#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Confidence	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNP_AF	i_dbSNP_PopFreq	i_dbSNP_Strength	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
ORM1	5004	hgsc.bcm.edu	37	9	117088618	117088620	+	In_Frame_Del	DEL	AGG	AGG	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117088618_117088620delAGG	ENST00000259396.8	+	6	665_667	c.587_589delAGG	c.(586-591)caggag>cag	p.E198del		NM_000607.2	NP_000598.2	P02763	A1AG1_HUMAN	orosomucoid 1	198					acute-phase response (GO:0006953)|inflammatory response (GO:0006954)|regulation of immune system process (GO:0002682)|transport (GO:0006810)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				endometrium(2)|large_intestine(4)|lung(2)	8		Myeloproliferative disorder(63;0.163)			Abiraterone(DB05812)|Acenocoumarol(DB01418)|Ajmaline(DB01426)|Alfentanil(DB00802)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Aprindine(DB01429)|Bupropion(DB01156)|Canagliflozin(DB08907)|Celecoxib(DB00482)|Chlorpromazine(DB00477)|Desipramine(DB01151)|Disopyramide(DB00280)|Doxazosin(DB00590)|Doxepin(DB01142)|Erlotinib(DB00530)|Fluoxetine(DB00472)|Gefitinib(DB00317)|Imatinib(DB00619)|Imipramine(DB00458)|Ivacaftor(DB08820)|Maprotiline(DB00934)|Mirabegron(DB08893)|Nateglinide(DB00731)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxycodone(DB00497)|Penbutolol(DB01359)|Pethidine(DB00454)|Phenprocoumon(DB00946)|Pitavastatin(DB08860)|Prazosin(DB00457)|Propranolol(DB00571)|Quinidine(DB00908)|Saquinavir(DB01232)|Tacrolimus(DB00864)|Tamsulosin(DB00706)|Telaprevir(DB05521)|Thalidomide(DB01041)|Trazodone(DB00656)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Vismodegib(DB08828)|Warfarin(DB00682)	GAGAGGAAACAGGAGGAGGGGGA	0.581																																					p.196_196del		Atlas-Indel	.											.	ORM1	20	.	0			c.586_588del						PASS	.																																			SO:0001651	inframe_deletion	5004	exon6			.		CCDS6803.1	9q32	2013-09-19			ENSG00000229314	ENSG00000229314		"""Lipocalins"""	8498	protein-coding gene	gene with protein product		138600					Standard	NM_000607		Approved		uc004bik.4	P02763	OTTHUMG00000021012	ENST00000259396.8:c.587_589delAGG	9.37:g.117088624_117088626delAGG	ENSP00000259396:p.Glu198del	915.0	0.0	0		979.0	178.0	0.181818	NM_000607	B7ZKQ5|Q5T539|Q5U067|Q8TC16	In_Frame_Del	DEL	ENST00000259396.8	37	CCDS6803.1																																																																																			.	.	none		0.581	ORM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055426.1		
LRRC37A2	474170	hgsc.bcm.edu	37	17	44590963	44590965	+	In_Frame_Del	DEL	CAA	CAA	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:44590963_44590965delCAA	ENST00000576629.1	+	2	1380_1382	c.885_887delCAA	c.(883-888)cccaac>ccc	p.N296del	LRRC37A2_ENST00000333412.3_In_Frame_Del_p.N296del			A6NM11	L37A2_HUMAN	leucine rich repeat containing 37, member A2	296						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|pancreas(4)|prostate(2)	15		Melanoma(429;0.211)		BRCA - Breast invasive adenocarcinoma(366;0.232)		ATCACTTGCCCAACATTACAGTT	0.473																																					p.295_296del		Atlas-Indel	.											.	LRRC37A2	37	.	0			c.884_886del						PASS	.																																			SO:0001651	inframe_deletion	474170	exon1			.	AY386262	CCDS42353.1	17q21.31	2013-05-14			ENSG00000238083	ENSG00000238083			32404	protein-coding gene	gene with protein product	"""c114 SLIT-like testicular protein"""						Standard	NM_001006607		Approved	FLJ45049	uc002ikn.1	A6NM11	OTTHUMG00000178032	ENST00000576629.1:c.885_887delCAA	17.37:g.44590963_44590965delCAA	ENSP00000459551:p.Asn296del	238.0	0.0	0		305.0	20.0	0.0655738	NM_001006607	B7ZMC3	In_Frame_Del	DEL	ENST00000576629.1	37	CCDS42353.1																																																																																			.	.	none		0.473	LRRC37A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440299.2	NM_001006607	
FOXD4L6	653404	hgsc.bcm.edu	37	9	69201361	69201362	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:69201361_69201362delTG	ENST00000377473.1	-	1	842_843	c.251_252delCA	c.(250-252)tcafs	p.S84fs		NM_001085476.1	NP_001078945.1	Q3SYB3	FX4L6_HUMAN	forkhead box D4-like 6	84					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TGCCAAACTCTGAGGGGTCGCT	0.698																																					p.84_85del		Atlas-Indel	.											.	.	.	.	0			c.252_253del						PASS	.																																			SO:0001589	frameshift_variant	653404	exon1			.		CCDS43826.1	9q12	2014-05-06			ENSG00000204793	ENSG00000273514			31986	protein-coding gene	gene with protein product							Standard	NM_001085476		Approved	OTTHUMG00000066822	uc004afi.2	Q3SYB3	OTTHUMG00000188618	ENST00000377473.1:c.251_252delCA	9.37:g.69201361_69201362delTG	ENSP00000366693:p.Ser84fs	354.0	0.0	0		547.0	86.0	0.157221	NM_001085476	B2RPC4|Q4V336	Frame_Shift_Del	DEL	ENST00000377473.1	37	CCDS43826.1																																																																																			.	.	none		0.698	FOXD4L6-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143174.1	NM_001085476	
LCNL1	401562	hgsc.bcm.edu	37	9	139879429	139879429	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139879429delT	ENST00000408973.2	+	3	1055	c.461delT	c.(460-462)ctcfs	p.L154fs	LCNL1_ENST00000432827.1_Intron	NM_207510.3	NP_997393.3	Q6ZST4	LCNL1_HUMAN	lipocalin-like 1	154																	tgcccctctctccctctcttc	0.682																																					p.L154fs		Atlas-Indel	.											.	LCNL1	4	.	0			c.460delC						PASS	.						8.0	11.0	10.0					9																	139879429		1791	3853	5644	SO:0001589	frameshift_variant	401562	exon3			.		CCDS43908.1	9q34.3	2014-01-22			ENSG00000214402	ENSG00000214402		"""Lipocalins"""	34436	protein-coding gene	gene with protein product							Standard	NM_207510		Approved	FLJ45224	uc004ckh.1	Q6ZST4	OTTHUMG00000159546	ENST00000408973.2:c.461delT	9.37:g.139879429delT	ENSP00000386162:p.Leu154fs	315.0	0.0	0		209.0	15.0	0.0717703	NM_207510		Frame_Shift_Del	DEL	ENST00000408973.2	37	CCDS43908.1																																																																																			.	.	none		0.682	LCNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356128.1	NM_207510	
C6orf48	50854	hgsc.bcm.edu	37	6	31807372	31807373	+	Frame_Shift_Ins	INS	-	-	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31807372_31807373insA	ENST00000375640.3	+	4	887_888	c.160_161insA	c.(160-162)tacfs	p.Y54fs	SNORD52_ENST00000364884.1_RNA|C6orf48_ENST00000395788.3_Frame_Shift_Ins_p.Y54fs|C6orf48_ENST00000375642.2_Frame_Shift_Ins_p.Y54fs|C6orf48_ENST00000375633.1_Frame_Shift_Ins_p.Y54fs|C6orf48_ENST00000375641.2_Frame_Shift_Ins_p.Y54fs|C6orf48_ENST00000375639.2_Frame_Shift_Ins_p.Y54fs|C6orf48_ENST00000375638.3_Frame_Shift_Ins_p.Y54fs|C6orf48_ENST00000395789.1_Frame_Shift_Ins_p.Y54fs|C6orf48_ENST00000375635.2_Frame_Shift_Ins_p.Y54fs	NM_001040438.1	NP_001035528.1	Q9UBA6	G8_HUMAN	chromosome 6 open reading frame 48	54										breast(1)|large_intestine(1)|lung(1)|skin(1)	4						CCTAAGAACTTACAACTTTCCT	0.391																																					p.Y54_N55delinsX		Pindel,Atlas-Indel	.											.	C6orf48	8	.	0			c.160_161insA						PASS	.																																			SO:0001589	frameshift_variant	50854	exon5			.	AJ249732	CCDS34416.1	6p21.33	2011-12-13			ENSG00000204387	ENSG00000204387			19078	protein-coding gene	gene with protein product		605447				8096093	Standard	NM_001287483		Approved	D6S57, G8	uc003rjy.2	Q9UBA6	OTTHUMG00000031175	ENST00000375640.3:c.161dupA	6.37:g.31807373_31807373dupA	ENSP00000364791:p.Tyr54fs	119.0	0.0	.		120.0	41.0	0.342	NM_001040437	Q9BW21|Q9UBA7|Q9UBA8	Frame_Shift_Ins	INS	ENST00000375640.3	37	CCDS34416.1																																																																																			.	.	none		0.391	C6orf48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076332.2	NM_001040437	
NAP1L5	266812	hgsc.bcm.edu	37	4	89618415	89618426	+	In_Frame_Del	DEL	GCAGCCTCTGCC	GCAGCCTCTGCC	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GCAGCCTCTGCC	GCAGCCTCTGCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:89618415_89618426delGCAGCCTCTGCC	ENST00000323061.5	-	1	960_971	c.480_491delGGCAGAGGCTGC	c.(478-492)gcggcagaggctgcc>gcc	p.160_164AAEAA>A	HERC3_ENST00000543130.1_Intron|HERC3_ENST00000264345.3_Intron|HERC3_ENST00000402738.1_Intron	NM_153757.2	NP_715638.1	Q96NT1	NP1L5_HUMAN	nucleosome assembly protein 1-like 5	160	Glu-rich.				nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				endometrium(2)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(123;0.000181)		GGCCCCCGCGGCAGCCTCTGCCGCAGcctcct	0.608																																					p.161_164del		Pindel,Atlas-Indel	.											.	NAP1L5	23	.	0			c.481_492del						PASS	.		,	4,4262		1,2,2130					,	-3.3	0.0			93	0,8252		0,0,4126	no	coding,intron	HERC3,NAP1L5	NM_153757.2,NM_014606.1	,	1,2,6256	A1A1,A1R,RR		0.0,0.0938,0.032	,	,		4,12514				SO:0001651	inframe_deletion	266812	exon1			.	NM_153757	CCDS3632.1	4q21-q22	2006-04-12			ENSG00000177432	ENSG00000177432			19968	protein-coding gene	gene with protein product		612203				12383514	Standard	NM_153757		Approved	DRLM	uc003hrx.3	Q96NT1	OTTHUMG00000130950	ENST00000323061.5:c.480_491delGGCAGAGGCTGC	4.37:g.89618415_89618426delGCAGCCTCTGCC	ENSP00000320488:p.Ala160_Ala163del	279.0	0.0	.		285.0	66.0	0.232	NM_153757		In_Frame_Del	DEL	ENST00000323061.5	37	CCDS3632.1																																																																																			.	.	none		0.608	NAP1L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253551.1	NM_153757	
LRRC37A	9884	hgsc.bcm.edu	37	17	44373384	44373386	+	In_Frame_Del	DEL	CAA	CAA	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CAA	CAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:44373384_44373386delCAA	ENST00000320254.5	+	1	888_890	c.885_887delCAA	c.(883-888)cccaac>ccc	p.N296del	ARL17B_ENST00000570618.1_Intron|LRRC37A_ENST00000393465.3_In_Frame_Del_p.N296del|LRRC37A_ENST00000496930.1_Intron	NM_014834.4	NP_055649.4	A6NMS7	L37A1_HUMAN	leucine rich repeat containing 37A	296						integral component of membrane (GO:0016021)				endometrium(1)|lung(2)|pancreas(6)|prostate(1)|skin(1)	11		Melanoma(429;0.211)		BRCA - Breast invasive adenocarcinoma(366;0.232)		ATCACTTGCCCAACATTACAGTT	0.473																																					p.295_296del		Atlas-Indel	.											.	LRRC37A	19	.	0			c.884_886del						PASS	.																																			SO:0001651	inframe_deletion	9884	exon1			.	BC040501	CCDS11504.2	17q21.31	2014-04-01			ENSG00000176681	ENSG00000176681			29069	protein-coding gene	gene with protein product						9628581, 15533724	Standard	NM_014834		Approved	KIAA0563	uc031rbr.1	A6NMS7	OTTHUMG00000149841	ENST00000320254.5:c.885_887delCAA	17.37:g.44373384_44373386delCAA	ENSP00000326324:p.Asn296del	235.0	0.0	0		305.0	21.0	0.0688525	NM_014834	Q68DY2|Q8IWC7	In_Frame_Del	DEL	ENST00000320254.5	37	CCDS11504.2																																																																																			.	.	none		0.473	LRRC37A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313519.3	NM_014834	
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1643073	1643073	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1643073delC	ENST00000399682.1	-	1	295	c.251delG	c.(250-252)tgtfs	p.C84fs		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				NS(1)|endometrium(9)|kidney(2)|lung(2)|pancreas(1)|prostate(3)|skin(2)	20		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		GGAACCCCCACAAGAGCCATA	0.667																																					p.C84fs		Atlas-Indel	.											KRTAP5-4,NS,carcinoma,0,1	KRTAP5-4	78	1	0			c.252delT						PASS	.						9.0	15.0	13.0					11																	1643073		682	1575	2257	SO:0001589	frameshift_variant	387267	exon1			.	AB126073		11p15.5	2012-04-19			ENSG00000241598	ENSG00000241598		"""Keratin associated proteins"""	23599	protein-coding gene	gene with protein product						15144888	Standard	NM_001012709		Approved	KRTAP5.4	uc009ycy.1	Q6L8H1	OTTHUMG00000057553	ENST00000399682.1:c.251delG	11.37:g.1643073delC	ENSP00000382590:p.Cys84fs	225.0	0.0	0		284.0	23.0	0.0809859	NM_001012709		Frame_Shift_Del	DEL	ENST00000399682.1	37																																																																																				.	.	none		0.667	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709	
FANCE	2178	hgsc.bcm.edu	37	6	35424008	35424010	+	In_Frame_Del	DEL	GGA	GGA	-	rs45451605|rs397897540	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:35424008_35424010delGGA	ENST00000229769.2	+	2	918_920	c.733_735delGGA	c.(733-735)ggadel	p.G246del		NM_021922.2	NP_068741.1	Q9HB96	FANCE_HUMAN	Fanconi anemia, complementation group E	246	Interaction with FANCC.				DNA repair (GO:0006281)	Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|ovary(1)|skin(2)	13						CCTGGCAGATGGAGGAAGTGCAT	0.507			"""N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia					17	0.00339457	0.0113	0.0014	5008	,	,		22003	0.0		0.0	False		,,,				2504	0.001				p.244_245del		Pindel,Atlas-Indel	.	yes	Rec		Fanconi anaemia E	6	6p21-p22	2178	"""Fanconi anemia, complementation group E"""		L	.	FANCE	45	.	0			c.732_734del						PASS	.			70,4194		2,66,2064						-4.1	0.0		dbSNP_127	120	5,8249		0,5,4122	no	coding	FANCE	NM_021922.2		2,71,6186	A1A1,A1R,RR		0.0606,1.6417,0.5991				75,12443				SO:0001651	inframe_deletion	2178	exon2	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	.	AF265210	CCDS4805.1	6p22-p21	2014-09-17			ENSG00000112039	ENSG00000112039		"""Fanconi anemia, complementation groups"""	3586	protein-coding gene	gene with protein product		613976		FACE		7662964, 11001585	Standard	XM_005248885		Approved	FAE	uc003oko.1	Q9HB96	OTTHUMG00000014565	ENST00000229769.2:c.733_735delGGA	6.37:g.35424011_35424013delGGA	ENSP00000229769:p.Gly246del	138.0	0.0	.		142.0	42.0	0.296	NM_021922	A8K907|Q4ZGH2	In_Frame_Del	DEL	ENST00000229769.2	37	CCDS4805.1																																																																																			GGA|0.979;-|0.021	0.021	strong		0.507	FANCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040282.1		
HYDIN	54768	hgsc.bcm.edu	37	16	71007312	71007312	+	Frame_Shift_Del	DEL	G	G	-	rs373616607		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:71007312delG	ENST00000393567.2	-	35	5463	c.5313delC	c.(5311-5313)cccfs	p.P1771fs		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	1771					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				CTCCAGAAATGGGCTGGATTT	0.403																																					p.I1772fs		Pindel,Atlas-Indel	.											.	HYDIN	788	.	0			c.5314delA						PASS	.						1.0	1.0	1.0					16																	71007312		454	1000	1454	SO:0001589	frameshift_variant	54768	exon35			.	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.5313delC	16.37:g.71007312delG	ENSP00000377197:p.Pro1771fs	101.0	0.0	.		140.0	25.0	0.179	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Frame_Shift_Del	DEL	ENST00000393567.2	37	CCDS59269.1																																																																																			.	.	weak		0.403	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
SSPO	23145	hgsc.bcm.edu	37	7	149480091	149480092	+	RNA	INS	-	-	C	rs144883973	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149480091_149480092insC	ENST00000378016.2	+	0	2057_2058							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			ATCACCCTGGACCCCCGCCATG	0.653													CCCCC|CCCCC|CCCCCC|insertion	131	0.0261581	0.0946	0.0086	5008	,	,		17227	0.0		0.0	False		,,,				2504	0.0				p.D686fs		Pindel,Atlas-Indel	.											.	.	.	.	0			c.2057_2058insC						PASS	.			263,3523		27,209,1657						4.2	1.0		dbSNP_134	31	27,7833		1,25,3904	no	frameshift	SSPO	NM_198455.2		28,234,5561	A1A1,A1R,RR		0.3435,6.9466,2.4901				290,11356						23145	exon15			.	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149480096_149480096dupC		217.0	0.0	.		217.0	71.0	0.327	NM_198455	Q76B61	Frame_Shift_Ins	INS	ENST00000378016.2	37																																																																																				-|0.979;C|0.021	0.021	strong		0.653	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
TIGD6	81789	hgsc.bcm.edu	37	5	149375721	149375721	+	Frame_Shift_Del	DEL	C	C	-	rs33910807|rs575130996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149375721delC	ENST00000296736.3	-	2	965	c.191delG	c.(190-192)ggafs	p.G64fs	TIGD6_ENST00000515406.2_Frame_Shift_Del_p.G64fs	NM_030953.3	NP_112215.1	Q17RP2	TIGD6_HUMAN	tigger transposable element derived 6	64						nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|stomach(1)	10			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			CCGCTGGGGTCCCACGGATGC	0.433													CCC|CCC|CC|deletion	476	0.0950479	0.3449	0.0231	5008	,	,		21862	0.0		0.004	False		,,,				2504	0.0				p.G64fs		Pindel,Atlas-Indel	.											.	TIGD6	29	.	0			c.192delA						PASS	.			1204,3060		171,862,1099	71.0	98.0	89.0			-2.9	0.2	5	dbSNP_126	99	16,8222		2,12,4105	yes	frameshift	TIGD6	NM_030953.3		173,874,5204	A1A1,A1R,RR		0.1942,28.2364,9.7584			149375721	1220,11282	2188	4300	6488	SO:0001589	frameshift_variant	81789	exon2			.	AK056604	CCDS4301.1	5q33.1	2008-02-05			ENSG00000164296	ENSG00000164296			18332	protein-coding gene	gene with protein product						11230166	Standard	NM_030953		Approved	DKFZp761E2110	uc003lrj.3	Q17RP2	OTTHUMG00000130045	ENST00000296736.3:c.191delG	5.37:g.149375721delC	ENSP00000296736:p.Gly64fs	66.0	0.0	.		82.0	32.0	0.390	NM_030953	B3KTZ8|Q96MQ4|Q9H0X7	Frame_Shift_Del	DEL	ENST00000296736.3	37	CCDS4301.1																																																																																			C|0.913;-|0.087	0.087	strong		0.433	TIGD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252324.1	NM_030953	
SCARA5	286133	hgsc.bcm.edu	37	8	27779652	27779672	+	In_Frame_Del	DEL	GCAGCGGAGCCTGCAGCAGCC	GCAGCGGAGCCTGCAGCAGCC	-	rs556775167|rs370651084|rs544481270	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GCAGCGGAGCCTGCAGCAGCC	GCAGCGGAGCCTGCAGCAGCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:27779652_27779672delGCAGCGGAGCCTGCAGCAGCC	ENST00000354914.3	-	4	817_837	c.332_352delGGCTGCTGCAGGCTCCGCTGC	c.(331-354)cggctgctgcaggctccgctgcaa>caa	p.RLLQAPL111del	SCARA5_ENST00000518030.1_In_Frame_Del_p.RLLQAPL68del|SCARA5_ENST00000301906.4_In_Frame_Del_p.RLLQAPL68del|SCARA5_ENST00000524352.1_In_Frame_Del_p.RLLQAPL111del|SCARA5_ENST00000380385.2_Intron	NM_173833.5	NP_776194.2	Q6ZMJ2	SCAR5_HUMAN	scavenger receptor class A, member 5	111					cellular iron ion homeostasis (GO:0006879)|cellular response to heat (GO:0034605)|endocytosis (GO:0006897)|iron ion transmembrane transport (GO:0034755)|protein homotrimerization (GO:0070207)|receptor-mediated endocytosis (GO:0006898)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)	ferritin receptor activity (GO:0070287)|scavenger receptor activity (GO:0005044)			central_nervous_system(1)|large_intestine(6)|lung(5)|prostate(3)|skin(3)	18		Ovarian(32;0.0218)		UCEC - Uterine corpus endometrioid carcinoma (27;0.023)|KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)|Colorectal(74;0.228)		AGGTCCGCTTGCAGCGGAGCCTGCAGCAGCCGCAGCTGCAA	0.67														4	0.000798722	0.003	0.0	5008	,	,		20679	0.0		0.0	False		,,,				2504	0.0				p.111_118del		Pindel,Atlas-Indel	.											.	SCARA5	53	.	0			c.333_353del						PASS	.			5,4237		1,3,2117						3.1	1.0			13	9,8227		3,3,4112	no	coding	SCARA5	NM_173833.5		4,6,6229	A1A1,A1R,RR		0.1093,0.1179,0.1122				14,12464				SO:0001651	inframe_deletion	286133	exon4			.	AK172746	CCDS6064.1	8p21.1	2014-07-08	2014-07-08		ENSG00000168079	ENSG00000168079			28701	protein-coding gene	gene with protein product		611306	"""scavenger receptor class A, member 5 (putative)"""			19154717	Standard	NM_173833		Approved	FLJ23907, MGC45780, NET33	uc003xgj.3	Q6ZMJ2	OTTHUMG00000132172	ENST00000354914.3:c.332_352delGGCTGCTGCAGGCTCCGCTGC	8.37:g.27779652_27779672delGCAGCGGAGCCTGCAGCAGCC	ENSP00000346990:p.Arg111_Leu117del	97.0	0.0	.		53.0	26.0	0.491	NM_173833	Q6UXZ1|Q7Z4A1|Q8N4Z7	In_Frame_Del	DEL	ENST00000354914.3	37	CCDS6064.1																																																																																			.	.	none		0.670	SCARA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255223.2	NM_173833	
SLC39A8	64116	hgsc.bcm.edu	37	4	103188834	103188836	+	Intron	DEL	AGA	AGA	-	rs370986625|rs71813938	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:103188834_103188836delAGA	ENST00000394833.2	-	7	1525				SLC39A8_ENST00000424970.2_Intron|SLC39A8_ENST00000356736.4_Intron	NM_001135148.1|NM_022154.5	NP_001128620.1|NP_071437.3	Q9C0K1	S39A8_HUMAN	solute carrier family 39 (zinc transporter), member 8						transmembrane transport (GO:0055085)|zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)|plasma membrane (GO:0005886)	metal ion transmembrane transporter activity (GO:0046873)			large_intestine(1)|lung(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Hepatocellular(203;0.217)		all cancers(1;9.78e-10)|OV - Ovarian serous cystadenocarcinoma(123;1.52e-09)|GBM - Glioblastoma multiforme(1;0.000142)		AAAGTCTCCTAGAAGAAGAAGAA	0.369														302	0.0603035	0.2179	0.0173	5008	,	,		19711	0.0		0.002	False		,,,				2504	0.0				.		Atlas-Indel	.											SLC39A8,NS,carcinoma,0,1	SLC39A8	24	1	0			.						PASS	.		,,,	882,3384		101,680,1352					,,,	4.9	1.0		dbSNP_130	74	16,8232		0,16,4108	no	intron,intron,intron,intron	SLC39A8	NM_022154.5,NM_001135148.1,NM_001135147.1,NM_001135146.1	,,,	101,696,5460	A1A1,A1R,RR		0.194,20.6751,7.176	,,,	,,,		898,11616				SO:0001627	intron_variant	64116	.			.		CCDS3656.1, CCDS47117.1	4q22-q24	2013-05-22			ENSG00000138821	ENSG00000138821		"""Solute carriers"""	20862	protein-coding gene	gene with protein product		608732	"""solute carrier family 39 (metal ion transporter), member 8"""			12504855, 12659941	Standard	NM_001135146		Approved	BIGM103	uc003hwc.2	Q9C0K1	OTTHUMG00000131120	ENST00000394833.2:c.1049-3TCT>-	4.37:g.103188843_103188845delAGA		166.0	0.0	0		160.0	55.0	0.34375	.	B4E2H3|Q96SM9|Q9BVC0|Q9NSA4	Splice_Site	DEL	ENST00000394833.2	37	CCDS3656.1																																																																																			AGA|0.950;-|0.050	0.050	strong		0.369	SLC39A8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253798.1	NM_022154	
NBPF3	84224	hgsc.bcm.edu	37	1	21801436	21801444	+	Splice_Site	DEL	GTCTCCCAG	GTCTCCCAG	-	rs139002241|rs570380722|rs372317136	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GTCTCCCAG	GTCTCCCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:21801436_21801444delGTCTCCCAG	ENST00000318249.5	+	8	1334_1342	c.984_992delGTCTCCCAG	c.(982-993)gtgtctcccagg>gtg	p.SPR329del	NBPF3_ENST00000318220.6_Splice_Site_p.SPR273del|NBPF3_ENST00000342104.5_Splice_Site_p.SPR329del|NBPF3_ENST00000454000.2_Splice_Site_p.SPR259del	NM_032264.3	NP_115640.1	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3	329	NBPF 2. {ECO:0000255|PROSITE- ProRule:PRU00647}.					cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	20		all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		AAGGGCCAGTGTCTCCCAGGTAATGCCAT	0.388														277	0.0553115	0.1551	0.0937	5008	,	,		21818	0.001		0.002	False		,,,				2504	0.0041				p.328_331del		Pindel,Atlas-Indel	.											.	NBPF3	55	.	0			c.983_991del						PASS	.			506,3760		32,442,1659						-1.6	0.0		dbSNP_134	214	59,8193		1,57,4068	no	coding-near-splice	NBPF3	NM_032264.2		33,499,5727	A1A1,A1R,RR		0.715,11.8612,4.5135				565,11953				SO:0001630	splice_region_variant	84224	exon8			.	BC024011	CCDS216.1, CCDS57976.1, CCDS57977.1	1p36.12	2013-01-17			ENSG00000142794	ENSG00000142794		"""neuroblastoma breakpoint family"""	25076	protein-coding gene	gene with protein product		612992				11230166, 16079250	Standard	NM_032264		Approved	AE2	uc001ber.4	Q9H094	OTTHUMG00000002944	ENST00000318249.5:c.992+1GTCTCCCAG>-	1.37:g.21801436_21801444delGTCTCCCAG		85.0	0.0	.		88.0	17.0	0.193	NM_032264	A8K965|B4DSP2|I3L0I8|Q3BBW1|Q5VTG2|Q5VTG3|Q5VTG4|Q8IX78|Q8ND86|Q8TC96	In_Frame_Del	DEL	ENST00000318249.5	37	CCDS216.1																																																																																			GTCTCCCAG|0.948;-|0.052	0.052	strong		0.388	NBPF3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_032264	In_Frame_Del
ING3	54556	hgsc.bcm.edu	37	7	120610847	120610849	+	In_Frame_Del	DEL	AAC	AAC	-	rs539687500	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AAC	AAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:120610847_120610849delAAC	ENST00000315870.5	+	10	1162_1164	c.1014_1016delAAC	c.(1012-1017)caaaca>caa	p.T340del	ING3_ENST00000431467.1_In_Frame_Del_p.T325del	NM_019071.2	NP_061944.2	Q9NXR8	ING3_HUMAN	inhibitor of growth family, member 3	340					chromatin organization (GO:0006325)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|positive regulation of apoptotic process (GO:0043065)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|NuA4 histone acetyltransferase complex (GO:0035267)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Piccolo NuA4 histone acetyltransferase complex (GO:0032777)|Swr1 complex (GO:0000812)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			NS(1)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	12	all_neural(327;0.117)					TCTCTCAACAAACAACTGTAGTG	0.394														6	0.00119808	0.0045	0.0	5008	,	,		17162	0.0		0.0	False		,,,				2504	0.0				p.338_339del		Pindel,Atlas-Indel	.											.	ING3	36	.	0			c.1013_1015del						PASS	.																																			SO:0001651	inframe_deletion	54556	exon10			.	AF074968	CCDS5778.1, CCDS35497.1	7q31	2013-01-28			ENSG00000071243	ENSG00000071243		"""Zinc fingers, PHD-type"""	14587	protein-coding gene	gene with protein product		607493				12080476	Standard	NM_019071		Approved	p47ING3, FLJ20089, Eaf4, MEAF4	uc003vjn.3	Q9NXR8	OTTHUMG00000141270	ENST00000315870.5:c.1014_1016delAAC	7.37:g.120610850_120610852delAAC	ENSP00000320566:p.Thr340del	112.0	0.0	.		92.0	37.0	0.402	NM_019071	A8K790|O60394|Q567P3|Q6GMT3|Q7Z762|Q969G0|Q96DT4|Q9HC99|Q9P081	In_Frame_Del	DEL	ENST00000315870.5	37	CCDS5778.1																																																																																			.	.	none		0.394	ING3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280453.2	NM_019071	
NAIP	4671	hgsc.bcm.edu	37	5	70281620	70281621	+	Frame_Shift_Del	DEL	AT	AT	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:70281620_70281621delAT	ENST00000517649.1	-	12	1545_1546	c.1255_1256delAT	c.(1255-1257)atgfs	p.M419fs	NAIP_ENST00000194097.4_Frame_Shift_Del_p.M419fs|NAIP_ENST00000508426.2_Frame_Shift_Del_p.M419fs|NAIP_ENST00000523981.1_Frame_Shift_Del_p.M257fs|NAIP_ENST00000503719.2_Frame_Shift_Del_p.M257fs	NM_004536.2	NP_004527.2	Q13075	BIRC1_HUMAN	NLR family, apoptosis inhibitory protein	419					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|metal ion binding (GO:0046872)			central_nervous_system(1)	1		Lung NSC(167;4.15e-05)|Prostate(74;0.00996)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;3.04e-60)|Epithelial(20;7.09e-58)|all cancers(19;1.13e-53)|Lung(70;0.0174)		AAGCAAAGACATGTGGCGGAAA	0.5																																					p.419_419del		Atlas-Indel	.											.	NAIP	38	.	0			c.1256_1257del						PASS	.																																			SO:0001589	frameshift_variant	4671	exon12			.	U19251	CCDS4009.1, CCDS43327.1	5q13.2	2010-06-16	2006-12-08	2006-12-08	ENSG00000249437	ENSG00000249437		"""Baculoviral IAP repeat containing"", ""Nucleotide-binding domain and leucine rich repeat containing"""	7634	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and BIR domain containing 1"", ""NLR family, BIR domain containing 1"""	600355	"""baculoviral IAP repeat-containing 1"""	BIRC1		7813013	Standard	NM_022892		Approved	NLRB1	uc003jyj.1	Q13075	OTTHUMG00000163318	ENST00000517649.1:c.1255_1256delAT	5.37:g.70281620_70281621delAT	ENSP00000428657:p.Met419fs	214.0	0.0	0		205.0	32.0	0.156098	NM_004536	B9EG72|E9PHD1|O75857|Q13730|Q59GI6|Q8TDZ4|Q99796	Frame_Shift_Del	DEL	ENST00000517649.1	37	CCDS4009.1																																																																																			.	.	none		0.500	NAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372649.6	NM_004536	
ARID4B	51742	hgsc.bcm.edu	37	1	235377279	235377281	+	In_Frame_Del	DEL	TCC	TCC	-	rs113894806|rs10588817|rs113458177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:235377279_235377281delTCC	ENST00000264183.3	-	17	2141_2143	c.1644_1646delGGA	c.(1642-1647)gaggaa>gaa	p.548_549EE>E	ARID4B_ENST00000349213.3_Intron|ARID4B_ENST00000366603.2_In_Frame_Del_p.548_549EE>E	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	548	Glu-rich.				histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.E548E(2)		NS(1)|breast(2)|large_intestine(2)|lung(1)|ovary(2)	8	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			ttcttcttcttcctcctcctcct	0.414														183	0.0365415	0.1203	0.0144	5008	,	,		17403	0.001		0.008	False		,,,				2504	0.0051				p.549_549del		Pindel,Atlas-Indel	.											.	ARID4B	142	.	2	Substitution - coding silent(2)	endometrium(1)|kidney(1)	c.1645_1647del						PASS	.																																			SO:0001651	inframe_deletion	51742	exon17			.	AF214114	CCDS31060.1, CCDS31061.1	1q42.1-q43	2013-02-07	2006-11-08	2004-01-30	ENSG00000054267	ENSG00000054267		"""-"""	15550	protein-coding gene	gene with protein product		609696	"""retinoblastoma binding protein 1-like 1"", ""AT rich interactive domain 4B (RBP1- like)"""	RBP1L1		11481388	Standard	NM_016374		Approved	BCAA, BRCAA1, SAP180	uc001hwq.3	Q4LE39	OTTHUMG00000039621	ENST00000264183.3:c.1644_1646delGGA	1.37:g.235377288_235377290delTCC	ENSP00000264183:p.Glu553del	137.0	0.0	.		176.0	28.0	0.159	NM_016374	A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	In_Frame_Del	DEL	ENST00000264183.3	37	CCDS31061.1																																																																																			TCC|0.967;-|0.033	0.033	strong		0.414	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095566.3	NM_016374	
CMA1	1215	hgsc.bcm.edu	37	14	24976605	24976605	+	Frame_Shift_Del	DEL	T	T	-	rs542619483	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24976605delT	ENST00000250378.3	-	2	195	c.166delA	c.(166-168)atafs	p.I56fs	CMA1_ENST00000206446.4_Intron|RP11-80A15.1_ENST00000555109.1_Intron	NM_001836.3	NP_001827.1	P23946	CMA1_HUMAN	chymase 1, mast cell	56	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				angiotensin maturation (GO:0002003)|cellular protein metabolic process (GO:0044267)|cellular response to glucose stimulus (GO:0071333)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|interleukin-1 beta biosynthetic process (GO:0050720)|midbrain development (GO:0030901)|peptide metabolic process (GO:0006518)|positive regulation of angiogenesis (GO:0045766)|regulation of inflammatory response (GO:0050727)	extracellular region (GO:0005576)|intracellular (GO:0005622)	peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			kidney(1)|lung(8)|pancreas(1)|prostate(1)	11				GBM - Glioblastoma multiforme(265;0.0271)		TTCCGTCTTATAAGGAAACCA	0.488													?|T|-|unsure	8	0.00159744	0.0061	0.0	5008	,	,		19307	0.0		0.0	False		,,,				2504	0.0				p.I56fs		Pindel,Atlas-Indel	.											.	CMA1	21	.	0			c.167delT						PASS	.			12,4252		0,12,2120	143.0	139.0	140.0			5.0	0.2	14		140	0,8254		0,0,4127	no	frameshift	CMA1	NM_001836.2		0,12,6247	A1A1,A1R,RR		0.0,0.2814,0.0959			24976605	12,12506	2203	4300	6503	SO:0001589	frameshift_variant	1215	exon2			.		CCDS9630.1	14q12	2012-08-30			ENSG00000092009	ENSG00000092009	3.4.21.39		2097	protein-coding gene	gene with protein product		118938				8468056	Standard	NM_001836		Approved		uc001wpp.1	P23946	OTTHUMG00000140181	ENST00000250378.3:c.166delA	14.37:g.24976605delT	ENSP00000250378:p.Ile56fs	147.0	0.0	.		120.0	39.0	0.325	NM_001836	B5BUM8|Q16018|Q3SY36|Q3SY37|Q9UDH5	Frame_Shift_Del	DEL	ENST00000250378.3	37	CCDS9630.1																																																																																			.	.	none		0.488	CMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276535.2		
MTFP1	51537	hgsc.bcm.edu	37	22	30824659	30824660	+	3'UTR	INS	-	-	A	rs527818803|rs149958301	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30824659_30824660insA	ENST00000266263.5	+	0	989_990				MTFP1_ENST00000355143.4_Stop_Codon_Ins|MTFP1_ENST00000407550.3_3'UTR|RP4-539M6.19_ENST00000439838.1_3'UTR	NM_016498.4	NP_057582.2	Q9UDX5	MTFP1_HUMAN	mitochondrial fission process 1						apoptotic process (GO:0006915)|mitochondrial fission (GO:0000266)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(1)|large_intestine(1)|lung(2)	4						GACAGAAGCTTAGAGACAAAGG	0.559													A|A|AA|insertion	54	0.0107827	0.0393	0.0029	5008	,	,		20262	0.0		0.0	False		,,,				2504	0.0				p.X136delinsX		Pindel,Atlas-Indel	.											.	MTFP1	7	.	0			c.406_407insA						PASS	.		,	105,4159		0,105,2027					,	-0.6	0.0		dbSNP_134	38	1,8253		0,1,4126	yes	utr-3,frameshift	MTFP1	NM_016498.4,NM_001003704.2	,	0,106,6153	A1A1,A1R,RR		0.0121,2.4625,0.8468	,	,		106,12412				SO:0001624	3_prime_UTR_variant	51537	exon3			.	AF151076	CCDS33634.1, CCDS33635.1	22q	2010-09-02			ENSG00000242114	ENSG00000242114			26945	protein-coding gene	gene with protein product		610235				15155745, 15985469	Standard	NM_016498		Approved	MTP18, HSPC242		Q9UDX5	OTTHUMG00000151057	ENST00000266263.5:c.*139->A	22.37:g.30824660_30824660dupA		72.0	0.0	.		75.0	27.0	0.360	NM_001003704	A6NFQ5|Q9H3K1|Q9P0N6	Frame_Shift_Ins	INS	ENST00000266263.5	37	CCDS33635.1																																																																																			-|0.993;A|0.007	0.007	strong		0.559	MTFP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321126.3	NM_016498	
SSPO	23145	hgsc.bcm.edu	37	7	149484830	149484830	+	RNA	DEL	G	G	-	rs137977793	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149484830delG	ENST00000378016.2	+	0	3652							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			ATTATGCCACGCGGAGGTCCC	0.667													G|G|-|deletion	82	0.0163738	0.0598	0.0029	5008	,	,		17852	0.0		0.001	False		,,,				2504	0.0				p.H1217fs		Pindel,Atlas-Indel	.											.	.	.	.	0			c.3651delC						PASS	.			183,3691		17,149,1771	8.0	12.0	11.0			-4.0	0.0	7	dbSNP_134	11	3,7937		1,1,3968	no	frameshift	SSPO	NM_198455.2		18,150,5739	A1A1,A1R,RR		0.0378,4.7238,1.5744			149484830	186,11628	2003	4151	6154			23145	exon25			.	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149484830delG		52.0	0.0	.		46.0	11.0	0.239	NM_198455	Q76B61	Frame_Shift_Del	DEL	ENST00000378016.2	37																																																																																				G|0.985;-|0.015	0.015	strong		0.667	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
KRTAP6-2	337967	hgsc.bcm.edu	37	21	31971075	31971076	+	Frame_Shift_Ins	INS	-	-	A	rs74773890|rs113467703|rs113674499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31971075_31971076insA	ENST00000334897.3	-	1	143_144	c.118_119insT	c.(118-120)tatfs	p.Y40fs	KRTAP22-1_ENST00000334680.2_5'Flank	NM_181604.1	NP_853635.1	Q3LI66	KRA62_HUMAN	keratin associated protein 6-2	40						intermediate filament (GO:0005882)				endometrium(2)|kidney(1)|large_intestine(4)|lung(4)	11						GCCATGACCATAGCCACAGCAG	0.564													A|A|AA|insertion	66	0.0131789	0.0484	0.0029	5008	,	,		15138	0.0		0.0	False		,,,				2504	0.0				p.Y40fs		Pindel,Atlas-Indel	.											.	KRTAP6-2	24	.	0			c.119_120insT						PASS	.			171,4093		4,163,1965						-6.6	0.0		dbSNP_132	106	1,8253		0,1,4126	no	frameshift	KRTAP6-2	NM_181604.1		4,164,6091	A1A1,A1R,RR		0.0121,4.0103,1.374				172,12346				SO:0001589	frameshift_variant	337967	exon1			.	AP001708	CCDS13600.1	21q22.1	2011-02-10			ENSG00000186930	ENSG00000186930		"""Keratin associated proteins"""	18932	protein-coding gene	gene with protein product						12359730	Standard	NM_181604		Approved	KAP6.2	uc011adc.2	Q3LI66	OTTHUMG00000057794	ENST00000334897.3:c.119dupT	21.37:g.31971076_31971076dupA	ENSP00000334560:p.Tyr40fs	206.0	0.0	.		200.0	60.0	0.300	NM_181604		Frame_Shift_Ins	INS	ENST00000334897.3	37	CCDS13600.1																																																																																			-|0.990;A|0.010	0.010	strong		0.564	KRTAP6-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128246.3		
ZSCAN29	146050	hgsc.bcm.edu	37	15	43658416	43658418	+	In_Frame_Del	DEL	CCT	CCT	-	rs377169169|rs151154169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:43658416_43658418delCCT	ENST00000396976.2	-	3	1246_1248	c.1112_1114delAGG	c.(1111-1116)gaggga>gga	p.E371del	ZSCAN29_ENST00000568898.1_Intron|ZSCAN29_ENST00000562072.1_In_Frame_Del_p.E370del|ZSCAN29_ENST00000396972.1_Intron	NM_152455.3	NP_689668.3	Q8IWY8	ZSC29_HUMAN	zinc finger and SCAN domain containing 29	371					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(7)|skin(2)	24		all_cancers(109;2.12e-14)|all_epithelial(112;1.99e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;8.97e-07)		TCTTCTGCTCCCTCCTCATGCTG	0.601														118	0.0235623	0.0855	0.0058	5008	,	,		18099	0.0		0.001	False		,,,				2504	0.0				p.371_372del		Pindel,Atlas-Indel	.											.	ZSCAN29	57	.	0			c.1113_1115del						PASS	.			330,3934		28,274,1830						-9.0	0.0		dbSNP_119	68	3,8251		0,3,4124	no	coding	ZSCAN29	NM_152455.3		28,277,5954	A1A1,A1R,RR		0.0363,7.7392,2.6602				333,12185				SO:0001651	inframe_deletion	146050	exon3			.	AF525399	CCDS10095.2	15q15.3	2013-01-08	2007-03-08	2007-03-08	ENSG00000140265	ENSG00000140265		"""-"", ""Zinc fingers, C2H2-type"""	26673	protein-coding gene	gene with protein product			"""zinc finger protein 690"""	ZNF690		12434312	Standard	NM_152455		Approved	FLJ35867, Zfp690	uc001zrk.1	Q8IWY8	OTTHUMG00000130767	ENST00000396976.2:c.1112_1114delAGG	15.37:g.43658419_43658421delCCT	ENSP00000380174:p.Glu371del	61.0	0.0	.		74.0	25.0	0.338	NM_152455	B3KVB9|Q32M75|Q32M76|Q8NA40	In_Frame_Del	DEL	ENST00000396976.2	37	CCDS10095.2																																																																																			CCT|0.977;-|0.023	0.023	strong		0.601	ZSCAN29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253278.1	NM_152455	
DCHS2	54798	hgsc.bcm.edu	37	4	155158259	155158260	+	In_Frame_Ins	INS	-	-	GTT	rs138652483|rs376550327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:155158259_155158260insGTT	ENST00000357232.4	-	25	6178_6179	c.6179_6180insAAC	c.(6178-6180)act>acAACt	p.2060_2060T>TT		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2060	Cadherin 18. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		CAAGAAATTGAGTTGTTGATAT	0.376														103	0.0205671	0.0734	0.0058	5008	,	,		19389	0.0		0.002	False		,,,				2504	0.0				p.T2060delinsTT		Pindel,Atlas-Indel	.											.	DCHS2	594	.	0			c.6180_6181insAAC						PASS	.			254,4010		7,240,1885						3.4	0.1		dbSNP_134	82	6,8246		0,6,4120	no	coding	DCHS2	NM_017639.3		7,246,6005	A1A1,A1R,RR		0.0727,5.9568,2.0773				260,12256				SO:0001652	inframe_insertion	54798	exon25			.	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.6177_6179dupAAC	4.37:g.155158263_155158265dupGTT	ENSP00000349768:p.Thr2060dup	140.0	0.0	.		126.0	40.0	0.317	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	In_Frame_Ins	INS	ENST00000357232.4	37	CCDS3785.1																																																																																			-|0.988;GTT|0.012	0.012	strong		0.376	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
LCNL1	401562	hgsc.bcm.edu	37	9	139879427	139879428	+	Frame_Shift_Ins	INS	-	-	GG			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139879427_139879428insGG	ENST00000408973.2	+	3	1053_1054	c.459_460insGG	c.(460-462)ctcfs	p.L154fs	LCNL1_ENST00000432827.1_Intron	NM_207510.3	NP_997393.3	Q6ZST4	LCNL1_HUMAN	lipocalin-like 1	154																	cctgcccctctctccctctctt	0.678																																					p.S153fs		Atlas-Indel	.											.	LCNL1	4	.	0			c.459_460insGG						PASS	.			103,3313		9,85,1614						-1.1	0.0			10	3,7317		0,3,3657	no	frameshift	LCNL1	NM_207510.3		9,88,5271	A1A1,A1R,RR		0.041,3.0152,0.9873				106,10630				SO:0001589	frameshift_variant	401562	exon3			.		CCDS43908.1	9q34.3	2014-01-22			ENSG00000214402	ENSG00000214402		"""Lipocalins"""	34436	protein-coding gene	gene with protein product							Standard	NM_207510		Approved	FLJ45224	uc004ckh.1	Q6ZST4	OTTHUMG00000159546	Exception_encountered	9.37:g.139879427_139879428insGG	ENSP00000386162:p.Leu154fs	314.0	0.0	0		217.0	14.0	0.0645161	NM_207510		Frame_Shift_Ins	INS	ENST00000408973.2	37	CCDS43908.1																																																																																			.	.	none		0.678	LCNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356128.1	NM_207510	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057775	46057804	+	In_Frame_Del	DEL	TGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	TGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	-	rs138406502|rs587625812|rs587722247|rs146378555|rs587701287	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	TGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46057775_46057804delTGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	ENST00000380095.1	+	1	503_532	c.441_470delTGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	c.(439-471)tgtgtgcctgtctgctctaagtccgtctgctat>tgt	p.VPVCSKSVCY148del	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	148	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						AGGCCTGCTGTGTGCCTGTCTGCTCTAAGTCCGTCTGCTATGTGCCTGTG	0.622																																					p.147_157del		Atlas-Indel	.											.	KRTAP10-10	37	.	0			c.440_469del						PASS	.		,	9,4255		1,7,2124					,	2.3	0.0			280	5,8249		2,1,4124	no	coding,intron	TSPEAR,KRTAP10-10	NM_181688.1,NM_144991.2	,	3,8,6248	A1A1,A1R,RR		0.0606,0.2111,0.1118	,	,		14,12504				SO:0001651	inframe_deletion	353333	exon1			.	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.441_470delTGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	21.37:g.46057775_46057804delTGTGCCTGTCTGCTCTAAGTCCGTCTGCTA	ENSP00000369438:p.Val148_Tyr157del	151.0	0.0	0		167.0	45.0	0.269461	NM_181688		In_Frame_Del	DEL	ENST00000380095.1	37	CCDS33585.1																																																																																			.	.	none		0.622	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
MN1	4330	hgsc.bcm.edu	37	22	28194912	28194913	+	In_Frame_Ins	INS	-	-	TGC			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:28194912_28194913insTGC	ENST00000302326.4	-	1	2573_2574	c.1619_1620insGCA	c.(1618-1620)caa>caGCAa	p.540_540Q>QQ		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	540	Poly-Gln.				intramembranous ossification (GO:0001957)					NS(1)|breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	45						gctgttgctgttgctgctgctg	0.658			T	ETV6	"""AML, meningioma"""																																p.Q540delinsQQ		Atlas-Indel	.		Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		"""L, O"""	MN1,NS,carcinoma,0,1	MN1	122	1	0			c.1620_1621insGCA						PASS	.																																			SO:0001652	inframe_insertion	4330	exon1			.	X82209	CCDS42998.1	22q12.1	2010-09-29			ENSG00000169184	ENSG00000169184			7180	protein-coding gene	gene with protein product	"""probable tumor suppressor protein MN1"""	156100	"""meningioma chromosome region"""	MGCR		7731706, 12569362	Standard	NM_002430		Approved	MGCR1-PEN, MGCR1	uc003adj.3	Q10571	OTTHUMG00000150975	ENST00000302326.4:c.1617_1619dupGCA	22.37:g.28194919_28194921dupTGC	ENSP00000304956:p.Gln550dup	42.0	0.0	0		56.0	27.0	0.482143	NM_002430	A9Z1V9	In_Frame_Ins	INS	ENST00000302326.4	37	CCDS42998.1																																																																																			.	.	weak		0.658	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320737.1	NM_002430	
CLCA4	22802	hgsc.bcm.edu	37	1	87045903	87045908	+	In_Frame_Del	DEL	CCTACT	CCTACT	-	rs56040873|rs77594462	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCTACT	CCTACT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:87045903_87045908delCCTACT	ENST00000370563.3	+	14	2677_2682	c.2635_2640delCCTACT	c.(2635-2640)cctactdel	p.PT885del	RP4-651E10.4_ENST00000456587.1_RNA	NM_012128.3	NP_036260.2	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	885					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44		Lung NSC(277;0.238)		all cancers(265;0.0202)|Epithelial(280;0.0404)		TGAtcctacacctactcctactccta	0.345																																					p.878_880del		Pindel,Atlas-Indel	.											.	CLCA4	131	.	0			c.2634_2639del						PASS	.			2247,6,1315		606,4,1031,1,0,142						-0.9	0.0		dbSNP_108	97	5524,10,2288		1973,7,1571,1,1,358	no	codingComplex	CLCA4	NM_012128.3		2579,11,2602,2,1,500	A1A1,A1A2,A1R,A2A2,A2R,RR		29.3787,37.0235,31.7735				7771,16,3603				SO:0001651	inframe_deletion	22802	exon14			.	AF127035	CCDS41355.1	1p31-p22	2012-02-26	2009-01-29		ENSG00000016602	ENSG00000016602			2018	protein-coding gene	gene with protein product			"""chloride channel, calcium activated, family member 4"", ""chloride channel regulator 4"""			10437792	Standard	NM_012128		Approved	CaCC2	uc009wcs.3	Q14CN2	OTTHUMG00000010260	ENST00000370563.3:c.2635_2640delCCTACT	1.37:g.87045909_87045914delCCTACT	ENSP00000359594:p.Pro885_Thr886del	146.0	0.0	.		181.0	46.0	0.254	NM_012128	A8MQC9|B7Z1Q5|Q6UX81|Q9UNF7	In_Frame_Del	DEL	ENST00000370563.3	37	CCDS41355.1																																																																																			.	.	weak		0.345	CLCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028292.1	NM_012128	
SEC63	11231	hgsc.bcm.edu	37	6	108214734	108214735	+	In_Frame_Ins	INS	-	-	GTA			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:108214734_108214735insGTA	ENST00000369002.4	-	16	1804_1805	c.1625_1626insTAC	c.(1624-1626)cca>ccTACa	p.542_543insT		NM_007214.4	NP_009145.1	Q9UGP8	SEC63_HUMAN	SEC63 homolog (S. cerevisiae)	542					liver development (GO:0001889)|multicellular organismal aging (GO:0010259)|nitrogen compound metabolic process (GO:0006807)|posttranslational protein targeting to membrane (GO:0006620)|posttranslational protein targeting to membrane, translocation (GO:0031204)|protein targeting to membrane (GO:0006612)|renal system development (GO:0072001)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)	p.P542Q(1)		endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36		all_cancers(87;5.35e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.00225)|Colorectal(196;0.0294)		BRCA - Breast invasive adenocarcinoma(108;0.0079)|Epithelial(106;0.0356)|all cancers(137;0.0525)|OV - Ovarian serous cystadenocarcinoma(136;0.054)		GCTTTGACTGTGGTAATAGCAC	0.322																																					p.P542delinsPT		Pindel,Atlas-Indel	.											.	SEC63	79	.	1	Substitution - Missense(1)	lung(1)	c.1626_1627insTAC						PASS	.			6,4258		0,6,2126						-3.9	0.9			138	0,8254		0,0,4127	no	coding	SEC63	NM_007214.4		0,6,6253	A1A1,A1R,RR		0.0,0.1407,0.0479				6,12512				SO:0001652	inframe_insertion	11231	exon16			.	BC048287	CCDS5061.1	6q21	2011-09-05	2006-09-12		ENSG00000025796	ENSG00000025796		"""Heat shock proteins / DNAJ (HSP40)"""	21082	protein-coding gene	gene with protein product		608648	"""SEC63-like (S. cerevisiae)"""			10219736, 10543453	Standard	NM_007214		Approved	SEC63L, PRO2507, ERdj2, DNAJC23	uc003psc.4	Q9UGP8	OTTHUMG00000015316	ENST00000369002.4:c.1625_1626insTAC	6.37:g.108214734_108214735insGTA	ENSP00000357998:p.Pro542_Gln543insThr	104.0	0.0	.		110.0	39.0	0.355	NM_007214	O95380|Q5THN4|Q86VS9|Q8IWL0|Q9NTE0	In_Frame_Ins	INS	ENST00000369002.4	37	CCDS5061.1																																																																																			.	.	none		0.322	SEC63-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041705.4	NM_007214	
RNF34	80196	hgsc.bcm.edu	37	12	121858078	121858080	+	In_Frame_Del	DEL	GAT	GAT	-	rs370767127|rs72059744|rs185279212	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GAT	GAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:121858078_121858080delGAT	ENST00000392464.2	+	4	736_738	c.667_669delGAT	c.(667-669)gatdel	p.D229del	RNF34_ENST00000361234.5_In_Frame_Del_p.D229del|RNF34_ENST00000555076.1_Intron|RNF34_ENST00000392465.3_In_Frame_Del_p.D230del					ring finger protein 34, E3 ubiquitin protein ligase											breast(1)|large_intestine(1)	2	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000432)|Epithelial(86;0.00233)		AAACACAGAAgatgatgatgacg	0.404														186	0.0371406	0.1339	0.013	5008	,	,		22592	0.0		0.0	False		,,,				2504	0.0				p.223_224del		Pindel,Atlas-Indel	.											.	RNF34	54	.	0			c.669_671del						PASS	.		,	485,3779		29,427,1676					,	-2.2	0.9		dbSNP_130	70	6,8246		0,6,4120	no	coding,coding	RNF34	NM_194271.1,NM_025126.2	,	29,433,5796	A1A1,A1R,RR		0.0727,11.3743,3.923	,	,		491,12025				SO:0001651	inframe_deletion	80196	exon5			.	AF306709, AB084914	CCDS9221.1, CCDS31915.1, CCDS73538.1	12q24.31	2012-02-23	2012-02-23			ENSG00000170633		"""RING-type (C3HC4) zinc fingers"""	17297	protein-coding gene	gene with protein product		608299	"""ring finger protein 34"""			12118383	Standard	NM_025126		Approved	RIFF, FLJ21786, RIF	uc001ual.2	Q969K3		ENST00000392464.2:c.667_669delGAT	12.37:g.121858084_121858086delGAT	ENSP00000376257:p.Asp229del	66.0	0.0	.		92.0	35.0	0.380	NM_194271		In_Frame_Del	DEL	ENST00000392464.2	37																																																																																				GAT|0.969;-|0.031	0.031	strong		0.404	RNF34-005	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000413892.1	NM_194271	
TBC1D5	9779	hgsc.bcm.edu	37	3	17208285	17208286	+	Frame_Shift_Del	DEL	CG	CG	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CG	CG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:17208285_17208286delCG	ENST00000253692.7	-	21	3731_3732	c.2067_2068delCG	c.(2065-2070)agcgttfs	p.V690fs	TBC1D5_ENST00000429383.4_Frame_Shift_Del_p.V690fs|TBC1D5_ENST00000414318.2_5'UTR|TBC1D5_ENST00000446818.2_Frame_Shift_Del_p.V712fs	NM_014744.2	NP_055559.1	Q92609	TBCD5_HUMAN	TBC1 domain family, member 5	690						retromer complex (GO:0030904)	Rab GTPase activator activity (GO:0005097)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	36						GACATTTGAACGCTCTGGCCTT	0.51																																					p.712_712del		Pindel,Atlas-Indel	.											.	TBC1D5	69	.	0			c.2134_2135del						PASS	.																																			SO:0001589	frameshift_variant	9779	exon23			.	D86965	CCDS33714.1, CCDS46770.1	3p24.3	2013-07-09			ENSG00000131374	ENSG00000131374			19166	protein-coding gene	gene with protein product		615740				19531583	Standard	NM_014744		Approved	KIAA0210	uc003cbe.3	Q92609	OTTHUMG00000155488	ENST00000253692.7:c.2067_2068delCG	3.37:g.17208285_17208286delCG	ENSP00000253692:p.Val690fs	165.0	0.0	.		180.0	46.0	0.256	NM_001134381	A6NP25|C9JP52	Frame_Shift_Del	DEL	ENST00000253692.7	37	CCDS33714.1																																																																																			.	.	none		0.510	TBC1D5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340301.3	NM_014744	
SERPINB3	6317	hgsc.bcm.edu	37	18	61323014	61323014	+	Frame_Shift_Del	DEL	T	T	-	rs201374310|rs386804125|rs60286570	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61323014delT	ENST00000283752.5	-	8	1193	c.1050delA	c.(1048-1050)gtafs	p.V350fs	SERPINB11_ENST00000489748.1_RNA|SERPINB3_ENST00000332821.8_Frame_Shift_Del_p.V298fs	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	350					negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						ATCCGAATCCTACTACAGCGG	0.493																																					p.G351fs		Atlas-Indel	.											.	SERPINB3	90	.	0			c.1051delG						PASS	.			402,3860		46,310,1775	115.0	125.0	122.0			-4.0	0.0	18	dbSNP_130	124	9,8245		0,9,4118	no	frameshift	SERPINB3	NM_006919.2		46,319,5893	A1A1,A1R,RR		0.109,9.4322,3.2838			61323014	411,12105	2202	4300	6502	SO:0001589	frameshift_variant	6317	exon8			.	U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"""Serine (or cysteine) peptidase inhibitors"""	10569	protein-coding gene	gene with protein product		600517	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"""	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.1050delA	18.37:g.61323014delT	ENSP00000283752:p.Val350fs	209.0	0.0	0		182.0	49.0	0.269231	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	Frame_Shift_Del	DEL	ENST00000283752.5	37	CCDS11987.1																																																																																			T|0.960;-|0.040	0.040	strong		0.493	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919	
ORM2	5005	hgsc.bcm.edu	37	9	117095395	117095397	+	In_Frame_Del	DEL	AGG	AGG	-	rs530796283|rs537714275	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGG	AGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117095395_117095397delAGG	ENST00000431067.2	+	6	623_625	c.587_589delAGG	c.(586-591)caggag>cag	p.E198del		NM_000608.2	NP_000599.1	P19652	A1AG2_HUMAN	orosomucoid 2	198					acute-phase response (GO:0006953)|regulation of immune system process (GO:0002682)|transport (GO:0006810)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(1)	7		Myeloproliferative disorder(63;0.163)			Chlorpromazine(DB00477)|Oxycodone(DB00497)|Thalidomide(DB01041)	GAGAGGAAACAGGAGGAGGGGGA	0.581														13	0.00259585	0.0083	0.0014	5008	,	,		22543	0.0		0.001	False		,,,				2504	0.0				p.196_196del	NSCLC(65;867 1308 1814 2391 12508)	Atlas-Indel	.											.	ORM2	13	.	0			c.586_588del						PASS	.			39,3131		1,37,1547						1.8	0.0			15	1,5925		0,1,2962	no	coding	ORM2	NM_000608.2		1,38,4509	A1A1,A1R,RR		0.0169,1.2303,0.4398				40,9056				SO:0001651	inframe_deletion	5005	exon6			.		CCDS6804.1	9q32	2013-09-19			ENSG00000228278	ENSG00000228278		"""Lipocalins"""	8499	protein-coding gene	gene with protein product	"""alpha-1-acid glycoprotein, type 2"""	138610				4711474, 2970990	Standard	NM_000608		Approved	AGP-B, AGP-B', AGP2		P19652	OTTHUMG00000021014	ENST00000431067.2:c.587_589delAGG	9.37:g.117095401_117095403delAGG	ENSP00000394936:p.Glu198del	871.0	0.0	0		888.0	290.0	0.326577	NM_000608	B2R5L2|Q16571|Q5T538|Q6IB74	In_Frame_Del	DEL	ENST00000431067.2	37	CCDS6804.1																																																																																			.	.	none		0.581	ORM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055432.1	NM_000608	
TRIM16	10626	hgsc.bcm.edu	37	17	15546132	15546133	+	Splice_Site	INS	-	-	A	rs577610193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:15546132_15546133insA	ENST00000578237.1	-	7	1375		c.e7-2		RP11-385D13.1_ENST00000455584.2_Splice_Site|TRIM16_ENST00000416464.2_Splice_Site|TRIM16_ENST00000579219.1_5'UTR|TRIM16_ENST00000577886.1_5'UTR|TRIM16_ENST00000336708.7_Splice_Site|TRIM16_ENST00000581224.1_Splice_Site			O95361	TRI16_HUMAN	tripartite motif containing 16						histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription, DNA-templated (GO:0045893)|response to growth hormone (GO:0060416)|response to organophosphorus (GO:0046683)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)|PML body (GO:0016605)	DNA binding (GO:0003677)|interleukin-1 binding (GO:0019966)|NACHT domain binding (GO:0032089)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	19				UCEC - Uterine corpus endometrioid carcinoma (92;0.0839)|Epithelial(1;8.4e-29)|all cancers(1;3.06e-28)|Colorectal(1;1.57e-19)|OV - Ovarian serous cystadenocarcinoma(1;6.1e-17)|COAD - Colon adenocarcinoma(1;3.38e-12)|READ - Rectum adenocarcinoma(2;1.46e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0559)		GAGTTCAGCCTAAAAGTGGAAA	0.515													AAAAA|AAAA|AAAAA|deletion	377	0.0752796	0.2511	0.0173	5008	,	,		20717	0.0		0.0099	False		,,,				2504	0.0235				.		Atlas-Indel	.											.	TRIM16	45	.	0			c.520-2->T						PASS	.			457,1595		140,177,709						3.8	0.9			2	44,3468		15,14,1727	no	splice-3	TRIM16	NM_006470.3		155,191,2436	A1A1,A1R,RR		1.2528,22.271,9.0043				501,5063				SO:0001630	splice_region_variant	10626	exon6			.	AF096870	CCDS11171.1	17p11.2	2011-04-20	2011-01-25		ENSG00000221926	ENSG00000221926		"""Tripartite motif containing / Tripartite motif containing"""	17241	protein-coding gene	gene with protein product	"""estrogen-responsive B box protein"""	609505	"""tripartite motif-containing 16"""			11331580	Standard	NM_006470		Approved	EBBP	uc002gor.1	O95361	OTTHUMG00000059067	ENST00000578237.1:c.520-2->T	17.37:g.15546136_15546136dupA		335.0	0.0	0		402.0	88.0	0.218905	NM_006470	Q6IAL8|Q7Z6I2|Q96BE8|Q96J43	Splice_Site	INS	ENST00000578237.1	37	CCDS11171.1																																																																																			.	.	none		0.515	TRIM16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130700.2	NM_006470	Intron
LTF	4057	hgsc.bcm.edu	37	3	46496843	46496843	+	Frame_Shift_Del	DEL	C	C	-	rs571988865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:46496843delC	ENST00000231751.4	-	5	884	c.589delG	c.(589-591)gaafs	p.E197fs	LTF_ENST00000417439.1_Frame_Shift_Del_p.E197fs|LTF_ENST00000426532.2_Frame_Shift_Del_p.E153fs	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	197	Transferrin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00741}.				antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		CATTTGTTTTCCCCTGTCCCC	0.562													CCCC|CCCC|CCC|deletion	12	0.00239617	0.0091	0.0	5008	,	,		22260	0.0		0.0	False		,,,				2504	0.0				p.E197fs		Pindel,Atlas-Indel	.											.	LTF	98	.	0			c.590delA						PASS	.		,	55,4211		13,29,2091	144.0	122.0	129.0		,	-9.6	0.0	3		130	74,8180		37,0,4090	no	frameshift,frameshift	LTF	NM_002343.3,NM_001199149.1	,	50,29,6181	A1A1,A1R,RR		0.8965,1.2893,1.0304	,	,	46496843	129,12391	2203	4300	6503	SO:0001589	frameshift_variant	4057	exon5			.		CCDS33747.1, CCDS56251.1	3p21.31	2012-10-02			ENSG00000012223	ENSG00000012223			6720	protein-coding gene	gene with protein product		150210				17476971, 3356163	Standard	NM_001199149		Approved	HLF2	uc003cpq.3	P02788	OTTHUMG00000156325	ENST00000231751.4:c.589delG	3.37:g.46496843delC	ENSP00000231751:p.Glu197fs	128.0	0.0	.		143.0	43.0	0.301	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Frame_Shift_Del	DEL	ENST00000231751.4	37	CCDS33747.1																																																																																			.	.	none		0.562	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343	
Unknown	0	hgsc.bcm.edu	37	2	98129757	98129758	+	IGR	INS	-	-	T	rs367988895|rs567331785	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:98129757_98129758insT								AC159540.1 (38708 upstream) : ANKRD36B (34269 downstream)																							TTATTCTTAACTTTTCCCTAAC	0.337																																					p.K897fs		Atlas-Indel	.											.	.	.	.	0			c.2691_2692insA						PASS	.																																			SO:0001628	intergenic_variant	57730	exon38			.																													2.37:g.98129761_98129761dupT		1139.0	0.0	0		678.0	61.0	0.0899705	NM_025190		Frame_Shift_Ins	INS		37																																																																																				.	.	weak	0	0.337								
PROL1	58503	hgsc.bcm.edu	37	4	71275631	71275632	+	Frame_Shift_Ins	INS	-	-	C	rs573505950|rs201259916	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:71275631_71275632insC	ENST00000399575.2	+	3	760_761	c.586_587insC	c.(586-588)accfs	p.T196fs		NM_021225.4	NP_067048.4	Q99935	PROL1_HUMAN	proline rich, lacrimal 1	196	Thr-rich.				negative regulation of endopeptidase activity (GO:0010951)|regulation of sensory perception of pain (GO:0051930)|retina homeostasis (GO:0001895)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	endopeptidase inhibitor activity (GO:0004866)|peptidase inhibitor activity (GO:0030414)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(3)	15		all_hematologic(202;0.196)				ATCAGCAGCAACCCCCGCAGCA	0.49													CCCCC|CCCCC|CCCCCC|insertion	10	0.00199681	0.0068	0.0014	5008	,	,		19421	0.0		0.0	False		,,,				2504	0.0				p.T196fs		Pindel,Atlas-Indel	.											.	PROL1	46	.	0			c.586_587insC						PASS	.			26,3928		2,22,1953						0.2	0.0			139	0,8034		0,0,4017	no	frameshift	PROL1	NM_021225.4		2,22,5970	A1A1,A1R,RR		0.0,0.6576,0.2169				26,11962				SO:0001589	frameshift_variant	58503	exon3			.	S83198	CCDS43235.1	4q13.3	2011-10-28	2005-02-07		ENSG00000171199	ENSG00000171199			17279	protein-coding gene	gene with protein product		608936	"""proline rich 1"""			8670737	Standard	NM_021225		Approved	BPLP, PRL1, opiorphin	uc003hfi.3	Q99935	OTTHUMG00000160845	ENST00000399575.2:c.591dupC	4.37:g.71275636_71275636dupC	ENSP00000382485:p.Thr196fs	167.0	0.0	.		197.0	65.0	0.330	NM_021225	A8MZ07|P85047	Frame_Shift_Ins	INS	ENST00000399575.2	37	CCDS43235.1																																																																																			.	.	none		0.490	PROL1-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000362639.1	NM_021225	
LINC00471	151477	hgsc.bcm.edu	37	2	232373857	232373860	+	RNA	DEL	TTCT	TTCT	-	rs374163700|rs150545131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TTCT	TTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:232373857_232373860delTTCT	ENST00000313064.2	-	0	558_561					NR_024079.1		Q8N535	CB052_HUMAN	long intergenic non-protein coding RNA 471																		TACAGAAGGATTCTTTATCTTCCT	0.5														25	0.00499201	0.0182	0.0014	5008	,	,		18054	0.0		0.0	False		,,,				2504	0.0				.		Pindel,Atlas-Indel	.											.	.	.	.	0			.						PASS	.			63,4203		3,57,2073						-2.7	0.0		dbSNP_131	199	2,8252		0,2,4125	no	intergenic				3,59,6198	A1A1,A1R,RR		0.0242,1.4768,0.5192				65,12455						151477	.			.	BC033054		2q37.1	2012-10-12	2011-08-31	2011-08-31	ENSG00000181798	ENSG00000181798		"""Long non-coding RNAs"""	28668	non-coding RNA	RNA, long non-coding			"""chromosome 2 open reading frame 52"""	C2orf52		12477932	Standard	NR_024079		Approved	MGC43122	uc002vrx.1	Q8N535	OTTHUMG00000133227		2.37:g.232373857_232373860delTTCT		237.0	0.0	.		251.0	69.0	0.275	.		RNA	DEL	ENST00000313064.2	37																																																																																				TTCT|0.994;-|0.006	0.006	strong		0.500	LINC00471-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000256963.2	NM_173513	
OR5L2	26338	hgsc.bcm.edu	37	11	55594980	55594980	+	Frame_Shift_Del	DEL	G	G	-	rs571342053|rs144106069	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55594980delG	ENST00000378397.1	+	1	286	c.286delG	c.(286-288)gggfs	p.G96fs		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	96						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|large_intestine(1)|lung(42)|ovary(1)|prostate(3)|skin(1)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	59		all_epithelial(135;0.208)				CTCCTTCCTAGGGTGCATGGT	0.473										HNSCC(27;0.073)			|||unknown(ALL_OTHER_Ns)	28	0.00559105	0.0189	0.0043	5008	,	,		23720	0.0		0.0	False		,,,				2504	0.0				p.L95fs		Pindel,Atlas-Indel	.											OR5L2,NS,carcinoma,+2,2	OR5L2	135	2	0			c.285delA						PASS	.			101,4161		1,99,2031	187.0	181.0	183.0			-0.1	0.0	11	dbSNP_134	184	4,8248		0,4,4122	no	frameshift	OR5L2	NM_001004739.1		1,103,6153	A1A1,A1R,RR		0.0485,2.3698,0.8391			55594980	105,12409	2200	4296	6496	SO:0001589	frameshift_variant	26338	exon1			.	AB065782	CCDS31511.1	11q11	2012-08-09			ENSG00000205030	ENSG00000205030		"""GPCR / Class A : Olfactory receptors"""	8351	protein-coding gene	gene with protein product						1370859	Standard	NM_001004739		Approved	HTPCRX16, HSHTPCRX16	uc001nhy.1	Q8NGL0	OTTHUMG00000166812	ENST00000378397.1:c.286delG	11.37:g.55594980delG	ENSP00000367650:p.Gly96fs	201.0	0.0	.		141.0	37.0	0.262	NM_001004739	Q6IF66|Q96RB2	Frame_Shift_Del	DEL	ENST00000378397.1	37	CCDS31511.1																																																																																			G|0.995;-|0.005	0.005	strong		0.473	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739	
CEP85L	387119	hgsc.bcm.edu	37	6	118812811	118812813	+	Intron	DEL	TGT	TGT	-	rs71866282	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:118812811_118812813delTGT	ENST00000368491.3	-	6	2059				CEP85L_ENST00000368488.5_Intron|CEP85L_ENST00000392500.3_In_Frame_Del_p.Q494del|CEP85L_ENST00000419517.2_In_Frame_Del_p.Q491del|CEP85L_ENST00000360290.3_In_Frame_Del_p.Q389del	NM_001042475.2	NP_001035940.1	Q5SZL2	CE85L_HUMAN	centrosomal protein 85kDa-like							centrosome (GO:0005813)|cytoplasm (GO:0005737)											GCTGAGGAAATGTTGTTGACCTA	0.32														166	0.033147	0.059	0.0173	5008	,	,		18299	0.0		0.0189	False		,,,				2504	0.0583				p.492_492del		Pindel,Atlas-Indel	.											.	CEP85L	26	.	0			c.1474_1476del						PASS	.		,,	241,4015		6,229,1893					,,	3.5	0.0		dbSNP_130	43	164,8084		2,160,3962	no	coding,intron,intron	C6orf204	NM_206921.2,NM_001178035.1,NM_001042475.2	,,	8,389,5855	A1A1,A1R,RR		1.9884,5.6626,3.239	,,	,,		405,12099				SO:0001627	intron_variant	387119	exon6			.	AF308284	CCDS5119.2, CCDS43498.1, CCDS55052.1	6q22.31	2011-11-25	2011-11-25	2011-11-25	ENSG00000111860	ENSG00000111860			21638	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 204"""	C6orf204			Standard	NM_206921		Approved	NY-BR-15, bA57K17.2	uc003pya.2	Q5SZL2	OTTHUMG00000015465	ENST00000368491.3:c.1437+35ACA>-	6.37:g.118812814_118812816delTGT		77.0	0.0	.		70.0	30.0	0.429	NM_206921	A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289	In_Frame_Del	DEL	ENST00000368491.3	37	CCDS43498.1																																																																																			TGT|0.979;-|0.021	0.021	strong		0.320	CEP85L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041996.2	NM_001042475	
PCDHAC2	56134	hgsc.bcm.edu	37	5	140346446	140346451	+	In_Frame_Del	DEL	TGCTGC	TGCTGC	-	rs148181752		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TGCTGC	TGCTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140346446_140346451delTGCTGC	ENST00000289269.5	+	1	627_632	c.95_100delTGCTGC	c.(94-102)ttgctgctg>ttg	p.32_34LLL>L	PCDHA11_ENST00000398640.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA3_ENST00000522353.2_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	32					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|liver(2)|lung(9)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	45			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ctgctgctgttgctgctgctgctACC	0.704																																					p.32_33del	Melanoma(190;638 2083 3390 11909 52360)	Pindel,Atlas-Indel	.											.	PCDHAC2	142	.	0			c.94_99del						PASS	.		,,,,,,,,,,,,,,,,,,	283,11,3622		45,0,193,0,11,1709					,,,,,,,,,,,,,,,,,,	0.2	0.7		dbSNP_134	8	13,29,7600		3,0,7,1,27,3783	no	codingComplex,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,codingComplex,intron	PCDHA9,PCDHAC2,PCDHAC1,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_031883.2,NM_031860.1,NM_031857.1,NM_031849.1,NM_031411.1,NM_018911.2,NM_018910.2,NM_018909.2,NM_018908.2,NM_018907.2,NM_018906.2,NM_018905.2,NM_018904.2,NM_018903.2,NM_018902.3,NM_018901.2,NM_018900.2,NM_018899.5,NM_018898.3	,,,,,,,,,,,,,,,,,,	48,0,200,1,38,5492	A1A1,A1A2,A1R,A2A2,A2R,RR		0.5496,7.5077,2.9071	,,,,,,,,,,,,,,,,,,	,,,,,,,,,,,,,,,,,,		296,40,11222				SO:0001651	inframe_deletion	56134	exon1			.	AF152474	CCDS4242.1	5q31	2010-11-26			ENSG00000243232	ENSG00000243232		"""Cadherins / Protocadherins : Clustered"""	8677	other	complex locus constituent		606321				10380929	Standard	NM_031883		Approved	PCDH-ALPHA-C2		Q9Y5I4	OTTHUMG00000129607	ENST00000289269.5:c.95_100delTGCTGC	5.37:g.140346452_140346457delTGCTGC	ENSP00000289269:p.Leu34_Leu35del	90.0	0.0	.		80.0	17.0	0.213	NM_031883	Q2M3V1|Q9Y5F4	In_Frame_Del	DEL	ENST00000289269.5	37	CCDS4242.1																																																																																			TGCTGC|0.974;-|0.026	0.026	strong		0.704	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899	
ZNF594	84622	hgsc.bcm.edu	37	17	5085878	5085879	+	Frame_Shift_Del	DEL	CT	CT	-	rs146837771	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5085878_5085879delCT	ENST00000399604.4	-	1	1813_1814	c.1673_1674delAG	c.(1672-1674)gagfs	p.E558fs	ZNF594_ENST00000575779.1_Frame_Shift_Del_p.E558fs			Q96JF6	ZN594_HUMAN	zinc finger protein 594	558					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						GAATTTTCTGCTCTCCCCTAAG	0.47														55	0.0109824	0.0378	0.0029	5008	,	,		21001	0.0		0.003	False		,,,				2504	0.0				p.558_559del		Pindel,Atlas-Indel	.											.	ZNF594	89	.	0			c.1674_1675del						PASS	.			154,3700		12,130,1785						-0.1	0.0		dbSNP_134	128	1,8047		0,1,4023	no	frameshift	ZNF594	NM_032530.1		12,131,5808	A1A1,A1R,RR		0.0124,3.9958,1.3023				155,11747				SO:0001589	frameshift_variant	84622	exon2			.	AB058774	CCDS42241.1	17p13	2013-01-08			ENSG00000180626	ENSG00000180626		"""Zinc fingers, C2H2-type"""	29392	protein-coding gene	gene with protein product						11347906	Standard	NM_032530		Approved	KIAA1871	uc010cla.1	Q96JF6	OTTHUMG00000132059	ENST00000399604.4:c.1673_1674delAG	17.37:g.5085880_5085881delCT	ENSP00000382513:p.Glu558fs	120.0	0.0	.		117.0	33.0	0.282	NM_032530	Q6RFS0	Frame_Shift_Del	DEL	ENST00000399604.4	37	CCDS42241.1																																																																																			CT|0.987;-|0.013	0.013	strong		0.470	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737	
TNRC6A	27327	hgsc.bcm.edu	37	16	24788401	24788402	+	In_Frame_Ins	INS	-	-	GCA	rs112426081|rs575176088	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:24788401_24788402insGCA	ENST00000395799.3	+	5	440_441	c.311_312insGCA	c.(310-315)ccgcag>ccGCAgcag	p.108_109insQ	TNRC6A_ENST00000315183.7_In_Frame_Ins_p.108_109insQ	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	108	Gln-rich.|Interaction with argonaute family proteins.				cellular response to starvation (GO:0009267)|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)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		cagcagcagccgcagcagcagc	0.589														11	0.00219649	0.0083	0.0	5008	,	,		10840	0.0		0.0	False		,,,				2504	0.0				p.P104delinsPQ		Atlas-Indel	.											TNRC6A,NS,carcinoma,0,1	TNRC6A	171	1	0			c.311_312insGCA						PASS	.			43,3543		6,31,1756						-2.9	0.0		dbSNP_132	22	8,7216		1,6,3605	no	coding	TNRC6A	NM_014494.2		7,37,5361	A1A1,A1R,RR		0.1107,1.1991,0.4718				51,10759				SO:0001652	inframe_insertion	27327	exon5			.	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"""Trinucleotide (CAG) repeat containing"""	11969	protein-coding gene	gene with protein product		610739	"""trinucleotide repeat containing 6"""	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.321_323dupGCA	16.37:g.24788408_24788410dupGCA	ENSP00000379144:p.Gln111_Gln112dup	48.0	0.0	0		55.0	11.0	0.2	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	In_Frame_Ins	INS	ENST00000395799.3	37	CCDS10624.2																																																																																			-|0.500;GCA|0.500	0.500	weak		0.589	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
SLC4A2	6522	hgsc.bcm.edu	37	7	150763616	150763621	+	In_Frame_Del	DEL	GGAGGC	GGAGGC	-	rs150330052|rs199537782|rs374531279	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGAGGC	GGAGGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150763616_150763621delGGAGGC	ENST00000485713.1	+	6	1631_1636	c.591_596delGGAGGC	c.(589-597)gaggaggcg>gag	p.EA202del	SLC4A2_ENST00000413384.2_In_Frame_Del_p.EA202del|SLC4A2_ENST00000310317.5_In_Frame_Del_p.EA120del|SLC4A2_ENST00000461735.1_In_Frame_Del_p.EA188del|SLC4A2_ENST00000392826.2_In_Frame_Del_p.EA193del	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	202	Pro-rich.		E -> V (in dbSNP:rs2229551). {ECO:0000269|Ref.2}.		anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(14)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCCAGGTGGAGGAGGCGGAGGCGGAG	0.733														191	0.038139	0.1316	0.0173	5008	,	,		15101	0.001		0.003	False		,,,				2504	0.001				p.197_199del		Pindel,Atlas-Indel	.											.	SLC4A2	98	.	0			c.590_595del						PASS	.		,,,	390,3074		94,202,1436					,,,	4.7	1.0		dbSNP_130	8	34,6758		8,18,3370	no	coding,coding,coding,coding	SLC4A2	NM_003040.3,NM_001199694.1,NM_001199693.1,NM_001199692.1	,,,	102,220,4806	A1A1,A1R,RR		0.5006,11.2587,4.1342	,,,	,,,		424,9832				SO:0001651	inframe_deletion	6522	exon6			.		CCDS5917.1, CCDS56520.1, CCDS56521.1	7q36.1	2013-07-19	2013-07-19		ENSG00000164889	ENSG00000164889		"""Solute carriers"""	11028	protein-coding gene	gene with protein product	"""anion exchanger 2 type a"", ""anion exchanger 2 type b1"", ""anion exchanger 2 type b2"""	109280	"""erythrocyte membrane protein band 3-like 1"", ""solute carrier family 4, anion exchanger, member 2 (erythrocyte membrane protein band 3-like 1)"""	EPB3L1, AE2		8434259	Standard	NM_003040		Approved	HKB3, BND3L, NBND3	uc003wit.4	P04920	OTTHUMG00000158443	ENST00000485713.1:c.591_596delGGAGGC	7.37:g.150763622_150763627delGGAGGC	ENSP00000419412:p.Glu202_Ala203del	56.0	0.0	.		49.0	12.0	0.245	NM_001199692	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	In_Frame_Del	DEL	ENST00000485713.1	37	CCDS5917.1																																																																																			GGAGGC|0.962;-|0.038	0.038	strong		0.733	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040	
C8orf82	414919	hgsc.bcm.edu	37	8	145753431	145753431	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145753431delT	ENST00000524821.1	-	2	397	c.182delA	c.(181-183)aagfs	p.K61fs	C8orf82_ENST00000313465.5_Frame_Shift_Del_p.K61fs|LRRC24_ENST00000529415.2_5'Flank|LRRC24_ENST00000533758.1_5'Flank			Q6P1X6	CH082_HUMAN	chromosome 8 open reading frame 82	61										endometrium(1)|urinary_tract(1)	2						GATGAAATTCTTCATTTTGGA	0.582																																					p.K61fs		Pindel,Atlas-Indel	.											C8orf82,bladder,carcinoma,0,1	C8orf82	7	1	0			c.183delG						PASS	.			1,4263		0,1,2131	86.0	84.0	85.0			3.7	1.0	8		85	0,8254		0,0,4127	no	frameshift	C8orf82	NM_001001795.1		0,1,6258	A1A1,A1R,RR		0.0,0.0235,0.0080			145753431	1,12517	2203	4300	6503	SO:0001589	frameshift_variant	414919	exon2			.		CCDS34970.1	8q24	2012-04-18			ENSG00000213563	ENSG00000213563			33826	protein-coding gene	gene with protein product						12477932	Standard	NM_001001795		Approved	MGC70857	uc003zdp.1	Q6P1X6	OTTHUMG00000165181	ENST00000524821.1:c.182delA	8.37:g.145753431delT	ENSP00000436621:p.Lys61fs	51.0	0.0	.		57.0	28.0	0.491	NM_001001795	Q6GMR2|Q6P2Q7	Frame_Shift_Del	DEL	ENST00000524821.1	37	CCDS34970.1																																																																																			.	.	none		0.582	C8orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382503.1	NM_001001795	
OR52D1	390066	hgsc.bcm.edu	37	11	5510498	5510499	+	Frame_Shift_Ins	INS	-	-	C	rs571241475|rs386750177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5510498_5510499insC	ENST00000322641.5	+	1	584_585	c.562_563insC	c.(562-564)gccfs	p.A188fs	HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron	NM_001005163.2	NP_001005163.1	Q9H346	O52D1_HUMAN	olfactory receptor, family 52, subfamily D, member 1	188					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)		TATGGGCATTGCCCGACTGGCC	0.51													CCC|CCC|CCCC|insertion	9	0.00179712	0.0053	0.0029	5008	,	,		22033	0.0		0.0	False		,,,				2504	0.0				p.A188fs		Atlas-Indel	.											.	OR52D1	66	.	0			c.562_563insC						PASS	.																																			SO:0001589	frameshift_variant	390066	exon1			.	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.565dupC	11.37:g.5510501_5510501dupC	ENSP00000326232:p.Ala188fs	121.0	0.0	0		134.0	54.0	0.402985	NM_001005163	B9EGY9|Q6IFI6	Frame_Shift_Ins	INS	ENST00000322641.5	37	CCDS31384.1																																																																																			.	.	none		0.510	OR52D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143372.1	NM_001005163	
RBPJL	11317	hgsc.bcm.edu	37	20	43940531	43940542	+	In_Frame_Del	DEL	CAGCGCGTCCGG	CAGCGCGTCCGG	-	rs142744285|rs367731607	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CAGCGCGTCCGG	CAGCGCGTCCGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43940531_43940542delCAGCGCGTCCGG	ENST00000343694.3	+	5	453_464	c.381_392delCAGCGCGTCCGG	c.(379-393)gacagcgcgtccggc>gac	p.SASG128del	RBPJL_ENST00000372741.3_In_Frame_Del_p.SASG128del|RBPJL_ENST00000372743.1_In_Frame_Del_p.SASG128del	NM_001281448.1|NM_001281449.1|NM_014276.2	NP_001268377.1|NP_001268378.1|NP_055091.2	Q9UBG7	RBPJL_HUMAN	recombination signal binding protein for immunoglobulin kappa J region-like	128					positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Myeloproliferative disorder(115;0.0122)				TGGGACTGGACAGCGCGTCCGGCAGCGCCACT	0.66											OREG0025979	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		73	0.0145767	0.0454	0.0072	5008	,	,		19337	0.0		0.004	False		,,,				2504	0.0041				p.127_131del		Pindel,Atlas-Indel	.											.	RBPJL	67	.	0			c.380_391del						PASS	.			129,3693		18,93,1800						4.2	1.0		dbSNP_134	9	24,7388		7,10,3689	no	coding	RBPJL	NM_014276.2		25,103,5489	A1A1,A1R,RR		0.3238,3.3752,1.3619				153,11081				SO:0001651	inframe_deletion	11317	exon5			.	AB024964	CCDS13349.1, CCDS63283.1, CCDS63284.1	20q13.12	2013-10-18	2007-02-26	2007-02-26	ENSG00000124232	ENSG00000124232			13761	protein-coding gene	gene with protein product			"""recombining binding protein suppressor of hairless (Drosophila)-like"""	RBPSUHL		9929984	Standard	NM_014276		Approved	RBP-L, SUH, SUHL	uc002xns.3	Q9UBG7	OTTHUMG00000033055	ENST00000343694.3:c.381_392delCAGCGCGTCCGG	20.37:g.43940531_43940542delCAGCGCGTCCGG	ENSP00000341243:p.Ser128_Gly131del	127.0	0.0	.	920	118.0	45.0	0.381	NM_014276	O95723|Q5QPU9|Q5QPV0|Q9ULV9	In_Frame_Del	DEL	ENST00000343694.3	37	CCDS13349.1																																																																																			CAGCGCGTCCGG|0.987;-|0.013	0.013	strong		0.660	RBPJL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080391.1	NM_014276	
ATP2C2	9914	hgsc.bcm.edu	37	16	84497336	84497337	+	Stop_Codon_Ins	INS	-	-	AGTGGA	rs149491518|rs568403499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84497336_84497337insAGTGGA	ENST00000262429.4	+	0	2928_2929				RP11-517C16.2_ENST00000565700.1_RNA|ATP2C2_ENST00000420010.2_3'UTR|ATP2C2_ENST00000416219.2_Stop_Codon_Ins	NM_014861.2	NP_055676.2	O75185	AT2C2_HUMAN	ATPase, Ca++ transporting, type 2C, member 2						ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(3)|skin(5)|urinary_tract(1)	33						TGAAGATGTGTAGTGGACCGCA	0.54														67	0.0133786	0.0499	0.0014	5008	,	,		19122	0.0		0.0	False		,,,				2504	0.0				p.X947delinsX		Pindel,Atlas-Indel	.											.	ATP2C2	75	.	0			c.2839_2840insAGTGGA						PASS	.			151,3647		1,149,1749						3.1	0.0		dbSNP_134	118	1,7939		0,1,3969	no	coding	ATP2C2	NM_014861.2		1,150,5718	A1A1,A1R,RR		0.0126,3.9758,1.2949				152,11586				SO:0001567	stop_retained_variant	9914	exon27			.	AK091051	CCDS42207.1, CCDS67088.1	16q24.1	2010-04-20			ENSG00000064270	ENSG00000064270	3.6.3.8	"""ATPases / P-type"""	29103	protein-coding gene	gene with protein product	"""secretory pathway calcium ATPase 2"""	613082				9734811	Standard	XM_006721355		Approved	KIAA0703, SPCA2	uc002fhx.3	O75185		ENST00000262429.4:c.2839_2844dupAGTGGA	16.37:g.84497337_84497342dupAGTGGA		146.0	0.0	.		120.0	26.0	0.217	NM_014861	B4DU76|E7ES94|Q5HYC3|Q5S053|Q68CQ2	In_Frame_Ins	INS	ENST00000262429.4	37	CCDS42207.1																																																																																			-|0.987;AGTGGA|0.013	0.013	strong		0.540	ATP2C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433404.1	NM_014861	
LRRC46	90506	hgsc.bcm.edu	37	17	45914125	45914136	+	In_Frame_Del	DEL	AGGAGCTGGAGC	AGGAGCTGGAGC	-	rs142960476|rs377191761	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGGAGCTGGAGC	AGGAGCTGGAGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:45914125_45914136delAGGAGCTGGAGC	ENST00000269025.4	+	8	968_979	c.605_616delAGGAGCTGGAGC	c.(604-618)aaggagctggagcag>aag	p.ELEQ203del		NM_033413.3	NP_219481.1	Q96FV0	LRC46_HUMAN	leucine rich repeat containing 46	203										endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|ovary(1)	9						GGCTTCCTCAAGGAGCTGGAGCAGGAGCTGAG	0.684														156	0.0311502	0.1104	0.013	5008	,	,		19410	0.0		0.0	False		,,,				2504	0.001				p.202_205del		Pindel,Atlas-Indel	.											.	LRRC46	25	.	0			c.604_615del						PASS	.			383,3877		24,335,1771						-3.3	0.8		dbSNP_134	24	7,8231		1,5,4113	no	coding	LRRC46	NM_033413.3		25,340,5884	A1A1,A1R,RR		0.085,8.9906,3.1205				390,12108				SO:0001651	inframe_deletion	90506	exon8			.		CCDS11518.1	17q21.32	2005-08-09				ENSG00000141294			25047	protein-coding gene	gene with protein product						12477932	Standard	NM_033413		Approved	MGC16309	uc002ima.3	Q96FV0		ENST00000269025.4:c.605_616delAGGAGCTGGAGC	17.37:g.45914125_45914136delAGGAGCTGGAGC	ENSP00000269025:p.Glu203_Gln206del	184.0	0.0	.		131.0	35.0	0.267	NM_033413	A8K9Q0	In_Frame_Del	DEL	ENST00000269025.4	37	CCDS11518.1																																																																																			AGGAGCTGGAGC|0.978;-|0.022	0.022	strong		0.684	LRRC46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441377.1	NM_033413	
UPK3BL	100134938	hgsc.bcm.edu	37	7	102281151	102281152	+	Frame_Shift_Ins	INS	-	-	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:102281151_102281152insA	ENST00000340457.8	-	2	230_231	c.181_182insT	c.(181-183)tccfs	p.S61fs	POLR2J2_ENST00000591000.1_3'UTR|POLR2J2_ENST00000333432.6_Frame_Shift_Ins_p.V99fs|RP11-514P8.6_ENST00000519541.1_Frame_Shift_Ins_p.S61fs|POLR2J2_ENST00000476151.1_3'UTR	NM_001114403.2	NP_001107875.1	B0FP48	UPK3L_HUMAN	uroplakin 3B-like	61						integral component of membrane (GO:0016021)				kidney(2)|stomach(1)	3						CGTGAAGGTGGACAGGGTGAGC	0.609																																					p.S61fs		Atlas-Indel	.											.	UPK3BL	6	.	0			c.182_183insT						PASS	.																																			SO:0001589	frameshift_variant	100134938	exon2			.	EU341824	CCDS47675.1	7q22.1	2014-02-12	2010-03-03		ENSG00000267368	ENSG00000267368			37278	protein-coding gene	gene with protein product	"""uroplakin-like protein"""						Standard	NM_001114403		Approved	UPLP		B0FP48	OTTHUMG00000165036	ENST00000340457.8:c.182dupT	7.37:g.102281152_102281152dupA	ENSP00000342938:p.Ser61fs	134.0	0.0	0		78.0	27.0	0.346154	NM_001114403		Frame_Shift_Ins	INS	ENST00000340457.8	37	CCDS47675.1																																																																																			.	.	none		0.609	UPK3BL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381510.1	NM_001114403	
ARID1A	8289	hgsc.bcm.edu	37	1	27097616	27097618	+	In_Frame_Del	DEL	AAG	AAG	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:27097616_27097618delAAG	ENST00000324856.7	+	12	3576_3578	c.3205_3207delAAG	c.(3205-3207)aagdel	p.K1069del	ARID1A_ENST00000457599.2_In_Frame_Del_p.K1069del|ARID1A_ENST00000540690.1_5'Flank|ARID1A_ENST00000374152.2_In_Frame_Del_p.K686del	NM_006015.4	NP_006006.3	O14497	ARI1A_HUMAN	AT rich interactive domain 1A (SWI-like)	1069	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				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)		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)		ACAGGTCAACAAGAACAAAAAAT	0.483			"""Mis, N, F, S, D"""		"""clear cell ovarian carcinoma, RCC"""																																p.1068_1069del		Pindel,Atlas-Indel	.		Rec	yes		1	1p35.3	8289	AT rich interactive domain 1A (SWI-like)		E	.	ARID1A	842	.	0			c.3204_3206del						PASS	.																																			SO:0001651	inframe_deletion	8289	exon12			.	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.3205_3207delAAG	1.37:g.27097616_27097618delAAG	ENSP00000320485:p.Lys1069del	81.0	0.0	.		79.0	16.0	0.203	NM_139135	D3DPL1|Q53FK9|Q5T0W1|Q5T0W2|Q5T0W3|Q8NFD6|Q96T89|Q9BY33|Q9HBJ5|Q9UPZ1	In_Frame_Del	DEL	ENST00000324856.7	37	CCDS285.1																																																																																			.	.	none		0.483	ARID1A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011437.2	NM_139135	
RSPH10B2	728194	hgsc.bcm.edu	37	7	6838173	6838176	+	Stop_Codon_Del	DEL	AGAG	AGAG	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGAG	AGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:6838173_6838176delAGAG	ENST00000403107.1	+	0	2999_3002				CCZ1B_ENST00000597208.1_5'Flank|RSPH10B2_ENST00000359718.3_3'UTR|RSPH10B2_ENST00000297186.3_Stop_Codon_Del|CCZ1B_ENST00000316731.8_3'UTR|RSPH10B2_ENST00000433859.2_Stop_Codon_Del|RSPH10B2_ENST00000404077.1_Stop_Codon_Del			B2RC85	R10B2_HUMAN	radial spoke head 10 homolog B2 (Chlamydomonas)											breast(3)|endometrium(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|skin(2)	15						AAGAAAAAGTAGAGAGACACGAGG	0.49																																					p.871_871del		Atlas-Indel	.											.	RSPH10B	28	.	0			c.2611_2884del						PASS	.																																			SO:0001567	stop_retained_variant	222967	exon21			.		CCDS43552.1	7p22.1	2008-07-04			ENSG00000169402	ENSG00000169402			34385	protein-coding gene	gene with protein product							Standard	NM_001099697		Approved		uc003sqw.1	B2RC85	OTTHUMG00000151856	Exception_encountered	7.37:g.6838173_6838176delAGAG		497.0	0.0	0		379.0	34.0	0.0897098	NM_173565	A6NMW7|B2RXI4|B2RXJ0|Q86ST9|Q8NE68	Frame_Shift_Del	DEL	ENST00000403107.1	37	CCDS43552.1																																																																																			.	.	none		0.490	RSPH10B2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324184.4	NM_001099697	
ANKRD40	91369	hgsc.bcm.edu	37	17	48777220	48777221	+	In_Frame_Ins	INS	-	-	TCA	rs377717183|rs138572332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48777220_48777221insTCA	ENST00000285243.6	-	3	586_587	c.317_318insTGA	c.(316-318)gac>gaTGAc	p.106_106D>DD		NM_052855.3	NP_443087.1	Q6AI12	ANR40_HUMAN	ankyrin repeat domain 40	106	Poly-Asp.									breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|skin(1)|urinary_tract(1)	11			BRCA - Breast invasive adenocarcinoma(22;2.03e-09)			GGGGGAGGTTGtcatcatcatc	0.406														235	0.0469249	0.0908	0.0807	5008	,	,		16671	0.0337		0.004	False		,,,				2504	0.0215				p.D106delinsDD		Atlas-Indel	.											.	ANKRD40	35	.	0			c.318_319insTGA						PASS	.																																			SO:0001652	inframe_insertion	91369	exon3			.	BC012978	CCDS11572.1	17q21.33	2013-01-10			ENSG00000154945	ENSG00000154945		"""Ankyrin repeat domain containing"""	28233	protein-coding gene	gene with protein product						12477932	Standard	NM_052855		Approved	MGC15396	uc002iso.3	Q6AI12	OTTHUMG00000162255	ENST00000285243.6:c.315_317dupTGA	17.37:g.48777227_48777229dupTCA	ENSP00000285243:p.Asp106dup	40.0	0.0	0		51.0	15.0	0.294118	NM_052855	Q96E32	In_Frame_Ins	INS	ENST00000285243.6	37	CCDS11572.1																																																																																			-|0.957;TCA|0.043	0.043	strong		0.406	ANKRD40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368201.2	NM_052855	
C11orf16	56673	hgsc.bcm.edu	37	11	8942889	8942890	+	Frame_Shift_Del	DEL	AT	AT	-	rs398102297|rs10583719	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:8942889_8942890delAT	ENST00000326053.5	-	6	1483_1484	c.1377_1378delAT	c.(1375-1380)atatgtfs	p.IC459fs	C11orf16_ENST00000525780.1_Intron	NM_020643.2	NP_065694.2	Q9NQ32	CK016_HUMAN	chromosome 11 open reading frame 16	459										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	22				Epithelial(150;4.11e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0234)		TTCCACTGACATATTGCAAGGC	0.54														164	0.0327476	0.1135	0.0173	5008	,	,		18882	0.0		0.002	False		,,,				2504	0.0				p.460_460del		Pindel,Atlas-Indel	.											.	C11orf16	43	.	0			c.1378_1379del						PASS	.			445,3819		22,401,1709						-1.1	0.0		dbSNP_119	130	6,8248		0,6,4121	no	frameshift	C11orf16	NM_020643.2		22,407,5830	A1A1,A1R,RR		0.0727,10.4362,3.6028				451,12067				SO:0001589	frameshift_variant	56673	exon6			.	AJ400877	CCDS7794.1	11p15.3	2008-06-25			ENSG00000176029	ENSG00000176029			1169	protein-coding gene	gene with protein product						11528127	Standard	NM_020643		Approved		uc001mhb.4	Q9NQ32	OTTHUMG00000165654	ENST00000326053.5:c.1377_1378delAT	11.37:g.8942891_8942892delAT	ENSP00000318999:p.Ile459fs	174.0	0.0	.		179.0	52.0	0.291	NM_020643	Q53FB2|Q8N6Y9	Frame_Shift_Del	DEL	ENST00000326053.5	37	CCDS7794.1																																																																																			AT|0.978;-|0.022	0.022	strong		0.540	C11orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385626.1	NM_020643	
TLDC1	57707	hgsc.bcm.edu	37	16	84529358	84529360	+	In_Frame_Del	DEL	CTC	CTC	-	rs200260198	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84529358_84529360delCTC	ENST00000343629.6	-	3	495_497	c.313_315delGAG	c.(313-315)gagdel	p.E105del	TLDC1_ENST00000561807.1_5'UTR|TLDC1_ENST00000535580.1_In_Frame_Del_p.E78del|RP11-517C16.4_ENST00000568771.1_RNA	NM_020947.3	NP_065998.3	Q6P9B6	TLDC1_HUMAN	TBC/LysM-associated domain containing 1	105						lysosomal membrane (GO:0005765)											TGAGACTCTTCTCCTCGGAGTTT	0.542														32	0.00638978	0.0219	0.0029	5008	,	,		19194	0.0		0.001	False		,,,				2504	0.0				p.105_106del		Pindel,Atlas-Indel	.											.	KIAA1609	39	.	0			c.314_316del						PASS	.			120,4144		5,110,2017						4.2	0.9			119	32,8222		12,8,4107	no	coding	KIAA1609	NM_020947.3		17,118,6124	A1A1,A1R,RR		0.3877,2.8143,1.2143				152,12366				SO:0001651	inframe_deletion	57707	exon3			.	AB046829	CCDS32498.1	16q24.1	2013-03-14	2013-03-14	2013-03-14	ENSG00000140950	ENSG00000140950			29325	protein-coding gene	gene with protein product	"""TLD domain containing 1"""		"""KIAA1609"""	KIAA1609		10997877	Standard	NM_020947		Approved		uc002fib.3	Q6P9B6	OTTHUMG00000176739	ENST00000343629.6:c.313_315delGAG	16.37:g.84529361_84529363delCTC	ENSP00000343635:p.Glu105del	226.0	0.0	.		184.0	53.0	0.288	NM_020947	Q8IZ64|Q9HCG3|Q9NTE8	In_Frame_Del	DEL	ENST00000343629.6	37	CCDS32498.1																																																																																			CTC|0.994;-|0.006	0.006	strong		0.542	TLDC1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433421.1	NM_020947	
OR6P1	128366	hgsc.bcm.edu	37	1	158533298	158533299	+	Frame_Shift_Ins	INS	-	-	A	rs201077183		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158533298_158533299insA	ENST00000334632.1	-	1	95_96	c.96_97insT	c.(94-99)tttgcafs	p.A33fs		NM_001160325.1	NP_001153797.1	Q8NGX9	OR6P1_HUMAN	olfactory receptor, family 6, subfamily P, member 1	33						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(4)|lung(1)	6						AGGTAAATTGCAAAAAAAAGGA	0.47																																					p.A33fs		Pindel,Atlas-Indel	.											.	OR6P1	47	.	0			c.97_98insT						PASS	.																																			SO:0001589	frameshift_variant	128366	exon1			.	BK004193	CCDS53391.1	1q23.1	2012-08-09			ENSG00000186440	ENSG00000186440		"""GPCR / Class A : Olfactory receptors"""	15036	protein-coding gene	gene with protein product							Standard	NM_001160325		Approved		uc010pim.2	Q8NGX9	OTTHUMG00000019633	ENST00000334632.1:c.97dupT	1.37:g.158533306_158533306dupA	ENSP00000334721:p.Ala33fs	94.0	0.0	.		95.0	28.0	0.295	NM_001160325	Q6IFR9	Frame_Shift_Ins	INS	ENST00000334632.1	37	CCDS53391.1																																																																																			-|0.995;A|0.005	0.005	strong		0.470	OR6P1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051848.1		
FOXD4L3	286380	hgsc.bcm.edu	37	9	70919085	70919085	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:70919085delC	ENST00000342833.2	+	1	1810	c.1218delC	c.(1216-1218)tgcfs	p.C406fs		NM_199135.4	NP_954586.4	Q6VB84	FX4L3_HUMAN	forkhead box D4-like 3	406						nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			ovary(1)	1				all cancers(8;0.00136)|Epithelial(8;0.0288)|GBM - Glioblastoma multiforme(74;0.0402)|OV - Ovarian serous cystadenocarcinoma(323;0.18)		GGGCGCGGTGCTGGGCGGGCA	0.677																																					p.C406fs		Atlas-Indel	.											.	FOXD4L3	7	.	0			c.1217delG						PASS	.						2.0	3.0	2.0					9																	70919085		917	2379	3296	SO:0001589	frameshift_variant	286380	exon1			.	AY344642	CCDS43833.1	9q13	2008-05-13				ENSG00000187559			18523	protein-coding gene	gene with protein product		611086				12421752	Standard	NM_199135		Approved	OTTHUMG00000019959, FOXD6	uc004agm.1	Q6VB84	OTTHUMG00000019959	ENST00000342833.2:c.1218delC	9.37:g.70919085delC	ENSP00000341961:p.Cys406fs	668.0	0.0	0		931.0	76.0	0.0816327	NM_199135	Q5JTX9	Frame_Shift_Del	DEL	ENST00000342833.2	37	CCDS43833.1																																																																																			.	.	none		0.677	FOXD4L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052539.2	NM_199358	
PODXL2	50512	hgsc.bcm.edu	37	3	127379364	127379369	+	In_Frame_Del	DEL	GAAGAG	GAAGAG	-	rs200281996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GAAGAG	GAAGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:127379364_127379369delGAAGAG	ENST00000342480.6	+	3	532_537	c.493_498delGAAGAG	c.(493-498)gaagagdel	p.EE171del		NM_015720.2	NP_056535.1	Q9NZ53	PDXL2_HUMAN	podocalyxin-like 2	171	Glu-rich.				leukocyte tethering or rolling (GO:0050901)	integral component of plasma membrane (GO:0005887)	glycosaminoglycan binding (GO:0005539)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	26						agaggaggaagaagaggaagaggaag	0.553														37	0.00738818	0.0212	0.0014	5008	,	,		22508	0.005		0.0	False		,,,				2504	0.0031				p.164_166del		Pindel,Atlas-Indel	.											.	PODXL2	53	.	0			c.492_497del						PASS	.			61,4203		1,59,2072						-4.8	0.4			53	3,8251		1,1,4125	no	coding	PODXL2	NM_015720.2		2,60,6197	A1A1,A1R,RR		0.0363,1.4306,0.5113				64,12454				SO:0001651	inframe_deletion	50512	exon3			.	AF219137	CCDS3044.1	3q21.3	2005-02-18			ENSG00000114631	ENSG00000114631			17936	protein-coding gene	gene with protein product	"""endoglycan"""					10722749	Standard	NM_015720		Approved	PODLX2, endoglycan	uc003ejq.3	Q9NZ53	OTTHUMG00000159642	ENST00000342480.6:c.493_498delGAAGAG	3.37:g.127379370_127379375delGAAGAG	ENSP00000345359:p.Glu171_Glu172del	95.0	0.0	.		79.0	29.0	0.367	NM_015720	Q6UVY4|Q8WUV6	In_Frame_Del	DEL	ENST00000342480.6	37	CCDS3044.1																																																																																			GAAGAG|0.992;-|0.008	0.008	strong		0.553	PODXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356638.1	NM_015720	
OR2T27	403239	hgsc.bcm.edu	37	1	248813309	248813310	+	Frame_Shift_Ins	INS	-	-	A	rs141113411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248813309_248813310insA	ENST00000344889.3	-	1	875_876	c.876_877insT	c.(874-879)cttaggfs	p.R293fs		NM_001001824.1	NP_001001824.1	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T, member 27	293						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(2)|large_intestine(4)|lung(20)|skin(3)|stomach(1)	32	all_cancers(71;1.15e-05)|all_epithelial(71;5.29e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.089)|Lung NSC(105;0.0969)|Melanoma(84;0.199)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCCTTGTTCCTAAGGCTGTAAA	0.485													AA|AA|AAA|insertion	231	0.0461262	0.1664	0.013	5008	,	,		19512	0.0		0.0	False		,,,				2504	0.002				p.R293_N294delinsX		Atlas-Indel	.											.	OR2T27	52	.	0			c.877_878insT						PASS	.			510,3700		101,308,1696						0.7	0.2		dbSNP_134	74	5,8185		0,5,4090	no	frameshift	OR2T27	NM_001001824.1		101,313,5786	A1A1,A1R,RR		0.0611,12.114,4.1532				515,11885				SO:0001589	frameshift_variant	403239	exon1			.		CCDS31124.1	1q44	2012-08-09			ENSG00000187701	ENSG00000187701		"""GPCR / Class A : Olfactory receptors"""	31252	protein-coding gene	gene with protein product							Standard	NM_001001824		Approved		uc010pzo.2	Q8NH04	OTTHUMG00000040376	ENST00000344889.3:c.877dupT	1.37:g.248813311_248813311dupA	ENSP00000342008:p.Arg293fs	280.0	0.0	0		251.0	39.0	0.155378	NM_001001824		Frame_Shift_Ins	INS	ENST00000344889.3	37	CCDS31124.1																																																																																			-|0.960;A|0.040	0.040	strong		0.485	OR2T27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097124.1	NM_001001824	
CIC	23152	hgsc.bcm.edu	37	19	42794829	42794831	+	In_Frame_Del	DEL	AAG	AAG	-	rs587778196		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42794829_42794831delAAG	ENST00000575354.2	+	10	1949_1951	c.1909_1911delAAG	c.(1909-1911)aagdel	p.K637del	CIC_ENST00000572681.2_In_Frame_Del_p.K1546del|CIC_ENST00000160740.3_In_Frame_Del_p.K637del	NM_015125.3	NP_055940.3	Q96RK0	CIC_HUMAN	capicua transcriptional repressor	637	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|breast(5)|central_nervous_system(32)|endometrium(10)|kidney(2)|large_intestine(7)|lung(9)|ovary(7)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	82		Prostate(69;0.00682)				GCCCCCAAACAAGGAGGAGCAAG	0.695			"""Mis, F, S"""		oligodendroglioma																																p.636_637del		Pindel,Atlas-Indel	.		Rec	yes		19	19q13.2	23152	capicua homolog		O	.	CIC	249	.	0			c.1908_1910del						PASS	.																																			SO:0001651	inframe_deletion	23152	exon10			.	AB002304	CCDS12601.1	19q13.2	2013-03-15	2013-03-15		ENSG00000079432	ENSG00000079432			14214	protein-coding gene	gene with protein product		612082	"""capicua (Drosophila) homolog"", ""capicua homolog (Drosophila)"""			12393275, 15981098	Standard	NM_015125		Approved	KIAA0306	uc002otf.1	Q96RK0		ENST00000575354.2:c.1909_1911delAAG	19.37:g.42794829_42794831delAAG	ENSP00000458663:p.Lys637del	87.0	0.0	.		107.0	33.0	0.308	NM_015125	Q7LGI1|Q9UEG5|Q9Y6T1	In_Frame_Del	DEL	ENST00000575354.2	37	CCDS12601.1																																																																																			.	.	none		0.695	CIC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438532.2		
SMPD2	6610	hgsc.bcm.edu	37	6	109764875	109764877	+	In_Frame_Del	DEL	GGA	GGA	-	rs142982624|rs370460899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GGA	GGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:109764875_109764877delGGA	ENST00000258052.3	+	10	1398_1400	c.1039_1041delGGA	c.(1039-1041)ggadel	p.G349del	PPIL6_ENST00000440797.2_5'Flank|PPIL6_ENST00000424445.2_5'Flank|PPIL6_ENST00000521072.2_5'Flank	NM_003080.2	NP_003071.2	O60906	NSMA_HUMAN	sphingomyelin phosphodiesterase 2, neutral membrane (neutral sphingomyelinase)	349					apoptotic signaling pathway (GO:0097190)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|neurotrophin TRK receptor signaling pathway (GO:0048011)|response to mechanical stimulus (GO:0009612)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin metabolic process (GO:0006684)	caveola (GO:0005901)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|sphingomyelin phosphodiesterase activity (GO:0004767)			endometrium(2)|lung(3)|stomach(1)|upper_aerodigestive_tract(2)	8		all_cancers(87;1.1e-06)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;0.000144)|all_lung(197;0.0221)|Colorectal(196;0.0488)|Lung SC(18;0.0548)		Epithelial(106;0.0137)|all cancers(137;0.0188)|OV - Ovarian serous cystadenocarcinoma(136;0.0228)|BRCA - Breast invasive adenocarcinoma(108;0.0566)		CCTGGCGGCTGGAGGAGGGGCCG	0.635														223	0.0445288	0.1573	0.0159	5008	,	,		16679	0.0		0.004	False		,,,				2504	0.0				p.346_347del		Pindel,Atlas-Indel	.											.	SMPD2	25	.	0			c.1038_1040del						PASS	.			602,3662		46,510,1576						-8.7	0.0		dbSNP_134	49	14,8240		3,8,4116	no	coding	SMPD2	NM_003080.2		49,518,5692	A1A1,A1R,RR		0.1696,14.1182,4.9209				616,11902				SO:0001651	inframe_deletion	6610	exon10			.	AJ222801	CCDS5075.1	6q21	2009-10-23			ENSG00000135587	ENSG00000135587	3.1.4.12		11121	protein-coding gene	gene with protein product		603498				9520418	Standard	XM_005267109		Approved	nSMase, ISC1	uc003pti.3	O60906	OTTHUMG00000015348	ENST00000258052.3:c.1039_1041delGGA	6.37:g.109764878_109764880delGGA	ENSP00000258052:p.Gly349del	123.0	0.0	.		102.0	34.0	0.333	NM_003080	Q5TED1|Q9BWR3	In_Frame_Del	DEL	ENST00000258052.3	37	CCDS5075.1																																																																																			GGA|0.957;-|0.043	0.043	strong		0.635	SMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041755.1		
USP34	9736	hgsc.bcm.edu	37	2	61575022	61575023	+	In_Frame_Ins	INS	-	-	TGG			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:61575022_61575023insTGG	ENST00000398571.2	-	15	2343_2344	c.2267_2268insCCA	c.(2266-2268)cat>caCCAt	p.756_756H>HH		NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	756					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			ggtggtggtgatggtggtggtg	0.386																																					p.H756delinsHH		Pindel,Atlas-Indel	.											.	USP34	334	.	0			c.2268_2269insCCA						PASS	.																																			SO:0001652	inframe_insertion	9736	exon15			.	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"""Ubiquitin-specific peptidases"""	20066	protein-coding gene	gene with protein product		615295	"""ubiquitin specific protease 34"""			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.2265_2267dupCCA	2.37:g.61575029_61575031dupTGG	ENSP00000381577:p.His760dup	41.0	0.0	.		54.0	17.0	0.315	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	In_Frame_Ins	INS	ENST00000398571.2	37	CCDS42686.1																																																																																			.	.	none		0.386	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4		
DMXL1	1657	hgsc.bcm.edu	37	5	118529595	118529597	+	In_Frame_Del	DEL	AAT	AAT	-	rs200335120|rs374810198|rs146526208|rs150940354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AAT	AAT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:118529595_118529597delAAT	ENST00000311085.8	+	30	7467_7469	c.7387_7389delAAT	c.(7387-7389)aatdel	p.N2463del	DMXL1_ENST00000539542.1_In_Frame_Del_p.N2463del	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	2463	Poly-Asp.									breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		tgatgatgacaatgatgatgatg	0.315														32	0.00638978	0.0234	0.0014	5008	,	,		16171	0.0		0.0	False		,,,				2504	0.0				p.2462_2463del		Pindel,Atlas-Indel	.											.	DMXL1	268	.	0			c.7386_7388del						PASS	.			93,4171		1,91,2040						-10.3	0.2			98	1,8253		0,1,4126	no	coding	DMXL1	NM_005509.4		1,92,6166	A1A1,A1R,RR		0.0121,2.1811,0.7509				94,12424				SO:0001651	inframe_deletion	1657	exon30			.	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"""WD repeat domain containing"""	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.7387_7389delAAT	5.37:g.118529595_118529597delAAT	ENSP00000309690:p.Asn2463del	52.0	0.0	.		55.0	10.0	0.182	NM_005509		In_Frame_Del	DEL	ENST00000311085.8	37	CCDS4125.1																																																																																			.	.	weak		0.315	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509	
FOXD4L6	653404	hgsc.bcm.edu	37	9	69200395	69200395	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:69200395delG	ENST00000377473.1	-	1	1809	c.1218delC	c.(1216-1218)tgcfs	p.C406fs		NM_001085476.1	NP_001078945.1	Q3SYB3	FX4L6_HUMAN	forkhead box D4-like 6	406					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TGCCCGCCCAGCACCGCGCCC	0.677																																					p.W407fs		Atlas-Indel	.											.	.	.	.	0			c.1219delT						PASS	.						1.0	2.0	2.0					9																	69200395		633	1796	2429	SO:0001589	frameshift_variant	653404	exon1			.		CCDS43826.1	9q12	2014-05-06			ENSG00000204793	ENSG00000273514			31986	protein-coding gene	gene with protein product							Standard	NM_001085476		Approved	OTTHUMG00000066822	uc004afi.2	Q3SYB3	OTTHUMG00000188618	ENST00000377473.1:c.1218delC	9.37:g.69200395delG	ENSP00000366693:p.Cys406fs	643.0	0.0	0		1099.0	96.0	0.0873521	NM_001085476	B2RPC4|Q4V336	Frame_Shift_Del	DEL	ENST00000377473.1	37	CCDS43826.1																																																																																			.	.	none		0.677	FOXD4L6-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143174.1	NM_001085476	
SLC22A25	387601	hgsc.bcm.edu	37	11	62996774	62996775	+	Frame_Shift_Ins	INS	-	-	A	rs112260121	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:62996774_62996775insA	ENST00000306494.6	-	1	349_350	c.350_351insT	c.(349-351)gtgfs	p.V117fs	SLC22A10_ENST00000525620.1_Intron|SLC22A25_ENST00000403374.2_5'Flank|SLC22A10_ENST00000535888.1_Intron	NM_199352.3	NP_955384.3			solute carrier family 22, member 25											NS(2)|breast(2)|endometrium(4)|kidney(2)|large_intestine(7)|lung(7)|ovary(3)|skin(7)	34						CCCAGCCATCCACACAGGGCTC	0.51													A|A|AA|insertion	42	0.00838658	0.0318	0.0	5008	,	,		19685	0.0		0.0	False		,,,				2504	0.0				p.V117fs		Pindel,Atlas-Indel	.											.	SLC22A25	87	.	0			c.351_352insT						PASS	.			104,4160		2,100,2030						1.9	1.0		dbSNP_132	130	4,8250		0,4,4123	yes	frameshift	SLC22A25	NM_199352.3		2,104,6153	A1A1,A1R,RR		0.0485,2.439,0.8628				108,12410				SO:0001589	frameshift_variant	387601	exon1			.	AY437532	CCDS31592.1	11q12.3	2014-05-20			ENSG00000196600	ENSG00000196600		"""Solute carriers"""	32935	protein-coding gene	gene with protein product		610792	"""MGI:2442751, MGI:2385316, MGI:3042283, MGI:3645714, MGI:3605624, MGI:2442750"""			17714910	Standard	NM_199352		Approved	UST6, HIMTP, MGC120420	uc001nwr.1	Q6T423	OTTHUMG00000165340	ENST00000306494.6:c.351dupT	11.37:g.62996775_62996775dupA	ENSP00000307443:p.Val117fs	235.0	0.0	.		200.0	57.0	0.285	NM_199352		Frame_Shift_Ins	INS	ENST00000306494.6	37	CCDS31592.1																																																																																			-|0.990;A|0.010	0.010	strong		0.510	SLC22A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383519.3	NM_199352	
ADRM1	11047	hgsc.bcm.edu	37	20	60883770	60883778	+	In_Frame_Del	DEL	GACACGAAG	GACACGAAG	-	rs374034164		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GACACGAAG	GACACGAAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:60883770_60883778delGACACGAAG	ENST00000253003.2	+	10	1223_1231	c.1177_1185delGACACGAAG	c.(1177-1185)gacacgaagdel	p.DTK393del	LAMA5_ENST00000492698.1_Intron|RP11-157P1.4_ENST00000414042.1_RNA	NM_007002.2|NM_175573.1	NP_008933.2|NP_783163.1	Q16186	ADRM1_HUMAN	adhesion regulating molecule 1	393	Interaction with UCHL5.				positive regulation of endopeptidase activity (GO:0010950)|proteasome assembly (GO:0043248)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|proteasome complex (GO:0000502)	endopeptidase activator activity (GO:0061133)|protease binding (GO:0002020)|proteasome binding (GO:0070628)			central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|urinary_tract(1)	5	Breast(26;7.76e-09)		BRCA - Breast invasive adenocarcinoma(19;2.51e-06)			GAAAGAGGGCGACACGAAGGACAAGAAGG	0.574																																					p.392_395del		Pindel,Atlas-Indel	.											.	ADRM1	28	.	0			c.1176_1184del						PASS	.		,	23,2,4215		0,0,23,0,2,2095					,	-0.2	0.8			134	185,0,8059		3,0,179,0,0,3940	no	codingComplex,codingComplex	ADRM1	NM_175573.1,NM_007002.2	,	3,0,202,0,2,6035	A1A1,A1A2,A1R,A2A2,A2R,RR		2.2441,0.5896,1.6822	,	,		208,2,12274				SO:0001651	inframe_deletion	11047	exon10			.	D64154	CCDS13496.1, CCDS74747.1	20q13.33	2008-05-22			ENSG00000130706	ENSG00000130706			15759	protein-coding gene	gene with protein product		610650				8033103	Standard	NM_007002		Approved	GP110, Rpn13, ARM1	uc002yco.3	Q16186	OTTHUMG00000032904	ENST00000253003.2:c.1177_1185delGACACGAAG	20.37:g.60883770_60883778delGACACGAAG	ENSP00000253003:p.Asp393_Lys395del	250.0	0.0	.		243.0	56.0	0.230	NM_007002	A0PKB1|Q96FJ7|Q9H1P2	In_Frame_Del	DEL	ENST00000253003.2	37	CCDS13496.1																																																																																			GACACGAAG|0.012;-|0.988	0.988	strong		0.574	ADRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080007.1		
HRC	3270	hgsc.bcm.edu	37	19	49657889	49657890	+	In_Frame_Ins	INS	-	-	TCCTCCTCC	rs369248456|rs57199624|rs147238387|rs551367394|rs542091249		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49657889_49657890insTCCTCCTCC	ENST00000252825.4	-	1	791_792	c.605_606insGGAGGAGGA	c.(604-606)gaa>gaGGAGGAGGAa	p.202_202E>EEEE	HRC_ENST00000595625.1_In_Frame_Ins_p.202_202E>EEEE	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	202	4 X tandem repeats, acidic.|6 X approximate tandem repeats.|Glu-rich (acidic).				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		AGGcctcctcttcctcctcctc	0.569																																					p.E202delinsEEEE	Melanoma(37;75 1097 24567 25669 30645)	Atlas-Indel	.											.	HRC	85	.	0			c.606_607insGGAGGAGGA						PASS	.																																			SO:0001652	inframe_insertion	3270	exon1			.		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"""histidine-rich calcium-binding protein"""			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.597_605dupGGAGGAGGA	19.37:g.49657890_49657898dupTCCTCCTCC	ENSP00000252825:p.GluGluGlu202dup	165.0	0.0	0		170.0	31.0	0.182353	NM_002152	Q504Y6	In_Frame_Ins	INS	ENST00000252825.4	37	CCDS12759.1																																																																																			.	.	alt		0.569	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152	
ONECUT2	9480	hgsc.bcm.edu	37	18	55103476	55103477	+	In_Frame_Ins	INS	-	-	CAC			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:55103476_55103477insCAC	ENST00000491143.2	+	1	560_561	c.528_529insCAC	c.(529-531)cac>CACcac	p.177_177H>HH	AC090340.1_ENST00000581316.1_RNA	NM_004852.2	NP_004843.2	O95948	ONEC2_HUMAN	one cut homeobox 2	177	Poly-His.				cell fate commitment (GO:0045165)|cilium assembly (GO:0042384)|endocrine pancreas development (GO:0031018)|epithelial cell development (GO:0002064)|liver development (GO:0001889)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|organ morphogenesis (GO:0009887)|peripheral nervous system neuron development (GO:0048935)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell-matrix adhesion (GO:0001952)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|lung(4)|ovary(2)|skin(1)	15		Colorectal(73;0.234)		READ - Rectum adenocarcinoma(59;0.227)|Colorectal(16;0.245)		accaccatccgcaccaccacca	0.658																																					p.P176delinsPH		Pindel,Atlas-Indel	.											.	ONECUT2	42	.	0			c.528_529insCAC						PASS	.																																			SO:0001652	inframe_insertion	9480	exon1			.	Y18198	CCDS42440.1	18q21.31	2012-03-09	2007-07-16		ENSG00000119547	ENSG00000119547		"""Homeoboxes / CUT class"""	8139	protein-coding gene	gene with protein product		604894	"""one cut domain, family member 2"""			9915796	Standard	NM_004852		Approved	OC-2	uc002lgo.3	O95948	OTTHUMG00000159776	ENST00000491143.2:c.550_552dupCAC	18.37:g.55103483_55103485dupCAC	ENSP00000419185:p.His184dup	63.0	0.0	.		66.0	11.0	0.167	NM_004852		In_Frame_Ins	INS	ENST00000491143.2	37	CCDS42440.1																																																																																			.	.	none		0.658	ONECUT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357264.3		
OSBPL1A	114876	hgsc.bcm.edu	37	18	21740032	21740033	+	IGR	DEL	TG	TG	-	rs149126027	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:21740032_21740033delTG	ENST00000319481.3	-	0	4195				CABYR_ENST00000399499.1_3'UTR|CABYR_ENST00000581397.1_3'UTR|RP11-799B12.4_ENST00000583267.1_lincRNA|CABYR_ENST00000327201.6_3'UTR|CABYR_ENST00000415309.2_3'UTR|CABYR_ENST00000399496.3_3'UTR	NM_080597.3	NP_542164.2	Q9BXW6	OSBL1_HUMAN	oxysterol binding protein-like 1A						antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|nucleus (GO:0005634)	cholesterol binding (GO:0015485)|phospholipid binding (GO:0005543)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(16)|ovary(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	36	all_cancers(21;0.000396)|all_epithelial(16;4.36e-06)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0505)|Ovarian(20;0.17)					AACTGAAAACTGGTAGGTACAC	0.406														131	0.0261581	0.0976	0.0029	5008	,	,		21848	0.0		0.0	False		,,,				2504	0.0				p.379_380del		Pindel,Atlas-Indel	.											.	CABYR	51	.	0			c.1137_1138del						PASS	.		,,,,,	310,3948		19,272,1838					,,,,,	2.1	1.0		dbSNP_134	57	0,8248		0,0,4124	no	frameshift-near-splice,frameshift-near-splice,utr-3,frameshift-near-splice,frameshift-near-splice,utr-3	CABYR	NM_153770.1,NM_153769.1,NM_153768.1,NM_138644.1,NM_138643.1,NM_012189.2	,,,,,	19,272,5962	A1A1,A1R,RR		0.0,7.2804,2.4788	,,,,,	,,,,,		310,12196				SO:0001628	intergenic_variant	26256	exon5			.	AF392449, AF274714	CCDS11884.1, CCDS11885.1, CCDS56056.1	18q11.2	2014-06-03	2014-06-03	2014-06-03	ENSG00000141447	ENSG00000141447		"""Oxysterol binding proteins"", ""Ankyrin repeat domain containing"""	16398	protein-coding gene	gene with protein product		606730	"""oxysterol binding protein-like 1B"""	OSBPL1B		11279184, 10588946	Standard	NM_080597		Approved	ORP-1, ORP1	uc002kve.3	Q9BXW6	OTTHUMG00000131944		18.37:g.21740032_21740033delTG		57.0	0.0	.		77.0	26.0	0.338	NM_153769	B7Z7D3|Q9BZF5|Q9NW87	Frame_Shift_Del	DEL	ENST00000319481.3	37	CCDS11884.1																																																																																			TG|0.978;-|0.022	0.022	strong		0.406	OSBPL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254902.1	NM_080597	
SERPINB3	6317	hgsc.bcm.edu	37	18	61323011	61323012	+	Frame_Shift_Ins	INS	-	-	GCCA	rs60533853|rs3180227|rs386804125|rs72132327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61323011_61323012insGCCA	ENST00000283752.5	-	8	1195_1196	c.1052_1053insTGGC	c.(1051-1053)ggafs	p.G351fs	SERPINB11_ENST00000489748.1_RNA|SERPINB3_ENST00000332821.8_Frame_Shift_Ins_p.G299fs	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	351			G -> A (increased antiprotease activity and increased MAPK8 inhibition activity; dbSNP:rs3180227). {ECO:0000269|PubMed:12975381, ECO:0000269|PubMed:14970861, ECO:0000269|PubMed:21383048, ECO:0000269|Ref.6}.		negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						ATGATCCGAATCCTACTACAGC	0.49																																					p.G351fs		Atlas-Indel	.											.	SERPINB3	90	.	0			c.1053_1054insTGGC						PASS	.																																			SO:0001589	frameshift_variant	6317	exon8			.	U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"""Serine (or cysteine) peptidase inhibitors"""	10569	protein-coding gene	gene with protein product		600517	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"""	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.1052_1053insTGGC	18.37:g.61323011_61323012insGCCA	ENSP00000283752:p.Gly351fs	212.0	0.0	0		192.0	49.0	0.255208	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	Frame_Shift_Ins	INS	ENST00000283752.5	37	CCDS11987.1																																																																																			.	.	alt		0.490	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919	
DUPD1	338599	hgsc.bcm.edu	37	10	76803600	76803602	+	In_Frame_Del	DEL	AGA	AGA	-	rs571550955|rs370448554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:76803600_76803602delAGA	ENST00000338487.5	-	2	373_375	c.374_376delTCT	c.(373-378)ttctac>tac	p.F125del		NM_001003892.1	NP_001003892.1	Q68J44	DUPD1_HUMAN	dual specificity phosphatase and pro isomerase domain containing 1	125	Tyrosine-protein phosphatase.				protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(2)|lung(5)|ovary(2)|urinary_tract(1)	11	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)					GCCGCCGGGTAGAAGAAGACACT	0.68														33	0.00658946	0.0219	0.0058	5008	,	,		9789	0.0		0.0	False		,,,				2504	0.0				p.125_126del		Pindel,Atlas-Indel	.											.	DUPD1	30	.	0			c.375_377del						PASS	.			103,4161		6,91,2035						2.5	0.2			84	42,8212		16,10,4101	no	coding	DUPD1	NM_001003892.1		22,101,6136	A1A1,A1R,RR		0.5088,2.4156,1.1583				145,12373				SO:0001651	inframe_deletion	338599	exon2			.		CCDS31223.1	10q22.3	2011-06-09			ENSG00000188716	ENSG00000188716		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	23481	protein-coding gene	gene with protein product							Standard	NM_001003892		Approved	DUSP27	uc001jwq.1	Q68J44	OTTHUMG00000018512	ENST00000338487.5:c.374_376delTCT	10.37:g.76803606_76803608delAGA	ENSP00000340609:p.Phe125del	44.0	0.0	.		56.0	18.0	0.321	NM_001003892	B2RP93	In_Frame_Del	DEL	ENST00000338487.5	37	CCDS31223.1																																																																																			.	.	none		0.680	DUPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048777.2	XM_291741	
DEFB119	245932	hgsc.bcm.edu	37	20	29965208	29965211	+	Frame_Shift_Del	DEL	ACTG	ACTG	-	rs374993061	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	ACTG	ACTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:29965208_29965211delACTG	ENST00000376321.3	-	2	212_215	c.93_96delCAGT	c.(91-96)aacagtfs	p.NS31fs	SNORA40_ENST00000390832.1_RNA|DEFB119_ENST00000339144.3_3'UTR|DEFB119_ENST00000492344.1_5'UTR	NM_153289.3	NP_695021.2	Q8N690	DB119_HUMAN	defensin, beta 119	31					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				large_intestine(2)|lung(1)|prostate(1)	4	all_hematologic(12;0.158)		Colorectal(19;0.00254)|COAD - Colon adenocarcinoma(19;0.0347)			TACAAATTCCACTGTTACCCATGC	0.431														26	0.00519169	0.0182	0.0029	5008	,	,		21220	0.0		0.0	False		,,,				2504	0.0				p.32_33del		Pindel,Atlas-Indel	.											DEFB119_ENST00000376321,NS,malignant_melanoma,+1,2	DEFB119	37	2	0			c.94_97del						PASS	.		,	106,4154		3,100,2027					,	3.3	0.3			168	2,8248		0,2,4123	no	utr-3,frameshift	DEFB119	NM_173460.1,NM_153289.2	,	3,102,6150	A1A1,A1R,RR		0.0242,2.4883,0.8633	,	,		108,12402				SO:0001589	frameshift_variant	245932	exon2			.	AA939044	CCDS13178.1, CCDS33455.1	20q11.21	2007-02-19	2003-10-06		ENSG00000180483	ENSG00000180483		"""Defensins, beta"""	18099	protein-coding gene	gene with protein product			"""defensin, beta 120"""	DEFB120		11854508	Standard	NM_153289		Approved	DEFB-19, DEFB-20	uc002wvu.2	Q8N690	OTTHUMG00000032172	ENST00000376321.3:c.93_96delCAGT	20.37:g.29965208_29965211delACTG	ENSP00000365499:p.Asn31fs	110.0	0.0	.		88.0	36.0	0.409	NM_153289	Q5GRG1|Q5JWP1|Q5TH42|Q8N689	Frame_Shift_Del	DEL	ENST00000376321.3	37	CCDS13178.1																																																																																			.	.	weak		0.431	DEFB119-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078514.1	NM_153289	
HABP2	3026	hgsc.bcm.edu	37	10	115348749	115348751	+	3'UTR	DEL	CTT	CTT	-	rs141729427|rs148467563|rs200486696|rs11575787|rs144589482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:115348749_115348751delCTT	ENST00000351270.3	+	0	2400_2402				NRAP_ENST00000359988.3_In_Frame_Del_p.K1726del|NRAP_ENST00000369358.4_In_Frame_Del_p.K1734del|NRAP_ENST00000369360.3_In_Frame_Del_p.K1699del|NRAP_ENST00000360478.3_In_Frame_Del_p.K1691del|HABP2_ENST00000542051.1_3'UTR	NM_004132.3	NP_004123.1	Q14520	HABP2_HUMAN	hyaluronan binding protein 2						cell adhesion (GO:0007155)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	glycosaminoglycan binding (GO:0005539)|serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.0233)|Breast(234;0.0672)		Epithelial(162;0.00319)|all cancers(201;0.0112)	Hyaluronan(DB08818)	ACAGCAGGGCCTTCTTCTTTTTG	0.537														34	0.00678914	0.025	0.0014	5008	,	,		16073	0.0		0.0	False		,,,				2504	0.0				p.1727_1728del		Pindel,Atlas-Indel	.											.	NRAP	208	.	0			c.5180_5182del						PASS	.		,,,	162,4102		7,148,1977					,,,	3.8	1.0		dbSNP_120	163	28,8226		11,6,4110	no	coding,coding,utr-3,utr-3	HABP2,NRAP	NM_198060.2,NM_006175.3,NM_004132.3,NM_001177660.1	,,,	18,154,6087	A1A1,A1R,RR		0.3392,3.7992,1.5178	,,,	,,,		190,12328				SO:0001624	3_prime_UTR_variant	4892	exon42			.		CCDS7577.1, CCDS53579.1	10q25.3	2008-08-01	2001-11-28		ENSG00000148702	ENSG00000148702			4798	protein-coding gene	gene with protein product	"""plasma hyaluronan binding protein"", ""factor VII activating protein"""	603924	"""hyaluronan-binding protein 2"""			8827452, 12437095	Standard	NM_004132		Approved	HABP, PHBP, HGFAL, FSAP	uc001lai.4	Q14520	OTTHUMG00000019073	ENST00000351270.3:c.*623CTT>-	10.37:g.115348755_115348757delCTT		144.0	0.0	.		187.0	61.0	0.326	NM_001261463	A8K467|B7Z8U5|F5H5M6|O00663	In_Frame_Del	DEL	ENST00000351270.3	37	CCDS7577.1																																																																																			CTT|0.992;-|0.008	0.008	strong		0.537	HABP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050428.1	NM_004132	
FMO2	2327	hgsc.bcm.edu	37	1	171162551	171162552	+	In_Frame_Ins	INS	-	-	GAC	rs2020868|rs397844260	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:171162551_171162552insGAC	ENST00000209929.7	+	3	368_369	c.210_211insGAC	c.(211-213)gac>GACgac	p.71_71D>DD	FMO2_ENST00000529935.1_3'UTR|FMO2_ENST00000441535.1_In_Frame_Ins_p.71_71D>DD			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	71					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	22	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					CCTGTTTCAGTGACTTTCCAAT	0.342														516	0.103035	0.298	0.0476	5008	,	,		17166	0.002		0.0447	False		,,,				2504	0.0429				p.S70delinsSD		Pindel,Atlas-Indel	.											.	FMO2	66	.	0			c.210_211insGAC						PASS	.			1054,3212		148,758,1227						4.3	1.0		dbSNP_98	103	398,7856		12,374,3741	no	coding	FMO2	NM_001460.2		160,1132,4968	A1A1,A1R,RR		4.8219,24.707,11.5974				1452,11068				SO:0001652	inframe_insertion	2327	exon3			.	BC005894	CCDS1293.1	1q24.3	2011-08-04	2006-07-17		ENSG00000094963	ENSG00000094963			3770	protein-coding gene	gene with protein product		603955	"""flavin containing monooxygenase 2"""			1417778, 9804831	Standard	XR_426768		Approved		uc001ghk.1	Q99518	OTTHUMG00000035504	ENST00000209929.7:c.211_213dupGAC	1.37:g.171162552_171162554dupGAC	ENSP00000209929:p.Asp71dup	76.0	0.0	.		58.0	19.0	0.328	NM_001460	Q53XR0	In_Frame_Ins	INS	ENST00000209929.7	37	CCDS1293.1																																																																																			-|0.904;GAC|0.096	0.096	strong		0.342	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460	
OR2A1	346528	hgsc.bcm.edu	37	7	144015524	144015527	+	Frame_Shift_Del	DEL	TGTT	TGTT	-	rs559439902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TGTT	TGTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:144015524_144015527delTGTT	ENST00000408951.1	+	1	307_310	c.307_310delTGTT	c.(307-312)tgtttgfs	p.CL103fs	OR2A1-AS1_ENST00000478925.1_RNA|OR2A1-AS1_ENST00000476560.1_RNA|OR2A1-AS1_ENST00000496968.1_RNA|OR2A1-AS1_ENST00000475089.1_RNA|OR2A1-AS1_ENST00000467944.1_RNA|OR2A1-AS1_ENST00000463561.1_RNA|OR2A1-AS1_ENST00000478806.1_RNA|OR2A1-AS1_ENST00000486094.1_RNA|OR2A1-AS1_ENST00000461843.1_RNA|OR2A1-AS1_ENST00000488041.1_RNA|OR2A1-AS1_ENST00000489488.1_RNA|OR2A1-AS1_ENST00000493539.1_RNA|OR2A1-AS1_ENST00000487102.1_RNA	NM_001005287.1	NP_001005287.1	Q8NGT9	OR2A1_HUMAN	olfactory receptor, family 2, subfamily A, member 1	103						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(1)|lung(3)|skin(2)	6	Melanoma(164;0.14)					GACCTTTCTCTGTTTGAGTTTTGG	0.569														126	0.0251597	0.0908	0.0086	5008	,	,		44510	0.0		0.0	False		,,,				2504	0.0				p.102_103del		Atlas-Indel	.											.	OR2A1	10	.	0			c.306_309del						PASS	.			296,3480		1,294,1593						-5.2	0.1			171	15,6777		4,7,3385	no	frameshift	OR2A1	NM_001005287.1		5,301,4978	A1A1,A1R,RR		0.2208,7.839,2.9428				311,10257				SO:0001589	frameshift_variant	346528	exon1			.		CCDS43673.1	7q35	2013-09-20			ENSG00000221970	ENSG00000221970		"""GPCR / Class A : Olfactory receptors"""	8229	protein-coding gene	gene with protein product							Standard	NM_001005287		Approved		uc011kub.2	Q8NGT9	OTTHUMG00000158005	ENST00000408951.1:c.307_310delTGTT	7.37:g.144015524_144015527delTGTT	ENSP00000386175:p.Cys103fs	626.0	0.0	0		1136.0	133.0	0.117077	NM_001005287	Q6IF44|Q96R46	Frame_Shift_Del	DEL	ENST00000408951.1	37	CCDS43673.1																																																																																			.	.	none		0.569	OR2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349985.1		
LIPM	340654	hgsc.bcm.edu	37	10	90562801	90562802	+	Splice_Site	INS	-	-	T	rs535896941|rs554915830	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:90562801_90562802insT	ENST00000404743.4	+	1	314		c.e1+1		LIPM_ENST00000539337.1_Splice_Site	NM_001128215.1	NP_001121687.1	Q5VYY2	LIPM_HUMAN	lipase, family member M						lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	hydrolase activity, acting on ester bonds (GO:0016788)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(2)|pancreas(1)|skin(1)	7						CATGAATATTGTAAGTTGGGAT	0.347													T|T|TT|insertion	3	0.000599042	0.0023	0.0	5008	,	,		21071	0.0		0.0	False		,,,				2504	0.0				.		Pindel,Atlas-Indel	.											.	LIPM	17	.	0			c.147+1->T						PASS	.			4,2254		1,2,1126						4.9	1.0			127	0,4458		0,0,2229	no	splice-5	LIPM	NM_001128215.1		1,2,3355	A1A1,A1R,RR		0.0,0.1771,0.0596				4,6712				SO:0001630	splice_region_variant	340654	exon1			.		CCDS44457.1	10q23.31	2008-02-04	2007-02-27	2007-02-27	ENSG00000173239	ENSG00000173239			23455	protein-coding gene	gene with protein product		613923	"""lipase-like, ab-hydrolase domain containing 3"""	LIPL3			Standard	NM_001128215		Approved	bA304I5.1	uc009xtm.1	Q5VYY2	OTTHUMG00000018698	ENST00000404743.4:c.147+1->T	10.37:g.90562802_90562802dupT		129.0	0.0	.		104.0	35.0	0.337	NM_001128215	A6PVS3|B2RXK7|B5MCR3	Splice_Site	INS	ENST00000404743.4	37	CCDS44457.1																																																																																			.	.	none		0.347	LIPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049261.3	XM_291663	Intron
TRPM3	80036	hgsc.bcm.edu	37	9	73151130	73151133	+	Frame_Shift_Del	DEL	TCTC	TCTC	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCTC	TCTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:73151130_73151133delTCTC	ENST00000377110.3	-	25	5103_5106	c.4860_4863delGAGA	c.(4858-4863)gagagafs	p.ER1620fs	TRPM3_ENST00000396292.4_Frame_Shift_Del_p.ER1492fs|TRPM3_ENST00000358082.3_Frame_Shift_Del_p.ER1482fs|TRPM3_ENST00000377105.1_Frame_Shift_Del_p.ER1479fs|TRPM3_ENST00000377111.2_Intron|TRPM3_ENST00000396280.5_Frame_Shift_Del_p.ER1469fs|TRPM3_ENST00000408909.2_Frame_Shift_Del_p.ER1479fs|TRPM3_ENST00000357533.2_Frame_Shift_Del_p.ER1624fs|TRPM3_ENST00000377106.1_Frame_Shift_Del_p.ER1492fs|TRPM3_ENST00000396285.1_Frame_Shift_Del_p.ER1479fs|TRPM3_ENST00000423814.3_Frame_Shift_Del_p.ER1647fs|TRPM3_ENST00000360823.2_Frame_Shift_Del_p.ER1482fs			Q9HCF6	TRPM3_HUMAN	transient receptor potential cation channel, subfamily M, member 3	1645					calcium ion transmembrane transport (GO:0070588)|cation transport (GO:0006812)|detection of temperature stimulus (GO:0016048)|ion transmembrane transport (GO:0034220)|sensory perception of temperature stimulus (GO:0050951)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)			NS(2)|breast(4)|central_nervous_system(2)|endometrium(6)|kidney(1)|large_intestine(18)|liver(1)|lung(46)|ovary(3)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(1)	95						TGGACAGGGTTCTCTCTGAGTTAT	0.544																																					p.1621_1622del		Pindel,Atlas-Indel	.											.	TRPM3	700	.	0			c.4861_4864del						PASS	.		,,,,,,	5,4259		0,5,2127					,,,,,,	-3.5	0.6			363	0,8254		0,0,4127	no	frameshift,frameshift,frameshift,frameshift,frameshift,frameshift,frameshift	TRPM3	NM_206947.3,NM_206946.3,NM_206945.3,NM_206944.3,NM_024971.5,NM_020952.4,NM_001007471.2	,,,,,,	0,5,6254	A1A1,A1R,RR		0.0,0.1173,0.0399	,,,,,,	,,,,,,		5,12513				SO:0001589	frameshift_variant	80036	exon25			.	AB046836	CCDS6634.1, CCDS6635.1, CCDS6636.1, CCDS6637.1, CCDS43835.1, CCDS65064.1	9q21.11	2011-12-14			ENSG00000083067	ENSG00000083067		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17992	protein-coding gene	gene with protein product	"""melastatin 2"""	608961				16382100	Standard	NM_206946		Approved	KIAA1616, LTRPC3, GON-2	uc004aid.3	Q9HCF6	OTTHUMG00000019997	ENST00000377110.3:c.4860_4863delGAGA	9.37:g.73151130_73151133delTCTC	ENSP00000366314:p.Glu1620fs	439.0	0.0	.		453.0	86.0	0.190	NM_001007471	A2A3F6|A9Z1Y7|Q5VW02|Q5VW03|Q5VW04|Q5W5T7|Q86SH0|Q86SH6|Q86UL0|Q86WK1|Q86WK2|Q86WK3|Q86WK4|Q86YZ9|Q86Z00|Q86Z01|Q9H0X2	Frame_Shift_Del	DEL	ENST00000377110.3	37	CCDS43835.1																																																																																			.	.	none		0.544	TRPM3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214158.3	NM_206945	
PLIN5	440503	hgsc.bcm.edu	37	19	4529255	4529257	+	In_Frame_Del	DEL	GAG	GAG	-	rs140507757	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4529255_4529257delGAG	ENST00000381848.3	-	5	428_430	c.348_350delCTC	c.(346-351)acctca>aca	p.S117del	CTB-50L17.14_ENST00000586020.1_3'UTR	NM_001013706.2	NP_001013728.2	Q00G26	PLIN5_HUMAN	perilipin 5	117	Essential for lipid droplet targeting. {ECO:0000250}.				lipid particle organization (GO:0034389)|lipid storage (GO:0019915)|mitochondrion localization (GO:0051646)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of lipase activity (GO:0060192)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of triglyceride catabolic process (GO:0010897)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of lipase activity (GO:0060193)|positive regulation of lipid storage (GO:0010884)|positive regulation of sequestering of triglyceride (GO:0010890)|positive regulation of triglyceride biosynthetic process (GO:0010867)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lipid particle (GO:0005811)|mitochondrion (GO:0005739)				endometrium(4)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	10						GTCCTTGGCTGAGGTCACCACCT	0.67														54	0.0107827	0.0401	0.0014	5008	,	,		14860	0.0		0.0	False		,,,				2504	0.0				p.117_117del		Pindel,Atlas-Indel	.											.	PLIN5	27	.	0			c.349_351del						PASS	.			141,3831		9,123,1854						-7.4	1.0		dbSNP_134	48	0,8030		0,0,4015	no	coding	PLIN5	NM_001013706.2		9,123,5869	A1A1,A1R,RR		0.0,3.5498,1.1748				141,11861				SO:0001651	inframe_deletion	440503	exon5			.	DQ839131	CCDS42473.1	19p13.3	2009-08-12			ENSG00000214456	ENSG00000214456		"""Perilipins"""	33196	protein-coding gene	gene with protein product	"""lipid storage droplet protein 5"""	613248				17234449, 19638644	Standard	NM_001013706		Approved	LSDP5, LSDA5, OXPAT, MLDP	uc002mas.3	Q00G26		ENST00000381848.3:c.348_350delCTC	19.37:g.4529255_4529257delGAG	ENSP00000371272:p.Ser117del	143.0	0.0	.		118.0	36.0	0.305	NM_001013706	A2RRC1|Q6ZS68	In_Frame_Del	DEL	ENST00000381848.3	37	CCDS42473.1																																																																																			GAG|0.986;-|0.014	0.014	strong		0.670	PLIN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458647.1	NM_001013706	
ADAM28	10863	hgsc.bcm.edu	37	8	24184128	24184129	+	In_Frame_Ins	INS	-	-	ATC	rs111491080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24184128_24184129insATC	ENST00000265769.4	+	10	1062_1063	c.952_953insATC	c.(952-954)tat>tATCat	p.318_319insH	RP11-624C23.1_ENST00000518988.1_RNA|ADAM28_ENST00000518516.1_3'UTR|ADAM28_ENST00000397649.3_In_Frame_Ins_p.65_66insH|RP11-624C23.1_ENST00000523700.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA|ADAM28_ENST00000540823.1_In_Frame_Ins_p.85_86insH|ADAM28_ENST00000437154.2_In_Frame_Ins_p.318_319insH|RP11-624C23.1_ENST00000523578.1_RNA	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	318	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		GTGTTCTCCTTATTCTGTTGGC	0.332														3	0.000599042	0.0023	0.0	5008	,	,		18291	0.0		0.0	False		,,,				2504	0.0				p.Y318delinsYH	NSCLC(193;488 2149 22258 34798 40734)	Pindel,Atlas-Indel	.											.	ADAM28	100	.	0			c.952_953insATC						PASS	.		,	20,4244		0,20,2112					,	4.3	1.0		dbSNP_132	294	0,8252		0,0,4126	no	coding,coding	ADAM28	NM_021777.3,NM_014265.4	,	0,20,6238	A1A1,A1R,RR		0.0,0.469,0.1598	,	,		20,12496				SO:0001652	inframe_insertion	10863	exon10			.	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	Exception_encountered	8.37:g.24184128_24184129insATC	ENSP00000265769:p.Tyr318_Ser319insHis	269.0	0.0	.		282.0	83.0	0.294	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	In_Frame_Ins	INS	ENST00000265769.4	37	CCDS34865.1																																																																																			-|0.500;ATC|0.500	0.500	weak		0.332	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778	
ARID1B	57492	hgsc.bcm.edu	37	6	157099402	157099403	+	In_Frame_Ins	INS	-	-	CAGCAG			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:157099402_157099403insCAGCAG	ENST00000350026.5	+	1	340_341	c.339_340insCAGCAG	c.(340-342)cag>CAGCAGcag	p.114_114Q>QQQ	ARID1B_ENST00000275248.4_In_Frame_Ins_p.56_56Q>QQQ|RP11-230C9.3_ENST00000604792.1_RNA|ARID1B_ENST00000367148.1_In_Frame_Ins_p.114_114Q>QQQ|MIR4466_ENST00000606121.1_RNA|RP11-230C9.2_ENST00000603191.1_lincRNA|ARID1B_ENST00000346085.5_In_Frame_Ins_p.114_114Q>QQQ	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	114	Gln-rich.|Poly-Gln.				chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		TAAACCAGTTCcagcagcagca	0.639																																					p.F113delinsFQQ		Atlas-Indel	.											.	ARID1B	320	.	0			c.339_340insCAGCAG						PASS	.																																			SO:0001652	inframe_insertion	57492	exon1			.	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"""-"""	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.352_357dupCAGCAG	6.37:g.157099403_157099408dupCAGCAG	ENSP00000055163:p.GlnGln130dup	30.0	0.0	0		27.0	12.0	0.444444	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	In_Frame_Ins	INS	ENST00000350026.5	37	CCDS5251.2																																																																																			.	.	none		0.639	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732	
FMO2	2327	hgsc.bcm.edu	37	1	171165803	171165803	+	Frame_Shift_Del	DEL	G	G	-	rs28369860	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:171165803delG	ENST00000209929.7	+	4	495	c.337delG	c.(337-339)gtgfs	p.V113fs	RP1-127D3.4_ENST00000422841.1_RNA|RP1-127D3.4_ENST00000445290.1_RNA|RP1-127D3.4_ENST00000445909.1_RNA|FMO2_ENST00000529935.1_3'UTR|FMO2_ENST00000441535.1_Frame_Shift_Del_p.V113fs			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	113					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	22	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TGTCCTTAGTGTGAGAAAATG	0.453													G|G|-|deletion	515	0.102835	0.2973	0.0476	5008	,	,		22626	0.002		0.0447	False		,,,				2504	0.0429				p.S112fs		Pindel,Atlas-Indel	.											.	FMO2	66	.	0			c.336delT	GRCh37	CD033950	FMO2	D	rs28369860	PASS	.			1055,3211		149,757,1227	106.0	106.0	106.0			2.2	1.0	1	dbSNP_125	115	398,7856		12,374,3741	no	frameshift	FMO2	NM_001460.2		161,1131,4968	A1A1,A1R,RR		4.8219,24.7304,11.6054			171165803	1453,11067	2093	4290	6383	SO:0001589	frameshift_variant	2327	exon4			.	BC005894	CCDS1293.1	1q24.3	2011-08-04	2006-07-17		ENSG00000094963	ENSG00000094963			3770	protein-coding gene	gene with protein product		603955	"""flavin containing monooxygenase 2"""			1417778, 9804831	Standard	XR_426768		Approved		uc001ghk.1	Q99518	OTTHUMG00000035504	ENST00000209929.7:c.337delG	1.37:g.171165803delG	ENSP00000209929:p.Val113fs	184.0	0.0	.		155.0	43.0	0.277	NM_001460	Q53XR0	Frame_Shift_Del	DEL	ENST00000209929.7	37	CCDS1293.1																																																																																			.	.	weak		0.453	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460	
SSPO	23145	hgsc.bcm.edu	37	7	149519007	149519007	+	RNA	DEL	G	G	-	rs568158666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149519007delG	ENST00000378016.2	+	0	12811							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CTCCTGTGGAGGTGGAAACCA	0.682													GG|GG|G|deletion	26	0.00519169	0.0197	0.0	5008	,	,		16479	0.0		0.0	False		,,,				2504	0.0				p.G4270fs		Pindel,Atlas-Indel	.											.	.	.	.	0			c.12810delA						PASS	.			63,3869		2,59,1905	16.0	19.0	18.0			3.2	1.0	7		18	2,7986		1,0,3993	no	frameshift	SSPO	NM_198455.2		3,59,5898	A1A1,A1R,RR		0.025,1.6022,0.5453			149519007	65,11855	2040	4183	6223			23145	exon90			.	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149519007delG		181.0	0.0	.		198.0	54.0	0.273	NM_198455	Q76B61	Frame_Shift_Del	DEL	ENST00000378016.2	37																																																																																				.	.	none		0.682	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
CDCP2	200008	hgsc.bcm.edu	37	1	54610404	54610405	+	Frame_Shift_Del	DEL	TG	TG	-	rs558673127	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:54610404_54610405delTG	ENST00000371330.1	-	2	1008_1009	c.161_162delCA	c.(160-162)acafs	p.T54fs	RP11-446E24.4_ENST00000525949.1_5'UTR|RP11-446E24.4_ENST00000311841.7_3'UTR	NM_201546.2	NP_963840.2	Q5VXM1	CDCP2_HUMAN	CUB domain containing protein 2	54	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.					extracellular region (GO:0005576)				kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|stomach(1)	24						AGCTGCACTCTGTGTTGTAGGG	0.559														3	0.000599042	0.0015	0.0014	5008	,	,		20392	0.0		0.0	False		,,,				2504	0.0				p.54_55del		Pindel,Atlas-Indel	.											.	CDCP2	52	.	0			c.162_163del						PASS	.			66,4200		31,4,2098						4.5	1.0			74	145,8109		72,1,4054	no	frameshift	CDCP2	NM_201546.2		103,5,6152	A1A1,A1R,RR		1.7567,1.5471,1.6853				211,12309				SO:0001589	frameshift_variant	200008	exon2			.		CCDS588.2	1p32.3	2011-02-10			ENSG00000157211	ENSG00000157211			27297	protein-coding gene	gene with protein product		612320				12477932	Standard	NM_201546		Approved		uc001cwv.2	Q5VXM1	OTTHUMG00000155307	ENST00000371330.1:c.161_162delCA	1.37:g.54610406_54610407delTG	ENSP00000360381:p.Thr54fs	138.0	0.0	.		119.0	33.0	0.277	NM_201546	Q6ZWJ3	Frame_Shift_Del	DEL	ENST00000371330.1	37	CCDS588.2																																																																																			.	.	none		0.559	CDCP2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000022209.2	NM_201546	
NOTCH1	4851	hgsc.bcm.edu	37	9	139390649	139390650	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139390649_139390650delAG	ENST00000277541.6	-	34	7616_7617	c.7541_7542delCT	c.(7540-7542)cctfs	p.P2514fs		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	2514					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P2515fs*4(145)|p.T2512fs*1(1)|p.E2515fs*3(1)		breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		CAGGGGACTCAGGGGACGGGGT	0.663			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)																											p.2514_2515del		Pindel,Atlas-Indel	.		Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	.	NOTCH1	1980	.	147	Complex - frameshift(145)|Deletion - Frameshift(2)	haematopoietic_and_lymphoid_tissue(147)	c.7542_7543del						PASS	.																																			SO:0001589	frameshift_variant	4851	exon34			.	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.7541_7542delCT	9.37:g.139390649_139390650delAG	ENSP00000277541:p.Pro2514fs	113.0	0.0	.		118.0	38.0	0.322	NM_017617	Q59ED8|Q5SXM3	Frame_Shift_Del	DEL	ENST00000277541.6	37	CCDS43905.1																																																																																			.	.	none		0.663	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
DHRS11	79154	hgsc.bcm.edu	37	17	34958760	34958761	+	IGR	INS	-	-	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34958760_34958761insG	ENST00000251312.5	+	0	1598				MRM1_ENST00000250156.7_Frame_Shift_Ins_p.I175fs|MRM1_ENST00000585770.1_Intron	NM_024308.3	NP_077284.2	Q6UWP2	DHR11_HUMAN	dehydrogenase/reductase (SDR family) member 11							extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			endometrium(1)|lung(4)	5						GTGGATAAGGTCATCACCAGCC	0.594																																					p.V174fs		Pindel,Atlas-Indel	.											.	MRM1	19	.	0			c.521_522insG						PASS	.																																			SO:0001628	intergenic_variant	79922	exon1			.		CCDS11315.2	17q12	2014-05-06			ENSG00000108272	ENSG00000278535		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	28639	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 24C, member 1"""					12975309, 19027726	Standard	NM_024308		Approved	MGC4172, SDR24C1	uc002hnd.3	Q6UWP2	OTTHUMG00000188442		17.37:g.34958760_34958761insG		29.0	0.0	.		33.0	12.0	0.364	NM_024864	B2RDZ3|Q9BUC7|Q9H674	Frame_Shift_Ins	INS	ENST00000251312.5	37	CCDS11315.2																																																																																			.	.	none		0.594	DHRS11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256681.2	NM_024308	
CCDC34	91057	hgsc.bcm.edu	37	11	27384449	27384466	+	In_Frame_Del	DEL	TCATCCACGTCTTCCTCA	TCATCCACGTCTTCCTCA	-	rs368035683|rs138931796|rs377198931|rs3207371|rs558321598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCATCCACGTCTTCCTCA	TCATCCACGTCTTCCTCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:27384449_27384466delTCATCCACGTCTTCCTCA	ENST00000328697.6	-	1	949_966	c.276_293delTGAGGAAGACGTGGATGA	c.(274-294)gatgaggaagacgtggatgaa>gaa	p.DEEDVD92del	CCDC34_ENST00000317945.6_In_Frame_Del_p.DEEDVD92del	NM_030771.1	NP_110398.1	Q96HJ3	CCD34_HUMAN	coiled-coil domain containing 34	92	Asp-rich.									endometrium(2)|large_intestine(4)|lung(1)|prostate(1)|urinary_tract(1)	9						ATGGGCATCTTCATCCACGTCTTCCTCATCATCCACGT	0.592														162	0.0323482	0.1097	0.0144	5008	,	,		19380	0.001		0.004	False		,,,				2504	0.002				p.93_98del		Pindel,Atlas-Indel	.											.	CCDC34	48	.	0			c.277_294del						PASS	.		,	353,3911		23,307,1802					,	0.9	0.0		dbSNP_134	173	50,8204		11,28,4088	no	coding,coding	CCDC34	NM_080654.2,NM_030771.1	,	34,335,5890	A1A1,A1R,RR		0.6058,8.2786,3.2194	,	,		403,12115				SO:0001651	inframe_deletion	91057	exon1			.	AF382034	CCDS7863.1, CCDS31448.1	11p14.1	2010-03-30			ENSG00000109881	ENSG00000109881			25079	protein-coding gene	gene with protein product		612324				11173847	Standard	NM_080654		Approved	NY-REN-41, L15, RAMA3	uc001mrh.1	Q96HJ3	OTTHUMG00000166211	ENST00000328697.6:c.276_293delTGAGGAAGACGTGGATGA	11.37:g.27384449_27384466delTCATCCACGTCTTCCTCA	ENSP00000330240:p.Asp92_Asp97del	294.0	0.0	.		215.0	39.0	0.181	NM_030771	B2R8G2|Q8IX69|Q9H2A6|Q9Y599	In_Frame_Del	DEL	ENST00000328697.6	37	CCDS31448.1																																																																																			TCATCCACGTCTTCCTCA|0.966;-|0.034	0.034	strong		0.592	CCDC34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388396.2	NM_030771	
ZFHX3	463	hgsc.bcm.edu	37	16	72831357	72831358	+	In_Frame_Ins	INS	-	-	TTG	rs568545014|rs34918837|rs552138038|rs372909378	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:72831357_72831358insTTG	ENST00000268489.5	-	9	5895_5896	c.5223_5224insCAA	c.(5221-5226)caagca>caaCAAgca	p.1741_1742insQ	ZFHX3_ENST00000397992.5_In_Frame_Ins_p.827_828insQ	NM_006885.3	NP_008816.3	Q15911	ZFHX3_HUMAN	zinc finger homeobox 3	1741	Poly-Gln.				brain development (GO:0007420)|cell cycle arrest (GO:0007050)|muscle organ development (GO:0007517)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|regulation of neuron differentiation (GO:0045664)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	enzyme binding (GO:0019899)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(3)|breast(7)|cervix(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(22)|liver(1)|lung(46)|ovary(5)|pancreas(1)|prostate(15)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(11)	153		Ovarian(137;0.13)				AGCGTTTGTGCttgttgttgtt	0.53														242	0.0483227	0.1755	0.0115	5008	,	,		29749	0.002		0.0	False		,,,				2504	0.0				p.A1742delinsQA		Atlas-Indel	.											.	ZFHX3	404	.	0			c.5224_5225insCAA						PASS	.																																			SO:0001652	inframe_insertion	463	exon9			.	D10250	CCDS10908.1, CCDS54035.1	16q22.3	2012-03-09	2007-08-09	2007-08-09	ENSG00000140836	ENSG00000140836		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	777	protein-coding gene	gene with protein product		104155	"""AT-binding transcription factor 1"""	ATBF1		1719379, 7592926	Standard	NM_006885		Approved	ZNF927	uc002fck.3	Q15911	OTTHUMG00000137599	ENST00000268489.5:c.5221_5223dupCAA	16.37:g.72831364_72831366dupTTG	ENSP00000268489:p.Gln1742_Gln1743dup	198.0	0.0	0		184.0	51.0	0.277174	NM_006885	D3DWS8|O15101|Q13719	In_Frame_Ins	INS	ENST00000268489.5	37	CCDS10908.1																																																																																			.	.	weak		0.530	ZFHX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269008.1	NM_006885	
PDE6H	5149	hgsc.bcm.edu	37	12	15134337	15134337	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:15134337delT	ENST00000266395.2	+	4	285	c.179delT	c.(178-180)atcfs	p.I60fs		NM_006205.2	NP_006196.1	Q13956	CNCG_HUMAN	phosphodiesterase 6H, cGMP-specific, cone, gamma	60					activation of MAPK activity (GO:0000187)|negative regulation of catalytic activity (GO:0043086)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|response to stimulus (GO:0050896)|visual perception (GO:0007601)		3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|cGMP binding (GO:0030553)|enzyme inhibitor activity (GO:0004857)			endometrium(1)|lung(6)|ovary(1)|skin(2)	10					Sildenafil(DB00203)|Vardenafil(DB00862)	CTTGCAGATATCACAGTGATT	0.498																																					p.I60fs		Pindel,Atlas-Indel	.											.	PDE6H	13	.	0			c.178delA						PASS	.						180.0	154.0	163.0					12																	15134337		2203	4300	6503	SO:0001589	frameshift_variant	5149	exon4			.		CCDS8672.1	12p13	2008-03-18					3.1.4.17	"""Phosphodiesterases"""	8790	protein-coding gene	gene with protein product		601190				8786098	Standard	NM_006205		Approved		uc001rcr.3	Q13956		ENST00000266395.2:c.179delT	12.37:g.15134337delT	ENSP00000266395:p.Ile60fs	110.0	0.0	.		106.0	33.0	0.311	NM_006205	Q52LY7	Frame_Shift_Del	DEL	ENST00000266395.2	37	CCDS8672.1																																																																																			.	.	none		0.498	PDE6H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400880.1		
ST6GALNAC5	81849	hgsc.bcm.edu	37	1	77334292	77334293	+	In_Frame_Ins	INS	-	-	CAGCAA	rs60179124|rs201548881|rs62637703	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:77334292_77334293insCAGCAA	ENST00000477717.1	+	2	361_362	c.126_127insCAGCAA	c.(127-129)cag>CAGCAAcag	p.43_43Q>QQQ	ST6GALNAC5_ENST00000496845.1_3'UTR	NM_030965.1	NP_112227.1	Q9BVH7	SIA7E_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 5	43	Poly-Gln.				glycosphingolipid biosynthetic process (GO:0006688)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	integral component of Golgi membrane (GO:0030173)	alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase activity (GO:0001665)|sialyltransferase activity (GO:0008373)			endometrium(2)|kidney(1)|large_intestine(6)|lung(5)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)	18						agcagcagcagcagcagcaaca	0.713														341	0.0680911	0.2216	0.0288	5008	,	,		11798	0.0		0.0258	False		,,,				2504	0.002				p.Q42delinsQQQ		Atlas-Indel	.											.	ST6GALNAC5	59	.	0			c.126_127insCAGCAA						PASS	.			818,37,3099		139,15,525,4,14,1280						2.2	1.0		dbSNP_129	13	373,14,7183		30,0,313,2,10,3430	no	codingComplex	ST6GALNAC5	NM_030965.1		169,15,838,6,24,4710	A1A1,A1A2,A1R,A2A2,A2R,RR		5.1123,21.6237,10.7775				1191,51,10282				SO:0001652	inframe_insertion	81849	exon2			.		CCDS673.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000117069	ENSG00000117069		"""Sialyltransferases"""	19342	protein-coding gene	gene with protein product		610134	"""sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) E"""	SIAT7E		10521438, 10601645	Standard	NM_030965		Approved	MGC3184, ST6GalNAcV	uc001dhi.3	Q9BVH7	OTTHUMG00000009687	Exception_encountered	1.37:g.77334292_77334293insCAGCAA	ENSP00000417583:p.GlnGln49dup	93.0	0.0	0		136.0	63.0	0.463235	NM_030965	B1AK82	In_Frame_Ins	INS	ENST00000477717.1	37	CCDS673.1																																																																																			-|0.929;CAGCAA|0.071	0.071	strong		0.713	ST6GALNAC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026692.2	NM_030965	
SUMF2	25870	hgsc.bcm.edu	37	7	56140760	56140761	+	Frame_Shift_Del	DEL	TT	TT	-	rs146946713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TT	TT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:56140760_56140761delTT	ENST00000413756.1	+	3	318_319	c.295_296delTT	c.(295-297)tttfs	p.F99fs	SUMF2_ENST00000342190.6_Frame_Shift_Del_p.F118fs|SUMF2_ENST00000275607.9_Frame_Shift_Del_p.F11fs|SUMF2_ENST00000395436.2_Frame_Shift_Del_p.F118fs|SUMF2_ENST00000437307.2_Frame_Shift_Del_p.F99fs|SUMF2_ENST00000434526.2_Frame_Shift_Del_p.F118fs|SUMF2_ENST00000395435.2_Frame_Shift_Del_p.F118fs			Q8NBJ7	SUMF2_HUMAN	sulfatase modifying factor 2	99					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)	endoplasmic reticulum lumen (GO:0005788)	metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(1)|lung(6)|ovary(2)|skin(1)	14	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			CTTTGAGGACTTTGTCTCTGAT	0.48														49	0.00978435	0.034	0.0058	5008	,	,		19873	0.0		0.0	False		,,,				2504	0.0				p.117_118del		Pindel,Atlas-Indel	.											.	SUMF2	56	.	0			c.351_352del						PASS	.		,,,,	133,4131		2,129,2001					,,,,	0.9	0.9		dbSNP_134	120	0,8254		0,0,4127	yes	frameshift,frameshift,frameshift,frameshift,frameshift	SUMF2	NM_015411.2,NM_001146333.1,NM_001130069.2,NM_001042470.1,NM_001042469.1	,,,,	2,129,6128	A1A1,A1R,RR		0.0,3.1191,1.0625	,,,,	,,,,		133,12385				SO:0001589	frameshift_variant	25870	exon3			.	AK075477	CCDS5524.2, CCDS43588.2, CCDS43589.2, CCDS47589.1, CCDS55111.1	7q11.1	2004-04-30			ENSG00000129103	ENSG00000129103			20415	protein-coding gene	gene with protein product		607940				12757706	Standard	NM_015411		Approved	DKFZp566I1024	uc003trv.3	Q8NBJ7	OTTHUMG00000129373	ENST00000413756.1:c.295_296delTT	7.37:g.56140760_56140761delTT	ENSP00000406445:p.Phe99fs	105.0	0.0	.		101.0	43.0	0.426	NM_001130069	B4DU41|B4DWQ0|Q14DW5|Q53ZE3|Q96BH2|Q9BRN3|Q9BWI1|Q9Y405	Frame_Shift_Del	DEL	ENST00000413756.1	37																																																																																				TT|0.993;-|0.007	0.007	strong		0.480	SUMF2-013	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000341457.2	NM_015411	
RPGR	6103	hgsc.bcm.edu	37	X	38145694	38145717	+	Intron	DEL	TCCTCCTCTTCCCCCTCCCCTTCC	TCCTCCTCTTCCCCCTCCCCTTCC	-			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCCTCCTCTTCCCCCTCCCCTTCC	TCCTCCTCTTCCCCCTCCCCTTCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:38145694_38145717delTCCTCCTCTTCCCCCTCCCCTTCC	ENST00000339363.3	-	14	2688				RPGR_ENST00000378505.2_In_Frame_Del_p.845_853EEGEGEEEE>E|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000309513.3_Intron|RPGR_ENST00000318842.7_Intron|RPGR_ENST00000342811.3_Intron|RPGR_ENST00000338898.3_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						cccttctccttcctcctcttccccctccccttcctcctcttccc	0.607																																					p.846_853del		Pindel	.											.	RPGR	175	.	0			c.2536_2559del	GRCh37	CD022920|CD077431|CI033306|CM004110|CM066945	orf15	D|I|M		PASS	.																																			SO:0001627	intron_variant	6103	exon15			.	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+629GGAAGGGGAGGGGGAAGAGGAGGA>-	X.37:g.38145694_38145717delTCCTCCTCTTCCCCCTCCCCTTCC		100.0	0.0	.		120.0	24.0	0.200	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	In_Frame_Del	DEL	ENST00000339363.3	37																																																																																				.	.	none		0.607	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
ZNF271	10778	hgsc.bcm.edu	37	18	32889822	32889823	+	RNA	INS	-	-	ATTGGTGTCCAAAACTGACACA	rs569387923|rs58173030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:32889822_32889823insATTGGTGTCCAAAACTGACACA	ENST00000399070.3	+	0	4216_4217					NR_024565.1|NR_024566.1		Q14591	ZN271_HUMAN	zinc finger protein 271						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(3)|lung(9)	12						atggacatgagattggtgtcca	0.411														9	0.00179712	0.0061	0.0014	5008	,	,		19822	0.0		0.0	False		,,,				2504	0.0				.		Pindel	.											.	ZNF271	16	.	0			.						PASS	.																																					10778	.			.	X78930		18q12.2	2013-04-03			ENSG00000257267	ENSG00000257267		"""Zinc fingers, C2H2-type"""	13065	other	unknown		604754				7865130, 11777961	Standard	NR_024565		Approved	HZF7, ZNFEB	uc002kyp.4	Q14591	OTTHUMG00000132563		18.37:g.32889822_32889823insATTGGTGTCCAAAACTGACACA		43.0	0.0	.		44.0	16.0	0.364	.	B3KN34|Q96T29|Q9BSX2|Q9UN33|Q9Y5B7	RNA	INS	ENST00000399070.3	37																																																																																				.	.	none		0.411	ZNF271-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000255767.2	NR_024565	
TMEM255B	348013	hgsc.bcm.edu	37	13	114503876	114503916	+	Splice_Site	DEL	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACA	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACA	-	rs9577890|rs111667140|rs41284485|rs9577889|rs114746443|rs66696122|rs371072437|rs115620789|rs550352190|rs386775130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACA	CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:114503876_114503916delCCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACA	ENST00000375353.3	+	6	527_536	c.500_509delCCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACA	c.(499-510)gcctgcgggagg>gg	p.ACGR167fs		NM_182614.2	NP_872420.1	Q8WV15	T255B_HUMAN	transmembrane protein 255B	167						integral component of membrane (GO:0016021)											GACCTCTATGCCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACACCTGCGGGAG	0.643																																					p.167_170del		Pindel	.											.	.	.	.	0			c.499_509del						PASS	.																																			SO:0001630	splice_region_variant	348013	exon6			.	BC018995	CCDS45071.1	13q34	2012-11-30	2012-11-30	2012-11-30	ENSG00000184497	ENSG00000184497			28297	protein-coding gene	gene with protein product			"""family with sequence similarity 70, member B"""	FAM70B		12477932	Standard	NM_182614		Approved	MGC20579	uc001vuh.3	Q8WV15	OTTHUMG00000017398	ENST00000375353.3:c.509+1CCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACA>-	13.37:g.114503876_114503916delCCTGCGGGAGGTGAGGGGCACCGGGGACCCCCATATCTACA		199.0	0.0	.		138.0	25.0	0.181	NM_182614		Frame_Shift_Del	DEL	ENST00000375353.3	37	CCDS45071.1																																																																																			.	.	none		0.643	TMEM255B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045953.4	NM_182614	Frame_Shift_Del
SERPINB3	6317	hgsc.bcm.edu	37	18	61323012	61323014	+	In_Frame_Del	DEL	CCT	CCT	-	rs3180227|rs60286570|rs386804125|rs72132327|rs201374310	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCT	CCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61323012_61323014delCCT	ENST00000283752.5	-	8	1193_1195	c.1050_1052delAGG	c.(1048-1053)gtagga>gta	p.G351del	SERPINB11_ENST00000489748.1_RNA|SERPINB3_ENST00000332821.8_In_Frame_Del_p.G299del	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	351			G -> A (increased antiprotease activity and increased MAPK8 inhibition activity; dbSNP:rs3180227). {ECO:0000269|PubMed:12975381, ECO:0000269|PubMed:14970861, ECO:0000269|PubMed:21383048, ECO:0000269|Ref.6}.		negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						TGATCCGAATCCTACTACAGCGG	0.488																																					p.351_351del		Pindel	.											.	SERPINB3	90	.	0			c.1051_1053del						PASS	.																																			SO:0001651	inframe_deletion	6317	exon8			.	U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"""Serine (or cysteine) peptidase inhibitors"""	10569	protein-coding gene	gene with protein product		600517	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"""	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.1050_1052delAGG	18.37:g.61323012_61323014delCCT	ENSP00000283752:p.Gly351del	211.0	0.0	.		190.0	42.0	0.221	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	In_Frame_Del	DEL	ENST00000283752.5	37	CCDS11987.1																																																																																			.	.	alt		0.488	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919	
RPGR	6103	hgsc.bcm.edu	37	X	38145199	38145201	+	Intron	DEL	TCC	TCC	-	rs200955614		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:38145199_38145201delTCC	ENST00000339363.3	-	14	2688				RPGR_ENST00000378505.2_In_Frame_Del_p.1017_1018EE>E|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000309513.3_Intron|RPGR_ENST00000318842.7_Intron|RPGR_ENST00000342811.3_Intron|RPGR_ENST00000338898.3_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						cacttccccttcctcttcttcct	0.581														38	0.0100662	0.0265	0.0043	3775	,	,		8305	0.0		0.0	False		,,,				2504	0.0				p.1018_1018del		Pindel	.											.	RPGR	175	.	0			c.3052_3054del	GRCh37	CD004123	orf15	D		PASS	.		,	173,3490		4,136,29,1439,476					,	-0.5	0.0			35	175,6221		2,108,63,2240,1633	no	coding,intron	RPGR	NM_001034853.1,NM_000328.2	,	6,244,92,3679,2109	A1A1,A1R,A1,RR,R		2.7361,4.7229,3.4596	,	,		348,9711				SO:0001627	intron_variant	6103	exon15			.	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+1145GGA>-	X.37:g.38145199_38145201delTCC		29.0	0.0	.		55.0	10.0	0.182	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	In_Frame_Del	DEL	ENST00000339363.3	37																																																																																				TCC|0.992;-|0.008	0.008	strong		0.581	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
DMKN	93099	hgsc.bcm.edu	37	19	36002371	36002394	+	In_Frame_Del	DEL	CCACTGCTGCCGCCACTGCTGCCG	CCACTGCTGCCGCCACTGCTGCCG	-	rs112672248|rs142519211|rs11667007|rs12981076|rs146822312|rs148799704|rs56743379|rs371511253|rs117522133|rs59309505|rs58579970	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	CCACTGCTGCCGCCACTGCTGCCG	CCACTGCTGCCGCCACTGCTGCCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36002371_36002394delCCACTGCTGCCGCCACTGCTGCCG	ENST00000339686.3	-	5	1013_1036	c.837_860delCGGCAGCAGTGGCGGCAGCAGTGG	c.(835-861)ggcggcagcagtggcggcagcagtggt>ggt	p.279_287GGSSGGSSG>G	DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000447113.2_In_Frame_Del_p.279_287GGSSGGSSG>G|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000451297.2_In_Frame_Del_p.279_287GGSSGGSSG>G|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000440396.1_In_Frame_Del_p.279_287GGSSGGSSG>G|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000424570.2_In_Frame_Del_p.279_287GGSSGGSSG>G|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000418261.1_In_Frame_Del_p.279_287GGSSGGSSG>G	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	279	Gly-rich.		G -> S (in dbSNP:rs11667007). {ECO:0000269|PubMed:17380110}.	G -> GSSSG (in Ref. 4; AAQ88778). {ECO:0000305}.		extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.S274_S290del(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			actgctgccaccactgctgccgccactgctgccgccactgctgc	0.638																																					p.280_287del		Pindel	.											.	DMKN	116	.	1	Deletion - In frame(1)	ovary(1)	c.838_861del						PASS	.																																			SO:0001651	inframe_deletion	93099	exon5			.	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.837_860delCGGCAGCAGTGGCGGCAGCAGTGG	19.37:g.36002371_36002394delCCACTGCTGCCGCCACTGCTGCCG	ENSP00000342012:p.Gly279_Ser286del	91.0	0.0	.		90.0	25.0	0.278	NM_033317	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	In_Frame_Del	DEL	ENST00000339686.3	37	CCDS12463.1																																																																																			.	.	none		0.638	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46012225	46012226	+	In_Frame_Ins	INS	-	-	CAGCAGCTGGGGGCA			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46012225_46012226insCAGCAGCTGGGGGCA	ENST00000400368.1	-	1	160_161	c.140_141insTGCCCCCAGCTGCTG	c.(139-141)tgc>tgTGCCCCCAGCTGCTGc	p.47_47C>CAPSCC	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	47	29 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(6)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23						GGGCCGGGGCGCAGCAGGGGGG	0.683																																					p.C47delinsCAPSCC		Pindel	.											.	KRTAP10-6	57	.	0			c.141_142insTGCCCCCAGCTGCTG						PASS	.																																			SO:0001652	inframe_insertion	386674	exon1			.	AB076353	CCDS42959.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000188155	ENSG00000188155		"""Keratin associated proteins"""	20523	protein-coding gene	gene with protein product			"""keratin associated protein 18-6"""	KRTAP18-6			Standard	NM_198688		Approved	KRTAP18.6, KAP18.6, KAP10.6	uc002zfm.3	P60371	OTTHUMG00000057634	ENST00000400368.1:c.140_141insTGCCCCCAGCTGCTG	21.37:g.46012225_46012226insCAGCAGCTGGGGGCA	Exception_encountered	93.0	0.0	.		58.0	14.0	0.241	NM_198688		In_Frame_Ins	INS	ENST00000400368.1	37	CCDS42959.1																																																																																			.	.	none		0.683	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688	
GPR39	2863	hgsc.bcm.edu	37	2	133403034	133403036	+	In_Frame_Del	DEL	AGA	AGA	-	rs557760477|rs113224054	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:133403034_133403036delAGA	ENST00000329321.3	+	2	1686_1688	c.1217_1219delAGA	c.(1216-1221)gagaag>gag	p.K407del	GPR39_ENST00000470071.1_3'UTR|LYPD1_ENST00000397463.2_3'UTR	NM_001508.2	NP_001499.1	O43194	GPR39_HUMAN	G protein-coupled receptor 39	407					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						AGGAGAACTGAGAAGATTTTCTT	0.601														13	0.00259585	0.0098	0.0	5008	,	,		18521	0.0		0.0	False		,,,				2504	0.0				p.406_406del		Pindel	.											.	GPR39	60	.	0			c.1216_1218del						PASS	.		,,	25,4241		2,21,2110					,,	-1.8	0.0		dbSNP_132	52	2,8252		1,0,4126	no	utr-3,coding,utr-3	GPR39,LYPD1	NM_144586.5,NM_001508.2,NM_001077427.2	,,	3,21,6236	A1A1,A1R,RR		0.0242,0.586,0.2157	,,	,,		27,12493				SO:0001651	inframe_deletion	2863	exon2			.	AF034633	CCDS2170.1	2q21-q22	2012-08-21			ENSG00000183840	ENSG00000183840		"""GPCR / Class A : Orphans"""	4496	protein-coding gene	gene with protein product		602886				9441746	Standard	NM_001508		Approved		uc002ttl.3	O43194	OTTHUMG00000131679	ENST00000329321.3:c.1217_1219delAGA	2.37:g.133403037_133403039delAGA	ENSP00000327417:p.Lys407del	26.0	0.0	.		23.0	10.0	0.435	NM_001508	B2RC12|B6V9G4|Q08AS2|Q53R01	In_Frame_Del	DEL	ENST00000329321.3	37	CCDS2170.1																																																																																			AGA|0.500;-|0.500	0.500	weak		0.601	GPR39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254582.1		
RPF2	84154	hgsc.bcm.edu	37	6	111310252	111310252	+	Missense_Mutation	SNP	G	G	A	rs6909298	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:111310252G>A	ENST00000441448.2	+	3	270	c.178G>A	c.(178-180)Ggt>Agt	p.G60S		NM_032194.1	NP_115570.1	Q9H7B2	RPF2_HUMAN	ribosome production factor 2 homolog (S. cerevisiae)	60	Brix. {ECO:0000255|PROSITE- ProRule:PRU00034}.		G -> S (in dbSNP:rs6909298).			nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|ovary(2)	7						AAAACCATACGGTGTACTATA	0.254													G|||	113	0.0225639	0.0809	0.0086	5008	,	,		15215	0.0		0.0	False		,,,				2504	0.0				p.G60S		Atlas-SNP	.											.	RPF2	26	.	0			c.G178A						PASS	.	G	SER/GLY	308,4064	152.2+/-185.9	17,274,1895	41.0	44.0	43.0		178	3.1	0.9	6	dbSNP_116	43	0,8588		0,0,4294	yes	missense	RPF2	NM_032194.1	56	17,274,6189	AA,AG,GG		0.0,7.0448,2.3765	benign	60/307	111310252	308,12652	2186	4294	6480	SO:0001583	missense	84154	exon3			CCATACGGTGTAC	AK024740	CCDS5088.1	6q21	2009-09-25	2009-09-25	2009-09-25	ENSG00000197498	ENSG00000197498			20870	protein-coding gene	gene with protein product	"""ribosomal processing factor 2 homolog (S. cerevisiae)"""		"""brix domain containing 1"""	BXDC1		12048200	Standard	NM_032194		Approved	FLJ21087, bA397G5.4	uc003pun.3	Q9H7B2	OTTHUMG00000015368	ENST00000441448.2:c.178G>A	6.37:g.111310252G>A	ENSP00000402338:p.Gly60Ser	113.0	0.0	0		133.0	66.0	0.496241	NM_032194	Q5VXN1|Q8N4A1	Missense_Mutation	SNP	ENST00000441448.2	37	CCDS5088.1	41	0.018772893772893772	41	0.08333333333333333	0	0.0	0	0.0	0	0.0	g	6.952	0.545509	0.13312	0.070448	0.0	ENSG00000197498	ENST00000441448;ENST00000368864;ENST00000425871	T;T;T	0.18960	2.18;2.18;2.18	4.92	3.11	0.35812	Brix domain (3);	0.105052	0.64402	D	0.000005	T	0.02380	0.0073	N	0.00765	-1.205	0.36277	D	0.855568	B	0.06786	0.001	B	0.10450	0.005	T	0.27297	-1.0078	10	0.33940	T	0.23	-35.436	11.9222	0.52797	0.1536:0.0:0.8463:0.0	rs6909298;rs52791590;rs6909298	60	Q9H7B2	RPF2_HUMAN	S	60;21;27	ENSP00000402338:G60S;ENSP00000357857:G21S;ENSP00000414026:G27S	ENSP00000357857:G21S	G	+	1	0	RPF2	111416945	1.000000	0.71417	0.914000	0.36105	0.019000	0.09904	4.189000	0.58358	1.209000	0.43321	-0.448000	0.05591	GGT	G|0.977;A|0.023	0.023	strong		0.254	RPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041813.2	NM_032194	
SEC16A	9919	hgsc.bcm.edu	37	9	139370829	139370829	+	Silent	SNP	G	G	A	rs114386206	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139370829G>A	ENST00000371706.3	-	1	738	c.705C>T	c.(703-705)ccC>ccT	p.P235P	SEC16A_ENST00000290037.6_Silent_p.P235P|SEC16A_ENST00000313050.7_Silent_p.P413P|SEC16A_ENST00000431893.2_Silent_p.P235P			O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	235					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|protein transport (GO:0015031)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				breast(1)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(15)|lung(14)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		GTGTAGGTGCGGGCGGACGGC	0.592													g|||	19	0.00379393	0.0136	0.0014	5008	,	,		16416	0.0		0.0	False		,,,				2504	0.0				p.P413P		Atlas-SNP	.											.	SEC16A	249	.	0			c.C1239T						PASS	.	C		42,3906		0,42,1932	21.0	24.0	23.0		1239	-7.4	0.0	9	dbSNP_132	23	9,8283		0,9,4137	no	coding-synonymous	SEC16A	NM_014866.1		0,51,6069	AA,AG,GG		0.1085,1.0638,0.4167		413/2358	139370829	51,12189	1974	4146	6120	SO:0001819	synonymous_variant	9919	exon3			AGGTGCGGGCGGA	AK074565	CCDS55351.1, CCDS75936.1	9q34.3	2007-06-20	2007-06-20	2007-06-20	ENSG00000148396	ENSG00000148396			29006	protein-coding gene	gene with protein product		612854	"""KIAA0310"""	KIAA0310		9205841	Standard	NM_014866		Approved	p250	uc004chx.3	O15027	OTTHUMG00000020932	ENST00000371706.3:c.705C>T	9.37:g.139370829G>A		89.0	0.0	0		121.0	45.0	0.371901	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Silent	SNP	ENST00000371706.3	37																																																																																				G|0.996;A|0.004	0.004	strong		0.592	SEC16A-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000055077.1	XM_088459	
EIF2A	83939	hgsc.bcm.edu	37	3	150285535	150285535	+	Silent	SNP	T	T	C	rs376872417	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:150285535T>C	ENST00000460851.1	+	7	640	c.531T>C	c.(529-531)ccT>ccC	p.P177P	EIF2A_ENST00000273435.5_Silent_p.P172P|EIF2A_ENST00000487799.1_Silent_p.P152P|SERP1_ENST00000490945.1_Intron|EIF2A_ENST00000406576.3_Silent_p.P116P|EIF2A_ENST00000383043.3_5'Flank|SERP1_ENST00000479209.1_Intron			Q9BY44	EIF2A_HUMAN	eukaryotic translation initiation factor 2A, 65kDa	177					positive regulation of signal transduction (GO:0009967)|protein phosphorylation (GO:0006468)|regulation of translation (GO:0006417)|ribosome assembly (GO:0042255)|SREBP signaling pathway (GO:0032933)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|eukaryotic translation initiation factor 2 complex (GO:0005850)|extracellular space (GO:0005615)	ribosome binding (GO:0043022)|translation initiation factor activity (GO:0003743)|tRNA binding (GO:0000049)			cervix(1)|endometrium(2)|kidney(1)|lung(3)	7		Melanoma(1037;0.0575)	LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			TATTATCACCTGGACCCCAAC	0.279													T|||	3	0.000599042	0.0023	0.0	5008	,	,		19889	0.0		0.0	False		,,,				2504	0.0				p.P177P		Atlas-SNP	.											.	EIF2A	59	.	0			c.T531C						PASS	.	T		3,3595		0,3,1796	77.0	67.0	70.0		531	2.2	1.0	3		70	0,8122		0,0,4061	no	coding-synonymous	EIF2A	NM_032025.3		0,3,5857	CC,CT,TT		0.0,0.0834,0.0256		177/586	150285535	3,11717	1799	4061	5860	SO:0001819	synonymous_variant	83939	exon7			ATCACCTGGACCC	AF212241	CCDS46935.1	3q25.1	2011-01-19	2006-01-24		ENSG00000144895	ENSG00000144895			3254	protein-coding gene	gene with protein product		609234				12133843, 1620067	Standard	NM_032025		Approved	EIF-2A	uc003eya.3	Q9BY44	OTTHUMG00000159775	ENST00000460851.1:c.531T>C	3.37:g.150285535T>C		174.0	0.0	0		187.0	95.0	0.508021	NM_032025	A8MPS6|B4DF96|B4DQ14|D3DNI9|Q5QTR2|Q7Z4E9|Q8NFM1|Q96EW9|Q96K81	Silent	SNP	ENST00000460851.1	37	CCDS46935.1																																																																																			.	.	weak		0.279	EIF2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000357259.2	NM_032025	
TNPO2	30000	hgsc.bcm.edu	37	19	12813683	12813683	+	Silent	SNP	T	T	C	rs16978630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12813683T>C	ENST00000592287.1	-	20	2367	c.2259A>G	c.(2257-2259)gaA>gaG	p.E753E	TNPO2_ENST00000588216.1_Silent_p.E753E|TNPO2_ENST00000425528.1_Silent_p.E753E|TNPO2_ENST00000441499.1_Silent_p.E753E|TNPO2_ENST00000356861.5_Silent_p.E753E|TNPO2_ENST00000450764.2_Silent_p.E753E	NM_001136196.1	NP_001129668.1	O14787	TNPO2_HUMAN	transportin 2	753					intracellular protein transport (GO:0006886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						GGTTAATGATTTCCACCAGGT	0.632													C|||	747	0.149161	0.5333	0.0461	5008	,	,		16704	0.0		0.0099	False		,,,				2504	0.0				p.E753E		Atlas-SNP	.											.	TNPO2	108	.	0			c.A2259G						PASS	.	C	,,	1692,2404		359,974,715	244.0	265.0	258.0		2259,2259,2259	1.0	1.0	19	dbSNP_123	258	127,8261		1,125,4068	no	coding-synonymous,coding-synonymous,coding-synonymous	TNPO2	NM_001136195.1,NM_001136196.1,NM_013433.4	,,	360,1099,4783	CC,CT,TT		1.5141,41.3086,14.5707	,,	753/888,753/898,753/888	12813683	1819,10665	2048	4194	6242	SO:0001819	synonymous_variant	30000	exon20			AATGATTTCCACC	AF019039	CCDS45991.1, CCDS45992.1	19p13.13	2009-01-12	2009-01-12			ENSG00000105576		"""Importins"""	19998	protein-coding gene	gene with protein product	"""importin 3"", ""karyopherin beta 2b"""	603002				9298975, 12384575	Standard	NM_013433		Approved	IPO3, KPNB2B, FLJ12155, TRN2	uc002muo.3	O14787		ENST00000592287.1:c.2259A>G	19.37:g.12813683T>C		310.0	0.0	0		314.0	141.0	0.449045	NM_013433	O14655|Q6IN77	Silent	SNP	ENST00000592287.1	37	CCDS45991.1																																																																																			T|0.866;C|0.134	0.134	strong		0.632	TNPO2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450785.1	NM_013433	
LRP4	4038	hgsc.bcm.edu	37	11	46917868	46917868	+	Missense_Mutation	SNP	A	A	G	rs7926667	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:46917868A>G	ENST00000378623.1	-	9	1183	c.941T>C	c.(940-942)tTg>tCg	p.L314S		NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	314	LDL-receptor class A 8. {ECO:0000255|PROSITE-ProRule:PRU00124}.		L -> S (in dbSNP:rs7926667).		dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		GAACTGGTCCAAGGCACATTG	0.562													G|||	306	0.0611022	0.2216	0.0173	5008	,	,		20751	0.0		0.001	False		,,,				2504	0.0				p.L314S		Atlas-SNP	.											.	LRP4	160	.	0			c.T941C						PASS	.	G	SER/LEU	769,3633	752.8+/-412.3	67,635,1499	90.0	86.0	87.0		941	6.0	0.9	11	dbSNP_116	87	3,8595	818.6+/-406.8	0,3,4296	yes	missense	LRP4	NM_002334.3	145	67,638,5795	GG,GA,AA		0.0349,17.4693,5.9385	benign	314/1906	46917868	772,12228	2201	4299	6500	SO:0001583	missense	4038	exon9			TGGTCCAAGGCAC	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"""Low density lipoprotein receptors"""	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.941T>C	11.37:g.46917868A>G	ENSP00000367888:p.Leu314Ser	28.0	0.0	0		22.0	7.0	0.318182	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Missense_Mutation	SNP	ENST00000378623.1	37	CCDS31478.1	100	0.045787545787545784	92	0.18699186991869918	8	0.022099447513812154	0	0.0	0	0.0	G	4.491	0.091136	0.08632	0.174693	3.49E-4	ENSG00000134569	ENST00000378623	T	0.55234	0.53	5.96	5.96	0.96718	.	0.074366	0.56097	N	0.000024	T	0.00039	0.0001	N	0.02368	-0.58	0.42982	P	0.005531999999999981	B	0.02656	0.0	B	0.06405	0.002	T	0.08806	-1.0704	9	0.07482	T	0.82	.	10.2442	0.43330	0.0677:0.0:0.7975:0.1348	rs7926667;rs52792198;rs7926667	314	O75096	LRP4_HUMAN	S	314	ENSP00000367888:L314S	ENSP00000367888:L314S	L	-	2	0	LRP4	46874444	1.000000	0.71417	0.886000	0.34754	0.907000	0.53573	4.687000	0.61708	1.543000	0.49345	-0.119000	0.15052	TTG	A|0.948;G|0.052	0.052	strong		0.562	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334	
DTX4	23220	hgsc.bcm.edu	37	11	58949852	58949852	+	Silent	SNP	C	C	T	rs75403375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:58949852C>T	ENST00000227451.3	+	2	956	c.852C>T	c.(850-852)acC>acT	p.T284T	DTX4_ENST00000532982.1_Silent_p.T178T	NM_015177.1	NP_055992.1	Q9Y2E6	DTX4_HUMAN	deltex 4, E3 ubiquitin ligase	284					innate immune response (GO:0045087)|Notch signaling pathway (GO:0007219)|positive regulation of type I interferon production (GO:0032481)|protein ubiquitination (GO:0016567)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(11)|prostate(1)|upper_aerodigestive_tract(1)	20		all_epithelial(135;0.125)				ACAGCAAGACCGGAAGGGTGG	0.637													C|||	135	0.0269569	0.0983	0.0072	5008	,	,		19567	0.0		0.0	False		,,,				2504	0.0				p.T284T		Atlas-SNP	.											.	DTX4	84	.	0			c.C852T						PASS	.	C		245,3755		7,231,1762	30.0	40.0	37.0		852	-9.1	0.0	11	dbSNP_132	37	0,8320		0,0,4160	no	coding-synonymous	DTX4	NM_015177.1		7,231,5922	TT,TC,CC		0.0,6.125,1.9886		284/620	58949852	245,12075	2000	4160	6160	SO:0001819	synonymous_variant	23220	exon2			CAAGACCGGAAGG	AB023154	CCDS44612.1	11q12.2	2014-01-28	2014-01-28		ENSG00000110042	ENSG00000110042		"""RING-type (C3HC4) zinc fingers"""	29151	protein-coding gene	gene with protein product			"""deltex 4 homolog (Drosophila)"", ""deltex homolog 4 (Drosophila)"""			10231032, 22388039	Standard	NM_015177		Approved	KIAA0937, RNF155	uc001nns.2	Q9Y2E6	OTTHUMG00000167336	ENST00000227451.3:c.852C>T	11.37:g.58949852C>T		45.0	0.0	0		49.0	25.0	0.510204	NM_015177	Q0VF38	Silent	SNP	ENST00000227451.3	37	CCDS44612.1																																																																																			C|0.975;T|0.025	0.025	strong		0.637	DTX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394228.1	XM_166213	
ZNF804B	219578	hgsc.bcm.edu	37	7	88965040	88965040	+	Missense_Mutation	SNP	C	C	T	rs56948780	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:88965040C>T	ENST00000333190.4	+	4	3353	c.2744C>T	c.(2743-2745)aCt>aTt	p.T915I		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	915			T -> I (in dbSNP:rs56948780).				metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			GAATCAAACACTGCAGAAGGA	0.433										HNSCC(36;0.09)			T|||	199	0.0397364	0.1445	0.0101	5008	,	,		18290	0.0		0.001	False		,,,				2504	0.0				p.T915I		Atlas-SNP	.											.	ZNF804B	322	.	0			c.C2744T						PASS	.	T	ILE/THR	522,3884	769.0+/-413.6	33,456,1714	93.0	99.0	97.0		2744	2.7	0.0	7	dbSNP_129	97	7,8593	818.2+/-406.9	0,7,4293	yes	missense	ZNF804B	NM_181646.2	89	33,463,6007	TT,TC,CC		0.0814,11.8475,4.0674	benign	915/1350	88965040	529,12477	2203	4300	6503	SO:0001583	missense	219578	exon4			CAAACACTGCAGA	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"""zinc finger 804B"""				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.2744C>T	7.37:g.88965040C>T	ENSP00000329638:p.Thr915Ile	135.0	0.0	0		130.0	65.0	0.5	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	37	CCDS5613.1	67	0.030677655677655676	63	0.12804878048780488	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	T	0.047	-1.263638	0.01445	0.118475	8.14E-4	ENSG00000182348	ENST00000333190	T	0.04406	3.63	5.02	2.67	0.31697	.	1.602880	0.03170	N	0.170660	T	0.00039	0.0001	N	0.01168	-0.975	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.41875	-0.9484	10	0.02654	T	1	3.734	4.3373	0.11092	0.1723:0.2578:0.0:0.5699	rs56948780	915	A4D1E1	Z804B_HUMAN	I	915	ENSP00000329638:T915I	ENSP00000329638:T915I	T	+	2	0	ZNF804B	88802976	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	0.929000	0.28844	0.092000	0.17331	-0.254000	0.11334	ACT	C|0.964;T|0.036	0.036	strong		0.433	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646	
IFNA13	3447	hgsc.bcm.edu	37	9	21367519	21367519	+	Missense_Mutation	SNP	G	G	C	rs145283706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21367519G>C	ENST00000449498.1	-	1	556	c.491C>G	c.(490-492)gCc>gGc	p.A164G		NM_006900.3	NP_008831.3	P01562	IFNA1_HUMAN	interferon, alpha 13	163					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)|type I interferon receptor binding (GO:0005132)			breast(2)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)|skin(1)	9				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.0173)		AACCTCCCAGGCACAAGGGCT	0.443																																					p.A164G		Atlas-SNP	.											.	IFNA13	19	.	0			c.C491G						PASS	.						108.0	102.0	104.0					9																	21367519		2202	4280	6482	SO:0001583	missense	3447	exon1			TCCCAGGCACAAG		CCDS6505.2	9p22	2010-12-10			ENSG00000233816	ENSG00000233816		"""Interferons"""	5419	protein-coding gene	gene with protein product		147578				1385305	Standard	NM_006900		Approved		uc003zpa.2	P01562	OTTHUMG00000019675	ENST00000449498.1:c.491C>G	9.37:g.21367519G>C	ENSP00000394494:p.Ala164Gly	569.0	1.0	0.00175747		592.0	229.0	0.386824	NM_006900	D4Q9M8|Q14605|Q2M1L8|Q52LB8|Q5VYQ2|Q7M4Q1|Q8WZ68|Q9UMJ3	Missense_Mutation	SNP	ENST00000449498.1	37	CCDS6505.2	.	.	.	.	.	.	.	.	.	.	G	19.57	3.852515	0.71719	.	.	ENSG00000233816	ENST00000449498	T	0.18960	2.18	2.56	1.64	0.23874	.	0.126331	0.52532	D	0.000075	T	0.50446	0.1616	M	0.92317	3.295	0.27386	N	0.95527	P	0.39847	0.691	D	0.65140	0.932	T	0.42899	-0.9424	10	0.87932	D	0	.	6.7704	0.23591	0.1469:0.0:0.8531:0.0	.	164	E9PB07	.	G	164	ENSP00000394494:A164G	ENSP00000394494:A164G	A	-	2	0	IFNA13	21357519	1.000000	0.71417	0.994000	0.49952	0.928000	0.56348	2.320000	0.43797	0.402000	0.25451	0.313000	0.20887	GCC	G|0.832;C|0.168	0.168	strong		0.443	IFNA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051904.2	NM_006900	
ZNF492	57615	hgsc.bcm.edu	37	19	22846962	22846962	+	Missense_Mutation	SNP	G	G	C	rs138844698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22846962G>C	ENST00000456783.2	+	4	735	c.491G>C	c.(490-492)aGt>aCt	p.S164T	CTC-457E21.9_ENST00000601860.1_RNA	NM_020855.2	NP_065906.1	Q9P255	ZN492_HUMAN	zinc finger protein 492	164					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				AGAATTCATAGTGGAGAGAAA	0.338													N|||	246	0.0491214	0.1778	0.0115	5008	,	,		17962	0.0		0.003	False		,,,				2504	0.0				p.S164T		Atlas-SNP	.											.	ZNF492	129	.	0			c.G491C						PASS	.						14.0	20.0	18.0					19																	22846962		1994	4214	6208	SO:0001583	missense	57615	exon4			TTCATAGTGGAGA	AB040906	CCDS46032.1	19p13.11	2013-01-08				ENSG00000229676		"""Zinc fingers, C2H2-type"""	23707	protein-coding gene	gene with protein product			"""zinc finger protein 115 (Y20)"""	ZNF115		10819331	Standard	NM_020855		Approved	KIAA1473	uc002nqw.3	Q9P255		ENST00000456783.2:c.491G>C	19.37:g.22846962G>C	ENSP00000413660:p.Ser164Thr	281.0	2.0	0.00711744		160.0	119.0	0.74375	NM_020855	Q08EI7|Q08EI8	Missense_Mutation	SNP	ENST00000456783.2	37	CCDS46032.1	93	0.042582417582417584	87	0.17682926829268292	4	0.011049723756906077	0	0.0	2	0.002638522427440633	.	0.004	-2.252690	0.00268	.	.	ENSG00000229676	ENST00000456783	T	0.12879	2.64	1.3	1.3	0.21679	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00890	-1.11	0.52501	P	4.999999999999449E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.44452	-0.9327	8	0.02654	T	1	.	6.7224	0.23338	0.0:0.7004:0.2996:0.0	.	164	Q9P255	ZN492_HUMAN	T	164	ENSP00000413660:S164T	ENSP00000413660:S164T	S	+	2	0	ZNF492	22638802	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-3.346000	0.00503	-0.381000	0.07882	-1.146000	0.01853	AGT	G|0.957;C|0.043	0.043	strong		0.338	ZNF492-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464581.1	NM_020855	
ALDH16A1	126133	hgsc.bcm.edu	37	19	49969501	49969501	+	Silent	SNP	G	G	A	rs61732839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49969501G>A	ENST00000293350.4	+	14	2062	c.1899G>A	c.(1897-1899)gcG>gcA	p.A633A	ALDH16A1_ENST00000540132.1_Silent_p.A470A|ALDH16A1_ENST00000455361.2_Silent_p.A582A|CTD-3148I10.9_ENST00000599536.1_Intron|ALDH16A1_ENST00000433981.2_Silent_p.A468A	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	633						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|skin(2)|urinary_tract(3)	20		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)		GACTTCGGGCGTGGGGGGCCC	0.716													G|||	188	0.0375399	0.1324	0.0159	5008	,	,		14127	0.001		0.001	False		,,,				2504	0.0				p.A633A		Atlas-SNP	.											.	ALDH16A1	54	.	0			c.G1899A						PASS	.	G	,	360,3874		8,344,1765	9.0	11.0	11.0		1746,1899	-8.7	0.0	19	dbSNP_129	11	9,8349		0,9,4170	no	coding-synonymous,coding-synonymous	ALDH16A1	NM_001145396.1,NM_153329.3	,	8,353,5935	AA,AG,GG		0.1077,8.5026,2.9304	,	582/752,633/803	49969501	369,12223	2117	4179	6296	SO:0001819	synonymous_variant	126133	exon14			TCGGGCGTGGGGG	AY007096	CCDS12766.1, CCDS46141.1	19q13.33	2014-08-12			ENSG00000161618	ENSG00000161618		"""Aldehyde dehydrogenases"""	28114	protein-coding gene	gene with protein product		613358					Standard	NM_153329		Approved	MGC10204	uc002pnt.3	Q8IZ83	OTTHUMG00000183163	ENST00000293350.4:c.1899G>A	19.37:g.49969501G>A		40.0	0.0	0		50.0	20.0	0.4	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Silent	SNP	ENST00000293350.4	37	CCDS12766.1																																																																																			G|0.975;A|0.025	0.025	strong		0.716	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329	
FAM214A	56204	hgsc.bcm.edu	37	15	52901109	52901109	+	Missense_Mutation	SNP	T	T	C	rs61731676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:52901109T>C	ENST00000261844.7	-	6	2154	c.2002A>G	c.(2002-2004)Aaa>Gaa	p.K668E	FAM214A_ENST00000546305.2_Missense_Mutation_p.K675E	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A	668																	CCAAAGAATTTTGGATTATAG	0.269													T|||	98	0.0195687	0.0726	0.0029	5008	,	,		17454	0.0		0.0	False		,,,				2504	0.0				p.K668E		Atlas-SNP	.											.	.	.	.	0			c.A2002G						PASS	.	T	GLU/LYS	195,3367		6,183,1592	51.0	47.0	48.0		2002	5.2	0.2	15	dbSNP_129	48	1,8081		0,1,4040	yes	missense	KIAA1370	NM_019600.2	56	6,184,5632	CC,CT,TT		0.0124,5.4745,1.6833	benign	668/1077	52901109	196,11448	1781	4041	5822	SO:0001583	missense	56204	exon6			AGAATTTTGGATT	AB037791	CCDS45263.1, CCDS66773.1	15q21.2-q21.3	2011-12-01	2011-12-01	2011-12-01	ENSG00000047346	ENSG00000047346			25609	protein-coding gene	gene with protein product			"""KIAA1370"""	KIAA1370		10718198	Standard	XM_005254547		Approved	FLJ10980	uc002acg.4	Q32MH5		ENST00000261844.7:c.2002A>G	15.37:g.52901109T>C	ENSP00000261844:p.Lys668Glu	55.0	0.0	0		83.0	38.0	0.457831	NM_019600	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Missense_Mutation	SNP	ENST00000261844.7	37	CCDS45263.1	35	0.016025641025641024	34	0.06910569105691057	1	0.0027624309392265192	0	0.0	0	0.0	T	0	-2.662882	0.00107	0.054745	1.24E-4	ENSG00000047346	ENST00000261844;ENST00000399202;ENST00000534964;ENST00000546305	T;T;T	0.29397	1.65;1.57;1.65	6.16	5.24	0.73138	.	0.435251	0.24628	N	0.036918	T	0.00524	0.0017	N	0.00368	-1.59	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.21314	-1.0249	10	0.02654	T	1	.	11.867	0.52499	0.0:0.859:0.0:0.141	.	675;668	F5H8G0;Q32MH5	.;K1370_HUMAN	E	668;668;667;675	ENSP00000261844:K668E;ENSP00000382153:K668E;ENSP00000443598:K675E	ENSP00000261844:K668E	K	-	1	0	KIAA1370	50688401	0.012000	0.17670	0.195000	0.23364	0.037000	0.13140	1.798000	0.38814	1.598000	0.50083	-0.248000	0.11899	AAA	T|0.982;C|0.018	0.018	strong		0.269	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419914.1	NM_019600	
DPH7	92715	hgsc.bcm.edu	37	9	140472034	140472034	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140472034G>C	ENST00000277540.2	-	2	332	c.175C>G	c.(175-177)Cct>Gct	p.P59A	DPH7_ENST00000479650.1_Intron	NM_138778.2	NP_620133.1	Q9BTV6	DPH7_HUMAN	diphthamide biosynthesis 7	59					peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)												CGGACCTGAGGCTCCTTAACT	0.458																																					p.P59A		Atlas-SNP	.											.	WDR85	20	.	0			c.C175G						PASS	.						110.0	98.0	102.0					9																	140472034		2203	4300	6503	SO:0001583	missense	92715	exon2			CCTGAGGCTCCTT	AK075115	CCDS7047.1	9q34.3	2013-06-20	2013-06-20	2013-06-20	ENSG00000148399	ENSG00000148399		"""WD repeat domain containing"""	25199	protein-coding gene	gene with protein product		613210	"""chromosome 9 open reading frame 112"", ""WD repeat domain 85"""	C9orf112, WDR85		23486472	Standard	NM_138778		Approved	FLJ90634, RRT2	uc004cnk.1	Q9BTV6	OTTHUMG00000020991	ENST00000277540.2:c.175C>G	9.37:g.140472034G>C	ENSP00000277540:p.Pro59Ala	106.0	0.0	0		133.0	92.0	0.691729	NM_138778	Q96AB7	Missense_Mutation	SNP	ENST00000277540.2	37	CCDS7047.1	.	.	.	.	.	.	.	.	.	.	G	14.22	2.471496	0.43942	.	.	ENSG00000148399	ENST00000277540	T	0.12569	2.67	5.11	4.2	0.49525	.	0.243332	0.33875	N	0.004464	T	0.09468	0.0233	L	0.32530	0.975	0.29436	N	0.859517	B	0.33549	0.417	B	0.30105	0.111	T	0.11690	-1.0577	10	0.21540	T	0.41	.	10.6122	0.45429	0.0936:0.0:0.9064:0.0	.	59	Q9BTV6	WDR85_HUMAN	A	59	ENSP00000277540:P59A	ENSP00000277540:P59A	P	-	1	0	WDR85	139591855	0.998000	0.40836	0.361000	0.25849	0.016000	0.09150	1.030000	0.30153	2.363000	0.80096	0.455000	0.32223	CCT	.	.	none		0.458	DPH7-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055350.1	NM_138778	
PCSK7	9159	hgsc.bcm.edu	37	11	117097931	117097931	+	Silent	SNP	C	C	T	rs45528535	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117097931C>T	ENST00000320934.3	-	5	1341	c.711G>A	c.(709-711)gcG>gcA	p.A237A		NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	237	Peptidase S8.				peptide hormone processing (GO:0016486)|protein processing (GO:0016485)	integral component of Golgi membrane (GO:0030173)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	16	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)		TGGGCACAGCCGCGATCTCTC	0.607			T	IGH@	MLCLS						OREG0021371	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	227	0.0453275	0.1415	0.0375	5008	,	,		18045	0.0		0.0119	False		,,,				2504	0.002				p.A237A		Atlas-SNP	.		Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	PCSK7,NS,carcinoma,-2,1	PCSK7	59	1	0			c.G711A						PASS	.	C		535,3867	243.1+/-252.9	28,479,1694	114.0	94.0	101.0		711	-11.2	0.0	11	dbSNP_127	101	31,8561	22.2+/-67.0	0,31,4265	no	coding-synonymous	PCSK7	NM_004716.2		28,510,5959	TT,TC,CC		0.3608,12.1536,4.3559		237/786	117097931	566,12428	2201	4296	6497	SO:0001819	synonymous_variant	9159	exon5			CACAGCCGCGATC	U40623	CCDS8382.1	11q23-q24	2008-02-01			ENSG00000160613	ENSG00000160613			8748	protein-coding gene	gene with protein product		604872				8615762, 9820811	Standard	XM_006718938		Approved	PC7, PC8, LPC, SPC7	uc001pqr.3	Q16549	OTTHUMG00000165640	ENST00000320934.3:c.711G>A	11.37:g.117097931C>T		78.0	0.0	0	1478	79.0	28.0	0.35443	NM_004716	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Silent	SNP	ENST00000320934.3	37	CCDS8382.1																																																																																			C|0.956;T|0.044	0.044	strong		0.607	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716	
ADRB1	153	hgsc.bcm.edu	37	10	115805057	115805057	+	Missense_Mutation	SNP	G	G	T	rs17875445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:115805057G>T	ENST00000369295.2	+	1	1252	c.1166G>T	c.(1165-1167)gGa>gTa	p.G389V		NM_000684.2	NP_000675.1	P08588	ADRB1_HUMAN	adrenoceptor beta 1	389			R -> G (reduced binding to G proteins; dbSNP:rs1801253). {ECO:0000269|PubMed:10212248, ECO:0000269|PubMed:10477438, ECO:0000269|PubMed:15164054, ECO:0000269|Ref.3}.|R -> L. {ECO:0000269|Ref.3}.		activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|aging (GO:0007568)|apoptotic process (GO:0006915)|brown fat cell differentiation (GO:0050873)|diet induced thermogenesis (GO:0002024)|fear response (GO:0042596)|glycogen catabolic process (GO:0005980)|heat generation (GO:0031649)|lipid homeostasis (GO:0055088)|memory (GO:0007613)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of smooth muscle contraction (GO:0045986)|negative regulation of urine volume (GO:0035811)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cation channel activity (GO:2001259)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of heart rate by epinephrine-norepinephrine (GO:0001996)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of renin secretion into blood stream (GO:1900135)|positive regulation of saliva secretion (GO:0046878)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of the force of heart contraction by norepinephrine (GO:0003061)|protein localization to organelle (GO:0033365)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|response to cold (GO:0009409)|Rho protein signal transduction (GO:0007266)|sensory perception of pain (GO:0019233)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)|wound healing (GO:0042060)	early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|beta-adrenergic receptor activity (GO:0004939)|beta1-adrenergic receptor activity (GO:0004940)|dopamine binding (GO:0035240)|drug binding (GO:0008144)|epinephrine binding (GO:0051379)|norepinephrine binding (GO:0051380)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|receptor signaling protein activity (GO:0005057)			large_intestine(4)|lung(1)|upper_aerodigestive_tract(1)	6		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0124)|all cancers(201;0.0298)	Acebutolol(DB01193)|Alprenolol(DB00866)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Asenapine(DB06216)|Atenolol(DB00335)|Betaxolol(DB00195)|Bethanidine(DB00217)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bopindolol(DB08807)|Bupranolol(DB08808)|Cabergoline(DB00248)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Dobutamine(DB00841)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Esmolol(DB00187)|Fenoterol(DB01288)|Isoetarine(DB00221)|Isoprenaline(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Loxapine(DB00408)|Mephentermine(DB01365)|Metipranolol(DB01214)|Metoprolol(DB00264)|Mirtazapine(DB00370)|Nadolol(DB01203)|Nebivolol(DB04861)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Phenylpropanolamine(DB00397)|Pindolol(DB00960)|Pirbuterol(DB01291)|Practolol(DB01297)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Salbutamol(DB01001)|Sotalol(DB00489)|Timolol(DB00373)|Trimipramine(DB00726)	GCCTTCCAGGGACTGCTCTGC	0.721													G|||	27	0.00539137	0.0197	0.0014	5008	,	,		5822	0.0		0.0	False		,,,				2504	0.0				p.G389V		Atlas-SNP	.											.	ADRB1	16	.	0			c.G1166T						PASS	.	G	VAL/GLY	35,4029		0,35,1997	15.0	13.0	13.0		1166	1.7	1.0	10	dbSNP_124	13	0,7986		0,0,3993	no	missense	ADRB1	NM_000684.2	109	0,35,5990	TT,TG,GG		0.0,0.8612,0.2905		389/478	115805057	35,12015	2032	3993	6025	SO:0001583	missense	153	exon1			TCCAGGGACTGCT	J03019	CCDS7586.1	10q25.3	2012-08-08	2012-05-09		ENSG00000043591	ENSG00000043591		"""GPCR / Class A : Adrenoceptors : beta"""	285	protein-coding gene	gene with protein product		109630	"""adrenergic, beta-1-, receptor"""	ADRB1R			Standard	NM_000684		Approved		uc001lba.3	P08588	OTTHUMG00000019079	ENST00000369295.2:c.1166G>T	10.37:g.115805057G>T	ENSP00000358301:p.Gly389Val	36.0	0.0	0		37.0	17.0	0.459459	NM_000684	B0LPE2|Q5T5Y4|Q9UKG7|Q9UKG8	Missense_Mutation	SNP	ENST00000369295.2	37	CCDS7586.1	11	0.005036630036630037	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	0	0.0	G	8.144	0.785930	0.16189	0.008612	0.0	ENSG00000043591	ENST00000369295	T	0.37235	1.21	3.81	1.72	0.24424	.	0.000000	0.85682	U	0.000000	T	0.26484	0.0647	M	0.64404	1.975	0.36477	D	0.867582	.	.	.	.	.	.	T	0.37079	-0.9721	8	0.62326	D	0.03	.	7.2309	0.26043	0.3079:0.0:0.6921:0.0	rs17875445	.	.	.	V	389	ENSP00000358301:G389V	ENSP00000358301:G389V	G	+	2	0	ADRB1	115795047	1.000000	0.71417	0.998000	0.56505	0.291000	0.27294	3.494000	0.53273	0.129000	0.18514	0.484000	0.47621	GGA	G|0.994;T|0.006	0.006	strong		0.721	ADRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050448.1		
TMEM63A	9725	hgsc.bcm.edu	37	1	226050503	226050503	+	Silent	SNP	G	G	A	rs10915888	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:226050503G>A	ENST00000366835.3	-	11	1065	c.795C>T	c.(793-795)aaC>aaT	p.N265N	TMEM63A_ENST00000537914.1_De_novo_Start_OutOfFrame|TMEM63A_ENST00000474478.1_5'UTR	NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A	265					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	nucleotide binding (GO:0000166)			breast(2)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24	Breast(184;0.197)					GTTTGGCCACGTTGTAGCACA	0.572													G|||	199	0.0397364	0.1392	0.0202	5008	,	,		18776	0.0		0.0	False		,,,				2504	0.001				p.N265N		Atlas-SNP	.											.	TMEM63A	75	.	0			c.C795T						PASS	.	G		574,3832	255.8+/-260.9	35,504,1664	114.0	81.0	92.0		795	-1.0	0.8	1	dbSNP_120	92	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TMEM63A	NM_014698.2		35,506,5962	AA,AG,GG		0.0233,13.0277,4.4287		265/808	226050503	576,12430	2203	4300	6503	SO:0001819	synonymous_variant	9725	exon11			GGCCACGTTGTAG		CCDS31042.1	1q42.12	2008-02-05	2005-07-25	2005-07-25	ENSG00000196187	ENSG00000196187			29118	protein-coding gene	gene with protein product			"""KIAA0792"""	KIAA0792		9872452, 9455484	Standard	NM_014698		Approved		uc001hpm.2	O94886	OTTHUMG00000037442	ENST00000366835.3:c.795C>T	1.37:g.226050503G>A		170.0	0.0	0		203.0	108.0	0.53202	NM_014698	Q53GI7|Q5TE96|Q8N2U2	Silent	SNP	ENST00000366835.3	37	CCDS31042.1																																																																																			G|0.956;A|0.044	0.044	strong		0.572	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	NM_014698	
SVEP1	79987	hgsc.bcm.edu	37	9	113265448	113265448	+	Silent	SNP	A	A	G	rs10120982	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:113265448A>G	ENST00000401783.2	-	6	1689	c.1353T>C	c.(1351-1353)tgT>tgC	p.C451C	SVEP1_ENST00000302728.8_Silent_p.C451C|SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000374461.1_Silent_p.C428C|SVEP1_ENST00000374469.1_Silent_p.C428C	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	451	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				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						CCCTTGTAGAACAGCTGATGT	0.393													A|||	56	0.0111821	0.0378	0.0072	5008	,	,		20793	0.0		0.001	False		,,,				2504	0.0				p.C451C		Atlas-SNP	.											SVEP1,NS,carcinoma,-1,2	SVEP1	326	2	0			c.T1353C						PASS	.	A		130,3830		4,122,1854	152.0	149.0	150.0		1353	0.9	1.0	9	dbSNP_119	150	2,8308		0,2,4153	no	coding-synonymous	SVEP1	NM_153366.3		4,124,6007	GG,GA,AA		0.0241,3.2828,1.0758		451/3572	113265448	132,12138	1980	4155	6135	SO:0001819	synonymous_variant	79987	exon6			TGTAGAACAGCTG	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.1353T>C	9.37:g.113265448A>G		186.0	0.0	0		202.0	59.0	0.292079	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	37	CCDS48004.1																																																																																			A|0.992;G|0.008	0.008	strong		0.393	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
ALX4	60529	hgsc.bcm.edu	37	11	44286722	44286722	+	Silent	SNP	C	C	T	rs145904583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:44286722C>T	ENST00000329255.3	-	4	1021	c.918G>A	c.(916-918)ccG>ccA	p.P306P		NM_021926.3	NP_068745.2	Q9H161	ALX4_HUMAN	ALX homeobox 4	306			P -> L. {ECO:0000269|PubMed:22829454}.		anterior/posterior pattern specification (GO:0009952)|digestive tract development (GO:0048565)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal system morphogenesis (GO:0048704)|hair follicle development (GO:0001942)|muscle organ development (GO:0007517)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|regulation of apoptotic process (GO:0042981)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P306P(1)		central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	16						CGAGCCAGGACGGGTTCTGAA	0.687													C|||	47	0.00938498	0.0325	0.0043	5008	,	,		16566	0.0		0.0	False		,,,				2504	0.001				p.P306P		Atlas-SNP	.											ALX4,NS,carcinoma,0,1	ALX4	58	1	1	Substitution - coding silent(1)	prostate(1)	c.G918A						PASS	.	C		100,4198		1,98,2050	17.0	16.0	16.0		918	-7.6	0.3	11	dbSNP_134	16	5,8425		0,5,4210	no	coding-synonymous	ALX4	NM_021926.3		1,103,6260	TT,TC,CC		0.0593,2.3267,0.825		306/412	44286722	105,12623	2149	4215	6364	SO:0001819	synonymous_variant	60529	exon4			CCAGGACGGGTTC	AF294629	CCDS31468.1	11p11.2	2011-06-20	2008-11-04		ENSG00000052850	ENSG00000052850		"""Homeoboxes / PRD class"""	450	protein-coding gene	gene with protein product		605420	"""parietal foramina 2"", ""aristaless-like homeobox 4"""	PFM2		11017806, 8644736	Standard	NM_021926		Approved	FPP, PFM, KIAA1788	uc001myb.3	Q9H161	OTTHUMG00000166557	ENST00000329255.3:c.918G>A	11.37:g.44286722C>T		267.0	0.0	0		221.0	109.0	0.493213	NM_021926	Q96JN7|Q9H198|Q9HAY9	Silent	SNP	ENST00000329255.3	37	CCDS31468.1																																																																																			C|0.991;T|0.009	0.009	strong		0.687	ALX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390399.1		
ADAMTS15	170689	hgsc.bcm.edu	37	11	130318935	130318935	+	Silent	SNP	C	C	A	rs146878786	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:130318935C>A	ENST00000299164.2	+	1	67	c.67C>A	c.(67-69)Cgg>Agg	p.R23R		NM_139055.2	NP_620686.1	Q8TE58	ATS15_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 15	23						proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(16)|pancreas(1)|prostate(1)|skin(8)|urinary_tract(1)	36	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0631)|Lung(977;0.215)		TGAGCCAGAGCGGGAGGTAGT	0.662													C|||	14	0.00279553	0.0098	0.0014	5008	,	,		14248	0.0		0.0	False		,,,				2504	0.0				p.R23R		Atlas-SNP	.											.	ADAMTS15	103	.	0			c.C67A						PASS	.	C		46,4356	44.6+/-78.6	0,46,2155	29.0	30.0	30.0		67	2.4	0.4	11	dbSNP_134	30	0,8594		0,0,4297	no	coding-synonymous	ADAMTS15	NM_139055.2		0,46,6452	AA,AC,CC		0.0,1.045,0.354		23/951	130318935	46,12950	2201	4297	6498	SO:0001819	synonymous_variant	170689	exon1			CCAGAGCGGGAGG	AJ315733	CCDS8488.1	11q25	2008-02-01	2005-08-19		ENSG00000166106	ENSG00000166106		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	16305	protein-coding gene	gene with protein product		607509	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 15"""			11867212	Standard	NM_139055		Approved		uc010scd.2	Q8TE58	OTTHUMG00000165657	ENST00000299164.2:c.67C>A	11.37:g.130318935C>A		82.0	0.0	0		59.0	24.0	0.40678	NM_139055	Q32MI6	Silent	SNP	ENST00000299164.2	37	CCDS8488.1																																																																																			C|0.997;A|0.003	0.003	strong		0.662	ADAMTS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385638.1	NM_139055	
PKP2	5318	hgsc.bcm.edu	37	12	33031023	33031023	+	Missense_Mutation	SNP	G	G	A	rs62001016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:33031023G>A	ENST00000070846.6	-	3	815	c.791C>T	c.(790-792)gCa>gTa	p.A264V	PKP2_ENST00000340811.4_Missense_Mutation_p.A264V	NM_004572.3	NP_004563.2	Q99959	PKP2_HUMAN	plakophilin 2	264					adherens junction maintenance (GO:0034334)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential (GO:0086001)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cell-cell signaling involved in cardiac conduction (GO:0086019)|desmosome assembly (GO:0002159)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|intermediate filament bundle assembly (GO:0045110)|lipid homeostasis (GO:0055088)|maintenance of organ identity (GO:0048496)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of tight junction assembly (GO:2000810)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	adherens junction (GO:0005912)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|protein kinase C binding (GO:0005080)|sodium channel regulator activity (GO:0017080)			NS(1)|breast(2)|endometrium(1)|kidney(9)|large_intestine(8)|lung(21)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	50	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					AGTGAGCCCTGCCGTCAGGTA	0.647													G|||	58	0.0115815	0.0408	0.0058	5008	,	,		18240	0.0		0.0	False		,,,				2504	0.0				p.A264V		Atlas-SNP	.											.	PKP2	110	.	0			c.C791T						PASS	.	G	VAL/ALA,VAL/ALA	137,4269	96.7+/-135.4	1,135,2067	52.0	48.0	49.0		791,791	3.8	0.0	12	dbSNP_129	49	0,8600		0,0,4300	yes	missense,missense	PKP2	NM_001005242.2,NM_004572.3	64,64	1,135,6367	AA,AG,GG		0.0,3.1094,1.0534	benign,benign	264/838,264/882	33031023	137,12869	2203	4300	6503	SO:0001583	missense	5318	exon3			AGCCCTGCCGTCA	X97675	CCDS8731.1, CCDS31771.1	12p11	2014-09-17				ENSG00000057294		"""Armadillo repeat containing"""	9024	protein-coding gene	gene with protein product		602861				8922383	Standard	NM_001005242		Approved		uc001rlj.4	Q99959	OTTHUMG00000169500	ENST00000070846.6:c.791C>T	12.37:g.33031023G>A	ENSP00000070846:p.Ala264Val	85.0	0.0	0		97.0	47.0	0.484536	NM_004572	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	Missense_Mutation	SNP	ENST00000070846.6	37	CCDS8731.1	24	0.01098901098901099	22	0.044715447154471545	2	0.0055248618784530384	0	0.0	0	0.0	G	1.719	-0.497156	0.04291	0.031094	0.0	ENSG00000057294	ENST00000340811;ENST00000070846;ENST00000537278	T;T	0.81163	-1.46;-1.39	4.73	3.84	0.44239	.	5.091870	0.00357	N	0.000025	T	0.42944	0.1225	N	0.22421	0.69	0.09310	N	1	B;B;B	0.19200	0.034;0.02;0.006	B;B;B	0.21708	0.036;0.016;0.01	T	0.49862	-0.8894	10	0.21540	T	0.41	-14.3867	10.8315	0.46663	0.0896:0.0:0.9104:0.0	.	264;264;264	Q99959-2;A0AV37;Q99959	.;.;PKP2_HUMAN	V	264	ENSP00000342800:A264V;ENSP00000070846:A264V	ENSP00000070846:A264V	A	-	2	0	PKP2	32922290	0.001000	0.12720	0.001000	0.08648	0.008000	0.06430	0.892000	0.28322	0.994000	0.38892	0.650000	0.86243	GCA	G|0.988;A|0.012	0.012	strong		0.647	PKP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404449.1	NM_004572	
SSPO	23145	hgsc.bcm.edu	37	7	149488991	149488991	+	RNA	SNP	T	T	C	rs893601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149488991T>C	ENST00000378016.2	+	0	5332							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GCAGTGCCACTCACCCCAGAA	0.662													C|||	202	0.0403355	0.1029	0.0144	5008	,	,		16534	0.004		0.003	False		,,,				2504	0.0501				p.S1778P		Atlas-SNP	.											.	.	.	.	0			c.T5332C						PASS	.	C		297,3797		12,273,1762	19.0	23.0	22.0		5336	4.8	0.1	7	dbSNP_86	22	18,8330		0,18,4156	yes	coding-notMod3	SSPO	NM_198455.2		12,291,5918	CC,CT,TT		0.2156,7.2545,2.5317			149488991	315,12127	2047	4174	6221			23145	exon35			TGCCACTCACCCC	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149488991T>C		95.0	0.0	0		83.0	40.0	0.481928	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				T|0.976;C|0.024	0.024	strong		0.662	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
ZNF286A	57335	hgsc.bcm.edu	37	17	15604508	15604508	+	Missense_Mutation	SNP	C	C	G	rs144115902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:15604508C>G	ENST00000464847.2	+	2	633	c.80C>G	c.(79-81)aCa>aGa	p.T27R	ZNF286A_ENST00000395893.2_Missense_Mutation_p.T27R|ZNF286A_ENST00000580259.1_Missense_Mutation_p.T27R|ZNF286A_ENST00000472486.1_Missense_Mutation_p.T17R|ZNF286A_ENST00000585194.1_Missense_Mutation_p.T27R|ZNF286A_ENST00000581529.1_Missense_Mutation_p.T17R|ZNF286A_ENST00000421016.1_Missense_Mutation_p.T27R|ZNF286A_ENST00000585171.1_3'UTR|ZNF286A_ENST00000583566.1_Missense_Mutation_p.T27R|ZNF286A_ENST00000413242.2_Missense_Mutation_p.T27R|ZNF286A_ENST00000593105.1_Missense_Mutation_p.T17R|ZNF286A_ENST00000395894.2_Missense_Mutation_p.T27R			Q9HBT8	Z286A_HUMAN	zinc finger protein 286A	27					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)|READ - Rectum adenocarcinoma(1115;0.0222)|BRCA - Breast invasive adenocarcinoma(8;0.0781)		GAGAAGAGCACAGAAGAGGGA	0.478													C|||	121	0.0241613	0.0855	0.0115	5008	,	,		21616	0.0		0.0	False		,,,				2504	0.0				p.T27R		Atlas-SNP	.											.	ZNF286A	58	.	0			c.C80G						PASS	.	C	ARG/THR,ARG/THR	334,4072		6,322,1875	220.0	201.0	207.0		80,80	4.3	0.8	17	dbSNP_134	207	4,8592		0,4,4294	no	missense,missense	ZNF286A	NM_001130842.1,NM_020652.2	71,71	6,326,6169	GG,GC,CC		0.0465,7.5806,2.5996	benign,benign	27/522,27/522	15604508	338,12664	2203	4298	6501	SO:0001583	missense	57335	exon3			AGAGCACAGAAGA	AF217226	CCDS11172.1, CCDS73997.1	17p11.2	2013-02-14	2007-01-05	2007-01-05		ENSG00000187607		"""Zinc fingers, C2H2-type"", ""-"""	13501	protein-coding gene	gene with protein product			"""zinc finger protein 286"""	ZNF286		11347906	Standard	NM_020652		Approved	KIAA1874	uc010cot.3	Q9HBT8	OTTHUMG00000166448	ENST00000464847.2:c.80C>G	17.37:g.15604508C>G	ENSP00000464218:p.Thr27Arg	263.0	0.0	0		222.0	110.0	0.495495	NM_020652	B4DKF9|Q96JF3	Missense_Mutation	SNP	ENST00000464847.2	37	CCDS11172.1	49	0.022435897435897436	41	0.08333333333333333	6	0.016574585635359115	0	0.0	2	0.002638522427440633	.	12.15	1.851494	0.32699	0.075806	4.65E-4	ENSG00000187607	ENST00000421016;ENST00000412988;ENST00000395894;ENST00000395893	T;T;T;T	0.07327	3.55;3.2;5.46;5.59	4.3	4.3	0.51218	.	1.408720	0.05359	N	0.533364	T	0.00384	0.0012	N	0.14661	0.345	0.26812	N	0.968979	B	0.19583	0.037	B	0.20955	0.032	T	0.25152	-1.0140	10	0.14252	T	0.57	-0.6478	12.9853	0.58588	0.0:1.0:0.0:0.0	.	27	Q9HBT8	Z286A_HUMAN	R	27;17;27;27	ENSP00000397163:T27R;ENSP00000408168:T17R;ENSP00000379231:T27R;ENSP00000379230:T27R	ENSP00000435872:T27R	T	+	2	0	ZNF286A	15545233	0.001000	0.12720	0.848000	0.33437	0.905000	0.53344	0.004000	0.13106	2.320000	0.78422	0.555000	0.69702	ACA	C|0.978;G|0.022	0.022	strong		0.478	ZNF286A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130696.4	NM_020652	
ITIH6	347365	hgsc.bcm.edu	37	X	54815065	54815065	+	Missense_Mutation	SNP	G	G	C	rs140757238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:54815065G>C	ENST00000218436.6	-	5	663	c.634C>G	c.(634-636)Cca>Gca	p.P212A	ITIH6_ENST00000498398.1_5'Flank	NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	212					hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										CTGGTGGATGGGGGTGAATCC	0.587													G|||	52	0.0137748	0.0371	0.0043	3775	,	,		11601	0.0		0.0	False		,,,				2504	0.0				p.P212A		Atlas-SNP	.											.	.	.	.	0			c.C634G						PASS	.	G	ALA/PRO	212,3623		3,177,29,1452,542	65.0	44.0	51.0		634	1.7	0.0	X	dbSNP_134	51	3,6725		0,1,2,2427,1870	yes	missense	ITIH5L	NM_198510.2	27	3,178,31,3879,2412	CC,CG,C,GG,G		0.0446,5.528,2.0354	possibly-damaging	212/1314	54815065	215,10348	2203	4300	6503	SO:0001583	missense	347365	exon5			TGGATGGGGGTGA	AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313			28907	protein-coding gene	gene with protein product			"""inter-alpha (globulin) inhibitor H5-like"""	ITIH5L		12975309	Standard	NM_198510		Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.634C>G	X.37:g.54815065G>C	ENSP00000218436:p.Pro212Ala	81.0	0.0	0		105.0	50.0	0.47619	NM_198510	A6NN03	Missense_Mutation	SNP	ENST00000218436.6	37	CCDS14361.1	24	0.014466546112115732	11	0.023404255319148935	0	0.0	0	0.0	0	0.0	G	1.845	-0.466354	0.04476	0.05528	4.46E-4	ENSG00000102313	ENST00000218436	T	0.02177	4.41	3.88	1.7	0.24286	.	0.424226	0.19726	U	0.107470	T	0.00271	0.0008	L	0.39898	1.24	0.42463	P	0.007206000000000046	B	0.14805	0.011	B	0.19148	0.024	T	0.37888	-0.9686	9	0.14656	T	0.56	.	6.3923	0.21593	0.1233:0.0:0.6815:0.1952	.	212	Q6UXX5	ITH5L_HUMAN	A	212	ENSP00000218436:P212A	ENSP00000218436:P212A	P	-	1	0	ITIH5L	54831790	1.000000	0.71417	0.042000	0.18584	0.218000	0.24690	1.253000	0.32886	0.488000	0.27723	0.171000	0.16805	CCA	G|0.976;C|0.024	0.024	strong		0.587	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510	
SNX20	124460	hgsc.bcm.edu	37	16	50709792	50709792	+	Silent	SNP	C	C	T	rs35435054	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:50709792C>T	ENST00000330943.4	-	3	342	c.171G>A	c.(169-171)acG>acA	p.T57T	SNX20_ENST00000423026.2_Silent_p.T57T|SNX20_ENST00000300590.3_Silent_p.T57T	NM_182854.2	NP_878274.1	Q7Z614	SNX20_HUMAN	sorting nexin 20	57					protein transport (GO:0015031)	endosome (GO:0005768)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)			kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|skin(2)|stomach(1)	15						GAAGCTCCCGCGTGGTCATGC	0.552													C|||	70	0.0139776	0.0499	0.0043	5008	,	,		21120	0.0		0.001	False		,,,				2504	0.0				p.T57T		Atlas-SNP	.											SNX20_ENST00000300590,NS,carcinoma,-1,2	SNX20	50	2	0			c.G171A						PASS	.	C	,,	220,4176	132.1+/-168.6	5,210,1983	103.0	92.0	96.0		171,171,171	-11.3	0.1	16	dbSNP_126	96	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	SNX20	NM_001144972.1,NM_153337.2,NM_182854.2	,,	5,211,6282	TT,TC,CC		0.0116,5.0045,1.7005	,,	57/103,57/130,57/317	50709792	221,12775	2198	4300	6498	SO:0001819	synonymous_variant	124460	exon3			CTCCCGCGTGGTC	AK055837	CCDS10745.1, CCDS10744.1, CCDS45481.1	16q12.1	2008-03-25	2008-03-25		ENSG00000167208	ENSG00000167208		"""Sorting nexins"""	30390	protein-coding gene	gene with protein product	"""selectin ligand interactor cytoplasmic 1"""	613281				18196517, 16782399	Standard	NM_182854		Approved	SLIC-1, SLIC1	uc002egk.2	Q7Z614	OTTHUMG00000133173	ENST00000330943.4:c.171G>A	16.37:g.50709792C>T		66.0	0.0	0		80.0	34.0	0.425	NM_001144972	A8K9D5|Q08E98|Q6P4H2|Q8IV59	Silent	SNP	ENST00000330943.4	37	CCDS10745.1																																																																																			C|0.981;T|0.019	0.019	strong		0.552	SNX20-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256879.2	NM_153337	
IGSF22	283284	hgsc.bcm.edu	37	11	18743529	18743529	+	Missense_Mutation	SNP	T	T	C	rs115954314	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:18743529T>C	ENST00000513874.1	-	3	308	c.169A>G	c.(169-171)Agc>Ggc	p.S57G	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	57										NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						ATGTTTGAGCTCCGGGTCACT	0.627											OREG0020822	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	34	0.00678914	0.025	0.0014	5008	,	,		17155	0.0		0.0	False		,,,				2504	0.0				p.S57G		Atlas-SNP	.											.	IGSF22	211	.	0			c.A169G						PASS	.	T	GLY/SER	74,3986		0,74,1956	74.0	81.0	79.0		169	3.0	0.0	11	dbSNP_132	79	1,8327		0,1,4163	yes	missense	IGSF22	NM_173588.3	56	0,75,6119	CC,CT,TT		0.012,1.8227,0.6054	possibly-damaging	57/1327	18743529	75,12313	2030	4164	6194	SO:0001583	missense	283284	exon3			TTGAGCTCCGGGT	AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.169A>G	11.37:g.18743529T>C	ENSP00000421191:p.Ser57Gly	50.0	0.0	0	90	71.0	30.0	0.422535	NM_173588	A6NNA0|D6RGV7	Missense_Mutation	SNP	ENST00000513874.1	37	CCDS41625.2	17	0.007783882783882784	17	0.034552845528455285	0	0.0	0	0.0	0	0.0	T	13.41	2.229888	0.39399	0.018227	1.2E-4	ENSG00000179057	ENST00000513874	T	0.53640	0.61	4.23	3.05	0.35203	.	0.206612	0.23787	U	0.044561	T	0.09423	0.0232	N	0.14661	0.345	0.09310	N	1	B	0.20261	0.043	B	0.17433	0.018	T	0.08700	-1.0709	10	0.28530	T	0.3	.	5.4317	0.16456	0.1745:0.0:0.1813:0.6442	.	57	D6RGV7	.	G	57	ENSP00000421191:S57G	ENSP00000322422:S57G	S	-	1	0	IGSF22	18700105	0.780000	0.28664	0.001000	0.08648	0.989000	0.77384	2.349000	0.44054	0.471000	0.27319	0.533000	0.62120	AGC	T|0.992;C|0.008	0.008	strong		0.627	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588	
LRSAM1	90678	hgsc.bcm.edu	37	9	130263362	130263362	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:130263362C>T	ENST00000323301.4	+	24	2590	c.1986C>T	c.(1984-1986)tcC>tcT	p.S662S	LRSAM1_ENST00000300417.6_Silent_p.S662S|LRSAM1_ENST00000483302.1_3'UTR|LRSAM1_ENST00000373322.1_Silent_p.S662S|LRSAM1_ENST00000373324.4_Silent_p.S635S	NM_138361.5	NP_612370.3	Q6UWE0	LRSM1_HUMAN	leucine rich repeat and sterile alpha motif containing 1	662					cell death (GO:0008219)|negative regulation of endocytosis (GO:0045806)|protein autoubiquitination (GO:0051865)|protein catabolic process (GO:0030163)|protein polyubiquitination (GO:0000209)|ubiquitin-dependent endocytosis (GO:0070086)|viral budding (GO:0046755)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(2)	16						TGAGGCCATCCGCTCCCCCTG	0.662																																					p.S662S		Atlas-SNP	.											.	LRSAM1	40	.	0			c.C1986T						PASS	.						57.0	55.0	56.0					9																	130263362		2203	4300	6503	SO:0001819	synonymous_variant	90678	exon25			GCCATCCGCTCCC	AK056203	CCDS6873.1, CCDS55347.1	9q34.13	2014-09-17			ENSG00000148356	ENSG00000148356		"""Sterile alpha motif (SAM) domain containing"""	25135	protein-coding gene	gene with protein product		610933				12975309	Standard	NM_001005373		Approved	FLJ31641	uc004brd.2	Q6UWE0	OTTHUMG00000020701	ENST00000323301.4:c.1986C>T	9.37:g.130263362C>T		63.0	0.0	0		68.0	20.0	0.294118	NM_001005373	Q5VVV0|Q8NB40|Q96GT5|Q96MX5|Q96MZ7	Silent	SNP	ENST00000323301.4	37	CCDS6873.1																																																																																			.	.	none		0.662	LRSAM1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054164.1	NM_138361	
ZBTB18	10472	hgsc.bcm.edu	37	1	244217662	244217662	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:244217662T>C	ENST00000358704.4	+	2	735	c.586T>C	c.(586-588)Ttg>Ctg	p.L196L		NM_001278196.1|NM_006352.4|NM_205768.2	NP_001265125.1|NP_006343.2|NP_991331.1	Q99592	ZBT18_HUMAN	zinc finger and BTB domain containing 18	187				KLNILPSKRDLAAEPGNMWMRLPSDSAGIPQAGGEAEPHAT AAGKTVASPCSSTESLSQRSVTSVRDSADVDCVLDLSVKSS LSGVENLNSSYFSSQ -> IEHPAQQKGLGGRAWEHVDAIA LRLSRHPPGWRRGRATRHSSWKNSSQPLQLNRVFVPE (in Ref. 1; AAA81368). {ECO:0000305}.	cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron development (GO:0048666)|regulation of cell division (GO:0051302)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GTGGATGCGATTGCCCTCAGA	0.567																																					p.L196L		Atlas-SNP	.											.	.	.	.	0			c.T586C						PASS	.						51.0	57.0	55.0					1																	244217662		2203	4300	6503	SO:0001819	synonymous_variant	10472	exon2			ATGCGATTGCCCT	U38896	CCDS1622.1	1q44	2013-09-19	2013-01-09	2013-01-09	ENSG00000179456	ENSG00000179456		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	13030	protein-coding gene	gene with protein product		608433	"""zinc finger protein 238"""	ZNF238		9568537, 9013868	Standard	NM_205768		Approved	C2H2-171, TAZ-1, RP58	uc031psv.1	Q99592	OTTHUMG00000040013	ENST00000358704.4:c.586T>C	1.37:g.244217662T>C		169.0	0.0	0		167.0	91.0	0.54491	NM_205768	A8K5U3|Q13397|Q5VU40|Q8N463|Q9UD99	Silent	SNP	ENST00000358704.4	37	CCDS1622.1																																																																																			.	.	none		0.567	ZBTB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096513.2	NM_205768	
EHMT1	79813	hgsc.bcm.edu	37	9	140671147	140671147	+	Silent	SNP	C	C	T	rs7868455	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140671147C>T	ENST00000460843.1	+	12	1896	c.1869C>T	c.(1867-1869)aaC>aaT	p.N623N	EHMT1_ENST00000371394.2_3'UTR|EHMT1_ENST00000334856.6_Silent_p.N592N|EHMT1_ENST00000462484.1_Silent_p.N623N	NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	623					chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|embryo development (GO:0009790)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|methyltransferase activity (GO:0008168)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		GAGTCAATAACGCCAGCTATT	0.527													C|||	315	0.0628994	0.2315	0.0115	5008	,	,		18209	0.0		0.001	False		,,,				2504	0.0				p.N623N		Atlas-SNP	.											.	EHMT1	196	.	0			c.C1869T						PASS	.	C	,	712,3694	297.3+/-284.7	63,586,1554	126.0	111.0	116.0		1869,1869	-6.8	0.8	9	dbSNP_116	116	11,8589	7.7+/-29.5	0,11,4289	no	coding-synonymous,coding-synonymous	EHMT1	NM_001145527.1,NM_024757.4	,	63,597,5843	TT,TC,CC		0.1279,16.1598,5.559	,	623/809,623/1299	140671147	723,12283	2203	4300	6503	SO:0001819	synonymous_variant	79813	exon12			CAATAACGCCAGC	AY083210	CCDS7050.1, CCDS7050.2, CCDS56595.1	9q34.3	2013-09-20			ENSG00000181090	ENSG00000181090	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"", ""Ankyrin repeat domain containing"""	24650	protein-coding gene	gene with protein product		607001	"""euchromatic histone methyltransferase 1"""			11347906, 12004135	Standard	NM_024757		Approved	Eu-HMTase1, FLJ12879, KIAA1876, bA188C12.1, KMT1D	uc011mfc.2	Q9H9B1	OTTHUMG00000020995	ENST00000460843.1:c.1869C>T	9.37:g.140671147C>T		122.0	0.0	0		126.0	126.0	1	NM_001145527	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Silent	SNP	ENST00000460843.1	37	CCDS7050.2																																																																																			C|0.939;T|0.061	0.061	strong		0.527	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757	
ITGA11	22801	hgsc.bcm.edu	37	15	68631920	68631920	+	Silent	SNP	C	C	T	rs9302249	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:68631920C>T	ENST00000315757.7	-	11	1280	c.1194G>A	c.(1192-1194)acG>acA	p.T398T	ITGA11_ENST00000423218.2_Silent_p.T398T	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	398					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						TCCCGGCACTCGTCTCCTTTA	0.582													C|||	302	0.0603035	0.2201	0.013	5008	,	,		17677	0.0		0.001	False		,,,				2504	0.001				p.T398T		Atlas-SNP	.											ITGA11,colon,carcinoma,-1,1	ITGA11	110	1	0			c.G1194A						PASS	.	C		666,3374		51,564,1405	69.0	75.0	73.0		1194	-3.1	0.2	15	dbSNP_119	73	4,8346		0,4,4171	no	coding-synonymous	ITGA11	NM_001004439.1		51,568,5576	TT,TC,CC		0.0479,16.4851,5.4076		398/1189	68631920	670,11720	2020	4175	6195	SO:0001819	synonymous_variant	22801	exon11			GGCACTCGTCTCC	AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"""Integrins"""	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.1194G>A	15.37:g.68631920C>T		56.0	0.0	0		78.0	32.0	0.410256	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Silent	SNP	ENST00000315757.7	37	CCDS45291.1																																																																																			C|0.956;T|0.044	0.044	strong		0.582	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211	
DOCK11	139818	hgsc.bcm.edu	37	X	117680019	117680019	+	Silent	SNP	G	G	C	rs61740837	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:117680019G>C	ENST00000276202.7	+	6	561	c.498G>C	c.(496-498)gtG>gtC	p.V166V	DOCK11_ENST00000276204.6_Silent_p.V166V	NM_144658.3	NP_653259.3	Q5JSL3	DOC11_HUMAN	dedicator of cytokinesis 11	166	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(4)|cervix(2)|endometrium(8)|kidney(5)|large_intestine(17)|liver(1)|lung(35)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(1)	84						AGGGTGGTGTGATAAAACAAG	0.338													G|||	33	0.00874172	0.0234	0.0014	3775	,	,		12505	0.0		0.001	False		,,,				2504	0.0				p.V166V		Atlas-SNP	.											.	DOCK11	185	.	0			c.G498C						PASS	.	G		75,3760		0,67,8,1565,563	143.0	120.0	128.0		498	2.2	1.0	X	dbSNP_129	128	0,6728		0,0,0,2428,1872	no	coding-synonymous	DOCK11	NM_144658.3		0,67,8,3993,2435	CC,CG,C,GG,G		0.0,1.9557,0.71		166/2074	117680019	75,10488	2203	4300	6503	SO:0001819	synonymous_variant	139818	exon6			TGGTGTGATAAAA	AK125641	CCDS35373.1	Xq24	2013-10-25			ENSG00000147251	ENSG00000147251		"""Pleckstrin homology (PH) domain containing"""	23483	protein-coding gene	gene with protein product	"""zizimin2"""	300681				12432077, 16968698	Standard	NM_144658		Approved	FLJ32122, FLJ43653, ZIZ2, ACG	uc004eqp.2	Q5JSL3	OTTHUMG00000022256	ENST00000276202.7:c.498G>C	X.37:g.117680019G>C		192.0	0.0	0		201.0	77.0	0.383085	NM_144658	A6NMF0|Q66M66|Q6ZUJ5|Q86VU8|Q96MN3	Silent	SNP	ENST00000276202.7	37	CCDS35373.1																																																																																			G|0.993;C|0.007	0.007	strong		0.338	DOCK11-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000356002.1	NM_144658	
COL28A1	340267	hgsc.bcm.edu	37	7	7410391	7410391	+	Missense_Mutation	SNP	A	A	C	rs76240858	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:7410391A>C	ENST00000399429.3	-	33	3171	c.3031T>G	c.(3031-3033)Tct>Gct	p.S1011A		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	1011					cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		TCTGGAGTAGATTCACTGAGT	0.373													A|||	17	0.00339457	0.0113	0.0	5008	,	,		16003	0.0		0.002	False		,,,				2504	0.0				p.S1011A		Atlas-SNP	.											.	COL28A1	113	.	0			c.T3031G						PASS	.	A	ALA/SER	37,3663		0,37,1813	127.0	116.0	120.0		3031	0.1	0.0	7	dbSNP_131	120	2,8168		0,2,4083	yes	missense	COL28A1	NM_001037763.2	99	0,39,5896	CC,CA,AA		0.0245,1.0,0.3286	possibly-damaging	1011/1126	7410391	39,11831	1850	4085	5935	SO:0001583	missense	340267	exon33			GAGTAGATTCACT	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"""Collagens"""	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.3031T>G	7.37:g.7410391A>C	ENSP00000382356:p.Ser1011Ala	84.0	0.0	0		97.0	32.0	0.329897	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Missense_Mutation	SNP	ENST00000399429.3	37	CCDS43553.1	9	0.004120879120879121	8	0.016260162601626018	0	0.0	0	0.0	1	0.0013192612137203166	A	10.22	1.291183	0.23564	0.01	2.45E-4	ENSG00000215018	ENST00000399429	D	0.88509	-2.39	3.85	0.134	0.14771	.	1.902650	0.03097	U	0.160580	T	0.69415	0.3108	L	0.27053	0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.60556	-0.7240	10	0.18710	T	0.47	0.0019	6.0507	0.19785	0.6632:0.0:0.3368:0.0	.	1011	Q2UY09	COSA1_HUMAN	A	1011	ENSP00000382356:S1011A	ENSP00000382356:S1011A	S	-	1	0	COL28A1	7376916	0.764000	0.28473	0.033000	0.17914	0.275000	0.26752	0.791000	0.26915	0.014000	0.14944	-0.290000	0.09829	TCT	A|0.997;C|0.003	0.003	strong		0.373	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763	
PLD3	23646	hgsc.bcm.edu	37	19	40882588	40882588	+	Silent	SNP	C	C	T	rs57187324	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40882588C>T	ENST00000409587.1	+	11	1489	c.1092C>T	c.(1090-1092)atC>atT	p.I364I	PLD3_ENST00000409735.4_Silent_p.I364I|PLD3_ENST00000356508.5_Silent_p.I364I|PLD3_ENST00000409281.1_Silent_p.I364I|PLD3_ENST00000409419.1_Silent_p.I364I			Q8IV08	PLD3_HUMAN	phospholipase D family, member 3	364					cell death (GO:0008219)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phospholipase D activity (GO:0004630)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	20			Lung(22;0.000636)|LUSC - Lung squamous cell carcinoma(20;0.00248)			GCCTGCTCATCAGCTGCTGGG	0.632													c|||	39	0.00778754	0.0295	0.0	5008	,	,		16027	0.0		0.0	False		,,,				2504	0.0				p.I364I		Atlas-SNP	.											.	PLD3	71	.	0			c.C1092T						PASS	.		,	124,4282	92.0+/-130.7	2,120,2081	79.0	72.0	74.0		1092,1092	3.2	1.0	19	dbSNP_129	74	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PLD3	NM_001031696.2,NM_012268.2	,	2,120,6381	TT,TC,CC		0.0,2.8143,0.9534	,	364/491,364/491	40882588	124,12882	2203	4300	6503	SO:0001819	synonymous_variant	23646	exon11			GCTCATCAGCTGC	BC000553	CCDS33027.1	19q13.2	2014-03-14	2005-05-20		ENSG00000105223	ENSG00000105223			17158	protein-coding gene	gene with protein product		615698	"""phospholipase D3"""			9140189, 15794758	Standard	XM_005258704		Approved	HU-K4	uc002onj.4	Q8IV08	OTTHUMG00000152736	ENST00000409587.1:c.1092C>T	19.37:g.40882588C>T		62.0	0.0	0		49.0	23.0	0.469388	NM_012268	Q92853|Q9BW87	Silent	SNP	ENST00000409587.1	37	CCDS33027.1																																																																																			C|0.990;T|0.010	0.010	strong		0.632	PLD3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327721.1	NM_012268	
ADCY9	115	hgsc.bcm.edu	37	16	4043415	4043415	+	Missense_Mutation	SNP	T	T	C	rs113187435	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4043415T>C	ENST00000294016.3	-	4	2519	c.1981A>G	c.(1981-1983)Agc>Ggc	p.S661G	ADCY9_ENST00000571889.1_5'UTR	NM_001116.3	NP_001107.2	O60503	ADCY9_HUMAN	adenylate cyclase 9	661					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						ACCTTGGTGCTGTTTTTATGC	0.532													T|||	37	0.00738818	0.0272	0.0014	5008	,	,		19275	0.0		0.0	False		,,,				2504	0.0				p.S661G		Atlas-SNP	.											.	ADCY9	151	.	0			c.A1981G						PASS	.	T	GLY/SER	111,4283	85.8+/-124.5	1,109,2087	235.0	202.0	213.0		1981	4.2	0.8	16	dbSNP_132	213	0,8600		0,0,4300	yes	missense	ADCY9	NM_001116.3	56	1,109,6387	CC,CT,TT		0.0,2.5262,0.8542	benign	661/1354	4043415	111,12883	2197	4300	6497	SO:0001583	missense	115	exon4			TGGTGCTGTTTTT	AF036927	CCDS32382.1	16p13.3	2013-02-04				ENSG00000162104	4.6.1.1	"""Adenylate cyclases"""	240	protein-coding gene	gene with protein product		603302				9628827	Standard	NM_001116		Approved	AC9	uc002cvx.3	O60503		ENST00000294016.3:c.1981A>G	16.37:g.4043415T>C	ENSP00000294016:p.Ser661Gly	269.0	0.0	0		245.0	116.0	0.473469	NM_001116	A7E2V5|A7E2X2|D3DUD1|O60273|Q4ZHT9|Q4ZIR5|Q9BWT4|Q9UGP2	Missense_Mutation	SNP	ENST00000294016.3	37	CCDS32382.1	9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	T	11.87	1.769081	0.31320	0.025262	0.0	ENSG00000162104	ENST00000294016	D	0.84070	-1.8	5.36	4.24	0.50183	.	0.368925	0.31884	N	0.006919	T	0.43366	0.1244	N	0.14661	0.345	0.31169	N	0.703441	B	0.02656	0.0	B	0.01281	0.0	T	0.54977	-0.8212	10	0.28530	T	0.3	.	8.1862	0.31341	0.0:0.1581:0.0:0.8419	.	661	O60503	ADCY9_HUMAN	G	661	ENSP00000294016:S661G	ENSP00000294016:S661G	S	-	1	0	ADCY9	3983416	1.000000	0.71417	0.842000	0.33263	0.993000	0.82548	1.848000	0.39309	0.845000	0.35118	0.445000	0.29226	AGC	T|0.991;C|0.009	0.009	strong		0.532	ADCY9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438076.1		
DNAH9	1770	hgsc.bcm.edu	37	17	11622729	11622729	+	Silent	SNP	C	C	T	rs61739488	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:11622729C>T	ENST00000262442.4	+	27	5699	c.5631C>T	c.(5629-5631)acC>acT	p.T1877T	DNAH9_ENST00000454412.2_Silent_p.T1877T	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	1877	AAA 1. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		CAGGCAAGACCGAGACCACCA	0.607													c|||	256	0.0511182	0.1861	0.0115	5008	,	,		16870	0.0		0.001	False		,,,				2504	0.001				p.T1877T		Atlas-SNP	.											.	DNAH9	695	.	0			c.C5631T						PASS	.	G		706,3700	294.1+/-283.0	52,602,1549	92.0	79.0	83.0		5631	-10.4	0.0	17	dbSNP_129	83	7,8593	4.3+/-15.6	0,7,4293	no	coding-synonymous	DNAH9	NM_001372.3		52,609,5842	TT,TC,CC		0.0814,16.0236,5.4821		1877/4487	11622729	713,12293	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon27			CAAGACCGAGACC	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.5631C>T	17.37:g.11622729C>T		114.0	0.0	0		106.0	47.0	0.443396	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			C|0.950;T|0.050	0.050	strong		0.607	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
LUZP1	7798	hgsc.bcm.edu	37	1	23415518	23415518	+	Missense_Mutation	SNP	C	C	T	rs12066671	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:23415518C>T	ENST00000302291.4	-	5	3902	c.3101G>A	c.(3100-3102)aGt>aAt	p.S1034N	LUZP1_ENST00000418342.1_Missense_Mutation_p.S1034N|LUZP1_ENST00000374623.3_Missense_Mutation_p.S1034N|RP1-184J9.2_ENST00000427154.1_RNA			Q86V48	LUZP1_HUMAN	leucine zipper protein 1	1034			S -> N (in dbSNP:rs12066671).		artery development (GO:0060840)|neural fold bending (GO:0021503)|ventricular septum development (GO:0003281)	membrane (GO:0016020)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(2)	31		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Ovarian(437;0.00373)|Breast(348;0.00815)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;4.88e-27)|Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;4.31e-06)|GBM - Glioblastoma multiforme(114;8.64e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00176)|STAD - Stomach adenocarcinoma(196;0.0146)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0967)|LUSC - Lung squamous cell carcinoma(448;0.199)		CCTGTAGACACTGAGTGTACA	0.552													C|||	381	0.0760783	0.2693	0.0331	5008	,	,		19540	0.0		0.002	False		,,,				2504	0.0				p.S1034N		Atlas-SNP	.											.	LUZP1	83	.	0			c.G3101A						PASS	.	C	ASN/SER,ASN/SER	921,3485	353.1+/-312.0	102,717,1384	117.0	109.0	112.0		3101,3101	2.3	0.0	1	dbSNP_120	112	8,8592	6.4+/-24.3	0,8,4292	yes	missense,missense	LUZP1	NM_001142546.1,NM_033631.3	46,46	102,725,5676	TT,TC,CC		0.093,20.9033,7.1429	benign,benign	1034/1077,1034/1077	23415518	929,12077	2203	4300	6503	SO:0001583	missense	7798	exon5			TAGACACTGAGTG	BC051733	CCDS30628.1	1p36	2008-02-05			ENSG00000169641	ENSG00000169641			14985	protein-coding gene	gene with protein product		601422				8812416	Standard	NM_033631		Approved	LUZP	uc010odv.1	Q86V48	OTTHUMG00000003227	ENST00000302291.4:c.3101G>A	1.37:g.23415518C>T	ENSP00000303758:p.Ser1034Asn	273.0	0.0	0		328.0	166.0	0.506098	NM_033631	Q5TH93|Q8N4X3|Q8TEH1	Missense_Mutation	SNP	ENST00000302291.4	37	CCDS30628.1	125	0.05723443223443223	115	0.23373983739837398	10	0.027624309392265192	0	0.0	0	0.0	C	7.770	0.707239	0.15239	0.209033	9.3E-4	ENSG00000169641	ENST00000418342;ENST00000374623;ENST00000302291	T;T;T	0.13420	2.59;2.59;2.59	5.53	2.34	0.29019	.	0.527164	0.17464	N	0.173327	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.30281	0.275	B	0.27076	0.076	T	0.44697	-0.9311	9	0.39692	T	0.17	.	9.0334	0.36273	0.1575:0.5558:0.2867:0.0	rs12066671;rs52805088;rs12066671	1034	Q86V48	LUZP1_HUMAN	N	1034	ENSP00000393460:S1034N;ENSP00000363752:S1034N;ENSP00000303758:S1034N	ENSP00000303758:S1034N	S	-	2	0	LUZP1	23288105	0.000000	0.05858	0.008000	0.14137	0.279000	0.26890	0.390000	0.20768	0.750000	0.32877	0.655000	0.94253	AGT	C|0.925;T|0.075	0.075	strong		0.552	LUZP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008900.3	NM_033631	
PRODH2	58510	hgsc.bcm.edu	37	19	36302897	36302897	+	Silent	SNP	G	G	A	rs145376615	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36302897G>A	ENST00000301175.3	-	5	809	c.792C>T	c.(790-792)ccC>ccT	p.P264P		NM_021232.1	NP_067055.1	Q9UF12	PROD2_HUMAN	proline dehydrogenase (oxidase) 2	264					proline catabolic process to glutamate (GO:0010133)	mitochondrial inner membrane (GO:0005743)	proline dehydrogenase activity (GO:0004657)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CCAGCCTCTCGGGGCTCAGCT	0.637													G|||	30	0.00599042	0.0212	0.0029	5008	,	,		18798	0.0		0.0	False		,,,				2504	0.0				p.P264P		Atlas-SNP	.											.	PRODH2	68	.	0			c.C792T						PASS	.	G		87,4319	72.5+/-110.5	0,87,2116	51.0	47.0	48.0		792	-9.5	0.2	19	dbSNP_134	48	0,8600		0,0,4300	no	coding-synonymous	PRODH2	NM_021232.1		0,87,6416	AA,AG,GG		0.0,1.9746,0.6689		264/537	36302897	87,12919	2203	4300	6503	SO:0001819	synonymous_variant	58510	exon5			CCTCTCGGGGCTC	U80018	CCDS12478.1	19q13.1	2014-07-11				ENSG00000250799			17325	protein-coding gene	gene with protein product							Standard	NM_021232		Approved	HSPOX1	uc002obx.1	Q9UF12		ENST00000301175.3:c.792C>T	19.37:g.36302897G>A		97.0	0.0	0		97.0	51.0	0.525773	NM_021232		Silent	SNP	ENST00000301175.3	37	CCDS12478.1																																																																																			A|0.006;G|0.994;T|0.000	0.006	strong		0.637	PRODH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452552.2	NM_021232	
MYL9	10398	hgsc.bcm.edu	37	20	35176541	35176541	+	Silent	SNP	G	G	A	rs11553089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:35176541G>A	ENST00000279022.2	+	3	395	c.291G>A	c.(289-291)acG>acA	p.T97T	MYL9_ENST00000346786.2_Intron|RP5-977B1.7_ENST00000439595.1_RNA|RP5-977B1.7_ENST00000425233.1_RNA|RP5-977B1.11_ENST00000561134.1_RNA	NM_006097.4	NP_006088.2	P24844	MYL9_HUMAN	myosin, light chain 9, regulatory	97					axon guidance (GO:0007411)|muscle contraction (GO:0006936)|platelet aggregation (GO:0070527)|regulation of muscle contraction (GO:0006937)	cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|stress fiber (GO:0001725)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|structural constituent of muscle (GO:0008307)			endometrium(2)|kidney(1)|large_intestine(3)|lung(2)	8	Breast(12;0.0192)	Myeloproliferative disorder(115;0.00878)				TGAACGGCACGGACCCCGAGG	0.607													G|||	112	0.0223642	0.0787	0.0101	5008	,	,		17578	0.0		0.0	False		,,,				2504	0.001				p.T97T		Atlas-SNP	.											.	MYL9	13	.	0			c.G291A						PASS	.	G	,	262,4144	151.0+/-185.0	10,242,1951	114.0	78.0	91.0		291,	-9.7	0.1	20	dbSNP_120	91	1,8599		0,1,4299	no	coding-synonymous,intron	MYL9	NM_006097.3,NM_181526.1	,	10,243,6250	AA,AG,GG		0.0116,5.9464,2.0221	,	97/173,	35176541	263,12743	2203	4300	6503	SO:0001819	synonymous_variant	10398	exon3			CGGCACGGACCCC	J02854	CCDS13276.1, CCDS13277.1	20q11.23	2013-01-10	2006-09-29		ENSG00000101335	ENSG00000101335		"""Myosins / Light chain"", ""EF-hand domain containing"""	15754	protein-coding gene	gene with protein product	"""myosin regulatory light chain 2, smooth muscle isoform"", ""myosin regulatory light chain 1"""	609905	"""myosin, light polypeptide 9, regulatory"""			2526655	Standard	NM_006097		Approved	MYRL2, MLC2, LC20, MRLC1	uc002xfl.2	P24844	OTTHUMG00000032387	ENST00000279022.2:c.291G>A	20.37:g.35176541G>A		117.0	0.0	0		101.0	60.0	0.594059	NM_006097	E1P5T6|Q9BQL9|Q9BUF9|Q9H136	Silent	SNP	ENST00000279022.2	37	CCDS13276.1																																																																																			G|0.975;A|0.025	0.025	strong		0.607	MYL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079015.2	NM_006097	
OR2T27	403239	hgsc.bcm.edu	37	1	248813352	248813352	+	Silent	SNP	G	G	A	rs147773385	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248813352G>A	ENST00000344889.3	-	1	833	c.834C>T	c.(832-834)taC>taT	p.Y278Y		NM_001001824.1	NP_001001824.1	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T, member 27	278						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.Y278*(1)		breast(2)|endometrium(2)|large_intestine(4)|lung(20)|skin(3)|stomach(1)	32	all_cancers(71;1.15e-05)|all_epithelial(71;5.29e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.089)|Lung NSC(105;0.0969)|Melanoma(84;0.199)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TAAGGATGGTGTAGAAGGCAG	0.522													G|||	106	0.0211661	0.0772	0.0058	5008	,	,		16990	0.0		0.0	False		,,,				2504	0.0				p.Y278Y		Atlas-SNP	.											OR2T27,colon,carcinoma,0,1	OR2T27	52	1	1	Substitution - Nonsense(1)	large_intestine(1)	c.C834T						scavenged	.	G		158,4196		8,142,2027	78.0	73.0	74.0		834	0.4	1.0	1	dbSNP_134	74	0,8548		0,0,4274	no	coding-synonymous	OR2T27	NM_001001824.1		8,142,6301	AA,AG,GG		0.0,3.6288,1.2246		278/318	248813352	158,12744	2177	4274	6451	SO:0001819	synonymous_variant	403239	exon1			GATGGTGTAGAAG		CCDS31124.1	1q44	2012-08-09			ENSG00000187701	ENSG00000187701		"""GPCR / Class A : Olfactory receptors"""	31252	protein-coding gene	gene with protein product							Standard	NM_001001824		Approved		uc010pzo.2	Q8NH04	OTTHUMG00000040376	ENST00000344889.3:c.834C>T	1.37:g.248813352G>A		246.0	0.0	0		166.0	26.0	0.156627	NM_001001824		Silent	SNP	ENST00000344889.3	37	CCDS31124.1																																																																																			G|0.986;A|0.014	0.014	strong		0.522	OR2T27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097124.1	NM_001001824	
LRTM1	57408	hgsc.bcm.edu	37	3	54958884	54958884	+	Silent	SNP	A	A	G	rs35757787	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:54958884A>G	ENST00000273286.5	-	2	528	c.366T>C	c.(364-366)ccT>ccC	p.P122P	CACNA2D3_ENST00000490478.1_Intron|CACNA2D3_ENST00000474759.1_Intron|LRTM1_ENST00000493075.1_Silent_p.P46P|CACNA2D3_ENST00000415676.2_Intron|CACNA2D3_ENST00000288197.5_Intron	NM_020678.2	NP_065729.1	Q9HBL6	LRTM1_HUMAN	leucine-rich repeats and transmembrane domains 1	122						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(7)|lung(6)|prostate(1)|skin(4)	21				KIRC - Kidney renal clear cell carcinoma(284;0.00975)|Kidney(284;0.0112)|OV - Ovarian serous cystadenocarcinoma(275;0.0502)		CCCTCAGCTGAGGGAGGGAAT	0.478													A|||	154	0.0307508	0.1127	0.0058	5008	,	,		20302	0.0		0.001	False		,,,				2504	0.0				p.P122P		Atlas-SNP	.											.	LRTM1	52	.	0			c.T366C						PASS	.	A	,	420,3986	205.8+/-227.6	14,392,1797	76.0	75.0	75.0		,366	-11.5	0.0	3	dbSNP_126	75	2,8598	2.2+/-6.3	0,2,4298	no	intron,coding-synonymous	CACNA2D3,LRTM1	NM_018398.2,NM_020678.2	,	14,394,6095	GG,GA,AA		0.0233,9.5325,3.2447	,	,122/346	54958884	422,12584	2203	4300	6503	SO:0001819	synonymous_variant	57408	exon2			CAGCTGAGGGAGG	AF225421	CCDS2876.1	3p14.3	2006-01-02			ENSG00000144771	ENSG00000144771			25023	protein-coding gene	gene with protein product						12477932	Standard	NM_020678		Approved	HT017	uc003dhl.3	Q9HBL6	OTTHUMG00000158578	ENST00000273286.5:c.366T>C	3.37:g.54958884A>G		122.0	0.0	0		124.0	67.0	0.540323	NM_020678	Q8IUU2	Silent	SNP	ENST00000273286.5	37	CCDS2876.1																																																																																			A|0.971;G|0.029	0.029	strong		0.478	LRTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351399.1	NM_020678	
CAMK4	814	hgsc.bcm.edu	37	5	110820116	110820116	+	Silent	SNP	T	T	G	rs6886469	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:110820116T>G	ENST00000282356.4	+	11	1772	c.1374T>G	c.(1372-1374)gcT>gcG	p.A458A	CAMK4_ENST00000512890.1_3'UTR|CAMK4_ENST00000512453.1_Silent_p.A458A	NM_001744.4	NP_001735.1	Q16566	KCC4_HUMAN	calcium/calmodulin-dependent protein kinase IV	458					activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|long-term memory (GO:0007616)|myeloid dendritic cell differentiation (GO:0043011)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleocytoplasmic transport (GO:0006913)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of osteoclast differentiation (GO:0045670)|regulation of T cell differentiation in thymus (GO:0033081)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(3)|prostate(2)|skin(1)|urinary_tract(1)	30		all_cancers(142;1.49e-05)|all_epithelial(76;1.82e-07)|Prostate(80;0.00964)|all_lung(232;0.0181)|Lung NSC(167;0.0298)|Ovarian(225;0.0446)|Colorectal(57;0.0478)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;3.79e-08)|Epithelial(69;5.29e-08)|all cancers(49;1.1e-05)|COAD - Colon adenocarcinoma(37;0.109)		GAAGCTCTGCTGTGGGTTTTG	0.512													T|||	46	0.0091853	0.034	0.0014	5008	,	,		19121	0.0		0.0	False		,,,				2504	0.0				p.A458A		Atlas-SNP	.											.	CAMK4	77	.	0			c.T1374G						PASS	.	T		114,4290	87.3+/-125.9	3,108,2091	47.0	47.0	47.0		1374	-3.5	0.0	5	dbSNP_116	47	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	CAMK4	NM_001744.4		3,110,6389	GG,GT,TT		0.0233,2.5886,0.892		458/474	110820116	116,12888	2202	4300	6502	SO:0001819	synonymous_variant	814	exon11			CTCTGCTGTGGGT	D30742	CCDS4103.1	5q22.1	2012-09-20			ENSG00000152495	ENSG00000152495	2.7.11.17		1464	protein-coding gene	gene with protein product	"""brain Ca++-calmodulin-dependent protein kinase type IV"", ""calcium/calmodulin-dependent protein kinase type IV catalytic chain"", ""CAM kinase IV"", ""CAM kinase- GR"""	114080				2536634	Standard	NM_001744		Approved	CaMK-GR	uc003kpf.3	Q16566	OTTHUMG00000128792	ENST00000282356.4:c.1374T>G	5.37:g.110820116T>G		78.0	0.0	0		69.0	40.0	0.57971	NM_001744	D3DSZ7	Silent	SNP	ENST00000282356.4	37	CCDS4103.1																																																																																			T|0.991;G|0.009	0.009	strong		0.512	CAMK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250719.2	NM_001744	
TSSK3	81629	hgsc.bcm.edu	37	1	32829261	32829261	+	Missense_Mutation	SNP	A	A	G	rs35508255	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:32829261A>G	ENST00000373534.3	+	2	716	c.211A>G	c.(211-213)Atc>Gtc	p.I71V	FAM229A_ENST00000415596.1_Intron|FAM229A_ENST00000432622.1_5'Flank	NM_052841.3	NP_443073.1	Q96PN8	TSSK3_HUMAN	testis-specific serine kinase 3	71	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		I -> V (in dbSNP:rs35508255).		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein phosphorylation (GO:0006468)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|large_intestine(6)|lung(5)|skin(2)|stomach(1)	15		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.17)|Breast(348;0.212)				CAAGAACATCATCCAGGTGTA	0.562													A|||	81	0.0161741	0.0582	0.0058	5008	,	,		19728	0.0		0.0	False		,,,				2504	0.0				p.I71V		Atlas-SNP	.											.	TSSK3	22	.	0			c.A211G						PASS	.	A	VAL/ILE	208,4198	128.2+/-165.1	5,198,2000	79.0	84.0	82.0		211	1.9	1.0	1	dbSNP_126	82	3,8597	3.0+/-9.4	0,3,4297	yes	missense	TSSK3	NM_052841.3	29	5,201,6297	GG,GA,AA		0.0349,4.7208,1.6223	benign	71/269	32829261	211,12795	2203	4300	6503	SO:0001583	missense	81629	exon2			AACATCATCCAGG	AF296450	CCDS362.1	1p35-p34	2008-02-05	2005-03-10	2005-03-12	ENSG00000162526	ENSG00000162526			15473	protein-coding gene	gene with protein product		607660	"""serine/threonine kinase 22C (spermiogenesis associated)"""	STK22C		11597141	Standard	NM_052841		Approved	SPOGA3	uc001bvf.3	Q96PN8	OTTHUMG00000007585	ENST00000373534.3:c.211A>G	1.37:g.32829261A>G	ENSP00000362634:p.Ile71Val	120.0	0.0	0		147.0	82.0	0.557823	NM_052841	Q5TEE5	Missense_Mutation	SNP	ENST00000373534.3	37	CCDS362.1	39	0.017857142857142856	36	0.07317073170731707	3	0.008287292817679558	0	0.0	0	0.0	A	9.836	1.189629	0.21954	0.047208	3.49E-4	ENSG00000162526	ENST00000373534	T	0.15372	2.43	5.42	1.88	0.25563	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.086426	0.49916	N	0.000121	T	0.00496	0.0016	N	0.02379	-0.575	0.80722	D	1	P	0.45715	0.865	P	0.45232	0.474	T	0.45512	-0.9256	10	0.13470	T	0.59	.	8.5454	0.33417	0.7713:0.0:0.2287:0.0	rs35508255;rs61742632	71	Q96PN8	TSSK3_HUMAN	V	71	ENSP00000362634:I71V	ENSP00000362634:I71V	I	+	1	0	TSSK3	32601848	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	1.475000	0.35409	0.456000	0.26937	-0.274000	0.10170	ATC	A|0.981;G|0.019	0.019	strong		0.562	TSSK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020049.1		
ERBB2	2064	hgsc.bcm.edu	37	17	37872035	37872035	+	Missense_Mutation	SNP	G	G	T	rs4252633	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:37872035G>T	ENST00000269571.5	+	12	1515	c.1356G>T	c.(1354-1356)tgG>tgT	p.W452C	ERBB2_ENST00000406381.2_Missense_Mutation_p.W422C|ERBB2_ENST00000541774.1_Missense_Mutation_p.W437C|ERBB2_ENST00000445658.2_Missense_Mutation_p.W176C|ERBB2_ENST00000540042.1_Missense_Mutation_p.W422C|ERBB2_ENST00000584450.1_Missense_Mutation_p.W452C|ERBB2_ENST00000578199.1_Missense_Mutation_p.W422C|ERBB2_ENST00000584601.1_Missense_Mutation_p.W422C|ERBB2_ENST00000540147.1_Missense_Mutation_p.W422C			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	452			W -> C (in dbSNP:rs4252633). {ECO:0000269|Ref.3}.		axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	GCATCAGCTGGCTGGGGCTGC	0.627		1	"""A, Mis, O"""		"""breast, ovarian, other tumour types, NSCLC, gastric"""					TCGA GBM(5;<1E-08)			G|||	90	0.0179712	0.0673	0.0014	5008	,	,		19038	0.0		0.0	False		,,,				2504	0.0				p.W452C		Atlas-SNP	.		Dom	yes		17	17q21.1	2064	"""v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"""		E	.	ERBB2	429	.	0			c.G1356T						PASS	.	G	CYS/TRP,CYS/TRP	210,4196	129.0+/-165.8	6,198,1999	98.0	81.0	86.0		1266,1356	2.8	1.0	17	dbSNP_111	86	0,8600		0,0,4300	yes	missense,missense	ERBB2	NM_001005862.1,NM_004448.2	215,215	6,198,6299	TT,TG,GG		0.0,4.7662,1.6146	possibly-damaging,possibly-damaging	422/1226,452/1256	37872035	210,12796	2203	4300	6503	SO:0001583	missense	2064	exon12			CAGCTGGCTGGGG	X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"""CD molecules"""	3430	protein-coding gene	gene with protein product	"""neuro/glioblastoma derived oncogene homolog"""	164870	"""v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"""	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.1356G>T	17.37:g.37872035G>T	ENSP00000269571:p.Trp452Cys	42.0	0.0	0		66.0	32.0	0.484848	NM_004448	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	37	CCDS32642.1	39	0.017857142857142856	38	0.07723577235772358	1	0.0027624309392265192	0	0.0	0	0.0	G	8.363	0.833490	0.16820	0.047662	0.0	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147;ENST00000540042	T;T;T;T;T;T	0.79247	-1.25;-1.25;-1.25;-1.25;-1.25;-1.25	5.93	2.79	0.32731	EGF receptor, L domain (1);	.	.	.	.	T	0.16685	0.0401	L	0.34521	1.04	0.35496	D	0.799411	P;D;D;P	0.57257	0.951;0.979;0.965;0.903	P;P;P;P	0.62885	0.88;0.874;0.762;0.908	T	0.62680	-0.6803	9	0.72032	D	0.01	.	3.232	0.06751	0.1435:0.2503:0.4775:0.1287	rs4252633	176;422;437;452	B4DTR1;F5H1T4;P04626-4;P04626	.;.;.;ERBB2_HUMAN	C	422;437;176;452;422;422	ENSP00000385185:W422C;ENSP00000446466:W437C;ENSP00000404047:W176C;ENSP00000269571:W452C;ENSP00000443562:W422C;ENSP00000446382:W422C	ENSP00000269571:W452C	W	+	3	0	ERBB2	35125561	0.528000	0.26314	0.995000	0.50966	0.899000	0.52679	-0.034000	0.12225	0.381000	0.24851	-0.305000	0.09177	TGG	G|0.979;T|0.021	0.021	strong		0.627	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2		
ACIN1	22985	hgsc.bcm.edu	37	14	23549948	23549948	+	Missense_Mutation	SNP	C	C	T	rs11555803	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:23549948C>T	ENST00000262710.1	-	6	1097	c.770G>A	c.(769-771)aGa>aAa	p.R257K	ACIN1_ENST00000605057.1_Missense_Mutation_p.R199K|ACIN1_ENST00000457657.1_Missense_Mutation_p.R217K|ACIN1_ENST00000555053.1_Missense_Mutation_p.R257K|ACIN1_ENST00000555352.1_5'Flank	NM_001164814.1|NM_014977.3	NP_001158286.1|NP_055792	Q9UKV3	ACINU_HUMAN	apoptotic chromatin condensation inducer 1	257	Glu-rich.		R -> K (in dbSNP:rs11555803).		apoptotic chromosome condensation (GO:0030263)|apoptotic process (GO:0006915)|ATP catabolic process (GO:0006200)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|erythrocyte differentiation (GO:0030218)|mRNA processing (GO:0006397)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|positive regulation of apoptotic process (GO:0043065)|positive regulation of monocyte differentiation (GO:0045657)|RNA splicing (GO:0008380)	ASAP complex (GO:0061574)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATPase activity (GO:0016887)|enzyme binding (GO:0019899)|nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|kidney(4)|large_intestine(9)|lung(10)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	37	all_cancers(95;1.36e-05)			GBM - Glioblastoma multiforme(265;0.00816)		CCTTAGGTTTCTGGAAGGTGT	0.473													C|||	114	0.0227636	0.0825	0.0072	5008	,	,		20266	0.0		0.0	False		,,,				2504	0.0				p.R257K		Atlas-SNP	.											.	ACIN1	147	.	0			c.G770A						PASS	.	C	LYS/ARG,LYS/ARG,LYS/ARG	356,4050	183.6+/-211.2	16,324,1863	175.0	179.0	178.0		770,650,770	5.5	1.0	14	dbSNP_120	178	8,8592	6.4+/-24.3	0,8,4292	yes	missense,missense,missense	ACIN1	NM_001164814.1,NM_001164815.1,NM_014977.3	26,26,26	16,332,6155	TT,TC,CC		0.093,8.0799,2.7987	probably-damaging,probably-damaging,probably-damaging	257/1329,217/1302,257/1342	23549948	364,12642	2203	4300	6503	SO:0001583	missense	22985	exon6			AGGTTTCTGGAAG	AB014570	CCDS9587.1, CCDS53887.1, CCDS53888.1, CCDS53889.1, CCDS55905.1	14q11.2	2008-11-25	2004-03-31	2004-04-01	ENSG00000100813	ENSG00000100813			17066	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 152"""	604562	"""apoptotic chromatin condensation inducer in the nucleus"""	ACINUS		9734811, 10490026	Standard	NM_014977		Approved	KIAA0670, fSAP152	uc001wit.4	Q9UKV3	OTTHUMG00000028716	ENST00000262710.1:c.770G>A	14.37:g.23549948C>T	ENSP00000262710:p.Arg257Lys	102.0	0.0	0		92.0	48.0	0.521739	NM_001164814	B2RTT4|D3DS45|O75158|Q9UG91|Q9UKV1|Q9UKV2	Missense_Mutation	SNP	ENST00000262710.1	37	CCDS9587.1	39	0.017857142857142856	38	0.07723577235772358	1	0.0027624309392265192	0	0.0	0	0.0	C	22.9	4.351242	0.82132	0.080799	9.3E-4	ENSG00000100813	ENST00000262710;ENST00000457657;ENST00000555053	T;T;T	0.27890	2.05;1.64;2.04	5.47	5.47	0.80525	.	0.000000	0.43260	D	0.000591	T	0.03178	0.0093	L	0.43152	1.355	0.38624	D	0.951213	D;P	0.53312	0.959;0.932	D;P	0.65684	0.937;0.867	T	0.01039	-1.1472	10	0.17832	T	0.49	-10.3899	14.8326	0.70159	0.0:1.0:0.0:0.0	rs11555803;rs52803485;rs11555803	257;257	G3V3M7;Q9UKV3	.;ACINU_HUMAN	K	257;217;257	ENSP00000262710:R257K;ENSP00000405677:R217K;ENSP00000451328:R257K	ENSP00000262710:R257K	R	-	2	0	ACIN1	22619788	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	3.549000	0.53681	2.569000	0.86673	0.650000	0.86243	AGA	C|0.971;T|0.029	0.029	strong		0.473	ACIN1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071707.3	NM_014977	
SYCE1L	100130958	hgsc.bcm.edu	37	16	77246093	77246093	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:77246093G>A	ENST00000378644.4	+	8	545	c.490G>A	c.(490-492)Gag>Aag	p.E164K	RP11-538I12.2_ENST00000569032.1_RNA	NM_001129979.1	NP_001123451.1	A8MT33	SYC1L_HUMAN	synaptonemal complex central element protein 1-like	164					synaptonemal complex assembly (GO:0007130)	synaptonemal complex (GO:0000795)				breast(1)|prostate(1)	2						GCTGCTCTCGGAGAGTGAGCC	0.721																																					p.E164K		Atlas-SNP	.											.	SYCE1L	10	.	0			c.G490A						PASS	.						8.0	11.0	10.0					16																	77246093		690	1581	2271	SO:0001583	missense	100130958	exon8			CTCTCGGAGAGTG		CCDS45533.1	16q23.1	2009-10-06			ENSG00000205078	ENSG00000205078			37236	protein-coding gene	gene with protein product	"""meiosis-related protein"""					16328886	Standard	NM_001129979		Approved	MRP2	uc010vnh.1	A8MT33		ENST00000378644.4:c.490G>A	16.37:g.77246093G>A	ENSP00000367911:p.Glu164Lys	73.0	0.0	0		123.0	67.0	0.544715	NM_001129979	A6NF23	Missense_Mutation	SNP	ENST00000378644.4	37	CCDS45533.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.999402	0.74818	.	.	ENSG00000205078	ENST00000378644	T	0.38560	1.13	3.47	1.38	0.22167	.	0.000000	0.41396	U	0.000894	T	0.58004	0.2092	M	0.72118	2.19	0.20975	N	0.999814	D	0.76494	0.999	D	0.80764	0.994	T	0.48747	-0.9008	10	0.72032	D	0.01	.	9.4908	0.38958	0.0:0.4243:0.5757:0.0	.	164	A8MT33	SYC1L_HUMAN	K	164	ENSP00000367911:E164K	ENSP00000367911:E164K	E	+	1	0	SYCE1L	75803594	0.957000	0.32711	0.327000	0.25402	0.186000	0.23388	1.540000	0.36115	0.416000	0.25844	0.471000	0.43371	GAG	.	.	none		0.721	SYCE1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433889.1	NM_001129979	
UGT3A2	167127	hgsc.bcm.edu	37	5	36049324	36049324	+	Silent	SNP	G	G	A	rs148290056	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:36049324G>A	ENST00000282507.3	-	4	611	c.510C>T	c.(508-510)ttC>ttT	p.F170F	UGT3A2_ENST00000545528.1_Intron|UGT3A2_ENST00000504954.1_Intron|UGT3A2_ENST00000513300.1_Silent_p.F136F	NM_174914.3	NP_777574.2	Q3SY77	UD3A2_HUMAN	UDP glycosyltransferase 3 family, polypeptide A2	170					cellular response to genistein (GO:0071412)	integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)|UDP-glycosyltransferase activity (GO:0008194)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	43	all_lung(31;0.000179)		Lung(74;0.111)|Epithelial(62;0.113)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CCAAAGAGCCGAATGAAGTGG	0.453																																					p.F170F		Atlas-SNP	.											.	UGT3A2	117	.	0			c.C510T						PASS	.	G	,	33,4373	39.2+/-71.8	0,33,2170	87.0	82.0	84.0		408,510	-2.3	0.0	5	dbSNP_134	84	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	UGT3A2	NM_001168316.1,NM_174914.3	,	0,33,6470	AA,AG,GG		0.0,0.749,0.2537	,	136/490,170/524	36049324	33,12973	2203	4300	6503	SO:0001819	synonymous_variant	167127	exon4			AGAGCCGAATGAA		CCDS3914.1, CCDS54842.1	5p13.2	2014-05-20			ENSG00000168671	ENSG00000168671		"""UDP glucuronosyltransferases"""	27266	protein-coding gene	gene with protein product						12975309	Standard	NM_174914		Approved		uc003jjz.2	Q3SY77	OTTHUMG00000131108	ENST00000282507.3:c.510C>T	5.37:g.36049324G>A		101.0	0.0	0		112.0	46.0	0.410714	NM_174914	B4DUQ7|E9PFK7|Q6UXC4|Q8NBP2	Silent	SNP	ENST00000282507.3	37	CCDS3914.1																																																																																			G|0.996;A|0.004	0.004	strong		0.453	UGT3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253771.2	NM_174914	
GPR87	53836	hgsc.bcm.edu	37	3	151017855	151017855	+	Splice_Site	SNP	T	T	G	rs141290943	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:151017855T>G	ENST00000260843.4	-	2	498	c.34A>C	c.(34-36)Aat>Cat	p.N12H	MED12L_ENST00000273432.4_Intron|MED12L_ENST00000474524.1_Intron|MED12L_ENST00000491549.1_Intron	NM_023915.3	NP_076404.3	Q9BY21	GPR87_HUMAN	G protein-coupled receptor 87	12					negative regulation of adenylate cyclase activity (GO:0007194)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled purinergic nucleotide receptor activity (GO:0045028)			endometrium(6)|large_intestine(6)|lung(5)|skin(1)|upper_aerodigestive_tract(1)	19			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GACGGCTTACTTGGTAATTTT	0.413													T|||	4	0.000798722	0.003	0.0	5008	,	,		18522	0.0		0.0	False		,,,				2504	0.0				p.N12H		Atlas-SNP	.											.	GPR87	52	.	0			c.A34C						PASS	.	T	HIS/ASN,	32,4374	37.6+/-69.7	0,32,2171	102.0	94.0	97.0		34,	1.4	1.0	3	dbSNP_134	97	1,8599	1.2+/-3.3	0,1,4299	yes	missense-near-splice,intron	GPR87,MED12L	NM_023915.3,NM_053002.4	68,	0,33,6470	GG,GT,TT		0.0116,0.7263,0.2537	benign,	12/359,	151017855	33,12973	2203	4300	6503	SO:0001630	splice_region_variant	53836	exon2			GCTTACTTGGTAA	AF237763	CCDS3157.1	3q24	2012-08-21			ENSG00000138271	ENSG00000138271		"""GPCR / Class A : Orphans"""	4538	protein-coding gene	gene with protein product		606379		GPR95		11273702	Standard	NM_023915		Approved		uc003eyt.2	Q9BY21	OTTHUMG00000159858	ENST00000260843.4:c.34+1A>C	3.37:g.151017855T>G		76.0	0.0	0		73.0	44.0	0.60274	NM_023915	Q5KU35|Q96JZ8|Q9BXC2	Missense_Mutation	SNP	ENST00000260843.4	37	CCDS3157.1	.	.	.	.	.	.	.	.	.	.	T	9.296	1.051901	0.19827	0.007263	1.16E-4	ENSG00000138271	ENST00000260843	T	0.62232	0.04	4.49	1.38	0.22167	.	0.688041	0.13625	N	0.374112	T	0.28067	0.0692	N	0.08118	0	0.80722	D	1	B	0.17268	0.021	B	0.13407	0.009	T	0.04855	-1.0922	9	.	.	.	-0.5324	7.7237	0.28746	0.0:0.8001:0.0:0.1999	.	12	Q9BY21	GPR87_HUMAN	H	12	ENSP00000260843:N12H	.	N	-	1	0	GPR87	152500545	1.000000	0.71417	1.000000	0.80357	0.606000	0.37113	1.189000	0.32114	0.152000	0.19188	0.533000	0.62120	AAT	T|0.998;G|0.002	0.002	strong		0.413	GPR87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357788.1		Missense_Mutation
MAP10	54627	hgsc.bcm.edu	37	1	232943513	232943513	+	Missense_Mutation	SNP	A	A	T	rs61735509	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:232943513A>T	ENST00000418460.1	+	1	2871	c.2744A>T	c.(2743-2745)cAc>cTc	p.H915L		NM_019090.2	NP_061963.2	Q9P2G4	MAP10_HUMAN	microtubule-associated protein 10	773					cytoplasmic microtubule organization (GO:0031122)|positive regulation of cytokinesis (GO:0032467)|regulation of microtubule-based process (GO:0032886)|spindle midzone assembly involved in mitosis (GO:0051256)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)	microtubule binding (GO:0008017)										TCACCTGTACACTCATACAGA	0.388													A|||	96	0.0191693	0.0696	0.0058	5008	,	,		19105	0.0		0.0	False		,,,				2504	0.0				p.H915L		Atlas-SNP	.											.	.	.	.	0			c.A2744T						PASS	.	A	LEU/HIS	220,3454		5,210,1622	47.0	47.0	47.0		2744	-4.8	0.0	1	dbSNP_129	47	6,8134		0,6,4064	yes	missense	KIAA1383	NM_019090.2	99	5,216,5686	TT,TA,AA		0.0737,5.988,1.913	benign	915/1048	232943513	226,11588	1837	4070	5907	SO:0001583	missense	54627	exon1			CTGTACACTCATA	AB037804	CCDS44334.1	1q42.2	2013-02-12	2013-02-12	2013-02-12	ENSG00000212916	ENSG00000212916			29265	protein-coding gene	gene with protein product	"""microtubule regulator 120 KDa"""		"""KIAA1383"""	KIAA1383		23264731	Standard	NM_019090		Approved	MTR120	uc001hvh.2	Q9P2G4	OTTHUMG00000037819	ENST00000418460.1:c.2744A>T	1.37:g.232943513A>T	ENSP00000403208:p.His915Leu	89.0	0.0	0		106.0	55.0	0.518868	NM_019090	A8K2F1|Q32MI1|Q58EZ9|Q5VV83	Missense_Mutation	SNP	ENST00000418460.1	37	CCDS44334.1	26	0.011904761904761904	24	0.04878048780487805	2	0.0055248618784530384	0	0.0	0	0.0	A	0.104	-1.148237	0.01714	0.05988	7.37E-4	ENSG00000212916	ENST00000418460	.	.	.	5.94	-4.76	0.03229	.	1.184600	0.06521	N	0.739754	T	0.01489	0.0048	N	0.16307	0.4	0.09310	N	1	B	0.15141	0.012	B	0.14578	0.011	T	0.20207	-1.0282	9	0.11485	T	0.65	0.0447	0.8514	0.01173	0.2763:0.1074:0.2072:0.409	rs61735509	773	Q9P2G4	K1383_HUMAN	L	915	.	ENSP00000403208:H915L	H	+	2	0	KIAA1383	231010136	0.000000	0.05858	0.012000	0.15200	0.035000	0.12851	0.776000	0.26704	-0.904000	0.03876	0.482000	0.46254	CAC	A|0.989;T|0.011	0.011	strong		0.388	MAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092317.3	NM_019090	
CLEC4F	165530	hgsc.bcm.edu	37	2	71043607	71043607	+	Silent	SNP	G	G	C	rs114209954	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71043607G>C	ENST00000272367.2	-	4	982	c.906C>G	c.(904-906)acC>acG	p.T302T	CLEC4F_ENST00000426626.1_Silent_p.T302T	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	302					endocytosis (GO:0006897)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			endometrium(1)|large_intestine(5)|lung(18)|ovary(5)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	37						TAAAGGCCTGGGTCTGGGAGT	0.403													G|||	63	0.0125799	0.0461	0.0029	5008	,	,		19886	0.0		0.0	False		,,,				2504	0.0				p.T302T	Colon(107;10 2157 6841 26035)	Atlas-SNP	.											.	CLEC4F	95	.	0			c.C906G						PASS	.	G		214,4192	126.1+/-163.2	4,206,1993	89.0	95.0	93.0		906	-0.9	0.3	2	dbSNP_132	93	1,8599		0,1,4299	no	coding-synonymous	CLEC4F	NM_173535.2		4,207,6292	CC,CG,GG		0.0116,4.857,1.6531		302/590	71043607	215,12791	2203	4300	6503	SO:0001819	synonymous_variant	165530	exon4			GGCCTGGGTCTGG	AK096429	CCDS1910.1	2p13.3	2008-02-05	2005-02-09	2005-02-11	ENSG00000152672	ENSG00000152672		"""C-type lectin domain containing"""	25357	protein-coding gene	gene with protein product			"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 13"""	CLECSF13		8889548, 1846367	Standard	NM_001258027		Approved	FLJ39110, KCLR	uc002shf.3	Q8N1N0	OTTHUMG00000129713	ENST00000272367.2:c.906C>G	2.37:g.71043607G>C		186.0	0.0	0		171.0	82.0	0.479532	NM_173535	A4QPA5	Silent	SNP	ENST00000272367.2	37	CCDS1910.1																																																																																			G|0.985;C|0.015	0.015	strong		0.403	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535	
TNFRSF18	8784	hgsc.bcm.edu	37	1	1141824	1141824	+	Missense_Mutation	SNP	G	G	C	rs11466676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1141824G>C	ENST00000379268.2	-	1	247	c.128C>G	c.(127-129)aCg>aGg	p.T43R	TNFRSF18_ENST00000328596.6_Missense_Mutation_p.T43R|TNFRSF18_ENST00000486728.1_5'Flank|TNFRSF18_ENST00000379265.5_Missense_Mutation_p.T43R	NM_004195.2|NM_148902.1	NP_004186.1|NP_683700.1	Q9Y5U5	TNR18_HUMAN	tumor necrosis factor receptor superfamily, member 18	43			T -> R (in dbSNP:rs11466676).		apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	tumor necrosis factor-activated receptor activity (GO:0005031)			lung(1)	1	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.73e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.01e-21)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		GTCCGTTCCCGTCCCAAGCAG	0.716													g|||	238	0.047524	0.1702	0.0173	5008	,	,		12979	0.0		0.001	False		,,,				2504	0.0				p.T43R	GBM(157;472 1934 13810 14591 35952)	Atlas-SNP	.											.	TNFRSF18	13	.	0			c.C128G						PASS	.	G	ARG/THR,ARG/THR,ARG/THR	308,3220		10,288,1466	4.0	5.0	5.0		128,128,128	2.1	0.0	1	dbSNP_120	5	2,7088		0,2,3543	no	missense,missense,missense	TNFRSF18	NM_004195.2,NM_148901.1,NM_148902.1	71,71,71	10,290,5009	CC,CG,GG		0.0282,8.7302,2.9196	benign,benign,benign	43/242,43/256,43/235	1141824	310,10308	1764	3545	5309	SO:0001583	missense	8784	exon1			GTTCCCGTCCCAA	AF125304	CCDS9.1, CCDS10.1, CCDS30552.1	1p36.3	2011-08-11			ENSG00000186891	ENSG00000186891		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11914	protein-coding gene	gene with protein product		603905				9177197, 10037686	Standard	NM_004195		Approved	AITR, GITR, CD357	uc001add.3	Q9Y5U5	OTTHUMG00000001414	ENST00000379268.2:c.128C>G	1.37:g.1141824G>C	ENSP00000368570:p.Thr43Arg	33.0	0.0	0		22.0	9.0	0.409091	NM_148902	B1AME1|O95851|Q5U0I4|Q9NYJ9	Missense_Mutation	SNP	ENST00000379268.2	37	CCDS10.1	84	0.038461538461538464	75	0.1524390243902439	6	0.016574585635359115	2	0.0034965034965034965	1	0.0013192612137203166	G	12.07	1.828233	0.32329	0.087302	2.82E-4	ENSG00000186891	ENST00000328596;ENST00000379268;ENST00000379265	T;T;T	0.60171	1.64;0.31;0.21	3.1	2.14	0.27477	.	0.907582	0.08998	U	0.863377	T	0.00524	0.0017	L	0.50333	1.59	0.80722	P	0.0	D;D;D	0.57571	0.98;0.98;0.98	P;P;P	0.52309	0.695;0.673;0.582	T	0.11084	-1.0602	9	0.87932	D	0	-4.6596	8.7668	0.34708	0.0:0.233:0.767:0.0	rs11466676	43;43;43	Q9Y5U5-2;Q9Y5U5;B1AME3	.;TNR18_HUMAN;.	R	43	ENSP00000328207:T43R;ENSP00000368570:T43R;ENSP00000368567:T43R	ENSP00000328207:T43R	T	-	2	0	TNFRSF18	1131687	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.161000	0.10026	0.563000	0.29222	0.462000	0.41574	ACG	G|0.955;C|0.045	0.045	strong		0.716	TNFRSF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004083.2	NM_004195	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240611	39240611	+	Silent	SNP	G	G	A	rs529043715	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39240611G>A	ENST00000391417.4	+	1	153	c.153G>A	c.(151-153)agG>agA	p.R51R		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	51	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						GCTGCTGCAGGCCCCAGTGCT	0.647													g|||	99	0.0197684	0.0726	0.0029	5008	,	,		18224	0.0		0.001	False		,,,				2504	0.0				p.R51R		Atlas-SNP	.											KRTAP4-9_ENST00000377734,NS,carcinoma,+1,2	KRTAP4-7	49	2	0			c.G153A						PASS	.						15.0	24.0	21.0					17																	39240611		691	1591	2282	SO:0001819	synonymous_variant	100132476	exon1			CTGCAGGCCCCAG	AJ406939	CCDS45673.1	17q21.2	2013-06-25			ENSG00000240871	ENSG00000240871		"""Keratin associated proteins"""	18898	protein-coding gene	gene with protein product						11279113	Standard	NM_033061		Approved	KAP4.7	uc010wfn.2	Q9BYR0	OTTHUMG00000133582	ENST00000391417.4:c.153G>A	17.37:g.39240611G>A		113.0	0.0	0		176.0	35.0	0.198864	NM_033061	A0AVM6|A8MQ08|A8MTL4	Silent	SNP	ENST00000391417.4	37	CCDS45673.1																																																																																			.	.	none		0.647	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
MUC4	4585	hgsc.bcm.edu	37	3	195507780	195507780	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195507780G>A	ENST00000463781.3	-	2	11130	c.10671C>T	c.(10669-10671)gaC>gaT	p.D3557D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.D3557D	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)		CCGAGGAAGCGTCGGTGACAG	0.592																																					p.D3557D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-2,2	MUC4	1505	2	0			c.C10671T						scavenged	.						25.0	21.0	23.0					3																	195507780		653	1573	2226	SO:0001819	synonymous_variant	4585	exon2			GGAAGCGTCGGTG	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.10671C>T	3.37:g.195507780G>A		336.0	0.0	0		183.0	52.0	0.284153	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
AHNAK2	113146	hgsc.bcm.edu	37	14	105417732	105417732	+	Silent	SNP	G	G	A	rs190986194	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105417732G>A	ENST00000333244.5	-	7	4175	c.4056C>T	c.(4054-4056)gaC>gaT	p.D1352D	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1352						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GTGCAGACAGGTCCACGGAGG	0.597													.|||	283	0.0565096	0.0113	0.1297	5008	,	,		13768	0.0129		0.1153	False		,,,				2504	0.0501				p.D1352D		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C4056T						PASS	.						126.0	107.0	114.0					14																	105417732		1812	2877	4689	SO:0001819	synonymous_variant	113146	exon7			AGACAGGTCCACG	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.4056C>T	14.37:g.105417732G>A		363.0	0.0	0		258.0	105.0	0.406977	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			G|0.914;A|0.086	0.086	strong		0.597	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
ITGAD	3681	hgsc.bcm.edu	37	16	31422071	31422071	+	Missense_Mutation	SNP	C	C	G	rs142278416	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31422071C>G	ENST00000389202.2	+	12	1277	c.1228C>G	c.(1228-1230)Cta>Gta	p.L410V		NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	410					activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						CTCCACCGAGCTAGCCCTGTG	0.667													c|||	38	0.00758786	0.0265	0.0043	5008	,	,		7588	0.0		0.0	False		,,,				2504	0.0				p.L410V		Atlas-SNP	.											.	ITGAD	154	.	0			c.C1228G						PASS	.	C	VAL/LEU	110,4284		2,106,2089	28.0	30.0	29.0		1228	1.0	0.0	16	dbSNP_134	29	1,8597		0,1,4298	yes	missense	ITGAD	NM_005353.2	32	2,107,6387	GG,GC,CC		0.0116,2.5034,0.8544	benign	410/1162	31422071	111,12881	2197	4299	6496	SO:0001583	missense	3681	exon12			ACCGAGCTAGCCC	U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"""CD molecules"", ""Integrins"""	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.1228C>G	16.37:g.31422071C>G	ENSP00000373854:p.Leu410Val	209.0	0.0	0		190.0	89.0	0.468421	NM_005353	Q15575|Q15576	Missense_Mutation	SNP	ENST00000389202.2	37	CCDS32438.1	14	0.00641025641025641	13	0.026422764227642278	1	0.0027624309392265192	0	0.0	0	0.0	c	0.001	-2.980833	0.00046	0.025034	1.16E-4	ENSG00000156886	ENST00000444228;ENST00000389202	T	0.15139	2.45	4.4	1.04	0.20106	.	.	.	.	.	T	0.01387	0.0045	N	0.01446	-0.86	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.06405	0.002;0.001	T	0.40232	-0.9574	9	0.02654	T	1	.	7.4596	0.27287	0.0:0.3542:0.5324:0.1134	.	426;410	Q59H14;Q13349	.;ITAD_HUMAN	V	426;410	ENSP00000373854:L410V	ENSP00000373854:L410V	L	+	1	2	ITGAD	31329572	0.949000	0.32298	0.037000	0.18230	0.014000	0.08584	-0.348000	0.07740	0.286000	0.22352	0.197000	0.17608	CTA	C|0.991;G|0.009	0.009	strong		0.667	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353	
AHNAK2	113146	hgsc.bcm.edu	37	14	105416344	105416344	+	Missense_Mutation	SNP	T	T	G	rs368838079		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105416344T>G	ENST00000333244.5	-	7	5563	c.5444A>C	c.(5443-5445)gAt>gCt	p.D1815A	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1815						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GGCAGTCACATCCTTGTCGGC	0.612																																					p.D1815A		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A5444C						PASS	.	T	ALA/ASP	15,3901		2,11,1945	157.0	191.0	180.0		5444	0.1	0.0	14		180	0,8254		0,0,4127	no	missense	AHNAK2	NM_138420.2	126	2,11,6072	GG,GT,TT		0.0,0.383,0.1233	benign	1815/5796	105416344	15,12155	1958	4127	6085	SO:0001583	missense	113146	exon7			GTCACATCCTTGT	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.5444A>C	14.37:g.105416344T>G	ENSP00000353114:p.Asp1815Ala	290.0	0.0	0		301.0	16.0	0.0531561	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	t	13.76	2.332517	0.41297	0.00383	0.0	ENSG00000185567	ENST00000333244	T	0.01947	4.54	4.3	0.0484	0.14285	.	.	.	.	.	T	0.04861	0.0131	M	0.92317	3.295	0.09310	N	1	B	0.33637	0.42	B	0.25506	0.061	T	0.18524	-1.0334	9	0.34782	T	0.22	-8.5499	7.3574	0.26727	0.0:0.0901:0.4093:0.5005	.	1815	Q8IVF2	AHNK2_HUMAN	A	1815	ENSP00000353114:D1815A	ENSP00000353114:D1815A	D	-	2	0	AHNAK2	104487389	0.291000	0.24352	0.004000	0.12327	0.019000	0.09904	2.523000	0.45580	0.079000	0.16929	0.374000	0.22700	GAT	.	.	weak		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
ZC3H12C	85463	hgsc.bcm.edu	37	11	110007834	110007834	+	Silent	SNP	T	T	C	rs78240010	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:110007834T>C	ENST00000278590.3	+	2	519	c.468T>C	c.(466-468)ccT>ccC	p.P156P	ZC3H12C_ENST00000528673.1_Silent_p.P157P|ZC3H12C_ENST00000453089.2_Silent_p.P125P	NM_033390.1	NP_203748.1	Q9C0D7	ZC12C_HUMAN	zinc finger CCCH-type containing 12C	156							endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37		all_cancers(61;3.24e-13)|all_epithelial(67;1.27e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.72e-06)|BRCA - Breast invasive adenocarcinoma(274;1.17e-05)|all cancers(92;9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0279)		AGAAACCACCTGATGTGGTGC	0.413													N|||	66	0.0131789	0.0431	0.0043	5008	,	,		22894	0.003		0.0	False		,,,				2504	0.0031				p.P156P		Atlas-SNP	.											.	ZC3H12C	83	.	0			c.T468C						PASS	.	C		127,3593		4,119,1737	71.0	66.0	67.0		468	-8.4	0.9	11	dbSNP_132	67	0,8192		0,0,4096	no	coding-synonymous	ZC3H12C	NM_033390.1		4,119,5833	CC,CT,TT		0.0,3.414,1.0662		156/884	110007834	127,11785	1860	4096	5956	SO:0001819	synonymous_variant	85463	exon2			ACCACCTGATGTG		CCDS44727.1	11q22.3	2012-07-05			ENSG00000149289	ENSG00000149289		"""Zinc fingers, CCCH-type domain containing"""	29362	protein-coding gene	gene with protein product	"""MCP induced protein 3"""	615001				11214970, 18178554	Standard	NM_033390		Approved	KIAA1726, MCPIP3	uc009yxw.3	Q9C0D7	OTTHUMG00000166572	ENST00000278590.3:c.468T>C	11.37:g.110007834T>C		91.0	0.0	0		54.0	24.0	0.444444	NM_033390	B4DI65|B4DR47	Silent	SNP	ENST00000278590.3	37	CCDS44727.1																																																																																			T|0.992;C|0.008	0.008	strong		0.413	ZC3H12C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390491.1	NM_033390	
PTAFR	5724	hgsc.bcm.edu	37	1	28476520	28476520	+	Missense_Mutation	SNP	T	T	C	rs5939	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:28476520T>C	ENST00000373857.3	-	2	1647	c.1013A>G	c.(1012-1014)aAt>aGt	p.N338S	PTAFR_ENST00000539896.1_Missense_Mutation_p.N338S|PTAFR_ENST00000305392.3_Missense_Mutation_p.N338S	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	338			N -> S (in dbSNP:rs5939). {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)			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)		TTTGAGGGAATTGCCAGGGAT	0.527													T|||	120	0.0239617	0.0862	0.0086	5008	,	,		21965	0.0		0.0	False		,,,				2504	0.0				p.N338S		Atlas-SNP	.											.	PTAFR	30	.	0			c.A1013G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN,SER/ASN	324,4082	173.4+/-203.2	12,300,1891	100.0	107.0	105.0		1013,1013,1013,1013	-1.5	0.0	1	dbSNP_52	105	7,8593	5.7+/-21.5	0,7,4293	yes	missense,missense,missense,missense	PTAFR	NM_000952.4,NM_001164721.1,NM_001164722.2,NM_001164723.2	46,46,46,46	12,307,6184	CC,CT,TT		0.0814,7.3536,2.545	benign,benign,benign,benign	338/343,338/343,338/343,338/343	28476520	331,12675	2203	4300	6503	SO:0001583	missense	5724	exon3			AGGGAATTGCCAG	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.1013A>G	1.37:g.28476520T>C	ENSP00000362965:p.Asn338Ser	121.0	0.0	0		151.0	68.0	0.450331	NM_001164723	A3KMC8|A8K2H5	Missense_Mutation	SNP	ENST00000373857.3	37	CCDS318.1	30	0.013736263736263736	26	0.052845528455284556	4	0.011049723756906077	0	0.0	0	0.0	T	3.748	-0.052169	0.07362	0.073536	8.14E-4	ENSG00000169403	ENST00000373857;ENST00000539896;ENST00000305392	T;T;T	0.70399	-0.48;-0.48;-0.48	5.38	-1.47	0.08772	.	1.433670	0.04726	N	0.420206	T	0.04363	0.0120	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.04495	-1.0947	10	0.07813	T	0.8	.	1.6592	0.02787	0.1391:0.3175:0.1355:0.408	rs5939;rs5939	338	P25105	PTAFR_HUMAN	S	338	ENSP00000362965:N338S;ENSP00000442658:N338S;ENSP00000301974:N338S	ENSP00000301974:N338S	N	-	2	0	PTAFR	28349107	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-0.242000	0.08928	-0.555000	0.06142	-0.418000	0.06021	AAT	T|0.975;C|0.025	0.025	strong		0.527	PTAFR-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011258.1	NM_000952	
OR4D9	390199	hgsc.bcm.edu	37	11	59282651	59282651	+	Missense_Mutation	SNP	C	C	T	rs76276934	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:59282651C>T	ENST00000329328.3	+	1	266	c.266C>T	c.(265-267)aCa>aTa	p.T89I		NM_001004711.1	NP_001004711.1	Q8NGE8	OR4D9_HUMAN	olfactory receptor, family 4, subfamily D, member 9	89						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(3)|lung(14)|prostate(5)|upper_aerodigestive_tract(1)	26						CTATCAGAGACAAAAACCATC	0.483													c|||	108	0.0215655	0.0802	0.0029	5008	,	,		20793	0.0		0.0	False		,,,				2504	0.0				p.T89I		Atlas-SNP	.											.	OR4D9	47	.	0			c.C266T						PASS	.	C	ILE/THR	263,4139	149.5+/-183.7	9,245,1947	122.0	118.0	119.0		266	-6.1	0.0	11	dbSNP_131	119	1,8589		0,1,4294	yes	missense	OR4D9	NM_001004711.1	89	9,246,6241	TT,TC,CC		0.0116,5.9746,2.032	benign	89/315	59282651	264,12728	2201	4295	6496	SO:0001583	missense	390199	exon1			CAGAGACAAAAAC	AB065861	CCDS31564.1	11q12.1	2012-08-09	2003-12-15		ENSG00000172742	ENSG00000172742		"""GPCR / Class A : Olfactory receptors"""	15178	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily D, member 9 pseudogene"""				Standard	NM_001004711		Approved		uc010rkv.2	Q8NGE8	OTTHUMG00000167343	ENST00000329328.3:c.266C>T	11.37:g.59282651C>T	ENSP00000328563:p.Thr89Ile	177.0	0.0	0		174.0	88.0	0.505747	NM_001004711	Q6IFF3	Missense_Mutation	SNP	ENST00000329328.3	37	CCDS31564.1	53	0.024267399267399268	52	0.10569105691056911	1	0.0027624309392265192	0	0.0	0	0.0	C	1.435	-0.569257	0.03910	0.059746	1.16E-4	ENSG00000172742	ENST00000329328	T	0.01397	4.94	4.02	-6.07	0.02158	GPCR, rhodopsin-like superfamily (1);	0.913714	0.08973	U	0.866909	T	0.00039	0.0001	L	0.39085	1.19	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46076	-0.9217	10	0.52906	T	0.07	.	2.2328	0.04001	0.3788:0.3173:0.1962:0.1076	.	89	Q8NGE8	OR4D9_HUMAN	I	89	ENSP00000328563:T89I	ENSP00000328563:T89I	T	+	2	0	OR4D9	59039227	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-2.882000	0.00714	-1.736000	0.01352	-1.265000	0.01443	ACA	C|0.979;T|0.021	0.021	strong		0.483	OR4D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394237.1	NM_001004711	
SPATC1L	84221	hgsc.bcm.edu	37	21	47588365	47588365	+	Missense_Mutation	SNP	G	G	A	rs73908565	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:47588365G>A	ENST00000291672.5	-	3	1462	c.401C>T	c.(400-402)tCc>tTc	p.S134F	SPATC1L_ENST00000330205.6_5'UTR	NM_001142854.1	NP_001136326.1	Q9H0A9	SPC1L_HUMAN	spermatogenesis and centriole associated 1-like	134																	CAGGAGCGGGGACAGCTTCCT	0.647													G|||	123	0.0245607	0.09	0.0058	5008	,	,		16558	0.0		0.0	False		,,,				2504	0.0				p.S134F		Atlas-SNP	.											.	.	.	.	0			c.C401T						PASS	.	G	PHE/SER,	106,1278		7,92,593	49.0	52.0	51.0		401,	3.2	0.7	21	dbSNP_130	51	1,3181		0,1,1590	yes	missense,utr-5	C21orf56	NM_001142854.1,NM_032261.4	155,	7,93,2183	AA,AG,GG		0.0314,7.659,2.3434	probably-damaging,	134/341,	47588365	107,4459	692	1591	2283	SO:0001583	missense	84221	exon3			AGCGGGGACAGCT	BC009497	CCDS13732.1, CCDS46653.1	21q22.3	2013-01-21	2012-11-12	2012-11-12	ENSG00000160284	ENSG00000160284			1298	protein-coding gene	gene with protein product	"""speriolin-like protein"""	612412	"""chromosome 21 open reading frame 56"""	C21orf56			Standard	NM_032261		Approved		uc011afu.2	Q9H0A9	OTTHUMG00000090487	ENST00000291672.5:c.401C>T	21.37:g.47588365G>A	ENSP00000291672:p.Ser134Phe	116.0	0.0	0		127.0	57.0	0.448819	NM_001142854	B4E323|Q52LS9|Q6FIH5|Q6P0L3|Q9NSE5	Missense_Mutation	SNP	ENST00000291672.5	37	CCDS46653.1	46	0.021062271062271064	44	0.08943089430894309	2	0.0055248618784530384	0	0.0	0	0.0	G	10.80	1.453781	0.26161	0.07659	3.14E-4	ENSG00000160284	ENST00000291672	T	0.55588	0.51	5.21	3.23	0.37069	.	0.477138	0.17215	N	0.182544	T	0.02193	0.0068	L	0.29908	0.895	0.09310	N	0.999992	P	0.44195	0.828	P	0.45138	0.471	T	0.00449	-1.1732	10	0.31617	T	0.26	-26.6257	12.7958	0.57558	0.0:0.3352:0.6648:0.0	.	134	Q9H0A9	CU056_HUMAN	F	134	ENSP00000291672:S134F	ENSP00000291672:S134F	S	-	2	0	C21orf56	46412793	0.073000	0.21202	0.739000	0.30968	0.521000	0.34408	0.543000	0.23237	1.164000	0.42652	0.467000	0.42956	TCC	G|0.978;A|0.022	0.022	strong		0.647	SPATC1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376654.1	NM_032261	
CHCHD3	54927	hgsc.bcm.edu	37	7	132470419	132470419	+	Silent	SNP	G	G	A	rs147050556	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:132470419G>A	ENST00000262570.5	-	8	807	c.663C>T	c.(661-663)agC>agT	p.S221S	CHCHD3_ENST00000476546.1_5'UTR|CHCHD3_ENST00000448878.1_Silent_p.S226S	NM_017812.2	NP_060282.1	Q9NX63	MIC19_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 3	221					inner mitochondrial membrane organization (GO:0007007)|mitochondrial fusion (GO:0008053)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein complex scaffold (GO:0032947)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	7						TCTCAAGCATGCTCTGCAAGA	0.353													G|||	5	0.000998403	0.0038	0.0	5008	,	,		19096	0.0		0.0	False		,,,				2504	0.0				p.S221S		Atlas-SNP	.											.	CHCHD3	21	.	0			c.C663T						PASS	.	G		18,4388	25.3+/-52.1	0,18,2185	100.0	95.0	97.0		663	5.8	1.0	7	dbSNP_134	97	0,8600		0,0,4300	no	coding-synonymous	CHCHD3	NM_017812.2		0,18,6485	AA,AG,GG		0.0,0.4085,0.1384		221/228	132470419	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	54927	exon8			AAGCATGCTCTGC	BC011596	CCDS5828.1	7q33	2012-10-02			ENSG00000106554	ENSG00000106554		"""Coiled-coil-helix-coiled-coil-helix domain containing"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	21906	protein-coding gene	gene with protein product	"""mitochondrial inner membrane organizing system 3"", ""protein phosphatase 1, regulatory subunit 22"""	613748				22252321, 23019327, 21081504, 17624330	Standard	NM_017812		Approved	FLJ20420, MINOS3, PPP1R22	uc003vre.3	Q9NX63	OTTHUMG00000155231	ENST00000262570.5:c.663C>T	7.37:g.132470419G>A		329.0	0.0	0		324.0	186.0	0.574074	NM_017812		Silent	SNP	ENST00000262570.5	37	CCDS5828.1																																																																																			G|0.998;A|0.002	0.002	strong		0.353	CHCHD3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000338899.1	NM_017812	
NOL10	79954	hgsc.bcm.edu	37	2	10729257	10729257	+	Missense_Mutation	SNP	T	T	C	rs34359340	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:10729257T>C	ENST00000381685.5	-	19	1861	c.1756A>G	c.(1756-1758)Aca>Gca	p.T586A	NOL10_ENST00000542668.1_Missense_Mutation_p.T536A|NOL10_ENST00000345985.3_Missense_Mutation_p.T536A|NOL10_ENST00000538384.1_Missense_Mutation_p.T560A|AC092687.5_ENST00000414538.1_RNA	NM_024894.3	NP_079170.2	Q9BSC4	NOL10_HUMAN	nucleolar protein 10	586						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)					Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)		TTTAGGACTGTCTGCTGGTCC	0.473													T|||	179	0.0357428	0.1301	0.0101	5008	,	,		18410	0.0		0.0	False		,,,				2504	0.0				p.T586A		Atlas-SNP	.											.	NOL10	22	.	0			c.A1756G						PASS	.	T	ALA/THR	471,3935	223.0+/-239.6	22,427,1754	167.0	172.0	170.0		1756	2.9	1.0	2	dbSNP_126	170	0,8600		0,0,4300	yes	missense	NOL10	NM_024894.2	58	22,427,6054	CC,CT,TT		0.0,10.69,3.6214	probably-damaging	586/689	10729257	471,12535	2203	4300	6503	SO:0001583	missense	79954	exon19			GGACTGTCTGCTG	AK024137	CCDS1673.2, CCDS58697.1, CCDS58698.1	2p25.1	2008-05-23			ENSG00000115761	ENSG00000115761			25862	protein-coding gene	gene with protein product			"""polyglutamine binding protein 5"""	PQBP5		12477932	Standard	NM_024894		Approved	FLJ14075	uc002raq.3	Q9BSC4	OTTHUMG00000119023	ENST00000381685.5:c.1756A>G	2.37:g.10729257T>C	ENSP00000371101:p.Thr586Ala	239.0	0.0	0		247.0	116.0	0.469636	NM_024894	A8K3R5|B4DLV0|Q53RC9|Q96TA5|Q9H7Y7|Q9H855	Missense_Mutation	SNP	ENST00000381685.5	37	CCDS1673.2	59	0.027014652014652016	57	0.11585365853658537	2	0.0055248618784530384	0	0.0	0	0.0	T	4.966	0.179358	0.09443	0.1069	0.0	ENSG00000115761	ENST00000345985;ENST00000381685;ENST00000542668;ENST00000538384	T;T;T;T	0.40756	1.02;2.21;1.61;2.21	5.35	2.93	0.34026	.	0.131457	0.64402	N	0.000001	T	0.00496	0.0016	M	0.65975	2.015	0.58432	D	0.999992	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.06405	0.001;0.001;0.002	T	0.04737	-1.0930	10	0.07644	T	0.81	-16.2693	8.127	0.31005	0.0:0.0702:0.1358:0.794	rs34359340	560;586;536	B4DLV0;Q9BSC4;Q9BSC4-2	.;NOL10_HUMAN;.	A	536;586;536;560	ENSP00000263837:T536A;ENSP00000371101:T586A;ENSP00000437625:T536A;ENSP00000439663:T560A	ENSP00000263837:T536A	T	-	1	0	NOL10	10646708	1.000000	0.71417	0.966000	0.40874	0.758000	0.43043	2.567000	0.45956	0.415000	0.25817	-0.435000	0.05868	ACA	T|0.964;C|0.036	0.036	strong		0.473	NOL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239227.1	NM_024894	
RNF130	55819	hgsc.bcm.edu	37	5	179393867	179393867	+	Silent	SNP	T	T	C	rs10060093	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:179393867T>C	ENST00000261947.4	-	7	1487	c.1089A>G	c.(1087-1089)tcA>tcG	p.S363S	RNF130_ENST00000521389.1_Silent_p.S363S|CTC-563A5.2_ENST00000510240.1_RNA|RNF130_ENST00000522208.2_Silent_p.S363S	NM_001280801.1	NP_001267730.1			ring finger protein 130											breast(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|upper_aerodigestive_tract(2)	17	all_cancers(89;5.49e-05)|all_epithelial(37;1.94e-05)|Renal(175;0.000159)|Lung NSC(126;0.00118)|all_lung(126;0.00212)	all_cancers(40;0.0294)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GAGGAAGAGGTGAGATCCCCG	0.582													C|||	123	0.0245607	0.0893	0.0029	5008	,	,		17689	0.002		0.001	False		,,,				2504	0.0				p.S363S	GBM(24;432 554 38471 39699 51728)	Atlas-SNP	.											.	RNF130	49	.	0			c.A1089G						PASS	.	C		291,4115	799.7+/-415.5	9,273,1921	100.0	91.0	94.0		1089	-6.4	0.4	5	dbSNP_119	94	4,8596	819.1+/-406.8	0,4,4296	no	coding-synonymous	RNF130	NM_018434.4		9,277,6217	CC,CT,TT		0.0465,6.6046,2.2682		363/420	179393867	295,12711	2203	4300	6503	SO:0001819	synonymous_variant	55819	exon7			AAGAGGTGAGATC	AF155650	CCDS4451.1, CCDS64340.1	5q35.3	2013-01-09			ENSG00000113269	ENSG00000113269		"""RING-type (C3HC4) zinc fingers"""	18280	protein-coding gene	gene with protein product						10806348	Standard	NM_018434		Approved	GP, G1RZFP, GOLIATH	uc003mll.1	Q86XS8	OTTHUMG00000130909	ENST00000261947.4:c.1089A>G	5.37:g.179393867T>C		148.0	0.0	0		182.0	82.0	0.450549	NM_018434		Silent	SNP	ENST00000261947.4	37																																																																																				T|0.972;C|0.028	0.028	strong		0.582	RNF130-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000374205.1	NM_018434	
RIMKLB	57494	hgsc.bcm.edu	37	12	8926015	8926015	+	Silent	SNP	C	C	T	rs386760122|rs2302488	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:8926015C>T	ENST00000538135.1	+	6	1621	c.796C>T	c.(796-798)Ctg>Ttg	p.L266L	RIMKLB_ENST00000299673.5_3'UTR|RIMKLB_ENST00000535829.1_Silent_p.L266L|A2ML1-AS1_ENST00000537288.1_RNA|RIMKLB_ENST00000357529.3_Silent_p.L266L			Q9ULI2	RIMKB_HUMAN	ribosomal modification protein rimK-like family member B	266	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.				cellular protein modification process (GO:0006464)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|citrate-L-glutamate ligase activity (GO:0072591)|metal ion binding (GO:0046872)|N-acetyl-L-aspartate-L-glutamate ligase activity (GO:0072590)			central_nervous_system(2)|kidney(3)|large_intestine(5)|lung(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						CATTGATCTGCTGATGAAAGA	0.473													T|||	384	0.0766773	0.2602	0.0259	5008	,	,		-128	0.0159		0.003	False		,,,				2504	0.0031				p.L266L		Atlas-SNP	.											.	RIMKLB	47	.	0			c.C796T						PASS	.	T		905,3245		101,703,1271	189.0	193.0	191.0		796	0.6	0.9	12	dbSNP_100	191	24,8424		0,24,4200	yes	coding-synonymous	RIMKLB	NM_020734.2		101,727,5471	TT,TC,CC		0.2841,21.8072,7.3742		266/387	8926015	929,11669	2075	4224	6299	SO:0001819	synonymous_variant	57494	exon7			GATCTGCTGATGA	AB033064	CCDS41748.1	12p13.31	2011-09-21	2008-10-13	2008-10-13	ENSG00000166532	ENSG00000166532	6.3.2.N6		29228	protein-coding gene	gene with protein product	"""N-acetylaspartyl-glutamate synthetase"""	614054	"""family with sequence similarity 80, member B"""	FAM80B		10574462, 20643647	Standard	XM_006719116		Approved	KIAA1238, NAAGS, NAAGS-I	uc001qux.2	Q9ULI2		ENST00000538135.1:c.796C>T	12.37:g.8926015C>T		263.0	0.0	0		267.0	116.0	0.434457	NM_020734	B7Z834|D3DUV2|Q8N4P4|Q8WTW6	Silent	SNP	ENST00000538135.1	37	CCDS41748.1																																																																																			C|0.911;T|0.089	0.089	strong		0.473	RIMKLB-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398874.1	NM_020734	
GRM1	2911	hgsc.bcm.edu	37	6	146755561	146755561	+	Missense_Mutation	SNP	C	C	G	rs146753539	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:146755561C>G	ENST00000282753.1	+	8	3449	c.3214C>G	c.(3214-3216)Ccg>Gcg	p.P1072A	GRM1_ENST00000492807.2_3'UTR|GRM1_ENST00000507907.1_3'UTR|GRM1_ENST00000355289.4_3'UTR|GRM1_ENST00000392299.2_3'UTR|GRM1_ENST00000361719.2_Missense_Mutation_p.P1072A			Q13255	GRM1_HUMAN	glutamate receptor, metabotropic 1	1072	Gln/Pro-rich.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|cell death (GO:0008219)|cellular response to electrical stimulus (GO:0071257)|dimeric G-protein coupled receptor signaling pathway (GO:0038042)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|G-protein coupled receptor signaling pathway (GO:0007186)|locomotory behavior (GO:0007626)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of sensory perception of pain (GO:0051930)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of pain (GO:0019233)|synaptic transmission (GO:0007268)	dendrite (GO:0030425)|G-protein coupled receptor dimeric complex (GO:0038037)|G-protein coupled receptor homodimeric complex (GO:0038038)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(2)|breast(5)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(54)|ovary(7)|pancreas(2)|prostate(5)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	126		Ovarian(120;0.0387)		OV - Ovarian serous cystadenocarcinoma(155;5.35e-08)|GBM - Glioblastoma multiforme(68;0.00762)		CCCGCCACCTCCGCAGCACCT	0.682													C|||	28	0.00559105	0.0174	0.0043	5008	,	,		14178	0.0		0.002	False		,,,				2504	0.0				p.P1072A		Atlas-SNP	.											GRM1,NS,carcinoma,-1,1	GRM1	419	1	0			c.C3214G						PASS	.	C	ALA/PRO,	67,4321		0,67,2127	29.0	33.0	32.0		3214,	2.9	0.5	6	dbSNP_134	32	12,8572		0,12,4280	yes	missense,utr-3	GRM1	NM_000838.3,NM_001114329.1	27,	0,79,6407	GG,GC,CC		0.1398,1.5269,0.609	benign,	1072/1195,	146755561	79,12893	2194	4292	6486	SO:0001583	missense	2911	exon9			CCACCTCCGCAGC	U31215	CCDS5209.1, CCDS47497.1, CCDS64548.1	6q24	2014-06-12			ENSG00000152822	ENSG00000152822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4593	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 85"""	604473				9076744, 9376535	Standard	NM_001278064		Approved	GPRC1A, mGlu1, MGLUR1, PPP1R85	uc010khw.2	Q13255	OTTHUMG00000015752	ENST00000282753.1:c.3214C>G	6.37:g.146755561C>G	ENSP00000282753:p.Pro1072Ala	63.0	0.0	0		68.0	23.0	0.338235	NM_000838	B9EG79|F8W805|Q13256|Q14757|Q14758|Q5VTF7|Q5VTF8|Q9NU10|Q9UGS9|Q9UGT0	Missense_Mutation	SNP	ENST00000282753.1	37	CCDS5209.1	13	0.005952380952380952	10	0.02032520325203252	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	C	9.887	1.203100	0.22121	0.015269	0.001398	ENSG00000152822	ENST00000361719;ENST00000282753	D;D	0.87809	-2.3;-2.3	5.71	2.87	0.33458	.	0.283949	0.40144	N	0.001180	T	0.65386	0.2686	L	0.29908	0.895	0.22142	N	0.999333	B	0.13594	0.008	B	0.16722	0.016	T	0.60383	-0.7274	10	0.51188	T	0.08	.	9.181	0.37141	0.0:0.7456:0.1201:0.1343	.	1072	Q13255	GRM1_HUMAN	A	1072	ENSP00000354896:P1072A;ENSP00000282753:P1072A	ENSP00000282753:P1072A	P	+	1	0	GRM1	146797254	0.024000	0.19004	0.468000	0.27192	0.601000	0.36947	0.978000	0.29488	0.730000	0.32425	0.462000	0.41574	CCG	C|0.993;G|0.007	0.007	strong		0.682	GRM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042574.1	NM_000838	
TSKS	60385	hgsc.bcm.edu	37	19	50251701	50251701	+	Missense_Mutation	SNP	C	C	T	rs199829146		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50251701C>T	ENST00000246801.3	-	3	507	c.425G>A	c.(424-426)cGc>cAc	p.R142H	TSKS_ENST00000358830.3_5'Flank	NM_021733.1	NP_068379.1	Q9UJT2	TSKS_HUMAN	testis-specific serine kinase substrate	142					negative regulation of phosphatase activity (GO:0010923)	centriole (GO:0005814)	protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|prostate(3)|skin(3)	38		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)		GTCTTTGGCGCGGACCAATCC	0.557																																					p.R142H		Atlas-SNP	.											TSKS,NS,carcinoma,+1,2	TSKS	97	2	0			c.G425A						PASS	.	C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	115.0	94.0	101.0		425	3.8	0.8	19		101	0,8600		0,0,4300	yes	missense	TSKS	NM_021733.1	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging	142/593	50251701	1,13005	2203	4300	6503	SO:0001583	missense	60385	exon3			TTGGCGCGGACCA	BC058862	CCDS12780.1	19q13.3	2014-06-13							30719	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 161"""	608253				11444856, 18495105	Standard	NM_021733		Approved	TSSKS, PPP1R161	uc002ppm.3	Q9UJT2		ENST00000246801.3:c.425G>A	19.37:g.50251701C>T	ENSP00000246801:p.Arg142His	167.0	0.0	0		165.0	71.0	0.430303	NM_021733	Q8WXJ0	Missense_Mutation	SNP	ENST00000246801.3	37	CCDS12780.1	.	.	.	.	.	.	.	.	.	.	C	14.73	2.621834	0.46840	2.27E-4	0.0	ENSG00000126467	ENST00000246801	T	0.48522	0.81	4.85	3.82	0.43975	.	0.122950	0.34628	N	0.003810	T	0.35098	0.0920	L	0.29908	0.895	0.80722	D	1	B	0.20459	0.045	B	0.16722	0.016	T	0.23440	-1.0188	10	0.72032	D	0.01	-9.0121	10.2244	0.43216	0.0:0.9063:0.0:0.0937	.	142	Q9UJT2	TSKS_HUMAN	H	142	ENSP00000246801:R142H	ENSP00000246801:R142H	R	-	2	0	TSKS	54943513	0.829000	0.29322	0.834000	0.33040	0.990000	0.78478	1.653000	0.37323	1.274000	0.44362	0.462000	0.41574	CGC	.	.	weak		0.557	TSKS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465795.1	NM_021733	
SLC9C2	284525	hgsc.bcm.edu	37	1	173526520	173526520	+	Missense_Mutation	SNP	C	C	T	rs116588526	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:173526520C>T	ENST00000367714.3	-	10	1596	c.1174G>A	c.(1174-1176)Gtt>Att	p.V392I	SLC9C2_ENST00000536496.1_Missense_Mutation_p.V290I|SLC9C2_ENST00000466087.1_5'UTR|RP3-436N22.3_ENST00000431459.1_RNA	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	392					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										AGATTATAAACATCAGGAGCC	0.343													C|||	61	0.0121805	0.0454	0.0014	5008	,	,		17169	0.0		0.0	False		,,,				2504	0.0				p.V392I		Atlas-SNP	.											.	.	.	.	0			c.G1174A						PASS	.	C	ILE/VAL	125,4281	89.7+/-128.4	3,119,2081	112.0	124.0	120.0		1174	-9.1	0.1	1	dbSNP_132	120	0,8600		0,0,4300	yes	missense	SLC9A11	NM_178527.3	29	3,119,6381	TT,TC,CC		0.0,2.837,0.9611	benign	392/1125	173526520	125,12881	2203	4300	6503	SO:0001583	missense	284525	exon10			TATAAACATCAGG	AK128104	CCDS1308.1	1q25.1	2013-07-18	2013-07-18	2012-03-22	ENSG00000162753	ENSG00000162753		"""Solute carriers"""	28664	protein-coding gene	gene with protein product			"""solute carrier family 9, isoform 11"", ""solute carrier family 9, member 11"", ""solute carrier family 9, member C2"""	SLC9A11			Standard	NM_178527		Approved	MGC43026	uc001giz.2	Q5TAH2	OTTHUMG00000034800	ENST00000367714.3:c.1174G>A	1.37:g.173526520C>T	ENSP00000356687:p.Val392Ile	238.0	0.0	0		223.0	118.0	0.529148	NM_178527	Q86UF3	Missense_Mutation	SNP	ENST00000367714.3	37	CCDS1308.1	21	0.009615384615384616	20	0.04065040650406504	1	0.0027624309392265192	0	0.0	0	0.0	C	0.013	-1.635886	0.00806	0.02837	0.0	ENSG00000162753	ENST00000367714;ENST00000536496	T;T	0.22945	1.93;1.93	5.57	-9.13	0.00704	Cation/H+ exchanger (1);	1.176240	0.06215	N	0.685727	T	0.02342	0.0072	N	0.02539	-0.55	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.39440	-0.9614	10	0.21014	T	0.42	-6.9326	11.2419	0.48974	0.1172:0.6529:0.0:0.2299	.	392	Q5TAH2	S9A11_HUMAN	I	392;290	ENSP00000356687:V392I;ENSP00000445437:V290I	ENSP00000356687:V392I	V	-	1	0	SLC9A11	171793143	0.001000	0.12720	0.050000	0.19076	0.051000	0.14879	-1.894000	0.01607	-1.269000	0.02436	-1.130000	0.01982	GTT	C|0.989;T|0.011	0.011	strong		0.343	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527	
GPATCH2	55105	hgsc.bcm.edu	37	1	217793718	217793718	+	Silent	SNP	A	A	G	rs34839777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:217793718A>G	ENST00000366935.3	-	2	290	c.180T>C	c.(178-180)ccT>ccC	p.P60P	GPATCH2_ENST00000366934.3_Silent_p.P60P	NM_018040.2	NP_060510.1	Q9NW75	GPTC2_HUMAN	G patch domain containing 2	60					negative regulation of phosphatase activity (GO:0010923)		nucleic acid binding (GO:0003676)			NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)	35				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)		GGCGTTTCAGAGGGCAAGATA	0.498													A|||	38	0.00758786	0.0265	0.0043	5008	,	,		17711	0.0		0.0	False		,,,				2504	0.0				p.P60P		Atlas-SNP	.											.	GPATCH2	53	.	0			c.T180C						PASS	.	A		114,4292	85.3+/-124.0	3,108,2092	136.0	123.0	128.0		180	-4.0	1.0	1	dbSNP_126	128	0,8600		0,0,4300	no	coding-synonymous	GPATCH2	NM_018040.2		3,108,6392	GG,GA,AA		0.0,2.5874,0.8765		60/529	217793718	114,12892	2203	4300	6503	SO:0001819	synonymous_variant	55105	exon2			TTTCAGAGGGCAA	AK001114	CCDS1518.1, CCDS73031.1	1q41	2013-01-28		2006-12-13	ENSG00000092978	ENSG00000092978		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""G patch domain containing"""	25499	protein-coding gene	gene with protein product	"""cancer/testis antigen 110"", ""protein phosphatase 1, regulatory subunit 30"""			GPATC2		19432882, 15375528	Standard	XM_005273174		Approved	FLJ10252, CT110, PPP1R30	uc001hlf.1	Q9NW75	OTTHUMG00000000527	ENST00000366935.3:c.180T>C	1.37:g.217793718A>G		51.0	0.0	0		51.0	22.0	0.431373	NM_018040	Q5VYK7|Q5VYK8|Q86YE7	Silent	SNP	ENST00000366935.3	37	CCDS1518.1																																																																																			A|0.990;G|0.010	0.010	strong		0.498	GPATCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001272.1	NM_018040	
CYP4F12	66002	hgsc.bcm.edu	37	19	15793282	15793282	+	Silent	SNP	A	A	G	rs35352350		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15793282A>G	ENST00000550308.1	+	6	989	c.609A>G	c.(607-609)ctA>ctG	p.L203L	CYP4F12_ENST00000324632.10_Silent_p.L203L	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	203					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	TGGACAGTCTACAGAAATGCA	0.527																																					p.L203L		Atlas-SNP	.											.	CYP4F12	89	.	0			c.A609G						PASS	.	G		62,4344		0,62,2141	115.0	108.0	111.0		609	1.3	1.0	19	dbSNP_126	111	0,8600		0,0,4300	no	coding-synonymous	CYP4F12	NM_023944.3		0,62,6441	GG,GA,AA		0.0,1.4072,0.4767		203/525	15793282	62,12944	2203	4300	6503	SO:0001819	synonymous_variant	66002	exon6			CAGTCTACAGAAA	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.609A>G	19.37:g.15793282A>G		326.0	0.0	0		395.0	56.0	0.141772	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Silent	SNP	ENST00000550308.1	37	CCDS42517.1																																																																																			A|0.991;G|0.009	0.009	strong		0.527	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
SNX27	81609	hgsc.bcm.edu	37	1	151638486	151638486	+	Splice_Site	SNP	T	T	C	rs150091333	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:151638486T>C	ENST00000458013.2	+	6	1104	c.984T>C	c.(982-984)ttT>ttC	p.F328F	SNX27_ENST00000368838.1_Splice_Site_p.F235F|SNX27_ENST00000482791.1_3'UTR|SNX27_ENST00000368843.3_Splice_Site_p.F328F			Q96L92	SNX27_HUMAN	sorting nexin family member 27	328	FERM-like region F1.|Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|establishment of natural killer cell polarity (GO:0001770)|intracellular protein transport (GO:0006886)|retrograde transport, endosome to plasma membrane (GO:1990126)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|immunological synapse (GO:0001772)|nucleus (GO:0005634)	phosphatidylinositol-3-phosphate binding (GO:0032266)			central_nervous_system(1)|large_intestine(2)|ovary(2)	5	Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			GTCACTCCTTTGGTAAGTACC	0.403													T|||	19	0.00379393	0.0144	0.0	5008	,	,		21524	0.0		0.0	False		,,,				2504	0.0				p.F328F	Colon(46;291 966 40145 41237 41888)	Atlas-SNP	.											.	SNX27	44	.	0			c.T984C						PASS	.	T		62,4344	58.1+/-94.6	0,62,2141	169.0	146.0	154.0		984	3.9	1.0	1	dbSNP_134	154	6,8594	5.0+/-18.6	0,6,4294	yes	coding-synonymous-near-splice	SNX27	NM_030918.5		0,68,6435	CC,CT,TT		0.0698,1.4072,0.5228		328/529	151638486	68,12938	2203	4300	6503	SO:0001630	splice_region_variant	81609	exon6			CTCCTTTGGTAAG	AB007957	CCDS1001.1	1q21.3	2008-03-11			ENSG00000143376	ENSG00000143376		"""Sorting nexins"""	20073	protein-coding gene	gene with protein product		611541				12461558	Standard	XM_005245509		Approved	MY014, KIAA0488, MGC20471	uc001eyn.1	Q96L92	OTTHUMG00000013052	ENST00000458013.2:c.985+1T>C	1.37:g.151638486T>C		95.0	0.0	0		110.0	50.0	0.454545	NM_030918	Q32Q36|Q4AEJ5|Q5VWB0|Q5VWB1|Q5VWB2|Q6IPP6|Q86UB1|Q96D79|Q9H3K8	Silent	SNP	ENST00000458013.2	37																																																																																				T|0.994;C|0.006	0.006	strong		0.403	SNX27-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000036624.3	NM_030918	Silent
GNA14	9630	hgsc.bcm.edu	37	9	80144099	80144099	+	Silent	SNP	G	G	A	rs12346870	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:80144099G>A	ENST00000341700.6	-	2	708	c.195C>T	c.(193-195)gaC>gaT	p.D65D	RP11-466A17.1_ENST00000439145.1_RNA	NM_004297.3	NP_004288.1	O95837	GNA14_HUMAN	guanine nucleotide binding protein (G protein), alpha 14	65					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			endometrium(3)|kidney(1)|large_intestine(7)|lung(4)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	24						TTCTGTCTTCGTCGCTGTAAC	0.448													G|||	114	0.0227636	0.0809	0.0086	5008	,	,		21370	0.0		0.001	False		,,,				2504	0.0				p.D65D		Atlas-SNP	.											.	GNA14	50	.	0			c.C195T						PASS	.	G		273,4133	154.0+/-187.5	12,249,1942	339.0	317.0	324.0		195	-0.6	1.0	9	dbSNP_120	324	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	GNA14	NM_004297.3		12,251,6240	AA,AG,GG		0.0233,6.1961,2.1144		65/356	80144099	275,12731	2203	4300	6503	SO:0001819	synonymous_variant	9630	exon2			GTCTTCGTCGCTG	AF105201	CCDS6657.1	9q21	2008-05-23			ENSG00000156049	ENSG00000156049			4382	protein-coding gene	gene with protein product		604397				10191087, 17620339	Standard	NM_004297		Approved		uc004aku.3	O95837	OTTHUMG00000020058	ENST00000341700.6:c.195C>T	9.37:g.80144099G>A		291.0	0.0	0		324.0	213.0	0.657407	NM_004297	B1ALW3	Silent	SNP	ENST00000341700.6	37	CCDS6657.1																																																																																			G|0.976;A|0.024	0.024	strong		0.448	GNA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052759.1		
IGSF22	283284	hgsc.bcm.edu	37	11	18735480	18735480	+	Missense_Mutation	SNP	G	G	A	rs111397851	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:18735480G>A	ENST00000513874.1	-	14	2153	c.2014C>T	c.(2014-2016)Cgt>Tgt	p.R672C	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	672	Ig-like 4.									NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						CTGTCTTCACGCACACAGTTG	0.602													g|||	236	0.0471246	0.1415	0.0317	5008	,	,		23327	0.0		0.0258	False		,,,				2504	0.001				p.R672C		Atlas-SNP	.											.	IGSF22	211	.	0			c.C2014T						PASS	.		CYS/ARG	491,3899	207.2+/-228.6	24,443,1728	88.0	95.0	93.0		2014	1.0	0.0	11	dbSNP_132	93	219,8353	90.4+/-152.6	3,213,4070	yes	missense	IGSF22	NM_173588.3	180	27,656,5798	AA,AG,GG		2.5548,11.1845,5.4775	probably-damaging	672/1327	18735480	710,12252	2195	4286	6481	SO:0001583	missense	283284	exon14			CTTCACGCACACA	AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.2014C>T	11.37:g.18735480G>A	ENSP00000421191:p.Arg672Cys	165.0	0.0	0		194.0	107.0	0.551546	NM_173588	A6NNA0|D6RGV7	Missense_Mutation	SNP	ENST00000513874.1	37	CCDS41625.2	94	0.04304029304029304	61	0.12398373983739837	15	0.04143646408839779	0	0.0	18	0.023746701846965697	G	11.60	1.686151	0.29962	0.111845	0.025548	ENSG00000179057	ENST00000513874	T	0.46063	0.88	3.98	0.959	0.19624	.	0.000000	0.33327	U	0.005033	T	0.02418	0.0074	H	0.97896	4.1	0.09310	N	1	D	0.89917	1.0	D	0.79784	0.993	T	0.16129	-1.0413	10	0.62326	D	0.03	.	3.8194	0.08828	0.1944:0.0:0.384:0.4215	.	672	D6RGV7	.	C	672	ENSP00000421191:R672C	ENSP00000322422:R672C	R	-	1	0	IGSF22	18692056	0.003000	0.15002	0.002000	0.10522	0.321000	0.28281	0.178000	0.16820	0.027000	0.15297	0.448000	0.29417	CGT	G|0.961;A|0.039	0.039	strong		0.602	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588	
ABCA3	21	hgsc.bcm.edu	37	16	2373687	2373687	+	Silent	SNP	C	C	T	rs74002800	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2373687C>T	ENST00000301732.5	-	7	1150	c.450G>A	c.(448-450)gtG>gtA	p.V150V	ABCA3_ENST00000567910.1_Silent_p.V150V|ABCA3_ENST00000382381.3_Silent_p.V150V	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	150					response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)	alveolar lamellar body (GO:0097208)|alveolar lamellar body membrane (GO:0097233)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(7)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(7)|prostate(5)|skin(6)|upper_aerodigestive_tract(1)	70		Ovarian(90;0.17)			Imatinib(DB00619)	GGTGATATTTCACCTGTGGAA	0.517													C|||	172	0.034345	0.1218	0.0159	5008	,	,		18945	0.0		0.0	False		,,,				2504	0.0				p.V150V		Atlas-SNP	.											.	ABCA3	176	.	0			c.G450A						PASS	.	C		498,3898	228.8+/-243.5	29,440,1729	170.0	192.0	185.0		450	0.9	0.9	16	dbSNP_130	185	6,8594	3.7+/-12.6	0,6,4294	no	coding-synonymous	ABCA3	NM_001089.2		29,446,6023	TT,TC,CC		0.0698,11.3285,3.8781		150/1705	2373687	504,12492	2198	4300	6498	SO:0001819	synonymous_variant	21	exon7			ATATTTCACCTGT	U78735	CCDS10466.1	16p13.3	2012-03-14			ENSG00000167972	ENSG00000167972		"""ATP binding cassette transporters / subfamily A"""	33	protein-coding gene	gene with protein product		601615		ABC3		8706931	Standard	NM_001089		Approved	ABC-C, EST111653, LBM180	uc002cpy.1	Q99758	OTTHUMG00000128845	ENST00000301732.5:c.450G>A	16.37:g.2373687C>T		111.0	0.0	0		126.0	46.0	0.365079	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Silent	SNP	ENST00000301732.5	37	CCDS10466.1																																																																																			C|0.963;T|0.037	0.037	strong		0.517	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089	
INSL6	11172	hgsc.bcm.edu	37	9	5185365	5185365	+	Missense_Mutation	SNP	A	A	G	rs2149554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:5185365A>G	ENST00000381641.3	-	1	303	c.238T>C	c.(238-240)Ttc>Ctc	p.F80L		NM_007179.2	NP_009110.2	Q9Y581	INSL6_HUMAN	insulin-like 6	80			F -> L (in dbSNP:rs2149554).		fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|lung(2)	15	all_hematologic(13;0.137)	Breast(48;0.147)|Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0128)|Lung(218;0.145)		GGGCTTTCGAACTGGTATGGG	0.537													A|||	503	0.100439	0.3646	0.0274	5008	,	,		16500	0.0		0.001	False		,,,				2504	0.001				p.F80L		Atlas-SNP	.											INSL6,NS,carcinoma,+2,1	INSL6	35	1	0			c.T238C						scavenged	.	A	LEU/PHE	1275,3131	436.4+/-344.6	176,923,1104	118.0	126.0	123.0		238	0.5	0.0	9	dbSNP_96	123	10,8590	6.4+/-24.3	0,10,4290	yes	missense	INSL6	NM_007179.2	22	176,933,5394	GG,GA,AA		0.1163,28.9378,9.8801	benign	80/214	5185365	1285,11721	2203	4300	6503	SO:0001583	missense	11172	exon1			TTTCGAACTGGTA	AF156094	CCDS6458.1	9p24	2008-07-21			ENSG00000120210	ENSG00000120210			6089	protein-coding gene	gene with protein product	"""relaxin/insulin-like factor 1"""	606414				10819760	Standard	NM_007179		Approved	RIF1	uc003zix.3	Q9Y581	OTTHUMG00000019489	ENST00000381641.3:c.238T>C	9.37:g.5185365A>G	ENSP00000371054:p.Phe80Leu	84.0	1.0	0.0119048		117.0	61.0	0.521368	NM_007179	A0AVS0|Q9NS16	Missense_Mutation	SNP	ENST00000381641.3	37	CCDS6458.1	184	0.08424908424908426	174	0.35365853658536583	10	0.027624309392265192	0	0.0	0	0.0	A	5.443	0.266871	0.10294	0.289378	0.001163	ENSG00000120210	ENST00000381641	T	0.40476	1.03	4.39	0.455	0.16649	Insulin-like (3);	3.103370	0.00944	N	0.002876	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.06786	0.001	B	0.10450	0.005	T	0.29427	-1.0012	9	0.11485	T	0.65	-13.6373	3.4873	0.07625	0.5569:0.1995:0.2435:0.0	rs2149554;rs52816055;rs56640305;rs2149554	80	Q9Y581	INSL6_HUMAN	L	80	ENSP00000371054:F80L	ENSP00000371054:F80L	F	-	1	0	INSL6	5175365	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.553000	0.06012	0.067000	0.16545	0.533000	0.62120	TTC	A|0.897;G|0.103	0.103	strong		0.537	INSL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051608.3	NM_007179	
ICAM5	7087	hgsc.bcm.edu	37	19	10404588	10404588	+	Silent	SNP	T	T	C	rs116688659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:10404588T>C	ENST00000221980.4	+	7	1743	c.1680T>C	c.(1678-1680)tcT>tcC	p.S560S		NM_003259.3	NP_003250.3	Q9UMF0	ICAM5_HUMAN	intercellular adhesion molecule 5, telencephalin	560	Ig-like C2-type 6.				phagocytosis (GO:0006909)|single organismal cell-cell adhesion (GO:0016337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|prostate(2)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(20;2.64e-09)|Epithelial(33;4.31e-06)|all cancers(31;9.75e-06)			CTCGGGGCTCTGCGGCCAAAA	0.662													T|||	24	0.00479233	0.0182	0.0	5008	,	,		17413	0.0		0.0	False		,,,				2504	0.0				p.S560S		Atlas-SNP	.											.	ICAM5	53	.	0			c.T1680C						PASS	.	T		55,4349	54.2+/-90.2	0,55,2147	42.0	49.0	47.0		1680	-9.2	0.0	19	dbSNP_132	47	0,8600		0,0,4300	no	coding-synonymous	ICAM5	NM_003259.3		0,55,6447	CC,CT,TT		0.0,1.2489,0.4229		560/925	10404588	55,12949	2202	4300	6502	SO:0001819	synonymous_variant	7087	exon7			GGGCTCTGCGGCC	U72671	CCDS12233.1	19p13.2	2013-01-14				ENSG00000105376		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5348	protein-coding gene	gene with protein product	"""telencephalin"""	601852		TLCN		8995416, 9828136	Standard	NM_003259		Approved	TLN	uc002mnu.4	Q9UMF0		ENST00000221980.4:c.1680T>C	19.37:g.10404588T>C		45.0	0.0	0		36.0	12.0	0.333333	NM_003259	Q9Y6F3	Silent	SNP	ENST00000221980.4	37	CCDS12233.1																																																																																			T|0.995;C|0.005	0.005	strong		0.662	ICAM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451217.1	NM_003259	
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274360	39274360	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39274360A>T	ENST00000391413.2	-	1	246	c.208T>A	c.(208-210)Tgc>Agc	p.C70S		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	70	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].		Missing (in allele KAP4.14). {ECO:0000269|PubMed:15955084}.			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)			CTGGAGATGCAGCATCTGGGG	0.667																																					p.C70S		Atlas-SNP	.											KRTAP4-11,NS,carcinoma,0,1	KRTAP4-11	94	1	0			c.T208A						scavenged	.						7.0	12.0	11.0					17																	39274360		677	1580	2257	SO:0001583	missense	653240	exon1			AGATGCAGCATCT	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.208T>A	17.37:g.39274360A>T	ENSP00000375232:p.Cys70Ser	189.0	2.0	0.010582		169.0	15.0	0.0887574	NM_033059	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	13.38	2.219303	0.39201	.	.	ENSG00000212721	ENST00000391413	T	0.02280	4.36	3.77	1.34	0.21922	.	0.000000	0.36972	U	0.002304	T	0.04770	0.0129	M	0.90252	3.1	0.23636	N	0.997233	B	0.17268	0.021	B	0.17722	0.019	T	0.23048	-1.0199	10	0.54805	T	0.06	.	4.9719	0.14119	0.7038:0.1861:0.1101:0.0	.	70	Q9BYQ6	KR411_HUMAN	S	70	ENSP00000375232:C70S	ENSP00000375232:C70S	C	-	1	0	KRTAP4-11	36527886	0.844000	0.29557	0.494000	0.27515	0.120000	0.20174	1.052000	0.30429	0.644000	0.30656	0.496000	0.49642	TGC	.	.	none		0.667	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
DNAH14	127602	hgsc.bcm.edu	37	1	225355716	225355716	+	Missense_Mutation	SNP	T	T	C	rs78614986	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:225355716T>C	ENST00000445597.2	+	23	4240	c.4240T>C	c.(4240-4242)Tat>Cat	p.Y1414H	DNAH14_ENST00000439375.2_Missense_Mutation_p.Y1819H|DNAH14_ENST00000430092.1_Missense_Mutation_p.Y1819H			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	1414					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						TATACAGTTTTATAATCAACT	0.269													T|||	28	0.00559105	0.0204	0.0014	5008	,	,		16127	0.0		0.0	False		,,,				2504	0.0				p.Y1819H		Atlas-SNP	.											.	DNAH14	300	.	0			c.T5455C						PASS	.	T	HIS/TYR	41,1343		0,41,651	50.0	50.0	50.0		5455	-2.7	1.0	1	dbSNP_132	50	0,3156		0,0,1578	no	missense	DNAH14	NM_001373.1	83	0,41,2229	CC,CT,TT		0.0,2.9624,0.9031	probably-damaging	1819/4516	225355716	41,4499	692	1578	2270	SO:0001583	missense	127602	exon35			CAGTTTTATAATC	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.4240T>C	1.37:g.225355716T>C	ENSP00000409472:p.Tyr1414His	271.0	0.0	0		279.0	131.0	0.469534	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	T	10.64	1.405909	0.25378	0.029624	0.0	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375;ENST00000328556	T;T;T;T	0.39997	2.15;1.05;1.05;1.42	5.24	-2.69	0.06022	.	.	.	.	.	T	0.13372	0.0324	L	0.43598	1.365	0.80722	D	1	B	0.12630	0.006	B	0.16722	0.016	T	0.08785	-1.0705	9	0.54805	T	0.06	.	12.5268	0.56091	0.0:0.5994:0.0:0.4006	.	1819	Q0VDD8-4	.	H	1414;1819;1819;913	ENSP00000409472:Y1414H;ENSP00000414402:Y1819H;ENSP00000392061:Y1819H;ENSP00000332424:Y913H	ENSP00000332424:Y913H	Y	+	1	0	DNAH14	223422339	0.356000	0.24930	0.977000	0.42913	0.834000	0.47266	-1.031000	0.03578	-0.549000	0.06191	-0.237000	0.12165	TAT	T|0.993;C|0.007	0.007	strong		0.269	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
SLC37A3	84255	hgsc.bcm.edu	37	7	140051116	140051116	+	Missense_Mutation	SNP	G	G	A	rs76089276	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140051116G>A	ENST00000326232.9	-	9	1042	c.839C>T	c.(838-840)gCg>gTg	p.A280V	SLC37A3_ENST00000447932.2_Missense_Mutation_p.A280V|SLC37A3_ENST00000429996.2_3'UTR|SLC37A3_ENST00000340308.3_Missense_Mutation_p.A280V	NM_207113.1	NP_996996.1	Q8NCC5	SPX3_HUMAN	solute carrier family 37, member 3	280					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|stomach(3)	24	Melanoma(164;0.0142)					GAAGCTTATCGCCTTGACTTG	0.468													G|||	167	0.0333466	0.1188	0.0115	5008	,	,		20455	0.0		0.002	False		,,,				2504	0.0				p.A280V	Esophageal Squamous(133;211 1716 4665 11387 37873)	Atlas-SNP	.											.	SLC37A3	80	.	0			c.C839T						PASS	.	G	VAL/ALA,VAL/ALA	454,3952	216.4+/-235.1	19,416,1768	152.0	129.0	137.0		839,839	5.2	1.0	7	dbSNP_131	137	8,8592	5.0+/-18.6	0,8,4292	yes	missense,missense	SLC37A3	NM_032295.2,NM_207113.1	64,64	19,424,6060	AA,AG,GG		0.093,10.3041,3.5522	probably-damaging,probably-damaging	280/444,280/495	140051116	462,12544	2203	4300	6503	SO:0001583	missense	84255	exon9			CTTATCGCCTTGA	AK074823	CCDS5858.1, CCDS5859.1, CCDS75669.1	7q34	2013-07-17	2013-07-17		ENSG00000157800	ENSG00000157800		"""Solute carriers"""	20651	protein-coding gene	gene with protein product							Standard	NM_001287498		Approved	DKFZp761N0624	uc003vvo.3	Q8NCC5	OTTHUMG00000157343	ENST00000326232.9:c.839C>T	7.37:g.140051116G>A	ENSP00000321498:p.Ala280Val	171.0	0.0	0		187.0	83.0	0.44385	NM_207113	Q6PIU7|Q86SS4|Q9BQG7	Missense_Mutation	SNP	ENST00000326232.9	37	CCDS5859.1	71|71	0.03250915750915751|0.03250915750915751	66|66	0.13414634146341464|0.13414634146341464	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	0|0	0.0|0.0	G|G	20.6|20.6	4.022383|4.022383	0.75275|0.75275	0.103041|0.103041	9.3E-4|9.3E-4	ENSG00000157800|ENSG00000157800	ENST00000340308;ENST00000447932;ENST00000326232|ENST00000485734	T;T;T|.	0.58060|.	0.36;0.36;0.36|.	5.2|5.2	5.2|5.2	0.72013|0.72013	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.04407|.	0.0121|.	M|M	0.86097|0.86097	2.795|2.795	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.79108|.	0.981;0.992;0.979|.	T|.	0.49716|.	-0.8910|.	10|.	0.62326|.	D|.	0.03|.	-43.077|-43.077	18.7136|18.7136	0.91667|0.91667	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	280;280;280|.	Q8NCC5-2;Q8NCC5-3;Q8NCC5|.	.;.;SPX3_HUMAN|.	V|X	280|59	ENSP00000343358:A280V;ENSP00000397481:A280V;ENSP00000321498:A280V|.	ENSP00000321498:A280V|.	A|R	-|-	2|1	0|2	SLC37A3|SLC37A3	139697585|139697585	1.000000|1.000000	0.71417|0.71417	0.951000|0.951000	0.38953|0.38953	0.262000|0.262000	0.26303|0.26303	7.710000|7.710000	0.84655|0.84655	2.575000|2.575000	0.86900|0.86900	0.563000|0.563000	0.77884|0.77884	GCG|CGA	G|0.969;A|0.031	0.031	strong		0.468	SLC37A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348492.1	NM_032295	
MGAM	8972	hgsc.bcm.edu	37	7	141754625	141754625	+	Silent	SNP	C	C	T	rs115294234	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:141754625C>T	ENST00000549489.2	+	27	3326	c.3231C>T	c.(3229-3231)acC>acT	p.T1077T	MGAM_ENST00000475668.2_Silent_p.T1077T	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1077	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)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	CATCCAGCACCCCTGAGGGTC	0.448													c|||	56	0.0111821	0.0401	0.0043	5008	,	,		19007	0.0		0.0	False		,,,				2504	0.0				p.T1077T		Atlas-SNP	.											.	MGAM	767	.	0			c.C3231T						PASS	.	C		137,3699		4,129,1785	142.0	135.0	137.0		3231	1.1	0.2	7	dbSNP_132	137	0,8226		0,0,4113	no	coding-synonymous	MGAM	NM_004668.2		4,129,5898	TT,TC,CC		0.0,3.5714,1.1358		1077/1858	141754625	137,11925	1918	4113	6031	SO:0001819	synonymous_variant	8972	exon27			CAGCACCCCTGAG	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.3231C>T	7.37:g.141754625C>T		169.0	0.0	0		190.0	95.0	0.5	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000549489.2	37	CCDS47727.1																																																																																			C|0.985;T|0.015	0.015	strong		0.448	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
CLDN22	53842	hgsc.bcm.edu	37	4	184240777	184240777	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:184240777A>G	ENST00000323319.5	-	1	1150	c.595T>C	c.(595-597)Tac>Cac	p.Y199H	WWC2_ENST00000403733.3_3'UTR	NM_001111319.1	NP_001104789.1	Q8N7P3	CLD22_HUMAN	claudin 22	199					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			cervix(1)|kidney(1)|lung(3)|prostate(1)|skin(1)	7		all_lung(41;6.9e-12)|Lung NSC(41;1.28e-11)|Colorectal(36;0.0172)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)|Esophageal squamous(56;0.176)		all cancers(43;4.1e-26)|Epithelial(43;6.45e-22)|OV - Ovarian serous cystadenocarcinoma(60;7.64e-10)|Colorectal(24;5.87e-06)|GBM - Glioblastoma multiforme(59;6.5e-06)|STAD - Stomach adenocarcinoma(60;2.09e-05)|COAD - Colon adenocarcinoma(29;5.15e-05)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.155)		GCCACTGCGTAGTGGCCCGAA	0.542																																					p.Y199H		Atlas-SNP	.											CLDN22,NS,carcinoma,+2,1	CLDN22	20	1	0			c.T595C						scavenged	.						232.0	210.0	217.0					4																	184240777		1568	3582	5150	SO:0001583	missense	53842	exon1			CTGCGTAGTGGCC	AK098064	CCDS43286.1	4q35.1	2010-08-05			ENSG00000177300	ENSG00000177300		"""Claudins"""	2044	protein-coding gene	gene with protein product							Standard	NM_001111319		Approved	CLDN21	uc010isa.1	Q8N7P3	OTTHUMG00000160627	ENST00000323319.5:c.595T>C	4.37:g.184240777A>G	ENSP00000318113:p.Tyr199His	243.0	2.0	0.00823045		300.0	153.0	0.51	NM_001111319		Missense_Mutation	SNP	ENST00000323319.5	37	CCDS43286.1	.	.	.	.	.	.	.	.	.	.	A	11.23	1.577764	0.28180	.	.	ENSG00000177300	ENST00000323319	D	0.85411	-1.98	6.07	2.4	0.29515	.	0.831349	0.11145	N	0.594777	T	0.80974	0.4727	M	0.63843	1.955	0.09310	N	1	B	0.29508	0.246	B	0.26094	0.066	T	0.69135	-0.5225	10	0.54805	T	0.06	.	6.5842	0.22612	0.7044:0.0:0.1875:0.108	.	199	Q8N7P3	CLD22_HUMAN	H	199	ENSP00000318113:Y199H	ENSP00000318113:Y199H	Y	-	1	0	CLDN22	184477771	0.029000	0.19370	0.651000	0.29564	0.026000	0.11368	0.963000	0.29293	0.176000	0.19873	-1.139000	0.01908	TAC	.	.	none		0.542	CLDN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361493.1		
NAA16	79612	hgsc.bcm.edu	37	13	41929296	41929296	+	Missense_Mutation	SNP	A	A	G	rs17062054	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:41929296A>G	ENST00000379406.3	+	10	1355	c.1031A>G	c.(1030-1032)gAa>gGa	p.E344G	RNU6-57P_ENST00000411348.1_RNA|NAA16_ENST00000379367.3_Missense_Mutation_p.E344G|NAA16_ENST00000403412.3_Missense_Mutation_p.E344G	NM_024561.4	NP_078837.3	Q6N069	NAA16_HUMAN	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	344			E -> G (in dbSNP:rs17062054).		N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ribosome binding (GO:0043022)			breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|urinary_tract(2)	31						ATAATCCAGGAACTTGTTACT	0.254													A|||	379	0.0756789	0.2723	0.0259	5008	,	,		14616	0.0		0.001	False		,,,				2504	0.0				p.E344G		Atlas-SNP	.											.	NAA16	74	.	0			c.A1031G						PASS	.	A	GLY/GLU,,GLY/GLU	1062,3342	336.3+/-304.3	129,804,1269	92.0	103.0	99.0		1031,924,1031	5.2	1.0	13	dbSNP_123	99	17,8567	6.4+/-24.3	0,17,4275	yes	missense,coding-synonymous,missense	NAA16	NM_001110798.1,NM_018527.3,NM_024561.4	98,,98	129,821,5544	GG,GA,AA		0.198,24.1144,8.3077	possibly-damaging,,possibly-damaging	344/430,308/312,344/865	41929296	1079,11909	2202	4292	6494	SO:0001583	missense	79612	exon10			TCCAGGAACTTGT	AL833341	CCDS9379.1, CCDS45044.1	13q14.11	2013-01-10	2010-01-14	2010-01-14	ENSG00000172766	ENSG00000172766		"""N(alpha)-acetyltransferase subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	26164	protein-coding gene	gene with protein product			"""NMDA receptor regulated 1-like"""	NARG1L		11483580, 19660095	Standard	NM_024561		Approved	FLJ22054, MGC40612, PRO2435	uc001uyf.2	Q6N069	OTTHUMG00000016791	ENST00000379406.3:c.1031A>G	13.37:g.41929296A>G	ENSP00000368716:p.Glu344Gly	33.0	0.0	0		36.0	13.0	0.361111	NM_001110798	B0QZ59|Q5VSP9|Q6P2D5|Q8N5J3|Q8N870	Missense_Mutation	SNP	ENST00000379406.3	37	CCDS9379.1	122	0.055860805860805864	111	0.22560975609756098	11	0.03038674033149171	0	0.0	0	0.0	A	20.6	4.024646	0.75390	0.241144	0.00198	ENSG00000172766	ENST00000379367;ENST00000379406;ENST00000403412	T;T;T	0.50001	0.76;0.76;0.76	5.23	5.23	0.72850	.	0.074309	0.56097	D	0.000039	T	0.00039	0.0001	.	.	.	0.18873	P	0.9999871049	P;P	0.48640	0.866;0.913	P;P	0.57548	0.61;0.823	T	0.00814	-1.1555	8	0.72032	D	0.01	-14.8273	15.0951	0.72226	1.0:0.0:0.0:0.0	rs17062054;rs52827917;rs59013357;rs17062054	344;344	Q6N069;Q6N069-4	NAA16_HUMAN;.	G	344	ENSP00000368674:E344G;ENSP00000368716:E344G;ENSP00000386103:E344G	ENSP00000368674:E344G	E	+	2	0	NAA16	40827296	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.480000	0.81109	1.980000	0.57719	0.533000	0.62120	GAA	A|0.919;G|0.081	0.081	strong		0.254	NAA16-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044672.2	NM_018527	
PELP1	27043	hgsc.bcm.edu	37	17	4586220	4586220	+	Silent	SNP	G	G	A	rs35109567	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4586220G>A	ENST00000574876.1	-	4	465	c.448C>T	c.(448-450)Ctg>Ttg	p.L150L	PELP1_ENST00000436683.2_Silent_p.L3L|AC091153.4_ENST00000441700.2_RNA|PELP1_ENST00000269230.7_Silent_p.L150L|PELP1_ENST00000301396.4_Silent_p.L150L|PELP1_ENST00000572293.1_Silent_p.L200L|PELP1_ENST00000570823.1_5'Flank			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	150					cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						GCCACGGCCAGCTCCATTGTG	0.557													g|||	138	0.0275559	0.1014	0.0058	5008	,	,		16714	0.0		0.0	False		,,,				2504	0.0				p.L150L		Atlas-SNP	.											.	PELP1	102	.	0			c.C448T						PASS	.			338,3568		15,308,1630	24.0	28.0	27.0		448	-3.3	1.0	17	dbSNP_126	27	5,8279		0,5,4137	no	coding-synonymous	PELP1	NM_014389.2		15,313,5767	AA,AG,GG		0.0604,8.6534,2.8138		150/1131	4586220	343,11847	1953	4142	6095	SO:0001819	synonymous_variant	27043	exon4			CGGCCAGCTCCAT		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"""proline, glutamic acid and leucine rich protein 1"""			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8		ENST00000574876.1:c.448C>T	17.37:g.4586220G>A		185.0	0.0	0		176.0	84.0	0.477273	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Silent	SNP	ENST00000574876.1	37	CCDS58503.1																																																																																			G|0.974;A|0.026	0.026	strong		0.557	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389	
AHSG	197	hgsc.bcm.edu	37	3	186338634	186338634	+	Missense_Mutation	SNP	G	G	A	rs77385737	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:186338634G>A	ENST00000273784.5	+	7	1098	c.1022G>A	c.(1021-1023)cGc>cAc	p.R341H	AHSG_ENST00000411641.2_Missense_Mutation_p.R340H	NM_001622.2	NP_001613.2	P02765	FETUA_HUMAN	alpha-2-HS-glycoprotein	340					acute-phase response (GO:0006953)|negative regulation of bone mineralization (GO:0030502)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of phosphorylation (GO:0042326)|ossification (GO:0001503)|pinocytosis (GO:0006907)|positive regulation of phagocytosis (GO:0050766)|regulation of bone mineralization (GO:0030500)|regulation of inflammatory response (GO:0050727)|skeletal system development (GO:0001501)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|kinase inhibitor activity (GO:0019210)			central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(2)|stomach(1)	22	all_cancers(143;3.64e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;3.27e-20)	GBM - Glioblastoma multiforme(93;0.0463)		CGGAAAACACGCACAGTGGTG	0.602													.|||	17	0.00339457	0.0121	0.0	5008	,	,		21835	0.0		0.001	False		,,,				2504	0.0				p.R340H		Atlas-SNP	.											AHSG,NS,carcinoma,+1,1	AHSG	40	1	0			c.G1019A						scavenged	.	G	HIS/ARG	59,4347	58.1+/-94.6	1,57,2145	81.0	77.0	79.0		1019	1.7	0.0	3	dbSNP_132	79	2,8598	2.2+/-6.3	0,2,4298	yes	missense	AHSG	NM_001622.2	29	1,59,6443	AA,AG,GG		0.0233,1.3391,0.469	probably-damaging	340/368	186338634	61,12945	2203	4300	6503	SO:0001583	missense	197	exon7			AAACACGCACAGT	D67013, M16961	CCDS3278.1	3q27.3	2006-02-22			ENSG00000145192	ENSG00000145192			349	protein-coding gene	gene with protein product		138680				9322749, 7736783	Standard	NM_001622		Approved	FETUA, A2HS, HSGA	uc003fqk.4	P02765	OTTHUMG00000156605	ENST00000273784.5:c.1022G>A	3.37:g.186338634G>A	ENSP00000273784:p.Arg341His	124.0	1.0	0.00806452		169.0	86.0	0.508876	NM_001622	A8K9N6|B2R7G1|O14961|O14962|Q9P152	Missense_Mutation	SNP	ENST00000273784.5	37		5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	g	9.995	1.232001	0.22626	0.013391	2.33E-4	ENSG00000145192	ENST00000411641;ENST00000541510;ENST00000273784	T;T	0.05258	3.47;3.47	4.63	1.7	0.24286	.	0.972799	0.08447	N	0.944617	T	0.04634	0.0126	L	0.44542	1.39	0.09310	N	1	B;B;B	0.10296	0.003;0.002;0.001	B;B;B	0.06405	0.002;0.0;0.0	T	0.38436	-0.9661	10	0.44086	T	0.13	-0.6739	7.4138	0.27032	0.3211:0.508:0.1709:0.0	.	406;340;341	F5H0Q5;P02765;C9JV77	.;FETUA_HUMAN;.	H	340;406;341	ENSP00000393887:R340H;ENSP00000273784:R341H	ENSP00000273784:R341H	R	+	2	0	AHSG	187821328	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.305000	0.08188	0.216000	0.20781	-0.344000	0.07964	CGC	G|0.996;A|0.004	0.004	strong		0.602	AHSG-002	NOVEL	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000344762.1	NM_001622	
GEMIN4	50628	hgsc.bcm.edu	37	17	649164	649164	+	Missense_Mutation	SNP	G	G	A	rs34519093	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:649164G>A	ENST00000319004.5	-	2	2237	c.2119C>T	c.(2119-2121)Cgc>Tgc	p.R707C	GEMIN4_ENST00000576778.1_Missense_Mutation_p.R696C	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	707					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		TTGCTGAAGCGGTCCAAGAGC	0.542													T|||	116	0.0231629	0.0832	0.0058	5008	,	,		19134	0.0		0.002	False		,,,				2504	0.0				p.R707C		Atlas-SNP	.											.	GEMIN4	116	.	0			c.C2119T						PASS	.	T	CYS/ARG	263,3613		6,251,1681	28.0	29.0	29.0		2119	-6.4	0.0	17	dbSNP_126	29	4,8282		0,4,4139	yes	missense	GEMIN4	NM_015721.2	180	6,255,5820	AA,AG,GG		0.0483,6.7853,2.1954	benign	707/1059	649164	267,11895	1938	4143	6081	SO:0001583	missense	50628	exon2			TGAAGCGGTCCAA	AF177341	CCDS45559.1	17p13.3	2008-07-18				ENSG00000179409			15717	protein-coding gene	gene with protein product	"""HCC-associated protein 1"", ""component of gems 4"""	606969				10725331	Standard	NM_015721		Approved	HHRF-1, DKFZP434B131, p97, DKFZP434D174, HC56, HCAP1	uc002frs.1	P57678		ENST00000319004.5:c.2119C>T	17.37:g.649164G>A	ENSP00000321706:p.Arg707Cys	46.0	0.0	0		35.0	22.0	0.628571	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Missense_Mutation	SNP	ENST00000319004.5	37	CCDS45559.1	50	0.022893772893772892	46	0.09349593495934959	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	T	8.559	0.877352	0.17395	0.067853	4.83E-4	ENSG00000179409	ENST00000319004	T	0.05855	3.38	5.56	-6.42	0.01932	.	0.696678	0.15313	N	0.268978	T	0.00109	0.0003	N	0.02011	-0.69	0.25173	N	0.990269	B	0.02656	0.0	B	0.01281	0.0	T	0.37454	-0.9705	10	0.48119	T	0.1	-0.0898	4.5907	0.12306	0.2625:0.4379:0.0738:0.2258	rs34519093	707	P57678	GEMI4_HUMAN	C	707	ENSP00000321706:R707C	ENSP00000321706:R707C	R	-	1	0	GEMIN4	595914	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.501000	0.02281	-2.443000	0.00548	-3.149000	0.00058	CGC	G|0.978;A|0.022	0.022	strong		0.542	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721	
INTS1	26173	hgsc.bcm.edu	37	7	1538174	1538174	+	Silent	SNP	C	C	T	rs143126716	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:1538174C>T	ENST00000404767.3	-	10	1384	c.1299G>A	c.(1297-1299)gcG>gcA	p.A433A	INTS1_ENST00000389470.4_Silent_p.A561A|INTS1_ENST00000493531.1_5'Flank	NM_001080453.2	NP_001073922.2	Q8N201	INT1_HUMAN	integrator complex subunit 1	433					inner cell mass cell proliferation (GO:0001833)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|snRNA processing (GO:0016180)|U2 snRNA 3'-end processing (GO:0034474)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				autonomic_ganglia(1)|cervix(1)|endometrium(14)|kidney(3)|large_intestine(7)|lung(24)|ovary(1)|prostate(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	62		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|OV - Ovarian serous cystadenocarcinoma(56;6.99e-15)		TGTCCTTGTGCGCGCTCAGCA	0.652													C|||	63	0.0125799	0.0431	0.0086	5008	,	,		10067	0.0		0.0	False		,,,				2504	0.0				p.A433A		Atlas-SNP	.											INTS1,NS,carcinoma,-1,1	INTS1	145	1	0			c.G1299A						PASS	.			125,4145		4,117,2014	85.0	97.0	93.0		1299	-9.7	0.0	7	dbSNP_134	93	6,8488		0,6,4241	no	coding-synonymous	INTS1	NM_001080453.2		4,123,6255	TT,TC,CC		0.0706,2.9274,1.0263		433/2191	1538174	131,12633	2135	4247	6382	SO:0001819	synonymous_variant	26173	exon10			CTTGTGCGCGCTC	AB037861	CCDS47526.1	7p22.3	2009-11-06			ENSG00000164880	ENSG00000164880			24555	protein-coding gene	gene with protein product		611345				16239144	Standard	NM_001080453		Approved	DKFZp586J0619, KIAA1440, INT1, NET28	uc003skn.2	Q8N201	OTTHUMG00000151449	ENST00000404767.3:c.1299G>A	7.37:g.1538174C>T		131.0	0.0	0		166.0	166.0	1	NM_001080453	A6NJ44|Q6NT70|Q6UX74|Q8WV40|Q96D36|Q9NTD1|Q9P2A8|Q9Y3W8	Silent	SNP	ENST00000404767.3	37	CCDS47526.1																																																																																			C|0.988;T|0.012	0.012	strong		0.652	INTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323683.1		
AWAT1	158833	hgsc.bcm.edu	37	X	69455671	69455671	+	Missense_Mutation	SNP	G	G	A	rs61995694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:69455671G>A	ENST00000374521.3	+	2	223	c.182G>A	c.(181-183)cGa>cAa	p.R61Q	AWAT1_ENST00000480702.1_3'UTR	NM_001013579.2	NP_001013597.1	Q58HT5	AWAT1_HUMAN	acyl-CoA wax alcohol acyltransferase 1	61					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	long-chain-alcohol O-fatty-acyltransferase activity (GO:0047196)			breast(2)|central_nervous_system(1)|large_intestine(4)|lung(3)|ovary(4)|skin(1)	15						ACCCCAGAGCGAGGTAAGACT	0.512													g|||	113	0.0299338	0.0825	0.0058	3775	,	,		15173	0.0		0.0	False		,,,				2504	0.0				p.R61Q		Atlas-SNP	.											.	AWAT1	74	.	0			c.G182A						PASS	.		GLN/ARG	342,3493		13,270,46,1349,525	184.0	144.0	158.0		182	1.1	0.6	X	dbSNP_129	158	2,6726		0,2,0,2426,1872	yes	missense	AWAT1	NM_001013579.2	43	13,272,46,3775,2397	AA,AG,A,GG,G		0.0297,8.9179,3.2567	benign	61/329	69455671	344,10219	2203	4300	6503	SO:0001583	missense	158833	exon2			CAGAGCGAGGTAA	BC039181	CCDS35321.1	Xq13.1	2010-01-25	2009-02-23	2009-02-23	ENSG00000204195	ENSG00000204195			23252	protein-coding gene	gene with protein product		300924	"""diacylglycerol O-acyltransferase 2-like 3"""	DGAT2L3		14970677, 15671038	Standard	NM_001013579		Approved		uc004dxy.3	Q58HT5	OTTHUMG00000021773	ENST00000374521.3:c.182G>A	X.37:g.69455671G>A	ENSP00000363645:p.Arg61Gln	127.0	0.0	0		119.0	49.0	0.411765	NM_001013579	Q5JT21|Q6IEE4	Missense_Mutation	SNP	ENST00000374521.3	37	CCDS35321.1	46	0.027727546714888487	32	0.06808510638297872	3	0.008287292817679558	0	0.0	0	0.0	g	2.423	-0.332574	0.05314	0.089179	2.97E-4	ENSG00000204195	ENST00000374521	T	0.17528	2.27	5.03	1.06	0.20224	.	0.715401	0.13082	N	0.415230	T	0.00241	0.0007	N	0.04162	-0.26	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.09377	0.004	T	0.42749	-0.9433	9	0.02654	T	1	-0.016	7.6926	0.28577	0.6396:0.0:0.3604:0.0	rs61995694	61	Q58HT5	AWAT1_HUMAN	Q	61	ENSP00000363645:R61Q	ENSP00000363645:R61Q	R	+	2	0	AWAT1	69372396	0.002000	0.14202	0.579000	0.28588	0.849000	0.48306	0.034000	0.13776	-0.029000	0.13827	-0.372000	0.07161	CGA	G|0.967;A|0.033	0.033	strong		0.512	AWAT1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057066.3	NM_001013579	
SCAF11	9169	hgsc.bcm.edu	37	12	46339033	46339033	+	Splice_Site	SNP	A	A	G	rs11183245	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:46339033A>G	ENST00000369367.3	-	6	695	c.462T>C	c.(460-462)caT>caC	p.H154H	SCAF11_ENST00000419565.2_Splice_Site_p.H154H	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	154					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(17)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	69						GTAACTTACTATGTATCCACT	0.318													A|||	66	0.0131789	0.0477	0.0029	5008	,	,		17740	0.0		0.001	False		,,,				2504	0.0				p.H154H		Atlas-SNP	.											.	SCAF11	145	.	0			c.T462C						PASS	.	A		167,3485		4,159,1663	111.0	105.0	107.0		462	-1.8	0.0	12	dbSNP_120	107	0,8134		0,0,4067	yes	coding-synonymous-near-splice	SCAF11	NM_004719.2		4,159,5730	GG,GA,AA		0.0,4.5728,1.4169		154/1464	46339033	167,11619	1826	4067	5893	SO:0001630	splice_region_variant	9169	exon6			CTTACTATGTATC	Y11251	CCDS8748.2	12q13.11	2013-01-09	2011-01-10	2011-01-10	ENSG00000139218	ENSG00000139218		"""RING-type (C3HC4) zinc fingers"""	10784	protein-coding gene	gene with protein product		603668	"""splicing factor, arginine/serine-rich 2, interacting protein"", ""serine/arginine-rich splicing factor 2, interacting protein"""	SFRS2IP, SRSF2IP		9224939, 9447963	Standard	NM_004719		Approved	SIP1, SRRP129, CASP11	uc001rox.3	Q99590	OTTHUMG00000149930	ENST00000369367.3:c.463+1T>C	12.37:g.46339033A>G		97.0	0.0	0		90.0	42.0	0.466667	NM_004719	A6NEU9|A6NLW5|Q8IW59	Silent	SNP	ENST00000369367.3	37	CCDS8748.2																																																																																			A|0.972;G|0.028	0.028	strong		0.318	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719	Silent
SYNE2	23224	hgsc.bcm.edu	37	14	64450479	64450479	+	Missense_Mutation	SNP	A	A	G	rs78191145	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:64450479A>G	ENST00000344113.4	+	18	2238	c.2026A>G	c.(2026-2028)Aaa>Gaa	p.K676E	SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Missense_Mutation_p.K676E|SYNE2_ENST00000358025.3_Missense_Mutation_p.K676E	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	676					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		ACTGATGATAAAAAAACAGGA	0.303													A|||	31	0.0061901	0.0234	0.0	5008	,	,		14554	0.0		0.0	False		,,,				2504	0.0				p.K676E		Atlas-SNP	.											.	SYNE2	577	.	0			c.A2026G						PASS	.	A	GLU/LYS,GLU/LYS	85,3501		3,79,1711	40.0	39.0	39.0		2026,2026	3.0	0.1	14	dbSNP_131	39	0,8130		0,0,4065	yes	missense,missense	SYNE2	NM_015180.4,NM_182914.2	56,56	3,79,5776	GG,GA,AA		0.0,2.3703,0.7255	probably-damaging,probably-damaging	676/6886,676/6908	64450479	85,11631	1793	4065	5858	SO:0001583	missense	23224	exon18			ATGATAAAAAAAC	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.2026A>G	14.37:g.64450479A>G	ENSP00000341781:p.Lys676Glu	149.0	0.0	0		138.0	80.0	0.57971	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Missense_Mutation	SNP	ENST00000344113.4	37	CCDS41963.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	A	10.57	1.387852	0.25031	0.023703	0.0	ENSG00000054654	ENST00000358025;ENST00000344113;ENST00000554584;ENST00000261678	T;T;T	0.57436	0.76;0.76;0.4	5.56	3.05	0.35203	.	0.110909	0.38778	N	0.001580	T	0.24160	0.0585	L	0.44542	1.39	0.20196	N	0.999925	P;P	0.46064	0.798;0.872	B;P	0.45856	0.3;0.495	T	0.16100	-1.0414	10	0.52906	T	0.07	.	11.2166	0.48830	0.565:0.435:0.0:0.0	.	676;676	Q8WXH0;Q8WXH0-2	SYNE2_HUMAN;.	E	676	ENSP00000350719:K676E;ENSP00000341781:K676E;ENSP00000452570:K676E	ENSP00000261678:K676E	K	+	1	0	SYNE2	63520232	0.770000	0.28543	0.119000	0.21687	0.552000	0.35366	1.368000	0.34216	0.909000	0.36697	0.528000	0.53228	AAA	A|0.996;G|0.004	0.004	strong		0.303	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
SDC3	9672	hgsc.bcm.edu	37	1	31349795	31349795	+	Silent	SNP	G	G	A	rs142879690	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:31349795G>A	ENST00000339394.6	-	3	648	c.474C>T	c.(472-474)acC>acT	p.T158T	SDC3_ENST00000471567.1_5'UTR|SDC3_ENST00000336798.7_Silent_p.T100T	NM_014654.3	NP_055469.3	O75056	SDC3_HUMAN	syndecan 3	158	Ser/Thr-rich (mucin-like).				carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Myeloproliferative disorder(586;0.0393)|Colorectal(325;0.0466)|all_neural(195;0.0966)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)		STAD - Stomach adenocarcinoma(196;0.0197)|READ - Rectum adenocarcinoma(331;0.0649)		TAGTGGAGACGGTGGTGGCTC	0.667													G|||	5	0.000998403	0.0038	0.0	5008	,	,		12182	0.0		0.0	False		,,,				2504	0.0				p.T158T		Atlas-SNP	.											.	SDC3	45	.	0			c.C474T						PASS	.	G		21,4385	25.3+/-52.1	0,21,2182	36.0	38.0	37.0		474	-1.0	0.3	1	dbSNP_134	37	0,8598		0,0,4299	no	coding-synonymous	SDC3	NM_014654.3		0,21,6481	AA,AG,GG		0.0,0.4766,0.1615		158/443	31349795	21,12983	2203	4299	6502	SO:0001819	synonymous_variant	9672	exon3			GGAGACGGTGGTG	AF248634	CCDS30661.1	1p35.2	2013-09-19	2007-02-15		ENSG00000162512	ENSG00000162512		"""Proteoglycans / Cell Surface : Syndecans"""	10660	protein-coding gene	gene with protein product	"""syndecan proteoglycan 3"""	186357	"""syndecan 3 (N-syndecan)"""			1556152, 11527150	Standard	NM_014654		Approved	N-syndecan, SYND3	uc001bse.2	O75056	OTTHUMG00000043646	ENST00000339394.6:c.474C>T	1.37:g.31349795G>A		119.0	0.0	0		141.0	70.0	0.496454	NM_014654	Q5T1Z6|Q5T1Z7|Q96CT3|Q96PR8	Silent	SNP	ENST00000339394.6	37	CCDS30661.1																																																																																			G|0.998;A|0.002	0.002	strong		0.667	SDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102017.1	NM_014654	
ELL	8178	hgsc.bcm.edu	37	19	18561420	18561420	+	Silent	SNP	C	C	T	rs34078075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18561420C>T	ENST00000262809.4	-	8	1403	c.1332G>A	c.(1330-1332)tcG>tcA	p.S444S	ELL_ENST00000596124.3_Silent_p.S311S	NM_006532.3	NP_006523.1	P55199	ELL_HUMAN	elongation factor RNA polymerase II	444					gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of viral transcription (GO:0050434)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	phosphatase binding (GO:0019902)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(5)|prostate(1)	19				GBM - Glioblastoma multiforme(1328;7.81e-07)		GCTTGCTGCGCGAGGGGCTGC	0.687			T	MLL	AL								C|||	107	0.0213658	0.0681	0.0144	5008	,	,		14591	0.0		0.007	False		,,,				2504	0.0				p.S444S		Atlas-SNP	.		Dom	yes		19	19p13.1	8178	ELL gene (11-19 lysine-rich leukemia gene)		L	.	ELL	52	.	0			c.G1332A						PASS	.	C		273,4131		5,263,1934	35.0	21.0	26.0		1332	-5.8	0.0	19	dbSNP_126	26	55,8539		0,55,4242	no	coding-synonymous	ELL	NM_006532.3		5,318,6176	TT,TC,CC		0.64,6.1989,2.5235		444/622	18561420	328,12670	2202	4297	6499	SO:0001819	synonymous_variant	8178	exon8			GCTGCGCGAGGGG	U16282	CCDS12380.1	19p13.1	2012-04-17	2005-05-23			ENSG00000105656		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23114	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 68"""	600284	"""chromosome 19 open reading frame 17"""	C19orf17		7991593, 8596958	Standard	NM_006532		Approved	Men, ELL1, PPP1R68	uc002njh.3	P55199		ENST00000262809.4:c.1332G>A	19.37:g.18561420C>T		189.0	0.0	0		266.0	134.0	0.503759	NM_006532		Silent	SNP	ENST00000262809.4	37	CCDS12380.1																																																																																			C|0.976;T|0.024	0.024	strong		0.687	ELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466362.1	NM_006532	
DDX27	55661	hgsc.bcm.edu	37	20	47858695	47858695	+	Missense_Mutation	SNP	G	G	A	rs143843778	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:47858695G>A	ENST00000371764.4	+	18	2170	c.2161G>A	c.(2161-2163)Gcc>Acc	p.A721T	ZNFX1_ENST00000371754.4_Intron|DDX27_ENST00000484427.1_3'UTR|ZNFX1_ENST00000469991.1_Intron	NM_017895.7	NP_060365.7	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	721						nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	45			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			GAATCGCAGAGCCAAGCGGGC	0.567													G|||	17	0.00339457	0.0121	0.0014	5008	,	,		17319	0.0		0.0	False		,,,				2504	0.0				p.A721T		Atlas-SNP	.											.	DDX27	74	.	0			c.G2161A						PASS	.	G	THR/ALA	54,4352	54.9+/-90.9	0,54,2149	48.0	45.0	46.0		2161	1.7	1.0	20	dbSNP_134	46	0,8600		0,0,4300	yes	missense	DDX27	NM_017895.7	58	0,54,6449	AA,AG,GG		0.0,1.2256,0.4152	benign	721/797	47858695	54,12952	2203	4300	6503	SO:0001583	missense	55661	exon18			CGCAGAGCCAAGC	AL049766	CCDS13416.1	20q13.13	2010-07-06	2003-06-13		ENSG00000124228	ENSG00000124228		"""DEAD-boxes"""	15837	protein-coding gene	gene with protein product			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 27"""				Standard	NM_017895		Approved	dJ686N3.1, DRS1	uc002xuh.3	Q96GQ7	OTTHUMG00000033072	ENST00000371764.4:c.2161G>A	20.37:g.47858695G>A	ENSP00000360828:p.Ala721Thr	139.0	0.0	0		133.0	56.0	0.421053	NM_017895	A0AVB6|B7ZLY1|Q5VXM7|Q8WYG4|Q969N7|Q96F57|Q96L97|Q9BWY9|Q9BXF0|Q9H990|Q9NWU3|Q9P0C2|Q9UGD6	Missense_Mutation	SNP	ENST00000371764.4	37	CCDS13416.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	G	12.62	1.992729	0.35131	0.012256	0.0	ENSG00000124228	ENST00000371764	T	0.01438	4.89	5.83	1.74	0.24563	.	0.354569	0.32473	N	0.006059	T	0.00695	0.0023	N	0.22421	0.69	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.58222	-0.7674	10	0.17369	T	0.5	-2.8822	4.7211	0.12918	0.3373:0.1498:0.513:0.0	.	721	Q96GQ7	DDX27_HUMAN	T	721	ENSP00000360828:A721T	ENSP00000360828:A721T	A	+	1	0	DDX27	47292102	0.998000	0.40836	0.996000	0.52242	0.995000	0.86356	0.954000	0.29175	0.098000	0.17522	0.561000	0.74099	GCC	G|0.996;A|0.004	0.004	strong		0.567	DDX27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080485.1		
OR8D2	283160	hgsc.bcm.edu	37	11	124190036	124190036	+	Missense_Mutation	SNP	G	G	A	rs61735123	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124190036G>A	ENST00000357438.2	-	1	148	c.58C>T	c.(58-60)Cgc>Tgc	p.R20C		NM_001002918.1	NP_001002918.1	Q9GZM6	OR8D2_HUMAN	olfactory receptor, family 8, subfamily D, member 2	20						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	25		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0525)		AGTTCTGGGCGTTGTGTCAAG	0.438													A|||	134	0.0267572	0.093	0.013	5008	,	,		17109	0.001		0.0	False		,,,				2504	0.001				p.R20C		Atlas-SNP	.											.	OR8D2	65	.	0			c.C58T						PASS	.	A	CYS/ARG	378,4022	188.5+/-214.9	16,346,1838	67.0	67.0	67.0		58	-6.8	0.0	11	dbSNP_129	67	5,8593	4.3+/-15.6	0,5,4294	yes	missense	OR8D2	NM_001002918.1	180	16,351,6132	AA,AG,GG		0.0582,8.5909,2.9466	benign	20/312	124190036	383,12615	2200	4299	6499	SO:0001583	missense	283160	exon1			CTGGGCGTTGTGT	AF162668	CCDS31707.1	11q24.1	2012-08-09			ENSG00000197263	ENSG00000197263		"""GPCR / Class A : Olfactory receptors"""	8482	protein-coding gene	gene with protein product							Standard	NM_001002918		Approved		uc010sah.2	Q9GZM6	OTTHUMG00000165978	ENST00000357438.2:c.58C>T	11.37:g.124190036G>A	ENSP00000350022:p.Arg20Cys	61.0	0.0	0		66.0	28.0	0.424242	NM_001002918	B9EH49|Q6IFR0	Missense_Mutation	SNP	ENST00000357438.2	37	CCDS31707.1	33	0.01510989010989011	28	0.056910569105691054	5	0.013812154696132596	0	0.0	0	0.0	g	6.776	0.512072	0.12944	0.085909	5.82E-4	ENSG00000197263	ENST00000357438	T	0.00438	7.42	3.42	-6.85	0.01681	.	1.442220	0.04657	N	0.408191	T	0.00012	0.0000	N	0.25380	0.74	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.35943	-0.9768	10	0.72032	D	0.01	.	6.2183	0.20667	0.4743:0.0:0.1929:0.3328	.	20	Q9GZM6	OR8D2_HUMAN	C	20	ENSP00000350022:R20C	ENSP00000350022:R20C	R	-	1	0	OR8D2	123695246	0.000000	0.05858	0.000000	0.03702	0.072000	0.16883	-2.227000	0.01210	-3.085000	0.00249	-0.684000	0.03749	CGC	G|0.972;A|0.028	0.028	strong		0.438	OR8D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387286.1	NM_001002918	
CCHCR1	54535	hgsc.bcm.edu	37	6	31118304	31118304	+	Silent	SNP	C	C	T	rs139910767		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31118304C>T	ENST00000376266.5	-	7	995	c.873G>A	c.(871-873)gcG>gcA	p.A291A	CCHCR1_ENST00000480060.1_Intron|CCHCR1_ENST00000451521.2_Silent_p.A344A|CCHCR1_ENST00000396263.2_Silent_p.A291A|CCHCR1_ENST00000396268.3_Silent_p.A380A	NM_019052.3	NP_061925.2	Q8TD31	CCHCR_HUMAN	coiled-coil alpha-helical rod protein 1	291					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein export from nucleus (GO:0006611)	centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(13)|skin(1)	23						GCAGCAGCTCCGCGGTGGCAT	0.657													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19191	0.0		0.0	False		,,,				2504	0.0				p.A380A		Atlas-SNP	.											.	CCHCR1	68	.	0			c.G1140A						PASS	.	C	,,	3,3019		0,3,1508	48.0	34.0	39.0		1032,1140,873	-9.5	0.0	6	dbSNP_134	39	0,5414		0,0,2707	no	coding-synonymous,coding-synonymous,coding-synonymous	CCHCR1	NM_001105563.1,NM_001105564.1,NM_019052.3	,,	0,3,4215	TT,TC,CC		0.0,0.0993,0.0356	,,	344/836,380/872,291/783	31118304	3,8433	1511	2707	4218	SO:0001819	synonymous_variant	54535	exon7			CAGCTCCGCGGTG	AF216493	CCDS4695.1, CCDS43445.1, CCDS47397.1	6p21.3	2007-08-01	2005-02-15	2005-02-16	ENSG00000204536	ENSG00000204536			13930	protein-coding gene	gene with protein product		605310	"""chromosome 6 open reading frame 18"""	C6orf18		10888604, 10545595	Standard	NM_019052		Approved	HCR	uc003nsp.4	Q8TD31	OTTHUMG00000031112	ENST00000376266.5:c.873G>A	6.37:g.31118304C>T		76.0	0.0	0		93.0	45.0	0.483871	NM_001105564	A2ABH6|E9PE84|Q2TB67|Q5SQ82|Q5STE9|Q9NRK8|Q9NWY9|Q9NXJ4|Q9NXK3|Q9Y6W1|Q9Y6W2	Silent	SNP	ENST00000376266.5	37	CCDS4695.1																																																																																			C|0.999;T|0.001	0.001	strong		0.657	CCHCR1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076190.5	NM_019052	
LRP4	4038	hgsc.bcm.edu	37	11	46914526	46914526	+	Silent	SNP	C	C	T	rs61741501	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:46914526C>T	ENST00000378623.1	-	13	1937	c.1695G>A	c.(1693-1695)gaG>gaA	p.E565E		NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	565					dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		CAACTTACCCCTCCATGGGAT	0.567													C|||	306	0.0611022	0.2216	0.0173	5008	,	,		17231	0.0		0.001	False		,,,				2504	0.0				p.E565E		Atlas-SNP	.											.	LRP4	160	.	0			c.G1695A						PASS	.	C		763,3639	303.2+/-287.8	67,629,1505	43.0	41.0	42.0		1695	2.7	1.0	11	dbSNP_129	42	3,8595	2.2+/-6.3	0,3,4296	no	coding-synonymous	LRP4	NM_002334.3		67,632,5801	TT,TC,CC		0.0349,17.333,5.8923		565/1906	46914526	766,12234	2201	4299	6500	SO:0001819	synonymous_variant	4038	exon13			TTACCCCTCCATG	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"""Low density lipoprotein receptors"""	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.1695G>A	11.37:g.46914526C>T		66.0	0.0	0		56.0	29.0	0.517857	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Silent	SNP	ENST00000378623.1	37	CCDS31478.1																																																																																			C|0.947;T|0.053	0.053	strong		0.567	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334	
CATSPER3	347732	hgsc.bcm.edu	37	5	134347241	134347241	+	Silent	SNP	T	T	C	rs7719874	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:134347241T>C	ENST00000282611.6	+	8	1211	c.1125T>C	c.(1123-1125)caT>caC	p.H375H		NM_178019.2	NP_821138.1	Q86XQ3	CTSR3_HUMAN	cation channel, sperm associated 3	375					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|endoplasmic reticulum (GO:0005783)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AGATCGTGCATGTGCTGAGCC	0.562													T|||	293	0.0585064	0.2126	0.0144	5008	,	,		19649	0.0		0.002	False		,,,				2504	0.0				p.H375H		Atlas-SNP	.											.	CATSPER3	38	.	0			c.T1125C						PASS	.	T		785,3621	317.2+/-295.0	66,653,1484	88.0	76.0	80.0		1125	-5.6	0.1	5	dbSNP_116	80	7,8593	6.4+/-24.3	0,7,4293	no	coding-synonymous	CATSPER3	NM_178019.2		66,660,5777	CC,CT,TT		0.0814,17.8166,6.0895		375/399	134347241	792,12214	2203	4300	6503	SO:0001819	synonymous_variant	347732	exon8			CGTGCATGTGCTG	AF432876	CCDS4181.1	5q31.2	2011-07-05			ENSG00000152705	ENSG00000152705		"""Voltage-gated ion channels / Cation channels, sperm associated"""	20819	protein-coding gene	gene with protein product		609120				12646162, 12932298, 17227845, 16382101	Standard	NM_178019		Approved	CACRC	uc003lag.3	Q86XQ3	OTTHUMG00000129137	ENST00000282611.6:c.1125T>C	5.37:g.134347241T>C		77.0	0.0	0		83.0	39.0	0.46988	NM_178019	Q86XS6	Silent	SNP	ENST00000282611.6	37	CCDS4181.1																																																																																			T|0.929;C|0.071	0.071	strong		0.562	CATSPER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251191.2	NM_178019	
ASMTL	8623	hgsc.bcm.edu	37	X	1522330	1522330	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:1522330C>T	ENST00000381317.3	-	13	1730	c.1698G>A	c.(1696-1698)gcG>gcA	p.A566A	ASMTL_ENST00000534940.1_Silent_p.A508A|ASMTL_ENST00000381333.4_Silent_p.A550A|ASMTL-AS1_ENST00000420411.2_RNA|ASMTL-AS1_ENST00000602357.1_RNA|ASMTL_ENST00000416733.2_Silent_p.A490A|ASMTL-AS1_ENST00000419737.2_RNA|ASMTL-AS1_ENST00000443929.1_RNA|ASMTL-AS1_ENST00000425740.2_RNA	NM_004192.3	NP_004183.2	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like	566	ASMT-like.					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)				GGGCGCGCTGCGCCACCCTCT	0.652													c|||	79	0.0157748	0.059	0.0014	5008	,	,		19966	0.0		0.0	False		,,,				2504	0.0				p.A566A		Atlas-SNP	.											.	ASMTL	56	.	0			c.G1698A						PASS	.		,,	259,3999		9,241,1879	76.0	84.0	81.0		1524,1650,1698	0.3	0.0	X	dbSNP_134	81	2,8470		0,2,4234	no	coding-synonymous,coding-synonymous,coding-synonymous	ASMTL	NM_001173473.1,NM_001173474.1,NM_004192.3	,,	9,243,6113	TT,TC,CC		0.0236,6.0827,2.0503	,,	508/564,550/606,566/622	1522330	261,12469	2129	4236	6365	SO:0001819	synonymous_variant	8623	exon13			GCGCTGCGCCACC	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.1698G>A	X.37:g.1522330C>T		154.0	0.0	0		189.0	98.0	0.518519	NM_004192	B4DX75|F5GXH4|J3JS33|Q5JQ53|Q8NBH5|Q96G02|Q9BUL6	Silent	SNP	ENST00000381317.3	37	CCDS43917.1																																																																																			C|0.982;T|0.018	0.018	strong		0.652	ASMTL-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055595.1	NM_004192	
ABCC1	4363	hgsc.bcm.edu	37	16	16184366	16184366	+	Silent	SNP	G	G	T	rs28364004	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:16184366G>T	ENST00000399410.3	+	19	2740	c.2565G>T	c.(2563-2565)ctG>ctT	p.L855L	ABCC1_ENST00000399408.2_Silent_p.L855L|ABCC1_ENST00000351154.5_Silent_p.L796L|ABCC1_ENST00000345148.5_Silent_p.L855L|ABCC1_ENST00000349029.5_Silent_p.L740L|ABCC1_ENST00000346370.5_Silent_p.L799L	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	855	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	ACCAGGAGCTGCTGGCTCGAG	0.607													G|||	24	0.00479233	0.0136	0.0072	5008	,	,		19519	0.0		0.001	False		,,,				2504	0.0				p.L855L		Atlas-SNP	.											.	ABCC1	156	.	0			c.G2565T						PASS	.	G	,,,,	40,4072		0,40,2016	34.0	36.0	36.0		2565,2388,2397,2220,2565	3.3	1.0	16	dbSNP_126	36	7,8397		0,7,4195	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ABCC1	NM_004996.3,NM_019862.2,NM_019898.2,NM_019899.2,NM_019900.2	,,,,	0,47,6211	TT,TG,GG		0.0833,0.9728,0.3755	,,,,	855/1532,796/1473,799/1476,740/1417,855/1467	16184366	47,12469	2056	4202	6258	SO:0001819	synonymous_variant	4363	exon19			GGAGCTGCTGGCT	L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"""ATP binding cassette transporters / subfamily C"""	51	protein-coding gene	gene with protein product		158343	"""multidrug resistance associated protein 1"""	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.2565G>T	16.37:g.16184366G>T		66.0	0.0	0		72.0	31.0	0.430556	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Silent	SNP	ENST00000399410.3	37	CCDS42122.1																																																																																			G|0.983;T|0.017	0.017	strong		0.607	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996	
MAN2B1	4125	hgsc.bcm.edu	37	19	12766624	12766624	+	Missense_Mutation	SNP	C	C	A	rs377104016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12766624C>A	ENST00000456935.2	-	14	1754	c.1714G>T	c.(1714-1716)Gcc>Tcc	p.A572S	MAN2B1_ENST00000495617.1_5'Flank|MAN2B1_ENST00000221363.4_Missense_Mutation_p.A571S	NM_000528.3|NM_001173498.1	NP_000519.2|NP_001166969.1	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	572					cellular protein modification process (GO:0006464)|mannose metabolic process (GO:0006013)|protein deglycosylation (GO:0006517)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)	p.A572T(1)		breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						AAGCCCAGGGCGGGCAGTGAG	0.612													C|||	2	0.000399361	0.0	0.0	5008	,	,		17585	0.0		0.0	False		,,,				2504	0.002				p.A572S		Atlas-SNP	.											MAN2B1,NS,carcinoma,0,1	MAN2B1	91	1	1	Substitution - Missense(1)	prostate(1)	c.G1714T						PASS	.	C	SER/ALA,SER/ALA	3,4403	8.1+/-20.4	0,3,2200	58.0	64.0	62.0		1714,1711	4.0	1.0	19		62	0,8600		0,0,4300	no	missense,missense	MAN2B1	NM_000528.3,NM_001173498.1	99,99	0,3,6500	AA,AC,CC		0.0,0.0681,0.0231	benign,benign	572/1012,571/1011	12766624	3,13003	2203	4300	6503	SO:0001583	missense	4125	exon14			CCAGGGCGGGCAG		CCDS32919.1, CCDS54224.1	19p13.2	2013-09-20			ENSG00000104774	ENSG00000104774	3.2.1.24		6826	protein-coding gene	gene with protein product		609458		MANB			Standard	NM_000528		Approved	LAMAN	uc002mub.2	O00754	OTTHUMG00000156397	ENST00000456935.2:c.1714G>T	19.37:g.12766624C>A	ENSP00000395473:p.Ala572Ser	32.0	0.0	0		37.0	21.0	0.567568	NM_000528	G5E928|O15330|Q16680|Q93094|Q9BW13	Missense_Mutation	SNP	ENST00000456935.2	37	CCDS32919.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.66|19.66	3.869012|3.869012	0.72065|0.72065	6.81E-4|6.81E-4	0.0|0.0	ENSG00000104774|ENSG00000104774	ENST00000456935;ENST00000536796;ENST00000221363|ENST00000433513	T;T|.	0.81163|.	-1.46;-1.46|.	5.16|5.16	4.03|4.03	0.46877|0.46877	Glycosyl hydrolases 38, C-terminal (1);Glycosyl hydrolase, family 13, all-beta (1);Glycoside hydrolase-type carbohydrate-binding (1);|.	0.000000|.	0.33712|.	N|.	0.004633|.	T|T	0.76593|0.76593	0.4009|0.4009	M|M	0.85041|0.85041	2.73|2.73	0.39975|0.39975	D|D	0.974849|0.974849	P;D|.	0.58970|.	0.928;0.984|.	P;P|.	0.59288|.	0.774;0.855|.	T|T	0.80151|0.80151	-0.1502|-0.1502	10|5	0.54805|.	T|.	0.06|.	-16.9432|-16.9432	12.4629|12.4629	0.55741|0.55741	0.0:0.8153:0.1847:0.0|0.0:0.8153:0.1847:0.0	.|.	571;572|.	G5E928;O00754|.	.;MA2B1_HUMAN|.	S|L	572;511;571|107	ENSP00000395473:A572S;ENSP00000221363:A571S|.	ENSP00000221363:A571S|.	A|R	-|-	1|2	0|0	MAN2B1|MAN2B1	12627624|12627624	0.995000|0.995000	0.38212|0.38212	0.986000|0.986000	0.45419|0.45419	0.762000|0.762000	0.43233|0.43233	2.575000|2.575000	0.46025|0.46025	2.389000|2.389000	0.81357|0.81357	0.313000|0.313000	0.20887|0.20887	GCC|CGC	.	.	weak		0.612	MAN2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344062.1		
ACVR2B	93	hgsc.bcm.edu	37	3	38523754	38523754	+	Silent	SNP	C	C	T	rs149695736	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:38523754C>T	ENST00000352511.4	+	9	1612	c.1140C>T	c.(1138-1140)gcC>gcT	p.A380A		NM_001106.3	NP_001097.2	Q13705	AVR2B_HUMAN	activin A receptor, type IIB	380	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|determination of left/right symmetry (GO:0007368)|embryonic foregut morphogenesis (GO:0048617)|gastrulation with mouth forming second (GO:0001702)|heart development (GO:0007507)|insulin secretion (GO:0030073)|kidney development (GO:0001822)|lung development (GO:0030324)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm development (GO:0007498)|odontogenesis of dentin-containing tooth (GO:0042475)|organ growth (GO:0035265)|palate development (GO:0060021)|pancreas development (GO:0031016)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|post-embryonic development (GO:0009791)|regulation of transcription, DNA-templated (GO:0006355)|response to glucose (GO:0009749)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|venous blood vessel development (GO:0060841)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)			lung(1)	1	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0565)|Kidney(284;0.071)		AGAGAGATGCCTTCCTGCGCA	0.572													C|||	8	0.00159744	0.0061	0.0	5008	,	,		21138	0.0		0.0	False		,,,				2504	0.0				p.A380A		Atlas-SNP	.											ACVR2B_ENST00000352511,caecum,carcinoma,0,2	ACVR2B	88	2	0			c.C1140T						PASS	.	C		10,4396	16.8+/-37.8	0,10,2193	128.0	96.0	107.0		1140	3.5	1.0	3	dbSNP_134	107	0,8600		0,0,4300	yes	coding-synonymous	ACVR2B	NM_001106.3		0,10,6493	TT,TC,CC		0.0,0.227,0.0769		380/513	38523754	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	93	exon9			AGATGCCTTCCTG	X77533	CCDS2679.1	3p22	2006-11-06			ENSG00000114739	ENSG00000114739			174	protein-coding gene	gene with protein product		602730				8161782, 9621519	Standard	NM_001106		Approved	ActR-IIB	uc003cif.3	Q13705	OTTHUMG00000131291	ENST00000352511.4:c.1140C>T	3.37:g.38523754C>T		218.0	1.0	0.00458716		277.0	141.0	0.509025	NM_001106	Q4VAV0	Silent	SNP	ENST00000352511.4	37	CCDS2679.1																																																																																			C|0.999;T|0.001	0.001	strong		0.572	ACVR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254059.3	NM_001106	
CEP85L	387119	hgsc.bcm.edu	37	6	118791804	118791804	+	Missense_Mutation	SNP	T	T	C	rs7743702	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:118791804T>C	ENST00000368491.3	-	11	2539	c.1918A>G	c.(1918-1920)Atg>Gtg	p.M640V	CEP85L_ENST00000368488.5_Missense_Mutation_p.M643V	NM_001042475.2	NP_001035940.1	Q5SZL2	CE85L_HUMAN	centrosomal protein 85kDa-like	640			M -> V (in dbSNP:rs7743702).			centrosome (GO:0005813)|cytoplasm (GO:0005737)											TTTCCTTGCATAGACTAGAAT	0.318													T|||	166	0.033147	0.059	0.0173	5008	,	,		15160	0.0		0.0189	False		,,,				2504	0.0583				p.M643V		Atlas-SNP	.											.	CEP85L	26	.	0			c.A1927G						PASS	.	T	VAL/MET,VAL/MET	199,3401		4,191,1605	74.0	70.0	72.0		1918,1927	1.6	1.0	6	dbSNP_116	72	166,7950		2,162,3894	yes	missense,missense	C6orf204	NM_001042475.2,NM_001178035.1	21,21	6,353,5499	CC,CT,TT		2.0453,5.5278,3.1154	benign,benign	640/806,643/809	118791804	365,11351	1800	4058	5858	SO:0001583	missense	387119	exon12			CTTGCATAGACTA	AF308284	CCDS5119.2, CCDS43498.1, CCDS55052.1	6q22.31	2011-11-25	2011-11-25	2011-11-25	ENSG00000111860	ENSG00000111860			21638	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 204"""	C6orf204			Standard	NM_206921		Approved	NY-BR-15, bA57K17.2	uc003pya.2	Q5SZL2	OTTHUMG00000015465	ENST00000368491.3:c.1918A>G	6.37:g.118791804T>C	ENSP00000357477:p.Met640Val	127.0	0.0	0		131.0	69.0	0.526718	NM_001178035	A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289	Missense_Mutation	SNP	ENST00000368491.3	37	CCDS43498.1	46	0.021062271062271064	26	0.052845528455284556	6	0.016574585635359115	0	0.0	14	0.018469656992084433	T	12.46	1.943229	0.34283	0.055278	0.020453	ENSG00000111860	ENST00000368491;ENST00000368488	T;T	0.10960	2.82;2.82	5.69	1.6	0.23607	.	0.484848	0.22127	N	0.064253	T	0.02304	0.0071	L	0.36672	1.1	0.29229	N	0.873412	B	0.21225	0.053	B	0.18561	0.022	T	0.36601	-0.9741	10	0.49607	T	0.09	-6.4463	2.3369	0.04250	0.257:0.0736:0.133:0.5364	rs7743702;rs52838185;rs7743702	640	Q5SZL2	CF204_HUMAN	V	640;643	ENSP00000357477:M640V;ENSP00000357474:M643V	ENSP00000357474:M643V	M	-	1	0	C6orf204	118898497	0.926000	0.31397	1.000000	0.80357	0.939000	0.58152	0.058000	0.14301	0.932000	0.37266	0.533000	0.62120	ATG	T|0.975;C|0.025	0.025	strong		0.318	CEP85L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041996.2	NM_001042475	
C3orf22	152065	hgsc.bcm.edu	37	3	126272160	126272160	+	Missense_Mutation	SNP	T	T	C	rs146981008	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:126272160T>C	ENST00000318225.2	-	2	452	c.74A>G	c.(73-75)aAg>aGg	p.K25R		NM_152533.1	NP_689746.1	Q8N5N4	CC022_HUMAN	chromosome 3 open reading frame 22	25										large_intestine(1)|lung(3)|ovary(2)|prostate(1)	7				GBM - Glioblastoma multiforme(114;0.147)		CGGAAACTTCTTGGCAAAATT	0.562													T|||	5	0.000998403	0.0008	0.0058	5008	,	,		17166	0.0		0.0	False		,,,				2504	0.0				p.K25R		Atlas-SNP	.											.	C3orf22	17	.	0			c.A74G						PASS	.	T	ARG/LYS	5,4401	9.9+/-24.2	0,5,2198	242.0	246.0	245.0		74	1.9	0.5	3	dbSNP_134	245	0,8600		0,0,4300	yes	missense	C3orf22	NM_152533.1	26	0,5,6498	CC,CT,TT		0.0,0.1135,0.0384	possibly-damaging	25/142	126272160	5,13001	2203	4300	6503	SO:0001583	missense	152065	exon2			AACTTCTTGGCAA		CCDS3040.1	3q21.3	2011-09-30			ENSG00000180697	ENSG00000180697			28534	protein-coding gene	gene with protein product						12477932	Standard	NM_152533		Approved	MGC34728	uc003ejb.3	Q8N5N4	OTTHUMG00000162731	ENST00000318225.2:c.74A>G	3.37:g.126272160T>C	ENSP00000316644:p.Lys25Arg	114.0	0.0	0		75.0	34.0	0.453333	NM_152533	B3KUS9	Missense_Mutation	SNP	ENST00000318225.2	37	CCDS3040.1	3	0.0013736263736263737	0	0.0	3	0.008287292817679558	0	0.0	0	0.0	T	9.445	1.088997	0.20390	0.001135	0.0	ENSG00000180697	ENST00000318225	.	.	.	2.96	1.87	0.25490	.	0.557035	0.13645	N	0.372704	T	0.11750	0.0286	N	0.12746	0.255	0.21604	N	0.999627	B	0.17667	0.023	B	0.17433	0.018	T	0.19877	-1.0292	9	0.22109	T	0.4	.	3.4088	0.07351	0.0:0.2278:0.0:0.7722	.	25	Q8N5N4	CC022_HUMAN	R	25	.	ENSP00000316644:K25R	K	-	2	0	C3orf22	127754850	0.013000	0.17824	0.465000	0.27155	0.240000	0.25518	0.519000	0.22862	0.602000	0.29896	0.402000	0.26972	AAG	T|0.999;C|0.001	0.001	strong		0.562	C3orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370231.2	NM_152533	
GYS2	2998	hgsc.bcm.edu	37	12	21692210	21692210	+	Silent	SNP	T	T	C	rs142883971	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:21692210T>C	ENST00000261195.2	-	15	2126	c.1872A>G	c.(1870-1872)gaA>gaG	p.E624E		NM_021957.3	NP_068776.2	P54840	GYS2_HUMAN	glycogen synthase 2 (liver)	624					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|response to glucose (GO:0009749)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|ectoplasm (GO:0043265)	glycogen (starch) synthase activity (GO:0004373)|glycogen synthase activity, transferring glucose-1-phosphate (GO:0061547)|protein homodimerization activity (GO:0042803)			NS(1)|breast(2)|endometrium(5)|kidney(1)|large_intestine(14)|lung(14)|prostate(6)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						GTGATGTTAGTTCCACATGGA	0.303													T|||	17	0.00339457	0.0121	0.0014	5008	,	,		16759	0.0		0.0	False		,,,				2504	0.0				p.E624E	Colon(149;9 1820 3690 10544 50424)	Atlas-SNP	.											GYS2,NS,carcinoma,-2,1	GYS2	110	1	0			c.A1872G						PASS	.	T		72,4334	63.5+/-100.7	0,72,2131	166.0	173.0	171.0		1872	-3.7	0.0	12	dbSNP_134	171	0,8600		0,0,4300	no	coding-synonymous	GYS2	NM_021957.3		0,72,6431	CC,CT,TT		0.0,1.6341,0.5536		624/704	21692210	72,12934	2203	4300	6503	SO:0001819	synonymous_variant	2998	exon15			TGTTAGTTCCACA		CCDS8690.1	12p12.2-p11.2	2013-02-22			ENSG00000111713	ENSG00000111713	2.4.1.11	"""Glycosyltransferase group 1 domain containing"""	4707	protein-coding gene	gene with protein product		138571					Standard	NM_021957		Approved		uc001rfb.3	P54840	OTTHUMG00000169135	ENST00000261195.2:c.1872A>G	12.37:g.21692210T>C		88.0	0.0	0		91.0	46.0	0.505495	NM_021957	A0AVD8	Silent	SNP	ENST00000261195.2	37	CCDS8690.1																																																																																			T|0.995;C|0.005	0.005	strong		0.303	GYS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402396.1	NM_021957	
VPS13A	23230	hgsc.bcm.edu	37	9	79959197	79959197	+	Splice_Site	SNP	G	G	A	rs73449933	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:79959197G>A	ENST00000360280.3	+	51	7415	c.7155G>A	c.(7153-7155)gaG>gaA	p.E2385E	VPS13A_ENST00000376636.3_Splice_Site_p.E2346E|VPS13A_ENST00000376634.4_Splice_Site_p.E2385E|VPS13A_ENST00000357409.5_Splice_Site_p.E2385E	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	2385					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						TAGATAACGAGGTAAGTTTTT	0.289													G|||	71	0.0141773	0.053	0.0014	5008	,	,		13508	0.0		0.0	False		,,,				2504	0.0				p.E2385E		Atlas-SNP	.											.	VPS13A	735	.	0			c.G7155A						PASS	.	G	,,,	169,4237	101.2+/-139.8	3,163,2037	80.0	91.0	87.0		7038,7155,7155,7155	2.7	1.0	9	dbSNP_130	87	1,8585	1.2+/-3.3	0,1,4292	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	VPS13A	NM_001018037.1,NM_001018038.2,NM_015186.3,NM_033305.2	,,,	3,164,6329	AA,AG,GG		0.0116,3.8357,1.3085	,,,	2346/3136,2385/3070,2385/3096,2385/3175	79959197	170,12822	2203	4293	6496	SO:0001630	splice_region_variant	23230	exon51			TAACGAGGTAAGT	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"""chorein"""	605978	"""chorea acanthocytosis"", ""vacuolar protein sorting 13A (yeast)"""	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.7155+1G>A	9.37:g.79959197G>A		69.0	0.0	0		81.0	57.0	0.703704	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Silent	SNP	ENST00000360280.3	37	CCDS6655.1																																																																																			G|0.986;A|0.014	0.014	strong		0.289	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	Silent
ADAM18	8749	hgsc.bcm.edu	37	8	39581417	39581417	+	Missense_Mutation	SNP	A	A	G	rs76378145	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:39581417A>G	ENST00000265707.5	+	19	2213	c.2168A>G	c.(2167-2169)gAg>gGg	p.E723G	ADAM18_ENST00000523755.1_3'UTR|ADAM18_ENST00000379866.1_Missense_Mutation_p.E699G|ADAM18_ENST00000541111.1_Missense_Mutation_p.E137G	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	723					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(31)|ovary(1)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)	71		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)			GAGAATGCAGAGTATAATCGG	0.274													A|||	127	0.0253594	0.0893	0.0101	5008	,	,		14686	0.0		0.002	False		,,,				2504	0.0				p.E723G		Atlas-SNP	.											.	ADAM18	169	.	0			c.A2168G						PASS	.		GLY/GLU	371,4033	172.3+/-202.3	20,331,1851	84.0	89.0	87.0		2168	3.6	0.0	8	dbSNP_132	87	2,8588	2.2+/-6.3	0,2,4293	yes	missense	ADAM18	NM_014237.2	98	20,333,6144	GG,GA,AA		0.0233,8.4242,2.8706	benign	723/740	39581417	373,12621	2202	4295	6497	SO:0001583	missense	8749	exon19			ATGCAGAGTATAA	AJ133004	CCDS6113.1, CCDS55225.1	8p11.22	2008-08-07	2005-08-18		ENSG00000168619	ENSG00000168619		"""ADAM metallopeptidase domain containing"""	196	protein-coding gene	gene with protein product			"""a disintegrin and metalloproteinase domain 18"""			12200459	Standard	NM_014237		Approved	tMDCIII, ADAM27	uc003xni.3	Q9Y3Q7	OTTHUMG00000164040	ENST00000265707.5:c.2168A>G	8.37:g.39581417A>G	ENSP00000265707:p.Glu723Gly	55.0	0.0	0		52.0	52.0	1	NM_014237	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Missense_Mutation	SNP	ENST00000265707.5	37	CCDS6113.1	51	0.023351648351648352	45	0.09146341463414634	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	a	9.078	0.998571	0.19121	0.084242	2.33E-4	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000541111	D;D;D	0.93953	-3.32;-3.32;-3.32	4.77	3.61	0.41365	.	0.638567	0.13741	N	0.365922	T	0.38241	0.1033	M	0.68593	2.085	0.09310	N	1	B;B	0.27910	0.193;0.046	B;B	0.27170	0.077;0.035	T	0.67333	-0.5697	10	0.52906	T	0.07	.	7.6055	0.28100	0.9001:0.0:0.0999:0.0	.	699;723	Q9Y3Q7-2;Q9Y3Q7	.;ADA18_HUMAN	G	723;699;137	ENSP00000265707:E723G;ENSP00000369195:E699G;ENSP00000444729:E137G	ENSP00000265707:E723G	E	+	2	0	ADAM18	39700574	0.174000	0.23070	0.007000	0.13788	0.001000	0.01503	2.076000	0.41548	0.933000	0.37291	-0.393000	0.06486	GAG	A|0.972;G|0.028	0.028	strong		0.274	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237	
ST6GALNAC3	256435	hgsc.bcm.edu	37	1	76878097	76878097	+	Silent	SNP	G	G	A	rs17098940	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:76878097G>A	ENST00000328299.3	+	3	766	c.618G>A	c.(616-618)aaG>aaA	p.K206K	ST6GALNAC3_ENST00000464140.1_3'UTR	NM_152996.2	NP_694541.2	Q8NDV1	SIA7C_HUMAN	ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3	206					glycoprotein metabolic process (GO:0009100)|glycosphingolipid metabolic process (GO:0006687)|glycosylceramide metabolic process (GO:0006677)|protein glycosylation (GO:0006486)|sialylation (GO:0097503)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sialyltransferase activity (GO:0008373)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(20)|ovary(3)|prostate(1)|skin(2)	36						AAACTGGGAAGGACAGGTGAG	0.383													A|||	213	0.0425319	0.1558	0.0101	5008	,	,		18401	0.0		0.0	False		,,,				2504	0.0				p.K206K		Atlas-SNP	.											.	ST6GALNAC3	71	.	0			c.G618A						PASS	.	A	,	562,3844		36,490,1677	45.0	43.0	44.0		618,618	2.4	1.0	1	dbSNP_123	44	4,8590		0,4,4293	no	coding-synonymous,coding-synonymous	ST6GALNAC3	NM_001160011.1,NM_152996.2	,	36,494,5970	AA,AG,GG		0.0465,12.7553,4.3538	,	206/211,206/306	76878097	566,12434	2203	4297	6500	SO:0001819	synonymous_variant	256435	exon3			TGGGAAGGACAGG		CCDS672.1	1p31.1	2013-03-01	2005-02-07	2005-02-07	ENSG00000184005	ENSG00000184005		"""Sialyltransferases"""	19343	protein-coding gene	gene with protein product	"""ST6GALNAC III"""	610133	"""sialyltransferase 7 ((alpha-N-acetylneuraminyl-2,3-beta-galactosyl-1,3)-N-acetyl galactosaminide alpha-2,6-sialyltransferase) C"""	SIAT7C			Standard	NM_152996		Approved		uc001dhh.2	Q8NDV1	OTTHUMG00000009615	ENST00000328299.3:c.618G>A	1.37:g.76878097G>A		42.0	0.0	0		67.0	35.0	0.522388	NM_001160011	Q6PCE0|Q6UX29|Q8N259	Silent	SNP	ENST00000328299.3	37	CCDS672.1																																																																																			G|0.955;A|0.045	0.045	strong		0.383	ST6GALNAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026501.1	NM_152996	
MROH6	642475	hgsc.bcm.edu	37	8	144652780	144652780	+	Silent	SNP	T	T	A	rs11990485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144652780T>A	ENST00000398882.3	-	5	1024	c.768A>T	c.(766-768)ggA>ggT	p.G256G	MROH6_ENST00000524906.1_5'Flank|MROH6_ENST00000532704.1_5'Flank|RP11-661A12.9_ENST00000531730.1_RNA|MROH6_ENST00000533679.1_5'Flank|MROH6_ENST00000534459.1_5'Flank	NM_001100878.1	NP_001094348.1	A6NGR9	MROH6_HUMAN	maestro heat-like repeat family member 6	256																	CCCTCGTGGCTCCCACGCAGC	0.662													T|||	70	0.0139776	0.0522	0.0014	5008	,	,		12771	0.0		0.0	False		,,,				2504	0.0				p.G256G		Atlas-SNP	.											.	.	.	.	0			c.A768T						PASS	.	T		171,3991		2,167,1912	30.0	35.0	34.0		768	-0.9	1.0	8	dbSNP_120	34	1,8441		0,1,4220	no	coding-synonymous	C8orf73	NM_001100878.1		2,168,6132	AA,AT,TT		0.0118,4.1086,1.3646		256/720	144652780	172,12432	2081	4221	6302	SO:0001819	synonymous_variant	642475	exon5			CGTGGCTCCCACG	AF289596	CCDS47928.1	8q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000204839	ENSG00000204839		"""maestro heat-like repeat containing"""	27814	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 73"""	C8orf73		12477932	Standard	NM_001100878		Approved		uc010mff.3	A6NGR9	OTTHUMG00000165164	ENST00000398882.3:c.768A>T	8.37:g.144652780T>A		14.0	0.0	0		27.0	14.0	0.518519	NM_001100878	A8MWB1	Silent	SNP	ENST00000398882.3	37	CCDS47928.1																																																																																			T|0.989;A|0.011	0.011	strong		0.662	MROH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382330.3	NM_001100878	
KIF6	221458	hgsc.bcm.edu	37	6	39688551	39688551	+	Missense_Mutation	SNP	T	T	C	rs114269617	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:39688551T>C	ENST00000287152.7	-	2	197	c.103A>G	c.(103-105)Agc>Ggc	p.S35G	KIF6_ENST00000538893.1_Missense_Mutation_p.S35G|KIF6_ENST00000373216.3_Missense_Mutation_p.S35G|KIF6_ENST00000373215.3_Missense_Mutation_p.S35G	NM_145027.4	NP_659464.3	Q6ZMV9	KIF6_HUMAN	kinesin family member 6	35	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|male germ cell nucleus (GO:0001673)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(16)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						ATTTCCAAGCTAGGTATTAAT	0.318													T|||	48	0.00958466	0.0325	0.0014	5008	,	,		18134	0.0		0.004	False		,,,				2504	0.0				p.S35G		Atlas-SNP	.											.	KIF6	233	.	0			c.A103G						PASS	.	T	GLY/SER	184,4222	117.5+/-155.4	2,180,2021	97.0	101.0	100.0		103	0.2	0.4	6	dbSNP_132	100	3,8597	1.2+/-3.3	0,3,4297	yes	missense	KIF6	NM_145027.4	56	2,183,6318	CC,CT,TT		0.0349,4.1761,1.4378	possibly-damaging	35/815	39688551	187,12819	2203	4300	6503	SO:0001583	missense	221458	exon2			CCAAGCTAGGTAT	AL832634	CCDS4844.1, CCDS75449.1	6p21.2	2010-03-30			ENSG00000164627	ENSG00000164627		"""Kinesins"""	21202	protein-coding gene	gene with protein product		613919	"""chromosome 6 open reading frame 102"""	C6orf102			Standard	NM_145027		Approved	dJ1043E3.1, MGC33317, dJ137F1.4, dJ188D3.1, DKFZp451I2418	uc003oot.2	Q6ZMV9	OTTHUMG00000014648	ENST00000287152.7:c.103A>G	6.37:g.39688551T>C	ENSP00000287152:p.Ser35Gly	68.0	0.0	0		59.0	31.0	0.525424	NM_145027	Q2MDE3|Q2MDE4|Q5T8J6|Q6ZWE3|Q86T87|Q8WTV4	Missense_Mutation	SNP	ENST00000287152.7	37	CCDS4844.1	27	0.012362637362637362	23	0.046747967479674794	0	0.0	0	0.0	4	0.005277044854881266	T	11.68	1.711929	0.30322	0.041761	3.49E-4	ENSG00000164627	ENST00000287152;ENST00000373216;ENST00000373215;ENST00000538893	T;T;T;T	0.72725	-0.68;-0.68;-0.68;-0.68	6.06	0.196	0.15159	Kinesin, motor domain (3);	.	.	.	.	T	0.43590	0.1254	L	0.47190	1.495	0.09310	N	1	B;B;B	0.25390	0.021;0.005;0.125	B;B;B	0.34452	0.018;0.008;0.183	T	0.46992	-0.9151	9	0.42905	T	0.14	.	4.8731	0.13642	0.3772:0.0982:0.0:0.5246	.	35;35;35	E7EUN7;F6VGH2;Q6ZMV9	.;.;KIF6_HUMAN	G	35	ENSP00000287152:S35G;ENSP00000362312:S35G;ENSP00000362311:S35G;ENSP00000441435:S35G	ENSP00000287152:S35G	S	-	1	0	KIF6	39796529	0.318000	0.24598	0.387000	0.26183	0.989000	0.77384	0.951000	0.29135	0.492000	0.27815	0.533000	0.62120	AGC	T|0.984;C|0.016	0.016	strong		0.318	KIF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040455.2	NM_145027	
OR1E2	8388	hgsc.bcm.edu	37	17	3336723	3336723	+	Missense_Mutation	SNP	A	A	G	rs73296096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3336723A>G	ENST00000248384.1	-	1	412	c.413T>C	c.(412-414)cTc>cCc	p.L138P		NM_003554.1	NP_003545.1	P47887	OR1E2_HUMAN	olfactory receptor, family 1, subfamily E, member 2	138					sensory perception of chemical stimulus (GO:0007606)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|receptor activity (GO:0004872)			endometrium(3)|large_intestine(3)|lung(3)	9						GTAGTGCAGGAGGAAGCAGAT	0.552													G|||	153	0.0305511	0.1112	0.0072	5008	,	,		19727	0.0		0.001	False		,,,				2504	0.0				p.L138P		Atlas-SNP	.											.	OR1E2	25	.	0			c.T413C						PASS	.	-	PRO/LEU	356,4050	793.7+/-415.2	24,308,1871	90.0	75.0	80.0		413		1.0	17	dbSNP_130	80	2,8598	819.2+/-406.8	0,2,4298	yes	missense	OR1E2	NM_003554.1	98	24,310,6169	GG,GA,AA		0.0233,8.0799,2.7526		138/324	3336723	358,12648	2203	4300	6503	SO:0001583	missense	8388	exon1			TGCAGGAGGAAGC	U04686	CCDS11026.1	17p13.3	2012-08-09			ENSG00000127780	ENSG00000127780		"""GPCR / Class A : Olfactory receptors"""	8190	protein-coding gene	gene with protein product				OR1E4		8004088, 9500546	Standard	NM_003554		Approved	OR17-93, OR17-135	uc010vre.2	P47887	OTTHUMG00000090651	ENST00000248384.1:c.413T>C	17.37:g.3336723A>G	ENSP00000248384:p.Leu138Pro	214.0	0.0	0		223.0	98.0	0.439462	NM_003554	O43877|O95632|Q0VAD5|Q0VAD6|Q9UL13	Missense_Mutation	SNP	ENST00000248384.1	37	CCDS11026.1	49	0.022435897435897436	49	0.09959349593495935	0	0.0	0	0.0	0	0.0	G	2.920	-0.223476	0.06061	0.080799	2.33E-4	ENSG00000127780	ENST00000248384	T	0.02890	4.12	.	.	.	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00073	0.0002	N	0.08118	0	0.25307	N	0.989232	.	.	.	.	.	.	T	0.50825	-0.8782	5	0.72032	D	0.01	.	.	.	.	.	138	P47887	OR1E2_HUMAN	P	138	ENSP00000248384:L138P	ENSP00000248384:L138P	L	-	2	0	OR1E2	3283473	.	.	0.977000	0.42913	0.222000	0.24845	.	.	0.000000	0.14550	0.000000	0.15137	CTC	A|0.975;G|0.025	0.025	strong		0.552	OR1E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207311.1		
C3orf33	285315	hgsc.bcm.edu	37	3	155493497	155493497	+	Silent	SNP	T	T	C	rs377018605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:155493497T>C	ENST00000340171.2	-	3	413	c.315A>G	c.(313-315)tcA>tcG	p.S105S	C3orf33_ENST00000534941.1_Silent_p.S62S			Q6P1S2	CC033_HUMAN	chromosome 3 open reading frame 33	105					negative regulation of ERK1 and ERK2 cascade (GO:0070373)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)			breast(1)|kidney(1)|large_intestine(3)|lung(3)	8			Lung(72;0.11)|LUSC - Lung squamous cell carcinoma(72;0.114)			TACTTCTCAATGAAGCTATAA	0.269													T|||	6	0.00119808	0.0038	0.0014	5008	,	,		15710	0.0		0.0	False		,,,				2504	0.0				p.S62S		Atlas-SNP	.											.	C3orf33	18	.	0			c.A186G						PASS	.	T		16,3586		0,16,1785	67.0	70.0	69.0		186	-4.1	0.7	3		69	1,8111		0,1,4055	no	coding-synonymous	C3orf33	NM_173657.1		0,17,5840	CC,CT,TT		0.0123,0.4442,0.1451		62/252	155493497	17,11697	1801	4056	5857	SO:0001819	synonymous_variant	285315	exon4			TCTCAATGAAGCT	AF115515	CCDS54659.1	3q25.31	2012-10-31			ENSG00000174928	ENSG00000174928			26434	protein-coding gene	gene with protein product						20680465	Standard	NM_173657		Approved	FLJ31139, AC3-33	uc003fal.1	Q6P1S2	OTTHUMG00000158496	ENST00000340171.2:c.315A>G	3.37:g.155493497T>C		111.0	0.0	0		100.0	55.0	0.55	NM_173657	A8K1H5|Q86YE6|Q8IXA7|Q96NB5	Silent	SNP	ENST00000340171.2	37																																																																																				.	.	weak		0.269	C3orf33-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351167.1	NM_173657	
COL6A3	1293	hgsc.bcm.edu	37	2	238253332	238253332	+	Silent	SNP	G	G	A	rs10084221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:238253332G>A	ENST00000295550.4	-	36	7781	c.7329C>T	c.(7327-7329)gcC>gcT	p.A2443A	COL6A3_ENST00000346358.4_Silent_p.A2243A|COL6A3_ENST00000353578.4_Silent_p.A2237A|COL6A3_ENST00000347401.3_Silent_p.A2242A|COL6A3_ENST00000472056.1_Silent_p.A1836A|COL6A3_ENST00000409809.1_Silent_p.A2237A	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	2443	Nonhelical region.|VWFA 11. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CAGCCACCCGGGCCCCCCGTG	0.557													G|||	355	0.0708866	0.2171	0.0375	5008	,	,		19167	0.005		0.0189	False		,,,				2504	0.0184				p.A2443A		Atlas-SNP	.											.	COL6A3	608	.	0			c.C7329T						PASS	.	G	,,	801,3605	296.7+/-284.4	54,693,1456	55.0	61.0	59.0		7329,5508,6711	3.4	1.0	2	dbSNP_119	59	177,8423	78.6+/-141.3	1,175,4124	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	,,	55,868,5580	AA,AG,GG		2.0581,18.1798,7.5196	,,	2443/3178,1836/2571,2237/2972	238253332	978,12028	2203	4300	6503	SO:0001819	synonymous_variant	1293	exon36			CACCCGGGCCCCC	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.7329C>T	2.37:g.238253332G>A		54.0	0.0	0		77.0	34.0	0.441558	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			G|0.935;A|0.065	0.065	strong		0.557	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
FAT3	120114	hgsc.bcm.edu	37	11	92568196	92568196	+	Silent	SNP	C	C	T	rs374591402	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:92568196C>T	ENST00000298047.6	+	14	10049	c.10032C>T	c.(10030-10032)gaC>gaT	p.D3344D	FAT3_ENST00000525166.1_Silent_p.D3194D|FAT3_ENST00000409404.2_Silent_p.D3344D			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3344	Cadherin 31. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TCAGCCAAGACGTCTACAGTG	0.527										TCGA Ovarian(4;0.039)			C|||	4	0.000798722	0.0023	0.0	5008	,	,		17326	0.0		0.0	False		,,,				2504	0.001				p.D3344D		Atlas-SNP	.											.	FAT3	1822	.	0			c.C10032T						PASS	.	C		7,3905		0,7,1949	55.0	55.0	55.0		10032	-1.9	1.0	11		55	0,8324		0,0,4162	no	coding-synonymous	FAT3	NM_001008781.2		0,7,6111	TT,TC,CC		0.0,0.1789,0.0572		3344/4558	92568196	7,12229	1956	4162	6118	SO:0001819	synonymous_variant	120114	exon14			CCAAGACGTCTAC	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.10032C>T	11.37:g.92568196C>T		195.0	0.0	0		150.0	83.0	0.553333	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				.	.	weak		0.527	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
URB2	9816	hgsc.bcm.edu	37	1	229783328	229783328	+	Silent	SNP	G	G	C	rs115914317	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229783328G>C	ENST00000258243.2	+	7	4114	c.3978G>C	c.(3976-3978)ctG>ctC	p.L1326L		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	1326						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						TAGATGTCCTGGCTGCACTGC	0.552													G|||	17	0.00339457	0.0129	0.0	5008	,	,		17934	0.0		0.0	False		,,,				2504	0.0				p.L1326L		Atlas-SNP	.											.	URB2	152	.	0			c.G3978C						PASS	.	G		51,4355	53.6+/-89.4	0,51,2152	78.0	71.0	73.0		3978	4.7	1.0	1	dbSNP_132	73	0,8600		0,0,4300	no	coding-synonymous	URB2	NM_014777.2		0,51,6452	CC,CG,GG		0.0,1.1575,0.3921		1326/1525	229783328	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	9816	exon7			TGTCCTGGCTGCA	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.3978G>C	1.37:g.229783328G>C		163.0	0.0	0		147.0	76.0	0.517007	NM_014777	Q5VYC9	Silent	SNP	ENST00000258243.2	37	CCDS31052.1																																																																																			G|0.997;C|0.003	0.003	strong		0.552	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777	
ERCC5	2073	hgsc.bcm.edu	37	13	103506690	103506690	+	Missense_Mutation	SNP	G	G	A	rs4987063	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:103506690G>A	ENST00000355739.4	+	4	1856	c.433G>A	c.(433-435)Gtt>Att	p.V145I	ERCC5_ENST00000535557.1_Missense_Mutation_p.V145I|BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.C570Y	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	145			V -> I (in dbSNP:rs4987063).		DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|response to UV (GO:0009411)|response to UV-C (GO:0010225)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	51	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					CGACCTCTATGTTTTGCCTCC	0.363			"""Mis, N, F"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				G|||	35	0.00698882	0.0257	0.0014	5008	,	,		19977	0.0		0.0	False		,,,				2504	0.0				p.V599I		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (G)	13	13q33	2073	"""excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))"""		E	.	.	.	.	0			c.G1795A						PASS	.	G	ILE/VAL,ILE/VAL	91,4315	74.7+/-112.8	2,87,2114	123.0	116.0	118.0		1795,433	2.4	0.2	13	dbSNP_111	118	0,8600		0,0,4300	yes	missense,missense	ERCC5,BIVM-ERCC5	NM_001204425.1,NM_000123.3	29,29	2,87,6414	AA,AG,GG		0.0,2.0654,0.6997	benign,benign	599/1641,145/1187	103506690	91,12915	2203	4300	6503	SO:0001583	missense	0	exon12	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	CTCTATGTTTTGC	X71342	CCDS32004.1	13q22-q34	2014-09-17	2014-03-07		ENSG00000134899	ENSG00000134899			3437	protein-coding gene	gene with protein product	"""Cockayne syndrome"""	133530	"""xeroderma pigmentosum, complementation group G"", ""excision repair cross-complementing rodent repair deficiency, complementation group 5"""	ERCM2, XPGC		8088806	Standard	NM_000123		Approved			P28715	OTTHUMG00000017310	ENST00000355739.4:c.433G>A	13.37:g.103506690G>A	ENSP00000347978:p.Val145Ile	93.0	0.0	0		96.0	35.0	0.364583	NM_001204425	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Missense_Mutation	SNP	ENST00000355739.4	37	CCDS32004.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	G	4.272	0.049520	0.08243	0.020654	0.0	ENSG00000134899	ENST00000418659;ENST00000355739;ENST00000535557	T;T	0.23147	3.49;1.92	6.03	2.39	0.29439	.	0.420080	0.25570	N	0.029763	T	0.07413	0.0187	L	0.28556	0.865	0.26071	N	0.981225	B;B;B	0.22080	0.038;0.064;0.051	B;B;B	0.23275	0.045;0.014;0.01	T	0.18209	-1.0344	10	0.25751	T	0.34	-2.6138	5.2232	0.15379	0.2217:0.0:0.6337:0.1446	rs4987063	145;145;570	B4DSI5;P28715;Q59FZ7	.;ERCC5_HUMAN;.	I	570;145;145	ENSP00000347978:V145I;ENSP00000442117:V145I	ENSP00000347978:V145I	V	+	1	0	ERCC5	102304691	0.999000	0.42202	0.227000	0.23927	0.161000	0.22273	3.038000	0.49783	0.424000	0.26061	-0.136000	0.14681	GTT	G|0.993;A|0.007	0.007	strong		0.363	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1		
UVSSA	57654	hgsc.bcm.edu	37	4	1374769	1374769	+	Silent	SNP	G	G	A	rs115722661	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:1374769G>A	ENST00000389851.4	+	12	2301	c.1854G>A	c.(1852-1854)gaG>gaA	p.E618E	UVSSA_ENST00000511216.1_Silent_p.E618E|UVSSA_ENST00000507531.1_Silent_p.E618E|UVSSA_ENST00000512728.1_Silent_p.E169E|UVSSA_ENST00000511563.1_Silent_p.E169E	NM_020894.2	NP_065945.2	Q2YD98	UVSSA_HUMAN	UV-stimulated scaffold protein A	618					protein ubiquitination (GO:0016567)|response to UV (GO:0009411)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)	RNA polymerase II core binding (GO:0000993)										AGAAGCAGGAGCGCCCGGGTA	0.667													G|||	14	0.00279553	0.0098	0.0014	5008	,	,		15251	0.0		0.0	False		,,,				2504	0.0				p.E618E		Atlas-SNP	.											.	.	.	.	0			c.G1854A						PASS	.	G		67,4331	61.1+/-98.1	0,67,2132	30.0	34.0	33.0		1854	-3.4	0.0	4	dbSNP_133	33	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	KIAA1530	NM_020894.2		0,68,6430	AA,AG,GG		0.0116,1.5234,0.5232		618/710	1374769	68,12928	2199	4299	6498	SO:0001819	synonymous_variant	57654	exon12			GCAGGAGCGCCCG	BC021930	CCDS33938.1	4p16.3	2012-04-27	2012-04-27	2012-04-27		ENSG00000163945			29304	protein-coding gene	gene with protein product		614632	"""KIAA1530"""	KIAA1530		10819331, 22466610, 22466611, 22466612	Standard	NM_020894		Approved		uc003gde.4	Q2YD98		ENST00000389851.4:c.1854G>A	4.37:g.1374769G>A		213.0	0.0	0		202.0	97.0	0.480198	NM_020894	A8K9E6|B2RU11|Q8WTX4|Q9P1Z8	Silent	SNP	ENST00000389851.4	37	CCDS33938.1																																																																																			G|0.995;A|0.005	0.005	strong		0.667	UVSSA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359480.1	NM_020894	
FBN3	84467	hgsc.bcm.edu	37	19	8137052	8137052	+	Silent	SNP	G	G	A	rs10420783	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8137052G>A	ENST00000600128.1	-	63	8382	c.7968C>T	c.(7966-7968)ccC>ccT	p.P2656P	FBN3_ENST00000601739.1_Silent_p.P2656P|FBN3_ENST00000270509.2_Silent_p.P2656P			Q75N90	FBN3_HUMAN	fibrillin 3	2656						proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						CCTGGGGTCCGGGGCTGAAGC	0.672													G|||	256	0.0511182	0.1846	0.0173	5008	,	,		19707	0.0		0.0	False		,,,				2504	0.0				p.P2656P		Atlas-SNP	.											.	FBN3	300	.	0			c.C7968T						PASS	.	G		653,3753	279.0+/-274.6	45,563,1595	99.0	107.0	104.0		7968	-7.2	0.0	19	dbSNP_119	104	12,8588	7.7+/-29.5	0,12,4288	no	coding-synonymous	FBN3	NM_032447.3		45,575,5883	AA,AG,GG		0.1395,14.8207,5.113		2656/2810	8137052	665,12341	2203	4300	6503	SO:0001819	synonymous_variant	84467	exon62			GGGTCCGGGGCTG		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.7968C>T	19.37:g.8137052G>A		72.0	0.0	0		72.0	72.0	1	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																			G|0.949;A|0.051	0.051	strong		0.672	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
NMU	10874	hgsc.bcm.edu	37	4	56475330	56475330	+	Missense_Mutation	SNP	T	T	C	rs35892915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:56475330T>C	ENST00000264218.3	-	4	341	c.236A>G	c.(235-237)gAg>gGg	p.E79G	NMU_ENST00000507338.1_Missense_Mutation_p.E79G|NMU_ENST00000511469.1_Missense_Mutation_p.E63G|NMU_ENST00000515325.1_5'UTR|NMU_ENST00000505262.1_Missense_Mutation_p.E79G	NM_006681.2	NP_006672.1	P48645	NMU_HUMAN	neuromedin U	79			E -> G (in dbSNP:rs35892915).		digestion (GO:0007586)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|gastric acid secretion (GO:0001696)|neuropeptide signaling pathway (GO:0007218)|photoperiodism (GO:0009648)|positive regulation of hormone secretion (GO:0046887)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of synaptic transmission (GO:0050806)|regulation of smooth muscle contraction (GO:0006940)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|terminal bouton (GO:0043195)	receptor binding (GO:0005102)			lung(3)|ovary(1)|urinary_tract(1)	5	Lung NSC(11;0.00256)|all_epithelial(27;0.075)|Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.103)	LUSC - Lung squamous cell carcinoma(4;6.72e-08)|Lung(4;6.22e-07)|Epithelial(7;0.00559)	LUSC - Lung squamous cell carcinoma(721;0.0115)		GCAAAGCTCCTCCAGTGCGTT	0.363													T|||	114	0.0227636	0.0847	0.0029	5008	,	,		19593	0.0		0.0	False		,,,				2504	0.0				p.E79G		Atlas-SNP	.											.	NMU	17	.	0			c.A236G						PASS	.	T	GLY/GLU	312,4094	168.0+/-198.9	9,294,1900	111.0	111.0	111.0		236	1.7	0.9	4	dbSNP_126	111	5,8595	3.0+/-9.4	0,5,4295	yes	missense	NMU	NM_006681.2	98	9,299,6195	CC,CT,TT		0.0581,7.0813,2.4373	possibly-damaging	79/175	56475330	317,12689	2203	4300	6503	SO:0001583	missense	10874	exon4			AGCTCCTCCAGTG	X76029	CCDS3501.1, CCDS75125.1	4q12	2013-02-26			ENSG00000109255	ENSG00000109255		"""Endogenous ligands"""	7859	protein-coding gene	gene with protein product	"""prepro-NMU"""	605103				7619205	Standard	XM_005265713		Approved		uc003hbc.3	P48645	OTTHUMG00000102161	ENST00000264218.3:c.236A>G	4.37:g.56475330T>C	ENSP00000264218:p.Glu79Gly	71.0	0.0	0		87.0	43.0	0.494253	NM_006681		Missense_Mutation	SNP	ENST00000264218.3	37	CCDS3501.1	32	0.014652014652014652	31	0.06300813008130081	1	0.0027624309392265192	0	0.0	0	0.0	T	13.36	2.215110	0.39102	0.070813	5.81E-4	ENSG00000109255	ENST00000511469;ENST00000264218;ENST00000505262;ENST00000541393;ENST00000507338	T;T;T;T	0.51574	0.7;0.7;1.31;0.7	5.51	1.72	0.24424	.	0.342720	0.28778	N	0.014164	T	0.04363	0.0120	M	0.65498	2.005	0.34244	D	0.67794	P	0.38922	0.651	B	0.35859	0.212	T	0.26538	-1.0100	10	0.66056	D	0.02	-11.2	8.6898	0.34260	0.0:0.2134:0.0:0.7866	rs35892915	79	P48645	NMU_HUMAN	G	63;79;79;79;79	ENSP00000422399:E63G;ENSP00000264218:E79G;ENSP00000424246:E79G;ENSP00000422870:E79G	ENSP00000264218:E79G	E	-	2	0	NMU	56170087	1.000000	0.71417	0.873000	0.34254	0.350000	0.29205	2.040000	0.41203	0.073000	0.16731	0.533000	0.62120	GAG	T|0.978;C|0.022	0.022	strong		0.363	NMU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220006.2		
NCOA6	23054	hgsc.bcm.edu	37	20	33338099	33338099	+	Silent	SNP	G	G	A	rs61736335	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33338099G>A	ENST00000374796.2	-	10	4469	c.1899C>T	c.(1897-1899)ggC>ggT	p.G633G	NCOA6_ENST00000359003.2_Silent_p.G633G			Q14686	NCOA6_HUMAN	nuclear receptor coactivator 6	633	CREBBP-binding region.|Gln-rich.|NCOA1-binding region.|TBP/GTF2A-binding region.				brain development (GO:0007420)|cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA-templated transcription, initiation (GO:0006352)|glucocorticoid receptor signaling pathway (GO:0042921)|heart development (GO:0007507)|intracellular estrogen receptor signaling pathway (GO:0030520)|labyrinthine layer blood vessel development (GO:0060716)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)	histone methyltransferase complex (GO:0035097)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(2)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(8)|large_intestine(16)|lung(37)|ovary(4)|prostate(5)|skin(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	107						GGACCATCTGGCCCTGGGAGG	0.587													G|||	11	0.00219649	0.0083	0.0	5008	,	,		17579	0.0		0.0	False		,,,				2504	0.0				p.G633G		Atlas-SNP	.											.	NCOA6	219	.	0			c.C1899T						PASS	.	G	,	60,4346	58.1+/-94.6	0,60,2143	112.0	100.0	104.0		1899,1899	-0.8	1.0	20	dbSNP_129	104	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	NCOA6	NM_001242539.1,NM_014071.3	,	0,61,6442	AA,AG,GG		0.0116,1.3618,0.469	,	633/1071,633/2064	33338099	61,12945	2203	4300	6503	SO:0001819	synonymous_variant	23054	exon9			CATCTGGCCCTGG	AF128458	CCDS13241.1, CCDS74720.1	20q11	2008-08-01			ENSG00000198646	ENSG00000198646			15936	protein-coding gene	gene with protein product	"""nuclear receptor coactivator RAP250"", ""activating signal cointegrator-2"", ""peroxisome proliferator-activated receptor interacting protein"""	605299				8724849, 8263591	Standard	NM_014071		Approved	KIAA0181, RAP250, ASC2, AIB3, PRIP, TRBP, NRC	uc002xaw.3	Q14686	OTTHUMG00000032311	ENST00000374796.2:c.1899C>T	20.37:g.33338099G>A		155.0	0.0	0		198.0	101.0	0.510101	NM_014071	A6NLF1|B2RMN5|E1P5P7|Q9NTZ9|Q9UH74|Q9UK86	Silent	SNP	ENST00000374796.2	37	CCDS13241.1																																																																																			G|0.996;A|0.004	0.004	strong		0.587	NCOA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078811.2	NM_014071	
LIPG	9388	hgsc.bcm.edu	37	18	47088741	47088741	+	Silent	SNP	C	C	T	rs874566	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:47088741C>T	ENST00000261292.4	+	1	341	c.63C>T	c.(61-63)agC>agT	p.S21S	LIPG_ENST00000427224.2_Silent_p.S21S|LIPG_ENST00000577628.1_Intron|LIPG_ENST00000580036.1_Silent_p.S21S	NM_006033.2	NP_006024.1	Q9Y5X9	LIPE_HUMAN	lipase, endothelial	21					cell proliferation (GO:0008283)|cholesterol homeostasis (GO:0042632)|high-density lipoprotein particle remodeling (GO:0034375)|lipid metabolic process (GO:0006629)|phospholipid catabolic process (GO:0009395)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol transport (GO:0032376)|positive regulation of high-density lipoprotein particle clearance (GO:0010983)|regulation of lipoprotein metabolic process (GO:0050746)|response to nutrient (GO:0007584)|reverse cholesterol transport (GO:0043691)	extracellular space (GO:0005615)	heparin binding (GO:0008201)|lipoprotein lipase activity (GO:0004465)|phosphatidylcholine 1-acylhydrolase activity (GO:0008970)|phospholipase activity (GO:0004620)			autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)|skin(2)	18						CTGCGGGGAGCCCCGTACCTT	0.557													C|||	224	0.0447284	0.1551	0.0216	5008	,	,		14167	0.0		0.004	False		,,,				2504	0.0				p.S21S	Pancreas(126;280 1778 12814 26243 34948)	Atlas-SNP	.											.	LIPG	47	.	0			c.C63T						PASS	.	C		677,3729	285.7+/-278.4	57,563,1583	81.0	81.0	81.0		63	2.6	0.0	18	dbSNP_86	81	37,8563	25.1+/-72.6	0,37,4263	no	coding-synonymous	LIPG	NM_006033.2		57,600,5846	TT,TC,CC		0.4302,15.3654,5.4898		21/501	47088741	714,12292	2203	4300	6503	SO:0001819	synonymous_variant	9388	exon1			GGGGAGCCCCGTA	AF118767	CCDS11938.1	18q21.1	2006-04-22				ENSG00000101670			6623	protein-coding gene	gene with protein product		603684				10318835, 10192396	Standard	XM_005258390		Approved	EDL	uc002ldv.3	Q9Y5X9		ENST00000261292.4:c.63C>T	18.37:g.47088741C>T		113.0	0.0	0		93.0	46.0	0.494624	NM_006033	B0LPG6|Q6P9C8|Q6UW82	Silent	SNP	ENST00000261292.4	37	CCDS11938.1																																																																																			C|0.953;T|0.047	0.047	strong		0.557	LIPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447546.1	NM_006033	
NRXN1	9378	hgsc.bcm.edu	37	2	50280469	50280469	+	Silent	SNP	C	C	T	rs74714098	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:50280469C>T	ENST00000406316.2	-	20	5454	c.3978G>A	c.(3976-3978)acG>acA	p.T1326T	NRXN1_ENST00000401710.1_Silent_p.T344T|NRXN1_ENST00000401669.2_Silent_p.T1356T|NRXN1_ENST00000402717.3_Silent_p.T1348T|NRXN1_ENST00000404971.1_Silent_p.T1396T|NRXN1_ENST00000342183.5_Silent_p.T291T|NRXN1_ENST00000405472.3_Silent_p.T1348T|NRXN1_ENST00000406859.3_Silent_p.T1326T	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	1326	Poly-Thr.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			TAGCCAGGGTCGTGGTAGTCT	0.473													C|||	82	0.0163738	0.0575	0.0043	5008	,	,		16560	0.0		0.001	False		,,,				2504	0.002				p.T1396T		Atlas-SNP	.											.	NRXN1	1118	.	0			c.G4188A						PASS	.	C	,,	186,4220	119.2+/-156.9	6,174,2023	135.0	131.0	132.0		4188,3978,873	-7.8	0.8	2	dbSNP_131	132	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	NRXN1	NM_001135659.1,NM_004801.4,NM_138735.2	,,	6,175,6322	TT,TC,CC		0.0116,4.2215,1.4378	,,	1396/1548,1326/1478,291/443	50280469	187,12819	2203	4300	6503	SO:0001819	synonymous_variant	9378	exon22			CAGGGTCGTGGTA	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.3978G>A	2.37:g.50280469C>T		198.0	0.0	0		204.0	104.0	0.509804	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	37	CCDS54360.1																																																																																			C|0.983;T|0.017	0.017	strong		0.473	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2		
NWD1	284434	hgsc.bcm.edu	37	19	16860602	16860602	+	Silent	SNP	T	T	C	rs61731252	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16860602T>C	ENST00000552788.1	+	4	1149	c.1149T>C	c.(1147-1149)cgT>cgC	p.R383R	NWD1_ENST00000379808.3_Silent_p.R383R|NWD1_ENST00000523826.1_Silent_p.R177R|NWD1_ENST00000339803.6_Silent_p.R248R|NWD1_ENST00000524140.2_Silent_p.R383R|NWD1_ENST00000549814.1_Silent_p.R383R			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	383	NACHT.						ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						CAGATGCCCGTGGCCTGCTGA	0.622													t|||	337	0.0672923	0.1838	0.0274	5008	,	,		17972	0.0079		0.0288	False		,,,				2504	0.0389				p.R383R		Atlas-SNP	.											.	NWD1	303	.	0			c.T1149C						PASS	.			733,3673		58,617,1528	32.0	34.0	33.0		1149	-4.7	0.0	19	dbSNP_129	33	320,8280		7,306,3987	no	coding-synonymous	NWD1	NM_001007525.3		65,923,5515	CC,CT,TT		3.7209,16.6364,8.0963		383/1433	16860602	1053,11953	2203	4300	6503	SO:0001819	synonymous_variant	284434	exon6			TGCCCGTGGCCTG	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"""WD repeat domain containing"""	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.1149T>C	19.37:g.16860602T>C		52.0	0.0	0		56.0	55.0	0.982143	NM_001007525	C9J021|Q68CT3	Silent	SNP	ENST00000552788.1	37																																																																																				T|0.927;C|0.073	0.073	strong		0.622	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525	
IGSF5	150084	hgsc.bcm.edu	37	21	41143018	41143018	+	Missense_Mutation	SNP	T	T	A	rs74817033	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:41143018T>A	ENST00000380588.4	+	4	697	c.594T>A	c.(592-594)agT>agA	p.S198R	IGSF5_ENST00000479378.1_3'UTR	NM_001080444.1	NP_001073913.1	Q9NSI5	IGSF5_HUMAN	immunoglobulin superfamily, member 5	198	Ig-like V-type 2.				single organismal cell-cell adhesion (GO:0016337)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(7)|skin(2)|stomach(1)	23		Prostate(19;5.35e-06)				ACCTTCAAAGTGCAGTGAGCA	0.557													T|||	215	0.0429313	0.1551	0.0144	5008	,	,		15696	0.0		0.0	False		,,,				2504	0.0				p.S198R		Atlas-SNP	.											.	IGSF5	62	.	0			c.T594A						PASS	.	T	ARG/SER	560,3846	251.8+/-258.4	34,492,1677	76.0	72.0	73.0		594	-3.7	0.0	21	dbSNP_131	73	5,8595	3.7+/-12.6	0,5,4295	yes	missense	IGSF5	NM_001080444.1	110	34,497,5972	AA,AT,TT		0.0581,12.7099,4.3441	benign	198/408	41143018	565,12441	2203	4300	6503	SO:0001583	missense	150084	exon4			TCAAAGTGCAGTG		CCDS33562.1	21q22.2	2013-01-29			ENSG00000183067	ENSG00000183067		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5952	protein-coding gene	gene with protein product	"""junctional adhesion molecule 4"""	610638					Standard	NM_001080444		Approved	JAM4	uc002yyo.3	Q9NSI5	OTTHUMG00000086724	ENST00000380588.4:c.594T>A	21.37:g.41143018T>A	ENSP00000369962:p.Ser198Arg	64.0	0.0	0		70.0	35.0	0.5	NM_001080444		Missense_Mutation	SNP	ENST00000380588.4	37	CCDS33562.1	87	0.03983516483516483	78	0.15853658536585366	9	0.024861878453038673	0	0.0	0	0.0	T	17.24	3.339873	0.60963	0.127099	5.81E-4	ENSG00000183067	ENST00000380588	T	0.12147	2.71	5.11	-3.69	0.04450	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.194230	0.52532	N	0.000061	T	0.00039	0.0001	L	0.40543	1.245	0.80722	P	0.0	P	0.37708	0.606	B	0.37198	0.243	T	0.40175	-0.9577	9	0.14252	T	0.57	-6.954	5.6797	0.17769	0.0:0.2935:0.239:0.4676	.	198	Q9NSI5	IGSF5_HUMAN	R	198	ENSP00000369962:S198R	ENSP00000369962:S198R	S	+	3	2	IGSF5	40064888	0.001000	0.12720	0.000000	0.03702	0.931000	0.56810	-0.287000	0.08388	-0.719000	0.04942	0.528000	0.53228	AGT	T|0.959;A|0.041	0.041	strong		0.557	IGSF5-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195005.1		
FOCAD	54914	hgsc.bcm.edu	37	9	20820346	20820346	+	Silent	SNP	A	A	T	rs147147351		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:20820346A>T	ENST00000380249.1	+	15	1948	c.1584A>T	c.(1582-1584)cgA>cgT	p.R528R	FOCAD_ENST00000338382.6_Silent_p.R528R|FOCAD_ENST00000605086.1_5'UTR	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	528						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											AAATTCTACGAATAATACAAC	0.378													A|||	1	0.000199681	0.0008	0.0	5008	,	,		17668	0.0		0.0	False		,,,				2504	0.0				p.R528R		Atlas-SNP	.											KIAA1797,rectum,carcinoma,+1,1	.	.	1	0			c.A1584T						PASS	.	A		3,4403	6.2+/-15.9	0,3,2200	101.0	96.0	98.0		1584	1.8	1.0	9	dbSNP_134	98	0,8600		0,0,4300	no	coding-synonymous	KIAA1797	NM_017794.3		0,3,6500	TT,TA,AA		0.0,0.0681,0.0231		528/1802	20820346	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	54914	exon15			TCTACGAATAATA	AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"""KIAA1797"""	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.1584A>T	9.37:g.20820346A>T		127.0	0.0	0		123.0	55.0	0.447154	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Silent	SNP	ENST00000380249.1	37	CCDS34993.1																																																																																			A|1.000;T|0.000	0.000	strong		0.378	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794	
RGS13	6003	hgsc.bcm.edu	37	1	192613522	192613522	+	Missense_Mutation	SNP	C	C	T	rs146420296		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:192613522C>T	ENST00000391995.2	+	4	346	c.58C>T	c.(58-60)Cct>Tct	p.P20S	RGS13_ENST00000543215.1_Missense_Mutation_p.P20S	NM_002927.4	NP_002918.1	O14921	RGS13_HUMAN	regulator of G-protein signaling 13	20					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			endometrium(1)|kidney(1)|large_intestine(4)|lung(12)|skin(1)	19						TAAGAGGCCCCCTTCAAAGTA	0.289																																					p.P20S		Atlas-SNP	.											.	RGS13	31	.	0			c.C58T						PASS	.	C	SER/PRO,SER/PRO	1,4405	2.1+/-5.4	0,1,2202	122.0	135.0	131.0		58,58	3.7	0.5	1	dbSNP_134	131	0,8598		0,0,4299	no	missense,missense	RGS13	NM_002927.4,NM_144766.2	74,74	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	benign,benign	20/160,20/160	192613522	1,13003	2203	4299	6502	SO:0001583	missense	6003	exon4			AGGCCCCCTTCAA	AF030107	CCDS1376.1	1q31.2	2008-02-05	2007-08-14		ENSG00000127074	ENSG00000127074		"""Regulators of G-protein signaling"""	9995	protein-coding gene	gene with protein product		607190	"""regulator of G-protein signalling 13"""			11875076	Standard	NM_144766		Approved		uc001gsk.3	O14921	OTTHUMG00000035601	ENST00000391995.2:c.58C>T	1.37:g.192613522C>T	ENSP00000375853:p.Pro20Ser	235.0	0.0	0		214.0	96.0	0.448598	NM_002927	Q6PGR2|Q8TD63|Q9BX45	Missense_Mutation	SNP	ENST00000391995.2	37	CCDS1376.1	.	.	.	.	.	.	.	.	.	.	C	4.758	0.140916	0.09083	2.27E-4	0.0	ENSG00000127074	ENST00000391995;ENST00000543215	T;T	0.29655	1.56;1.56	5.62	3.67	0.42095	.	0.906400	0.09503	N	0.793331	T	0.18130	0.0435	N	0.24115	0.695	0.23653	N	0.997194	B	0.06786	0.001	B	0.06405	0.002	T	0.28073	-1.0055	10	0.07175	T	0.84	.	8.174	0.31270	0.0:0.7495:0.1625:0.0881	.	20	O14921	RGS13_HUMAN	S	20	ENSP00000375853:P20S;ENSP00000442837:P20S	ENSP00000375853:P20S	P	+	1	0	RGS13	190880145	0.086000	0.21541	0.478000	0.27316	0.701000	0.40568	1.077000	0.30741	1.460000	0.47911	0.655000	0.94253	CCT	C|1.000;T|0.000	0.000	weak		0.289	RGS13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086400.1	NM_002927	
MBOAT7	79143	hgsc.bcm.edu	37	19	54682538	54682538	+	Silent	SNP	C	C	T	rs116423748	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54682538C>T	ENST00000245615.1	-	7	1455	c.975G>A	c.(973-975)caG>caA	p.Q325Q	MBOAT7_ENST00000431666.2_Silent_p.Q252Q|MBOAT7_ENST00000391754.1_Silent_p.Q325Q|MBOAT7_ENST00000338624.6_Silent_p.Q252Q	NM_024298.3	NP_077274.3	Q96N66	MBOA7_HUMAN	membrane bound O-acyltransferase domain containing 7	325					glycerophospholipid biosynthetic process (GO:0046474)|layer formation in cerebral cortex (GO:0021819)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)|ventricular system development (GO:0021591)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	lysophospholipid acyltransferase activity (GO:0071617)			endometrium(4)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	10	all_cancers(19;0.0065)|all_epithelial(19;0.00348)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)					CCAGCCACCACTGCACCGTCA	0.567													C|||	37	0.00738818	0.0272	0.0014	5008	,	,		19150	0.0		0.0	False		,,,				2504	0.0				p.Q325Q	NSCLC(97;826 2151 10470 22540)	Atlas-SNP	.											.	MBOAT7	37	.	0			c.G975A						PASS	.	C	,,,	116,4290	86.3+/-125.0	2,112,2089	85.0	63.0	70.0		756,975,756,975	2.5	1.0	19	dbSNP_132	70	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MBOAT7	NM_001146056.1,NM_001146082.1,NM_001146083.1,NM_024298.3	,,,	2,113,6388	TT,TC,CC		0.0116,2.6328,0.8996	,,,	252/400,325/345,252/400,325/473	54682538	117,12889	2203	4300	6503	SO:0001819	synonymous_variant	79143	exon7			CCACCACTGCACC	AF211969	CCDS12883.1, CCDS54315.1, CCDS54316.1	19q13.4	2008-12-15	2008-01-17	2008-01-17	ENSG00000125505	ENSG00000125505			15505	protein-coding gene	gene with protein product	"""lysophosphatidylinositol acyltransferase"""	606048	"""leukocyte receptor cluster (LRC) member 4"""	LENG4		10941842, 8702217, 18094042	Standard	NM_024298		Approved	BB1, hMBOA-7, LPIAT	uc002qdr.3	Q96N66	OTTHUMG00000066516	ENST00000245615.1:c.975G>A	19.37:g.54682538C>T		100.0	0.0	0		121.0	61.0	0.504132	NM_001146082	A9C4B6|B0V3I5|B4DQ87|Q05DF0|Q7L5N2|Q99908|Q9BPV2|Q9BRE9	Silent	SNP	ENST00000245615.1	37	CCDS12883.1																																																																																			C|0.991;T|0.009	0.009	strong		0.567	MBOAT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142203.1	NM_024298	
NFAM1	150372	hgsc.bcm.edu	37	22	42805444	42805444	+	Missense_Mutation	SNP	G	G	C	rs17003048	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:42805444G>C	ENST00000329021.5	-	3	598	c.561C>G	c.(559-561)aaC>aaG	p.N187K		NM_145912.5	NP_666017.1	Q8NET5	NFAM1_HUMAN	NFAT activating protein with ITAM motif 1	187			N -> K (in dbSNP:rs17003048).		B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of cytokine production (GO:0001819)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of B cell differentiation (GO:0045577)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			large_intestine(1)|lung(3)	4						CCCGTACCTTGTTCCAGAGCA	0.662													C|||	158	0.0315495	0.1157	0.0058	5008	,	,		16803	0.0		0.001	False		,,,				2504	0.0				p.N187K		Atlas-SNP	.											.	NFAM1	12	.	0			c.C561G						PASS	.	C	LYS/ASN	450,3956	785.4+/-414.7	22,406,1775	102.0	96.0	98.0		561	4.8	1.0	22	dbSNP_123	98	3,8597	818.9+/-406.8	0,3,4297	yes	missense	NFAM1	NM_145912.5	94	22,409,6072	CC,CG,GG		0.0349,10.2133,3.483	benign	187/271	42805444	453,12553	2203	4300	6503	SO:0001583	missense	150372	exon3			TACCTTGTTCCAG	BC038241	CCDS14034.1	22q13.2	2005-02-01			ENSG00000235568	ENSG00000235568			29872	protein-coding gene	gene with protein product		608740				12615919	Standard	NM_145912		Approved	CNAIP	uc003bcn.4	Q8NET5	OTTHUMG00000150923	ENST00000329021.5:c.561C>G	22.37:g.42805444G>C	ENSP00000333680:p.Asn187Lys	72.0	0.0	0		80.0	42.0	0.525	NM_145912	B0QYD0|Q20WL2|Q5JZ96|Q8IUY8|Q8TEM8	Missense_Mutation	SNP	ENST00000329021.5	37	CCDS14034.1	55	0.025183150183150184	53	0.10772357723577236	2	0.0055248618784530384	0	0.0	0	0.0	C	0.145	-1.097589	0.01843	0.102133	3.49E-4	ENSG00000235568	ENST00000329021	T	0.18174	2.23	4.8	4.8	0.61643	.	0.000000	0.46145	N	0.000311	T	0.00073	0.0002	N	0.00159	-1.955	0.19300	N	0.99998	B	0.02656	0.0	B	0.01281	0.0	T	0.39354	-0.9618	10	0.02654	T	1	-15.1863	11.2161	0.48827	0.0:0.8139:0.1861:0.0	rs17003048;rs17003048	187	Q8NET5	NFAM1_HUMAN	K	187	ENSP00000333680:N187K	ENSP00000333680:N187K	N	-	3	2	NFAM1	41135388	1.000000	0.71417	1.000000	0.80357	0.058000	0.15608	1.335000	0.33839	1.036000	0.39998	-0.322000	0.08575	AAC	G|0.962;C|0.038	0.038	strong		0.662	NFAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320541.1	NM_145912	
UTP3	57050	hgsc.bcm.edu	37	4	71555656	71555656	+	Missense_Mutation	SNP	T	T	G	rs111975570	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:71555656T>G	ENST00000254803.2	+	1	1461	c.1262T>G	c.(1261-1263)cTt>cGt	p.L421R		NM_020368.2	NP_065101.1	Q9NQZ2	SAS10_HUMAN	UTP3, small subunit (SSU) processome component, homolog (S. cerevisiae)	421					brain development (GO:0007420)|chromatin modification (GO:0016568)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(4)	18			Lung(101;0.235)			AATAGGGGACTTACTCCTAGG	0.388													T|||	36	0.0071885	0.0272	0.0	5008	,	,		17360	0.0		0.0	False		,,,				2504	0.0				p.L421R		Atlas-SNP	.											.	UTP3	40	.	0			c.T1262G						PASS	.	T	ARG/LEU	64,4342	61.1+/-98.1	0,64,2139	89.0	95.0	93.0		1262	5.5	1.0	4	dbSNP_132	93	0,8600		0,0,4300	yes	missense	UTP3	NM_020368.2	102	0,64,6439	GG,GT,TT		0.0,1.4526,0.4921	probably-damaging	421/480	71555656	64,12942	2203	4300	6503	SO:0001583	missense	57050	exon1			GGGGACTTACTCC	AL136590	CCDS3546.1	4q13.3	2008-02-05			ENSG00000132467	ENSG00000132467			24477	protein-coding gene	gene with protein product	"""disrupter of silencing 10"""	611614				12477932	Standard	NM_020368		Approved	FLJ23256, DKFZp761F222, SAS10, CRLZ1	uc003hfo.3	Q9NQZ2	OTTHUMG00000129911	ENST00000254803.2:c.1262T>G	4.37:g.71555656T>G	ENSP00000254803:p.Leu421Arg	71.0	0.0	0		76.0	37.0	0.486842	NM_020368	Q6FI82	Missense_Mutation	SNP	ENST00000254803.2	37	CCDS3546.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	T	20.6	4.011830	0.75046	0.014526	0.0	ENSG00000132467	ENST00000254803	T	0.62788	-0.0	5.46	5.46	0.80206	Something about silencing protein 10 (Sas10), C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.70710	0.3255	H	0.96111	3.77	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.85360	0.1107	10	0.72032	D	0.01	-6.9132	15.8384	0.78818	0.0:0.0:0.0:1.0	.	421	Q9NQZ2	SAS10_HUMAN	R	421	ENSP00000254803:L421R	ENSP00000254803:L421R	L	+	2	0	UTP3	71774520	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.366000	0.79548	2.191000	0.70037	0.533000	0.62120	CTT	T|0.994;G|0.006	0.006	strong		0.388	UTP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252163.2	NM_020368	
ATOH1	474	hgsc.bcm.edu	37	4	94750227	94750227	+	Silent	SNP	G	G	A	rs138388359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:94750227G>A	ENST00000306011.3	+	1	186	c.150G>A	c.(148-150)ccG>ccA	p.P50P		NM_005172.1	NP_005163.1	Q92858	ATOH1_HUMAN	atonal homolog 1 (Drosophila)	50					auditory receptor cell fate determination (GO:0042668)|auditory receptor cell fate specification (GO:0042667)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|cerebral cortex development (GO:0021987)|inner ear morphogenesis (GO:0042472)|negative regulation of apoptotic process (GO:0043066)|neuron migration (GO:0001764)|positive regulation of auditory receptor cell differentiation (GO:0045609)|positive regulation of neuron differentiation (GO:0045666)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|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)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	11		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;3.57e-07)		CCGTCTACCCGCCTGAGCTGT	0.672													G|||	8	0.00159744	0.0061	0.0	5008	,	,		13999	0.0		0.0	False		,,,				2504	0.0				p.P50P		Atlas-SNP	.											.	ATOH1	40	.	0			c.G150A						PASS	.	G		30,4376	32.6+/-62.9	0,30,2173	34.0	36.0	35.0		150	-6.8	0.4	4	dbSNP_134	35	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous	ATOH1	NM_005172.1		0,31,6470	AA,AG,GG		0.0116,0.6809,0.2384		50/355	94750227	31,12971	2203	4298	6501	SO:0001819	synonymous_variant	474	exon1			CTACCCGCCTGAG	U61148	CCDS3638.1	4q22	2013-05-21			ENSG00000172238	ENSG00000172238		"""Basic helix-loop-helix proteins"""	797	protein-coding gene	gene with protein product		601461				8872459	Standard	NM_005172		Approved	HATH1, MATH-1, Math1, bHLHa14	uc003hta.1	Q92858	OTTHUMG00000130972	ENST00000306011.3:c.150G>A	4.37:g.94750227G>A		133.0	0.0	0		115.0	52.0	0.452174	NM_005172	Q14CT9	Silent	SNP	ENST00000306011.3	37	CCDS3638.1																																																																																			A|0.001;G|0.999;T|0.000	0.001	strong		0.672	ATOH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253585.1	NM_005172	
SRCIN1	80725	hgsc.bcm.edu	37	17	36708277	36708277	+	Missense_Mutation	SNP	C	C	T	rs7222929	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:36708277C>T	ENST00000264659.7	-	14	2796	c.2572G>A	c.(2572-2574)Gtg>Atg	p.V858M	SRCIN1_ENST00000578925.1_Missense_Mutation_p.V892M|SRCIN1_ENST00000398579.4_5'UTR	NM_025248.2	NP_079524.2	Q9C0H9	SRCN1_HUMAN	SRC kinase signaling inhibitor 1	730	Pro-rich.				exocytosis (GO:0006887)|negative regulation of protein tyrosine kinase activity (GO:0061099)|positive regulation of protein tyrosine kinase activity (GO:0061098)|regulation of cell migration (GO:0030334)|regulation of dendritic spine morphogenesis (GO:0061001)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	protein kinase binding (GO:0019901)	p.V858M(1)		endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)	19						TCGAAGTCCACGCTCTTGTTG	0.622													C|||	237	0.0473243	0.1679	0.0144	5008	,	,		17220	0.0		0.0	False		,,,				2504	0.0051				p.V858M		Atlas-SNP	.											SRCIN1,rectum,carcinoma,0,1	SRCIN1	66	1	1	Substitution - Missense(1)	large_intestine(1)	c.G2572A						scavenged	.	C	MET/VAL	600,3358		49,502,1428	40.0	47.0	45.0		2572	-1.4	0.4	17	dbSNP_116	45	10,8258		0,10,4124	yes	missense	SRCIN1	NM_025248.2	21	49,512,5552	TT,TC,CC		0.1209,15.1592,4.9894	benign	858/1184	36708277	610,11616	1979	4134	6113	SO:0001583	missense	80725	exon14			AGTCCACGCTCTT		CCDS45660.1	17q12	2009-12-14			ENSG00000017373	ENSG00000277363			29506	protein-coding gene	gene with protein product	"""p130Cas-associated protein"", ""SNAP-25-interacting protein"""	610786				11214970	Standard	NM_025248		Approved	SNIP, p140Cap, KIAA1684	uc002hqd.3	Q9C0H9		ENST00000264659.7:c.2572G>A	17.37:g.36708277C>T	ENSP00000264659:p.Val858Met	90.0	1.0	0.0111111		124.0	62.0	0.5	NM_025248	Q75T46|Q8N4W8	Missense_Mutation	SNP	ENST00000264659.7	37	CCDS45660.1	90	0.04120879120879121	84	0.17073170731707318	6	0.016574585635359115	0	0.0	0	0.0	C	6.675	0.493112	0.12702	0.151592	0.001209	ENSG00000017373	ENST00000264659;ENST00000542707;ENST00000398579	T	0.43688	0.94	4.69	-1.42	0.08913	.	0.364146	0.27420	N	0.019451	T	0.00039	0.0001	L	0.29908	0.895	0.51233	P	8.900000000000574E-5	P;B;B;B	0.36110	0.537;0.216;0.216;0.015	B;B;B;B	0.13407	0.009;0.004;0.004;0.002	T	0.14671	-1.0464	9	0.44086	T	0.13	-10.5966	0.5426	0.00648	0.3992:0.1273:0.2332:0.2403	rs7222929;rs52804512;rs7222929	164;730;730;858	Q9C0H9-4;Q9C0H9-2;Q9C0H9;Q9C0H9-5	.;.;SRCN1_HUMAN;.	M	858;639;712	ENSP00000264659:V858M	ENSP00000264659:V858M	V	-	1	0	SRCIN1	33961803	0.447000	0.25673	0.424000	0.26647	0.293000	0.27360	-0.300000	0.08243	-0.160000	0.11002	-1.334000	0.01262	GTG	C|0.930;T|0.070	0.070	strong		0.622	SRCIN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000441878.4	NM_025248	
PRSS36	146547	hgsc.bcm.edu	37	16	31151622	31151622	+	Missense_Mutation	SNP	C	C	T	rs61729752	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31151622C>T	ENST00000268281.4	-	14	2340	c.2282G>A	c.(2281-2283)aGg>aAg	p.R761K	PRSS36_ENST00000418068.2_Intron|PRSS36_ENST00000569305.1_Missense_Mutation_p.R756K	NM_001258290.1|NM_173502.4	NP_001245219.1|NP_775773.2	Q5K4E3	POLS2_HUMAN	protease, serine, 36	761	Peptidase S1 3. {ECO:0000255|PROSITE- ProRule:PRU00274}.					cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)	serine-type endopeptidase activity (GO:0004252)			kidney(2)|large_intestine(4)|lung(8)|ovary(3)	17						TACCTCACACCTGTTCTCCTG	0.537													c|||	78	0.0155751	0.0545	0.0086	5008	,	,		17560	0.0		0.0	False		,,,				2504	0.0				p.R761K		Atlas-SNP	.											.	PRSS36	50	.	0			c.G2282A						PASS	.		LYS/ARG	237,4157	139.6+/-175.2	8,221,1968	57.0	54.0	55.0		2282	2.9	1.0	16	dbSNP_129	55	1,8599	1.2+/-3.3	0,1,4299	yes	missense	PRSS36	NM_173502.3	26	8,222,6267	TT,TC,CC		0.0116,5.3937,1.8316	benign	761/856	31151622	238,12756	2197	4300	6497	SO:0001583	missense	146547	exon14			TCACACCTGTTCT	AK075142	CCDS32436.1, CCDS58452.1, CCDS58453.1	16p11.2	2014-09-04			ENSG00000178226			"""Serine peptidases / Serine peptidases"""	26906	protein-coding gene	gene with protein product	"""polyserase 2"""	610560				15536082	Standard	NM_173502		Approved	FLJ90661	uc002ebd.4	Q5K4E3	OTTHUMG00000176751	ENST00000268281.4:c.2282G>A	16.37:g.31151622C>T	ENSP00000268281:p.Arg761Lys	93.0	0.0	0		96.0	50.0	0.520833	NM_173502	A8K2P5|B4DW80|B7ZMK8|E7EX56|Q8NBY4	Missense_Mutation	SNP	ENST00000268281.4	37	CCDS32436.1	31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	C	10.18	1.279325	0.23307	0.053937	1.16E-4	ENSG00000178226	ENST00000268281	T	0.58940	0.3	4.92	2.86	0.33363	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.07818	0.0196	L	0.40543	1.245	0.21740	N	0.99957	B;B	0.09022	0.002;0.002	B;B	0.12156	0.007;0.007	T	0.12967	-1.0527	9	0.59425	D	0.04	.	6.1003	0.20043	0.0:0.7536:0.0:0.2464	.	756;761	B7ZMK8;Q5K4E3	.;POLS2_HUMAN	K	761	ENSP00000268281:R761K	ENSP00000268281:R761K	R	-	2	0	PRSS36	31059123	0.001000	0.12720	1.000000	0.80357	0.981000	0.71138	-0.769000	0.04710	1.125000	0.41998	0.555000	0.69702	AGG	C|0.982;T|0.018	0.018	strong		0.537	PRSS36-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000433542.1	NM_173502	
CCDC168	643677	hgsc.bcm.edu	37	13	103387667	103387667	+	Missense_Mutation	SNP	G	G	A	rs79455872	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:103387667G>A	ENST00000322527.2	-	1	1492	c.1493C>T	c.(1492-1494)tCa>tTa	p.S498L		NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168	498																	TACATCACTTGAAAGTTCTCC	0.428													G|||	160	0.0319489	0.1172	0.0043	5008	,	,		21385	0.0		0.001	False		,,,				2504	0.001				p.S5127L		Atlas-SNP	.											.	.	.	.	0			c.C15380T						PASS	.	G	LEU/SER	166,1218		11,144,537	93.0	72.0	78.0		15380	0.7	0.0	13	dbSNP_132	78	6,3176		0,6,1585	yes	missense	CCDC168	NM_001146197.1	145	11,150,2122	AA,AG,GG		0.1886,11.9942,3.767	probably-damaging	5127/7082	103387667	172,4394	692	1591	2283	SO:0001583	missense	643677	exon4			TCACTTGAAAGTT		CCDS73596.1	13q33.1	2014-06-17	2011-08-09	2011-08-09	ENSG00000175820	ENSG00000175820			26851	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 40"""	C13orf40			Standard	NM_001146197		Approved	FLJ40176	uc001vpm.3	Q8NDH2	OTTHUMG00000187287	ENST00000322527.2:c.1493C>T	13.37:g.103387667G>A	ENSP00000320232:p.Ser498Leu	271.0	0.0	0		286.0	132.0	0.461538	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	37		57	0.0260989010989011	56	0.11382113821138211	1	0.0027624309392265192	0	0.0	0	0.0	G	13.70	2.316654	0.40996	0.119942	0.001886	ENSG00000175820	ENST00000322527	T	0.03580	3.88	3.59	0.657	0.17850	.	0.303088	0.18152	N	0.150052	T	0.00109	0.0003	L	0.54323	1.7	0.09310	N	1	D	0.61697	0.99	P	0.58077	0.832	T	0.40040	-0.9584	10	0.21014	T	0.42	.	6.3169	0.21196	0.0:0.3699:0.4233:0.2068	.	498	Q8NDH2	CC168_HUMAN	L	498	ENSP00000320232:S498L	ENSP00000320232:S498L	S	-	2	0	CCDC168	102185668	0.000000	0.05858	0.000000	0.03702	0.089000	0.18198	0.183000	0.16919	0.082000	0.17018	0.467000	0.42956	TCA	G|0.970;A|0.030	0.030	strong		0.428	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
CTC1	80169	hgsc.bcm.edu	37	17	8141779	8141779	+	Silent	SNP	T	T	C	rs73244859	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:8141779T>C	ENST00000315684.8	-	3	373	c.366A>G	c.(364-366)gcA>gcG	p.A122A	CTC1_ENST00000581671.1_5'UTR	NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	122					bone marrow development (GO:0048539)|cellular response to DNA damage stimulus (GO:0006974)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organism growth (GO:0035264)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|replicative senescence (GO:0090399)|spleen development (GO:0048536)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)|thymus development (GO:0048538)	nuclear chromosome, telomeric region (GO:0000784)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|skin(4)	29						GTTCCAAGTCTGCCGATAGGT	0.547													C|||	111	0.0221645	0.0787	0.0	5008	,	,		19305	0.003		0.001	False		,,,				2504	0.0031				p.A122A		Atlas-SNP	.											.	CTC1	75	.	0			c.A366G						PASS	.	C		248,3754		8,232,1761	125.0	125.0	125.0		366	1.5	0.0	17	dbSNP_130	125	0,8334		0,0,4167	no	coding-synonymous	CTC1	NM_025099.5		8,232,5928	CC,CT,TT		0.0,6.1969,2.0104		122/1218	8141779	248,12088	2001	4167	6168	SO:0001819	synonymous_variant	80169	exon3			CAAGTCTGCCGAT	AL831955	CCDS42259.1	17p13.1	2011-02-21	2011-02-21	2011-02-21	ENSG00000178971	ENSG00000178971			26169	protein-coding gene	gene with protein product	"""conserved telomere maintenance component 1"", ""alpha accessory factor 132"", ""conserved telomere capping protein 1"""	613129	"""tmp494178"", ""chromosome 17 open reading frame 68"""	C17orf68		19854130, 19854131	Standard	NM_025099		Approved	FLJ22170, AAF132	uc002gkq.4	Q2NKJ3		ENST00000315684.8:c.366A>G	17.37:g.8141779T>C		208.0	0.0	0		201.0	102.0	0.507463	NM_025099	B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Silent	SNP	ENST00000315684.8	37	CCDS42259.1																																																																																			T|0.984;C|0.016	0.016	strong		0.547	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442012.1	NM_025099	
TNXB	7148	hgsc.bcm.edu	37	6	32014190	32014190	+	Silent	SNP	G	G	A	rs116701346	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32014190G>A	ENST00000375244.3	-	31	10569	c.10368C>T	c.(10366-10368)acC>acT	p.T3456T	TNXB_ENST00000375247.2_Silent_p.T3454T|TNXB_ENST00000451343.1_5'Flank			P22105	TENX_HUMAN	tenascin XB	3501	Fibronectin type-III 26. {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						CCTCAGCCACGGTCAGTTCCC	0.632													G|||	18	0.00359425	0.0129	0.0014	5008	,	,		18563	0.0		0.0	False		,,,				2504	0.0				p.T3454T		Atlas-SNP	.											.	TNXB	553	.	0			c.C10362T						PASS	.	G		13,2817		0,13,1402	27.0	32.0	30.0		10362	-4.5	0.2	6	dbSNP_132	30	2,5274		0,2,2636	no	coding-synonymous	TNXB	NM_019105.6		0,15,4038	AA,AG,GG		0.0379,0.4594,0.185		3454/4243	32014190	15,8091	1415	2638	4053	SO:0001819	synonymous_variant	7148	exon31			AGCCACGGTCAGT	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.10368C>T	6.37:g.32014190G>A		82.0	0.0	0		79.0	47.0	0.594937	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	37																																																																																				G|0.996;A|0.004	0.004	strong		0.632	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
NETO1	81832	hgsc.bcm.edu	37	18	70417378	70417378	+	Missense_Mutation	SNP	G	G	C	rs17086286	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:70417378G>C	ENST00000327305.6	-	9	2117	c.1460C>G	c.(1459-1461)gCa>gGa	p.A487G	NETO1_ENST00000583169.1_Missense_Mutation_p.A487G|NETO1_ENST00000299430.2_Missense_Mutation_p.A486G|RNA5SP460_ENST00000516789.1_RNA	NM_138966.3	NP_620416	Q8TDF5	NETO1_HUMAN	neuropilin (NRP) and tolloid (TLL)-like 1	487			A -> G (in dbSNP:rs17086286).		memory (GO:0007613)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|receptor localization to synapse (GO:0097120)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|visual learning (GO:0008542)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|kainate selective glutamate receptor complex (GO:0032983)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				NS(3)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(36)|ovary(2)|prostate(3)|skin(3)|stomach(1)	63		Esophageal squamous(42;0.129)		READ - Rectum adenocarcinoma(1;0.0487)		ACAGGCATCTGCAGCATCTTG	0.488													G|||	94	0.01877	0.0688	0.0043	5008	,	,		18531	0.0		0.0	False		,,,				2504	0.0				p.A487G		Atlas-SNP	.											.	NETO1	178	.	0			c.C1460G						PASS	.	G	GLY/ALA,GLY/ALA	265,4141	149.9+/-184.0	4,257,1942	165.0	141.0	149.0		1460,1460	4.9	0.8	18	dbSNP_123	149	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense	NETO1	NM_001201465.1,NM_138966.3	60,60	4,260,6239	CC,CG,GG		0.0349,6.0145,2.0606	possibly-damaging,possibly-damaging	487/534,487/534	70417378	268,12738	2203	4300	6503	SO:0001583	missense	81832	exon9			GCATCTGCAGCAT	AF448838	CCDS12000.1, CCDS42444.1	18q22.2	2008-08-01			ENSG00000166342	ENSG00000166342			13823	protein-coding gene	gene with protein product		607973				11943477, 12810072	Standard	NM_138999		Approved	BTCL1, BCTL1	uc002lkw.3	Q8TDF5	OTTHUMG00000132834	ENST00000327305.6:c.1460C>G	18.37:g.70417378G>C	ENSP00000313088:p.Ala487Gly	181.0	0.0	0		212.0	93.0	0.438679	NM_001201465	Q86W85|Q8ND78|Q8TDF4	Missense_Mutation	SNP	ENST00000327305.6	37	CCDS12000.1	34	0.015567765567765568	34	0.06910569105691057	0	0.0	0	0.0	0	0.0	G	17.20	3.327871	0.60743	0.060145	3.49E-4	ENSG00000166342	ENST00000327305;ENST00000299430	T;T	0.26518	1.74;1.73	5.76	4.86	0.63082	.	0.000000	0.64402	D	0.000014	T	0.02012	0.0063	L	0.42245	1.32	0.80722	D	1	P;P	0.40731	0.728;0.608	B;B	0.41036	0.346;0.188	T	0.00389	-1.1770	10	0.41790	T	0.15	-3.6568	16.2419	0.82418	0.0:0.0:0.8668:0.1332	rs17086286;rs52790393;rs17086286	486;487	Q8TDF5-2;Q8TDF5	.;NETO1_HUMAN	G	487;486	ENSP00000313088:A487G;ENSP00000299430:A486G	ENSP00000299430:A486G	A	-	2	0	NETO1	68568358	1.000000	0.71417	0.836000	0.33094	0.968000	0.65278	7.044000	0.76578	2.725000	0.93324	0.460000	0.39030	GCA	G|0.978;C|0.022	0.022	strong		0.488	NETO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256301.2	NM_138999	
PRR21	643905	hgsc.bcm.edu	37	2	240982009	240982009	+	Missense_Mutation	SNP	G	G	A	rs202192655		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:240982009G>A	ENST00000408934.1	-	1	390	c.391C>T	c.(391-393)Ccc>Tcc	p.P131S		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	131	Pro-rich.							p.P131S(2)		NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(5)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	29						AGGGCCGTGGGTGAAGAGGCA	0.647																																					p.P131S		Atlas-SNP	.											PRR21,NS,malignant_melanoma,0,2	PRR21	53	2	2	Substitution - Missense(2)	NS(2)	c.C391T						scavenged	.						4.0	3.0	3.0					2																	240982009		1301	2740	4041	SO:0001583	missense	643905	exon1			CCGTGGGTGAAGA	AF453950	CCDS33417.1	2q37.3	2009-04-20			ENSG00000221961	ENSG00000221961			33866	protein-coding gene	gene with protein product							Standard	NM_001080835		Approved		uc010zod.2	Q8WXC7	OTTHUMG00000159174	ENST00000408934.1:c.391C>T	2.37:g.240982009G>A	ENSP00000386166:p.Pro131Ser	35.0	0.0	0		12.0	2.0	0.166667	NM_001080835		Missense_Mutation	SNP	ENST00000408934.1	37	CCDS33417.1	.	.	.	.	.	.	.	.	.	.	-	0.018	-1.469388	0.01044	.	.	ENSG00000221961	ENST00000408934;ENST00000486799	T;T	0.13307	2.6;2.6	1.73	-3.03	0.05429	.	.	.	.	.	T	0.10766	0.0263	N	0.08118	0	0.09310	N	1	D	0.63880	0.993	P	0.61940	0.896	T	0.12993	-1.0526	9	0.10111	T	0.7	.	7.6745	0.28478	0.3709:0.0:0.6291:0.0	.	131	Q8WXC7	PRR21_HUMAN	S	131	ENSP00000386166:P131S;ENSP00000418240:P131S	ENSP00000386166:P131S	P	-	1	0	PRR21	240630682	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.053000	0.03500	-0.874000	0.04027	-0.481000	0.04817	CCC	.	.	weak		0.647	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
SPOCK2	9806	hgsc.bcm.edu	37	10	73826775	73826775	+	Silent	SNP	G	G	A	rs7079142	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73826775G>A	ENST00000373109.2	-	8	1257	c.813C>T	c.(811-813)gcC>gcT	p.A271A	SPOCK2_ENST00000460053.1_5'UTR|SPOCK2_ENST00000536168.1_Silent_p.A271A|SPOCK2_ENST00000317376.4_Silent_p.A271A	NM_001244950.1	NP_001231879.1	Q92563	TICN2_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 2	271					extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)|regulation of cell differentiation (GO:0045595)|signal transduction (GO:0007165)|synapse assembly (GO:0007416)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix binding (GO:0050840)|glycosaminoglycan binding (GO:0005539)			endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						GGTTGATGGCGGCCAGCTCCG	0.582													G|||	46	0.0091853	0.034	0.0014	5008	,	,		18389	0.0		0.0	False		,,,				2504	0.0				p.A271A		Atlas-SNP	.											.	SPOCK2	32	.	0			c.C813T						PASS	.	G		112,4294	85.8+/-124.5	0,112,2091	121.0	106.0	111.0		813	-7.5	0.6	10	dbSNP_116	111	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	SPOCK2	NM_014767.2		0,115,6388	AA,AG,GG		0.0349,2.542,0.8842		271/425	73826775	115,12891	2203	4300	6503	SO:0001819	synonymous_variant	9806	exon8			GATGGCGGCCAGC	AJ001453	CCDS7313.1, CCDS44431.1	10q22.1	2013-09-19			ENSG00000107742	ENSG00000107742			13564	protein-coding gene	gene with protein product		607988				10386950	Standard	NM_014767		Approved	KIAA0275, testican-2	uc001jso.2	Q92563	OTTHUMG00000018430	ENST00000373109.2:c.813C>T	10.37:g.73826775G>A		58.0	0.0	0		74.0	34.0	0.459459	NM_001244950	C9J767|Q6UW87	Silent	SNP	ENST00000373109.2	37	CCDS7313.1																																																																																			G|0.990;A|0.010	0.010	strong		0.582	SPOCK2-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048560.2		
PGLYRP2	114770	hgsc.bcm.edu	37	19	15587067	15587067	+	Silent	SNP	T	T	A	rs35927052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15587067T>A	ENST00000340880.4	-	2	894	c.414A>T	c.(412-414)atA>atT	p.I138I	PGLYRP2_ENST00000292609.4_Silent_p.I138I	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	138					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptide amidation (GO:0001519)|peptidoglycan catabolic process (GO:0009253)|regulation of inflammatory response (GO:0050727)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(2)|skin(3)|stomach(2)|urinary_tract(1)	28						AGGGCAAATTTATGACCCTGC	0.607													T|||	123	0.0245607	0.0477	0.0058	5008	,	,		18627	0.006		0.008	False		,,,				2504	0.0429				p.I138I		Atlas-SNP	.											.	PGLYRP2	116	.	0			c.A414T						PASS	.	T		193,4213	121.7+/-159.2	3,187,2013	85.0	77.0	79.0		414	-9.2	0.0	19	dbSNP_126	79	75,8525	44.9+/-103.4	0,75,4225	no	coding-synonymous	PGLYRP2	NM_052890.3		3,262,6238	AA,AT,TT		0.8721,4.3804,2.0606		138/577	15587067	268,12738	2203	4300	6503	SO:0001819	synonymous_variant	114770	exon2			CAAATTTATGACC	AY358156	CCDS12330.2	19p13.12	2010-04-27			ENSG00000161031	ENSG00000161031	3.5.1.28		30013	protein-coding gene	gene with protein product	"""peptidoglycan recognition protein L precursor"", ""peptidoglycan recognition protein-like"", ""N-acetylmuramoyl-L-alanine amidase"""	608199				11461926, 12669421, 14506276	Standard	NM_052890		Approved	PGRP-L, PGLYRPL, TAGL-like, tagL, tagL-alpha, tagl-beta, PGRPL	uc002nbf.4	Q96PD5	OTTHUMG00000150690	ENST00000340880.4:c.414A>T	19.37:g.15587067T>A		116.0	0.0	0		109.0	59.0	0.541284	NM_052890	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Silent	SNP	ENST00000340880.4	37	CCDS12330.2																																																																																			T|0.981;A|0.019	0.019	strong		0.607	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890	
WDR87	83889	hgsc.bcm.edu	37	19	38377404	38377404	+	Missense_Mutation	SNP	C	C	T	rs201328117		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38377404C>T	ENST00000303868.5	-	6	7014	c.6790G>A	c.(6790-6792)Gag>Aag	p.E2264K	WDR87_ENST00000447313.2_Missense_Mutation_p.E2303K	NM_031951.3	NP_114157.3	Q6ZQQ6	WDR87_HUMAN	WD repeat domain 87	2264	Glu-rich.									NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|prostate(1)|skin(3)|stomach(1)	36						tcctcctcctcccttacctcc	0.488																																					p.E2264K		Atlas-SNP	.											.	WDR87	191	.	0			c.G6790A						PASS	.						66.0	49.0	54.0					19																	38377404		692	1591	2283	SO:0001583	missense	83889	exon6			CCTCCTCCCTTAC	AK128826	CCDS46063.1, CCDS74356.1	19q13.13	2013-01-09			ENSG00000171804	ENSG00000171804		"""WD repeat domain containing"""	29934	protein-coding gene	gene with protein product							Standard	XM_005259304		Approved	NYD-SP11	uc010efu.2	Q6ZQQ6	OTTHUMG00000048187	ENST00000303868.5:c.6790G>A	19.37:g.38377404C>T	ENSP00000368025:p.Glu2264Lys	30.0	0.0	0		67.0	12.0	0.179104	NM_031951	Q9BWV9	Missense_Mutation	SNP	ENST00000303868.5	37	CCDS46063.1	.	.	.	.	.	.	.	.	.	.	C	10.21	1.286996	0.23478	.	.	ENSG00000171804	ENST00000447313;ENST00000303868	T;T	0.41400	1.0;1.0	4.47	4.47	0.54385	.	.	.	.	.	T	0.39682	0.1087	L	0.29908	0.895	0.09310	N	1	D;D	0.69078	0.997;0.997	P;P	0.58577	0.841;0.841	T	0.13872	-1.0493	9	0.06099	T	0.92	.	9.1387	0.36890	0.0:0.8956:0.0:0.1044	.	2264;2303	Q6ZQQ6;E7ESW6	WDR87_HUMAN;.	K	2303;2264	ENSP00000405012:E2303K;ENSP00000368025:E2264K	ENSP00000368025:E2264K	E	-	1	0	WDR87	43069244	0.001000	0.12720	0.064000	0.19789	0.078000	0.17371	0.800000	0.27042	2.412000	0.81896	0.450000	0.29827	GAG	.	.	weak		0.488	WDR87-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314628.2	XM_940478	
ZNF285	26974	hgsc.bcm.edu	37	19	44891748	44891748	+	Missense_Mutation	SNP	T	T	C	rs60800862	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44891748T>C	ENST00000330997.4	-	4	723	c.659A>G	c.(658-660)gAa>gGa	p.E220G	CTC-512J12.6_ENST00000588212.1_Intron|ZNF285_ENST00000591679.1_Missense_Mutation_p.E227G|ZNF285_ENST00000544719.2_Missense_Mutation_p.E220G	NM_152354.3	NP_689567.3	Q96NJ3	ZN285_HUMAN	zinc finger protein 285	220					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|prostate(5)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	44						ATTACGTTTTTCAACCGTTGA	0.463													T|||	110	0.0219649	0.0809	0.0043	5008	,	,		19447	0.0		0.0	False		,,,				2504	0.0				p.E220G		Atlas-SNP	.											.	ZNF285	86	.	0			c.A659G						PASS	.	T	GLY/GLU	255,4151	145.4+/-180.2	6,243,1954	103.0	100.0	101.0		659	-0.2	0.0	19	dbSNP_129	101	1,8599		0,1,4299	yes	missense	ZNF285	NM_152354.3	98	6,244,6253	CC,CT,TT		0.0116,5.7876,1.9683		220/591	44891748	256,12750	2203	4300	6503	SO:0001583	missense	26974	exon4			CGTTTTTCAACCG	AK055309	CCDS12638.1, CCDS74389.1	19q13.32	2013-01-08	2010-04-14	2010-04-14		ENSG00000267508		"""Zinc fingers, C2H2-type"", ""-"""	13079	protein-coding gene	gene with protein product			"""zinc finger protein 285A"""	ZNF285A			Standard	XM_005258734		Approved			Q96NJ3	OTTHUMG00000178848	ENST00000330997.4:c.659A>G	19.37:g.44891748T>C	ENSP00000333595:p.Glu220Gly	134.0	0.0	0		133.0	60.0	0.451128	NM_152354	Q17RJ3|Q6B0A8|Q6ISR5	Missense_Mutation	SNP	ENST00000330997.4	37	CCDS12638.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	T	6.112	0.388881	0.11581	0.057876	1.16E-4	ENSG00000062370	ENST00000544719;ENST00000330997	T	0.28454	1.61	3.27	-0.157	0.13387	.	.	.	.	.	T	0.01905	0.0060	L	0.38175	1.15	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.21075	-1.0256	9	0.24483	T	0.36	.	3.8075	0.08783	0.1682:0.3505:0.0:0.4813	rs60800862	244;220	B7ZLR9;Q96NJ3	.;ZN285_HUMAN	G	243;220	ENSP00000333595:E220G	ENSP00000333595:E220G	E	-	2	0	ZNF285	49583588	0.000000	0.05858	0.002000	0.10522	0.168000	0.22595	-0.057000	0.11768	0.046000	0.15833	0.373000	0.22412	GAA	T|0.983;C|0.017	0.017	strong		0.463	ZNF285-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443600.1	NM_152354	
MT-CO1	4512	hgsc.bcm.edu	37	M	6253	6253	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:6253T>C	ENST00000361624.2	+	1	350	c.350T>C	c.(349-351)aTa>aCa	p.I117T	MT-TL1_ENST00000386347.1_RNA|MT-ATP6_ENST00000361899.2_5'Flank|MT-TD_ENST00000387419.1_RNA|MT-CO3_ENST00000362079.2_5'Flank|MT-TA_ENST00000387392.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-TY_ENST00000387409.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ATP8_ENST00000361851.1_5'Flank|MT-TN_ENST00000387400.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-TI_ENST00000387365.1_RNA|MT-CO2_ENST00000361739.1_5'Flank			P00395	COX1_HUMAN	mitochondrially encoded cytochrome c oxidase I	117					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex IV (GO:0005751)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(4)|endometrium(25)|kidney(19)|lung(3)|prostate(3)	54						CGCATCTGCTATAGTGGAGGC	0.537																																					p.M117T		Atlas-SNP	.											.	.	.	.	0			c.T350C						PASS	.																																			SO:0001583	missense	5742	exon1			CTGCTATAGTGGA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198804	ENSG00000198804		"""Mitochondrial respiratory chain complex / Complex IV"""	7419	protein-coding gene	gene with protein product		516030	"""cytochrome c oxidase I"""	MTCO1		7219534	Standard			Approved	COX1, COI		P00395		ENST00000361624.2:c.350T>C	M.37:g.6253T>C	ENSP00000354499:p.Ile117Thr	11.0	0.0	0		12.0	12.0	1	ENST00000361624	Q34770	Missense_Mutation	SNP	ENST00000361624.2	37																																																																																				.	.	none		0.537	MT-CO1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024028	
BDP1	55814	hgsc.bcm.edu	37	5	70845400	70845400	+	Missense_Mutation	SNP	A	A	G	rs59354595	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:70845400A>G	ENST00000358731.4	+	34	7225	c.6962A>G	c.(6961-6963)aAa>aGa	p.K2321R	BDP1_ENST00000380675.2_Intron	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	2321					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		ATATTGGTCAAATCAGTGAAT	0.418													A|||	204	0.0407348	0.146	0.013	5008	,	,		18672	0.0		0.002	False		,,,				2504	0.0				p.K2321R		Atlas-SNP	.											.	BDP1	204	.	0			c.A6962G						PASS	.	A	ARG/LYS	479,3309		28,423,1443	93.0	88.0	89.0		6962	2.3	0.8	5	dbSNP_129	89	3,8211		0,3,4104	yes	missense	BDP1	NM_018429.2	26	28,426,5547	GG,GA,AA		0.0365,12.6452,4.016	benign	2321/2625	70845400	482,11520	1894	4107	6001	SO:0001583	missense	55814	exon34			TGGTCAAATCAGT	AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"""TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"""	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.6962A>G	5.37:g.70845400A>G	ENSP00000351575:p.Lys2321Arg	218.0	0.0	0		228.0	103.0	0.451754	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	37	CCDS43328.1	79	0.036172161172161175	73	0.1483739837398374	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	A	12.53	1.964625	0.34659	0.126452	3.65E-4	ENSG00000145734	ENST00000358731;ENST00000451951	T	0.04551	3.6	5.96	2.27	0.28462	.	0.277827	0.31577	N	0.007413	T	0.00012	0.0000	N	0.21448	0.665	0.80722	D	1	B	0.28178	0.202	B	0.26202	0.067	T	0.61033	-0.7144	10	0.12766	T	0.61	.	4.5339	0.12019	0.6602:0.1661:0.1737:0.0	rs59354595;rs61734266	2321	A6H8Y1	BDP1_HUMAN	R	2321;1869	ENSP00000351575:K2321R	ENSP00000351575:K2321R	K	+	2	0	BDP1	70881156	0.700000	0.27796	0.848000	0.33437	0.954000	0.61252	0.169000	0.16641	0.157000	0.19338	0.533000	0.62120	AAA	A|0.963;G|0.037	0.037	strong		0.418	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429	
FCGR3A	2214	hgsc.bcm.edu	37	1	161518233	161518233	+	Silent	SNP	C	C	A	rs139622799	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:161518233C>A	ENST00000436743.1	-	4	451	c.297G>T	c.(295-297)ccG>ccT	p.P99P	FCGR3A_ENST00000367969.3_Silent_p.P135P|RP11-25K21.6_ENST00000537821.2_RNA|FCGR3A_ENST00000476031.1_5'UTR|FCGR3A_ENST00000443193.1_Silent_p.P134P|FCGR3A_ENST00000540048.1_Silent_p.P99P	NM_001127593.1|NM_001127595.1|NM_001127596.1	NP_001121065.1|NP_001121067.1|NP_001121068.1	P08637	FCG3A_HUMAN	Fc fragment of IgG, low affinity IIIa, receptor (CD16a)	99	Ig-like C2-type 1.				Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	24	all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	CTAGCTGCACCGGGTCACTGA	0.512																																					p.P135P		Atlas-SNP	.											FCGR3A,lower_third,carcinoma,-2,1	FCGR3A	38	1	0			c.G405T						scavenged	.	C	,,,,	144,4262	81.4+/-119.9	0,144,2059	114.0	112.0	113.0		405,402,297,297,294	-8.9	0.0	1	dbSNP_134	113	7,8587	5.0+/-18.6	0,7,4290	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FCGR3A	NM_000569.6,NM_001127592.1,NM_001127593.1,NM_001127595.1,NM_001127596.1	,,,,	0,151,6349	AA,AC,CC		0.0815,3.2683,1.1615	,,,,	135/291,134/290,99/255,99/255,98/254	161518233	151,12849	2203	4297	6500	SO:0001819	synonymous_variant	2214	exon3			CTGCACCGGGTCA	BC036723	CCDS1232.1, CCDS44266.1	1q23	2014-09-17	2005-02-02		ENSG00000203747	ENSG00000203747		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3619	protein-coding gene	gene with protein product		146740	"""Fc fragment of IgG, low affinity IIIa, receptor for (CD16)"""	FCGR3, FCG3		2139735	Standard	NM_001127592		Approved	CD16, CD16a	uc001gar.3	P08637	OTTHUMG00000034466	ENST00000436743.1:c.297G>T	1.37:g.161518233C>A		488.0	2.0	0.00409836		585.0	181.0	0.309402	NM_000569	A2N6W9|Q53FJ0|Q53FL6|Q5EBR4|Q65ZM6|Q6PIJ0	Silent	SNP	ENST00000436743.1	37	CCDS44266.1	32	0.014652014652014652	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	C	11.25	1.583746	0.28268	0.032683	8.15E-4	ENSG00000203747	ENST00000426740	.	.	.	4.43	-8.86	0.00795	.	.	.	.	.	T	0.26011	0.0634	.	.	.	0.38428	D	0.94635	.	.	.	.	.	.	T	0.47873	-0.9083	4	.	.	.	.	7.0855	0.25255	0.2513:0.1676:0.0:0.5811	.	.	.	.	L	116	.	.	R	-	2	0	FCGR3A	159784857	0.000000	0.05858	0.029000	0.17559	0.763000	0.43281	-5.433000	0.00123	-3.094000	0.00246	-0.218000	0.12543	CGG	C|0.985;A|0.015	0.015	strong		0.512	FCGR3A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102169.2	NM_000569	
TLR3	7098	hgsc.bcm.edu	37	4	187004544	187004544	+	Silent	SNP	C	C	T	rs35111588	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:187004544C>T	ENST00000296795.3	+	4	1808	c.1704C>T	c.(1702-1704)aaC>aaT	p.N568N	TLR3_ENST00000504367.1_Silent_p.N291N	NM_003265.2	NP_003256.1	O15455	TLR3_HUMAN	toll-like receptor 3	568					activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to drug (GO:0035690)|cellular response to exogenous dsRNA (GO:0071360)|cellular response to interferon-beta (GO:0035458)|cellular response to interferon-gamma (GO:0071346)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to virus (GO:0051607)|detection of virus (GO:0009597)|extrinsic apoptotic signaling pathway (GO:0097191)|hyperosmotic response (GO:0006972)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|microglial cell activation involved in immune response (GO:0002282)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|necroptotic signaling pathway (GO:0097527)|negative regulation of osteoclast differentiation (GO:0045671)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chemokine biosynthetic process (GO:0045080)|positive regulation of chemokine production (GO:0032722)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha biosynthetic process (GO:0045356)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type III interferon production (GO:0034346)|response to exogenous dsRNA (GO:0043330)|signal transduction (GO:0007165)|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)|endolysosome membrane (GO:0036020)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	double-stranded RNA binding (GO:0003725)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.47e-11)|BRCA - Breast invasive adenocarcinoma(30;1.14e-05)|GBM - Glioblastoma multiforme(59;0.000107)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.16)		ACATCCTTAACTTGGAGTCCA	0.423													C|||	296	0.0591054	0.2156	0.013	5008	,	,		20763	0.0		0.002	False		,,,				2504	0.0				p.N568N		Atlas-SNP	.											.	TLR3	83	.	0			c.C1704T						PASS	.	C		714,3692	297.8+/-285.0	60,594,1549	92.0	90.0	91.0		1704	-2.8	0.9	4	dbSNP_126	91	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	TLR3	NM_003265.2		60,602,5841	TT,TC,CC		0.093,16.2052,5.5513		568/905	187004544	722,12284	2203	4300	6503	SO:0001819	synonymous_variant	7098	exon4			CCTTAACTTGGAG	U88879	CCDS3846.1	4q35	2014-09-17				ENSG00000164342		"""CD molecules"""	11849	protein-coding gene	gene with protein product		603029				9435236	Standard	NM_003265		Approved	CD283	uc003iyq.3	O15455		ENST00000296795.3:c.1704C>T	4.37:g.187004544C>T		116.0	0.0	0		109.0	45.0	0.412844	NM_003265	B2RAI7|B7Z7K0|E6Y0F0|E6Y0F1|E9PGH4|Q4VAL2|Q504W0	Silent	SNP	ENST00000296795.3	37	CCDS3846.1																																																																																			C|0.949;T|0.051	0.051	strong		0.423	TLR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360313.4		
ORAOV1	220064	hgsc.bcm.edu	37	11	69490001	69490001	+	Missense_Mutation	SNP	C	C	T	rs56107468	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:69490001C>T	ENST00000535657.1	-	1	88	c.7G>A	c.(7-9)Ggc>Agc	p.G3S	ORAOV1_ENST00000542341.1_Missense_Mutation_p.G3S|ORAOV1_ENST00000539414.1_Missense_Mutation_p.G3S|ORAOV1_ENST00000279147.4_Missense_Mutation_p.G3S|ORAOV1_ENST00000536870.1_Missense_Mutation_p.G3S			Q8WV07	ORAV1_HUMAN	oral cancer overexpressed 1	3			G -> S (in dbSNP:rs56107468).							NS(1)|endometrium(1)|large_intestine(2)|lung(1)	5	all_cancers(3;5.53e-114)|all_epithelial(3;1.34e-121)|Breast(3;9.28e-34)|all_lung(4;1.99e-21)|Lung NSC(4;4.65e-21)|Hepatocellular(3;6.15e-15)|Melanoma(5;1.89e-05)|Ovarian(3;0.0348)		Epithelial(3;5.64e-57)|all cancers(3;5.98e-51)|BRCA - Breast invasive adenocarcinoma(2;5.49e-48)|Lung(3;1.13e-16)|LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)|LUAD - Lung adenocarcinoma(13;0.0537)			TCCTGACTGCCAGCCATAGCG	0.677													C|||	111	0.0221645	0.0802	0.0072	5008	,	,		15446	0.0		0.0	False		,,,				2504	0.0				p.G3S		Atlas-SNP	.											.	ORAOV1	11	.	0			c.G7A						PASS	.	C	SER/GLY	279,4109		8,263,1923	28.0	26.0	26.0		7	1.8	0.1	11	dbSNP_129	26	3,8577		0,3,4287	yes	missense	ORAOV1	NM_153451.2	56	8,266,6210	TT,TC,CC		0.035,6.3582,2.1746	benign	3/138	69490001	282,12686	2194	4290	6484	SO:0001583	missense	220064	exon1			GACTGCCAGCCAT		CCDS8192.1	11q13.2	2010-11-23			ENSG00000149716	ENSG00000149716			17589	protein-coding gene	gene with protein product	"""oral cancer overexpressed protein 1-A"""	607224				12172009	Standard	NM_153451		Approved	TAOS1	uc001opc.3	Q8WV07		ENST00000535657.1:c.7G>A	11.37:g.69490001C>T	ENSP00000446129:p.Gly3Ser	227.0	0.0	0		218.0	101.0	0.463303	NM_153451	B2R4R2|Q8NFK0	Missense_Mutation	SNP	ENST00000535657.1	37	CCDS8192.1	46	0.021062271062271064	42	0.08536585365853659	4	0.011049723756906077	0	0.0	0	0.0	C	12.95	2.091045	0.36855	0.063582	3.5E-4	ENSG00000149716	ENST00000538554;ENST00000376587;ENST00000279147;ENST00000536870;ENST00000535657;ENST00000539414;ENST00000441922;ENST00000542341;ENST00000355486;ENST00000543023	T;T;T;T;T;T;T	0.44083	0.95;1.04;0.93;1.04;1.03;0.97;1.03	3.78	1.83	0.25207	.	0.922530	0.09022	N	0.859968	T	0.01029	0.0034	L	0.40543	1.245	0.09310	N	1	B;B;B;B	0.34015	0.435;0.034;0.004;0.041	B;B;B;B	0.35510	0.204;0.017;0.01;0.017	T	0.09662	-1.0664	10	0.09338	T	0.73	-25.5519	3.1767	0.06571	0.209:0.5597:0.0:0.2313	rs56107468	3;3;3;3	B4DFA5;F5H6T8;F5GWS9;Q8WV07	.;.;.;ORAV1_HUMAN	S	3	ENSP00000446428:G3S;ENSP00000279147:G3S;ENSP00000441984:G3S;ENSP00000446129:G3S;ENSP00000444112:G3S;ENSP00000409643:G3S;ENSP00000437367:G3S	ENSP00000279147:G3S	G	-	1	0	ORAOV1	69199182	0.000000	0.05858	0.060000	0.19600	0.298000	0.27526	0.050000	0.14120	0.878000	0.35920	0.561000	0.74099	GGC	C|0.978;T|0.022	0.022	strong		0.677	ORAOV1-009	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000396821.1	NM_153451	
USP17L2	377630	hgsc.bcm.edu	37	8	11995276	11995276	+	Missense_Mutation	SNP	C	C	T	rs372605534	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11995276C>T	ENST00000333796.3	-	1	1310	c.994G>A	c.(994-996)Gac>Aac	p.D332N	FAM66D_ENST00000434078.2_RNA	NM_001256869.1|NM_001256871.1|NM_001256872.1|NM_001256873.1|NM_001256874.1|NM_201402.2	NP_001243798.1|NP_001243800.1|NP_001243801.1|NP_001243802.1|NP_001243803.1|NP_958804.2	Q6R6M4	U17L2_HUMAN	ubiquitin specific peptidase 17-like family member 2	332	USP.			D -> N (in Ref. 1; AAR91701). {ECO:0000305}.	apoptotic process (GO:0006915)|CAAX-box protein processing (GO:0071586)|cell cycle checkpoint (GO:0000075)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of histone deacetylation (GO:0031064)|negative regulation of protein processing (GO:0010955)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of Ras GTPase activity (GO:0034261)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of RIG-I signaling pathway (GO:1900246)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of apoptotic process (GO:0042981)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of defense response to virus by host (GO:0050691)|regulation of ruffle assembly (GO:1900027)|ubiquitin-dependent protein catabolic process (GO:0006511)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.D332N(1)		central_nervous_system(1)|kidney(1)|large_intestine(11)|liver(1)|lung(8)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	29						TAATGTCCGTCGTGACAACTC	0.493													T|||	288	0.057508	0.1876	0.0288	5008	,	,		20795	0.005		0.003	False		,,,				2504	0.0123				p.D332N		Atlas-SNP	.											USP17L2,NS,carcinoma,0,1	USP17L2	47	1	1	Substitution - Missense(1)	ovary(1)	c.G994A						scavenged	.						21.0	24.0	23.0					8																	11995276		1690	3931	5621	SO:0001583	missense	377630	exon1			GTCCGTCGTGACA	BC156290	CCDS43713.1	8p23.1	2012-10-09	2012-10-09		ENSG00000223443	ENSG00000223443			34434	protein-coding gene	gene with protein product	"""deubiquitinating enzyme 3"""	610186	"""ubiquitin specific peptidase 17-like 2"""				Standard	NM_201402		Approved	DUB3	uc003wvc.1	Q6R6M4	OTTHUMG00000165295	ENST00000333796.3:c.994G>A	8.37:g.11995276C>T	ENSP00000333329:p.Asp332Asn	322.0	2.0	0.00621118		351.0	148.0	0.421652	NM_201402		Missense_Mutation	SNP	ENST00000333796.3	37	CCDS43713.1	.	.	.	.	.	.	.	.	.	.	T	4.883	0.164168	0.09287	.	.	ENSG00000223443	ENST00000333796	T	0.28895	1.59	0.935	-0.328	0.12690	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2, conserved site (1);Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.717965	0.12292	N	0.481969	T	0.12817	0.0311	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42378	-0.9455	8	0.08381	T	0.77	.	6.32	0.21213	0.0:0.6535:0.0:0.3465	.	332	Q6R6M4	U17L2_HUMAN	N	332	ENSP00000333329:D332N	ENSP00000333329:D332N	D	-	1	0	USP17L2	12032685	1.000000	0.71417	0.001000	0.08648	0.007000	0.05969	2.426000	0.44731	-0.621000	0.05633	-0.849000	0.03036	GAC	.	.	weak		0.493	USP17L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383303.2	NM_201402	
RACGAP1	29127	hgsc.bcm.edu	37	12	50384469	50384469	+	Silent	SNP	A	A	G	rs56699050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:50384469A>G	ENST00000427314.2	-	18	2044	c.1821T>C	c.(1819-1821)ccT>ccC	p.P607P	RACGAP1_ENST00000434422.1_Silent_p.P607P|RACGAP1_ENST00000454520.2_Silent_p.P607P|RACGAP1_ENST00000548961.1_Intron|RACGAP1_ENST00000547905.1_Silent_p.P607P|RACGAP1_ENST00000551016.1_Silent_p.P607P|RACGAP1_ENST00000312377.5_Silent_p.P607P	NM_013277.3	NP_037409.2			Rac GTPase activating protein 1											cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(6)	14						CTGCATACCTAGGAGTGTTCT	0.403													G|||	407	0.08127	0.2988	0.0173	5008	,	,		18804	0.0		0.0	False		,,,				2504	0.0				p.P607P		Atlas-SNP	.											.	RACGAP1	36	.	0			c.T1821C						PASS	.	G	,,	1092,3314	721.2+/-409.1	136,820,1247	106.0	109.0	108.0		1821,1821,1821	2.9	1.0	12	dbSNP_129	108	5,8595	819.1+/-406.8	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	RACGAP1	NM_001126103.1,NM_001126104.1,NM_013277.3	,,	136,825,5542	GG,GA,AA		0.0581,24.7844,8.4346	,,	607/633,607/633,607/633	50384469	1097,11909	2203	4300	6503	SO:0001819	synonymous_variant	29127	exon18			ATACCTAGGAGTG		CCDS8795.1	12q13	2004-05-17				ENSG00000161800			9804	protein-coding gene	gene with protein product		604980				9497316	Standard	NM_013277		Approved	MgcRacGAP	uc001rvs.2	Q9H0H5		ENST00000427314.2:c.1821T>C	12.37:g.50384469A>G		136.0	0.0	0		132.0	70.0	0.530303	NM_013277		Silent	SNP	ENST00000427314.2	37	CCDS8795.1																																																																																			A|0.918;G|0.082	0.082	strong		0.403	RACGAP1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405997.1	NM_013277	
ZNF80	7634	hgsc.bcm.edu	37	3	113955726	113955726	+	Nonsense_Mutation	SNP	G	G	A	rs79892855	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:113955726G>A	ENST00000482457.2	-	1	699	c.196C>T	c.(196-198)Cga>Tga	p.R66*	RP11-553L6.2_ENST00000481773.1_RNA|RP11-553L6.2_ENST00000493033.1_RNA	NM_007136.3	NP_009067.2	P51504	ZNF80_HUMAN	zinc finger protein 80	66					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)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|urinary_tract(2)	32		Lung NSC(201;0.0233)|all_neural(597;0.0837)				TGCTGATGTCGAACAAGGAGG	0.483													G|||	74	0.0147764	0.053	0.0043	5008	,	,		24200	0.0		0.0	False		,,,				2504	0.001				p.R66X	GBM(23;986 1114 21716)	Atlas-SNP	.											.	ZNF80	75	.	0			c.C196T						PASS	.	G	stop/ARG	188,4218	120.4+/-158.0	5,178,2020	105.0	90.0	95.0		196	-1.3	0.0	3	dbSNP_131	95	0,8600		0,0,4300	yes	stop-gained	ZNF80	NM_007136.3		5,178,6320	AA,AG,GG		0.0,4.2669,1.4455		66/274	113955726	188,12818	2203	4300	6503	SO:0001587	stop_gained	7634	exon1			GATGTCGAACAAG	X65233	CCDS2979.1	3q13.31	2013-01-08	2006-05-12		ENSG00000174255	ENSG00000174255		"""Zinc fingers, C2H2-type"""	13155	protein-coding gene	gene with protein product		194553	"""zinc finger protein 80 (pT17)"""			8478004	Standard	NM_007136		Approved	pT17	uc010hqo.3	P51504	OTTHUMG00000159332	ENST00000482457.2:c.196C>T	3.37:g.113955726G>A	ENSP00000417192:p.Arg66*	88.0	0.0	0		89.0	40.0	0.449438	NM_007136	Q6NSW4|Q6NT14	Nonsense_Mutation	SNP	ENST00000482457.2	37	CCDS2979.1	28	0.01282051282051282	26	0.052845528455284556	2	0.0055248618784530384	0	0.0	0	0.0	G	33	5.211008	0.95069	0.042669	0.0	ENSG00000174255	ENST00000482457	.	.	.	3.01	-1.33	0.09172	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.18276	T	0.48	.	0.2983	0.00269	0.2292:0.1648:0.2619:0.3441	.	.	.	.	X	66	.	ENSP00000309812:R66X	R	-	1	2	ZNF80	115438416	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.585000	0.00423	-0.318000	0.08665	-0.136000	0.14681	CGA	G|0.987;A|0.013	0.013	strong		0.483	ZNF80-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354696.2	NM_007136	
VWF	7450	hgsc.bcm.edu	37	12	6182828	6182828	+	Missense_Mutation	SNP	A	A	T	rs1800387	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:6182828A>T	ENST00000261405.5	-	8	1208	c.954T>A	c.(952-954)aaT>aaA	p.N318K		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	318	TIL 1.		N -> K (in dbSNP:rs1800387).		blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	GACACATTTCATTGATGTGCA	0.537													A|||	779	0.155551	0.4705	0.0735	5008	,	,		20376	0.001		0.0328	False		,,,				2504	0.0736				p.N318K		Atlas-SNP	.											.	VWF	338	.	0			c.T954A						PASS	.	A	LYS/ASN	1814,2592	532.8+/-373.5	380,1054,769	121.0	101.0	108.0		954	-3.5	0.0	12	dbSNP_89	108	222,8378	92.8+/-154.8	1,220,4079	yes	missense	VWF	NM_000552.3	94	381,1274,4848	TT,TA,AA		2.5814,41.1711,15.6543	benign	318/2814	6182828	2036,10970	2203	4300	6503	SO:0001583	missense	7450	exon8			CATTTCATTGATG		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.954T>A	12.37:g.6182828A>T	ENSP00000261405:p.Asn318Lys	77.0	0.0	0		88.0	28.0	0.318182	NM_000552	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	283	0.1295787545787546	235	0.47764227642276424	30	0.08287292817679558	0	0.0	18	0.023746701846965697	A	13.32	2.203429	0.38905	0.411711	0.025814	ENSG00000110799	ENST00000261405	D	0.90069	-2.61	5.07	-3.54	0.04653	Protease inhibitor I8, cysteine-rich trypsin inhibitor-like (2);	1.028730	0.07777	N	0.952644	T	0.00012	0.0000	L	0.42632	1.34	0.09310	P	0.99999999821589	B;P	0.42161	0.005;0.772	B;B	0.40444	0.02;0.329	T	0.09357	-1.0678	9	0.32370	T	0.25	.	1.2239	0.01929	0.3764:0.2668:0.2306:0.1262	rs1800387;rs56444638;rs1800387	318;318	B4DNX0;P04275	.;VWF_HUMAN	K	318	ENSP00000261405:N318K	ENSP00000261405:N318K	N	-	3	2	VWF	6053089	0.916000	0.31088	0.012000	0.15200	0.881000	0.50899	0.118000	0.15605	-0.694000	0.05113	0.402000	0.26972	AAT	A|0.839;T|0.161	0.161	strong		0.537	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
KRT75	9119	hgsc.bcm.edu	37	12	52822464	52822464	+	Missense_Mutation	SNP	T	T	C	rs2232402	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52822464T>C	ENST00000252245.5	-	6	1319	c.1099A>G	c.(1099-1101)Atc>Gtc	p.I367V	RP11-1020M18.10_ENST00000548135.1_RNA	NM_004693.2	NP_004684.2	O95678	K2C75_HUMAN	keratin 75	367	Coil 2.|Rod.		I -> V (in dbSNP:rs2232402).		hematopoietic progenitor cell differentiation (GO:0002244)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(13)|lung(10)|prostate(1)|skin(1)	28				BRCA - Breast invasive adenocarcinoma(357;0.192)		ATTTCAGAGATCTCTTGTTTG	0.512													T|||	103	0.0205671	0.0764	0.0029	5008	,	,		21269	0.0		0.0	False		,,,				2504	0.0				p.I367V		Atlas-SNP	.											KRT75,NS,carcinoma,+2,3	KRT75	75	3	0			c.A1099G						PASS	.	T	VAL/ILE	373,4033	189.2+/-215.4	16,341,1846	193.0	158.0	170.0		1099	5.2	1.0	12	dbSNP_98	170	1,8599		0,1,4299	yes	missense	KRT75	NM_004693.2	29	16,342,6145	CC,CT,TT		0.0116,8.4657,2.8756	probably-damaging	367/552	52822464	374,12632	2203	4300	6503	SO:0001583	missense	9119	exon6			CAGAGATCTCTTG	Y19212	CCDS8827.1	12q13.13	2013-06-25			ENSG00000170454	ENSG00000170454		"""-"", ""Intermediate filaments type II, keratins (basic)"""	24431	protein-coding gene	gene with protein product		609025				9856802, 10692104, 16831889	Standard	NM_004693		Approved	K6HF	uc001saj.2	O95678	OTTHUMG00000169592	ENST00000252245.5:c.1099A>G	12.37:g.52822464T>C	ENSP00000252245:p.Ile367Val	153.0	0.0	0		149.0	73.0	0.489933	NM_004693	B4DQU4|Q9NSA9	Missense_Mutation	SNP	ENST00000252245.5	37	CCDS8827.1	34	0.015567765567765568	33	0.06707317073170732	1	0.0027624309392265192	0	0.0	0	0.0	T	18.53	3.644098	0.67244	0.084657	1.16E-4	ENSG00000170454	ENST00000252245	D	0.89617	-2.54	5.18	5.18	0.71444	Prefoldin (1);Filament (1);	0.000000	0.51477	D	0.000081	T	0.59128	0.2171	M	0.81802	2.56	0.42420	D	0.992635	D	0.69078	0.997	D	0.70935	0.971	T	0.77680	-0.2497	10	0.66056	D	0.02	.	15.0403	0.71785	0.0:0.0:0.0:1.0	rs2232402;rs52796316;rs60556458;rs2232402	367	O95678	K2C75_HUMAN	V	367	ENSP00000252245:I367V	ENSP00000252245:I367V	I	-	1	0	KRT75	51108731	1.000000	0.71417	1.000000	0.80357	0.611000	0.37282	5.064000	0.64338	1.966000	0.57179	0.459000	0.35465	ATC	T|0.969;C|0.031	0.031	strong		0.512	KRT75-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404968.1	NM_004693	
LOXHD1	125336	hgsc.bcm.edu	37	18	44102193	44102193	+	Silent	SNP	G	G	A	rs187103862		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:44102193G>A	ENST00000398722.4	-	25	4121	c.4122C>T	c.(4120-4122)atC>atT	p.I1374I	LOXHD1_ENST00000441893.2_Silent_p.I585I|LOXHD1_ENST00000300591.6_Silent_p.I541I|LOXHD1_ENST00000536736.1_Silent_p.I1652I|LOXHD1_ENST00000441551.2_Silent_p.I1446I|LOXHD1_ENST00000579038.1_Silent_p.I445I|LOXHD1_ENST00000582408.1_Silent_p.I541I			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	1374	PLAT 10. {ECO:0000255|PROSITE- ProRule:PRU00152}.				calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|sensory perception of sound (GO:0007605)	membrane (GO:0016020)|stereocilium (GO:0032420)	calcium channel activity (GO:0005262)	p.I1374I(1)|p.I1652I(1)		NS(3)|autonomic_ganglia(1)|breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|pancreas(1)|prostate(4)|skin(4)|stomach(1)	36						CATCCTCCCCGATGAGAAAGA	0.572													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19237	0.0		0.0	False		,,,				2504	0.0				p.I1652I		Atlas-SNP	.											LOXHD1_ENST00000398722,NS,carcinoma,0,2	LOXHD1	367	2	2	Substitution - coding silent(2)	endometrium(2)	c.C4956T						PASS	.	G	,	1,1383		0,1,691	114.0	101.0	105.0		1623,4956	-5.2	0.4	18		105	0,3182		0,0,1591	no	coding-synonymous,coding-synonymous	LOXHD1	NM_001145472.2,NM_144612.6	,	0,1,2282	AA,AG,GG		0.0,0.0723,0.0219	,	541/1115,1652/2212	44102193	1,4565	692	1591	2283	SO:0001819	synonymous_variant	125336	exon32			CTCCCCGATGAGA	AK057232	CCDS45861.1, CCDS45862.1, CCDS54184.1	18q21.1	2009-09-11			ENSG00000167210	ENSG00000167210			26521	protein-coding gene	gene with protein product		613072	"""deafness, autosomal recessive 77"""	DFNB77		19732867	Standard	NM_144612		Approved	FLJ32670, LH2D1	uc010xcw.1	Q8IVV2	OTTHUMG00000132644	ENST00000398722.4:c.4122C>T	18.37:g.44102193G>A		94.0	0.0	0		102.0	44.0	0.431373	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Silent	SNP	ENST00000398722.4	37																																																																																				G|1.000;A|0.000	0.000	strong		0.572	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
TEX19	400629	hgsc.bcm.edu	37	17	80320303	80320303	+	Missense_Mutation	SNP	G	G	T	rs147220016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:80320303G>T	ENST00000333437.4	+	2	587	c.277G>T	c.(277-279)Ggg>Tgg	p.G93W		NM_207459.3	NP_997342.1	Q8NA77	TEX19_HUMAN	testis expressed 19	93					cell differentiation (GO:0030154)|meiotic nuclear division (GO:0007126)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(1)|lung(2)|upper_aerodigestive_tract(1)	6						GCCTGTGCAGGGGGGCTCTGA	0.652													.|||	10	0.00199681	0.0008	0.0086	5008	,	,		18460	0.0		0.002	False		,,,				2504	0.001				p.G93W		Atlas-SNP	.											.	TEX19	17	.	0			c.G277T						PASS	.	G	TRP/GLY	2,4404	4.2+/-10.8	0,2,2201	39.0	42.0	41.0		277	1.9	0.0	17	dbSNP_134	41	32,8566	21.0+/-64.5	0,32,4267	yes	missense	TEX19	NM_207459.3	184	0,34,6468	TT,TG,GG		0.3722,0.0454,0.2615	probably-damaging	93/165	80320303	34,12970	2203	4299	6502	SO:0001583	missense	400629	exon2			GTGCAGGGGGGCT	BC016939	CCDS11809.1	17q25.3	2009-04-14			ENSG00000182459	ENSG00000182459			33802	protein-coding gene	gene with protein product		615647					Standard	NM_207459		Approved	FLJ35767	uc002keq.3	Q8NA77	OTTHUMG00000132857	ENST00000333437.4:c.277G>T	17.37:g.80320303G>T	ENSP00000331500:p.Gly93Trp	51.0	0.0	0		74.0	26.0	0.351351	NM_207459		Missense_Mutation	SNP	ENST00000333437.4	37	CCDS11809.1	5	0.0022893772893772895	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	G	13.50	2.255828	0.39896	4.54E-4	0.003722	ENSG00000182459	ENST00000333437	.	.	.	3.22	1.94	0.25998	.	.	.	.	.	T	0.39627	0.1085	L	0.29908	0.895	0.09310	N	1	D	0.69078	0.997	D	0.71870	0.975	T	0.20739	-1.0266	8	0.66056	D	0.02	-41.824	8.5403	0.33388	0.0:0.4168:0.5832:0.0	.	93	Q8NA77	TEX19_HUMAN	W	93	.	ENSP00000331500:G93W	G	+	1	0	TEX19	77913592	0.022000	0.18835	0.005000	0.12908	0.002000	0.02628	0.388000	0.20735	0.628000	0.30357	0.462000	0.41574	GGG	G|0.997;T|0.003	0.003	strong		0.652	TEX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256331.1	NM_207459	
CNGB3	54714	hgsc.bcm.edu	37	8	87680282	87680282	+	Missense_Mutation	SNP	C	C	T	rs16916632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:87680282C>T	ENST00000320005.5	-	5	655	c.608G>A	c.(607-609)cGa>cAa	p.R203Q		NM_019098.4	NP_061971.3	Q9NQW8	CNGB3_HUMAN	cyclic nucleotide gated channel beta 3	203			R -> Q (in ACHM3; unknown pathological significance; dbSNP:rs16916632). {ECO:0000269|PubMed:15712225}.		cation transport (GO:0006812)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|transmembrane transporter complex (GO:1902495)	cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(15)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	80						AAGTTTAATTCGCTTTAAGTA	0.398													C|||	278	0.0555112	0.1952	0.0101	5008	,	,		14978	0.003		0.0	False		,,,				2504	0.0102				p.R203Q		Atlas-SNP	.											.	CNGB3	176	.	0			c.G608A						PASS	.	C	GLN/ARG	679,3727	286.0+/-278.5	46,587,1570	238.0	228.0	231.0		608	-6.8	0.0	8	dbSNP_123	231	2,8598	1.2+/-3.3	0,2,4298	yes	missense	CNGB3	NM_019098.4	43	46,589,5868	TT,TC,CC		0.0233,15.4108,5.236	benign	203/810	87680282	681,12325	2203	4300	6503	SO:0001583	missense	54714	exon5			TTAATTCGCTTTA	AF228520	CCDS6244.1	8q21.3	2013-01-23	2003-06-25		ENSG00000170289	ENSG00000170289		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2153	protein-coding gene	gene with protein product		605080	"""achromatopsia (rod monochromacy) 3"", ""achromatopsia (rod monochromacy) 1"""	ACHM3, ACHM1, RMCH		10888875, 10958649, 16382102	Standard	NM_019098		Approved		uc003ydx.3	Q9NQW8	OTTHUMG00000163738	ENST00000320005.5:c.608G>A	8.37:g.87680282C>T	ENSP00000316605:p.Arg203Gln	163.0	0.0	0		185.0	86.0	0.464865	NM_019098	C9JA51|Q9NRE9	Missense_Mutation	SNP	ENST00000320005.5	37	CCDS6244.1	73	0.033424908424908424	72	0.14634146341463414	1	0.0027624309392265192	0	0.0	0	0.0	C	12.18	1.862010	0.32884	0.154108	2.33E-4	ENSG00000170289	ENST00000320005	D	0.97016	-4.21	6.1	-6.81	0.01704	.	1.625600	0.03560	N	0.226891	T	0.07369	0.0186	L	0.40543	1.245	0.80722	P	0.0	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.68375	-0.5425	9	0.23891	T	0.37	.	13.0899	0.59162	0.1009:0.116:0.0:0.7831	rs16916632;rs52789907;rs16916632	203;203	Q9NQW8-2;Q9NQW8	.;CNGB3_HUMAN	Q	203	ENSP00000316605:R203Q	ENSP00000316605:R203Q	R	-	2	0	CNGB3	87749398	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.590000	0.05760	-1.332000	0.02249	-0.143000	0.13931	CGA	C|0.951;T|0.049	0.049	strong		0.398	CNGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375107.1	NM_019098	
DLK1	8788	hgsc.bcm.edu	37	14	101201206	101201206	+	Silent	SNP	C	C	T	rs139584149	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:101201206C>T	ENST00000341267.4	+	5	1367	c.1125C>T	c.(1123-1125)agC>agT	p.S375S	DLK1_ENST00000331224.6_Silent_p.S302S|RP11-566J3.4_ENST00000608876.1_lincRNA	NM_003836.5	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog (Drosophila)	375					cell differentiation (GO:0030154)|embryonic skeletal system development (GO:0048706)|multicellular organismal development (GO:0007275)|negative regulation of Notch signaling pathway (GO:0045746)|Notch signaling pathway (GO:0007219)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)	external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(16)|ovary(2)|prostate(1)|skin(1)	29		Melanoma(154;0.155)				CCACCTTCAGCAAGGAGGCCG	0.552													C|||	50	0.00998403	0.0371	0.0	5008	,	,		16616	0.0		0.001	False		,,,				2504	0.0				p.S375S		Atlas-SNP	.											.	DLK1	57	.	0			c.C1125T						PASS	.	C		105,4301	82.4+/-120.9	1,103,2099	92.0	92.0	92.0		1125	3.5	0.9	14	dbSNP_134	92	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	DLK1	NM_003836.5		1,107,6395	TT,TC,CC		0.0465,2.3831,0.8381		375/384	101201206	109,12897	2203	4300	6503	SO:0001819	synonymous_variant	8788	exon5			CTTCAGCAAGGAG	U15979	CCDS9963.1	14q32	2011-12-05	2001-12-03			ENSG00000185559			2907	protein-coding gene	gene with protein product		176290	"""delta-like homolog (Drosophila)"""			8095043, 7925474	Standard	NM_003836		Approved	FA1, pG2, Pref-1, ZOG, Delta1	uc001yhs.4	P80370		ENST00000341267.4:c.1125C>T	14.37:g.101201206C>T		30.0	0.0	0		26.0	16.0	0.615385	NM_003836	P15803|Q96DW5	Silent	SNP	ENST00000341267.4	37	CCDS9963.1																																																																																			C|0.991;T|0.009	0.009	strong		0.552	DLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414389.1		
WBP4	11193	hgsc.bcm.edu	37	13	41639377	41639377	+	Silent	SNP	C	C	T	rs61740513	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:41639377C>T	ENST00000379487.3	+	4	616	c.216C>T	c.(214-216)gcC>gcT	p.A72A	WBP4_ENST00000542082.1_Silent_p.A51A	NM_007187.3	NP_009118.1	O75554	WBP4_HUMAN	WW domain binding protein 4	72					mRNA cis splicing, via spliceosome (GO:0045292)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spliceosomal complex (GO:0005681)	nucleic acid binding (GO:0003676)|proline-rich region binding (GO:0070064)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|prostate(1)|skin(1)	12		Lung NSC(96;3.55e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;3.11e-09)|Epithelial(112;3.37e-06)|OV - Ovarian serous cystadenocarcinoma(117;8.3e-05)|GBM - Glioblastoma multiforme(144;0.00102)|BRCA - Breast invasive adenocarcinoma(63;0.07)		AGGCAGCTGCCCTGAAAGCAT	0.368													C|||	126	0.0251597	0.0908	0.0072	5008	,	,		14418	0.0		0.001	False		,,,				2504	0.0				p.A72A		Atlas-SNP	.											.	WBP4	40	.	0			c.C216T						PASS	.	C		411,3995	201.5+/-224.5	14,383,1806	64.0	69.0	67.0		216	2.8	1.0	13	dbSNP_129	67	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	WBP4	NM_007187.3		14,385,6104	TT,TC,CC		0.0233,9.3282,3.1755		72/377	41639377	413,12593	2203	4300	6503	SO:0001819	synonymous_variant	11193	exon4			AGCTGCCCTGAAA	AF071185	CCDS9375.1	13q13.3	2012-10-17	2012-10-17		ENSG00000120688	ENSG00000120688			12739	protein-coding gene	gene with protein product	"""formin binding protein 21"""	604981				9724750	Standard	NM_007187		Approved	FBP21, MGC117310	uc001uxt.3	O75554	OTTHUMG00000016784	ENST00000379487.3:c.216C>T	13.37:g.41639377C>T		56.0	0.0	0		65.0	37.0	0.569231	NM_007187	B7Z4M2|Q32P29	Silent	SNP	ENST00000379487.3	37	CCDS9375.1																																																																																			C|0.967;T|0.033	0.033	strong		0.368	WBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044655.2	NM_007187	
SSRP1	6749	hgsc.bcm.edu	37	11	57101000	57101000	+	Silent	SNP	G	G	C	rs7932705	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:57101000G>C	ENST00000278412.2	-	4	521	c.255C>G	c.(253-255)ctC>ctG	p.L85L		NM_003146.2	NP_003137.1	Q08945	SSRP1_HUMAN	structure specific recognition protein 1	85					DNA repair (GO:0006281)|DNA replication (GO:0006260)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|prostate(4)	23						AGAAATCAGAGAGTTTCTCAA	0.468													G|||	76	0.0151757	0.0537	0.0072	5008	,	,		19918	0.0		0.0	False		,,,				2504	0.0				p.L85L	Colon(89;1000 1340 6884 23013 41819)	Atlas-SNP	.											.	SSRP1	75	.	0			c.C255G						PASS	.	G		189,4213	122.1+/-159.5	2,185,2014	90.0	87.0	88.0		255	-0.2	1.0	11	dbSNP_116	88	5,8587	3.7+/-12.6	0,5,4291	no	coding-synonymous	SSRP1	NM_003146.2		2,190,6305	CC,CG,GG		0.0582,4.2935,1.493		85/710	57101000	194,12800	2201	4296	6497	SO:0001819	synonymous_variant	6749	exon4			ATCAGAGAGTTTC	M86737	CCDS7952.1	11q12	2008-02-05			ENSG00000149136	ENSG00000149136			11327	protein-coding gene	gene with protein product	"""facilitates chromatin remodeling 80 kDa subunit"""	604328				1372440	Standard	NM_003146		Approved	FACT80	uc001njt.3	Q08945	OTTHUMG00000167024	ENST00000278412.2:c.255C>G	11.37:g.57101000G>C		144.0	0.0	0		111.0	63.0	0.567568	NM_003146	Q5BJG8	Silent	SNP	ENST00000278412.2	37	CCDS7952.1																																																																																			G|0.986;C|0.014	0.014	strong		0.468	SSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392460.1	NM_003146	
BACE2	25825	hgsc.bcm.edu	37	21	42551183	42551183	+	Intron	SNP	G	G	A	rs202000983	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:42551183G>A	ENST00000330333.6	+	1	775				PLAC4_ENST00000430327.2_RNA|PLAC4_ENST00000440221.2_RNA|PLAC4_ENST00000414699.1_RNA|BACE2-IT1_ENST00000433378.1_RNA|BACE2_ENST00000328735.6_Intron|PLAC4_ENST00000536486.1_RNA|BACE2_ENST00000347667.5_Intron	NM_012105.3	NP_036237.2	Q9Y5Z0	BACE2_HUMAN	beta-site APP-cleaving enzyme 2						membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(2)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14		Prostate(19;1.57e-07)|all_epithelial(19;0.0251)				gaggagtgagggagtccaggg	0.607													G|||	14	0.00279553	0.0098	0.0014	5008	,	,		20303	0.0		0.0	False		,,,				2504	0.0				p.P125S		Atlas-SNP	.											.	.	.	.	0			c.C373T						PASS	.	G	,,,SER/PRO	16,4350		0,16,2167	126.0	106.0	113.0		,,,373	0.2	0.0	21		113	0,8470		0,0,4235	yes	intron,intron,intron,missense	BACE2,PLAC4	NM_012105.3,NM_138991.1,NM_138992.1,NM_182832.2	,,,74	0,16,6402	AA,AG,GG		0.0,0.3665,0.1246	,,,possibly-damaging	,,,125/151	42551183	16,12820	2183	4235	6418	SO:0001627	intron_variant	191585	exon1			AGTGAGGGAGTCC	AF117892	CCDS13668.1, CCDS13669.1, CCDS13670.1	21q22.3	2011-08-11			ENSG00000182240	ENSG00000182240			934	protein-coding gene	gene with protein product		605668		AEPLC		10965118, 10830953	Standard	NM_138991		Approved	CEAP1, DRAP, ALP56	uc002yyw.3	Q9Y5Z0	OTTHUMG00000086742	ENST00000330333.6:c.312+10681G>A	21.37:g.42551183G>A		263.0	1.0	0.00380228		297.0	158.0	0.531987	NM_182832	A8K7P1|Q5DIH8|Q8N2D4|Q9H2V8|Q9NZL1|Q9NZL2|Q9UJT6	Missense_Mutation	SNP	ENST00000330333.6	37	CCDS13668.1																																																																																			.	.	weak		0.607	BACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195056.1		
ERCC4	2072	hgsc.bcm.edu	37	16	14031695	14031695	+	Silent	SNP	A	A	G	rs2020958	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:14031695A>G	ENST00000311895.7	+	9	1893	c.1884A>G	c.(1882-1884)gaA>gaG	p.E628E	CTD-2135D7.2_ENST00000570663.1_RNA|CTD-2135D7.2_ENST00000575137.1_RNA	NM_005236.2	NP_005227.1	Q92889	XPF_HUMAN	excision repair cross-complementation group 4	628					DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|negative regulation of telomere maintenance (GO:0032205)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair involved in interstrand cross-link repair (GO:1901255)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)|resolution of meiotic recombination intermediates (GO:0000712)|response to UV (GO:0009411)|telomere maintenance (GO:0000723)|telomere maintenance via telomere shortening (GO:0010834)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	chromosome, telomeric region (GO:0000781)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleotide-excision repair factor 1 complex (GO:0000110)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	damaged DNA binding (GO:0003684)|endodeoxyribonuclease activity (GO:0004520)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(5)|lung(12)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	38						AAGAAAAGGAAGCTTTTGAAA	0.393			"""Mis, N, F"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				A|||	77	0.0153754	0.0582	0.0	5008	,	,		16132	0.0		0.0	False		,,,				2504	0.0				p.E628E		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (F)	16	16p13.3-p13.13	2072	"""excision repair cross-complementing rodent repair deficiency, complementation group 4"""		E	.	ERCC4	100	.	0			c.A1884G						PASS	.	A		170,4224	105.2+/-143.6	3,164,2030	76.0	75.0	75.0		1884	4.2	1.0	16	dbSNP_94	75	0,8600		0,0,4300	no	coding-synonymous	ERCC4	NM_005236.2		3,164,6330	GG,GA,AA		0.0,3.8689,1.3083		628/917	14031695	170,12824	2197	4300	6497	SO:0001819	synonymous_variant	2072	exon9	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	AAAGGAAGCTTTT	L76568	CCDS32390.1	16p13.3	2014-09-17	2014-03-07		ENSG00000175595	ENSG00000175595			3436	protein-coding gene	gene with protein product	"""xeroderma pigmentosum, complementation group F"""	133520	"""excision repair cross-complementing rodent repair deficiency, complementation group 4"""	XPF		9579555, 8887684	Standard	NM_005236		Approved	RAD1, FANCQ	uc002dce.2	Q92889	OTTHUMG00000048194	ENST00000311895.7:c.1884A>G	16.37:g.14031695A>G		70.0	0.0	0		81.0	41.0	0.506173	NM_005236	A5PKV6|A8K111|O00140|Q8TD83	Silent	SNP	ENST00000311895.7	37	CCDS32390.1																																																																																			A|0.982;G|0.018	0.018	strong		0.393	ERCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109634.2	NM_005236	
TRMT2B	79979	hgsc.bcm.edu	37	X	100278558	100278558	+	Silent	SNP	T	T	C	rs61745518	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:100278558T>C	ENST00000372936.3	-	8	1429	c.657A>G	c.(655-657)gtA>gtG	p.V219V	TRMT2B_ENST00000478422.1_5'Flank|TRMT2B_ENST00000372939.1_Silent_p.V174V|TRMT2B_ENST00000338687.7_Silent_p.V174V|TRMT2B_ENST00000545398.1_Silent_p.V219V|TRMT2B_ENST00000372931.5_Silent_p.V219V|TRMT2B_ENST00000372935.1_Silent_p.V219V	NM_024917.5	NP_079193.2	Q96GJ1	TRM2_HUMAN	tRNA methyltransferase 2 homolog B (S. cerevisiae)	219						mitochondrion (GO:0005739)	S-adenosylmethionine-dependent tRNA (m5U54) methyltransferase activity (GO:0030697)			breast(3)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	24						CTTCATGAAATACAAGGCAGG	0.458													T|||	74	0.0196026	0.0545	0.0029	3775	,	,		14763	0.0		0.0	False		,,,				2504	0.0				p.V219V		Atlas-SNP	.											.	TRMT2B	33	.	0			c.A657G						PASS	.	T	,,,	236,3599		8,187,33,1437,538	142.0	110.0	121.0		657,522,657,657	0.3	0.6	X	dbSNP_129	121	1,6727		0,1,0,2427,1872	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRMT2B	NM_001167970.1,NM_001167971.1,NM_001167972.1,NM_024917.5	,,,	8,188,33,3864,2410	CC,CT,C,TT,T		0.0149,6.1538,2.2437	,,,	219/505,174/460,219/505,219/505	100278558	237,10326	2203	4300	6503	SO:0001819	synonymous_variant	79979	exon7			ATGAAATACAAGG	BC020116	CCDS14477.1, CCDS55464.1	Xq22.1	2012-06-12	2012-06-12	2008-09-17	ENSG00000188917	ENSG00000188917			25748	protein-coding gene	gene with protein product			"""chromosome X open reading frame 34"""	CXorf34		14702039	Standard	NM_024917		Approved	FLJ12687	uc004egq.3	Q96GJ1	OTTHUMG00000022017	ENST00000372936.3:c.657A>G	X.37:g.100278558T>C		165.0	0.0	0		180.0	175.0	0.972222	NM_001167972	A6NDG5|A6NEI9|A6NMG6|Q5JPF0|Q5JVY6|Q96HU7|Q96IH9|Q9H9K2	Silent	SNP	ENST00000372936.3	37	CCDS14477.1																																																																																			T|0.979;C|0.021	0.021	strong		0.458	TRMT2B-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057512.1	NM_024917	
CAPN5	726	hgsc.bcm.edu	37	11	76796022	76796022	+	Silent	SNP	C	C	A	rs34236021	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:76796022C>A	ENST00000278559.3	+	2	279	c.90C>A	c.(88-90)ccC>ccA	p.P30P	CAPN5_ENST00000531028.1_Silent_p.P30P|CAPN5_ENST00000456580.2_Silent_p.P30P|CAPN5_ENST00000529629.1_Silent_p.P30P	NM_004055.4	NP_004046.2	O15484	CAN5_HUMAN	calpain 5	30	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(1)|breast(2)|endometrium(2)|large_intestine(7)|lung(17)|urinary_tract(1)	30						TCGAGGACCCCCTCTTCCCCG	0.637													c|||	176	0.0351438	0.1278	0.0072	5008	,	,		14704	0.0		0.002	False		,,,				2504	0.0				p.P30P		Atlas-SNP	.											.	CAPN5	67	.	0			c.C90A						PASS	.	C		424,3976	186.0+/-213.0	16,392,1792	33.0	37.0	36.0		90	0.5	1.0	11	dbSNP_126	36	9,8575	6.4+/-24.3	0,9,4283	no	coding-synonymous	CAPN5	NM_004055.4		16,401,6075	AA,AC,CC		0.1048,9.6364,3.3349		30/641	76796022	433,12551	2200	4292	6492	SO:0001819	synonymous_variant	726	exon2			GGACCCCCTCTTC		CCDS8248.1	11q14	2014-01-29				ENSG00000149260			1482	protein-coding gene	gene with protein product		602537	"""vitreoretinopathy, neovascular inflammatory"""	VRNI		9503024, 9367857, 23055945	Standard	NM_004055		Approved	nCL-3, HTRA3, ADNIV	uc001oxx.3	O15484		ENST00000278559.3:c.90C>A	11.37:g.76796022C>A		85.0	0.0	0		73.0	24.0	0.328767	NM_004055	O00263	Silent	SNP	ENST00000278559.3	37	CCDS8248.1																																																																																			C|0.973;A|0.027	0.027	strong		0.637	CAPN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382564.2	NM_004055	
SSR2	6746	hgsc.bcm.edu	37	1	155988108	155988108	+	Silent	SNP	A	A	G	rs34428308	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:155988108A>G	ENST00000295702.4	-	3	278	c.207T>C	c.(205-207)ttT>ttC	p.F69F	SSR2_ENST00000480567.1_Silent_p.F69F|SSR2_ENST00000496742.1_Intron|SSR2_ENST00000529008.1_Silent_p.F69F	NM_003145.3	NP_003136.1	P43308	SSRB_HUMAN	signal sequence receptor, beta (translocon-associated protein beta)	69					cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|stomach(1)	10	Hepatocellular(266;0.133)|all_hematologic(923;0.145)|all_neural(408;0.195)					ACACAATGCCAAAGTCTTCTG	0.468													A|||	43	0.00858626	0.0318	0.0014	5008	,	,		20208	0.0		0.0	False		,,,				2504	0.0				p.F69F		Atlas-SNP	.											.	SSR2	20	.	0			c.T207C						PASS	.	A		164,4242	108.2+/-146.6	4,156,2043	114.0	105.0	108.0		207	1.1	1.0	1	dbSNP_126	108	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SSR2	NM_003145.3		4,157,6342	GG,GA,AA		0.0116,3.7222,1.2686		69/184	155988108	165,12841	2203	4300	6503	SO:0001819	synonymous_variant	6746	exon3			AATGCCAAAGTCT	BC000341	CCDS1126.1	1q21-q23	2008-02-05			ENSG00000163479	ENSG00000163479			11324	protein-coding gene	gene with protein product		600867				7789174	Standard	NM_003145		Approved	TLAP, TRAPB	uc001fmx.3	P43308	OTTHUMG00000017456	ENST00000295702.4:c.207T>C	1.37:g.155988108A>G		61.0	0.0	0		66.0	37.0	0.560606	NM_003145	B2R9K9|D3DVA7|Q53HI0|Q5VY95|Q5VY96|Q6IB31|Q9BWE4	Silent	SNP	ENST00000295702.4	37	CCDS1126.1																																																																																			A|0.990;G|0.010	0.010	strong		0.468	SSR2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046172.2	NM_003145	
TRIM29	23650	hgsc.bcm.edu	37	11	119996490	119996490	+	Silent	SNP	G	G	A	rs61753082	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:119996490G>A	ENST00000341846.5	-	4	1663	c.1242C>T	c.(1240-1242)gaC>gaT	p.D414D	TRIM29_ENST00000529044.1_Silent_p.D153D|TRIM29_ENST00000524816.3_5'Flank|TRIM29_ENST00000528870.1_5'Flank|TRIM29_ENST00000541857.1_Silent_p.D147D	NM_012101.3	NP_036233.2	Q14134	TRI29_HUMAN	tripartite motif containing 29	414					negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(17)|ovary(1)|pancreas(1)|skin(3)|urinary_tract(1)	30		Breast(109;0.00117)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)		TGAGCAGGTCGTCCTTGAAGT	0.562													G|||	105	0.0209665	0.0719	0.0144	5008	,	,		11882	0.0		0.0	False		,,,				2504	0.0				p.D414D		Atlas-SNP	.											.	TRIM29	78	.	0			c.C1242T						PASS	.	G		298,4100	162.2+/-194.2	15,268,1916	101.0	87.0	92.0		1242	-8.7	0.6	11	dbSNP_129	92	0,8590		0,0,4295	no	coding-synonymous	TRIM29	NM_012101.3		15,268,6211	AA,AG,GG		0.0,6.7758,2.2944		414/589	119996490	298,12690	2199	4295	6494	SO:0001819	synonymous_variant	23650	exon4			CAGGTCGTCCTTG	AF230388	CCDS8428.1	11q23.3	2011-04-20	2011-01-25		ENSG00000137699	ENSG00000137699		"""Tripartite motif containing / Tripartite motif containing"""	17274	protein-coding gene	gene with protein product	"""tripartite motif protein TRIM29"", ""ataxia-telangiectasia group D-associated protein"""	610658	"""tripartite motif-containing 29"""			11331580	Standard	NM_012101		Approved	ATDC, FLJ36085	uc001pwz.3	Q14134	OTTHUMG00000140377	ENST00000341846.5:c.1242C>T	11.37:g.119996490G>A		151.0	0.0	0		118.0	78.0	0.661017	NM_012101	Q96AA9|Q9BZY7	Silent	SNP	ENST00000341846.5	37	CCDS8428.1																																																																																			G|0.979;A|0.021	0.021	strong		0.562	TRIM29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277108.2	NM_012101	
CYP4F12	66002	hgsc.bcm.edu	37	19	15791212	15791212	+	Silent	SNP	A	A	C	rs386807228|rs142773675	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15791212A>C	ENST00000550308.1	+	5	788	c.408A>C	c.(406-408)atA>atC	p.I136I	CYP4F12_ENST00000324632.10_Silent_p.I136I	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	136					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	GAGAAGGGATACTGCTGAGTG	0.567													.|||	100	0.0199681	0.0711	0.0072	5008	,	,		19609	0.0		0.001	False		,,,				2504	0.0				p.I136I		Atlas-SNP	.											.	CYP4F12	89	.	0			c.A408C						PASS	.						30.0	35.0	33.0					19																	15791212		2202	4298	6500	SO:0001819	synonymous_variant	66002	exon5			AGGGATACTGCTG	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.408A>C	19.37:g.15791212A>C		211.0	0.0	0		258.0	48.0	0.186047	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Silent	SNP	ENST00000550308.1	37	CCDS42517.1																																																																																			A|0.969;C|0.031	0.031	strong		0.567	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
ABCC12	94160	hgsc.bcm.edu	37	16	48145742	48145742	+	Missense_Mutation	SNP	T	T	A	rs34135219	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:48145742T>A	ENST00000311303.3	-	14	2414	c.2069A>T	c.(2068-2070)gAg>gTg	p.E690V	ABCC12_ENST00000416054.1_3'UTR|ABCC12_ENST00000448542.1_Missense_Mutation_p.E690V	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	690	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.		E -> V (in dbSNP:rs34135219).			integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|liver(1)|lung(43)|ovary(2)|prostate(3)|skin(7)|urinary_tract(1)	90		all_cancers(37;0.0474)|all_lung(18;0.047)				CCCTCTCTCCTCCATTAACTC	0.458													T|||	249	0.0497204	0.1399	0.0159	5008	,	,		20912	0.0149		0.003	False		,,,				2504	0.0358				p.E690V		Atlas-SNP	.											.	ABCC12	190	.	0			c.A2069T						PASS	.	T	VAL/GLU	506,3896	237.7+/-249.4	28,450,1723	160.0	150.0	154.0		2069	3.1	1.0	16	dbSNP_126	154	33,8567	21.6+/-65.8	0,33,4267	yes	missense	ABCC12	NM_033226.2	121	28,483,5990	AA,AT,TT		0.3837,11.4948,4.1455	benign	690/1360	48145742	539,12463	2201	4300	6501	SO:0001583	missense	94160	exon14			CTCTCCTCCATTA	AY040220	CCDS10730.1	16q12.1	2012-03-14			ENSG00000140798	ENSG00000140798		"""ATP binding cassette transporters / subfamily C"""	14640	protein-coding gene	gene with protein product		607041				11435397, 11483364	Standard	NM_033226		Approved	MRP9	uc002efc.1	Q96J65	OTTHUMG00000133143	ENST00000311303.3:c.2069A>T	16.37:g.48145742T>A	ENSP00000311030:p.Glu690Val	224.0	0.0	0		235.0	118.0	0.502128	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Missense_Mutation	SNP	ENST00000311303.3	37	CCDS10730.1	71	0.03250915750915751	62	0.12601626016260162	6	0.016574585635359115	3	0.005244755244755245	0	0.0	T	12.35	1.912301	0.33721	0.114948	0.003837	ENSG00000140798	ENST00000311303;ENST00000448542;ENST00000449939	T;T	0.68331	-0.32;-0.32	5.56	3.08	0.35506	ABC transporter-like (1);	0.429810	0.26623	N	0.023346	T	0.00936	0.0031	L	0.55213	1.73	0.58432	D	0.999997	B	0.19445	0.036	B	0.22880	0.042	T	0.03060	-1.1077	10	0.45353	T	0.12	.	7.8142	0.29249	0.1333:0.0777:0.0:0.789	rs34135219;rs58143374	690	Q96J65	MRP9_HUMAN	V	690;690;632	ENSP00000311030:E690V;ENSP00000401855:E690V	ENSP00000311030:E690V	E	-	2	0	ABCC12	46703243	0.815000	0.29118	1.000000	0.80357	0.501000	0.33797	1.779000	0.38624	0.951000	0.37770	0.459000	0.35465	GAG	T|0.963;A|0.037	0.037	strong		0.458	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226	
SALL4	57167	hgsc.bcm.edu	37	20	50406892	50406892	+	Silent	SNP	C	C	T	rs61737143	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:50406892C>T	ENST00000217086.4	-	2	2241	c.2130G>A	c.(2128-2130)acG>acA	p.T710T	SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000371539.3_Intron|SALL4_ENST00000395997.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	710					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TGGGAAGAGGCGTGGGGACCT	0.587													C|||	91	0.0181709	0.0643	0.0072	5008	,	,		18206	0.0		0.001	False		,,,				2504	0.0				p.T710T		Atlas-SNP	.											.	SALL4	168	.	0			c.G2130A						PASS	.	C		253,4153	143.5+/-178.5	11,231,1961	41.0	38.0	39.0		2130	-6.0	0.0	20	dbSNP_129	39	0,8600		0,0,4300	no	coding-synonymous	SALL4	NM_020436.3		11,231,6261	TT,TC,CC		0.0,5.7422,1.9453		710/1054	50406892	253,12753	2203	4300	6503	SO:0001819	synonymous_variant	57167	exon2			AAGAGGCGTGGGG	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"""Zinc fingers, C2H2-type"""	15924	protein-coding gene	gene with protein product		607343	"""sal (Drosophila)-like 4"", ""sal-like 4 (Drosophila)"""				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.2130G>A	20.37:g.50406892C>T		171.0	0.0	0		158.0	55.0	0.348101	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	37	CCDS13438.1																																																																																			C|0.982;T|0.018	0.018	strong		0.587	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
ITSN2	50618	hgsc.bcm.edu	37	2	24498674	24498674	+	Silent	SNP	C	C	T	rs77507357	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:24498674C>T	ENST00000355123.4	-	18	2432	c.1989G>A	c.(1987-1989)caG>caA	p.Q663Q	SCARNA21_ENST00000515996.1_RNA|ITSN2_ENST00000361999.3_Silent_p.Q636Q|ITSN2_ENST00000406921.3_Silent_p.Q663Q	NM_006277.2	NP_006268.2	Q9NZM3	ITSN2_HUMAN	intersectin 2	663					endocytosis (GO:0006897)|positive regulation of signal transduction (GO:0009967)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|SH3/SH2 adaptor activity (GO:0005070)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(8)|large_intestine(11)|liver(3)|lung(28)|ovary(2)|stomach(1)	61	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TCTTATAAAGCTGTTCAAGGG	0.338													T|||	40	0.00798722	0.0303	0.0	5008	,	,		17795	0.0		0.0	False		,,,				2504	0.0				p.Q663Q		Atlas-SNP	.											.	ITSN2	224	.	0			c.G1989A						PASS	.	T	,,	143,4263	812.9+/-416.1	4,135,2064	147.0	140.0	142.0		1989,1908,1989	-4.5	0.9	2	dbSNP_132	142	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	ITSN2	NM_006277.2,NM_019595.3,NM_147152.2	,,	4,135,6364	TT,TC,CC		0.0,3.2456,1.0995	,,	663/1698,636/1671,663/1250	24498674	143,12863	2203	4300	6503	SO:0001819	synonymous_variant	50618	exon18			ATAAAGCTGTTCA	AB033082	CCDS1710.2, CCDS1711.2, CCDS46230.1	2p23.3	2013-09-19	2002-10-30		ENSG00000198399	ENSG00000198399		"""Rho guanine nucleotide exchange factors"", ""EF-hand domain containing"""	6184	protein-coding gene	gene with protein product	"""SH3 domain protein 1B"", ""SH3P18-like WASP associated protein"""	604464	"""SH3 domain protein 1B"""	SH3D1B		10922467, 11748279	Standard	NM_006277		Approved	KIAA1256, SWAP, SH3P18, SWA, PRO2015	uc002rfe.2	Q9NZM3	OTTHUMG00000090818	ENST00000355123.4:c.1989G>A	2.37:g.24498674C>T		172.0	0.0	0		201.0	104.0	0.517413	NM_147152	O95062|Q15812|Q9HAK4|Q9NXE6|Q9NYG0|Q9NZM2|Q9ULG4	Silent	SNP	ENST00000355123.4	37	CCDS1710.2																																																																																			C|0.989;T|0.011	0.011	strong		0.338	ITSN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207620.2	NM_006277	
RTP5	285093	hgsc.bcm.edu	37	2	242814604	242814604	+	Silent	SNP	G	G	C	rs78628254	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242814604G>C	ENST00000343216.3	+	2	925	c.897G>C	c.(895-897)ccG>ccC	p.P299P		NM_173821.2	NP_776182.2																					TCTGCAGCCCGGTTGGCGTGG	0.667													G|||	228	0.0455272	0.1664	0.0086	5008	,	,		18709	0.0		0.002	False		,,,				2504	0.0				p.P299P		Atlas-SNP	.											.	.	.	.	0			c.G897C						PASS	.			556,3250		37,482,1384	36.0	41.0	39.0		897	-5.6	0.0	2	dbSNP_131	39	3,8227		0,3,4112	no	coding-synonymous	C2orf85	NM_173821.2		37,485,5496	CC,CG,GG		0.0365,14.6085,4.6444		299/573	242814604	559,11477	1903	4115	6018	SO:0001819	synonymous_variant	285093	exon2			CAGCCCGGTTGGC																												ENST00000343216.3:c.897G>C	2.37:g.242814604G>C		56.0	0.0	0		73.0	40.0	0.547945	NM_173821		Silent	SNP	ENST00000343216.3	37	CCDS42843.1																																																																																			G|0.967;C|0.033	0.033	strong		0.667	CXXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322310.1		
UBE2U	148581	hgsc.bcm.edu	37	1	64686577	64686577	+	Missense_Mutation	SNP	C	C	T	rs139887828	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:64686577C>T	ENST00000371076.3	+	6	737	c.493C>T	c.(493-495)Cgt>Tgt	p.R165C	UBE2U_ENST00000464349.1_3'UTR	NM_152489.1	NP_689702.1	Q5VVX9	UBE2U_HUMAN	ubiquitin-conjugating enzyme E2U (putative)	165					protein ubiquitination (GO:0016567)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)			large_intestine(3)|lung(2)|skin(1)	6						TAAAGACCCACGTAAATGTAT	0.284													C|||	38	0.00758786	0.0272	0.0029	5008	,	,		13978	0.0		0.0	False		,,,				2504	0.0				p.R165C		Atlas-SNP	.											.	UBE2U	16	.	0			c.C493T						PASS	.	C	CYS/ARG	138,4268	98.5+/-137.1	0,138,2065	92.0	99.0	96.0		493	-5.5	0.0	1	dbSNP_134	96	1,8589	1.2+/-3.3	0,1,4294	yes	missense	UBE2U	NM_152489.1	180	0,139,6359	TT,TC,CC		0.0116,3.1321,1.0696	benign	165/227	64686577	139,12857	2203	4295	6498	SO:0001583	missense	148581	exon6			GACCCACGTAAAT	BC029895	CCDS627.1	1p31.3	2008-02-05			ENSG00000177414	ENSG00000177414		"""Ubiquitin-conjugating enzymes E2"""	28559	protein-coding gene	gene with protein product						12477932	Standard	NM_152489		Approved	MGC35130	uc001dbn.1	Q5VVX9	OTTHUMG00000009023	ENST00000371076.3:c.493C>T	1.37:g.64686577C>T	ENSP00000360116:p.Arg165Cys	187.0	0.0	0		159.0	78.0	0.490566	NM_152489	Q8N1D4	Missense_Mutation	SNP	ENST00000371076.3	37	CCDS627.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	C	7.130	0.579790	0.13686	0.031321	1.16E-4	ENSG00000177414	ENST00000371077;ENST00000371076	T;T	0.72942	-0.7;-0.69	4.12	-5.54	0.02544	Ubiquitin-conjugating enzyme/RWD-like (1);	2.859510	0.01357	N	0.012095	T	0.25419	0.0618	N	0.14661	0.345	0.09310	N	1	B	0.24043	0.096	B	0.09377	0.004	T	0.18366	-1.0339	10	0.87932	D	0	.	3.3218	0.07053	0.095:0.4157:0.2415:0.2478	.	165	Q5VVX9	UBE2U_HUMAN	C	165	ENSP00000360117:R165C;ENSP00000360116:R165C	ENSP00000360116:R165C	R	+	1	0	UBE2U	64459165	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.259000	0.08721	-1.248000	0.02503	-0.229000	0.12294	CGT	C|0.991;T|0.009	0.009	strong		0.284	UBE2U-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025005.1	NM_152489	
LAMB4	22798	hgsc.bcm.edu	37	7	107706208	107706208	+	Splice_Site	SNP	C	C	T	rs73725316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:107706208C>T	ENST00000388781.3	-	21	2918	c.2835G>A	c.(2833-2835)acG>acA	p.T945T	LAMB4_ENST00000388780.3_Splice_Site_p.T945T|LAMB4_ENST00000205386.4_Splice_Site_p.T945T	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	945	Laminin EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00460}.				cell adhesion (GO:0007155)	basement membrane (GO:0005604)				NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						ACTGCATACCCGTATAACCTT	0.373													C|||	42	0.00838658	0.0303	0.0029	5008	,	,		20016	0.0		0.0	False		,,,				2504	0.0				p.T945T		Atlas-SNP	.											.	LAMB4	253	.	0			c.G2835A						PASS	.	C		113,4293	85.3+/-124.0	2,109,2092	123.0	116.0	118.0		2835	2.2	0.6	7	dbSNP_130	118	0,8600		0,0,4300	yes	coding-synonymous-near-splice	LAMB4	NM_007356.2		2,109,6392	TT,TC,CC		0.0,2.5647,0.8688		945/1762	107706208	113,12893	2203	4300	6503	SO:0001630	splice_region_variant	22798	exon21			CATACCCGTATAA	AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"""Laminins"""	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.2836+1G>A	7.37:g.107706208C>T		118.0	0.0	0		108.0	51.0	0.472222	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Silent	SNP	ENST00000388781.3	37	CCDS34732.1																																																																																			C|0.992;T|0.008	0.008	strong		0.373	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857	Silent
PKD1	5310	hgsc.bcm.edu	37	16	2152850	2152850	+	Silent	SNP	A	A	G	rs9926309	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2152850A>G	ENST00000262304.4	-	24	9121	c.8913T>C	c.(8911-8913)gcT>gcC	p.A2971A	PKD1_ENST00000561991.1_5'Flank|PKD1_ENST00000423118.1_Silent_p.A2971A	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	2971					anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						GCCGGTGGTCAGCACCCTGGA	0.642													g|||	190	0.0379393	0.1369	0.0115	5008	,	,		11693	0.001		0.0	False		,,,				2504	0.0				p.A2971A		Atlas-SNP	.											.	PKD1	184	.	0			c.T8913C						PASS	.	G	,	394,3996	767.2+/-413.5	22,350,1823	62.0	72.0	69.0		8913,8913	-9.1	0.0	16	dbSNP_119	69	5,8575	816.3+/-406.9	0,5,4285	no	coding-synonymous,coding-synonymous	PKD1	NM_000296.3,NM_001009944.2	,	22,355,6108	GG,GA,AA		0.0583,8.9749,3.0763	,	2971/4303,2971/4304	2152850	399,12571	2195	4290	6485	SO:0001819	synonymous_variant	5310	exon24			GTGGTCAGCACCC	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9008	protein-coding gene	gene with protein product	"""polycystin 1"", ""transient receptor potential cation channel, subfamily P, member 1"""	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.8913T>C	16.37:g.2152850A>G		80.0	0.0	0		68.0	24.0	0.352941	NM_000296	Q15140|Q15141	Silent	SNP	ENST00000262304.4	37	CCDS32369.1	49	0.022435897435897436	45	0.09146341463414634	4	0.011049723756906077	0	0.0	0	0.0	G	0.702	-0.790596	0.02884	0.089749	5.83E-4	ENSG00000008710	ENST00000382481	.	.	.	4.55	-9.1	0.00714	.	.	.	.	.	T	0.04137	0.0115	.	.	.	0.58432	D	0.999995	.	.	.	.	.	.	T	0.65701	-0.6104	5	0.87932	D	0	.	9.2021	0.37265	0.2909:0.5516:0.0851:0.0724	rs9926309	.	.	.	P	1209	.	ENSP00000371921:L1209P	L	-	2	0	PKD1	2092851	0.000000	0.05858	0.001000	0.08648	0.014000	0.08584	-2.024000	0.01436	-1.933000	0.01052	-1.087000	0.02190	CTG	A|0.976;G|0.024	0.024	strong		0.642	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
WDFY4	57705	hgsc.bcm.edu	37	10	50019740	50019740	+	Missense_Mutation	SNP	T	T	C	rs114590878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:50019740T>C	ENST00000325239.5	+	29	5228	c.5201T>C	c.(5200-5202)aTg>aCg	p.M1734T	WDFY4_ENST00000413659.2_3'UTR	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	1734						integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						ACAGAGCTGATGGACGGGCCC	0.527													c|||	68	0.0135783	0.0446	0.0115	5008	,	,		21523	0.0		0.001	False		,,,				2504	0.0				p.M1734T		Atlas-SNP	.											.	WDFY4	205	.	0			c.T5201C						PASS	.		THR/MET	55,1329		1,53,638	127.0	116.0	120.0		5201	-9.3	0.0	10	dbSNP_132	120	2,3180		0,2,1589	yes	missense	WDFY4	NM_020945.1	81	1,55,2227	CC,CT,TT		0.0629,3.974,1.2484	benign	1734/3185	50019740	57,4509	692	1591	2283	SO:0001583	missense	57705	exon30			AGCTGATGGACGG	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.5201T>C	10.37:g.50019740T>C	ENSP00000320563:p.Met1734Thr	112.0	0.0	0		123.0	69.0	0.560976	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	37	CCDS44385.1	17	0.007783882783882784	15	0.03048780487804878	2	0.0055248618784530384	0	0.0	0	0.0	C	1.196	-0.633873	0.03584	0.03974	6.29E-4	ENSG00000128815	ENST00000426033;ENST00000325239	T	0.53857	0.6	5.62	-9.26	0.00662	.	0.878748	0.09893	N	0.742057	T	0.01940	0.0061	N	0.00170	-1.935	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.17077	-1.0381	9	.	.	.	.	4.1195	0.10099	0.0879:0.2511:0.1727:0.4883	.	262;1734	F2Z372;Q6ZS81	.;WDFY4_HUMAN	T	1734	ENSP00000320563:M1734T	.	M	+	2	0	WDFY4	49689746	0.000000	0.05858	0.000000	0.03702	0.051000	0.14879	-1.181000	0.03085	-3.275000	0.00198	-1.367000	0.01198	ATG	T|0.992;C|0.008	0.008	strong		0.527	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
CEP250	11190	hgsc.bcm.edu	37	20	34089679	34089679	+	Silent	SNP	C	C	T	rs224379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34089679C>T	ENST00000397527.1	+	29	4626	c.3906C>T	c.(3904-3906)tcC>tcT	p.S1302S	CEP250_ENST00000342580.4_Silent_p.S1246S	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	1302	Gln/Glu-rich.				centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			AAGAGAAATCCAAGTGGGAAG	0.493													C|||	14	0.00279553	0.0106	0.0	5008	,	,		22493	0.0		0.0	False		,,,				2504	0.0				p.S1302S		Atlas-SNP	.											.	CEP250	141	.	0			c.C3906T						PASS	.	C		58,4346	56.2+/-92.4	0,58,2144	50.0	50.0	50.0		3906	1.9	1.0	20	dbSNP_79	50	0,8600		0,0,4300	no	coding-synonymous	CEP250	NM_007186.3		0,58,6444	TT,TC,CC		0.0,1.317,0.446		1302/2443	34089679	58,12946	2202	4300	6502	SO:0001819	synonymous_variant	11190	exon29			GAAATCCAAGTGG	AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"""centrosomal protein 2"""	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.3906C>T	20.37:g.34089679C>T		31.0	0.0	0		35.0	21.0	0.6	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Silent	SNP	ENST00000397527.1	37	CCDS13255.1																																																																																			C|0.996;T|0.004	0.004	strong		0.493	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186	
NLRP14	338323	hgsc.bcm.edu	37	11	7064271	7064271	+	Silent	SNP	T	T	C	rs116753166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:7064271T>C	ENST00000299481.4	+	4	1360	c.1014T>C	c.(1012-1014)taT>taC	p.Y338Y		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	338	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)			breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		GAGAGGAGTATATTTACCAGT	0.398													T|||	87	0.0173722	0.0613	0.0072	5008	,	,		22160	0.0		0.001	False		,,,				2504	0.0				p.Y338Y		Atlas-SNP	.											.	NLRP14	187	.	0			c.T1014C						PASS	.	T		260,4142	146.9+/-181.5	14,232,1955	100.0	105.0	103.0		1014	2.2	0.4	11	dbSNP_132	103	1,8591	1.2+/-3.3	0,1,4295	no	coding-synonymous	NLRP14	NM_176822.3		14,233,6250	CC,CT,TT		0.0116,5.9064,2.0086		338/1094	7064271	261,12733	2201	4296	6497	SO:0001819	synonymous_variant	338323	exon4			GGAGTATATTTAC	BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"""Nucleotide-binding domain and leucine rich repeat containing"""	22939	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"""	609665	"""NACHT, leucine rich repeat and PYD containing 14"""	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.1014T>C	11.37:g.7064271T>C		127.0	0.0	0		166.0	82.0	0.493976	NM_176822	Q7RTR6	Silent	SNP	ENST00000299481.4	37	CCDS7776.1																																																																																			T|0.983;C|0.017	0.017	strong		0.398	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822	
ALDH16A1	126133	hgsc.bcm.edu	37	19	49965956	49965956	+	Missense_Mutation	SNP	G	G	A	rs10406757	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49965956G>A	ENST00000293350.4	+	8	1205	c.1042G>A	c.(1042-1044)Gcc>Acc	p.A348T	ALDH16A1_ENST00000540132.1_Missense_Mutation_p.A185T|ALDH16A1_ENST00000455361.2_Missense_Mutation_p.A297T|CTD-3148I10.9_ENST00000599536.1_5'Flank|ALDH16A1_ENST00000433981.2_Missense_Mutation_p.A183T	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	348						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|skin(2)|urinary_tract(3)	20		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)		CCGGGGGGCTGCCGCATGTGA	0.687													G|||	187	0.0373403	0.1324	0.0159	5008	,	,		12025	0.0		0.001	False		,,,				2504	0.0				p.A348T		Atlas-SNP	.											.	ALDH16A1	54	.	0			c.G1042A						PASS	.	G	THR/ALA,THR/ALA	423,3981		21,381,1800	23.0	26.0	25.0		889,1042	2.8	0.5	19	dbSNP_119	25	4,8592		0,4,4294	yes	missense,missense	ALDH16A1	NM_001145396.1,NM_153329.3	58,58	21,385,6094	AA,AG,GG		0.0465,9.6049,3.2846	probably-damaging,probably-damaging	297/752,348/803	49965956	427,12573	2202	4298	6500	SO:0001583	missense	126133	exon8			GGGGCTGCCGCAT	AY007096	CCDS12766.1, CCDS46141.1	19q13.33	2014-08-12			ENSG00000161618	ENSG00000161618		"""Aldehyde dehydrogenases"""	28114	protein-coding gene	gene with protein product		613358					Standard	NM_153329		Approved	MGC10204	uc002pnt.3	Q8IZ83	OTTHUMG00000183163	ENST00000293350.4:c.1042G>A	19.37:g.49965956G>A	ENSP00000293350:p.Ala348Thr	275.0	0.0	0		323.0	171.0	0.529412	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Missense_Mutation	SNP	ENST00000293350.4	37	CCDS12766.1	52	0.023809523809523808	45	0.09146341463414634	7	0.019337016574585635	0	0.0	0	0.0	G	13.56	2.274535	0.40194	0.096049	4.65E-4	ENSG00000161618	ENST00000293350;ENST00000455361;ENST00000540132;ENST00000433981	T;T;T;T	0.77489	-1.1;-1.1;-1.1;-1.1	5.03	2.77	0.32553	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, C-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.412335	0.24688	N	0.036418	T	0.11410	0.0278	L	0.55834	1.745	0.09310	N	1	D;D;D	0.76494	0.999;0.998;0.997	D;D;D	0.69307	0.943;0.963;0.932	T	0.22906	-1.0203	10	0.32370	T	0.25	-22.8219	6.9006	0.24281	0.0956:0.0:0.7322:0.1723	rs10406757	185;297;348	F5H4B6;B4DLQ1;Q8IZ83	.;.;A16A1_HUMAN	T	348;297;185;183	ENSP00000293350:A348T;ENSP00000410142:A297T;ENSP00000445088:A185T;ENSP00000398675:A183T	ENSP00000293350:A348T	A	+	1	0	ALDH16A1	54657768	0.494000	0.26043	0.530000	0.27963	0.649000	0.38597	3.254000	0.51477	1.286000	0.44565	0.485000	0.47835	GCC	A|0.034;C|0.000;G|0.965	0.034	strong		0.687	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329	
FGF6	2251	hgsc.bcm.edu	37	12	4554549	4554549	+	Missense_Mutation	SNP	G	G	A	rs17183529	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:4554549G>A	ENST00000228837.2	-	1	231	c.188C>T	c.(187-189)gCc>gTc	p.A63V		NM_020996.1	NP_066276.2	P10767	FGF6_HUMAN	fibroblast growth factor 6	63			A -> V (in dbSNP:rs17183529). {ECO:0000269|Ref.2}.		angiogenesis (GO:0001525)|cartilage condensation (GO:0001502)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|myoblast differentiation (GO:0045445)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|sarcolemma (GO:0042383)	growth factor activity (GO:0008083)	p.A63V(1)		NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	20			Colorectal(7;0.00165)|COAD - Colon adenocarcinoma(12;0.0229)			AGCTAGCCCGGCGCGAGACCT	0.642													G|||	21	0.00419329	0.0159	0.0	5008	,	,		17319	0.0		0.0	False		,,,				2504	0.0				p.A63V		Atlas-SNP	.											FGF6,colon,carcinoma,-1,2	FGF6	40	2	1	Substitution - Missense(1)	large_intestine(1)	c.C188T						PASS	.	G	VAL/ALA	57,4349	51.6+/-87.1	0,57,2146	88.0	83.0	85.0		188	4.1	0.0	12	dbSNP_123	85	0,8600		0,0,4300	no	missense	FGF6	NM_020996.1	64	0,57,6446	AA,AG,GG		0.0,1.2937,0.4383	benign	63/209	4554549	57,12949	2203	4300	6503	SO:0001583	missense	2251	exon1			AGCCCGGCGCGAG	X63454	CCDS8527.1	12p13	2014-01-30				ENSG00000111241		"""Endogenous ligands"""	3684	protein-coding gene	gene with protein product		134921				16597617	Standard	NM_020996		Approved		uc001qmr.1	P10767		ENST00000228837.2:c.188C>T	12.37:g.4554549G>A	ENSP00000228837:p.Ala63Val	59.0	0.0	0		89.0	44.0	0.494382	NM_020996	Q0VAE1	Missense_Mutation	SNP	ENST00000228837.2	37	CCDS8527.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	10.67	1.415816	0.25552	0.012937	0.0	ENSG00000111241	ENST00000228837	T	0.26810	1.71	5.0	4.09	0.47781	.	0.553031	0.20578	N	0.089588	T	0.18257	0.0438	L	0.49126	1.545	0.09310	N	0.999998	B	0.30146	0.27	B	0.34991	0.193	T	0.12578	-1.0542	10	0.36615	T	0.2	.	9.216	0.37348	0.0768:0.1473:0.7759:0.0	rs17183529	63	P10767	FGF6_HUMAN	V	63	ENSP00000228837:A63V	ENSP00000228837:A63V	A	-	2	0	FGF6	4424810	0.756000	0.28383	0.004000	0.12327	0.229000	0.25112	3.566000	0.53805	1.215000	0.43411	0.561000	0.74099	GCC	G|0.996;A|0.004	0.004	strong		0.642	FGF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398939.1	NM_020996	
SUPT7L	9913	hgsc.bcm.edu	37	2	27883958	27883958	+	Silent	SNP	C	C	T	rs6756254	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27883958C>T	ENST00000337768.5	-	3	881	c.312G>A	c.(310-312)tcG>tcA	p.S104S	SUPT7L_ENST00000404798.2_Intron|SUPT7L_ENST00000464789.2_Silent_p.S102S|SUPT7L_ENST00000405491.1_Silent_p.S102S|SUPT7L_ENST00000406540.1_Silent_p.S102S|SLC4A1AP_ENST00000326019.6_5'Flank	NM_001282729.1|NM_014860.1	NP_001269658.1|NP_055675.1	O94864	ST65G_HUMAN	suppressor of Ty 7 (S. cerevisiae)-like	104					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|maintenance of protein location in nucleus (GO:0051457)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|STAGA complex (GO:0030914)	transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|prostate(2)|skin(2)|urinary_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)					ACCCAGGGCACGAGGGAAGAG	0.527													C|||	333	0.0664936	0.2307	0.0187	5008	,	,		20175	0.0		0.0129	False		,,,				2504	0.002				p.S104S		Atlas-SNP	.											.	SUPT7L	36	.	0			c.G312A						PASS	.	C		690,3508		61,568,1470	117.0	123.0	121.0		312	-2.7	0.3	2	dbSNP_116	121	65,8345		0,65,4140	no	coding-synonymous	SUPT7L	NM_014860.1		61,633,5610	TT,TC,CC		0.7729,16.4364,5.9883		104/415	27883958	755,11853	2099	4205	6304	SO:0001819	synonymous_variant	9913	exon3			AGGGCACGAGGGA	AF197954	CCDS42667.1, CCDS62885.1, CCDS62886.1	2p23.3	2008-02-05			ENSG00000119760	ENSG00000119760			30632	protein-coding gene	gene with protein product		612762				9872452, 11564863	Standard	NM_001282732		Approved	STAF65, gamma, KIAA0764, SPT7L	uc002rli.1	O94864	OTTHUMG00000151947	ENST00000337768.5:c.312G>A	2.37:g.27883958C>T		358.0	0.0	0		440.0	194.0	0.440909	NM_014860	B4E3W3|Q6IB21|Q9H2T6	Silent	SNP	ENST00000337768.5	37	CCDS42667.1																																																																																			C|0.940;T|0.060	0.060	strong		0.527	SUPT7L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324568.1	NM_014860	
IL1A	3552	hgsc.bcm.edu	37	2	113539224	113539224	+	Silent	SNP	G	G	A	rs20540	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:113539224G>A	ENST00000263339.3	-	4	431	c.276C>T	c.(274-276)atC>atT	p.I92I		NM_000575.3	NP_000566.3	P01583	IL1A_HUMAN	interleukin 1, alpha	92					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|cytokine-mediated signaling pathway (GO:0019221)|ectopic germ cell programmed cell death (GO:0035234)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fever generation (GO:0001660)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell division (GO:0051781)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of mitosis (GO:0045840)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation vascular endothelial growth factor production (GO:0010575)|response to copper ion (GO:0046688)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	copper ion binding (GO:0005507)|cytokine activity (GO:0005125)			breast(2)|large_intestine(1)|lung(9)	12					Rilonacept(DB06372)	CATCATCAGTGATGGATTGGC	0.453													G|||	96	0.0191693	0.0719	0.0014	5008	,	,		23080	0.0		0.0	False		,,,				2504	0.0				p.I92I		Atlas-SNP	.											.	IL1A	19	.	0			c.C276T						PASS	.	G		263,4143	149.9+/-184.0	9,245,1949	218.0	203.0	208.0		276	0.0	0.0	2	dbSNP_67	208	0,8600		0,0,4300	no	coding-synonymous	IL1A	NM_000575.3		9,245,6249	AA,AG,GG		0.0,5.9691,2.0221		92/272	113539224	263,12743	2203	4300	6503	SO:0001819	synonymous_variant	3552	exon4			ATCAGTGATGGAT	M28983	CCDS2101.1	2q14	2014-01-30			ENSG00000115008	ENSG00000115008		"""Interleukins and interleukin receptors"", ""Endogenous ligands"""	5991	protein-coding gene	gene with protein product	"""preinterleukin 1 alpha"", ""hematopoietin-1"", ""pro-interleukin-1-alpha"""	147760		IL1		8188271, 2989698	Standard	NM_000575		Approved	IL1F1, IL-1A, IL1-ALPHA	uc002tig.3	P01583	OTTHUMG00000131315	ENST00000263339.3:c.276C>T	2.37:g.113539224G>A		243.0	1.0	0.00411523		242.0	112.0	0.46281	NM_000575	Q53QF9|Q7RU02	Silent	SNP	ENST00000263339.3	37	CCDS2101.1																																																																																			G|0.980;A|0.020	0.020	strong		0.453	IL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254084.1	NM_000575	
PREX1	57580	hgsc.bcm.edu	37	20	47295906	47295906	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:47295906C>T	ENST00000371941.3	-	13	1603	c.1581G>A	c.(1579-1581)ccG>ccA	p.P527P	PREX1_ENST00000396220.1_Silent_p.P527P	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	527	DEP 2. {ECO:0000255|PROSITE- ProRule:PRU00066}.				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)			ACTTGATCACCGGGGTGTAGA	0.512																																					p.P527P		Atlas-SNP	.											.	PREX1	441	.	0			c.G1581A						PASS	.						117.0	112.0	114.0					20																	47295906		2203	4300	6503	SO:0001819	synonymous_variant	57580	exon13			GATCACCGGGGTG	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.1581G>A	20.37:g.47295906C>T		36.0	0.0	0		34.0	16.0	0.470588	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Silent	SNP	ENST00000371941.3	37	CCDS13410.1																																																																																			.	.	none		0.512	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820	
CCDC88C	440193	hgsc.bcm.edu	37	14	91770308	91770308	+	Silent	SNP	C	C	T	rs112741231	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:91770308C>T	ENST00000389857.6	-	20	3458	c.3372G>A	c.(3370-3372)acG>acA	p.T1124T		NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	1124					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				GGGAACTCAGCGTGGAGTTCT	0.662													c|||	111	0.0221645	0.0772	0.013	5008	,	,		16262	0.0		0.0	False		,,,				2504	0.0				p.T1124T		Atlas-SNP	.											CCDC88C_ENST00000389857,NS,carcinoma,0,2	CCDC88C	192	2	0			c.G3372A						PASS	.	C		250,3982		8,234,1874	43.0	49.0	47.0		3372	-11.0	0.2	14	dbSNP_132	47	9,8477		0,9,4234	no	coding-synonymous	CCDC88C	NM_001080414.3		8,243,6108	TT,TC,CC		0.1061,5.9074,2.0365		1124/2029	91770308	259,12459	2116	4243	6359	SO:0001819	synonymous_variant	440193	exon20			ACTCAGCGTGGAG		CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"""Dvl-associating protein with a high frequency of leucine residues"", ""spinocerebellar ataxia 40"""	611204	"""KIAA1509"""	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.3372G>A	14.37:g.91770308C>T		54.0	0.0	0		58.0	31.0	0.534483	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Silent	SNP	ENST00000389857.6	37	CCDS45151.1																																																																																			C|0.983;T|0.017	0.017	strong		0.662	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353	
MYO7A	4647	hgsc.bcm.edu	37	11	76922208	76922208	+	Silent	SNP	G	G	A	rs111033209	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:76922208G>A	ENST00000409709.3	+	45	6335	c.6063G>A	c.(6061-6063)aaG>aaA	p.K2021K	MYO7A_ENST00000409619.2_Silent_p.K1972K|MYO7A_ENST00000605744.1_3'UTR|MYO7A_ENST00000458637.2_Silent_p.K1983K	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	2021	FERM 2. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						AGTTGCCCAAGTATCTCCGAG	0.617													G|||	155	0.0309505	0.1142	0.0043	5008	,	,		19584	0.0		0.001	False		,,,				2504	0.0				p.K2021K		Atlas-SNP	.											.	MYO7A	164	.	0			c.G6063A						PASS	.	G	,	352,3800		22,308,1746	19.0	23.0	22.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	6063,5949	1.4	1.0	11	dbSNP_132	22	6,8398		0,6,4196	no	coding-synonymous,coding-synonymous	MYO7A	NM_000260.3,NM_001127180.1	,	22,314,5942	AA,AG,GG		0.0714,8.4778,2.8512	,	2021/2216,1983/2176	76922208	358,12198	2076	4202	6278	SO:0001819	synonymous_variant	4647	exon45			GCCCAAGTATCTC	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"""A-kinase anchor proteins"", ""Myosins / Myosin superfamily : Class VII"""	7606	protein-coding gene	gene with protein product		276903	"""myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"""	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.6063G>A	11.37:g.76922208G>A		83.0	0.0	0		62.0	24.0	0.387097	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Silent	SNP	ENST00000409709.3	37	CCDS53683.1																																																																																			G|0.966;A|0.034	0.034	strong		0.617	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
MSLN	10232	hgsc.bcm.edu	37	16	816973	816973	+	Missense_Mutation	SNP	A	A	G	rs35317722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:816973A>G	ENST00000382862.3	+	14	1581	c.1486A>G	c.(1486-1488)Aac>Gac	p.N496D	MSLN_ENST00000566549.1_Missense_Mutation_p.N488D|MSLN_ENST00000563941.1_Missense_Mutation_p.N488D|MSLN_ENST00000545450.2_Missense_Mutation_p.N488D	NM_013404.4	NP_037536.2	Q13421	MSLN_HUMAN	mesothelin	496					cell adhesion (GO:0007155)|pancreas development (GO:0031016)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|kidney(2)|lung(11)|pancreas(1)|prostate(1)|skin(3)	20		Hepatocellular(780;0.00335)				CCAGAACATGAACGGGTCCGA	0.627													A|||	151	0.0301518	0.1104	0.0072	5008	,	,		18480	0.0		0.0	False		,,,				2504	0.0				p.N496D		Atlas-SNP	.											.	MSLN	109	.	0			c.A1486G						PASS	.	A	ASP/ASN,ASP/ASN,ASP/ASN	341,4039	175.5+/-204.9	19,303,1868	79.0	80.0	79.0		1462,1462,1486	-0.5	0.0	16	dbSNP_126	79	3,8581	3.0+/-9.4	0,3,4289	yes	missense,missense,missense	MSLN	NM_001177355.1,NM_005823.5,NM_013404.4	23,23,23	19,306,6157	GG,GA,AA		0.0349,7.7854,2.6535	benign,benign,benign	488/623,488/623,496/631	816973	344,12620	2190	4292	6482	SO:0001583	missense	10232	exon14			AACATGAACGGGT	U40434	CCDS32356.1, CCDS45370.1	16p13.3	2008-04-16			ENSG00000102854	ENSG00000102854			7371	protein-coding gene	gene with protein product		601051				7665620, 8552591	Standard	NM_005823		Approved	CAK1, MPF	uc002cjw.2	Q13421	OTTHUMG00000047992	ENST00000382862.3:c.1486A>G	16.37:g.816973A>G	ENSP00000372313:p.Asn496Asp	58.0	0.0	0		77.0	38.0	0.493506	NM_013404	D3DU65|Q14859|Q4VQD5|Q96GR6|Q96KJ5|Q9BR17|Q9BTR2|Q9UCB2|Q9UK57	Missense_Mutation	SNP	ENST00000382862.3	37	CCDS32356.1	66	0.03021978021978022	63	0.12804878048780488	3	0.008287292817679558	0	0.0	0	0.0	A	5.121	0.207947	0.09704	0.077854	3.49E-4	ENSG00000102854	ENST00000446427;ENST00000445361;ENST00000545450;ENST00000382862	T;T	0.12039	2.72;2.72	5.13	-0.498	0.12019	.	0.811867	0.11375	N	0.570445	T	0.00073	0.0002	N	0.19112	0.55	0.09310	N	1	B;B;B;B	0.15719	0.004;0.009;0.014;0.004	B;B;B;B	0.13407	0.005;0.009;0.005;0.005	T	0.44620	-0.9316	10	0.11485	T	0.65	-15.2008	5.1406	0.14957	0.4492:0.2783:0.0:0.2724	rs35317722	487;496;488;488	Q13421-4;Q13421;Q13421-2;Q13421-3	.;MSLN_HUMAN;.;.	D	496;488;488;496	ENSP00000442965:N488D;ENSP00000372313:N496D	ENSP00000372313:N496D	N	+	1	0	MSLN	756974	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.121000	0.15667	0.222000	0.20900	0.443000	0.29094	AAC	A|0.970;G|0.030	0.030	strong		0.627	MSLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109253.2		
MEGF8	1954	hgsc.bcm.edu	37	19	42873089	42873089	+	Silent	SNP	G	G	A	rs10425783	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42873089G>A	ENST00000251268.6	+	37	6576	c.6576G>A	c.(6574-6576)acG>acA	p.T2192T	MEGF8_ENST00000334370.4_Silent_p.T2125T|MEGF8_ENST00000378073.4_5'Flank	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	2192	EGF-like 5. {ECO:0000255|PROSITE- ProRule:PRU00076}.				BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				GCAACGAGACGCAGAATTGCC	0.662													G|||	133	0.0265575	0.093	0.0115	5008	,	,		17876	0.0		0.002	False		,,,				2504	0.0				p.T2192T		Atlas-SNP	.											.	MEGF8	358	.	0			c.G6576A						PASS	.	G		335,4071	176.9+/-206.0	17,301,1885	82.0	84.0	83.0		6375	-9.5	0.0	19	dbSNP_119	83	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous	MEGF8	NM_001410.2		17,311,6175	AA,AG,GG		0.1163,7.6033,2.6526		2125/2779	42873089	345,12661	2203	4300	6503	SO:0001819	synonymous_variant	1954	exon37			CGAGACGCAGAAT	AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"""HBV pre s2 binding protein 1"""	604267	"""EGF-like-domain, multiple 4"", ""chromosome 19 open reading frame 49"""	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.6576G>A	19.37:g.42873089G>A		78.0	0.0	0		89.0	48.0	0.539326	NM_001271938	A8KAY0|O75097	Silent	SNP	ENST00000251268.6	37																																																																																				G|0.969;A|0.031	0.031	strong		0.662	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410	
SACS	26278	hgsc.bcm.edu	37	13	23914286	23914286	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:23914286T>C	ENST00000382292.3	-	9	4002	c.3729A>G	c.(3727-3729)gaA>gaG	p.E1243E	SACS_ENST00000382298.3_Silent_p.E1243E|SACS_ENST00000402364.1_Silent_p.E493E			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	1243					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		GATAGTAGTCTTCATCACTAA	0.323																																					p.E1243E		Atlas-SNP	.											.	SACS	871	.	0			c.A3729G						PASS	.						44.0	43.0	43.0					13																	23914286		2202	4300	6502	SO:0001819	synonymous_variant	26278	exon10			GTAGTCTTCATCA	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.3729A>G	13.37:g.23914286T>C		79.0	0.0	0		121.0	62.0	0.512397	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	37	CCDS9300.2																																																																																			.	.	none		0.323	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
CLEC16A	23274	hgsc.bcm.edu	37	16	11272227	11272227	+	Missense_Mutation	SNP	C	C	T	rs61744103	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:11272227C>T	ENST00000409790.1	+	24	3072	c.2842C>T	c.(2842-2844)Ctt>Ttt	p.L948F	CLEC16A_ENST00000381822.2_Missense_Mutation_p.L35F	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A									p.0?(1)		breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						TAAGCCTCACCTTCCTGACCA	0.592													C|||	90	0.0179712	0.0658	0.0043	5008	,	,		6774	0.0		0.0	False		,,,				2504	0.0				p.L948F		Atlas-SNP	.											.	CLEC16A	101	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.C2842T						PASS	.	C	PHE/LEU	177,4103		3,171,1966	100.0	111.0	107.0		2842	2.0	0.9	16	dbSNP_129	107	1,8491		0,1,4245	yes	missense	CLEC16A	NM_015226.2	22	3,172,6211	TT,TC,CC		0.0118,4.1355,1.3937	benign	948/1054	11272227	178,12594	2140	4246	6386	SO:0001583	missense	23274	exon23			CCTCACCTTCCTG	AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"""C-type lectin domain containing"""	29013	protein-coding gene	gene with protein product		611303	"""KIAA0350"""	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.2842C>T	16.37:g.11272227C>T	ENSP00000387122:p.Leu948Phe	73.0	0.0	0		77.0	46.0	0.597403	NM_015226		Missense_Mutation	SNP	ENST00000409790.1	37	CCDS45409.1	20	0.009157509157509158	18	0.036585365853658534	2	0.0055248618784530384	0	0.0	0	0.0	C	10.65	1.409444	0.25378	0.041355	1.18E-4	ENSG00000038532	ENST00000409790;ENST00000542102;ENST00000381822	T	0.50548	0.74	4.13	2.02	0.26589	.	1.046110	0.07487	N	0.904880	T	0.11879	0.0289	N	0.03608	-0.345	0.09310	N	1	D;B	0.69078	0.997;0.0	D;B	0.63283	0.913;0.0	T	0.21895	-1.0232	10	0.32370	T	0.25	-2.4515	5.4981	0.16813	0.3727:0.5235:0.0:0.1038	rs61744103	35;948	Q2KHT3-3;Q2KHT3	.;CL16A_HUMAN	F	948;948;35	ENSP00000387122:L948F	ENSP00000371244:L35F	L	+	1	0	CLEC16A	11179728	0.120000	0.22244	0.917000	0.36280	0.855000	0.48748	0.314000	0.19432	0.815000	0.34398	0.563000	0.77884	CTT	C|0.991;T|0.009	0.009	strong		0.592	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226	
CCL18	6362	hgsc.bcm.edu	37	17	34391721	34391721	+	Missense_Mutation	SNP	G	G	A	rs73290772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34391721G>A	ENST00000004921.3	+	1	82	c.19G>A	c.(19-21)Gcc>Acc	p.A7T		NM_002988.2	NP_002979.1	P55774	CCL18_HUMAN	chemokine (C-C motif) ligand 18 (pulmonary and activation-regulated)	7					cell chemotaxis (GO:0060326)|cell communication (GO:0007154)|cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|immune response (GO:0006955)|inflammatory response (GO:0006954)|response to biotic stimulus (GO:0009607)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	chemokine activity (GO:0008009)			endometrium(1)|large_intestine(2)|lung(1)	4		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		CCTTGCAGCTGCCCTCCTTGT	0.587													G|||	32	0.00638978	0.0227	0.0014	5008	,	,		20323	0.0		0.001	False		,,,				2504	0.0				p.A7T		Atlas-SNP	.											.	CCL18	9	.	0			c.G19A						PASS	.	G	THR/ALA	83,4323	70.9+/-108.8	1,81,2121	175.0	144.0	154.0		19	-4.2	0.0	17	dbSNP_130	154	4,8596	3.7+/-12.6	0,4,4296	yes	missense	CCL18	NM_002988.2	58	1,85,6417	AA,AG,GG		0.0465,1.8838,0.6689	possibly-damaging	7/90	34391721	87,12919	2203	4300	6503	SO:0001583	missense	6362	exon1			GCAGCTGCCCTCC	Y13710	CCDS11306.1	17q11.2	2014-05-06	2002-08-22	2002-08-23	ENSG00000006074	ENSG00000275385		"""Chemokine ligands"""	10616	protein-coding gene	gene with protein product		603757	"""small inducible cytokine subfamily A (Cys-Cys), member 18, pulmonary and activation-regulated"""	SCYA18		9233607, 10049593	Standard	NM_002988		Approved	DC-CK1, PARC, AMAC-1, DCCK1, MIP-4, CKb7	uc002hku.3	P55774	OTTHUMG00000188410	ENST00000004921.3:c.19G>A	17.37:g.34391721G>A	ENSP00000004921:p.Ala7Thr	115.0	0.0	0		150.0	74.0	0.493333	NM_002988	B5BUM2|Q53X71	Missense_Mutation	SNP	ENST00000004921.3	37	CCDS11306.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	15.95	2.982703	0.53827	0.018838	4.65E-4	ENSG00000006074	ENST00000004921	T	0.03468	3.92	4.63	-4.23	0.03789	.	0.749621	0.12687	N	0.447482	T	0.02418	0.0074	.	.	.	0.09310	N	1	D	0.65815	0.995	P	0.53954	0.738	T	0.10382	-1.0632	9	0.37606	T	0.19	.	5.6346	0.17530	0.3533:0.0:0.5254:0.1213	.	7	P55774	CCL18_HUMAN	T	7	ENSP00000004921:A7T	ENSP00000004921:A7T	A	+	1	0	CCL18	31415834	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.697000	0.05098	-0.814000	0.04352	-0.311000	0.09066	GCC	G|0.994;A|0.006	0.006	strong		0.587	CCL18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256583.1	NM_002988	
LMAN1L	79748	hgsc.bcm.edu	37	15	75111530	75111530	+	Missense_Mutation	SNP	G	G	A	rs62621375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:75111530G>A	ENST00000309664.5	+	6	774	c.635G>A	c.(634-636)gGt>gAt	p.G212D	LMAN1L_ENST00000379709.3_Missense_Mutation_p.G212D|RP11-414J4.2_ENST00000564823.1_RNA	NM_021819.2	NP_068591.2	Q9HAT1	LMA1L_HUMAN	lectin, mannose-binding, 1 like	212	L-type lectin-like. {ECO:0000255|PROSITE- ProRule:PRU00658}.					integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						AGTGATCCAGGTGAGTTCTGT	0.612													A|||	374	0.0746805	0.2723	0.0144	5008	,	,		19129	0.001		0.003	False		,,,				2504	0.0				p.G212D		Atlas-SNP	.											.	LMAN1L	43	.	0			c.G635A						PASS	.	A	ASP/GLY	1009,3385	728.8+/-410.0	126,757,1314	207.0	185.0	193.0		635	5.7	0.0	15	dbSNP_129	193	6,8586	818.6+/-406.8	0,6,4290	yes	missense	LMAN1L	NM_021819.2	94	126,763,5604	AA,AG,GG		0.0698,22.9631,7.8161	benign	212/527	75111530	1015,11971	2197	4296	6493	SO:0001583	missense	79748	exon6			ATCCAGGTGAGTT	AF303398	CCDS10270.1	15q24.1	2005-08-05			ENSG00000140506	ENSG00000140506			6632	protein-coding gene	gene with protein product		609548				11255007	Standard	NM_021819		Approved	ERGL, ERGIC-53L	uc002ayt.1	Q9HAT1	OTTHUMG00000142813	ENST00000309664.5:c.635G>A	15.37:g.75111530G>A	ENSP00000310431:p.Gly212Asp	236.0	0.0	0		225.0	224.0	0.995556	NM_021819	Q6UWN2	Missense_Mutation	SNP	ENST00000309664.5	37	CCDS10270.1	151	0.06913919413919414	143	0.29065040650406504	5	0.013812154696132596	1	0.0017482517482517483	2	0.002638522427440633	A	4.989	0.183651	0.09495	0.229631	6.98E-4	ENSG00000140506	ENST00000309664;ENST00000456603;ENST00000379709	T;T	0.63255	-0.03;-0.03	5.67	5.67	0.87782	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.744014	0.12971	N	0.424120	T	0.00012	0.0000	N	0.00072	-2.265	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.0;0.001;0.0	T	0.20174	-1.0283	8	.	.	.	.	8.6109	0.33801	0.9131:0.0:0.0869:0.0	rs62621375	104;212;140;212	B4DGW5;Q9HAT1-3;B4DU67;Q9HAT1	.;.;.;LMA1L_HUMAN	D	212;104;212	ENSP00000310431:G212D;ENSP00000369031:G212D	.	G	+	2	0	LMAN1L	72898583	0.706000	0.27856	0.008000	0.14137	0.095000	0.18619	2.764000	0.47613	0.987000	0.38709	-0.332000	0.08345	GGT	G|0.924;A|0.076	0.076	strong		0.612	LMAN1L-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286397.4		
THBS2	7058	hgsc.bcm.edu	37	6	169648723	169648723	+	Missense_Mutation	SNP	G	G	C	rs36088849	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:169648723G>C	ENST00000366787.3	-	4	647	c.398C>G	c.(397-399)aCc>aGc	p.T133S		NM_003247.2	NP_003238.2	P35442	TSP2_HUMAN	thrombospondin 2	133	Heparin-binding. {ECO:0000255}.|Laminin G-like.		T -> S (in dbSNP:rs36088849).		cell adhesion (GO:0007155)|negative regulation of angiogenesis (GO:0016525)|positive regulation of synapse assembly (GO:0051965)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|platelet alpha granule (GO:0031091)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			NS(3)|biliary_tract(1)|endometrium(8)|kidney(3)|large_intestine(23)|liver(1)|lung(56)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	111		Breast(66;1.78e-05)|Ovarian(120;0.0728)|Esophageal squamous(34;0.247)		OV - Ovarian serous cystadenocarcinoma(33;1.85e-21)|BRCA - Breast invasive adenocarcinoma(81;1.43e-06)|GBM - Glioblastoma multiforme(31;0.000379)		CACATGCCGGGTGCCGTCAAT	0.652													G|||	119	0.023762	0.0885	0.0029	5008	,	,		18772	0.0		0.0	False		,,,				2504	0.0				p.T133S	Esophageal Squamous(91;219 1934 18562 44706)	Atlas-SNP	.											.	THBS2	230	.	0			c.C398G						PASS	.	G	SER/THR	345,4061	168.7+/-199.5	15,315,1873	84.0	70.0	75.0		398	0.2	0.0	6	dbSNP_126	75	3,8597	3.0+/-9.4	0,3,4297	yes	missense	THBS2	NM_003247.2	58	15,318,6170	CC,CG,GG		0.0349,7.8302,2.6757	benign	133/1173	169648723	348,12658	2203	4300	6503	SO:0001583	missense	7058	exon4			TGCCGGGTGCCGT		CCDS34574.1	6q27	2008-07-28			ENSG00000186340	ENSG00000186340			11786	protein-coding gene	gene with protein product		188061				18455130	Standard	NM_003247		Approved	TSP2	uc003qwt.3	P35442	OTTHUMG00000045408	ENST00000366787.3:c.398C>G	6.37:g.169648723G>C	ENSP00000355751:p.Thr133Ser	84.0	0.0	0		110.0	60.0	0.545455	NM_003247	A6H8N1|A7E232|Q5RI52	Missense_Mutation	SNP	ENST00000366787.3	37	CCDS34574.1	35	0.016025641025641024	34	0.06910569105691057	1	0.0027624309392265192	0	0.0	0	0.0	G	1.088	-0.664792	0.03428	0.078302	3.49E-4	ENSG00000186340	ENST00000366787	T	0.01998	4.51	4.61	0.151	0.14888	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G, thrombospondin-type, N-terminal (1);	1.763740	0.03486	U	0.215882	T	0.00384	0.0012	N	0.04203	-0.255	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46952	-0.9154	10	0.22706	T	0.39	-3.9265	3.3224	0.07054	0.1616:0.2494:0.4685:0.1205	rs36088849	133	P35442	TSP2_HUMAN	S	133	ENSP00000355751:T133S	ENSP00000355751:T133S	T	-	2	0	THBS2	169390648	0.018000	0.18449	0.000000	0.03702	0.012000	0.07955	1.512000	0.35812	0.080000	0.16959	0.563000	0.77884	ACC	G|0.977;C|0.023	0.023	strong		0.652	THBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105439.1	NM_003247	
FGD3	89846	hgsc.bcm.edu	37	9	95768396	95768396	+	Silent	SNP	C	C	T	rs199786328		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95768396C>T	ENST00000375482.3	+	6	1267	c.771C>T	c.(769-771)gcC>gcT	p.A257A	FGD3_ENST00000337352.6_Silent_p.A257A|FGD3_ENST00000416701.2_Silent_p.A257A	NM_001083536.1	NP_001077005.1	Q5JSP0	FGD3_HUMAN	FYVE, RhoGEF and PH domain containing 3	257	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	17						TTGACCGAGCCGTAGGGCTGG	0.587																																					p.A257A		Atlas-SNP	.											.	FGD3	116	.	0			c.C771T						PASS	.	C	,	1,4327		0,1,2163	64.0	71.0	69.0		771,771	-7.4	0.0	9		69	0,8568		0,0,4284	no	coding-synonymous,coding-synonymous	FGD3	NM_001083536.1,NM_033086.2	,	0,1,6447	TT,TC,CC		0.0,0.0231,0.0078	,	257/726,257/726	95768396	1,12895	2164	4284	6448	SO:0001819	synonymous_variant	89846	exon6			CCGAGCCGTAGGG	AK000004	CCDS43849.1, CCDS69619.1	9q22	2013-01-10	2004-08-24		ENSG00000127084	ENSG00000127084		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	16027	protein-coding gene	gene with protein product			"""FGD1 family, member 3"""			11214971	Standard	NM_001083536		Approved	FLJ00004, ZFYVE5	uc004asz.2	Q5JSP0	OTTHUMG00000021032	ENST00000375482.3:c.771C>T	9.37:g.95768396C>T		68.0	0.0	0		85.0	56.0	0.658824	NM_001083536	F8W7P2|Q4VX84|Q7Z7D9|Q8N5G1	Silent	SNP	ENST00000375482.3	37	CCDS43849.1																																																																																			C|1.000;T|0.000	0.000	strong		0.587	FGD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055493.1	NM_033086	
JAG1	182	hgsc.bcm.edu	37	20	10624502	10624502	+	Silent	SNP	G	G	A	rs56225585	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:10624502G>A	ENST00000254958.5	-	20	2897	c.2382C>T	c.(2380-2382)agC>agT	p.S794S	JAG1_ENST00000488480.1_RNA|JAG1_ENST00000423891.2_Silent_p.S635S	NM_000214.2	NP_000205.1	P78504	JAG1_HUMAN	jagged 1	794	EGF-like 15; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				angiogenesis (GO:0001525)|aorta morphogenesis (GO:0035909)|auditory receptor cell differentiation (GO:0042491)|blood vessel remodeling (GO:0001974)|cardiac neural crest cell development involved in outflow tract morphogenesis (GO:0061309)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac septum morphogenesis (GO:0060411)|cell fate determination (GO:0001709)|ciliary body morphogenesis (GO:0061073)|distal tubule development (GO:0072017)|endocardial cushion cell development (GO:0061444)|endothelial cell differentiation (GO:0045446)|hemopoiesis (GO:0030097)|keratinocyte differentiation (GO:0030216)|loop of Henle development (GO:0072070)|morphogenesis of an epithelial sheet (GO:0002011)|myoblast differentiation (GO:0045445)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of stem cell differentiation (GO:2000737)|nervous system development (GO:0007399)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|response to muramyl dipeptide (GO:0032495)|T cell mediated immunity (GO:0002456)	apical part of cell (GO:0045177)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|pancreas(1)|urinary_tract(1)	44						CACAGGTGCCGCTGTTGTAAC	0.522									Alagille Syndrome				G|||	475	0.0948482	0.3396	0.0375	5008	,	,		16433	0.0		0.0	False		,,,				2504	0.0				p.S794S		Atlas-SNP	.											.	JAG1	213	.	0			c.C2382T						PASS	.	G		1227,3179	422.3+/-339.7	166,895,1142	72.0	60.0	64.0		2382	-5.8	0.8	20	dbSNP_129	64	22,8578	15.3+/-51.7	0,22,4278	no	coding-synonymous	JAG1	NM_000214.2		166,917,5420	AA,AG,GG		0.2558,27.8484,9.6033		794/1219	10624502	1249,11757	2203	4300	6503	SO:0001819	synonymous_variant	182	exon20	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	GGTGCCGCTGTTG	U61276	CCDS13112.1	20p12.1-p11.23	2011-05-12	2010-06-24		ENSG00000101384	ENSG00000101384		"""CD molecules"""	6188	protein-coding gene	gene with protein product		601920	"""Alagille syndrome"""	AGS, JAGL1		7697721, 9207788	Standard	NM_000214		Approved	AHD, AWS, HJ1, CD339	uc002wnw.2	P78504	OTTHUMG00000031872	ENST00000254958.5:c.2382C>T	20.37:g.10624502G>A		58.0	0.0	0		58.0	58.0	1	NM_000214	A0AV43|B4DYR1|E9PCF9|O14902|O15122|Q15816	Silent	SNP	ENST00000254958.5	37	CCDS13112.1																																																																																			G|0.914;A|0.086	0.086	strong		0.522	JAG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_000214	
NEFM	4741	hgsc.bcm.edu	37	8	24771318	24771318	+	Silent	SNP	G	G	A	rs61735462	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24771318G>A	ENST00000221166.5	+	1	794	c.12G>A	c.(10-12)acG>acA	p.T4T	RP11-624C23.1_ENST00000519689.1_RNA|NEFM_ENST00000433454.2_5'Flank|NEFM_ENST00000437366.2_Silent_p.T4T|NEFM_ENST00000521540.1_3'UTR|NEFM_ENST00000518131.1_Silent_p.T4T|GS1-72M22.1_ENST00000607058.1_RNA			P07197	NFM_HUMAN	neurofilament, medium polypeptide	4	Head.				axon cargo transport (GO:0008088)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|regulation of axon diameter (GO:0031133)	axon (GO:0030424)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)|neuromuscular junction (GO:0031594)	microtubule binding (GO:0008017)|structural constituent of cytoskeleton (GO:0005200)	p.?(1)		breast(3)|endometrium(7)|kidney(4)|large_intestine(5)|lung(14)|ovary(1)|prostate(1)|urinary_tract(1)	36		Prostate(55;0.157)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0197)|Epithelial(17;2.44e-10)|Colorectal(74;0.0108)|COAD - Colon adenocarcinoma(73;0.0375)		TGAGCTACACGTTGGACTCGC	0.697													g|||	42	0.00838658	0.031	0.0	5008	,	,		13480	0.0		0.001	False		,,,				2504	0.0				p.T4T		Atlas-SNP	.											.	NEFM	115	.	1	Unknown(1)	breast(1)	c.G12A						PASS	.			92,4278		0,92,2093	13.0	16.0	15.0		12	-0.2	0.9	8	dbSNP_129	15	3,8561		0,3,4279	no	coding-synonymous	NEFM	NM_005382.2		0,95,6372	AA,AG,GG		0.035,2.1053,0.7345		4/917	24771318	95,12839	2185	4282	6467	SO:0001819	synonymous_variant	4741	exon1			CTACACGTTGGAC	BC002421	CCDS6046.1, CCDS47831.1	8p21	2013-01-16	2008-09-19	2006-11-20	ENSG00000104722	ENSG00000104722		"""Intermediate filaments type IV"""	7734	protein-coding gene	gene with protein product		162250	"""neurofilament, medium polypeptide 150kDa"""	NEF3		1348579	Standard	NM_001105541		Approved	NFM, NF-M	uc003xed.4	P07197	OTTHUMG00000131990	ENST00000221166.5:c.12G>A	8.37:g.24771318G>A		68.0	0.0	0		81.0	34.0	0.419753	NM_005382	B4DGN2|E9PBF7|Q4QRK6	Silent	SNP	ENST00000221166.5	37	CCDS6046.1																																																																																			G|0.992;A|0.008	0.008	strong		0.697	NEFM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254954.2	NM_005382	
SEC31B	25956	hgsc.bcm.edu	37	10	102262227	102262227	+	Silent	SNP	C	C	G	rs143541316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:102262227C>G	ENST00000370345.3	-	11	1291	c.1194G>C	c.(1192-1194)ctG>ctC	p.L398L	SEC31B_ENST00000451524.1_Silent_p.L398L|SEC31B_ENST00000494350.1_5'Flank	NM_015490.3	NP_056305.1	Q9NQW1	SC31B_HUMAN	SEC31 homolog B (S. cerevisiae)	398					protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|vesicle coat (GO:0030120)				NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(3)|lung(17)|ovary(1)|urinary_tract(1)	36		Colorectal(252;0.117)		Epithelial(162;2.36e-10)|all cancers(201;2.09e-08)		CAAAAGTAACCAGCTTCCCTC	0.483													c|||	34	0.00678914	0.0219	0.0043	5008	,	,		19175	0.0		0.002	False		,,,				2504	0.0				p.L398L		Atlas-SNP	.											.	SEC31B	84	.	0			c.G1194C						PASS	.			126,4280	92.5+/-131.2	3,120,2080	40.0	42.0	41.0		1194	4.5	1.0	10	dbSNP_134	41	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	SEC31B	NM_015490.3		3,126,6374	GG,GC,CC		0.0698,2.8597,1.0149		398/1180	102262227	132,12874	2203	4300	6503	SO:0001819	synonymous_variant	25956	exon11			AGTAACCAGCTTC	AF274863	CCDS7495.1	10q24.32	2013-01-10	2006-10-05	2006-09-07	ENSG00000075826	ENSG00000075826		"""WD repeat domain containing"""	23197	protein-coding gene	gene with protein product		610258	"""SEC31-like 2 (S. cerevisiae)"""	SEC31L2		16495487	Standard	NM_015490		Approved	SEC31B-1, DKFZP434M183	uc001krc.1	Q9NQW1	OTTHUMG00000019342	ENST00000370345.3:c.1194G>C	10.37:g.102262227C>G		42.0	0.0	0		40.0	18.0	0.45	NM_015490	B7ZM75|Q6MZS3|Q86UF0|Q9Y4Q8	Silent	SNP	ENST00000370345.3	37	CCDS7495.1																																																																																			C|0.990;G|0.010	0.010	strong		0.483	SEC31B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051198.1	NM_015490	
PIK3C3	5289	hgsc.bcm.edu	37	18	39576682	39576682	+	Silent	SNP	G	G	A	rs140083392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:39576682G>A	ENST00000262039.4	+	9	1058	c.972G>A	c.(970-972)acG>acA	p.T324T	PIK3C3_ENST00000398870.3_Silent_p.T261T	NM_002647.2	NP_002638.2	Q8NEB9	PK3C3_HUMAN	phosphatidylinositol 3-kinase, catalytic subunit type 3	324	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.				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						ATTATCTTACGAATCAAGAAA	0.279										TSP Lung(28;0.18)			G|||	5	0.000998403	0.0038	0.0	5008	,	,		15613	0.0		0.0	False		,,,				2504	0.0				p.T324T	NSCLC(37;552 1060 2683 16430 37914)	Atlas-SNP	.											PIK3C3,NS,carcinoma,+1,1	PIK3C3	138	1	0			c.G972A						scavenged	.	G		4,4392	8.1+/-20.4	0,4,2194	66.0	70.0	68.0		972	-5.3	1.0	18	dbSNP_134	68	0,8550		0,0,4275	no	coding-synonymous	PIK3C3	NM_002647.2		0,4,6469	AA,AG,GG		0.0,0.091,0.0309		324/888	39576682	4,12942	2198	4275	6473	SO:0001819	synonymous_variant	5289	exon9			TCTTACGAATCAA	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.972G>A	18.37:g.39576682G>A		186.0	1.0	0.00537634		163.0	65.0	0.398773	NM_002647	Q15134	Silent	SNP	ENST00000262039.4	37	CCDS11920.1																																																																																			G|0.999;A|0.001	0.001	strong		0.279	PIK3C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255804.1	NM_002647	
RHPN2	85415	hgsc.bcm.edu	37	19	33486992	33486992	+	Missense_Mutation	SNP	A	A	C	rs75351369	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33486992A>C	ENST00000254260.3	-	11	1395	c.1360T>G	c.(1360-1362)Tac>Gac	p.Y454D	RHPN2_ENST00000400226.4_Missense_Mutation_p.Y303D	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	454	BRO1. {ECO:0000255|PROSITE- ProRule:PRU00526}.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(5)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(3)|urinary_tract(1)	44	Esophageal squamous(110;0.137)					TGCTGGGCGTACGTGAGCCGG	0.627													A|||	129	0.0257588	0.0915	0.0115	5008	,	,		18136	0.0		0.0	False		,,,				2504	0.0				p.Y454D		Atlas-SNP	.											.	RHPN2	107	.	0			c.T1360G						PASS	.	A	ASP/TYR	312,4094	167.6+/-198.6	8,296,1899	82.0	66.0	72.0		1360	3.8	0.8	19	dbSNP_131	72	5,8595	5.0+/-18.6	0,5,4295	no	missense	RHPN2	NM_033103.4	160	8,301,6194	CC,CA,AA		0.0581,7.0813,2.4373	probably-damaging	454/687	33486992	317,12689	2203	4300	6503	SO:0001583	missense	85415	exon11			GGGCGTACGTGAG	AF268032	CCDS12427.1	19q13.12	2008-02-05				ENSG00000131941			19974	protein-coding gene	gene with protein product						12221077	Standard	NM_033103		Approved		uc002nuf.3	Q8IUC4		ENST00000254260.3:c.1360T>G	19.37:g.33486992A>C	ENSP00000254260:p.Tyr454Asp	311.0	0.0	0		290.0	143.0	0.493103	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	50	0.022893772893772892	47	0.09552845528455285	3	0.008287292817679558	0	0.0	0	0.0	A	15.96	2.987827	0.53934	0.070813	5.81E-4	ENSG00000131941	ENST00000254260;ENST00000544458;ENST00000400226	T;T	0.18502	2.21;2.21	4.86	3.82	0.43975	BRO1 domain (3);	0.230044	0.46758	D	0.000279	T	0.01387	0.0045	M	0.89287	3.02	0.41757	D	0.989692	D	0.56968	0.978	D	0.65233	0.933	T	0.00111	-1.2045	10	0.87932	D	0	0.6788	9.3929	0.38383	0.9165:0.0:0.0835:0.0	.	454	Q8IUC4	RHPN2_HUMAN	D	454;184;303	ENSP00000254260:Y454D;ENSP00000402244:Y303D	ENSP00000254260:Y454D	Y	-	1	0	RHPN2	38178832	0.997000	0.39634	0.822000	0.32727	0.459000	0.32528	2.550000	0.45811	0.669000	0.31146	0.477000	0.44152	TAC	A|0.973;C|0.027	0.027	strong		0.627	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103	
UNC45B	146862	hgsc.bcm.edu	37	17	33475426	33475426	+	Silent	SNP	C	C	T	rs16970656	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:33475426C>T	ENST00000268876.5	+	2	241	c.144C>T	c.(142-144)aaC>aaT	p.N48N	UNC45B_ENST00000433649.1_Silent_p.N48N|UNC45B_ENST00000394570.2_Silent_p.N48N|UNC45B_ENST00000591048.1_Silent_p.N48N|UNC45B_ENST00000378449.1_Silent_p.N48N	NM_173167.2	NP_775259.1	Q8IWX7	UN45B_HUMAN	unc-45 homolog B (C. elegans)	48					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(10)|lung(24)|ovary(3)|prostate(2)|skin(1)|stomach(1)|urinary_tract(3)	59		Ovarian(249;0.17)				TTTATCGGAACCGGGCAGCCT	0.637													C|||	90	0.0179712	0.0658	0.0043	5008	,	,		18215	0.0		0.0	False		,,,				2504	0.0				p.N48N		Atlas-SNP	.											.	UNC45B	133	.	0			c.C144T						PASS	.	C	,	259,4147	144.2+/-179.2	2,255,1946	54.0	51.0	52.0		144,144	1.8	1.0	17	dbSNP_123	52	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	UNC45B	NM_001033576.1,NM_173167.2	,	2,257,6244	TT,TC,CC		0.0233,5.8783,2.0068	,	48/930,48/932	33475426	261,12745	2203	4300	6503	SO:0001819	synonymous_variant	146862	exon2			TCGGAACCGGGCA	AW755253	CCDS11292.1, CCDS45648.1	17q12	2008-02-05	2005-11-17	2005-11-17	ENSG00000141161	ENSG00000141161			14304	protein-coding gene	gene with protein product		611220	"""cardiomyopathy associated 4"""	CMYA4		12356907	Standard	NM_001267052		Approved	UNC45	uc002hja.3	Q8IWX7	OTTHUMG00000132931	ENST00000268876.5:c.144C>T	17.37:g.33475426C>T		77.0	0.0	0		86.0	41.0	0.476744	NM_001267052	Q495Q8|Q495Q9	Silent	SNP	ENST00000268876.5	37	CCDS11292.1																																																																																			C|0.975;T|0.025	0.025	strong		0.637	UNC45B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256458.2	NM_173167	
FES	2242	hgsc.bcm.edu	37	15	91434277	91434277	+	Silent	SNP	C	C	T	rs2229074	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:91434277C>T	ENST00000328850.3	+	11	1528	c.1386C>T	c.(1384-1386)caC>caT	p.H462H	FES_ENST00000450438.2_Intron|FES_ENST00000444422.2_Intron|FES_ENST00000394300.3_Silent_p.H404H|FES_ENST00000414248.2_Intron|FES_ENST00000394302.1_Intron	NM_002005.3	NP_001996.1	P07332	FES_HUMAN	FES proto-oncogene, tyrosine kinase	462	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				axon guidance (GO:0007411)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of neuron projection development (GO:0010976)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell adhesion (GO:0030155)|regulation of cell differentiation (GO:0045595)|regulation of cell motility (GO:2000145)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of mast cell degranulation (GO:0043304)|regulation of vesicle-mediated transport (GO:0060627)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule cytoskeleton (GO:0015630)	ATP binding (GO:0005524)|immunoglobulin receptor binding (GO:0034987)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol binding (GO:0035091)|protein tyrosine kinase activity (GO:0004713)			lung(2)|ovary(1)	3	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			TGTGGTACCACGGGGCCATCC	0.647													C|||	297	0.0593051	0.2126	0.0202	5008	,	,		18427	0.0		0.002	False		,,,				2504	0.0				p.H462H		Atlas-SNP	.											.	FES	102	.	0			c.C1386T						PASS	.	C	,,,	799,3595		75,649,1473	58.0	49.0	52.0		1212,,,1386	-8.0	0.8	15	dbSNP_98	52	9,8581		0,9,4286	no	coding-synonymous,intron,intron,coding-synonymous	FES	NM_001143783.1,NM_001143784.1,NM_001143785.1,NM_002005.3	,,,	75,658,5759	TT,TC,CC		0.1048,18.1839,6.223	,,,	404/765,,,462/823	91434277	808,12176	2197	4295	6492	SO:0001819	synonymous_variant	2242	exon11			GTACCACGGGGCC	X52192	CCDS10365.1, CCDS45349.1, CCDS45350.1, CCDS45351.1	15q26.1	2014-06-26	2014-06-26		ENSG00000182511	ENSG00000182511	2.7.10.1	"""SH2 domain containing"""	3657	protein-coding gene	gene with protein product	"""Oncogene FES, feline sarcoma virus"", ""c-fes/fps protein"""	190030	"""feline sarcoma (Snyder-Theilen) viral (v-fes)/Fujinami avian sarcoma (PRCII) viral (v-fps) oncogene homolog"", ""feline sarcoma oncogene"""			1870997	Standard	NM_002005		Approved	FPS	uc002bpv.3	P07332	OTTHUMG00000044456	ENST00000328850.3:c.1386C>T	15.37:g.91434277C>T		75.0	0.0	0		100.0	98.0	0.98	NM_002005	B2R6E6|B4DUD0|E9PC94|E9PC95|Q2VXS7|Q2VXS8|Q2VXT0|Q6GTU5	Silent	SNP	ENST00000328850.3	37	CCDS10365.1																																																																																			C|0.935;T|0.065	0.065	strong		0.647	FES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313497.1	NM_002005	
CPXM2	119587	hgsc.bcm.edu	37	10	125651150	125651150	+	Missense_Mutation	SNP	G	G	A	rs112027854	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:125651150G>A	ENST00000241305.3	-	1	180	c.26C>T	c.(25-27)cCa>cTa	p.P9L	CPXM2_ENST00000368854.3_Intron	NM_198148.2	NP_937791.2	Q8N436	CPXM2_HUMAN	carboxypeptidase X (M14 family), member 2	9					cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(7)|kidney(2)|large_intestine(13)|lung(15)|ovary(2)|prostate(2)|skin(3)	47		all_lung(145;0.174)|Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)|Lung NSC(174;0.233)		COAD - Colon adenocarcinoma(40;0.212)|Colorectal(40;0.237)		GGCCAGCGCTGGGGTAGCGGT	0.751													g|||	131	0.0261581	0.0938	0.0101	5008	,	,		8004	0.0		0.0	False		,,,				2504	0.0				p.P9L		Atlas-SNP	.											CPXM2,rectum,carcinoma,0,1	CPXM2	120	1	0			c.C26T						PASS	.		LEU/PRO	153,2681		2,149,1266	4.0	6.0	5.0		26	-2.5	0.0	10	dbSNP_132	5	3,5397		0,3,2697	no	missense	CPXM2	NM_198148.2	98	2,152,3963	AA,AG,GG		0.0556,5.3987,1.8946	benign	9/757	125651150	156,8078	1417	2700	4117	SO:0001583	missense	119587	exon1			AGCGCTGGGGTAG	AY358565	CCDS7637.1	10q26	2012-02-10			ENSG00000121898	ENSG00000121898			26977	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase"""					12975309	Standard	NM_198148		Approved	UNQ676, CPX2	uc001lhk.1	Q8N436	OTTHUMG00000019206	ENST00000241305.3:c.26C>T	10.37:g.125651150G>A	ENSP00000241305:p.Pro9Leu	12.0	0.0	0		18.0	7.0	0.388889	NM_198148	B4E3Q2	Missense_Mutation	SNP	ENST00000241305.3	37	CCDS7637.1	.	.	.	.	.	.	.	.	.	.	g	12.37	1.916952	0.33815	0.053987	5.56E-4	ENSG00000121898	ENST00000241305;ENST00000418782	D	0.96716	-4.1	3.45	-2.48	0.06423	.	3.521810	0.01155	N	0.006503	T	0.66406	0.2786	N	0.08118	0	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.78841	-0.2045	10	0.30078	T	0.28	0.0228	7.7622	0.28959	0.6768:0.0:0.3232:0.0	.	9	Q8N436	CPXM2_HUMAN	L	9	ENSP00000241305:P9L	ENSP00000241305:P9L	P	-	2	0	CPXM2	125641140	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	-0.090000	0.11163	-0.418000	0.07450	-0.701000	0.03672	CCA	G|0.500;A|0.500	0.500	weak		0.751	CPXM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050853.1	NM_198148	
KRT6C	286887	hgsc.bcm.edu	37	12	52865924	52865924	+	Silent	SNP	G	G	A	rs77218649	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52865924G>A	ENST00000252250.6	-	2	728	c.681C>T	c.(679-681)agC>agT	p.S227S		NM_173086.4	NP_775109.2	P48668	K2C6C_HUMAN	keratin 6C	227	Coil 1B.|Rod.		S -> N (in dbSNP:rs17099602). {ECO:0000269|PubMed:7543104}.		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)		CCCCGACGATGCTGTCCAGCT	0.592													G|||	128	0.0255591	0.0961	0.0014	5008	,	,		17326	0.0		0.0	False		,,,				2504	0.0				p.S227S		Atlas-SNP	.											.	KRT6C	55	.	0			c.C681T						PASS	.	G		354,4050		39,276,1887	135.0	87.0	103.0		681	-2.5	0.0	12	dbSNP_131	103	4,8524		1,2,4261	no	coding-synonymous	KRT6C	NM_173086.4		40,278,6148	AA,AG,GG		0.0469,8.0381,2.7683		227/565	52865924	358,12574	2202	4264	6466	SO:0001819	synonymous_variant	286887	exon2			GACGATGCTGTCC	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.681C>T	12.37:g.52865924G>A		340.0	0.0	0		398.0	189.0	0.474874	NM_173086	A1L4L5|P48666|Q2TAZ9|Q7RTN9	Silent	SNP	ENST00000252250.6	37	CCDS8829.1																																																																																			G|0.976;A|0.024	0.024	strong		0.592	KRT6C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404976.1	NM_173086	
DSP	1832	hgsc.bcm.edu	37	6	7565596	7565596	+	Missense_Mutation	SNP	C	C	T	rs139509870	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:7565596C>T	ENST00000379802.3	+	7	1123	c.782C>T	c.(781-783)gCg>gTg	p.A261V	DSP_ENST00000418664.2_Missense_Mutation_p.A261V	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	261	Globular 1.|Interacts with plakophilin 1 and junction plakoglobin.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		GTGCAGAAAGCGTCCTTTGAG	0.473													C|||	2	0.000399361	0.0	0.0029	5008	,	,		19062	0.0		0.0	False		,,,				2504	0.0				p.A261V		Atlas-SNP	.											.	DSP	306	.	0			c.C782T						PASS	.	C	VAL/ALA,VAL/ALA	5,4401	9.9+/-24.2	0,5,2198	106.0	95.0	98.0		782,782	4.6	0.7	6	dbSNP_134	98	0,8600		0,0,4300	no	missense,missense	DSP	NM_001008844.1,NM_004415.2	64,64	0,5,6498	TT,TC,CC		0.0,0.1135,0.0384	benign,benign	261/2273,261/2872	7565596	5,13001	2203	4300	6503	SO:0001583	missense	1832	exon7			AGAAAGCGTCCTT	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"""desmoplakin (DPI, DPII)"""			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.782C>T	6.37:g.7565596C>T	ENSP00000369129:p.Ala261Val	58.0	0.0	0		50.0	22.0	0.44	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	37	CCDS4501.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	14.58	2.579212	0.46006	0.001135	0.0	ENSG00000096696	ENST00000379802;ENST00000418664;ENST00000397483	D;D	0.92752	-3.1;-3.1	5.42	4.55	0.56014	.	0.366306	0.23134	N	0.051542	T	0.74854	0.3771	L	0.29908	0.895	0.25172	N	0.990271	B;B	0.26483	0.15;0.15	B;B	0.14578	0.006;0.011	T	0.66484	-0.5912	10	0.45353	T	0.12	.	7.1237	0.25458	0.1483:0.7018:0.0:0.1499	.	308;261	Q4LE79;P15924	.;DESP_HUMAN	V	261;261;66	ENSP00000369129:A261V;ENSP00000396591:A261V	ENSP00000369129:A261V	A	+	2	0	DSP	7510595	0.687000	0.27671	0.682000	0.30024	0.913000	0.54294	1.332000	0.33805	1.284000	0.44531	0.563000	0.77884	GCG	C|1.000;T|0.000	0.000	strong		0.473	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
ABCA8	10351	hgsc.bcm.edu	37	17	66928470	66928470	+	Silent	SNP	C	C	T	rs28385895|rs386798698|rs202032826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:66928470C>T	ENST00000269080.2	-	6	893	c.756G>A	c.(754-756)aaG>aaA	p.K252K	ABCA8_ENST00000586539.1_Silent_p.K252K|ABCA8_ENST00000430352.2_Silent_p.K252K	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	252					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					TCATCAAGGCCTTCATCCTTT	0.393													C|||	383	0.0764776	0.2738	0.0231	5008	,	,		20456	0.0		0.005	False		,,,				2504	0.0				p.K252K		Atlas-SNP	.											.	ABCA8	213	.	0			c.G756A						PASS	.																																			SO:0001819	synonymous_variant	10351	exon6			CAAGGCCTTCATC	AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"""ATP binding cassette transporters / subfamily A"""	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.756G>A	17.37:g.66928470C>T		80.0	0.0	0		102.0	48.0	0.470588	NM_007168	A1L3U3|C9JQE6|Q86WW0	Silent	SNP	ENST00000269080.2	37	CCDS11680.1																																																																																			C|0.959;T|0.041	0.041	strong		0.393	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168	
KDM4C	23081	hgsc.bcm.edu	37	9	6986589	6986589	+	Missense_Mutation	SNP	A	A	C	rs111451391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:6986589A>C	ENST00000381309.3	+	11	2165	c.1600A>C	c.(1600-1602)Agc>Cgc	p.S534R	KDM4C_ENST00000543771.1_Missense_Mutation_p.S534R|KDM4C_ENST00000536108.1_Missense_Mutation_p.S353R|KDM4C_ENST00000428870.2_Missense_Mutation_p.S221R|KDM4C_ENST00000535193.1_Missense_Mutation_p.S556R|KDM4C_ENST00000442236.2_Intron|KDM4C_ENST00000381306.3_Missense_Mutation_p.S534R	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	534					histone H3-K9 demethylation (GO:0033169)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	androgen receptor binding (GO:0050681)|dioxygenase activity (GO:0051213)|enzyme binding (GO:0019899)|histone demethylase activity (H3-K9 specific) (GO:0032454)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43						TGATGTGGAGAGCCATGGGAA	0.498													A|||	63	0.0125799	0.0023	0.0865	5008	,	,		19983	0.0		0.0	False		,,,				2504	0.0				p.S556R		Atlas-SNP	.											KDM4C,NS,carcinoma,-2,1	KDM4C	186	1	0			c.A1666C						scavenged	.	A	ARG/SER,ARG/SER,ARG/SER,ARG/SER	5,4401	9.9+/-24.2	0,5,2198	101.0	90.0	94.0		1600,1600,1666,1600	4.2	1.0	9	dbSNP_132	94	1,8599		0,1,4299	yes	missense,missense,missense,missense	KDM4C	NM_001146694.1,NM_001146695.1,NM_001146696.1,NM_015061.3	110,110,110,110	0,6,6497	CC,CA,AA		0.0116,0.1135,0.0461	benign,benign,benign,benign	534/1048,534/814,556/836,534/1057	6986589	6,13000	2203	4300	6503	SO:0001583	missense	23081	exon11			GTGGAGAGCCATG	AB018323	CCDS6471.1, CCDS55285.1, CCDS55286.1, CCDS55287.1	9p24-p23	2013-01-23	2009-04-06	2009-04-06	ENSG00000107077	ENSG00000107077		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	17071	protein-coding gene	gene with protein product	"""tudor domain containing 14C"""	605469	"""jumonji domain containing 2C"""	JMJD2C		9872452, 15138608	Standard	NM_015061		Approved	GASC1, KIAA0780, TDRD14C	uc003zkh.3	Q9H3R0	OTTHUMG00000019536	ENST00000381309.3:c.1600A>C	9.37:g.6986589A>C	ENSP00000370710:p.Ser534Arg	162.0	1.0	0.00617284		174.0	89.0	0.511494	NM_001146696	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	37	CCDS6471.1	31	0.014194139194139194	1	0.0020325203252032522	30	0.08287292817679558	0	0.0	0	0.0	A	13.15	2.149919	0.37923	0.001135	1.16E-4	ENSG00000107077	ENST00000535193;ENST00000543771;ENST00000381309;ENST00000381306;ENST00000536108;ENST00000428870	T;T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6;0.6	5.3	4.17	0.49024	.	2.061340	0.01784	N	0.031882	T	0.04952	0.0133	M	0.66939	2.045	0.29043	N	0.884963	P;P;B;P	0.42203	0.773;0.603;0.112;0.603	B;B;B;B	0.38616	0.277;0.202;0.064;0.246	T	0.14671	-1.0464	10	0.13470	T	0.59	-1.3627	8.4932	0.33112	0.8984:0.0:0.1016:0.0	.	534;556;534;534	F5H347;F5H7P0;Q9H3R0;Q9H3R0-2	.;.;KDM4C_HUMAN;.	R	556;534;534;534;353;221	ENSP00000442382:S556R;ENSP00000445427:S534R;ENSP00000370710:S534R;ENSP00000370707:S534R;ENSP00000440656:S353R;ENSP00000405739:S221R	ENSP00000370707:S534R	S	+	1	0	KDM4C	6976589	1.000000	0.71417	0.979000	0.43373	0.845000	0.48019	4.096000	0.57734	1.040000	0.40099	0.533000	0.62120	AGC	A|0.995;C|0.004;T|0.000	0.004	strong		0.498	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061	
MICALL2	79778	hgsc.bcm.edu	37	7	1481983	1481983	+	Missense_Mutation	SNP	G	G	A	rs4075307	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:1481983G>A	ENST00000297508.7	-	7	1731	c.1556C>T	c.(1555-1557)cCg>cTg	p.P519L	MICALL2_ENST00000405088.4_Missense_Mutation_p.P307L	NM_182924.3	NP_891554.1	Q8IY33	MILK2_HUMAN	MICAL-like 2	519	Mediates targeting to the cell plasma membrane. {ECO:0000250}.		P -> L (in dbSNP:rs4075307).		actin cytoskeleton reorganization (GO:0031532)|actin filament polymerization (GO:0030041)|endocytic recycling (GO:0032456)|neuron projection development (GO:0031175)|substrate adhesion-dependent cell spreading (GO:0034446)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin filament binding (GO:0051015)|filamin binding (GO:0031005)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(8)|ovary(2)|skin(2)	19		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)		CGTGCTCAGCGGGGCTGGCGG	0.647													G|||	174	0.0347444	0.1241	0.013	5008	,	,		14709	0.0		0.001	False		,,,				2504	0.0				p.P519L		Atlas-SNP	.											.	MICALL2	63	.	0			c.C1556T						PASS	.		LEU/PRO	437,3969	208.8+/-229.8	24,389,1790	121.0	118.0	119.0		1556	1.3	0.0	7	dbSNP_108	119	5,8595	3.7+/-12.6	0,5,4295	yes	missense	MICALL2	NM_182924.3	98	24,394,6085	AA,AG,GG		0.0581,9.9183,3.3984	possibly-damaging	519/905	1481983	442,12564	2203	4300	6503	SO:0001583	missense	79778	exon7			CTCAGCGGGGCTG	BC037988	CCDS5324.1	7p22.3	2006-11-24			ENSG00000164877	ENSG00000164877			29672	protein-coding gene	gene with protein product	"""junctional Rab13-binding protein"""					12110185, 16525024	Standard	NM_182924		Approved	MGC46023, FLJ23471, MICAL-L2, JRAB	uc003skj.4	Q8IY33	OTTHUMG00000119021	ENST00000297508.7:c.1556C>T	7.37:g.1481983G>A	ENSP00000297508:p.Pro519Leu	86.0	0.0	0		76.0	76.0	1	NM_182924	D3YTD2|Q7RTP4|Q7Z655|Q8TEQ4|Q9H5F9	Missense_Mutation	SNP	ENST00000297508.7	37	CCDS5324.1	55	0.025183150183150184	50	0.1016260162601626	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	13.70	2.314588	0.40996	0.099183	5.81E-4	ENSG00000164877	ENST00000405088;ENST00000297508	T;T	0.69806	2.37;-0.43	3.76	1.29	0.21616	.	0.235349	0.21901	N	0.067446	T	0.01156	0.0038	L	0.32530	0.975	0.09310	N	0.999999	B;D	0.53312	0.136;0.959	B;B	0.33690	0.006;0.168	T	0.04140	-1.0974	10	0.17832	T	0.49	.	3.0549	0.06181	0.2049:0.2804:0.5147:0.0	rs4075307;rs16870427;rs4075307	519;307	Q8IY33;D3YTD2	MILK2_HUMAN;.	L	307;519	ENSP00000385928:P307L;ENSP00000297508:P519L	ENSP00000297508:P519L	P	-	2	0	MICALL2	1448509	0.001000	0.12720	0.001000	0.08648	0.008000	0.06430	0.665000	0.25083	0.674000	0.31244	0.561000	0.74099	CCG	G|0.965;A|0.035	0.035	strong		0.647	MICALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239223.2	NM_182924	
E4F1	1877	hgsc.bcm.edu	37	16	2273676	2273676	+	Missense_Mutation	SNP	C	C	A	rs200831818	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2273676C>A	ENST00000301727.4	+	1	110	c.62C>A	c.(61-63)gCc>gAc	p.A21D	E4F1_ENST00000565090.1_Missense_Mutation_p.A21D|E4F1_ENST00000564139.1_Missense_Mutation_p.A21D	NM_004424.3	NP_004415.2	Q66K89	E4F1_HUMAN	E4F transcription factor 1	21					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|mitotic cell cycle arrest (GO:0071850)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|regulation of cell cycle process (GO:0010564)|regulation of growth (GO:0040008)|regulation of mitotic cell cycle, embryonic (GO:0009794)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	cAMP response element binding (GO:0035497)|DNA binding (GO:0003677)|ligase activity (GO:0016874)|metal ion binding (GO:0046872)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			ovary(1)	1						CAGGCCGAAGCCGGGCGGGAA	0.711													C|||	11	0.00219649	0.0076	0.0014	5008	,	,		11713	0.0		0.0	False		,,,				2504	0.0				p.A21D		Atlas-SNP	.											.	E4F1	53	.	0			c.C62A						PASS	.	C	ASP/ALA	26,4326		0,26,2150	12.0	16.0	15.0		62	4.7	1.0	16		15	0,8536		0,0,4268	yes	missense	E4F1	NM_004424.3	126	0,26,6418	AA,AC,CC		0.0,0.5974,0.2017	probably-damaging	21/785	2273676	26,12862	2176	4268	6444	SO:0001583	missense	1877	exon1			CCGAAGCCGGGCG	U87269	CCDS32370.1, CCDS73809.1, CCDS73810.1	16p13.3	2013-01-08				ENSG00000167967		"""Zinc fingers, C2H2-type"""	3121	protein-coding gene	gene with protein product		603022				9763670, 8828041	Standard	XM_005255155		Approved	E4F	uc002cpm.3	Q66K89		ENST00000301727.4:c.62C>A	16.37:g.2273676C>A	ENSP00000301727:p.Ala21Asp	8.0	0.0	0		20.0	12.0	0.6	NM_004424	A8K2R4|O00146	Missense_Mutation	SNP	ENST00000301727.4	37	CCDS32370.1	.	.	.	.	.	.	.	.	.	.	C	10.88	1.476414	0.26511	0.005974	0.0	ENSG00000167967	ENST00000301727	T	0.09723	2.95	4.68	4.68	0.58851	.	0.718111	0.13054	N	0.417418	T	0.11537	0.0281	N	0.14661	0.345	0.44523	D	0.997474	D;D;D	0.64830	0.985;0.994;0.985	P;P;P	0.57911	0.767;0.829;0.767	T	0.18241	-1.0343	10	0.59425	D	0.04	-23.6911	16.3289	0.83001	0.0:1.0:0.0:0.0	.	17;21;21	E9PFZ8;E7EMF7;Q66K89	.;.;E4F1_HUMAN	D	21	ENSP00000301727:A21D	ENSP00000301727:A21D	A	+	2	0	E4F1	2213677	1.000000	0.71417	1.000000	0.80357	0.858000	0.48976	1.236000	0.32683	2.425000	0.82216	0.655000	0.94253	GCC	.	.	weak		0.711	E4F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435225.1	NM_004424	
OR8J1	219477	hgsc.bcm.edu	37	11	56128226	56128226	+	Silent	SNP	T	T	C	rs11823483	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:56128226T>C	ENST00000303039.3	+	1	536	c.504T>C	c.(502-504)taT>taC	p.Y168Y		NM_001005205.2	NP_001005205.2	Q8NGP2	OR8J1_HUMAN	olfactory receptor, family 8, subfamily J, member 1	168						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	47	Esophageal squamous(21;0.00448)					CTGTGTCTTATTGCTCTTCTA	0.388													T|||	240	0.0479233	0.1687	0.0231	5008	,	,		18982	0.0		0.001	False		,,,				2504	0.0				p.Y168Y		Atlas-SNP	.											.	OR8J1	87	.	0			c.T504C						PASS	.	T		628,3774	272.5+/-270.8	48,532,1621	120.0	108.0	112.0		504	-2.3	1.0	11	dbSNP_120	112	9,8583	4.3+/-15.6	0,9,4287	no	coding-synonymous	OR8J1	NM_001005205.2		48,541,5908	CC,CT,TT		0.1047,14.2662,4.9023		168/317	56128226	637,12357	2201	4296	6497	SO:0001819	synonymous_variant	219477	exon1			GTCTTATTGCTCT	AB065748	CCDS31529.1	11q11	2012-08-09			ENSG00000172487	ENSG00000172487		"""GPCR / Class A : Olfactory receptors"""	14855	protein-coding gene	gene with protein product							Standard	NM_001005205		Approved		uc010rjh.2	Q8NGP2	OTTHUMG00000166859	ENST00000303039.3:c.504T>C	11.37:g.56128226T>C		146.0	0.0	0		161.0	73.0	0.453416	NM_001005205	B2RNQ6|B9EH63|Q6IFC2|Q96RC3	Silent	SNP	ENST00000303039.3	37	CCDS31529.1																																																																																			T|0.955;C|0.045	0.045	strong		0.388	OR8J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391606.2	NM_001005205	
OR6C68	403284	hgsc.bcm.edu	37	12	55887054	55887054	+	Missense_Mutation	SNP	C	C	G	rs56760228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:55887054C>G	ENST00000548615.1	+	1	893	c.893C>G	c.(892-894)gCc>gGc	p.A298G	RP11-110A12.2_ENST00000554049.1_RNA|RP11-110A12.2_ENST00000555138.1_RNA|RP11-110A12.2_ENST00000556750.1_RNA|OR6C68_ENST00000379662.1_Missense_Mutation_p.A303G	NM_001005519.2	NP_001005519.2	A6NDL8	O6C68_HUMAN	olfactory receptor, family 6, subfamily C, member 68	298						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(2)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	15						GTTAAACAAGCCTTTCATGAC	0.289													C|||	306	0.0611022	0.2163	0.0288	5008	,	,		17663	0.0		0.0	False		,,,				2504	0.0				p.A298G		Atlas-SNP	.											.	OR6C68	36	.	0			c.C893G						PASS	.	G	GLY/ALA	793,3609		73,647,1481	32.0	36.0	35.0		893	3.2	0.2	12	dbSNP_129	35	9,8583		0,9,4287	yes	missense	OR6C68	NM_001005519.2	60	73,656,5768	GG,GC,CC		0.1047,18.0145,6.1721	benign	298/313	55887054	802,12192	2201	4296	6497	SO:0001583	missense	403284	exon1			AACAAGCCTTTCA		CCDS31826.1, CCDS31826.2	12q13.2	2013-09-23			ENSG00000205327	ENSG00000205327		"""GPCR / Class A : Olfactory receptors"""	31297	protein-coding gene	gene with protein product							Standard	NM_001005519		Approved		uc031qhq.1	A6NDL8	OTTHUMG00000169958	ENST00000548615.1:c.893C>G	12.37:g.55887054C>G	ENSP00000448811:p.Ala298Gly	61.0	0.0	0		62.0	23.0	0.370968	NM_001005519		Missense_Mutation	SNP	ENST00000548615.1	37	CCDS31826.2	104	0.047619047619047616	93	0.18902439024390244	11	0.03038674033149171	0	0.0	0	0.0	c	4.988	0.183559	0.09495	0.180145	0.001047	ENSG00000205327	ENST00000379662;ENST00000548615	T;T	0.45276	0.9;0.9	5.03	3.19	0.36642	.	0.288458	0.24461	N	0.038338	T	0.00073	0.0002	M	0.61703	1.905	0.80722	P	0.0	B	0.30914	0.3	B	0.38296	0.27	T	0.09185	-1.0686	9	0.72032	D	0.01	.	7.1754	0.25742	0.1288:0.6768:0.1243:0.0702	rs56760228	298	A6NDL8	O6C68_HUMAN	G	303;298	ENSP00000368983:A303G;ENSP00000448811:A298G	ENSP00000368983:A303G	A	+	2	0	OR6C68	54173321	0.000000	0.05858	0.226000	0.23910	0.035000	0.12851	0.005000	0.13129	0.628000	0.30357	-3.065000	0.00067	GCC	C|0.953;G|0.047	0.047	strong		0.289	OR6C68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406677.1		
CAMK1	8536	hgsc.bcm.edu	37	3	9804658	9804658	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:9804658G>A	ENST00000256460.3	-	5	546	c.369C>T	c.(367-369)ttC>ttT	p.F123F	OGG1_ENST00000302008.8_Intron|OGG1_ENST00000449570.2_Intron|OGG1_ENST00000383826.5_Intron|OGG1_ENST00000302036.7_Intron|OGG1_ENST00000349503.5_Intron	NM_003656.4	NP_003647.1	Q14012	KCC1A_HUMAN	calcium/calmodulin-dependent protein kinase I	123	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|nucleocytoplasmic transport (GO:0006913)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of synapse structural plasticity (GO:0051835)|protein phosphorylation (GO:0006468)|regulation of muscle cell differentiation (GO:0051147)|regulation of protein binding (GO:0043393)|regulation of protein localization (GO:0032880)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)	12	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.0475)		CCAGCACCTGGAAGATGAGGC	0.597																																					p.F123F		Atlas-SNP	.											.	CAMK1	32	.	0			c.C369T						PASS	.						71.0	63.0	66.0					3																	9804658		2203	4300	6503	SO:0001819	synonymous_variant	8536	exon5			CACCTGGAAGATG	L41816	CCDS2582.1	3p25.3	2004-02-27			ENSG00000134072	ENSG00000134072			1459	protein-coding gene	gene with protein product		604998				7641687	Standard	NM_003656		Approved	CaMKI	uc003bst.3	Q14012	OTTHUMG00000128419	ENST00000256460.3:c.369C>T	3.37:g.9804658G>A		127.0	0.0	0		121.0	70.0	0.578512	NM_003656	Q3KPF6	Silent	SNP	ENST00000256460.3	37	CCDS2582.1																																																																																			.	.	none		0.597	CAMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250206.1	NM_003656	
KIAA1107	23285	hgsc.bcm.edu	37	1	92646431	92646431	+	Missense_Mutation	SNP	A	A	G	rs7523466	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:92646431A>G	ENST00000370378.4	+	8	1975	c.1877A>G	c.(1876-1878)gAt>gGt	p.D626G	KIAA1107_ENST00000409154.4_Missense_Mutation_p.D681G	NM_015237.2	NP_056052.2	Q9UPP5	K1107_HUMAN	KIAA1107	681										breast(4)|central_nervous_system(1)|endometrium(3)|kidney(2)|prostate(1)|skin(3)	14						GAAACAGATGATTGCGATGCA	0.318													A|||	20	0.00399361	0.0144	0.0014	5008	,	,		21343	0.0		0.0	False		,,,				2504	0.0				p.D626G		Atlas-SNP	.											.	KIAA1107	60	.	0			c.A1877G						PASS	.	A	GLY/ASP	16,1368		0,16,676	46.0	40.0	42.0		1877	3.3	0.0	1	dbSNP_116	42	0,3182		0,0,1591	yes	missense	KIAA1107	NM_015237.2	94	0,16,2267	GG,GA,AA		0.0,1.1561,0.3504	benign	626/1355	92646431	16,4550	692	1591	2283	SO:0001583	missense	23285	exon8			CAGATGATTGCGA	AB029030	CCDS44172.1	1p22.1	2008-02-05			ENSG00000069712	ENSG00000069712			29192	protein-coding gene	gene with protein product						10470851	Standard	NM_015237		Approved		uc010otd.2	Q9UPP5	OTTHUMG00000010292	ENST00000370378.4:c.1877A>G	1.37:g.92646431A>G	ENSP00000359404:p.Asp626Gly	80.0	0.0	0		86.0	44.0	0.511628	NM_015237	O14767|Q8N3X7	Missense_Mutation	SNP	ENST00000370378.4	37	CCDS44172.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	A	0.013	-1.646340	0.00792	0.011561	0.0	ENSG00000069712	ENST00000409154;ENST00000370378	T;T	0.05382	3.45;3.49	5.62	3.32	0.38043	.	1.054050	0.07354	N	0.882889	T	0.01523	0.0049	N	0.19112	0.55	0.09310	N	1	B	0.12630	0.006	B	0.12837	0.008	T	0.48681	-0.9014	10	0.27785	T	0.31	.	9.7427	0.40429	0.8607:0.0:0.1393:0.0	rs7523466;rs52806057;rs7523466	626	E9PEZ5	.	G	681;626	ENSP00000386957:D681G;ENSP00000359404:D626G	ENSP00000359404:D626G	D	+	2	0	KIAA1107	92419019	0.014000	0.17966	0.001000	0.08648	0.062000	0.15995	1.181000	0.32017	0.436000	0.26393	-0.256000	0.11100	GAT	A|0.994;G|0.006	0.006	strong		0.318	KIAA1107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028375.3	XM_034086	
AHNAK2	113146	hgsc.bcm.edu	37	14	105415899	105415899	+	Silent	SNP	A	A	G	rs11850869	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105415899A>G	ENST00000333244.5	-	7	6008	c.5889T>C	c.(5887-5889)gcT>gcC	p.A1963A	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1963						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CATCCAGCTTAGCCTTCTGGG	0.597													.|||	339	0.0676917	0.2315	0.013	5008	,	,		18512	0.0218		0.001	False		,,,				2504	0.001				p.A1963A		Atlas-SNP	.											.	AHNAK2	719	.	0			c.T5889C						PASS	.	G		716,3310		132,452,1429	142.0	155.0	151.0		5889	-2.9	0.0	14	dbSNP_120	151	7,8261		1,5,4128	no	coding-synonymous	AHNAK2	NM_138420.2		133,457,5557	GG,GA,AA		0.0847,17.7844,5.8809		1963/5796	105415899	723,11571	2013	4134	6147	SO:0001819	synonymous_variant	113146	exon7			CAGCTTAGCCTTC	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.5889T>C	14.37:g.105415899A>G		276.0	0.0	0		296.0	294.0	0.993243	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.965;G|0.035	0.035	strong		0.597	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
GSE1	23199	hgsc.bcm.edu	37	16	85695298	85695298	+	Silent	SNP	C	C	T	rs61737039	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:85695298C>T	ENST00000253458.7	+	9	2363	c.2187C>T	c.(2185-2187)ttC>ttT	p.F729F	GSE1_ENST00000393243.1_Silent_p.F656F|RN7SL381P_ENST00000577658.1_RNA|GSE1_ENST00000405402.2_Silent_p.F625F	NM_014615.2	NP_055430.1	Q14687	GSE1_HUMAN	Gse1 coiled-coil protein	729																	ATGATGAGTTCCTGCAGCAGC	0.716													C|||	66	0.0131789	0.0469	0.0043	5008	,	,		14613	0.0		0.001	False		,,,				2504	0.0				p.F729F		Atlas-SNP	.											.	.	.	.	0			c.C2187T						PASS	.	C	,	139,4221		2,135,2043	11.0	14.0	13.0		1875,2187	-1.5	1.0	16	dbSNP_129	13	3,8533		0,3,4265	no	coding-synonymous,coding-synonymous	KIAA0182	NM_001134473.1,NM_014615.2	,	2,138,6308	TT,TC,CC		0.0351,3.1881,1.1011	,	625/1114,729/1218	85695298	142,12754	2180	4268	6448	SO:0001819	synonymous_variant	23199	exon9			TGAGTTCCTGCAG	D80004	CCDS10952.1, CCDS45539.1, CCDS62007.1	16q24.1	2012-12-07	2012-12-07	2012-10-02	ENSG00000131149	ENSG00000131149			28979	protein-coding gene	gene with protein product	"""genetic suppressor element 1"""		"""KIAA0182"", ""Gse1 coiled-coil protein homolog (mouse)"""	KIAA0182		8724849, 8786132	Standard	NM_014615		Approved		uc002fix.4	Q14687	OTTHUMG00000137650	ENST00000253458.7:c.2187C>T	16.37:g.85695298C>T		125.0	0.0	0		126.0	61.0	0.484127	NM_014615	D3DUM4|Q8IY61|Q96GA4|Q9BW09	Silent	SNP	ENST00000253458.7	37	CCDS10952.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	C	5.452	0.268528	0.10349	0.031881	3.51E-4	ENSG00000131149	ENST00000412692	.	.	.	4.88	-1.45	0.08828	.	.	.	.	.	T	0.17238	0.0414	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.31052	-0.9957	4	.	.	.	-10.3922	10.1383	0.42719	0.0:0.4732:0.0:0.5268	rs61737039	.	.	.	F	536	.	.	S	+	2	0	KIAA0182	84252799	0.988000	0.35896	0.990000	0.47175	0.473000	0.32948	0.303000	0.19210	-0.171000	0.10797	-0.291000	0.09656	TCC	C|0.988;T|0.012	0.012	strong		0.716	GSE1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325527.1	NM_014615	
C2orf16	84226	hgsc.bcm.edu	37	2	27803810	27803810	+	Silent	SNP	C	C	T	rs13408423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27803810C>T	ENST00000408964.2	+	1	4422	c.4371C>T	c.(4369-4371)ccC>ccT	p.P1457P	ZNF512_ENST00000413371.2_5'Flank|ZNF512_ENST00000379717.1_5'Flank|AC074091.1_ENST00000408604.1_RNA|ZNF512_ENST00000416005.2_5'Flank|ZNF512_ENST00000556601.1_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000355467.4_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1457						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					TGCCCAAGCCCACAGATTCCC	0.493													C|||	55	0.0109824	0.0378	0.0043	5008	,	,		18436	0.0		0.002	False		,,,				2504	0.0				p.P1457P		Atlas-SNP	.											.	C2orf16	357	.	0			c.C4371T						PASS	.	C		118,3726		3,112,1807	97.0	100.0	99.0		4371	2.5	0.0	2	dbSNP_121	99	2,8260		0,2,4129	no	coding-synonymous	C2orf16	NM_032266.3		3,114,5936	TT,TC,CC		0.0242,3.0697,0.9912		1457/1985	27803810	120,11986	1922	4131	6053	SO:0001819	synonymous_variant	84226	exon1			CAAGCCCACAGAT	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.4371C>T	2.37:g.27803810C>T		62.0	0.0	0		68.0	42.0	0.617647	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Silent	SNP	ENST00000408964.2	37	CCDS42666.1																																																																																			C|0.986;T|0.014	0.014	strong		0.493	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
PDZD2	23037	hgsc.bcm.edu	37	5	32087828	32087828	+	Missense_Mutation	SNP	C	C	T	rs36097367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:32087828C>T	ENST00000438447.1	+	20	4662	c.4274C>T	c.(4273-4275)aCg>aTg	p.T1425M	PDZD2_ENST00000282493.3_Missense_Mutation_p.T1425M			O15018	PDZD2_HUMAN	PDZ domain containing 2	1425			T -> M (in dbSNP:rs36097367).		cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						AGCCCTGTGACGGACATTGAC	0.607													C|||	183	0.0365415	0.1346	0.0058	5008	,	,		18447	0.0		0.001	False		,,,				2504	0.0				p.T1425M		Atlas-SNP	.											PDZD2,NS,carcinoma,-1,1	PDZD2	306	1	0			c.C4274T						PASS	.	C	MET/THR	527,3879	232.0+/-245.7	27,473,1703	40.0	41.0	41.0		4274	4.7	0.8	5	dbSNP_126	41	5,8595	4.3+/-15.6	0,5,4295	yes	missense	PDZD2	NM_178140.2	81	27,478,5998	TT,TC,CC		0.0581,11.961,4.0904	probably-damaging	1425/2840	32087828	532,12474	2203	4300	6503	SO:0001583	missense	23037	exon19			CTGTGACGGACAT	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"""PDZ domain containing 3"""	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.4274C>T	5.37:g.32087828C>T	ENSP00000402033:p.Thr1425Met	95.0	0.0	0		149.0	89.0	0.597315	NM_178140	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	50	0.022893772893772892	48	0.0975609756097561	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	17.75	3.467294	0.63625	0.11961	5.81E-4	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.09723	2.95;2.95	5.55	4.67	0.58626	.	0.000000	0.45867	D	0.000323	T	0.00384	0.0012	L	0.59436	1.845	0.38283	D	0.942477	D	0.89917	1.0	D	0.71656	0.974	T	0.00203	-1.1924	10	0.87932	D	0	.	13.494	0.61414	0.1575:0.8425:0.0:0.0	rs36097367	1425	O15018	PDZD2_HUMAN	M	1425;1226;1425	ENSP00000402033:T1425M;ENSP00000282493:T1425M	ENSP00000282493:T1425M	T	+	2	0	PDZD2	32123585	0.993000	0.37304	0.800000	0.32199	0.624000	0.37722	3.702000	0.54800	1.331000	0.45412	0.655000	0.94253	ACG	C|0.961;T|0.039	0.039	strong		0.607	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1		
KIAA0319	9856	hgsc.bcm.edu	37	6	24596433	24596433	+	Missense_Mutation	SNP	A	A	C	rs73727343	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:24596433A>C	ENST00000378214.3	-	3	993	c.469T>G	c.(469-471)Tca>Gca	p.S157A	KIAA0319_ENST00000535378.1_Missense_Mutation_p.S148A|KIAA0319_ENST00000430948.2_Missense_Mutation_p.S112A|KIAA0319_ENST00000543707.1_Missense_Mutation_p.S157A|KIAA0319_ENST00000537886.1_Missense_Mutation_p.S157A	NM_001168375.1|NM_014809.3	NP_001161847.1|NP_055624.2	Q5VV43	K0319_HUMAN	KIAA0319	157				S -> A (in Ref. 1; BAA20777 and 5; AAI52461). {ECO:0000305}.	negative regulation of dendrite development (GO:2000171)|neuron migration (GO:0001764)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|endometrium(6)|kidney(3)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	53						TAGTCATCTGAGTACTCAGAC	0.597													A|||	134	0.0267572	0.0961	0.0072	5008	,	,		17776	0.0		0.002	False		,,,				2504	0.0				p.S157A		Atlas-SNP	.											.	KIAA0319	117	.	0			c.T469G						PASS	.	A	ALA/SER,ALA/SER,ALA/SER,ALA/SER,ALA/SER	322,4084	170.5+/-200.9	9,304,1890	75.0	79.0	78.0		442,469,334,469,469	-3.2	0.1	6	dbSNP_130	78	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense,missense,missense	KIAA0319	NM_001168374.1,NM_001168375.1,NM_001168376.1,NM_001168377.1,NM_014809.3	99,99,99,99,99	9,307,6187	CC,CA,AA		0.0349,7.3082,2.4988	benign,benign,benign,benign,benign	148/1064,157/1073,112/1028,157/1012,157/1073	24596433	325,12681	2203	4300	6503	SO:0001583	missense	9856	exon3			CATCTGAGTACTC	AB002317	CCDS34348.1, CCDS54969.1, CCDS54970.1, CCDS54971.1, CCDS75409.1	6p22.3	2013-12-13			ENSG00000137261	ENSG00000137261			21580	protein-coding gene	gene with protein product	"""neuronal migration"""	609269				9205841, 15514892	Standard	NM_014809		Approved	NMIG	uc003neh.1	Q5VV43	OTTHUMG00000014358	ENST00000378214.3:c.469T>G	6.37:g.24596433A>C	ENSP00000367459:p.Ser157Ala	55.0	0.0	0		54.0	25.0	0.462963	NM_001168377	A7MD37|B2RTU7|B4DHA7|B4DK75|B7ZML3|F5H123|Q9UJC8|Q9Y4G7	Missense_Mutation	SNP	ENST00000378214.3	37	CCDS34348.1	65	0.02976190476190476	58	0.11788617886178862	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	A	4.600	0.111504	0.08831	0.073082	3.49E-4	ENSG00000137261	ENST00000537886;ENST00000535378;ENST00000430948;ENST00000378214;ENST00000543707	T;T;T;T;T	0.06371	3.31;3.32;3.32;3.31;3.31	4.43	-3.24	0.05094	.	1.418230	0.04637	N	0.404692	T	0.01156	0.0038	L	0.29908	0.895	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.10450	0.005;0.003;0.001	T	0.48375	-0.9041	10	0.29301	T	0.29	-0.0017	0.6264	0.00786	0.3156:0.2275:0.2714:0.1855	.	157;148;157	F5H123;Q5VV43-2;Q5VV43	.;.;K0319_HUMAN	A	157;148;112;157;157	ENSP00000439700:S157A;ENSP00000442403:S148A;ENSP00000401086:S112A;ENSP00000367459:S157A;ENSP00000437656:S157A	ENSP00000367459:S157A	S	-	1	0	KIAA0319	24704412	0.000000	0.05858	0.057000	0.19452	0.884000	0.51177	-1.251000	0.02882	-0.187000	0.10516	0.421000	0.28195	TCA	A|0.970;C|0.030	0.030	strong		0.597	KIAA0319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040009.1	NM_014809	
AHNAK	79026	hgsc.bcm.edu	37	11	62291912	62291912	+	Missense_Mutation	SNP	C	C	T	rs115362908	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:62291912C>T	ENST00000378024.4	-	5	10251	c.9977G>A	c.(9976-9978)aGt>aAt	p.S3326N	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	3326					protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				TATATCCAAACTGGGAGCTTT	0.413													C|||	16	0.00319489	0.0098	0.0043	5008	,	,		19033	0.0		0.0	False		,,,				2504	0.0				p.S3326N		Atlas-SNP	.											.	AHNAK	532	.	0			c.G9977A						PASS	.	C	ASN/SER,	53,4351	52.3+/-87.9	3,47,2152	58.0	53.0	55.0		9977,	1.6	0.1	11	dbSNP_132	55	1,8597	1.2+/-3.3	0,1,4298	yes	missense,intron	AHNAK	NM_001620.1,NM_024060.2	46,	3,48,6450	TT,TC,CC		0.0116,1.2035,0.4153	benign,	3326/5891,	62291912	54,12948	2202	4299	6501	SO:0001583	missense	79026	exon5			TCCAAACTGGGAG	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.9977G>A	11.37:g.62291912C>T	ENSP00000367263:p.Ser3326Asn	80.0	0.0	0		76.0	45.0	0.592105	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	8	0.003663003663003663	6	0.012195121951219513	2	0.0055248618784530384	0	0.0	0	0.0	C	1.856	-0.463832	0.04476	0.012035	1.16E-4	ENSG00000124942	ENST00000378024	T	0.00672	5.89	4.07	1.61	0.23674	.	.	.	.	.	T	0.00608	0.0020	L	0.28556	0.865	0.09310	N	1	B	0.25719	0.132	B	0.35278	0.199	T	0.48747	-0.9008	9	0.20519	T	0.43	.	6.9065	0.24311	0.0:0.2034:0.0:0.7966	.	3326	Q09666	AHNK_HUMAN	N	3326	ENSP00000367263:S3326N	ENSP00000367263:S3326N	S	-	2	0	AHNAK	62048488	0.000000	0.05858	0.067000	0.19924	0.419000	0.31324	0.794000	0.26958	0.089000	0.17243	0.305000	0.20034	AGT	C|0.996;T|0.004	0.004	strong		0.413	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
NOL10	79954	hgsc.bcm.edu	37	2	10797952	10797952	+	Silent	SNP	G	G	A	rs61737663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:10797952G>A	ENST00000381685.5	-	11	927	c.822C>T	c.(820-822)ccC>ccT	p.P274P	NOL10_ENST00000542668.1_Silent_p.P224P|NOL10_ENST00000345985.3_Intron|NOL10_ENST00000538384.1_Silent_p.P248P	NM_024894.3	NP_079170.2	Q9BSC4	NOL10_HUMAN	nucleolar protein 10	274						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)					Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.207)		CGGACTTAATGGGCAGCCCAT	0.348													G|||	83	0.0165735	0.0582	0.0086	5008	,	,		18192	0.0		0.0	False		,,,				2504	0.0				p.P274P		Atlas-SNP	.											.	NOL10	22	.	0			c.C822T						PASS	.	G		67,1317		0,67,625	131.0	122.0	124.0		822	3.5	1.0	2	dbSNP_129	124	0,3182		0,0,1591	no	coding-synonymous	NOL10	NM_024894.2		0,67,2216	AA,AG,GG		0.0,4.841,1.4674		274/689	10797952	67,4499	692	1591	2283	SO:0001819	synonymous_variant	79954	exon11			CTTAATGGGCAGC	AK024137	CCDS1673.2, CCDS58697.1, CCDS58698.1	2p25.1	2008-05-23			ENSG00000115761	ENSG00000115761			25862	protein-coding gene	gene with protein product			"""polyglutamine binding protein 5"""	PQBP5		12477932	Standard	NM_024894		Approved	FLJ14075	uc002raq.3	Q9BSC4	OTTHUMG00000119023	ENST00000381685.5:c.822C>T	2.37:g.10797952G>A		199.0	0.0	0		192.0	92.0	0.479167	NM_024894	A8K3R5|B4DLV0|Q53RC9|Q96TA5|Q9H7Y7|Q9H855	Silent	SNP	ENST00000381685.5	37	CCDS1673.2																																																																																			G|0.988;A|0.012	0.012	strong		0.348	NOL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239227.1	NM_024894	
DCHS2	54798	hgsc.bcm.edu	37	4	155158104	155158104	+	Missense_Mutation	SNP	G	G	A	rs17031279	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:155158104G>A	ENST00000357232.4	-	25	6334	c.6335C>T	c.(6334-6336)aCg>aTg	p.T2112M		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2112	Cadherin 19. {ECO:0000255|PROSITE- ProRule:PRU00043}.		T -> M (in dbSNP:rs17031279).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		TGTAACAAGCGTGCTTCCAAC	0.383													G|||	106	0.0211661	0.0749	0.0058	5008	,	,		22095	0.0		0.002	False		,,,				2504	0.001				p.T2112M		Atlas-SNP	.											.	DCHS2	594	.	0			c.C6335T						PASS	.	G	MET/THR	258,4148	149.2+/-183.4	6,246,1951	158.0	152.0	154.0		6335	4.1	0.1	4	dbSNP_123	154	5,8595	4.3+/-15.6	0,5,4295	yes	missense	DCHS2	NM_017639.3	81	6,251,6246	AA,AG,GG		0.0581,5.8557,2.0221	probably-damaging	2112/2917	155158104	263,12743	2203	4300	6503	SO:0001583	missense	54798	exon25			ACAAGCGTGCTTC	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.6335C>T	4.37:g.155158104G>A	ENSP00000349768:p.Thr2112Met	162.0	0.0	0		178.0	90.0	0.505618	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	26	0.011904761904761904	26	0.052845528455284556	0	0.0	0	0.0	0	0.0	G	10.93	1.488688	0.26686	0.058557	5.81E-4	ENSG00000197410	ENST00000357232	T	0.52754	0.65	5.82	4.09	0.47781	Cadherin (3);Cadherin-like (1);	0.347781	0.26669	N	0.023120	T	0.14614	0.0353	M	0.76002	2.32	0.30495	N	0.770966	D	0.89917	1.0	D	0.66847	0.947	T	0.47995	-0.9073	10	0.42905	T	0.14	.	4.1039	0.10028	0.147:0.1359:0.5918:0.1253	rs17031279;rs52827899;rs17031279	2112	Q6V1P9	PCD23_HUMAN	M	2112	ENSP00000349768:T2112M	ENSP00000349768:T2112M	T	-	2	0	DCHS2	155377554	0.994000	0.37717	0.138000	0.22173	0.167000	0.22549	2.937000	0.48979	1.459000	0.47892	0.557000	0.71058	ACG	G|0.979;A|0.021	0.021	strong		0.383	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
USP2	9099	hgsc.bcm.edu	37	11	119243612	119243612	+	Silent	SNP	T	T	C	rs4938649	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:119243612T>C	ENST00000260187.2	-	2	873	c.579A>G	c.(577-579)gaA>gaG	p.E193E	USP2_ENST00000455332.2_Intron|RP11-334E6.3_ENST00000530918.2_RNA	NM_004205.4	NP_004196.4	O75604	UBP2_HUMAN	ubiquitin specific peptidase 2	193	Necessary for interaction with MDM4.				cell cycle (GO:0007049)|muscle organ development (GO:0007517)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of skeletal muscle tissue development (GO:0048643)|protein deubiquitination (GO:0016579)|protein stabilization (GO:0050821)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell cortex (GO:0005938)|centrosome (GO:0005813)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cyclin binding (GO:0030332)|cysteine-type endopeptidase activity (GO:0004197)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	24		all_hematologic(192;4.65e-05)|Breast(348;0.0101)|all_neural(223;0.0218)|Medulloblastoma(222;0.0425)|Renal(330;0.157)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.000513)|Colorectal(284;0.0116)|Lung(307;0.0853)|LUSC - Lung squamous cell carcinoma(976;0.0889)		CGACCAGGTATTCAGGGCAGC	0.637													C|||	239	0.0477236	0.1195	0.0274	5008	,	,		17377	0.0407		0.002	False		,,,				2504	0.0194				p.E193E		Atlas-SNP	.											.	USP2	71	.	0			c.A579G						PASS	.	C		503,3895	779.2+/-414.3	28,447,1724	66.0	69.0	68.0		579	1.2	0.9	11	dbSNP_111	68	8,8582	818.2+/-406.9	0,8,4287	no	coding-synonymous	USP2	NM_004205.4		28,455,6011	CC,CT,TT		0.0931,11.437,3.9344		193/606	119243612	511,12477	2199	4295	6494	SO:0001819	synonymous_variant	9099	exon2			CAGGTATTCAGGG	AF079564	CCDS8422.1, CCDS8423.1, CCDS58189.1	11q23.3	2008-02-05	2005-08-08			ENSG00000036672		"""Ubiquitin-specific peptidases"""	12618	protein-coding gene	gene with protein product		604725	"""ubiquitin specific protease 2"""			12838346	Standard	NM_004205		Approved	UBP41	uc001pwm.4	O75604		ENST00000260187.2:c.579A>G	11.37:g.119243612T>C		55.0	0.0	0		46.0	29.0	0.630435	NM_004205	B0YJB8|E9PPM2|Q8IUM2|Q8IW04|Q96MB9|Q9BQ21	Silent	SNP	ENST00000260187.2	37	CCDS8422.1																																																																																			T|0.959;C|0.041	0.041	strong		0.637	USP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388361.2	NM_171997	
CNST	163882	hgsc.bcm.edu	37	1	246755204	246755204	+	Missense_Mutation	SNP	C	C	T	rs116182112	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:246755204C>T	ENST00000366513.4	+	2	609	c.340C>T	c.(340-342)Cca>Tca	p.P114S	CNST_ENST00000366512.3_Missense_Mutation_p.P114S|CNST_ENST00000483271.1_3'UTR	NM_152609.2	NP_689822.2	Q6PJW8	CNST_HUMAN	consortin, connexin sorting protein	114					negative regulation of phosphatase activity (GO:0010923)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)	connexin binding (GO:0071253)|phosphatase binding (GO:0019902)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|prostate(1)|urinary_tract(2)	28						AAAAAGAAGTCCAAGAAGCAA	0.393													C|||	10	0.00199681	0.0076	0.0	5008	,	,		20543	0.0		0.0	False		,,,				2504	0.0				p.P114S		Atlas-SNP	.											.	CNST	73	.	0			c.C340T						PASS	.	C	SER/PRO,SER/PRO	22,4376		0,22,2177	30.0	31.0	31.0		340,340	-12.3	0.0	1	dbSNP_132	31	1,8591		0,1,4295	yes	missense,missense	CNST	NM_001139459.1,NM_152609.2	74,74	0,23,6472	TT,TC,CC		0.0116,0.5002,0.1771	benign,benign	114/617,114/726	246755204	23,12967	2199	4296	6495	SO:0001583	missense	163882	exon2			AGAAGTCCAAGAA	AK056563	CCDS1628.1, CCDS44343.1	1q44	2012-04-17	2009-11-03	2009-11-03	ENSG00000162852	ENSG00000162852		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	26486	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 64"""	613439	"""chromosome 1 open reading frame 71"""	C1orf71		19864490	Standard	NM_152609		Approved	FLJ32001, PPP1R64	uc001ibp.3	Q6PJW8	OTTHUMG00000040090	ENST00000366513.4:c.340C>T	1.37:g.246755204C>T	ENSP00000355470:p.Pro114Ser	54.0	0.0	0		45.0	22.0	0.488889	NM_152609	Q5VSY9|Q5VTM7|Q8IYA9|Q8N3L5|Q8NB09|Q8TEI2|Q96MR5	Missense_Mutation	SNP	ENST00000366513.4	37	CCDS1628.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	0.124	-1.122387	0.01785	0.005002	1.16E-4	ENSG00000162852	ENST00000366513;ENST00000366512;ENST00000366511	T;T;T	0.21734	1.99;1.99;1.99	6.17	-12.3	0.00002	.	1.657020	0.02939	N	0.140268	T	0.08268	0.0206	L	0.39633	1.23	0.09310	N	0.999998	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.14559	-1.0468	10	0.25751	T	0.34	-0.1849	3.0934	0.06301	0.2575:0.3466:0.279:0.1169	.	114;114	Q6PJW8;Q6PJW8-2	CNST_HUMAN;.	S	114	ENSP00000355470:P114S;ENSP00000355469:P114S;ENSP00000355468:P114S	ENSP00000355468:P114S	P	+	1	0	CNST	244821827	0.031000	0.19500	0.002000	0.10522	0.852000	0.48524	-1.106000	0.03319	-4.388000	0.00052	-1.094000	0.02160	CCA	C|0.998;T|0.002	0.002	strong		0.393	CNST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096780.1	NM_152609	
MRPL23	6150	hgsc.bcm.edu	37	11	1972229	1972229	+	Missense_Mutation	SNP	G	G	A	rs377324983		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1972229G>A	ENST00000397298.3	+	2	203	c.118G>A	c.(118-120)Gtg>Atg	p.V40M	MRPL23_ENST00000381514.3_Missense_Mutation_p.V40M|MRPL23_ENST00000397294.3_Missense_Mutation_p.V40M|MRPL23_ENST00000397297.3_Missense_Mutation_p.V40M|MRPL23_ENST00000486931.1_3'UTR|MRPL23_ENST00000381519.1_Missense_Mutation_p.V40M	NM_021134.3	NP_066957.3	Q16540	RM23_HUMAN	mitochondrial ribosomal protein L23	40					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			large_intestine(2)|lung(1)|ovary(1)	4		all_epithelial(84;6.24e-05)|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;0.0026)|Lung(200;0.0171)|LUSC - Lung squamous cell carcinoma(625;0.0842)		CGAGGACACCGTGCAGTTCCG	0.657													G|||	1	0.000199681	0.0	0.0	5008	,	,		15615	0.001		0.0	False		,,,				2504	0.0				p.V40M		Atlas-SNP	.											.	MRPL23	14	.	0			c.G118A						PASS	.						38.0	31.0	33.0					11																	1972229		2198	4297	6495	SO:0001583	missense	6150	exon2			GACACCGTGCAGT	AB051340	CCDS31336.1	11p15.5	2012-09-13			ENSG00000214026	ENSG00000214026		"""Mitochondrial ribosomal proteins / large subunits"""	10322	protein-coding gene	gene with protein product		600789		RPL23L		8541832	Standard	NM_021134		Approved	L23MRP	uc001lux.3	Q16540	OTTHUMG00000012476	ENST00000397298.3:c.118G>A	11.37:g.1972229G>A	ENSP00000380466:p.Val40Met	64.0	0.0	0		70.0	37.0	0.528571	NM_021134	A8MT29|Q96Q71	Missense_Mutation	SNP	ENST00000397298.3	37	CCDS31336.1	.	.	.	.	.	.	.	.	.	.	G	25.7	4.663671	0.88251	.	.	ENSG00000214026	ENST00000397298;ENST00000381519;ENST00000397297;ENST00000381514;ENST00000397294	T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93	4.46	4.46	0.54185	Ribosomal protein L23/L15e (1);Nucleotide-binding, alpha-beta plait (1);	0.159427	0.41097	U	0.000941	T	0.71921	0.3397	M	0.91196	3.185	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.80522	-0.1345	10	0.72032	D	0.01	.	17.4877	0.87693	0.0:0.0:1.0:0.0	.	40	Q16540	RM23_HUMAN	M	40	ENSP00000380466:V40M;ENSP00000370930:V40M;ENSP00000380465:V40M;ENSP00000370925:V40M;ENSP00000380462:V40M	ENSP00000370925:V40M	V	+	1	0	MRPL23	1928805	1.000000	0.71417	0.996000	0.52242	0.876000	0.50452	5.989000	0.70587	2.199000	0.70637	0.491000	0.48974	GTG	.	.	weak		0.657	MRPL23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034765.2	NM_021134	
FCER2	2208	hgsc.bcm.edu	37	19	7754101	7754101	+	Missense_Mutation	SNP	G	G	A	rs34694289	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7754101G>A	ENST00000346664.5	-	11	1156	c.944C>T	c.(943-945)cCc>cTc	p.P315L	FCER2_ENST00000597921.1_Missense_Mutation_p.P315L|FCER2_ENST00000360067.4_Missense_Mutation_p.P314L	NM_001220500.1|NM_002002.4	NP_001207429.1|NP_001993.2	P06734	FCER2_HUMAN	Fc fragment of IgE, low affinity II, receptor for (CD23)	315					Notch signaling pathway (GO:0007219)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	10						AGGGGCAGAGGGGGTGGGCAG	0.637													G|||	51	0.0101837	0.0386	0.0	5008	,	,		14053	0.0		0.0	False		,,,				2504	0.0				p.P315L		Atlas-SNP	.											.	FCER2	19	.	0			c.C944T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO	130,4276	87.3+/-125.9	4,122,2077	33.0	32.0	32.0		941,944,944	-0.9	0.0	19	dbSNP_126	32	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	FCER2	NM_001207019.2,NM_001220500.1,NM_002002.4	98,98,98	4,123,6376	AA,AG,GG		0.0116,2.9505,1.0072	probably-damaging,probably-damaging,probably-damaging	314/321,315/322,315/322	7754101	131,12875	2203	4300	6503	SO:0001583	missense	2208	exon11			GCAGAGGGGGTGG	M15059	CCDS12184.1	19p13.3	2011-08-30	2006-03-09			ENSG00000104921		"""C-type lectin domain containing"", ""CD molecules"""	3612	protein-coding gene	gene with protein product		151445	"""Fc fragment of IgE, low affinity II, receptor for (CD23A)"""	CD23A, FCE2			Standard	NM_002002		Approved	CLEC4J, CD23	uc002mhm.2	P06734		ENST00000346664.5:c.944C>T	19.37:g.7754101G>A	ENSP00000264072:p.Pro315Leu	156.0	0.0	0		235.0	138.0	0.587234	NM_002002		Missense_Mutation	SNP	ENST00000346664.5	37	CCDS12184.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	G	12.45	1.942513	0.34283	0.029505	1.16E-4	ENSG00000104921	ENST00000346664;ENST00000360067	T;T	0.04156	3.69;3.71	2.72	-0.925	0.10458	.	.	.	.	.	T	0.00815	0.0027	N	0.08118	0	0.09310	N	1	B	0.14012	0.009	B	0.12156	0.007	T	0.44544	-0.9321	9	0.87932	D	0	.	4.2641	0.10754	0.1588:0.4449:0.3963:0.0	rs34694289	315	P06734	FCER2_HUMAN	L	315;314	ENSP00000264072:P315L;ENSP00000353178:P314L	ENSP00000264072:P315L	P	-	2	0	FCER2	7660101	0.000000	0.05858	0.000000	0.03702	0.306000	0.27790	-0.171000	0.09883	0.008000	0.14787	0.298000	0.19748	CCC	G|0.990;A|0.010	0.010	strong		0.637	FCER2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461832.1	NM_002002	
PCSK7	9159	hgsc.bcm.edu	37	11	117089801	117089801	+	Missense_Mutation	SNP	T	T	C	rs61729982	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117089801T>C	ENST00000320934.3	-	11	2033	c.1403A>G	c.(1402-1404)aAc>aGc	p.N468S	PCSK7_ENST00000540028.1_Missense_Mutation_p.N109S	NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	468	Peptidase S8.				peptide hormone processing (GO:0016486)|protein processing (GO:0016485)	integral component of Golgi membrane (GO:0030173)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	16	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)		CCTCCAGGCGTTGAGGAGGCC	0.607			T	IGH@	MLCLS								T|||	20	0.00399361	0.0151	0.0	5008	,	,		21331	0.0		0.0	False		,,,				2504	0.0				p.N468S		Atlas-SNP	.		Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	.	PCSK7	59	.	0			c.A1403G						PASS	.	T	SER/ASN	48,4354	49.6+/-84.7	0,48,2153	67.0	53.0	57.0		1403	5.2	0.9	11	dbSNP_129	57	0,8592		0,0,4296	yes	missense	PCSK7	NM_004716.2	46	0,48,6449	CC,CT,TT		0.0,1.0904,0.3694	benign	468/786	117089801	48,12946	2201	4296	6497	SO:0001583	missense	9159	exon11			CAGGCGTTGAGGA	U40623	CCDS8382.1	11q23-q24	2008-02-01			ENSG00000160613	ENSG00000160613			8748	protein-coding gene	gene with protein product		604872				8615762, 9820811	Standard	XM_006718938		Approved	PC7, PC8, LPC, SPC7	uc001pqr.3	Q16549	OTTHUMG00000165640	ENST00000320934.3:c.1403A>G	11.37:g.117089801T>C	ENSP00000325917:p.Asn468Ser	44.0	0.0	0		41.0	29.0	0.707317	NM_004716	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Missense_Mutation	SNP	ENST00000320934.3	37	CCDS8382.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	T	13.08	2.129420	0.37630	0.010904	0.0	ENSG00000160613	ENST00000320934;ENST00000540028;ENST00000543900	D;D	0.83163	-1.69;-1.69	5.2	5.2	0.72013	Peptidase S8/S53, subtilisin/kexin/sedolisin (2);	0.050433	0.85682	D	0.000000	T	0.65688	0.2715	L	0.43923	1.385	0.52501	D	0.999951	B	0.18013	0.025	B	0.17722	0.019	T	0.71583	-0.4549	10	0.59425	D	0.04	-22.611	13.9011	0.63804	0.0:0.0:0.0:1.0	.	468	Q16549	PCSK7_HUMAN	S	468;109;468	ENSP00000325917:N468S;ENSP00000441944:N109S	ENSP00000325917:N468S	N	-	2	0	PCSK7	116595011	0.999000	0.42202	0.924000	0.36721	0.523000	0.34469	3.028000	0.49705	1.977000	0.57605	0.482000	0.46254	AAC	T|0.996;C|0.004	0.004	strong		0.607	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716	
CMTR2	55783	hgsc.bcm.edu	37	16	71317567	71317567	+	Missense_Mutation	SNP	A	A	G	rs16970857	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:71317567A>G	ENST00000338099.5	-	3	2593	c.2257T>C	c.(2257-2259)Ttc>Ctc	p.F753L	CMTR2_ENST00000434935.2_Missense_Mutation_p.F753L			Q8IYT2	CMTR2_HUMAN	cap methyltransferase 2	753			F -> L (in dbSNP:rs16970857).		7-methylguanosine mRNA capping (GO:0006370)|cap2 mRNA methylation (GO:0097310)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)										TGAATAATGAAATGCAAATGC	0.368													A|||	159	0.0317492	0.1165	0.0072	5008	,	,		19301	0.0		0.0	False		,,,				2504	0.0				p.F753L		Atlas-SNP	.											.	FTSJD1	70	.	0			c.T2257C						PASS	.	A	LEU/PHE,LEU/PHE	481,3915	216.8+/-235.3	32,417,1749	41.0	44.0	43.0		2257,2257	3.6	1.0	16	dbSNP_123	43	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense	FTSJD1	NM_001099642.1,NM_018348.5	22,22	32,420,6046	GG,GA,AA		0.0349,10.9418,3.7242	benign,benign	753/771,753/771	71317567	484,12512	2198	4300	6498	SO:0001583	missense	55783	exon3			TAATGAAATGCAA	BC035005	CCDS10898.1	16q22.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000180917	ENSG00000180917			25635	protein-coding gene	gene with protein product	"""adrift homolog (Drosophila)"""		"""FtsJ methyltransferase domain containing 1"""	FTSJD1		21310715	Standard	NM_018348		Approved	FLJ11171, AFT, MTr2	uc010cga.3	Q8IYT2	OTTHUMG00000137587	ENST00000338099.5:c.2257T>C	16.37:g.71317567A>G	ENSP00000337512:p.Phe753Leu	178.0	0.0	0		180.0	88.0	0.488889	NM_018348	B2RCD5|D3DWS1|Q8NE77|Q8NFR5|Q9H8Z4|Q9NUS3|Q9NXF5	Missense_Mutation	SNP	ENST00000338099.5	37	CCDS10898.1	44	0.020146520146520148	42	0.08536585365853659	2	0.0055248618784530384	0	0.0	0	0.0	A	4.716	0.133141	0.09032	0.109418	3.49E-4	ENSG00000180917	ENST00000338099;ENST00000434935	T;T	0.09445	2.98;2.98	5.8	3.58	0.41010	.	0.463445	0.21366	N	0.075705	T	0.00073	0.0002	N	0.01168	-0.975	0.21499	N	0.99967	B	0.02656	0.0	B	0.01281	0.0	T	0.45600	-0.9250	10	0.02654	T	1	-21.5732	6.5334	0.22339	0.7212:0.147:0.1318:0.0	rs16970857;rs52837568;rs16970857	753	Q8IYT2	FTSJ1_HUMAN	L	753	ENSP00000337512:F753L;ENSP00000411148:F753L	ENSP00000337512:F753L	F	-	1	0	FTSJD1	69875068	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	0.876000	0.28092	1.020000	0.39573	0.477000	0.44152	TTC	A|0.964;G|0.036	0.036	strong		0.368	CMTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268984.2	NM_018348	
KIF20A	10112	hgsc.bcm.edu	37	5	137520025	137520025	+	Missense_Mutation	SNP	G	G	A	rs142495138	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:137520025G>A	ENST00000394894.3	+	12	1676	c.1450G>A	c.(1450-1452)Gtg>Atg	p.V484M	KIF20A_ENST00000508792.1_Missense_Mutation_p.V466M	NM_005733.2	NP_005724.1	O95235	KI20A_HUMAN	kinesin family member 20A	484	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cytokinesis (GO:0000910)|metabolic process (GO:0008152)|microtubule bundle formation (GO:0001578)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)|transporter activity (GO:0005215)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(3)|liver(2)|lung(9)|prostate(2)|upper_aerodigestive_tract(1)	27			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0109)			GATTGTCAATGTGAATCCCTG	0.512																																					p.V484M		Atlas-SNP	.											.	KIF20A	53	.	0			c.G1450A						PASS	.	G	MET/VAL	4,4402	8.1+/-20.4	0,4,2199	170.0	163.0	165.0		1450	3.7	1.0	5	dbSNP_134	165	0,8600		0,0,4300	no	missense	KIF20A	NM_005733.2	21	0,4,6499	AA,AG,GG		0.0,0.0908,0.0308	probably-damaging	484/891	137520025	4,13002	2203	4300	6503	SO:0001583	missense	10112	exon12			GTCAATGTGAATC	AF070672	CCDS4199.1	5q31	2008-02-05	2003-01-13	2003-01-17	ENSG00000112984	ENSG00000112984		"""Kinesins"""	9787	protein-coding gene	gene with protein product		605664	"""RAB6 interacting, kinesin-like (rabkinesin6)"""	RAB6KIFL		11416179, 10806357	Standard	NM_005733		Approved		uc003lcj.3	O95235	OTTHUMG00000129195	ENST00000394894.3:c.1450G>A	5.37:g.137520025G>A	ENSP00000378356:p.Val484Met	217.0	0.0	0		208.0	107.0	0.514423	NM_005733	B4DL79|D3DQB6	Missense_Mutation	SNP	ENST00000394894.3	37	CCDS4199.1	.	.	.	.	.	.	.	.	.	.	G	12.38	1.921838	0.33908	9.08E-4	0.0	ENSG00000112984	ENST00000394894;ENST00000508792	T;T	0.55930	0.49;0.49	5.49	3.72	0.42706	Kinesin, motor domain (3);	0.175916	0.27164	N	0.020639	T	0.46268	0.1384	L	0.50919	1.6	0.40300	D	0.978593	B;B	0.25272	0.122;0.036	B;B	0.32149	0.141;0.051	T	0.47341	-0.9125	10	0.72032	D	0.01	-5.3957	6.3677	0.21463	0.3825:0.0:0.6175:0.0	.	466;484	B4DL79;O95235	.;KI20A_HUMAN	M	484;466	ENSP00000378356:V484M;ENSP00000420880:V466M	ENSP00000378356:V484M	V	+	1	0	KIF20A	137547924	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	3.399000	0.52586	0.874000	0.35823	0.643000	0.83706	GTG	G|1.000;A|0.000	0.000	strong		0.512	KIF20A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251272.1	NM_005733	
OR8U1	219417	hgsc.bcm.edu	37	11	56143952	56143952	+	Silent	SNP	T	T	C	rs78408319	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:56143952T>C	ENST00000302270.1	+	1	853	c.853T>C	c.(853-855)Ttg>Ctg	p.L285L		NM_001005204.1	NP_001005204.1	Q8NH10	OR8U1_HUMAN	olfactory receptor, family 8, subfamily U, member 1	285						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(23)|ovary(4)|skin(1)|stomach(1)	39	Esophageal squamous(21;0.00448)					CATTCCCATGTTGAATCCCTT	0.388													T|||	237	0.0473243	0.1664	0.0231	5008	,	,		18826	0.0		0.001	False		,,,				2504	0.0				p.L285L		Atlas-SNP	.											.	OR8U1	59	.	0			c.T853C						PASS	.	T		535,3441		39,457,1492	139.0	144.0	142.0		853	-11.4	0.2	11	dbSNP_132	142	8,8396		0,8,4194	no	coding-synonymous	OR8U1	NM_001005204.1		39,465,5686	CC,CT,TT		0.0952,13.4557,4.3861		285/310	56143952	543,11837	1988	4202	6190	SO:0001819	synonymous_variant	219417	exon1			CCCATGTTGAATC	AB065603	CCDS41647.1	11q11	2012-08-09			ENSG00000172199	ENSG00000172199		"""GPCR / Class A : Olfactory receptors"""	19611	protein-coding gene	gene with protein product							Standard	NM_001005204		Approved			Q8NH10	OTTHUMG00000166860	ENST00000302270.1:c.853T>C	11.37:g.56143952T>C		114.0	0.0	0		125.0	60.0	0.48	NM_001005204		Silent	SNP	ENST00000302270.1	37	CCDS41647.1																																																																																			T|0.973;C|0.027	0.027	strong		0.388	OR8U1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391607.1	NM_001005204	
OR7C1	26664	hgsc.bcm.edu	37	19	14910900	14910900	+	Missense_Mutation	SNP	A	A	T	rs149561973	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14910900A>T	ENST00000248073.2	-	1	123	c.49T>A	c.(49-51)Ttt>Att	p.F17I	OR7A5_ENST00000601611.1_Intron	NM_198944.1	NP_945182.1	O76099	OR7C1_HUMAN	olfactory receptor, family 7, subfamily C, member 1	17					spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(2)|ovary(2)|prostate(1)	18						GTTGCTGAAAATCCCAGGAGG	0.438													.|||	27	0.00539137	0.0204	0.0	5008	,	,		18932	0.0		0.0	False		,,,				2504	0.0				p.F17I		Atlas-SNP	.											.	OR7C1	58	.	0			c.T49A						PASS	.	A	ILE/PHE	29,4371		0,29,2171	94.0	90.0	91.0		49	2.6	0.9	19	dbSNP_134	91	0,8592		0,0,4296	yes	missense	OR7C1	NM_198944.1	21	0,29,6467	TT,TA,AA		0.0,0.6591,0.2232	possibly-damaging	17/321	14910900	29,12963	2200	4296	6496	SO:0001583	missense	26664	exon1			CTGAAAATCCCAG	X89676	CCDS12317.1	19p13.1	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	8373	protein-coding gene	gene with protein product				OR7C4			Standard	NM_198944		Approved	OR19-5	uc010xnz.2	O76099		ENST00000248073.2:c.49T>A	19.37:g.14910900A>T	ENSP00000248073:p.Phe17Ile	68.0	0.0	0		61.0	31.0	0.508197	NM_198944	Q15621|Q6IFP2|Q96R94	Missense_Mutation	SNP	ENST00000248073.2	37	CCDS12317.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	a	13.45	2.240147	0.39598	0.006591	0.0	ENSG00000127530	ENST00000248073	T	0.06608	3.28	3.67	2.6	0.31112	.	0.214512	0.23239	U	0.050361	T	0.01870	0.0059	L	0.50919	1.6	0.24836	N	0.992496	P	0.41748	0.761	B	0.37267	0.245	T	0.28170	-1.0052	10	0.54805	T	0.06	.	7.5523	0.27804	0.8084:0.0:0.0:0.1915	.	17	O76099	OR7C1_HUMAN	I	17	ENSP00000248073:F17I	ENSP00000248073:F17I	F	-	1	0	OR7C1	14771900	0.001000	0.12720	0.913000	0.36048	0.090000	0.18270	-0.216000	0.09266	0.552000	0.29026	0.433000	0.28618	TTT	A|0.994;T|0.006	0.006	strong		0.438	OR7C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466519.1		
ZMYM6	9204	hgsc.bcm.edu	37	1	35454115	35454115	+	Silent	SNP	A	A	G	rs61745582	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:35454115A>G	ENST00000357182.4	-	16	2795	c.2568T>C	c.(2566-2568)taT>taC	p.Y856Y	ZMYM6_ENST00000493328.1_5'UTR|ZMYM6_ENST00000487874.1_Intron|ZMYM6_ENST00000373340.2_Intron	NM_007167.3	NP_009098.3	O95789	ZMYM6_HUMAN	zinc finger, MYM-type 6	856					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(10)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	44		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.13)				tttctactaaatatggtttaa	0.338													A|||	214	0.0427316	0.1513	0.0187	5008	,	,		17989	0.0		0.001	False		,,,				2504	0.0				p.Y856Y		Atlas-SNP	.											.	ZMYM6	110	.	0			c.T2568C						PASS	.	A		249,2077		15,219,929	17.0	16.0	16.0		2568	2.4	1.0	1	dbSNP_129	16	5,5061		0,5,2528	no	coding-synonymous	ZMYM6	NM_007167.3		15,224,3457	GG,GA,AA		0.0987,10.7051,3.4361		856/1326	35454115	254,7138	1163	2533	3696	SO:0001819	synonymous_variant	9204	exon16			TACTAAATATGGT	AF055470	CCDS387.2	1p34.2	2014-05-12	2005-09-12	2005-09-12	ENSG00000163867	ENSG00000163867		"""Zinc fingers, MYM type"", ""Zinc fingers, BED-type"""	13050	protein-coding gene	gene with protein product	"""zinc finger, BED-type containing 7"""	613567	"""zinc finger protein 258"", ""zinc finger, MYM-type containing 6"""	ZNF258		10486218, 23533661	Standard	NM_007167		Approved	ZNF198L4, MYM, Buster2, ZBED7	uc001byh.3	O95789	OTTHUMG00000004163	ENST00000357182.4:c.2568T>C	1.37:g.35454115A>G		245.0	0.0	0		229.0	112.0	0.489083	NM_007167	B4DRJ6|Q32Q23|Q4G108|Q5SVZ9|Q5SW00|Q69YL4|Q96IY0|Q9NWF1|Q9P2J4	Silent	SNP	ENST00000357182.4	37	CCDS387.2																																																																																			A|0.962;G|0.038	0.038	strong		0.338	ZMYM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011999.1	NM_007167	
CCDC107	203260	hgsc.bcm.edu	37	9	35661057	35661057	+	Missense_Mutation	SNP	C	C	G	rs10441685	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35661057C>G	ENST00000426546.2	+	5	791	c.725C>G	c.(724-726)tCc>tGc	p.S242C	CCDC107_ENST00000378407.3_3'UTR|CCDC107_ENST00000378409.3_Missense_Mutation_p.S215C|ARHGEF39_ENST00000343259.3_3'UTR|ARHGEF39_ENST00000378395.2_3'UTR|CCDC107_ENST00000378406.1_3'UTR|ARHGEF39_ENST00000490970.1_5'Flank|ARHGEF39_ENST00000378387.3_3'UTR|CCDC107_ENST00000421582.2_3'UTR|CCDC107_ENST00000327351.2_3'UTR	NM_001195200.1|NM_001195201.1|NM_001195217.1|NM_174923.2	NP_001182129.1|NP_001182130.1|NP_001182146.1|NP_777583.2	Q8WV48	CC107_HUMAN	coiled-coil domain containing 107	242			S -> C (in dbSNP:rs10441685).			integral component of membrane (GO:0016021)				endometrium(1)|lung(3)|skin(1)	5	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CTAGCTACTTCCTGGGAGGTG	0.597													C|||	358	0.0714856	0.1982	0.0216	5008	,	,		19531	0.0139		0.0338	False		,,,				2504	0.0337				p.S242C		Atlas-SNP	.											.	CCDC107	12	.	0			c.C725G						PASS	.	C	CYS/SER,,,,CYS/SER	698,3708	290.4+/-280.9	47,604,1552	72.0	71.0	71.0		644,,,,725	4.4	0.0	9	dbSNP_119	71	229,8371	93.1+/-155.1	2,225,4073	no	missense,utr-3,utr-3,utr-3,missense	C9orf100,CCDC107	NM_001195200.1,NM_001195201.1,NM_001195217.1,NM_032818.2,NM_174923.2	112,,,,112	49,829,5625	GG,GC,CC		2.6628,15.842,7.1275	possibly-damaging,,,,possibly-damaging	215/257,,,,242/284	35661057	927,12079	2203	4300	6503	SO:0001583	missense	203260	exon5			CTACTTCCTGGGA	AK075523	CCDS6583.1, CCDS56573.1, CCDS56574.1, CCDS56575.1	9q13.3	2008-02-05			ENSG00000159884	ENSG00000159884			28465	protein-coding gene	gene with protein product						12477932	Standard	NM_174923		Approved	MGC31967	uc011lox.2	Q8WV48	OTTHUMG00000019868	ENST00000426546.2:c.725C>G	9.37:g.35661057C>G	ENSP00000414964:p.Ser242Cys	119.0	0.0	0		116.0	52.0	0.448276	NM_174923	A6XND6|Q5T4R5|Q5T4R8|Q5T4R9|Q86VB6|Q8N2E4	Missense_Mutation	SNP	ENST00000426546.2	37	CCDS6583.1	145	0.06639194139194139	99	0.20121951219512196	10	0.027624309392265192	9	0.015734265734265736	27	0.03562005277044855	C	10.84	1.464832	0.26335	0.15842	0.026628	ENSG00000159884	ENST00000426546;ENST00000378409	T;T	0.39592	1.48;1.07	5.34	4.44	0.53790	.	0.688813	0.13667	N	0.371165	T	0.00039	0.0001	L	0.34521	1.04	0.40203	P	0.022464999999999957	D;D	0.61697	0.99;0.99	P;P	0.53549	0.729;0.729	T	0.06058	-1.0848	9	0.48119	T	0.1	-0.1448	9.9115	0.41408	0.0:0.9082:0.0:0.0918	rs10441685	215;242	F8W8S5;Q8WV48	.;CC107_HUMAN	C	242;215	ENSP00000414964:S242C;ENSP00000367665:S215C	ENSP00000367665:S215C	S	+	2	0	CCDC107	35651057	0.014000	0.17966	0.007000	0.13788	0.048000	0.14542	1.958000	0.40402	1.487000	0.48415	0.655000	0.94253	TCC	C|0.929;G|0.071	0.071	strong		0.597	CCDC107-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052325.1	NM_174923	
SQSTM1	8878	hgsc.bcm.edu	37	5	179260661	179260661	+	Silent	SNP	G	G	A	rs10058037	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:179260661G>A	ENST00000389805.4	+	7	1222	c.1044G>A	c.(1042-1044)ccG>ccA	p.P348P	SQSTM1_ENST00000510187.1_Intron|SQSTM1_ENST00000376929.3_Silent_p.P264P|SQSTM1_ENST00000402874.3_Silent_p.P264P|SQSTM1_ENST00000360718.5_Silent_p.P264P	NM_003900.4	NP_003891.1	Q13501	SQSTM_HUMAN	sequestosome 1	348	Interaction with NTRK1. {ECO:0000250}.				apoptotic signaling pathway (GO:0097190)|autophagy (GO:0006914)|cell differentiation (GO:0030154)|endosomal transport (GO:0016197)|immune system process (GO:0002376)|intracellular signal transduction (GO:0035556)|macroautophagy (GO:0016236)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of macroautophagy (GO:0016239)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein heterooligomerization (GO:0051291)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of Ras protein signal transduction (GO:0046578)|response to stress (GO:0006950)|ubiquitin-dependent protein catabolic process (GO:0006511)	aggresome (GO:0016235)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|lysosome (GO:0005764)|nucleoplasm (GO:0005654)|PML body (GO:0016605)|pre-autophagosomal structure (GO:0000407)	identical protein binding (GO:0042802)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|receptor tyrosine kinase binding (GO:0030971)|SH2 domain binding (GO:0042169)|ubiquitin binding (GO:0043130)|zinc ion binding (GO:0008270)		SQSTM1/ALK(2)	NS(1)|breast(1)|endometrium(1)|large_intestine(2)|liver(2)|lung(5)|ovary(1)	13	all_cancers(89;0.000205)|all_epithelial(37;7.15e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0395)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AAGTGGACCCGTCTACAGGTG	0.542													G|||	165	0.0329473	0.118	0.0086	5008	,	,		19610	0.001		0.001	False		,,,				2504	0.001				p.P348P		Atlas-SNP	.											SQSTM1,NS,carcinoma,+1,1	SQSTM1	30	1	0			c.G1044A						PASS	.	G	,,	415,3991	205.8+/-227.6	17,381,1805	93.0	87.0	89.0		792,792,1044	-10.5	0.0	5	dbSNP_119	89	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	SQSTM1	NM_001142298.1,NM_001142299.1,NM_003900.4	,,	17,383,6103	AA,AG,GG		0.0233,9.419,3.2062	,,	264/357,264/357,348/441	179260661	417,12589	2203	4300	6503	SO:0001819	synonymous_variant	8878	exon7			GGACCCGTCTACA	U46751	CCDS34317.1, CCDS47355.1	5q35	2008-02-05	2004-04-15		ENSG00000161011	ENSG00000161011			11280	protein-coding gene	gene with protein product		601530	"""Paget disease of bone 3"", ""oxidative stress induced like"""	PDB3, OSIL		8650207, 8551575	Standard	NM_003900		Approved	p62, p60, p62B, A170	uc003mkw.4	Q13501	OTTHUMG00000150643	ENST00000389805.4:c.1044G>A	5.37:g.179260661G>A		82.0	0.0	0		82.0	36.0	0.439024	NM_003900	A6NFN7|B2R661|B3KUW5|Q13446|Q9BUV7|Q9BVS6|Q9UEU1	Silent	SNP	ENST00000389805.4	37	CCDS34317.1																																																																																			G|0.960;A|0.040	0.040	strong		0.542	SQSTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319344.1		
TLN1	7094	hgsc.bcm.edu	37	9	35714269	35714269	+	Silent	SNP	G	G	A	rs35844106	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35714269G>A	ENST00000314888.9	-	24	3440	c.3087C>T	c.(3085-3087)acC>acT	p.T1029T	TLN1_ENST00000540444.1_Silent_p.T1029T	NM_006289.3	NP_006280.3	Q9Y490	TLN1_HUMAN	talin 1	1029					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-cell junction assembly (GO:0007043)|cell-substrate junction assembly (GO:0007044)|cellular component movement (GO:0006928)|cellular protein metabolic process (GO:0044267)|cortical actin cytoskeleton organization (GO:0030866)|cytoskeletal anchoring at plasma membrane (GO:0007016)|endoplasmic reticulum unfolded protein response (GO:0030968)|muscle contraction (GO:0006936)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|microtubule organizing center (GO:0005815)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	integrin binding (GO:0005178)|LIM domain binding (GO:0030274)|structural constituent of cytoskeleton (GO:0005200)|vinculin binding (GO:0017166)			NS(2)|breast(8)|central_nervous_system(2)|endometrium(10)|kidney(5)|large_intestine(9)|lung(32)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(6)	85	all_epithelial(49;0.167)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CAGCCAGCGCGGTGCCCAGGT	0.582													G|||	22	0.00439297	0.0166	0.0	5008	,	,		21795	0.0		0.0	False		,,,				2504	0.0				p.T1029T		Atlas-SNP	.											.	TLN1	185	.	0			c.C3087T						PASS	.	G		63,4343	58.1+/-94.6	0,63,2140	58.0	55.0	56.0		3087	-11.8	0.0	9	dbSNP_126	56	0,8600		0,0,4300	yes	coding-synonymous	TLN1	NM_006289.3		0,63,6440	AA,AG,GG		0.0,1.4299,0.4844		1029/2542	35714269	63,12943	2203	4300	6503	SO:0001819	synonymous_variant	7094	exon24			CAGCGCGGTGCCC	AB028950	CCDS35009.1	9p23-p21	2008-02-05			ENSG00000137076	ENSG00000137076			11845	protein-coding gene	gene with protein product		186745		TLN		7635475, 10610730	Standard	NM_006289		Approved	ILWEQ	uc003zxt.2	Q9Y490	OTTHUMG00000019874	ENST00000314888.9:c.3087C>T	9.37:g.35714269G>A		98.0	0.0	0		87.0	45.0	0.517241	NM_006289	A6NMY0|Q86YD0|Q9NZQ2|Q9UHH8|Q9UPX3	Silent	SNP	ENST00000314888.9	37	CCDS35009.1																																																																																			G|0.995;A|0.005	0.005	strong		0.582	TLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052353.2	NM_006289	
ARID4B	51742	hgsc.bcm.edu	37	1	235357460	235357460	+	Silent	SNP	A	A	G	rs62000435	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:235357460A>G	ENST00000264183.3	-	19	2490	c.1993T>C	c.(1993-1995)Ttg>Ctg	p.L665L	ARID4B_ENST00000349213.3_Silent_p.L579L|ARID4B_ENST00000366603.2_Silent_p.L665L	NM_016374.5	NP_057458.4	Q4LE39	ARI4B_HUMAN	AT rich interactive domain 4B (RBP1-like)	665					histone H3-K9 trimethylation (GO:0036124)|histone H4-K20 trimethylation (GO:0034773)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|large_intestine(2)|lung(1)|ovary(2)	8	Ovarian(103;0.0473)|Breast(184;0.23)	all_cancers(173;0.000782)|Prostate(94;0.0132)|all_epithelial(177;0.0808)|Lung SC(1967;0.24)	OV - Ovarian serous cystadenocarcinoma(106;2.86e-05)			GGTTTGGACAAGCGCCGAAGT	0.343													A|||	25	0.00499201	0.0174	0.0029	5008	,	,		16650	0.0		0.0	False		,,,				2504	0.0				p.L665L		Atlas-SNP	.											.	ARID4B	142	.	0			c.T1993C						PASS	.	A	,,	112,4294	82.4+/-120.9	1,110,2092	144.0	135.0	138.0		1993,1993,1735	3.9	1.0	1	dbSNP_129	138	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	ARID4B	NM_001206794.1,NM_016374.5,NM_031371.3	,,	1,112,6390	GG,GA,AA		0.0233,2.542,0.8765	,,	665/1313,665/1313,579/1227	235357460	114,12892	2203	4300	6503	SO:0001819	synonymous_variant	51742	exon19			TGGACAAGCGCCG	AF214114	CCDS31060.1, CCDS31061.1	1q42.1-q43	2013-02-07	2006-11-08	2004-01-30	ENSG00000054267	ENSG00000054267		"""-"""	15550	protein-coding gene	gene with protein product		609696	"""retinoblastoma binding protein 1-like 1"", ""AT rich interactive domain 4B (RBP1- like)"""	RBP1L1		11481388	Standard	NM_016374		Approved	BCAA, BRCAA1, SAP180	uc001hwq.3	Q4LE39	OTTHUMG00000039621	ENST00000264183.3:c.1993T>C	1.37:g.235357460A>G		181.0	0.0	0		191.0	100.0	0.52356	NM_016374	A1L465|Q3MHV4|Q5HY99|Q5T2C2|Q5T2C3|Q5T2C4|Q5T2C5|Q5T2C6|Q6P600|Q86UX1|Q86WR4|Q9H915|Q9NYU3|Q9NZB6|Q9NZG4|Q9P2W4|Q9UF62|Q9Y6E1	Silent	SNP	ENST00000264183.3	37	CCDS31061.1																																																																																			A|0.992;G|0.008	0.008	strong		0.343	ARID4B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095566.3	NM_016374	
ATP6V0A4	50617	hgsc.bcm.edu	37	7	138417642	138417642	+	Missense_Mutation	SNP	C	C	T	rs73730479	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:138417642C>T	ENST00000310018.2	-	17	2170	c.1888G>A	c.(1888-1890)Gca>Aca	p.A630T	ATP6V0A4_ENST00000393054.1_Missense_Mutation_p.A630T|ATP6V0A4_ENST00000353492.4_Missense_Mutation_p.A630T	NM_020632.2|NM_130840.2	NP_065683.2|NP_570855.2	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a4	630					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|regulation of pH (GO:0006885)|sensory perception of sound (GO:0007605)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)			NS(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						TAGAGGGGTGCGTTGGAAGAG	0.373													C|||	210	0.0419329	0.121	0.0245	5008	,	,		16608	0.0268		0.002	False		,,,				2504	0.0041				p.A630T		Atlas-SNP	.											.	ATP6V0A4	93	.	0			c.G1888A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	470,3936	220.0+/-237.6	22,426,1755	99.0	96.0	97.0		1888,1888,1888	1.5	0.0	7	dbSNP_130	97	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense,missense	ATP6V0A4	NM_020632.2,NM_130840.2,NM_130841.2	58,58,58	22,432,6049	TT,TC,CC		0.0698,10.6673,3.6598	benign,benign,benign	630/841,630/841,630/841	138417642	476,12530	2203	4300	6503	SO:0001583	missense	50617	exon16			GGGGTGCGTTGGA	AF245517	CCDS5849.1	7q34	2011-06-09	2006-01-20	2002-05-10	ENSG00000105929	ENSG00000105929		"""ATPases / V-type"""	866	protein-coding gene	gene with protein product		605239	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1B"", ""ATPase, H+ transporting, lysosomal V0 subunit a isoform 4"", ""ATPase, H+ transporting, lysosomal V0 subunit A4"""	ATP6N1B, ATP6N2, RTA1C		10577919, 10973252	Standard	XM_005250393		Approved	RDRTA2, VPP2, RTADR, a4, Vph1, Stv1	uc003vuf.3	Q9HBG4	OTTHUMG00000157122	ENST00000310018.2:c.1888G>A	7.37:g.138417642C>T	ENSP00000308122:p.Ala630Thr	108.0	0.0	0		90.0	38.0	0.422222	NM_130841	A4D1R4|A8KA80|Q32M47	Missense_Mutation	SNP	ENST00000310018.2	37	CCDS5849.1	92	0.04212454212454213	61	0.12398373983739837	9	0.024861878453038673	20	0.03496503496503497	2	0.002638522427440633	C	9.110	1.006311	0.19199	0.106673	6.98E-4	ENSG00000105929	ENST00000310018;ENST00000393054;ENST00000353492	D;D;D	0.85702	-2.02;-2.02;-2.02	5.88	1.49	0.22878	.	0.899723	0.09437	N	0.802370	T	0.02807	0.0084	L	0.37750	1.13	0.09310	N	1	P	0.47350	0.894	B	0.34452	0.183	T	0.01639	-1.1306	10	0.17369	T	0.5	-0.0025	8.1138	0.30930	0.0:0.5837:0.215:0.2013	.	630	Q9HBG4	VPP4_HUMAN	T	630	ENSP00000308122:A630T;ENSP00000376774:A630T;ENSP00000253856:A630T	ENSP00000308122:A630T	A	-	1	0	ATP6V0A4	138068182	0.000000	0.05858	0.001000	0.08648	0.020000	0.10135	0.199000	0.17237	0.383000	0.24910	0.655000	0.94253	GCA	C|0.963;T|0.037	0.037	strong		0.373	ATP6V0A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347514.1	NM_020632	
MDN1	23195	hgsc.bcm.edu	37	6	90424458	90424458	+	Silent	SNP	C	C	T	rs114422841	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:90424458C>T	ENST00000369393.3	-	46	6988	c.6873G>A	c.(6871-6873)tcG>tcA	p.S2291S	MDN1_ENST00000428876.1_Silent_p.S2291S			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	2291					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		CAGGATCCATCGAGAGGAAAA	0.433													C|||	13	0.00259585	0.0083	0.0	5008	,	,		20221	0.0		0.001	False		,,,				2504	0.001				p.S2291S		Atlas-SNP	.											.	MDN1	478	.	0			c.G6873A						PASS	.	C		54,4352	52.3+/-87.9	0,54,2149	67.0	64.0	65.0		6873	-4.0	1.0	6	dbSNP_132	65	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	MDN1	NM_014611.1		0,56,6447	TT,TC,CC		0.0233,1.2256,0.4306		2291/5597	90424458	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	23195	exon46			ATCCATCGAGAGG	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.6873G>A	6.37:g.90424458C>T		71.0	0.0	0		64.0	35.0	0.546875	NM_014611	O15019|Q5T794	Silent	SNP	ENST00000369393.3	37	CCDS5024.1																																																																																			C|0.996;T|0.004	0.004	strong		0.433	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
FCRL5	83416	hgsc.bcm.edu	37	1	157514685	157514685	+	Silent	SNP	G	G	A	rs11803066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:157514685G>A	ENST00000361835.3	-	4	652	c.495C>T	c.(493-495)cgC>cgT	p.R165R	FCRL5_ENST00000368190.3_Silent_p.R165R|FCRL5_ENST00000368189.3_Silent_p.R165R|FCRL5_ENST00000368191.3_Silent_p.R80R|FCRL5_ENST00000356953.4_Silent_p.R165R	NM_001195388.1|NM_031281.2	NP_001182317.1|NP_112571.2	Q96RD9	FCRL5_HUMAN	Fc receptor-like 5	165					negative regulation of B cell receptor signaling pathway (GO:0050859)|negative regulation of release of sequestered calcium ion into cytosol (GO:0051280)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)				breast(5)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(45)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	85	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.231)				ATCCAGTACAGCGATATGCAC	0.368													G|||	72	0.014377	0.053	0.0029	5008	,	,		21706	0.0		0.0	False		,,,				2504	0.0				p.R165R		Atlas-SNP	.											.	FCRL5	177	.	0			c.C495T						PASS	.	G	,	233,4173	138.8+/-174.5	5,223,1975	153.0	142.0	146.0		495,495	-3.5	0.0	1	dbSNP_120	146	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	FCRL5	NM_001195388.1,NM_031281.2	,	5,223,6275	AA,AG,GG		0.0,5.2882,1.7915	,	165/999,165/978	157514685	233,12773	2203	4300	6503	SO:0001819	synonymous_variant	83416	exon4			AGTACAGCGATAT	AF369794	CCDS1165.1	1q21	2013-01-11			ENSG00000143297	ENSG00000143297		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18508	protein-coding gene	gene with protein product		605877				11027651, 11290337	Standard	NM_031281		Approved	FCRH5, IRTA2, BXMAS1, CD307e	uc009wsm.3	Q96RD9	OTTHUMG00000017481	ENST00000361835.3:c.495C>T	1.37:g.157514685G>A		155.0	0.0	0		190.0	103.0	0.542105	NM_031281	A0N0M2|B7WNT9|B7WP94|Q495Q2|Q495Q4|Q5VYK9|Q6UY46	Silent	SNP	ENST00000361835.3	37	CCDS1165.1																																																																																			G|0.982;A|0.018	0.018	strong		0.368	FCRL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046263.1	NM_031281	
AFF2	2334	hgsc.bcm.edu	37	X	148035200	148035200	+	Silent	SNP	G	G	A	rs12011040	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:148035200G>A	ENST00000370460.2	+	10	1967	c.1488G>A	c.(1486-1488)tcG>tcA	p.S496S	AFF2_ENST00000342251.3_Silent_p.S463S|AFF2_ENST00000286437.5_Silent_p.S137S|AFF2_ENST00000370457.5_Silent_p.S463S	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	496					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)			breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					GCTCTGAGTCGGATTCAGACA	0.587													A|||	536	0.141987	0.3381	0.0476	3775	,	,		11768	0.003		0.0388	False		,,,				2504	0.0143				p.S496S		Atlas-SNP	.											.	AFF2	679	.	0			c.G1488A						PASS	.	A	,,,,,	1531,2304		268,774,221,590,350	126.0	118.0	121.0		1389,1458,1383,1371,411,1488	-10.0	0.0	X	dbSNP_120	121	287,6441		3,196,85,2229,1787	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	AFF2	NM_001169122.1,NM_001169123.1,NM_001169124.1,NM_001169125.1,NM_001170628.1,NM_002025.3	,,,,,	271,970,306,2819,2137	AA,AG,A,GG,G		4.2658,39.9218,17.211	,,,,,	463/1277,486/1302,461/1277,457/1273,137/953,496/1312	148035200	1818,8745	2203	4300	6503	SO:0001819	synonymous_variant	2334	exon10			TGAGTCGGATTCA	U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"""fragile X mental retardation 2"""	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.1488G>A	X.37:g.148035200G>A		352.0	0.0	0		415.0	140.0	0.337349	NM_002025	A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Silent	SNP	ENST00000370460.2	37	CCDS14684.1																																																																																			0|0.003;A|0.180	0.180	strong		0.587	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025	
NCOR2	9612	hgsc.bcm.edu	37	12	124821705	124821705	+	Silent	SNP	G	G	A	rs3741512	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124821705G>A	ENST00000405201.1	-	38	5709	c.5709C>T	c.(5707-5709)ccC>ccT	p.P1903P	NCOR2_ENST00000397355.1_Silent_p.P1894P|NCOR2_ENST00000404621.1_Silent_p.P1893P|NCOR2_ENST00000429285.2_Silent_p.P1893P|NCOR2_ENST00000356219.3_Silent_p.P1910P|NCOR2_ENST00000404121.2_Silent_p.P1464P			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1914					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|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)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		CCGGGCGAACGGGTGAGGAGG	0.667													g|||	120	0.0239617	0.0862	0.0086	5008	,	,		14245	0.0		0.0	False		,,,				2504	0.0				p.P1903P		Atlas-SNP	.											.	NCOR2	475	.	0			c.C5709T						PASS	.		,,	227,3647		6,215,1716	12.0	17.0	15.0		5679,5679,5709	-6.6	0.7	12	dbSNP_107	15	2,7984		0,2,3991	no	coding-synonymous,coding-synonymous,coding-synonymous	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	,,	6,217,5707	AA,AG,GG		0.025,5.8596,1.9309	,,	1893/2459,1893/2505,1903/2515	124821705	229,11631	1937	3993	5930	SO:0001819	synonymous_variant	9612	exon40			GCGAACGGGTGAG	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"""nuclear receptor co-repressor 2"""			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.5709C>T	12.37:g.124821705G>A		252.0	0.0	0		269.0	131.0	0.486989	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Silent	SNP	ENST00000405201.1	37	CCDS41858.2	70	0.03205128205128205	67	0.13617886178861788	3	0.008287292817679558	0	0.0	0	0.0	g	6.208	0.406498	0.11754	0.058596	2.5E-4	ENSG00000196498	ENST00000440187	.	.	.	4.36	-6.64	0.01801	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.99999815647	.	.	.	.	.	.	T	0.31613	-0.9937	3	.	.	.	-11.6142	1.0444	0.01566	0.3119:0.1788:0.3193:0.1901	rs3741512	.	.	.	C	138	.	.	R	-	1	0	NCOR2	123387658	0.000000	0.05858	0.747000	0.31113	0.653000	0.38743	-2.100000	0.01345	-0.547000	0.06207	-2.034000	0.00421	CGT	G|0.966;A|0.034	0.034	strong		0.667	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
SLC22A25	387601	hgsc.bcm.edu	37	11	62931547	62931547	+	Splice_Site	SNP	T	T	C	rs114205803	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:62931547T>C	ENST00000306494.6	-	9	1394		c.e9-2		SLC22A10_ENST00000525620.1_Intron|SLC22A10_ENST00000535888.1_Intron	NM_199352.3	NP_955384.3			solute carrier family 22, member 25											NS(2)|breast(2)|endometrium(4)|kidney(2)|large_intestine(7)|lung(7)|ovary(3)|skin(7)	34						GCTCTTCCCCTTGGAGTAAAA	0.403													T|||	18	0.00359425	0.0136	0.0	5008	,	,		20838	0.0		0.0	False		,,,				2504	0.0				.		Atlas-SNP	.											.	SLC22A25	87	.	0			c.1395-2A>G						PASS	.	T		48,4354	35.2+/-66.4	1,46,2154	102.0	113.0	110.0			3.9	0.7	11	dbSNP_132	110	0,8596		0,0,4298	yes	splice-3	SLC22A25	NM_199352.3		1,46,6452	CC,CT,TT		0.0,1.0904,0.3693			62931547	48,12950	2201	4298	6499	SO:0001630	splice_region_variant	387601	exon10			TTCCCCTTGGAGT	AY437532	CCDS31592.1	11q12.3	2014-05-20			ENSG00000196600	ENSG00000196600		"""Solute carriers"""	32935	protein-coding gene	gene with protein product		610792	"""MGI:2442751, MGI:2385316, MGI:3042283, MGI:3645714, MGI:3605624, MGI:2442750"""			17714910	Standard	NM_199352		Approved	UST6, HIMTP, MGC120420	uc001nwr.1	Q6T423	OTTHUMG00000165340	ENST00000306494.6:c.1395-2A>G	11.37:g.62931547T>C		230.0	0.0	0		230.0	91.0	0.395652	NM_199352		Splice_Site	SNP	ENST00000306494.6	37	CCDS31592.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	T	10.76	1.441510	0.25900	0.010904	0.0	ENSG00000196600	ENST00000306494	.	.	.	3.88	3.88	0.44766	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.2959	0.37815	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	SLC22A25	62688123	0.077000	0.21312	0.693000	0.30195	0.010000	0.07245	1.743000	0.38258	1.768000	0.52137	0.477000	0.44152	.	T|0.996;C|0.004	0.004	strong		0.403	SLC22A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383519.3	NM_199352	Intron
GRM3	2913	hgsc.bcm.edu	37	7	86479694	86479694	+	Silent	SNP	G	G	A	rs76035289	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:86479694G>A	ENST00000361669.2	+	5	3499	c.2400G>A	c.(2398-2400)acG>acA	p.T800T	GRM3_ENST00000439827.1_Missense_Mutation_p.D445N|GRM3_ENST00000394720.2_Missense_Mutation_p.D443N|GRM3_ENST00000536043.1_Silent_p.T672T|GRM3_ENST00000546348.1_Silent_p.T392T	NM_000840.2	NP_000831.2	Q14832	GRM3_HUMAN	glutamate receptor, metabotropic 3	800					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of adenylate cyclase activity (GO:0007194)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|axon (GO:0030424)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	calcium channel regulator activity (GO:0005246)|G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group II metabotropic glutamate receptor activity (GO:0001641)			NS(2)|breast(6)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(43)|ovary(3)|pancreas(2)|prostate(4)|skin(25)|upper_aerodigestive_tract(5)	109	Esophageal squamous(14;0.0058)|all_lung(186;0.132)|Lung NSC(181;0.142)					AGGTGCAGACGACAACCATGT	0.458													G|||	68	0.0135783	0.0469	0.0058	5008	,	,		21770	0.001		0.001	False		,,,				2504	0.0				p.T800T	GBM(52;969 1098 3139 52280)	Atlas-SNP	.											.	GRM3	237	.	0			c.G2400A						PASS	.	G		178,4228	115.0+/-153.0	2,174,2027	218.0	151.0	173.0		2400	-11.9	0.1	7	dbSNP_131	173	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	GRM3	NM_000840.2		2,181,6320	AA,AG,GG		0.0814,4.0399,1.4224		800/880	86479694	185,12821	2203	4300	6503	SO:0001819	synonymous_variant	2913	exon5			GCAGACGACAACC		CCDS5600.1	7q21.1-q21.2	2012-08-29			ENSG00000198822	ENSG00000198822		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4595	protein-coding gene	gene with protein product		601115				8824806	Standard	NM_000840		Approved	GPRC1C, mGlu3, MGLUR3	uc003uid.3	Q14832	OTTHUMG00000022884	ENST00000361669.2:c.2400G>A	7.37:g.86479694G>A		162.0	0.0	0		156.0	82.0	0.525641	NM_000840	Q2PNZ6|Q75MV4|Q75N17|Q86YG6|Q8TBH9	Silent	SNP	ENST00000361669.2	37	CCDS5600.1	30	0.013736263736263736	29	0.05894308943089431	0	0.0	0	0.0	1	0.0013192612137203166	G	9.085	1.000326	0.19121	0.040399	8.14E-4	ENSG00000198822	ENST00000439827;ENST00000394720	D;D	0.85773	-2.03;-2.03	5.97	-11.9	0.00025	.	.	.	.	.	T	0.21841	0.0526	.	.	.	0.09310	N	0.999991	B	0.02656	0.0	B	0.01281	0.0	T	0.49799	-0.8901	8	0.66056	D	0.02	.	2.9374	0.05819	0.4424:0.2623:0.1692:0.1262	.	445	G5E9K2	.	N	445;443	ENSP00000398767:D445N;ENSP00000378209:D443N	ENSP00000378209:D443N	D	+	1	0	GRM3	86317630	0.000000	0.05858	0.132000	0.22025	0.766000	0.43426	-1.862000	0.01653	-2.006000	0.00958	-1.779000	0.00650	GAC	G|0.985;A|0.015	0.015	strong		0.458	GRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253362.2		
CD1E	913	hgsc.bcm.edu	37	1	158325765	158325765	+	Silent	SNP	C	C	T	rs61734677	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158325765C>T	ENST00000368167.3	+	4	1013	c.774C>T	c.(772-774)gaC>gaT	p.D258D	CD1E_ENST00000368160.3_Silent_p.D258D|CD1E_ENST00000368157.1_Intron|CD1E_ENST00000452291.2_Silent_p.D69D|CD1E_ENST00000368165.3_Silent_p.D168D|CD1E_ENST00000368164.3_Silent_p.D69D|CD1E_ENST00000368163.3_Intron|CD1E_ENST00000368156.1_Silent_p.D168D|CD1E_ENST00000368166.3_Silent_p.D69D|CD1E_ENST00000368155.3_Intron|CD1E_ENST00000368154.1_Intron|CD1E_ENST00000444681.2_Silent_p.D159D|CD1E_ENST00000434258.1_Silent_p.D256D|CD1E_ENST00000368161.3_Silent_p.D258D	NM_030893.3	NP_112155.2	P15812	CD1E_HUMAN	CD1e molecule	258	Ig-like.				antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(27)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|urinary_tract(1)	49	all_hematologic(112;0.0378)					AGCGAGGGGACGTCCTGCCTA	0.617													C|||	198	0.0395367	0.1483	0.0029	5008	,	,		15430	0.0		0.0	False		,,,				2504	0.0				p.D258D		Atlas-SNP	.											.	CD1E	129	.	0			c.C774T						PASS	.	C	,,,,,,,,,,,,	609,3797	265.9+/-266.9	48,513,1642	115.0	111.0	112.0		774,774,,207,207,504,,,207,,477,504,774	-5.1	0.0	1	dbSNP_129	112	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous,intron,intron,coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous	CD1E	NM_001042583.2,NM_001042584.2,NM_001042585.2,NM_001042586.2,NM_001042587.2,NM_001185107.1,NM_001185108.1,NM_001185110.1,NM_001185112.1,NM_001185113.1,NM_001185114.1,NM_001185115.1,NM_030893.3	,,,,,,,,,,,,	48,519,5936	TT,TC,CC		0.0698,13.8221,4.7286	,,,,,,,,,,,,	258/377,258/291,,69/188,69/102,168/299,,,69/200,,159/290,168/287,258/389	158325765	615,12391	2203	4300	6503	SO:0001819	synonymous_variant	913	exon4			AGGGGACGTCCTG	AJ289111	CCDS41417.1, CCDS41418.1, CCDS41419.1, CCDS41420.1, CCDS41421.1, CCDS41422.1, CCDS53387.1, CCDS53388.1, CCDS53389.1, CCDS53390.1, CCDS53384.1, CCDS53385.1, CCDS53386.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158488	ENSG00000158488		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1638	protein-coding gene	gene with protein product		188411	"""CD1E antigen, e polypeptide"", ""CD1e antigen"""			10948205	Standard	NM_001042585		Approved		uc001fse.3	P15812	OTTHUMG00000017515	ENST00000368167.3:c.774C>T	1.37:g.158325765C>T		296.0	0.0	0		313.0	162.0	0.517572	NM_001042584	B4DZV3|E7EP01|Q5TDJ9|Q5TDK3|Q5TDK4|Q5TDK5|Q5TDK6|Q5TDK8|Q5TDL1|Q712E4|Q712E5|Q712E6|Q712E7|Q712E8|Q712E9|Q712F0|Q712F1|Q712F2|Q712F3|Q712F4|Q712F5|Q96TD0|Q96TD1|Q9UMM1|Q9Y5M3	Silent	SNP	ENST00000368167.3	37	CCDS41417.1	66	0.03021978021978022	65	0.13211382113821138	1	0.0027624309392265192	0	0.0	0	0.0	C	0.065	-1.215843	0.01542	0.138221	6.98E-4	ENSG00000158488	ENST00000368162	.	.	.	4.6	-5.12	0.02893	.	.	.	.	.	T	0.10551	0.0258	.	.	.	0.20074	N	0.999933	.	.	.	.	.	.	T	0.29701	-1.0003	4	.	.	.	-27.8278	6.6347	0.22877	0.1308:0.2718:0.0:0.5974	rs61734677	.	.	.	C	28	.	.	R	+	1	0	CD1E	156592389	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-4.235000	0.00269	-1.234000	0.02548	-1.008000	0.02478	CGT	C|0.978;T|0.022	0.022	strong		0.617	CD1E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046353.3	NM_030893	
BCL2A1	597	hgsc.bcm.edu	37	15	80263111	80263111	+	Missense_Mutation	SNP	C	C	A	rs34080999	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:80263111C>A	ENST00000267953.3	-	1	677	c.351G>T	c.(349-351)gaG>gaT	p.E117D	BCL2A1_ENST00000335661.6_Missense_Mutation_p.E117D	NM_004049.3	NP_004040.1	Q16548	B2LA1_HUMAN	BCL2-related protein A1	117			E -> D (in dbSNP:rs34080999).		extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)	mitochondrial outer membrane (GO:0005741)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(2)|large_intestine(4)|lung(3)|pancreas(1)|upper_aerodigestive_tract(1)	12						AATATGAAATCTCCTTATAGG	0.383													C|||	191	0.038139	0.1384	0.0086	5008	,	,		17180	0.0		0.002	False		,,,				2504	0.0				p.E117D		Atlas-SNP	.											.	BCL2A1	28	.	0			c.G351T						PASS	.	C	ASP/GLU,ASP/GLU	472,3934	219.1+/-236.9	26,420,1757	118.0	125.0	123.0		351,351	-5.0	0.0	15	dbSNP_126	123	7,8593	6.4+/-24.3	0,7,4293	yes	missense,missense	BCL2A1	NM_001114735.1,NM_004049.3	45,45	26,427,6050	AA,AC,CC		0.0814,10.7127,3.6829	benign,benign	117/164,117/176	80263111	479,12527	2203	4300	6503	SO:0001583	missense	597	exon1			TGAAATCTCCTTA		CCDS10312.1, CCDS45322.1	15q24.3	2014-05-20			ENSG00000140379	ENSG00000140379			991	protein-coding gene	gene with protein product		601056		HBPA1		8589678, 12771180	Standard	NM_004049		Approved	GRS, BFL1, BCL2L5, ACC-1, ACC-2	uc002bfc.4	Q16548	OTTHUMG00000144173	ENST00000267953.3:c.351G>T	15.37:g.80263111C>A	ENSP00000267953:p.Glu117Asp	244.0	0.0	0		224.0	105.0	0.46875	NM_001114735	Q6FGZ4|Q6FH19|Q86W13|Q99524	Missense_Mutation	SNP	ENST00000267953.3	37	CCDS10312.1	55	0.025183150183150184	50	0.1016260162601626	5	0.013812154696132596	0	0.0	0	0.0	C	11.44	1.639200	0.29157	0.107127	8.14E-4	ENSG00000140379	ENST00000267953;ENST00000335661	T;T	0.11604	2.76;2.76	4.98	-5.04	0.02964	Apoptosis regulator, Bcl2-like (1);Apoptosis regulator, Bcl-2, BH (3);	1.167600	0.06235	N	0.689282	T	0.00144	0.0004	N	0.21448	0.665	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.44742	-0.9308	10	0.15499	T	0.54	-25.672	8.3287	0.32173	0.0:0.3478:0.4258:0.2264	rs34080999	117;117	Q86W13;Q16548	.;B2LA1_HUMAN	D	117	ENSP00000267953:E117D;ENSP00000335250:E117D	ENSP00000267953:E117D	E	-	3	2	BCL2A1	78050166	0.457000	0.25752	0.000000	0.03702	0.018000	0.09664	-0.218000	0.09240	-0.861000	0.04094	0.655000	0.94253	GAG	C|0.968;A|0.032	0.032	strong		0.383	BCL2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291372.1	NM_004049	
STARD13	90627	hgsc.bcm.edu	37	13	33704346	33704346	+	Silent	SNP	C	C	T	rs114088950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:33704346C>T	ENST00000336934.5	-	5	584	c.468G>A	c.(466-468)gtG>gtA	p.V156V	STARD13_ENST00000399365.3_Silent_p.V38V|STARD13_ENST00000255486.4_Silent_p.V148V	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	156					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)		AGAGGTCGTCCACACGAGACC	0.557													C|||	86	0.0171725	0.0492	0.0014	5008	,	,		21153	0.0		0.0	False		,,,				2504	0.0204				p.V156V		Atlas-SNP	.											.	STARD13	100	.	0			c.G468A						PASS	.	C	,,	147,4259	103.8+/-142.4	3,141,2059	82.0	62.0	69.0		114,468,444	5.4	1.0	13	dbSNP_132	69	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	STARD13	NM_052851.2,NM_178006.3,NM_178007.2	,,	3,142,6358	TT,TC,CC		0.0116,3.3364,1.1379	,,	38/996,156/1114,148/1106	33704346	148,12858	2203	4300	6503	SO:0001819	synonymous_variant	90627	exon5			GTCGTCCACACGA	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.468G>A	13.37:g.33704346C>T		33.0	0.0	0		43.0	18.0	0.418605	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Silent	SNP	ENST00000336934.5	37	CCDS9348.1																																																																																			C|0.986;T|0.014	0.014	strong		0.557	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466	
SLC38A6	145389	hgsc.bcm.edu	37	14	61445981	61445981	+	5'Flank	SNP	C	C	T	rs114005374	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:61445981C>T	ENST00000267488.4	+	0	0				TRMT5_ENST00000261249.6_Missense_Mutation_p.R212Q|RP11-193F5.1_ENST00000553946.1_RNA|SLC38A6_ENST00000354886.2_5'Flank|SLC38A6_ENST00000456840.2_5'Flank	NM_153811.2	NP_722518.2	Q8IZM9	S38A6_HUMAN	solute carrier family 38, member 6						amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)		p.R212Q(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(5)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(108;0.0981)		CTGATGATCTCGAAGGTTTAG	0.353													C|||	11	0.00219649	0.0083	0.0	5008	,	,		21341	0.0		0.0	False		,,,				2504	0.0				p.R212Q		Atlas-SNP	.											TRMT5,caecum,carcinoma,0,1	TRMT5	44	1	1	Substitution - Missense(1)	large_intestine(1)	c.G635A						PASS	.	C	GLN/ARG	11,4395	17.9+/-39.9	0,11,2192	99.0	93.0	95.0		635	4.8	1.0	14	dbSNP_132	95	0,8600		0,0,4300	yes	missense	TRMT5	NM_020810.2	43	0,11,6492	TT,TC,CC		0.0,0.2497,0.0846	probably-damaging	212/510	61445981	11,12995	2203	4300	6503	SO:0001631	upstream_gene_variant	57570	exon2			TGATCTCGAAGGT	AF070578	CCDS9751.1, CCDS53900.1	14q23.1	2013-05-22			ENSG00000139974	ENSG00000139974		"""Solute carriers"""	19863	protein-coding gene	gene with protein product							Standard	NM_153811		Approved	NAT-1	uc001xfh.2	Q8IZM9	OTTHUMG00000140335		14.37:g.61445981C>T	Exception_encountered	119.0	0.0	0		129.0	61.0	0.472868	NM_020810	C9JWA6|Q86SY5	Missense_Mutation	SNP	ENST00000267488.4	37	CCDS9751.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	35	5.439965	0.96168	0.002497	0.0	ENSG00000126814	ENST00000261249	T	0.23754	1.89	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	T	0.51856	0.1699	M	0.91920	3.255	0.58432	D	0.999998	D	0.76494	0.999	D	0.73708	0.981	T	0.65709	-0.6102	10	0.46703	T	0.11	-9.0897	18.1347	0.89614	0.0:1.0:0.0:0.0	.	212	Q32P41	TRM5_HUMAN	Q	212	ENSP00000261249:R212Q	ENSP00000261249:R212Q	R	-	2	0	TRMT5	60515734	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.317000	0.79018	2.489000	0.83994	0.655000	0.94253	CGA	C|0.999;T|0.001	0.001	strong		0.353	SLC38A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276957.1		
CENPJ	55835	hgsc.bcm.edu	37	13	25480616	25480616	+	Silent	SNP	T	T	A	rs17081368	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:25480616T>A	ENST00000381884.4	-	7	1745	c.1560A>T	c.(1558-1560)acA>acT	p.T520T	CENPJ_ENST00000545981.1_Silent_p.T520T	NM_018451.4	NP_060921.3	Q9HC77	CENPJ_HUMAN	centromere protein J	520					cell division (GO:0051301)|centriole replication (GO:0007099)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|microtubule polymerization (GO:0046785)|mitotic cell cycle (GO:0000278)|regulation of centriole replication (GO:0046599)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)|gamma-tubulin small complex (GO:0008275)|microtubule (GO:0005874)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|tubulin binding (GO:0015631)			endometrium(5)|kidney(4)|large_intestine(14)|lung(13)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47		Lung SC(185;0.0225)|Breast(139;0.0602)		all cancers(112;0.00793)|Epithelial(112;0.0411)|OV - Ovarian serous cystadenocarcinoma(117;0.139)		CTTTACCTTGTGTCTTATTCC	0.448													T|||	248	0.0495208	0.1785	0.0159	5008	,	,		17190	0.0		0.001	False		,,,				2504	0.0				p.T520T		Atlas-SNP	.											.	CENPJ	116	.	0			c.A1560T						PASS	.	T		656,3750	274.3+/-271.8	47,562,1594	73.0	77.0	76.0		1560	0.4	0.0	13	dbSNP_123	76	12,8586	8.4+/-32.0	0,12,4287	no	coding-synonymous	CENPJ	NM_018451.3		47,574,5881	AA,AT,TT		0.1396,14.8888,5.1369		520/1339	25480616	668,12336	2203	4299	6502	SO:0001819	synonymous_variant	55835	exon7			ACCTTGTGTCTTA	AF139625	CCDS9310.1	13q12.12	2013-11-05			ENSG00000151849	ENSG00000151849			17272	protein-coding gene	gene with protein product	"""centrosomal P4.1-associated protein"""	609279	"""microcephaly, primary autosomal recessive 6"""	MCPH6		11003675, 22699936	Standard	NM_018451		Approved	CPAP, BM032, LAP, LIP1, Sas-4, SASS4, SCKL4	uc001upt.5	Q9HC77	OTTHUMG00000016595	ENST00000381884.4:c.1560A>T	13.37:g.25480616T>A		88.0	0.0	0		118.0	60.0	0.508475	NM_018451	Q2KHM6|Q5JPD5|Q5T6R5|Q96KS5|Q9C067	Silent	SNP	ENST00000381884.4	37	CCDS9310.1																																																																																			T|0.950;A|0.050	0.050	strong		0.448	CENPJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044209.1	NM_018451	
S100A3	6274	hgsc.bcm.edu	37	1	153520954	153520954	+	Missense_Mutation	SNP	C	C	T	rs36022742	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:153520954C>T	ENST00000368713.3	-	2	204	c.8G>A	c.(7-9)aGg>aAg	p.R3K	S100A4_ENST00000368716.4_5'Flank|S100A4_ENST00000354332.4_5'Flank|S100A4_ENST00000368714.1_Intron|S100A3_ENST00000368712.1_Missense_Mutation_p.R3K	NM_002960.1	NP_002951.1	P33764	S10A3_HUMAN	S100 calcium binding protein A3	3			R -> K (in dbSNP:rs36022742).			cytoplasm (GO:0005737)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(1)|liver(1)|lung(1)	3	all_lung(78;5.98e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			CTCCAGAGGCCTGGCCATCCT	0.602													C|||	713	0.142372	0.3896	0.0994	5008	,	,		17421	0.0149		0.0517	False		,,,				2504	0.0634				p.R3K		Atlas-SNP	.											.	S100A3	7	.	0			c.G8A						PASS	.	C	LYS/ARG	1514,2892	471.8+/-356.2	272,970,961	105.0	105.0	105.0		8	0.8	0.0	1	dbSNP_126	105	465,8135	135.4+/-192.6	16,433,3851	yes	missense	S100A3	NM_002960.1	26	288,1403,4812	TT,TC,CC		5.407,34.3622,15.2161	benign	3/102	153520954	1979,11027	2203	4300	6503	SO:0001583	missense	6274	exon2			AGAGGCCTGGCCA	BC012893	CCDS1043.1	1q21	2008-02-05	2001-11-28		ENSG00000188015	ENSG00000188015		"""S100 calcium binding proteins"""	10493	protein-coding gene	gene with protein product		176992	"""S100 calcium-binding protein A3"""	S100E		8341667	Standard	NM_002960		Approved		uc001fca.1	P33764	OTTHUMG00000013550	ENST00000368713.3:c.8G>A	1.37:g.153520954C>T	ENSP00000357702:p.Arg3Lys	45.0	0.0	0		48.0	22.0	0.458333	NM_002960	D3DV51|Q6FGE4	Missense_Mutation	SNP	ENST00000368713.3	37	CCDS1043.1	255	0.11675824175824176	180	0.36585365853658536	33	0.09116022099447514	9	0.015734265734265736	33	0.04353562005277045	C	7.322	0.617075	0.14129	0.343622	0.05407	ENSG00000188015	ENST00000368713;ENST00000368712	T;T	0.13538	2.58;2.58	5.05	0.817	0.18773	EF-hand-like domain (1);	0.427486	0.25430	N	0.030730	T	0.02418	0.0074	N	0.14661	0.345	0.80722	P	0.0	B	0.22276	0.067	B	0.15052	0.012	T	0.40739	-0.9547	9	0.56958	D	0.05	.	8.5814	0.33630	0.0:0.4703:0.4447:0.085	rs36022742;rs59565142;rs61732314	3	P33764	S10A3_HUMAN	K	3	ENSP00000357702:R3K;ENSP00000357701:R3K	ENSP00000357701:R3K	R	-	2	0	S100A3	151787578	0.000000	0.05858	0.002000	0.10522	0.038000	0.13279	-0.160000	0.10041	-0.025000	0.13918	-0.163000	0.13421	AGG	C|0.861;T|0.139	0.139	strong		0.602	S100A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037726.1	NM_002960	
C2CD5	9847	hgsc.bcm.edu	37	12	22680809	22680809	+	Silent	SNP	T	T	C	rs12322490	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:22680809T>C	ENST00000333957.4	-	4	450	c.195A>G	c.(193-195)ttA>ttG	p.L65L	C2CD5_ENST00000536386.1_Silent_p.L65L|C2CD5_ENST00000446597.1_Silent_p.L65L|C2CD5_ENST00000540703.1_5'Flank|C2CD5_ENST00000545552.1_Silent_p.L65L|C2CD5_ENST00000544930.1_5'UTR|C2CD5_ENST00000396028.2_Silent_p.L65L|C2CD5_ENST00000542676.1_Silent_p.L65L	NM_014802.1	NP_055617.1	Q86YS7	C2CD5_HUMAN	C2 calcium-dependent domain containing 5	65	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				cellular response to insulin stimulus (GO:0032869)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|intracellular protein transmembrane transport (GO:0065002)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of vesicle fusion (GO:0031340)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)										GTTCATCTTGTAAGTCTTCAT	0.303													T|||	229	0.0457268	0.1649	0.0159	5008	,	,		16020	0.0		0.0	False		,,,				2504	0.0				p.L65L		Atlas-SNP	.											.	.	.	.	0			c.A195G						PASS	.	T		560,3846	250.0+/-257.2	37,486,1680	142.0	130.0	134.0		195	0.2	1.0	12	dbSNP_120	134	7,8593	5.0+/-18.6	0,7,4293	yes	coding-synonymous	KIAA0528	NM_014802.1		37,493,5973	CC,CT,TT		0.0814,12.7099,4.3595		65/1001	22680809	567,12439	2203	4300	6503	SO:0001819	synonymous_variant	9847	exon4			ATCTTGTAAGTCT	AB011100	CCDS31758.1, CCDS66337.1, CCDS66338.1, CCDS66339.1, CCDS66340.1	12p12.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000111731	ENSG00000111731			29062	protein-coding gene	gene with protein product	"""138 kDa C2 domain-containing phosphoprotein"""		"""KIAA0528"""	KIAA0528		21907143	Standard	XM_005253538		Approved	CDP138	uc001rfq.3	Q86YS7	OTTHUMG00000169100	ENST00000333957.4:c.195A>G	12.37:g.22680809T>C		119.0	0.0	0		135.0	93.0	0.688889	NM_014802	B4DJ03|B4DRN7|B7ZLL0|F5H2A1|F5H5R1|O60280|Q17RY7|Q7Z619|Q86SU3	Silent	SNP	ENST00000333957.4	37	CCDS31758.1																																																																																			T|0.950;C|0.050	0.050	strong		0.303	C2CD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402257.1	NM_014802	
CEP85	64793	hgsc.bcm.edu	37	1	26581981	26581981	+	Silent	SNP	G	G	A	rs34867486	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:26581981G>A	ENST00000252992.4	+	4	659	c.528G>A	c.(526-528)gcG>gcA	p.A176A	CEP85_ENST00000451429.2_Silent_p.A125A	NM_001281517.1|NM_022778.2	NP_001268446.1|NP_073615.2	Q6P2H3	CEP85_HUMAN	centrosomal protein 85kDa	176						centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|spindle pole (GO:0000922)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(11)|skin(2)	25						AAGAAGAGGCGAGGAAGTTTG	0.473													G|||	105	0.0209665	0.0749	0.0086	5008	,	,		21433	0.0		0.0	False		,,,				2504	0.0				p.A176A		Atlas-SNP	.											CEP85,NS,carcinoma,+2,1	CEP85	61	1	0			c.G528A						PASS	.	G		236,4170	141.1+/-176.5	3,230,1970	87.0	85.0	86.0		528	3.6	0.7	1	dbSNP_126	86	3,8597	3.0+/-9.4	0,3,4297	yes	coding-synonymous	CEP85	NM_022778.2		3,233,6267	AA,AG,GG		0.0349,5.3563,1.8376		176/763	26581981	239,12767	2203	4300	6503	SO:0001819	synonymous_variant	64793	exon4			AGAGGCGAGGAAG	AK024038	CCDS277.1, CCDS60038.1	1p36.11	2014-02-20	2011-05-06	2011-05-06	ENSG00000130695	ENSG00000130695			25309	protein-coding gene	gene with protein product			"""coiled-coil domain containing 21"""	CCDC21		12477932	Standard	NM_022778		Approved	DKFZP434L0117	uc001bls.1	Q6P2H3	OTTHUMG00000003380	ENST00000252992.4:c.528G>A	1.37:g.26581981G>A		110.0	0.0	0		114.0	58.0	0.508772	NM_022778	B4DRL1|D3DPK4|F8W7K4|Q5VY68|Q5VY70|Q9H6Q1|Q9H828|Q9UF52	Silent	SNP	ENST00000252992.4	37	CCDS277.1																																																																																			G|0.979;A|0.021	0.021	strong		0.473	CEP85-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009492.2	NM_022778	
HECTD2	143279	hgsc.bcm.edu	37	10	93260363	93260363	+	Silent	SNP	C	C	T	rs34553731	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:93260363C>T	ENST00000298068.5	+	19	2149	c.2055C>T	c.(2053-2055)gaC>gaT	p.D685D	HECTD2_ENST00000446394.1_Silent_p.D689D|HECTD2_ENST00000536715.1_Silent_p.D274D|HECTD2_ENST00000371667.1_Silent_p.D335D	NM_182765.3	NP_877497	Q5U5R9	HECD2_HUMAN	HECT domain containing E3 ubiquitin protein ligase 2	685	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|endometrium(2)|kidney(4)|large_intestine(10)|lung(7)|skin(1)|urinary_tract(1)	27						CAAAAACGGACTTAACTATAA	0.418													C|||	61	0.0121805	0.0439	0.0029	5008	,	,		16343	0.0		0.001	False		,,,				2504	0.0				p.D685D	NSCLC(12;376 469 1699 39910 41417)	Atlas-SNP	.											.	HECTD2	60	.	0			c.C2055T						PASS	.	C		205,4201	127.0+/-164.0	5,195,2003	103.0	95.0	98.0		2055	3.9	0.6	10	dbSNP_126	98	6,8594	3.0+/-9.4	0,6,4294	no	coding-synonymous	HECTD2	NM_182765.3		5,201,6297	TT,TC,CC		0.0698,4.6527,1.6223		685/777	93260363	211,12795	2203	4300	6503	SO:0001819	synonymous_variant	143279	exon19			AACGGACTTAACT	AK094625	CCDS7414.1, CCDS7415.1, CCDS60591.1	10q23.32	2013-09-20	2012-02-23		ENSG00000165338	ENSG00000165338			26736	protein-coding gene	gene with protein product			"""HECT domain containing 2"""			8619474, 9110174	Standard	NM_001284274		Approved	FLJ37306	uc001khl.2	Q5U5R9	OTTHUMG00000018742	ENST00000298068.5:c.2055C>T	10.37:g.93260363C>T		50.0	0.0	0		61.0	29.0	0.47541	NM_182765	Q5VZ97|Q5VZ98|Q5VZ99|Q8N1X7|Q8TCP5	Silent	SNP	ENST00000298068.5	37	CCDS7414.1																																																																																			C|0.985;T|0.015	0.015	strong		0.418	HECTD2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098620.1		
KIAA1377	57562	hgsc.bcm.edu	37	11	101829070	101829070	+	Silent	SNP	C	C	T	rs61742070	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:101829070C>T	ENST00000263468.8	+	5	948	c.678C>T	c.(676-678)ctC>ctT	p.L226L	KIAA1377_ENST00000537689.1_Silent_p.L27L	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	226										breast(4)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(18)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	53	all_epithelial(12;0.0104)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00931)		BRCA - Breast invasive adenocarcinoma(274;0.038)		AGAAACTCCTCGAAGATCAAC	0.343													C|||	49	0.00978435	0.0371	0.0	5008	,	,		18452	0.0		0.0	False		,,,				2504	0.0				p.L226L		Atlas-SNP	.											.	KIAA1377	111	.	0			c.C678T						PASS	.	C		129,4277	90.2+/-128.9	0,129,2074	105.0	113.0	110.0		678	0.7	1.0	11	dbSNP_129	110	0,8598		0,0,4299	no	coding-synonymous	KIAA1377	NM_020802.2		0,129,6373	TT,TC,CC		0.0,2.9278,0.992		226/1118	101829070	129,12875	2203	4299	6502	SO:0001819	synonymous_variant	57562	exon5			ACTCCTCGAAGAT	AK095004	CCDS31658.1	11q22.2	2006-02-03			ENSG00000110318	ENSG00000110318			29264	protein-coding gene	gene with protein product		614634				10718198	Standard	XM_005271627		Approved		uc001pgm.3	Q9P2H0	OTTHUMG00000167319	ENST00000263468.8:c.678C>T	11.37:g.101829070C>T		68.0	0.0	0		67.0	32.0	0.477612	NM_020802	Q4G0U6	Silent	SNP	ENST00000263468.8	37	CCDS31658.1																																																																																			C|0.989;T|0.011	0.011	strong		0.343	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802	
CAPN12	147968	hgsc.bcm.edu	37	19	39234674	39234674	+	Silent	SNP	G	G	A	rs111831826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39234674G>A	ENST00000328867.4	-	1	440	c.132C>T	c.(130-132)atC>atT	p.I44I	CAPN12_ENST00000601953.1_Intron	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	44					proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(60;2.87e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)			CGCGGAACAGGATCCCCGAAT	0.637													g|||	11	0.00219649	0.0083	0.0	5008	,	,		16631	0.0		0.0	False		,,,				2504	0.0				p.I44I		Atlas-SNP	.											.	CAPN12	43	.	0			c.C132T						PASS	.	G		27,4379	32.6+/-62.9	0,27,2176	82.0	67.0	72.0		132	2.6	1.0	19	dbSNP_132	72	0,8600		0,0,4300	no	coding-synonymous	CAPN12	NM_144691.3		0,27,6476	AA,AG,GG		0.0,0.6128,0.2076		44/720	39234674	27,12979	2203	4300	6503	SO:0001819	synonymous_variant	147968	exon1			GAACAGGATCCCC	BC014027	CCDS12519.1	19q13.2	2014-08-12			ENSG00000182472	ENSG00000182472		"""EF-hand domain containing"""	13249	protein-coding gene	gene with protein product		608839					Standard	NM_144691		Approved		uc002ojd.1	Q6ZSI9	OTTHUMG00000182525	ENST00000328867.4:c.132C>T	19.37:g.39234674G>A		69.0	0.0	0		79.0	37.0	0.468354	NM_144691		Silent	SNP	ENST00000328867.4	37	CCDS12519.1																																																																																			G|0.998;A|0.002	0.002	strong		0.637	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1		
PREX2	80243	hgsc.bcm.edu	37	8	69104701	69104701	+	Silent	SNP	G	G	A	rs116570374	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:69104701G>A	ENST00000288368.4	+	37	4822	c.4545G>A	c.(4543-4545)tcG>tcA	p.S1515S		NM_024870.2|NM_025170.4	NP_079146.2|NP_079446.3	Q70Z35	PREX2_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2	1515					adult locomotory behavior (GO:0008344)|dendrite morphogenesis (GO:0048813)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|positive regulation of Rac GTPase activity (GO:0032855)		Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(6)|biliary_tract(1)|breast(4)|endometrium(11)|kidney(16)|large_intestine(25)|liver(4)|lung(57)|ovary(2)|pancreas(4)|prostate(3)|skin(42)|upper_aerodigestive_tract(1)|urinary_tract(2)	178						CAGTTTCCTCGGAGCTGTGCA	0.557													G|||	28	0.00559105	0.0204	0.0014	5008	,	,		12376	0.0		0.0	False		,,,				2504	0.0				p.S1515S		Atlas-SNP	.											.	PREX2	614	.	0			c.G4545A						PASS	.	G		93,4313	75.7+/-113.9	1,91,2111	57.0	47.0	50.0		4545	-3.1	1.0	8	dbSNP_132	50	2,8598		0,2,4298	no	coding-synonymous	PREX2	NM_024870.2		1,93,6409	AA,AG,GG		0.0233,2.1108,0.7304		1515/1607	69104701	95,12911	2203	4300	6503	SO:0001819	synonymous_variant	80243	exon37			TTCCTCGGAGCTG	AK024079	CCDS6201.1	8q13.1	2014-06-13	2008-09-15	2008-09-15	ENSG00000046889	ENSG00000046889		"""Rho guanine nucleotide exchange factors"""	22950	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 129"""	612139	"""DEP domain containing 2"""	DEPDC2		15304342, 15304343	Standard	NM_024870		Approved	DEP.2, FLJ12987, P-REX2, PPP1R129	uc003xxv.1	Q70Z35	OTTHUMG00000164402	ENST00000288368.4:c.4545G>A	8.37:g.69104701G>A		65.0	0.0	0		101.0	51.0	0.504951	NM_024870	B4DFX0|Q32KL0|Q32KL1|Q6R7Q3|Q6R7Q4|Q9H805|Q9H961	Silent	SNP	ENST00000288368.4	37	CCDS6201.1																																																																																			G|0.993;A|0.007	0.007	strong		0.557	PREX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378620.1	NM_025170	
HTR4	3360	hgsc.bcm.edu	37	5	147845463	147845463	+	Missense_Mutation	SNP	G	G	A	rs73266449	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:147845463G>A	ENST00000314512.6	-	7	1265	c.1102C>T	c.(1102-1104)Ctc>Ttc	p.L368F	HTR4_ENST00000521530.1_Intron|HTR4_ENST00000354217.2_Intron|HTR4_ENST00000521735.1_Missense_Mutation_p.L368F	NM_199453.3	NP_955525.1	Q13639	5HT4R_HUMAN	5-hydroxytryptamine (serotonin) receptor 4, G protein-coupled	0					G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cell proliferation (GO:0008284)|regulation of appetite (GO:0032098)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)			endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		Cinitapride(DB08810)|Cisapride(DB00604)|Ergoloid mesylate(DB01049)|Metoclopramide(DB01233)|Ondansetron(DB00904)	AAGAGCAGGAGGAAGCTGGAG	0.433													G|||	200	0.0399361	0.1437	0.0144	5008	,	,		17221	0.0		0.0	False		,,,				2504	0.0				p.L368F	GBM(120;370 1604 14007 17804 41573)	Atlas-SNP	.											.	HTR4	161	.	0			c.C1102T						PASS	.	G	,PHE/LEU	459,3947	219.4+/-237.2	28,403,1772	150.0	163.0	158.0		,1102	-7.4	0.3	5	dbSNP_130	158	3,8597	3.0+/-9.4	0,3,4297	yes	intron,missense	HTR4	NM_001040169.2,NM_199453.3	,22	28,406,6069	AA,AG,GG		0.0349,10.4176,3.5522	,	,368/379	147845463	462,12544	2203	4300	6503	SO:0001583	missense	3360	exon6			GCAGGAGGAAGCT	Y08756	CCDS4291.1, CCDS34270.1, CCDS34271.1, CCDS34272.1, CCDS34273.1, CCDS34273.2, CCDS75353.1	5q31-q33	2012-08-08	2012-02-03		ENSG00000164270	ENSG00000164270		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5299	protein-coding gene	gene with protein product		602164	"""5-hydroxytryptamine (serotonin) receptor 4"""			9371406, 9276448	Standard	NM_199453		Approved	5-HT4	uc021yfj.1	Q13639	OTTHUMG00000129931	ENST00000314512.6:c.1102C>T	5.37:g.147845463G>A	ENSP00000314906:p.Leu368Phe	257.0	0.0	0		255.0	118.0	0.462745	NM_199453	C4WYH4|Q546Q1|Q684M0|Q712M9|Q96KH9|Q96KI0|Q9H199|Q9NY73|Q9UBM6|Q9UBT4|Q9UE22|Q9UE23|Q9UQR6	Missense_Mutation	SNP	ENST00000314512.6	37	CCDS34271.1	77	0.035256410256410256	72	0.14634146341463414	5	0.013812154696132596	0	0.0	0	0.0	G	9.178	1.022933	0.19433	0.104176	3.49E-4	ENSG00000164270	ENST00000314512;ENST00000521735	T;T	0.71817	-0.6;-0.6	5.06	-7.41	0.01392	.	.	.	.	.	T	0.00356	0.0011	.	.	.	0.31926	P	0.612866	B	0.02656	0.0	B	0.01281	0.0	T	0.18745	-1.0327	7	0.09843	T	0.71	.	16.3003	0.82806	0.6695:0.0:0.3305:0.0	.	368	Q684M0	.	F	368	ENSP00000314906:L368F;ENSP00000430979:L368F	ENSP00000314906:L368F	L	-	1	0	HTR4	147825656	0.873000	0.30073	0.266000	0.24541	0.912000	0.54170	-0.283000	0.08433	-2.141000	0.00805	-2.010000	0.00438	CTC	G|0.967;A|0.033	0.033	strong		0.433	HTR4-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000374235.1	NM_000870	
FCRL1	115350	hgsc.bcm.edu	37	1	157771979	157771979	+	Silent	SNP	C	C	T	rs12035302	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:157771979C>T	ENST00000368176.3	-	5	679	c.612G>A	c.(610-612)ccG>ccA	p.P204P	FCRL1_ENST00000489998.1_5'UTR|FCRL1_ENST00000491942.1_Silent_p.P204P|FCRL1_ENST00000358292.3_Silent_p.P204P	NM_001159398.1|NM_052938.4	NP_001152870.1|NP_443170.1	Q96LA6	FCRL1_HUMAN	Fc receptor-like 1	204						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(24)|ovary(4)|prostate(1)|skin(6)	42	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			GGCGAGACACCGGGACTGAGG	0.582													C|||	122	0.024361	0.0832	0.0058	5008	,	,		19850	0.006		0.001	False		,,,				2504	0.001				p.P204P	GBM(54;482 1003 11223 30131 35730)	Atlas-SNP	.											.	FCRL1	164	.	0			c.G612A						PASS	.	C	,,	291,4115	141.5+/-176.9	15,261,1927	34.0	36.0	35.0		612,612,612	1.2	1.0	1	dbSNP_120	35	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	FCRL1	NM_001159397.1,NM_001159398.1,NM_052938.4	,,	15,266,6222	TT,TC,CC		0.0581,6.6046,2.2759	,,	204/367,204/429,204/430	157771979	296,12710	2203	4300	6503	SO:0001819	synonymous_variant	115350	exon5			AGACACCGGGACT	BC033690	CCDS1170.1, CCDS53382.1, CCDS53383.1	1q21-q22	2013-01-14			ENSG00000163534	ENSG00000163534		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18509	protein-coding gene	gene with protein product		606508				11493702, 11929751	Standard	NM_052938		Approved	FCRH1, IRTA5, IFGP1, CD307a	uc001frg.3	Q96LA6	OTTHUMG00000019398	ENST00000368176.3:c.612G>A	1.37:g.157771979C>T		134.0	0.0	0		136.0	65.0	0.477941	NM_001159397	B2RE05|Q8N759|Q8NDI0|Q96PJ6	Silent	SNP	ENST00000368176.3	37	CCDS1170.1																																																																																			C|0.978;T|0.022	0.022	strong		0.582	FCRL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051401.1	NM_052938	
PDHX	8050	hgsc.bcm.edu	37	11	34969150	34969150	+	Silent	SNP	C	C	T	rs34582941	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:34969150C>T	ENST00000227868.4	+	3	423	c.339C>T	c.(337-339)atC>atT	p.I113I	PDHX_ENST00000430469.2_Silent_p.I113I|PDHX_ENST00000448838.3_Silent_p.I98I			O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X	113	Lipoyl-binding. {ECO:0000255|PROSITE- ProRule:PRU01066}.				cellular metabolic process (GO:0044237)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	transferase activity, transferring acyl groups (GO:0016746)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)	16	all_epithelial(35;0.115)|Lung NSC(22;0.218)|all_lung(20;0.242)	all_hematologic(20;0.124)	STAD - Stomach adenocarcinoma(6;0.00113)			TGGCCAAAATCGTGGTAAGTT	0.353													C|||	272	0.0543131	0.1974	0.0159	5008	,	,		15319	0.0		0.0	False		,,,				2504	0.0				p.I113I		Atlas-SNP	.											.	PDHX	40	.	0			c.C339T						PASS	.	C	,,	720,3684	299.3+/-285.7	67,586,1549	163.0	154.0	157.0		294,339,339	-2.9	1.0	11	dbSNP_126	157	10,8586	5.7+/-21.5	0,10,4288	no	coding-synonymous,coding-synonymous,coding-synonymous	PDHX	NM_001135024.1,NM_001166158.1,NM_003477.2	,,	67,596,5837	TT,TC,CC		0.1163,16.3488,5.6154	,,	98/487,113/275,113/502	34969150	730,12270	2202	4298	6500	SO:0001819	synonymous_variant	8050	exon3			CAAAATCGTGGTA	U82328	CCDS7896.1, CCDS44569.1, CCDS53616.1	11p13	2008-02-05			ENSG00000110435	ENSG00000110435			21350	protein-coding gene	gene with protein product		608769				9467010, 12372595	Standard	NM_003477		Approved	E3BP, proX, PDX1, OPDX, DLDBP	uc001mvt.3	O00330	OTTHUMG00000166491	ENST00000227868.4:c.339C>T	11.37:g.34969150C>T		36.0	0.0	0		70.0	33.0	0.471429	NM_003477	B4DW62|D3DR11|E9PB14|E9PBP7|O60221|Q96FV8|Q99783	Silent	SNP	ENST00000227868.4	37	CCDS7896.1																																																																																			C|0.951;T|0.049	0.049	strong		0.353	PDHX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390017.1	NM_003477	
CARD11	84433	hgsc.bcm.edu	37	7	2969689	2969689	+	Missense_Mutation	SNP	T	T	G	rs41515445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:2969689T>G	ENST00000396946.4	-	12	1993	c.1590A>C	c.(1588-1590)gaA>gaC	p.E530D		NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	530					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		CGTCCGTGCCTTCTTCCTCGT	0.622			Mis		DLBCL								T|||	141	0.028155	0.1036	0.0058	5008	,	,		16650	0.0		0.0	False		,,,				2504	0.0				p.E530D		Atlas-SNP	.		Dom	yes		7	7p22	84433	"""caspase recruitment domain family, member 11"""		L	.	CARD11	339	.	0			c.A1590C						PASS	.	T	ASP/GLU	398,4008	195.3+/-220.0	17,364,1822	115.0	78.0	91.0		1590	-5.4	0.0	7	dbSNP_127	91	2,8598	1.2+/-3.3	0,2,4298	yes	missense	CARD11	NM_032415.4	45	17,366,6120	GG,GT,TT		0.0233,9.0331,3.0755	benign	530/1155	2969689	400,12606	2203	4300	6503	SO:0001583	missense	84433	exon12			CGTGCCTTCTTCC	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"""card-maguk protein 1"", ""bcl10-interacting maguk protein 3"""	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.1590A>C	7.37:g.2969689T>G	ENSP00000380150:p.Glu530Asp	111.0	0.0	0		123.0	62.0	0.504065	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	50	0.022893772893772892	46	0.09349593495934959	4	0.011049723756906077	0	0.0	0	0.0	T	4.090	0.014638	0.07959	0.090331	2.33E-4	ENSG00000198286	ENST00000396946;ENST00000355508	T;T	0.30981	1.51;2.48	3.85	-5.41	0.02648	.	1.090360	0.06781	N	0.785380	T	0.00384	0.0012	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.23868	-1.0176	10	0.02654	T	1	-2.0525	5.5885	0.17287	0.3319:0.0:0.5015:0.1665	rs41515445;rs58644294	530	Q9BXL7	CAR11_HUMAN	D	530;2	ENSP00000380150:E530D;ENSP00000347695:E2D	ENSP00000347695:E2D	E	-	3	2	CARD11	2936215	0.001000	0.12720	0.000000	0.03702	0.021000	0.10359	-0.891000	0.04135	-0.959000	0.03618	0.459000	0.35465	GAA	T|0.972;G|0.028	0.028	strong		0.622	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415	
HK2	3099	hgsc.bcm.edu	37	2	75107671	75107671	+	Silent	SNP	C	C	T	rs28363033	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:75107671C>T	ENST00000290573.2	+	10	2145	c.1545C>T	c.(1543-1545)taC>taT	p.Y515Y	HK2_ENST00000409174.1_Silent_p.Y487Y	NM_000189.4	NP_000180.2	P52789	HXK2_HUMAN	hexokinase 2	515	Catalytic.|Hexokinase type-1 2.				apoptotic mitochondrial changes (GO:0008637)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|lactation (GO:0007595)|regulation of glucose import (GO:0046324)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	43						TGCCCACCTACGTGTGTGCTA	0.597													C|||	56	0.0111821	0.0393	0.0043	5008	,	,		19072	0.0		0.001	False		,,,				2504	0.0				p.Y515Y		Atlas-SNP	.											.	HK2	85	.	0			c.C1545T						PASS	.	C		155,4251	107.3+/-145.7	4,147,2052	64.0	63.0	63.0		1545	-4.0	0.9	2	dbSNP_125	63	0,8600		0,0,4300	no	coding-synonymous	HK2	NM_000189.4		4,147,6352	TT,TC,CC		0.0,3.5179,1.1918		515/918	75107671	155,12851	2203	4300	6503	SO:0001819	synonymous_variant	3099	exon10			CACCTACGTGTGT		CCDS1956.1	2p13	2010-03-19			ENSG00000159399	ENSG00000159399	2.7.1.1		4923	protein-coding gene	gene with protein product		601125					Standard	NM_000189		Approved		uc002snd.3	P52789	OTTHUMG00000129972	ENST00000290573.2:c.1545C>T	2.37:g.75107671C>T		129.0	0.0	0		163.0	62.0	0.380368	NM_000189	D6W5J2|Q8WU87|Q9UN82	Silent	SNP	ENST00000290573.2	37	CCDS1956.1																																																																																			C|0.988;T|0.012	0.012	strong		0.597	HK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252238.2	NM_000189	
ZNF592	9640	hgsc.bcm.edu	37	15	85326315	85326315	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:85326315A>C	ENST00000560079.2	+	4	697	c.409A>C	c.(409-411)Acc>Ccc	p.T137P	ZNF592_ENST00000299927.3_Missense_Mutation_p.T137P	NM_014630.2	NP_055445.2	Q92610	ZN592_HUMAN	zinc finger protein 592	137					cell death (GO:0008219)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(143;0.0587)			GCCATTACCCACCTTCAACCA	0.478																																					p.T137P		Atlas-SNP	.											.	ZNF592	95	.	0			c.A409C						PASS	.						99.0	105.0	103.0					15																	85326315		2203	4299	6502	SO:0001583	missense	9640	exon4			TTACCCACCTTCA	D86966	CCDS32317.1	15q25.2	2011-03-15				ENSG00000166716		"""Zinc fingers, C2H2-type"""	28986	protein-coding gene	gene with protein product		613624	"""spinocerebellar ataxia, autosomal recessive 5"""	SCAR5		9039502, 12030328, 20531441	Standard	NM_014630		Approved	KIAA0211, CAMOS	uc002bld.3	Q92610		ENST00000560079.2:c.409A>C	15.37:g.85326315A>C	ENSP00000452877:p.Thr137Pro	80.0	0.0	0		62.0	29.0	0.467742	NM_014630	Q2M1T2|Q504Y9	Missense_Mutation	SNP	ENST00000560079.2	37	CCDS32317.1	.	.	.	.	.	.	.	.	.	.	A	16.70	3.196504	0.58126	.	.	ENSG00000166716	ENST00000299927	T	0.00640	6.03	6.06	6.06	0.98353	.	0.249606	0.46145	D	0.000302	T	0.02156	0.0067	L	0.48642	1.525	0.43852	D	0.99644	D	0.65815	0.995	D	0.63381	0.914	T	0.64580	-0.6374	10	0.72032	D	0.01	-20.196	14.5614	0.68140	1.0:0.0:0.0:0.0	.	137	Q92610	ZN592_HUMAN	P	137	ENSP00000299927:T137P	ENSP00000299927:T137P	T	+	1	0	ZNF592	83127319	0.986000	0.35501	0.998000	0.56505	0.999000	0.98932	3.000000	0.49481	2.324000	0.78689	0.533000	0.62120	ACC	.	.	none		0.478	ZNF592-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418779.2	NM_014630	
ABHD11	83451	hgsc.bcm.edu	37	7	73151643	73151643	+	Missense_Mutation	SNP	C	C	T	rs61745525|rs386714666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:73151643C>T	ENST00000222800.3	-	4	610	c.541G>A	c.(541-543)Gtg>Atg	p.V181M	LINC00035_ENST00000427153.1_RNA|ABHD11_ENST00000458339.1_Intron|ABHD11_ENST00000437775.2_Missense_Mutation_p.V174M|ABHD11_ENST00000395147.4_Intron|ABHD11_ENST00000468998.1_5'Flank	NM_148912.2	NP_683710.1	Q8NFV4	ABHDB_HUMAN	abhydrolase domain containing 11	181						mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			breast(1)|endometrium(1)|large_intestine(1)|lung(1)	4		Lung NSC(55;0.0908)|all_lung(88;0.198)				ATGGCTGCCACATAGGTTGCA	0.557													C|||	228	0.0455272	0.1649	0.0144	5008	,	,		21333	0.0		0.0	False		,,,				2504	0.0				p.V181M		Atlas-SNP	.											.	ABHD11	11	.	0			c.G541A						PASS	.	C	,MET/VAL,MET/VAL	436,3970		29,378,1796	89.0	73.0	79.0		,541,520	-9.2	0.0	7	dbSNP_129	79	3,8597		0,3,4297	yes	intron,missense,missense	ABHD11	NM_001145364.1,NM_148912.2,NM_148913.2	,21,21	29,381,6093	TT,TC,CC		0.0349,9.8956,3.3754	,benign,benign	,181/316,174/309	73151643	439,12567	2203	4300	6503	SO:0001583	missense	83451	exon4			CTGCCACATAGGT	AF217971	CCDS5558.1, CCDS47607.1, CCDS47608.1, CCDS75615.1	7q11.23	2010-08-05	2005-01-24	2005-01-27	ENSG00000106077	ENSG00000106077		"""Abhydrolase domain containing"""	16407	protein-coding gene	gene with protein product			"""Williams Beuren syndrome chromosome region 21"""	WBSCR21		12073013	Standard	NR_026910		Approved	PP1226	uc003tzb.3	Q8NFV4	OTTHUMG00000130029	ENST00000222800.3:c.541G>A	7.37:g.73151643C>T	ENSP00000222800:p.Val181Met	59.0	0.0	0		63.0	63.0	1	NM_148912	H7BYM8|Q6PJU0|Q8N722|Q8N723|Q8NFV2|Q8NFV3|Q9HBS8	Missense_Mutation	SNP	ENST00000222800.3	37	CCDS5558.1	73	0.033424908424908424	67	0.13617886178861788	6	0.016574585635359115	0	0.0	0	0.0	C	6.139	0.393893	0.11638	0.098956	3.49E-4	ENSG00000106077	ENST00000437775;ENST00000222800	T;T	0.68479	-0.33;-0.33	4.62	-9.25	0.00666	.	0.399068	0.28388	N	0.015523	T	0.00328	0.0010	L	0.31578	0.945	0.09310	P	0.99999999628235	B;B	0.18310	0.027;0.017	B;B	0.19666	0.015;0.026	T	0.01456	-1.1350	9	0.36615	T	0.2	-0.2939	3.1353	0.06437	0.2531:0.453:0.1175:0.1763	.	174;181	Q8NFV4-4;Q8NFV4	.;ABHDB_HUMAN	M	174;181	ENSP00000416970:V174M;ENSP00000222800:V181M	ENSP00000222800:V181M	V	-	1	0	ABHD11	72789579	0.406000	0.25344	0.004000	0.12327	0.014000	0.08584	-0.283000	0.08433	-1.427000	0.01992	-0.367000	0.07326	GTG	C|0.963;T|0.037	0.037	strong		0.557	ABHD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252306.1		
ZNF420	147923	hgsc.bcm.edu	37	19	37618157	37618157	+	Silent	SNP	T	T	C	rs78427535	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:37618157T>C	ENST00000337995.3	+	5	479	c.264T>C	c.(262-264)gaT>gaC	p.D88D	ZNF585A_ENST00000588723.1_Intron|CTC-454I21.4_ENST00000587645.1_RNA|ZNF420_ENST00000304239.7_Silent_p.D88D	NM_144689.3	NP_653290.2	Q8TAQ5	ZN420_HUMAN	zinc finger protein 420	88					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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(2)|large_intestine(9)|lung(10)|prostate(1)|skin(3)	27			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ATTCCAGGGATTATTTGGAAG	0.373													T|||	88	0.0175719	0.0628	0.0072	5008	,	,		18952	0.0		0.0	False		,,,				2504	0.0				p.D88D		Atlas-SNP	.											.	ZNF420	71	.	0			c.T264C						PASS	.	T		250,4156	145.0+/-179.8	7,236,1960	83.0	83.0	83.0		264	-4.2	0.0	19	dbSNP_131	83	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	ZNF420	NM_144689.3		7,243,6253	CC,CT,TT		0.0814,5.6741,1.976		88/689	37618157	257,12749	2203	4300	6503	SO:0001819	synonymous_variant	147923	exon5			CAGGGATTATTTG	AK056695	CCDS12498.1	19q13.12	2013-01-08			ENSG00000197050	ENSG00000197050		"""Zinc fingers, C2H2-type"", ""-"""	20649	protein-coding gene	gene with protein product							Standard	NM_144689		Approved	FLJ32191	uc002ofl.3	Q8TAQ5	OTTHUMG00000048168	ENST00000337995.3:c.264T>C	19.37:g.37618157T>C		141.0	0.0	0		148.0	72.0	0.486486	NM_144689	B2RDY6|Q96ML5	Silent	SNP	ENST00000337995.3	37	CCDS12498.1																																																																																			T|0.984;C|0.016	0.016	strong		0.373	ZNF420-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109587.3	NM_144689	
BDNF	627	hgsc.bcm.edu	37	11	27679976	27679976	+	Missense_Mutation	SNP	C	C	T	rs146354977	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:27679976C>T	ENST00000525528.1	-	1	1229	c.136G>A	c.(136-138)Gtg>Atg	p.V46M	BDNF_ENST00000525950.1_Missense_Mutation_p.V46M|BDNF_ENST00000314915.6_Missense_Mutation_p.V54M|BDNF_ENST00000584049.1_5'UTR|BDNF_ENST00000395983.3_Missense_Mutation_p.V46M|BDNF_ENST00000438929.1_Missense_Mutation_p.V128M|BDNF_ENST00000420794.1_Missense_Mutation_p.V46M|BDNF_ENST00000533246.1_Missense_Mutation_p.V46M|BDNF-AS_ENST00000532965.1_RNA|BDNF_ENST00000395980.2_Missense_Mutation_p.V46M|BDNF-AS_ENST00000530686.1_RNA|BDNF_ENST00000418212.1_Missense_Mutation_p.V46M|BDNF-AS_ENST00000502161.2_RNA|BDNF_ENST00000356660.4_Missense_Mutation_p.V46M|BDNF-AS_ENST00000530313.1_RNA|BDNF_ENST00000533131.1_Missense_Mutation_p.V46M|BDNF_ENST00000395978.3_Missense_Mutation_p.V46M|BDNF_ENST00000530861.1_Missense_Mutation_p.V46M|BDNF_ENST00000395981.3_Missense_Mutation_p.V46M|BDNF-AS_ENST00000499008.3_RNA|BDNF-AS_ENST00000501176.2_RNA|BDNF-AS_ENST00000500662.2_RNA|BDNF_ENST00000532997.1_Missense_Mutation_p.V46M|BDNF_ENST00000439476.2_Missense_Mutation_p.V46M|BDNF-AS_ENST00000499568.2_RNA|BDNF_ENST00000395986.2_Missense_Mutation_p.V61M	NM_170735.5	NP_733931.1	P23560	BDNF_HUMAN	brain-derived neurotrophic factor	46					axon extension (GO:0048675)|axon guidance (GO:0007411)|axon target recognition (GO:0007412)|behavioral fear response (GO:0001662)|chronic inflammatory response (GO:0002544)|circadian rhythm (GO:0007623)|dendrite development (GO:0016358)|dendrite extension (GO:0097484)|feeding behavior (GO:0007631)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glutamate secretion (GO:0014047)|inner ear development (GO:0048839)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of synaptic transmission, GABAergic (GO:0032229)|nerve development (GO:0021675)|nervous system development (GO:0007399)|neuron recognition (GO:0008038)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of synapse assembly (GO:0051965)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of retinal cell programmed cell death (GO:0046668)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|response to anesthetic (GO:0072347)|response to fluoxetine (GO:0014076)|response to hormone (GO:0009725)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to vitamin A (GO:0033189)|taste bud development (GO:0061193)|ureteric bud development (GO:0001657)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)|synaptic vesicle (GO:0008021)	growth factor activity (GO:0008083)			breast(1)|large_intestine(3)|lung(2)	6						GGCCCATTCACGCTCTCCAGA	0.547													C|||	3	0.000599042	0.0023	0.0	5008	,	,		18690	0.0		0.0	False		,,,				2504	0.0				p.V128M		Atlas-SNP	.											.	BDNF	63	.	0			c.G382A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	1,4403	2.1+/-5.4	0,1,2201	149.0	149.0	149.0		136,136,136,136,223,382,136,136,136,136,136,136,160,136,136,181,136	-1.7	1.0	11	dbSNP_134	149	0,8598		0,0,4299	no	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	BDNF	NM_001143805.1,NM_001143806.1,NM_001143807.1,NM_001143808.1,NM_001143809.1,NM_001143810.1,NM_001143811.1,NM_001143812.1,NM_001143813.1,NM_001143814.1,NM_001143816.1,NM_001709.4,NM_170731.4,NM_170732.4,NM_170733.3,NM_170734.3,NM_170735.5	21,21,21,21,21,21,21,21,21,21,21,21,21,21,21,21,21	0,1,6500	TT,TC,CC		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	46/248,46/248,46/248,46/248,75/277,128/330,46/248,46/248,46/248,46/248,46/248,46/248,54/256,46/248,46/248,61/263,46/248	27679976	1,13001	2202	4299	6501	SO:0001583	missense	627	exon3			CATTCACGCTCTC	AB038670	CCDS7865.1, CCDS7866.1, CCDS44558.1, CCDS41628.1	11p14.1	2014-01-30			ENSG00000176697	ENSG00000176697		"""Endogenous ligands"""	1033	protein-coding gene	gene with protein product	"""neurotrophin"""	113505				2236018, 1889806, 17942328, 17493809	Standard	NM_170731		Approved		uc009yje.3	P23560	OTTHUMG00000178797	ENST00000525528.1:c.136G>A	11.37:g.27679976C>T	ENSP00000437138:p.Val46Met	139.0	0.0	0		131.0	61.0	0.465649	NM_001143810	A7LA85|A7LA92|D3DQZ2|Q598Q1|Q6DN19|Q6YNR2|Q6YNR3|Q9BYY7|Q9UC24	Missense_Mutation	SNP	ENST00000525528.1	37	CCDS7866.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	6.658	0.489860	0.12702	2.27E-4	0.0	ENSG00000176697	ENST00000439476;ENST00000525528;ENST00000395986;ENST00000533131;ENST00000356660;ENST00000418212;ENST00000533246;ENST00000530861;ENST00000395983;ENST00000438929;ENST00000395980;ENST00000532997;ENST00000395981;ENST00000395978;ENST00000525950;ENST00000314915;ENST00000420794;ENST00000528035	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.53423	0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62;0.62	6.16	-1.67	0.08238	.	0.752012	0.13050	N	0.417798	T	0.20495	0.0493	N	0.14661	0.345	0.26003	N	0.98209	B;B;B;B;B	0.19445	0.012;0.013;0.014;0.002;0.036	B;B;B;B;B	0.16722	0.016;0.002;0.01;0.003;0.01	T	0.20306	-1.0279	10	0.87932	D	0	-29.8815	9.1961	0.37228	0.0:0.2875:0.1522:0.5603	.	75;128;54;46;61	P23560-5;P23560-4;P23560-2;P23560;P23560-3	.;.;.;BDNF_HUMAN;.	M	46;46;61;46;46;46;46;46;46;128;46;46;46;46;46;54;46;46	ENSP00000389345:V46M;ENSP00000437138:V46M;ENSP00000379309:V61M;ENSP00000432727:V46M;ENSP00000349084:V46M;ENSP00000400502:V46M;ENSP00000432376:V46M;ENSP00000435564:V46M;ENSP00000379307:V46M;ENSP00000414303:V128M;ENSP00000379304:V46M;ENSP00000435805:V46M;ENSP00000379305:V46M;ENSP00000379302:V46M;ENSP00000432035:V46M;ENSP00000320002:V54M;ENSP00000389564:V46M	ENSP00000320002:V54M	V	-	1	0	BDNF	27636552	0.977000	0.34250	0.957000	0.39632	0.991000	0.79684	0.156000	0.16382	-0.215000	0.10063	-0.142000	0.14014	GTG	C|0.999;T|0.001	0.001	strong		0.547	BDNF-016	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388135.1	NM_170735	
SLC9A3	6550	hgsc.bcm.edu	37	5	491906	491906	+	Silent	SNP	G	G	A	rs6870920	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:491906G>A	ENST00000264938.3	-	2	501	c.492C>T	c.(490-492)ggC>ggT	p.G164G	SLC9A3_ENST00000514375.1_Silent_p.G164G	NM_004174.2	NP_004165.2	P48764	SL9A3_HUMAN	solute carrier family 9, subfamily A (NHE3, cation proton antiporter 3), member 3	164					ion transport (GO:0006811)|regulation of pH (GO:0006885)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|sodium:proton antiporter activity (GO:0015385)			NS(2)|biliary_tract(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|liver(2)|lung(16)|prostate(3)|skin(2)|urinary_tract(1)	37			Epithelial(17;0.000529)|OV - Ovarian serous cystadenocarcinoma(19;0.00153)|all cancers(22;0.00186)|Lung(60;0.0863)			TGAGGAAGACGCCGTAGAGGG	0.672													G|||	181	0.0361422	0.1301	0.0101	5008	,	,		11795	0.0		0.002	False		,,,				2504	0.0				p.G164G		Atlas-SNP	.											SLC9A3,head_neck,malignant_melanoma,-1,1	SLC9A3	89	1	0			c.C492T						PASS	.	G		407,3969		28,351,1809	27.0	20.0	22.0		492	-8.3	0.5	5	dbSNP_116	22	11,8555		0,11,4272	no	coding-synonymous	SLC9A3	NM_004174.2		28,362,6081	AA,AG,GG		0.1284,9.3007,3.2298		164/835	491906	418,12524	2188	4283	6471	SO:0001819	synonymous_variant	6550	exon2			GAAGACGCCGTAG		CCDS3855.1, CCDS64116.1	5p15.3	2013-05-22	2012-03-22		ENSG00000066230	ENSG00000066230		"""Solute carriers"""	11073	protein-coding gene	gene with protein product		182307	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 3"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 3"""	NHE3		8096830	Standard	NM_004174		Approved		uc003jbe.2	P48764	OTTHUMG00000090315	ENST00000264938.3:c.492C>T	5.37:g.491906G>A		81.0	0.0	0		83.0	43.0	0.518072	NM_004174	B7ZKR2|E9PF67|Q3MIW3	Silent	SNP	ENST00000264938.3	37	CCDS3855.1																																																																																			G|0.958;A|0.042	0.042	strong		0.672	SLC9A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206677.2	NM_004174	
PITPNM1	9600	hgsc.bcm.edu	37	11	67267636	67267636	+	Silent	SNP	G	G	A	rs59249357	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:67267636G>A	ENST00000534749.1	-	5	1085	c.897C>T	c.(895-897)gcC>gcT	p.A299A	PITPNM1_ENST00000436757.2_Silent_p.A299A|PITPNM1_ENST00000356404.3_Silent_p.A299A			O00562	PITM1_HUMAN	phosphatidylinositol transfer protein, membrane-associated 1	299					brain development (GO:0007420)|lipid metabolic process (GO:0006629)|phospholipid transport (GO:0015914)|phototransduction (GO:0007602)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lipid particle (GO:0005811)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phosphatidylinositol transporter activity (GO:0008526)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(3)	18						CATCGGGGGAGGCATCTGGGC	0.687													G|||	68	0.0135783	0.0492	0.0043	5008	,	,		14719	0.0		0.0	False		,,,				2504	0.0				p.A299A	GBM(28;144 709 4607 5525)	Atlas-SNP	.											.	PITPNM1	84	.	0			c.C897T						PASS	.						26.0	32.0	30.0					11																	67267636		2172	4257	6429	SO:0001819	synonymous_variant	9600	exon6			GGGGGAGGCATCT	X98654	CCDS31620.1, CCDS44659.1	11q13	2008-07-21		2003-05-16	ENSG00000110697	ENSG00000110697			9003	protein-coding gene	gene with protein product	"""PYK2 N-terminal domain-interacting receptor 2"", ""retinal degeneration B alpha 1"""	608794		PITPNM		9680295	Standard	NM_004910		Approved	DRES9, NIR2, RDGB1, RDGBA1, Rd9, RDGB	uc001oly.3	O00562	OTTHUMG00000167675	ENST00000534749.1:c.897C>T	11.37:g.67267636G>A		15.0	0.0	0		29.0	13.0	0.448276	NM_001130848	A6NME4|Q6T7X3|Q8TBN3|Q9BZ73	Silent	SNP	ENST00000534749.1	37	CCDS31620.1																																																																																			A|0.006;C|0.005;G|0.988	0.006	strong		0.687	PITPNM1-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395520.1	NM_004910	
IGFALS	3483	hgsc.bcm.edu	37	16	1840777	1840777	+	Missense_Mutation	SNP	G	G	A	rs9282731	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1840777G>A	ENST00000215539.3	-	2	1752	c.1642C>T	c.(1642-1644)Cgg>Tgg	p.R548W	IGFALS_ENST00000415638.3_Missense_Mutation_p.R586W			P35858	ALS_HUMAN	insulin-like growth factor binding protein, acid labile subunit	548	LRRCT.		R -> W (in dbSNP:rs9282731).		cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin-like growth factor binding (GO:0005520)			endometrium(2)|lung(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	8						GCGAAGTCCCGCAGCGCCTTG	0.667													G|||	458	0.0914537	0.2837	0.0159	5008	,	,		13459	0.003		0.004	False		,,,				2504	0.0665				p.R586W		Atlas-SNP	.											.	IGFALS	29	.	0			c.C1756T						PASS	.	G	TRP/ARG,TRP/ARG	1035,3305		125,785,1260	21.0	18.0	19.0		1756,1642	-2.2	0.0	16	dbSNP_118	19	14,8548		0,14,4267	yes	missense,missense	IGFALS	NM_001146006.1,NM_004970.2	101,101	125,799,5527	AA,AG,GG		0.1635,23.8479,8.1305	probably-damaging,probably-damaging	586/644,548/606	1840777	1049,11853	2170	4281	6451	SO:0001583	missense	3483	exon2			AGTCCCGCAGCGC	M86826	CCDS10446.1, CCDS53982.1	16p13.3	2008-07-28			ENSG00000099769	ENSG00000099769			5468	protein-coding gene	gene with protein product		601489				1379671, 16114275	Standard	NM_004970		Approved	ALS	uc010uvn.2	P35858	OTTHUMG00000128638	ENST00000215539.3:c.1642C>T	16.37:g.1840777G>A	ENSP00000215539:p.Arg548Trp	103.0	0.0	0		109.0	61.0	0.559633	NM_001146006	B4DZY8|E9PGU3	Missense_Mutation	SNP	ENST00000215539.3	37	CCDS10446.1	124	0.056776556776556776	117	0.23780487804878048	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	G	12.57	1.976387	0.34848	0.238479	0.001635	ENSG00000099769	ENST00000215539;ENST00000415638	T;T	0.25749	1.78;1.78	4.54	-2.24	0.06909	Cysteine-rich flanking region, C-terminal (1);	0.186351	0.45361	N	0.000368	T	0.00012	0.0000	L	0.53780	1.695	0.09310	P	0.9999999850705	B;B	0.33135	0.399;0.399	B;B	0.23275	0.045;0.045	T	0.27571	-1.0070	9	0.40728	T	0.16	.	6.0748	0.19909	0.1844:0.0:0.5355:0.2801	rs9282731;rs9282731	586;548	E9PGU3;P35858	.;ALS_HUMAN	W	548;586	ENSP00000215539:R548W;ENSP00000416683:R586W	ENSP00000215539:R548W	R	-	1	2	IGFALS	1780778	0.001000	0.12720	0.006000	0.13384	0.033000	0.12548	-0.195000	0.09546	-0.354000	0.08212	-0.219000	0.12488	CGG	G|0.909;A|0.091	0.091	strong		0.667	IGFALS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250509.2		
HS3ST2	9956	hgsc.bcm.edu	37	16	22826321	22826321	+	Silent	SNP	G	G	A	rs111703383	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:22826321G>A	ENST00000261374.3	+	1	824	c.390G>A	c.(388-390)gtG>gtA	p.V130V		NM_006043.1	NP_006034.1	Q9Y278	HS3S2_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 2	130					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)		CCCGGGCCGTGCTGGAGTTTA	0.637													G|||	271	0.0541134	0.1959	0.0173	5008	,	,		13590	0.0		0.0	False		,,,				2504	0.0				p.V130V		Atlas-SNP	.											.	HS3ST2	59	.	0			c.G390A						PASS	.	G		724,3626		47,630,1498	15.0	19.0	17.0		390	4.1	1.0	16	dbSNP_132	17	4,8560		0,4,4278	no	coding-synonymous	HS3ST2	NM_006043.1		47,634,5776	AA,AG,GG		0.0467,16.6437,5.6373		130/368	22826321	728,12186	2175	4282	6457	SO:0001819	synonymous_variant	9956	exon1			GGCCGTGCTGGAG	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.390G>A	16.37:g.22826321G>A		106.0	0.0	0		94.0	94.0	1	NM_006043	Q52LZ1	Silent	SNP	ENST00000261374.3	37	CCDS10606.1																																																																																			G|0.949;A|0.051	0.051	strong		0.637	HS3ST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211598.1	NM_006043	
SCAMP5	192683	hgsc.bcm.edu	37	15	75305058	75305058	+	Silent	SNP	G	G	T	rs60910940	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:75305058G>T	ENST00000361900.6	+	4	255	c.48G>T	c.(46-48)ccG>ccT	p.P16P	SCAMP5_ENST00000545456.1_5'UTR|SCAMP5_ENST00000425597.3_Silent_p.P16P|SCAMP5_ENST00000562212.1_Silent_p.P16P|SCAMP5_ENST00000565923.1_3'UTR	NM_001178111.1	NP_001171582.1	Q8TAC9	SCAM5_HUMAN	secretory carrier membrane protein 5	16					exocytosis (GO:0006887)|negative regulation of endocytosis (GO:0045806)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|positive regulation of cytokine secretion (GO:0050715)|protein transport (GO:0015031)|response to endoplasmic reticulum stress (GO:0034976)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|synapse (GO:0045202)|trans-Golgi network membrane (GO:0032588)				large_intestine(1)|lung(1)|ovary(1)|urinary_tract(2)	5						AATTCATCCCGCTGAAGCCAT	0.507													G|||	168	0.0335463	0.1241	0.0043	5008	,	,		19935	0.0		0.001	False		,,,				2504	0.0				p.P16P		Atlas-SNP	.											.	SCAMP5	34	.	0			c.G48T						PASS	.	G	,,	388,3722		14,360,1681	97.0	102.0	101.0		48,48,48	-10.7	0.4	15	dbSNP_129	101	3,8399		0,3,4198	no	coding-synonymous,coding-synonymous,coding-synonymous	SCAMP5	NM_001178111.1,NM_001178112.1,NM_138967.3	,,	14,363,5879	TT,TG,GG		0.0357,9.4404,3.125	,,	16/236,16/236,16/236	75305058	391,12121	2055	4201	6256	SO:0001819	synonymous_variant	192683	exon4			CATCCCGCTGAAG	AL833230	CCDS45306.1	15q24.2	2014-05-20			ENSG00000198794	ENSG00000198794		"""Secretory carrier membrane proteins"""	30386	protein-coding gene	gene with protein product		613766				12477932	Standard	NM_001178111		Approved	MGC24969	uc002azk.2	Q8TAC9	OTTHUMG00000172704	ENST00000361900.6:c.48G>T	15.37:g.75305058G>T		164.0	1.0	0.00609756		167.0	167.0	1	NM_001178111	B3KPJ7|B7Z762|D3DW71|Q8N3M4	Silent	SNP	ENST00000361900.6	37	CCDS45306.1																																																																																			G|0.966;T|0.034	0.034	strong		0.507	SCAMP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420015.2	NM_138967	
SFXN3	81855	hgsc.bcm.edu	37	10	102795819	102795819	+	Missense_Mutation	SNP	A	A	T	rs35361377	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:102795819A>T	ENST00000224807.5	+	5	860	c.404A>T	c.(403-405)aAc>aTc	p.N135I	SFXN3_ENST00000393459.1_Missense_Mutation_p.N131I	NM_030971.3	NP_112233.2	Q9BWM7	SFXN3_HUMAN	sideroflexin 3	135					iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	cation transmembrane transporter activity (GO:0008324)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	9		Colorectal(252;0.234)		Epithelial(162;6.98e-09)|all cancers(201;3.55e-07)		GCCATTGTTAACTACTCCAAC	0.572													A|||	59	0.0117812	0.0431	0.0029	5008	,	,		18920	0.0		0.0	False		,,,				2504	0.0				p.N135I		Atlas-SNP	.											.	SFXN3	19	.	0			c.A404T						PASS	.	A	ILE/ASN	161,4245	109.1+/-147.4	3,155,2045	173.0	153.0	159.0		404	5.4	1.0	10	dbSNP_126	159	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SFXN3	NM_030971.3	149	3,156,6344	TT,TA,AA		0.0116,3.6541,1.2456	probably-damaging	135/326	102795819	162,12844	2203	4300	6503	SO:0001583	missense	81855	exon5			TTGTTAACTACTC	AK074707	CCDS7508.2	10q24.32	2008-09-04			ENSG00000107819	ENSG00000107819		"""Sideroflexins"""	16087	protein-coding gene	gene with protein product		615571					Standard	NM_030971		Approved	SFX3	uc001ksp.3	Q9BWM7	OTTHUMG00000018921	ENST00000224807.5:c.404A>T	10.37:g.102795819A>T	ENSP00000224807:p.Asn135Ile	113.0	0.0	0		116.0	67.0	0.577586	NM_030971	Q8NCJ0|Q9NTP4	Missense_Mutation	SNP	ENST00000224807.5	37	CCDS7508.2	21	0.009615384615384616	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	0	0.0	A	29.2	4.982999	0.93044	0.036541	1.16E-4	ENSG00000107819	ENST00000393459;ENST00000224807	T;T	0.54279	0.58;0.58	5.36	5.36	0.76844	.	0.041188	0.85682	D	0.000000	T	0.54886	0.1886	H	0.96111	3.77	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.996;0.996	T	0.80699	-0.1266	10	0.87932	D	0	-24.293	15.3508	0.74384	1.0:0.0:0.0:0.0	rs35361377	139;135;135	B4DRS6;A6NCZ6;Q9BWM7	.;.;SFXN3_HUMAN	I	131;135	ENSP00000377103:N131I;ENSP00000224807:N135I	ENSP00000224807:N135I	N	+	2	0	SFXN3	102785809	1.000000	0.71417	0.991000	0.47740	0.988000	0.76386	9.329000	0.96413	2.024000	0.59613	0.379000	0.24179	AAC	A|0.986;T|0.014	0.014	strong		0.572	SFXN3-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_030971	
ANKRD24	170961	hgsc.bcm.edu	37	19	4216931	4216931	+	Missense_Mutation	SNP	A	A	G	rs61741405	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4216931A>G	ENST00000600132.1	+	18	2050	c.1774A>G	c.(1774-1776)Aca>Gca	p.T592A	ANKRD24_ENST00000318934.4_Missense_Mutation_p.T592A|ANKRD24_ENST00000262970.5_Missense_Mutation_p.T682A	NM_133475.1	NP_597732.1	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24	592										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0233)|STAD - Stomach adenocarcinoma(1328;0.181)		AGCTGAGGCCACAGGAGCCAA	0.562													A|||	46	0.0091853	0.0325	0.0043	5008	,	,		19640	0.0		0.0	False		,,,				2504	0.0				p.T592A		Atlas-SNP	.											.	ANKRD24	180	.	0			c.A1774G						PASS	.	A	ALA/THR	159,3919		5,149,1885	31.0	36.0	35.0		1774	-6.7	0.0	19	dbSNP_129	35	1,8381		0,1,4190	yes	missense	ANKRD24	NM_133475.1	58	5,150,6075	GG,GA,AA		0.0119,3.899,1.2841	benign	592/1147	4216931	160,12300	2039	4191	6230	SO:0001583	missense	170961	exon18			GAGGCCACAGGAG	AB075861	CCDS45925.1	19p13.3	2013-01-10				ENSG00000089847		"""Ankyrin repeat domain containing"""	29424	protein-coding gene	gene with protein product						11853319	Standard	NM_133475		Approved	KIAA1981	uc010dtt.1	Q8TF21		ENST00000600132.1:c.1774A>G	19.37:g.4216931A>G	ENSP00000471252:p.Thr592Ala	46.0	0.0	0		28.0	16.0	0.571429	NM_133475	O75268|O95781	Missense_Mutation	SNP	ENST00000600132.1	37	CCDS45925.1	27	0.012362637362637362	26	0.052845528455284556	1	0.0027624309392265192	0	0.0	0	0.0	a	2.619	-0.288978	0.05605	0.03899	1.19E-4	ENSG00000089847	ENST00000318934;ENST00000262970	T;T	0.33216	1.47;1.42	3.39	-6.68	0.01778	.	2.468300	0.02265	N	0.067899	T	0.02455	0.0075	N	0.24115	0.695	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.10086	-1.0645	10	0.21540	T	0.41	3.2671	5.3297	0.15926	0.5536:0.0:0.1925:0.2539	rs61741405	592;682	Q8TF21;Q8TF21-2	ANR24_HUMAN;.	A	592;682	ENSP00000321731:T592A;ENSP00000262970:T682A	ENSP00000262970:T682A	T	+	1	0	ANKRD24	4167931	0.000000	0.05858	0.000000	0.03702	0.068000	0.16541	-0.277000	0.08502	-0.988000	0.03489	0.172000	0.16884	ACA	A|0.987;G|0.013	0.013	strong		0.562	ANKRD24-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458188.1	XM_114000	
COPA	1314	hgsc.bcm.edu	37	1	160302298	160302298	+	Missense_Mutation	SNP	T	T	C	rs57425682	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:160302298T>C	ENST00000241704.7	-	6	665	c.436A>G	c.(436-438)Aca>Gca	p.T146A	COPA_ENST00000368069.3_Missense_Mutation_p.T146A	NM_001098398.1|NM_004371.3	NP_001091868.1|NP_004362.2	P53621	COPA_HUMAN	coatomer protein complex, subunit alpha	146					COPI coating of Golgi vesicle (GO:0048205)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|pancreatic juice secretion (GO:0030157)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(2)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(2)	46	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			AAGTCTTCTGTGGGGTGGAAC	0.473													C|||	275	0.0549121	0.177	0.0202	5008	,	,		16356	0.0238		0.0	False		,,,				2504	0.0031				p.T146A		Atlas-SNP	.											.	COPA	181	.	0			c.A436G						PASS	.	C	ALA/THR,ALA/THR	633,3773	767.1+/-413.5	60,513,1630	132.0	118.0	123.0		436,436	3.9	1.0	1	dbSNP_129	123	8,8592	818.9+/-406.8	0,8,4292	yes	missense,missense	COPA	NM_001098398.1,NM_004371.3	58,58	60,521,5922	CC,CT,TT		0.093,14.3668,4.9285	benign,benign	146/1234,146/1225	160302298	641,12365	2203	4300	6503	SO:0001583	missense	1314	exon6			CTTCTGTGGGGTG	U24105	CCDS1202.1, CCDS41424.1	1q23.2	2014-01-30			ENSG00000122218	ENSG00000122218		"""WD repeat domain containing"", ""Endogenous ligands"""	2230	protein-coding gene	gene with protein product	"""proxenin"", ""xenin"""	601924				8647451	Standard	NM_004371		Approved	HEP-COP	uc001fvv.4	P53621	OTTHUMG00000033111	ENST00000241704.7:c.436A>G	1.37:g.160302298T>C	ENSP00000241704:p.Thr146Ala	52.0	0.0	0		50.0	29.0	0.58	NM_001098398	Q5T201|Q8IXZ9	Missense_Mutation	SNP	ENST00000241704.7	37	CCDS1202.1	95	0.043498168498168496	66	0.13414634146341464	9	0.024861878453038673	20	0.03496503496503497	0	0.0	C	13.43	2.233892	0.39498	0.143668	9.3E-4	ENSG00000122218	ENST00000368069;ENST00000241704	T;T	0.59906	0.23;0.23	5.05	3.92	0.45320	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.119729	0.64402	N	0.000017	T	0.26340	0.0643	L	0.39020	1.185	0.42906	P	0.005758999999999959	B;B	0.06786	0.001;0.001	B;B	0.16289	0.012;0.015	T	0.05517	-1.0880	9	0.54805	T	0.06	-2.4504	7.7922	0.29127	0.7177:0.1453:0.0:0.137	rs57425682;rs61739741	146;146	P53621;P53621-2	COPA_HUMAN;.	A	146	ENSP00000357048:T146A;ENSP00000241704:T146A	ENSP00000241704:T146A	T	-	1	0	COPA	158568922	1.000000	0.71417	0.999000	0.59377	0.678000	0.39670	4.802000	0.62539	0.403000	0.25479	-1.641000	0.00772	ACA	T|0.956;C|0.044	0.044	strong		0.473	COPA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080638.1	NM_004371	
ELMOD1	55531	hgsc.bcm.edu	37	11	107501428	107501428	+	Missense_Mutation	SNP	A	A	T	rs201717101	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:107501428A>T	ENST00000265840.7	+	4	431	c.166A>T	c.(166-168)Aca>Tca	p.T56S	ELMOD1_ENST00000531234.1_Missense_Mutation_p.T50S|ELMOD1_ENST00000443271.2_Missense_Mutation_p.T56S	NM_018712.3	NP_061182.3	Q8N336	ELMD1_HUMAN	ELMO/CED-12 domain containing 1	56					phagocytosis (GO:0006909)|positive regulation of GTPase activity (GO:0043547)	cytoskeleton (GO:0005856)	GTPase activator activity (GO:0005096)			endometrium(2)|large_intestine(5)|liver(2)|lung(7)|pancreas(2)|prostate(1)	19		Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00304)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)|Epithelial(105;0.00027)|all cancers(92;0.00481)		TTTCACAGAAACATCACTGAG	0.313													A|||	6	0.00119808	0.0045	0.0	5008	,	,		19465	0.0		0.0	False		,,,				2504	0.0				p.T56S		Atlas-SNP	.											.	ELMOD1	40	.	0			c.A166T						PASS	.	A	SER/THR,SER/THR	8,3684		0,8,1838	93.0	89.0	90.0		166,166	3.2	1.0	11		90	0,8158		0,0,4079	yes	missense,missense	ELMOD1	NM_001130037.1,NM_018712.3	58,58	0,8,5917	TT,TA,AA		0.0,0.2167,0.0675	benign,benign	56/327,56/335	107501428	8,11842	1846	4079	5925	SO:0001583	missense	55531	exon4			ACAGAAACATCAC	AL359601	CCDS44723.1, CCDS44724.1	11q23.1	2012-10-15	2006-01-20		ENSG00000110675	ENSG00000110675			25334	protein-coding gene	gene with protein product		615456	"""ELMO domain containing 1"""			12477932	Standard	NM_018712		Approved	DKFZp547C176	uc010rvs.2	Q8N336	OTTHUMG00000166361	ENST00000265840.7:c.166A>T	11.37:g.107501428A>T	ENSP00000265840:p.Thr56Ser	122.0	0.0	0		152.0	58.0	0.381579	NM_018712	B4E167|G5E9S5|Q9NPW3	Missense_Mutation	SNP	ENST00000265840.7	37	CCDS44723.1	.	.	.	.	.	.	.	.	.	.	A	10.08	1.251659	0.22880	0.002167	0.0	ENSG00000110675	ENST00000531234;ENST00000265840;ENST00000443271	.	.	.	5.62	3.19	0.36642	.	0.250304	0.42294	D	0.000737	T	0.09686	0.0238	N	0.01277	-0.915	0.30939	N	0.726031	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.20538	-1.0272	9	0.08381	T	0.77	.	4.3202	0.11013	0.5821:0.0:0.178:0.2399	.	56;56	Q8N336;G5E9S5	ELMD1_HUMAN;.	S	50;56;56	.	ENSP00000265840:T56S	T	+	1	0	ELMOD1	107006638	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	1.228000	0.32588	0.957000	0.37930	0.533000	0.62120	ACA	.	.	weak		0.313	ELMOD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389406.1	NM_018712	
DCC	1630	hgsc.bcm.edu	37	18	50705370	50705370	+	Missense_Mutation	SNP	A	A	T	rs116498325	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:50705370A>T	ENST00000442544.2	+	9	2073	c.1457A>T	c.(1456-1458)cAg>cTg	p.Q486L	DCC_ENST00000581580.1_Missense_Mutation_p.Q141L|DCC_ENST00000412726.1_Missense_Mutation_p.Q334L	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	486	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		GGGTCCCTTCAGCTCACTGTG	0.463													A|||	15	0.00299521	0.0106	0.0014	5008	,	,		16535	0.0		0.0	False		,,,				2504	0.0				p.Q486L		Atlas-SNP	.											.	DCC	360	.	0			c.A1457T						PASS	.	A	LEU/GLN	43,4363	46.0+/-80.4	1,41,2161	100.0	90.0	94.0		1457	5.6	1.0	18	dbSNP_132	94	0,8600		0,0,4300	yes	missense	DCC	NM_005215.3	113	1,41,6461	TT,TA,AA		0.0,0.9759,0.3306	possibly-damaging	486/1448	50705370	43,12963	2203	4300	6503	SO:0001583	missense	1630	exon9			CCCTTCAGCTCAC	X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2701	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 1"""	120470	"""deleted in colorectal carcinoma"""			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.1457A>T	18.37:g.50705370A>T	ENSP00000389140:p.Gln486Leu	107.0	0.0	0		164.0	78.0	0.47561	NM_005215		Missense_Mutation	SNP	ENST00000442544.2	37	CCDS11952.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	A	15.68	2.903669	0.52333	0.009759	0.0	ENSG00000187323	ENST00000442544;ENST00000304775;ENST00000412726	T;T	0.57752	0.38;0.38	5.62	5.62	0.85841	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.076791	0.52532	D	0.000063	T	0.63534	0.2519	M	0.72894	2.215	0.53688	D	0.999971	P;P;D	0.58970	0.769;0.769;0.984	P;P;D	0.65874	0.593;0.593;0.939	T	0.71533	-0.4564	10	0.87932	D	0	.	15.0981	0.72250	1.0:0.0:0.0:0.0	.	334;334;486	E7EQM8;B4DYX2;P43146	.;.;DCC_HUMAN	L	486;419;334	ENSP00000389140:Q486L;ENSP00000397322:Q334L	ENSP00000304146:Q419L	Q	+	2	0	DCC	48959368	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	8.534000	0.90620	2.266000	0.75297	0.533000	0.62120	CAG	A|0.996;T|0.004	0.004	strong		0.463	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215	
ETAA1	54465	hgsc.bcm.edu	37	2	67624739	67624739	+	Silent	SNP	C	C	A	rs182131786	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:67624739C>A	ENST00000272342.5	+	1	289	c.159C>A	c.(157-159)ccC>ccA	p.P53P		NM_019002.3	NP_061875.2	Q9NY74	ETAA1_HUMAN	Ewing tumor-associated antigen 1	53						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	33						AGGGGCCTCCCGGGCCAGTGC	0.721													C|||	5	0.000998403	0.0038	0.0	5008	,	,		11612	0.0		0.0	False		,,,				2504	0.0				p.P53P		Atlas-SNP	.											ETAA1,colon,carcinoma,+2,1	ETAA1	88	1	0			c.C159A						PASS	.	C		10,4090		0,10,2040	5.0	7.0	6.0		159	-0.4	0.0	2		6	1,8047		0,1,4023	no	coding-synonymous	ETAA1	NM_019002.3		0,11,6063	AA,AC,CC		0.0124,0.2439,0.0905		53/927	67624739	11,12137	2050	4024	6074	SO:0001819	synonymous_variant	54465	exon1			GCCTCCCGGGCCA	AJ242682	CCDS1882.1	2p14	2014-02-12	2007-10-04		ENSG00000143971	ENSG00000143971			24648	protein-coding gene	gene with protein product		613196	"""Ewing's tumor-associated antigen 1"""			16003559	Standard	XM_005264374		Approved	ETAA16	uc002sdz.1	Q9NY74	OTTHUMG00000129545	ENST00000272342.5:c.159C>A	2.37:g.67624739C>A		12.0	0.0	0		33.0	23.0	0.69697	NM_019002	Q05BT7|Q53SC4	Silent	SNP	ENST00000272342.5	37	CCDS1882.1																																																																																			C|0.999;A|0.001	0.001	strong		0.721	ETAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251735.1	NM_019002	
FAT2	2196	hgsc.bcm.edu	37	5	150946444	150946444	+	Silent	SNP	G	G	A	rs142348925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:150946444G>A	ENST00000261800.5	-	1	2061	c.2049C>T	c.(2047-2049)atC>atT	p.I683I		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	683					epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TAAAGTGGAGGATAGTCTTTG	0.408													G|||	2	0.000399361	0.0015	0.0	5008	,	,		22771	0.0		0.0	False		,,,				2504	0.0				p.I683I		Atlas-SNP	.											.	FAT2	465	.	0			c.C2049T						PASS	.	G		6,4400	11.4+/-27.6	0,6,2197	117.0	110.0	112.0		2049	2.8	1.0	5	dbSNP_134	112	0,8600		0,0,4300	no	coding-synonymous	FAT2	NM_001447.2		0,6,6497	AA,AG,GG		0.0,0.1362,0.0461		683/4350	150946444	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon1			GTGGAGGATAGTC	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.2049C>T	5.37:g.150946444G>A		132.0	0.0	0		220.0	98.0	0.445455	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																			G|0.999;A|0.001	0.001	strong		0.408	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
COX7B	1349	hgsc.bcm.edu	37	X	77158147	77158147	+	Missense_Mutation	SNP	C	C	A	rs61752458	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:77158147C>A	ENST00000481445.1	+	2	164	c.48C>A	c.(46-48)agC>agA	p.S16R	COX7B_ENST00000475465.1_3'UTR	NM_001866.2	NP_001857.1	P24311	COX7B_HUMAN	cytochrome c oxidase subunit VIIb	16					cellular metabolic process (GO:0044237)|central nervous system development (GO:0007417)|hydrogen ion transmembrane transport (GO:1902600)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)	cytochrome-c oxidase activity (GO:0004129)			endometrium(2)	2						AAGTTCGAAGCATTCAGCAAA	0.388													C|||	49	0.0129801	0.0356	0.0029	3775	,	,		15718	0.0		0.0	False		,,,				2504	0.0				p.S16R		Atlas-SNP	.											.	COX7B	8	.	0			c.C48A						PASS	.	C	ARG/SER	101,3734		1,83,16,1548,555	138.0	107.0	118.0		48	3.1	1.0	X	dbSNP_129	118	0,6728		0,0,0,2428,1872	yes	missense	COX7B	NM_001866.2	110	1,83,16,3976,2427	AA,AC,A,CC,C		0.0,2.6336,0.9562	benign	16/81	77158147	101,10462	2203	4300	6503	SO:0001583	missense	1349	exon2			TCGAAGCATTCAG	Z14244	CCDS14437.1	Xq21.1	2011-07-04			ENSG00000131174	ENSG00000131174		"""Mitochondrial respiratory chain complex / Complex IV"""	2291	protein-coding gene	gene with protein product		300885				8382530	Standard	NM_001866		Approved		uc004ecu.1	P24311	OTTHUMG00000022718	ENST00000481445.1:c.48C>A	X.37:g.77158147C>A	ENSP00000417656:p.Ser16Arg	78.0	0.0	0		87.0	42.0	0.482759	NM_001866	B2R4M3|Q6ICR1	Missense_Mutation	SNP	ENST00000481445.1	37	CCDS14437.1	11	0.006630500301386378	4	0.008298755186721992	1	0.002777777777777778	0	0.0	0	0.0	C	17.45	3.392912	0.62066	0.026336	0.0	ENSG00000131174	ENST00000481445	T	0.48836	0.8	4.92	3.13	0.36017	.	0.349121	0.32401	N	0.006153	T	0.29288	0.0729	.	.	.	0.40351	P	0.02086100000000002	P	0.43542	0.81	P	0.53062	0.717	T	0.56619	-0.7949	8	0.52906	T	0.07	-0.0019	6.4067	0.21668	0.1816:0.7202:0.0:0.0982	rs61752458	16	P24311	COX7B_HUMAN	R	16	ENSP00000417656:S16R	ENSP00000417656:S16R	S	+	3	2	COX7B	77044803	1.000000	0.71417	0.997000	0.53966	0.814000	0.46013	0.699000	0.25586	0.330000	0.23485	0.523000	0.50628	AGC	C|0.991;A|0.009	0.009	strong		0.388	COX7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058970.1	NM_001866	
ITPRIPL2	162073	hgsc.bcm.edu	37	16	19126492	19126492	+	Missense_Mutation	SNP	T	T	A	rs8051801	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:19126492T>A	ENST00000381440.3	+	1	1239	c.709T>A	c.(709-711)Tgc>Agc	p.C237S	CTD-2349B8.1_ENST00000564808.2_Intron	NM_001034841.3	NP_001030013.1	Q3MIP1	IPIL2_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein-like 2	237			C -> S (in dbSNP:rs8051801).			integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						TGATGCCTTCTGCGTGGATGT	0.657											OREG0023657	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	43	0.00858626	0.0325	0.0	5008	,	,		17049	0.0		0.0	False		,,,				2504	0.0				p.C237S		Atlas-SNP	.											.	ITPRIPL2	40	.	0			c.T709A						PASS	.	T	SER/CYS	146,4248	100.7+/-139.4	3,140,2054	74.0	78.0	77.0		709	4.7	1.0	16	dbSNP_116	77	0,8600		0,0,4300	yes	missense	ITPRIPL2	NM_001034841.3	112	3,140,6354	AA,AT,TT		0.0,3.3227,1.1236	probably-damaging	237/536	19126492	146,12848	2197	4300	6497	SO:0001583	missense	162073	exon1			GCCTTCTGCGTGG		CCDS32395.1	16p12.3	2011-04-28	2011-04-28		ENSG00000205730	ENSG00000205730			27257	protein-coding gene	gene with protein product			"""inositol 1,4,5-triphosphate receptor interacting protein-like 2"""				Standard	NM_001034841		Approved	FLJ22994, MGC126798, MGC126800, LOC162073	uc002dfu.4	Q3MIP1		ENST00000381440.3:c.709T>A	16.37:g.19126492T>A	ENSP00000370849:p.Cys237Ser	86.0	0.0	0	730	85.0	36.0	0.423529	NM_001034841		Missense_Mutation	SNP	ENST00000381440.3	37	CCDS32395.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	T	22.2	4.253591	0.80135	0.033227	0.0	ENSG00000205730	ENST00000381440	T	0.16597	2.33	4.71	4.71	0.59529	.	0.382932	0.21183	U	0.078791	T	0.10895	0.0266	L	0.27053	0.805	0.46521	D	0.999086	D	0.71674	0.998	D	0.78314	0.991	T	0.01452	-1.1351	10	0.72032	D	0.01	-13.7638	13.3495	0.60593	0.0:0.0:0.0:1.0	rs8051801;rs8051801	237	Q3MIP1	IPIL2_HUMAN	S	237	ENSP00000370849:C237S	ENSP00000370849:C237S	C	+	1	0	ITPRIPL2	19033993	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.264000	0.58859	1.743000	0.51761	0.533000	0.62120	TGC	T|0.989;A|0.011	0.011	strong		0.657	ITPRIPL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435827.3	NM_001034841	
NOL8	55035	hgsc.bcm.edu	37	9	95077498	95077498	+	Missense_Mutation	SNP	C	C	T	rs58545014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95077498C>T	ENST00000535387.1	-	6	1408	c.1409G>A	c.(1408-1410)gGa>gAa	p.G470E	NOL8_ENST00000542053.1_Missense_Mutation_p.G402E|NOL8_ENST00000545558.1_Missense_Mutation_p.G470E|NOL8_ENST00000358855.4_Missense_Mutation_p.G402E|NOL8_ENST00000442668.2_Missense_Mutation_p.G470E					nucleolar protein 8											endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						CTCCTCACCTCCTTCAGAGTC	0.433													C|||	166	0.033147	0.1172	0.0159	5008	,	,		20446	0.0		0.0	False		,,,				2504	0.0				p.G470E		Atlas-SNP	.											.	NOL8	118	.	0			c.G1409A						PASS	.	C	GLU/GLY	379,3445		15,349,1548	67.0	62.0	63.0		1409	-2.3	0.0	9	dbSNP_129	63	9,8283		0,9,4137	yes	missense	NOL8	NM_017948.5	98	15,358,5685	TT,TC,CC		0.1085,9.9111,3.2024	benign	470/1168	95077498	388,11728	1912	4146	6058	SO:0001583	missense	55035	exon7			TCACCTCCTTCAG	AB109030	CCDS47993.1, CCDS59135.1	9q22.32	2013-02-12	2004-01-12	2004-01-14	ENSG00000198000	ENSG00000198000		"""RNA binding motif (RRM) containing"""	23387	protein-coding gene	gene with protein product		611534	"""chromosome 9 open reading frame 34"""	C9orf34		12477932	Standard	NM_017948		Approved	FLJ20736, Nop132	uc022bjx.1	Q76FK4	OTTHUMG00000020221	ENST00000535387.1:c.1409G>A	9.37:g.95077498C>T	ENSP00000441300:p.Gly470Glu	178.0	0.0	0		161.0	118.0	0.732919	NM_017948		Missense_Mutation	SNP	ENST00000535387.1	37	CCDS47993.1	73	0.033424908424908424	67	0.13617886178861788	6	0.016574585635359115	0	0.0	0	0.0	C	2.889	-0.230150	0.05983	0.099111	0.001085	ENSG00000198000	ENST00000442668;ENST00000375594;ENST00000358855;ENST00000545558;ENST00000535387;ENST00000542053;ENST00000432670	T;T;T;T;T;T	0.15256	2.71;2.7;2.71;2.93;2.7;2.44	5.69	-2.34	0.06704	.	1.014810	0.07869	N	0.967526	T	0.00039	0.0001	N	0.16656	0.425	0.80722	P	0.0	B	0.15141	0.012	B	0.11329	0.006	T	0.41124	-0.9526	9	0.10377	T	0.69	-5.5238	1.3463	0.02164	0.171:0.3053:0.1593:0.3644	rs58545014;rs61740235	470	Q76FK4	NOL8_HUMAN	E	470;472;402;470;470;402;470	ENSP00000401177:G470E;ENSP00000351723:G402E;ENSP00000441140:G470E;ENSP00000441300:G470E;ENSP00000440709:G402E;ENSP00000414112:G470E	ENSP00000351723:G402E	G	-	2	0	NOL8	94117319	0.000000	0.05858	0.000000	0.03702	0.182000	0.23217	-1.648000	0.01995	-0.302000	0.08869	-0.345000	0.07892	GGA	C|0.972;T|0.028	0.028	strong		0.433	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948	
RPGR	6103	hgsc.bcm.edu	37	X	38145715	38145715	+	Intron	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:38145715T>C	ENST00000339363.3	-	14	2688				RPGR_ENST00000378505.2_Missense_Mutation_p.E846G|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000309513.3_Intron|RPGR_ENST00000318842.7_Intron|RPGR_ENST00000342811.3_Intron|RPGR_ENST00000338898.3_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						cccctccccttcctcctcttc	0.602																																					p.E846G		Atlas-SNP	.											.	RPGR	175	.	0			c.A2537G						PASS	.						39.0	26.0	31.0					X																	38145715		1741	3341	5082	SO:0001627	intron_variant	6103	exon15			TCCCCTTCCTCCT	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+631A>G	X.37:g.38145715T>C		113.0	0.0	0		115.0	8.0	0.0695652	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Missense_Mutation	SNP	ENST00000339363.3	37		.	.	.	.	.	.	.	.	.	.	t	5.065	0.197625	0.09652	.	.	ENSG00000156313	ENST00000378505	T	0.02525	4.26	1.54	1.54	0.23209	.	1.854680	0.04946	U	0.459387	T	0.04137	0.0115	L	0.50333	1.59	0.45676	D	0.998598	B	0.13594	0.008	B	0.06405	0.002	T	0.32745	-0.9895	10	0.66056	D	0.02	.	4.6898	0.12776	0.0:0.1904:0.0:0.8096	.	846	E9PE28	.	G	846	ENSP00000367766:E846G	ENSP00000367766:E846G	E	-	2	0	RPGR	38030659	0.004000	0.15560	0.004000	0.12327	0.000000	0.00434	0.336000	0.19823	0.671000	0.31185	0.000000	0.15137	GAA	.	.	none		0.602	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
BAIAP3	8938	hgsc.bcm.edu	37	16	1391362	1391362	+	Silent	SNP	A	A	G	rs75271587	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1391362A>G	ENST00000324385.5	+	8	866	c.708A>G	c.(706-708)gcA>gcG	p.A236A	BAIAP3_ENST00000421665.2_Silent_p.A201A|BAIAP3_ENST00000426824.3_Silent_p.A201A|BAIAP3_ENST00000568887.1_Silent_p.A173A|BAIAP3_ENST00000397489.1_Silent_p.A218A|BAIAP3_ENST00000397488.2_Silent_p.A218A|BAIAP3_ENST00000562208.1_Silent_p.A178A	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	236	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				G-protein coupled receptor signaling pathway (GO:0007186)|neurotransmitter secretion (GO:0007269)		protein C-terminus binding (GO:0008022)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(25)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42		Hepatocellular(780;0.0893)				AGCCCCGTGCACAGAAGGAGC	0.682													G|||	52	0.0103834	0.0386	0.0014	5008	,	,		17448	0.0		0.0	False		,,,				2504	0.0				p.A236A		Atlas-SNP	.											.	BAIAP3	88	.	0			c.A708G						PASS	.	G	,,,,	126,4260		1,124,2068	37.0	36.0	36.0		603,603,534,519,708	-5.2	0.0	16	dbSNP_131	36	0,8590		0,0,4295	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BAIAP3	NM_001199096.1,NM_001199097.1,NM_001199098.1,NM_001199099.1,NM_003933.4	,,,,	1,124,6363	GG,GA,AA		0.0,2.8728,0.971	,,,,	201/1117,201/1153,178/1130,173/1125,236/1188	1391362	126,12850	2193	4295	6488	SO:0001819	synonymous_variant	8938	exon8			CCGTGCACAGAAG	AB017111	CCDS10434.1, CCDS55978.1, CCDS55979.1, CCDS58402.1, CCDS58403.1, CCDS66894.1	16p13.3	2008-07-04			ENSG00000007516	ENSG00000007516			948	protein-coding gene	gene with protein product		604009				9790924	Standard	NM_003933		Approved	BAP3, KIAA0734	uc002clk.2	O94812	OTTHUMG00000047833	ENST00000324385.5:c.708A>G	16.37:g.1391362A>G		74.0	0.0	0		53.0	24.0	0.45283	NM_003933	A2A2B2|B2RCD7|B4DGS5|B4DIK3|B4DRK9|B4DRP1|E7EUB9|H3BUH8|H3BVI3|H7C2Q1|O94839|Q2M226|Q658J2|Q76N05|Q96RZ3|Q9UJK1	Silent	SNP	ENST00000324385.5	37	CCDS10434.1																																																																																			A|0.988;G|0.012	0.012	strong		0.682	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3		
KDR	3791	hgsc.bcm.edu	37	4	55956183	55956183	+	Silent	SNP	G	G	T	rs145298133	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:55956183G>T	ENST00000263923.4	-	23	3427	c.3132C>A	c.(3130-3132)atC>atA	p.I1044I	RP11-530I17.1_ENST00000511222.1_RNA	NM_002253.2	NP_002244.1	P35968	VGFR2_HUMAN	kinase insert domain receptor (a type III receptor tyrosine kinase)	1044	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion homeostasis (GO:0055074)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|cell fate commitment (GO:0045165)|cell maturation (GO:0048469)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic hemopoiesis (GO:0035162)|endothelial cell differentiation (GO:0045446)|endothelium development (GO:0003158)|extracellular matrix organization (GO:0030198)|lung alveolus development (GO:0048286)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine autophosphorylation (GO:0038083)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vasculogenesis (GO:2001214)|protein autophosphorylation (GO:0046777)|regulation of cell shape (GO:0008360)|signal transduction by phosphorylation (GO:0023014)|surfactant homeostasis (GO:0043129)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sorting endosome (GO:0097443)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|Hsp90 protein binding (GO:0051879)|integrin binding (GO:0005178)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(16)|lung(71)|ovary(2)|prostate(2)|skin(10)|soft_tissue(4)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	135	all_cancers(7;0.0255)|all_lung(4;0.00175)|Lung NSC(11;0.00384)|all_epithelial(27;0.034)|Glioma(25;0.08)|all_neural(26;0.101)		Epithelial(7;0.189)		Axitinib(DB06626)|Cabozantinib(DB08875)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CAAAGTCACAGATTTTAACCA	0.428			Mis		"""NSCLC, angiosarcoma"""					TSP Lung(20;0.16)			G|||	3	0.000599042	0.0023	0.0	5008	,	,		18361	0.0		0.0	False		,,,				2504	0.0				p.I1044I		Atlas-SNP	.		Dom	yes		4	4q11-q12	3791	vascular endothelial growth factor receptor 2		E	.	KDR	307	.	0			c.C3132A						PASS	.	G		10,4396	16.8+/-37.8	0,10,2193	94.0	93.0	94.0		3132	5.7	1.0	4	dbSNP_134	94	0,8600		0,0,4300	no	coding-synonymous	KDR	NM_002253.2		0,10,6493	TT,TG,GG		0.0,0.227,0.0769		1044/1357	55956183	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	3791	exon23			GTCACAGATTTTA	AF035121	CCDS3497.1	4q11-q12	2013-01-29			ENSG00000128052	ENSG00000128052	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6307	protein-coding gene	gene with protein product		191306				1417831	Standard	NM_002253		Approved	FLK1, VEGFR, VEGFR2, CD309	uc003has.3	P35968	OTTHUMG00000128734	ENST00000263923.4:c.3132C>A	4.37:g.55956183G>T		68.0	0.0	0		80.0	28.0	0.35	NM_002253	A2RRS0|B5A925|C5IFA0|O60723|Q14178	Silent	SNP	ENST00000263923.4	37	CCDS3497.1																																																																																			G|0.999;T|0.001	0.001	strong		0.428	KDR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250645.1		
GH2	2689	hgsc.bcm.edu	37	17	61957610	61957610	+	3'UTR	SNP	G	G	T	rs58696130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:61957610G>T	ENST00000423893.2	-	0	786				GH2_ENST00000456543.2_Missense_Mutation_p.P241T|GH2_ENST00000332800.7_3'UTR|GH2_ENST00000449787.2_3'UTR			P01242	SOM2_HUMAN	growth hormone 2						JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			breast(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)	24						AAGGCTGGTGGGCACTGGAGT	0.552													G|||	144	0.028754	0.1044	0.0072	5008	,	,		19214	0.0		0.001	False		,,,				2504	0.0				p.P241T		Atlas-SNP	.											.	GH2	73	.	0			c.C721A						PASS	.	G	,,,THR/PRO	304,2350		17,270,1040	36.0	38.0	37.0		,,,721	0.8	0.0	17	dbSNP_129	37	1,4617		0,1,2308	yes	utr-3,utr-3,utr-3,missense	GH2	NM_002059.3,NM_022556.2,NM_022557.2,NM_022558.2	,,,38	17,271,3348	TT,TG,GG		0.0217,11.4544,4.1942	,,,	,,,241/246	61957610	305,6967	1327	2309	3636	SO:0001624	3_prime_UTR_variant	2689	exon5			CTGGTGGGCACTG	J03756	CCDS11647.1, CCDS11648.1, CCDS45757.1, CCDS45758.1	17q22-q24	2014-01-30						"""Endogenous ligands"""	4262	protein-coding gene	gene with protein product	"""placental-specific growth hormone"", ""placenta-specific growth hormone"""	139240				6306568	Standard	NM_002059		Approved	GH-V, GHV, GHL, hGH-V	uc002jcl.2	P01242		ENST00000423893.2:c.*71C>A	17.37:g.61957610G>T		82.0	0.0	0		132.0	71.0	0.537879	NM_022558	B1A4H5|B1A4H7|O14643|O14644|P09587	Missense_Mutation	SNP	ENST00000423893.2	37	CCDS11647.1	35	0.016025641025641024	34	0.06910569105691057	1	0.0027624309392265192	0	0.0	0	0.0	g	10.77	1.444668	0.25987	0.114544	2.17E-4	ENSG00000136487	ENST00000456543	D	0.89552	-2.53	1.79	0.797	0.18654	.	.	.	.	.	T	0.06735	0.0172	N	0.24115	0.695	0.09310	N	1	B	0.14012	0.009	B	0.09377	0.004	T	0.45279	-0.9272	9	0.87932	D	0	.	4.4826	0.11774	0.2024:0.0:0.7976:0.0	rs58696130;rs61764021	241	O14644	.	T	241	ENSP00000394122:P241T	ENSP00000394122:P241T	P	-	1	0	GH2	59311342	0.006000	0.16342	0.002000	0.10522	0.048000	0.14542	0.969000	0.29370	0.321000	0.23259	-0.699000	0.03677	CCA	G|0.983;T|0.017	0.017	strong		0.552	GH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417665.1	NM_002059	
GPC3	2719	hgsc.bcm.edu	37	X	132670269	132670269	+	Silent	SNP	T	T	C	rs61754631	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:132670269T>C	ENST00000370818.3	-	8	2071	c.1626A>G	c.(1624-1626)gcA>gcG	p.A542A	GPC3_ENST00000394299.2_Silent_p.A565A|GPC3_ENST00000543339.1_Silent_p.A488A	NM_001164618.1|NM_004484.3	NP_001158090.1|NP_004475.1	P51654	GPC3_HUMAN	glypican 3	542					anatomical structure morphogenesis (GO:0009653)|anterior/posterior axis specification (GO:0009948)|body morphogenesis (GO:0010171)|bone mineralization (GO:0030282)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cell proliferation involved in metanephros development (GO:0072203)|chondroitin sulfate metabolic process (GO:0030204)|coronary vasculature development (GO:0060976)|embryonic hindlimb morphogenesis (GO:0035116)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lung development (GO:0030324)|mesenchymal cell proliferation involved in ureteric bud development (GO:0072138)|mesonephric duct morphogenesis (GO:0072180)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of growth (GO:0045926)|negative regulation of smoothened signaling pathway (GO:0045879)|osteoclast differentiation (GO:0030316)|phototransduction, visible light (GO:0007603)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of endocytosis (GO:0045807)|positive regulation of glucose import (GO:0046326)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of plasma membrane (GO:0046658)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	peptidyl-dipeptidase inhibitor activity (GO:0060422)			breast(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|prostate(1)|skin(2)	36	Acute lymphoblastic leukemia(192;0.000127)					CCTTCGGAGTTGCCTGCTGAC	0.502			"""T, D, Mis, N, F, S"""			Wilms tumour			Simpson-Golabi-Behmel syndrome				C|||	203	0.0537748	0.1505	0.0058	3775	,	,		12135	0.0		0.0	False		,,,				2504	0.0				p.A565A		Atlas-SNP	.	yes	Rec/X		Simpson-Golabi-Behmel syndrome	X	Xq26.1	2719	glypican 3		O	.	GPC3	88	.	0			c.A1695G						PASS	.	C	,,,	741,3094		68,494,111,1070,460	274.0	217.0	236.0		1695,1578,1464,1626	2.1	0.0	X	dbSNP_129	236	5,6723		0,2,3,2426,1869	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GPC3	NM_001164617.1,NM_001164618.1,NM_001164619.1,NM_004484.3	,,,	68,496,114,3496,2329	CC,CT,C,TT,T		0.0743,19.322,7.0624	,,,	565/604,526/565,488/527,542/581	132670269	746,9817	2203	4300	6503	SO:0001819	synonymous_variant	2719	exon9	Familial Cancer Database	SGBS	CGGAGTTGCCTGC	L47125	CCDS14638.1, CCDS55496.1	Xq26	2014-09-17			ENSG00000147257	ENSG00000147257		"""Proteoglycans / Cell Surface : Glypicans"""	4451	protein-coding gene	gene with protein product	"""glypican proteoglycan 3"""	300037		SDYS		8589713, 9787072	Standard	NM_004484		Approved	OCI-5, SGBS, SGBS1, SGB, DGSX	uc010nrn.2	P51654	OTTHUMG00000022448	ENST00000370818.3:c.1626A>G	X.37:g.132670269T>C		172.0	0.0	0		193.0	119.0	0.61658	NM_001164617	C9JLE3|G3V1R0|Q2L880|Q2L882	Silent	SNP	ENST00000370818.3	37	CCDS14638.1																																																																																			T|0.927;C|0.073	0.073	strong		0.502	GPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058356.1	NM_004484	
DPY19L2	283417	hgsc.bcm.edu	37	12	64057543	64057543	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:64057543C>T	ENST00000324472.4	-	3	628	c.445G>A	c.(445-447)Gaa>Aaa	p.E149K	RP11-415I12.3_ENST00000509615.2_RNA	NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	149					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	transferase activity, transferring glycosyl groups (GO:0016757)	p.E149*(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	45			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		CTAACCATTTCAGTGCGAAAA	0.333																																					p.E149K		Atlas-SNP	.											DPY19L2,caecum,carcinoma,0,1	DPY19L2	97	1	1	Substitution - Nonsense(1)	large_intestine(1)	c.G445A						scavenged	.						58.0	55.0	56.0					12																	64057543		2203	4299	6502	SO:0001583	missense	283417	exon3			CCATTTCAGTGCG		CCDS31851.1	12q14.2	2012-11-14			ENSG00000177990	ENSG00000177990			19414	protein-coding gene	gene with protein product	"""spermatogenesis associated 34"""	613893				12975309	Standard	XM_006719348		Approved	FLJ32949, SPATA34	uc001srp.1	Q6NUT2	OTTHUMG00000168712	ENST00000324472.4:c.445G>A	12.37:g.64057543C>T	ENSP00000315988:p.Glu149Lys	317.0	0.0	0		344.0	21.0	0.0610465	NM_173812	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Missense_Mutation	SNP	ENST00000324472.4	37	CCDS31851.1	.	.	.	.	.	.	.	.	.	.	C	15.97	2.990830	0.54041	.	.	ENSG00000177990	ENST00000324472;ENST00000538147	T;T	0.68331	-0.32;-0.32	2.5	2.5	0.30297	.	0.000000	0.85682	U	0.000000	T	0.81230	0.4779	M	0.86740	2.835	0.80722	D	1	D	0.76494	0.999	D	0.76071	0.987	T	0.83031	-0.0162	9	.	.	.	.	10.7323	0.46104	0.0:1.0:0.0:0.0	.	149	Q6NUT2	D19L2_HUMAN	K	149;6	ENSP00000315988:E149K;ENSP00000439567:E6K	.	E	-	1	0	DPY19L2	62343810	1.000000	0.71417	0.999000	0.59377	0.753000	0.42808	6.967000	0.76079	1.389000	0.46526	0.184000	0.17185	GAA	.	.	none		0.333	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400689.2	NM_173812	
MTUS1	57509	hgsc.bcm.edu	37	8	17612064	17612064	+	Missense_Mutation	SNP	A	A	C	rs75253845	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:17612064A>C	ENST00000262102.6	-	2	1477	c.1253T>G	c.(1252-1254)aTg>aGg	p.M418R	MTUS1_ENST00000381869.3_Missense_Mutation_p.M418R|MTUS1_ENST00000519263.1_Missense_Mutation_p.M418R|MTUS1_ENST00000381862.3_Missense_Mutation_p.M418R	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	418					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		GCTAATGACCATATCATTTGC	0.443													A|||	134	0.0267572	0.0991	0.0043	5008	,	,		19985	0.0		0.0	False		,,,				2504	0.0				p.M418R		Atlas-SNP	.											.	MTUS1	144	.	0			c.T1253G						PASS	.	A	ARG/MET,ARG/MET	262,3548		9,244,1652	97.0	92.0	93.0		1253,1253	-3.9	0.0	8	dbSNP_131	93	0,8240		0,0,4120	yes	missense,missense	MTUS1	NM_001001924.2,NM_001001925.2	91,91	9,244,5772	CC,CA,AA		0.0,6.8766,2.1743	benign,benign	418/1271,418/1217	17612064	262,11788	1905	4120	6025	SO:0001583	missense	57509	exon2			ATGACCATATCAT	AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"""AT2 receptor-interacting protein"", ""AT2R binding protein"", ""mitochondrial tumor suppressor gene 1"""	609589	"""mitochondrial tumor suppressor 1"""			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.1253T>G	8.37:g.17612064A>C	ENSP00000262102:p.Met418Arg	147.0	0.0	0		134.0	68.0	0.507463	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	45	0.020604395604395604	44	0.08943089430894309	1	0.0027624309392265192	0	0.0	0	0.0	A	0.005	-2.138056	0.00335	0.068766	0.0	ENSG00000129422	ENST00000381869;ENST00000262102;ENST00000519263;ENST00000381862	T;T;T;T	0.17854	3.24;3.27;3.24;2.25	5.0	-3.89	0.04193	.	1.334190	0.04473	N	0.376484	T	0.00356	0.0011	N	0.24115	0.695	0.09310	N	1	B;B;B	0.30824	0.296;0.296;0.296	B;B;B	0.27380	0.079;0.037;0.053	T	0.23048	-1.0199	10	0.66056	D	0.02	1.3614	1.2801	0.02039	0.384:0.2677:0.2254:0.1229	.	418;418;418	Q9ULD2-5;Q9ULD2-2;Q9ULD2	.;.;MTUS1_HUMAN	R	418	ENSP00000371293:M418R;ENSP00000262102:M418R;ENSP00000430167:M418R;ENSP00000371286:M418R	ENSP00000262102:M418R	M	-	2	0	MTUS1	17656344	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	0.074000	0.14662	-0.755000	0.04709	-0.336000	0.08194	ATG	A|0.978;C|0.022	0.022	strong		0.443	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031	
OBSCN	84033	hgsc.bcm.edu	37	1	228461655	228461655	+	Silent	SNP	C	C	T	rs138055037	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228461655C>T	ENST00000422127.1	+	18	5366	c.5322C>T	c.(5320-5322)caC>caT	p.H1774H	RP5-1139B12.3_ENST00000602947.1_RNA|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000570156.2_Silent_p.H2149H|RP5-1139B12.2_ENST00000602517.1_RNA|OBSCN_ENST00000359599.6_Silent_p.H621H|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Silent_p.H1774H|RP5-1139B12.3_ENST00000602529.1_RNA	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1774	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GGGACACCCACACCCTGACCG	0.662													C|||	35	0.00698882	0.0265	0.0	5008	,	,		17285	0.0		0.0	False		,,,				2504	0.0				p.H2149H		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C6447T						PASS	.	C	,	115,4115		1,113,2001	19.0	23.0	22.0		5322,5322	1.3	1.0	1	dbSNP_134	22	0,8446		0,0,4223	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	1,113,6224	TT,TC,CC		0.0,2.7187,0.9072	,	1774/7969,1774/6621	228461655	115,12561	2115	4223	6338	SO:0001819	synonymous_variant	84033	exon22			CACCCACACCCTG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.5322C>T	1.37:g.228461655C>T		185.0	0.0	0		184.0	103.0	0.559783	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			C|0.996;T|0.004	0.004	strong		0.662	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
SBF1	6305	hgsc.bcm.edu	37	22	50899103	50899103	+	Silent	SNP	G	G	A	rs77064034	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50899103G>A	ENST00000390679.3	-	24	3190	c.3006C>T	c.(3004-3006)gaC>gaT	p.D1002D	SBF1_ENST00000348911.6_Silent_p.D1003D|SBF1_ENST00000380817.3_Silent_p.D1002D			O95248	MTMR5_HUMAN	SET binding factor 1	1002					cell death (GO:0008219)|positive regulation of Rab GTPase activity (GO:0032851)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(8)|large_intestine(3)|lung(18)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	43		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)		GCTCGGCGCTGTCAGACCCCA	0.627													G|||	99	0.0197684	0.0711	0.0072	5008	,	,		16560	0.0		0.0	False		,,,				2504	0.0				p.D1002D		Atlas-SNP	.											.	SBF1	211	.	0			c.C3006T						PASS	.	G		270,3750		8,254,1748	87.0	92.0	90.0		3006	-3.9	1.0	22	dbSNP_131	90	1,8301		0,1,4150	no	coding-synonymous	SBF1	NM_002972.2		8,255,5898	AA,AG,GG		0.012,6.7164,2.1993		1002/1894	50899103	271,12051	2010	4151	6161	SO:0001819	synonymous_variant	6305	exon24			GGCGCTGTCAGAC	U93181	CCDS14091.1, CCDS14091.2	22q13.33	2013-01-10			ENSG00000100241	ENSG00000100241		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"", ""DENN/MADD domain containing"", ""Pleckstrin homology (PH) domain containing"""	10542	protein-coding gene	gene with protein product	"""myotubularin related 5"", ""DENN/MADD domain containing 7A"""	603560				9537414, 9736772	Standard	NM_002972		Approved	MTMR5, DENND7A	uc003blh.3	O95248	OTTHUMG00000150204	ENST00000390679.3:c.3006C>T	22.37:g.50899103G>A		96.0	0.0	0		96.0	43.0	0.447917	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Silent	SNP	ENST00000390679.3	37																																																																																				G|0.990;A|0.010	0.010	strong		0.627	SBF1-201	KNOWN	basic	protein_coding	protein_coding			
CETP	1071	hgsc.bcm.edu	37	16	57003846	57003846	+	Missense_Mutation	SNP	C	C	T	rs34716057	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57003846C>T	ENST00000566128.1	+	5	532	c.265C>T	c.(265-267)Cgg>Tgg	p.R89W	CETP_ENST00000200676.3_Missense_Mutation_p.R154W|CETP_ENST00000569082.1_3'UTR|CETP_ENST00000379780.2_Missense_Mutation_p.R154W					cholesteryl ester transfer protein, plasma											NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(4)|skin(3)	23						TGGTAGAGTGCGGACCGATGC	0.597													C|||	41	0.0081869	0.0295	0.0029	5008	,	,		19510	0.0		0.0	False		,,,				2504	0.0				p.R154W		Atlas-SNP	.											.	CETP	50	.	0			c.C460T						PASS	.	C	TRP/ARG	116,4280	88.7+/-127.4	3,110,2085	133.0	80.0	98.0		460	-2.7	0.0	16	dbSNP_126	98	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CETP	NM_000078.2	101	3,112,6383	TT,TC,CC		0.0233,2.6388,0.908	probably-damaging	154/494	57003846	118,12878	2198	4300	6498	SO:0001583	missense	1071	exon5			AGAGTGCGGACCG	M30185	CCDS10772.1, CCDS67032.1	16q13	2012-10-02			ENSG00000087237	ENSG00000087237		"""BPI fold containing"""	1869	protein-coding gene	gene with protein product	"""BPI fold containing family F"""	118470				3600759, 2334701	Standard	NM_000078		Approved	BPIFF	uc002eki.2	P11597	OTTHUMG00000133279	ENST00000566128.1:c.265C>T	16.37:g.57003846C>T	ENSP00000456276:p.Arg89Trp	136.0	0.0	0		139.0	72.0	0.517986	NM_000078		Missense_Mutation	SNP	ENST00000566128.1	37		17	0.007783882783882784	17	0.034552845528455285	0	0.0	0	0.0	0	0.0	C	9.523	1.108810	0.20714	0.026388	2.33E-4	ENSG00000087237	ENST00000200676;ENST00000379780	T;T	0.06768	3.26;3.26	4.05	-2.74	0.05932	Lipid-binding serum glycoprotein, N-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.824610	0.10339	U	0.686590	T	0.01730	0.0055	N	0.12182	0.205	0.09310	N	1	D;B	0.71674	0.998;0.066	P;B	0.50754	0.649;0.021	T	0.18935	-1.0321	10	0.66056	D	0.02	-16.4666	2.4134	0.04430	0.1231:0.3542:0.3268:0.1959	rs34716057;rs35242580;rs59039225	154;154	P11597-2;P11597	.;CETP_HUMAN	W	154	ENSP00000200676:R154W;ENSP00000369106:R154W	ENSP00000200676:R154W	R	+	1	2	CETP	55561347	0.074000	0.21230	0.000000	0.03702	0.001000	0.01503	0.020000	0.13466	-0.956000	0.03631	-1.961000	0.00478	CGG	C|0.992;T|0.008	0.008	strong		0.597	CETP-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432305.1	NM_000078	
NLRP6	171389	hgsc.bcm.edu	37	11	285256	285256	+	Silent	SNP	G	G	A	rs144727560	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:285256G>A	ENST00000312165.5	+	8	2631	c.2631G>A	c.(2629-2631)gcG>gcA	p.A877A	RP11-326C3.2_ENST00000525217.1_RNA|RP11-326C3.2_ENST00000534742.1_RNA|NLRP6_ENST00000534750.1_Silent_p.A876A|RP11-326C3.2_ENST00000533924.1_RNA	NM_138329.1	NP_612202.2	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	877					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|regulation of inflammatory response (GO:0050727)|response to bacterium (GO:0009617)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|vasopressin receptor activity (GO:0005000)			breast(1)|skin(1)|upper_aerodigestive_tract(2)	4		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)		CACACCCAGCGCTGGACGGCC	0.597													G|||	19	0.00379393	0.0106	0.0029	5008	,	,		15333	0.0		0.0	False		,,,				2504	0.0031				p.A877A		Atlas-SNP	.											.	NLRP6	4	.	0			c.G2631A						PASS	.	G		49,4357	45.3+/-79.5	0,49,2154	84.0	69.0	74.0		2631	-4.3	0.0	11	dbSNP_134	74	0,8600		0,0,4300	no	coding-synonymous	NLRP6	NM_138329.1		0,49,6454	AA,AG,GG		0.0,1.1121,0.3767		877/893	285256	49,12957	2203	4300	6503	SO:0001819	synonymous_variant	171389	exon8			CCCAGCGCTGGAC	AF479748	CCDS7693.1, CCDS60680.1	11p15	2006-12-08	2006-12-08	2006-12-08	ENSG00000174885	ENSG00000174885		"""Nucleotide-binding domain and leucine rich repeat containing"""	22944	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 6"""	609650	"""NACHT, leucine rich repeat and PYD containing 6"""	NALP6		12563287, 12019269	Standard	NM_138329		Approved	PYPAF5, PAN3, CLR11.4	uc010qvs.3	P59044	OTTHUMG00000119070	ENST00000312165.5:c.2631G>A	11.37:g.285256G>A		70.0	0.0	0		78.0	36.0	0.461538	NM_138329	A8K9F3|E9PJZ8	Silent	SNP	ENST00000312165.5	37	CCDS7693.1																																																																																			G|0.995;A|0.005	0.005	strong		0.597	NLRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239283.1	NM_138329	
PDLIM5	10611	hgsc.bcm.edu	37	4	95539204	95539204	+	Missense_Mutation	SNP	C	C	T	rs141653509	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:95539204C>T	ENST00000317968.4	+	8	1106	c.970C>T	c.(970-972)Cgg>Tgg	p.R324W	PDLIM5_ENST00000542407.1_Missense_Mutation_p.R202W|PDLIM5_ENST00000514743.1_Missense_Mutation_p.R353W|PDLIM5_ENST00000380176.3_3'UTR|PDLIM5_ENST00000437932.1_Missense_Mutation_p.R215W	NM_001256428.1|NM_006457.4	NP_001243357.1|NP_006448	Q96HC4	PDLI5_HUMAN	PDZ and LIM domain 5	324					regulation of dendritic spine morphogenesis (GO:0061001)|regulation of synapse assembly (GO:0051963)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytosol (GO:0005829)|membrane (GO:0016020)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	actin binding (GO:0003779)|actinin binding (GO:0042805)|protein kinase C binding (GO:0005080)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	22		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.84e-09)		AGCTTCCACACGGAGCATGCC	0.547													C|||	7	0.00139776	0.0045	0.0	5008	,	,		15988	0.001		0.0	False		,,,				2504	0.0				p.R353W		Atlas-SNP	.											PDLIM5,NS,carcinoma,-1,1	PDLIM5	76	1	0			c.C1057T						PASS	.	C	TRP/ARG,TRP/ARG	25,4381	30.8+/-60.4	0,25,2178	48.0	48.0	48.0		643,970	0.8	0.0	4	dbSNP_134	48	0,8600		0,0,4300	yes	missense,missense	PDLIM5	NM_001011513.2,NM_006457.3	101,101	0,25,6478	TT,TC,CC		0.0,0.5674,0.1922	probably-damaging,probably-damaging	215/488,324/597	95539204	25,12981	2203	4300	6503	SO:0001583	missense	10611	exon12			TCCACACGGAGCA	AF061258	CCDS3641.1, CCDS47103.1, CCDS47104.1, CCDS58915.1, CCDS58916.1, CCDS58917.1, CCDS75166.1	4q22	2006-04-12			ENSG00000163110	ENSG00000163110			17468	protein-coding gene	gene with protein product		605904				15346770	Standard	NM_006457		Approved	LIM, Enh	uc003htk.4	Q96HC4	OTTHUMG00000130973	ENST00000317968.4:c.970C>T	4.37:g.95539204C>T	ENSP00000321746:p.Arg324Trp	83.0	0.0	0		115.0	64.0	0.556522	NM_001256426	A8K6F9|D6RB78|E9PBF5|O60705|Q56VN4|Q5UW38|Q8WVK0	Missense_Mutation	SNP	ENST00000317968.4	37	CCDS3641.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	10.95	1.494439	0.26774	0.005674	0.0	ENSG00000163110	ENST00000437932;ENST00000317968;ENST00000503974;ENST00000542407;ENST00000514743	T;T;T;T;T	0.59364	0.48;0.67;0.48;0.27;0.46	5.14	0.821	0.18799	.	0.458336	0.23654	N	0.045883	T	0.33323	0.0859	L	0.47716	1.5	0.09310	N	1	B;B;B;B	0.23490	0.009;0.086;0.005;0.006	B;B;B;B	0.10450	0.002;0.004;0.003;0.005	T	0.29671	-1.0004	10	0.59425	D	0.04	.	2.7512	0.05281	0.4316:0.3432:0.1293:0.0959	.	221;353;324;215	E9PBF5;D6RB78;Q96HC4;Q96HC4-4	.;.;PDLI5_HUMAN;.	W	215;324;221;202;353	ENSP00000398469:R215W;ENSP00000321746:R324W;ENSP00000424297:R221W;ENSP00000442187:R202W;ENSP00000424360:R353W	ENSP00000321746:R324W	R	+	1	2	PDLIM5	95758227	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-0.059000	0.11731	0.187000	0.20147	0.585000	0.79938	CGG	C|0.999;T|0.001	0.001	strong		0.547	PDLIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253586.1		
CPA3	1359	hgsc.bcm.edu	37	3	148601596	148601596	+	Silent	SNP	G	G	A	rs140411214	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:148601596G>A	ENST00000296046.3	+	9	1027	c.975G>A	c.(973-975)gaG>gaA	p.E325E	RP11-680B3.2_ENST00000488190.1_RNA	NM_001870.2	NP_001861.2	P15088	CBPA3_HUMAN	carboxypeptidase A3 (mast cell)	325					angiotensin maturation (GO:0002003)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|secretory granule (GO:0030141)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(1)|large_intestine(3)|lung(20)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	35			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)			CTAACCATGAGGACTTGGTAC	0.398													G|||	21	0.00419329	0.0151	0.0014	5008	,	,		20428	0.0		0.0	False		,,,				2504	0.0				p.E325E		Atlas-SNP	.											.	CPA3	75	.	0			c.G975A						PASS	.	G		66,4340	62.3+/-99.4	0,66,2137	96.0	80.0	86.0		975	0.8	0.1	3	dbSNP_134	86	0,8600		0,0,4300	no	coding-synonymous	CPA3	NM_001870.2		0,66,6437	AA,AG,GG		0.0,1.498,0.5075		325/418	148601596	66,12940	2203	4300	6503	SO:0001819	synonymous_variant	1359	exon9			CCATGAGGACTTG		CCDS3138.1	3q24	2012-02-10			ENSG00000163751	ENSG00000163751	3.4.17.1		2298	protein-coding gene	gene with protein product	"""mast cell carboxypeptidase A"", ""tissue carboxypeptidase A"""	114851					Standard	NM_001870		Approved		uc003ewm.3	P15088	OTTHUMG00000159526	ENST00000296046.3:c.975G>A	3.37:g.148601596G>A		136.0	0.0	0		143.0	67.0	0.468531	NM_001870	Q96E94	Silent	SNP	ENST00000296046.3	37	CCDS3138.1																																																																																			G|0.995;A|0.005	0.005	strong		0.398	CPA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355974.1	NM_001870	
MYO19	80179	hgsc.bcm.edu	37	17	34858985	34858985	+	Missense_Mutation	SNP	A	A	G	rs61743158	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34858985A>G	ENST00000431794.3	-	21	2554	c.2032T>C	c.(2032-2034)Tgc>Cgc	p.C678R	MYO19_ENST00000268852.9_Missense_Mutation_p.C478R	NM_001163735.1	NP_001157207.1	Q96H55	MYO19_HUMAN	myosin XIX	678	Myosin motor.					cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|urinary_tract(1)	20		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		GAGGATGTGCAAGGATGAAGC	0.493													G|||	24	0.00479233	0.0174	0.0014	5008	,	,		18666	0.0		0.0	False		,,,				2504	0.0				p.C678R		Atlas-SNP	.											.	MYO19	130	.	0			c.T2032C						PASS	.	G	ARG/CYS,ARG/CYS	77,3859		3,71,1894	191.0	202.0	198.0		2032,1432	4.3	0.6	17	dbSNP_129	198	0,8298		0,0,4149	yes	missense,missense	MYO19	NM_001163735.1,NM_025109.5	180,180	3,71,6043	GG,GA,AA		0.0,1.9563,0.6294	benign,benign	678/971,478/771	34858985	77,12157	1968	4149	6117	SO:0001583	missense	80179	exon22			ATGTGCAAGGATG	BC008900	CCDS45654.1, CCDS54112.1, CCDS59283.1	17q12	2014-08-12	2007-09-26	2007-09-26	ENSG00000278259	ENSG00000278259		"""Myosins / Myosin superfamily : Class XIX"""	26234	protein-coding gene	gene with protein product			"""myosin head domain containing 1"""	MYOHD1		17877792, 19932026	Standard	NM_001033580		Approved	FLJ22865	uc010wcy.2	Q96H55	OTTHUMG00000188437	ENST00000431794.3:c.2032T>C	17.37:g.34858985A>G	ENSP00000409936:p.Cys678Arg	149.0	0.0	0		154.0	65.0	0.422078	NM_001163735	Q59GS4|Q9H5X2	Missense_Mutation	SNP	ENST00000431794.3	37	CCDS54112.1	8	0.003663003663003663	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	G	4.905	0.168151	0.09339	0.019563	0.0	ENSG00000141140	ENST00000431794;ENST00000268852	D;D	0.94966	-3.57;-3.57	5.25	4.27	0.50696	Myosin head, motor domain (1);	.	.	.	.	T	0.70141	0.3190	N	0.00926	-1.1	0.23515	N	0.997514	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.67360	-0.5690	9	0.23302	T	0.38	.	7.8717	0.29569	0.0883:0.1733:0.7385:0.0	.	678;478	Q96H55;Q96H55-4	MYO19_HUMAN;.	R	678;478	ENSP00000409936:C678R;ENSP00000268852:C478R	ENSP00000268852:C478R	C	-	1	0	MYO19	31933098	0.261000	0.24063	0.559000	0.28332	0.034000	0.12701	1.018000	0.30002	0.706000	0.31912	-0.213000	0.12676	TGC	A|0.995;G|0.005	0.005	strong		0.493	MYO19-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451074.1	NM_025109	
TPM4	7171	hgsc.bcm.edu	37	19	16186865	16186865	+	5'Flank	SNP	G	G	A	rs114042568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16186865G>A	ENST00000300933.4	+	0	0				TPM4_ENST00000538887.1_Silent_p.E41E|TPM4_ENST00000344824.6_Silent_p.E41E	NM_003290.2	NP_003281.1	P67936	TPM4_HUMAN	tropomyosin 4						cellular component movement (GO:0006928)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|osteoblast differentiation (GO:0001649)	cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|membrane (GO:0016020)|muscle thin filament tropomyosin (GO:0005862)|podosome (GO:0002102)|stress fiber (GO:0001725)	calcium ion binding (GO:0005509)|structural constituent of muscle (GO:0008307)		TPM4/ALK(12)	breast(1)|large_intestine(3)	4						AGGTGGAGGAGGAGCTGACGC	0.617			T	ALK	ALCL								G|||	90	0.0179712	0.062	0.0115	5008	,	,		14293	0.0		0.0	False		,,,				2504	0.0				p.E41E		Atlas-SNP	.		Dom	yes		19	19p13.1	7171	tropomyosin 4		L	.	TPM4	28	.	0			c.G123A						PASS	.	G		143,2989		7,129,1430	30.0	31.0	31.0		123	1.8	1.0	19	dbSNP_132	31	1,7153		0,1,3576	no	coding-synonymous	TPM4	NM_001145160.1		7,130,5006	AA,AG,GG		0.014,4.5658,1.4		41/285	16186865	144,10142	1566	3577	5143	SO:0001631	upstream_gene_variant	7171	exon2			GGAGGAGGAGCTG		CCDS12338.1, CCDS46007.1	19p13.1	2013-03-11			ENSG00000167460	ENSG00000167460		"""Tropomyosins"""	12013	protein-coding gene	gene with protein product		600317				8641132	Standard	NM_003290		Approved		uc002ndi.2	P67936	OTTHUMG00000182134		19.37:g.16186865G>A	Exception_encountered	108.0	0.0	0		137.0	67.0	0.489051	NM_001145160	P07226|Q15659|Q5U0D9|Q9BU85|Q9H8Q3|Q9UCS1|Q9UCS2|Q9UCS3|Q9UCS4	Silent	SNP	ENST00000300933.4	37	CCDS12338.1																																																																																			G|0.989;A|0.011	0.011	strong		0.617	TPM4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459673.2	NM_003290	
FCGRT	2217	hgsc.bcm.edu	37	19	50017191	50017191	+	Silent	SNP	G	G	T	rs11551281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50017191G>T	ENST00000221466.5	+	3	612	c.126G>T	c.(124-126)ccG>ccT	p.P42P	FCGRT_ENST00000596975.1_Silent_p.P42P|FCGRT_ENST00000426395.3_Silent_p.P42P|FCGRT_ENST00000594823.1_3'UTR|FCGRT_ENST00000599988.1_Intron	NM_001136019.2	NP_001129491.1	P55899	FCGRN_HUMAN	Fc fragment of IgG, receptor, transporter, alpha	42	Alpha-1.				antigen processing and presentation (GO:0019882)|IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor (GO:0002416)|immune response (GO:0006955)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	IgG binding (GO:0019864)			endometrium(3)|kidney(2)|lung(1)|ovary(1)|prostate(1)|skin(1)	9		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00291)|GBM - Glioblastoma multiforme(134;0.0156)		CGCCTGCCCCGGGGACTCCTG	0.652													G|||	98	0.0195687	0.0363	0.0029	5008	,	,		13393	0.0456		0.0	False		,,,				2504	0.002				p.P42P		Atlas-SNP	.											.	FCGRT	23	.	0			c.G126T						PASS	.	G	,	151,4255	103.0+/-141.5	3,145,2055	108.0	109.0	109.0		126,126	-5.5	0.0	19	dbSNP_120	109	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous	FCGRT	NM_001136019.2,NM_004107.4	,	3,148,6352	TT,TG,GG		0.0349,3.4271,1.1841	,	42/366,42/366	50017191	154,12852	2203	4300	6503	SO:0001819	synonymous_variant	2217	exon3			TGCCCCGGGGACT	U12255	CCDS12770.1	19q13.3	2013-01-11				ENSG00000104870		"""Immunoglobulin superfamily / C1-set domain containing"""	3621	protein-coding gene	gene with protein product		601437				7964511, 8646894	Standard	NM_001136019		Approved	FCRN, alpha-chain	uc002pog.2	P55899		ENST00000221466.5:c.126G>T	19.37:g.50017191G>T		170.0	0.0	0		162.0	88.0	0.54321	NM_001136019	Q5HYM5|Q9HBV7|Q9NZ19	Silent	SNP	ENST00000221466.5	37	CCDS12770.1																																																																																			G|0.984;T|0.016	0.016	strong		0.652	FCGRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465267.1		
MYO5B	4645	hgsc.bcm.edu	37	18	47462657	47462657	+	Silent	SNP	G	G	A	rs1627232	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:47462657G>A	ENST00000285039.7	-	16	2267	c.1968C>T	c.(1966-1968)cgC>cgT	p.R656R		NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	656	Actin-binding. {ECO:0000255}.|Myosin motor.		R -> C (in DIAR2). {ECO:0000269|PubMed:18724368}.		endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		GCTTGATGCAGCGGACATAGT	0.537													g|||	167	0.0333466	0.0923	0.0043	5008	,	,		19813	0.0268		0.0109	False		,,,				2504	0.0041				p.R656R		Atlas-SNP	.											.	MYO5B	178	.	0			c.C1968T						PASS	.	A		271,3913		12,247,1833	96.0	99.0	98.0		1968	1.7	1.0	18	dbSNP_89	98	15,8451		0,15,4218	no	coding-synonymous	MYO5B	NM_001080467.2		12,262,6051	AA,AG,GG		0.1772,6.4771,2.2609		656/1849	47462657	286,12364	2092	4233	6325	SO:0001819	synonymous_variant	4645	exon16			GATGCAGCGGACA	AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"""Myosins / Myosin superfamily : Class V"""	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.1968C>T	18.37:g.47462657G>A		145.0	0.0	0		143.0	63.0	0.440559	NM_001080467	B0I1R3|Q0P656|Q9H6Y6	Silent	SNP	ENST00000285039.7	37	CCDS42436.1																																																																																			G|0.961;A|0.039	0.039	strong		0.537	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2		
HLA-DMA	3108	hgsc.bcm.edu	37	6	32917126	32917126	+	Missense_Mutation	SNP	C	C	T	rs9469319	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32917126C>T	ENST00000374843.4	-	4	788	c.703G>A	c.(703-705)Gtg>Atg	p.V235M	HLA-DMA_ENST00000464392.1_5'UTR|HLA-DMA_ENST00000395305.3_Missense_Mutation_p.V140M|XXbac-BPG181M17.5_ENST00000429234.1_Intron|HLA-DMA_ENST00000395303.3_Missense_Mutation_p.V201M	NM_006120.3	NP_006111.2	P28067	DMA_HUMAN	major histocompatibility complex, class II, DM alpha	235			V -> M (in dbSNP:rs9469319).		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|chaperone mediated protein folding requiring cofactor (GO:0051085)|immunoglobulin mediated immune response (GO:0016064)|inner ear development (GO:0048839)|peptide antigen assembly with MHC class II protein complex (GO:0002503)|positive regulation of immune response (GO:0050778)|positive regulation of T cell differentiation (GO:0045582)|positive thymic T cell selection (GO:0045059)|protein transport (GO:0015031)	cell surface (GO:0009986)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)	MHC class II protein complex binding (GO:0023026)			kidney(1)|large_intestine(2)|lung(8)	11						CCAAAGGCCACGCCACACAGC	0.592													C|||	11	0.00219649	0.0076	0.0014	5008	,	,		19854	0.0		0.0	False		,,,				2504	0.0				p.V235M		Atlas-SNP	.											.	HLA-DMA	20	.	0			c.G703A						PASS	.	C	MET/VAL	21,4385	28.1+/-56.4	0,21,2182	91.0	85.0	87.0		703	-2.8	0.0	6	dbSNP_119	87	1,8599	1.2+/-3.3	0,1,4299	yes	missense	HLA-DMA	NM_006120.3	21	0,22,6481	TT,TC,CC		0.0116,0.4766,0.1692	possibly-damaging	235/262	32917126	22,12984	2203	4300	6503	SO:0001583	missense	3108	exon4			AGGCCACGCCACA		CCDS4761.1	6p21.3	2013-01-11			ENSG00000204257	ENSG00000204257		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4934	protein-coding gene	gene with protein product		142855				1922385	Standard	NM_006120		Approved	D6S222E, RING6	uc003ocm.2	P28067	OTTHUMG00000031173	ENST00000374843.4:c.703G>A	6.37:g.32917126C>T	ENSP00000363976:p.Val235Met	87.0	0.0	0		100.0	50.0	0.5	NM_006120	Q29639|Q29640	Missense_Mutation	SNP	ENST00000374843.4	37	CCDS4761.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	11.77	1.739075	0.30774	0.004766	1.16E-4	ENSG00000204257	ENST00000395305;ENST00000395303;ENST00000374843;ENST00000456800	T;T;T;T	0.01821	5.12;4.62;5.63;5.55	5.0	-2.84	0.05751	.	0.963671	0.08623	N	0.918117	T	0.00724	0.0024	M	0.71581	2.175	0.09310	N	1	P	0.52316	0.952	B	0.37780	0.258	T	0.41840	-0.9486	10	0.87932	D	0	.	1.2422	0.01965	0.127:0.2689:0.2786:0.3255	rs9469319;rs9469319	235	Q31604	.	M	140;201;235;265	ENSP00000378716:V140M;ENSP00000378714:V201M;ENSP00000363976:V235M;ENSP00000409668:V265M	ENSP00000363976:V235M	V	-	1	0	HLA-DMA	33025104	0.000000	0.05858	0.006000	0.13384	0.598000	0.36846	-1.977000	0.01495	-0.428000	0.07339	0.551000	0.68910	GTG	C|0.997;T|0.003	0.003	strong		0.592	HLA-DMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076325.2	NM_006120	
HTR3A	3359	hgsc.bcm.edu	37	11	113857661	113857661	+	Missense_Mutation	SNP	G	G	A	rs35815285	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:113857661G>A	ENST00000504030.2	+	8	1476	c.1031G>A	c.(1030-1032)cGt>cAt	p.R344H	HTR3A_ENST00000535865.1_Missense_Mutation_p.R88H|HTR3A_ENST00000375498.2_Missense_Mutation_p.R350H|HTR3A_ENST00000299961.5_Missense_Mutation_p.R329H|HTR3A_ENST00000506841.2_Missense_Mutation_p.R376H|HTR3A_ENST00000355556.2_Missense_Mutation_p.R382H			P46098	5HT3A_HUMAN	5-hydroxytryptamine (serotonin) receptor 3A, ionotropic	344			R -> H (in dbSNP:rs35815285). {ECO:0000269|PubMed:16487942}.		cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cellular response to growth factor stimulus (GO:0071363)|digestion (GO:0007586)|ion transmembrane transport (GO:0034220)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	36		all_cancers(61;2.31e-17)|all_epithelial(67;2.1e-10)|all_hematologic(158;4.64e-05)|Melanoma(852;0.000312)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0294)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.71e-06)|Epithelial(105;2.58e-05)|all cancers(92;0.000238)|OV - Ovarian serous cystadenocarcinoma(223;0.191)	Alosetron(DB00969)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Chloroprocaine(DB01161)|Cisapride(DB00604)|Clozapine(DB00363)|Dolasetron(DB00757)|Ergoloid mesylate(DB01049)|Granisetron(DB00889)|Loxapine(DB00408)|Memantine(DB01043)|Methadone(DB00333)|Metoclopramide(DB01233)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Ondansetron(DB00904)|Palonosetron(DB00377)|Procaine(DB00721)|Quetiapine(DB01224)|Rocuronium(DB00728)|Tapentadol(DB06204)|Trimipramine(DB00726)|Tubocurarine(DB01199)|Ziprasidone(DB00246)	GCTTGGCTGCGTCACCTGGTT	0.592													G|||	172	0.034345	0.121	0.0144	5008	,	,		17839	0.0		0.002	False		,,,				2504	0.0				p.R382H		Atlas-SNP	.											HTR3A,NS,carcinoma,+1,1	HTR3A	93	1	0			c.G1145A	GRCh37	CM011786	HTR3A	M	rs35815285	scavenged	.	G	HIS/ARG,HIS/ARG,HIS/ARG	419,3983	205.2+/-227.1	17,385,1799	55.0	50.0	52.0		1049,986,1145	3.5	0.6	11	dbSNP_126	52	6,8586	5.0+/-18.6	0,6,4290	yes	missense,missense,missense	HTR3A	NM_000869.5,NM_001161772.2,NM_213621.3	29,29,29	17,391,6089	AA,AG,GG		0.0698,9.5184,3.2707	possibly-damaging,possibly-damaging,possibly-damaging	350/485,329/464,382/517	113857661	425,12569	2201	4296	6497	SO:0001583	missense	3359	exon7			GGCTGCGTCACCT	D49394	CCDS8365.1, CCDS8366.1, CCDS8365.2, CCDS8366.2, CCDS53710.1	11q23.1-q23.2	2012-05-22	2012-02-03					"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	5297	protein-coding gene	gene with protein product		182139	"""5-hydroxytryptamine (serotonin) receptor 3A"""	HTR3		8530095, 12867984	Standard	NM_000869		Approved	5-HT3R, 5-HT3A	uc010rxb.2	P46098		ENST00000504030.2:c.1031G>A	11.37:g.113857661G>A	ENSP00000424189:p.Arg344His	119.0	1.0	0.00840336		119.0	69.0	0.579832	NM_213621	B4DSY6|G5E986|O60854|Q7KZM7|Q99918|Q9BSZ9	Missense_Mutation	SNP	ENST00000504030.2	37		59	0.027014652014652016	52	0.10569105691056911	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	G	18.10	3.548612	0.65311	0.095184	6.98E-4	ENSG00000166736	ENST00000504030;ENST00000355556;ENST00000375498;ENST00000506841;ENST00000535865;ENST00000299961	D;T;D;T;D;D	0.87966	-2.32;-0.77;-2.32;-0.77;-2.32;-2.32	5.37	3.51	0.40186	.	0.166108	0.48767	D	0.000170	T	0.12603	0.0306	L	0.45581	1.43	0.44104	D	0.996877	P;D;D	0.58970	0.944;0.98;0.984	P;P;P	0.52957	0.602;0.681;0.714	T	0.55405	-0.8146	10	0.59425	D	0.04	-19.81	6.9616	0.24599	0.3829:0.0:0.6171:0.0	rs35815285	329;382;350	B4DSY6;G5E986;Q7KZM7	.;.;.	H	344;382;350;376;88;329	ENSP00000424189:R344H;ENSP00000347754:R382H;ENSP00000364648:R350H;ENSP00000424776:R376H;ENSP00000437776:R88H;ENSP00000299961:R329H	ENSP00000299961:R329H	R	+	2	0	HTR3A	113362871	1.000000	0.71417	0.646000	0.29493	0.545000	0.35147	4.552000	0.60747	0.765000	0.33221	0.561000	0.74099	CGT	G|0.965;A|0.035	0.035	strong		0.592	HTR3A-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000360822.2	NM_000869	
UNC79	57578	hgsc.bcm.edu	37	14	94173098	94173098	+	Missense_Mutation	SNP	G	G	A	rs76642035	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:94173098G>A	ENST00000393151.2	+	50	7756	c.7756G>A	c.(7756-7758)Gtg>Atg	p.V2586M	UNC79_ENST00000256339.4_Missense_Mutation_p.V2409M|UNC79_ENST00000555664.1_Missense_Mutation_p.V2547M|UNC79_ENST00000553484.1_Missense_Mutation_p.V2608M			Q9P2D8	UNC79_HUMAN	unc-79 homolog (C. elegans)	2586					behavioral response to ethanol (GO:0048149)|ion transmembrane transport (GO:0034220)|multicellular organism growth (GO:0035264)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|cervix(2)|endometrium(10)|kidney(7)|large_intestine(18)|liver(1)|lung(64)|ovary(1)|prostate(5)|skin(3)|urinary_tract(4)	118						TCAGAACCACGTGAACCACCA	0.557													G|||	22	0.00439297	0.0159	0.0014	5008	,	,		17791	0.0		0.0	False		,,,				2504	0.0				p.V2409M		Atlas-SNP	.											.	UNC79	366	.	0			c.G7225A						PASS	.	G	MET/VAL	61,4345	57.4+/-93.9	1,59,2143	69.0	74.0	73.0		7225	5.8	1.0	14	dbSNP_131	73	0,8600		0,0,4300	yes	missense	UNC79	NM_020818.3	21	1,59,6443	AA,AG,GG		0.0,1.3845,0.469	probably-damaging	2409/2459	94173098	61,12945	2203	4300	6503	SO:0001583	missense	57578	exon50			AACCACGTGAACC	AB037830	CCDS9911.2	14q32.13	2011-08-18	2011-08-18	2011-08-18	ENSG00000133958	ENSG00000133958			19966	protein-coding gene	gene with protein product			"""KIAA1409"""	KIAA1409		20714347, 21040849	Standard	NM_020818		Approved		uc001ybs.1	Q9P2D8	OTTHUMG00000029783	ENST00000393151.2:c.7756G>A	14.37:g.94173098G>A	ENSP00000376858:p.Val2586Met	104.0	0.0	0		96.0	48.0	0.5	NM_020818	B5MDL6|Q6ZUT7	Missense_Mutation	SNP	ENST00000393151.2	37		6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	G	23.0	4.363881	0.82353	0.013845	0.0	ENSG00000133958	ENST00000256339;ENST00000555664;ENST00000553484;ENST00000393151;ENST00000393153	T;T;T;T	0.19806	2.12;2.14;2.12;2.12	5.79	5.79	0.91817	.	0.000000	0.85682	D	0.000000	T	0.36110	0.0955	L	0.53249	1.67	0.80722	D	1	D	0.76494	0.999	D	0.71656	0.974	T	0.05037	-1.0910	10	0.52906	T	0.07	-21.9581	20.0407	0.97588	0.0:0.0:1.0:0.0	.	2608	C9JQL1	.	M	2409;2547;2608;2586;2608	ENSP00000256339:V2409M;ENSP00000450868:V2547M;ENSP00000451360:V2608M;ENSP00000376858:V2586M	ENSP00000256339:V2409M	V	+	1	0	KIAA1409	93242851	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	9.869000	0.99810	2.746000	0.94184	0.561000	0.74099	GTG	G|0.996;A|0.004	0.004	strong		0.557	UNC79-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412766.1	XM_028395	
NWD1	284434	hgsc.bcm.edu	37	19	16860558	16860558	+	Missense_Mutation	SNP	G	G	A	rs61733271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16860558G>A	ENST00000552788.1	+	4	1105	c.1105G>A	c.(1105-1107)Gtc>Atc	p.V369I	NWD1_ENST00000379808.3_Missense_Mutation_p.V369I|NWD1_ENST00000523826.1_Missense_Mutation_p.V163I|NWD1_ENST00000339803.6_Missense_Mutation_p.V234I|NWD1_ENST00000524140.2_Missense_Mutation_p.V369I|NWD1_ENST00000549814.1_Missense_Mutation_p.V369I			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	369	NACHT.						ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GACAGTGACCGTCCTGCGGCT	0.622													g|||	330	0.0658946	0.1785	0.0274	5008	,	,		18889	0.0079		0.0288	False		,,,				2504	0.0389				p.V369I		Atlas-SNP	.											.	NWD1	303	.	0			c.G1105A						PASS	.		ILE/VAL	715,3691		56,603,1544	32.0	33.0	32.0		1105	1.0	0.2	19	dbSNP_129	32	322,8276		8,306,3985	yes	missense	NWD1	NM_001007525.3	29	64,909,5529	AA,AG,GG		3.7451,16.2279,7.9745	benign	369/1433	16860558	1037,11967	2203	4299	6502	SO:0001583	missense	284434	exon6			GTGACCGTCCTGC	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"""WD repeat domain containing"""	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.1105G>A	19.37:g.16860558G>A	ENSP00000447224:p.Val369Ile	61.0	0.0	0		63.0	63.0	1	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		121	0.0554029304029304	87	0.17682926829268292	14	0.03867403314917127	1	0.0017482517482517483	19	0.025065963060686015	N	3.273	-0.148788	0.06627	0.162279	0.037451	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.76839	-1.05;-1.05;-1.05;-1.05;-1.05;-1.05	4.42	1.02	0.19986	.	0.069867	0.56097	N	0.000032	T	0.00210	0.0006	L	0.28115	0.83	0.33929	P	0.358212	B;B;B	0.27166	0.17;0.066;0.081	B;B;B	0.32624	0.149;0.017;0.029	T	0.04103	-1.0977	9	0.12103	T	0.63	-23.6771	8.4041	0.32603	0.2739:0.0:0.7261:0.0	rs61733271	369;369;234	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	I	234;369;369;369;163;369;234	ENSP00000428579:V369I;ENSP00000447548:V369I;ENSP00000369136:V369I;ENSP00000428955:V163I;ENSP00000447224:V369I;ENSP00000340159:V234I	ENSP00000340159:V234I	V	+	1	0	NWD1	16721558	0.407000	0.25352	0.207000	0.23584	0.656000	0.38851	0.720000	0.25896	0.094000	0.17404	-0.155000	0.13514	GTC	G|0.927;A|0.073	0.073	strong		0.622	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525	
IGDCC4	57722	hgsc.bcm.edu	37	15	65681648	65681648	+	Missense_Mutation	SNP	A	A	G	rs144676391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:65681648A>G	ENST00000352385.2	-	14	2719	c.2510T>C	c.(2509-2511)gTg>gCg	p.V837A		NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	837	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	44						GCGCTCCACCACAGAGCCGAA	0.572													A|||	21	0.00419329	0.0159	0.0	5008	,	,		16119	0.0		0.0	False		,,,				2504	0.0				p.V837A		Atlas-SNP	.											.	IGDCC4	95	.	0			c.T2510C						PASS	.	A	ALA/VAL	46,4356	48.2+/-83.0	0,46,2155	82.0	63.0	69.0		2510	4.3	1.0	15	dbSNP_134	69	0,8598		0,0,4299	yes	missense	IGDCC4	NM_020962.1	64	0,46,6454	GG,GA,AA		0.0,1.045,0.3538	benign	837/1251	65681648	46,12954	2201	4299	6500	SO:0001583	missense	57722	exon14			TCCACCACAGAGC		CCDS10206.1	15q22.31	2013-02-11			ENSG00000103742	ENSG00000103742		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	13770	protein-coding gene	gene with protein product	"""likely ortholog of mouse neighbor of Punc E11"""						Standard	NM_020962		Approved	NOPE, LOC57722	uc002aou.1	Q8TDY8	OTTHUMG00000133136	ENST00000352385.2:c.2510T>C	15.37:g.65681648A>G	ENSP00000319623:p.Val837Ala	79.0	0.0	0		50.0	18.0	0.36	NM_020962	Q9HCE4	Missense_Mutation	SNP	ENST00000352385.2	37	CCDS10206.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	A	13.90	2.373757	0.42105	0.01045	0.0	ENSG00000103742	ENST00000352385;ENST00000356152	T	0.54279	0.58	5.37	4.26	0.50523	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.256570	0.38058	N	0.001833	T	0.18676	0.0448	N	0.13098	0.295	0.30508	N	0.76971	B	0.23377	0.084	B	0.17722	0.019	T	0.15925	-1.0420	10	0.35671	T	0.21	-20.1912	10.6197	0.45472	0.9248:0.0:0.0752:0.0	.	837	Q8TDY8	IGDC4_HUMAN	A	837;566	ENSP00000319623:V837A	ENSP00000319623:V837A	V	-	2	0	IGDCC4	63468701	1.000000	0.71417	0.996000	0.52242	0.975000	0.68041	5.865000	0.69583	2.043000	0.60533	0.454000	0.30748	GTG	A|0.995;G|0.005	0.005	strong		0.572	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962	
DNASE1	1773	hgsc.bcm.edu	37	16	3707262	3707262	+	Silent	SNP	G	G	A	rs8176920	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3707262G>A	ENST00000246949.5	+	7	3833	c.624G>A	c.(622-624)ctG>ctA	p.L208L	DNASE1_ENST00000407479.1_Silent_p.L208L|DNASE1_ENST00000414110.2_Silent_p.L91L	NM_005223.3	NP_005214.2	P24855	DNAS1_HUMAN	deoxyribonuclease I	208					apoptotic process (GO:0006915)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	deoxyribonuclease I activity (GO:0004530)			lung(1)	1		Ovarian(90;0.0261)		Kidney(780;0.0556)		CCATCCGCCTGTGGACAAGCC	0.617													G|||	160	0.0319489	0.1195	0.0029	5008	,	,		18167	0.0		0.0	False		,,,				2504	0.0				p.L208L		Atlas-SNP	.											.	DNASE1	16	.	0			c.G624A						PASS	.	G		370,4024	189.9+/-215.9	14,342,1841	86.0	69.0	75.0		624	1.8	1.0	16	dbSNP_117	75	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	DNASE1	NM_005223.3		14,345,6138	AA,AG,GG		0.0349,8.4206,2.8706		208/283	3707262	373,12621	2197	4300	6497	SO:0001819	synonymous_variant	1773	exon7			CCGCCTGTGGACA		CCDS10507.1	16p13.3	2008-02-05			ENSG00000213918	ENSG00000213918	3.1.21.1		2956	protein-coding gene	gene with protein product		125505		DNL1		2349940	Standard	XM_005255148		Approved		uc002cvr.3	P24855	OTTHUMG00000129426	ENST00000246949.5:c.624G>A	16.37:g.3707262G>A		120.0	0.0	0		115.0	115.0	1	NM_005223	B4DV35|Q14UU9|Q14UV0	Silent	SNP	ENST00000246949.5	37	CCDS10507.1																																																																																			G|0.970;A|0.030	0.030	strong		0.617	DNASE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251585.2		
TFDP3	51270	hgsc.bcm.edu	37	X	132352230	132352230	+	Missense_Mutation	SNP	C	C	G	rs28455963	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:132352230C>G	ENST00000310125.4	-	1	146	c.58G>C	c.(58-60)Gag>Cag	p.E20Q		NM_016521.2	NP_057605.3	Q5H9I0	TFDP3_HUMAN	transcription factor Dp family, member 3	20					cellular response to DNA damage stimulus (GO:0006974)|G1/S transition of mitotic cell cycle (GO:0000082)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(4)|large_intestine(1)|lung(8)|ovary(1)|prostate(2)	19	Acute lymphoblastic leukemia(192;0.000127)					GTCTGGTTCTCGTCCATTAAG	0.483													G|||	383	0.101457	0.2247	0.0389	3775	,	,		13274	0.002		0.0288	False		,,,				2504	0.0286				p.E20Q		Atlas-SNP	.											.	TFDP3	92	.	0			c.G58C						PASS	.	G	GLN/GLU	304,905		40,182,42,295,133	63.0	47.0	52.0		58	0.2	0.0	X	dbSNP_125	52	85,2306		3,62,17,735,774	yes	missense	TFDP3	NM_016521.2	29	43,244,59,1030,907	GG,GC,G,CC,C		3.555,25.1447,10.8056	benign	20/406	132352230	389,3211	692	1591	2283	SO:0001583	missense	51270	exon1			GGTTCTCGTCCAT	AF219119	CCDS14636.2	Xq26.2	2009-03-25			ENSG00000183434	ENSG00000183434			24603	protein-coding gene	gene with protein product	"""E2F-like protein"", ""cancer/testis antigen 30"""	300772				12097419	Standard	NM_016521		Approved	HCA661, E2F-like, CT30	uc004exb.1	Q5H9I0	OTTHUMG00000022433	ENST00000310125.4:c.58G>C	X.37:g.132352230C>G	ENSP00000385461:p.Glu20Gln	186.0	0.0	0		170.0	116.0	0.682353	NM_016521	Q6DK49|Q9NZ54	Missense_Mutation	SNP	ENST00000310125.4	37	CCDS14636.2	154	0.09282700421940929	74	0.17703349282296652	13	0.03651685393258427	2	0.0034965034965034965	14	0.01907356948228883	G	0.008	-1.897626	0.00517	0.251447	0.03555	ENSG00000183434	ENST00000310125	T	0.19806	2.12	0.235	0.235	0.15431	.	.	.	.	.	T	0.00012	0.0000	N	0.00260	-1.75	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.34378	-0.9831	7	0.02654	T	1	.	.	.	.	rs28455963	20	Q5H9I0	TFDP3_HUMAN	Q	20	ENSP00000385461:E20Q	ENSP00000385461:E20Q	E	-	1	0	TFDP3	132179896	0.988000	0.35896	0.016000	0.15963	0.016000	0.09150	0.556000	0.23438	-0.705000	0.05035	-0.699000	0.03677	GAG	C|0.877;G|0.123	0.123	strong		0.483	TFDP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058337.1	NM_016521	
C6orf52	347744	hgsc.bcm.edu	37	6	10687325	10687325	+	Silent	SNP	C	C	T	rs144052767	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:10687325C>T	ENST00000426700.2	-	2	143	c.144G>A	c.(142-144)gcG>gcA	p.A48A	C6orf52_ENST00000503680.1_5'UTR|C6orf52_ENST00000259983.3_Silent_p.A48A|C6orf52_ENST00000460742.2_5'UTR|C6orf52_ENST00000379586.1_Intron|C6orf52_ENST00000467832.2_Intron			Q5T4I8	CF052_HUMAN	chromosome 6 open reading frame 52	48										endometrium(1)|prostate(1)	2						CGTGCTGTCGCGCATACCAGT	0.507													C|||	61	0.0121805	0.0431	0.0043	5008	,	,		20327	0.0		0.001	False		,,,				2504	0.0				p.A48A		Atlas-SNP	.											C6orf52,caecum,carcinoma,0,1	C6orf52	9	1	0			c.G144A						scavenged	.	C		74,1310		1,72,619	105.0	93.0	97.0		144	1.1	0.0	6	dbSNP_134	97	2,3180		0,2,1589	no	coding-synonymous	C6orf52	NM_001145020.1		1,74,2208	TT,TC,CC		0.0629,5.3468,1.6645		48/153	10687325	76,4490	692	1591	2283	SO:0001819	synonymous_variant	347744	exon3			CTGTCGCGCATAC	BC016820	CCDS47371.1	6p24.2	2009-09-22	2007-06-07	2007-06-07	ENSG00000137434	ENSG00000137434			20881	protein-coding gene	gene with protein product						12477932	Standard	NM_001145020		Approved		uc011dij.2	Q5T4I8	OTTHUMG00000014240	ENST00000426700.2:c.144G>A	6.37:g.10687325C>T		121.0	1.0	0.00826446		116.0	53.0	0.456897	NM_001145020	Q5T4I7|Q96AS6	Silent	SNP	ENST00000426700.2	37	CCDS47371.1																																																																																			C|0.990;T|0.010	0.010	strong		0.507	C6orf52-002	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039825.2	NM_001145020	
HDAC7	51564	hgsc.bcm.edu	37	12	48185449	48185449	+	Missense_Mutation	SNP	G	G	A	rs73291234	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:48185449G>A	ENST00000427332.2	-	15	1892	c.1736C>T	c.(1735-1737)tCg>tTg	p.S579L	HDAC7_ENST00000552960.1_Missense_Mutation_p.S601L|HDAC7_ENST00000354334.3_Missense_Mutation_p.S581L|HDAC7_ENST00000380610.4_Missense_Mutation_p.S635L|HDAC7_ENST00000080059.7_Missense_Mutation_p.S618L|HDAC7_ENST00000488927.1_5'UTR			Q8WUI4	HDAC7_HUMAN	histone deacetylase 7	579	Histone deacetylase.				cell-cell junction assembly (GO:0007043)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|transcription, DNA-templated (GO:0006351)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein kinase binding (GO:0019901)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25				GBM - Glioblastoma multiforme(48;0.137)		AGAGTGGACCGACTGCAGCTC	0.632													G|||	51	0.0101837	0.0356	0.0058	5008	,	,		13311	0.0		0.0	False		,,,				2504	0.0				p.S618L		Atlas-SNP	.											.	HDAC7	71	.	0			c.C1853T						PASS	.	G	LEU/SER,LEU/SER	134,4272	96.2+/-134.9	4,126,2073	41.0	43.0	42.0		1742,1853	3.5	0.8	12	dbSNP_130	42	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	HDAC7	NM_001098416.2,NM_015401.3	145,145	4,127,6372	AA,AG,GG		0.0116,3.0413,1.038	possibly-damaging,possibly-damaging	581/955,618/992	48185449	135,12871	2203	4300	6503	SO:0001583	missense	51564	exon15			TGGACCGACTGCA	AF239243	CCDS8756.2, CCDS41776.1	12q13.1	2008-02-25	2008-02-25	2008-02-25	ENSG00000061273	ENSG00000061273			14067	protein-coding gene	gene with protein product		606542	"""histone deacetylase 7A"""	HDAC7A		10922406, 10640276	Standard	NM_015401		Approved	DKFZP586J0917	uc010slo.2	Q8WUI4	OTTHUMG00000152968	ENST00000427332.2:c.1736C>T	12.37:g.48185449G>A	ENSP00000404394:p.Ser579Leu	178.0	0.0	0		172.0	79.0	0.459302	NM_015401	B3KY08|B4DWI0|B4E0Q5|Q6P1W9|Q6W9G7|Q7Z4K2|Q7Z5I1|Q96K01|Q9BR73|Q9H7L0|Q9NW41|Q9NWA9|Q9NYK9|Q9UFU7	Missense_Mutation	SNP	ENST00000427332.2	37		17|17	0.007783882783882784|0.007783882783882784	15|15	0.03048780487804878|0.03048780487804878	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	G|G	16.73|16.73	3.204615|3.204615	0.58234|0.58234	0.030413|0.030413	1.16E-4|1.16E-4	ENSG00000061273|ENSG00000061273	ENST00000548080|ENST00000080059;ENST00000354334;ENST00000552960;ENST00000380610;ENST00000427332	.|T;T;T;T;T	.|0.68903	.|-0.36;-0.36;-0.36;-0.36;-0.36	5.3|5.3	3.48|3.48	0.39840|0.39840	.|.	.|0.194140	.|0.45606	.|N	.|0.000346	T|T	0.19127|0.19127	0.0459|0.0459	N|N	0.02539|0.02539	-0.55|-0.55	0.45295|0.45295	D|D	0.998291|0.998291	.|D;D;D	.|0.59767	.|0.963;0.986;0.978	.|B;P;B	.|0.48627	.|0.209;0.584;0.398	T|T	0.07654|0.07654	-1.0761|-1.0761	5|10	.|0.21540	.|T	.|0.41	.|.	7.5367|7.5367	0.27714|0.27714	0.1551:0.1369:0.708:0.0|0.1551:0.1369:0.708:0.0	.|.	.|618;601;581	.|Q8WUI4-5;Q8WUI4-6;Q8WUI4-7	.|.;.;.	W|L	59|618;581;601;635;579	.|ENSP00000080059:S618L;ENSP00000351326:S581L;ENSP00000448532:S601L;ENSP00000369984:S635L;ENSP00000404394:S579L	.|ENSP00000080059:S618L	R|S	-|-	1|2	2|0	HDAC7|HDAC7	46471716|46471716	1.000000|1.000000	0.71417|0.71417	0.765000|0.765000	0.31456|0.31456	0.970000|0.970000	0.65996|0.65996	5.572000|5.572000	0.67411|0.67411	0.759000|0.759000	0.33084|0.33084	-0.261000|-0.261000	0.10672|0.10672	CGG|TCG	G|0.989;A|0.011	0.011	strong		0.632	HDAC7-013	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000328804.2		
SKIV2L	6499	hgsc.bcm.edu	37	6	31928039	31928039	+	Silent	SNP	C	C	G	rs11541400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31928039C>G	ENST00000375394.2	+	4	392	c.279C>G	c.(277-279)gtC>gtG	p.V93V	SKIV2L_ENST00000488648.1_3'UTR|NELFE_ENST00000375425.5_5'Flank|SKIV2L_ENST00000544581.1_Intron|NELFE_ENST00000444811.2_5'Flank|NELFE_ENST00000375429.3_5'Flank	NM_006929.4	NP_008860.4	Q15477	SKIV2_HUMAN	superkiller viralicidic activity 2-like (S. cerevisiae)	93					ATP catabolic process (GO:0006200)	nucleus (GO:0005634)|Ski complex (GO:0055087)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|large_intestine(1)|ovary(1)	4						TTTTGGCTGTCCTGGGAGCCC	0.517													C|||	22	0.00439297	0.0121	0.0058	5008	,	,		19192	0.0		0.002	False		,,,				2504	0.0				p.V93V		Atlas-SNP	.											.	SKIV2L	97	.	0			c.C279G						PASS	.	C		28,2994		0,28,1483	140.0	173.0	161.0		279	0.1	0.0	6	dbSNP_120	161	33,5385		0,33,2676	no	coding-synonymous	SKIV2L	NM_006929.4		0,61,4159	GG,GC,CC		0.6091,0.9265,0.7227		93/1247	31928039	61,8379	1511	2709	4220	SO:0001819	synonymous_variant	6499	exon4			GGCTGTCCTGGGA		CCDS4731.1	6p21	2010-02-17	2001-11-28		ENSG00000204351	ENSG00000204351			10898	protein-coding gene	gene with protein product		600478	"""superkiller viralicidic activity 2 (S. cerevisiae homolog)-like"""	SKIV2		7759100, 9799600	Standard	XM_006715168		Approved	HLP, DDX13, SKI2W, 170A	uc003nyn.1	Q15477	OTTHUMG00000031146	ENST00000375394.2:c.279C>G	6.37:g.31928039C>G		113.0	0.0	0		116.0	53.0	0.456897	NM_006929	O15005|Q12902|Q15476|Q5ST66	Silent	SNP	ENST00000375394.2	37	CCDS4731.1																																																																																			C|0.993;G|0.007	0.007	strong		0.517	SKIV2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076264.3		
NKD2	85409	hgsc.bcm.edu	37	5	1036482	1036482	+	Missense_Mutation	SNP	C	C	A	rs35679233	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:1036482C>A	ENST00000296849.5	+	9	999	c.770C>A	c.(769-771)aCg>aAg	p.T257K	NKD2_ENST00000537972.1_Missense_Mutation_p.T257K|NKD2_ENST00000382730.2_5'Flank|NKD2_ENST00000274150.4_Missense_Mutation_p.T257K	NM_033120.3	NP_149111.1	Q969F2	NKD2_HUMAN	naked cuticle homolog 2 (Drosophila)	257			T -> K (in dbSNP:rs35679233).		exocytosis (GO:0006887)|Golgi vesicle fusion to target membrane (GO:0048210)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein processing (GO:0010954)|protein targeting to plasma membrane (GO:0072661)|Wnt signaling pathway (GO:0016055)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cytoplasmic vesicle (GO:0031410)	calcium ion binding (GO:0005509)|growth factor binding (GO:0019838)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(3)|large_intestine(1)|lung(8)|pancreas(1)	14	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;3.28e-09)		Epithelial(17;0.00093)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00417)|Lung(60;0.165)			GAGAACTACACGTCCAGATTC	0.647													C|||	35	0.00698882	0.0242	0.0043	5008	,	,		10087	0.0		0.0	False		,,,				2504	0.0				p.T257K		Atlas-SNP	.											.	NKD2	39	.	0			c.C770A						PASS	.	C	LYS/THR	64,4342	58.7+/-95.3	0,64,2139	100.0	78.0	85.0		770	2.7	0.2	5	dbSNP_126	85	1,8599	1.2+/-3.3	0,1,4299	yes	missense	NKD2	NM_033120.2	78	0,65,6438	AA,AC,CC		0.0116,1.4526,0.4998	probably-damaging	257/452	1036482	65,12941	2203	4300	6503	SO:0001583	missense	85409	exon9			ACTACACGTCCAG	AF358137	CCDS3859.1, CCDS59486.1	5p15.3	2013-01-10			ENSG00000145506	ENSG00000145506		"""EF-hand domain containing"""	17046	protein-coding gene	gene with protein product	"""naked cuticle-2"", ""Dvl-binding protein NKD2"""	607852				11356022, 11604995	Standard	NM_033120		Approved	Naked2	uc003jbt.2	Q969F2	OTTHUMG00000090348	ENST00000296849.5:c.770C>A	5.37:g.1036482C>A	ENSP00000296849:p.Thr257Lys	72.0	0.0	0		84.0	44.0	0.52381	NM_001271082	Q96EK8|Q9BSN0	Missense_Mutation	SNP	ENST00000296849.5	37	CCDS3859.1	11	0.005036630036630037	8	0.016260162601626018	3	0.008287292817679558	0	0.0	0	0.0	C	14.85	2.658436	0.47467	0.014526	1.16E-4	ENSG00000145506	ENST00000296849;ENST00000274150;ENST00000537972	T;T;T	0.75589	0.25;-0.95;-0.95	4.5	2.69	0.31865	.	0.066054	0.64402	D	0.000014	T	0.71056	0.3295	M	0.76170	2.325	0.80722	D	1	D;D	0.71674	0.998;0.998	D;D	0.68039	0.938;0.955	T	0.76066	-0.3095	10	0.87932	D	0	-4.1939	7.4699	0.27342	0.0:0.7924:0.0:0.2076	rs35679233	257;257	Q969F2-2;Q969F2	.;NKD2_HUMAN	K	257	ENSP00000296849:T257K;ENSP00000274150:T257K;ENSP00000440925:T257K	ENSP00000274150:T257K	T	+	2	0	NKD2	1089482	0.977000	0.34250	0.199000	0.23439	0.223000	0.24884	2.475000	0.45162	0.339000	0.23719	0.491000	0.48974	ACG	C|0.994;A|0.006	0.006	strong		0.647	NKD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206720.2	NM_033120	
RPL37	6167	hgsc.bcm.edu	37	5	40834595	40834595	+	Silent	SNP	G	G	A	rs6495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:40834595G>A	ENST00000274242.5	-	2	266	c.117C>T	c.(115-117)taC>taT	p.Y39Y	RPL37_ENST00000504562.1_5'UTR|SNORD72_ENST00000390994.1_RNA|RPL37_ENST00000508493.1_Silent_p.Y39Y|RPL37_ENST00000509877.1_Silent_p.Y39Y	NM_000997.4	NP_000988.1	P61927	RL37_HUMAN	ribosomal protein L37	39					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)	metal ion binding (GO:0046872)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)|structural constituent of ribosome (GO:0003735)			lung(3)|ovary(1)	4		Breast(839;0.238)				GCTTGGCAGGGTAGCCACATT	0.483													G|||	19	0.00379393	0.0136	0.0014	5008	,	,		19990	0.0		0.0	False		,,,				2504	0.0				p.Y39Y	Colon(188;1411 2035 4978 19588 31462)	Atlas-SNP	.											.	RPL37	7	.	0			c.C117T						PASS	.	G		41,4365	44.6+/-78.6	0,41,2162	58.0	53.0	55.0		117	2.9	1.0	5	dbSNP_52	55	0,8600		0,0,4300	no	coding-synonymous	RPL37	NM_000997.4		0,41,6462	AA,AG,GG		0.0,0.9305,0.3152		39/98	40834595	41,12965	2203	4300	6503	SO:0001819	synonymous_variant	6167	exon2			GGCAGGGTAGCCA	L11567	CCDS3934.1	5p13.1	2013-09-23			ENSG00000145592	ENSG00000145592		"""L ribosomal proteins"""	10347	protein-coding gene	gene with protein product	"""60S ribosomal protein L37a"""	604181				7545944, 9582194	Standard	NM_000997		Approved	L37	uc003jme.1	P61927	OTTHUMG00000094774	ENST00000274242.5:c.117C>T	5.37:g.40834595G>A		62.0	0.0	0		100.0	44.0	0.44	NM_000997	B2R4H2|P02403|Q6IBB4|Q99883	Silent	SNP	ENST00000274242.5	37	CCDS3934.1																																																																																			G|0.996;A|0.004	0.004	strong		0.483	RPL37-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000211583.2	NM_000997	
TRPM2	7226	hgsc.bcm.edu	37	21	45799018	45799018	+	Missense_Mutation	SNP	G	G	A	rs45485992	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45799018G>A	ENST00000397928.1	+	8	1598	c.1153G>A	c.(1153-1155)Gtg>Atg	p.V385M	TRPM2_ENST00000300482.5_Missense_Mutation_p.V385M|TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000397932.2_Missense_Mutation_p.V385M|TRPM2_ENST00000300481.9_Missense_Mutation_p.V385M	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	385			V -> M (in dbSNP:rs45485992). {ECO:0000269|Ref.6}.		calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)			breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						GAAACTGAGCGTGTTCTTCCA	0.587													G|||	14	0.00279553	0.0106	0.0	5008	,	,		22548	0.0		0.0	False		,,,				2504	0.0				p.V385M		Atlas-SNP	.											.	TRPM2	196	.	0			c.G1153A						PASS	.	G	MET/VAL	53,4353	54.2+/-90.2	2,49,2152	127.0	92.0	104.0		1153	-7.7	0.0	21	dbSNP_127	104	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TRPM2	NM_003307.3	21	2,50,6451	AA,AG,GG		0.0116,1.2029,0.4152	benign	385/1504	45799018	54,12952	2203	4300	6503	SO:0001583	missense	7226	exon8			CTGAGCGTGTTCT	AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Nudix motif containing"""	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.1153G>A	21.37:g.45799018G>A	ENSP00000381023:p.Val385Met	75.0	0.0	0		78.0	38.0	0.487179	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	37	CCDS13710.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	3.161	-0.172171	0.06421	0.012029	1.16E-4	ENSG00000142185	ENST00000300482;ENST00000397928;ENST00000300481;ENST00000397932	T;T;T;T	0.36699	1.24;1.24;1.24;1.24	3.84	-7.69	0.01263	.	1.065880	0.07211	N	0.859284	T	0.10380	0.0254	L	0.36672	1.1	0.09310	N	1	B;B	0.25743	0.133;0.133	B;B	0.13407	0.009;0.003	T	0.09037	-1.0693	10	0.45353	T	0.12	-4.1705	3.8491	0.08948	0.4825:0.2381:0.193:0.0864	rs45485992;rs61737083	385;385	E9PGK7;O94759	.;TRPM2_HUMAN	M	385	ENSP00000300482:V385M;ENSP00000381023:V385M;ENSP00000300481:V385M;ENSP00000381026:V385M	ENSP00000300481:V385M	V	+	1	0	TRPM2	44623446	0.000000	0.05858	0.002000	0.10522	0.332000	0.28634	-0.968000	0.03817	-2.737000	0.00381	-1.087000	0.02190	GTG	G|0.994;A|0.006	0.006	strong		0.587	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307	
MYO15A	51168	hgsc.bcm.edu	37	17	18022385	18022385	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18022385C>A	ENST00000205890.5	+	2	609	c.271C>A	c.(271-273)Cgc>Agc	p.R91S		NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	91					inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					GACGCAGATGCGCATGGGCAA	0.662																																					p.R91S		Atlas-SNP	.											.	MYO15A	268	.	0			c.C271A						PASS	.						12.0	15.0	14.0					17																	18022385		1990	4132	6122	SO:0001583	missense	51168	exon2			CAGATGCGCATGG	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"""Myosins / Myosin superfamily : Class XV"""	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.271C>A	17.37:g.18022385C>A	ENSP00000205890:p.Arg91Ser	53.0	0.0	0		84.0	48.0	0.571429	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	CCDS42271.1	.	.	.	.	.	.	.	.	.	.	C	15.86	2.957666	0.53400	.	.	ENSG00000091536	ENST00000205890	D	0.91407	-2.84	5.05	2.82	0.32997	.	.	.	.	.	D	0.85961	0.5819	L	0.29908	0.895	0.80722	D	1	D	0.54207	0.965	P	0.46479	0.518	D	0.86392	0.1736	9	0.72032	D	0.01	.	10.2951	0.43618	0.2213:0.6572:0.1215:0.0	.	91	Q9UKN7	MYO15_HUMAN	S	91	ENSP00000205890:R91S	ENSP00000205890:R91S	R	+	1	0	MYO15A	17963110	0.968000	0.33430	0.999000	0.59377	0.455000	0.32408	0.304000	0.19228	2.333000	0.79357	0.561000	0.74099	CGC	.	.	none		0.662	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
STAG1	10274	hgsc.bcm.edu	37	3	136062724	136062724	+	Missense_Mutation	SNP	C	C	G	rs34149860	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:136062724C>G	ENST00000383202.2	-	30	3652	c.3396G>C	c.(3394-3396)caG>caC	p.Q1132H	STAG1_ENST00000236698.5_Missense_Mutation_p.Q1132H|STAG1_ENST00000536929.1_Missense_Mutation_p.Q716H|STAG1_ENST00000434713.2_Missense_Mutation_p.Q872H	NM_005862.2	NP_005853.2	Q8WVM7	STAG1_HUMAN	stromal antigen 1	1132			Q -> H (in dbSNP:rs34149860).		chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(16)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58						GTTCTTGAATCTGGTCTCCCA	0.448													C|||	436	0.0870607	0.3124	0.0303	5008	,	,		20341	0.0		0.002	False		,,,				2504	0.0				p.Q1132H		Atlas-SNP	.											.	STAG1	135	.	0			c.G3396C						PASS	.	C	HIS/GLN	1218,3188	421.7+/-339.5	170,878,1155	100.0	99.0	99.0		3396	3.5	1.0	3	dbSNP_126	99	12,8588	8.4+/-32.0	0,12,4288	yes	missense	STAG1	NM_005862.2	24	170,890,5443	GG,GC,CC		0.1395,27.6441,9.4572	benign	1132/1259	136062724	1230,11776	2203	4300	6503	SO:0001583	missense	10274	exon30			TTGAATCTGGTCT	Z75330	CCDS3090.1	3q22.2-q22.3	2011-08-12			ENSG00000118007	ENSG00000118007			11354	protein-coding gene	gene with protein product		604358				9305759	Standard	XM_006713471		Approved	SA-1, SCC3A	uc003era.1	Q8WVM7	OTTHUMG00000159798	ENST00000383202.2:c.3396G>C	3.37:g.136062724C>G	ENSP00000372689:p.Gln1132His	136.0	0.0	0		160.0	87.0	0.54375	NM_005862	O00539|Q6P275	Missense_Mutation	SNP	ENST00000383202.2	37	CCDS3090.1	157	0.07188644688644688	145	0.29471544715447157	11	0.03038674033149171	0	0.0	1	0.0013192612137203166	C	8.880	0.951348	0.18431	0.276441	0.001395	ENSG00000118007	ENST00000383202;ENST00000236698;ENST00000434713;ENST00000536929	T;T;T;T	0.32272	1.87;1.9;1.85;1.46	5.48	3.45	0.39498	.	0.196262	0.47455	D	0.000221	T	0.00012	0.0000	N	0.11201	0.11	0.26204	P	0.9793941	B;B	0.06786	0.001;0.001	B;B	0.10450	0.005;0.002	T	0.34725	-0.9817	9	0.41790	T	0.15	.	9.8937	0.41304	0.0:0.7454:0.0:0.2546	rs34149860	1132;1132	Q6P275;Q8WVM7	.;STAG1_HUMAN	H	1132;1132;872;716	ENSP00000372689:Q1132H;ENSP00000236698:Q1132H;ENSP00000404396:Q872H;ENSP00000445787:Q716H	ENSP00000236698:Q1132H	Q	-	3	2	STAG1	137545414	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	1.602000	0.36783	1.316000	0.45131	-0.137000	0.14449	CAG	C|0.914;G|0.086	0.086	strong		0.448	STAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357366.1	NM_005862	
RXFP3	51289	hgsc.bcm.edu	37	5	33937215	33937215	+	Silent	SNP	C	C	T	rs78710898	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:33937215C>T	ENST00000330120.3	+	1	725	c.370C>T	c.(370-372)Ctg>Ttg	p.L124L		NM_016568.3	NP_057652.1	Q9NSD7	RL3R1_HUMAN	relaxin/insulin-like family peptide receptor 3	124					G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled peptide receptor activity (GO:0008528)|G-protein coupled receptor activity (GO:0004930)			endometrium(4)|large_intestine(9)|lung(24)|ovary(1)|skin(1)|upper_aerodigestive_tract(3)	42						CGTCACCAACCTGGCGCTGAC	0.582													C|||	66	0.0131789	0.0469	0.0058	5008	,	,		19766	0.0		0.0	False		,,,				2504	0.0				p.L124L		Atlas-SNP	.											.	RXFP3	114	.	0			c.C370T						PASS	.	C		146,4260	101.2+/-139.8	5,136,2062	137.0	126.0	129.0		370	4.8	1.0	5	dbSNP_132	129	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RXFP3	NM_016568.3		5,137,6361	TT,TC,CC		0.0116,3.3137,1.1302		124/470	33937215	147,12859	2203	4300	6503	SO:0001819	synonymous_variant	51289	exon1			ACCAACCTGGCGC	D88437	CCDS3900.1	5p15.1-p14	2012-08-08	2006-05-09	2006-03-15	ENSG00000182631	ENSG00000182631		"""GPCR / Class A : Relaxin family peptide receptors"""	24883	protein-coding gene	gene with protein product		609445	"""relaxin 3 receptor 1"", ""relaxin family peptide receptor 3"""	RLN3R1		15956688, 16507880	Standard	NM_016568		Approved	SALPR, GPCR135, RXFPR3	uc003jic.2	Q9NSD7	OTTHUMG00000090685	ENST00000330120.3:c.370C>T	5.37:g.33937215C>T		111.0	0.0	0		139.0	76.0	0.546763	NM_016568	Q14DA5	Silent	SNP	ENST00000330120.3	37	CCDS3900.1																																																																																			C|0.989;T|0.011	0.011	strong		0.582	RXFP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207369.1	NM_016568	
MED24	9862	hgsc.bcm.edu	37	17	38189659	38189659	+	Missense_Mutation	SNP	C	C	T	rs34585432	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38189659C>T	ENST00000394128.2	-	7	691	c.610G>A	c.(610-612)Gcc>Acc	p.A204T	MED24_ENST00000394127.2_Missense_Mutation_p.A191T|MED24_ENST00000356271.3_Missense_Mutation_p.A191T|MED24_ENST00000501516.3_Missense_Mutation_p.A223T|MED24_ENST00000479829.1_5'Flank|MED24_ENST00000394126.1_Missense_Mutation_p.A229T	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	204			A -> T (in dbSNP:rs34585432). {ECO:0000269|PubMed:8590280}.		androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					CTGAGATTGGCCAGGATCTCT	0.567													C|||	29	0.00579073	0.0204	0.0029	5008	,	,		19434	0.0		0.0	False		,,,				2504	0.0				p.A204T		Atlas-SNP	.											.	MED24	89	.	0			c.G610A						PASS	.	C	THR/ALA,THR/ALA	92,4314	70.9+/-108.8	1,90,2112	43.0	38.0	40.0		571,610	3.7	1.0	17	dbSNP_126	40	0,8600		0,0,4300	yes	missense,missense	MED24	NM_001079518.1,NM_014815.3	58,58	1,90,6412	TT,TC,CC		0.0,2.0881,0.7074	benign,benign	191/977,204/990	38189659	92,12914	2203	4300	6503	SO:0001583	missense	9862	exon7			GATTGGCCAGGAT	AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"""thyroid hormone receptor associated protein 4"", ""cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"""	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.610G>A	17.37:g.38189659C>T	ENSP00000377686:p.Ala204Thr	93.0	0.0	0		101.0	47.0	0.465347	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Missense_Mutation	SNP	ENST00000394128.2	37	CCDS11359.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	C	13.03	2.115269	0.37339	0.020881	0.0	ENSG00000008838	ENST00000394126;ENST00000356271;ENST00000394128;ENST00000535071;ENST00000394127;ENST00000536318;ENST00000543759;ENST00000535508;ENST00000431269;ENST00000428757	T;T;T	0.42131	0.98;0.98;0.98	5.67	3.69	0.42338	Mediator complex, subunit Med24, N-terminal (1);	0.307388	0.34314	N	0.004079	T	0.23054	0.0557	N	0.08118	0	0.25781	N	0.984725	B;B;B;B;B;B;B;B;D	0.71674	0.367;0.166;0.166;0.357;0.034;0.017;0.034;0.042;0.998	B;B;B;B;B;B;B;B;D	0.78314	0.253;0.096;0.096;0.257;0.04;0.005;0.025;0.042;0.991	T	0.07233	-1.0783	10	0.33141	T	0.24	-14.6106	8.965	0.35872	0.0:0.7801:0.0:0.2199	rs34585432	178;191;154;133;154;114;191;204;146	B9TX63;B9TX65;B4DV99;B4DDR8;F5H5K2;F8W9R9;O75448-2;O75448;F5H0K1	.;.;.;.;.;.;.;MED24_HUMAN;.	T	204;204;204;154;191;146;178;178;114;223	ENSP00000377686:A204T;ENSP00000443344:A154T;ENSP00000377685:A191T	ENSP00000348610:A204T	A	-	1	0	MED24	35443185	0.924000	0.31332	1.000000	0.80357	0.613000	0.37349	0.946000	0.29069	1.402000	0.46780	0.655000	0.94253	GCC	C|0.993;T|0.007	0.007	strong		0.567	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815	
PLXNA4	91584	hgsc.bcm.edu	37	7	131864657	131864657	+	Silent	SNP	G	G	A	rs374317794	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:131864657G>A	ENST00000359827.3	-	20	4625	c.3663C>T	c.(3661-3663)taC>taT	p.Y1221Y	PLXNA4_ENST00000321063.4_Silent_p.Y1221Y			Q9HCM2	PLXA4_HUMAN	plexin A4	1221	IPT/TIG 4.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						TCCCCGGGGAGTACTCCATGC	0.637													G|||	6	0.00119808	0.0045	0.0	5008	,	,		16981	0.0		0.0	False		,,,				2504	0.0				p.Y1221Y		Atlas-SNP	.											.	PLXNA4	873	.	0			c.C3663T						PASS	.	G		9,4255		0,9,2123	15.0	17.0	17.0		3663	4.0	1.0	7		17	0,8480		0,0,4240	no	coding-synonymous	PLXNA4	NM_020911.1		0,9,6363	AA,AG,GG		0.0,0.2111,0.0706		1221/1895	131864657	9,12735	2132	4240	6372	SO:0001819	synonymous_variant	91584	exon20			CGGGGAGTACTCC	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.3663C>T	7.37:g.131864657G>A		49.0	0.0	0		56.0	26.0	0.464286	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	37	CCDS43646.1																																																																																			.	.	weak		0.637	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
KRTAP9-9	81870	hgsc.bcm.edu	37	17	39411711	39411711	+	Missense_Mutation	SNP	C	C	G	rs150962386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39411711C>G	ENST00000394008.1	+	1	76	c.74C>G	c.(73-75)aCc>aGc	p.T25S		NM_030975.2	NP_112237.2	Q9BYP9	KRA99_HUMAN	keratin associated protein 9-9	30	14 X 5 AA repeats of C-C-[RQVGE]- [SPSTNQ]-[TASL].					keratin filament (GO:0045095)				endometrium(3)|skin(2)|upper_aerodigestive_tract(1)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			ACCACTGTGACCACCTGCAGC	0.627													.|||	219	0.04373	0.1566	0.0159	5008	,	,		17225	0.0		0.001	False		,,,				2504	0.0				p.T25S		Atlas-SNP	.											.	KRTAP9-9	24	.	0			c.C74G						PASS	.																																			SO:0001583	missense	81870	exon1			CTGTGACCACCTG	AJ406951	CCDS54127.1	17q21.2	2010-06-03			ENSG00000198083	ENSG00000198083		"""Keratin associated proteins"""	16773	protein-coding gene	gene with protein product			"""keratin associated protein 9-5"""	KRTAP9-5		11279113	Standard	NM_030975		Approved	KAP9.9, KAP9.5	uc021txh.1	Q9BYP9	OTTHUMG00000133602	ENST00000394008.1:c.74C>G	17.37:g.39411711C>G	ENSP00000377576:p.Thr25Ser	39.0	0.0	0		85.0	43.0	0.505882	NM_030975	B5MDD6|Q9BYQ1	Missense_Mutation	SNP	ENST00000394008.1	37	CCDS54127.1	82	0.037545787545787544	72	0.14634146341463414	10	0.027624309392265192	0	0.0	0	0.0	.	6.971	0.549071	0.13312	.	.	ENSG00000198083	ENST00000394008	T	0.00724	5.78	2.19	1.14	0.20703	.	.	.	.	.	T	0.00012	0.0000	N	0.13168	0.305	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.40997	-0.9533	9	0.08381	T	0.77	.	7.4223	0.27079	0.0:0.8514:0.0:0.1486	.	30	Q9BYP9	KRA99_HUMAN	S	25	ENSP00000377576:T25S	ENSP00000377576:T25S	T	+	2	0	KRTAP9-9	36665237	0.931000	0.31567	0.005000	0.12908	0.354000	0.29330	2.718000	0.47236	0.474000	0.27392	0.456000	0.33151	ACC	C|0.962;G|0.038	0.038	strong		0.627	KRTAP9-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257710.1	NM_030975	
RHNO1	83695	hgsc.bcm.edu	37	12	2994562	2994562	+	Silent	SNP	T	T	C	rs371402573	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:2994562T>C	ENST00000489288.2	+	2	182	c.30T>C	c.(28-30)ccT>ccC	p.P10P	RHNO1_ENST00000461997.2_Silent_p.P10P|RHNO1_ENST00000464682.2_Intron	NM_001252499.2|NM_001257097.1|NM_001257098.1	NP_001239428.1|NP_001244026.1|NP_001244027.1	Q9BSD3	RHNO1_HUMAN	RAD9-HUS1-RAD1 interacting nuclear orphan 1	10					cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|DNA damage checkpoint (GO:0000077)|positive regulation of G0 to G1 transition (GO:0070318)|recombinational repair (GO:0000725)	chromosome (GO:0005694)|nucleus (GO:0005634)											GCCGCCAGCCTTCCCAGAAAG	0.552													T|||	3	0.000599042	0.0015	0.0014	5008	,	,		13532	0.0		0.0	False		,,,				2504	0.0				p.P10P		Atlas-SNP	.											.	.	.	.	0			c.T30C						PASS	.	T		1,4405	2.1+/-5.4	0,1,2202	68.0	67.0	67.0			-10.7	0.0	12		67	0,8600		0,0,4300	no	intergenic				0,1,6502	CC,CT,TT		0.0,0.0227,0.0077			2994562	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	83695	exon2			CCAGCCTTCCCAG	AK021945	CCDS8518.1, CCDS58199.1	12p13.33	2012-08-23	2012-08-23	2012-08-23	ENSG00000171792	ENSG00000171792			28206	protein-coding gene	gene with protein product	"""Rad9, Rad1, Hus1 interacting nuclear orphan"""	614085	"""chromosome 12 open reading frame 32"""	C12orf32		20811708, 21659603	Standard	NM_001252499		Approved	HKMT1188, MGC13204, RHINO	uc031qfq.1	Q9BSD3	OTTHUMG00000158557	ENST00000489288.2:c.30T>C	12.37:g.2994562T>C		178.0	0.0	0		162.0	94.0	0.580247	NM_001257098	B7Z989	Silent	SNP	ENST00000489288.2	37	CCDS8518.1																																																																																			.	.	weak		0.552	RHNO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351286.2	NM_031465	
FAT3	120114	hgsc.bcm.edu	37	11	92534968	92534968	+	Missense_Mutation	SNP	G	G	A	rs370539148	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:92534968G>A	ENST00000298047.6	+	9	8806	c.8789G>A	c.(8788-8790)cGa>cAa	p.R2930Q	FAT3_ENST00000525166.1_Missense_Mutation_p.R2780Q|FAT3_ENST00000409404.2_Missense_Mutation_p.R2930Q			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2930	Cadherin 27. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				GAAGTGTACCGAGGGAATGTG	0.552										TCGA Ovarian(4;0.039)			G|||	4	0.000798722	0.003	0.0	5008	,	,		21033	0.0		0.0	False		,,,				2504	0.0				p.R2930Q		Atlas-SNP	.											.	FAT3	1822	.	0			c.G8789A						PASS	.	G	GLN/ARG	7,4033		0,7,2013	94.0	93.0	93.0		8789	5.1	1.0	11		93	0,8374		0,0,4187	no	missense	FAT3	NM_001008781.2	43	0,7,6200	AA,AG,GG		0.0,0.1733,0.0564	possibly-damaging	2930/4558	92534968	7,12407	2020	4187	6207	SO:0001583	missense	120114	exon9			TGTACCGAGGGAA	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.8789G>A	11.37:g.92534968G>A	ENSP00000298047:p.Arg2930Gln	98.0	0.0	0		90.0	49.0	0.544444	NM_001008781	B5MDB0|Q96AU6	Missense_Mutation	SNP	ENST00000298047.6	37		.	.	.	.	.	.	.	.	.	.	G	16.93	3.257586	0.59321	0.001733	0.0	ENSG00000165323	ENST00000298047;ENST00000409404;ENST00000525166	T;T;T	0.01725	4.67;4.67;4.67	6.04	5.08	0.68730	.	.	.	.	.	T	0.02455	0.0075	N	0.20766	0.605	0.80722	D	1	D	0.59357	0.985	P	0.52267	0.694	T	0.71206	-0.4661	9	0.24483	T	0.36	.	10.4452	0.44490	0.157:0.0:0.843:0.0	.	2930	Q8TDW7-3	.	Q	2930;2930;2780	ENSP00000298047:R2930Q;ENSP00000387040:R2930Q;ENSP00000432586:R2780Q	ENSP00000298047:R2930Q	R	+	2	0	FAT3	92174616	1.000000	0.71417	1.000000	0.80357	0.719000	0.41307	1.983000	0.40648	1.433000	0.47394	0.563000	0.77884	CGA	.	.	weak		0.552	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
TACC1	6867	hgsc.bcm.edu	37	8	38677242	38677242	+	Silent	SNP	G	G	A	rs16887780	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:38677242G>A	ENST00000317827.4	+	3	859	c.480G>A	c.(478-480)acG>acA	p.T160T	TACC1_ENST00000518415.1_Silent_p.T115T|TACC1_ENST00000379931.3_Silent_p.T160T|TACC1_ENST00000443286.2_Silent_p.T176T|TACC1_ENST00000522752.1_Intron|TACC1_ENST00000276520.8_Intron|TACC1_ENST00000330691.6_Intron|TACC1_ENST00000520615.1_5'UTR|TACC1_ENST00000520340.1_Silent_p.T124T|TACC1_ENST00000520973.1_5'UTR|TACC1_ENST00000348567.4_Intron|TACC1_ENST00000519416.1_5'UTR|TACC1_ENST00000520611.1_5'Flank	NM_006283.2	NP_006274.2	O75410	TACC1_HUMAN	transforming, acidic coiled-coil containing protein 1	160	Interaction with TDRD7.				cell cycle (GO:0007049)|cell division (GO:0051301)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)				breast(4)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|skin(3)	17		all_lung(54;0.00292)|Lung NSC(58;0.0115)|Hepatocellular(245;0.065)	LUSC - Lung squamous cell carcinoma(45;1.7e-09)|COAD - Colon adenocarcinoma(9;0.235)			AGGATTCCACGGATATCTCGG	0.493													G|||	61	0.0121805	0.0454	0.0014	5008	,	,		20225	0.0		0.0	False		,,,				2504	0.0				p.T160T		Atlas-SNP	.											.	TACC1	98	.	0			c.G480A						PASS	.	G	,,	120,4286	89.7+/-128.4	1,118,2084	101.0	101.0	101.0		,,480	-1.6	0.0	8	dbSNP_123	101	1,8599	1.2+/-3.3	0,1,4299	yes	intron,utr-5,coding-synonymous	TACC1	NM_001122824.1,NM_001146216.2,NM_006283.2	,,	1,119,6383	AA,AG,GG		0.0116,2.7236,0.9303	,,	,,160/806	38677242	121,12885	2203	4300	6503	SO:0001819	synonymous_variant	6867	exon3			TTCCACGGATATC	AF049910	CCDS6109.1, CCDS47845.1, CCDS55224.1	8p11	2012-12-20			ENSG00000147526	ENSG00000147526			11522	protein-coding gene	gene with protein product		605301					Standard	NM_006283		Approved		uc010lwp.3	O75410	OTTHUMG00000164018	ENST00000317827.4:c.480G>A	8.37:g.38677242G>A		225.0	1.0	0.00444444		230.0	117.0	0.508696	NM_006283	B2RBD9|D3DSX6|Q6Y687|Q86YG7|Q8IUJ2|Q8IUJ3|Q8IUJ4|Q8IZG2|Q8NEY7|Q9UPP9	Silent	SNP	ENST00000317827.4	37	CCDS6109.1																																																																																			G|0.991;A|0.009	0.009	strong		0.493	TACC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000376768.1	NM_006283	
RERE	473	hgsc.bcm.edu	37	1	8420966	8420966	+	Silent	SNP	G	G	A	rs77608355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:8420966G>A	ENST00000337907.3	-	19	3235	c.2601C>T	c.(2599-2601)ggC>ggT	p.G867G	RERE_ENST00000476556.1_Silent_p.G313G|RERE_ENST00000400908.2_Silent_p.G867G|RERE_ENST00000400907.2_Intron|RERE_ENST00000377464.1_Silent_p.G599G	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	867	Pro-rich.				chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		GCTGTGGGGGGCCTGGGTGCT	0.726													G|||	162	0.0323482	0.1165	0.0115	5008	,	,		10147	0.0		0.0	False		,,,				2504	0.0				p.G867G		Atlas-SNP	.											.	RERE	129	.	0			c.C2601T						PASS	.	G	,,	201,3379		0,201,1589	3.0	3.0	3.0		2601,939,2601	-10.4	0.5	1	dbSNP_131	3	2,7358		0,2,3678	no	coding-synonymous,coding-synonymous,coding-synonymous	RERE	NM_001042681.1,NM_001042682.1,NM_012102.3	,,	0,203,5267	AA,AG,GG		0.0272,5.6145,1.8556	,,	867/1567,313/1013,867/1567	8420966	203,10737	1790	3680	5470	SO:0001819	synonymous_variant	473	exon19			TGGGGGGCCTGGG	AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"""GATA zinc finger domain containing"""	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.2601C>T	1.37:g.8420966G>A		10.0	0.0	0		11.0	9.0	0.818182	NM_012102	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Silent	SNP	ENST00000337907.3	37	CCDS95.1																																																																																			G|0.972;A|0.028	0.028	strong		0.726	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1		
THRAP3	9967	hgsc.bcm.edu	37	1	36752687	36752687	+	Missense_Mutation	SNP	A	A	G	rs58840555	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:36752687A>G	ENST00000354618.5	+	4	1080	c.856A>G	c.(856-858)Act>Gct	p.T286A	THRAP3_ENST00000469141.2_Missense_Mutation_p.T286A	NM_005119.3	NP_005110.2	Q9Y2W1	TR150_HUMAN	thyroid hormone receptor associated protein 3	286	Ser-rich.				androgen receptor signaling pathway (GO:0030521)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|nuclear-transcribed mRNA catabolic process (GO:0000956)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|phosphoprotein binding (GO:0051219)|poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(5)|stomach(1)	37		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GATGGGCTCAACTCTGCCGAG	0.597			T	USP6	aneurysmal bone cysts								A|||	283	0.0565096	0.1997	0.0274	5008	,	,		19531	0.0		0.0	False		,,,				2504	0.0				p.T286A	Pancreas(129;785 1795 20938 23278 32581)	Atlas-SNP	.		Dom	yes		1	1p34.3	9967	thyroid hormone receptor associated protein 3 (TRAP150)		M	.	THRAP3	93	.	0			c.A856G						PASS	.	A	ALA/THR	773,3633	311.1+/-291.9	88,597,1518	75.0	77.0	76.0		856	-10.2	0.1	1	dbSNP_129	76	9,8591	7.1+/-27.0	0,9,4291	no	missense	THRAP3	NM_005119.3	58	88,606,5809	GG,GA,AA		0.1047,17.5443,6.0126	benign	286/956	36752687	782,12224	2203	4300	6503	SO:0001583	missense	9967	exon4			GGCTCAACTCTGC	AF117756	CCDS405.1	1p34.3	2008-02-05			ENSG00000054118	ENSG00000054118			22964	protein-coding gene	gene with protein product		603809					Standard	NM_005119		Approved	TRAP150	uc001cae.4	Q9Y2W1	OTTHUMG00000007866	ENST00000354618.5:c.856A>G	1.37:g.36752687A>G	ENSP00000346634:p.Thr286Ala	115.0	0.0	0		121.0	49.0	0.404959	NM_005119	D3DPS5|Q5VTK6	Missense_Mutation	SNP	ENST00000354618.5	37	CCDS405.1	101	0.04624542124542125	89	0.18089430894308944	12	0.03314917127071823	0	0.0	0	0.0	A	0.128	-1.116496	0.01799	0.175443	0.001047	ENSG00000054118	ENST00000354618;ENST00000469141	T;T	0.12774	2.65;2.65	5.85	-10.2	0.00374	.	0.656822	0.15045	N	0.283624	T	0.00012	0.0000	N	0.00538	-1.39	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.12967	-1.0527	9	0.06365	T	0.9	0.3741	7.9158	0.29816	0.1879:0.0:0.445:0.3671	rs58840555;rs61732681	286	Q9Y2W1	TR150_HUMAN	A	286	ENSP00000346634:T286A;ENSP00000433825:T286A	ENSP00000346634:T286A	T	+	1	0	THRAP3	36525274	0.000000	0.05858	0.133000	0.22050	0.263000	0.26337	-0.599000	0.05700	-2.368000	0.00604	-2.215000	0.00298	ACT	A|0.946;G|0.054	0.054	strong		0.597	THRAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021688.2	NM_005119	
ACOX1	51	hgsc.bcm.edu	37	17	73944496	73944496	+	Missense_Mutation	SNP	G	G	A	rs35629489	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73944496G>A	ENST00000301608.4	-	13	1831	c.1771C>T	c.(1771-1773)Cgt>Tgt	p.R591C	ACOX1_ENST00000293217.5_Missense_Mutation_p.R591C|ACOX1_ENST00000537812.1_Missense_Mutation_p.R553C	NM_007292.5	NP_009223.2	Q15067	ACOX1_HUMAN	acyl-CoA oxidase 1, palmitoyl	591					alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|fatty acid oxidation (GO:0019395)|generation of precursor metabolites and energy (GO:0006091)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|peroxisome fission (GO:0016559)|positive regulation of cholesterol homeostasis (GO:2000189)|prostaglandin metabolic process (GO:0006693)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)|FAD binding (GO:0071949)|fatty acid binding (GO:0005504)|flavin adenine dinucleotide binding (GO:0050660)|palmitoyl-CoA oxidase activity (GO:0016401)|PDZ domain binding (GO:0030165)|protein N-terminus binding (GO:0047485)|receptor binding (GO:0005102)			large_intestine(2)|lung(7)|ovary(2)|prostate(2)|skin(1)	14					Flavin adenine dinucleotide(DB03147)	TCCTTTACACGCTGGTTTACT	0.388													G|||	69	0.013778	0.0461	0.0043	5008	,	,		18689	0.0		0.002	False		,,,				2504	0.0031				p.R591C		Atlas-SNP	.											ACOX1_ENST00000301608,caecum,carcinoma,0,2	ACOX1	85	2	0			c.C1771T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG	111,4295	85.8+/-124.5	1,109,2093	152.0	132.0	139.0		1657,1771,1771	5.2	0.1	17	dbSNP_126	139	12,8588	9.1+/-34.3	0,12,4288	yes	missense,missense,missense	ACOX1	NM_001185039.1,NM_004035.6,NM_007292.5	180,180,180	1,121,6381	AA,AG,GG		0.1395,2.5193,0.9457	probably-damaging,probably-damaging,probably-damaging	553/623,591/661,591/661	73944496	123,12883	2203	4300	6503	SO:0001583	missense	51	exon13			TTACACGCTGGTT	U03254	CCDS11734.1, CCDS11735.1	17q25.1	2012-10-04	2010-04-30		ENSG00000161533	ENSG00000161533	1.3.3.6		119	protein-coding gene	gene with protein product		609751	"""acyl-Coenzyme A oxidase 1, palmitoyl"""			8159712	Standard	NM_007292		Approved	PALMCOX	uc002jqe.3	Q15067	OTTHUMG00000180027	ENST00000301608.4:c.1771C>T	17.37:g.73944496G>A	ENSP00000301608:p.Arg591Cys	58.0	0.0	0		39.0	12.0	0.307692	NM_007292	A8K6X8|A8KAA0|B4DK61|F5GYQ8|Q12863|Q15068|Q15101|Q16131|Q7Z3W5|Q9UD31	Missense_Mutation	SNP	ENST00000301608.4	37	CCDS11735.1	25	0.011446886446886446	23	0.046747967479674794	0	0.0	0	0.0	2	0.002638522427440633	G	15.54	2.864717	0.51482	0.025193	0.001395	ENSG00000161533	ENST00000301608;ENST00000293217;ENST00000537812;ENST00000539791;ENST00000538781	T;T;T	0.47177	0.85;0.85;0.85	5.25	5.25	0.73442	Acyl-CoA oxidase, C-terminal (1);Acyl-CoA dehydrogenase/oxidase C-terminal (2);	0.099482	0.64402	D	0.000003	T	0.31575	0.0801	M	0.86178	2.8	0.38755	D	0.954204	D;D;P;B	0.76494	0.999;0.998;0.47;0.268	P;P;B;B	0.60117	0.869;0.869;0.106;0.045	T	0.65796	-0.6081	10	0.72032	D	0.01	-11.4201	19.7385	0.96217	0.0:0.0:1.0:0.0	rs35629489	523;553;591;591	F5H0M0;F5GYQ8;Q15067;Q15067-2	.;.;ACOX1_HUMAN;.	C	591;591;553;591;523	ENSP00000301608:R591C;ENSP00000293217:R591C;ENSP00000441257:R553C	ENSP00000293217:R591C	R	-	1	0	ACOX1	71456091	1.000000	0.71417	0.099000	0.21106	0.405000	0.30901	5.538000	0.67193	2.838000	0.97847	0.655000	0.94253	CGT	G|0.989;A|0.011	0.011	strong		0.388	ACOX1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439503.1		
BIN1	274	hgsc.bcm.edu	37	2	127827598	127827598	+	Silent	SNP	C	C	T	rs61748158	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:127827598C>T	ENST00000316724.5	-	5	795	c.384G>A	c.(382-384)acG>acA	p.T128T	BIN1_ENST00000259238.4_Silent_p.T128T|BIN1_ENST00000393040.3_Silent_p.T128T|BIN1_ENST00000348750.4_Silent_p.T128T|BIN1_ENST00000357970.3_Silent_p.T128T|BIN1_ENST00000409400.1_Silent_p.T128T|BIN1_ENST00000393041.3_Silent_p.T128T|BIN1_ENST00000376113.2_Silent_p.T128T|BIN1_ENST00000346226.3_Silent_p.T128T|BIN1_ENST00000351659.3_Silent_p.T128T|BIN1_ENST00000352848.3_Silent_p.T128T	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1	128	BAR. {ECO:0000255|PROSITE- ProRule:PRU00361}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|lipid tube assembly (GO:0060988)|muscle cell differentiation (GO:0042692)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of endocytosis (GO:0045807)|positive regulation of GTPase activity (GO:0043547)|regulation of cell cycle arrest (GO:0071156)|regulation of neuron differentiation (GO:0045664)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|axon initial segment (GO:0043194)|axon terminus (GO:0043679)|cerebellar mossy fiber (GO:0044300)|cytoplasm (GO:0005737)|I band (GO:0031674)|lipid tube (GO:0060987)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)|T-tubule (GO:0030315)|varicosity (GO:0043196)|Z disc (GO:0030018)	identical protein binding (GO:0042802)|tau protein binding (GO:0048156)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(3)|skin(3)	24	Colorectal(110;0.0831)			BRCA - Breast invasive adenocarcinoma(221;0.073)		GGCCCAGGTACGTGTCCATGG	0.597													C|||	18	0.00359425	0.0106	0.0014	5008	,	,		19793	0.003		0.0	False		,,,				2504	0.0				p.T128T		Atlas-SNP	.											.	BIN1	85	.	0			c.G384A						PASS	.	C	,,,,,,,,,	24,4382		0,24,2179	138.0	108.0	118.0		384,384,384,384,384,384,384,384,384,384	-9.6	0.6	2	dbSNP_129	118	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BIN1	NM_004305.3,NM_139343.2,NM_139344.2,NM_139345.2,NM_139346.2,NM_139347.2,NM_139348.2,NM_139349.2,NM_139350.2,NM_139351.2	,,,,,,,,,	0,24,6479	TT,TC,CC		0.0,0.5447,0.1845	,,,,,,,,,	128/455,128/594,128/551,128/507,128/498,128/519,128/483,128/476,128/440,128/410	127827598	24,12982	2203	4300	6503	SO:0001819	synonymous_variant	274	exon5			CAGGTACGTGTCC	U68485	CCDS2137.1, CCDS2138.1, CCDS2139.1, CCDS2140.1, CCDS2141.1, CCDS2142.1, CCDS2143.1, CCDS42743.1, CCDS42744.1, CCDS46403.1	2q14	2014-09-17			ENSG00000136717	ENSG00000136717			1052	protein-coding gene	gene with protein product	"""amphiphysin II"""	601248		AMPHL		8725406, 8782822, 17676042	Standard	NM_004305		Approved	SH3P9, AMPH2	uc002tns.2	O00499	OTTHUMG00000131465	ENST00000316724.5:c.384G>A	2.37:g.127827598C>T		67.0	0.0	0		64.0	32.0	0.5	NM_139346	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Silent	SNP	ENST00000316724.5	37	CCDS2138.1																																																																																			C|0.998;T|0.002	0.002	strong		0.597	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343	
TGIF1	7050	hgsc.bcm.edu	37	18	3452262	3452262	+	Silent	SNP	C	C	T	rs8098291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:3452262C>T	ENST00000330513.5	+	1	588	c.285C>T	c.(283-285)tcC>tcT	p.S95S	TGIF1_ENST00000343820.5_Intron|TGIF1_ENST00000345133.5_Intron|TGIF1_ENST00000400167.2_5'Flank|TGIF1_ENST00000551541.1_Intron|TGIF1_ENST00000551402.1_Intron|TGIF1_ENST00000405385.3_Intron|TGIF1_ENST00000548489.2_Intron|TGIF1_ENST00000407501.2_Intron|TGIF1_ENST00000577543.1_Intron|TGIF1_ENST00000401449.1_Intron	NM_170695.2	NP_733796.2	Q15583	TGIF1_HUMAN	TGFB-induced factor homeobox 1	95					determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|negative regulation of cell proliferation (GO:0008285)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|nodal signaling pathway (GO:0038092)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of neuron differentiation (GO:0045666)|regulation of gastrulation (GO:0010470)|response to drug (GO:0042493)|retina development in camera-type eye (GO:0060041)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(3)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	13	Esophageal squamous(4;0.0859)	Colorectal(8;0.0104)				GTGCCCTCTCCCCGGAGCTGG	0.771													C|||	265	0.0529153	0.1861	0.0245	5008	,	,		9736	0.0		0.002	False		,,,				2504	0.0				p.S95S		Atlas-SNP	.											.	TGIF1	41	.	0			c.C285T						PASS	.	C	,,,,,,	598,3670		33,532,1569	8.0	9.0	9.0		,285,,,,,	3.5	0.0	18	dbSNP_116	9	17,8359		0,17,4171	no	intron,coding-synonymous,intron,intron,intron,intron,intron	TGIF1	NM_003244.2,NM_170695.2,NM_173207.1,NM_173208.1,NM_173209.1,NM_173210.1,NM_174886.1	,,,,,,	33,549,5740	TT,TC,CC		0.203,14.0112,4.864	,,,,,,	,95/402,,,,,	3452262	615,12029	2134	4188	6322	SO:0001819	synonymous_variant	7050	exon1			CCTCTCCCCGGAG	X89750	CCDS11832.1, CCDS11833.1, CCDS11834.1, CCDS11835.1	18p11.31	2011-06-20	2007-01-30	2007-01-30	ENSG00000177426	ENSG00000177426		"""Homeoboxes / TALE class"""	11776	protein-coding gene	gene with protein product		602630	"""TGFB-induced factor (TALE family homeobox)"""	HPE4, TGIF		8537382, 10835638	Standard	NM_173211		Approved		uc002klz.3	Q15583	OTTHUMG00000131511	ENST00000330513.5:c.285C>T	18.37:g.3452262C>T		16.0	0.0	0		22.0	14.0	0.636364	NM_170695	A6NE42|A6NLU7|F8VZB6|Q6ICR0|Q8N5X9|Q9NRS0	Silent	SNP	ENST00000330513.5	37	CCDS11834.1																																																																																			C|0.953;T|0.047	0.047	strong		0.771	TGIF1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254368.4	NM_170695	
PIEZO1	9780	hgsc.bcm.edu	37	16	88800122	88800122	+	Silent	SNP	C	C	G	rs9928479	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88800122C>G	ENST00000301015.9	-	18	2607	c.2361G>C	c.(2359-2361)cgG>cgC	p.R787R	RP5-1142A6.2_ENST00000440406.2_RNA	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	787					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1)	10						GCTCCAGCAGCCGCTCAGCCA	0.662													c|||	303	0.0605032	0.2194	0.0187	5008	,	,		15726	0.0		0.0	False		,,,				2504	0.0				p.R787R		Atlas-SNP	.											.	PIEZO1	79	.	0			c.G2361C						PASS	.						4.0	9.0	8.0					16																	88800122		636	1499	2135	SO:0001819	synonymous_variant	9780	exon18			CAGCAGCCGCTCA	D87071	CCDS54058.1	16q24.3	2011-08-31	2011-08-31	2011-08-31	ENSG00000103335	ENSG00000103335			28993	protein-coding gene	gene with protein product		611184	"""family with sequence similarity 38, member A"""	FAM38A		20813920, 21056836, 21299953, 21696149	Standard	NM_001142864		Approved	KIAA0233	uc010vpb.2	Q92508	OTTHUMG00000156776	ENST00000301015.9:c.2361G>C	16.37:g.88800122C>G		54.0	0.0	0		64.0	21.0	0.328125	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Silent	SNP	ENST00000301015.9	37	CCDS54058.1	93	0.042582417582417584	85	0.17276422764227642	6	0.016574585635359115	0	0.0	2	0.002638522427440633	C	11.51	1.659600	0.29515	.	.	ENSG00000103335	ENST00000451779	.	.	.	4.7	0.207	0.15214	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.09310	P	0.9999999999997674	.	.	.	.	.	.	T	0.13683	-1.0500	3	.	.	.	-48.0889	6.7645	0.23558	0.1152:0.2818:0.5236:0.0793	rs9928479;rs61498906	.	.	.	P	733	.	.	A	-	1	0	FAM38A	87327623	1.000000	0.71417	0.996000	0.52242	0.970000	0.65996	1.524000	0.35942	-0.107000	0.12088	0.556000	0.70494	GCT	C|0.955;G|0.045	0.045	strong		0.662	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
LGI3	203190	hgsc.bcm.edu	37	8	22009053	22009053	+	Silent	SNP	G	G	A	rs35142808	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22009053G>A	ENST00000306317.2	-	7	1067	c.778C>T	c.(778-780)Ctg>Ttg	p.L260L	LGI3_ENST00000424267.2_Silent_p.L236L	NM_139278.2	NP_644807.1	Q8N145	LGI3_HUMAN	leucine-rich repeat LGI family, member 3	260					exocytosis (GO:0006887)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|extracellular region (GO:0005576)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	catalytic activity (GO:0003824)			endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	17				Colorectal(74;0.00189)|COAD - Colon adenocarcinoma(73;0.0612)|READ - Rectum adenocarcinoma(644;0.0999)		TCCCACTTCAGGATGGTGCAG	0.602													G|||	174	0.0347444	0.1203	0.0043	5008	,	,		19819	0.0		0.003	False		,,,				2504	0.0092				p.L260L		Atlas-SNP	.											.	LGI3	44	.	0			c.C778T						PASS	.	G		467,3939	219.4+/-237.2	32,403,1768	87.0	89.0	89.0		778	4.2	0.8	8	dbSNP_126	89	25,8575	17.9+/-57.8	1,23,4276	no	coding-synonymous	LGI3	NM_139278.2		33,426,6044	AA,AG,GG		0.2907,10.5992,3.7829		260/549	22009053	492,12514	2203	4300	6503	SO:0001819	synonymous_variant	203190	exon7			ACTTCAGGATGGT	AJ487518	CCDS6025.1	8p21.2	2008-07-28			ENSG00000168481	ENSG00000168481			18711	protein-coding gene	gene with protein product		608302				12023020, 18628660	Standard	NM_139278		Approved		uc003xav.3	Q8N145	OTTHUMG00000131599	ENST00000306317.2:c.778C>T	8.37:g.22009053G>A		96.0	0.0	0		113.0	55.0	0.486726	NM_139278	A5PLP2|Q86TL4|Q8N296	Silent	SNP	ENST00000306317.2	37	CCDS6025.1																																																																																			G|0.968;A|0.032	0.032	strong		0.602	LGI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254482.1		
DCHS2	54798	hgsc.bcm.edu	37	4	155407595	155407595	+	Nonstop_Mutation	SNP	C	C	A	rs140554741	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:155407595C>A	ENST00000456341.2	-	2	2108	c.2109G>T	c.(2107-2109)taG>taT	p.*703Y	DCHS2_ENST00000443500.1_Nonstop_Mutation_p.*710Y|DCHS2_ENST00000339452.1_Intron			Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	0	Cadherin 6. {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.*710Y(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		TACAGGAAATCTAGGCAAGAT	0.353													C|||	93	0.0185703	0.0008	0.0086	5008	,	,		21542	0.001		0.0298	False		,,,				2504	0.0562				p.X710Y		Atlas-SNP	.											DCHS2_ENST00000443500,NS,carcinoma,0,1	DCHS2	594	1	1	Nonstop extension(1)	kidney(1)	c.G2130T						PASS	.						268.0	215.0	231.0					4																	155407595		692	1591	2283	SO:0001578	stop_lost	54798	exon2			GGAAATCTAGGCA	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000456341.2:c.2109G>T	4.37:g.155407595C>A		113.0	0.0	0		97.0	36.0	0.371134	NM_001142553	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000456341.2	37		24	0.01098901098901099	0	0.0	3	0.008287292817679558	0	0.0	21	0.027704485488126648	C	13.13	2.144810	0.37825	.	.	ENSG00000197410	ENST00000456341;ENST00000443500	.	.	.	2.87	-2.53	0.06326	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.6935	0.05127	0.3797:0.2807:0.0:0.3396	.	.	.	.	Y	703;710	.	.	X	-	3	2	DCHS2	155627045	0.000000	0.05858	0.000000	0.03702	0.592000	0.36648	-0.749000	0.04813	-0.726000	0.04895	0.561000	0.74099	TAG	C|0.989;A|0.011	0.011	strong		0.353	DCHS2-005	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000365285.1	NM_001142552	
TECTA	7007	hgsc.bcm.edu	37	11	121016424	121016424	+	Missense_Mutation	SNP	A	A	G	rs200852252	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:121016424A>G	ENST00000392793.1	+	12	3975	c.3704A>G	c.(3703-3705)aAc>aGc	p.N1235S	TECTA_ENST00000264037.2_Missense_Mutation_p.N1235S|TECTA_ENST00000478058.1_3'UTR			O75443	TECTA_HUMAN	tectorin alpha	1235	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		AGCATGCAGAACAGCACCTAT	0.532													A|||	4	0.000798722	0.0015	0.0029	5008	,	,		22478	0.0		0.0	False		,,,				2504	0.0				p.N1235S		Atlas-SNP	.											.	TECTA	329	.	0			c.A3704G						PASS	.	A	SER/ASN	2,4404	4.2+/-10.8	0,2,2201	157.0	126.0	136.0		3704	4.6	1.0	11		136	0,8598		0,0,4299	no	missense	TECTA	NM_005422.2	46	0,2,6500	GG,GA,AA		0.0,0.0454,0.0154	probably-damaging	1235/2156	121016424	2,13002	2203	4299	6502	SO:0001583	missense	7007	exon11			TGCAGAACAGCAC	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.3704A>G	11.37:g.121016424A>G	ENSP00000376543:p.Asn1235Ser	189.0	0.0	0		150.0	71.0	0.473333	NM_005422		Missense_Mutation	SNP	ENST00000392793.1	37	CCDS8434.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	A	17.08	3.298372	0.60195	4.54E-4	0.0	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.62788	-0.0;-0.0	5.76	4.57	0.56435	von Willebrand factor, type D domain (3);	0.000000	0.85682	D	0.000000	T	0.72463	0.3463	L	0.55213	1.73	0.40504	D	0.980674	D	0.76494	0.999	D	0.83275	0.996	T	0.70927	-0.4739	10	0.31617	T	0.26	.	12.6018	0.56501	0.8617:0.1383:0.0:0.0	.	1235	O75443	TECTA_HUMAN	S	1235	ENSP00000376543:N1235S;ENSP00000264037:N1235S	ENSP00000264037:N1235S	N	+	2	0	TECTA	120521634	1.000000	0.71417	0.970000	0.41538	0.986000	0.74619	5.257000	0.65473	2.196000	0.70406	0.482000	0.46254	AAC	A|1.000;G|0.000	0.000	strong		0.532	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422	
DNAH10	196385	hgsc.bcm.edu	37	12	124401172	124401172	+	Missense_Mutation	SNP	G	G	A	rs61740383	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124401172G>A	ENST00000409039.3	+	62	10562	c.10537G>A	c.(10537-10539)Gac>Aac	p.D3513N		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3513	AAA 5. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		TATCCTGGGAGACAAGGAAGT	0.433													G|||	327	0.0652955	0.2322	0.0231	5008	,	,		21713	0.0		0.003	False		,,,				2504	0.001				p.D3513N		Atlas-SNP	.											.	DNAH10	888	.	0			c.G10537A						PASS	.	G	ASN/ASP	688,3042		58,572,1235	71.0	72.0	72.0		10537	4.7	1.0	12	dbSNP_129	72	38,8150		1,36,4057	yes	missense	DNAH10	NM_207437.3	23	59,608,5292	AA,AG,GG		0.4641,18.445,6.0916	probably-damaging	3513/4472	124401172	726,11192	1865	4094	5959	SO:0001583	missense	196385	exon62			CTGGGAGACAAGG	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.10537G>A	12.37:g.124401172G>A	ENSP00000386770:p.Asp3513Asn	83.0	0.0	0		98.0	52.0	0.530612	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	113	0.051739926739926737	100	0.2032520325203252	11	0.03038674033149171	0	0.0	2	0.002638522427440633	G	32	5.137071	0.94517	0.18445	0.004641	ENSG00000197653	ENST00000409039	T	0.33654	1.4	4.74	4.74	0.60224	.	0.000000	0.85682	D	0.000000	T	0.00144	0.0004	M	0.90425	3.115	0.09310	P	0.999999878792	D	0.89917	1.0	D	0.87578	0.998	T	0.02471	-1.1154	9	0.87932	D	0	.	17.7267	0.88367	0.0:0.0:1.0:0.0	rs61740383	3513	Q8IVF4	DYH10_HUMAN	N	3513	ENSP00000386770:D3513N	ENSP00000386770:D3513N	D	+	1	0	DNAH10	122967125	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.869000	0.99810	2.177000	0.69029	0.561000	0.74099	GAC	G|0.957;A|0.043	0.043	strong		0.433	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
DNPEP	23549	hgsc.bcm.edu	37	2	220250769	220250769	+	Missense_Mutation	SNP	T	T	C	rs6742404	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220250769T>C	ENST00000273075.4	-	6	731	c.511A>G	c.(511-513)Att>Gtt	p.I171V	AC053503.4_ENST00000420563.1_RNA|DNPEP_ENST00000373972.1_Missense_Mutation_p.I96V|DNPEP_ENST00000523282.1_Missense_Mutation_p.I179V	NM_012100.2	NP_036232	Q9ULA0	DNPEP_HUMAN	aspartyl aminopeptidase	161					peptide metabolic process (GO:0006518)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Renal(207;0.0474)		Epithelial(149;1.09e-06)|all cancers(144;0.000179)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		ATGCGAAGAATGGGCCGCTCC	0.627													T|||	134	0.0267572	0.0961	0.0101	5008	,	,		19551	0.0		0.0	False		,,,				2504	0.0				p.I171V		Atlas-SNP	.											.	DNPEP	40	.	0			c.A511G						PASS	.	T	VAL/ILE	385,3907		26,333,1787	83.0	94.0	90.0		511	3.7	1.0	2	dbSNP_116	90	1,8519		0,1,4259	yes	missense	DNPEP	NM_012100.2	29	26,334,6046	CC,CT,TT		0.0117,8.9702,3.0128	benign	171/486	220250769	386,12426	2146	4260	6406	SO:0001583	missense	23549	exon6			GAAGAATGGGCCG		CCDS42823.1	2q36.1	2008-05-22			ENSG00000123992	ENSG00000123992			2981	protein-coding gene	gene with protein product		611367				9632644	Standard	NM_012100		Approved	DAP, ASPEP	uc002vle.2	Q9ULA0	OTTHUMG00000058919	ENST00000273075.4:c.511A>G	2.37:g.220250769T>C	ENSP00000273075:p.Ile171Val	182.0	0.0	0		210.0	111.0	0.528571	NM_012100	Q9BW44|Q9NUV5	Missense_Mutation	SNP	ENST00000273075.4	37	CCDS42823.1	43	0.019688644688644688	41	0.08333333333333333	2	0.0055248618784530384	0	0.0	0	0.0	T	12.99	2.104829	0.37145	0.089702	1.17E-4	ENSG00000123992	ENST00000273075;ENST00000337010;ENST00000373972;ENST00000523282;ENST00000535056;ENST00000457935;ENST00000429013;ENST00000521459;ENST00000322176;ENST00000434339;ENST00000430206	.	.	.	4.87	3.71	0.42584	Peptidase M18, domain 2 (1);	0.138463	0.51477	D	0.000095	T	0.03477	0.0100	L	0.46614	1.455	0.49798	D	0.999821	B;B;B;B;B	0.21606	0.005;0.058;0.033;0.005;0.002	B;B;B;B;B	0.24269	0.033;0.052;0.052;0.015;0.02	T	0.04017	-1.0984	9	0.49607	T	0.09	-6.0541	10.134	0.42695	0.0:0.0791:0.0:0.9209	rs6742404	179;171;179;161;171	E7ETB3;B7Z822;B7Z7F0;Q9ULA0;Q53SB6	.;.;.;DNPEP_HUMAN;.	V	171;171;96;179;64;179;157;171;171;96;96	.	ENSP00000273075:I171V	I	-	1	0	DNPEP	219959013	0.580000	0.26733	0.998000	0.56505	0.850000	0.48378	0.182000	0.16900	0.718000	0.32166	0.459000	0.35465	ATT	T|0.962;C|0.038	0.038	strong		0.627	DNPEP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000130212.1	NM_012100	
FLG	2312	hgsc.bcm.edu	37	1	152275559	152275559	+	Missense_Mutation	SNP	A	A	G	rs3126065	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152275559A>G	ENST00000368799.1	-	3	11838	c.11803T>C	c.(11803-11805)Tca>Cca	p.S3935P	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3935	Ser-rich.		S -> P (in dbSNP:rs3126065).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GAATCTTGTGAAAGACTACTA	0.468									Ichthyosis				A|||	548	0.109425	0.3979	0.0303	5008	,	,		22781	0.0		0.001	False		,,,				2504	0.0				p.S3935P		Atlas-SNP	.											.	FLG	900	.	0			c.T11803C						PASS	.	A	PRO/SER	1446,2960	468.3+/-355.1	228,990,985	138.0	133.0	135.0		11803	-0.9	0.0	1	dbSNP_103	135	14,8586	9.8+/-36.6	0,14,4286	yes	missense	FLG	NM_002016.1	74	228,1004,5271	GG,GA,AA		0.1628,32.8189,11.2256	probably-damaging	3935/4062	152275559	1460,11546	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTTGTGAAAGACT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.11803T>C	1.37:g.152275559A>G	ENSP00000357789:p.Ser3935Pro	177.0	1.0	0.00564972		178.0	178.0	1	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	185	0.08470695970695971	174	0.35365853658536583	11	0.03038674033149171	0	0.0	0	0.0	A	4.914	0.169897	0.09339	0.328189	0.001628	ENSG00000143631	ENST00000368799	T	0.03772	3.81	2.35	-0.929	0.10444	.	.	.	.	.	T	0.01661	0.0053	L	0.52573	1.65	0.80722	P	0.0	D	0.53885	0.963	B	0.44108	0.441	T	0.39461	-0.9613	8	0.46703	T	0.11	.	1.6209	0.02713	0.4417:0.0:0.2748:0.2835	rs3126065;rs3126065	3935	P20930	FILA_HUMAN	P	3935	ENSP00000357789:S3935P	ENSP00000357789:S3935P	S	-	1	0	FLG	150542183	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.627000	0.05521	-0.321000	0.08627	0.533000	0.62120	TCA	A|0.871;G|0.129	0.129	strong		0.468	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
ADAMDEC1	27299	hgsc.bcm.edu	37	8	24256389	24256389	+	Silent	SNP	A	A	T	rs7001097	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24256389A>T	ENST00000256412.4	+	9	985	c.765A>T	c.(763-765)atA>atT	p.I255I	RP11-624C23.1_ENST00000519689.1_RNA|ADAMDEC1_ENST00000522298.1_Silent_p.I176I|RP11-624C23.1_ENST00000523578.1_RNA|ADAMDEC1_ENST00000538205.1_Silent_p.I176I	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	255	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				immune response (GO:0006955)|negative regulation of cell adhesion (GO:0007162)	extracellular region (GO:0005576)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|large_intestine(4)|skin(2)|stomach(1)	9		Prostate(55;0.0181)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)		TTCCACAGATATATAACACCA	0.413													T|||	88	0.0175719	0.0635	0.0058	5008	,	,		20707	0.0		0.0	False		,,,				2504	0.0				p.I255I	Ovarian(147;687 1849 3699 25981 31337)	Atlas-SNP	.											.	ADAMDEC1	69	.	0			c.A765T						PASS	.	T	,,	261,4145	803.2+/-415.7	11,239,1953	92.0	91.0	91.0		528,528,765	0.2	0.9	8	dbSNP_116	91	2,8598	818.9+/-406.8	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	ADAMDEC1	NM_001145271.1,NM_001145272.1,NM_014479.3	,,	11,241,6251	TT,TA,AA		0.0233,5.9237,2.0221	,,	176/392,176/392,255/471	24256389	263,12743	2203	4300	6503	SO:0001819	synonymous_variant	27299	exon9			ACAGATATATAAC	Y13323	CCDS6044.1, CCDS55212.1	8p12	2008-08-07			ENSG00000134028	ENSG00000134028			16299	protein-coding gene	gene with protein product		606393				9271581, 12037602	Standard	NM_001145271		Approved	M12.219	uc003xdz.2	O15204	OTTHUMG00000097858	ENST00000256412.4:c.765A>T	8.37:g.24256389A>T		80.0	0.0	0		113.0	51.0	0.451327	NM_014479	B7ZAK5	Silent	SNP	ENST00000256412.4	37	CCDS6044.1																																																																																			A|0.977;T|0.023	0.023	strong		0.413	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479	
DLG5	9231	hgsc.bcm.edu	37	10	79556305	79556305	+	Missense_Mutation	SNP	C	C	T	rs74140334	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:79556305C>T	ENST00000372391.2	-	28	5217	c.5212G>A	c.(5212-5214)Gct>Act	p.A1738T	DLG5_ENST00000459739.1_5'UTR|DLG5_ENST00000372388.2_Missense_Mutation_p.A1398T	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	1738	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				apical protein localization (GO:0045176)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|intracellular signal transduction (GO:0035556)|metanephric collecting duct development (GO:0072205)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|polarized epithelial cell differentiation (GO:0030859)|protein complex assembly (GO:0006461)|protein localization to adherens junction (GO:0071896)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|zonula adherens assembly (GO:0045186)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cytoskeletal protein binding (GO:0008092)|receptor signaling complex scaffold activity (GO:0030159)			breast(9)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(17)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	60	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)			GGCCTCAGAGCGGTGCAGTCC	0.597													C|||	70	0.0139776	0.0514	0.0014	5008	,	,		19795	0.0		0.001	False		,,,				2504	0.0				p.A1738T		Atlas-SNP	.											.	DLG5	154	.	0			c.G5212A						PASS	.	C	THR/ALA	164,4242	110.4+/-148.6	2,160,2041	100.0	85.0	90.0		5212	2.4	0.1	10	dbSNP_130	90	2,8598	2.2+/-6.3	0,2,4298	yes	missense	DLG5	NM_004747.3	58	2,162,6339	TT,TC,CC		0.0233,3.7222,1.2763	benign	1738/1920	79556305	166,12840	2203	4300	6503	SO:0001583	missense	9231	exon28			TCAGAGCGGTGCA	U61843	CCDS7353.2	10q23	2008-07-09	2001-11-28		ENSG00000151208	ENSG00000151208			2904	protein-coding gene	gene with protein product		604090	"""discs, large (Drosophila) homolog 5"""			9738934	Standard	XM_005270276		Approved	P-dlg, KIAA0583	uc001jzk.3	Q8TDM6	OTTHUMG00000018548	ENST00000372391.2:c.5212G>A	10.37:g.79556305C>T	ENSP00000361467:p.Ala1738Thr	241.0	0.0	0		210.0	96.0	0.457143	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Missense_Mutation	SNP	ENST00000372391.2	37	CCDS7353.2	29	0.013278388278388278	28	0.056910569105691054	1	0.0027624309392265192	0	0.0	0	0.0	C	6.638	0.486271	0.12641	0.037222	2.33E-4	ENSG00000151208	ENST00000372391;ENST00000424842;ENST00000372388	T;T;T	0.16457	2.34;2.34;2.34	5.97	2.38	0.29361	Guanylate kinase/L-type calcium channel (1);	0.200014	0.25233	N	0.032160	T	0.00552	0.0018	N	0.03608	-0.345	0.29378	N	0.863515	B;B	0.27882	0.0;0.192	B;B	0.21360	0.0;0.034	T	0.39333	-0.9619	10	0.02654	T	1	.	8.5372	0.33371	0.6271:0.2508:0.0:0.1221	.	1738;1398	Q8TDM6;Q8TDM6-2	DLG5_HUMAN;.	T	1738;699;1398	ENSP00000361467:A1738T;ENSP00000394797:A699T;ENSP00000361464:A1398T	ENSP00000361464:A1398T	A	-	1	0	DLG5	79226311	0.996000	0.38824	0.059000	0.19551	0.082000	0.17680	3.446000	0.52928	0.153000	0.19213	-0.262000	0.10625	GCT	C|0.988;T|0.012	0.012	strong		0.597	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2		
PIWIL4	143689	hgsc.bcm.edu	37	11	94320300	94320300	+	Silent	SNP	C	C	T	rs145516372	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:94320300C>T	ENST00000299001.6	+	7	1012	c.801C>T	c.(799-801)gtC>gtT	p.V267V	RP11-867G2.8_ENST00000536540.1_RNA|RP11-867G2.8_ENST00000537874.1_RNA	NM_152431.2	NP_689644.2	Q7Z3Z4	PIWL4_HUMAN	piwi-like RNA-mediated gene silencing 4	267					cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|P granule (GO:0043186)|piP-body (GO:0071547)	piRNA binding (GO:0034584)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|urinary_tract(2)	30		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.0123)				GTTACAAAGTCCTCCGGAATG	0.433													C|||	51	0.0101837	0.0371	0.0029	5008	,	,		18230	0.0		0.0	False		,,,				2504	0.0				p.V267V		Atlas-SNP	.											.	PIWIL4	70	.	0			c.C801T						PASS	.	C		116,4286	88.7+/-127.4	2,112,2087	188.0	191.0	190.0		801	1.8	0.9	11	dbSNP_134	190	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous	PIWIL4	NM_152431.2		2,113,6384	TT,TC,CC		0.0116,2.6352,0.9001		267/853	94320300	117,12881	2201	4298	6499	SO:0001819	synonymous_variant	143689	exon7			CAAAGTCCTCCGG	AB079366	CCDS31656.1	11q12	2013-02-15	2013-02-15			ENSG00000134627		"""Argonaute/PIWI family"""	18444	protein-coding gene	gene with protein product		610315	"""piwi-like 4 (Drosophila)"""			12906857	Standard	NM_152431		Approved	FLJ36156, HIWI2, Miwi2	uc001pfa.3	Q7Z3Z4		ENST00000299001.6:c.801C>T	11.37:g.94320300C>T		119.0	0.0	0		124.0	47.0	0.379032	NM_152431	B4DEG5|Q68CZ4|Q8N8G9|Q8N9V8|Q8NEH2	Silent	SNP	ENST00000299001.6	37	CCDS31656.1																																																																																			C|0.992;T|0.008	0.008	strong		0.433	PIWIL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396388.1	NM_152431	
BPIFA3	128861	hgsc.bcm.edu	37	20	31812949	31812949	+	Silent	SNP	C	C	T	rs147632261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31812949C>T	ENST00000375454.3	+	4	642	c.432C>T	c.(430-432)atC>atT	p.I144I	BPIFA3_ENST00000490499.1_3'UTR|BPIFA3_ENST00000375452.3_Silent_p.I108I	NM_178466.3	NP_848561.2	Q9BQP9	BPIA3_HUMAN	BPI fold containing family A, member 3	144						extracellular region (GO:0005576)	lipid binding (GO:0008289)										ATATGAGCATCGTTGTGGAGT	0.522													C|||	24	0.00479233	0.0136	0.0029	5008	,	,		22489	0.0		0.004	False		,,,				2504	0.0				p.I144I		Atlas-SNP	.											.	.	.	.	0			c.C432T						PASS	.	C	,	54,4352	52.9+/-88.7	0,54,2149	205.0	196.0	199.0		324,432	2.5	0.1	20	dbSNP_134	199	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous,coding-synonymous	BPIFA3	NM_001042439.1,NM_178466.3	,	0,64,6439	TT,TC,CC		0.1163,1.2256,0.4921	,	108/219,144/255	31812949	64,12942	2203	4300	6503	SO:0001819	synonymous_variant	128861	exon4			GAGCATCGTTGTG		CCDS13216.2, CCDS42865.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131059	ENSG00000131059		"""BPI fold containing"""	16204	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 71"""	C20orf71		11971875, 21787333	Standard	XR_244132		Approved	bA49G10.4, SPLUNC3	uc002wyr.3	Q9BQP9	OTTHUMG00000032245	ENST00000375454.3:c.432C>T	20.37:g.31812949C>T		136.0	0.0	0		162.0	84.0	0.518519	NM_178466	Q5JWG8|Q6NZ38	Silent	SNP	ENST00000375454.3	37	CCDS13216.2																																																																																			C|0.995;T|0.005	0.005	strong		0.522	BPIFA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078672.1	NM_178466	
MUC4	4585	hgsc.bcm.edu	37	3	195511486	195511486	+	Missense_Mutation	SNP	G	G	T	rs71180962|rs202186297	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195511486G>T	ENST00000463781.3	-	2	7424	c.6965C>A	c.(6964-6966)cCt>cAt	p.P2322H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P2322H	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)		GCTGGTGACAGGAAGAGGGGT	0.592																																					p.P2322H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.C6965A						scavenged	.						6.0	6.0	6.0					3																	195511486		588	1429	2017	SO:0001583	missense	4585	exon2			GTGACAGGAAGAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.6965C>A	3.37:g.195511486G>T	ENSP00000417498:p.Pro2322His	113.0	0.0	0		113.0	26.0	0.230089	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	G	5.604	0.296160	0.10622	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33654	1.4;1.41	.	.	.	.	0.000000	0.25881	U	0.027698	T	0.14527	0.0351	N	0.08118	0	0.20489	N	0.999896	B	0.22909	0.077	B	0.11329	0.006	T	0.21518	-1.0243	8	.	.	.	.	6.7067	0.23254	2.0E-4:0.0:0.9998:0.0	.	2322	E7ESK3	.	H	2322	ENSP00000417498:P2322H;ENSP00000420243:P2322H	.	P	-	2	0	MUC4	196995881	0.000000	0.05858	0.002000	0.10522	0.095000	0.18619	-2.721000	0.00811	0.488000	0.27723	0.064000	0.15345	CCT	G|0.996;T|0.005	0.005	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
OR8H3	390152	hgsc.bcm.edu	37	11	55889918	55889918	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55889918G>A	ENST00000313472.3	+	1	70	c.70G>A	c.(70-72)Gtc>Atc	p.V24I		NM_001005201.1	NP_001005201.1	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H, member 3	24						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(30)|ovary(2)|prostate(1)|skin(3)|stomach(1)	42	Esophageal squamous(21;0.00693)					CTCTGAAGAGGTCCAGATGGC	0.453																																					p.V24I		Atlas-SNP	.											.	OR8H3	92	.	0			c.G70A						PASS	.						204.0	194.0	198.0					11																	55889918		2201	4296	6497	SO:0001583	missense	390152	exon1			GAAGAGGTCCAGA	AB065840	CCDS31519.1	11q11	2012-08-09			ENSG00000181761	ENSG00000181761		"""GPCR / Class A : Olfactory receptors"""	15309	protein-coding gene	gene with protein product							Standard	NM_001005201		Approved		uc001nii.1	Q8N146	OTTHUMG00000166833	ENST00000313472.3:c.70G>A	11.37:g.55889918G>A	ENSP00000323928:p.Val24Ile	196.0	0.0	0		231.0	18.0	0.0779221	NM_001005201	Q6IFB7	Missense_Mutation	SNP	ENST00000313472.3	37	CCDS31519.1	.	.	.	.	.	.	.	.	.	.	G	1.503	-0.551434	0.03996	.	.	ENSG00000181761	ENST00000313472	T	0.01359	4.98	3.43	-6.36	0.01969	.	1.100610	0.06932	N	0.811320	T	0.00552	0.0018	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.49504	-0.8933	10	0.54805	T	0.06	.	2.0752	0.03623	0.3689:0.211:0.3126:0.1075	.	24	Q8N146	OR8H3_HUMAN	I	24	ENSP00000323928:V24I	ENSP00000323928:V24I	V	+	1	0	OR8H3	55646494	0.000000	0.05858	0.104000	0.21259	0.032000	0.12392	-5.175000	0.00144	-0.849000	0.04158	-1.252000	0.01501	GTC	.	.	none		0.453	OR8H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391541.1	NM_001005201	
ARHGAP8	23779	hgsc.bcm.edu	37	22	45221404	45221404	+	Missense_Mutation	SNP	C	C	T	rs74393756	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:45221404C>T	ENST00000389774.2	+	8	761	c.620C>T	c.(619-621)cCg>cTg	p.P207L	PRR5-ARHGAP8_ENST00000352766.7_Missense_Mutation_p.P386L|ARHGAP8_ENST00000336963.4_Missense_Mutation_p.P176L|ARHGAP8_ENST00000517296.3_Missense_Mutation_p.P386L|ARHGAP8_ENST00000389773.5_Missense_Mutation_p.P298L|PRR5-ARHGAP8_ENST00000361473.5_Missense_Mutation_p.P307L|ARHGAP8_ENST00000356099.6_Missense_Mutation_p.P176L	NM_001017526.1	NP_001017526.1	P85298	RHG08_HUMAN	Rho GTPase activating protein 8	207					positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(9)|prostate(1)|skin(7)	29		all_neural(38;0.00409)|Ovarian(80;0.00976)|Glioma(61;0.0649)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0204)		GGCCGGACGCCGCCTCCCACC	0.647													c|||	92	0.0183706	0.0666	0.0043	5008	,	,		12937	0.0		0.0	False		,,,				2504	0.001				p.P298L		Atlas-SNP	.											.	PRR5-ARHGAP8	53	.	0			c.C893T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	258,4146	146.1+/-180.8	6,246,1950	35.0	37.0	36.0		620,527,893,527	1.2	0.0	22	dbSNP_131	36	4,8594	3.7+/-12.6	0,4,4295	yes	missense,missense,missense,missense	ARHGAP8,PRR5-ARHGAP8	NM_001017526.1,NM_001198726.1,NM_181334.4,NM_181335.2	98,98,98,98	6,250,6245	TT,TC,CC		0.0465,5.8583,2.0151	benign,benign,benign,benign	207/465,176/306,298/556,176/434	45221404	262,12740	2202	4299	6501	SO:0001583	missense	553158	exon10			GGACGCCGCCTCC	AF177331	CCDS14060.2, CCDS33664.1, CCDS56233.1	22q13.3	2010-05-11			ENSG00000241484	ENSG00000241484		"""Rho GTPase activating proteins"""	677	protein-coding gene	gene with protein product		609405				10591208	Standard	NM_001198726		Approved	FLJ20185, BPGAP1		P85298	OTTHUMG00000030234	ENST00000389774.2:c.620C>T	22.37:g.45221404C>T	ENSP00000374424:p.Pro207Leu	150.0	0.0	0		185.0	83.0	0.448649	NM_181334	A6ZJ79|A6ZJ80|O75983|O95695|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Missense_Mutation	SNP	ENST00000389774.2	37	CCDS33664.1	32|32	0.014652014652014652|0.014652014652014652	30|30	0.06097560975609756|0.06097560975609756	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	c|c	11.26|11.26	1.586905|1.586905	0.28268|0.28268	0.058583|0.058583	4.65E-4|4.65E-4	ENSG00000248405;ENSG00000248405;ENSG00000241484;ENSG00000241484;ENSG00000241484;ENSG00000241484;ENSG00000241484|ENSG00000248405	ENST00000361473;ENST00000352766;ENST00000517296;ENST00000389773;ENST00000389774;ENST00000336963;ENST00000356099|ENST00000515632	T;T;T;T;T;T;T|.	0.60548|.	2.27;2.25;2.25;2.27;2.2;0.18;2.21|.	4.6|4.6	1.18|1.18	0.20946|0.20946	.|.	1.887620|.	0.03242|.	N|.	0.180497|.	T|T	0.07863|0.07863	0.0197|0.0197	M|M	0.67953|0.67953	2.075|2.075	0.09310|0.09310	N|N	0.999994|0.999994	B;B;P;B;B;B;B|.	0.48640|.	0.214;0.007;0.913;0.318;0.049;0.002;0.328|.	B;B;B;B;B;B;B|.	0.28553|.	0.018;0.002;0.091;0.018;0.004;0.001;0.011|.	T|T	0.07597|0.07597	-1.0764|-1.0764	10|5	0.52906|.	T|.	0.07|.	.|.	7.5251|7.5251	0.27650|0.27650	0.0:0.7049:0.0:0.2951|0.0:0.7049:0.0:0.2951	.|.	212;176;212;207;217;386;307|.	B7ZMA4;A6ZJ79;A2RU51;P85298;Q6PCC7;B1AHC4;B1AHC3|.	.;.;.;RHG08_HUMAN;.;.;.|.	L|C	307;386;386;298;207;176;176|230	ENSP00000354732:P307L;ENSP00000262731:P386L;ENSP00000429240:P386L;ENSP00000374423:P298L;ENSP00000374424:P207L;ENSP00000337287:P176L;ENSP00000348407:P176L|.	ENSP00000337287:P176L|.	P|R	+|+	2|1	0|0	PRR5-ARHGAP8;ARHGAP8|PRR5-ARHGAP8	43600068|43600068	0.001000|0.001000	0.12720|0.12720	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.734000|0.734000	0.26101|0.26101	0.120000|0.120000	0.18254|0.18254	-0.130000|-0.130000	0.14895|0.14895	CCG|CGC	C|0.978;T|0.022	0.022	strong		0.647	ARHGAP8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000075088.4	NM_017701	
SIMC1	375484	hgsc.bcm.edu	37	5	175722243	175722243	+	Missense_Mutation	SNP	A	A	G	rs7736723	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:175722243A>G	ENST00000443967.1	+	5	1992	c.1585A>G	c.(1585-1587)Atg>Gtg	p.M529V	SIMC1_ENST00000341199.6_Missense_Mutation_p.M114V|SIMC1_ENST00000429602.2_Missense_Mutation_p.M548V|SIMC1_ENST00000430704.2_Missense_Mutation_p.M114V			Q8NDZ2	SIMC1_HUMAN	SUMO-interacting motifs containing 1	529							SUMO polymer binding (GO:0032184)										GGAGGCCTACATGCTTCTCAT	0.483													A|||	81	0.0161741	0.059	0.0043	5008	,	,		16361	0.0		0.0	False		,,,				2504	0.0				p.M114V		Atlas-SNP	.											.	.	.	.	0			c.A340G						PASS	.	A	VAL/MET	276,4128	150.7+/-184.7	3,270,1929	39.0	32.0	34.0		340	4.2	1.0	5	dbSNP_129	34	1,8595	1.2+/-3.3	0,1,4297	no	missense	C5orf25	NM_198567.4	21	3,271,6226	GG,GA,AA		0.0116,6.267,2.1308	possibly-damaging	114/458	175722243	277,12723	2202	4298	6500	SO:0001583	missense	375484	exon2			GCCTACATGCTTC	BC037298	CCDS4398.2	5q35.2	2013-08-14	2012-11-14	2012-11-14	ENSG00000170085	ENSG00000170085			24779	protein-coding gene	gene with protein product	"""oocyte maturation associated 1"", ""platform element for inhibition of autolytic degradation"""		"""chromosome 5 open reading frame 25"""	C5orf25		23086935, 23707407	Standard	NM_198567		Approved	FLJ44216, OOMA1, PLEIAD	uc003mds.4	Q8NDZ2	OTTHUMG00000130663	ENST00000443967.1:c.1585A>G	5.37:g.175722243A>G	ENSP00000406571:p.Met529Val	321.0	0.0	0		323.0	134.0	0.414861	NM_198567	J3KQQ8|Q6NXN8|Q6ZTU4|Q8IZ15	Missense_Mutation	SNP	ENST00000443967.1	37		32	0.014652014652014652	32	0.06504065040650407	0	0.0	0	0.0	0	0.0	A	16.45	3.127921	0.56721	0.06267	1.16E-4	ENSG00000170085	ENST00000341199;ENST00000430704;ENST00000443967;ENST00000429602	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	4.24	4.24	0.50183	.	0.174470	0.43747	D	0.000531	T	0.05686	0.0149	L	0.48642	1.525	0.25231	N	0.989824	P;P;D	0.57257	0.865;0.782;0.979	B;B;P	0.53401	0.391;0.327;0.725	T	0.01238	-1.1409	10	0.51188	T	0.08	-16.7421	12.4812	0.55844	1.0:0.0:0.0:0.0	rs55844480	548;114;529	B4DRM7;Q8NDZ2-3;Q8NDZ2	.;.;CE025_HUMAN	V	114;114;529;548	ENSP00000342075:M114V;ENSP00000409287:M114V;ENSP00000406571:M529V;ENSP00000410552:M548V	ENSP00000342075:M114V	M	+	1	0	C5orf25	175654849	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.371000	0.59523	1.775000	0.52247	0.496000	0.49642	ATG	A|1.000;|0.000	.	weak		0.483	SIMC1-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000253155.2	NM_198567	
COL5A1	1289	hgsc.bcm.edu	37	9	137630361	137630361	+	Splice_Site	SNP	G	G	A	rs61729545	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:137630361G>A	ENST00000371817.3	+	10	1845	c.1431G>A	c.(1429-1431)gcG>gcA	p.A477A		NM_000093.3|NM_001278074.1	NP_000084.3|NP_001265003.1	P20908	CO5A1_HUMAN	collagen, type V, alpha 1	477	Interrupted collagenous region.				axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|heart morphogenesis (GO:0003007)|integrin biosynthetic process (GO:0045112)|negative regulation of endodermal cell differentiation (GO:1903225)|regulation of cellular component organization (GO:0051128)|skin development (GO:0043588)|tendon development (GO:0035989)|wound healing, spreading of epidermal cells (GO:0035313)	basement membrane (GO:0005604)|collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|proteoglycan binding (GO:0043394)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(26)|liver(2)|lung(36)|ovary(4)|pancreas(4)|prostate(5)|skin(10)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	115		Myeloproliferative disorder(178;0.0341)		all cancers(34;2.28e-08)|OV - Ovarian serous cystadenocarcinoma(145;6.03e-08)|Epithelial(140;6.4e-08)|GBM - Glioblastoma multiforme(294;0.131)		AAGGCCCCGCGGTGAGTATCC	0.637													G|||	351	0.0700879	0.2549	0.0202	5008	,	,		15920	0.0		0.0	False		,,,				2504	0.0				p.A477A		Atlas-SNP	.											COL5A1,NS,carcinoma,+1,1	COL5A1	323	1	0			c.G1431A						PASS	.	G		894,3512	343.1+/-307.5	90,714,1399	42.0	46.0	44.0		1431	-5.2	0.9	9	dbSNP_129	44	13,8587	7.1+/-27.0	0,13,4287	yes	coding-synonymous-near-splice	COL5A1	NM_000093.3		90,727,5686	AA,AG,GG		0.1512,20.2905,6.9737		477/1839	137630361	907,12099	2203	4300	6503	SO:0001630	splice_region_variant	1289	exon10			CCCCGCGGTGAGT	D90279	CCDS6982.1, CCDS75932.1	9q34.2-q34.3	2014-09-17			ENSG00000130635	ENSG00000130635		"""Collagens"""	2209	protein-coding gene	gene with protein product	"""alpha 1 type V collagen"""	120215				1572660	Standard	NM_001278074		Approved		uc031tfl.1	P20908	OTTHUMG00000020891	ENST00000371817.3:c.1431+1G>A	9.37:g.137630361G>A		128.0	0.0	0		160.0	100.0	0.625	NM_000093	Q15094|Q5SUX4	Silent	SNP	ENST00000371817.3	37	CCDS6982.1																																																																																			G|0.937;A|0.063	0.063	strong		0.637	COL5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054954.2	NM_000093	Silent
ATP2B3	492	hgsc.bcm.edu	37	X	152830495	152830495	+	Silent	SNP	T	T	C	rs5986910	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:152830495T>C	ENST00000349466.2	+	20	3602	c.3276T>C	c.(3274-3276)caT>caC	p.H1092H	ATP2B3_ENST00000393842.1_Silent_p.H1078H|ATP2B3_ENST00000263519.4_Silent_p.H1092H|ATP2B3_ENST00000370181.2_Silent_p.H1078H|ATP2B3_ENST00000370186.1_Silent_p.H1078H|ATP2B3_ENST00000359149.3_Silent_p.H1092H			Q16720	AT2B3_HUMAN	ATPase, Ca++ transporting, plasma membrane 3	1092					blood coagulation (GO:0007596)|cell death (GO:0008219)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			NS(2)|breast(5)|endometrium(7)|large_intestine(8)|lung(23)|ovary(1)|pancreas(1)|skin(3)	50	all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					AGATCGACCATGCCGAGCGGG	0.672													C|||	206	0.0545695	0.1467	0.0144	3775	,	,		12860	0.0		0.002	False		,,,				2504	0.0				p.H1092H		Atlas-SNP	.											.	ATP2B3	552	.	0			c.T3276C						PASS	.		,	667,3161		51,473,92,1107,474	24.0	23.0	23.0		3276,3276	0.6	1.0	X	dbSNP_114	23	13,6711		0,8,5,2420,1863	no	coding-synonymous,coding-synonymous	ATP2B3	NM_001001344.2,NM_021949.3	,	51,481,97,3527,2337	CC,CT,C,TT,T		0.1933,17.4242,6.4443	,	1092/1221,1092/1174	152830495	680,9872	2197	4296	6493	SO:0001819	synonymous_variant	492	exon19			CGACCATGCCGAG	U60414	CCDS14722.1, CCDS35440.1	Xq28	2014-07-18			ENSG00000067842	ENSG00000067842	3.6.3.8	"""ATPases / P-type"""	816	protein-coding gene	gene with protein product	"""plasma membrane calcium-transporting ATPase 3"", ""cilia and flagella associated protein 39"""	300014	"""spinocerebellar ataxia, X-linked 1"", ""cerebellar ataxia 2 (X-linked)"""	SCAX1, CLA2		8187550, 22912398	Standard	NM_021949		Approved	PMCA3, CFAP39	uc004fht.1	Q16720	OTTHUMG00000024202	ENST00000349466.2:c.3276T>C	X.37:g.152830495T>C		185.0	0.0	0		194.0	64.0	0.329897	NM_001001344	B7WNR8|B7WNY5|Q12995|Q16858	Silent	SNP	ENST00000349466.2	37	CCDS35440.1																																																																																			T|0.920;C|0.080	0.080	strong		0.672	ATP2B3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060957.1	NM_021949	
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39262121	39262121	+	Missense_Mutation	SNP	C	C	T	rs200757692	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39262121C>T	ENST00000391415.1	+	1	538	c.481C>T	c.(481-483)Cgc>Tgc	p.R161C		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	161	29 X 5 AA repeats of C-C-[RQVHIEK]- [SPTR]-[VSTQCRNP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.R149C(1)|p.R161C(1)		central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						cagctgctgccgcccctcttg	0.657																																					p.R161C		Atlas-SNP	.											KRTAP4-9_ENST00000377734,NS,carcinoma,0,2	KRTAP4-9	110	2	2	Substitution - Missense(2)	endometrium(2)	c.C481T						scavenged	.						7.0	11.0	10.0					17																	39262121		682	1570	2252	SO:0001583	missense	100132386	exon1			TGCTGCCGCCCCT	AJ406941	CCDS54124.1	17q21.2	2013-06-25			ENSG00000212722	ENSG00000212722		"""Keratin associated proteins"""	18910	protein-coding gene	gene with protein product							Standard	NM_001146041		Approved	KAP4.9	uc010wfp.2	Q9BYQ8	OTTHUMG00000133584	ENST00000391415.1:c.481C>T	17.37:g.39262121C>T	ENSP00000375234:p.Arg161Cys	129.0	0.0	0		151.0	17.0	0.112583	NM_001146041		Missense_Mutation	SNP	ENST00000391415.1	37	CCDS54124.1	.	.	.	.	.	.	.	.	.	.	.	11.80	1.746361	0.30955	.	.	ENSG00000212722	ENST00000377734;ENST00000391415;ENST00000333994	T	0.00605	6.27	2.98	0.469	0.16741	.	0.000000	0.40640	U	0.001042	T	0.00552	0.0018	M	0.70275	2.135	0.09310	N	1	P	0.34587	0.458	B	0.19391	0.025	T	0.50857	-0.8778	10	0.52906	T	0.07	.	1.9066	0.03278	0.202:0.4678:0.1985:0.1317	.	161	Q9BYQ8	KRA49_HUMAN	C	149;161;152	ENSP00000375234:R161C	ENSP00000334461:R152C	R	+	1	0	KRTAP4-9	36515647	0.000000	0.05858	0.321000	0.25320	0.226000	0.24999	-1.001000	0.03690	0.325000	0.23359	0.197000	0.17608	CGC	.	.	none		0.657	KRTAP4-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257688.1	NM_001146041	
PTPRJ	5795	hgsc.bcm.edu	37	11	48166642	48166642	+	Silent	SNP	C	C	T	rs34300475	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:48166642C>T	ENST00000418331.2	+	14	3229	c.2877C>T	c.(2875-2877)cgC>cgT	p.R959R		NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	959					contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						CCTTCAGTCGCTACTCAGATG	0.532													C|||	350	0.0698882	0.2564	0.013	5008	,	,		22420	0.0		0.002	False		,,,				2504	0.0				p.R959R		Atlas-SNP	.											.	PTPRJ	225	.	0			c.C2877T						PASS	.	C		789,3613	319.1+/-295.9	68,653,1480	164.0	145.0	151.0		2877	2.3	0.0	11	dbSNP_126	151	5,8591	3.0+/-9.4	0,5,4293	no	coding-synonymous	PTPRJ	NM_002843.3		68,658,5773	TT,TC,CC		0.0582,17.9237,6.1086		959/1338	48166642	794,12204	2201	4298	6499	SO:0001819	synonymous_variant	5795	exon14			CAGTCGCTACTCA	U10886	CCDS7945.1, CCDS44596.1	11p11.2	2013-02-11			ENSG00000149177	ENSG00000149177		"""CD molecules"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9673	protein-coding gene	gene with protein product		600925				7937872, 7994032	Standard	NM_001098503		Approved	DEP1, HPTPeta, CD148	uc001ngp.4	Q12913	OTTHUMG00000166573	ENST00000418331.2:c.2877C>T	11.37:g.48166642C>T		206.0	0.0	0		198.0	100.0	0.50505	NM_002843	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Silent	SNP	ENST00000418331.2	37	CCDS7945.1																																																																																			C|0.944;T|0.056	0.056	strong		0.532	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1		
ZNF570	148268	hgsc.bcm.edu	37	19	37975400	37975400	+	Silent	SNP	T	T	C	rs78317808	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:37975400T>C	ENST00000330173.1	+	5	1405	c.876T>C	c.(874-876)caT>caC	p.H292H	ZNF570_ENST00000586475.1_Silent_p.H348H|ZNF570_ENST00000388801.3_Silent_p.H89H	NM_144694.1	NP_653295.1	Q96NI8	ZN570_HUMAN	zinc finger protein 570	292					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)|kidney(3)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(1)	27			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TAGTTCAACATCTGCGAGTTC	0.423													T|||	91	0.0181709	0.0651	0.0072	5008	,	,		21985	0.0		0.0	False		,,,				2504	0.0				p.H292H		Atlas-SNP	.											.	ZNF570	58	.	0			c.T876C						PASS	.	T		263,4143	148.0+/-182.4	8,247,1948	77.0	73.0	74.0		876	2.2	1.0	19	dbSNP_131	74	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	ZNF570	NM_144694.1		8,253,6242	CC,CT,TT		0.0698,5.9691,2.0683		292/537	37975400	269,12737	2203	4300	6503	SO:0001819	synonymous_variant	148268	exon5			TCAACATCTGCGA	AK055353	CCDS12504.1, CCDS74355.1	19q13.12	2013-09-20			ENSG00000171827	ENSG00000171827		"""Zinc fingers, C2H2-type"", ""-"""	26416	protein-coding gene	gene with protein product							Standard	XM_005258567		Approved	FLJ30791	uc002ogk.1	Q96NI8	OTTHUMG00000048176	ENST00000330173.1:c.876T>C	19.37:g.37975400T>C		68.0	0.0	0		61.0	36.0	0.590164	NM_144694	A1L472|B4DMP1	Silent	SNP	ENST00000330173.1	37	CCDS12504.1																																																																																			T|0.983;C|0.017	0.017	strong		0.423	ZNF570-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109600.1	NM_144694	
MOAP1	64112	hgsc.bcm.edu	37	14	93649552	93649552	+	Silent	SNP	A	A	G	rs114256363	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:93649552A>G	ENST00000556883.1	-	2	1520	c.1036T>C	c.(1036-1038)Ttg>Ctg	p.L346L	TMEM251_ENST00000283534.4_5'Flank|TMEM251_ENST00000415050.2_5'Flank|MOAP1_ENST00000298894.4_Silent_p.L346L|RP11-371E8.4_ENST00000557574.1_5'Flank			Q96BY2	MOAP1_HUMAN	modulator of apoptosis 1	346					apoptotic signaling pathway (GO:0097190)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of apoptotic process (GO:0043065)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:0001844)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)	13		all_cancers(154;0.00528)|Acute lymphoblastic leukemia(33;0.0497)|all_epithelial(191;0.125)|all_neural(303;0.13)		Epithelial(152;0.178)|all cancers(159;0.2)|COAD - Colon adenocarcinoma(157;0.204)		TTACCTTCCAATATTGCCTGG	0.473													A|||	96	0.0191693	0.0696	0.0058	5008	,	,		21495	0.0		0.0	False		,,,				2504	0.0				p.L346L		Atlas-SNP	.											.	MOAP1	32	.	0			c.T1036C						PASS	.	A		233,4173	139.2+/-174.8	8,217,1978	99.0	90.0	93.0		1036	-4.4	0.0	14	dbSNP_132	93	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MOAP1	NM_022151.4		8,218,6277	GG,GA,AA		0.0116,5.2882,1.7992		346/352	93649552	234,12772	2203	4300	6503	SO:0001819	synonymous_variant	64112	exon3			CTTCCAATATTGC	BC015044	CCDS9908.1	14q32.12	2012-02-09			ENSG00000165943	ENSG00000165943		"""Paraneoplastic Ma antigens"""	16658	protein-coding gene	gene with protein product	"""paraneoplastic Ma antigen family member 4"""	609485				11060313	Standard	NM_022151		Approved	MAP-1, PNMA4	uc001ybj.3	Q96BY2	OTTHUMG00000169184	ENST00000556883.1:c.1036T>C	14.37:g.93649552A>G		118.0	0.0	0		111.0	48.0	0.432432	NM_022151	B2RDF6|Q9H833|Q9HAS1	Silent	SNP	ENST00000556883.1	37	CCDS9908.1																																																																																			A|0.982;G|0.018	0.018	strong		0.473	MOAP1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412685.1		
WDR87	83889	hgsc.bcm.edu	37	19	38383386	38383386	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38383386C>T	ENST00000303868.5	-	4	3064	c.2840G>A	c.(2839-2841)cGt>cAt	p.R947H	WDR87_ENST00000447313.2_Missense_Mutation_p.R986H	NM_031951.3	NP_114157.3	Q6ZQQ6	WDR87_HUMAN	WD repeat domain 87	947										NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|prostate(1)|skin(3)|stomach(1)	36						CATTCCTAGACGCTTCAGCCC	0.512																																					p.R947H		Atlas-SNP	.											WDR87,colon,carcinoma,0,1	WDR87	191	1	0			c.G2840A						PASS	.						191.0	153.0	164.0					19																	38383386		692	1591	2283	SO:0001583	missense	83889	exon4			CCTAGACGCTTCA	AK128826	CCDS46063.1, CCDS74356.1	19q13.13	2013-01-09			ENSG00000171804	ENSG00000171804		"""WD repeat domain containing"""	29934	protein-coding gene	gene with protein product							Standard	XM_005259304		Approved	NYD-SP11	uc010efu.2	Q6ZQQ6	OTTHUMG00000048187	ENST00000303868.5:c.2840G>A	19.37:g.38383386C>T	ENSP00000368025:p.Arg947His	225.0	0.0	0		248.0	133.0	0.53629	NM_031951	Q9BWV9	Missense_Mutation	SNP	ENST00000303868.5	37	CCDS46063.1	.	.	.	.	.	.	.	.	.	.	C	15.35	2.806795	0.50421	.	.	ENSG00000171804	ENST00000447313;ENST00000303868	T;T	0.64618	-0.11;-0.11	5.27	1.93	0.25924	.	0.124727	0.33457	N	0.004882	T	0.54919	0.1888	M	0.66939	2.045	0.25293	N	0.989346	B;B	0.25486	0.127;0.127	B;B	0.18263	0.021;0.021	T	0.54503	-0.8284	10	0.87932	D	0	-5.9939	8.0083	0.30338	0.0:0.7327:0.0:0.2673	.	947;986	Q6ZQQ6;E7ESW6	WDR87_HUMAN;.	H	986;947	ENSP00000405012:R986H;ENSP00000368025:R947H	ENSP00000368025:R947H	R	-	2	0	WDR87	43075226	0.501000	0.26099	0.982000	0.44146	0.996000	0.88848	0.382000	0.20635	0.611000	0.30052	0.549000	0.68633	CGT	.	.	none		0.512	WDR87-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314628.2	XM_940478	
ZDHHC23	254887	hgsc.bcm.edu	37	3	113673098	113673098	+	Missense_Mutation	SNP	C	C	T	rs149202494		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:113673098C>T	ENST00000330212.3	+	3	1012	c.713C>T	c.(712-714)aCa>aTa	p.T238I	ZDHHC23_ENST00000498275.1_Missense_Mutation_p.T232I	NM_173570.3	NP_775841.2	Q8IYP9	ZDH23_HUMAN	zinc finger, DHHC-type containing 23	238					protein localization to plasma membrane (GO:0072659)|protein palmitoylation (GO:0018345)	integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|urinary_tract(2)	16						AATCGCACAACAAAGGATGAC	0.597													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18066	0.0		0.0	False		,,,				2504	0.0				p.T238I		Atlas-SNP	.											.	ZDHHC23	38	.	0			c.C713T						PASS	.	C	ILE/THR	2,4404	4.2+/-10.8	0,2,2201	81.0	79.0	80.0		713	-1.8	0.0	3	dbSNP_134	80	0,8600		0,0,4300	no	missense	ZDHHC23	NM_173570.3	89	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	benign	238/410	113673098	2,13004	2203	4300	6503	SO:0001583	missense	254887	exon3			GCACAACAAAGGA	AK127025	CCDS33827.1	3q13.31	2008-05-02			ENSG00000184307	ENSG00000184307		"""Zinc fingers, DHHC-type"""	28654	protein-coding gene	gene with protein product						12477932	Standard	NM_173570		Approved	MGC42530	uc003eau.3	Q8IYP9	OTTHUMG00000159335	ENST00000330212.3:c.713C>T	3.37:g.113673098C>T	ENSP00000330485:p.Thr238Ile	151.0	0.0	0		168.0	84.0	0.5	NM_173570	D3DN76	Missense_Mutation	SNP	ENST00000330212.3	37	CCDS33827.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	0.022	-1.410585	0.01145	4.54E-4	0.0	ENSG00000184307	ENST00000330212;ENST00000498275	T;T	0.24723	1.84;1.84	5.11	-1.77	0.07982	.	1.393810	0.04616	N	0.401098	T	0.09555	0.0235	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25363	-1.0134	10	0.20519	T	0.43	-12.359	5.4023	0.16303	0.0:0.3117:0.1628:0.5255	.	238	Q8IYP9	ZDH23_HUMAN	I	238;232	ENSP00000330485:T238I;ENSP00000417840:T232I	ENSP00000330485:T238I	T	+	2	0	ZDHHC23	115155788	0.000000	0.05858	0.001000	0.08648	0.007000	0.05969	-0.478000	0.06575	-0.376000	0.07943	-0.459000	0.05422	ACA	C|1.000;T|0.000	0.000	strong		0.597	ZDHHC23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354702.1	NM_173570	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057949	46057949	+	Silent	SNP	C	C	T	rs78352751	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46057949C>T	ENST00000380095.1	+	1	677	c.615C>T	c.(613-615)ccC>ccT	p.P205P	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	205	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						GCTGCGTGCCCGTCCCCTCCT	0.701													C|||	103	0.0205671	0.0756	0.0043	5008	,	,		20099	0.0		0.0	False		,,,				2504	0.0				p.P205P		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.C615T						PASS	.						95.0	98.0	97.0					21																	46057949		2203	4300	6503	SO:0001819	synonymous_variant	353333	exon1			CGTGCCCGTCCCC	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.615C>T	21.37:g.46057949C>T		297.0	0.0	0		471.0	121.0	0.2569	NM_181688		Silent	SNP	ENST00000380095.1	37	CCDS33585.1																																																																																			C|0.982;T|0.018	0.018	strong		0.701	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
CLEC16A	23274	hgsc.bcm.edu	37	16	11133642	11133642	+	Silent	SNP	G	G	A	rs61740101	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:11133642G>A	ENST00000409790.1	+	14	1799	c.1569G>A	c.(1567-1569)caG>caA	p.Q523Q	CLEC16A_ENST00000465491.1_3'UTR|CLEC16A_ENST00000409552.3_Silent_p.Q505Q	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A									p.0?(1)		breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						AGCGAATCCAGCTCCCCGTGC	0.547													G|||	64	0.0127796	0.0477	0.0014	5008	,	,		18325	0.0		0.0	False		,,,				2504	0.0				p.Q523Q		Atlas-SNP	.											.	CLEC16A	101	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.G1569A						PASS	.	G		137,3891		6,125,1883	51.0	55.0	54.0		1569	3.3	1.0	16	dbSNP_129	54	0,8358		0,0,4179	no	coding-synonymous	CLEC16A	NM_015226.2		6,125,6062	AA,AG,GG		0.0,3.4012,1.1061		523/1054	11133642	137,12249	2014	4179	6193	SO:0001819	synonymous_variant	23274	exon13			AATCCAGCTCCCC	AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"""C-type lectin domain containing"""	29013	protein-coding gene	gene with protein product		611303	"""KIAA0350"""	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.1569G>A	16.37:g.11133642G>A		89.0	0.0	0		93.0	46.0	0.494624	NM_015226		Silent	SNP	ENST00000409790.1	37	CCDS45409.1																																																																																			G|0.989;A|0.011	0.011	strong		0.547	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226	
NCOR1	9611	hgsc.bcm.edu	37	17	16001756	16001756	+	Silent	SNP	G	G	A	rs79413281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:16001756G>A	ENST00000268712.3	-	21	3002	c.2745C>T	c.(2743-2745)ctC>ctT	p.L915L	NCOR1_ENST00000395848.1_Silent_p.L822L|NCOR1_ENST00000395851.1_Silent_p.L931L|RNU6-314P_ENST00000516574.1_RNA	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	915					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)			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)		GAGATGAGACGAGTATAGATC	0.378													a|||	109	0.0217652	0.0764	0.0115	5008	,	,		17847	0.0		0.0	False		,,,				2504	0.0				p.L931L		Atlas-SNP	.											.	NCOR1	240	.	0			c.C2793T						PASS	.	A	,,	262,4144	802.4+/-415.7	7,248,1948	87.0	87.0	87.0		2466,2793,2745	-5.2	0.8	17	dbSNP_132	87	4,8596	819.1+/-406.8	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	NCOR1	NM_001190438.1,NM_001190440.1,NM_006311.3	,,	7,252,6244	AA,AG,GG		0.0465,5.9464,2.0452	,,	822/915,931/2338,915/2441	16001756	266,12740	2203	4300	6503	SO:0001819	synonymous_variant	9611	exon20			TGAGACGAGTATA	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.2745C>T	17.37:g.16001756G>A		130.0	0.0	0		119.0	51.0	0.428571	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Silent	SNP	ENST00000268712.3	37	CCDS11175.1																																																																																			G|0.981;A|0.019	0.019	strong		0.378	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311	
RICTOR	253260	hgsc.bcm.edu	37	5	38950761	38950761	+	Silent	SNP	A	A	G	rs150422546	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:38950761A>G	ENST00000357387.3	-	31	3219	c.3189T>C	c.(3187-3189)gaT>gaC	p.D1063D	RICTOR_ENST00000296782.5_Silent_p.D1063D	NM_152756.3	NP_689969.2			RPTOR independent companion of MTOR, complex 2											NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|prostate(3)|skin(5)	75	all_lung(31;0.000396)					CTTCATTGATATCAAGGAAAA	0.348													A|||	6	0.00119808	0.0045	0.0	5008	,	,		17156	0.0		0.0	False		,,,				2504	0.0				p.D1063D		Atlas-SNP	.											.	RICTOR	182	.	0			c.T3189C						PASS	.	A		9,4395	15.5+/-35.6	0,9,2193	98.0	106.0	103.0		3189	-0.0	1.0	5	dbSNP_134	103	0,8592		0,0,4296	yes	coding-synonymous	RICTOR	NM_152756.3		0,9,6489	GG,GA,AA		0.0,0.2044,0.0693		1063/1709	38950761	9,12987	2202	4296	6498	SO:0001819	synonymous_variant	253260	exon31			ATTGATATCAAGG		CCDS34148.1, CCDS68861.1	5p13.1	2009-07-09			ENSG00000164327	ENSG00000164327			28611	protein-coding gene	gene with protein product	"""rapamycin-insensitive companion of mTOR"", ""pianissimo"""	609022				12477932	Standard	XM_005248278		Approved	MGC39830, AVO3, PIA, KIAA1999	uc003jlp.2	Q6R327	OTTHUMG00000162037	ENST00000357387.3:c.3189T>C	5.37:g.38950761A>G		207.0	0.0	0		210.0	111.0	0.528571	NM_152756		Silent	SNP	ENST00000357387.3	37	CCDS34148.1																																																																																			A|0.999;G|0.001	0.001	strong		0.348	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756	
ERI1	90459	hgsc.bcm.edu	37	8	8869129	8869129	+	Missense_Mutation	SNP	T	T	G	rs112570397	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:8869129T>G	ENST00000523898.1	+	4	1044	c.365T>G	c.(364-366)tTt>tGt	p.F122C	ERI1_ENST00000519292.1_Missense_Mutation_p.F122C|ERI1_ENST00000250263.7_Missense_Mutation_p.F122C			Q8IV48	ERI1_HUMAN	exoribonuclease 1	122					gene silencing by RNA (GO:0031047)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|rRNA 3'-end processing (GO:0031125)	cytoplasm (GO:0005737)|histone pre-mRNA 3'end processing complex (GO:0071204)|nucleolus (GO:0005730)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|histone pre-mRNA stem-loop binding (GO:0071207)|metal ion binding (GO:0046872)|ribosome binding (GO:0043022)|rRNA binding (GO:0019843)			NS(1)|endometrium(2)|large_intestine(1)|lung(6)|prostate(1)	11						GAGAGCAATTTTGCTGACAGT	0.348													G|||	41	0.0081869	0.0303	0.0014	5008	,	,		17758	0.0		0.0	False		,,,				2504	0.0				p.F122C		Atlas-SNP	.											.	ERI1	20	.	0			c.T365G						PASS	.	G	CYS/PHE	121,4285	813.8+/-416.2	1,119,2083	82.0	82.0	82.0		365	1.7	0.0	8	dbSNP_132	82	0,8600		0,0,4300	yes	missense	ERI1	NM_153332.3	205	1,119,6383	GG,GT,TT		0.0,2.7463,0.9303	benign	122/350	8869129	121,12885	2203	4300	6503	SO:0001583	missense	90459	exon3			GCAATTTTGCTGA	BC035279	CCDS5972.1	8p23.1	2008-12-16	2008-12-16	2008-12-16	ENSG00000104626	ENSG00000104626		"""Enhanced RNAi three prime mRNA exonucleases"""	23994	protein-coding gene	gene with protein product	"""exoribonuclease 1"", ""enhanced RNAi three prime mRNA exonuclease homolog 1 (C.elegans)"""	608739	"""three prime histone mRNA exonuclease 1"""	THEX1		14536070	Standard	NM_153332		Approved	3'HEXO	uc003wsk.2	Q8IV48	OTTHUMG00000129328	ENST00000523898.1:c.365T>G	8.37:g.8869129T>G	ENSP00000429615:p.Phe122Cys	51.0	0.0	0		75.0	45.0	0.6	NM_153332	A8K4U7|Q9NSX3	Missense_Mutation	SNP	ENST00000523898.1	37	CCDS5972.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	G	10.23	1.293512	0.23564	0.027463	0.0	ENSG00000104626	ENST00000523898;ENST00000250263;ENST00000519292	T;T;T	0.43688	0.94;0.94;0.94	5.79	1.69	0.24217	.	1.091090	0.06714	N	0.773725	T	0.09992	0.0245	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18272	-1.0342	10	0.46703	T	0.11	-26.669	3.9327	0.09293	0.1405:0.3665:0.3736:0.1193	.	122	Q8IV48	ERI1_HUMAN	C	122	ENSP00000429615:F122C;ENSP00000250263:F122C;ENSP00000430190:F122C	ENSP00000250263:F122C	F	+	2	0	ERI1	8906539	0.000000	0.05858	0.000000	0.03702	0.943000	0.58893	-0.253000	0.08794	0.078000	0.16900	-0.231000	0.12243	TTT	T|0.991;G|0.009	0.009	strong		0.348	ERI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251471.2	NM_153332	
TCTE1	202500	hgsc.bcm.edu	37	6	44249939	44249939	+	Silent	SNP	G	G	A	rs34405945	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:44249939G>A	ENST00000371505.4	-	4	1326	c.1204C>T	c.(1204-1206)Ctg>Ttg	p.L402L	TCTE1_ENST00000371504.1_Intron|TCTE1_ENST00000371503.3_Intron|RP11-444E17.6_ENST00000505802.1_Intron|TMEM151B_ENST00000438774.2_Intron	NM_182539.3	NP_872345.2	Q5JU00	TCTE1_HUMAN	t-complex-associated-testis-expressed 1	402										breast(1)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(9)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			GGCTCAGACAGCTCATTGCCA	0.602													G|||	60	0.0119808	0.0446	0.0014	5008	,	,		18613	0.0		0.0	False		,,,				2504	0.0				p.L402L		Atlas-SNP	.											.	TCTE1	77	.	0			c.C1204T						PASS	.	G		113,4293	85.8+/-124.5	0,113,2090	159.0	127.0	138.0		1204	2.4	1.0	6	dbSNP_126	138	1,8599		0,1,4299	yes	coding-synonymous	TCTE1	NM_182539.3		0,114,6389	AA,AG,GG		0.0116,2.5647,0.8765		402/502	44249939	114,12892	2203	4300	6503	SO:0001819	synonymous_variant	202500	exon4			CAGACAGCTCATT	BC035022	CCDS4910.1	6q21.1	2014-07-18			ENSG00000146221	ENSG00000146221			11693	protein-coding gene	gene with protein product		186975				2568335, 8646886	Standard	NM_182539		Approved	D6S46, MGC33600, FAP155	uc003oxi.2	Q5JU00	OTTHUMG00000014763	ENST00000371505.4:c.1204C>T	6.37:g.44249939G>A		135.0	0.0	0		183.0	98.0	0.535519	NM_182539	B4DX59|Q8IYS6	Silent	SNP	ENST00000371505.4	37	CCDS4910.1																																																																																			G|0.988;A|0.012	0.012	strong		0.602	TCTE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040736.1	NM_182539	
BOC	91653	hgsc.bcm.edu	37	3	112993412	112993412	+	Silent	SNP	C	C	T	rs7615578	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:112993412C>T	ENST00000495514.1	+	9	2129	c.1425C>T	c.(1423-1425)ccC>ccT	p.P475P	BOC_ENST00000273395.4_Silent_p.P475P|BOC_ENST00000355385.3_Silent_p.P475P|BOC_ENST00000497495.1_3'UTR			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	475	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			CCGAGGCTCCCATCATCCTCA	0.672													C|||	55	0.0109824	0.0401	0.0029	5008	,	,		17614	0.0		0.0	False		,,,				2504	0.0				p.P475P		Atlas-SNP	.											.	BOC	139	.	0			c.C1425T						PASS	.	C		178,4226		3,172,2027	29.0	34.0	32.0		1425	-2.2	0.3	3	dbSNP_116	32	2,8596		0,2,4297	no	coding-synonymous	BOC	NM_033254.2		3,174,6324	TT,TC,CC		0.0233,4.0418,1.3844		475/1115	112993412	180,12822	2202	4299	6501	SO:0001819	synonymous_variant	91653	exon9			GGCTCCCATCATC	AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17173	protein-coding gene	gene with protein product	"""brother of CDO"", ""brother of CDON"", ""cell adhesion associated, oncogene regulated 2"""	608708	"""Boc homolog (mouse)"""			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.1425C>T	3.37:g.112993412C>T		169.0	0.0	0		215.0	104.0	0.483721	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Silent	SNP	ENST00000495514.1	37	CCDS2971.1																																																																																			C|0.985;T|0.015	0.015	strong		0.672	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254	
LRP12	29967	hgsc.bcm.edu	37	8	105503401	105503401	+	Missense_Mutation	SNP	T	T	C	rs16871494	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:105503401T>C	ENST00000276654.5	-	7	2188	c.2080A>G	c.(2080-2082)Agt>Ggt	p.S694G	LRP12_ENST00000424843.2_Missense_Mutation_p.S675G|LRP12_ENST00000518375.1_5'UTR	NM_013437.4	NP_038465.1	Q9Y561	LRP12_HUMAN	low density lipoprotein receptor-related protein 12	694			S -> G (in dbSNP:rs16871494).		endocytosis (GO:0006897)|receptor-mediated endocytosis (GO:0006898)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	low-density lipoprotein receptor activity (GO:0005041)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48			OV - Ovarian serous cystadenocarcinoma(57;1.21e-06)|STAD - Stomach adenocarcinoma(118;0.229)			GTTGAGGAACTTGCACATGCT	0.532													T|||	177	0.0353435	0.1286	0.0072	5008	,	,		19333	0.0		0.002	False		,,,				2504	0.0				p.S694G		Atlas-SNP	.											.	LRP12	124	.	0			c.A2080G						PASS	.	T	GLY/SER,GLY/SER	469,3937	220.4+/-237.8	15,439,1749	99.0	84.0	90.0		2023,2080	3.1	0.8	8	dbSNP_123	90	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	LRP12	NM_001135703.2,NM_013437.4	56,56	15,444,6044	CC,CT,TT		0.0581,10.6446,3.6445	benign,benign	675/841,694/860	105503401	474,12532	2203	4300	6503	SO:0001583	missense	29967	exon7			AGGAACTTGCACA	AF166350	CCDS6303.1, CCDS47907.1	8q22.2	2013-02-27	2010-01-26		ENSG00000147650	ENSG00000147650		"""Low density lipoprotein receptors"""	31708	protein-coding gene	gene with protein product						12809483, 14676824	Standard	NM_013437		Approved	ST7, FLJ12929	uc003yma.3	Q9Y561	OTTHUMG00000164892	ENST00000276654.5:c.2080A>G	8.37:g.105503401T>C	ENSP00000276654:p.Ser694Gly	170.0	0.0	0		189.0	93.0	0.492063	NM_013437	A8K137|B4DRQ2	Missense_Mutation	SNP	ENST00000276654.5	37	CCDS6303.1	80	0.03663003663003663	78	0.15853658536585366	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	8.256	0.809999	0.16537	0.106446	5.81E-4	ENSG00000147650	ENST00000424843;ENST00000276654;ENST00000520873	D;D	0.85484	-1.99;-1.94	5.49	3.13	0.36017	.	0.595743	0.20652	N	0.088183	T	0.00608	0.0020	N	0.14661	0.345	0.09310	N	0.999997	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.00857	-1.1538	10	0.38643	T	0.18	-5.7539	8.0472	0.30555	0.0:0.2201:0.0:0.7799	rs16871494;rs52835469;rs16871494	675;694	Q9Y561-2;Q9Y561	.;LRP12_HUMAN	G	675;694;59	ENSP00000399148:S675G;ENSP00000276654:S694G	ENSP00000276654:S694G	S	-	1	0	LRP12	105572577	0.961000	0.32948	0.772000	0.31596	0.845000	0.48019	1.626000	0.37039	0.482000	0.27582	0.528000	0.53228	AGT	T|0.957;C|0.043	0.043	strong		0.532	LRP12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380821.1	NM_013437	
ITGA2B	3674	hgsc.bcm.edu	37	17	42455126	42455126	+	Silent	SNP	C	C	T	rs114232872	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:42455126C>T	ENST00000262407.5	-	21	2158	c.2127G>A	c.(2125-2127)aaG>aaA	p.K709K	ITGA2B_ENST00000353281.4_Silent_p.K709K	NM_000419.3	NP_000410.2	P08514	ITA2B_HUMAN	integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41)	709					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of leukocyte migration (GO:0002687)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)	extracellular matrix binding (GO:0050840)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			biliary_tract(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.191)	Abciximab(DB00054)|Tirofiban(DB00775)	TCTCATTCTCCTTCTTCTGAT	0.502													C|||	24	0.00479233	0.0159	0.0043	5008	,	,		14353	0.0		0.0	False		,,,				2504	0.0				p.K709K		Atlas-SNP	.											.	ITGA2B	88	.	0			c.G2127A						PASS	.	C		57,4349	54.9+/-90.9	0,57,2146	86.0	75.0	79.0		2127	-0.0	1.0	17	dbSNP_132	79	0,8600		0,0,4300	no	coding-synonymous	ITGA2B	NM_000419.3		0,57,6446	TT,TC,CC		0.0,1.2937,0.4383		709/1040	42455126	57,12949	2203	4300	6503	SO:0001819	synonymous_variant	3674	exon21			ATTCTCCTTCTTC		CCDS32665.1	17q21.32	2014-09-17	2006-02-22			ENSG00000005961		"""CD molecules"", ""Integrins"""	6138	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 93"""	607759	"""integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B)"""	GP2B			Standard	NM_000419		Approved	CD41B, CD41, PPP1R93	uc002igt.1	P08514		ENST00000262407.5:c.2127G>A	17.37:g.42455126C>T		69.0	0.0	0		69.0	36.0	0.521739	NM_000419	B2RCY8|O95366|Q14443|Q17R67	Silent	SNP	ENST00000262407.5	37	CCDS32665.1																																																																																			C|0.995;T|0.005	0.005	strong		0.502	ITGA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439823.1		
EVA1C	59271	hgsc.bcm.edu	37	21	33867447	33867447	+	Missense_Mutation	SNP	G	G	A	rs61744983	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:33867447G>A	ENST00000300255.2	+	5	1218	c.745G>A	c.(745-747)Gtg>Atg	p.V249M	EVA1C_ENST00000401402.3_Intron|EVA1C_ENST00000485488.1_3'UTR|EVA1C_ENST00000382699.3_Missense_Mutation_p.V249M	NM_058187.3	NP_478067.2	P58658	EVA1C_HUMAN	eva-1 homolog C (C. elegans)	249	SUEL-type lectin 2. {ECO:0000255|PROSITE- ProRule:PRU00260}.					integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)										TTTGCCAGGCGTGAAAAAATA	0.507													G|||	16	0.00319489	0.0121	0.0	5008	,	,		18504	0.0		0.0	False		,,,				2504	0.0				p.V249M		Atlas-SNP	.											.	.	.	.	0			c.G745A						PASS	.	G	MET/VAL	36,4370	40.0+/-72.8	0,36,2167	133.0	106.0	115.0		745	5.6	1.0	21	dbSNP_129	115	0,8600		0,0,4300	yes	missense	C21orf63	NM_058187.3	21	0,36,6467	AA,AG,GG		0.0,0.8171,0.2768	possibly-damaging	249/442	33867447	36,12970	2203	4300	6503	SO:0001583	missense	59271	exon5			CCAGGCGTGAAAA	AF358258	CCDS13614.1, CCDS68186.1	21q22.11	2012-11-05	2012-11-05	2012-11-05	ENSG00000166979	ENSG00000166979			13239	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 64"", ""chromosome 21 open reading frame 63"", ""family with sequence similarity 176, member C"""	C21orf64, C21orf63, FAM176C		11707072, 19470522	Standard	NM_058187		Approved	B18, PRED34, B19	uc002ypr.1	P58658	OTTHUMG00000064922	ENST00000300255.2:c.745G>A	21.37:g.33867447G>A	ENSP00000300255:p.Val249Met	145.0	0.0	0		159.0	88.0	0.553459	NM_058187	A6ND58|Q8IXZ0	Missense_Mutation	SNP	ENST00000300255.2	37	CCDS13614.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	24.5	4.540898	0.85917	0.008171	0.0	ENSG00000166979	ENST00000300255;ENST00000382699	T;T	0.19250	2.16;2.16	5.62	5.62	0.85841	D-galactoside/L-rhamnose binding SUEL lectin domain (2);	0.245509	0.41605	D	0.000854	T	0.41766	0.1173	M	0.75884	2.315	0.46564	D	0.999108	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.987	T	0.40664	-0.9551	10	0.56958	D	0.05	0.1652	19.264	0.93979	0.0:0.0:1.0:0.0	rs61744983	249;249	A6ND58;P58658	.;CU063_HUMAN	M	249	ENSP00000300255:V249M;ENSP00000372146:V249M	ENSP00000300255:V249M	V	+	1	0	C21orf63	32789318	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	6.445000	0.73456	2.631000	0.89168	0.655000	0.94253	GTG	G|0.997;A|0.003	0.003	strong		0.507	EVA1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139403.1	NM_058187	
MAK	4117	hgsc.bcm.edu	37	6	10792040	10792040	+	Missense_Mutation	SNP	C	C	A	rs62000445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:10792040C>A	ENST00000313243.2	-	10	1566	c.1184G>T	c.(1183-1185)cGt>cTt	p.R395L	MAK_ENST00000354489.2_Missense_Mutation_p.R395L|SYCP2L_ENST00000543878.1_Intron|MAK_ENST00000536370.1_3'UTR|MAK_ENST00000538030.1_Missense_Mutation_p.R395L|MAK_ENST00000474039.1_Missense_Mutation_p.R395L|RP11-637O19.3_ENST00000480294.1_Intron			P20794	MAK_HUMAN	male germ cell-associated kinase	395					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|photoreceptor cell maintenance (GO:0045494)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(8)|prostate(1)|skin(1)	22	Breast(50;0.107)|Ovarian(93;0.107)	all_hematologic(90;0.117)				CTGACCCCAACGCCTCCTACC	0.448													C|||	48	0.00958466	0.0348	0.0029	5008	,	,		17957	0.0		0.0	False		,,,				2504	0.0				p.R395L		Atlas-SNP	.											MAK,NS,carcinoma,-1,1	MAK	47	1	0			c.G1184T						PASS	.	C	LEU/ARG,LEU/ARG	125,4281	93.4+/-132.2	3,119,2081	114.0	104.0	107.0		1184,1184	5.0	0.9	6	dbSNP_129	107	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	MAK	NM_001242385.1,NM_005906.4	102,102	3,120,6380	AA,AC,CC		0.0116,2.837,0.9688	probably-damaging,probably-damaging	395/584,395/624	10792040	126,12880	2203	4300	6503	SO:0001583	missense	4117	exon10			CCCCAACGCCTCC		CCDS4516.1, CCDS75398.1, CCDS75399.1	6p24.2	2014-01-28			ENSG00000111837	ENSG00000111837			6816	protein-coding gene	gene with protein product		154235				16951154	Standard	NM_005906		Approved	dJ417M14.2, RP62	uc021ylk.1	P20794	OTTHUMG00000014247	ENST00000313243.2:c.1184G>T	6.37:g.10792040C>A	ENSP00000313021:p.Arg395Leu	133.0	0.0	0		150.0	73.0	0.486667	NM_005906	F1T0K6|G1FL29|Q547D0|Q9NUH7	Missense_Mutation	SNP	ENST00000313243.2	37	CCDS4516.1	21	0.009615384615384616	20	0.04065040650406504	1	0.0027624309392265192	0	0.0	0	0.0	C	22.3	4.265065	0.80358	0.02837	1.16E-4	ENSG00000111837	ENST00000313243;ENST00000354489;ENST00000538030	T;T;T	0.77877	-1.13;-1.13;-0.92	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	D	0.86230	0.5883	M	0.77103	2.36	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.87928	0.2708	10	0.87932	D	0	.	16.8762	0.86052	0.0:1.0:0.0:0.0	.	395	P20794	MAK_HUMAN	L	395	ENSP00000313021:R395L;ENSP00000346484:R395L;ENSP00000442250:R395L	ENSP00000313021:R395L	R	-	2	0	MAK	10900026	0.999000	0.42202	0.902000	0.35471	0.522000	0.34438	5.363000	0.66104	2.487000	0.83934	0.655000	0.94253	CGT	C|0.991;A|0.009	0.009	strong		0.448	MAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039841.1	NM_005906	
HLA-DOA	3111	hgsc.bcm.edu	37	6	32975896	32975896	+	Silent	SNP	A	A	G	rs364950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32975896A>G	ENST00000229829.5	-	2	300	c.225T>C	c.(223-225)ggT>ggC	p.G75G	HLA-DOA_ENST00000450833.2_Silent_p.G45G|HLA-DOA_ENST00000495532.1_5'UTR	NM_002119.3	NP_002110.1	P06340	DOA_HUMAN	major histocompatibility complex, class II, DO alpha	75	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|immune response (GO:0006955)|negative regulation of antigen processing and presentation of peptide antigen via MHC class II (GO:0002587)|regulation of T cell differentiation (GO:0045580)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)	MHC class II protein complex binding (GO:0023026)|MHC class II receptor activity (GO:0032395)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(1)	9						GGGCAAAGTCACCAAACTCAG	0.612													G|||	401	0.0800719	0.233	0.0749	5008	,	,		16847	0.0		0.0408	False		,,,				2504	0.0				p.G75G		Atlas-SNP	.											.	HLA-DOA	22	.	0			c.T225C						PASS	.	G		616,2406		51,514,946	58.0	52.0	54.0		225	1.6	0.1	6	dbSNP_80	54	141,5277		1,139,2569	no	coding-synonymous	HLA-DOA	NM_002119.3		52,653,3515	GG,GA,AA		2.6024,20.3839,8.9692		75/251	32975896	757,7683	1511	2709	4220	SO:0001819	synonymous_variant	3111	exon2			AAAGTCACCAAAC	M31525	CCDS4763.1	6p21.3	2013-01-11		2001-10-05	ENSG00000204252	ENSG00000204252		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4936	protein-coding gene	gene with protein product		142930		HLA-DZA, HLA-DNA		2370084	Standard	XM_005272804		Approved	HLA-D0-alpha	uc003ocr.3	P06340	OTTHUMG00000031211	ENST00000229829.5:c.225T>C	6.37:g.32975896A>G		78.0	0.0	0		88.0	39.0	0.443182	NM_002119	Q58HU0|Q58HU1|Q5STC7|Q9TQC6|Q9TQC7|Q9TQC8|Q9TQC9|Q9TQD0|Q9TQD1|Q9TQD2|Q9TQD3	Silent	SNP	ENST00000229829.5	37	CCDS4763.1																																																																																			A|0.906;G|0.094	0.094	strong		0.612	HLA-DOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076426.2	NM_002119	
MUC4	4585	hgsc.bcm.edu	37	3	195511447	195511447	+	Missense_Mutation	SNP	G	G	A	rs577730605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195511447G>A	ENST00000463781.3	-	2	7463	c.7004C>T	c.(7003-7005)aCg>aTg	p.T2335M	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T2335M	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.T2335M(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)		AGGAAGAGGCGTGGTGTCACC	0.597													.|||	23	0.00459265	0.0159	0.0	5008	,	,		17550	0.0		0.001	False		,,,				2504	0.001				p.T2335M		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	1	Substitution - Missense(1)	endometrium(1)	c.C7004T						scavenged	.						5.0	6.0	6.0					3																	195511447		581	1479	2060	SO:0001583	missense	4585	exon2			AGAGGCGTGGTGT	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.7004C>T	3.37:g.195511447G>A	ENSP00000417498:p.Thr2335Met	214.0	0.0	0		119.0	7.0	0.0588235	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	G	3.781	-0.045698	0.07452	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.36699	1.24;1.28	.	.	.	.	1.329500	0.07018	U	0.826373	T	0.30978	0.0782	N	0.19112	0.55	0.09310	N	1	D	0.64830	0.994	P	0.52909	0.713	T	0.26677	-1.0096	8	.	.	.	.	5.844	0.18652	9.0E-4:0.0:0.9991:0.0	.	2335	E7ESK3	.	M	2335	ENSP00000417498:T2335M;ENSP00000420243:T2335M	.	T	-	2	0	MUC4	196995842	0.000000	0.05858	0.018000	0.16275	0.025000	0.11179	-0.545000	0.06069	0.064000	0.16427	0.064000	0.15345	ACG	.	.	none		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CTTN	2017	hgsc.bcm.edu	37	11	70279759	70279759	+	Missense_Mutation	SNP	G	G	A	rs56162978	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:70279759G>A	ENST00000301843.8	+	17	1657	c.1451G>A	c.(1450-1452)aGc>aAc	p.S484N	CTTN_ENST00000538675.1_Missense_Mutation_p.S168N|CTTN_ENST00000346329.3_Missense_Mutation_p.S447N|CTTN_ENST00000376561.3_Missense_Mutation_p.S447N	NM_005231.3	NP_005222.2	Q14247	SRC8_HUMAN	cortactin	484					negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|mitotic spindle midzone (GO:1990023)|ruffle (GO:0001726)				breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|urinary_tract(1)	31			BRCA - Breast invasive adenocarcinoma(2;4.34e-41)|LUSC - Lung squamous cell carcinoma(11;1.51e-13)|STAD - Stomach adenocarcinoma(18;0.0513)	Lung(977;0.0234)|LUSC - Lung squamous cell carcinoma(976;0.133)		TTAGAGGACAGCACCTACGAT	0.517													G|||	261	0.0521166	0.1884	0.0173	5008	,	,		16431	0.0		0.0	False		,,,				2504	0.0				p.S484N		Atlas-SNP	.											.	CTTN	162	.	0			c.G1451A						PASS	.		ASN/SER,ASN/SER,ASN/SER	788,3612	319.1+/-295.9	55,678,1467	159.0	153.0	155.0		1340,1451,1340	-0.8	0.0	11	dbSNP_129	155	5,8583	3.7+/-12.6	0,5,4289	yes	missense,missense,missense	CTTN	NM_001184740.1,NM_005231.3,NM_138565.2	46,46,46	55,683,5756	AA,AG,GG		0.0582,17.9091,6.1056	benign,benign,benign	447/635,484/551,447/514	70279759	793,12195	2200	4294	6494	SO:0001583	missense	2017	exon17			AGGACAGCACCTA	AJ288897	CCDS8197.1, CCDS41680.1, CCDS53676.1	11q13	2008-02-05	2004-06-08	2004-06-09	ENSG00000085733	ENSG00000085733			3338	protein-coding gene	gene with protein product		164765	"""ems1 sequence (mammary tumor and squamous cell carcinoma-associated (p80/85 src substrate)"""	EMS1		7685625	Standard	NM_005231		Approved		uc001opu.3	Q14247	OTTHUMG00000134307	ENST00000301843.8:c.1451G>A	11.37:g.70279759G>A	ENSP00000301843:p.Ser484Asn	121.0	0.0	0		138.0	64.0	0.463768	NM_005231	Q8N707|Q96H99	Missense_Mutation	SNP	ENST00000301843.8	37	CCDS41680.1	85	0.03891941391941392	81	0.16463414634146342	4	0.011049723756906077	0	0.0	0	0.0	G	1.497	-0.553053	0.03996	0.179091	5.82E-4	ENSG00000085733	ENST00000346329;ENST00000301843;ENST00000376561;ENST00000538675;ENST00000529736	T;T;T;T;T	0.32753	1.44;1.45;1.48;1.88;1.86	4.86	-0.816	0.10839	Src homology-3 domain (1);	0.722113	0.13537	N	0.380525	T	0.00039	0.0001	N	0.14661	0.345	0.09310	N	1	B;B;B;B	0.09022	0.002;0.0;0.0;0.0	B;B;B;B	0.10450	0.005;0.0;0.0;0.001	T	0.21143	-1.0254	10	0.05525	T	0.97	-27.692	5.4208	0.16400	0.6072:0.1347:0.258:0.0	rs56162978;rs58344286	168;447;484;447	B4E358;Q96H99;Q14247;Q8N707	.;.;SRC8_HUMAN;.	N	447;484;447;168;141	ENSP00000317189:S447N;ENSP00000301843:S484N;ENSP00000365745:S447N;ENSP00000439762:S168N;ENSP00000431421:S141N	ENSP00000301843:S484N	S	+	2	0	CTTN	69957407	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.316000	0.19469	-0.462000	0.06984	-0.891000	0.02926	AGC	G|0.941;A|0.059	0.059	strong		0.517	CTTN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259233.2	NM_138565	
CCDC173	129881	hgsc.bcm.edu	37	2	170502509	170502509	+	Missense_Mutation	SNP	G	G	A	rs112720712	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170502509G>A	ENST00000447353.1	-	9	1606	c.1501C>T	c.(1501-1503)Cct>Tct	p.P501S		NM_001085447.1	NP_001078916.1	Q0VFZ6	CC173_HUMAN	coiled-coil domain containing 173	501																	CCACCTCCAGGTCCTTCCTGT	0.433													G|||	49	0.00978435	0.034	0.0043	5008	,	,		17210	0.0		0.001	False		,,,				2504	0.0				p.P501S		Atlas-SNP	.											.	.	.	.	0			c.C1501T						PASS	.	G	SER/PRO	119,3659		2,115,1772	169.0	173.0	171.0		1501	2.0	1.0	2	dbSNP_132	171	0,8212		0,0,4106	yes	missense	C2orf77	NM_001085447.1	74	2,115,5878	AA,AG,GG		0.0,3.1498,0.9925	benign	501/553	170502509	119,11871	1889	4106	5995	SO:0001583	missense	129881	exon9			CTCCAGGTCCTTC	BC015980, BC117445	CCDS46445.1	2q31.1	2012-08-07	2012-08-07	2012-08-07	ENSG00000154479	ENSG00000154479			25064	protein-coding gene	gene with protein product	"""hypothetical LOC129881"""		"""chromosome 2 open reading frame 77"""	C2orf77		12477932	Standard	NM_001085447		Approved	LOC129881	uc002ufe.2	Q0VFZ6	OTTHUMG00000154116	ENST00000447353.1:c.1501C>T	2.37:g.170502509G>A	ENSP00000391504:p.Pro501Ser	122.0	0.0	0		109.0	49.0	0.449541	NM_001085447	Q6PJF6	Missense_Mutation	SNP	ENST00000447353.1	37	CCDS46445.1	20	0.009157509157509158	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	13.71	2.319074	0.41096	0.031498	0.0	ENSG00000154479	ENST00000447353	.	.	.	5.87	2.01	0.26516	.	0.916393	0.09355	N	0.813572	T	0.06462	0.0166	L	0.40543	1.245	0.20074	N	0.999938	B	0.09022	0.002	B	0.08055	0.003	T	0.24657	-1.0154	9	0.07482	T	0.82	.	1.5507	0.02574	0.229:0.2733:0.3648:0.1329	.	501	Q0VFZ6	CB077_HUMAN	S	501	.	ENSP00000391504:P501S	P	-	1	0	C2orf77	170210755	0.219000	0.23619	0.992000	0.48379	0.992000	0.81027	0.199000	0.17237	0.467000	0.27218	0.655000	0.94253	CCT	G|0.990;A|0.010	0.010	strong		0.433	CCDC173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333954.2	NM_001085447	
MARK3	4140	hgsc.bcm.edu	37	14	103941392	103941392	+	Missense_Mutation	SNP	A	A	G	rs56305318	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:103941392A>G	ENST00000429436.2	+	13	1837	c.1327A>G	c.(1327-1329)Agt>Ggt	p.S443G	MARK3_ENST00000303622.9_Missense_Mutation_p.S443G|MARK3_ENST00000335102.5_Missense_Mutation_p.S466G|MARK3_ENST00000561071.1_Intron|MARK3_ENST00000216288.7_Missense_Mutation_p.S427G|MARK3_ENST00000416682.2_Missense_Mutation_p.S466G|MARK3_ENST00000440884.3_Missense_Mutation_p.S364G|MARK3_ENST00000553942.1_Missense_Mutation_p.S443G	NM_001128918.1|NM_001128919.1	NP_001122390.1|NP_001122391.1	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3	443			S -> G (in dbSNP:rs56305318). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9543386, ECO:0000269|Ref.2}.			plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30		Melanoma(154;0.155)	Epithelial(46;0.241)			CACTGCAGATAGTGACCTCAA	0.448													A|||	242	0.0483227	0.1793	0.0072	5008	,	,		20680	0.0		0.0	False		,,,				2504	0.0				p.S443G		Atlas-SNP	.											.	MARK3	86	.	0			c.A1327G						PASS	.	A	GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER	577,3417		51,475,1471	59.0	61.0	60.0		1327,1327,1279,1090,1327	2.0	0.8	14	dbSNP_129	60	1,8343		0,1,4171	yes	missense,missense,missense,missense,missense	MARK3	NM_001128918.1,NM_001128919.1,NM_001128920.1,NM_001128921.1,NM_002376.5	56,56,56,56,56	51,476,5642	GG,GA,AA		0.012,14.4467,4.6847	benign,benign,benign,benign,benign	443/754,443/745,427/714,364/660,443/730	103941392	578,11760	1997	4172	6169	SO:0001583	missense	4140	exon13			GCAGATAGTGACC	M80359	CCDS41993.1, CCDS45165.1, CCDS45166.1, CCDS45167.1, CCDS55947.1	14q32.32	2014-04-07			ENSG00000075413	ENSG00000075413			6897	protein-coding gene	gene with protein product		602678				9533022	Standard	NM_002376		Approved	CTAK1, KP78, PAR-1A	uc001ymz.4	P27448	OTTHUMG00000171789	ENST00000429436.2:c.1327A>G	14.37:g.103941392A>G	ENSP00000411397:p.Ser443Gly	86.0	0.0	0		85.0	48.0	0.564706	NM_001128919	O60219|Q86TT8|Q8TB41|Q8WX83|Q96RG1|Q9UMY9|Q9UN34	Missense_Mutation	SNP	ENST00000429436.2	37	CCDS45165.1	87|87	0.03983516483516483|0.03983516483516483	83|83	0.16869918699186992|0.16869918699186992	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	0|0	0.0|0.0	A|A	12.87|12.87	2.068525|2.068525	0.36470|0.36470	0.144467|0.144467	1.2E-4|1.2E-4	ENSG00000075413|ENSG00000075413	ENST00000554627|ENST00000335102;ENST00000411530;ENST00000440884;ENST00000416682;ENST00000429436;ENST00000303622;ENST00000216288;ENST00000553942	.|T;T;T;T;T;T;T	.|0.55234	.|0.53;0.53;0.53;0.53;0.53;0.53;0.53	5.78|5.78	2.0|2.0	0.26442|0.26442	.|.	.|0.269900	.|0.46758	.|N	.|0.000264	T|T	0.00144|0.00144	0.0004|0.0004	L|L	0.40543|0.40543	1.245|1.245	0.27271|0.27271	P|P	0.9583608|0.9583608	.|B;B;B;B;B;B;B	.|0.02656	.|0.0;0.0;0.0;0.0;0.0;0.0;0.0	.|B;B;B;B;B;B;B	.|0.10450	.|0.001;0.004;0.001;0.001;0.0;0.005;0.001	T|T	0.07868|0.07868	-1.0750|-1.0750	4|9	.|0.29301	.|T	.|0.29	.|.	9.2811|9.2811	0.37729|0.37729	0.781:0.0:0.219:0.0|0.781:0.0:0.219:0.0	rs56305318;rs61730317|rs56305318;rs61730317	.|450;466;427;443;364;443;443	.|P27448-7;P27448-2;P27448-6;P27448;Q86TT8;P27448-4;P27448-3	.|.;.;.;MARK3_HUMAN;.;.;.	M|G	194|466;92;364;466;443;443;427;443	.|ENSP00000335347:S466G;ENSP00000402104:S364G;ENSP00000408092:S466G;ENSP00000411397:S443G;ENSP00000303698:S443G;ENSP00000216288:S427G;ENSP00000450772:S443G	.|ENSP00000216288:S443G	I|S	+|+	3|1	3|0	MARK3|MARK3	103011145|103011145	0.979000|0.979000	0.34478|0.34478	0.769000|0.769000	0.31535|0.31535	0.720000|0.720000	0.41350|0.41350	1.621000|1.621000	0.36986|0.36986	0.090000|0.090000	0.17273|0.17273	0.533000|0.533000	0.62120|0.62120	ATA|AGT	A|0.958;G|0.042	0.042	strong		0.448	MARK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415144.1	NM_001128918	
STARD13	90627	hgsc.bcm.edu	37	13	33741716	33741716	+	Silent	SNP	C	C	T	rs17078661	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:33741716C>T	ENST00000336934.5	-	2	329	c.213G>A	c.(211-213)ggG>ggA	p.G71G	STARD13_ENST00000399365.3_5'UTR|STARD13_ENST00000255486.4_Silent_p.G63G|STARD13_ENST00000487412.1_5'UTR	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	71	SAM.				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)		ATTGCGGGAACCCGGCAGCAC	0.483													C|||	178	0.0355431	0.1301	0.0086	5008	,	,		18769	0.0		0.0	False		,,,				2504	0.0				p.G71G		Atlas-SNP	.											STARD13,NS,carcinoma,-1,1	STARD13	100	1	0			c.G213A						PASS	.	C	,,	558,3848	250.9+/-257.8	30,498,1675	96.0	93.0	94.0		,213,189	-3.2	1.0	13	dbSNP_123	94	7,8593	5.7+/-21.5	0,7,4293	no	utr-5,coding-synonymous,coding-synonymous	STARD13	NM_052851.2,NM_178006.3,NM_178007.2	,,	30,505,5968	TT,TC,CC		0.0814,12.6645,4.3441	,,	,71/1114,63/1106	33741716	565,12441	2203	4300	6503	SO:0001819	synonymous_variant	90627	exon2			CGGGAACCCGGCA	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.213G>A	13.37:g.33741716C>T		63.0	0.0	0		69.0	33.0	0.478261	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Silent	SNP	ENST00000336934.5	37	CCDS9348.1																																																																																			C|0.960;T|0.040	0.040	strong		0.483	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466	
ZNF506	440515	hgsc.bcm.edu	37	19	19906131	19906131	+	Missense_Mutation	SNP	T	T	G	rs16996376	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:19906131T>G	ENST00000540806.2	-	4	653	c.565A>C	c.(565-567)Act>Cct	p.T189P	CTC-559E9.4_ENST00000590274.1_lincRNA|CTC-559E9.6_ENST00000591884.1_RNA|ZNF506_ENST00000443905.2_Missense_Mutation_p.T189P|ZNF506_ENST00000587461.1_Intron|ZNF506_ENST00000450683.2_Missense_Mutation_p.T157P|CTC-559E9.6_ENST00000589657.1_RNA			Q5JVG8	ZN506_HUMAN	zinc finger protein 506	189			T -> P (in dbSNP:rs16996376).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|large_intestine(7)|lung(3)|skin(1)|stomach(1)	14						TTATATGTAGTACGGGTTGAA	0.303													t|||	327	0.0652955	0.2262	0.0288	5008	,	,		19010	0.0		0.007	False		,,,				2504	0.001				p.T189P		Atlas-SNP	.											.	ZNF506	36	.	0			c.A565C						PASS	.	T	PRO/THR,PRO/THR	787,3387		71,645,1371	51.0	53.0	52.0		565,469	1.0	0.1	19	dbSNP_123	52	66,8426		1,64,4181	yes	missense,missense	ZNF506	NM_001099269.2,NM_001145404.1	38,38	72,709,5552	GG,GT,TT		0.7772,18.8548,6.7346	possibly-damaging,possibly-damaging	189/445,157/413	19906131	853,11813	2087	4246	6333	SO:0001583	missense	440515	exon4			ATGTAGTACGGGT	AK095575	CCDS42531.1, CCDS46027.1	19p13.11	2013-01-08				ENSG00000081665		"""Zinc fingers, C2H2-type"", ""-"""	23780	protein-coding gene	gene with protein product							Standard	NM_001099269		Approved	DKFZp761G1812	uc010eci.2	Q5JVG8		ENST00000540806.2:c.565A>C	19.37:g.19906131T>G	ENSP00000440625:p.Thr189Pro	66.0	0.0	0		50.0	22.0	0.44	NM_001099269	B3KTH6	Missense_Mutation	SNP	ENST00000540806.2	37	CCDS42531.1	131	0.059981684981684984	115	0.23373983739837398	13	0.03591160220994475	0	0.0	3	0.00395778364116095	t	13.27	2.185989	0.38609	0.188548	0.007772	ENSG00000081665	ENST00000443905;ENST00000540806;ENST00000450683	T;T;T	0.01172	5.23;5.23;5.23	0.974	0.974	0.19715	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	M	0.85373	2.75	0.80722	P	0.0	D;D	0.67145	0.996;0.967	D;P	0.65874	0.939;0.75	T	0.41980	-0.9478	8	0.87932	D	0	.	4.0711	0.09882	0.0:0.0:0.0:1.0	rs16996376;rs60499475;rs16996376	189;157	Q5JVG8;Q5JVG8-2	ZN506_HUMAN;.	P	189;189;157	ENSP00000393835:T189P;ENSP00000440625:T189P;ENSP00000408892:T157P	ENSP00000393835:T189P	T	-	1	0	ZNF506	19767131	0.000000	0.05858	0.061000	0.19648	0.058000	0.15608	-0.102000	0.10956	0.358000	0.24211	0.347000	0.21830	ACT	T|0.935;G|0.065	0.065	strong		0.303	ZNF506-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460794.1	XM_036218	
WNT8B	7479	hgsc.bcm.edu	37	10	102242030	102242030	+	Silent	SNP	G	G	A	rs9420786	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:102242030G>A	ENST00000343737.5	+	6	641	c.513G>A	c.(511-513)gcG>gcA	p.A171A		NM_003393.3	NP_003384.2	Q93098	WNT8B_HUMAN	wingless-type MMTV integration site family, member 8B	171					cell fate commitment (GO:0045165)|cellular response to retinoic acid (GO:0071300)|determination of dorsal identity (GO:0048263)|gastrulation (GO:0007369)|negative regulation of gene expression (GO:0010629)|nervous system development (GO:0007399)|neuron differentiation (GO:0030182)|positive regulation of gene expression (GO:0010628)|response to estradiol (GO:0032355)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|large_intestine(1)|ovary(1)|skin(1)	4		Colorectal(252;0.117)		Epithelial(162;1.87e-10)|all cancers(201;1.64e-08)		CTCCCCAGGCGGTGAAGGGCA	0.622											OREG0020440	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	90	0.0179712	0.0514	0.0029	5008	,	,		16675	0.002		0.001	False		,,,				2504	0.0174				p.A171A		Atlas-SNP	.											.	WNT8B	31	.	0			c.G513A						PASS	.	G		247,4131		4,239,1946	15.0	16.0	16.0		513	-3.3	0.9	10	dbSNP_119	16	2,8544		0,2,4271	no	coding-synonymous	WNT8B	NM_003393.3		4,241,6217	AA,AG,GG		0.0234,5.6418,1.9266		171/352	102242030	249,12675	2189	4273	6462	SO:0001819	synonymous_variant	7479	exon6			CCAGGCGGTGAAG	X91940	CCDS7494.1	10q24	2003-11-12			ENSG00000075290	ENSG00000075290		"""Wingless-type MMTV integration sites"""	12789	protein-coding gene	gene with protein product		601396				8661156	Standard	NM_003393		Approved		uc001krb.3	Q93098	OTTHUMG00000018912	ENST00000343737.5:c.513G>A	10.37:g.102242030G>A		17.0	0.0	0	1365	29.0	12.0	0.413793	NM_003393	O00771|Q5VX55|Q8WYK9	Silent	SNP	ENST00000343737.5	37	CCDS7494.1																																																																																			G|0.978;A|0.022	0.022	strong		0.622	WNT8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049867.1	NM_003393	
CDC6	990	hgsc.bcm.edu	37	17	38447569	38447569	+	Silent	SNP	T	T	C	rs1130199	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38447569T>C	ENST00000209728.4	+	3	909	c.438T>C	c.(436-438)tgT>tgC	p.C146C		NM_001254.3	NP_001245.1	Q99741	CDC6_HUMAN	cell division cycle 6	146					DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|positive regulation of chromosome segregation (GO:0051984)|positive regulation of cytokinesis (GO:0032467)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|traversing start control point of mitotic cell cycle (GO:0007089)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|kinase binding (GO:0019900)|nucleotide binding (GO:0000166)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	21						AATCTGCATGTGTGAGACTAT	0.403													T|||	557	0.111222	0.3994	0.0375	5008	,	,		24231	0.0		0.003	False		,,,				2504	0.0				p.C146C		Atlas-SNP	.											.	CDC6	53	.	0			c.T438C						PASS	.	T		1438,2968	453.6+/-350.4	230,978,995	87.0	90.0	89.0		438	0.9	0.0	17	dbSNP_86	89	10,8590	6.4+/-24.3	0,10,4290	no	coding-synonymous	CDC6	NM_001254.3		230,988,5285	CC,CT,TT		0.1163,32.6373,11.1333		146/561	38447569	1448,11558	2203	4300	6503	SO:0001819	synonymous_variant	990	exon3			TGCATGTGTGAGA	U77949	CCDS11365.1	17q21.3	2013-01-17	2013-01-17		ENSG00000094804	ENSG00000094804			1744	protein-coding gene	gene with protein product		602627	"""CDC6 (cell division cycle 6, S. cerevisiae) homolog"", ""CDC6 cell division cycle 6 homolog (S. cerevisiae)"", ""cell division cycle 6 homolog (S. cerevisiae)"""	CDC18L		8990175, 9566895	Standard	NM_001254		Approved		uc002huj.1	Q99741	OTTHUMG00000133324	ENST00000209728.4:c.438T>C	17.37:g.38447569T>C		154.0	1.0	0.00649351		140.0	139.0	0.992857	NM_001254	Q8TB30	Silent	SNP	ENST00000209728.4	37	CCDS11365.1																																																																																			T|0.886;C|0.114	0.114	strong		0.403	CDC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257129.1		
DNAJB9	4189	hgsc.bcm.edu	37	7	108213545	108213545	+	Silent	SNP	T	T	C	rs376971670		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:108213545T>C	ENST00000249356.3	+	3	966	c.420T>C	c.(418-420)caT>caC	p.H140H	DNAJB9_ENST00000465725.1_Intron	NM_012328.2	NP_036460.1	Q9UBS3	DNJB9_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 9	140					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	misfolded protein binding (GO:0051787)			central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(4)|urinary_tract(1)	13						TTGAAAATCATTTCCAGACAC	0.363																																					p.H140H		Atlas-SNP	.											DNAJB9,NS,carcinoma,+1,1	DNAJB9	25	1	0			c.T420C						PASS	.	T		2,4404	4.2+/-10.8	0,2,2201	110.0	109.0	109.0		420	0.7	1.0	7		109	0,8600		0,0,4300	no	coding-synonymous	DNAJB9	NM_012328.2		0,2,6501	CC,CT,TT		0.0,0.0454,0.0154		140/224	108213545	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	4189	exon3			AAATCATTTCCAG	AB026908	CCDS5752.1	7q31	2011-09-02			ENSG00000128590	ENSG00000128590		"""Heat shock proteins / DNAJ (HSP40)"""	6968	protein-coding gene	gene with protein product		602634		MDG1		9533036, 11147971	Standard	NM_012328		Approved		uc003vfn.3	Q9UBS3	OTTHUMG00000154866	ENST00000249356.3:c.420T>C	7.37:g.108213545T>C		172.0	0.0	0		176.0	83.0	0.471591	NM_012328		Silent	SNP	ENST00000249356.3	37	CCDS5752.1																																																																																			.	.	weak		0.363	DNAJB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337414.1		
SELE	6401	hgsc.bcm.edu	37	1	169697218	169697218	+	Silent	SNP	G	G	A	rs5365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:169697218G>A	ENST00000333360.7	-	8	1399	c.1260C>T	c.(1258-1260)aaC>aaT	p.N420N	SELE_ENST00000367777.1_Silent_p.N420N|SELE_ENST00000367774.1_Intron|C1orf112_ENST00000498289.1_Intron|SELE_ENST00000367776.1_Intron|SELE_ENST00000367780.4_Intron|SELE_ENST00000367781.4_Intron|SELE_ENST00000367779.4_Intron|SELE_ENST00000367782.4_Silent_p.N420N|SELE_ENST00000367775.1_Intron	NM_000450.2	NP_000441.2	P16581	LYAM2_HUMAN	selectin E	420	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				actin filament-based process (GO:0030029)|activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|leukocyte tethering or rolling (GO:0050901)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of receptor internalization (GO:0002092)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)	caveola (GO:0005901)|coated pit (GO:0005905)|cortical cytoskeleton (GO:0030863)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	oligosaccharide binding (GO:0070492)|phospholipase binding (GO:0043274)|sialic acid binding (GO:0033691)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(3)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	all_hematologic(923;0.208)				Carvedilol(DB01136)	TGGGCTTCTCGTTGTCCCACT	0.448													G|||	101	0.0201677	0.0756	0.0014	5008	,	,		19018	0.0		0.0	False		,,,				2504	0.0				p.N420N		Atlas-SNP	.											.	SELE	84	.	0			c.C1260T						PASS	.	G		284,4122	157.0+/-190.0	5,274,1924	96.0	109.0	104.0		1260	-10.5	0.0	1	dbSNP_52	104	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SELE	NM_000450.2		5,276,6222	AA,AG,GG		0.0233,6.4458,2.199		420/611	169697218	286,12720	2203	4300	6503	SO:0001819	synonymous_variant	6401	exon8			CTTCTCGTTGTCC	M30640	CCDS1283.1	1q22-q25	2008-07-31	2008-07-31		ENSG00000007908	ENSG00000007908		"""CD molecules"""	10718	protein-coding gene	gene with protein product		131210	"""endothelial adhesion molecule 1"""	ELAM1, ELAM		1375831	Standard	NM_000450		Approved	ESEL, CD62E	uc001ggm.4	P16581	OTTHUMG00000034851	ENST00000333360.7:c.1260C>T	1.37:g.169697218G>A		67.0	0.0	0		60.0	27.0	0.45	NM_000450	A2RRD6|P16111	Silent	SNP	ENST00000333360.7	37	CCDS1283.1																																																																																			G|0.982;A|0.018	0.018	strong		0.448	SELE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084333.1	NM_000450	
TMEM14B	81853	hgsc.bcm.edu	37	6	10751379	10751379	+	Silent	SNP	C	C	T	rs1046427	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:10751379C>T	ENST00000379542.5	+	4	281	c.114C>T	c.(112-114)tcC>tcT	p.S38S	TMEM14B_ENST00000379530.3_Intron|TMEM14B_ENST00000461342.1_Intron|TMEM14B_ENST00000473276.1_Intron|TMEM14B_ENST00000481240.1_Intron|TMEM14B_ENST00000475942.1_Silent_p.S38S|SYCP2L_ENST00000543878.1_Intron|TMEM14B_ENST00000491103.1_3'UTR|TMEM14B_ENST00000467317.1_Silent_p.S38S|RP11-637O19.3_ENST00000480294.1_Intron|RNA5SP203_ENST00000410451.1_RNA	NM_030969.3	NP_112231.3	Q9NUH8	TM14B_HUMAN	transmembrane protein 14B	38						integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(2)|skin(2)	11	Ovarian(93;0.107)|Breast(50;0.137)	all_hematologic(90;0.135)				GCGTGCCGTCCCTGGCTGCAG	0.542													C|||	117	0.0233626	0.0779	0.0115	5008	,	,		20713	0.0		0.004	False		,,,				2504	0.002				p.S38S		Atlas-SNP	.											.	TMEM14B	19	.	0			c.C114T						PASS	.	C	,	262,4142	148.4+/-182.8	15,232,1955	129.0	112.0	118.0		,114	3.1	0.9	6	dbSNP_86	118	28,8572	18.5+/-59.3	0,28,4272	no	intron,coding-synonymous	TMEM14B	NM_001127711.1,NM_030969.3	,	15,260,6227	TT,TC,CC		0.3256,5.9491,2.2301	,	,38/115	10751379	290,12714	2202	4300	6502	SO:0001819	synonymous_variant	81853	exon4			GCCGTCCCTGGCT	AL024498	CCDS4515.1, CCDS47372.1, CCDS75395.1, CCDS75396.1, CCDS75397.1	6p25.1-p23	2008-08-12			ENSG00000137210	ENSG00000137210			21384	protein-coding gene	gene with protein product							Standard	NM_030969		Approved	MGC1223	uc003mzk.4	Q9NUH8	OTTHUMG00000014246	ENST00000379542.5:c.114C>T	6.37:g.10751379C>T		110.0	0.0	0		122.0	59.0	0.483607	NM_030969	Q5THN7|Q5THN8|Q96IX7|Q9BVN8	Silent	SNP	ENST00000379542.5	37	CCDS4515.1																																																																																			C|0.979;T|0.021	0.021	strong		0.542	TMEM14B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039836.1	NM_030969	
ANKRD33	341405	hgsc.bcm.edu	37	12	52282865	52282865	+	Silent	SNP	C	C	T	rs35851809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52282865C>T	ENST00000340970.4	+	3	377	c.6C>T	c.(4-6)gtC>gtT	p.V2V	ANKRD33_ENST00000547119.1_3'UTR|ANKRD33_ENST00000538991.1_Intron|ANKRD33_ENST00000301190.6_Silent_p.V137V			Q7Z3H0	ANR33_HUMAN	ankyrin repeat domain 33	2					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|skeletal muscle cell differentiation (GO:0035914)	cytosol (GO:0005829)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	22				BRCA - Breast invasive adenocarcinoma(357;0.0969)		GCCTCATGGTCGCATGCTACC	0.607													c|||	7	0.00139776	0.0053	0.0	5008	,	,		18277	0.0		0.0	False		,,,				2504	0.0				p.V137V		Atlas-SNP	.											.	ANKRD33	33	.	0			c.C411T						PASS	.	T	,	29,4377	35.2+/-66.4	1,27,2175	91.0	96.0	95.0		6,411	-1.1	0.7	12	dbSNP_126	95	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ANKRD33	NM_001130015.1,NM_182608.3	,	1,27,6475	TT,TC,CC		0.0,0.6582,0.223	,	2/273,137/453	52282865	29,12977	2203	4300	6503	SO:0001819	synonymous_variant	341405	exon3			CATGGTCGCATGC		CCDS8815.1, CCDS44892.1	12q13.13	2013-01-10	2005-01-07	2005-01-07		ENSG00000167612		"""Ankyrin repeat domain containing"""	13788	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 7"""	C12orf7		20026326	Standard	NM_182608		Approved	DKFZp686O1689, PANKY	uc001rzd.3	Q7Z3H0	OTTHUMG00000169506	ENST00000340970.4:c.6C>T	12.37:g.52282865C>T		135.0	0.0	0		93.0	42.0	0.451613	NM_182608	Q0VAA7|Q5K619|Q5K621|Q5K622|Q5K623|Q5K624|Q6ZUN0	Silent	SNP	ENST00000340970.4	37	CCDS44892.1																																																																																			C|0.998;T|0.002	0.002	strong		0.607	ANKRD33-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404515.1	NM_182608	
MS4A7	58475	hgsc.bcm.edu	37	11	60161273	60161273	+	Missense_Mutation	SNP	C	C	T	rs372900689		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:60161273C>T	ENST00000300184.3	+	7	858	c.662C>T	c.(661-663)tCg>tTg	p.S221L	MS4A14_ENST00000531787.1_Intron|MS4A7_ENST00000358246.1_Missense_Mutation_p.S176L|MS4A7_ENST00000530234.2_Intron|MS4A14_ENST00000395001.1_5'Flank|MS4A14_ENST00000531783.1_5'Flank|MS4A14_ENST00000300187.6_5'Flank|MS4A7_ENST00000534016.1_Missense_Mutation_p.S176L|MS4A14_ENST00000395005.2_5'Flank	NM_021201.4|NM_206939.1	NP_067024.1|NP_996822.1	Q9GZW8	MS4A7_HUMAN	membrane-spanning 4-domains, subfamily A, member 7	221						integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|liver(2)|lung(8)|ovary(1)|skin(1)	20						TCATTTTCCTCGACCCAGTCA	0.348																																					p.S221L		Atlas-SNP	.											.	MS4A7	38	.	0			c.C662T						PASS	.	C	LEU/SER,LEU/SER,LEU/SER,LEU/SER	1,4405	2.1+/-5.4	0,1,2202	103.0	105.0	104.0		527,662,527,662	-0.0	0.0	11		104	0,8600		0,0,4300	no	missense,missense,missense,missense	MS4A7	NM_206940.1,NM_206939.1,NM_206938.1,NM_021201.4	145,145,145,145	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign,benign,benign	176/196,221/241,176/196,221/241	60161273	1,13005	2203	4300	6503	SO:0001583	missense	58475	exon7			TTTCCTCGACCCA	AB026043	CCDS7985.1, CCDS7986.1	11q12	2008-03-25				ENSG00000166927			13378	protein-coding gene	gene with protein product		606502				11245982, 11401424	Standard	NM_021201		Approved	CD20L4, CFFM4, MS4A8	uc001npf.3	Q9GZW8		ENST00000300184.3:c.662C>T	11.37:g.60161273C>T	ENSP00000300184:p.Ser221Leu	75.0	0.0	0		70.0	41.0	0.585714	NM_021201	A6NP53|Q6IAG8	Missense_Mutation	SNP	ENST00000300184.3	37	CCDS7985.1	.	.	.	.	.	.	.	.	.	.	c	0.019	-1.453245	0.01071	2.27E-4	0.0	ENSG00000166927	ENST00000300184;ENST00000358246;ENST00000534016;ENST00000530027	T;T;T;T	0.12984	3.36;2.63;2.63;2.9	3.79	-0.0112	0.13993	.	2.053890	0.03732	N	0.253570	T	0.05640	0.0148	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27434	-1.0074	10	0.02654	T	1	-35.547	3.542	0.07815	0.0:0.2192:0.1969:0.5839	.	176;221	Q9GZW8-2;Q9GZW8	.;MS4A7_HUMAN	L	221;176;176;157	ENSP00000300184:S221L;ENSP00000350983:S176L;ENSP00000434637:S176L;ENSP00000434819:S157L	ENSP00000300184:S221L	S	+	2	0	MS4A7	59917849	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.094000	0.11094	-0.015000	0.14150	-0.592000	0.04112	TCG	.	.	weak		0.348	MS4A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394299.1		
HSPB3	8988	hgsc.bcm.edu	37	5	53751818	53751818	+	Missense_Mutation	SNP	G	G	A	rs35258119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:53751818G>A	ENST00000302005.1	+	1	374	c.199G>A	c.(199-201)Ggc>Agc	p.G67S		NM_006308.2	NP_006299.1	Q12988	HSPB3_HUMAN	heat shock 27kDa protein 3	67			G -> S (in dbSNP:rs35258119).		cell death (GO:0008219)|response to unfolded protein (GO:0006986)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|large_intestine(4)|prostate(3)	8		Lung NSC(810;0.00104)				ACCCCGAGAAGGCAAATCCCA	0.552													G|||	41	0.0081869	0.028	0.0058	5008	,	,		19929	0.0		0.0	False		,,,				2504	0.0				p.G67S		Atlas-SNP	.											.	HSPB3	17	.	0			c.G199A						PASS	.	G	SER/GLY	90,4316	75.7+/-113.9	0,90,2113	84.0	76.0	79.0		199	2.1	0.0	5	dbSNP_126	79	0,8600		0,0,4300	yes	missense	HSPB3	NM_006308.2	56	0,90,6413	AA,AG,GG		0.0,2.0427,0.692	benign	67/151	53751818	90,12916	2203	4300	6503	SO:0001583	missense	8988	exon1			CGAGAAGGCAAAT	Y17782	CCDS3961.1	5q11.2	2011-09-02	2002-08-29		ENSG00000169271	ENSG00000169271		"""Heat shock proteins / HSPB"""	5248	protein-coding gene	gene with protein product		604624	"""heat shock 27kD protein 3"""			8972725, 9858786	Standard	NM_006308		Approved	HSPL27	uc003jph.2	Q12988	OTTHUMG00000096995	ENST00000302005.1:c.199G>A	5.37:g.53751818G>A	ENSP00000303394:p.Gly67Ser	139.0	0.0	0		146.0	144.0	0.986301	NM_006308		Missense_Mutation	SNP	ENST00000302005.1	37	CCDS3961.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	G	9.517	1.107277	0.20714	0.020427	0.0	ENSG00000169271	ENST00000302005	D	0.91124	-2.79	5.89	2.12	0.27331	Heat shock protein Hsp20 (2);HSP20-like chaperone (1);	0.364101	0.27415	N	0.019475	T	0.69628	0.3132	N	0.16708	0.43	0.09310	N	1	B	0.19445	0.036	B	0.17722	0.019	T	0.65742	-0.6094	10	0.36615	T	0.2	-30.5173	10.6026	0.45375	0.2571:0.0:0.7429:0.0	rs35258119	67	Q12988	HSPB3_HUMAN	S	67	ENSP00000303394:G67S	ENSP00000303394:G67S	G	+	1	0	HSPB3	53787575	0.686000	0.27661	0.045000	0.18777	0.039000	0.13416	0.902000	0.28459	0.813000	0.34350	0.655000	0.94253	GGC	G|0.992;A|0.008	0.008	strong		0.552	HSPB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214074.2		
C2orf16	84226	hgsc.bcm.edu	37	2	27804690	27804690	+	Missense_Mutation	SNP	C	C	T	rs555322236	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27804690C>T	ENST00000408964.2	+	1	5302	c.5251C>T	c.(5251-5253)Cac>Tac	p.H1751Y	ZNF512_ENST00000413371.2_5'Flank|ZNF512_ENST00000379717.1_5'Flank|AC074091.1_ENST00000408604.1_RNA|ZNF512_ENST00000416005.2_5'Flank|ZNF512_ENST00000556601.1_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000355467.4_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1751	27 X 8 AA approximative tandem repeat of P-S-E-R-S-H-H-S.|Arg-rich.					extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					GAGAAGACATCACAGTCCCTC	0.557													C|||	6	0.00119808	0.0038	0.0	5008	,	,		20958	0.001		0.0	False		,,,				2504	0.0				p.H1751Y		Atlas-SNP	.											.	C2orf16	357	.	0			c.C5251T						PASS	.						192.0	196.0	195.0					2																	27804690		1920	4145	6065	SO:0001583	missense	84226	exon1			AGACATCACAGTC	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.5251C>T	2.37:g.27804690C>T	ENSP00000386190:p.His1751Tyr	171.0	0.0	0		158.0	13.0	0.0822785	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	.	.	.	.	.	.	.	.	.	.	C	14.08	2.428580	0.43122	.	.	ENSG00000221843	ENST00000408964	T	0.05199	3.48	3.97	2.1	0.27182	.	.	.	.	.	T	0.04770	0.0129	L	0.34521	1.04	0.09310	N	1	P	0.47604	0.898	B	0.37550	0.253	T	0.41520	-0.9504	9	0.30078	T	0.28	.	8.7197	0.34434	0.1703:0.6649:0.1648:0.0	.	1751	Q68DN1	CB016_HUMAN	Y	1751	ENSP00000386190:H1751Y	ENSP00000386190:H1751Y	H	+	1	0	C2orf16	27658194	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.020000	0.13466	0.607000	0.29982	0.456000	0.33151	CAC	.	.	none		0.557	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
LMO7	4008	hgsc.bcm.edu	37	13	76195833	76195833	+	Missense_Mutation	SNP	A	A	G	rs143470231	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:76195833A>G	ENST00000341547.4	+	1	1264	c.4A>G	c.(4-6)Aag>Gag	p.K2E	LMO7_ENST00000357063.3_Missense_Mutation_p.K2E|RP11-173B14.5_ENST00000568302.1_RNA|LMO7_ENST00000377534.3_Missense_Mutation_p.K2E|RP11-173B14.5_ENST00000568735.1_RNA|RP11-29G8.3_ENST00000563635.1_RNA	NM_005358.5	NP_005349.3	Q8WWI1	LMO7_HUMAN	LIM domain 7	2					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		AACTGCTATGAAGAAAATTAG	0.363													A|||	57	0.0113818	0.0378	0.0101	5008	,	,		17645	0.0		0.0	False		,,,				2504	0.0				p.K2E		Atlas-SNP	.											LMO7_ENST00000357063,colon,carcinoma,-2,2	LMO7	334	2	0			c.A4G						PASS	.	A	GLU/LYS	168,4238	101.6+/-140.2	4,160,2039	40.0	38.0	39.0		4	1.0	0.2	13	dbSNP_134	39	0,8600		0,0,4300	yes	missense	LMO7	NM_005358.5	56	4,160,6339	GG,GA,AA		0.0,3.813,1.2917		2/1350	76195833	168,12838	2203	4300	6503	SO:0001583	missense	4008	exon1			GCTATGAAGAAAA	AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"""F-box only protein 20"""	604362	"""LIM domain only 7"""	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000341547.4:c.4A>G	13.37:g.76195833A>G	ENSP00000342112:p.Lys2Glu	33.0	0.0	0		28.0	13.0	0.464286	NM_005358	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000341547.4	37	CCDS9454.1	18	0.008241758241758242	16	0.032520325203252036	2	0.0055248618784530384	0	0.0	0	0.0	A	15.96	2.985987	0.53934	0.03813	0.0	ENSG00000136153	ENST00000341547;ENST00000357063;ENST00000377534	T;T;T	0.35048	1.33;1.39;1.44	5.23	1.02	0.19986	.	.	.	.	.	T	0.11707	0.0285	.	.	.	0.09310	N	1	D	0.57257	0.979	P	0.53266	0.722	T	0.11891	-1.0569	8	0.87932	D	0	.	1.7898	0.03049	0.5679:0.1723:0.0937:0.166	.	2	Q8WWI1-3	.	E	2	ENSP00000342112:K2E;ENSP00000349571:K2E;ENSP00000366757:K2E	ENSP00000342112:K2E	K	+	1	0	LMO7	75093834	0.987000	0.35691	0.226000	0.23910	0.335000	0.28730	2.364000	0.44187	0.796000	0.33947	0.460000	0.39030	AAG	A|0.987;G|0.013	0.013	strong		0.363	LMO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045297.1	NM_005358	
OR51I2	390064	hgsc.bcm.edu	37	11	5474894	5474894	+	Missense_Mutation	SNP	T	T	C	rs74049540	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5474894T>C	ENST00000341449.2	+	1	257	c.176T>C	c.(175-177)aTg>aCg	p.M59T	HBG2_ENST00000380259.2_Intron|HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron	NM_001004754.2	NP_001004754.1	Q9H344	O51I2_HUMAN	olfactory receptor, family 51, subfamily I, member 2	59					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)			endometrium(3)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	29		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;1.09e-10)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CATGAGCCCATGTACTACTTC	0.572													T|||	291	0.058107	0.2118	0.0144	5008	,	,		21590	0.0		0.001	False		,,,				2504	0.0				p.M59T		Atlas-SNP	.											.	OR51I2	76	.	0			c.T176C						PASS	.	T	THR/MET	709,3693	295.6+/-283.7	60,589,1552	109.0	98.0	102.0		176	5.6	1.0	11	dbSNP_130	102	9,8585	5.0+/-18.6	0,9,4288	yes	missense	OR51I2	NM_001004754.2	81	60,598,5840	CC,CT,TT		0.1047,16.1063,5.5248	possibly-damaging	59/313	5474894	718,12278	2201	4297	6498	SO:0001583	missense	390064	exon1			AGCCCATGTACTA	BK004381	CCDS31383.1	11p15.4	2012-08-09			ENSG00000187918	ENSG00000187918		"""GPCR / Class A : Olfactory receptors"""	15201	protein-coding gene	gene with protein product							Standard	NM_001004754		Approved		uc010qzf.2	Q9H344	OTTHUMG00000066902	ENST00000341449.2:c.176T>C	11.37:g.5474894T>C	ENSP00000341987:p.Met59Thr	125.0	0.0	0		135.0	64.0	0.474074	NM_001004754	Q6IF81	Missense_Mutation	SNP	ENST00000341449.2	37	CCDS31383.1	128	0.05860805860805861	123	0.25	5	0.013812154696132596	0	0.0	0	0.0	T	13.85	2.359159	0.41801	0.161063	0.001047	ENSG00000187918	ENST00000341449	T	0.09817	2.94	5.57	5.57	0.84162	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	H	0.94771	3.58	0.25314	P	0.9891777	D	0.55800	0.973	P	0.61201	0.885	T	0.04621	-1.0938	9	0.72032	D	0.01	.	14.7065	0.69194	0.0:0.0:0.0:1.0	.	59	Q9H344	O51I2_HUMAN	T	59	ENSP00000341987:M59T	ENSP00000341987:M59T	M	+	2	0	OR51I2	5431470	1.000000	0.71417	1.000000	0.80357	0.364000	0.29643	4.672000	0.61597	2.340000	0.79590	0.528000	0.53228	ATG	T|0.937;C|0.063	0.063	strong		0.572	OR51I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143385.1	NM_001004754	
RP1L1	94137	hgsc.bcm.edu	37	8	10470794	10470794	+	Missense_Mutation	SNP	G	G	C	rs77833234	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10470794G>C	ENST00000382483.3	-	4	1037	c.814C>G	c.(814-816)Cca>Gca	p.P272A		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	272					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		GGCAGCCGTGGCGTGCTGCCT	0.647													G|||	19	0.00379393	0.0144	0.0	5008	,	,		15506	0.0		0.0	False		,,,				2504	0.0				p.P272A		Atlas-SNP	.											.	RP1L1	453	.	0			c.C814G						PASS	.	G	ALA/PRO	38,3946		0,38,1954	53.0	59.0	57.0		814	0.2	0.0	8	dbSNP_131	57	2,8342		0,2,4170	no	missense	RP1L1	NM_178857.5	27	0,40,6124	CC,CG,GG		0.024,0.9538,0.3245	probably-damaging	272/2401	10470794	40,12288	1992	4172	6164	SO:0001583	missense	94137	exon4			GCCGTGGCGTGCT	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.814C>G	8.37:g.10470794G>C	ENSP00000371923:p.Pro272Ala	33.0	0.0	0		21.0	9.0	0.428571	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	20	0.009157509157509158	13	0.026422764227642278	2	0.0055248618784530384	2	0.0034965034965034965	3	0.00395778364116095	G	1.225	-0.625730	0.03610	0.009538	2.4E-4	ENSG00000183638	ENST00000382483	T	0.04194	3.68	5.33	0.147	0.14838	.	1.942830	0.03465	N	0.212853	T	0.01287	0.0042	L	0.38175	1.15	0.09310	N	1	B	0.22683	0.073	B	0.20767	0.031	T	0.43048	-0.9415	10	0.21014	T	0.42	-0.1152	0.8756	0.01223	0.251:0.3733:0.1891:0.1866	.	272	A6NKC6	.	A	272	ENSP00000371923:P272A	ENSP00000371923:P272A	P	-	1	0	RP1L1	10508204	0.087000	0.21565	0.000000	0.03702	0.005000	0.04900	1.861000	0.39438	0.162000	0.19483	-0.293000	0.09583	CCA	G|0.993;C|0.007	0.007	strong		0.647	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
SHROOM4	57477	hgsc.bcm.edu	37	X	50350751	50350751	+	Missense_Mutation	SNP	G	G	C	rs201290098		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:50350751G>C	ENST00000289292.7	-	6	3674	c.3391C>G	c.(3391-3393)Cag>Gag	p.Q1131E	SHROOM4_ENST00000376020.2_Missense_Mutation_p.Q1131E|SHROOM4_ENST00000460112.3_Missense_Mutation_p.Q1015E			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1131	Gln-rich.			KQQ -> QQQQKQQE (in Ref. 1; BAA86516 and 3; AAI51241). {ECO:0000305}.	actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					tcctcctcctgttgcttctgc	0.582																																					p.Q1131E		Atlas-SNP	.											.	SHROOM4	171	.	0			c.C3391G						PASS	.						15.0	14.0	15.0					X																	50350751		2199	4294	6493	SO:0001583	missense	57477	exon6			CCTCCTGTTGCTT	AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3391C>G	X.37:g.50350751G>C	ENSP00000289292:p.Gln1131Glu	111.0	0.0	0		70.0	6.0	0.0857143	NM_020717	A7E2X9|D6RFW0|Q96LA0	Missense_Mutation	SNP	ENST00000289292.7	37	CCDS35277.1	.	.	.	.	.	.	.	.	.	.	G	0.015	-1.554911	0.00918	.	.	ENSG00000158352	ENST00000289292;ENST00000376020;ENST00000460112	T;T;T	0.06449	3.3;3.3;3.3	4.89	-0.0454	0.13851	.	1.383290	0.04423	N	0.367895	T	0.03827	0.0108	N	0.24115	0.695	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.36456	-0.9747	10	0.02654	T	1	.	4.0399	0.09746	0.093:0.4322:0.3193:0.1556	.	1131	Q9ULL8	SHRM4_HUMAN	E	1131;1131;1015	ENSP00000289292:Q1131E;ENSP00000365188:Q1131E;ENSP00000421450:Q1015E	ENSP00000289292:Q1131E	Q	-	1	0	SHROOM4	50367491	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	0.374000	0.20501	-0.047000	0.13423	-0.434000	0.05882	CAG	.	.	weak		0.582	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717	
EMR3	84658	hgsc.bcm.edu	37	19	14740942	14740942	+	Missense_Mutation	SNP	G	G	A	rs78700925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14740942G>A	ENST00000253673.5	-	14	1821	c.1721C>T	c.(1720-1722)cCa>cTa	p.P574L	EMR3_ENST00000599900.1_Missense_Mutation_p.P359L|EMR3_ENST00000344373.4_Missense_Mutation_p.P522L|EMR3_ENST00000443157.2_Missense_Mutation_p.P448L	NM_032571.3	NP_115960.2	Q9BY15	EMR3_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 3	574					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|autonomic_ganglia(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(12)|lung(14)|ovary(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	50						CTGGGCAGCTGGACCCACCTG	0.542													G|||	94	0.01877	0.0688	0.0043	5008	,	,		14251	0.0		0.0	False		,,,				2504	0.0				p.P574L		Atlas-SNP	.											.	EMR3	99	.	0			c.C1721T						PASS	.	G	LEU/PRO	203,4203	126.6+/-163.6	4,195,2004	109.0	92.0	98.0		1721	2.7	0.0	19	dbSNP_131	98	1,8599	1.2+/-3.3	0,1,4299	yes	missense	EMR3	NM_032571.3	98	4,196,6303	AA,AG,GG		0.0116,4.6074,1.5685	possibly-damaging	574/653	14740942	204,12802	2203	4300	6503	SO:0001583	missense	84658	exon14			GCAGCTGGACCCA	AF239764	CCDS12315.1, CCDS74296.1, CCDS74297.1	19p13.1	2014-08-08				ENSG00000131355		"""-"", ""GPCR / Class B : Orphans"""	23647	protein-coding gene	gene with protein product		606101				11279179, 12975309	Standard	XM_005260118		Approved		uc002mzi.4	Q9BY15		ENST00000253673.5:c.1721C>T	19.37:g.14740942G>A	ENSP00000253673:p.Pro574Leu	126.0	0.0	0		117.0	56.0	0.478632	NM_032571		Missense_Mutation	SNP	ENST00000253673.5	37	CCDS12315.1	29	0.013278388278388278	29	0.05894308943089431	0	0.0	0	0.0	0	0.0	G	10.10	1.256668	0.22965	0.046074	1.16E-4	ENSG00000131355	ENST00000443157;ENST00000253673;ENST00000344373	T;T;T	0.41065	1.03;1.01;1.01	3.76	2.72	0.32119	GPCR, family 2-like (1);	.	.	.	.	T	0.19805	0.0476	M	0.88570	2.965	0.20489	N	0.999896	D;D;D	0.89917	1.0;1.0;0.992	D;D;D	0.87578	0.996;0.998;0.968	T	0.17319	-1.0373	9	0.87932	D	0	.	9.204	0.37278	0.1094:0.0:0.8906:0.0	.	448;522;574	E7EW83;Q9BY15-2;Q9BY15	.;.;EMR3_HUMAN	L	448;574;522	ENSP00000396208:P448L;ENSP00000253673:P574L;ENSP00000340758:P522L	ENSP00000253673:P574L	P	-	2	0	EMR3	14601942	0.037000	0.19845	0.031000	0.17742	0.029000	0.11900	2.165000	0.42396	0.923000	0.37045	-0.136000	0.14681	CCA	G|0.984;A|0.016	0.016	strong		0.542	EMR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466488.1	NM_032571	
TBC1D9B	23061	hgsc.bcm.edu	37	5	179297352	179297352	+	Silent	SNP	A	A	G	rs384668	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:179297352A>G	ENST00000356834.3	-	16	2665	c.2628T>C	c.(2626-2628)tgT>tgC	p.C876C	TBC1D9B_ENST00000519746.1_Silent_p.C52C|TBC1D9B_ENST00000355235.3_Silent_p.C876C|TBC1D9B_ENST00000444477.2_Silent_p.C34C	NM_198868.2	NP_942568.2	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	876						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	28	all_cancers(89;0.000197)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0236)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TGTGGGAGCCACAGGCCCAGG	0.617													G|||	623	0.124401	0.444	0.0432	5008	,	,		19003	0.001		0.005	False		,,,				2504	0.0				p.C876C		Atlas-SNP	.											.	TBC1D9B	157	.	0			c.T2628C						PASS	.	G	,	1543,2863	671.2+/-402.4	287,969,947	99.0	102.0	101.0		2628,2628	-7.3	0.3	5	dbSNP_80	101	15,8585	818.3+/-406.9	0,15,4285	no	coding-synonymous,coding-synonymous	TBC1D9B	NM_015043.3,NM_198868.2	,	287,984,5232	GG,GA,AA		0.1744,35.0204,11.9791	,	876/1234,876/1251	179297352	1558,11448	2203	4300	6503	SO:0001819	synonymous_variant	23061	exon16			GGAGCCACAGGCC	AB014576	CCDS4450.1, CCDS43408.1	5q35.3	2013-01-10			ENSG00000197226	ENSG00000197226		"""EF-hand domain containing"""	29097	protein-coding gene	gene with protein product						9734811	Standard	NM_198868		Approved	KIAA0676	uc003mlh.3	Q66K14	OTTHUMG00000130911	ENST00000356834.3:c.2628T>C	5.37:g.179297352A>G		119.0	0.0	0		120.0	56.0	0.466667	NM_198868	D3DWQ5|D3DWQ6|O75163|Q53EY0|Q6MZI2|Q96H49	Silent	SNP	ENST00000356834.3	37	CCDS43408.1																																																																																			A|0.890;G|0.110	0.110	strong		0.617	TBC1D9B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253501.3	NM_015043	
SPTBN1	6711	hgsc.bcm.edu	37	2	54895682	54895682	+	Silent	SNP	C	C	T	rs2229505	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:54895682C>T	ENST00000356805.4	+	36	7352	c.7071C>T	c.(7069-7071)ttC>ttT	p.F2357F		NM_003128.2	NP_003119.2	Q01082	SPTB2_HUMAN	spectrin, beta, non-erythrocytic 1	2357					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi to plasma membrane protein transport (GO:0043001)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|plasma membrane organization (GO:0007009)|protein targeting to plasma membrane (GO:0072661)	axolemma (GO:0030673)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|ankyrin binding (GO:0030506)|phospholipid binding (GO:0005543)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(8)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(27)|ovary(4)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	82			Lung(47;0.24)			AGAAGCGGTTCAGCCTTTTTG	0.522													C|||	178	0.0355431	0.1165	0.0245	5008	,	,		17151	0.001		0.005	False		,,,				2504	0.001				p.F2357F		Atlas-SNP	.											.	SPTBN1	378	.	0			c.C7071T						PASS	.	C		429,3977		18,393,1792	25.0	23.0	24.0		7071	3.7	1.0	2	dbSNP_98	24	14,8584		0,14,4285	no	coding-synonymous	SPTBN1	NM_003128.2		18,407,6077	TT,TC,CC		0.1628,9.7367,3.4066		2357/2365	54895682	443,12561	2203	4299	6502	SO:0001819	synonymous_variant	6711	exon36			GCGGTTCAGCCTT		CCDS33198.1, CCDS33199.1	2p21	2013-01-10			ENSG00000115306	ENSG00000115306		"""Pleckstrin homology (PH) domain containing"""	11275	protein-coding gene	gene with protein product		182790					Standard	NM_003128		Approved		uc002rxu.3	Q01082	OTTHUMG00000133746	ENST00000356805.4:c.7071C>T	2.37:g.54895682C>T		94.0	0.0	0		97.0	43.0	0.443299	NM_003128	B2RP63|O60837|Q16057|Q53R99|Q59ER3|Q8IX99	Silent	SNP	ENST00000356805.4	37	CCDS33198.1																																																																																			C|0.962;T|0.038	0.038	strong		0.522	SPTBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258115.3		
PTPRF	5792	hgsc.bcm.edu	37	1	44019305	44019305	+	Silent	SNP	C	C	T	rs6684279	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:44019305C>T	ENST00000359947.4	+	4	574	c.234C>T	c.(232-234)ttC>ttT	p.F78F	PTPRF_ENST00000438120.1_Silent_p.F78F|PTPRF_ENST00000372414.3_Silent_p.F78F|PTPRF_ENST00000372413.3_Silent_p.F78F	NM_002840.3	NP_002831.2	P10586	PTPRF_HUMAN	protein tyrosine phosphatase, receptor type, F	78	Ig-like C2-type 1.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|negative regulation of receptor binding (GO:1900121)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(24)|ovary(4)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)	72	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				CCCAGCGCTTCGAGGTGCGTC	0.597													C|||	165	0.0329473	0.118	0.0072	5008	,	,		21711	0.0		0.004	False		,,,				2504	0.0				p.F78F		Atlas-SNP	.											.	PTPRF	172	.	0			c.C234T						PASS	.	C	,	440,3966	210.2+/-230.7	23,394,1786	126.0	121.0	122.0		234,234	-9.8	0.6	1	dbSNP_116	122	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	PTPRF	NM_002840.3,NM_130440.2	,	23,395,6085	TT,TC,CC		0.0116,9.9864,3.3907	,	78/1908,78/1899	44019305	441,12565	2203	4300	6503	SO:0001819	synonymous_variant	5792	exon4			GCGCTTCGAGGTG	Y00815	CCDS489.2, CCDS490.2	1p34	2013-02-11			ENSG00000142949	ENSG00000142949		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9670	protein-coding gene	gene with protein product		179590		LAR		7558042	Standard	NM_130440		Approved		uc001cjr.3	P10586	OTTHUMG00000007501	ENST00000359947.4:c.234C>T	1.37:g.44019305C>T		89.0	0.0	0		81.0	41.0	0.506173	NM_002840	D3DPX6|D3DPX7|Q5T021|Q5T022|Q5W9G2|Q86WS0	Silent	SNP	ENST00000359947.4	37	CCDS489.2																																																																																			C|0.964;T|0.036	0.036	strong		0.597	PTPRF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000019710.1		
GPR55	9290	hgsc.bcm.edu	37	2	231775371	231775371	+	Missense_Mutation	SNP	C	C	T	rs80290067	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:231775371C>T	ENST00000392040.1	-	2	499	c.307G>A	c.(307-309)Gtc>Atc	p.V103I	GPR55_ENST00000392039.2_Missense_Mutation_p.V103I|AC012507.4_ENST00000454890.1_RNA	NM_005683.3	NP_005674.2	Q9Y2T6	GPR55_HUMAN	G protein-coupled receptor 55	103					activation of phospholipase C activity (GO:0007202)|bone resorption (GO:0045453)|cannabinoid signaling pathway (GO:0038171)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of osteoclast differentiation (GO:0045671)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rho protein signal transduction (GO:0035025)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)|G-protein coupled receptor activity (GO:0004930)			endometrium(1)|large_intestine(1)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		Renal(207;0.0112)|all_lung(227;0.0741)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)|Lung NSC(271;0.204)		Epithelial(121;1.04e-11)|all cancers(144;4.22e-09)|LUSC - Lung squamous cell carcinoma(224;0.0119)|Lung(119;0.0145)		TACATGCTGACGAAGTAAAGG	0.597													c|||	144	0.028754	0.1051	0.0072	5008	,	,		21034	0.0		0.0	False		,,,				2504	0.0				p.V103I		Atlas-SNP	.											.	GPR55	46	.	0			c.G307A						PASS	.	C	ILE/VAL	423,3983	197.1+/-221.3	26,371,1806	66.0	44.0	52.0		307	-5.3	0.7	2	dbSNP_131	52	5,8595	4.3+/-15.6	0,5,4295	yes	missense	GPR55	NM_005683.3	29	26,376,6101	TT,TC,CC		0.0581,9.6005,3.2908	benign	103/320	231775371	428,12578	2203	4300	6503	SO:0001583	missense	9290	exon2			TGCTGACGAAGTA	AF096786	CCDS2480.1	2q37	2012-08-21			ENSG00000135898	ENSG00000135898		"""GPCR / Class A : Orphans"""	4511	protein-coding gene	gene with protein product		604107				9931487	Standard	NM_005683		Approved		uc002vrg.3	Q9Y2T6	OTTHUMG00000133224	ENST00000392040.1:c.307G>A	2.37:g.231775371C>T	ENSP00000375894:p.Val103Ile	43.0	0.0	0		47.0	20.0	0.425532	NM_005683	Q8N580	Missense_Mutation	SNP	ENST00000392040.1	37	CCDS2480.1	53	0.024267399267399268	49	0.09959349593495935	4	0.011049723756906077	0	0.0	0	0.0	c	0.687	-0.795929	0.02862	0.096005	5.81E-4	ENSG00000135898	ENST00000392040;ENST00000392039;ENST00000438398	T;T;T	0.72835	-0.69;-0.69;-0.69	5.38	-5.31	0.02730	GPCR, rhodopsin-like superfamily (1);	0.408961	0.25774	N	0.028383	T	0.01254	0.0041	N	0.12569	0.235	0.24899	N	0.992118	B	0.17465	0.022	B	0.15870	0.014	T	0.13442	-1.0509	10	0.02654	T	1	-33.6109	12.2542	0.54615	0.0:0.5177:0.0:0.4823	.	103	Q9Y2T6	GPR55_HUMAN	I	103	ENSP00000375894:V103I;ENSP00000375893:V103I;ENSP00000412768:V103I	ENSP00000375893:V103I	V	-	1	0	GPR55	231483615	0.000000	0.05858	0.728000	0.30774	0.241000	0.25554	-0.686000	0.05161	-0.943000	0.03691	-1.598000	0.00824	GTC	C|0.971;T|0.029	0.029	strong		0.597	GPR55-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332618.1	NM_005683	
KIAA0556	23247	hgsc.bcm.edu	37	16	27709812	27709812	+	Silent	SNP	C	C	T	rs61740294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27709812C>T	ENST00000261588.4	+	9	1123	c.1104C>T	c.(1102-1104)agC>agT	p.S368S	KIAA0556_ENST00000567894.1_3'UTR|CTD-2049O4.1_ENST00000564893.1_RNA	NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	368						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						AGCCAGCCAGCCCACTGCAGG	0.637													C|||	81	0.0161741	0.0575	0.0072	5008	,	,		17048	0.0		0.0	False		,,,				2504	0.0				p.S368S		Atlas-SNP	.											.	KIAA0556	348	.	0			c.C1104T						PASS	.	C		254,4140		7,240,1950	20.0	21.0	21.0		1104	1.3	0.2	16	dbSNP_129	21	0,8600		0,0,4300	no	coding-synonymous	KIAA0556	NM_015202.2		7,240,6250	TT,TC,CC		0.0,5.7806,1.9547		368/1619	27709812	254,12740	2197	4300	6497	SO:0001819	synonymous_variant	23247	exon9			AGCCAGCCCACTG	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.1104C>T	16.37:g.27709812C>T		29.0	0.0	0		42.0	18.0	0.428571	NM_015202	A7E2C2	Silent	SNP	ENST00000261588.4	37	CCDS32415.1																																																																																			C|0.978;T|0.022	0.022	strong		0.637	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202	
CDC42BPB	9578	hgsc.bcm.edu	37	14	103434985	103434985	+	Silent	SNP	G	G	A	rs55659700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:103434985G>A	ENST00000361246.2	-	15	2352	c.2064C>T	c.(2062-2064)tcC>tcT	p.S688S		NM_006035.3	NP_006026.3			CDC42 binding protein kinase beta (DMPK-like)											NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(11)|liver(1)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	49		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		TCTCCAGCTCGGATTTGATTT	0.453													G|||	45	0.00898562	0.0257	0.0159	5008	,	,		19256	0.0		0.0	False		,,,				2504	0.0				p.S688S		Atlas-SNP	.											.	CDC42BPB	123	.	0			c.C2064T						PASS	.	G		111,4295	85.8+/-124.5	2,107,2094	83.0	90.0	88.0		2064	-9.2	0.2	14	dbSNP_129	88	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CDC42BPB	NM_006035.3		2,108,6393	AA,AG,GG		0.0116,2.5193,0.8611		688/1712	103434985	112,12894	2203	4300	6503	SO:0001819	synonymous_variant	9578	exon15			CAGCTCGGATTTG	AF128625	CCDS9978.1	14q32.32	2010-05-12	2001-11-28		ENSG00000198752	ENSG00000198752			1738	protein-coding gene	gene with protein product		614062	"""CDC42-binding protein kinase beta (DMPK-like)"""			10198171	Standard	NM_006035		Approved	MRCKB, KIAA1124	uc001ymi.1	Q9Y5S2		ENST00000361246.2:c.2064C>T	14.37:g.103434985G>A		106.0	0.0	0		98.0	47.0	0.479592	NM_006035		Silent	SNP	ENST00000361246.2	37	CCDS9978.1																																																																																			G|0.992;A|0.008	0.008	strong		0.453	CDC42BPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415711.1	NM_006035	
SEMG1	6406	hgsc.bcm.edu	37	20	43837053	43837053	+	Missense_Mutation	SNP	G	G	T	rs2233887	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43837053G>T	ENST00000372781.3	+	2	1172	c.1115G>T	c.(1114-1116)cGc>cTc	p.R372L	SEMG1_ENST00000244069.6_Missense_Mutation_p.R312L	NM_003007.3	NP_002998.1	P04279	SEMG1_HUMAN	semenogelin I	372	2 X 60 AA tandem repeats, type 1.|Repeat-rich region. {ECO:0000250}.		R -> L (in dbSNP:rs2233887). {ECO:0000269|PubMed:14629036}.		insemination (GO:0007320)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	32		Myeloproliferative disorder(115;0.0122)				GTATCCCAACGCAGTATTTAT	0.413													G|||	63	0.0125799	0.0371	0.0086	5008	,	,		22334	0.0		0.004	False		,,,				2504	0.0041				p.R372L		Atlas-SNP	.											SEMG1,bladder,carcinoma,+1,3	SEMG1	71	3	0			c.G1115T						PASS	.	G	LEU/ARG	143,4263	100.3+/-138.9	1,141,2061	75.0	70.0	72.0		1115	-0.4	0.0	20	dbSNP_98	72	18,8582	12.6+/-44.7	0,18,4282	yes	missense	SEMG1	NM_003007.3	102	1,159,6343	TT,TG,GG		0.2093,3.2456,1.2379		372/463	43837053	161,12845	2203	4300	6503	SO:0001583	missense	6406	exon2			CCCAACGCAGTAT		CCDS13345.1	20q12-q13.2	2009-08-06			ENSG00000124233	ENSG00000124233			10742	protein-coding gene	gene with protein product	"""semen coagulating protein"", ""cancer/testis antigen 103"""	182140		SEMG		2912989, 15563730	Standard	NM_003007		Approved	CT103		P04279	OTTHUMG00000032565	ENST00000372781.3:c.1115G>T	20.37:g.43837053G>T	ENSP00000361867:p.Arg372Leu	151.0	0.0	0		166.0	85.0	0.512048	NM_003007	Q53ZV0|Q53ZV1|Q53ZV2|Q6X4I9|Q6Y809|Q6Y822|Q6Y823|Q86U64|Q96QM3	Missense_Mutation	SNP	ENST00000372781.3	37	CCDS13345.1	23	0.010531135531135532	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	6.094	0.385541	0.11524	0.032456	0.002093	ENSG00000124233	ENST00000244069;ENST00000372781	T;T	0.06218	3.33;3.33	0.951	-0.436	0.12275	.	.	.	.	.	T	0.00967	0.0032	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.42849	-0.9427	9	0.72032	D	0.01	.	3.6742	0.08286	0.0:0.0:0.5676:0.4324	rs2233887;rs52805273;rs2233887	312;372	P04279-2;P04279	.;SEMG1_HUMAN	L	312;372	ENSP00000244069:R312L;ENSP00000361867:R372L	ENSP00000244069:R312L	R	+	2	0	SEMG1	43270467	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.312000	0.08113	-0.121000	0.11787	0.404000	0.27445	CGC	G|0.984;T|0.016	0.016	strong		0.413	SEMG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079416.3	NM_003007	
MUC5B	727897	hgsc.bcm.edu	37	11	1268528	1268528	+	Missense_Mutation	SNP	C	C	T	rs202008769	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1268528C>T	ENST00000529681.1	+	31	10476	c.10418C>T	c.(10417-10419)tCg>tTg	p.S3473L	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.S3476L	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	3473	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)		GCCTGGACTTCGGCCACCTCG	0.672													-|||	12	0.00239617	0.0083	0.0014	5008	,	,		18693	0.0		0.0	False		,,,				2504	0.0				p.S3473L		Atlas-SNP	.											MUC5B,colon,carcinoma,0,4	MUC5B	473	4	0			c.C10418T						PASS	.	C	LEU/SER	11,4213		0,11,2101	60.0	85.0	77.0		10418	0.0	0.0	11		77	2,8406		0,2,4202	no	missense	MUC5B	NM_002458.2	145	0,13,6303	TT,TC,CC		0.0238,0.2604,0.1029	benign	3473/5763	1268528	13,12619	2112	4204	6316	SO:0001583	missense	727897	exon31			GGACTTCGGCCAC	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.10418C>T	11.37:g.1268528C>T	ENSP00000436812:p.Ser3473Leu	462.0	0.0	0		657.0	250.0	0.380518	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	c	4.864	0.160630	0.09287	0.002604	2.38E-4	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.20598	2.06;2.24	2.0	0.00491	0.14060	.	.	.	.	.	T	0.16811	0.0404	L	0.50333	1.59	0.09310	N	1	B;B	0.33494	0.414;0.001	B;B	0.29716	0.106;0.0	T	0.18745	-1.0327	9	0.87932	D	0	.	5.899	0.18955	0.0:0.6851:0.0:0.3149	.	4001;3476	A7Y9J9;E9PBJ0	.;.	L	3473;3476;3445;3378	ENSP00000436812:S3473L;ENSP00000415793:S3476L	ENSP00000343037:S3445L	S	+	2	0	MUC5B	1225104	0.000000	0.05858	0.002000	0.10522	0.028000	0.11728	-1.189000	0.03061	0.007000	0.14760	-0.712000	0.03635	TCG	.	.	weak		0.672	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
FOXRED2	80020	hgsc.bcm.edu	37	22	36902259	36902259	+	Missense_Mutation	SNP	G	G	A	rs56767103	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:36902259G>A	ENST00000397224.4	-	2	304	c.211C>T	c.(211-213)Cgc>Tgc	p.R71C	FOXRED2_ENST00000397223.4_Missense_Mutation_p.R71C|FOXRED2_ENST00000216187.6_Missense_Mutation_p.R71C	NM_001102371.1	NP_001095841.1	Q8IWF2	FXRD2_HUMAN	FAD-dependent oxidoreductase domain containing 2	71			R -> C (in dbSNP:rs56767103).		ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum lumen (GO:0005788)	flavin adenine dinucleotide binding (GO:0050660)|glycoprotein binding (GO:0001948)|oxidoreductase activity (GO:0016491)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						CGCGGGTAGCGTGTGAAGAAG	0.667													G|||	144	0.028754	0.1059	0.0043	5008	,	,		16027	0.0		0.001	False		,,,				2504	0.0				p.R71C		Atlas-SNP	.											.	FOXRED2	48	.	0			c.C211T						PASS	.	G	CYS/ARG,CYS/ARG	385,4021	193.3+/-218.5	22,341,1840	70.0	52.0	59.0		211,211	5.0	1.0	22	dbSNP_129	59	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	FOXRED2	NM_001102371.1,NM_024955.5	180,180	22,344,6137	AA,AG,GG		0.0349,8.7381,2.9832	possibly-damaging,possibly-damaging	71/685,71/685	36902259	388,12618	2203	4300	6503	SO:0001583	missense	80020	exon2			GGTAGCGTGTGAA	BC027716	CCDS13929.1	22q12.3	2006-07-05			ENSG00000100350	ENSG00000100350			26264	protein-coding gene	gene with protein product		613777				12477932	Standard	NM_024955		Approved	FLJ23322	uc003app.4	Q8IWF2	OTTHUMG00000044614	ENST00000397224.4:c.211C>T	22.37:g.36902259G>A	ENSP00000380401:p.Arg71Cys	93.0	0.0	0		93.0	49.0	0.526882	NM_001102371	B2RDI4|Q8N378|Q96BD1|Q9H5L5|Q9H6M8	Missense_Mutation	SNP	ENST00000397224.4	37	CCDS13929.1	46	0.021062271062271064	44	0.08943089430894309	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	22.6	4.317138	0.81469	0.087381	3.49E-4	ENSG00000100350	ENST00000397224;ENST00000216187;ENST00000397223;ENST00000423980	T;T;T;T	0.23950	1.88;1.88;1.88;1.88	5.04	5.04	0.67666	Pyridine nucleotide-disulphide oxidoreductase, FAD/NAD(P)-binding domain (1);	0.201070	0.44097	D	0.000489	T	0.02083	0.0065	M	0.79123	2.44	0.40354	D	0.979162	D	0.65815	0.995	P	0.59703	0.862	T	0.00936	-1.1508	10	0.48119	T	0.1	-31.9668	7.8809	0.29621	0.0837:0.0:0.7553:0.161	rs56767103	71	Q8IWF2	FXRD2_HUMAN	C	71	ENSP00000380401:R71C;ENSP00000216187:R71C;ENSP00000380400:R71C;ENSP00000409692:R71C	ENSP00000216187:R71C	R	-	1	0	FOXRED2	35232205	1.000000	0.71417	0.977000	0.42913	0.953000	0.61014	4.550000	0.60733	2.337000	0.79520	0.561000	0.74099	CGC	G|0.974;A|0.026	0.026	strong		0.667	FOXRED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104098.2	NM_024955	
CSTA	1475	hgsc.bcm.edu	37	3	122060390	122060390	+	Missense_Mutation	SNP	G	G	T	rs34021626	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122060390G>T	ENST00000264474.3	+	3	322	c.273G>T	c.(271-273)aaG>aaT	p.K91N		NM_005213.3	NP_005204.1	P01040	CYTA_HUMAN	cystatin A (stefin A)	91					keratinocyte differentiation (GO:0030216)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|peptide cross-linking (GO:0018149)|single organismal cell-cell adhesion (GO:0016337)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|protease binding (GO:0002020)|protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			large_intestine(2)|lung(2)	4				GBM - Glioblastoma multiforme(114;0.155)		ACAAAAACAAGGATGACGAGC	0.408													G|||	96	0.0191693	0.0688	0.0072	5008	,	,		18439	0.0		0.0	False		,,,				2504	0.0				p.K91N	Pancreas(26;157 1503 12440)	Atlas-SNP	.											.	CSTA	11	.	0			c.G273T						PASS	.	G	ASN/LYS	255,4151	147.6+/-182.1	8,239,1956	122.0	120.0	120.0		273	3.6	0.0	3	dbSNP_126	120	1,8599	1.2+/-3.3	0,1,4299	yes	missense	CSTA	NM_005213.3	94	8,240,6255	TT,TG,GG		0.0116,5.7876,1.9683	benign	91/99	122060390	256,12750	2203	4300	6503	SO:0001583	missense	1475	exon3			AAACAAGGATGAC		CCDS3011.1	3q21	2008-04-15			ENSG00000121552	ENSG00000121552			2481	protein-coding gene	gene with protein product		184600		STF1, STFA		1674139	Standard	NM_005213		Approved		uc003eex.3	P01040	OTTHUMG00000159488	ENST00000264474.3:c.273G>T	3.37:g.122060390G>T	ENSP00000264474:p.Lys91Asn	83.0	0.0	0		86.0	48.0	0.55814	NM_005213	Q6IB90	Missense_Mutation	SNP	ENST00000264474.3	37	CCDS3011.1	33	0.01510989010989011	29	0.05894308943089431	4	0.011049723756906077	0	0.0	0	0.0	G	16.40	3.111876	0.56398	0.057876	1.16E-4	ENSG00000121552	ENST00000264474	T	0.77098	-1.07	5.34	3.56	0.40772	Proteinase inhibitor I25, cystatin (2);	0.284783	0.37053	N	0.002270	T	0.37945	0.1022	.	.	.	0.18873	N	0.999989	P	0.52577	0.954	P	0.57057	0.812	T	0.55541	-0.8125	9	0.49607	T	0.09	-9.3656	7.8305	0.29340	0.1844:0.0:0.8156:0.0	rs34021626	91	P01040	CYTA_HUMAN	N	91	ENSP00000264474:K91N	ENSP00000264474:K91N	K	+	3	2	CSTA	123543080	0.006000	0.16342	0.013000	0.15412	0.046000	0.14306	0.259000	0.18405	0.824000	0.34613	0.655000	0.94253	AAG	G|0.984;T|0.016	0.016	strong		0.408	CSTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355751.1	NM_005213	
NXPE1	120400	hgsc.bcm.edu	37	11	114393757	114393757	+	Missense_Mutation	SNP	C	C	T	rs79538449	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:114393757C>T	ENST00000424269.1	-	4	951	c.952G>A	c.(952-954)Ggt>Agt	p.G318S	NXPE1_ENST00000251921.2_Missense_Mutation_p.G176S|NXPE1_ENST00000536271.1_Missense_Mutation_p.G34S			Q8N323	NXPE1_HUMAN	neurexophilin and PC-esterase domain family, member 1	318						extracellular region (GO:0005576)											AAAGTATAACCACCAGGGACA	0.363													C|||	16	0.00319489	0.0121	0.0	5008	,	,		19211	0.0		0.0	False		,,,				2504	0.0				p.G176S		Atlas-SNP	.											.	NXPE1	8	.	0			c.G526A						PASS	.	C	SER/GLY	56,4346	56.2+/-92.4	0,56,2145	101.0	91.0	95.0		526	4.4	0.2	11	dbSNP_131	95	1,8591	1.2+/-3.3	0,1,4295	yes	missense	FAM55A	NM_152315.2	56	0,57,6440	TT,TC,CC		0.0116,1.2721,0.4387	probably-damaging	176/406	114393757	57,12937	2201	4296	6497	SO:0001583	missense	120400	exon5			TATAACCACCAGG	BC029049	CCDS8372.1	11q23.2	2012-06-14	2012-06-11	2012-06-11	ENSG00000095110	ENSG00000095110			28527	protein-coding gene	gene with protein product			"""family with sequence similarity 55, member A"""	FAM55A		12477932	Standard	NM_152315		Approved	MGC34290	uc001ppa.3	Q8N323	OTTHUMG00000168284	ENST00000424269.1:c.952G>A	11.37:g.114393757C>T	ENSP00000411690:p.Gly318Ser	145.0	0.0	0		166.0	99.0	0.596386	NM_152315	B0YJ13	Missense_Mutation	SNP	ENST00000424269.1	37		3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	33	5.276316	0.95459	0.012721	1.16E-4	ENSG00000095110	ENST00000536271;ENST00000251921;ENST00000424269	T;T;T	0.60797	0.55;0.29;0.16	4.4	4.4	0.53042	.	0.000000	0.64402	D	0.000003	T	0.72011	0.3408	M	0.84585	2.705	0.42372	D	0.992458	D	0.89917	1.0	D	0.97110	1.0	T	0.80777	-0.1231	10	0.87932	D	0	.	15.2699	0.73693	0.0:1.0:0.0:0.0	.	318	Q8N323	FA55A_HUMAN	S	34;176;318	ENSP00000445200:G34S;ENSP00000251921:G176S;ENSP00000411690:G318S	ENSP00000251921:G176S	G	-	1	0	FAM55A	113898967	0.425000	0.25498	0.152000	0.22495	0.689000	0.40095	2.280000	0.43443	2.372000	0.80975	0.650000	0.86243	GGT	C|0.997;T|0.003	0.003	strong		0.363	NXPE1-201	KNOWN	basic	protein_coding	protein_coding		NM_152315	
GAD1	2571	hgsc.bcm.edu	37	2	171715387	171715387	+	Missense_Mutation	SNP	G	G	A	rs769402	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:171715387G>A	ENST00000358196.3	+	16	2145	c.1595G>A	c.(1594-1596)cGg>cAg	p.R532Q		NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	532			R -> Q (in dbSNP:rs769402). {ECO:0000269|Ref.9}.		gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate catabolic process (GO:0006538)|glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|protein-pyridoxal-5-phosphate linkage (GO:0018352)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(15)|ovary(1)|urinary_tract(2)	35						CCTCAACGACGGGAAAAGCTA	0.453													G|||	305	0.0609026	0.2216	0.0159	5008	,	,		20178	0.0		0.001	False		,,,				2504	0.0				p.R532Q		Atlas-SNP	.											.	GAD1	79	.	0			c.G1595A						PASS	.	G	GLN/ARG	807,3599	321.3+/-297.0	68,671,1464	82.0	83.0	83.0		1595	3.8	1.0	2	dbSNP_98	83	13,8587	9.1+/-34.3	0,13,4287	yes	missense	GAD1	NM_000817.2	43	68,684,5751	AA,AG,GG		0.1512,18.3159,6.3048	benign	532/595	171715387	820,12186	2203	4300	6503	SO:0001583	missense	2571	exon16			AACGACGGGAAAA		CCDS2239.1, CCDS2240.1	2q31	2008-02-05	2002-08-29		ENSG00000128683	ENSG00000128683	4.1.1.15		4092	protein-coding gene	gene with protein product		605363	"""glutamate decarboxylase 1 (brain, 67kD)"""	GAD		1549570	Standard	XM_005246443		Approved		uc002ugi.3	Q99259	OTTHUMG00000044175	ENST00000358196.3:c.1595G>A	2.37:g.171715387G>A	ENSP00000350928:p.Arg532Gln	111.0	0.0	0		118.0	61.0	0.516949	NM_000817	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Missense_Mutation	SNP	ENST00000358196.3	37	CCDS2239.1	105	0.04807692307692308	96	0.1951219512195122	9	0.024861878453038673	0	0.0	0	0.0	G	13.06	2.125053	0.37533	0.183159	0.001512	ENSG00000128683	ENST00000358196	T	0.16597	2.33	5.63	3.84	0.44239	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.174131	0.50627	N	0.000104	T	0.00012	0.0000	L	0.31526	0.94	0.09310	P	1.0	B	0.14012	0.009	B	0.04013	0.001	T	0.39440	-0.9614	9	0.12430	T	0.62	-7.3586	9.081	0.36552	0.2195:0.0:0.7805:0.0	rs769402;rs2229844;rs2266645;rs10209273;rs52821361;rs769402	532	Q99259	DCE1_HUMAN	Q	532	ENSP00000350928:R532Q	ENSP00000350928:R532Q	R	+	2	0	GAD1	171423633	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.305000	0.59110	0.736000	0.32559	0.655000	0.94253	CGG	G|0.935;A|0.065	0.065	strong		0.453	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2		
EVX2	344191	hgsc.bcm.edu	37	2	176948445	176948445	+	Silent	SNP	C	C	G	rs61731351	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:176948445C>G	ENST00000308618.4	-	1	196	c.60G>C	c.(58-60)acG>acC	p.T20T		NM_001080458.1	NP_001073927.1	Q03828	EVX2_HUMAN	even-skipped homeobox 2	20					limb morphogenesis (GO:0035108)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			kidney(1)|large_intestine(3)|liver(1)|lung(8)|ovary(3)	16			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	READ - Rectum adenocarcinoma(9;0.0678)|Colorectal(32;0.115)		TCTTGCCCGCCGTAGGGCTGT	0.547													C|||	188	0.0375399	0.1369	0.0086	5008	,	,		16189	0.0		0.001	False		,,,				2504	0.0				p.T20T		Atlas-SNP	.											EVX2,NS,carcinoma,0,1	EVX2	51	1	0			c.G60C						PASS	.	C		572,3834	242.8+/-252.7	42,488,1673	68.0	79.0	75.0		60	0.0	1.0	2	dbSNP_129	75	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	EVX2	NM_001080458.1		42,489,5972	GG,GC,CC		0.0116,12.9823,4.4057		20/477	176948445	573,12433	2203	4300	6503	SO:0001819	synonymous_variant	344191	exon1			GCCCGCCGTAGGG		CCDS33333.1	2q31.1	2012-03-09	2007-02-15		ENSG00000174279	ENSG00000174279		"""Homeoboxes / ANTP class : HOXL subclass"""	3507	protein-coding gene	gene with protein product		142991	"""eve, even-skipped homeobox homolog 2 (Drosophila)"""			1675198	Standard	NM_001080458		Approved		uc010zeu.2	Q03828	OTTHUMG00000154173	ENST00000308618.4:c.60G>C	2.37:g.176948445C>G		72.0	0.0	0		104.0	54.0	0.519231	NM_001080458		Silent	SNP	ENST00000308618.4	37	CCDS33333.1																																																																																			C|0.930;G|0.070	0.070	strong		0.547	EVX2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359252.1		
IL18BP	10068	hgsc.bcm.edu	37	11	71711438	71711438	+	Missense_Mutation	SNP	G	G	A	rs376290357		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71711438G>A	ENST00000393703.4	+	3	607	c.70G>A	c.(70-72)Gtc>Atc	p.V24I	IL18BP_ENST00000497194.2_Missense_Mutation_p.V24I|IL18BP_ENST00000393707.4_Missense_Mutation_p.V24I|IL18BP_ENST00000260049.5_Missense_Mutation_p.V24I|IL18BP_ENST00000393705.4_Missense_Mutation_p.V24I|IL18BP_ENST00000531053.1_Missense_Mutation_p.V24I|IL18BP_ENST00000337131.5_Missense_Mutation_p.V24I|IL18BP_ENST00000404792.1_Missense_Mutation_p.V24I	NM_001039660.1	NP_001034749.1	O95998	I18BP_HUMAN	interleukin 18 binding protein	24					cellular response to hydrogen peroxide (GO:0070301)|cellular response to tumor necrosis factor (GO:0071356)|extracellular negative regulation of signal transduction (GO:1900116)|response to lipopolysaccharide (GO:0032496)|T-helper 1 type immune response (GO:0042088)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	interleukin-18 binding (GO:0042007)|receptor antagonist activity (GO:0048019)			endometrium(2)|kidney(1)|large_intestine(3)|lung(1)	7						TGCCCACGTCGTCACTCTCCT	0.617																																					p.V24I		Atlas-SNP	.											.	IL18BP	15	.	0			c.G70A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	3,4255		0,3,2126	98.0	107.0	104.0		70,70,70,70,70,70,70	-8.2	0.0	11		104	0,8508		0,0,4254	no	missense,missense,missense,missense,missense,missense,missense	IL18BP	NM_001039659.1,NM_001039660.1,NM_001145055.1,NM_001145057.1,NM_005699.3,NM_173042.2,NM_173044.2	29,29,29,29,29,29,29	0,3,6380	AA,AG,GG		0.0,0.0705,0.0235	benign,benign,benign,benign,benign,benign,benign	24/195,24/195,24/116,24/195,24/200,24/195,24/164	71711438	3,12763	2129	4254	6383	SO:0001583	missense	10068	exon3			CACGTCGTCACTC	AF110798	CCDS8206.2, CCDS44666.1	11q13	2013-01-11			ENSG00000137496	ENSG00000137496		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5987	protein-coding gene	gene with protein product	"""MC51L-53L-54L homolog gene product"""	604113				10023777	Standard	NM_001145055		Approved	IL18BPa	uc001orf.1	O95998	OTTHUMG00000133713	ENST00000393703.4:c.70G>A	11.37:g.71711438G>A	ENSP00000377306:p.Val24Ile	91.0	0.0	0		85.0	44.0	0.517647	NM_001145057	B3KUZ0|B7WPK4|O95993|O96027|Q9NZA9|Q9UBR7	Missense_Mutation	SNP	ENST00000393703.4	37	CCDS8206.2	.	.	.	.	.	.	.	.	.	.	G	0	-2.676183	0.00102	7.05E-4	0.0	ENSG00000137496	ENST00000393703;ENST00000497194;ENST00000393705;ENST00000337131;ENST00000531053;ENST00000404792;ENST00000260049;ENST00000393707	T;T;T;T;T;T;T	0.35236	1.35;1.32;1.35;1.35;1.32;1.35;1.35	4.08	-8.16	0.01061	.	1.862160	0.02902	N	0.135517	T	0.13329	0.0323	N	0.04043	-0.29	0.09310	N	1	B;B;B	0.12013	0.001;0.005;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.20273	-1.0280	10	0.06099	T	0.92	-2.0645	7.9891	0.30229	0.1145:0.1776:0.6198:0.0881	.	24;24;24	O95998-3;G3V1C5;O95998	.;.;I18BP_HUMAN	I	24	ENSP00000377306:V24I;ENSP00000434717:V24I;ENSP00000377308:V24I;ENSP00000338723:V24I;ENSP00000434835:V24I;ENSP00000384212:V24I;ENSP00000260049:V24I	ENSP00000260049:V24I	V	+	1	0	IL18BP	71389086	0.000000	0.05858	0.000000	0.03702	0.070000	0.16714	-2.169000	0.01269	-3.683000	0.00121	-0.340000	0.08031	GTC	.	.	weak		0.617	IL18BP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258012.2	NM_173042	
PTPRT	11122	hgsc.bcm.edu	37	20	41408886	41408886	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:41408886G>A	ENST00000373187.1	-	4	539	c.540C>T	c.(538-540)gaC>gaT	p.D180D	PTPRT_ENST00000373193.3_Silent_p.D180D|PTPRT_ENST00000373190.1_Silent_p.D180D|PTPRT_ENST00000373184.1_Silent_p.D180D|PTPRT_ENST00000356100.2_Silent_p.D180D|PTPRT_ENST00000373201.1_Silent_p.D180D|PTPRT_ENST00000373198.4_Silent_p.D180D			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	180	MAM. {ECO:0000255|PROSITE- ProRule:PRU00128}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				CCCGGACCTCGTCCACGGCGA	0.532																																					p.D180D		Atlas-SNP	.											PTPRT,NS,carcinoma,0,2	PTPRT	372	2	0			c.C540T						scavenged	.						131.0	131.0	131.0					20																	41408886		2076	4217	6293	SO:0001819	synonymous_variant	11122	exon4			GACCTCGTCCACG	AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.540C>T	20.37:g.41408886G>A		52.0	1.0	0.0192308		65.0	20.0	0.307692	NM_007050	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Silent	SNP	ENST00000373187.1	37	CCDS42874.1																																																																																			.	.	none		0.532	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1		
UBXN11	91544	hgsc.bcm.edu	37	1	26620761	26620761	+	Missense_Mutation	SNP	T	T	C	rs6695966	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:26620761T>C	ENST00000374222.1	-	9	958	c.494A>G	c.(493-495)gAg>gGg	p.E165G	UBXN11_ENST00000374223.1_Intron|UBXN11_ENST00000374217.2_Missense_Mutation_p.E132G|UBXN11_ENST00000535108.1_Missense_Mutation_p.E7G|UBXN11_ENST00000374221.3_Missense_Mutation_p.E165G|UBXN11_ENST00000357089.4_Missense_Mutation_p.E132G|UBXN11_ENST00000436301.2_Missense_Mutation_p.E90G|UBXN11_ENST00000314675.7_Intron			Q5T124	UBX11_HUMAN	UBX domain protein 11	165			E -> G (in dbSNP:rs6695966).			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						TGTCTTGCTCTCTGAGTCCTC	0.607													T|||	98	0.0195687	0.0696	0.0086	5008	,	,		18835	0.0		0.0	False		,,,				2504	0.0				p.E165G		Atlas-SNP	.											.	UBXN11	54	.	0			c.A494G						PASS	.	T	,GLY/GLU,GLY/GLU	200,3930		2,196,1867	99.0	98.0	98.0		,395,494	4.5	0.1	1	dbSNP_116	98	3,8407		0,3,4202	yes	intron,missense,missense	UBXN11	NM_001077262.1,NM_145345.2,NM_183008.2	,98,98	2,199,6069	CC,CT,TT		0.0357,4.8426,1.6188	,possibly-damaging,possibly-damaging	,132/488,165/521	26620761	203,12337	2065	4205	6270	SO:0001583	missense	91544	exon9			TTGCTCTCTGAGT	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.494A>G	1.37:g.26620761T>C	ENSP00000363339:p.Glu165Gly	97.0	0.0	0		77.0	36.0	0.467532	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Missense_Mutation	SNP	ENST00000374222.1	37	CCDS41288.1	32	0.014652014652014652	29	0.05894308943089431	3	0.008287292817679558	0	0.0	0	0.0	T	20.1	3.936518	0.73442	0.048426	3.57E-4	ENSG00000158062	ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217;ENST00000389235;ENST00000535108;ENST00000436301;ENST00000374215;ENST00000452980;ENST00000442942;ENST00000450041;ENST00000423664	T;T;T;T;T;T;T;T;T;T;T	0.54675	0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56;0.56	4.47	4.47	0.54385	.	0.322809	0.32655	N	0.005820	T	0.11965	0.0291	M	0.61703	1.905	0.18873	N	0.999983	P;P;P;P;P	0.44139	0.734;0.799;0.827;0.827;0.799	B;B;P;P;B	0.46758	0.398;0.272;0.526;0.526;0.214	T	0.22277	-1.0221	10	0.72032	D	0.01	-25.9901	10.3196	0.43758	0.0:0.0:0.0:1.0	rs6695966;rs52794001;rs6695966	7;90;132;127;165	B7Z1T8;B7Z3N8;Q5T124-2;Q5T124-4;Q5T124	.;.;.;.;UBX11_HUMAN	G	132;165;165;132;132;7;90;127;132;132;90;127	ENSP00000349601:E132G;ENSP00000363338:E165G;ENSP00000363339:E165G;ENSP00000363334:E132G;ENSP00000446034:E7G;ENSP00000393858:E90G;ENSP00000363332:E127G;ENSP00000410357:E132G;ENSP00000404956:E132G;ENSP00000413448:E90G;ENSP00000394036:E127G	ENSP00000349601:E132G	E	-	2	0	UBXN11	26493348	0.829000	0.29322	0.059000	0.19551	0.483000	0.33249	2.735000	0.47377	2.013000	0.59113	0.459000	0.35465	GAG	T|0.974;C|0.026	0.026	strong		0.607	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
ITIH5	80760	hgsc.bcm.edu	37	10	7628027	7628027	+	Silent	SNP	C	C	T	rs11255206	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:7628027C>T	ENST00000256861.6	-	8	1023	c.945G>A	c.(943-945)aaG>aaA	p.K315K	ITIH5_ENST00000446830.2_Silent_p.K97K|ITIH5_ENST00000434980.1_5'UTR|ITIH5_ENST00000397146.2_Silent_p.K315K|ITIH5_ENST00000298441.6_Silent_p.K101K|ITIH5_ENST00000397145.2_Silent_p.K315K	NM_030569.6	NP_085046.5	Q86UX2	ITIH5_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 5	315	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|kidney(6)|large_intestine(21)|lung(25)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(3)	75						AGAGGGCATCCTTGGTCTAGG	0.493													C|||	98	0.0195687	0.0643	0.0043	5008	,	,		17370	0.0069		0.002	False		,,,				2504	0.001				p.K315K		Atlas-SNP	.											.	ITIH5	343	.	0			c.G945A						PASS	.	C	,,	215,4191	126.6+/-163.6	5,205,1993	94.0	84.0	87.0		945,945,303	-0.6	1.0	10	dbSNP_120	87	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	ITIH5	NM_001001851.2,NM_030569.6,NM_032817.5	,,	5,209,6289	TT,TC,CC		0.0465,4.8797,1.6838	,,	315/703,315/943,101/729	7628027	219,12787	2203	4300	6503	SO:0001819	synonymous_variant	80760	exon8			GGCATCCTTGGTC			10p14	2011-10-26	2011-10-26		ENSG00000123243	ENSG00000123243			21449	protein-coding gene	gene with protein product		609783	"""inter-alpha (globulin) inhibitor H5"""			14744536	Standard	NM_001001851		Approved	MGC10848	uc021pmv.1	Q86UX2	OTTHUMG00000017635	ENST00000256861.6:c.945G>A	10.37:g.7628027C>T		77.0	0.0	0		96.0	41.0	0.427083	NM_001001851	Q5T664|Q5T665|Q5T666|Q6AI60|Q6UXB7|Q8TF48|Q8WYV2|Q96K70	Silent	SNP	ENST00000256861.6	37																																																																																				C|0.983;T|0.017	0.017	strong		0.493	ITIH5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000046688.1	NM_030569	
RBPJL	11317	hgsc.bcm.edu	37	20	43945487	43945487	+	Missense_Mutation	SNP	T	T	C	rs34078698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43945487T>C	ENST00000343694.3	+	12	1514	c.1442T>C	c.(1441-1443)gTg>gCg	p.V481A	RBPJL_ENST00000464504.1_3'UTR|RBPJL_ENST00000372741.3_3'UTR|RBPJL_ENST00000372743.1_Missense_Mutation_p.V480A	NM_001281448.1|NM_001281449.1|NM_014276.2	NP_001268377.1|NP_001268378.1|NP_055091.2	Q9UBG7	RBPJL_HUMAN	recombination signal binding protein for immunoglobulin kappa J region-like	481	IPT/TIG.				positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Myeloproliferative disorder(115;0.0122)				GAATACAGCGTGCGGCCGGGT	0.667													C|||	84	0.0167732	0.0484	0.0086	5008	,	,		13248	0.0		0.004	False		,,,				2504	0.0102				p.V481A		Atlas-SNP	.											RBPJL,colon,carcinoma,+1,1	RBPJL	67	1	0			c.T1442C						PASS	.	C	ALA/VAL	200,4206	790.0+/-415.0	4,192,2007	41.0	50.0	47.0		1442	-1.1	0.3	20	dbSNP_126	47	17,8583	809.0+/-407.2	0,17,4283	yes	missense	RBPJL	NM_014276.2	64	4,209,6290	CC,CT,TT		0.1977,4.5393,1.6685	benign	481/518	43945487	217,12789	2203	4300	6503	SO:0001583	missense	11317	exon12			ACAGCGTGCGGCC	AB024964	CCDS13349.1, CCDS63283.1, CCDS63284.1	20q13.12	2013-10-18	2007-02-26	2007-02-26	ENSG00000124232	ENSG00000124232			13761	protein-coding gene	gene with protein product			"""recombining binding protein suppressor of hairless (Drosophila)-like"""	RBPSUHL		9929984	Standard	NM_014276		Approved	RBP-L, SUH, SUHL	uc002xns.3	Q9UBG7	OTTHUMG00000033055	ENST00000343694.3:c.1442T>C	20.37:g.43945487T>C	ENSP00000341243:p.Val481Ala	66.0	0.0	0		57.0	24.0	0.421053	NM_014276	O95723|Q5QPU9|Q5QPV0|Q9ULV9	Missense_Mutation	SNP	ENST00000343694.3	37	CCDS13349.1	33	0.01510989010989011	25	0.0508130081300813	4	0.011049723756906077	0	0.0	4	0.005277044854881266	C	1.885	-0.456982	0.04540	0.045393	0.001977	ENSG00000124232	ENST00000372743;ENST00000343694	T;T	0.35789	1.29;1.29	5.06	-1.14	0.09741	.	1.055390	0.07430	N	0.895594	T	0.01156	0.0038	N	0.00436	-1.5	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20405	-1.0276	10	0.18710	T	0.47	-0.9329	2.3328	0.04239	0.1025:0.2059:0.3513:0.3403	rs34078698;rs60037526	481	Q9UBG7	RBPJL_HUMAN	A	480;481	ENSP00000361828:V480A;ENSP00000341243:V481A	ENSP00000341243:V481A	V	+	2	0	RBPJL	43378901	0.000000	0.05858	0.271000	0.24616	0.392000	0.30506	-0.499000	0.06413	-0.341000	0.08376	-0.386000	0.06593	GTG	T|0.986;C|0.014	0.014	strong		0.667	RBPJL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080391.1	NM_014276	
WIPF3	644150	hgsc.bcm.edu	37	7	29924002	29924002	+	Missense_Mutation	SNP	C	C	A	rs371924598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:29924002C>A	ENST00000409290.1	+	4	892	c.892C>A	c.(892-894)Cct>Act	p.P298T	WIPF3_ENST00000242140.5_Missense_Mutation_p.P298T|WIPF3_ENST00000409123.1_Missense_Mutation_p.P298T	NM_001080529.2	NP_001073998.2	A6NGB9	WIPF3_HUMAN	WAS/WASL interacting protein family, member 3	298	Poly-Pro.				cell differentiation (GO:0030154)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)				breast(2)|large_intestine(3)|lung(6)|ovary(1)	12						CCCGCTCCCCCCTTATGCTTC	0.672													C|||	18	0.00359425	0.0129	0.0	5008	,	,		5386	0.001		0.0	False		,,,				2504	0.0				p.P298T		Atlas-SNP	.											.	WIPF3	46	.	0			c.C892A						PASS	.	C	THR/PRO	24,3134		0,24,1555	4.0	4.0	4.0		892	1.0	0.0	7		4	2,7334		0,2,3666	no	missense	WIPF3	NM_001080529.2	38	0,26,5221	AA,AC,CC		0.0273,0.76,0.2478	benign	298/484	29924002	26,10468	1579	3668	5247	SO:0001583	missense	644150	exon5			CTCCCCCCTTATG	AK094250	CCDS56472.1	7p15.1	2006-10-12			ENSG00000122574	ENSG00000122574			22004	protein-coding gene	gene with protein product		612432					Standard	NM_001080529		Approved	CR16, FLJ36931	uc022aaz.1	A6NGB9	OTTHUMG00000152761	ENST00000409290.1:c.892C>A	7.37:g.29924002C>A	ENSP00000386878:p.Pro298Thr	117.0	0.0	0		140.0	69.0	0.492857	NM_001080529	B8ZZV2	Missense_Mutation	SNP	ENST00000409290.1	37	CCDS56472.1	.	.	.	.	.	.	.	.	.	.	C	6.789	0.514559	0.12944	0.0076	2.73E-4	ENSG00000122574	ENST00000409123;ENST00000409290;ENST00000242140	T;T;T	0.43688	0.94;0.94;0.94	4.02	0.979	0.19745	.	0.460073	0.18939	N	0.126985	T	0.16300	0.0392	N	0.12746	0.255	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.15350	-1.0440	10	0.21014	T	0.42	.	11.6236	0.51132	0.4549:0.5451:0.0:0.0	.	298	A6NGB9	WIPF3_HUMAN	T	298	ENSP00000386790:P298T;ENSP00000386878:P298T;ENSP00000242140:P298T	ENSP00000242140:P298T	P	+	1	0	WIPF3	29890527	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.063000	0.11655	-0.325000	0.08577	-1.624000	0.00789	CCT	.	.	weak		0.672	WIPF3-002	NOVEL	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000327705.1		
NWD1	284434	hgsc.bcm.edu	37	19	16899852	16899852	+	Missense_Mutation	SNP	G	G	T	rs140602425		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16899852G>T	ENST00000552788.1	+	11	2791	c.2791G>T	c.(2791-2793)Gat>Tat	p.D931Y	NWD1_ENST00000379808.3_Missense_Mutation_p.D931Y|NWD1_ENST00000523826.1_Missense_Mutation_p.D725Y|NWD1_ENST00000339803.6_Missense_Mutation_p.D796Y|NWD1_ENST00000524140.2_Missense_Mutation_p.D931Y|NWD1_ENST00000549814.1_Missense_Mutation_p.D931Y			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	931							ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						TGCTTCAAAGGATTACACGCT	0.498																																					p.D931Y		Atlas-SNP	.											.	NWD1	303	.	0			c.G2791T						PASS	.	G	TYR/ASP	2,4404	4.2+/-10.8	0,2,2201	116.0	112.0	113.0		2791	5.7	0.3	19	dbSNP_134	113	0,8600		0,0,4300	no	missense	NWD1	NM_001007525.3	160	0,2,6501	TT,TG,GG		0.0,0.0454,0.0154	probably-damaging	931/1433	16899852	2,13004	2203	4300	6503	SO:0001583	missense	284434	exon13			TCAAAGGATTACA	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"""WD repeat domain containing"""	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.2791G>T	19.37:g.16899852G>T	ENSP00000447224:p.Asp931Tyr	113.0	0.0	0		126.0	55.0	0.436508	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		.	.	.	.	.	.	.	.	.	.	G	13.13	2.144107	0.37825	4.54E-4	0.0	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	D;D;D;D;D;D	0.89415	-2.51;-2.51;-2.51;-2.51;-2.51;-2.51	5.65	5.65	0.86999	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.96914	0.8992	H	0.98701	4.305	0.32370	N	0.55603	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	D	0.98435	1.0584	10	0.87932	D	0	-35.093	15.2049	0.73173	0.0:0.0:1.0:0.0	.	931;931;796	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	Y	796;931;931;931;725;931;796	ENSP00000428579:D931Y;ENSP00000447548:D931Y;ENSP00000369136:D931Y;ENSP00000428955:D725Y;ENSP00000447224:D931Y;ENSP00000340159:D796Y	ENSP00000340159:D796Y	D	+	1	0	NWD1	16760852	1.000000	0.71417	0.252000	0.24328	0.003000	0.03518	5.303000	0.65738	2.661000	0.90470	0.591000	0.81541	GAT	G|1.000;T|0.000	0.000	weak		0.498	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525	
FUS	2521	hgsc.bcm.edu	37	16	31193948	31193948	+	Silent	SNP	C	C	T	rs61733962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31193948C>T	ENST00000254108.7	+	3	258	c.153C>T	c.(151-153)ggC>ggT	p.G51G	RP11-388M20.6_ENST00000564743.1_RNA|FUS_ENST00000568685.1_Silent_p.G51G|FUS_ENST00000380244.3_Silent_p.G51G	NM_001170634.1|NM_001170937.1|NM_004960.3	NP_001164105.1|NP_001164408.1|NP_004951.1	P35637	FUS_HUMAN	FUS RNA binding protein	51	Gln/Gly/Ser/Tyr-rich.				cell death (GO:0008219)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		FUS/ERG(167)|FUS/DDIT3(631)|FUS/FEV(2)|FUS/ATF1(4)|FUS/CREB3L1(6)|FUS/CREB3L2(158)	breast(3)|endometrium(5)|kidney(3)|large_intestine(1)|lung(5)|prostate(3)|skin(1)|urinary_tract(1)	22		Renal(780;0.000219)|Breast(268;0.00957)|Hepatocellular(780;0.121)		GBM - Glioblastoma multiforme(240;2.31e-05)|Kidney(780;0.000209)		CAGGCTATGGCCAGAGCAGCT	0.522			T	"""DDIT3, ERG, FEV, ATF1, CREB3L2, CREB3L1"""	"""liposarcoma, AML, Ewing sarcoma, angiomatoid fibrous histiocytoma, fibromyxoid sarcoma"""								C|||	169	0.033746	0.1097	0.0187	5008	,	,		19819	0.0		0.005	False		,,,				2504	0.0061				p.G51G		Atlas-SNP	.		Dom	yes		16	16p11.2	2521	"""fusion, derived from t(12;16) malignant liposarcoma"""		"""M, L"""	.	FUS	52	.	0			c.C153T						PASS	.	C	,,	427,3967	210.8+/-231.2	24,379,1794	100.0	95.0	97.0		153,153,153	1.4	1.0	16	dbSNP_129	97	30,8570	20.4+/-63.3	0,30,4270	no	coding-synonymous,coding-synonymous,coding-synonymous	FUS	NM_001170634.1,NM_001170937.1,NM_004960.3	,,	24,409,6064	TT,TC,CC		0.3488,9.7178,3.517	,,	51/526,51/523,51/527	31193948	457,12537	2197	4300	6497	SO:0001819	synonymous_variant	2521	exon3			CTATGGCCAGAGC	AF071213	CCDS10707.1, CCDS58454.1	16p11.2	2014-09-17	2014-05-09		ENSG00000089280	ENSG00000089280		"""RNA binding motif (RRM) containing"""	4010	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein P2"", ""translocated in liposarcoma"""	137070	"""fusion, derived from t(12;16) malignant liposarcoma"", ""amyotrophic lateral sclerosis 6"", ""fusion (involved in t(12;16) in malignant liposarcoma)"", ""fused in sarcoma"""	ALS6		2372777, 7503811, 19251628, 19251627	Standard	NM_004960		Approved	TLS, FUS1, hnRNP-P2, HNRNPP2	uc002ebe.2	P35637	OTTHUMG00000132395	ENST00000254108.7:c.153C>T	16.37:g.31193948C>T		193.0	0.0	0		183.0	94.0	0.513661	NM_001170634	Q9H4A8	Silent	SNP	ENST00000254108.7	37	CCDS10707.1																																																																																			C|0.965;T|0.035	0.035	strong		0.522	FUS-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255526.2	NM_004960	
C22orf23	84645	hgsc.bcm.edu	37	22	38341124	38341124	+	Missense_Mutation	SNP	T	T	G	rs35562630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:38341124T>G	ENST00000249079.2	-	5	662	c.406A>C	c.(406-408)Atg>Ctg	p.M136L	C22orf23_ENST00000403026.1_Missense_Mutation_p.M136L|C22orf23_ENST00000403305.1_Missense_Mutation_p.M136L			Q9BZE7	EVG1_HUMAN	chromosome 22 open reading frame 23	136			M -> L (in dbSNP:rs35562630).							endometrium(3)|kidney(2)|large_intestine(7)	12	Melanoma(58;0.045)					CGTTCCTCCATGTCCTTCCCT	0.512													G|||	204	0.0407348	0.1513	0.0043	5008	,	,		16932	0.0		0.001	False		,,,				2504	0.0				p.M136L		Atlas-SNP	.											.	C22orf23	21	.	0			c.A406C						PASS	.	G	LEU/MET,LEU/MET	504,3902	779.8+/-414.4	23,458,1722	162.0	158.0	159.0		343,406	-8.1	0.0	22	dbSNP_126	159	7,8593	819.0+/-406.8	0,7,4293	yes	missense,missense	C22orf23	NM_001207062.1,NM_032561.4	15,15	23,465,6015	GG,GT,TT		0.0814,11.4389,3.929	benign,benign	115/197,136/218	38341124	511,12495	2203	4300	6503	SO:0001583	missense	84645	exon5			CCTCCATGTCCTT	AF324466	CCDS13962.1, CCDS74860.1	22q13.1	2013-10-11			ENSG00000128346	ENSG00000128346			18589	protein-coding gene	gene with protein product						11237012	Standard	NM_032561		Approved	FLJ32787, EVG1, LOC84645	uc003auj.2	Q9BZE7	OTTHUMG00000150672	ENST00000249079.2:c.406A>C	22.37:g.38341124T>G	ENSP00000249079:p.Met136Leu	348.0	0.0	0		368.0	163.0	0.442935	NM_032561	Q5JYU9|Q96M68	Missense_Mutation	SNP	ENST00000249079.2	37	CCDS13962.1	74	0.03388278388278388	72	0.14634146341463414	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	13.88	2.367954	0.42003	0.114389	8.14E-4	ENSG00000128346	ENST00000403305;ENST00000249079;ENST00000403026;ENST00000418863	T;T;T;T	0.40476	1.03;1.03;1.03;1.03	5.27	-8.07	0.01098	.	2.120180	0.02082	N	0.052461	T	0.00073	0.0002	N	0.02202	-0.64	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.05599	-1.0875	9	0.25751	T	0.34	8.7692	3.5531	0.07854	0.1443:0.121:0.2065:0.5283	rs35562630	136	Q9BZE7	EVG1_HUMAN	L	136	ENSP00000384667:M136L;ENSP00000249079:M136L;ENSP00000384618:M136L;ENSP00000395077:M136L	ENSP00000249079:M136L	M	-	1	0	C22orf23	36671070	0.000000	0.05858	0.000000	0.03702	0.465000	0.32709	-0.628000	0.05515	-1.268000	0.02439	-0.121000	0.15023	ATG	T|0.946;G|0.054	0.054	strong		0.512	C22orf23-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319564.1	NM_032561	
NTRK1	4914	hgsc.bcm.edu	37	1	156838432	156838432	+	Missense_Mutation	SNP	C	C	T	rs55909005	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156838432C>T	ENST00000524377.1	+	6	751	c.710C>T	c.(709-711)aCg>aTg	p.T237M	NTRK1_ENST00000392302.2_Missense_Mutation_p.T207M|NTRK1_ENST00000368196.3_Missense_Mutation_p.T237M|NTRK1_ENST00000358660.3_Missense_Mutation_p.T237M	NM_002529.3	NP_002520.2	P04629	NTRK1_HUMAN	neurotrophic tyrosine kinase, receptor, type 1	237	Ig-like C2-type 1.		T -> M (in dbSNP:rs55909005). {ECO:0000269|PubMed:17344846}.		activation of adenylate cyclase activity (GO:0007190)|activation of MAPKK activity (GO:0000186)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|axon guidance (GO:0007411)|axonogenesis involved in innervation (GO:0060385)|B cell differentiation (GO:0030183)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to nicotine (GO:0071316)|circadian rhythm (GO:0007623)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|detection of temperature stimulus involved in sensory perception of pain (GO:0050965)|developmental programmed cell death (GO:0010623)|learning or memory (GO:0007611)|mechanoreceptor differentiation (GO:0042490)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory nerve development (GO:0021553)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of programmed cell death (GO:0043068)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|response to activity (GO:0014823)|response to axon injury (GO:0048678)|response to drug (GO:0042493)|response to electrical stimulus (GO:0051602)|response to ethanol (GO:0045471)|response to hydrostatic pressure (GO:0051599)|response to nutrient levels (GO:0031667)|response to radiation (GO:0009314)|Sertoli cell development (GO:0060009)|small GTPase mediated signal transduction (GO:0007264)|sympathetic nervous system development (GO:0048485)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|early endosome (GO:0005769)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|nerve growth factor binding (GO:0048406)|nerve growth factor receptor activity (GO:0010465)|neurotrophin binding (GO:0043121)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(35)|ovary(8)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	74	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)				Amitriptyline(DB00321)|Imatinib(DB00619)|Regorafenib(DB08896)	CAGTCAGCCACGGTGATGGTG	0.637			T	"""TPM3, TPR, TFG"""	papillary thyroid					TSP Lung(10;0.080)			C|||	87	0.0173722	0.0598	0.0115	5008	,	,		15696	0.0		0.0	False		,,,				2504	0.0				p.T237M		Atlas-SNP	.		Dom	yes		1	1q21-q22	4914	"""neurotrophic tyrosine kinase, receptor, type 1"""		E	.	NTRK1	287	.	0			c.C710T						PASS	.	C	MET/THR,MET/THR,MET/THR	196,3896		4,188,1854	14.0	14.0	14.0		620,710,710	2.5	0.5	1	dbSNP_129	14	5,8021		0,5,4008	yes	missense,missense,missense	NTRK1	NM_001007792.1,NM_001012331.1,NM_002529.3	81,81,81	4,193,5862	TT,TC,CC		0.0623,4.7898,1.6587	probably-damaging,probably-damaging,probably-damaging	207/761,237/791,237/797	156838432	201,11917	2046	4013	6059	SO:0001583	missense	4914	exon6			CAGCCACGGTGAT	Y09028	CCDS1161.1, CCDS30890.1, CCDS30891.1	1q21-q22	2014-09-17			ENSG00000198400	ENSG00000198400	2.7.10.1	"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	8031	protein-coding gene	gene with protein product	"""high affinity nerve growth factor receptor"""	191315				2869410	Standard	NM_001007792		Approved	TRK, TRKA, MTC	uc001fqh.1	P04629	OTTHUMG00000041304	ENST00000524377.1:c.710C>T	1.37:g.156838432C>T	ENSP00000431418:p.Thr237Met	93.0	0.0	0		103.0	53.0	0.514563	NM_001012331	B2R6T5|B7ZM34|P08119|Q15655|Q15656|Q5D056|Q5VZS2|Q7Z5C3|Q9UIU7	Missense_Mutation	SNP	ENST00000524377.1	37	CCDS1161.1	27	0.012362637362637362	22	0.044715447154471545	5	0.013812154696132596	0	0.0	0	0.0	C	13.13	2.144047	0.37825	0.047898	6.23E-4	ENSG00000198400	ENST00000392302;ENST00000368196;ENST00000524377;ENST00000358660	T;T;T;T	0.16073	2.37;2.37;2.37;2.37	4.38	2.47	0.30058	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.432209	0.19724	N	0.107503	T	0.16514	0.0397	L	0.52573	1.65	0.32458	N	0.544507	P;D;D;D	0.89917	0.791;1.0;1.0;0.998	B;P;D;P	0.85130	0.248;0.806;0.997;0.886	T	0.03354	-1.1045	10	0.35671	T	0.21	.	6.7504	0.23483	0.0:0.782:0.0:0.218	rs55909005	237;237;237;207	A8K3Z4;P04629-2;P04629;A6NF12	.;.;NTRK1_HUMAN;.	M	207;237;237;237	ENSP00000376120:T207M;ENSP00000357179:T237M;ENSP00000431418:T237M;ENSP00000351486:T237M	ENSP00000351486:T237M	T	+	2	0	NTRK1	155105056	0.172000	0.23043	0.531000	0.27976	0.749000	0.42624	0.489000	0.22387	0.577000	0.29470	0.462000	0.41574	ACG	C|0.987;T|0.013	0.013	strong		0.637	NTRK1-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392279.1	NM_002529	
SCGB1D1	10648	hgsc.bcm.edu	37	11	61959636	61959636	+	Missense_Mutation	SNP	C	C	T	rs116188604	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61959636C>T	ENST00000306238.3	+	2	233	c.164C>T	c.(163-165)gCt>gTt	p.A55V		NM_006552.1	NP_006543.1	O95968	SG1D1_HUMAN	secretoglobin, family 1D, member 1	55						extracellular space (GO:0005615)	protein heterodimerization activity (GO:0046982)			endometrium(1)|large_intestine(2)|lung(4)|skin(1)|stomach(1)	9						CCTCTGGAAGCTGTTGCAGCC	0.423													C|||	69	0.013778	0.0484	0.0058	5008	,	,		21854	0.0		0.001	False		,,,				2504	0.0				p.A55V		Atlas-SNP	.											SCGB1D1,NS,carcinoma,0,1	SCGB1D1	18	1	0			c.C164T						PASS	.	C	VAL/ALA	192,4212	122.1+/-159.5	6,180,2016	132.0	126.0	128.0		164	-4.4	0.0	11	dbSNP_132	128	4,8594	3.7+/-12.6	0,4,4295	yes	missense	SCGB1D1	NM_006552.1	64	6,184,6311	TT,TC,CC		0.0465,4.3597,1.5075	probably-damaging	55/91	61959636	196,12806	2202	4299	6501	SO:0001583	missense	10648	exon2			TGGAAGCTGTTGC	AJ224171	CCDS8015.1	11q13	2011-12-14			ENSG00000168515	ENSG00000168515		"""Secretoglobins"""	18395	protein-coding gene	gene with protein product	"""prostatein-like lipophilin A"", ""lipophilin A (uteroglobin family member)"""	615060				9720917, 10066439, 22155607	Standard	NM_006552		Approved	LPHA, LIPA, MGC71958	uc001nsz.1	O95968	OTTHUMG00000167505	ENST00000306238.3:c.164C>T	11.37:g.61959636C>T	ENSP00000303070:p.Ala55Val	151.0	0.0	0		165.0	88.0	0.533333	NM_006552		Missense_Mutation	SNP	ENST00000306238.3	37	CCDS8015.1	36	0.016483516483516484	30	0.06097560975609756	3	0.008287292817679558	0	0.0	3	0.00395778364116095	C	13.33	2.203741	0.38905	0.043597	4.65E-4	ENSG00000168515	ENST00000306238	T	0.15372	2.43	3.88	-4.42	0.03579	.	1.484950	0.04929	N	0.456544	T	0.01029	0.0034	.	.	.	0.09310	N	1	P	0.42735	0.788	B	0.37144	0.242	T	0.14309	-1.0477	9	0.51188	T	0.08	.	3.9086	0.09193	0.269:0.2885:0.0:0.4425	.	55	O95968	SG1D1_HUMAN	V	55	ENSP00000303070:A55V	ENSP00000303070:A55V	A	+	2	0	SCGB1D1	61716212	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.404000	0.02494	-1.026000	0.03330	-0.857000	0.03018	GCT	C|0.982;T|0.018	0.018	strong		0.423	SCGB1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394856.1	NM_006552	
ILDR1	286676	hgsc.bcm.edu	37	3	121712098	121712098	+	Missense_Mutation	SNP	G	G	A	rs34284625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:121712098G>A	ENST00000344209.5	-	7	1624	c.1498C>T	c.(1498-1500)Cac>Tac	p.H500Y	ILDR1_ENST00000273691.3_Missense_Mutation_p.H456Y|ILDR1_ENST00000460554.1_5'UTR|ILDR1_ENST00000393631.1_Missense_Mutation_p.H411Y|ILDR1_ENST00000462014.1_Missense_Mutation_p.H468Y	NM_001199799.1	NP_001186728.1	Q86SU0	ILDR1_HUMAN	immunoglobulin-like domain containing receptor 1	500					positive regulation of peptide hormone secretion (GO:0090277)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-density lipoprotein particle receptor activity (GO:0070506)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(114;0.156)		TGTGGGGAGTGCGAGCCGCGG	0.632													G|||	201	0.0401358	0.1445	0.0144	5008	,	,		15335	0.0		0.0	False		,,,				2504	0.0				p.H500Y		Atlas-SNP	.											.	ILDR1	120	.	0			c.C1498T						PASS	.	G	TYR/HIS,TYR/HIS,TYR/HIS	520,3882		26,468,1707	23.0	24.0	24.0		1498,1231,1366	4.0	0.0	3	dbSNP_126	24	8,8590		0,8,4291	yes	missense,missense,missense	ILDR1	NM_001199799.1,NM_001199800.1,NM_175924.3	83,83,83	26,476,5998	AA,AG,GG		0.093,11.8128,4.0615	benign,benign,benign	500/547,411/458,456/503	121712098	528,12472	2201	4299	6500	SO:0001583	missense	286676	exon7			GGGAGTGCGAGCC	BC044240	CCDS3008.1, CCDS56270.1, CCDS56271.1	3q21.1	2013-10-11			ENSG00000145103	ENSG00000145103			28741	protein-coding gene	gene with protein product		609739	"""deafness, autosomal recessive 42"""	DFNB42		15641023, 21255762	Standard	NM_175924		Approved	MGC50831	uc003ees.3	Q86SU0	OTTHUMG00000159481	ENST00000344209.5:c.1498C>T	3.37:g.121712098G>A	ENSP00000345667:p.His500Tyr	152.0	0.0	0		173.0	81.0	0.468208	NM_001199799	Q6ZP61|Q7Z578	Missense_Mutation	SNP	ENST00000344209.5	37	CCDS56271.1	78	0.03571428571428571	74	0.15040650406504066	4	0.011049723756906077	0	0.0	0	0.0	G	11.04	1.522102	0.27211	0.118128	9.3E-4	ENSG00000145103	ENST00000273691;ENST00000344209;ENST00000393631;ENST00000462014	T;T;T;T	0.76709	-0.44;-0.44;-1.04;-0.04	5.76	3.99	0.46301	.	1.592350	0.03082	N	0.158662	T	0.00784	0.0026	N	0.22421	0.69	0.80722	P	0.0	B;B;B;B	0.32620	0.378;0.165;0.378;0.378	B;B;B;B	0.28849	0.095;0.044;0.095;0.095	T	0.22661	-1.0210	9	0.56958	D	0.05	-1.8466	11.555	0.50741	0.1185:0.0:0.8815:0.0	rs34284625	411;500;456;468	Q86SU0-5;Q86SU0;Q86SU0-2;Q86SU0-6	.;ILDR1_HUMAN;.;.	Y	456;500;411;468	ENSP00000273691:H456Y;ENSP00000345667:H500Y;ENSP00000377251:H411Y;ENSP00000419414:H468Y	ENSP00000273691:H456Y	H	-	1	0	ILDR1	123194788	0.109000	0.22037	0.001000	0.08648	0.252000	0.25951	2.180000	0.42537	0.802000	0.34089	0.563000	0.77884	CAC	G|0.956;A|0.044	0.044	strong		0.632	ILDR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355666.1	NM_175924	
LMNTD1	160492	hgsc.bcm.edu	37	12	25672880	25672880	+	Missense_Mutation	SNP	T	T	C	rs34732786	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:25672880T>C	ENST00000282881.6	-	6	1014	c.865A>G	c.(865-867)Aca>Gca	p.T289A	IFLTD1_ENST00000539744.1_Missense_Mutation_p.T192A|IFLTD1_ENST00000458174.2_Missense_Mutation_p.T310A|IFLTD1_ENST00000413632.2_Missense_Mutation_p.T270A|IFLTD1_ENST00000445693.1_Missense_Mutation_p.T226A	NM_152590.3	NP_689803.2	Q8N9Z9	LMTD1_HUMAN		289			T -> A (in dbSNP:rs34732786).		cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22	all_lung(3;2.75e-22)|Lung NSC(3;1.77e-21)|all_hematologic(7;0.00656)|Colorectal(261;0.0847)					ATTGTAGCTGTAGATGCTGTC	0.378													T|||	88	0.0175719	0.0628	0.0072	5008	,	,		13206	0.0		0.0	False		,,,				2504	0.0				p.T310A		Atlas-SNP	.											.	IFLTD1	121	.	0			c.A928G						PASS	.	T	ALA/THR,ALA/THR,ALA/THR,ALA/THR	251,4155	146.5+/-181.1	5,241,1957	211.0	187.0	195.0		676,928,808,865	-7.0	0.0	12	dbSNP_126	195	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense,missense	IFLTD1	NM_001145727.1,NM_001145728.1,NM_001145729.1,NM_152590.2	58,58,58,58	5,242,6256	CC,CT,TT		0.0116,5.6968,1.9376	benign,benign,benign,benign	226/326,310/410,270/370,289/389	25672880	252,12754	2203	4300	6503	SO:0001583	missense	160492	exon7			TAGCTGTAGATGC																												ENST00000282881.6:c.865A>G	12.37:g.25672880T>C	ENSP00000282881:p.Thr289Ala	160.0	0.0	0		121.0	51.0	0.421488	NM_001145728	B4DL27|B4DY70|Q8IY38	Missense_Mutation	SNP	ENST00000282881.6	37	CCDS8704.1	20|20	0.009157509157509158|0.009157509157509158	17|17	0.034552845528455285|0.034552845528455285	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	T|T	8.850|8.850	0.944302|0.944302	0.18356|0.18356	0.056968|0.056968	1.16E-4|1.16E-4	ENSG00000152936|ENSG00000152936	ENST00000282881;ENST00000539744;ENST00000458174;ENST00000445693;ENST00000413632;ENST00000539523;ENST00000545543|ENST00000543629	T;T;T;T;T;T;T|.	0.22945|.	2.72;2.75;2.72;2.72;2.54;1.93;2.5|.	4.84|4.84	-7.02|-7.02	0.01589|0.01589	.|.	.|.	.|.	.|.	.|.	T|T	0.02267|0.02267	0.0070|0.0070	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	B;B;B;B|.	0.17667|.	0.023;0.023;0.023;0.013|.	B;B;B;B|.	0.11329|.	0.003;0.006;0.006;0.002|.	T|T	0.21861|0.21861	-1.0233|-1.0233	9|5	0.62326|.	D|.	0.03|.	-0.6199|-0.6199	9.436|9.436	0.38639|0.38639	0.0:0.5472:0.2462:0.2065|0.0:0.5472:0.2462:0.2065	rs34732786|rs34732786	226;310;270;289|.	Q8N9Z9-3;Q8N9Z9-5;Q8N9Z9-4;Q8N9Z9|.	.;.;.;ILFT1_HUMAN|.	A|C	289;192;310;226;270;6;119|63	ENSP00000282881:T289A;ENSP00000443132:T192A;ENSP00000407353:T310A;ENSP00000407043:T226A;ENSP00000393150:T270A;ENSP00000438160:T6A;ENSP00000443596:T119A|.	ENSP00000282881:T289A|.	T|Y	-|-	1|2	0|0	IFLTD1|IFLTD1	25564147|25564147	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.013000|0.013000	0.08279|0.08279	-2.565000|-2.565000	0.00918|0.00918	-1.326000|-1.326000	0.02266|0.02266	0.477000|0.477000	0.44152|0.44152	ACA|TAC	T|0.980;C|0.020	0.020	strong		0.378	IFLTD1-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402279.1		
CCDC40	55036	hgsc.bcm.edu	37	17	78014024	78014024	+	Silent	SNP	G	G	A	rs2885349	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78014024G>A	ENST00000397545.4	+	3	534	c.507G>A	c.(505-507)tcG>tcA	p.S169S	CCDC40_ENST00000374876.4_Silent_p.S169S|CCDC40_ENST00000374877.3_Silent_p.S169S|CCDC40_ENST00000269318.5_Silent_p.S169S	NM_017950.3	NP_060420.2	Q4G0X9	CCD40_HUMAN	coiled-coil domain containing 40	169					axonemal dynein complex assembly (GO:0070286)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement (GO:0003351)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)|regulation of cilium beat frequency (GO:0003356)	cilium (GO:0005929)|cytoplasm (GO:0005737)				NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(7)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	38	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.149)			TAGGCCCGTCGGAGCAAATGG	0.612													G|||	316	0.063099	0.1884	0.0173	5008	,	,		14983	0.001		0.004	False		,,,				2504	0.0511				p.S169S		Atlas-SNP	.											CCDC40_ENST00000374877,rectum,carcinoma,+1,2	CCDC40	198	2	0			c.G507A						PASS	.	G		614,3338		46,522,1408	30.0	34.0	33.0		507	-1.7	0.0	17	dbSNP_101	33	14,8316		0,14,4151	no	coding-synonymous	CCDC40	NM_017950.3		46,536,5559	AA,AG,GG		0.1681,15.5364,5.1132		169/1143	78014024	628,11654	1976	4165	6141	SO:0001819	synonymous_variant	55036	exon3			CCCGTCGGAGCAA	AB046860	CCDS42395.1, CCDS58604.1	17q25.3	2013-11-15			ENSG00000141519	ENSG00000141519			26090	protein-coding gene	gene with protein product		613799				21131974	Standard	NM_017950		Approved	FLJ20753, KIAA1640, FLJ32021, CILD15, FAP172	uc010dht.3	Q4G0X9	OTTHUMG00000132707	ENST00000397545.4:c.507G>A	17.37:g.78014024G>A		56.0	0.0	0		64.0	32.0	0.5	NM_017950	A8MTD2|C9JTI9|C9JTJ0|C9JXW1|Q6PE47|Q9HCD2|Q9NWL5	Silent	SNP	ENST00000397545.4	37	CCDS42395.1																																																																																			G|0.968;A|0.032	0.032	strong		0.612	CCDC40-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256005.2	XM_371082	
FMNL2	114793	hgsc.bcm.edu	37	2	153475556	153475556	+	Missense_Mutation	SNP	T	T	C	rs11897929	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:153475556T>C	ENST00000288670.9	+	14	1878	c.1511T>C	c.(1510-1512)aTg>aCg	p.M504T	FMNL2_ENST00000475377.2_5'Flank	NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	504			M -> T (in dbSNP:rs11897929).		cortical actin cytoskeleton organization (GO:0030866)|cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)				central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(2)|lung(3)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	23						ACATTGTCCATGGGGTCAGAA	0.537													T|||	386	0.0770767	0.2769	0.0259	5008	,	,		16892	0.0		0.002	False		,,,				2504	0.0				p.M504T		Atlas-SNP	.											.	FMNL2	75	.	0			c.T1511C						PASS	.	T	THR/MET	828,3056		87,654,1201	67.0	70.0	69.0		1511	-2.1	0.0	2	dbSNP_120	69	3,8279		0,3,4138	yes	missense	FMNL2	NM_052905.3	81	87,657,5339	CC,CT,TT		0.0362,21.3182,6.8305	benign	504/1093	153475556	831,11335	1942	4141	6083	SO:0001583	missense	114793	exon14			TGTCCATGGGGTC	AB067489	CCDS46429.1	2q23.3	2008-02-05	2003-12-02	2003-12-03	ENSG00000157827	ENSG00000157827			18267	protein-coding gene	gene with protein product			"""formin homology 2 domain containing 2"""	FHOD2			Standard	XM_005246263		Approved	KIAA1902	uc002tye.3	Q96PY5	OTTHUMG00000154035	ENST00000288670.9:c.1511T>C	2.37:g.153475556T>C	ENSP00000288670:p.Met504Thr	181.0	0.0	0		172.0	93.0	0.540698	NM_052905	B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Missense_Mutation	SNP	ENST00000288670.9	37	CCDS46429.1	136	0.06227106227106227	128	0.2601626016260163	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	T	0.957	-0.704556	0.03255	0.213182	3.62E-4	ENSG00000157827	ENST00000288670;ENST00000421344	D	0.90004	-2.6	5.57	-2.14	0.07123	.	0.947878	0.08957	N	0.869194	T	0.00039	0.0001	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.01520	-1.1334	9	0.13108	T	0.6	.	11.4827	0.50335	0.0:0.5749:0.0:0.4251	rs11897929;rs11897929	504	Q96PY5-3	.	T	504;1	ENSP00000288670:M504T	ENSP00000288670:M504T	M	+	2	0	FMNL2	153183802	0.000000	0.05858	0.000000	0.03702	0.103000	0.19146	-0.531000	0.06171	-0.792000	0.04480	-0.973000	0.02599	ATG	T|0.920;C|0.080	0.080	strong		0.537	FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905	
FARP2	9855	hgsc.bcm.edu	37	2	242352768	242352768	+	Missense_Mutation	SNP	A	A	C	rs16843643	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242352768A>C	ENST00000264042.3	+	7	725	c.555A>C	c.(553-555)aaA>aaC	p.K185N	FARP2_ENST00000373287.4_Missense_Mutation_p.K185N|FARP2_ENST00000545004.1_Missense_Mutation_p.K185N	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	185	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.		K -> N (in dbSNP:rs16843643).		actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		AGCACCTCAAAGTGAACGAGT	0.403													A|||	203	0.0405351	0.146	0.013	5008	,	,		20493	0.001		0.0	False		,,,				2504	0.0				p.K185N		Atlas-SNP	.											.	FARP2	92	.	0			c.A555C						PASS	.	A	ASN/LYS	514,3892	231.7+/-245.5	32,450,1721	104.0	82.0	90.0		555	-5.4	0.0	2	dbSNP_123	90	10,8590	7.7+/-29.5	0,10,4290	yes	missense	FARP2	NM_014808.2	94	32,460,6011	CC,CA,AA		0.1163,11.6659,4.0289	probably-damaging	185/1055	242352768	524,12482	2203	4300	6503	SO:0001583	missense	9855	exon7			CCTCAAAGTGAAC	AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.555A>C	2.37:g.242352768A>C	ENSP00000264042:p.Lys185Asn	50.0	0.0	0		58.0	32.0	0.551724	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Missense_Mutation	SNP	ENST00000264042.3	37	CCDS33424.1	69	0.03159340659340659	64	0.13008130081300814	5	0.013812154696132596	0	0.0	0	0.0	A	8.513	0.866895	0.17250	0.116659	0.001163	ENSG00000006607	ENST00000264042;ENST00000545004;ENST00000373287	T;T;T	0.30714	1.52;1.52;1.52	5.34	-5.39	0.02664	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.312765	0.32533	N	0.005966	T	0.00241	0.0007	L	0.41124	1.26	0.09310	N	1	D;B;P	0.54772	0.968;0.116;0.947	P;B;P	0.50791	0.598;0.078;0.65	T	0.03034	-1.1080	10	0.59425	D	0.04	.	3.6724	0.08279	0.3864:0.1157:0.3863:0.1116	rs16843643;rs52827477;rs59890453;rs16843643	185;185;185	O94887-2;F5GZ84;O94887	.;.;FARP2_HUMAN	N	185	ENSP00000264042:K185N;ENSP00000443876:K185N;ENSP00000362384:K185N	ENSP00000264042:K185N	K	+	3	2	FARP2	242001441	0.001000	0.12720	0.000000	0.03702	0.336000	0.28762	0.092000	0.15066	-1.367000	0.02152	0.528000	0.53228	AAA	A|0.960;C|0.040	0.040	strong		0.403	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1		
ZNF385C	201181	hgsc.bcm.edu	37	17	40183707	40183707	+	Silent	SNP	G	G	C	rs75049227	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:40183707G>C	ENST00000436535.3	-	4	606	c.606C>G	c.(604-606)gcC>gcG	p.A202A	ZNF385C_ENST00000461831.1_5'Flank			Q66K41	Z385C_HUMAN	zinc finger protein 385C	121						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	3		all_cancers(22;0.00127)|Breast(137;0.00104)|all_epithelial(22;0.0126)				CCCCATCCTGGGCCTGGGTGT	0.587													G|||	55	0.0109824	0.0416	0.0	5008	,	,		19297	0.0		0.0	False		,,,				2504	0.0				p.A123A		Atlas-SNP	.											.	ZNF385C	7	.	0			c.C369G						PASS	.																																			SO:0001819	synonymous_variant	201181	exon4			ATCCTGGGCCTGG	BC067901	CCDS74065.1	17q21.2	2012-10-05			ENSG00000187595	ENSG00000187595			33722	protein-coding gene	gene with protein product							Standard	NM_001242704		Approved		uc021txr.1	Q66K41	OTTHUMG00000132073	ENST00000436535.3:c.606C>G	17.37:g.40183707G>C		352.0	0.0	0		358.0	172.0	0.480447	NM_001242704	Q4G0J1	Silent	SNP	ENST00000436535.3	37																																																																																				G|0.994;C|0.006	0.006	strong		0.587	ZNF385C-001	NOVEL	not_organism_supported|mRNA_end_NF|cds_end_NF|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000347740.3	NM_001013624	
NECAB2	54550	hgsc.bcm.edu	37	16	84027966	84027966	+	Missense_Mutation	SNP	C	C	T	rs79514285	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84027966C>T	ENST00000305202.4	+	7	673	c.656C>T	c.(655-657)cCc>cTc	p.P219L	NECAB2_ENST00000567703.1_3'UTR|NECAB2_ENST00000565691.1_Missense_Mutation_p.P136L	NM_019065.2	NP_061938.2	Q7Z6G3	NECA2_HUMAN	N-terminal EF-hand calcium binding protein 2	219						cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	19						AGCCCCACTCCCGCCTCTGCC	0.617													C|||	12	0.00239617	0.0083	0.0014	5008	,	,		16456	0.0		0.0	False		,,,				2504	0.0				p.P219L		Atlas-SNP	.											.	NECAB2	36	.	0			c.C656T						PASS	.	C	LEU/PRO	49,4351	50.2+/-85.5	0,49,2151	56.0	55.0	55.0		656	2.6	0.0	16	dbSNP_131	55	1,8599	1.2+/-3.3	0,1,4299	yes	missense	NECAB2	NM_019065.2	98	0,50,6450	TT,TC,CC		0.0116,1.1136,0.3846	possibly-damaging	219/387	84027966	50,12950	2200	4300	6500	SO:0001583	missense	54550	exon7			CCACTCCCGCCTC	AY299331	CCDS10940.1	16q23.3-q24.1	2013-01-10	2007-12-06	2007-12-06	ENSG00000103154	ENSG00000103154		"""N-terminal EF-hand calcium binding proteins"", ""EF-hand domain containing"""	23746	protein-coding gene	gene with protein product			"""EF-hand calcium binding protein 2"""	EFCBP2		12044471	Standard	NM_019065		Approved		uc002fhd.3	Q7Z6G3	OTTHUMG00000137636	ENST00000305202.4:c.656C>T	16.37:g.84027966C>T	ENSP00000307449:p.Pro219Leu	100.0	0.0	0		99.0	50.0	0.50505	NM_019065	A2RRG3|O75547|Q6ZSK0	Missense_Mutation	SNP	ENST00000305202.4	37	CCDS10940.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	6.435	0.448444	0.12223	0.011136	1.16E-4	ENSG00000103154	ENST00000305202	T	0.18338	2.22	4.58	2.62	0.31277	.	0.326488	0.32868	N	0.005554	T	0.09598	0.0236	L	0.44542	1.39	0.09310	N	0.999999	B	0.06786	0.001	B	0.06405	0.002	T	0.27773	-1.0064	10	0.21540	T	0.41	-9.3808	10.4175	0.44331	0.0:0.7817:0.1375:0.0809	.	219	Q7Z6G3	NECA2_HUMAN	L	219	ENSP00000307449:P219L	ENSP00000307449:P219L	P	+	2	0	NECAB2	82585467	0.004000	0.15560	0.000000	0.03702	0.000000	0.00434	1.654000	0.37334	0.128000	0.18479	-1.872000	0.00552	CCC	C|0.996;T|0.004	0.004	strong		0.617	NECAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269077.2	NM_019065	
MMP20	9313	hgsc.bcm.edu	37	11	102487643	102487643	+	Missense_Mutation	SNP	T	T	C	rs61730848	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:102487643T>C	ENST00000260228.2	-	2	286	c.274A>G	c.(274-276)Atg>Gtg	p.M92V	RP11-817J15.2_ENST00000542119.1_RNA	NM_004771.3	NP_004762.2	Q9NPA2	MMP25_HUMAN	matrix metallopeptidase 20	82					hard palate development (GO:0060022)|inflammatory response (GO:0006954)|proteolysis (GO:0006508)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(4)|large_intestine(3)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(8;8.95e-05)|all_epithelial(12;0.00227)|Lung NSC(15;0.139)	Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0033)	Epithelial(9;0.0216)|Lung(13;0.0711)|all cancers(10;0.0889)|LUSC - Lung squamous cell carcinoma(19;0.13)	BRCA - Breast invasive adenocarcinoma(274;0.0161)	Marimastat(DB00786)	ATCACGTTCATTGTGGTCTGG	0.458													T|||	12	0.00239617	0.0083	0.0014	5008	,	,		20171	0.0		0.0	False		,,,				2504	0.0				p.M92V		Atlas-SNP	.											.	MMP20	52	.	0			c.A274G						PASS	.	T	VAL/MET	31,4375	36.8+/-68.6	0,31,2172	174.0	149.0	158.0		274	4.0	0.4	11	dbSNP_129	158	0,8598		0,0,4299	yes	missense	MMP20	NM_004771.3	21	0,31,6471	CC,CT,TT		0.0,0.7036,0.2384	benign	92/484	102487643	31,12973	2203	4299	6502	SO:0001583	missense	9313	exon2			CGTTCATTGTGGT	Y12779	CCDS8318.1	11q22.3	2008-05-22	2008-05-22			ENSG00000137674			7167	protein-coding gene	gene with protein product	"""enamelysin"""	604629	"""matrix metalloproteinase 20 (enamelysin)"""			9398237	Standard	NM_004771		Approved		uc001phc.3	O60882		ENST00000260228.2:c.274A>G	11.37:g.102487643T>C	ENSP00000260228:p.Met92Val	222.0	0.0	0		223.0	91.0	0.408072	NM_004771	D3DUA8|Q9H3Q0	Missense_Mutation	SNP	ENST00000260228.2	37	CCDS8318.1	3	0.0013736263736263737	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	0	0.0	T	8.312	0.822400	0.16678	0.007036	0.0	ENSG00000137674	ENST00000260228	T	0.34072	1.38	5.09	3.95	0.45737	Peptidoglycan binding-like (2);Metallopeptidase, catalytic domain (1);	0.248296	0.48286	D	0.000186	T	0.22126	0.0533	L	0.48174	1.505	0.31775	N	0.631573	B	0.10296	0.003	B	0.12837	0.008	T	0.24368	-1.0162	10	0.54805	T	0.06	.	7.274	0.26273	0.1337:0.0:0.2769:0.5894	.	92	O60882	MMP20_HUMAN	V	92	ENSP00000260228:M92V	ENSP00000260228:M92V	M	-	1	0	MMP20	101992853	0.016000	0.18221	0.382000	0.26119	0.387000	0.30353	0.103000	0.15292	1.044000	0.40200	0.533000	0.62120	ATG	T|0.998;C|0.002	0.002	strong		0.458	MMP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398012.1		
PPP1R12C	54776	hgsc.bcm.edu	37	19	55623871	55623871	+	Missense_Mutation	SNP	T	T	G	rs116840455	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55623871T>G	ENST00000263433.3	-	3	550	c.535A>C	c.(535-537)Atg>Ctg	p.M179L	PPP1R12C_ENST00000435544.2_Missense_Mutation_p.M105L|PPP1R12C_ENST00000376393.2_Missense_Mutation_p.M179L	NM_001271618.1|NM_017607.2	NP_001258547.1|NP_060077.1			protein phosphatase 1, regulatory subunit 12C											central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	22			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0449)		AGCCCCTCCATGGCGTCCGAC	0.701													T|||	47	0.00938498	0.0356	0.0	5008	,	,		12736	0.0		0.0	False		,,,				2504	0.0				p.M179L		Atlas-SNP	.											.	PPP1R12C	46	.	0			c.A535C						PASS	.	T	LEU/MET	136,4270		0,136,2067	22.0	28.0	26.0		535	2.0	1.0	19	dbSNP_132	26	0,8596		0,0,4298	yes	missense	PPP1R12C	NM_017607.2	15	0,136,6365	GG,GT,TT		0.0,3.0867,1.046	possibly-damaging	179/783	55623871	136,12866	2203	4298	6501	SO:0001583	missense	54776	exon3			CCTCCATGGCGTC	AF312028	CCDS12916.1	19q13.42	2013-01-10	2011-10-04		ENSG00000125503	ENSG00000125503		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	14947	protein-coding gene	gene with protein product	"""myosin-binding subunit 85"""	613245	"""leukocyte receptor cluster (LRC) member 3"", ""protein phosphatase 1, regulatory (inhibitor) subunit 12C"""	LENG3		11399775	Standard	NM_017607		Approved	DKFZP434D0412, p84, MBS85, p85	uc002qix.4	Q9BZL4		ENST00000263433.3:c.535A>C	19.37:g.55623871T>G	ENSP00000263433:p.Met179Leu	122.0	0.0	0		93.0	38.0	0.408602	NM_017607		Missense_Mutation	SNP	ENST00000263433.3	37	CCDS12916.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	T	17.05	3.291102	0.59976	0.030867	0.0	ENSG00000125503	ENST00000263433;ENST00000376393;ENST00000435544	T;T;T	0.51574	0.7;0.7;0.7	5.24	2.02	0.26589	Ankyrin repeat-containing domain (3);	0.106312	0.64402	D	0.000009	T	0.12263	0.0298	L	0.31578	0.945	0.41995	D	0.990866	B;B;B	0.25441	0.126;0.122;0.075	B;B;B	0.23150	0.02;0.044;0.02	T	0.03875	-1.0996	10	0.44086	T	0.13	.	7.5728	0.27918	0.0:0.2535:0.0:0.7465	.	105;179;179	B4DME2;Q9BZL4-3;Q9BZL4	.;.;PP12C_HUMAN	L	179;179;105	ENSP00000263433:M179L;ENSP00000365573:M179L;ENSP00000387833:M105L	ENSP00000263433:M179L	M	-	1	0	PPP1R12C	60315683	1.000000	0.71417	0.994000	0.49952	0.926000	0.56050	2.280000	0.43443	0.421000	0.25980	0.459000	0.35465	ATG	T|0.990;G|0.010	0.010	strong		0.701	PPP1R12C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451814.2	NM_017607	
SLITRK4	139065	hgsc.bcm.edu	37	X	142717383	142717383	+	Silent	SNP	A	A	G	rs73577386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:142717383A>G	ENST00000381779.4	-	2	1767	c.1542T>C	c.(1540-1542)agT>agC	p.S514S	SLITRK4_ENST00000338017.4_Silent_p.S514S|SLITRK4_ENST00000356928.1_Silent_p.S514S	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	514						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					CAAGGACCCCACTGACAGGCA	0.473													A|||	528	0.139868	0.3812	0.0317	3775	,	,		13652	0.0		0.002	False		,,,				2504	0.0				p.S514S		Atlas-SNP	.											.	SLITRK4	162	.	0			c.T1542C						PASS	.	A	,,	1667,2168		315,787,250,530,321	133.0	136.0	135.0		1542,1542,1542	-3.0	1.0	X	dbSNP_130	135	17,6711		0,11,6,2417,1866	no	coding-synonymous,coding-synonymous,coding-synonymous	SLITRK4	NM_001184749.1,NM_001184750.1,NM_173078.3	,,	315,798,256,2947,2187	GG,GA,G,AA,A		0.2527,43.4681,15.9424	,,	514/838,514/838,514/838	142717383	1684,8879	2203	4300	6503	SO:0001819	synonymous_variant	139065	exon2			GACCCCACTGACA	BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.1542T>C	X.37:g.142717383A>G		199.0	1.0	0.00502513		168.0	168.0	1	NM_001184750	Q5JXG3|Q8TCM8|Q96DL3	Silent	SNP	ENST00000381779.4	37	CCDS14679.1																																																																																			A|0.836;G|0.164	0.164	strong		0.473	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078	
GPR68	8111	hgsc.bcm.edu	37	14	91700319	91700319	+	Missense_Mutation	SNP	A	A	G	rs151219229	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:91700319A>G	ENST00000531499.2	-	2	1415	c.1076T>C	c.(1075-1077)tTc>tCc	p.F359S	GPR68_ENST00000238699.3_Missense_Mutation_p.F369S|GPR68_ENST00000529300.1_5'Flank|GPR68_ENST00000535815.1_Missense_Mutation_p.F359S			Q15743	OGR1_HUMAN	G protein-coupled receptor 68	359					cellular response to pH (GO:0071467)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of monocyte differentiation (GO:0045656)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of osteoclast development (GO:2001206)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(2)|endometrium(1)|kidney(1)|lung(2)|skin(1)|urinary_tract(1)	8		all_cancers(154;0.0555)		COAD - Colon adenocarcinoma(157;0.21)		GCCCGTGGGGAACCCGCCCGA	0.711													G|||	53	0.0105831	0.0393	0.0014	5008	,	,		13610	0.0		0.0	False		,,,				2504	0.0				p.F359S		Atlas-SNP	.											.	GPR68	32	.	0			c.T1076C						PASS	.	G	SER/PHE,SER/PHE	50,3832		0,50,1891	10.0	13.0	12.0		1076,1076	1.6	0.0	14	dbSNP_134	12	0,7436		0,0,3718	no	missense,missense	GPR68	NM_003485.3,NM_001177676.1	155,155	0,50,5609	GG,GA,AA		0.0,1.288,0.4418	benign,benign	359/366,359/366	91700319	50,11268	1941	3718	5659	SO:0001583	missense	8111	exon2			GTGGGGAACCCGC	U48405	CCDS9894.1, CCDS9894.2	14q31	2012-08-21				ENSG00000119714		"""GPCR / Class A : Orphans"""	4519	protein-coding gene	gene with protein product		601404				8661159	Standard	NM_001177676		Approved	OGR1	uc001xzg.3	Q15743		ENST00000531499.2:c.1076T>C	14.37:g.91700319A>G	ENSP00000434045:p.Phe359Ser	46.0	0.0	0		42.0	11.0	0.261905	NM_001177676	Q13334|Q4VBB4|Q6IX34	Missense_Mutation	SNP	ENST00000531499.2	37	CCDS9894.2	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	G	4.035	0.004003	0.07866	0.01288	0.0	ENSG00000119714	ENST00000531499;ENST00000238699;ENST00000535815	T;T;T	0.61040	0.14;0.15;0.14	4.46	1.59	0.23543	.	0.406139	0.19168	N	0.121014	T	0.11324	0.0276	N	0.02539	-0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.16719	-1.0393	10	0.07175	T	0.84	.	4.0511	0.09796	0.2953:0.1741:0.5306:0.0	.	359;359	Q6NWR5;Q15743	.;OGR1_HUMAN	S	359;369;359	ENSP00000434045:F359S;ENSP00000238699:F369S;ENSP00000440797:F359S	ENSP00000238699:F369S	F	-	2	0	GPR68	90770072	.	.	0.005000	0.12908	0.002000	0.02628	.	.	-0.069000	0.12931	-0.227000	0.12334	TTC	A|0.995;G|0.005	0.005	strong		0.711	GPR68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395245.2		
PXDNL	137902	hgsc.bcm.edu	37	8	52320786	52320786	+	Missense_Mutation	SNP	G	G	A	rs74731075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:52320786G>A	ENST00000356297.4	-	17	3498	c.3398C>T	c.(3397-3399)gCg>gTg	p.A1133V	PXDNL_ENST00000543296.1_Missense_Mutation_p.A1133V	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	1133					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				ATCCACGGCCGCAGAATAAGC	0.547													G|||	131	0.0261581	0.0946	0.0072	5008	,	,		14026	0.0		0.001	False		,,,				2504	0.0				p.A1133V		Atlas-SNP	.											.	PXDNL	414	.	0			c.C3398T						PASS	.	G	VAL/ALA	264,3518		11,242,1638	73.0	79.0	77.0		3398	1.3	0.0	8	dbSNP_131	77	5,8231		0,5,4113	yes	missense	PXDNL	NM_144651.4	64	11,247,5751	AA,AG,GG		0.0607,6.9804,2.2383	benign	1133/1464	52320786	269,11749	1891	4118	6009	SO:0001583	missense	137902	exon17			ACGGCCGCAGAAT		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.3398C>T	8.37:g.52320786G>A	ENSP00000348645:p.Ala1133Val	68.0	0.0	0		81.0	40.0	0.493827	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	51|51	0.023351648351648352|0.023351648351648352	48|48	0.0975609756097561|0.0975609756097561	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	G|G	0.006|0.006	-2.030686|-2.030686	0.00410|0.00410	0.069804|0.069804	6.07E-4|6.07E-4	ENSG00000147485|ENSG00000147485	ENST00000356297;ENST00000543296|ENST00000522933	T;T|.	0.69040|.	-0.37;-0.37|.	3.82|3.82	1.31|1.31	0.21738|0.21738	.|.	0.495534|.	0.16394|.	N|.	0.216355|.	T|T	0.00109|0.00109	0.0003|0.0003	N|N	0.00055|0.00055	-2.37|-2.37	0.25903|0.25903	N|N	0.983334|0.983334	B|.	0.11235|.	0.004|.	B|.	0.01281|.	0.0|.	T|T	0.35425|0.35425	-0.9789|-0.9789	10|5	0.02654|.	T|.	1|.	.|.	3.9194|3.9194	0.09237|0.09237	0.6521:0.2101:0.1378:0.0|0.6521:0.2101:0.1378:0.0	.|.	1133|.	A1KZ92|.	PXDNL_HUMAN|.	V|W	1133|252	ENSP00000348645:A1133V;ENSP00000444865:A1133V|.	ENSP00000348645:A1133V|.	A|R	-|-	2|1	0|2	PXDNL|PXDNL	52483339|52483339	1.000000|1.000000	0.71417|0.71417	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	6.058000|6.058000	0.71126|0.71126	-0.039000|-0.039000	0.13602|0.13602	-0.175000|-0.175000	0.13238|0.13238	GCG|CGG	G|0.973;A|0.027	0.027	strong		0.547	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
MAPK7	5598	hgsc.bcm.edu	37	17	19285392	19285392	+	Silent	SNP	G	G	A	rs2233079	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:19285392G>A	ENST00000308406.5	+	5	2162	c.1776G>A	c.(1774-1776)gcG>gcA	p.A592A	MAPK7_ENST00000395602.4_Silent_p.A592A|MAPK7_ENST00000571657.1_Intron|MAPK7_ENST00000395604.3_Silent_p.A592A|MFAP4_ENST00000574313.2_5'Flank|MAPK7_ENST00000299612.7_Silent_p.A453A	NM_139033.2	NP_620602.2	Q13164	MK07_HUMAN	mitogen-activated protein kinase 7	592	May not be required for kinase activity; required to stimulate MEF2C activity. {ECO:0000250}.|Pro-rich.				cAMP-mediated signaling (GO:0019933)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to transforming growth factor beta stimulus (GO:0071560)|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 cAMP catabolic process (GO:0030821)|negative regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051344)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NFAT protein import into nucleus (GO:0051534)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of response to cytokine stimulus (GO:0060761)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|regulation of angiogenesis (GO:0045765)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|mitogen-activated protein kinase binding (GO:0051019)			autonomic_ganglia(1)|central_nervous_system(4)|endometrium(5)|kidney(2)|large_intestine(4)|lung(9)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	30	all_cancers(12;2.87e-05)|all_epithelial(12;0.00114)|Hepatocellular(7;0.00345)|Breast(13;0.206)					ctgccccagcgccaacgccaa	0.657													G|||	165	0.0329473	0.118	0.013	5008	,	,		9722	0.0		0.0	False		,,,				2504	0.0				p.A592A		Atlas-SNP	.											.	MAPK7	72	.	0			c.G1776A						PASS	.	G	,,,	433,3955		29,375,1790	14.0	13.0	13.0		1776,1359,1776,1776	-8.4	0.0	17	dbSNP_98	13	9,8573		0,9,4282	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MAPK7	NM_002749.3,NM_139032.2,NM_139033.2,NM_139034.2	,,,	29,384,6072	AA,AG,GG		0.1049,9.8678,3.4079	,,,	592/817,453/678,592/817,592/817	19285392	442,12528	2194	4291	6485	SO:0001819	synonymous_variant	5598	exon5			CCCAGCGCCAACG	U25278	CCDS11206.1, CCDS11207.1	17p11.2	2011-06-09			ENSG00000166484	ENSG00000166484	2.7.11.24	"""Mitogen-activated protein kinase cascade / Kinases"""	6880	protein-coding gene	gene with protein product	"""BMK1 kinase"", ""extracellular-signal-regulated kinase 5"""	602521		PRKM7		10072598, 7759517	Standard	NM_139032		Approved	BMK1, ERK5	uc002gvp.3	Q13164	OTTHUMG00000059587	ENST00000308406.5:c.1776G>A	17.37:g.19285392G>A		144.0	0.0	0		200.0	114.0	0.57	NM_002749	Q16634|Q59F50|Q6QLU7|Q7L4P4|Q969G1|Q96G51	Silent	SNP	ENST00000308406.5	37	CCDS11206.1																																																																																			G|0.959;A|0.041	0.041	strong		0.657	MAPK7-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132506.1	NM_139033	
OR8J3	81168	hgsc.bcm.edu	37	11	55904422	55904422	+	Missense_Mutation	SNP	A	A	G	rs114758947	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55904422A>G	ENST00000301529.1	-	1	772	c.773T>C	c.(772-774)aTg>aCg	p.M258T		NM_001004064.1	NP_001004064.1	Q8NGG0	OR8J3_HUMAN	olfactory receptor, family 8, subfamily J, member 3	258						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(1)|lung(38)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	59	Esophageal squamous(21;0.00693)					CTGCAAATACATAAATAGCAT	0.428													A|||	88	0.0175719	0.0628	0.0058	5008	,	,		18131	0.0		0.001	False		,,,				2504	0.0				p.M258T		Atlas-SNP	.											.	OR8J3	112	.	0			c.T773C						PASS	.	A	THR/MET	235,4167	139.2+/-174.8	7,221,1973	138.0	133.0	135.0		773	2.1	0.5	11	dbSNP_132	135	2,8590	2.2+/-6.3	0,2,4294	yes	missense	OR8J3	NM_001004064.1	81	7,223,6267	GG,GA,AA		0.0233,5.3385,1.8239	probably-damaging	258/316	55904422	237,12757	2201	4296	6497	SO:0001583	missense	81168	exon1			AAATACATAAATA		CCDS31520.1	11q12.2	2012-08-09			ENSG00000167822	ENSG00000167822		"""GPCR / Class A : Olfactory receptors"""	15312	protein-coding gene	gene with protein product							Standard	NM_001004064		Approved		uc010riz.2	Q8NGG0	OTTHUMG00000166834	ENST00000301529.1:c.773T>C	11.37:g.55904422A>G	ENSP00000301529:p.Met258Thr	183.0	0.0	0		236.0	127.0	0.538136	NM_001004064	Q6IFB6|Q96RC2	Missense_Mutation	SNP	ENST00000301529.1	37	CCDS31520.1	41	0.018772893772893772	38	0.07723577235772358	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	A	7.537	0.659897	0.14645	0.053385	2.33E-4	ENSG00000167822	ENST00000301529	T	0.00164	8.64	3.27	2.11	0.27256	GPCR, rhodopsin-like superfamily (1);	0.136411	0.52532	D	0.000070	T	0.00039	0.0001	L	0.53561	1.675	0.09310	N	1	D	0.53619	0.961	P	0.62298	0.9	T	0.47169	-0.9138	10	0.72032	D	0.01	.	5.506	0.16854	0.6758:0.0:0.3242:0.0	.	258	Q8NGG0	OR8J3_HUMAN	T	258	ENSP00000301529:M258T	ENSP00000301529:M258T	M	-	2	0	OR8J3	55660998	0.000000	0.05858	0.453000	0.27007	0.065000	0.16274	-0.305000	0.08188	1.272000	0.44329	0.247000	0.18012	ATG	A|0.983;G|0.017	0.017	strong		0.428	OR8J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391542.1	NM_001004064	
GPR124	25960	hgsc.bcm.edu	37	8	37690615	37690615	+	Silent	SNP	G	G	A	rs61738775	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:37690615G>A	ENST00000412232.2	+	9	1198	c.1185G>A	c.(1183-1185)ccG>ccA	p.P395P	GPR124_ENST00000315215.7_Silent_p.P395P	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124	395					central nervous system development (GO:0007417)|endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuropeptide signaling pathway (GO:0007218)|positive regulation of endothelial cell migration (GO:0010595)|regulation of angiogenesis (GO:0045765)|regulation of chemotaxis (GO:0050920)|regulation of establishment of blood-brain barrier (GO:0090210)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(16)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			GGGGTGCCCCGGGCACCCGAG	0.682													G|||	321	0.0640974	0.2284	0.0159	5008	,	,		11914	0.005		0.002	False		,,,				2504	0.001				p.P395P		Atlas-SNP	.											.	GPR124	85	.	0			c.G1185A						PASS	.	G		846,3560	318.5+/-295.7	69,708,1426	41.0	47.0	45.0		1185	-10.2	0.3	8	dbSNP_129	45	8,8592	5.0+/-18.6	0,8,4292	no	coding-synonymous	GPR124	NM_032777.9		69,716,5718	AA,AG,GG		0.093,19.2011,6.5662		395/1339	37690615	854,12152	2203	4300	6503	SO:0001819	synonymous_variant	25960	exon9			TGCCCCGGGCACC	AB040964	CCDS6097.2	8p11.22	2014-08-08			ENSG00000020181	ENSG00000020181		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17849	protein-coding gene	gene with protein product	"""tumor endothelial marker 5"""	606823				11559528, 12565841	Standard	NM_032777		Approved	TEM5, DKFZp434C211, DKFZp434J0911, KIAA1531, FLJ14390	uc003xkj.3	Q96PE1	OTTHUMG00000156182	ENST00000412232.2:c.1185G>A	8.37:g.37690615G>A		14.0	0.0	0		17.0	15.0	0.882353	NM_032777	A6H8W3|D3DSW4|Q8N3R1|Q8TEM3|Q96KB2|Q9P1Z7|Q9UFY4	Silent	SNP	ENST00000412232.2	37	CCDS6097.2																																																																																			G|0.934;A|0.066	0.066	strong		0.682	GPR124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343331.2		
USP50	373509	hgsc.bcm.edu	37	15	50836846	50836846	+	Silent	SNP	G	G	C	rs114737323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:50836846G>C	ENST00000532404.1	-	2	359	c.186C>G	c.(184-186)ctC>ctG	p.L62L	USP50_ENST00000530218.1_Intron	NM_203494.4	NP_987090.2	Q70EL3	UBP50_HUMAN	ubiquitin specific peptidase 50	62	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|kidney(2)|large_intestine(4)|liver(1)|lung(5)	13				all cancers(107;0.000519)|GBM - Glioblastoma multiforme(94;0.00288)		AGATGCTGCAGAGACACTGTG	0.537													G|||	166	0.033147	0.121	0.0086	5008	,	,		16271	0.0		0.0	False		,,,				2504	0.0				p.L62L		Atlas-SNP	.											.	USP50	24	.	0			c.C186G						PASS	.	G		364,3704		20,324,1690	55.0	58.0	57.0		186	1.7	1.0	15	dbSNP_132	57	2,8376		0,2,4187	no	coding-synonymous	USP50	NM_203494.4		20,326,5877	CC,CG,GG		0.0239,8.9479,2.9407		62/335	50836846	366,12080	2034	4189	6223	SO:0001819	synonymous_variant	373509	exon2			GCTGCAGAGACAC	AI990110	CCDS53944.1	15q21.1	2008-02-05	2005-08-08			ENSG00000170236		"""Ubiquitin-specific peptidases"""	20079	protein-coding gene	gene with protein product			"""ubiquitin specific protease 50"""			12838346	Standard	NM_203494		Approved		uc021sky.1	Q70EL3		ENST00000532404.1:c.186C>G	15.37:g.50836846G>C		53.0	0.0	0		86.0	43.0	0.5	NM_203494	E9PP86	Silent	SNP	ENST00000532404.1	37	CCDS53944.1																																																																																			G|0.957;C|0.043	0.043	strong		0.537	USP50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395249.1		
PPFIBP1	8496	hgsc.bcm.edu	37	12	27829369	27829369	+	Silent	SNP	T	T	C	rs35150305	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:27829369T>C	ENST00000318304.8	+	18	1753	c.1470T>C	c.(1468-1470)gcT>gcC	p.A490A	PPFIBP1_ENST00000542629.1_Silent_p.A459A|PPFIBP1_ENST00000537927.1_Silent_p.A337A|PPFIBP1_ENST00000228425.6_Silent_p.A473A	NM_001198916.1|NM_177444.2	NP_001185845.1|NP_803193	Q86W92	LIPB1_HUMAN	PTPRF interacting protein, binding protein 1 (liprin beta 1)	490					cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)			PPFIBP1/ALK(3)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(13)|prostate(2)|skin(1)	32	Lung SC(9;0.0873)					AGGACAGAGCTCCGGCAGAAA	0.547													T|||	123	0.0245607	0.0915	0.0029	5008	,	,		17752	0.0		0.0	False		,,,				2504	0.0				p.A490A		Atlas-SNP	.											.	PPFIBP1	153	.	0			c.T1470C						PASS	.	T	,,,	340,4066	176.2+/-205.4	9,322,1872	61.0	63.0	62.0		1011,1377,1419,1470	-2.5	0.0	12	dbSNP_126	62	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PPFIBP1	NM_001198915.1,NM_001198916.1,NM_003622.3,NM_177444.2	,,,	9,325,6169	CC,CT,TT		0.0349,7.7167,2.6372	,,,	337/859,459/981,473/1006,490/1012	27829369	343,12663	2203	4300	6503	SO:0001819	synonymous_variant	8496	exon18			CAGAGCTCCGGCA	AF034802	CCDS8713.1, CCDS55812.1, CCDS55813.1, CCDS55814.1	12p12.1	2013-01-10						"""Sterile alpha motif (SAM) domain containing"""	9249	protein-coding gene	gene with protein product		603141				9624153, 11836260	Standard	NM_003622		Approved	L2, hSGT2, hSgt2p, SGT2	uc001ric.2	Q86W92		ENST00000318304.8:c.1470T>C	12.37:g.27829369T>C		93.0	0.0	0		130.0	71.0	0.546154	NM_177444	O75336|Q86X70|Q9NY03|Q9ULJ0	Silent	SNP	ENST00000318304.8	37	CCDS55812.1																																																																																			T|0.978;C|0.022	0.022	strong		0.547	PPFIBP1-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402877.1	NM_003622	
KIAA0895L	653319	hgsc.bcm.edu	37	16	67210855	67210855	+	Missense_Mutation	SNP	G	G	C	rs61733789	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67210855G>C	ENST00000290881.7	-	8	2201	c.1275C>G	c.(1273-1275)caC>caG	p.H425Q	KIAA0895L_ENST00000561621.1_3'UTR|KIAA0895L_ENST00000563831.2_5'UTR|KIAA0895L_ENST00000563902.1_Missense_Mutation_p.H425Q			Q68EN5	K895L_HUMAN	KIAA0895-like	425										breast(2)|endometrium(5)|kidney(2)|large_intestine(3)|lung(2)|prostate(2)|skin(1)	17						GGGGCCGCAGGTGGTCCACAT	0.627													G|||	334	0.0666933	0.1929	0.0086	5008	,	,		17791	0.003		0.003	False		,,,				2504	0.0685				p.H425Q		Atlas-SNP	.											.	KIAA0895L	32	.	0			c.C1275G						PASS	.	G	GLN/HIS	589,3435		38,513,1461	61.0	66.0	64.0		1275	-3.4	1.0	16	dbSNP_129	64	8,8370		0,8,4181	yes	missense	KIAA0895L	NM_001040715.1	24	38,521,5642	CC,CG,GG		0.0955,14.6372,4.8137	benign	425/472	67210855	597,11805	2012	4189	6201	SO:0001583	missense	653319	exon7			CCGCAGGTGGTCC	AK092303	CCDS42177.1	16q22.1	2008-11-27				ENSG00000196123			34408	protein-coding gene	gene with protein product							Standard	NM_001040715		Approved	LOC653319	uc002ert.3	Q68EN5		ENST00000290881.7:c.1275C>G	16.37:g.67210855G>C	ENSP00000290881:p.His425Gln	99.0	0.0	0		94.0	49.0	0.521277	NM_001040715	A2VCS8|Q8N3H9|Q8NAQ5|Q96IE5	Missense_Mutation	SNP	ENST00000290881.7	37	CCDS42177.1	101	0.04624542124542125	95	0.19308943089430894	4	0.011049723756906077	2	0.0034965034965034965	0	0.0	G	11.37	1.618724	0.28801	0.146372	9.55E-4	ENSG00000196123	ENST00000290881	.	.	.	4.59	-3.36	0.04913	.	0.520084	0.22311	N	0.061738	T	0.00012	0.0000	N	0.11560	0.145	0.43271	P	0.004773000000000027	B;B	0.10296	0.001;0.003	B;B	0.11329	0.006;0.005	T	0.23868	-1.0176	8	0.17369	T	0.5	-13.5417	1.6114	0.02694	0.2829:0.364:0.2227:0.1304	rs61733789	425;270	Q68EN5;Q68EN5-3	K895L_HUMAN;.	Q	425	.	ENSP00000290881:H425Q	H	-	3	2	KIAA0895L	65768356	0.060000	0.20803	0.971000	0.41717	0.993000	0.82548	-0.536000	0.06135	-0.345000	0.08325	0.555000	0.69702	CAC	G|0.923;C|0.077	0.077	strong		0.627	KIAA0895L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421193.4	NM_001040715	
BANK1	55024	hgsc.bcm.edu	37	4	102965016	102965016	+	Missense_Mutation	SNP	A	A	G	rs140337324		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:102965016A>G	ENST00000322953.4	+	11	2195	c.1921A>G	c.(1921-1923)Aga>Gga	p.R641G	BANK1_ENST00000444316.2_Missense_Mutation_p.R611G|BANK1_ENST00000508653.1_Missense_Mutation_p.R508G|BANK1_ENST00000504592.1_Missense_Mutation_p.R626G|BANK1_ENST00000428908.1_Missense_Mutation_p.R508G	NM_017935.4	NP_060405	Q8NDB2	BANK1_HUMAN	B-cell scaffold protein with ankyrin repeats 1	641					B cell activation (GO:0042113)					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)		AAAGACAGCCAGAAGACAATC	0.333													A|||	1	0.000199681	0.0008	0.0	5008	,	,		16410	0.0		0.0	False		,,,				2504	0.0				p.R641G		Atlas-SNP	.											.	BANK1	95	.	0			c.A1921G						PASS	.	A	GLY/ARG,GLY/ARG,GLY/ARG	7,4399	12.9+/-30.5	0,7,2196	130.0	137.0	135.0		1831,1522,1921	2.8	1.0	4	dbSNP_134	135	0,8598		0,0,4299	yes	missense,missense,missense	BANK1	NM_001083907.2,NM_001127507.2,NM_017935.4	125,125,125	0,7,6495	GG,GA,AA		0.0,0.1589,0.0538	probably-damaging,probably-damaging,probably-damaging	611/756,508/653,641/786	102965016	7,12997	2203	4299	6502	SO:0001583	missense	55024	exon11			ACAGCCAGAAGAC	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.1921A>G	4.37:g.102965016A>G	ENSP00000320509:p.Arg641Gly	56.0	0.0	0		60.0	26.0	0.433333	NM_017935	A8K7W8|B0F3S2|Q8N5K8|Q8NB56|Q8WYN5|Q9NWP2	Missense_Mutation	SNP	ENST00000322953.4	37	CCDS34038.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	15.88	2.962531	0.53400	0.001589	0.0	ENSG00000153064	ENST00000504592;ENST00000322953;ENST00000428908;ENST00000508653;ENST00000444316	T;T;T;T;T	0.56103	0.48;0.48;0.48;0.48;0.48	5.4	2.84	0.33178	.	0.152125	0.42172	D	0.000760	T	0.61739	0.2371	L	0.47716	1.5	0.27143	N	0.961604	P;D;D	0.89917	0.951;1.0;1.0	P;D;D	0.87578	0.631;0.998;0.998	T	0.53865	-0.8378	10	0.44086	T	0.13	.	9.7001	0.40180	0.6632:0.3368:0.0:0.0	.	508;641;626	Q8NDB2-4;Q8NDB2;Q8NDB2-2	.;BANK1_HUMAN;.	G	626;641;508;508;611	ENSP00000421443:R626G;ENSP00000320509:R641G;ENSP00000412748:R508G;ENSP00000422314:R508G;ENSP00000388817:R611G	ENSP00000320509:R641G	R	+	1	2	BANK1	103184039	0.998000	0.40836	0.999000	0.59377	0.930000	0.56654	0.952000	0.29149	0.311000	0.23014	0.402000	0.26972	AGA	A|0.999;G|0.001	0.001	strong		0.333	BANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363161.1	NM_017935	
NIM1K	167359	hgsc.bcm.edu	37	5	43277283	43277283	+	Silent	SNP	G	G	A	rs61734291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:43277283G>A	ENST00000512796.1	+	3	1916	c.417G>A	c.(415-417)gtG>gtA	p.V139V	NIM1_ENST00000326035.2_Silent_p.V139V			Q8IY84	NIM1_HUMAN		139	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein phosphorylation (GO:0006468)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)										TTTACGAAGTGGTGGAGACCC	0.507													A|||	201	0.0401358	0.1437	0.0159	5008	,	,		20135	0.0		0.0	False		,,,				2504	0.0				p.V139V		Atlas-SNP	.											.	.	.	.	0			c.G417A						PASS	.	A		468,3938	783.5+/-414.6	26,416,1761	103.0	98.0	100.0		417	-8.7	0.5	5	dbSNP_129	100	4,8596	819.2+/-406.8	0,4,4296	no	coding-synonymous	NIM1	NM_153361.2		26,420,6057	AA,AG,GG		0.0465,10.6219,3.6291		139/437	43277283	472,12534	2203	4300	6503	SO:0001819	synonymous_variant	0	exon3			CGAAGTGGTGGAG																												ENST00000512796.1:c.417G>A	5.37:g.43277283G>A		79.0	0.0	0		112.0	58.0	0.517857	NM_153361	B3KVM1	Silent	SNP	ENST00000512796.1	37	CCDS3943.1																																																																																			G|0.965;A|0.035	0.035	strong		0.507	NIM1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368017.1		
PSRC1	84722	hgsc.bcm.edu	37	1	109824361	109824361	+	Silent	SNP	A	A	C	rs11800211	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:109824361A>C	ENST00000438534.2	-	4	537	c.399T>G	c.(397-399)tcT>tcG	p.S133S	PSRC1_ENST00000369907.3_Silent_p.S133S|PSRC1_ENST00000369904.3_Silent_p.S133S|PSRC1_ENST00000409138.2_Silent_p.S133S|PSRC1_ENST00000369903.2_Silent_p.S133S|PSRC1_ENST00000409267.1_Silent_p.S133S|PSRC1_ENST00000369909.2_Silent_p.S133S	NM_001005290.3	NP_001005290.1	Q6PGN9	PSRC1_HUMAN	proline/serine-rich coiled-coil 1	133	4 X 4 AA repeats of P-X-X-P.				microtubule bundle formation (GO:0001578)|mitotic metaphase plate congression (GO:0007080)|negative regulation of cell growth (GO:0030308)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of mitotic spindle organization (GO:0060236)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)	microtubule binding (GO:0008017)			endometrium(1)|large_intestine(1)|lung(2)|prostate(2)|skin(1)	7		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)|Breast(1374;0.244)		Colorectal(144;0.0286)|Lung(183;0.0658)|COAD - Colon adenocarcinoma(174;0.112)|Epithelial(280;0.188)|all cancers(265;0.213)		TCCGCGTCAAAGAGTTCACAG	0.627													A|||	250	0.0499201	0.1831	0.0101	5008	,	,		18059	0.0		0.001	False		,,,				2504	0.0				p.S133S		Atlas-SNP	.											.	PSRC1	12	.	0			c.T399G						PASS	.	A	,,	768,3638	311.9+/-292.3	61,646,1496	59.0	62.0	61.0		399,399,399	0.7	0.9	1	dbSNP_120	61	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous,coding-synonymous,coding-synonymous	PSRC1	NM_001005290.3,NM_001032291.2,NM_032636.7	,,	61,654,5788	CC,CA,AA		0.093,17.4308,5.9665	,,	133/311,133/334,133/334	109824361	776,12230	2203	4300	6503	SO:0001819	synonymous_variant	84722	exon4			CGTCAAAGAGTTC		CCDS797.1, CCDS30791.1	1p13.3	2008-02-05			ENSG00000134222	ENSG00000134222			24472	protein-coding gene	gene with protein product	"""differential display and activated by p53"""	613126				12427559, 10618717	Standard	NM_001032291		Approved	DDA3	uc001dxd.3	Q6PGN9	OTTHUMG00000012000	ENST00000438534.2:c.399T>G	1.37:g.109824361A>C		126.0	0.0	0		146.0	83.0	0.568493	NM_001032291	Q5T2Z3|Q6ZTI8|Q71MG3|Q9BV77	Silent	SNP	ENST00000438534.2	37																																																																																				A|0.938;C|0.062	0.062	strong		0.627	PSRC1-202	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000335567.3	NM_032636	
KLHL26	55295	hgsc.bcm.edu	37	19	18778879	18778879	+	Silent	SNP	C	C	T	rs79044993	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18778879C>T	ENST00000300976.4	+	3	762	c.672C>T	c.(670-672)atC>atT	p.I224I	KLHL26_ENST00000599006.1_Intron	NM_018316.1	NP_060786.1	Q53HC5	KLH26_HUMAN	kelch-like family member 26	224	BACK.									breast(1)|central_nervous_system(1)|kidney(1)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						GTGCCGAGATCGACCTGTTCC	0.677													C|||	49	0.00978435	0.034	0.0043	5008	,	,		14950	0.0		0.001	False		,,,				2504	0.0				p.I224I		Atlas-SNP	.											.	KLHL26	43	.	0			c.C672T						PASS	.	C		121,4285	89.2+/-127.9	1,119,2083	38.0	38.0	38.0		672	-8.3	0.9	19	dbSNP_131	38	4,8592	3.7+/-12.6	0,4,4294	no	coding-synonymous	KLHL26	NM_018316.1		1,123,6377	TT,TC,CC		0.0465,2.7463,0.9614		224/616	18778879	125,12877	2203	4298	6501	SO:0001819	synonymous_variant	55295	exon3			CGAGATCGACCTG		CCDS12384.1	19p13.11	2013-10-15	2013-02-22		ENSG00000167487	ENSG00000167487		"""Kelch-like"", ""BTB/POZ domain containing"""	25623	protein-coding gene	gene with protein product			"""kelch-like 26 (Drosophila)"""				Standard	XM_006722785		Approved		uc002njz.1	Q53HC5	OTTHUMG00000183114	ENST00000300976.4:c.672C>T	19.37:g.18778879C>T		41.0	0.0	0		71.0	32.0	0.450704	NM_018316	Q8TAP0|Q9NUX3	Silent	SNP	ENST00000300976.4	37	CCDS12384.1																																																																																			C|0.988;T|0.012	0.012	strong		0.677	KLHL26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465145.1	NM_018316	
ALPPL2	251	hgsc.bcm.edu	37	2	233271852	233271852	+	Silent	SNP	C	C	T	rs61730280	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:233271852C>T	ENST00000295453.3	+	2	205	c.153C>T	c.(151-153)gcC>gcT	p.A51A		NM_031313.2	NP_112603.2	P10696	PPBN_HUMAN	alkaline phosphatase, placental-like 2	51					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|large_intestine(1)|liver(2)|lung(6)|skin(1)	13		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)	Amifostine(DB01143)	CACAGACAGCCGCCAAGAACC	0.672													c|||	45	0.00898562	0.034	0.0	5008	,	,		15470	0.0		0.0	False		,,,				2504	0.0				p.A51A		Atlas-SNP	.											.	ALPPL2	36	.	0			c.C153T						PASS	.	C		143,4263	100.7+/-139.4	0,143,2060	67.0	81.0	76.0		153	-2.5	0.2	2	dbSNP_129	76	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ALPPL2	NM_031313.2		0,145,6358	TT,TC,CC		0.0233,3.2456,1.1149		51/533	233271852	145,12861	2203	4300	6503	SO:0001819	synonymous_variant	251	exon2			GACAGCCGCCAAG	J04948	CCDS2491.1	2q37	2008-05-20			ENSG00000163286	ENSG00000163286			441	protein-coding gene	gene with protein product		171810					Standard	NM_031313		Approved		uc002vss.4	P10696	OTTHUMG00000133257	ENST00000295453.3:c.153C>T	2.37:g.233271852C>T		93.0	0.0	0		116.0	54.0	0.465517	NM_031313	A8KAF2|Q16727|Q53S81|Q96CM1	Silent	SNP	ENST00000295453.3	37	CCDS2491.1																																																																																			C|0.990;T|0.010	0.010	strong		0.672	ALPPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257034.2	NM_031313	
ZNF175	7728	hgsc.bcm.edu	37	19	52090671	52090671	+	Missense_Mutation	SNP	T	T	A	rs60097262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52090671T>A	ENST00000262259.2	+	5	1445	c.1087T>A	c.(1087-1089)Tat>Aat	p.Y363N	ZNF175_ENST00000436511.2_Intron	NM_007147.2	NP_009078.1	Q9Y473	ZN175_HUMAN	zinc finger protein 175	363			Y -> N (in dbSNP:rs60097262).		defense response to virus (GO:0051607)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	24		all_neural(266;0.0299)		GBM - Glioblastoma multiforme(134;0.000426)|OV - Ovarian serous cystadenocarcinoma(262;0.0257)		AAAGAAGCCCTATAAATGCCA	0.398													T|||	100	0.0199681	0.0711	0.0086	5008	,	,		22349	0.0		0.0	False		,,,				2504	0.0				p.Y363N		Atlas-SNP	.											.	ZNF175	65	.	0			c.T1087A						PASS	.	T	ASN/TYR	232,4174	138.4+/-174.2	5,222,1976	105.0	109.0	108.0		1087	0.1	1.0	19	dbSNP_129	108	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ZNF175	NM_007147.2	143	5,223,6275	AA,AT,TT		0.0116,5.2655,1.7915	benign	363/712	52090671	233,12773	2203	4300	6503	SO:0001583	missense	7728	exon5			AAGCCCTATAAAT	D50419	CCDS12837.1	19q13.4	2013-01-08			ENSG00000105497	ENSG00000105497		"""Zinc fingers, C2H2-type"", ""-"""	12964	protein-coding gene	gene with protein product		601139				8838321	Standard	NM_007147		Approved	OTK18	uc002pxb.3	Q9Y473	OTTHUMG00000167771	ENST00000262259.2:c.1087T>A	19.37:g.52090671T>A	ENSP00000262259:p.Tyr363Asn	99.0	0.0	0		130.0	56.0	0.430769	NM_007147	A8K9H2	Missense_Mutation	SNP	ENST00000262259.2	37	CCDS12837.1	30	0.013736263736263736	29	0.05894308943089431	1	0.0027624309392265192	0	0.0	0	0.0	T	10.98	1.503898	0.26949	0.052655	1.16E-4	ENSG00000105497	ENST00000262259	T	0.25749	1.78	2.3	0.113	0.14631	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03520	0.0101	M	0.89030	3	0.80722	D	1	P	0.41041	0.736	B	0.37304	0.246	T	0.02437	-1.1159	9	0.87932	D	0	.	4.9985	0.14253	0.0:0.4369:0.0:0.5631	rs60097262;rs61736481	363	Q9Y473	ZN175_HUMAN	N	363	ENSP00000262259:Y363N	ENSP00000262259:Y363N	Y	+	1	0	ZNF175	56782483	0.001000	0.12720	0.972000	0.41901	0.872000	0.50106	1.063000	0.30567	0.020000	0.15106	0.460000	0.39030	TAT	T|0.983;A|0.017	0.017	strong		0.398	ZNF175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396205.1	NM_007147	
OR2B2	81697	hgsc.bcm.edu	37	6	27879093	27879093	+	Silent	SNP	G	G	A	rs73392698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:27879093G>A	ENST00000303324.2	-	1	1081	c.1005C>T	c.(1003-1005)tcC>tcT	p.S335S		NM_033057.2	NP_149046.2	Q9GZK3	OR2B2_HUMAN	olfactory receptor, family 2, subfamily B, member 2	335						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(4)|large_intestine(5)|lung(10)|prostate(1)|urinary_tract(1)	22						GACAACTTGCGGAGAAGTTAG	0.318													G|||	86	0.0171725	0.0582	0.0101	5008	,	,		18973	0.0		0.002	False		,,,				2504	0.0				p.S335S		Atlas-SNP	.											.	OR2B2	54	.	0			c.C1005T						PASS	.	G		226,4180	133.3+/-169.7	3,220,1980	81.0	84.0	83.0		1005	-2.2	0.0	6	dbSNP_130	83	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous	OR2B2	NM_033057.2		3,225,6275	AA,AG,GG		0.0581,5.1294,1.7761		335/358	27879093	231,12775	2203	4300	6503	SO:0001819	synonymous_variant	81697	exon1			ACTTGCGGAGAAG	Z98744	CCDS4641.1	6p22.3-p21.3	2014-02-19	2002-02-28		ENSG00000168131	ENSG00000168131		"""GPCR / Class A : Olfactory receptors"""	13966	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily B, member 9"""	OR2B9			Standard	NM_033057		Approved	hs6M1-10, OR6-1, OR2B2Q	uc011dkw.2	Q9GZK3	OTTHUMG00000014495	ENST00000303324.2:c.1005C>T	6.37:g.27879093G>A		59.0	0.0	0		55.0	31.0	0.563636	NM_033057	B2RNH2|Q9GZL2|Q9Y299	Silent	SNP	ENST00000303324.2	37	CCDS4641.1																																																																																			G|0.984;A|0.016	0.016	strong		0.318	OR2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040163.1		
PGLYRP2	114770	hgsc.bcm.edu	37	19	15580694	15580694	+	Missense_Mutation	SNP	G	G	A	rs61734899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15580694G>A	ENST00000340880.4	-	4	1870	c.1390C>T	c.(1390-1392)Cac>Tac	p.H464Y	PGLYRP2_ENST00000292609.4_Missense_Mutation_p.H464Y	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	464					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptide amidation (GO:0001519)|peptidoglycan catabolic process (GO:0009253)|regulation of inflammatory response (GO:0050727)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(2)|skin(3)|stomach(2)|urinary_tract(1)	28						CCCACCCAGTGCCAGCCGCGT	0.716													G|||	124	0.0247604	0.0484	0.0058	5008	,	,		13687	0.006		0.008	False		,,,				2504	0.0429				p.H464Y		Atlas-SNP	.											.	PGLYRP2	116	.	0			c.C1390T						PASS	.	G	TYR/HIS	161,4189		2,157,2016	11.0	15.0	14.0		1390	2.9	1.0	19	dbSNP_129	14	65,8451		0,65,4193	yes	missense	PGLYRP2	NM_052890.3	83	2,222,6209	AA,AG,GG		0.7633,3.7011,1.7566	benign	464/577	15580694	226,12640	2175	4258	6433	SO:0001583	missense	114770	exon4			CCCAGTGCCAGCC	AY358156	CCDS12330.2	19p13.12	2010-04-27			ENSG00000161031	ENSG00000161031	3.5.1.28		30013	protein-coding gene	gene with protein product	"""peptidoglycan recognition protein L precursor"", ""peptidoglycan recognition protein-like"", ""N-acetylmuramoyl-L-alanine amidase"""	608199				11461926, 12669421, 14506276	Standard	NM_052890		Approved	PGRP-L, PGLYRPL, TAGL-like, tagL, tagL-alpha, tagl-beta, PGRPL	uc002nbf.4	Q96PD5	OTTHUMG00000150690	ENST00000340880.4:c.1390C>T	19.37:g.15580694G>A	ENSP00000345968:p.His464Tyr	71.0	0.0	0		61.0	24.0	0.393443	NM_052890	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Missense_Mutation	SNP	ENST00000340880.4	37	CCDS12330.2	34	0.015567765567765568	21	0.042682926829268296	3	0.008287292817679558	2	0.0034965034965034965	8	0.010554089709762533	G	12.80	2.046263	0.36085	0.037011	0.007633	ENSG00000161031	ENST00000340880;ENST00000292609	T;T	0.17213	2.29;2.29	5.04	2.91	0.33838	Peptidoglycan recognition protein family domain, metazoa/bacteria (1);N-acetylmuramoyl-L-alanine amidase domain (4);	0.380248	0.27554	N	0.018848	T	0.03564	0.0102	M	0.66378	2.025	0.35512	D	0.80071	B;B	0.09022	0.001;0.002	B;B	0.13407	0.008;0.009	T	0.08249	-1.0731	10	0.35671	T	0.21	-13.9263	4.8686	0.13620	0.1811:0.0:0.6507:0.1682	.	464;464	Q96PD5-2;Q96PD5	.;PGRP2_HUMAN	Y	464	ENSP00000345968:H464Y;ENSP00000292609:H464Y	ENSP00000292609:H464Y	H	-	1	0	PGLYRP2	15441694	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	0.700000	0.25601	0.540000	0.28808	-0.448000	0.05591	CAC	G|0.983;A|0.017	0.017	strong		0.716	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890	
SLC4A11	83959	hgsc.bcm.edu	37	20	3209254	3209254	+	Silent	SNP	G	G	A	rs139086376	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:3209254G>A	ENST00000380056.3	-	17	2387	c.2340C>T	c.(2338-2340)ccC>ccT	p.P780P	SLC4A11_ENST00000488544.1_5'Flank|SLC4A11_ENST00000380059.3_Silent_p.P807P|SLC4A11_ENST00000539553.2_Silent_p.P764P	NM_032034.3	NP_114423.1	Q8NBS3	S4A11_HUMAN	solute carrier family 4, sodium borate transporter, member 11	780	Membrane (bicarbonate transporter).				bicarbonate transport (GO:0015701)|borate transmembrane transport (GO:0035445)|borate transport (GO:0046713)|cellular cation homeostasis (GO:0030003)|fluid transport (GO:0042044)|proton transport (GO:0015992)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	bicarbonate transmembrane transporter activity (GO:0015106)|borate transmembrane transporter activity (GO:0046715)|hydrogen ion channel activity (GO:0015252)|inorganic anion exchanger activity (GO:0005452)|protein dimerization activity (GO:0046983)|sodium channel activity (GO:0005272)|symporter activity (GO:0015293)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(4)|soft_tissue(1)|urinary_tract(1)	40						GCACGGGCTTGGGGATCCACT	0.652													G|||	31	0.0061901	0.0219	0.0029	5008	,	,		17235	0.0		0.0	False		,,,				2504	0.0				p.P807P	NSCLC(190;922 2139 10266 10292 38692)	Atlas-SNP	.											.	SLC4A11	188	.	0			c.C2421T						PASS	.	G	,,	78,4328	65.8+/-103.3	0,78,2125	75.0	69.0	71.0		2292,2421,2340	4.0	1.0	20	dbSNP_134	71	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC4A11	NM_001174089.1,NM_001174090.1,NM_032034.3	,,	0,79,6424	AA,AG,GG		0.0116,1.7703,0.6074	,,	764/876,807/919,780/892	3209254	79,12927	2203	4300	6503	SO:0001819	synonymous_variant	83959	exon18			GGGCTTGGGGATC	AF336127	CCDS13052.1, CCDS54445.1, CCDS54446.1	20p13	2014-02-14	2007-08-03		ENSG00000088836	ENSG00000088836		"""Solute carriers"""	16438	protein-coding gene	gene with protein product		610206	"""corneal endothelial dystrophy 2 (autosomal recessive)"", ""solute carrier family 4, sodium bicarbonate transporter-like, member 11"", ""corneal dystrophy and perceptive deafness 1"""	CHED2, CDPD1		10843999, 11302728, 16767101	Standard	NM_001174089		Approved	dJ794I6.2, BTR1, NaBC1, FECD4	uc010zqe.2	Q8NBS3	OTTHUMG00000031740	ENST00000380056.3:c.2340C>T	20.37:g.3209254G>A		184.0	0.0	0		153.0	72.0	0.470588	NM_001174090	B4DKC8|B4DKX9|G3V1M3|Q2TB62|Q2TB63|Q9BXF4|Q9NTW9	Silent	SNP	ENST00000380056.3	37	CCDS13052.1																																																																																			G|0.994;A|0.006	0.006	strong		0.652	SLC4A11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077728.1		
PRMT9	90826	hgsc.bcm.edu	37	4	148575601	148575601	+	Missense_Mutation	SNP	T	T	C	rs17023638	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:148575601T>C	ENST00000322396.6	-	9	1689	c.1447A>G	c.(1447-1449)Agt>Ggt	p.S483G	PRMT10_ENST00000541232.1_Missense_Mutation_p.S370G|TMEM184C_ENST00000508208.1_Intron	NM_138364.2	NP_612373.2	Q6P2P2	ANM9_HUMAN		483			S -> G (in dbSNP:rs17023638).			cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28						TGGGTAAAACTTTTTGCAACA	0.403													T|||	127	0.0253594	0.0938	0.0043	5008	,	,		19860	0.0		0.0	False		,,,				2504	0.0				p.S483G		Atlas-SNP	.											.	PRMT10	68	.	0			c.A1447G						PASS	.	T	GLY/SER	301,4105	161.8+/-193.9	10,281,1912	108.0	108.0	108.0		1447	0.4	0.4	4	dbSNP_123	108	1,8599	1.2+/-3.3	0,1,4299	yes	missense	PRMT10	NM_138364.2	56	10,282,6211	CC,CT,TT		0.0116,6.8316,2.322	benign	483/846	148575601	302,12704	2203	4300	6503	SO:0001583	missense	90826	exon9			TAAAACTTTTTGC																												ENST00000322396.6:c.1447A>G	4.37:g.148575601T>C	ENSP00000314396:p.Ser483Gly	68.0	0.0	0		102.0	43.0	0.421569	NM_138364	A8KA39|B3KU92|Q6ZR58|Q8N383|Q9BT55|Q9NT98	Missense_Mutation	SNP	ENST00000322396.6	37	CCDS3771.1	64	0.029304029304029304	64	0.13008130081300814	0	0.0	0	0.0	0	0.0	T	10.31	1.315040	0.23908	0.068316	1.16E-4	ENSG00000164169	ENST00000322396;ENST00000541232	T;T	0.45668	0.89;0.89	6.04	0.437	0.16555	.	0.391208	0.33792	N	0.004547	T	0.00241	0.0007	L	0.31294	0.92	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.15150	-1.0447	9	0.13853	T	0.58	-20.9041	5.4198	0.16394	0.1195:0.2119:0.0:0.6686	rs17023638;rs17023638	483	Q6P2P2	ANM10_HUMAN	G	483;370	ENSP00000314396:S483G;ENSP00000439508:S370G	ENSP00000314396:S483G	S	-	1	0	PRMT10	148795051	0.002000	0.14202	0.389000	0.26208	0.971000	0.66376	0.093000	0.15086	0.116000	0.18110	0.459000	0.35465	AGT	T|0.963;C|0.037	0.037	strong		0.403	PRMT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364650.1		
CCDC14	64770	hgsc.bcm.edu	37	3	123633665	123633665	+	Silent	SNP	T	T	C	rs13319634	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:123633665T>C	ENST00000488653.2	-	13	2913	c.2823A>G	c.(2821-2823)agA>agG	p.R941R	CCDC14_ENST00000485727.1_Silent_p.R741R|CCDC14_ENST00000433542.2_Silent_p.R900R|CCDC14_ENST00000489746.1_Silent_p.R741R|CCDC14_ENST00000483247.1_5'UTR|CCDC14_ENST00000310351.4_Silent_p.R781R			Q49A88	CCD14_HUMAN	coiled-coil domain containing 14	941					substantia nigra development (GO:0021762)	centrosome (GO:0005813)				NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)	21		Lung NSC(201;0.0371)|Prostate(884;0.0405)|Myeloproliferative disorder(1037;0.205)		Lung(219;0.00942)|GBM - Glioblastoma multiforme(114;0.159)		ACTTCTGGAGTCTAGCTATGT	0.403													T|||	124	0.0247604	0.09	0.0072	5008	,	,		477	0.0		0.0	False		,,,				2504	0.0				p.R900R		Atlas-SNP	.											.	CCDC14	97	.	0			c.A2700G						PASS	.	T		317,4089		15,287,1901	20.0	20.0	20.0		2700	-3.3	0.8	3	dbSNP_121	20	7,8589		0,7,4291	no	coding-synonymous	CCDC14	NM_022757.4		15,294,6192	CC,CT,TT		0.0814,7.1947,2.4919		900/913	123633665	324,12678	2203	4298	6501	SO:0001819	synonymous_variant	64770	exon12			CTGGAGTCTAGCT	AL122079	CCDS3025.2	3q21.1	2014-03-20			ENSG00000175455	ENSG00000175455			25766	protein-coding gene	gene with protein product						12477932	Standard	NM_022757		Approved	FLJ12892, DKFZp434L1050	uc010hrt.3	Q49A88	OTTHUMG00000153005	ENST00000488653.2:c.2823A>G	3.37:g.123633665T>C		167.0	0.0	0		197.0	82.0	0.416244	NM_022757	B7Z2T2|B8ZZ41|B8ZZ58|D3DN98|Q7Z3N3|Q86T30|Q8IWF8|Q8WUJ8|Q96K47|Q9H9A3|Q9UFH0	Silent	SNP	ENST00000488653.2	37																																																																																				T|0.970;C|0.030	0.030	strong		0.403	CCDC14-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_022757	
OR10H5	284433	hgsc.bcm.edu	37	19	15904914	15904914	+	Missense_Mutation	SNP	C	C	T	rs150835909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15904914C>T	ENST00000308940.8	+	1	154	c.56C>T	c.(55-57)gCc>gTc	p.A19V		NM_001004466.1	NP_001004466.1	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H, member 5	19						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(9)|ovary(1)	20						GGCTTCTCTGCCTTCCCCCAC	0.582													.|||	34	0.00678914	0.025	0.0014	5008	,	,		19279	0.0		0.0	False		,,,				2504	0.0				p.A19V		Atlas-SNP	.											.	OR10H5	49	.	0			c.C56T						PASS	.	C	VAL/ALA	159,4247		6,147,2050	252.0	210.0	225.0		56	-1.8	0.2	19	dbSNP_134	225	2,8598		0,2,4298	no	missense	OR10H5	NM_001004466.1	64	6,149,6348	TT,TC,CC		0.0233,3.6087,1.2379	benign	19/316	15904914	161,12845	2203	4300	6503	SO:0001583	missense	284433	exon1			TCTCTGCCTTCCC	AC011537	CCDS32940.1	19p13.12	2013-09-24			ENSG00000172519	ENSG00000172519		"""GPCR / Class A : Olfactory receptors"""	15389	protein-coding gene	gene with protein product							Standard	NM_001004466		Approved		uc010xos.2	Q8NGA6	OTTHUMG00000182284	ENST00000308940.8:c.56C>T	19.37:g.15904914C>T	ENSP00000310704:p.Ala19Val	146.0	0.0	0		179.0	86.0	0.480447	NM_001004466	Q6IFJ0|Q96R60	Missense_Mutation	SNP	ENST00000308940.8	37	CCDS32940.1	11	0.005036630036630037	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	0	0.0	.	4.228	0.041170	0.08196	0.036087	2.33E-4	ENSG00000172519	ENST00000308940	T	0.00330	8.08	3.45	-1.79	0.07932	.	0.432269	0.19564	N	0.111245	T	0.00039	0.0001	N	0.05199	-0.095	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.27673	-1.0067	10	0.41790	T	0.15	.	6.7765	0.23622	0.4443:0.2643:0.2914:0.0	.	19	Q8NGA6	O10H5_HUMAN	V	19	ENSP00000310704:A19V	ENSP00000310704:A19V	A	+	2	0	OR10H5	15765914	0.000000	0.05858	0.153000	0.22517	0.262000	0.26303	-1.472000	0.02341	-0.540000	0.06265	0.573000	0.79308	GCC	C|0.990;T|0.010	0.010	strong		0.582	OR10H5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460363.1		
NOC2L	26155	hgsc.bcm.edu	37	1	889421	889421	+	Missense_Mutation	SNP	C	C	T	rs3828050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:889421C>T	ENST00000327044.6	-	7	789	c.740G>A	c.(739-741)cGt>cAt	p.R247H	NOC2L_ENST00000487214.1_5'Flank	NM_015658.3	NP_056473	Q9Y3T9	NOC2L_HUMAN	nucleolar complex associated 2 homolog (S. cerevisiae)	247					apoptotic process (GO:0006915)|cellular response to UV (GO:0034644)|chromatin assembly (GO:0031497)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of histone acetylation (GO:0035067)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleolus to nucleoplasm transport (GO:0032066)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|nucleosome binding (GO:0031491)|poly(A) RNA binding (GO:0044822)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)	p.R247L(1)		endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	16	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;1.86e-38)|OV - Ovarian serous cystadenocarcinoma(86;6.08e-23)|Colorectal(212;0.000161)|COAD - Colon adenocarcinoma(227;0.000194)|BRCA - Breast invasive adenocarcinoma(365;0.000475)|Kidney(185;0.00231)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0344)|Lung(427;0.2)		GATGTCCACACGAAGCTTCCC	0.647													C|||	2	0.000399361	0.0	0.0	5008	,	,		16641	0.002		0.0	False		,,,				2504	0.0				p.R247H		Atlas-SNP	.											NOC2L,NS,carcinoma,0,1	NOC2L	42	1	1	Substitution - Missense(1)	lung(1)	c.G740A						PASS	.						87.0	84.0	85.0					1																	889421		2203	4300	6503	SO:0001583	missense	26155	exon7			TCCACACGAAGCT	AL050019	CCDS3.1	1p36.33	2014-06-12			ENSG00000188976	ENSG00000188976			24517	protein-coding gene	gene with protein product	"""novel INHAT repressor"", ""protein phosphatase 1, regulatory subunit 12"""	610770					Standard	NM_015658		Approved	DKFZP564C186, NET7, NET15, NIR, PPP1R112	uc001abz.4	Q9Y3T9	OTTHUMG00000040720	ENST00000327044.6:c.740G>A	1.37:g.889421C>T	ENSP00000317992:p.Arg247His	288.0	1.0	0.00347222		275.0	143.0	0.52	NM_015658	Q5SVA3|Q9BTN6	Missense_Mutation	SNP	ENST00000327044.6	37	CCDS3.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	C	11.92	1.783028	0.31593	.	.	ENSG00000188976	ENST00000327044	T	0.67698	-0.28	4.11	4.11	0.48088	Armadillo-type fold (1);	0.152310	0.44688	D	0.000440	T	0.62732	0.2452	L	0.53249	1.67	0.51767	D	0.99993	B;B;B	0.22146	0.065;0.065;0.031	B;B;B	0.18561	0.022;0.022;0.01	T	0.65730	-0.6097	10	0.66056	D	0.02	-17.7817	15.5423	0.76062	0.0:1.0:0.0:0.0	rs3828050	247;247;14	B3KNC3;Q9Y3T9;Q9H9J5	.;NOC2L_HUMAN;.	H	247	ENSP00000317992:R247H	ENSP00000317992:R247H	R	-	2	0	NOC2L	879284	0.999000	0.42202	0.993000	0.49108	0.561000	0.35649	4.286000	0.58995	2.135000	0.66039	0.306000	0.20318	CGT	C|0.999;T|0.001	0.001	strong		0.647	NOC2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097869.1	NM_015658	
AGBL4	84871	hgsc.bcm.edu	37	1	49005351	49005351	+	Missense_Mutation	SNP	C	C	T	rs60977321	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:49005351C>T	ENST00000371839.1	-	12	1443	c.1327G>A	c.(1327-1329)Gtg>Atg	p.V443M	AGBL4_ENST00000334103.7_Missense_Mutation_p.V176M	NM_032785.3	NP_116174.3	Q5VU57	CBPC6_HUMAN	ATP/GTP binding protein-like 4	443			V -> M (in dbSNP:rs60977321).		C-terminal protein deglutamylation (GO:0035609)|protein side chain deglutamylation (GO:0035610)	cytosol (GO:0005829)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|stomach(1)	15				Colorectal(2;0.00349)|COAD - Colon adenocarcinoma(2;0.0037)		TTTTCAACCACGGGGTTCAGC	0.512													C|||	322	0.0642971	0.233	0.0144	5008	,	,		17535	0.0		0.004	False		,,,				2504	0.0				p.V443M		Atlas-SNP	.											.	AGBL4	54	.	0			c.G1327A						PASS	.	C	MET/VAL	287,1097		31,225,436	134.0	111.0	118.0		1327	-2.2	1.0	1	dbSNP_129	118	4,3178		0,4,1587	yes	missense	AGBL4	NM_032785.3	21	31,229,2023	TT,TC,CC		0.1257,20.737,6.3732	benign	443/504	49005351	291,4275	692	1591	2283	SO:0001583	missense	84871	exon12			CAACCACGGGGTT	AK027348	CCDS44137.1	1p33	2014-06-23			ENSG00000186094	ENSG00000186094			25892	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 6"""					21074048	Standard	NM_032785		Approved	FLJ14442, CCP6	uc001cru.2	Q5VU57	OTTHUMG00000007793	ENST00000371839.1:c.1327G>A	1.37:g.49005351C>T	ENSP00000360905:p.Val443Met	109.0	0.0	0		129.0	57.0	0.44186	NM_032785	B3KT26|B4DG37	Missense_Mutation	SNP	ENST00000371839.1	37	CCDS44137.1	103	0.04716117216117216	100	0.2032520325203252	3	0.008287292817679558	0	0.0	0	0.0	C	4.542	0.100554	0.08731	0.20737	0.001257	ENSG00000186094	ENST00000371839;ENST00000411952;ENST00000334103	T;T	0.44881	2.53;0.91	4.65	-2.18	0.07037	.	2.280690	0.01719	N	0.028181	T	0.00012	0.0000	N	0.08118	0	0.52099	P	5.3999999999998494E-5	B;B;B	0.19583	0.0;0.002;0.037	B;B;B	0.08055	0.0;0.001;0.003	T	0.12863	-1.0531	9	0.25751	T	0.34	-0.0068	1.605	0.02682	0.2303:0.0994:0.4078:0.2624	rs60977321	455;176;443	Q5VU57-2;B4DGK1;Q5VU57	.;.;CBPC6_HUMAN	M	443;437;176	ENSP00000360905:V443M;ENSP00000335516:V176M	ENSP00000335516:V176M	V	-	1	0	AGBL4	48777938	0.020000	0.18652	0.992000	0.48379	0.242000	0.25591	-1.494000	0.02296	-0.194000	0.10399	-1.708000	0.00717	GTG	C|0.961;T|0.039	0.039	strong		0.512	AGBL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021346.4	NM_032785	
NIPBL	25836	hgsc.bcm.edu	37	5	36985751	36985751	+	Silent	SNP	A	A	G	rs293756	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:36985751A>G	ENST00000282516.8	+	10	2968	c.2469A>G	c.(2467-2469)aaA>aaG	p.K823K	NIPBL_ENST00000448238.2_Silent_p.K823K|NIPBL_ENST00000504430.1_3'UTR	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	823					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			ATAAACAAAAATCAGATGACA	0.443													A|||	183	0.0365415	0.1354	0.0058	5008	,	,		19980	0.0		0.0	False		,,,				2504	0.0				p.K823K		Atlas-SNP	.											.	NIPBL	513	.	0			c.A2469G						PASS	.	A	,	506,3900	231.0+/-245.0	27,452,1724	68.0	67.0	67.0		2469,2469	-0.5	1.0	5	dbSNP_79	67	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	NIPBL	NM_015384.4,NM_133433.3	,	27,453,6023	GG,GA,AA		0.0116,11.4843,3.8982	,	823/2698,823/2805	36985751	507,12499	2203	4300	6503	SO:0001819	synonymous_variant	25836	exon10			ACAAAAATCAGAT	AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"""sister chromatid cohesion 2 homolog (yeast)"""	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.2469A>G	5.37:g.36985751A>G		169.0	0.0	0		185.0	101.0	0.545946	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Silent	SNP	ENST00000282516.8	37	CCDS3920.1																																																																																			A|0.961;G|0.039	0.039	strong		0.443	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384	
C5orf42	65250	hgsc.bcm.edu	37	5	37115116	37115116	+	Missense_Mutation	SNP	C	C	T	rs7702892	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37115116C>T	ENST00000508244.1	-	49	9277	c.9184G>A	c.(9184-9186)Gga>Aga	p.G3062R	C5orf42_ENST00000274258.7_Missense_Mutation_p.G1960R|C5orf42_ENST00000425232.2_Missense_Mutation_p.G3062R			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	3062			G -> R (in dbSNP:rs7702892).			integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			GCTTTGGCTCCACCAGCTTTT	0.363													C|||	124	0.0247604	0.0908	0.0058	5008	,	,		18889	0.0		0.0	False		,,,				2504	0.0				p.G3062R		Atlas-SNP	.											C5orf42_ENST00000425232,bladder,carcinoma,+1,2	C5orf42	422	2	0			c.G9184A						PASS	.	C	ARG/GLY	340,4066	175.5+/-204.9	13,314,1876	101.0	90.0	93.0		9184	2.0	0.0	5	dbSNP_116	93	2,8598	2.2+/-6.3	0,2,4298	yes	missense	C5orf42	NM_023073.3	125	13,316,6174	TT,TC,CC		0.0233,7.7167,2.6296	benign	3062/3198	37115116	342,12664	2203	4300	6503	SO:0001583	missense	65250	exon50			TGGCTCCACCAGC		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.9184G>A	5.37:g.37115116C>T	ENSP00000421690:p.Gly3062Arg	64.0	0.0	0		74.0	39.0	0.527027	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	45	0.020604395604395604	43	0.08739837398373984	2	0.0055248618784530384	0	0.0	0	0.0	C	13.98	2.398422	0.42512	0.077167	2.33E-4	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429	T;T;T;T	0.22945	1.94;1.94;1.93;1.93	3.78	1.97	0.26223	.	1.267940	0.05991	U	0.646004	T	0.00608	0.0020	N	0.22421	0.69	0.09310	N	1	B;B	0.12013	0.005;0.005	B;B	0.15052	0.012;0.01	T	0.26224	-1.0109	10	0.25751	T	0.34	.	6.7291	0.23373	0.0:0.7655:0.0:0.2345	rs7702892;rs52808859;rs7702892	3062;1960	E9PH94;Q9H799	.;CE042_HUMAN	R	3062;3062;1960;2128	ENSP00000421690:G3062R;ENSP00000389014:G3062R;ENSP00000274258:G1960R;ENSP00000424223:G2128R	ENSP00000274258:G1960R	G	-	1	0	C5orf42	37150873	0.000000	0.05858	0.013000	0.15412	0.825000	0.46686	0.020000	0.13466	0.353000	0.24079	-0.137000	0.14449	GGA	C|0.970;T|0.030	0.030	strong		0.363	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073	
DPH6	89978	hgsc.bcm.edu	37	15	35830665	35830665	+	Missense_Mutation	SNP	C	C	T	rs34907758	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:35830665C>T	ENST00000256538.4	-	3	148	c.122G>A	c.(121-123)gGg>gAg	p.G41E	DPH6_ENST00000440392.2_Missense_Mutation_p.G41E	NM_080650.3	NP_542381.1	Q7L8W6	DPH6_HUMAN	diphthamine biosynthesis 6	41			G -> E (in dbSNP:rs34907758).		peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)		ATP binding (GO:0005524)|diphthine-ammonia ligase activity (GO:0017178)										TTCATCAGACCCCACTGCAAC	0.433													C|||	152	0.0303514	0.1097	0.0101	5008	,	,		17189	0.0		0.0	False		,,,				2504	0.0				p.G41E		Atlas-SNP	.											.	ATPBD4	30	.	0			c.G122A						PASS	.	C	GLU/GLY,GLU/GLY	311,4091	161.4+/-193.6	13,285,1903	73.0	62.0	66.0		122,122	2.9	1.0	15	dbSNP_126	66	5,8589	3.7+/-12.6	0,5,4292	no	missense,missense	ATPBD4	NM_001141972.1,NM_080650.3	98,98	13,290,6195	TT,TC,CC		0.0582,7.065,2.4315	benign,benign	41/166,41/268	35830665	316,12680	2201	4297	6498	SO:0001583	missense	89978	exon3			TCAGACCCCACTG		CCDS10043.1, CCDS45213.1	15q14	2013-06-19	2013-06-19	2013-05-02	ENSG00000134146	ENSG00000134146	6.3.1.14		30543	protein-coding gene	gene with protein product	"""diphthine--ammonia ligase"""		"""ATP binding domain 4"", ""DPH6 homolog (S. cerevisiae)"""	ATPBD4		23169644, 23468660	Standard	NM_080650		Approved	MGC14798		Q7L8W6	OTTHUMG00000129759	ENST00000256538.4:c.122G>A	15.37:g.35830665C>T	ENSP00000256538:p.Gly41Glu	117.0	0.0	0		103.0	49.0	0.475728	NM_001141972	B3KWG1|Q96HJ6	Missense_Mutation	SNP	ENST00000256538.4	37	CCDS10043.1	50	0.022893772893772892	44	0.08943089430894309	6	0.016574585635359115	0	0.0	0	0.0	C	8.198	0.797575	0.16327	0.07065	5.82E-4	ENSG00000134146	ENST00000256538;ENST00000440392	T;T	0.42900	1.54;0.96	5.8	2.88	0.33553	Domain of unknown function DUF71, ATP-binding domain (2);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.676327	0.14999	N	0.286217	T	0.00524	0.0017	N	0.02708	-0.52	0.22851	N	0.998659	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.20638	-1.0269	10	0.02654	T	1	-0.1968	7.3765	0.26831	0.0:0.5948:0.0:0.4052	rs34907758	41;41	B3KWG1;Q7L8W6	.;ATBD4_HUMAN	E	41	ENSP00000256538:G41E;ENSP00000406976:G41E	ENSP00000256538:G41E	G	-	2	0	ATPBD4	33617957	0.000000	0.05858	0.998000	0.56505	0.692000	0.40212	-0.022000	0.12480	0.362000	0.24319	-0.142000	0.14014	GGG	C|0.972;T|0.028	0.028	strong		0.433	DPH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251973.1	NM_080650	
OR7D2	162998	hgsc.bcm.edu	37	19	9297196	9297196	+	Missense_Mutation	SNP	G	G	A	rs61739064	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9297196G>A	ENST00000344248.2	+	1	918	c.739G>A	c.(739-741)Gtc>Atc	p.V247I		NM_175883.2	NP_787079.1	Q96RA2	OR7D2_HUMAN	olfactory receptor, family 7, subfamily D, member 2	247					regulation of transcription, DNA-templated (GO:0006355)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(2)|upper_aerodigestive_tract(2)	20						TCACCTCTCCGTCGTTTCTTT	0.468													G|||	64	0.0127796	0.0484	0.0	5008	,	,		17847	0.0		0.0	False		,,,				2504	0.0				p.V247I		Atlas-SNP	.											.	OR7D2	55	.	0			c.G739A						PASS	.	G	ILE/VAL	210,4196	127.8+/-164.7	2,206,1995	91.0	76.0	81.0		739	2.2	0.0	19	dbSNP_129	81	1,8599	1.2+/-3.3	0,1,4299	yes	missense	OR7D2	NM_175883.2	29	2,207,6294	AA,AG,GG		0.0116,4.7662,1.6223	benign	247/313	9297196	211,12795	2203	4300	6503	SO:0001583	missense	162998	exon1			CTCTCCGTCGTTT	AK095468	CCDS32900.1	19p13.2	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	8378	protein-coding gene	gene with protein product							Standard	NM_175883		Approved	OR19-4, HTPCRH03, FLJ38149	uc002mkz.1	Q96RA2		ENST00000344248.2:c.739G>A	19.37:g.9297196G>A	ENSP00000345563:p.Val247Ile	66.0	0.0	0		70.0	33.0	0.471429	NM_175883	Q6IFJ7|Q8N133	Missense_Mutation	SNP	ENST00000344248.2	37	CCDS32900.1	23	0.010531135531135532	23	0.046747967479674794	0	0.0	0	0.0	0	0.0	G	9.760	1.169781	0.21621	0.047662	1.16E-4	ENSG00000188000	ENST00000344248	T	0.00253	8.43	2.2	2.2	0.27929	GPCR, rhodopsin-like superfamily (1);	0.000000	0.35970	U	0.002872	T	0.00039	0.0001	M	0.78801	2.425	0.09310	N	1	P	0.40197	0.706	B	0.38378	0.272	T	0.38693	-0.9649	10	0.59425	D	0.04	.	11.9676	0.53044	0.0:0.0:1.0:0.0	rs61739064	247	Q96RA2	OR7D2_HUMAN	I	247	ENSP00000345563:V247I	ENSP00000345563:V247I	V	+	1	0	OR7D2	9158196	0.163000	0.22920	0.047000	0.18901	0.020000	0.10135	2.174000	0.42482	1.578000	0.49821	0.505000	0.49811	GTC	G|0.983;A|0.017	0.017	strong		0.468	OR7D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449002.1		
UPP2	151531	hgsc.bcm.edu	37	2	158977928	158977928	+	Silent	SNP	A	A	C	rs10186677	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:158977928A>C	ENST00000005756.4	+	5	656	c.462A>C	c.(460-462)gcA>gcC	p.A154A	UPP2_ENST00000460456.1_Intron|UPP2_ENST00000605860.1_Silent_p.A211A|UPP2_ENST00000409859.4_Silent_p.A211A	NM_173355.3	NP_775491.1	O95045	UPP2_HUMAN	uridine phosphorylase 2	154					nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|nucleotide catabolic process (GO:0009166)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)|uridine metabolic process (GO:0046108)	cytosol (GO:0005829)|type III intermediate filament (GO:0045098)	uridine phosphorylase activity (GO:0004850)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31					Fluorouracil(DB00544)	CAGGGATTGCACCAGGGACTG	0.383													A|||	84	0.0167732	0.0605	0.0058	5008	,	,		18783	0.0		0.0	False		,,,				2504	0.0				p.A211A		Atlas-SNP	.											.	UPP2	60	.	0			c.A633C						PASS	.	A	,	210,4196	129.0+/-165.8	5,200,1998	201.0	207.0	205.0		633,462	-4.8	0.0	2	dbSNP_119	205	4,8594	3.7+/-12.6	0,4,4295	no	coding-synonymous,coding-synonymous	UPP2	NM_001135098.1,NM_173355.3	,	5,204,6293	CC,CA,AA		0.0465,4.7662,1.6456	,	211/375,154/318	158977928	214,12790	2203	4299	6502	SO:0001819	synonymous_variant	151531	exon7			GATTGCACCAGGG	AY225131	CCDS2207.1, CCDS46435.1	2q24.2	2008-02-05			ENSG00000007001	ENSG00000007001			23061	protein-coding gene	gene with protein product						12849978	Standard	NM_173355		Approved	UPASE2, UP2, UDRPASE2	uc002tzo.3	O95045	OTTHUMG00000131969	ENST00000005756.4:c.462A>C	2.37:g.158977928A>C		382.0	0.0	0		303.0	185.0	0.610561	NM_001135098	B3KV87	Silent	SNP	ENST00000005756.4	37	CCDS2207.1																																																																																			A|0.980;C|0.020	0.020	strong		0.383	UPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254929.2	NM_173355	
IGSF5	150084	hgsc.bcm.edu	37	21	41142958	41142958	+	Silent	SNP	C	C	T	rs61737685	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:41142958C>T	ENST00000380588.4	+	4	637	c.534C>T	c.(532-534)ctC>ctT	p.L178L	IGSF5_ENST00000479378.1_3'UTR	NM_001080444.1	NP_001073913.1	Q9NSI5	IGSF5_HUMAN	immunoglobulin superfamily, member 5	178	Ig-like V-type 2.				single organismal cell-cell adhesion (GO:0016337)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(7)|skin(2)|stomach(1)	23		Prostate(19;5.35e-06)				CCTGGGAGCTCGGTCTCCTGG	0.517													C|||	230	0.0459265	0.1664	0.0144	5008	,	,		15063	0.0		0.0	False		,,,				2504	0.0				p.L178L		Atlas-SNP	.											.	IGSF5	62	.	0			c.C534T						PASS	.	C		580,3826	258.3+/-262.4	35,510,1658	68.0	66.0	66.0		534	-2.5	0.0	21	dbSNP_129	66	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	IGSF5	NM_001080444.1		35,516,5952	TT,TC,CC		0.0698,13.1639,4.5056		178/408	41142958	586,12420	2203	4300	6503	SO:0001819	synonymous_variant	150084	exon4			GGAGCTCGGTCTC		CCDS33562.1	21q22.2	2013-01-29			ENSG00000183067	ENSG00000183067		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5952	protein-coding gene	gene with protein product	"""junctional adhesion molecule 4"""	610638					Standard	NM_001080444		Approved	JAM4	uc002yyo.3	Q9NSI5	OTTHUMG00000086724	ENST00000380588.4:c.534C>T	21.37:g.41142958C>T		47.0	0.0	0		53.0	30.0	0.566038	NM_001080444		Silent	SNP	ENST00000380588.4	37	CCDS33562.1																																																																																			C|0.957;T|0.043	0.043	strong		0.517	IGSF5-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195005.1		
INMT	11185	hgsc.bcm.edu	37	7	30795419	30795419	+	Silent	SNP	C	C	T	rs35221354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:30795419C>T	ENST00000013222.5	+	3	760	c.744C>T	c.(742-744)gcC>gcT	p.A248A	INMT_ENST00000484180.1_3'UTR|INMT_ENST00000409539.1_Silent_p.A247A|INMT-FAM188B_ENST00000458257.1_Intron	NM_001199219.1|NM_006774.4	NP_001186148.1|NP_006765.4	O95050	INMT_HUMAN	indolethylamine N-methyltransferase	248					amine metabolic process (GO:0009308)|methylation (GO:0032259)|response to toxic substance (GO:0009636)	cytosol (GO:0005829)	amine N-methyltransferase activity (GO:0030748)|thioether S-methyltransferase activity (GO:0004790)			kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|stomach(1)	23						CCAATGCTGCCAACAATGGGG	0.592													C|||	272	0.0543131	0.1921	0.0259	5008	,	,		20160	0.0		0.0	False		,,,				2504	0.0				p.A248A		Atlas-SNP	.											INMT,NS,carcinoma,+1,1	INMT	38	1	0			c.C744T						PASS	.	C	,	710,3696	297.3+/-284.7	54,602,1547	99.0	96.0	97.0		741,744	3.4	0.1	7	dbSNP_126	97	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous,coding-synonymous	INMT	NM_001199219.1,NM_006774.4	,	54,609,5840	TT,TC,CC		0.0814,16.1144,5.5128	,	247/263,248/264	30795419	717,12289	2203	4300	6503	SO:0001819	synonymous_variant	11185	exon3			TGCTGCCAACAAT		CCDS5430.1, CCDS56479.1	7p14.3	2011-08-30			ENSG00000241644	ENSG00000241644	2.1.1.49		6069	protein-coding gene	gene with protein product		604854				10552930	Standard	NM_001199219		Approved		uc003tbs.1	O95050	OTTHUMG00000167163	ENST00000013222.5:c.744C>T	7.37:g.30795419C>T		78.0	0.0	0		71.0	30.0	0.422535	NM_006774	B8ZZ69|Q3KP49|Q9P1Y2|Q9UBY4|Q9UHQ0	Silent	SNP	ENST00000013222.5	37	CCDS5430.1																																																																																			C|0.947;T|0.053	0.053	strong		0.592	INMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214993.3	NM_006774	
PCDHA10	56139	hgsc.bcm.edu	37	5	140237094	140237094	+	Silent	SNP	C	C	G	rs60872775	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140237094C>G	ENST00000307360.5	+	1	1461	c.1461C>G	c.(1459-1461)gcC>gcG	p.A487A	PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA10_ENST00000506939.2_Silent_p.A487A|PCDHA4_ENST00000512229.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	487	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGAGAACGCCCTGGTGTCCT	0.662													.|||	56	0.0111821	0.0416	0.0014	5008	,	,		16717	0.0		0.0	False		,,,				2504	0.0				p.A487A		Atlas-SNP	.											.	PCDHA10	358	.	0			c.C1461G						PASS	.	C	,,,,,,,,,,,,,	141,4251	805.5+/-415.8	11,119,2066	76.0	78.0	78.0		,1461,,,,,,,,,,,1461,1461	1.8	1.0	5	dbSNP_129	78	0,8546		0,0,4273	no	intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,coding-synonymous	PCDHA9,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031859.1,NM_031860.1	,,,,,,,,,,,,,	11,119,6339	GG,GC,CC		0.0,3.2104,1.0898	,,,,,,,,,,,,,	,487/949,,,,,,,,,,,487/845,487/686	140237094	141,12797	2196	4273	6469	SO:0001819	synonymous_variant	56139	exon1			GAACGCCCTGGTG	AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"""Cadherins / Protocadherins : Clustered"""	8664	other	complex locus constituent	"""KIAA0345-like 4"", ""ortholog to mouse CNR8"""	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.1461C>G	5.37:g.140237094C>G		365.0	0.0	0		309.0	157.0	0.508091	NM_031859	A1L493|O75280|Q9NRU2	Silent	SNP	ENST00000307360.5	37	CCDS54921.1																																																																																			C|0.989;G|0.011	0.011	strong		0.662	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901	
SYCP2	10388	hgsc.bcm.edu	37	20	58496438	58496438	+	Missense_Mutation	SNP	A	A	G	rs61730337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:58496438A>G	ENST00000357552.3	-	4	320	c.95T>C	c.(94-96)aTt>aCt	p.I32T	SYCP2_ENST00000476314.1_5'UTR|SYCP2_ENST00000371001.2_Missense_Mutation_p.I32T			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	32					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			ACAAATATCAATTTGCAAAAG	0.308													A|||	98	0.0195687	0.0711	0.0043	5008	,	,		15338	0.0		0.001	False		,,,				2504	0.0				p.I32T		Atlas-SNP	.											.	SYCP2	204	.	0			c.T95C						PASS	.	A	THR/ILE	248,4154	140.0+/-175.5	7,234,1960	55.0	52.0	53.0		95	1.3	1.0	20	dbSNP_129	53	2,8578	2.2+/-6.3	0,2,4288	yes	missense	SYCP2	NM_014258.2	89	7,236,6248	GG,GA,AA		0.0233,5.6338,1.9257	possibly-damaging	32/1531	58496438	250,12732	2201	4290	6491	SO:0001583	missense	10388	exon3			ATATCAATTTGCA	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.95T>C	20.37:g.58496438A>G	ENSP00000350162:p.Ile32Thr	165.0	0.0	0		193.0	101.0	0.523316	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Missense_Mutation	SNP	ENST00000357552.3	37	CCDS13482.1	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	A	0.025	-1.384165	0.01194	0.056338	2.33E-4	ENSG00000196074	ENST00000371001;ENST00000357552;ENST00000446834;ENST00000425931	T;T;T;T	0.39997	2.62;2.62;2.37;1.05	5.04	1.3	0.21679	.	0.654897	0.15121	N	0.279380	T	0.01421	0.0046	N	0.22421	0.69	0.21553	N	0.999649	B	0.20052	0.041	B	0.14578	0.011	T	0.10706	-1.0618	10	0.12766	T	0.61	-9.6108	1.5416	0.02557	0.3441:0.1539:0.3533:0.1487	.	32	Q9BX26	SYCP2_HUMAN	T	32;32;32;31	ENSP00000360040:I32T;ENSP00000350162:I32T;ENSP00000402456:I32T;ENSP00000399300:I31T	ENSP00000350162:I32T	I	-	2	0	SYCP2	57929833	0.892000	0.30473	0.999000	0.59377	0.442000	0.32017	0.388000	0.20735	0.357000	0.24183	-0.538000	0.04264	ATT	A|0.979;G|0.021	0.021	strong		0.308	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258	
UBTF	7343	hgsc.bcm.edu	37	17	42284951	42284951	+	Silent	SNP	A	A	G	rs113823176	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:42284951A>G	ENST00000302904.4	-	20	2532	c.2040T>C	c.(2038-2040)gaT>gaC	p.D680D	UBTF_ENST00000526094.1_Silent_p.D643D|UBTF_ENST00000527034.1_Missense_Mutation_p.M642T|UBTF_ENST00000533177.1_Silent_p.D643D|CTB-175E5.7_ENST00000586560.1_RNA|UBTF_ENST00000393606.3_Silent_p.D643D|UBTF_ENST00000529383.1_Silent_p.D680D|UBTF_ENST00000436088.1_Silent_p.D680D|UBTF_ENST00000343638.5_Silent_p.D643D			P17480	UBF1_HUMAN	upstream binding transcription factor, RNA polymerase I	680	Asp/Glu/Ser-rich (acidic).				chromatin silencing at rDNA (GO:0000183)|gene expression (GO:0010467)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|regulation of transcription from RNA polymerase I promoter (GO:0006356)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(1)|large_intestine(9)|lung(10)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00765)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.114)		cctcttcatcatcctcctcGG	0.587													A|||	59	0.0117812	0.0431	0.0029	5008	,	,		17778	0.0		0.0	False		,,,				2504	0.0				p.D680D		Atlas-SNP	.											.	UBTF	65	.	0			c.T2040C						PASS	.	A	,,	105,4301	82.4+/-120.9	1,103,2099	156.0	104.0	122.0		1929,1929,2040	-5.1	0.5	17	dbSNP_132	122	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	UBTF	NM_001076683.1,NM_001076684.2,NM_014233.3	,,	1,103,6399	GG,GA,AA		0.0,2.3831,0.8073	,,	643/728,643/728,680/765	42284951	105,12901	2203	4300	6503	SO:0001819	synonymous_variant	7343	exon20			TTCATCATCCTCC	BC042297	CCDS11480.1, CCDS42346.1	17q21.31	2014-03-25			ENSG00000108312	ENSG00000108312			12511	protein-coding gene	gene with protein product		600673				9126496	Standard	NM_001076683		Approved	UBF, NOR-90, UBF1, UBF2	uc010czs.3	P17480	OTTHUMG00000167585	ENST00000302904.4:c.2040T>C	17.37:g.42284951A>G		177.0	0.0	0		223.0	118.0	0.529148	NM_014233	A8K6R8	Silent	SNP	ENST00000302904.4	37	CCDS11480.1	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	A	10.81	1.455714	0.26161	0.023831	0.0	ENSG00000108312	ENST00000527034	D	0.98280	-4.84	5.05	-5.13	0.02884	.	.	.	.	.	D	0.84840	0.5561	.	.	.	0.80722	D	1	.	.	.	.	.	.	D	0.84157	0.0426	6	0.33940	T	0.23	-7.4078	5.2771	0.15655	0.2064:0.218:0.469:0.1066	.	.	.	.	T	642	ENSP00000431539:M642T	ENSP00000431539:M642T	M	-	2	0	UBTF	39640477	0.000000	0.05858	0.464000	0.27143	0.990000	0.78478	-2.032000	0.01426	-1.382000	0.02109	0.402000	0.26972	ATG	A|0.990;G|0.010	0.010	strong		0.587	UBTF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395205.1	NM_014233	
SPIDR	23514	hgsc.bcm.edu	37	8	48511729	48511729	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:48511729C>T	ENST00000297423.4	+	10	1899	c.1515C>T	c.(1513-1515)agC>agT	p.S505S	SPIDR_ENST00000521214.1_3'UTR|SPIDR_ENST00000518074.1_Silent_p.S445S|SPIDR_ENST00000541342.1_Silent_p.S435S	NM_001080394.2|NM_001282916.1	NP_001073863.1|NP_001269845.1	Q14159	SPIDR_HUMAN	scaffolding protein involved in DNA repair	505					cellular response to camptothecin (GO:0072757)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydroxyurea (GO:0072711)|cellular response to ionizing radiation (GO:0071479)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of double-strand break repair (GO:2000781)|positive regulation of protein complex assembly (GO:0031334)|regulation of double-strand break repair via homologous recombination (GO:0010569)|regulation of establishment of protein localization to chromosome (GO:0070202)	nuclear chromosome (GO:0000228)											AGGGGGCCAGCTCAGGACACA	0.592																																					p.S505S		Atlas-SNP	.											.	KIAA0146	64	.	0			c.C1515T						PASS	.						29.0	36.0	33.0					8																	48511729		2051	4183	6234	SO:0001819	synonymous_variant	23514	exon10			GGCCAGCTCAGGA	AK055680	CCDS43737.1, CCDS64890.1, CCDS64891.1	8q11.21	2013-07-02	2013-07-02	2013-07-02	ENSG00000164808	ENSG00000164808			28971	protein-coding gene	gene with protein product		615384	"""KIAA0146"""	KIAA0146		8590280, 23509288	Standard	XM_005251189		Approved		uc003xqd.3	Q14159	OTTHUMG00000164176	ENST00000297423.4:c.1515C>T	8.37:g.48511729C>T		102.0	0.0	0		101.0	41.0	0.405941	NM_001080394	B4DFV2|B4E0Y6|Q96BI5	Silent	SNP	ENST00000297423.4	37	CCDS43737.1	.	.	.	.	.	.	.	.	.	.	C	3.747	-0.052466	0.07362	.	.	ENSG00000164808	ENST00000519401	.	.	.	4.68	0.555	0.17247	.	.	.	.	.	T	0.23846	0.0577	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.24764	-1.0151	4	.	.	.	.	3.972	0.09457	0.1661:0.488:0.0:0.3459	.	.	.	.	V	187	.	.	A	+	2	0	KIAA0146	48674282	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-0.473000	0.06615	0.134000	0.18681	0.585000	0.79938	GCT	.	.	none		0.592	SPIDR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377611.1	NM_001080394	
ZSCAN25	221785	hgsc.bcm.edu	37	7	99226981	99226981	+	Missense_Mutation	SNP	C	C	G	rs10239632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99226981C>G	ENST00000394152.2	+	8	1300	c.973C>G	c.(973-975)Cct>Gct	p.P325A	ZSCAN25_ENST00000466948.1_Intron|ZSCAN25_ENST00000262941.6_Missense_Mutation_p.P253A|ZSCAN25_ENST00000334715.3_Missense_Mutation_p.P325A	NM_145115.2	NP_660090.2	Q6NSZ9	ZSC25_HUMAN	zinc finger and SCAN domain containing 25	325			P -> A (in dbSNP:rs10239632).		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)										GCCTGGGCTTCCTCCTCCCCA	0.627													C|||	185	0.0369409	0.1263	0.0216	5008	,	,		17584	0.0		0.003	False		,,,				2504	0.0				p.P325A		Atlas-SNP	.											.	.	.	.	0			c.C973G						PASS	.	C	ALA/PRO	449,3957	211.8+/-231.9	28,393,1782	59.0	54.0	56.0		973	2.7	0.0	7	dbSNP_119	56	7,8593	3.7+/-12.6	0,7,4293	yes	missense	ZNF498	NM_145115.2	27	28,400,6075	GG,GC,CC		0.0814,10.1906,3.5061	benign	325/545	99226981	456,12550	2203	4300	6503	SO:0001583	missense	221785	exon8			GGGCTTCCTCCTC	AK057030	CCDS5671.2	7q22.1	2013-01-09	2013-01-09	2013-01-09	ENSG00000197037	ENSG00000197037		"""-"", ""Zinc fingers, C2H2-type"""	21961	protein-coding gene	gene with protein product			"""zinc finger protein 498"""	ZNF498		11179890	Standard	XM_005250194		Approved	FLJ32468	uc003url.1	Q6NSZ9	OTTHUMG00000074055	ENST00000394152.2:c.973C>G	7.37:g.99226981C>G	ENSP00000377708:p.Pro325Ala	52.0	0.0	0		58.0	35.0	0.603448	NM_145115	A4D290|D6W5T5|Q14C82|Q14C99|Q5EBM9|Q6DJZ0|Q6N032|Q6ZML3	Missense_Mutation	SNP	ENST00000394152.2	37	CCDS5671.2	82	0.037545787545787544	71	0.1443089430894309	10	0.027624309392265192	0	0.0	1	0.0013192612137203166	C	0.010	-1.757120	0.00657	0.101906	8.14E-4	ENSG00000197037	ENST00000394152;ENST00000334715;ENST00000262941	T;T;T	0.08807	3.06;3.06;3.05	4.82	2.66	0.31614	.	0.503847	0.16909	N	0.194576	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.42616	-0.9441	9	0.09590	T	0.72	-0.7741	2.5036	0.04639	0.2459:0.4907:0.1618:0.1016	rs10239632;rs10239632	253;325	Q6NSZ9-2;Q6NSZ9	.;ZN498_HUMAN	A	325;325;253	ENSP00000377708:P325A;ENSP00000334800:P325A;ENSP00000262941:P253A	ENSP00000262941:P253A	P	+	1	0	ZNF498	99064917	0.000000	0.05858	0.006000	0.13384	0.006000	0.05464	0.695000	0.25527	1.140000	0.42260	-0.502000	0.04539	CCT	C|0.966;G|0.034	0.034	strong		0.627	ZSCAN25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157203.4	NM_145115	
BMX	660	hgsc.bcm.edu	37	X	15555339	15555339	+	Silent	SNP	G	G	A	rs376617024		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:15555339G>A	ENST00000357607.2	+	14	1493	c.1305G>A	c.(1303-1305)aaG>aaA	p.K435K	BMX_ENST00000348343.6_Silent_p.K435K|BMX_ENST00000342014.6_Silent_p.K435K			P51813	BMX_HUMAN	BMX non-receptor tyrosine kinase	435	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to stress (GO:0006950)|signal transduction (GO:0007165)	cytosol (GO:0005829)|ruffle membrane (GO:0032587)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|signal transducer activity (GO:0004871)			breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(14)|ovary(2)|urinary_tract(3)	30	Hepatocellular(33;0.183)					AGCTGGGCAAGTGGAAGGGGC	0.473													g|||	2	0.000529801	0.0	0.0	3775	,	,		13134	0.002		0.0	False		,,,				2504	0.0				p.K435K		Atlas-SNP	.											.	BMX	73	.	0			c.G1305A						PASS	.	G	,	1,3834		0,1,1631,571	187.0	167.0	174.0		1305,1305	3.5	1.0	X		174	0,6728		0,0,2428,1872	no	coding-synonymous,coding-synonymous	BMX	NM_001721.6,NM_203281.2	,	0,1,4059,2443	AA,AG,GG,G		0.0,0.0261,0.0095	,	435/676,435/676	15555339	1,10562	2203	4300	6503	SO:0001819	synonymous_variant	660	exon14			GGGCAAGTGGAAG	AF045459	CCDS14168.1	Xp22.2	2013-05-14			ENSG00000102010	ENSG00000102010		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	1079	protein-coding gene	gene with protein product	"""BTK-like on X chromosome"""	300101				7970727	Standard	NM_203281		Approved	ETK, PSCTK3	uc004cwx.4	P51813	OTTHUMG00000021180	ENST00000357607.2:c.1305G>A	X.37:g.15555339G>A		177.0	0.0	0		217.0	100.0	0.460829	NM_001721	A6NIH9|O60564|Q12871	Silent	SNP	ENST00000357607.2	37	CCDS14168.1																																																																																			.	.	weak		0.473	BMX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055877.1	NM_001721	
GPR110	266977	hgsc.bcm.edu	37	6	46977894	46977894	+	Missense_Mutation	SNP	C	C	T	rs115292676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:46977894C>T	ENST00000371253.2	-	11	1492	c.1277G>A	c.(1276-1278)cGg>cAg	p.R426Q	GPR110_ENST00000449332.2_5'UTR|GPR110_ENST00000283297.5_Missense_Mutation_p.R229Q	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	426					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)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	29						AATGAATTTCCGAGAAAAATT	0.428													C|||	59	0.0117812	0.0431	0.0014	5008	,	,		19836	0.0		0.0	False		,,,				2504	0.001				p.R426Q		Atlas-SNP	.											GPR110,colon,carcinoma,-1,2	GPR110	102	2	0			c.G1277A						PASS	.	C	GLN/ARG	135,4271	97.1+/-135.8	4,127,2072	80.0	77.0	78.0		1277	1.6	0.1	6	dbSNP_132	78	7,8593	5.7+/-21.5	0,7,4293	yes	missense	GPR110	NM_153840.2	43	4,134,6365	TT,TC,CC		0.0814,3.064,1.0918	possibly-damaging	426/911	46977894	142,12864	2203	4300	6503	SO:0001583	missense	266977	exon11			AATTTCCGAGAAA	AB083618	CCDS4920.1, CCDS34471.1	6p21.1	2014-08-08			ENSG00000153292	ENSG00000153292		"""-"", ""GPCR / Class B : Orphans"""	18990	protein-coding gene	gene with protein product						12435584, 14623098	Standard	XM_005249006		Approved	hGPCR36, PGR19	uc003oyt.3	Q5T601	OTTHUMG00000014795	ENST00000371253.2:c.1277G>A	6.37:g.46977894C>T	ENSP00000360299:p.Arg426Gln	180.0	0.0	0		178.0	100.0	0.561798	NM_153840	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Missense_Mutation	SNP	ENST00000371253.2	37	CCDS34471.1	17	0.007783882783882784	17	0.034552845528455285	0	0.0	0	0.0	0	0.0	C	8.645	0.896884	0.17686	0.03064	8.14E-4	ENSG00000153292	ENST00000371252;ENST00000371253;ENST00000283297	T;T	0.32515	1.45;1.45	5.35	1.57	0.23409	.	0.603370	0.14993	N	0.286596	T	0.08935	0.0221	M	0.67953	2.075	0.09310	N	1	B	0.22604	0.072	B	0.09377	0.004	T	0.38200	-0.9672	10	0.09843	T	0.71	-0.0889	5.8064	0.18442	0.0:0.5882:0.1282:0.2836	.	426	Q5T601	GP110_HUMAN	Q	426;426;229	ENSP00000360299:R426Q;ENSP00000283297:R229Q	ENSP00000283297:R229Q	R	-	2	0	GPR110	47085853	0.000000	0.05858	0.104000	0.21259	0.823000	0.46562	-0.323000	0.07997	0.340000	0.23745	0.555000	0.69702	CGG	C|0.989;T|0.011	0.011	strong		0.428	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840	
SLC26A11	284129	hgsc.bcm.edu	37	17	78201686	78201686	+	Silent	SNP	C	C	T	rs61011315	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78201686C>T	ENST00000361193.3	+	7	943	c.663C>T	c.(661-663)caC>caT	p.H221H	SLC26A11_ENST00000411502.3_Silent_p.H221H|SLC26A11_ENST00000546047.2_Silent_p.H221H|SLC26A11_ENST00000572725.1_Silent_p.H221H	NM_001166347.1|NM_173626.3	NP_001159819.1|NP_775897.3			solute carrier family 26 (anion exchanger), member 11											central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(7)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	28	all_neural(118;0.0538)		OV - Ovarian serous cystadenocarcinoma(97;0.0344)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			TGCGGGACCACGTGCCTCCCG	0.667													C|||	260	0.0519169	0.1808	0.0115	5008	,	,		13801	0.0		0.0109	False		,,,				2504	0.002				p.H221H		Atlas-SNP	.											.	SLC26A11	60	.	0			c.C663T						PASS	.	C	,,,	718,3688	297.6+/-284.8	61,596,1546	84.0	67.0	72.0		663,663,663,663	-0.2	0.1	17	dbSNP_129	72	113,8487	60.2+/-122.0	2,109,4189	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC26A11	NM_001166347.1,NM_001166348.1,NM_001166349.1,NM_173626.3	,,,	63,705,5735	TT,TC,CC		1.314,16.296,6.3894	,,,	221/607,221/607,221/607,221/607	78201686	831,12175	2203	4300	6503	SO:0001819	synonymous_variant	284129	exon7			GGACCACGTGCCT		CCDS11771.2	17q25	2013-07-18	2013-07-18		ENSG00000181045	ENSG00000181045		"""Solute carriers"""	14471	protein-coding gene	gene with protein product		610117	"""solute carrier family 26, member 11"""				Standard	NM_001166347		Approved		uc010dhv.2	Q86WA9	OTTHUMG00000133419	ENST00000361193.3:c.663C>T	17.37:g.78201686C>T		39.0	0.0	0		45.0	23.0	0.511111	NM_173626		Silent	SNP	ENST00000361193.3	37	CCDS11771.2																																																																																			C|0.944;T|0.056	0.056	strong		0.667	SLC26A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257281.1		
RACGAP1	29127	hgsc.bcm.edu	37	12	50384542	50384542	+	Missense_Mutation	SNP	T	T	C	rs140590023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:50384542T>C	ENST00000427314.2	-	18	1971	c.1748A>G	c.(1747-1749)cAt>cGt	p.H583R	RACGAP1_ENST00000434422.1_Missense_Mutation_p.H583R|RACGAP1_ENST00000454520.2_Missense_Mutation_p.H583R|RACGAP1_ENST00000548961.1_Intron|RACGAP1_ENST00000547905.1_Missense_Mutation_p.H583R|RACGAP1_ENST00000551016.1_Missense_Mutation_p.H583R|RACGAP1_ENST00000312377.5_Missense_Mutation_p.H583R	NM_013277.3	NP_037409.2			Rac GTPase activating protein 1											cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(6)	14						GAGAAGCTGATGTTCAGGAGT	0.448													T|||	7	0.00139776	0.0053	0.0	5008	,	,		18657	0.0		0.0	False		,,,				2504	0.0				p.H583R		Atlas-SNP	.											.	RACGAP1	36	.	0			c.A1748G						PASS	.	T	ARG/HIS,ARG/HIS,ARG/HIS	24,4382	30.8+/-60.4	0,24,2179	99.0	100.0	100.0		1748,1748,1748	4.3	1.0	12	dbSNP_134	100	0,8600		0,0,4300	yes	missense,missense,missense	RACGAP1	NM_001126103.1,NM_001126104.1,NM_013277.3	29,29,29	0,24,6479	CC,CT,TT		0.0,0.5447,0.1845	benign,benign,benign	583/633,583/633,583/633	50384542	24,12982	2203	4300	6503	SO:0001583	missense	29127	exon18			AGCTGATGTTCAG		CCDS8795.1	12q13	2004-05-17				ENSG00000161800			9804	protein-coding gene	gene with protein product		604980				9497316	Standard	NM_013277		Approved	MgcRacGAP	uc001rvs.2	Q9H0H5		ENST00000427314.2:c.1748A>G	12.37:g.50384542T>C	ENSP00000404190:p.His583Arg	159.0	0.0	0		167.0	67.0	0.401198	NM_013277		Missense_Mutation	SNP	ENST00000427314.2	37	CCDS8795.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	10.23	1.292278	0.23564	0.005447	0.0	ENSG00000161800	ENST00000427314;ENST00000312377;ENST00000434422;ENST00000454520;ENST00000551016;ENST00000547905	T;T;T;T;T;T	0.25250	1.81;1.81;1.81;1.81;1.81;1.81	5.44	4.26	0.50523	.	0.261377	0.45606	D	0.000346	T	0.12347	0.0300	L	0.40543	1.245	0.32252	N	0.571354	B	0.02656	0.0	B	0.04013	0.001	T	0.21042	-1.0257	10	0.12103	T	0.63	-5.0933	7.5935	0.28035	0.1299:0.0708:0.0:0.7993	.	583	Q9H0H5	RGAP1_HUMAN	R	583	ENSP00000404190:H583R;ENSP00000309871:H583R;ENSP00000413241:H583R;ENSP00000404808:H583R;ENSP00000449374:H583R;ENSP00000449370:H583R	ENSP00000309871:H583R	H	-	2	0	RACGAP1	48670809	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.825000	0.62708	0.955000	0.37878	0.533000	0.62120	CAT	T|0.998;C|0.002	0.002	strong		0.448	RACGAP1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405997.1	NM_013277	
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011406	46011406	+	Silent	SNP	G	G	T	rs374116165	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46011406G>T	ENST00000400368.1	-	1	980	c.960C>A	c.(958-960)gtC>gtA	p.V320V	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	320	29 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(6)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23						CACAGGAGGGGACGGGCACGC	0.701													.|||	155	0.0309505	0.1127	0.0086	5008	,	,		19947	0.0		0.0	False		,,,				2504	0.0				p.V320V		Atlas-SNP	.											.	KRTAP10-6	57	.	0			c.C960A						PASS	.						68.0	83.0	78.0					21																	46011406		2201	4300	6501	SO:0001819	synonymous_variant	386674	exon1			GGAGGGGACGGGC	AB076353	CCDS42959.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000188155	ENSG00000188155		"""Keratin associated proteins"""	20523	protein-coding gene	gene with protein product			"""keratin associated protein 18-6"""	KRTAP18-6			Standard	NM_198688		Approved	KRTAP18.6, KAP18.6, KAP10.6	uc002zfm.3	P60371	OTTHUMG00000057634	ENST00000400368.1:c.960C>A	21.37:g.46011406G>T		362.0	0.0	0		258.0	46.0	0.178295	NM_198688		Silent	SNP	ENST00000400368.1	37	CCDS42959.1																																																																																			.	.	weak		0.701	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688	
AKIRIN2	55122	hgsc.bcm.edu	37	6	88385579	88385579	+	Splice_Site	SNP	G	G	A	rs63749091	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:88385579G>A	ENST00000257787.5	-	4	1124	c.600C>T	c.(598-600)agC>agT	p.S200S		NM_018064.3	NP_060534.1	Q53H80	AKIR2_HUMAN	akirin 2	200					embryo development (GO:0009790)|innate immune response (GO:0045087)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endopeptidase activity (GO:0010950)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to lipopolysaccharide (GO:0032496)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)			large_intestine(4)	4						AATACTTACAGCTAGCAGGCT	0.303													A|||	164	0.0327476	0.1165	0.0144	5008	,	,		19800	0.0		0.0	False		,,,				2504	0.0				p.S200S		Atlas-SNP	.											.	AKIRIN2	13	.	0			c.C600T						PASS	.	A		466,3938	782.5+/-414.6	26,414,1762	71.0	69.0	70.0		600	4.6	1.0	6	dbSNP_129	70	1,8599	818.3+/-406.9	0,1,4299	yes	coding-synonymous-near-splice	AKIRIN2	NM_018064.3		26,415,6061	AA,AG,GG		0.0116,10.5813,3.5912		200/204	88385579	467,12537	2202	4300	6502	SO:0001630	splice_region_variant	55122	exon4			CTTACAGCTAGCA	BC000764	CCDS5013.1	6q15	2009-04-17	2008-06-23	2008-06-23	ENSG00000135334	ENSG00000135334			21407	protein-coding gene	gene with protein product		615165	"""chromosome 6 open reading frame 166"""	C6orf166			Standard	NM_018064		Approved	FLJ10342, dJ486L4.2	uc003pmk.3	Q53H80	OTTHUMG00000015180	ENST00000257787.5:c.601+1C>T	6.37:g.88385579G>A		107.0	0.0	0		133.0	61.0	0.458647	NM_018064	Q9BQB1	Silent	SNP	ENST00000257787.5	37	CCDS5013.1																																																																																			G|0.968;A|0.032	0.032	strong		0.303	AKIRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041455.1	NM_018064	Silent
TOX	9760	hgsc.bcm.edu	37	8	59727966	59727966	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:59727966C>T	ENST00000361421.1	-	7	1543	c.1323G>A	c.(1321-1323)atG>atA	p.M441I	RNU4-50P_ENST00000364361.1_RNA	NM_014729.2	NP_055544.1	O94900	TOX_HUMAN	thymocyte selection-associated high mobility group box	441						nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(13)|prostate(1)|skin(2)|stomach(1)	33		all_cancers(86;0.165)|Myeloproliferative disorder(644;0.00452)|all_lung(136;0.036)|Lung NSC(129;0.0464)|all_epithelial(80;0.0607)				GGGGCTGCTGCATGGTGAGCG	0.577																																					p.M441I	Pancreas(161;610 1969 17913 21374 22725)	Atlas-SNP	.											.	TOX	83	.	0			c.G1323A						PASS	.						69.0	73.0	72.0					8																	59727966		2203	4300	6503	SO:0001583	missense	9760	exon7			CTGCTGCATGGTG		CCDS34897.1	8q12.2-q12.3	2009-04-17			ENSG00000198846	ENSG00000198846			18988	protein-coding gene	gene with protein product		606863				9872452, 11850626	Standard	NM_014729		Approved	KIAA0808, TOX1	uc003xtw.1	O94900	OTTHUMG00000164331	ENST00000361421.1:c.1323G>A	8.37:g.59727966C>T	ENSP00000354842:p.Met441Ile	274.0	0.0	0		334.0	166.0	0.497006	NM_014729	Q96AV5	Missense_Mutation	SNP	ENST00000361421.1	37	CCDS34897.1	.	.	.	.	.	.	.	.	.	.	C	17.67	3.447063	0.63178	.	.	ENSG00000198846	ENST00000361421;ENST00000456290	T	0.12255	2.7	5.98	5.98	0.97165	.	0.196250	0.56097	D	0.000022	T	0.32675	0.0837	L	0.55213	1.73	0.80722	D	1	P	0.45126	0.851	P	0.58391	0.838	T	0.00031	-1.2282	9	.	.	.	.	20.4366	0.99092	0.0:1.0:0.0:0.0	.	441	O94900	TOX_HUMAN	I	441;191	ENSP00000354842:M441I	.	M	-	3	0	TOX	59890520	1.000000	0.71417	1.000000	0.80357	0.796000	0.44982	6.711000	0.74675	2.837000	0.97791	0.591000	0.81541	ATG	.	.	none		0.577	TOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378307.1	NM_014729	
SSPO	23145	hgsc.bcm.edu	37	7	149489048	149489048	+	RNA	SNP	C	C	T	rs893602	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149489048C>T	ENST00000378016.2	+	0	5389							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GCACAGCACCCGCCAGACCAG	0.652													C|||	131	0.0261581	0.0946	0.0086	5008	,	,		18478	0.0		0.0	False		,,,				2504	0.0				p.R1797C		Atlas-SNP	.											.	.	.	.	0			c.C5389T						PASS	.	C		257,3869		9,239,1815	28.0	32.0	31.0		5393	3.0	0.0	7	dbSNP_86	31	4,8368		0,4,4182	yes	coding-notMod3	SSPO	NM_198455.2		9,243,5997	TT,TC,CC		0.0478,6.2288,2.0883			149489048	261,12237	2063	4186	6249			23145	exon35			AGCACCCGCCAGA	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149489048C>T		60.0	0.0	0		77.0	37.0	0.480519	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.979;T|0.021	0.021	strong		0.652	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
NRIP1	8204	hgsc.bcm.edu	37	21	16337448	16337448	+	Silent	SNP	C	C	A	rs28707654	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:16337448C>A	ENST00000400202.1	-	3	3778	c.3066G>T	c.(3064-3066)ggG>ggT	p.G1022G	AF127577.10_ENST00000446301.1_RNA|NRIP1_ENST00000318948.4_Silent_p.G1022G|NRIP1_ENST00000400199.1_Silent_p.G1022G			P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	1022	Interaction with ZNF366.				androgen receptor signaling pathway (GO:0030521)|lipid storage (GO:0019915)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ovarian follicle rupture (GO:0001543)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|glucocorticoid receptor binding (GO:0035259)|nuclear hormone receptor binding (GO:0035257)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			cervix(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(13)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	39				Epithelial(23;1.19e-05)|all cancers(11;4.64e-05)|COAD - Colon adenocarcinoma(22;0.000232)|Colorectal(24;0.0006)|OV - Ovarian serous cystadenocarcinoma(11;0.00418)|Lung(58;0.199)|LUSC - Lung squamous cell carcinoma(23;0.24)		CTGGTCTAGACCCTGCACAGC	0.478													C|||	112	0.0223642	0.0787	0.0115	5008	,	,		19106	0.0		0.0	False		,,,				2504	0.0				p.G1022G		Atlas-SNP	.											.	NRIP1	103	.	0			c.G3066T						PASS	.	C		332,4072	171.6+/-201.8	15,302,1885	51.0	49.0	50.0		3066	-4.7	0.0	21	dbSNP_125	50	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	NRIP1	NM_003489.3		15,303,6183	AA,AC,CC		0.0116,7.5386,2.5611		1022/1159	16337448	333,12669	2202	4299	6501	SO:0001819	synonymous_variant	8204	exon4			TCTAGACCCTGCA	X84373	CCDS13568.1	21q11.2	2008-07-31			ENSG00000180530	ENSG00000180530			8001	protein-coding gene	gene with protein product	"""receptor interacting protein 140"", ""nuclear factor RIP140"""	602490				7641693, 9521594	Standard	NM_003489		Approved	RIP140	uc002yjx.2	P48552	OTTHUMG00000074323	ENST00000400202.1:c.3066G>T	21.37:g.16337448C>A		48.0	0.0	0		78.0	43.0	0.551282	NM_003489	Q8IWE8	Silent	SNP	ENST00000400202.1	37	CCDS13568.1																																																																																			C|0.978;A|0.022	0.022	strong		0.478	NRIP1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157926.1	NM_003489	
PCNXL4	64430	hgsc.bcm.edu	37	14	60585282	60585282	+	Missense_Mutation	SNP	G	G	A	rs144345462	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:60585282G>A	ENST00000406854.1	+	7	2368	c.1814G>A	c.(1813-1815)cGa>cAa	p.R605Q	PCNXL4_ENST00000535349.1_5'UTR|PCNXL4_ENST00000406949.1_Missense_Mutation_p.R371Q|PCNXL4_ENST00000317623.4_Missense_Mutation_p.R371Q|PCNXL4_ENST00000404681.2_Missense_Mutation_p.R605Q			Q63HM2	PCX4_HUMAN	pecanex-like 4 (Drosophila)	605						integral component of membrane (GO:0016021)											GGGTTTCCCCGACCTATTCAG	0.493													G|||	32	0.00638978	0.0242	0.0	5008	,	,		16639	0.0		0.0	False		,,,				2504	0.0				p.R371Q		Atlas-SNP	.											.	.	.	.	0			c.G1112A						PASS	.	G	GLN/ARG	39,4367	42.3+/-75.8	0,39,2164	70.0	63.0	65.0		1112	6.1	1.0	14	dbSNP_134	65	0,8600		0,0,4300	yes	missense	C14orf135	NM_022495.5	43	0,39,6464	AA,AG,GG		0.0,0.8852,0.2999	probably-damaging	371/939	60585282	39,12967	2203	4300	6503	SO:0001583	missense	64430	exon6			TTCCCCGACCTAT	AK022861		14q23.1	2012-07-18	2012-07-18	2012-07-18	ENSG00000126773	ENSG00000126773			20349	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 135"""	C14orf135			Standard	NM_022495		Approved		uc001xer.4	Q63HM2	OTTHUMG00000150361	ENST00000406854.1:c.1814G>A	14.37:g.60585282G>A	ENSP00000384801:p.Arg605Gln	294.0	1.0	0.00340136		323.0	148.0	0.458204	NM_022495	A8MXM2|Q9BQG8|Q9H9F2	Missense_Mutation	SNP	ENST00000406854.1	37		20	0.009157509157509158	20	0.04065040650406504	0	0.0	0	0.0	0	0.0	G	36	5.921833	0.97105	0.008852	0.0	ENSG00000126773	ENST00000317623;ENST00000406854;ENST00000406949;ENST00000404681	T;T;T;T	0.57436	0.4;0.43;0.65;0.43	6.07	6.07	0.98685	.	.	.	.	.	T	0.46521	0.1397	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.67304	-0.5704	9	0.87932	D	0	.	20.6439	0.99570	0.0:0.0:1.0:0.0	.	605;371	Q63HM2;B5MC47	CN135_HUMAN;.	Q	371;605;371;605	ENSP00000317396:R371Q;ENSP00000384801:R605Q;ENSP00000385201:R371Q;ENSP00000385713:R605Q	ENSP00000317396:R371Q	R	+	2	0	C14orf135	59655035	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	9.126000	0.94411	2.890000	0.99128	0.650000	0.86243	CGA	G|0.991;A|0.009	0.009	strong		0.493	PCNXL4-005	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000317847.1	NM_022495	
KCNK17	89822	hgsc.bcm.edu	37	6	39267315	39267315	+	Missense_Mutation	SNP	C	C	T	rs2758910	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:39267315C>T	ENST00000373231.4	-	5	1119	c.887G>A	c.(886-888)cGg>cAg	p.R296Q	KCNK17_ENST00000453413.2_3'UTR	NM_031460.3	NP_113648.2	Q96T54	KCNKH_HUMAN	potassium channel, subfamily K, member 17	296			R -> Q (in dbSNP:rs2758910).		potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(2)	14						CTCTGGCTCCCGGTCAGGTCC	0.587													c|||	39	0.00778754	0.0287	0.0014	5008	,	,		20167	0.0		0.0	False		,,,				2504	0.0				p.R296Q		Atlas-SNP	.											KCNK17,NS,carcinoma,-1,1	KCNK17	61	1	0			c.G887A						PASS	.	T	,GLN/ARG	142,4264	101.2+/-139.8	1,140,2062	90.0	79.0	83.0		,887	-2.5	0.0	6	dbSNP_100	83	0,8600		0,0,4300	yes	utr-3,missense	KCNK17	NM_001135111.1,NM_031460.3	,43	1,140,6362	TT,TC,CC		0.0,3.2229,1.0918	,benign	,296/333	39267315	142,12864	2203	4300	6503	SO:0001583	missense	89822	exon5			GGCTCCCGGTCAG	AF358910	CCDS4842.1, CCDS47419.1	6p21	2012-03-07			ENSG00000124780	ENSG00000124780		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	14465	protein-coding gene	gene with protein product		607370				16382106	Standard	NM_031460		Approved	K2p17.1, TALK-2, TALK2, TASK4, TASK-4	uc003ooo.3	Q96T54	OTTHUMG00000014646	ENST00000373231.4:c.887G>A	6.37:g.39267315C>T	ENSP00000362328:p.Arg296Gln	151.0	0.0	0		165.0	80.0	0.484848	NM_031460	E9PB46|Q5TCF4|Q8TAW4|Q9BXD1|Q9H592	Missense_Mutation	SNP	ENST00000373231.4	37	CCDS4842.1	13	0.005952380952380952	12	0.024390243902439025	1	0.0027624309392265192	0	0.0	0	0.0	c	10.09	1.254922	0.22965	0.032229	0.0	ENSG00000124780	ENST00000373231	T	0.15603	2.41	4.25	-2.45	0.06481	.	.	.	.	.	T	0.01765	0.0056	N	0.14661	0.345	0.09310	N	1	B	0.12013	0.005	B	0.06405	0.002	T	0.47262	-0.9131	9	0.11182	T	0.66	.	5.3132	0.15841	0.0:0.4054:0.1426:0.452	rs2758910;rs52820365;rs2758910	296	Q96T54	KCNKH_HUMAN	Q	296	ENSP00000362328:R296Q	ENSP00000362328:R296Q	R	-	2	0	KCNK17	39375293	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.463000	0.06696	-0.926000	0.03770	-0.119000	0.15052	CGG	C|0.989;T|0.011	0.011	strong		0.587	KCNK17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040453.2	NM_031460	
DNAH1	25981	hgsc.bcm.edu	37	3	52365223	52365223	+	Missense_Mutation	SNP	G	G	A	rs55931436	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:52365223G>A	ENST00000420323.2	+	7	1192	c.931G>A	c.(931-933)Gac>Aac	p.D311N		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	311	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|response to mechanical stimulus (GO:0009612)	axonemal dynein complex (GO:0005858)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			cervix(2)|endometrium(18)|kidney(6)|large_intestine(3)|lung(31)|prostate(1)|urinary_tract(1)	62				BRCA - Breast invasive adenocarcinoma(193;2.02e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000207)|Kidney(197;0.0022)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CCTGGACTACGACGAGGAGAA	0.567													G|||	89	0.0177716	0.0643	0.0058	5008	,	,		20717	0.0		0.0	False		,,,				2504	0.0				p.D311N		Atlas-SNP	.											.	DNAH1	534	.	0			c.G931A						PASS	.	G	ASN/ASP	167,3917		5,157,1880	56.0	59.0	58.0		931	3.6	0.0	3	dbSNP_129	58	1,8383		0,1,4191	yes	missense	DNAH1	NM_015512.4	23	5,158,6071	AA,AG,GG		0.0119,4.0891,1.3474	benign	311/4266	52365223	168,12300	2042	4192	6234	SO:0001583	missense	25981	exon7			GACTACGACGAGG	U61738	CCDS46842.1	3p21-p14	2008-02-05	2006-09-04		ENSG00000114841	ENSG00000114841		"""Axonemal dyneins"""	2940	protein-coding gene	gene with protein product		603332	"""dynein, axonemal, heavy polypeptide 1"""			8812413, 9256245	Standard	NM_015512		Approved	XLHSRF-1, DNAHC1, HDHC7, HL-11, HL11	uc011bef.2	Q9P2D7	OTTHUMG00000158378	ENST00000420323.2:c.931G>A	3.37:g.52365223G>A	ENSP00000401514:p.Asp311Asn	150.0	0.0	0		194.0	91.0	0.469072	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Missense_Mutation	SNP	ENST00000420323.2	37	CCDS46842.1	33	0.01510989010989011	32	0.06504065040650407	1	0.0027624309392265192	0	0.0	0	0.0	G	10.94	1.491737	0.26774	0.040891	1.19E-4	ENSG00000114841	ENST00000420323	T	0.23348	1.91	5.38	3.58	0.41010	.	0.000000	0.53938	D	0.000051	T	0.01627	0.0052	L	0.46885	1.475	0.26172	N	0.979848	B;P	0.39326	0.07;0.668	B;B	0.36186	0.022;0.219	T	0.01452	-1.1351	10	0.52906	T	0.07	.	11.8483	0.52397	0.1429:0.0:0.8571:0.0	rs55931436;rs61734655	311;311	C9JXH6;Q9P2D7-3	.;.	N	311	ENSP00000401514:D311N	ENSP00000401514:D311N	D	+	1	0	DNAH1	52340263	0.986000	0.35501	0.008000	0.14137	0.151000	0.21798	2.173000	0.42472	0.643000	0.30638	0.462000	0.41574	GAC	G|0.984;A|0.016	0.016	strong		0.567	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512	
OGFOD1	55239	hgsc.bcm.edu	37	16	56496469	56496469	+	Missense_Mutation	SNP	G	G	A	rs147797412	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:56496469G>A	ENST00000566157.1	+	4	494	c.371G>A	c.(370-372)cGg>cAg	p.R124Q	OGFOD1_ENST00000565209.1_3'UTR|OGFOD1_ENST00000568397.1_Missense_Mutation_p.R124Q	NM_018233.3	NP_060703.3	Q8N543	OGFD1_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 1	124					cell proliferation (GO:0008283)|peptidyl-proline hydroxylation (GO:0019511)|protein hydroxylation (GO:0018126)|regulation of translational termination (GO:0006449)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|peptidyl-proline 3-dioxygenase activity (GO:0031544)|peptidyl-proline dioxygenase activity (GO:0031543)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	8					Vitamin C(DB00126)	GAAGATTTCCGGTCCTGGCTT	0.393													G|||	5	0.000998403	0.0008	0.0029	5008	,	,		19961	0.0		0.0	False		,,,				2504	0.002				p.R124Q		Atlas-SNP	.											.	OGFOD1	31	.	0			c.G371A						PASS	.	G	GLN/ARG	4,4392	8.1+/-20.4	0,4,2194	80.0	77.0	78.0		371	5.6	1.0	16	dbSNP_134	78	0,8600		0,0,4300	yes	missense	OGFOD1	NM_018233.3	43	0,4,6494	AA,AG,GG		0.0,0.091,0.0308	possibly-damaging	124/543	56496469	4,12992	2198	4300	6498	SO:0001583	missense	55239	exon4			ATTTCCGGTCCTG	BC032919	CCDS10761.2	16q12.2	2010-11-23			ENSG00000087263	ENSG00000087263			25585	protein-coding gene	gene with protein product	"""TPA1, termination and polyadenylation 1, homolog (S. cerevisiae)"""	615857				10997877	Standard	NM_018233		Approved	KIAA1612, FLJ10826, TPA1	uc002ejb.3	Q8N543	OTTHUMG00000133237	ENST00000566157.1:c.371G>A	16.37:g.56496469G>A	ENSP00000457258:p.Arg124Gln	95.0	0.0	0		56.0	27.0	0.482143	NM_018233	H3BUQ2|Q9H7U5|Q9H9J9|Q9HA87|Q9HCG0|Q9NVB6	Missense_Mutation	SNP	ENST00000566157.1	37	CCDS10761.2	.	.	.	.	.	.	.	.	.	.	G	23.9	4.474261	0.84640	9.1E-4	0.0	ENSG00000087263	ENST00000336111	.	.	.	5.61	5.61	0.85477	Prolyl 4-hydroxylase, alpha subunit (1);	0.000000	0.85682	D	0.000000	T	0.59582	0.2204	M	0.79258	2.445	0.80722	D	1	D	0.58268	0.982	B	0.41510	0.359	T	0.67616	-0.5625	9	0.59425	D	0.04	-17.5224	13.8776	0.63662	0.0748:0.0:0.9252:0.0	.	124	Q8N543	OGFD1_HUMAN	Q	124	.	ENSP00000337196:R124Q	R	+	2	0	OGFOD1	55053970	1.000000	0.71417	0.989000	0.46669	0.997000	0.91878	6.847000	0.75404	2.658000	0.90341	0.585000	0.79938	CGG	G|1.000;A|0.000	0.000	weak		0.393	OGFOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256976.3	NM_018233	
MUC5B	727897	hgsc.bcm.edu	37	11	1272246	1272246	+	Silent	SNP	G	G	A	rs115045504	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1272246G>A	ENST00000529681.1	+	31	14194	c.14136G>A	c.(14134-14136)acG>acA	p.T4712T	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Silent_p.T4715T	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4712	23 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.		T -> M (in dbSNP:rs2943511). {ECO:0000269|PubMed:9013550}.		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)		tgaccagcacggccaccacac	0.617													g|||	69	0.013778	0.0477	0.0086	5008	,	,		18297	0.0		0.0	False		,,,				2504	0.0				p.T4712T		Atlas-SNP	.											MUC5B,colon,carcinoma,+1,2	MUC5B	473	2	0			c.G14136A						PASS	.	G		97,4189		3,91,2049	108.0	139.0	128.0		14136	-3.3	0.0	11	dbSNP_132	128	0,8456		0,0,4228	no	coding-synonymous	MUC5B	NM_002458.2		3,91,6277	AA,AG,GG		0.0,2.2632,0.7613		4712/5763	1272246	97,12645	2143	4228	6371	SO:0001819	synonymous_variant	727897	exon31			CAGCACGGCCACC	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.14136G>A	11.37:g.1272246G>A		551.0	2.0	0.00362976		520.0	253.0	0.486538	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			G|0.988;A|0.012	0.012	strong		0.617	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
ZNF799	90576	hgsc.bcm.edu	37	19	12502155	12502155	+	Missense_Mutation	SNP	T	T	G	rs201335235		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12502155T>G	ENST00000430385.3	-	4	1257	c.1057A>C	c.(1057-1059)Aaa>Caa	p.K353Q	ZNF799_ENST00000419318.1_Missense_Mutation_p.K321Q|CTD-3105H18.14_ENST00000435033.1_Intron	NM_001080821.2	NP_001074290.1	Q96GE5	ZN799_HUMAN	zinc finger protein 799	353					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						TCATGACTTTTCAGTGAACTA	0.413																																					p.K353Q		Atlas-SNP	.											.	ZNF799	111	.	0			c.A1057C						PASS	.						160.0	156.0	157.0					19																	12502155		2203	4300	6503	SO:0001583	missense	90576	exon4			GACTTTTCAGTGA	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.1057A>C	19.37:g.12502155T>G	ENSP00000411084:p.Lys353Gln	91.0	0.0	0		111.0	8.0	0.0720721	NM_001080821		Missense_Mutation	SNP	ENST00000430385.3	37	CCDS45989.1	.	.	.	.	.	.	.	.	.	.	G	0.033	-1.323810	0.01309	.	.	ENSG00000196466	ENST00000419318;ENST00000430385	T;T	0.04406	3.63;3.63	1.31	-1.61	0.08399	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02418	0.0074	N	0.12527	0.23	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.49041	-0.8980	9	0.14252	T	0.57	.	6.8386	0.23951	0.0:0.0:0.2963:0.7037	.	353	Q96GE5	ZN799_HUMAN	Q	321;353	ENSP00000415278:K321Q;ENSP00000411084:K353Q	ENSP00000415278:K321Q	K	-	1	0	ZNF799	12363155	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.687000	0.05156	-0.936000	0.03723	-1.919000	0.00516	AAA	.	.	weak		0.413	ZNF799-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344099.2	NM_001080821	
UQCC1	55245	hgsc.bcm.edu	37	20	33971876	33971876	+	Missense_Mutation	SNP	T	T	C	rs114745625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33971876T>C	ENST00000374385.5	-	3	367	c.190A>G	c.(190-192)Ata>Gta	p.I64V	UQCC1_ENST00000349714.5_Missense_Mutation_p.I64V|UQCC1_ENST00000374384.2_Missense_Mutation_p.I64V|UQCC1_ENST00000407996.2_Missense_Mutation_p.I64V|UQCC1_ENST00000491125.1_5'UTR|UQCC1_ENST00000397556.3_Intron|UQCC1_ENST00000540457.1_Intron|UQCC1_ENST00000374377.5_Intron|UQCC1_ENST00000542501.1_Missense_Mutation_p.I64V|UQCC1_ENST00000359226.2_Missense_Mutation_p.I64V|UQCC1_ENST00000397554.1_Missense_Mutation_p.I64V|UQCC1_ENST00000374380.2_Intron	NM_018244.4	NP_060714.3	Q9NVA1	UQCC1_HUMAN	ubiquinol-cytochrome c reductase complex assembly factor 1	64						cytoplasmic membrane-bounded vesicle (GO:0016023)|mitochondrion (GO:0005739)											TTCAGCTGTATGTCTATTCCA	0.438													T|||	13	0.00259585	0.0098	0.0	5008	,	,		21480	0.0		0.0	False		,,,				2504	0.0				p.I64V		Atlas-SNP	.											.	UQCC	41	.	0			c.A190G						PASS	.	T	,VAL/ILE,VAL/ILE	57,4349	56.2+/-92.4	1,55,2147	184.0	149.0	161.0		,190,190	-1.4	0.0	20	dbSNP_132	161	0,8600		0,0,4300	yes	intron,missense,missense	UQCC	NM_001184977.1,NM_018244.4,NM_199487.2	,29,29	1,55,6447	CC,CT,TT		0.0,1.2937,0.4383	,benign,benign	,64/300,64/274	33971876	57,12949	2203	4300	6503	SO:0001583	missense	55245	exon3			GCTGTATGTCTAT	AK001712	CCDS13252.1, CCDS13253.1, CCDS13253.2, CCDS54458.1	20q11.22	2013-09-20	2013-09-20	2013-09-20	ENSG00000101019	ENSG00000101019		"""Mitochondrial respiratory chain complex assembly factors"""	15891	protein-coding gene	gene with protein product	"""Basic FGF-repressed Zic-binding protein"", ""cytochrome B protein synthesis 3 homolog (S. cerevisiae)"""	611797	"""chromosome 20 open reading frame 44"", ""ubiquinol-cytochrome c reductase complex chaperone"""	C20orf44, UQCC			Standard	NM_018244		Approved	FLJ10850, CBP3, BFZB	uc002xcd.3	Q9NVA1	OTTHUMG00000032335	ENST00000374385.5:c.190A>G	20.37:g.33971876T>C	ENSP00000363506:p.Ile64Val	217.0	0.0	0		218.0	104.0	0.477064	NM_018244	B1AKV5|Q0VF37|Q5T348|Q5T351|Q5T353|Q86YU3|Q86YU4|Q96H66|Q9H438|Q9H452|Q9H9K8|Q9H9R5	Missense_Mutation	SNP	ENST00000374385.5	37	CCDS13252.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	T	0.042	-1.280171	0.01398	0.012937	0.0	ENSG00000101019	ENST00000349714;ENST00000359226;ENST00000374384;ENST00000374385;ENST00000407996;ENST00000542501;ENST00000438533;ENST00000397554	T;T;T;T;T;T;T;T	0.42900	1.55;1.57;1.66;1.66;0.96;1.54;1.62;1.62	5.02	-1.38	0.09027	.	0.874131	0.10138	N	0.711165	T	0.13500	0.0327	N	0.12961	0.28	0.09310	N	1	B;B;B;B;B	0.14012	0.009;0.0;0.002;0.0;0.0	B;B;B;B;B	0.13407	0.009;0.0;0.001;0.0;0.0	T	0.18777	-1.0326	10	0.27785	T	0.31	-3.4421	0.9374	0.01347	0.1611:0.3029:0.1662:0.3698	.	64;64;64;64;64	B7Z7J8;B7ZBG3;B1AKV2;B7ZBG4;Q9NVA1	.;.;.;.;UQCC_HUMAN	V	64;64;64;64;64;64;78;64	ENSP00000335364:I64V;ENSP00000352161:I64V;ENSP00000363505:I64V;ENSP00000363506:I64V;ENSP00000386064:I64V;ENSP00000445059:I64V;ENSP00000398531:I78V;ENSP00000380686:I64V	ENSP00000335364:I64V	I	-	1	0	UQCC	33435290	0.000000	0.05858	0.004000	0.12327	0.135000	0.20990	-0.025000	0.12413	0.080000	0.16959	0.533000	0.62120	ATA	T|0.997;C|0.003	0.003	strong		0.438	UQCC1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078866.1	NM_018244	
LOXHD1	125336	hgsc.bcm.edu	37	18	44157797	44157797	+	Silent	SNP	G	G	T	rs112463030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:44157797G>T	ENST00000398722.4	-	7	1008	c.1009C>A	c.(1009-1011)Cgg>Agg	p.R337R	LOXHD1_ENST00000536736.1_Silent_p.R615R|LOXHD1_ENST00000441551.2_Silent_p.R615R			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	337	PLAT 3. {ECO:0000255|PROSITE- ProRule:PRU00152}.				calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|sensory perception of sound (GO:0007605)	membrane (GO:0016020)|stereocilium (GO:0032420)	calcium channel activity (GO:0005262)			NS(3)|autonomic_ganglia(1)|breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|pancreas(1)|prostate(4)|skin(4)|stomach(1)	36						CTCACATTCCGCATGGTGACA	0.592													G|||	24	0.00479233	0.0166	0.0014	5008	,	,		20177	0.0		0.001	False		,,,				2504	0.0				p.R615R		Atlas-SNP	.											.	LOXHD1	367	.	0			c.C1843A						PASS	.	G		34,1350		1,32,659	62.0	64.0	63.0		1843	-2.2	1.0	18	dbSNP_132	63	0,3182		0,0,1591	no	coding-synonymous	LOXHD1	NM_144612.6		1,32,2250	TT,TG,GG		0.0,2.4566,0.7446		615/2212	44157797	34,4532	692	1591	2283	SO:0001819	synonymous_variant	125336	exon14			CATTCCGCATGGT	AK057232	CCDS45861.1, CCDS45862.1, CCDS54184.1	18q21.1	2009-09-11			ENSG00000167210	ENSG00000167210			26521	protein-coding gene	gene with protein product		613072	"""deafness, autosomal recessive 77"""	DFNB77		19732867	Standard	NM_144612		Approved	FLJ32670, LH2D1	uc010xcw.1	Q8IVV2	OTTHUMG00000132644	ENST00000398722.4:c.1009C>A	18.37:g.44157797G>T		81.0	0.0	0		95.0	49.0	0.515789	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Silent	SNP	ENST00000398722.4	37		13	0.005952380952380952	12	0.024390243902439025	0	0.0	0	0.0	1	0.0013192612137203166	G	1.684	-0.505763	0.04261	0.024566	0.0	ENSG00000167210	ENST00000441551	.	.	.	5.66	-2.15	0.07102	.	.	.	.	.	T	0.54447	0.1859	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68205	-0.5470	4	.	.	.	.	18.5598	0.91096	0.0:0.0:0.2663:0.7337	.	.	.	.	E	595	.	.	A	-	2	0	LOXHD1	42411795	1.000000	0.71417	0.994000	0.49952	0.066000	0.16364	0.835000	0.27531	-0.232000	0.09811	-0.314000	0.08810	GCG	G|0.994;T|0.006	0.006	strong		0.592	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
TTN	7273	hgsc.bcm.edu	37	2	179430224	179430224	+	Missense_Mutation	SNP	G	G	T	rs79926414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179430224G>T	ENST00000591111.1	-	276	75936	c.75712C>A	c.(75712-75714)Cag>Aag	p.Q25238K	TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.Q18006K|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.Q24311K|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.Q17939K|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.Q17814K|TTN_ENST00000589042.1_Missense_Mutation_p.Q26879K			Q8WZ42	TITIN_HUMAN	titin	25238					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)			AAACTAGGCTGTATAGTCAAG	0.388													G|||	79	0.0157748	0.0567	0.0058	5008	,	,		22772	0.0		0.0	False		,,,				2504	0.0				p.Q26879K		Atlas-SNP	.											.	TTN	18412	.	0			c.C80635A						PASS	.	G	LYS/GLN,LYS/GLN,LYS/GLN,LYS/GLN	176,3544		5,166,1689	130.0	127.0	128.0		54016,53815,72931,53440	5.5	1.0	2	dbSNP_131	128	1,8199		0,1,4099	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	53,53,53,53	5,167,5788	TT,TG,GG		0.0122,4.7312,1.4849	benign,benign,benign,benign	18006/27119,17939/27052,24311/33424,17814/26927	179430224	177,11743	1860	4100	5960	SO:0001583	missense	7273	exon326			TAGGCTGTATAGT	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.75712C>A	2.37:g.179430224G>T	ENSP00000465570:p.Gln25238Lys	199.0	1.0	0.00502513		151.0	90.0	0.596026	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		42	0.019230769230769232	39	0.07926829268292683	3	0.008287292817679558	0	0.0	0	0.0	G	9.263	1.043608	0.19748	0.047312	1.22E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.61980	0.06;0.33;0.3;0.3	5.49	5.49	0.81192	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.01835	0.0058	N	0.00465	-1.465	0.26115	N	0.980629	B;B;B;B	0.09022	0.001;0.002;0.002;0.001	B;B;B;B	0.04013	0.0;0.001;0.001;0.0	T	0.07028	-1.0794	9	0.87932	D	0	.	14.8449	0.70254	0.0:0.2548:0.7452:0.0	.	17814;17939;18006;25238	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	K	24311;17814;18006;17939;17812	ENSP00000343764:Q24311K;ENSP00000434586:Q17814K;ENSP00000340554:Q18006K;ENSP00000352154:Q17939K	ENSP00000340554:Q18006K	Q	-	1	0	TTN	179138470	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.169000	0.50809	2.595000	0.87683	0.484000	0.47621	CAG	G|0.976;T|0.024	0.024	strong		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
FOXRED2	80020	hgsc.bcm.edu	37	22	36886178	36886178	+	Silent	SNP	A	A	G	rs73409777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:36886178A>G	ENST00000397224.4	-	9	2025	c.1932T>C	c.(1930-1932)taT>taC	p.Y644Y	FOXRED2_ENST00000397223.4_Silent_p.Y644Y|FOXRED2_ENST00000366463.3_Silent_p.Y196Y|FOXRED2_ENST00000216187.6_Silent_p.Y644Y	NM_001102371.1	NP_001095841.1	Q8IWF2	FXRD2_HUMAN	FAD-dependent oxidoreductase domain containing 2	644					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum lumen (GO:0005788)	flavin adenine dinucleotide binding (GO:0050660)|glycoprotein binding (GO:0001948)|oxidoreductase activity (GO:0016491)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						CTGTGGGGGCATAGTCCCGCA	0.652													A|||	142	0.0283546	0.1044	0.0043	5008	,	,		16850	0.0		0.001	False		,,,				2504	0.0				p.Y644Y		Atlas-SNP	.											.	FOXRED2	48	.	0			c.T1932C						PASS	.	A	,	385,4021	187.8+/-214.3	21,343,1839	47.0	51.0	50.0		1932,1932	-3.8	0.0	22	dbSNP_130	50	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	FOXRED2	NM_001102371.1,NM_024955.5	,	21,346,6136	GG,GA,AA		0.0349,8.7381,2.9832	,	644/685,644/685	36886178	388,12618	2203	4300	6503	SO:0001819	synonymous_variant	80020	exon9			GGGGGCATAGTCC	BC027716	CCDS13929.1	22q12.3	2006-07-05			ENSG00000100350	ENSG00000100350			26264	protein-coding gene	gene with protein product		613777				12477932	Standard	NM_024955		Approved	FLJ23322	uc003app.4	Q8IWF2	OTTHUMG00000044614	ENST00000397224.4:c.1932T>C	22.37:g.36886178A>G		68.0	0.0	0		81.0	39.0	0.481481	NM_001102371	B2RDI4|Q8N378|Q96BD1|Q9H5L5|Q9H6M8	Silent	SNP	ENST00000397224.4	37	CCDS13929.1																																																																																			A|0.975;G|0.025	0.025	strong		0.652	FOXRED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104098.2	NM_024955	
IPO13	9670	hgsc.bcm.edu	37	1	44422367	44422367	+	Silent	SNP	A	A	G	rs36061711	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:44422367A>G	ENST00000372343.3	+	4	1760	c.1098A>G	c.(1096-1098)acA>acG	p.T366T	IPO13_ENST00000492152.1_3'UTR	NM_014652.3	NP_055467.3	O94829	IPO13_HUMAN	importin 13	366					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0821)				TCTGGTACACACTGCAGGTGT	0.532													A|||	196	0.0391374	0.1415	0.013	5008	,	,		20746	0.0		0.0	False		,,,				2504	0.0				p.T366T		Atlas-SNP	.											.	IPO13	86	.	0			c.A1098G						PASS	.	A		497,3909	231.4+/-245.2	31,435,1737	125.0	116.0	119.0		1098	-11.5	0.2	1	dbSNP_126	119	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	IPO13	NM_014652.3		31,437,6035	GG,GA,AA		0.0233,11.2801,3.8367		366/964	44422367	499,12507	2203	4300	6503	SO:0001819	synonymous_variant	9670	exon4			GTACACACTGCAG	AB018267	CCDS503.1	1p34.1	2008-02-05			ENSG00000117408	ENSG00000117408		"""Importins"""	16853	protein-coding gene	gene with protein product		610411				9872452, 11447110	Standard	NM_014652		Approved	IMP13, KIAA0724, RANBP13	uc001ckx.3	O94829	OTTHUMG00000008297	ENST00000372343.3:c.1098A>G	1.37:g.44422367A>G		129.0	0.0	0		164.0	83.0	0.506098	NM_014652	D3DPY4|Q5T4X3|Q7LC04|Q96HS3|Q9H8N3|Q9UFR1	Silent	SNP	ENST00000372343.3	37	CCDS503.1																																																																																			A|0.964;G|0.036	0.036	strong		0.532	IPO13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022846.1	NM_014652	
NPR2	4882	hgsc.bcm.edu	37	9	35811749	35811749	+	IGR	SNP	C	C	T	rs79261709	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35811749C>T	ENST00000342694.2	+	0	3686				TMEM8B_ENST00000377996.1_5'Flank|AL133410.1_ENST00000582432.1_RNA|HINT2_ENST00000474908.1_5'Flank|SPAG8_ENST00000484764.1_Silent_p.A96A|SPAG8_ENST00000396638.2_Silent_p.A98A|SPAG8_ENST00000340291.2_Silent_p.A98A|SPAG8_ENST00000479751.1_5'Flank	NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2						bone development (GO:0060348)|cell surface receptor signaling pathway (GO:0007166)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cGMP biosynthetic process (GO:0006182)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of oocyte maturation (GO:1900194)|ossification (GO:0001503)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|signal transduction (GO:0007165)|single organism reproductive process (GO:0044702)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(2)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)	AGCCGGGTCCCGCACAGGGCT	0.547													c|||	68	0.0135783	0.0492	0.0043	5008	,	,		17978	0.0		0.0	False		,,,				2504	0.0				p.A98A		Atlas-SNP	.											.	SPAG8	67	.	0			c.G294A						PASS	.	C	,	184,4222	115.0+/-153.0	2,180,2021	56.0	68.0	64.0		294,294	-2.2	0.0	9	dbSNP_131	64	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SPAG8	NM_001039592.1,NM_172312.1	,	2,180,6321	TT,TC,CC		0.0,4.1761,1.4147	,	98/486,98/502	35811749	184,12822	2203	4300	6503	SO:0001628	intergenic_variant	26206	exon2			GGGTCCCGCACAG	AJ005282	CCDS6590.1	9p21-p12	2014-03-03	2014-03-03		ENSG00000159899	ENSG00000159899			7944	protein-coding gene	gene with protein product	"""guanylate cyclase B"""	108961	"""acromesomelic dysplasia, Maroteaux type"", ""atrionatriuretic peptide receptor B"", ""natriuretic peptide receptor B"""	ANPRB, NPRB, AMDM		9634515, 15146390	Standard	XM_005251478		Approved	GUCY2B, ANPb	uc003zyd.3	P20594	OTTHUMG00000019871		9.37:g.35811749C>T		80.0	0.0	0		76.0	44.0	0.578947	NM_001039592	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Silent	SNP	ENST00000342694.2	37	CCDS6590.1	19	0.0086996336996337	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	c	5.786	0.329334	0.10956	0.041761	0.0	ENSG00000137098	ENST00000497810	.	.	.	5.3	-2.21	0.06973	.	.	.	.	.	T	0.04003	0.0112	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.20538	-1.0272	4	.	.	.	3.7726	0.3647	0.00370	0.3138:0.2293:0.2557:0.2013	.	.	.	.	Q	96	.	.	R	-	2	0	SPAG8	35801749	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.424000	0.07025	-0.264000	0.09365	-0.710000	0.03640	CGG	C|0.988;T|0.012	0.012	strong		0.547	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1		
CPPED1	55313	hgsc.bcm.edu	37	16	12798724	12798724	+	Missense_Mutation	SNP	C	C	T	rs145004672	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:12798724C>T	ENST00000381774.4	-	3	712	c.472G>A	c.(472-474)Gtc>Atc	p.V158I	CPPED1_ENST00000261660.4_Intron|CPPED1_ENST00000433677.2_Intron	NM_018340.2	NP_060810.2	Q9BRF8	CPPED_HUMAN	calcineurin-like phosphoesterase domain containing 1	158	Catalytic.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	metal ion binding (GO:0046872)|phosphoprotein phosphatase activity (GO:0004721)	p.V158I(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|skin(1)|urinary_tract(1)	18						AGGAACAGGACGCCCCCGACC	0.612													C|||	42	0.00838658	0.0272	0.0029	5008	,	,		17716	0.003		0.0	False		,,,				2504	0.001				p.V158I		Atlas-SNP	.											CPPED1,rectum,carcinoma,0,1	CPPED1	41	1	1	Substitution - Missense(1)	large_intestine(1)	c.G472A						scavenged	.	C	,ILE/VAL	69,3929		1,67,1931	57.0	62.0	60.0		,472	4.4	0.8	16	dbSNP_134	60	1,8319		0,1,4159	yes	intron,missense	CPPED1	NM_001099455.1,NM_018340.2	,29	1,68,6090	TT,TC,CC		0.012,1.7259,0.5683	,possibly-damaging	,158/315	12798724	70,12248	1999	4160	6159	SO:0001583	missense	55313	exon3			ACAGGACGCCCCC	AK022710	CCDS42119.1, CCDS42120.1	16p13.12	2014-02-12	2009-03-13		ENSG00000103381	ENSG00000103381			25632	protein-coding gene	gene with protein product	"""complete S transactivated protein 1"""	615603				12477932	Standard	NM_018340		Approved	CSTP1, FLJ11151	uc002dca.4	Q9BRF8	OTTHUMG00000167711	ENST00000381774.4:c.472G>A	16.37:g.12798724C>T	ENSP00000371193:p.Val158Ile	94.0	1.0	0.0106383		83.0	45.0	0.542169	NM_018340	B4DQ68|Q6MZY9|Q9H9M9|Q9NUT6	Missense_Mutation	SNP	ENST00000381774.4	37	CCDS42120.1	27	0.012362637362637362	23	0.046747967479674794	1	0.0027624309392265192	3	0.005244755244755245	0	0.0	C	16.61	3.171078	0.57584	0.017259	1.2E-4	ENSG00000103381	ENST00000381774	T	0.72505	-0.66	5.32	4.37	0.52481	Metallophosphoesterase domain (1);	0.053983	0.64402	D	0.000001	T	0.29882	0.0747	M	0.67397	2.05	0.80722	D	1	P	0.47191	0.891	B	0.43194	0.411	T	0.56165	-0.8024	10	0.46703	T	0.11	-31.751	12.0777	0.53653	0.0:0.9163:0.0:0.0837	.	158	Q9BRF8	CPPED_HUMAN	I	158	ENSP00000371193:V158I	ENSP00000371193:V158I	V	-	1	0	CPPED1	12706225	0.998000	0.40836	0.840000	0.33206	0.315000	0.28087	3.848000	0.55903	1.256000	0.44068	-0.128000	0.14901	GTC	C|0.988;T|0.012	0.012	strong		0.612	CPPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395795.2	NM_018340	
ABCB8	11194	hgsc.bcm.edu	37	7	150730712	150730712	+	Missense_Mutation	SNP	G	G	A	rs6975981	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150730712G>A	ENST00000297504.6	+	3	233	c.167G>A	c.(166-168)aGc>aAc	p.S56N	ABCB8_ENST00000477719.1_Missense_Mutation_p.S39N|ABCB8_ENST00000477092.1_Missense_Mutation_p.S39N|ABCB8_ENST00000356058.4_Missense_Mutation_p.S76N|ABCB8_ENST00000542328.1_Intron|ABCB8_ENST00000493338.1_3'UTR|ABCB8_ENST00000358849.4_Missense_Mutation_p.S39N|ABCB8_ENST00000498578.1_Missense_Mutation_p.S39N			Q9NUT2	ABCB8_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 8	56					transmembrane transport (GO:0055085)|transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	26			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Doxorubicin(DB00997)	GGCTACCGCAGCTCCTCCCTC	0.677													G|||	161	0.0321486	0.1157	0.0115	5008	,	,		16274	0.0		0.0	False		,,,				2504	0.0				p.S39N		Atlas-SNP	.											.	ABCB8	65	.	0			c.G116A						PASS	.	G	ASN/SER	340,4066	168.7+/-199.5	13,314,1876	41.0	45.0	44.0		116	2.2	0.0	7	dbSNP_116	44	10,8590	7.7+/-29.5	0,10,4290	yes	missense	ABCB8	NM_007188.3	46	13,324,6166	AA,AG,GG		0.1163,7.7167,2.6911	benign	39/719	150730712	350,12656	2203	4300	6503	SO:0001583	missense	11194	exon2			ACCGCAGCTCCTC	AF047690	CCDS5913.1, CCDS64798.1, CCDS64799.1, CCDS64800.1	7q36.1	2012-05-16			ENSG00000197150	ENSG00000197150		"""ATP binding cassette transporters / subfamily B"""	49	protein-coding gene	gene with protein product	"""mitochondrial ABC protein"""	605464				8894702	Standard	NM_001282291		Approved	EST328128, M-ABC1, MABC1	uc003wik.4	Q9NUT2	OTTHUMG00000158686	ENST00000297504.6:c.167G>A	7.37:g.150730712G>A	ENSP00000297504:p.Ser56Asn	118.0	0.0	0		107.0	49.0	0.457944	NM_007188	A5D8W3|B2RBL8|B3KND2|B4DG02|G3XAP3|O95787|Q53GM0	Missense_Mutation	SNP	ENST00000297504.6	37		65	0.02976190476190476	61	0.12398373983739837	4	0.011049723756906077	0	0.0	0	0.0	G	10.99	1.505996	0.26949	0.077167	0.001163	ENSG00000197150	ENST00000461373;ENST00000358849;ENST00000360651;ENST00000297504;ENST00000498578;ENST00000356058;ENST00000477719;ENST00000477092	D;D;D;D;D;D	0.91011	-2.65;-2.66;-2.77;-2.01;-2.07;-2.1	4.07	2.23	0.28157	.	0.502250	0.22050	N	0.065324	T	0.05410	0.0143	N	0.24115	0.695	0.09310	N	1	B;B;B;B;P	0.40000	0.079;0.361;0.277;0.361;0.698	B;B;B;B;B	0.38562	0.035;0.051;0.109;0.081;0.276	T	0.29212	-1.0019	10	0.38643	T	0.18	0.0796	5.7097	0.17929	0.1091:0.1985:0.6924:0.0	rs6975981;rs60484309	39;56;39;39;76	A5D8W3;Q9NUT2;Q9NUT2-2;C9JTY4;E7ENE8	.;ABCB8_HUMAN;.;.;.	N	76;39;39;56;39;76;39;39	ENSP00000351717:S39N;ENSP00000297504:S56N;ENSP00000418271:S39N;ENSP00000348353:S76N;ENSP00000419891:S39N;ENSP00000419558:S39N	ENSP00000297504:S56N	S	+	2	0	ABCB8	150361645	0.849000	0.29639	0.002000	0.10522	0.015000	0.08874	1.842000	0.39250	0.474000	0.27392	0.561000	0.74099	AGC	G|0.973;A|0.027	0.027	strong		0.677	ABCB8-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351733.2	NM_007188	
ERO1L	30001	hgsc.bcm.edu	37	14	53133134	53133134	+	Silent	SNP	A	A	G	rs34388088	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:53133134A>G	ENST00000395686.3	-	7	811	c.588T>C	c.(586-588)gcT>gcC	p.A196A		NM_014584.1	NP_055399.1	Q96HE7	ERO1A_HUMAN	ERO1-like (S. cerevisiae)	196					4-hydroxyproline metabolic process (GO:0019471)|brown fat cell differentiation (GO:0050873)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|chaperone mediated protein folding requiring cofactor (GO:0051085)|endoplasmic reticulum unfolded protein response (GO:0030968)|extracellular matrix organization (GO:0030198)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|protein folding (GO:0006457)|protein maturation by protein folding (GO:0022417)|release of sequestered calcium ion into cytosol (GO:0051209)|response to endoplasmic reticulum stress (GO:0034976)|response to temperature stimulus (GO:0009266)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)		ERO1L/FERMT2(2)	breast(1)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	12	Breast(41;0.226)					ATATTTTCCAAGCATCTGGTC	0.333													A|||	76	0.0151757	0.0537	0.0072	5008	,	,		17663	0.0		0.0	False		,,,				2504	0.0				p.A196A		Atlas-SNP	.											.	ERO1L	35	.	0			c.T588C						PASS	.	A		219,4187	129.4+/-166.1	8,203,1992	79.0	79.0	79.0		588	0.9	1.0	14	dbSNP_126	79	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	ERO1L	NM_014584.1		8,208,6287	GG,GA,AA		0.0581,4.9705,1.7223		196/469	53133134	224,12782	2203	4300	6503	SO:0001819	synonymous_variant	30001	exon7			TTTCCAAGCATCT	AF081886	CCDS9709.1	14q22.1	2010-10-06	2001-11-28		ENSG00000197930	ENSG00000197930			13280	protein-coding gene	gene with protein product		615435	"""ERO1 (S. cerevisiae)-like"""			10671517	Standard	NM_014584		Approved	ERO1A, ERO1-alpha	uc001wzv.3	Q96HE7	OTTHUMG00000140301	ENST00000395686.3:c.588T>C	14.37:g.53133134A>G		230.0	0.0	0		199.0	84.0	0.422111	NM_014584	A8K9X4|A8MYW1|Q7LD45|Q9P1Q9|Q9UKV6	Silent	SNP	ENST00000395686.3	37	CCDS9709.1																																																																																			A|0.985;G|0.015	0.015	strong		0.333	ERO1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276892.1	NM_014584	
SYNE2	23224	hgsc.bcm.edu	37	14	64461914	64461914	+	Silent	SNP	A	A	G	rs34001379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:64461914A>G	ENST00000344113.4	+	23	3146	c.2934A>G	c.(2932-2934)gaA>gaG	p.E978E	SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Silent_p.E978E|SYNE2_ENST00000358025.3_Silent_p.E978E	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	978					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TCATCAAAGAACATGAGGTAC	0.318													A|||	32	0.00638978	0.0242	0.0	5008	,	,		18525	0.0		0.0	False		,,,				2504	0.0				p.E978E		Atlas-SNP	.											SYNE2,rectum,carcinoma,+2,1	SYNE2	577	1	0			c.A2934G						PASS	.	A	,	93,3593		3,87,1753	47.0	46.0	46.0		2934,2934	-0.1	1.0	14	dbSNP_126	46	0,8152		0,0,4076	no	coding-synonymous,coding-synonymous	SYNE2	NM_015180.4,NM_182914.2	,	3,87,5829	GG,GA,AA		0.0,2.5231,0.7856	,	978/6886,978/6908	64461914	93,11745	1843	4076	5919	SO:0001819	synonymous_variant	23224	exon23			CAAAGAACATGAG	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.2934A>G	14.37:g.64461914A>G		171.0	0.0	0		158.0	78.0	0.493671	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																			A|0.995;G|0.005	0.005	strong		0.318	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
KLC3	147700	hgsc.bcm.edu	37	19	45848946	45848946	+	Silent	SNP	G	G	A	rs114640964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45848946G>A	ENST00000391946.2	+	2	249	c.147G>A	c.(145-147)gcG>gcA	p.A49A	KLC3_ENST00000470402.1_Silent_p.A63A|KLC3_ENST00000585434.1_Silent_p.A49A	NM_177417.2	NP_803136.2	Q6P597	KLC3_HUMAN	kinesin light chain 3	49					axon cargo transport (GO:0008088)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|motile cilium (GO:0031514)|neuron projection (GO:0043005)	microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	8		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		GGCACCTGGCGGAGGCCCTGG	0.716													g|||	75	0.014976	0.0552	0.0029	5008	,	,		13066	0.0		0.0	False		,,,				2504	0.0				p.A49A		Atlas-SNP	.											.	KLC3	37	.	0			c.G147A						PASS	.	A		150,3632		0,150,1741	5.0	8.0	7.0		147	-4.1	0.9	19	dbSNP_132	7	2,7914		0,2,3956	no	coding-synonymous	KLC3	NM_177417.2		0,152,5697	AA,AG,GG		0.0253,3.9662,1.2994		49/505	45848946	152,11546	1891	3958	5849	SO:0001819	synonymous_variant	147700	exon2			CCTGGCGGAGGCC	AK092481	CCDS12660.2	19q13	2013-01-10			ENSG00000104892	ENSG00000104892		"""Tetratricopeptide (TTC) repeat domain containing"""	20717	protein-coding gene	gene with protein product		601334					Standard	XM_005258536		Approved	KLC2L, KNS2B, KLCt	uc002pbf.1	Q6P597	OTTHUMG00000143722	ENST00000391946.2:c.147G>A	19.37:g.45848946G>A		42.0	0.0	0		42.0	22.0	0.52381	NM_177417	A0AVM3|A2RUT6|Q6GMU2|Q8NAL1|Q8WWJ9	Silent	SNP	ENST00000391946.2	37	CCDS12660.2																																																																																			G|0.990;A|0.010	0.010	strong		0.716	KLC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289776.1	NM_145275	
KALRN	8997	hgsc.bcm.edu	37	3	124374487	124374487	+	Silent	SNP	T	T	C	rs55750661	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:124374487T>C	ENST00000291478.5	+	6	904	c.741T>C	c.(739-741)taT>taC	p.Y247Y	KALRN_ENST00000459915.1_Silent_p.Y36Y|KALRN_ENST00000428018.2_Silent_p.Y215Y|KALRN_ENST00000360013.3_Silent_p.Y1944Y|KALRN_ENST00000393496.1_Silent_p.Y285Y	NM_007064.3	NP_008995.2	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1943					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						AGAAAGACTATGTCAAGGATC	0.493													t|||	8	0.00159744	0.0038	0.0029	5008	,	,		20398	0.0		0.001	False		,,,				2504	0.0				p.Y1944Y		Atlas-SNP	.											.	KALRN	556	.	0			c.T5832C						PASS	.	C	,	22,4384	29.0+/-57.7	0,22,2181	203.0	186.0	191.0		5832,741	-2.5	1.0	3	dbSNP_129	191	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	KALRN	NM_001024660.3,NM_007064.3	,	0,24,6479	CC,CT,TT		0.0233,0.4993,0.1845	,	1944/2987,247/1290	124374487	24,12982	2203	4300	6503	SO:0001819	synonymous_variant	8997	exon39			AGACTATGTCAAG	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	4814	protein-coding gene	gene with protein product	"""serine/threonine kinase with Dbl and pleckstrin homology domains"""	604605	"""huntingtin-associated protein interacting protein (duo)"""	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000291478.5:c.741T>C	3.37:g.124374487T>C		138.0	0.0	0		140.0	67.0	0.478571	NM_001024660	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000291478.5	37	CCDS3028.1	3	0.0013736263736263737	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	0	0.0	t	10.36	1.329889	0.24167	0.004993	2.33E-4	ENSG00000160145	ENST00000354186	.	.	.	5.42	-2.53	0.06326	.	.	.	.	.	T	0.55465	0.1922	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59112	-0.7515	4	.	.	.	.	13.5294	0.61613	0.0:0.5623:0.0:0.4377	rs55750661	.	.	.	T	1913	.	.	M	+	2	0	KALRN	125857177	0.434000	0.25570	0.977000	0.42913	0.995000	0.86356	-0.455000	0.06762	-0.595000	0.05828	-0.253000	0.11424	ATG	T|0.998;C|0.002	0.002	strong		0.493	KALRN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000246891.5	NM_003947	
KIAA0226L	80183	hgsc.bcm.edu	37	13	46919719	46919719	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:46919719C>T	ENST00000429979.1	-	13	2252	c.1648G>A	c.(1648-1650)Gag>Aag	p.E550K	KIAA0226L_ENST00000534925.1_Missense_Mutation_p.E415K|KIAA0226L_ENST00000378781.3_3'UTR|KIAA0226L_ENST00000409879.2_Missense_Mutation_p.E393K|KIAA0226L_ENST00000378784.4_Missense_Mutation_p.E483K|KIAA0226L_ENST00000389908.3_Missense_Mutation_p.E550K|KIAA0226L_ENST00000378787.3_Intron|KIAA0226L_ENST00000378797.2_Intron|KIAA0226L_ENST00000322896.6_Missense_Mutation_p.E393K	NM_025113.2	NP_079389.2	Q9H714	K226L_HUMAN	KIAA0226-like	550										NS(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|pancreas(1)	26						GGCACCTGCTCGAACTCCTTT	0.527																																					p.E550K		Atlas-SNP	.											.	KIAA0226L	63	.	0			c.G1648A						PASS	.						43.0	42.0	42.0					13																	46919719		1942	4138	6080	SO:0001583	missense	80183	exon13			CCTGCTCGAACTC	AK025215	CCDS31970.2, CCDS66543.1, CCDS66544.1, CCDS66545.1, CCDS73569.1	13q14.11	2011-08-09	2011-08-09	2011-08-09	ENSG00000102445	ENSG00000102445			20420	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 18"""	C13orf18			Standard	NM_001286766		Approved	FLJ21562	uc010acl.3	Q9H714	OTTHUMG00000016868	ENST00000429979.1:c.1648G>A	13.37:g.46919719C>T	ENSP00000396935:p.Glu550Lys	48.0	0.0	0		47.0	25.0	0.531915	NM_025113	A8KAG9|A8XR19|B3KS87|Q5W051|Q5W053|Q6PJ74|Q6PK94|Q86XH7|Q8N5J6	Missense_Mutation	SNP	ENST00000429979.1	37	CCDS31970.2	.	.	.	.	.	.	.	.	.	.	C	18.22	3.574834	0.65878	.	.	ENSG00000102445	ENST00000429979;ENST00000378784;ENST00000389908;ENST00000409879;ENST00000322896;ENST00000534925	T;T;T;T	0.46819	0.86;0.87;0.86;0.89	5.35	4.51	0.55191	.	.	.	.	.	T	0.41396	0.1157	M	0.77616	2.38	0.80722	D	1	B;B;P;B;B	0.38677	0.231;0.231;0.642;0.251;0.434	B;B;B;B;B	0.33521	0.064;0.064;0.163;0.041;0.165	T	0.35599	-0.9782	9	0.08179	T	0.78	-17.8147	9.4511	0.38727	0.0:0.8394:0.0:0.1606	.	393;393;550;415;483	B7ZBN5;B7Z6E4;Q9H714;A8KAG9;Q9H714-3	.;.;K226L_HUMAN;.;.	K	550;483;550;393;393;415	ENSP00000396935:E550K;ENSP00000368061:E483K;ENSP00000374558:E550K;ENSP00000437501:E415K	ENSP00000315633:E393K	E	-	1	0	KIAA0226L	45817720	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	3.410000	0.52664	1.251000	0.43983	0.655000	0.94253	GAG	.	.	none		0.527	KIAA0226L-204	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044809.2	NM_025113	
TREM1	54210	hgsc.bcm.edu	37	6	41243926	41243926	+	Missense_Mutation	SNP	G	G	C	rs2234245	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:41243926G>C	ENST00000244709.4	-	4	705	c.642C>G	c.(640-642)ttC>ttG	p.F214L	TREM1_ENST00000334475.6_Missense_Mutation_p.S150C|TREM1_ENST00000589614.1_Intron	NM_018643.3	NP_061113.1	Q9NP99	TREM1_HUMAN	triggering receptor expressed on myeloid cells 1	214			F -> L (in dbSNP:rs2234245).		blood coagulation (GO:0007596)|chemokine metabolic process (GO:0050755)|cytokine secretion involved in immune response (GO:0002374)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|leukocyte migration (GO:0050900)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|neutrophil mediated killing of gram-negative bacterium (GO:0070945)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|scaffold protein binding (GO:0097110)			NS(1)|breast(2)|endometrium(2)|large_intestine(5)|lung(5)|skin(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					TCTTACTCAGGAATCCACCAG	0.547													G|||	140	0.0279553	0.1006	0.0101	5008	,	,		19431	0.0		0.0	False		,,,				2504	0.0				p.F214L		Atlas-SNP	.											.	TREM1	38	.	0			c.C642G						PASS	.	G	CYS/SER,LEU/PHE	299,4107	162.5+/-194.5	11,277,1915	174.0	143.0	154.0		449,642	1.0	0.1	6	dbSNP_98	154	7,8593	5.0+/-18.6	0,7,4293	yes	missense,missense	TREM1	NM_001242590.1,NM_018643.3	112,22	11,284,6208	CC,CG,GG		0.0814,6.7862,2.3528	possibly-damaging,possibly-damaging	150/151,214/235	41243926	306,12700	2203	4300	6503	SO:0001583	missense	54210	exon4			ACTCAGGAATCCA	AF196329	CCDS4854.1, CCDS56427.1, CCDS59499.1	6p21.1	2013-01-11			ENSG00000124731	ENSG00000124731		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	17760	protein-coding gene	gene with protein product		605085				11922939, 10799849	Standard	NM_018643		Approved	TREM-1, CD354	uc003oqf.2	Q9NP99	OTTHUMG00000014674	ENST00000244709.4:c.642C>G	6.37:g.41243926G>C	ENSP00000244709:p.Phe214Leu	90.0	0.0	0		102.0	48.0	0.470588	NM_018643	B4DWG2|K7EJW1|Q53FL8|Q5T2C9|Q86YU1	Missense_Mutation	SNP	ENST00000244709.4	37	CCDS4854.1	46|46	0.021062271062271064|0.021062271062271064	41|41	0.08333333333333333|0.08333333333333333	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	0|0	0.0|0.0	G|G	18.63|18.63	3.665281|3.665281	0.67700|0.67700	0.067862|0.067862	8.14E-4|8.14E-4	ENSG00000124731|ENSG00000124731	ENST00000244709|ENST00000334475	T|T	0.04194|0.14144	3.68|2.53	4.86|4.86	1.0|1.0	0.19881|0.19881	.|.	0.883988|.	0.09394|.	N|.	0.808190|.	T|T	0.04543|0.04543	0.0124|0.0124	.|.	.|.	.|.	0.20196|0.20196	N|N	0.999924|0.999924	B|P	0.02656|0.41546	0.0|0.754	B|B	0.01281|0.41299	0.0|0.353	T|T	0.30650|0.30650	-0.9971|-0.9971	9|8	0.02654|0.87932	T|D	1|0	-4.1779|-4.1779	4.7266|4.7266	0.12943|0.12943	0.2677:0.1574:0.5749:0.0|0.2677:0.1574:0.5749:0.0	rs2234245|rs2234245	214|150	Q9NP99|Q9NP99-2	TREM1_HUMAN|.	L|C	214|150	ENSP00000244709:F214L|ENSP00000334284:S150C	ENSP00000244709:F214L|ENSP00000334284:S150C	F|S	-|-	3|2	2|0	TREM1|TREM1	41351904|41351904	0.593000|0.593000	0.26840|0.26840	0.056000|0.056000	0.19401|0.19401	0.730000|0.730000	0.41778|0.41778	0.268000|0.268000	0.18571|0.18571	0.059000|0.059000	0.16252|0.16252	0.655000|0.655000	0.94253|0.94253	TTC|TCC	G|0.979;C|0.021	0.021	strong		0.547	TREM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040505.2	NM_018643	
PTX4	390667	hgsc.bcm.edu	37	16	1536117	1536117	+	Silent	SNP	G	G	A	rs58192896	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1536117G>A	ENST00000447419.2	-	3	1285	c.1260C>T	c.(1258-1260)ttC>ttT	p.F420F	PTX4_ENST00000293922.1_Silent_p.F415F|PTX4_ENST00000440447.2_3'UTR			Q96A99	PTX4_HUMAN	pentraxin 4, long	420	Pentaxin.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						TGCTCCCCACGAAGGCCTCGG	0.647													G|||	277	0.0553115	0.1974	0.0231	5008	,	,		17589	0.0		0.0	False		,,,				2504	0.0				p.F415F		Atlas-SNP	.											.	PTX4	46	.	0			c.C1245T						PASS	.	G		831,3567	324.8+/-298.8	76,679,1444	65.0	62.0	63.0		1245	-10.4	0.5	16	dbSNP_129	63	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	PTX4	NM_001013658.1		76,682,5741	AA,AG,GG		0.0349,18.895,6.4164		415/474	1536117	834,12164	2199	4300	6499	SO:0001819	synonymous_variant	390667	exon3			CCCCACGAAGGCC		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"""chromosome 16 open reading frame 38"""	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.1260C>T	16.37:g.1536117G>A		73.0	0.0	0		79.0	36.0	0.455696	NM_001013658		Silent	SNP	ENST00000447419.2	37																																																																																				G|0.941;A|0.059	0.059	strong		0.647	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
MYO18B	84700	hgsc.bcm.edu	37	22	26168333	26168333	+	Silent	SNP	C	C	T	rs185388626	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:26168333C>T	ENST00000407587.2	+	7	1894	c.1725C>T	c.(1723-1725)gaC>gaT	p.D575D	MYO18B_ENST00000536101.1_Silent_p.D575D|MYO18B_ENST00000335473.7_Silent_p.D575D			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	575	Myosin motor.					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						AGGTCGAGGACCTGGCCTCTC	0.607													C|||	18	0.00359425	0.0136	0.0	5008	,	,		11926	0.0		0.0	False		,,,				2504	0.0				p.D575D		Atlas-SNP	.											.	MYO18B	322	.	0			c.C1725T						PASS	.	C		70,3950		0,70,1940	108.0	107.0	107.0		1725	2.0	1.0	22		107	0,8346		0,0,4173	no	coding-synonymous	MYO18B	NM_032608.5		0,70,6113	TT,TC,CC		0.0,1.7413,0.5661		575/2568	26168333	70,12296	2010	4173	6183	SO:0001819	synonymous_variant	84700	exon7			CGAGGACCTGGCC	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.1725C>T	22.37:g.26168333C>T		82.0	0.0	0		94.0	53.0	0.56383	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37																																																																																				C|0.998;T|0.002	0.002	strong		0.607	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
LTF	4057	hgsc.bcm.edu	37	3	46501308	46501308	+	Splice_Site	SNP	T	T	C	rs61740461	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:46501308T>C	ENST00000231751.4	-	2	340	c.45A>G	c.(43-45)ggA>ggG	p.G15G	LTF_ENST00000417439.1_Splice_Site_p.G15G|LTF_ENST00000426532.2_5'UTR	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	15					antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		CCAGACACAGTCCTGGGAGAG	0.562													T|||	351	0.0700879	0.2549	0.0202	5008	,	,		17512	0.0		0.0	False		,,,				2504	0.0				p.G15G		Atlas-SNP	.											.	LTF	98	.	0			c.A45G						PASS	.	T	,	855,3551	318.8+/-295.8	83,689,1431	58.0	50.0	52.0		,45	0.4	1.0	3	dbSNP_129	52	6,8594	3.7+/-12.6	0,6,4294	yes	utr-5,coding-synonymous-near-splice	LTF	NM_001199149.1,NM_002343.3	,	83,695,5725	CC,CT,TT		0.0698,19.4054,6.62	,	,15/711	46501308	861,12145	2203	4300	6503	SO:0001630	splice_region_variant	4057	exon2			ACACAGTCCTGGG		CCDS33747.1, CCDS56251.1	3p21.31	2012-10-02			ENSG00000012223	ENSG00000012223			6720	protein-coding gene	gene with protein product		150210				17476971, 3356163	Standard	NM_001199149		Approved	HLF2	uc003cpq.3	P02788	OTTHUMG00000156325	ENST00000231751.4:c.44-1A>G	3.37:g.46501308T>C		135.0	0.0	0		120.0	65.0	0.541667	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Silent	SNP	ENST00000231751.4	37	CCDS33747.1																																																																																			T|0.931;C|0.069	0.069	strong		0.562	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343	Silent
ULK1	8408	hgsc.bcm.edu	37	12	132404110	132404110	+	Silent	SNP	C	C	T	rs113954208	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132404110C>T	ENST00000321867.4	+	25	3129	c.2778C>T	c.(2776-2778)ctC>ctT	p.L926L	ULK1_ENST00000540647.1_Silent_p.L171L	NM_003565.2	NP_003556	O75385	ULK1_HUMAN	unc-51 like autophagy activating kinase 1	926					autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|cellular response to nutrient levels (GO:0031669)|cerebellar granule cell differentiation (GO:0021707)|negative regulation of collateral sprouting (GO:0048671)|neuron projection development (GO:0031175)|neuron projection regeneration (GO:0031102)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|protein autophosphorylation (GO:0046777)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|radial glia guided migration of cerebellar granule cell (GO:0021933)|Ras protein signal transduction (GO:0007265)|receptor internalization (GO:0031623)|regulation of autophagy (GO:0010506)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|response to starvation (GO:0042594)	ATG1/UKL1 signaling complex (GO:0034273)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extrinsic component of autophagic vacuole membrane (GO:0097635)|extrinsic component of omegasome membrane (GO:0097629)|extrinsic component of pre-autophagosomal structure membrane (GO:0097632)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)	ATP binding (GO:0005524)|protein complex binding (GO:0032403)|protein serine/threonine kinase activity (GO:0004674)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	29	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)		CCGGCAAGCTCTGCCTGTCGT	0.657													C|||	16	0.00319489	0.0121	0.0	5008	,	,		16514	0.0		0.0	False		,,,				2504	0.0				p.L926L		Atlas-SNP	.											.	ULK1	92	.	0			c.C2778T						PASS	.	C		72,4334	63.5+/-100.7	1,70,2132	63.0	68.0	66.0		2778	1.7	1.0	12	dbSNP_132	66	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	ULK1	NM_003565.2		1,71,6430	TT,TC,CC		0.0116,1.6341,0.5614		926/1051	132404110	73,12931	2203	4299	6502	SO:0001819	synonymous_variant	8408	exon25			CAAGCTCTGCCTG	AF045458	CCDS9274.1	12q24.3	2014-02-12	2013-07-02		ENSG00000177169	ENSG00000177169			12558	protein-coding gene	gene with protein product	"""ATG1 autophagy related 1 homolog (S. cerevisiae)"""	603168	"""unc-51 (C. elegans)-like kinase 1"", ""unc-51-like kinase 1 (C. elegans)"""			9693035	Standard	NM_003565		Approved	ATG1, ATG1A	uc001uje.3	O75385	OTTHUMG00000168052	ENST00000321867.4:c.2778C>T	12.37:g.132404110C>T		90.0	0.0	0		69.0	41.0	0.594203	NM_003565	Q9UQ28	Silent	SNP	ENST00000321867.4	37	CCDS9274.1																																																																																			C|0.994;T|0.006	0.006	strong		0.657	ULK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397769.3		
MUC16	94025	hgsc.bcm.edu	37	19	8996460	8996460	+	Missense_Mutation	SNP	A	A	C	rs115933306	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8996460A>C	ENST00000397910.4	-	61	41315	c.41112T>G	c.(41110-41112)gaT>gaG	p.D13704E	MUC16_ENST00000380951.5_Missense_Mutation_p.D345E	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13706	SEA 11. {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						TGCAGATGGCATCCACTCCAG	0.547													-|||	174	0.0347444	0.1271	0.0086	5008	,	,		19097	0.0		0.0	False		,,,				2504	0.0				p.D13704E		Atlas-SNP	.											.	MUC16	4315	.	0			c.T41112G						PASS	.	A	GLU/ASP	326,3522		18,290,1616	71.0	66.0	68.0		41112	-4.6	0.0	19	dbSNP_132	68	4,8262		0,4,4129	yes	missense	MUC16	NM_024690.2	45	18,294,5745	CC,CA,AA		0.0484,8.4719,2.7241	probably-damaging	13704/14508	8996460	330,11784	1924	4133	6057	SO:0001583	missense	94025	exon61			GATGGCATCCACT	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.41112T>G	19.37:g.8996460A>C	ENSP00000381008:p.Asp13704Glu	204.0	0.0	0		170.0	170.0	1	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	43|43	0.019688644688644688|0.019688644688644688	39|39	0.07926829268292683|0.07926829268292683	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	0|0	0.0|0.0	.|.	13.79|13.79	2.342264|2.342264	0.41498|0.41498	0.084719|0.084719	4.84E-4|4.84E-4	ENSG00000181143|ENSG00000181143	ENST00000397910;ENST00000380951|ENST00000542240	T;T|.	0.35048|.	1.33;1.33|.	3.36|3.36	-4.56|-4.56	0.03431|0.03431	SEA (1);|.	0.216241|.	0.23120|.	U|.	0.051715|.	T|T	0.09468|0.09468	0.0233|0.0233	M|M	0.90082|0.90082	3.085|3.085	.|.	.|.	.|.	D;D|.	0.65815|.	0.995;0.959|.	P;D|.	0.67103|.	0.901;0.949|.	T|T	0.61197|0.61197	-0.7111|-0.7111	9|4	0.72032|.	D|.	0.01|.	-11.1203|-11.1203	8.9526|8.9526	0.35799|0.35799	0.6401:0.0:0.3599:0.0|0.6401:0.0:0.3599:0.0	.|.	21349;13704|.	Q8WXI7;B5ME49|.	MUC16_HUMAN;.|.	E|R	13704;345|544	ENSP00000381008:D13704E;ENSP00000370338:D345E|.	ENSP00000370338:D345E|.	D|M	-|-	3|2	2|0	MUC16|MUC16	8857460|8857460	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.010000|0.010000	0.07245|0.07245	-1.743000|-1.743000	0.01834|0.01834	-0.764000|-0.764000	0.04651|0.04651	-0.415000|-0.415000	0.06103|0.06103	GAT|ATG	A|0.974;C|0.026	0.026	strong		0.547	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
CXCR2	3579	hgsc.bcm.edu	37	2	218999798	218999798	+	Silent	SNP	T	T	C	rs142747099	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:218999798T>C	ENST00000318507.2	+	3	701	c.274T>C	c.(274-276)Ttg>Ctg	p.L92L		NM_001557.3	NP_001548.1	P25025	CXCR2_HUMAN	chemokine (C-X-C motif) receptor 2	92					cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|inflammatory response (GO:0006954)|interleukin-8-mediated signaling pathway (GO:0038112)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|interleukin-8 binding (GO:0019959)|interleukin-8 receptor activity (GO:0004918)|signal transducer activity (GO:0004871)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(11)|skin(1)|stomach(1)	22						GAACCTAGCCTTGGCCGACCT	0.567																																					p.L92L		Atlas-SNP	.											.	CXCR2	54	.	0			c.T274C						PASS	.	T	,	6,4400	11.4+/-27.6	0,6,2197	144.0	136.0	138.0		274,274	-0.1	0.8	2	dbSNP_134	138	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CXCR2	NM_001168298.1,NM_001557.3	,	0,6,6497	CC,CT,TT		0.0,0.1362,0.0461	,	92/361,92/361	218999798	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	3579	exon4			CTAGCCTTGGCCG	U11869	CCDS2408.1	2q35	2012-08-08	2009-11-25	2009-11-25	ENSG00000180871	ENSG00000180871		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : C-X-C motif"", ""Interleukins and interleukin receptors"""	6027	protein-coding gene	gene with protein product		146928	"""interleukin 8 receptor, beta"""	IL8RB		1427896	Standard	NM_001557		Approved	CMKAR2, CD182	uc002vha.2	P25025	OTTHUMG00000133107	ENST00000318507.2:c.274T>C	2.37:g.218999798T>C		249.0	1.0	0.00401606		238.0	109.0	0.457983	NM_001168298	Q8IUZ1|Q9P2T6|Q9P2T7	Silent	SNP	ENST00000318507.2	37	CCDS2408.1																																																																																			T|0.999;C|0.001	0.001	strong		0.567	CXCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256772.2	NM_001557	
PPP1R3F	89801	hgsc.bcm.edu	37	X	49142987	49142987	+	Missense_Mutation	SNP	C	C	T	rs372361395		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:49142987C>T	ENST00000055335.6	+	4	1851	c.1835C>T	c.(1834-1836)aCg>aTg	p.T612M	PPP1R3F_ENST00000495799.1_Missense_Mutation_p.T266M|PPP1R3F_ENST00000466508.1_Missense_Mutation_p.T266M|PPP1R3F_ENST00000376188.1_Missense_Mutation_p.T266M|PPP1R3F_ENST00000438316.1_Missense_Mutation_p.T283M	NM_033215.4	NP_149992.3	Q6ZSY5	PPR3F_HUMAN	protein phosphatase 1, regulatory subunit 3F	612					regulation of glycogen (starch) synthase activity (GO:2000465)|regulation of glycogen biosynthetic process (GO:0005979)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	glycogen binding (GO:2001069)|protein phosphatase binding (GO:0019903)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(4)	27	Ovarian(276;0.236)					GTGGTAGCCACGATGGGAGAT	0.612													C|||	1	0.000264901	0.0	0.0	3775	,	,		12213	0.001		0.0	False		,,,				2504	0.0				p.T612M		Atlas-SNP	.											.	PPP1R3F	56	.	0			c.C1835T						PASS	.		MET/THR,MET/THR	1,3833		0,1,1631,570	36.0	26.0	29.0		797,1835	3.8	0.9	X		29	0,6728		0,0,2428,1872	no	missense,missense	PPP1R3F	NM_001184745.1,NM_033215.4	81,81	0,1,4059,2442	TT,TC,CC,C		0.0,0.0261,0.0095	probably-damaging,probably-damaging	266/454,612/800	49142987	1,10561	2202	4300	6502	SO:0001583	missense	89801	exon4			TAGCCACGATGGG		CCDS35254.1, CCDS55415.1	Xp11.23	2012-04-17	2011-10-04		ENSG00000049769	ENSG00000049769		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14944	protein-coding gene	gene with protein product			"""protein phosphatase 1, regulatory (inhibitor) subunit 3F"""			11948623	Standard	NM_033215		Approved	Hb2E	uc004dnh.2	Q6ZSY5	OTTHUMG00000024139	ENST00000055335.6:c.1835C>T	X.37:g.49142987C>T	ENSP00000055335:p.Thr612Met	89.0	0.0	0		110.0	54.0	0.490909	NM_033215	A2VDJ8|B3KPW2|E9PCM3	Missense_Mutation	SNP	ENST00000055335.6	37	CCDS35254.1	.	.	.	.	.	.	.	.	.	.	C	13.75	2.331209	0.41297	2.61E-4	0.0	ENSG00000049769	ENST00000466508;ENST00000438316;ENST00000055335;ENST00000495799;ENST00000376188	T;T;T;T;T	0.59224	0.7;0.71;0.28;0.7;0.7	4.71	3.82	0.43975	.	0.521490	0.17939	N	0.156901	T	0.60625	0.2283	L	0.27053	0.805	0.26861	N	0.967952	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.65987	0.917;0.917;0.94	T	0.53408	-0.8443	10	0.87932	D	0	-0.2653	10.192	0.43032	0.0:0.8014:0.1986:0.0	.	283;297;612	F5H262;A2VDJ8;Q6ZSY5	.;.;PPR3F_HUMAN	M	266;283;612;266;266	ENSP00000420687:T266M;ENSP00000415548:T283M;ENSP00000055335:T612M;ENSP00000417535:T266M;ENSP00000365359:T266M	ENSP00000055335:T612M	T	+	2	0	PPP1R3F	49029931	0.942000	0.31987	0.876000	0.34364	0.775000	0.43874	0.261000	0.18442	1.027000	0.39758	0.509000	0.49947	ACG	.	.	weak		0.612	PPP1R3F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060819.2	NM_033215	
ADAMTS1	9510	hgsc.bcm.edu	37	21	28214238	28214238	+	Silent	SNP	T	T	C	rs77718820	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:28214238T>C	ENST00000284984.3	-	3	1603	c.1149A>G	c.(1147-1149)agA>agG	p.R383R		NM_006988.3	NP_008919.3	Q9UHI8	ATS1_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 1	383	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				heart trabecula formation (GO:0060347)|integrin-mediated signaling pathway (GO:0007229)|kidney development (GO:0001822)|negative regulation of cell proliferation (GO:0008285)|ovulation from ovarian follicle (GO:0001542)	basement membrane (GO:0005604)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(20)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	42		Breast(209;0.000962)		Lung(58;0.215)		CGGAGCAGCTTCTGCTCGGAT	0.433													T|||	59	0.0117812	0.0439	0.0014	5008	,	,		17992	0.0		0.0	False		,,,				2504	0.0				p.R383R		Atlas-SNP	.											.	ADAMTS1	131	.	0			c.A1149G						PASS	.	T		150,4256	103.4+/-141.9	3,144,2056	119.0	102.0	108.0		1149	0.5	1.0	21	dbSNP_131	108	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ADAMTS1	NM_006988.3		3,145,6355	CC,CT,TT		0.0116,3.4044,1.161		383/968	28214238	151,12855	2203	4300	6503	SO:0001819	synonymous_variant	9510	exon3			GCAGCTTCTGCTC	AF060152	CCDS33524.1	21q21.3	2008-05-14	2005-08-19		ENSG00000154734	ENSG00000154734		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	217	protein-coding gene	gene with protein product		605174	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1"""			10438512	Standard	NM_006988		Approved	C3-C5, METH1, KIAA1346	uc002ymf.3	Q9UHI8	OTTHUMG00000078688	ENST00000284984.3:c.1149A>G	21.37:g.28214238T>C		146.0	0.0	0		131.0	67.0	0.51145	NM_006988	D3DSD5|Q9NSJ8|Q9P2K0|Q9UH83|Q9UP80	Silent	SNP	ENST00000284984.3	37	CCDS33524.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	T	11.14	1.552302	0.27739	0.034044	1.16E-4	ENSG00000154734	ENST00000451462	.	.	.	5.55	0.507	0.16967	.	.	.	.	.	T	0.14743	0.0356	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.06862	-1.0803	4	.	.	.	.	6.0716	0.19893	0.0:0.3189:0.3426:0.3385	.	.	.	.	G	165	.	.	E	-	2	0	ADAMTS1	27136109	0.985000	0.35326	0.995000	0.50966	0.974000	0.67602	0.136000	0.15974	-0.047000	0.13423	0.533000	0.62120	GAA	T|0.990;C|0.010	0.010	strong		0.433	ADAMTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171650.2		
NWD1	284434	hgsc.bcm.edu	37	19	16860001	16860001	+	Missense_Mutation	SNP	A	A	T	rs76739123	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16860001A>T	ENST00000552788.1	+	4	548	c.548A>T	c.(547-549)cAg>cTg	p.Q183L	NWD1_ENST00000379808.3_Missense_Mutation_p.Q183L|NWD1_ENST00000523826.1_De_novo_Start_OutOfFrame|NWD1_ENST00000339803.6_Missense_Mutation_p.Q48L|NWD1_ENST00000524140.2_Missense_Mutation_p.Q183L|NWD1_ENST00000549814.1_Missense_Mutation_p.Q183L			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	183							ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GACCGGGAACAGGGAGCCACC	0.572													A|||	120	0.0239617	0.0825	0.0101	5008	,	,		17868	0.0		0.001	False		,,,				2504	0.0031				p.Q183L		Atlas-SNP	.											.	NWD1	303	.	0			c.A548T						PASS	.	A	LEU/GLN	279,4127	157.0+/-190.0	5,269,1929	72.0	57.0	62.0		548	-7.3	0.0	19	dbSNP_131	62	10,8590	6.4+/-24.3	0,10,4290	yes	missense	NWD1	NM_001007525.3	113	5,279,6219	TT,TA,AA		0.1163,6.3323,2.2221	benign	183/1433	16860001	289,12717	2203	4300	6503	SO:0001583	missense	284434	exon6			GGGAACAGGGAGC	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"""WD repeat domain containing"""	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.548A>T	19.37:g.16860001A>T	ENSP00000447224:p.Gln183Leu	115.0	0.0	0		143.0	79.0	0.552448	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		49	0.022435897435897436	42	0.08536585365853659	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	a	2.726	-0.265505	0.05754	0.063323	0.001163	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000552788;ENST00000339803	T;T;T;T;T	0.56444	2.07;2.07;2.07;2.07;0.46	4.45	-7.35	0.01422	.	1.747030	0.02870	N	0.131458	T	0.01523	0.0049	L	0.39397	1.21	0.18873	N	0.999986	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.10474	-1.0628	10	0.54805	T	0.06	-3.4934	2.1523	0.03803	0.2044:0.3718:0.2881:0.1356	.	183;48	Q149M9-3;C9J2Y8	.;.	L	48;183;183;183;183;48	ENSP00000428579:Q183L;ENSP00000447548:Q183L;ENSP00000369136:Q183L;ENSP00000447224:Q183L;ENSP00000340159:Q48L	ENSP00000340159:Q48L	Q	+	2	0	NWD1	16721001	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.401000	0.07232	-1.070000	0.03149	-0.499000	0.04595	CAG	A|0.975;T|0.025	0.025	strong		0.572	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525	
ZNF286B	729288	hgsc.bcm.edu	37	17	18566386	18566386	+	Missense_Mutation	SNP	G	G	A	rs143643706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18566386G>A	ENST00000545289.1	-	5	683	c.433C>T	c.(433-435)Cgg>Tgg	p.R145W	ZNF286B_ENST00000285274.5_3'UTR	NM_001145045.1	NP_001138517.1	P0CG31	Z286B_HUMAN	zinc finger protein 286B	145					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						ACACTATTCCGTGTCAGTCTG	0.408													.|||	424	0.0846645	0.3071	0.0202	5008	,	,		22256	0.0		0.002	False		,,,				2504	0.002				p.R145W		Atlas-SNP	.											.	ZNF286B	75	.	0			c.C433T						PASS	.	G	TRP/ARG	315,1069		31,253,408	111.0	99.0	102.0		433	-3.4	0.0	17	dbSNP_134	102	11,3169		0,11,1579	no	missense	ZNF286B	NM_001145045.1	101	31,264,1987	AA,AG,GG		0.3459,22.7601,7.1429	probably-damaging	145/523	18566386	326,4238	692	1590	2282	SO:0001583	missense	729288	exon5			TATTCCGTGTCAG		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.433C>T	17.37:g.18566386G>A	ENSP00000461413:p.Arg145Trp	390.0	0.0	0		353.0	137.0	0.388102	NM_001145045		Missense_Mutation	SNP	ENST00000545289.1	37	CCDS58523.1																																																																																			G|0.945;A|0.055	0.055	strong		0.408	ZNF286B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_001723047	
KRTAP27-1	643812	hgsc.bcm.edu	37	21	31709935	31709935	+	Missense_Mutation	SNP	G	G	A	rs149814034	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31709935G>A	ENST00000382835.2	-	1	77	c.52C>T	c.(52-54)Ctc>Ttc	p.L18F		NM_001077711.1	NP_001071179.1	Q3LI81	KR271_HUMAN	keratin associated protein 27-1	18						intermediate filament (GO:0005882)				endometrium(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(1)	18						ATGGCAGAGAGTGGTGGGGCA	0.453													G|||	9	0.00179712	0.0061	0.0014	5008	,	,		19096	0.0		0.0	False		,,,				2504	0.0				p.L18F		Atlas-SNP	.											.	KRTAP27-1	53	.	0			c.C52T						PASS	.	G	PHE/LEU	23,4383	30.8+/-60.4	0,23,2180	103.0	98.0	100.0		52	4.3	1.0	21	dbSNP_134	100	0,8600		0,0,4300	yes	missense	KRTAP27-1	NM_001077711.1	22	0,23,6480	AA,AG,GG		0.0,0.522,0.1768	probably-damaging	18/208	31709935	23,12983	2203	4300	6503	SO:0001583	missense	643812	exon1			CAGAGAGTGGTGG	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.52C>T	21.37:g.31709935G>A	ENSP00000372286:p.Leu18Phe	192.0	0.0	0		211.0	94.0	0.445498	NM_001077711		Missense_Mutation	SNP	ENST00000382835.2	37	CCDS33532.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	G	14.33	2.502796	0.44558	0.00522	0.0	ENSG00000206107	ENST00000382835	T	0.03330	3.97	4.29	4.29	0.51040	.	0.619122	0.14168	U	0.336909	T	0.10594	0.0259	M	0.63428	1.95	0.36763	D	0.88338	D	0.89917	1.0	D	0.91635	0.999	T	0.00862	-1.1536	10	0.59425	D	0.04	-6.9941	12.5116	0.56009	0.0:0.0:1.0:0.0	.	18	Q3LI81	KR271_HUMAN	F	18	ENSP00000372286:L18F	ENSP00000372286:L18F	L	-	1	0	KRTAP27-1	30631806	0.995000	0.38212	0.952000	0.39060	0.168000	0.22595	3.701000	0.54793	2.665000	0.90641	0.579000	0.79373	CTC	G|0.997;A|0.003	0.003	strong		0.453	KRTAP27-1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132470.3	NM_001077711	
KRTAP19-6	337973	hgsc.bcm.edu	37	21	31914019	31914019	+	Missense_Mutation	SNP	C	C	T	rs77807247	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31914019C>T	ENST00000334046.5	-	1	164	c.134G>A	c.(133-135)cGc>cAc	p.R45H		NM_181612.2	NP_853643.1	Q3LI70	KR196_HUMAN	keratin associated protein 19-6	45						intermediate filament (GO:0005882)				breast(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	9						GCATGATGGGCGGCAGCAGCC	0.498													c|||	161	0.0321486	0.1135	0.0115	5008	,	,		14661	0.0		0.001	False		,,,				2504	0.002				p.R45H		Atlas-SNP	.											.	KRTAP19-6	16	.	0			c.G134A						PASS	.	C	HIS/ARG	371,4035	188.5+/-214.9	13,345,1845	110.0	120.0	116.0		134	-6.1	0.0	21	dbSNP_131	116	12,8588	9.8+/-36.6	0,12,4288	yes	missense	KRTAP19-6	NM_181612.2	29	13,357,6133	TT,TC,CC		0.1395,8.4203,2.9448	benign	45/59	31914019	383,12623	2203	4300	6503	SO:0001583	missense	337973	exon1			GATGGGCGGCAGC	AP001708	CCDS13598.1	21q22.1	2010-09-30			ENSG00000186925	ENSG00000186925		"""Keratin associated proteins"""	18941	protein-coding gene	gene with protein product						12359730	Standard	NM_181612		Approved	KAP19.6	uc002yok.1	Q3LI70	OTTHUMG00000057779	ENST00000334046.5:c.134G>A	21.37:g.31914019C>T	ENSP00000375107:p.Arg45His	94.0	0.0	0		97.0	43.0	0.443299	NM_181612	Q3LI71	Missense_Mutation	SNP	ENST00000334046.5	37	CCDS13598.1	64	0.029304029304029304	58	0.11788617886178862	6	0.016574585635359115	0	0.0	0	0.0	c	6.926	0.540492	0.13250	0.084203	0.001395	ENSG00000186925	ENST00000334046;ENST00000437381	T	0.11169	2.8	4.39	-6.09	0.02145	.	0.598882	0.13443	N	0.387478	T	0.00109	0.0003	.	.	.	0.09310	N	1	B	0.12013	0.005	B	0.04013	0.001	T	0.32587	-0.9901	9	0.87932	D	0	-1.818	7.3473	0.26670	0.1168:0.3112:0.0:0.5719	.	45	Q3LI70	KR196_HUMAN	H	45	ENSP00000375107:R45H	ENSP00000375107:R45H	R	-	2	0	KRTAP19-6	30835890	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.929000	0.03976	-1.347000	0.02208	-1.903000	0.00527	CGC	C|0.969;T|0.031	0.031	strong		0.498	KRTAP19-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128231.4		
PCSK5	5125	hgsc.bcm.edu	37	9	78506181	78506181	+	Silent	SNP	C	C	A	rs34813806	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:78506181C>A	ENST00000545128.1	+	1	622	c.84C>A	c.(82-84)ccC>ccA	p.P28P	PCSK5_ENST00000376752.4_Silent_p.P28P|PCSK5_ENST00000376767.3_Silent_p.P28P	NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	28					anterior/posterior pattern specification (GO:0009952)|cell-cell signaling (GO:0007267)|cytokine biosynthetic process (GO:0042089)|embryo implantation (GO:0007566)|embryonic digestive tract development (GO:0048566)|embryonic skeletal system development (GO:0048706)|heart development (GO:0007507)|kidney development (GO:0001822)|limb morphogenesis (GO:0035108)|nerve growth factor processing (GO:0032455)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|renin secretion into blood stream (GO:0002001)|respiratory tube development (GO:0030323)|signal peptide processing (GO:0006465)|viral life cycle (GO:0019058)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|secretory granule (GO:0030141)	peptidase activity (GO:0008233)|peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						GCCTGCTCCCCGTGTGTCGGA	0.677													C|||	55	0.0109824	0.0386	0.0058	5008	,	,		12564	0.0		0.0	False		,,,				2504	0.0				p.P28P		Atlas-SNP	.											.	PCSK5	329	.	0			c.C84A						PASS	.	C	,	116,4290	76.8+/-115.0	3,110,2090	42.0	51.0	48.0		84,84	-4.0	1.0	9	dbSNP_126	48	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous,coding-synonymous	PCSK5	NM_001190482.1,NM_006200.3	,	3,116,6384	AA,AC,CC		0.0698,2.6328,0.938	,	28/1861,28/914	78506181	122,12884	2203	4300	6503	SO:0001819	synonymous_variant	5125	exon1			GCTCCCCGTGTGT		CCDS6652.1, CCDS55320.1	9q21.13	2013-09-24			ENSG00000099139	ENSG00000099139			8747	protein-coding gene	gene with protein product		600488				7782070	Standard	NM_001190482		Approved	PC5, PC6, SPC6	uc004akc.2	Q92824	OTTHUMG00000020039	ENST00000545128.1:c.84C>A	9.37:g.78506181C>A		74.0	0.0	0		104.0	77.0	0.740385	NM_006200	F5H2G7|Q13527|Q96EP4	Silent	SNP	ENST00000545128.1	37	CCDS55320.1																																																																																			C|0.990;A|0.010	0.010	strong		0.677	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
VNN1	8876	hgsc.bcm.edu	37	6	133013576	133013576	+	Missense_Mutation	SNP	G	G	T	rs34535050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:133013576G>T	ENST00000367928.4	-	5	987	c.974C>A	c.(973-975)gCg>gAg	p.A325E		NM_004666.2	NP_004657.2	O95497	VNN1_HUMAN	vanin 1	325	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.		A -> E (in dbSNP:rs34535050). {ECO:0000269|Ref.4}.		acute inflammatory response (GO:0002526)|cellular component movement (GO:0006928)|chronic inflammatory response (GO:0002544)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|pantothenate metabolic process (GO:0015939)|positive regulation of T cell differentiation in thymus (GO:0033089)|response to oxidative stress (GO:0006979)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	GPI anchor binding (GO:0034235)|pantetheine hydrolase activity (GO:0017159)			NS(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)	31	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.0027)|GBM - Glioblastoma multiforme(226;0.0189)		TGATGAGAGCGCTTCTATACT	0.448													G|||	124	0.0247604	0.09	0.0058	5008	,	,		18388	0.0		0.001	False		,,,				2504	0.0				p.A325E		Atlas-SNP	.											.	VNN1	69	.	0			c.C974A						PASS	.	G	GLU/ALA	329,4077	173.7+/-203.5	15,299,1889	76.0	74.0	75.0		974	4.1	0.0	6	dbSNP_126	75	3,8597	2.2+/-6.3	0,3,4297	yes	missense	VNN1	NM_004666.2	107	15,302,6186	TT,TG,GG		0.0349,7.4671,2.5527	benign	325/514	133013576	332,12674	2203	4300	6503	SO:0001583	missense	8876	exon5			GAGAGCGCTTCTA	AJ132099	CCDS5159.1	6q23-q24	2013-02-13			ENSG00000112299	ENSG00000112299	3.5.1.92	"""Vanins"""	12705	protein-coding gene	gene with protein product		603570				9790769	Standard	NM_004666		Approved	Tiff66	uc003qdo.3	O95497	OTTHUMG00000015587	ENST00000367928.4:c.974C>A	6.37:g.133013576G>T	ENSP00000356905:p.Ala325Glu	63.0	0.0	0		67.0	33.0	0.492537	NM_004666	A8K310|Q4JFW6|Q4VAS7|Q4VAS8|Q4VAS9|Q9UF16|Q9UJF4	Missense_Mutation	SNP	ENST00000367928.4	37	CCDS5159.1	39	0.017857142857142856	36	0.07317073170731707	3	0.008287292817679558	0	0.0	0	0.0	G	0.747	-0.774241	0.02951	0.074671	3.49E-4	ENSG00000112299	ENST00000367928	D	0.87256	-2.23	5.85	4.05	0.47172	Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (1);	1.202920	0.05711	N	0.595981	T	0.67316	0.2880	L	0.46157	1.445	0.09310	N	1	B	0.15141	0.012	B	0.20767	0.031	T	0.55082	-0.8196	10	0.15952	T	0.53	-14.8515	5.0557	0.14531	0.067:0.23:0.4724:0.2306	rs34535050	325	O95497	VNN1_HUMAN	E	325	ENSP00000356905:A325E	ENSP00000356905:A325E	A	-	2	0	VNN1	133055269	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.013000	0.13310	0.796000	0.33947	0.563000	0.77884	GCG	G|0.975;T|0.025	0.025	strong		0.448	VNN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042263.1		
PDE4C	5143	hgsc.bcm.edu	37	19	18330144	18330144	+	Missense_Mutation	SNP	C	C	T	rs34503849	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18330144C>T	ENST00000355502.3	-	12	1737	c.866G>A	c.(865-867)cGg>cAg	p.R289Q	PDE4C_ENST00000594465.3_Missense_Mutation_p.R289Q|AC068499.10_ENST00000594805.3_RNA|PDE4C_ENST00000597297.1_Missense_Mutation_p.R59Q|PDE4C_ENST00000539010.1_Missense_Mutation_p.R58Q|PDE4C_ENST00000447275.3_Missense_Mutation_p.R183Q|PDE4C_ENST00000598111.2_Missense_Mutation_p.R59Q|PDE4C_ENST00000594617.3_Missense_Mutation_p.R289Q|PDE4C_ENST00000262805.12_Missense_Mutation_p.R257Q			Q08493	PDE4C_HUMAN	phosphodiesterase 4C, cAMP-specific	289			R -> Q (in dbSNP:rs34503849).		cAMP catabolic process (GO:0006198)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular space (GO:0005615)|primary cilium (GO:0072372)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33					Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	GCCACTGATCCGGGACATGGG	0.642													C|||	87	0.0173722	0.0613	0.0058	5008	,	,		16374	0.001		0.001	False		,,,				2504	0.0				p.R289Q		Atlas-SNP	.											.	PDE4C	80	.	0			c.G866A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	201,4205	125.7+/-162.9	4,193,2006	52.0	50.0	51.0		866,770,548	3.7	1.0	19	dbSNP_126	51	0,8600		0,0,4300	yes	missense,missense,missense	PDE4C	NM_000923.4,NM_001098818.2,NM_001098819.2	43,43,43	4,193,6306	TT,TC,CC		0.0,4.562,1.5454	benign,benign,benign	289/713,257/681,183/607	18330144	201,12805	2203	4300	6503	SO:0001583	missense	5143	exon9			CTGATCCGGGACA		CCDS12373.1, CCDS42523.1, CCDS46016.1	19p13.11	2010-06-24	2010-06-24			ENSG00000105650	3.1.4.17	"""Phosphodiesterases"""	8782	protein-coding gene	gene with protein product	"""phosphodiesterase E1 dunce homolog (Drosophila)"""	600128	"""phosphodiesterase 4C, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E1)"""	DPDE1			Standard	NM_001098818		Approved		uc002nik.4	Q08493		ENST00000355502.3:c.866G>A	19.37:g.18330144C>T	ENSP00000347689:p.Arg289Gln	81.0	0.0	0		94.0	55.0	0.585106	NM_000923	B3KTC4|Q9UN44|Q9UN45|Q9UN46|Q9UPJ6	Missense_Mutation	SNP	ENST00000355502.3	37	CCDS12373.1	37	0.01694139194139194	33	0.06707317073170732	3	0.008287292817679558	1	0.0017482517482517483	0	0.0	C	0.914	-0.718231	0.03182	0.04562	0.0	ENSG00000105650	ENST00000536045;ENST00000355502;ENST00000536507;ENST00000262805;ENST00000447275;ENST00000545961;ENST00000336173;ENST00000539010;ENST00000543547	T;T;T;T	0.68479	-0.31;-0.33;-0.32;-0.02	4.75	3.65	0.41850	.	1.896290	0.02956	N	0.142375	T	0.01730	0.0055	N	0.00038	-2.52	0.28550	N	0.911646	B;B;B;B	0.11235	0.0;0.004;0.001;0.0	B;B;B;B	0.06405	0.001;0.002;0.002;0.001	T	0.48570	-0.9024	10	0.02654	T	1	.	8.4709	0.32984	0.0:0.0967:0.0:0.9033	rs34503849	289;257;95;59	Q08493;Q08493-3;O43850;O76104	PDE4C_HUMAN;.;.;.	Q	368;289;277;257;183;95;58;58;398	ENSP00000347689:R289Q;ENSP00000262805:R257Q;ENSP00000402091:R183Q;ENSP00000439470:R58Q	ENSP00000262805:R257Q	R	-	2	0	PDE4C	18191144	1.000000	0.71417	0.991000	0.47740	0.118000	0.20060	4.475000	0.60210	0.657000	0.30906	-0.657000	0.03884	CGG	C|0.982;T|0.018	0.018	strong		0.642	PDE4C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466295.1		
PAN3	255967	hgsc.bcm.edu	37	13	28750683	28750683	+	Silent	SNP	A	A	G	rs142608239	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:28750683A>G	ENST00000380958.3	+	3	758	c.606A>G	c.(604-606)ccA>ccG	p.P202P	PAN3_ENST00000399613.1_Silent_p.P56P	NM_175854.7	NP_787050.6			PAN3 poly(A) specific ribonuclease subunit											endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)	Colorectal(13;0.000334)	all cancers(112;0.0102)|Epithelial(112;0.0803)|GBM - Glioblastoma multiforme(144;0.121)|OV - Ovarian serous cystadenocarcinoma(117;0.13)|Lung(94;0.174)		GTGCCAAGCCATATTCAGCCC	0.338													A|||	17	0.00339457	0.0121	0.0014	5008	,	,		18080	0.0		0.0	False		,,,				2504	0.0				p.P202P		Atlas-SNP	.											.	PAN3	123	.	0			c.A606G						PASS	.	A		60,4346	58.7+/-95.3	1,58,2144	125.0	122.0	123.0		606	4.4	1.0	13	dbSNP_134	123	0,8600		0,0,4300	no	coding-synonymous	PAN3	NM_175854.7		1,58,6444	GG,GA,AA		0.0,1.3618,0.4613		202/888	28750683	60,12946	2203	4300	6503	SO:0001819	synonymous_variant	255967	exon3			CAAGCCATATTCA	AK091307	CCDS9329.1, CCDS9329.2	13q12.2	2014-03-27	2014-03-27		ENSG00000152520	ENSG00000152520			29991	protein-coding gene	gene with protein product			"""PAN3 poly(A) specific ribonuclease subunit homolog (S. cerevisiae)"""			14583602	Standard	NM_175854		Approved		uc001urz.3	Q58A45	OTTHUMG00000016645	ENST00000380958.3:c.606A>G	13.37:g.28750683A>G		86.0	0.0	0		123.0	72.0	0.585366	NM_175854		Silent	SNP	ENST00000380958.3	37	CCDS9329.2																																																																																			A|0.995;G|0.005	0.005	strong		0.338	PAN3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044318.4	NM_175854	
ECHDC3	79746	hgsc.bcm.edu	37	10	11797484	11797484	+	Silent	SNP	A	A	G	rs34878615	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:11797484A>G	ENST00000379215.4	+	4	679	c.468A>G	c.(466-468)caA>caG	p.Q156Q	ECHDC3_ENST00000496136.1_3'UTR	NM_024693.4	NP_078969	Q96DC8	ECHD3_HUMAN	enoyl CoA hydratase domain containing 3	156						mitochondrion (GO:0005739)	catalytic activity (GO:0003824)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)	4						CCGGCTGTCAACTGGTTGCCA	0.607													A|||	94	0.01877	0.0681	0.0043	5008	,	,		13971	0.0		0.001	False		,,,				2504	0.0				p.Q156Q		Atlas-SNP	.											.	ECHDC3	12	.	0			c.A468G						PASS	.	A		251,4155	144.6+/-179.5	10,231,1962	51.0	42.0	45.0		468	3.4	1.0	10	dbSNP_126	45	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	ECHDC3	NM_024693.4		10,235,6258	GG,GA,AA		0.0465,5.6968,1.9606		156/304	11797484	255,12751	2203	4300	6503	SO:0001819	synonymous_variant	79746	exon4			CTGTCAACTGGTT	AF275677	CCDS7084.1	10p14	2010-04-30	2010-04-30		ENSG00000134463	ENSG00000134463			23489	protein-coding gene	gene with protein product			"""enoyl Coenzyme A hydratase domain containing 3"""			12477932	Standard	NM_024693		Approved	FLJ20909	uc001ikw.4	Q96DC8	OTTHUMG00000017675	ENST00000379215.4:c.468A>G	10.37:g.11797484A>G		104.0	0.0	0		100.0	53.0	0.53	NM_024693	Q53HR9|Q5W0J7|Q8WYY8|Q9BVL8|Q9H7G4	Silent	SNP	ENST00000379215.4	37	CCDS7084.1																																																																																			A|0.981;G|0.019	0.019	strong		0.607	ECHDC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046771.1	NM_024693	
GPD2	2820	hgsc.bcm.edu	37	2	157425931	157425931	+	Missense_Mutation	SNP	A	A	C	rs35096779	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:157425931A>C	ENST00000310454.6	+	11	1729	c.1357A>C	c.(1357-1359)Aaa>Caa	p.K453Q	GPD2_ENST00000540309.1_Intron|GPD2_ENST00000438166.2_Missense_Mutation_p.K453Q|GPD2_ENST00000409125.4_Missense_Mutation_p.K226Q|GPD2_ENST00000409674.1_Missense_Mutation_p.K453Q	NM_001083112.2	NP_001076581.2	P43304	GPDM_HUMAN	glycerol-3-phosphate dehydrogenase 2 (mitochondrial)	453			K -> Q (in dbSNP:rs35096779).		camera-type eye development (GO:0043010)|cellular lipid metabolic process (GO:0044255)|gluconeogenesis (GO:0006094)|glycerol catabolic process (GO:0019563)|glycerol-3-phosphate metabolic process (GO:0006072)|multicellular organism growth (GO:0035264)|small molecule metabolic process (GO:0044281)	glycerol-3-phosphate dehydrogenase complex (GO:0009331)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|glycerol-3-phosphate dehydrogenase activity (GO:0004368)|sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity (GO:0052591)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(1)|stomach(1)	22						TGCTGCTGTCAAAACTCATAA	0.423													A|||	166	0.033147	0.1165	0.0159	5008	,	,		17986	0.0		0.001	False		,,,				2504	0.0				p.K453Q		Atlas-SNP	.											.	GPD2	59	.	0			c.A1357C						PASS	.	A	GLN/LYS,GLN/LYS	527,3879	239.6+/-250.7	30,467,1706	79.0	78.0	78.0		1357,1357	3.3	0.8	2	dbSNP_126	78	6,8594	3.7+/-12.6	0,6,4294	yes	missense,missense	GPD2	NM_000408.4,NM_001083112.2	53,53	30,473,6000	CC,CA,AA		0.0698,11.961,4.0981	benign,benign	453/728,453/728	157425931	533,12473	2203	4300	6503	SO:0001583	missense	2820	exon11			GCTGTCAAAACTC		CCDS2202.1	2q24.1	2013-01-10			ENSG00000115159	ENSG00000115159	1.1.1.8	"""EF-hand domain containing"""	4456	protein-coding gene	gene with protein product		138430					Standard	NM_001083112		Approved		uc002tzd.4	P43304	OTTHUMG00000131951	ENST00000310454.6:c.1357A>C	2.37:g.157425931A>C	ENSP00000308610:p.Lys453Gln	85.0	0.0	0		120.0	55.0	0.458333	NM_001083112	A8K4V0|B3KSA9|Q59FR1|Q9HAP9	Missense_Mutation	SNP	ENST00000310454.6	37	CCDS2202.1	63	0.028846153846153848	56	0.11382113821138211	7	0.019337016574585635	0	0.0	0	0.0	A	14.01	2.408743	0.42715	0.11961	6.98E-4	ENSG00000115159	ENST00000310454;ENST00000409125;ENST00000438166;ENST00000409674	T;T;T;T	0.60171	0.21;0.42;0.21;0.21	5.78	3.34	0.38264	.	0.179590	0.56097	N	0.000021	T	0.00967	0.0032	L	0.48877	1.53	0.39253	D	0.96407	B	0.06786	0.001	B	0.13407	0.009	T	0.02288	-1.1182	10	0.52906	T	0.07	.	13.5438	0.61690	0.6092:0.3908:0.0:0.0	rs35096779	453	P43304	GPDM_HUMAN	Q	453;226;453;453	ENSP00000308610:K453Q;ENSP00000386484:K226Q;ENSP00000409708:K453Q;ENSP00000386425:K453Q	ENSP00000308610:K453Q	K	+	1	0	GPD2	157134177	0.997000	0.39634	0.775000	0.31657	0.987000	0.75469	2.271000	0.43364	0.427000	0.26145	0.528000	0.53228	AAA	A|0.963;C|0.037	0.037	strong		0.423	GPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254910.3		
HEPACAM	220296	hgsc.bcm.edu	37	11	124794763	124794763	+	Silent	SNP	T	T	G	rs36089266	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124794763T>G	ENST00000298251.4	-	2	693	c.288A>C	c.(286-288)cgA>cgC	p.R96R		NM_152722.4	NP_689935.2			hepatic and glial cell adhesion molecule											breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|pancreas(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22	all_hematologic(175;0.215)	Breast(109;0.00222)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.54e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0308)		GGATACGGTCTCGATAGTCAG	0.587													T|||	27	0.00539137	0.0204	0.0	5008	,	,		21438	0.0		0.0	False		,,,				2504	0.0				p.R96R		Atlas-SNP	.											HEPACAM,NS,carcinoma,-1,4	HEPACAM	64	4	0			c.A288C						PASS	.	T		52,4350	53.6+/-89.4	1,50,2150	142.0	125.0	131.0		288	1.8	1.0	11	dbSNP_126	131	0,8598		0,0,4299	no	coding-synonymous	HEPACAM	NM_152722.4		1,50,6449	GG,GT,TT		0.0,1.1813,0.4		96/417	124794763	52,12948	2201	4299	6500	SO:0001819	synonymous_variant	220296	exon2			ACGGTCTCGATAG	AK098396	CCDS8456.1	11q24.2	2013-01-29	2011-02-11		ENSG00000165478	ENSG00000165478		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26361	protein-coding gene	gene with protein product	"""glial cell adhesion molecule"""	611642	"""hepatocyte cell adhesion molecule"""			15885354, 15917256	Standard	NM_152722		Approved	FLJ25530, hepaCAM, GLIALCAM	uc001qbk.3	Q14CZ8	OTTHUMG00000165938	ENST00000298251.4:c.288A>C	11.37:g.124794763T>G		127.0	0.0	0		111.0	57.0	0.513514	NM_152722		Silent	SNP	ENST00000298251.4	37	CCDS8456.1																																																																																			T|0.994;G|0.006	0.006	strong		0.587	HEPACAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387125.1	NM_152722	
BCAT1	586	hgsc.bcm.edu	37	12	25031515	25031515	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:25031515T>C	ENST00000261192.7	-	5	985	c.459A>G	c.(457-459)ccA>ccG	p.P153P	BCAT1_ENST00000342945.5_Silent_p.P92P|BCAT1_ENST00000538118.1_Silent_p.P152P|BCAT1_ENST00000539282.1_Silent_p.P165P|BCAT1_ENST00000539780.1_Silent_p.P116P|BCAT1_ENST00000544418.1_5'UTR	NM_001178091.1|NM_005504.6	NP_001171562.1|NP_005495.2	P54687	BCAT1_HUMAN	branched chain amino-acid transaminase 1, cytosolic	153					branched-chain amino acid biosynthetic process (GO:0009082)|branched-chain amino acid catabolic process (GO:0009083)|cell proliferation (GO:0008283)|cellular nitrogen compound metabolic process (GO:0034641)|G1/S transition of mitotic cell cycle (GO:0000082)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	branched-chain-amino-acid transaminase activity (GO:0004084)|L-isoleucine transaminase activity (GO:0052656)|L-leucine transaminase activity (GO:0052654)|L-valine transaminase activity (GO:0052655)			breast(1)|large_intestine(1)|lung(3)|prostate(2)	7	Acute lymphoblastic leukemia(6;0.00112)|all_hematologic(7;0.00152)|Ovarian(17;0.107)|Colorectal(261;0.196)				Gabapentin(DB00996)|L-Isoleucine(DB00167)|L-Leucine(DB00149)|L-Valine(DB00161)	ATGTTGAATATGGGACCCATT	0.363																																					p.P165P		Atlas-SNP	.											.	BCAT1	44	.	0			c.A495G						PASS	.						94.0	91.0	92.0					12																	25031515		1894	4128	6022	SO:0001819	synonymous_variant	586	exon5			TGAATATGGGACC		CCDS44845.1, CCDS53760.1, CCDS53761.1, CCDS53762.1, CCDS53763.1	12p12.1	2012-10-02	2010-05-07		ENSG00000060982	ENSG00000060982	2.6.1.42		976	protein-coding gene	gene with protein product		113520	"""branched chain aminotransferase 1, cytosolic"""	BCT1		9165094	Standard	NM_005504		Approved		uc010six.2	P54687	OTTHUMG00000169053	ENST00000261192.7:c.459A>G	12.37:g.25031515T>C		112.0	0.0	0		106.0	9.0	0.0849057	NM_001178093	B3KY27|B7Z2M5|B7Z5L0|F5H5E4|Q68DQ7|Q96MY9	Silent	SNP	ENST00000261192.7	37	CCDS44845.1																																																																																			.	.	none		0.363	BCAT1-001	KNOWN	upstream_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402080.1	NM_005504	
CST4	1472	hgsc.bcm.edu	37	20	23669488	23669488	+	Missense_Mutation	SNP	T	T	C	rs73902130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:23669488T>C	ENST00000217423.3	-	1	189	c.119A>G	c.(118-120)aAt>aGt	p.N40S		NM_001899.2	NP_001890.1	P01036	CYTS_HUMAN	cystatin S	40					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	16	Lung NSC(19;0.0789)|Colorectal(13;0.0993)|all_lung(19;0.169)					CCACTCATCATTGAGGTCTGC	0.577													.|||	170	0.0339457	0.1225	0.0115	5008	,	,		18118	0.0		0.0	False		,,,				2504	0.0				p.N40S		Atlas-SNP	.											CST4,colon,carcinoma,-1,1	CST4	37	1	0			c.A119G						PASS	.	T	SER/ASN	409,3997	201.1+/-224.2	18,373,1812	145.0	124.0	131.0		119	1.0	0.0	20	dbSNP_130	131	3,8597	2.2+/-6.3	0,3,4297	yes	missense	CST4	NM_001899.2	46	18,376,6109	CC,CT,TT		0.0349,9.2828,3.1678	benign	40/142	23669488	412,12594	2203	4300	6503	SO:0001583	missense	1472	exon1			TCATCATTGAGGT		CCDS13159.1	20p11.2	2008-04-15			ENSG00000101441	ENSG00000101441			2476	protein-coding gene	gene with protein product		123857				1801729	Standard	NM_001899		Approved		uc002wto.1	P01036	OTTHUMG00000032083	ENST00000217423.3:c.119A>G	20.37:g.23669488T>C	ENSP00000217423:p.Asn40Ser	217.0	0.0	0		274.0	144.0	0.525547	NM_001899	Q9UBI5|Q9UCS9	Missense_Mutation	SNP	ENST00000217423.3	37	CCDS13159.1	58	0.026556776556776556	51	0.10365853658536585	7	0.019337016574585635	0	0.0	0	0.0	T	5.380	0.255435	0.10185	0.092828	3.49E-4	ENSG00000101441	ENST00000217423	T	0.15256	2.44	2.19	1.01	0.19927	Proteinase inhibitor I25, cystatin (2);	0.362807	0.27236	N	0.020294	T	0.00241	0.0007	N	0.26042	0.785	0.09310	N	1	B	0.10296	0.003	B	0.08055	0.003	T	0.36286	-0.9754	10	0.20519	T	0.43	.	4.081	0.09925	0.0:0.1933:0.0:0.8067	.	40	P01036	CYTS_HUMAN	S	40	ENSP00000217423:N40S	ENSP00000217423:N40S	N	-	2	0	CST4	23617488	0.000000	0.05858	0.001000	0.08648	0.015000	0.08874	0.251000	0.18257	0.094000	0.17404	0.358000	0.22013	AAT	T|0.964;C|0.036	0.036	strong		0.577	CST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078349.2	NM_001899	
ENPP2	5168	hgsc.bcm.edu	37	8	120575112	120575112	+	Silent	SNP	G	G	A	rs61740048	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:120575112G>A	ENST00000075322.6	-	24	2464	c.2406C>T	c.(2404-2406)aaC>aaT	p.N802N	ENPP2_ENST00000427067.2_Silent_p.N823N|ENPP2_ENST00000522826.1_Silent_p.N827N|ENPP2_ENST00000522167.1_Silent_p.N437N|ENPP2_ENST00000259486.6_Silent_p.N854N	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2	802					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylcholine catabolic process (GO:0034638)|phospholipid catabolic process (GO:0009395)|regulation of cell migration (GO:0030334)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alkylglycerophosphoethanolamine phosphodiesterase activity (GO:0047391)|calcium ion binding (GO:0005509)|hydrolase activity (GO:0016787)|lysophospholipase activity (GO:0004622)|nucleic acid binding (GO:0003676)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.N854N(1)		breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(30)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)	69	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			AGCTCTCCTCGTTGTCAGGCC	0.478													G|||	21	0.00419329	0.0159	0.0	5008	,	,		19836	0.0		0.0	False		,,,				2504	0.0				p.N854N	Melanoma(20;305 879 2501 4818 31020)	Atlas-SNP	.											ENPP2_ENST00000522826,colon,carcinoma,0,7	ENPP2	254	7	1	Substitution - coding silent(1)	kidney(1)	c.C2562T						PASS	.	G	,,	48,4358	48.2+/-83.0	0,48,2155	109.0	97.0	101.0		2406,2481,2562	-6.0	0.2	8	dbSNP_129	101	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	ENPP2	NM_001040092.1,NM_001130863.1,NM_006209.3	,,	0,49,6454	AA,AG,GG		0.0116,1.0894,0.3767	,,	802/864,827/889,854/916	120575112	49,12957	2203	4300	6503	SO:0001819	synonymous_variant	5168	exon25			CTCCTCGTTGTCA	D45421	CCDS6329.1, CCDS34936.1, CCDS47914.1	8q24.12	2014-04-09	2008-08-01		ENSG00000136960	ENSG00000136960	3.1.4.1, 3.6.1.9		3357	protein-coding gene	gene with protein product	"""autotaxin"""	601060		PDNP2		8586446	Standard	NM_001040092		Approved	ATX, PD-IALPHA	uc003yos.2	Q13822	OTTHUMG00000164995	ENST00000075322.6:c.2406C>T	8.37:g.120575112G>A		101.0	0.0	0		121.0	61.0	0.504132	NM_006209	A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Silent	SNP	ENST00000075322.6	37	CCDS34936.1																																																																																			G|0.997;A|0.003	0.003	strong		0.478	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1		
ALK	238	hgsc.bcm.edu	37	2	29445425	29445425	+	Silent	SNP	G	G	A	rs56146053	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:29445425G>A	ENST00000389048.3	-	21	4314	c.3408C>T	c.(3406-3408)tcC>tcT	p.S1136S	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1136	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)		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)	TGGGCATTCCGGACACCTGGC	0.572			"""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				G|||	167	0.0333466	0.1225	0.0072	5008	,	,		16613	0.0		0.0	False		,,,				2504	0.0				p.S1136S		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	ALK,colon,carcinoma,0,1	ALK	533	1	0			c.C3408T						PASS	.	G		379,4027	193.0+/-218.2	13,353,1837	57.0	55.0	56.0		3408	-5.2	0.9	2	dbSNP_129	56	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ALK	NM_004304.4		13,354,6136	AA,AG,GG		0.0116,8.6019,2.9217		1136/1621	29445425	380,12626	2203	4300	6503	SO:0001819	synonymous_variant	238	exon21	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	CATTCCGGACACC	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.3408C>T	2.37:g.29445425G>A		125.0	0.0	0		138.0	57.0	0.413043	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			G|0.970;A|0.030	0.030	strong		0.572	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
TMEM132B	114795	hgsc.bcm.edu	37	12	125900104	125900104	+	Silent	SNP	A	A	T	rs143188464	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:125900104A>T	ENST00000299308.3	+	3	980	c.972A>T	c.(970-972)atA>atT	p.I324I		NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	324						integral component of membrane (GO:0016021)				NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		GTGTGAAGATAACGGCAGTGA	0.468													A|||	30	0.00599042	0.0219	0.0014	5008	,	,		18015	0.0		0.0	False		,,,				2504	0.0				p.I324I		Atlas-SNP	.											.	TMEM132B	207	.	0			c.A972T						PASS	.	A		118,4212		0,118,2047	77.0	92.0	87.0		972	-11.3	0.0	12	dbSNP_134	87	1,8527		0,1,4263	no	coding-synonymous	TMEM132B	NM_052907.2		0,119,6310	TT,TA,AA		0.0117,2.7252,0.9255		324/1079	125900104	119,12739	2165	4264	6429	SO:0001819	synonymous_variant	114795	exon3			GAAGATAACGGCA	AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.972A>T	12.37:g.125900104A>T		157.0	0.0	0		156.0	81.0	0.519231	NM_052907	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Silent	SNP	ENST00000299308.3	37	CCDS41859.1																																																																																			A|0.994;T|0.006	0.006	strong		0.468	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1	NM_052907	
CYFIP2	26999	hgsc.bcm.edu	37	5	156742033	156742033	+	Silent	SNP	C	C	T	rs17054446	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:156742033C>T	ENST00000521420.1	+	12	1300	c.1209C>T	c.(1207-1209)ggC>ggT	p.G403G	CYFIP2_ENST00000541131.1_Silent_p.G354G|CYFIP2_ENST00000377576.3_Silent_p.G429G|CYFIP2_ENST00000522463.1_Silent_p.G233G|CYFIP2_ENST00000435847.2_Silent_p.G103G|CYFIP2_ENST00000347377.6_Silent_p.G429G|CYFIP2_ENST00000318218.6_Silent_p.G429G|CYFIP2_ENST00000442283.2_5'UTR					cytoplasmic FMR1 interacting protein 2											breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ACTGTCCTGGCACCGCGGAGG	0.512													C|||	33	0.00658946	0.0234	0.0029	5008	,	,		19474	0.0		0.0	False		,,,				2504	0.0				p.G429G		Atlas-SNP	.											.	CYFIP2	354	.	0			c.C1287T						PASS	.	C	,,	65,4037		0,65,1986	64.0	64.0	64.0		1287,1287,1287	4.6	1.0	5	dbSNP_123	64	0,8400		0,0,4200	no	coding-synonymous,coding-synonymous,coding-synonymous	CYFIP2	NM_001037332.2,NM_001037333.1,NM_014376.2	,,	0,65,6186	TT,TC,CC		0.0,1.5846,0.5199	,,	429/1254,429/1254,429/1254	156742033	65,12437	2051	4200	6251	SO:0001819	synonymous_variant	26999	exon13			TCCTGGCACCGCG	AF160973	CCDS75364.1	5q34	2008-07-18				ENSG00000055163			13760	protein-coding gene	gene with protein product	"""p53 inducible protein"""	606323				11438699	Standard	NM_001037333		Approved	PIR121	uc021ygm.1	Q96F07		ENST00000521420.1:c.1209C>T	5.37:g.156742033C>T		116.0	0.0	0		104.0	49.0	0.471154	NM_001037332		Silent	SNP	ENST00000521420.1	37																																																																																				C|0.993;T|0.007	0.007	strong		0.512	CYFIP2-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000373710.1	NM_001037332	
BTK	695	hgsc.bcm.edu	37	X	100617218	100617218	+	Silent	SNP	A	A	G	rs148358153	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:100617218A>G	ENST00000308731.7	-	7	694	c.531T>C	c.(529-531)ccT>ccC	p.P177P	BTK_ENST00000372880.1_Silent_p.P177P	NM_000061.2	NP_000052.1	Q06187	BTK_HUMAN	Bruton agammaglobulinemia tyrosine kinase	177					adaptive immune response (GO:0002250)|apoptotic signaling pathway (GO:0097190)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|calcium-mediated signaling (GO:0019722)|cell maturation (GO:0048469)|Fc-epsilon receptor signaling pathway (GO:0038095)|histamine secretion by mast cell (GO:0002553)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm development (GO:0007498)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of B cell apoptotic process (GO:0002902)|regulation of B cell cytokine production (GO:0002721)|response to organic substance (GO:0010033)|response to reactive oxygen species (GO:0000302)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|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, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein tyrosine kinase activity (GO:0004713)			breast(4)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(25)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50						GAGAACTCCCAGGTTTTAAGC	0.498									Agammaglobulinemia, X-linked				A|||	26	0.00688742	0.0182	0.0029	3775	,	,		13779	0.0		0.0	False		,,,				2504	0.0				p.P177P		Atlas-SNP	.											.	BTK	87	.	0			c.T531C						PASS	.	A		73,3762		0,67,6,1565,565	111.0	95.0	100.0		531	2.7	1.0	X	dbSNP_134	100	0,6728		0,0,0,2428,1872	no	coding-synonymous	BTK	NM_000061.2		0,67,6,3993,2437	GG,GA,G,AA,A		0.0,1.9035,0.6911		177/660	100617218	73,10490	2203	4300	6503	SO:0001819	synonymous_variant	695	exon7	Familial Cancer Database	Bruton Type Agammaglobulinemia	ACTCCCAGGTTTT	AK057105	CCDS14482.1, CCDS76002.1, CCDS76003.1	Xq21.33-q22	2014-09-17			ENSG00000010671	ENSG00000010671	2.7.10.1	"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	1133	protein-coding gene	gene with protein product		300300		AGMX1, IMD1		8380905	Standard	NM_000061		Approved	ATK, XLA, PSCTK1	uc004ehg.2	Q06187	OTTHUMG00000022022	ENST00000308731.7:c.531T>C	X.37:g.100617218A>G		126.0	0.0	0		101.0	46.0	0.455446	NM_000061	B2RAW1|Q32ML5	Silent	SNP	ENST00000308731.7	37	CCDS14482.1																																																																																			A|0.993;G|0.007	0.007	strong		0.498	BTK-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057532.2	NM_000061	
MUC4	4585	hgsc.bcm.edu	37	3	195513425	195513425	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195513425C>G	ENST00000463781.3	-	2	5485	c.5026G>C	c.(5026-5028)Ggt>Cgt	p.G1676R	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.G1676R	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)		GTGGCGTGACCGGTGGATGCT	0.607																																					p.G1676R		Atlas-SNP	.											MUC4_ENST00000463781,rectum,carcinoma,0,1	MUC4	1505	1	0			c.G5026C						scavenged	.						36.0	34.0	34.0					3																	195513425		689	1583	2272	SO:0001583	missense	4585	exon2			CGTGACCGGTGGA	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.5026G>C	3.37:g.195513425C>G	ENSP00000417498:p.Gly1676Arg	523.0	0.0	0		468.0	61.0	0.130342	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	2.575	-0.298681	0.05532	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32515	1.49;1.45	0.423	-0.846	0.10734	.	.	.	.	.	T	0.22936	0.0554	N	0.08118	0	0.09310	N	1	D	0.64830	0.994	P	0.59546	0.859	T	0.12993	-1.0526	8	.	.	.	.	4.1233	0.10116	0.651:0.3489:1.0E-4:0.0	.	1676	E7ESK3	.	R	1676	ENSP00000417498:G1676R;ENSP00000420243:G1676R	.	G	-	1	0	MUC4	196997820	0.000000	0.05858	0.006000	0.13384	0.006000	0.05464	-0.235000	0.09016	-0.784000	0.04528	0.089000	0.15464	GGT	.	.	none		0.607	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
KRTAP10-12	386685	hgsc.bcm.edu	37	21	46117746	46117746	+	Silent	SNP	C	C	T	rs112431728	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46117746C>T	ENST00000400365.3	+	1	660	c.630C>T	c.(628-630)ccC>ccT	p.P210P	TSPEAR_ENST00000323084.4_Intron	NM_198699.1	NP_941972.1	P60413	KR10C_HUMAN	keratin associated protein 10-12	210	19 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(8)	9						GCCGCGTGCCCGTCCCCTCCT	0.721													a|||	33	0.00658946	0.0242	0.0014	5008	,	,		14658	0.0		0.0	False		,,,				2504	0.0				p.P210P		Atlas-SNP	.											.	KRTAP10-12	21	.	0			c.C630T						PASS	.	A	,	115,4287		1,113,2087	53.0	68.0	63.0		,630	0.8	0.4	21	dbSNP_132	63	1,8581		0,1,4290	no	intron,coding-synonymous	TSPEAR,KRTAP10-12	NM_144991.2,NM_198699.1	,	1,114,6377	TT,TC,CC		0.0117,2.6124,0.8934	,	,210/246	46117746	116,12868	2201	4291	6492	SO:0001819	synonymous_variant	386685	exon1			CGTGCCCGTCCCC	AB076364	CCDS42967.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000189169	ENSG00000189169		"""Keratin associated proteins"""	20533	protein-coding gene	gene with protein product			"""keratin associated protein 18-12"""	KRTAP18-12			Standard	NM_198699		Approved	KRTAP18.12, KAP10.12	uc002zfw.1	P60413	OTTHUMG00000057629	ENST00000400365.3:c.630C>T	21.37:g.46117746C>T		83.0	0.0	0		81.0	44.0	0.54321	NM_198699	B2RPA3	Silent	SNP	ENST00000400365.3	37	CCDS42967.1																																																																																			C|0.994;T|0.006	0.006	strong		0.721	KRTAP10-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128032.1	NM_198699	
NIPBL	25836	hgsc.bcm.edu	37	5	36986297	36986297	+	Silent	SNP	A	A	G	rs1669445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:36986297A>G	ENST00000282516.8	+	10	3514	c.3015A>G	c.(3013-3015)ctA>ctG	p.L1005L	NIPBL_ENST00000448238.2_Silent_p.L1005L|NIPBL_ENST00000504430.1_3'UTR	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	1005					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			TAGTTGTGCTACAAAAACTGT	0.333													A|||	184	0.0367412	0.1362	0.0058	5008	,	,		17335	0.0		0.0	False		,,,				2504	0.0				p.L1005L		Atlas-SNP	.											.	NIPBL	513	.	0			c.A3015G						PASS	.	A	,	504,3902	228.1+/-243.1	27,450,1726	130.0	147.0	141.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3015,3015	1.7	1.0	5	dbSNP_89	141	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	NIPBL	NM_015384.4,NM_133433.3	,	27,451,6025	GG,GA,AA		0.0116,11.4389,3.8828	,	1005/2698,1005/2805	36986297	505,12501	2203	4300	6503	SO:0001819	synonymous_variant	25836	exon10			TGTGCTACAAAAA	AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"""sister chromatid cohesion 2 homolog (yeast)"""	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.3015A>G	5.37:g.36986297A>G		33.0	0.0	0		45.0	22.0	0.488889	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Silent	SNP	ENST00000282516.8	37	CCDS3920.1																																																																																			A|0.961;G|0.039	0.039	strong		0.333	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384	
KPRP	448834	hgsc.bcm.edu	37	1	152732998	152732998	+	Missense_Mutation	SNP	C	C	T	rs140912923	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152732998C>T	ENST00000606109.1	+	1	962	c.934C>T	c.(934-936)Cgc>Tgc	p.R312C	KPRP_ENST00000368773.1_Missense_Mutation_p.R312C			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	312	Pro-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGTCCTCGCCGCCCCATTTC	0.597													C|||	24	0.00479233	0.0174	0.0014	5008	,	,		16798	0.0		0.0	False		,,,				2504	0.0				p.R312C		Atlas-SNP	.											KPRP,NS,carcinoma,0,3	KPRP	152	3	0			c.C934T						PASS	.	C	CYS/ARG	69,4337	62.9+/-100.1	2,65,2136	48.0	47.0	48.0		934	-8.3	0.0	1	dbSNP_134	48	0,8600		0,0,4300	no	missense	KPRP	NM_001025231.1	180	2,65,6436	TT,TC,CC		0.0,1.566,0.5305	possibly-damaging	312/580	152732998	69,12937	2203	4300	6503	SO:0001583	missense	448834	exon2			CCTCGCCGCCCCA	AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"""chromosome 1 open reading frame 45"""	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.934C>T	1.37:g.152732998C>T	ENSP00000475216:p.Arg312Cys	72.0	0.0	0		110.0	55.0	0.5	NM_001025231		Missense_Mutation	SNP	ENST00000606109.1	37	CCDS30862.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	C	9.290	1.050327	0.19827	0.01566	0.0	ENSG00000203786	ENST00000368773	T	0.16196	2.36	5.3	-8.26	0.01021	.	1.822830	0.02592	N	0.100084	T	0.03305	0.0096	N	0.19112	0.55	0.09310	N	1	B	0.12013	0.005	B	0.09377	0.004	T	0.43909	-0.9362	10	0.72032	D	0.01	-0.013	9.3493	0.38129	0.1476:0.6376:0.1235:0.0913	.	312	Q5T749	KPRP_HUMAN	C	312	ENSP00000357762:R312C	ENSP00000357762:R312C	R	+	1	0	KPRP	150999622	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.771000	0.04699	-1.006000	0.03412	-0.502000	0.04539	CGC	C|0.994;T|0.006	0.006	strong		0.597	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231	
COL6A5	256076	hgsc.bcm.edu	37	3	130095598	130095598	+	Missense_Mutation	SNP	A	A	G	rs115250607	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:130095598A>G	ENST00000432398.2	+	3	1080	c.586A>G	c.(586-588)Agc>Ggc	p.S196G	COL6A5_ENST00000265379.6_Missense_Mutation_p.S196G	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	196	Nonhelical region.|VWFA 1. {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						CAGAGACCTCAGCACATTTTC	0.463													A|||	97	0.019369	0.0703	0.0058	5008	,	,		20670	0.0		0.0	False		,,,				2504	0.0				p.S196G		Atlas-SNP	.											.	COL6A5	205	.	0			c.A586G						PASS	.	A	GLY/SER	75,1309		0,75,617	92.0	79.0	83.0		586	0.6	0.9	3	dbSNP_132	83	0,3182		0,0,1591	yes	missense	COL6A5	NM_153264.5	56	0,75,2208	GG,GA,AA		0.0,5.4191,1.6426	benign	196/2527	130095598	75,4491	692	1591	2283	SO:0001583	missense	256076	exon3			GACCTCAGCACAT	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.586A>G	3.37:g.130095598A>G	ENSP00000390895:p.Ser196Gly	165.0	0.0	0		175.0	73.0	0.417143	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		30	0.013736263736263736	28	0.056910569105691054	2	0.0055248618784530384	0	0.0	0	0.0	A	7.887	0.731439	0.15507	0.054191	0.0	ENSG00000172752	ENST00000432398;ENST00000265379	T;T	0.77877	-1.13;-1.13	4.91	0.623	0.17654	.	.	.	.	.	T	0.12689	0.0308	N	0.11313	0.125	0.09310	N	0.999998	B	0.13145	0.007	B	0.19666	0.026	T	0.07731	-1.0757	9	0.20046	T	0.44	.	8.6998	0.34318	0.6916:0.0:0.3084:0.0	.	196	A8TX70-2	.	G	196	ENSP00000390895:S196G;ENSP00000265379:S196G	ENSP00000265379:S196G	S	+	1	0	COL6A5	131578288	0.000000	0.05858	0.929000	0.37066	0.781000	0.44180	-0.161000	0.10026	0.278000	0.22164	0.374000	0.22700	AGC	A|0.983;G|0.017	0.017	strong		0.463	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
GPKOW	27238	hgsc.bcm.edu	37	X	48970655	48970655	+	Silent	SNP	C	C	T	rs34057359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:48970655C>T	ENST00000156109.5	-	11	1413	c.1335G>A	c.(1333-1335)cgG>cgA	p.R445R		NM_015698.4	NP_056513.2	Q92917	GPKOW_HUMAN	G patch domain and KOW motifs	445						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(11)|ovary(2)	21						GCACCAAAGCCCGGCTCCGTG	0.562													C|||	409	0.108344	0.289	0.0375	3775	,	,		16222	0.0		0.001	False		,,,				2504	0.0				p.R445R		Atlas-SNP	.											.	GPKOW	38	.	0			c.G1335A						PASS	.	C		1294,2541		185,734,190,713,381	148.0	110.0	123.0		1335	0.5	0.4	X	dbSNP_126	123	8,6720		0,8,0,2420,1872	no	coding-synonymous	GPKOW	NM_015698.4		185,742,190,3133,2253	TT,TC,T,CC,C		0.1189,33.7419,12.326		445/477	48970655	1302,9261	2203	4300	6503	SO:0001819	synonymous_variant	27238	exon11			CAAAGCCCGGCTC	U66359	CCDS35251.1	Xp11.23	2013-01-28			ENSG00000068394	ENSG00000068394		"""G patch domain containing"""	30677	protein-coding gene	gene with protein product	"""G patch domain containing 5"""					21880142, 22365833	Standard	NM_015698		Approved	T54, GPATC5, GPATCH5, Spp2	uc004dmr.3	Q92917	OTTHUMG00000021511	ENST00000156109.5:c.1335G>A	X.37:g.48970655C>T		231.0	0.0	0		207.0	102.0	0.492754	NM_015698	Q59EK5|Q9BQA8	Silent	SNP	ENST00000156109.5	37	CCDS35251.1																																																																																			C|0.873;T|0.127	0.127	strong		0.562	GPKOW-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056535.2	NM_015698	
POC5	134359	hgsc.bcm.edu	37	5	75001590	75001590	+	Missense_Mutation	SNP	T	T	A	rs77025299	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:75001590T>A	ENST00000428202.2	-	4	435	c.246A>T	c.(244-246)gaA>gaT	p.E82D	POC5_ENST00000380475.2_5'UTR|POC5_ENST00000446329.2_Missense_Mutation_p.E57D|POC5_ENST00000514838.2_Intron|POC5_ENST00000504862.1_5'UTR|POC5_ENST00000510798.1_5'UTR	NM_001099271.1	NP_001092741.1	Q8NA72	POC5_HUMAN	POC5 centriolar protein	82					cell cycle (GO:0007049)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						CTATTGCAGTTTCTCTTACTT	0.284													T|||	295	0.0589058	0.211	0.0202	5008	,	,		16251	0.0		0.002	False		,,,				2504	0.0				p.E82D		Atlas-SNP	.											.	POC5	82	.	0			c.A246T						PASS	.	T	ASP/GLU,ASP/GLU	586,2982		47,492,1245	79.0	71.0	74.0		246,171	2.4	0.4	5	dbSNP_131	74	4,8068		0,4,4032	yes	missense,missense	POC5	NM_001099271.1,NM_152408.2	45,45	47,496,5277	AA,AT,TT		0.0496,16.4238,5.0687	benign,benign	82/576,57/551	75001590	590,11050	1784	4036	5820	SO:0001583	missense	134359	exon4			TGCAGTTTCTCTT	AK093098	CCDS47236.1, CCDS47237.1	5q13.3	2013-08-05	2013-08-05	2010-03-26	ENSG00000152359	ENSG00000152359			26658	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 37"", ""POC5 centriolar protein homolog (Chlamydomonas)"""	C5orf37		19349582	Standard	NM_152408		Approved	FLJ35779, MGC120442, MGC120443, MGC120444, hPOC5	uc003keh.4	Q8NA72	OTTHUMG00000162487	ENST00000428202.2:c.246A>T	5.37:g.75001590T>A	ENSP00000410216:p.Glu82Asp	67.0	0.0	0		55.0	19.0	0.345455	NM_001099271	B4DJG7|Q494X7|Q494X9|Q6P085	Missense_Mutation	SNP	ENST00000428202.2	37	CCDS47236.1	96	0.04395604395604396	88	0.17886178861788618	8	0.022099447513812154	0	0.0	0	0.0	T	7.456	0.643625	0.14451	0.164238	4.96E-4	ENSG00000152359	ENST00000428202;ENST00000446329	T;T	0.25414	1.81;1.8	4.91	2.36	0.29203	.	0.396419	0.27609	N	0.018614	T	0.00039	0.0001	L	0.43701	1.375	0.09310	P	0.9999988642	B;B	0.12630	0.006;0.006	B;B	0.13407	0.009;0.006	T	0.16571	-1.0398	9	0.34782	T	0.22	-13.4474	9.2644	0.37632	0.0:0.0:0.3522:0.6478	.	82;57	Q8NA72;Q8NA72-3	POC5_HUMAN;.	D	82;57	ENSP00000410216:E82D;ENSP00000399481:E57D	ENSP00000410216:E82D	E	-	3	2	POC5	75037346	0.911000	0.30947	0.398000	0.26321	0.137000	0.21094	1.191000	0.32138	0.392000	0.25172	0.528000	0.53228	GAA	T|0.965;A|0.035	0.035	strong		0.284	POC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369124.1	NM_152408	
PTGIR	5739	hgsc.bcm.edu	37	19	47124742	47124742	+	Missense_Mutation	SNP	G	G	C	rs28590598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:47124742G>C	ENST00000291294.2	-	3	1089	c.956C>G	c.(955-957)tCg>tGg	p.S319W	PTGIR_ENST00000594275.1_Missense_Mutation_p.S76W|PTGIR_ENST00000597185.1_Missense_Mutation_p.S48W|PTGIR_ENST00000598865.1_Missense_Mutation_p.S107W	NM_000960.3	NP_000951.1	P43119	PI2R_HUMAN	prostaglandin I2 (prostacyclin) receptor (IP)	319			S -> W (in dbSNP:rs28590598).		adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of GTPase activity (GO:0043547)|response to lipopolysaccharide (GO:0032496)	cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	13		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000327)|all cancers(93;0.000641)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0331)	Dinoprost Tromethamine(DB01160)|Epoprostenol(DB01240)|Iloprost(DB01088)|Treprostinil(DB00374)	GGGTGTCTGCGAGTCTCCGTG	0.647													G|||	136	0.0271565	0.0968	0.0101	5008	,	,		18475	0.0		0.001	False		,,,				2504	0.0				p.S319W		Atlas-SNP	.											.	PTGIR	31	.	0			c.C956G						PASS	.	G	TRP/SER	405,4001	184.3+/-211.7	22,361,1820	42.0	48.0	46.0		956	0.2	0.0	19	dbSNP_125	46	2,8598	2.2+/-6.3	0,2,4298	yes	missense	PTGIR	NM_000960.3	177	22,363,6118	CC,CG,GG		0.0233,9.192,3.1293	probably-damaging	319/387	47124742	407,12599	2203	4300	6503	SO:0001583	missense	5739	exon3			GTCTGCGAGTCTC		CCDS12686.1	19q13.3	2012-08-08				ENSG00000160013		"""GPCR / Class A : Prostanoid receptors"""	9602	protein-coding gene	gene with protein product		600022				7759114	Standard	NM_000960		Approved	IP	uc002pex.3	P43119		ENST00000291294.2:c.956C>G	19.37:g.47124742G>C	ENSP00000291294:p.Ser319Trp	114.0	0.0	0		115.0	59.0	0.513043	NM_000960		Missense_Mutation	SNP	ENST00000291294.2	37	CCDS12686.1	52	0.023809523809523808	49	0.09959349593495935	3	0.008287292817679558	0	0.0	0	0.0	G	13.66	2.304672	0.40795	0.09192	2.33E-4	ENSG00000160013	ENST00000291294	T	0.41065	1.01	4.39	0.217	0.15264	.	0.792252	0.10334	N	0.687165	T	0.00998	0.0033	N	0.24115	0.695	0.09310	N	1	D	0.63046	0.992	P	0.51866	0.682	T	0.03202	-1.1061	10	0.66056	D	0.02	-8.4268	6.0489	0.19775	0.5271:0.0:0.4729:0.0	rs28590598	319	P43119	PI2R_HUMAN	W	319	ENSP00000291294:S319W	ENSP00000291294:S319W	S	-	2	0	PTGIR	51816582	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	0.177000	0.16801	-0.057000	0.13199	-0.258000	0.10820	TCG	G|0.973;C|0.027	0.027	strong		0.647	PTGIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466581.1		
SOWAHC	65124	hgsc.bcm.edu	37	2	110372688	110372688	+	Missense_Mutation	SNP	C	C	G	rs72938294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:110372688C>G	ENST00000356454.3	+	1	778	c.622C>G	c.(622-624)Ctg>Gtg	p.L208V	SEPT10_ENST00000356688.4_5'Flank|SEPT10_ENST00000397714.2_5'Flank|SEPT10_ENST00000334001.6_5'Flank|SEPT10_ENST00000397712.2_5'Flank|SEPT10_ENST00000545389.1_5'Flank|SEPT10_ENST00000437928.1_5'Flank|SEPT10_ENST00000415095.1_5'Flank	NM_023016.3	NP_075392.2	Q53LP3	SWAHC_HUMAN	sosondowah ankyrin repeat domain family member C	208																	CCTCCGTGACCTGGTGATGGG	0.736													C|||	95	0.0189696	0.0688	0.0058	5008	,	,		11693	0.0		0.0	False		,,,				2504	0.0				p.L208V		Atlas-SNP	.											.	.	.	.	0			c.C622G						PASS	.	C	VAL/LEU	168,3274		1,166,1554	8.0	9.0	9.0		622	1.7	0.0	2	dbSNP_130	9	3,6469		0,3,3233	yes	missense	ANKRD57	NM_023016.3	32	1,169,4787	GG,GC,CC		0.0464,4.8809,1.7248	possibly-damaging	208/526	110372688	171,9743	1721	3236	4957	SO:0001583	missense	65124	exon1			CGTGACCTGGTGA	AK023346	CCDS33270.1	2q13	2013-01-10	2012-01-12	2012-01-12	ENSG00000198142	ENSG00000198142		"""Ankyrin repeat domain containing"""	26149	protein-coding gene	gene with protein product			"""ankyrin repeat domain 57"""	C2orf26, ANKRD57		22234889	Standard	NM_023016		Approved	FLJ21870	uc002tfb.3	Q53LP3	OTTHUMG00000153219	ENST00000356454.3:c.622C>G	2.37:g.110372688C>G	ENSP00000365830:p.Leu208Val	68.0	0.0	0		83.0	40.0	0.481928	NM_023016	Q8NE15|Q9H6U1	Missense_Mutation	SNP	ENST00000356454.3	37	CCDS33270.1	36	0.016483516483516484	31	0.06300813008130081	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	0.725	-0.782051	0.02907	0.048809	4.64E-4	ENSG00000198142	ENST00000356454	T	0.26373	1.74	3.58	1.66	0.24008	.	1.034310	0.07796	N	0.955796	T	0.01661	0.0053	N	0.22421	0.69	0.09310	N	1	B	0.22003	0.063	B	0.22386	0.039	T	0.27971	-1.0058	10	0.38643	T	0.18	-1.0053	4.8489	0.13528	0.1515:0.615:0.147:0.0865	.	208	Q53LP3	ANR57_HUMAN	V	208	ENSP00000365830:L208V	ENSP00000365830:L208V	L	+	1	2	ANKRD57	109729977	0.000000	0.05858	0.037000	0.18230	0.225000	0.24961	0.616000	0.24344	0.273000	0.22049	0.462000	0.41574	CTG	C|0.983;G|0.017	0.017	strong		0.736	SOWAHC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330168.1	NM_023016	
UCP3	7352	hgsc.bcm.edu	37	11	73717263	73717263	+	Silent	SNP	G	G	A	rs2229706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:73717263G>A	ENST00000314032.4	-	3	840	c.288C>T	c.(286-288)atC>atT	p.I96I	UCP3_ENST00000426995.2_Silent_p.I96I|UCP3_ENST00000348534.4_Silent_p.I96I	NM_003356.3	NP_003347.1	P55916	UCP3_HUMAN	uncoupling protein 3 (mitochondrial, proton carrier)	96					aging (GO:0007568)|cellular metabolic process (GO:0044237)|cellular response to hormone stimulus (GO:0032870)|fatty acid metabolic process (GO:0006631)|lipid metabolic process (GO:0006629)|mitochondrial transport (GO:0006839)|proton transport (GO:0015992)|respiratory electron transport chain (GO:0022904)|respiratory gaseous exchange (GO:0007585)|response to activity (GO:0014823)|response to cold (GO:0009409)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|response to superoxide (GO:0000303)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	oxidative phosphorylation uncoupler activity (GO:0017077)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	12	Breast(11;2.08e-05)					CATAGAGGCCGATGCGGATGG	0.627													G|||	34	0.00678914	0.0242	0.0029	5008	,	,		18530	0.0		0.0	False		,,,				2504	0.0				p.I96I		Atlas-SNP	.											.	UCP3	31	.	0			c.C288T						PASS	.	G	,	102,4298	80.9+/-119.3	1,100,2099	44.0	43.0	43.0		288,288	-4.0	1.0	11	dbSNP_98	43	1,8585	1.2+/-3.3	0,1,4292	no	coding-synonymous,coding-synonymous	UCP3	NM_003356.3,NM_022803.2	,	1,101,6391	AA,AG,GG		0.0116,2.3182,0.7932	,	96/313,96/276	73717263	103,12883	2200	4293	6493	SO:0001819	synonymous_variant	7352	exon3			GAGGCCGATGCGG	AF001787	CCDS8229.1, CCDS44677.1	11q13.4	2013-05-22				ENSG00000175564		"""Solute carriers"""	12519	protein-coding gene	gene with protein product		602044				9480760, 9196039	Standard	NM_003356		Approved	SLC25A9	uc001our.3	P55916		ENST00000314032.4:c.288C>T	11.37:g.73717263G>A		66.0	0.0	0		70.0	39.0	0.557143	NM_003356	O60475|Q96HL3	Silent	SNP	ENST00000314032.4	37	CCDS8229.1																																																																																			G|0.991;A|0.009	0.009	strong		0.627	UCP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398200.1	NM_003356	
DPY19L4	286148	hgsc.bcm.edu	37	8	95746883	95746883	+	Silent	SNP	G	G	A	rs113391412	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:95746883G>A	ENST00000414645.2	+	3	252	c.153G>A	c.(151-153)aaG>aaA	p.K51K		NM_181787.2	NP_861452.2	Q7Z388	D19L4_HUMAN	dpy-19-like 4 (C. elegans)	51						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(6)|ovary(2)|prostate(2)	21	Breast(36;3.85e-06)					GCTTTGCAAAGATTTTCATTG	0.348													G|||	49	0.00978435	0.0363	0.0014	5008	,	,		19614	0.0		0.0	False		,,,				2504	0.0				p.K51K		Atlas-SNP	.											.	DPY19L4	60	.	0			c.G153A						PASS	.	G		136,4270	93.9+/-132.6	1,134,2068	89.0	84.0	85.0		153	4.2	1.0	8	dbSNP_132	85	0,8600		0,0,4300	no	coding-synonymous	DPY19L4	NM_181787.2		1,134,6368	AA,AG,GG		0.0,3.0867,1.0457		51/724	95746883	136,12870	2203	4300	6503	SO:0001819	synonymous_variant	286148	exon3			TGCAAAGATTTTC		CCDS34924.1	8q22.1	2006-11-24			ENSG00000156162	ENSG00000156162			27829	protein-coding gene	gene with protein product		613895					Standard	NM_181787		Approved		uc003ygx.2	Q7Z388	OTTHUMG00000164589	ENST00000414645.2:c.153G>A	8.37:g.95746883G>A		90.0	0.0	0		114.0	67.0	0.587719	NM_181787	Q6ZW32|Q6ZW42|Q7Z329	Silent	SNP	ENST00000414645.2	37	CCDS34924.1																																																																																			G|0.988;A|0.012	0.012	strong		0.348	DPY19L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379339.1	NM_181787	
LRRC73	221424	hgsc.bcm.edu	37	6	43475195	43475195	+	Splice_Site	SNP	G	G	A	rs61746927	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43475195G>A	ENST00000372441.1	-	5	1779	c.879C>T	c.(877-879)agC>agT	p.S293S		NM_001012974.1	NP_001012992.1	Q5JTD7	LRC73_HUMAN	leucine rich repeat containing 73	293																	GGTTCTTACCGCTGGGGCACA	0.632													G|||	74	0.0147764	0.0469	0.0144	5008	,	,		18063	0.0		0.002	False		,,,				2504	0.0				p.S293S		Atlas-SNP	.											.	.	.	.	0			c.C879T						PASS	.	G		237,4169	134.9+/-171.1	9,219,1975	33.0	38.0	36.0		879	-1.7	0.9	6	dbSNP_129	36	4,8596	3.7+/-12.6	0,4,4296	yes	coding-synonymous-near-splice	C6orf154	NM_001012974.1		9,223,6271	AA,AG,GG		0.0465,5.379,1.853		293/317	43475195	241,12765	2203	4300	6503	SO:0001630	splice_region_variant	221424	exon5			CTTACCGCTGGGG		CCDS34456.1	6p21.1	2011-11-25	2011-11-25	2011-11-25	ENSG00000204052	ENSG00000204052			21375	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 154"""	C6orf154			Standard	NM_001012974		Approved	dJ337H4.2	uc003ovk.2	Q5JTD7	OTTHUMG00000014737	ENST00000372441.1:c.880+1C>T	6.37:g.43475195G>A		50.0	0.0	0		52.0	25.0	0.480769	NM_001012974		Silent	SNP	ENST00000372441.1	37	CCDS34456.1																																																																																			G|0.980;A|0.020	0.020	strong		0.632	LRRC73-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040635.1	NM_001012974	Silent
PER3	8863	hgsc.bcm.edu	37	1	7880585	7880585	+	Silent	SNP	A	A	T	rs17031601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:7880585A>T	ENST00000361923.2	+	15	1993	c.1818A>T	c.(1816-1818)atA>atT	p.I606I	PER3_ENST00000377532.3_Silent_p.I614I|RP3-467L1.4_ENST00000451646.1_RNA	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	606	CSNK1E binding domain. {ECO:0000250}.				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)			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)		GACGGTCCATAGACACAGGAG	0.507													A|||	67	0.0133786	0.0477	0.0058	5008	,	,		18040	0.0		0.0	False		,,,				2504	0.0				p.I606I		Atlas-SNP	.											.	PER3	95	.	0			c.A1818T						PASS	.	A		174,4232	115.4+/-153.4	3,168,2032	79.0	65.0	70.0		1818	-0.2	0.0	1	dbSNP_123	70	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	PER3	NM_016831.1		3,171,6329	TT,TA,AA		0.0349,3.9492,1.3609		606/1202	7880585	177,12829	2203	4300	6503	SO:0001819	synonymous_variant	8863	exon15			GTCCATAGACACA	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.1818A>T	1.37:g.7880585A>T		183.0	0.0	0		213.0	113.0	0.530516	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Silent	SNP	ENST00000361923.2	37	CCDS89.1																																																																																			A|0.985;T|0.015	0.015	strong		0.507	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
MARVELD2	153562	hgsc.bcm.edu	37	5	68715576	68715576	+	Missense_Mutation	SNP	G	G	A	rs140764671	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:68715576G>A	ENST00000325631.5	+	2	438	c.364G>A	c.(364-366)Gca>Aca	p.A122T	MARVELD2_ENST00000413223.2_Missense_Mutation_p.A122T	NM_001038603.2|NM_001244734.1	NP_001033692.2|NP_001231663.1	Q8N4S9	MALD2_HUMAN	MARVEL domain containing 2	122					cell-cell junction organization (GO:0045216)|establishment of endothelial barrier (GO:0061028)|sensory perception of sound (GO:0007605)|tight junction assembly (GO:0070830)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|paranodal junction (GO:0033010)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(1)|lung(4)|skin(1)|urinary_tract(1)	15		Lung NSC(167;0.000937)|Prostate(74;0.0187)|Ovarian(174;0.16)		OV - Ovarian serous cystadenocarcinoma(47;7.31e-57)|Epithelial(20;1.05e-52)|all cancers(19;2.63e-48)|Lung(70;0.0183)		AGCCTCTCCAGCAAGACCAAA	0.532													G|||	21	0.00419329	0.0151	0.0014	5008	,	,		18849	0.0		0.0	False		,,,				2504	0.0				p.A122T		Atlas-SNP	.											.	MARVELD2	49	.	0			c.G364A						PASS	.	G	THR/ALA	75,4331	65.3+/-102.7	1,73,2129	53.0	54.0	54.0		364	-0.0	0.0	5	dbSNP_134	54	0,8600		0,0,4300	yes	missense	MARVELD2	NM_001038603.2	58	1,73,6429	AA,AG,GG		0.0,1.7022,0.5767	benign	122/559	68715576	75,12931	2203	4300	6503	SO:0001583	missense	153562	exon2			TCTCCAGCAAGAC	AK055094	CCDS34175.1, CCDS58956.1	5q13.1	2007-05-01	2004-07-12	2004-07-14	ENSG00000152939	ENSG00000152939			26401	protein-coding gene	gene with protein product	"""tricellulin"""	610572	"""MARVEL (membrane-associating) domain containing 2"", ""deafness, autosomal recessive 49"""	MRVLDC2, DFNB49		17186462	Standard	NM_001038603		Approved	FLJ30532, TRIC	uc003jwq.3	Q8N4S9	OTTHUMG00000162512	ENST00000325631.5:c.364G>A	5.37:g.68715576G>A	ENSP00000323264:p.Ala122Thr	69.0	0.0	0		88.0	43.0	0.488636	NM_001244734	A1BQX0|A1BQX1|A8KA97|Q96NM9	Missense_Mutation	SNP	ENST00000325631.5	37	CCDS34175.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	2.825	-0.243931	0.05906	0.017022	0.0	ENSG00000152939	ENST00000325631;ENST00000282886;ENST00000454295;ENST00000515844;ENST00000512803;ENST00000436532;ENST00000413223	T;T;T;T;T;T	0.47869	1.48;0.9;0.83;1.48;1.45;1.45	5.07	-0.0336	0.13900	.	0.712658	0.14187	N	0.335596	T	0.12305	0.0299	N	0.12746	0.255	0.09310	N	1	B;B;B	0.09022	0.001;0.002;0.0	B;B;B	0.11329	0.004;0.006;0.002	T	0.10337	-1.0634	10	0.33940	T	0.23	-24.4939	4.5252	0.11978	0.4245:0.0:0.4294:0.1461	.	122;122;122	Q8N4S9-3;Q8N4S9-2;Q8N4S9	.;.;MALD2_HUMAN	T	122	ENSP00000323264:A122T;ENSP00000396244:A122T;ENSP00000421902:A122T;ENSP00000423490:A122T;ENSP00000414776:A122T;ENSP00000398922:A122T	ENSP00000282886:A122T	A	+	1	0	MARVELD2	68751332	0.000000	0.05858	0.001000	0.08648	0.022000	0.10575	-0.332000	0.07904	-0.087000	0.12528	-0.140000	0.14226	GCA	G|0.995;A|0.005	0.005	strong		0.532	MARVELD2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369583.1	NM_144724	
APP	351	hgsc.bcm.edu	37	21	27326977	27326977	+	Silent	SNP	A	A	G	rs45537238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:27326977A>G	ENST00000346798.3	-	13	1647	c.1614T>C	c.(1612-1614)taT>taC	p.Y538Y	APP_ENST00000358918.3_Silent_p.Y538Y|APP_ENST00000448388.2_Silent_p.Y428Y|APP_ENST00000354192.3_Silent_p.Y407Y|APP_ENST00000359726.3_Silent_p.Y482Y|APP_ENST00000357903.3_Silent_p.Y519Y|APP_ENST00000440126.3_Silent_p.Y514Y|APP_ENST00000439274.2_Silent_p.Y482Y|APP_ENST00000348990.5_Silent_p.Y463Y	NM_000484.3	NP_000475.1	P05067	A4_HUMAN	amyloid beta (A4) precursor protein	538	Collagen-binding.				adult locomotory behavior (GO:0008344)|axon cargo transport (GO:0008088)|axon midline choice point recognition (GO:0016199)|axonogenesis (GO:0007409)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|collateral sprouting in absence of injury (GO:0048669)|dendrite development (GO:0016358)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|ionotropic glutamate receptor signaling pathway (GO:0035235)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|mRNA polyadenylation (GO:0006378)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron differentiation (GO:0045665)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of multicellular organism growth (GO:0040014)|regulation of protein binding (GO:0043393)|regulation of synapse structure and activity (GO:0050803)|regulation of translation (GO:0006417)|response to oxidative stress (GO:0006979)|smooth endoplasmic reticulum calcium ion homeostasis (GO:0051563)|suckling behavior (GO:0001967)|synaptic growth at neuromuscular junction (GO:0051124)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|ciliary rootlet (GO:0035253)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endosome (GO:0005768)|ER to Golgi transport vesicle (GO:0030134)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|receptor complex (GO:0043235)|spindle midzone (GO:0051233)|synapse (GO:0045202)	acetylcholine receptor binding (GO:0033130)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|peptidase activator activity (GO:0016504)|PTB domain binding (GO:0051425)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			endometrium(5)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(209;0.00295)				TCATGCGCTCATAAATCACAC	0.458													G|||	124	0.0247604	0.0893	0.0072	5008	,	,		20225	0.0		0.001	False		,,,				2504	0.0				p.Y538Y		Atlas-SNP	.											.	APP	90	.	0			c.T1614C						PASS	.	G	,,,,,,,,,	332,4074	796.0+/-415.3	16,300,1887	104.0	81.0	89.0		1614,1542,1221,1446,1284,1614,1557,1389,1557,1389	-9.4	0.7	21	dbSNP_127	89	5,8595	818.8+/-406.8	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	APP	NM_000484.3,NM_001136016.3,NM_001136129.2,NM_001136130.2,NM_001136131.2,NM_001204301.1,NM_001204302.1,NM_001204303.1,NM_201413.2,NM_201414.2	,,,,,,,,,	16,305,6182	GG,GA,AA		0.0581,7.5352,2.5911	,,,,,,,,,	538/771,514/747,407/640,482/715,428/661,538/753,519/734,463/678,519/752,463/696	27326977	337,12669	2203	4300	6503	SO:0001819	synonymous_variant	351	exon13			GCGCTCATAAATC	M15533	CCDS13576.1, CCDS13577.1, CCDS33523.1, CCDS46638.1, CCDS46639.1, CCDS56211.1, CCDS56212.1, CCDS56213.1	21q21.2	2014-01-30	2008-07-31		ENSG00000142192	ENSG00000142192		"""Endogenous ligands"""	620	protein-coding gene	gene with protein product	"""peptidase nexin-II"""	104760	"""Alzheimer disease"""	AD1		1679289	Standard	NM_001136130		Approved		uc002ylz.3	P05067	OTTHUMG00000078438	ENST00000346798.3:c.1614T>C	21.37:g.27326977A>G		140.0	0.0	0		153.0	81.0	0.529412	NM_000484	B2R5V1|B4DII8|D3DSD1|D3DSD2|D3DSD3|P09000|P78438|Q13764|Q13778|Q13793|Q16011|Q16014|Q16019|Q16020|Q6GSC0|Q8WZ99|Q9BT38|Q9UC33|Q9UCA9|Q9UCB6|Q9UCC8|Q9UCD1|Q9UQ58	Silent	SNP	ENST00000346798.3	37	CCDS13576.1	40	0.018315018315018316	36	0.07317073170731707	4	0.011049723756906077	0	0.0	0	0.0	G	8.620	0.891207	0.17613	0.075352	5.81E-4	ENSG00000142192	ENST00000448850	.	.	.	5.52	-9.36	0.00629	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-19.8727	19.7142	0.96108	0.2996:0.0:0.7004:0.0	rs45537238;rs60681122	.	.	.	R	441	.	.	X	-	1	0	APP	26248848	0.000000	0.05858	0.669000	0.29828	0.984000	0.73092	-1.770000	0.01791	-2.333000	0.00631	-1.115000	0.02055	TGA	A|0.977;G|0.023	0.023	strong		0.458	APP-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171340.1	NM_000484	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057943	46057943	+	Silent	SNP	C	C	T	rs77446663		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46057943C>T	ENST00000380095.1	+	1	671	c.609C>T	c.(607-609)tgC>tgT	p.C203C	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	203	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						CCACCTGCTGCGTGCCCGTCC	0.692																																					p.C203C		Atlas-SNP	.											KRTAP10-10,NS,carcinoma,+2,1	KRTAP10-10	37	1	0			c.C609T						PASS	.						97.0	100.0	99.0					21																	46057943		2203	4300	6503	SO:0001819	synonymous_variant	353333	exon1			CTGCTGCGTGCCC	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.609C>T	21.37:g.46057943C>T		293.0	0.0	0		456.0	117.0	0.256579	NM_181688		Silent	SNP	ENST00000380095.1	37	CCDS33585.1																																																																																			C|0.982;T|0.018	0.018	strong		0.692	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
PCDHA5	56143	hgsc.bcm.edu	37	5	140202418	140202418	+	Missense_Mutation	SNP	C	C	A	rs61735511	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140202418C>A	ENST00000529859.1	+	1	1058	c.1058C>A	c.(1057-1059)aCc>aAc	p.T353N	PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000378126.3_Missense_Mutation_p.T353N|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Missense_Mutation_p.T353N	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	353	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(3)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCATAACCACCCTTTTCCTG	0.502													.|||	317	0.0632987	0.2322	0.013	5008	,	,		19770	0.0		0.001	False		,,,				2504	0.0				p.T353N		Atlas-SNP	.											PCDHA5_ENST00000529859,NS,carcinoma,-1,2	PCDHA5	361	2	0			c.C1058A						PASS	.	C	,,,,ASN/THR,,ASN/THR	861,3545	337.0+/-304.7	78,705,1420	87.0	80.0	83.0		,,,,1058,,1058	4.0	0.2	5	dbSNP_129	83	2,8598	2.2+/-6.3	0,2,4298	yes	intron,intron,intron,intron,missense,intron,missense	PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_031411.1,NM_031501.1	,,,,65,,65	78,707,5718	AA,AC,CC		0.0233,19.5415,6.6354	,,,,,,	,,,,353/937,,353/817	140202418	863,12143	2203	4300	6503	SO:0001583	missense	56143	exon1			TAACCACCCTTTT	AF152483	CCDS54917.1	5q31	2010-11-26				ENSG00000204965		"""Cadherins / Protocadherins : Clustered"""	8671	other	complex locus constituent	"""ortholog of mouse CNR6"", ""KIAA0345-like 9"""	606311		CNRS6		10380929, 10662547	Standard	NM_018908		Approved	CNR6, CRNR6, CNRN6, PCDH-ALPHA5		Q9Y5H7		ENST00000529859.1:c.1058C>A	5.37:g.140202418C>A	ENSP00000436557:p.Thr353Asn	161.0	0.0	0		168.0	86.0	0.511905	NM_018908	O75284|Q8N4R3	Missense_Mutation	SNP	ENST00000529859.1	37	CCDS54917.1	96	0.04395604395604396	90	0.18292682926829268	6	0.016574585635359115	0	0.0	0	0.0	C	12.70	2.018078	0.35606	0.195415	2.33E-4	ENSG00000204965	ENST00000529619;ENST00000529859;ENST00000378126	T;T;T	0.61510	0.1;0.1;0.24	3.97	3.97	0.46021	Cadherin (2);Cadherin-like (1);	.	.	.	.	T	0.00073	0.0002	L	0.28400	0.85	0.35989	P	0.16346499999999997	B;B;B	0.25743	0.024;0.133;0.063	B;B;B	0.28709	0.093;0.043;0.042	T	0.16928	-1.0386	8	0.87932	D	0	.	16.4	0.83637	0.0:1.0:0.0:0.0	rs61735511	353;353;353	Q9Y5H7;Q9Y5H7-3;Q9Y5H7-2	PCDA5_HUMAN;.;.	N	353	ENSP00000433416:T353N;ENSP00000436557:T353N;ENSP00000367366:T353N	ENSP00000367366:T353N	T	+	2	0	PCDHA5	140182602	1.000000	0.71417	0.240000	0.24138	0.827000	0.46813	7.800000	0.85949	1.900000	0.55004	0.655000	0.94253	ACC	C|0.940;A|0.060	0.060	strong		0.502	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908	
GGN	199720	hgsc.bcm.edu	37	19	38876944	38876944	+	Missense_Mutation	SNP	C	C	T	rs151268424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38876944C>T	ENST00000334928.6	-	3	1090	c.958G>A	c.(958-960)Gaa>Aaa	p.E320K	GGN_ENST00000591809.1_Intron|AC005789.9_ENST00000585411.1_RNA|SPRED3_ENST00000587013.1_5'Flank	NM_152657.3	NP_689870.3	Q86UU5	GGN_HUMAN	gametogenetin	320	Interaction with GGNBP1. {ECO:0000250}.|Pro-rich.				cell differentiation (GO:0030154)|gamete generation (GO:0007276)|multicellular organismal development (GO:0007275)|protein localization (GO:0008104)|spermatogenesis (GO:0007283)	nucleolus (GO:0005730)|perinuclear region of cytoplasm (GO:0048471)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(60;3.4e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			GAGCACCCTTCGCCGTCTCCA	0.682													C|||	14	0.00279553	0.0106	0.0	5008	,	,		13386	0.0		0.0	False		,,,				2504	0.0				p.E320K		Atlas-SNP	.											.	GGN	50	.	0			c.G958A						PASS	.	C	LYS/GLU	53,4345		0,53,2146	24.0	28.0	27.0		958	3.3	1.0	19	dbSNP_134	27	0,8600		0,0,4300	yes	missense	GGN	NM_152657.3	56	0,53,6446	TT,TC,CC		0.0,1.2051,0.4078	possibly-damaging	320/653	38876944	53,12945	2199	4300	6499	SO:0001583	missense	199720	exon3			ACCCTTCGCCGTC	AF538035	CCDS12516.1	19q13.2	2008-09-04				ENSG00000179168			18869	protein-coding gene	gene with protein product		609966				12574169	Standard	NM_152657		Approved	FLJ35713, MGC33369	uc002oij.1	Q86UU5		ENST00000334928.6:c.958G>A	19.37:g.38876944C>T	ENSP00000334940:p.Glu320Lys	33.0	0.0	0		32.0	10.0	0.3125	NM_152657	Q7RTU6|Q86UU4|Q8NAA1	Missense_Mutation	SNP	ENST00000334928.6	37	CCDS12516.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	15.63	2.891749	0.52014	0.012051	0.0	ENSG00000179168	ENST00000334928	.	.	.	3.33	3.33	0.38152	.	0.000000	0.38005	N	0.001858	T	0.37183	0.0994	L	0.29908	0.895	0.30484	N	0.77204	D;D	0.76494	0.999;0.999	D;D	0.76071	0.987;0.987	T	0.28235	-1.0050	9	0.17369	T	0.5	-7.3092	10.004	0.41946	0.0:1.0:0.0:0.0	.	237;320	Q86UU5-2;Q86UU5	.;GGN_HUMAN	K	320	.	ENSP00000334940:E320K	E	-	1	0	GGN	43568784	0.987000	0.35691	1.000000	0.80357	0.788000	0.44548	1.158000	0.31737	1.679000	0.50963	0.462000	0.41574	GAA	C|0.996;T|0.004	0.004	strong		0.682	GGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459205.1	NM_152657	
DBH	1621	hgsc.bcm.edu	37	9	136521749	136521749	+	Silent	SNP	G	G	A	rs78516399	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136521749G>A	ENST00000393056.2	+	10	1551	c.1539G>A	c.(1537-1539)caG>caA	p.Q513Q	DBH-AS1_ENST00000425189.1_RNA	NM_000787.3	NP_000778.3	P09172	DOPO_HUMAN	dopamine beta-hydroxylase (dopamine beta-monooxygenase)	513					behavioral response to ethanol (GO:0048149)|blood vessel remodeling (GO:0001974)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cytokine production (GO:0001816)|dopamine catabolic process (GO:0042420)|fear response (GO:0042596)|glucose homeostasis (GO:0042593)|homoiothermy (GO:0042309)|leukocyte mediated immunity (GO:0002443)|leukocyte migration (GO:0050900)|locomotory behavior (GO:0007626)|maternal behavior (GO:0042711)|memory (GO:0007613)|norepinephrine biosynthetic process (GO:0042421)|positive regulation of vasoconstriction (GO:0045907)|regulation of cell proliferation (GO:0042127)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|response to amphetamine (GO:0001975)|response to pain (GO:0048265)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|secretory granule lumen (GO:0034774)	catalytic activity (GO:0003824)|copper ion binding (GO:0005507)|dopamine beta-monooxygenase activity (GO:0004500)|L-ascorbic acid binding (GO:0031418)			central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(9)|liver(1)|lung(6)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	36				OV - Ovarian serous cystadenocarcinoma(145;2.33e-07)|Epithelial(140;1.5e-06)|all cancers(34;1.66e-05)	Disulfiram(DB00822)|Dopamine(DB00988)|Propylthiouracil(DB00550)|Vitamin C(DB00126)	GCTTCCTGCAGAAGTACTTCC	0.622													G|||	33	0.00658946	0.025	0.0	5008	,	,		17798	0.0		0.0	False		,,,				2504	0.0				p.Q513Q		Atlas-SNP	.											.	DBH	86	.	0			c.G1539A						PASS	.	G		77,4329	68.7+/-106.4	0,77,2126	47.0	44.0	45.0		1539	1.7	1.0	9	dbSNP_131	45	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DBH	NM_000787.3		0,78,6425	AA,AG,GG		0.0116,1.7476,0.5997		513/618	136521749	78,12928	2203	4300	6503	SO:0001819	synonymous_variant	1621	exon10			CCTGCAGAAGTAC	X13256	CCDS6977.2	9q34	2013-06-03			ENSG00000123454	ENSG00000123454	1.14.17.1		2689	protein-coding gene	gene with protein product		609312					Standard	NM_000787		Approved	DBM	uc004cel.3	P09172	OTTHUMG00000020878	ENST00000393056.2:c.1539G>A	9.37:g.136521749G>A		52.0	0.0	0		31.0	18.0	0.580645	NM_000787	Q5T381|Q96AG2	Silent	SNP	ENST00000393056.2	37	CCDS6977.2																																																																																			G|0.993;A|0.007	0.007	strong		0.622	DBH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054929.2	NM_000787	
PROK2	60675	hgsc.bcm.edu	37	3	71821933	71821933	+	Missense_Mutation	SNP	G	G	T	rs60239864	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:71821933G>T	ENST00000295619.3	-	4	340	c.332C>A	c.(331-333)cCa>cAa	p.P111Q	PROK2_ENST00000353065.3_Missense_Mutation_p.P90Q	NM_001126128.1	NP_001119600.1	Q9HC23	PROK2_HUMAN	prokineticin 2	111					activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|cell proliferation (GO:0008283)|chemotaxis (GO:0006935)|circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|negative regulation of apoptotic process (GO:0043066)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of smooth muscle contraction (GO:0045987)|sensory perception of pain (GO:0019233)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)	G-protein coupled receptor binding (GO:0001664)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	6		Prostate(10;0.00899)		BRCA - Breast invasive adenocarcinoma(55;1.89e-05)|Epithelial(33;0.000173)|LUSC - Lung squamous cell carcinoma(21;0.00168)|Lung(16;0.00306)		GGCCAAGCCTGGCAGACATGG	0.408													G|||	33	0.00658946	0.0242	0.0014	5008	,	,		16471	0.0		0.0	False		,,,				2504	0.0				p.P111Q		Atlas-SNP	.											.	PROK2	13	.	0			c.C332A						PASS	.	G	GLN/PRO,GLN/PRO	86,4320	73.1+/-111.1	1,84,2118	79.0	85.0	83.0		332,269	5.8	1.0	3	dbSNP_129	83	0,8600		0,0,4300	yes	missense,missense	PROK2	NM_001126128.1,NM_021935.3	76,76	1,84,6418	TT,TG,GG		0.0,1.9519,0.6612	probably-damaging,probably-damaging	111/130,90/109	71821933	86,12920	2203	4300	6503	SO:0001583	missense	60675	exon4			AAGCCTGGCAGAC	AF333025	CCDS2916.1, CCDS46868.1	3p21.1	2013-02-28			ENSG00000163421	ENSG00000163421		"""Endogenous ligands"""	18455	protein-coding gene	gene with protein product	"""protein Bv8 homolog"""	607002				11054548, 11259612	Standard	NM_021935		Approved	PK2, BV8, MIT1, KAL4	uc003dpa.4	Q9HC23	OTTHUMG00000158809	ENST00000295619.3:c.332C>A	3.37:g.71821933G>T	ENSP00000295619:p.Pro111Gln	121.0	0.0	0		152.0	94.0	0.618421	NM_001126128	Q53Z79|Q6ISR0	Missense_Mutation	SNP	ENST00000295619.3	37	CCDS46868.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	G	27.9	4.873120	0.91664	0.019519	0.0	ENSG00000163421	ENST00000353065;ENST00000295619	T;T	0.72725	-0.68;-0.68	5.85	5.85	0.93711	Prokineticin domain (2);	0.000000	0.85682	D	0.000000	T	0.72020	0.3409	L	0.59436	1.845	0.58432	D	0.999998	D;D	0.89917	1.0;0.999	D;D	0.97110	1.0;0.974	T	0.77600	-0.2527	10	0.51188	T	0.08	-11.9075	18.9291	0.92558	0.0:0.0:1.0:0.0	rs60239864	111;90	Q9HC23;Q6ISR0	PROK2_HUMAN;.	Q	90;111	ENSP00000295618:P90Q;ENSP00000295619:P111Q	ENSP00000295619:P111Q	P	-	2	0	PROK2	71904623	1.000000	0.71417	0.980000	0.43619	0.999000	0.98932	8.067000	0.89488	2.773000	0.95371	0.650000	0.86243	CCA	G|0.994;T|0.006	0.006	strong		0.408	PROK2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352302.1	NM_001126128	
OTOL1	131149	hgsc.bcm.edu	37	3	161221262	161221262	+	Silent	SNP	T	T	A	rs113998122	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:161221262T>A	ENST00000327928.4	+	4	966	c.966T>A	c.(964-966)acT>acA	p.T322T		NM_001080440.1	NP_001073909.1	A6NHN0	OTOL1_HUMAN	otolin 1	322	Collagen-like 3.					collagen trimer (GO:0005581)|extracellular region (GO:0005576)				central_nervous_system(2)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)	27						GAGGCCCCACTGGGAAGAAGG	0.572													T|||	50	0.00998403	0.0378	0.0	5008	,	,		13649	0.0		0.0	False		,,,				2504	0.0				p.T322T		Atlas-SNP	.											.	OTOL1	63	.	0			c.T966A						PASS	.	T		116,3608		0,116,1746	30.0	30.0	30.0		966	-7.4	0.0	3	dbSNP_132	30	2,8184		0,2,4091	no	coding-synonymous	OTOL1	NM_001080440.1		0,118,5837	AA,AT,TT		0.0244,3.1149,0.9908		322/478	161221262	118,11792	1862	4093	5955	SO:0001819	synonymous_variant	131149	exon4			CCCCACTGGGAAG		CCDS46948.1	3q26.1	2011-05-19	2011-05-19			ENSG00000182447			34071	protein-coding gene	gene with protein product	"""C1q and tumor necrosis factor related protein 15"""		"""otolin 1 homolog (zebrafish)"""			17544811, 15905077	Standard	NM_001080440		Approved	C1QTNF15	uc011bpb.2	A6NHN0		ENST00000327928.4:c.966T>A	3.37:g.161221262T>A		108.0	0.0	0		107.0	60.0	0.560748	NM_001080440		Silent	SNP	ENST00000327928.4	37	CCDS46948.1																																																																																			T|0.990;A|0.010	0.010	strong		0.572	OTOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353184.1	NM_001080440	
CCDC168	643677	hgsc.bcm.edu	37	13	103386496	103386496	+	Silent	SNP	T	T	G	rs7988702	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:103386496T>G	ENST00000322527.2	-	1	2663	c.2664A>C	c.(2662-2664)ccA>ccC	p.P888P		NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168	888																	TATGTGACATTGGTGAAATCC	0.368													T|||	134	0.0267572	0.0976	0.0058	5008	,	,		24575	0.0		0.001	False		,,,				2504	0.0				p.P5517P		Atlas-SNP	.											.	.	.	.	0			c.A16551C						PASS	.	T		137,1247		10,117,565	160.0	130.0	139.0		16551	-0.0	0.1	13	dbSNP_116	139	4,3178		0,4,1587	no	coding-synonymous	CCDC168	NM_001146197.1		10,121,2152	GG,GT,TT		0.1257,9.8988,3.088		5517/7082	103386496	141,4425	692	1591	2283	SO:0001819	synonymous_variant	643677	exon4			TGACATTGGTGAA		CCDS73596.1	13q33.1	2014-06-17	2011-08-09	2011-08-09	ENSG00000175820	ENSG00000175820			26851	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 40"""	C13orf40			Standard	NM_001146197		Approved	FLJ40176	uc001vpm.3	Q8NDH2	OTTHUMG00000187287	ENST00000322527.2:c.2664A>C	13.37:g.103386496T>G		227.0	0.0	0		263.0	129.0	0.490494	NM_001146197	Q8N800	Silent	SNP	ENST00000322527.2	37																																																																																				T|0.974;G|0.026	0.026	strong		0.368	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
SLC22A5	6584	hgsc.bcm.edu	37	5	131729935	131729935	+	Missense_Mutation	SNP	C	C	T	rs11568525	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:131729935C>T	ENST00000245407.3	+	10	1866	c.1645C>T	c.(1645-1647)Ccc>Tcc	p.P549S	SLC22A5_ENST00000435065.2_Missense_Mutation_p.P573S	NM_003060.3	NP_003051.1	O76082	S22A5_HUMAN	solute carrier family 22 (organic cation/carnitine transporter), member 5	549			P -> S (associated with CDSP; unclassified missense variant; dbSNP:rs11568525). {ECO:0000269|PubMed:16931768, ECO:0000269|PubMed:20574985}.		carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|positive regulation of intestinal epithelial structure maintenance (GO:0060731)|quaternary ammonium group transport (GO:0015697)|quorum sensing involved in interaction with host (GO:0052106)|sodium ion transport (GO:0006814)|sodium-dependent organic cation transport (GO:0070715)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antibiotic transporter activity (GO:0042895)|ATP binding (GO:0005524)|carnitine transmembrane transporter activity (GO:0015226)|drug transmembrane transporter activity (GO:0015238)|PDZ domain binding (GO:0030165)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|symporter activity (GO:0015293)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|stomach(1)	8		all_cancers(142;0.0751)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Acetylcarnitine(DB08842)|Aminohippurate(DB00345)|Amphetamine(DB00182)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benzylpenicillin(DB01053)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefradine(DB01333)|Ceftazidime(DB00438)|Cephalexin(DB00567)|Cephaloglycin(DB00689)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Creatine(DB00148)|Cyclacillin(DB01000)|Dactinomycin(DB00970)|Desipramine(DB01151)|Diphenhydramine(DB01075)|Dopamine(DB00988)|Epinephrine(DB00668)|Furosemide(DB00695)|Guanidine(DB00536)|Histamine Phosphate(DB00667)|Ipratropium bromide(DB00332)|L-Arginine(DB00125)|L-Carnitine(DB00583)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Mepyramine(DB06691)|Methamphetamine(DB01577)|Niacin(DB00627)|Nicotine(DB00184)|Norepinephrine(DB00368)|Norfloxacin(DB01059)|Ofloxacin(DB01165)|Probenecid(DB01032)|Procainamide(DB01035)|Quinidine(DB00908)|Quinine(DB00468)|Sparfloxacin(DB01208)|Thiamine(DB00152)|Tiotropium(DB01409)|Valproic Acid(DB00313)|Verapamil(DB00661)	TCAAGAAAGGCCCACAATCCT	0.388													C|||	110	0.0219649	0.0809	0.0043	5008	,	,		21710	0.0		0.0	False		,,,				2504	0.0				p.P549S		Atlas-SNP	.											.	SLC22A5	34	.	0			c.C1645T						PASS	.	C	SER/PRO	307,4099	166.9+/-198.0	5,297,1901	124.0	117.0	119.0		1645	4.4	1.0	5	dbSNP_126	119	0,8600		0,0,4300	yes	missense	SLC22A5	NM_003060.3	74	5,297,6201	TT,TC,CC		0.0,6.9678,2.3604	benign	549/558	131729935	307,12699	2203	4300	6503	SO:0001583	missense	6584	exon10			GAAAGGCCCACAA	AF057164	CCDS4154.1	5q23.3	2013-05-22	2008-01-11		ENSG00000197375	ENSG00000197375		"""Solute carriers"""	10969	protein-coding gene	gene with protein product		603377		CDSP		9618255, 9916797, 9685390	Standard	NM_003060		Approved	OCTN2, SCD	uc003kww.4	O76082	OTTHUMG00000059634	ENST00000245407.3:c.1645C>T	5.37:g.131729935C>T	ENSP00000245407:p.Pro549Ser	168.0	0.0	0		139.0	55.0	0.395683	NM_003060	A2Q0V1|B2R844|D3DQ87|Q6ZQZ8|Q96EH6	Missense_Mutation	SNP	ENST00000245407.3	37	CCDS4154.1	39	0.017857142857142856	37	0.07520325203252033	2	0.0055248618784530384	0	0.0	0	0.0	C	10.62	1.402298	0.25291	0.069678	0.0	ENSG00000197375	ENST00000245407;ENST00000435065	T;T	0.72725	-0.64;-0.68	5.28	4.38	0.52667	.	0.594079	0.17842	N	0.160148	T	0.04815	0.0130	N	0.24115	0.695	0.29262	N	0.871235	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.002	T	0.04178	-1.0971	10	0.09084	T	0.74	.	10.2464	0.43343	0.0:0.9041:0.0:0.0959	rs11568525;rs45558436;rs52826155;rs57292152;rs11568525	573;549	A2Q0V1;O76082	.;S22A5_HUMAN	S	549;573	ENSP00000245407:P549S;ENSP00000402760:P573S	ENSP00000245407:P549S	P	+	1	0	SLC22A5	131757834	0.935000	0.31712	0.985000	0.45067	0.319000	0.28217	1.735000	0.38176	1.392000	0.46585	0.655000	0.94253	CCC	C|0.972;T|0.028	0.028	strong		0.388	SLC22A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132631.1	NM_003060	
OBSCN	84033	hgsc.bcm.edu	37	1	228473959	228473959	+	Missense_Mutation	SNP	T	T	G	rs202022683	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228473959T>G	ENST00000422127.1	+	34	9229	c.9185T>G	c.(9184-9186)gTg>gGg	p.V3062G	OBSCN_ENST00000366707.4_Missense_Mutation_p.V181G|OBSCN_ENST00000570156.2_Missense_Mutation_p.V3491G|OBSCN_ENST00000359599.6_Missense_Mutation_p.V1909G|OBSCN_ENST00000366709.4_Missense_Mutation_p.V181G|OBSCN_ENST00000284548.11_Missense_Mutation_p.V3062G	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3062	Ig-like 30.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GGCTACCACGTGCTGACCCTG	0.662													T|||	36	0.0071885	0.0272	0.0	5008	,	,		17519	0.0		0.0	False		,,,				2504	0.0				p.V3491G		Atlas-SNP	.											OBSCN_ENST00000570156,NS,haematopoietic_neoplasm,0,4	OBSCN	2142	4	0			c.T10472G						scavenged	.	T	GLY/VAL,GLY/VAL	98,4070		1,96,1987	26.0	33.0	31.0		9185,9185	4.5	1.0	1	dbSNP_134	31	0,8434		0,0,4217	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	109,109	1,96,6204	GG,GT,TT		0.0,2.3512,0.7777	possibly-damaging,possibly-damaging	3062/7969,3062/6621	228473959	98,12504	2084	4217	6301	SO:0001583	missense	84033	exon39			ACCACGTGCTGAC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.9185T>G	1.37:g.228473959T>G	ENSP00000409493:p.Val3062Gly	192.0	2.0	0.0104167		204.0	101.0	0.495098	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.084154	0.76642	0.023512	0.0	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709;ENST00000359599	T;T;T;T;T	0.66815	-0.23;-0.23;-0.23;-0.23;-0.23	5.67	4.49	0.54785	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.638941	0.14451	N	0.318802	T	0.59555	0.2202	M	0.66939	2.045	0.39455	D	0.967471	P;D	0.54207	0.877;0.965	P;P	0.62435	0.818;0.902	T	0.66208	-0.5981	10	0.23891	T	0.37	.	6.0668	0.19868	0.1444:0.0756:0.0:0.7801	.	3062;3062	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	G	3062;3062;181;181;1909	ENSP00000284548:V3062G;ENSP00000409493:V3062G;ENSP00000355668:V181G;ENSP00000355670:V181G;ENSP00000352613:V1909G	ENSP00000284548:V3062G	V	+	2	0	OBSCN	226540582	0.533000	0.26354	0.959000	0.39883	0.795000	0.44927	1.070000	0.30653	2.155000	0.67459	0.459000	0.35465	GTG	.	.	weak		0.662	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
PLK4	10733	hgsc.bcm.edu	37	4	128808620	128808620	+	Silent	SNP	A	A	T	rs112831813	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:128808620A>T	ENST00000270861.5	+	6	1702	c.1428A>T	c.(1426-1428)gtA>gtT	p.V476V	PLK4_ENST00000513090.1_Silent_p.V444V|PLK4_ENST00000514379.1_Silent_p.V435V|PLK4_ENST00000515069.1_Silent_p.V476V|PLK4_ENST00000507249.1_Silent_p.V442V	NM_014264.4	NP_055079.3	O00444	PLK4_HUMAN	polo-like kinase 4	476					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						CTGAAACCGTACAACAGTGGT	0.363													A|||	26	0.00519169	0.0182	0.0029	5008	,	,		16496	0.0		0.0	False		,,,				2504	0.0				p.V476V	Colon(135;508 1718 19061 31832 42879)	Atlas-SNP	.											.	PLK4	65	.	0			c.A1428T						PASS	.	A	,,	76,4330	65.8+/-103.3	0,76,2127	65.0	66.0	65.0		1332,1305,1428	-5.6	0.9	4	dbSNP_132	65	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	PLK4	NM_001190799.1,NM_001190801.1,NM_014264.4	,,	0,77,6426	TT,TA,AA		0.0116,1.7249,0.592	,,	444/939,435/930,476/971	128808620	77,12929	2203	4300	6503	SO:0001819	synonymous_variant	10733	exon6			AACCGTACAACAG	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.1428A>T	4.37:g.128808620A>T		406.0	0.0	0		482.0	238.0	0.493776	NM_014264	B2RAL0|B7Z837|B7Z8G7|Q8IYF0|Q96Q95|Q9UD84|Q9UDE2	Silent	SNP	ENST00000270861.5	37	CCDS3735.1																																																																																			A|0.993;T|0.007	0.007	strong		0.363	PLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257095.3		
MN1	4330	hgsc.bcm.edu	37	22	28193097	28193097	+	Silent	SNP	C	C	T	rs45471598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:28193097C>T	ENST00000302326.4	-	1	4389	c.3435G>A	c.(3433-3435)ccG>ccA	p.P1145P		NM_002430.2	NP_002421.3	Q10571	MN1_HUMAN	meningioma (disrupted in balanced translocation) 1	1145					intramembranous ossification (GO:0001957)					NS(1)|breast(2)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	45						CGTCGGGTGGCGGGGCGCCGC	0.711			T	ETV6	"""AML, meningioma"""								C|||	265	0.0529153	0.1936	0.013	5008	,	,		13060	0.0		0.0	False		,,,				2504	0.0				p.P1145P		Atlas-SNP	.		Dom	yes		22	22q13	4330	meningioma (disrupted in balanced translocation) 1		"""L, O"""	MN1,colon,carcinoma,0,1	MN1	122	1	0			c.G3435A						PASS	.	C		505,3385		19,467,1459	6.0	7.0	7.0		3435	-3.9	0.0	22	dbSNP_127	7	8,8188		0,8,4090	no	coding-synonymous	MN1	NM_002430.2		19,475,5549	TT,TC,CC		0.0976,12.982,4.2446		1145/1321	28193097	513,11573	1945	4098	6043	SO:0001819	synonymous_variant	4330	exon1			GGGTGGCGGGGCG	X82209	CCDS42998.1	22q12.1	2010-09-29			ENSG00000169184	ENSG00000169184			7180	protein-coding gene	gene with protein product	"""probable tumor suppressor protein MN1"""	156100	"""meningioma chromosome region"""	MGCR		7731706, 12569362	Standard	NM_002430		Approved	MGCR1-PEN, MGCR1	uc003adj.3	Q10571	OTTHUMG00000150975	ENST00000302326.4:c.3435G>A	22.37:g.28193097C>T		22.0	0.0	0		38.0	18.0	0.473684	NM_002430	A9Z1V9	Silent	SNP	ENST00000302326.4	37	CCDS42998.1																																																																																			C|0.962;T|0.038	0.038	strong		0.711	MN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320737.1	NM_002430	
DPF2	5977	hgsc.bcm.edu	37	11	65113459	65113459	+	Silent	SNP	G	G	T	rs61736579	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:65113459G>T	ENST00000528416.1	+	8	967	c.834G>T	c.(832-834)ggG>ggT	p.G278G	DPF2_ENST00000415073.2_Intron|DPF2_ENST00000532264.1_3'UTR|DPF2_ENST00000252268.4_Silent_p.G292G	NM_006268.4	NP_006259.1	Q92785	REQU_HUMAN	D4, zinc and double PHD fingers family 2	278					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|prostate(1)	23						TCTGCCTGGGGGACTCAAAGA	0.537													G|||	57	0.0113818	0.0295	0.0029	5008	,	,		18964	0.0149		0.001	False		,,,				2504	0.0				p.G278G		Atlas-SNP	.											.	DPF2	54	.	0			c.G834T						PASS	.	G		96,4306	78.3+/-116.7	0,96,2105	118.0	123.0	121.0		834	-7.1	0.6	11	dbSNP_129	121	2,8592	1.2+/-3.3	0,2,4295	no	coding-synonymous	DPF2	NM_006268.4		0,98,6400	TT,TG,GG		0.0233,2.1808,0.7541		278/392	65113459	98,12898	2201	4297	6498	SO:0001819	synonymous_variant	5977	exon8			CCTGGGGGACTCA	U94585	CCDS8100.1	11q13.1	2014-05-13	2003-10-06	2003-10-08	ENSG00000133884	ENSG00000133884		"""Zinc fingers, PHD-type"""	9964	protein-coding gene	gene with protein product		601671	"""requiem, apoptosis response zinc finger gene"""	REQ		11845289	Standard	NM_006268		Approved	ubi-d4, BAF45d	uc001odm.3	Q92785	OTTHUMG00000165985	ENST00000528416.1:c.834G>T	11.37:g.65113459G>T		78.0	0.0	0		103.0	51.0	0.495146	NM_006268	A8K7C9|B4DT58	Silent	SNP	ENST00000528416.1	37	CCDS8100.1	26	0.011904761904761904	19	0.03861788617886179	0	0.0	7	0.012237762237762238	0	0.0	G	12.47	1.947810	0.34377	0.021808	2.33E-4	ENSG00000133884	ENST00000531989	D	0.90504	-2.68	5.92	-7.09	0.01553	.	0.000000	0.38005	N	0.001851	T	0.61515	0.2353	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.69187	-0.5211	7	0.24483	T	0.36	-20.6054	6.2509	0.20845	0.5834:0.0898:0.2361:0.0906	rs61736579	.	.	.	V	41	ENSP00000435887:G41V	ENSP00000435887:G41V	G	+	2	0	DPF2	64870035	0.000000	0.05858	0.648000	0.29521	0.864000	0.49448	-1.570000	0.02140	-1.394000	0.02077	-2.076000	0.00381	GGG	G|0.989;T|0.011	0.011	strong		0.537	DPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387293.3	NM_006268	
ZNF98	148198	hgsc.bcm.edu	37	19	22575504	22575504	+	Missense_Mutation	SNP	C	C	G	rs116270361	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22575504C>G	ENST00000357774.5	-	4	654	c.533G>C	c.(532-534)gGa>gCa	p.G178A		NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	178					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				AGATTTCTTTCCAGTATGTCC	0.303													c|||	102	0.0203674	0.0741	0.0058	5008	,	,		17746	0.0		0.0	False		,,,				2504	0.0				p.G178A		Atlas-SNP	.											.	ZNF98	230	.	0			c.G533C						PASS	.	C	ALA/GLY	286,3752		6,274,1739	26.0	27.0	27.0		533	-1.8	0.0	19	dbSNP_132	27	2,8428		0,2,4213	no	missense	ZNF98	NM_001098626.1	60	6,276,5952	GG,GC,CC		0.0237,7.0827,2.3099	possibly-damaging	178/573	22575504	288,12180	2019	4215	6234	SO:0001583	missense	148198	exon4			TTCTTTCCAGTAT		CCDS46031.1	19p12	2014-02-14	2010-04-20	2008-06-12	ENSG00000197360	ENSG00000197360		"""Zinc fingers, C2H2-type"", ""-"""	13174	protein-coding gene	gene with protein product	"""zinc finger protein 739"""	603980					Standard	NM_001098626		Approved	ZNF739, F7175	uc002nqt.2	A6NK75	OTTHUMG00000182940	ENST00000357774.5:c.533G>C	19.37:g.22575504C>G	ENSP00000350418:p.Gly178Ala	280.0	0.0	0		287.0	152.0	0.529617	NM_001098626		Missense_Mutation	SNP	ENST00000357774.5	37	CCDS46031.1	42	0.019230769230769232	40	0.08130081300813008	2	0.0055248618784530384	0	0.0	0	0.0	.	12.41	1.928642	0.34002	0.070827	2.37E-4	ENSG00000197360	ENST00000357774	T	0.35236	1.32	1.28	-1.83	0.07833	Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02767	0.0083	L	0.52905	1.665	0.30794	N	0.740644	P	0.45827	0.867	P	0.55713	0.782	T	0.22103	-1.0226	9	0.66056	D	0.02	.	4.2412	0.10648	0.2247:0.6036:0.0:0.1717	.	178	A6NK75	ZNF98_HUMAN	A	178	ENSP00000350418:G178A	ENSP00000350418:G178A	G	-	2	0	ZNF98	22367344	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	0.168000	0.16622	-0.223000	0.09943	0.305000	0.20034	GGA	C|0.976;G|0.024	0.024	strong		0.303	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626	
KALRN	8997	hgsc.bcm.edu	37	3	124174062	124174062	+	Silent	SNP	C	C	T	rs61747979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:124174062C>T	ENST00000240874.3	+	22	3742	c.3585C>T	c.(3583-3585)gcC>gcT	p.A1195A	KALRN_ENST00000460856.1_Silent_p.A1186A|KALRN_ENST00000360013.3_Silent_p.A1195A	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1195					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.A1195A(2)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						TTCAGCTGGCCGATAGCTTTG	0.483													C|||	160	0.0319489	0.1172	0.0072	5008	,	,		21547	0.0		0.0	False		,,,				2504	0.0				p.A1195A		Atlas-SNP	.											.	KALRN	556	.	2	Substitution - coding silent(2)	lung(2)	c.C3585T						PASS	.	C	,	413,3993	203.5+/-225.9	25,363,1815	118.0	109.0	112.0		3585,3585	-9.4	0.0	3	dbSNP_129	112	3,8597	1.2+/-3.3	0,3,4297	no	coding-synonymous,coding-synonymous	KALRN	NM_001024660.3,NM_003947.4	,	25,366,6112	TT,TC,CC		0.0349,9.3736,3.1985	,	1195/2987,1195/1664	124174062	416,12590	2203	4300	6503	SO:0001819	synonymous_variant	8997	exon22			GCTGGCCGATAGC	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	4814	protein-coding gene	gene with protein product	"""serine/threonine kinase with Dbl and pleckstrin homology domains"""	604605	"""huntingtin-associated protein interacting protein (duo)"""	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.3585C>T	3.37:g.124174062C>T		108.0	0.0	0		104.0	51.0	0.490385	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000240874.3	37	CCDS3027.1	68	0.031135531135531136	66	0.13414634146341464	2	0.0055248618784530384	0	0.0	0	0.0	C	6.766	0.510205	0.12883	0.093736	3.49E-4	ENSG00000160145	ENST00000354186	.	.	.	4.71	-9.42	0.00610	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.09310	P	0.9999999999999124	.	.	.	.	.	.	T	0.01925	-1.1246	3	.	.	.	.	3.8289	0.08865	0.2842:0.1245:0.0655:0.5257	rs61747979	.	.	.	L	1164	.	.	P	+	2	0	KALRN	125656752	0.000000	0.05858	0.027000	0.17364	0.936000	0.57629	-4.076000	0.00300	-4.614000	0.00039	-1.741000	0.00685	CCG	C|0.969;T|0.031	0.031	strong		0.483	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947	
ADARB2	105	hgsc.bcm.edu	37	10	1405835	1405835	+	Silent	SNP	G	G	A	rs35398040	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:1405835G>A	ENST00000381312.1	-	3	790	c.465C>T	c.(463-465)gtC>gtT	p.V155V	RP11-398B16.2_ENST00000432987.1_RNA	NM_018702.3	NP_061172.1	Q9NS39	RED2_HUMAN	adenosine deaminase, RNA-specific, B2 (non-functional)	155	DRBM 1. {ECO:0000255|PROSITE- ProRule:PRU00266}.				mRNA processing (GO:0006397)	nucleus (GO:0005634)	adenosine deaminase activity (GO:0004000)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|single-stranded RNA binding (GO:0003727)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(17)|prostate(2)|skin(1)|urinary_tract(1)	41		all_epithelial(10;0.059)|Colorectal(49;0.0815)		all cancers(11;0.0224)|GBM - Glioblastoma multiforme(2;0.0414)|Epithelial(11;0.165)		CTACCGCGAAGACCGGGGCAT	0.692													g|||	72	0.014377	0.0522	0.0043	5008	,	,		9729	0.0		0.0	False		,,,				2504	0.0				p.V155V		Atlas-SNP	.											.	ADARB2	95	.	0			c.C465T						PASS	.			185,4221	107.8+/-146.2	5,175,2023	35.0	30.0	32.0		465	1.2	1.0	10	dbSNP_126	32	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ADARB2	NM_018702.3		5,176,6322	AA,AG,GG		0.0116,4.1988,1.4301		155/740	1405835	186,12820	2203	4300	6503	SO:0001819	synonymous_variant	105	exon3			CGCGAAGACCGGG	AF034837	CCDS7058.1	10p15.3	2013-05-20	2013-05-20		ENSG00000185736	ENSG00000185736	3.5.-.-		227	protein-coding gene	gene with protein product	"""RED2 homolog (rat)"""	602065	"""adenosine deaminase, RNA-specific, B2 (RED2 homolog rat)"", ""adenosine deaminase, RNA-specific, B2"""			9272162, 10836796	Standard	NM_018702		Approved	RED2, hRED2, ADAR3	uc009xhq.3	Q9NS39	OTTHUMG00000017543	ENST00000381312.1:c.465C>T	10.37:g.1405835G>A		74.0	0.0	0		115.0	114.0	0.991304	NM_018702	B2RPJ5|Q5VUT6|Q5VW42	Silent	SNP	ENST00000381312.1	37	CCDS7058.1																																																																																			G|0.981;A|0.019	0.019	strong		0.692	ADARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046426.1	NM_018702	
SYNGR3	9143	hgsc.bcm.edu	37	16	2042086	2042086	+	Missense_Mutation	SNP	G	G	A	rs199784173	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2042086G>A	ENST00000248121.2	+	2	369	c.211G>A	c.(211-213)Ggc>Agc	p.G71S	SYNGR3_ENST00000562045.1_5'UTR	NM_004209.5	NP_004200.2	O43761	SNG3_HUMAN	synaptogyrin 3	71	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				positive regulation of transporter activity (GO:0032411)|substantia nigra development (GO:0021762)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|synaptic vesicle (GO:0008021)				endometrium(1)|lung(2)	3						CTGCCGCTTCGGCGTCGCGCT	0.716													G|||	18	0.00359425	0.0113	0.0043	5008	,	,		8658	0.0		0.0	False		,,,				2504	0.0				p.G71S		Atlas-SNP	.											.	SYNGR3	10	.	0			c.G211A						PASS	.	G	SER/GLY	21,3953		0,21,1966	6.0	6.0	6.0		211	4.2	1.0	16		6	0,8028		0,0,4014	no	missense	SYNGR3	NM_004209.5	56	0,21,5980	AA,AG,GG		0.0,0.5284,0.175	probably-damaging	71/230	2042086	21,11981	1987	4014	6001	SO:0001583	missense	9143	exon2			CGCTTCGGCGTCG	AJ002309	CCDS10456.1	16p13.3	2008-05-19			ENSG00000127561	ENSG00000127561			11501	protein-coding gene	gene with protein product		603927				9760194	Standard	NM_004209		Approved		uc002cod.3	O43761	OTTHUMG00000128711	ENST00000248121.2:c.211G>A	16.37:g.2042086G>A	ENSP00000248121:p.Gly71Ser	5.0	0.0	0		11.0	10.0	0.909091	NM_004209	B2R9S0	Missense_Mutation	SNP	ENST00000248121.2	37	CCDS10456.1	13	0.005952380952380952	11	0.022357723577235773	1	0.0027624309392265192	1	0.0017482517482517483	0	0.0	g	23.6	4.432249	0.83776	0.005284	0.0	ENSG00000127561	ENST00000248121;ENST00000320633	T	0.24908	1.83	4.2	4.2	0.49525	Marvel (1);MARVEL-like domain (1);	0.056575	0.64402	D	0.000001	T	0.31575	0.0801	M	0.66378	2.025	0.80722	D	1	D	0.89917	1.0	D	0.68621	0.959	T	0.40590	-0.9555	10	0.62326	D	0.03	.	15.6377	0.76966	0.0:0.0:1.0:0.0	.	71	O43761	SNG3_HUMAN	S	71	ENSP00000248121:G71S	ENSP00000248121:G71S	G	+	1	0	SYNGR3	1982087	1.000000	0.71417	1.000000	0.80357	0.135000	0.20990	9.184000	0.94893	2.340000	0.79590	0.561000	0.74099	GGC	G|0.994;A|0.006	0.006	strong		0.716	SYNGR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250616.1		
C17orf64	124773	hgsc.bcm.edu	37	17	58506785	58506785	+	Silent	SNP	G	G	T	rs9913666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:58506785G>T	ENST00000269127.4	+	5	576	c.492G>T	c.(490-492)ctG>ctT	p.L164L		NM_181707.2	NP_859058.2	Q86WR6	CQ064_HUMAN	chromosome 17 open reading frame 64	164										breast(2)|large_intestine(1)|lung(3)	6	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;5.81e-13)|all cancers(12;2.17e-11)|Colorectal(3;0.01)			AAGACAGTCTGCCCAAGCTCT	0.622													G|||	541	0.108027	0.3858	0.0418	5008	,	,		17929	0.0		0.002	False		,,,				2504	0.0				p.L164L		Atlas-SNP	.											.	C17orf64	19	.	0			c.G492T						PASS	.	G		1342,3064	443.9+/-347.2	217,908,1078	47.0	47.0	47.0		492	1.7	1.0	17	dbSNP_119	47	14,8586	9.8+/-36.6	0,14,4286	no	coding-synonymous	C17orf64	NM_181707.2		217,922,5364	TT,TG,GG		0.1628,30.4585,10.426		164/237	58506785	1356,11650	2203	4300	6503	SO:0001819	synonymous_variant	124773	exon5			CAGTCTGCCCAAG	BC048806	CCDS32698.2	17q23.2	2005-12-16			ENSG00000141371	ENSG00000141371			26990	protein-coding gene	gene with protein product						12477932	Standard	NM_181707		Approved		uc002iyq.3	Q86WR6	OTTHUMG00000157171	ENST00000269127.4:c.492G>T	17.37:g.58506785G>T		104.0	0.0	0		127.0	62.0	0.488189	NM_181707	Q8IY87	Silent	SNP	ENST00000269127.4	37	CCDS32698.2																																																																																			G|0.912;T|0.088	0.088	strong		0.622	C17orf64-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000347743.1	NM_181707	
ENTPD4	9583	hgsc.bcm.edu	37	8	23299225	23299225	+	Missense_Mutation	SNP	C	C	T	rs34849865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:23299225C>T	ENST00000358689.4	-	8	974	c.739G>A	c.(739-741)Gtt>Att	p.V247I	ENTPD4_ENST00000356206.6_Missense_Mutation_p.V247I|ENTPD4_ENST00000417069.2_Missense_Mutation_p.V247I	NM_001128930.2|NM_004901.4	NP_001122402.1|NP_004892.1	Q9Y227	ENTP4_HUMAN	ectonucleoside triphosphate diphosphohydrolase 4	247					UDP catabolic process (GO:0006256)	cytoplasmic vesicle (GO:0031410)|integral component of Golgi membrane (GO:0030173)|intracellular membrane-bounded organelle (GO:0043231)	uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	25		Prostate(55;0.114)		Colorectal(74;0.0161)|COAD - Colon adenocarcinoma(73;0.0649)		ACTTCCACAACGGCCTCATCA	0.473													C|||	26	0.00519169	0.0197	0.0	5008	,	,		21884	0.0		0.0	False		,,,				2504	0.0				p.V247I		Atlas-SNP	.											.	ENTPD4	56	.	0			c.G739A						PASS	.	C	ILE/VAL,ILE/VAL	101,4305	81.9+/-120.4	1,99,2103	65.0	56.0	59.0		739,739	3.1	0.4	8	dbSNP_126	59	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	ENTPD4	NM_001128930.2,NM_004901.4	29,29	1,101,6401	TT,TC,CC		0.0233,2.2923,0.7919	benign,benign	247/609,247/617	23299225	103,12903	2203	4300	6503	SO:0001583	missense	9583	exon8			CCACAACGGCCTC	AJ131358	CCDS6041.1, CCDS47827.1	8p21.3	2014-05-16	2004-09-22	2004-09-22	ENSG00000197217	ENSG00000197217			14573	protein-coding gene	gene with protein product		607577	"""lysosomal apyrase-like 1"""	LYSAL1		10393803, 9205841	Standard	NM_001128930		Approved	LALP70, LAP70, KIAA0392, NTPDase-4, UDPase	uc003xdl.3	Q9Y227	OTTHUMG00000097852	ENST00000358689.4:c.739G>A	8.37:g.23299225C>T	ENSP00000351520:p.Val247Ile	55.0	0.0	0		59.0	39.0	0.661017	NM_004901	D3DSS3|O15092	Missense_Mutation	SNP	ENST00000358689.4	37	CCDS6041.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	C	12.07	1.826131	0.32237	0.022923	2.33E-4	ENSG00000197217	ENST00000356206;ENST00000358689;ENST00000417069	T;T;T	0.14144	2.57;2.53;2.58	5.87	3.1	0.35709	.	0.431567	0.26307	N	0.025140	T	0.05686	0.0149	L	0.49126	1.545	0.31429	N	0.673388	B;B;B	0.13594	0.008;0.003;0.003	B;B;B	0.15870	0.014;0.003;0.005	T	0.12192	-1.0557	10	0.25751	T	0.34	-13.4993	8.0326	0.30474	0.0:0.7229:0.1325:0.1446	rs34849865	247;247;247	Q8NE73;Q9Y227-2;Q9Y227	.;.;ENTP4_HUMAN	I	247	ENSP00000348536:V247I;ENSP00000351520:V247I;ENSP00000408573:V247I	ENSP00000348536:V247I	V	-	1	0	ENTPD4	23355170	0.005000	0.15991	0.412000	0.26496	0.832000	0.47134	0.266000	0.18534	0.385000	0.24970	0.655000	0.94253	GTT	C|0.993;T|0.007	0.007	strong		0.473	ENTPD4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215142.1	NM_004901	
IPO13	9670	hgsc.bcm.edu	37	1	44424525	44424525	+	Silent	SNP	G	G	A	rs74073335	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:44424525G>A	ENST00000372343.3	+	11	2654	c.1992G>A	c.(1990-1992)gaG>gaA	p.E664E		NM_014652.3	NP_055467.3	O94829	IPO13_HUMAN	importin 13	664					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0821)				AAGGCCCTGAGCTTCGGAAGC	0.562													G|||	38	0.00758786	0.0287	0.0	5008	,	,		20073	0.0		0.0	False		,,,				2504	0.0				p.E664E		Atlas-SNP	.											.	IPO13	86	.	0			c.G1992A						PASS	.	G		124,4282	90.6+/-129.3	1,122,2080	84.0	78.0	80.0		1992	3.8	1.0	1	dbSNP_130	80	0,8600		0,0,4300	no	coding-synonymous	IPO13	NM_014652.3		1,122,6380	AA,AG,GG		0.0,2.8143,0.9534		664/964	44424525	124,12882	2203	4300	6503	SO:0001819	synonymous_variant	9670	exon11			CCCTGAGCTTCGG	AB018267	CCDS503.1	1p34.1	2008-02-05			ENSG00000117408	ENSG00000117408		"""Importins"""	16853	protein-coding gene	gene with protein product		610411				9872452, 11447110	Standard	NM_014652		Approved	IMP13, KIAA0724, RANBP13	uc001ckx.3	O94829	OTTHUMG00000008297	ENST00000372343.3:c.1992G>A	1.37:g.44424525G>A		165.0	0.0	0		166.0	96.0	0.578313	NM_014652	D3DPY4|Q5T4X3|Q7LC04|Q96HS3|Q9H8N3|Q9UFR1	Silent	SNP	ENST00000372343.3	37	CCDS503.1																																																																																			G|0.991;A|0.009	0.009	strong		0.562	IPO13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022846.1	NM_014652	
BAALC	79870	hgsc.bcm.edu	37	8	104240275	104240275	+	Missense_Mutation	SNP	G	G	C	rs34542607	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:104240275G>C	ENST00000297574.6	+	4	630	c.491G>C	c.(490-492)aGc>aCc	p.S164T	RP11-318M2.2_ENST00000499522.2_RNA|BAALC_ENST00000309982.5_Missense_Mutation_p.S129T|BAALC_ENST00000438105.2_3'UTR|RP11-318M2.2_ENST00000523614.2_RNA|BAALC_ENST00000523754.1_3'UTR|RP11-318M2.3_ENST00000523775.1_RNA			Q8WXS3	BAALC_HUMAN	brain and acute leukemia, cytoplasmic	164			S -> T (in dbSNP:rs34542607).			cytoplasm (GO:0005737)|membrane (GO:0016020)				kidney(1)|large_intestine(3)|lung(3)	7			OV - Ovarian serous cystadenocarcinoma(57;3.49e-05)|STAD - Stomach adenocarcinoma(118;0.133)			GTAACAGATAGCATCCAACAG	0.408													G|||	124	0.0247604	0.0908	0.0058	5008	,	,		24074	0.0		0.0	False		,,,				2504	0.0				p.S129T		Atlas-SNP	.											.	BAALC	15	.	0			c.G386C						PASS	.	G	,THR/SER	395,4011	198.1+/-222.0	21,353,1829	127.0	109.0	115.0		,386	3.9	0.9	8	dbSNP_126	115	1,8599	1.2+/-3.3	0,1,4299	yes	utr-3,missense	BAALC	NM_001024372.1,NM_024812.2	,58	21,354,6128	CC,CG,GG		0.0116,8.965,3.0447	,benign	,129/146	104240275	396,12610	2203	4300	6503	SO:0001583	missense	79870	exon3			CAGATAGCATCCA	AF363578	CCDS6297.1, CCDS47906.1	8q22.3	2008-07-29			ENSG00000164929	ENSG00000164929			14333	protein-coding gene	gene with protein product		606602				11707601	Standard	NM_024812		Approved		uc003yld.3	Q8WXS3	OTTHUMG00000164782	ENST00000297574.6:c.491G>C	8.37:g.104240275G>C	ENSP00000297574:p.Ser164Thr	72.0	0.0	0		81.0	47.0	0.580247	NM_024812	Q8WTP6|Q8WXS0|Q8WXS1|Q8WXS2|Q9HA93	Missense_Mutation	SNP	ENST00000297574.6	37		56	0.02564102564102564	55	0.11178861788617886	1	0.0027624309392265192	0	0.0	0	0.0	G	12.02	1.813455	0.32053	0.08965	1.16E-4	ENSG00000164929	ENST00000309982;ENST00000297574	T;T	0.50813	0.73;0.73	4.8	3.9	0.45041	.	0.129605	0.48286	D	0.000192	T	0.00524	0.0017	.	.	.	0.80722	D	1	P;B	0.40970	0.734;0.447	B;B	0.32342	0.14;0.144	T	0.01894	-1.1252	9	0.22109	T	0.4	-12.8881	8.4904	0.33098	0.1123:0.0:0.8877:0.0	rs34542607	164;129	Q8WXS3;Q8WXS3-2	BAALC_HUMAN;.	T	129;164	ENSP00000312457:S129T;ENSP00000297574:S164T	ENSP00000297574:S164T	S	+	2	0	BAALC	104309451	1.000000	0.71417	0.886000	0.34754	0.987000	0.75469	2.175000	0.42491	1.113000	0.41760	0.591000	0.81541	AGC	G|0.971;C|0.029	0.029	strong		0.408	BAALC-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000380257.1		
BHLHB9	80823	hgsc.bcm.edu	37	X	102004046	102004046	+	Silent	SNP	G	G	A	rs17003869	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102004046G>A	ENST00000372735.1	+	4	708	c.123G>A	c.(121-123)agG>agA	p.R41R	BHLHB9_ENST00000447531.1_Silent_p.R41R|BHLHB9_ENST00000361229.4_Silent_p.R41R|BHLHB9_ENST00000457056.1_Silent_p.R41R|BHLHB9_ENST00000448867.1_Silent_p.R41R			Q6PI77	BHLH9_HUMAN	basic helix-loop-helix domain containing, class B, 9	41					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						CCAAGACCAGGGCCAAAGCAA	0.502													G|||	50	0.013245	0.0371	0.0014	3775	,	,		15788	0.0		0.0	False		,,,				2504	0.0				p.R41R		Atlas-SNP	.											.	BHLHB9	60	.	0			c.G123A						PASS	.	G	,,,,,,,	149,3686		2,117,28,1513,543	120.0	102.0	108.0		123,123,123,123,123,123,123,123	-3.2	0.0	X	dbSNP_123	108	0,6728		0,0,0,2428,1872	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BHLHB9	NM_001142524.1,NM_001142525.1,NM_001142526.1,NM_001142527.1,NM_001142528.1,NM_001142529.1,NM_001142530.1,NM_030639.2	,,,,,,,	2,117,28,3941,2415	AA,AG,A,GG,G		0.0,3.8853,1.4106	,,,,,,,	41/548,41/548,41/548,41/548,41/548,41/548,41/548,41/548	102004046	149,10414	2203	4300	6503	SO:0001819	synonymous_variant	80823	exon2			GACCAGGGCCAAA	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.123G>A	X.37:g.102004046G>A		322.0	0.0	0		412.0	145.0	0.351942	NM_001142530	Q9C0G2	Silent	SNP	ENST00000372735.1	37	CCDS14502.1																																																																																			0|0.003;A|0.015	0.015	strong		0.502	BHLHB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057630.1	NM_030639	
ZBTB40	9923	hgsc.bcm.edu	37	1	22816687	22816687	+	Silent	SNP	A	A	G	rs115103344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:22816687A>G	ENST00000375647.4	+	2	453	c.246A>G	c.(244-246)aaA>aaG	p.K82K	ZBTB40_ENST00000374651.4_Silent_p.K82K|ZBTB40_ENST00000404138.1_Silent_p.K82K	NM_014870.3	NP_055685.3	Q9NUA8	ZBT40_HUMAN	zinc finger and BTB domain containing 40	82	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				bone mineralization (GO:0030282)|cellular response to DNA damage stimulus (GO:0006974)|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(4)|kidney(4)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	26		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;2.86e-26)|Colorectal(126;8.55e-08)|COAD - Colon adenocarcinoma(152;4.1e-06)|GBM - Glioblastoma multiforme(114;1.39e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000712)|KIRC - Kidney renal clear cell carcinoma(1967;0.00374)|STAD - Stomach adenocarcinoma(196;0.00645)|READ - Rectum adenocarcinoma(331;0.0693)|Lung(427;0.216)		ACACGGGCAAACTACCTGTGG	0.473													A|||	31	0.0061901	0.0204	0.0043	5008	,	,		21552	0.0		0.001	False		,,,				2504	0.0				p.K82K		Atlas-SNP	.											.	ZBTB40	87	.	0			c.A246G						PASS	.	A	,	74,4332	65.3+/-102.7	0,74,2129	90.0	85.0	87.0		246,246	-3.0	0.6	1	dbSNP_132	87	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	ZBTB40	NM_001083621.1,NM_014870.3	,	0,75,6428	GG,GA,AA		0.0116,1.6795,0.5767	,	82/1240,82/1240	22816687	75,12931	2203	4300	6503	SO:0001819	synonymous_variant	9923	exon3			GGGCAAACTACCT	AB007947	CCDS224.1	1p36	2013-01-08			ENSG00000184677	ENSG00000184677		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	29045	protein-coding gene	gene with protein product		612106					Standard	NM_014870		Approved	KIAA0478, ZNF923	uc001bfu.2	Q9NUA8	OTTHUMG00000002897	ENST00000375647.4:c.246A>G	1.37:g.22816687A>G		107.0	0.0	0		122.0	62.0	0.508197	NM_001083621	O75066|Q5TFU5|Q8N1R1	Silent	SNP	ENST00000375647.4	37	CCDS224.1																																																																																			A|0.993;G|0.007	0.007	strong		0.473	ZBTB40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008094.1	NM_014870	
FAM124A	220108	hgsc.bcm.edu	37	13	51855114	51855114	+	Missense_Mutation	SNP	G	G	T	rs74087446	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:51855114G>T	ENST00000322475.8	+	4	1498	c.1363G>T	c.(1363-1365)Gca>Tca	p.A455S	FAM124A_ENST00000280057.6_Missense_Mutation_p.A491S	NM_001242312.1	NP_001229241.1	Q86V42	F124A_HUMAN	family with sequence similarity 124A	455										breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(6)|ovary(1)|prostate(2)|skin(1)	26		Acute lymphoblastic leukemia(7;0.000334)|Breast(56;0.00156)|Prostate(109;0.00538)|Lung NSC(96;0.0216)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;4.25e-07)		CAGCCACTGGGCAGCTCACAA	0.587													G|||	93	0.0185703	0.0696	0.0014	5008	,	,		18065	0.0		0.0	False		,,,				2504	0.0				p.A491S		Atlas-SNP	.											.	FAM124A	61	.	0			c.G1471T						PASS	.	G	SER/ALA,SER/ALA	315,4091	168.3+/-199.2	15,285,1903	55.0	54.0	54.0		1363,1471	-8.6	0.0	13	dbSNP_130	54	0,8600		0,0,4300	yes	missense,missense	FAM124A	NM_001242312.1,NM_145019.3	99,99	15,285,6203	TT,TG,GG		0.0,7.1493,2.422	benign,benign	455/547,491/583	51855114	315,12691	2203	4300	6503	SO:0001583	missense	220108	exon5			CACTGGGCAGCTC	AK096364	CCDS9427.1, CCDS55900.1	13q14.3	2006-08-11			ENSG00000150510	ENSG00000150510			26413	protein-coding gene	gene with protein product						12975309	Standard	NM_145019		Approved	FLJ30707	uc001vff.2	Q86V42	OTTHUMG00000016942	ENST00000322475.8:c.1363G>T	13.37:g.51855114G>T	ENSP00000324625:p.Ala455Ser	113.0	0.0	0		111.0	51.0	0.459459	NM_145019	A2A324|Q8N8P9|Q8NE66|Q96NJ9	Missense_Mutation	SNP	ENST00000322475.8	37	CCDS55900.1	38	0.0173992673992674	37	0.07520325203252033	1	0.0027624309392265192	0	0.0	0	0.0	G	6.025	0.373042	0.11409	0.071493	0.0	ENSG00000150510	ENST00000322475;ENST00000280057	T;T	0.39406	1.13;1.08	5.07	-8.56	0.00904	.	2.466230	0.01371	N	0.012590	T	0.00440	0.0014	N	0.00368	-1.59	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.001;0.002	T	0.13818	-1.0495	10	0.05620	T	0.96	-11.5191	5.727	0.18018	0.0847:0.4204:0.3398:0.1551	.	455;491	Q86V42;Q86V42-2	F124A_HUMAN;.	S	455;491	ENSP00000324625:A455S;ENSP00000280057:A491S	ENSP00000280057:A491S	A	+	1	0	FAM124A	50753115	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.686000	0.05161	-1.642000	0.01521	-0.284000	0.09977	GCA	G|0.975;T|0.026	0.026	strong		0.587	FAM124A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045019.3	NM_145019	
TTN	7273	hgsc.bcm.edu	37	2	179560847	179560847	+	Missense_Mutation	SNP	C	C	T	rs73038324	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179560847C>T	ENST00000591111.1	-	112	30225	c.30001G>A	c.(30001-30003)Gaa>Aaa	p.E10001K	TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.E9074K|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.E10318K			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TAAGGTTCTTCGAAAGATTCA	0.383													C|||	194	0.038738	0.1377	0.0159	5008	,	,		19287	0.0		0.001	False		,,,				2504	0.0				p.E10318K		Atlas-SNP	.											.	TTN	18412	.	0			c.G30952A						PASS	.	C	,,,LYS/GLU	347,3211		17,313,1449	126.0	105.0	111.0		,,,27220	5.8	0.9	2	dbSNP_130	111	9,7899		0,9,3945	yes	intron,intron,intron,missense	TTN	NM_003319.4,NM_133432.3,NM_133437.3,NM_133378.4	,,,56	17,322,5394	TT,TC,CC		0.1138,9.7527,3.1048	,,,benign	,,,9074/33424	179560847	356,11110	1779	3954	5733	SO:0001583	missense	7273	exon114			GTTCTTCGAAAGA	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.30001G>A	2.37:g.179560847C>T	ENSP00000465570:p.Glu10001Lys	242.0	0.0	0		234.0	119.0	0.508547	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		84	0.038461538461538464	77	0.1565040650406504	7	0.019337016574585635	0	0.0	0	0.0	C	18.27	3.586510	0.66105	0.097527	0.001138	ENSG00000155657	ENST00000342992;ENST00000414766	T	0.64260	-0.09	5.78	5.78	0.91487	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.00356	0.0011	M	0.66939	2.045	0.09310	P	1.0	B;P	0.50710	0.327;0.938	B;B	0.36845	0.026;0.234	T	0.36915	-0.9728	8	0.87932	D	0	.	15.5205	0.75862	0.0:1.0:0.0:0.0	.	10001;10001	Q8WZ42;Q8WZ42-5	TITIN_HUMAN;.	K	9074;196	ENSP00000343764:E9074K	ENSP00000343764:E9074K	E	-	1	0	TTN	179269092	0.966000	0.33281	0.949000	0.38748	0.899000	0.52679	2.415000	0.44635	2.729000	0.93468	0.650000	0.86243	GAA	C|0.968;T|0.032	0.032	strong		0.383	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
UACA	55075	hgsc.bcm.edu	37	15	70968850	70968850	+	Silent	SNP	A	A	G	rs61741196	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:70968850A>G	ENST00000322954.6	-	13	1298	c.1113T>C	c.(1111-1113)aaT>aaC	p.N371N	UACA_ENST00000379983.2_Silent_p.N358N|UACA_ENST00000560441.1_Silent_p.N358N|UACA_ENST00000539319.1_Silent_p.N262N	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	371					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						ATTTAAATCTATTTTTCAGAG	0.318													A|||	49	0.00978435	0.0356	0.0029	5008	,	,		16930	0.0		0.0	False		,,,				2504	0.0				p.N371N		Atlas-SNP	.											.	UACA	235	.	0			c.T1113C						PASS	.	A	,	142,4254	98.0+/-136.7	1,140,2057	61.0	63.0	62.0		1074,1113	-5.5	0.7	15	dbSNP_129	62	0,8584		0,0,4292	no	coding-synonymous,coding-synonymous	UACA	NM_001008224.1,NM_018003.2	,	1,140,6349	GG,GA,AA		0.0,3.2302,1.094	,	358/1404,371/1417	70968850	142,12838	2198	4292	6490	SO:0001819	synonymous_variant	55075	exon13			AAATCTATTTTTC	AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"""Ankyrin repeat domain containing"""	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.1113T>C	15.37:g.70968850A>G		50.0	0.0	0		52.0	30.0	0.576923	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Silent	SNP	ENST00000322954.6	37	CCDS10235.1																																																																																			A|0.989;G|0.011	0.011	strong		0.318	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2		
DDX60L	91351	hgsc.bcm.edu	37	4	169342926	169342926	+	Silent	SNP	G	G	A	rs73863330	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:169342926G>A	ENST00000511577.1	-	17	2626	c.2379C>T	c.(2377-2379)taC>taT	p.Y793Y	DDX60L_ENST00000505890.1_Silent_p.Y793Y|DDX60L_ENST00000260184.7_Silent_p.Y793Y			Q5H9U9	DDX6L_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60-like	793	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.						ATP binding (GO:0005524)|helicase activity (GO:0004386)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(23)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.175)		CGGGTGCAACGTACACAACCA	0.468													g|||	24	0.00479233	0.0182	0.0	5008	,	,		23719	0.0		0.0	False		,,,				2504	0.0				p.Y793Y		Atlas-SNP	.											DDX60L,NS,carcinoma,-1,1	DDX60L	116	1	0			c.C2379T						PASS	.	A		61,4345	57.4+/-93.9	0,61,2142	225.0	226.0	226.0		2379	1.4	0.0	4	dbSNP_130	226	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous	DDX60L	NM_001012967.1		0,72,6431	AA,AG,GG		0.1279,1.3845,0.5536		793/1707	169342926	72,12934	2203	4300	6503	SO:0001819	synonymous_variant	91351	exon17			TGCAACGTACACA	AK092461	CCDS47161.1	4q32.3	2008-01-08				ENSG00000181381			26429	protein-coding gene	gene with protein product							Standard	XM_005263341		Approved	FLJ31033	uc003irq.4	Q5H9U9		ENST00000511577.1:c.2379C>T	4.37:g.169342926G>A		110.0	0.0	0		106.0	62.0	0.584906	NM_001012967	Q96ND6	Silent	SNP	ENST00000511577.1	37																																																																																				G|0.994;A|0.006	0.006	strong		0.468	DDX60L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000364839.1	NM_001012967	
DAW1	164781	hgsc.bcm.edu	37	2	228750106	228750106	+	Missense_Mutation	SNP	C	C	T	rs11894733	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:228750106C>T	ENST00000309931.2	+	2	163	c.80C>T	c.(79-81)aCt>aTt	p.T27I	DAW1_ENST00000373666.2_Missense_Mutation_p.T27I|DAW1_ENST00000545118.1_Missense_Mutation_p.T12I|SNORA25_ENST00000607153.1_RNA	NM_178821.1	NP_849143.1	Q8N136	DAW1_HUMAN	dynein assembly factor with WDR repeat domains 1	27			T -> I (in dbSNP:rs11894733).			cilium (GO:0005929)											GAATTAAAGACTAAGTCCATA	0.343													C|||	299	0.0597045	0.2179	0.0159	5008	,	,		14283	0.0		0.0	False		,,,				2504	0.0				p.T27I		Atlas-SNP	.											.	.	.	.	0			c.C80T						PASS	.	C	ILE/THR	760,3646	307.2+/-289.9	67,626,1510	113.0	118.0	116.0		80	4.6	1.0	2	dbSNP_120	116	9,8591	7.1+/-27.0	0,9,4291	yes	missense	WDR69	NM_178821.1	89	67,635,5801	TT,TC,CC		0.1047,17.2492,5.9127	possibly-damaging	27/416	228750106	769,12237	2203	4300	6503	SO:0001583	missense	164781	exon2			TAAAGACTAAGTC		CCDS2470.1	2q36.3	2013-09-03	2013-02-19	2013-02-19	ENSG00000123977	ENSG00000123977		"""WD repeat domain containing"""	26383	protein-coding gene	gene with protein product	"""outer row dynein assembly 16 homolog (Chlamydomonas)"""		"""WD repeat domain 69"""	WDR69		20568242, 21953912	Standard	NM_178821		Approved	FLJ25955, ODA16	uc002vpn.1	Q8N136	OTTHUMG00000133190	ENST00000309931.2:c.80C>T	2.37:g.228750106C>T	ENSP00000311899:p.Thr27Ile	70.0	0.0	0		67.0	28.0	0.41791	NM_178821	Q6ZRY1|Q8N776	Missense_Mutation	SNP	ENST00000309931.2	37	CCDS2470.1	109	0.04990842490842491	102	0.2073170731707317	7	0.019337016574585635	0	0.0	0	0.0	C	12.91	2.079117	0.36662	0.172492	0.001047	ENSG00000123977	ENST00000373666;ENST00000309931;ENST00000440997;ENST00000545118	T;T;T;T	0.53423	0.69;0.64;0.71;0.62	5.52	4.61	0.57282	.	0.172732	0.50627	D	0.000108	T	0.00073	0.0002	M	0.81341	2.54	0.19575	P	0.9999648258	P	0.52170	0.951	P	0.44394	0.448	T	0.08638	-1.0712	9	0.41790	T	0.15	.	10.7579	0.46247	0.0:0.9014:0.0:0.0986	rs11894733;rs52813204;rs56552186;rs58221385;rs11894733	27	Q8N136	WDR69_HUMAN	I	27;27;12;12	ENSP00000362770:T27I;ENSP00000311899:T27I;ENSP00000394853:T12I;ENSP00000437887:T12I	ENSP00000311899:T27I	T	+	2	0	WDR69	228458350	1.000000	0.71417	0.995000	0.50966	0.330000	0.28571	4.893000	0.63199	1.234000	0.43709	0.655000	0.94253	ACT	C|0.939;T|0.061	0.061	strong		0.343	DAW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331745.1	NM_178821	
ZBTB11	27107	hgsc.bcm.edu	37	3	101370091	101370091	+	Silent	SNP	C	C	T	rs34525894	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:101370091C>T	ENST00000312938.4	-	11	3661	c.3081G>A	c.(3079-3081)caG>caA	p.Q1027Q		NM_014415.3	NP_055230.2	O95625	ZBT11_HUMAN	zinc finger and BTB domain containing 11	1027					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						TCTGTCCTTGCTGTTGTGCTA	0.378													C|||	258	0.0515176	0.1891	0.0115	5008	,	,		24052	0.0		0.0	False		,,,				2504	0.0				p.Q1027Q		Atlas-SNP	.											.	ZBTB11	77	.	0			c.G3081A						PASS	.	C		757,3649	309.7+/-291.2	72,613,1518	132.0	129.0	130.0		3081	5.4	1.0	3	dbSNP_126	130	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ZBTB11	NM_014415.3		72,615,5816	TT,TC,CC		0.0233,17.1811,5.8358		1027/1054	101370091	759,12247	2203	4300	6503	SO:0001819	synonymous_variant	27107	exon11			TCCTTGCTGTTGT	U69274	CCDS2943.1	3q12.3	2013-01-09			ENSG00000066422	ENSG00000066422		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	16740	protein-coding gene	gene with protein product							Standard	NM_014415		Approved	ZNF-U69274, ZNF913	uc003dve.4	O95625	OTTHUMG00000159133	ENST00000312938.4:c.3081G>A	3.37:g.101370091C>T		209.0	0.0	0		221.0	95.0	0.429864	NM_014415	Q2NKP9	Silent	SNP	ENST00000312938.4	37	CCDS2943.1																																																																																			C|0.948;T|0.052	0.052	strong		0.378	ZBTB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353441.2	NM_014415	
MCF2L	23263	hgsc.bcm.edu	37	13	113729414	113729414	+	Missense_Mutation	SNP	C	C	T	rs74926660	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:113729414C>T	ENST00000375608.3	+	12	1367	c.1309C>T	c.(1309-1311)Cgg>Tgg	p.R437W	MCF2L_ENST00000423482.2_Missense_Mutation_p.R405W|MCF2L_ENST00000434480.2_Missense_Mutation_p.R413W|MCF2L_ENST00000375604.2_Missense_Mutation_p.R464W|MCF2L_ENST00000442652.2_Missense_Mutation_p.R437W|MCF2L_ENST00000397030.1_Missense_Mutation_p.R440W|MCF2L_ENST00000375597.4_Missense_Mutation_p.R405W|MCF2L_ENST00000421756.1_Missense_Mutation_p.R411W|MCF2L_ENST00000535094.2_Missense_Mutation_p.R407W|MCF2L_ENST00000375601.3_Missense_Mutation_p.R411W			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	437					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular space (GO:0005615)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			kidney(1)|large_intestine(5)|ovary(1)|stomach(1)	8	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				CCAGGAGCTCCGGCACCTCTG	0.667													C|||	67	0.0133786	0.0204	0.0231	5008	,	,		14912	0.0208		0.0	False		,,,				2504	0.0031				p.R407W		Atlas-SNP	.											.	MCF2L	182	.	0			c.C1219T						PASS	.	C	TRP/ARG,TRP/ARG	89,4317	75.2+/-113.4	0,89,2114	60.0	68.0	65.0		1219,1213	4.9	0.9	13	dbSNP_131	65	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	MCF2L	NM_001112732.2,NM_024979.4	101,101	0,91,6412	TT,TC,CC		0.0233,2.02,0.6997	probably-damaging,probably-damaging	407/1126,405/1124	113729414	91,12915	2203	4300	6503	SO:0001583	missense	23263	exon11			GAGCTCCGGCACC	AB002360	CCDS9527.2, CCDS45070.1, CCDS9527.3, CCDS45070.2	13q34	2013-01-10			ENSG00000126217	ENSG00000126217		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	14576	protein-coding gene	gene with protein product		609499				9205841	Standard	NM_001112732		Approved	KIAA0362, DBS, OST, ARHGEF14	uc010tjr.2	O15068	OTTHUMG00000017377	ENST00000375608.3:c.1309C>T	13.37:g.113729414C>T	ENSP00000364758:p.Arg437Trp	81.0	0.0	0		83.0	41.0	0.493976	NM_001112732	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Missense_Mutation	SNP	ENST00000375608.3	37		32|32	0.014652014652014652|0.014652014652014652	14|14	0.028455284552845527|0.028455284552845527	4|4	0.011049723756906077|0.011049723756906077	12|12	0.02097902097902098|0.02097902097902098	2|2	0.002638522427440633|0.002638522427440633	C|C	14.59|14.59	2.580228|2.580228	0.46006|0.46006	0.0202|0.0202	2.33E-4|2.33E-4	ENSG00000126217|ENSG00000126217	ENST00000397017|ENST00000375608;ENST00000442652;ENST00000375604;ENST00000397030;ENST00000535094;ENST00000421756;ENST00000375601;ENST00000434480;ENST00000423482;ENST00000375597;ENST00000440749	.|T;T;T;T;T;T;T;T;T;T	.|0.18016	.|2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24	4.88|4.88	4.88|4.88	0.63580|0.63580	.|.	.|0.622889	.|0.16873	.|N	.|0.196041	T|T	0.19565|0.19565	0.0470|0.0470	M|M	0.77616|0.77616	2.38|2.38	0.09310|0.09310	N|N	0.999999|0.999999	.|D;D;D;D;D;D	.|0.89917	.|0.999;0.996;0.999;1.0;0.985;0.999	.|P;P;P;D;P;D	.|0.70016	.|0.88;0.88;0.888;0.967;0.828;0.954	T|T	0.06180|0.06180	-1.0841|-1.0841	5|10	.|0.87932	.|D	.|0	.|.	13.7445|13.7445	0.62868|0.62868	0.0:0.8458:0.1542:0.0|0.0:0.8458:0.1542:0.0	.|.	.|405;407;464;369;405;437	.|E9PDN8;O15068-9;G5E9A1;E2QRA2;O15068-4;O15068	.|.;.;.;.;.;MCF2L_HUMAN	L|W	67|437;437;464;440;407;411;411;413;405;405;248	.|ENSP00000364758:R437W;ENSP00000401422:R437W;ENSP00000364754:R464W;ENSP00000380225:R440W;ENSP00000440374:R407W;ENSP00000397285:R411W;ENSP00000364751:R411W;ENSP00000407722:R413W;ENSP00000405639:R405W;ENSP00000364747:R405W	.|ENSP00000364747:R405W	P|R	+|+	2|1	0|2	MCF2L|MCF2L	112777415|112777415	0.609000|0.609000	0.26975|0.26975	0.886000|0.886000	0.34754|0.34754	0.181000|0.181000	0.23173|0.23173	1.666000|1.666000	0.37460|0.37460	2.239000|2.239000	0.73571|0.73571	0.561000|0.561000	0.74099|0.74099	CCG|CGG	C|0.990;T|0.010	0.010	strong		0.667	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4		
GRIK5	2901	hgsc.bcm.edu	37	19	42560893	42560893	+	Missense_Mutation	SNP	G	G	A	rs139340543	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42560893G>A	ENST00000262895.3	-	7	823	c.824C>T	c.(823-825)cCc>cTc	p.P275L	GRIK5_ENST00000593562.1_Missense_Mutation_p.P275L|GRIK5_ENST00000301218.4_Missense_Mutation_p.P275L	NM_002088.4	NP_002079.3	Q16478	GRIK5_HUMAN	glutamate receptor, ionotropic, kainate 5	275					cellular response to glucose stimulus (GO:0071333)|establishment of localization in cell (GO:0051649)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|positive regulation of neuron apoptotic process (GO:0043525)|protein retention in ER lumen (GO:0006621)|receptor clustering (GO:0043113)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic vesicle fusion to presynaptic membrane (GO:0031630)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|kainate selective glutamate receptor complex (GO:0032983)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(11)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	35		Prostate(69;0.059)				AGGGTAGAAGGGGTGGGACGT	0.577													G|||	7	0.00139776	0.0053	0.0	5008	,	,		20492	0.0		0.0	False		,,,				2504	0.0				p.P275L		Atlas-SNP	.											.	GRIK5	220	.	0			c.C824T						PASS	.	G	LEU/PRO	7,4399	12.9+/-30.5	0,7,2196	135.0	120.0	125.0		824	4.9	1.0	19	dbSNP_134	125	0,8600		0,0,4300	yes	missense	GRIK5	NM_002088.3	98	0,7,6496	AA,AG,GG		0.0,0.1589,0.0538	possibly-damaging	275/981	42560893	7,12999	2203	4300	6503	SO:0001583	missense	2901	exon7			TAGAAGGGGTGGG		CCDS12595.1	19q13.2	2012-08-29			ENSG00000105737	ENSG00000105737		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4583	protein-coding gene	gene with protein product		600283		GRIK2		7527545	Standard	NM_002088		Approved	GluK5, KA2	uc002osj.2	Q16478	OTTHUMG00000044573	ENST00000262895.3:c.824C>T	19.37:g.42560893G>A	ENSP00000262895:p.Pro275Leu	126.0	0.0	0		122.0	54.0	0.442623	NM_002088	Q8WWG8	Missense_Mutation	SNP	ENST00000262895.3	37	CCDS12595.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	21.6	4.178464	0.78564	0.001589	0.0	ENSG00000105737	ENST00000262895;ENST00000301218	D;D	0.84873	-1.91;-1.91	4.93	4.93	0.64822	Extracellular ligand-binding receptor (1);	0.073753	0.53938	D	0.000048	D	0.88209	0.6375	M	0.64170	1.965	0.80722	D	1	B	0.33637	0.42	P	0.45138	0.471	D	0.88944	0.3382	10	0.72032	D	0.01	.	17.2807	0.87127	0.0:0.0:1.0:0.0	.	275	Q16478	GRIK5_HUMAN	L	275	ENSP00000262895:P275L;ENSP00000301218:P275L	ENSP00000262895:P275L	P	-	2	0	GRIK5	47252733	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.555000	0.82223	2.442000	0.82660	0.467000	0.42956	CCC	G|0.999;A|0.001	0.001	strong		0.577	GRIK5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463453.1		
SPHK2	56848	hgsc.bcm.edu	37	19	49132646	49132646	+	Silent	SNP	G	G	A	rs75629654	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49132646G>A	ENST00000245222.4	+	7	1947	c.1581G>A	c.(1579-1581)ctG>ctA	p.L527L	SPHK2_ENST00000443164.1_Silent_p.L589L|SPHK2_ENST00000600537.1_Silent_p.L468L|SPHK2_ENST00000598088.1_Silent_p.L527L|SPHK2_ENST00000599029.1_Silent_p.L491L|SPHK2_ENST00000340932.3_Silent_p.L489L|SPHK2_ENST00000599748.1_Silent_p.L491L	NM_001204158.2|NM_001243876.1|NM_020126.4	NP_001191087.1|NP_001230805.1|NP_064511.2	Q9NRA0	SPHK2_HUMAN	sphingosine kinase 2	527					blood vessel development (GO:0001568)|brain development (GO:0007420)|cell proliferation (GO:0008283)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|small molecule metabolic process (GO:0044281)|sphinganine-1-phosphate biosynthetic process (GO:0006669)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	ATP binding (GO:0005524)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|Ras GTPase binding (GO:0017016)|sphinganine kinase activity (GO:0008481)			NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	19		all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		GCACCCCGCTGCCCCCAGACT	0.711													G|||	273	0.0545128	0.1944	0.0216	5008	,	,		12771	0.001		0.0	False		,,,				2504	0.0				p.L527L		Atlas-SNP	.											.	SPHK2	62	.	0			c.G1581A						PASS	.	G	,,,	717,3679		52,613,1533	19.0	21.0	20.0		1404,1581,1473,1581	0.3	0.9	19	dbSNP_131	20	4,8590		0,4,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPHK2	NM_001204158.2,NM_001204159.2,NM_001204160.2,NM_020126.4	,,,	52,617,5826	AA,AG,GG		0.0465,16.3103,5.5504	,,,	468/596,527/655,491/619,527/655	49132646	721,12269	2198	4297	6495	SO:0001819	synonymous_variant	56848	exon7			CCCGCTGCCCCCA	AF245447	CCDS12727.1, CCDS59404.1, CCDS59405.1, CCDS74414.1	19q13.33	2013-09-20			ENSG00000063176	ENSG00000063176			18859	protein-coding gene	gene with protein product		607092				10751414, 17895250	Standard	NM_020126		Approved		uc002pjs.3	Q9NRA0	OTTHUMG00000183318	ENST00000245222.4:c.1581G>A	19.37:g.49132646G>A		29.0	0.0	0		56.0	56.0	1	NM_020126	A0T4C8|B4DU87|Q9BRN1|Q9H0Q2|Q9NWU7	Silent	SNP	ENST00000245222.4	37	CCDS12727.1																																																																																			G|0.940;A|0.060	0.060	strong		0.711	SPHK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466153.1		
MST1L	11223	hgsc.bcm.edu	37	1	17087509	17087509	+	RNA	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17087509C>T	ENST00000455405.2	-	0	0							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										CCACATCCTCCTGCCAAGGCC	0.632																																					p.Q52Q		Atlas-SNP	.											.	.	.	.	0			c.G156A						PASS	.																																					11223	exon2			ATCCTCCTGCCAA	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.17087509C>T		713.0	0.0	0		896.0	71.0	0.0792411	NM_001271733	B7WPB1|Q13209	Silent	SNP	ENST00000455405.2	37																																																																																				.	.	none		0.632	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
TAF1	6872	hgsc.bcm.edu	37	X	70627477	70627477	+	Silent	SNP	G	G	A	rs7050748	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:70627477G>A	ENST00000373790.4	+	27	4209	c.4158G>A	c.(4156-4158)tcG>tcA	p.S1386S	TAF1_ENST00000276072.3_Silent_p.S1407S|TAF1_ENST00000449580.1_Silent_p.S1386S|TAF1_ENST00000423759.1_Silent_p.S1407S	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	1386	Interaction with ASF1A and ASF1B.				cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				TGACGCTGTCGTCCATCTTGG	0.438													A|||	293	0.0776159	0.2012	0.0274	3775	,	,		15657	0.0		0.005	False		,,,				2504	0.0031				p.S1407S		Atlas-SNP	.											.	TAF1	439	.	0			c.G4221A						PASS	.	A	,	921,2914		89,609,134,934,437	129.0	111.0	117.0		4221,4158	0.9	1.0	X	dbSNP_116	117	39,6689		0,29,10,2399,1862	no	coding-synonymous,coding-synonymous	TAF1	NM_004606.3,NM_138923.2	,	89,638,144,3333,2299	AA,AG,A,GG,G		0.5797,24.0156,9.0883	,	1407/1894,1386/1873	70627477	960,9603	2203	4300	6503	SO:0001819	synonymous_variant	6872	exon27			GCTGTCGTCCATC		CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"""Chromatin-modifying enzymes / K-acetyltransferases"""	11535	protein-coding gene	gene with protein product		313650	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD"", ""dystonia 3 (with Parkinsonism)"""	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.4158G>A	X.37:g.70627477G>A		316.0	0.0	0		316.0	136.0	0.43038	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Silent	SNP	ENST00000373790.4	37	CCDS35325.1	117	0.0705244122965642	71	0.1658878504672897	6	0.01694915254237288	0	0.0	3	0.003968253968253968	.	8.199	0.797814	0.16327	0.240156	0.005797	ENSG00000147133	ENST00000463163;ENST00000437147	.	.	.	4.95	0.941	0.19519	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999999938	.	.	.	.	.	.	T	0.28396	-1.0045	3	.	.	.	.	1.3732	0.02215	0.2938:0.111:0.1437:0.4515	rs7050748	.	.	.	H	52;41	.	.	R	+	2	0	TAF1	70544202	0.020000	0.18652	0.992000	0.48379	0.891000	0.51852	-0.742000	0.04850	-0.381000	0.07882	-0.574000	0.04147	CGT	0|0.003;A|0.098	0.098	strong		0.438	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606	
KIT	3815	hgsc.bcm.edu	37	4	55602765	55602765	+	Silent	SNP	G	G	C	rs3733542	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:55602765G>C	ENST00000288135.5	+	18	2683	c.2586G>C	c.(2584-2586)ctG>ctC	p.L862L		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	862	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.L862L(6)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TTTGGGAGCTGTTCTCTTTAG	0.418		1	"""Mis, O"""		"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""	"""GIST, epithelioma"""	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors				G|||	822	0.164137	0.3759	0.0793	5008	,	,		19674	0.0565		0.0954	False		,,,				2504	0.1196				p.L862L		Atlas-SNP	.	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"""L, M, O, E"""	KIT,colon,carcinoma,0,10	KIT	7396	10	6	Substitution - coding silent(6)	haematopoietic_and_lymphoid_tissue(3)|bone(2)|stomach(1)	c.G2586C						PASS	.	G	,	1433,2973	466.2+/-354.4	229,975,999	142.0	144.0	143.0		2586,2574	-2.3	1.0	4	dbSNP_107	143	1078,7522	226.8+/-262.4	74,930,3296	no	coding-synonymous,coding-synonymous	KIT	NM_000222.2,NM_001093772.1	,	303,1905,4295	CC,CG,GG		12.5349,32.5238,19.3065	,	862/977,858/973	55602765	2511,10495	2203	4300	6503	SO:0001819	synonymous_variant	3815	exon18	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	GGAGCTGTTCTCT	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6342	protein-coding gene	gene with protein product		164920	"""piebald trait"""	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.2586G>C	4.37:g.55602765G>C		106.0	0.0	0		95.0	31.0	0.326316	NM_000222	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Silent	SNP	ENST00000288135.5	37	CCDS3496.1																																																																																			G|0.828;C|0.172	0.172	strong		0.418	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1		
ZNF74	7625	hgsc.bcm.edu	37	22	20760106	20760106	+	Silent	SNP	C	C	T	rs2229316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:20760106C>T	ENST00000400451.2	+	5	1297	c.783C>T	c.(781-783)tcC>tcT	p.S261S	ZNF74_ENST00000356671.5_Silent_p.S261S|ZNF74_ENST00000405993.1_Silent_p.S229S|ZNF74_ENST00000403682.3_3'UTR|ZNF74_ENST00000357502.5_3'UTR	NM_003426.3	NP_003417.2	Q16587	ZNF74_HUMAN	zinc finger protein 74	261					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19	Melanoma(16;0.000465)|Ovarian(15;0.0025)|Colorectal(54;0.0221)|all_neural(72;0.219)	Lung SC(17;0.0262)|all_lung(157;0.248)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)			GCCAGAGCTCCTCCCTCACGC	0.687													C|||	95	0.0189696	0.0696	0.0043	5008	,	,		15500	0.0		0.0	False		,,,				2504	0.0				p.S261S		Atlas-SNP	.											.	ZNF74	54	.	0			c.C783T						PASS	.	C		188,4216		6,176,2020	21.0	25.0	23.0		783	-7.0	0.0	22	dbSNP_98	23	3,8593		0,3,4295	no	coding-synonymous	ZNF74	NM_003426.2		6,179,6315	TT,TC,CC		0.0349,4.2688,1.4692		261/645	20760106	191,12809	2202	4298	6500	SO:0001819	synonymous_variant	7625	exon5			GAGCTCCTCCCTC	X71623	CCDS42982.1, CCDS58794.1	22q11.2	2013-01-08	2006-05-12		ENSG00000185252	ENSG00000185252		"""Zinc fingers, C2H2-type"", ""-"""	13144	protein-coding gene	gene with protein product		194548	"""zinc finger protein 74 (Cos52)"""			1639391, 10591208	Standard	NM_003426		Approved	Cos52, Zfp520, ZNF520	uc010gsm.4	Q16587	OTTHUMG00000150687	ENST00000400451.2:c.783C>T	22.37:g.20760106C>T		39.0	0.0	0		42.0	42.0	1	NM_003426	B5MCE3|B7Z5Y2|Q6IBV2|Q6PJP1|Q9UC04|Q9UF05|Q9UF06|Q9UF07	Silent	SNP	ENST00000400451.2	37	CCDS42982.1																																																																																			C|0.982;T|0.018	0.018	strong		0.687	ZNF74-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319648.2	NM_003426	
PLEKHA5	54477	hgsc.bcm.edu	37	12	19440471	19440471	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:19440471A>G	ENST00000299275.6	+	12	1832	c.1826A>G	c.(1825-1827)cAg>cGg	p.Q609R	PLEKHA5_ENST00000510738.2_3'UTR|PLEKHA5_ENST00000543806.1_Missense_Mutation_p.Q501R|PLEKHA5_ENST00000317589.4_Missense_Mutation_p.Q609R|PLEKHA5_ENST00000309364.4_Missense_Mutation_p.Q609R|PLEKHA5_ENST00000538714.1_Missense_Mutation_p.Q609R|PLEKHA5_ENST00000355397.3_Missense_Mutation_p.Q609R|PLEKHA5_ENST00000539256.1_Missense_Mutation_p.Q367R|PLEKHA5_ENST00000424268.1_Missense_Mutation_p.Q501R|PLEKHA5_ENST00000429027.2_Missense_Mutation_p.Q615R|PLEKHA5_ENST00000359180.3_Missense_Mutation_p.Q609R	NM_019012.5	NP_061885.2	Q9HAU0	PKHA5_HUMAN	pleckstrin homology domain containing, family A member 5	609					reproductive system development (GO:0061458)	cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.00804)					GTTAGTCCCCAGAGCCTCCAA	0.403																																					p.Q615R	Pancreas(196;329 2193 11246 14234 19524)	Atlas-SNP	.											.	PLEKHA5	198	.	0			c.A1844G						PASS	.						105.0	104.0	105.0					12																	19440471		2203	4300	6503	SO:0001583	missense	54477	exon13			GTCCCCAGAGCCT	AF302150	CCDS8682.1, CCDS44840.1, CCDS44840.2, CCDS55809.1, CCDS58213.1, CCDS58214.1	12p12	2013-01-10			ENSG00000052126	ENSG00000052126		"""Pleckstrin homology (PH) domain containing"""	30036	protein-coding gene	gene with protein product		607770				11214970, 11001876	Standard	NM_001143821		Approved	PEPP2, KIAA1686, FLJ10667	uc031qgo.1	Q9HAU0	OTTHUMG00000167921	ENST00000299275.6:c.1826A>G	12.37:g.19440471A>G	ENSP00000299275:p.Gln609Arg	175.0	0.0	0		160.0	83.0	0.51875	NM_001256470	A0JP03|B4DGS1|E9PHQ3|F5H0I0|Q6NSF8|Q86ST7|Q8N3K6|Q96DY9|Q9BVR4|Q9C0H7|Q9H924|Q9NVK8	Missense_Mutation	SNP	ENST00000299275.6	37	CCDS8682.1	.	.	.	.	.	.	.	.	.	.	A	18.64	3.668063	0.67814	.	.	ENSG00000052126	ENST00000317589;ENST00000355397;ENST00000359180;ENST00000542828;ENST00000309364;ENST00000429027;ENST00000299275;ENST00000539256;ENST00000538714;ENST00000424268;ENST00000543806;ENST00000536974	T;T;T;T;T;T;T;T;T;T;T	0.35048	2.5;1.33;2.5;2.5;1.33;2.5;2.5;1.33;1.57;1.57;2.5	5.86	4.73	0.59995	.	0.115083	0.64402	D	0.000011	T	0.52757	0.1754	M	0.70595	2.14	0.39754	D	0.971935	D;D;D;P;D;D;D	0.76494	0.988;0.999;0.998;0.584;0.995;0.986;0.999	P;D;D;B;D;P;D	0.85130	0.883;0.997;0.993;0.445;0.978;0.835;0.997	T	0.52571	-0.8558	10	0.10111	T	0.7	-14.8584	11.3548	0.49609	0.9297:0.0:0.0703:0.0	.	609;501;501;615;615;609;609	Q9HAU0-4;F5H0I0;E7EME8;B4DHK5;E9PHQ3;Q9HAU0;Q9HAU0-2	.;.;.;.;.;PKHA5_HUMAN;.	R	609;609;609;616;609;615;609;367;609;501;501;501	ENSP00000325155:Q609R;ENSP00000347560:Q609R;ENSP00000352104:Q609R;ENSP00000311239:Q609R;ENSP00000404296:Q615R;ENSP00000299275:Q609R;ENSP00000440611:Q367R;ENSP00000439673:Q609R;ENSP00000400411:Q501R;ENSP00000439837:Q501R;ENSP00000440371:Q501R	ENSP00000299275:Q609R	Q	+	2	0	PLEKHA5	19331738	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.067000	0.71193	2.241000	0.73720	0.482000	0.46254	CAG	.	.	none		0.403	PLEKHA5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397013.1	NM_019012	
SMCO1	255798	hgsc.bcm.edu	37	3	196234777	196234777	+	Missense_Mutation	SNP	A	A	G	rs187809363	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:196234777A>G	ENST00000397537.2	-	3	782	c.626T>C	c.(625-627)aTa>aCa	p.I209T		NM_001077657.1	NP_001071125.1	Q147U7	SMCO1_HUMAN	single-pass membrane protein with coiled-coil domains 1	209						integral component of membrane (GO:0016021)											gacagatggtatcaaCTCTTC	0.428													A|||	7	0.00139776	0.0053	0.0	5008	,	,		17582	0.0		0.0	False		,,,				2504	0.0				p.I209T		Atlas-SNP	.											C3orf43,NS,malignant_melanoma,+1,1	C3orf43	25	1	0			c.T626C						PASS	.	A	THR/ILE	15,3743		0,15,1864	111.0	102.0	105.0		626	4.0	0.0	3		105	0,8236		0,0,4118	yes	missense	C3orf43	NM_001077657.1	89	0,15,5982	GG,GA,AA		0.0,0.3991,0.1251	benign	209/215	196234777	15,11979	1879	4118	5997	SO:0001583	missense	255798	exon3			GATGGTATCAACT	AK123917	CCDS43192.1	3q29	2013-03-08	2013-03-08	2013-03-08	ENSG00000214097	ENSG00000214097			27407	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 43"""	C3orf43			Standard	NM_001077657		Approved	FLJ41923, DKFZp313B0440		Q147U7	OTTHUMG00000155581	ENST00000397537.2:c.626T>C	3.37:g.196234777A>G	ENSP00000380671:p.Ile209Thr	187.0	0.0	0		208.0	97.0	0.466346	NM_001077657	B3KW20	Missense_Mutation	SNP	ENST00000397537.2	37	CCDS43192.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	A	11.14	1.550303	0.27739	0.003991	0.0	ENSG00000214097	ENST00000397537	T	0.36340	1.26	5.39	4.03	0.46877	.	.	.	.	.	T	0.28067	0.0692	L	0.29908	0.895	0.09310	N	1	B;B	0.26195	0.144;0.144	B;B	0.27715	0.051;0.082	T	0.18999	-1.0319	9	0.72032	D	0.01	-4.7237	9.3415	0.38082	0.9032:0.0:0.0968:0.0	.	209;201	Q147U7;E9PGG7	CC043_HUMAN;.	T	209	ENSP00000380671:I209T	ENSP00000380671:I209T	I	-	2	0	C3orf43	197719174	0.957000	0.32711	0.010000	0.14722	0.013000	0.08279	2.479000	0.45197	2.054000	0.61138	0.533000	0.62120	ATA	A|0.999;G|0.001	0.001	strong		0.428	SMCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340776.1	NM_001006109	
DNA2	1763	hgsc.bcm.edu	37	10	70218890	70218890	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:70218890C>T	ENST00000358410.3	-	5	740	c.690G>A	c.(688-690)tcG>tcA	p.S230S	DNA2_ENST00000399179.2_Silent_p.S230S|DNA2_ENST00000399180.2_Silent_p.S316S|RNA5SP319_ENST00000362768.1_RNA	NM_001080449.2	NP_001073918.2	P51530	DNA2_HUMAN	DNA replication helicase/nuclease 2	230	Nuclease activity. {ECO:0000250}.				ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing (GO:0000729)|DNA duplex unwinding (GO:0032508)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|DNA replication, Okazaki fragment processing (GO:0033567)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|mitochondrial DNA repair (GO:0043504)|mitochondrial DNA replication (GO:0006264)|mitotic cell cycle (GO:0000278)|positive regulation of DNA replication (GO:0045740)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)	mitochondrial nucleoid (GO:0042645)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|5'-3' DNA helicase activity (GO:0043139)|5'-flap endonuclease activity (GO:0017108)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|nuclease activity (GO:0004518)|single-stranded DNA-dependent ATPase activity (GO:0043142)|site-specific endodeoxyribonuclease activity, specific for altered base (GO:0016890)			breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)	20						GGAAGTCAGTCGAAGTGTTTT	0.358																																					p.S230S		Atlas-SNP	.											DNA2L,NS,carcinoma,-1,4	DNA2	76	4	0			c.G690A						PASS	.						88.0	78.0	81.0					10																	70218890		1845	4099	5944	SO:0001819	synonymous_variant	1763	exon5			GTCAGTCGAAGTG	D42046	CCDS44415.1, CCDS44415.2	10q21.3-q22.1	2013-05-13	2013-05-13	2008-01-08	ENSG00000138346	ENSG00000138346			2939	protein-coding gene	gene with protein product		601810	"""DNA2 DNA replication helicase 2-like (yeast)"", ""DNA replication helicase 2 homolog (yeast)"""	DNA2L		8938459, 17032657, 23352259	Standard	NM_001080449		Approved	KIAA0083	uc031pvh.1	P51530	OTTHUMG00000018352	ENST00000358410.3:c.690G>A	10.37:g.70218890C>T		91.0	0.0	0		103.0	5.0	0.0485437	NM_001080449	Q2NKM1|Q5TC49|Q5TC50|Q6P455|Q6PI80|Q7Z6H9|Q8N346	Silent	SNP	ENST00000358410.3	37																																																																																				.	.	none		0.358	DNA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000048334.2		
C5orf42	65250	hgsc.bcm.edu	37	5	37173977	37173977	+	Silent	SNP	A	A	G	rs61746147	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37173977A>G	ENST00000508244.1	-	31	6144	c.6051T>C	c.(6049-6051)gcT>gcC	p.A2017A	C5orf42_ENST00000274258.7_Silent_p.A897A|C5orf42_ENST00000425232.2_Silent_p.A2017A			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	2017						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			GTGGTTGTGAAGCAACATTGA	0.418													A|||	122	0.024361	0.09	0.0043	5008	,	,		16616	0.0		0.0	False		,,,				2504	0.0				p.A2017A		Atlas-SNP	.											.	C5orf42	422	.	0			c.T6051C						PASS	.	A		341,4065	178.0+/-206.8	13,315,1875	140.0	133.0	135.0		6051	1.9	0.9	5	dbSNP_129	135	2,8598	2.2+/-6.3	0,2,4298	yes	coding-synonymous	C5orf42	NM_023073.3		13,317,6173	GG,GA,AA		0.0233,7.7394,2.6372		2017/3198	37173977	343,12663	2203	4300	6503	SO:0001819	synonymous_variant	65250	exon32			TTGTGAAGCAACA		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.6051T>C	5.37:g.37173977A>G		85.0	0.0	0		90.0	43.0	0.477778	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Silent	SNP	ENST00000508244.1	37	CCDS34146.2																																																																																			A|0.974;G|0.026	0.026	strong		0.418	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073	
GSN	2934	hgsc.bcm.edu	37	9	124091256	124091256	+	Missense_Mutation	SNP	G	G	T	rs9696578	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:124091256G>T	ENST00000373818.4	+	14	2072	c.2003G>T	c.(2002-2004)cGc>cTc	p.R668L	GSN_ENST00000436847.1_Missense_Mutation_p.R628L|GSN_ENST00000373823.3_Missense_Mutation_p.R617L|GSN_ENST00000373807.1_Missense_Mutation_p.R399L|GSN_ENST00000545652.1_Missense_Mutation_p.R625L|GSN_ENST00000341272.2_Missense_Mutation_p.R617L|GSN_ENST00000412819.1_Missense_Mutation_p.R617L|GSN_ENST00000394353.2_Missense_Mutation_p.R628L|GSN_ENST00000373808.2_Missense_Mutation_p.R617L|GSN_ENST00000449733.1_Missense_Mutation_p.R617L|GSN_ENST00000373806.1_Missense_Mutation_p.R93L	NM_000177.4|NM_001258029.1	NP_000168.1|NP_001244958.1	P06396	GELS_HUMAN	gelsolin	668	Actin-binding, Ca-sensitive. {ECO:0000255}.		R -> L (in dbSNP:rs9696578).		actin filament polymerization (GO:0030041)|actin filament severing (GO:0051014)|aging (GO:0007568)|apoptotic process (GO:0006915)|barbed-end actin filament capping (GO:0051016)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to cadmium ion (GO:0071276)|cilium morphogenesis (GO:0060271)|oligodendrocyte development (GO:0014003)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of cell adhesion (GO:0030155)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|tissue regeneration (GO:0042246)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)	21						CATCCTCCTCGCCTCTTTGCC	0.622													G|||	18	0.00359425	0.0129	0.0	5008	,	,		21562	0.0		0.001	False		,,,				2504	0.0				p.R668L		Atlas-SNP	.											.	GSN	81	.	0			c.G2003T						PASS	.	G	LEU/ARG,LEU/ARG,LEU/ARG,LEU/ARG,LEU/ARG,LEU/ARG,LEU/ARG,LEU/ARG	46,4360	49.6+/-84.7	0,46,2157	89.0	74.0	79.0		2003,1850,1850,1850,1850,1883,1883,1850	4.7	1.0	9	dbSNP_119	79	1,8599	2.2+/-6.3	0,1,4299	yes	missense,missense,missense,missense,missense,missense,missense,missense	GSN	NM_000177.4,NM_001127662.1,NM_001127663.1,NM_001127664.1,NM_001127665.1,NM_001127666.1,NM_001127667.1,NM_198252.2	102,102,102,102,102,102,102,102	0,47,6456	TT,TG,GG		0.0116,1.044,0.3614	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	668/783,617/732,617/732,617/732,617/732,628/743,628/743,617/732	124091256	47,12959	2203	4300	6503	SO:0001583	missense	2934	exon14			CTCCTCGCCTCTT	X04412	CCDS6828.1, CCDS6829.1, CCDS48011.1, CCDS65118.1, CCDS75890.1, CCDS75891.1	9q33	2010-04-27	2010-04-27		ENSG00000148180	ENSG00000148180			4620	protein-coding gene	gene with protein product	"""amyloidosis, Finnish type"""	137350	"""gelsolin (amyloidosis, Finnish type)"""			1652889	Standard	NM_001127662		Approved	DKFZp313L0718	uc004blf.1	P06396	OTTHUMG00000020584	ENST00000373818.4:c.2003G>T	9.37:g.124091256G>T	ENSP00000362924:p.Arg668Leu	38.0	0.0	0		49.0	25.0	0.510204	NM_000177	A2A418|A8MUD1|A8MYN7|B7Z373|B7Z5V1|F5H1A8|Q5T0I2|Q8WVV7	Missense_Mutation	SNP	ENST00000373818.4	37	CCDS6828.1	7	0.003205128205128205	6	0.012195121951219513	0	0.0	0	0.0	1	0.0013192612137203166	G	27.6	4.842728	0.91197	0.01044	1.16E-4	ENSG00000148180	ENST00000373823;ENST00000436847;ENST00000394353;ENST00000449733;ENST00000412819;ENST00000341272;ENST00000373808;ENST00000394352;ENST00000456109;ENST00000545652;ENST00000373818;ENST00000373807;ENST00000373806;ENST00000373805	T;T;T;T;T;T;T;T;T;T;T	0.57595	1.62;1.62;1.62;1.62;1.62;1.62;1.62;1.62;1.62;2.41;0.39	5.56	4.66	0.58398	.	0.110224	0.64402	D	0.000005	T	0.74527	0.3728	H	0.94964	3.605	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.994;0.999;0.999;0.992;0.999	D	0.84690	0.0722	10	0.87932	D	0	-20.0116	15.541	0.76048	0.0:0.1383:0.8617:0.0	rs9696578;rs9696578	641;625;628;399;668	B7Z9A0;F5H1A8;B7Z373;Q5T0H9;P06396	.;.;.;.;GELS_HUMAN	L	617;628;628;617;617;617;617;601;591;625;668;399;93;93	ENSP00000362929:R617L;ENSP00000411293:R628L;ENSP00000377882:R628L;ENSP00000409358:R617L;ENSP00000416586:R617L;ENSP00000340888:R617L;ENSP00000362914:R617L;ENSP00000445823:R625L;ENSP00000362924:R668L;ENSP00000362913:R399L;ENSP00000362912:R93L	ENSP00000340888:R617L	R	+	2	0	GSN	123131077	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	9.362000	0.97126	1.322000	0.45245	0.655000	0.94253	CGC	G|0.993;T|0.007	0.007	strong		0.622	GSN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053861.1	NM_000177	
TM7SF3	51768	hgsc.bcm.edu	37	12	27148324	27148324	+	Missense_Mutation	SNP	G	G	C	rs34735713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:27148324G>C	ENST00000343028.4	-	5	761	c.536C>G	c.(535-537)cCa>cGa	p.P179R	TM7SF3_ENST00000542667.1_5'UTR	NM_016551.2	NP_057635.1	Q9NS93	TM7S3_HUMAN	transmembrane 7 superfamily member 3	179			P -> R (in dbSNP:rs34735713).			extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	18	Colorectal(261;0.0847)					AGCGTCACATGGTGGGGGATC	0.468													G|||	109	0.0217652	0.0779	0.0086	5008	,	,		21417	0.0		0.0	False		,,,				2504	0.0				p.P179R		Atlas-SNP	.											.	TM7SF3	41	.	0			c.C536G						PASS	.	G	ARG/PRO	360,4046	183.3+/-210.9	16,328,1859	68.0	56.0	60.0		536	2.5	0.0	12	dbSNP_126	60	5,8595	3.7+/-12.6	0,5,4295	yes	missense	TM7SF3	NM_016551.2	103	16,333,6154	CC,CG,GG		0.0581,8.1707,2.8064	possibly-damaging	179/571	27148324	365,12641	2203	4300	6503	SO:0001583	missense	51768	exon5			TCACATGGTGGGG	AB032470	CCDS8710.1	12q11-q12	2012-08-10			ENSG00000064115	ENSG00000064115			23049	protein-coding gene	gene with protein product		605181				10828615	Standard	NM_016551		Approved		uc010sjl.2	Q9NS93	OTTHUMG00000169243	ENST00000343028.4:c.536C>G	12.37:g.27148324G>C	ENSP00000342322:p.Pro179Arg	80.0	0.0	0		119.0	61.0	0.512605	NM_016551	B3KMZ3|Q9NUS4	Missense_Mutation	SNP	ENST00000343028.4	37	CCDS8710.1	32	0.014652014652014652	31	0.06300813008130081	1	0.0027624309392265192	0	0.0	0	0.0	G	13.61	2.289340	0.40494	0.081707	5.81E-4	ENSG00000064115	ENST00000343028;ENST00000543803;ENST00000539741;ENST00000543088	T;T;T;T	0.44881	1.5;0.92;0.91;0.93	4.27	2.45	0.29901	.	0.491723	0.22200	N	0.063241	T	0.01870	0.0059	L	0.60455	1.87	0.09310	N	1	P	0.42409	0.779	B	0.33690	0.168	T	0.02184	-1.1199	10	0.66056	D	0.02	-0.8778	8.9426	0.35740	0.2425:0.0:0.7575:0.0	rs34735713	179	Q9NS93	TM7S3_HUMAN	R	179;77;57;57	ENSP00000342322:P179R;ENSP00000442617:P77R;ENSP00000441027:P57R;ENSP00000444632:P57R	ENSP00000342322:P179R	P	-	2	0	TM7SF3	27039591	0.546000	0.26457	0.001000	0.08648	0.002000	0.02628	3.800000	0.55537	0.574000	0.29417	-0.157000	0.13467	CCA	G|0.971;C|0.029	0.029	strong		0.468	TM7SF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403033.1	NM_016551	
KRT73	319101	hgsc.bcm.edu	37	12	53005004	53005004	+	Missense_Mutation	SNP	T	T	C	rs607426	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53005004T>C	ENST00000305748.3	-	6	1128	c.1094A>G	c.(1093-1095)gAg>gGg	p.E365G	RP11-641A6.2_ENST00000552364.1_RNA|RP11-641A6.2_ENST00000549180.1_RNA|RP11-641A6.2_ENST00000551089.1_RNA	NM_175068.2	NP_778238.1	Q86Y46	K2C73_HUMAN	keratin 73	365	Coil 2.|Rod.		E -> G (in dbSNP:rs607426).			extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.189)		CTTCACACTCTCAATCTCCGA	0.567													T|||	104	0.0207668	0.0764	0.0043	5008	,	,		20476	0.0		0.0	False		,,,				2504	0.0				p.E365G		Atlas-SNP	.											.	KRT73	101	.	0			c.A1094G						PASS	.	T	GLY/GLU	214,4192	129.8+/-166.5	5,204,1994	144.0	125.0	131.0		1094	5.6	1.0	12	dbSNP_83	131	1,8599		0,1,4299	yes	missense	KRT73	NM_175068.2	98	5,205,6293	CC,CT,TT		0.0116,4.857,1.6531	benign	365/541	53005004	215,12791	2203	4300	6503	SO:0001583	missense	319101	exon6			ACACTCTCAATCT	AJ508776	CCDS8834.1	12q13.13	2013-06-25			ENSG00000186049	ENSG00000186049		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28928	protein-coding gene	gene with protein product		608247				12648212, 16831889	Standard	NM_175068		Approved	KRT6IRS3, K6IRS3	uc001sas.3	Q86Y46	OTTHUMG00000169746	ENST00000305748.3:c.1094A>G	12.37:g.53005004T>C	ENSP00000307014:p.Glu365Gly	218.0	0.0	0		211.0	97.0	0.459716	NM_175068	Q32MB2	Missense_Mutation	SNP	ENST00000305748.3	37	CCDS8834.1	29	0.013278388278388278	27	0.054878048780487805	2	0.0055248618784530384	0	0.0	0	0.0	T	12.93	2.086766	0.36855	0.04857	1.16E-4	ENSG00000186049	ENST00000305748;ENST00000552855	D;D	0.89746	-2.56;-2.56	5.61	5.61	0.85477	Filament (1);	0.000000	0.53938	D	0.000057	T	0.63896	0.2550	M	0.83603	2.65	0.37997	D	0.934108	B	0.06786	0.001	B	0.13407	0.009	T	0.79019	-0.1974	10	0.44086	T	0.13	.	11.2067	0.48773	0.0:0.0715:0.0:0.9285	rs607426;rs1352442;rs1707745	365	Q86Y46	K2C73_HUMAN	G	365;110	ENSP00000307014:E365G;ENSP00000449081:E110G	ENSP00000307014:E365G	E	-	2	0	KRT73	51291271	0.995000	0.38212	0.995000	0.50966	0.919000	0.55068	3.762000	0.55250	2.276000	0.75962	0.454000	0.30748	GAG	T|0.980;C|0.020	0.020	strong		0.567	KRT73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405700.1	NM_175068	
SPATC1L	84221	hgsc.bcm.edu	37	21	47581508	47581508	+	Missense_Mutation	SNP	C	C	A	rs74518516	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:47581508C>A	ENST00000291672.5	-	5	1869	c.808G>T	c.(808-810)Gtg>Ttg	p.V270L	SPATC1L_ENST00000330205.6_Missense_Mutation_p.V116L	NM_001142854.1	NP_001136326.1	Q9H0A9	SPC1L_HUMAN	spermatogenesis and centriole associated 1-like	270																	GCCGGGTGCACGTCGCGGCTG	0.692													C|||	122	0.024361	0.0877	0.0086	5008	,	,		12794	0.0		0.0	False		,,,				2504	0.0				p.V270L		Atlas-SNP	.											.	.	.	.	0			c.G808T						PASS	.	C	LEU/VAL,LEU/VAL	406,3986		22,362,1812	23.0	25.0	24.0		808,346	4.3	1.0	21	dbSNP_131	24	4,8584		0,4,4290	yes	missense,missense	C21orf56	NM_001142854.1,NM_032261.4	32,32	22,366,6102	AA,AC,CC		0.0466,9.2441,3.1587	benign,benign	270/341,116/187	47581508	410,12570	2196	4294	6490	SO:0001583	missense	84221	exon5			GGTGCACGTCGCG	BC009497	CCDS13732.1, CCDS46653.1	21q22.3	2013-01-21	2012-11-12	2012-11-12	ENSG00000160284	ENSG00000160284			1298	protein-coding gene	gene with protein product	"""speriolin-like protein"""	612412	"""chromosome 21 open reading frame 56"""	C21orf56			Standard	NM_032261		Approved		uc011afu.2	Q9H0A9	OTTHUMG00000090487	ENST00000291672.5:c.808G>T	21.37:g.47581508C>A	ENSP00000291672:p.Val270Leu	67.0	0.0	0		99.0	57.0	0.575758	NM_001142854	B4E323|Q52LS9|Q6FIH5|Q6P0L3|Q9NSE5	Missense_Mutation	SNP	ENST00000291672.5	37	CCDS46653.1	57	0.0260989010989011	52	0.10569105691056911	5	0.013812154696132596	0	0.0	0	0.0	C	13.27	2.188243	0.38609	0.092441	4.66E-4	ENSG00000160284	ENST00000330205;ENST00000291672	T;T	0.50001	0.76;0.76	4.27	4.27	0.50696	.	0.098443	0.41938	D	0.000800	T	0.00637	0.0021	L	0.38838	1.175	0.27740	N	0.944518	B	0.32968	0.392	B	0.27380	0.079	T	0.02411	-1.1163	10	0.51188	T	0.08	-27.6288	8.1902	0.31363	0.0:0.8871:0.0:0.1129	.	270	Q9H0A9	CU056_HUMAN	L	116;270	ENSP00000333869:V116L;ENSP00000291672:V270L	ENSP00000291672:V270L	V	-	1	0	C21orf56	46405936	0.803000	0.28956	0.979000	0.43373	0.918000	0.54935	1.358000	0.34102	1.929000	0.55896	0.591000	0.81541	GTG	C|0.971;A|0.029	0.029	strong		0.692	SPATC1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376654.1	NM_032261	
SSBP3	23648	hgsc.bcm.edu	37	1	54747176	54747176	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:54747176C>T	ENST00000371320.3	-	5	711	c.301G>A	c.(301-303)Gtg>Atg	p.V101M	SSBP3_ENST00000417664.2_De_novo_Start_InFrame|SSBP3_ENST00000371319.3_Missense_Mutation_p.V101M|SSBP3_ENST00000357475.4_Missense_Mutation_p.V101M|SSBP3_ENST00000326956.7_5'UTR	NM_145716.2	NP_663768.1	Q9BWW4	SSBP3_HUMAN	single stranded DNA binding protein 3	101	Pro-rich.				head morphogenesis (GO:0060323)|hematopoietic progenitor cell differentiation (GO:0002244)|midbrain-hindbrain boundary initiation (GO:0021547)|positive regulation of anterior head development (GO:2000744)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prechordal plate formation (GO:0021501)|protein complex assembly (GO:0006461)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|protein complex (GO:0043234)	single-stranded DNA binding (GO:0003697)			central_nervous_system(2)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	11						TTGCCAAGCACGGGGCTCGGG	0.617																																					p.V101M		Atlas-SNP	.											.	SSBP3	65	.	0			c.G301A						PASS	.						16.0	15.0	15.0					1																	54747176		2194	4286	6480	SO:0001583	missense	23648	exon5			CAAGCACGGGGCT		CCDS590.1, CCDS591.1, CCDS30726.1	1p32.3	2008-02-05	2001-11-28		ENSG00000157216	ENSG00000157216			15674	protein-coding gene	gene with protein product		607390	"""single-stranded DNA-binding protein 3"""			12079286	Standard	NM_145716		Approved	CSDP, SSDP, FLJ10355, SSDP1	uc001cxe.4	Q9BWW4	OTTHUMG00000008264	ENST00000371320.3:c.301G>A	1.37:g.54747176C>T	ENSP00000360371:p.Val101Met	80.0	0.0	0		105.0	35.0	0.333333	NM_145716	A8K0A9|Q5T860|Q5T861|Q9BTM0|Q9BWW3	Missense_Mutation	SNP	ENST00000371320.3	37	CCDS591.1	.	.	.	.	.	.	.	.	.	.	C	24.7	4.555184	0.86231	.	.	ENSG00000157216	ENST00000371320;ENST00000371319;ENST00000357475	.	.	.	4.83	4.83	0.62350	.	0.000000	0.64402	U	0.000001	T	0.77818	0.4187	M	0.68317	2.08	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.80764	0.994;0.981;0.973	T	0.78311	-0.2253	9	0.46703	T	0.11	-0.63	18.3318	0.90271	0.0:1.0:0.0:0.0	.	101;101;101	Q9BWW4-2;Q9BWW4-3;Q9BWW4	.;.;SSBP3_HUMAN	M	101	.	ENSP00000350067:V101M	V	-	1	0	SSBP3	54519764	1.000000	0.71417	0.977000	0.42913	0.991000	0.79684	7.369000	0.79578	2.409000	0.81822	0.563000	0.77884	GTG	.	.	none		0.617	SSBP3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022721.1	NM_018070	
AKNA	80709	hgsc.bcm.edu	37	9	117129921	117129921	+	Missense_Mutation	SNP	G	G	C	rs62640865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117129921G>C	ENST00000307564.4	-	6	1791	c.1630C>G	c.(1630-1632)Ctg>Gtg	p.L544V	AKNA_ENST00000374075.5_Missense_Mutation_p.L463V|AKNA_ENST00000374088.3_Missense_Mutation_p.L544V|AKNA_ENST00000312033.3_Missense_Mutation_p.L544V|AKNA_ENST00000223791.3_Missense_Mutation_p.L4V	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	544					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						AGCCACCCCAGGGTGGGCATG	0.607													G|||	180	0.0359425	0.1324	0.0072	5008	,	,		20087	0.0		0.0	False		,,,				2504	0.0				p.L544V		Atlas-SNP	.											.	AKNA	119	.	0			c.C1630G						PASS	.	G	VAL/LEU	445,3961	213.8+/-233.3	20,405,1778	50.0	50.0	50.0		1630	3.2	0.0	9	dbSNP_129	50	3,8597	2.2+/-6.3	0,3,4297	yes	missense	AKNA	NM_030767.4	32	20,408,6075	CC,CG,GG		0.0349,10.0999,3.4446	benign	544/1440	117129921	448,12558	2203	4300	6503	SO:0001583	missense	80709	exon6			ACCCCAGGGTGGG	AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.1630C>G	9.37:g.117129921G>C	ENSP00000303769:p.Leu544Val	72.0	0.0	0		76.0	32.0	0.421053	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	SNP	ENST00000307564.4	37	CCDS6805.1	71	0.03250915750915751	68	0.13821138211382114	3	0.008287292817679558	0	0.0	0	0.0	G	8.010	0.757277	0.15846	0.100999	3.49E-4	ENSG00000106948	ENST00000307564;ENST00000394582;ENST00000374088;ENST00000223791;ENST00000374075;ENST00000312033	T;T;T;T;T	0.30714	2.72;2.72;2.46;2.72;1.52	5.05	3.17	0.36434	.	0.310451	0.23710	N	0.045338	T	0.00109	0.0003	N	0.14661	0.345	0.09310	N	0.999998	B;B	0.17268	0.005;0.021	B;B	0.15484	0.004;0.013	T	0.21042	-1.0257	10	0.30078	T	0.28	-0.342	6.9494	0.24536	0.0931:0.1751:0.7318:0.0	rs62640865	544;463	Q7Z591;Q7Z591-2	AKNA_HUMAN;.	V	544;385;544;4;463;544	ENSP00000303769:L544V;ENSP00000363201:L544V;ENSP00000223791:L4V;ENSP00000363188:L463V;ENSP00000309222:L544V	ENSP00000223791:L4V	L	-	1	2	AKNA	116169742	0.004000	0.15560	0.002000	0.10522	0.008000	0.06430	1.056000	0.30480	0.802000	0.34089	0.655000	0.94253	CTG	G|0.957;C|0.043	0.043	strong		0.607	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767	
TSSK1B	83942	hgsc.bcm.edu	37	5	112770054	112770054	+	Silent	SNP	G	G	A	rs111560230	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:112770054G>A	ENST00000390666.3	-	1	674	c.483C>T	c.(481-483)tgC>tgT	p.C161C	CTD-2201G3.1_ENST00000383058.4_RNA|MCC_ENST00000408903.3_Intron|CTD-2201G3.1_ENST00000416046.2_RNA|CTD-2201G3.1_ENST00000510381.2_RNA	NM_032028.3	NP_114417.1	Q9BXA7	TSSK1_HUMAN	testis-specific serine kinase 1B	161	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				multicellular organismal development (GO:0007275)|protein phosphorylation (GO:0006468)|spermatid development (GO:0007286)	cytoplasmic vesicle (GO:0031410)|motile cilium (GO:0031514)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			large_intestine(8)|ovary(2)|skin(2)|stomach(1)	13		all_cancers(142;0.0138)|all_epithelial(76;0.000445)|Colorectal(10;0.00814)|Prostate(80;0.0115)|Ovarian(225;0.156)		Epithelial(69;4.15e-08)|OV - Ovarian serous cystadenocarcinoma(64;4.49e-08)|all cancers(49;3.2e-06)|COAD - Colon adenocarcinoma(37;0.0371)|Colorectal(14;0.0449)		CATCCCGCAGGCAGCGCTTGG	0.577													G|||	2	0.000399361	0.0015	0.0	5008	,	,		21131	0.0		0.0	False		,,,				2504	0.0				p.C161C		Atlas-SNP	.											.	TSSK1B	89	.	0			c.C483T						PASS	.	G	,	2,4402	4.2+/-10.8	0,2,2200	81.0	77.0	78.0		,483	1.2	1.0	5	dbSNP_132	78	0,8600		0,0,4300	no	intron,coding-synonymous	MCC,TSSK1B	NM_001085377.1,NM_032028.3	,	0,2,6500	AA,AG,GG		0.0,0.0454,0.0154	,	,161/368	112770054	2,13002	2202	4300	6502	SO:0001819	synonymous_variant	83942	exon1			CCGCAGGCAGCGC	AF348076	CCDS4112.1	5q22.2	2008-10-23	2007-01-30	2007-01-30	ENSG00000212122	ENSG00000212122			14968	protein-coding gene	gene with protein product		610709	"""serine/threonine kinase 22D (spermiogenesis associated)"", ""testis-specific serine kinase 1"""	STK22D, TSSK1		15044604	Standard	NM_032028		Approved	SPOGA4, FKSG81	uc003kqm.2	Q9BXA7	OTTHUMG00000128835	ENST00000390666.3:c.483C>T	5.37:g.112770054G>A		81.0	0.0	0		80.0	36.0	0.45	NM_032028	B2R8D9	Silent	SNP	ENST00000390666.3	37	CCDS4112.1																																																																																			G|0.500;A|0.500	0.500	strong		0.577	TSSK1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250774.2	NM_032028	
MBOAT4	619373	hgsc.bcm.edu	37	8	29990075	29990075	+	Missense_Mutation	SNP	C	C	T	rs16876563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:29990075C>T	ENST00000320542.3	-	3	776	c.692G>A	c.(691-693)gGa>gAa	p.G231E	LEPROTL1_ENST00000523116.1_Intron|LEPROTL1_ENST00000442880.2_Intron	NM_001100916.1	NP_001094386.1	Q96T53	MBOA4_HUMAN	membrane bound O-acyltransferase domain containing 4	231			G -> E (in dbSNP:rs16876563).		cellular protein metabolic process (GO:0044267)|peptidyl-serine octanoylation (GO:0018191)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	serine O-acyltransferase activity (GO:0016412)			endometrium(1)	1						ATCAGTCAGTCCCGCTCCTGC	0.557													C|||	227	0.0453275	0.1649	0.0115	5008	,	,		20664	0.0		0.001	False		,,,				2504	0.0				p.G231E		Atlas-SNP	.											MBOAT4_ENST00000320542,NS,carcinoma,+1,1	MBOAT4	31	1	0			c.G692A						PASS	.	C	GLU/GLY,	202,1182		14,174,504	142.0	133.0	135.0		692,	2.0	0.0	8	dbSNP_123	135	1,3181		0,1,1590	yes	missense,intron	LEPROTL1,MBOAT4	NM_001100916.1,NM_001128208.1	98,	14,175,2094	TT,TC,CC		0.0314,14.5954,4.4459	benign,	231/436,	29990075	203,4363	692	1591	2283	SO:0001583	missense	619373	exon3			GTCAGTCCCGCTC	AF359269	CCDS47835.1	8p12	2008-08-04	2006-06-29	2006-06-29	ENSG00000177669	ENSG00000177669			32311	protein-coding gene	gene with protein product	"""ghrelin O-acyltransferase"""	611940	"""O-acyltransferase (membrane bound) domain containing 4"""	OACT4		18443287	Standard	NM_001100916		Approved	FKSG89, GOAT	uc010lvg.3	Q96T53	OTTHUMG00000163824	ENST00000320542.3:c.692G>A	8.37:g.29990075C>T	ENSP00000314196:p.Gly231Glu	125.0	0.0	0		136.0	64.0	0.470588	NM_001100916	B1Q003	Missense_Mutation	SNP	ENST00000320542.3	37	CCDS47835.1	78	0.03571428571428571	76	0.15447154471544716	2	0.0055248618784530384	0	0.0	0	0.0	C	3.261	-0.151211	0.06585	0.145954	3.14E-4	ENSG00000177669	ENST00000320542	T	0.73363	-0.74	4.87	1.96	0.26148	.	0.744599	0.12002	N	0.508753	T	0.00695	0.0023	M	0.63428	1.95	0.80722	P	0.0	B	0.26602	0.154	B	0.31101	0.124	T	0.24404	-1.0161	8	.	.	.	.	4.3137	0.10982	0.0:0.6049:0.1904:0.2047	rs16876563;rs52827595;rs16876563	231	Q96T53	MBOA4_HUMAN	E	231	ENSP00000314196:G231E	.	G	-	2	0	MBOAT4	30109617	0.000000	0.05858	0.041000	0.18516	0.046000	0.14306	0.566000	0.23593	1.277000	0.44412	0.563000	0.77884	GGA	C|0.952;T|0.048	0.048	strong		0.557	MBOAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375795.1		
MACC1	346389	hgsc.bcm.edu	37	7	20199835	20199835	+	Missense_Mutation	SNP	G	G	A	rs17142503	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:20199835G>A	ENST00000400331.5	-	5	457	c.149C>T	c.(148-150)cCg>cTg	p.P50L	MACC1_ENST00000589011.1_Missense_Mutation_p.P50L|MACC1_ENST00000332878.4_Missense_Mutation_p.P50L	NM_182762.3	NP_877439.3	Q6ZN28	MACC1_HUMAN	metastasis associated in colon cancer 1	50			P -> L (in dbSNP:rs17142503).		positive regulation of cell division (GO:0051781)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(15)|lung(12)|ovary(2)|prostate(1)|skin(3)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(1)	39						GAAAGCATCCGGCCAATTGTG	0.398													G|||	117	0.0233626	0.0802	0.0043	5008	,	,		16736	0.001		0.001	False		,,,				2504	0.0061				p.P50L		Atlas-SNP	.											MACC1,colon,carcinoma,-1,1	MACC1	99	1	0			c.C149T						PASS	.	G	LEU/PRO	269,4137	140.0+/-175.5	6,257,1940	75.0	76.0	76.0		149	4.9	0.1	7	dbSNP_123	76	6,8594	5.0+/-18.6	0,6,4294	yes	missense	MACC1	NM_182762.3	98	6,263,6234	AA,AG,GG		0.0698,6.1053,2.1144	benign	50/853	20199835	275,12731	2203	4300	6503	SO:0001583	missense	346389	exon5			GCATCCGGCCAAT		CCDS5369.1	7p15.3	2008-10-14			ENSG00000183742	ENSG00000183742			30215	protein-coding gene	gene with protein product		612646					Standard	NM_182762		Approved	7A5, SH3BP4L	uc003sus.4	Q6ZN28	OTTHUMG00000128415	ENST00000400331.5:c.149C>T	7.37:g.20199835G>A	ENSP00000383185:p.Pro50Leu	56.0	0.0	0		69.0	36.0	0.521739	NM_182762	A8MUS5|B2RNR9|Q6ZQN8|Q7Z5A5	Missense_Mutation	SNP	ENST00000400331.5	37	CCDS5369.1	23	0.010531135531135532	20	0.04065040650406504	2	0.0055248618784530384	1	0.0017482517482517483	0	0.0	G	10.20	1.284308	0.23392	0.061053	6.98E-4	ENSG00000183742	ENST00000400331;ENST00000332878	T;T	0.09538	2.97;2.97	5.82	4.95	0.65309	.	0.520649	0.21203	N	0.078429	T	0.01029	0.0034	L	0.40543	1.245	0.44469	D	0.997404	P	0.52692	0.955	B	0.42087	0.375	T	0.12192	-1.0557	10	0.54805	T	0.06	-2.2911	10.037	0.42135	0.0689:0.0:0.795:0.1362	rs17142503;rs17142503	50	Q6ZN28	MACC1_HUMAN	L	50	ENSP00000383185:P50L;ENSP00000328410:P50L	ENSP00000328410:P50L	P	-	2	0	MACC1	20166360	0.878000	0.30173	0.135000	0.22099	0.025000	0.11179	3.709000	0.54853	1.484000	0.48361	-0.198000	0.12761	CCG	G|0.982;A|0.018	0.018	strong		0.398	MACC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250202.5	NM_182762	
COBL	23242	hgsc.bcm.edu	37	7	51096992	51096992	+	Missense_Mutation	SNP	G	G	A	rs61737866	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:51096992G>A	ENST00000265136.7	-	10	1966	c.1801C>T	c.(1801-1803)Cac>Tac	p.H601Y	COBL_ENST00000395542.2_Missense_Mutation_p.H683Y	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	601				H -> Y (in Ref. 5; AAH45771). {ECO:0000305}.	actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)			NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					GAAGCGGGGTGCAGGGCAGGT	0.562													G|||	130	0.0259585	0.0976	0.0	5008	,	,		20023	0.0		0.001	False		,,,				2504	0.0				p.H601Y	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-SNP	.											.	COBL	167	.	0			c.C1801T						PASS	.	G	TYR/HIS	393,4013	196.4+/-220.7	22,349,1832	79.0	70.0	73.0		1801	-7.0	0.0	7	dbSNP_129	73	4,8596	3.0+/-9.4	0,4,4296	yes	missense	COBL	NM_015198.3	83	22,353,6128	AA,AG,GG		0.0465,8.9197,3.0524	benign	601/1262	51096992	397,12609	2203	4300	6503	SO:0001583	missense	23242	exon10			CGGGGTGCAGGGC	AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"""cordon-bleu homolog (mouse)"""				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.1801C>T	7.37:g.51096992G>A	ENSP00000265136:p.His601Tyr	207.0	0.0	0		249.0	112.0	0.449799	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Missense_Mutation	SNP	ENST00000265136.7	37	CCDS34637.1	40|40	0.018315018315018316|0.018315018315018316	39|39	0.07926829268292683|0.07926829268292683	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	G|G	0.509|0.509	-0.867489|-0.867489	0.02590|0.02590	0.089197|0.089197	4.65E-4|4.65E-4	ENSG00000106078|ENSG00000106078	ENST00000452534|ENST00000265136;ENST00000445054;ENST00000431948;ENST00000395542;ENST00000457306	.|T;T;T;T	.|0.21734	.|1.99;1.99;1.99;1.99	5.59|5.59	-6.98|-6.98	0.01611|0.01611	.|.	.|2.903440	.|0.00947	.|N	.|0.002915	T|T	0.00271|0.00271	0.0008|0.0008	N|N	0.02539|0.02539	-0.55|-0.55	0.09310|0.09310	N|N	1|1	.|B;B;B;B;B	.|0.02656	.|0.0;0.0;0.0;0.0;0.0	.|B;B;B;B;B	.|0.04013	.|0.0;0.0;0.0;0.0;0.001	T|T	0.36866|0.36866	-0.9730|-0.9730	5|10	.|0.02654	.|T	.|1	.|.	11.0652|11.0652	0.47972|0.47972	0.6443:0.0913:0.2644:0.0|0.6443:0.0913:0.2644:0.0	.|.	.|601;658;601;683;143	.|O75128-3;O75128-7;O75128;O75128-2;O75128-6	.|.;.;COBL_HUMAN;.;.	V|Y	576|601;493;486;683;99	.|ENSP00000265136:H601Y;ENSP00000401204:H493Y;ENSP00000413498:H486Y;ENSP00000378912:H683Y	.|ENSP00000265136:H601Y	A|H	-|-	2|1	0|0	COBL|COBL	51064486|51064486	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	0.066000|0.066000	0.14489|0.14489	-1.290000|-1.290000	0.02372|0.02372	-0.145000|-0.145000	0.13849|0.13849	GCA|CAC	G|0.974;A|0.026	0.026	strong		0.562	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198	
C1orf177	163747	hgsc.bcm.edu	37	1	55272743	55272743	+	Missense_Mutation	SNP	A	A	G	rs115158797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55272743A>G	ENST00000371273.3	+	2	194	c.179A>G	c.(178-180)tAt>tGt	p.Y60C	C1orf177_ENST00000358193.3_Missense_Mutation_p.Y60C	NM_001110533.1	NP_001104003	Q3ZCV2	CA177_HUMAN	chromosome 1 open reading frame 177	60										breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(6)|prostate(2)	17						TCCACGCGTTATTCTACCCAA	0.572													A|||	49	0.00978435	0.0363	0.0014	5008	,	,		16140	0.0		0.0	False		,,,				2504	0.0				p.Y60C		Atlas-SNP	.											.	C1orf177	36	.	0			c.A179G						PASS	.	A	CYS/TYR,CYS/TYR	127,4279	93.9+/-132.6	2,123,2078	205.0	186.0	192.0		179,179	1.3	0.0	1	dbSNP_132	192	0,8600		0,0,4300	yes	missense,missense	C1orf177	NM_001110533.1,NM_152607.2	194,194	2,123,6378	GG,GA,AA		0.0,2.8824,0.9765	possibly-damaging,possibly-damaging	60/419,60/415	55272743	127,12879	2203	4300	6503	SO:0001583	missense	163747	exon2			CGCGTTATTCTAC	AK097520	CCDS599.1, CCDS44153.1	1p32.3	2012-07-25			ENSG00000162398	ENSG00000162398			26854	protein-coding gene	gene with protein product							Standard	NM_152607		Approved	FLJ40201	uc001cyb.4	Q3ZCV2	OTTHUMG00000009986	ENST00000371273.3:c.179A>G	1.37:g.55272743A>G	ENSP00000360320:p.Tyr60Cys	157.0	0.0	0		159.0	78.0	0.490566	NM_001110533	B7WPL2|Q8N7Y9	Missense_Mutation	SNP	ENST00000371273.3	37	CCDS44153.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	A	10.43	1.348922	0.24426	0.028824	0.0	ENSG00000162398	ENST00000358193;ENST00000371273	T;T	0.26518	1.73;1.73	3.72	1.32	0.21799	.	1.288330	0.05479	N	0.554456	T	0.06462	0.0166	N	0.25647	0.755	0.09310	N	1	D;D	0.57257	0.979;0.979	P;P	0.53313	0.723;0.723	T	0.08249	-1.0731	10	0.39692	T	0.17	.	3.1969	0.06636	0.498:0.0:0.108:0.394	.	60;60	Q3ZCV2;Q3ZCV2-2	CA177_HUMAN;.	C	60	ENSP00000350924:Y60C;ENSP00000360320:Y60C	ENSP00000350924:Y60C	Y	+	2	0	C1orf177	55045331	0.001000	0.12720	0.000000	0.03702	0.013000	0.08279	1.170000	0.31883	0.264000	0.21851	0.379000	0.24179	TAT	A|0.989;G|0.011	0.011	strong		0.572	C1orf177-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027674.1	NM_152607	
TBC1D17	79735	hgsc.bcm.edu	37	19	50386253	50386253	+	Silent	SNP	C	C	T	rs61741174	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50386253C>T	ENST00000221543.5	+	9	1250	c.951C>T	c.(949-951)cgC>cgT	p.R317R	TBC1D17_ENST00000535102.2_Silent_p.R284R	NM_024682.2	NP_078958	Q9HA65	TBC17_HUMAN	TBC1 domain family, member 17	317	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				autophagy (GO:0006914)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)	Rab GTPase activator activity (GO:0005097)			NS(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15		all_lung(116;0.000338)|Lung NSC(112;0.000446)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.017)		GCCTGCGGCGCGAGGCCTGGA	0.637													C|||	49	0.00978435	0.0348	0.0043	5008	,	,		19944	0.0		0.0	False		,,,				2504	0.0				p.R317R		Atlas-SNP	.											.	TBC1D17	39	.	0			c.C951T						PASS	.	C	,	146,4258		5,136,2061	31.0	32.0	32.0		852,951	-10.1	0.0	19	dbSNP_129	32	0,8592		0,0,4296	no	coding-synonymous,coding-synonymous	TBC1D17	NM_001168222.1,NM_024682.2	,	5,136,6357	TT,TC,CC		0.0,3.3152,1.1234	,	284/616,317/649	50386253	146,12850	2202	4296	6498	SO:0001819	synonymous_variant	79735	exon9			GCGGCGCGAGGCC	AK090606	CCDS12785.1, CCDS54294.1	19q13.33	2013-07-09				ENSG00000104946			25699	protein-coding gene	gene with protein product						22854040	Standard	NM_024682		Approved	FLJ12168	uc002pqo.3	Q9HA65		ENST00000221543.5:c.951C>T	19.37:g.50386253C>T		99.0	0.0	0		113.0	62.0	0.548673	NM_024682	B4DT12|B9A6L8|F5H1W7	Silent	SNP	ENST00000221543.5	37	CCDS12785.1																																																																																			C|0.989;T|0.011	0.011	strong		0.637	TBC1D17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466404.1	NM_024682	
CDK6	1021	hgsc.bcm.edu	37	7	92462572	92462572	+	Silent	SNP	G	G	A	rs189208543	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:92462572G>A	ENST00000265734.4	-	2	477	c.66C>T	c.(64-66)ggC>ggT	p.G22G	CDK6_ENST00000491250.1_5'Flank|CDK6_ENST00000424848.2_Silent_p.G22G	NM_001259.6	NP_001250.1	Q00534	CDK6_HUMAN	cyclin-dependent kinase 6	22	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				astrocyte development (GO:0014002)|cell cycle arrest (GO:0007050)|cell dedifferentiation (GO:0043697)|cell division (GO:0051301)|dentate gyrus development (GO:0021542)|G1/S transition of mitotic cell cycle (GO:0000082)|generation of neurons (GO:0048699)|gliogenesis (GO:0042063)|hematopoietic stem cell differentiation (GO:0060218)|lateral ventricle development (GO:0021670)|mitotic cell cycle (GO:0000278)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular senescence (GO:2000773)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of osteoblast differentiation (GO:0045668)|Notch signaling pathway (GO:0007219)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of gene expression (GO:0010628)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of erythrocyte differentiation (GO:0045646)|regulation of gene expression (GO:0010468)|response to virus (GO:0009615)|T cell differentiation in thymus (GO:0033077)|type B pancreatic cell development (GO:0003323)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|ruffle (GO:0001726)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|skin(1)|urinary_tract(1)	11	all_cancers(62;8.72e-12)|all_epithelial(64;3.65e-10)|Breast(17;0.000675)|all_lung(186;0.0392)|Lung NSC(181;0.053)|all_neural(327;0.219)|all_hematologic(106;0.237)		STAD - Stomach adenocarcinoma(4;6.16e-07)|GBM - Glioblastoma multiforme(5;1.2e-06)|all cancers(6;3.1e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			TCCCATAGGCGCCCTCCCCGA	0.706			T	MLLT10	ALL								G|||	7	0.00139776	0.0053	0.0	5008	,	,		13163	0.0		0.0	False		,,,				2504	0.0				p.G22G		Atlas-SNP	.		Dom	yes		7	7q21-q22	1021	cyclin-dependent kinase 6		L	.	CDK6	30	.	0			c.C66T						PASS	.	G	,	1,4401		0,1,2200	26.0	19.0	21.0		66,66	2.5	1.0	7		21	0,8594		0,0,4297	no	coding-synonymous,coding-synonymous	CDK6	NM_001145306.1,NM_001259.6	,	0,1,6497	AA,AG,GG		0.0,0.0227,0.0077	,	22/327,22/327	92462572	1,12995	2201	4297	6498	SO:0001819	synonymous_variant	1021	exon2			ATAGGCGCCCTCC		CCDS5628.1	7q21-q22	2011-11-08			ENSG00000105810	ENSG00000105810		"""Cyclin-dependent kinases"""	1777	protein-coding gene	gene with protein product		603368				1639063	Standard	NM_001259		Approved	PLSTIRE	uc010lez.3	Q00534	OTTHUMG00000131697	ENST00000265734.4:c.66C>T	7.37:g.92462572G>A		67.0	0.0	0		94.0	45.0	0.478723	NM_001259	A4D1G0	Silent	SNP	ENST00000265734.4	37	CCDS5628.1																																																																																			G|0.998;A|0.002	0.002	strong		0.706	CDK6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254605.2		
OR8H2	390151	hgsc.bcm.edu	37	11	55873401	55873401	+	Missense_Mutation	SNP	A	A	G	rs115405120	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55873401A>G	ENST00000313503.1	+	1	883	c.883A>G	c.(883-885)Aaa>Gaa	p.K295E		NM_001005200.1	NP_001005200.1	Q8N162	OR8H2_HUMAN	olfactory receptor, family 8, subfamily H, member 2	295						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(38)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	61	Esophageal squamous(21;0.00693)					TCTTAGAAACAAAGAGGTGAA	0.368										HNSCC(53;0.14)			a|||	35	0.00698882	0.0219	0.0086	5008	,	,		17201	0.0		0.0	False		,,,				2504	0.0				p.K295E		Atlas-SNP	.											.	OR8H2	117	.	0			c.A883G						PASS	.	A	GLU/LYS	102,4298	78.8+/-117.2	1,100,2099	81.0	89.0	87.0		883	3.3	1.0	11	dbSNP_132	87	2,8586	3.0+/-9.4	0,2,4292	yes	missense	OR8H2	NM_001005200.1	56	1,102,6391	GG,GA,AA		0.0233,2.3182,0.8007	possibly-damaging	295/313	55873401	104,12884	2200	4294	6494	SO:0001583	missense	390151	exon1			AGAAACAAAGAGG	AB065657	CCDS31518.1	11q11	2012-08-09			ENSG00000181767	ENSG00000181767		"""GPCR / Class A : Olfactory receptors"""	15308	protein-coding gene	gene with protein product							Standard	NM_001005200		Approved		uc010riy.2	Q8N162	OTTHUMG00000166832	ENST00000313503.1:c.883A>G	11.37:g.55873401A>G	ENSP00000323982:p.Lys295Glu	121.0	0.0	0		111.0	61.0	0.54955	NM_001005200	Q6IFC1	Missense_Mutation	SNP	ENST00000313503.1	37	CCDS31518.1	19	0.0086996336996337	16	0.032520325203252036	3	0.008287292817679558	0	0.0	0	0.0	a	8.777	0.927390	0.18056	0.023182	2.33E-4	ENSG00000181767	ENST00000313503	T	0.44083	0.93	3.35	3.35	0.38373	.	0.000000	0.56097	D	0.000025	T	0.18341	0.0440	M	0.76170	2.325	0.25971	N	0.982491	B	0.28378	0.209	B	0.27380	0.079	T	0.35301	-0.9794	10	0.87932	D	0	.	8.3251	0.32151	0.9009:0.0:0.0991:0.0	.	295	Q8N162	OR8H2_HUMAN	E	295	ENSP00000323982:K295E	ENSP00000323982:K295E	K	+	1	0	OR8H2	55629977	0.009000	0.17119	0.992000	0.48379	0.067000	0.16453	2.182000	0.42556	1.497000	0.48584	0.362000	0.22060	AAA	A|0.991;G|0.009	0.009	strong		0.368	OR8H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391540.1	NM_001005200	
RGS14	10636	hgsc.bcm.edu	37	5	176798996	176798996	+	Missense_Mutation	SNP	G	G	A	rs149981884	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:176798996G>A	ENST00000408923.3	+	15	1809	c.1621G>A	c.(1621-1623)Gag>Aag	p.E541K	RGS14_ENST00000506944.1_3'UTR	NM_006480.4	NP_006471.2	O43566	RGS14_HUMAN	regulator of G-protein signaling 14	541					cell division (GO:0051301)|chromosome segregation (GO:0007059)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|mitotic nuclear division (GO:0007067)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of synaptic plasticity (GO:0031914)|nucleocytoplasmic transport (GO:0006913)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of GTPase activity (GO:0043547)|positive regulation of neurogenesis (GO:0050769)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|response to oxidative stress (GO:0006979)|spindle organization (GO:0007051)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual learning (GO:0008542)|zygote asymmetric cell division (GO:0010070)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|microtubule (GO:0005874)|nuclear body (GO:0016604)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|spindle (GO:0005819)|spindle pole (GO:0000922)	GDP-dissociation inhibitor activity (GO:0005092)|GTPase activator activity (GO:0005096)|microtubule binding (GO:0008017)|receptor signaling complex scaffold activity (GO:0030159)|receptor signaling protein activity (GO:0005057)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(3)|skin(3)|upper_aerodigestive_tract(1)	12	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	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)			GCCCAGCTCCGAGGAGACCCC	0.632													C|||	36	0.0071885	0.0265	0.0	5008	,	,		15334	0.0		0.001	False		,,,				2504	0.0				p.E541K	NSCLC(47;353 1896 28036)	Atlas-SNP	.											.	RGS14	34	.	0			c.G1621A						PASS	.	C	LYS/GLU	74,3978		0,74,1952	109.0	131.0	124.0		1621	2.9	0.0	5	dbSNP_134	124	3,8353		0,3,4175	yes	missense	RGS14	NM_006480.4	56	0,77,6127	AA,AG,GG		0.0359,1.8263,0.6206	benign	541/567	176798996	77,12331	2026	4178	6204	SO:0001583	missense	10636	exon15			AGCTCCGAGGAGA	AF037195	CCDS43405.1	5q35.3	2008-02-05	2007-08-14		ENSG00000169220	ENSG00000169220		"""Regulators of G-protein signaling"""	9996	protein-coding gene	gene with protein product		602513	"""regulator of G-protein signalling 14"""				Standard	NM_006480		Approved		uc003mgf.3	O43566	OTTHUMG00000163324	ENST00000408923.3:c.1621G>A	5.37:g.176798996G>A	ENSP00000386229:p.Glu541Lys	66.0	0.0	0		80.0	44.0	0.55	NM_006480	O43565|Q506M1|Q6ZWA4|Q8TD62	Missense_Mutation	SNP	ENST00000408923.3	37	CCDS43405.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	C	5.842	0.339577	0.11069	0.018263	3.59E-4	ENSG00000169220	ENST00000408923;ENST00000336477	T	0.37584	1.19	4.84	2.9	0.33743	.	1.710450	0.02865	N	0.130773	T	0.09818	0.0241	N	0.14661	0.345	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.21827	-1.0234	10	0.06625	T	0.88	-0.2211	2.9504	0.05860	0.0:0.4578:0.2389:0.3033	.	312;389;541	B3KUX0;O43566-5;O43566	.;.;RGS14_HUMAN	K	541;322	ENSP00000386229:E541K	ENSP00000336864:E322K	E	+	1	0	RGS14	176731602	0.001000	0.12720	0.009000	0.14445	0.018000	0.09664	1.463000	0.35277	0.678000	0.31325	-0.756000	0.03474	GAG	G|0.995;A|0.005	0.005	strong		0.632	RGS14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372676.1	NM_006480	
POTEG	404785	hgsc.bcm.edu	37	14	19553494	19553494	+	Missense_Mutation	SNP	G	G	C	rs200256710	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:19553494G>C	ENST00000409832.3	+	1	130	c.78G>C	c.(76-78)aaG>aaC	p.K26N		NM_001005356.2	NP_001005356.1	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	26										cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(31)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	47						AGATGGGCAAGTGGTGCCGCC	0.582																																					p.K26N		Atlas-SNP	.											POTEG,NS,carcinoma,0,1	POTEG	118	1	0			c.G78C						scavenged	.						4.0	7.0	6.0					14																	19553494		1219	2779	3998	SO:0001583	missense	404785	exon1			GGGCAAGTGGTGC		CCDS73610.1	14q11.2	2013-01-10	2008-11-26	2008-11-26	ENSG00000222036	ENSG00000222036		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33896	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 4"""	608916	"""ANKRD26-like family C, member 2"""	A26C2			Standard	NR_027480		Approved	POTE14, POTE-14, POTE14alpha, CT104.4	uc001vuz.1	Q6S5H5	OTTHUMG00000170340	ENST00000409832.3:c.78G>C	14.37:g.19553494G>C	ENSP00000386971:p.Lys26Asn	1363.0	1.0	0.000733676		2158.0	285.0	0.132067	NM_001005356	A1L153|A6NMI9|Q6S5H6|Q6S8J2	Missense_Mutation	SNP	ENST00000409832.3	37	CCDS32018.1	.	.	.	.	.	.	.	.	.	.	g	9.693	1.152413	0.21371	.	.	ENSG00000222036	ENST00000409832	T	0.46819	0.86	.	.	.	.	.	.	.	.	T	0.52025	0.1709	L	0.29908	0.895	0.09310	N	1	D	0.89917	1.0	D	0.83275	0.996	T	0.37934	-0.9684	7	0.87932	D	0	.	.	.	.	.	26	Q6S5H5	POTEG_HUMAN	N	26	ENSP00000386971:K26N	ENSP00000386971:K26N	K	+	3	2	POTEG	18623494	0.003000	0.15002	0.038000	0.18304	0.017000	0.09413	-0.275000	0.08525	0.459000	0.27016	0.152000	0.16155	AAG	G|0.996;A|0.004	.	alt		0.582	POTEG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408579.1	NM_001005356	
CLU	1191	hgsc.bcm.edu	37	8	27457507	27457507	+	Silent	SNP	G	G	C	rs9331937	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:27457507G>C	ENST00000316403.10	-	7	1359	c.954C>G	c.(952-954)ccC>ccG	p.P318P	CLU_ENST00000405140.3_Silent_p.P318P|CLU_ENST00000523500.1_Silent_p.P318P|CLU_ENST00000546343.1_Silent_p.P329P|CLU_ENST00000560366.1_Silent_p.P370P			P10909	CLUS_HUMAN	clusterin	318					blood coagulation (GO:0007596)|cell morphogenesis (GO:0000902)|central nervous system myelin maintenance (GO:0032286)|chaperone-mediated protein complex assembly (GO:0051131)|chaperone-mediated protein folding (GO:0061077)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|lipid metabolic process (GO:0006629)|microglial cell activation (GO:0001774)|microglial cell proliferation (GO:0061518)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of protein homooligomerization (GO:0032463)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of neurofibrillary tangle assembly (GO:1902998)|positive regulation of neuron death (GO:1901216)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of tau-protein kinase activity (GO:1902949)|positive regulation of tumor necrosis factor production (GO:0032760)|protein import (GO:0017038)|protein stabilization (GO:0050821)|regulation of beta-amyloid clearance (GO:1900221)|regulation of neuron death (GO:1901214)|regulation of neuronal signal transduction (GO:1902847)|release of cytochrome c from mitochondria (GO:0001836)|response to misfolded protein (GO:0051788)|response to virus (GO:0009615)|reverse cholesterol transport (GO:0043691)	apical dendrite (GO:0097440)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|spherical high-density lipoprotein particle (GO:0034366)	misfolded protein binding (GO:0051787)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)	21		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|Colorectal(74;0.132)		TAGCCTGGGAGGGGTTGTTGG	0.522													G|||	144	0.028754	0.1059	0.0058	5008	,	,		20885	0.0		0.0	False		,,,				2504	0.0				p.P318P		Atlas-SNP	.											.	CLU	54	.	0			c.C954G						PASS	.	G		375,4031	191.2+/-216.9	12,351,1840	57.0	54.0	55.0		954	-8.3	0.0	8	dbSNP_119	55	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	CLU	NM_203339.2		12,353,6138	CC,CG,GG		0.0233,8.5111,2.8987		318/450	27457507	377,12629	2203	4300	6503	SO:0001819	synonymous_variant	1191	exon7			CTGGGAGGGGTTG	M64722	CCDS47832.1	8p21-p12	2012-11-30	2006-02-10		ENSG00000120885	ENSG00000120885			2095	protein-coding gene	gene with protein product	"""complement lysis inhibitor"", ""sulfated glycoprotein 2"", ""testosterone-repressed prostate message 2"", ""apolipoprotein J"""	185430	"""clusterin (complement lysis inhibitor, SP-40,40, sulfated glycoprotein 2, testosterone-repressed prostate message 2, apolipoprotein J)"""	CLI, APOJ		1585460	Standard	NR_038335		Approved	SGP-2, SP-40, TRPM-2, KUB1, CLU1, CLU2	uc003xfz.2	P10909	OTTHUMG00000102114	ENST00000316403.10:c.954C>G	8.37:g.27457507G>C		84.0	0.0	0		86.0	38.0	0.44186	NM_001831	B2R9Q1|B3KSE6|P11380|P11381|Q2TU75|Q5HYC1|Q7Z5B9	Silent	SNP	ENST00000316403.10	37	CCDS47832.1	54|54	0.024725274725274724|0.024725274725274724	51|51	0.10365853658536585|0.10365853658536585	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	G|G	5.885|5.885	0.347360|0.347360	0.11126|0.11126	0.085111|0.085111	2.33E-4|2.33E-4	ENSG00000120885|ENSG00000120885	ENST00000522098|ENST00000521770	.|T	.|0.38401	.|1.14	5.62|5.62	-8.32|-8.32	0.00996|0.00996	.|.	.|0.050523	.|0.85682	.|D	.|0.000000	T|T	0.00724|0.00724	0.0024|0.0024	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.38134|0.38134	-0.9675|-0.9675	4|7	.|0.87932	.|D	.|0	-28.8002|-28.8002	0.2978|0.2978	0.00268|0.00268	0.2607:0.255:0.2311:0.2532|0.2607:0.255:0.2311:0.2532	rs9331937;rs9331937|rs9331937;rs9331937	.|.	.|.	.|.	V|R	181|9	.|ENSP00000428033:P9R	.|ENSP00000428033:P9R	L|P	-|-	1|2	0|0	CLU|CLU	27513424|27513424	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.009000|0.009000	0.06853|0.06853	-3.122000|-3.122000	0.00594|0.00594	-1.333000|-1.333000	0.02247|0.02247	0.655000|0.655000	0.94253|0.94253	CTC|CCT	G|0.973;C|0.027	0.027	strong		0.522	CLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219953.3	NM_001831	
ZBTB42	100128927	hgsc.bcm.edu	37	14	105268701	105268701	+	Silent	SNP	G	G	A	rs61734768	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105268701G>A	ENST00000342537.7	+	1	1452	c.1167G>A	c.(1165-1167)ccG>ccA	p.P389P	ZBTB42_ENST00000555360.1_Silent_p.P389P	NM_001137601.1	NP_001131073.1	B2RXF5	ZBT42_HUMAN	zinc finger and BTB domain containing 42	389					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										GAGAGAAGCCGCATGCCTGCC	0.592													G|||	269	0.0537141	0.1377	0.0274	5008	,	,		18458	0.005		0.0139	False		,,,				2504	0.0501				p.P389P		Atlas-SNP	.											.	ZBTB42	10	.	0			c.G1167A						PASS	.	G		148,1234		7,134,550	39.0	50.0	46.0		1167	-8.3	0.7	14	dbSNP_129	46	34,3138		1,32,1553	no	coding-synonymous	ZBTB42	NM_001137601.1		8,166,2103	AA,AG,GG		1.0719,10.7091,3.9965		389/423	105268701	182,4372	691	1586	2277	SO:0001819	synonymous_variant	100128927	exon2			GAAGCCGCATGCC	AX721091	CCDS45174.1	14q32.33	2013-01-09				ENSG00000179627		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	32550	protein-coding gene	gene with protein product		613915					Standard	NM_001137601		Approved	ZNF925	uc001ypp.3	B2RXF5		ENST00000342537.7:c.1167G>A	14.37:g.105268701G>A		89.0	0.0	0		97.0	50.0	0.515464	NM_001137601	B7ZW21	Silent	SNP	ENST00000342537.7	37	CCDS45174.1																																																																																			G|0.959;A|0.041	0.041	strong		0.592	ZBTB42-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410372.1		
ZNF689	115509	hgsc.bcm.edu	37	16	30616488	30616488	+	Silent	SNP	G	G	A	rs9937653	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:30616488G>A	ENST00000287461.3	-	3	937	c.600C>T	c.(598-600)tcC>tcT	p.S200S	ZNF689_ENST00000566673.1_5'UTR|RP11-146F11.5_ENST00000563540.1_RNA	NM_138447.1	NP_612456.1	Q96CS4	ZN689_HUMAN	zinc finger protein 689	200					regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(1)	14			Colorectal(24;0.198)			GGCACTCGCCGGAGTGTGCCC	0.577													G|||	155	0.0309505	0.1135	0.0072	5008	,	,		14868	0.0		0.0	False		,,,				2504	0.0				p.S200S		Atlas-SNP	.											.	ZNF689	48	.	0			c.C600T						PASS	.	G		371,4023	190.2+/-216.2	14,343,1840	65.0	65.0	65.0		600	-9.9	0.1	16	dbSNP_119	65	4,8596	2.2+/-6.3	0,4,4296	no	coding-synonymous	ZNF689	NM_138447.1		14,347,6136	AA,AG,GG		0.0465,8.4433,2.8859		200/501	30616488	375,12619	2197	4300	6497	SO:0001819	synonymous_variant	115509	exon3			CTCGCCGGAGTGT	BC014000	CCDS10686.1	16p11.2	2013-01-08			ENSG00000156853	ENSG00000156853		"""Zinc fingers, C2H2-type"", ""-"""	25173	protein-coding gene	gene with protein product							Standard	NM_138447		Approved	FLJ90415	uc031qvq.1	Q96CS4	OTTHUMG00000132415	ENST00000287461.3:c.600C>T	16.37:g.30616488G>A		125.0	0.0	0		120.0	51.0	0.425	NM_138447	Q658J5	Silent	SNP	ENST00000287461.3	37	CCDS10686.1																																																																																			G|0.972;A|0.028	0.028	strong		0.577	ZNF689-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255552.1	NM_138447	
EXOC8	149371	hgsc.bcm.edu	37	1	231472916	231472916	+	Silent	SNP	G	G	A	rs73116365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:231472916G>A	ENST00000360394.2	-	1	662	c.576C>T	c.(574-576)taC>taT	p.Y192Y	SPRTN_ENST00000391858.4_5'UTR|SPRTN_ENST00000008440.9_5'Flank|EXOC8_ENST00000366645.1_Silent_p.Y188Y|SPRTN_ENST00000295050.7_5'Flank	NM_175876.3	NP_787072.2	Q8IYI6	EXOC8_HUMAN	exocyst complex component 8	192	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cellular protein localization (GO:0034613)|cellular protein metabolic process (GO:0044267)|exocytosis (GO:0006887)|membrane organization (GO:0061024)|protein transport (GO:0015031)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|exocyst (GO:0000145)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(2)|endometrium(1)|large_intestine(2)|liver(1)|lung(5)|prostate(1)|skin(1)|stomach(1)	14	Breast(184;0.0871)	all_cancers(173;0.151)|Prostate(94;0.183)				GGTCCGCATCGTATTCCACTA	0.587													G|||	77	0.0153754	0.0537	0.0072	5008	,	,		17457	0.0		0.001	False		,,,				2504	0.0				p.Y192Y		Atlas-SNP	.											.	EXOC8	42	.	0			c.C576T						PASS	.	G		215,4191	130.2+/-166.9	7,201,1995	77.0	66.0	70.0		576	1.2	1.0	1	dbSNP_130	70	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	EXOC8	NM_175876.3		7,203,6293	AA,AG,GG		0.0233,4.8797,1.6685		192/726	231472916	217,12789	2203	4300	6503	SO:0001819	synonymous_variant	149371	exon1			CGCATCGTATTCC	AL117352	CCDS1593.1	1q42.2	2013-01-22			ENSG00000116903	ENSG00000116903			24659	protein-coding gene	gene with protein product		615283				12477932	Standard	NM_175876		Approved	SEC84, EXO84, Exo84p	uc001huq.3	Q8IYI6	OTTHUMG00000038025	ENST00000360394.2:c.576C>T	1.37:g.231472916G>A		95.0	0.0	0		108.0	53.0	0.490741	NM_175876	B3KU33|Q5TE82	Silent	SNP	ENST00000360394.2	37	CCDS1593.1																																																																																			G|0.983;A|0.017	0.017	strong		0.587	EXOC8-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_175876	
MMP13	4322	hgsc.bcm.edu	37	11	102818662	102818662	+	Missense_Mutation	SNP	T	T	C	rs17860568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:102818662T>C	ENST00000260302.3	-	8	1197	c.1169A>G	c.(1168-1170)gAt>gGt	p.D390G	MMP13_ENST00000340273.4_Missense_Mutation_p.D390G	NM_002427.3	NP_002418.1	P45452	MMP13_HUMAN	matrix metallopeptidase 13 (collagenase 3)	390	Interaction with collagen.		D -> G (in dbSNP:rs17860568). {ECO:0000269|Ref.4}.		bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cartilage development (GO:0051216)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|skin(1)|stomach(1)	27		all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)		BRCA - Breast invasive adenocarcinoma(274;0.0144)	Marimastat(DB00786)	CTTGCCTGTATCCTCAAAGTG	0.438													T|||	41	0.0081869	0.0287	0.0014	5008	,	,		16765	0.0		0.002	False		,,,				2504	0.0				p.D390G		Atlas-SNP	.											.	MMP13	75	.	0			c.A1169G						PASS	.	T	GLY/ASP	75,4329	67.0+/-104.6	2,71,2129	135.0	113.0	120.0		1169	2.0	0.2	11	dbSNP_123	120	1,8597		0,1,4298	yes	missense	MMP13	NM_002427.3	94	2,72,6427	CC,CT,TT		0.0116,1.703,0.5845	benign	390/472	102818662	76,12926	2202	4299	6501	SO:0001583	missense	4322	exon8			CCTGTATCCTCAA	X75308	CCDS8324.1	11q22.3	2014-01-30	2005-08-08		ENSG00000137745	ENSG00000137745		"""Endogenous ligands"""	7159	protein-coding gene	gene with protein product	"""collagenase 3"""	600108	"""matrix metalloproteinase 13 (collagenase 3)"""			8207000	Standard	NM_002427		Approved	CLG3	uc001phl.3	P45452	OTTHUMG00000165850	ENST00000260302.3:c.1169A>G	11.37:g.102818662T>C	ENSP00000260302:p.Asp390Gly	85.0	0.0	0		89.0	32.0	0.359551	NM_002427	A8K846|B2RCZ3|Q6NWN6	Missense_Mutation	SNP	ENST00000260302.3	37	CCDS8324.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	T	12.68	2.009730	0.35415	0.01703	1.16E-4	ENSG00000137745	ENST00000260302;ENST00000340273	T;T	0.02863	4.13;4.13	5.82	1.98	0.26296	Hemopexin/matrixin (2);	0.232869	0.49916	D	0.000139	T	0.01061	0.0035	L	0.39566	1.225	0.35073	D	0.762662	B	0.18741	0.03	B	0.30716	0.119	T	0.37407	-0.9707	10	0.44086	T	0.13	.	7.3488	0.26678	0.0:0.1373:0.2092:0.6535	rs17860568	390	P45452	MMP13_HUMAN	G	390	ENSP00000260302:D390G;ENSP00000339672:D390G	ENSP00000260302:D390G	D	-	2	0	MMP13	102323872	0.008000	0.16893	0.234000	0.24042	0.991000	0.79684	1.812000	0.38952	0.479000	0.27511	0.533000	0.62120	GAT	T|0.991;C|0.009	0.009	strong		0.438	MMP13-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386648.1	NM_002427	
LRIT2	340745	hgsc.bcm.edu	37	10	85982075	85982075	+	Silent	SNP	A	A	G	rs7901410	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:85982075A>G	ENST00000372113.4	-	3	1259	c.1254T>C	c.(1252-1254)taT>taC	p.Y418Y	LRIT2_ENST00000538192.1_Silent_p.Y428Y	NM_001017924.2	NP_001017924.1	A6NDA9	LRIT2_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 2	418	Fibronectin type-III.					integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|prostate(6)|urinary_tract(1)	32						CATCCACAGCATAAGTATTGA	0.537													A|||	227	0.0453275	0.1672	0.0086	5008	,	,		21319	0.0		0.0	False		,,,				2504	0.0				p.Y418Y		Atlas-SNP	.											.	LRIT2	81	.	0			c.T1254C						PASS	.	A		602,3804	265.9+/-266.9	50,502,1651	121.0	114.0	116.0		1254	-10.1	0.0	10	dbSNP_116	116	18,8582	12.6+/-44.7	0,18,4282	no	coding-synonymous	LRIT2	NM_001017924.2		50,520,5933	GG,GA,AA		0.2093,13.6632,4.767		418/551	85982075	620,12386	2203	4300	6503	SO:0001819	synonymous_variant	340745	exon3			CACAGCATAAGTA		CCDS31234.1, CCDS60581.1	10q23.2	2013-01-11	2007-06-19	2007-06-19	ENSG00000204033	ENSG00000204033		"""Immunoglobulin superfamily / I-set domain containing"""	23443	protein-coding gene	gene with protein product			"""leucine rich repeat containing 22"""	LRRC22			Standard	NM_001017924		Approved	AC022389.4	uc001kcy.3	A6NDA9	OTTHUMG00000018633	ENST00000372113.4:c.1254T>C	10.37:g.85982075A>G		56.0	0.0	0		78.0	41.0	0.525641	NM_001017924	B7ZME6	Silent	SNP	ENST00000372113.4	37	CCDS31234.1																																																																																			A|0.945;G|0.055	0.055	strong		0.537	LRIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049110.4	XM_291697	
MBTPS1	8720	hgsc.bcm.edu	37	16	84097021	84097021	+	Missense_Mutation	SNP	C	C	G	rs35417190	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84097021C>G	ENST00000343411.3	-	19	2956	c.2461G>C	c.(2461-2463)Gtt>Ctt	p.V821L		NM_003791.2	NP_003782.1	Q14703	MBTP1_HUMAN	membrane-bound transcription factor peptidase, site 1	821					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cholesterol metabolic process (GO:0008203)|endoplasmic reticulum unfolded protein response (GO:0030968)|lipid metabolic process (GO:0006629)|lysosome organization (GO:0007040)|proteolysis (GO:0006508)|regulation of transcription factor import into nucleus (GO:0042990)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(10)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41						TTTTCAACAACTGCTGTTTCC	0.438											OREG0023981	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	15	0.00299521	0.0091	0.0043	5008	,	,		17016	0.0		0.0	False		,,,				2504	0.0				p.V821L		Atlas-SNP	.											.	MBTPS1	85	.	0			c.G2461C						PASS	.	C	LEU/VAL	40,4360	43.8+/-77.6	0,40,2160	78.0	75.0	76.0		2461	2.4	0.1	16	dbSNP_126	76	0,8600		0,0,4300	yes	missense	MBTPS1	NM_003791.2	32	0,40,6460	GG,GC,CC		0.0,0.9091,0.3077	benign	821/1053	84097021	40,12960	2200	4300	6500	SO:0001583	missense	8720	exon19			CAACAACTGCTGT	D42053	CCDS10941.1	16q24	2008-08-04	2005-08-17		ENSG00000140943	ENSG00000140943			15456	protein-coding gene	gene with protein product		603355	"""membrane-bound transcription factor protease, site 1"""			9809072, 10944850	Standard	NM_003791		Approved	S1P, KIAA0091, SKI-1, PCSK8	uc002fhi.3	Q14703	OTTHUMG00000137639	ENST00000343411.3:c.2461G>C	16.37:g.84097021C>G	ENSP00000344223:p.Val821Leu	123.0	0.0	0	1226	120.0	53.0	0.441667	NM_003791	A8K6V8|Q24JQ2|Q9UF67	Missense_Mutation	SNP	ENST00000343411.3	37	CCDS10941.1	3	0.0013736263736263737	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	0	0.0	C	10.63	1.403350	0.25291	0.009091	0.0	ENSG00000140943	ENST00000343411;ENST00000347334	T	0.30182	1.54	5.44	2.36	0.29203	.	0.294067	0.37261	N	0.002176	T	0.10465	0.0256	N	0.16656	0.425	0.40773	D	0.983105	B	0.02656	0.0	B	0.04013	0.001	T	0.10730	-1.0617	10	0.25106	T	0.35	-6.6213	4.5503	0.12108	0.2657:0.5222:0.0:0.2121	rs35417190	821	Q14703	MBTP1_HUMAN	L	821;266	ENSP00000344223:V821L	ENSP00000344223:V821L	V	-	1	0	MBTPS1	82654522	0.002000	0.14202	0.082000	0.20525	0.989000	0.77384	0.019000	0.13444	0.335000	0.23614	0.491000	0.48974	GTT	C|0.997;G|0.003	0.003	strong		0.438	MBTPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269080.2	NM_003791	
MYO10	4651	hgsc.bcm.edu	37	5	16754991	16754991	+	Silent	SNP	C	C	T	rs61736777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:16754991C>T	ENST00000513610.1	-	19	2329	c.1875G>A	c.(1873-1875)acG>acA	p.T625T		NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	625	Myosin motor.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						AGGAGCTTAGCGTTGCCATTA	0.398													C|||	153	0.0305511	0.1112	0.0072	5008	,	,		15693	0.0		0.001	False		,,,				2504	0.0				p.T625T		Atlas-SNP	.											.	MYO10	198	.	0			c.G1875A						PASS	.	C		322,3610		11,300,1655	69.0	66.0	67.0		1875	-11.5	0.0	5	dbSNP_129	67	4,8360		0,4,4178	no	coding-synonymous	MYO10	NM_012334.2		11,304,5833	TT,TC,CC		0.0478,8.1892,2.6513		625/2059	16754991	326,11970	1966	4182	6148	SO:0001819	synonymous_variant	4651	exon19			GCTTAGCGTTGCC	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"""Myosins / Myosin superfamily : Class X"", ""Pleckstrin homology (PH) domain containing"""	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.1875G>A	5.37:g.16754991C>T		71.0	0.0	0		78.0	33.0	0.423077	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	37	CCDS54834.1																																																																																			C|0.973;T|0.027	0.027	strong		0.398	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
PRF1	5551	hgsc.bcm.edu	37	10	72358407	72358407	+	Missense_Mutation	SNP	C	C	T	rs140787739	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:72358407C>T	ENST00000441259.1	-	3	1230	c.1070G>A	c.(1069-1071)cGg>cAg	p.R357Q	PRF1_ENST00000373209.2_Missense_Mutation_p.R357Q	NM_001083116.1|NM_005041.4	NP_001076585.1|NP_005032.2	P14222	PERF_HUMAN	perforin 1 (pore forming protein)	357	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				apoptotic process (GO:0006915)|cellular defense response (GO:0006968)|cytolysis (GO:0019835)|defense response to tumor cell (GO:0002357)|defense response to virus (GO:0051607)|immune response to tumor cell (GO:0002418)|protein homooligomerization (GO:0051260)|transmembrane transport (GO:0055085)	cytolytic granule (GO:0044194)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|wide pore channel activity (GO:0022829)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(1)|prostate(3)|urinary_tract(3)	23						CAGTGCCTCCCGCCGCGGGTC	0.697			M			"""various leukaemia, lymphoma"""	Type 2 familial hemophagocytic lymphohistiocytosis		Familial Hemophagocytic Lymphohistiocytosis				C|||	2	0.000399361	0.0008	0.0	5008	,	,		16023	0.0		0.0	False		,,,				2504	0.001				p.R357Q		Atlas-SNP	.	yes	Rec			10	10q22	5551	perforin 1 (pore forming protein)		L	PRF1,caecum,carcinoma,-1,1	PRF1	64	1	0			c.G1070A						PASS	.	C	GLN/ARG,GLN/ARG	5,4399		0,5,2197	19.0	23.0	22.0		1070,1070	4.9	1.0	10	dbSNP_134	22	2,8588		0,2,4293	yes	missense,missense	PRF1	NM_001083116.1,NM_005041.4	43,43	0,7,6490	TT,TC,CC		0.0233,0.1135,0.0539	probably-damaging,probably-damaging	357/556,357/556	72358407	7,12987	2202	4295	6497	SO:0001583	missense	5551	exon3	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GCCTCCCGCCGCG	BC047695	CCDS7305.1	10q22	2014-09-17			ENSG00000180644	ENSG00000180644			9360	protein-coding gene	gene with protein product	"""Perforin"", ""perforin 1 (preforming protein)"""	170280				1505959, 2592021	Standard	NM_005041		Approved	PFP, P1, HPLH2	uc001jrf.4	P14222	OTTHUMG00000018412	ENST00000441259.1:c.1070G>A	10.37:g.72358407C>T	ENSP00000398568:p.Arg357Gln	74.0	0.0	0		68.0	35.0	0.514706	NM_001083116	B2R6X4|Q59F57|Q86WX7	Missense_Mutation	SNP	ENST00000441259.1	37	CCDS7305.1	.	.	.	.	.	.	.	.	.	.	C	18.09	3.547379	0.65311	0.001135	2.33E-4	ENSG00000180644	ENST00000373209;ENST00000441259;ENST00000318971	D;D	0.85013	-1.93;-1.93	5.83	4.92	0.64577	Membrane attack complex component/perforin (MACPF) domain (3);	0.263415	0.37669	N	0.001991	D	0.88463	0.6443	M	0.66378	2.025	0.41451	D	0.987985	D	0.76494	0.999	P	0.61940	0.896	D	0.87239	0.2265	10	0.44086	T	0.13	-49.1524	7.9431	0.29969	0.0:0.8314:0.0:0.1686	.	357	P14222	PERF_HUMAN	Q	357	ENSP00000362305:R357Q;ENSP00000398568:R357Q	ENSP00000316746:R357Q	R	-	2	0	PRF1	72028413	0.050000	0.20438	0.966000	0.40874	0.070000	0.16714	0.384000	0.20668	2.741000	0.93983	0.655000	0.94253	CGG	C|0.999;T|0.001	0.001	strong		0.697	PRF1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048517.2	NM_005041	
LRRC56	115399	hgsc.bcm.edu	37	11	549949	549949	+	Missense_Mutation	SNP	G	G	A	rs371135949		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:549949G>A	ENST00000270115.7	+	7	874	c.374G>A	c.(373-375)cGc>cAc	p.R125H		NM_198075.3	NP_932341.1	Q8IYG6	LRC56_HUMAN	leucine rich repeat containing 56	125										kidney(1)|lung(4)|skin(1)	6		all_cancers(49;2.16e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TGGCTGGCTCGCTGTGGCCTC	0.667													G|||	1	0.000199681	0.0	0.0	5008	,	,		18623	0.001		0.0	False		,,,				2504	0.0				p.R125H		Atlas-SNP	.											.	LRRC56	23	.	0			c.G374A						PASS	.	G	HIS/ARG	0,4406		0,0,2203	64.0	56.0	59.0		374	3.8	1.0	11		59	1,8599	1.2+/-3.3	0,1,4299	no	missense	LRRC56	NM_198075.3	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	125/543	549949	1,13005	2203	4300	6503	SO:0001583	missense	115399	exon7			TGGCTCGCTGTGG		CCDS7700.1	11p15.5	2005-10-18			ENSG00000161328	ENSG00000161328			25430	protein-coding gene	gene with protein product						12477932	Standard	NM_198075		Approved	FLJ00101, DKFZp761L1518	uc010qvz.2	Q8IYG6	OTTHUMG00000132003	ENST00000270115.7:c.374G>A	11.37:g.549949G>A	ENSP00000270115:p.Arg125His	79.0	0.0	0		75.0	27.0	0.36	NM_198075	Q8N3Q4	Missense_Mutation	SNP	ENST00000270115.7	37	CCDS7700.1	.	.	.	.	.	.	.	.	.	.	G	19.34	3.809742	0.70797	0.0	1.16E-4	ENSG00000161328	ENST00000270115	T	0.09538	2.97	4.71	3.8	0.43715	.	0.119263	0.64402	D	0.000014	T	0.21921	0.0528	L	0.46819	1.47	0.40148	D	0.976912	D	0.89917	1.0	D	0.81914	0.995	T	0.01256	-1.1404	10	0.72032	D	0.01	-17.8379	7.3187	0.26515	0.1956:0.0:0.8044:0.0	.	125	Q8IYG6	LRC56_HUMAN	H	125	ENSP00000270115:R125H	ENSP00000270115:R125H	R	+	2	0	LRRC56	539949	1.000000	0.71417	0.999000	0.59377	0.977000	0.68977	3.731000	0.55013	1.219000	0.43474	-0.186000	0.12905	CGC	.	.	weak		0.667	LRRC56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254969.1	NM_198075	
RBMXL1	494115	hgsc.bcm.edu	37	1	89449168	89449168	+	Silent	SNP	T	T	A	rs59048247	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:89449168T>A	ENST00000321792.5	-	2	769	c.342A>T	c.(340-342)ggA>ggT	p.G114G	CCBL2_ENST00000446900.2_Intron|RBMXL1_ENST00000413769.1_5'UTR|CCBL2_ENST00000260508.4_Intron|RBMXL1_ENST00000399794.2_Silent_p.G114G|CCBL2_ENST00000370485.2_Intron|CCBL2_ENST00000370491.3_Intron	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	114					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										CTCCACTTCCTCCTCTTCCAG	0.512													.|||	318	0.0634984	0.2292	0.0187	5008	,	,		19592	0.0		0.002	False		,,,				2504	0.0				p.G114G		Atlas-SNP	.											.	.	.	.	0			c.A342T						PASS	.	T	,,,	876,3530	339.1+/-305.6	83,710,1410	90.0	98.0	96.0		,,342,342	-0.4	0.5	1	dbSNP_129	96	10,8590	7.1+/-27.0	0,10,4290	no	intron,intron,coding-synonymous,coding-synonymous	CCBL2,RBMXL1	NM_001008661.2,NM_001008662.2,NM_001162536.2,NM_019610.5	,,,	83,720,5700	AA,AT,TT		0.1163,19.882,6.8122	,,,	,,114/391,114/391	89449168	886,12120	2203	4300	6503	SO:0001819	synonymous_variant	494115	exon3			ACTTCCTCCTCTT	BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"""RNA binding motif (RRM) containing"""	25073	protein-coding gene	gene with protein product	"""kynurenine aminotransferase III"""					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.342A>T	1.37:g.89449168T>A		394.0	0.0	0		338.0	150.0	0.443787	NM_001162536		Silent	SNP	ENST00000321792.5	37	CCDS716.1																																																																																			T|0.940;A|0.060	0.060	strong		0.512	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610	
MAGI3	260425	hgsc.bcm.edu	37	1	113933814	113933814	+	Silent	SNP	C	C	T	rs182574963	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:113933814C>T	ENST00000307546.9	+	1	234	c.159C>T	c.(157-159)ggC>ggT	p.G53G	MAGI3_ENST00000369615.1_Silent_p.G53G|MAGI3_ENST00000369611.4_Silent_p.G53G|MAGI3_ENST00000486456.1_3'UTR|MAGI3_ENST00000369617.4_Silent_p.G53G	NM_001142782.1	NP_001136254.1	Q5TCQ9	MAGI3_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 3	53	Interaction with ADRB1 and TGFA. {ECO:0000250}.|PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|nucleotide phosphorylation (GO:0046939)|positive regulation of JUN kinase activity (GO:0043507)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)|ovary(3)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	41	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-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)		AGGAGCCCGGCGGGGGCACCT	0.746													C|||	31	0.0061901	0.0204	0.0058	5008	,	,		9388	0.0		0.0	False		,,,				2504	0.0				p.G53G		Atlas-SNP	.											.	MAGI3	181	.	0			c.C159T						PASS	.	C	,	45,4037		0,45,1996	5.0	7.0	6.0		159,159	2.9	1.0	1		6	2,8118		0,2,4058	no	coding-synonymous,coding-synonymous	MAGI3	NM_001142782.1,NM_152900.2	,	0,47,6054	TT,TC,CC		0.0246,1.1024,0.3852	,	53/1482,53/1126	113933814	47,12155	2041	4060	6101	SO:0001819	synonymous_variant	260425	exon1			GCCCGGCGGGGGC	AF213259	CCDS860.1, CCDS44196.1	1p12-p11.2	2008-02-05			ENSG00000081026	ENSG00000081026			29647	protein-coding gene	gene with protein product		615943				10997877, 10748157	Standard	NM_152900		Approved	MAGI-3	uc001edk.3	Q5TCQ9	OTTHUMG00000011737	ENST00000307546.9:c.159C>T	1.37:g.113933814C>T		26.0	0.0	0		35.0	26.0	0.742857	NM_152900	Q5TCQ8|Q5TCR0|Q9H2V6|Q9H5Y8|Q9HBC4|Q9HCD8	Silent	SNP	ENST00000307546.9	37	CCDS44196.1																																																																																			C|0.994;T|0.006	0.006	strong		0.746	MAGI3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000032429.1	NM_152900	
IFNA4	3441	hgsc.bcm.edu	37	9	21187146	21187146	+	Missense_Mutation	SNP	C	C	T	rs201186279		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21187146C>T	ENST00000421715.1	-	1	452	c.385G>A	c.(385-387)Gtg>Atg	p.V129M		NM_021068.2	NP_066546.1	P05014	IFNA4_HUMAN	interferon, alpha 4	129					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)|response to virus (GO:0009615)|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)|type I interferon receptor binding (GO:0005132)	p.V129M(1)		breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17				GBM - Glioblastoma multiforme(5;2.69e-202)|Lung(24;2.26e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		GTCTCTTCCACCCCAACCTCC	0.458													C|||	1	0.000199681	0.0	0.0014	5008	,	,		19919	0.0		0.0	False		,,,				2504	0.0				p.V129M	NSCLC(154;890 1986 23660 27800 51138)	Atlas-SNP	.											IFNA4,NS,carcinoma,0,1	IFNA4	34	1	1	Substitution - Missense(1)	endometrium(1)	c.G385A						scavenged	.						35.0	38.0	37.0					9																	21187146		2182	4253	6435	SO:0001583	missense	3441	exon1			CTTCCACCCCAAC		CCDS6498.1	9p22	2010-08-24			ENSG00000236637	ENSG00000236637		"""Interferons"""	5425	protein-coding gene	gene with protein product		147564				1385305	Standard	NM_021068		Approved	MGC142200, IFN-alpha4a	uc003zon.2	P05014	OTTHUMG00000019660	ENST00000421715.1:c.385G>A	9.37:g.21187146C>T	ENSP00000412897:p.Val129Met	513.0	2.0	0.00389864		736.0	68.0	0.0923913	NM_021068	P13358|Q14CS4|Q5VV15	Missense_Mutation	SNP	ENST00000421715.1	37	CCDS6498.1	.	.	.	.	.	.	.	.	.	.	-	4.271	0.049496	0.08243	.	.	ENSG00000236637	ENST00000421715	T	0.03441	3.93	2.96	-5.93	0.02254	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	1.507550	0.03550	N	0.225260	T	0.05593	0.0147	M	0.73319	2.225	0.09310	N	1	B	0.18741	0.03	B	0.28305	0.088	T	0.38351	-0.9665	10	0.52906	T	0.07	.	1.8132	0.03095	0.1267:0.2025:0.3717:0.2991	.	129	P05014	IFNA4_HUMAN	M	129	ENSP00000412897:V129M	ENSP00000412897:V129M	V	-	1	0	IFNA4	21177146	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.851000	0.01669	-1.988000	0.00980	-1.417000	0.01113	GTG	.	.	weak		0.458	IFNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051889.1	NM_021068	
YTHDC2	64848	hgsc.bcm.edu	37	5	112871458	112871458	+	Silent	SNP	C	C	G	rs77052070	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:112871458C>G	ENST00000161863.4	+	7	1278	c.1065C>G	c.(1063-1065)ctC>ctG	p.L355L	YTHDC2_ENST00000515883.1_Silent_p.L355L	NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	355	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)			NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		ATGTAAATCTCTTTATAAGAT	0.279													C|||	63	0.0125799	0.0477	0.0	5008	,	,		17937	0.0		0.0	False		,,,				2504	0.0				p.L355L		Atlas-SNP	.											.	YTHDC2	118	.	0			c.C1065G						PASS	.	C		214,4190	128.6+/-165.4	2,210,1990	49.0	54.0	52.0		1065	-5.6	0.5	5	dbSNP_131	52	0,8594		0,0,4297	no	coding-synonymous	YTHDC2	NM_022828.3		2,210,6287	GG,GC,CC		0.0,4.8592,1.6464		355/1431	112871458	214,12784	2202	4297	6499	SO:0001819	synonymous_variant	64848	exon7			AAATCTCTTTATA	AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.1065C>G	5.37:g.112871458C>G		96.0	0.0	0		109.0	41.0	0.376147	NM_022828	B2RP66	Silent	SNP	ENST00000161863.4	37	CCDS4113.1																																																																																			C|0.984;G|0.016	0.016	strong		0.279	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2	NM_022828	
NOL8	55035	hgsc.bcm.edu	37	9	95076833	95076833	+	Missense_Mutation	SNP	C	C	G	rs373764183		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95076833C>G	ENST00000535387.1	-	6	2073	c.2074G>C	c.(2074-2076)Ggc>Cgc	p.G692R	NOL8_ENST00000542053.1_Missense_Mutation_p.G624R|NOL8_ENST00000545558.1_Missense_Mutation_p.G692R|NOL8_ENST00000358855.4_Missense_Mutation_p.G624R|NOL8_ENST00000442668.2_Missense_Mutation_p.G692R					nucleolar protein 8											endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						TTGTCAAAGCCTATGTTGTGA	0.433																																					p.G692R		Atlas-SNP	.											.	NOL8	118	.	0			c.G2074C						PASS	.	C	ARG/GLY	1,3761		0,1,1880	37.0	33.0	35.0		2074	1.5	0.0	9		35	0,8226		0,0,4113	no	missense	NOL8	NM_017948.5	125	0,1,5993	GG,GC,CC		0.0,0.0266,0.0083	probably-damaging	692/1168	95076833	1,11987	1881	4113	5994	SO:0001583	missense	55035	exon7			CAAAGCCTATGTT	AB109030	CCDS47993.1, CCDS59135.1	9q22.32	2013-02-12	2004-01-12	2004-01-14	ENSG00000198000	ENSG00000198000		"""RNA binding motif (RRM) containing"""	23387	protein-coding gene	gene with protein product		611534	"""chromosome 9 open reading frame 34"""	C9orf34		12477932	Standard	NM_017948		Approved	FLJ20736, Nop132	uc022bjx.1	Q76FK4	OTTHUMG00000020221	ENST00000535387.1:c.2074G>C	9.37:g.95076833C>G	ENSP00000441300:p.Gly692Arg	76.0	0.0	0		97.0	65.0	0.670103	NM_017948		Missense_Mutation	SNP	ENST00000535387.1	37	CCDS47993.1	.	.	.	.	.	.	.	.	.	.	C	11.25	1.582405	0.28180	2.66E-4	0.0	ENSG00000198000	ENST00000442668;ENST00000375594;ENST00000358855;ENST00000545558;ENST00000535387;ENST00000542053;ENST00000432670	T;T;T;T;T;T	0.49720	0.77;0.77;0.77;0.77;0.77;0.77	5.48	1.52	0.23074	.	1.217900	0.05599	N	0.576075	T	0.33556	0.0867	L	0.29908	0.895	0.09310	N	1	P	0.41265	0.744	B	0.39068	0.289	T	0.21793	-1.0235	10	0.52906	T	0.07	0.5806	1.5277	0.02529	0.1481:0.4632:0.1439:0.2448	.	692	Q76FK4	NOL8_HUMAN	R	692;694;624;692;692;624;692	ENSP00000401177:G692R;ENSP00000351723:G624R;ENSP00000441140:G692R;ENSP00000441300:G692R;ENSP00000440709:G624R;ENSP00000414112:G692R	ENSP00000351723:G624R	G	-	1	0	NOL8	94116654	0.000000	0.05858	0.000000	0.03702	0.089000	0.18198	0.191000	0.17076	0.018000	0.15052	0.561000	0.74099	GGC	.	.	weak		0.433	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948	
KRTAP9-9	81870	hgsc.bcm.edu	37	17	39412125	39412125	+	Missense_Mutation	SNP	G	G	C	rs144403228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39412125G>C	ENST00000394008.1	+	1	490	c.488G>C	c.(487-489)tGc>tCc	p.C163S		NM_030975.2	NP_112237.2	Q9BYP9	KRA99_HUMAN	keratin associated protein 9-9	148						keratin filament (GO:0045095)				endometrium(3)|skin(2)|upper_aerodigestive_tract(1)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			GTGTCCAGCTGCTGCCAGCCT	0.557													.|||	77	0.0153754	0.056	0.0043	5008	,	,		22420	0.0		0.0	False		,,,				2504	0.0				p.C163S		Atlas-SNP	.											.	KRTAP9-9	24	.	0			c.G488C						PASS	.	G	SER/CYS	216,4190		6,204,1993	163.0	170.0	167.0		488	3.7	1.0	17	dbSNP_134	167	2,8598		0,2,4298	yes	missense	KRTAP9-9	NM_030975.2	112	6,206,6291	CC,CG,GG		0.0233,4.9024,1.6761	possibly-damaging	163/170	39412125	218,12788	2203	4300	6503	SO:0001583	missense	81870	exon1			CCAGCTGCTGCCA	AJ406951	CCDS54127.1	17q21.2	2010-06-03			ENSG00000198083	ENSG00000198083		"""Keratin associated proteins"""	16773	protein-coding gene	gene with protein product			"""keratin associated protein 9-5"""	KRTAP9-5		11279113	Standard	NM_030975		Approved	KAP9.9, KAP9.5	uc021txh.1	Q9BYP9	OTTHUMG00000133602	ENST00000394008.1:c.488G>C	17.37:g.39412125G>C	ENSP00000377576:p.Cys163Ser	262.0	1.0	0.00381679		263.0	129.0	0.490494	NM_030975	B5MDD6|Q9BYQ1	Missense_Mutation	SNP	ENST00000394008.1	37	CCDS54127.1	28	0.01282051282051282	24	0.04878048780487805	4	0.011049723756906077	0	0.0	0	0.0	.	23.2	4.383020	0.82792	0.049024	2.33E-4	ENSG00000198083	ENST00000431129;ENST00000394008	T	0.02323	4.34	3.68	3.68	0.42216	.	.	.	.	.	T	0.01976	0.0062	M	0.81497	2.545	0.30835	N	0.736277	D	0.89917	1.0	D	0.72982	0.979	T	0.00388	-1.1771	9	0.46703	T	0.11	.	11.5975	0.50981	0.0:0.0:1.0:0.0	.	148	Q9BYP9	KRA99_HUMAN	S	169;163	ENSP00000377576:C163S	ENSP00000377576:C163S	C	+	2	0	KRTAP9-9	36665651	0.998000	0.40836	0.998000	0.56505	0.904000	0.53231	1.282000	0.33226	1.971000	0.57363	0.462000	0.41574	TGC	G|0.987;C|0.013	0.013	strong		0.557	KRTAP9-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257710.1	NM_030975	
IKBKE	9641	hgsc.bcm.edu	37	1	206666601	206666601	+	Silent	SNP	C	C	A	rs144382861	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:206666601C>A	ENST00000367120.3	+	20	2308	c.1935C>A	c.(1933-1935)ctC>ctA	p.L645L	IKBKE_ENST00000537984.1_Silent_p.L560L|C1orf147_ENST00000367119.1_Intron	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	645	Interaction with DDX3X.				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)					CCCTGCAGCTCCTGGAAGAGC	0.587													C|||	5	0.000998403	0.0038	0.0	5008	,	,		17760	0.0		0.0	False		,,,				2504	0.0				p.L645L		Atlas-SNP	.											.	IKBKE	77	.	0			c.C1935A						PASS	.	C	,,	21,4385	28.1+/-56.4	0,21,2182	61.0	68.0	65.0		1680,,1935	2.0	1.0	1	dbSNP_134	65	0,8600		0,0,4300	no	coding-synonymous,intron,coding-synonymous	IKBKE	NM_001193321.1,NM_001193322.1,NM_014002.3	,,	0,21,6482	AA,AC,CC		0.0,0.4766,0.1615	,,	560/632,,645/717	206666601	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	9641	exon20			GCAGCTCCTGGAA	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.1935C>A	1.37:g.206666601C>A		93.0	0.0	0		95.0	47.0	0.494737	NM_014002	D3DT78|Q3B754|Q3KR43|Q5JTS6	Silent	SNP	ENST00000367120.3	37	CCDS30996.1																																																																																			C|0.999;A|0.001	0.001	strong		0.587	IKBKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088484.1		
MYO7B	4648	hgsc.bcm.edu	37	2	128367433	128367433	+	Missense_Mutation	SNP	G	G	A	rs61741454	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128367433G>A	ENST00000409816.2	+	23	3066	c.3034G>A	c.(3034-3036)Gtc>Atc	p.V1012I	MYO7B_ENST00000389524.4_Missense_Mutation_p.V1012I|MYO7B_ENST00000428314.1_Missense_Mutation_p.V1012I			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1012	MyTH4 1. {ECO:0000255|PROSITE- ProRule:PRU00359}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		GGCCGCCCTGGTCATATGGAA	0.592													G|||	36	0.0071885	0.0234	0.0072	5008	,	,		18749	0.0		0.0	False		,,,				2504	0.0				p.V1012I		Atlas-SNP	.											.	MYO7B	359	.	0			c.G3034A						PASS	.	G	ILE/VAL	91,4015		2,87,1964	48.0	52.0	51.0		3034	2.6	0.0	2	dbSNP_129	51	2,8426		0,2,4212	yes	missense	MYO7B	NM_001080527.1	29	2,89,6176	AA,AG,GG		0.0237,2.2163,0.742	benign	1012/2117	128367433	93,12441	2053	4214	6267	SO:0001583	missense	4648	exon24			GCCCTGGTCATAT		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"""Myosins / Myosin superfamily : Class VII"""	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.3034G>A	2.37:g.128367433G>A	ENSP00000386461:p.Val1012Ile	207.0	1.0	0.00483092		203.0	105.0	0.517241	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	37	CCDS46405.1	12	0.005494505494505495	9	0.018292682926829267	3	0.008287292817679558	0	0.0	0	0.0	G	8.417	0.845525	0.16963	0.022163	2.37E-4	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000409816	D;D;D	0.87103	-2.21;-2.21;-2.21	5.47	2.57	0.30868	MyTH4 domain (2);	0.485163	0.20625	N	0.088698	T	0.62122	0.2402	N	0.17474	0.49	0.09310	N	1	B	0.12630	0.006	B	0.08055	0.003	T	0.63328	-0.6662	10	0.72032	D	0.01	.	8.5581	0.33494	0.1397:0.1265:0.7338:0.0	rs61741454	1012	Q6PIF6	MYO7B_HUMAN	I	1012	ENSP00000374175:V1012I;ENSP00000415090:V1012I;ENSP00000386461:V1012I	ENSP00000374175:V1012I	V	+	1	0	MYO7B	128083903	0.888000	0.30383	0.039000	0.18376	0.011000	0.07611	2.293000	0.43558	0.678000	0.31325	0.655000	0.94253	GTC	G|0.993;A|0.007	0.007	strong		0.592	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
CLU	1191	hgsc.bcm.edu	37	8	27468005	27468005	+	Silent	SNP	G	G	A	rs9331892	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:27468005G>A	ENST00000316403.10	-	2	489	c.84C>T	c.(82-84)gaC>gaT	p.D28D	CLU_ENST00000405140.3_Silent_p.D28D|CLU_ENST00000523500.1_Silent_p.D28D|CLU_ENST00000546343.1_Silent_p.D39D|CLU_ENST00000560366.1_Silent_p.D80D			P10909	CLUS_HUMAN	clusterin	28				D -> S (in Ref. 9; AA sequence and 13; AA sequence). {ECO:0000305}.	blood coagulation (GO:0007596)|cell morphogenesis (GO:0000902)|central nervous system myelin maintenance (GO:0032286)|chaperone-mediated protein complex assembly (GO:0051131)|chaperone-mediated protein folding (GO:0061077)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|lipid metabolic process (GO:0006629)|microglial cell activation (GO:0001774)|microglial cell proliferation (GO:0061518)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of protein homooligomerization (GO:0032463)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of neurofibrillary tangle assembly (GO:1902998)|positive regulation of neuron death (GO:1901216)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of tau-protein kinase activity (GO:1902949)|positive regulation of tumor necrosis factor production (GO:0032760)|protein import (GO:0017038)|protein stabilization (GO:0050821)|regulation of beta-amyloid clearance (GO:1900221)|regulation of neuron death (GO:1901214)|regulation of neuronal signal transduction (GO:1902847)|release of cytochrome c from mitochondria (GO:0001836)|response to misfolded protein (GO:0051788)|response to virus (GO:0009615)|reverse cholesterol transport (GO:0043691)	apical dendrite (GO:0097440)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|spherical high-density lipoprotein particle (GO:0034366)	misfolded protein binding (GO:0051787)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)	21		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|Colorectal(74;0.132)		GGAGCTCATTGTCTGAGACCG	0.562													G|||	286	0.0571086	0.2095	0.013	5008	,	,		20395	0.0		0.0	False		,,,				2504	0.0				p.D28D		Atlas-SNP	.											.	CLU	54	.	0			c.C84T						PASS	.	G		775,3631	313.3+/-293.0	65,645,1493	114.0	103.0	107.0		84	2.2	0.0	8	dbSNP_119	107	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	CLU	NM_203339.2		65,653,5785	AA,AG,GG		0.093,17.5897,6.0203		28/450	27468005	783,12223	2203	4300	6503	SO:0001819	synonymous_variant	1191	exon2			CTCATTGTCTGAG	M64722	CCDS47832.1	8p21-p12	2012-11-30	2006-02-10		ENSG00000120885	ENSG00000120885			2095	protein-coding gene	gene with protein product	"""complement lysis inhibitor"", ""sulfated glycoprotein 2"", ""testosterone-repressed prostate message 2"", ""apolipoprotein J"""	185430	"""clusterin (complement lysis inhibitor, SP-40,40, sulfated glycoprotein 2, testosterone-repressed prostate message 2, apolipoprotein J)"""	CLI, APOJ		1585460	Standard	NR_038335		Approved	SGP-2, SP-40, TRPM-2, KUB1, CLU1, CLU2	uc003xfz.2	P10909	OTTHUMG00000102114	ENST00000316403.10:c.84C>T	8.37:g.27468005G>A		116.0	0.0	0		138.0	53.0	0.384058	NM_001831	B2R9Q1|B3KSE6|P11380|P11381|Q2TU75|Q5HYC1|Q7Z5B9	Silent	SNP	ENST00000316403.10	37	CCDS47832.1																																																																																			G|0.944;A|0.056	0.056	strong		0.562	CLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219953.3	NM_001831	
INF2	64423	hgsc.bcm.edu	37	14	105180977	105180977	+	Missense_Mutation	SNP	G	G	A	rs9672065	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105180977G>A	ENST00000392634.4	+	21	3590	c.3478G>A	c.(3478-3480)Ggt>Agt	p.G1160S	INF2_ENST00000330634.7_Missense_Mutation_p.G1160S	NM_022489.3	NP_071934.3	Q27J81	INF2_HUMAN	inverted formin, FH2 and WH2 domain containing	1160					actin cytoskeleton organization (GO:0030036)|cell death (GO:0008219)|regulation of cellular component size (GO:0032535)|regulation of mitochondrial fission (GO:0090140)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	8		all_cancers(154;0.0896)|Melanoma(154;0.155)|all_epithelial(191;0.172)	all cancers(16;0.00188)|OV - Ovarian serous cystadenocarcinoma(23;0.0191)|Epithelial(46;0.047)|GBM - Glioblastoma multiforme(11;0.116)	Epithelial(152;0.176)		CCACAGCCGTGGTGCCAGACC	0.652													G|||	110	0.0219649	0.0734	0.0144	5008	,	,		16731	0.0		0.003	False		,,,				2504	0.0				p.G1160S		Atlas-SNP	.											.	INF2	148	.	0			c.G3478A						PASS	.	G	SER/GLY,SER/GLY	221,3991		2,217,1887	38.0	46.0	43.0		3478,3478	-8.5	0.0	14	dbSNP_119	43	6,8424		0,6,4209	yes	missense,missense	INF2	NM_022489.3,NM_001031714.3	56,56	2,223,6096	AA,AG,GG		0.0712,5.2469,1.7956	benign,benign	1160/1250,1160/1241	105180977	227,12415	2106	4215	6321	SO:0001583	missense	64423	exon21			AGCCGTGGTGCCA	AK025709	CCDS9989.2, CCDS45173.1	14q32.33	2009-09-07	2007-11-29	2007-11-29	ENSG00000203485	ENSG00000203485			23791	protein-coding gene	gene with protein product	"""inverted formin 2"""	610982	"""chromosome 14 open reading frame 151"", ""chromosome 14 open reading frame 173"""	C14orf151, C14orf173		16818491	Standard	NM_001031714		Approved	MGC13251	uc001ypb.2	Q27J81	OTTHUMG00000029811	ENST00000392634.4:c.3478G>A	14.37:g.105180977G>A	ENSP00000376410:p.Gly1160Ser	44.0	0.0	0		39.0	26.0	0.666667	NM_022489	Q27J83|Q69YL8|Q6P1X7|Q6PK22|Q86TR7|Q9BRM1|Q9H6N1	Missense_Mutation	SNP	ENST00000392634.4	37	CCDS9989.2	48	0.02197802197802198	44	0.08943089430894309	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	G	2.964	-0.214005	0.06101	0.052469	7.12E-4	ENSG00000203485	ENST00000330634;ENST00000392634	T;T	0.79940	-1.3;-1.32	4.24	-8.47	0.00939	.	1.401710	0.05279	N	0.519086	T	0.02807	0.0084	N	0.02539	-0.55	0.09310	N	0.999998	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.38929	-0.9638	10	0.02654	T	1	.	10.5338	0.44992	0.7803:0.1044:0.1153:0.0	rs9672065	1160;1160	Q27J81-2;Q27J81	.;INF2_HUMAN	S	1160	ENSP00000376406:G1160S;ENSP00000376410:G1160S	ENSP00000252527:G628S	G	+	1	0	INF2	104252022	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.762000	0.01803	-2.735000	0.00382	-0.948000	0.02665	GGT	G|0.978;A|0.022	0.022	strong		0.652	INF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000074371.4	NM_022489	
TTC4	7268	hgsc.bcm.edu	37	1	55197320	55197320	+	Silent	SNP	G	G	A	rs1062700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55197320G>A	ENST00000371281.3	+	7	930	c.843G>A	c.(841-843)ctG>ctA	p.L281L	MROH7-TTC4_ENST00000414150.2_3'UTR|TTC4_ENST00000371284.5_3'UTR	NM_004623.4	NP_004614.3	O95801	TTC4_HUMAN	tetratricopeptide repeat domain 4	281										breast(2)|endometrium(3)|kidney(1)|lung(2)|stomach(1)	9						TGCTCTTTCTGTACCCAGAGT	0.557													G|||	248	0.0495208	0.0651	0.0216	5008	,	,		18066	0.004		0.0606	False		,,,				2504	0.0838				p.L281L		Atlas-SNP	.											.	TTC4	21	.	0			c.G843A						PASS	.	G		311,4095	166.5+/-197.7	16,279,1908	79.0	69.0	72.0		843	0.9	1.0	1	dbSNP_86	72	399,8201	126.8+/-185.2	7,385,3908	no	coding-synonymous	TTC4	NM_004623.4		23,664,5816	AA,AG,GG		4.6395,7.0586,5.459		281/388	55197320	710,12296	2203	4300	6503	SO:0001819	synonymous_variant	7268	exon7			CTTTCTGTACCCA		CCDS596.1	1p32	2013-01-11			ENSG00000243725	ENSG00000243725		"""Tetratricopeptide (TTC) repeat domain containing"""	12394	protein-coding gene	gene with protein product		606753				9933562	Standard	NM_004623		Approved	MGC5097, FLJ41930	uc001cxx.4	O95801	OTTHUMG00000009914	ENST00000371281.3:c.843G>A	1.37:g.55197320G>A		83.0	0.0	0		76.0	29.0	0.381579	NM_004623	Q53Y95|Q5TA96|Q9H3I2	Silent	SNP	ENST00000371281.3	37	CCDS596.1																																																																																			G|0.946;A|0.054	0.054	strong		0.557	TTC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027432.1	NM_004623	
KIAA0556	23247	hgsc.bcm.edu	37	16	27689137	27689137	+	Missense_Mutation	SNP	G	G	T	rs147094899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27689137G>T	ENST00000261588.4	+	7	647	c.628G>T	c.(628-630)Gac>Tac	p.D210Y	KIAA0556_ENST00000567894.1_3'UTR|CTD-2049O4.1_ENST00000564893.1_RNA	NM_015202.2	NP_056017.2	O60303	K0556_HUMAN	KIAA0556	210						extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(4)|endometrium(7)|kidney(8)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	76						TATTGAGGAAGACATACTCTC	0.507													G|||	40	0.00798722	0.028	0.0014	5008	,	,		16870	0.001		0.001	False		,,,				2504	0.0				p.D210Y		Atlas-SNP	.											.	KIAA0556	348	.	0			c.G628T						PASS	.	G	TYR/ASP	81,4313	71.4+/-109.4	0,81,2116	65.0	59.0	61.0		628	4.5	1.0	16	dbSNP_134	61	1,8599	1.2+/-3.3	0,1,4299	yes	missense	KIAA0556	NM_015202.2	160	0,82,6415	TT,TG,GG		0.0116,1.8434,0.6311	benign	210/1619	27689137	82,12912	2197	4300	6497	SO:0001583	missense	23247	exon7			GAGGAAGACATAC	AB011128	CCDS32415.1	16p12.1-p11.2	2012-11-30			ENSG00000047578	ENSG00000047578			29068	protein-coding gene	gene with protein product						9628581	Standard	NM_015202		Approved		uc002dow.3	O60303	OTTHUMG00000176780	ENST00000261588.4:c.628G>T	16.37:g.27689137G>T	ENSP00000261588:p.Asp210Tyr	89.0	0.0	0		124.0	54.0	0.435484	NM_015202	A7E2C2	Missense_Mutation	SNP	ENST00000261588.4	37	CCDS32415.1	12	0.005494505494505495	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	13.62	2.290322	0.40494	0.018434	1.16E-4	ENSG00000047578	ENST00000261588;ENST00000327217	T	0.49432	0.78	5.48	4.53	0.55603	.	0.296062	0.32175	N	0.006462	T	0.43612	0.1255	L	0.54323	1.7	0.36190	D	0.850035	D;D	0.76494	0.999;0.979	D;P	0.66497	0.944;0.81	T	0.65014	-0.6271	10	0.87932	D	0	-4.2839	10.458	0.44561	0.09:0.0:0.91:0.0	.	118;210	Q8N803;O60303	.;K0556_HUMAN	Y	210;117	ENSP00000261588:D210Y	ENSP00000261588:D210Y	D	+	1	0	KIAA0556	27596638	1.000000	0.71417	0.973000	0.42090	0.021000	0.10359	3.790000	0.55461	1.320000	0.45209	-0.137000	0.14449	GAC	G|0.993;T|0.007	0.007	strong		0.507	KIAA0556-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433724.1	NM_015202	
KIT	3815	hgsc.bcm.edu	37	4	55561862	55561862	+	Silent	SNP	G	G	T	rs56411694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:55561862G>T	ENST00000288135.5	+	2	349	c.252G>T	c.(250-252)acG>acT	p.T84T		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	84	Ig-like C2-type 1.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AATGGATCACGGAAAAGGCAG	0.443		1	"""Mis, O"""		"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""	"""GIST, epithelioma"""	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors				G|||	99	0.0197684	0.0696	0.0101	5008	,	,		19742	0.0		0.0	False		,,,				2504	0.0				p.T84T		Atlas-SNP	.	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"""L, M, O, E"""	.	KIT	7396	.	0			c.G252T						PASS	.	G	,	273,4133	155.5+/-188.7	9,255,1939	96.0	89.0	92.0		252,252	-10.4	0.0	4	dbSNP_129	92	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	KIT	NM_000222.2,NM_001093772.1	,	9,260,6234	TT,TG,GG		0.0581,6.1961,2.1375	,	84/977,84/973	55561862	278,12728	2203	4300	6503	SO:0001819	synonymous_variant	3815	exon2	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	GATCACGGAAAAG	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6342	protein-coding gene	gene with protein product		164920	"""piebald trait"""	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.252G>T	4.37:g.55561862G>T		112.0	0.0	0		98.0	46.0	0.469388	NM_000222	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Silent	SNP	ENST00000288135.5	37	CCDS3496.1																																																																																			G|0.981;T|0.019	0.019	strong		0.443	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1		
PSMD2	5708	hgsc.bcm.edu	37	3	184023918	184023918	+	Silent	SNP	A	A	G	rs34477849	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184023918A>G	ENST00000310118.4	+	14	2337	c.1779A>G	c.(1777-1779)acA>acG	p.T593T	PSMD2_ENST00000435761.1_Silent_p.T434T|PSMD2_ENST00000439383.1_Silent_p.T463T|EIF2B5_ENST00000444495.1_Intron	NM_002808.3	NP_002799.3	Q13200	PSMD2_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 2	593					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)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|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 polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of protein catabolic process (GO:0042176)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	enzyme regulator activity (GO:0030234)			breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(5)|liver(1)|lung(12)|prostate(3)|upper_aerodigestive_tract(2)	27	all_cancers(143;1.54e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)		Bortezomib(DB00188)	TTGCCAACACACTGGTGGATG	0.507											OREG0015947	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	103	0.0205671	0.0741	0.0072	5008	,	,		22790	0.0		0.0	False		,,,				2504	0.0				p.T593T	Colon(24;313 636 6917 9932 15554)	Atlas-SNP	.											.	PSMD2	56	.	0			c.A1779G						PASS	.	A		261,4145	150.3+/-184.3	8,245,1950	150.0	112.0	125.0		1779	-12.0	0.0	3	dbSNP_126	125	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	PSMD2	NM_002808.3		8,247,6248	GG,GA,AA		0.0233,5.9237,2.0221		593/909	184023918	263,12743	2203	4300	6503	SO:0001819	synonymous_variant	5708	exon14			CAACACACTGGTG	AK095245	CCDS3258.1, CCDS63853.1, CCDS63854.1	3q27.3	2008-05-22			ENSG00000175166	ENSG00000175166		"""Proteasome (prosome, macropain) subunits"""	9559	protein-coding gene	gene with protein product		606223				8774743	Standard	NM_002808		Approved	S2, P97, TRAP2, MGC14274, Rpn1	uc003fnn.1	Q13200	OTTHUMG00000156796	ENST00000310118.4:c.1779A>G	3.37:g.184023918A>G		284.0	1.0	0.00352113	1988	362.0	189.0	0.522099	NM_002808	B4DX07|B4DXY1|E7EW34|E9PCS3|Q12932|Q15321|Q53XQ4|Q96I12	Silent	SNP	ENST00000310118.4	37	CCDS3258.1	35	0.016025641025641024	33	0.06707317073170732	2	0.0055248618784530384	0	0.0	0	0.0	A	9.215	1.031899	0.19590	0.059237	2.33E-4	ENSG00000175166	ENST00000432855	.	.	.	6.0	-12.0	0.00017	.	.	.	.	.	T	0.04907	0.0132	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54077	-0.8347	4	.	.	.	-13.3765	7.9576	0.30051	0.2487:0.1375:0.4867:0.1271	rs34477849;rs34477849	.	.	.	R	54	.	.	H	+	2	0	PSMD2	185506612	0.000000	0.05858	0.009000	0.14445	0.973000	0.67179	-2.546000	0.00932	-2.989000	0.00280	-1.179000	0.01719	CAC	A|0.976;G|0.024	0.024	strong		0.507	PSMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345843.1	NM_002808	
SLC19A2	10560	hgsc.bcm.edu	37	1	169446639	169446639	+	Silent	SNP	C	C	A	rs150548640	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:169446639C>A	ENST00000236137.5	-	2	797	c.561G>T	c.(559-561)ctG>ctT	p.L187L	SLC19A2_ENST00000367804.4_Intron	NM_006996.2	NP_008927.1	O60779	S19A2_HUMAN	solute carrier family 19 (thiamine transporter), member 2	187					folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|thiamine transport (GO:0015888)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	folic acid transporter activity (GO:0008517)|thiamine transmembrane transporter activity (GO:0015234)|thiamine uptake transmembrane transporter activity (GO:0015403)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(2)|upper_aerodigestive_tract(1)	11	all_hematologic(923;0.208)				Thiamine(DB00152)	TCAGGCTGAACAGCGACCAGC	0.498													C|||	17	0.00339457	0.0106	0.0043	5008	,	,		19254	0.0		0.0	False		,,,				2504	0.0				p.L187L		Atlas-SNP	.											.	SLC19A2	35	.	0			c.G561T						PASS	.	C		48,4358	49.6+/-84.7	1,46,2156	57.0	59.0	58.0		561	-1.5	1.0	1	dbSNP_134	58	0,8600		0,0,4300	no	coding-synonymous	SLC19A2	NM_006996.2		1,46,6456	AA,AC,CC		0.0,1.0894,0.3691		187/498	169446639	48,12958	2203	4300	6503	SO:0001819	synonymous_variant	10560	exon2			GCTGAACAGCGAC	AF135488	CCDS1280.1	1q23.3	2013-05-22			ENSG00000117479	ENSG00000117479		"""Solute carriers"""	10938	protein-coding gene	gene with protein product		603941		TRMA		9399900, 10391221	Standard	NM_006996		Approved	THTR1	uc001gge.4	O60779	OTTHUMG00000035452	ENST00000236137.5:c.561G>T	1.37:g.169446639C>A		76.0	0.0	0		82.0	50.0	0.609756	NM_006996	B2R9H0|B4E1X4|Q8WV87|Q9UBL7|Q9UKJ2|Q9UN31|Q9UN43	Silent	SNP	ENST00000236137.5	37	CCDS1280.1																																																																																			C|0.996;A|0.004	0.004	strong		0.498	SLC19A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086106.1	NM_006996	
UBAP2	55833	hgsc.bcm.edu	37	9	33927880	33927880	+	Nonstop_Mutation	SNP	C	C	G	rs16935295	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:33927880C>G	ENST00000418786.2	-	17	2152	c.2060G>C	c.(2059-2061)tGa>tCa	p.*687S	UBAP2_ENST00000539807.1_Missense_Mutation_p.M517I|UBAP2_ENST00000449054.1_Missense_Mutation_p.M762I|UBAP2_ENST00000379238.1_Missense_Mutation_p.M762I|UBAP2_ENST00000379235.1_Start_Codon_SNP_p.M1I|UBAP2_ENST00000360802.1_Missense_Mutation_p.M762I|UBAP2_ENST00000379239.4_Missense_Mutation_p.M495I					ubiquitin associated protein 2											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)		TCGCGGTGTTCATGCTACTGG	0.637													C|||	151	0.0301518	0.1104	0.0058	5008	,	,		19308	0.0		0.001	False		,,,				2504	0.0				p.M762I		Atlas-SNP	.											.	UBAP2	82	.	0			c.G2286C						PASS	.	C	ILE/MET	448,3958	214.8+/-234.0	24,400,1779	90.0	87.0	88.0		2286	4.8	0.7	9	dbSNP_123	88	6,8594	5.0+/-18.6	0,6,4294	yes	missense	UBAP2	NM_018449.2	10	24,406,6073	GG,GC,CC		0.0698,10.168,3.4907	benign	762/1120	33927880	454,12552	2203	4300	6503	SO:0001578	stop_lost	55833	exon20			GGTGTTCATGCTA	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	ENST00000418786.2:c.2060G>C	9.37:g.33927880C>G		140.0	0.0	0		142.0	88.0	0.619718	NM_018449		Missense_Mutation	SNP	ENST00000418786.2	37		43|43	0.019688644688644688|0.019688644688644688	40|40	0.08130081300813008|0.08130081300813008	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	C|C	11.68|11.68	1.711377|1.711377	0.30322|0.30322	0.10168|0.10168	6.98E-4|6.98E-4	ENSG00000137073|ENSG00000137073	ENST00000379238;ENST00000449054;ENST00000360802;ENST00000431417;ENST00000379235;ENST00000379239;ENST00000539807;ENST00000351580|ENST00000418786	T;T;T;T;T;T|.	0.33216|.	1.66;1.66;1.66;1.42;1.66;1.66|.	5.77|5.77	4.85|4.85	0.62838|0.62838	.|.	0.315392|.	0.42682|.	D|.	0.000678|.	T|.	0.02267|.	0.0070|.	L|L	0.50919|0.50919	1.6|1.6	0.09310|0.09310	N|N	1|1	B;B;B;B;B|.	0.12013|.	0.005;0.002;0.002;0.002;0.003|.	B;B;B;B;B|.	0.09377|.	0.004;0.004;0.004;0.004;0.002|.	T|.	0.00761|.	-1.1577|.	10|.	0.23891|.	T|.	0.37|.	-1.1258|-1.1258	16.2411|16.2411	0.82409|0.82409	0.0:0.8668:0.1332:0.0|0.0:0.8668:0.1332:0.0	rs16935295;rs52823002;rs16935295|rs16935295;rs52823002;rs16935295	687;517;495;671;762|.	F5H4D5;F5H2U4;A6NCA8;F5H2C8;Q5T6F2|.	.;.;.;.;UBAP2_HUMAN|.	I|S	762;762;762;671;1;495;517;198|687	ENSP00000368540:M762I;ENSP00000416932:M762I;ENSP00000354039:M762I;ENSP00000368537:M1I;ENSP00000368541:M495I;ENSP00000439329:M517I|.	ENSP00000259602:M198I|.	M|X	-|-	3|2	0|2	UBAP2|UBAP2	33917880|33917880	1.000000|1.000000	0.71417|0.71417	0.710000|0.710000	0.30468|0.30468	0.061000|0.061000	0.15899|0.15899	1.399000|1.399000	0.34566|0.34566	1.383000|1.383000	0.46405|0.46405	0.655000|0.655000	0.94253|0.94253	ATG|TGA	C|0.965;G|0.035	0.035	strong		0.637	UBAP2-203	KNOWN	basic	protein_coding	protein_coding		NM_018449	
CD33	945	hgsc.bcm.edu	37	19	51738465	51738465	+	Missense_Mutation	SNP	G	G	A	rs58981829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51738465G>A	ENST00000262262.4	+	5	820	c.799G>A	c.(799-801)Gtt>Att	p.V267I	CD33_ENST00000421133.2_Missense_Mutation_p.V140I|CD33_ENST00000436584.2_Missense_Mutation_p.V140I|CD33_ENST00000391796.3_Missense_Mutation_p.V267I	NM_001772.3	NP_001763.3	P20138	CD33_HUMAN	CD33 molecule	267			V -> I (in dbSNP:rs58981829).		cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|negative regulation of cell proliferation (GO:0008285)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(15)|skin(1)|stomach(1)	24		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000224)|OV - Ovarian serous cystadenocarcinoma(262;0.00468)	Gemtuzumab ozogamicin(DB00056)	AGGAGCTGGTGTTACAGCCCT	0.502													g|||	203	0.0405351	0.1399	0.0245	5008	,	,		19411	0.0		0.001	False		,,,				2504	0.0				p.V267I		Atlas-SNP	.											CD33,NS,carcinoma,0,1	CD33	55	1	0			c.G799A						PASS	.	A	ILE/VAL,ILE/VAL,ILE/VAL	521,3885		29,463,1711	151.0	123.0	133.0		418,799,799	1.9	0.0	19	dbSNP_129	133	5,8595		0,5,4295	yes	missense,missense,missense	CD33	NM_001082618.1,NM_001177608.1,NM_001772.3	29,29,29	29,468,6006	AA,AG,GG		0.0581,11.8248,4.0443	benign,benign,benign	140/238,267/311,267/365	51738465	526,12480	2203	4300	6503	SO:0001583	missense	945	exon5			GCTGGTGTTACAG	M23197	CCDS33084.1, CCDS46157.1, CCDS54299.1	19q13.3	2013-01-29	2006-03-28		ENSG00000105383	ENSG00000105383		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1659	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 3"""	159590	"""CD33 antigen (gp67)"""			3139766, 9465907	Standard	NM_001772		Approved	SIGLEC3, SIGLEC-3, p67, FLJ00391	uc002pwa.2	P20138		ENST00000262262.4:c.799G>A	19.37:g.51738465G>A	ENSP00000262262:p.Val267Ile	212.0	0.0	0		224.0	121.0	0.540179	NM_001772	B4E3P8|C9JEN7|F8WAL2|Q8TD24	Missense_Mutation	SNP	ENST00000262262.4	37	CCDS33084.1	67	0.030677655677655676	54	0.10975609756097561	12	0.03314917127071823	0	0.0	1	0.0013192612137203166	.	6.151	0.396010	0.11638	0.118248	5.81E-4	ENSG00000105383	ENST00000436584;ENST00000262262;ENST00000421133;ENST00000391796	T;T;T;T	0.39997	1.05;2.69;2.69;2.16	4.13	1.93	0.25924	.	1.922710	0.03611	N	0.234840	T	0.00524	0.0017	L	0.35644	1.08	0.80722	P	0.0	B;B;B	0.10296	0.0;0.003;0.001	B;B;B	0.12156	0.002;0.007;0.002	T	0.10405	-1.0631	9	0.26408	T	0.33	.	9.5522	0.39317	0.195:0.0:0.805:0.0	rs58981829;rs61736474	140;267;267	C9JEN7;F8WAL2;P20138	.;.;CD33_HUMAN	I	140;267;140;267	ENSP00000403331:V140I;ENSP00000262262:V267I;ENSP00000410126:V140I;ENSP00000375673:V267I	ENSP00000262262:V267I	V	+	1	0	CD33	56430277	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	0.249000	0.18216	0.169000	0.19679	-0.939000	0.02691	GTT	G|0.955;A|0.045	0.045	strong		0.502	CD33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464199.2	NM_001772	
DLK1	8788	hgsc.bcm.edu	37	14	101200780	101200780	+	Silent	SNP	T	T	C	rs2295660	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:101200780T>C	ENST00000341267.4	+	5	941	c.699T>C	c.(697-699)tgT>tgC	p.C233C	DLK1_ENST00000331224.6_Intron	NM_003836.5	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog (Drosophila)	233	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|embryonic skeletal system development (GO:0048706)|multicellular organismal development (GO:0007275)|negative regulation of Notch signaling pathway (GO:0045746)|Notch signaling pathway (GO:0007219)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)	external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(16)|ovary(2)|prostate(1)|skin(1)	29		Melanoma(154;0.155)				GCTACGAGTGTCTGTGCAAGC	0.662													T|||	107	0.0213658	0.0371	0.0058	5008	,	,		15534	0.0506		0.003	False		,,,				2504	0.0				p.C233C		Atlas-SNP	.											.	DLK1	57	.	0			c.T699C						PASS	.	T		104,4300		1,102,2099	38.0	44.0	42.0		699	3.1	1.0	14	dbSNP_100	42	8,8590		0,8,4291	no	coding-synonymous	DLK1	NM_003836.5		1,110,6390	CC,CT,TT		0.093,2.3615,0.8614		233/384	101200780	112,12890	2202	4299	6501	SO:0001819	synonymous_variant	8788	exon5			CGAGTGTCTGTGC	U15979	CCDS9963.1	14q32	2011-12-05	2001-12-03			ENSG00000185559			2907	protein-coding gene	gene with protein product		176290	"""delta-like homolog (Drosophila)"""			8095043, 7925474	Standard	NM_003836		Approved	FA1, pG2, Pref-1, ZOG, Delta1	uc001yhs.4	P80370		ENST00000341267.4:c.699T>C	14.37:g.101200780T>C		39.0	0.0	0		46.0	15.0	0.326087	NM_003836	P15803|Q96DW5	Silent	SNP	ENST00000341267.4	37	CCDS9963.1																																																																																			T|0.981;C|0.019	0.019	strong		0.662	DLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414389.1		
KIAA0196	9897	hgsc.bcm.edu	37	8	126079867	126079867	+	Silent	SNP	T	T	C	rs10429323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:126079867T>C	ENST00000318410.7	-	10	1594	c.1245A>G	c.(1243-1245)ttA>ttG	p.L415L	KIAA0196_ENST00000517845.1_Silent_p.L267L	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	415					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)			GTGCAGTATCTAACAGCAGCT	0.358													C|||	160	0.0319489	0.1157	0.0101	5008	,	,		15835	0.0		0.0	False		,,,				2504	0.0				p.L415L		Atlas-SNP	.											.	KIAA0196	90	.	0			c.A1245G						PASS	.	C		358,4048	793.9+/-415.2	17,324,1862	166.0	155.0	158.0		1245	4.7	1.0	8	dbSNP_119	158	1,8599	819.2+/-406.8	0,1,4299	no	coding-synonymous	KIAA0196	NM_014846.3		17,325,6161	CC,CT,TT		0.0116,8.1253,2.7603		415/1160	126079867	359,12647	2203	4300	6503	SO:0001819	synonymous_variant	9897	exon10			AGTATCTAACAGC		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.1245A>G	8.37:g.126079867T>C		132.0	0.0	0		150.0	72.0	0.48	NM_014846	A8K4R7|Q3KQX5|Q8TBQ2	Silent	SNP	ENST00000318410.7	37	CCDS6355.1	51	0.023351648351648352	45	0.09146341463414634	6	0.016574585635359115	0	0.0	0	0.0	C	8.635	0.894613	0.17613	0.081253	1.16E-4	ENSG00000164961	ENST00000523273	.	.	.	5.61	4.7	0.59300	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-12.6356	10.9586	0.47372	0.1293:0.8033:0.0:0.0675	rs10429323;rs10429323	.	.	.	W	32	.	.	X	-	2	0	KIAA0196	126149049	0.998000	0.40836	0.996000	0.52242	0.751000	0.42716	0.645000	0.24782	1.393000	0.46605	-0.320000	0.08662	TAG	T|0.971;C|0.029	0.029	strong		0.358	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846	
DMD	1756	hgsc.bcm.edu	37	X	32716110	32716110	+	Silent	SNP	C	C	T	rs1800265	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:32716110C>T	ENST00000357033.4	-	9	1043	c.837G>A	c.(835-837)acG>acA	p.T279T	DMD_ENST00000288447.4_Silent_p.T271T|DMD_ENST00000378677.2_Silent_p.T275T	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	279			T -> A (in CMD3B). {ECO:0000269|PubMed:9170407}.		cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				CTAGACTGACCGTGATCTGCA	0.488													T|||	570	0.150993	0.3805	0.0865	3775	,	,		11752	0.002		0.002	False		,,,				2504	0.0031				p.T279T		Atlas-SNP	.											.	DMD	2127	.	0			c.G837A						PASS	.	T	,,,,	1838,1995		386,779,287,466,284	105.0	73.0	84.0		813,837,468,825,468	-1.6	1.0	X	dbSNP_89	84	21,6701		0,17,4,2410,1864	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DMD	NM_000109.3,NM_004006.2,NM_004007.2,NM_004009.3,NM_004010.3	,,,,	386,796,291,2876,2148	TT,TC,T,CC,C		0.3124,47.952,17.6125	,,,,	271/3678,279/3686,156/3563,275/3682,156/3563	32716110	1859,8696	2202	4295	6497	SO:0001819	synonymous_variant	1756	exon9			ACTGACCGTGATC	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.837G>A	X.37:g.32716110C>T		121.0	0.0	0		150.0	77.0	0.513333	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Silent	SNP	ENST00000357033.4	37	CCDS14233.1																																																																																			C|0.852;T|0.148	0.148	strong		0.488	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
CXorf38	159013	hgsc.bcm.edu	37	X	40496354	40496354	+	Missense_Mutation	SNP	T	T	C	rs17145855	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:40496354T>C	ENST00000327877.5	-	4	552	c.526A>G	c.(526-528)Acg>Gcg	p.T176A	CXorf38_ENST00000378421.1_Missense_Mutation_p.T57A|CXorf38_ENST00000440784.2_Missense_Mutation_p.T91A|CXorf38_ENST00000378426.1_Missense_Mutation_p.T57A	NM_144970.2	NP_659407.1	Q8TB03	CX038_HUMAN	chromosome X open reading frame 38	176			T -> A (in dbSNP:rs17145855).							NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	12						CGAAGCCACGTAGAAGATACT	0.358													T|||	57	0.0150993	0.0424	0.0014	3775	,	,		14154	0.0		0.0	False		,,,				2504	0.0				p.T176A		Atlas-SNP	.											.	CXorf38	29	.	0			c.A526G						PASS	.	T	ALA/THR	179,3656		2,151,24,1479,547	56.0	51.0	53.0		526	-7.7	0.0	X	dbSNP_123	53	0,6728		0,0,0,2428,1872	yes	missense	CXorf38	NM_144970.2	58	2,151,24,3907,2419	CC,CT,C,TT,T		0.0,4.6675,1.6946	benign	176/320	40496354	179,10384	2203	4300	6503	SO:0001583	missense	159013	exon4			GCCACGTAGAAGA	AL832829	CCDS14253.1	Xp11	2008-02-05			ENSG00000185753	ENSG00000185753			28589	protein-coding gene	gene with protein product							Standard	NM_144970		Approved	MGC39350	uc004dew.3	Q8TB03	OTTHUMG00000024104	ENST00000327877.5:c.526A>G	X.37:g.40496354T>C	ENSP00000330488:p.Thr176Ala	319.0	0.0	0		323.0	155.0	0.479876	NM_144970	B3KW28|D3DWB5|Q5JPF5|Q8N941	Missense_Mutation	SNP	ENST00000327877.5	37	CCDS14253.1	16	0.009644364074743821	9	0.01882845188284519	0	0.0	0	0.0	0	0.0	T	0.117	-1.130194	0.01756	0.046675	0.0	ENSG00000185753	ENST00000378426;ENST00000327877;ENST00000378421;ENST00000440784	T;T;T;T	0.40476	1.03;1.03;1.03;1.03	4.95	-7.7	0.01259	.	1.658950	0.02974	N	0.144773	T	0.02610	0.0079	N	0.14661	0.345	0.34371	P	0.30793899999999996	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.10776	-1.0615	9	0.08837	T	0.75	0.4805	2.9505	0.05860	0.1431:0.3119:0.0909:0.4542	rs17145855;rs52818878;rs17145855	91;176	E7EN46;Q8TB03	.;CX038_HUMAN	A	57;176;57;91	ENSP00000367683:T57A;ENSP00000330488:T176A;ENSP00000367677:T57A;ENSP00000400019:T91A	ENSP00000330488:T176A	T	-	1	0	CXorf38	40381298	0.000000	0.05858	0.003000	0.11579	0.414000	0.31173	-1.312000	0.02720	-1.183000	0.02723	-0.537000	0.04273	ACG	0|0.003;C|0.018	0.018	strong		0.358	CXorf38-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060685.3	NM_144970	
GLRA4	441509	hgsc.bcm.edu	37	X	102962343	102962343	+	Missense_Mutation	SNP	T	T	C	rs61744012		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102962343T>C	ENST00000372617.4	-	9	1603	c.1183A>G	c.(1183-1185)Att>Gtt	p.I395V		NM_001024452.2	NP_001019623.2	Q5JXX5	GLRA4_HUMAN	glycine receptor, alpha 4	395						cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|glycine binding (GO:0016594)|transmitter-gated ion channel activity (GO:0022824)			cervix(1)|endometrium(2)|large_intestine(2)|lung(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	21						GGACTATAAATGCCAGAACCT	0.527													T|||	48	0.0127152	0.0348	0.0029	3775	,	,		14232	0.0		0.0	False		,,,				2504	0.0				p.I395V		Atlas-SNP	.											.	GLRA4	86	.	0			c.A1183G						PASS	.	T	VAL/ILE	94,3180		0,77,17,1275,553	105.0	100.0	102.0		1183	5.0	1.0	X	dbSNP_129	102	1,6426		0,1,0,2321,1783	yes	missense	GLRA4	NM_001024452.2	29	0,78,17,3596,2336	CC,CT,C,TT,T		0.0156,2.8711,0.9793	benign	395/418	102962343	95,9606	1922	4105	6027	SO:0001583	missense	441509	exon9			TATAAATGCCAGA	Z93848	CCDS43980.2	Xq22.2	2012-01-16			ENSG00000188828	ENSG00000188828		"""Ligand-gated ion channels / Glycine receptors"""	31715	protein-coding gene	gene with protein product							Standard	NM_001024452		Approved		uc011mse.2	Q5JXX5	OTTHUMG00000022110	ENST00000372617.4:c.1183A>G	X.37:g.102962343T>C	ENSP00000361700:p.Ile395Val	116.0	0.0	0		136.0	84.0	0.617647	NM_001024452		Missense_Mutation	SNP	ENST00000372617.4	37	CCDS43980.2	16	0.009644364074743821	12	0.024691358024691357	1	0.0027624309392265192	0	0.0	0	0.0	t	2.377	-0.343098	0.05243	0.028711	1.56E-4	ENSG00000188828	ENST00000372617	T	0.77877	-1.13	4.99	4.99	0.66335	.	1.027970	0.07653	N	0.932363	T	0.31263	0.0791	N	0.02539	-0.55	0.27370	N	0.955726	B	0.02656	0.0	B	0.01281	0.0	T	0.31223	-0.9951	10	0.25106	T	0.35	.	9.8284	0.40925	0.0:0.0:0.0:1.0	.	395	Q5JXX5	GLRA4_HUMAN	V	395	ENSP00000361700:I395V	ENSP00000361700:I395V	I	-	1	0	GLRA4	102848999	0.380000	0.25131	0.999000	0.59377	0.987000	0.75469	0.625000	0.24477	1.844000	0.53588	0.441000	0.28932	ATT	T|0.990;C|0.010	0.010	strong		0.527	GLRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057742.2	NM_001024452	
ZNF814	730051	hgsc.bcm.edu	37	19	58385987	58385987	+	Missense_Mutation	SNP	C	C	G	rs111291730	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58385987C>G	ENST00000435989.2	-	3	1005	c.771G>C	c.(769-771)ttG>ttC	p.L257F	ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597832.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	257					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						GATGATTACTCAAGCTAGCAT	0.398													.|||	16	0.00319489	0.0121	0.0	5008	,	,		23651	0.0		0.0	False		,,,				2504	0.0				p.L257F		Atlas-SNP	.											.	ZNF814	93	.	0			c.G771C						PASS	.						120.0	91.0	100.0					19																	58385987		692	1591	2283	SO:0001583	missense	730051	exon3			ATTACTCAAGCTA		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"""Zinc fingers, C2H2-type"", ""-"""	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.771G>C	19.37:g.58385987C>G	ENSP00000410545:p.Leu257Phe	234.0	1.0	0.0042735		257.0	126.0	0.490272	NM_001144989	A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	CCDS46212.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	.	6.736	0.504632	0.12822	.	.	ENSG00000204514	ENST00000435989	T	0.52057	0.68	2.23	-1.06	0.10002	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.32010	0.0815	M	0.62723	1.935	0.09310	N	1	B	0.14805	0.011	B	0.12156	0.007	T	0.30208	-0.9986	9	0.49607	T	0.09	.	5.757	0.18178	0.2141:0.4859:0.3:0.0	.	257	B7Z6K7	ZN814_HUMAN	F	257	ENSP00000410545:L257F	ENSP00000410545:L257F	L	-	3	2	ZNF814	63077799	0.005000	0.15991	0.000000	0.03702	0.011000	0.07611	0.213000	0.17521	-0.743000	0.04784	-2.575000	0.00170	TTG	C|0.998;G|0.002	0.002	strong		0.398	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708	
GAS6	2621	hgsc.bcm.edu	37	13	114526504	114526504	+	Silent	SNP	G	G	A	rs74118435	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:114526504G>A	ENST00000327773.6	-	13	1643	c.1497C>T	c.(1495-1497)gtC>gtT	p.V499V	GAS6_ENST00000355761.4_Silent_p.V445V|GAS6_ENST00000418959.3_Silent_p.V200V|GAS6-AS1_ENST00000458001.1_RNA|GAS6_ENST00000450766.1_Silent_p.V226V|GAS6_ENST00000357389.3_Silent_p.V542V	NM_000820.2	NP_000811.1	Q14393	GAS6_HUMAN	growth arrest-specific 6	542	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				activation of protein kinase B activity (GO:0032148)|apoptotic cell clearance (GO:0043277)|B cell chemotaxis (GO:0035754)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell-substrate adhesion (GO:0031589)|cellular protein metabolic process (GO:0044267)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth factor stimulus (GO:0071363)|cellular response to interferon-alpha (GO:0035457)|cellular response to starvation (GO:0009267)|cellular response to vitamin K (GO:0071307)|dendritic cell differentiation (GO:0097028)|enzyme linked receptor protein signaling pathway (GO:0007167)|extracellular matrix assembly (GO:0085029)|fusion of virus membrane with host plasma membrane (GO:0019064)|hematopoietic stem cell migration to bone marrow (GO:0097241)|leukocyte migration (GO:0050900)|macrophage cytokine production (GO:0010934)|negative regulation of apoptotic process (GO:0043066)|negative regulation of biomineral tissue development (GO:0070168)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-1 secretion (GO:0050711)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-6 secretion (GO:1900165)|negative regulation of oligodendrocyte apoptotic process (GO:1900142)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of renal albumin absorption (GO:2000533)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|neuron migration (GO:0001764)|organ regeneration (GO:0031100)|peptidyl-glutamic acid carboxylation (GO:0017187)|peptidyl-serine phosphorylation (GO:0018105)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of dendritic cell chemotaxis (GO:2000510)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of gene expression (GO:0010628)|positive regulation of glomerular filtration (GO:0003104)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of phagocytosis (GO:0050766)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of TOR signaling (GO:0032008)|post-translational protein modification (GO:0043687)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|protein targeting to plasma membrane (GO:0072661)|proteolysis (GO:0006508)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)|viral entry into host cell (GO:0046718)|viral genome replication (GO:0019079)	cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|platelet alpha granule lumen (GO:0031093)	binding, bridging (GO:0060090)|calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|phosphatidylserine binding (GO:0001786)|protein tyrosine kinase activator activity (GO:0030296)|receptor agonist activity (GO:0048018)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|voltage-gated calcium channel activity (GO:0005245)			central_nervous_system(4)|ovary(1)	5	Lung NSC(43;0.00976)|all_neural(89;0.0337)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0176)|all_epithelial(44;0.0104)|all_lung(25;0.0249)|Lung NSC(25;0.0908)|Breast(118;0.188)				ATTCAGTCCCGACGTCCAGAG	0.627													G|||	111	0.0221645	0.0809	0.0058	5008	,	,		19406	0.0		0.0	False		,,,				2504	0.0				p.V499V		Atlas-SNP	.											.	GAS6	75	.	0			c.C1497T						PASS	.	G	,,	282,4122	157.4+/-190.3	8,266,1928	96.0	79.0	85.0		1497,678,600	-9.1	0.0	13	dbSNP_130	85	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	GAS6	NM_000820.2,NM_001143945.1,NM_001143946.1	,,	8,269,6225	AA,AG,GG		0.0349,6.4033,2.1916	,,	499/679,226/406,200/380	114526504	285,12719	2202	4300	6502	SO:0001819	synonymous_variant	2621	exon13			AGTCCCGACGTCC		CCDS45072.1	13q34	2008-07-18			ENSG00000183087	ENSG00000183087			4168	protein-coding gene	gene with protein product	"""AXL stimulatory factor"""	600441		AXLLG		8336730	Standard	NM_000820		Approved	AXSF, FLJ34709, DKFZp666G247	uc001vud.3	Q14393	OTTHUMG00000017395	ENST00000327773.6:c.1497C>T	13.37:g.114526504G>A		86.0	0.0	0		95.0	54.0	0.568421	NM_000820	B3KRQ7|B3KVL4|E9PBL7|Q6IMN1|Q7Z7N3	Silent	SNP	ENST00000327773.6	37	CCDS45072.1																																																																																			G|0.971;A|0.029	0.029	strong		0.627	GAS6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045946.2	NM_000820	
TTC3	7267	hgsc.bcm.edu	37	21	38524226	38524226	+	Silent	SNP	A	A	G	rs2835632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:38524226A>G	ENST00000399017.2	+	26	5057	c.2310A>G	c.(2308-2310)aaA>aaG	p.K770K	TTC3_ENST00000355666.1_Silent_p.K770K|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000540756.1_Silent_p.K460K|TTC3_ENST00000354749.2_Silent_p.K770K	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	770					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				AAGACAAAAAATTGAAGAGAA	0.338													A|||	528	0.105431	0.2466	0.1715	5008	,	,		18165	0.0407		0.003	False		,,,				2504	0.0399				p.K770K	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.A2310G						PASS	.	A	,	912,3494	336.3+/-304.3	94,724,1385	67.0	66.0	66.0		2310,2310	0.3	0.2	21	dbSNP_100	66	16,8582	11.2+/-40.8	0,16,4283	no	coding-synonymous,coding-synonymous	TTC3	NM_001001894.1,NM_003316.3	,	94,740,5668	GG,GA,AA		0.1861,20.699,7.1363	,	770/2026,770/2026	38524226	928,12076	2203	4299	6502	SO:0001819	synonymous_variant	7267	exon26			CAAAAAATTGAAG	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.2310A>G	21.37:g.38524226A>G		193.0	0.0	0		192.0	105.0	0.546875	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Silent	SNP	ENST00000399017.2	37	CCDS13651.1	197	0.0902014652014652	113	0.22967479674796748	51	0.1408839779005525	31	0.05419580419580419	2	0.002638522427440633	A	6.749	0.507112	0.12883	0.20699	0.001861	ENSG00000182670	ENST00000414818	.	.	.	5.42	0.33	0.15929	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.25717	P	0.9854106	.	.	.	.	.	.	T	0.17561	-1.0365	3	.	.	.	-5.4385	8.4056	0.32612	0.6847:0.0:0.3153:0.0	rs2835632;rs3737425	.	.	.	S	134	.	.	N	+	2	0	TTC3	37446096	0.645000	0.27286	0.218000	0.23776	0.987000	0.75469	1.103000	0.31062	-0.103000	0.12175	-0.274000	0.10170	AAT	A|0.931;G|0.069	0.069	strong		0.338	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		
HMCN1	83872	hgsc.bcm.edu	37	1	186057347	186057347	+	Silent	SNP	A	A	T	rs61745374	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:186057347A>T	ENST00000271588.4	+	62	9745	c.9516A>T	c.(9514-9516)acA>acT	p.T3172T	HMCN1_ENST00000367492.2_Silent_p.T3172T	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	3172	Ig-like C2-type 30.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TGACATTAACATGTGATGCCA	0.428													A|||	206	0.0411342	0.1498	0.0101	5008	,	,		17561	0.0		0.001	False		,,,				2504	0.0				p.T3172T		Atlas-SNP	.											.	HMCN1	797	.	0			c.A9516T						PASS	.	A		558,3848	250.9+/-257.8	49,460,1694	98.0	87.0	91.0		9516	-11.3	0.0	1	dbSNP_129	91	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	HMCN1	NM_031935.2		49,466,5988	TT,TA,AA		0.0698,12.6645,4.3365		3172/5636	186057347	564,12442	2203	4300	6503	SO:0001819	synonymous_variant	83872	exon62			ATTAACATGTGAT	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.9516A>T	1.37:g.186057347A>T		71.0	0.0	0		73.0	50.0	0.684932	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	37	CCDS30956.1																																																																																			A|0.953;T|0.047	0.047	strong		0.428	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
ALKBH8	91801	hgsc.bcm.edu	37	11	107427616	107427616	+	Silent	SNP	C	C	G	rs17107135	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:107427616C>G	ENST00000428149.2	-	3	394	c.243G>C	c.(241-243)ccG>ccC	p.P81P	ALKBH8_ENST00000389568.3_Silent_p.P81P|ALKBH8_ENST00000530933.1_5'UTR|ALKBH8_ENST00000417449.2_Silent_p.P84P|ALKBH8_ENST00000429370.1_Silent_p.P81P	NM_138775.2	NP_620130.2	Q96BT7	ALKB8_HUMAN	alkB, alkylation repair homolog 8 (E. coli)	81	RRM.				cellular response to DNA damage stimulus (GO:0006974)|tRNA methylation (GO:0030488)	cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|RNA binding (GO:0003723)|tRNA (uracil) methyltransferase activity (GO:0016300)			breast(2)|large_intestine(2)|lung(5)	9		Melanoma(852;0.000288)|Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00301)|all_epithelial(67;0.00512)|Breast(348;0.104)		BRCA - Breast invasive adenocarcinoma(274;3.53e-05)|Epithelial(105;0.00029)|all cancers(92;0.00518)		CAAATGAGTACGGCTTGTTAG	0.443													G|||	545	0.108826	0.3918	0.036	5008	,	,		14479	0.001		0.001	False		,,,				2504	0.0				p.P81P		Atlas-SNP	.											.	ALKBH8	88	.	0			c.G243C						PASS	.	G		1354,3048	692.3+/-405.5	220,914,1067	130.0	121.0	124.0		243	2.7	1.0	11	dbSNP_123	124	24,8572	818.1+/-406.9	0,24,4274	no	coding-synonymous	ALKBH8	NM_138775.2		220,938,5341	GG,GC,CC		0.2792,30.7587,10.6016		81/665	107427616	1378,11620	2201	4298	6499	SO:0001819	synonymous_variant	91801	exon3			TGAGTACGGCTTG	AF086489	CCDS8337.2, CCDS73376.1	11q22.3	2013-10-04			ENSG00000137760	ENSG00000137760	2.1.1.229	"""Alkylation repair homologs"", ""RNA binding motif (RRM) containing"""	25189	protein-coding gene	gene with protein product		613306				20123966	Standard	NM_138775		Approved	MGC10235	uc009yxp.3	Q96BT7	OTTHUMG00000157008	ENST00000428149.2:c.243G>C	11.37:g.107427616C>G		158.0	1.0	0.00632911		152.0	152.0	1	NM_138775	B1Q2M0|B4DEF6|Q8N989	Silent	SNP	ENST00000428149.2	37	CCDS8337.2																																																																																			C|0.896;G|0.104	0.104	strong		0.443	ALKBH8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000347071.2	NM_138775	
RUFY4	285180	hgsc.bcm.edu	37	2	218953991	218953991	+	Missense_Mutation	SNP	T	T	G	rs201137688	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:218953991T>G	ENST00000344321.7	+	12	2037	c.1519T>G	c.(1519-1521)Tgg>Ggg	p.W507G	RUFY4_ENST00000374155.3_Missense_Mutation_p.W527G|RUFY4_ENST00000441828.2_3'UTR	NM_198483.3	NP_940885.2	Q6ZNE9	RUFY4_HUMAN	RUN and FYVE domain containing 4	507							metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(1)	10		Renal(207;0.0915)		Epithelial(149;4.11e-06)|all cancers(144;0.000519)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		GGACCGCCTGTGGCAGAGGCT	0.527													T|||	2	0.000399361	0.0	0.0	5008	,	,		19104	0.0		0.001	False		,,,				2504	0.001				p.W507G		Atlas-SNP	.											.	RUFY4	59	.	0			c.T1519G						PASS	.	T	GLY/TRP	3,3833		0,3,1915	48.0	50.0	49.0		1519	4.9	1.0	2		49	14,8270		0,14,4128	yes	missense	RUFY4	NM_198483.3	184	0,17,6043	GG,GT,TT		0.169,0.0782,0.1403	probably-damaging	507/572	218953991	17,12103	1918	4142	6060	SO:0001583	missense	285180	exon12			CGCCTGTGGCAGA	AK128393		2q35	2007-01-29			ENSG00000188282	ENSG00000188282		"""Zinc fingers, FYVE domain containing"""	24804	protein-coding gene	gene with protein product							Standard	NM_198483		Approved	FLJ46536	uc010fvl.2	Q6ZNE9	OTTHUMG00000155235	ENST00000344321.7:c.1519T>G	2.37:g.218953991T>G	ENSP00000345900:p.Trp507Gly	141.0	0.0	0		183.0	74.0	0.404372	NM_198483	Q6ZR96	Missense_Mutation	SNP	ENST00000344321.7	37		.	.	.	.	.	.	.	.	.	.	T	16.23	3.064752	0.55432	7.82E-4	0.00169	ENSG00000188282	ENST00000344321;ENST00000374155	T;T	0.66280	1.15;-0.2	4.92	4.92	0.64577	Zinc finger, FYVE/PHD-type (1);	0.000000	0.49305	D	0.000154	T	0.76842	0.4044	M	0.80616	2.505	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.75545	-0.3280	10	0.27082	T	0.32	-16.7446	10.8813	0.46939	0.0:0.0:0.0:1.0	.	507	Q6ZNE9	RUFY4_HUMAN	G	507;527	ENSP00000345900:W507G;ENSP00000363270:W527G	ENSP00000345900:W507G	W	+	1	0	RUFY4	218662236	1.000000	0.71417	0.962000	0.40283	0.771000	0.43674	3.616000	0.54174	2.079000	0.62486	0.454000	0.30748	TGG	T|0.999;G|0.001	0.001	weak		0.527	RUFY4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_198483	
ADAMDEC1	27299	hgsc.bcm.edu	37	8	24261518	24261518	+	Silent	SNP	G	G	A	rs61731545	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24261518G>A	ENST00000256412.4	+	13	1543	c.1323G>A	c.(1321-1323)gaG>gaA	p.E441E	RP11-624C23.1_ENST00000519689.1_RNA|ADAMDEC1_ENST00000522298.1_Silent_p.E362E|RP11-624C23.1_ENST00000523578.1_RNA|ADAMDEC1_ENST00000538205.1_Silent_p.E362E	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	441	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				immune response (GO:0006955)|negative regulation of cell adhesion (GO:0007162)	extracellular region (GO:0005576)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|large_intestine(4)|skin(2)|stomach(1)	9		Prostate(55;0.0181)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)		CTTTGAAGGAGTGTACCAATC	0.433													A|||	87	0.0173722	0.0628	0.0058	5008	,	,		17414	0.0		0.0	False		,,,				2504	0.0				p.E441E	Ovarian(147;687 1849 3699 25981 31337)	Atlas-SNP	.											.	ADAMDEC1	69	.	0			c.G1323A						PASS	.	A	,,	259,4147	802.9+/-415.7	10,239,1954	210.0	177.0	188.0		1086,1086,1323	-2.6	0.7	8	dbSNP_129	188	2,8598	818.9+/-406.8	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	ADAMDEC1	NM_001145271.1,NM_001145272.1,NM_014479.3	,,	10,241,6252	AA,AG,GG		0.0233,5.8783,2.0068	,,	362/392,362/392,441/471	24261518	261,12745	2203	4300	6503	SO:0001819	synonymous_variant	27299	exon13			GAAGGAGTGTACC	Y13323	CCDS6044.1, CCDS55212.1	8p12	2008-08-07			ENSG00000134028	ENSG00000134028			16299	protein-coding gene	gene with protein product		606393				9271581, 12037602	Standard	NM_001145271		Approved	M12.219	uc003xdz.2	O15204	OTTHUMG00000097858	ENST00000256412.4:c.1323G>A	8.37:g.24261518G>A		113.0	0.0	0		121.0	61.0	0.504132	NM_014479	B7ZAK5	Silent	SNP	ENST00000256412.4	37	CCDS6044.1																																																																																			G|0.979;A|0.021	0.021	strong		0.433	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479	
CARD9	64170	hgsc.bcm.edu	37	9	139264827	139264827	+	Silent	SNP	C	C	T	rs115057256	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139264827C>T	ENST00000371732.5	-	6	1035	c.870G>A	c.(868-870)gcG>gcA	p.A290A	CARD9_ENST00000371734.3_Silent_p.A290A|CARD9_ENST00000460290.1_5'Flank|CARD9_ENST00000315908.7_Silent_p.A290A	NM_052813.4	NP_434700.2	Q9H257	CARD9_HUMAN	caspase recruitment domain family, member 9	290					defense response to Gram-positive bacterium (GO:0050830)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of apoptotic process (GO:0042981)|regulation of interleukin-2 biosynthetic process (GO:0045076)|regulation of interleukin-6 biosynthetic process (GO:0045408)|regulation of tumor necrosis factor biosynthetic process (GO:0042534)|response to drug (GO:0042493)|response to exogenous dsRNA (GO:0043330)|response to fungus (GO:0009620)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)	cytoplasm (GO:0005737)	CARD domain binding (GO:0050700)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)|prostate(3)|skin(1)	15		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;4.58e-06)|Epithelial(140;5.65e-06)		GGTCCCGCAGCGCCTGCCGCC	0.687													C|||	50	0.00998403	0.0363	0.0029	5008	,	,		16294	0.0		0.0	False		,,,				2504	0.0				p.A290A		Atlas-SNP	.											CARD9,NS,NS,-1,1	CARD9	47	1	0			c.G870A						PASS	.	C	,	145,4233	94.8+/-133.5	2,141,2046	33.0	36.0	35.0		870,870	-8.2	0.2	9	dbSNP_132	35	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous,coding-synonymous	CARD9	NM_052813.4,NM_052814.3	,	2,142,6343	TT,TC,CC		0.0116,3.312,1.1253	,	290/537,290/493	139264827	146,12828	2189	4298	6487	SO:0001819	synonymous_variant	64170	exon6			CCGCAGCGCCTGC	AF311287	CCDS6997.1, CCDS48057.1	9q34	2014-09-17			ENSG00000187796	ENSG00000187796			16391	protein-coding gene	gene with protein product		607212				11053425	Standard	NM_052813		Approved		uc004chg.3	Q9H257	OTTHUMG00000020925	ENST00000371732.5:c.870G>A	9.37:g.139264827C>T		87.0	0.0	0		91.0	71.0	0.78022	NM_052813	Q5SXM5|Q5SXM6|Q9H854	Silent	SNP	ENST00000371732.5	37	CCDS6997.1																																																																																			C|0.989;T|0.011	0.011	strong		0.687	CARD9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055053.1	NM_052813	
ATF4	468	hgsc.bcm.edu	37	22	39918323	39918323	+	Missense_Mutation	SNP	C	C	G	rs1803323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:39918323C>G	ENST00000337304.2	+	2	1654	c.772C>G	c.(772-774)Ccc>Gcc	p.P258A	ATF4_ENST00000396680.1_Missense_Mutation_p.P258A|ATF4_ENST00000404241.2_Missense_Mutation_p.P258A	NM_001675.2	NP_001666.2	P18848	ATF4_HUMAN	activating transcription factor 4	258			P -> A (in dbSNP:rs1803323).		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular amino acid metabolic process (GO:0006520)|cellular protein metabolic process (GO:0044267)|circadian regulation of gene expression (GO:0032922)|endoplasmic reticulum unfolded protein response (GO:0030968)|gamma-aminobutyric acid signaling pathway (GO:0007214)|gluconeogenesis (GO:0006094)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress (GO:1990440)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to endoplasmic reticulum stress (GO:0034976)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite membrane (GO:0032590)|Lewy body core (GO:1990037)|neuron projection (GO:0043005)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter sequence-specific DNA binding (GO:0001046)|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 RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	11	Melanoma(58;0.04)				Pseudoephedrine(DB00852)	GTCTGCCCGTCCCAAACCTTA	0.522													C|||	86	0.0171725	0.0628	0.0043	5008	,	,		19286	0.0		0.0	False		,,,				2504	0.0				p.P258A		Atlas-SNP	.											.	ATF4	27	.	0			c.C772G						PASS	.	C	ALA/PRO,ALA/PRO	169,4237	99.8+/-138.5	5,159,2039	24.0	25.0	24.0		772,772	2.0	0.2	22	dbSNP_89	24	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	ATF4	NM_001675.2,NM_182810.1	27,27	5,161,6337	GG,GC,CC		0.0233,3.8357,1.3148	possibly-damaging,possibly-damaging	258/352,258/352	39918323	171,12835	2203	4300	6503	SO:0001583	missense	468	exon2			GCCCGTCCCAAAC	D90209	CCDS13996.1	22q13.1	2013-05-23	2013-05-23		ENSG00000128272	ENSG00000128272		"""basic leucine zipper proteins"""	786	protein-coding gene	gene with protein product	"""tax-responsive enhancer element B67"""	604064	"""activating transcription factor 4 (tax-responsive enhancer element B67)"""	TXREB		1847461, 1534408	Standard	NM_182810		Approved	TAXREB67, CREB-2	uc003axz.3	P18848	OTTHUMG00000151099	ENST00000337304.2:c.772C>G	22.37:g.39918323C>G	ENSP00000336790:p.Pro258Ala	303.0	0.0	0		329.0	178.0	0.541033	NM_001675	Q9UH31	Missense_Mutation	SNP	ENST00000337304.2	37	CCDS13996.1	23	0.010531135531135532	23	0.046747967479674794	0	0.0	0	0.0	0	0.0	C	10.09	1.255962	0.22965	0.038357	2.33E-4	ENSG00000128272	ENST00000404241;ENST00000337304;ENST00000396680	T;T;T	0.24350	1.86;1.86;1.86	5.24	2.04	0.26737	.	0.251601	0.40640	N	0.001054	T	0.04998	0.0134	M	0.68952	2.095	0.28571	N	0.910626	P	0.48294	0.908	B	0.44224	0.444	T	0.03784	-1.1004	10	0.87932	D	0	-11.5679	9.0061	0.36113	0.0:0.6756:0.0:0.3244	rs1803323;rs52835171;rs1803323	258	P18848	ATF4_HUMAN	A	258	ENSP00000384587:P258A;ENSP00000336790:P258A;ENSP00000379912:P258A	ENSP00000336790:P258A	P	+	1	0	ATF4	38248269	0.003000	0.15002	0.178000	0.23040	0.066000	0.16364	0.129000	0.15830	0.219000	0.20840	0.462000	0.41574	CCC	C|0.987;G|0.013	0.013	strong		0.522	ATF4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321305.1	NM_001675	
SPEM1	374768	hgsc.bcm.edu	37	17	7324340	7324340	+	Missense_Mutation	SNP	G	G	A	rs61741352	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7324340G>A	ENST00000323675.3	+	3	371	c.346G>A	c.(346-348)Ggc>Agc	p.G116S	RP11-104H15.7_ENST00000575310.1_RNA	NM_199339.2	NP_955371.2	Q8N4L4	SPEM1_HUMAN	spermatid maturation 1	116					sperm individualization (GO:0007291)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	12		Prostate(122;0.173)				TCGCCGTCGAGGCTCTCCCAC	0.602													G|||	229	0.0457268	0.1672	0.0115	5008	,	,		18927	0.0		0.0	False		,,,				2504	0.0				p.G116S		Atlas-SNP	.											.	SPEM1	41	.	0			c.G346A						PASS	.	G	SER/GLY	547,3757		37,473,1642	70.0	76.0	74.0		346	2.7	0.0	17	dbSNP_129	74	3,8483		0,3,4240	yes	missense	SPEM1	NM_199339.2	56	37,476,5882	AA,AG,GG		0.0354,12.7091,4.3002	possibly-damaging	116/310	7324340	550,12240	2152	4243	6395	SO:0001583	missense	374768	exon3			CGTCGAGGCTCTC	AK097400	CCDS42254.1	17p13.1	2011-12-12	2008-02-04	2008-02-04	ENSG00000181323	ENSG00000181323			32429	protein-coding gene	gene with protein product		615116	"""chromosome 17 open reading frame 83"""	C17orf83		17426145, 20558241, 21184802	Standard	NM_199339		Approved	FLJ40081	uc002ggv.3	Q8N4L4		ENST00000323675.3:c.346G>A	17.37:g.7324340G>A	ENSP00000315554:p.Gly116Ser	134.0	0.0	0		165.0	74.0	0.448485	NM_199339		Missense_Mutation	SNP	ENST00000323675.3	37	CCDS42254.1	83	0.038003663003663	78	0.15853658536585366	5	0.013812154696132596	0	0.0	0	0.0	G	10.79	1.449713	0.26074	0.127091	3.54E-4	ENSG00000181323	ENST00000323383;ENST00000323675	.	.	.	4.7	2.67	0.31697	.	1.055190	0.07527	N	0.911526	T	0.00109	0.0003	L	0.32530	0.975	0.09310	N	1	B	0.32829	0.386	B	0.31101	0.124	T	0.12528	-1.0544	9	0.46703	T	0.11	-0.4131	6.202	0.20581	0.1006:0.1883:0.7111:0.0	rs61741352	116	Q8N4L4	SPEM1_HUMAN	S	65;116	.	ENSP00000315511:G65S	G	+	1	0	SPEM1	7265064	0.004000	0.15560	0.001000	0.08648	0.146000	0.21551	1.315000	0.33608	0.566000	0.29273	0.655000	0.94253	GGC	G|0.962;A|0.038	0.038	strong		0.602	SPEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440932.1	NM_199339	
DIDO1	11083	hgsc.bcm.edu	37	20	61525488	61525488	+	Silent	SNP	A	A	G	rs112062101	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61525488A>G	ENST00000266070.4	-	12	2956	c.2631T>C	c.(2629-2631)tcT>tcC	p.S877S	DIDO1_ENST00000395340.1_Silent_p.S877S|DIDO1_ENST00000395335.2_Silent_p.S877S|DIDO1_ENST00000395343.1_Silent_p.S877S	NM_033081.2	NP_149072.2	Q9BTC0	DIDO1_HUMAN	death inducer-obliterator 1	877					apoptotic signaling pathway (GO:0097190)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(6)|breast(5)|central_nervous_system(1)|cervix(3)|endometrium(6)|kidney(1)|large_intestine(17)|lung(39)|ovary(8)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)	99	Breast(26;5.68e-08)					CTTTCTTAACAGAAGCTGACA	0.517													A|||	38	0.00758786	0.0265	0.0043	5008	,	,		19309	0.0		0.0	False		,,,				2504	0.0				p.S877S	Melanoma(25;381 482 3385 5362 7955 17159 17174 40604 47095)	Atlas-SNP	.											DIDO1,NS,carcinoma,-1,1	DIDO1	321	1	0			c.T2631C						PASS	.	A	,,,	111,4295	80.9+/-119.3	0,111,2092	102.0	117.0	112.0		2631,2631,2631,2631	-5.0	0.0	20	dbSNP_132	112	1,8593		0,1,4296	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DIDO1	NM_001193369.1,NM_001193370.1,NM_033081.2,NM_080797.3	,,,	0,112,6388	GG,GA,AA		0.0116,2.5193,0.8615	,,,	877/2241,877/1190,877/2241,877/1190	61525488	112,12888	2203	4297	6500	SO:0001819	synonymous_variant	11083	exon12			CTTAACAGAAGCT	AB002331	CCDS13508.2, CCDS13509.1, CCDS33506.1	20q13.33	2013-01-28	2005-11-11	2005-11-11	ENSG00000101191	ENSG00000101191		"""Zinc fingers, PHD-type"""	2680	protein-coding gene	gene with protein product		604140	"""chromosome 20 open reading frame 158"", ""death associated transcription factor 1"""	C20orf158, DATF1		10393935	Standard	NM_033081		Approved	DIO1, dJ885L7.8, FLJ11265, KIAA0333, DIO-1, BYE1	uc002ydr.2	Q9BTC0	OTTHUMG00000032945	ENST00000266070.4:c.2631T>C	20.37:g.61525488A>G		82.0	0.0	0		79.0	39.0	0.493671	NM_080797	A8MY65|B9EH82|E1P5I1|O15043|Q3ZTL7|Q3ZTL8|Q4VXS1|Q4VXS2|Q4VXV8|Q4VXV9|Q96D72|Q9BQW0|Q9BW03|Q9H4G6|Q9H4G7|Q9NTU8|Q9NUM8|Q9UFB6	Silent	SNP	ENST00000266070.4	37	CCDS33506.1																																																																																			A|0.994;G|0.006	0.006	strong		0.517	DIDO1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080091.2	NM_080796	
GPRIN3	285513	hgsc.bcm.edu	37	4	90169025	90169025	+	Missense_Mutation	SNP	C	C	T	rs17015286	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:90169025C>T	ENST00000609438.1	-	2	2755	c.2237G>A	c.(2236-2238)aGa>aAa	p.R746K	GPRIN3_ENST00000333209.4_Missense_Mutation_p.R746K	NM_198281.2	NP_938022.2	Q6ZVF9	GRIN3_HUMAN	GPRIN family member 3	746			R -> K (in dbSNP:rs17015286).							breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|prostate(2)|skin(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;5.67e-05)		CTGCCTTCCTCTGAGCTTCTT	0.468													T|||	299	0.0597045	0.2163	0.0173	5008	,	,		17742	0.0		0.0	False		,,,				2504	0.001				p.R746K		Atlas-SNP	.											.	GPRIN3	90	.	0			c.G2237A						PASS	.	T	LYS/ARG	800,3606	751.2+/-412.2	79,642,1482	108.0	110.0	109.0		2237	5.3	1.0	4	dbSNP_123	109	16,8584	818.7+/-406.8	0,16,4284	yes	missense	GPRIN3	NM_198281.2	26	79,658,5766	TT,TC,CC		0.186,18.1571,6.274	benign	746/777	90169025	816,12190	2203	4300	6503	SO:0001583	missense	285513	exon2			CTTCCTCTGAGCT	AK124616	CCDS34030.1	4q22.1	2006-08-24				ENSG00000185477			27733	protein-coding gene	gene with protein product		611241				15488195	Standard	NM_198281		Approved	GRIN3, FLJ42625	uc003hsm.1	Q6ZVF9		ENST00000609438.1:c.2237G>A	4.37:g.90169025C>T	ENSP00000476603:p.Arg746Lys	169.0	0.0	0		176.0	92.0	0.522727	NM_198281	Q8IVE4	Missense_Mutation	SNP	ENST00000609438.1	37	CCDS34030.1	112	0.05128205128205128	107	0.21747967479674796	5	0.013812154696132596	0	0.0	0	0.0	T	9.991	1.230900	0.22542	0.181571	0.00186	ENSG00000185477	ENST00000333209	T	0.19394	2.15	5.26	5.26	0.73747	.	0.000000	0.36234	N	0.002708	T	0.00012	0.0000	N	0.01228	-0.945	0.49130	P	2.4299999999999322E-4	B	0.02656	0.0	B	0.01281	0.0	T	0.33420	-0.9869	9	0.02654	T	1	-13.2449	11.2596	0.49074	0.0:0.0711:0.0:0.9289	rs17015286;rs52823204;rs56606122;rs61213802;rs17015286	746	Q6ZVF9	GRIN3_HUMAN	K	746	ENSP00000328672:R746K	ENSP00000328672:R746K	R	-	2	0	GPRIN3	90388048	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	4.662000	0.61525	1.023000	0.39654	-0.254000	0.11334	AGA	C|0.933;T|0.067	0.067	strong		0.468	GPRIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363540.2	NM_198281	
GSDMC	56169	hgsc.bcm.edu	37	8	130762732	130762732	+	Missense_Mutation	SNP	T	T	C	rs76700535	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:130762732T>C	ENST00000276708.4	-	11	1909	c.1028A>G	c.(1027-1029)tAc>tGc	p.Y343C		NM_031415.2	NP_113603.1	Q9BYG8	GSDMC_HUMAN	gasdermin C	343						cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)				autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	26						CAGGATACTGTAGAACATGAC	0.473													T|||	53	0.0105831	0.0393	0.0014	5008	,	,		20490	0.0		0.0	False		,,,				2504	0.0				p.Y343C		Atlas-SNP	.											.	GSDMC	71	.	0			c.A1028G						PASS	.	T	CYS/TYR	190,4216	120.0+/-157.7	6,178,2019	136.0	119.0	125.0		1028	-4.0	0.0	8	dbSNP_131	125	1,8599	1.2+/-3.3	0,1,4299	yes	missense	GSDMC	NM_031415.2	194	6,179,6318	CC,CT,TT		0.0116,4.3123,1.4686	probably-damaging	343/509	130762732	191,12815	2203	4300	6503	SO:0001583	missense	56169	exon11			ATACTGTAGAACA	AB042405	CCDS6360.1	8q24.21	2014-05-14	2008-07-31	2008-07-31	ENSG00000147697	ENSG00000147697			7151	protein-coding gene	gene with protein product		608384	"""melanoma-derived leucine zipper, extra-nuclear factor"""	MLZE		17350798	Standard	NM_031415		Approved		uc003ysr.3	Q9BYG8	OTTHUMG00000164851	ENST00000276708.4:c.1028A>G	8.37:g.130762732T>C	ENSP00000276708:p.Tyr343Cys	101.0	0.0	0		117.0	47.0	0.401709	NM_031415	Q5XKF3|Q6P494	Missense_Mutation	SNP	ENST00000276708.4	37	CCDS6360.1	25	0.011446886446886446	25	0.0508130081300813	0	0.0	0	0.0	0	0.0	T	9.583	1.124120	0.20959	0.043123	1.16E-4	ENSG00000147697	ENST00000276708	T	0.22134	1.97	5.14	-4.01	0.04045	.	1.565630	0.03508	N	0.219111	T	0.02688	0.0081	N	0.08118	0	0.09310	N	1	D	0.59357	0.985	P	0.55667	0.781	T	0.12993	-1.0526	10	0.38643	T	0.18	.	8.1941	0.31385	0.0:0.1621:0.5701:0.2678	.	343	Q9BYG8	GSDMC_HUMAN	C	343	ENSP00000276708:Y343C	ENSP00000276708:Y343C	Y	-	2	0	GSDMC	130831914	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-0.577000	0.05847	-0.432000	0.07297	-0.389000	0.06534	TAC	T|0.985;C|0.015	0.015	strong		0.473	GSDMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380586.1		
APOBEC3B	9582	hgsc.bcm.edu	37	22	39381957	39381957	+	Silent	SNP	C	C	T	rs150187552	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:39381957C>T	ENST00000333467.3	+	3	360	c.315C>T	c.(313-315)gcC>gcT	p.A105A	APOBEC3B_ENST00000407298.3_Silent_p.A105A|APOBEC3B_ENST00000402182.3_Silent_p.A105A	NM_001270411.1|NM_004900.4	NP_001257340.1|NP_004891	Q9UH17	ABC3B_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B	105					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)					CGAAGCTGGCCGAATTCCTGT	0.572													C|||	20	0.00399361	0.0151	0.0	5008	,	,		14653	0.0		0.0	False		,,,				2504	0.0				p.A105A		Atlas-SNP	.											.	APOBEC3B	32	.	0			c.C315T						PASS	.	C		28,4376		3,22,2177	156.0	149.0	151.0		315	-4.2	0.0	22	dbSNP_134	151	0,8596		0,0,4298	no	coding-synonymous	APOBEC3B	NM_004900.3		3,22,6475	TT,TC,CC		0.0,0.6358,0.2154		105/383	39381957	28,12972	2202	4298	6500	SO:0001819	synonymous_variant	9582	exon3			GCTGGCCGAATTC	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.315C>T	22.37:g.39381957C>T		306.0	0.0	0		323.0	112.0	0.346749	NM_004900	B0QYD2|O95618|Q20WL1|Q5IFJ4|Q7Z2N3|Q7Z6D6|Q9UE74	Silent	SNP	ENST00000333467.3	37	CCDS13982.1																																																																																			C|0.998;T|0.002	0.002	strong		0.572	APOBEC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321233.1	NM_004900	
CILP	8483	hgsc.bcm.edu	37	15	65496624	65496624	+	Missense_Mutation	SNP	C	C	G	rs140625947	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:65496624C>G	ENST00000261883.4	-	6	1067	c.901G>C	c.(901-903)Gca>Cca	p.A301P		NM_003613.3	NP_003604	O75339	CILP1_HUMAN	cartilage intermediate layer protein, nucleotide pyrophosphohydrolase	301					negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				breast(5)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(14)|lung(17)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|urinary_tract(1)	55						ACAAACTCTGCCTTGATGGTG	0.473													C|||	13	0.00259585	0.0008	0.0	5008	,	,		20367	0.0119		0.0	False		,,,				2504	0.0				p.A301P		Atlas-SNP	.											.	CILP	124	.	0			c.G901C						PASS	.	C	PRO/ALA	4,4398	8.1+/-20.4	0,4,2197	83.0	82.0	83.0		901	5.6	0.8	15	dbSNP_134	83	0,8598		0,0,4299	yes	missense	CILP	NM_003613.3	27	0,4,6496	GG,GC,CC		0.0,0.0909,0.0308	possibly-damaging	301/1185	65496624	4,12996	2201	4299	6500	SO:0001583	missense	8483	exon6			ACTCTGCCTTGAT	AY358904	CCDS10203.1	15q22	2013-01-14			ENSG00000138615	ENSG00000138615		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1980	protein-coding gene	gene with protein product		603489				9722584, 9722583	Standard	NM_003613		Approved	HsT18872	uc002aon.2	O75339	OTTHUMG00000133140	ENST00000261883.4:c.901G>C	15.37:g.65496624C>G	ENSP00000261883:p.Ala301Pro	137.0	0.0	0		164.0	75.0	0.457317	NM_003613	B2R8F7|Q6UW99|Q8IYI5	Missense_Mutation	SNP	ENST00000261883.4	37	CCDS10203.1	7	0.003205128205128205	1	0.0020325203252032522	0	0.0	6	0.01048951048951049	0	0.0	C	18.99	3.738884	0.69304	9.09E-4	0.0	ENSG00000138615	ENST00000261883	T	0.40476	1.03	5.63	5.63	0.86233	.	0.163750	0.52532	D	0.000061	T	0.37019	0.0988	L	0.50333	1.59	0.43058	D	0.994673	P	0.50943	0.94	B	0.44044	0.439	T	0.44862	-0.9300	10	0.72032	D	0.01	-27.6493	18.6742	0.91523	0.0:1.0:0.0:0.0	.	301	O75339	CILP1_HUMAN	P	301	ENSP00000261883:A301P	ENSP00000261883:A301P	A	-	1	0	CILP	63283677	0.983000	0.35010	0.798000	0.32154	0.651000	0.38670	2.711000	0.47177	2.659000	0.90383	0.563000	0.77884	GCA	C|0.999;G|0.001	0.001	strong		0.473	CILP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256829.1	NM_003613	
ELOVL5	60481	hgsc.bcm.edu	37	6	53159233	53159233	+	Intron	SNP	G	G	A	rs9474477	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:53159233G>A	ENST00000542638.1	-	2	506				ELOVL5_ENST00000304434.6_Intron|ELOVL5_ENST00000486973.1_Intron|ELOVL5_ENST00000370913.5_Silent_p.L39L|ELOVL5_ENST00000541407.1_Intron|ELOVL5_ENST00000370918.4_Intron			Q9NYP7	ELOV5_HUMAN	ELOVL fatty acid elongase 5						alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|fatty acid elongation, monounsaturated fatty acid (GO:0034625)|fatty acid elongation, polyunsaturated fatty acid (GO:0034626)|linoleic acid metabolic process (GO:0043651)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|unsaturated fatty acid biosynthetic process (GO:0006636)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	fatty acid elongase activity (GO:0009922)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	7	Lung NSC(77;0.116)					agctgctgtagccatcctaca	0.453													G|||	126	0.0251597	0.0938	0.0014	5008	,	,		20012	0.0		0.001	False		,,,				2504	0.0				p.L39L		Atlas-SNP	.											.	ELOVL5	25	.	0			c.C115T						PASS	.	G	,,,	68,1520		1,66,727	3.0	3.0	3.0		,,115,	2.0	0.0	6	dbSNP_119	3	4,3590		0,4,1793	no	intron,intron,coding-synonymous,intron	ELOVL5	NM_001242828.1,NM_001242830.1,NM_001242831.1,NM_021814.4	,,,	1,70,2520	AA,AG,GG		0.1113,4.2821,1.3894	,,,	,,39/89,	53159233	72,5110	794	1797	2591	SO:0001627	intron_variant	60481	exon3			GCTGTAGCCATCC	AF052129	CCDS4951.1, CCDS56433.1, CCDS56434.1, CCDS75470.1	6p21.1-p12.1	2014-07-30	2011-05-25		ENSG00000012660	ENSG00000012660			21308	protein-coding gene	gene with protein product		611805	"""ELOVL family member 5, elongation of long chain fatty acids (FEN1/Elo2, SUR4/Elo3-like, yeast)"", ""spinocerebellar ataxia 38"""	SCA38		10970790, 25065913	Standard	NM_021814		Approved	HELO1, dJ483K16.1	uc011dwx.2	Q9NYP7	OTTHUMG00000016249	ENST00000542638.1:c.58+1206C>T	6.37:g.53159233G>A		124.0	0.0	0		139.0	76.0	0.546763	NM_001242831	B4DZJ2|F6SH78|Q59EL3|Q5TGH5|Q6NXE7|Q7L2S5|Q8NCG4|Q9UI22	Silent	SNP	ENST00000542638.1	37	CCDS4951.1																																																																																			G|0.973;A|0.027	0.027	strong		0.453	ELOVL5-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043566.1	NM_021814	
RFX7	64864	hgsc.bcm.edu	37	15	56387421	56387421	+	Silent	SNP	T	T	C	rs34255389	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:56387421T>C	ENST00000559447.2	-	9	2485	c.2214A>G	c.(2212-2214)ctA>ctG	p.L738L	RFX7_ENST00000317318.6_Silent_p.L835L|RFX7_ENST00000422057.1_Silent_p.L738L|RFX7_ENST00000423270.1_Silent_p.L835L			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	738					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						TCTGGCTATGTAGCTGCTGGC	0.393													T|||	16	0.00319489	0.0113	0.0014	5008	,	,		20635	0.0		0.0	False		,,,				2504	0.0				p.L835L		Atlas-SNP	.											.	RFX7	170	.	0			c.A2505G						PASS	.	T		40,3758		0,40,1859	115.0	113.0	114.0		2505	-10.9	0.0	15	dbSNP_126	114	0,8254		0,0,4127	no	coding-synonymous	RFX7	NM_022841.5		0,40,5986	CC,CT,TT		0.0,1.0532,0.3319		835/1461	56387421	40,12012	1899	4127	6026	SO:0001819	synonymous_variant	64864	exon9			GCTATGTAGCTGC			15q21.3	2008-08-04	2008-08-04	2008-08-04		ENSG00000181827			25777	protein-coding gene	gene with protein product		612660	"""regulatory factor X domain containing 2"""	RFXDC2			Standard	NM_022841		Approved	FLJ12994	uc010bfn.3	Q2KHR2		ENST00000559447.2:c.2214A>G	15.37:g.56387421T>C		137.0	0.0	0		172.0	82.0	0.476744	NM_022841	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Silent	SNP	ENST00000559447.2	37																																																																																				T|0.996;C|0.004	0.004	strong		0.393	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841	
SVEP1	79987	hgsc.bcm.edu	37	9	113149612	113149612	+	Missense_Mutation	SNP	T	T	C	rs114581956	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:113149612T>C	ENST00000401783.2	-	42	10349	c.10013A>G	c.(10012-10014)cAc>cGc	p.H3338R	SVEP1_ENST00000374469.1_Missense_Mutation_p.H3315R|SVEP1_ENST00000297826.5_Missense_Mutation_p.H1264R	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	3338	Sushi 32. {ECO:0000255|PROSITE- ProRule:PRU00302}.				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						TTCTGTGCAGTGTGCCTCAGA	0.468													T|||	47	0.00938498	0.0333	0.0029	5008	,	,		17065	0.0		0.001	False		,,,				2504	0.0				p.H3338R		Atlas-SNP	.											.	SVEP1	326	.	0			c.A10013G						PASS	.	T	ARG/HIS	94,3784		1,92,1846	140.0	140.0	140.0		10013	1.4	0.0	9	dbSNP_132	140	0,8258		0,0,4129	yes	missense	SVEP1	NM_153366.3	29	1,92,5975	CC,CT,TT		0.0,2.4239,0.7746	benign	3338/3572	113149612	94,12042	1939	4129	6068	SO:0001583	missense	79987	exon42			GTGCAGTGTGCCT	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.10013A>G	9.37:g.113149612T>C	ENSP00000384917:p.His3338Arg	247.0	0.0	0		241.0	80.0	0.33195	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	27	0.012362637362637362	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	3.480	-0.106077	0.06924	0.024239	0.0	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826	T;T;T	0.63580	-0.05;-0.05;-0.05	5.09	1.42	0.22433	Complement control module (2);Sushi/SCR/CCP (3);	0.889971	0.09909	N	0.740049	T	0.08133	0.0203	N	0.11892	0.195	0.09310	N	0.999999	B	0.18013	0.025	B	0.22152	0.038	T	0.09662	-1.0664	10	0.21014	T	0.42	.	3.9589	0.09403	0.1226:0.0714:0.1426:0.6634	.	3338	Q4LDE5	SVEP1_HUMAN	R	3338;3315;1264	ENSP00000384917:H3338R;ENSP00000363593:H3315R;ENSP00000297826:H1264R	ENSP00000297826:H1264R	H	-	2	0	SVEP1	112189433	0.005000	0.15991	0.021000	0.16686	0.386000	0.30323	1.484000	0.35508	0.055000	0.16094	0.529000	0.55759	CAC	T|0.987;C|0.013	0.013	strong		0.468	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
CAPN14	440854	hgsc.bcm.edu	37	2	31417290	31417290	+	Missense_Mutation	SNP	T	T	C	rs76523220	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:31417290T>C	ENST00000403897.3	-	9	1076	c.935A>G	c.(934-936)aAt>aGt	p.N312S	CAPN14_ENST00000444918.2_Missense_Mutation_p.N312S	NM_001145122.1	NP_001138594.1	A8MX76	CAN14_HUMAN	calpain 14	312	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(1)|endometrium(2)|prostate(1)|skin(1)|stomach(2)	7						TTCTCCGTCATTGTCTTTCCT	0.448													T|||	210	0.0419329	0.1112	0.0245	5008	,	,		19529	0.0		0.0378	False		,,,				2504	0.0082				p.N312S		Atlas-SNP	.											.	CAPN14	36	.	0			c.A935G						PASS	.	T	SER/ASN	157,1227		12,133,547	87.0	80.0	82.0		935	3.6	0.5	2	dbSNP_131	82	92,3090		4,84,1503	yes	missense	CAPN14	NM_001145122.1	46	16,217,2050	CC,CT,TT		2.8913,11.3439,5.4534	benign	312/685	31417290	249,4317	692	1591	2283	SO:0001583	missense	440854	exon9			CCGTCATTGTCTT	AC015980	CCDS46254.1	2p23.1-p21	2013-01-10			ENSG00000214711	ENSG00000214711		"""EF-hand domain containing"""	16664	protein-coding gene	gene with protein product		610229				11675017	Standard	NM_001145122		Approved		uc010yms.2	A8MX76	OTTHUMG00000152039	ENST00000403897.3:c.935A>G	2.37:g.31417290T>C	ENSP00000385247:p.Asn312Ser	64.0	0.0	0		73.0	37.0	0.506849	NM_001145122	B3KRU9	Missense_Mutation	SNP	ENST00000403897.3	37	CCDS46254.1	85	0.03891941391941392	45	0.09146341463414634	12	0.03314917127071823	0	0.0	28	0.036939313984168866	T	12.26	1.885840	0.33348	0.113439	0.028913	ENSG00000214711	ENST00000444918;ENST00000403897	D;D	0.97352	-4.35;-4.35	3.61	3.61	0.41365	Peptidase C2, calpain, catalytic domain (3);	0.309811	0.29046	U	0.013315	T	0.26702	0.0653	N	0.14661	0.345	0.32099	N	0.590856	B;B	0.30563	0.285;0.187	B;B	0.28916	0.096;0.04	T	0.75439	-0.3317	10	0.87932	D	0	.	12.5311	0.56115	0.0:0.0:0.0:1.0	.	312;136	A8MX76;A8MX76-2	CAN14_HUMAN;.	S	312	ENSP00000398670:N312S;ENSP00000385247:N312S	ENSP00000385247:N312S	N	-	2	0	CAPN14	31270794	0.993000	0.37304	0.453000	0.27007	0.636000	0.38137	5.177000	0.65032	1.411000	0.46957	0.533000	0.62120	AAT	T|0.964;C|0.036	0.036	strong		0.448	CAPN14-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325010.1	NM_001145122	
FBLIM1	54751	hgsc.bcm.edu	37	1	16091700	16091700	+	Silent	SNP	G	G	A	rs61733331	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:16091700G>A	ENST00000375766.3	+	3	862	c.222G>A	c.(220-222)ccG>ccA	p.P74P	FBLIM1_ENST00000441801.2_Silent_p.P74P|FBLIM1_ENST00000332305.5_Silent_p.P74P|FBLIM1_ENST00000400773.1_Silent_p.P74P|FBLIM1_ENST00000375771.1_Silent_p.P74P	NM_017556.2	NP_060026.2	Q8WUP2	FBLI1_HUMAN	filamin binding LIM protein 1	74	Intrinsically disordered.|Pro-rich.				cell junction assembly (GO:0034329)|regulation of cell shape (GO:0008360)|regulation of integrin activation (GO:0033623)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|stress fiber (GO:0001725)	filamin binding (GO:0031005)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	16		Colorectal(325;0.000257)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.56e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|READ - Rectum adenocarcinoma(331;0.0649)|STAD - Stomach adenocarcinoma(313;0.138)		CCACAGTGCCGGCTGCACCTA	0.662													A|||	84	0.0167732	0.0477	0.0043	5008	,	,		13729	0.0069		0.002	False		,,,				2504	0.0092				p.P74P		Atlas-SNP	.											.	FBLIM1	46	.	0			c.G222A						PASS	.	A	,,	157,4227		2,153,2037	21.0	24.0	23.0		222,222,222	-2.8	0.0	1	dbSNP_129	23	18,8566		0,18,4274	no	coding-synonymous,coding-synonymous,coding-synonymous	FBLIM1	NM_001024215.1,NM_001024216.1,NM_017556.2	,,	2,171,6311	AA,AG,GG		0.2097,3.5812,1.3495	,,	74/375,74/277,74/374	16091700	175,12793	2192	4292	6484	SO:0001819	synonymous_variant	54751	exon2			AGTGCCGGCTGCA		CCDS163.1, CCDS30609.1, CCDS44064.1	1p36.13	2014-04-07			ENSG00000162458	ENSG00000162458			24686	protein-coding gene	gene with protein product		607747				12679033, 12496242	Standard	XM_005245900		Approved	FBLP-1, CAL, migfilin	uc001axe.1	Q8WUP2	OTTHUMG00000003079	ENST00000375766.3:c.222G>A	1.37:g.16091700G>A		117.0	0.0	0		123.0	67.0	0.544715	NM_001024215	B3KNY0|Q5VVE0|Q5VVE1|Q8IX23|Q96T00|Q9UFD6	Silent	SNP	ENST00000375766.3	37	CCDS163.1																																																																																			G|0.988;A|0.012	0.012	strong		0.662	FBLIM1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008511.3	NM_001024215	
SLC16A6	9120	hgsc.bcm.edu	37	17	66267734	66267734	+	Silent	SNP	T	T	C	rs61740584	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:66267734T>C	ENST00000327268.4	-	6	731	c.567A>G	c.(565-567)ctA>ctG	p.L189L	SLC16A6_ENST00000580666.1_Silent_p.L189L|ARSG_ENST00000448504.2_Intron	NM_001174166.1	NP_001167637.1	O15403	MOT7_HUMAN	solute carrier family 16, member 6	189					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)			large_intestine(3)|lung(8)|prostate(1)|skin(1)|urinary_tract(2)	15	all_cancers(12;1.24e-09)		BRCA - Breast invasive adenocarcinoma(8;3.17e-08)|LUSC - Lung squamous cell carcinoma(166;0.24)		Pyruvic acid(DB00119)	TGTTTAACTGTAGTAGGCCCA	0.473													T|||	118	0.0235623	0.087	0.0043	5008	,	,		18475	0.0		0.0	False		,,,				2504	0.0				p.L189L		Atlas-SNP	.											.	SLC16A6	56	.	0			c.A567G						PASS	.	T	,,	400,4006	199.1+/-222.7	18,364,1821	76.0	73.0	74.0		567,567,	-2.4	0.3	17	dbSNP_129	74	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,intron	SLC16A6,ARSG	NM_001174166.1,NM_004694.4,NM_014960.3	,,	18,365,6120	CC,CT,TT		0.0116,9.0785,3.0832	,,	189/524,189/524,	66267734	401,12605	2203	4300	6503	SO:0001819	synonymous_variant	9120	exon6			TAACTGTAGTAGG	U79745	CCDS11675.1	17q24.2	2013-07-18	2013-07-18		ENSG00000108932	ENSG00000108932		"""Solute carriers"""	10927	protein-coding gene	gene with protein product		603880	"""solute carrier family 16 (monocarboxylic acid transporters), member 6"", ""solute carrier family 16, member 6 (monocarboxylic acid transporter 7)"""			9425115	Standard	NM_004694		Approved	MCT6, MCT7	uc002jgz.2	O15403	OTTHUMG00000179812	ENST00000327268.4:c.567A>G	17.37:g.66267734T>C		134.0	0.0	0		119.0	54.0	0.453782	NM_001174166	Q6P1X3	Silent	SNP	ENST00000327268.4	37	CCDS11675.1																																																																																			T|0.969;C|0.031	0.031	strong		0.473	SLC16A6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448323.1	NM_004694	
CHD1L	9557	hgsc.bcm.edu	37	1	146763171	146763171	+	Missense_Mutation	SNP	T	T	A	rs61756300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:146763171T>A	ENST00000369258.4	+	20	2348	c.2328T>A	c.(2326-2328)agT>agA	p.S776R	CHD1L_ENST00000467213.1_3'UTR|CHD1L_ENST00000369259.3_Missense_Mutation_p.S572R|CHD1L_ENST00000361293.5_Missense_Mutation_p.S495R|CHD1L_ENST00000431239.1_Missense_Mutation_p.S682R	NM_001256336.1|NM_004284.4|NM_024568.2	NP_001243265.1|NP_004275.4|NP_078844.2	Q86WJ1	CHD1L_HUMAN	chromodomain helicase DNA binding protein 1-like	776	Macro. {ECO:0000255|PROSITE- ProRule:PRU00490}.				ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|nucleotide binding (GO:0000166)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(923;0.0487)					CAGACCTGAGTTTGGGAGGTG	0.403													T|||	101	0.0201677	0.0749	0.0029	5008	,	,		20473	0.0		0.0	False		,,,				2504	0.0				p.S776R		Atlas-SNP	.											.	CHD1L	72	.	0			c.T2328A						PASS	.	T	ARG/SER	265,4141	152.5+/-186.2	6,253,1944	196.0	162.0	173.0		2328	4.6	1.0	1	dbSNP_129	173	6,8594	4.3+/-15.6	0,6,4294	yes	missense	CHD1L	NM_004284.3	110	6,259,6238	AA,AT,TT		0.0698,6.0145,2.0837	benign	776/898	146763171	271,12735	2203	4300	6503	SO:0001583	missense	9557	exon20			CCTGAGTTTGGGA	AF054177	CCDS927.1, CCDS58021.1, CCDS58022.1, CCDS72882.1	1q21.1	2008-02-05			ENSG00000131778	ENSG00000131778			1916	protein-coding gene	gene with protein product		613039				9653160	Standard	NM_004284		Approved	ALC1	uc001epm.5	Q86WJ1	OTTHUMG00000150271	ENST00000369258.4:c.2328T>A	1.37:g.146763171T>A	ENSP00000358262:p.Ser776Arg	383.0	0.0	0		378.0	182.0	0.481481	NM_004284	A5YM64|B4DDE1|B5MDZ7|Q53EZ3|Q5VXX7|Q6DD94|Q6PK83|Q86XH3|Q96HF7|Q96SP3|Q9BVJ1|Q9NVV8	Missense_Mutation	SNP	ENST00000369258.4	37	CCDS927.1	30	0.013736263736263736	28	0.056910569105691054	2	0.0055248618784530384	0	0.0	0	0.0	T	12.55	1.970529	0.34754	0.060145	6.98E-4	ENSG00000131778	ENST00000431239;ENST00000369259;ENST00000369258;ENST00000361293	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	5.82	4.63	0.57726	Appr-1-p processing (1);	0.600804	0.20767	N	0.086044	T	0.11836	0.0288	N	0.25647	0.755	0.26362	N	0.977023	P;B;B	0.40476	0.718;0.063;0.032	B;B;B	0.35470	0.203;0.055;0.021	T	0.04650	-1.0936	10	0.23302	T	0.38	.	9.3476	0.38118	0.0:0.0:0.1803:0.8197	rs61756300	682;572;776	Q86WJ1-2;Q86WJ1-3;Q86WJ1	.;.;CHD1L_HUMAN	R	682;572;776;495	ENSP00000389031:S682R;ENSP00000358263:S572R;ENSP00000358262:S776R;ENSP00000355100:S495R	ENSP00000355100:S495R	S	+	3	2	CHD1L	145229795	0.305000	0.24481	1.000000	0.80357	0.902000	0.53008	0.451000	0.21779	2.223000	0.72356	0.454000	0.30748	AGT	T|0.984;A|0.016	0.016	strong		0.403	CHD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040377.1	NM_004284	
MIPEP	4285	hgsc.bcm.edu	37	13	24463414	24463414	+	Missense_Mutation	SNP	C	C	A	rs112735196	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:24463414C>A	ENST00000382172.3	-	1	144	c.46G>T	c.(46-48)Gct>Tct	p.A16S	C1QTNF9B_ENST00000556521.1_5'Flank|C1QTNF9B-AS1_ENST00000417034.1_RNA|MIPEP_ENST00000469167.1_5'UTR|C1QTNF9B-AS1_ENST00000435039.2_RNA|C1QTNF9B-AS1_ENST00000382133.4_RNA	NM_005932.3	NP_005923	Q99797	MIPEP_HUMAN	mitochondrial intermediate peptidase	16					protein processing involved in protein targeting to mitochondrion (GO:0006627)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|liver(1)|lung(12)|prostate(2)|skin(1)	27		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)		ggcggcAGAGCTGCTGCTCTG	0.692													C|||	24	0.00479233	0.0182	0.0	5008	,	,		11162	0.0		0.0	False		,,,				2504	0.0				p.A16S		Atlas-SNP	.											.	MIPEP	53	.	0			c.G46T						PASS	.						2.0	3.0	3.0					13																	24463414		1592	3189	4781	SO:0001583	missense	4285	exon1			GCAGAGCTGCTGC		CCDS9303.1	13q12	2011-01-17			ENSG00000027001	ENSG00000027001	3.4.24.59		7104	protein-coding gene	gene with protein product		602241				9073519	Standard	NM_005932		Approved	MIP	uc001uox.4	Q99797	OTTHUMG00000016573	ENST00000382172.3:c.46G>T	13.37:g.24463414C>A	ENSP00000371607:p.Ala16Ser	4.0	0.0	0		18.0	17.0	0.944444	NM_005932	Q5JV15|Q5T9Q9|Q96G65	Missense_Mutation	SNP	ENST00000382172.3	37	CCDS9303.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	c	11.93	1.786749	0.31593	.	.	ENSG00000027001	ENST00000382172	T	0.10005	2.92	4.11	2.28	0.28536	.	0.834312	0.10422	N	0.676614	T	0.04363	0.0120	L	0.36672	1.1	0.09310	N	1	B	0.20052	0.041	B	0.17098	0.017	T	0.26849	-1.0091	10	0.59425	D	0.04	-18.1677	7.5781	0.27948	0.0:0.7411:0.1649:0.094	.	16	Q99797	MIPEP_HUMAN	S	16	ENSP00000371607:A16S	ENSP00000371607:A16S	A	-	1	0	MIPEP	23361414	0.002000	0.14202	0.108000	0.21378	0.376000	0.30014	0.683000	0.25349	0.920000	0.36970	0.491000	0.48974	GCT	C|0.994;A|0.006	0.006	strong		0.692	MIPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044169.1		
PSMC5	5705	hgsc.bcm.edu	37	17	61902011	61902011	+	5'Flank	SNP	C	C	T	rs9910549	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:61902011C>T	ENST00000310144.6	+	0	0				FTSJ3_ENST00000427159.2_Silent_p.G301G|FTSJ3_ENST00000580295.1_5'Flank|PSMC5_ENST00000580864.1_5'Flank	NM_002805.5	NP_002796.4	P62195	PRS8_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 5						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)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of inclusion body assembly (GO:0090261)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|extracellular vesicular exosome (GO:0070062)|inclusion body (GO:0016234)|membrane (GO:0016020)|nuclear proteasome complex (GO:0031595)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|thyrotropin-releasing hormone receptor binding (GO:0031531)|transcription cofactor activity (GO:0003712)|transcription factor binding (GO:0008134)			endometrium(3)|kidney(2)|large_intestine(8)|lung(3)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	20						GCTCCTTGCGCCCCAACACTC	0.562													C|||	99	0.0197684	0.0734	0.0029	5008	,	,		19798	0.0		0.0	False		,,,				2504	0.0				p.G301G		Atlas-SNP	.											.	FTSJ3	63	.	0			c.G903A						PASS	.	C		211,4195	130.2+/-166.9	6,199,1998	191.0	171.0	178.0		903	0.5	1.0	17	dbSNP_119	178	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	FTSJ3	NM_017647.3		6,201,6296	TT,TC,CC		0.0233,4.7889,1.6377		301/848	61902011	213,12793	2203	4300	6503	SO:0001631	upstream_gene_variant	117246	exon10			CTTGCGCCCCAAC	L38810	CCDS11645.1, CCDS56043.1	17q23.3	2010-04-21			ENSG00000087191	ENSG00000087191		"""Proteasome (prosome, macropain) subunits"", ""ATPases / AAA-type"""	9552	protein-coding gene	gene with protein product		601681				9473509, 9048938	Standard	NM_002805		Approved	SUG1, p45/SUG, TBP10, p45, S8, TRIP1, SUG-1	uc002jcb.3	P62195			17.37:g.61902011C>T	Exception_encountered	209.0	0.0	0		207.0	103.0	0.497585	NM_017647	A8K3Z3|A8K763|O35051|O43208|P47210|P52915|P52916	Silent	SNP	ENST00000310144.6	37	CCDS11645.1																																																																																			C|0.976;T|0.024	0.024	strong		0.562	PSMC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444404.1	NM_002805	
ZNF628	89887	hgsc.bcm.edu	37	19	55994975	55994975	+	Silent	SNP	G	G	T	rs114065657	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55994975G>T	ENST00000598519.1	+	3	2968	c.2415G>T	c.(2413-2415)gtG>gtT	p.V805V	NAT14_ENST00000587400.1_5'Flank|ZNF628_ENST00000391718.2_Silent_p.V801V|NAT14_ENST00000205194.4_5'Flank|NAT14_ENST00000591590.1_5'Flank			Q5EBL2	ZN628_HUMAN	zinc finger protein 628	805	Gly-rich.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(4)|kidney(1)|lung(2)	7	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0531)		TGCAGAATGTGGGGGGTGGGG	0.692													g|||	82	0.0163738	0.0598	0.0029	5008	,	,		13204	0.0		0.001	False		,,,				2504	0.0				p.V805V		Atlas-SNP	.											.	ZNF628	75	.	0			c.G2415T						PASS	.	G		212,4192		2,208,1992	32.0	41.0	38.0		2403	-1.7	0.8	19	dbSNP_132	38	2,8592		0,2,4295	no	coding-synonymous	ZNF628	NM_033113.2		2,210,6287	TT,TG,GG		0.0233,4.8138,1.6464		801/1056	55994975	214,12784	2202	4297	6499	SO:0001819	synonymous_variant	89887	exon3			GAATGTGGGGGGT	AF367249	CCDS33116.3	19q13.43	2013-01-08			ENSG00000197483	ENSG00000197483		"""Zinc fingers, C2H2-type"""	28054	protein-coding gene	gene with protein product	"""Zinc finger expressed in Embryonal cells and Certain adult organs"""	610671					Standard	NM_033113		Approved	ZEC, Zfp628	uc002qld.3	Q5EBL2	OTTHUMG00000150396	ENST00000598519.1:c.2415G>T	19.37:g.55994975G>T		72.0	0.0	0		93.0	50.0	0.537634	NM_033113	Q86X34	Silent	SNP	ENST00000598519.1	37	CCDS33116.3																																																																																			G|0.980;T|0.020	0.020	strong		0.692	ZNF628-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317934.2	XM_058964	
GPRASP1	9737	hgsc.bcm.edu	37	X	101912465	101912465	+	Silent	SNP	G	G	T	rs1124050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:101912465G>T	ENST00000361600.5	+	5	4425	c.3624G>T	c.(3622-3624)ccG>ccT	p.P1208P	RP4-769N13.7_ENST00000602441.1_RNA|GPRASP1_ENST00000537097.1_Silent_p.P1208P|GPRASP1_ENST00000444152.1_Silent_p.P1208P|GPRASP1_ENST00000415986.1_Silent_p.P1208P	NM_014710.4	NP_055525.3	Q5JY77	GASP1_HUMAN	G protein-coupled receptor associated sorting protein 1	1208	OPRD1-binding.				endosome to lysosome transport (GO:0008333)|G-protein coupled receptor catabolic process (GO:1990172)	cytoplasm (GO:0005737)				NS(1)|breast(3)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(10)|lung(29)|ovary(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	60						TTAATTATCCGTCCTCCCGAG	0.383													G|||	50	0.013245	0.0371	0.0014	3775	,	,		15018	0.0		0.0	False		,,,				2504	0.0				p.P1208P		Atlas-SNP	.											.	GPRASP1	140	.	0			c.G3624T						PASS	.	G	,,,,	148,3687		2,116,28,1514,543	103.0	93.0	97.0		3624,3624,3624,,3624	-5.8	0.1	X	dbSNP_86	97	0,6728		0,0,0,2428,1872	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous	GPRASP1,ARMCX5-GPRASP2	NM_001099410.1,NM_001099411.1,NM_001184727.1,NM_001199818.1,NM_014710.4	,,,,	2,116,28,3942,2415	TT,TG,T,GG,G		0.0,3.8592,1.4011	,,,,	1208/1396,1208/1396,1208/1396,,1208/1396	101912465	148,10415	2203	4300	6503	SO:0001819	synonymous_variant	9737	exon3			TTATCCGTCCTCC	AB007903	CCDS35352.1	Xq22.1	2014-03-21			ENSG00000198932	ENSG00000198932		"""Armadillo repeat containing"""	24834	protein-coding gene	gene with protein product		300417				9455477, 15086532, 16221301	Standard	NM_014710		Approved	GASP, GASP1	uc010nod.3	Q5JY77	OTTHUMG00000022061	ENST00000361600.5:c.3624G>T	X.37:g.101912465G>T		280.0	1.0	0.00357143		293.0	107.0	0.365188	NM_001099411	O43168|Q96LA1	Silent	SNP	ENST00000361600.5	37	CCDS35352.1																																																																																			0|0.003;A|0.000;G|0.981;T|0.016	0.016	strong		0.383	GPRASP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057634.2	NM_014710	
RBBP8NL	140893	hgsc.bcm.edu	37	20	60989243	60989243	+	Silent	SNP	T	T	C	rs34446012	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:60989243T>C	ENST00000252998.1	-	10	1320	c.1164A>G	c.(1162-1164)ctA>ctG	p.L388L		NM_080833.2	NP_543023.2	Q8NC74	RB8NL_HUMAN	RBBP8 N-terminal like	388						extracellular space (GO:0005615)											AGCCGACTGGTAGGGAGGGCA	0.701													T|||	25	0.00499201	0.0174	0.0029	5008	,	,		12717	0.0		0.0	False		,,,				2504	0.0				p.L388L		Atlas-SNP	.											.	.	.	.	0			c.A1164G						PASS	.	T		45,4287		0,45,2121	13.0	14.0	13.0		1164	-10.1	0.0	20	dbSNP_126	13	0,8462		0,0,4231	no	coding-synonymous	C20orf151	NM_080833.2		0,45,6352	CC,CT,TT		0.0,1.0388,0.3517		388/665	60989243	45,12749	2166	4231	6397	SO:0001819	synonymous_variant	140893	exon10			GACTGGTAGGGAG	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.1164A>G	20.37:g.60989243T>C		61.0	0.0	0		65.0	33.0	0.507692	NM_080833	B2RP98|Q8N4Z9|Q9BR75|Q9H0Y9	Silent	SNP	ENST00000252998.1	37	CCDS13498.1																																																																																			T|0.996;C|0.004	0.004	strong		0.701	RBBP8NL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080029.1	NM_080833	
NT5E	4907	hgsc.bcm.edu	37	6	86195098	86195098	+	Silent	SNP	C	C	T	rs35478984	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:86195098C>T	ENST00000257770.3	+	4	946	c.897C>T	c.(895-897)aaC>aaT	p.N299N	NT5E_ENST00000369651.3_Silent_p.N299N	NM_002526.3	NP_002517.1	P21589	5NTD_HUMAN	5'-nucleotidase, ecto (CD73)	299					adenosine biosynthetic process (GO:0046086)|AMP catabolic process (GO:0006196)|dephosphorylation (GO:0016311)|DNA metabolic process (GO:0006259)|negative regulation of inflammatory response (GO:0050728)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	5'-nucleotidase activity (GO:0008253)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(76;0.000215)|Acute lymphoblastic leukemia(125;3.66e-08)|all_hematologic(105;8.61e-05)|all_epithelial(107;0.0427)		BRCA - Breast invasive adenocarcinoma(108;0.0417)	Cytarabine(DB00987)|Pentoxifylline(DB00806)	AAAGAGGAAACGTCATCTCTT	0.438													C|||	97	0.019369	0.0703	0.0058	5008	,	,		20130	0.0		0.0	False		,,,				2504	0.0				p.N299N	Melanoma(140;797 1765 2035 2752 18208)	Atlas-SNP	.											.	NT5E	56	.	0			c.C897T						PASS	.	C	,	287,4119	159.6+/-192.1	8,271,1924	151.0	136.0	141.0		897,897	-0.1	0.9	6	dbSNP_126	141	2,8598	3.0+/-9.4	0,2,4298	no	coding-synonymous,coding-synonymous	NT5E	NM_001204813.1,NM_002526.3	,	8,273,6222	TT,TC,CC		0.0233,6.5138,2.2221	,	299/525,299/575	86195098	289,12717	2203	4300	6503	SO:0001819	synonymous_variant	4907	exon4			AGGAAACGTCATC	X55740	CCDS5002.1, CCDS56439.1	6q14-q21	2013-08-28	2002-04-18	2002-04-19	ENSG00000135318	ENSG00000135318	3.1.3.5	"""CD molecules"""	8021	protein-coding gene	gene with protein product		129190	"""5' nucleotidase (CD73)"""	NT5			Standard	NM_002526		Approved	CD73, eN, eNT, CALJA	uc003pko.4	P21589	OTTHUMG00000015139	ENST00000257770.3:c.897C>T	6.37:g.86195098C>T		109.0	0.0	0		109.0	47.0	0.431193	NM_001204813	B3KQI8|O75520|Q5W116	Silent	SNP	ENST00000257770.3	37	CCDS5002.1	44	0.020146520146520148	42	0.08536585365853659	2	0.0055248618784530384	0	0.0	0	0.0	C	6.940	0.543124	0.13250	0.065138	2.33E-4	ENSG00000135318	ENST00000416334	.	.	.	5.36	-0.104	0.13605	.	.	.	.	.	T	0.44561	0.1299	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42732	-0.9434	4	.	.	.	-7.7038	11.3536	0.49602	0.0:0.1944:0.0:0.8056	rs35478984	.	.	.	M	64	.	.	T	+	2	0	NT5E	86251817	0.963000	0.33076	0.937000	0.37676	0.836000	0.47400	0.030000	0.13688	-0.211000	0.10124	-1.744000	0.00683	ACG	C|0.977;T|0.023	0.023	strong		0.438	NT5E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041388.1		
GHITM	27069	hgsc.bcm.edu	37	10	85902479	85902479	+	Silent	SNP	A	A	T	rs146877821	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:85902479A>T	ENST00000372134.3	+	3	391	c.198A>T	c.(196-198)gcA>gcT	p.A66A	RP11-338I21.1_ENST00000606511.1_RNA	NM_014394.2	NP_055209.2	Q9H3K2	GHITM_HUMAN	growth hormone inducible transmembrane protein	66					apoptotic process (GO:0006915)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				breast(1)|endometrium(1)|large_intestine(3)|lung(3)|prostate(2)	10						AAGAGGCAGCATTGGAACCAT	0.408													A|||	29	0.00579073	0.0212	0.0014	5008	,	,		15827	0.0		0.0	False		,,,				2504	0.0				p.A66A		Atlas-SNP	.											.	GHITM	30	.	0			c.A198T						PASS	.	A		53,3701		0,53,1824	100.0	102.0	101.0		198	-9.6	0.0	10	dbSNP_134	101	0,8224		0,0,4112	no	coding-synonymous	GHITM	NM_014394.2		0,53,5936	TT,TA,AA		0.0,1.4118,0.4425		66/346	85902479	53,11925	1877	4112	5989	SO:0001819	synonymous_variant	27069	exon3			GGCAGCATTGGAA	AB009685	CCDS41542.1	10q23.1	2008-02-01			ENSG00000165678	ENSG00000165678			17281	protein-coding gene	gene with protein product	"""transmembrane BAX inhibitor motif containing 5"""					8619474, 9110174	Standard	NM_014394		Approved	HSPC282, PTD010, DERP2, My021, TMBIM5	uc001kcs.1	Q9H3K2	OTTHUMG00000018637	ENST00000372134.3:c.198A>T	10.37:g.85902479A>T		61.0	0.0	0		97.0	46.0	0.474227	NM_014394	A8K9Z9|D3DWE0|O95894|Q5VT95|Q9H0P2	Silent	SNP	ENST00000372134.3	37	CCDS41542.1																																																																																			A|0.995;T|0.005	0.005	strong		0.408	GHITM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049125.1	NM_014394	
RHPN1	114822	hgsc.bcm.edu	37	8	144464073	144464073	+	Missense_Mutation	SNP	G	G	A	rs34746679	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144464073G>A	ENST00000289013.6	+	14	1833	c.1732G>A	c.(1732-1734)Gcg>Acg	p.A578T		NM_052924.2	NP_443156.2	Q8TCX5	RHPN1_HUMAN	rhophilin, Rho GTPase binding protein 1	603	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				signal transduction (GO:0007165)		small GTPase regulator activity (GO:0005083)			endometrium(1)|large_intestine(1)|lung(7)	9	all_cancers(97;7.39e-11)|all_epithelial(106;5.44e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.107)|BRCA - Breast invasive adenocarcinoma(115;0.156)			GCTGAAGGCTGCGGGAGAGGC	0.682													G|||	39	0.00778754	0.0287	0.0014	5008	,	,		15201	0.0		0.0	False		,,,				2504	0.0				p.A578T		Atlas-SNP	.											RHPN1_ENST00000289013,NS,carcinoma,-1,2	RHPN1	76	2	0			c.G1732A						PASS	.	G	THR/ALA	90,4180		3,84,2048	29.0	46.0	41.0		1732	1.7	0.0	8	dbSNP_126	41	3,8489		0,3,4243	yes	missense	RHPN1	NM_052924.2	58	3,87,6291	AA,AG,GG		0.0353,2.1077,0.7287	benign	578/671	144464073	93,12669	2135	4246	6381	SO:0001583	missense	114822	exon14			AAGGCTGCGGGAG	AB067516	CCDS47927.1	8q24.3	2003-02-06			ENSG00000158106	ENSG00000158106			19973	protein-coding gene	gene with protein product		601031				11572484	Standard	NM_052924		Approved	KIAA1929, RHPN, ODF5	uc003yyb.3	Q8TCX5	OTTHUMG00000165006	ENST00000289013.6:c.1732G>A	8.37:g.144464073G>A	ENSP00000289013:p.Ala578Thr	125.0	0.0	0		139.0	79.0	0.568345	NM_052924	Q8TAV1|Q96PV9	Missense_Mutation	SNP	ENST00000289013.6	37	CCDS47927.1	23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	G	6.274	0.418750	0.11870	0.021077	3.53E-4	ENSG00000158106	ENST00000289013	T	0.27557	1.66	4.59	1.73	0.24493	.	0.587122	0.17709	N	0.164651	T	0.04092	0.0114	N	0.25789	0.76	0.09310	N	1	B	0.17852	0.024	B	0.17979	0.02	T	0.16719	-1.0393	10	0.25751	T	0.34	-10.2882	6.9391	0.24483	0.4169:0.0:0.5831:0.0	rs34746679	578	Q8TCX5-2	.	T	578	ENSP00000289013:A578T	ENSP00000289013:A578T	A	+	1	0	RHPN1	144535216	0.000000	0.05858	0.001000	0.08648	0.017000	0.09413	0.119000	0.15626	0.349000	0.23975	0.462000	0.41574	GCG	G|0.989;A|0.011	0.011	strong		0.682	RHPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381417.1		
BPI	671	hgsc.bcm.edu	37	20	36954790	36954790	+	Missense_Mutation	SNP	G	G	A	rs5743524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:36954790G>A	ENST00000262865.4	+	10	1218	c.1129G>A	c.(1129-1131)Gtc>Atc	p.V377I	BPI_ENST00000489102.1_3'UTR|CTD-2308N23.2_ENST00000437016.1_RNA	NM_001725.2	NP_001716.2	P17213	BPI_HUMAN	bactericidal/permeability-increasing protein	377			V -> I (in dbSNP:rs5743524).		defense response to bacterium (GO:0042742)|immune response (GO:0006955)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of macrophage activation (GO:0043031)|negative regulation of tumor necrosis factor production (GO:0032720)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	lipopolysaccharide binding (GO:0001530)			kidney(1)|large_intestine(6)|lung(15)|ovary(4)|prostate(2)|stomach(1)|urinary_tract(1)	30		Myeloproliferative disorder(115;0.00878)				GGCCTTTGCCGTCCTCCCCAA	0.597													g|||	209	0.0417332	0.1475	0.0187	5008	,	,		19366	0.0		0.001	False		,,,				2504	0.0				p.V377I		Atlas-SNP	.											.	BPI	67	.	0			c.G1129A						PASS	.	A	ILE/VAL	508,3898	235.5+/-248.0	28,452,1723	90.0	70.0	77.0		1129	-3.8	0.0	20	dbSNP_114	77	8,8592	6.4+/-24.3	0,8,4292	yes	missense	BPI	NM_001725.2	29	28,460,6015	AA,AG,GG		0.093,11.5297,3.9674	benign	377/488	36954790	516,12490	2203	4300	6503	SO:0001583	missense	671	exon10			TTTGCCGTCCTCC	J04739	CCDS13303.1	20q11.23	2011-08-16			ENSG00000101425	ENSG00000101425		"""BPI fold containing"""	1095	protein-coding gene	gene with protein product	"""BPI fold containing family D, member 1"""	109195				8432532	Standard	NM_001725		Approved	BPIFD1	uc002xia.2	P17213	OTTHUMG00000032441	ENST00000262865.4:c.1129G>A	20.37:g.36954790G>A	ENSP00000262865:p.Val377Ile	143.0	0.0	0		123.0	52.0	0.422764	NM_001725	B2RCY2|Q1ZZU8|Q5JRW0|Q8IW58|Q9BYZ9|Q9H1L2|Q9H1M8|Q9H203|Q9UCT4|Q9UD65	Missense_Mutation	SNP	ENST00000262865.4	37	CCDS13303.1	85	0.03891941391941392	80	0.16260162601626016	5	0.013812154696132596	0	0.0	0	0.0	g	3.739	-0.053900	0.07362	0.115297	9.3E-4	ENSG00000101425	ENST00000262865	T	0.09163	3.01	4.39	-3.78	0.04333	Lipid-binding serum glycoprotein, C-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	1.053620	0.07393	N	0.889378	T	0.00039	0.0001	N	0.11927	0.2	0.53688	P	2.8000000000028002E-5	B	0.20988	0.05	B	0.11329	0.006	T	0.48175	-0.9058	9	0.06757	T	0.87	-18.082	13.0633	0.59020	0.743:0.0:0.257:0.0	rs5743524;rs5743524	377	P17213	BPI_HUMAN	I	377	ENSP00000262865:V377I	ENSP00000262865:V377I	V	+	1	0	BPI	36388204	0.008000	0.16893	0.003000	0.11579	0.011000	0.07611	-0.063000	0.11655	-0.933000	0.03737	-2.146000	0.00336	GTC	G|0.949;A|0.051	0.051	strong		0.597	BPI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079157.2	NM_001725	
TG	7038	hgsc.bcm.edu	37	8	133953740	133953740	+	Missense_Mutation	SNP	A	A	C	rs61744749	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133953740A>C	ENST00000220616.4	+	26	5226	c.5186A>C	c.(5185-5187)gAc>gCc	p.D1729A	TG_ENST00000542445.1_Intron|TG_ENST00000377869.1_Missense_Mutation_p.D1672A	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1729					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		CTTGCATGCGACCGTGATCTG	0.527													A|||	140	0.0279553	0.1014	0.0086	5008	,	,		23318	0.0		0.0	False		,,,				2504	0.0				p.D1729A		Atlas-SNP	.											TG,NS,carcinoma,+1,1	TG	416	1	0			c.A5186C						PASS	.	A	ALA/ASP	382,4024	193.0+/-218.2	19,344,1840	176.0	141.0	153.0		5186	5.6	1.0	8	dbSNP_129	153	3,8597	3.0+/-9.4	0,3,4297	yes	missense	TG	NM_003235.4	126	19,347,6137	CC,CA,AA		0.0349,8.67,2.9602	possibly-damaging	1729/2769	133953740	385,12621	2203	4300	6503	SO:0001583	missense	7038	exon26			CATGCGACCGTGA	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.5186A>C	8.37:g.133953740A>C	ENSP00000220616:p.Asp1729Ala	292.0	1.0	0.00342466		311.0	147.0	0.472669	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	61	0.027930402930402932	57	0.11585365853658537	4	0.011049723756906077	0	0.0	0	0.0	A	11.79	1.743661	0.30865	0.0867	3.49E-4	ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616	T;T	0.70282	-0.47;-0.47	5.61	5.61	0.85477	.	0.387653	0.24873	N	0.034902	T	0.02230	0.0069	M	0.72118	2.19	0.36596	D	0.874396	B	0.31581	0.329	B	0.27170	0.077	T	0.47898	-0.9081	10	0.66056	D	0.02	.	12.1945	0.54290	1.0:0.0:0.0:0.0	rs61744749	1729	P01266	THYG_HUMAN	A	1672;535;1729	ENSP00000367100:D1672A;ENSP00000220616:D1729A	ENSP00000220616:D1729A	D	+	2	0	TG	134022922	0.998000	0.40836	0.981000	0.43875	0.150000	0.21749	3.679000	0.54634	2.142000	0.66516	0.379000	0.24179	GAC	A|0.964;C|0.036	0.036	strong		0.527	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
ZNF790	388536	hgsc.bcm.edu	37	19	37309790	37309790	+	Missense_Mutation	SNP	T	T	A	rs4369791	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:37309790T>A	ENST00000356725.4	-	5	1576	c.1456A>T	c.(1456-1458)Acc>Tcc	p.T486S	CTD-2162K18.5_ENST00000587278.1_RNA|CTD-2162K18.5_ENST00000588906.1_RNA	NM_001242802.1|NM_206894.3	NP_001229731.1|NP_996777.2	Q6PG37	ZN790_HUMAN	zinc finger protein 790	486			T -> S (in dbSNP:rs4369791).		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)			biliary_tract(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(7)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	32	Esophageal squamous(110;0.183)		COAD - Colon adenocarcinoma(19;0.0454)|Colorectal(19;0.065)			CGAAAAAAGGTCTTTCCACAT	0.388													T|||	20	0.00399361	0.0151	0.0	5008	,	,		20361	0.0		0.0	False		,,,				2504	0.0				p.T486S		Atlas-SNP	.											.	ZNF790	89	.	0			c.A1456T						PASS	.	T	SER/THR,SER/THR,SER/THR,SER/THR	72,4334	65.3+/-102.7	1,70,2132	83.0	80.0	81.0		1456,1456,1456,1456	-1.0	0.0	19	dbSNP_111	81	0,8600		0,0,4300	yes	missense,missense,missense,missense	ZNF790	NM_001242800.1,NM_001242801.1,NM_001242802.1,NM_206894.3	58,58,58,58	1,70,6432	AA,AT,TT		0.0,1.6341,0.5536	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	486/637,486/637,486/637,486/637	37309790	72,12934	2203	4300	6503	SO:0001583	missense	388536	exon5			AAAAGGTCTTTCC	BC057245	CCDS12496.1	19q13.12	2013-01-08			ENSG00000197863	ENSG00000197863		"""Zinc fingers, C2H2-type"", ""-"""	33114	protein-coding gene	gene with protein product							Standard	NM_206894		Approved	MGC62100, FLJ20350	uc021utm.1	Q6PG37	OTTHUMG00000165616	ENST00000356725.4:c.1456A>T	19.37:g.37309790T>A	ENSP00000349161:p.Thr486Ser	48.0	0.0	0		41.0	19.0	0.463415	NM_206894		Missense_Mutation	SNP	ENST00000356725.4	37	CCDS12496.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	T	8.684	0.905767	0.17760	0.016341	0.0	ENSG00000197863	ENST00000356725	T	0.19105	2.17	3.14	-0.997	0.10215	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.03477	0.0100	N	0.03903	-0.33	0.09310	N	1	B	0.22604	0.072	B	0.23018	0.043	T	0.32079	-0.9920	9	0.41790	T	0.15	.	4.173	0.10339	0.2887:0.4551:0.0:0.2562	rs4369791;rs52825956;rs4369791	486	Q6PG37	ZN790_HUMAN	S	486	ENSP00000349161:T486S	ENSP00000349161:T486S	T	-	1	0	ZNF790	42001630	0.000000	0.05858	0.034000	0.17996	0.389000	0.30415	0.069000	0.14552	-0.105000	0.12132	0.402000	0.26972	ACC	T|0.995;A|0.005	0.005	strong		0.388	ZNF790-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385341.2	NM_206894	
SPRYD3	84926	hgsc.bcm.edu	37	12	53467230	53467230	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53467230G>T	ENST00000301463.4	-	6	619	c.533C>A	c.(532-534)tCc>tAc	p.S178Y	SPRYD3_ENST00000547837.1_Missense_Mutation_p.S215Y	NM_032840.2	NP_116229.1	Q8NCJ5	SPRY3_HUMAN	SPRY domain containing 3	178	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.									central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	17						TCCATCTGGGGACATGGGCAT	0.607																																					p.S178Y		Atlas-SNP	.											.	SPRYD3	29	.	0			c.C533A						PASS	.						57.0	43.0	47.0					12																	53467230		2203	4292	6495	SO:0001583	missense	84926	exon6			TCTGGGGACATGG	AK074694	CCDS8845.1	12q13.13	2006-11-29		2006-02-02		ENSG00000167778			25920	protein-coding gene	gene with protein product						14702039	Standard	NM_032840		Approved	FLJ14800	uc001sbt.2	Q8NCJ5	OTTHUMG00000170101	ENST00000301463.4:c.533C>A	12.37:g.53467230G>T	ENSP00000301463:p.Ser178Tyr	53.0	0.0	0		54.0	22.0	0.407407	NM_032840	B9EG99|Q96SK5	Missense_Mutation	SNP	ENST00000301463.4	37	CCDS8845.1	.	.	.	.	.	.	.	.	.	.	G	19.45	3.830680	0.71258	.	.	ENSG00000167778	ENST00000301463;ENST00000547837	T;T	0.60040	0.22;0.22	5.17	5.17	0.71159	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.060021	0.64402	D	0.000002	T	0.60143	0.2246	L	0.42245	1.32	0.53005	D	0.999964	D	0.56968	0.978	P	0.50708	0.648	T	0.59484	-0.7446	10	0.45353	T	0.12	-19.5437	16.5838	0.84722	0.0:0.0:1.0:0.0	.	178	Q8NCJ5	SPRY3_HUMAN	Y	178;215	ENSP00000301463:S178Y;ENSP00000449452:S215Y	ENSP00000301463:S178Y	S	-	2	0	SPRYD3	51753497	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.182000	0.94881	2.861000	0.98227	0.655000	0.94253	TCC	.	.	none		0.607	SPRYD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407264.1	NM_032840	
BPHL	670	hgsc.bcm.edu	37	6	3152760	3152760	+	Missense_Mutation	SNP	T	T	C	rs2231370	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:3152760T>C	ENST00000380379.5	+	7	876	c.827T>C	c.(826-828)tTg>tCg	p.L276S	RP1-40E16.11_ENST00000447644.1_RNA|BPHL_ENST00000434640.1_Missense_Mutation_p.L259S|BPHL_ENST00000380368.2_3'UTR|BPHL_ENST00000380375.3_Missense_Mutation_p.L259S|TUBB2A_ENST00000489942.1_5'Flank|BPHL_ENST00000464040.1_3'UTR	NM_004332.2	NP_004323.2	Q86WA6	BPHL_HUMAN	biphenyl hydrolase-like (serine hydrolase)	276					cellular amino acid metabolic process (GO:0006520)|response to toxic substance (GO:0009636)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)			endometrium(4)|kidney(1)|large_intestine(2)|lung(6)	13	Ovarian(93;0.0386)	all_hematologic(90;0.108)				AACCTGCATTTGCGTTTTGCA	0.438													T|||	250	0.0499201	0.1747	0.0173	5008	,	,		21159	0.001		0.005	False		,,,				2504	0.001				p.L276S		Atlas-SNP	.											.	BPHL	32	.	0			c.T827C						PASS	.	T	SER/LEU	588,3818	261.0+/-264.0	42,504,1657	168.0	153.0	158.0		827	4.7	0.1	6	dbSNP_98	158	31,8569	21.0+/-64.5	0,31,4269	yes	missense	BPHL	NM_004332.2	145	42,535,5926	CC,CT,TT		0.3605,13.3454,4.7593	probably-damaging	276/292	3152760	619,12387	2203	4300	6503	SO:0001583	missense	670	exon7			TGCATTTGCGTTT	X81372	CCDS4483.2	6p25	2008-08-29	2008-08-29		ENSG00000137274	ENSG00000137274			1094	protein-coding gene	gene with protein product	"""breast epithelial mucin-associated antigen"""	603156		MCNAA		7759552, 9721218, 15832508	Standard	NM_004332		Approved	Bph-rp	uc003mva.3	Q86WA6	OTTHUMG00000014140	ENST00000380379.5:c.827T>C	6.37:g.3152760T>C	ENSP00000369739:p.Leu276Ser	146.0	0.0	0		168.0	84.0	0.5	NM_004332	Q00306|Q13855|Q3KP51	Missense_Mutation	SNP	ENST00000380379.5	37	CCDS4483.2	104	0.047619047619047616	92	0.18699186991869918	5	0.013812154696132596	1	0.0017482517482517483	6	0.0079155672823219	T	19.10	3.761514	0.69763	0.133454	0.003605	ENSG00000137274	ENST00000434640;ENST00000380375;ENST00000380379	T;T;T	0.72051	-0.62;-0.62;-0.62	5.9	4.74	0.60224	.	0.069235	0.64402	D	0.000014	T	0.77061	0.4075	M	0.73430	2.235	0.22354	P	0.999176454	D;D	0.76494	0.999;0.999	D;D	0.79784	0.993;0.988	T	0.80801	-0.1220	9	0.56958	D	0.05	-17.8489	11.8569	0.52441	0.0:0.0677:0.0:0.9323	rs2231370;rs52831698;rs2231370	276;259	Q86WA6;Q86WA6-2	BPHL_HUMAN;.	S	259;259;276	ENSP00000390472:L259S;ENSP00000369734:L259S;ENSP00000369739:L276S	ENSP00000369734:L259S	L	+	2	0	BPHL	3097759	0.996000	0.38824	0.080000	0.20451	0.991000	0.79684	5.961000	0.70356	1.064000	0.40671	0.528000	0.53228	TTG	T|0.949;C|0.051	0.051	strong		0.438	BPHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039670.5		
HOXD3	3232	hgsc.bcm.edu	37	2	177034130	177034130	+	Silent	SNP	G	G	A	rs77818566	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:177034130G>A	ENST00000468418.3	+	3	2378	c.288G>A	c.(286-288)ggG>ggA	p.G96G	HOXD3_ENST00000249440.3_Silent_p.G96G|HOXD3_ENST00000410016.1_Silent_p.G96G			P31249	HXD3_HUMAN	homeobox D3	96					anterior/posterior pattern specification (GO:0009952)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|embryonic skeletal system morphogenesis (GO:0048704)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron differentiation (GO:0045666)|thyroid gland development (GO:0030878)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(11)|prostate(1)|upper_aerodigestive_tract(2)	23			OV - Ovarian serous cystadenocarcinoma(117;0.00569)|Epithelial(96;0.0864)|all cancers(119;0.226)	Colorectal(32;0.247)		CGGGCACTGGGAACAGCCAGG	0.647													G|||	289	0.0577077	0.2133	0.0101	5008	,	,		14552	0.0		0.0	False		,,,				2504	0.0				p.G96G		Atlas-SNP	.											.	HOXD3	65	.	0			c.G288A						PASS	.	G		749,3657	262.5+/-264.9	73,603,1527	24.0	26.0	25.0		288	3.6	1.0	2	dbSNP_131	25	18,8582	9.8+/-36.6	0,18,4282	no	coding-synonymous	HOXD3	NM_006898.4		73,621,5809	AA,AG,GG		0.2093,16.9995,5.8973		96/433	177034130	767,12239	2203	4300	6503	SO:0001819	synonymous_variant	3232	exon2			CACTGGGAACAGC		CCDS2270.1	2q31.1	2011-06-20	2005-12-22		ENSG00000128652	ENSG00000128652		"""Homeoboxes / ANTP class : HOXL subclass"""	5137	protein-coding gene	gene with protein product		142980	"""homeo box D3"""	HOX4A, HOX4, HOX1D		1973146, 1358459	Standard	NM_006898		Approved		uc002ukt.1	P31249	OTTHUMG00000132517	ENST00000468418.3:c.288G>A	2.37:g.177034130G>A		141.0	0.0	0		116.0	56.0	0.482759	NM_006898	Q99955|Q9BSC5	Silent	SNP	ENST00000468418.3	37	CCDS2270.1																																																																																			G|0.949;A|0.051	0.051	strong		0.647	HOXD3-005	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334246.4		
COL15A1	1306	hgsc.bcm.edu	37	9	101816873	101816873	+	Missense_Mutation	SNP	A	A	G	rs35642150	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:101816873A>G	ENST00000375001.3	+	32	3389	c.2966A>G	c.(2965-2967)aAa>aGa	p.K989R		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	989	Triple-helical region 6 (COL6).		K -> R (in dbSNP:rs35642150).		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)				AAAGGAGAGAAAGGATCCTGG	0.433													A|||	71	0.0141773	0.0514	0.0043	5008	,	,		19547	0.0		0.0	False		,,,				2504	0.0				p.K989R		Atlas-SNP	.											.	COL15A1	211	.	0			c.A2966G						PASS	.	A	ARG/LYS	123,4283	91.1+/-129.8	1,121,2081	79.0	84.0	82.0		2966	5.7	1.0	9	dbSNP_126	82	1,8599	1.2+/-3.3	0,1,4299	yes	missense	COL15A1	NM_001855.3	26	1,122,6380	GG,GA,AA		0.0116,2.7916,0.9534	probably-damaging	989/1389	101816873	124,12882	2203	4300	6503	SO:0001583	missense	1306	exon32			GAGAGAAAGGATC	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.2966A>G	9.37:g.101816873A>G	ENSP00000364140:p.Lys989Arg	131.0	0.0	0		134.0	94.0	0.701493	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	37	CCDS35081.1	23	0.010531135531135532	21	0.042682926829268296	2	0.0055248618784530384	0	0.0	0	0.0	A	16.86	3.239791	0.58995	0.027916	1.16E-4	ENSG00000204291	ENST00000375001	T	0.30448	1.53	5.67	5.67	0.87782	C-type lectin fold (1);	0.172969	0.41396	D	0.000883	T	0.13030	0.0316	L	0.33753	1.03	0.41059	D	0.985365	D	0.63880	0.993	D	0.72625	0.978	T	0.02560	-1.1141	10	0.20046	T	0.44	-17.3435	12.5857	0.56416	1.0:0.0:0.0:0.0	rs35642150	989	P39059	COFA1_HUMAN	R	989	ENSP00000364140:K989R	ENSP00000364140:K989R	K	+	2	0	COL15A1	100856694	0.999000	0.42202	1.000000	0.80357	0.990000	0.78478	1.712000	0.37940	2.288000	0.76882	0.533000	0.62120	AAA	A|0.988;G|0.012	0.012	strong		0.433	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	
FTO	79068	hgsc.bcm.edu	37	16	53922838	53922838	+	Missense_Mutation	SNP	C	C	T	rs16952624	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:53922838C>T	ENST00000471389.1	+	7	1436	c.1214C>T	c.(1213-1215)gCa>gTa	p.A405V	FTO_ENST00000431610.2_Missense_Mutation_p.A6V|FTO_ENST00000394647.3_Missense_Mutation_p.A109V|FTO_ENST00000460382.1_Missense_Mutation_p.A6V	NM_001080432.2	NP_001073901.1	Q9C0B1	FTO_HUMAN	fat mass and obesity associated	405			A -> V (in dbSNP:rs16952624).		adipose tissue development (GO:0060612)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA demethylation (GO:0080111)|oxidative demethylation (GO:0070989)|oxidative single-stranded DNA demethylation (GO:0035552)|oxidative single-stranded RNA demethylation (GO:0035553)|regulation of lipid storage (GO:0010883)|regulation of multicellular organism growth (GO:0040014)|regulation of respiratory system process (GO:0044065)|regulation of white fat cell proliferation (GO:0070350)|RNA repair (GO:0042245)|temperature homeostasis (GO:0001659)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA-N1-methyladenine dioxygenase activity (GO:0043734)|ferrous iron binding (GO:0008198)|oxidative DNA demethylase activity (GO:0035516)|oxidative RNA demethylase activity (GO:0035515)			endometrium(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						CAACTGGAAGCACTGTGGAAG	0.502													C|||	37	0.00738818	0.0272	0.0014	5008	,	,		18970	0.0		0.0	False		,,,				2504	0.0				p.A405V		Atlas-SNP	.											FTO,NS,carcinoma,-1,1	FTO	51	1	0			c.C1214T						PASS	.	C	VAL/ALA	124,4272	93.0+/-131.7	4,116,2078	287.0	257.0	267.0		1214	-3.4	0.0	16	dbSNP_123	267	0,8600		0,0,4300	yes	missense	FTO	NM_001080432.2	64	4,116,6378	TT,TC,CC		0.0,2.8207,0.9541	benign	405/506	53922838	124,12872	2198	4300	6498	SO:0001583	missense	79068	exon7			TGGAAGCACTGTG	BC003583	CCDS32448.1	16q12.2	2013-11-15			ENSG00000140718	ENSG00000140718		"""Alkylation repair homologs"""	24678	protein-coding gene	gene with protein product	"""AlkB homolog 9"", ""alpha-ketoglutarate-dependent dioxygenase"""	610966				17434869, 17991826, 22002720	Standard	NM_001080432		Approved	KIAA1752, MGC5149, ALKBH9	uc002ehr.3	Q9C0B1	OTTHUMG00000158780	ENST00000471389.1:c.1214C>T	16.37:g.53922838C>T	ENSP00000418823:p.Ala405Val	299.0	0.0	0		326.0	156.0	0.478528	NM_001080432	A2RUH1|B2RNS0|Q0P676|Q7Z785	Missense_Mutation	SNP	ENST00000471389.1	37	CCDS32448.1	21	0.009615384615384616	20	0.04065040650406504	1	0.0027624309392265192	0	0.0	0	0.0	C	8.234	0.805364	0.16467	0.028207	0.0	ENSG00000140718	ENST00000471389;ENST00000394647;ENST00000431610;ENST00000460382;ENST00000476894	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	5.84	-3.41	0.04839	Alpha-ketoglutarate-dependent dioxygenase FTO, C-terminal (1);	0.513654	0.22753	N	0.056043	T	0.04724	0.0128	N	0.14661	0.345	0.09310	N	0.999998	B	0.18013	0.025	B	0.18871	0.023	T	0.06552	-1.0820	10	0.46703	T	0.11	-3.9788	7.7201	0.28727	0.3262:0.2045:0.4693:0.0	rs16952624;rs52815989;rs16952624	405	Q9C0B1	FTO_HUMAN	V	405;109;6;6;6	ENSP00000418823:A405V;ENSP00000378142:A109V;ENSP00000415636:A6V;ENSP00000417422:A6V	ENSP00000378142:A109V	A	+	2	0	FTO	52480339	0.643000	0.27269	0.004000	0.12327	0.166000	0.22503	0.621000	0.24418	-0.639000	0.05502	-0.275000	0.10095	GCA	C|0.988;T|0.012	0.012	strong		0.502	FTO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352196.1	NM_001080432	
PIEZO1	9780	hgsc.bcm.edu	37	16	88801457	88801457	+	Silent	SNP	G	G	A	rs115016757	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88801457G>A	ENST00000301015.9	-	14	1920	c.1674C>T	c.(1672-1674)ccC>ccT	p.P558P	RP5-1142A6.2_ENST00000440406.2_RNA|RP5-1142A6.2_ENST00000567968.1_RNA	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	558					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1)	10						GCGTCCGCGTGGGCTCTGTGG	0.657													G|||	223	0.0445288	0.1611	0.0144	5008	,	,		14944	0.0		0.0	False		,,,				2504	0.0				p.P558P		Atlas-SNP	.											.	PIEZO1	79	.	0			c.C1674T						PASS	.	G		155,1229		9,137,546	68.0	65.0	66.0		1674	3.0	1.0	16	dbSNP_132	66	2,3180		0,2,1589	no	coding-synonymous	PIEZO1	NM_001142864.2		9,139,2135	AA,AG,GG		0.0629,11.1994,3.4385		558/2522	88801457	157,4409	692	1591	2283	SO:0001819	synonymous_variant	9780	exon14			CCGCGTGGGCTCT	D87071	CCDS54058.1	16q24.3	2011-08-31	2011-08-31	2011-08-31	ENSG00000103335	ENSG00000103335			28993	protein-coding gene	gene with protein product		611184	"""family with sequence similarity 38, member A"""	FAM38A		20813920, 21056836, 21299953, 21696149	Standard	NM_001142864		Approved	KIAA0233	uc010vpb.2	Q92508	OTTHUMG00000156776	ENST00000301015.9:c.1674C>T	16.37:g.88801457G>A		85.0	0.0	0		88.0	36.0	0.409091	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Silent	SNP	ENST00000301015.9	37	CCDS54058.1	58	0.026556776556776556	55	0.11178861788617886	3	0.008287292817679558	0	0.0	0	0.0	G	3.774	-0.047036	0.07407	0.111994	6.29E-4	ENSG00000103335	ENST00000451779	.	.	.	4.03	3.05	0.35203	.	.	.	.	.	T	0.00906	0.0030	.	.	.	0.09310	P	0.9999999968917	.	.	.	.	.	.	T	0.12293	-1.0553	3	.	.	.	-33.9642	6.4507	0.21902	0.0988:0.0:0.7192:0.1819	.	.	.	.	Y	504	.	.	H	-	1	0	FAM38A	87328958	0.271000	0.24162	0.986000	0.45419	0.301000	0.27625	0.787000	0.26858	0.786000	0.33708	0.313000	0.20887	CAC	G|0.966;A|0.034	0.034	strong		0.657	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
NCAPD3	23310	hgsc.bcm.edu	37	11	134048592	134048592	+	Missense_Mutation	SNP	G	G	T	rs34739733	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:134048592G>T	ENST00000534548.2	-	22	2783	c.2719C>A	c.(2719-2721)Ccc>Acc	p.P907T	RP11-700F16.3_ENST00000531710.1_RNA	NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	907			P -> T (in dbSNP:rs34739733).		mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	germinal vesicle (GO:0042585)|membrane (GO:0016020)|nuclear condensin complex (GO:0000799)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)	methylated histone binding (GO:0035064)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		ACCTGGGGGGGTGGCTGAGAC	0.522													G|||	20	0.00399361	0.0136	0.0029	5008	,	,		18713	0.0		0.0	False		,,,				2504	0.0				p.P907T		Atlas-SNP	.											.	NCAPD3	141	.	0			c.C2719A						PASS	.	G	THR/PRO	55,4347	54.2+/-90.2	0,55,2146	92.0	94.0	93.0		2719	4.1	0.0	11	dbSNP_126	93	0,8594		0,0,4297	yes	missense	NCAPD3	NM_015261.2	38	0,55,6443	TT,TG,GG		0.0,1.2494,0.4232	benign	907/1499	134048592	55,12941	2201	4297	6498	SO:0001583	missense	23310	exon22			GGGGGGGTGGCTG	AK124878	CCDS31723.1	11q25	2008-02-04			ENSG00000151503	ENSG00000151503			28952	protein-coding gene	gene with protein product		609276				7584044, 8619474, 14532007	Standard	NM_015261		Approved	hCAP-D3, CAP-D3, hHCP-6, KIAA0056, FLJ42888, hcp-6	uc001qhd.1	P42695	OTTHUMG00000167172	ENST00000534548.2:c.2719C>A	11.37:g.134048592G>T	ENSP00000433681:p.Pro907Thr	106.0	0.0	0		138.0	66.0	0.478261	NM_015261	A6NFS2|Q4KMQ9	Missense_Mutation	SNP	ENST00000534548.2	37	CCDS31723.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	G	8.015	0.758394	0.15846	0.012494	0.0	ENSG00000151503	ENST00000534548	T	0.21734	1.99	6.03	4.13	0.48395	Armadillo-like helical (1);Armadillo-type fold (1);	0.330969	0.32918	N	0.005489	T	0.09512	0.0234	L	0.31664	0.95	0.40749	D	0.982908	B	0.33413	0.411	B	0.29353	0.101	T	0.09530	-1.0670	10	0.14656	T	0.56	-4.2164	11.7991	0.52116	0.0:0.1196:0.6321:0.2483	rs34739733	907	P42695	CNDD3_HUMAN	T	907	ENSP00000433681:P907T	ENSP00000434168:P907T	P	-	1	0	NCAPD3	133553802	1.000000	0.71417	0.001000	0.08648	0.115000	0.19883	4.737000	0.62066	0.850000	0.35239	0.655000	0.94253	CCC	G|0.995;T|0.005	0.005	strong		0.522	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261	
RGS13	6003	hgsc.bcm.edu	37	1	192628623	192628623	+	Missense_Mutation	SNP	G	G	C	rs16834603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:192628623G>C	ENST00000391995.2	+	7	738	c.450G>C	c.(448-450)ttG>ttC	p.L150F	RGS13_ENST00000543215.1_Missense_Mutation_p.L150F|RGS13_ENST00000482095.1_3'UTR	NM_002927.4	NP_002918.1	O14921	RGS13_HUMAN	regulator of G-protein signaling 13	150	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.		L -> F (in dbSNP:rs16834603). {ECO:0000269|Ref.2}.		G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			endometrium(1)|kidney(1)|large_intestine(4)|lung(12)|skin(1)	19						AAAAACTTTTGAAAACTATGC	0.323													G|||	207	0.0413339	0.1513	0.0101	5008	,	,		16977	0.0		0.0	False		,,,				2504	0.0				p.L150F		Atlas-SNP	.											.	RGS13	31	.	0			c.G450C						PASS	.	G	PHE/LEU,PHE/LEU	577,3829	246.2+/-254.9	48,481,1674	46.0	45.0	45.0		450,450	2.7	1.0	1	dbSNP_123	45	4,8596	3.0+/-9.4	0,4,4296	yes	missense,missense	RGS13	NM_002927.4,NM_144766.2	22,22	48,485,5970	CC,CG,GG		0.0465,13.0958,4.4672	benign,benign	150/160,150/160	192628623	581,12425	2203	4300	6503	SO:0001583	missense	6003	exon7			ACTTTTGAAAACT	AF030107	CCDS1376.1	1q31.2	2008-02-05	2007-08-14		ENSG00000127074	ENSG00000127074		"""Regulators of G-protein signaling"""	9995	protein-coding gene	gene with protein product		607190	"""regulator of G-protein signalling 13"""			11875076	Standard	NM_144766		Approved		uc001gsk.3	O14921	OTTHUMG00000035601	ENST00000391995.2:c.450G>C	1.37:g.192628623G>C	ENSP00000375853:p.Leu150Phe	156.0	0.0	0		181.0	94.0	0.519337	NM_002927	Q6PGR2|Q8TD63|Q9BX45	Missense_Mutation	SNP	ENST00000391995.2	37	CCDS1376.1	71	0.03250915750915751	70	0.14227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	G	13.88	2.368730	0.42003	0.130958	4.65E-4	ENSG00000127074	ENST00000391995;ENST00000543215	T;T	0.36157	1.27;1.27	5.89	2.73	0.32206	Regulator of G protein signalling (2);Regulator of G protein signalling superfamily (1);	0.277274	0.34725	N	0.003740	T	0.00300	0.0009	M	0.75085	2.285	0.31991	P	0.6046279999999999	B	0.29531	0.247	B	0.35470	0.203	T	0.11743	-1.0575	9	0.62326	D	0.03	.	5.6215	0.17459	0.0815:0.1835:0.6077:0.1273	rs16834603;rs52813648;rs16834603	150	O14921	RGS13_HUMAN	F	150	ENSP00000375853:L150F;ENSP00000442837:L150F	ENSP00000375853:L150F	L	+	3	2	RGS13	190895246	0.082000	0.21442	1.000000	0.80357	0.888000	0.51559	0.259000	0.18405	1.497000	0.48584	0.591000	0.81541	TTG	G|0.955;C|0.045	0.045	strong		0.323	RGS13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086400.1	NM_002927	
OR1E2	8388	hgsc.bcm.edu	37	17	3336699	3336699	+	Missense_Mutation	SNP	C	C	G	rs78339092	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3336699C>G	ENST00000248384.1	-	1	436	c.437G>C	c.(436-438)aGc>aCc	p.S146T		NM_003554.1	NP_003545.1	P47887	OR1E2_HUMAN	olfactory receptor, family 1, subfamily E, member 2	146					sensory perception of chemical stimulus (GO:0007606)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|receptor activity (GO:0004872)			endometrium(3)|large_intestine(3)|lung(3)	9						GAGCATGGGGCTCATGATGGC	0.562													C|||	120	0.0239617	0.0885	0.0043	5008	,	,		19338	0.0		0.0	False		,,,				2504	0.0				p.S146T		Atlas-SNP	.											OR1E2,right_upper_lobe,carcinoma,+1,1	OR1E2	25	1	0			c.G437C						PASS	.																																			SO:0001583	missense	8388	exon1			ATGGGGCTCATGA	U04686	CCDS11026.1	17p13.3	2012-08-09			ENSG00000127780	ENSG00000127780		"""GPCR / Class A : Olfactory receptors"""	8190	protein-coding gene	gene with protein product				OR1E4		8004088, 9500546	Standard	NM_003554		Approved	OR17-93, OR17-135	uc010vre.2	P47887	OTTHUMG00000090651	ENST00000248384.1:c.437G>C	17.37:g.3336699C>G	ENSP00000248384:p.Ser146Thr	225.0	0.0	0		228.0	96.0	0.421053	NM_003554	O43877|O95632|Q0VAD5|Q0VAD6|Q9UL13	Missense_Mutation	SNP	ENST00000248384.1	37	CCDS11026.1	45	0.020604395604395604	45	0.09146341463414634	0	0.0	0	0.0	0	0.0	C	7.609	0.674467	0.14841	.	.	ENSG00000127780	ENST00000248384;ENST00000454364	T	0.03717	3.83	5.47	2.44	0.29823	GPCR, rhodopsin-like superfamily (1);	0.148993	0.48286	N	0.000187	T	0.00109	0.0003	N	0.08118	0	0.25052	N	0.99113	B	0.21225	0.053	B	0.26693	0.072	T	0.49495	-0.8934	10	0.33940	T	0.23	.	9.9959	0.41898	0.0:0.7793:0.0:0.2207	.	146	P47887	OR1E2_HUMAN	T	146;136	ENSP00000248384:S146T	ENSP00000248384:S146T	S	-	2	0	OR1E2	3283449	0.000000	0.05858	0.958000	0.39756	0.329000	0.28539	-0.448000	0.06820	0.439000	0.26476	0.650000	0.86243	AGC	C|0.987;G|0.013	0.013	strong		0.562	OR1E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207311.1		
TMPRSS11B	132724	hgsc.bcm.edu	37	4	69098115	69098115	+	Silent	SNP	A	A	G	rs10018067	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:69098115A>G	ENST00000332644.5	-	6	650	c.489T>C	c.(487-489)tcT>tcC	p.S163S		NM_182502.3	NP_872308.2	Q86T26	TM11B_HUMAN	transmembrane protease, serine 11B	163						extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)	27						TAAGCATTTCAGAAGCAGCCT	0.289													a|||	141	0.028155	0.1006	0.0086	5008	,	,		13924	0.0		0.0	False		,,,				2504	0.002				p.S163S		Atlas-SNP	.											.	TMPRSS11B	66	.	0			c.T489C						PASS	.	G		346,4054	754.8+/-412.5	17,312,1871	49.0	56.0	53.0		489	1.9	0.0	4	dbSNP_119	53	14,8572	810.0+/-407.1	0,14,4279	no	coding-synonymous	TMPRSS11B	NM_182502.3		17,326,6150	GG,GA,AA		0.1631,7.8636,2.7722		163/417	69098115	360,12626	2200	4293	6493	SO:0001819	synonymous_variant	132724	exon6			CATTTCAGAAGCA	BX537945	CCDS3521.1	4q13.2	2010-04-13			ENSG00000185873	ENSG00000185873		"""Serine peptidases / Transmembrane"""	25398	protein-coding gene	gene with protein product							Standard	NM_182502		Approved		uc003hdw.4	Q86T26	OTTHUMG00000129301	ENST00000332644.5:c.489T>C	4.37:g.69098115A>G		114.0	0.0	0		158.0	80.0	0.506329	NM_182502	A8K4D9	Silent	SNP	ENST00000332644.5	37	CCDS3521.1																																																																																			A|0.973;G|0.027	0.027	strong		0.289	TMPRSS11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251431.2	NM_182502	
SNAI1	6615	hgsc.bcm.edu	37	20	48600475	48600475	+	Missense_Mutation	SNP	C	C	T	rs34261470	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:48600475C>T	ENST00000244050.2	+	2	258	c.197C>T	c.(196-198)gCg>gTg	p.A66V		NM_005985.3	NP_005976.2	O95863	SNAI1_HUMAN	snail family zinc finger 1	66			A -> V (in dbSNP:rs34261470).		cartilage morphogenesis (GO:0060536)|cell migration (GO:0016477)|epithelial to mesenchymal transition (GO:0001837)|hair follicle morphogenesis (GO:0031069)|left/right pattern formation (GO:0060972)|mesoderm formation (GO:0001707)|negative regulation of cell differentiation involved in embryonic placenta development (GO:0060806)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|Notch signaling involved in heart development (GO:0061314)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of tight junction assembly (GO:2000810)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	kinase binding (GO:0019900)|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 regulatory region sequence-specific DNA binding (GO:0000977)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)|ovary(2)	17			BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			TCTGTCCTGGCGCCCCAAGCC	0.657													C|||	140	0.0279553	0.093	0.0101	5008	,	,		14457	0.0		0.0	False		,,,				2504	0.0102				p.A66V		Atlas-SNP	.											.	SNAI1	28	.	0			c.C197T						PASS	.	C	VAL/ALA	321,4085	168.3+/-199.2	18,285,1900	45.0	50.0	48.0		197	1.8	0.9	20	dbSNP_126	48	7,8593	5.7+/-21.5	0,7,4293	no	missense	SNAI1	NM_005985.3	64	18,292,6193	TT,TC,CC		0.0814,7.2855,2.5219	benign	66/265	48600475	328,12678	2203	4300	6503	SO:0001583	missense	6615	exon2			TCCTGGCGCCCCA	AF125377	CCDS13423.1	20q13.2	2013-05-23	2013-05-23		ENSG00000124216	ENSG00000124216		"""Snail homologs"", ""Zinc fingers, C2H2-type"""	11128	protein-coding gene	gene with protein product		604238	"""snail 1 (drosophila homolog), zinc finger protein"", ""snail homolog 1 (Drosophila)"""			10585766	Standard	NM_005985		Approved	SNA, SLUGH2, SNAH, SNAIL1, SNAIL	uc002xuz.3	O95863	OTTHUMG00000033048	ENST00000244050.2:c.197C>T	20.37:g.48600475C>T	ENSP00000244050:p.Ala66Val	43.0	0.0	0		50.0	19.0	0.38	NM_005985	B2R842|Q9P113|Q9UBP7|Q9UHH7	Missense_Mutation	SNP	ENST00000244050.2	37	CCDS13423.1	38	0.0173992673992674	32	0.06504065040650407	6	0.016574585635359115	0	0.0	0	0.0	C	12.23	1.875633	0.33162	0.072855	8.14E-4	ENSG00000124216	ENST00000244050	T	0.20332	2.08	4.94	1.81	0.25067	.	1.159810	0.06133	N	0.670998	T	0.01061	0.0035	L	0.33485	1.01	0.23704	N	0.997068	B	0.11235	0.004	B	0.04013	0.001	T	0.32134	-0.9918	10	0.13853	T	0.58	-4.3384	7.28	0.26306	0.0:0.6314:0.0:0.3686	rs34261470	66	O95863	SNAI1_HUMAN	V	66	ENSP00000244050:A66V	ENSP00000244050:A66V	A	+	2	0	SNAI1	48033882	0.003000	0.15002	0.936000	0.37596	0.943000	0.58893	1.315000	0.33608	0.429000	0.26202	0.557000	0.71058	GCG	C|0.979;T|0.021	0.021	strong		0.657	SNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080350.1		
ADAM19	8728	hgsc.bcm.edu	37	5	156964944	156964944	+	Missense_Mutation	SNP	G	G	C	rs11134804	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:156964944G>C	ENST00000517905.1	-	4	351	c.307C>G	c.(307-309)Caa>Gaa	p.Q103E	ADAM19_ENST00000430702.2_5'UTR|ADAM19_ENST00000257527.4_Missense_Mutation_p.Q103E|ADAM19_ENST00000394020.1_Missense_Mutation_p.Q105E			Q9H013	ADA19_HUMAN	ADAM metallopeptidase domain 19	103					heart development (GO:0007507)|membrane protein ectodomain proteolysis (GO:0006509)	integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Renal(175;0.00488)	Medulloblastoma(196;0.0359)|all_neural(177;0.14)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GTGGTGGTTTGAGGGTTACCA	0.443													G|||	136	0.0271565	0.0968	0.0086	5008	,	,		18034	0.0		0.0	False		,,,				2504	0.002				p.Q103E		Atlas-SNP	.											.	ADAM19	216	.	0			c.C307G						PASS	.	G	GLU/GLN	377,4029	191.9+/-217.4	13,351,1839	207.0	192.0	197.0		307	5.2	1.0	5	dbSNP_120	197	4,8596	3.0+/-9.4	0,4,4296	yes	missense	ADAM19	NM_033274.3	29	13,355,6135	CC,CG,GG		0.0465,8.5565,2.9294	benign	103/919	156964944	381,12625	2203	4300	6503	SO:0001583	missense	8728	exon4			TGGTTTGAGGGTT	AF311317	CCDS4338.1	5q33.3	2010-06-24	2010-06-24		ENSG00000135074	ENSG00000135074		"""ADAM metallopeptidase domain containing"""	197	protein-coding gene	gene with protein product	"""meltrin beta"""	603640	"""a disintegrin and metalloproteinase domain 19 (meltrin beta)"""			9806848	Standard	NM_033274		Approved	MLTNB	uc003lwz.4	Q9H013	OTTHUMG00000130242	ENST00000517905.1:c.307C>G	5.37:g.156964944G>C	ENSP00000428654:p.Gln103Glu	91.0	0.0	0		91.0	44.0	0.483516	NM_033274	Q9BZL5|Q9UHP2	Missense_Mutation	SNP	ENST00000517905.1	37		51	0.023351648351648352	47	0.09552845528455285	4	0.011049723756906077	0	0.0	0	0.0	G	14.59	2.579496	0.46006	0.085565	4.65E-4	ENSG00000135074	ENST00000257527;ENST00000394020;ENST00000517905	T;T;T	0.05199	3.48;3.48;3.48	5.17	5.17	0.71159	.	0.462253	0.20288	N	0.095302	T	0.00241	0.0007	L	0.41906	1.305	0.80722	D	1	B	0.23249	0.082	B	0.24394	0.053	T	0.39941	-0.9589	10	0.72032	D	0.01	.	14.5834	0.68308	0.0:0.0:1.0:0.0	rs11134804;rs56446321;rs11134804	103	Q9H013-2	.	E	103;105;103	ENSP00000257527:Q103E;ENSP00000377588:Q105E;ENSP00000428654:Q103E	ENSP00000257527:Q103E	Q	-	1	0	ADAM19	156897522	1.000000	0.71417	0.979000	0.43373	0.883000	0.51084	3.257000	0.51500	2.584000	0.87258	0.563000	0.77884	CAA	G|0.965;C|0.035	0.035	strong		0.443	ADAM19-003	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000373918.1	NM_033274	
NOTCH2NL	388677	hgsc.bcm.edu	37	1	145281413	145281413	+	Missense_Mutation	SNP	G	G	A	rs76765512	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:145281413G>A	ENST00000369340.3	+	5	787	c.343G>A	c.(343-345)Gca>Aca	p.A115T	NOTCH2NL_ENST00000362074.6_Missense_Mutation_p.A115T|RP11-458D21.5_ENST00000468030.1_Missense_Mutation_p.A115T|NOTCH2NL_ENST00000344859.3_Missense_Mutation_p.A115T			Q7Z3S9	NT2NL_HUMAN	notch 2 N-terminal like	115	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|Notch signaling pathway (GO:0007219)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	27						TCATCCCTGTGCAAATGGAAG	0.502																																					p.A115T		Atlas-SNP	.											.	NOTCH2NL	100	.	0			c.G343A						PASS	.	G	THR/ALA	228,4178	115.4+/-153.4	0,228,1975	339.0	343.0	342.0		343	2.9	1.0	1	dbSNP_131	342	2,8596	1.2+/-3.3	0,2,4297	no	missense	NOTCH2NL	NM_203458.3	58	0,230,6272	AA,AG,GG		0.0233,5.1748,1.7687	possibly-damaging	115/237	145281413	230,12774	2203	4299	6502	SO:0001583	missense	388677	exon4			CCCTGTGCAAATG		CCDS72880.1	1q21.2	2010-06-24	2010-06-24		ENSG00000213240	ENSG00000213240			31862	protein-coding gene	gene with protein product			"""Notch homolog 2 (Drosophila) N-terminal like"""			14673143	Standard	NM_203458		Approved	N2N	uc001emn.4	Q7Z3S9	OTTHUMG00000013754	ENST00000369340.3:c.343G>A	1.37:g.145281413G>A	ENSP00000358346:p.Ala115Thr	1344.0	2.0	0.0014881		1480.0	388.0	0.262162	NM_203458	Q5BKT8|Q5VTG9|Q5XG84|Q6P192|Q8NC23|Q8WUQ9|Q96FY1	Missense_Mutation	SNP	ENST00000369340.3	37	CCDS909.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.233634	0.79688	0.051748	2.33E-4	ENSG00000213240	ENST00000362074;ENST00000344859;ENST00000369340	D;D;D	0.87491	-2.26;-2.26;-2.26	2.87	2.87	0.33458	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	.	.	.	.	T	0.76835	0.4043	L	0.37507	1.11	0.32769	N	0.504048	P;P	0.49783	0.825;0.928	B;P	0.48571	0.342;0.582	T	0.70378	-0.4888	9	0.29301	T	0.29	.	11.5361	0.50639	0.0:0.0:1.0:0.0	.	115;115	Q7Z3S9-2;Q7Z3S9	.;NT2NL_HUMAN	T	115	ENSP00000354929:A115T;ENSP00000344557:A115T;ENSP00000358346:A115T	ENSP00000344557:A115T	A	+	1	0	NOTCH2NL	143992770	1.000000	0.71417	0.999000	0.59377	0.982000	0.71751	7.645000	0.83430	1.601000	0.50113	0.400000	0.26472	GCA	G|0.980;A|0.020	0.020	strong		0.502	NOTCH2NL-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038546.1	NM_203458	
ARSK	153642	hgsc.bcm.edu	37	5	94936744	94936744	+	Silent	SNP	G	G	A	rs61733083	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:94936744G>A	ENST00000380009.4	+	7	1495	c.1290G>A	c.(1288-1290)tcG>tcA	p.S430S		NM_198150.2	NP_937793.1	Q6UWY0	ARSK_HUMAN	arylsulfatase family, member K	430					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(1)	16		all_cancers(142;3.38e-06)|all_epithelial(76;6.57e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473)		all cancers(79;6.5e-16)		TAGCCTATTCGGATGGTGCAT	0.383													G|||	47	0.00938498	0.034	0.0029	5008	,	,		20862	0.0		0.0	False		,,,				2504	0.0				p.S430S		Atlas-SNP	.											.	ARSK	29	.	0			c.G1290A						PASS	.	G		120,4286	88.7+/-127.4	0,120,2083	125.0	119.0	121.0		1290	-1.4	0.7	5	dbSNP_129	121	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ARSK	NM_198150.2		0,121,6382	AA,AG,GG		0.0116,2.7236,0.9303		430/537	94936744	121,12885	2203	4300	6503	SO:0001819	synonymous_variant	153642	exon7			CTATTCGGATGGT		CCDS4073.1	5q15	2013-02-14	2006-03-07		ENSG00000164291	ENSG00000164291		"""Arylsulfatase family"""	25239	protein-coding gene	gene with protein product		610011	"""arylsulfatase K"""			12975309, 16174644	Standard	NM_198150		Approved	DKFZp313G1735, TSULF	uc003kld.3	Q6UWY0	OTTHUMG00000121166	ENST00000380009.4:c.1290G>A	5.37:g.94936744G>A		112.0	0.0	0		130.0	56.0	0.430769	NM_198150	A2BDE3|B4E1I4|Q3ZCW3|Q8N3Q8	Silent	SNP	ENST00000380009.4	37	CCDS4073.1																																																																																			G|0.990;A|0.010	0.010	strong		0.383	ARSK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241652.2	NM_198150	
GPRIN2	9721	hgsc.bcm.edu	37	10	46999385	46999385	+	Missense_Mutation	SNP	C	C	T	rs113256776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:46999385C>T	ENST00000374317.1	+	3	778	c.505C>T	c.(505-507)Cct>Tct	p.P169S	GPRIN2_ENST00000374314.4_Missense_Mutation_p.P169S	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	169										breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						TGGCCAGGCCCCTGCAGGCCT	0.637													C|||	128	0.0255591	0.09	0.0115	5008	,	,		39000	0.0		0.001	False		,,,				2504	0.0				p.P169S		Atlas-SNP	.											.	GPRIN2	94	.	0			c.C505T						PASS	.	C	SER/PRO	231,4175		0,231,1972	39.0	40.0	40.0		505	0.7	0.0	10	dbSNP_132	40	1,8599		0,1,4299	yes	missense	GPRIN2	NM_014696.3	74	0,232,6271	TT,TC,CC		0.0116,5.2429,1.7838	probably-damaging	169/459	46999385	232,12774	2203	4300	6503	SO:0001583	missense	9721	exon3			CAGGCCCCTGCAG	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.505C>T	10.37:g.46999385C>T	ENSP00000363436:p.Pro169Ser	37.0	0.0	0		70.0	15.0	0.214286	NM_014696	Q5SVF0	Missense_Mutation	SNP	ENST00000374317.1	37	CCDS31192.1	.	.	.	.	.	.	.	.	.	.	C	9.805	1.181582	0.21787	0.052429	1.16E-4	ENSG00000204175	ENST00000374317;ENST00000374314	T;T	0.03330	3.97;3.97	4.71	0.695	0.18070	.	0.700953	0.12491	N	0.464220	T	0.00695	0.0023	M	0.63428	1.95	0.09310	N	1	B	0.22909	0.077	B	0.20767	0.031	T	0.39165	-0.9627	10	0.87932	D	0	-0.5548	3.3753	0.07235	0.1809:0.5265:0.0:0.2926	.	169	O60269	GRIN2_HUMAN	S	169	ENSP00000363436:P169S;ENSP00000363433:P169S	ENSP00000363433:P169S	P	+	1	0	GPRIN2	46419391	0.000000	0.05858	0.003000	0.11579	0.063000	0.16089	0.087000	0.14958	0.036000	0.15547	0.650000	0.86243	CCT	C|0.975;T|0.025	0.025	strong		0.637	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696	
SLC2A8	29988	hgsc.bcm.edu	37	9	130162230	130162230	+	Silent	SNP	C	C	G	rs36057295	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:130162230C>G	ENST00000373371.3	+	4	560	c.471C>G	c.(469-471)ctC>ctG	p.L157L	SLC2A8_ENST00000373360.3_Silent_p.L157L|SLC2A8_ENST00000373352.1_5'UTR	NM_001271712.1|NM_014580.3	NP_001258641.1|NP_055395.2	Q9NY64	GTR8_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 8	157					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						GGGGGTTGCTCGGCTCCTGTG	0.557													C|||	130	0.0259585	0.0968	0.0029	5008	,	,		17695	0.0		0.0	False		,,,				2504	0.0				p.L157L		Atlas-SNP	.											.	SLC2A8	27	.	0			c.C471G						PASS	.	C		315,4091	169.1+/-199.8	9,297,1897	137.0	134.0	135.0		471	-5.9	1.0	9	dbSNP_126	135	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SLC2A8	NM_014580.3		9,299,6195	GG,GC,CC		0.0233,7.1493,2.4373		157/478	130162230	317,12689	2203	4300	6503	SO:0001819	synonymous_variant	29988	exon4			GTTGCTCGGCTCC	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.471C>G	9.37:g.130162230C>G		155.0	0.0	0		108.0	32.0	0.296296	NM_014580	Q8WUZ9|Q9NSC4	Silent	SNP	ENST00000373371.3	37	CCDS6870.1	38	0.0173992673992674	37	0.07520325203252033	1	0.0027624309392265192	0	0.0	0	0.0	C	1.094	-0.663174	0.03428	0.071493	2.33E-4	ENSG00000136856	ENST00000419132	.	.	.	5.35	-5.92	0.02261	.	.	.	.	.	T	0.04003	0.0112	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40701	-0.9549	4	.	.	.	.	7.9566	0.30047	0.0948:0.1228:0.603:0.1794	rs36057295	.	.	.	W	67	.	.	S	+	2	0	SLC2A8	129202051	0.005000	0.15991	0.967000	0.41034	0.066000	0.16364	-2.012000	0.01451	-0.659000	0.05359	-0.302000	0.09304	TCG	C|0.975;G|0.025	0.025	strong		0.557	SLC2A8-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054177.1	NM_014580	
NARS2	79731	hgsc.bcm.edu	37	11	78279744	78279744	+	Silent	SNP	T	T	C	rs60510975	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:78279744T>C	ENST00000281038.5	-	3	681	c.306A>G	c.(304-306)ccA>ccG	p.P102P	NARS2_ENST00000528850.1_5'UTR	NM_001243251.1|NM_024678.5	NP_001230180.1|NP_078954.4	Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial (putative)	102					asparaginyl-tRNA aminoacylation (GO:0006421)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	asparagine-tRNA ligase activity (GO:0004816)|ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)	27	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)	GCCTTTTGGATGGACTTTTTA	0.333													T|||	225	0.0449281	0.1657	0.0072	5008	,	,		17073	0.0		0.001	False		,,,				2504	0.0				p.P102P		Atlas-SNP	.											NARS2,lower_third,carcinoma,-2,1	NARS2	62	1	0			c.A306G						PASS	.	T		604,3796	264.1+/-265.8	41,522,1637	182.0	174.0	177.0		306	-1.5	1.0	11	dbSNP_129	177	3,8579	3.0+/-9.4	0,3,4288	no	coding-synonymous	NARS2	NM_024678.5		41,525,5925	CC,CT,TT		0.035,13.7273,4.6757		102/478	78279744	607,12375	2200	4291	6491	SO:0001819	synonymous_variant	79731	exon3			TTTGGATGGACTT	BC007800	CCDS8261.1, CCDS58164.1	11q14.1	2011-07-01	2007-02-23		ENSG00000137513	ENSG00000137513	6.1.1.22	"""Aminoacyl tRNA synthetases / Class II"""	26274	protein-coding gene	gene with protein product	"""asparagine tRNA ligase 2, mitochondrial (putative)"""	612803				15779907	Standard	NM_024678		Approved	FLJ23441, SLM5	uc001ozi.3	Q96I59	OTTHUMG00000166702	ENST00000281038.5:c.306A>G	11.37:g.78279744T>C		185.0	0.0	0		193.0	97.0	0.502591	NM_024678	G3V178	Silent	SNP	ENST00000281038.5	37	CCDS8261.1																																																																																			T|0.960;C|0.040	0.040	strong		0.333	NARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391138.2	NM_024678	
MDN1	23195	hgsc.bcm.edu	37	6	90461235	90461235	+	Missense_Mutation	SNP	T	T	C	rs115558420	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:90461235T>C	ENST00000369393.3	-	23	3257	c.3142A>G	c.(3142-3144)Aag>Gag	p.K1048E	MDN1_ENST00000428876.1_Missense_Mutation_p.K1048E			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	1048					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		GTAGGCTCCTTGTCTCCCACC	0.478													T|||	9	0.00179712	0.0068	0.0	5008	,	,		18332	0.0		0.0	False		,,,				2504	0.0				p.K1048E		Atlas-SNP	.											MDN1,NS,carcinoma,+2,1	MDN1	478	1	0			c.A3142G						PASS	.	T	GLU/LYS	41,4365	44.6+/-78.6	0,41,2162	155.0	133.0	140.0		3142	4.5	1.0	6	dbSNP_132	140	0,8600		0,0,4300	yes	missense	MDN1	NM_014611.1	56	0,41,6462	CC,CT,TT		0.0,0.9305,0.3152	possibly-damaging	1048/5597	90461235	41,12965	2203	4300	6503	SO:0001583	missense	23195	exon23			GCTCCTTGTCTCC	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.3142A>G	6.37:g.90461235T>C	ENSP00000358400:p.Lys1048Glu	165.0	0.0	0		186.0	90.0	0.483871	NM_014611	O15019|Q5T794	Missense_Mutation	SNP	ENST00000369393.3	37	CCDS5024.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	T	15.19	2.759315	0.49468	0.009305	0.0	ENSG00000112159	ENST00000369393;ENST00000428876;ENST00000439638	T;T;T	0.39592	1.07;1.07;1.07	5.71	4.48	0.54585	.	0.162096	0.53938	D	0.000057	T	0.13200	0.0320	N	0.22421	0.69	0.38581	D	0.950177	B;B	0.19331	0.035;0.003	B;B	0.15484	0.008;0.013	T	0.06409	-1.0828	10	0.14656	T	0.56	.	12.5357	0.56140	0.0:0.0:0.1389:0.8611	.	975;1048	Q5T795;Q9NU22	.;MDN1_HUMAN	E	1048;1048;975	ENSP00000358400:K1048E;ENSP00000413970:K1048E;ENSP00000409664:K975E	ENSP00000358400:K1048E	K	-	1	0	MDN1	90517956	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	3.063000	0.49978	2.172000	0.68678	0.533000	0.62120	AAG	T|0.997;C|0.003	0.003	strong		0.478	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
TTN	7273	hgsc.bcm.edu	37	2	179594590	179594590	+	Silent	SNP	T	T	A	rs66523653	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179594590T>A	ENST00000591111.1	-	61	17663	c.17439A>T	c.(17437-17439)acA>acT	p.T5813T	TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Silent_p.T4886T|RP11-171I2.1_ENST00000590024.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Silent_p.T6130T			Q8WZ42	TITIN_HUMAN	titin	12614	Ig-like 39.				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)			TAGGAGTGCCTGTTATTTGGC	0.408													T|||	78	0.0155751	0.0537	0.0101	5008	,	,		18115	0.0		0.0	False		,,,				2504	0.0				p.T6130T		Atlas-SNP	.											.	TTN	18412	.	0			c.A18390T						PASS	.	T	,,,	168,3604		3,162,1721	58.0	56.0	57.0		,14658,,	2.1	1.0	2	dbSNP_130	57	1,8225		0,1,4112	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	3,163,5833	AA,AT,TT		0.0122,4.4539,1.4086	,,,	,4886/33424,,	179594590	169,11829	1886	4113	5999	SO:0001819	synonymous_variant	7273	exon63			AGTGCCTGTTATT	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.17439A>T	2.37:g.179594590T>A		253.0	0.0	0		237.0	118.0	0.49789	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|0.984;A|0.016	0.016	strong		0.408	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TJP2	9414	hgsc.bcm.edu	37	9	71851080	71851080	+	Silent	SNP	C	C	T	rs12340440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:71851080C>T	ENST00000377245.4	+	13	2125	c.1917C>T	c.(1915-1917)gaC>gaT	p.D639D	TJP2_ENST00000265384.7_Silent_p.D639D|TJP2_ENST00000453658.2_Silent_p.D616D|TJP2_ENST00000535702.1_Silent_p.D643D|TJP2_ENST00000348208.4_Silent_p.D639D|TJP2_ENST00000539225.1_Silent_p.D670D	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	639	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|hippo signaling (GO:0035329)|nucleotide phosphorylation (GO:0046939)|response to organic substance (GO:0010033)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	guanylate kinase activity (GO:0004385)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(5)|lung(9)|prostate(3)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	35						CACTGTATGACGGCAAGCTGG	0.502													C|||	75	0.014976	0.0545	0.0043	5008	,	,		19727	0.0		0.0	False		,,,				2504	0.0				p.D670D		Atlas-SNP	.											TJP2,colon,carcinoma,0,1	TJP2	120	1	0			c.C2010T						scavenged	.	C	,,,,,	188,4218	120.4+/-158.0	5,178,2020	106.0	97.0	100.0		1848,1929,2010,1917,1917,1917	-3.3	1.0	9	dbSNP_120	100	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TJP2	NM_001170414.1,NM_001170415.1,NM_001170416.1,NM_001170630.1,NM_004817.3,NM_201629.3	,,,,,	5,179,6319	TT,TC,CC		0.0116,4.2669,1.4532	,,,,,	616/1021,643/1158,670/1222,639/994,639/1191,639/1044	71851080	189,12817	2203	4300	6503	SO:0001819	synonymous_variant	9414	exon13			GTATGACGGCAAG	L27476	CCDS6627.1, CCDS6628.1, CCDS55314.1, CCDS55315.1, CCDS55316.1, CCDS55317.1	9q13-q21	2012-07-12	2012-07-12		ENSG00000119139	ENSG00000119139			11828	protein-coding gene	gene with protein product	"""Friedreich ataxia region gene X104 (tight junction protein ZO-2)"", ""zona occludens 2"""	607709	"""deafness, autosomal dominant 51"""	DFNA51		7951235, 20602916	Standard	NM_001170630		Approved	ZO-2, X104, ZO2	uc011lrv.2	Q9UDY2	OTTHUMG00000019978	ENST00000377245.4:c.1917C>T	9.37:g.71851080C>T		54.0	1.0	0.0185185		57.0	36.0	0.631579	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Silent	SNP	ENST00000377245.4	37	CCDS6627.1																																																																																			C|0.983;T|0.017	0.017	strong		0.502	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629	
ZNF598	90850	hgsc.bcm.edu	37	16	2050151	2050151	+	Silent	SNP	A	A	G	rs114023844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2050151A>G	ENST00000563630.1	-	9	1476	c.1234T>C	c.(1234-1236)Ttg>Ctg	p.L412L	ZNF598_ENST00000562103.1_Silent_p.L412L|ZNF598_ENST00000431526.1_Silent_p.L467L|AC005606.15_ENST00000567515.1_lincRNA			Q86UK7	ZN598_HUMAN	zinc finger protein 598	467							poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|skin(1)|urinary_tract(1)	16						GGCAGCGCCAACCCCACAGGG	0.687													A|||	137	0.0273562	0.0998	0.0072	5008	,	,		16236	0.0		0.0	False		,,,				2504	0.0				p.L467L		Atlas-SNP	.											.	ZNF598	55	.	0			c.T1399C						PASS	.	A		210,3608		6,198,1705	22.0	26.0	25.0		1401	-6.5	0.0	16	dbSNP_132	25	0,8050		0,0,4025	no	coding-synonymous	ZNF598	NM_178167.2		6,198,5730	GG,GA,AA		0.0,5.5003,1.7695		467/905	2050151	210,11658	1909	4025	5934	SO:0001819	synonymous_variant	90850	exon11			GCGCCAACCCCAC	BC029270		16p13.3	2008-05-02				ENSG00000167962		"""Zinc fingers, C2H2-type"""	28079	protein-coding gene	gene with protein product							Standard	NM_178167		Approved	FLJ00086	uc002cof.2	Q86UK7		ENST00000563630.1:c.1234T>C	16.37:g.2050151A>G		35.0	0.0	0		43.0	19.0	0.44186	NM_178167	Q8IW49|Q8N3D9|Q96FG3|Q9H7J3	Silent	SNP	ENST00000563630.1	37																																																																																				A|0.978;G|0.022	0.022	strong		0.687	ZNF598-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000434439.1	NM_178167	
MAP1B	4131	hgsc.bcm.edu	37	5	71489695	71489695	+	Silent	SNP	C	C	T	rs2227915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:71489695C>T	ENST00000296755.7	+	5	811	c.513C>T	c.(511-513)atC>atT	p.I171I		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	171					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		AAACCCAGATCGGGGAGTTAC	0.433													C|||	156	0.0311502	0.1135	0.0086	5008	,	,		20619	0.0		0.0	False		,,,				2504	0.0				p.I171I	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											.	MAP1B	243	.	0			c.C513T						PASS	.	C		353,4053	182.9+/-210.6	14,325,1864	48.0	47.0	48.0		513	2.3	1.0	5	dbSNP_123	48	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	MAP1B	NM_005909.3		14,329,6160	TT,TC,CC		0.0465,8.0118,2.7449		171/2469	71489695	357,12649	2203	4300	6503	SO:0001819	synonymous_variant	4131	exon5			CCAGATCGGGGAG	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 102"""	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.513C>T	5.37:g.71489695C>T		52.0	0.0	0		49.0	28.0	0.571429	NM_005909	A2BDK5	Silent	SNP	ENST00000296755.7	37	CCDS4012.1																																																																																			C|0.968;T|0.032	0.032	strong		0.433	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909	
ARL11	115761	hgsc.bcm.edu	37	13	50205165	50205165	+	Missense_Mutation	SNP	G	G	C	rs35835937	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:50205165G>C	ENST00000282026.1	+	2	917	c.582G>C	c.(580-582)aaG>aaC	p.K194N	ARL11_ENST00000490932.1_Intron	NM_138450.5	NP_612459.1	Q969Q4	ARL11_HUMAN	ADP-ribosylation factor-like 11	194					hematopoietic progenitor cell differentiation (GO:0002244)|small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			kidney(1)|large_intestine(4)|ovary(1)	6		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.119)|Kidney(9;0.169)	GBM - Glioblastoma multiforme(99;1.67e-09)		GAGACAGCAAGAGATCTTGAT	0.522													G|||	38	0.00758786	0.028	0.0014	5008	,	,		20145	0.0		0.0	False		,,,				2504	0.0				p.K194N		Atlas-SNP	.											.	ARL11	26	.	0			c.G582C						PASS	.	G	ASN/LYS	90,4200		1,88,2056	6.0	6.0	6.0		582	0.8	0.0	13	dbSNP_126	6	0,8320		0,0,4160	yes	missense	ARL11	NM_138450.5	94	1,88,6216	CC,CG,GG		0.0,2.0979,0.7137	benign	194/197	50205165	90,12520	2145	4160	6305	SO:0001583	missense	115761	exon2			CAGCAAGAGATCT	AF441378	CCDS9419.1	13q14.12	2014-05-09			ENSG00000152213	ENSG00000152213		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	24046	protein-coding gene	gene with protein product		609351				12477932	Standard	NM_138450		Approved	ARLTS1, FLJ33930	uc001vdf.2	Q969Q4	OTTHUMG00000016919	ENST00000282026.1:c.582G>C	13.37:g.50205165G>C	ENSP00000282026:p.Lys194Asn	167.0	0.0	0		160.0	91.0	0.56875	NM_138450		Missense_Mutation	SNP	ENST00000282026.1	37	CCDS9419.1	15	0.006868131868131868	15	0.03048780487804878	0	0.0	0	0.0	0	0.0	G	12.80	2.047801	0.36085	0.020979	0.0	ENSG00000152213	ENST00000282026	T	0.61158	0.13	4.85	0.84	0.18912	.	.	.	.	.	T	0.17280	0.0415	N	0.22421	0.69	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.20140	-1.0284	9	0.87932	D	0	.	5.8114	0.18467	0.1723:0.2988:0.5288:0.0	rs35835937	194	Q969Q4	ARL11_HUMAN	N	194	ENSP00000282026:K194N	ENSP00000282026:K194N	K	+	3	2	ARL11	49103166	0.006000	0.16342	0.000000	0.03702	0.014000	0.08584	0.717000	0.25851	0.195000	0.20347	0.561000	0.74099	AAG	G|0.993;C|0.007	0.007	strong		0.522	ARL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044929.2	NM_138450	
ZPBP2	124626	hgsc.bcm.edu	37	17	38028635	38028635	+	Silent	SNP	T	T	C	rs61737283	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38028635T>C	ENST00000348931.4	+	5	710	c.519T>C	c.(517-519)agT>agC	p.S173S	ZPBP2_ENST00000377940.3_Silent_p.S151S|ZPBP2_ENST00000584588.1_Intron	NM_199321.2	NP_955353.1	Q6X784	ZPBP2_HUMAN	zona pellucida binding protein 2	173			S -> I (in dbSNP:rs11557467). {ECO:0000269|PubMed:14702039}.		acrosome assembly (GO:0001675)|binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|extracellular region (GO:0005576)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)				kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	15	Colorectal(19;0.000442)		Lung(15;0.00849)|LUSC - Lung squamous cell carcinoma(15;0.171)			TCTTGGATAGTCTAATTTCTG	0.358													T|||	148	0.0295527	0.1089	0.0058	5008	,	,		14981	0.0		0.0	False		,,,				2504	0.0				p.S173S		Atlas-SNP	.											.	ZPBP2	33	.	0			c.T519C						PASS	.																																			SO:0001819	synonymous_variant	124626	exon5			GGATAGTCTAATT	BC043152	CCDS11352.1, CCDS11353.2	17q21.1	2013-01-11			ENSG00000186075	ENSG00000186075		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	20678	protein-coding gene	gene with protein product		608499					Standard	XM_005257031		Approved	ZPBPL, MGC41930	uc002hte.3	Q6X784	OTTHUMG00000133022	ENST00000348931.4:c.519T>C	17.37:g.38028635T>C		76.0	0.0	0		89.0	48.0	0.539326	NM_199321	A8K8L8|Q6X783|Q86XL5	Silent	SNP	ENST00000348931.4	37	CCDS11352.1																																																																																			T|0.868;C|0.132	0.132	strong		0.358	ZPBP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256609.2	NM_198844	
DNAH6	1768	hgsc.bcm.edu	37	2	84924783	84924783	+	Missense_Mutation	SNP	G	G	C	rs73943384	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:84924783G>C	ENST00000237449.6	+	46	7617	c.7609G>C	c.(7609-7611)Gag>Cag	p.E2537Q	DNAH6_ENST00000389394.3_Missense_Mutation_p.E2537Q|DNAH6_ENST00000398278.2_Missense_Mutation_p.E2488Q|DNAH6_ENST00000602588.1_Missense_Mutation_p.E509Q			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	2537	AAA 4. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						GGATGAACTGGAGCAGGTTTT	0.428													G|||	68	0.0135783	0.0499	0.0029	5008	,	,		16198	0.0		0.0	False		,,,				2504	0.0				p.E2537Q		Atlas-SNP	.											.	DNAH6	194	.	0			c.G7609C						PASS	.	G	GLN/GLU	42,1342		0,42,650	138.0	126.0	130.0		7609	5.7	1.0	2	dbSNP_130	130	1,3181		0,1,1590	yes	missense	DNAH6	NM_001370.1	29	0,43,2240	CC,CG,GG		0.0314,3.0347,0.9417	probably-damaging	2537/4159	84924783	43,4523	692	1591	2283	SO:0001583	missense	1768	exon47			GAACTGGAGCAGG	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.7609G>C	2.37:g.84924783G>C	ENSP00000237449:p.Glu2537Gln	77.0	0.0	0		75.0	37.0	0.493333	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Missense_Mutation	SNP	ENST00000237449.6	37	CCDS46348.1	23	0.010531135531135532	21	0.042682926829268296	2	0.0055248618784530384	0	0.0	0	0.0	G	25.4	4.630590	0.87660	0.030347	3.14E-4	ENSG00000115423	ENST00000389394;ENST00000398278;ENST00000237449	T;T;T	0.56103	0.73;0.48;0.73	5.67	5.67	0.87782	Dynein heavy chain, P-loop containing D4 domain (1);ATPase, AAA+ type, core (1);	.	.	.	.	T	0.38401	0.1039	L	0.57130	1.785	0.47949	D	0.999553	D;D	0.67145	0.996;0.99	D;D	0.70716	0.97;0.962	T	0.57751	-0.7757	9	0.49607	T	0.09	.	18.5426	0.91035	0.0:0.0:1.0:0.0	.	2537;2488	Q9C0G6;Q9C0G6-4	DYH6_HUMAN;.	Q	2537;2488;2537	ENSP00000374045:E2537Q;ENSP00000381326:E2488Q;ENSP00000237449:E2537Q	ENSP00000237449:E2537Q	E	+	1	0	DNAH6	84778294	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	4.379000	0.59575	2.682000	0.91365	0.484000	0.47621	GAG	G|0.989;C|0.011	0.011	strong		0.428	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
GABRB1	2560	hgsc.bcm.edu	37	4	47408850	47408850	+	Silent	SNP	C	C	T	rs115114447	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:47408850C>T	ENST00000295454.3	+	8	1279	c.987C>T	c.(985-987)taC>taT	p.Y329Y	GABRB1_ENST00000538619.1_Silent_p.Y259Y	NM_000812.3	NP_000803.2	P18505	GBRB1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 1	329					cellular response to histamine (GO:0071420)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|ligand-gated ion channel activity (GO:0015276)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(22)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44					Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Gamma Hydroxybutyric Acid(DB01440)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lindane(DB00431)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TTGTAAATTACATCTTCTTTG	0.423													C|||	77	0.0153754	0.056	0.0043	5008	,	,		19488	0.0		0.0	False		,,,				2504	0.0				p.Y329Y		Atlas-SNP	.											GABRB1,colon,carcinoma,+1,1	GABRB1	107	1	0			c.C987T						PASS	.	C		236,4170	138.4+/-174.2	4,228,1971	167.0	161.0	163.0		987	1.1	1.0	4	dbSNP_132	163	4,8596	1.2+/-3.3	0,4,4296	no	coding-synonymous	GABRB1	NM_000812.3		4,232,6267	TT,TC,CC		0.0465,5.3563,1.8453		329/475	47408850	240,12766	2203	4300	6503	SO:0001819	synonymous_variant	2560	exon8			AAATTACATCTTC		CCDS3474.1	4p12	2012-06-22			ENSG00000163288	ENSG00000163288		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4081	protein-coding gene	gene with protein product	"""GABA(A) receptor, beta 1"""	137190					Standard	NM_000812		Approved		uc003gxh.3	P18505	OTTHUMG00000044269	ENST00000295454.3:c.987C>T	4.37:g.47408850C>T		222.0	0.0	0		235.0	235.0	1	NM_000812	B2R6U7|D6REL3|Q16166|Q8TBK3	Silent	SNP	ENST00000295454.3	37	CCDS3474.1																																																																																			C|0.982;T|0.018	0.018	strong		0.423	GABRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216896.1		
DNAH10	196385	hgsc.bcm.edu	37	12	124417989	124417989	+	Missense_Mutation	SNP	C	C	T	rs61746561	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124417989C>T	ENST00000409039.3	+	76	13079	c.13054C>T	c.(13054-13056)Cgc>Tgc	p.R4352C	RP11-380L11.3_ENST00000602292.1_RNA|DNAH10OS_ENST00000514254.2_Intron|CCDC92_ENST00000544798.1_Intron	NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	4352					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)		GCCACTGGACCGCTCCACCTT	0.617													C|||	70	0.0139776	0.0507	0.0014	5008	,	,		18672	0.0		0.001	False		,,,				2504	0.001				p.R4352C		Atlas-SNP	.											.	DNAH10	888	.	0			c.C13054T						PASS	.	C	CYS/ARG	149,3855		4,141,1857	40.0	43.0	42.0		13054	5.2	1.0	12	dbSNP_129	42	7,8303		0,7,4148	yes	missense	DNAH10	NM_207437.3	180	4,148,6005	TT,TC,CC		0.0842,3.7213,1.2669	probably-damaging	4352/4472	124417989	156,12158	2002	4155	6157	SO:0001583	missense	196385	exon76			CTGGACCGCTCCA	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.13054C>T	12.37:g.124417989C>T	ENSP00000386770:p.Arg4352Cys	76.0	0.0	0		105.0	43.0	0.409524	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	C	34	5.328033	0.95733	0.037213	8.42E-4	ENSG00000197653	ENST00000409039	T	0.09255	3.0	5.18	5.18	0.71444	Dynein heavy chain (1);	0.139800	0.49305	D	0.000149	T	0.11410	0.0278	M	0.83118	2.625	0.80722	D	1	D	0.89917	1.0	D	0.70487	0.969	T	0.02942	-1.1091	10	0.66056	D	0.02	.	18.3051	0.90177	0.0:1.0:0.0:0.0	rs61746561	4352	Q8IVF4	DYH10_HUMAN	C	4352	ENSP00000386770:R4352C	ENSP00000386770:R4352C	R	+	1	0	DNAH10	122983942	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	5.889000	0.69766	2.413000	0.81919	0.561000	0.74099	CGC	C|0.991;T|0.009	0.009	strong		0.617	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057635	46057635	+	Missense_Mutation	SNP	G	G	A	rs114397261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46057635G>A	ENST00000380095.1	+	1	363	c.301G>A	c.(301-303)Gtg>Atg	p.V101M	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	101	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						tgtctgctgtgtgcccgtctg	0.632													A|||	306	0.0611022	0.2118	0.0173	5008	,	,		18765	0.002		0.001	False		,,,				2504	0.0112				p.V101M		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.G301A						PASS	.	A	,MET/VAL	438,3968		76,286,1841	130.0	123.0	125.0		,301	-1.7	0.0	21	dbSNP_132	125	2,8594		0,2,4296	no	intron,missense	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,21	76,288,6137	AA,AG,GG		0.0233,9.941,3.3841	,possibly-damaging	,101/252	46057635	440,12562	2203	4298	6501	SO:0001583	missense	353333	exon1			TGCTGTGTGCCCG	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.301G>A	21.37:g.46057635G>A	ENSP00000369438:p.Val101Met	204.0	0.0	0		273.0	120.0	0.43956	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	.	.	.	.	.	.	.	.	.	.	a	1.285	-0.609223	0.03690	0.09941	2.33E-4	ENSG00000221859	ENST00000380095	T	0.01430	4.9	2.86	-1.68	0.08212	.	.	.	.	.	T	0.00073	0.0002	L	0.36672	1.1	0.09310	N	1	B	0.26195	0.144	B	0.34452	0.183	T	0.44128	-0.9348	9	0.44086	T	0.13	.	9.7593	0.40522	0.4446:0.0:0.5554:0.0	.	101	P60014	KR10A_HUMAN	M	101	ENSP00000369438:V101M	ENSP00000369438:V101M	V	+	1	0	KRTAP10-10	44882063	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-0.140000	0.10342	-1.728000	0.01366	-2.786000	0.00116	GTG	G|0.928;A|0.072	0.072	strong		0.632	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
UNC5B	219699	hgsc.bcm.edu	37	10	73039594	73039594	+	Silent	SNP	C	C	T	rs80333477	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73039594C>T	ENST00000335350.6	+	2	512	c.96C>T	c.(94-96)agC>agT	p.S32S	UNC5B_ENST00000373192.4_Silent_p.S32S	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	32					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(4)|skin(4)	49						ATTCTGGCAGCGAGGTGCTCC	0.657													C|||	79	0.0157748	0.0582	0.0029	5008	,	,		17163	0.0		0.0	False		,,,				2504	0.0				p.S32S		Atlas-SNP	.											.	UNC5B	123	.	0			c.C96T						PASS	.	C		186,4220	118.8+/-156.5	4,178,2021	37.0	32.0	34.0		96	-3.5	0.3	10	dbSNP_132	34	0,8600		0,0,4300	no	coding-synonymous	UNC5B	NM_170744.4		4,178,6321	TT,TC,CC		0.0,4.2215,1.4301		32/946	73039594	186,12820	2203	4300	6503	SO:0001819	synonymous_variant	219699	exon2			TGGCAGCGAGGTG	AB096256	CCDS7309.1, CCDS58083.1	10q22.2	2013-01-11	2001-11-28		ENSG00000107731	ENSG00000107731		"""Immunoglobulin superfamily / I-set domain containing"""	12568	protein-coding gene	gene with protein product		607870	"""unc5 (C.elegans homolog) b"""				Standard	NM_170744		Approved	UNC5H2, p53RDL1	uc001jro.3	Q8IZJ1	OTTHUMG00000018422	ENST00000335350.6:c.96C>T	10.37:g.73039594C>T		147.0	0.0	0		177.0	97.0	0.548023	NM_001244889	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Silent	SNP	ENST00000335350.6	37	CCDS7309.1																																																																																			C|0.987;T|0.013	0.013	strong		0.657	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744	
C5orf42	65250	hgsc.bcm.edu	37	5	37245935	37245935	+	Missense_Mutation	SNP	C	C	T	rs73750959	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37245935C>T	ENST00000508244.1	-	2	187	c.94G>A	c.(94-96)Gtt>Att	p.V32I	C5orf42_ENST00000274258.7_5'UTR|RN7SL37P_ENST00000490461.2_RNA|C5orf42_ENST00000425232.2_Missense_Mutation_p.V32I			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	32						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			AAAAGAAAAACGGCTTCTTTT	0.328													C|||	152	0.0303514	0.1127	0.0043	5008	,	,		15998	0.0		0.0	False		,,,				2504	0.0				p.V32I		Atlas-SNP	.											.	C5orf42	422	.	0			c.G94A						PASS	.	C	ILE/VAL	145,1239		8,129,555	77.0	69.0	71.0		94	4.3	1.0	5	dbSNP_130	71	0,3176		0,0,1588	yes	missense	C5orf42	NM_023073.3	29	8,129,2143	TT,TC,CC		0.0,10.4769,3.1798	possibly-damaging	32/3198	37245935	145,4415	692	1588	2280	SO:0001583	missense	65250	exon3			GAAAAACGGCTTC		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.94G>A	5.37:g.37245935C>T	ENSP00000421690:p.Val32Ile	87.0	0.0	0		74.0	36.0	0.486486	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	53	0.024267399267399268	52	0.10569105691056911	1	0.0027624309392265192	0	0.0	0	0.0	C	12.59	1.983446	0.35036	0.104769	0.0	ENSG00000197603	ENST00000508244;ENST00000425232	T;T	0.51817	0.69;0.69	5.34	4.35	0.52113	.	0.391851	0.21991	U	0.066147	T	0.00724	0.0024	L	0.41824	1.3	0.80722	D	1	P	0.51351	0.944	B	0.37198	0.243	T	0.00783	-1.1568	10	0.59425	D	0.04	-10.2005	12.5366	0.56145	0.0:0.8874:0.0:0.1126	.	32	E9PH94	.	I	32	ENSP00000421690:V32I;ENSP00000389014:V32I	ENSP00000389014:V32I	V	-	1	0	C5orf42	37281692	1.000000	0.71417	1.000000	0.80357	0.430000	0.31655	3.683000	0.54663	2.497000	0.84241	0.313000	0.20887	GTT	C|0.980;T|0.020	0.020	strong		0.328	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073	
N4BP2	55728	hgsc.bcm.edu	37	4	40122377	40122377	+	Missense_Mutation	SNP	G	G	A	rs78767806	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:40122377G>A	ENST00000261435.6	+	9	3062	c.2646G>A	c.(2644-2646)atG>atA	p.M882I		NM_018177.4	NP_060647.2	Q86UW6	N4BP2_HUMAN	NEDD4 binding protein 2	882					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						TCAACATTATGGGTGACTGGC	0.388													G|||	127	0.0253594	0.0938	0.0043	5008	,	,		21899	0.0		0.0	False		,,,				2504	0.0				p.M882I		Atlas-SNP	.											.	N4BP2	166	.	0			c.G2646A						PASS	.	G	ILE/MET	297,4109	155.5+/-188.7	7,283,1913	55.0	56.0	55.0		2646	3.7	0.2	4	dbSNP_131	55	3,8595	2.2+/-6.3	0,3,4296	yes	missense	N4BP2	NM_018177.4	10	7,286,6209	AA,AG,GG		0.0349,6.7408,2.307	benign	882/1771	40122377	300,12704	2203	4299	6502	SO:0001583	missense	55728	exon9			CATTATGGGTGAC	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.2646G>A	4.37:g.40122377G>A	ENSP00000261435:p.Met882Ile	250.0	0.0	0		240.0	104.0	0.433333	NM_018177	A0AVR3|Q9NVK2|Q9P2D4	Missense_Mutation	SNP	ENST00000261435.6	37	CCDS3457.1	44|44	0.020146520146520148|0.020146520146520148	42|42	0.08536585365853659|0.08536585365853659	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	G|G	6.953|6.953	0.545704|0.545704	0.13312|0.13312	0.067408|0.067408	3.49E-4|3.49E-4	ENSG00000078177|ENSG00000078177	ENST00000513269|ENST00000261435;ENST00000381804	.|T	.|0.16073	.|2.37	5.48|5.48	3.72|3.72	0.42706|0.42706	.|.	.|0.426709	.|0.19802	.|N	.|0.105727	T|T	0.00300|0.00300	0.0009|0.0009	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.06405	.|0.002;0.001	T|T	0.34502|0.34502	-0.9826|-0.9826	5|10	.|0.35671	.|T	.|0.21	-1.4935|-1.4935	5.7473|5.7473	0.18128|0.18128	0.1425:0.0:0.5811:0.2764|0.1425:0.0:0.5811:0.2764	.|.	.|882;882	.|Q86UW6-2;Q86UW6	.|.;N4BP2_HUMAN	R|I	529|882;802	.|ENSP00000261435:M882I	.|ENSP00000261435:M882I	G|M	+|+	1|3	0|0	N4BP2|N4BP2	39798772|39798772	0.070000|0.070000	0.21116|0.21116	0.168000|0.168000	0.22838|0.22838	0.735000|0.735000	0.41995|0.41995	0.254000|0.254000	0.18314|0.18314	0.778000|0.778000	0.33520|0.33520	0.655000|0.655000	0.94253|0.94253	GGG|ATG	G|0.975;A|0.025	0.025	strong		0.388	N4BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250458.2	NM_018177	
FANCA	2175	hgsc.bcm.edu	37	16	89857880	89857880	+	Silent	SNP	C	C	T	rs1800332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89857880C>T	ENST00000389301.3	-	14	1320	c.1290G>A	c.(1288-1290)gcG>gcA	p.A430A	FANCA_ENST00000568369.1_Silent_p.A430A	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	430					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)		CAACCAGGAACGCAGTGACCA	0.557			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				C|||	163	0.0325479	0.1195	0.0072	5008	,	,		20326	0.0		0.0	False		,,,				2504	0.0				p.A430A		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	FANCA,NS,lymphoid_neoplasm,-1,1	FANCA	99	1	0			c.G1290A						PASS	.	C		453,3943	217.1+/-235.6	20,413,1765	63.0	51.0	55.0		1290	-10.9	0.0	16	dbSNP_89	55	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	FANCA	NM_000135.2		20,415,6063	TT,TC,CC		0.0233,10.3048,3.5011		430/1456	89857880	455,12541	2198	4300	6498	SO:0001819	synonymous_variant	2175	exon14	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CAGGAACGCAGTG	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.1290G>A	16.37:g.89857880C>T		86.0	0.0	0		96.0	37.0	0.385417	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Silent	SNP	ENST00000389301.3	37	CCDS32515.1																																																																																			C|0.967;T|0.033	0.033	strong		0.557	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
COL28A1	340267	hgsc.bcm.edu	37	7	7571420	7571420	+	Silent	SNP	T	T	C	rs17168526	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:7571420T>C	ENST00000399429.3	-	3	380	c.240A>G	c.(238-240)caA>caG	p.Q80Q		NM_001037763.2	NP_001032852.2	Q2UY09	COSA1_HUMAN	collagen, type XXVIII, alpha 1	80	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	42		Ovarian(82;0.0789)		UCEC - Uterine corpus endometrioid carcinoma (126;0.228)		CAGGAGTCAATTGGAAAATCT	0.418													T|||	127	0.0253594	0.0923	0.0058	5008	,	,		18415	0.0		0.001	False		,,,				2504	0.0				p.Q80Q		Atlas-SNP	.											.	COL28A1	113	.	0			c.A240G						PASS	.	T		280,3454		9,262,1596	70.0	69.0	70.0		240	-8.4	0.0	7	dbSNP_123	70	6,8210		0,6,4102	no	coding-synonymous	COL28A1	NM_001037763.2		9,268,5698	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	0.073,7.4987,2.3933		80/1126	7571420	286,11664	1867	4108	5975	SO:0001819	synonymous_variant	340267	exon3			AGTCAATTGGAAA	AJ890451	CCDS43553.1	7p21.3	2013-01-16			ENSG00000215018	ENSG00000215018		"""Collagens"""	22442	protein-coding gene	gene with protein product		609996				16330543	Standard	NM_001037763		Approved		uc003src.1	Q2UY09	OTTHUMG00000150034	ENST00000399429.3:c.240A>G	7.37:g.7571420T>C		283.0	0.0	0		318.0	131.0	0.41195	NM_001037763	A4D101|A4D106|A4D107|A8MVR2|B9EGX9|Q2UY07|Q2UY08	Silent	SNP	ENST00000399429.3	37	CCDS43553.1																																																																																			T|0.969;C|0.031	0.031	strong		0.418	COL28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315899.1	NM_001037763	
FAM214A	56204	hgsc.bcm.edu	37	15	52901887	52901887	+	Silent	SNP	A	A	G	rs75512966	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:52901887A>G	ENST00000261844.7	-	6	1376	c.1224T>C	c.(1222-1224)ctT>ctC	p.L408L	FAM214A_ENST00000546305.2_Silent_p.L415L	NM_019600.2	NP_062546.2	Q32MH5	F214A_HUMAN	family with sequence similarity 214, member A	408																	AAACCCGGAAAAGTTTTGAAT	0.403													A|||	99	0.0197684	0.0734	0.0029	5008	,	,		19310	0.0		0.0	False		,,,				2504	0.0				p.L408L		Atlas-SNP	.											.	.	.	.	0			c.T1224C						PASS	.	A		198,3438		6,186,1626	60.0	56.0	57.0		1224	0.5	0.0	15	dbSNP_132	57	1,8143		0,1,4071	no	coding-synonymous	KIAA1370	NM_019600.2		6,187,5697	GG,GA,AA		0.0123,5.4455,1.6893		408/1077	52901887	199,11581	1818	4072	5890	SO:0001819	synonymous_variant	56204	exon6			CCGGAAAAGTTTT	AB037791	CCDS45263.1, CCDS66773.1	15q21.2-q21.3	2011-12-01	2011-12-01	2011-12-01	ENSG00000047346	ENSG00000047346			25609	protein-coding gene	gene with protein product			"""KIAA1370"""	KIAA1370		10718198	Standard	XM_005254547		Approved	FLJ10980	uc002acg.4	Q32MH5		ENST00000261844.7:c.1224T>C	15.37:g.52901887A>G		47.0	0.0	0		58.0	29.0	0.5	NM_019600	A8KA52|B4DEP5|B4DF40|F5H8G0|Q32MH6|Q4G0R7|Q5XJ16|Q6PDA3|Q9NV24|Q9P2H7	Silent	SNP	ENST00000261844.7	37	CCDS45263.1																																																																																			A|0.981;G|0.019	0.019	strong		0.403	FAM214A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419914.1	NM_019600	
CFAP46	54777	hgsc.bcm.edu	37	10	134622046	134622046	+	Missense_Mutation	SNP	C	C	T	rs73387072	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:134622046C>T	ENST00000368586.5	-	58	8127	c.8027G>A	c.(8026-8028)cGt>cAt	p.R2676H	TTC40_ENST00000263170.5_Missense_Mutation_p.R837H	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						CCAGCCCCGACGCAGACCCCA	0.677													C|||	131	0.0261581	0.0885	0.0173	5008	,	,		15164	0.0		0.002	False		,,,				2504	0.0				p.R2676H		Atlas-SNP	.											.	TTC40	100	.	0			c.G8027A						PASS	.	C	HIS/ARG	341,4065	166.9+/-198.0	17,307,1879	36.0	44.0	41.0		2963	0.2	0.0	10	dbSNP_130	41	9,8587	5.7+/-21.5	0,9,4289	yes	missense	C10orf92	NM_001200049.1	29	17,316,6168	TT,TC,CC		0.1047,7.7394,2.6919	possibly-damaging	988/1028	134622046	350,12652	2203	4298	6501	SO:0001583	missense	54777	exon58			CCCCGACGCAGAC																												ENST00000368586.5:c.8027G>A	10.37:g.134622046C>T	ENSP00000357575:p.Arg2676His	94.0	0.0	0		123.0	72.0	0.585366	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	51	0.023351648351648352	45	0.09146341463414634	6	0.016574585635359115	0	0.0	0	0.0	C	11.21	1.571070	0.28003	0.077394	0.001047	ENSG00000171811	ENST00000368586;ENST00000263170	T;T	0.16073	2.71;2.37	1.36	0.248	0.15526	.	.	.	.	.	T	0.00241	0.0007	N	0.08118	0	0.09310	N	0.999999	P	0.49559	0.925	B	0.29862	0.108	T	0.36744	-0.9735	9	0.87932	D	0	.	5.3024	0.15785	0.0:0.6333:0.3667:0.0	.	837	Q8IYW2	CJ092_HUMAN	H	2676;837	ENSP00000357575:R2676H;ENSP00000263170:R837H	ENSP00000263170:R837H	R	-	2	0	C10orf93	134472036	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.082000	0.03400	-0.076000	0.12775	-0.531000	0.04308	CGT	C|0.975;T|0.025	0.025	strong		0.677	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
OR2K2	26248	hgsc.bcm.edu	37	9	114089883	114089883	+	Silent	SNP	G	G	A	rs61748722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:114089883G>A	ENST00000374428.1	-	1	917	c.918C>T	c.(916-918)taC>taT	p.Y306Y	OR2K2_ENST00000302681.1_Silent_p.Y277Y			Q8NGT1	OR2K2_HUMAN	olfactory receptor, family 2, subfamily K, member 2	306						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)	20						TAAGCACTCCGTAAAGCAACG	0.383													A|||	74	0.0147764	0.053	0.0058	5008	,	,		22259	0.0		0.0	False		,,,				2504	0.0				p.Y277Y		Atlas-SNP	.											.	OR2K2	77	.	0			c.C831T						PASS	.	A		233,4173	805.1+/-415.8	5,223,1975	131.0	124.0	126.0		831	4.6	1.0	9	dbSNP_129	126	1,8599	819.2+/-406.8	0,1,4299	no	coding-synonymous	OR2K2	NM_205859.1		5,224,6274	AA,AG,GG		0.0116,5.2882,1.7992		277/317	114089883	234,12772	2203	4300	6503	SO:0001819	synonymous_variant	26248	exon1			CACTCCGTAAAGC	X64977	CCDS6778.1	9q31.3	2012-08-09			ENSG00000171133	ENSG00000171133		"""GPCR / Class A : Olfactory receptors"""	8264	protein-coding gene	gene with protein product				OR2AR1P		1370859, 17010214	Standard	NM_205859		Approved	HTPCRH06, HSHTPCRH06	uc011lwp.2	Q8NGT1	OTTHUMG00000020488	ENST00000374428.1:c.918C>T	9.37:g.114089883G>A		167.0	0.0	0		171.0	123.0	0.719298	NM_205859	Q2TA61|Q5VYK4|Q6IFI5	Silent	SNP	ENST00000374428.1	37																																																																																				G|0.982;A|0.018	0.018	strong		0.383	OR2K2-201	KNOWN	basic	protein_coding	protein_coding		NM_205859	
ATP10A	57194	hgsc.bcm.edu	37	15	25928508	25928508	+	Silent	SNP	C	C	T	rs142960034	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:25928508C>T	ENST00000356865.6	-	17	3528	c.3417G>A	c.(3415-3417)ggG>ggA	p.G1139G		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	1139					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|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)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		TGTCCAGCACCCCAGTCACGA	0.537													C|||	19	0.00379393	0.0144	0.0	5008	,	,		17004	0.0		0.0	False		,,,				2504	0.0				p.G1139G		Atlas-SNP	.											.	ATP10A	270	.	0			c.G3417A						PASS	.	C		63,4343	59.3+/-96.0	0,63,2140	75.0	66.0	69.0		3417	2.5	1.0	15	dbSNP_134	69	0,8600		0,0,4300	no	coding-synonymous	ATP10A	NM_024490.3		0,63,6440	TT,TC,CC		0.0,1.4299,0.4844		1139/1500	25928508	63,12943	2203	4300	6503	SO:0001819	synonymous_variant	57194	exon17			CAGCACCCCAGTC	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.3417G>A	15.37:g.25928508C>T		142.0	0.0	0		148.0	73.0	0.493243	NM_024490	Q4G0S9|Q969I4	Silent	SNP	ENST00000356865.6	37	CCDS32178.1																																																																																			C|0.996;T|0.004	0.004	strong		0.537	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	
PCDHA6	56142	hgsc.bcm.edu	37	5	140209429	140209429	+	Missense_Mutation	SNP	C	C	G	rs60309716	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140209429C>G	ENST00000529310.1	+	1	1867	c.1753C>G	c.(1753-1755)Ctg>Gtg	p.L585V	PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	585	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.		L -> V (in dbSNP:rs60309716).		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCCGCGGTCACTGGGTGCAGG	0.677													.|||	317	0.0632987	0.2322	0.013	5008	,	,		16721	0.0		0.001	False		,,,				2504	0.0				p.L585V		Atlas-SNP	.											.	PCDHA6	442	.	0			c.C1753G						PASS	.	G	,,,,,VAL/LEU,,VAL/LEU,	863,3543	743.4+/-411.5	78,707,1418	87.0	87.0	87.0		,,,,,1753,,1753,	1.0	0.0	5	dbSNP_129	87	2,8596	819.0+/-406.8	0,2,4297	no	intron,intron,intron,intron,intron,missense,intron,missense,intron	PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_031411.1,NM_031848.1,NM_031849.1	,,,,,32,,32,	78,709,5715	GG,GC,CC		0.0233,19.5869,6.6518	,,,,,,,,	,,,,,585/951,,585/804,	140209429	865,12139	2203	4299	6502	SO:0001583	missense	56142	exon1			CGGTCACTGGGTG	AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842		"""Cadherins / Protocadherins : Clustered"""	8672	other	complex locus constituent	"""KIAA0345-like 8"""	606312		CNRS2		10380929, 10662547	Standard	NM_018909		Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.1753C>G	5.37:g.140209429C>G	ENSP00000433378:p.Leu585Val	210.0	0.0	0		274.0	141.0	0.514599	NM_018909	O75283|Q9NRT8	Missense_Mutation	SNP	ENST00000529310.1	37	CCDS47281.1	96	0.04395604395604396	90	0.18292682926829268	6	0.016574585635359115	0	0.0	0	0.0	G	0.001	-3.111828	0.00032	0.195869	2.33E-4	ENSG00000081842	ENST00000529310	T	0.50001	0.76	3.87	0.98	0.19750	Cadherin (2);Cadherin-like (1);	0.000000	0.33199	N	0.005169	T	0.00012	0.0000	N	0.00237	-1.79	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.19484	-1.0304	9	0.07482	T	0.82	.	3.3104	0.07015	0.0814:0.2713:0.3691:0.2783	rs60309716;rs61730776	585;585	Q9UN73-3;Q9UN73	.;PCDA6_HUMAN	V	585	ENSP00000433378:L585V	ENSP00000433378:L585V	L	+	1	2	PCDHA6	140189613	0.013000	0.17824	0.005000	0.12908	0.002000	0.02628	1.103000	0.31062	-0.149000	0.11215	-0.671000	0.03813	CTG	C|0.940;G|0.060	0.060	strong		0.677	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909	
EIF4G3	8672	hgsc.bcm.edu	37	1	21177800	21177800	+	Missense_Mutation	SNP	A	A	T	rs2230572	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:21177800A>T	ENST00000264211.8	-	22	3749	c.3555T>A	c.(3553-3555)gaT>gaA	p.D1185E	EIF4G3_ENST00000536266.1_Missense_Mutation_p.D789E|EIF4G3_ENST00000602326.1_Missense_Mutation_p.D1191E|EIF4G3_ENST00000374937.3_Missense_Mutation_p.D1191E|EIF4G3_ENST00000374935.3_Missense_Mutation_p.D905E|EIF4G3_ENST00000400422.1_Missense_Mutation_p.D1185E|EIF4G3_ENST00000537738.1_Missense_Mutation_p.D675E	NM_003760.4	NP_003751.2	O43432	IF4G3_HUMAN	eukaryotic translation initiation factor 4 gamma, 3	1185			D -> E (in dbSNP:rs2230572).		cytokine-mediated signaling pathway (GO:0019221)|positive regulation of meiosis I (GO:0060903)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|regulation of translational initiation (GO:0006446)|spermatogenesis (GO:0007283)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(18)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(1)|urinary_tract(3)	70		all_lung(284;2.61e-06)|Lung NSC(340;2.81e-06)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00149)|Ovarian(437;0.00338)|Myeloproliferative disorder(586;0.0256)		UCEC - Uterine corpus endometrioid carcinoma (279;0.023)|COAD - Colon adenocarcinoma(152;5.42e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000327)|GBM - Glioblastoma multiforme(114;0.000696)|Kidney(64;0.0018)|STAD - Stomach adenocarcinoma(196;0.00644)|KIRC - Kidney renal clear cell carcinoma(64;0.0185)|READ - Rectum adenocarcinoma(331;0.124)|Lung(427;0.191)		TCCTCTCCACATCCACACCTC	0.498													A|||	14	0.00279553	0.0091	0.0029	5008	,	,		16789	0.0		0.0	False		,,,				2504	0.0				p.D1221E		Atlas-SNP	.											EIF4G3_ENST00000374937,NS,carcinoma,-2,2	EIF4G3	300	2	0			c.T3663A						PASS	.	A	GLU/ASP,GLU/ASP,GLU/ASP	50,4356	52.9+/-88.7	0,50,2153	163.0	147.0	152.0		3663,3573,3555	-7.4	0.0	1	dbSNP_98	152	0,8600		0,0,4300	yes	missense,missense,missense	EIF4G3	NM_001198801.1,NM_001198802.1,NM_003760.4	45,45,45	0,50,6453	TT,TA,AA		0.0,1.1348,0.3844	benign,benign,benign	1221/1622,1191/1592,1185/1586	21177800	50,12956	2203	4300	6503	SO:0001583	missense	8672	exon26			CTCCACATCCACA	AF012072	CCDS214.1, CCDS55580.1, CCDS59192.1, CCDS72723.1	1p36.12	2008-02-05			ENSG00000075151	ENSG00000075151			3298	protein-coding gene	gene with protein product		603929				9418880	Standard	NM_001198801		Approved	eIF4GII	uc001bef.3	O43432	OTTHUMG00000002624	ENST00000264211.8:c.3555T>A	1.37:g.21177800A>T	ENSP00000264211:p.Asp1185Glu	172.0	0.0	0		197.0	101.0	0.51269	NM_001198801	B9EGQ7|Q15597|Q504Z1|Q5SWC3|Q8NEN1	Missense_Mutation	SNP	ENST00000264211.8	37	CCDS214.1	10	0.004578754578754579	8	0.016260162601626018	2	0.0055248618784530384	0	0.0	0	0.0	A	14.94	2.685816	0.47991	0.011348	0.0	ENSG00000075151	ENST00000264211;ENST00000400415;ENST00000400422;ENST00000374935;ENST00000537738;ENST00000374937;ENST00000536266	T;T;T;T;T;T	0.06849	3.87;3.87;3.68;3.25;3.87;3.55	5.73	-7.44	0.01379	.	0.243758	0.46758	N	0.000265	T	0.01222	0.0040	N	0.14661	0.345	0.26519	N	0.974465	B;B;B;B;B	0.06786	0.001;0.0;0.0;0.001;0.0	B;B;B;B;B	0.09377	0.001;0.001;0.001;0.004;0.002	T	0.39035	-0.9633	10	0.07644	T	0.81	-6.5184	6.1684	0.20404	0.2584:0.1981:0.4652:0.0783	rs2230572;rs35634957	1380;905;789;1191;1185	Q59GJ0;Q504Z1;F5H564;B9EGQ7;O43432	.;.;.;.;IF4G3_HUMAN	E	1185;1381;1185;905;675;1191;789	ENSP00000264211:D1185E;ENSP00000383274:D1185E;ENSP00000364071:D905E;ENSP00000442010:D675E;ENSP00000364073:D1191E;ENSP00000444693:D789E	ENSP00000264211:D1185E	D	-	3	2	EIF4G3	21050387	0.000000	0.05858	0.006000	0.13384	0.482000	0.33219	-2.045000	0.01410	-1.357000	0.02180	0.482000	0.46254	GAT	A|0.995;T|0.005	0.005	strong		0.498	EIF4G3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000007467.3	NM_003760	
C21orf2	755	hgsc.bcm.edu	37	21	45750725	45750725	+	Missense_Mutation	SNP	G	G	A	rs148023924	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45750725G>A	ENST00000339818.4	-	6	830	c.623C>T	c.(622-624)tCg>tTg	p.S208L	C21orf2_ENST00000325223.7_Missense_Mutation_p.S207L|AP001062.8_ENST00000422357.1_RNA|C21orf2_ENST00000397956.3_Missense_Mutation_p.S207L|AP001062.7_ENST00000448927.1_RNA|C21orf2_ENST00000496321.1_5'UTR	NM_001271440.1|NM_004928.2	NP_001258369.1|NP_004919.1	O43822	CU002_HUMAN	chromosome 21 open reading frame 2	208					cilium morphogenesis (GO:0060271)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				endometrium(2)	2				Colorectal(79;0.0806)		GTGGCTGCTCGAGGCATCCCT	0.682													G|||	12	0.00239617	0.0068	0.0	5008	,	,		13283	0.0		0.001	False		,,,				2504	0.002				p.S208L		Atlas-SNP	.											.	C21orf2	10	.	0			c.C623T						PASS	.	G	LEU/SER	23,4355		0,23,2166	14.0	15.0	15.0		623	-5.4	0.0	21	dbSNP_134	15	0,8590		0,0,4295	yes	missense	C21orf2	NM_004928.2	145	0,23,6461	AA,AG,GG		0.0,0.5254,0.1774	benign	208/257	45750725	23,12945	2189	4295	6484	SO:0001583	missense	755	exon6			CTGCTCGAGGCAT	Y11392	CCDS13709.1, CCDS59444.1, CCDS59445.1	21q22.3	2014-03-24			ENSG00000160226	ENSG00000160226			1260	protein-coding gene	gene with protein product	"""nuclear encoded mitochondrial protein"", ""leucine rich repeat containing 76"""	603191				9465297	Standard	NM_004928		Approved	YF5, A2, LRRC76	uc002zeq.2	O43822	OTTHUMG00000086909	ENST00000339818.4:c.623C>T	21.37:g.45750725G>A	ENSP00000344566:p.Ser208Leu	166.0	0.0	0		160.0	79.0	0.49375	NM_004928	A8MPS9|O14993|Q8N5X6|Q99837|Q99838	Missense_Mutation	SNP	ENST00000339818.4	37	CCDS13709.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	9.377	1.072041	0.20147	0.005254	0.0	ENSG00000160226	ENST00000339818;ENST00000397956;ENST00000325223	T;T;T	0.35973	1.61;1.28;1.61	4.25	-5.4	0.02656	.	2.084300	0.02418	N	0.082253	T	0.08223	0.0205	N	0.02011	-0.69	0.09310	N	1	B;B;B;B	0.06786	0.001;0.001;0.0;0.001	B;B;B;B	0.04013	0.001;0.0;0.0;0.001	T	0.09292	-1.0681	10	0.28530	T	0.3	-0.0966	1.5726	0.02618	0.5044:0.1437:0.2077:0.1442	.	207;207;208;167	G5E952;Q8N5X6;O43822;O43822-2	.;.;CU002_HUMAN;.	L	208;207;207	ENSP00000344566:S208L;ENSP00000381047:S207L;ENSP00000317302:S207L	ENSP00000317302:S207L	S	-	2	0	C21orf2	44575153	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.798000	0.04565	-0.617000	0.05664	-0.137000	0.14449	TCG	G|0.997;A|0.003	0.003	strong		0.682	C21orf2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195799.1	NM_004928	
SEC14L5	9717	hgsc.bcm.edu	37	16	5050678	5050678	+	Silent	SNP	C	C	T	rs61745575	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:5050678C>T	ENST00000251170.7	+	9	1173	c.993C>T	c.(991-993)ctC>ctT	p.L331L		NM_014692.1	NP_055507.1	O43304	S14L5_HUMAN	SEC14-like 5 (S. cerevisiae)	331	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	transporter activity (GO:0005215)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|skin(1)	29						TCTACATCCTCCGCCTGGGCC	0.632													C|||	132	0.0263578	0.0923	0.0115	5008	,	,		16872	0.0		0.002	False		,,,				2504	0.0				p.L331L		Atlas-SNP	.											SEC14L5,NS,carcinoma,+2,1	SEC14L5	79	1	0			c.C993T						PASS	.	C		191,3593		4,183,1705	11.0	12.0	12.0		993	1.2	1.0	16	dbSNP_129	12	2,7978		0,2,3988	no	coding-synonymous	SEC14L5	NM_014692.1		4,185,5693	TT,TC,CC		0.0251,5.0476,1.6406		331/697	5050678	193,11571	1892	3990	5882	SO:0001819	synonymous_variant	9717	exon9			CATCCTCCGCCTG	AB007880	CCDS45403.1	16p13.3	2008-02-05				ENSG00000103184			29032	protein-coding gene	gene with protein product						9455477	Standard	NM_014692		Approved	KIAA0420, PRELID4B	uc002cye.2	O43304		ENST00000251170.7:c.993C>T	16.37:g.5050678C>T		125.0	0.0	0		104.0	50.0	0.480769	NM_014692		Silent	SNP	ENST00000251170.7	37	CCDS45403.1																																																																																			C|0.975;T|0.025	0.025	strong		0.632	SEC14L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434379.1		
TRIM67	440730	hgsc.bcm.edu	37	1	231298970	231298970	+	Silent	SNP	T	T	C	rs372035563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:231298970T>C	ENST00000366653.5	+	1	255	c.255T>C	c.(253-255)gcT>gcC	p.A85A	TRIM67_ENST00000366652.2_Silent_p.A85A|TRIM67_ENST00000444294.3_Silent_p.A85A|TRIM67_ENST00000449018.3_Silent_p.A45A			Q6ZTA4	TRI67_HUMAN	tripartite motif containing 67	85	Gly-rich.				negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Breast(184;0.0871)	all_cancers(173;0.189)|Prostate(94;0.167)				GGAGTGCAGCTGGCGGCCTCG	0.756													T|||	20	0.00399361	0.0151	0.0	5008	,	,		9536	0.0		0.0	False		,,,				2504	0.0				p.A85A		Atlas-SNP	.											.	TRIM67	160	.	0			c.T255C						PASS	.	T		1,2915		0,1,1457	2.0	2.0	2.0		255	-8.1	0.0	1		2	0,6030		0,0,3015	no	coding-synonymous	TRIM67	NM_001004342.3		0,1,4472	CC,CT,TT		0.0,0.0343,0.0112		85/784	231298970	1,8945	1458	3015	4473	SO:0001819	synonymous_variant	440730	exon1			TGCAGCTGGCGGC	AK126782	CCDS44333.1, CCDS73048.1	1q42.2	2014-02-17	2011-01-25		ENSG00000119283	ENSG00000119283		"""Tripartite motif containing / Tripartite motif containing"", ""Fibronectin type III domain containing"", ""RING-type (C3HC4) zinc fingers"""	31859	protein-coding gene	gene with protein product		610584	"""tripartite motif-containing 67"""				Standard	NM_001004342		Approved	TNL	uc009xfn.1	Q6ZTA4	OTTHUMG00000037958	ENST00000366653.5:c.255T>C	1.37:g.231298970T>C		11.0	0.0	0		17.0	5.0	0.294118	NM_001004342	Q5TER7|Q5TER8|Q7Z4K7	Silent	SNP	ENST00000366653.5	37	CCDS44333.1																																																																																			.	.	none		0.756	TRIM67-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092649.3	NM_001004342	
SGMS2	166929	hgsc.bcm.edu	37	4	108816880	108816880	+	Silent	SNP	G	G	A	rs150784082	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:108816880G>A	ENST00000394684.4	+	3	728	c.171G>A	c.(169-171)ccG>ccA	p.P57P	SGMS2_ENST00000359079.4_Silent_p.P57P|RP11-286E11.1_ENST00000499098.1_RNA|RP11-286E11.1_ENST00000513071.1_RNA|SGMS2_ENST00000394686.3_Silent_p.P57P	NM_001136258.1	NP_001129730.1	Q8NHU3	SMS2_HUMAN	sphingomyelin synthase 2	57					small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingomyelin biosynthetic process (GO:0006686)	Golgi apparatus (GO:0005794)|integral component of cell outer membrane (GO:0045203)|integral component of Golgi membrane (GO:0030173)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ceramide cholinephosphotransferase activity (GO:0047493)|kinase activity (GO:0016301)|sphingomyelin synthase activity (GO:0033188)			central_nervous_system(1)|endometrium(2)|large_intestine(8)|liver(2)|lung(6)|prostate(1)	20				OV - Ovarian serous cystadenocarcinoma(123;2.95e-05)		AAAAGTACCCGGACTATATCC	0.443													G|||	22	0.00439297	0.0159	0.0014	5008	,	,		20353	0.0		0.0	False		,,,				2504	0.0				p.P57P		Atlas-SNP	.											.	SGMS2	39	.	0			c.G171A						PASS	.	G	,,	56,4350	55.5+/-91.7	0,56,2147	98.0	94.0	95.0		171,171,171	-5.7	0.7	4	dbSNP_134	95	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	SGMS2	NM_001136257.1,NM_001136258.1,NM_152621.5	,,	0,57,6446	AA,AG,GG		0.0116,1.271,0.4383	,,	57/366,57/366,57/366	108816880	57,12949	2203	4300	6503	SO:0001819	synonymous_variant	166929	exon2			GTACCCGGACTAT	BC041369	CCDS3677.1	4q25	2008-02-05			ENSG00000164023	ENSG00000164023	2.7.8.27		28395	protein-coding gene	gene with protein product		611574				14685263	Standard	NM_152621		Approved	MGC26963, SMS2	uc003hyl.4	Q8NHU3	OTTHUMG00000131811	ENST00000394684.4:c.171G>A	4.37:g.108816880G>A		101.0	0.0	0		98.0	52.0	0.530612	NM_001136257	A8K2S9|B2RA61	Silent	SNP	ENST00000394684.4	37	CCDS3677.1																																																																																			G|0.996;A|0.004	0.004	strong		0.443	SGMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254752.1	NM_152621	
ADAMDEC1	27299	hgsc.bcm.edu	37	8	24259600	24259600	+	Missense_Mutation	SNP	C	C	T	rs76707982	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24259600C>T	ENST00000256412.4	+	12	1535	c.1315C>T	c.(1315-1317)Cct>Tct	p.P439S	RP11-624C23.1_ENST00000519689.1_RNA|ADAMDEC1_ENST00000522298.1_Missense_Mutation_p.P360S|RP11-624C23.1_ENST00000523578.1_RNA|ADAMDEC1_ENST00000538205.1_Missense_Mutation_p.P360S	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	439	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.				immune response (GO:0006955)|negative regulation of cell adhesion (GO:0007162)	extracellular region (GO:0005576)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|large_intestine(4)|skin(2)|stomach(1)	9		Prostate(55;0.0181)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)		TTGTGGCTCTCCTAAGGTATT	0.368													C|||	72	0.014377	0.053	0.0029	5008	,	,		16709	0.0		0.0	False		,,,				2504	0.0				p.P439S	Ovarian(147;687 1849 3699 25981 31337)	Atlas-SNP	.											ADAMDEC1_ENST00000256412,NS,malignant_melanoma,-1,1	ADAMDEC1	69	1	0			c.C1315T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO	219,4187	127.8+/-164.7	6,207,1990	77.0	79.0	78.0		1078,1078,1315	3.4	1.0	8	dbSNP_131	78	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	ADAMDEC1	NM_001145271.1,NM_001145272.1,NM_014479.3	74,74,74	6,208,6289	TT,TC,CC		0.0116,4.9705,1.6915	probably-damaging,probably-damaging,probably-damaging	360/392,360/392,439/471	24259600	220,12786	2203	4300	6503	SO:0001583	missense	27299	exon12			GGCTCTCCTAAGG	Y13323	CCDS6044.1, CCDS55212.1	8p12	2008-08-07			ENSG00000134028	ENSG00000134028			16299	protein-coding gene	gene with protein product		606393				9271581, 12037602	Standard	NM_001145271		Approved	M12.219	uc003xdz.2	O15204	OTTHUMG00000097858	ENST00000256412.4:c.1315C>T	8.37:g.24259600C>T	ENSP00000256412:p.Pro439Ser	53.0	0.0	0		61.0	39.0	0.639344	NM_014479	B7ZAK5	Missense_Mutation	SNP	ENST00000256412.4	37	CCDS6044.1	29	0.013278388278388278	28	0.056910569105691054	1	0.0027624309392265192	0	0.0	0	0.0	C	12.49	1.952501	0.34471	0.049705	1.16E-4	ENSG00000134028	ENST00000256412;ENST00000538205;ENST00000522298	T;T;T	0.10860	2.83;2.83;2.83	6.16	3.43	0.39272	Blood coagulation inhibitor, Disintegrin (3);	0.377504	0.26176	N	0.025893	T	0.01156	0.0038	L	0.47190	1.495	0.44188	D	0.997006	P	0.35192	0.489	B	0.39935	0.314	T	0.20472	-1.0274	10	0.38643	T	0.18	-5.4888	8.4866	0.33076	0.0:0.7617:0.0:0.2383	.	439	O15204	ADEC1_HUMAN	S	439;360;360	ENSP00000256412:P439S;ENSP00000442592:P360S;ENSP00000428993:P360S	ENSP00000256412:P439S	P	+	1	0	ADAMDEC1	24315545	0.000000	0.05858	1.000000	0.80357	0.989000	0.77384	-0.002000	0.12924	0.486000	0.27676	0.650000	0.86243	CCT	C|0.983;T|0.017	0.017	strong		0.368	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479	
AMN	81693	hgsc.bcm.edu	37	14	103395212	103395212	+	Missense_Mutation	SNP	G	G	T	rs568801729		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:103395212G>T	ENST00000299155.5	+	5	446	c.413G>T	c.(412-414)cGc>cTc	p.R138L		NM_030943.3	NP_112205.2	Q9BXJ7	AMNLS_HUMAN	amnion associated transmembrane protein	138					cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|excretion (GO:0007588)|Golgi to plasma membrane protein transport (GO:0043001)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			kidney(2)|large_intestine(1)|lung(2)|skin(1)	6				Colorectal(3;0.00739)|READ - Rectum adenocarcinoma(2;0.0336)|Epithelial(152;0.0363)|all cancers(159;0.147)	Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GTGCCCTGCCGCCACGACGAC	0.706																																					p.R138L		Atlas-SNP	.											.	AMN	13	.	0			c.G413T						PASS	.						30.0	28.0	29.0					14																	103395212		2203	4297	6500	SO:0001583	missense	81693	exon5			CCTGCCGCCACGA	AF328788	CCDS9977.1	14q32.32	2014-09-17	2012-12-07		ENSG00000166126	ENSG00000166126			14604	protein-coding gene	gene with protein product		605799	"""amnionless homolog (mouse)"""			11279523	Standard	NM_030943		Approved	amnionless	uc001ymg.4	Q9BXJ7		ENST00000299155.5:c.413G>T	14.37:g.103395212G>T	ENSP00000299155:p.Arg138Leu	45.0	0.0	0		93.0	54.0	0.580645	NM_030943	Q6UX83	Missense_Mutation	SNP	ENST00000299155.5	37	CCDS9977.1	.	.	.	.	.	.	.	.	.	.	G	14.55	2.570223	0.45798	.	.	ENSG00000166126	ENST00000299155;ENST00000541086	D	0.88664	-2.41	4.03	0.969	0.19686	.	0.560105	0.18314	U	0.145003	D	0.84083	0.5394	M	0.61703	1.905	0.26626	N	0.972569	P	0.38020	0.615	B	0.38954	0.286	T	0.76173	-0.3056	10	0.62326	D	0.03	-1.9881	2.5302	0.04701	0.11:0.1861:0.5126:0.1913	.	138	Q9BXJ7	AMNLS_HUMAN	L	138;84	ENSP00000299155:R138L	ENSP00000299155:R138L	R	+	2	0	AMN	102464965	0.003000	0.15002	0.737000	0.30932	0.919000	0.55068	0.296000	0.19083	-0.112000	0.11979	0.306000	0.20318	CGC	.	.	none		0.706	AMN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415704.1		
ROGDI	79641	hgsc.bcm.edu	37	16	4849726	4849726	+	Missense_Mutation	SNP	G	G	C	rs143095485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4849726G>C	ENST00000322048.7	-	6	771	c.393C>G	c.(391-393)gaC>gaG	p.D131E	ROGDI_ENST00000586336.1_5'UTR	NM_024589.2	NP_078865.1	Q9GZN7	ROGDI_HUMAN	rogdi homolog (Drosophila)	131					hemopoiesis (GO:0030097)|positive regulation of cell proliferation (GO:0008284)	intracellular (GO:0005622)|nucleus (GO:0005634)				endometrium(2)|lung(1)|ovary(1)|skin(1)	5						GGTAGCTCTGGTCCCGGCTGG	0.602													G|||	88	0.0175719	0.0643	0.0043	5008	,	,		12956	0.0		0.0	False		,,,				2504	0.0				p.D131E		Atlas-SNP	.											.	ROGDI	11	.	0			c.C393G						PASS	.	G	GLU/ASP	269,4125	152.5+/-186.2	5,259,1933	99.0	79.0	86.0		393	-9.8	0.4	16	dbSNP_134	86	0,8600		0,0,4300	yes	missense	ROGDI	NM_024589.1	45	5,259,6233	CC,CG,GG		0.0,6.122,2.0702	benign	131/288	4849726	269,12725	2197	4300	6497	SO:0001583	missense	79641	exon6			GCTCTGGTCCCGG	AK026039	CCDS10523.1	16p13.3	2014-09-17			ENSG00000067836	ENSG00000067836			29478	protein-coding gene	gene with protein product		614574				11230166	Standard	NM_024589		Approved	FLJ22386	uc002cxv.4	Q9GZN7	OTTHUMG00000129479	ENST00000322048.7:c.393C>G	16.37:g.4849726G>C	ENSP00000322832:p.Asp131Glu	119.0	0.0	0		129.0	59.0	0.457364	NM_024589	Q6IA00	Missense_Mutation	SNP	ENST00000322048.7	37	CCDS10523.1	21	0.009615384615384616	21	0.042682926829268296	0	0.0	0	0.0	0	0.0	G	6.305	0.424431	0.11928	0.06122	0.0	ENSG00000067836	ENST00000322048	T	0.41065	1.01	4.91	-9.82	0.00484	.	0.057101	0.64402	D	0.000002	T	0.01870	0.0059	L	0.39020	1.185	0.32051	N	0.596972	B	0.10296	0.003	B	0.14023	0.01	T	0.11227	-1.0596	10	0.17369	T	0.5	1.2912	4.1989	0.10457	0.1965:0.3057:0.4049:0.0929	.	131	Q9GZN7	ROGDI_HUMAN	E	131	ENSP00000322832:D131E	ENSP00000322832:D131E	D	-	3	2	ROGDI	4789727	0.003000	0.15002	0.407000	0.26434	0.258000	0.26162	-0.702000	0.05069	-2.194000	0.00753	-0.254000	0.11334	GAC	G|0.980;C|0.020	0.020	strong		0.602	ROGDI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251643.3	NM_024589	
HOXB8	3218	hgsc.bcm.edu	37	17	46690623	46690623	+	Missense_Mutation	SNP	G	G	C	rs112046402	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:46690623G>C	ENST00000239144.4	-	2	907	c.673C>G	c.(673-675)Ctg>Gtg	p.L225V	HOXB7_ENST00000567101.2_Intron|HOXB7_ENST00000239165.7_5'Flank|HOXB8_ENST00000576562.1_Missense_Mutation_p.L224V	NM_024016.3	NP_076921.1	P17481	HXB8_HUMAN	homeobox B8	225					adult locomotory behavior (GO:0008344)|anterior/posterior pattern specification (GO:0009952)|dorsal spinal cord development (GO:0021516)|embryonic skeletal system morphogenesis (GO:0048704)|grooming behavior (GO:0007625)|negative regulation of myeloid cell differentiation (GO:0045638)|sensory perception of pain (GO:0019233)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|lung(8)|urinary_tract(2)	11						GCCCGCTCCAGCTTCTGTTTC	0.612													G|||	155	0.0309505	0.1142	0.0058	5008	,	,		8098	0.0		0.0	False		,,,				2504	0.0				p.L225V		Atlas-SNP	.											.	HOXB8	26	.	0			c.C673G						PASS	.	G	VAL/LEU	341,4065	176.2+/-205.4	7,327,1869	81.0	83.0	83.0		673	1.9	1.0	17	dbSNP_132	83	1,8599		0,1,4299	yes	missense	HOXB8	NM_024016.3	32	7,328,6168	CC,CG,GG		0.0116,7.7394,2.6296	benign	225/244	46690623	342,12664	2203	4300	6503	SO:0001583	missense	3218	exon2			GCTCCAGCTTCTG		CCDS11533.1	17q21.32	2011-06-20	2005-12-22		ENSG00000120068	ENSG00000120068		"""Homeoboxes / ANTP class : HOXL subclass"""	5119	protein-coding gene	gene with protein product		142963	"""homeo box B8"""	HOX2, HOX2D		1973146, 1358459	Standard	XM_005257286		Approved		uc002inw.3	P17481	OTTHUMG00000159904	ENST00000239144.4:c.673C>G	17.37:g.46690623G>C	ENSP00000239144:p.Leu225Val	143.0	0.0	0		141.0	65.0	0.460993	NM_024016	Q9H1I2	Missense_Mutation	SNP	ENST00000239144.4	37	CCDS11533.1	46	0.021062271062271064	44	0.08943089430894309	2	0.0055248618784530384	0	0.0	0	0.0	G	7.810	0.715510	0.15306	0.077394	1.16E-4	ENSG00000120068	ENST00000239144	D	0.90324	-2.65	3.04	1.94	0.25998	.	0.473524	0.13687	U	0.369761	T	0.15046	0.0363	N	0.14661	0.345	0.25211	N	0.989973	B	0.12013	0.005	B	0.12156	0.007	T	0.43956	-0.9359	10	0.29301	T	0.29	.	8.2888	0.31946	0.0:0.0:0.4932:0.5068	.	225	P17481	HXB8_HUMAN	V	225	ENSP00000239144:L225V	ENSP00000239144:L225V	L	-	1	2	HOXB8	44045622	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	2.900000	0.48687	1.734000	0.51633	0.479000	0.44913	CTG	G|0.977;C|0.023	0.023	strong		0.612	HOXB8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358092.3		
GABRG3	2567	hgsc.bcm.edu	37	15	27222266	27222266	+	Silent	SNP	A	A	G	rs35752220	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:27222266A>G	ENST00000333743.6	+	2	425	c.171A>G	c.(169-171)gaA>gaG	p.E57E	GABRG3_ENST00000555083.1_Silent_p.E57E	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	57					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(23)|skin(1)|upper_aerodigestive_tract(4)	42		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TGCTAAGAGAATATGATAAAA	0.348													A|||	182	0.0363419	0.1316	0.0101	5008	,	,		19188	0.0		0.001	False		,,,				2504	0.0				p.E57E	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											.	GABRG3	115	.	0			c.A171G						PASS	.	A		345,3291		16,313,1489	99.0	99.0	99.0		171	3.0	1.0	15	dbSNP_126	99	3,8149		0,3,4073	no	coding-synonymous	GABRG3	NM_033223.4		16,316,5562	GG,GA,AA		0.0368,9.4884,2.9522		57/468	27222266	348,11440	1818	4076	5894	SO:0001819	synonymous_variant	2567	exon2			AAGAGAATATGAT		CCDS45195.1, CCDS59251.1	15q12	2012-06-22			ENSG00000182256	ENSG00000182256		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4088	protein-coding gene	gene with protein product	"""GABA(G) receptor, gamma 3"""	600233				7601451	Standard	NM_033223		Approved		uc001zbg.2	Q99928	OTTHUMG00000044462	ENST00000333743.6:c.171A>G	15.37:g.27222266A>G		105.0	0.0	0		122.0	53.0	0.434426	NM_001270873	G3V594|Q9HD46|Q9NYT2	Silent	SNP	ENST00000333743.6	37	CCDS45195.1																																																																																			A|0.970;G|0.030	0.030	strong		0.348	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2		
CEMIP	57214	hgsc.bcm.edu	37	15	81172064	81172064	+	Silent	SNP	G	G	A	rs35541581	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:81172064G>A	ENST00000394685.3	+	5	668	c.249G>A	c.(247-249)ctG>ctA	p.L83L	KIAA1199_ENST00000220244.3_Silent_p.L83L|KIAA1199_ENST00000356249.5_Silent_p.L83L			Q8WUJ3	CEMIP_HUMAN		83	G8. {ECO:0000255|PROSITE- ProRule:PRU00817}.				hyaluronan catabolic process (GO:0030214)|positive regulation of cell migration (GO:0030335)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase C activity (GO:1900020)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|sensory perception of sound (GO:0007605)	clathrin-coated vesicle membrane (GO:0030665)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	clathrin heavy chain binding (GO:0032050)|ER retention sequence binding (GO:0046923)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						CAGGCAAGCTGGTCATTAAAG	0.527													A|||	357	0.0712859	0.2481	0.0389	5008	,	,		19880	0.0		0.002	False		,,,				2504	0.0				p.L83L		Atlas-SNP	.											.	KIAA1199	118	.	0			c.G249A						PASS	.	A		941,3465	736.2+/-410.7	102,737,1364	78.0	70.0	73.0		249	-12.1	0.0	15	dbSNP_126	73	29,8571	817.9+/-406.9	0,29,4271	no	coding-synonymous	KIAA1199	NM_018689.1		102,766,5635	AA,AG,GG		0.3372,21.3572,7.4581		83/1362	81172064	970,12036	2203	4300	6503	SO:0001819	synonymous_variant	57214	exon4			CAAGCTGGTCATT																												ENST00000394685.3:c.249G>A	15.37:g.81172064G>A		112.0	0.0	0		125.0	62.0	0.496	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Silent	SNP	ENST00000394685.3	37	CCDS10315.1																																																																																			G|0.928;A|0.072	0.072	strong		0.527	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1		
CYB561	1534	hgsc.bcm.edu	37	17	61513509	61513509	+	Silent	SNP	C	C	T	rs35447397	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:61513509C>T	ENST00000392976.1	-	3	506	c.207G>A	c.(205-207)ctG>ctA	p.L69L	CYB561_ENST00000582297.1_Silent_p.L69L|CYB561_ENST00000582034.1_Silent_p.L40L|CYB561_ENST00000581163.1_5'UTR|CYB561_ENST00000581573.1_Silent_p.L69L|CYB561_ENST00000584031.1_Silent_p.L69L|CYB561_ENST00000448884.2_Silent_p.L69L|CYB561_ENST00000542042.1_Silent_p.L136L|CYB561_ENST00000582997.1_Silent_p.L76L|CYB561_ENST00000392975.2_Silent_p.L69L|CYB561_ENST00000360793.3_Silent_p.L69L	NM_001017916.1	NP_001017916.1	P49447	CY561_HUMAN	cytochrome b561	69	Cytochrome b561. {ECO:0000255|PROSITE- ProRule:PRU00242}.				electron transport chain (GO:0022900)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	ferric-chelate reductase activity (GO:0000293)|metal ion binding (GO:0046872)|transmembrane electron transfer carrier (GO:0022865)			lung(2)|ovary(1)|prostate(1)	4				READ - Rectum adenocarcinoma(1115;0.0689)		GGTAAACCAGCAGGGCTGTGG	0.607													C|||	41	0.0081869	0.031	0.0	5008	,	,		17487	0.0		0.0	False		,,,				2504	0.0				p.L69L		Atlas-SNP	.											.	CYB561	15	.	0			c.G207A						PASS	.	C	,,	114,4290	87.8+/-126.4	1,112,2089	128.0	94.0	106.0		207,207,207	3.9	1.0	17	dbSNP_126	106	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	CYB561	NM_001017916.1,NM_001017917.1,NM_001915.3	,,	1,112,6389	TT,TC,CC		0.0,2.5886,0.8767	,,	69/252,69/252,69/252	61513509	114,12890	2202	4300	6502	SO:0001819	synonymous_variant	1534	exon3			AACCAGCAGGGCT		CCDS11636.1	17q23.3	2013-03-14	2013-03-14		ENSG00000008283	ENSG00000008283		"""Cytochrome b genes"""	2571	protein-coding gene	gene with protein product	"""ferric-chelate reductase 2"", ""cytochrome b561 family, member A1"""	600019				7959749, 23249217	Standard	XM_005257091		Approved	FRRS2, CYB561A1	uc002jas.3	P49447		ENST00000392976.1:c.207G>A	17.37:g.61513509C>T		85.0	0.0	0		76.0	35.0	0.460526	NM_001915	B2RE96|B7Z775|D3DU11|Q5BJG9|Q9BU05|Q9BWR9	Silent	SNP	ENST00000392976.1	37	CCDS11636.1																																																																																			C|0.989;T|0.011	0.011	strong		0.607	CYB561-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444843.1	NM_001915	
ATF6B	1388	hgsc.bcm.edu	37	6	32093922	32093922	+	Silent	SNP	G	G	A	rs204894	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32093922G>A	ENST00000375203.3	-	5	482	c.450C>T	c.(448-450)aaC>aaT	p.N150N	ATF6B_ENST00000468502.1_5'UTR|ATF6B_ENST00000375201.4_Silent_p.N147N	NM_001136153.1|NM_004381.4	NP_001129625.1|NP_004372.3	Q99941	ATF6B_HUMAN	activating transcription factor 6 beta	150					response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	22						TGGGGATAACGTTGATCTGGA	0.512													G|||	244	0.048722	0.115	0.0648	5008	,	,		15085	0.001		0.0457	False		,,,				2504	0.0				p.N150N		Atlas-SNP	.											.	ATF6B	40	.	0			c.C450T						PASS	.	G	,	453,3953	216.4+/-235.1	21,411,1771	157.0	137.0	144.0		441,450	-0.3	1.0	6	dbSNP_79	144	404,8196	127.2+/-185.5	7,390,3903	yes	coding-synonymous,coding-synonymous	ATF6B	NM_001136153.1,NM_004381.4	,	28,801,5674	AA,AG,GG		4.6977,10.2814,6.5893	,	147/701,150/704	32093922	857,12149	2203	4300	6503	SO:0001819	synonymous_variant	1388	exon5			GATAACGTTGATC		CCDS47408.1, CCDS4737.1	6p21.3	2013-01-10	2008-10-21	2008-10-21	ENSG00000213676	ENSG00000213676		"""basic leucine zipper proteins"""	2349	protein-coding gene	gene with protein product		600984	"""cAMP responsive element binding protein-like 1"""	CREBL1		11256944, 14973138	Standard	NM_004381		Approved	G13	uc003nzn.3	Q99941	OTTHUMG00000031296	ENST00000375203.3:c.450C>T	6.37:g.32093922G>A		120.0	0.0	0		132.0	70.0	0.530303	NM_004381	B0UYX6|Q13269|Q14343|Q14345|Q5SSW7|Q99635|Q99637|Q9H3V9|Q9H3W1|Q9NPL0	Silent	SNP	ENST00000375203.3	37	CCDS4737.1																																																																																			G|0.945;A|0.055	0.055	strong		0.512	ATF6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076638.2		
CDK12	51755	hgsc.bcm.edu	37	17	37682200	37682200	+	Missense_Mutation	SNP	A	A	G	rs61747430	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:37682200A>G	ENST00000447079.4	+	13	3424	c.3391A>G	c.(3391-3393)Atc>Gtc	p.I1131V	CDK12_ENST00000430627.2_Missense_Mutation_p.I1131V	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	1131					mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						CGACCTGAGCATCCCTCAAAT	0.507			"""Mis, N, F"""		serous ovarian					TCGA Ovarian(9;0.13)			A|||	43	0.00858626	0.0325	0.0	5008	,	,		19029	0.0		0.0	False		,,,				2504	0.0				p.I1131V		Atlas-SNP	.		Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	.	CDK12	161	.	0			c.A3391G						PASS	.	A	VAL/ILE,VAL/ILE	148,4258	103.0+/-141.5	3,142,2058	88.0	75.0	80.0		3391,3391	2.6	1.0	17	dbSNP_129	80	1,8599		0,1,4299	yes	missense,missense	CDK12	NM_016507.2,NM_015083.1	29,29	3,143,6357	GG,GA,AA		0.0116,3.3591,1.1456	benign,benign	1131/1491,1131/1482	37682200	149,12857	2203	4300	6503	SO:0001583	missense	51755	exon13			CTGAGCATCCCTC	AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258		"""Cyclin-dependent kinases"""	24224	protein-coding gene	gene with protein product	"""CDC2 related protein kinase 7"""	615514	"""Cdc2-related kinase, arginine/serine-rich"""	CRKRS		10048485, 11683387, 19884882	Standard	XM_005257456		Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.3391A>G	17.37:g.37682200A>G	ENSP00000398880:p.Ile1131Val	202.0	0.0	0		239.0	106.0	0.443515	NM_016507	A7E2B2|B4DYX4|B9EIQ6|O94978	Missense_Mutation	SNP	ENST00000447079.4	37	CCDS11337.1	15	0.006868131868131868	15	0.03048780487804878	0	0.0	0	0.0	0	0.0	A	4.981	0.182220	0.09495	0.033591	1.16E-4	ENSG00000167258	ENST00000430627;ENST00000447079	T;T	0.67171	-0.23;-0.25	4.82	2.59	0.31030	.	0.151372	0.30374	N	0.009776	T	0.13457	0.0326	N	0.01668	-0.77	0.30087	N	0.808665	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.10917	-1.0609	10	0.30854	T	0.27	-6.9124	7.0706	0.25177	0.6741:0.0:0.3259:0.0	rs61747430	1130;1131;1131	E7EUM9;Q9NYV4;Q9NYV4-2	.;CDK12_HUMAN;.	V	1131	ENSP00000407720:I1131V;ENSP00000398880:I1131V	ENSP00000407720:I1131V	I	+	1	0	CDK12	34935726	0.995000	0.38212	0.998000	0.56505	0.771000	0.43674	1.586000	0.36611	0.811000	0.34303	-0.385000	0.06624	ATC	A|0.989;G|0.011	0.011	strong		0.507	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507	
NR1I2	8856	hgsc.bcm.edu	37	3	119530546	119530546	+	Silent	SNP	T	T	C	rs12721611	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119530546T>C	ENST00000337940.4	+	4	657	c.609T>C	c.(607-609)acT>acC	p.T203T	NR1I2_ENST00000466380.1_Silent_p.T164T|NR1I2_ENST00000393716.2_Silent_p.T164T	NM_022002.2	NP_071285.1	O75469	NR1I2_HUMAN	nuclear receptor subfamily 1, group I, member 2	164	Hinge.				drug export (GO:0046618)|exogenous drug catabolic process (GO:0042738)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|steroid metabolic process (GO:0008202)|transcription initiation from RNA polymerase II promoter (GO:0006367)|xenobiotic metabolic process (GO:0006805)|xenobiotic transport (GO:0042908)	nucleoplasm (GO:0005654)	drug binding (GO:0008144)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|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)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(2)|prostate(2)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.175)	Docetaxel(DB01248)|Erlotinib(DB00530)|Estradiol(DB00783)|Ethinyl Estradiol(DB00977)|Paclitaxel(DB01229)|Rifampicin(DB01045)|Rifaximin(DB01220)|Rilpivirine(DB08864)|Vitamin E(DB00163)	CCTTTGACACTACCTTCTCCC	0.527													T|||	76	0.0151757	0.0545	0.0058	5008	,	,		20683	0.0		0.0	False		,,,				2504	0.0				p.T203T		Atlas-SNP	.											.	NR1I2	44	.	0			c.T609C						PASS	.	T	,,	232,4174	136.5+/-172.5	3,226,1974	110.0	97.0	101.0		492,609,492	3.0	1.0	3	dbSNP_126	101	6,8594	2.2+/-6.3	1,4,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	NR1I2	NM_003889.3,NM_022002.2,NM_033013.2	,,	4,230,6269	CC,CT,TT		0.0698,5.2655,1.8299	,,	164/435,203/474,164/398	119530546	238,12768	2203	4300	6503	SO:0001819	synonymous_variant	8856	exon4			TGACACTACCTTC	AF061056	CCDS2995.1, CCDS43136.1, CCDS54627.1	3q12-q13.3	2013-03-25			ENSG00000144852	ENSG00000144852		"""Nuclear hormone receptors"""	7968	protein-coding gene	gene with protein product	"""pregnane X receptor"", ""orphan nuclear receptor PXR"""	603065				9727070, 9770465	Standard	NM_003889		Approved	ONR1, PXR, BXR, SXR, PAR2	uc003edk.3	O75469	OTTHUMG00000159400	ENST00000337940.4:c.609T>C	3.37:g.119530546T>C		83.0	0.0	0		89.0	48.0	0.539326	NM_022002	Q006P5|Q008C8|Q96AC7|Q9UJ22|Q9UJ23|Q9UJ24|Q9UJ25|Q9UJ26|Q9UJ27|Q9UNW4	Silent	SNP	ENST00000337940.4	37	CCDS2995.1																																																																																			T|0.981;C|0.019	0.019	strong		0.527	NR1I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355126.1		
PCDHB2	56133	hgsc.bcm.edu	37	5	140475514	140475514	+	Missense_Mutation	SNP	C	C	A	rs73793576	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140475514C>A	ENST00000194155.4	+	1	1288	c.1140C>A	c.(1138-1140)aaC>aaA	p.N380K		NM_018936.2	NP_061759.1	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2	380	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(22)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCGGAGACAACGGAAGGATGG	0.473													C|||	44	0.00878594	0.0325	0.0014	5008	,	,		19966	0.0		0.0	False		,,,				2504	0.0				p.N380K		Atlas-SNP	.											.	PCDHB2	163	.	0			c.C1140A						PASS	.	C	LYS/ASN	116,4290	90.2+/-128.9	2,112,2089	81.0	73.0	76.0		1140	-1.8	1.0	5	dbSNP_130	76	0,8600		0,0,4300	yes	missense	PCDHB2	NM_018936.2	94	2,112,6389	AA,AC,CC		0.0,2.6328,0.8919	probably-damaging	380/799	140475514	116,12890	2203	4300	6503	SO:0001583	missense	56133	exon1			AGACAACGGAAGG	AF152495	CCDS4244.1	5q31	2010-01-26			ENSG00000112852	ENSG00000112852		"""Cadherins / Protocadherins : Clustered"""	8687	other	protocadherin		606328				10380929	Standard	NM_018936		Approved	PCDH-BETA2	uc003lil.3	Q9Y5E7	OTTHUMG00000129606	ENST00000194155.4:c.1140C>A	5.37:g.140475514C>A	ENSP00000194155:p.Asn380Lys	135.0	0.0	0		138.0	72.0	0.521739	NM_018936	Q4KMU1	Missense_Mutation	SNP	ENST00000194155.4	37	CCDS4244.1	16	0.007326007326007326	15	0.03048780487804878	1	0.0027624309392265192	0	0.0	0	0.0	C	11.52	1.663243	0.29515	0.026328	0.0	ENSG00000112852	ENST00000194155	T	0.59906	0.23	5.15	-1.8	0.07907	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.60945	0.2308	H	0.97390	3.995	0.35381	D	0.789909	D	0.71674	0.998	P	0.62435	0.902	T	0.82259	-0.0546	9	0.72032	D	0.01	.	12.3358	0.55067	0.0:0.4067:0.0:0.5933	.	380	Q9Y5E7	PCDB2_HUMAN	K	380	ENSP00000194155:N380K	ENSP00000194155:N380K	N	+	3	2	PCDHB2	140455698	0.014000	0.17966	0.990000	0.47175	0.260000	0.26232	-0.975000	0.03790	-0.310000	0.08766	0.655000	0.94253	AAC	C|0.991;A|0.009	0.009	strong		0.473	PCDHB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251801.2	NM_018936	
KIF5C	3800	hgsc.bcm.edu	37	2	149861927	149861927	+	Silent	SNP	G	G	A	rs184488465	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:149861927G>A	ENST00000435030.1	+	22	2762	c.2394G>A	c.(2392-2394)ctG>ctA	p.L798L	KIF5C_ENST00000397413.1_Silent_p.L566L|KIF5C_ENST00000414838.2_Silent_p.L703L|KIF5C_ENST00000464066.1_3'UTR			O60282	KIF5C_HUMAN	kinesin family member 5C	798					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mRNA transport (GO:0051028)|organelle organization (GO:0006996)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(12)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(221;0.108)		TGCAGACACTGCACAACCTTC	0.428													G|||	12	0.00239617	0.0091	0.0	5008	,	,		16356	0.0		0.0	False		,,,				2504	0.0				p.L798L		Atlas-SNP	.											.	KIF5C	166	.	0			c.G2394A						PASS	.	G		16,3708		0,16,1846	73.0	71.0	72.0		2105	-0.9	1.0	2		72	0,8218		0,0,4109	no	coding-synonymous	KIF5C	NM_004522.1		0,16,5955	AA,AG,GG		0.0,0.4296,0.134		798/958	149861927	16,11926	1862	4109	5971	SO:0001819	synonymous_variant	3800	exon22			GACACTGCACAAC	AB011103	CCDS74586.1	2q23	2008-02-05			ENSG00000168280	ENSG00000168280		"""Kinesins"""	6325	protein-coding gene	gene with protein product		604593				7514426	Standard	NM_004522		Approved		uc010zbu.2	O60282	OTTHUMG00000153779	ENST00000435030.1:c.2394G>A	2.37:g.149861927G>A		69.0	0.0	0		66.0	44.0	0.666667	NM_004522	O95079|Q2YDC5	Silent	SNP	ENST00000435030.1	37																																																																																				G|0.999;A|0.001	0.001	strong		0.428	KIF5C-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000332562.3	NM_004522	
BRD7	29117	hgsc.bcm.edu	37	16	50368670	50368670	+	Missense_Mutation	SNP	C	C	A	rs113038433	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:50368670C>A	ENST00000394688.3	-	7	998	c.839G>T	c.(838-840)gGa>gTa	p.G280V	BRD7_ENST00000394689.2_Missense_Mutation_p.G280V			Q9NPI1	BRD7_HUMAN	bromodomain containing 7	280					cell cycle (GO:0007049)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|urinary_tract(2)	22		all_cancers(37;0.0127)				TTCGGCATCTCCAGAGTCCTC	0.473													C|||	60	0.0119808	0.0431	0.0043	5008	,	,		17122	0.0		0.0	False		,,,				2504	0.0				p.G280V		Atlas-SNP	.											.	BRD7	61	.	0			c.G839T						PASS	.	C	VAL/GLY,VAL/GLY	129,4267	94.4+/-133.1	1,127,2070	138.0	142.0	141.0		839,839	4.4	0.4	16	dbSNP_132	141	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	BRD7	NM_001173984.2,NM_013263.4	109,109	1,128,6369	AA,AC,CC		0.0116,2.9345,1.0003	benign,benign	280/653,280/652	50368670	130,12866	2198	4300	6498	SO:0001583	missense	29117	exon7			GCATCTCCAGAGT	AF213969	CCDS10742.1, CCDS54007.1	16q12.1	2008-11-18	2002-01-14		ENSG00000166164	ENSG00000166164			14310	protein-coding gene	gene with protein product			"""bromodomain-containing 7"""			10526152, 18809673	Standard	NM_013263		Approved	CELTIX1, BP75	uc002ege.2	Q9NPI1	OTTHUMG00000133170	ENST00000394688.3:c.839G>T	16.37:g.50368670C>A	ENSP00000378180:p.Gly280Val	136.0	0.0	0		192.0	59.0	0.307292	NM_013263	Q4VC09|Q8N2L9|Q96KA4|Q9BV48|Q9UH59	Missense_Mutation	SNP	ENST00000394688.3	37	CCDS10742.1	25	0.011446886446886446	24	0.04878048780487805	1	0.0027624309392265192	0	0.0	0	0.0	C	10.22	1.289343	0.23478	0.029345	1.16E-4	ENSG00000166164	ENST00000394688;ENST00000394689	T;T	0.30448	1.54;1.53	5.47	4.41	0.53225	.	0.486780	0.23583	N	0.046637	T	0.02193	0.0068	N	0.08118	0	0.24366	N	0.994853	B;B	0.06786	0.0;0.001	B;B	0.09377	0.002;0.004	T	0.07121	-1.0789	10	0.27082	T	0.32	-13.1079	10.8718	0.46887	0.3081:0.6919:0.0:0.0	.	280;280	Q9NPI1;Q9NPI1-2	BRD7_HUMAN;.	V	280	ENSP00000378180:G280V;ENSP00000378181:G280V	ENSP00000378180:G280V	G	-	2	0	BRD7	48926171	0.945000	0.32115	0.424000	0.26647	0.782000	0.44232	2.285000	0.43487	2.733000	0.93635	0.650000	0.86243	GGA	C|0.988;A|0.012	0.012	strong		0.473	BRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256874.3	NM_013263	
PPP1R12C	54776	hgsc.bcm.edu	37	19	55607447	55607447	+	Silent	SNP	G	G	A	rs35641913	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55607447G>A	ENST00000263433.3	-	8	1140	c.1125C>T	c.(1123-1125)gaC>gaT	p.D375D	PPP1R12C_ENST00000435544.2_Silent_p.D301D|PPP1R12C_ENST00000376393.2_Silent_p.D375D	NM_001271618.1|NM_017607.2	NP_001258547.1|NP_060077.1			protein phosphatase 1, regulatory subunit 12C											central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	22			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0449)		CCTCATCCTCGTCCTGGATGG	0.642													G|||	111	0.0221645	0.0825	0.0029	5008	,	,		14673	0.0		0.0	False		,,,				2504	0.0				p.D375D		Atlas-SNP	.											PPP1R12C,NS,carcinoma,0,1	PPP1R12C	46	1	0			c.C1125T						PASS	.	G		328,4078	163.6+/-195.4	9,310,1884	53.0	66.0	62.0		1125	-7.5	0.4	19	dbSNP_126	62	1,8595		0,1,4297	no	coding-synonymous	PPP1R12C	NM_017607.2		9,311,6181	AA,AG,GG		0.0116,7.4444,2.5304		375/783	55607447	329,12673	2203	4298	6501	SO:0001819	synonymous_variant	54776	exon8			ATCCTCGTCCTGG	AF312028	CCDS12916.1	19q13.42	2013-01-10	2011-10-04		ENSG00000125503	ENSG00000125503		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	14947	protein-coding gene	gene with protein product	"""myosin-binding subunit 85"""	613245	"""leukocyte receptor cluster (LRC) member 3"", ""protein phosphatase 1, regulatory (inhibitor) subunit 12C"""	LENG3		11399775	Standard	NM_017607		Approved	DKFZP434D0412, p84, MBS85, p85	uc002qix.4	Q9BZL4		ENST00000263433.3:c.1125C>T	19.37:g.55607447G>A		29.0	0.0	0		40.0	20.0	0.5	NM_017607		Silent	SNP	ENST00000263433.3	37	CCDS12916.1																																																																																			G|0.976;A|0.024	0.024	strong		0.642	PPP1R12C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451814.2	NM_017607	
ANGPT4	51378	hgsc.bcm.edu	37	20	854973	854973	+	Silent	SNP	T	T	G	rs62641668	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:854973T>G	ENST00000381922.3	-	8	1407	c.1305A>C	c.(1303-1305)tcA>tcC	p.S435S	ANGPT4_ENST00000546022.1_Intron	NM_015985.2	NP_057069.1	Q9Y264	ANGP4_HUMAN	angiopoietin 4	435	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to hypoxia (GO:0071456)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)	27						GGTCGTTGTCTGAGTCAAGGG	0.612													T|||	75	0.014976	0.0416	0.0144	5008	,	,		20786	0.004		0.006	False		,,,				2504	0.0				p.S435S	Pancreas(181;481 2077 3259 31286 49856)	Atlas-SNP	.											ANGPT4,bladder,carcinoma,-1,1	ANGPT4	77	1	0			c.A1305C						PASS	.	T		163,4243	109.9+/-148.2	5,153,2045	123.0	93.0	103.0		1305	-10.3	0.0	20	dbSNP_129	103	52,8548	32.8+/-85.7	0,52,4248	no	coding-synonymous	ANGPT4	NM_015985.2		5,205,6293	GG,GT,TT		0.6047,3.6995,1.6531		435/504	854973	215,12791	2203	4300	6503	SO:0001819	synonymous_variant	51378	exon8			GTTGTCTGAGTCA	AF074332	CCDS13009.1	20p13	2013-02-06			ENSG00000101280	ENSG00000101280		"""Fibrinogen C domain containing"""	487	protein-coding gene	gene with protein product		603705				10051567, 10218486	Standard	NM_015985		Approved		uc002wei.3	Q9Y264	OTTHUMG00000031652	ENST00000381922.3:c.1305A>C	20.37:g.854973T>G		176.0	0.0	0		216.0	103.0	0.476852	NM_015985	B4E3J9|Q5TFF4|Q9H4Z4	Silent	SNP	ENST00000381922.3	37	CCDS13009.1																																																																																			T|0.983;G|0.017	0.017	strong		0.612	ANGPT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077493.1	NM_015985	
ARHGEF10	9639	hgsc.bcm.edu	37	8	1808343	1808343	+	Silent	SNP	C	C	T	rs147914724	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:1808343C>T	ENST00000398564.1	+	4	546	c.546C>T	c.(544-546)gaC>gaT	p.D182D	ARHGEF10_ENST00000518288.1_Silent_p.D182D|ARHGEF10_ENST00000398560.1_Silent_p.D182D|ARHGEF10_ENST00000262112.6_Silent_p.D182D|ARHGEF10_ENST00000520359.1_Silent_p.D158D|ARHGEF10_ENST00000349830.3_Silent_p.D158D			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	182					centrosome duplication (GO:0051298)|myelination in peripheral nervous system (GO:0022011)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cytosol (GO:0005829)	kinesin binding (GO:0019894)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.D182D(1)		endometrium(3)|large_intestine(11)|lung(11)|prostate(3)|skin(3)|stomach(3)|urinary_tract(1)	35		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		CGTCCCTGGACGAAGAAGGTA	0.657													C|||	2	0.000399361	0.0008	0.0	5008	,	,		17485	0.0		0.0	False		,,,				2504	0.001				p.D158D		Atlas-SNP	.											ARHGEF10_ENST00000398564,colon,carcinoma,0,1	ARHGEF10	255	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C474T						PASS	.	C		14,4392	21.2+/-45.6	0,14,2189	80.0	72.0	74.0		474	-10.6	0.0	8	dbSNP_134	74	0,8600		0,0,4300	no	coding-synonymous	ARHGEF10	NM_014629.2		0,14,6489	TT,TC,CC		0.0,0.3177,0.1076		158/1345	1808343	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	9639	exon4			CCTGGACGAAGAA	AF009205	CCDS34794.1	8p23	2014-09-17			ENSG00000104728	ENSG00000104728		"""Rho guanine nucleotide exchange factors"""	14103	protein-coding gene	gene with protein product		608136				9205841, 16896804	Standard	XM_005266039		Approved	KIAA0294, Gef10	uc003wpr.3	O15013	OTTHUMG00000163626	ENST00000398564.1:c.546C>T	8.37:g.1808343C>T		67.0	0.0	0		95.0	41.0	0.431579	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Silent	SNP	ENST00000398564.1	37																																																																																				C|0.999;T|0.001	0.001	strong		0.657	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding			
CCNG2	901	hgsc.bcm.edu	37	4	78079768	78079768	+	Missense_Mutation	SNP	A	A	G	rs4150051	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:78079768A>G	ENST00000316355.5	+	2	439	c.83A>G	c.(82-84)gAa>gGa	p.E28G	CCNG2_ENST00000502280.1_Missense_Mutation_p.E28G|CCNG2_ENST00000395640.1_Missense_Mutation_p.E28G|CCNG2_ENST00000509972.1_Missense_Mutation_p.E28G|CCNG2_ENST00000497512.1_3'UTR|CCNG2_ENST00000354403.5_Missense_Mutation_p.E28G	NM_004354.2	NP_004345.1	Q16589	CCNG2_HUMAN	cyclin G2	28			E -> G (in dbSNP:rs4150051). {ECO:0000269|Ref.3}.		cell cycle checkpoint (GO:0000075)|mitotic nuclear division (GO:0007067)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)				breast(1)|kidney(2)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	10						CTGGAACAAGAAGAGAGATTC	0.502													A|||	22	0.00439297	0.0144	0.0043	5008	,	,		16831	0.0		0.0	False		,,,				2504	0.0				p.E28G		Atlas-SNP	.											.	CCNG2	27	.	0			c.A83G						PASS	.	A	GLY/GLU	67,4339	62.3+/-99.4	2,63,2138	112.0	112.0	112.0		83	5.6	1.0	4	dbSNP_110	112	1,8599		0,1,4299	yes	missense	CCNG2	NM_004354.2	98	2,64,6437	GG,GA,AA		0.0116,1.5207,0.5228	probably-damaging	28/345	78079768	68,12938	2203	4300	6503	SO:0001583	missense	901	exon2			AACAAGAAGAGAG	BC032518	CCDS3581.1	4q21.22	2009-05-07			ENSG00000138764	ENSG00000138764			1593	protein-coding gene	gene with protein product		603203				8806701	Standard	NM_004354		Approved		uc003hkq.4	Q16589	OTTHUMG00000130100	ENST00000316355.5:c.83A>G	4.37:g.78079768A>G	ENSP00000315743:p.Glu28Gly	132.0	0.0	0		125.0	61.0	0.488	NM_004354	B4DF25|Q6FGA7|Q6FGC6	Missense_Mutation	SNP	ENST00000316355.5	37	CCDS3581.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	24.2	4.508863	0.85282	0.015207	1.16E-4	ENSG00000138764	ENST00000316355;ENST00000354403;ENST00000502280;ENST00000395640;ENST00000512918;ENST00000509972	T;T;T;T;T;T	0.57436	0.4;0.4;0.4;0.4;1.69;1.69	5.57	5.57	0.84162	Cyclin-like (1);	0.000000	0.85682	D	0.000000	T	0.64125	0.2570	M	0.88979	2.995	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.78046	-0.2357	10	0.87932	D	0	-16.452	15.3858	0.74699	1.0:0.0:0.0:0.0	rs4150051	28;28	B4DF25;Q16589	.;CCNG2_HUMAN	G	28	ENSP00000315743:E28G;ENSP00000346379:E28G;ENSP00000424665:E28G;ENSP00000379002:E28G;ENSP00000426085:E28G;ENSP00000426476:E28G	ENSP00000315743:E28G	E	+	2	0	CCNG2	78298792	1.000000	0.71417	1.000000	0.80357	0.550000	0.35303	7.252000	0.78309	2.126000	0.65437	0.459000	0.35465	GAA	A|0.996;G|0.004	0.004	strong		0.502	CCNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252404.3	NM_004354	
SPPL2C	162540	hgsc.bcm.edu	37	17	43922535	43922535	+	Missense_Mutation	SNP	C	C	T	rs116482551	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:43922535C>T	ENST00000329196.5	+	1	280	c.263C>T	c.(262-264)cCc>cTc	p.P88L	MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579244.1_RNA|MAPT-AS1_ENST00000579599.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	88	PA.					endoplasmic reticulum membrane (GO:0005789)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)										AGCCAGCGGCCCCTCCGCCAG	0.682													C|||	19	0.00379393	0.0144	0.0	5008	,	,		15160	0.0		0.0	False		,,,				2504	0.0				p.P88L		Atlas-SNP	.											.	.	.	.	0			c.C263T						PASS	.	C	LEU/PRO	68,4338	56.2+/-92.4	1,66,2136	25.0	26.0	26.0		263	4.8	0.6	17	dbSNP_132	26	0,8598		0,0,4299	yes	missense	IMP5	NM_175882.2	98	1,66,6435	TT,TC,CC		0.0,1.5433,0.5229	probably-damaging	88/685	43922535	68,12936	2203	4299	6502	SO:0001583	missense	162540	exon1			AGCGGCCCCTCCG		CCDS32673.1	17q21.31	2014-02-12			ENSG00000185294	ENSG00000185294			28902	protein-coding gene	gene with protein product	"""intramembrane protease 5"""	608284				12139484	Standard	NM_175882		Approved	IMP5	uc010wka.2	Q8IUH8		ENST00000329196.5:c.263C>T	17.37:g.43922535C>T	ENSP00000332488:p.Pro88Leu	84.0	0.0	0		87.0	47.0	0.54023	NM_175882	Q8TC67|Q8WVZ6	Missense_Mutation	SNP	ENST00000329196.5	37	CCDS32673.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	15.63	2.890707	0.52014	0.015433	0.0	ENSG00000185294	ENST00000329196	T	0.06068	3.35	4.8	4.8	0.61643	Protease-associated domain, PA (1);	0.000000	0.42172	D	0.000759	T	0.10637	0.0260	M	0.73217	2.22	0.58432	D	0.999998	D	0.69078	0.997	D	0.68943	0.961	T	0.00203	-1.1924	10	0.33940	T	0.23	-5.2725	13.2146	0.59851	0.0:1.0:0.0:0.0	.	88	Q8IUH8	IMP5_HUMAN	L	88	ENSP00000332488:P88L	ENSP00000332488:P88L	P	+	2	0	AC217771.1	41278315	0.895000	0.30542	0.640000	0.29408	0.454000	0.32378	2.391000	0.44424	2.481000	0.83766	0.650000	0.86243	CCC	C|0.995;T|0.005	0.005	strong		0.682	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
GBGT1	26301	hgsc.bcm.edu	37	9	136029474	136029474	+	Silent	SNP	C	C	T	rs35808997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136029474C>T	ENST00000372040.3	-	7	845	c.534G>A	c.(532-534)gaG>gaA	p.E178E	RALGDS_ENST00000542690.1_Intron|GBGT1_ENST00000372038.3_3'UTR|GBGT1_ENST00000472281.1_5'UTR|GBGT1_ENST00000372043.3_Missense_Mutation_p.R172K|GBGT1_ENST00000540636.1_Silent_p.E161E	NM_001282629.1	NP_001269558.1	Q8N5D6	GBGT1_HUMAN	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	178					glycolipid biosynthetic process (GO:0009247)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	globoside alpha-N-acetylgalactosaminyltransferase activity (GO:0047277)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(4)|lung(2)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;3.49e-06)|Epithelial(140;2.59e-05)		GCATGGATGTCTCCTCCCAGT	0.607													C|||	364	0.0726837	0.2632	0.0202	5008	,	,		17590	0.0		0.002	False		,,,				2504	0.0				p.E178E		Atlas-SNP	.											.	GBGT1	25	.	0			c.G534A						PASS	.	C		957,3449	360.1+/-315.1	109,739,1355	59.0	47.0	51.0		534	2.9	0.6	9	dbSNP_126	51	6,8592	4.3+/-15.6	0,6,4293	no	coding-synonymous	GBGT1	NM_021996.4		109,745,5648	TT,TC,CC		0.0698,21.7204,7.4054		178/348	136029474	963,12041	2203	4299	6502	SO:0001819	synonymous_variant	26301	exon7			GGATGTCTCCTCC	AY358175	CCDS6960.1, CCDS65175.1, CCDS65176.1	9q34.13-q34.3	2014-07-18			ENSG00000148288	ENSG00000148288		"""Glycosyltransferase family 6 domain containing"""	20460	protein-coding gene	gene with protein product	"""Forssman glycolipid synthetase (FS)"", ""Forssman synthetase"""	606074				10506200, 8855242	Standard	NM_021996		Approved	UDP-GalNAc, A3GALNT, MGC44848, FS		Q8N5D6	OTTHUMG00000020853	ENST00000372040.3:c.534G>A	9.37:g.136029474C>T		88.0	0.0	0		118.0	69.0	0.584746	NM_021996	A8K633|B2RA95|B7Z8S5|Q45F07|Q5T7U9|Q5T7V1|Q8N2K4|Q9UKI5	Silent	SNP	ENST00000372040.3	37	CCDS6960.1	115	0.052655677655677656	109	0.22154471544715448	6	0.016574585635359115	0	0.0	0	0.0	C	6.220	0.408804	0.11812	0.217204	6.98E-4	ENSG00000148288	ENST00000372043	T	0.22134	1.97	5.16	2.91	0.33838	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999742809	.	.	.	.	.	.	T	0.13575	-1.0504	5	0.87932	D	0	-9.1051	9.1909	0.37197	0.0:0.6371:0.2769:0.086	rs35808997;rs62638706	.	.	.	K	172	ENSP00000361113:R172K	ENSP00000361113:R172K	R	-	2	0	GBGT1	135019295	0.950000	0.32346	0.650000	0.29550	0.003000	0.03518	0.078000	0.14761	1.145000	0.42336	-0.479000	0.04858	AGA	C|0.934;T|0.066	0.066	strong		0.607	GBGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054815.1	NM_021996	
SYT8	90019	hgsc.bcm.edu	37	11	1858076	1858076	+	Missense_Mutation	SNP	C	C	T	rs115217397	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1858076C>T	ENST00000381968.3	+	7	945	c.817C>T	c.(817-819)Cgt>Tgt	p.R273C	TNNI2_ENST00000252898.7_5'Flank|SYT8_ENST00000535046.1_3'UTR|TNNI2_ENST00000381906.1_5'Flank|SYT8_ENST00000341958.3_Missense_Mutation_p.R259C|TNNI2_ENST00000381911.1_5'Flank	NM_138567.3	NP_612634	Q8NBV8	SYT8_HUMAN	synaptotagmin VIII	273	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)		TCGAGGCCTGCGTCCAGGACT	0.682													C|||	38	0.00758786	0.0272	0.0014	5008	,	,		16027	0.0		0.0	False		,,,				2504	0.001				p.R273C		Atlas-SNP	.											.	SYT8	29	.	0			c.C817T						PASS	.	C	CYS/ARG	108,4292	82.4+/-120.9	2,104,2094	37.0	38.0	38.0		817	0.6	0.2	11	dbSNP_132	38	1,8595	1.2+/-3.3	0,1,4297	yes	missense	SYT8	NM_138567.3	180	2,105,6391	TT,TC,CC		0.0116,2.4545,0.8387	probably-damaging	273/402	1858076	109,12887	2200	4298	6498	SO:0001583	missense	90019	exon7			GGCCTGCGTCCAG	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.817C>T	11.37:g.1858076C>T	ENSP00000371394:p.Arg273Cys	55.0	0.0	0		57.0	21.0	0.368421	NM_138567	A6NFJ4|Q9NSV9	Missense_Mutation	SNP	ENST00000381968.3	37	CCDS7726.2	17|17	0.007783882783882784|0.007783882783882784	17|17	0.034552845528455285|0.034552845528455285	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	c|c	13.17|13.17	2.156344|2.156344	0.38021|0.38021	0.024545|0.024545	1.16E-4|1.16E-4	ENSG00000149043|ENSG00000149043	ENST00000381978|ENST00000381968;ENST00000341958	.|T;T	.|0.69685	.|-0.42;-0.42	3.07|3.07	0.632|0.632	0.17705|0.17705	.|C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	.|.	.|.	.|.	.|.	T|T	0.35278|0.35278	0.0926|0.0926	L|L	0.33245|0.33245	0.995|0.995	0.18873|0.18873	N|N	0.999986|0.999986	.|D;D	.|0.63046	.|0.992;0.992	.|P;P	.|0.51918	.|0.684;0.684	T|T	0.40136|0.40136	-0.9579|-0.9579	5|9	.|0.87932	.|D	.|0	.|.	5.0271|5.0271	0.14391|0.14391	0.6967:0.1957:0.1076:0.0|0.6967:0.1957:0.1076:0.0	.|.	.|273;259	.|Q8NBV8;A6NCR4	.|SYT8_HUMAN;.	V|C	271|273;259	.|ENSP00000371394:R273C;ENSP00000343691:R259C	.|ENSP00000343691:R259C	A|R	+|+	2|1	0|0	SYT8|SYT8	1814652|1814652	0.012000|0.012000	0.17670|0.17670	0.210000|0.210000	0.23637|0.23637	0.473000|0.473000	0.32948|0.32948	-0.050000|-0.050000	0.11904|0.11904	0.015000|0.015000	0.14971|0.14971	0.313000|0.313000	0.20887|0.20887	GCG|CGT	C|0.991;T|0.009	0.009	strong		0.682	SYT8-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000025013.4		
SMARCA4	6597	hgsc.bcm.edu	37	19	11094903	11094903	+	Missense_Mutation	SNP	G	G	A	rs145867502		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11094903G>A	ENST00000429416.3	+	3	357	c.76G>A	c.(76-78)Gcc>Acc	p.A26T	SMARCA4_ENST00000358026.2_Missense_Mutation_p.A26T|SMARCA4_ENST00000590574.1_Missense_Mutation_p.A26T|SMARCA4_ENST00000413806.3_Missense_Mutation_p.A26T|SMARCA4_ENST00000541122.2_Missense_Mutation_p.A26T|SMARCA4_ENST00000450717.3_Missense_Mutation_p.A26T|SMARCA4_ENST00000344626.4_Missense_Mutation_p.A26T|SMARCA4_ENST00000589677.1_Missense_Mutation_p.A26T|SMARCA4_ENST00000444061.3_Missense_Mutation_p.A26T	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	26	Necessary for interaction with SS18L1/CREST. {ECO:0000250}.				aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				TTCCCCTGGAGCCATGCTGGG	0.721			"""F, N, Mis"""		NSCLC								G|||	1	0.000199681	0.0008	0.0	5008	,	,		15706	0.0		0.0	False		,,,				2504	0.0				p.A26T		Atlas-SNP	.		Rec	yes		19	19p13.2	6597	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"""		E	.	SMARCA4	502	.	1	Unknown(1)	lung(1)	c.G76A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	12,4366		0,12,2177	19.0	24.0	23.0		76,76,76,76,76,76,76	4.9	1.0	19	dbSNP_134	23	0,8566		0,0,4283	no	missense,missense,missense,missense,missense,missense,missense	SMARCA4	NM_003072.3,NM_001128849.1,NM_001128848.1,NM_001128847.1,NM_001128846.1,NM_001128845.1,NM_001128844.1	58,58,58,58,58,58,58	0,12,6460	AA,AG,GG		0.0,0.2741,0.0927	benign,benign,benign,benign,benign,benign,benign	26/1648,26/1680,26/1614,26/1615,26/1617,26/1618,26/1648	11094903	12,12932	2189	4283	6472	SO:0001583	missense	6597	exon2			CCTGGAGCCATGC	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"""SNF2-like 4"", ""global transcription activator homologous sequence"", ""sucrose nonfermenting-like 4"", ""mitotic growth and transcription activator"", ""BRM/SWI2-related gene 1"", ""homeotic gene regulator"", ""nuclear protein GRB1"", ""brahma protein-like 1"", ""ATP-dependent helicase SMARCA4"""	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.76G>A	19.37:g.11094903G>A	ENSP00000395654:p.Ala26Thr	58.0	0.0	0		76.0	36.0	0.473684	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	CCDS12253.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	21.4	4.144345	0.77888	0.002741	0.0	ENSG00000127616	ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	D;D;D;D;D;D;D	0.86956	-2.18;-2.19;-2.18;-2.17;-2.17;-2.18;-2.17	4.95	4.95	0.65309	.	0.130808	0.49305	D	0.000154	D	0.82879	0.5133	L	0.36672	1.1	0.48087	D	0.999582	B;B;B;B;B;B;B	0.10296	0.003;0.003;0.003;0.0;0.003;0.001;0.003	B;B;B;B;B;B;B	0.08055	0.003;0.003;0.003;0.001;0.003;0.001;0.003	T	0.79579	-0.1745	10	0.66056	D	0.02	-16.4285	17.1334	0.86732	0.0:0.0:1.0:0.0	.	26;26;26;26;26;26;26	B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;A7E2E1;P51532	.;.;.;.;.;.;SMCA4_HUMAN	T	26	ENSP00000395654:A26T;ENSP00000350720:A26T;ENSP00000343896:A26T;ENSP00000445036:A26T;ENSP00000392837:A26T;ENSP00000397783:A26T;ENSP00000414727:A26T	ENSP00000343896:A26T	A	+	1	0	SMARCA4	10955903	0.994000	0.37717	1.000000	0.80357	0.996000	0.88848	2.131000	0.42074	2.563000	0.86464	0.655000	0.94253	GCC	G|0.999;A|0.001	0.001	strong		0.721	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072	
TSSK2	23617	hgsc.bcm.edu	37	22	19118992	19118992	+	Missense_Mutation	SNP	A	A	G	rs3747052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:19118992A>G	ENST00000399635.2	+	1	672	c.80A>G	c.(79-81)aAa>aGa	p.K27R	DGCR14_ENST00000252137.6_3'UTR	NM_053006.4	NP_443732.3	Q96PF2	TSSK2_HUMAN	testis-specific serine kinase 2	27	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		K -> R (may be associated with infertility; dbSNP:rs3747052). {ECO:0000269|PubMed:17344846}.		multicellular organismal development (GO:0007275)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|centriole (GO:0005814)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(2)|lung(2)|prostate(4)|stomach(1)	11	Colorectal(54;0.0993)					GCAAAAGTCAAATCTGCCTAC	0.517													.|||	196	0.0391374	0.1165	0.0144	5008	,	,		22180	0.0198		0.008	False		,,,				2504	0.0041				p.K27R		Atlas-SNP	.											.	TSSK2	29	.	0			c.A80G						PASS	.	A	,ARG/LYS	482,3924	225.9+/-241.6	25,432,1746	82.0	70.0	74.0		,80	4.6	1.0	22	dbSNP_107	74	5,8595	3.7+/-12.6	0,5,4295	yes	utr-3,missense	DGCR14,TSSK2	NM_022719.2,NM_053006.4	,26	25,437,6041	GG,GA,AA		0.0581,10.9396,3.7444	,benign	,27/359	19118992	487,12519	2203	4300	6503	SO:0001583	missense	23617	exon1			AAGTCAAATCTGC	AF362953	CCDS13755.1	22q11.21	2007-01-30	2005-03-10	2005-03-12	ENSG00000206203	ENSG00000206203			11401	protein-coding gene	gene with protein product		610710	"""serine/threonine kinase 22B (spermiogenesis associated)"""	STK22B		10591208	Standard	NM_053006		Approved	SPOGA2, FLJ38613	uc002zow.2	Q96PF2	OTTHUMG00000150118	ENST00000399635.2:c.80A>G	22.37:g.19118992A>G	ENSP00000382544:p.Lys27Arg	107.0	0.0	0		95.0	60.0	0.631579	NM_053006	Q8IY55	Missense_Mutation	SNP	ENST00000399635.2	37	CCDS13755.1	89	0.04075091575091575	63	0.12804878048780488	6	0.016574585635359115	13	0.022727272727272728	7	0.009234828496042216	A	16.33	3.091896	0.55968	0.109396	5.81E-4	ENSG00000206203	ENST00000399635	D	0.82619	-1.63	5.62	4.56	0.56223	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.53938	D	0.000060	T	0.02727	0.0082	N	0.13327	0.33	0.32898	D	0.51277	B	0.23185	0.081	B	0.42882	0.401	T	0.58446	-0.7635	10	0.72032	D	0.01	.	9.692	0.40134	0.845:0.0:0.0:0.155	rs3747052;rs3747052	27	Q96PF2	TSSK2_HUMAN	R	27	ENSP00000382544:K27R	ENSP00000382544:K27R	K	+	2	0	TSSK2	17498992	1.000000	0.71417	0.984000	0.44739	0.986000	0.74619	5.829000	0.69316	0.912000	0.36772	0.460000	0.39030	AAA	A|0.959;G|0.041	0.041	strong		0.517	TSSK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316431.1		
DHRS2	10202	hgsc.bcm.edu	37	14	24114490	24114490	+	3'UTR	SNP	G	G	A	rs7150155	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24114490G>A	ENST00000250383.6	+	0	1347				DHRS2_ENST00000344777.7_Silent_p.V294V	NM_005794.3	NP_005785.1	Q13268	DHRS2_HUMAN	dehydrogenase/reductase (SDR family) member 2						C21-steroid hormone metabolic process (GO:0008207)|cellular response to oxidative stress (GO:0034599)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|response to toxic substance (GO:0009636)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	carbonyl reductase (NADPH) activity (GO:0004090)			endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00659)		GCGTAGCTGTGGTCCCAGGCC	0.597													g|||	370	0.0738818	0.267	0.0216	5008	,	,		17143	0.0		0.002	False		,,,				2504	0.0				p.V294V		Atlas-SNP	.											DHRS2_ENST00000344777,NS,carcinoma,+1,1	DHRS2	78	1	0			c.G882A						scavenged	.		,	963,3443	362.4+/-316.1	113,737,1353	58.0	60.0	59.0		,882	2.3	0.0	14	dbSNP_116	59	13,8587	9.1+/-34.3	0,13,4287	no	utr-3,coding-synonymous	DHRS2	NM_005794.3,NM_182908.4	,	113,750,5640	AA,AG,GG		0.1512,21.8566,7.5042	,	,294/301	24114490	976,12030	2203	4300	6503	SO:0001624	3_prime_UTR_variant	10202	exon9			AGCTGTGGTCCCA		CCDS9604.1, CCDS41927.1	14q11.2	2011-09-14			ENSG00000100867	ENSG00000100867		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	18349	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 1"""	615194				7556196, 11944995, 16685466, 19027726	Standard	NM_182908		Approved	HEP27, SDR25C1	uc001wkt.4	Q13268	OTTHUMG00000028771	ENST00000250383.6:c.*28G>A	14.37:g.24114490G>A		61.0	1.0	0.0163934		71.0	39.0	0.549296	NM_182908	D3DS54|Q53GS4|Q7Z789|Q9H2R2	Silent	SNP	ENST00000250383.6	37	CCDS9604.1																																																																																			G|0.966;A|0.034	0.034	strong		0.597	DHRS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000071842.2	NM_182908	
GFM1	85476	hgsc.bcm.edu	37	3	158372389	158372389	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:158372389A>C	ENST00000486715.1	+	8	1409	c.1052A>C	c.(1051-1053)cAc>cCc	p.H351P	GFM1_ENST00000478576.1_Missense_Mutation_p.H351P|GFM1_ENST00000264263.5_Missense_Mutation_p.H370P	NM_024996.5	NP_079272.4			G elongation factor, mitochondrial 1											breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|urinary_tract(2)	22			Lung(72;0.00309)|LUSC - Lung squamous cell carcinoma(72;0.0043)			GACAATTCCCACCCATTTGTA	0.308																																					p.H351P		Atlas-SNP	.											.	GFM1	83	.	0			c.A1052C						PASS	.																																			SO:0001583	missense	85476	exon8			ATTCCCACCCATT	AF309777	CCDS33885.1	3q25	2008-02-05			ENSG00000168827	ENSG00000168827			13780	protein-coding gene	gene with protein product		606639	"""G translation elongation factor, mitochondrial"""			11374907, 11735030	Standard	NM_024996		Approved	EFGM, GFM, EGF1	uc003fce.3	Q96RP9	OTTHUMG00000158804	ENST00000486715.1:c.1052A>C	3.37:g.158372389A>C	ENSP00000419038:p.His351Pro	110.0	0.0	0		127.0	62.0	0.488189	NM_024996		Missense_Mutation	SNP	ENST00000486715.1	37	CCDS33885.1	.	.	.	.	.	.	.	.	.	.	A	13.40	2.225950	0.39300	.	.	ENSG00000168827	ENST00000486715;ENST00000478576;ENST00000264263;ENST00000312756	T;T;T	0.79845	-1.31;-1.31;-1.31	5.66	5.66	0.87406	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.216872	0.49305	D	0.000147	T	0.72930	0.3522	N	0.22421	0.69	0.80722	D	1	B;B;B	0.34161	0.439;0.203;0.047	B;B;B	0.39660	0.306;0.162;0.112	T	0.75445	-0.3315	10	0.72032	D	0.01	-10.9205	11.6275	0.51153	0.867:0.0:0.0:0.133	.	370;351;351	Q96RP9-2;Q96RP9;C9IZ01	.;EFGM_HUMAN;.	P	351;351;370;85	ENSP00000419038:H351P;ENSP00000418755:H351P;ENSP00000264263:H370P	ENSP00000264263:H370P	H	+	2	0	GFM1	159855083	0.996000	0.38824	0.988000	0.46212	0.739000	0.42172	5.152000	0.64882	2.140000	0.66376	0.533000	0.62120	CAC	.	.	none		0.308	GFM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352271.1	NM_024996	
USP10	9100	hgsc.bcm.edu	37	16	84778261	84778261	+	Silent	SNP	G	G	A	rs77170713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84778261G>A	ENST00000219473.7	+	4	287	c.174G>A	c.(172-174)gaG>gaA	p.E58E	USP10_ENST00000562743.1_3'UTR|USP10_ENST00000570191.1_Silent_p.E62E	NM_001272075.1|NM_005153.2	NP_001259004.1|NP_005144.2	Q14694	UBP10_HUMAN	ubiquitin specific peptidase 10	58	Interaction with p53/TP53.				autophagy (GO:0006914)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA repair (GO:0006281)|protein deubiquitination (GO:0016579)|regulation of autophagy (GO:0010506)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ion channel binding (GO:0044325)|p53 binding (GO:0002039)|poly(A) RNA binding (GO:0044822)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			endometrium(3)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|stomach(1)|urinary_tract(1)	17						AGAGAATTGAGTTTGGTGTCG	0.403													G|||	27	0.00539137	0.0204	0.0	5008	,	,		16411	0.0		0.0	False		,,,				2504	0.0				p.E62E		Atlas-SNP	.											.	USP10	51	.	0			c.G186A						PASS	.	G		55,3637		0,55,1791	45.0	43.0	43.0		174	-3.0	1.0	16	dbSNP_131	43	1,8163		0,1,4081	no	coding-synonymous	USP10	NM_005153.2		0,56,5872	AA,AG,GG		0.0122,1.4897,0.4723		58/799	84778261	56,11800	1846	4082	5928	SO:0001819	synonymous_variant	9100	exon5			AATTGAGTTTGGT	D80012	CCDS45537.1, CCDS62004.1	16q	2008-03-25	2005-08-08			ENSG00000103194		"""Ubiquitin-specific peptidases"""	12608	protein-coding gene	gene with protein product		609818	"""ubiquitin specific protease 10"""			12838346	Standard	NM_005153		Approved	UBPO, KIAA0190	uc002fii.3	Q14694		ENST00000219473.7:c.174G>A	16.37:g.84778261G>A		119.0	0.0	0		145.0	77.0	0.531034	NM_001272075	B2RDJ8|B4DS84|Q9BWG7|Q9NSL7	Silent	SNP	ENST00000219473.7	37	CCDS45537.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	12.78	2.039111	0.35989	0.014897	1.22E-4	ENSG00000103194	ENST00000540269	.	.	.	5.06	-3.04	0.05412	.	.	.	.	.	T	0.59609	0.2206	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.67538	-0.5645	5	0.66056	D	0.02	-22.7486	11.4442	0.50114	0.7447:0.0:0.2553:0.0	.	.	.	.	N	38	.	ENSP00000445589:S38N	S	+	2	0	USP10	83335762	1.000000	0.71417	0.969000	0.41365	0.892000	0.51952	0.653000	0.24902	-0.665000	0.05317	-0.339000	0.08088	AGT	G|0.997;A|0.003	0.003	strong		0.403	USP10-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433660.1		
NUP88	4927	hgsc.bcm.edu	37	17	5291126	5291126	+	Missense_Mutation	SNP	T	T	C	rs149760662	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5291126T>C	ENST00000573584.1	-	12	2251	c.1742A>G	c.(1741-1743)gAc>gGc	p.D581G	NUP88_ENST00000573169.1_5'Flank	NM_002532.4	NP_002523.2	Q99567	NUP88_HUMAN	nucleoporin 88kDa	581					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)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	transporter activity (GO:0005215)			endometrium(4)|kidney(4)|large_intestine(4)|lung(3)	15						CTTTGCCAAGTCCTGTTTGAG	0.522													T|||	5	0.000998403	0.0	0.0014	5008	,	,		15835	0.0		0.003	False		,,,				2504	0.001				p.D581G		Atlas-SNP	.											.	NUP88	47	.	0			c.A1742G						PASS	.	T	GLY/ASP	6,4400	11.4+/-27.6	0,6,2197	96.0	96.0	96.0		1742	4.8	1.0	17	dbSNP_134	96	44,8556	27.9+/-77.7	0,44,4256	yes	missense	NUP88	NM_002532.4	94	0,50,6453	CC,CT,TT		0.5116,0.1362,0.3844	benign	581/742	5291126	50,12956	2203	4300	6503	SO:0001583	missense	4927	exon12			GCCAAGTCCTGTT	Y08612	CCDS11070.1	17p13	2004-02-18	2002-08-29		ENSG00000108559	ENSG00000108559			8067	protein-coding gene	gene with protein product		602552	"""nucleoporin 88kD"""			9049309	Standard	NM_002532		Approved	MGC8530	uc002gbo.2	Q99567	OTTHUMG00000099453	ENST00000573584.1:c.1742A>G	17.37:g.5291126T>C	ENSP00000458954:p.Asp581Gly	86.0	0.0	0		119.0	61.0	0.512605	NM_002532	D3DTM2|Q9BWE5	Missense_Mutation	SNP	ENST00000573584.1	37	CCDS11070.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	T	19.11	3.764327	0.69878	0.001362	0.005116	ENSG00000108559	ENST00000225696;ENST00000543132	.	.	.	4.76	4.76	0.60689	.	0.047661	0.85682	D	0.000000	T	0.48822	0.1521	L	0.38838	1.175	0.52501	D	0.999951	P;B	0.52692	0.955;0.046	P;B	0.51615	0.675;0.04	T	0.51196	-0.8736	9	0.32370	T	0.25	-20.571	13.9189	0.63919	0.0:0.0:0.0:1.0	.	466;581	B4DP20;Q99567	.;NUP88_HUMAN	G	581;466	.	ENSP00000225696:D581G	D	-	2	0	NUP88	5231850	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	5.299000	0.65716	2.137000	0.66172	0.454000	0.30748	GAC	T|0.998;C|0.002	0.002	strong		0.522	NUP88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216918.3	NM_002532	
ATF7IP2	80063	hgsc.bcm.edu	37	16	10527404	10527404	+	Missense_Mutation	SNP	G	G	A	rs141089693	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:10527404G>A	ENST00000396560.2	+	4	1085	c.858G>A	c.(856-858)atG>atA	p.M286I	ATF7IP2_ENST00000543967.1_Intron|ATF7IP2_ENST00000396559.1_Missense_Mutation_p.M286I|ATF7IP2_ENST00000356427.2_Missense_Mutation_p.M286I|ATF7IP2_ENST00000324570.5_Missense_Mutation_p.M286I	NM_024997.3	NP_079273.2	Q5U623	MCAF2_HUMAN	activating transcription factor 7 interacting protein 2	286					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				large_intestine(3)	3						AGAAGAGGATGTTTTCAGAAA	0.338													G|||	5	0.000998403	0.0038	0.0	5008	,	,		21095	0.0		0.0	False		,,,				2504	0.0				p.M286I		Atlas-SNP	.											.	ATF7IP2	40	.	0			c.G858A						PASS	.	G	ILE/MET	30,4362	32.6+/-62.9	1,28,2167	54.0	56.0	55.0		858	1.8	1.0	16	dbSNP_134	55	0,8598		0,0,4299	yes	missense	ATF7IP2	NM_024997.2	10	1,28,6466	AA,AG,GG		0.0,0.6831,0.2309	possibly-damaging	286/683	10527404	30,12960	2196	4299	6495	SO:0001583	missense	80063	exon4			GAGGATGTTTTCA	AK022730	CCDS10540.1, CCDS58422.1	16p13.2	2008-02-05			ENSG00000166669	ENSG00000166669			20397	protein-coding gene	gene with protein product		613645					Standard	NM_001256160		Approved	FLJ12668	uc002czu.3	Q5U623	OTTHUMG00000129749	ENST00000396560.2:c.858G>A	16.37:g.10527404G>A	ENSP00000379808:p.Met286Ile	152.0	0.0	0		159.0	81.0	0.509434	NM_024997	B2RNR2|Q53EZ7|Q658U2|Q6IS97|Q8N9X8|Q9H9L6	Missense_Mutation	SNP	ENST00000396560.2	37	CCDS10540.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	13.62	2.292811	0.40594	0.006831	0.0	ENSG00000166669	ENST00000396559;ENST00000396560;ENST00000535850;ENST00000356427;ENST00000324570	T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93	5.02	1.79	0.24919	.	0.492757	0.20948	N	0.082817	T	0.25269	0.0614	L	0.55481	1.735	0.21822	N	0.999525	B;B	0.27656	0.184;0.161	B;B	0.29353	0.101;0.053	T	0.13522	-1.0506	10	0.33940	T	0.23	-6.0402	5.1577	0.15044	0.1856:0.0:0.6499:0.1645	.	286;286	Q5U623-2;Q5U623	.;MCAF2_HUMAN	I	286	ENSP00000379807:M286I;ENSP00000379808:M286I;ENSP00000440791:M286I;ENSP00000348799:M286I;ENSP00000322811:M286I	ENSP00000322811:M286I	M	+	3	0	ATF7IP2	10434905	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	1.462000	0.35266	0.648000	0.30732	-0.145000	0.13849	ATG	G|0.999;A|0.001	0.001	strong		0.338	ATF7IP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251961.1	NM_024997	
MRPL28	10573	hgsc.bcm.edu	37	16	417691	417691	+	Missense_Mutation	SNP	C	C	G	rs114486517	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:417691C>G	ENST00000199706.8	-	6	790	c.755G>C	c.(754-756)aGa>aCa	p.R252T	MRPL28_ENST00000389675.2_Missense_Mutation_p.R252T|MRPL28_ENST00000429738.1_Intron	NM_006428.4	NP_006419.2	Q13084	RM28_HUMAN	mitochondrial ribosomal protein L28	252				R -> T (in Ref. 6; AAC50181). {ECO:0000305}.	translation (GO:0006412)	cytoplasm (GO:0005737)|mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|kidney(1)|lung(1)|ovary(1)|prostate(1)	5		Hepatocellular(16;0.000105)|Lung NSC(18;0.0324)|all_lung(18;0.064)				GCCACTGGCTCTCTTCTGCAC	0.617													C|||	327	0.0652955	0.2194	0.0303	5008	,	,		18217	0.0		0.008	False		,,,				2504	0.0082				p.R252T		Atlas-SNP	.											.	MRPL28	15	.	0			c.G755C						PASS	.	C	THR/ARG	811,3595	316.1+/-294.4	77,657,1469	53.0	48.0	50.0		755	-3.0	0.0	16	dbSNP_132	50	57,8543	33.3+/-86.6	1,55,4244	yes	missense	MRPL28	NM_006428.4	71	78,712,5713	GG,GC,CC		0.6628,18.4067,6.6738	benign	252/257	417691	868,12138	2203	4300	6503	SO:0001583	missense	10573	exon6			CTGGCTCTCTTCT	U19796	CCDS32349.1	16p13.12	2012-09-26	2002-11-13		ENSG00000086504	ENSG00000086504		"""Mitochondrial ribosomal proteins / large subunits"""	14484	protein-coding gene	gene with protein product		604853	"""melanoma-associated antigen recognised by cytotoxic T lymphocytes"""	MAAT1		11551941, 19753307	Standard	NM_006428		Approved	p15	uc002cgs.2	Q13084	OTTHUMG00000047994	ENST00000199706.8:c.755G>C	16.37:g.417691C>G	ENSP00000199706:p.Arg252Thr	119.0	0.0	0		134.0	69.0	0.514925	NM_006428	B2RCM4|D3DU46|Q4TT39|Q96S26|Q9BQD8|Q9BR04	Missense_Mutation	SNP	ENST00000199706.8	37	CCDS32349.1	109	0.04990842490842491	98	0.1991869918699187	9	0.024861878453038673	0	0.0	2	0.002638522427440633	C	8.839	0.941748	0.18281	0.184067	0.006628	ENSG00000086504	ENST00000397735;ENST00000199706;ENST00000397734;ENST00000389675	T;T	0.23950	1.88;1.88	4.86	-2.96	0.05547	.	0.400839	0.27000	N	0.021425	T	0.00012	0.0000	L	0.31294	0.92	0.80722	P	0.0	B;B	0.22003	0.063;0.063	B;B	0.15484	0.013;0.013	T	0.23940	-1.0174	9	0.49607	T	0.09	-0.0185	4.4593	0.11659	0.0:0.2928:0.309:0.3982	.	252;252	Q13084;Q4TT38	RM28_HUMAN;.	T	252	ENSP00000199706:R252T;ENSP00000374326:R252T	ENSP00000199706:R252T	R	-	2	0	MRPL28	357692	0.007000	0.16637	0.004000	0.12327	0.779000	0.44077	-0.411000	0.07142	-0.118000	0.11851	0.637000	0.83480	AGA	C|0.937;G|0.063	0.063	strong		0.617	MRPL28-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139285.2		
IL4R	3566	hgsc.bcm.edu	37	16	27356271	27356271	+	Silent	SNP	T	T	C	rs112497527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27356271T>C	ENST00000395762.2	+	5	550	c.291T>C	c.(289-291)gaT>gaC	p.D97D	IL4R_ENST00000170630.2_Silent_p.D97D|IL4R_ENST00000543915.2_Silent_p.D97D|IL4R_ENST00000380922.3_Silent_p.D82D|IL4R_ENST00000449195.1_Silent_p.D97D	NM_000418.3	NP_000409.1	P24394	IL4RA_HUMAN	interleukin 4 receptor	97		Major IL4 binding determinant.			defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|ovulation (GO:0030728)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of macrophage activation (GO:0043032)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|production of molecular mediator involved in inflammatory response (GO:0002532)|regulation of cell proliferation (GO:0042127)|response to estrogen (GO:0043627)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	interleukin-4 receptor activity (GO:0004913)|receptor signaling protein activity (GO:0005057)			breast(3)|endometrium(2)|kidney(2)|large_intestine(2)|lung(15)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	33						TCAGTGCGGATAACTATACAC	0.642													C|||	66	0.0131789	0.0469	0.0058	5008	,	,		14225	0.0		0.0	False		,,,				2504	0.0				p.D97D		Atlas-SNP	.											.	IL4R	70	.	0			c.T291C						PASS	.	C	,	198,4196	807.2+/-415.9	3,192,2002	108.0	92.0	98.0		291,291	2.4	0.0	16	dbSNP_132	98	2,8598	819.2+/-406.8	0,2,4298	no	coding-synonymous,coding-synonymous	IL4R	NM_000418.2,NM_001008699.1	,	3,194,6300	CC,CT,TT		0.0233,4.5061,1.5392	,	97/826,97/228	27356271	200,12794	2197	4300	6497	SO:0001819	synonymous_variant	3566	exon5			TGCGGATAACTAT	X52425	CCDS10629.1, CCDS58441.1	16p12.1-p11.2	2008-05-14			ENSG00000077238	ENSG00000077238		"""Interleukins and interleukin receptors"", ""CD molecules"""	6015	protein-coding gene	gene with protein product		147781				1679753	Standard	NM_000418		Approved	CD124	uc010bxy.4	P24394	OTTHUMG00000097015	ENST00000395762.2:c.291T>C	16.37:g.27356271T>C		127.0	0.0	0		111.0	50.0	0.45045	NM_000418	B4E076|B9EKU8|H3BSY5|Q96P01|Q9H181|Q9H182|Q9H183|Q9H184|Q9H185|Q9H186|Q9H187|Q9H188	Silent	SNP	ENST00000395762.2	37	CCDS10629.1																																																																																			T|0.988;C|0.012	0.012	strong		0.642	IL4R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214104.4		
CCDC73	493860	hgsc.bcm.edu	37	11	32622233	32622233	+	IGR	SNP	A	A	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:32622233A>T	ENST00000335185.5	-	0	3849				EIF3M_ENST00000531120.1_Splice_Site|EIF3M_ENST00000524896.1_Splice_Site	NM_001008391.2	NP_001008392.2	Q6ZRK6	CCD73_HUMAN	coiled-coil domain containing 73											NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	51	Breast(20;0.112)					TCTGTTTTCTAGGCCTGTTAC	0.333																																					.		Atlas-SNP	.											.	EIF3M	37	.	0			c.800-2A>T						PASS	.						65.0	63.0	63.0					11																	32622233		2202	4299	6501	SO:0001628	intergenic_variant	10480	exon9			TTTTCTAGGCCTG	AK128159	CCDS41630.1	11p13	2006-02-11			ENSG00000186714	ENSG00000186714			23261	protein-coding gene	gene with protein product		612328					Standard	NM_001008391		Approved	NY-SAR-79	uc001mtv.4	Q6ZRK6	OTTHUMG00000166279		11.37:g.32622233A>T		86.0	0.0	0		108.0	12.0	0.111111	NM_006360	Q6P5Q7|Q6ZMW0|Q86WE7	Splice_Site	SNP	ENST00000335185.5	37	CCDS41630.1	.	.	.	.	.	.	.	.	.	.	A	31	5.076612	0.94000	.	.	ENSG00000149100	ENST00000531120;ENST00000524896;ENST00000526267	.	.	.	5.93	5.93	0.95920	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3871	0.83514	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	EIF3M	32578809	1.000000	0.71417	0.634000	0.29324	0.673000	0.39480	8.701000	0.91331	2.270000	0.75569	0.482000	0.46254	.	.	.	none		0.333	CCDC73-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388874.2	NM_001008391	
LHFPL2	10184	hgsc.bcm.edu	37	5	77784810	77784810	+	Silent	SNP	A	A	C	rs35110604	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:77784810A>C	ENST00000515007.2	-	3	907	c.597T>G	c.(595-597)gcT>gcG	p.A199A	LHFPL2_ENST00000380345.2_Silent_p.A199A			Q6ZUX7	LHPL2_HUMAN	lipoma HMGIC fusion partner-like 2	199						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(1)|upper_aerodigestive_tract(1)	6		all_lung(232;0.000409)|Lung NSC(167;0.00108)|Ovarian(174;0.0107)|Prostate(461;0.218)		OV - Ovarian serous cystadenocarcinoma(54;6.48e-46)|Epithelial(54;8.43e-42)|all cancers(79;1.42e-36)		CAGAGAAGACAGCACAGATGA	0.473													A|||	116	0.0231629	0.0825	0.0101	5008	,	,		21336	0.0		0.0	False		,,,				2504	0.0				p.A199A		Atlas-SNP	.											.	LHFPL2	9	.	0			c.T597G						PASS	.	A		282,4124	157.4+/-190.3	7,268,1928	134.0	131.0	132.0		597	-4.5	1.0	5	dbSNP_126	132	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	LHFPL2	NM_005779.2		7,271,6225	CC,CA,AA		0.0349,6.4004,2.1913		199/229	77784810	285,12721	2203	4300	6503	SO:0001819	synonymous_variant	10184	exon5			GAAGACAGCACAG	D86961	CCDS4042.1	5q13	2008-02-05			ENSG00000145685	ENSG00000145685			6588	protein-coding gene	gene with protein product		609718				10329012	Standard	NM_005779		Approved	KIAA0206	uc003kfo.3	Q6ZUX7	OTTHUMG00000107579	ENST00000515007.2:c.597T>G	5.37:g.77784810A>C		163.0	0.0	0		167.0	83.0	0.497006	NM_005779	B2RMQ6|Q7Z5P0|Q92605	Silent	SNP	ENST00000515007.2	37	CCDS4042.1																																																																																			A|0.982;C|0.018	0.018	strong		0.473	LHFPL2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369098.2	NM_005779	
TMEM232	642987	hgsc.bcm.edu	37	5	109904249	109904249	+	Missense_Mutation	SNP	C	C	T	rs61734250	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:109904249C>T	ENST00000455884.2	-	11	1404	c.1354G>A	c.(1354-1356)Gaa>Aaa	p.E452K	TMEM232_ENST00000515518.2_5'UTR|TMEM232_ENST00000429839.2_Missense_Mutation_p.E452K			C9JQI7	TM232_HUMAN	transmembrane protein 232	452						integral component of membrane (GO:0016021)				breast(1)|kidney(2)	3						TCCTGTTCTTCGTCTCCTTGA	0.363													C|||	109	0.0217652	0.0802	0.0029	5008	,	,		17280	0.0		0.001	False		,,,				2504	0.0				p.E452K		Atlas-SNP	.											TMEM232_ENST00000455884,rectum,carcinoma,0,2	TMEM232	57	2	0			c.G1354A						PASS	.	C	LYS/GLU	71,1313		2,67,623	443.0	343.0	373.0		1354	3.1	0.7	5	dbSNP_129	373	0,3182		0,0,1591	yes	missense	TMEM232	NM_001039763.3	56	2,67,2214	TT,TC,CC		0.0,5.1301,1.555	benign	452/658	109904249	71,4495	692	1591	2283	SO:0001583	missense	642987	exon11			GTTCTTCGTCTCC	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.1354G>A	5.37:g.109904249C>T	ENSP00000401477:p.Glu452Lys	213.0	0.0	0		201.0	97.0	0.482587	NM_001039763	B4DKF4	Missense_Mutation	SNP	ENST00000455884.2	37	CCDS47253.2	43	0.019688644688644688	42	0.08536585365853659	1	0.0027624309392265192	0	0.0	0	0.0	C	11.26	1.584993	0.28268	0.051301	0.0	ENSG00000186952	ENST00000429839;ENST00000455884	.	.	.	5.88	3.09	0.35607	.	0.688144	0.13800	N	0.361872	T	0.00695	0.0023	N	0.21448	0.665	0.21290	N	0.999739	B;B;B	0.27971	0.196;0.055;0.03	B;B;B	0.17722	0.019;0.011;0.007	T	0.13522	-1.0506	8	.	.	.	-3.5222	5.5928	0.17311	0.0:0.6568:0.1618:0.1814	.	452;452;334	C9JQI7;C9JQI7-2;E9PFK0	TM232_HUMAN;.;.	K	452	.	.	E	-	1	0	TMEM232	109932148	0.949000	0.32298	0.655000	0.29622	0.924000	0.55760	0.721000	0.25911	0.364000	0.24374	0.557000	0.71058	GAA	C|0.977;T|0.023	0.023	strong		0.363	TMEM232-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372488.2	NM_001039763	
ABL1	25	hgsc.bcm.edu	37	9	133761001	133761001	+	Silent	SNP	A	A	G	rs1056171	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:133761001A>G	ENST00000318560.5	+	11	3705	c.3324A>G	c.(3322-3324)ccA>ccG	p.P1108P		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	1108	F-actin-binding.				actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	GCAGTGGTCCAGCGGCCACTC	0.557			"""T, Mis"""	"""BCR, ETV6, NUP214"""	"""CML, ALL, T-ALL"""								G|||	3276	0.654153	0.882	0.6974	5008	,	,		18771	0.5952		0.4881	False		,,,				2504	0.547				p.P1127P		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	ABL1,scalp,carcinoma,+2,1	ABL1	1632	1	0			c.A3381G						PASS	.	G	,	3592,814	300.1+/-286.2	1470,652,81	29.0	34.0	32.0		3324,3381	-10.5	0.2	9	dbSNP_86	32	4015,4585	586.5+/-392.0	924,2167,1209	no	coding-synonymous,coding-synonymous	ABL1	NM_005157.4,NM_007313.2	,	2394,2819,1290	GG,GA,AA		46.686,18.4748,41.5116	,	1108/1131,1127/1150	133761001	7607,5399	2203	4300	6503	SO:0001819	synonymous_variant	25	exon11			TGGTCCAGCGGCC	M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"""SH2 domain containing"""	76	protein-coding gene	gene with protein product		189980	"""v-abl Abelson murine leukemia viral oncogene homolog 1"", ""c-abl oncogene 1, receptor tyrosine kinase"", ""c-abl oncogene 1, non-receptor tyrosine kinase"""	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.3324A>G	9.37:g.133761001A>G		141.0	1.0	0.0070922		122.0	122.0	1	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	37	CCDS35166.1																																																																																			A|0.391;G|0.609	0.609	strong		0.557	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313	
AKTIP	64400	hgsc.bcm.edu	37	16	53526366	53526366	+	Silent	SNP	T	T	C	rs16952272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:53526366T>C	ENST00000394657.7	-	10	1011	c.837A>G	c.(835-837)tcA>tcG	p.S279S	AKTIP_ENST00000570004.1_Silent_p.S279S|AKTIP_ENST00000300245.4_Silent_p.S280S	NM_001012398.1|NM_022476.2	NP_001012398.1|NP_071921.1	Q9H8T0	AKTIP_HUMAN	AKT interacting protein	279					apoptotic process (GO:0006915)|early endosome to late endosome transport (GO:0045022)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|protein transport (GO:0015031)	FHF complex (GO:0070695)|plasma membrane (GO:0005886)	acid-amino acid ligase activity (GO:0016881)			large_intestine(1)|lung(2)|prostate(2)	5		all_cancers(37;0.14)				AAGGCTGTACTGAGCCAGGCT	0.433													T|||	36	0.0071885	0.025	0.0029	5008	,	,		20673	0.0		0.001	False		,,,				2504	0.0				p.S279S		Atlas-SNP	.											.	AKTIP	16	.	0			c.A837G						PASS	.	T	,	119,4277	89.2+/-127.9	2,115,2081	115.0	112.0	113.0		837,837	1.3	1.0	16	dbSNP_123	113	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	AKTIP	NM_001012398.1,NM_022476.2	,	2,116,6380	CC,CT,TT		0.0116,2.707,0.9234	,	279/293,279/293	53526366	120,12876	2198	4300	6498	SO:0001819	synonymous_variant	64400	exon10			CTGTACTGAGCCA	AK023320	CCDS10749.1	16q12.2	2010-01-14	2007-01-16	2007-01-16	ENSG00000166971	ENSG00000166971		"""Ubiquitin-conjugating enzymes E2"""	16710	protein-coding gene	gene with protein product		608483	"""fused toes (mouse) homolog"", ""fused toes homolog (mouse)"""	FTS		7818539, 8626685	Standard	XM_005256094		Approved	FLJ13258	uc002ehl.3	Q9H8T0	OTTHUMG00000133199	ENST00000394657.7:c.837A>G	16.37:g.53526366T>C		180.0	0.0	0		184.0	87.0	0.472826	NM_022476	Q503B1|Q53H38	Silent	SNP	ENST00000394657.7	37	CCDS10749.1																																																																																			T|0.990;C|0.010	0.010	strong		0.433	AKTIP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256909.4	NM_022476	
SLC9A4	389015	hgsc.bcm.edu	37	2	103148868	103148868	+	Silent	SNP	G	G	A	rs59687519	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:103148868G>A	ENST00000295269.4	+	12	2575	c.2118G>A	c.(2116-2118)gaG>gaA	p.E706E		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	706					epithelial cell development (GO:0002064)|gastric acid secretion (GO:0001696)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						AGAAGCAAGAGGCACAAGAAA	0.468													G|||	88	0.0175719	0.062	0.0086	5008	,	,		21876	0.0		0.0	False		,,,				2504	0.0				p.E706E		Atlas-SNP	.											.	SLC9A4	115	.	0			c.G2118A						PASS	.	G		265,4141	150.3+/-184.3	9,247,1947	93.0	90.0	91.0		2118	0.7	0.0	2	dbSNP_129	91	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SLC9A4	NM_001011552.3		9,249,6245	AA,AG,GG		0.0233,6.0145,2.0529		706/799	103148868	267,12739	2203	4300	6503	SO:0001819	synonymous_variant	389015	exon12			GCAAGAGGCACAA		CCDS33264.1	2q12.1	2013-05-22	2012-03-22		ENSG00000180251	ENSG00000180251		"""Solute carriers"""	11077	protein-coding gene	gene with protein product		600531	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 4"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 4"""			8199403	Standard	NM_001011552		Approved	NHE4	uc002tbz.4	Q6AI14	OTTHUMG00000153093	ENST00000295269.4:c.2118G>A	2.37:g.103148868G>A		80.0	0.0	0		102.0	59.0	0.578431	NM_001011552	Q69YK0	Silent	SNP	ENST00000295269.4	37	CCDS33264.1																																																																																			G|0.981;A|0.019	0.019	strong		0.468	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3	
TRPS1	7227	hgsc.bcm.edu	37	8	116631902	116631902	+	Silent	SNP	C	C	A	rs7823278	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:116631902C>A	ENST00000220888.5	-	2	543	c.384G>T	c.(382-384)ccG>ccT	p.P128P	TRPS1_ENST00000395715.3_Silent_p.P141P|TRPS1_ENST00000519076.1_Silent_p.P82P|TRPS1_ENST00000519674.1_Silent_p.P128P|TRPS1_ENST00000520276.1_Silent_p.P132P			Q9UHF7	TRPS1_HUMAN	trichorhinophalangeal syndrome I	128					chondrocyte differentiation (GO:0002062)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|NLS-bearing protein import into nucleus (GO:0006607)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|regulation of chondrocyte differentiation (GO:0032330)|regulation of histone deacetylation (GO:0031063)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(25)|lung(58)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|urinary_tract(2)	111	all_cancers(13;5.44e-23)|all_epithelial(1;2.14e-27)|Lung NSC(37;2.55e-05)|Ovarian(258;0.0219)		Epithelial(1;9.78e-37)|all cancers(1;3.14e-31)|BRCA - Breast invasive adenocarcinoma(1;2.56e-12)			CTGCTCTTTGCGGAGACTTCA	0.522									Langer-Giedion syndrome				A|||	844	0.16853	0.5734	0.049	5008	,	,		18881	0.0		0.002	False		,,,				2504	0.0511				p.P141P		Atlas-SNP	.											TRPS1_ENST00000395715,NS,carcinoma,-1,2	TRPS1	516	2	0			c.G423T						PASS	.	A		1632,2214		341,950,632	58.0	58.0	58.0		423	5.8	1.0	8	dbSNP_116	58	20,8250		0,20,4115	no	coding-synonymous	TRPS1	NM_014112.2		341,970,4747	AA,AC,CC		0.2418,42.4337,13.6349		141/1295	116631902	1652,10464	1923	4135	6058	SO:0001819	synonymous_variant	7227	exon3	Familial Cancer Database	Trichorhinophalangeal syndrome type 2, TRPS II	TCTTTGCGGAGAC	AF183810	CCDS6318.2, CCDS64957.1	8q23.3	2014-06-23			ENSG00000104447	ENSG00000104447		"""GATA zinc finger domain containing"", ""Zinc fingers, C2H2-type"""	12340	protein-coding gene	gene with protein product		604386				8530105, 10615131, 10647898	Standard	NM_001282903		Approved	LGCR	uc003yny.3	Q9UHF7	OTTHUMG00000142829	ENST00000220888.5:c.384G>T	8.37:g.116631902C>A		97.0	0.0	0		110.0	110.0	1	NM_014112	B4E1Z5|Q08AU2|Q9NWE1|Q9UHH6	Silent	SNP	ENST00000220888.5	37																																																																																				C|0.873;A|0.127	0.127	strong		0.522	TRPS1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000286436.3	NM_014112	
SLC25A22	79751	hgsc.bcm.edu	37	11	800186	800186	+	5'Flank	SNP	C	C	T	rs148849040		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:800186C>T	ENST00000531214.1	-	0	0				PIDD_ENST00000411829.2_Missense_Mutation_p.R723Q|PIDD_ENST00000347755.5_Missense_Mutation_p.R740Q	NM_001191060.1	NP_001177989.1	Q9H936	GHC1_HUMAN	solute carrier family 25 (mitochondrial carrier: glutamate), member 22						L-glutamate transport (GO:0015813)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			endometrium(1)|kidney(1)|lung(2)|urinary_tract(1)	5		all_cancers(49;4.75e-06)|all_epithelial(84;0.00204)|Breast(177;0.00234)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;6.27e-26)|Epithelial(43;4.84e-25)|OV - Ovarian serous cystadenocarcinoma(40;2.72e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CTTCCTCTGCCGGGCAGCCTC	0.692													C|||	1	0.000199681	0.0008	0.0	5008	,	,		14878	0.0		0.0	False		,,,				2504	0.0				p.R740Q	Colon(93;848 1468 3270 23355 49636)	Atlas-SNP	.											.	PIDD	76	.	0			c.G2219A						PASS	.	C	GLN/ARG,GLN/ARG	5,4369		0,5,2182	15.0	17.0	16.0		2219,2168	3.3	1.0	11	dbSNP_134	16	0,8574		0,0,4287	yes	missense,missense	PIDD	NM_145886.3,NM_145887.3	43,43	0,5,6469	TT,TC,CC		0.0,0.1143,0.0386	probably-damaging,probably-damaging	740/911,723/894	800186	5,12943	2187	4287	6474	SO:0001631	upstream_gene_variant	55367	exon14			CTCTGCCGGGCAG	AJ428202	CCDS7715.1	11p15.5	2013-05-22			ENSG00000177542	ENSG00000177542		"""Solute carriers"""	19954	protein-coding gene	gene with protein product		609302				11897791	Standard	NM_024698		Approved	GC1, FLJ13044, NET44, EIEE3	uc001lrj.3	Q9H936	OTTHUMG00000133310		11.37:g.800186C>T	Exception_encountered	61.0	0.0	0		60.0	41.0	0.683333	NM_145886	A8K366|C9J1H6|E9PJD3|E9PKB2|E9PL68|E9PN26|E9PNQ3|E9PP01|E9PR97|Q8TBU8	Missense_Mutation	SNP	ENST00000531214.1	37	CCDS7715.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.238462	0.79800	0.001143	0.0	ENSG00000177595	ENST00000411829;ENST00000347755	T;T	0.48201	0.82;0.94	4.24	3.29	0.37713	.	0.138436	0.46145	N	0.000315	T	0.49236	0.1545	L	0.29908	0.895	0.32961	D	0.521066	D;D;D;D	0.76494	0.999;0.999;0.996;0.999	D;P;P;D	0.64776	0.929;0.886;0.806;0.928	T	0.58429	-0.7638	10	0.54805	T	0.06	.	7.9393	0.29948	0.0:0.7476:0.0:0.2524	.	451;740;583;723	Q9HB75-5;Q9HB75;Q9HB75-3;Q9HB75-2	.;PIDD_HUMAN;.;.	Q	723;740	ENSP00000416801:R723Q;ENSP00000337797:R740Q	ENSP00000337797:R740Q	R	-	2	0	PIDD	790186	1.000000	0.71417	0.999000	0.59377	0.828000	0.46876	1.731000	0.38135	2.193000	0.70182	0.462000	0.41574	CGG	C|1.000;T|0.000	0.000	weak		0.692	SLC25A22-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384124.1		
FREM2	341640	hgsc.bcm.edu	37	13	39265558	39265558	+	Silent	SNP	T	T	A	rs41292757	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:39265558T>A	ENST00000280481.7	+	1	4293	c.4077T>A	c.(4075-4077)ggT>ggA	p.G1359G		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	1359					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		AACCTACTGGTGCCTTTGAAA	0.398													T|||	59	0.0117812	0.0008	0.0216	5008	,	,		21033	0.0		0.0378	False		,,,				2504	0.0051				p.G1359G		Atlas-SNP	.											.	FREM2	385	.	0			c.T4077A						PASS	.	T		43,4363	44.6+/-78.6	0,43,2160	63.0	64.0	63.0		4077	0.2	0.8	13	dbSNP_127	63	324,8276	114.8+/-174.7	5,314,3981	no	coding-synonymous	FREM2	NM_207361.4		5,357,6141	AA,AT,TT		3.7674,0.9759,2.8218		1359/3170	39265558	367,12639	2203	4300	6503	SO:0001819	synonymous_variant	341640	exon1			TACTGGTGCCTTT	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.4077T>A	13.37:g.39265558T>A		101.0	0.0	0		128.0	61.0	0.476562	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	37	CCDS31960.1																																																																																			T|0.972;A|0.028	0.028	strong		0.398	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
C4orf22	255119	hgsc.bcm.edu	37	4	81866010	81866010	+	Missense_Mutation	SNP	A	A	C	rs201959026		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:81866010A>C	ENST00000358105.3	+	5	572	c.523A>C	c.(523-525)Aac>Cac	p.N175H	C4orf22_ENST00000508675.1_Missense_Mutation_p.N192H	NM_152770.2	NP_689983.2	Q6V702	CD022_HUMAN	chromosome 4 open reading frame 22	175										NS(1)|large_intestine(3)|lung(5)|prostate(1)|skin(5)	15						TTCAAGTCCCAACTATCAAGT	0.313													A|||	1	0.000199681	0.0008	0.0	5008	,	,		16588	0.0		0.0	False		,,,				2504	0.0				p.N192H		Atlas-SNP	.											.	C4orf22	35	.	0			c.A574C						PASS	.	A	HIS/ASN,HIS/ASN	8,4396	12.9+/-30.5	0,8,2194	70.0	71.0	71.0		574,523	5.8	1.0	4		71	0,8594		0,0,4297	yes	missense,missense	C4orf22	NM_001206997.1,NM_152770.2	68,68	0,8,6491	CC,CA,AA		0.0,0.1817,0.0615	possibly-damaging,possibly-damaging	192/251,175/234	81866010	8,12990	2202	4297	6499	SO:0001583	missense	255119	exon6			AGTCCCAACTATC	BC034296	CCDS3587.1, CCDS56336.1	4q21.21	2008-02-05			ENSG00000197826	ENSG00000197826			28554	protein-coding gene	gene with protein product						12477932	Standard	NM_152770		Approved		uc010ijp.3	Q6V702	OTTHUMG00000130289	ENST00000358105.3:c.523A>C	4.37:g.81866010A>C	ENSP00000350818:p.Asn175His	282.0	1.0	0.0035461		328.0	148.0	0.451219	NM_001206997	E7EQ13|Q6ZQY4|Q8N4G9	Missense_Mutation	SNP	ENST00000358105.3	37	CCDS3587.1	.	.	.	.	.	.	.	.	.	.	A	17.34	3.364872	0.61513	0.001817	0.0	ENSG00000197826	ENST00000358105;ENST00000508675	T;T	0.36878	1.23;1.23	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.55609	0.1931	M	0.77616	2.38	0.46203	D	0.998921	P;D	0.54397	0.956;0.966	P;P	0.55667	0.73;0.781	T	0.60010	-0.7346	10	0.56958	D	0.05	.	15.1462	0.72653	1.0:0.0:0.0:0.0	.	192;175	E7EQ13;Q6V702	.;CD022_HUMAN	H	175;192	ENSP00000350818:N175H;ENSP00000425786:N192H	ENSP00000350818:N175H	N	+	1	0	C4orf22	82085034	1.000000	0.71417	1.000000	0.80357	0.650000	0.38633	6.456000	0.73501	2.216000	0.71823	0.533000	0.62120	AAC	.	.	weak		0.313	C4orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252629.2	NM_152770	
DNAH14	127602	hgsc.bcm.edu	37	1	225152298	225152298	+	Missense_Mutation	SNP	A	A	T	rs79645812	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:225152298A>T	ENST00000445597.2	+	6	866	c.866A>T	c.(865-867)aAg>aTg	p.K289M	DNAH14_ENST00000366849.1_Missense_Mutation_p.K162M|DNAH14_ENST00000366850.3_Missense_Mutation_p.K162M|DNAH14_ENST00000439375.2_Missense_Mutation_p.K162M|DNAH14_ENST00000400952.3_Missense_Mutation_p.K162M|DNAH14_ENST00000366848.1_Missense_Mutation_p.K162M|DNAH14_ENST00000430092.1_Missense_Mutation_p.K162M			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	289					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						GCAATTCAGAAGATTACTTTA	0.259													A|||	28	0.00559105	0.0204	0.0014	5008	,	,		13586	0.0		0.0	False		,,,				2504	0.0				p.K162M		Atlas-SNP	.											.	DNAH14	300	.	0			c.A485T						PASS	.	A	MET/LYS,MET/LYS,MET/LYS	82,3478		0,82,1698	70.0	69.0	69.0		485,485,485	4.2	0.0	1	dbSNP_131	69	0,8100		0,0,4050	yes	missense,missense,missense	DNAH14	NM_001145154.1,NM_001373.1,NM_144989.2	95,95,95	0,82,5748	TT,TA,AA		0.0,2.3034,0.7033	probably-damaging,probably-damaging,probably-damaging	162/454,162/4516,162/229	225152298	82,11578	1780	4050	5830	SO:0001583	missense	127602	exon5			TTCAGAAGATTAC	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.866A>T	1.37:g.225152298A>T	ENSP00000409472:p.Lys289Met	134.0	0.0	0		97.0	47.0	0.484536	NM_144989	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		10|10	0.004578754578754579|0.004578754578754579	10|10	0.02032520325203252|0.02032520325203252	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	A|A	15.26|15.26	2.781749|2.781749	0.49891|0.49891	0.023034|0.023034	0.0|0.0	ENSG00000185842|ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000366850;ENST00000400952;ENST00000366849;ENST00000366848;ENST00000439375|ENST00000433124	T;T;T;T;T;T;T|.	0.36878|.	2.32;1.42;1.23;1.26;1.27;1.23;1.42|.	5.33|5.33	4.17|4.17	0.49024|0.49024	.|.	0.553031|.	0.17085|.	N|.	0.187621|.	T|.	0.22859|.	0.0552|.	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	D;D;D;D|.	0.89917|.	0.999;1.0;1.0;0.999|.	D;D;D;D|.	0.76071|.	0.912;0.987;0.967;0.927|.	T|.	0.12091|.	-1.0561|.	9|.	0.87932|.	D|.	0|.	.|.	9.497|9.497	0.38995|0.38995	0.9159:0.0:0.0841:0.0|0.9159:0.0:0.0841:0.0	.|.	162;162;162;289|.	Q0VDD8-4;Q0VDD8-3;Q0VDD8-2;Q0VDD8|.	.;.;.;DYH14_HUMAN|.	M|X	289;162;162;162;162;162;162|60	ENSP00000409472:K289M;ENSP00000414402:K162M;ENSP00000355815:K162M;ENSP00000383737:K162M;ENSP00000355814:K162M;ENSP00000355813:K162M;ENSP00000392061:K162M|.	ENSP00000355813:K162M|.	K|R	+|+	2|1	0|2	DNAH14|DNAH14	223218921|223218921	0.789000|0.789000	0.28775|0.28775	0.040000|0.040000	0.18447|0.18447	0.068000|0.068000	0.16541|0.16541	1.785000|1.785000	0.38684|0.38684	0.929000|0.929000	0.37192|0.37192	0.413000|0.413000	0.27773|0.27773	AAG|AGA	A|0.995;T|0.005	0.005	strong		0.259	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
PEPD	5184	hgsc.bcm.edu	37	19	33968991	33968991	+	Missense_Mutation	SNP	T	T	A	rs61748998	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33968991T>A	ENST00000244137.7	-	7	542	c.509A>T	c.(508-510)gAa>gTa	p.E170V	PEPD_ENST00000436370.3_Missense_Mutation_p.E106V|PEPD_ENST00000397032.4_Missense_Mutation_p.E170V	NM_000285.3	NP_000276.2	P12955	PEPD_HUMAN	peptidase D	170					cellular amino acid metabolic process (GO:0006520)|collagen catabolic process (GO:0030574)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)	aminopeptidase activity (GO:0004177)|dipeptidase activity (GO:0016805)|manganese ion binding (GO:0030145)|metallocarboxypeptidase activity (GO:0004181)			endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)	17	Esophageal squamous(110;0.137)					ATTGTTGACTTCGAACCTGTA	0.488													T|||	77	0.0153754	0.0567	0.0	5008	,	,		21814	0.0		0.002	False		,,,				2504	0.0				p.E170V		Atlas-SNP	.											.	PEPD	48	.	0			c.A509T						PASS	.	T	VAL/GLU,VAL/GLU,VAL/GLU	155,3897		4,147,1875	87.0	88.0	88.0		509,509,317	3.6	1.0	19	dbSNP_129	88	1,8361		0,1,4180	yes	missense,missense,missense	PEPD	NM_000285.3,NM_001166056.1,NM_001166057.1	121,121,121	4,148,6055	AA,AT,TT		0.012,3.8253,1.2566	benign,benign,benign	170/494,170/453,106/430	33968991	156,12258	2026	4181	6207	SO:0001583	missense	5184	exon7			TTGACTTCGAACC	BC015027	CCDS42544.1, CCDS54244.1, CCDS54245.1	19q13.11	2008-02-05				ENSG00000124299	3.4.13.9		8840	protein-coding gene	gene with protein product	"""prolidase"""	613230				2925654, 1972707	Standard	NM_000285		Approved		uc002nur.4	P12955		ENST00000244137.7:c.509A>T	19.37:g.33968991T>A	ENSP00000244137:p.Glu170Val	194.0	0.0	0		157.0	80.0	0.509554	NM_000285	A8K3Z1|A8K416|A8K696|A8MX47|B4DDB7|B4DGJ1|E9PCE8|Q8TBN9|Q9BT75	Missense_Mutation	SNP	ENST00000244137.7	37	CCDS42544.1	19	0.0086996336996337	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	T	8.903	0.956821	0.18507	0.038253	1.2E-4	ENSG00000124299	ENST00000244137;ENST00000397032;ENST00000436370	T;T;T	0.79749	-1.03;-0.93;-1.3	5.7	3.56	0.40772	.	0.722777	0.15080	N	0.281739	T	0.32194	0.0821	N	0.13168	0.305	0.80722	D	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.06405	0.001;0.002;0.001	T	0.31052	-0.9957	10	0.24483	T	0.36	-4.3759	10.1383	0.42719	0.0:0.0:0.3228:0.6772	rs61748998	106;170;170	E9PCE8;A8MX47;P12955	.;.;PEPD_HUMAN	V	170;170;106	ENSP00000244137:E170V;ENSP00000380226:E170V;ENSP00000391890:E106V	ENSP00000244137:E170V	E	-	2	0	PEPD	38660831	1.000000	0.71417	0.994000	0.49952	0.574000	0.36063	0.933000	0.28897	0.387000	0.25024	0.533000	0.62120	GAA	T|0.978;A|0.022	0.022	strong		0.488	PEPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451432.3	NM_000285	
LRGUK	136332	hgsc.bcm.edu	37	7	133881794	133881794	+	Silent	SNP	T	T	C	rs35258804	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:133881794T>C	ENST00000285928.2	+	13	1551	c.1482T>C	c.(1480-1482)aaT>aaC	p.N494N		NM_144648.1	NP_653249.1	Q96M69	LRGUK_HUMAN	leucine-rich repeats and guanylate kinase domain containing	494	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)			breast(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	49						ATGGATTAAATAGGGACACCG	0.358													T|||	188	0.0375399	0.1324	0.013	5008	,	,		18959	0.0		0.001	False		,,,				2504	0.0031				p.N494N		Atlas-SNP	.											.	LRGUK	113	.	0			c.T1482C						PASS	.	T		484,3922	226.9+/-242.2	40,404,1759	164.0	154.0	158.0		1482	0.7	0.4	7	dbSNP_126	158	22,8578	16.0+/-53.3	0,22,4278	no	coding-synonymous	LRGUK	NM_144648.1		40,426,6037	CC,CT,TT		0.2558,10.985,3.8905		494/826	133881794	506,12500	2203	4300	6503	SO:0001819	synonymous_variant	136332	exon13			ATTAAATAGGGAC	AK057348	CCDS5830.1	7q33	2006-10-27			ENSG00000155530	ENSG00000155530			21964	protein-coding gene	gene with protein product							Standard	NM_144648		Approved	FLJ32786	uc003vrm.1	Q96M69	OTTHUMG00000155320	ENST00000285928.2:c.1482T>C	7.37:g.133881794T>C		135.0	0.0	0		98.0	54.0	0.55102	NM_144648	Q2M3I1	Silent	SNP	ENST00000285928.2	37	CCDS5830.1																																																																																			T|0.963;C|0.037	0.037	strong		0.358	LRGUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339442.1	NM_144648	
SPTBN5	51332	hgsc.bcm.edu	37	15	42179424	42179424	+	Missense_Mutation	SNP	C	C	T	rs890499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42179424C>T	ENST00000320955.6	-	6	1102	c.875G>A	c.(874-876)aGg>aAg	p.R292K		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	292					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		AGTGAGTCTCCTCTGGACAGT	0.612													C|||	306	0.0611022	0.2239	0.013	5008	,	,		19925	0.0		0.001	False		,,,				2504	0.0				p.R257K		Atlas-SNP	.											.	SPTBN5	171	.	0			c.G770A						PASS	.	C	LYS/ARG	563,2887		35,493,1197	25.0	33.0	30.0		770	1.1	0.8	15	dbSNP_86	30	9,6849		0,9,3420	yes	missense	SPTBN5	NM_016642.2	26	35,502,4617	TT,TC,CC		0.1312,16.3188,5.5491	possibly-damaging	257/3640	42179424	572,9736	1725	3429	5154	SO:0001583	missense	51332	exon6			AGTCTCCTCTGGA	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.875G>A	15.37:g.42179424C>T	ENSP00000317790:p.Arg292Lys	231.0	0.0	0		274.0	140.0	0.510949	NM_016642		Missense_Mutation	SNP	ENST00000320955.6	37		106	0.048534798534798536	103	0.20934959349593496	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	C	5.966	0.362219	0.11296	0.163188	0.001312	ENSG00000137877	ENST00000320955	T	0.69806	-0.43	4.49	1.08	0.20341	.	0.076889	0.48286	D	0.000197	T	0.00039	0.0001	N	0.05383	-0.06	0.43540	P	0.00416099999999997	P	0.35612	0.512	B	0.24541	0.054	T	0.22906	-1.0203	9	0.02654	T	1	.	5.7068	0.17913	0.0:0.3579:0.0:0.6421	rs890499;rs1704358;rs890499	292	Q9NRC6	SPTN5_HUMAN	K	292	ENSP00000317790:R292K	ENSP00000317790:R292K	R	-	2	0	SPTBN5	39966716	0.982000	0.34865	0.797000	0.32132	0.954000	0.61252	0.676000	0.25247	0.357000	0.24183	0.591000	0.81541	AGG	C|0.929;T|0.071	0.071	strong		0.612	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
URB2	9816	hgsc.bcm.edu	37	1	229783361	229783361	+	Silent	SNP	C	C	T	rs137900306	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229783361C>T	ENST00000258243.2	+	7	4147	c.4011C>T	c.(4009-4011)atC>atT	p.I1337I		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	1337						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						AGGAGGCCATCGGCAACCCCC	0.612													C|||	5	0.000998403	0.0038	0.0	5008	,	,		14676	0.0		0.0	False		,,,				2504	0.0				p.I1337I		Atlas-SNP	.											.	URB2	152	.	0			c.C4011T						PASS	.	C		11,4395	17.9+/-39.9	0,11,2192	90.0	74.0	79.0		4011	-0.1	0.1	1	dbSNP_134	79	0,8600		0,0,4300	no	coding-synonymous	URB2	NM_014777.2		0,11,6492	TT,TC,CC		0.0,0.2497,0.0846		1337/1525	229783361	11,12995	2203	4300	6503	SO:0001819	synonymous_variant	9816	exon7			GGCCATCGGCAAC	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.4011C>T	1.37:g.229783361C>T		168.0	0.0	0		142.0	74.0	0.521127	NM_014777	Q5VYC9	Silent	SNP	ENST00000258243.2	37	CCDS31052.1																																																																																			C|0.999;T|0.001	0.001	strong		0.612	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777	
TNXB	7148	hgsc.bcm.edu	37	6	32032689	32032689	+	Silent	SNP	C	C	T	rs35206129	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32032689C>T	ENST00000375244.3	-	19	6951	c.6750G>A	c.(6748-6750)tcG>tcA	p.S2250S	TNXB_ENST00000375247.2_Silent_p.S2250S			P22105	TENX_HUMAN	tenascin XB	2322	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						GCTCCAGGCCCGAGATGGTGA	0.612													C|||	18	0.00359425	0.0129	0.0014	5008	,	,		17765	0.0		0.0	False		,,,				2504	0.0				p.S2250S		Atlas-SNP	.											.	TNXB	553	.	0			c.G6750A						PASS	.	C		11,2531		0,11,1260	49.0	55.0	53.0		6750	-9.6	0.7	6	dbSNP_126	53	0,5100		0,0,2550	no	coding-synonymous	TNXB	NM_019105.6		0,11,3810	TT,TC,CC		0.0,0.4327,0.1439		2250/4243	32032689	11,7631	1271	2550	3821	SO:0001819	synonymous_variant	7148	exon19			CAGGCCCGAGATG	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.6750G>A	6.37:g.32032689C>T		128.0	0.0	0		133.0	64.0	0.481203	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	37																																																																																				C|0.995;T|0.005	0.005	strong		0.612	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
RXRB	6257	hgsc.bcm.edu	37	6	33162507	33162507	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33162507G>A	ENST00000374680.3	-	10	1765	c.1554C>T	c.(1552-1554)atC>atT	p.I518I	RXRB_ENST00000544186.1_Silent_p.I332I|COL11A2_ENST00000374712.1_5'Flank|COL11A2_ENST00000374713.1_5'Flank|COL11A2_ENST00000361917.1_5'Flank|COL11A2_ENST00000374708.4_5'Flank|COL11A2_ENST00000395197.1_5'Flank|COL11A2_ENST00000341947.2_5'Flank|COL11A2_ENST00000395194.1_5'Flank|COL11A2_ENST00000357486.1_5'Flank|COL11A2_ENST00000374714.1_5'Flank|RXRB_ENST00000374685.4_Silent_p.I522I	NM_001270401.1|NM_021976.4	NP_001257330.1|NP_068811.1	P28702	RXRB_HUMAN	retinoid X receptor, beta	518	Ligand-binding. {ECO:0000250}.				cardiac muscle cell proliferation (GO:0060038)|cellular response to retinoic acid (GO:0071300)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|maternal placenta development (GO:0001893)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle cell differentiation (GO:0055012)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	9-cis retinoic acid receptor activity (GO:0004886)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(1)|skin(2)	15					Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Tazarotene(DB00799)|Tretinoin(DB00755)	GGAAGGTGTCGATGGGGGTGT	0.547																																					p.I522I		Atlas-SNP	.											RXRB,colon,carcinoma,0,1	RXRB	34	1	0			c.C1566T						PASS	.						97.0	88.0	91.0					6																	33162507		1511	2709	4220	SO:0001819	synonymous_variant	6257	exon10			GGTGTCGATGGGG	M84820	CCDS4768.1, CCDS59007.1	6p21.3	2013-01-16			ENSG00000204231	ENSG00000204231		"""Nuclear hormone receptors"""	10478	protein-coding gene	gene with protein product	"""nuclear receptor subfamily 2 group B member 2"""	180246				8257090	Standard	NM_021976		Approved	NR2B2, H-2RIIBP, RCoR-1	uc003odc.4	P28702	OTTHUMG00000031298	ENST00000374680.3:c.1554C>T	6.37:g.33162507G>A		60.0	0.0	0		90.0	42.0	0.466667	NM_001270401	P28703|Q59G65|Q5JP92|Q5STQ1	Silent	SNP	ENST00000374680.3	37	CCDS4768.1																																																																																			.	.	none		0.547	RXRB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076642.2	NM_021976	
NSFL1C	55968	hgsc.bcm.edu	37	20	1433171	1433171	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1433171T>C	ENST00000216879.4	-	7	1619	c.752A>G	c.(751-753)aAa>aGa	p.K251R	NSFL1C_ENST00000461211.1_5'UTR|NSFL1C_ENST00000381658.4_Missense_Mutation_p.K140R|NSFL1C_ENST00000476071.1_Missense_Mutation_p.K253R|NSFL1C_ENST00000353088.2_Missense_Mutation_p.K220R|NSFL1C_ENST00000350991.4_Missense_Mutation_p.K253R	NM_016143.4	NP_057227.2	Q9UNZ2	NSF1C_HUMAN	NSFL1 (p97) cofactor (p47)	251						chromosome (GO:0005694)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			breast(1)|large_intestine(5)|lung(6)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	16						AGTGAAGGCTTTGAAGGCTCC	0.577																																					p.K251R		Atlas-SNP	.											.	NSFL1C	38	.	0			c.A752G						PASS	.						158.0	139.0	146.0					20																	1433171		2203	4300	6503	SO:0001583	missense	55968	exon7			AAGGCTTTGAAGG	AF112211	CCDS13015.1, CCDS13016.1, CCDS56175.1	20p13	2011-06-28			ENSG00000088833	ENSG00000088833		"""UBX domain containing"""	15912	protein-coding gene	gene with protein product	"""SHP1 homolog (S. cerevisiae)"", ""UBX domain protein 2C"""	606610				11042152	Standard	NM_016143		Approved	dJ776F14.1, p47, UBXD10, UBX1, UBXN2C	uc002wfc.3	Q9UNZ2	OTTHUMG00000031665	ENST00000216879.4:c.752A>G	20.37:g.1433171T>C	ENSP00000216879:p.Lys251Arg	99.0	0.0	0		96.0	34.0	0.354167	NM_016143	A2A2L1|B2RD74|Q5JXA4|Q5JXA5|Q7Z533|Q9H102|Q9NVL9|Q9UI06	Missense_Mutation	SNP	ENST00000216879.4	37	CCDS13015.1	.	.	.	.	.	.	.	.	.	.	T	16.27	3.076548	0.55753	.	.	ENSG00000088833	ENST00000353088;ENST00000476071;ENST00000216879;ENST00000381658;ENST00000350991	T;T;T;T;T	0.49432	0.79;0.78;0.78;0.82;0.78	5.13	2.85	0.33270	SEP domain (3);	0.000000	0.85682	D	0.000000	T	0.42337	0.1198	M	0.62016	1.91	0.58432	D	0.999995	B;B;B	0.11235	0.004;0.001;0.001	B;B;B	0.12156	0.007;0.005;0.005	T	0.30937	-0.9961	10	0.51188	T	0.08	-10.0824	8.1784	0.31296	0.0:0.294:0.0:0.706	.	220;140;251	Q9UNZ2-4;Q9UNZ2-6;Q9UNZ2	.;.;NSF1C_HUMAN	R	220;253;251;140;253	ENSP00000338643:K220R;ENSP00000418529:K253R;ENSP00000216879:K251R;ENSP00000371074:K140R;ENSP00000202584:K253R	ENSP00000216879:K251R	K	-	2	0	NSFL1C	1381171	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.908000	0.28545	0.503000	0.28060	0.533000	0.62120	AAA	.	.	none		0.577	NSFL1C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077525.2	NM_016143	
AP4E1	23431	hgsc.bcm.edu	37	15	51233881	51233881	+	Missense_Mutation	SNP	A	A	G	rs58909326	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:51233881A>G	ENST00000261842.5	+	10	1191	c.1085A>G	c.(1084-1086)tAt>tGt	p.Y362C	AP4E1_ENST00000560508.1_Missense_Mutation_p.Y287C	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	362					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)				breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		GCTCTTACCTATGTTATCCAA	0.353													A|||	72	0.014377	0.053	0.0029	5008	,	,		16104	0.0		0.0	False		,,,				2504	0.0				p.Y362C		Atlas-SNP	.											.	AP4E1	78	.	0			c.A1085G						PASS	.	A	CYS/TYR	216,4176	131.8+/-168.3	5,206,1985	147.0	137.0	141.0		1085	4.9	1.0	15	dbSNP_129	141	2,8586	2.2+/-6.3	0,2,4292	yes	missense	AP4E1	NM_007347.3	194	5,208,6277	GG,GA,AA		0.0233,4.918,1.6795	benign	362/1138	51233881	218,12762	2196	4294	6490	SO:0001583	missense	23431	exon10			TTACCTATGTTAT	AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014			573	protein-coding gene	gene with protein product		607244				10436028, 21620353	Standard	NM_007347		Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.1085A>G	15.37:g.51233881A>G	ENSP00000261842:p.Tyr362Cys	114.0	0.0	0		128.0	62.0	0.484375	NM_007347	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Missense_Mutation	SNP	ENST00000261842.5	37	CCDS32240.1	35	0.016025641025641024	35	0.07113821138211382	0	0.0	0	0.0	0	0.0	A	11.86	1.763436	0.31228	0.04918	2.33E-4	ENSG00000081014	ENST00000261842	T	0.25414	1.8	6.04	4.93	0.64822	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.061436	0.64402	D	0.000002	T	0.01029	0.0034	N	0.16098	0.37	0.58432	D	0.999997	B	0.22800	0.075	B	0.21917	0.037	T	0.10823	-1.0613	10	0.37606	T	0.19	-17.2068	9.7604	0.40528	0.8689:0.0:0.1311:0.0	rs58909326	362	Q9UPM8	AP4E1_HUMAN	C	362	ENSP00000261842:Y362C	ENSP00000261842:Y362C	Y	+	2	0	AP4E1	49021173	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	4.930000	0.63462	2.317000	0.78254	0.460000	0.39030	TAT	A|0.982;G|0.018	0.018	strong		0.353	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1		
SLCO4A1	28231	hgsc.bcm.edu	37	20	61292475	61292475	+	Missense_Mutation	SNP	C	C	T	rs201057493		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61292475C>T	ENST00000370507.1	+	4	1165	c.1069C>T	c.(1069-1071)Cgt>Tgt	p.R357C	RP11-93B14.5_ENST00000433126.1_RNA|SLCO4A1_ENST00000217159.1_Missense_Mutation_p.R357C|RP11-93B14.5_ENST00000411824.1_RNA|RP11-93B14.5_ENST00000451648.1_RNA			Q96BD0	SO4A1_HUMAN	solute carrier organic anion transporter family, member 4A1	357					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			endometrium(6)|kidney(2)|large_intestine(1)|lung(7)|ovary(3)|prostate(2)	21	Breast(26;3.65e-08)		BRCA - Breast invasive adenocarcinoma(19;2.33e-06)		Benzylpenicillin(DB01053)|Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)	GGACAGCAGCCGTGGGGAGGC	0.622													c|||	1	0.000199681	0.0	0.0	5008	,	,		11244	0.0		0.001	False		,,,				2504	0.0				p.R357C	Pancreas(168;741 2006 10379 40139 45334)	Atlas-SNP	.											SLCO4A1,uveal_tract,malignant_melanoma,0,1	SLCO4A1	65	1	0			c.C1069T						PASS	.		CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	89.0	80.0	83.0		1069	3.2	0.0	20		83	0,8600		0,0,4300	no	missense	SLCO4A1	NM_016354.3	180	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	357/723	61292475	1,13005	2203	4300	6503	SO:0001583	missense	28231	exon5			AGCAGCCGTGGGG	AB031051	CCDS13501.1	20q13.1	2013-05-22	2003-11-25	2003-11-26	ENSG00000101187	ENSG00000101187		"""Solute carriers"""	10953	protein-coding gene	gene with protein product		612436	"""solute carrier family 21 (organic anion transporter), member 12"""	SLC21A12		10873595	Standard	NM_016354		Approved	OATP-E, OATP4A1	uc002ydb.1	Q96BD0	OTTHUMG00000032923	ENST00000370507.1:c.1069C>T	20.37:g.61292475C>T	ENSP00000359538:p.Arg357Cys	40.0	0.0	0		62.0	25.0	0.403226	NM_016354	Q9H4T7|Q9H4T8|Q9H8P2|Q9NWX8|Q9UI35|Q9UIG7	Missense_Mutation	SNP	ENST00000370507.1	37	CCDS13501.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	c	6.688	0.495496	0.12762	2.27E-4	0.0	ENSG00000101187	ENST00000217159;ENST00000370512;ENST00000370507	T;T	0.41400	1.0;1.0	4.25	3.22	0.36961	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	6.950440	0.00447	N	0.000090	T	0.42810	0.1219	L	0.54323	1.7	0.19300	N	0.999972	B	0.15473	0.013	B	0.15484	0.013	T	0.30707	-0.9969	10	0.56958	D	0.05	.	7.3638	0.26762	0.0:0.7375:0.1713:0.0912	.	357	Q96BD0	SO4A1_HUMAN	C	357	ENSP00000217159:R357C;ENSP00000359538:R357C	ENSP00000217159:R357C	R	+	1	0	SLCO4A1	60762920	0.092000	0.21681	0.008000	0.14137	0.002000	0.02628	2.568000	0.45965	1.940000	0.56252	0.450000	0.29827	CGT	C|1.000;T|0.000	0.000	strong		0.622	SLCO4A1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080048.2	NM_016354	
GPR144	347088	hgsc.bcm.edu	37	9	127230864	127230864	+	Missense_Mutation	SNP	G	G	A	rs7854446	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:127230864G>A	ENST00000334810.1	+	14	2221	c.2221G>A	c.(2221-2223)Gtg>Atg	p.V741M				Q7Z7M1	GP144_HUMAN	G protein-coupled receptor 144	741					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)			central_nervous_system(1)|endometrium(3)	4						CTGGATGCTGGTGGAGGGGCT	0.637													G|||	92	0.0183706	0.0666	0.0058	5008	,	,		17950	0.0		0.0	False		,,,				2504	0.0				p.V741M		Atlas-SNP	.											.	GPR144	33	.	0			c.G2221A						PASS	.	G	MET/VAL	114,1270		6,102,584	100.0	88.0	92.0		2221	4.7	1.0	9	dbSNP_116	92	1,3181		0,1,1590	yes	missense	GPR144	NM_001161808.1	21	6,103,2174	AA,AG,GG		0.0314,8.237,2.5186	probably-damaging	741/964	127230864	115,4451	692	1591	2283	SO:0001583	missense	347088	exon14			ATGCTGGTGGAGG	AY278562		9q34.11	2014-08-08			ENSG00000180264	ENSG00000180264		"""-"", ""GPCR / Class B : Orphans"""	18651	protein-coding gene	gene with protein product							Standard	XM_006710216		Approved	PGR24	uc010mwn.3	Q7Z7M1	OTTHUMG00000020652	ENST00000334810.1:c.2221G>A	9.37:g.127230864G>A	ENSP00000335156:p.Val741Met	174.0	1.0	0.00574713		121.0	119.0	0.983471	NM_001161808	Q86SL4|Q8NH12	Missense_Mutation	SNP	ENST00000334810.1	37	CCDS48016.1	39|39	0.017857142857142856|0.017857142857142856	37|37	0.07520325203252033|0.07520325203252033	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	G|G	21.8|21.8	4.205019|4.205019	0.79127|0.79127	0.08237|0.08237	3.14E-4|3.14E-4	ENSG00000180264|ENSG00000180264	ENST00000446588|ENST00000334810	.|T	.|0.41400	.|1.0	4.7|4.7	4.7|4.7	0.59300|0.59300	.|GPCR, family 2-like (1);	.|.	.|.	.|.	.|.	T|T	0.09202|0.09202	0.0227|0.0227	M|M	0.76170|0.76170	2.325|2.325	0.49582|0.49582	D|D	0.999802|0.999802	D|D	0.89917|0.89917	1.0|1.0	D|D	0.91635|0.91635	0.999|0.999	T|T	0.45249|0.45249	-0.9274|-0.9274	8|9	0.87932|0.72032	D|D	0|0.01	.|.	16.2217|16.2217	0.82262|0.82262	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs7854446;rs7854446|rs7854446;rs7854446	9|741	A1E4E8|Q7Z7M1	.|GP144_HUMAN	D|M	9|741	.|ENSP00000335156:V741M	ENSP00000414478:G9D|ENSP00000335156:V741M	G|V	+|+	2|1	0|0	GPR144|GPR144	126270685|126270685	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.838000|0.838000	0.47535|0.47535	6.672000|6.672000	0.74477|0.74477	2.147000|2.147000	0.66899|0.66899	0.561000|0.561000	0.74099|0.74099	GGT|GTG	G|0.967;A|0.033	0.033	strong		0.637	GPR144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054026.2	NM_182611	
CASP4	837	hgsc.bcm.edu	37	11	104819333	104819333	+	Missense_Mutation	SNP	C	C	A	rs55901059	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:104819333C>A	ENST00000444739.2	-	6	1762	c.852G>T	c.(850-852)gaG>gaT	p.E284D	CASP4_ENST00000531333.1_5'Flank|CASP4_ENST00000393150.3_Missense_Mutation_p.E228D	NM_001225.3	NP_001216.1	P49662	CASP4_HUMAN	caspase 4, apoptosis-related cysteine peptidase	284			E -> D (in dbSNP:rs55901059).		apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of inflammatory response (GO:0050727)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|IPAF inflammasome complex (GO:0072557)|membrane (GO:0016020)|mitochondrion (GO:0005739)|NLRP3 inflammasome complex (GO:0072559)	cysteine-type endopeptidase activity (GO:0004197)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(1)|skin(1)|urinary_tract(2)	23		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000854)|Epithelial(105;0.00879)|all cancers(92;0.0357)		CCTCTAGGTTCTCAGATGACT	0.493													c|||	93	0.0185703	0.0688	0.0029	5008	,	,		19215	0.0		0.0	False		,,,				2504	0.0				p.E284D		Atlas-SNP	.											.	CASP4	57	.	0			c.G852T						PASS	.	C	ASP/GLU,ASP/GLU	287,4117	157.8+/-190.6	12,263,1927	157.0	117.0	131.0		852,684	-2.6	0.0	11	dbSNP_129	131	1,8597		0,1,4298	yes	missense,missense	CASP4	NM_001225.3,NM_033306.2	45,45	12,264,6225	AA,AC,CC		0.0116,6.5168,2.215	benign,benign	284/378,228/322	104819333	288,12714	2202	4299	6501	SO:0001583	missense	837	exon6			TAGGTTCTCAGAT	U25804	CCDS8327.1, CCDS41704.1	11q22.2-q22.3	2006-02-17	2005-08-17		ENSG00000196954	ENSG00000196954		"""Caspases"""	1505	protein-coding gene	gene with protein product		602664	"""caspase 4, apoptosis-related cysteine protease"""			7797510, 9250871	Standard	NM_001225		Approved	ICE(rel)II, ICH-2, TX	uc001pid.1	P49662	OTTHUMG00000166078	ENST00000444739.2:c.852G>T	11.37:g.104819333C>A	ENSP00000388566:p.Glu284Asp	147.0	0.0	0		141.0	86.0	0.609929	NM_001225	A2NHL8|A2NHM0	Missense_Mutation	SNP	ENST00000444739.2	37	CCDS8327.1	43	0.019688644688644688	42	0.08536585365853659	1	0.0027624309392265192	0	0.0	0	0.0	C	9.595	1.127085	0.20959	0.065168	1.16E-4	ENSG00000196954	ENST00000444739;ENST00000393150;ENST00000355546	T;T	0.20738	2.05;2.05	5.08	-2.61	0.06171	Peptidase C14, caspase catalytic (1);Peptidase C14, caspase precursor p45, core (1);	1.203310	0.05999	N	0.647483	T	0.00580	0.0019	L	0.37800	1.135	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.32587	-0.9901	10	0.19590	T	0.45	.	12.8207	0.57692	0.0:0.3484:0.58:0.0716	rs55901059;rs61735787	284	P49662	CASP4_HUMAN	D	284;228;237	ENSP00000388566:E284D;ENSP00000376857:E228D	ENSP00000347741:E237D	E	-	3	2	CASP4	104324543	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-1.270000	0.02831	-0.407000	0.07576	-0.494000	0.04653	GAG	C|0.979;A|0.021	0.021	strong		0.493	CASP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387751.1	NM_001225	
BRDT	676	hgsc.bcm.edu	37	1	92445179	92445179	+	Missense_Mutation	SNP	G	G	A	rs114276662	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:92445179G>A	ENST00000362005.3	+	9	1570	c.1152G>A	c.(1150-1152)atG>atA	p.M384I	BRDT_ENST00000394530.3_Missense_Mutation_p.M338I|BRDT_ENST00000399546.2_Missense_Mutation_p.M384I|BRDT_ENST00000402388.1_Missense_Mutation_p.M384I|BRDT_ENST00000370389.2_Missense_Mutation_p.M311I	NM_001242805.1	NP_001229734	Q58F21	BRDT_HUMAN	bromodomain, testis-specific	384					cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|histone displacement (GO:0001207)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|mRNA processing (GO:0006397)|positive regulation of transcription during meiosis (GO:0051039)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(24)|ovary(1)|prostate(4)|skin(2)|stomach(2)|urinary_tract(2)	56		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)		TTGAGAGTATGCCTTTATGTT	0.348													G|||	22	0.00439297	0.0144	0.0029	5008	,	,		16690	0.0		0.001	False		,,,				2504	0.0				p.M388I		Atlas-SNP	.											.	BRDT	133	.	0			c.G1164A						PASS	.	G	ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET	67,4339	61.7+/-98.7	0,67,2136	103.0	103.0	103.0		1152,1164,1014,1014,933,1152,1152	3.5	0.0	1	dbSNP_133	103	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense,missense	BRDT	NM_001242805.1,NM_001242806.1,NM_001242807.1,NM_001242808.1,NM_001242810.1,NM_001726.3,NM_207189.2	10,10,10,10,10,10,10	0,67,6436	AA,AG,GG		0.0,1.5207,0.5151	benign,benign,benign,benign,benign,benign,benign	384/948,388/952,338/902,338/902,311/875,384/948,384/948	92445179	67,12939	2203	4300	6503	SO:0001583	missense	676	exon8			GAGTATGCCTTTA	AF019085	CCDS735.1, CCDS55615.1, CCDS55616.1, CCDS72820.1	1p22.1	2010-12-23			ENSG00000137948	ENSG00000137948			1105	protein-coding gene	gene with protein product	"""cancer/testis antigen 9"""	602144				9367677	Standard	NM_001726		Approved	BRD6, CT9	uc010osz.2	Q58F21	OTTHUMG00000010113	ENST00000362005.3:c.1152G>A	1.37:g.92445179G>A	ENSP00000354568:p.Met384Ile	195.0	0.0	0		206.0	92.0	0.446602	NM_001242806	A6NF68|B7Z811|B7Z890|B7ZAX7|D3DT32|O14789|Q05DQ4|Q6P5T1|Q7Z4A6|Q8IWI6	Missense_Mutation	SNP	ENST00000362005.3	37	CCDS735.1	7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	G	7.998	0.754682	0.15778	0.015207	0.0	ENSG00000137948	ENST00000362005;ENST00000370389;ENST00000399546;ENST00000539070;ENST00000394530;ENST00000426141;ENST00000402388	T;T;T;T;T;T	0.09163	3.33;3.34;3.33;3.38;3.01;3.33	5.41	3.49	0.39957	Bromodomain (1);	0.456653	0.24005	N	0.042435	T	0.02230	0.0069	L	0.29908	0.895	0.09310	N	1	B;B;B;B	0.18863	0.031;0.031;0.0;0.031	B;B;B;B	0.09377	0.004;0.004;0.002;0.002	T	0.43032	-0.9416	10	0.38643	T	0.18	-0.2883	5.9499	0.19239	0.1483:0.0:0.5637:0.288	.	338;338;388;384	B7ZAX7;B7Z811;B7Z890;Q58F21	.;.;.;BRDT_HUMAN	I	384;311;384;384;338;384;384	ENSP00000354568:M384I;ENSP00000359416:M311I;ENSP00000387822:M384I;ENSP00000378038:M338I;ENSP00000404969:M384I;ENSP00000384051:M384I	ENSP00000354568:M384I	M	+	3	0	BRDT	92217767	0.008000	0.16893	0.016000	0.15963	0.543000	0.35085	1.606000	0.36826	0.631000	0.30412	0.655000	0.94253	ATG	G|0.995;A|0.005	0.005	strong		0.348	BRDT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027980.2	NM_207189	
UBA5	79876	hgsc.bcm.edu	37	3	132384704	132384704	+	Missense_Mutation	SNP	G	G	A	rs61748106	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:132384704G>A	ENST00000356232.4	+	2	1271	c.199G>A	c.(199-201)Gac>Aac	p.D67N	UBA5_ENST00000493720.2_Missense_Mutation_p.D67N|UBA5_ENST00000473651.1_Missense_Mutation_p.D67N|UBA5_ENST00000494238.2_Missense_Mutation_p.D11N|UBA5_ENST00000264991.4_Missense_Mutation_p.D11N	NM_024818.3	NP_079094.1	Q9GZZ9	UBA5_HUMAN	ubiquitin-like modifier activating enzyme 5	67					protein ufmylation (GO:0071569)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|UFM1 activating enzyme activity (GO:0071566)			breast(2)|endometrium(4)|kidney(4)|large_intestine(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16						AATTGTAAGCGACTATGAGGT	0.303													G|||	2	0.000399361	0.0015	0.0	5008	,	,		18495	0.0		0.0	False		,,,				2504	0.0				p.D67N		Atlas-SNP	.											UBA5,colon,carcinoma,0,1	UBA5	33	1	0			c.G199A						PASS	.	G	ASN/ASP,ASN/ASP	7,4399	12.9+/-30.5	0,7,2196	90.0	98.0	96.0		199,31	4.3	0.7	3	dbSNP_129	96	0,8600		0,0,4300	yes	missense,missense	UBA5	NM_024818.3,NM_198329.2	23,23	0,7,6496	AA,AG,GG		0.0,0.1589,0.0538	benign,benign	67/405,11/349	132384704	7,12999	2203	4300	6503	SO:0001583	missense	79876	exon2			GTAAGCGACTATG	AY253672	CCDS3076.1, CCDS3077.1	3q22	2007-11-30	2007-11-30	2007-11-30	ENSG00000081307	ENSG00000081307		"""Ubiquitin-like modifier activating enzymes"""	23230	protein-coding gene	gene with protein product	"""UBA5, ubiquitin-activating enzyme E1 homolog (yeast)"""	610552	"""ubiquitin-activating enzyme E1-domain containing 1"""	UBE1DC1		11230166, 15071506	Standard	NM_198329		Approved	FLJ23251	uc003epa.4	Q9GZZ9	OTTHUMG00000159759	ENST00000356232.4:c.199G>A	3.37:g.132384704G>A	ENSP00000348565:p.Asp67Asn	102.0	0.0	0		99.0	44.0	0.444444	NM_024818	A6NJL3|D3DNC8|Q96ST1	Missense_Mutation	SNP	ENST00000356232.4	37	CCDS3076.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	4.515	0.095620	0.08681	0.001589	0.0	ENSG00000081307	ENST00000264991;ENST00000356232;ENST00000493720;ENST00000468022;ENST00000473651;ENST00000494238;ENST00000489361	T;T;T;T;T;T;T	0.29142	1.58;1.58;1.58;1.58;1.58;1.58;1.58	6.03	4.26	0.50523	Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.14056	0.0340	N	0.04959	-0.14	0.80722	D	1	B;B	0.11235	0.004;0.002	B;B	0.09377	0.004;0.002	T	0.07616	-1.0763	10	0.12103	T	0.63	-19.1821	11.318	0.49403	0.1873:0.0:0.8127:0.0	rs61748106	67;67	E7EWE1;Q9GZZ9	.;UBA5_HUMAN	N	11;67;67;11;67;11;11	ENSP00000264991:D11N;ENSP00000348565:D67N;ENSP00000417879:D67N;ENSP00000418569:D11N;ENSP00000424984:D67N;ENSP00000418807:D11N;ENSP00000417905:D11N	ENSP00000264991:D11N	D	+	1	0	UBA5	133867394	1.000000	0.71417	0.700000	0.30305	0.868000	0.49771	4.654000	0.61469	0.898000	0.36418	-0.794000	0.03295	GAC	G|0.999;A|0.001	0.001	strong		0.303	UBA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357187.2	NM_024818	
PXDNL	137902	hgsc.bcm.edu	37	8	52321293	52321293	+	Missense_Mutation	SNP	T	T	A	rs562911693		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:52321293T>A	ENST00000356297.4	-	17	2991	c.2891A>T	c.(2890-2892)cAt>cTt	p.H964L	PXDNL_ENST00000543296.1_Missense_Mutation_p.H964L	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	964					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				CAGAGCCAGATGCTCGTTGGC	0.647																																					p.H964L		Atlas-SNP	.											.	PXDNL	414	.	0			c.A2891T						PASS	.						13.0	15.0	14.0					8																	52321293		1980	4147	6127	SO:0001583	missense	137902	exon17			GCCAGATGCTCGT		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.2891A>T	8.37:g.52321293T>A	ENSP00000348645:p.His964Leu	106.0	0.0	0		103.0	54.0	0.524272	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	7.567|7.567	0.665851|0.665851	0.14710|0.14710	.|.	.|.	ENSG00000147485|ENSG00000147485	ENST00000356297;ENST00000543296|ENST00000522933	T;T|.	0.71698|.	-0.59;-0.59|.	3.73|3.73	1.18|1.18	0.20946|0.20946	.|.	0.164545|.	0.29508|.	N|.	0.011960|.	T|T	0.19208|0.19208	0.0461|0.0461	N|N	0.17082|0.17082	0.46|0.46	0.26667|0.26667	N|N	0.971805|0.971805	B|.	0.11235|.	0.004|.	B|.	0.17979|.	0.02|.	T|T	0.24657|0.24657	-1.0154|-1.0154	10|5	0.59425|.	D|.	0.04|.	.|.	3.9824|3.9824	0.09501|0.09501	0.1835:0.1097:0.0:0.7068|0.1835:0.1097:0.0:0.7068	.|.	964|.	A1KZ92|.	PXDNL_HUMAN|.	L|F	964|83	ENSP00000348645:H964L;ENSP00000444865:H964L|.	ENSP00000348645:H964L|.	H|I	-|-	2|1	0|0	PXDNL|PXDNL	52483846|52483846	1.000000|1.000000	0.71417|0.71417	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	5.173000|5.173000	0.65010|0.65010	-0.052000|-0.052000	0.13311|0.13311	-0.371000|-0.371000	0.07208|0.07208	CAT|ATC	.	.	none		0.647	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
MT-ND4L	4539	hgsc.bcm.edu	37	M	10688	10688	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:10688G>A	ENST00000361335.1	+	1	219	c.219G>A	c.(217-219)gtG>gtA	p.V73V	MT-TR_ENST00000387439.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-ND4_ENST00000361381.2_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-TK_ENST00000387421.1_RNA			P03901	NU4LM_HUMAN	mitochondrially encoded NADH dehydrogenase 4L	73					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(2)|kidney(2)	5						GAAGCAGCGGTGGGCCTAGCC	0.458																																					p.V73V		Atlas-SNP	.											.	.	.	.	0			c.G219A						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			AGCGGTGGGCCTA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000212907	ENSG00000212907	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7460	protein-coding gene	gene with protein product	"""complex I ND4L subunit"", ""NADH-ubiquinone oxidoreductase chain 4L"""	516004	"""NADH dehydrogenase 4L"""	MTND4L			Standard			Approved	ND4L, NAD4L		P03901		ENST00000361335.1:c.219G>A	M.37:g.10688G>A		11.0	0.0	0		9.0	9.0	1	ENST00000361335		Silent	SNP	ENST00000361335.1	37																																																																																				.	.	none		0.458	MT-ND4L-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024034	
PKMYT1	9088	hgsc.bcm.edu	37	16	3023185	3023185	+	Missense_Mutation	SNP	G	G	A	rs150931982	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3023185G>A	ENST00000262300.8	-	8	1850	c.1342C>T	c.(1342-1344)Cgg>Tgg	p.R448W	PKMYT1_ENST00000574385.1_Missense_Mutation_p.R439W|PAQR4_ENST00000572687.1_3'UTR|PKMYT1_ENST00000431515.2_Missense_Mutation_p.R448W|PKMYT1_ENST00000573944.1_Missense_Mutation_p.R439W|PAQR4_ENST00000318782.8_3'UTR|PKMYT1_ENST00000571102.1_5'Flank|PAQR4_ENST00000293978.8_3'UTR|PKMYT1_ENST00000574730.1_Missense_Mutation_p.R379W|PKMYT1_ENST00000440027.2_Silent_p.P460P	NM_001258450.1|NM_004203.4|NM_182687.2	NP_001245379.1|NP_004194.3|NP_872629.1	Q99640	PMYT1_HUMAN	protein kinase, membrane associated tyrosine/threonine 1	448	Interaction with CDC2-CCNB1.|Interaction with PIN1.				G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	10						CCCACAGTCCGGGCCAGGACA	0.657													G|||	17	0.00339457	0.0129	0.0	5008	,	,		15724	0.0		0.0	False		,,,				2504	0.0				p.R448W		Atlas-SNP	.											.	PKMYT1	23	.	0			c.C1342T						PASS	.	G	TRP/ARG,,	34,4316		0,34,2141	28.0	27.0	28.0		1342,,1380	2.5	0.8	16	dbSNP_134	28	0,8560		0,0,4280	yes	missense,utr-3,coding-synonymous	PKMYT1,PAQR4	NM_004203.4,NM_152341.3,NM_182687.2	101,,	0,34,6421	AA,AG,GG		0.0,0.7816,0.2634	probably-damaging,,	448/500,,460/481	3023185	34,12876	2175	4280	6455	SO:0001583	missense	9088	exon8			CAGTCCGGGCCAG	AK097642	CCDS10486.1, CCDS45391.1, CCDS58414.1, CCDS58415.1	16p13.3	2014-06-13			ENSG00000127564	ENSG00000127564			29650	protein-coding gene	gene with protein product	"""membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase"", ""protein phosphatase 1, regulatory subunit 126"""	602474				9001210, 12606722	Standard	NM_004203		Approved	MYT1, PPP1R126	uc002csn.3	Q99640	OTTHUMG00000128975	ENST00000262300.8:c.1342C>T	16.37:g.3023185G>A	ENSP00000262300:p.Arg448Trp	65.0	0.0	0		108.0	48.0	0.444444	NM_004203	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Missense_Mutation	SNP	ENST00000262300.8	37	CCDS10486.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	13.73	2.324957	0.41197	0.007816	0.0	ENSG00000127564	ENST00000431515;ENST00000262300;ENST00000402679	T;T	0.62941	-0.01;0.15	4.75	2.47	0.30058	.	0.463681	0.22806	N	0.055404	T	0.41719	0.1171	L	0.32530	0.975	0.80722	D	1	D;D	0.60575	0.988;0.988	P;P	0.52424	0.698;0.698	T	0.53514	-0.8428	10	0.59425	D	0.04	-16.2832	9.4789	0.38889	0.0:0.0:0.6461:0.3539	.	379;448	B4DXD4;Q99640	.;PMYT1_HUMAN	W	448	ENSP00000392855:R448W;ENSP00000262300:R448W	ENSP00000262300:R448W	R	-	1	2	PKMYT1	2963186	0.954000	0.32549	0.808000	0.32385	0.023000	0.10783	1.549000	0.36212	1.104000	0.41587	0.655000	0.94253	CGG	G|0.995;A|0.005	0.005	strong		0.657	PKMYT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250963.2	NM_004203	
IGF2R	3482	hgsc.bcm.edu	37	6	160482929	160482929	+	Missense_Mutation	SNP	C	C	G	rs8191844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:160482929C>G	ENST00000356956.1	+	25	3699	c.3551C>G	c.(3550-3552)aCc>aGc	p.T1184S		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	1184			T -> S (in dbSNP:rs8191844). {ECO:0000269|Ref.5}.		insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	CGCTTCTCCACCAGGATCACG	0.522													C|||	40	0.00798722	0.0287	0.0029	5008	,	,		18416	0.0		0.0	False		,,,				2504	0.0				p.T1184S		Atlas-SNP	.											.	IGF2R	251	.	0			c.C3551G						PASS	.	C	SER/THR	127,4279	93.0+/-131.7	1,125,2077	159.0	148.0	152.0		3551	5.5	1.0	6	dbSNP_117	152	0,8600		0,0,4300	yes	missense	IGF2R	NM_000876.2	58	1,125,6377	GG,GC,CC		0.0,2.8824,0.9765	probably-damaging	1184/2492	160482929	127,12879	2203	4300	6503	SO:0001583	missense	3482	exon25			TCTCCACCAGGAT	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"""CD molecules"""	5467	protein-coding gene	gene with protein product	"""cation-independent mannose-6 phosphate receptor"""	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.3551C>G	6.37:g.160482929C>G	ENSP00000349437:p.Thr1184Ser	156.0	0.0	0		152.0	73.0	0.480263	NM_000876	Q7Z7G9|Q96PT5	Missense_Mutation	SNP	ENST00000356956.1	37	CCDS5273.1	14	0.00641025641025641	12	0.024390243902439025	2	0.0055248618784530384	0	0.0	0	0.0	C	23.0	4.365286	0.82463	0.028824	0.0	ENSG00000197081	ENST00000356956	T	0.04275	3.66	5.5	5.5	0.81552	Mannose-6-phosphate receptor, binding (1);	0.000000	0.85682	D	0.000000	T	0.14270	0.0345	M	0.75615	2.305	0.52501	D	0.999957	D	0.89917	1.0	D	0.87578	0.998	T	0.01810	-1.1269	10	0.32370	T	0.25	-13.6676	17.5389	0.87841	0.0:1.0:0.0:0.0	rs8191844;rs52837912;rs8191844	1184	P11717	MPRI_HUMAN	S	1184	ENSP00000349437:T1184S	ENSP00000349437:T1184S	T	+	2	0	IGF2R	160402919	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.514000	0.67043	2.735000	0.93741	0.655000	0.94253	ACC	C|0.991;G|0.009	0.009	strong		0.522	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
DNAH5	1767	hgsc.bcm.edu	37	5	13841066	13841066	+	Silent	SNP	G	G	A	rs6880264	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:13841066G>A	ENST00000265104.4	-	34	5762	c.5658C>T	c.(5656-5658)taC>taT	p.Y1886Y		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	1886	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TCAGAGTCTCGTATTTCACTC	0.388									Kartagener syndrome				G|||	74	0.0147764	0.0545	0.0029	5008	,	,		19415	0.0		0.0	False		,,,				2504	0.0				p.Y1886Y		Atlas-SNP	.											.	DNAH5	868	.	0			c.C5658T						PASS	.	G		192,4214	122.9+/-160.3	2,188,2013	149.0	136.0	141.0		5658	-2.4	1.0	5	dbSNP_116	141	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	DNAH5	NM_001369.2		2,191,6310	AA,AG,GG		0.0349,4.3577,1.4993		1886/4625	13841066	195,12811	2203	4300	6503	SO:0001819	synonymous_variant	1767	exon34	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AGTCTCGTATTTC	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.5658C>T	5.37:g.13841066G>A		127.0	0.0	0		141.0	63.0	0.446809	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Silent	SNP	ENST00000265104.4	37	CCDS3882.1																																																																																			G|0.985;A|0.015	0.015	strong		0.388	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
LRRFIP2	9209	hgsc.bcm.edu	37	3	37154417	37154417	+	Missense_Mutation	SNP	T	T	C	rs34902788	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:37154417T>C	ENST00000336686.4	-	8	507	c.427A>G	c.(427-429)Aaa>Gaa	p.K143E	LRRFIP2_ENST00000354379.4_Intron|LRRFIP2_ENST00000421307.1_Missense_Mutation_p.K143E|LRRFIP2_ENST00000440230.1_Intron|LRRFIP2_ENST00000421276.2_Intron|LRRFIP2_ENST00000396428.2_Missense_Mutation_p.K112E			Q9Y608	LRRF2_HUMAN	leucine rich repeat (in FLII) interacting protein 2	143	DVL3-binding.|Ser-rich.		K -> E (in dbSNP:rs34902788).		Wnt signaling pathway (GO:0016055)		LRR domain binding (GO:0030275)	p.0?(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						AGTAGGTCTTTATGAGAATCA	0.368													T|||	72	0.014377	0.0514	0.0058	5008	,	,		18111	0.0		0.0	False		,,,				2504	0.0				p.K143E		Atlas-SNP	.											.	LRRFIP2	71	.	1	Whole gene deletion(1)	ovary(1)	c.A427G						PASS	.	T	,GLU/LYS,	190,4216	120.4+/-158.0	7,176,2020	128.0	128.0	128.0		,427,	4.3	1.0	3	dbSNP_126	128	2,8598	1.2+/-3.3	0,2,4298	yes	intron,missense,intron	LRRFIP2	NM_001134369.1,NM_006309.2,NM_017724.2	,56,	7,178,6318	CC,CT,TT		0.0233,4.3123,1.4762	,possibly-damaging,	,143/722,	37154417	192,12814	2203	4300	6503	SO:0001583	missense	9209	exon9			GGTCTTTATGAGA	AF115509	CCDS2664.1, CCDS2665.1, CCDS46791.1, CCDS63592.1	3p22.1	2008-07-18			ENSG00000093167	ENSG00000093167			6703	protein-coding gene	gene with protein product		614043				10366446	Standard	NM_017724		Approved	HUFI-2	uc003cgp.2	Q9Y608	OTTHUMG00000130796	ENST00000336686.4:c.427A>G	3.37:g.37154417T>C	ENSP00000338727:p.Lys143Glu	43.0	0.0	0		46.0	16.0	0.347826	NM_006309	A8K649|A8MXR0|B4DY63|Q68CV3|Q9NXH5	Missense_Mutation	SNP	ENST00000336686.4	37	CCDS2664.1	17	0.007783882783882784	15	0.03048780487804878	2	0.0055248618784530384	0	0.0	0	0.0	T	10.81	1.454776	0.26161	0.043123	2.33E-4	ENSG00000093167	ENST00000421307;ENST00000336686;ENST00000396428	T;T;T	0.48201	0.82;0.82;0.87	5.52	4.29	0.51040	.	0.266541	0.34959	N	0.003544	T	0.06554	0.0168	N	0.08118	0	0.29065	N	0.883669	B;B	0.27853	0.076;0.191	B;B	0.28465	0.077;0.09	T	0.04153	-1.0973	10	0.12766	T	0.61	-16.635	12.8465	0.57833	0.0:0.0:0.1352:0.8648	rs34902788	112;143	A8MXR0;Q9Y608	.;LRRF2_HUMAN	E	143;143;112	ENSP00000392217:K143E;ENSP00000338727:K143E;ENSP00000379705:K112E	ENSP00000338727:K143E	K	-	1	0	LRRFIP2	37129421	1.000000	0.71417	0.981000	0.43875	0.935000	0.57460	3.954000	0.56708	2.232000	0.73038	0.482000	0.46254	AAA	T|0.987;C|0.013	0.013	strong		0.368	LRRFIP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253335.3	NM_006309	
NR1D1	9572	hgsc.bcm.edu	37	17	38253469	38253469	+	Silent	SNP	G	G	A	rs9905506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38253469G>A	ENST00000246672.3	-	2	849	c.219C>T	c.(217-219)ccC>ccT	p.P73P		NM_021724.3	NP_068370.1	P20393	NR1D1_HUMAN	nuclear receptor subfamily 1, group D, member 1	73	Crucial for activation of GJA1. {ECO:0000250}.|Modulating.				cell differentiation (GO:0030154)|cellular response to lipopolysaccharide (GO:0071222)|circadian regulation of gene expression (GO:0032922)|circadian temperature homeostasis (GO:0060086)|gene expression (GO:0010467)|glycogen biosynthetic process (GO:0005978)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of receptor biosynthetic process (GO:0010871)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of bile acid biosynthetic process (GO:0070859)|positive regulation of transcription, DNA-templated (GO:0045893)|proteasomal protein catabolic process (GO:0010498)|regulation of cholesterol homeostasis (GO:2000188)|regulation of circadian rhythm (GO:0042752)|regulation of fat cell differentiation (GO:0045598)|regulation of gluconeogenesis by regulation of transcription from RNA polymerase II promoter (GO:0035947)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of lipid metabolic process (GO:0019216)|regulation of type B pancreatic cell proliferation (GO:0061469)|response to leptin (GO:0044321)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|heme binding (GO:0020037)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|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)|steroid hormone receptor activity (GO:0003707)|transcription corepressor activity (GO:0003714)|transcription corepressor binding (GO:0001222)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(5)|lung(2)|skin(1)|upper_aerodigestive_tract(2)	11	Colorectal(19;0.000442)					CACTCAGGCTGGGTGGAATGC	0.607													G|||	123	0.0245607	0.0908	0.0043	5008	,	,		18042	0.0		0.0	False		,,,				2504	0.0				p.P73P		Atlas-SNP	.											.	NR1D1	45	.	0			c.C219T						PASS	.	G		290,4116	160.3+/-192.7	5,280,1918	75.0	76.0	76.0		219	1.6	1.0	17	dbSNP_119	76	0,8600		0,0,4300	no	coding-synonymous	NR1D1	NM_021724.3		5,280,6218	AA,AG,GG		0.0,6.5819,2.2297		73/615	38253469	290,12716	2203	4300	6503	SO:0001819	synonymous_variant	9572	exon2			CAGGCTGGGTGGA	X72631	CCDS11361.1	17q11.2	2013-01-16			ENSG00000126368	ENSG00000126368		"""Nuclear hormone receptors"""	7962	protein-coding gene	gene with protein product		602408		THRAL		1971514	Standard	NM_021724		Approved	ear-1, hRev, Rev-ErbAalpha, THRA1	uc002htz.3	P20393	OTTHUMG00000133327	ENST00000246672.3:c.219C>T	17.37:g.38253469G>A		153.0	0.0	0		176.0	84.0	0.477273	NM_021724	Q0P5Z4|Q15304	Silent	SNP	ENST00000246672.3	37	CCDS11361.1																																																																																			G|0.979;A|0.021	0.021	strong		0.607	NR1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257135.1		
DDX51	317781	hgsc.bcm.edu	37	12	132625884	132625884	+	Missense_Mutation	SNP	C	C	T	rs142395492	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132625884C>T	ENST00000397333.3	-	8	1224	c.1186G>A	c.(1186-1188)Gag>Aag	p.E396K		NM_175066.3	NP_778236.2	Q8N8A6	DDX51_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 51	396	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(1)|lung(5)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.59e-08)|Epithelial(86;3.62e-07)|all cancers(50;2.13e-05)		GCGGGGTCCTCGCTCTGGAAG	0.682													C|||	46	0.0091853	0.0318	0.0043	5008	,	,		14725	0.0		0.001	False		,,,				2504	0.0				p.E396K		Atlas-SNP	.											.	DDX51	33	.	0			c.G1186A						PASS	.	C	LYS/GLU	117,3883		6,105,1889	43.0	54.0	51.0		1186	1.9	0.0	12	dbSNP_134	51	5,8245		0,5,4120	no	missense	DDX51	NM_175066.3	56	6,110,6009	TT,TC,CC		0.0606,2.925,0.9959	benign	396/667	132625884	122,12128	2000	4125	6125	SO:0001583	missense	317781	exon8			GGTCCTCGCTCTG	BC040185	CCDS41865.1	12q24.33	2005-10-12				ENSG00000185163		"""DEAD-boxes"""	20082	protein-coding gene	gene with protein product							Standard	NM_175066		Approved		uc001ujy.4	Q8N8A6		ENST00000397333.3:c.1186G>A	12.37:g.132625884C>T	ENSP00000380495:p.Glu396Lys	13.0	0.0	0		28.0	18.0	0.642857	NM_175066	A8MPT9|Q5CZ71|Q8IXK5|Q96ED1	Missense_Mutation	SNP	ENST00000397333.3	37	CCDS41865.1	18	0.008241758241758242	14	0.028455284552845527	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	11.56	1.674865	0.29783	0.02925	6.06E-4	ENSG00000185163	ENST00000397333	T	0.12255	2.7	4.79	1.92	0.25849	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.770658	0.12492	N	0.464146	T	0.01661	0.0053	N	0.08118	0	0.09310	N	1	B	0.24721	0.11	B	0.20184	0.028	T	0.44221	-0.9342	10	0.14252	T	0.57	-14.9068	5.9048	0.18986	0.0:0.6566:0.1608:0.1826	.	396	Q8N8A6	DDX51_HUMAN	K	396	ENSP00000380495:E396K	ENSP00000380495:E396K	E	-	1	0	DDX51	131191837	0.000000	0.05858	0.005000	0.12908	0.004000	0.04260	0.982000	0.29539	0.438000	0.26450	-0.229000	0.12294	GAG	C|0.992;T|0.008	0.008	strong		0.682	DDX51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398978.1	NM_175066	
NCAM2	4685	hgsc.bcm.edu	37	21	22790831	22790831	+	Silent	SNP	T	T	C	rs986371	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:22790831T>C	ENST00000400546.1	+	11	1671	c.1422T>C	c.(1420-1422)aaT>aaC	p.N474N	NCAM2_ENST00000284894.7_Silent_p.N332N	NM_004540.3	NP_004531.2	O15394	NCAM2_HUMAN	neural cell adhesion molecule 2	474	Ig-like C2-type 5.				axonal fasciculation (GO:0007413)|neuron cell-cell adhesion (GO:0007158)|sensory perception of smell (GO:0007608)	axon (GO:0030424)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(4)|cervix(2)|endometrium(8)|kidney(6)|large_intestine(22)|liver(4)|lung(49)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	108		Lung NSC(9;0.195)		all cancers(11;0.00102)|OV - Ovarian serous cystadenocarcinoma(11;0.00121)|Epithelial(23;0.00147)|Colorectal(24;0.174)		GACGCTATAATTGCACAGCCA	0.299													T|||	30	0.00599042	0.0204	0.0043	5008	,	,		16315	0.0		0.0	False		,,,				2504	0.0				p.N474N		Atlas-SNP	.											.	NCAM2	220	.	0			c.T1422C						PASS	.	T		102,3546		0,102,1722	110.0	109.0	109.0		1422	-3.3	1.0	21	dbSNP_86	109	0,8166		0,0,4083	no	coding-synonymous	NCAM2	NM_004540.3		0,102,5805	CC,CT,TT		0.0,2.7961,0.8634		474/838	22790831	102,11712	1824	4083	5907	SO:0001819	synonymous_variant	4685	exon11			CTATAATTGCACA		CCDS42910.1	21q21	2013-02-11			ENSG00000154654	ENSG00000154654		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7657	protein-coding gene	gene with protein product		602040				9226371	Standard	NM_004540		Approved	NCAM21, MGC51008	uc002yld.2	O15394	OTTHUMG00000078121	ENST00000400546.1:c.1422T>C	21.37:g.22790831T>C		237.0	0.0	0		290.0	139.0	0.47931	NM_004540	A8MQ06|B7Z841|Q7Z7F2	Silent	SNP	ENST00000400546.1	37	CCDS42910.1																																																																																			T|0.992;C|0.008	0.008	strong		0.299	NCAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000170915.1	NM_004540	
SIGLEC1	6614	hgsc.bcm.edu	37	20	3674170	3674170	+	Silent	SNP	G	G	A	rs61734520	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:3674170G>A	ENST00000344754.4	-	13	3431	c.3432C>T	c.(3430-3432)gcC>gcT	p.A1144A	SIGLEC1_ENST00000202578.4_Silent_p.A1144A	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	1144	Ig-like C2-type 11.				cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						GGTAGGAGGTGGCATCCCTGA	0.662													G|||	103	0.0205671	0.0772	0.0014	5008	,	,		15685	0.0		0.0	False		,,,				2504	0.0				p.A1144A		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.C3432T						PASS	.	G		233,4173	136.9+/-172.8	7,219,1977	53.0	47.0	49.0		3432	-3.0	0.7	20	dbSNP_129	49	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	SIGLEC1	NM_023068.3		7,223,6273	AA,AG,GG		0.0465,5.2882,1.8222		1144/1710	3674170	237,12769	2203	4300	6503	SO:0001819	synonymous_variant	6614	exon13			GGAGGTGGCATCC	AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	11127	protein-coding gene	gene with protein product		600751	"""sialoadhesin"""	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.3432C>T	20.37:g.3674170G>A		130.0	0.0	0		119.0	69.0	0.579832	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Silent	SNP	ENST00000344754.4	37	CCDS13060.1																																																																																			G|0.980;A|0.020	0.020	strong		0.662	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068	
NAV2	89797	hgsc.bcm.edu	37	11	20070349	20070349	+	Silent	SNP	C	C	T	rs78806867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:20070349C>T	ENST00000396087.3	+	16	4146	c.4047C>T	c.(4045-4047)tcC>tcT	p.S1349S	NAV2_ENST00000527559.2_Silent_p.S1278S|NAV2_ENST00000311043.8_Silent_p.S412S|NAV2_ENST00000533917.1_Silent_p.S412S|NAV2_ENST00000360655.4_Silent_p.S1262S|NAV2_ENST00000540292.1_Silent_p.S1280S|NAV2_ENST00000396085.1_Silent_p.S1326S|NAV2_ENST00000349880.4_Silent_p.S1326S|NAV2-AS2_ENST00000533767.1_RNA	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	1349					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						TGGTCATCTCCAATCCTCATG	0.522													C|||	63	0.0125799	0.0454	0.0014	5008	,	,		21187	0.0		0.002	False		,,,				2504	0.0				p.S1349S		Atlas-SNP	.											.	NAV2	255	.	0			c.C4047T						PASS	.	C	,,,	145,4261	101.2+/-139.8	5,135,2063	136.0	113.0	121.0		3786,1236,3978,3978	1.9	1.0	11	dbSNP_131	121	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NAV2	NM_001111018.1,NM_001111019.1,NM_145117.4,NM_182964.5	,,,	5,136,6362	TT,TC,CC		0.0116,3.291,1.1226	,,,	1262/2366,412/1494,1326/2430,1326/2433	20070349	146,12860	2203	4300	6503	SO:0001819	synonymous_variant	89797	exon16			CATCTCCAATCCT	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.4047C>T	11.37:g.20070349C>T		141.0	0.0	0		155.0	76.0	0.490323	NM_001244963	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Silent	SNP	ENST00000396087.3	37	CCDS58126.1																																																																																			C|0.988;T|0.012	0.012	strong		0.522	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
ANKRD16	54522	hgsc.bcm.edu	37	10	5920244	5920244	+	Missense_Mutation	SNP	T	T	C	rs61729846	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:5920244T>C	ENST00000380094.5	-	7	1478	c.935A>G	c.(934-936)cAt>cGt	p.H312R	ANKRD16_ENST00000191063.8_Missense_Mutation_p.I286V|ANKRD16_ENST00000380092.4_Missense_Mutation_p.H312R	NM_019046.2	NP_061919.1	Q6P6B7	ANR16_HUMAN	ankyrin repeat domain 16	312										breast(1)|endometrium(1)|large_intestine(5)|lung(3)|stomach(2)	12						ACAGGCCAGATGCAGGGCTGA	0.502													T|||	310	0.061901	0.2247	0.0173	5008	,	,		19150	0.0		0.001	False		,,,				2504	0.0				p.H312R		Atlas-SNP	.											.	ANKRD16	32	.	0			c.A935G						PASS	.	T	ARG/HIS,VAL/ILE,ARG/HIS	885,3521	343.8+/-307.8	98,689,1416	67.0	66.0	66.0		935,856,935	5.0	1.0	10	dbSNP_129	66	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense,missense	ANKRD16	NM_001009941.2,NM_001009943.2,NM_019046.2	29,29,29	98,694,5711	CC,CT,TT		0.0581,20.0862,6.843	probably-damaging,probably-damaging,probably-damaging	312/362,286/305,312/362	5920244	890,12116	2203	4300	6503	SO:0001583	missense	54522	exon7			GCCAGATGCAGGG	AL137614	CCDS31136.1, CCDS31137.1	10p15.1	2013-01-10			ENSG00000134461	ENSG00000134461		"""Ankyrin repeat domain containing"""	23471	protein-coding gene	gene with protein product							Standard	NM_019046		Approved	DKFZP434N1511	uc010qat.2	Q6P6B7	OTTHUMG00000017610	ENST00000380094.5:c.935A>G	10.37:g.5920244T>C	ENSP00000369436:p.His312Arg	33.0	0.0	0		47.0	30.0	0.638298	NM_001009941	A6NEF0|F8WEI4|Q9NT01	Missense_Mutation	SNP	ENST00000380094.5	37	CCDS31136.1	102|102	0.046703296703296704|0.046703296703296704	96|96	0.1951219512195122|0.1951219512195122	6|6	0.016574585635359115|0.016574585635359115	0|0	0.0|0.0	0|0	0.0|0.0	T|T	12.88|12.88	2.071823|2.071823	0.36566|0.36566	0.200862|0.200862	5.81E-4|5.81E-4	ENSG00000134461|ENSG00000134461	ENST00000380094;ENST00000380092|ENST00000191063	T;T|T	0.71461|0.58797	-0.57;-0.57|0.31	4.97|4.97	4.97|4.97	0.65823|0.65823	Ankyrin repeat-containing domain (4);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.00144|0.00144	0.0004|0.0004	M|M	0.85099|0.85099	2.735|2.735	0.35597|0.35597	P|P	0.192465|0.192465	D|B	0.89917|0.19073	1.0|0.033	D|B	0.91635|0.21917	0.999|0.037	T|T	0.20672|0.20672	-1.0268|-1.0268	9|8	0.51188|0.62326	T|D	0.08|0.03	-15.6176|-15.6176	13.4896|13.4896	0.61386|0.61386	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	312|286	Q6P6B7|F8WEI4	ANR16_HUMAN|.	R|V	312|286	ENSP00000369436:H312R;ENSP00000369434:H312R|ENSP00000352361:I286V	ENSP00000369434:H312R|ENSP00000352361:I286V	H|I	-|-	2|1	0|0	ANKRD16|ANKRD16	5960250|5960250	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.852000|0.852000	0.48524|0.48524	6.409000|6.409000	0.73289|0.73289	1.858000|1.858000	0.53909|0.53909	0.254000|0.254000	0.18369|0.18369	CAT|ATC	T|0.928;C|0.072	0.072	strong		0.502	ANKRD16-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046611.2	XM_166138	
FASTKD1	79675	hgsc.bcm.edu	37	2	170403106	170403106	+	Silent	SNP	G	G	A	rs16857030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170403106G>A	ENST00000453153.2	-	8	1669	c.1323C>T	c.(1321-1323)gcC>gcT	p.A441A	FASTKD1_ENST00000453929.2_Silent_p.A441A	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	441					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(5)|large_intestine(10)|lung(9)|ovary(4)|prostate(3)	37						GTGGTAAAACGGCTTCAATTC	0.428													G|||	494	0.0986422	0.2496	0.0764	5008	,	,		19180	0.003		0.0636	False		,,,				2504	0.045				p.A441A		Atlas-SNP	.											.	FASTKD1	86	.	0			c.C1323T						PASS	.	G		878,3528	338.9+/-305.5	90,698,1415	70.0	72.0	72.0		1323	-1.6	0.9	2	dbSNP_123	72	483,8117	139.5+/-196.2	10,463,3827	no	coding-synonymous	FASTKD1	NM_024622.3		100,1161,5242	AA,AG,GG		5.6163,19.9274,10.4644		441/848	170403106	1361,11645	2203	4300	6503	SO:0001819	synonymous_variant	79675	exon8			TAAAACGGCTTCA	AL832058	CCDS33318.1, CCDS63051.1	2q31.1	2008-02-05			ENSG00000138399	ENSG00000138399			26150	protein-coding gene	gene with protein product						11347906	Standard	NM_024622		Approved	FLJ21901	uc002uev.4	Q53R41	OTTHUMG00000154953	ENST00000453153.2:c.1323C>T	2.37:g.170403106G>A		228.0	0.0	0		173.0	70.0	0.404624	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Silent	SNP	ENST00000453153.2	37	CCDS33318.1																																																																																			G|0.902;A|0.098	0.098	strong		0.428	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622	
MTMR3	8897	hgsc.bcm.edu	37	22	30403307	30403307	+	Splice_Site	SNP	C	C	T	rs146523702	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30403307C>T	ENST00000401950.2	+	10	1218	c.876C>T	c.(874-876)ttC>ttT	p.F292F	MTMR3_ENST00000406629.1_Splice_Site_p.F292F|MTMR3_ENST00000351488.3_Splice_Site_p.F292F|MTMR3_ENST00000333027.3_Splice_Site_p.F292F|CTA-85E5.10_ENST00000429350.1_RNA|MTMR3_ENST00000323630.5_Splice_Site_p.F156F	NM_021090.3	NP_066576.1	Q13615	MTMR3_HUMAN	myotubularin related protein 3	292	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|large_intestine(3)|ovary(2)|skin(8)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(5;0.00204)|Epithelial(10;0.06)|all cancers(5;0.107)			ACGTGGAGTTCGGTAAGGTGC	0.458													C|||	12	0.00239617	0.0091	0.0	5008	,	,		21375	0.0		0.0	False		,,,				2504	0.0				p.F292F		Atlas-SNP	.											MTMR3_ENST00000401950,NS,lymphoid_neoplasm,+2,1	MTMR3	106	1	0			c.C876T						PASS	.	C	,,	47,4359	46.0+/-80.4	0,47,2156	46.0	40.0	42.0		876,876,876	-3.0	1.0	22	dbSNP_134	42	2,8598	2.2+/-6.3	0,2,4298	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	MTMR3	NM_021090.3,NM_153050.2,NM_153051.2	,,	0,49,6454	TT,TC,CC		0.0233,1.0667,0.3767	,,	292/1199,292/1171,292/1162	30403307	49,12957	2203	4300	6503	SO:0001630	splice_region_variant	8897	exon10			GGAGTTCGGTAAG	U58034	CCDS13870.1, CCDS13871.1, CCDS46682.1	22q12.2	2011-06-09			ENSG00000100330	ENSG00000100330		"""Zinc fingers, FYVE domain containing"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7451	protein-coding gene	gene with protein product		603558				8640223, 9736772	Standard	NM_153050		Approved	KIAA0371, ZFYVE10, FYVE-DSP1	uc003agv.4	Q13615	OTTHUMG00000151278	ENST00000401950.2:c.877+1C>T	22.37:g.30403307C>T		63.0	0.0	0		64.0	64.0	1	NM_021090	A5PL26|A7MD32|Q9NYN5|Q9NYN6|Q9UDX6|Q9UEG3	Silent	SNP	ENST00000401950.2	37	CCDS13870.1																																																																																			C|0.997;T|0.003	0.003	strong		0.458	MTMR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322066.1	NM_021090	Silent
CYP4F11	57834	hgsc.bcm.edu	37	19	16024605	16024605	+	Silent	SNP	C	C	G	rs75284625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16024605C>G	ENST00000402119.4	-	12	1938	c.1512G>C	c.(1510-1512)ctG>ctC	p.L504L	CYP4F11_ENST00000326742.8_3'UTR|CYP4F11_ENST00000248041.8_Silent_p.L504L|CYP4F11_ENST00000591841.1_Silent_p.L179L	NM_021187.3	NP_067010.3			cytochrome P450, family 4, subfamily F, polypeptide 11											NS(1)|breast(3)|endometrium(4)|large_intestine(2)|lung(11)|ovary(1)|skin(3)	25						CGCGCAATATCAGCTCGGGTT	0.632													.|||	36	0.0071885	0.0257	0.0029	5008	,	,		15991	0.0		0.0	False		,,,				2504	0.0				p.L504L		Atlas-SNP	.											.	CYP4F11	83	.	0			c.G1512C						PASS	.	C	,	190,4216	120.8+/-158.4	8,174,2021	62.0	57.0	59.0		1512,1512	1.6	0.2	19	dbSNP_132	59	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	CYP4F11	NM_001128932.1,NM_021187.3	,	8,175,6320	GG,GC,CC		0.0116,4.3123,1.4686	,	504/525,504/525	16024605	191,12815	2203	4300	6503	SO:0001819	synonymous_variant	57834	exon13			CAATATCAGCTCG	AF236085	CCDS12337.1	19p13.1	2011-07-29	2003-01-14		ENSG00000171903	ENSG00000171903		"""Cytochrome P450s"""	13265	protein-coding gene	gene with protein product		611517	"""cytochrome P450, subfamily IVF, polypeptide 11"""			10964514, 9068972	Standard	NM_021187		Approved		uc002nbu.2	Q9HBI6		ENST00000402119.4:c.1512G>C	19.37:g.16024605C>G		130.0	0.0	0		150.0	81.0	0.54	NM_001128932		Silent	SNP	ENST00000402119.4	37	CCDS12337.1																																																																																			C|0.990;G|0.010	0.010	strong		0.632	CYP4F11-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460385.2	NM_021187	
CAAP1	79886	hgsc.bcm.edu	37	9	26842506	26842506	+	Silent	SNP	G	G	A	rs10967558	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:26842506G>A	ENST00000333916.5	-	6	967	c.879C>T	c.(877-879)gaC>gaT	p.D293D	CAAP1_ENST00000535437.1_Silent_p.D148D|CAAP1_ENST00000520187.1_3'UTR	NM_001167575.1|NM_024828.3	NP_001161047.1|NP_079104.3	Q9H8G2	CAAP1_HUMAN	caspase activity and apoptosis inhibitor 1	293					apoptotic process (GO:0006915)												CTTTCTCCAGGTCATCTATCT	0.502													G|||	242	0.0483227	0.1747	0.0144	5008	,	,		18187	0.0		0.001	False		,,,				2504	0.0				p.D293D		Atlas-SNP	.											.	.	.	.	0			c.C879T						PASS	.	G	,	585,3821	259.5+/-263.1	32,521,1650	244.0	228.0	233.0		444,879	2.9	1.0	9	dbSNP_120	233	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous	C9orf82	NM_001167575.1,NM_024828.3	,	32,525,5946	AA,AG,GG		0.0465,13.2773,4.5287	,	148/217,293/362	26842506	589,12417	2203	4300	6503	SO:0001819	synonymous_variant	79886	exon6			CTCCAGGTCATCT	BC014658	CCDS6516.1	9p21.2	2012-04-20	2012-04-20	2012-04-20	ENSG00000120159	ENSG00000120159			25834	protein-coding gene	gene with protein product	"""conserved anti-apoptotic protein"""		"""chromosome 9 open reading frame 82"""	C9orf82		21980415	Standard	NM_024828		Approved	FLJ13657, CAAP	uc003zqc.3	Q9H8G2	OTTHUMG00000019706	ENST00000333916.5:c.879C>T	9.37:g.26842506G>A		289.0	0.0	0		295.0	140.0	0.474576	NM_024828	B4DWT4|D3DRK4|Q5VY32|Q6IPE6|Q96C59	Silent	SNP	ENST00000333916.5	37	CCDS6516.1																																																																																			G|0.941;A|0.059	0.059	strong		0.502	CAAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051954.1	NM_024828	
TMEM203	94107	hgsc.bcm.edu	37	9	140099675	140099675	+	Silent	SNP	G	G	A	rs113235610	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140099675G>A	ENST00000343666.5	-	1	415	c.192C>T	c.(190-192)acC>acT	p.T64T	NDOR1_ENST00000371521.4_5'Flank|TMEM203_ENST00000537254.1_Silent_p.T64T|NDOR1_ENST00000427047.2_5'Flank|TPRN_ENST00000541945.1_5'Flank|NDOR1_ENST00000458322.2_5'Flank|NDOR1_ENST00000344894.5_5'Flank	NM_053045.1	NP_444273.1	Q969S6	TM203_HUMAN	transmembrane protein 203	64						integral component of membrane (GO:0016021)				central_nervous_system(1)|kidney(1)	2	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		ACACGATGGTGGTGAAGTAGG	0.617													G|||	33	0.00658946	0.0212	0.0072	5008	,	,		15733	0.0		0.0	False		,,,				2504	0.0				p.T64T		Atlas-SNP	.											TMEM203,NS,carcinoma,0,1	TMEM203	8	1	0			c.C192T						PASS	.	G		83,4319	70.3+/-108.2	1,81,2119	45.0	47.0	46.0		192	3.1	1.0	9	dbSNP_132	46	0,8584		0,0,4292	no	coding-synonymous	TMEM203	NM_053045.1		1,81,6411	AA,AG,GG		0.0,1.8855,0.6391		64/137	140099675	83,12903	2201	4292	6493	SO:0001819	synonymous_variant	94107	exon1			GATGGTGGTGAAG	BC009283	CCDS35185.1	9q34.3	2007-12-18			ENSG00000187713	ENSG00000187713			28217	protein-coding gene	gene with protein product	"""HBeAg-binding protein 1"""					12477932	Standard	NM_053045		Approved	MGC14327, HBEBP1	uc004clv.3	Q969S6	OTTHUMG00000020985	ENST00000343666.5:c.192C>T	9.37:g.140099675G>A		77.0	0.0	0		80.0	56.0	0.7	NM_053045	Q6NW08	Silent	SNP	ENST00000343666.5	37	CCDS35185.1																																																																																			G|0.992;A|0.008	0.008	strong		0.617	TMEM203-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055325.2	NM_053045	
BPTF	2186	hgsc.bcm.edu	37	17	65914911	65914911	+	Silent	SNP	T	T	C	rs80201495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:65914911T>C	ENST00000321892.4	+	14	5824	c.5763T>C	c.(5761-5763)gaT>gaC	p.D1921D	BPTF_ENST00000424123.3_Silent_p.D1782D|BPTF_ENST00000335221.5_Silent_p.D1921D|BPTF_ENST00000306378.6_Silent_p.D1795D			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	1921					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			GATGGGATGATATGGCGGCCA	0.458													C|||	95	0.0189696	0.0666	0.0086	5008	,	,		16414	0.0		0.001	False		,,,				2504	0.0				p.D1921D		Atlas-SNP	.											.	BPTF	415	.	0			c.T5763C						PASS	.	C	,	247,4159	804.1+/-415.7	7,233,1963	149.0	145.0	147.0		5763,5385	3.2	1.0	17	dbSNP_131	147	8,8592	818.9+/-406.8	0,8,4292	no	coding-synonymous,coding-synonymous	BPTF	NM_004459.6,NM_182641.3	,	7,241,6255	CC,CT,TT		0.093,5.606,1.9606	,	1921/2904,1795/2921	65914911	255,12751	2203	4300	6503	SO:0001819	synonymous_variant	2186	exon14			GGATGATATGGCG	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"""Zinc fingers, PHD-type"""	3581	protein-coding gene	gene with protein product		601819	"""fetal Alzheimer antigen"""	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.5763T>C	17.37:g.65914911T>C		153.0	0.0	0		148.0	76.0	0.513514	NM_004459	Q6NX67|Q7Z7D6|Q9UIG2	Silent	SNP	ENST00000321892.4	37																																																																																				T|0.981;C|0.019	0.019	strong		0.458	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459	
GOLGA3	2802	hgsc.bcm.edu	37	12	133398638	133398638	+	Missense_Mutation	SNP	G	G	A	rs141852501	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:133398638G>A	ENST00000450791.2	-	1	260	c.77C>T	c.(76-78)gCc>gTc	p.A26V	GOLGA3_ENST00000204726.3_Missense_Mutation_p.A26V|GOLGA3_ENST00000537452.1_Missense_Mutation_p.A26V|GOLGA3_ENST00000545875.1_Missense_Mutation_p.A26V|GOLGA3_ENST00000456883.2_Missense_Mutation_p.A26V			Q08378	GOGA3_HUMAN	golgin A3	26	Pro-rich.				intra-Golgi vesicle-mediated transport (GO:0006891)	cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		CTTCAGTGGGGCCTCGGGGAG	0.647													G|||	8	0.00159744	0.0061	0.0	5008	,	,		14431	0.0		0.0	False		,,,				2504	0.0				p.A26V		Atlas-SNP	.											.	GOLGA3	234	.	0			c.C77T						PASS	.	G	VAL/ALA,VAL/ALA	28,4378	32.6+/-62.9	0,28,2175	44.0	47.0	46.0		77,77	-3.7	0.0	12	dbSNP_134	46	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	GOLGA3	NM_001172557.1,NM_005895.3	64,64	0,29,6474	AA,AG,GG		0.0116,0.6355,0.223	benign,benign	26/1135,26/1499	133398638	29,12977	2203	4300	6503	SO:0001583	missense	2802	exon2			AGTGGGGCCTCGG	AF485338	CCDS9281.1, CCDS53846.1	12q24.33	2010-02-12	2010-02-12		ENSG00000090615	ENSG00000090615			4426	protein-coding gene	gene with protein product	"""SY2/SY10 protein"", ""Golgi complex-associated protein of 170 kD"""	602581	"""golgi autoantigen, golgin subfamily a, 3"""			8315394, 15829563	Standard	NM_001172557		Approved	golgin-160, GCP170, MEA-2	uc001ukz.1	Q08378	OTTHUMG00000168023	ENST00000450791.2:c.77C>T	12.37:g.133398638G>A	ENSP00000410378:p.Ala26Val	112.0	0.0	0		111.0	58.0	0.522523	NM_001172557	A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	Missense_Mutation	SNP	ENST00000450791.2	37	CCDS9281.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	G	11.20	1.568083	0.28003	0.006355	1.16E-4	ENSG00000090615	ENST00000204726;ENST00000450791;ENST00000456883;ENST00000537452;ENST00000545875	T;T;T;T;T	0.32988	1.86;1.86;1.86;1.43;1.43	5.4	-3.7	0.04437	.	1.125330	0.06702	N	0.771525	T	0.16896	0.0406	L	0.44542	1.39	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.002;0.001	T	0.33574	-0.9863	10	0.41790	T	0.15	.	7.4989	0.27505	0.069:0.4444:0.3435:0.1431	.	26;26;26	Q08378-4;Q08378-2;Q08378	.;.;GOGA3_HUMAN	V	26	ENSP00000204726:A26V;ENSP00000410378:A26V;ENSP00000409303:A26V;ENSP00000442143:A26V;ENSP00000442603:A26V	ENSP00000204726:A26V	A	-	2	0	GOLGA3	131908711	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.762000	0.04745	-0.565000	0.06061	-2.362000	0.00238	GCC	G|0.997;A|0.003	0.003	strong		0.647	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397569.2	NM_005895	
KRTAP13-4	284827	hgsc.bcm.edu	37	21	31802621	31802621	+	Missense_Mutation	SNP	T	T	A	rs73899382	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31802621T>A	ENST00000334068.2	+	1	50	c.28T>A	c.(28-30)Ttc>Atc	p.F10I		NM_181600.1	NP_853631.1	Q3LI77	KR134_HUMAN	keratin associated protein 13-4	10						intermediate filament (GO:0005882)				NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	15						CTCTAGAAACTTCTCCTCCCG	0.542													-|||	32	0.00638978	0.0234	0.0014	5008	,	,		18495	0.0		0.0	False		,,,				2504	0.0				p.F10I	NSCLC(196;2401 3038 18004 35753)	Atlas-SNP	.											.	KRTAP13-4	46	.	0			c.T28A						PASS	.	T	ILE/PHE	90,4316	74.7+/-112.8	1,88,2114	112.0	113.0	113.0		28	2.5	1.0	21	dbSNP_130	113	0,8600		0,0,4300	yes	missense	KRTAP13-4	NM_181600.1	21	1,88,6414	AA,AT,TT		0.0,2.0427,0.692	probably-damaging	10/161	31802621	90,12916	2203	4300	6503	SO:0001583	missense	284827	exon1			AGAAACTTCTCCT	AP001708	CCDS13592.1	21q22.1	2006-03-13			ENSG00000186971	ENSG00000186971		"""Keratin associated proteins"""	18926	protein-coding gene	gene with protein product						12359730	Standard	NM_181600		Approved	KAP13.4	uc011acw.2	Q3LI77	OTTHUMG00000057770	ENST00000334068.2:c.28T>A	21.37:g.31802621T>A	ENSP00000334834:p.Phe10Ile	206.0	0.0	0		238.0	102.0	0.428571	NM_181600	A2RRL3	Missense_Mutation	SNP	ENST00000334068.2	37	CCDS13592.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	t	14.16	2.452391	0.43531	0.020427	0.0	ENSG00000186971	ENST00000334068	T	0.03496	3.91	4.95	2.47	0.30058	.	0.000000	0.46442	D	0.000291	T	0.06096	0.0158	M	0.87971	2.92	0.26406	N	0.976344	D	0.89917	1.0	D	0.91635	0.999	T	0.01345	-1.1379	10	0.66056	D	0.02	.	9.5117	0.39080	0.0:0.0:0.3442:0.6558	.	10	Q3LI77	KR134_HUMAN	I	10	ENSP00000334834:F10I	ENSP00000334834:F10I	F	+	1	0	KRTAP13-4	30724492	0.999000	0.42202	0.996000	0.52242	0.025000	0.11179	1.211000	0.32382	0.388000	0.25054	-0.321000	0.08615	TTC	T|0.992;A|0.008	0.008	strong		0.542	KRTAP13-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128222.1		
ATPAF2	91647	hgsc.bcm.edu	37	17	17924447	17924447	+	Missense_Mutation	SNP	T	T	C	rs34607655	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:17924447T>C	ENST00000474627.3	-	7	876	c.722A>G	c.(721-723)gAg>gGg	p.E241G	ATPAF2_ENST00000469327.1_5'UTR|ATPAF2_ENST00000585101.1_Intron	NM_145691.3	NP_663729.1	Q8N5M1	ATPF2_HUMAN	ATP synthase mitochondrial F1 complex assembly factor 2	241					proton-transporting ATP synthase complex assembly (GO:0043461)	mitochondrion (GO:0005739)|nuclear speck (GO:0016607)				breast(2)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|urinary_tract(1)	8	all_neural(463;0.228)					CTGGTACTCCTCCTCCAGGCG	0.577													T|||	19	0.00379393	0.0136	0.0014	5008	,	,		20341	0.0		0.0	False		,,,				2504	0.0				p.E241G		Atlas-SNP	.											.	ATPAF2	15	.	0			c.A722G						PASS	.	T	GLY/GLU	39,4367	41.6+/-74.8	0,39,2164	43.0	35.0	38.0		722	5.7	1.0	17	dbSNP_126	38	0,8600		0,0,4300	yes	missense	ATPAF2	NM_145691.3	98	0,39,6464	CC,CT,TT		0.0,0.8852,0.2999	probably-damaging	241/290	17924447	39,12967	2203	4300	6503	SO:0001583	missense	91647	exon7			TACTCCTCCTCCA	AF052185	CCDS32585.1	17p11.2	2012-10-12			ENSG00000171953	ENSG00000171953		"""Mitochondrial respiratory chain complex assembly factors"""	18802	protein-coding gene	gene with protein product		608918				11410595, 11997338	Standard	NM_145691		Approved	Atp12p, ATP12, LP3663, MGC29736	uc002gse.1	Q8N5M1	OTTHUMG00000059354	ENST00000474627.3:c.722A>G	17.37:g.17924447T>C	ENSP00000417190:p.Glu241Gly	81.0	0.0	0		107.0	56.0	0.523364	NM_145691	A6NDE5|A8K2J2|Q6XYC7	Missense_Mutation	SNP	ENST00000474627.3	37	CCDS32585.1	8	0.003663003663003663	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	T	28.0	4.877445	0.91664	0.008852	0.0	ENSG00000171953	ENST00000474627	T	0.81330	-1.48	5.7	5.7	0.88788	ATPase assembly, ATP12, domain (1);	0.000000	0.85682	D	0.000000	D	0.84982	0.5593	M	0.88105	2.93	0.80722	D	1	D	0.57257	0.979	P	0.52554	0.702	D	0.88744	0.3245	10	0.66056	D	0.02	-18.6937	15.9482	0.79809	0.0:0.0:0.0:1.0	rs34607655	241	Q8N5M1	ATPF2_HUMAN	G	241	ENSP00000417190:E241G	ENSP00000417190:E241G	E	-	2	0	ATPAF2	17865172	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.945000	0.87732	2.170000	0.68504	0.528000	0.53228	GAG	T|0.996;C|0.004	0.004	strong		0.577	ATPAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131934.3	NM_145691	
LYST	1130	hgsc.bcm.edu	37	1	235933535	235933535	+	Missense_Mutation	SNP	C	C	G	rs6665568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:235933535C>G	ENST00000389794.3	-	20	6021	c.5847G>C	c.(5845-5847)caG>caC	p.Q1949H	LYST_ENST00000536965.1_3'UTR|LYST_ENST00000389793.2_Missense_Mutation_p.Q1949H			Q99698	LYST_HUMAN	lysosomal trafficking regulator	1949			Q -> H (in dbSNP:rs6665568).		blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			TAAACATCTGCTGGTGGTGAT	0.388													C|||	308	0.0615016	0.2194	0.0245	5008	,	,		17686	0.0		0.001	False		,,,				2504	0.0				p.Q1949H		Atlas-SNP	.											.	LYST	370	.	0			c.G5847C						PASS	.	C	HIS/GLN	828,3578	327.5+/-300.1	76,676,1451	128.0	132.0	131.0		5847	0.8	0.7	1	dbSNP_116	131	10,8590	6.4+/-24.3	0,10,4290	yes	missense	LYST	NM_000081.2	24	76,686,5741	GG,GC,CC		0.1163,18.7926,6.4432	benign	1949/3802	235933535	838,12168	2203	4300	6503	SO:0001583	missense	1130	exon20			CATCTGCTGGTGG	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"""WD repeat domain containing"""	1968	protein-coding gene	gene with protein product		606897	"""Chediak-Higashi syndrome 1"""	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.5847G>C	1.37:g.235933535C>G	ENSP00000374444:p.Gln1949His	172.0	0.0	0		154.0	74.0	0.480519	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Missense_Mutation	SNP	ENST00000389794.3	37	CCDS31062.1	115	0.052655677655677656	108	0.21951219512195122	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	C	8.986	0.976514	0.18736	0.187926	0.001163	ENSG00000143669	ENST00000389794;ENST00000389793	T;T	0.61158	0.13;0.13	5.48	0.809	0.18725	.	0.630262	0.18067	N	0.152750	T	0.00012	0.0000	N	0.17082	0.46	0.09310	P	1.0	B	0.02656	0.0	B	0.04013	0.001	T	0.11966	-1.0566	9	0.13853	T	0.58	.	2.9878	0.05973	0.217:0.4875:0.1067:0.1888	rs6665568;rs52790740;rs6665568	1949	Q99698	LYST_HUMAN	H	1949	ENSP00000374444:Q1949H;ENSP00000374443:Q1949H	ENSP00000374443:Q1949H	Q	-	3	2	LYST	234000158	0.152000	0.22762	0.656000	0.29637	0.957000	0.61999	-0.438000	0.06905	0.266000	0.21894	0.650000	0.86243	CAG	C|0.943;G|0.057	0.057	strong		0.388	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5		
ABCA9	10350	hgsc.bcm.edu	37	17	67031882	67031882	+	Silent	SNP	A	A	G	rs16973534	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:67031882A>G	ENST00000340001.4	-	7	1072	c.861T>C	c.(859-861)ctT>ctC	p.L287L	ABCA9_ENST00000453985.2_Silent_p.L287L|ABCA9_ENST00000370732.2_Silent_p.L287L	NM_080283.3	NP_525022.2	Q8IUA7	ABCA9_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 9	287					transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			NS(2)|breast(4)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(21)|lung(35)|ovary(4)|prostate(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	91	Breast(10;1.47e-12)					ATTTTACAATAAGAGCCATTA	0.423													A|||	141	0.028155	0.1036	0.0058	5008	,	,		16263	0.0		0.0	False		,,,				2504	0.0				p.L287L		Atlas-SNP	.											.	ABCA9	192	.	0			c.T861C						PASS	.	A		442,3964	213.8+/-233.3	27,388,1788	71.0	67.0	68.0		861	-1.6	0.0	17	dbSNP_123	68	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	ABCA9	NM_080283.3		27,391,6085	GG,GA,AA		0.0349,10.0318,3.4215		287/1625	67031882	445,12561	2203	4300	6503	SO:0001819	synonymous_variant	10350	exon7			TACAATAAGAGCC	AF423307	CCDS11681.1	17q24	2012-03-14			ENSG00000154258	ENSG00000154258		"""ATP binding cassette transporters / subfamily A"""	39	protein-coding gene	gene with protein product		612507					Standard	XM_005256934		Approved	EST640918	uc002jhu.3	Q8IUA7	OTTHUMG00000140371	ENST00000340001.4:c.861T>C	17.37:g.67031882A>G		435.0	0.0	0		430.0	196.0	0.455814	NM_080283	Q6P655|Q8N2S4|Q8WWZ5|Q96MD8	Silent	SNP	ENST00000340001.4	37	CCDS11681.1																																																																																			A|0.970;G|0.030	0.030	strong		0.423	ABCA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277072.2	NM_172386	
ASH1L	55870	hgsc.bcm.edu	37	1	155451343	155451343	+	Missense_Mutation	SNP	A	A	C	rs114218266	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:155451343A>C	ENST00000368346.3	-	3	1957	c.1318T>G	c.(1318-1320)Tgt>Ggt	p.C440G	ASH1L_ENST00000392403.3_Missense_Mutation_p.C440G|ASH1L_ENST00000548830.1_3'UTR			Q9NR48	ASH1L_HUMAN	ash1 (absent, small, or homeotic)-like (Drosophila)	440					cell-cell signaling (GO:0007267)|DNA packaging (GO:0006323)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|tight junction (GO:0005923)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(13)|large_intestine(28)|lung(39)|ovary(2)|pancreas(1)|prostate(6)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(4)	124	Hepatocellular(266;0.0997)|all_neural(408;0.129)|all_hematologic(923;0.145)		Epithelial(20;1.74e-08)|all cancers(21;3.29e-08)|BRCA - Breast invasive adenocarcinoma(34;0.021)			TTTGTACTACAAGAAGCCTTA	0.423													A|||	103	0.0205671	0.0734	0.0058	5008	,	,		19464	0.002		0.0	False		,,,				2504	0.0				p.C440G		Atlas-SNP	.											.	ASH1L	279	.	0			c.T1318G						PASS	.	A	GLY/CYS	299,4107	155.5+/-188.7	12,275,1916	61.0	60.0	60.0		1318	3.6	1.0	1	dbSNP_132	60	2,8598	1.2+/-3.3	0,2,4298	yes	missense	ASH1L	NM_018489.2	159	12,277,6214	CC,CA,AA		0.0233,6.7862,2.3143	possibly-damaging	440/2965	155451343	301,12705	2203	4300	6503	SO:0001583	missense	55870	exon3			TACTACAAGAAGC	AB037841	CCDS1113.2	1q22	2013-01-28			ENSG00000116539	ENSG00000116539		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	19088	protein-coding gene	gene with protein product		607999				10860993, 16545939	Standard	NM_018489		Approved	huASH1, ASH1, ASH1L1, KMT2H	uc001fkt.3	Q9NR48	OTTHUMG00000014011	ENST00000368346.3:c.1318T>G	1.37:g.155451343A>C	ENSP00000357330:p.Cys440Gly	137.0	0.0	0		179.0	77.0	0.430168	NM_018489	Q59GP1|Q5T714|Q5T715|Q9P2C7	Missense_Mutation	SNP	ENST00000368346.3	37		35	0.016025641025641024	34	0.06910569105691057	1	0.0027624309392265192	0	0.0	0	0.0	A	15.65	2.897292	0.52121	0.067862	2.33E-4	ENSG00000116539	ENST00000368346;ENST00000392403	D;D	0.91407	-2.84;-2.83	4.73	3.6	0.41247	.	0.327762	0.30538	N	0.009409	T	0.74772	0.3760	N	0.14661	0.345	0.80722	D	1	P;P	0.50528	0.895;0.936	B;P	0.44477	0.264;0.451	T	0.78445	-0.2201	10	0.72032	D	0.01	.	7.8358	0.29369	0.8353:0.0:0.1647:0.0	.	440;440	Q9NR48;Q9NR48-2	ASH1L_HUMAN;.	G	440	ENSP00000357330:C440G;ENSP00000376204:C440G	ENSP00000357330:C440G	C	-	1	0	ASH1L	153717967	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.294000	0.59043	0.936000	0.37367	0.460000	0.39030	TGT	A|0.981;C|0.019	0.019	strong		0.423	ASH1L-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000039400.1	NM_018489	
PLCD4	84812	hgsc.bcm.edu	37	2	219483526	219483526	+	Missense_Mutation	SNP	G	G	C	rs200863393		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:219483526G>C	ENST00000450993.2	+	4	745	c.406G>C	c.(406-408)Gac>Cac	p.D136H	PLCD4_ENST00000432688.1_Missense_Mutation_p.D136H|PLCD4_ENST00000417849.1_Missense_Mutation_p.D136H|U3_ENST00000516996.1_RNA	NM_032726.3	NP_116115.1	Q9BRC7	PLCD4_HUMAN	phospholipase C, delta 4	136	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				acrosome reaction (GO:0007340)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phosphatidylinositol metabolic process (GO:0046488)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|urinary_tract(3)	23		Renal(207;0.0915)		Epithelial(149;5.11e-07)|all cancers(144;0.000104)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		GGAGCGCCTGGACCAGTATCG	0.582													G|||	1	0.000199681	0.0	0.0	5008	,	,		20288	0.0		0.001	False		,,,				2504	0.0				p.D136H		Atlas-SNP	.											.	PLCD4	51	.	0			c.G406C						PASS	.	G	HIS/ASP	0,4162		0,0,2081	18.0	18.0	18.0		406	4.9	1.0	2		18	2,8408		0,2,4203	yes	missense	PLCD4	NM_032726.3	81	0,2,6284	CC,CG,GG		0.0238,0.0,0.0159	probably-damaging	136/763	219483526	2,12570	2081	4205	6286	SO:0001583	missense	84812	exon4			CGCCTGGACCAGT	AI366170	CCDS46516.1	2q35	2013-01-10			ENSG00000115556	ENSG00000115556	3.1.4.11	"""EF-hand domain containing"""	9062	protein-coding gene	gene with protein product		605939				10702683, 9056492	Standard	NM_032726		Approved		uc021vwx.1	Q9BRC7	OTTHUMG00000154743	ENST00000450993.2:c.406G>C	2.37:g.219483526G>C	ENSP00000388631:p.Asp136His	88.0	0.0	0		101.0	48.0	0.475248	NM_032726	Q53FS8	Missense_Mutation	SNP	ENST00000450993.2	37	CCDS46516.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	18.34	3.603570	0.66445	0.0	2.38E-4	ENSG00000115556	ENST00000450993;ENST00000251959;ENST00000457426;ENST00000417849;ENST00000432688	T;T;T	0.43688	0.94;0.94;0.94	4.89	4.89	0.63831	.	1.041430	0.07513	N	0.909165	T	0.69441	0.3111	M	0.76838	2.35	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.61063	-0.7138	10	0.51188	T	0.08	.	16.8055	0.85626	0.0:0.0:1.0:0.0	.	83;136	B4DN84;Q9BRC7	.;PLCD4_HUMAN	H	136	ENSP00000388631:D136H;ENSP00000396942:D136H;ENSP00000396185:D136H	ENSP00000251959:D136H	D	+	1	0	PLCD4	219191770	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.473000	0.97714	2.553000	0.86117	0.655000	0.94253	GAC	G|1.000;C|0.000	0.000	strong		0.582	PLCD4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336876.1		
TENM3	55714	hgsc.bcm.edu	37	4	183594275	183594275	+	Missense_Mutation	SNP	T	T	C	rs201144002		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:183594275T>C	ENST00000511685.1	+	7	1352	c.1229T>C	c.(1228-1230)aTt>aCt	p.I410T	TENM3_ENST00000406950.2_Missense_Mutation_p.I410T			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	410					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										CAGCTCTTCATTGATCAGCCA	0.438																																					p.I410T		Atlas-SNP	.											.	.	.	.	0			c.T1229C						PASS	.	T	THR/ILE	0,3630		0,0,1815	63.0	59.0	60.0		1229	4.9	1.0	4		60	1,8189		0,1,4094	yes	missense	ODZ3	NM_001080477.1	89	0,1,5909	CC,CT,TT		0.0122,0.0,0.0085	possibly-damaging	410/2700	183594275	1,11819	1815	4095	5910	SO:0001583	missense	55714	exon6			TCTTCATTGATCA	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"""odz, odd Oz/ten-m homolog 3 (Drosophila)"""	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.1229T>C	4.37:g.183594275T>C	ENSP00000424226:p.Ile410Thr	210.0	1.0	0.0047619		195.0	100.0	0.512821	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	T	17.79	3.476907	0.63849	0.0	1.22E-4	ENSG00000218336	ENST00000511685;ENST00000406950	T;T	0.29397	1.57;1.57	4.91	4.91	0.64330	.	.	.	.	.	T	0.31765	0.0807	M	0.67397	2.05	0.53688	D	0.999978	B	0.33694	0.421	B	0.26864	0.074	T	0.15780	-1.0425	9	0.44086	T	0.13	.	15.0662	0.71996	0.0:0.0:0.0:1.0	.	410	Q9P273	TEN3_HUMAN	T	410	ENSP00000424226:I410T;ENSP00000385276:I410T	ENSP00000385276:I410T	I	+	2	0	ODZ3	183831269	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	7.822000	0.86651	2.197000	0.70478	0.456000	0.33151	ATT	.	.	weak		0.438	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1		
CTXN3	613212	hgsc.bcm.edu	37	5	126993262	126993262	+	Missense_Mutation	SNP	G	G	A	rs386692235|rs61743797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:126993262G>A	ENST00000379445.3	+	3	600	c.49G>A	c.(49-51)Gaa>Aaa	p.E17K	CTXN3_ENST00000395322.3_Missense_Mutation_p.E17K|CTC-548H10.2_ENST00000512352.1_RNA	NM_001048252.2	NP_001041717.1	Q4LDR2	CTXN3_HUMAN	cortexin 3	17			E -> V (in dbSNP:rs248709). {ECO:0000269|Ref.2}.			integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(2)|lung(1)	4		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	Epithelial(69;0.0128)|COAD - Colon adenocarcinoma(49;0.0234)|OV - Ovarian serous cystadenocarcinoma(64;0.038)		CCTTGGGAACGAATCAGCAGA	0.478													G|||	11	0.00219649	0.0076	0.0	5008	,	,		21036	0.0		0.001	False		,,,				2504	0.0				p.E17K		Atlas-SNP	.											.	CTXN3	19	.	0			c.G49A						PASS	.						128.0	111.0	117.0					5																	126993262		2203	4300	6503	SO:0001583	missense	613212	exon3			GGGAACGAATCAG	AB219764	CCDS34221.1	5q23.2	2006-09-21				ENSG00000205279			31110	protein-coding gene	gene with protein product							Standard	NM_001048252		Approved		uc003kum.4	Q4LDR2		ENST00000379445.3:c.49G>A	5.37:g.126993262G>A	ENSP00000368758:p.Glu17Lys	68.0	0.0	0		83.0	49.0	0.590361	NM_001048252	B2RV32|D3DQ82	Missense_Mutation	SNP	ENST00000379445.3	37	CCDS34221.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	1.635	-0.518074	0.04171	.	.	ENSG00000205279	ENST00000379445;ENST00000395322	T;T	0.30714	1.52;1.52	4.52	-5.44	0.02624	.	1.776230	0.02356	N	0.076391	T	0.08670	0.0215	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.17623	-1.0363	9	0.09084	T	0.74	0.374	4.8394	0.13483	0.4246:0.0873:0.3994:0.0887	rs61743797	17	Q4LDR2	CTXN3_HUMAN	K	17	ENSP00000368758:E17K;ENSP00000378732:E17K	ENSP00000368758:E17K	E	+	1	0	CTXN3	127021161	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-1.490000	0.02304	-1.410000	0.02035	-0.940000	0.02684	GAA	G|0.998;A|0.002	0.002	strong		0.478	CTXN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372467.1	XM_932841	
CELSR1	9620	hgsc.bcm.edu	37	22	46777896	46777896	+	Missense_Mutation	SNP	C	C	G	rs7287089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46777896C>G	ENST00000262738.3	-	21	6934	c.6935G>C	c.(6934-6936)cGc>cCc	p.R2312P		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2312			R -> P (does not affect protein localization to the cell membrane; dbSNP:rs7287089). {ECO:0000269|PubMed:22095531}.		anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		AGGCCCCGGGCGCGTGGTCTG	0.682													.|||	85	0.0169728	0.0605	0.0072	5008	,	,		12386	0.0		0.0	False		,,,				2504	0.0				p.R2312P		Atlas-SNP	.											.	CELSR1	242	.	0			c.G6935C						PASS	.	C	PRO/ARG	163,4111		1,161,1975	8.0	9.0	9.0		6935	-3.2	0.0	22	dbSNP_116	9	2,8374		0,2,4186	no	missense	CELSR1	NM_014246.1	103	1,163,6161	GG,GC,CC		0.0239,3.8138,1.3043	benign	2312/3015	46777896	165,12485	2137	4188	6325	SO:0001583	missense	9620	exon21			CCCGGGCGCGTGG	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	1850	protein-coding gene	gene with protein product	"""flamingo homolog 2 (Drosophila)"""	604523	"""cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"""			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.6935G>C	22.37:g.46777896C>G	ENSP00000262738:p.Arg2312Pro	15.0	0.0	0		29.0	12.0	0.413793	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	32	0.014652014652014652	31	0.06300813008130081	1	0.0027624309392265192	0	0.0	0	0.0	C	9.166	1.020045	0.19433	0.038138	2.39E-4	ENSG00000075275	ENST00000262738	T	0.67698	-0.28	4.89	-3.18	0.05186	Domain of unknown function DUF3497 (1);	1.362770	0.05247	N	0.513271	T	0.05777	0.0151	N	0.08118	0	0.09310	N	1	B;B	0.10296	0.003;0.001	B;B	0.11329	0.006;0.002	T	0.04413	-1.0953	10	0.20519	T	0.43	.	3.427	0.07414	0.1112:0.33:0.384:0.1748	rs7287089	633;2312	B7Z7U7;Q9NYQ6	.;CELR1_HUMAN	P	2312	ENSP00000262738:R2312P	ENSP00000262738:R2312P	R	-	2	0	CELSR1	45156560	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.121000	0.03270	-0.119000	0.11830	0.555000	0.69702	CGC	C|0.985;G|0.015	0.015	strong		0.682	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
DHX8	1659	hgsc.bcm.edu	37	17	41570819	41570819	+	Silent	SNP	G	G	A	rs146528228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:41570819G>A	ENST00000262415.3	+	7	942	c.870G>A	c.(868-870)cgG>cgA	p.R290R	DHX8_ENST00000540306.1_Silent_p.R290R	NM_004941.1	NP_004932.1	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	290	S1 motif. {ECO:0000255|PROSITE- ProRule:PRU00180}.				ATP catabolic process (GO:0006200)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		TCAGGAAGCGGTGGGAAGGCC	0.512													G|||	5	0.000998403	0.0038	0.0	5008	,	,		19930	0.0		0.0	False		,,,				2504	0.0				p.R290R	NSCLC(56;1548 1661 49258 49987)	Atlas-SNP	.											.	DHX8	98	.	0			c.G870A						PASS	.	G		31,4375	36.8+/-68.6	0,31,2172	96.0	92.0	93.0		870	0.8	1.0	17	dbSNP_134	93	0,8600		0,0,4300	no	coding-synonymous	DHX8	NM_004941.1		0,31,6472	AA,AG,GG		0.0,0.7036,0.2384		290/1221	41570819	31,12975	2203	4300	6503	SO:0001819	synonymous_variant	1659	exon7			GAAGCGGTGGGAA	D50487	CCDS11464.1	17q21.31	2005-08-19	2003-06-13	2003-06-20		ENSG00000067596		"""DEAH-boxes"""	2749	protein-coding gene	gene with protein product		600396	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 8 (RNA helicase)"""	DDX8		7935475	Standard	NM_004941		Approved	HRH1, PRP22, PRPF22	uc002idu.1	Q14562		ENST00000262415.3:c.870G>A	17.37:g.41570819G>A		109.0	0.0	0		127.0	60.0	0.472441	NM_004941		Silent	SNP	ENST00000262415.3	37	CCDS11464.1																																																																																			G|0.998;A|0.002	0.002	strong		0.512	DHX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453485.1		
CLEC12B	387837	hgsc.bcm.edu	37	12	10163381	10163381	+	Missense_Mutation	SNP	C	C	T	rs11833101|rs386760228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:10163381C>T	ENST00000338896.5	+	1	151	c.23C>T	c.(22-24)gCg>gTg	p.A8V	CLEC1B_ENST00000428126.2_Intron|CLEC12B_ENST00000396502.1_Missense_Mutation_p.A8V	NM_001129998.1	NP_001123470.1	Q2HXU8	CL12B_HUMAN	C-type lectin domain family 12, member B	8						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(2)|large_intestine(2)|lung(5)	9						GTGACCTACGCGACACTCACA	0.398													C|||	160	0.0319489	0.1135	0.0144	5008	,	,		20629	0.0		0.0	False		,,,				2504	0.0				p.A8V		Atlas-SNP	.											.	CLEC12B	25	.	0			c.C23T						PASS	.	C	VAL/ALA,VAL/ALA	334,4072	170.1+/-200.6	12,310,1881	61.0	58.0	59.0		23,23	4.0	0.3	12	dbSNP_120	59	0,8600		0,0,4300	yes	missense,missense	CLEC12B	NM_001129998.1,NM_205852.2	64,64	12,310,6181	TT,TC,CC		0.0,7.5806,2.568	possibly-damaging,possibly-damaging	8/277,8/233	10163381	334,12672	2203	4300	6503	SO:0001583	missense	387837	exon1			CCTACGCGACACT	AK128243	CCDS8610.1, CCDS44830.1	12p13.2	2010-08-17			ENSG00000256660	ENSG00000256660		"""C-type lectin domain containing"""	31966	protein-coding gene	gene with protein product						17562706	Standard	NM_205852		Approved		uc001qwz.2	Q2HXU8	OTTHUMG00000168397	ENST00000338896.5:c.23C>T	12.37:g.10163381C>T	ENSP00000344563:p.Ala8Val	67.0	0.0	0		77.0	28.0	0.363636	NM_001129998	Q6UWF2|Q6ZRG0	Missense_Mutation	SNP	ENST00000338896.5	37	CCDS44830.1	60	0.027472527472527472	54	0.10975609756097561	6	0.016574585635359115	0	0.0	0	0.0	C	12.83	2.054910	0.36277	0.075806	0.0	ENSG00000256660	ENST00000396502;ENST00000338896	T;T	0.01629	4.72;5.01	4.88	4.0	0.46444	.	0.368895	0.22840	N	0.054991	T	0.00073	0.0002	M	0.69823	2.125	0.18873	N	0.999986	B;P;P	0.44690	0.206;0.454;0.841	B;B;B	0.33690	0.022;0.049;0.168	T	0.50841	-0.8780	10	0.62326	D	0.03	.	9.8308	0.40941	0.0:0.9025:0.0:0.0975	rs11833101;rs56980128	8;8;8	Q2HXU8;Q2HXU8-2;F5H4H7	CL12B_HUMAN;.;.	V	8	ENSP00000379759:A8V;ENSP00000344563:A8V	ENSP00000344563:A8V	A	+	2	0	CLEC12B	10054648	0.000000	0.05858	0.322000	0.25334	0.601000	0.36947	0.634000	0.24614	1.390000	0.46547	0.561000	0.74099	GCG	C|0.976;T|0.024	0.024	strong		0.398	CLEC12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399554.2	NM_205852	
ZNF444	55311	hgsc.bcm.edu	37	19	56669889	56669889	+	Silent	SNP	G	G	A	rs61736530	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56669889G>A	ENST00000337080.3	+	4	691	c.324G>A	c.(322-324)tcG>tcA	p.S108S	ZNF444_ENST00000592171.1_3'UTR|ZNF444_ENST00000592949.1_Silent_p.S108S	NM_001253792.1|NM_018337.3	NP_001240721.1|NP_060807.2	Q8N0Y2	ZN444_HUMAN	zinc finger protein 444	108					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|endometrium(1)|lung(5)	7		Colorectal(82;3.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0531)		CCGATGGGTCGTCAGCAACGA	0.597													g|||	64	0.0127796	0.0461	0.0014	5008	,	,		17153	0.001		0.001	False		,,,				2504	0.0				p.S108S		Atlas-SNP	.											.	ZNF444	15	.	0			c.G324A						PASS	.	A		220,4186	131.8+/-168.3	3,214,1986	74.0	64.0	68.0		324	-5.4	0.0	19	dbSNP_129	68	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	ZNF444	NM_018337.2		3,216,6284	AA,AG,GG		0.0233,4.9932,1.7069		108/328	56669889	222,12784	2203	4300	6503	SO:0001819	synonymous_variant	55311	exon4			TGGGTCGTCAGCA	AB052954	CCDS12939.1, CCDS59426.1	19q13.43	2013-01-09			ENSG00000167685	ENSG00000167685		"""-"", ""Zinc fingers, C2H2-type"""	16052	protein-coding gene	gene with protein product		607874				11978792, 19760602	Standard	NM_001253792		Approved	ZSCAN17, FLJ11137, EZF2	uc002qmm.3	Q8N0Y2		ENST00000337080.3:c.324G>A	19.37:g.56669889G>A		214.0	0.0	0		214.0	214.0	1	NM_001253792	Q8TEQ9|Q8WU35|Q9NUU1	Silent	SNP	ENST00000337080.3	37	CCDS12939.1																																																																																			G|0.981;A|0.019	0.019	strong		0.597	ZNF444-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457503.1	NM_018337	
CSF1	1435	hgsc.bcm.edu	37	1	110466776	110466776	+	Silent	SNP	C	C	T	rs3208449	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:110466776C>T	ENST00000329608.6	+	6	1924	c.1533C>T	c.(1531-1533)gcC>gcT	p.A511A	CSF1_ENST00000369802.3_Silent_p.A511A|CSF1_ENST00000420111.2_Silent_p.A213A|CSF1_ENST00000369801.1_Silent_p.A395A|CSF1_ENST00000344188.5_Silent_p.A395A	NM_000757.5|NM_172211.3	NP_000748|NP_757350.1	P09603	CSF1_HUMAN	colony stimulating factor 1 (macrophage)	511					branching involved in mammary gland duct morphogenesis (GO:0060444)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|developmental process involved in reproduction (GO:0003006)|hemopoiesis (GO:0030097)|homeostasis of number of cells within a tissue (GO:0048873)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary duct terminal end bud growth (GO:0060763)|mammary gland fat development (GO:0060611)|monocyte activation (GO:0042117)|odontogenesis (GO:0042476)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|osteoclast proliferation (GO:0002158)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of monocyte differentiation (GO:0045657)|positive regulation of mononuclear cell proliferation (GO:0032946)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of odontogenesis of dentin-containing tooth (GO:0042488)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of macrophage derived foam cell differentiation (GO:0010743)|regulation of ossification (GO:0030278)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|macrophage colony-stimulating factor receptor binding (GO:0005157)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(3)|large_intestine(3)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	20		all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Acute lymphoblastic leukemia(138;0.204)		Lung(183;0.0238)|Colorectal(144;0.112)|all cancers(265;0.117)|Epithelial(280;0.127)|LUSC - Lung squamous cell carcinoma(189;0.135)		TCTTGCTGGCCGTCGGAGGCC	0.637													C|||	14	0.00279553	0.0106	0.0	5008	,	,		16807	0.0		0.0	False		,,,				2504	0.0				p.A511A		Atlas-SNP	.											.	CSF1	40	.	0			c.C1533T						PASS	.	C	,,,	28,4376		0,28,2174	34.0	34.0	34.0		1533,1185,639,1533	-8.4	0.1	1	dbSNP_105	34	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CSF1	NM_000757.5,NM_172210.2,NM_172211.2,NM_172212.2	,,,	0,29,6473	TT,TC,CC		0.0116,0.6358,0.223	,,,	511/555,395/439,213/257,511/555	110466776	29,12975	2202	4300	6502	SO:0001819	synonymous_variant	1435	exon6			GCTGGCCGTCGGA	BC021117	CCDS816.1, CCDS817.1, CCDS30797.1	1p13.3	2012-09-20			ENSG00000184371	ENSG00000184371			2432	protein-coding gene	gene with protein product		120420				1540160	Standard	NM_172210		Approved	M-CSF, MCSF, MGC31930	uc001dyw.4	P09603	OTTHUMG00000011646	ENST00000329608.6:c.1533C>T	1.37:g.110466776C>T		69.0	0.0	0		96.0	51.0	0.53125	NM_000757	A8K6J5|Q13130|Q14086|Q14806|Q5VVF3|Q5VVF4|Q9UQR8	Silent	SNP	ENST00000329608.6	37	CCDS816.1																																																																																			C|0.996;T|0.004	0.004	strong		0.637	CSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032208.1	NM_000757	
BLZF1	8548	hgsc.bcm.edu	37	1	169345883	169345883	+	Missense_Mutation	SNP	A	A	G	rs112226207	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:169345883A>G	ENST00000367808.3	+	3	557	c.134A>G	c.(133-135)cAt>cGt	p.H45R	BLZF1_ENST00000329281.2_Missense_Mutation_p.H45R|BLZF1_ENST00000367807.3_Missense_Mutation_p.H45R			Q9H2G9	GO45_HUMAN	basic leucine zipper nuclear factor 1	45					cell proliferation (GO:0008283)|Golgi organization (GO:0007030)|Golgi to plasma membrane protein transport (GO:0043001)|mitotic cell cycle (GO:0000278)|regulation of cell growth (GO:0001558)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cytoplasm (GO:0005737)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|sequence-specific DNA binding transcription factor activity (GO:0003700)|ubiquitin protein ligase binding (GO:0031625)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|prostate(1)|skin(1)	14	all_hematologic(923;0.208)					AGAAAGCATCATAGTCTTCAG	0.453													A|||	8	0.00159744	0.0053	0.0014	5008	,	,		18203	0.0		0.0	False		,,,				2504	0.0				p.H45R		Atlas-SNP	.											.	BLZF1	57	.	0			c.A134G						PASS	.	A	ARG/HIS	30,4376	36.0+/-67.5	0,30,2173	95.0	95.0	95.0		134	-1.9	0.0	1	dbSNP_132	95	0,8600		0,0,4300	yes	missense	BLZF1	NM_003666.2	29	0,30,6473	GG,GA,AA		0.0,0.6809,0.2307	benign	45/401	169345883	30,12976	2203	4300	6503	SO:0001583	missense	8548	exon3			AGCATCATAGTCT	U79751	CCDS1278.1	1q24	2008-08-01	2008-08-01		ENSG00000117475	ENSG00000117475			1065	protein-coding gene	gene with protein product		608692				9129147	Standard	NM_003666		Approved	JEM-1	uc001gfy.3	Q9H2G9	OTTHUMG00000035453	ENST00000367808.3:c.134A>G	1.37:g.169345883A>G	ENSP00000356782:p.His45Arg	143.0	0.0	0		144.0	71.0	0.493056	NM_003666	O15298|Q5T531|Q5T533|Q9GZX4	Missense_Mutation	SNP	ENST00000367808.3	37	CCDS1278.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	A	4.096	0.015897	0.07959	0.006809	0.0	ENSG00000117475	ENST00000367808;ENST00000329281;ENST00000367807;ENST00000420531;ENST00000426663	T;T;T;T;T	0.42513	1.57;1.57;0.97;0.97;1.57	5.27	-1.89	0.07689	.	0.566329	0.20243	N	0.096258	T	0.07234	0.0183	N	0.22421	0.69	0.26193	N	0.979556	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.08055	0.001;0.001;0.003	T	0.34279	-0.9835	9	0.09590	T	0.72	-2.9441	6.7849	0.23668	0.5046:0.3627:0.1328:0.0	.	45;45;45	A8K6R0;Q9H2G9;Q9H2G9-2	.;GO45_HUMAN;.	R	45	ENSP00000356782:H45R;ENSP00000327541:H45R;ENSP00000356781:H45R;ENSP00000414668:H45R;ENSP00000404408:H45R	ENSP00000327541:H45R	H	+	2	0	BLZF1	167612507	0.001000	0.12720	0.000000	0.03702	0.695000	0.40330	0.633000	0.24598	-0.247000	0.09597	-0.389000	0.06534	CAT	A|0.997;G|0.003	0.003	strong		0.453	BLZF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086109.1	NM_003666	
PASK	23178	hgsc.bcm.edu	37	2	242065635	242065635	+	Missense_Mutation	SNP	A	A	G	rs77674262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242065635A>G	ENST00000405260.1	-	10	3393	c.2695T>C	c.(2695-2697)Tac>Cac	p.Y899H	PASK_ENST00000539818.1_Missense_Mutation_p.Y683H|PASK_ENST00000544142.1_Missense_Mutation_p.Y713H|PASK_ENST00000234040.4_Missense_Mutation_p.Y899H|PASK_ENST00000403638.3_Missense_Mutation_p.Y899H|PASK_ENST00000358649.4_Missense_Mutation_p.Y899H	NM_001252120.1	NP_001239049.1	Q96RG2	PASK_HUMAN	PAS domain containing serine/threonine kinase	899				Y -> H (in Ref. 1; AAK69752). {ECO:0000305}.	negative regulation of glycogen biosynthetic process (GO:0045719)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of energy homeostasis (GO:2000505)|regulation of glucagon secretion (GO:0070092)|regulation of respiratory gaseous exchange (GO:0043576)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(20)|ovary(4)|prostate(4)|skin(1)|stomach(1)|urinary_tract(2)	53		all_cancers(19;4.46e-39)|all_epithelial(40;1.34e-17)|Breast(86;1.53e-05)|Renal(207;0.00179)|all_lung(227;0.00481)|Lung NSC(271;0.017)|Ovarian(221;0.0228)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|all_neural(83;0.243)|Hepatocellular(293;0.244)		Epithelial(32;1.34e-31)|all cancers(36;1e-28)|OV - Ovarian serous cystadenocarcinoma(60;3.53e-14)|Kidney(56;4.31e-09)|KIRC - Kidney renal clear cell carcinoma(57;4.35e-08)|BRCA - Breast invasive adenocarcinoma(100;5.64e-06)|Lung(119;0.000596)|LUSC - Lung squamous cell carcinoma(224;0.00481)|Colorectal(34;0.014)|COAD - Colon adenocarcinoma(134;0.0968)		TCTCGATGGTAGCAGCTCCCG	0.637													A|||	109	0.0217652	0.0764	0.0115	5008	,	,		17584	0.0		0.0	False		,,,				2504	0.0				p.Y899H		Atlas-SNP	.											.	PASK	230	.	0			c.T2695C						PASS	.	A	HIS/TYR	255,4151	142.3+/-177.5	10,235,1958	70.0	56.0	61.0		2695	2.4	0.9	2	dbSNP_131	61	0,8600		0,0,4300	yes	missense	PASK	NM_015148.2	83	10,235,6258	GG,GA,AA		0.0,5.7876,1.9606	benign	899/1324	242065635	255,12751	2203	4300	6503	SO:0001583	missense	23178	exon10			GATGGTAGCAGCT	U79240	CCDS2545.1, CCDS58758.1, CCDS58759.1	2q37.3	2008-05-23			ENSG00000115687	ENSG00000115687			17270	protein-coding gene	gene with protein product		607505				11688972, 11459942, 15148392	Standard	NM_001252119		Approved	PASKIN, KIAA0135, STK37	uc010fzl.2	Q96RG2	OTTHUMG00000133392	ENST00000405260.1:c.2695T>C	2.37:g.242065635A>G	ENSP00000384016:p.Tyr899His	126.0	0.0	0		143.0	74.0	0.517483	NM_015148	G5E9F1|Q05BE4|Q68DY3|Q6GSJ5|Q86XH6|Q99763|Q9UFR7	Missense_Mutation	SNP	ENST00000405260.1	37	CCDS2545.1	42	0.019230769230769232	38	0.07723577235772358	4	0.011049723756906077	0	0.0	0	0.0	A	6.136	0.393272	0.11638	0.057876	0.0	ENSG00000115687	ENST00000234040;ENST00000544142;ENST00000405260;ENST00000358649;ENST00000539818;ENST00000403638	T;T;T;T;T;T	0.69175	-0.38;-0.38;-0.38;-0.33;-0.37;0.57	4.94	2.43	0.29744	.	0.703722	0.12909	N	0.429094	T	0.06872	0.0175	M	0.62723	1.935	0.28200	N	0.927392	B;B;B;B;B	0.18013	0.014;0.025;0.025;0.015;0.014	B;B;B;B;B	0.18561	0.01;0.022;0.022;0.022;0.01	T	0.24440	-1.0160	10	0.45353	T	0.12	.	5.2611	0.15573	0.758:0.0:0.0873:0.1548	.	864;713;899;899;899	B7Z7R6;F5GYW7;Q96RG2-2;G5E9F1;Q96RG2	.;.;.;.;PASK_HUMAN	H	899;713;899;899;683;899	ENSP00000234040:Y899H;ENSP00000441374:Y713H;ENSP00000384016:Y899H;ENSP00000351475:Y899H;ENSP00000443083:Y683H;ENSP00000384438:Y899H	ENSP00000234040:Y899H	Y	-	1	0	PASK	241714308	1.000000	0.71417	0.911000	0.35937	0.022000	0.10575	2.054000	0.41335	0.734000	0.32515	-0.411000	0.06167	TAC	A|0.979;G|0.021	0.021	strong		0.637	PASK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000323753.1	NM_015148	
USP46	64854	hgsc.bcm.edu	37	4	53494283	53494283	+	Silent	SNP	G	G	A	rs115007179	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:53494283G>A	ENST00000441222.3	-	3	349	c.165C>T	c.(163-165)ttC>ttT	p.F55F	USP46_ENST00000504078.1_5'Flank|USP46_ENST00000508499.1_Silent_p.F48F|USP46_ENST00000451218.2_Silent_p.F28F	NM_022832.3	NP_073743.2	P62068	UBP46_HUMAN	ubiquitin specific peptidase 46	55	USP.				adult feeding behavior (GO:0008343)|behavioral fear response (GO:0001662)|behavioral response to ethanol (GO:0048149)|protein deubiquitination (GO:0016579)|regulation of synaptic transmission, GABAergic (GO:0032228)|righting reflex (GO:0060013)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(2)	12			LUSC - Lung squamous cell carcinoma(32;0.0295)			ATGGACGGCAGAAGTACAATG	0.522													G|||	43	0.00858626	0.031	0.0029	5008	,	,		21730	0.0		0.0	False		,,,				2504	0.0				p.F55F		Atlas-SNP	.											.	USP46	38	.	0			c.C165T						PASS	.	G	,	110,3966		2,106,1930	90.0	85.0	86.0		144,165	5.2	1.0	4	dbSNP_132	86	3,8385		0,3,4191	no	coding-synonymous,coding-synonymous	USP46	NM_001134223.1,NM_022832.3	,	2,109,6121	AA,AG,GG		0.0358,2.6987,0.9066	,	48/360,55/367	53494283	113,12351	2038	4194	6232	SO:0001819	synonymous_variant	64854	exon3			ACGGCAGAAGTAC	AK022614	CCDS47053.1, CCDS47054.1	4q12	2008-02-05	2005-08-08		ENSG00000109189	ENSG00000109189		"""Ubiquitin-specific peptidases"""	20075	protein-coding gene	gene with protein product		612849	"""ubiquitin specific protease 46"""			12838346	Standard	NM_022832		Approved	FLJ12552	uc003gzn.3	P62068	OTTHUMG00000160640	ENST00000441222.3:c.165C>T	4.37:g.53494283G>A		102.0	0.0	0		102.0	101.0	0.990196	NM_022832	B7Z3Y7|B7Z675|B7Z7S3|G8ACC7|Q80V95|Q9H7U4|Q9H9T8	Silent	SNP	ENST00000441222.3	37	CCDS47053.1																																																																																			G|0.997;A|0.003	0.003	strong		0.522	USP46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361516.2	NM_022832	
TTC17	55761	hgsc.bcm.edu	37	11	43413028	43413028	+	Missense_Mutation	SNP	A	A	C	rs12099204	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:43413028A>C	ENST00000039989.4	+	4	447	c.433A>C	c.(433-435)Ata>Cta	p.I145L	RP11-484D2.4_ENST00000394183.2_RNA|TTC17_ENST00000299240.6_Missense_Mutation_p.I145L	NM_018259.5	NP_060729.2	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17	145			I -> L (in dbSNP:rs12099204).		actin filament polymerization (GO:0030041)|cilium organization (GO:0044782)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(27)|ovary(5)|prostate(3)|skin(3)	53						TGAAGATTATATAGACACAGA	0.328													A|||	528	0.105431	0.382	0.0317	5008	,	,		16846	0.0		0.001	False		,,,				2504	0.0				p.I145L		Atlas-SNP	.											.	TTC17	112	.	0			c.A433C						PASS	.	A	LEU/ILE	1459,2947	469.6+/-355.5	256,947,1000	80.0	82.0	82.0		433	5.2	1.0	11	dbSNP_120	82	9,8591	6.4+/-24.3	0,9,4291	yes	missense	TTC17	NM_018259.5	5	256,956,5291	CC,CA,AA		0.1047,33.1139,11.2871	benign	145/1142	43413028	1468,11538	2203	4300	6503	SO:0001583	missense	55761	exon4			GATTATATAGACA	AK001540	CCDS31466.1	11p11.2	2013-01-10			ENSG00000052841	ENSG00000052841		"""Tetratricopeptide (TTC) repeat domain containing"""	25596	protein-coding gene	gene with protein product						12477932	Standard	NM_018259		Approved	FLJ10890	uc001mxi.3	Q96AE7	OTTHUMG00000166398	ENST00000039989.4:c.433A>C	11.37:g.43413028A>C	ENSP00000039989:p.Ile145Leu	195.0	1.0	0.00512821		203.0	203.0	1	NM_018259	G3XAB3|Q8NEC0	Missense_Mutation	SNP	ENST00000039989.4	37	CCDS31466.1	202	0.0924908424908425	193	0.39227642276422764	9	0.024861878453038673	0	0.0	0	0.0	A	12.70	2.015330	0.35511	0.331139	0.001047	ENSG00000052841	ENST00000299240;ENST00000039989	T;T	0.31510	1.49;1.59	5.2	5.2	0.72013	.	0.264075	0.45606	D	0.000357	T	0.00012	0.0000	N	0.08118	0	0.34987	P	0.245382	B;B;B	0.16802	0.011;0.007;0.019	B;B;B	0.17433	0.008;0.006;0.018	T	0.41088	-0.9528	9	0.09338	T	0.73	-16.7019	9.8335	0.40956	0.9228:0.0:0.0772:0.0	rs12099204;rs12099204	145;145;145	Q8NEC0;Q96AE7;G3XAB3	.;TTC17_HUMAN;.	L	145	ENSP00000299240:I145L;ENSP00000039989:I145L	ENSP00000039989:I145L	I	+	1	0	TTC17	43369604	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.614000	0.36911	2.091000	0.63221	0.460000	0.39030	ATA	A|0.883;C|0.117	0.117	strong		0.328	TTC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389577.2	NM_018259	
PIK3C2G	5288	hgsc.bcm.edu	37	12	18499629	18499629	+	Missense_Mutation	SNP	A	A	T	rs77656456	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:18499629A>T	ENST00000266497.5	+	10	1522	c.1484A>T	c.(1483-1485)aAt>aTt	p.N495I	PIK3C2G_ENST00000538779.1_Missense_Mutation_p.N495I|PIK3C2G_ENST00000535651.1_Missense_Mutation_p.N495I|PIK3C2G_ENST00000433979.1_Missense_Mutation_p.N495I			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	495	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.				chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				CAGCTAATCAATGTCTACTGT	0.418													A|||	9	0.00179712	0.0061	0.0014	5008	,	,		17734	0.0		0.0	False		,,,				2504	0.0				p.N495I		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.A1484T						PASS	.	A	ILE/ASN	17,3835		0,17,1909	183.0	183.0	183.0		1484	1.6	0.0	12	dbSNP_131	183	0,8256		0,0,4128	yes	missense	PIK3C2G	NM_004570.4	149	0,17,6037	TT,TA,AA		0.0,0.4413,0.1404	benign	495/1446	18499629	17,12091	1926	4128	6054	SO:0001583	missense	5288	exon11			TAATCAATGTCTA	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"""phosphoinositide-3-kinase, class 2, gamma polypeptide"""			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.1484A>T	12.37:g.18499629A>T	ENSP00000266497:p.Asn495Ile	119.0	0.0	0		149.0	73.0	0.489933	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	37	CCDS44839.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	A	10.11	1.260049	0.23051	0.004413	0.0	ENSG00000139144	ENST00000535651;ENST00000433979;ENST00000266497;ENST00000538779	T;T;T;T	0.60797	1.49;0.17;0.17;0.16	3.98	1.61	0.23674	Phosphoinositide 3-kinase, C2 (1);	1.592470	0.03319	N	0.191731	T	0.30727	0.0774	N	0.08118	0	0.09310	N	1	B;B;B	0.30281	0.04;0.066;0.275	B;B;B	0.28232	0.033;0.073;0.087	T	0.35871	-0.9771	10	0.66056	D	0.02	-1.4578	6.9084	0.24321	0.6849:0.0:0.3151:0.0	.	494;495;495	B7ZLY6;F5H369;O75747	.;.;P3C2G_HUMAN	I	495	ENSP00000443850:N495I;ENSP00000404845:N495I;ENSP00000266497:N495I;ENSP00000445381:N495I	ENSP00000266497:N495I	N	+	2	0	PIK3C2G	18390896	0.000000	0.05858	0.019000	0.16419	0.908000	0.53690	0.199000	0.17237	0.344000	0.23847	0.454000	0.30748	AAT	A|0.998;T|0.002	0.002	strong		0.418	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570	
NWD1	284434	hgsc.bcm.edu	37	19	16860685	16860685	+	Missense_Mutation	SNP	C	C	T	rs61998161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16860685C>T	ENST00000552788.1	+	4	1232	c.1232C>T	c.(1231-1233)aCc>aTc	p.T411I	NWD1_ENST00000379808.3_Missense_Mutation_p.T411I|NWD1_ENST00000523826.1_Missense_Mutation_p.T205I|NWD1_ENST00000339803.6_Missense_Mutation_p.T276I|NWD1_ENST00000524140.2_Missense_Mutation_p.T411I|NWD1_ENST00000549814.1_Missense_Mutation_p.T411I			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	411	NACHT.						ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GACGCCCACACCAGGGTGGTC	0.587													c|||	120	0.0239617	0.0825	0.0101	5008	,	,		18238	0.0		0.001	False		,,,				2504	0.0031				p.T411I		Atlas-SNP	.											.	NWD1	303	.	0			c.C1232T						PASS	.		ILE/THR	266,4134		5,256,1939	55.0	56.0	56.0		1232	-8.4	0.0	19	dbSNP_129	56	10,8590		0,10,4290	yes	missense	NWD1	NM_001007525.3	89	5,266,6229	TT,TC,CC		0.1163,6.0455,2.1231	benign	411/1433	16860685	276,12724	2200	4300	6500	SO:0001583	missense	284434	exon6			CCCACACCAGGGT	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"""WD repeat domain containing"""	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.1232C>T	19.37:g.16860685C>T	ENSP00000447224:p.Thr411Ile	70.0	0.0	0		85.0	42.0	0.494118	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		49	0.022435897435897436	42	0.08536585365853659	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	c	5.508	0.278633	0.10458	0.060455	0.001163	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.81078	-1.45;-1.45;-1.45;-1.45;-1.45;-1.45	4.77	-8.37	0.00976	.	1.739930	0.02884	N	0.133179	T	0.07234	0.0183	N	0.19112	0.55	0.09310	N	1	P;B;P	0.39022	0.655;0.435;0.491	B;B;B	0.37198	0.243;0.157;0.243	T	0.48547	-0.9026	10	0.33940	T	0.23	-0.9905	16.403	0.83649	0.0991:0.1543:0.7466:0.0	rs61998161	411;411;276	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	I	276;411;411;411;205;411;276	ENSP00000428579:T411I;ENSP00000447548:T411I;ENSP00000369136:T411I;ENSP00000428955:T205I;ENSP00000447224:T411I;ENSP00000340159:T276I	ENSP00000340159:T276I	T	+	2	0	NWD1	16721685	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.167000	0.09940	-0.626000	0.05596	-0.194000	0.12790	ACC	C|0.979;T|0.021	0.021	strong		0.587	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525	
SSPO	23145	hgsc.bcm.edu	37	7	149499254	149499254	+	RNA	SNP	G	G	A	rs59522380	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149499254G>A	ENST00000378016.2	+	0	7622							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CCGCGTGACCGGTTCCGAAGC	0.687													G|||	298	0.0595048	0.2171	0.0159	5008	,	,		15602	0.0		0.0	False		,,,				2504	0.0				p.R2541Q		Atlas-SNP	.											.	.	.	.	0			c.G7622A						PASS	.	G		441,3035		13,415,1310	4.0	6.0	5.0		7626	-4.0	0.0	7	dbSNP_129	5	7,7421		0,7,3707	no	coding-notMod3	SSPO	NM_198455.2		13,422,5017	AA,AG,GG		0.0942,12.687,4.1086			149499254	448,10456	1738	3714	5452			23145	exon51			GTGACCGGTTCCG	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149499254G>A		26.0	0.0	0		44.0	21.0	0.477273	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				G|0.945;A|0.055	0.055	strong		0.687	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
PTPRA	5786	hgsc.bcm.edu	37	20	2969015	2969015	+	Silent	SNP	C	C	G	rs61742610	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:2969015C>G	ENST00000216877.6	+	8	1006	c.606C>G	c.(604-606)tcC>tcG	p.S202S	PTPRA_ENST00000425918.2_Silent_p.S222S|PTPRA_ENST00000356147.3_Silent_p.S202S|PTPRA_ENST00000318266.5_Silent_p.S202S|PTPRA_ENST00000380393.3_Silent_p.S211S|PTPRA_ENST00000358719.4_Silent_p.S67S|PTPRA_ENST00000399903.2_Silent_p.S211S	NM_080840.2	NP_543030.1	P18433	PTPRA_HUMAN	protein tyrosine phosphatase, receptor type, A	211					axon guidance (GO:0007411)|insulin receptor signaling pathway (GO:0008286)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein phosphorylation (GO:0006468)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(5)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17						TGGCCAGATCCCCAAGCACCA	0.547													C|||	147	0.029353	0.0802	0.0231	5008	,	,		17950	0.001		0.003	False		,,,				2504	0.0215				p.S211S		Atlas-SNP	.											.	PTPRA	75	.	0			c.C633G						PASS	.	C	,,	279,4127	155.5+/-188.7	9,261,1933	96.0	95.0	96.0		633,606,606	0.8	1.0	20	dbSNP_129	96	16,8584	11.9+/-42.8	0,16,4284	no	coding-synonymous,coding-synonymous,coding-synonymous	PTPRA	NM_002836.3,NM_080840.2,NM_080841.2	,,	9,277,6217	GG,GC,CC		0.186,6.3323,2.2682	,,	211/803,202/794,202/794	2969015	295,12711	2203	4300	6503	SO:0001819	synonymous_variant	5786	exon13			CAGATCCCCAAGC		CCDS13038.1, CCDS13039.1	20p13	2011-06-09			ENSG00000132670	ENSG00000132670		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9664	protein-coding gene	gene with protein product		176884		PTPRL2, PTPA		2172030, 2169617	Standard	NM_080840		Approved	LRP, HLPR, HPTPA, RPTPA	uc002whn.3	P18433	OTTHUMG00000031718	ENST00000216877.6:c.606C>G	20.37:g.2969015C>G		133.0	0.0	0		145.0	80.0	0.551724	NM_002836	A8K2G8|D3DVX5|Q14513|Q7Z2I2|Q96TD9	Silent	SNP	ENST00000216877.6	37	CCDS13039.1																																																																																			C|0.977;G|0.023	0.023	strong		0.547	PTPRA-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077682.3		
MS4A14	84689	hgsc.bcm.edu	37	11	60183401	60183401	+	Missense_Mutation	SNP	G	G	T	rs376669252		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:60183401G>T	ENST00000300187.6	+	5	1237	c.960G>T	c.(958-960)ttG>ttT	p.L320F	MS4A14_ENST00000395005.2_Missense_Mutation_p.L303F|MS4A14_ENST00000531783.1_Missense_Mutation_p.L353F|MS4A14_ENST00000395001.1_3'UTR|MS4A14_ENST00000531787.1_Missense_Mutation_p.L208F	NM_032597.4	NP_115986.3	Q96JA4	M4A14_HUMAN	membrane-spanning 4-domains, subfamily A, member 14	320						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(9)|lung(31)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	62						CTGAAGACTTGCCATCCCAAG	0.448																																					p.L353F		Atlas-SNP	.											.	MS4A14	120	.	0			c.G1059T						PASS	.	G	PHE/LEU,PHE/LEU	1,4405	2.1+/-5.4	0,1,2202	99.0	91.0	94.0		909,960	-0.6	0.0	11		94	0,8600		0,0,4300	no	missense,missense	MS4A14	NM_001079692.1,NM_032597.3	22,22	0,1,6502	TT,TG,GG		0.0,0.0227,0.0077	possibly-damaging,possibly-damaging	303/663,320/680	60183401	1,13005	2203	4300	6503	SO:0001583	missense	84689	exon6			AGACTTGCCATCC	AY584610	CCDS31569.1, CCDS41652.1, CCDS58136.1, CCDS73295.1	11q12.2	2008-04-10	2008-04-10	2008-04-10		ENSG00000166928			30706	protein-coding gene	gene with protein product			"""membrane-spanning 4-domains, subfamily A, member 16"""	MS4A16			Standard	NM_032597		Approved	NYD-SP21, FLJ32856, DKFZp434H092	uc031qbd.1	Q96JA4		ENST00000300187.6:c.960G>T	11.37:g.60183401G>T	ENSP00000300187:p.Leu320Phe	168.0	0.0	0		164.0	77.0	0.469512	NM_001261828	E9PJE3|Q2TVT5|Q3B7W3|Q86XH8|Q9NTC2	Missense_Mutation	SNP	ENST00000300187.6	37	CCDS31569.1	.	.	.	.	.	.	.	.	.	.	G	9.851	1.193578	0.22037	2.27E-4	0.0	ENSG00000166928	ENST00000531787;ENST00000300187;ENST00000395005;ENST00000531783	T;T;T;T	0.39787	1.07;2.31;1.06;2.67	3.83	-0.63	0.11530	.	3.820730	0.00986	N	0.003454	T	0.32071	0.0817	L	0.36672	1.1	0.09310	N	1	P;P	0.40107	0.703;0.578	B;B	0.35413	0.202;0.099	T	0.27331	-1.0077	10	0.52906	T	0.07	-0.0477	5.6589	0.17658	0.0999:0.0:0.3621:0.5381	.	303;320	Q96JA4-2;Q96JA4	.;M4A14_HUMAN	F	208;320;303;353	ENSP00000437222:L208F;ENSP00000300187:L320F;ENSP00000378453:L303F;ENSP00000433761:L353F	ENSP00000300187:L320F	L	+	3	2	MS4A14	59939977	0.000000	0.05858	0.007000	0.13788	0.081000	0.17604	-0.924000	0.03996	-0.103000	0.12175	-0.143000	0.13931	TTG	.	.	weak		0.448	MS4A14-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000395383.2		
LBP	3929	hgsc.bcm.edu	37	20	36982785	36982785	+	Missense_Mutation	SNP	C	C	G	rs2232586	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:36982785C>G	ENST00000217407.2	+	4	631	c.470C>G	c.(469-471)tCc>tGc	p.S157C		NM_004139.3	NP_004130.2	P18428	LBP_HUMAN	lipopolysaccharide binding protein	157			S -> C (in dbSNP:rs2232586).	VTAS -> GYCL (in Ref. 1; AAA59493). {ECO:0000305}.	acute-phase response (GO:0006953)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of molecule of bacterial origin (GO:0032490)|innate immune response (GO:0045087)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation involved in immune response (GO:0002281)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of tumor necrosis factor production (GO:0032720)|opsonization (GO:0008228)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage activation (GO:0043032)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of respiratory burst involved in inflammatory response (GO:0060265)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|response to lipopolysaccharide (GO:0032496)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)|lipoteichoic acid binding (GO:0070891)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(1)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				GTTACTGCCTCCAGCTGCAGC	0.592													C|||	28	0.00559105	0.0204	0.0014	5008	,	,		17413	0.0		0.0	False		,,,				2504	0.0				p.S157C		Atlas-SNP	.											.	LBP	60	.	0			c.C470G						PASS	.	C	CYS/SER	45,4361	46.7+/-81.2	1,43,2159	66.0	56.0	59.0		470	3.8	0.2	20	dbSNP_98	59	0,8600		0,0,4300	yes	missense	LBP	NM_004139.2	112	1,43,6459	GG,GC,CC		0.0,1.0213,0.346	probably-damaging	157/482	36982785	45,12961	2203	4300	6503	SO:0001583	missense	3929	exon4			CTGCCTCCAGCTG		CCDS13304.1	20q11.23	2011-08-16	2001-11-28		ENSG00000129988	ENSG00000129988		"""BPI fold containing"""	6517	protein-coding gene	gene with protein product	"""BPI fold containing family D, member 2"""	151990	"""lipopolysaccharide-binding protein"""			8432532	Standard	NM_004139		Approved	BPIFD2	uc002xic.2	P18428	OTTHUMG00000032447	ENST00000217407.2:c.470C>G	20.37:g.36982785C>G	ENSP00000217407:p.Ser157Cys	66.0	0.0	0		56.0	32.0	0.571429	NM_004139	B2R938|O43438|Q92672|Q9H403|Q9UD66	Missense_Mutation	SNP	ENST00000217407.2	37	CCDS13304.1	17	0.007783882783882784	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	0	0.0	C	11.79	1.743153	0.30865	0.010213	0.0	ENSG00000129988	ENST00000217407;ENST00000538599	T	0.07688	3.17	4.77	3.75	0.43078	Lipid-binding serum glycoprotein, N-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.281808	0.30437	N	0.009628	T	0.10766	0.0263	M	0.85041	2.73	0.09310	N	1	D	0.89917	1.0	D	0.80764	0.994	T	0.00759	-1.1578	10	0.62326	D	0.03	-21.3368	9.7646	0.40552	0.2055:0.7945:0.0:0.0	rs2232586	157	P18428	LBP_HUMAN	C	157	ENSP00000217407:S157C	ENSP00000217407:S157C	S	+	2	0	LBP	36416199	0.012000	0.17670	0.193000	0.23327	0.108000	0.19459	2.151000	0.42263	2.648000	0.89879	0.561000	0.74099	TCC	C|0.994;G|0.006	0.006	strong		0.592	LBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079174.2	NM_004139	
PSAPL1	768239	hgsc.bcm.edu	37	4	7436151	7436151	+	Silent	SNP	T	T	C	rs61738663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:7436151T>C	ENST00000319098.4	-	1	549	c.456A>G	c.(454-456)ccA>ccG	p.P152P	SORCS2_ENST00000329016.9_Intron|SORCS2_ENST00000507866.2_Intron|SORCS2_ENST00000511199.1_Intron	NM_001085382.1	NP_001078851.1	Q6NUJ1	SAPL1_HUMAN	prosaposin-like 1 (gene/pseudogene)	152					sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)				lung(4)	4						CTTTGGAGAGTGGCCTCAGGG	0.662													T|||	233	0.0465256	0.1634	0.0231	5008	,	,		16972	0.0		0.0	False		,,,				2504	0.001				p.P152P		Atlas-SNP	.											.	PSAPL1	51	.	0			c.A456G						PASS	.	T	,	545,3441		36,473,1484	11.0	13.0	12.0		456,	-5.4	0.0	4	dbSNP_129	12	3,8305		0,3,4151	no	coding-synonymous,intron	SORCS2,PSAPL1	NM_001085382.1,NM_020777.2	,	36,476,5635	CC,CT,TT		0.0361,13.6729,4.4575	,	152/522,	7436151	548,11746	1993	4154	6147	SO:0001819	synonymous_variant	768239	exon1			GGAGAGTGGCCTC	DQ991252	CCDS47009.1	4p16.1	2010-03-12	2010-03-12			ENSG00000178597			33131	protein-coding gene	gene with protein product			"""prosaposin-like 1"""				Standard	NM_001085382		Approved		uc011bwj.2	Q6NUJ1		ENST00000319098.4:c.456A>G	4.37:g.7436151T>C		66.0	0.0	0		51.0	22.0	0.431373	NM_001085382	A0A184|Q8N7T4	Silent	SNP	ENST00000319098.4	37	CCDS47009.1																																																																																			T|0.963;C|0.037	0.037	strong		0.662	PSAPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358859.1		
USP2	9099	hgsc.bcm.edu	37	11	119243912	119243912	+	Silent	SNP	C	C	T	rs536224379|rs79464246	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:119243912C>T	ENST00000260187.2	-	2	573	c.279G>A	c.(277-279)gaG>gaA	p.E93E	USP2_ENST00000455332.2_Intron|RP11-334E6.3_ENST00000530918.2_RNA	NM_004205.4	NP_004196.4	O75604	UBP2_HUMAN	ubiquitin specific peptidase 2	93	Necessary for interaction with MDM4.				cell cycle (GO:0007049)|muscle organ development (GO:0007517)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of skeletal muscle tissue development (GO:0048643)|protein deubiquitination (GO:0016579)|protein stabilization (GO:0050821)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell cortex (GO:0005938)|centrosome (GO:0005813)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cyclin binding (GO:0030332)|cysteine-type endopeptidase activity (GO:0004197)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	24		all_hematologic(192;4.65e-05)|Breast(348;0.0101)|all_neural(223;0.0218)|Medulloblastoma(222;0.0425)|Renal(330;0.157)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.000513)|Colorectal(284;0.0116)|Lung(307;0.0853)|LUSC - Lung squamous cell carcinoma(976;0.0889)		GGGTCTGGCTCTCTGCCCGCT	0.657													C|||	40	0.00798722	0.0265	0.0072	5008	,	,		16244	0.0		0.0	False		,,,				2504	0.0				p.E93E		Atlas-SNP	.											.	USP2	71	.	0			c.G279A						PASS	.	C		107,4291	82.9+/-121.4	2,103,2094	67.0	76.0	73.0		279	4.3	1.0	11	dbSNP_132	73	1,8589		0,1,4294	no	coding-synonymous	USP2	NM_004205.4		2,104,6388	TT,TC,CC		0.0116,2.4329,0.8315		93/606	119243912	108,12880	2199	4295	6494	SO:0001819	synonymous_variant	9099	exon2			CTGGCTCTCTGCC	AF079564	CCDS8422.1, CCDS8423.1, CCDS58189.1	11q23.3	2008-02-05	2005-08-08			ENSG00000036672		"""Ubiquitin-specific peptidases"""	12618	protein-coding gene	gene with protein product		604725	"""ubiquitin specific protease 2"""			12838346	Standard	NM_004205		Approved	UBP41	uc001pwm.4	O75604		ENST00000260187.2:c.279G>A	11.37:g.119243912C>T		73.0	0.0	0		90.0	50.0	0.555556	NM_004205	B0YJB8|E9PPM2|Q8IUM2|Q8IW04|Q96MB9|Q9BQ21	Silent	SNP	ENST00000260187.2	37	CCDS8422.1																																																																																			C|0.991;T|0.009	0.009	strong		0.657	USP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388361.2	NM_171997	
GPRC5D	55507	hgsc.bcm.edu	37	12	13103196	13103196	+	Silent	SNP	G	G	A	rs150759739	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:13103196G>A	ENST00000228887.1	-	1	122	c.123C>T	c.(121-123)ctC>ctT	p.L41L	RP11-392P7.6_ENST00000538231.1_RNA|RP11-392P7.6_ENST00000543515.2_RNA|RP11-392P7.6_ENST00000536029.1_RNA|RP11-392P7.6_ENST00000540198.1_RNA|GPRC5D_ENST00000396333.3_Silent_p.L41L|RP11-392P7.6_ENST00000545914.1_RNA|RP11-392P7.6_ENST00000394742.3_RNA|RP11-392P7.6_ENST00000542078.1_RNA	NM_018654.1	NP_061124.1	Q9NZD1	GPC5D_HUMAN	G protein-coupled receptor, class C, group 5, member D	41						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			kidney(2)|large_intestine(2)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9		Prostate(47;0.183)		BRCA - Breast invasive adenocarcinoma(232;0.15)		GAAATGCTAAGAGTAGCAGAA	0.547													G|||	16	0.00319489	0.0106	0.0014	5008	,	,		20686	0.001		0.0	False		,,,				2504	0.0				p.L41L		Atlas-SNP	.											.	GPRC5D	23	.	0			c.C123T						PASS	.	G		39,4367	44.6+/-78.6	0,39,2164	98.0	91.0	94.0		123	5.2	1.0	12	dbSNP_134	94	0,8600		0,0,4300	no	coding-synonymous	GPRC5D	NM_018654.1		0,39,6464	AA,AG,GG		0.0,0.8852,0.2999		41/346	13103196	39,12967	2203	4300	6503	SO:0001819	synonymous_variant	55507	exon1			TGCTAAGAGTAGC	AF209923	CCDS8658.1	12p13.3	2014-01-30	2014-01-30		ENSG00000111291	ENSG00000111291		"""GPCR / Class C : Orphans"""	13310	protein-coding gene	gene with protein product		607437	"""G protein-coupled receptor, family C, group 5, member D"""				Standard	XM_005253421		Approved		uc010shp.2	Q9NZD1	OTTHUMG00000168711	ENST00000228887.1:c.123C>T	12.37:g.13103196G>A		74.0	0.0	0		70.0	48.0	0.685714	NM_018654	Q3KNV3|Q7Z5J9|Q8TDS6	Silent	SNP	ENST00000228887.1	37	CCDS8658.1																																																																																			G|0.997;A|0.003	0.003	strong		0.547	GPRC5D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400687.1		
DVL1	1855	hgsc.bcm.edu	37	1	1277183	1277183	+	Missense_Mutation	SNP	C	C	T	rs61735963	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1277183C>T	ENST00000378888.5	-	5	753	c.469G>A	c.(469-471)Gcc>Acc	p.A157T	DVL1_ENST00000378891.5_Missense_Mutation_p.A157T			O14640	DVL1_HUMAN	dishevelled segment polarity protein 1	157				A -> P (in Ref. 1; AAB65242). {ECO:0000305}.	axon extension (GO:0048675)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|cochlea morphogenesis (GO:0090103)|collateral sprouting (GO:0048668)|convergent extension (GO:0060026)|convergent extension involved in neural plate elongation (GO:0022007)|cytoplasmic microtubule organization (GO:0031122)|dendrite morphogenesis (GO:0048813)|intracellular signal transduction (GO:0035556)|negative regulation of protein binding (GO:0032091)|negative regulation of protein kinase activity (GO:0006469)|neural tube development (GO:0021915)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuron projection development (GO:0010976)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|prepulse inhibition (GO:0060134)|protein localization to microtubule (GO:0035372)|protein localization to nucleus (GO:0034504)|receptor clustering (GO:0043113)|regulation of neurotransmitter levels (GO:0001505)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|social behavior (GO:0035176)|synapse organization (GO:0050808)|transcription from RNA polymerase II promoter (GO:0006366)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	axon (GO:0030424)|cell cortex (GO:0005938)|clathrin-coated vesicle (GO:0030136)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|growth cone (GO:0030426)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	enzyme binding (GO:0019899)|frizzled binding (GO:0005109)|identical protein binding (GO:0042802)|protein kinase binding (GO:0019901)|Rac GTPase binding (GO:0048365)			endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	13	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		TTGGTCCGGGCGGCTGTGGGG	0.687													c|||	329	0.0656949	0.2375	0.0202	5008	,	,		17330	0.0		0.001	False		,,,				2504	0.0				p.A157T		Atlas-SNP	.											.	DVL1	36	.	0			c.G469A						PASS	.	C	THR/ALA	898,3474		85,728,1373	14.0	14.0	14.0		469	-3.4	0.0	1	dbSNP_129	14	9,8557		0,9,4274	yes	missense	DVL1	NM_004421.2	58	85,737,5647	TT,TC,CC		0.1051,20.5398,7.0104	benign	157/671	1277183	907,12031	2186	4283	6469	SO:0001583	missense	1855	exon5			TCCGGGCGGCTGT	AF006011	CCDS22.1	1p36	2013-05-22	2013-05-22		ENSG00000107404	ENSG00000107404		"""Dishevelled homologs"""	3084	protein-coding gene	gene with protein product		601365	"""dishevelled 1 (homologous to Drosophila dsh)"", ""dishevelled, dsh homolog 1 (Drosophila)"""			8817329	Standard	NM_004421		Approved		uc001aer.4	O14640	OTTHUMG00000003069	ENST00000378888.5:c.469G>A	1.37:g.1277183C>T	ENSP00000368166:p.Ala157Thr	88.0	0.0	0		107.0	50.0	0.46729	NM_004421	Q5TA33|Q5TA35	Missense_Mutation	SNP	ENST00000378888.5	37		122	0.055860805860805864	114	0.23170731707317074	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	C	8.305	0.820817	0.16678	0.205398	0.001051	ENSG00000107404	ENST00000378891;ENST00000378888;ENST00000345100	T;T	0.04917	3.53;3.53	4.02	-3.44	0.04796	.	0.469288	0.22130	N	0.064219	T	0.00012	0.0000	N	0.04880	-0.145	0.45621	P	0.0014420000000000543	B	0.02656	0.0	B	0.04013	0.001	T	0.37572	-0.9700	9	0.07813	T	0.8	.	0.2996	0.00271	0.3245:0.167:0.1548:0.3536	.	157	O14640-2	.	T	157	ENSP00000368169:A157T;ENSP00000368166:A157T	ENSP00000340031:A157T	A	-	1	0	DVL1	1267046	0.188000	0.23250	0.019000	0.16419	0.398000	0.30690	0.396000	0.20867	-0.463000	0.06973	0.205000	0.17691	GCC	C|0.931;T|0.069	0.069	strong		0.687	DVL1-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000008490.1	NM_004421	
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39262103	39262103	+	Missense_Mutation	SNP	A	A	T	rs374629799	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39262103A>T	ENST00000391415.1	+	1	520	c.463A>T	c.(463-465)Agc>Tgc	p.S155C		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	155	29 X 5 AA repeats of C-C-[RQVHIEK]- [SPTR]-[VSTQCRNP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						ccccagctgcagcatctccag	0.672													a|||	152	0.0303514	0.0893	0.0216	5008	,	,		18051	0.001		0.0139	False		,,,				2504	0.0041				p.S155C		Atlas-SNP	.											KRTAP4-9_ENST00000377734,NS,carcinoma,0,2	KRTAP4-9	110	2	0			c.A463T						PASS	.						6.0	9.0	8.0					17																	39262103		679	1572	2251	SO:0001583	missense	100132386	exon1			AGCTGCAGCATCT	AJ406941	CCDS54124.1	17q21.2	2013-06-25			ENSG00000212722	ENSG00000212722		"""Keratin associated proteins"""	18910	protein-coding gene	gene with protein product							Standard	NM_001146041		Approved	KAP4.9	uc010wfp.2	Q9BYQ8	OTTHUMG00000133584	ENST00000391415.1:c.463A>T	17.37:g.39262103A>T	ENSP00000375234:p.Ser155Cys	125.0	0.0	0		186.0	42.0	0.225806	NM_001146041		Missense_Mutation	SNP	ENST00000391415.1	37	CCDS54124.1	.	.	.	.	.	.	.	.	.	.	.	0.091	-1.167638	0.01660	.	.	ENSG00000212722	ENST00000377734;ENST00000391415;ENST00000333994	T	0.00584	6.4	3.1	-1.38	0.09027	.	.	.	.	.	T	0.00109	0.0003	N	0.00041	-2.485	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48186	-0.9057	9	0.02654	T	1	.	0.2915	0.00259	0.1968:0.2502:0.1975:0.3554	.	155	Q9BYQ8	KRA49_HUMAN	C	143;155;146	ENSP00000375234:S155C	ENSP00000334461:S146C	S	+	1	0	KRTAP4-9	36515629	0.946000	0.32159	0.002000	0.10522	0.205000	0.24178	1.056000	0.30480	-0.110000	0.12022	-1.044000	0.02363	AGC	.	.	weak		0.672	KRTAP4-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257688.1	NM_001146041	
UMODL1	89766	hgsc.bcm.edu	37	21	43536047	43536047	+	Silent	SNP	C	C	T	rs141581454	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:43536047C>T	ENST00000408910.2	+	14	2427	c.2427C>T	c.(2425-2427)aaC>aaT	p.N809N	UMODL1_ENST00000400427.1_Silent_p.N865N|UMODL1_ENST00000400424.2_Silent_p.N737N|UMODL1_ENST00000408989.2_Silent_p.N937N	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	809	SEA 2. {ECO:0000255|PROSITE- ProRule:PRU00188}.				adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						CCTTTCGCAACGCAAGCAGCC	0.468													C|||	6	0.00119808	0.0038	0.0014	5008	,	,		17984	0.0		0.0	False		,,,				2504	0.0				p.N937N	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.C2811T						PASS	.	C	,,,	20,3852		0,20,1916	96.0	98.0	97.0		2427,2595,2211,2811	-6.4	0.0	21	dbSNP_134	97	0,8284		0,0,4142	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	UMODL1	NM_001004416.2,NM_001199527.1,NM_001199528.2,NM_173568.3	,,,	0,20,6058	TT,TC,CC		0.0,0.5165,0.1645	,,,	809/1319,865/1375,737/1247,937/1447	43536047	20,12136	1936	4142	6078	SO:0001819	synonymous_variant	89766	exon13			TCGCAACGCAAGC		CCDS42935.1, CCDS42936.1, CCDS56214.1, CCDS56215.1	21q22.3	2008-07-04			ENSG00000177398	ENSG00000177398			12560	protein-coding gene	gene with protein product	"""olfactorin"""	613859				16026467	Standard	NM_173568		Approved		uc002zag.1	Q5DID0	OTTHUMG00000086788	ENST00000408910.2:c.2427C>T	21.37:g.43536047C>T		212.0	0.0	0		233.0	116.0	0.497854	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Silent	SNP	ENST00000408910.2	37	CCDS42936.1																																																																																			C|0.998;T|0.002	0.002	strong		0.468	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
NDNL2	56160	hgsc.bcm.edu	37	15	29561467	29561467	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:29561467T>G	ENST00000332303.4	-	1	566	c.443A>C	c.(442-444)aAg>aCg	p.K148T	FAM189A1_ENST00000261275.4_Intron	NM_138704.3	NP_619649.1	Q96MG7	MAGG1_HUMAN	necdin-like 2	148	Interaction with NSMCE1.|MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				DNA recombination (GO:0006310)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)|regulation of growth (GO:0040008)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Smc5-Smc6 complex (GO:0030915)				breast(3)|large_intestine(2)|lung(3)	8		all_lung(180;4.69e-11)|Breast(32;0.0013)		all cancers(64;8.37e-11)|Epithelial(43;9.29e-10)|BRCA - Breast invasive adenocarcinoma(123;0.00736)|GBM - Glioblastoma multiforme(186;0.018)|Lung(196;0.153)		AGTGTTGCTCTTGGGTTCAAG	0.582																																					p.K148T		Atlas-SNP	.											.	NDNL2	19	.	0			c.A443C						PASS	.						81.0	74.0	76.0					15																	29561467		2203	4300	6503	SO:0001583	missense	56160	exon1			TTGCTCTTGGGTT	AF490510	CCDS10023.1	15q13.1	2008-02-01			ENSG00000185115	ENSG00000185115			7677	protein-coding gene	gene with protein product		608243				18086888	Standard	NM_138704		Approved	HCA4, MAGEG1, MAGEL3, NSE3, NSMCE3	uc001zco.3	Q96MG7	OTTHUMG00000129261	ENST00000332303.4:c.443A>C	15.37:g.29561467T>G	ENSP00000330694:p.Lys148Thr	111.0	0.0	0		116.0	58.0	0.5	NM_138704	Q8IW16|Q8TEI6|Q9H214	Missense_Mutation	SNP	ENST00000332303.4	37	CCDS10023.1	.	.	.	.	.	.	.	.	.	.	T	16.86	3.238898	0.58995	.	.	ENSG00000185115	ENST00000332303	T	0.05717	3.4	3.91	-1.44	0.08856	.	0.124104	0.52532	U	0.000070	T	0.03305	0.0096	N	0.20807	0.61	0.09310	N	0.999997	P	0.36712	0.566	B	0.42959	0.403	T	0.35051	-0.9804	10	0.02654	T	1	.	4.0573	0.09823	0.0:0.3563:0.1937:0.45	.	148	Q96MG7	MAGG1_HUMAN	T	148	ENSP00000330694:K148T	ENSP00000330694:K148T	K	-	2	0	NDNL2	27348759	1.000000	0.71417	0.007000	0.13788	0.969000	0.65631	0.975000	0.29449	-0.271000	0.09272	0.460000	0.39030	AAG	.	.	none		0.582	NDNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251370.1	NM_138704	
TRANK1	9881	hgsc.bcm.edu	37	3	36898699	36898699	+	Silent	SNP	G	G	A	rs187740236	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:36898699G>A	ENST00000429976.2	-	12	2629	c.2382C>T	c.(2380-2382)tgC>tgT	p.C794C	TRANK1_ENST00000301807.6_Silent_p.C244C|TRANK1_ENST00000428977.2_Silent_p.C244C	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	794							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						TTTCTGAAGTGCACTCGATCT	0.502													G|||	14	0.00279553	0.0106	0.0	5008	,	,		20254	0.0		0.0	False		,,,				2504	0.0				p.C794C		Atlas-SNP	.											.	TRANK1	398	.	0			c.C2382T						PASS	.	G		34,4008		1,32,1988	243.0	235.0	238.0		2382	-3.4	0.7	3		238	0,8392		0,0,4196	yes	coding-synonymous	TRANK1	NM_014831.2		1,32,6184	AA,AG,GG		0.0,0.8412,0.2734		794/2926	36898699	34,12400	2021	4196	6217	SO:0001819	synonymous_variant	9881	exon12			TGAAGTGCACTCG	AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29011	protein-coding gene	gene with protein product	"""lupus brain antigen 1"", ""KIAA0342"""					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.2382C>T	3.37:g.36898699G>A		54.0	0.0	0		74.0	35.0	0.472973	NM_014831	Q8N8K0	Silent	SNP	ENST00000429976.2	37	CCDS46789.2																																																																																			G|0.998;A|0.002	0.002	strong		0.502	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831	
GRM5	2915	hgsc.bcm.edu	37	11	88338074	88338074	+	Silent	SNP	G	G	A	rs61745770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:88338074G>A	ENST00000305447.4	-	4	1355	c.1206C>T	c.(1204-1206)aaC>aaT	p.N402N	GRM5_ENST00000393297.1_Silent_p.N402N|GRM5_ENST00000418177.2_Silent_p.N402N|GRM5_ENST00000455756.2_Silent_p.N402N|GRM5_ENST00000305432.5_Silent_p.N402N	NM_001143831.2	NP_001137303.1	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5	402					activation of MAPKKK activity (GO:0000185)|cognition (GO:0050890)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|learning (GO:0007612)|locomotory behavior (GO:0007626)|negative regulation of locomotion (GO:0040013)|phospholipase C-activating G-protein coupled glutamate receptor signaling pathway (GO:0007206)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(1)|breast(5)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(18)|lung(40)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)|Rufinamide(DB06201)	AATAGATGGCGTTGATCACAA	0.458													g|||	136	0.0271565	0.0946	0.0144	5008	,	,		20660	0.0		0.001	False		,,,				2504	0.0				p.N402N		Atlas-SNP	.											.	GRM5	414	.	0			c.C1206T						PASS	.	A	,	353,4049	183.3+/-210.9	14,325,1862	101.0	86.0	91.0		1206,1206	-2.1	1.0	11	dbSNP_129	91	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	GRM5	NM_000842.3,NM_001143831.2	,	14,325,6161	AA,AG,GG		0.0,8.0191,2.7154	,	402/1181,402/1213	88338074	353,12647	2201	4299	6500	SO:0001819	synonymous_variant	2915	exon5			GATGGCGTTGATC	D28538	CCDS8283.1, CCDS44694.1	11q14.3	2014-06-12			ENSG00000168959	ENSG00000168959		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4597	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 86"""	604102				7908515	Standard	NM_001143831		Approved	MGLUR5, GPRC1E, mGlu5, PPP1R86	uc001pcq.3	P41594	OTTHUMG00000134306	ENST00000305447.4:c.1206C>T	11.37:g.88338074G>A		65.0	0.0	0		71.0	40.0	0.56338	NM_000842	Q6J164	Silent	SNP	ENST00000305447.4	37	CCDS44694.1																																																																																			G|0.971;A|0.029	0.029	strong		0.458	GRM5-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259226.1	NM_000842	
ABCA13	154664	hgsc.bcm.edu	37	7	48452147	48452147	+	Silent	SNP	G	G	A	rs369363967	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:48452147G>A	ENST00000435803.1	+	41	12450	c.12426G>A	c.(12424-12426)acG>acA	p.T4142T		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	4142					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						TGCACCTGACGGGCTATGGGA	0.478													G|||	4	0.000798722	0.0023	0.0014	5008	,	,		17632	0.0		0.0	False		,,,				2504	0.0				p.T4142T		Atlas-SNP	.											.	ABCA13	1192	.	0			c.G12426A						PASS	.	G		24,3846		0,24,1911	80.0	75.0	77.0		12426	-9.9	0.0	7		77	0,8308		0,0,4154	no	coding-synonymous	ABCA13	NM_152701.3		0,24,6065	AA,AG,GG		0.0,0.6202,0.1971		4142/5059	48452147	24,12154	1935	4154	6089	SO:0001819	synonymous_variant	154664	exon41			CCTGACGGGCTAT	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"""ATP binding cassette transporters / subfamily A"""	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.12426G>A	7.37:g.48452147G>A		121.0	0.0	0		152.0	85.0	0.559211	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Silent	SNP	ENST00000435803.1	37	CCDS47584.1																																																																																			.	.	weak		0.478	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
CEP55	55165	hgsc.bcm.edu	37	10	95262980	95262980	+	Silent	SNP	C	C	T	rs62642530	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:95262980C>T	ENST00000371485.3	+	3	598	c.294C>T	c.(292-294)acC>acT	p.T98T		NM_001127182.1|NM_018131.4	NP_001120654|NP_060601	Q53EZ4	CEP55_HUMAN	centrosomal protein 55kDa	98					establishment of protein localization (GO:0045184)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|midbody (GO:0030496)				kidney(1)|large_intestine(5)|lung(6)|stomach(1)	13		Colorectal(252;0.207)				ATAGTACTACCACATTGCTTG	0.443													C|||	20	0.00399361	0.0129	0.0014	5008	,	,		19829	0.0		0.0	False		,,,				2504	0.002				p.T98T		Atlas-SNP	.											.	CEP55	35	.	0			c.C294T						PASS	.	C	,	38,4368	16.8+/-37.8	0,38,2165	147.0	131.0	136.0		294,294	-10.7	0.0	10	dbSNP_129	136	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CEP55	NM_001127182.1,NM_018131.4	,	0,38,6465	TT,TC,CC		0.0,0.8625,0.2922	,	98/465,98/465	95262980	38,12968	2203	4300	6503	SO:0001819	synonymous_variant	55165	exon3			TACTACCACATTG	AK001402	CCDS7428.1	10q24.1	2014-02-20	2005-12-01	2005-12-01	ENSG00000138180	ENSG00000138180			1161	protein-coding gene	gene with protein product	"""cancer/testis antigen 111"""	610000	"""chromosome 10 open reading frame 3"""	C10orf3		16198290	Standard	NM_018131		Approved	FLJ10540, CT111	uc009xug.3	Q53EZ4	OTTHUMG00000018774	ENST00000371485.3:c.294C>T	10.37:g.95262980C>T		102.0	0.0	0		82.0	43.0	0.52439	NM_018131	B2RDG8|Q32WF5|Q3MV20|Q5VY28|Q6N034|Q96H32|Q9NVS7	Silent	SNP	ENST00000371485.3	37	CCDS7428.1																																																																																			C|0.996;T|0.004	0.004	strong		0.443	CEP55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049434.1	NM_018131	
MYH1	4619	hgsc.bcm.edu	37	17	10404766	10404766	+	Silent	SNP	C	C	T	rs61730793	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:10404766C>T	ENST00000226207.5	-	27	3493	c.3399G>A	c.(3397-3399)cgG>cgA	p.R1133R	RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1133					muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						CTGCTTTGGCCCGGGAGGCCC	0.572													C|||	31	0.0061901	0.0227	0.0014	5008	,	,		16908	0.0		0.0	False		,,,				2504	0.0				p.R1133R		Atlas-SNP	.											.	MYH1	403	.	0			c.G3399A						PASS	.	C		90,4316		1,88,2114	40.0	45.0	44.0		3399	3.3	1.0	17	dbSNP_129	44	0,8588		0,0,4294	no	coding-synonymous	MYH1	NM_005963.3		1,88,6408	TT,TC,CC		0.0,2.0427,0.6926		1133/1940	10404766	90,12904	2203	4294	6497	SO:0001819	synonymous_variant	4619	exon27			TTTGGCCCGGGAG		CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"""Myosins / Myosin superfamily : Class II"""	7567	protein-coding gene	gene with protein product	"""myosin heavy chain IIx/d"""	160730	"""myosin, heavy polypeptide 1, skeletal muscle, adult"""			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.3399G>A	17.37:g.10404766C>T		144.0	0.0	0		160.0	86.0	0.5375	NM_005963	Q14CA4|Q9Y622	Silent	SNP	ENST00000226207.5	37	CCDS11155.1																																																																																			C|0.994;T|0.006	0.006	strong		0.572	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963	
POP5	51367	hgsc.bcm.edu	37	12	121019009	121019009	+	Silent	SNP	G	G	C	rs74750729	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:121019009G>C	ENST00000357500.4	-	2	107	c.72C>G	c.(70-72)ctC>ctG	p.L24L	POP5_ENST00000341039.2_Silent_p.L24L|POP5_ENST00000542776.1_5'UTR	NM_015918.3	NP_057002.2	Q969H6	POP5_HUMAN	processing of precursor 5, ribonuclease P/MRP subunit (S. cerevisiae)	24					tRNA processing (GO:0008033)	nucleolar ribonuclease P complex (GO:0005655)	ribonuclease P activity (GO:0004526)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|ovary(1)	7	all_neural(191;0.077)|Medulloblastoma(191;0.0922)					CTCGGTCATCGAGGCTTAGGC	0.672													G|||	8	0.00159744	0.0061	0.0	5008	,	,		16752	0.0		0.0	False		,,,				2504	0.0				p.L24L		Atlas-SNP	.											.	POP5	14	.	0			c.C72G						PASS	.	G	,	43,4363	44.6+/-78.6	0,43,2160	44.0	46.0	45.0		72,72	1.7	1.0	12	dbSNP_131	45	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	POP5	NM_015918.3,NM_198202.1	,	0,43,6460	CC,CG,GG		0.0,0.9759,0.3306	,	24/164,24/114	121019009	43,12963	2203	4300	6503	SO:0001819	synonymous_variant	51367	exon2			GTCATCGAGGCTT	AJ306296	CCDS9202.1, CCDS9203.1	12q24.31	2012-05-21			ENSG00000167272	ENSG00000167272			17689	protein-coding gene	gene with protein product		609992				11413139	Standard	NM_198202		Approved		uc001tys.3	Q969H6	OTTHUMG00000169023	ENST00000357500.4:c.72C>G	12.37:g.121019009G>C		88.0	0.0	0		85.0	45.0	0.529412	NM_198202	A6NL80|Q53FS5|Q9Y2Q6	Silent	SNP	ENST00000357500.4	37	CCDS9202.1																																																																																			G|0.998;C|0.002	0.002	strong		0.672	POP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401993.1	NM_015918	
LILRA2	11027	hgsc.bcm.edu	37	19	55098742	55098742	+	Missense_Mutation	SNP	G	G	T	rs73939008	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55098742G>T	ENST00000251377.3	+	9	1514	c.1381G>T	c.(1381-1383)Gtg>Ttg	p.V461L	LILRA2_ENST00000391737.1_Missense_Mutation_p.V432L|LILRA2_ENST00000251376.3_Missense_Mutation_p.V444L|CTB-83J4.2_ENST00000596330.1_lincRNA|LILRA2_ENST00000391738.3_Missense_Mutation_p.V461L|LILRB1_ENST00000448689.1_Intron|LILRB1_ENST00000418536.2_Intron|LILRB1_ENST00000396321.2_Intron			Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2	461					defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(33)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50				GBM - Glioblastoma multiforme(193;0.0963)		CTTGGTCCTGGTGGTCCTCGG	0.562													g|||	51	0.0101837	0.0378	0.0014	5008	,	,		17380	0.0		0.0	False		,,,				2504	0.0				p.V461L		Atlas-SNP	.											LILRA2,right_upper_lobe,carcinoma,0,1	LILRA2	99	1	0			c.G1381T						PASS	.	G	LEU/VAL,LEU/VAL	100,4306	78.3+/-116.7	0,100,2103	111.0	96.0	101.0		1381,1330	-4.3	0.0	19	dbSNP_130	101	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	LILRA2	NM_001130917.1,NM_006866.2	32,32	0,102,6401	TT,TG,GG		0.0233,2.2696,0.7843	,	461/484,444/467	55098742	102,12904	2203	4300	6503	SO:0001583	missense	11027	exon8			GTCCTGGTGGTCC	U82275	CCDS12900.1, CCDS46179.1, CCDS74453.1	19q13.4	2013-01-11			ENSG00000239998	ENSG00000239998		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6603	protein-coding gene	gene with protein product		604812				9079806, 9548455	Standard	XM_005258452		Approved	LIR-7, ILT1, CD85h, LIR7		Q8N149	OTTHUMG00000065703	ENST00000251377.3:c.1381G>T	19.37:g.55098742G>T	ENSP00000251377:p.Val461Leu	227.0	0.0	0		253.0	109.0	0.43083	NM_001130917	O75020	Missense_Mutation	SNP	ENST00000251377.3	37	CCDS46179.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	G	10.21	1.287724	0.23478	0.022696	2.33E-4	ENSG00000239998	ENST00000251377;ENST00000391738;ENST00000251376;ENST00000391737	T;T;T;T	0.00529	6.98;6.98;6.86;6.78	2.74	-4.29	0.03721	.	22.652400	0.00166	N	0.000016	T	0.00109	0.0003	N	0.25094	0.71	0.09310	N	0.999998	B;B;P	0.45126	0.341;0.09;0.851	B;B;P	0.47402	0.066;0.026;0.546	T	0.55755	-0.8091	10	0.02654	T	1	.	5.1841	0.15174	0.0:0.3589:0.2798:0.3612	.	432;461;444	A8MZH0;Q8N149;Q8N149-2	.;LIRA2_HUMAN;.	L	461;461;444;432	ENSP00000251377:V461L;ENSP00000375618:V461L;ENSP00000251376:V444L;ENSP00000375617:V432L	ENSP00000251376:V444L	V	+	1	0	LILRA2	59790554	0.003000	0.15002	0.035000	0.18076	0.160000	0.22226	-1.113000	0.03296	-0.357000	0.08175	0.609000	0.83330	GTG	G|0.991;T|0.009	0.009	strong		0.562	LILRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140813.2		
DMD	1756	hgsc.bcm.edu	37	X	32466654	32466654	+	Silent	SNP	G	G	A	rs143628111	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:32466654G>A	ENST00000357033.4	-	27	3911	c.3705C>T	c.(3703-3705)gcC>gcT	p.A1235A	DMD_ENST00000378677.2_Silent_p.A1231A	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	1235					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				CCTTTTTTAAGGCCTCTTGTG	0.438													G|||	71	0.0188079	0.0537	0.0	3775	,	,		13391	0.0		0.0	False		,,,				2504	0.0				p.A1235A		Atlas-SNP	.											.	DMD	2127	.	0			c.C3705T						PASS	.	G	,,,,	183,3650		3,143,34,1485,537	199.0	158.0	172.0		3681,3705,3336,3693,3336	4.0	1.0	X	dbSNP_134	172	2,6725		0,2,0,2426,1871	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DMD	NM_000109.3,NM_004006.2,NM_004007.2,NM_004009.3,NM_004010.3	,,,,	3,145,34,3911,2408	AA,AG,A,GG,G		0.0297,4.7743,1.7519	,,,,	1227/3678,1235/3686,1112/3563,1231/3682,1112/3563	32466654	185,10375	2202	4299	6501	SO:0001819	synonymous_variant	1756	exon27			TTTTAAGGCCTCT	AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.3705C>T	X.37:g.32466654G>A		269.0	0.0	0		258.0	127.0	0.492248	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Silent	SNP	ENST00000357033.4	37	CCDS14233.1																																																																																			G|0.983;A|0.017	0.017	strong		0.438	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
TICRR	90381	hgsc.bcm.edu	37	15	90167610	90167610	+	Missense_Mutation	SNP	G	G	T	rs115865608	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90167610G>T	ENST00000268138.7	+	20	4174	c.4069G>T	c.(4069-4071)Gtt>Ttt	p.V1357F	TICRR_ENST00000560985.1_Missense_Mutation_p.V1356F|KIF7_ENST00000558928.1_Intron			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	1357	Pro-rich.				cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|formation of translation preinitiation complex (GO:0001731)|mitotic DNA replication checkpoint (GO:0033314)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	chromatin binding (GO:0003682)										CTCCTGCCCTGTTCCCTCAAC	0.517													G|||	15	0.00299521	0.0098	0.0029	5008	,	,		20300	0.0		0.0	False		,,,				2504	0.0				p.V1357F		Atlas-SNP	.											.	.	.	.	0			c.G4069T						PASS	.	G	PHE/VAL	47,4353	48.9+/-83.8	1,45,2154	129.0	129.0	129.0		4069	0.1	0.0	15	dbSNP_132	129	0,8598		0,0,4299	yes	missense	C15orf42	NM_152259.3	50	1,45,6453	TT,TG,GG		0.0,1.0682,0.3616	possibly-damaging	1357/1911	90167610	47,12951	2200	4299	6499	SO:0001583	missense	90381	exon20			TGCCCTGTTCCCT	AK123612	CCDS10352.2	15q26.1	2012-07-11	2012-07-11	2012-07-11	ENSG00000140534	ENSG00000140534			28704	protein-coding gene	gene with protein product	"""TOPBP1-interacting replication-stimulating protein"", ""SLD3 homolog (S. cerevisiae)"""	613298	"""chromosome 15 open reading frame 42"""	C15orf42		20116089, 20080954	Standard	NM_152259		Approved	MGC45866, FLJ41618, Treslin, SLD3	uc002boe.3	Q7Z2Z1	OTTHUMG00000149648	ENST00000268138.7:c.4069G>T	15.37:g.90167610G>T	ENSP00000268138:p.Val1357Phe	63.0	0.0	0		60.0	34.0	0.566667	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Missense_Mutation	SNP	ENST00000268138.7	37	CCDS10352.2	3	0.0013736263736263737	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	0	0.0	G	8.278	0.814810	0.16607	0.010682	0.0	ENSG00000140534	ENST00000268138	T	0.08984	3.03	4.59	0.12	0.14691	.	1.919780	0.02660	N	0.107408	T	0.09598	0.0236	L	0.50333	1.59	0.09310	N	1	P	0.43701	0.815	P	0.46389	0.515	T	0.26883	-1.0090	10	0.40728	T	0.16	0.4344	7.2402	0.26092	0.2249:0.1216:0.6535:0.0	.	1357	Q7Z2Z1	TICRR_HUMAN	F	1357	ENSP00000268138:V1357F	ENSP00000268138:V1357F	V	+	1	0	C15orf42	87968614	0.003000	0.15002	0.002000	0.10522	0.216000	0.24613	0.321000	0.19558	0.118000	0.18165	-0.140000	0.14226	GTT	G|0.996;T|0.004	0.004	strong		0.517	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259	
C1orf112	55732	hgsc.bcm.edu	37	1	169796859	169796859	+	Silent	SNP	A	A	C	rs149832132	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:169796859A>C	ENST00000286031.6	+	12	1705	c.1005A>C	c.(1003-1005)ccA>ccC	p.P335P	C1orf112_ENST00000413811.2_Intron|C1orf112_ENST00000498289.1_3'UTR|C1orf112_ENST00000359326.4_Silent_p.P335P	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	335										breast(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|stomach(1)	34	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					AAGACCTGCCATGTGAACTGC	0.398													A|||	14	0.00279553	0.0106	0.0	5008	,	,		19847	0.0		0.0	False		,,,				2504	0.0				p.P335P		Atlas-SNP	.											.	C1orf112	74	.	0			c.A1005C						PASS	.	A		42,4364	45.3+/-79.5	0,42,2161	348.0	345.0	346.0		1005	-10.8	0.0	1	dbSNP_134	346	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	C1orf112	NM_018186.2		0,43,6460	CC,CA,AA		0.0116,0.9532,0.3306		335/854	169796859	43,12963	2203	4300	6503	SO:0001819	synonymous_variant	55732	exon12			CCTGCCATGTGAA	AL354614	CCDS1285.1	1q24.2	2012-06-26			ENSG00000000460	ENSG00000000460			25565	protein-coding gene	gene with protein product						12477932	Standard	NM_018186		Approved	FLJ10706	uc001ggq.3	Q9NSG2	OTTHUMG00000035821	ENST00000286031.6:c.1005A>C	1.37:g.169796859A>C		67.0	0.0	0		76.0	26.0	0.342105	NM_018186	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Silent	SNP	ENST00000286031.6	37	CCDS1285.1																																																																																			A|0.997;C|0.003	0.003	strong		0.398	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186	
C16orf82	162083	hgsc.bcm.edu	37	16	27078705	27078705	+	lincRNA	SNP	T	T	C	rs115398674	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27078705T>C	ENST00000505035.1	+	0	678				RP11-673P17.2_ENST00000565783.1_RNA			Q7Z2V1	TNT_HUMAN	chromosome 16 open reading frame 82																		CTGGGCTCCATAGACCCTCCC	0.652													C|||	96	0.0191693	0.0711	0.0014	5008	,	,		17209	0.0		0.001	False		,,,				2504	0.0				p.I130T		Atlas-SNP	.											.	.	.	.	0			c.T389C						PASS	.	C	THR/ILE	203,3827		4,195,1816	8.0	12.0	10.0		389	-4.4	0.0	16	dbSNP_132	10	4,8292		0,4,4144	yes	missense	C16orf82	NM_001145545.1	89	4,199,5960	CC,CT,TT		0.0482,5.0372,1.6794	benign	130/155	27078705	207,12119	2015	4148	6163			162083	exon1			GCTCCATAGACCC	BC031257		16p12.1	2013-01-24			ENSG00000234186	ENSG00000234186			30755	other	unknown						12477932	Standard	NM_001145545		Approved	TNT	uc010vcm.2	Q7Z2V1	OTTHUMG00000161986		16.37:g.27078705T>C		66.0	0.0	0		74.0	26.0	0.351351	NM_001145545	B9EGC2|Q8NEF0	Missense_Mutation	SNP	ENST00000505035.1	37																																																																																				T|0.980;C|0.020	0.020	strong		0.652	C16orf82-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000366634.1	NM_001145545	
NID2	22795	hgsc.bcm.edu	37	14	52493996	52493996	+	Missense_Mutation	SNP	C	C	T	rs28507587	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:52493996C>T	ENST00000216286.5	-	12	2596	c.2597G>A	c.(2596-2598)cGg>cAg	p.R866Q	NID2_ENST00000541773.1_Intron	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	866	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.		R -> Q (in dbSNP:rs28507587).		basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					GTGAACACACCGGGCCTGCCC	0.587													c|||	116	0.0231629	0.0847	0.0058	5008	,	,		19977	0.0		0.0	False		,,,				2504	0.0				p.R866Q		Atlas-SNP	.											NID2,NS,carcinoma,-1,1	NID2	201	1	0			c.G2597A						PASS	.	C	GLN/ARG	293,4113	160.3+/-192.7	12,269,1922	41.0	37.0	38.0		2597	-0.7	1.0	14	dbSNP_125	38	5,8595	3.0+/-9.4	0,5,4295	yes	missense	NID2	NM_007361.3	43	12,274,6217	TT,TC,CC		0.0581,6.65,2.2913	possibly-damaging	866/1376	52493996	298,12708	2203	4300	6503	SO:0001583	missense	22795	exon12			ACACACCGGGCCT	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.2597G>A	14.37:g.52493996C>T	ENSP00000216286:p.Arg866Gln	70.0	0.0	0		107.0	51.0	0.476636	NM_007361	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	37	CCDS9706.1	38	0.0173992673992674	35	0.07113821138211382	3	0.008287292817679558	0	0.0	0	0.0	C	9.202	1.028739	0.19512	0.0665	5.81E-4	ENSG00000087303	ENST00000216286;ENST00000316204;ENST00000395707	T	0.71934	-0.61	5.98	-0.687	0.11320	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.509728	0.21782	N	0.069185	T	0.05181	0.0138	L	0.33339	1.005	0.53688	D	0.999977	B;P;B	0.45044	0.012;0.849;0.04	B;B;B	0.26094	0.011;0.066;0.025	T	0.28138	-1.0053	10	0.10902	T	0.67	.	12.2116	0.54383	0.0:0.5941:0.0:0.4059	rs28507587;rs28507587	460;868;866	E7EPP3;Q5CZI2;Q14112	.;.;NID2_HUMAN	Q	866;460;868	ENSP00000216286:R866Q	ENSP00000216286:R866Q	R	-	2	0	NID2	51563746	0.000000	0.05858	0.956000	0.39512	0.155000	0.21991	-1.056000	0.03489	-0.047000	0.13423	-0.222000	0.12452	CGG	C|0.979;T|0.021	0.021	strong		0.587	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1		
FBXW9	84261	hgsc.bcm.edu	37	19	12800597	12800597	+	Missense_Mutation	SNP	T	T	C	rs73921601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12800597T>C	ENST00000380339.3	-	7	1250	c.1214A>G	c.(1213-1215)aAc>aGc	p.N405S	FBXW9_ENST00000544494.1_Missense_Mutation_p.N113S|CTD-2659N19.2_ENST00000585742.1_RNA|CTD-2192J16.26_ENST00000593554.1_lincRNA|FBXW9_ENST00000393261.3_Missense_Mutation_p.N375S|FBXW9_ENST00000587955.1_Missense_Mutation_p.N395S			Q5XUX1	FBXW9_HUMAN	F-box and WD repeat domain containing 9	405					SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)					cervix(1)|lung(4)|ovary(1)|prostate(1)	7						GAAGCAGCCGTTGCGGTTGGC	0.652													T|||	245	0.0489217	0.1679	0.0187	5008	,	,		17279	0.0		0.0099	False		,,,				2504	0.0				p.N375S		Atlas-SNP	.											FBXW9_ENST00000393261,caecum,carcinoma,+1,3	FBXW9	30	3	0			c.A1124G						PASS	.	T	SER/ASN	686,3720	270.4+/-269.6	52,582,1569	60.0	63.0	62.0		1124	-0.8	0.0	19	dbSNP_130	62	125,8475	61.3+/-123.2	0,125,4175	yes	missense	FBXW9	NM_032301.2	46	52,707,5744	CC,CT,TT		1.4535,15.5697,6.2356	benign	375/459	12800597	811,12195	2203	4300	6503	SO:0001583	missense	84261	exon7			CAGCCGTTGCGGT	BC004290	CCDS12278.2	19p13.2	2013-01-09	2007-02-08		ENSG00000132004	ENSG00000132004		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	28136	protein-coding gene	gene with protein product		609074	"""F-box and WD-40 domain protein 9"""			12477932	Standard	NM_032301		Approved	MGC10870, Fbw9	uc002mum.1	Q5XUX1	OTTHUMG00000150152	ENST00000380339.3:c.1214A>G	19.37:g.12800597T>C	ENSP00000369696:p.Asn405Ser	85.0	0.0	0		84.0	29.0	0.345238	NM_032301	B3KVP7|Q9BT89	Missense_Mutation	SNP	ENST00000380339.3	37		87	0.03983516483516483	73	0.1483739837398374	7	0.019337016574585635	0	0.0	7	0.009234828496042216	T	4.791	0.147100	0.09134	0.155697	0.014535	ENSG00000132004	ENST00000544494;ENST00000393261;ENST00000380339	T;T;T	0.75154	-0.91;-0.91;-0.91	4.32	-0.772	0.10998	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	2.425580	0.01961	N	0.043380	T	0.00384	0.0012	L	0.27053	0.805	0.80722	P	0.0	B;B;B	0.11235	0.001;0.004;0.001	B;B;B	0.12156	0.003;0.007;0.001	T	0.02326	-1.1176	9	0.21540	T	0.41	2.9217	4.636	0.12525	0.0:0.4404:0.1963:0.3633	.	395;405;375	Q5XUX1-2;Q5XUX1;Q5XUX1-3	.;FBXW9_HUMAN;.	S	113;375;405	ENSP00000442714:N113S;ENSP00000376945:N375S;ENSP00000369696:N405S	ENSP00000369696:N405S	N	-	2	0	FBXW9	12661597	0.000000	0.05858	0.001000	0.08648	0.064000	0.16182	-0.137000	0.10389	0.154000	0.19237	0.397000	0.26171	AAC	T|0.944;C|0.056	0.056	strong		0.652	FBXW9-201	KNOWN	basic	protein_coding	protein_coding		NM_032301	
UBR4	23352	hgsc.bcm.edu	37	1	19451090	19451090	+	Missense_Mutation	SNP	T	T	C	rs183578825	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19451090T>C	ENST00000375254.3	-	65	9560	c.9533A>G	c.(9532-9534)aAt>aGt	p.N3178S	UBR4_ENST00000375217.2_Missense_Mutation_p.N3171S|UBR4_ENST00000375226.2_Missense_Mutation_p.N3154S|UBR4_ENST00000375267.2_Missense_Mutation_p.N3178S	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	3178					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)		GATTCGAGAATTGGTGTCAGT	0.468													T|||	3	0.000599042	0.0023	0.0	5008	,	,		19837	0.0		0.0	False		,,,				2504	0.0				p.N3178S		Atlas-SNP	.											UBR4,NS,carcinoma,0,1	UBR4	415	1	0			c.A9533G						PASS	.						201.0	183.0	189.0					1																	19451090		2203	4300	6503	SO:0001583	missense	23352	exon65			CGAGAATTGGTGT	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.9533A>G	1.37:g.19451090T>C	ENSP00000364403:p.Asn3178Ser	164.0	0.0	0		167.0	79.0	0.473054	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	T	13.60	2.286447	0.40494	.	.	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000425413;ENST00000417040	T;T;T;T	0.21543	2.0;2.0;2.01;2.01	6.07	3.29	0.37713	.	0.196102	0.52532	N	0.000075	T	0.07999	0.0200	N	0.03608	-0.345	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.24693	-1.0153	10	0.16896	T	0.51	.	7.8597	0.29504	0.0:0.303:0.0:0.697	.	3178	Q5T4S7	UBR4_HUMAN	S	3178;3178;3171;3154;786;1864	ENSP00000364403:N3178S;ENSP00000364416:N3178S;ENSP00000364365:N3171S;ENSP00000364374:N3154S	ENSP00000364365:N3171S	N	-	2	0	UBR4	19323677	1.000000	0.71417	0.990000	0.47175	0.842000	0.47809	3.890000	0.56220	0.348000	0.23949	0.533000	0.62120	AAT	T|0.999;C|0.001	0.001	strong		0.468	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
ZDHHC19	131540	hgsc.bcm.edu	37	3	195935346	195935346	+	Missense_Mutation	SNP	C	C	T	rs75505676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195935346C>T	ENST00000296326.3	-	4	573	c.494G>A	c.(493-495)tGc>tAc	p.C165Y	ZDHHC19_ENST00000488508.1_5'UTR	NM_001039617.1	NP_001034706.1	Q8WVZ1	ZDH19_HUMAN	zinc finger, DHHC-type containing 19	165						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(1)|liver(1)|lung(7)|ovary(3)	14	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.89e-25)|all cancers(36;1.46e-23)|OV - Ovarian serous cystadenocarcinoma(49;2.1e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0022)		CGAGTAGAGGCACAGGGACAG	0.602													C|||	15	0.00299521	0.0098	0.0029	5008	,	,		16054	0.0		0.0	False		,,,				2504	0.0				p.C165Y		Atlas-SNP	.											.	ZDHHC19	25	.	0			c.G494A						PASS	.	C	TYR/CYS	41,4341		0,41,2150	117.0	137.0	130.0		494	4.7	1.0	3	dbSNP_131	130	0,8560		0,0,4280	yes	missense	ZDHHC19	NM_001039617.1	194	0,41,6430	TT,TC,CC		0.0,0.9356,0.3168	probably-damaging	165/310	195935346	41,12901	2191	4280	6471	SO:0001583	missense	131540	exon4			TAGAGGCACAGGG	BC022078	CCDS43190.1	3q29	2008-05-02			ENSG00000163958	ENSG00000163958		"""Zinc fingers, DHHC-type"""	20713	protein-coding gene	gene with protein product							Standard	XR_246038		Approved	MGC33345	uc003fwc.3	Q8WVZ1	OTTHUMG00000133642	ENST00000296326.3:c.494G>A	3.37:g.195935346C>T	ENSP00000296326:p.Cys165Tyr	242.0	0.0	0		244.0	116.0	0.47541	NM_001039617	A8MSY6|B3KVI1	Missense_Mutation	SNP	ENST00000296326.3	37	CCDS43190.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	C	19.39	3.817947	0.71028	0.009356	0.0	ENSG00000163958	ENST00000296326	T	0.24350	1.86	5.61	4.72	0.59763	Zinc finger, DHHC-type, palmitoyltransferase (1);	0.000000	0.64402	D	0.000008	T	0.44912	0.1316	M	0.93328	3.405	0.36364	D	0.860879	P	0.52463	0.953	P	0.54544	0.755	T	0.69262	-0.5191	10	0.66056	D	0.02	-33.5711	11.8273	0.52275	0.1753:0.8247:0.0:0.0	.	165	Q8WVZ1	ZDH19_HUMAN	Y	165	ENSP00000296326:C165Y	ENSP00000296326:C165Y	C	-	2	0	ZDHHC19	197419743	0.937000	0.31787	0.983000	0.44433	0.650000	0.38633	0.889000	0.28282	1.342000	0.45619	0.561000	0.74099	TGC	C|0.996;T|0.004	0.004	strong		0.602	ZDHHC19-007	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341533.1	NM_144637	
BRWD1	54014	hgsc.bcm.edu	37	21	40590176	40590176	+	Silent	SNP	G	G	T	rs76171323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:40590176G>T	ENST00000333229.2	-	31	3888	c.3561C>A	c.(3559-3561)ggC>ggA	p.G1187G	BRWD1-IT1_ENST00000435608.1_RNA|BRWD1_ENST00000380800.3_Silent_p.G1187G|BRWD1_ENST00000342449.3_Silent_p.G1187G	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	1187	Bromo 1. {ECO:0000255|PROSITE- ProRule:PRU00035}.				cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				AATCAACAGGGCCTGCAAAAG	0.378													G|||	75	0.014976	0.0545	0.0014	5008	,	,		15406	0.0		0.002	False		,,,				2504	0.0				p.G1187G	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											BRWD1_ENST00000333229,NS,lymphoid_neoplasm,0,2	BRWD1	325	2	0			c.C3561A						PASS	.	G	,	182,4224	118.8+/-156.5	1,180,2022	108.0	107.0	107.0		3561,3561	-0.7	1.0	21	dbSNP_131	107	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	BRWD1	NM_018963.4,NM_033656.3	,	1,181,6321	TT,TG,GG		0.0116,4.1307,1.407	,	1187/2321,1187/2270	40590176	183,12823	2203	4300	6503	SO:0001819	synonymous_variant	54014	exon31			AACAGGGCCTGCA	AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"""WD repeat domain containing"""	12760	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 107"", ""WD repeat domain 9"""	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.3561C>A	21.37:g.40590176G>T		114.0	0.0	0		112.0	66.0	0.589286	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Silent	SNP	ENST00000333229.2	37	CCDS13662.1	40	0.018315018315018316	40	0.08130081300813008	0	0.0	0	0.0	0	0.0	G	9.823	1.186196	0.21870	0.041307	1.16E-4	ENSG00000185658	ENST00000424441	.	.	.	5.56	-0.669	0.11388	.	.	.	.	.	T	0.04861	0.0131	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.04115	-1.0976	4	.	.	.	-8.3462	7.2761	0.26286	0.5235:0.1169:0.3596:0.0	.	.	.	.	T	173	.	.	P	-	1	0	BRWD1	39512046	0.888000	0.30383	0.993000	0.49108	0.904000	0.53231	0.108000	0.15396	-0.032000	0.13758	0.462000	0.41574	CCC	G|0.984;T|0.016	0.016	strong		0.378	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656	
WDR4	10785	hgsc.bcm.edu	37	21	44273691	44273691	+	Silent	SNP	G	G	A	rs146863277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:44273691G>A	ENST00000398208.2	-	9	1022	c.963C>T	c.(961-963)ggC>ggT	p.G321G	WDR4_ENST00000330317.2_Silent_p.G321G|WDR4_ENST00000492742.1_5'UTR	NM_001260474.1|NM_001260475.1|NM_001260476.1|NM_018669.5	NP_001247403.1|NP_001247404.1|NP_001247405.1|NP_061139.2			WD repeat domain 4											haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(3)|ovary(2)	11				Colorectal(79;0.0165)|Lung(125;0.0484)|STAD - Stomach adenocarcinoma(101;0.0624)|COAD - Colon adenocarcinoma(84;0.128)|LUSC - Lung squamous cell carcinoma(216;0.244)		GCCACTGGTCGCCCACAGGCC	0.622													G|||	23	0.00459265	0.0151	0.0029	5008	,	,		15951	0.0		0.001	False		,,,				2504	0.0				p.G321G		Atlas-SNP	.											.	WDR4	35	.	0			c.C963T						PASS	.	G	,	65,4339	56.2+/-92.4	1,63,2138	26.0	26.0	26.0		963,963	-6.0	0.0	21	dbSNP_134	26	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	WDR4	NM_018669.4,NM_033661.3	,	1,66,6435	AA,AG,GG		0.0349,1.4759,0.5229	,	321/413,321/413	44273691	68,12936	2202	4300	6502	SO:0001819	synonymous_variant	10785	exon9			CTGGTCGCCCACA	AJ243912	CCDS13691.1	21q22.3	2013-01-09			ENSG00000160193	ENSG00000160193		"""WD repeat domain containing"""	12756	protein-coding gene	gene with protein product	"""TRM82 tRNA methyltransferase 82 homolog (S. cerevisiae)"""	605924				12403464	Standard	NM_018669		Approved	TRM82, TRMT82	uc002zci.4	P57081	OTTHUMG00000086826	ENST00000398208.2:c.963C>T	21.37:g.44273691G>A		61.0	0.0	0		69.0	43.0	0.623188	NM_018669		Silent	SNP	ENST00000398208.2	37	CCDS13691.1																																																																																			G|0.995;A|0.005	0.005	strong		0.622	WDR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195479.1		
ZNF780A	284323	hgsc.bcm.edu	37	19	40580426	40580426	+	Silent	SNP	A	A	G	rs399405	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40580426A>G	ENST00000595687.2	-	6	2132	c.1923T>C	c.(1921-1923)tcT>tcC	p.S641S	ZNF780A_ENST00000340963.5_Silent_p.S641S|ZNF780A_ENST00000455521.1_Silent_p.S642S|AC005614.5_ENST00000595508.1_RNA|ZNF780A_ENST00000594395.1_Silent_p.S642S|ZNF780A_ENST00000414720.2_Intron|ZNF780A_ENST00000450241.2_Silent_p.S607S	NM_001010880.2	NP_001010880.2	O75290	Z780A_HUMAN	zinc finger protein 780A	641					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|upper_aerodigestive_tract(3)|urinary_tract(1)	31	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					CTTACATTCAAGATGCCTTCT	0.418													a|||	547	0.109225	0.3449	0.0403	5008	,	,		22537	0.0069		0.0109	False		,,,				2504	0.046				p.S642S		Atlas-SNP	.											.	ZNF780A	156	.	0			c.T1926C						PASS	.	A	,,,	1370,3036	454.7+/-350.8	220,930,1053	153.0	148.0	150.0		1923,1926,1923,	-2.3	0.0	19	dbSNP_80	150	68,8532	41.7+/-99.0	1,66,4233	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	ZNF780A	NM_001010880.2,NM_001142577.1,NM_001142578.1,NM_001142579.1	,,,	221,996,5286	GG,GA,AA		0.7907,31.094,11.0564	,,,	641/642,642/643,641/642,	40580426	1438,11568	2203	4300	6503	SO:0001819	synonymous_variant	284323	exon6			CATTCAAGATGCC	AK091274	CCDS33026.2, CCDS46078.1, CCDS46079.1	19q13.2	2014-02-12	2006-08-15		ENSG00000197782	ENSG00000197782		"""Zinc fingers, C2H2-type"", ""-"""	27603	protein-coding gene	gene with protein product							Standard	NM_001142577		Approved	ZNF780	uc010xvh.2	O75290	OTTHUMG00000155119	ENST00000595687.2:c.1923T>C	19.37:g.40580426A>G		247.0	0.0	0		268.0	268.0	1	NM_001142577	E9PB48|Q6ZN87	Silent	SNP	ENST00000595687.2	37	CCDS33026.2																																																																																			A|0.899;G|0.101	0.101	strong		0.418	ZNF780A-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000470066.1	NM_001010880	
FLG	2312	hgsc.bcm.edu	37	1	152285188	152285188	+	Missense_Mutation	SNP	G	G	A	rs3120655	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152285188G>A	ENST00000368799.1	-	3	2209	c.2174C>T	c.(2173-2175)aCt>aTt	p.T725I	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	725	Ser-rich.		T -> I (in dbSNP:rs3120655).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCCGTGCCCAGTGCCTGAGTG	0.567									Ichthyosis				-|||	562	0.11222	0.407	0.0331	5008	,	,		21307	0.0		0.001	False		,,,				2504	0.0				p.T725I		Atlas-SNP	.											.	FLG	900	.	0			c.C2174T						PASS	.	G	ILE/THR	1483,2923		249,985,969	379.0	400.0	393.0		2174	3.0	0.0	1	dbSNP_103	393	19,8581		0,19,4281	no	missense	FLG	NM_002016.1	89	249,1004,5250	AA,AG,GG		0.2209,33.6586,11.5485	possibly-damaging	725/4062	152285188	1502,11504	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TGCCCAGTGCCTG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.2174C>T	1.37:g.152285188G>A	ENSP00000357789:p.Thr725Ile	243.0	1.0	0.00411523		274.0	272.0	0.992701	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	165	0.07554945054945054	152	0.3089430894308943	12	0.03314917127071823	1	0.0017482517482517483	0	0.0	-	6.095	0.385885	0.11524	0.336586	0.002209	ENSG00000143631	ENST00000368799	T	0.03358	3.96	3.89	2.97	0.34412	.	.	.	.	.	T	0.00580	0.0019	N	0.03281	-0.365	0.80722	P	0.0	B	0.14805	0.011	B	0.17979	0.02	T	0.46317	-0.9200	8	0.16896	T	0.51	1.9131	8.0676	0.30669	0.1154:0.0:0.8846:0.0	.	725	P20930	FILA_HUMAN	I	725	ENSP00000357789:T725I	ENSP00000357789:T725I	T	-	2	0	FLG	150551812	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.408000	0.07169	0.832000	0.34804	-0.663000	0.03849	ACT	.	.	weak		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
EFEMP1	2202	hgsc.bcm.edu	37	2	56145110	56145110	+	Silent	SNP	G	G	T	rs12292	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:56145110G>T	ENST00000394555.2	-	4	642	c.207C>A	c.(205-207)ctC>ctA	p.L69L	EFEMP1_ENST00000355426.3_Silent_p.L69L|EFEMP1_ENST00000424836.2_Silent_p.L11L|EFEMP1_ENST00000394554.1_Silent_p.L69L	NM_001039348.2|NM_001039349.2	NP_001034437.1|NP_001034438.1	Q12805	FBLN3_HUMAN	EGF containing fibulin-like extracellular matrix protein 1	69	EGF-like 1; atypical. {ECO:0000255|PROSITE-ProRule:PRU00076}.				epidermal growth factor receptor signaling pathway (GO:0007173)|extracellular matrix organization (GO:0030198)|negative regulation of chondrocyte differentiation (GO:0032331)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|epidermal growth factor-activated receptor activity (GO:0005006)			NS(1)|breast(2)|endometrium(4)|large_intestine(6)|lung(5)|ovary(5)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	28			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			TCGGAAGGCAGAGGTATCCTC	0.458													G|||	193	0.0385383	0.1369	0.0159	5008	,	,		21544	0.0		0.001	False		,,,				2504	0.0				p.L69L	GBM(92;934 1319 7714 28760 40110)	Atlas-SNP	.											.	EFEMP1	81	.	0			c.C207A						PASS	.	G	,	526,3880	239.6+/-250.7	28,470,1705	111.0	112.0	112.0		207,207	1.7	1.0	2	dbSNP_52	112	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	EFEMP1	NM_001039348.2,NM_001039349.2	,	28,473,6002	TT,TG,GG		0.0349,11.9383,4.0674	,	69/494,69/494	56145110	529,12477	2203	4300	6503	SO:0001819	synonymous_variant	2202	exon4			AAGGCAGAGGTAT	U03877	CCDS1857.1	2p16	2013-01-08	2011-01-25		ENSG00000115380	ENSG00000115380		"""Fibulins"""	3218	protein-coding gene	gene with protein product	"""fibulin 3"""	601548	"""fibrillin-like"", ""EGF-containing fibulin-like extracellular matrix protein 1"""	DHRD, FBNL		8812496, 7799918	Standard	NM_001039348		Approved	S1-5, FBLN3, MTLV	uc002rzi.3	Q12805	OTTHUMG00000129343	ENST00000394555.2:c.207C>A	2.37:g.56145110G>T		248.0	0.0	0		229.0	122.0	0.532751	NM_001039349	A8K3I4|B4DW75|D6W5D2|Q541U7	Silent	SNP	ENST00000394555.2	37	CCDS1857.1	58	0.026556776556776556	53	0.10772357723577236	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	9.474	1.096510	0.20552	0.119383	3.49E-4	ENSG00000115380	ENST00000405693	.	.	.	5.68	1.67	0.24075	.	.	.	.	.	T	0.00695	0.0023	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.01600	-1.1315	5	0.27785	T	0.31	.	3.1782	0.06576	0.1297:0.1199:0.5058:0.2445	rs12292;rs12292	.	.	.	Y	5	.	ENSP00000384951:S5Y	S	-	2	0	EFEMP1	55998614	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.101000	0.31037	0.288000	0.22398	0.650000	0.86243	TCT	G|0.951;T|0.049	0.049	strong		0.458	EFEMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251491.2		
APPBP2	10513	hgsc.bcm.edu	37	17	58603185	58603185	+	Silent	SNP	G	G	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:58603185G>C	ENST00000083182.3	-	1	395	c.108C>G	c.(106-108)ccC>ccG	p.P36P	RP11-15E18.1_ENST00000558027.1_RNA|RP11-15E18.1_ENST00000559739.1_RNA	NM_001282476.1|NM_006380.2	NP_001269405.1|NP_006371.2	Q92624	APBP2_HUMAN	amyloid beta precursor protein (cytoplasmic tail) binding protein 2	36					intracellular protein transport (GO:0006886)|intracellular transport (GO:0046907)|metabolic process (GO:0008152)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nucleus (GO:0005634)	microtubule motor activity (GO:0003777)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(17)|pancreas(1)|urinary_tract(1)	25	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;3.67e-13)|all cancers(12;1.44e-11)|Colorectal(3;0.01)			GGATGTTCTCGGGCAAGGAGC	0.602																																					p.P36P		Atlas-SNP	.											.	APPBP2	48	.	0			c.C108G						PASS	.						136.0	110.0	119.0					17																	58603185		2203	4300	6503	SO:0001819	synonymous_variant	10513	exon1			GTTCTCGGGCAAG	AF017782	CCDS32699.1	17q23.2	2012-09-20	2001-11-28		ENSG00000062725	ENSG00000062725			622	protein-coding gene	gene with protein product	"""protein interacting with APP tail 1"""	605324	"""amyloid beta precursor protein (cytoplasmic tail)-binding protein 2"""			9843960	Standard	NM_006380		Approved	KIAA0228, Hs.84084, PAT1	uc002iys.1	Q92624		ENST00000083182.3:c.108C>G	17.37:g.58603185G>C		134.0	0.0	0		134.0	73.0	0.544776	NM_006380	A8K862|O95095|Q8WVC9	Silent	SNP	ENST00000083182.3	37	CCDS32699.1																																																																																			.	.	none		0.602	APPBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449465.1	NM_006380	
AEBP1	165	hgsc.bcm.edu	37	7	44146151	44146151	+	Missense_Mutation	SNP	C	C	T	rs75107445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:44146151C>T	ENST00000223357.3	+	2	565	c.260C>T	c.(259-261)cCg>cTg	p.P87L		NM_001129.3	NP_001120.3	Q8IUX7	AEBP1_HUMAN	AE binding protein 1	87	Pro-rich.				cell adhesion (GO:0007155)|muscle organ development (GO:0007517)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(13)|upper_aerodigestive_tract(2)	33						ACAGTGCCTCCGGAAAAGACC	0.587													C|||	9	0.00179712	0.0061	0.0	5008	,	,		15644	0.0		0.0	False		,,,				2504	0.001				p.P87L		Atlas-SNP	.											AEBP1,larynx,carcinoma,-1,1	AEBP1	102	1	0			c.C260T						PASS	.	C	LEU/PRO	23,4365	26.2+/-53.5	0,23,2171	36.0	45.0	42.0		260	1.9	0.1	7	dbSNP_131	42	0,8586		0,0,4293	yes	missense	AEBP1	NM_001129.3	98	0,23,6464	TT,TC,CC		0.0,0.5242,0.1773	benign	87/1159	44146151	23,12951	2194	4293	6487	SO:0001583	missense	165	exon2			TGCCTCCGGAAAA	D86479	CCDS5476.1	7p	2008-07-18	2001-11-28		ENSG00000106624	ENSG00000106624			303	protein-coding gene	gene with protein product	"""aortic carboxypeptidase-like protein"", ""adipocyte enhancer binding protein 1"""	602981	"""AE-binding protein 1"""			8920928	Standard	NM_001129		Approved	ACLP	uc003tkb.4	Q8IUX7	OTTHUMG00000023362	ENST00000223357.3:c.260C>T	7.37:g.44146151C>T	ENSP00000223357:p.Pro87Leu	40.0	0.0	0		46.0	19.0	0.413043	NM_001129	Q14113|Q59ER7|Q6ZSC7|Q7KZ79	Missense_Mutation	SNP	ENST00000223357.3	37	CCDS5476.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	16.09	3.025082	0.54683	0.005242	0.0	ENSG00000106624	ENST00000223357;ENST00000449162	D	0.94828	-3.53	4.9	1.92	0.25849	.	0.598172	0.14954	N	0.288777	D	0.84853	0.5564	L	0.27053	0.805	0.34323	D	0.68679	B	0.14805	0.011	B	0.08055	0.003	T	0.81575	-0.0870	10	0.87932	D	0	-1.0442	6.299	0.21101	0.0:0.6427:0.0:0.3573	.	87	Q8IUX7	AEBP1_HUMAN	L	87;3	ENSP00000223357:P87L	ENSP00000223357:P87L	P	+	2	0	AEBP1	44112676	0.000000	0.05858	0.071000	0.20095	0.651000	0.38670	0.214000	0.17541	0.079000	0.16929	0.462000	0.41574	CCG	C|0.999;T|0.001	0.001	strong		0.587	AEBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250993.2	NM_001129	
PKMYT1	9088	hgsc.bcm.edu	37	16	3026956	3026956	+	Silent	SNP	T	T	C	rs4149786	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3026956T>C	ENST00000262300.8	-	3	595	c.87A>G	c.(85-87)ccA>ccG	p.P29P	PKMYT1_ENST00000574385.1_Silent_p.P20P|PKMYT1_ENST00000431515.2_Silent_p.P29P|PKMYT1_ENST00000573944.1_Silent_p.P20P|PKMYT1_ENST00000574730.1_Intron|PKMYT1_ENST00000440027.2_Silent_p.P29P	NM_001258450.1|NM_004203.4|NM_182687.2	NP_001245379.1|NP_004194.3|NP_872629.1	Q99640	PMYT1_HUMAN	protein kinase, membrane associated tyrosine/threonine 1	29	Pro-rich.				G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of mitosis (GO:0007088)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	10						GGAAGTAGGCTGGGACTGGGA	0.692													C|||	5	0.000998403	0.0	0.0	5008	,	,		16125	0.0		0.0	False		,,,				2504	0.0051				p.P29P		Atlas-SNP	.											.	PKMYT1	23	.	0			c.A87G						PASS	.	C	,	10,4286		0,10,2138	12.0	15.0	14.0		87,87	-3.7	1.0	16	dbSNP_110	14	0,8510		0,0,4255	no	coding-synonymous,coding-synonymous	PKMYT1	NM_004203.4,NM_182687.2	,	0,10,6393	CC,CT,TT		0.0,0.2328,0.0781	,	29/500,29/481	3026956	10,12796	2148	4255	6403	SO:0001819	synonymous_variant	9088	exon3			GTAGGCTGGGACT	AK097642	CCDS10486.1, CCDS45391.1, CCDS58414.1, CCDS58415.1	16p13.3	2014-06-13			ENSG00000127564	ENSG00000127564			29650	protein-coding gene	gene with protein product	"""membrane-associated tyrosine- and threonine-specific cdc2-inhibitory kinase"", ""protein phosphatase 1, regulatory subunit 126"""	602474				9001210, 12606722	Standard	NM_004203		Approved	MYT1, PPP1R126	uc002csn.3	Q99640	OTTHUMG00000128975	ENST00000262300.8:c.87A>G	16.37:g.3026956T>C		76.0	0.0	0		65.0	21.0	0.323077	NM_182687	B3KUN8|B4DXD4|D3DUA4|F8W164|I3L1V2|O14731|Q7LE24|Q8TCM9	Silent	SNP	ENST00000262300.8	37	CCDS10486.1																																																																																			T|0.993;C|0.007	0.007	strong		0.692	PKMYT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250963.2	NM_004203	
LILRA3	11026	hgsc.bcm.edu	37	19	54803141	54803141	+	Missense_Mutation	SNP	C	C	T	rs147561158	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54803141C>T	ENST00000251390.3	-	4	627	c.536G>A	c.(535-537)cGg>cAg	p.R179Q	LILRA3_ENST00000391744.3_Intron|LILRA3_ENST00000391745.1_Missense_Mutation_p.R196Q	NM_006865.3	NP_006856.3	Q8N6C8	LIRA3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (without TM domain), member 3	179	Ig-like C2-type 2.				defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			NS(3)|breast(1)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GAAGATGGCCCGGGATGACCC	0.567													.|||	5	0.000998403	0.0038	0.0	5008	,	,		15432	0.0		0.0	False		,,,				2504	0.0				p.R179Q		Atlas-SNP	.											LILRA3,right_upper_lobe,carcinoma,0,2	LILRA3	65	2	0			c.G536A						scavenged	.	C	,GLN/ARG	25,4365		1,23,2171	139.0	115.0	123.0		,536	-0.2	0.0	19	dbSNP_134	123	0,8332		0,0,4166	yes	intron,missense	LILRA3	NM_001172654.1,NM_006865.3	,43	1,23,6337	TT,TC,CC		0.0,0.5695,0.1965	,	,179/440	54803141	25,12697	2195	4166	6361	SO:0001583	missense	11026	exon4			ATGGCCCGGGATG	U91926		19q13.4	2013-01-11						"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6604	protein-coding gene	gene with protein product		604818				9278324, 9548455	Standard	XM_006710242		Approved	LIR-4, HM43, ILT6, HM31, LIR4, CD85e		Q8N6C8		ENST00000251390.3:c.536G>A	19.37:g.54803141C>T	ENSP00000251390:p.Arg179Gln	315.0	2.0	0.00634921		346.0	167.0	0.482659	NM_006865	J3KPM2|O15469|O15470|O75016|Q8N151|Q8N154|Q8NHJ1|Q8NHJ2|Q8NHJ3|Q8NHJ4	Missense_Mutation	SNP	ENST00000251390.3	37	CCDS12887.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	0.015	-1.559568	0.00910	0.005695	0.0	ENSG00000170866	ENST00000251390;ENST00000391745	T;T	0.02890	4.12;4.12	2.07	-0.183	0.13284	Immunoglobulin-like fold (1);	0.611757	0.12604	N	0.454468	T	0.00695	0.0023	N	0.02391	-0.57	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.46693	-0.9173	10	0.02654	T	1	.	4.3936	0.11351	0.0:0.4019:0.0:0.5981	.	179	Q8N6C8	LIRA3_HUMAN	Q	179;196	ENSP00000251390:R179Q;ENSP00000375625:R196Q	ENSP00000251390:R179Q	R	-	2	0	LILRA3	59494953	0.000000	0.05858	0.003000	0.11579	0.000000	0.00434	-0.534000	0.06150	-0.089000	0.12484	-0.350000	0.07774	CGG	C|0.998;T|0.002	0.002	strong		0.567	LILRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140236.1		
OTC	5009	hgsc.bcm.edu	37	X	38260570	38260570	+	Silent	SNP	T	T	C	rs145777402	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:38260570T>C	ENST00000039007.4	+	5	581	c.429T>C	c.(427-429)taT>taC	p.Y143Y	OTC_ENST00000488812.1_3'UTR|TM4SF2_ENST00000465127.1_Intron	NM_000531.5	NP_000522.3	P00480	OTC_HUMAN	ornithine carbamoyltransferase	143					ammonia homeostasis (GO:0097272)|arginine biosynthetic process (GO:0006526)|cellular nitrogen compound metabolic process (GO:0034641)|citrulline biosynthetic process (GO:0019240)|liver development (GO:0001889)|midgut development (GO:0007494)|ornithine catabolic process (GO:0006593)|protein homotrimerization (GO:0070207)|response to biotin (GO:0070781)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|ornithine carbamoyltransferase activity (GO:0004585)|phosphate ion binding (GO:0042301)|phospholipid binding (GO:0005543)			breast(2)|endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22					L-Citrulline(DB00155)|L-Ornithine(DB00129)	CTCGAGTGTATAAACAATCAG	0.393													T|||	12	0.00317881	0.0091	0.0	3775	,	,		10235	0.0		0.0	False		,,,				2504	0.0				p.Y143Y		Atlas-SNP	.											.	OTC	60	.	0			c.T429C						PASS	.	T		45,3788		0,40,5,1591,566	103.0	78.0	86.0		429	-0.4	1.0	X	dbSNP_134	86	0,6728		0,0,0,2428,1872	no	coding-synonymous	OTC	NM_000531.5		0,40,5,4019,2438	CC,CT,C,TT,T		0.0,1.174,0.4261		143/355	38260570	45,10516	2202	4300	6502	SO:0001819	synonymous_variant	5009	exon5			AGTGTATAAACAA	K02100	CCDS14247.1	Xp21.1	2014-06-28			ENSG00000036473	ENSG00000036473	2.1.3.3		8512	protein-coding gene	gene with protein product		300461					Standard	NM_000531		Approved		uc004def.4	P00480	OTTHUMG00000022727	ENST00000039007.4:c.429T>C	X.37:g.38260570T>C		229.0	0.0	0		179.0	74.0	0.413408	NM_000531	A8K9P2|D3DWB0|Q3KNR1|Q6B0I1|Q9NYJ5	Silent	SNP	ENST00000039007.4	37	CCDS14247.1																																																																																			T|0.994;C|0.006	0.006	strong		0.393	OTC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059006.2		
ODF1	4956	hgsc.bcm.edu	37	8	103573024	103573024	+	Missense_Mutation	SNP	G	G	A	rs568456031|rs143802899|rs111689913|rs58232162|rs386728348	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:103573024G>A	ENST00000285402.3	+	2	821	c.665G>A	c.(664-666)aGc>aAc	p.S222N	ODF1_ENST00000518835.1_Missense_Mutation_p.S15N	NM_024410.3	NP_077721.2	Q14990	ODFP1_HUMAN	outer dense fiber of sperm tails 1	222	C-X-P repeat region.		Missing. {ECO:0000269|PubMed:8111388}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|outer dense fiber (GO:0001520)		p.C218_P226delCNPCSPCNP(1)		NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(14;2.76e-05)|all_epithelial(15;4.54e-08)|Lung NSC(17;4.08e-05)|all_lung(17;9.15e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000125)|STAD - Stomach adenocarcinoma(118;0.0826)			aacccctgcagcccctgcaac	0.567													A|||	442	0.0882588	0.3011	0.0303	5008	,	,		16173	0.0129		0.0099	False		,,,				2504	0.0				p.S222N		Atlas-SNP	.											.	ODF1	55	.	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.G665A						PASS	.	A	ASN/SER	1013,3353		178,657,1348	60.0	59.0	59.0		665	-4.1	0.0	8	dbSNP_132	59	30,8398		1,28,4185	no	missense	ODF1	NM_024410.3	46	179,685,5533	AA,AG,GG		0.356,23.202,8.1523	benign	222/251	103573024	1043,11751	2183	4214	6397	SO:0001583	missense	4956	exon2			CCTGCAGCCCCTG	M93131	CCDS6293.1	8q22	2011-09-05	2002-10-21		ENSG00000155087	ENSG00000155087		"""Heat shock proteins / HSPB"""	8113	protein-coding gene	gene with protein product	"""cancer/testis antigen 133"""	182878	"""outer dense fibre of sperm tails 1"""			8305202	Standard	NM_024410		Approved	ODFPG, ODF27, RT7, HSPB10, CT133	uc003ykt.2	Q14990	OTTHUMG00000164719	ENST00000285402.3:c.665G>A	8.37:g.103573024G>A	ENSP00000285402:p.Ser222Asn	145.0	0.0	0		106.0	42.0	0.396226	NM_024410	Q3SX72	Missense_Mutation	SNP	ENST00000285402.3	37	CCDS6293.1	188	0.08608058608058608	164	0.3333333333333333	11	0.03038674033149171	9	0.015734265734265736	4	0.005277044854881266	A	0.034	-1.317862	0.01320	0.23202	0.00356	ENSG00000155087	ENST00000285402;ENST00000518835	D;T	0.86164	-2.08;1.89	4.92	-4.11	0.03928	.	1.048210	0.07416	N	0.893166	T	0.00012	0.0000	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.00688	-1.1609	10	0.22706	T	0.39	-12.522	13.0969	0.59197	0.6974:0.0:0.3026:0.0	.	222	Q14990	ODFP1_HUMAN	N	222;15	ENSP00000285402:S222N;ENSP00000430023:S15N	ENSP00000285402:S222N	S	+	2	0	ODF1	103642200	0.004000	0.15560	0.004000	0.12327	0.002000	0.02628	-1.097000	0.03349	-1.135000	0.02895	-1.581000	0.00855	AGC	G|0.893;A|0.107	0.107	strong		0.567	ODF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379884.1		
TSC22D2	9819	hgsc.bcm.edu	37	3	150176316	150176316	+	Missense_Mutation	SNP	C	C	A	rs149526922	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:150176316C>A	ENST00000361875.3	+	4	3252	c.2236C>A	c.(2236-2238)Cca>Aca	p.P746T	TSC22D2_ENST00000361136.2_Missense_Mutation_p.P722T	NM_014779.2	NP_055594.1	O75157	T22D2_HUMAN	TSC22 domain family, member 2	746					response to osmotic stress (GO:0006970)		sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	18			LUSC - Lung squamous cell carcinoma(72;0.0538)|Lung(72;0.066)			ATCCCAACTCCCAACCCAACA	0.438													C|||	2	0.000399361	0.0015	0.0	5008	,	,		19128	0.0		0.0	False		,,,				2504	0.0				p.P746T		Atlas-SNP	.											.	TSC22D2	42	.	0			c.C2236A						PASS	.	C	THR/PRO	9,4397	15.5+/-35.6	0,9,2194	117.0	113.0	115.0		2236	4.3	1.0	3	dbSNP_134	115	0,8600		0,0,4300	yes	missense	TSC22D2	NM_014779.2	38	0,9,6494	AA,AC,CC		0.0,0.2043,0.0692	possibly-damaging	746/781	150176316	9,12997	2203	4300	6503	SO:0001583	missense	9819	exon4			CAACTCCCAACCC	AB014569	CCDS3149.1	3q25.1	2005-03-01			ENSG00000196428	ENSG00000196428			29095	protein-coding gene	gene with protein product						9734811	Standard	NM_014779		Approved	KIAA0669, TILZ4a, TILZ4b, TILZ4c	uc003exv.3	O75157	OTTHUMG00000159744	ENST00000361875.3:c.2236C>A	3.37:g.150176316C>A	ENSP00000354543:p.Pro746Thr	272.0	0.0	0		275.0	129.0	0.469091	NM_014779	D3DNI5|Q6PI50|Q9H2Z6|Q9H2Z7|Q9H2Z8	Missense_Mutation	SNP	ENST00000361875.3	37	CCDS3149.1	1|1	4.578754578754579E-4|4.578754578754579E-4	1|1	0.0020325203252032522|0.0020325203252032522	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	0.007|0.007	-1.972930|-1.972930	0.00452|0.00452	0.002043|0.002043	0.0|0.0	ENSG00000196428|ENSG00000196428	ENST00000466814|ENST00000543241;ENST00000361875;ENST00000361136	.|T;T	.|0.29917	.|1.55;1.56	5.38|5.38	4.27|4.27	0.50696|0.50696	.|.	0.273316|0.273316	0.25256|0.25256	N|N	0.031991|0.031991	T|T	0.09949|0.09949	0.0244|0.0244	N|N	0.04508|0.04508	-0.205|-0.205	0.28151|0.28151	N|N	0.92938|0.92938	.|B;B	.|0.33919	.|0.037;0.432	.|B;B	.|0.33196	.|0.023;0.159	T|T	0.35871|0.35871	-0.9771|-0.9771	6|10	.|0.02654	.|T	.|1	.|.	4.617|4.617	0.12432|0.12432	0.0:0.765:0.0:0.235|0.0:0.765:0.0:0.235	.|.	.|722;746	.|O75157-2;O75157	.|.;T22D2_HUMAN	H|T	169|195;746;722	.|ENSP00000354543:P746T;ENSP00000354893:P722T	.|ENSP00000354893:P722T	P|P	+|+	2|1	0|0	TSC22D2|TSC22D2	151659006|151659006	0.996000|0.996000	0.38824|0.38824	1.000000|1.000000	0.80357|0.80357	0.032000|0.032000	0.12392|0.12392	0.943000|0.943000	0.29030|0.29030	2.693000|2.693000	0.91896|0.91896	0.655000|0.655000	0.94253|0.94253	CCC|CCA	C|0.999;A|0.001	0.001	strong		0.438	TSC22D2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357123.2	NM_014779	
FAM207A	85395	hgsc.bcm.edu	37	21	46380068	46380068	+	Missense_Mutation	SNP	G	G	A	rs141593051	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46380068G>A	ENST00000291634.6	+	3	385	c.337G>A	c.(337-339)Gag>Aag	p.E113K	FAM207A_ENST00000479127.1_3'UTR|FAM207A_ENST00000397826.3_Missense_Mutation_p.E98K	NM_058190.2	NP_478070.1	Q9NSI2	F207A_HUMAN	family with sequence similarity 207, member A	113																	GCTGAGGCGTGAGCAATGGTT	0.572													G|||	2	0.000399361	0.0015	0.0	5008	,	,		21685	0.0		0.0	False		,,,				2504	0.0				p.E113K		Atlas-SNP	.											.	.	.	.	0			c.G337A						PASS	.	G	LYS/GLU	5,4401	11.4+/-27.6	0,5,2198	128.0	101.0	110.0		337	3.2	0.4	21	dbSNP_134	110	0,8600		0,0,4300	yes	missense	FAM207A	NM_058190.2	56	0,5,6498	AA,AG,GG		0.0,0.1135,0.0384	benign	113/231	46380068	5,13001	2203	4300	6503	SO:0001583	missense	85395	exon3			AGGCGTGAGCAAT		CCDS13718.1	21q22.3	2011-08-15	2011-08-15	2011-08-15	ENSG00000160256	ENSG00000160256			15811	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 70"""	C21orf70			Standard	NM_058190		Approved	PRED56	uc002zgl.3	Q9NSI2	OTTHUMG00000090293	ENST00000291634.6:c.337G>A	21.37:g.46380068G>A	ENSP00000291634:p.Glu113Lys	114.0	0.0	0		95.0	47.0	0.494737	NM_058190		Missense_Mutation	SNP	ENST00000291634.6	37	CCDS13718.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	10.04	1.240186	0.22711	0.001135	0.0	ENSG00000160256	ENST00000291634;ENST00000397826;ENST00000458015	T;T;T	0.47177	0.85;0.85;0.85	3.24	3.24	0.37175	.	0.168860	0.50627	D	0.000105	T	0.36276	0.0961	L	0.55743	1.74	0.40834	D	0.983615	P;B	0.46142	0.873;0.021	B;B	0.44044	0.439;0.037	T	0.48281	-0.9049	10	0.62326	D	0.03	-19.5017	10.2398	0.43305	0.0:0.0:1.0:0.0	.	98;113	Q9NSI2-2;Q9NSI2	.;F207A_HUMAN	K	113;98;98	ENSP00000291634:E113K;ENSP00000380926:E98K;ENSP00000404964:E98K	ENSP00000291634:E113K	E	+	1	0	C21orf70	45204496	0.782000	0.28689	0.427000	0.26684	0.158000	0.22134	2.095000	0.41729	2.110000	0.64415	0.650000	0.86243	GAG	G|0.999;A|0.001	0.001	strong		0.572	FAM207A-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206639.1	NM_058190	
LEFTY1	10637	hgsc.bcm.edu	37	1	226076598	226076598	+	Missense_Mutation	SNP	C	C	T	rs35273824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:226076598C>T	ENST00000272134.5	-	1	248	c.169G>A	c.(169-171)Gtg>Atg	p.V57M	RP4-559A3.7_ENST00000432920.2_Intron|LEFTY1_ENST00000492457.1_Intron	NM_020997.3	NP_066277.1	O75610	LFTY1_HUMAN	left-right determination factor 1	57			V -> M (in dbSNP:rs35273824).		cell growth (GO:0016049)|determination of left/right symmetry (GO:0007368)|heart morphogenesis (GO:0003007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)				cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	10	Breast(184;0.197)					TGGGCCCTCACGTGGGTGGGG	0.697													C|||	194	0.038738	0.1346	0.0216	5008	,	,		17711	0.0		0.0	False		,,,				2504	0.001				p.V57M		Atlas-SNP	.											.	LEFTY1	30	.	0			c.G169A						PASS	.	C	MET/VAL	581,3825	246.8+/-255.3	33,515,1655	30.0	32.0	31.0		169	1.0	0.1	1	dbSNP_126	31	0,8598		0,0,4299	yes	missense	LEFTY1	NM_020997.3	21	33,515,5954	TT,TC,CC		0.0,13.1866,4.4679	probably-damaging	57/367	226076598	581,12423	2203	4299	6502	SO:0001583	missense	10637	exon1			CCCTCACGTGGGT	AF081507	CCDS1548.1	1q42.1	2008-02-05	2004-11-17	2004-11-17	ENSG00000243709	ENSG00000243709			6552	protein-coding gene	gene with protein product		603037	"""left-right determination, factor B"""	LEFTB		10053005, 10886363	Standard	NM_020997		Approved	LEFTYB	uc001hpo.3	O75610	OTTHUMG00000037443	ENST00000272134.5:c.169G>A	1.37:g.226076598C>T	ENSP00000272134:p.Val57Met	187.0	0.0	0		194.0	103.0	0.530928	NM_020997	B2R7U0|Q53H67|Q5TE94	Missense_Mutation	SNP	ENST00000272134.5	37	CCDS1548.1	78	0.03571428571428571	70	0.14227642276422764	8	0.022099447513812154	0	0.0	0	0.0	c	11.47	1.647249	0.29246	0.131866	0.0	ENSG00000243709	ENST00000272134	T	0.58940	0.3	4.18	0.96	0.19631	Transforming growth factor-beta, N-terminal (1);	0.188005	0.47093	D	0.000242	T	0.00967	0.0032	M	0.74881	2.28	0.44789	P	0.0022060000000000413	D;D	0.89917	1.0;1.0	D;D	0.75020	0.985;0.985	T	0.29305	-1.0016	9	0.34782	T	0.22	.	4.8349	0.13460	0.0:0.613:0.177:0.21	rs35273824	57;57	B2R7U0;O75610	.;LFTY1_HUMAN	M	57	ENSP00000272134:V57M	ENSP00000272134:V57M	V	-	1	0	LEFTY1	224143221	0.997000	0.39634	0.125000	0.21846	0.032000	0.12392	2.679000	0.46909	0.249000	0.21456	0.313000	0.20887	GTG	C|0.956;T|0.044	0.044	strong		0.697	LEFTY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091155.1	NM_020997	
FGF4	2249	hgsc.bcm.edu	37	11	69588798	69588798	+	Silent	SNP	A	A	G	rs61738964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:69588798A>G	ENST00000168712.1	-	2	756	c.438T>C	c.(436-438)taT>taC	p.Y146Y	AP001888.1_ENST00000602104.1_5'Flank|FGF4_ENST00000538040.1_Intron	NM_002007.2	NP_001998.1	P08620	FGF4_HUMAN	fibroblast growth factor 4	146					apoptotic process involved in morphogenesis (GO:0060561)|cartilage condensation (GO:0001502)|cell-cell signaling (GO:0007267)|chondroblast differentiation (GO:0060591)|cranial suture morphogenesis (GO:0060363)|embryonic hindlimb morphogenesis (GO:0035116)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|mesenchymal cell proliferation (GO:0010463)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction (GO:0007165)|stem cell maintenance (GO:0019827)	cytosol (GO:0005829)|extracellular region (GO:0005576)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)			lung(3)	3	Melanoma(5;1.89e-05)		LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)		Pentosan Polysulfate(DB00686)	TCACCGAGCCATAGAGCTTGC	0.657													A|||	31	0.0061901	0.0212	0.0043	5008	,	,		17189	0.0		0.0	False		,,,				2504	0.0				p.Y146Y		Atlas-SNP	.											.	FGF4	13	.	0			c.T438C						PASS	.	A		100,4300	77.8+/-116.1	3,94,2103	38.0	34.0	35.0		438	1.5	1.0	11	dbSNP_129	35	0,8588		0,0,4294	no	coding-synonymous	FGF4	NM_002007.2		3,94,6397	GG,GA,AA		0.0,2.2727,0.7699		146/207	69588798	100,12888	2200	4294	6494	SO:0001819	synonymous_variant	2249	exon2			CGAGCCATAGAGC	M17446	CCDS8194.1	11q13.3	2014-01-30	2008-08-01		ENSG00000075388	ENSG00000075388		"""Endogenous ligands"""	3682	protein-coding gene	gene with protein product	"""human stomach cancer, transforming factor from FGF-related oncogene"", ""kaposi sarcoma oncogene"", ""transforming protein KS3"""	164980	"""heparin secretory transforming protein 1"""	HSTF1		1611909	Standard	NM_002007		Approved	K-FGF, HBGF-4, HST, HST-1, KFGF	uc001opg.1	P08620	OTTHUMG00000167887	ENST00000168712.1:c.438T>C	11.37:g.69588798A>G		131.0	0.0	0		174.0	83.0	0.477012	NM_002007	B7U994	Silent	SNP	ENST00000168712.1	37	CCDS8194.1																																																																																			A|0.994;G|0.006	0.006	strong		0.657	FGF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396834.2	NM_002007	
APC2	10297	hgsc.bcm.edu	37	19	1469078	1469078	+	Silent	SNP	G	G	A	rs79021820	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1469078G>A	ENST00000535453.1	+	14	7491	c.5778G>A	c.(5776-5778)tcG>tcA	p.S1926S	APC2_ENST00000233607.2_Silent_p.S1926S|C19orf25_ENST00000588427.1_Intron|APC2_ENST00000238483.4_Silent_p.S1652S			P02655	APOC2_HUMAN	adenomatosis polyposis coli 2	0					cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|chylomicron remnant clearance (GO:0034382)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle clearance (GO:0034384)|lipid catabolic process (GO:0016042)|lipoprotein metabolic process (GO:0042157)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of lipid metabolic process (GO:0045833)|negative regulation of receptor-mediated endocytosis (GO:0048261)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipid catabolic process (GO:0060697)|positive regulation of triglyceride catabolic process (GO:0010898)|positive regulation of very-low-density lipoprotein particle remodeling (GO:0010902)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)|very-low-density lipoprotein particle remodeling (GO:0034372)	chylomicron (GO:0042627)|early endosome (GO:0005769)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate-density lipoprotein particle (GO:0034363)|low-density lipoprotein particle (GO:0034362)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	lipase inhibitor activity (GO:0055102)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|kidney(4)|large_intestine(2)|lung(5)|pancreas(1)|skin(2)	18		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|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)		CGCAGAGATCGCCCGTGCGGA	0.771													G|||	198	0.0395367	0.1475	0.0043	5008	,	,		6607	0.0		0.0	False		,,,				2504	0.0				p.S1926S		Atlas-SNP	.											.	APC2	50	.	0			c.G5778A						PASS	.	G		162,2148		1,160,994	1.0	2.0	2.0		5778	-7.8	0.5	19	dbSNP_131	2	3,5457		0,3,2727	no	coding-synonymous	APC2	NM_005883.2		1,163,3721	AA,AG,GG		0.0549,7.013,2.1236		1926/2304	1469078	165,7605	1155	2730	3885	SO:0001819	synonymous_variant	10297	exon15			GAGATCGCCCGTG		CCDS12068.1	19p13.3	2013-02-14			ENSG00000115266	ENSG00000115266		"""Armadillo repeat containing"""	24036	protein-coding gene	gene with protein product	"""adenomatous polyposis coli like"""	612034				9823329, 10021369	Standard	XM_005259475		Approved	APCL	uc002lsr.1	O95996		ENST00000535453.1:c.5778G>A	19.37:g.1469078G>A		11.0	0.0	0		29.0	19.0	0.655172	NM_005883	C0JYY4|Q9BS39|Q9UDE3|Q9UNK3	Silent	SNP	ENST00000535453.1	37	CCDS12068.1																																																																																			G|0.949;A|0.051	0.051	strong		0.771	APC2-004	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449539.2	NM_005883	
FRAS1	80144	hgsc.bcm.edu	37	4	79351542	79351542	+	Missense_Mutation	SNP	C	C	T	rs34271211	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:79351542C>T	ENST00000325942.6	+	37	5380	c.4940C>T	c.(4939-4941)aCa>aTa	p.T1647I	FRAS1_ENST00000264895.6_Missense_Mutation_p.T1647I	NM_001166133.1	NP_001159605.1	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	1647					cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						CTTAAGCATACAGCTGAGTTC	0.498													C|||	41	0.0081869	0.031	0.0	5008	,	,		19131	0.0		0.0	False		,,,				2504	0.0				p.T1647I		Atlas-SNP	.											.	FRAS1	779	.	0			c.C4940T						PASS	.	C	ILE/THR,ILE/THR	123,3785		2,119,1833	59.0	61.0	61.0		4940,4940	4.0	0.0	4	dbSNP_126	61	0,8324		0,0,4162	yes	missense,missense	FRAS1	NM_001166133.1,NM_025074.6	89,89	2,119,5995	TT,TC,CC		0.0,3.1474,1.0056	possibly-damaging,possibly-damaging	1647/1977,1647/4013	79351542	123,12109	1954	4162	6116	SO:0001583	missense	80144	exon37			AGCATACAGCTGA	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000325942.6:c.4940C>T	4.37:g.79351542C>T	ENSP00000326330:p.Thr1647Ile	100.0	0.0	0		86.0	38.0	0.44186	NM_001166133	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Missense_Mutation	SNP	ENST00000325942.6	37	CCDS54772.1	18	0.008241758241758242	18	0.036585365853658534	0	0.0	0	0.0	0	0.0	C	13.88	2.368547	0.42003	0.031474	0.0	ENSG00000138759	ENST00000325942;ENST00000264895;ENST00000545316	T;T	0.26810	1.71;1.71	5.68	3.98	0.46160	.	0.367128	0.29307	N	0.012540	T	0.04272	0.0118	L	0.57536	1.79	0.09310	N	1	P;P	0.47302	0.565;0.893	B;B	0.39876	0.205;0.312	T	0.10613	-1.0622	10	0.20046	T	0.44	.	2.3609	0.04307	0.2218:0.458:0.1775:0.1427	rs34271211	1647;1647	E9PHH6;A2RRR8	.;.	I	1647;1647;67	ENSP00000326330:T1647I;ENSP00000264895:T1647I	ENSP00000264895:T1647I	T	+	2	0	FRAS1	79570566	0.019000	0.18553	0.003000	0.11579	0.001000	0.01503	2.837000	0.48191	0.883000	0.36040	-0.229000	0.12294	ACA	C|0.992;T|0.008	0.008	strong		0.498	FRAS1-001	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000362706.2		
CAAP1	79886	hgsc.bcm.edu	37	9	26861106	26861106	+	Missense_Mutation	SNP	C	C	T	rs12342214	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:26861106C>T	ENST00000333916.5	-	5	785	c.697G>A	c.(697-699)Gtg>Atg	p.V233M	CAAP1_ENST00000535437.1_Missense_Mutation_p.V88M|CAAP1_ENST00000520187.1_Intron|CAAP1_ENST00000495958.1_5'UTR	NM_001167575.1|NM_024828.3	NP_001161047.1|NP_079104.3	Q9H8G2	CAAP1_HUMAN	caspase activity and apoptosis inhibitor 1	233			V -> M (in dbSNP:rs12342214).		apoptotic process (GO:0006915)												TTCTCTCTCACGGATGAAGCA	0.318													T|||	257	0.0513179	0.1868	0.013	5008	,	,		15800	0.0		0.001	False		,,,				2504	0.0				p.V233M		Atlas-SNP	.											.	.	.	.	0			c.G697A						PASS	.	T	MET/VAL,MET/VAL	602,3804	769.0+/-413.6	30,542,1631	95.0	104.0	101.0		262,697	0.6	0.4	9	dbSNP_120	101	3,8597	818.4+/-406.9	0,3,4297	yes	missense,missense	C9orf82	NM_001167575.1,NM_024828.3	21,21	30,545,5928	TT,TC,CC		0.0349,13.6632,4.6517	benign,benign	88/217,233/362	26861106	605,12401	2203	4300	6503	SO:0001583	missense	79886	exon5			CTCTCACGGATGA	BC014658	CCDS6516.1	9p21.2	2012-04-20	2012-04-20	2012-04-20	ENSG00000120159	ENSG00000120159			25834	protein-coding gene	gene with protein product	"""conserved anti-apoptotic protein"""		"""chromosome 9 open reading frame 82"""	C9orf82		21980415	Standard	NM_024828		Approved	FLJ13657, CAAP	uc003zqc.3	Q9H8G2	OTTHUMG00000019706	ENST00000333916.5:c.697G>A	9.37:g.26861106C>T	ENSP00000369431:p.Val233Met	175.0	0.0	0		170.0	72.0	0.423529	NM_024828	B4DWT4|D3DRK4|Q5VY32|Q6IPE6|Q96C59	Missense_Mutation	SNP	ENST00000333916.5	37	CCDS6516.1	94	0.04304029304029304	89	0.18089430894308944	5	0.013812154696132596	0	0.0	0	0.0	T	11.16	1.556553	0.27827	0.136632	3.49E-4	ENSG00000120159	ENST00000333916;ENST00000535437	T;T	0.44881	0.91;0.92	5.71	0.612	0.17591	.	0.254994	0.31381	N	0.007741	T	0.00039	0.0001	N	0.08118	0	0.58432	P	1.0000000000287557E-6	B	0.06786	0.001	B	0.06405	0.002	T	0.18272	-1.0342	9	0.33940	T	0.23	0.0412	1.6248	0.02721	0.1489:0.2564:0.3337:0.261	rs12342214;rs52805377;rs12342214	233	Q9H8G2	CI082_HUMAN	M	233;88	ENSP00000369431:V233M;ENSP00000444885:V88M	ENSP00000369431:V233M	V	-	1	0	C9orf82	26851106	0.831000	0.29352	0.434000	0.26772	0.937000	0.57800	-0.048000	0.11944	-0.404000	0.07610	-1.904000	0.00526	GTG	C|0.939;T|0.061	0.061	strong		0.318	CAAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051954.1	NM_024828	
TXNDC5	81567	hgsc.bcm.edu	37	6	7883386	7883386	+	Silent	SNP	G	G	A	rs9502656	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:7883386G>A	ENST00000379757.4	-	10	1327	c.1290C>T	c.(1288-1290)gaC>gaT	p.D430D	TXNDC5_ENST00000539054.1_Silent_p.D358D|BLOC1S5-TXNDC5_ENST00000439343.2_3'UTR|TXNDC5_ENST00000473453.1_Silent_p.D322D	NM_030810.3	NP_110437.2	Q8NBS9	TXND5_HUMAN	thioredoxin domain containing 5 (endoplasmic reticulum)	430					apoptotic cell clearance (GO:0043277)|cell redox homeostasis (GO:0045454)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	protein disulfide isomerase activity (GO:0003756)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|skin(2)	22	Ovarian(93;0.0398)					CCTAAAGTTCGTCTTTCGCTT	0.557													G|||	375	0.0748802	0.2466	0.0331	5008	,	,		17755	0.0		0.0209	False		,,,				2504	0.0051				p.D430D	Ovarian(119;1430 1625 3928 26125 34589)	Atlas-SNP	.											.	TXNDC5	33	.	0			c.C1290T						PASS	.	G	,	895,3511	345.9+/-308.8	94,707,1402	159.0	117.0	131.0		966,1290	-10.3	0.0	6	dbSNP_119	131	184,8416	82.9+/-145.4	4,176,4120	no	coding-synonymous,coding-synonymous	TXNDC5	NM_001145549.2,NM_030810.3	,	98,883,5522	AA,AG,GG		2.1395,20.3132,8.2962	,	322/325,430/433	7883386	1079,11927	2203	4300	6503	SO:0001819	synonymous_variant	81567	exon10			AAGTTCGTCTTTC	AK025006	CCDS4505.1, CCDS47369.1	6p24.3	2011-10-19	2009-02-23		ENSG00000239264	ENSG00000239264		"""Protein disulfide isomerases"""	21073	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 15"""		"""thioredoxin domain containing 5"""				Standard	NM_001145549		Approved	MGC3178, FLJ21353, FLJ90810, EndoPDI, Hcc-2, ERp46, PDIA15	uc003mxv.3	Q8NBS9	OTTHUMG00000014216	ENST00000379757.4:c.1290C>T	6.37:g.7883386G>A		67.0	0.0	0		65.0	25.0	0.384615	NM_030810	B2RDM2|Q5TCQ0|Q8ND33|Q8TCT2|Q9BVH9	Silent	SNP	ENST00000379757.4	37	CCDS4505.1																																																																																			G|0.920;A|0.080	0.080	strong		0.557	TXNDC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039792.1	NM_030810	
PGAM2	5224	hgsc.bcm.edu	37	7	44104805	44104805	+	Silent	SNP	C	C	T	rs112828964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:44104805C>T	ENST00000297283.3	-	1	381	c.324G>A	c.(322-324)ggG>ggA	p.G108G	AC017116.11_ENST00000445938.1_RNA	NM_000290.3	NP_000281.2	P15259	PGAM2_HUMAN	phosphoglycerate mutase 2 (muscle)	108					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|response to mercury ion (GO:0046689)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|striated muscle contraction (GO:0006941)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity (GO:0046538)|bisphosphoglycerate 2-phosphatase activity (GO:0004083)|bisphosphoglycerate mutase activity (GO:0004082)|cofactor binding (GO:0048037)|phosphoglycerate mutase activity (GO:0004619)			large_intestine(2)|lung(4)|ovary(1)|stomach(1)	8						CCTGCTCCTCCCCGTGCTTGG	0.632													C|||	159	0.0317492	0.1188	0.0029	5008	,	,		16305	0.0		0.0	False		,,,				2504	0.0				p.G108G		Atlas-SNP	.											.	PGAM2	20	.	0			c.G324A						PASS	.	C		422,3984	206.5+/-228.1	19,384,1800	62.0	61.0	62.0		324	-4.1	0.9	7	dbSNP_132	62	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	PGAM2	NM_000290.3		19,386,6098	TT,TC,CC		0.0233,9.5778,3.26		108/254	44104805	424,12582	2203	4300	6503	SO:0001819	synonymous_variant	5224	exon1			CTCCTCCCCGTGC		CCDS34624.1	7p13-p12	2008-11-17			ENSG00000164708	ENSG00000164708	5.4.2.1, 3.1.3.13, 5.4.2.4		8889	protein-coding gene	gene with protein product		612931					Standard	NM_000290		Approved	PGAM-M	uc003tjs.3	P15259	OTTHUMG00000155355	ENST00000297283.3:c.324G>A	7.37:g.44104805C>T		256.0	0.0	0		280.0	131.0	0.467857	NM_000290		Silent	SNP	ENST00000297283.3	37	CCDS34624.1																																																																																			C|0.968;T|0.032	0.032	strong		0.632	PGAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339614.1		
PUM2	23369	hgsc.bcm.edu	37	2	20508156	20508156	+	Silent	SNP	C	C	T	rs34057700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:20508156C>T	ENST00000361078.2	-	5	730	c.708G>A	c.(706-708)caG>caA	p.Q236Q	PUM2_ENST00000536417.1_Silent_p.Q180Q|PUM2_ENST00000420234.1_5'Flank|PUM2_ENST00000338086.5_Silent_p.Q236Q|PUM2_ENST00000403432.1_Silent_p.Q236Q|PUM2_ENST00000319801.5_Silent_p.Q236Q			Q8TB72	PUM2_HUMAN	pumilio RNA-binding family member 2	236	Interaction with SNAPIN.				regulation of translation (GO:0006417)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nuclear membrane (GO:0031965)|perinuclear region of cytoplasm (GO:0048471)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(7)|lung(13)|ovary(2)|prostate(4)|urinary_tract(3)	42	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GATAGTCAAACTGTAAGGATT	0.408													C|||	145	0.0289537	0.1021	0.013	5008	,	,		17612	0.0		0.001	False		,,,				2504	0.0				p.Q236Q		Atlas-SNP	.											.	PUM2	91	.	0			c.G708A						PASS	.	C		404,4002	200.8+/-224.0	18,368,1817	83.0	81.0	81.0		708	5.2	1.0	2	dbSNP_126	81	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	PUM2	NM_015317.1		18,370,6115	TT,TC,CC		0.0233,9.1693,3.1216		236/1065	20508156	406,12600	2203	4300	6503	SO:0001819	synonymous_variant	23369	exon5			GTCAAACTGTAAG	AF315591	CCDS1698.1, CCDS74486.1, CCDS74487.1	2p22-p21	2013-09-02	2013-09-02		ENSG00000055917	ENSG00000055917			14958	protein-coding gene	gene with protein product		607205	"""pumilio (Drosphila) homolog 2"", ""pumilio homolog 2 (Drosophila)"""			9039502, 12459267, 12511597	Standard	XM_005262607		Approved	PUMH2, KIAA0235	uc002rds.1	Q8TB72	OTTHUMG00000122098	ENST00000361078.2:c.708G>A	2.37:g.20508156C>T		177.0	0.0	0		180.0	85.0	0.472222	NM_015317	B3KSL0|B4E2B6|D6W527|O00234|Q53TV7|Q8WY43|Q9HAN2	Silent	SNP	ENST00000361078.2	37																																																																																				C|0.974;T|0.026	0.026	strong		0.408	PUM2-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015317	
FAT1	2195	hgsc.bcm.edu	37	4	187542432	187542432	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:187542432A>G	ENST00000441802.2	-	10	5517	c.5308T>C	c.(5308-5310)Tat>Cat	p.Y1770H		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1770	Cadherin 16. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						AGTCCTGTATATTCTGCCTGC	0.443										HNSCC(5;0.00058)																											p.Y1770H	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.T5308C						PASS	.						106.0	99.0	101.0					4																	187542432		1947	4150	6097	SO:0001583	missense	2195	exon10			CTGTATATTCTGC	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.5308T>C	4.37:g.187542432A>G	ENSP00000406229:p.Tyr1770His	244.0	0.0	0		264.0	125.0	0.473485	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	A	14.22	2.471201	0.43942	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.66638	-0.22	5.5	5.5	0.81552	Cadherin (2);Cadherin-like (1);	0.055265	0.85682	D	0.000000	D	0.85517	0.5715	H	0.94542	3.55	0.58432	D	0.999999	D	0.67145	0.996	D	0.63381	0.914	D	0.89615	0.3844	10	0.72032	D	0.01	.	15.7759	0.78214	1.0:0.0:0.0:0.0	.	1770	Q14517	FAT1_HUMAN	H	1770;1772	ENSP00000406229:Y1770H	ENSP00000260147:Y1772H	Y	-	1	0	FAT1	187779426	1.000000	0.71417	0.279000	0.24732	0.057000	0.15508	9.139000	0.94554	2.308000	0.77769	0.533000	0.62120	TAT	.	.	none		0.443	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
RNF207	388591	hgsc.bcm.edu	37	1	6278425	6278425	+	Missense_Mutation	SNP	G	G	A	rs61746089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:6278425G>A	ENST00000377939.4	+	17	1856	c.1729G>A	c.(1729-1731)Gcc>Acc	p.A577T	RNF207_ENST00000483336.1_3'UTR|RNF207_ENST00000377948.2_3'UTR	NM_207396.2	NP_997279.2	Q6ZRF8	RN207_HUMAN	ring finger protein 207	577						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(2)	16	Ovarian(185;0.0634)	all_cancers(23;1.22e-38)|all_epithelial(116;4.25e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;4.84e-38)|GBM - Glioblastoma multiforme(13;5.77e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.88e-19)|Colorectal(212;6.9e-08)|COAD - Colon adenocarcinoma(227;8.13e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)		CGCGGCCTCAGCCAGGTAAAG	0.577													G|||	29	0.00579073	0.0204	0.0029	5008	,	,		20029	0.0		0.0	False		,,,				2504	0.0				p.A577T		Atlas-SNP	.											.	RNF207	45	.	0			c.G1729A						PASS	.	G	THR/ALA	79,4175		0,79,2048	59.0	70.0	66.0		1729	-1.1	0.7	1	dbSNP_129	66	0,8490		0,0,4245	yes	missense	RNF207	NM_207396.2	58	0,79,6293	AA,AG,GG		0.0,1.8571,0.6199	benign	577/635	6278425	79,12665	2127	4245	6372	SO:0001583	missense	388591	exon17			GCCTCAGCCAGGT	AK128246	CCDS59.2	1p36.31	2008-11-19			ENSG00000158286	ENSG00000158286		"""RING-type (C3HC4) zinc fingers"""	32947	protein-coding gene	gene with protein product	"""OTTHUMG00000001089"""		"""chromosome 1 open reading frame 188"""	C1orf188			Standard	NM_207396		Approved	FLJ46380, FLJ32096	uc001amg.3	Q6ZRF8	OTTHUMG00000001089	ENST00000377939.4:c.1729G>A	1.37:g.6278425G>A	ENSP00000367173:p.Ala577Thr	91.0	0.0	0		96.0	51.0	0.53125	NM_207396	A2VCM8|B4DFR6|Q5TGS6|Q6ZS63|Q96MP2	Missense_Mutation	SNP	ENST00000377939.4	37	CCDS59.2	17	0.007783882783882784	15	0.03048780487804878	2	0.0055248618784530384	0	0.0	0	0.0	G	12.17	1.856674	0.32791	0.018571	0.0	ENSG00000158286	ENST00000377939	T	0.17691	2.26	5.1	-1.12	0.09808	.	1.899990	0.03308	N	0.190106	T	0.02807	0.0084	N	0.16478	0.41	0.53005	D	0.999968	B	0.06786	0.001	B	0.08055	0.003	T	0.39502	-0.9611	10	0.13470	T	0.59	-18.452	4.6334	0.12513	0.3114:0.3955:0.293:0.0	rs61746089	577	Q6ZRF8	RN207_HUMAN	T	577	ENSP00000367173:A577T	ENSP00000367173:A577T	A	+	1	0	RNF207	6201012	0.008000	0.16893	0.657000	0.29651	0.042000	0.13812	-0.175000	0.09825	0.123000	0.18342	-0.222000	0.12452	GCC	G|0.991;A|0.009	0.009	strong		0.577	RNF207-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003669.2	NM_207396	
ANKRD36B	57730	hgsc.bcm.edu	37	2	98206012	98206012	+	RNA	SNP	G	G	A	rs185401750	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:98206012G>A	ENST00000443455.1	-	0	315							Q8N2N9	AN36B_HUMAN	ankyrin repeat domain 36B																		TCTCTTATTGGCGTCATAATA	0.522													.|||	73	0.0145767	0.0469	0.0043	5008	,	,		11591	0.006		0.001	False		,,,				2504	0.001				p.A46V		Atlas-SNP	.											.	.	.	.	0			c.C137T						PASS	.	G	VAL/ALA	41,1343		2,37,653	106.0	82.0	89.0		137	0.8	0.0	2		89	0,3182		0,0,1591	no	missense	ANKRD36B	NM_025190.3	64	2,37,2244	AA,AG,GG		0.0,2.9624,0.8979	benign	46/1354	98206012	41,4525	692	1591	2283			57730	exon1			TTATTGGCGTCAT	AK024934	CCDS74543.1	2q11.2	2013-01-11	2008-03-25	2008-03-25	ENSG00000196912	ENSG00000196912		"""Ankyrin repeat domain containing"""	29333	protein-coding gene	gene with protein product	"""melanoma-associated antigen"", ""CLL-associated antigen KW-1"""		"""KIAA1641"""	KIAA1641		10997877	Standard	NM_025190		Approved	FLJ21281	uc010yvc.1	Q8N2N9	OTTHUMG00000130547		2.37:g.98206012G>A		292.0	1.0	0.00342466		259.0	124.0	0.478764	NM_025190	Q08AK5|Q6IPR0|Q6PI49|Q8IZM7|Q8TDH6|Q96N30|Q9H759	Missense_Mutation	SNP	ENST00000443455.1	37																																																																																				G|0.989;A|0.011	0.011	strong		0.522	ANKRD36B-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000328967.2	NM_025190	
SEMA3E	9723	hgsc.bcm.edu	37	7	83035289	83035289	+	Silent	SNP	A	A	G	rs28505908	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:83035289A>G	ENST00000307792.3	-	8	1367	c.900T>C	c.(898-900)aaT>aaC	p.N300N	SEMA3E_ENST00000427262.1_Silent_p.N240N	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	300	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)				TGTCAATTCCATTCATTCCTG	0.353													A|||	60	0.0119808	0.0454	0.0	5008	,	,		18888	0.0		0.0	False		,,,				2504	0.0				p.N300N		Atlas-SNP	.											.	SEMA3E	125	.	0			c.T900C						PASS	.	A	,	154,4252	106.0+/-144.5	1,152,2050	159.0	145.0	150.0		720,900	3.3	1.0	7	dbSNP_125	150	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	SEMA3E	NM_001178129.1,NM_012431.2	,	1,154,6348	GG,GA,AA		0.0233,3.4952,1.1994	,	240/716,300/776	83035289	156,12850	2203	4300	6503	SO:0001819	synonymous_variant	9723	exon8			AATTCCATTCATT	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.900T>C	7.37:g.83035289A>G		89.0	0.0	0		104.0	51.0	0.490385	NM_012431	B4E1P1|Q75M94|Q75M97	Silent	SNP	ENST00000307792.3	37	CCDS34674.1																																																																																			A|0.987;G|0.013	0.013	strong		0.353	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431	
HYI	81888	hgsc.bcm.edu	37	1	43917098	43917098	+	Missense_Mutation	SNP	C	C	G	rs79439514	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:43917098C>G	ENST00000372425.4	-	7	938	c.743G>C	c.(742-744)tGt>tCt	p.C248S	SZT2_ENST00000562955.1_3'UTR|HYI_ENST00000372434.1_Missense_Mutation_p.C273S|HYI_ENST00000372426.1_Missense_Mutation_p.C200S|HYI_ENST00000372432.1_Splice_Site|HYI_ENST00000583037.1_Missense_Mutation_p.C175S|SZT2_ENST00000372442.1_3'UTR|HYI-AS1_ENST00000444386.1_RNA|HYI_ENST00000486909.1_Missense_Mutation_p.C248S|SZT2-AS1_ENST00000396885.2_RNA			Q5T013	HYI_HUMAN	hydroxypyruvate isomerase (putative)	248							hydroxypyruvate isomerase activity (GO:0008903)			large_intestine(1)|lung(2)|ovary(1)|urinary_tract(2)	6	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CTGATACTCACAGCCCACGAA	0.627													C|||	146	0.0291534	0.1051	0.0086	5008	,	,		18840	0.0		0.001	False		,,,				2504	0.0				p.C248S		Atlas-SNP	.											.	HYI	23	.	0			c.G743C						PASS	.	C	SER/CYS,,	377,4029	189.5+/-215.6	21,335,1847	61.0	66.0	64.0		743,,	5.5	1.0	1	dbSNP_131	64	2,8598	2.2+/-6.3	0,2,4298	yes	missense,utr-3,splice-5	SZT2,HYI	NM_001190880.2,NM_015284.3,NM_031207.5	112,,	21,337,6145	GG,GC,CC		0.0233,8.5565,2.914	probably-damaging,,	248/278,,	43917098	379,12627	2203	4300	6503	SO:0001583	missense	81888	exon7			TACTCACAGCCCA		CCDS488.1, CCDS488.2, CCDS53309.1, CCDS72771.1	1p34.2	2010-06-24	2010-06-24		ENSG00000178922	ENSG00000178922	5.3.1.22		26948	protein-coding gene	gene with protein product			"""hydroxypyruvate isomerase homolog (E. coli)"""			10561547	Standard	NM_031207		Approved	HT036	uc001cjo.3	Q5T013	OTTHUMG00000007502	ENST00000372425.4:c.743G>C	1.37:g.43917098C>G	ENSP00000361502:p.Cys248Ser	37.0	0.0	0		42.0	18.0	0.428571	NM_001190880	D3DPX4|D3DPX5|Q5Q9A2|Q7Z778|Q96S83|Q9BZR3|Q9BZR4	Missense_Mutation	SNP	ENST00000372425.4	37	CCDS53309.1	56|56	0.02564102564102564|0.02564102564102564	54|54	0.10975609756097561|0.10975609756097561	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	C|C	20.9|20.9	4.070255|4.070255	0.76301|0.76301	0.085565|0.085565	2.33E-4|2.33E-4	ENSG00000178922|ENSG00000178922	ENST00000372425;ENST00000372434;ENST00000372430;ENST00000372426;ENST00000486909|ENST00000470662	T;T;T|.	0.43294|.	0.95;0.95;0.95|.	5.52|5.52	5.52|5.52	0.82312|0.82312	Xylose isomerase-like, TIM barrel domain (2);|.	.|.	.|.	.|.	.|.	T|T	0.17492|0.17492	0.0420|0.0420	M|M	0.93638|0.93638	3.44|3.44	0.09310|0.09310	P|P	0.9999999792184|0.9999999792184	D|.	0.54601|.	0.967|.	P|.	0.56865|.	0.808|.	T|T	0.69239|0.69239	-0.5197|-0.5197	8|4	0.87932|.	D|.	0|.	.|.	19.8124|19.8124	0.96553|0.96553	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	248|.	Q5T013|.	HYI_HUMAN|.	S|L	248;200;175;200;248|157	ENSP00000361502:C248S;ENSP00000361503:C200S;ENSP00000428399:C248S|.	ENSP00000361502:C248S|.	C|V	-|-	2|1	0|0	HYI|HYI	43689685|43689685	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.785000|0.785000	0.44390|0.44390	7.729000|7.729000	0.84864|0.84864	2.764000|2.764000	0.94973|0.94973	0.563000|0.563000	0.77884|0.77884	TGT|GTG	C|0.974;G|0.026	0.026	strong		0.627	HYI-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_031207	
SMARCA2	6595	hgsc.bcm.edu	37	9	2039776	2039776	+	Silent	SNP	A	A	G	rs376509101|rs13296987	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	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|RP11-264I13.2_ENST00000426860.1_RNA|SMARCA2_ENST00000382194.1_Silent_p.Q222Q			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						scavenged	.						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		90.0	1.0	0.0111111		100.0	52.0	0.52	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	
UBA1	7317	hgsc.bcm.edu	37	X	47070468	47070468	+	Missense_Mutation	SNP	A	A	C	rs143044923	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:47070468A>C	ENST00000335972.6	+	20	2491	c.2308A>C	c.(2308-2310)Aac>Cac	p.N770H	UBA1_ENST00000377351.4_Missense_Mutation_p.N770H|UBA1_ENST00000377269.3_Missense_Mutation_p.N218H	NM_003334.3	NP_003325.2	P22314	UBA1_HUMAN	ubiquitin-like modifier activating enzyme 1	770					cell death (GO:0008219)|cellular response to DNA damage stimulus (GO:0006974)|modification-dependent protein catabolic process (GO:0019941)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						GGCTGCTGCCAACCTGTTTGC	0.622													A|||	15	0.00397351	0.0106	0.0014	3775	,	,		14662	0.0		0.0	False		,,,				2504	0.0				p.N770H		Atlas-SNP	.											.	UBA1	89	.	0			c.A2308C						PASS	.	A	HIS/ASN,HIS/ASN	80,3755		1,63,15,1568,556	94.0	71.0	79.0		2308,2308	4.7	1.0	X	dbSNP_134	79	1,6727		0,1,0,2427,1872	yes	missense,missense	UBA1	NM_003334.3,NM_153280.2	68,68	1,64,15,3995,2428	CC,CA,C,AA,A		0.0149,2.086,0.7668	probably-damaging,probably-damaging	770/1059,770/1059	47070468	81,10482	2203	4300	6503	SO:0001583	missense	7317	exon20			GCTGCCAACCTGT	AF258566	CCDS14275.1	Xp11.23	2014-08-13	2007-11-30	2007-11-30	ENSG00000130985	ENSG00000130985	6.3.2.19	"""Ubiquitin-like modifier activating enzymes"""	12469	protein-coding gene	gene with protein product	"""UBA1, ubiquitin-activating enzyme E1 homolog (yeast)"", ""POC20 centriolar protein homolog (Chlamydomonas)"""	314370	"""ubiquitin-activating enzyme E1 (A1S9T and BN75 temperature sensitivity complementing)"", ""ubiquitin-activating enzyme E1"""	A1S9T, GXP1, UBE1		1845793	Standard	NM_153280		Approved	UBE1X, POC20, CFAP124	uc004dhj.4	P22314	OTTHUMG00000021436	ENST00000335972.6:c.2308A>C	X.37:g.47070468A>C	ENSP00000338413:p.Asn770His	128.0	0.0	0		143.0	69.0	0.482517	NM_153280	Q5JRR8|Q96E13	Missense_Mutation	SNP	ENST00000335972.6	37	CCDS14275.1	5	0.0030138637733574444	2	0.004098360655737705	0	0.0	0	0.0	0	0.0	A	21.3	4.124412	0.77436	0.02086	1.49E-4	ENSG00000130985	ENST00000377351;ENST00000335972;ENST00000377269	T;T;T	0.74632	-0.86;-0.86;-0.86	4.66	4.66	0.58398	Molybdenum cofactor biosynthesis, MoeB (1);Ubiquitin-like 1 activating enzyme, catalytic cysteine domain (1);	0.043287	0.85682	D	0.000000	T	0.82125	0.4969	H	0.95114	3.625	0.58432	D	0.999996	D;D	0.89917	0.999;1.0	D;D	0.91635	0.985;0.999	D	0.87031	0.2135	10	0.40728	T	0.16	-28.4035	12.3807	0.55305	1.0:0.0:0.0:0.0	.	218;770	Q5JRR6;P22314	.;UBA1_HUMAN	H	770;770;218	ENSP00000366568:N770H;ENSP00000338413:N770H;ENSP00000366481:N218H	ENSP00000338413:N770H	N	+	1	0	UBA1	46955412	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.197000	0.51028	1.837000	0.53436	0.430000	0.28490	AAC	A|0.994;C|0.006	0.006	strong		0.622	UBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056389.1	NM_003334	
POM121L12	285877	hgsc.bcm.edu	37	7	53103540	53103540	+	Missense_Mutation	SNP	C	C	G	rs78135827	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:53103540C>G	ENST00000408890.4	+	1	192	c.176C>G	c.(175-177)aCt>aGt	p.T59S		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	59										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						AGGTCCCTGACTCAGAGCCAT	0.706													C|||	168	0.0335463	0.1248	0.0043	5008	,	,		12626	0.0		0.0	False		,,,				2504	0.0				p.T59S		Atlas-SNP	.											POM121L12,NS,carcinoma,0,1	POM121L12	146	1	0			c.C176G						PASS	.	C	SER/THR	438,3494		27,384,1555	29.0	35.0	33.0		176	-1.1	0.0	7	dbSNP_131	33	4,8306		0,4,4151	yes	missense	POM121L12	NM_182595.3	58	27,388,5706	GG,GC,CC		0.0481,11.1394,3.6105	probably-damaging	59/297	53103540	442,11800	1966	4155	6121	SO:0001583	missense	285877	exon1			CCCTGACTCAGAG		CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 12"""				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.176C>G	7.37:g.53103540C>G	ENSP00000386133:p.Thr59Ser	57.0	0.0	0		78.0	33.0	0.423077	NM_182595	Q8NDI9	Missense_Mutation	SNP	ENST00000408890.4	37	CCDS43584.1	74	0.03388278388278388	71	0.1443089430894309	2	0.0055248618784530384	1	0.0017482517482517483	0	0.0	C	0.374	-0.932216	0.02359	0.111394	4.81E-4	ENSG00000221900	ENST00000408890	T	0.22539	1.95	1.81	-1.11	0.09840	.	.	.	.	.	T	0.00073	0.0002	N	0.08118	0	0.80722	P	0.0	B	0.16603	0.018	B	0.20767	0.031	T	0.41052	-0.9530	8	0.22109	T	0.4	.	2.491	0.04610	0.0:0.3885:0.2856:0.3259	.	59	Q8N7R1	P1L12_HUMAN	S	59	ENSP00000386133:T59S	ENSP00000386133:T59S	T	+	2	0	POM121L12	53071034	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	0.353000	0.20130	-0.287000	0.09064	0.313000	0.20887	ACT	C|0.965;G|0.035	0.035	strong		0.706	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
C2orf16	84226	hgsc.bcm.edu	37	2	27804691	27804691	+	Missense_Mutation	SNP	A	A	G	rs573591891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27804691A>G	ENST00000408964.2	+	1	5303	c.5252A>G	c.(5251-5253)cAc>cGc	p.H1751R	ZNF512_ENST00000413371.2_5'Flank|ZNF512_ENST00000379717.1_5'Flank|AC074091.1_ENST00000408604.1_RNA|ZNF512_ENST00000416005.2_5'Flank|ZNF512_ENST00000556601.1_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000355467.4_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1751	27 X 8 AA approximative tandem repeat of P-S-E-R-S-H-H-S.|Arg-rich.					extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					AGAAGACATCACAGTCCCTCT	0.552													A|||	8	0.00159744	0.0053	0.0	5008	,	,		20961	0.001		0.0	False		,,,				2504	0.0				p.H1751R		Atlas-SNP	.											.	C2orf16	357	.	0			c.A5252G						PASS	.						192.0	196.0	195.0					2																	27804691		1917	4144	6061	SO:0001583	missense	84226	exon1			GACATCACAGTCC	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.5252A>G	2.37:g.27804691A>G	ENSP00000386190:p.His1751Arg	169.0	0.0	0		157.0	13.0	0.0828025	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	.	.	.	.	.	.	.	.	.	.	A	0.005	-2.199397	0.00299	.	.	ENSG00000221843	ENST00000408964	T	0.04706	3.57	3.97	-7.95	0.01148	.	.	.	.	.	T	0.01592	0.0051	N	0.01729	-0.75	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.42682	-0.9437	9	0.02654	T	1	.	14.4295	0.67240	0.7984:0.0:0.1133:0.0882	.	1751	Q68DN1	CB016_HUMAN	R	1751	ENSP00000386190:H1751R	ENSP00000386190:H1751R	H	+	2	0	C2orf16	27658195	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-11.276000	0.00004	-2.917000	0.00306	-1.919000	0.00516	CAC	.	.	none		0.552	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
HSD17B13	345275	hgsc.bcm.edu	37	4	88243832	88243832	+	Silent	SNP	A	A	G	rs137887488	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88243832A>G	ENST00000328546.4	-	1	226	c.162T>C	c.(160-162)taT>taC	p.Y54Y	HSD17B13_ENST00000302219.6_Silent_p.Y54Y|RP11-529H2.2_ENST00000508163.1_RNA	NM_178135.3	NP_835236.2	Q7Z5P4	DHB13_HUMAN	hydroxysteroid (17-beta) dehydrogenase 13	54						extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|urinary_tract(1)	8		Acute lymphoblastic leukemia(40;0.244)|all_hematologic(202;0.248)		OV - Ovarian serous cystadenocarcinoma(123;0.000308)		TTGCAAATTCATAAGTAGTCT	0.388													A|||	10	0.00199681	0.0068	0.0014	5008	,	,		20127	0.0		0.0	False		,,,				2504	0.0				p.Y54Y		Atlas-SNP	.											.	HSD17B13	27	.	0			c.T162C						PASS	.	A	,	39,4367	43.1+/-76.7	0,39,2164	109.0	110.0	110.0		162,162	-0.3	1.0	4	dbSNP_134	110	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	HSD17B13	NM_001136230.1,NM_178135.3	,	0,39,6464	GG,GA,AA		0.0,0.8852,0.2999	,	54/265,54/301	88243832	39,12967	2203	4300	6503	SO:0001819	synonymous_variant	345275	exon1			AAATTCATAAGTA		CCDS3618.1, CCDS47097.1	4q22.1	2011-09-20			ENSG00000170509	ENSG00000170509	1.1.-.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	18685	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 16C, member 3"""	612127				19027726	Standard	NM_178135		Approved	SCDR9, SDR16C3	uc003hqo.2	Q7Z5P4	OTTHUMG00000130602	ENST00000328546.4:c.162T>C	4.37:g.88243832A>G		173.0	0.0	0		186.0	89.0	0.478495	NM_178135	A8K9R9|Q2M1L5|Q86W22|Q86W23	Silent	SNP	ENST00000328546.4	37	CCDS3618.1																																																																																			A|0.996;G|0.004	0.004	strong		0.388	HSD17B13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253052.1	NM_178135	
SPHK2	56848	hgsc.bcm.edu	37	19	49131317	49131317	+	Silent	SNP	G	G	T	rs116785119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49131317G>T	ENST00000245222.4	+	5	1113	c.747G>T	c.(745-747)ctG>ctT	p.L249L	SPHK2_ENST00000443164.1_Silent_p.L311L|SPHK2_ENST00000600537.1_Silent_p.L190L|SPHK2_ENST00000601712.1_Silent_p.L213L|SPHK2_ENST00000598088.1_Silent_p.L249L|SPHK2_ENST00000599029.1_Silent_p.L213L|SPHK2_ENST00000340932.3_Silent_p.L213L|SPHK2_ENST00000599748.1_Silent_p.L213L	NM_001204158.2|NM_001243876.1|NM_020126.4	NP_001191087.1|NP_001230805.1|NP_064511.2	Q9NRA0	SPHK2_HUMAN	sphingosine kinase 2	249	DAGKc. {ECO:0000255|PROSITE- ProRule:PRU00783}.				blood vessel development (GO:0001568)|brain development (GO:0007420)|cell proliferation (GO:0008283)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|small molecule metabolic process (GO:0044281)|sphinganine-1-phosphate biosynthetic process (GO:0006669)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	ATP binding (GO:0005524)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|Ras GTPase binding (GO:0017016)|sphinganine kinase activity (GO:0008481)			NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	19		all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		GAGACGGGCTGCTCCATGAGG	0.647													G|||	17	0.00339457	0.0121	0.0014	5008	,	,		16367	0.0		0.0	False		,,,				2504	0.0				p.L249L		Atlas-SNP	.											.	SPHK2	62	.	0			c.G747T						PASS	.	G	,,,	56,4350	55.5+/-91.7	1,54,2148	55.0	60.0	58.0		570,747,639,747	4.6	1.0	19	dbSNP_132	58	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SPHK2	NM_001204158.2,NM_001204159.2,NM_001204160.2,NM_020126.4	,,,	1,54,6448	TT,TG,GG		0.0,1.271,0.4306	,,,	190/596,249/655,213/619,249/655	49131317	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	56848	exon5			CGGGCTGCTCCAT	AF245447	CCDS12727.1, CCDS59404.1, CCDS59405.1, CCDS74414.1	19q13.33	2013-09-20			ENSG00000063176	ENSG00000063176			18859	protein-coding gene	gene with protein product		607092				10751414, 17895250	Standard	NM_020126		Approved		uc002pjs.3	Q9NRA0	OTTHUMG00000183318	ENST00000245222.4:c.747G>T	19.37:g.49131317G>T		61.0	0.0	0		65.0	37.0	0.569231	NM_020126	A0T4C8|B4DU87|Q9BRN1|Q9H0Q2|Q9NWU7	Silent	SNP	ENST00000245222.4	37	CCDS12727.1																																																																																			G|0.996;T|0.004	0.004	strong		0.647	SPHK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466153.1		
SVEP1	79987	hgsc.bcm.edu	37	9	113169816	113169816	+	Silent	SNP	T	T	C	rs116159392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:113169816T>C	ENST00000401783.2	-	38	8400	c.8064A>G	c.(8062-8064)ggA>ggG	p.G2688G	SVEP1_ENST00000374469.1_Silent_p.G2665G|SVEP1_ENST00000297826.5_Silent_p.G614G	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2688	Sushi 21. {ECO:0000255|PROSITE- ProRule:PRU00302}.				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						GAAGTTCATATCCTGGATTAC	0.453													T|||	207	0.0413339	0.149	0.0144	5008	,	,		22581	0.0		0.0	False		,,,				2504	0.0				p.G2688G		Atlas-SNP	.											SVEP1,NS,carcinoma,0,1	SVEP1	326	1	0			c.A8064G						PASS	.	T		461,3353		27,407,1473	169.0	166.0	167.0		8064	-6.8	0.9	9	dbSNP_132	167	5,8265		0,5,4130	no	coding-synonymous	SVEP1	NM_153366.3		27,412,5603	CC,CT,TT		0.0605,12.087,3.8563		2688/3572	113169816	466,11618	1907	4135	6042	SO:0001819	synonymous_variant	79987	exon38			TTCATATCCTGGA	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.8064A>G	9.37:g.113169816T>C		151.0	0.0	0		118.0	75.0	0.635593	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	37	CCDS48004.1																																																																																			T|0.959;C|0.041	0.041	strong		0.453	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
MYO10	4651	hgsc.bcm.edu	37	5	16701717	16701717	+	Silent	SNP	C	C	T	rs149110	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:16701717C>T	ENST00000513610.1	-	25	3241	c.2787G>A	c.(2785-2787)agG>agA	p.R929R	MYO10_ENST00000515803.1_Silent_p.R268R|MYO10_ENST00000427430.2_Silent_p.R286R|MYO10_ENST00000512061.1_5'Flank|MYO10_ENST00000505695.1_Silent_p.R268R|MYO10_ENST00000274203.9_Silent_p.R286R	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	929	Mediates antiparallel dimerization.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						CCTCCTCCAGCCTGCGGAGCT	0.637													C|||	327	0.0652955	0.2277	0.0288	5008	,	,		13912	0.0		0.006	False		,,,				2504	0.0				p.R929R		Atlas-SNP	.											.	MYO10	198	.	0			c.G2787A						PASS	.	C		850,3468		77,696,1386	24.0	29.0	27.0		2787	3.2	0.9	5	dbSNP_79	27	49,8505		1,47,4229	no	coding-synonymous	MYO10	NM_012334.2		78,743,5615	TT,TC,CC		0.5728,19.685,6.9842		929/2059	16701717	899,11973	2159	4277	6436	SO:0001819	synonymous_variant	4651	exon25			CTCCAGCCTGCGG	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"""Myosins / Myosin superfamily : Class X"", ""Pleckstrin homology (PH) domain containing"""	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.2787G>A	5.37:g.16701717C>T		90.0	0.0	0		93.0	46.0	0.494624	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	37	CCDS54834.1																																																																																			C|0.928;T|0.072	0.072	strong		0.637	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
CAP2	10486	hgsc.bcm.edu	37	6	17507504	17507504	+	Silent	SNP	C	C	G	rs146710056	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:17507504C>G	ENST00000229922.2	+	5	937	c.405C>G	c.(403-405)gcC>gcG	p.A135A	CAP2_ENST00000465994.1_Silent_p.A135A|CAP2_ENST00000489374.1_Intron|CAP2_ENST00000378990.2_Silent_p.A109A|CAP2_ENST00000493172.1_Intron	NM_006366.2	NP_006357.1	P40123	CAP2_HUMAN	CAP, adenylate cyclase-associated protein, 2 (yeast)	135					activation of adenylate cyclase activity (GO:0007190)|axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|establishment or maintenance of cell polarity (GO:0007163)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)				breast(3)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(4)|urinary_tract(1)	27	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)			ATCTTTCGGCCGTCAGCGAAA	0.483													C|||	4	0.000798722	0.003	0.0	5008	,	,		19667	0.0		0.0	False		,,,				2504	0.0				p.A135A		Atlas-SNP	.											.	CAP2	61	.	0			c.C405G						PASS	.	C		18,4388	26.2+/-53.5	0,18,2185	128.0	102.0	111.0		405	-3.8	0.8	6	dbSNP_134	111	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CAP2	NM_006366.2		0,19,6484	GG,GC,CC		0.0116,0.4085,0.1461		135/478	17507504	19,12987	2203	4300	6503	SO:0001819	synonymous_variant	10486	exon5			TTCGGCCGTCAGC	BC008481	CCDS4539.1	6p22.3	2008-02-05			ENSG00000112186	ENSG00000112186			20039	protein-coding gene	gene with protein product						7962207, 8761950	Standard	NM_006366		Approved		uc003ncb.3	P40123	OTTHUMG00000014311	ENST00000229922.2:c.405C>G	6.37:g.17507504C>G		134.0	0.0	0		128.0	66.0	0.515625	NM_006366	B2R5Y3|B7Z1C4|B7Z214|Q6IAY2	Silent	SNP	ENST00000229922.2	37	CCDS4539.1																																																																																			C|0.998;G|0.002	0.002	strong		0.483	CAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039952.2		
ATP8B1	5205	hgsc.bcm.edu	37	18	55334339	55334339	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:55334339T>C	ENST00000283684.4	-	19	2269	c.2270A>G	c.(2269-2271)tAt>tGt	p.Y757C	RP11-35G9.3_ENST00000599199.1_RNA|ATP8B1_ENST00000536015.1_Missense_Mutation_p.Y757C|RP11-35G9.3_ENST00000592201.1_RNA|RP11-35G9.5_ENST00000588925.1_RNA|RP11-35G9.3_ENST00000591854.1_RNA			O43520	AT8B1_HUMAN	ATPase, aminophospholipid transporter, class I, type 8B, member 1	757					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|drug transmembrane transport (GO:0006855)|inner ear receptor cell development (GO:0060119)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|phospholipid translocation (GO:0045332)|regulation of microvillus assembly (GO:0032534)|sensory perception of sound (GO:0007605)|transmembrane transport (GO:0055085)|vestibulocochlear nerve formation (GO:0021650)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|cardiolipin binding (GO:1901612)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(6)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(19)|ovary(3)|prostate(1)	53		Colorectal(73;0.229)				ATCCTCCCCATAGCAGATGGT	0.368																																					p.Y757C		Atlas-SNP	.											.	ATP8B1	126	.	0			c.A2270G						PASS	.						114.0	107.0	109.0					18																	55334339		2203	4300	6503	SO:0001583	missense	5205	exon20			TCCCCATAGCAGA	AF038007	CCDS11965.1	18q21	2010-04-28	2010-04-28		ENSG00000081923	ENSG00000081923		"""ATPases / P-type"""	3706	protein-coding gene	gene with protein product		602397	"""ATPase, Class I, type 8B, member 1"", ""ATPase, class I, type 8B, member 1"""	FIC1, BRIC, PFIC1		9500542, 7655458	Standard	NM_005603		Approved	ATPIC, PFIC	uc002lgw.3	O43520	OTTHUMG00000132739	ENST00000283684.4:c.2270A>G	18.37:g.55334339T>C	ENSP00000283684:p.Tyr757Cys	91.0	0.0	0		95.0	4.0	0.0421053	NM_005603	Q9BTP8	Missense_Mutation	SNP	ENST00000283684.4	37	CCDS11965.1	.	.	.	.	.	.	.	.	.	.	T	15.76	2.928583	0.52759	.	.	ENSG00000081923	ENST00000283684;ENST00000536015	T;T	0.67698	-0.28;-0.28	5.15	5.15	0.70609	HAD-like domain (2);	0.000000	0.85682	D	0.000000	T	0.77738	0.4175	L	0.59436	1.845	0.80722	D	1	D	0.65815	0.995	D	0.65773	0.938	T	0.79999	-0.1566	10	0.66056	D	0.02	.	14.945	0.71023	0.0:0.0:0.0:1.0	.	757	O43520	AT8B1_HUMAN	C	757	ENSP00000283684:Y757C;ENSP00000445359:Y757C	ENSP00000283684:Y757C	Y	-	2	0	ATP8B1	53485337	1.000000	0.71417	0.990000	0.47175	0.593000	0.36681	5.781000	0.68964	2.063000	0.61619	0.528000	0.53228	TAT	.	.	none		0.368	ATP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256097.1	NM_005603	
CT47B1	643311	hgsc.bcm.edu	37	X	120008932	120008932	+	Missense_Mutation	SNP	T	T	C	rs193289998		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:120008932T>C	ENST00000371311.3	-	1	847	c.593A>G	c.(592-594)gAg>gGg	p.E198G		NM_001145718.1	NP_001139190.1	P0C2W7	CT47B_HUMAN	cancer/testis antigen family 47, member B1	198										breast(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|lung(9)|ovary(1)|skin(1)	22						CGACGCGGCCTCCTGGACCGA	0.711													N|||	78	0.0206623	0.053	0.0115	3775	,	,		9887	0.0		0.0	False		,,,				2504	0.0				p.E198G		Atlas-SNP	.											.	CT47B1	67	.	0			c.A593G						PASS	.	T	GLY/GLU	86,1123		1,78,6,438,169	28.0	28.0	28.0		593	0.7	0.0	X		28	0,2389		0,0,0,800,789	no	missense	CT47B1	NM_001145718.1	98	1,78,6,1238,958	CC,CT,C,TT,T		0.0,7.1133,2.3902	benign	198/300	120008932	86,3512	692	1589	2281	SO:0001583	missense	643311	exon1			GCGGCCTCCTGGA		CCDS48161.1	Xq24	2014-05-06	2011-03-24		ENSG00000236446	ENSG00000236446			33293	protein-coding gene	gene with protein product	"""cancer/testis CT47 family, member 13"""	300790				16382448	Standard	NM_001145718		Approved	CT47.13	uc011muc.2	P0C2W7	OTTHUMG00000187483	ENST00000371311.3:c.593A>G	X.37:g.120008932T>C	ENSP00000360360:p.Glu198Gly	94.0	0.0	0		77.0	22.0	0.285714	NM_001145718	A6NM97	Missense_Mutation	SNP	ENST00000371311.3	37	CCDS48161.1	25	0.015069318866787222	15	0.03125	2	0.00558659217877095	0	0.0	0	0.0	T	10.45	1.352922	0.24512	0.071133	0.0	ENSG00000236446	ENST00000371311	.	.	.	1.89	0.714	0.18180	.	.	.	.	.	T	0.01029	0.0034	N	0.08118	0	0.80722	P	0.0	B	0.19817	0.039	B	0.08055	0.003	T	0.15492	-1.0435	7	0.35671	T	0.21	.	3.0134	0.06052	0.0:0.4121:0.0:0.5879	.	198	P0C2W7	CT47B_HUMAN	G	198	.	ENSP00000360360:E198G	E	-	2	0	CT47B1	119892960	0.000000	0.05858	0.000000	0.03702	0.093000	0.18481	-1.020000	0.03618	0.129000	0.18514	0.143000	0.16000	GAG	T|0.985;C|0.015	0.015	strong		0.711	CT47B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058121.1	NM_001145718	
ABCC3	8714	hgsc.bcm.edu	37	17	48734136	48734136	+	Missense_Mutation	SNP	G	G	A	rs35777968	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48734136G>A	ENST00000285238.8	+	3	376	c.296G>A	c.(295-297)cGg>cAg	p.R99Q	ABCC3_ENST00000427699.1_Missense_Mutation_p.R99Q	NM_003786.3	NP_003777.2	O15438	MRP3_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 3	99					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|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)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	33			BRCA - Breast invasive adenocarcinoma(22;3.05e-09)		Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Doxorubicin(DB00997)|Etoposide(DB00773)|Ezetimibe(DB00973)|Fluorouracil(DB00544)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indomethacin(DB00328)|Lamivudine(DB00709)|Leucovorin(DB00650)|Methotrexate(DB00563)|Metyrapone(DB01011)|Nifedipine(DB01115)|Omeprazole(DB00338)|Phenobarbital(DB01174)|Probenecid(DB01032)|Rifampicin(DB01045)|Sulfinpyrazone(DB01138)|Verapamil(DB00661)|Vincristine(DB00541)	GTCCATGGCCGGGCCCCTGCC	0.617													G|||	61	0.0121805	0.0454	0.0014	5008	,	,		16262	0.0		0.0	False		,,,				2504	0.0				p.R99Q		Atlas-SNP	.											.	ABCC3	138	.	0			c.G296A						PASS	.	G	GLN/ARG,GLN/ARG	157,4249	103.4+/-141.9	2,153,2048	70.0	71.0	71.0		296,296	-2.1	0.0	17	dbSNP_126	71	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	ABCC3	NM_001144070.1,NM_003786.3	43,43	2,155,6346	AA,AG,GG		0.0233,3.5633,1.2225	benign,benign	99/573,99/1528	48734136	159,12847	2203	4300	6503	SO:0001583	missense	8714	exon3			ATGGCCGGGCCCC	Y17151	CCDS32681.1, CCDS45739.1	17q21	2012-03-14			ENSG00000108846	ENSG00000108846		"""ATP binding cassette transporters / subfamily C"""	54	protein-coding gene	gene with protein product	"""canalicular multispecific organic anion transporter 2"""	604323				8894702, 9827529	Standard	NM_003786		Approved	MRP3, cMOAT2, EST90757, MLP2, MOAT-D	uc002isl.3	O15438	OTTHUMG00000162245	ENST00000285238.8:c.296G>A	17.37:g.48734136G>A	ENSP00000285238:p.Arg99Gln	115.0	0.0	0		106.0	51.0	0.481132	NM_003786	B2RPA9|D3DTX9|O60265|O60922|O75621|O95078|O95289|O95290|Q86X85|Q9UN52	Missense_Mutation	SNP	ENST00000285238.8	37	CCDS32681.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	G	11.08	1.534357	0.27475	0.035633	2.33E-4	ENSG00000108846	ENST00000427699;ENST00000285238	T;T	0.35236	1.32;1.32	5.53	-2.14	0.07123	.	1.579970	0.03817	N	0.266872	T	0.04137	0.0115	N	0.12182	0.205	0.09310	N	1	B;B	0.17038	0.01;0.02	B;B	0.13407	0.002;0.009	T	0.12372	-1.0550	10	0.12430	T	0.62	0.3777	6.1119	0.20106	0.4088:0.2585:0.3327:0.0	rs35777968;rs45584534;rs59497545	99;99	O15438;O15438-5	MRP3_HUMAN;.	Q	99	ENSP00000395160:R99Q;ENSP00000285238:R99Q	ENSP00000285238:R99Q	R	+	2	0	ABCC3	46089135	0.000000	0.05858	0.018000	0.16275	0.347000	0.29111	0.356000	0.20181	-0.007000	0.14345	0.591000	0.81541	CGG	G|0.987;A|0.013	0.013	strong		0.617	ABCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368083.2	NM_020038	
KMT2D	8085	hgsc.bcm.edu	37	12	49433356	49433356	+	Silent	SNP	G	G	A	rs116686402	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:49433356G>A	ENST00000301067.7	-	32	8090	c.8091C>T	c.(8089-8091)cgC>cgT	p.R2697R	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	2697					chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										GCAGGGTGTTGCGCTGGATCT	0.587													G|||	93	0.0185703	0.0696	0.0014	5008	,	,		18946	0.0		0.0	False		,,,				2504	0.0				p.R2697R		Atlas-SNP	.											.	MLL2	1173	.	0			c.C8091T						PASS	.	G		239,3787		8,223,1782	17.0	19.0	18.0		8091	0.2	1.0	12	dbSNP_132	18	2,8382		0,2,4190	no	coding-synonymous	MLL2	NM_003482.3		8,225,5972	AA,AG,GG		0.0239,5.9364,1.942		2697/5538	49433356	241,12169	2013	4192	6205	SO:0001819	synonymous_variant	8085	exon32			GGTGTTGCGCTGG	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.8091C>T	12.37:g.49433356G>A		30.0	0.0	0		43.0	17.0	0.395349	NM_003482	O14687	Silent	SNP	ENST00000301067.7	37	CCDS44873.1																																																																																			G|0.986;A|0.014	0.014	strong		0.587	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
ALDH16A1	126133	hgsc.bcm.edu	37	19	49969522	49969522	+	Silent	SNP	C	C	T	rs116631301	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49969522C>T	ENST00000293350.4	+	14	2083	c.1920C>T	c.(1918-1920)gcC>gcT	p.A640A	ALDH16A1_ENST00000540132.1_Silent_p.A477A|ALDH16A1_ENST00000455361.2_Silent_p.A589A|CTD-3148I10.9_ENST00000599536.1_Intron|ALDH16A1_ENST00000433981.2_Silent_p.A475A	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	640						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|skin(2)|urinary_tract(3)	20		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)		GGGTGCAGGCCCAAGGCCACA	0.701													C|||	44	0.00878594	0.031	0.0043	5008	,	,		14666	0.0		0.0	False		,,,				2504	0.0				p.A640A		Atlas-SNP	.											.	ALDH16A1	54	.	0			c.C1920T						PASS	.	C	,	145,4033		0,145,1944	7.0	9.0	8.0		1767,1920	3.3	1.0	19	dbSNP_132	8	3,8237		0,3,4117	no	coding-synonymous,coding-synonymous	ALDH16A1	NM_001145396.1,NM_153329.3	,	0,148,6061	TT,TC,CC		0.0364,3.4706,1.1918	,	589/752,640/803	49969522	148,12270	2089	4120	6209	SO:0001819	synonymous_variant	126133	exon14			GCAGGCCCAAGGC	AY007096	CCDS12766.1, CCDS46141.1	19q13.33	2014-08-12			ENSG00000161618	ENSG00000161618		"""Aldehyde dehydrogenases"""	28114	protein-coding gene	gene with protein product		613358					Standard	NM_153329		Approved	MGC10204	uc002pnt.3	Q8IZ83	OTTHUMG00000183163	ENST00000293350.4:c.1920C>T	19.37:g.49969522C>T		34.0	0.0	0		34.0	16.0	0.470588	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Silent	SNP	ENST00000293350.4	37	CCDS12766.1																																																																																			C|0.992;T|0.008	0.008	strong		0.701	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329	
SOX10	6663	hgsc.bcm.edu	37	22	38379543	38379543	+	Silent	SNP	G	G	A	rs73415876	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:38379543G>A	ENST00000396884.2	-	2	531	c.249C>T	c.(247-249)taC>taT	p.Y83Y	POLR2F_ENST00000407936.1_Intron|POLR2F_ENST00000405557.1_Intron|SOX10_ENST00000360880.2_Silent_p.Y83Y|SOX10_ENST00000470555.1_Intron	NM_006941.3	NP_008872.1	P56693	SOX10_HUMAN	SRY (sex determining region Y)-box 10	83					anatomical structure morphogenesis (GO:0009653)|cell maturation (GO:0048469)|developmental growth (GO:0048589)|digestive tract morphogenesis (GO:0048546)|enteric nervous system development (GO:0048484)|in utero embryonic development (GO:0001701)|melanocyte differentiation (GO:0030318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of transcription, DNA-templated (GO:0045892)|neural crest cell migration (GO:0001755)|oligodendrocyte differentiation (GO:0048709)|peripheral nervous system development (GO:0007422)|positive regulation of gliogenesis (GO:0014015)|positive regulation of neuroblast proliferation (GO:0002052)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	extrinsic component of mitochondrial outer membrane (GO:0031315)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|transcription coactivator activity (GO:0003713)			NS(6)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(4)|skin(2)	20	Melanoma(58;0.045)					GCGTCCAGTCGTAGCCGCTGA	0.657													G|||	205	0.0409345	0.152	0.0043	5008	,	,		11391	0.0		0.001	False		,,,				2504	0.0				p.Y83Y	Melanoma(39;342 1098 6220 32775 40068)|GBM(21;140 497 5227 16059 19275)	Atlas-SNP	.											.	SOX10	48	.	0			c.C249T	GRCh37	CM981855	SOX10	M	rs73415876	PASS	.	G		496,3910	215.5+/-234.4	22,452,1729	64.0	40.0	48.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	249	1.1	1.0	22	dbSNP_130	48	7,8591	4.3+/-15.6	0,7,4292	no	coding-synonymous	SOX10	NM_006941.3		22,459,6021	AA,AG,GG		0.0814,11.2574,3.868		83/467	38379543	503,12501	2203	4299	6502	SO:0001819	synonymous_variant	6663	exon2			CCAGTCGTAGCCG		CCDS13964.1	22q13.1	2014-09-17			ENSG00000100146	ENSG00000100146		"""SRY (sex determining region Y)-boxes"""	11190	protein-coding gene	gene with protein product	"""dominant megacolon, mouse, human homolog of"""	602229				9462749, 10441344, 12944398	Standard	NM_006941		Approved	DOM, WS4, WS2E	uc003aun.1	P56693	OTTHUMG00000149913	ENST00000396884.2:c.249C>T	22.37:g.38379543G>A		84.0	0.0	0		120.0	65.0	0.541667	NM_006941	B4DV62|Q6FHW7	Silent	SNP	ENST00000396884.2	37	CCDS13964.1																																																																																			A|0.044;G|0.956	0.044	strong		0.657	SOX10-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313875.1	NM_006941	
CLCN6	1185	hgsc.bcm.edu	37	1	11884586	11884586	+	Silent	SNP	G	G	A	rs60602304	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11884586G>A	ENST00000346436.6	+	8	676	c.624G>A	c.(622-624)tcG>tcA	p.S208S	CLCN6_ENST00000376492.3_3'UTR|CLCN6_ENST00000376496.3_Silent_p.S208S|CLCN6_ENST00000376487.3_Silent_p.S186S|CLCN6_ENST00000312413.6_Silent_p.S208S	NM_001286.3	NP_001277	P51797	CLCN6_HUMAN	chloride channel, voltage-sensitive 6	208					cell volume homeostasis (GO:0006884)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|response to mechanical stimulus (GO:0009612)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|voltage-gated chloride channel activity (GO:0005247)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(4)	36	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;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		ACAGTGGTTCGGTGGTGGGAG	0.597													G|||	115	0.0229633	0.0794	0.0043	5008	,	,		18300	0.004		0.001	False		,,,				2504	0.002				p.S208S		Atlas-SNP	.											.	CLCN6	77	.	0			c.G624A						PASS	.	G	,,,	421,3985	204.8+/-226.9	19,383,1801	75.0	68.0	71.0		624,624,624,624	-11.6	0.1	1	dbSNP_129	71	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CLCN6	NM_001286.2,NM_021735.2,NM_021736.2,NM_021737.2	,,,	19,391,6093	AA,AG,GG		0.093,9.5552,3.2985	,,,	208/870,208/321,208/354,208/309	11884586	429,12577	2203	4300	6503	SO:0001819	synonymous_variant	1185	exon8			TGGTTCGGTGGTG	X83378	CCDS138.1, CCDS57972.1	1p36	2012-09-26	2012-02-23		ENSG00000011021	ENSG00000011021		"""Ion channels / Chloride channels : Voltage-sensitive"""	2024	protein-coding gene	gene with protein product		602726	"""chloride channel 6"""			8543009	Standard	NM_001286		Approved	CLC-6, KIAA0046, ClC-6	uc001ate.5	P51797	OTTHUMG00000002299	ENST00000346436.6:c.624G>A	1.37:g.11884586G>A		105.0	0.0	0		99.0	53.0	0.535354	NM_001286	A8K1T4|B4DGT7|F8W9R3|O60818|O60819|O60820|O60821|P78520|P78521|Q17R81|Q5SNW2|Q5SNW3|Q5SNX1|Q5SNX2|Q5SNX3|Q99427|Q99428|Q99429	Silent	SNP	ENST00000346436.6	37	CCDS138.1																																																																																			G|0.970;A|0.030	0.030	strong		0.597	CLCN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006639.2	NM_001286	
RAPGEF3	10411	hgsc.bcm.edu	37	12	48134768	48134768	+	Missense_Mutation	SNP	A	A	T	rs80097705	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:48134768A>T	ENST00000449771.2	-	20	2067	c.1979T>A	c.(1978-1980)cTg>cAg	p.L660Q	RAPGEF3_ENST00000548919.1_Missense_Mutation_p.L569Q|RAPGEF3_ENST00000171000.4_Missense_Mutation_p.L618Q|RAPGEF3_ENST00000389212.3_Missense_Mutation_p.L660Q|RAPGEF3_ENST00000405493.2_Missense_Mutation_p.L618Q|RP1-197B17.3_ENST00000547799.1_lincRNA|RAPGEF3_ENST00000549151.1_Missense_Mutation_p.L618Q			O95398	RPGF3_HUMAN	Rap guanine nucleotide exchange factor (GEF) 3	660					angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cAMP-mediated signaling (GO:0019933)|cell proliferation (GO:0008283)|cellular response to cAMP (GO:0071320)|energy reserve metabolic process (GO:0006112)|establishment of endothelial barrier (GO:0061028)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cAMP catabolic process (GO:0030822)|positive regulation of Rap GTPase activity (GO:0032854)|positive regulation of stress fiber assembly (GO:0051496)|Rap protein signal transduction (GO:0032486)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Rap guanyl-nucleotide exchange factor activity (GO:0017034)			endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|pancreas(1)|prostate(1)|skin(7)	25	Lung SC(27;0.192)			GBM - Glioblastoma multiforme(48;0.0375)		GGCACTCACCAGGTCCAGCCC	0.657													A|||	149	0.0297524	0.1059	0.0115	5008	,	,		15902	0.0		0.001	False		,,,				2504	0.0				p.L660Q		Atlas-SNP	.											.	RAPGEF3	98	.	0			c.T1979A						PASS	.	A	GLN/LEU,GLN/LEU,GLN/LEU	441,3965	204.5+/-226.7	16,409,1778	28.0	26.0	27.0		1979,1853,1853	2.8	1.0	12	dbSNP_131	27	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense	RAPGEF3	NM_001098531.2,NM_001098532.2,NM_006105.5	113,113,113	16,412,6075	TT,TA,AA		0.0349,10.0091,3.4138	benign,benign,benign	660/924,618/882,618/882	48134768	444,12562	2203	4300	6503	SO:0001583	missense	10411	exon20			CTCACCAGGTCCA	AK092448	CCDS31784.1, CCDS41775.1	12q13.1	2006-04-12	2004-03-26		ENSG00000079337	ENSG00000079337			16629	protein-coding gene	gene with protein product	"""exchange protein directly activated by cAMP 1"""	606057	"""RAP guanine-nucleotide-exchange factor (GEF) 3"""			10777494, 9856955	Standard	NM_001098531		Approved	cAMP-GEFI, EPAC, bcm910	uc001rpz.4	O95398	OTTHUMG00000133667	ENST00000449771.2:c.1979T>A	12.37:g.48134768A>T	ENSP00000395708:p.Leu660Gln	118.0	0.0	0		134.0	61.0	0.455224	NM_001098531	A8K2G5|E7EQC8|O95634|Q8WVN0	Missense_Mutation	SNP	ENST00000449771.2	37	CCDS41775.1	64	0.029304029304029304	60	0.12195121951219512	4	0.011049723756906077	0	0.0	0	0.0	A	15.33	2.801075	0.50315	0.100091	3.49E-4	ENSG00000079337	ENST00000405493;ENST00000449771;ENST00000541821;ENST00000549151;ENST00000171000;ENST00000389211;ENST00000389212;ENST00000397089;ENST00000548919	T;T;T;T;T;T	0.29655	1.56;1.56;1.56;1.56;1.56;1.56	4.0	2.85	0.33270	Guanine-nucleotide dissociation stimulator CDC25 (2);Ras guanine nucleotide exchange factor, domain (1);	0.318780	0.26567	N	0.023652	T	0.00271	0.0008	N	0.25332	0.735	0.25580	P	0.9868038	B	0.13145	0.007	B	0.15484	0.013	T	0.05007	-1.0912	9	0.52906	T	0.07	.	7.9374	0.29937	0.898:0.0:0.102:0.0	.	660	O95398	RPGF3_HUMAN	Q	618;660;307;618;618;618;660;623;569	ENSP00000384521:L618Q;ENSP00000395708:L660Q;ENSP00000448619:L618Q;ENSP00000171000:L618Q;ENSP00000373864:L660Q;ENSP00000448480:L569Q	ENSP00000171000:L618Q	L	-	2	0	RAPGEF3	46421035	0.352000	0.24895	1.000000	0.80357	0.997000	0.91878	1.101000	0.31037	1.609000	0.50190	0.459000	0.35465	CTG	A|0.965;T|0.035	0.035	strong		0.657	RAPGEF3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257848.1	NM_006105	
RANBP2	5903	hgsc.bcm.edu	37	2	109384665	109384665	+	Missense_Mutation	SNP	A	A	G	rs145613015	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:109384665A>G	ENST00000283195.6	+	20	7796	c.7670A>G	c.(7669-7671)aAt>aGt	p.N2557S		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	2557					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)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						AAAAGTAACAATAGTGAAACT	0.363													A|||	10	0.00199681	0.0068	0.0014	5008	,	,		20419	0.0		0.0	False		,,,				2504	0.0				p.N2557S		Atlas-SNP	.											.	RANBP2	488	.	0			c.A7670G						PASS	.	A	SER/ASN	27,4379	30.8+/-60.4	1,25,2177	84.0	98.0	93.0		7670	-1.0	0.0	2	dbSNP_134	93	0,8594		0,0,4297	no	missense	RANBP2	NM_006267.4	46	1,25,6474	GG,GA,AA		0.0,0.6128,0.2077	benign	2557/3225	109384665	27,12973	2203	4297	6500	SO:0001583	missense	5903	exon20			GTAACAATAGTGA	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"""Tetratricopeptide (TTC) repeat domain containing"""	9848	protein-coding gene	gene with protein product		601181	"""acute necrotizing encephalopathy 1 (autosomal dominant)"""	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.7670A>G	2.37:g.109384665A>G	ENSP00000283195:p.Asn2557Ser	369.0	0.0	0		378.0	186.0	0.492063	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	A	0.024	-1.385684	0.01194	0.006128	0.0	ENSG00000153201	ENST00000409491;ENST00000283195	T	0.25250	1.81	5.31	-1.03	0.10102	.	.	.	.	.	T	0.04679	0.0127	N	0.00926	-1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39292	-0.9621	9	0.07644	T	0.81	-6.4079	10.0576	0.42255	0.5205:0.0:0.4795:0.0	.	2557	P49792	RBP2_HUMAN	S	1581;2557	ENSP00000283195:N2557S	ENSP00000283195:N2557S	N	+	2	0	RANBP2	108751097	0.000000	0.05858	0.007000	0.13788	0.682000	0.39822	-0.668000	0.05268	-0.097000	0.12307	0.377000	0.23210	AAT	.	.	weak		0.363	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267	
PALD1	27143	hgsc.bcm.edu	37	10	72294192	72294192	+	Missense_Mutation	SNP	C	C	T	rs141167395	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:72294192C>T	ENST00000263563.6	+	9	1302	c.1034C>T	c.(1033-1035)aCg>aTg	p.T345M		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	345						cytosol (GO:0005829)											GCTGCCCCCACGCAGGCCAAG	0.622													C|||	6	0.00119808	0.0038	0.0	5008	,	,		16332	0.001		0.0	False		,,,				2504	0.0				p.T345M		Atlas-SNP	.											.	.	.	.	0			c.C1034T						PASS	.	C	MET/THR	13,4391	20.2+/-43.8	0,13,2189	38.0	35.0	36.0		1034	-4.0	0.0	10	dbSNP_134	36	0,8598		0,0,4299	yes	missense	KIAA1274	NM_014431.2	81	0,13,6488	TT,TC,CC		0.0,0.2952,0.1	benign	345/857	72294192	13,12989	2202	4299	6501	SO:0001583	missense	27143	exon9			CCCCCACGCAGGC	AB033100	CCDS31215.1	10q22.2	2012-07-17	2012-07-17	2012-07-17	ENSG00000107719	ENSG00000107719			23530	protein-coding gene	gene with protein product		614656	"""paladin"", ""KIAA1274"""	PALD, KIAA1274			Standard	NM_014431		Approved		uc001jrd.4	Q9ULE6	OTTHUMG00000018411	ENST00000263563.6:c.1034C>T	10.37:g.72294192C>T	ENSP00000263563:p.Thr345Met	93.0	0.0	0		92.0	40.0	0.434783	NM_014431	B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Missense_Mutation	SNP	ENST00000263563.6	37	CCDS31215.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	0	0.0	C	9.315	1.056639	0.19907	0.002952	0.0	ENSG00000107719	ENST00000263563;ENST00000373214	T	0.24908	1.83	4.62	-3.99	0.04069	.	1.808830	0.02724	N	0.114334	T	0.13628	0.0330	N	0.11201	0.11	0.09310	N	1	B	0.18610	0.029	B	0.15052	0.012	T	0.23619	-1.0183	10	0.45353	T	0.12	0.2671	6.7714	0.23596	0.1154:0.3697:0.0:0.5148	.	345	Q9ULE6	PALD_HUMAN	M	345	ENSP00000263563:T345M	ENSP00000263563:T345M	T	+	2	0	KIAA1274	71964198	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-2.206000	0.01231	-1.208000	0.02634	-0.448000	0.05591	ACG	C|0.999;T|0.001	0.001	strong		0.622	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431	
SLC43A2	124935	hgsc.bcm.edu	37	17	1494660	1494660	+	Silent	SNP	G	G	A	rs73976240	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:1494660G>A	ENST00000301335.5	-	8	922	c.834C>T	c.(832-834)tcC>tcT	p.S278S	SLC43A2_ENST00000412517.3_Silent_p.S141S|SLC43A2_ENST00000574274.1_5'UTR|SLC43A2_ENST00000571650.1_Silent_p.S278S|SLC43A2_ENST00000382147.4_Silent_p.S278S	NM_001284498.1|NM_001284499.1	NP_001271427.1|NP_001271428.1	Q8N370	LAT4_HUMAN	solute carrier family 43 (amino acid system L transporter), member 2	278					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-amino acid transmembrane transporter activity (GO:0015179)			endometrium(4)|large_intestine(4)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (25;0.0883)		CACTCCTCATGGAGCTGCCCA	0.622													G|||	129	0.0257588	0.0961	0.0029	5008	,	,		10550	0.0		0.0	False		,,,				2504	0.0				p.S278S		Atlas-SNP	.											.	SLC43A2	37	.	0			c.C834T						PASS	.	G		311,4095	167.3+/-198.3	13,285,1905	76.0	70.0	72.0		834	5.1	1.0	17	dbSNP_130	72	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	SLC43A2	NM_152346.1		13,288,6202	AA,AG,GG		0.0349,7.0586,2.4143		278/570	1494660	314,12692	2203	4300	6503	SO:0001819	synonymous_variant	124935	exon8			CCTCATGGAGCTG	BC027923	CCDS11006.1, CCDS67107.1, CCDS67108.1	17p13.3	2013-07-17	2013-07-17		ENSG00000167703	ENSG00000167703		"""Solute carriers"""	23087	protein-coding gene	gene with protein product		610791				23268354	Standard	NM_001284498		Approved	MGC34680	uc002fsv.3	Q8N370	OTTHUMG00000090345	ENST00000301335.5:c.834C>T	17.37:g.1494660G>A		74.0	0.0	0		83.0	48.0	0.578313	NM_152346	B7Z6X9|C9JNU8|D3DTH9|Q5CD75|Q6IPM1|Q8NBX1|Q8NC21|Q8WZ00	Silent	SNP	ENST00000301335.5	37	CCDS11006.1																																																																																			G|0.971;A|0.029	0.029	strong		0.622	SLC43A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206717.4	NM_152346	
APLNR	187	hgsc.bcm.edu	37	11	57003581	57003581	+	Missense_Mutation	SNP	C	C	T	rs7943508	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:57003581C>T	ENST00000606794.1	-	1	1094	c.898G>A	c.(898-900)Gtc>Atc	p.V300I		NM_005161.4	NP_005152.1	P35414	APJ_HUMAN	apelin receptor	300			V -> I (in dbSNP:rs7943508).		G-protein coupled receptor signaling pathway (GO:0007186)|gastrulation (GO:0007369)|heart development (GO:0007507)|regulation of body fluid levels (GO:0050878)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)	p.V300F(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						CAGCTGTTGACGTAGCTGATG	0.597													C|||	71	0.0141773	0.0492	0.0086	5008	,	,		22043	0.0		0.0	False		,,,				2504	0.0				p.V300I		Atlas-SNP	.											APLNR,caecum,carcinoma,0,2	APLNR	62	2	1	Substitution - Missense(1)	lung(1)	c.G898A						PASS	.	C	ILE/VAL	180,4222	112.5+/-150.6	4,172,2025	115.0	62.0	80.0		898	2.6	1.0	11	dbSNP_116	80	3,8589	1.2+/-3.3	0,3,4293	yes	missense	APLNR	NM_005161.4	29	4,175,6318	TT,TC,CC		0.0349,4.0891,1.4083	benign	300/381	57003581	183,12811	2201	4296	6497	SO:0001583	missense	187	exon1			TGTTGACGTAGCT	U03642	CCDS7950.1	11q12.1	2012-08-08	2008-05-12	2008-05-12	ENSG00000134817	ENSG00000134817			339	protein-coding gene	gene with protein product	"""APJ (apelin) receptor"""	600052	"""angiotensin II receptor-like 1"""	AGTRL1		8294032, 14622440	Standard	NM_005161		Approved	FLJ90771, APJ, APJR	uc001njo.3	P35414	OTTHUMG00000167021	ENST00000606794.1:c.898G>A	11.37:g.57003581C>T	ENSP00000475344:p.Val300Ile	124.0	0.0	0		152.0	86.0	0.565789	NM_005161		Missense_Mutation	SNP	ENST00000606794.1	37	CCDS7950.1	38	0.0173992673992674	36	0.07317073170731707	2	0.0055248618784530384	0	0.0	0	0.0	C	7.586	0.669656	0.14776	0.040891	3.49E-4	ENSG00000134817	ENST00000257254;ENST00000326830;ENST00000444275	T	0.37411	1.2	5.46	2.62	0.31277	GPCR, rhodopsin-like superfamily (1);	0.326514	0.28067	N	0.016724	T	0.01558	0.0050	L	0.31845	0.965	0.26372	N	0.976879	B	0.30824	0.296	B	0.23852	0.049	T	0.07654	-1.0761	10	0.20519	T	0.43	-43.2768	8.7044	0.34345	0.0:0.6322:0.0:0.3678	rs7943508;rs52819082;rs7943508	300	P35414	APJ_HUMAN	I	300;181;219	ENSP00000257254:V300I	ENSP00000257254:V300I	V	-	1	0	APLNR	56760157	0.163000	0.22920	1.000000	0.80357	0.982000	0.71751	-0.359000	0.07632	0.292000	0.22492	-0.751000	0.03497	GTC	C|0.986;T|0.014	0.014	strong		0.597	APLNR-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470575.1	NM_005161	
SLC4A8	9498	hgsc.bcm.edu	37	12	51855009	51855009	+	Silent	SNP	T	T	G	rs150970094	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:51855009T>G	ENST00000453097.2	+	9	1252	c.1035T>G	c.(1033-1035)ggT>ggG	p.G345G	SLC4A8_ENST00000514353.3_Silent_p.G292G|SLC4A8_ENST00000358657.3_Silent_p.G372G|SLC4A8_ENST00000535225.2_Silent_p.G292G|SLC4A8_ENST00000394856.1_Silent_p.G292G	NM_001039960.2|NM_001258401.2	NP_001035049.1|NP_001245330.1			solute carrier family 4, sodium bicarbonate cotransporter, member 8											NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(18)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(2)|urinary_tract(5)	55				BRCA - Breast invasive adenocarcinoma(357;0.15)		TCTTATTGGGTCCAGTAGGGA	0.398													T|||	18	0.00359425	0.0136	0.0	5008	,	,		18676	0.0		0.0	False		,,,				2504	0.0				p.G345G		Atlas-SNP	.											SLC4A8,back,malignant_melanoma,+2,1	SLC4A8	292	1	0			c.T1035G						PASS	.	T	,	38,4368	42.3+/-75.8	0,38,2165	155.0	142.0	147.0		1035,1035	-2.6	1.0	12	dbSNP_134	147	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SLC4A8	NM_001039960.1,NM_004858.2	,	0,38,6465	GG,GT,TT		0.0,0.8625,0.2922	,	345/1094,345/1045	51855009	38,12968	2203	4300	6503	SO:0001819	synonymous_variant	9498	exon9			ATTGGGTCCAGTA	AB018282	CCDS44890.1, CCDS58232.1, CCDS58233.1, CCDS73470.1	12q13.13	2013-05-22			ENSG00000050438	ENSG00000050438		"""Solute carriers"""	11034	protein-coding gene	gene with protein product		605024				11133997	Standard	NM_001039960		Approved	NBC3	uc001rys.2	Q2Y0W8	OTTHUMG00000169489	ENST00000453097.2:c.1035T>G	12.37:g.51855009T>G		151.0	0.0	0		164.0	78.0	0.47561	NM_001039960		Silent	SNP	ENST00000453097.2	37	CCDS44890.1																																																																																			T|0.997;G|0.003	0.003	strong		0.398	SLC4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404356.1	NM_004858	
DLG5	9231	hgsc.bcm.edu	37	10	79556301	79556301	+	Missense_Mutation	SNP	A	A	G	rs74140333	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:79556301A>G	ENST00000372391.2	-	28	5221	c.5216T>C	c.(5215-5217)cTg>cCg	p.L1739P	DLG5_ENST00000459739.1_5'UTR|DLG5_ENST00000372388.2_Missense_Mutation_p.L1399P	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	1739	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				apical protein localization (GO:0045176)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|intracellular signal transduction (GO:0035556)|metanephric collecting duct development (GO:0072205)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|polarized epithelial cell differentiation (GO:0030859)|protein complex assembly (GO:0006461)|protein localization to adherens junction (GO:0071896)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|zonula adherens assembly (GO:0045186)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cytoskeletal protein binding (GO:0008092)|receptor signaling complex scaffold activity (GO:0030159)			breast(9)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(17)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	60	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)			GACAGGCCTCAGAGCGGTGCA	0.602													A|||	68	0.0135783	0.0499	0.0014	5008	,	,		20065	0.0		0.001	False		,,,				2504	0.0				p.L1739P		Atlas-SNP	.											.	DLG5	154	.	0			c.T5216C						PASS	.	A	PRO/LEU	150,4256	104.3+/-142.8	2,146,2055	100.0	85.0	90.0		5216	3.6	1.0	10	dbSNP_130	90	2,8598	2.2+/-6.3	0,2,4298	yes	missense	DLG5	NM_004747.3	98	2,148,6353	GG,GA,AA		0.0233,3.4044,1.1687	benign	1739/1920	79556301	152,12854	2203	4300	6503	SO:0001583	missense	9231	exon28			GGCCTCAGAGCGG	U61843	CCDS7353.2	10q23	2008-07-09	2001-11-28		ENSG00000151208	ENSG00000151208			2904	protein-coding gene	gene with protein product		604090	"""discs, large (Drosophila) homolog 5"""			9738934	Standard	XM_005270276		Approved	P-dlg, KIAA0583	uc001jzk.3	Q8TDM6	OTTHUMG00000018548	ENST00000372391.2:c.5216T>C	10.37:g.79556301A>G	ENSP00000361467:p.Leu1739Pro	249.0	0.0	0		211.0	98.0	0.464455	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Missense_Mutation	SNP	ENST00000372391.2	37	CCDS7353.2	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	A	12.73	2.026468	0.35701	0.034044	2.33E-4	ENSG00000151208	ENST00000372391;ENST00000424842;ENST00000372388	T;T;T	0.20598	2.06;2.06;2.06	5.97	3.63	0.41609	Guanylate kinase/L-type calcium channel (1);	0.000000	0.31519	N	0.007516	T	0.00784	0.0026	N	0.00652	-1.29	0.58432	D	0.999999	B;B	0.10296	0.001;0.003	B;B	0.17433	0.002;0.018	T	0.31586	-0.9938	10	0.24483	T	0.36	.	4.6381	0.12534	0.5759:0.0:0.4241:0.0	.	1739;1399	Q8TDM6;Q8TDM6-2	DLG5_HUMAN;.	P	1739;700;1399	ENSP00000361467:L1739P;ENSP00000394797:L700P;ENSP00000361464:L1399P	ENSP00000361464:L1399P	L	-	2	0	DLG5	79226307	1.000000	0.71417	0.970000	0.41538	0.687000	0.40016	4.450000	0.60041	1.069000	0.40788	0.533000	0.62120	CTG	A|0.989;G|0.011	0.011	strong		0.602	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2		
SPECC1L	23384	hgsc.bcm.edu	37	22	24761502	24761502	+	Silent	SNP	G	G	A	rs139166286	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:24761502G>A	ENST00000314328.9	+	13	3171	c.2886G>A	c.(2884-2886)tcG>tcA	p.S962S	SPECC1L-ADORA2A_ENST00000358654.2_3'UTR|SPECC1L_ENST00000437398.1_Silent_p.S962S|SPECC1L_ENST00000541492.1_Silent_p.S962S	NM_001254733.1|NM_015330.3	NP_001241662.1|NP_056145	Q69YQ0	CYTSA_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1-like	962					actin cytoskeleton organization (GO:0030036)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell migration (GO:0016477)|negative regulation of actin filament depolymerization (GO:0030835)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|gap junction (GO:0005921)|microtubule organizing center (GO:0005815)				breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(6)|ovary(1)|prostate(1)|skin(3)|stomach(2)|urinary_tract(1)	27						AGGGAGCGTCGCCAGCCTCTC	0.502																																					p.S962S		Atlas-SNP	.											.	SPECC1L	85	.	0			c.G2886A						PASS	.	G	,	18,4388	25.3+/-52.1	0,18,2185	109.0	84.0	92.0		2886,2886	-11.1	0.0	22	dbSNP_134	92	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SPECC1L	NM_001145468.1,NM_015330.2	,	0,18,6485	AA,AG,GG		0.0,0.4085,0.1384	,	962/1118,962/1118	24761502	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	23384	exon12			AGCGTCGCCAGCC	AK025531	CCDS33619.1, CCDS58797.1	22q11.23	2012-12-20	2010-09-17	2010-09-17	ENSG00000100014	ENSG00000100014			29022	protein-coding gene	gene with protein product	"""cytokinesis and spindle organization A"", ""cytospin A"""	614140	"""SPECC1-like"""			9205841	Standard	NM_001254733		Approved	KIAA0376, CYTSA	uc002zzv.4	Q69YQ0	OTTHUMG00000171450	ENST00000314328.9:c.2886G>A	22.37:g.24761502G>A		67.0	0.0	0		72.0	36.0	0.5	NM_001145468	B7Z758|F5H1H6|O15081	Silent	SNP	ENST00000314328.9	37	CCDS33619.1																																																																																			A|0.002;G|0.998	0.002	strong		0.502	SPECC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319986.2	NM_015330	
CDC27	996	hgsc.bcm.edu	37	17	45214623	45214623	+	Missense_Mutation	SNP	G	G	A	rs75637741		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:45214623G>A	ENST00000066544.3	-	14	1901	c.1808C>T	c.(1807-1809)gCc>gTc	p.A603V	CDC27_ENST00000531206.1_Missense_Mutation_p.A609V|CDC27_ENST00000446365.2_Missense_Mutation_p.A542V|CDC27_ENST00000527547.1_Missense_Mutation_p.A602V	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	603					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)			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						TAGAGTATAGGCATAAGCGTA	0.383																																					p.A609V		Atlas-SNP	.											CDC27_ENST00000531206,rectum,carcinoma,0,2	CDC27	337	2	0			c.C1826T						scavenged	.																																			SO:0001583	missense	996	exon14			GTATAGGCATAAG	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.1808C>T	17.37:g.45214623G>A	ENSP00000066544:p.Ala603Val	25.0	0.0	0		36.0	8.0	0.222222	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	G	36	5.873394	0.97049	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	5.81	5.81	0.92471	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.74382	0.3709	M	0.93594	3.435	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.997;0.993;0.993;0.994	T	0.80863	-0.1192	10	0.87932	D	0	-9.797	17.5633	0.87913	0.0:0.0:1.0:0.0	.	542;602;609;603	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	V	603;609;542;602	ENSP00000066544:A603V;ENSP00000434614:A609V;ENSP00000392802:A542V;ENSP00000437339:A602V	ENSP00000066544:A603V	A	-	2	0	CDC27	42569622	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.869000	0.99810	2.761000	0.94854	0.585000	0.79938	GCC	.	.	weak		0.383	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
ATP6V1C1	528	hgsc.bcm.edu	37	8	104054603	104054603	+	Silent	SNP	T	T	C	rs7009365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:104054603T>C	ENST00000395862.3	+	3	327	c.168T>C	c.(166-168)gaT>gaC	p.D56D	ATP6V1C1_ENST00000518738.1_Silent_p.D56D|ATP6V1C1_ENST00000521514.1_5'UTR|ATP6V1C1_ENST00000518857.1_Intron	NM_001695.4	NP_001686.1	P21283	VATC1_HUMAN	ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C1	56					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)|proton transport (GO:0015992)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|proton-transporting two-sector ATPase complex (GO:0016469)|proton-transporting V-type ATPase, V1 domain (GO:0033180)	hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)|proton-transporting ATPase activity, rotational mechanism (GO:0046961)|transporter activity (GO:0005215)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(6)|urinary_tract(1)	13	Lung NSC(17;0.000427)|all_lung(17;0.000533)		OV - Ovarian serous cystadenocarcinoma(57;3.57e-05)|STAD - Stomach adenocarcinoma(118;0.133)			GCTTGTCAGATGAACTGGCTA	0.373													T|||	382	0.076278	0.2685	0.0375	5008	,	,		19747	0.0		0.0	False		,,,				2504	0.001				p.D56D		Atlas-SNP	.											.	ATP6V1C1	33	.	0			c.T168C						PASS	.	T		917,3489	353.1+/-312.0	113,691,1399	226.0	216.0	220.0		168	0.8	1.0	8	dbSNP_116	220	10,8590	4.3+/-15.6	1,8,4291	no	coding-synonymous	ATP6V1C1	NM_001695.4		114,699,5690	CC,CT,TT		0.1163,20.8125,7.1275		56/383	104054603	927,12079	2203	4300	6503	SO:0001819	synonymous_variant	528	exon3			GTCAGATGAACTG	X69151	CCDS6296.1	8p22.3	2011-05-24	2006-01-13	2002-05-10	ENSG00000155097	ENSG00000155097	3.6.3.14	"""ATPases / V-type"""	856	protein-coding gene	gene with protein product		603097	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump) 42kD"", ""ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C, isoform 1"""	ATP6D, ATP6C		8250920, 14580332	Standard	NM_001695		Approved	VATC, Vma5	uc003ykz.4	P21283	OTTHUMG00000164761	ENST00000395862.3:c.168T>C	8.37:g.104054603T>C		201.0	0.0	0		157.0	82.0	0.522293	NM_001695		Silent	SNP	ENST00000395862.3	37	CCDS6296.1																																																																																			T|0.922;C|0.078	0.078	strong		0.373	ATP6V1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380101.1	NM_001695	
PCDHB6	56130	hgsc.bcm.edu	37	5	140530534	140530534	+	Missense_Mutation	SNP	G	G	C	rs10076554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140530534G>C	ENST00000231136.1	+	1	696	c.696G>C	c.(694-696)ttG>ttC	p.L232F	PCDHB6_ENST00000543635.1_Missense_Mutation_p.L96F	NM_018939.2	NP_061762.1	Q9Y5E3	PCDB6_HUMAN	protocadherin beta 6	232	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.		L -> F (in dbSNP:rs10076554).		calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			cervix(1)|endometrium(14)|kidney(6)|large_intestine(16)|liver(1)|lung(33)|ovary(1)|pancreas(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	84			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TCCAGGTTTTGGACATCAATG	0.587													G|||	73	0.0145767	0.0537	0.0029	5008	,	,		17505	0.0		0.0	False		,,,				2504	0.0				p.L232F		Atlas-SNP	.											.	PCDHB6	161	.	0			c.G696C						PASS	.	G	PHE/LEU	193,4213	121.3+/-158.8	4,185,2014	44.0	48.0	47.0		696	0.6	0.5	5	dbSNP_119	47	0,8600		0,0,4300	yes	missense	PCDHB6	NM_018939.2	22	4,185,6314	CC,CG,GG		0.0,4.3804,1.4839	possibly-damaging	232/795	140530534	193,12813	2203	4300	6503	SO:0001583	missense	56130	exon1			GGTTTTGGACATC	AF152499	CCDS4248.1	5q31	2010-01-26			ENSG00000113211	ENSG00000113211		"""Cadherins / Protocadherins : Clustered"""	8691	other	protocadherin		606332				10380929	Standard	NM_018939		Approved	PCDH-BETA6	uc003lir.3	Q9Y5E3	OTTHUMG00000129623	ENST00000231136.1:c.696G>C	5.37:g.140530534G>C	ENSP00000231136:p.Leu232Phe	103.0	0.0	0		108.0	53.0	0.490741	NM_018939	B2R8R9	Missense_Mutation	SNP	ENST00000231136.1	37	CCDS4248.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	G	14.12	2.441466	0.43326	0.043804	0.0	ENSG00000113211	ENST00000543635;ENST00000231136;ENST00000542861	T;T	0.01804	4.63;4.63	4.85	0.653	0.17828	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.01320	0.0043	M	0.93106	3.38	0.26654	N	0.97205	D	0.57571	0.98	D	0.63381	0.914	T	0.08432	-1.0722	9	0.72032	D	0.01	.	3.9631	0.09420	0.3108:0.0:0.4427:0.2466	rs10076554;rs61376880;rs10076554	232	Q9Y5E3	PCDB6_HUMAN	F	96;232;17	ENSP00000438466:L96F;ENSP00000231136:L232F	ENSP00000231136:L232F	L	+	3	2	PCDHB6	140510718	0.118000	0.22208	0.455000	0.27031	0.888000	0.51559	-0.354000	0.07681	0.178000	0.19917	0.561000	0.74099	TTG	G|0.986;C|0.014	0.014	strong		0.587	PCDHB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251818.2	NM_018939	
DBNL	28988	hgsc.bcm.edu	37	7	44096482	44096482	+	Missense_Mutation	SNP	G	G	A	rs61735009	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:44096482G>A	ENST00000448521.1	+	5	552	c.454G>A	c.(454-456)Gtg>Atg	p.V152M	DBNL_ENST00000497184.1_3'UTR|DBNL_ENST00000468694.1_Missense_Mutation_p.V152M|DBNL_ENST00000494774.1_Missense_Mutation_p.V152M|DBNL_ENST00000456905.1_Intron|DBNL_ENST00000490734.2_Missense_Mutation_p.V57M|DBNL_ENST00000440166.1_Missense_Mutation_p.V49M|DBNL_ENST00000452943.1_Missense_Mutation_p.V127M	NM_001014436.2	NP_001014436.1	Q9UJU6	DBNL_HUMAN	drebrin-like	152					activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|endocytosis (GO:0006897)|immune system process (GO:0002376)|neuron projection morphogenesis (GO:0048812)|podosome assembly (GO:0071800)|Rac protein signal transduction (GO:0016601)|synapse assembly (GO:0007416)	cell cortex (GO:0005938)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|podosome (GO:0002102)|postsynaptic density (GO:0014069)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|enzyme activator activity (GO:0008047)	p.V152L(1)		breast(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|stomach(1)	12						CTTCCAGGACGTGGGACCCCA	0.617													G|||	73	0.0145767	0.0552	0.0	5008	,	,		19626	0.0		0.0	False		,,,				2504	0.0				p.V152M	NSCLC(68;573 1327 18604 34760 37992)	Atlas-SNP	.											.	DBNL	26	.	1	Substitution - Missense(1)	lung(1)	c.G454A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL	188,4218	120.8+/-158.4	4,180,2019	101.0	93.0	96.0		454,454,454	-6.3	0.0	7	dbSNP_129	96	0,8600		0,0,4300	yes	missense,missense,missense	DBNL	NM_001014436.2,NM_001122956.1,NM_014063.6	21,21,21	4,180,6319	AA,AG,GG		0.0,4.2669,1.4455	benign,benign,benign	152/431,152/440,152/432	44096482	188,12818	2203	4300	6503	SO:0001583	missense	28988	exon5			CAGGACGTGGGAC	AF151364	CCDS34622.1, CCDS34623.1, CCDS47579.1, CCDS64633.1, CCDS64634.1	7p13	2004-07-22			ENSG00000136279	ENSG00000136279			2696	protein-coding gene	gene with protein product		610106				10087302	Standard	NM_014063		Approved	SH3P7, HIP-55	uc003tjq.4	Q9UJU6	OTTHUMG00000155350	ENST00000448521.1:c.454G>A	7.37:g.44096482G>A	ENSP00000411701:p.Val152Met	66.0	0.0	0		104.0	45.0	0.432692	NM_001122956	A4D2I9|B4DEM2|C9J7P1|P84070|Q6IAI8|Q96F30|Q96K74|Q9HBN8|Q9NR72	Missense_Mutation	SNP	ENST00000448521.1	37	CCDS34623.1	23|23	0.010531135531135532|0.010531135531135532	23|23	0.046747967479674794|0.046747967479674794	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	6.385|6.385	0.439110|0.439110	0.12104|0.12104	0.042669|0.042669	0.0|0.0	ENSG00000136279|ENSG00000136279	ENST00000432854|ENST00000448521;ENST00000440166;ENST00000452943;ENST00000468694;ENST00000494774;ENST00000490734;ENST00000539475	.|T;T;T;T;T;T	.|0.30714	.|1.91;2.23;2.23;1.52;1.91;2.22	4.9|4.9	-6.34|-6.34	0.01982|0.01982	.|.	.|1.052620	.|0.07283	.|N	.|0.871083	T|T	0.02230|0.02230	0.0069|0.0069	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	.|B;B;B;B;B;B;B;B	.|0.25772	.|0.021;0.021;0.02;0.134;0.082;0.119;0.005;0.012	.|B;B;B;B;B;B;B;B	.|0.15052	.|0.005;0.003;0.005;0.012;0.003;0.008;0.001;0.004	T|T	0.25502|0.25502	-1.0130|-1.0130	5|10	.|0.41790	.|T	.|0.15	0.0525|0.0525	8.2112|8.2112	0.31483|0.31483	0.2474:0.0:0.6024:0.1502|0.2474:0.0:0.6024:0.1502	rs61735009|rs61735009	.|49;100;82;57;127;152;152;152	.|B4DEM2;B4DXL9;B4DDU5;C9J7P1;B4DDD6;Q9UJU6-3;Q9UJU6;Q9UJU6-2	.|.;.;.;.;.;.;DBNL_HUMAN;.	H|M	80|152;49;127;152;152;57;82	.|ENSP00000411701:V152M;ENSP00000415173:V49M;ENSP00000405343:V127M;ENSP00000417653:V152M;ENSP00000419992:V152M;ENSP00000417749:V57M	.|ENSP00000415173:V49M	R|V	+|+	2|1	0|0	DBNL|DBNL	44063007|44063007	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.088000|0.088000	0.18126|0.18126	-0.206000|-0.206000	0.09398|0.09398	-0.667000|-0.667000	0.05303|0.05303	-0.696000|-0.696000	0.03686|0.03686	CGT|GTG	A|0.013;C|0.000;G|0.987	0.013	strong		0.617	DBNL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339572.2	NM_014063	
FREM2	341640	hgsc.bcm.edu	37	13	39263422	39263422	+	Silent	SNP	C	C	T	rs41292751	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:39263422C>T	ENST00000280481.7	+	1	2157	c.1941C>T	c.(1939-1941)gaC>gaT	p.D647D		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	647					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		AGCAGCAGGACATAACAGAGG	0.532													C|||	61	0.0121805	0.0008	0.0216	5008	,	,		17077	0.0		0.0378	False		,,,				2504	0.0072				p.D647D		Atlas-SNP	.											.	FREM2	385	.	0			c.C1941T						PASS	.	C		43,4363	45.3+/-79.5	0,43,2160	72.0	66.0	68.0		1941	5.1	1.0	13	dbSNP_127	68	324,8276	114.8+/-174.7	5,314,3981	no	coding-synonymous	FREM2	NM_207361.4		5,357,6141	TT,TC,CC		3.7674,0.9759,2.8218		647/3170	39263422	367,12639	2203	4300	6503	SO:0001819	synonymous_variant	341640	exon1			GCAGGACATAACA	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.1941C>T	13.37:g.39263422C>T		92.0	0.0	0		95.0	49.0	0.515789	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	37	CCDS31960.1																																																																																			C|0.973;T|0.027	0.027	strong		0.532	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
VWCE	220001	hgsc.bcm.edu	37	11	61048322	61048322	+	Silent	SNP	G	G	C	rs61744427	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61048322G>C	ENST00000335613.5	-	8	1559	c.1173C>G	c.(1171-1173)gcC>gcG	p.A391A		NM_152718.2	NP_689931.2	Q96DN2	VWCE_HUMAN	von Willebrand factor C and EGF domains	391	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						ATTCATGCATGGCTCCCAGGT	0.662													G|||	142	0.0283546	0.0613	0.0058	5008	,	,		17203	0.0268		0.001	False		,,,				2504	0.0297				p.A391A		Atlas-SNP	.											.	VWCE	84	.	0			c.C1173G						PASS	.	G		240,4164		3,234,1965	12.0	14.0	13.0		1173	1.2	0.5	11	dbSNP_129	13	3,8587		0,3,4292	no	coding-synonymous	VWCE	NM_152718.2		3,237,6257	CC,CG,GG		0.0349,5.4496,1.8701		391/956	61048322	243,12751	2202	4295	6497	SO:0001819	synonymous_variant	220001	exon8			ATGCATGGCTCCC	AK056571	CCDS8002.1	11q12.2	2006-08-04			ENSG00000167992	ENSG00000167992			26487	protein-coding gene	gene with protein product		611115				12869306	Standard	NM_152718		Approved	URG11, FLJ32009, VWC1	uc001nra.3	Q96DN2	OTTHUMG00000168208	ENST00000335613.5:c.1173C>G	11.37:g.61048322G>C		51.0	0.0	0		67.0	36.0	0.537313	NM_152718	A5PKV0|Q7Z7L6|Q86WK8	Silent	SNP	ENST00000335613.5	37	CCDS8002.1																																																																																			G|0.971;C|0.029	0.029	strong		0.662	VWCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398811.1	NM_152718	
MFAP3L	9848	hgsc.bcm.edu	37	4	170912685	170912685	+	Silent	SNP	T	T	C	rs61740817	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:170912685T>C	ENST00000361618.3	-	3	1381	c.1074A>G	c.(1072-1074)gaA>gaG	p.E358E	RP11-6E9.4_ENST00000508955.1_RNA|MFAP3L_ENST00000393704.3_Silent_p.E255E	NM_021647.6	NP_067679.6	O75121	MFA3L_HUMAN	microfibrillar-associated protein 3-like	358						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		Prostate(90;0.00601)|Renal(120;0.0183)|all_neural(102;0.122)|Melanoma(52;0.17)		GBM - Glioblastoma multiforme(119;0.0201)|LUSC - Lung squamous cell carcinoma(193;0.116)		CGGTAGAAGGTTCTGCAGTTT	0.512													.|||	324	0.0646965	0.239	0.0101	5008	,	,		19333	0.0		0.001	False		,,,				2504	0.0				p.E358E		Atlas-SNP	.											MFAP3L,NS,carcinoma,-2,1	MFAP3L	59	1	0			c.A1074G						PASS	.	C	,	788,3618	751.8+/-412.2	79,630,1494	191.0	160.0	170.0		765,1074	2.5	1.0	4	dbSNP_129	170	8,8592	818.9+/-406.8	0,8,4292	no	coding-synonymous,coding-synonymous	MFAP3L	NM_001009554.2,NM_021647.6	,	79,638,5786	CC,CT,TT		0.093,17.8847,6.1203	,	255/307,358/410	170912685	796,12210	2203	4300	6503	SO:0001819	synonymous_variant	9848	exon3			AGAAGGTTCTGCA	AB014526	CCDS34103.1, CCDS43281.1	4q33	2014-08-12			ENSG00000198948	ENSG00000198948		"""Immunoglobulin superfamily / I-set domain containing"""	29083	protein-coding gene	gene with protein product						9734811	Standard	XM_005263366		Approved	KIAA0626, NYD-sp9	uc003isp.4	O75121	OTTHUMG00000160942	ENST00000361618.3:c.1074A>G	4.37:g.170912685T>C		168.0	0.0	0		213.0	105.0	0.492958	NM_021647	A8K1X6|D3DP35|Q4W5N7|Q4W5N9|Q6TNA8|Q9BVE1|Q9BXK0	Silent	SNP	ENST00000361618.3	37	CCDS34103.1																																																																																			T|0.933;C|0.067	0.067	strong		0.512	MFAP3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363043.2	NM_021647	
RAI14	26064	hgsc.bcm.edu	37	5	34814745	34814745	+	Missense_Mutation	SNP	T	T	C	rs150350937		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:34814745T>C	ENST00000265109.3	+	12	1197	c.910T>C	c.(910-912)Tcg>Ccg	p.S304P	RAI14_ENST00000512629.1_Missense_Mutation_p.S275P|RAI14_ENST00000503673.1_Missense_Mutation_p.S304P|RAI14_ENST00000397449.1_Missense_Mutation_p.S297P|RAI14_ENST00000515799.1_Missense_Mutation_p.S307P|RAI14_ENST00000506376.1_Missense_Mutation_p.S296P|RAI14_ENST00000428746.2_Missense_Mutation_p.S304P	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14	304						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					GGGAAAGGAATCGGTATTTTT	0.318																																					p.S307P		Atlas-SNP	.											RAI14,scalp,malignant_melanoma,-1,1	RAI14	100	1	0			c.T919C						PASS	.	T	PRO/SER,PRO/SER,PRO/SER,PRO/SER,PRO/SER,PRO/SER	8,4398	12.9+/-30.5	0,8,2195	174.0	155.0	162.0		910,910,823,886,919,910	3.4	1.0	5	dbSNP_134	162	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense	RAI14	NM_001145520.1,NM_001145521.1,NM_001145522.1,NM_001145523.1,NM_001145525.1,NM_015577.2	74,74,74,74,74,74	0,8,6495	CC,CT,TT		0.0,0.1816,0.0615	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	304/981,304/981,275/952,296/973,307/984,304/981	34814745	8,12998	2203	4300	6503	SO:0001583	missense	26064	exon14			AAGGAATCGGTAT	AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560		"""Ankyrin repeat domain containing"""	14873	protein-coding gene	gene with protein product	"""novel retinal pigment epithelial"""	606586				11042181	Standard	NM_015577		Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.910T>C	5.37:g.34814745T>C	ENSP00000265109:p.Ser304Pro	318.0	0.0	0		291.0	150.0	0.515464	NM_001145525	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Missense_Mutation	SNP	ENST00000265109.3	37	CCDS34142.1	.	.	.	.	.	.	.	.	.	.	T	12.81	2.050617	0.36181	0.001816	0.0	ENSG00000039560	ENST00000265109;ENST00000512629;ENST00000428746;ENST00000503673;ENST00000515799;ENST00000506376;ENST00000397449	T;T;T;T;T;T;T	0.38077	1.21;1.16;1.21;1.21;1.22;1.26;1.25	5.86	3.44	0.39384	.	.	.	.	.	T	0.20007	0.0481	N	0.14661	0.345	0.27353	N	0.956195	B;B;B;B	0.09022	0.001;0.001;0.002;0.001	B;B;B;B	0.09377	0.004;0.001;0.004;0.001	T	0.14309	-1.0477	9	0.31617	T	0.26	-4.3706	6.5518	0.22438	0.0:0.3208:0.0:0.6792	.	296;275;307;304	Q9P0K7-3;E9PED3;Q9P0K7-2;Q9P0K7	.;.;.;RAI14_HUMAN	P	304;275;304;304;307;296;297	ENSP00000265109:S304P;ENSP00000422377:S275P;ENSP00000388725:S304P;ENSP00000422942:S304P;ENSP00000427123:S307P;ENSP00000423854:S296P;ENSP00000380591:S297P	ENSP00000265109:S304P	S	+	1	0	RAI14	34850502	0.963000	0.33076	0.987000	0.45799	0.933000	0.57130	0.571000	0.23669	1.139000	0.42245	0.528000	0.53228	TCG	T|1.000;C|0.000	0.000	weak		0.318	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577	
ZNF808	388558	hgsc.bcm.edu	37	19	53057031	53057031	+	Missense_Mutation	SNP	A	A	G	rs116132766	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53057031A>G	ENST00000359798.4	+	5	1042	c.862A>G	c.(862-864)Aag>Gag	p.K288E		NM_001039886.3	NP_001034975.2	Q8N4W9	ZN808_HUMAN	zinc finger protein 808	288					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(8)|kidney(3)|lung(12)|urinary_tract(1)	24				OV - Ovarian serous cystadenocarcinoma(262;0.00501)|GBM - Glioblastoma multiforme(134;0.0213)		GAAACCTTACAAGTGTAAAGA	0.398													A|||	13	0.00259585	0.0083	0.0029	5008	,	,		22244	0.0		0.0	False		,,,				2504	0.0				p.K288E		Atlas-SNP	.											.	ZNF808	81	.	0			c.A862G						PASS	.	A	GLU/LYS	56,4350		0,56,2147	147.0	148.0	148.0		862	-1.1	0.0	19	dbSNP_132	148	1,8599		0,1,4299	no	missense	ZNF808	NM_001039886.3	56	0,57,6446	GG,GA,AA		0.0116,1.271,0.4383	possibly-damaging	288/904	53057031	57,12949	2203	4300	6503	SO:0001583	missense	388558	exon5			CCTTACAAGTGTA	CR749856	CCDS46167.1	19q13.41	2013-01-08			ENSG00000198482	ENSG00000198482		"""Zinc fingers, C2H2-type"", ""-"""	33230	protein-coding gene	gene with protein product							Standard	NM_001039886		Approved		uc010epq.1	Q8N4W9	OTTHUMG00000158230	ENST00000359798.4:c.862A>G	19.37:g.53057031A>G	ENSP00000352846:p.Lys288Glu	162.0	0.0	0		151.0	53.0	0.350993	NM_001039886	Q68CN7	Missense_Mutation	SNP	ENST00000359798.4	37	CCDS46167.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	.	0.202	-1.043775	0.01997	0.01271	1.16E-4	ENSG00000198482	ENST00000359798	T	0.16196	2.36	1.38	-1.15	0.09709	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09730	0.0239	L	0.49350	1.555	0.09310	N	1	P	0.42941	0.794	B	0.43754	0.43	T	0.20974	-1.0259	9	0.13470	T	0.59	.	3.8277	0.08861	0.6228:0.2188:0.1583:0.0	.	288	Q8N4W9	ZN808_HUMAN	E	288	ENSP00000352846:K288E	ENSP00000352846:K288E	K	+	1	0	ZNF808	57748843	0.000000	0.05858	0.009000	0.14445	0.029000	0.11900	-1.383000	0.02544	-0.207000	0.10187	-1.020000	0.02445	AAG	A|0.996;G|0.004	0.004	strong		0.398	ZNF808-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350447.3	NM_001039886	
FBXO34	55030	hgsc.bcm.edu	37	14	55818514	55818514	+	Missense_Mutation	SNP	C	C	T	rs59719421	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:55818514C>T	ENST00000313833.4	+	2	1651	c.1406C>T	c.(1405-1407)tCc>tTc	p.S469F	FBXO34_ENST00000440021.1_Missense_Mutation_p.S469F	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	469										breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						GACCAGCCTTCCATTTTAAAC	0.433													C|||	74	0.0147764	0.053	0.0058	5008	,	,		20569	0.0		0.0	False		,,,				2504	0.0				p.S469F		Atlas-SNP	.											.	FBXO34	61	.	0			c.C1406T						PASS	.	C	PHE/SER,PHE/SER	247,4159	143.1+/-178.2	7,233,1963	117.0	113.0	114.0		1406,1406	4.6	0.0	14	dbSNP_129	114	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	FBXO34	NM_017943.3,NM_152231.1	155,155	7,236,6260	TT,TC,CC		0.0349,5.606,1.9222	possibly-damaging,possibly-damaging	469/712,469/712	55818514	250,12756	2203	4300	6503	SO:0001583	missense	55030	exon2			AGCCTTCCATTTT	AK000732	CCDS32086.1	14q22.1	2004-08-24	2004-06-15			ENSG00000178974		"""F-boxes /  ""other"""""	20201	protein-coding gene	gene with protein product		609104	"""F-box only protein 34"""				Standard	NM_017943		Approved	FLJ20725, Fbx34	uc010aoo.3	Q9NWN3		ENST00000313833.4:c.1406C>T	14.37:g.55818514C>T	ENSP00000313159:p.Ser469Phe	200.0	0.0	0		223.0	97.0	0.434978	NM_017943	Q2VPB5|Q4VBP5|Q86TY4	Missense_Mutation	SNP	ENST00000313833.4	37	CCDS32086.1	30	0.013736263736263736	28	0.056910569105691054	2	0.0055248618784530384	0	0.0	0	0.0	C	9.052	0.992345	0.18966	0.05606	3.49E-4	ENSG00000178974	ENST00000313833;ENST00000440021	T;T	0.19938	2.11;2.11	5.48	4.6	0.57074	.	0.393578	0.20036	N	0.100616	T	0.04003	0.0112	L	0.51422	1.61	0.09310	N	1	D	0.53462	0.96	P	0.55965	0.788	T	0.01130	-1.1442	10	0.62326	D	0.03	-11.2954	9.7892	0.40695	0.0:0.7856:0.1416:0.0728	rs59719421	469	Q9NWN3	FBX34_HUMAN	F	469	ENSP00000313159:S469F;ENSP00000394117:S469F	ENSP00000313159:S469F	S	+	2	0	FBXO34	54888267	0.215000	0.23574	0.006000	0.13384	0.072000	0.16883	1.083000	0.30815	1.573000	0.49748	-0.127000	0.14921	TCC	C|0.979;T|0.021	0.021	strong		0.433	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1		
DHX36	170506	hgsc.bcm.edu	37	3	154002774	154002774	+	Silent	SNP	G	G	A	rs114098462	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:154002774G>A	ENST00000496811.1	-	18	2114	c.2034C>T	c.(2032-2034)aaC>aaT	p.N678N	DHX36_ENST00000308361.6_Silent_p.N678N|DHX36_ENST00000329463.5_Silent_p.N664N|DHX36_ENST00000544526.1_Silent_p.N664N	NM_020865.2	NP_065916.2	Q9H2U1	DHX36_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 36	678					ATP catabolic process (GO:0006200)|innate immune response (GO:0045087)|ossification (GO:0001503)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|transcription, DNA-templated (GO:0006351)	chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|core promoter binding (GO:0001047)|DNA-dependent ATPase activity (GO:0008094)|double-stranded RNA binding (GO:0003725)|G-quadruplex DNA binding (GO:0051880)|G-quadruplex RNA binding (GO:0002151)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|transcription regulatory region DNA binding (GO:0044212)			endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(11)|prostate(2)|skin(1)|urinary_tract(1)	35			LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.173)			TATCCAAAGCGTTCTGTAAAG	0.373													G|||	46	0.0091853	0.0325	0.0029	5008	,	,		19458	0.0		0.001	False		,,,				2504	0.0				p.N678N		Atlas-SNP	.											.	DHX36	98	.	0			c.C2034T						PASS	.	G	,	114,4292	87.8+/-126.4	1,112,2090	102.0	101.0	101.0		1992,2034	-4.6	0.8	3	dbSNP_132	101	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	DHX36	NM_001114397.1,NM_020865.2	,	1,112,6390	AA,AG,GG		0.0,2.5874,0.8765	,	664/995,678/1009	154002774	114,12892	2203	4300	6503	SO:0001819	synonymous_variant	170506	exon18			CAAAGCGTTCTGT	AF217190	CCDS3171.1, CCDS54657.1	3q25.2	2012-09-20	2003-06-13	2003-06-20	ENSG00000174953	ENSG00000174953		"""DEAH-boxes"""	14410	protein-coding gene	gene with protein product		612767	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 36"""	DDX36			Standard	NM_020865		Approved	MLEL1, KIAA1488	uc003ezy.4	Q9H2U1	OTTHUMG00000159109	ENST00000496811.1:c.2034C>T	3.37:g.154002774G>A		155.0	0.0	0		172.0	75.0	0.436047	NM_020865	B2RB00|Q70JU3|Q8IYE5|Q9P240	Silent	SNP	ENST00000496811.1	37	CCDS3171.1	15	0.006868131868131868	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	0	0.0	G	9.279	1.047589	0.19827	0.025874	0.0	ENSG00000174953	ENST00000469977	.	.	.	5.6	-4.64	0.03349	.	.	.	.	.	T	0.41096	0.1144	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61113	-0.7128	4	.	.	.	.	15.9172	0.79531	0.4712:0.0:0.5288:0.0	.	.	.	.	M	125	.	.	T	-	2	0	DHX36	155485468	0.990000	0.36364	0.828000	0.32881	0.775000	0.43874	0.509000	0.22707	-1.147000	0.02851	-0.880000	0.02959	ACG	G|0.992;A|0.008	0.008	strong		0.373	DHX36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353349.1	NM_020865	
TRIOBP	11078	hgsc.bcm.edu	37	22	38129311	38129311	+	Silent	SNP	C	C	T	rs200990219	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:38129311C>T	ENST00000406386.3	+	8	4209	c.3954C>T	c.(3952-3954)tcC>tcT	p.S1318S		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	1318					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					ATAGGAAGTCCGAGGCAGCGG	0.652													C|||	10	0.00199681	0.0076	0.0	5008	,	,		15854	0.0		0.0	False		,,,				2504	0.0				p.S1318S		Atlas-SNP	.											.	TRIOBP	262	.	0			c.C3954T						PASS	.	C		12,3732		0,12,1860	8.0	14.0	12.0		3954	-1.1	1.0	22		12	0,7806		0,0,3903	no	coding-synonymous	TRIOBP	NM_001039141.2		0,12,5763	TT,TC,CC		0.0,0.3205,0.1039		1318/2366	38129311	12,11538	1872	3903	5775	SO:0001819	synonymous_variant	11078	exon8			GAAGTCCGAGGCA	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.3954C>T	22.37:g.38129311C>T		171.0	0.0	0		170.0	80.0	0.470588	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Silent	SNP	ENST00000406386.3	37	CCDS43015.1																																																																																			C|0.998;T|0.002	0.002	strong		0.652	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
PRIMA1	145270	hgsc.bcm.edu	37	14	94187816	94187816	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:94187816C>G	ENST00000393140.1	-	5	538	c.436G>C	c.(436-438)Gta>Cta	p.V146L	PRIMA1_ENST00000316227.3_3'UTR|PRIMA1_ENST00000393143.1_Missense_Mutation_p.V146L	NM_178013.3	NP_821092.1	Q86XR5	PRIMA_HUMAN	proline rich membrane anchor 1	146					establishment of localization in cell (GO:0051649)|neurotransmitter catabolic process (GO:0042135)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|synapse (GO:0045202)				endometrium(1)|large_intestine(2)|lung(3)|skin(1)	7		all_cancers(154;0.127)		Epithelial(152;0.138)|COAD - Colon adenocarcinoma(157;0.229)		TTCACGTCTACTCCTTTGTTG	0.577																																					p.V146L		Atlas-SNP	.											.	PRIMA1	21	.	0			c.G436C						PASS	.						142.0	101.0	115.0					14																	94187816		2203	4300	6503	SO:0001583	missense	145270	exon5			CGTCTACTCCTTT		CCDS9912.1	14q32.13	2008-08-29			ENSG00000175785	ENSG00000175785			18319	protein-coding gene	gene with protein product	"""membrane anchor of acetylcholinesterase"""	613851				11804574	Standard	NM_178013		Approved	PRIMA	uc001ybw.1	Q86XR5	OTTHUMG00000141313	ENST00000393140.1:c.436G>C	14.37:g.94187816C>G	ENSP00000376848:p.Val146Leu	65.0	0.0	0		69.0	29.0	0.42029	NM_178013	Q86XR6	Missense_Mutation	SNP	ENST00000393140.1	37	CCDS9912.1	.	.	.	.	.	.	.	.	.	.	C	15.38	2.815771	0.50527	.	.	ENSG00000175785	ENST00000393140;ENST00000393143	.	.	.	4.65	3.72	0.42706	.	0.948209	0.08632	N	0.916915	T	0.45736	0.1357	L	0.27053	0.805	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.36407	-0.9749	9	0.49607	T	0.09	-3.289	10.1546	0.42814	0.1979:0.8021:0.0:0.0	.	146	Q86XR5	PRIMA_HUMAN	L	146	.	ENSP00000376848:V146L	V	-	1	0	PRIMA1	93257569	1.000000	0.71417	0.998000	0.56505	0.070000	0.16714	2.628000	0.46477	2.135000	0.66039	0.591000	0.81541	GTA	.	.	none		0.577	PRIMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280658.1	NM_178013	
CCDC183	84960	hgsc.bcm.edu	37	9	139698977	139698977	+	Silent	SNP	G	G	A	rs11145892	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139698977G>A	ENST00000338005.6	+	7	725	c.690G>A	c.(688-690)gcG>gcA	p.A230A	KIAA1984_ENST00000371682.3_3'UTR|RP11-216L13.19_ENST00000415992.1_RNA|KIAA1984-AS1_ENST00000414656.1_RNA|RP11-216L13.18_ENST00000471502.1_RNA	NM_001039374.4	NP_001034463.4	Q5T5S1	CC183_HUMAN		230										biliary_tract(1)|breast(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	13	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.33e-06)|Epithelial(140;0.000124)		AAAGGGAGGCGTCCTTCATCG	0.612													G|||	64	0.0127796	0.0424	0.0058	5008	,	,		18627	0.0		0.002	False		,,,				2504	0.002				p.A230A		Atlas-SNP	.											.	KIAA1984	39	.	0			c.G690A						PASS	.	G		120,3832		1,118,1857	39.0	44.0	42.0		690	-5.7	0.4	9	dbSNP_120	42	37,8243		0,37,4103	no	coding-synonymous	KIAA1984	NM_001039374.4		1,155,5960	AA,AG,GG		0.4469,3.0364,1.2835		230/535	139698977	157,12075	1976	4140	6116	SO:0001819	synonymous_variant	84960	exon7			GGAGGCGTCCTTC																												ENST00000338005.6:c.690G>A	9.37:g.139698977G>A		31.0	0.0	0		40.0	27.0	0.675	NM_001039374	B2RP89|C9JD38|Q6P2D9|Q8NAI4|Q8TF18	Silent	SNP	ENST00000338005.6	37	CCDS43906.1																																																																																			G|0.993;A|0.007	0.007	strong		0.612	KIAA1984-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354899.1		
CSF1R	1436	hgsc.bcm.edu	37	5	149460544	149460544	+	Silent	SNP	G	G	A	rs41424646		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149460544G>A	ENST00000286301.3	-	3	384	c.93C>T	c.(91-93)gtC>gtT	p.V31V	CSF1R_ENST00000543093.1_Silent_p.V31V	NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor	31	Ig-like C2-type 1.				cell proliferation (GO:0008283)|cell-cell junction maintenance (GO:0045217)|cellular response to cytokine stimulus (GO:0071345)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cytokine-mediated signaling pathway (GO:0019221)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary gland duct morphogenesis (GO:0060603)|monocyte differentiation (GO:0030224)|multicellular organismal development (GO:0007275)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of bone resorption (GO:0045124)|regulation of cell shape (GO:0008360)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|macrophage colony-stimulating factor receptor activity (GO:0005011)|protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(38)|kidney(2)|large_intestine(6)|liver(3)|lung(23)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	93			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	CTGGCTTCACGACCAGCTCAG	0.607																																					p.V31V		Atlas-SNP	.											CSF1R_ENST00000286301,caecum,carcinoma,-1,2	CSF1R	250	2	0			c.C93T						scavenged	.	G		6,4400	11.4+/-27.6	0,6,2197	98.0	69.0	78.0		93	-11.5	0.1	5	dbSNP_127	78	0,8600		0,0,4300	no	coding-synonymous	CSF1R	NM_005211.3		0,6,6497	AA,AG,GG		0.0,0.1362,0.0461		31/973	149460544	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	1436	exon3			CTTCACGACCAGC	U63963	CCDS4302.1	5q32	2013-01-11	2008-08-01		ENSG00000182578	ENSG00000182578		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	2433	protein-coding gene	gene with protein product		164770	"""McDonough feline sarcoma viral (v-fms) oncogene homolog"""	FMS		1611909	Standard	NM_005211		Approved	C-FMS, CSFR, CD115	uc003lrm.3	P07333	OTTHUMG00000130050	ENST00000286301.3:c.93C>T	5.37:g.149460544G>A		136.0	1.0	0.00735294		186.0	94.0	0.505376	NM_005211	B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	Silent	SNP	ENST00000286301.3	37	CCDS4302.1																																																																																			T|0.000;G|0.999;A|0.001	0.001	strong		0.607	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2	NM_005211	
ZNF765	91661	hgsc.bcm.edu	37	19	53901281	53901281	+	Missense_Mutation	SNP	C	C	G	rs141876832	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53901281C>G	ENST00000396408.3	+	2	130	c.13C>G	c.(13-15)Cag>Gag	p.Q5E	ZNF765_ENST00000594030.1_Missense_Mutation_p.Q5E	NM_001040185.1	NP_001035275.1	Q7L2R6	ZN765_HUMAN	zinc finger protein 765	5					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|lung(3)	4				GBM - Glioblastoma multiforme(134;0.00379)		GGCTCTTCCTCAGGTGAGATG	0.433													.|||	88	0.0175719	0.0651	0.0029	5008	,	,		21689	0.0		0.0	False		,,,				2504	0.0				p.Q5E		Atlas-SNP	.											ZNF765_ENST00000396408,NS,carcinoma,-2,1	ZNF765	61	1	0			c.C13G						PASS	.	C	GLU/GLN	237,4169	139.2+/-174.8	4,229,1970	183.0	155.0	164.0		13	0.9	0.0	19	dbSNP_134	164	2,8598	2.2+/-6.3	0,2,4298	no	missense	ZNF765	NM_001040185.1	29	4,231,6268	GG,GC,CC		0.0233,5.379,1.8376	benign	5/524	53901281	239,12767	2203	4300	6503	SO:0001583	missense	91661	exon2			CTTCCTCAGGTGA	BC017357	CCDS46171.1	19q13.41	2013-01-08				ENSG00000196417		"""Zinc fingers, C2H2-type"", ""-"""	25092	protein-coding gene	gene with protein product						12477932	Standard	XR_430215		Approved		uc002qbm.3	Q7L2R6		ENST00000396408.3:c.13C>G	19.37:g.53901281C>G	ENSP00000379689:p.Gln5Glu	68.0	0.0	0		79.0	37.0	0.468354	NM_001040185	A8MYG0|B4DF18|B7ZAI5|B9EIL1|Q9BV49	Missense_Mutation	SNP	ENST00000396408.3	37	CCDS46171.1	83	0.038003663003663	44	0.08943089430894309	11	0.03038674033149171	14	0.024475524475524476	14	0.018469656992084433	C	2.310	-0.358135	0.05138	0.05379	2.33E-4	ENSG00000196417	ENST00000396408	T	0.00940	5.52	0.924	0.924	0.19418	Krueppel-associated box (1);	.	.	.	.	T	0.00073	0.0002	M	0.72894	2.215	0.09310	N	1	D	0.54772	0.968	P	0.44732	0.459	T	0.53078	-0.8489	9	0.66056	D	0.02	.	5.23	0.15416	0.0:1.0:0.0:0.0	.	5	Q7L2R6	ZN765_HUMAN	E	5	ENSP00000379689:Q5E	ENSP00000379689:Q5E	Q	+	1	0	ZNF765	58593093	0.446000	0.25665	0.033000	0.17914	0.161000	0.22273	0.533000	0.23082	0.829000	0.34733	0.194000	0.17425	CAG	C|0.962;G|0.038	0.038	strong		0.433	ZNF765-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371603.1	NM_138372	
NEUROG1	4762	hgsc.bcm.edu	37	5	134871280	134871280	+	Missense_Mutation	SNP	C	C	T	rs34137563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:134871280C>T	ENST00000314744.4	-	1	359	c.101G>A	c.(100-102)aGa>aAa	p.R34K		NM_006161.2	NP_006152.2	Q92886	NGN1_HUMAN	neurogenin 1	34					cell fate commitment (GO:0045165)|inner ear morphogenesis (GO:0042472)|nervous system development (GO:0007399)|neuron differentiation (GO:0030182)|positive regulation of exit from mitosis (GO:0031536)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|perikaryon (GO:0043204)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|E-box binding (GO:0070888)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding transcription factor activity (GO:0000989)			endometrium(1)|liver(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CTGTTGGAGTCTGGCACAGTC	0.692													C|||	30	0.00599042	0.0212	0.0029	5008	,	,		13642	0.0		0.0	False		,,,				2504	0.0				p.R34K		Atlas-SNP	.											.	NEUROG1	18	.	0			c.G101A						PASS	.	C	LYS/ARG	63,4167		2,59,2054	13.0	12.0	12.0		101	3.8	1.0	5	dbSNP_126	12	0,8264		0,0,4132	yes	missense	NEUROG1	NM_006161.2	26	2,59,6186	TT,TC,CC		0.0,1.4894,0.5042	possibly-damaging	34/238	134871280	63,12431	2115	4132	6247	SO:0001583	missense	4762	exon1			TGGAGTCTGGCAC	U63842	CCDS4187.1	5q23-q31	2013-05-21			ENSG00000181965	ENSG00000181965		"""Basic helix-loop-helix proteins"""	7764	protein-coding gene	gene with protein product	"""neurogenic differentiation 3"""	601726		NEUROD3		9119405	Standard	NM_006161		Approved	AKA, Math4C, ngn1, bHLHa6	uc003lax.3	Q92886	OTTHUMG00000129138	ENST00000314744.4:c.101G>A	5.37:g.134871280C>T	ENSP00000317580:p.Arg34Lys	23.0	0.0	0		30.0	13.0	0.433333	NM_006161	Q5U0Q9|Q96HE1	Missense_Mutation	SNP	ENST00000314744.4	37	CCDS4187.1	19	0.0086996336996337	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	C	12.13	1.847045	0.32606	0.014894	0.0	ENSG00000181965	ENST00000314744	D	0.95103	-3.61	4.7	3.83	0.44106	.	0.656928	0.13766	N	0.364252	T	0.74489	0.3723	N	0.24115	0.695	0.26416	N	0.976176	P	0.37864	0.61	B	0.37989	0.262	T	0.72606	-0.4242	10	0.06099	T	0.92	-0.0177	10.6463	0.45621	0.0:0.904:0.0:0.096	rs34137563	34	Q92886	NGN1_HUMAN	K	34	ENSP00000317580:R34K	ENSP00000317580:R34K	R	-	2	0	NEUROG1	134899179	1.000000	0.71417	0.958000	0.39756	0.312000	0.27988	2.898000	0.48672	0.977000	0.38444	-0.258000	0.10820	AGA	C|0.993;T|0.007	0.007	strong		0.692	NEUROG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251192.1	NM_006161	
INMT	11185	hgsc.bcm.edu	37	7	30793532	30793532	+	Missense_Mutation	SNP	G	G	A	rs76338133	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:30793532G>A	ENST00000013222.5	+	2	356	c.340G>A	c.(340-342)Gcc>Acc	p.A114T	INMT_ENST00000484180.1_3'UTR|INMT_ENST00000409539.1_Missense_Mutation_p.A113T|INMT-FAM188B_ENST00000458257.1_Missense_Mutation_p.A113T	NM_001199219.1|NM_006774.4	NP_001186148.1|NP_006765.4	O95050	INMT_HUMAN	indolethylamine N-methyltransferase	114					amine metabolic process (GO:0009308)|methylation (GO:0032259)|response to toxic substance (GO:0009636)	cytosol (GO:0005829)	amine N-methyltransferase activity (GO:0030748)|thioether S-methyltransferase activity (GO:0004790)			kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(2)|stomach(1)	23						GGTGAAATTCGCCTGTGAGCT	0.577													G|||	66	0.0131789	0.0461	0.0072	5008	,	,		19308	0.0		0.0	False		,,,				2504	0.0				p.A114T		Atlas-SNP	.											.	INMT	38	.	0			c.G340A						PASS	.	G	THR/ALA,THR/ALA	191,4215	118.8+/-156.5	1,189,2013	55.0	63.0	60.0		337,340	3.0	0.1	7	dbSNP_131	60	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	INMT	NM_001199219.1,NM_006774.4	58,58	1,191,6311	AA,AG,GG		0.0233,4.335,1.4839	possibly-damaging,possibly-damaging	113/263,114/264	30793532	193,12813	2203	4300	6503	SO:0001583	missense	11185	exon2			AAATTCGCCTGTG		CCDS5430.1, CCDS56479.1	7p14.3	2011-08-30			ENSG00000241644	ENSG00000241644	2.1.1.49		6069	protein-coding gene	gene with protein product		604854				10552930	Standard	NM_001199219		Approved		uc003tbs.1	O95050	OTTHUMG00000167163	ENST00000013222.5:c.340G>A	7.37:g.30793532G>A	ENSP00000013222:p.Ala114Thr	71.0	0.0	0		76.0	35.0	0.460526	NM_006774	B8ZZ69|Q3KP49|Q9P1Y2|Q9UBY4|Q9UHQ0	Missense_Mutation	SNP	ENST00000013222.5	37	CCDS5430.1	27	0.012362637362637362	23	0.046747967479674794	4	0.011049723756906077	0	0.0	0	0.0	G	20.3	3.970206	0.74246	0.04335	2.33E-4	ENSG00000241644	ENST00000013222;ENST00000409539	T;T	0.03745	3.82;3.82	3.94	3.01	0.34805	.	0.359516	0.21052	N	0.080972	T	0.00524	0.0017	L	0.47716	1.5	0.26856	N	0.968062	P;P	0.42993	0.797;0.797	B;B	0.30855	0.121;0.121	T	0.44190	-0.9344	10	0.62326	D	0.03	-22.6315	8.8685	0.35300	0.1195:0.0:0.8805:0.0	.	113;114	B8ZZ69;O95050	.;INMT_HUMAN	T	114;113	ENSP00000013222:A114T;ENSP00000386961:A113T	ENSP00000013222:A114T	A	+	1	0	INMT	30760057	0.724000	0.28038	0.090000	0.20809	0.481000	0.33189	3.811000	0.55620	0.927000	0.37143	0.561000	0.74099	GCC	G|0.984;A|0.016	0.016	strong		0.577	INMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214993.3	NM_006774	
TIMELESS	8914	hgsc.bcm.edu	37	12	56815717	56815717	+	Missense_Mutation	SNP	T	T	C	rs61733875	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56815717T>C	ENST00000553532.1	-	21	2758	c.2608A>G	c.(2608-2610)Atg>Gtg	p.M870V	TIMELESS_ENST00000229201.4_Missense_Mutation_p.M869V|TIMELESS_ENST00000554616.1_Missense_Mutation_p.M367V					timeless circadian clock											NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						GCCAGTCCCATCTGTACCAGA	0.557													T|||	255	0.0509185	0.1823	0.0187	5008	,	,		21890	0.0		0.001	False		,,,				2504	0.0				p.M870V		Atlas-SNP	.											.	TIMELESS	107	.	0			c.A2608G						PASS	.	T	VAL/MET	704,3702	295.3+/-283.6	47,610,1546	140.0	127.0	131.0		2608	1.3	0.8	12	dbSNP_129	131	4,8596	3.0+/-9.4	0,4,4296	yes	missense	TIMELESS	NM_003920.3	21	47,614,5842	CC,CT,TT		0.0465,15.9782,5.4436	benign	870/1209	56815717	708,12298	2203	4300	6503	SO:0001583	missense	8914	exon21			GTCCCATCTGTAC	AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"""Tof1 homolog (S. cerevisiae)"", ""timeless circadian clock 1"""	603887	"""timeless (Drosophila) homolog"", ""timeless homolog (Drosophila)"""			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.2608A>G	12.37:g.56815717T>C	ENSP00000450607:p.Met870Val	71.0	0.0	0		114.0	57.0	0.5	NM_003920		Missense_Mutation	SNP	ENST00000553532.1	37	CCDS8918.1	111	0.050824175824175824	108	0.21951219512195122	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	T	7.065	0.567067	0.13560	0.159782	4.65E-4	ENSG00000111602	ENST00000229201;ENST00000553532;ENST00000554616	T;T;T	0.11604	2.76;2.76;2.76	5.29	1.26	0.21427	Timeless C-terminal (1);	0.478535	0.21599	N	0.071972	T	0.00012	0.0000	L	0.46157	1.445	0.80722	P	0.0	B	0.17852	0.024	B	0.20955	0.032	T	0.35325	-0.9793	9	0.51188	T	0.08	-2.3118	3.9116	0.09205	0.0713:0.2456:0.3032:0.3798	.	870	Q9UNS1	TIM_HUMAN	V	869;870;367	ENSP00000229201:M869V;ENSP00000450607:M870V;ENSP00000450848:M367V	ENSP00000229201:M870V	M	-	1	0	TIMELESS	55101984	0.560000	0.26570	0.789000	0.31954	0.285000	0.27093	0.692000	0.25482	0.031000	0.15407	-0.973000	0.02599	ATG	T|0.947;C|0.053	0.053	strong		0.557	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920	
RPE65	6121	hgsc.bcm.edu	37	1	68904645	68904645	+	Silent	SNP	C	C	A	rs61752907	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:68904645C>A	ENST00000262340.5	-	9	1031	c.978G>T	c.(976-978)gtG>gtT	p.V326V		NM_000329.2	NP_000320.1	Q16518	RPE65_HUMAN	retinal pigment epithelium-specific protein 65kDa	326					cellular response to electrical stimulus (GO:0071257)|detection of light stimulus involved in visual perception (GO:0050908)|insulin receptor signaling pathway (GO:0008286)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin gene expression (GO:0007468)|retina homeostasis (GO:0001895)|retina morphogenesis in camera-type eye (GO:0060042)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	all-trans-retinyl-ester hydrolase, 11-cis retinol forming activity (GO:0052885)|all-trans-retinyl-palmitate hydrolase, 11-cis retinol forming activity (GO:0052884)|metal ion binding (GO:0046872)|retinal isomerase activity (GO:0004744)			central_nervous_system(1)|kidney(3)|large_intestine(12)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	35						AGCAGAGATCCACAATCAGAA	0.418													C|||	12	0.00239617	0.0083	0.0	5008	,	,		18772	0.0		0.001	False		,,,				2504	0.0				p.V326V		Atlas-SNP	.											.	RPE65	87	.	0			c.G978T						PASS	.	C		17,4389	25.3+/-52.1	0,17,2186	281.0	279.0	280.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	978	3.0	1.0	1	dbSNP_129	280	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	RPE65	NM_000329.2		0,21,6482	AA,AC,CC		0.0465,0.3858,0.1615		326/534	68904645	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	6121	exon9			GAGATCCACAATC	U18991	CCDS643.1	1p31	2014-05-13	2002-08-29		ENSG00000116745	ENSG00000116745	3.1.1.64		10294	protein-coding gene	gene with protein product	"""retinol isomerase"", ""all-trans-retinyl-palmitate hydrolase"", ""retinoid isomerohydrolase"", ""BCO family, member 3"""	180069	"""retinal pigment epithelium-specific protein (65kD)"""	RP20		8340400	Standard	XM_006710811		Approved	LCA2, rd12, BCO3	uc001dei.1	Q16518	OTTHUMG00000009208	ENST00000262340.5:c.978G>T	1.37:g.68904645C>A		128.0	0.0	0		143.0	72.0	0.503497	NM_000329	A8K1L0|Q5T9U3	Silent	SNP	ENST00000262340.5	37	CCDS643.1																																																																																			C|0.998;A|0.002	0.002	strong		0.418	RPE65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025509.1	NM_000329	
OR6Y1	391112	hgsc.bcm.edu	37	1	158517099	158517099	+	Missense_Mutation	SNP	C	C	A	rs113154921	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158517099C>A	ENST00000302617.3	-	1	796	c.797G>T	c.(796-798)cGt>cTt	p.R266L		NM_001005189.1	NP_001005189.1	Q8NGX8	OR6Y1_HUMAN	olfactory receptor, family 6, subfamily Y, member 1	266						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30	all_hematologic(112;0.0378)					GAGTTTGGGACGGGCATAGGT	0.483													C|||	99	0.0197684	0.0719	0.0043	5008	,	,		24161	0.0		0.001	False		,,,				2504	0.0				p.R266L		Atlas-SNP	.											.	OR6Y1	73	.	0			c.G797T						PASS	.	C	LEU/ARG	264,4142	148.4+/-182.8	11,242,1950	208.0	195.0	200.0		797	3.5	1.0	1	dbSNP_132	200	5,8595	5.0+/-18.6	0,5,4295	yes	missense	OR6Y1	NM_001005189.1	102	11,247,6245	AA,AC,CC		0.0581,5.9918,2.0683	probably-damaging	266/326	158517099	269,12737	2203	4300	6503	SO:0001583	missense	391112	exon1			TTGGGACGGGCAT	BK004192	CCDS30899.1	1q23.1	2012-08-09			ENSG00000197532	ENSG00000197532		"""GPCR / Class A : Olfactory receptors"""	14823	protein-coding gene	gene with protein product				OR6Y2			Standard	NM_001005189		Approved		uc010pil.2	Q8NGX8	OTTHUMG00000019629	ENST00000302617.3:c.797G>T	1.37:g.158517099C>A	ENSP00000304807:p.Arg266Leu	152.0	0.0	0		142.0	68.0	0.478873	NM_001005189	Q6IFS0	Missense_Mutation	SNP	ENST00000302617.3	37	CCDS30899.1	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	C	18.23	3.577221	0.65878	0.059918	5.81E-4	ENSG00000197532	ENST00000302617	T	0.36699	1.24	5.34	3.49	0.39957	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42172	D	0.000750	T	0.35740	0.0942	M	0.73319	2.225	0.09310	N	1	D	0.64830	0.994	P	0.58660	0.843	T	0.18681	-1.0329	10	0.87932	D	0	.	8.5271	0.33311	0.0:0.7603:0.0:0.2397	.	266	Q8NGX8	OR6Y1_HUMAN	L	266	ENSP00000304807:R266L	ENSP00000304807:R266L	R	-	2	0	OR6Y1	156783723	0.000000	0.05858	0.983000	0.44433	0.927000	0.56198	-0.100000	0.10990	0.822000	0.34565	0.655000	0.94253	CGT	A|0.018;C|0.982;G|0.000	0.018	strong		0.483	OR6Y1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051844.1	NM_001005189	
C8orf31	286122	hgsc.bcm.edu	37	8	144126087	144126087	+	Missense_Mutation	SNP	C	C	A	rs73717943	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144126087C>A	ENST00000395172.1	+	4	560	c.208C>A	c.(208-210)Ccc>Acc	p.P70T	C8orf31_ENST00000517653.1_3'UTR	NM_173687.2	NP_775958.1	Q8N9H6	CH031_HUMAN	chromosome 8 open reading frame 31	70										breast(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)	10	all_cancers(97;1.89e-10)|all_epithelial(106;8.73e-09)|Lung NSC(106;0.000161)|all_lung(105;0.000447)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					TGCCCTGGCACCCCAGGGACT	0.627													c|||	115	0.0229633	0.084	0.0058	5008	,	,		14974	0.0		0.0	False		,,,				2504	0.0				p.P70T		Atlas-SNP	.											.	C8orf31	18	.	0			c.C208A						PASS	.	C	THR/PRO	323,4083	170.1+/-200.6	7,309,1887	69.0	60.0	63.0		208	-2.7	0.0	8	dbSNP_130	63	2,8598	2.2+/-6.3	0,2,4298	yes	missense	C8orf31	NM_173687.2	38	7,311,6185	AA,AC,CC		0.0233,7.3309,2.4988	benign	70/133	144126087	325,12681	2203	4300	6503	SO:0001583	missense	286122	exon4			CTGGCACCCCAGG		CCDS6395.1	8q24.3	2012-04-11			ENSG00000177335	ENSG00000177335			26731	protein-coding gene	gene with protein product							Standard	NM_173687		Approved	FLJ37131	uc003yxp.1	Q8N9H6	OTTHUMG00000164771	ENST00000395172.1:c.208C>A	8.37:g.144126087C>A	ENSP00000378601:p.Pro70Thr	57.0	0.0	0		59.0	33.0	0.559322	NM_173687	Q6GMU7	Missense_Mutation	SNP	ENST00000395172.1	37	CCDS6395.1	46	0.021062271062271064	43	0.08739837398373984	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	c	0.019	-1.466214	0.01053	0.073309	2.33E-4	ENSG00000177335	ENST00000395172	T	0.57595	0.39	1.37	-2.73	0.05950	.	.	.	.	.	T	0.00875	0.0029	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.08055	0.003	T	0.05500	-1.0881	9	0.87932	D	0	.	0.828	0.01124	0.2674:0.3758:0.1668:0.19	.	70	Q8N9H6	CH031_HUMAN	T	70	ENSP00000378601:P70T	ENSP00000378601:P70T	P	+	1	0	C8orf31	144197462	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.991000	0.01478	-2.249000	0.00702	-1.735000	0.00691	CCC	C|0.973;A|0.027	0.027	strong		0.627	C8orf31-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380167.1	NM_173687	
C2CD4C	126567	hgsc.bcm.edu	37	19	408200	408200	+	Silent	SNP	G	G	C	rs7252178	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:408200G>C	ENST00000332235.6	-	2	335	c.162C>G	c.(160-162)ccC>ccG	p.P54P		NM_001136263.1	NP_001129735.1	Q8TF44	C2C4C_HUMAN	C2 calcium-dependent domain containing 4C	54										large_intestine(1)|pancreas(1)	2						AGGGCAGCTTGGGGGGGATGA	0.716													g|||	158	0.0315495	0.1165	0.0058	5008	,	,		10623	0.0		0.0	False		,,,				2504	0.0				p.P54P		Atlas-SNP	.											C2CD4C,NS,carcinoma,0,1	C2CD4C	13	1	0			c.C162G						PASS	.						19.0	24.0	23.0					19																	408200		692	1589	2281	SO:0001819	synonymous_variant	126567	exon2			CAGCTTGGGGGGG	AB075837	CCDS45890.1	19p13.3	2009-09-28	2009-09-28	2009-09-28		ENSG00000183186			29417	protein-coding gene	gene with protein product	"""nuclear localized factor 3"""	610336	"""KIAA1957"", ""family with sequence similarity 148, member C"""	KIAA1957, FAM148C		11853319	Standard	NM_001136263		Approved	NLF3	uc002loo.3	Q8TF44		ENST00000332235.6:c.162C>G	19.37:g.408200G>C		150.0	0.0	0		180.0	98.0	0.544444	NM_001136263	Q8N3H7	Silent	SNP	ENST00000332235.6	37	CCDS45890.1																																																																																			G|0.971;C|0.029	0.029	strong		0.716	C2CD4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451789.2	XM_065166	
PIP4K2B	8396	hgsc.bcm.edu	37	17	36936846	36936846	+	Silent	SNP	C	C	T	rs16968328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:36936846C>T	ENST00000269554.3	-	4	846	c.366G>A	c.(364-366)acG>acA	p.T122T	PIP4K2B_ENST00000311500.6_5'UTR	NM_003559.4	NP_003550.1	P78356	PI42B_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, beta	122	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				cell surface receptor signaling pathway (GO:0007166)|intracellular signal transduction (GO:0035556)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)|receptor signaling protein activity (GO:0005057)			endometrium(3)|kidney(2)|large_intestine(4)|liver(1)|lung(8)|ovary(1)	19						GGGCGCTGCGCGTCACTGAAT	0.572													C|||	323	0.0644968	0.2352	0.013	5008	,	,		19211	0.001		0.002	False		,,,				2504	0.0				p.T122T		Atlas-SNP	.											.	PIP4K2B	35	.	0			c.G366A						PASS	.	C		767,3639	313.0+/-292.9	60,647,1496	79.0	73.0	75.0		366	-6.1	0.9	17	dbSNP_123	75	8,8592	5.0+/-18.6	0,8,4292	no	coding-synonymous	PIP4K2B	NM_003559.4		60,655,5788	TT,TC,CC		0.093,17.4081,5.9588		122/417	36936846	775,12231	2203	4300	6503	SO:0001819	synonymous_variant	8396	exon4			GCTGCGCGTCACT	U85245	CCDS11329.1	17q21.2	2007-08-14	2007-08-14	2007-08-14		ENSG00000276293	2.7.1.149		8998	protein-coding gene	gene with protein product		603261	"""phosphatidylinositol-4-phosphate 5-kinase, type II, beta"""	PIP5K2B		9038203, 14691457, 9367159	Standard	NM_003559		Approved	PIP5KIIB, PIP5KIIbeta	uc002hqs.3	P78356		ENST00000269554.3:c.366G>A	17.37:g.36936846C>T		71.0	0.0	0		78.0	33.0	0.423077	NM_003559	Q5U0E8|Q8TBP2	Silent	SNP	ENST00000269554.3	37	CCDS11329.1																																																																																			C|0.931;T|0.069	0.069	strong		0.572	PIP4K2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256791.1	NM_003559	
DPP8	54878	hgsc.bcm.edu	37	15	65793060	65793060	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:65793060G>A	ENST00000341861.5	-	4	2058	c.478C>T	c.(478-480)Cgc>Tgc	p.R160C	DPP8_ENST00000339244.5_Missense_Mutation_p.R160C|DPP8_ENST00000300141.6_Missense_Mutation_p.R144C|Y_RNA_ENST00000516408.1_RNA|DPP8_ENST00000321147.6_Missense_Mutation_p.R160C|DPP8_ENST00000321118.7_Missense_Mutation_p.R160C|DPP8_ENST00000358939.4_Missense_Mutation_p.R144C|DPP8_ENST00000559233.1_Missense_Mutation_p.R160C	NM_197960.2	NP_932064.1	Q6V1X1	DPP8_HUMAN	dipeptidyl-peptidase 8	160					immune response (GO:0006955)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	dipeptidyl-peptidase activity (GO:0008239)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(2)|endometrium(3)|large_intestine(11)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						GTTCCAATGCGTTTTCTTTCT	0.393																																					p.R160C		Atlas-SNP	.											DPP8,colon,carcinoma,+1,1	DPP8	78	1	0			c.C478T						PASS	.						204.0	196.0	199.0					15																	65793060		2201	4299	6500	SO:0001583	missense	54878	exon5			CAATGCGTTTTCT	AF221634	CCDS10207.1, CCDS10208.1, CCDS10209.1, CCDS10210.1	15q22	2008-07-18	2006-01-12		ENSG00000074603	ENSG00000074603			16490	protein-coding gene	gene with protein product	"""dipeptidyl peptidase VIII"", ""dipeptidyl peptidase IV-related protein-1"", ""prolyl dipeptidase DPP8"""	606819	"""dipeptidylpeptidase 8"""			11012666	Standard	XM_005254500		Approved	DP8, DPRP1, MSTP141, FLJ14920, FLJ20283, MGC26191	uc002aox.3	Q6V1X1	OTTHUMG00000133150	ENST00000341861.5:c.478C>T	15.37:g.65793060G>A	ENSP00000339208:p.Arg160Cys	190.0	0.0	0		179.0	62.0	0.346369	NM_197960	Q7Z4C8|Q7Z4D3|Q7Z4E1|Q8IWG7|Q8NEM5|Q96JX1|Q9HBM2|Q9HBM3|Q9HBM4|Q9HBM5|Q9NXF4	Missense_Mutation	SNP	ENST00000341861.5	37	CCDS10207.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.943085	0.92526	.	.	ENSG00000074603	ENST00000341861;ENST00000358939;ENST00000300141;ENST00000321147;ENST00000321118;ENST00000339244;ENST00000395652	T;T;T;T;T;T;T	0.31247	1.5;1.5;1.5;1.5;1.5;1.5;1.5	5.91	5.91	0.95273	.	0.000000	0.85682	D	0.000000	T	0.58864	0.2152	M	0.72479	2.2	0.40608	D	0.981643	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.996;1.0;1.0	T	0.60047	-0.7339	10	0.87932	D	0	-17.8264	20.2885	0.98538	0.0:0.0:1.0:0.0	.	144;144;160;160	Q6V1X1-3;Q6V1X1-4;Q6V1X1-2;Q6V1X1	.;.;.;DPP8_HUMAN	C	160;144;144;160;160;160;160	ENSP00000339208:R160C;ENSP00000351817:R144C;ENSP00000300141:R144C;ENSP00000318111:R160C;ENSP00000316373:R160C;ENSP00000341230:R160C;ENSP00000379013:R160C	ENSP00000300141:R144C	R	-	1	0	DPP8	63580113	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.896000	0.87350	2.791000	0.96007	0.650000	0.86243	CGC	.	.	none		0.393	DPP8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256847.1	NM_017743	
PLCG2	5336	hgsc.bcm.edu	37	16	81960783	81960783	+	Splice_Site	SNP	G	G	A	rs115583707	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:81960783G>A	ENST00000359376.3	+	23	2728	c.2514G>A	c.(2512-2514)caG>caA	p.Q838Q		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	838					B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						TAGAAAAGCAGGTGAGTCCCC	0.512													G|||	54	0.0107827	0.0356	0.0101	5008	,	,		20557	0.0		0.0	False		,,,				2504	0.0				p.Q838Q		Atlas-SNP	.											.	PLCG2	276	.	0			c.G2514A						PASS	.	G		149,3837		3,143,1847	109.0	107.0	107.0		2514	5.3	1.0	16	dbSNP_132	107	1,8337		0,1,4168	yes	coding-synonymous-near-splice	PLCG2	NM_002661.3		3,144,6015	AA,AG,GG		0.012,3.7381,1.2171		838/1266	81960783	150,12174	1993	4169	6162	SO:0001630	splice_region_variant	5336	exon23			AAAGCAGGTGAGT		CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"""SH2 domain containing"""	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.2514+1G>A	16.37:g.81960783G>A		81.0	0.0	0		74.0	39.0	0.527027	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Silent	SNP	ENST00000359376.3	37	CCDS42204.1																																																																																			G|0.984;A|0.016	0.016	strong		0.512	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1		Silent
SVEP1	79987	hgsc.bcm.edu	37	9	113169116	113169116	+	Missense_Mutation	SNP	T	T	C	rs16914996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:113169116T>C	ENST00000401783.2	-	38	9100	c.8764A>G	c.(8764-8766)Atc>Gtc	p.I2922V	SVEP1_ENST00000374469.1_Missense_Mutation_p.I2899V|SVEP1_ENST00000297826.5_Missense_Mutation_p.I848V	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2922	Sushi 25. {ECO:0000255|PROSITE- ProRule:PRU00302}.		I -> V (in dbSNP:rs16914996).		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						CCGTGCAAGATGTAGCCCTCG	0.527													T|||	207	0.0413339	0.149	0.0144	5008	,	,		21879	0.0		0.0	False		,,,				2504	0.0				p.I2922V		Atlas-SNP	.											.	SVEP1	326	.	0			c.A8764G						PASS	.	T	VAL/ILE	495,3643		27,441,1601	141.0	142.0	141.0		8764	-1.4	0.0	9	dbSNP_123	141	5,8423		0,5,4209	yes	missense	SVEP1	NM_153366.3	29	27,446,5810	CC,CT,TT		0.0593,11.9623,3.979	benign	2922/3572	113169116	500,12066	2069	4214	6283	SO:0001583	missense	79987	exon38			GCAAGATGTAGCC	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.8764A>G	9.37:g.113169116T>C	ENSP00000384917:p.Ile2922Val	66.0	0.0	0		74.0	52.0	0.702703	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	74	0.03388278388278388	71	0.1443089430894309	3	0.008287292817679558	0	0.0	0	0.0	T	0.008	-1.879969	0.00537	0.119623	5.93E-4	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826	T;T;T	0.61859	0.07;0.07;0.07	5.41	-1.41	0.08941	Complement control module (2);Sushi/SCR/CCP (3);	1.252220	0.05177	N	0.500598	T	0.00178	0.0005	N	0.01146	-0.985	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.03651	-1.1016	9	0.17369	T	0.5	.	6.9527	0.24554	0.1169:0.3452:0.0:0.5379	rs16914996;rs52792614;rs16914996	2922	Q4LDE5	SVEP1_HUMAN	V	2922;2899;848	ENSP00000384917:I2922V;ENSP00000363593:I2899V;ENSP00000297826:I848V	ENSP00000297826:I848V	I	-	1	0	SVEP1	112208937	0.000000	0.05858	0.002000	0.10522	0.079000	0.17450	-1.006000	0.03671	-0.630000	0.05567	-0.326000	0.08463	ATC	T|0.943;C|0.057	0.057	strong		0.527	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
NAV2	89797	hgsc.bcm.edu	37	11	19735325	19735325	+	Silent	SNP	C	C	A	rs11828836	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:19735325C>A	ENST00000396087.3	+	1	183	c.84C>A	c.(82-84)ccC>ccA	p.P28P	NAV2_ENST00000360655.4_Intron|NAV2_ENST00000396085.1_Silent_p.P28P|NAV2_ENST00000349880.4_Silent_p.P28P|RP11-359E10.1_ENST00000603468.1_lincRNA	NM_001244963.1	NP_001231892.1	Q8IVL1	NAV2_HUMAN	neuron navigator 2	28					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						TGCACGTgcccccggcccggg	0.662													C|||	112	0.0223642	0.0825	0.0043	5008	,	,		13608	0.0		0.0	False		,,,				2504	0.0				p.P28P		Atlas-SNP	.											.	NAV2	255	.	0			c.C84A						PASS	.	C	,,	269,4121		8,253,1934	20.0	22.0	21.0		,84,84	4.4	1.0	11	dbSNP_120	21	5,8571		0,5,4283	no	intron,coding-synonymous,coding-synonymous	NAV2	NM_001111018.1,NM_145117.4,NM_182964.5	,,	8,258,6217	AA,AC,CC		0.0583,6.1276,2.1132	,,	,28/2430,28/2433	19735325	274,12692	2195	4288	6483	SO:0001819	synonymous_variant	89797	exon1			CGTGCCCCCGGCC	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.84C>A	11.37:g.19735325C>A		18.0	0.0	0		38.0	28.0	0.736842	NM_145117	A6NEC1|Q8IVK3|Q8IVK4|Q8IVK5|Q8IVK6|Q8IVK7|Q8IVK8|Q8NHC9|Q8NHD0|Q8TDE9|Q8TDF0|Q8TEB3|Q96B30|Q9NUZ6|Q9NVM7|Q9P2C8	Silent	SNP	ENST00000396087.3	37	CCDS58126.1																																																																																			C|0.975;A|0.025	0.025	strong		0.662	NAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324112.1	NM_145117	
JPH3	57338	hgsc.bcm.edu	37	16	87717863	87717863	+	Missense_Mutation	SNP	C	C	T	rs138328691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:87717863C>T	ENST00000284262.2	+	3	1518	c.1276C>T	c.(1276-1278)Cgg>Tgg	p.R426W	JPH3_ENST00000563609.1_3'UTR	NM_020655.2	NP_065706.2	Q8WXH2	JPH3_HUMAN	junctophilin 3	426					calcium ion transport into cytosol (GO:0060402)|exploration behavior (GO:0035640)|learning (GO:0007612)|locomotion (GO:0040011)|memory (GO:0007613)|neuromuscular process controlling balance (GO:0050885)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)	calcium-release channel activity (GO:0015278)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(80;0.0287)		CTTCCAGCACCGGGAAAACGG	0.647																																					p.R426W		Atlas-SNP	.											JPH3,NS,carcinoma,-2,1	JPH3	95	1	0			c.C1276T						PASS	.	C	TRP/ARG	4,4392	6.2+/-15.9	0,4,2194	73.0	60.0	64.0		1276	-4.8	0.9	16	dbSNP_134	64	0,8600		0,0,4300	yes	missense	JPH3	NM_020655.2	101	0,4,6494	TT,TC,CC		0.0,0.091,0.0308	probably-damaging	426/749	87717863	4,12992	2198	4300	6498	SO:0001583	missense	57338	exon3			CAGCACCGGGAAA	AB042636	CCDS10962.1	16q24.3	2008-02-05	2002-11-13		ENSG00000154118	ENSG00000154118			14203	protein-coding gene	gene with protein product		605268	"""trinucleotide repeat containing 22"""	TNRC22		10949023, 10891348	Standard	NM_020655		Approved	JP-3, CAGL237, HDL2, JP3	uc002fkd.4	Q8WXH2	OTTHUMG00000137656	ENST00000284262.2:c.1276C>T	16.37:g.87717863C>T	ENSP00000284262:p.Arg426Trp	192.0	0.0	0		218.0	121.0	0.555046	NM_020655	D3DUN2|Q8N471|Q9HDC3|Q9HDC4	Missense_Mutation	SNP	ENST00000284262.2	37	CCDS10962.1	.	.	.	.	.	.	.	.	.	.	C	18.52	3.641510	0.67244	9.1E-4	0.0	ENSG00000154118	ENST00000537256;ENST00000284262	T	0.49720	0.77	4.64	-4.8	0.03190	.	0.326711	0.28371	N	0.015584	T	0.51517	0.1679	L	0.50333	1.59	0.43617	D	0.995991	D	0.76494	0.999	P	0.55871	0.786	T	0.57797	-0.7749	10	0.56958	D	0.05	.	16.5936	0.84789	0.5065:0.4935:0.0:0.0	.	426	Q8WXH2	JPH3_HUMAN	W	289;426	ENSP00000284262:R426W	ENSP00000284262:R426W	R	+	1	2	JPH3	86275364	0.404000	0.25328	0.947000	0.38551	0.966000	0.64601	-0.364000	0.07583	-1.153000	0.02829	-0.181000	0.13052	CGG	C|0.999;T|0.001	0.001	strong		0.647	JPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269108.2		
VWDE	221806	hgsc.bcm.edu	37	7	12420145	12420145	+	Silent	SNP	T	T	C	rs146236000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:12420145T>C	ENST00000275358.3	-	5	944	c.756A>G	c.(754-756)gaA>gaG	p.E252E		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	252						extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						TGCCATCAAGTTCTAAAAGAG	0.368													T|||	39	0.00778754	0.0287	0.0014	5008	,	,		14891	0.0		0.0	False		,,,				2504	0.0				p.E252E		Atlas-SNP	.											VWDE_ENST00000275358,NS,carcinoma,-2,1	VWDE	123	1	0			c.A756G						PASS	.	T		32,1352		1,30,661	62.0	55.0	57.0		756	-0.3	1.0	7	dbSNP_134	57	1,3181		0,1,1590	no	coding-synonymous	VWDE	NM_001135924.1		1,31,2251	CC,CT,TT		0.0314,2.3121,0.7227		252/1591	12420145	33,4533	692	1591	2283	SO:0001819	synonymous_variant	221806	exon5			ATCAAGTTCTAAA		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.756A>G	7.37:g.12420145T>C		47.0	0.0	0		76.0	42.0	0.552632	NM_001135924	B7ZM77|Q96SQ3	Silent	SNP	ENST00000275358.3	37	CCDS47544.1																																																																																			T|0.994;C|0.006	0.006	strong		0.368	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
ZNF91	7644	hgsc.bcm.edu	37	19	23556550	23556550	+	Missense_Mutation	SNP	G	G	A	rs148956643	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:23556550G>A	ENST00000300619.7	-	3	452	c.247C>T	c.(247-249)Ccc>Tcc	p.P83S	ZNF91_ENST00000397082.2_Intron|ZNF91_ENST00000599743.1_Missense_Mutation_p.P83S	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	83	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				CTACCTGTGGGTTCATCCACC	0.438													G|||	73	0.0145767	0.0514	0.0072	5008	,	,		12954	0.0		0.0	False		,,,				2504	0.0				p.P83S		Atlas-SNP	.											.	ZNF91	349	.	0			c.C247T						PASS	.	G	SER/PRO	210,4192	127.8+/-164.7	4,202,1995	75.0	78.0	77.0		247	-0.3	0.0	19	dbSNP_134	77	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ZNF91	NM_003430.2	74	4,203,6294	AA,AG,GG		0.0116,4.7706,1.6228	benign	83/1192	23556550	211,12791	2201	4300	6501	SO:0001583	missense	7644	exon3			CTGTGGGTTCATC	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"""Zinc fingers, C2H2-type"", ""-"""	13166	protein-coding gene	gene with protein product		603971	"""zinc finger protein 91 (HPF7, HTF10)"""			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.247C>T	19.37:g.23556550G>A	ENSP00000300619:p.Pro83Ser	132.0	0.0	0		128.0	58.0	0.453125	NM_003430	A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	37	CCDS42541.1	28	0.01282051282051282	24	0.04878048780487805	4	0.011049723756906077	0	0.0	0	0.0	G	0.005	-2.230572	0.00280	0.047706	1.16E-4	ENSG00000167232	ENST00000300619	T	0.05855	3.38	0.158	-0.317	0.12736	Krueppel-associated box (1);	.	.	.	.	T	0.00815	0.0027	L	0.59436	1.845	0.09310	N	1	B	0.24533	0.105	B	0.17979	0.02	T	0.46582	-0.9181	8	0.17369	T	0.5	.	.	.	.	.	83	Q05481	ZNF91_HUMAN	S	83	ENSP00000300619:P83S	ENSP00000300619:P83S	P	-	1	0	ZNF91	23348390	0.002000	0.14202	0.005000	0.12908	0.006000	0.05464	-0.167000	0.09940	-1.052000	0.03222	-1.038000	0.02383	CCC	G|0.992;A|0.008	0.008	strong		0.438	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430	
PPP1R3A	5506	hgsc.bcm.edu	37	7	113519267	113519267	+	Missense_Mutation	SNP	C	C	T	rs35067467	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:113519267C>T	ENST00000284601.3	-	4	1948	c.1880G>A	c.(1879-1881)aGg>aAg	p.R627K		NM_002711.3	NP_002702.2	Q16821	PPR3A_HUMAN	protein phosphatase 1, regulatory subunit 3A	627			R -> K (in dbSNP:rs35067467).		glycogen metabolic process (GO:0005977)	integral component of membrane (GO:0016021)				NS(2)|breast(8)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|liver(1)|lung(43)|ovary(10)|pancreas(7)|prostate(3)|skin(15)|stomach(1)|upper_aerodigestive_tract(2)	121						ATAATCATTCCTCAAAACATT	0.393													C|||	187	0.0373403	0.1339	0.0115	5008	,	,		20272	0.0		0.002	False		,,,				2504	0.0				p.R627K		Atlas-SNP	.											.	PPP1R3A	317	.	0			c.G1880A						PASS	.	C	LYS/ARG	455,3951	213.5+/-233.1	22,411,1770	83.0	81.0	82.0		1880	-3.9	0.0	7	dbSNP_126	82	9,8591	6.4+/-24.3	0,9,4291	yes	missense	PPP1R3A	NM_002711.3	26	22,420,6061	TT,TC,CC		0.1047,10.3268,3.5676	benign	627/1123	113519267	464,12542	2203	4300	6503	SO:0001583	missense	5506	exon4			TCATTCCTCAAAA	AF024578	CCDS5759.1	7q31.1	2012-04-17	2011-10-04	2001-07-02	ENSG00000154415	ENSG00000154415	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9291	protein-coding gene	gene with protein product	"""glycogen-associated regulatory subunit of protein phosphatase-1"", ""protein phosphatase 1 regulatory subunit GM"""	600917	"""protein phosphatase 1, regulatory (inhibitor) subunit 3A (glycogen and sarcoplasmic reticulum binding subunit, skeletal muscle)"", ""protein phosphatase 1, regulatory (inhibitor) subunit 3A"""	PPP1R3		7926294	Standard	NM_002711		Approved	GM	uc010ljy.1	Q16821	OTTHUMG00000156944	ENST00000284601.3:c.1880G>A	7.37:g.113519267C>T	ENSP00000284601:p.Arg627Lys	253.0	0.0	0		238.0	121.0	0.508403	NM_002711	A0AVQ2|A4D0T6|O43476|Q75LN8|Q7KYM8|Q86UI6	Missense_Mutation	SNP	ENST00000284601.3	37	CCDS5759.1	68	0.031135531135531136	61	0.12398373983739837	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	C	0.023	-1.404787	0.01155	0.103268	0.001047	ENSG00000154415	ENST00000284601	T	0.15256	2.44	6.02	-3.93	0.04143	.	1.218990	0.05550	N	0.567306	T	0.00178	0.0005	L	0.31294	0.92	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39881	-0.9592	9	0.15499	T	0.54	-0.3547	9.053	0.36387	0.0:0.3009:0.11:0.5891	rs35067467	627	Q16821	PPR3A_HUMAN	K	627	ENSP00000284601:R627K	ENSP00000284601:R627K	R	-	2	0	PPP1R3A	113306503	0.000000	0.05858	0.000000	0.03702	0.122000	0.20287	-0.502000	0.06390	-0.652000	0.05408	-1.106000	0.02097	AGG	C|0.959;T|0.041	0.041	strong		0.393	PPP1R3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346724.1	NM_002711	
FAM71B	153745	hgsc.bcm.edu	37	5	156589937	156589937	+	Missense_Mutation	SNP	G	G	A	rs115938677	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:156589937G>A	ENST00000302938.4	-	2	1434	c.1339C>T	c.(1339-1341)Cgc>Tgc	p.R447C		NM_130899.2	NP_570969.2	Q8TC56	FA71B_HUMAN	family with sequence similarity 71, member B	447						nucleus (GO:0005634)		p.R447G(1)		NS(3)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(32)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	68	Renal(175;0.00212)	Medulloblastoma(196;0.0523)|all_neural(177;0.21)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CCTGCCTTGCGGTGATGAGAA	0.498													G|||	32	0.00638978	0.0182	0.0014	5008	,	,		20598	0.0		0.0	False		,,,				2504	0.0072				p.R447C		Atlas-SNP	.											FAM71B,NS,carcinoma,0,1	FAM71B	145	1	1	Substitution - Missense(1)	lung(1)	c.C1339T						PASS	.	G	CYS/ARG	87,4319	72.5+/-110.5	2,83,2118	171.0	162.0	165.0		1339	3.8	0.6	5	dbSNP_132	165	1,8599	1.2+/-3.3	0,1,4299	yes	missense	FAM71B	NM_130899.2	180	2,84,6417	AA,AG,GG		0.0116,1.9746,0.6766	probably-damaging	447/606	156589937	88,12918	2203	4300	6503	SO:0001583	missense	153745	exon2			CCTTGCGGTGATG		CCDS4335.1	5q33.3	2005-08-09			ENSG00000170613	ENSG00000170613			28397	protein-coding gene	gene with protein product						12477932	Standard	NM_130899		Approved	MGC26988	uc003lwn.3	Q8TC56	OTTHUMG00000130246	ENST00000302938.4:c.1339C>T	5.37:g.156589937G>A	ENSP00000305596:p.Arg447Cys	78.0	0.0	0		64.0	24.0	0.375	NM_130899	Q1EDD9|Q8TC64|Q96LY8	Missense_Mutation	SNP	ENST00000302938.4	37	CCDS4335.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	16.74	3.208131	0.58343	0.019746	1.16E-4	ENSG00000170613	ENST00000302938	T	0.19394	2.15	4.64	3.76	0.43208	.	1.354870	0.05270	N	0.517312	T	0.21387	0.0515	M	0.65498	2.005	0.37788	D	0.927243	D	0.69078	0.997	P	0.50490	0.642	T	0.08743	-1.0707	10	0.87932	D	0	-0.0752	10.7971	0.46466	0.0:0.0:0.8103:0.1897	.	447	Q8TC56	FA71B_HUMAN	C	447	ENSP00000305596:R447C	ENSP00000305596:R447C	R	-	1	0	FAM71B	156522515	0.960000	0.32886	0.566000	0.28421	0.204000	0.24138	1.831000	0.39141	1.241000	0.43820	0.655000	0.94253	CGC	G|0.995;A|0.005	0.005	strong		0.498	FAM71B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252570.2	NM_130899	
TNRC18	84629	hgsc.bcm.edu	37	7	5410814	5410814	+	Silent	SNP	G	G	C	rs114987874	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:5410814G>C	ENST00000430969.1	-	11	3759	c.3411C>G	c.(3409-3411)ccC>ccG	p.P1137P	TNRC18_ENST00000399537.4_Silent_p.P1137P	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1137	Pro-rich.						chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		TGATCTTGGAGGGGGACAAGC	0.697													G|||	122	0.024361	0.0847	0.0101	5008	,	,		13301	0.0		0.003	False		,,,				2504	0.0				p.P1137P		Atlas-SNP	.											.	TNRC18	311	.	0			c.C3411G						PASS	.	G		322,3598		8,306,1646	15.0	17.0	16.0		3411	0.2	1.0	7	dbSNP_132	16	16,8234		0,16,4109	no	coding-synonymous	TNRC18	NM_001080495.2		8,322,5755	CC,CG,GG		0.1939,8.2143,2.7773		1137/2969	5410814	338,11832	1960	4125	6085	SO:0001819	synonymous_variant	84629	exon11			CTTGGAGGGGGAC	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.3411C>G	7.37:g.5410814G>C		79.0	0.0	0		83.0	33.0	0.39759	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	37	CCDS47534.1																																																																																			G|0.984;C|0.016	0.016	strong		0.697	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
PCDHA6	56142	hgsc.bcm.edu	37	5	140209593	140209593	+	Silent	SNP	A	A	G	rs61730636	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140209593A>G	ENST00000529310.1	+	1	2031	c.1917A>G	c.(1915-1917)gaA>gaG	p.E639E	PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron	NM_018909.2|NM_031848.2|NM_031849.1	NP_061732.1|NP_114036.1|NP_114037.1	Q9UN73	PCDA6_HUMAN	protocadherin alpha 6	639	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(42)|prostate(8)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	89			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCTGGACGAAGCGGACTCTC	0.667													.|||	317	0.0632987	0.2322	0.013	5008	,	,		16276	0.0		0.001	False		,,,				2504	0.0				p.E639E		Atlas-SNP	.											PCDHA6_ENST00000529310,NS,carcinoma,+2,6	PCDHA6	442	6	0			c.A1917G						scavenged	.	A	,,,,,,,,	857,3549	328.0+/-300.3	78,701,1424	58.0	66.0	64.0		,,,,,1917,,1917,	0.9	0.6	5	dbSNP_129	64	2,8596	2.2+/-6.3	0,2,4297	no	intron,intron,intron,intron,intron,coding-synonymous,intron,coding-synonymous,intron	PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_031411.1,NM_031848.1,NM_031849.1	,,,,,,,,	78,703,5721	GG,GA,AA		0.0233,19.4507,6.6057	,,,,,,,,	,,,,,639/951,,639/804,	140209593	859,12145	2203	4299	6502	SO:0001819	synonymous_variant	56142	exon1			GGACGAAGCGGAC	AF152484	CCDS47281.1, CCDS47282.1	5q31	2010-11-26			ENSG00000081842	ENSG00000081842		"""Cadherins / Protocadherins : Clustered"""	8672	other	complex locus constituent	"""KIAA0345-like 8"""	606312		CNRS2		10380929, 10662547	Standard	NM_018909		Approved	CNR2, CRNR2, PCDH-ALPHA6		Q9UN73	OTTHUMG00000163353	ENST00000529310.1:c.1917A>G	5.37:g.140209593A>G		140.0	1.0	0.00714286		147.0	72.0	0.489796	NM_018909	O75283|Q9NRT8	Silent	SNP	ENST00000529310.1	37	CCDS47281.1																																																																																			A|0.940;G|0.060	0.060	strong		0.667	PCDHA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372829.3	NM_018909	
CIT	11113	hgsc.bcm.edu	37	12	120139701	120139701	+	Silent	SNP	T	T	G	rs34140357	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:120139701T>G	ENST00000261833.7	-	41	5293	c.5241A>C	c.(5239-5241)ggA>ggC	p.G1747G	CIT_ENST00000537607.1_5'UTR|CIT_ENST00000392521.2_Silent_p.G1789G	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	1747	CNH. {ECO:0000255|PROSITE- ProRule:PRU00795}.				cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		ATTTATTGGTTCCAATGAGGA	0.512													T|||	252	0.0503195	0.1823	0.0159	5008	,	,		21657	0.0		0.0	False		,,,				2504	0.0				p.G1789G		Atlas-SNP	.											.	CIT	535	.	0			c.A5367C						PASS	.	T	,	639,3767	274.0+/-271.7	50,539,1614	203.0	195.0	198.0		5367,5241	-0.1	1.0	12	dbSNP_126	198	8,8592	4.3+/-15.6	0,8,4292	no	coding-synonymous,coding-synonymous	CIT	NM_001206999.1,NM_007174.2	,	50,547,5906	GG,GT,TT		0.093,14.503,4.9746	,	1789/2070,1747/2028	120139701	647,12359	2203	4300	6503	SO:0001819	synonymous_variant	11113	exon42			ATTGGTTCCAATG	AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"""serine/threonine kinase 21"""	605629	"""citron (rho-interacting, serine/threonine kinase 21)"""			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.5241A>C	12.37:g.120139701T>G		107.0	0.0	0		141.0	60.0	0.425532	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Silent	SNP	ENST00000261833.7	37	CCDS9192.1	97	0.044413919413919416	89	0.18089430894308944	8	0.022099447513812154	0	0.0	0	0.0	T	11.11	1.542516	0.27563	0.14503	9.3E-4	ENSG00000122966	ENST00000392520	.	.	.	5.68	-0.123	0.13527	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.14504	-1.0470	3	.	.	.	.	7.4878	0.27443	0.0:0.2091:0.1194:0.6715	rs34140357	.	.	.	A	1360	.	.	E	-	2	0	CIT	118624084	1.000000	0.71417	0.997000	0.53966	0.998000	0.95712	1.220000	0.32491	0.060000	0.16281	0.528000	0.53228	GAA	T|0.947;G|0.053	0.053	strong		0.512	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174	
MISP	126353	hgsc.bcm.edu	37	19	757354	757354	+	Silent	SNP	G	G	A	rs35090443	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:757354G>A	ENST00000215582.6	+	2	511	c.408G>A	c.(406-408)ctG>ctA	p.L136L		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	136					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											CCAGGAGGCTGTGTGACCTGG	0.672													G|||	94	0.01877	0.0681	0.0058	5008	,	,		17272	0.0		0.0	False		,,,				2504	0.0				p.L136L		Atlas-SNP	.											.	C19orf21	56	.	0			c.G408A						PASS	.	G		230,4172	124.5+/-161.8	8,214,1979	41.0	39.0	40.0		408	-8.1	0.0	19	dbSNP_126	40	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous	C19orf21	NM_173481.2		8,215,6276	AA,AG,GG		0.0116,5.2249,1.7772		136/680	757354	231,12767	2201	4298	6499	SO:0001819	synonymous_variant	126353	exon2			GAGGCTGTGTGAC	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.408G>A	19.37:g.757354G>A		95.0	0.0	0		126.0	61.0	0.484127	NM_173481		Silent	SNP	ENST00000215582.6	37	CCDS12042.1																																																																																			G|0.982;A|0.018	0.018	strong		0.672	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481	
CCNB2	9133	hgsc.bcm.edu	37	15	59406674	59406674	+	Missense_Mutation	SNP	T	T	C	rs16941036	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:59406674T>C	ENST00000288207.2	+	4	490	c.299T>C	c.(298-300)aTg>aCg	p.M100T	CCNB2_ENST00000559622.1_Missense_Mutation_p.M19T	NM_004701.3	NP_004692.1	O95067	CCNB2_HUMAN	cyclin B2	100			M -> T (in dbSNP:rs16941036). {ECO:0000269|Ref.5}.		G2/M transition of mitotic cell cycle (GO:0000086)|growth (GO:0040007)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|regulation of cell cycle (GO:0051726)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)	centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)				kidney(4)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	9						GATGTCTCCATGAAGGAAGAG	0.473													T|||	17	0.00339457	0.0121	0.0014	5008	,	,		20124	0.0		0.0	False		,,,				2504	0.0				p.M100T		Atlas-SNP	.											.	CCNB2	23	.	0			c.T299C						PASS	.	T	THR/MET	72,4310	64.1+/-101.4	0,72,2119	92.0	85.0	87.0		299	4.2	1.0	15	dbSNP_123	87	1,8581	1.2+/-3.3	0,1,4290	yes	missense	CCNB2	NM_004701.3	81	0,73,6409	CC,CT,TT		0.0117,1.6431,0.5631	benign	100/399	59406674	73,12891	2191	4291	6482	SO:0001583	missense	9133	exon4			TCTCCATGAAGGA	AF002822	CCDS10170.1	15q21.3	2004-01-19			ENSG00000157456	ENSG00000157456			1580	protein-coding gene	gene with protein product		602755					Standard	NM_004701		Approved	HsT17299	uc002afz.3	O95067	OTTHUMG00000132715	ENST00000288207.2:c.299T>C	15.37:g.59406674T>C	ENSP00000288207:p.Met100Thr	102.0	0.0	0		126.0	61.0	0.484127	NM_004701	B3KM93|Q6FI99	Missense_Mutation	SNP	ENST00000288207.2	37	CCDS10170.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	T	8.119	0.780523	0.16120	0.016431	1.17E-4	ENSG00000157456	ENST00000288207	T	0.13538	2.58	5.3	4.17	0.49024	.	0.590246	0.19354	N	0.116311	T	0.08133	0.0203	M	0.75777	2.31	0.43457	D	0.995659	B;B	0.19935	0.017;0.04	B;B	0.20384	0.029;0.029	T	0.03524	-1.1028	10	0.13853	T	0.58	.	10.3592	0.43982	0.0:0.0774:0.0:0.9226	rs16941036;rs52827002;rs16941036	100;100	Q53HG9;O95067	.;CCNB2_HUMAN	T	100	ENSP00000288207:M100T	ENSP00000288207:M100T	M	+	2	0	CCNB2	57193966	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.612000	0.46343	0.862000	0.35528	0.459000	0.35465	ATG	T|0.994;C|0.006	0.006	strong		0.473	CCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256016.1	NM_004701	
ARID1B	57492	hgsc.bcm.edu	37	6	157505478	157505478	+	Silent	SNP	G	G	A	rs61745451	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:157505478G>A	ENST00000350026.5	+	12	3421	c.3420G>A	c.(3418-3420)gaG>gaA	p.E1140E	ARID1B_ENST00000275248.4_Silent_p.E1135E|ARID1B_ENST00000346085.5_Silent_p.E1153E|ARID1B_ENST00000367148.1_Silent_p.E1193E	NM_017519.2	NP_059989.2	Q8NFD5	ARI1B_HUMAN	AT rich interactive domain 1B (SWI1-like)	1140	ARID. {ECO:0000255|PROSITE- ProRule:PRU00355}.				chromatin-mediated maintenance of transcription (GO:0048096)|nervous system development (GO:0007399)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|SWI/SNF complex (GO:0016514)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			NS(2)|breast(5)|central_nervous_system(4)|endometrium(12)|kidney(4)|large_intestine(11)|lung(30)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(3)	81		Breast(66;0.000162)|Ovarian(120;0.0265)		OV - Ovarian serous cystadenocarcinoma(65;3.19e-17)|BRCA - Breast invasive adenocarcinoma(81;1.01e-05)		TTGCCTTTGAGTGCAAGATCG	0.567													G|||	68	0.0135783	0.0492	0.0014	5008	,	,		18188	0.0		0.002	False		,,,				2504	0.0				p.E1153E		Atlas-SNP	.											.	ARID1B	320	.	0			c.G3459A						PASS	.	G	,	141,4265	99.8+/-138.5	1,139,2063	80.0	77.0	78.0		3420,3459	5.9	1.0	6	dbSNP_129	78	3,8589	3.0+/-9.4	0,3,4293	no	coding-synonymous,coding-synonymous	ARID1B	NM_017519.2,NM_020732.3	,	1,142,6356	AA,AG,GG		0.0349,3.2002,1.1079	,	1140/2237,1153/2250	157505478	144,12854	2203	4296	6499	SO:0001819	synonymous_variant	57492	exon13			CTTTGAGTGCAAG	AF521671	CCDS5251.1, CCDS5251.2, CCDS55072.1	6q25.3	2014-09-17			ENSG00000049618	ENSG00000049618		"""-"""	18040	protein-coding gene	gene with protein product		614556					Standard	NM_017519		Approved	KIAA1235, ELD/OSA1, p250R, BAF250b, DAN15, 6A3-5	uc003qqo.3	Q8NFD5	OTTHUMG00000015890	ENST00000350026.5:c.3420G>A	6.37:g.157505478G>A		150.0	0.0	0		162.0	75.0	0.462963	NM_020732	Q5JRD1|Q5VYC4|Q8IZY8|Q8TEV0|Q8TF02|Q99491|Q9ULI5	Silent	SNP	ENST00000350026.5	37	CCDS5251.2																																																																																			G|0.989;A|0.011	0.011	strong		0.567	ARID1B-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000372723.1	NM_020732	
STH	246744	hgsc.bcm.edu	37	17	44076711	44076711	+	Silent	SNP	G	G	A	rs73317018	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:44076711G>A	ENST00000537309.1	+	1	96	c.66G>A	c.(64-66)ccG>ccA	p.P22P	MAPT_ENST00000415613.2_Intron|MAPT_ENST00000535772.1_Intron|MAPT_ENST00000347967.5_Intron|MAPT_ENST00000571987.1_Intron|MAPT_ENST00000344290.5_Intron|MAPT_ENST00000420682.2_Intron|MAPT_ENST00000570299.1_Intron|MAPT_ENST00000340799.5_Intron|MAPT_ENST00000574436.1_Intron|MAPT_ENST00000446361.3_Intron|MAPT_ENST00000262410.5_Intron|MAPT_ENST00000334239.8_Intron|MAPT_ENST00000576518.1_Intron|MAPT_ENST00000351559.5_Intron|MAPT_ENST00000431008.3_Intron	NM_001007532.2	NP_001007533.1	Q8IWL8	STH_HUMAN	saitohin	22						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	7						gcaggtggccggccctcattg	0.537													G|||	178	0.0355431	0.1271	0.0144	5008	,	,		18789	0.0		0.0	False		,,,				2504	0.0				p.P22P		Atlas-SNP	.											.	STH	14	.	0			c.G66A						PASS	.	G	,,,,,,,,	452,3442		19,414,1514	66.0	65.0	65.0		66,,,,,,,,	-2.5	0.0	17	dbSNP_132	65	1,8263		0,1,4131	no	coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron	MAPT,STH	NM_001007532.2,NM_001123066.3,NM_001123067.3,NM_001203251.1,NM_001203252.1,NM_005910.5,NM_016834.4,NM_016835.4,NM_016841.4	,,,,,,,,	19,415,5645	AA,AG,GG		0.0121,11.6076,3.7259	,,,,,,,,	22/129,,,,,,,,	44076711	453,11705	1947	4132	6079	SO:0001819	synonymous_variant	246744	exon1			GTGGCCGGCCCTC	AA325304	CCDS54136.1	17q21.1	2008-01-22				ENSG00000256762			18839	protein-coding gene	gene with protein product	"""microtubule-associated protein tau (MAPT) intronic transcript"""	607067				12032355, 16186110	Standard	NM_001007532		Approved	MAPTIT	uc002ijy.2	Q8IWL8		ENST00000537309.1:c.66G>A	17.37:g.44076711G>A		164.0	0.0	0		180.0	90.0	0.5	NM_001007532	A1L3X7	Silent	SNP	ENST00000537309.1	37	CCDS54136.1																																																																																			A|0.027;C|0.000;G|0.972;T|0.000	0.027	strong		0.537	STH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400444.1		
WSB2	55884	hgsc.bcm.edu	37	12	118474238	118474238	+	Silent	SNP	G	G	A	rs34253698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:118474238G>A	ENST00000315436.3	-	6	879	c.738C>T	c.(736-738)gaC>gaT	p.D246D	WSB2_ENST00000441406.2_Silent_p.D263D|WSB2_ENST00000536738.1_5'UTR|WSB2_ENST00000542304.1_Silent_p.D21D|WSB2_ENST00000535496.1_Silent_p.D248D|WSB2_ENST00000544233.1_Silent_p.D36D	NM_001278557.1|NM_018639.3	NP_001265486.1|NP_061109.1	Q9NYS7	WSB2_HUMAN	WD repeat and SOCS box containing 2	246					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	17	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					CGGGGGAGAAGTCACAAGAGA	0.512													G|||	77	0.0153754	0.056	0.0043	5008	,	,		19879	0.0		0.0	False		,,,				2504	0.0				p.D246D		Atlas-SNP	.											.	WSB2	32	.	0			c.C738T						PASS	.	G		183,4223	117.1+/-155.0	4,175,2024	176.0	156.0	163.0		738	3.8	1.0	12	dbSNP_126	163	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	WSB2	NM_018639.3		4,178,6321	AA,AG,GG		0.0349,4.1534,1.4301		246/405	118474238	186,12820	2203	4300	6503	SO:0001819	synonymous_variant	55884	exon6			GGAGAAGTCACAA	AF038187	CCDS9186.1, CCDS61251.1, CCDS61252.1	12q24.23	2013-01-09	2011-01-25		ENSG00000176871	ENSG00000176871		"""WD repeat domain containing"""	19222	protein-coding gene	gene with protein product			"""WD repeat and SOCS box-containing 2"""			12076535	Standard	NM_018639		Approved	SBA2, MGC10210	uc001twr.2	Q9NYS7	OTTHUMG00000168885	ENST00000315436.3:c.738C>T	12.37:g.118474238G>A		140.0	0.0	0		132.0	59.0	0.44697	NM_018639	B4DIE6|B4DPV6|Q9NRX9	Silent	SNP	ENST00000315436.3	37	CCDS9186.1																																																																																			G|0.985;A|0.015	0.015	strong		0.512	WSB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401515.1	NM_018639	
CHTF18	63922	hgsc.bcm.edu	37	16	846012	846012	+	Silent	SNP	C	C	T	rs114461038	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:846012C>T	ENST00000262315.9	+	18	2454	c.2391C>T	c.(2389-2391)ctC>ctT	p.L797L	CHTF18_ENST00000455171.2_Silent_p.L825L|CHTF18_ENST00000317063.6_Silent_p.L1006L	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	797					cell cycle (GO:0007049)|DNA replication (GO:0006260)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(1)|kidney(3)|liver(2)|lung(4)|prostate(1)	11		Hepatocellular(780;0.00335)				GCACGATGCTCGCTTACAGCC	0.642													c|||	89	0.0177716	0.0643	0.0058	5008	,	,		14732	0.0		0.0	False		,,,				2504	0.0				p.L797L		Atlas-SNP	.											.	CHTF18	52	.	0			c.C2391T						PASS	.			175,4107		8,159,1974	29.0	36.0	34.0		2391	-8.6	0.6	16	dbSNP_132	34	3,8505		0,3,4251	no	coding-synonymous	CHTF18	NM_022092.2		8,162,6225	TT,TC,CC		0.0353,4.0869,1.3917		797/976	846012	178,12612	2141	4254	6395	SO:0001819	synonymous_variant	63922	exon18			GATGCTCGCTTAC	BC018184	CCDS45371.1	16p13.3	2010-04-21	2003-12-09		ENSG00000127586	ENSG00000127586		"""ATPases / AAA-type"""	18435	protein-coding gene	gene with protein product		613201	"""chromosome 16 open reading frame 41"""	C16orf41		12171929	Standard	NM_022092		Approved	CHL12, C321D2.4, Ctf18	uc002cke.4	Q8WVB6	OTTHUMG00000047838	ENST00000262315.9:c.2391C>T	16.37:g.846012C>T		92.0	0.0	0		90.0	40.0	0.444444	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Silent	SNP	ENST00000262315.9	37	CCDS45371.1																																																																																			C|0.979;T|0.021	0.021	strong		0.642	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092	
HYPM	25763	hgsc.bcm.edu	37	X	37850385	37850385	+	Missense_Mutation	SNP	C	C	T	rs61737321		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:37850385C>T	ENST00000341016.3	+	1	316	c.293C>T	c.(292-294)gCt>gTt	p.A98V	TM4SF2_ENST00000465127.1_Intron	NM_012274.1	NP_036406.1	O75409	HYPM_HUMAN		98										central_nervous_system(2)|endometrium(3)|large_intestine(1)|lung(2)	8						CCCCACAGCGCTGAGAGTGAT	0.527													C|||	50	0.013245	0.0356	0.0043	3775	,	,		15106	0.0		0.0	False		,,,				2504	0.0				p.A98V		Atlas-SNP	.											.	CXorf27	14	.	0			c.C293T						PASS	.	C	VAL/ALA	116,3567		3,85,25,1468,546	99.0	104.0	102.0		293	-6.5	0.0	X	dbSNP_129	102	0,6600		0,0,0,2392,1816	yes	missense	CXorf27	NM_012274.1	64	3,85,25,3860,2362	TT,TC,T,CC,C		0.0,3.1496,1.1281	benign	98/118	37850385	116,10167	2127	4208	6335	SO:0001583	missense	25763	exon1			ACAGCGCTGAGAG																												ENST00000341016.3:c.293C>T	X.37:g.37850385C>T	ENSP00000339511:p.Ala98Val	152.0	0.0	0		209.0	105.0	0.502392	NM_012274	A1A4D3	Missense_Mutation	SNP	ENST00000341016.3	37	CCDS43929.1	10	0.006027727546714889	5	0.010245901639344262	2	0.005555555555555556	0	0.0	0	0.0	C	4.372	0.068603	0.08436	0.031496	0.0	ENSG00000187516	ENST00000341016	T	0.39787	1.06	3.24	-6.47	0.01902	Histone-fold (1);	.	.	.	.	T	0.04952	0.0133	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.13202	-1.0518	9	0.25751	T	0.34	.	1.5554	0.02583	0.1509:0.3307:0.3038:0.2146	rs61737321	98	O75409	HYPM_HUMAN	V	98	ENSP00000339511:A98V	ENSP00000339511:A98V	A	+	2	0	CXorf27	37735329	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.422000	0.02453	-1.678000	0.01454	-0.505000	0.04504	GCT	C|0.994;T|0.006	0.006	strong		0.527	CXorf27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080888.1		
CHMP6	79643	hgsc.bcm.edu	37	17	78972902	78972902	+	Silent	SNP	C	C	T	rs35687235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78972902C>T	ENST00000325167.5	+	8	633	c.555C>T	c.(553-555)aaC>aaT	p.N185N	CTD-2561B21.7_ENST00000577061.2_RNA|CTD-2561B21.7_ENST00000576215.1_RNA	NM_024591.4	NP_078867.2	Q96FZ7	CHMP6_HUMAN	charged multivesicular body protein 6	185					endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|viral life cycle (GO:0019058)|viral process (GO:0016032)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein N-terminus binding (GO:0047485)			lung(2)|ovary(1)	3	all_neural(118;0.101)		BRCA - Breast invasive adenocarcinoma(99;0.0175)|OV - Ovarian serous cystadenocarcinoma(97;0.0524)			CCACAGAAAACGTCCCTGTCA	0.622													C|||	144	0.028754	0.1059	0.0043	5008	,	,		19893	0.0		0.001	False		,,,				2504	0.0				p.N185N		Atlas-SNP	.											.	CHMP6	16	.	0			c.C555T						PASS	.	C		370,4036	187.1+/-213.8	18,334,1851	129.0	108.0	115.0		555	1.3	0.1	17	dbSNP_126	115	0,8600		0,0,4300	no	coding-synonymous	CHMP6	NM_024591.4		18,334,6151	TT,TC,CC		0.0,8.3976,2.8448		185/202	78972902	370,12636	2203	4300	6503	SO:0001819	synonymous_variant	79643	exon8			AGAAAACGTCCCT	BC010108	CCDS11774.1	17q25.3	2014-08-13	2011-09-21		ENSG00000176108	ENSG00000176108		"""Charged multivesicular body proteins"""	25675	protein-coding gene	gene with protein product		610901	"""chromatin modifying protein 6"""			11559748, 15511219	Standard	NM_024591		Approved	FLJ11749, VPS20	uc002jyw.4	Q96FZ7	OTTHUMG00000177645	ENST00000325167.5:c.555C>T	17.37:g.78972902C>T		93.0	0.0	0		89.0	52.0	0.58427	NM_024591	A8K7U0|Q53FU4|Q9HAE8	Silent	SNP	ENST00000325167.5	37	CCDS11774.1																																																																																			C|0.968;T|0.032	0.032	strong		0.622	CHMP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438215.1	NM_024591	
TBC1D4	9882	hgsc.bcm.edu	37	13	75861001	75861001	+	Missense_Mutation	SNP	A	A	G	rs557337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:75861001A>G	ENST00000377636.3	-	21	4170	c.3824T>C	c.(3823-3825)gTc>gCc	p.V1275A	TBC1D4_ENST00000425511.1_Missense_Mutation_p.V439A|TBC1D4_ENST00000431480.2_Missense_Mutation_p.V1267A|TBC1D4_ENST00000377625.2_Missense_Mutation_p.V1212A	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	1275			V -> A (in dbSNP:rs557337). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:19077034, ECO:0000269|PubMed:9628581}.		cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		GTCACAATTGACTAGAGCATC	0.463													G|||	873	0.174321	0.556	0.0778	5008	,	,		16760	0.0		0.0666	False		,,,				2504	0.0174				p.V1275A		Atlas-SNP	.											.	TBC1D4	142	.	0			c.T3824C						PASS	.	G	ALA/VAL	1770,2058		428,914,572	104.0	107.0	106.0		3824	3.9	0.0	13	dbSNP_83	106	484,7778		13,458,3660	yes	missense	TBC1D4	NM_014832.2	64	441,1372,4232	GG,GA,AA		5.8581,46.2382,18.6435	benign	1275/1299	75861001	2254,9836	1914	4131	6045	SO:0001583	missense	9882	exon21			CAATTGACTAGAG	AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"""Akt substrate of 160 kDa"""	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.3824T>C	13.37:g.75861001A>G	ENSP00000366863:p.Val1275Ala	312.0	0.0	0		333.0	166.0	0.498498	NM_014832	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Missense_Mutation	SNP	ENST00000377636.3	37	CCDS41901.1	333	0.15247252747252749	256	0.5203252032520326	32	0.08839779005524862	0	0.0	45	0.059366754617414245	G	0.218	-1.030972	0.02029	0.462382	0.058581	ENSG00000136111	ENST00000377636;ENST00000431480;ENST00000377625;ENST00000425511	T;T;T;T	0.03358	4.23;4.23;4.23;3.96	5.63	3.87	0.44632	.	0.297360	0.28841	N	0.013979	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.001;0.0;0.0	T	0.38329	-0.9666	9	0.02654	T	1	-5.6523	10.4567	0.44555	0.2148:0.0:0.7852:0.0	rs557337;rs52811417;rs60191388;rs557337	439;1212;1267;1275	O60343-4;O60343-2;O60343-3;O60343	.;.;.;TBCD4_HUMAN	A	1275;1267;1212;439	ENSP00000366863:V1275A;ENSP00000395986:V1267A;ENSP00000366852:V1212A;ENSP00000390654:V439A	ENSP00000366852:V1212A	V	-	2	0	TBC1D4	74759002	1.000000	0.71417	0.008000	0.14137	0.004000	0.04260	4.134000	0.57990	0.847000	0.35167	-0.119000	0.15052	GTC	A|0.827;G|0.173	0.173	strong		0.463	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832	
DENND1C	79958	hgsc.bcm.edu	37	19	6480013	6480013	+	Missense_Mutation	SNP	C	C	T	rs10416003	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6480013C>T	ENST00000381480.2	-	2	179	c.67G>A	c.(67-69)Gcc>Acc	p.A23T	DENND1C_ENST00000591030.1_Intron|DENND1C_ENST00000543576.1_Intron	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	23	UDENN.		A -> T (in dbSNP:rs10416003).		positive regulation of Rab GTPase activity (GO:0032851)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(3)|kidney(3)|large_intestine(1)|lung(3)	10						TGCAGGGAGGCAGGGCAGGCC	0.607													c|||	50	0.00998403	0.0363	0.0014	5008	,	,		16807	0.0		0.001	False		,,,				2504	0.0				p.A23T		Atlas-SNP	.											.	DENND1C	93	.	0			c.G67A						PASS	.	C	THR/ALA	144,3742		2,140,1801	34.0	39.0	37.0		67	-1.7	0.1	19	dbSNP_119	37	1,8255		0,1,4127	yes	missense	DENND1C	NM_024898.2	58	2,141,5928	TT,TC,CC		0.0121,3.7056,1.1942	benign	23/802	6480013	145,11997	1943	4128	6071	SO:0001583	missense	79958	exon2			GGGAGGCAGGGCA	AL713770	CCDS45938.1	19p13.3	2014-02-06	2005-08-17	2005-08-17	ENSG00000205744	ENSG00000205744		"""DENN/MADD domain containing"""	26225	protein-coding gene	gene with protein product		613634	"""family with sequence similarity 31, member C"""	FAM31C		12477932	Standard	XM_005259646		Approved	FLJ22757	uc002mfe.3	Q8IV53	OTTHUMG00000180853	ENST00000381480.2:c.67G>A	19.37:g.6480013C>T	ENSP00000370889:p.Ala23Thr	102.0	0.0	0		145.0	77.0	0.531034	NM_024898	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Missense_Mutation	SNP	ENST00000381480.2	37	CCDS45938.1	18	0.008241758241758242	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	c	9.626	1.135185	0.21123	0.037056	1.21E-4	ENSG00000205744	ENST00000381480	T	0.08193	3.12	4.95	-1.69	0.08186	uDENN (3);	0.538503	0.18725	N	0.132907	T	0.00695	0.0023	N	0.08118	0	0.09310	N	0.999995	B	0.16396	0.017	B	0.13407	0.009	T	0.44360	-0.9333	10	0.18710	T	0.47	-2.0715	5.3304	0.15930	0.0:0.4706:0.1479:0.3814	rs10416003;rs10416003	23	Q8IV53	DEN1C_HUMAN	T	23	ENSP00000370889:A23T	ENSP00000370889:A23T	A	-	1	0	DENND1C	6431013	0.003000	0.15002	0.132000	0.22025	0.862000	0.49288	-0.763000	0.04740	-0.080000	0.12685	0.558000	0.71614	GCC	C|0.991;T|0.009	0.009	strong		0.607	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2	NM_024898	
SEC62	7095	hgsc.bcm.edu	37	3	169700525	169700525	+	Silent	SNP	C	C	G	rs35176867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:169700525C>G	ENST00000337002.4	+	4	340	c.282C>G	c.(280-282)gcC>gcG	p.A94A	SEC62-AS1_ENST00000479626.1_RNA|SEC62_ENST00000480708.1_Silent_p.A94A	NM_003262.3	NP_003253.1	Q99442	SEC62_HUMAN	SEC62 homolog (S. cerevisiae)	94					cotranslational protein targeting to membrane (GO:0006613)|posttranslational protein targeting to membrane (GO:0006620)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			NS(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	9						TTCACCGAGCCCTAAAAGTAA	0.323													C|||	102	0.0203674	0.0749	0.0043	5008	,	,		16024	0.0		0.0	False		,,,				2504	0.0				p.A94A		Atlas-SNP	.											.	SEC62	27	.	0			c.C282G						PASS	.	C		246,4122	129.0+/-165.8	11,224,1949	63.0	75.0	71.0		282	-2.3	0.9	3	dbSNP_126	71	0,8592		0,0,4296	no	coding-synonymous	SEC62	NM_003262.3		11,224,6245	GG,GC,CC		0.0,5.6319,1.8981		94/400	169700525	246,12714	2184	4296	6480	SO:0001819	synonymous_variant	7095	exon4			CCGAGCCCTAAAA	D87127	CCDS3210.1	3q26.2	2008-04-22	2008-04-22	2008-04-22	ENSG00000008952	ENSG00000008952			11846	protein-coding gene	gene with protein product		602173	"""translocation protein 1"""	TLOC1		9020021, 10799540	Standard	NM_003262		Approved	Dtrp1, HTP1	uc003fgh.3	Q99442	OTTHUMG00000158753	ENST00000337002.4:c.282C>G	3.37:g.169700525C>G		176.0	0.0	0		195.0	98.0	0.502564	NM_003262	D3DNQ0|O00682|O00729	Silent	SNP	ENST00000337002.4	37	CCDS3210.1																																																																																			C|0.983;G|0.017	0.017	strong		0.323	SEC62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352043.1		
PRKCG	5582	hgsc.bcm.edu	37	19	54410114	54410114	+	Missense_Mutation	SNP	A	A	G	rs73937614	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54410114A>G	ENST00000263431.3	+	18	2341	c.2059A>G	c.(2059-2061)Agc>Ggc	p.S687G	PRKCG_ENST00000540413.1_Missense_Mutation_p.S687G|PRKCG_ENST00000542049.1_Missense_Mutation_p.S538G|CACNG7_ENST00000391767.1_5'Flank	NM_002739.3	NP_002730.1	P05129	KPCG_HUMAN	protein kinase C, gamma	687					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cell death (GO:0008219)|chemosensory behavior (GO:0007635)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|learning or memory (GO:0007611)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of protein ubiquitination (GO:0031397)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of mismatch repair (GO:0032425)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to morphine (GO:0043278)|response to pain (GO:0048265)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|synaptic membrane (GO:0097060)	ATP binding (GO:0005524)|calcium-dependent protein kinase C activity (GO:0004698)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(4)|ovary(2)|pancreas(2)|skin(1)	10	all_cancers(19;0.0462)|all_epithelial(19;0.0258)|all_lung(19;0.185)|Ovarian(34;0.19)|Lung NSC(19;0.218)			GBM - Glioblastoma multiforme(134;0.0521)	Tamoxifen(DB00675)	GGATGCCCGCAGCCCCACCAG	0.677											OREG0025667	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	58	0.0115815	0.0408	0.0058	5008	,	,		12287	0.0		0.0	False		,,,				2504	0.0				p.S687G		Atlas-SNP	.											.	PRKCG	246	.	0			c.A2059G						PASS	.	A	GLY/SER	118,4288	81.9+/-120.4	1,116,2086	38.0	48.0	45.0		2059	2.1	1.0	19	dbSNP_130	45	1,8597		0,1,4298	yes	missense	PRKCG	NM_002739.3	56	1,117,6384	GG,GA,AA		0.0116,2.6782,0.9151	possibly-damaging	687/698	54410114	119,12885	2203	4299	6502	SO:0001583	missense	5582	exon18			GCCCGCAGCCCCA	M13977	CCDS12867.1	19q13.4	2014-09-17			ENSG00000126583	ENSG00000126583	2.7.11.1		9402	protein-coding gene	gene with protein product	"""PKC-gamma"""	176980		PKCG, SCA14		8432525, 3755548	Standard	NM_002739		Approved	PKCC, MGC57564	uc002qcq.1	P05129	OTTHUMG00000064846	ENST00000263431.3:c.2059A>G	19.37:g.54410114A>G	ENSP00000263431:p.Ser687Gly	180.0	0.0	0	1000	208.0	89.0	0.427885	NM_002739	B7Z8Q0	Missense_Mutation	SNP	ENST00000263431.3	37	CCDS12867.1	13	0.005952380952380952	12	0.024390243902439025	1	0.0027624309392265192	0	0.0	0	0.0	A	16.20	3.056968	0.55325	0.026782	1.16E-4	ENSG00000126583	ENST00000540413;ENST00000263431;ENST00000542049	T;T;T	0.70631	-0.5;-0.5;-0.5	4.23	2.1	0.27182	.	.	.	.	.	T	0.33527	0.0866	L	0.43152	1.355	0.24531	N	0.994117	B;B;B	0.26876	0.118;0.041;0.162	B;B;B	0.24394	0.017;0.004;0.053	T	0.45041	-0.9288	9	0.59425	D	0.04	.	4.5914	0.12307	0.7265:0.0:0.0996:0.1739	.	538;687;687	B7Z8Q0;F5H5C4;P05129	.;.;KPCG_HUMAN	G	687;687;538	ENSP00000443493:S687G;ENSP00000263431:S687G;ENSP00000438090:S538G	ENSP00000263431:S687G	S	+	1	0	PRKCG	59101926	0.991000	0.36638	1.000000	0.80357	0.980000	0.70556	1.765000	0.38481	0.752000	0.32923	-0.496000	0.04628	AGC	A|0.993;G|0.007	0.007	strong		0.677	PRKCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139233.3	NM_002739	
MUC4	4585	hgsc.bcm.edu	37	3	195505863	195505863	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195505863G>A	ENST00000463781.3	-	2	13047	c.12588C>T	c.(12586-12588)acC>acT	p.T4196T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.T4196T	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.T4196T(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)		AGGAAGTGTCGGTGACAGGAA	0.607																																					p.T4196T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - coding silent(1)	prostate(1)	c.C12588T						scavenged	.						19.0	14.0	16.0					3																	195505863		689	1578	2267	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.12588C>T	3.37:g.195505863G>A		198.0	0.0	0		297.0	15.0	0.050505	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		0.607	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
EGR4	1961	hgsc.bcm.edu	37	2	73518716	73518716	+	Missense_Mutation	SNP	C	C	T	rs141733943	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:73518716C>T	ENST00000545030.1	-	2	1713	c.1639G>A	c.(1639-1641)Ggc>Agc	p.G547S	EGR4_ENST00000436467.2_Missense_Mutation_p.G444S	NM_001965.3	NP_001956.3	Q05215	EGR4_HUMAN	early growth response 4	547					cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						AAGCGGCGGCCGCACACGTCG	0.662													C|||	2	0.000399361	0.0015	0.0	5008	,	,		12645	0.0		0.0	False		,,,				2504	0.0				p.G547S		Atlas-SNP	.											.	EGR4	52	.	0			c.G1639A						PASS	.	C	SER/GLY	2,4404		0,2,2201	24.0	28.0	27.0		1639	4.8	1.0	2	dbSNP_134	27	0,8596		0,0,4298	no	missense	EGR4	NM_001965.3	56	0,2,6499	TT,TC,CC		0.0,0.0454,0.0154	probably-damaging	547/590	73518716	2,13000	2203	4298	6501	SO:0001583	missense	1961	exon2			GGCGGCCGCACAC		CCDS1925.2	2p13	2013-01-08			ENSG00000135625	ENSG00000135625		"""Zinc fingers, C2H2-type"""	3241	protein-coding gene	gene with protein product		128992				1584812	Standard	NM_001965		Approved	NGFI-C, PAT133	uc010yrj.2	Q05215	OTTHUMG00000129774	ENST00000545030.1:c.1639G>A	2.37:g.73518716C>T	ENSP00000445626:p.Gly547Ser	146.0	0.0	0		176.0	99.0	0.5625	NM_001965	B2RAE3|G3V1T5|Q2Z1P5	Missense_Mutation	SNP	ENST00000545030.1	37	CCDS1925.2	.	.	.	.	.	.	.	.	.	.	C	31	5.103602	0.94245	4.54E-4	0.0	ENSG00000135625	ENST00000545030;ENST00000436467	T;T	0.07216	3.21;3.21	4.79	4.79	0.61399	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.64402	D	0.000005	T	0.20780	0.0500	L	0.37897	1.145	0.58432	D	0.999998	D;D	0.89917	1.0;1.0	D;D	0.77557	0.989;0.99	T	0.00715	-1.1597	10	0.87932	D	0	-21.0702	16.5595	0.84535	0.0:1.0:0.0:0.0	.	444;547	Q05215;G3V1T5	EGR4_HUMAN;.	S	547;444	ENSP00000445626:G547S;ENSP00000419687:G444S	ENSP00000419687:G444S	G	-	1	0	EGR4	73372224	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.631000	0.83237	2.478000	0.83669	0.655000	0.94253	GGC	C|1.000;T|0.000	0.000	weak		0.662	EGR4-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001965	
TTN	7273	hgsc.bcm.edu	37	2	179428061	179428061	+	Missense_Mutation	SNP	C	C	T	rs11896637	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179428061C>T	ENST00000591111.1	-	276	78099	c.77875G>A	c.(77875-77877)Gca>Aca	p.A25959T	TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.A18727T|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.A25032T|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.A18660T|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.A18535T|TTN_ENST00000589042.1_Missense_Mutation_p.A27600T			Q8WZ42	TITIN_HUMAN	titin	25959	Fibronectin type-III 89. {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)			TTAACAGGTGCGCCACCATCA	0.493													C|||	178	0.0355431	0.1256	0.0159	5008	,	,		21438	0.0		0.001	False		,,,				2504	0.0				p.A27600T		Atlas-SNP	.											.	TTN	18412	.	0			c.G82798A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA	398,3684		21,356,1664	72.0	71.0	71.0		56179,55978,75094,55603	3.9	0.3	2	dbSNP_120	71	8,8402		0,8,4197	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	58,58,58,58	21,364,5861	TT,TC,CC		0.0951,9.7501,3.2501	benign,benign,benign,benign	18727/27119,18660/27052,25032/33424,18535/26927	179428061	406,12086	2041	4205	6246	SO:0001583	missense	7273	exon326			CAGGTGCGCCACC	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.77875G>A	2.37:g.179428061C>T	ENSP00000465570:p.Ala25959Thr	198.0	0.0	0		238.0	115.0	0.483193	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		85	0.03891941391941392	77	0.1565040650406504	8	0.022099447513812154	0	0.0	0	0.0	C	18.20	3.570710	0.65765	0.097501	9.51E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57907	0.37;0.37;0.37;0.37	5.74	3.93	0.45458	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00241	0.0007	L	0.47190	1.495	0.19300	P	0.9999757677	B;B;B;B	0.22414	0.069;0.069;0.069;0.02	B;B;B;B	0.17433	0.018;0.018;0.018;0.018	T	0.06481	-1.0824	8	0.87932	D	0	.	12.9829	0.58575	0.0:0.8666:0.0:0.1334	rs11896637;rs52798942;rs11896637	18535;18660;18727;25959	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	25032;18535;18727;18660;18533	ENSP00000343764:A25032T;ENSP00000434586:A18535T;ENSP00000340554:A18727T;ENSP00000352154:A18660T	ENSP00000340554:A18727T	A	-	1	0	TTN	179136307	0.999000	0.42202	0.344000	0.25628	0.992000	0.81027	4.111000	0.57838	0.755000	0.32990	0.563000	0.77884	GCA	C|0.965;T|0.035	0.035	strong		0.493	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TNXB	7148	hgsc.bcm.edu	37	6	32041621	32041621	+	Missense_Mutation	SNP	G	G	A	rs6910390	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32041621G>A	ENST00000375244.3	-	12	4685	c.4484C>T	c.(4483-4485)aCa>aTa	p.T1495I	TNXB_ENST00000375247.2_Missense_Mutation_p.T1495I			P22105	TENX_HUMAN	tenascin XB	1582	Fibronectin type-III 7. {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						CTCGGGGACTGTCCAGGAGAG	0.627													G|||	27	0.00539137	0.0159	0.0058	5008	,	,		13775	0.0		0.002	False		,,,				2504	0.0				p.T1495I		Atlas-SNP	.											.	TNXB	553	.	0			c.C4484T						PASS	.	G	ILE/THR	33,2523		1,31,1246	29.0	31.0	30.0		4484	1.5	0.1	6	dbSNP_116	30	30,5096		0,30,2533	yes	missense	TNXB	NM_019105.6	89	1,61,3779	AA,AG,GG		0.5853,1.2911,0.8201	benign	1495/4243	32041621	63,7619	1278	2563	3841	SO:0001583	missense	7148	exon12			GGGACTGTCCAGG	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.4484C>T	6.37:g.32041621G>A	ENSP00000364393:p.Thr1495Ile	182.0	0.0	0		190.0	100.0	0.526316	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		18	0.008241758241758242	11	0.022357723577235773	3	0.008287292817679558	1	0.0017482517482517483	3	0.00395778364116095	G	4.859	0.159720	0.09287	0.012911	0.005853	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.59083	0.29;0.29	5.46	1.54	0.23209	.	0.993930	0.08149	N	0.990366	T	0.44456	0.1294	M	0.82823	2.61	0.19945	N	0.999944	B	0.28552	0.215	B	0.36845	0.234	T	0.51934	-0.8642	10	0.38643	T	0.18	.	7.6751	0.28481	0.3741:0.0:0.6259:0.0	rs6910390	1495	P22105-3	.	I	1495	ENSP00000364393:T1495I;ENSP00000364396:T1495I	ENSP00000364393:T1495I	T	-	2	0	TNXB	32149599	0.384000	0.25164	0.076000	0.20297	0.007000	0.05969	0.499000	0.22546	-0.013000	0.14199	-1.178000	0.01721	ACA	G|0.992;A|0.008	0.008	strong		0.627	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
SPINK1	6690	hgsc.bcm.edu	37	5	147207605	147207605	+	Silent	SNP	G	G	A	rs35737774	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:147207605G>A	ENST00000296695.5	-	3	382	c.174C>T	c.(172-174)tgC>tgT	p.C58C	SPINK1_ENST00000510027.2_Silent_p.C58C	NM_003122.3	NP_003113.2	P00995	ISK1_HUMAN	serine peptidase inhibitor, Kazal type 1	58	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				negative regulation of calcium ion import (GO:0090281)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of serine-type endopeptidase activity (GO:1900004)|regulation of acrosome reaction (GO:0060046)|regulation of store-operated calcium entry (GO:2001256)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(1)|skin(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AACATAACACGCATTCATTGG	0.323									Hereditary Pancreatitis																												p.C58C		Atlas-SNP	.											.	SPINK1	9	.	0			c.C174T						PASS	.	G		624,3782	272.5+/-270.8	42,540,1621	102.0	95.0	97.0		174	-1.0	0.0	5	dbSNP_126	97	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SPINK1	NM_003122.3		42,541,5920	AA,AG,GG		0.0116,14.1625,4.8055		58/80	147207605	625,12381	2203	4300	6503	SO:0001819	synonymous_variant	6690	exon3	Familial Cancer Database		TAACACGCATTCA		CCDS4286.1	5q32	2011-08-31	2005-08-17		ENSG00000164266	ENSG00000164266		"""Serine peptidase inhibitors, Kazal type"""	11244	protein-coding gene	gene with protein product		167790	"""serine protease inhibitor, Kazal type 1"""				Standard	XM_005268501		Approved	Spink3, PCTT, PSTI, TATI	uc003los.2	P00995	OTTHUMG00000129730	ENST00000296695.5:c.174C>T	5.37:g.147207605G>A		42.0	0.0	0		41.0	41.0	1	NM_003122		Silent	SNP	ENST00000296695.5	37	CCDS4286.1																																																																																			G|0.956;A|0.044	0.044	strong		0.323	SPINK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251940.2	NM_003122	
CSNK2A3	283106	hgsc.bcm.edu	37	11	11373631	11373631	+	Missense_Mutation	SNP	C	C	T	rs74507390	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:11373631C>T	ENST00000528848.2	-	1	1273	c.1036G>A	c.(1036-1038)Gtc>Atc	p.V346I	RP11-567I13.1_ENST00000526867.1_RNA|GALNT18_ENST00000227756.4_Intron	NM_001256686.1	NP_001243615.1	Q8NEV1	CSK23_HUMAN	casein kinase 2, alpha 3 polypeptide	346					positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)		ATP binding (GO:0005524)|protein phosphatase regulator activity (GO:0019888)|protein serine/threonine kinase activity (GO:0004674)										GCGCTGCTGACGGGCGTACTG	0.567													-|||	208	0.0415335	0.1483	0.0173	5008	,	,		18472	0.0		0.0	False		,,,				2504	0.0				p.V346I		Atlas-SNP	.											.	.	.	.	0			c.G1036A						PASS	.																																			SO:0001583	missense	283106	exon1			TGCTGACGGGCGT	X64692	CCDS59224.1	11p15.3	2013-01-18	2013-01-17	2013-01-17	ENSG00000254598	ENSG00000254598			2458	protein-coding gene	gene with protein product			"""casein kinase 2, alpha 1 polypeptide pseudogene"""	CSNK2A1P		12102635, 1610905, 20625391	Standard	NM_001256686		Approved		uc001mjp.4	Q8NEV1	OTTHUMG00000165708	ENST00000528848.2:c.1036G>A	11.37:g.11373631C>T	ENSP00000473553:p.Val346Ile	126.0	0.0	0		100.0	50.0	0.5	NM_001256686		Missense_Mutation	SNP	ENST00000528848.2	37	CCDS59224.1																																																																																			C|0.965;T|0.035	0.035	strong		0.567	CSNK2A3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385850.3	NM_001256686	
MYH9	4627	hgsc.bcm.edu	37	22	36678816	36678816	+	Silent	SNP	C	C	A	rs80050551	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:36678816C>A	ENST00000216181.5	-	41	6011	c.5781G>T	c.(5779-5781)ccG>ccT	p.P1927P	MYH9_ENST00000475726.1_5'Flank	NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1927					actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)	p.P1927P(1)		NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						GCACGACAAACGGCAGGTCCC	0.672			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated				.|||	138	0.0275559	0.0991	0.0101	5008	,	,		14735	0.0		0.0	False		,,,				2504	0.0				p.P1927P		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	MYH9,NS,NS,0,1	MYH9	225	1	1	Substitution - coding silent(1)	pancreas(1)	c.G5781T						PASS	.			364,4042	178.0+/-206.8	14,336,1853	34.0	30.0	32.0		5781	-7.5	0.7	22	dbSNP_131	32	5,8593	3.0+/-9.4	0,5,4294	no	coding-synonymous	MYH9	NM_002473.4		14,341,6147	AA,AC,CC		0.0582,8.2615,2.8376		1927/1961	36678816	369,12635	2203	4299	6502	SO:0001819	synonymous_variant	4627	exon41	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	GACAAACGGCAGG		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"""Myosins / Myosin superfamily : Class II"""	7579	protein-coding gene	gene with protein product	"""nonmuscle myosin heavy chain II-A"""	160775	"""myosin, heavy polypeptide 9, non-muscle"""	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.5781G>T	22.37:g.36678816C>A		28.0	0.0	0		42.0	26.0	0.619048	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Silent	SNP	ENST00000216181.5	37	CCDS13927.1																																																																																			C|0.969;A|0.031	0.031	strong		0.672	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473	
KRTAP10-4	386672	hgsc.bcm.edu	37	21	45993990	45993990	+	Missense_Mutation	SNP	T	T	C	rs79601471		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45993990T>C	ENST00000400374.3	+	1	385	c.355T>C	c.(355-357)Tgc>Cgc	p.C119R	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_5'Flank	NM_198687.1	NP_941960.1	P60372	KR104_HUMAN	keratin associated protein 10-4	119	36 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(1)	18						CAAGACTGTCTGCTGCAAGCC	0.647																																					p.C119R		Atlas-SNP	.											.	KRTAP10-4	44	.	0			c.T355C						PASS	.	T	ARG/CYS,	498,3906		0,498,1704	117.0	107.0	111.0		355,	3.2	0.5	21	dbSNP_131	111	2,8590		0,2,4294	no	missense,intron	TSPEAR,KRTAP10-4	NM_198687.1,NM_144991.2	180,	0,500,5998	CC,CT,TT		0.0233,11.3079,3.8473	probably-damaging,	119/402,	45993990	500,12496	2202	4296	6498	SO:0001583	missense	386672	exon1			ACTGTCTGCTGCA	AB076351	CCDS42957.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000215454	ENSG00000215454		"""Keratin associated proteins"""	20521	protein-coding gene	gene with protein product			"""keratin associated protein 18-4"""	KRTAP18-4			Standard	NM_198687		Approved	KRTAP18.4, KAP10.4	uc002zfk.1	P60372	OTTHUMG00000057641	ENST00000400374.3:c.355T>C	21.37:g.45993990T>C	ENSP00000383225:p.Cys119Arg	575.0	0.0	0		530.0	140.0	0.264151	NM_198687	Q08AS0	Missense_Mutation	SNP	ENST00000400374.3	37	CCDS42957.1	97	0.044413919413919416	86	0.17479674796747968	11	0.03038674033149171	0	0.0	0	0.0	N	6.327	0.428441	0.11987	0.113079	2.33E-4	ENSG00000215454	ENST00000400374	T	0.01043	5.41	4.37	3.18	0.36537	.	.	.	.	.	T	0.00012	0.0000	M	0.90870	3.155	0.23780	P	0.99686138	D	0.54772	0.968	P	0.50970	0.655	T	0.16928	-1.0386	8	0.87932	D	0	.	7.1933	0.25839	0.3572:0.0:0.0:0.6428	.	119	P60372	KR104_HUMAN	R	119	ENSP00000383225:C119R	ENSP00000383225:C119R	C	+	1	0	KRTAP10-4	44818418	0.622000	0.27085	0.456000	0.27044	0.149000	0.21700	0.699000	0.25586	0.514000	0.28300	0.386000	0.25728	TGC	T|0.955;C|0.045	0.045	strong		0.647	KRTAP10-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128045.1	NM_198687	
SIGLEC1	6614	hgsc.bcm.edu	37	20	3670646	3670646	+	Silent	SNP	C	C	T	rs8115679	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:3670646C>T	ENST00000344754.4	-	18	4856	c.4857G>A	c.(4855-4857)ctG>ctA	p.L1619L	SIGLEC1_ENST00000202578.4_Silent_p.L1619L	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	1619	Ig-like C2-type 16.				cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						AGGCAGAGCCCAGGACATTTG	0.597													C|||	117	0.0233626	0.0862	0.0043	5008	,	,		19707	0.0		0.0	False		,,,				2504	0.0				p.L1619L		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.G4857A						PASS	.	C		310,4094	164.4+/-196.0	11,288,1903	44.0	38.0	40.0		4857	4.6	1.0	20	dbSNP_116	40	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SIGLEC1	NM_023068.3		11,290,6201	TT,TC,CC		0.0233,7.0391,2.3993		1619/1710	3670646	312,12692	2202	4300	6502	SO:0001819	synonymous_variant	6614	exon18			AGAGCCCAGGACA	AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	11127	protein-coding gene	gene with protein product		600751	"""sialoadhesin"""	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.4857G>A	20.37:g.3670646C>T		178.0	0.0	0		178.0	75.0	0.421348	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Silent	SNP	ENST00000344754.4	37	CCDS13060.1	33	0.01510989010989011	32	0.06504065040650407	1	0.0027624309392265192	0	0.0	0	0.0	C	8.307	0.821130	0.16678	0.070391	2.33E-4	ENSG00000088827	ENST00000419548	.	.	.	5.55	4.6	0.57074	.	.	.	.	.	T	0.12305	0.0299	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.21211	-1.0252	4	.	.	.	.	12.3752	0.55275	0.0:0.8305:0.1695:0.0	rs8115679;rs8115679	.	.	.	R	433	.	.	G	-	1	0	SIGLEC1	3618646	1.000000	0.71417	0.996000	0.52242	0.785000	0.44390	1.377000	0.34317	1.320000	0.45209	0.561000	0.74099	GGG	C|0.974;T|0.026	0.026	strong		0.597	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068	
RAI14	26064	hgsc.bcm.edu	37	5	34687817	34687817	+	Intron	SNP	T	T	C	rs10521016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:34687817T>C	ENST00000265109.3	+	2	323				RAI14_ENST00000512629.1_Intron|RAI14_ENST00000503673.1_Intron|RAI14_ENST00000515799.1_Intron|RAI14_ENST00000506376.1_Start_Codon_SNP_p.M1T|RAI14_ENST00000428746.2_Intron	NM_001145522.1|NM_015577.2	NP_001138994.1|NP_056392.2	Q9P0K7	RAI14_HUMAN	retinoic acid induced 14							actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(19)|lung(22)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(31;0.000191)					GGGAATTAGATGGAAGCCAAG	0.413													T|||	143	0.0285543	0.1044	0.0072	5008	,	,		19536	0.0		0.0	False		,,,				2504	0.0				p.M1T		Atlas-SNP	.											.	RAI14	100	.	0			c.T2C						PASS	.						187.0	157.0	166.0					5																	34687817		692	1591	2283	SO:0001627	intron_variant	26064	exon1			ATTAGATGGAAGC	AB037755	CCDS34142.1, CCDS54837.1, CCDS54838.1, CCDS54839.1	5p13.3-p13.2	2013-01-10			ENSG00000039560	ENSG00000039560		"""Ankyrin repeat domain containing"""	14873	protein-coding gene	gene with protein product	"""novel retinal pigment epithelial"""	606586				11042181	Standard	NM_015577		Approved	NORPEG, KIAA1334, RAI13, DKFZp564G013	uc011coj.2	Q9P0K7	OTTHUMG00000162019	ENST00000265109.3:c.36+757T>C	5.37:g.34687817T>C		150.0	0.0	0		181.0	180.0	0.994475	NM_001145523	E9PED3|Q6V1W9|Q7Z5I4|Q7Z733|Q9P2L2|Q9Y3T5	Missense_Mutation	SNP	ENST00000265109.3	37	CCDS34142.1	67	0.030677655677655676	65	0.13211382113821138	2	0.0055248618784530384	0	0.0	0	0.0	T	7.737	0.700548	0.15106	.	.	ENSG00000039560	ENST00000506376	T	0.33654	1.4	5.19	-0.0796	0.13710	.	.	.	.	.	T	0.00210	0.0006	.	.	.	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.21518	-1.0243	8	0.56958	D	0.05	.	0.6567	0.00835	0.1705:0.1874:0.1658:0.4763	rs10521016;rs56487933;rs10521016	1	Q9P0K7-3	.	T	1	ENSP00000423854:M1T	ENSP00000423854:M1T	M	+	2	0	RAI14	34723574	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.023000	0.12456	-0.143000	0.11334	-1.087000	0.02190	ATG	T|0.955;C|0.045	0.045	strong		0.413	RAI14-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366786.1	NM_015577	
DCHS2	54798	hgsc.bcm.edu	37	4	155219373	155219373	+	Silent	SNP	A	A	G	rs17031391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:155219373A>G	ENST00000357232.4	-	18	4727	c.4728T>C	c.(4726-4728)gtT>gtC	p.V1576V		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1576	Cadherin 13. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		CATTGTCATTAACATCAGTGA	0.438													A|||	405	0.0808706	0.2602	0.0418	5008	,	,		19929	0.0109		0.0179	False		,,,				2504	0.0031				p.V1576V		Atlas-SNP	.											.	DCHS2	594	.	0			c.T4728C						PASS	.	A		945,3461	361.4+/-315.7	116,713,1374	103.0	102.0	102.0		4728	-1.4	1.0	4	dbSNP_123	102	148,8452	72.6+/-135.2	3,142,4155	no	coding-synonymous	DCHS2	NM_017639.3		119,855,5529	GG,GA,AA		1.7209,21.448,8.4038		1576/2917	155219373	1093,11913	2203	4300	6503	SO:0001819	synonymous_variant	54798	exon18			GTCATTAACATCA	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.4728T>C	4.37:g.155219373A>G		199.0	0.0	0		214.0	98.0	0.457944	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Silent	SNP	ENST00000357232.4	37	CCDS3785.1																																																																																			A|0.913;G|0.087	0.087	strong		0.438	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
OR5B2	390190	hgsc.bcm.edu	37	11	58190228	58190228	+	Silent	SNP	G	G	A	rs77952368	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:58190228G>A	ENST00000302581.2	-	1	558	c.507C>T	c.(505-507)tcC>tcT	p.S169S		NM_001005566.2	NP_001005566.1	Q96R09	OR5B2_HUMAN	olfactory receptor, family 5, subfamily B, member 2	169						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|large_intestine(2)|lung(19)|ovary(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				GTACCAGATTGGATTTACAGA	0.453													G|||	26	0.00519169	0.0182	0.0029	5008	,	,		22719	0.0		0.0	False		,,,				2504	0.0				p.S169S		Atlas-SNP	.											OR5B2,NS,carcinoma,-1,1	OR5B2	75	1	0			c.C507T						PASS	.	G		59,4343	56.2+/-92.4	1,57,2143	61.0	57.0	58.0		507	1.8	0.0	11	dbSNP_131	58	1,8589		0,1,4294	no	coding-synonymous	OR5B2	NM_001005566.2		1,58,6437	AA,AG,GG		0.0116,1.3403,0.4618		169/310	58190228	60,12932	2201	4295	6496	SO:0001819	synonymous_variant	390190	exon1			CAGATTGGATTTA	AB065852	CCDS31550.1	11q12.1	2012-08-09			ENSG00000172365	ENSG00000172365		"""GPCR / Class A : Olfactory receptors"""	8323	protein-coding gene	gene with protein product							Standard	NM_001005566		Approved	OST073	uc010rkg.2	Q96R09	OTTHUMG00000167517	ENST00000302581.2:c.507C>T	11.37:g.58190228G>A		60.0	0.0	0		72.0	43.0	0.597222	NM_001005566	B2RNJ6|B9EGY7|Q6IEV7|Q8NGF5	Silent	SNP	ENST00000302581.2	37	CCDS31550.1																																																																																			G|0.993;A|0.007	0.007	strong		0.453	OR5B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394887.2	NM_001005566	
IFNA5	3442	hgsc.bcm.edu	37	9	21305048	21305048	+	Missense_Mutation	SNP	G	G	C	rs138121530	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21305048G>C	ENST00000259555.4	-	1	264	c.208C>G	c.(208-210)Cag>Gag	p.Q70E		NM_002169.2	NP_002160.1	P01569	IFNA5_HUMAN	interferon, alpha 5	70					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)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)	7				Lung(24;2.34e-24)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		TTCTGGAACTGGTTGCCATCA	0.473													G|||	60	0.0119808	0.0439	0.0029	5008	,	,		23310	0.0		0.0	False		,,,				2504	0.0				p.Q70E		Atlas-SNP	.											.	IFNA5	21	.	0			c.C208G						PASS	.	G	GLU/GLN	212,4194	131.0+/-167.6	3,206,1994	139.0	130.0	133.0		208	4.2	0.0	9	dbSNP_134	133	2,8598	2.2+/-6.3	0,2,4298	no	missense	IFNA5	NM_002169.2	29	3,208,6292	CC,CG,GG		0.0233,4.8116,1.6454	benign	70/190	21305048	214,12792	2203	4300	6503	SO:0001583	missense	3442	exon1			GGAACTGGTTGCC		CCDS6502.1	9p22	2010-08-24			ENSG00000147873	ENSG00000147873		"""Interferons"""	5426	protein-coding gene	gene with protein product		147565				1385305	Standard	NM_002169		Approved	IFN-alphaG	uc011lnh.2	P01569	OTTHUMG00000019664	ENST00000259555.4:c.208C>G	9.37:g.21305048G>C	ENSP00000259555:p.Gln70Glu	332.0	0.0	0		288.0	138.0	0.479167	NM_002169	Q52LX3	Missense_Mutation	SNP	ENST00000259555.4	37	CCDS6502.1	18	0.008241758241758242	18	0.036585365853658534	0	0.0	0	0.0	0	0.0	G	13.34	2.206733	0.39003	0.048116	2.33E-4	ENSG00000147873	ENST00000259555	T	0.04275	3.66	4.16	4.16	0.48862	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.474897	0.22261	N	0.062416	T	0.02610	0.0079	M	0.85373	2.75	0.09310	N	1	B	0.25743	0.133	P	0.45712	0.491	T	0.02596	-1.1136	10	0.72032	D	0.01	.	10.4841	0.44711	0.0:0.1982:0.8018:0.0	.	70	P01569	IFNA5_HUMAN	E	70	ENSP00000259555:Q70E	ENSP00000259555:Q70E	Q	-	1	0	IFNA5	21295048	0.002000	0.14202	0.014000	0.15608	0.007000	0.05969	1.019000	0.30014	2.052000	0.61016	0.537000	0.68136	CAG	G|0.984;C|0.016	0.016	strong		0.473	IFNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051893.1	NM_002169	
CD33	945	hgsc.bcm.edu	37	19	51729594	51729594	+	Missense_Mutation	SNP	T	T	C	rs11882250|rs201473304	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51729594T>C	ENST00000262262.4	+	4	748	c.727T>C	c.(727-729)Ttt>Ctt	p.F243L	CD33_ENST00000421133.2_Missense_Mutation_p.F116L|CD33_ENST00000436584.2_Missense_Mutation_p.F116L|CD33_ENST00000391796.3_Missense_Mutation_p.F243L	NM_001772.3	NP_001763.3	P20138	CD33_HUMAN	CD33 molecule	243			F -> L (in dbSNP:rs11882250).		cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|negative regulation of cell proliferation (GO:0008285)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(15)|skin(1)|stomach(1)	24		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000224)|OV - Ovarian serous cystadenocarcinoma(262;0.00468)	Gemtuzumab ozogamicin(DB00056)	AACTGGTATCTTTCCAGGAGA	0.502													t|||	186	0.0371406	0.1271	0.0245	5008	,	,		18721	0.0		0.001	False		,,,				2504	0.0				p.F243L		Atlas-SNP	.											.	CD33	55	.	0			c.T727C						PASS	.	T	LEU/PHE,LEU/PHE,LEU/PHE	478,3928		26,426,1751	92.0	86.0	88.0		346,727,727	2.9	0.0	19	dbSNP_120	88	4,8596		0,4,4296	yes	missense,missense,missense	CD33	NM_001082618.1,NM_001177608.1,NM_001772.3	22,22,22	26,430,6047	CC,CT,TT		0.0465,10.8488,3.706	benign,benign,benign	116/238,243/311,243/365	51729594	482,12524	2203	4300	6503	SO:0001583	missense	945	exon4			GGTATCTTTCCAG	M23197	CCDS33084.1, CCDS46157.1, CCDS54299.1	19q13.3	2013-01-29	2006-03-28		ENSG00000105383	ENSG00000105383		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1659	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 3"""	159590	"""CD33 antigen (gp67)"""			3139766, 9465907	Standard	NM_001772		Approved	SIGLEC3, SIGLEC-3, p67, FLJ00391	uc002pwa.2	P20138		ENST00000262262.4:c.727T>C	19.37:g.51729594T>C	ENSP00000262262:p.Phe243Leu	94.0	0.0	0		108.0	56.0	0.518519	NM_001772	B4E3P8|C9JEN7|F8WAL2|Q8TD24	Missense_Mutation	SNP	ENST00000262262.4	37	CCDS33084.1	64	0.029304029304029304	51	0.10365853658536585	12	0.03314917127071823	0	0.0	1	0.0013192612137203166	.	9.409	1.079972	0.20309	0.108488	4.65E-4	ENSG00000105383	ENST00000436584;ENST00000262262;ENST00000421133;ENST00000391796	T;T;T;T	0.34667	1.35;2.53;1.55;2.36	2.88	2.88	0.33553	.	.	.	.	.	T	0.00496	0.0016	L	0.40543	1.245	0.80722	P	0.0	B;B;B	0.26975	0.066;0.165;0.048	B;B;B	0.23852	0.028;0.049;0.023	T	0.06935	-1.0799	8	0.33141	T	0.24	.	7.4754	0.27374	0.0:0.0:0.0:1.0	rs11882250;rs52835930;rs56510285;rs57266763;rs11882250	116;243;243	C9JEN7;F8WAL2;P20138	.;.;CD33_HUMAN	L	116;243;116;243	ENSP00000403331:F116L;ENSP00000262262:F243L;ENSP00000410126:F116L;ENSP00000375673:F243L	ENSP00000262262:F243L	F	+	1	0	CD33	56421406	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	0.212000	0.17497	1.322000	0.45245	0.379000	0.24179	TTT	T|0.958;C|0.042	0.042	strong		0.502	CD33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464199.2	NM_001772	
PDE3A	5139	hgsc.bcm.edu	37	12	20522487	20522487	+	Missense_Mutation	SNP	A	A	G	rs372953537	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:20522487A>G	ENST00000359062.3	+	1	309	c.269A>G	c.(268-270)gAg>gGg	p.E90G	RP11-284H19.1_ENST00000535755.1_RNA	NM_000921.4|NM_001244683.1	NP_000912.3|NP_001231612.1	Q14432	PDE3A_HUMAN	phosphodiesterase 3A, cGMP-inhibited	90					blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP-mediated signaling (GO:0019934)|diterpenoid metabolic process (GO:0016101)|lipid metabolic process (GO:0006629)|negative regulation of apoptotic process (GO:0043066)|negative regulation of vascular permeability (GO:0043116)|oocyte maturation (GO:0001556)|positive regulation of oocyte development (GO:0060282)|positive regulation of vascular permeability (GO:0043117)|regulation of meiosis (GO:0040020)|response to cAMP (GO:0051591)|response to drug (GO:0042493)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|cGMP-inhibited cyclic-nucleotide phosphodiesterase activity (GO:0004119)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(7)|lung(29)|ovary(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	58	Esophageal squamous(101;0.125)	Breast(259;0.134)			Aminophylline(DB01223)|Amrinone(DB01427)|Anagrelide(DB00261)|Caffeine(DB00201)|Cilostazol(DB01166)|Enoximone(DB04880)|Ibudilast(DB05266)|Levosimendan(DB00922)|Milrinone(DB00235)|Oxtriphylline(DB01303)|Theophylline(DB00277)|Tofisopam(DB08811)	TGTGACCTGGAGCAGTGTAAG	0.716													A|||	5	0.000998403	0.0038	0.0	5008	,	,		11878	0.0		0.0	False		,,,				2504	0.0				p.E90G		Atlas-SNP	.											.	PDE3A	184	.	0			c.A269G						PASS	.	A	GLY/GLU	6,4166		0,6,2080	5.0	5.0	5.0		269	-0.0	0.5	12		5	0,8264		0,0,4132	no	missense	PDE3A	NM_000921.4	98	0,6,6212	GG,GA,AA		0.0,0.1438,0.0482	possibly-damaging	90/1142	20522487	6,12430	2086	4132	6218	SO:0001583	missense	5139	exon1			ACCTGGAGCAGTG		CCDS31754.1	12p12.2	2011-04-15			ENSG00000172572	ENSG00000172572	3.1.4.17	"""Phosphodiesterases"""	8778	protein-coding gene	gene with protein product		123805				1315035, 10679291	Standard	NM_000921		Approved	CGI-PDE	uc001reh.2	Q14432	OTTHUMG00000168962	ENST00000359062.3:c.269A>G	12.37:g.20522487A>G	ENSP00000351957:p.Glu90Gly	68.0	0.0	0		74.0	34.0	0.459459	NM_000921	O60865|Q13348|Q17RD1	Missense_Mutation	SNP	ENST00000359062.3	37	CCDS31754.1	.	.	.	.	.	.	.	.	.	.	A	16.65	3.182736	0.57800	0.001438	0.0	ENSG00000172572	ENST00000359062	T	0.64260	-0.09	5.03	-0.0284	0.13922	.	4.081800	0.00633	N	0.000487	T	0.46639	0.1403	N	0.19112	0.55	0.25845	N	0.984007	B	0.02656	0.0	B	0.01281	0.0	T	0.35871	-0.9771	10	0.59425	D	0.04	.	3.9386	0.09316	0.5223:0.1842:0.2935:0.0	.	90	Q14432	PDE3A_HUMAN	G	90	ENSP00000351957:E90G	ENSP00000351957:E90G	E	+	2	0	PDE3A	20413754	0.929000	0.31497	0.519000	0.27824	0.703000	0.40648	0.632000	0.24583	-0.019000	0.14055	0.449000	0.29647	GAG	.	.	weak		0.716	PDE3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401756.2		
ITPR2	3709	hgsc.bcm.edu	37	12	26774089	26774089	+	Missense_Mutation	SNP	T	T	G	rs2230373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:26774089T>G	ENST00000381340.3	-	26	3845	c.3429A>C	c.(3427-3429)gaA>gaC	p.E1143D	RP11-666F17.1_ENST00000414098.2_RNA|ITPR2_ENST00000545902.1_5'Flank	NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	1143			E -> D (in dbSNP:rs16931091).		activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	TCACTTGACTTTCCCCTATTT	0.413													T|||	203	0.0405351	0.149	0.0072	5008	,	,		18812	0.0		0.001	False		,,,				2504	0.0				p.E1143D		Atlas-SNP	.											.	ITPR2	270	.	0			c.A3429C						PASS	.	T	ASP/GLU	488,3302		24,440,1431	380.0	359.0	366.0		3429	-0.8	0.6	12	dbSNP_123	366	1,8249		0,1,4124	yes	missense	ITPR2	NM_002223.2	45	24,441,5555	GG,GT,TT		0.0121,12.876,4.0615	benign	1143/2702	26774089	489,11551	1895	4125	6020	SO:0001583	missense	3709	exon26			TTGACTTTCCCCT	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.3429A>C	12.37:g.26774089T>G	ENSP00000370744:p.Glu1143Asp	254.0	1.0	0.00393701		281.0	139.0	0.494662	NM_002223	O94773	Missense_Mutation	SNP	ENST00000381340.3	37	CCDS41764.1	82	0.037545787545787544	81	0.16463414634146342	1	0.0027624309392265192	0	0.0	0	0.0	T	9.713	1.157689	0.21454	0.12876	1.21E-4	ENSG00000123104	ENST00000381340	D	0.91996	-2.95	4.36	-0.782	0.10961	.	0.222293	0.40554	N	0.001063	T	0.00754	0.0025	N	0.05574	-0.02	0.31748	P	0.634949	B	0.02656	0.0	B	0.01281	0.0	T	0.23726	-1.0180	9	0.14656	T	0.56	.	1.8975	0.03261	0.1237:0.3347:0.2527:0.2889	rs16931091;rs56635647;rs16931091	1143	Q14571	ITPR2_HUMAN	D	1143	ENSP00000370744:E1143D	ENSP00000370744:E1143D	E	-	3	2	ITPR2	26665356	0.003000	0.15002	0.552000	0.28243	0.721000	0.41392	-0.083000	0.11286	-0.216000	0.10048	0.454000	0.30748	GAA	T|0.944;G|0.056	0.056	strong		0.413	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
PLA2G4E	123745	hgsc.bcm.edu	37	15	42289456	42289456	+	Splice_Site	SNP	G	G	C	rs79040960	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42289456G>C	ENST00000399518.3	-	11	1462	c.976C>G	c.(976-978)Cct>Gct	p.P326A	PLA2G4E_ENST00000413860.2_Splice_Site_p.P297A|CTD-2382E5.1_ENST00000499478.2_RNA	NM_001206670.1	NP_001193599.1	Q3MJ16	PA24E_HUMAN	phospholipase A2, group IVE	314	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)|stomach(1)	16		all_cancers(109;8.09e-13)|all_epithelial(112;2.03e-11)|Lung NSC(122;2.17e-07)|all_lung(180;8.79e-07)|Melanoma(134;0.0273)		OV - Ovarian serous cystadenocarcinoma(18;7.61e-18)|GBM - Glioblastoma multiforme(94;3.07e-06)		AGTGTCTCAGGGCTGGAGGGA	0.607													G|||	125	0.0249601	0.0885	0.0115	5008	,	,		19005	0.0		0.0	False		,,,				2504	0.0				p.P326A		Atlas-SNP	.											.	PLA2G4E	60	.	0			c.C976G						PASS	.	G	ALA/PRO	214,3522		2,210,1656	11.0	14.0	13.0		976	-0.7	0.2	15	dbSNP_131	13	2,7470		0,2,3734	yes	missense-near-splice	PLA2G4E	NM_001206670.1	27	2,212,5390	CC,CG,GG		0.0268,5.7281,1.9272	benign	326/869	42289456	216,10992	1868	3736	5604	SO:0001630	splice_region_variant	123745	exon11			TCTCAGGGCTGGA		CCDS55962.1	15q15.1	2008-09-19			ENSG00000188089	ENSG00000188089	3.1.1.4		24791	protein-coding gene	gene with protein product						15866882	Standard	NM_001206670		Approved	FLJ45651	uc021sjp.1	Q3MJ16	OTTHUMG00000130371	ENST00000399518.3:c.975-1C>G	15.37:g.42289456G>C		125.0	0.0	0		106.0	53.0	0.5	NM_001206670	Q6ZSC0	Missense_Mutation	SNP	ENST00000399518.3	37	CCDS55962.1	33	0.01510989010989011	31	0.06300813008130081	2	0.0055248618784530384	0	0.0	0	0.0	G	12.97	2.097162	0.37048	0.057281	2.68E-4	ENSG00000188089	ENST00000399518;ENST00000413860	T;T	0.01599	4.86;4.74	5.68	-0.726	0.11170	.	0.499688	0.17527	U	0.171007	T	0.00356	0.0011	M	0.72118	2.19	0.22656	N	0.998886	B	0.32731	0.382	B	0.32677	0.15	T	0.37033	-0.9723	10	0.51188	T	0.08	-4.1952	10.0101	0.41981	0.4735:0.0:0.5265:0.0	.	297	C9JK77	.	A	326;297	ENSP00000382434:P326A;ENSP00000413897:P297A	ENSP00000382434:P326A	P	-	1	0	PLA2G4E	40076748	0.130000	0.22417	0.193000	0.23327	0.022000	0.10575	-0.429000	0.06982	0.048000	0.15891	-0.251000	0.11542	CCT	G|0.982;C|0.018	0.018	strong		0.607	PLA2G4E-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252738.2	NM_198442	Missense_Mutation
ZP4	57829	hgsc.bcm.edu	37	1	238049143	238049143	+	Missense_Mutation	SNP	G	G	A	rs34811980	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:238049143G>A	ENST00000366570.4	-	7	1041	c.883C>T	c.(883-885)Cca>Tca	p.P295S	RP11-193H5.1_ENST00000450451.1_RNA	NM_021186.3	NP_067009.1	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4	295	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.		P -> S (in dbSNP:rs34811980).		acrosomal vesicle exocytosis (GO:0060478)|binding of sperm to zona pellucida (GO:0007339)|intracellular signal transduction (GO:0035556)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of humoral immune response (GO:0002922)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of T cell proliferation (GO:0042102)|protein kinase A signaling (GO:0010737)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	acrosin binding (GO:0032190)|signal transducer activity (GO:0004871)			breast(6)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(42)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	73	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			ACATTGATTGGGAGAGAGTTG	0.502													G|||	157	0.0313498	0.1112	0.013	5008	,	,		18469	0.0		0.001	False		,,,				2504	0.0				p.P295S	NSCLC(166;160 2029 11600 18754 19936)	Atlas-SNP	.											.	ZP4	161	.	0			c.C883T						PASS	.	G	SER/PRO	393,4013	196.4+/-220.7	14,365,1824	167.0	161.0	163.0		883	4.8	0.1	1	dbSNP_126	163	6,8594	4.3+/-15.6	0,6,4294	yes	missense	ZP4	NM_021186.3	74	14,371,6118	AA,AG,GG		0.0698,8.9197,3.0678	probably-damaging	295/541	238049143	399,12607	2203	4300	6503	SO:0001583	missense	57829	exon7			TGATTGGGAGAGA	U05781	CCDS1615.1	1q43	2013-01-17			ENSG00000116996	ENSG00000116996		"""Zona pellucida glycoproteins"""	15770	protein-coding gene	gene with protein product		613514				7841460	Standard	NM_021186		Approved	ZPB	uc001hym.3	Q12836	OTTHUMG00000039586	ENST00000366570.4:c.883C>T	1.37:g.238049143G>A	ENSP00000355529:p.Pro295Ser	73.0	0.0	0		94.0	51.0	0.542553	NM_021186	B2RAE1	Missense_Mutation	SNP	ENST00000366570.4	37	CCDS1615.1	56	0.02564102564102564	52	0.10569105691056911	4	0.011049723756906077	0	0.0	0	0.0	G	18.15	3.560913	0.65538	0.089197	6.98E-4	ENSG00000116996	ENST00000366570	T	0.81163	-1.46	4.85	4.85	0.62838	Zona pellucida sperm-binding protein (3);	0.124427	0.53938	D	0.000041	T	0.13841	0.0335	M	0.70275	2.135	0.09310	N	1	D	0.76494	0.999	D	0.74023	0.982	T	0.48514	-0.9029	10	0.34782	T	0.22	-14.4465	10.7036	0.45942	0.0:0.0:0.8094:0.1905	rs34811980	295	Q12836	ZP4_HUMAN	S	295	ENSP00000355529:P295S	ENSP00000355529:P295S	P	-	1	0	ZP4	236115766	0.999000	0.42202	0.076000	0.20297	0.635000	0.38103	3.598000	0.54038	2.242000	0.73789	0.650000	0.86243	CCA	G|0.973;A|0.027	0.027	strong		0.502	ZP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095476.1		
PHPT1	29085	hgsc.bcm.edu	37	9	139745012	139745012	+	Intron	SNP	G	G	T	rs149543778	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139745012G>T	ENST00000247665.10	+	3	622				MAMDC4_ENST00000445819.1_5'Flank|PHPT1_ENST00000492540.1_3'UTR|PHPT1_ENST00000545326.1_Splice_Site_p.G114C|MAMDC4_ENST00000317446.2_5'Flank|PHPT1_ENST00000371661.1_Splice_Site_p.G114C	NM_014172.4	NP_054891.2	Q9NRX4	PHP14_HUMAN	phosphohistidine phosphatase 1						negative regulation of ATP citrate synthase activity (GO:2000984)|negative regulation of lyase activity (GO:0051350)|negative regulation of T cell receptor signaling pathway (GO:0050860)|peptidyl-histidine dephosphorylation (GO:0035971)|positive regulation of cell motility (GO:2000147)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|protein dephosphorylation (GO:0006470)|regulation of actin cytoskeleton reorganization (GO:2000249)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	calcium channel inhibitor activity (GO:0019855)|ion channel binding (GO:0044325)|phosphohistidine phosphatase activity (GO:0008969)|phosphoprotein phosphatase activity (GO:0004721)			NS(1)|large_intestine(1)|lung(1)	3	all_cancers(76;0.0763)|all_epithelial(76;0.198)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;1.52e-05)|Epithelial(140;0.000171)		CCACCATCAAGGTTTGCTTGC	0.637													G|||	26	0.00519169	0.0159	0.0072	5008	,	,		18692	0.0		0.0	False		,,,				2504	0.0				p.G114C		Atlas-SNP	.											.	PHPT1	14	.	0			c.G340T						PASS	.	G	CYS/GLY,	37,3091		0,37,1527	37.0	38.0	38.0		340,	1.5	0.0	9	dbSNP_134	38	0,7150		0,0,3575	yes	missense-near-splice,intron	PHPT1	NM_001135861.1,NM_014172.4	159,	0,37,5102	TT,TG,GG		0.0,1.1829,0.36	,	114/125,	139745012	37,10241	1564	3575	5139	SO:0001627	intron_variant	29085	exon3			CATCAAGGTTTGC	AF131857	CCDS7009.1, CCDS48060.1	9q34.3	2008-02-05			ENSG00000054148	ENSG00000054148	3.1.3.-		30033	protein-coding gene	gene with protein product	"""phosphohistidine phosphatase 14kDa"", "" sex-regulated protein janus-a"""	610167				11042152, 8619474	Standard	NM_014172		Approved	PHP14, HSPC141, CGI-202, DKFZp564M173, bA216L13.10	uc004cjq.4	Q9NRX4	OTTHUMG00000020950	ENST00000247665.10:c.286-195G>T	9.37:g.139745012G>T		50.0	0.0	0		61.0	36.0	0.590164	NM_001135861	B1AMX0|B1AMX1|Q9H0Y3	Missense_Mutation	SNP	ENST00000247665.10	37	CCDS7009.1	8	0.003663003663003663	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	.	11.23	1.576676	0.28092	0.011829	0.0	ENSG00000054148	ENST00000371661;ENST00000545326	.	.	.	1.54	1.54	0.23209	.	.	.	.	.	T	0.54549	0.1865	.	.	.	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.41875	-0.9484	7	0.54805	T	0.06	.	9.0668	0.36469	0.0:0.0:1.0:0.0	.	114	Q9NRX4-2	.	C	114	.	ENSP00000360724:G114C	G	+	1	0	PHPT1	138864833	0.000000	0.05858	0.002000	0.10522	0.044000	0.14063	0.167000	0.16602	1.174000	0.42811	0.462000	0.41574	GGC	G|0.996;T|0.004	0.004	strong		0.637	PHPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055150.1	NM_014172	
PRSS35	167681	hgsc.bcm.edu	37	6	84233325	84233325	+	Silent	SNP	G	G	A	rs147168330	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:84233325G>A	ENST00000369700.3	+	2	342	c.165G>A	c.(163-165)aaG>aaA	p.K55K	PRSS35_ENST00000536636.1_Silent_p.K55K	NM_153362.2	NP_699193.2	Q8N3Z0	PRS35_HUMAN	protease, serine, 35	55						extracellular region (GO:0005576)|mitochondrion (GO:0005739)	serine-type endopeptidase activity (GO:0004252)			breast(2)|endometrium(2)|large_intestine(12)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	32		all_cancers(76;0.000113)|Acute lymphoblastic leukemia(125;1.09e-08)|all_hematologic(105;3.12e-05)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0768)		CAGATGCTAAGATGATGGTAA	0.453													G|||	19	0.00379393	0.0144	0.0	5008	,	,		18836	0.0		0.0	False		,,,				2504	0.0				p.K55K		Atlas-SNP	.											.	PRSS35	60	.	0			c.G165A						PASS	.	G	,	32,4374	38.4+/-70.7	0,32,2171	129.0	127.0	128.0		165,165	2.0	0.0	6	dbSNP_134	128	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PRSS35	NM_001170423.1,NM_153362.2	,	0,32,6471	AA,AG,GG		0.0,0.7263,0.246	,	55/414,55/414	84233325	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	167681	exon2			TGCTAAGATGATG	BC037170	CCDS4999.1	6q14.2	2010-05-12	2004-07-09	2004-07-09	ENSG00000146250	ENSG00000146250		"""Serine peptidases / Serine peptidases"""	21387	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 158"""	C6orf158			Standard	NM_153362		Approved	MGC46520, dJ223E3.1	uc003pjz.3	Q8N3Z0	OTTHUMG00000015113	ENST00000369700.3:c.165G>A	6.37:g.84233325G>A		209.0	0.0	0		198.0	84.0	0.424242	NM_153362	A8K7B3|Q9BQP6	Silent	SNP	ENST00000369700.3	37	CCDS4999.1																																																																																			G|0.997;A|0.003	0.003	strong		0.453	PRSS35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041352.1	NM_153362	
SLC5A9	200010	hgsc.bcm.edu	37	1	48697713	48697713	+	Missense_Mutation	SNP	C	C	T	rs140292897	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:48697713C>T	ENST00000438567.2	+	7	839	c.787C>T	c.(787-789)Cgg>Tgg	p.R263W	SLC5A9_ENST00000236495.5_Missense_Mutation_p.R288W|SLC5A9_ENST00000420136.2_Intron|SLC5A9_ENST00000533824.1_Missense_Mutation_p.R284W|RP5-1024N4.4_ENST00000606809.1_RNA	NM_001011547.2	NP_001011547.2	Q2M3M2	SC5A9_HUMAN	solute carrier family 5 (sodium/sugar cotransporter), member 9	263					sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(1)|endometrium(3)|large_intestine(4)|liver(2)|lung(11)|ovary(3)|prostate(1)|urinary_tract(1)	26						TCACCTCCCACGGCCCGATGC	0.617													C|||	7	0.00139776	0.0045	0.0	5008	,	,		20299	0.0		0.001	False		,,,				2504	0.0				p.R288W		Atlas-SNP	.											.	SLC5A9	82	.	0			c.C862T						PASS	.	C	TRP/ARG,TRP/ARG	27,4379	34.3+/-65.2	0,27,2176	124.0	113.0	117.0		787,862	5.0	0.8	1	dbSNP_134	117	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	SLC5A9	NM_001011547.2,NM_001135181.1	101,101	0,30,6473	TT,TC,CC		0.0349,0.6128,0.2307	probably-damaging,probably-damaging	263/682,288/707	48697713	30,12976	2203	4300	6503	SO:0001583	missense	200010	exon8			CTCCCACGGCCCG	BX648549	CCDS30709.2, CCDS44136.1	1p33	2013-07-19	2013-07-19		ENSG00000117834	ENSG00000117834		"""Solute carriers"""	22146	protein-coding gene	gene with protein product			"""solute carrier family 5 (sodium/glucose cotransporter), member 9"""				Standard	NM_001011547		Approved	SGLT4	uc001crn.2	Q2M3M2	OTTHUMG00000007959	ENST00000438567.2:c.787C>T	1.37:g.48697713C>T	ENSP00000401730:p.Arg263Trp	248.0	0.0	0		233.0	232.0	0.995708	NM_001135181	B3KY87|B7ZL45|B7ZL47|E9PAK4|E9PJ08|Q5TET3	Missense_Mutation	SNP	ENST00000438567.2	37	CCDS30709.2	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	28.2	4.897309	0.91962	0.006128	3.49E-4	ENSG00000117834	ENST00000533824;ENST00000438567;ENST00000236495	D;D;D	0.89415	-2.46;-2.44;-2.51	5.95	5.02	0.67125	.	0.000000	0.85682	D	0.000000	D	0.94401	0.8199	M	0.93420	3.415	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;1.0	D	0.94931	0.8082	10	0.87932	D	0	.	15.4795	0.75514	0.1395:0.8605:0.0:0.0	.	284;263;288	E9PJ08;Q2M3M2;E9PAK4	.;SC5A9_HUMAN;.	W	284;263;288	ENSP00000431900:R284W;ENSP00000401730:R263W;ENSP00000236495:R288W	ENSP00000236495:R288W	R	+	1	2	SLC5A9	48470300	0.998000	0.40836	0.828000	0.32881	0.985000	0.73830	3.906000	0.56340	1.485000	0.48380	0.563000	0.77884	CGG	C|0.998;T|0.002	0.002	strong		0.617	SLC5A9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022061.3	XM_117174	
FER	2241	hgsc.bcm.edu	37	5	108294979	108294979	+	Silent	SNP	T	T	C	rs34869483	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:108294979T>C	ENST00000281092.4	+	13	1971	c.1587T>C	c.(1585-1587)gaT>gaC	p.D529D	FER_ENST00000536402.1_3'UTR|FER_ENST00000438717.2_Silent_p.D354D	NM_005246.2	NP_005237.2	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	529	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				actin cytoskeleton reorganization (GO:0031532)|cell proliferation (GO:0008283)|cell-cell adhesion mediated by cadherin (GO:0044331)|cellular response to insulin stimulus (GO:0032869)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to reactive oxygen species (GO:0034614)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|diapedesis (GO:0050904)|extracellular matrix-cell signaling (GO:0035426)|Fc-epsilon receptor signaling pathway (GO:0038095)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|interleukin-6-mediated signaling pathway (GO:0070102)|intracellular signal transduction (GO:0035556)|Kit signaling pathway (GO:0038109)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of mast cell activation involved in immune response (GO:0033007)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|regulation of fibroblast migration (GO:0010762)|regulation of lamellipodium assembly (GO:0010591)|regulation of protein phosphorylation (GO:0001932)|response to lipopolysaccharide (GO:0032496)|response to platelet-derived growth factor (GO:0036119)|substrate adhesion-dependent cell spreading (GO:0034446)|tyrosine phosphorylation of Stat3 protein (GO:0042503)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			NS(2)|biliary_tract(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	32		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)		AACTTATAGATCATCACTATA	0.363													T|||	30	0.00599042	0.0015	0.0043	5008	,	,		15833	0.0		0.0119	False		,,,				2504	0.0133				p.D529D	Colon(146;1051 1799 9836 27344 47401)	Atlas-SNP	.											.	FER	100	.	0			c.T1587C						PASS	.	T		14,4390	21.2+/-45.6	0,14,2188	138.0	131.0	133.0		1587	-7.7	0.9	5	dbSNP_126	133	193,8405	84.8+/-147.2	4,185,4110	no	coding-synonymous	FER	NM_005246.2		4,199,6298	CC,CT,TT		2.2447,0.3179,1.5921		529/823	108294979	207,12795	2202	4299	6501	SO:0001819	synonymous_variant	2241	exon13			TATAGATCATCAC	J03358	CCDS4098.1	5q21	2013-02-14	2008-02-07		ENSG00000151422	ENSG00000151422	2.7.10.1	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""SH2 domain containing"""	3655	protein-coding gene	gene with protein product	"""phosphoprotein NCP94"", ""protein phosphatase 1, regulatory subunit 74"""	176942					Standard	NM_005246		Approved	TYK3, PPP1R74	uc003kop.1	P16591	OTTHUMG00000128751	ENST00000281092.4:c.1587T>C	5.37:g.108294979T>C		122.0	0.0	0		112.0	44.0	0.392857	NM_005246	B2RCR4|B4DSQ2|H2FLB8	Silent	SNP	ENST00000281092.4	37	CCDS4098.1																																																																																			T|0.988;C|0.012	0.012	strong		0.363	FER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250664.1	NM_005246	
ADAM8	101	hgsc.bcm.edu	37	10	135077265	135077265	+	Missense_Mutation	SNP	A	A	G	rs3008319	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:135077265A>G	ENST00000445355.3	-	22	2374	c.2324T>C	c.(2323-2325)aTc>aCc	p.I775T	ADAM8_ENST00000485491.2_Intron|ADAM8_ENST00000415217.3_Silent_p.H719H	NM_001109.4	NP_001100.3	P78325	ADAM8_HUMAN	ADAM metallopeptidase domain 8	775			I -> T (in dbSNP:rs3008319).		activation of MAPK activity involved in innate immune response (GO:0035419)|angiogenesis (GO:0001525)|cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|leukocyte migration involved in inflammatory response (GO:0002523)|lymphocyte chemotaxis (GO:0048247)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of bone resorption (GO:0045780)|positive regulation of cell adhesion (GO:0045785)|positive regulation of eosinophil migration (GO:2000418)|positive regulation of fibronectin-dependent thymocyte migration (GO:2000415)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of neutrophil extravasation (GO:2000391)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein processing (GO:0010954)|positive regulation of protein secretion (GO:0050714)|positive regulation of T cell differentiation in thymus (GO:0033089)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000309)|regulation of cell-cell adhesion (GO:0022407)|single organismal cell-cell adhesion (GO:0016337)	alpha9-beta1 integrin-ADAM8 complex (GO:0071133)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dense core granule membrane (GO:0032127)|integral component of plasma membrane (GO:0005887)|phagolysosome (GO:0032010)|plasma membrane (GO:0005886)|podosome (GO:0002102)|specific granule (GO:0042581)|tertiary granule (GO:0070820)	calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|protein self-association (GO:0043621)|zinc ion binding (GO:0008270)	p.I775T(1)		central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)	17		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;7.72e-06)|OV - Ovarian serous cystadenocarcinoma(35;8.23e-06)|Epithelial(32;1.02e-05)		CGTTGGCTTGATGACCTGGGA	0.642													A|||	341	0.0680911	0.2421	0.0288	5008	,	,		15527	0.0		0.001	False		,,,				2504	0.0				p.I775T		Atlas-SNP	.											ADAM8,NS,carcinoma,0,1	ADAM8	41	1	1	Substitution - Missense(1)	prostate(1)	c.T2324C						PASS	.	A	THR/ILE,,	990,3408		102,786,1311	41.0	39.0	40.0		2324,2157,	1.0	0.1	10	dbSNP_101	40	12,8580		0,12,4284	yes	missense,coding-synonymous,intron	ADAM8	NM_001109.4,NM_001164489.1,NM_001164490.1	89,,	102,798,5595	GG,GA,AA		0.1397,22.5102,7.7136	benign,,	775/825,719/743,	135077265	1002,11988	2199	4296	6495	SO:0001583	missense	101	exon22			GGCTTGATGACCT	D26579	CCDS31319.2, CCDS58102.1, CCDS58103.1	10q26.3	2014-03-20	2005-08-18		ENSG00000151651	ENSG00000151651		"""ADAM metallopeptidase domain containing"", ""CD molecules"""	215	protein-coding gene	gene with protein product		602267	"""a disintegrin and metalloproteinase domain 8"""			9126482	Standard	NM_001109		Approved	CD156, MS2, CD156a	uc021qbe.1	P78325	OTTHUMG00000019309	ENST00000445355.3:c.2324T>C	10.37:g.135077265A>G	ENSP00000453302:p.Ile775Thr	58.0	0.0	0		52.0	22.0	0.423077	NM_001109	B4DVM6|H0YL36|H0YLR0|H0YN39	Missense_Mutation	SNP	ENST00000445355.3	37	CCDS31319.2																																																																																			A|0.917;G|0.083	0.083	strong		0.642	ADAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051118.4	NM_001109	
LY75	4065	hgsc.bcm.edu	37	2	160737717	160737717	+	Silent	SNP	G	G	A	rs79199281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160737717G>A	ENST00000263636.4	-	8	1308	c.1281C>T	c.(1279-1281)aaC>aaT	p.N427N	LY75_ENST00000554112.1_Silent_p.N427N|LY75-CD302_ENST00000505052.1_Silent_p.N427N|LY75_ENST00000553424.1_Silent_p.N427N|LY75-CD302_ENST00000504764.1_Silent_p.N427N	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	427	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)			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)		GTATGTTTATGTTCTTAAGGC	0.323													G|||	26	0.00519169	0.0197	0.0	5008	,	,		19352	0.0		0.0	False		,,,				2504	0.0				p.N427N		Atlas-SNP	.											.	LY75	151	.	0			c.C1281T						PASS	.	G	,,	59,4347	58.1+/-94.6	0,59,2144	177.0	164.0	168.0		1281,1281,1281	1.9	1.0	2	dbSNP_131	168	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	,,	0,59,6444	AA,AG,GG		0.0,1.3391,0.4536	,,	427/1874,427/1818,427/1723	160737717	59,12947	2203	4300	6503	SO:0001819	synonymous_variant	4065	exon8			GTTTATGTTCTTA	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.1281C>T	2.37:g.160737717G>A		88.0	0.0	0		89.0	23.0	0.258427	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Silent	SNP	ENST00000263636.4	37	CCDS2211.1																																																																																			G|0.994;A|0.006	0.006	strong		0.323	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
MT-ND4	4538	hgsc.bcm.edu	37	M	11164	11164	+	Silent	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:11164A>G	ENST00000361381.2	+	1	405	c.405A>G	c.(403-405)cgA>cgG	p.R135R	MT-TR_ENST00000387439.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-TK_ENST00000387421.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	135					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						ATCATCACCCGATGAGGCAAC	0.443																																					p.R135R		Atlas-SNP	.											.	.	.	.	0			c.A405G						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			CACCCGATGAGGC			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.405A>G	M.37:g.11164A>G		15.0	0.0	0		10.0	10.0	1	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Silent	SNP	ENST00000361381.2	37																																																																																				.	.	none		0.443	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
RREB1	6239	hgsc.bcm.edu	37	6	7246994	7246994	+	Silent	SNP	C	C	T	rs187908583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:7246994C>T	ENST00000349384.6	+	11	4460	c.4146C>T	c.(4144-4146)ggC>ggT	p.G1382G	RREB1_ENST00000379933.3_Silent_p.G1382G|RREB1_ENST00000379938.2_Silent_p.G1437G|RREB1_ENST00000334984.6_Intron	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1382					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				GCGAGGCAGGCGCCGGGGGCG	0.692													C|||	33	0.00658946	0.025	0.0	5008	,	,		11874	0.0		0.0	False		,,,				2504	0.0				p.G1437G		Atlas-SNP	.											.	RREB1	242	.	0			c.C4311T						PASS	.	C	,,,	60,4166		0,60,2053	11.0	13.0	13.0		4146,4311,,4146	-3.5	0.0	6		13	1,8303		0,1,4151	no	coding-synonymous,coding-synonymous,intron,coding-synonymous	RREB1	NM_001003698.3,NM_001003699.3,NM_001003700.1,NM_001168344.1	,,,	0,61,6204	TT,TC,CC		0.012,1.4198,0.4868	,,,	1382/1688,1437/1743,,1382/1688	7246994	61,12469	2113	4152	6265	SO:0001819	synonymous_variant	6239	exon12			GGCAGGCGCCGGG	U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"""Zinc fingers, C2H2-type"""	10449	protein-coding gene	gene with protein product	"""hindsight homolog (drosophila)"""	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.4146C>T	6.37:g.7246994C>T		14.0	0.0	0		16.0	10.0	0.625	NM_001003699	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Silent	SNP	ENST00000349384.6	37	CCDS34336.1																																																																																			C|0.993;T|0.007	0.007	strong		0.692	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1		
LRRIQ3	127255	hgsc.bcm.edu	37	1	74575141	74575141	+	Silent	SNP	G	G	A	rs182798407	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:74575141G>A	ENST00000395089.1	-	4	803	c.804C>T	c.(802-804)ctC>ctT	p.L268L	LRRIQ3_ENST00000468759.1_5'UTR|LRRIQ3_ENST00000370909.2_Silent_p.L160L|LRRIQ3_ENST00000354431.4_Silent_p.L268L			A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3	268										NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5)	73						GATCCTTAAGGAGCTTATCTT	0.289													G|||	15	0.00299521	0.0113	0.0	5008	,	,		12152	0.0		0.0	False		,,,				2504	0.0				p.L268L		Atlas-SNP	.											LRRIQ3,right_upper_lobe,carcinoma,-1,1	LRRIQ3	146	1	0			c.C804T						PASS	.	G		41,3525		2,37,1744	100.0	83.0	88.0		804	2.0	0.0	1		88	0,8096		0,0,4048	no	coding-synonymous	LRRIQ3	NM_001105659.1		2,37,5792	AA,AG,GG		0.0,1.1497,0.3516		268/625	74575141	41,11621	1783	4048	5831	SO:0001819	synonymous_variant	127255	exon5			CTTAAGGAGCTTA	BX647210	CCDS41350.1	1p31.1	2008-06-12	2008-06-12	2008-06-12	ENSG00000162620	ENSG00000162620			28318	protein-coding gene	gene with protein product			"""leucine rich repeat containing 44"""	LRRC44		12477932	Standard	NM_001105659		Approved	MGC22773	uc001dfy.4	A6PVS8	OTTHUMG00000009508	ENST00000395089.1:c.804C>T	1.37:g.74575141G>A		98.0	0.0	0		120.0	59.0	0.491667	NM_001105659	A6PVS9|Q6P5P7|Q6ZMV4|Q8WUE0	Silent	SNP	ENST00000395089.1	37	CCDS41350.1																																																																																			G|0.997;A|0.003	0.003	strong		0.289	LRRIQ3-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316539.1	NM_145258	
ABCC6	368	hgsc.bcm.edu	37	16	16248791	16248791	+	Missense_Mutation	SNP	C	C	T	rs57695665	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:16248791C>T	ENST00000205557.7	-	28	4009	c.3980G>A	c.(3979-3981)gGg>gAg	p.G1327E		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	1327	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	AATGGGGACCCCGTCGATCCA	0.672													C|||	27	0.00539137	0.0197	0.0014	5008	,	,		16551	0.0		0.0	False		,,,				2504	0.0				p.G1327E		Atlas-SNP	.											.	ABCC6	110	.	0			c.G3980A						PASS	.	C	GLU/GLY	51,4343		0,51,2146	29.0	25.0	26.0		3980	3.6	1.0	16	dbSNP_129	26	1,8597		0,1,4298	yes	missense	ABCC6	NM_001171.5	98	0,52,6444	TT,TC,CC		0.0116,1.1607,0.4002	probably-damaging	1327/1504	16248791	52,12940	2197	4299	6496	SO:0001583	missense	368	exon28			GGGACCCCGTCGA	AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"""ATP binding cassette transporters / subfamily C"""	57	protein-coding gene	gene with protein product		603234	"""pseudoxanthoma elasticum"""	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.3980G>A	16.37:g.16248791C>T	ENSP00000205557:p.Gly1327Glu	115.0	0.0	0		108.0	58.0	0.537037	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	37	CCDS10568.1	17	0.007783882783882784	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	0	0.0	C	18.13	3.554991	0.65425	0.011607	1.16E-4	ENSG00000091262	ENST00000205557;ENST00000205558	D	0.92149	-2.98	4.53	3.57	0.40892	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.000000	0.47852	U	0.000212	D	0.90232	0.6946	M	0.84773	2.715	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.90118	0.4197	10	0.62326	D	0.03	.	12.2401	0.54538	0.0:0.9153:0.0:0.0847	rs57695665	1327;1327	O95255;A8Y988	MRP6_HUMAN;.	E	1327;265	ENSP00000205557:G1327E	ENSP00000205557:G1327E	G	-	2	0	ABCC6	16156292	0.891000	0.30450	0.957000	0.39632	0.594000	0.36715	2.702000	0.47102	0.901000	0.36495	0.465000	0.42564	GGG	C|0.994;T|0.006	0.006	strong		0.672	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2		
RBBP4	5928	hgsc.bcm.edu	37	1	33134865	33134865	+	Silent	SNP	A	A	C	rs11551266	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:33134865A>C	ENST00000373493.5	+	7	954	c.795A>C	c.(793-795)ccA>ccC	p.P265P	RBBP4_ENST00000373485.1_Silent_p.P265P|RBBP4_ENST00000544435.1_Silent_p.P13P|RBBP4_ENST00000458695.2_Silent_p.P230P|RBBP4_ENST00000414241.3_Silent_p.P264P	NM_001135255.1|NM_005610.2	NP_001128727.1|NP_005601.1	Q09028	RBBP4_HUMAN	retinoblastoma binding protein 4	265					ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|CENP-A containing nucleosome assembly (GO:0034080)|chromatin assembly (GO:0031497)|chromatin remodeling (GO:0006338)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of cell proliferation (GO:0008285)|nucleosome assembly (GO:0006334)|regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|ESC/E(Z) complex (GO:0035098)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|NuRD complex (GO:0016581)|NURF complex (GO:0016589)|protein complex (GO:0043234)|Sin3 complex (GO:0016580)	histone binding (GO:0042393)|histone deacetylase binding (GO:0042826)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(4)|ovary(1)|prostate(4)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)				CTTCCAAACCAAGCCACTCAG	0.383													A|||	409	0.0816693	0.2927	0.0303	5008	,	,		17140	0.0		0.001	False		,,,				2504	0.0				p.P265P		Atlas-SNP	.											.	RBBP4	38	.	0			c.A795C						PASS	.	A	,,	1061,3345	373.0+/-320.6	139,783,1281	63.0	62.0	62.0		792,690,795	4.1	1.0	1	dbSNP_120	62	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous,coding-synonymous,coding-synonymous	RBBP4	NM_001135255.1,NM_001135256.1,NM_005610.2	,,	139,794,5570	CC,CA,AA		0.1279,24.0808,8.2423	,,	264/425,230/391,265/426	33134865	1072,11934	2203	4300	6503	SO:0001819	synonymous_variant	5928	exon7			CAAACCAAGCCAC	BC053904	CCDS366.1, CCDS44105.1, CCDS44106.1	1p35.1	2014-07-17	2001-11-28		ENSG00000162521	ENSG00000162521		"""WD repeat domain containing"""	9887	protein-coding gene	gene with protein product		602923	"""retinoblastoma-binding protein 4"""			8350924, 14609955, 17531812	Standard	NM_005610		Approved	RbAp48, NURF55, lin-53	uc001bvr.3	Q09028	OTTHUMG00000007998	ENST00000373493.5:c.795A>C	1.37:g.33134865A>C		236.0	1.0	0.00423729		215.0	94.0	0.437209	NM_005610	B2R6G9|B4DRH0|D3DPQ3|P31149|Q53H02|Q96BV9	Silent	SNP	ENST00000373493.5	37	CCDS366.1	158|158	0.07234432234432235|0.07234432234432235	151|151	0.30691056910569103|0.30691056910569103	7|7	0.019337016574585635|0.019337016574585635	0|0	0.0|0.0	0|0	0.0|0.0	A|A	8.870|8.870	0.948970|0.948970	0.18356|0.18356	0.240808|0.240808	0.001279|0.001279	ENSG00000162521|ENSG00000162521	ENST00000475321|ENST00000463378	.|.	.|.	.|.	5.23|5.23	4.08|4.08	0.47627|0.47627	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	1.0|1.0	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.34153|0.34153	-0.9840|-0.9840	3|3	.|.	.|.	.|.	.|.	6.6964|6.6964	0.23201|0.23201	0.5947:0.2729:0.0:0.1324|0.5947:0.2729:0.0:0.1324	rs11551266;rs17849722;rs56732244|rs11551266;rs17849722;rs56732244	.|.	.|.	.|.	Q|P	68|25	.|.	.|.	K|Q	+|+	1|2	0|0	RBBP4|RBBP4	32907452|32907452	0.838000|0.838000	0.29461|0.29461	1.000000|1.000000	0.80357|0.80357	0.954000|0.954000	0.61252|0.61252	0.081000|0.081000	0.14823|0.14823	0.910000|0.910000	0.36722|0.36722	0.402000|0.402000	0.26972|0.26972	AAG|CAA	A|0.925;C|0.075	0.075	strong		0.383	RBBP4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021957.3	NM_005610	
MAST1	22983	hgsc.bcm.edu	37	19	12978556	12978556	+	Silent	SNP	C	C	G	rs202159363	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12978556C>G	ENST00000251472.4	+	20	2370	c.2331C>G	c.(2329-2331)tcC>tcG	p.S777S		NM_014975.2	NP_055790.1			microtubule associated serine/threonine kinase 1											NS(1)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(20)|ovary(5)|prostate(5)|skin(3)	56						AGCGATTCTCCGCGTCCGAGG	0.687													C|||	59	0.0117812	0.0431	0.0029	5008	,	,		13407	0.0		0.0	False		,,,				2504	0.0				p.S777S		Atlas-SNP	.											.	MAST1	214	.	0			c.C2331G						PASS	.	C		118,4146		0,118,2014	7.0	7.0	7.0		2331	-9.0	0.1	19		7	1,8357		0,1,4178	no	coding-synonymous	MAST1	NM_014975.2		0,119,6192	GG,GC,CC		0.012,2.7674,0.9428		777/1571	12978556	119,12503	2132	4179	6311	SO:0001819	synonymous_variant	22983	exon20			ATTCTCCGCGTCC	AB023190	CCDS32921.1	19p13.2	2008-02-05				ENSG00000105613			19034	protein-coding gene	gene with protein product		612256					Standard	NM_014975		Approved	SAST, KIAA0973	uc002mvm.3	Q9Y2H9		ENST00000251472.4:c.2331C>G	19.37:g.12978556C>G		61.0	0.0	0		62.0	33.0	0.532258	NM_014975		Silent	SNP	ENST00000251472.4	37	CCDS32921.1																																																																																			C|0.995;G|0.005	0.005	strong		0.687	MAST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451733.2	NM_014975	
NEDD9	4739	hgsc.bcm.edu	37	6	11190859	11190859	+	Missense_Mutation	SNP	G	G	A	rs61755989	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:11190859G>A	ENST00000379446.5	-	5	1409	c.1243C>T	c.(1243-1245)Cgg>Tgg	p.R415W	NEDD9_ENST00000504387.1_Missense_Mutation_p.R415W|RP3-510L9.1_ENST00000500636.2_RNA	NM_001271033.1|NM_006403.3	NP_001257962.1|NP_006394.1	Q14511	CASL_HUMAN	neural precursor cell expressed, developmentally down-regulated 9	415					actin filament bundle assembly (GO:0051017)|cell adhesion (GO:0007155)|cytoskeleton organization (GO:0007010)|integrin-mediated signaling pathway (GO:0007229)|mitotic nuclear division (GO:0007067)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle pole (GO:0000922)				endometrium(3)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	Breast(50;0.0768)|Ovarian(93;0.152)	all_hematologic(90;0.135)	Epithelial(50;0.0647)|all cancers(50;0.179)			TGCTGGAGCCGCTGAAGTCTC	0.537													G|||	104	0.0207668	0.0741	0.0072	5008	,	,		19658	0.0		0.001	False		,,,				2504	0.0				p.R415W		Atlas-SNP	.											.	NEDD9	191	.	0			c.C1243T						PASS	.	G	TRP/ARG,TRP/ARG	272,4134	152.9+/-186.6	8,256,1939	68.0	64.0	65.0		1243,1243	3.2	0.3	6	dbSNP_129	65	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	NEDD9	NM_001142393.1,NM_006403.3	101,101	8,258,6237	AA,AG,GG		0.0233,6.1734,2.1067	benign,benign	415/835,415/835	11190859	274,12732	2203	4300	6503	SO:0001583	missense	4739	exon6			GGAGCCGCTGAAG	L43821	CCDS4520.1, CCDS34340.1, CCDS47373.1, CCDS75400.1	6p25-p24	2011-04-13			ENSG00000111859	ENSG00000111859		"""Cas scaffolding proteins"""	7733	protein-coding gene	gene with protein product	"""Cas scaffolding protein family member 2"", ""Cas-like"""	602265					Standard	NM_182966		Approved	HEF1, CAS-L, CASS2	uc003mzv.2	Q14511	OTTHUMG00000014255	ENST00000379446.5:c.1243C>T	6.37:g.11190859G>A	ENSP00000368759:p.Arg415Trp	95.0	0.0	0		105.0	51.0	0.485714	NM_001142393	A8K9G7|A8MSJ9|G5E9Y9|Q5T9R4|Q5XKI0	Missense_Mutation	SNP	ENST00000379446.5	37	CCDS4520.1	32	0.014652014652014652	29	0.05894308943089431	3	0.008287292817679558	0	0.0	0	0.0	G	8.301	0.819834	0.16678	0.061734	2.33E-4	ENSG00000111859	ENST00000379446;ENST00000504387	T;T	0.27256	1.68;1.68	5.92	3.16	0.36331	Serine rich protein interaction (1);	0.147556	0.64402	N	0.000009	T	0.12689	0.0308	M	0.77103	2.36	0.80722	D	1	B;B;B	0.33512	0.415;0.294;0.403	B;B;B	0.29176	0.081;0.099;0.045	T	0.02966	-1.1088	10	0.59425	D	0.04	-11.9291	5.1672	0.15092	0.1975:0.0:0.5527:0.2498	.	415;415;415	G5E9Y9;A8K9G7;Q14511	.;.;CASL_HUMAN	W	415	ENSP00000368759:R415W;ENSP00000422871:R415W	ENSP00000368759:R415W	R	-	1	2	NEDD9	11298845	0.969000	0.33509	0.350000	0.25708	0.084000	0.17831	1.794000	0.38774	0.395000	0.25257	-0.182000	0.12963	CGG	G|0.981;A|0.019	0.019	strong		0.537	NEDD9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039853.2	NM_006403	
KCNK18	338567	hgsc.bcm.edu	37	10	118969353	118969353	+	Missense_Mutation	SNP	C	C	T	rs363360	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:118969353C>T	ENST00000334549.1	+	3	698	c.698C>T	c.(697-699)gCg>gTg	p.A233V		NM_181840.1	NP_862823.1	Q7Z418	KCNKI_HUMAN	potassium channel, subfamily K, member 18	233			A -> V (in dbSNP:rs363360). {ECO:0000269|PubMed:20871611}.		cellular response to pH (GO:0071467)|potassium ion export (GO:0071435)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium-activated potassium channel activity (GO:0015269)|outward rectifier potassium channel activity (GO:0015271)|potassium channel activity (GO:0005267)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(24)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	41		Colorectal(252;0.19)		all cancers(201;0.0211)		AGATCTCATGCGCTAGAGAAA	0.527													C|||	163	0.0325479	0.1165	0.013	5008	,	,		20294	0.0		0.0	False		,,,				2504	0.0				p.A233V		Atlas-SNP	.											KCNK18,colon,carcinoma,0,1	KCNK18	70	1	0			c.C698T						scavenged	.	C	VAL/ALA	421,3985	204.1+/-226.4	22,377,1804	103.0	99.0	100.0		698	2.8	0.0	10	dbSNP_79	100	3,8597	2.2+/-6.3	0,3,4297	no	missense	KCNK18	NM_181840.1	64	22,380,6101	TT,TC,CC		0.0349,9.5552,3.26	benign	233/385	118969353	424,12582	2203	4300	6503	SO:0001583	missense	338567	exon3			CTCATGCGCTAGA	AB087138	CCDS7598.1	10q26.11	2012-03-07			ENSG00000186795	ENSG00000186795		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	19439	protein-coding gene	gene with protein product	"""TWIK related spinal cord K+ channel"""	613655				16382106	Standard	NM_181840		Approved	K2p18.1, TRESK-2, TRESK2, TRESK, TRIK	uc010qsr.2	Q7Z418	OTTHUMG00000019120	ENST00000334549.1:c.698C>T	10.37:g.118969353C>T	ENSP00000334650:p.Ala233Val	110.0	1.0	0.00909091		120.0	56.0	0.466667	NM_181840	Q5SQQ8	Missense_Mutation	SNP	ENST00000334549.1	37	CCDS7598.1	67	0.030677655677655676	59	0.11991869918699187	8	0.022099447513812154	0	0.0	0	0.0	C	4.454	0.084176	0.08583	0.095552	3.49E-4	ENSG00000186795	ENST00000334549	T	0.14640	2.49	4.87	2.83	0.33086	.	0.649699	0.15587	N	0.254599	T	0.00144	0.0004	L	0.32530	0.975	0.09310	N	1	P	0.36010	0.532	B	0.27380	0.079	T	0.37957	-0.9683	10	0.31617	T	0.26	.	9.2831	0.37740	0.0:0.648:0.2759:0.0761	rs363360;rs363360	233	Q7Z418	KCNKI_HUMAN	V	233	ENSP00000334650:A233V	ENSP00000334650:A233V	A	+	2	0	KCNK18	118959343	0.289000	0.24334	0.002000	0.10522	0.001000	0.01503	1.454000	0.35178	1.379000	0.46325	0.655000	0.94253	GCG	A|0.000;C|0.963;T|0.037	0.037	strong		0.527	KCNK18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050562.2	NM_181840	
RSF1	51773	hgsc.bcm.edu	37	11	77413223	77413223	+	Missense_Mutation	SNP	T	T	C	rs78433827	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:77413223T>C	ENST00000308488.6	-	6	1353	c.1051A>G	c.(1051-1053)Atc>Gtc	p.I351V	RSF1_ENST00000360355.2_Missense_Mutation_p.I320V|RSF1_ENST00000480887.1_Missense_Mutation_p.I99V			Q96T23	RSF1_HUMAN	remodeling and spacing factor 1	351	Glu-rich.				CENP-A containing nucleosome assembly (GO:0034080)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|negative regulation of DNA binding (GO:0043392)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral transcription (GO:0050434)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RSF complex (GO:0031213)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(14;1.54e-17)|all_epithelial(13;4.06e-20)|Ovarian(111;0.152)		Epithelial(5;3e-50)|all cancers(3;6.37e-47)|BRCA - Breast invasive adenocarcinoma(5;9.82e-31)			CCAAATTCGATCCTTTCAGGC	0.398													T|||	29	0.00579073	0.0197	0.0043	5008	,	,		18269	0.0		0.0	False		,,,				2504	0.0				p.I351V		Atlas-SNP	.											RSF1,caecum,carcinoma,+2,1	RSF1	105	1	0			c.A1051G						PASS	.	T	VAL/ILE	110,4290	86.8+/-125.4	1,108,2091	149.0	147.0	148.0		1051	-0.2	0.0	11	dbSNP_131	148	2,8582	2.2+/-6.3	0,2,4290	yes	missense	RSF1	NM_016578.3	29	1,110,6381	CC,CT,TT		0.0233,2.5,0.8626	benign	351/1442	77413223	112,12872	2200	4292	6492	SO:0001583	missense	51773	exon6			ATTCGATCCTTTC	AF380176, AF227948	CCDS8253.1	11q14.1	2013-01-28	2006-05-25	2006-05-25	ENSG00000048649	ENSG00000048649		"""Zinc fingers, PHD-type"""	18118	protein-coding gene	gene with protein product		608522	"""hepatitis B virus x associated protein"""	HBXAP		11788598, 12972596	Standard	NM_016578		Approved	XAP8, RSF-1, p325	uc001oyn.3	Q96T23	OTTHUMG00000150433	ENST00000308488.6:c.1051A>G	11.37:g.77413223T>C	ENSP00000311513:p.Ile351Val	256.0	1.0	0.00390625		288.0	162.0	0.5625	NM_016578	Q86X86|Q9H3L8|Q9NVZ8|Q9NYU0	Missense_Mutation	SNP	ENST00000308488.6	37	CCDS8253.1	9	0.004120879120879121	6	0.012195121951219513	3	0.008287292817679558	0	0.0	0	0.0	T	0.003	-2.567968	0.00133	0.025	2.33E-4	ENSG00000048649	ENST00000308488;ENST00000480887;ENST00000360355;ENST00000526324;ENST00000528095	D;D;D;D;T	0.84589	-1.85;-1.85;-1.87;-1.86;1.6	5.9	-0.187	0.13268	.	1.083410	0.07199	N	0.857181	T	0.41026	0.1141	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.41124	-0.9526	10	0.21014	T	0.42	3.5725	1.2586	0.01996	0.175:0.2018:0.3389:0.2843	.	351	Q96T23	RSF1_HUMAN	V	351;99;320;152;350	ENSP00000311513:I351V;ENSP00000434509:I99V;ENSP00000353511:I320V;ENSP00000432022:I152V;ENSP00000436408:I350V	ENSP00000311513:I351V	I	-	1	0	RSF1	77090871	0.000000	0.05858	0.014000	0.15608	0.387000	0.30353	-0.043000	0.12043	0.057000	0.16193	-0.313000	0.08912	ATC	T|0.992;C|0.008	0.008	strong		0.398	RSF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318075.2	NM_016578	
TSHZ3	57616	hgsc.bcm.edu	37	19	31768491	31768491	+	Silent	SNP	G	G	A	rs139947200	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:31768491G>A	ENST00000240587.4	-	2	2535	c.2208C>T	c.(2206-2208)gcC>gcT	p.A736A		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	736					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					AGGGCTTGGCGGCCTTGCCCA	0.627													G|||	3	0.000599042	0.0023	0.0	5008	,	,		17340	0.0		0.0	False		,,,				2504	0.0				p.A736A		Atlas-SNP	.											.	TSHZ3	549	.	0			c.C2208T						PASS	.	G		17,4389	22.3+/-47.3	0,17,2186	58.0	59.0	59.0		2208	-10.7	0.3	19	dbSNP_134	59	0,8600		0,0,4300	no	coding-synonymous	TSHZ3	NM_020856.2		0,17,6486	AA,AG,GG		0.0,0.3858,0.1307		736/1082	31768491	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	57616	exon2			CTTGGCGGCCTTG	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	30700	protein-coding gene	gene with protein product	"""teashirt 3"""	614119	"""zinc finger protein 537"", ""teashirt family zinc finger 3"""	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.2208C>T	19.37:g.31768491G>A		63.0	0.0	0		66.0	27.0	0.409091	NM_020856	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	37	CCDS12421.2																																																																																			G|0.999;A|0.001	0.001	strong		0.627	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856	
FBXO44	93611	hgsc.bcm.edu	37	1	11721321	11721321	+	Silent	SNP	G	G	A	rs12057383	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11721321G>A	ENST00000251547.5	+	6	841	c.759G>A	c.(757-759)ccG>ccA	p.P253P	FBXO44_ENST00000376762.4_Missense_Mutation_p.A212T|FBXO6_ENST00000376753.4_5'Flank|FBXO44_ENST00000376760.1_Missense_Mutation_p.A212T|FBXO44_ENST00000376770.1_Silent_p.P253P|FBXO44_ENST00000251546.4_Missense_Mutation_p.A212T|FBXO44_ENST00000376768.1_Missense_Mutation_p.A244T	NM_033182.5	NP_149438.2	Q9H4M3	FBX44_HUMAN	F-box protein 44	253						SCF ubiquitin ligase complex (GO:0019005)				kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	8	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.41e-06)|COAD - Colon adenocarcinoma(227;0.000255)|BRCA - Breast invasive adenocarcinoma(304;0.0003)|Kidney(185;0.000758)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)		TCGGGCCCCCGCTGCCCTGAC	0.637													G|||	406	0.0810703	0.2784	0.0187	5008	,	,		15749	0.002		0.007	False		,,,				2504	0.0164				p.A212T		Atlas-SNP	.											.	FBXO44	20	.	0			c.G634A						PASS	.	G	,,THR/ALA,THR/ALA	1089,3317	394.7+/-329.4	130,829,1244	66.0	70.0	69.0		759,759,634,634	-4.8	0.9	1	dbSNP_120	69	33,8567	22.8+/-68.1	0,33,4267	yes	coding-synonymous,coding-synonymous,missense,missense	FBXO44	NM_001014765.1,NM_033182.5,NM_183412.2,NM_183413.2	,,58,58	130,862,5511	AA,AG,GG		0.3837,24.7163,8.6268	,,,	253/256,253/256,212/225,212/225	11721321	1122,11884	2203	4300	6503	SO:0001819	synonymous_variant	93611	exon5			GCCCCCGCTGCCC	AY040878	CCDS131.1, CCDS132.1	1p36.21	2008-03-26			ENSG00000132879	ENSG00000132879		"""F-boxes /  ""other"""""	24847	protein-coding gene	gene with protein product		609111				12383498	Standard	XM_005263535		Approved	FBX30, FBG3, MGC14140, Fbxo6a, Fbx44	uc001asm.3	Q9H4M3	OTTHUMG00000002071	ENST00000251547.5:c.759G>A	1.37:g.11721321G>A		128.0	0.0	0		141.0	66.0	0.468085	NM_183412	B3KNZ2|B7Z743|Q5TGX2|Q5TGX4|Q5TGX5|Q68DJ9|Q8WWY2	Missense_Mutation	SNP	ENST00000251547.5	37	CCDS132.1	145	0.06639194139194139	135	0.27439024390243905	4	0.011049723756906077	0	0.0	6	0.0079155672823219	G	11.75	1.732499	0.30684	0.247163	0.003837	ENSG00000132879	ENST00000251546;ENST00000376768;ENST00000376762;ENST00000376760	T;T;T;T	0.38401	1.2;1.14;1.2;1.2	4.82	-4.76	0.03229	.	0.998809	0.08102	N	0.997570	T	0.00012	0.0000	.	.	.	0.23696	P	0.9970848	B;B	0.10296	0.0;0.003	B;B	0.06405	0.001;0.002	T	0.31251	-0.9950	8	0.62326	D	0.03	-13.878	10.7614	0.46266	0.1572:0.1065:0.7363:0.0	rs12057383;rs56815691	244;212	B7Z1P2;Q9H4M3-2	.;.	T	212;244;212;212	ENSP00000251546:A212T;ENSP00000365959:A244T;ENSP00000365953:A212T;ENSP00000365951:A212T	ENSP00000251546:A212T	A	+	1	0	FBXO44	11643908	0.000000	0.05858	0.924000	0.36721	0.260000	0.26232	-0.672000	0.05244	-1.124000	0.02936	-0.258000	0.10820	GCT	G|0.924;A|0.076	0.076	strong		0.637	FBXO44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005761.1	NM_183412	
CCDC17	149483	hgsc.bcm.edu	37	1	46086588	46086588	+	Missense_Mutation	SNP	T	T	C	rs16832629	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:46086588T>C	ENST00000528266.1	-	11	1733	c.1586A>G	c.(1585-1587)aAt>aGt	p.N529S	CCDC17_ENST00000343901.2_Missense_Mutation_p.N497S|CCDC17_ENST00000445048.2_Intron|CCDC17_ENST00000421127.2_Missense_Mutation_p.N520S|CCDC17_ENST00000464739.1_5'Flank			Q96LX7	CCD17_HUMAN	coiled-coil domain containing 17	529										kidney(1)|large_intestine(1)|lung(1)|ovary(2)	5	Acute lymphoblastic leukemia(166;0.155)					AGGAATCCCATTCAGCTGCCC	0.577													T|||	32	0.00638978	0.0227	0.0029	5008	,	,		22169	0.0		0.0	False		,,,				2504	0.0				p.N529S		Atlas-SNP	.											.	CCDC17	54	.	0			c.A1586G						PASS	.	T	SER/ASN,SER/ASN	81,4325	68.7+/-106.4	0,81,2122	49.0	44.0	46.0		1586,1559	4.8	0.8	1	dbSNP_123	46	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	CCDC17	NM_001114938.2,NM_001190182.1	46,46	0,82,6421	CC,CT,TT		0.0116,1.8384,0.6305	probably-damaging,probably-damaging	529/623,520/614	46086588	82,12924	2203	4300	6503	SO:0001583	missense	149483	exon11			ATCCCATTCAGCT		CCDS44131.1, CCDS44131.2, CCDS53314.1	1p34.1	2014-02-12			ENSG00000159588	ENSG00000159588			26574	protein-coding gene	gene with protein product							Standard	NM_001190182		Approved	FLJ33084	uc010olt.2	Q96LX7	OTTHUMG00000007822	ENST00000528266.1:c.1586A>G	1.37:g.46086588T>C	ENSP00000432172:p.Asn529Ser	128.0	0.0	0		140.0	57.0	0.407143	NM_001114938	A1A4Y7|B4DNX7|B4E1Q5|C9J8L2|Q0P683|Q5T629	Missense_Mutation	SNP	ENST00000528266.1	37	CCDS44131.2	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	T	20.8	4.050511	0.75960	0.018384	1.16E-4	ENSG00000159588	ENST00000421127;ENST00000343901;ENST00000528266	T;T;T	0.48201	0.82;0.82;0.82	5.92	4.77	0.60923	.	0.130657	0.52532	D	0.000077	T	0.49389	0.1554	M	0.71581	2.175	0.36900	D	0.890378	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.70227	0.954;0.968;0.954	T	0.68492	-0.5394	10	0.87932	D	0	-5.1285	11.5274	0.50588	0.1344:0.0:0.0:0.8656	rs16832629	529;520;497	Q96LX7;Q96LX7-5;F2Z395	CCD17_HUMAN;.;.	S	520;497;529	ENSP00000389415:N520S;ENSP00000341451:N497S;ENSP00000432172:N529S	ENSP00000341451:N497S	N	-	2	0	CCDC17	45859175	0.991000	0.36638	0.794000	0.32065	0.951000	0.60555	2.283000	0.43470	1.021000	0.39600	0.533000	0.62120	AAT	T|0.993;C|0.007	0.007	strong		0.577	CCDC17-008	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386833.1	NM_152500	
ENOX1	55068	hgsc.bcm.edu	37	13	43987003	43987003	+	Missense_Mutation	SNP	C	C	G	rs7338624	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:43987003C>G	ENST00000261488.6	-	4	625	c.48G>C	c.(46-48)gaG>gaC	p.E16D	ENOX1_ENST00000412891.1_Missense_Mutation_p.E16D	NM_001242863.1|NM_017993.3	NP_001229792.1|NP_060463.2	Q8TC92	ENOX1_HUMAN	ecto-NOX disulfide-thiol exchanger 1	16			E -> D (in dbSNP:rs7338624). {ECO:0000269|PubMed:19055324}.		rhythmic process (GO:0048511)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)	nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(3)|large_intestine(7)|lung(18)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(1)	34		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)		TCTGAGGAAGCTCCTGGGGAA	0.498													C|||	242	0.0483227	0.1778	0.0101	5008	,	,		16486	0.0		0.0	False		,,,				2504	0.0				p.E16D		Atlas-SNP	.											.	ENOX1	158	.	0			c.G48C						PASS	.	C	ASP/GLU,ASP/GLU,ASP/GLU	677,3729	286.3+/-278.7	49,579,1575	125.0	111.0	116.0		48,48,48	2.9	0.9	13	dbSNP_116	116	9,8591	5.7+/-21.5	0,9,4291	yes	missense,missense,missense	ENOX1	NM_001127615.1,NM_001242863.1,NM_017993.3	45,45,45	49,588,5866	GG,GC,CC		0.1047,15.3654,5.2745	benign,benign,benign	16/644,16/644,16/644	43987003	686,12320	2203	4300	6503	SO:0001583	missense	55068	exon4			AGGAAGCTCCTGG	EF432052	CCDS9389.1	13q14.11	2013-02-12			ENSG00000120658	ENSG00000120658		"""RNA binding motif (RRM) containing"""	25474	protein-coding gene	gene with protein product		610914				11360993	Standard	NM_001127615		Approved	FLJ10094, PIG38, CNOX, cCNOX	uc001uza.4	Q8TC92	OTTHUMG00000016818	ENST00000261488.6:c.48G>C	13.37:g.43987003C>G	ENSP00000261488:p.Glu16Asp	96.0	0.0	0		93.0	49.0	0.526882	NM_017993	A4GU15|A6NMH9|B7Z5K1|Q2TU81|Q5VT11|Q9NWE0	Missense_Mutation	SNP	ENST00000261488.6	37	CCDS9389.1	78	0.03571428571428571	74	0.15040650406504066	4	0.011049723756906077	0	0.0	0	0.0	C	11.61	1.690096	0.29962	0.153654	0.001047	ENSG00000120658	ENST00000261488;ENST00000412891	T;T	0.44083	0.93;0.93	5.91	2.88	0.33553	.	0.688144	0.14119	N	0.340181	T	0.00109	0.0003	N	0.08118	0	0.09310	P	0.99999166027	B	0.02656	0.0	B	0.01281	0.0	T	0.18241	-1.0343	9	0.19590	T	0.45	-0.328	2.7291	0.05222	0.2036:0.4159:0.0:0.3805	rs7338624;rs52798713;rs7338624	16	Q8TC92	ENOX1_HUMAN	D	16	ENSP00000261488:E16D;ENSP00000415054:E16D	ENSP00000261488:E16D	E	-	3	2	ENOX1	42885003	0.996000	0.38824	0.871000	0.34182	0.975000	0.68041	1.058000	0.30504	0.842000	0.35045	0.655000	0.94253	GAG	C|0.955;G|0.045	0.045	strong		0.498	ENOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044717.2	NM_017993	
CGN	57530	hgsc.bcm.edu	37	1	151493098	151493098	+	Silent	SNP	C	C	T	rs141884525	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:151493098C>T	ENST00000271636.7	+	5	1204	c.1071C>T	c.(1069-1071)gcC>gcT	p.A357A		NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	351	Interacts with ZO-2.				transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|myosin complex (GO:0016459)|tight junction (GO:0005923)	actin binding (GO:0003779)|motor activity (GO:0003774)			NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			CTACTAAGGCCGTGGCAGGGC	0.557													C|||	28	0.00559105	0.0106	0.0	5008	,	,		19386	0.0129		0.0	False		,,,				2504	0.001				p.A357A		Atlas-SNP	.											.	CGN	106	.	0			c.C1071T						PASS	.	C		31,4375	36.8+/-68.6	0,31,2172	76.0	68.0	71.0		1071	3.0	0.0	1	dbSNP_134	71	0,8600		0,0,4300	no	coding-synonymous	CGN	NM_020770.2		0,31,6472	TT,TC,CC		0.0,0.7036,0.2384		357/1204	151493098	31,12975	2203	4300	6503	SO:0001819	synonymous_variant	57530	exon5			TAAGGCCGTGGCA	AB037740	CCDS999.1	1q21	2008-02-05			ENSG00000143375	ENSG00000143375			17429	protein-coding gene	gene with protein product		609473				11042084, 12529927	Standard	NM_020770		Approved	KIAA1319	uc009wmw.3	Q9P2M7	OTTHUMG00000012497	ENST00000271636.7:c.1071C>T	1.37:g.151493098C>T		192.0	0.0	0		196.0	101.0	0.515306	NM_020770	A6H8L3|A7MD22|Q5T386|Q9NR25	Silent	SNP	ENST00000271636.7	37	CCDS999.1	5	0.0022893772893772895	2	0.0040650406504065045	0	0.0	3	0.005244755244755245	0	0.0	C	1.548	-0.540081	0.04053	0.007036	0.0	ENSG00000143375	ENST00000416743	.	.	.	4.97	3.02	0.34903	.	.	.	.	.	T	0.20495	0.0493	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.18461	-1.0336	4	.	.	.	0.3924	10.9367	0.47249	0.0:0.6821:0.2427:0.0752	.	.	.	.	L	66	.	.	P	+	2	0	CGN	149759722	0.026000	0.19158	0.030000	0.17652	0.001000	0.01503	0.384000	0.20668	0.266000	0.21894	-0.797000	0.03246	CCG	C|0.997;T|0.003	0.003	strong		0.557	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034900.3	NM_020770	
UNC5A	90249	hgsc.bcm.edu	37	5	176305523	176305523	+	Silent	SNP	C	C	T	rs146460064	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:176305523C>T	ENST00000329542.4	+	13	2341	c.2067C>T	c.(2065-2067)caC>caT	p.H689H	UNC5A_ENST00000261961.3_Silent_p.H649H	NM_133369.2	NP_588610.2	Q6ZN44	UNC5A_HUMAN	unc-5 homolog A (C. elegans)	689					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(4)|kidney(3)|large_intestine(2)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)	34	all_cancers(89;0.000119)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGTACTTGCACTGCACCTTCA	0.602													C|||	8	0.00159744	0.0061	0.0	5008	,	,		20146	0.0		0.0	False		,,,				2504	0.0				p.H689H		Atlas-SNP	.											.	UNC5A	76	.	0			c.C2067T						PASS	.	C		41,4365	44.6+/-78.6	0,41,2162	107.0	83.0	91.0		2067	3.8	1.0	5	dbSNP_134	91	0,8600		0,0,4300	no	coding-synonymous	UNC5A	NM_133369.2		0,41,6462	TT,TC,CC		0.0,0.9305,0.3152		689/843	176305523	41,12965	2203	4300	6503	SO:0001819	synonymous_variant	90249	exon13			CTTGCACTGCACC	AB075856	CCDS34299.1	5q35.3	2013-01-11	2001-11-28		ENSG00000113763	ENSG00000113763		"""Immunoglobulin superfamily / I-set domain containing"""	12567	protein-coding gene	gene with protein product		607869	"""unc5 (C.elegans homolog) a"""				Standard	XM_006714927		Approved	KIAA1976, UNC5H1	uc003mey.3	Q6ZN44	OTTHUMG00000163225	ENST00000329542.4:c.2067C>T	5.37:g.176305523C>T		223.0	1.0	0.00448431		222.0	116.0	0.522523	NM_133369	B2RXE6|Q8TF26|Q96GP4	Silent	SNP	ENST00000329542.4	37	CCDS34299.1																																																																																			C|0.996;T|0.004	0.004	strong		0.602	UNC5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372166.1	XM_030300	
C10orf71	118461	hgsc.bcm.edu	37	10	50532155	50532155	+	Missense_Mutation	SNP	T	T	G	rs61453891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:50532155T>G	ENST00000374144.3	+	3	1853	c.1565T>G	c.(1564-1566)gTg>gGg	p.V522G	C10orf71_ENST00000323868.4_Missense_Mutation_p.V522G			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	522			V -> G (in dbSNP:rs61453891).							endometrium(1)	1						CTCTTGAAAGTGCTTGATGAG	0.502													T|||	150	0.0299521	0.1067	0.0115	5008	,	,		21076	0.0		0.001	False		,,,				2504	0.0				p.V522G		Atlas-SNP	.											.	C10orf71	179	.	0			c.T1565G						PASS	.	T	GLY/VAL,GLY/VAL	381,3695		19,343,1676	71.0	75.0	74.0		1565,1565	3.6	0.7	10	dbSNP_129	74	6,8358		0,6,4176	yes	missense,missense	C10orf71	NM_001135196.1,NM_199459.3	109,109	19,349,5852	GG,GT,TT		0.0717,9.3474,3.1109	benign,benign	522/1436,522/720	50532155	387,12053	2038	4182	6220	SO:0001583	missense	118461	exon3			TGAAAGTGCTTGA	AL833265	CCDS44387.1	10q11.23	2012-05-31			ENSG00000177354	ENSG00000177354			26973	protein-coding gene	gene with protein product							Standard	NM_001135196		Approved	FLJ45913	uc021pqa.2	Q711Q0	OTTHUMG00000018190	ENST00000374144.3:c.1565T>G	10.37:g.50532155T>G	ENSP00000363259:p.Val522Gly	82.0	0.0	0		88.0	45.0	0.511364	NM_001135196	A0AVL8	Missense_Mutation	SNP	ENST00000374144.3	37	CCDS44387.1	49	0.022435897435897436	44	0.08943089430894309	5	0.013812154696132596	0	0.0	0	0.0	T	0.006	-2.028060	0.00410	0.093474	7.17E-4	ENSG00000177354	ENST00000323868;ENST00000374144	T;T	0.13196	2.61;3.75	5.52	3.62	0.41486	.	0.465425	0.15896	N	0.239327	T	0.00109	0.0003	N	0.00170	-1.935	0.37892	D	0.930737	B	0.02656	0.0	B	0.01281	0.0	T	0.35001	-0.9806	10	0.08599	T	0.76	.	4.4351	0.11547	0.071:0.3245:0.3604:0.2441	rs61453891	522	Q711Q0-3	.	G	522	ENSP00000318713:V522G;ENSP00000363259:V522G	ENSP00000318713:V522G	V	+	2	0	C10orf71	50202161	0.998000	0.40836	0.723000	0.30687	0.214000	0.24535	1.664000	0.37439	0.651000	0.30788	-0.202000	0.12741	GTG	T|0.977;G|0.023	0.023	strong		0.502	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
HIST3H3	8290	hgsc.bcm.edu	37	1	228612934	228612934	+	Silent	SNP	A	A	G	rs61740979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228612934A>G	ENST00000366696.1	-	1	92	c.93T>C	c.(91-93)ccT>ccC	p.P31P		NM_003493.2	NP_003484.1	Q16695	H31T_HUMAN	histone cluster 3, H3	31					telomere maintenance (GO:0000723)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(1)|lung(2)|prostate(2)|skin(1)	6		Prostate(94;0.0724)				CGCCAGTGGCAGGTGCGCTCT	0.667													g|||	80	0.0159744	0.0567	0.0058	5008	,	,		13386	0.0		0.001	False		,,,				2504	0.0				p.P31P		Atlas-SNP	.											.	HIST3H3	20	.	0			c.T93C						PASS	.	C		240,4162		1,238,1962	36.0	43.0	41.0		93	-6.5	0.0	1	dbSNP_129	41	0,8594		0,0,4297	no	coding-synonymous	HIST3H3	NM_003493.2		1,238,6259	GG,GA,AA		0.0,5.4521,1.8467		31/137	228612934	240,12756	2201	4297	6498	SO:0001819	synonymous_variant	8290	exon1			AGTGGCAGGTGCG	Z49861	CCDS1572.1	1q42.13	2012-09-19	2006-10-11	2003-02-21	ENSG00000168148	ENSG00000168148		"""Histones / Replication-dependent"""	4778	protein-coding gene	gene with protein product		602820	"""H3 histone family, member T"", ""histone 3, H3"""	H3FT		8834248, 12408966	Standard	NM_003493		Approved	H3t, H3/g, H3.4	uc001hsx.1	Q16695	OTTHUMG00000040044	ENST00000366696.1:c.93T>C	1.37:g.228612934A>G		93.0	0.0	0		64.0	24.0	0.375	NM_003493	B2R5K3|Q6FGU4	Silent	SNP	ENST00000366696.1	37	CCDS1572.1																																																																																			A|0.981;G|0.019	0.019	strong		0.667	HIST3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096595.2	NM_003493	
OR5T2	219464	hgsc.bcm.edu	37	11	55999879	55999879	+	Silent	SNP	C	C	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55999879C>A	ENST00000313264.4	-	1	858	c.783G>T	c.(781-783)ctG>ctT	p.L261L		NM_001004746.1	NP_001004746.1	Q8NGG2	OR5T2_HUMAN	olfactory receptor, family 5, subfamily T, member 2	261						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(6)|kidney(1)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(1)|stomach(3)	41	Esophageal squamous(21;0.00448)					GAATGGCCAACAGAATCAAAC	0.438																																					p.L261L		Atlas-SNP	.											OR5T2,NS,carcinoma,0,1	OR5T2	107	1	0			c.G783T						scavenged	.						129.0	120.0	123.0					11																	55999879		2201	4296	6497	SO:0001819	synonymous_variant	219464	exon1			GGCCAACAGAATC	AB065838	CCDS31523.1	11q11	2012-08-09			ENSG00000181718	ENSG00000181718		"""GPCR / Class A : Olfactory receptors"""	15296	protein-coding gene	gene with protein product							Standard	NM_001004746		Approved		uc010rjc.2	Q8NGG2	OTTHUMG00000166851	ENST00000313264.4:c.783G>T	11.37:g.55999879C>A		197.0	1.0	0.00507614		219.0	94.0	0.429224	NM_001004746	B9EGX5|Q6IFC8	Silent	SNP	ENST00000313264.4	37	CCDS31523.1																																																																																			.	.	none		0.438	OR5T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391598.1	NM_001004746	
GRHL1	29841	hgsc.bcm.edu	37	2	10101289	10101289	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:10101289C>T	ENST00000324907.9	+	4	529	c.393C>T	c.(391-393)ggC>ggT	p.G131G	GRHL1_ENST00000405379.2_Silent_p.G131G|GRHL1_ENST00000324883.5_5'UTR	NM_198182.2	NP_937825.2	Q9NZI5	GRHL1_HUMAN	grainyhead-like 1 (Drosophila)	131					cellular lipid metabolic process (GO:0044255)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(2)|lung(8)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	17	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.172)|OV - Ovarian serous cystadenocarcinoma(76;0.246)		ACCAGCTGGGCATTGATAAGA	0.498																																					p.G131G		Atlas-SNP	.											.	GRHL1	95	.	0			c.C393T						PASS	.						77.0	84.0	81.0					2																	10101289		1327	2309	3636	SO:0001819	synonymous_variant	29841	exon4			GCTGGGCATTGAT	AF198489	CCDS33144.1, CCDS33144.2	2p25.2	2008-02-05	2005-07-11	2005-07-11	ENSG00000134317	ENSG00000134317			17923	protein-coding gene	gene with protein product		609786	"""transcription factor CP2-like 2"""	TFCP2L2		10644752, 12393799	Standard	NM_198182		Approved	LBP-32, MGR	uc002raa.3	Q9NZI5	OTTHUMG00000151704	ENST00000324907.9:c.393C>T	2.37:g.10101289C>T		177.0	0.0	0		181.0	80.0	0.441989	NM_198182	A6NLA4|B2R7E4|B5MEC2|Q53T93|Q6NWN7|Q6NWN8|Q6NWN9|Q8NI33	Silent	SNP	ENST00000324907.9	37	CCDS33144.2																																																																																			.	.	none		0.498	GRHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323543.2	NM_014552	
MYO19	80179	hgsc.bcm.edu	37	17	34856697	34856697	+	Missense_Mutation	SNP	A	A	G	rs56919948	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34856697A>G	ENST00000431794.3	-	23	2872	c.2350T>C	c.(2350-2352)Tgg>Cgg	p.W784R	MYO19_ENST00000268852.9_Missense_Mutation_p.W584R	NM_001163735.1	NP_001157207.1	Q96H55	MYO19_HUMAN	myosin XIX	784	IQ 2. {ECO:0000255|PROSITE- ProRule:PRU00116}.					cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|urinary_tract(1)	20		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		ACGGCCCGCCACTGCCGCTCC	0.637													G|||	28	0.00559105	0.0204	0.0014	5008	,	,		18434	0.0		0.0	False		,,,				2504	0.0				p.W784R		Atlas-SNP	.											.	MYO19	130	.	0			c.T2350C						PASS	.	G	ARG/TRP,ARG/TRP	74,4174		1,72,2051	14.0	18.0	17.0		2350,1750	2.8	0.4	17	dbSNP_129	17	0,8448		0,0,4224	yes	missense,missense	MYO19	NM_001163735.1,NM_025109.5	101,101	1,72,6275	GG,GA,AA		0.0,1.742,0.5829	benign,benign	784/971,584/771	34856697	74,12622	2124	4224	6348	SO:0001583	missense	80179	exon24			CCCGCCACTGCCG	BC008900	CCDS45654.1, CCDS54112.1, CCDS59283.1	17q12	2014-08-12	2007-09-26	2007-09-26	ENSG00000278259	ENSG00000278259		"""Myosins / Myosin superfamily : Class XIX"""	26234	protein-coding gene	gene with protein product			"""myosin head domain containing 1"""	MYOHD1		17877792, 19932026	Standard	NM_001033580		Approved	FLJ22865	uc010wcy.2	Q96H55	OTTHUMG00000188437	ENST00000431794.3:c.2350T>C	17.37:g.34856697A>G	ENSP00000409936:p.Trp784Arg	73.0	0.0	0		72.0	26.0	0.361111	NM_001163735	Q59GS4|Q9H5X2	Missense_Mutation	SNP	ENST00000431794.3	37	CCDS54112.1	8	0.003663003663003663	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	G	0.005	-2.234560	0.00277	0.01742	0.0	ENSG00000141140	ENST00000431794;ENST00000268852	T;T	0.53640	0.61;0.61	5.12	2.82	0.32997	.	0.000000	0.42548	N	0.000694	T	0.04770	0.0129	N	0.00197	-1.87	0.24385	N	0.994776	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33727	-0.9857	10	0.05959	T	0.93	.	6.7399	0.23431	0.1403:0.0:0.3167:0.543	rs56919948;rs61753952	784;584	Q96H55;Q96H55-4	MYO19_HUMAN;.	R	784;584	ENSP00000409936:W784R;ENSP00000268852:W584R	ENSP00000268852:W584R	W	-	1	0	MYO19	31930810	0.989000	0.36119	0.423000	0.26634	0.007000	0.05969	1.804000	0.38873	0.033000	0.15463	-1.507000	0.00952	TGG	A|0.996;G|0.004	0.004	strong		0.637	MYO19-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451074.1	NM_025109	
TRPC4AP	26133	hgsc.bcm.edu	37	20	33588874	33588874	+	IGR	SNP	G	G	A	rs76931580	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33588874G>A	ENST00000252015.2	-	0	3226				MYH7B_ENST00000262873.7_Silent_p.T1838T			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein						calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|protein ubiquitination (GO:0016567)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process (GO:0006511)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|skin(1)|stomach(1)|urinary_tract(1)	32			BRCA - Breast invasive adenocarcinoma(18;0.00936)			TGGAGCAGACGGTGCGCGAGC	0.647													G|||	66	0.0131789	0.0469	0.0058	5008	,	,		17893	0.0		0.0	False		,,,				2504	0.0				p.T1838T		Atlas-SNP	.											.	MYH7B	145	.	0			c.G5514A						PASS	.	G		149,4255	97.1+/-135.8	0,149,2053	40.0	50.0	47.0		5514	-9.1	0.1	20	dbSNP_131	47	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	MYH7B	NM_020884.3		0,151,6351	AA,AG,GG		0.0233,3.3833,1.1612		1838/1984	33588874	151,12853	2202	4300	6502	SO:0001628	intergenic_variant	57644	exon41			GCAGACGGTGCGC	AF055022	CCDS13246.1, CCDS46591.1	20q11.23	2014-06-13	2003-10-06	2003-10-08	ENSG00000100991	ENSG00000100991			16181	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 158"""	608430	"""chromosome 20 open reading frame 188"""	C20orf188			Standard	NM_015638		Approved	DKFZP727M231, DKFZp586C1223, dJ756N5.2, TRRP4AP, PPP1R158	uc002xbk.3	Q8TEL6	OTTHUMG00000032319		20.37:g.33588874G>A		198.0	0.0	0		192.0	85.0	0.442708	NM_020884	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Silent	SNP	ENST00000252015.2	37	CCDS13246.1																																																																																			G|0.996;A|0.004	0.004	strong		0.647	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638	
SCN5A	6331	hgsc.bcm.edu	37	3	38592356	38592356	+	Missense_Mutation	SNP	A	A	G	rs45563942	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:38592356A>G	ENST00000333535.4	-	28	5656	c.5507T>C	c.(5506-5508)aTc>aCc	p.I1836T	SCN5A_ENST00000450102.2_Missense_Mutation_p.I1782T|SCN5A_ENST00000414099.2_Missense_Mutation_p.I1818T|SCN5A_ENST00000443581.1_Missense_Mutation_p.I1835T|SCN5A_ENST00000425664.1_Missense_Mutation_p.I1818T|SCN5A_ENST00000455624.2_Missense_Mutation_p.I1803T|SCN5A_ENST00000413689.1_Missense_Mutation_p.I1836T|SCN5A_ENST00000423572.2_Missense_Mutation_p.I1835T|SCN5A_ENST00000464652.1_5'Flank|SCN5A_ENST00000451551.2_Missense_Mutation_p.I1782T|SCN5A_ENST00000449557.2_Missense_Mutation_p.I1782T			Q14524	SCN5A_HUMAN	sodium channel, voltage-gated, type V, alpha subunit	1836					AV node cell to bundle of His cell communication (GO:0086067)|brainstem development (GO:0003360)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|cardiac ventricle development (GO:0003231)|cellular response to calcium ion (GO:0071277)|cerebellum development (GO:0021549)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane depolarization during SA node cell action potential (GO:0086046)|neuronal action potential (GO:0019228)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of action potential (GO:0045760)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of sodium ion transport (GO:0010765)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|telencephalon development (GO:0021537)|ventricular cardiac muscle cell action potential (GO:0086005)	caveola (GO:0005901)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)	ankyrin binding (GO:0030506)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|fibroblast growth factor binding (GO:0017134)|ion channel binding (GO:0044325)|nitric-oxide synthase binding (GO:0050998)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			NS(3)|breast(2)|central_nervous_system(3)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(25)|lung(27)|ovary(6)|pancreas(3)|prostate(10)|skin(9)|upper_aerodigestive_tract(4)	107	Medulloblastoma(35;0.163)			KIRC - Kidney renal clear cell carcinoma(284;0.0822)|Kidney(284;0.1)	Ajmaline(DB01426)|Aprindine(DB01429)|Benzonatate(DB00868)|Carbamazepine(DB00564)|Cinchocaine(DB00527)|Cocaine(DB00907)|Disopyramide(DB00280)|Encainide(DB01228)|Ethotoin(DB00754)|Flecainide(DB01195)|Fosphenytoin(DB01320)|Hexylcaine(DB00473)|Indecainide(DB00192)|Lidocaine(DB00281)|Mexiletine(DB00379)|Moricizine(DB00680)|Oxcarbazepine(DB00776)|Phenytoin(DB00252)|Prilocaine(DB00750)|Procainamide(DB01035)|Propafenone(DB01182)|Quinidine barbiturate(DB01346)|Quinidine(DB00908)|Ranolazine(DB00243)|Riluzole(DB00740)|Tocainide(DB01056)|Valproic Acid(DB00313)|Verapamil(DB00661)|Zonisamide(DB00909)	GTCCATGTTGATGAGGCTTAT	0.552													A|||	8	0.00159744	0.0061	0.0	5008	,	,		21013	0.0		0.0	False		,,,				2504	0.0				p.I1836T		Atlas-SNP	.											.	SCN5A	634	.	0			c.T5507C						PASS	.	A	THR/ILE,THR/ILE,THR/ILE,THR/ILE,THR/ILE,THR/ILE	11,4249		0,11,2119	85.0	92.0	90.0		5504,5507,5453,5408,5345,5507	4.8	1.0	3	dbSNP_127	90	0,8484		0,0,4242	yes	missense,missense,missense,missense,missense,missense	SCN5A	NM_000335.4,NM_001099404.1,NM_001099405.1,NM_001160160.1,NM_001160161.1,NM_198056.2	89,89,89,89,89,89	0,11,6361	GG,GA,AA		0.0,0.2582,0.0863	benign,benign,benign,benign,benign,benign	1835/2016,1836/2017,1818/1999,1803/1984,1782/1963,1836/2017	38592356	11,12733	2130	4242	6372	SO:0001583	missense	6331	exon28			ATGTTGATGAGGC	AJ310893	CCDS46796.1, CCDS46797.1, CCDS46798.1, CCDS46799.1, CCDS54569.1, CCDS54570.1	3p21	2014-09-17	2007-01-23		ENSG00000183873	ENSG00000183873		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10593	protein-coding gene	gene with protein product	"""long QT syndrome 3"""	600163	"""sodium channel, voltage-gated, type V, alpha (long QT syndrome 3)"""	CMD1E		7842012, 15466643, 16382098	Standard	NM_198056		Approved	Nav1.5, LQT3, HB1, HBBD, PFHB1, IVF, HB2, HH1, SSS1, CDCD2, CMPD2, ICCD	uc021wvl.1	Q14524	OTTHUMG00000156166	ENST00000333535.4:c.5507T>C	3.37:g.38592356A>G	ENSP00000328968:p.Ile1836Thr	72.0	0.0	0		72.0	37.0	0.513889	NM_198056	A5H1P8|A6N922|A6N923|B2RTU0|E7ET19|E9PEF3|E9PEK2|E9PFW7|Q59H93|Q75RX9|Q75RY0|Q86UR3|Q8IZC9|Q96J69	Missense_Mutation	SNP	ENST00000333535.4	37	CCDS46796.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	16.43	3.122483	0.56613	0.002582	0.0	ENSG00000183873	ENST00000414099;ENST00000423572;ENST00000413689;ENST00000451551;ENST00000443581;ENST00000425664;ENST00000333535;ENST00000455624;ENST00000450102;ENST00000449557	D;D;D;D;D;D;D;D;D;D	0.96427	-3.92;-3.93;-3.93;-4.0;-3.93;-3.92;-3.93;-4.01;-4.0;-4.0	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	D	0.97539	0.9194	M	0.89095	3.005	0.49213	D	0.999767	B;P;B;B;B;B	0.50710	0.146;0.938;0.07;0.17;0.065;0.261	B;D;B;P;B;P	0.73380	0.379;0.98;0.265;0.547;0.351;0.734	D	0.96083	0.9055	10	0.66056	D	0.02	.	14.5421	0.68002	1.0:0.0:0.0:0.0	rs45563942	1782;1803;1818;1836;1835;1836	E9PEF3;E9PHB6;E9PG18;Q14524;Q14524-2;E9PEK2	.;.;.;SCN5A_HUMAN;.;.	T	1818;1835;1836;1782;1835;1818;1836;1803;1782;1782	ENSP00000398962:I1818T;ENSP00000398266:I1835T;ENSP00000410257:I1836T;ENSP00000388797:I1782T;ENSP00000397915:I1835T;ENSP00000416634:I1818T;ENSP00000328968:I1836T;ENSP00000399524:I1803T;ENSP00000403355:I1782T;ENSP00000413996:I1782T	ENSP00000328968:I1836T	I	-	2	0	SCN5A	38567360	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.133000	0.94460	2.025000	0.59659	0.460000	0.39030	ATC	A|0.999;G|0.001	0.001	strong		0.552	SCN5A-014	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377958.1	NM_198056	
SIDT1	54847	hgsc.bcm.edu	37	3	113285272	113285272	+	Silent	SNP	A	A	C	rs61734094	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:113285272A>C	ENST00000264852.4	+	2	954	c.228A>C	c.(226-228)acA>acC	p.T76T	SIDT1_ENST00000393830.3_Silent_p.T76T	NM_017699.2	NP_060169.2	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1	76					dsRNA transport (GO:0033227)	integral component of membrane (GO:0016021)	RNA transmembrane transporter activity (GO:0051033)			breast(1)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|liver(2)|lung(15)|ovary(3)|pancreas(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50						TGCAGGTGACAGCCGTGAGGG	0.507													C|||	101	0.0201677	0.0545	0.0086	5008	,	,		19117	0.0079		0.0099	False		,,,				2504	0.0051				p.T76T		Atlas-SNP	.											.	SIDT1	99	.	0			c.A228C						PASS	.	C		265,4141	802.1+/-415.6	10,245,1948	246.0	191.0	210.0		228	-11.2	0.0	3	dbSNP_129	210	60,8540	816.6+/-406.9	2,56,4242	no	coding-synonymous	SIDT1	NM_017699.2		12,301,6190	CC,CA,AA		0.6977,6.0145,2.4988		76/828	113285272	325,12681	2203	4300	6503	SO:0001819	synonymous_variant	54847	exon2			GGTGACAGCCGTG	AK000181	CCDS2974.1	3q13.31	2009-11-26			ENSG00000072858	ENSG00000072858			25967	protein-coding gene	gene with protein product		606816					Standard	NM_017699		Approved	FLJ20174, SID-1	uc003eak.3	Q9NXL6	OTTHUMG00000159299	ENST00000264852.4:c.228A>C	3.37:g.113285272A>C		133.0	0.0	0		139.0	72.0	0.517986	NM_017699	Q17RR4	Silent	SNP	ENST00000264852.4	37	CCDS2974.1																																																																																			A|0.978;C|0.022	0.022	strong		0.507	SIDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317564.1	NM_017699	
FURIN	5045	hgsc.bcm.edu	37	15	91419098	91419098	+	Missense_Mutation	SNP	C	C	T	rs16944971	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:91419098C>T	ENST00000268171.3	+	2	407	c.128C>T	c.(127-129)gCg>gTg	p.A43V		NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	43			A -> V (in dbSNP:rs16944971).		cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of low-density lipoprotein particle receptor catabolic process (GO:0032804)|negative regulation of transforming growth factor beta1 production (GO:0032911)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-translational protein modification (GO:0043687)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)|regulation of protein catabolic process (GO:0042176)|secretion by cell (GO:0032940)|signal peptide processing (GO:0006465)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|nerve growth factor binding (GO:0048406)|peptidase activity (GO:0008233)|peptide binding (GO:0042277)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(4)|endometrium(4)|large_intestine(3)|liver(2)|lung(13)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	36	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			GGAGGCCCAGCGGTGGCCAAC	0.622													C|||	143	0.0285543	0.0938	0.0173	5008	,	,		18737	0.0		0.007	False		,,,				2504	0.0				p.A43V		Atlas-SNP	.											.	FURIN	85	.	0			c.C128T						PASS	.	C	VAL/ALA	340,4048		9,322,1863	54.0	39.0	44.0		128	3.8	0.0	15	dbSNP_123	44	30,8546		0,30,4258	yes	missense	FURIN	NM_002569.2	64	9,352,6121	TT,TC,CC		0.3498,7.7484,2.8541	benign	43/795	91419098	370,12594	2194	4288	6482	SO:0001583	missense	5045	exon2			GCCCAGCGGTGGC	X17094	CCDS10364.1	15q26.1	2007-01-24	2002-12-04	2002-12-06	ENSG00000140564	ENSG00000140564			8568	protein-coding gene	gene with protein product		136950	"""paired basic amino acid cleaving enzyme (furin, membrane associated receptor protein)"""	PCSK3, FUR, PACE		2251280, 1741956	Standard	NM_002569		Approved	SPC1	uc002bpu.1	P09958	OTTHUMG00000149831	ENST00000268171.3:c.128C>T	15.37:g.91419098C>T	ENSP00000268171:p.Ala43Val	59.0	0.0	0		57.0	57.0	1	NM_002569	Q14336|Q6LBS3|Q9UCZ5	Missense_Mutation	SNP	ENST00000268171.3	37	CCDS10364.1	52	0.023809523809523808	38	0.07723577235772358	11	0.03038674033149171	0	0.0	3	0.00395778364116095	C	3.280	-0.147217	0.06627	0.077484	0.003498	ENSG00000140564	ENST00000268171	T	0.31510	1.49	4.77	3.85	0.44370	Proteinase inhibitor, propeptide (1);	0.284147	0.31963	N	0.006784	T	0.00936	0.0031	L	0.35487	1.065	0.09310	N	1	B	0.14438	0.01	B	0.12156	0.007	T	0.09443	-1.0674	10	0.32370	T	0.25	-14.4547	4.2077	0.10497	0.2574:0.5633:0.0:0.1793	rs16944971;rs16944971	43	P09958	FURIN_HUMAN	V	43	ENSP00000268171:A43V	ENSP00000268171:A43V	A	+	2	0	FURIN	89220102	0.000000	0.05858	0.004000	0.12327	0.036000	0.12997	0.595000	0.24029	1.257000	0.44085	0.555000	0.69702	GCG	C|0.968;T|0.032	0.032	strong		0.622	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569	
STAB2	55576	hgsc.bcm.edu	37	12	104089586	104089586	+	Silent	SNP	C	C	T	rs17034395	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:104089586C>T	ENST00000388887.2	+	33	3750	c.3546C>T	c.(3544-3546)atC>atT	p.I1182I		NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						ACAATGCCATCGAGAATTACA	0.403													.|||	380	0.0758786	0.2269	0.0231	5008	,	,		24489	0.0		0.0	False		,,,				2504	0.0654				p.I1182I		Atlas-SNP	.											.	STAB2	370	.	0			c.C3546T						PASS	.	C		855,3551	335.5+/-303.9	98,659,1446	112.0	110.0	110.0		3546	-1.1	1.0	12	dbSNP_123	110	19,8581	12.6+/-44.7	0,19,4281	no	coding-synonymous	STAB2	NM_017564.9		98,678,5727	TT,TC,CC		0.2209,19.4054,6.72		1182/2552	104089586	874,12132	2203	4300	6503	SO:0001819	synonymous_variant	55576	exon33			TGCCATCGAGAAT	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"""hyaluronic acid receptor for endocytosis"""	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.3546C>T	12.37:g.104089586C>T		142.0	0.0	0		123.0	52.0	0.422764	NM_017564		Silent	SNP	ENST00000388887.2	37	CCDS31888.1																																																																																			C|0.930;T|0.070	0.070	strong		0.403	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
MAPK13	5603	hgsc.bcm.edu	37	6	36104468	36104468	+	Silent	SNP	C	C	G	rs115013068	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36104468C>G	ENST00000211287.4	+	7	793	c.531C>G	c.(529-531)gcC>gcG	p.A177A	MAPK13_ENST00000373766.5_Silent_p.A177A|MAPK13_ENST00000373759.1_Silent_p.A99A|MAPK13_ENST00000373761.6_Silent_p.A167A	NM_002754.4	NP_002745.1	O15264	MK13_HUMAN	mitogen-activated protein kinase 13	177	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell cycle (GO:0007049)|intracellular signal transduction (GO:0035556)|MAPK cascade (GO:0000165)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-6 production (GO:0032755)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|response to osmotic stress (GO:0006970)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(2)|lung(2)|prostate(2)|skin(1)	12						ATGCAGACGCCGAGATGACTG	0.577													C|||	54	0.0107827	0.034	0.013	5008	,	,		20219	0.0		0.0	False		,,,				2504	0.0				p.A177A		Atlas-SNP	.											.	MAPK13	65	.	0			c.C531G						PASS	.	C		134,4272	94.4+/-133.1	3,128,2072	29.0	29.0	29.0		531	-10.2	0.0	6	dbSNP_132	29	0,8600		0,0,4300	no	coding-synonymous	MAPK13	NM_002754.3		3,128,6372	GG,GC,CC		0.0,3.0413,1.0303		177/366	36104468	134,12872	2203	4300	6503	SO:0001819	synonymous_variant	5603	exon7			AGACGCCGAGATG	Y10488	CCDS4818.1	6p21	2011-06-09			ENSG00000156711	ENSG00000156711	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinases"""	6875	protein-coding gene	gene with protein product		602899		PRKM13		9295308, 9218798	Standard	NM_002754		Approved	SAPK4, p38delta	uc003ols.4	O15264	OTTHUMG00000014587	ENST00000211287.4:c.531C>G	6.37:g.36104468C>G		169.0	0.0	0		187.0	98.0	0.524064	NM_002754	O14739|O15124|Q5U4A5|Q6FI46|Q9UNU0	Silent	SNP	ENST00000211287.4	37	CCDS4818.1																																																																																			C|0.990;G|0.010	0.010	strong		0.577	MAPK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040328.1		
DEFB136	613210	hgsc.bcm.edu	37	8	11831557	11831557	+	Silent	SNP	G	G	A	rs73538682	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11831557G>A	ENST00000382209.2	-	2	125	c.126C>T	c.(124-126)ttC>ttT	p.F42F		NM_001033018.2	NP_001028190.2	Q30KP8	DB136_HUMAN	defensin, beta 136	42					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(2)|large_intestine(1)|lung(4)	7			STAD - Stomach adenocarcinoma(15;0.033)	COAD - Colon adenocarcinoma(149;0.163)		GCGGACACCCGAAGAAACATA	0.473													G|||	147	0.029353	0.1067	0.0058	5008	,	,		20997	0.0		0.002	False		,,,				2504	0.0				p.F42F		Atlas-SNP	.											.	DEFB136	16	.	0			c.C126T						PASS	.	G		356,3638		15,326,1656	169.0	174.0	173.0		126	-2.5	0.7	8	dbSNP_130	173	5,8353		0,5,4174	no	coding-synonymous	DEFB136	NM_001033018.2		15,331,5830	AA,AG,GG		0.0598,8.9134,2.9226		42/79	11831557	361,11991	1997	4179	6176	SO:0001819	synonymous_variant	613210	exon2			ACACCCGAAGAAA	DQ012026	CCDS43709.1	8p23.1	2011-07-19			ENSG00000205884	ENSG00000205884		"""Defensins, beta"""	34433	protein-coding gene	gene with protein product						16033865	Standard	NM_001033018		Approved	DEFB137	uc011kxm.2	Q30KP8	OTTHUMG00000158720	ENST00000382209.2:c.126C>T	8.37:g.11831557G>A		173.0	1.0	0.00578035		141.0	141.0	1	NM_001033018	Q4QY36	Silent	SNP	ENST00000382209.2	37	CCDS43709.1																																																																																			G|0.980;A|0.020	0.020	strong		0.473	DEFB136-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351889.1	NM_001033018	
TET1	80312	hgsc.bcm.edu	37	10	70406747	70406747	+	Missense_Mutation	SNP	A	A	G	rs144156611	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:70406747A>G	ENST00000373644.4	+	4	4470	c.4261A>G	c.(4261-4263)Acc>Gcc	p.T1421A		NM_030625.2	NP_085128.2	Q8NFU7	TET1_HUMAN	tet methylcytosine dioxygenase 1	1421					chromatin modification (GO:0016568)|DNA demethylation (GO:0080111)|inner cell mass cell differentiation (GO:0001826)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of DNA methylation (GO:0044030)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	iron ion binding (GO:0005506)|methylcytosine dioxygenase activity (GO:0070579)|structure-specific DNA binding (GO:0043566)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(2)|ovary(5)|prostate(1)|upper_aerodigestive_tract(2)	21						TGAACTGCCCACCTGCAGCTG	0.368													A|||	43	0.00858626	0.0008	0.0504	5008	,	,		19982	0.0		0.005	False		,,,				2504	0.002				p.T1421A		Atlas-SNP	.											.	TET1	255	.	0			c.A4261G						PASS	.	A	ALA/THR	4,4402	8.1+/-20.4	0,4,2199	61.0	58.0	59.0		4261	-10.4	0.0	10	dbSNP_134	59	39,8561	24.6+/-71.5	0,39,4261	yes	missense	TET1	NM_030625.2	58	0,43,6460	GG,GA,AA		0.4535,0.0908,0.3306	benign	1421/2137	70406747	43,12963	2203	4300	6503	SO:0001583	missense	80312	exon4			CTGCCCACCTGCA	AF430147	CCDS7281.1	10q21	2014-02-18	2011-09-30	2008-03-12	ENSG00000138336	ENSG00000138336			29484	protein-coding gene	gene with protein product	"""leukemia-associated protein with a CXXC domain"", ""ten-eleven translocation-1"""	607790	"""CXXC zinc finger 6"", ""tet oncogene 1"""	CXXC6		12124344, 12646957	Standard	NM_030625		Approved	LCX, KIAA1676, bA119F7.1	uc001jok.4	Q8NFU7	OTTHUMG00000018359	ENST00000373644.4:c.4261A>G	10.37:g.70406747A>G	ENSP00000362748:p.Thr1421Ala	140.0	0.0	0		127.0	54.0	0.425197	NM_030625	Q5VUP7|Q7Z6B6|Q8TCR1|Q9C0I7	Missense_Mutation	SNP	ENST00000373644.4	37	CCDS7281.1	22	0.010073260073260074	0	0.0	19	0.052486187845303865	0	0.0	3	0.00395778364116095	A	11.19	1.565969	0.27915	9.08E-4	0.004535	ENSG00000138336	ENST00000373644	T	0.20881	2.04	5.22	-10.4	0.00318	TET cysteine-rich domain (1);	2.737390	0.01161	N	0.006653	T	0.01661	0.0053	L	0.31926	0.97	0.09310	N	1	B	0.14012	0.009	B	0.14023	0.01	T	0.14392	-1.0474	10	0.66056	D	0.02	.	0.6454	0.00817	0.1857:0.2739:0.184:0.3564	.	1421	Q8NFU7	TET1_HUMAN	A	1421	ENSP00000362748:T1421A	ENSP00000362748:T1421A	T	+	1	0	TET1	70076753	0.001000	0.12720	0.000000	0.03702	0.862000	0.49288	-0.836000	0.04382	-2.685000	0.00406	0.455000	0.32223	ACC	A|0.995;G|0.005	0.005	strong		0.368	TET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048354.1	NM_030625	
EMX2	2018	hgsc.bcm.edu	37	10	119305282	119305282	+	Silent	SNP	C	C	A	rs424112	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:119305282C>A	ENST00000553456.3	+	2	1370	c.546C>A	c.(544-546)gcC>gcA	p.A182A	EMX2OS_ENST00000551288.1_RNA|EMX2_ENST00000442245.4_Intron|EMX2_ENST00000546446.1_3'UTR	NM_004098.3	NP_004089.1	Q04743	EMX2_HUMAN	empty spiracles homeobox 2	182					anterior/posterior pattern specification (GO:0009952)|cell proliferation in forebrain (GO:0021846)|cerebral cortex regionalization (GO:0021796)|dentate gyrus development (GO:0021542)|forebrain cell migration (GO:0021885)|neuron differentiation (GO:0030182)|regulation of transcription, DNA-templated (GO:0006355)|renal system development (GO:0072001)|response to drug (GO:0042493)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|large_intestine(5)|lung(2)|ovary(1)|prostate(2)	12		Colorectal(252;0.109)|Lung NSC(174;0.179)|all_lung(145;0.22)		all cancers(201;0.0133)		TGGTGGGCGCCGAAAGGAAGC	0.642													C|||	191	0.038139	0.1354	0.0159	5008	,	,		15931	0.0		0.001	False		,,,				2504	0.0				p.A182A		Atlas-SNP	.											.	EMX2	25	.	0			c.C546A						PASS	.	C	,	469,3937	219.7+/-237.4	28,413,1762	46.0	44.0	45.0		,546	-3.2	1.0	10	dbSNP_80	45	4,8596	3.7+/-12.6	0,4,4296	no	intron,coding-synonymous	EMX2	NM_001165924.1,NM_004098.3	,	28,417,6058	AA,AC,CC		0.0465,10.6446,3.6368	,	,182/253	119305282	473,12533	2203	4300	6503	SO:0001819	synonymous_variant	2018	exon2			GGGCGCCGAAAGG	AF301598	CCDS7601.1, CCDS53583.1	10q26.11	2011-06-20	2007-02-15		ENSG00000170370	ENSG00000170370		"""Homeoboxes / ANTP class : NKL subclass"""	3341	protein-coding gene	gene with protein product		600035	"""empty spiracles homolog 2 (Drosophila)"""			7959790	Standard	NM_004098		Approved		uc001ldh.4	Q04743	OTTHUMG00000019123	ENST00000553456.3:c.546C>A	10.37:g.119305282C>A		159.0	0.0	0		178.0	95.0	0.533708	NM_004098	G3V305|Q96NN8|Q9BQF4	Silent	SNP	ENST00000553456.3	37	CCDS7601.1																																																																																			C|0.962;A|0.038	0.038	strong		0.642	EMX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050569.4	NM_004098	
SERPINB2	5055	hgsc.bcm.edu	37	18	61565014	61565014	+	Silent	SNP	C	C	T	rs6106	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61565014C>T	ENST00000299502.4	+	5	551	c.471C>T	c.(469-471)gaC>gaT	p.D157D	SERPINB2_ENST00000457692.1_Silent_p.D157D|SERPINB2_ENST00000482254.1_3'UTR	NM_002575.2	NP_002566.1	P05120	PAI2_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 2	157					blood coagulation (GO:0007596)|fibrinolysis (GO:0042730)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|liver(1)|lung(12)|prostate(2)|skin(2)|stomach(1)	32		Esophageal squamous(42;0.131)			Tenecteplase(DB00031)|Urokinase(DB00013)	AGGCAGTAGACTTCCTAGAAT	0.343													C|||	313	0.0625	0.2216	0.0259	5008	,	,		19658	0.0		0.002	False		,,,				2504	0.0				p.D157D		Atlas-SNP	.											.	SERPINB2	63	.	0			c.C471T						PASS	.	C	,	781,3625	308.0+/-290.3	67,647,1489	62.0	67.0	65.0		471,471	2.9	0.9	18	dbSNP_52	65	12,8588	9.1+/-34.3	0,12,4288	no	coding-synonymous,coding-synonymous	SERPINB2	NM_001143818.1,NM_002575.2	,	67,659,5777	TT,TC,CC		0.1395,17.7258,6.0972	,	157/416,157/416	61565014	793,12213	2203	4300	6503	SO:0001819	synonymous_variant	5055	exon5			AGTAGACTTCCTA	Y00630	CCDS11989.1	18q21.3	2014-02-18	2005-08-18		ENSG00000197632	ENSG00000197632		"""Serine (or cysteine) peptidase inhibitors"""	8584	protein-coding gene	gene with protein product		173390	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 2"""	PLANH2, PAI2		24172014	Standard	NM_002575		Approved	HsT1201	uc002ljo.3	P05120	OTTHUMG00000060592	ENST00000299502.4:c.471C>T	18.37:g.61565014C>T		212.0	0.0	0		214.0	106.0	0.495327	NM_002575	Q96E96	Silent	SNP	ENST00000299502.4	37	CCDS11989.1	130	0.05952380952380952	117	0.23780487804878048	12	0.03314917127071823	0	0.0	1	0.0013192612137203166	C	8.325	0.825088	0.16678	0.177258	0.001395	ENSG00000242550	ENST00000397996;ENST00000418725	.	.	.	5.6	2.87	0.33458	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.09552	-1.0669	3	.	.	.	.	8.4939	0.33117	0.0:0.7035:0.0:0.2965	rs6106;rs6106	.	.	.	F	34	.	.	L	+	1	0	SERPINB10	59715994	1.000000	0.71417	0.946000	0.38457	0.866000	0.49608	0.916000	0.28651	0.418000	0.25898	-0.142000	0.14014	CTT	C|0.933;T|0.067	0.067	strong		0.343	SERPINB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134009.1	NM_002575	
ERCC4	2072	hgsc.bcm.edu	37	16	14038659	14038659	+	Missense_Mutation	SNP	T	T	C	rs2020955	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:14038659T>C	ENST00000311895.7	+	10	1993	c.1984T>C	c.(1984-1986)Tct>Cct	p.S662P		NM_005236.2	NP_005227.1	Q92889	XPF_HUMAN	excision repair cross-complementation group 4	662	Nuclease.		S -> P (in dbSNP:rs2020955). {ECO:0000269|Ref.2}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|negative regulation of telomere maintenance (GO:0032205)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair involved in interstrand cross-link repair (GO:1901255)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision (GO:0033683)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)|resolution of meiotic recombination intermediates (GO:0000712)|response to UV (GO:0009411)|telomere maintenance (GO:0000723)|telomere maintenance via telomere shortening (GO:0010834)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	chromosome, telomeric region (GO:0000781)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleotide-excision repair factor 1 complex (GO:0000110)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	damaged DNA binding (GO:0003684)|endodeoxyribonuclease activity (GO:0004520)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)|single-stranded DNA endodeoxyribonuclease activity (GO:0000014)			NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(5)|lung(12)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	38						AGGCACAGCATCTGCAGATGT	0.488			"""Mis, N, F"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				T|||	306	0.0611022	0.2209	0.0187	5008	,	,		19375	0.0		0.001	False		,,,				2504	0.0				p.S662P		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (F)	16	16p13.3-p13.13	2072	"""excision repair cross-complementing rodent repair deficiency, complementation group 4"""		E	.	ERCC4	100	.	0			c.T1984C						PASS	.	T	PRO/SER	845,3549	335.7+/-304.0	79,687,1431	103.0	93.0	97.0		1984	0.9	0.0	16	dbSNP_94	97	11,8589	8.4+/-32.0	0,11,4289	yes	missense	ERCC4	NM_005236.2	74	79,698,5720	CC,CT,TT		0.1279,19.2308,6.5877	benign	662/917	14038659	856,12138	2197	4300	6497	SO:0001583	missense	2072	exon10	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	ACAGCATCTGCAG	L76568	CCDS32390.1	16p13.3	2014-09-17	2014-03-07		ENSG00000175595	ENSG00000175595			3436	protein-coding gene	gene with protein product	"""xeroderma pigmentosum, complementation group F"""	133520	"""excision repair cross-complementing rodent repair deficiency, complementation group 4"""	XPF		9579555, 8887684	Standard	NM_005236		Approved	RAD1, FANCQ	uc002dce.2	Q92889	OTTHUMG00000048194	ENST00000311895.7:c.1984T>C	16.37:g.14038659T>C	ENSP00000310520:p.Ser662Pro	168.0	0.0	0		133.0	61.0	0.458647	NM_005236	A5PKV6|A8K111|O00140|Q8TD83	Missense_Mutation	SNP	ENST00000311895.7	37	CCDS32390.1	106	0.048534798534798536	100	0.2032520325203252	6	0.016574585635359115	0	0.0	0	0.0	T	8.372	0.835596	0.16820	0.192308	0.001279	ENSG00000175595	ENST00000311895;ENST00000389138	T	0.62105	0.05	5.8	0.884	0.19182	.	0.401079	0.30732	N	0.008982	T	0.00039	0.0001	N	0.05414	-0.055	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.06162	-1.0842	9	0.27082	T	0.32	-7.9859	1.9232	0.03312	0.1348:0.1162:0.2951:0.4539	rs2020955;rs2020955	662	Q92889	XPF_HUMAN	P	662;650	ENSP00000310520:S662P	ENSP00000310520:S662P	S	+	1	0	ERCC4	13946160	0.014000	0.17966	0.001000	0.08648	0.041000	0.13682	0.464000	0.21988	0.084000	0.17077	0.533000	0.62120	TCT	T|0.934;C|0.066	0.066	strong		0.488	ERCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109634.2	NM_005236	
MUC4	4585	hgsc.bcm.edu	37	3	195507060	195507060	+	Missense_Mutation	SNP	G	G	T	rs202129071	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195507060G>T	ENST00000463781.3	-	2	11850	c.11391C>A	c.(11389-11391)gaC>gaA	p.D3797E	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D3797E	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)		CTGAGGAAGTGTCGGTGACAG	0.602																																					p.D3797E		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-2,1	MUC4	1505	1	0			c.C11391A						scavenged	.						7.0	7.0	7.0					3																	195507060		641	1487	2128	SO:0001583	missense	4585	exon2			GGAAGTGTCGGTG	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.11391C>A	3.37:g.195507060G>T	ENSP00000417498:p.Asp3797Glu	159.0	0.0	0		157.0	15.0	0.0955414	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	8.187	0.795093	0.16327	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29917	1.55;1.55	.	.	.	.	0.282130	0.14041	U	0.345384	T	0.15349	0.0370	N	0.19112	0.55	0.09310	N	0.999997	B	0.15141	0.012	B	0.06405	0.002	T	0.25537	-1.0129	8	.	.	.	.	5.844	0.18652	9.0E-4:0.0:0.9991:0.0	.	3669	E7ESK3	.	E	3797	ENSP00000417498:D3797E;ENSP00000420243:D3797E	.	D	-	3	2	MUC4	196991839	0.001000	0.12720	0.041000	0.18516	0.041000	0.13682	0.608000	0.24223	0.064000	0.16427	0.064000	0.15345	GAC	G|0.956;A|0.044	.	alt		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CATSPER3	347732	hgsc.bcm.edu	37	5	134343766	134343766	+	Missense_Mutation	SNP	T	T	G	rs3896260	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:134343766T>G	ENST00000282611.6	+	4	698	c.612T>G	c.(610-612)aaT>aaG	p.N204K		NM_178019.2	NP_821138.1	Q86XQ3	CTSR3_HUMAN	cation channel, sperm associated 3	204			N -> K (in dbSNP:rs3896260).		calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|endoplasmic reticulum (GO:0005783)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CTCCAGACAATGGTGACCATG	0.552													G|||	646	0.128994	0.4584	0.0461	5008	,	,		15472	0.0		0.007	False		,,,				2504	0.001				p.N204K		Atlas-SNP	.											.	CATSPER3	38	.	0			c.T612G						PASS	.	G	LYS/ASN	1758,2648	644.5+/-398.0	347,1064,792	184.0	145.0	158.0		612	-2.1	0.0	5	dbSNP_108	158	24,8576	818.1+/-406.9	0,24,4276	yes	missense	CATSPER3	NM_178019.2	94	347,1088,5068	GG,GT,TT		0.2791,39.9001,13.7014	benign	204/399	134343766	1782,11224	2203	4300	6503	SO:0001583	missense	347732	exon4			AGACAATGGTGAC	AF432876	CCDS4181.1	5q31.2	2011-07-05			ENSG00000152705	ENSG00000152705		"""Voltage-gated ion channels / Cation channels, sperm associated"""	20819	protein-coding gene	gene with protein product		609120				12646162, 12932298, 17227845, 16382101	Standard	NM_178019		Approved	CACRC	uc003lag.3	Q86XQ3	OTTHUMG00000129137	ENST00000282611.6:c.612T>G	5.37:g.134343766T>G	ENSP00000282611:p.Asn204Lys	249.0	0.0	0		303.0	145.0	0.478548	NM_178019	Q86XS6	Missense_Mutation	SNP	ENST00000282611.6	37	CCDS4181.1	241	0.11034798534798534	221	0.4491869918699187	17	0.04696132596685083	0	0.0	3	0.00395778364116095	G	0.003	-2.468589	0.00169	0.399001	0.002791	ENSG00000152705	ENST00000282611	D	0.97553	-4.43	4.33	-2.08	0.07254	Ion transport (1);	1.918400	0.01976	N	0.044466	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	0.50440	-0.8828	8	.	.	.	1.4415	0.1834	0.00126	0.2523:0.1883:0.202:0.3574	rs3896260;rs52815255;rs60117234;rs3896260	204	Q86XQ3	CTSR3_HUMAN	K	204	ENSP00000282611:N204K	.	N	+	3	2	CATSPER3	134371665	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.154000	0.03166	-0.973000	0.03555	-0.358000	0.07595	AAT	T|0.860;G|0.140	0.140	strong		0.552	CATSPER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251191.2	NM_178019	
SMYD1	150572	hgsc.bcm.edu	37	2	88396213	88396213	+	Silent	SNP	G	G	A	rs13403507	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:88396213G>A	ENST00000419482.2	+	6	883	c.798G>A	c.(796-798)ctG>ctA	p.L266L	SMYD1_ENST00000438570.1_Intron|SMYD1_ENST00000444564.2_Silent_p.L253L	NM_198274.3	NP_938015.1	Q8NB12	SMYD1_HUMAN	SET and MYND domain containing 1	266					chromatin remodeling (GO:0006338)|heart development (GO:0007507)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myotube differentiation (GO:0010831)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			NS(1)|breast(4)|central_nervous_system(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	41						AGAGGCAGCTGAAGAAGCAGT	0.493													G|||	44	0.00878594	0.0333	0.0	5008	,	,		22022	0.0		0.0	False		,,,				2504	0.0				p.L266L		Atlas-SNP	.											.	SMYD1	95	.	0			c.G798A						PASS	.	G		105,4301	84.4+/-122.9	0,105,2098	106.0	98.0	101.0		798	-0.6	1.0	2	dbSNP_121	101	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SMYD1	NM_198274.3		0,106,6397	AA,AG,GG		0.0116,2.3831,0.815		266/491	88396213	106,12900	2203	4300	6503	SO:0001819	synonymous_variant	150572	exon6			GCAGCTGAAGAAG	AF086123	CCDS33240.1	2p11.1	2011-07-01			ENSG00000115593	ENSG00000115593		"""Zinc fingers, MYND-type"", ""Chromatin-modifying enzymes / K-methyltransferases"""	20986	protein-coding gene	gene with protein product		606846				11923873	Standard	NM_198274		Approved	BOP, ZMYND22, KMT3D	uc002ssr.3	Q8NB12	OTTHUMG00000155045	ENST00000419482.2:c.798G>A	2.37:g.88396213G>A		156.0	0.0	0		115.0	58.0	0.504348	NM_198274	A0AV30|A6NE13	Silent	SNP	ENST00000419482.2	37	CCDS33240.1																																																																																			G|0.992;A|0.008	0.008	strong		0.493	SMYD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338229.2	XM_097915	
GSDMC	56169	hgsc.bcm.edu	37	8	130762324	130762324	+	Silent	SNP	A	A	G	rs35085916	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:130762324A>G	ENST00000276708.4	-	12	2006	c.1125T>C	c.(1123-1125)ggT>ggC	p.G375G		NM_031415.2	NP_113603.1	Q9BYG8	GSDMC_HUMAN	gasdermin C	375						cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)				autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	26						TTAGGATGGCACCACCAGGGC	0.368													A|||	87	0.0173722	0.0628	0.0058	5008	,	,		18988	0.0		0.0	False		,,,				2504	0.0				p.G375G		Atlas-SNP	.											.	GSDMC	71	.	0			c.T1125C						PASS	.	A		286,4120	153.3+/-186.9	9,268,1926	36.0	36.0	36.0		1125	0.7	0.0	8	dbSNP_126	36	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	GSDMC	NM_031415.2		9,272,6222	GG,GA,AA		0.0465,6.4911,2.2297		375/509	130762324	290,12716	2203	4300	6503	SO:0001819	synonymous_variant	56169	exon12			GATGGCACCACCA	AB042405	CCDS6360.1	8q24.21	2014-05-14	2008-07-31	2008-07-31	ENSG00000147697	ENSG00000147697			7151	protein-coding gene	gene with protein product		608384	"""melanoma-derived leucine zipper, extra-nuclear factor"""	MLZE		17350798	Standard	NM_031415		Approved		uc003ysr.3	Q9BYG8	OTTHUMG00000164851	ENST00000276708.4:c.1125T>C	8.37:g.130762324A>G		102.0	0.0	0		111.0	67.0	0.603604	NM_031415	Q5XKF3|Q6P494	Silent	SNP	ENST00000276708.4	37	CCDS6360.1																																																																																			A|0.981;G|0.019	0.019	strong		0.368	GSDMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380586.1		
CDK12	51755	hgsc.bcm.edu	37	17	37619038	37619038	+	Silent	SNP	G	G	A	rs35896550	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:37619038G>A	ENST00000447079.4	+	1	747	c.714G>A	c.(712-714)tcG>tcA	p.S238S	CDK12_ENST00000430627.2_Silent_p.S238S	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	238					mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						ATAGCCCCTCGGGAGCTTCTT	0.483			"""Mis, N, F"""		serous ovarian					TCGA Ovarian(9;0.13)			G|||	291	0.058107	0.2073	0.0159	5008	,	,		18736	0.0		0.003	False		,,,				2504	0.0031				p.S238S		Atlas-SNP	.		Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	CDK12,NS,carcinoma,+1,1	CDK12	161	1	0			c.G714A						PASS	.	G	,	772,3634	306.9+/-289.7	55,662,1486	102.0	112.0	109.0		714,714	-9.9	0.3	17	dbSNP_126	109	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous	CDK12	NM_015083.1,NM_016507.2	,	55,665,5783	AA,AG,GG		0.0349,17.5216,5.9588	,	238/1482,238/1491	37619038	775,12231	2203	4300	6503	SO:0001819	synonymous_variant	51755	exon1			CCCCTCGGGAGCT	AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258		"""Cyclin-dependent kinases"""	24224	protein-coding gene	gene with protein product	"""CDC2 related protein kinase 7"""	615514	"""Cdc2-related kinase, arginine/serine-rich"""	CRKRS		10048485, 11683387, 19884882	Standard	XM_005257456		Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.714G>A	17.37:g.37619038G>A		45.0	0.0	0		57.0	29.0	0.508772	NM_016507	A7E2B2|B4DYX4|B9EIQ6|O94978	Silent	SNP	ENST00000447079.4	37	CCDS11337.1																																																																																			G|0.933;A|0.067	0.067	strong		0.483	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4	NM_016507	
ETV7	51513	hgsc.bcm.edu	37	6	36341251	36341251	+	Missense_Mutation	SNP	G	G	A	rs9470262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36341251G>A	ENST00000340181.4	-	4	653	c.412C>T	c.(412-414)Cac>Tac	p.H138Y	ETV7_ENST00000373737.4_Missense_Mutation_p.H138Y|ETV7_ENST00000538992.1_5'UTR|ETV7_ENST00000373738.1_Missense_Mutation_p.H83Y|ETV7_ENST00000339796.5_Missense_Mutation_p.H138Y	NM_001207037.1|NM_001207040.1|NM_016135.3	NP_001193966.1|NP_001193969.1|NP_057219.1	Q9Y603	ETV7_HUMAN	ets variant 7	138			H -> Y (in dbSNP:rs9470262).		cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ morphogenesis (GO:0009887)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	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)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(4)	10						ACTGGAGAGTGCTGGGTGGGC	0.602													G|||	59	0.0117812	0.0446	0.0	5008	,	,		11025	0.0		0.0	False		,,,				2504	0.0				p.H138Y		Atlas-SNP	.											.	ETV7	31	.	0			c.C412T						PASS	.	G	TYR/HIS,TYR/HIS,TYR/HIS,TYR/HIS,TYR/HIS,TYR/HIS,,TYR/HIS	156,4250		3,150,2050	27.0	25.0	25.0		412,247,235,412,247,169,,412	2.4	0.0	6	dbSNP_119	25	0,8598		0,0,4299	yes	missense,missense,missense,missense,missense,missense,utr-5,missense	ETV7	NM_001207035.1,NM_001207036.1,NM_001207037.1,NM_001207038.1,NM_001207039.1,NM_001207040.1,NM_001207041.1,NM_016135.3	83,83,83,83,83,83,,83	3,150,6349	AA,AG,GG		0.0,3.5406,1.1996	benign,benign,benign,benign,benign,benign,,benign	138/318,83/287,79/283,138/265,83/263,57/261,,138/342	36341251	156,12848	2203	4299	6502	SO:0001583	missense	51513	exon4			GAGAGTGCTGGGT	AF116508	CCDS4819.1, CCDS56422.1, CCDS56423.1, CCDS56424.1, CCDS56425.1, CCDS75440.1, CCDS75441.1	6p21	2008-09-12	2008-09-12		ENSG00000010030	ENSG00000010030			18160	protein-coding gene	gene with protein product	"""TEL2 oncogene"""	605255	"""ets variant gene 7 (TEL2 oncogene)"""			10828014, 11108721	Standard	NM_016135		Approved	TEL2, TEL-2	uc003omb.3	Q9Y603	OTTHUMG00000014594	ENST00000340181.4:c.412C>T	6.37:g.36341251G>A	ENSP00000341843:p.His138Tyr	130.0	0.0	0		142.0	63.0	0.443662	NM_001207035	B3KVC2|B4DVB6|B4E1G4|Q5R3L3|Q5R3L4|Q9NZ65|Q9NZ66|Q9NZ68|Q9NZR8|Q9UNJ7|Q9Y5K4|Q9Y604	Missense_Mutation	SNP	ENST00000340181.4	37	CCDS4819.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	G	9.065	0.995354	0.19043	0.035406	0.0	ENSG00000010030	ENST00000339796;ENST00000340181;ENST00000373737;ENST00000373738	T;T;T;T	0.13538	2.96;2.96;2.58;2.68	3.37	2.43	0.29744	.	7.870880	0.00616	U	0.000429	T	0.02727	0.0082	N	0.24115	0.695	0.34145	D	0.66687	B;B;B;B;B;B	0.33135	0.399;0.167;0.255;0.091;0.263;0.34	B;B;B;B;B;B	0.31686	0.134;0.065;0.041;0.105;0.044;0.134	T	0.34825	-0.9813	10	0.02654	T	1	.	9.2275	0.37416	0.0:0.0:0.503:0.497	rs9470262;rs52802542;rs9470262	79;138;83;138;83;138	Q9Y603-2;Q9Y603-7;Q9Y603-4;Q9Y603;Q9Y603-6;Q9Y603-5	.;.;.;ETV7_HUMAN;.;.	Y	138;138;138;83	ENSP00000342260:H138Y;ENSP00000341843:H138Y;ENSP00000362842:H138Y;ENSP00000362843:H83Y	ENSP00000342260:H138Y	H	-	1	0	ETV7	36449229	0.000000	0.05858	0.007000	0.13788	0.022000	0.10575	0.108000	0.15396	1.446000	0.47643	0.456000	0.33151	CAC	G|0.988;A|0.012	0.012	strong		0.602	ETV7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040341.1	NM_016135	
SEMA6C	10500	hgsc.bcm.edu	37	1	151107277	151107277	+	Missense_Mutation	SNP	C	C	T	rs149398166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:151107277C>T	ENST00000341697.3	-	16	3346	c.1655G>A	c.(1654-1656)gGt>gAt	p.G552D	SEMA6C_ENST00000479820.1_5'Flank			Q9H3T2	SEM6C_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6C	552					axon guidance (GO:0007411)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	28	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			CACTTACCCACCAGATCCCCT	0.527													C|||	19	0.00379393	0.0144	0.0	5008	,	,		19859	0.0		0.0	False		,,,				2504	0.0				p.G552D		Atlas-SNP	.											.	SEMA6C	70	.	0			c.G1655A						PASS	.	C	ASP/GLY,ASP/GLY,ASP/GLY	40,4366	43.8+/-77.6	2,36,2165	134.0	121.0	125.0		1655,1535,1655	3.2	1.0	1	dbSNP_134	125	0,8600		0,0,4300	yes	missense,missense,missense	SEMA6C	NM_001178061.1,NM_001178062.1,NM_030913.4	94,94,94	2,36,6465	TT,TC,CC		0.0,0.9079,0.3076	possibly-damaging,possibly-damaging,possibly-damaging	552/963,512/923,552/931	151107277	40,12966	2203	4300	6503	SO:0001583	missense	10500	exon16			TACCCACCAGATC	AF339154	CCDS984.1, CCDS53363.1, CCDS53364.1	1q21.2	2008-02-05			ENSG00000143434	ENSG00000143434		"""Semaphorins"""	10740	protein-coding gene	gene with protein product	"""m-Sema Y2"""	609294				12110693	Standard	NM_030913		Approved	KIAA1869	uc001ewv.3	Q9H3T2	OTTHUMG00000012261	ENST00000341697.3:c.1655G>A	1.37:g.151107277C>T	ENSP00000344148:p.Gly552Asp	178.0	0.0	0		206.0	107.0	0.519417	NM_001178061	D3DV15|Q5JR71|Q5JR72|Q5JR73|Q8WXT8|Q8WXT9|Q8WXU0|Q96JF8	Missense_Mutation	SNP	ENST00000341697.3	37	CCDS984.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	11.28	1.593364	0.28357	0.009079	0.0	ENSG00000143434	ENST00000368914;ENST00000368912;ENST00000368913;ENST00000341697	T;T;T;T	0.46063	0.88;0.88;0.88;0.88	5.25	3.22	0.36961	.	3.389920	0.00550	N	0.000248	T	0.33498	0.0865	L	0.44542	1.39	0.32800	D	0.500067	B;D;B;D	0.54772	0.002;0.96;0.1;0.968	B;P;B;P	0.50934	0.01;0.523;0.257;0.654	T	0.06232	-1.0838	10	0.37606	T	0.19	.	11.5843	0.50910	0.0:0.527:0.473:0.0	.	552;512;552;552	B4DZD4;Q9H3T2-2;Q9H3T2-3;Q9H3T2	.;.;.;SEM6C_HUMAN	D	552;512;552;552	ENSP00000357910:G552D;ENSP00000357908:G512D;ENSP00000357909:G552D;ENSP00000344148:G552D	ENSP00000344148:G552D	G	-	2	0	SEMA6C	149373901	0.981000	0.34729	1.000000	0.80357	0.599000	0.36880	1.049000	0.30392	1.349000	0.45751	0.561000	0.74099	GGT	C|0.995;T|0.005	0.005	strong		0.527	SEMA6C-004	KNOWN	alternative_5_UTR|mRNA_start_NF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000034074.1	NM_030913	
INCENP	3619	hgsc.bcm.edu	37	11	61906397	61906397	+	Missense_Mutation	SNP	A	A	G	rs138049815	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61906397A>G	ENST00000394818.3	+	7	1413	c.1211A>G	c.(1210-1212)aAt>aGt	p.N404S	INCENP_ENST00000278849.4_Missense_Mutation_p.N404S	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	404					chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	central element (GO:0000801)|chromocenter (GO:0010369)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lateral element (GO:0000800)|microtubule (GO:0005874)|midbody (GO:0030496)|pericentric heterochromatin (GO:0005721)|protein complex (GO:0043234)|spindle (GO:0005819)				breast(1)|endometrium(1)|kidney(6)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						TGGCCCCACAATGACACGGAG	0.587													A|||	13	0.00259585	0.0098	0.0	5008	,	,		17407	0.0		0.0	False		,,,				2504	0.0				p.N404S		Atlas-SNP	.											.	INCENP	122	.	0			c.A1211G						PASS	.	A	SER/ASN,SER/ASN	48,4356	49.6+/-84.7	0,48,2154	133.0	122.0	125.0		1211,1211	1.4	0.1	11	dbSNP_134	125	1,8597		0,1,4298	yes	missense,missense	INCENP	NM_020238.2,NM_001040694.1	46,46	0,49,6452	GG,GA,AA		0.0116,1.0899,0.3769	benign,benign	404/915,404/919	61906397	49,12953	2202	4299	6501	SO:0001583	missense	3619	exon7			CCCACAATGACAC	AF282265	CCDS31582.1, CCDS44624.1	11q12.3	2013-01-17	2002-08-29		ENSG00000149503	ENSG00000149503			6058	protein-coding gene	gene with protein product		604411	"""inner centromere protein antigens (135kD, 155kD)"""			1860899, 11453556	Standard	NM_001040694		Approved	FLJ31633	uc001nsw.1	Q9NQS7	OTTHUMG00000167470	ENST00000394818.3:c.1211A>G	11.37:g.61906397A>G	ENSP00000378295:p.Asn404Ser	64.0	0.0	0		124.0	68.0	0.548387	NM_001040694	A8MQD2|Q5Y192	Missense_Mutation	SNP	ENST00000394818.3	37	CCDS44624.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	A	0.939	-0.710017	0.03230	0.010899	1.16E-4	ENSG00000149503	ENST00000394818;ENST00000278849	T;T	0.13196	2.61;2.61	5.24	1.43	0.22495	.	0.301301	0.29113	N	0.013114	T	0.02156	0.0067	N	0.01410	-0.885	0.09310	N	1	B;B;B	0.18610	0.029;0.0;0.0	B;B;B	0.18871	0.023;0.001;0.001	T	0.44605	-0.9317	10	0.07325	T	0.83	.	6.0369	0.19712	0.4261:0.0:0.5739:0.0	.	404;404;404	B3KPD3;Q9NQS7-2;Q9NQS7	.;.;INCE_HUMAN	S	404	ENSP00000378295:N404S;ENSP00000278849:N404S	ENSP00000278849:N404S	N	+	2	0	INCENP	61662973	0.048000	0.20356	0.068000	0.19968	0.006000	0.05464	0.392000	0.20801	0.558000	0.29135	-0.242000	0.12053	AAT	A|0.996;G|0.004	0.004	strong		0.587	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2	NM_020238	
CCR2	729230	hgsc.bcm.edu	37	3	46401243	46401243	+	Silent	SNP	A	A	G	rs3918386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:46401243A>G	ENST00000400888.2	+	2	1056	c.1017A>G	c.(1015-1017)ccA>ccG	p.P339P	CCR2_ENST00000292301.4_Silent_p.P339P			P41597	CCR2_HUMAN	chemokine (C-C motif) receptor 2	339					blood vessel remodeling (GO:0001974)|cellular calcium ion homeostasis (GO:0006874)|cellular defense response (GO:0006968)|cellular homeostasis (GO:0019725)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell chemotaxis (GO:0002407)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|JAK-STAT cascade (GO:0007259)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of angiogenesis (GO:0016525)|negative regulation of eosinophil degranulation (GO:0043310)|negative regulation of type 2 immune response (GO:0002829)|positive regulation of alpha-beta T cell proliferation (GO:0046641)|positive regulation of astrocyte chemotaxis (GO:2000464)|positive regulation of CD8-positive, alpha-beta T cell extravasation (GO:2000451)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of hematopoietic stem cell migration (GO:2000473)|positive regulation of immune complex clearance by monocytes and macrophages (GO:0090265)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of monocyte chemotaxis (GO:0090026)|positive regulation of monocyte extravasation (GO:2000439)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of T-helper 1 type immune response (GO:0002827)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of vascular endothelial growth factor production (GO:0010574)|response to wounding (GO:0009611)|T-helper 17 cell chemotaxis (GO:0035705)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	C-C chemokine receptor activity (GO:0016493)|CCR2 chemokine receptor binding (GO:0031727)|chemokine receptor activity (GO:0004950)|protein homodimerization activity (GO:0042803)			breast(3)|endometrium(1)|large_intestine(1)|liver(2)|lung(7)	14				BRCA - Breast invasive adenocarcinoma(193;0.00114)|KIRC - Kidney renal clear cell carcinoma(197;0.0174)|Kidney(197;0.0206)		GAGTGAGACCAGGAAAGAATG	0.498													A|||	356	0.0710863	0.2595	0.0187	5008	,	,		19407	0.0		0.0	False		,,,				2504	0.0				p.P339P		Atlas-SNP	.											.	CCR2	103	.	0			c.A1017G						PASS	.	A		597,2539		60,477,1031	119.0	108.0	111.0		1017	-4.7	0.0	3	dbSNP_108	111	7,7157		0,7,3575	no	coding-synonymous	CCR2	NM_001123041.2		60,484,4606	GG,GA,AA		0.0977,19.037,5.8641		339/375	46401243	604,9696	1568	3582	5150	SO:0001819	synonymous_variant	729230	exon3			GAGACCAGGAAAG		CCDS43078.1, CCDS46813.1	3p21	2012-08-08			ENSG00000121807	ENSG00000121807		"""GPCR / Class A : Chemokine receptors : C-C motif"", ""CD molecules"""	1603	protein-coding gene	gene with protein product		601267		CMKBR2		8146186	Standard	NM_001123041		Approved	CC-CKR-2, CKR2, MCP-1-R, CD192, FLJ78302	uc003cpn.4	P41597	OTTHUMG00000156466	ENST00000400888.2:c.1017A>G	3.37:g.46401243A>G		87.0	0.0	0		74.0	32.0	0.432432	NM_001123041	A0AVQ3|B2RMT0|Q4VBL2	Silent	SNP	ENST00000400888.2	37	CCDS43078.1																																																																																			A|0.940;G|0.060	0.060	strong		0.498	CCR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344292.1	NM_000647	
CLEC14A	161198	hgsc.bcm.edu	37	14	38724043	38724043	+	Silent	SNP	G	G	A	rs530380827|rs78287081	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:38724043G>A	ENST00000342213.2	-	1	1531	c.1185C>T	c.(1183-1185)tcC>tcT	p.S395S		NM_175060.2	NP_778230.1	Q86T13	CLC14_HUMAN	C-type lectin domain family 14, member A	395						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			breast(1)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33	Hepatocellular(127;0.213)|Esophageal squamous(585;0.22)		Lung(238;3.93e-06)|LUAD - Lung adenocarcinoma(48;2.62e-05)|Epithelial(34;0.187)	GBM - Glioblastoma multiforme(112;0.00439)		CCACGGCAGAGGAGGAGTCGA	0.502													G|||	44	0.00878594	0.0333	0.0	5008	,	,		19714	0.0		0.0	False		,,,				2504	0.0				p.S395S		Atlas-SNP	.											.	CLEC14A	83	.	0			c.C1185T						PASS	.	G		119,4287	88.2+/-126.9	2,115,2086	52.0	49.0	50.0		1185	-0.7	0.9	14	dbSNP_132	50	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CLEC14A	NM_175060.1		2,116,6385	AA,AG,GG		0.0116,2.7009,0.9227		395/491	38724043	120,12886	2203	4300	6503	SO:0001819	synonymous_variant	161198	exon1			GGCAGAGGAGGAG		CCDS9667.1	14q21.1	2010-04-27	2005-02-11	2005-02-11	ENSG00000176435	ENSG00000176435		"""C-type lectin domain containing"""	19832	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 27"""	C14orf27			Standard	NM_175060		Approved		uc001wum.2	Q86T13	OTTHUMG00000140248	ENST00000342213.2:c.1185C>T	14.37:g.38724043G>A		72.0	0.0	0		76.0	38.0	0.5	NM_175060	Q695G9|Q6PWT6|Q8N5V5	Silent	SNP	ENST00000342213.2	37	CCDS9667.1																																																																																			G|0.992;A|0.008	0.008	strong		0.502	CLEC14A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276729.1	NM_175060	
KRTAP4-4	84616	hgsc.bcm.edu	37	17	39316482	39316482	+	Missense_Mutation	SNP	C	C	G	rs366700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39316482C>G	ENST00000390661.3	-	1	501	c.462G>C	c.(460-462)agG>agC	p.R154S		NM_032524.1	NP_115913.1	Q9BYR3	KRA44_HUMAN	keratin associated protein 4-4	154	26 X 5 AA repeats of C-C-[GRQVCH]-[SPT]- [VSTQR].		R -> S (in dbSNP:rs366700).			keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(5)	7		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			GCCTGTAGCACCTGGACACAC	0.617													c|||	523	0.104433	0.379	0.0288	5008	,	,		20637	0.0		0.002	False		,,,				2504	0.0				p.R154S		Atlas-SNP	.											.	KRTAP4-4	21	.	0			c.G462C						PASS	.	G	SER/ARG	1375,3019		224,927,1046	39.0	46.0	44.0		462	1.5	1.0	17	dbSNP_80	44	7,8585		0,7,4289	yes	missense	KRTAP4-4	NM_032524.1	110	224,934,5335	GG,GC,CC		0.0815,31.2927,10.6422	benign	154/167	39316482	1382,11604	2197	4296	6493	SO:0001583	missense	84616	exon1			GTAGCACCTGGAC	AJ406936	CCDS11383.1	17q21.2	2013-06-25			ENSG00000171396	ENSG00000171396		"""Keratin associated proteins"""	16928	protein-coding gene	gene with protein product			"""keratin associated protein 4-13"""	KRTAP4-13		11279113	Standard	NM_032524		Approved	KAP4.4, KAP4.13	uc002hwc.3	Q9BYR3	OTTHUMG00000133428	ENST00000390661.3:c.462G>C	17.37:g.39316482C>G	ENSP00000375076:p.Arg154Ser	218.0	0.0	0		251.0	250.0	0.996016	NM_032524	Q9BYU7	Missense_Mutation	SNP	ENST00000390661.3	37	CCDS11383.1	190	0.08699633699633699	179	0.3638211382113821	11	0.03038674033149171	0	0.0	0	0.0	.	2.548	-0.304815	0.05495	0.312927	8.15E-4	ENSG00000171396	ENST00000390661	T	0.00571	6.5	4.79	1.5	0.22942	.	0.286046	0.18063	U	0.152889	T	0.00012	0.0000	N	0.00159	-1.955	0.54753	P	1.8999999999991246E-5	B	0.02656	0.0	B	0.04013	0.001	T	0.03068	-1.1076	9	0.19147	T	0.46	.	4.8968	0.13755	0.2534:0.289:0.4576:0.0	rs366700;rs52806510;rs366700	154	Q9BYR3	KRA44_HUMAN	S	154	ENSP00000375076:R154S	ENSP00000375076:R154S	R	-	3	2	KRTAP4-4	36570008	0.000000	0.05858	0.990000	0.47175	0.502000	0.33828	-0.971000	0.03806	0.113000	0.18004	-0.335000	0.08231	AGG	C|0.938;G|0.062	0.062	strong		0.617	KRTAP4-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257291.1		
DSE	29940	hgsc.bcm.edu	37	6	116758004	116758004	+	Silent	SNP	C	C	T	rs367781233		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:116758004C>T	ENST00000331677.3	+	7	2817	c.2373C>T	c.(2371-2373)gaC>gaT	p.D791D	DSE_ENST00000452085.3_Silent_p.D791D|DSE_ENST00000359564.2_Silent_p.D791D|DSE_ENST00000537543.1_Silent_p.D810D			Q9UL01	DSE_HUMAN	dermatan sulfate epimerase	791					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin-glucuronate 5-epimerase activity (GO:0047757)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)		AGGCCATTGACAGGATTTTTG	0.473																																					p.D791D		Atlas-SNP	.											.	DSE	98	.	0			c.C2373T						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	68.0	72.0	70.0		2373,2373	1.9	1.0	6		70	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	DSE	NM_001080976.1,NM_013352.2	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	791/959,791/959	116758004	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	29940	exon6			CATTGACAGGATT	AF098066	CCDS5107.1	6q22	2008-02-05	2007-01-29	2007-01-29	ENSG00000111817	ENSG00000111817	5.1.3.19		21144	protein-coding gene	gene with protein product		605942	"""squamous cell carcinoma antigen recognized by T cells 2"""	SART2		11920522, 16505484	Standard	NM_001080976		Approved	DSEPI	uc003pws.3	Q9UL01	OTTHUMG00000015434	ENST00000331677.3:c.2373C>T	6.37:g.116758004C>T		113.0	0.0	0		142.0	64.0	0.450704	NM_001080976	Q5R3K6	Silent	SNP	ENST00000331677.3	37	CCDS5107.1																																																																																			.	.	weak		0.473	DSE-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041940.2	NM_013352	
CIAPIN1	57019	hgsc.bcm.edu	37	16	57468110	57468110	+	Silent	SNP	G	G	A	rs77773186	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57468110G>A	ENST00000569979.1	-	4	448	c.402C>T	c.(400-402)ccC>ccT	p.P134P	CIAPIN1_ENST00000568940.1_Silent_p.P134P|CIAPIN1_ENST00000394391.4_Silent_p.P134P|CIAPIN1_ENST00000569370.1_Silent_p.P134P|CIAPIN1_ENST00000567518.1_Silent_p.P121P|CIAPIN1_ENST00000569246.1_5'UTR|CIAPIN1_ENST00000565961.1_Silent_p.P107P					cytokine induced apoptosis inhibitor 1											cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	10						CAGGGGTTAGGGGCTCCCGCT	0.443													G|||	24	0.00479233	0.0182	0.0	5008	,	,		20722	0.0		0.0	False		,,,				2504	0.0				p.P134P		Atlas-SNP	.											.	CIAPIN1	17	.	0			c.C402T						PASS	.	G		40,3776		0,40,1868	108.0	102.0	104.0		402	2.2	0.1	16	dbSNP_131	104	1,8231		0,1,4115	no	coding-synonymous	CIAPIN1	NM_020313.2		0,41,5983	AA,AG,GG		0.0121,1.0482,0.3403		134/313	57468110	41,12007	1908	4116	6024	SO:0001819	synonymous_variant	57019	exon5			GGTTAGGGGCTCC	AF248964	CCDS10781.2	16q21	2012-09-20			ENSG00000005194	ENSG00000005194			28050	protein-coding gene	gene with protein product		608943				10493829, 11230166	Standard	XM_005256061		Approved	Anamorsin	uc002ell.1	Q6FI81	OTTHUMG00000133457	ENST00000569979.1:c.402C>T	16.37:g.57468110G>A		122.0	0.0	0		96.0	56.0	0.583333	NM_020313		Silent	SNP	ENST00000569979.1	37																																																																																				G|0.993;A|0.007	0.007	strong		0.443	CIAPIN1-010	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432580.1	NM_020313	
C1orf127	148345	hgsc.bcm.edu	37	1	11008594	11008594	+	Missense_Mutation	SNP	A	A	T	rs1281016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11008594A>T	ENST00000377008.4	-	11	1543	c.1097T>A	c.(1096-1098)gTc>gAc	p.V366D	C1orf127_ENST00000377004.4_Missense_Mutation_p.V533D			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	366			V -> D (in dbSNP:rs1281016).							NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		TGGTCCTGAGACCAGAAGTGA	0.612													A|||	346	0.0690895	0.2035	0.0144	5008	,	,		19200	0.004		0.0427	False		,,,				2504	0.0204				p.V533D		Atlas-SNP	.											.	C1orf127	134	.	0			c.T1598A						PASS	.	A	ASP/VAL	735,3671	303.5+/-288.0	65,605,1533	56.0	53.0	54.0		1598	0.5	0.0	1	dbSNP_87	54	343,8257	116.3+/-176.0	4,335,3961	yes	missense	C1orf127	NM_001170754.1	152	69,940,5494	TT,TA,AA		3.9884,16.6818,8.2885	probably-damaging	533/824	11008594	1078,11928	2203	4300	6503	SO:0001583	missense	148345	exon12			CCTGAGACCAGAA	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.1097T>A	1.37:g.11008594A>T	ENSP00000366207:p.Val366Asp	199.0	0.0	0		179.0	86.0	0.480447	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Missense_Mutation	SNP	ENST00000377008.4	37		167|167	0.07646520146520147|0.07646520146520147	123|123	0.25|0.25	4|4	0.011049723756906077|0.011049723756906077	1|1	0.0017482517482517483|0.0017482517482517483	39|39	0.051451187335092345|0.051451187335092345	A|A	13.05|13.05	2.122259|2.122259	0.37436|0.37436	0.166818|0.166818	0.039884|0.039884	ENSG00000175262|ENSG00000175262	ENST00000418570;ENST00000520253|ENST00000377004;ENST00000377008	.|T;T	.|0.26518	.|1.73;1.73	4.15|4.15	0.48|0.48	0.16804|0.16804	.|.	.|0.956786	.|0.08574	.|N	.|0.925628	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.24115|0.24115	0.695|0.695	0.80722|0.80722	P|P	0.0|0.0	.|P;P;P	.|0.46512	.|0.879;0.879;0.879	.|B;B;B	.|0.42163	.|0.378;0.378;0.378	T|T	0.19484|0.19484	-1.0304|-1.0304	4|9	.|0.15952	.|T	.|0.53	-5.9143|-5.9143	0.8883|0.8883	0.01249|0.01249	0.3866:0.3152:0.136:0.1622|0.3866:0.3152:0.136:0.1622	rs1281016;rs52819154;rs1281016|rs1281016;rs52819154;rs1281016	.|384;358;366	.|B7ZLG7;Q8N9H9-2;Q8N9H9	.|.;.;CA127_HUMAN	T|D	368;485|533;366	.|ENSP00000366203:V533D;ENSP00000366207:V366D	.|ENSP00000366203:V533D	S|V	-|-	1|2	0|0	C1orf127|C1orf127	10931181|10931181	0.000000|0.000000	0.05858|0.05858	0.008000|0.008000	0.14137|0.14137	0.057000|0.057000	0.15508|0.15508	-0.110000|-0.110000	0.10824|0.10824	0.317000|0.317000	0.23160|0.23160	0.402000|0.402000	0.26972|0.26972	TCT|GTC	A|0.922;T|0.078	0.078	strong		0.612	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	
ZBTB24	9841	hgsc.bcm.edu	37	6	109787596	109787596	+	Missense_Mutation	SNP	C	C	T	rs2232448	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:109787596C>T	ENST00000230122.3	-	7	1719	c.1552G>A	c.(1552-1554)Gct>Act	p.A518T	MICAL1_ENST00000368952.4_5'Flank	NM_001164313.1|NM_014797.2	NP_001157785.1|NP_055612.2	O43167	ZBT24_HUMAN	zinc finger and BTB domain containing 24	518			A -> T (in dbSNP:rs2232448).		hematopoietic progenitor cell differentiation (GO:0002244)|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)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)	22		all_cancers(87;0.000189)|Acute lymphoblastic leukemia(125;3.07e-08)|all_hematologic(75;3.33e-06)|all_epithelial(87;0.00686)|Lung SC(18;0.0743)|Colorectal(196;0.101)|all_lung(197;0.149)		Epithelial(106;0.0154)|all cancers(137;0.0216)|OV - Ovarian serous cystadenocarcinoma(136;0.0242)|BRCA - Breast invasive adenocarcinoma(108;0.059)		GCATCTGAAGCATGCTTCTCC	0.463													C|||	418	0.0834665	0.2776	0.0346	5008	,	,		19894	0.0		0.0099	False		,,,				2504	0.0174				p.A518T		Atlas-SNP	.											.	ZBTB24	64	.	0			c.G1552A						PASS	.	C	THR/ALA	1041,3365	383.0+/-324.7	128,785,1290	120.0	111.0	114.0		1552	0.9	0.0	6	dbSNP_98	114	129,8471	64.9+/-127.2	0,129,4171	yes	missense	ZBTB24	NM_014797.2	58	128,914,5461	TT,TC,CC		1.5,23.6269,8.9958	benign	518/698	109787596	1170,11836	2203	4300	6503	SO:0001583	missense	9841	exon7			CTGAAGCATGCTT	AB007901	CCDS34509.1	6q21	2014-09-17	2004-04-15	2004-04-16	ENSG00000112365	ENSG00000112365		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	21143	protein-coding gene	gene with protein product	"""POZ (BTB) and AT hook containing zinc finger 2"""	614064	"""zinc finger protein 450"""	ZNF450		9455477	Standard	NM_014797		Approved	KIAA0441, BIF1, PATZ2	uc003ptl.1	O43167	OTTHUMG00000015349	ENST00000230122.3:c.1552G>A	6.37:g.109787596C>T	ENSP00000230122:p.Ala518Thr	112.0	0.0	0		132.0	77.0	0.583333	NM_014797	Q17RC6|Q5TED5|Q8N455	Missense_Mutation	SNP	ENST00000230122.3	37	CCDS34509.1	150	0.06868131868131869	131	0.266260162601626	14	0.03867403314917127	0	0.0	5	0.006596306068601583	C	5.706	0.314802	0.10789	0.236269	0.015	ENSG00000112365	ENST00000230122	T	0.11277	2.79	6.06	0.896	0.19253	.	1.043490	0.07456	N	0.899772	T	0.01189	0.0039	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.47420	-0.9119	9	0.62326	D	0.03	0.2747	0.4792	0.00545	0.2407:0.3331:0.1937:0.2325	rs2232448;rs52798886;rs57567548;rs2232448	518	O43167	ZBT24_HUMAN	T	518	ENSP00000230122:A518T	ENSP00000230122:A518T	A	-	1	0	ZBTB24	109894289	0.000000	0.05858	0.000000	0.03702	0.170000	0.22686	0.142000	0.16096	0.444000	0.26612	0.655000	0.94253	GCT	C|0.918;T|0.082	0.082	strong		0.463	ZBTB24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041758.1	NM_014797	
ENDOG	2021	hgsc.bcm.edu	37	9	131584649	131584649	+	Silent	SNP	C	C	T	rs55985529	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131584649C>T	ENST00000372642.4	+	3	865	c.654C>T	c.(652-654)atC>atT	p.I218I	C9orf114_ENST00000361256.5_3'UTR	NM_004435.2	NP_004426.2	Q14249	NUCG_HUMAN	endonuclease G	218					apoptotic DNA fragmentation (GO:0006309)|DNA recombination (GO:0006310)|in utero embryonic development (GO:0001701)|positive regulation of apoptotic process (GO:0043065)|response to antibiotic (GO:0046677)|response to tumor necrosis factor (GO:0034612)	mitochondrion (GO:0005739)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|nuclease activity (GO:0004518)|nucleic acid binding (GO:0003676)										ACCAGGTCATCGGCAAGAACC	0.592													C|||	136	0.0271565	0.0961	0.0101	5008	,	,		20205	0.0		0.002	False		,,,				2504	0.0				p.I218I		Atlas-SNP	.											.	ENDOG	8	.	0			c.C654T						PASS	.	C	,	338,4068	177.3+/-206.3	10,318,1875	88.0	78.0	82.0		654,	-11.3	0.0	9	dbSNP_129	82	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous,utr-3	ENDOG,C9orf114	NM_004435.2,NM_016390.2	,	10,323,6170	TT,TC,CC		0.0581,7.6714,2.6372	,	218/298,	131584649	343,12663	2203	4300	6503	SO:0001819	synonymous_variant	2021	exon3			GGTCATCGGCAAG	X79444	CCDS6912.1	9q34.1	2008-06-04			ENSG00000167136	ENSG00000167136			3346	protein-coding gene	gene with protein product		600440				7789991	Standard	NM_004435		Approved		uc004bwc.3	Q14249	OTTHUMG00000020763	ENST00000372642.4:c.654C>T	9.37:g.131584649C>T		105.0	0.0	0		107.0	66.0	0.616822	NM_004435	Q5T281|Q9BSP2	Silent	SNP	ENST00000372642.4	37	CCDS6912.1																																																																																			C|0.970;T|0.030	0.030	strong		0.592	ENDOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054505.1	NM_004435	
LRRTM1	347730	hgsc.bcm.edu	37	2	80529706	80529706	+	Silent	SNP	A	A	G	rs35054232	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:80529706A>G	ENST00000295057.3	-	2	1895	c.1239T>C	c.(1237-1239)ctT>ctC	p.L413L	CTNNA2_ENST00000540488.1_Intron|CTNNA2_ENST00000466387.1_Intron|CTNNA2_ENST00000541047.1_Intron|CTNNA2_ENST00000402739.4_Intron|LRRTM1_ENST00000409148.1_Silent_p.L413L|CTNNA2_ENST00000361291.4_Intron|CTNNA2_ENST00000496558.1_Intron	NM_178839.4	NP_849161.2	Q86UE6	LRRT1_HUMAN	leucine rich repeat transmembrane neuronal 1	413					exploration behavior (GO:0035640)|locomotory behavior (GO:0007626)|long-term synaptic potentiation (GO:0060291)|negative regulation of receptor internalization (GO:0002091)|protein localization to synapse (GO:0035418)|synapse organization (GO:0050808)	axon (GO:0030424)|cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|excitatory synapse (GO:0060076)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				NS(1)|breast(1)|endometrium(5)|large_intestine(7)|liver(1)|lung(33)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(5)|urinary_tract(2)	63						CGCCGCCTGGAAGAGCCACGG	0.682										HNSCC(69;0.2)			G|||	228	0.0455272	0.1604	0.0115	5008	,	,		16729	0.004		0.001	False		,,,				2504	0.0031				p.L413L		Atlas-SNP	.											.	LRRTM1	251	.	0			c.T1239C						PASS	.	G	,,	569,3833	754.3+/-412.4	41,487,1673	49.0	45.0	47.0		,,1239	2.0	1.0	2	dbSNP_126	47	37,8557	806.0+/-407.3	0,37,4260	no	intron,intron,coding-synonymous	CTNNA2,LRRTM1	NM_001164883.1,NM_004389.3,NM_178839.4	,,	41,524,5933	GG,GA,AA		0.4305,12.9259,4.663	,,	,,413/523	80529706	606,12390	2201	4297	6498	SO:0001819	synonymous_variant	347730	exon2			GCCTGGAAGAGCC	AY358310	CCDS1966.1	2p12	2004-06-22			ENSG00000162951	ENSG00000162951			19408	protein-coding gene	gene with protein product		610867				12676565	Standard	XR_244930		Approved	FLJ32082	uc002sok.1	Q86UE6	OTTHUMG00000130021	ENST00000295057.3:c.1239T>C	2.37:g.80529706A>G		33.0	0.0	0		37.0	13.0	0.351351	NM_178839	A8K397|D6W5K1|Q96DN1	Silent	SNP	ENST00000295057.3	37	CCDS1966.1																																																																																			A|0.958;G|0.042	0.042	strong		0.682	LRRTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313614.1	NM_178839	
SEMG1	6406	hgsc.bcm.edu	37	20	43836237	43836237	+	Missense_Mutation	SNP	T	T	A	rs61729393	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43836237T>A	ENST00000372781.3	+	2	356	c.299T>A	c.(298-300)cTa>cAa	p.L100Q	SEMG1_ENST00000244069.6_Missense_Mutation_p.L100Q	NM_003007.3	NP_002998.1	P04279	SEMG1_HUMAN	semenogelin I	100	Repeat-rich region. {ECO:0000250}.			L -> Q (in Ref. 3; AAP82463). {ECO:0000305}.	insemination (GO:0007320)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	32		Myeloproliferative disorder(115;0.0122)				CAACGACATCTAGGTGGAAGT	0.393													T|||	63	0.0125799	0.0371	0.0086	5008	,	,		22065	0.0		0.004	False		,,,				2504	0.0041				p.L100Q		Atlas-SNP	.											.	SEMG1	71	.	0			c.T299A						PASS	.	T	GLN/LEU	144,4262	100.7+/-139.4	1,142,2060	143.0	123.0	130.0		299	-2.1	0.0	20	dbSNP_129	130	18,8582	12.6+/-44.7	0,18,4282	yes	missense	SEMG1	NM_003007.3	113	1,160,6342	AA,AT,TT		0.2093,3.2683,1.2456		100/463	43836237	162,12844	2203	4300	6503	SO:0001583	missense	6406	exon2			GACATCTAGGTGG		CCDS13345.1	20q12-q13.2	2009-08-06			ENSG00000124233	ENSG00000124233			10742	protein-coding gene	gene with protein product	"""semen coagulating protein"", ""cancer/testis antigen 103"""	182140		SEMG		2912989, 15563730	Standard	NM_003007		Approved	CT103		P04279	OTTHUMG00000032565	ENST00000372781.3:c.299T>A	20.37:g.43836237T>A	ENSP00000361867:p.Leu100Gln	157.0	0.0	0		193.0	92.0	0.476684	NM_003007	Q53ZV0|Q53ZV1|Q53ZV2|Q6X4I9|Q6Y809|Q6Y822|Q6Y823|Q86U64|Q96QM3	Missense_Mutation	SNP	ENST00000372781.3	37	CCDS13345.1	23	0.010531135531135532	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	T	10.92	1.485748	0.26686	0.032683	0.002093	ENSG00000124233	ENST00000244069;ENST00000372781	T;T	0.09445	2.98;2.98	1.07	-2.13	0.07144	.	.	.	.	.	T	0.07007	0.0178	L	0.54323	1.7	0.09310	N	1	D;D;D	0.63880	0.985;0.993;0.988	P;D;P	0.71414	0.693;0.973;0.796	T	0.08513	-1.0718	9	0.62326	D	0.03	.	4.0698	0.09877	0.0:0.4746:0.0:0.5254	rs61729393	100;100;100	P04279-2;P04279;E7EPD3	.;SEMG1_HUMAN;.	Q	100	ENSP00000244069:L100Q;ENSP00000361867:L100Q	ENSP00000244069:L100Q	L	+	2	0	SEMG1	43269651	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.238000	0.01199	-0.505000	0.06568	-0.321000	0.08615	CTA	T|0.988;A|0.012	0.012	strong		0.393	SEMG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079416.3	NM_003007	
ARHGEF2	9181	hgsc.bcm.edu	37	1	155931630	155931630	+	Silent	SNP	G	G	A	rs143812169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:155931630G>A	ENST00000361247.4	-	11	1389	c.1290C>T	c.(1288-1290)gaC>gaT	p.D430D	ARHGEF2_ENST00000313695.7_Silent_p.D402D|ARHGEF2_ENST00000462460.2_Silent_p.D475D|ARHGEF2_ENST00000368315.4_Silent_p.D431D|ARHGEF2_ENST00000368316.1_Silent_p.D402D|ARHGEF2_ENST00000313667.4_Silent_p.D429D|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	430	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				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)					AAATACCCTCGTCCACATTGG	0.632													G|||	21	0.00419329	0.0136	0.0	5008	,	,		17097	0.0		0.0	False		,,,				2504	0.0031				p.D430D	Melanoma(178;35 2768 6610 28839)	Atlas-SNP	.											.	ARHGEF2	81	.	0			c.C1290T						PASS	.	G	,,	90,4316	73.6+/-111.7	1,88,2114	74.0	73.0	73.0		1290,1287,1206	4.0	1.0	1	dbSNP_134	73	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	ARHGEF2	NM_001162383.1,NM_001162384.1,NM_004723.3	,,	1,89,6413	AA,AG,GG		0.0116,2.0427,0.6997	,,	430/987,429/986,402/959	155931630	91,12915	2203	4300	6503	SO:0001819	synonymous_variant	9181	exon11			ACCCTCGTCCACA	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.1290C>T	1.37:g.155931630G>A		201.0	0.0	0		189.0	95.0	0.502645	NM_001162383	D3DVA6|O75142|Q15079|Q5VY92|Q8TDA3|Q8WUG4|Q9H023	Silent	SNP	ENST00000361247.4	37	CCDS53376.1																																																																																			G|0.995;A|0.005	0.005	strong		0.632	ARHGEF2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046204.2	NM_004723	
AGT	183	hgsc.bcm.edu	37	1	230846305	230846305	+	Missense_Mutation	SNP	C	C	T	rs11568032	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:230846305C>T	ENST00000366667.4	-	2	506	c.292G>A	c.(292-294)Gaa>Aaa	p.E98K	RP11-99J16__A.2_ENST00000412344.1_RNA	NM_000029.3	NP_000020.1	P01019	ANGT_HUMAN	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	98			E -> K (in dbSNP:rs11568032).		activation of NF-kappaB-inducing kinase activity (GO:0007250)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|angiotensin maturation (GO:0002003)|angiotensin mediated vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001998)|angiotensin-mediated drinking behavior (GO:0003051)|artery smooth muscle contraction (GO:0014824)|astrocyte activation (GO:0048143)|blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|branching involved in ureteric bud morphogenesis (GO:0001658)|catenin import into nucleus (GO:0035411)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|cellular lipid metabolic process (GO:0044255)|cellular protein metabolic process (GO:0044267)|cellular response to mechanical stimulus (GO:0071260)|cellular sodium ion homeostasis (GO:0006883)|cytokine secretion (GO:0050663)|ERK1 and ERK2 cascade (GO:0070371)|establishment of blood-nerve barrier (GO:0008065)|excretion (GO:0007588)|extracellular matrix organization (GO:0030198)|fibroblast proliferation (GO:0048144)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|kidney development (GO:0001822)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of tissue remodeling (GO:0034104)|nitric oxide mediated signal transduction (GO:0007263)|ovarian follicle rupture (GO:0001543)|peristalsis (GO:0030432)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of cytokine production (GO:0001819)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of NAD(P)H oxidase activity (GO:0033864)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of organ growth (GO:0046622)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of blood volume by renin-angiotensin (GO:0002016)|regulation of calcium ion transport (GO:0051924)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of norepinephrine secretion (GO:0014061)|regulation of proteolysis (GO:0030162)|regulation of renal output by angiotensin (GO:0002019)|regulation of renal sodium excretion (GO:0035813)|regulation of vasoconstriction (GO:0019229)|renal response to blood flow involved in circulatory renin-angiotensin regulation of systemic arterial blood pressure (GO:0001999)|renal system process (GO:0003014)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to cold (GO:0009409)|response to muscle activity involved in regulation of muscle adaptation (GO:0014873)|response to salt stress (GO:0009651)|small molecule metabolic process (GO:0044281)|smooth muscle cell differentiation (GO:0051145)|smooth muscle cell proliferation (GO:0048659)|stress-activated MAPK cascade (GO:0051403)|uterine smooth muscle contraction (GO:0070471)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	growth factor activity (GO:0008083)|hormone activity (GO:0005179)|serine-type endopeptidase inhibitor activity (GO:0004867)|superoxide-generating NADPH oxidase activator activity (GO:0016176)|type 1 angiotensin receptor binding (GO:0031702)|type 2 angiotensin receptor binding (GO:0031703)			endometrium(5)|kidney(1)|large_intestine(6)|lung(7)|pancreas(1)|prostate(5)	25	Breast(184;0.0735)|Ovarian(103;0.183)	all_cancers(173;4.64e-23)|all_epithelial(177;3.61e-18)|Breast(1374;0.00093)|all_neural(198;0.0604)|Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;4.4e-06)|Colorectal(1306;5.46e-06)|COAD - Colon adenocarcinoma(196;0.000256)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		AACTTGTCTTCGGTGTCAAGT	0.562													C|||	17	0.00339457	0.0113	0.0029	5008	,	,		21719	0.0		0.0	False		,,,				2504	0.0				p.E98K		Atlas-SNP	.											.	AGT	62	.	0			c.G292A						PASS	.	C	LYS/GLU	62,4344	58.1+/-94.6	0,62,2141	90.0	88.0	89.0		292	4.2	0.0	1	dbSNP_120	89	0,8600		0,0,4300	yes	missense	AGT	NM_000029.3	56	0,62,6441	TT,TC,CC		0.0,1.4072,0.4767	benign	98/486	230846305	62,12944	2203	4300	6503	SO:0001583	missense	183	exon2			TGTCTTCGGTGTC	K02215	CCDS1585.1	1q42.2	2014-02-18	2005-08-18	2001-06-29	ENSG00000135744	ENSG00000135744		"""Serine (or cysteine) peptidase inhibitors"", ""Endogenous ligands"""	333	protein-coding gene	gene with protein product	"""alpha-1 antiproteinase, antitrypsin"""	106150		SERPINA8		6089875, 24172014	Standard	NM_000029		Approved		uc001hty.4	P01019	OTTHUMG00000037757	ENST00000366667.4:c.292G>A	1.37:g.230846305C>T	ENSP00000355627:p.Glu98Lys	193.0	0.0	0		183.0	86.0	0.469945	NM_000029	Q16358|Q16359|Q96F91	Missense_Mutation	SNP	ENST00000366667.4	37	CCDS1585.1	9	0.004120879120879121	7	0.014227642276422764	2	0.0055248618784530384	0	0.0	0	0.0	C	8.409	0.843741	0.16963	0.014072	0.0	ENSG00000135744	ENST00000366667;ENST00000430091	D	0.87412	-2.25	5.09	4.18	0.49190	Serpin domain (1);	0.637587	0.16103	N	0.229456	T	0.73621	0.3610	M	0.62723	1.935	0.09310	N	1	P;P;P	0.40794	0.685;0.729;0.685	B;B;B	0.29785	0.107;0.101;0.107	T	0.66135	-0.5999	10	0.23302	T	0.38	.	5.7631	0.18211	0.1411:0.6438:0.1367:0.0785	rs11568032;rs52801258;rs59896600;rs11568032	98;98;98	B0ZBE2;B2R5S1;P01019	.;.;ANGT_HUMAN	K	98	ENSP00000355627:E98K	ENSP00000355627:E98K	E	-	1	0	AGT	228912928	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	0.721000	0.25911	1.276000	0.44395	0.491000	0.48974	GAA	C|0.994;T|0.006	0.006	strong		0.562	AGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092102.1	NM_000029	
SPOCK1	6695	hgsc.bcm.edu	37	5	136448208	136448208	+	Silent	SNP	A	A	G	rs17170968	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:136448208A>G	ENST00000394945.1	-	5	559	c.390T>C	c.(388-390)ccT>ccC	p.P130P	SPOCK1_ENST00000282223.7_Silent_p.P130P	NM_004598.3	NP_004589.1	Q08629	TICN1_HUMAN	sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican) 1	130	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.				cell adhesion (GO:0007155)|central nervous system neuron differentiation (GO:0021953)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron projection development (GO:0010977)|nervous system development (GO:0007399)|neurogenesis (GO:0022008)|neuron migration (GO:0001764)|regulation of cell growth (GO:0001558)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|postsynaptic density (GO:0014069)|proteinaceous extracellular matrix (GO:0005578)|sarcoplasm (GO:0016528)	calcium ion binding (GO:0005509)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(2)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CCAAATTCGAAGGTCCAACCC	0.498													A|||	379	0.0756789	0.2769	0.0187	5008	,	,		18879	0.0		0.0	False		,,,				2504	0.0				p.P130P		Atlas-SNP	.											.	SPOCK1	58	.	0			c.T390C						PASS	.	A		1146,3260	407.3+/-334.2	151,844,1208	101.0	97.0	98.0		390	-1.0	1.0	5	dbSNP_123	98	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous	SPOCK1	NM_004598.3		151,854,5498	GG,GA,AA		0.1163,26.01,8.8882		130/440	136448208	1156,11850	2203	4300	6503	SO:0001819	synonymous_variant	6695	exon5			ATTCGAAGGTCCA	AF231124	CCDS4191.1	5q31.2	2008-02-05	2005-11-04	2005-11-04	ENSG00000152377	ENSG00000152377			11251	protein-coding gene	gene with protein product		602264	"""sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican)"""	TIC1, SPOCK		9545645	Standard	NM_004598		Approved	testican-1	uc003lbp.3	Q08629	OTTHUMG00000129157	ENST00000394945.1:c.390T>C	5.37:g.136448208A>G		75.0	0.0	0		62.0	25.0	0.403226	NM_004598	B3KSW3|Q59EW0|Q8N630|Q9UCL8	Silent	SNP	ENST00000394945.1	37	CCDS4191.1																																																																																			A|0.924;G|0.076	0.076	strong		0.498	SPOCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251222.1	NM_004598	
ABHD2	11057	hgsc.bcm.edu	37	15	89738475	89738475	+	Missense_Mutation	SNP	A	A	C	rs147106119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:89738475A>C	ENST00000352732.5	+	11	1619	c.1099A>C	c.(1099-1101)Atg>Ctg	p.M367L	ABHD2_ENST00000355100.3_Missense_Mutation_p.M367L|ABHD2_ENST00000565973.1_Missense_Mutation_p.M367L	NM_152924.4	NP_690888.1	P08910	ABHD2_HUMAN	abhydrolase domain containing 2	367					negative regulation of cell migration (GO:0030336)|response to wounding (GO:0009611)	integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)|prostate(2)|soft_tissue(1)	23	Lung NSC(78;0.0472)|all_lung(78;0.089)					AGAGAACGTCATGTTTGTGCT	0.557													A|||	5	0.000998403	0.0038	0.0	5008	,	,		20328	0.0		0.0	False		,,,				2504	0.0				p.M367L	Colon(11;252 417 24570 33239 41878)	Atlas-SNP	.											.	ABHD2	55	.	0			c.A1099C						PASS	.	A	LEU/MET,LEU/MET	16,4384	23.3+/-48.9	0,16,2184	142.0	124.0	130.0		1099,1099	4.6	1.0	15	dbSNP_134	130	0,8598		0,0,4299	yes	missense,missense	ABHD2	NM_007011.7,NM_152924.4	15,15	0,16,6483	CC,CA,AA		0.0,0.3636,0.1231	benign,benign	367/426,367/426	89738475	16,12982	2200	4299	6499	SO:0001583	missense	11057	exon15			AACGTCATGTTTG	X12433	CCDS10348.1	15q26.1	2006-10-06			ENSG00000140526	ENSG00000140526		"""Abhydrolase domain containing"""	18717	protein-coding gene	gene with protein product		612196					Standard	NM_152924		Approved	LABH2	uc002bnk.2	P08910	OTTHUMG00000148684	ENST00000352732.5:c.1099A>C	15.37:g.89738475A>C	ENSP00000268129:p.Met367Leu	115.0	0.0	0		115.0	55.0	0.478261	NM_007011	Q53G48|Q53GU0|Q5FVD9|Q8TC79	Missense_Mutation	SNP	ENST00000352732.5	37	CCDS10348.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	5.968	0.362642	0.11296	0.003636	0.0	ENSG00000140526	ENST00000352732;ENST00000355100	T;T	0.60299	0.2;0.2	5.75	4.6	0.57074	Alpha/beta hydrolase fold-1 (1);	0.166180	0.64402	D	0.000008	T	0.34019	0.0883	N	0.16307	0.4	0.41422	D	0.987801	B	0.10296	0.003	B	0.15052	0.012	T	0.10847	-1.0612	10	0.08179	T	0.78	-14.589	6.6357	0.22881	0.7918:0.0:0.0709:0.1373	.	367	P08910	ABHD2_HUMAN	L	367	ENSP00000268129:M367L;ENSP00000347217:M367L	ENSP00000268129:M367L	M	+	1	0	ABHD2	87539479	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.877000	0.63086	0.974000	0.38366	0.533000	0.62120	ATG	A|0.999;C|0.001	0.001	strong		0.557	ABHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309074.2		
UNC5B	219699	hgsc.bcm.edu	37	10	73051440	73051440	+	Missense_Mutation	SNP	G	G	A	rs10509332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73051440G>A	ENST00000335350.6	+	10	1962	c.1546G>A	c.(1546-1548)Gcc>Acc	p.A516T	UNC5B_ENST00000373192.4_Missense_Mutation_p.A505T	NM_170744.4	NP_734465.2	Q8IZJ1	UNC5B_HUMAN	unc-5 homolog B (C. elegans)	516			A -> T (in dbSNP:rs10509332).		anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(4)|skin(4)	49						TAGCGATTTCGCCCGGGACAC	0.682													g|||	174	0.0347444	0.0923	0.013	5008	,	,		16797	0.0		0.0169	False		,,,				2504	0.0266				p.A516T		Atlas-SNP	.											.	UNC5B	123	.	0			c.G1546A						PASS	.		THR/ALA	326,4080	175.9+/-205.1	12,302,1889	49.0	51.0	50.0		1546	-7.4	0.0	10	dbSNP_119	50	235,8363	96.3+/-158.1	3,229,4067	yes	missense	UNC5B	NM_170744.4	58	15,531,5956	AA,AG,GG		2.7332,7.399,4.3141	benign	516/946	73051440	561,12443	2203	4299	6502	SO:0001583	missense	219699	exon10			GATTTCGCCCGGG	AB096256	CCDS7309.1, CCDS58083.1	10q22.2	2013-01-11	2001-11-28		ENSG00000107731	ENSG00000107731		"""Immunoglobulin superfamily / I-set domain containing"""	12568	protein-coding gene	gene with protein product		607870	"""unc5 (C.elegans homolog) b"""				Standard	NM_170744		Approved	UNC5H2, p53RDL1	uc001jro.3	Q8IZJ1	OTTHUMG00000018422	ENST00000335350.6:c.1546G>A	10.37:g.73051440G>A	ENSP00000334329:p.Ala516Thr	75.0	0.0	0		87.0	45.0	0.517241	NM_170744	Q5T3R9|Q5T3S0|Q86SN3|Q8N1Y2|Q9H9F3	Missense_Mutation	SNP	ENST00000335350.6	37	CCDS7309.1	66	0.03021978021978022	44	0.08943089430894309	6	0.016574585635359115	0	0.0	16	0.021108179419525065	g	0.003	-2.576838	0.00131	0.07399	0.027332	ENSG00000107731	ENST00000335350;ENST00000373192	T;T	0.48836	0.86;0.8	3.71	-7.42	0.01388	.	1.034760	0.07589	N	0.921713	T	0.00754	0.0025	N	0.22421	0.69	0.09310	N	1	B;B	0.24483	0.104;0.063	B;B	0.15870	0.014;0.006	T	0.04128	-1.0975	10	0.14656	T	0.56	-3.517	0.8807	0.01233	0.1728:0.2213:0.3114:0.2946	rs10509332;rs10509332	505;516	Q8IZJ1-2;Q8IZJ1	.;UNC5B_HUMAN	T	516;505	ENSP00000334329:A516T;ENSP00000362288:A505T	ENSP00000334329:A516T	A	+	1	0	UNC5B	72721446	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.641000	0.02007	-3.747000	0.00112	-2.851000	0.00103	GCC	G|0.960;A|0.040	0.040	strong		0.682	UNC5B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048541.1	NM_170744	
PXDN	7837	hgsc.bcm.edu	37	2	1647186	1647186	+	Silent	SNP	G	G	A	rs111450110	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:1647186G>A	ENST00000252804.4	-	19	3956	c.3906C>T	c.(3904-3906)gaC>gaT	p.D1302D		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	1302					extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		TGGGGATCTCGTCACAGCTGC	0.612													G|||	57	0.0113818	0.0393	0.0072	5008	,	,		16011	0.0		0.0	False		,,,				2504	0.0				p.D1302D		Atlas-SNP	.											.	PXDN	255	.	0			c.C3906T						PASS	.	G		167,4063		5,157,1953	65.0	76.0	72.0		3906	-9.0	0.0	2	dbSNP_132	72	1,8443		0,1,4221	yes	coding-synonymous	PXDN	NM_012293.1		5,158,6174	AA,AG,GG		0.0118,3.948,1.3255		1302/1480	1647186	168,12506	2115	4222	6337	SO:0001819	synonymous_variant	7837	exon19			GATCTCGTCACAG	AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"""Immunoglobulin superfamily / I-set domain containing"""	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.3906C>T	2.37:g.1647186G>A		65.0	0.0	0		71.0	31.0	0.43662	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Silent	SNP	ENST00000252804.4	37	CCDS46221.1																																																																																			G|0.992;A|0.008	0.008	strong		0.612	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455	
CCT5	22948	hgsc.bcm.edu	37	5	10262607	10262607	+	Silent	SNP	G	G	A	rs113262482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:10262607G>A	ENST00000280326.4	+	9	1614	c.1194G>A	c.(1192-1194)gcG>gcA	p.A398A	CCT5_ENST00000506600.1_Silent_p.A305A|CTD-2256P15.4_ENST00000606194.1_RNA|CCT5_ENST00000515390.1_Silent_p.A343A|CCT5_ENST00000503026.1_Silent_p.A377A|CCT5_ENST00000515676.1_Silent_p.A360A	NM_012073.3	NP_036205.1	P48643	TCPE_HUMAN	chaperonin containing TCP1, subunit 5 (epsilon)	398					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|response to virus (GO:0009615)	cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleolus (GO:0005730)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|G-protein beta-subunit binding (GO:0031681)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(2)	26						TTGAGGAGGCGAAACGATCCC	0.468													G|||	40	0.00798722	0.0295	0.0	5008	,	,		20572	0.0		0.001	False		,,,				2504	0.0				p.A398A		Atlas-SNP	.											.	CCT5	49	.	0			c.G1194A						PASS	.	G		99,4307	79.3+/-117.8	1,97,2105	160.0	131.0	141.0		1194	-7.7	0.9	5	dbSNP_132	141	3,8597	3.0+/-9.4	0,3,4297	yes	coding-synonymous	CCT5	NM_012073.3		1,100,6402	AA,AG,GG		0.0349,2.2469,0.7843		398/542	10262607	102,12904	2203	4300	6503	SO:0001819	synonymous_variant	22948	exon9			GGAGGCGAAACGA	D43950	CCDS3877.1	5p15.2	2014-09-17			ENSG00000150753	ENSG00000150753		"""Heat Shock Proteins / Chaperonins"""	1618	protein-coding gene	gene with protein product		610150					Standard	NM_012073		Approved	KIAA0098	uc003jeq.3	P48643	OTTHUMG00000131042	ENST00000280326.4:c.1194G>A	5.37:g.10262607G>A		120.0	0.0	0		143.0	68.0	0.475524	NM_012073	A8JZY8|A8K2X8|B4DYD8	Silent	SNP	ENST00000280326.4	37	CCDS3877.1																																																																																			G|0.992;A|0.008	0.008	strong		0.468	CCT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253688.2		
PCDHB14	56122	hgsc.bcm.edu	37	5	140603248	140603248	+	Silent	SNP	G	G	A	rs7713000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140603248G>A	ENST00000239449.4	+	1	171	c.171G>A	c.(169-171)gaG>gaA	p.E57E	PCDHB14_ENST00000515856.2_Intron	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	57	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGGGGGTGGAGGAGCTGTCTT	0.478													g|||	103	0.0205671	0.0734	0.0072	5008	,	,		17325	0.0		0.001	False		,,,				2504	0.0				p.E57E	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.G171A						PASS	.	G		278,4128		6,266,1931	90.0	93.0	92.0		171	1.0	0.6	5	dbSNP_116	92	0,8600		0,0,4300	no	coding-synonymous	PCDHB14	NM_018934.2		6,266,6231	AA,AG,GG		0.0,6.3096,2.1375		57/799	140603248	278,12728	2203	4300	6503	SO:0001819	synonymous_variant	56122	exon1			GGTGGAGGAGCTG	AF152493	CCDS4256.1	5q31	2010-01-26			ENSG00000120327	ENSG00000120327		"""Cadherins / Protocadherins : Clustered"""	8685	other	protocadherin		606340				10380929	Standard	NM_018934		Approved	PCDH-BETA14	uc003ljb.3	Q9Y5E9	OTTHUMG00000129619	ENST00000239449.4:c.171G>A	5.37:g.140603248G>A		188.0	0.0	0		205.0	106.0	0.517073	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Silent	SNP	ENST00000239449.4	37	CCDS4256.1																																																																																			G|0.975;A|0.025	0.025	strong		0.478	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934	
GALNT10	55568	hgsc.bcm.edu	37	5	153792453	153792453	+	Missense_Mutation	SNP	G	G	A	rs142635658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:153792453G>A	ENST00000297107.6	+	10	1528	c.1391G>A	c.(1390-1392)cGa>cAa	p.R464Q	GALNT10_ENST00000377657.3_Missense_Mutation_p.R137Q|SAP30L-AS1_ENST00000519727.1_RNA|GALNT10_ENST00000377661.2_Missense_Mutation_p.R402Q|SAP30L-AS1_ENST00000524264.1_RNA	NM_198321.3	NP_938080.1	Q86SR1	GLT10_HUMAN	polypeptide N-acetylgalactosaminyltransferase 10	464	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(12)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	32	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)|all_hematologic(541;0.21)	Kidney(363;8.21e-05)|KIRC - Kidney renal clear cell carcinoma(527;0.000577)			TTTCAGATCCGAAATGTGGGC	0.612													G|||	14	0.00279553	0.0106	0.0	5008	,	,		18983	0.0		0.0	False		,,,				2504	0.0				p.R464Q		Atlas-SNP	.											.	GALNT10	70	.	0			c.G1391A						PASS	.	G	GLN/ARG	41,4365	44.6+/-78.6	0,41,2162	85.0	84.0	85.0		1391	3.8	0.4	5	dbSNP_134	85	0,8600		0,0,4300	yes	missense	GALNT10	NM_198321.3	43	0,41,6462	AA,AG,GG		0.0,0.9305,0.3152	benign	464/604	153792453	41,12965	2203	4300	6503	SO:0001583	missense	55568	exon10			AGATCCGAAATGT	AK023782	CCDS4325.1	5q34	2014-03-13	2014-03-13		ENSG00000164574	ENSG00000164574	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	19873	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 10"""	608043	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 10 (GalNAc-T10)"""			12417297	Standard	NM_198321		Approved	GalNAc-T10	uc003lvh.3	Q86SR1	OTTHUMG00000130145	ENST00000297107.6:c.1391G>A	5.37:g.153792453G>A	ENSP00000297107:p.Arg464Gln	41.0	0.0	0		31.0	17.0	0.548387	NM_198321	B3KXC9|Q6IN56|Q86VP8|Q8IXJ2|Q8TEJ2|Q96IV2|Q9H8E1|Q9Y4M4	Missense_Mutation	SNP	ENST00000297107.6	37	CCDS4325.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	12.24	1.879954	0.33162	0.009305	0.0	ENSG00000164574	ENST00000297107;ENST00000377661;ENST00000377657	T;T;T	0.28666	1.6;1.6;1.6	5.56	3.77	0.43336	Ricin B-related lectin (1);Ricin B lectin (2);	0.091610	0.85682	D	0.000000	T	0.17492	0.0420	L	0.49256	1.55	0.48571	D	0.99967	B;B;B	0.31752	0.054;0.338;0.04	B;B;B	0.22152	0.013;0.038;0.005	T	0.02736	-1.1117	10	0.26408	T	0.33	.	10.6774	0.45794	0.2076:0.0:0.7924:0.0	.	402;135;464	Q86SR1-2;D6R8Y1;Q86SR1	.;.;GLT10_HUMAN	Q	464;402;137	ENSP00000297107:R464Q;ENSP00000366889:R402Q;ENSP00000366885:R137Q	ENSP00000297107:R464Q	R	+	2	0	GALNT10	153772646	1.000000	0.71417	0.392000	0.26245	0.899000	0.52679	2.936000	0.48971	0.706000	0.31912	0.655000	0.94253	CGA	G|0.997;A|0.003	0.003	strong		0.612	GALNT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252453.1	NM_198321	
CEP78	84131	hgsc.bcm.edu	37	9	80881357	80881357	+	Splice_Site	SNP	G	G	C	rs146563928	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:80881357G>C	ENST00000424347.2	+	15	2086		c.e15-1		CEP78_ENST00000376597.4_Splice_Site|CEP78_ENST00000277082.5_Splice_Site|CEP78_ENST00000415759.2_Splice_Site|CEP78_ENST00000376598.2_Splice_Site			Q5JTW2	CEP78_HUMAN	centrosomal protein 78kDa						G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)				breast(1)|cervix(1)|endometrium(5)|large_intestine(7)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	21						TTTCCTTCTAGTTTCAGAAAA	0.378													G|||	2	0.000399361	0.0	0.0014	5008	,	,		18264	0.0		0.001	False		,,,				2504	0.0				.		Atlas-SNP	.											.	CEP78	79	.	0			c.1849-1G>C						PASS	.	G	,	1,3681		0,1,1840	40.0	40.0	40.0		,	4.0	1.0	9	dbSNP_134	40	21,8139		0,21,4059	yes	splice-3,splice-3	CEP78	NM_001098802.1,NM_032171.1	,	0,22,5899	CC,CG,GG		0.2574,0.0272,0.1858	,	,	80881357	22,11820	1841	4080	5921	SO:0001630	splice_region_variant	84131	exon16			CTTCTAGTTTCAG	BC058931	CCDS47984.1, CCDS47985.1	9q21.2	2014-02-20	2005-12-01	2005-12-01	ENSG00000148019	ENSG00000148019			25740	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 81"""	C9orf81		14654843	Standard	NM_001098802		Approved	FLJ12643	uc004aky.4	Q5JTW2	OTTHUMG00000020062	ENST00000424347.2:c.1798-1G>C	9.37:g.80881357G>C		34.0	0.0	0		29.0	10.0	0.344828	NM_001098802	A1A4S8|E9PHX5|Q5BJE3|Q5JTW0|Q5JTW1|Q9H9N3	Splice_Site	SNP	ENST00000424347.2	37		2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	14.72	2.618270	0.46736	2.72E-4	0.002574	ENSG00000148019	ENST00000424347;ENST00000415085;ENST00000415759;ENST00000376597;ENST00000277082;ENST00000376598	.	.	.	6.07	4.01	0.46588	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.3193	0.26517	0.1296:0.1641:0.7063:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CEP78	80071177	0.987000	0.35691	0.999000	0.59377	0.943000	0.58893	1.038000	0.30254	2.885000	0.99019	0.655000	0.94253	.	G|0.999;C|0.001	0.001	strong		0.378	CEP78-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000052766.2	XM_095991	Intron
AGMO	392636	hgsc.bcm.edu	37	7	15458194	15458194	+	Missense_Mutation	SNP	T	T	A	rs146442781	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:15458194T>A	ENST00000342526.3	-	5	767	c.598A>T	c.(598-600)Atc>Ttc	p.I200F		NM_001004320.1	NP_001004320.1	Q6ZNB7	ALKMO_HUMAN	alkylglycerol monooxygenase	200					ether lipid metabolic process (GO:0046485)|fatty acid biosynthetic process (GO:0006633)|membrane lipid metabolic process (GO:0006643)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glyceryl-ether monooxygenase activity (GO:0050479)|iron ion binding (GO:0005506)	p.I200V(1)		breast(1)|kidney(1)|large_intestine(6)|liver(1)|lung(30)|prostate(1)|skin(2)	42						TCTGTATGGATCCAAAATTGG	0.348													T|||	22	0.00439297	0.0151	0.0029	5008	,	,		13274	0.0		0.0	False		,,,				2504	0.0				p.I200F		Atlas-SNP	.											AGMO,NS,carcinoma,0,1	AGMO	98	1	1	Substitution - Missense(1)	prostate(1)	c.A598T						scavenged	.	T	PHE/ILE	50,4350		0,50,2150	35.0	42.0	40.0		598	5.8	1.0	7	dbSNP_134	40	0,8574		0,0,4287	yes	missense	AGMO	NM_001004320.1	21	0,50,6437	AA,AT,TT		0.0,1.1364,0.3854	probably-damaging	200/446	15458194	50,12924	2200	4287	6487	SO:0001583	missense	392636	exon5			TATGGATCCAAAA		CCDS34604.1	7p21.1	2013-03-04	2011-01-31	2011-01-31	ENSG00000187546	ENSG00000187546	1.14.16.5	"""Fatty acid hydroxylase domain containing"""	33784	protein-coding gene	gene with protein product		613738	"""transmembrane protein 195"""	TMEM195		20643956	Standard	NM_001004320		Approved	FLJ16237	uc003stb.1	Q6ZNB7	OTTHUMG00000152387	ENST00000342526.3:c.598A>T	7.37:g.15458194T>A	ENSP00000341662:p.Ile200Phe	140.0	1.0	0.00714286		162.0	81.0	0.5	NM_001004320	A4D114|A6NCH5	Missense_Mutation	SNP	ENST00000342526.3	37	CCDS34604.1	7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	T	22.8	4.342517	0.81911	0.011364	0.0	ENSG00000187546	ENST00000342526	D	0.84730	-1.89	5.8	5.8	0.92144	Fatty acid hydroxylase (1);	0.000000	0.85682	D	0.000000	D	0.91751	0.7391	M	0.93462	3.42	0.80722	D	1	D	0.56035	0.974	P	0.61328	0.887	D	0.93409	0.6767	10	0.72032	D	0.01	-30.639	16.1416	0.81528	0.0:0.0:0.0:1.0	.	200	Q6ZNB7	ALKMO_HUMAN	F	200	ENSP00000341662:I200F	ENSP00000341662:I200F	I	-	1	0	AGMO	15424719	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	5.600000	0.67599	2.209000	0.71365	0.482000	0.46254	ATC	T|0.997;A|0.003	0.003	strong		0.348	AGMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326049.2	NM_001004320	
DEFB1	1672	hgsc.bcm.edu	37	8	6728298	6728298	+	Missense_Mutation	SNP	C	C	T	rs2738047|rs397732952	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:6728298C>T	ENST00000297439.3	-	2	276	c.112G>A	c.(112-114)Gtc>Atc	p.V38I		NM_005218.3	NP_005209.1	P60022	DEFB1_HUMAN	defensin, beta 1	38			V -> I (in dbSNP:rs2738047).		acute inflammatory response (GO:0002526)|antibacterial humoral response (GO:0019731)|chemotaxis (GO:0006935)|defense response to Gram-positive bacterium (GO:0050830)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|response to bacterium (GO:0009617)|response to testosterone (GO:0033574)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				lung(1)	1			STAD - Stomach adenocarcinoma(24;0.0984)	COAD - Colon adenocarcinoma(149;0.0162)|READ - Rectum adenocarcinoma(644;0.128)		CCACTGCTGACGCAATTGTAA	0.498													C|||	199	0.0397364	0.1384	0.0043	5008	,	,		18887	0.0069		0.002	False		,,,				2504	0.0041				p.V38I	Pancreas(35;916 948 9612 33610 36642)	Atlas-SNP	.											.	DEFB1	4	.	0			c.G112A	GRCh37	CM020372	DEFB1	M	rs2738047	PASS	.	C	ILE/VAL	545,3861	249.6+/-257.0	36,473,1694	122.0	99.0	107.0		112	2.2	0.0	8	dbSNP_100	107	6,8594	5.0+/-18.6	0,6,4294	yes	missense	DEFB1	NM_005218.3	29	36,479,5988	TT,TC,CC		0.0698,12.3695,4.2365	benign	38/69	6728298	551,12455	2203	4300	6503	SO:0001583	missense	1672	exon2			TGCTGACGCAATT	X92744	CCDS5959.1	8p23.1	2012-03-27			ENSG00000164825	ENSG00000164825		"""Defensins, beta"""	2766	protein-coding gene	gene with protein product		602056				7628632	Standard	NM_005218		Approved	HBD-1, DEFB-1, DEFB101, HBD1, BD1, MGC51822	uc003wqs.2	P60022	OTTHUMG00000090367	ENST00000297439.3:c.112G>A	8.37:g.6728298C>T	ENSP00000297439:p.Val38Ile	122.0	0.0	0		128.0	71.0	0.554688	NM_005218	Q09753	Missense_Mutation	SNP	ENST00000297439.3	37	CCDS5959.1	62	0.028388278388278388	56	0.11382113821138211	0	0.0	6	0.01048951048951049	0	0.0	C	13.89	2.373486	0.42105	0.123695	6.98E-4	ENSG00000164825	ENST00000297439	T	0.21543	2.0	4.24	2.16	0.27623	.	1.226530	0.06201	N	0.683220	T	0.00178	0.0005	.	.	.	0.09310	N	1	P	0.49696	0.927	B	0.29440	0.102	T	0.28870	-1.0030	9	0.41790	T	0.15	-4.8641	9.8265	0.40914	0.0:0.589:0.411:0.0	rs2738047;rs52816296;rs60091306;rs2738047	38	P60022	DEFB1_HUMAN	I	38	ENSP00000297439:V38I	ENSP00000297439:V38I	V	-	1	0	DEFB1	6715708	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	0.025000	0.13577	1.041000	0.40125	0.563000	0.77884	GTC	T|0.041;C|0.959	0.041	strong		0.498	DEFB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251292.1	NM_005218	
SSPO	23145	hgsc.bcm.edu	37	7	149498945	149498945	+	RNA	SNP	C	C	T	rs73727615	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149498945C>T	ENST00000378016.2	+	0	7397							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CTCTGTTCCCCGAGCCAGCTG	0.657													C|||	90	0.0179712	0.0635	0.0086	5008	,	,		18616	0.0		0.0	False		,,,				2504	0.0				p.P2466L		Atlas-SNP	.											.	.	.	.	0			c.C7397T						PASS	.	C		208,4004		3,202,1901	31.0	34.0	33.0		7401	2.5	0.1	7	dbSNP_130	33	3,8429		0,3,4213	no	coding-notMod3	SSPO	NM_198455.2		3,205,6114	TT,TC,CC		0.0356,4.9383,1.6688			149498945	211,12433	2106	4216	6322			23145	exon50			GTTCCCCGAGCCA	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149498945C>T		105.0	0.0	0		78.0	44.0	0.564103	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.982;T|0.018	0.018	strong		0.657	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
ALPI	248	hgsc.bcm.edu	37	2	233323000	233323000	+	Silent	SNP	C	C	T	rs10195208	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:233323000C>T	ENST00000295463.3	+	9	1142	c.1065C>T	c.(1063-1065)gaC>gaT	p.D355D		NM_001631.3	NP_001622.2	P09923	PPBI_HUMAN	alkaline phosphatase, intestinal	355					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|protease binding (GO:0002020)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|prostate(2)|upper_aerodigestive_tract(1)	24		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;1.64e-16)|Kidney(3;9.71e-08)|KIRC - Kidney renal clear cell carcinoma(3;2.74e-06)|BRCA - Breast invasive adenocarcinoma(100;0.000763)|Lung(119;0.00564)|LUSC - Lung squamous cell carcinoma(224;0.00746)		TGTTCGACGACGCCATTGAGA	0.627													C|||	253	0.0505192	0.1884	0.0058	5008	,	,		17694	0.0		0.0	False		,,,				2504	0.0				p.D355D		Atlas-SNP	.											ALPI,NS,carcinoma,+2,1	ALPI	64	1	0			c.C1065T						PASS	.	C		624,3782	271.6+/-270.3	39,546,1618	86.0	76.0	79.0		1065	-8.9	0.0	2	dbSNP_119	79	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	ALPI	NM_001631.3		39,554,5910	TT,TC,CC		0.093,14.1625,4.8593		355/529	233323000	632,12374	2203	4300	6503	SO:0001819	synonymous_variant	248	exon9			CGACGACGCCATT	M15694	CCDS2492.1	2q37.1	2008-02-05			ENSG00000163295	ENSG00000163295	3.1.3.1		437	protein-coding gene	gene with protein product		171740				3468508, 3469665	Standard	NM_001631		Approved		uc002vst.4	P09923	OTTHUMG00000133258	ENST00000295463.3:c.1065C>T	2.37:g.233323000C>T		240.0	1.0	0.00416667		266.0	128.0	0.481203	NM_001631	B2R7Y4|Q53S80|Q9UBV5|Q9UCL2	Silent	SNP	ENST00000295463.3	37	CCDS2492.1																																																																																			C|0.950;T|0.050	0.050	strong		0.627	ALPI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257035.2	NM_001631	
ADIPOQ	9370	hgsc.bcm.edu	37	3	186570951	186570951	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:186570951C>T	ENST00000412955.2	+	2	245	c.104C>T	c.(103-105)gCc>gTc	p.A35V	ADIPOQ-AS1_ENST00000422718.1_RNA|ADIPOQ_ENST00000444204.2_Missense_Mutation_p.A35V|ADIPOQ_ENST00000320741.2_Missense_Mutation_p.A35V			Q15848	ADIPO_HUMAN	adiponectin, C1Q and collagen domain containing	35					adiponectin-activated signaling pathway (GO:0033211)|brown fat cell differentiation (GO:0050873)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to insulin stimulus (GO:0032869)|circadian rhythm (GO:0007623)|detection of oxidative stress (GO:0070994)|fatty acid beta-oxidation (GO:0006635)|fatty acid oxidation (GO:0019395)|generation of precursor metabolites and energy (GO:0006091)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|low-density lipoprotein particle clearance (GO:0034383)|membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|negative regulation of blood pressure (GO:0045776)|negative regulation of cell migration (GO:0030336)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of hormone secretion (GO:0046888)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of intracellular protein transport (GO:0090317)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metanephric mesenchymal cell migration (GO:2000590)|negative regulation of phagocytosis (GO:0050765)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of platelet-derived growth factor receptor-alpha signaling pathway (GO:2000584)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of receptor binding (GO:1900121)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of synaptic transmission (GO:0050805)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|positive regulation of blood pressure (GO:0045777)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of fatty acid metabolic process (GO:0045923)|positive regulation of glucose import (GO:0046326)|positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of metanephric glomerular visceral epithelial cell development (GO:2000478)|positive regulation of monocyte chemotactic protein-1 production (GO:0071639)|positive regulation of myeloid cell apoptotic process (GO:0033034)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein kinase A signaling (GO:0010739)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of renal albumin absorption (GO:2000534)|positive regulation of signal transduction (GO:0009967)|protein heterotrimerization (GO:0070208)|protein homooligomerization (GO:0051260)|protein localization to plasma membrane (GO:0072659)|regulation of glucose metabolic process (GO:0010906)|response to activity (GO:0014823)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to linoleic acid (GO:0070543)|response to nutrient (GO:0007584)|response to sucrose (GO:0009744)|response to tumor necrosis factor (GO:0034612)	cell surface (GO:0009986)|collagen trimer (GO:0005581)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)|hormone activity (GO:0005179)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|sialic acid binding (GO:0033691)			breast(1)|endometrium(2)|large_intestine(4)|lung(6)|ovary(1)|skin(2)	16	all_cancers(143;1.2e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;1.47e-19)	GBM - Glioblastoma multiforme(93;0.0776)		CCCAAGGGGGCCTGCACAGGT	0.627																																					p.A35V		Atlas-SNP	.											.	ADIPOQ	35	.	0			c.C104T						PASS	.						51.0	52.0	51.0					3																	186570951		2203	4300	6503	SO:0001583	missense	9370	exon3			AGGGGGCCTGCAC	D45371	CCDS3284.1	3q27	2013-02-26	2005-01-24	2005-01-27	ENSG00000181092	ENSG00000181092		"""Endogenous ligands"""	13633	protein-coding gene	gene with protein product	"""adipose most abundant gene transcript 1"", ""adiponectin precursor"""	605441	"""adipocyte, C1Q and collagen domain containing"""	ACDC		7592907, 8631877	Standard	NM_001177800		Approved	ACRP30, AdipoQ, apM1, GBP28, adiponectin	uc003fra.3	Q15848	OTTHUMG00000156521	ENST00000412955.2:c.104C>T	3.37:g.186570951C>T	ENSP00000405611:p.Ala35Val	235.0	1.0	0.00425532		241.0	128.0	0.53112	NM_001177800	Q58EX9	Missense_Mutation	SNP	ENST00000412955.2	37	CCDS3284.1	.	.	.	.	.	.	.	.	.	.	C	14.75	2.627218	0.46944	.	.	ENSG00000181092	ENST00000412955;ENST00000320741;ENST00000444204	D;D;D	0.90676	-2.71;-2.71;-2.71	5.21	0.744	0.18353	.	0.825880	0.10698	N	0.644378	T	0.80396	0.4615	N	0.24115	0.695	0.19300	N	0.999976	B	0.06786	0.001	B	0.08055	0.003	T	0.64326	-0.6434	10	0.27082	T	0.32	.	4.1548	0.10256	0.139:0.4701:0.2975:0.0934	.	35	Q15848	ADIPO_HUMAN	V	35	ENSP00000405611:A35V;ENSP00000320709:A35V;ENSP00000389814:A35V	ENSP00000320709:A35V	A	+	2	0	ADIPOQ	188053645	0.068000	0.21057	0.807000	0.32361	0.936000	0.57629	1.784000	0.38674	0.213000	0.20722	0.655000	0.94253	GCC	.	.	none		0.627	ADIPOQ-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344490.2	NM_004797	
SSPO	23145	hgsc.bcm.edu	37	7	149486726	149486726	+	RNA	SNP	T	T	C	rs855695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149486726T>C	ENST00000378016.2	+	0	4500							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			TGTCCTGTGTTGATGGCACCT	0.637													C|||	161	0.0321486	0.1059	0.0115	5008	,	,		18130	0.004		0.0	False		,,,				2504	0.0092				p.V1500V		Atlas-SNP	.											.	.	.	.	0			c.T4500C						PASS	.	C		300,3736		11,278,1729	24.0	31.0	29.0		4504	-9.6	0.0	7	dbSNP_86	29	6,8338		0,6,4166	yes	coding-notMod3	SSPO	NM_198455.2		11,284,5895	CC,CT,TT		0.0719,7.4331,2.4717			149486726	306,12074	2018	4172	6190			23145	exon31			CTGTGTTGATGGC	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149486726T>C		140.0	0.0	0		127.0	77.0	0.606299	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				T|0.974;C|0.026	0.026	strong		0.637	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
PLA2G4B	100137049	hgsc.bcm.edu	37	15	42138572	42138572	+	Missense_Mutation	SNP	C	C	T	rs36126315	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42138572C>T	ENST00000452633.1	+	18	2124	c.1772C>T	c.(1771-1773)aCa>aTa	p.T591I	PLA2G4B_ENST00000542534.2_Missense_Mutation_p.T822I|PLA2G4B_ENST00000458483.1_Missense_Mutation_p.T591I|JMJD7-PLA2G4B_ENST00000382448.4_Missense_Mutation_p.T822I|JMJD7-PLA2G4B_ENST00000342159.4_Missense_Mutation_p.T822I			P0C869	PA24B_HUMAN	phospholipase A2, group IVB (cytosolic)	591	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.		T -> I (in dbSNP:rs36126315).		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|arachidonic acid metabolic process (GO:0019369)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|parturition (GO:0007567)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)						all_cancers(109;1.84e-13)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		all cancers(2;1.08e-30)|Epithelial(2;1.43e-22)|OV - Ovarian serous cystadenocarcinoma(18;1.13e-17)|GBM - Glioblastoma multiforme(94;9.77e-07)|Colorectal(2;0.0129)|COAD - Colon adenocarcinoma(120;0.0371)		CACTTCTCCACATGGAAAGGT	0.547													C|||	76	0.0151757	0.0552	0.0029	5008	,	,		20192	0.0		0.001	False		,,,				2504	0.0				p.T822I		Atlas-SNP	.											.	JMJD7-PLA2G4B	90	.	0			c.C2465T						PASS	.	C	ILE/THR,ILE/THR,ILE/THR	194,4212		8,178,2017	99.0	97.0	98.0		1772,2465,2465	3.0	0.6	15	dbSNP_126	98	3,8597		0,3,4297	yes	missense,missense,missense	JMJD7-PLA2G4B,PLA2G4B	NM_001114633.1,NM_001198588.1,NM_005090.3	89,89,89	8,181,6314	TT,TC,CC		0.0349,4.4031,1.5147	benign,benign,benign	591/782,822/894,822/1013	42138572	197,12809	2203	4300	6503	SO:0001583	missense	8681	exon22			TCTCCACATGGAA	AF065215	CCDS45241.1	15q11.2-q21.3	2010-08-17			ENSG00000243708	ENSG00000243708	3.1.1.4		9036	protein-coding gene	gene with protein product		606088				9705332	Standard	NM_001114633		Approved	cPLA2-beta, HsT16992		P0C869	OTTHUMG00000156809	ENST00000452633.1:c.1772C>T	15.37:g.42138572C>T	ENSP00000396045:p.Thr591Ile	114.0	0.0	0		112.0	55.0	0.491071	NM_005090	B4DRT9|O95712|Q19KD5|Q19KD6|Q59GF9|Q8TB10|Q9UKV7	Missense_Mutation	SNP	ENST00000452633.1	37	CCDS45241.1	24	0.01098901098901099	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	.	15.97	2.990575	0.54041	0.044031	3.49E-4	ENSG00000168970;ENSG00000168970;ENSG00000168970;ENSG00000243708	ENST00000382448;ENST00000342159;ENST00000458483;ENST00000452633	T;T;T;T	0.12984	2.63;2.63;2.63;2.63	4.96	3.05	0.35203	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2);	1.072970	0.07218	N	0.860326	T	0.04452	0.0122	L	0.49778	1.585	0.23454	N	0.997645	P;B;B	0.45283	0.855;0.078;0.178	P;B;B	0.47470	0.548;0.055;0.086	T	0.16928	-1.0386	10	0.40728	T	0.16	-4.9065	7.2416	0.26100	0.0:0.6949:0.144:0.1611	rs36126315	591;822;822	P0C869;P0C869-7;P0C869-6	PA24B_HUMAN;.;.	I	822;822;591;591	ENSP00000371886:T822I;ENSP00000342785:T822I;ENSP00000416610:T591I;ENSP00000396045:T591I	ENSP00000342785:T822I	T	+	2	0	JMJD7-PLA2G4B;PLA2G4B	39925864	0.227000	0.23707	0.645000	0.29479	0.900000	0.52787	0.800000	0.27042	0.727000	0.32360	0.655000	0.94253	ACA	C|0.985;T|0.015	0.015	strong		0.547	PLA2G4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345969.1	NM_001114633	
SRRM2	23524	hgsc.bcm.edu	37	16	2813177	2813177	+	Missense_Mutation	SNP	C	C	G	rs17136053	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2813177C>G	ENST00000301740.8	+	11	3197	c.2648C>G	c.(2647-2649)tCt>tGt	p.S883C		NM_016333.3	NP_057417.3	Q9UQ35	SRRM2_HUMAN	serine/arginine repetitive matrix 2	883	Ser-rich.		S -> C (in dbSNP:rs17136053).		mRNA splicing, via spliceosome (GO:0000398)	Cajal body (GO:0015030)|catalytic step 2 spliceosome (GO:0071013)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	C2H2 zinc finger domain binding (GO:0070742)|poly(A) RNA binding (GO:0044822)|protein N-terminus binding (GO:0047485)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(20)|lung(34)|ovary(6)|pancreas(3)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(7)	105						GAGTTGAAATCTAGGACCCCT	0.517													C|||	127	0.0253594	0.0923	0.0072	5008	,	,		19890	0.0		0.0	False		,,,				2504	0.0				p.S883C		Atlas-SNP	.											.	SRRM2	263	.	0			c.C2648G						PASS	.	C	CYS/SER	373,4023	189.5+/-215.6	16,341,1841	82.0	74.0	77.0		2648	2.2	0.7	16	dbSNP_123	77	2,8598	2.2+/-6.3	0,2,4298	yes	missense	SRRM2	NM_016333.3	112	16,343,6139	GG,GC,CC		0.0233,8.485,2.8855	possibly-damaging	883/2753	2813177	375,12621	2198	4300	6498	SO:0001583	missense	23524	exon11			TGAAATCTAGGAC	AF201422	CCDS32373.1	16p13.3	2012-07-02			ENSG00000167978	ENSG00000167978			16639	protein-coding gene	gene with protein product		606032				10668804, 11004489	Standard	NM_016333		Approved	SRm300, SRL300, KIAA0324, Cwc21	uc002crk.3	Q9UQ35	OTTHUMG00000177358	ENST00000301740.8:c.2648C>G	16.37:g.2813177C>G	ENSP00000301740:p.Ser883Cys	47.0	0.0	0		49.0	21.0	0.428571	NM_016333	A6NKB9|D3DU97|O15038|O94803|Q6NSL3|Q6PIM3|Q6PK40|Q8IW17|Q96GY7|Q9P0G1|Q9UHA8|Q9UQ36|Q9UQ37|Q9UQ38|Q9UQ40	Missense_Mutation	SNP	ENST00000301740.8	37	CCDS32373.1	56	0.02564102564102564	53	0.10772357723577236	3	0.008287292817679558	0	0.0	0	0.0	C	4.788	0.146546	0.09134	0.08485	2.33E-4	ENSG00000167978	ENST00000301740;ENST00000382301;ENST00000544933;ENST00000426305	T	0.31247	1.5	5.37	2.21	0.28008	.	0.094270	0.47852	N	0.000215	T	0.00524	0.0017	L	0.58101	1.795	0.28061	N	0.932955	B	0.09022	0.002	B	0.04013	0.001	T	0.05354	-1.0890	10	0.59425	D	0.04	-0.8628	8.8449	0.35164	0.0:0.6364:0.2835:0.0801	rs17136053;rs52826498;rs17136053	883	Q9UQ35	SRRM2_HUMAN	C	883;883;135;848	ENSP00000301740:S883C	ENSP00000301740:S883C	S	+	2	0	SRRM2	2753178	0.942000	0.31987	0.690000	0.30148	0.967000	0.64934	1.873000	0.39558	0.215000	0.20761	0.650000	0.86243	TCT	C|0.969;G|0.031	0.031	strong		0.517	SRRM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436411.1		
HSPB8	26353	hgsc.bcm.edu	37	12	119631654	119631654	+	Silent	SNP	C	C	T	rs4628742	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:119631654C>T	ENST00000281938.2	+	3	1253	c.582C>T	c.(580-582)acC>acT	p.T194T		NM_014365.2	NP_055180.1	Q9UJY1	HSPB8_HUMAN	heat shock 22kDa protein 8	194					cell death (GO:0008219)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(9)|skin(1)	14	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AGGAAGTCACCTGTACCTGAG	0.502													C|||	412	0.0822684	0.2867	0.0159	5008	,	,		18743	0.0169		0.001	False		,,,				2504	0.0041				p.T194T		Atlas-SNP	.											.	HSPB8	45	.	0			c.C582T						PASS	.	C		1050,3356	383.5+/-324.9	125,800,1278	89.0	84.0	86.0		582	1.4	1.0	12	dbSNP_111	86	9,8591	4.3+/-15.6	0,9,4291	no	coding-synonymous	HSPB8	NM_014365.2		125,809,5569	TT,TC,CC		0.1047,23.8311,8.1424		194/197	119631654	1059,11947	2203	4300	6503	SO:0001819	synonymous_variant	26353	exon3			AGTCACCTGTACC	AF191017	CCDS9189.1	12q24.23	2014-09-17	2004-04-23					"""Heat shock proteins / HSPB"""	30171	protein-coding gene	gene with protein product		608014	"""heat shock 27kDa protein 8"""			10833516, 11085516	Standard	NM_014365		Approved	H11, E2IG1, HSP22, HspB8	uc001txb.3	Q9UJY1		ENST00000281938.2:c.582C>T	12.37:g.119631654C>T		156.0	0.0	0		160.0	74.0	0.4625	NM_014365	B2R6A6|Q6FIH3|Q9UKS3	Silent	SNP	ENST00000281938.2	37	CCDS9189.1																																																																																			C|0.917;T|0.083	0.083	strong		0.502	HSPB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401647.1	NM_014365	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46058043	46058043	+	Missense_Mutation	SNP	C	C	T	rs77109703	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46058043C>T	ENST00000380095.1	+	1	771	c.709C>T	c.(709-711)Cgc>Tgc	p.R237C	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	237						keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						CGTGTGCTCCCGCCCTGCCTG	0.692																																					p.R237C		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.C709T						PASS	.	C	,CYS/ARG	389,4017	164.7+/-196.3	0,389,1814	49.0	53.0	52.0		,709	-1.5	0.0	21	dbSNP_131	52	4,8590	1.2+/-3.3	0,4,4293	no	intron,missense	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,180	0,393,6107	TT,TC,CC		0.0465,8.8289,3.0231	,benign	,237/252	46058043	393,12607	2203	4297	6500	SO:0001583	missense	353333	exon1			TGCTCCCGCCCTG	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.709C>T	21.37:g.46058043C>T	ENSP00000369438:p.Arg237Cys	218.0	0.0	0		380.0	84.0	0.221053	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	48	0.02197802197802198	47	0.09552845528455285	1	0.0027624309392265192	0	0.0	0	0.0	c	4.111	0.018755	0.07959	0.088289	4.65E-4	ENSG00000221859	ENST00000380095	T	0.01422	4.91	3.52	-1.53	0.08611	.	.	.	.	.	T	0.00073	0.0002	M	0.78285	2.405	0.36787	D	0.884654	B	0.28636	0.218	B	0.18871	0.023	T	0.50466	-0.8825	9	0.66056	D	0.02	.	4.2298	0.10597	0.3112:0.4801:0.0:0.2088	.	237	P60014	KR10A_HUMAN	C	237	ENSP00000369438:R237C	ENSP00000369438:R237C	R	+	1	0	KRTAP10-10	44882471	0.000000	0.05858	0.038000	0.18304	0.008000	0.06430	-1.152000	0.03172	-0.202000	0.10268	-0.444000	0.05651	CGC	C|0.966;T|0.034	0.034	strong		0.692	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
SOGA3	387104	hgsc.bcm.edu	37	6	127797389	127797389	+	Silent	SNP	C	C	T	rs61741826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:127797389C>T	ENST00000525778.1	-	6	2527	c.1782G>A	c.(1780-1782)gtG>gtA	p.V594V	SOGA3_ENST00000465909.2_Silent_p.V594V|SOGA3_ENST00000481848.2_Silent_p.V594V|SOGA3_ENST00000474293.2_5'Flank|SOGA3_ENST00000556132.1_Silent_p.V594V|SOGA3_ENST00000368268.2_Silent_p.V594V			Q5TF21	SOGA3_HUMAN	SOGA family member 3	594					regulation of autophagy (GO:0010506)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											CTTCTTCCTCCACCAGCCTTA	0.577													C|||	9	0.00179712	0.0068	0.0	5008	,	,		18875	0.0		0.0	False		,,,				2504	0.0				p.V594V		Atlas-SNP	.											.	.	.	.	0			c.G1782A						PASS	.	C		14,4244		0,14,2115	120.0	129.0	126.0		1782	4.7	1.0	6	dbSNP_129	126	0,8480		0,0,4240	no	coding-synonymous	C6orf174	NM_001012279.2		0,14,6355	TT,TC,CC		0.0,0.3288,0.1099		594/948	127797389	14,12724	2129	4240	6369	SO:0001819	synonymous_variant	387104	exon6			TTCCTCCACCAGC	AK096490	CCDS43505.1	6q22.33	2013-03-28	2012-02-27	2012-02-27	ENSG00000214338	ENSG00000214338			21494	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 174"""	C6orf174			Standard	NM_001012279		Approved	dJ403A15.3	uc003qbd.3	Q5TF21	OTTHUMG00000166438	ENST00000525778.1:c.1782G>A	6.37:g.127797389C>T		89.0	0.0	0		85.0	38.0	0.447059	NM_001012279		Silent	SNP	ENST00000525778.1	37	CCDS43505.1																																																																																			C|0.999;T|0.001	0.001	strong		0.577	SOGA3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388246.1	NM_001012279	
TRIM41	90933	hgsc.bcm.edu	37	5	180661274	180661274	+	Missense_Mutation	SNP	C	C	G	rs78013120	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:180661274C>G	ENST00000315073.5	+	6	2102	c.1392C>G	c.(1390-1392)gaC>gaG	p.D464E	TRIM41_ENST00000351937.5_Missense_Mutation_p.D464E|TRIM41_ENST00000510072.1_3'UTR	NM_033549.4	NP_291027.3	Q8WV44	TRI41_HUMAN	tripartite motif containing 41	464	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(3)|prostate(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;9.17e-06)|all_epithelial(37;1.19e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGGTTGCTGACCATCCCAAGC	0.726													C|||	23	0.00459265	0.0174	0.0	5008	,	,		8455	0.0		0.0	False		,,,				2504	0.0				p.D464E		Atlas-SNP	.											.	TRIM41	96	.	0			c.C1392G						PASS	.	C	GLU/ASP,GLU/ASP	72,4296		0,72,2112	21.0	24.0	23.0		1392,1392	3.1	1.0	5	dbSNP_133	23	0,8498		0,0,4249	yes	missense,missense	TRIM41	NM_033549.3,NM_201627.1	45,45	0,72,6361	GG,GC,CC		0.0,1.6484,0.5596	possibly-damaging,possibly-damaging	464/631,464/519	180661274	72,12794	2184	4249	6433	SO:0001583	missense	90933	exon6			TGCTGACCATCCC	AF258579	CCDS4465.1, CCDS4466.1	5q35.3	2013-01-09	2011-01-25		ENSG00000146063	ENSG00000146063		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19013	protein-coding gene	gene with protein product	"""RING-finger protein that interacts with C kinase"""	610530	"""tripartite motif-containing 41"""			16022281	Standard	NM_033549		Approved	MGC1127, RINCK	uc003mne.2	Q8WV44	OTTHUMG00000130965	ENST00000315073.5:c.1392C>G	5.37:g.180661274C>G	ENSP00000320869:p.Asp464Glu	40.0	0.0	0		50.0	28.0	0.56	NM_201627	B3KNJ6|D3DWR9|Q5BKT0|Q7L484|Q96Q10|Q9BSL8	Missense_Mutation	SNP	ENST00000315073.5	37	CCDS4466.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	18.88	3.716930	0.68844	0.016484	0.0	ENSG00000146063	ENST00000515499;ENST00000351937;ENST00000315073;ENST00000438174	T;T;T	0.14391	2.51;2.51;2.51	4.97	3.14	0.36123	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);B30.2/SPRY domain (1);	0.183072	0.38837	N	0.001552	T	0.09247	0.0228	M	0.62088	1.915	0.26095	N	0.980893	P;B	0.51791	0.948;0.001	P;B	0.48627	0.584;0.005	T	0.04386	-1.0955	10	0.48119	T	0.1	.	7.2565	0.26179	0.1752:0.7342:0.0:0.0907	.	464;464	Q8WV44;Q8WV44-2	TRI41_HUMAN;.	E	174;464;464;149	ENSP00000426803:D174E;ENSP00000336749:D464E;ENSP00000320869:D464E	ENSP00000320869:D464E	D	+	3	2	TRIM41	180593880	0.827000	0.29292	1.000000	0.80357	0.981000	0.71138	1.423000	0.34837	0.645000	0.30675	0.557000	0.71058	GAC	C|0.995;G|0.005	0.005	strong		0.726	TRIM41-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253574.3	NM_201627	
TMEM204	79652	hgsc.bcm.edu	37	16	1584294	1584294	+	Silent	SNP	C	C	T	rs79579867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1584294C>T	ENST00000566264.1	+	1	721	c.18C>T	c.(16-18)ctC>ctT	p.L6L	IFT140_ENST00000426508.2_Intron|TMEM204_ENST00000253934.5_Silent_p.L6L|IFT140_ENST00000361339.5_5'Flank	NM_024600.5	NP_078876.2	Q9BSN7	TM204_HUMAN	transmembrane protein 204	6					lymph vessel development (GO:0001945)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|response to stress (GO:0006950)|smooth muscle cell differentiation (GO:0051145)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|cervix(1)|endometrium(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	11		Hepatocellular(780;0.219)				TGCAGAGACTCGTGGCCGCGG	0.672													C|||	103	0.0205671	0.0764	0.0029	5008	,	,		15087	0.0		0.0	False		,,,				2504	0.0				p.L6L		Atlas-SNP	.											.	TMEM204	29	.	0			c.C18T						PASS	.	C	,	263,3993		4,255,1869	32.0	39.0	37.0		,18	-10.6	0.1	16	dbSNP_131	37	2,8484		0,2,4241	no	intron,coding-synonymous	IFT140,TMEM204	NM_014714.3,NM_024600.4	,	4,257,6110	TT,TC,CC		0.0236,6.1795,2.0797	,	,6/227	1584294	265,12477	2128	4243	6371	SO:0001819	synonymous_variant	79652	exon1			GAGACTCGTGGCC		CCDS42098.1	16p13.3	2008-02-05	2008-01-08	2008-01-08		ENSG00000131634			14158	protein-coding gene	gene with protein product		611002	"""chromosome 16 open reading frame 30"""	C16orf30			Standard	NM_024600		Approved	FLJ20898	uc002cmc.3	Q9BSN7		ENST00000566264.1:c.18C>T	16.37:g.1584294C>T		182.0	0.0	0		202.0	98.0	0.485149	NM_024600	D3DU76|Q3KRC1|Q9H7G5	Silent	SNP	ENST00000566264.1	37	CCDS42098.1																																																																																			C|0.979;T|0.021	0.021	strong		0.672	TMEM204-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432610.1	NM_024600	
FAM135A	57579	hgsc.bcm.edu	37	6	71248046	71248046	+	Silent	SNP	A	A	G	rs9455152	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:71248046A>G	ENST00000418814.2	+	20	4784	c.4170A>G	c.(4168-4170)acA>acG	p.T1390T	FAM135A_ENST00000457062.2_Silent_p.T1177T|FAM135A_ENST00000505868.1_Silent_p.T1390T|FAM135A_ENST00000370479.3_Silent_p.T1177T|FAM135A_ENST00000505769.1_Silent_p.T970T|FAM135A_ENST00000361499.3_Silent_p.T1194T	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	1390										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						TGCAGCTGACATGTCGAGATC	0.323													A|||	101	0.0201677	0.0726	0.0043	5008	,	,		14384	0.0		0.002	False		,,,				2504	0.0				p.T1390T		Atlas-SNP	.											.	FAM135A	181	.	0			c.A4170G						PASS	.	A	,,	299,4107	162.5+/-194.5	7,285,1911	59.0	61.0	60.0		3582,4170,3531	2.9	1.0	6	dbSNP_119	60	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	FAM135A	NM_001105531.2,NM_001162529.1,NM_020819.4	,,	7,289,6207	GG,GA,AA		0.0465,6.7862,2.3297	,,	1194/1320,1390/1516,1177/1303	71248046	303,12703	2203	4300	6503	SO:0001819	synonymous_variant	57579	exon18			GCTGACATGTCGA	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.4170A>G	6.37:g.71248046A>G		204.0	0.0	0		174.0	96.0	0.551724	NM_001162529	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Silent	SNP	ENST00000418814.2	37	CCDS55028.1																																																																																			A|0.974;G|0.026	0.026	strong		0.323	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819	
HEATR5B	54497	hgsc.bcm.edu	37	2	37280711	37280711	+	Silent	SNP	T	T	C	rs10202107	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:37280711T>C	ENST00000233099.5	-	17	2534	c.2439A>G	c.(2437-2439)caA>caG	p.Q813Q	HEATR5B_ENST00000354531.2_Silent_p.Q813Q	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	813						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				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)				CACCTTTAGCTTGTTTAACAC	0.313													T|||	56	0.0111821	0.0416	0.0014	5008	,	,		17495	0.0		0.0	False		,,,				2504	0.0				p.Q813Q		Atlas-SNP	.											.	HEATR5B	185	.	0			c.A2439G						PASS	.	T		121,4285	91.1+/-129.8	2,117,2084	56.0	57.0	57.0		2439	2.3	1.0	2	dbSNP_119	57	0,8600		0,0,4300	no	coding-synonymous	HEATR5B	NM_019024.1		2,117,6384	CC,CT,TT		0.0,2.7463,0.9303		813/2072	37280711	121,12885	2203	4300	6503	SO:0001819	synonymous_variant	54497	exon17			TTTAGCTTGTTTA	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.2439A>G	2.37:g.37280711T>C		221.0	0.0	0		196.0	101.0	0.515306	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Silent	SNP	ENST00000233099.5	37	CCDS33181.1																																																																																			T|0.989;C|0.011	0.011	strong		0.313	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024	
DLK1	8788	hgsc.bcm.edu	37	14	101201219	101201219	+	Missense_Mutation	SNP	G	G	C	rs115349979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:101201219G>C	ENST00000341267.4	+	5	1380	c.1138G>C	c.(1138-1140)Gac>Cac	p.D380H	DLK1_ENST00000331224.6_Missense_Mutation_p.D307H|RP11-566J3.4_ENST00000608876.1_lincRNA	NM_003836.5	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog (Drosophila)	380					cell differentiation (GO:0030154)|embryonic skeletal system development (GO:0048706)|multicellular organismal development (GO:0007275)|negative regulation of Notch signaling pathway (GO:0045746)|Notch signaling pathway (GO:0007219)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)	external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(16)|ovary(2)|prostate(1)|skin(1)	29		Melanoma(154;0.155)				GGAGGCCGGCGACGAGGAGAT	0.552													G|||	62	0.0123802	0.0469	0.0	5008	,	,		16011	0.0		0.0	False		,,,				2504	0.0				p.D380H		Atlas-SNP	.											DLK1,NS,carcinoma,-2,2	DLK1	57	2	0			c.G1138C						PASS	.	G	HIS/ASP	130,4276	94.8+/-133.5	3,124,2076	85.0	86.0	86.0		1138	0.9	0.2	14	dbSNP_132	86	0,8600		0,0,4300	yes	missense	DLK1	NM_003836.5	81	3,124,6376	CC,CG,GG		0.0,2.9505,0.9995	benign	380/384	101201219	130,12876	2203	4300	6503	SO:0001583	missense	8788	exon5			GCCGGCGACGAGG	U15979	CCDS9963.1	14q32	2011-12-05	2001-12-03			ENSG00000185559			2907	protein-coding gene	gene with protein product		176290	"""delta-like homolog (Drosophila)"""			8095043, 7925474	Standard	NM_003836		Approved	FA1, pG2, Pref-1, ZOG, Delta1	uc001yhs.4	P80370		ENST00000341267.4:c.1138G>C	14.37:g.101201219G>C	ENSP00000340292:p.Asp380His	26.0	0.0	0		20.0	10.0	0.5	NM_003836	P15803|Q96DW5	Missense_Mutation	SNP	ENST00000341267.4	37	CCDS9963.1	22	0.010073260073260074	22	0.044715447154471545	0	0.0	0	0.0	0	0.0	G	9.764	1.170865	0.21621	0.029505	0.0	ENSG00000185559	ENST00000341267;ENST00000331224	D;D	0.88431	-2.38;-2.32	4.41	0.928	0.19443	.	1.200000	0.06159	N	0.675641	T	0.57844	0.2081	N	0.08118	0	0.09310	N	1	P;P	0.46220	0.874;0.8	P;P	0.54460	0.753;0.571	T	0.69351	-0.5168	10	0.87932	D	0	.	0.6745	0.00864	0.2119:0.1565:0.3728:0.2589	.	307;380	P80370-2;P80370	.;DLK1_HUMAN	H	380;307	ENSP00000340292:D380H;ENSP00000331081:D307H	ENSP00000331081:D307H	D	+	1	0	DLK1	100270972	0.002000	0.14202	0.191000	0.23289	0.049000	0.14656	0.031000	0.13710	0.860000	0.35481	-0.332000	0.08345	GAC	G|0.988;C|0.012	0.012	strong		0.552	DLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414389.1		
HELQ	113510	hgsc.bcm.edu	37	4	84350870	84350870	+	Silent	SNP	A	A	G	rs59255439	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:84350870A>G	ENST00000295488.3	-	12	2487	c.2325T>C	c.(2323-2325)caT>caC	p.H775H	HELQ_ENST00000510985.1_Silent_p.H708H	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	775					double-strand break repair via homologous recombination (GO:0000724)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						CATTCATGAAATGATAGATGT	0.328								Other identified genes with known or suspected DNA repair function					G|||	497	0.0992412	0.3563	0.036	5008	,	,		15251	0.0		0.001	False		,,,				2504	0.0				p.H775H		Atlas-SNP	.											.	HELQ	95	.	0			c.T2325C						PASS	.	G		1348,3052	683.1+/-404.2	191,966,1043	43.0	39.0	40.0		2325	1.2	1.0	4	dbSNP_129	40	18,8578	810.1+/-407.1	0,18,4280	no	coding-synonymous	HELQ	NM_133636.2		191,984,5323	GG,GA,AA		0.2094,30.6364,10.5109		775/1102	84350870	1366,11630	2200	4298	6498	SO:0001819	synonymous_variant	113510	exon12			CATGAAATGATAG	AF436845	CCDS3603.1, CCDS75158.1	4q21.23	2009-02-26			ENSG00000163312	ENSG00000163312			18536	protein-coding gene	gene with protein product		606769				11751861	Standard	XM_005262711		Approved	Hel308	uc003hom.3	Q8TDG4	OTTHUMG00000130423	ENST00000295488.3:c.2325T>C	4.37:g.84350870A>G		84.0	0.0	0		82.0	42.0	0.512195	NM_133636	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Silent	SNP	ENST00000295488.3	37	CCDS3603.1																																																																																			A|0.908;G|0.092	0.092	strong		0.328	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057636	46057636	+	Missense_Mutation	SNP	T	T	A	rs115298124	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46057636T>A	ENST00000380095.1	+	1	364	c.302T>A	c.(301-303)gTg>gAg	p.V101E	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	101	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						gtctgctgtgtgcccgtctgc	0.627													A|||	306	0.0611022	0.2118	0.0173	5008	,	,		19037	0.002		0.001	False		,,,				2504	0.0112				p.V101E		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.T302A						PASS	.	A	,GLU/VAL	550,3856		77,396,1730	131.0	124.0	126.0		,302	-5.7	0.0	21	dbSNP_132	126	2,8594		0,2,4296	no	intron,missense	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,121	77,398,6026	AA,AT,TT		0.0233,12.483,4.2455	,benign	,101/252	46057636	552,12450	2203	4298	6501	SO:0001583	missense	353333	exon1			GCTGTGTGCCCGT	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.302T>A	21.37:g.46057636T>A	ENSP00000369438:p.Val101Glu	205.0	0.0	0		273.0	120.0	0.43956	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	.	.	.	.	.	.	.	.	.	.	a	0.032	-1.330391	0.01298	0.12483	2.33E-4	ENSG00000221859	ENST00000380095	T	0.01323	5.01	2.86	-5.72	0.02406	.	.	.	.	.	T	0.00012	0.0000	N	0.10874	0.06	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.39165	-0.9627	9	0.22706	T	0.39	.	1.3737	0.02215	0.2016:0.1241:0.184:0.4903	.	101	P60014	KR10A_HUMAN	E	101	ENSP00000369438:V101E	ENSP00000369438:V101E	V	+	2	0	KRTAP10-10	44882064	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.107000	0.03316	-4.925000	0.00027	-3.683000	0.00024	GTG	T|0.928;A|0.072	0.072	strong		0.627	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
ALDH7A1	501	hgsc.bcm.edu	37	5	125928395	125928395	+	Silent	SNP	A	A	G	rs60720055	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:125928395A>G	ENST00000409134.3	-	3	492	c.273T>C	c.(271-273)acT>acC	p.T91T	ALDH7A1_ENST00000553117.1_Silent_p.T91T|ALDH7A1_ENST00000413020.1_5'UTR|ALDH7A1_ENST00000447989.2_Silent_p.T118T	NM_001182.4|NM_001201377.1	NP_001173.2|NP_001188306.1	P49419	AL7A1_HUMAN	aldehyde dehydrogenase 7 family, member A1	91					cellular aldehyde metabolic process (GO:0006081)|cellular nitrogen compound metabolic process (GO:0034641)|glycine betaine biosynthetic process from choline (GO:0019285)|lysine catabolic process (GO:0006554)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|betaine-aldehyde dehydrogenase activity (GO:0008802)|L-aminoadipate-semialdehyde dehydrogenase activity (GO:0004043)			endometrium(1)|kidney(4)|large_intestine(4)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	16		all_cancers(142;0.24)|Prostate(80;0.081)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0417)|OV - Ovarian serous cystadenocarcinoma(64;0.068)|all cancers(49;0.109)		CTTTCTTTACAGTTTCTTCAT	0.368													A|||	302	0.0603035	0.1717	0.0274	5008	,	,		18399	0.0		0.0288	False		,,,				2504	0.0276				p.T118T		Atlas-SNP	.											.	ALDH7A1	57	.	0			c.T354C						PASS	.	A	,,	657,3749	278.1+/-274.1	42,573,1588	111.0	105.0	107.0		273,189,354	-9.2	0.1	5	dbSNP_129	107	214,8386	88.9+/-151.2	2,210,4088	no	coding-synonymous,coding-synonymous,coding-synonymous	ALDH7A1	NM_001182.4,NM_001201377.1,NM_001202404.1	,,	44,783,5676	GG,GA,AA		2.4884,14.9115,6.6969	,,	91/540,63/512,118/503	125928395	871,12135	2203	4300	6503	SO:0001819	synonymous_variant	501	exon3			CTTTACAGTTTCT	S74728	CCDS4137.2, CCDS56380.1	5q31	2013-06-03			ENSG00000164904	ENSG00000164904	1.2.1.31	"""Aldehyde dehydrogenases"""	877	protein-coding gene	gene with protein product	"""antiquitin 1"", ""26g turgor protein homolog"", ""alpha-aminoadipic semialdehyde dehydrogenase"", ""alpha-AASA dehydrogenase"", ""delta1-piperideine-6-carboxylate dehydrogenease"", ""P6c dehydrogenase"""	107323		ATQ1		9417906	Standard	NM_001182		Approved	EPD, PDE	uc003ktx.3	P49419	OTTHUMG00000128942	ENST00000409134.3:c.273T>C	5.37:g.125928395A>G		118.0	0.0	0		126.0	63.0	0.5	NM_001202404	B2R669|B4DIC7|B4DMA0|E7EPT3|O14619|Q6IPU8|Q9BUL4	Silent	SNP	ENST00000409134.3	37	CCDS4137.2																																																																																			A|0.941;G|0.059	0.059	strong		0.368	ALDH7A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250921.2	NM_001182	
KIAA1244	57221	hgsc.bcm.edu	37	6	138584014	138584014	+	Missense_Mutation	SNP	C	C	G	rs116596107	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:138584014C>G	ENST00000251691.4	+	12	1560	c.1394C>G	c.(1393-1395)gCt>gGt	p.A465G		NM_020340.4	NP_065073.3			KIAA1244											NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(11)|lung(17)|ovary(2)|skin(2)	44	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00102)|GBM - Glioblastoma multiforme(68;0.00259)		AAGGATGGGGCTGAGTGGAGC	0.612													C|||	4	0.000798722	0.003	0.0	5008	,	,		21357	0.0		0.0	False		,,,				2504	0.0				p.A465G		Atlas-SNP	.											.	KIAA1244	236	.	0			c.C1394G						PASS	.	C	GLY/ALA	37,4369	42.3+/-75.8	0,37,2166	94.0	72.0	80.0		1394	1.7	0.1	6	dbSNP_132	80	0,8600		0,0,4300	yes	missense	KIAA1244	NM_020340.4	60	0,37,6466	GG,GC,CC		0.0,0.8398,0.2845	benign	465/2178	138584014	37,12969	2203	4300	6503	SO:0001583	missense	57221	exon12			ATGGGGCTGAGTG	AB033070	CCDS5189.2	6q23.3	2012-04-17			ENSG00000112379	ENSG00000112379		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	21213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 33"""		"""chromosome 6 open reading frame 92"""	C6orf92			Standard	NM_020340		Approved	dJ171N11.1, BIG3, PPP1R33	uc003qhu.3	Q5TH69	OTTHUMG00000015670	ENST00000251691.4:c.1394C>G	6.37:g.138584014C>G	ENSP00000251691:p.Ala465Gly	142.0	0.0	0		122.0	65.0	0.532787	NM_020340		Missense_Mutation	SNP	ENST00000251691.4	37	CCDS5189.2	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	9.329	1.060068	0.19987	0.008398	0.0	ENSG00000112379	ENST00000251691	T	0.18960	2.18	5.62	1.68	0.24146	.	0.330121	0.29544	N	0.011855	T	0.05456	0.0144	L	0.36672	1.1	0.20074	N	0.999932	B	0.02656	0.0	B	0.04013	0.001	T	0.39761	-0.9598	10	0.23302	T	0.38	-25.5355	11.5601	0.50772	0.0:0.4804:0.4521:0.0675	.	465	Q5TH69	BIG3_HUMAN	G	465	ENSP00000251691:A465G	ENSP00000251691:A465G	A	+	2	0	KIAA1244	138625707	0.965000	0.33210	0.081000	0.20488	0.953000	0.61014	2.466000	0.45084	0.266000	0.21894	0.655000	0.94253	GCT	C|0.998;G|0.002	0.002	strong		0.612	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340	
ARHGAP17	55114	hgsc.bcm.edu	37	16	24965975	24965975	+	Silent	SNP	C	C	G	rs111986765	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:24965975C>G	ENST00000289968.6	-	10	870	c.801G>C	c.(799-801)ctG>ctC	p.L267L	ARHGAP17_ENST00000441763.2_3'UTR|ARHGAP17_ENST00000303665.5_Silent_p.L267L|ARHGAP17_ENST00000575975.1_5'Flank	NM_001006634.1	NP_001006635.1	Q68EM7	RHG17_HUMAN	Rho GTPase activating protein 17	267	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	GTPase activator activity (GO:0005096)			breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|urinary_tract(2)	30				GBM - Glioblastoma multiforme(48;0.0407)		CTTCAATGGGCAGCGCAATCT	0.542													C|||	2	0.000399361	0.0015	0.0	5008	,	,		18487	0.0		0.0	False		,,,				2504	0.0				p.L267L		Atlas-SNP	.											.	ARHGAP17	138	.	0			c.G801C						PASS	.	C	,	1,4393	2.1+/-5.4	0,1,2196	138.0	132.0	134.0		801,801	-10.4	0.1	16	dbSNP_132	134	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ARHGAP17	NM_001006634.1,NM_018054.4	,	0,1,6496	GG,GC,CC		0.0,0.0228,0.0077	,	267/882,267/804	24965975	1,12993	2197	4300	6497	SO:0001819	synonymous_variant	55114	exon10			AATGGGCAGCGCA	AJ306731	CCDS32408.1, CCDS32409.1	16p12.2-p12.1	2011-06-29				ENSG00000140750		"""Rho GTPase activating proteins"""	18239	protein-coding gene	gene with protein product		608293				10967100, 11431473	Standard	XM_005255413		Approved	RICH1, FLJ10308, NADRIN, FLJ13219, WBP15	uc002dnb.3	Q68EM7		ENST00000289968.6:c.801G>C	16.37:g.24965975C>G		91.0	0.0	0		87.0	43.0	0.494253	NM_001006634	A8K6M6|Q6ZUS4|Q7Z2F2|Q8NDG2|Q96KS2|Q96KS3|Q96SS8|Q9BVF6|Q9H8U5|Q9NW54	Silent	SNP	ENST00000289968.6	37	CCDS32409.1																																																																																			C|0.999;G|0.001	0.001	strong		0.542	ARHGAP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436548.3	NM_018054	
MT-ATP8	4509	hgsc.bcm.edu	37	M	8468	8468	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:8468C>T	ENST00000361851.1	+	1	103	c.103C>T	c.(103-105)Cta>Tta	p.L35L	MT-TR_ENST00000387439.1_RNA|MT-ND3_ENST00000361227.2_5'Flank|MT-ATP6_ENST00000361899.2_5'Flank|MT-TD_ENST00000387419.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-CO3_ENST00000362079.2_5'Flank|MT-ND4L_ENST00000361335.1_5'Flank|MT-TA_ENST00000387392.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-TY_ENST00000387409.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-TC_ENST00000387405.1_RNA			P03928	ATP8_HUMAN	mitochondrially encoded ATP synthase 8	35					ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) (GO:0000276)	hydrogen ion transmembrane transporter activity (GO:0015078)|transmembrane transporter activity (GO:0022857)										CAAACTACCACCTACCTCCCT	0.393																																					p.L35L		Atlas-SNP	.											.	.	.	.	0			c.C103T						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			TACCACCTACCTC			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000228253	ENSG00000228253		"""Mitochondrial respiratory chain complex / Complex V"", ""ATPases / F-type"""	7415	protein-coding gene	gene with protein product		516070	"""ATP synthase 8"""	MTATP8			Standard			Approved	ATP8, A6L		P03928		ENST00000361851.1:c.103C>T	M.37:g.8468C>T		4.0	0.0	0		6.0	6.0	1	ENST00000361851	Q34771	Silent	SNP	ENST00000361851.1	37																																																																																				.	.	none		0.393	MT-ATP8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024030	
UQCC1	55245	hgsc.bcm.edu	37	20	33981906	33981906	+	Missense_Mutation	SNP	G	G	C	rs75909303	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33981906G>C	ENST00000374385.5	-	2	295	c.118C>G	c.(118-120)Cgc>Ggc	p.R40G	UQCC1_ENST00000349714.5_Missense_Mutation_p.R40G|UQCC1_ENST00000374384.2_Missense_Mutation_p.R40G|UQCC1_ENST00000407996.2_Missense_Mutation_p.R40G|UQCC1_ENST00000491125.1_5'UTR|UQCC1_ENST00000397556.3_5'UTR|UQCC1_ENST00000540457.1_Intron|UQCC1_ENST00000374377.5_Missense_Mutation_p.S20W|UQCC1_ENST00000542501.1_Missense_Mutation_p.R40G|UQCC1_ENST00000359226.2_Missense_Mutation_p.R40G|UQCC1_ENST00000397554.1_Missense_Mutation_p.R40G|UQCC1_ENST00000374380.2_Missense_Mutation_p.R40G	NM_018244.4	NP_060714.3	Q9NVA1	UQCC1_HUMAN	ubiquinol-cytochrome c reductase complex assembly factor 1	40						cytoplasmic membrane-bounded vesicle (GO:0016023)|mitochondrion (GO:0005739)											TGGGAAGTGCGAGACAGAGCC	0.433													C|||	31	0.0061901	0.0227	0.0014	5008	,	,		19195	0.0		0.0	False		,,,				2504	0.0				p.R40G		Atlas-SNP	.											UQCC,NS,carcinoma,0,1	UQCC	41	1	0			c.C118G						PASS	.	C	GLY/ARG,GLY/ARG,GLY/ARG	95,4311	817.7+/-416.3	2,91,2110	124.0	117.0	120.0		118,118,118	4.8	1.0	20	dbSNP_131	120	0,8600		0,0,4300	yes	missense,missense,missense	UQCC	NM_001184977.1,NM_018244.4,NM_199487.2	125,125,125	2,91,6410	CC,CG,GG		0.0,2.1562,0.7304	benign,benign,benign	40/232,40/300,40/274	33981906	95,12911	2203	4300	6503	SO:0001583	missense	55245	exon2			AAGTGCGAGACAG	AK001712	CCDS13252.1, CCDS13253.1, CCDS13253.2, CCDS54458.1	20q11.22	2013-09-20	2013-09-20	2013-09-20	ENSG00000101019	ENSG00000101019		"""Mitochondrial respiratory chain complex assembly factors"""	15891	protein-coding gene	gene with protein product	"""Basic FGF-repressed Zic-binding protein"", ""cytochrome B protein synthesis 3 homolog (S. cerevisiae)"""	611797	"""chromosome 20 open reading frame 44"", ""ubiquinol-cytochrome c reductase complex chaperone"""	C20orf44, UQCC			Standard	NM_018244		Approved	FLJ10850, CBP3, BFZB	uc002xcd.3	Q9NVA1	OTTHUMG00000032335	ENST00000374385.5:c.118C>G	20.37:g.33981906G>C	ENSP00000363506:p.Arg40Gly	77.0	0.0	0		75.0	35.0	0.466667	NM_018244	B1AKV5|Q0VF37|Q5T348|Q5T351|Q5T353|Q86YU3|Q86YU4|Q96H66|Q9H438|Q9H452|Q9H9K8|Q9H9R5	Missense_Mutation	SNP	ENST00000374385.5	37	CCDS13252.1	8|8	0.003663003663003663|0.003663003663003663	8|8	0.016260162601626018|0.016260162601626018	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	2.061|2.061	-0.415323|-0.415323	0.04766|0.04766	0.021562|0.021562	0.0|0.0	ENSG00000101019|ENSG00000101019	ENST00000349714;ENST00000359226;ENST00000374384;ENST00000374380;ENST00000374385;ENST00000407996;ENST00000424405;ENST00000542501;ENST00000438533;ENST00000397554|ENST00000374377	T;T;T;T;T;T;T;T;T;T|.	0.05382|.	3.45;3.45;3.45;3.45;3.45;3.45;3.45;3.45;3.45;3.45|.	4.76|4.76	4.76|4.76	0.60689|0.60689	.|.	0.246918|.	0.36034|.	N|.	0.002824|.	T|T	0.03959|0.03959	0.0111|0.0111	N|N	0.00182|0.00182	-1.905|-1.905	0.09310|0.09310	N|N	0.999994|0.999994	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|T	0.12863|0.12863	-1.0531|-1.0531	10|6	0.02654|0.87932	T|D	1|0	0.7758|0.7758	11.0424|11.0424	0.47838|0.47838	0.0:0.8127:0.1873:0.0|0.0:0.8127:0.1873:0.0	.|.	40;40;40;40;40|.	B1AKV5;B7Z7J8;B7ZBG3;B7ZBG4;Q9NVA1|.	.;.;.;.;UQCC_HUMAN|.	G|W	40|20	ENSP00000335364:R40G;ENSP00000352161:R40G;ENSP00000363505:R40G;ENSP00000363501:R40G;ENSP00000363506:R40G;ENSP00000386064:R40G;ENSP00000399713:R40G;ENSP00000445059:R40G;ENSP00000398531:R40G;ENSP00000380686:R40G|.	ENSP00000335364:R40G|ENSP00000363497:S20W	R|S	-|-	1|2	0|0	UQCC|UQCC	33445320|33445320	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.857000|0.857000	0.48899|0.48899	1.417000|1.417000	0.34770|0.34770	1.248000|1.248000	0.43934|0.43934	-0.127000|-0.127000	0.14921|0.14921	CGC|TCG	G|0.994;C|0.006	0.006	strong		0.433	UQCC1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078866.1	NM_018244	
PNPO	55163	hgsc.bcm.edu	37	17	46023295	46023295	+	Silent	SNP	C	C	G	rs35974730	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:46023295C>G	ENST00000225573.4	+	5	591	c.486C>G	c.(484-486)ccC>ccG	p.P162P	PNPO_ENST00000534893.1_Silent_p.P67P|RP11-6N17.9_ENST00000582262.1_RNA|PNPO_ENST00000434554.2_Intron|PNPO_ENST00000544840.1_Silent_p.P144P|RP11-6N17.6_ENST00000582142.1_RNA|RP11-6N17.6_ENST00000580372.1_RNA	NM_018129.3	NP_060599.1	Q9NVS9	PNPO_HUMAN	pyridoxamine 5'-phosphate oxidase	162					pyridoxine biosynthetic process (GO:0008615)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	FMN binding (GO:0010181)|pyridoxamine-phosphate oxidase activity (GO:0004733)			endometrium(2)|large_intestine(1)|lung(1)|urinary_tract(1)	5						ACTCCCGCCCCAAGAGCAGCC	0.607													C|||	93	0.0185703	0.0681	0.0029	5008	,	,		19973	0.0		0.001	False		,,,				2504	0.0				p.P162P		Atlas-SNP	.											.	PNPO	18	.	0			c.C486G						PASS	.	C		274,4132	155.9+/-189.0	10,254,1939	70.0	69.0	69.0		486	2.1	1.0	17	dbSNP_126	69	14,8586	9.1+/-34.3	0,14,4286	yes	coding-synonymous	PNPO	NM_018129.3		10,268,6225	GG,GC,CC		0.1628,6.2188,2.2144		162/262	46023295	288,12718	2203	4300	6503	SO:0001819	synonymous_variant	55163	exon5			CCGCCCCAAGAGC	AF468030	CCDS11522.1	17q21.32	2008-11-27	2006-07-12			ENSG00000108439	1.4.3.5		30260	protein-coding gene	gene with protein product		603287	"""pyridoxine 5'-phosphate oxidase"""			9601034, 15182361	Standard	NM_018129		Approved	PDXPO	uc002imo.3	Q9NVS9		ENST00000225573.4:c.486C>G	17.37:g.46023295C>G		71.0	0.0	0		54.0	30.0	0.555556	NM_018129	B4E0V0|B4E152|B4E1D7|D3DTT9	Silent	SNP	ENST00000225573.4	37	CCDS11522.1																																																																																			C|0.980;G|0.020	0.020	strong		0.607	PNPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441407.1	NM_018129	
TNC	3371	hgsc.bcm.edu	37	9	117810651	117810651	+	Silent	SNP	G	G	A	rs146504512	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117810651G>A	ENST00000350763.4	-	16	5151	c.4740C>T	c.(4738-4740)acC>acT	p.T1580T	TNC_ENST00000535648.1_Intron|TNC_ENST00000537320.1_Intron|TNC_ENST00000345230.3_Intron|TNC_ENST00000481475.1_5'UTR|TNC_ENST00000341037.4_Intron|TNC_ENST00000340094.3_Silent_p.T1216T|TNC_ENST00000423613.2_Intron|TNC_ENST00000346706.3_Intron|TNC_ENST00000542877.1_Intron	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	1580	Fibronectin type-III 11. {ECO:0000255|PROSITE-ProRule:PRU00316}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						GCTTCCTCTGGGTTCCTGAAA	0.527													G|||	26	0.00519169	0.0144	0.0072	5008	,	,		18220	0.0		0.001	False		,,,				2504	0.001				p.T1580T		Atlas-SNP	.											.	TNC	282	.	0			c.C4740T						PASS	.	G		39,4367	43.8+/-77.6	0,39,2164	89.0	82.0	84.0		4740	3.1	1.0	9	dbSNP_134	84	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	TNC	NM_002160.3		0,47,6456	AA,AG,GG		0.093,0.8852,0.3614		1580/2202	117810651	47,12959	2203	4300	6503	SO:0001819	synonymous_variant	3371	exon16			CCTCTGGGTTCCT		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	5318	protein-coding gene	gene with protein product	"""hexabrachion (tenascin)"""	187380	"""hexabrachion (tenascin C, cytotactin)"", ""deafness, autosomal dominant 56"""	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.4740C>T	9.37:g.117810651G>A		68.0	0.0	0		79.0	37.0	0.468354	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Silent	SNP	ENST00000350763.4	37	CCDS6811.1																																																																																			G|0.996;A|0.004	0.004	strong		0.527	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
AQP8	343	hgsc.bcm.edu	37	16	25228566	25228566	+	Silent	SNP	G	G	A	rs139992979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:25228566G>A	ENST00000219660.5	+	2	185	c.60G>A	c.(58-60)ccG>ccA	p.P20P	AQP8_ENST00000566125.1_Silent_p.P14P	NM_001169.2	NP_001160.2	O94778	AQP8_HUMAN	aquaporin 8	20					canalicular bile acid transport (GO:0015722)|cellular response to cAMP (GO:0071320)|transmembrane transport (GO:0055085)|transport (GO:0006810)|water transport (GO:0006833)	apical part of cell (GO:0045177)|integral component of plasma membrane (GO:0005887)|intracellular canaliculus (GO:0046691)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	water channel activity (GO:0015250)			NS(1)|breast(1)|large_intestine(3)|lung(8)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)	16				GBM - Glioblastoma multiforme(48;0.044)		CCAGGGAGCCGAGCGTGGGTG	0.577													G|||	50	0.00998403	0.031	0.0115	5008	,	,		18800	0.0		0.001	False		,,,				2504	0.0				p.P20P		Atlas-SNP	.											.	AQP8	75	.	0			c.G60A						PASS	.	G		105,4289	82.4+/-120.9	2,101,2094	190.0	187.0	188.0		60	-9.9	0.0	16	dbSNP_134	188	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	AQP8	NM_001169.2		2,106,6389	AA,AG,GG		0.0581,2.3896,0.8465		20/262	25228566	110,12884	2197	4300	6497	SO:0001819	synonymous_variant	343	exon2			GGAGCCGAGCGTG	BC040630	CCDS10626.1	16p12	2008-02-05			ENSG00000103375	ENSG00000103375		"""Ion channels / Aquaporins"""	642	protein-coding gene	gene with protein product		603750				9806845, 10393433	Standard	NM_001169		Approved		uc002doc.3	O94778	OTTHUMG00000097013	ENST00000219660.5:c.60G>A	16.37:g.25228566G>A		233.0	0.0	0		238.0	111.0	0.466387	NM_001169	Q8IUU3|Q9UIA4	Silent	SNP	ENST00000219660.5	37	CCDS10626.1																																																																																			G|0.993;A|0.007	0.007	strong		0.577	AQP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214102.2	NM_001169	
OR3A2	4995	hgsc.bcm.edu	37	17	3181677	3181677	+	Missense_Mutation	SNP	G	G	C	rs73977611	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3181677G>C	ENST00000408891.2	-	1	591	c.553C>G	c.(553-555)Cac>Gac	p.H185D	RP11-64J4.2_ENST00000573491.1_RNA	NM_002551.3	NP_002542.3	P47893	OR3A2_HUMAN	olfactory receptor, family 3, subfamily A, member 2	185					sensory perception of chemical stimulus (GO:0007606)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|receptor activity (GO:0004872)			ovary(1)	1						CAGTAGAAGTGATTGACCTCA	0.562													G|||	81	0.0161741	0.0575	0.0072	5008	,	,		21392	0.0		0.0	False		,,,				2504	0.0				p.H185D	GBM(166;478 2018 3875 5042 31983)|Esophageal Squamous(77;407 1232 1405 14297 15272)	Atlas-SNP	.											.	OR3A2	36	.	0			c.C553G						PASS	.	G	ASP/HIS	188,4216	120.8+/-158.4	4,180,2018	71.0	59.0	63.0		553	2.8	1.0	17	dbSNP_130	63	1,8559		0,1,4279	no	missense	OR3A2	NM_002551.3	81	4,181,6297	CC,CG,GG		0.0117,4.2688,1.4579	probably-damaging	185/322	3181677	189,12775	2202	4280	6482	SO:0001583	missense	4995	exon1			AGAAGTGATTGAC	U04713	CCDS42233.1	17p13.3	2012-08-09				ENSG00000221882		"""GPCR / Class A : Olfactory receptors"""	8283	protein-coding gene	gene with protein product						8921386, 10673334	Standard	NM_002551		Approved	OLFRA04, OR228, OR17-228	uc002fvg.3	P47893		ENST00000408891.2:c.553C>G	17.37:g.3181677G>C	ENSP00000386180:p.His185Asp	274.0	1.0	0.00364964		295.0	140.0	0.474576	NM_002551	Q6IFM3|Q9P1Q3	Missense_Mutation	SNP	ENST00000408891.2	37	CCDS42233.1	28	0.01282051282051282	24	0.04878048780487805	4	0.011049723756906077	0	0.0	0	0.0	G	15.06	2.721441	0.48728	0.042688	1.17E-4	ENSG00000221882	ENST00000408891	T	0.00174	8.62	4.9	2.85	0.33270	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000069	T	0.00144	0.0004	M	0.90425	3.115	0.31106	N	0.710527	D	0.59357	0.985	D	0.68039	0.955	T	0.03335	-1.1047	10	0.87932	D	0	-23.7752	13.1298	0.59375	0.0:0.0:0.7099:0.2901	.	185	P47893	OR3A2_HUMAN	D	185	ENSP00000386180:H185D	ENSP00000386180:H185D	H	-	1	0	OR3A2	3128427	0.630000	0.27155	0.983000	0.44433	0.377000	0.30045	1.081000	0.30791	0.745000	0.32763	0.561000	0.74099	CAC	G|0.991;C|0.009	0.009	strong		0.562	OR3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438370.1		
SLC26A11	284129	hgsc.bcm.edu	37	17	78199666	78199666	+	Missense_Mutation	SNP	C	C	G	rs115961261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78199666C>G	ENST00000361193.3	+	6	824	c.544C>G	c.(544-546)Ccg>Gcg	p.P182A	SLC26A11_ENST00000411502.3_Missense_Mutation_p.P182A|SLC26A11_ENST00000546047.2_Missense_Mutation_p.P182A|SLC26A11_ENST00000572725.1_Missense_Mutation_p.P182A	NM_001166347.1|NM_173626.3	NP_001159819.1|NP_775897.3			solute carrier family 26 (anion exchanger), member 11											central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(7)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	28	all_neural(118;0.0538)		OV - Ovarian serous cystadenocarcinoma(97;0.0344)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			CATCCCCAGGCCGTTCTTCCT	0.562													C|||	44	0.00878594	0.0333	0.0	5008	,	,		16297	0.0		0.0	False		,,,				2504	0.0				p.P182A		Atlas-SNP	.											SLC26A11,NS,carcinoma,-1,2	SLC26A11	60	2	0			c.C544G						PASS	.	C	ALA/PRO,ALA/PRO,ALA/PRO,ALA/PRO	141,4265	101.6+/-140.2	5,131,2067	200.0	158.0	173.0		544,544,544,544	4.1	1.0	17	dbSNP_132	173	0,8600		0,0,4300	yes	missense,missense,missense,missense	SLC26A11	NM_001166347.1,NM_001166348.1,NM_001166349.1,NM_173626.3	27,27,27,27	5,131,6367	GG,GC,CC		0.0,3.2002,1.0841	benign,benign,benign,benign	182/607,182/607,182/607,182/607	78199666	141,12865	2203	4300	6503	SO:0001583	missense	284129	exon6			CCCAGGCCGTTCT		CCDS11771.2	17q25	2013-07-18	2013-07-18		ENSG00000181045	ENSG00000181045		"""Solute carriers"""	14471	protein-coding gene	gene with protein product		610117	"""solute carrier family 26, member 11"""				Standard	NM_001166347		Approved		uc010dhv.2	Q86WA9	OTTHUMG00000133419	ENST00000361193.3:c.544C>G	17.37:g.78199666C>G	ENSP00000355384:p.Pro182Ala	116.0	0.0	0		131.0	65.0	0.496183	NM_173626		Missense_Mutation	SNP	ENST00000361193.3	37	CCDS11771.2	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	C	9.192	1.026307	0.19512	0.032002	0.0	ENSG00000181045	ENST00000411502;ENST00000546047;ENST00000361193	D;D;D	0.92647	-3.08;-3.08;-3.08	4.09	4.09	0.47781	Sulphate transporter (1);	0.424346	0.25997	N	0.026961	T	0.70413	0.3221	N	0.25286	0.73	0.24628	N	0.993634	B	0.22080	0.064	B	0.27170	0.077	T	0.66015	-0.6028	10	0.20519	T	0.43	-11.6618	12.7028	0.57043	0.0:0.8328:0.1672:0.0	.	182	Q86WA9	S2611_HUMAN	A	182	ENSP00000403998:P182A;ENSP00000440724:P182A;ENSP00000355384:P182A	ENSP00000355384:P182A	P	+	1	0	SLC26A11	75814261	0.998000	0.40836	0.970000	0.41538	0.955000	0.61496	3.003000	0.49505	1.811000	0.52892	0.467000	0.42956	CCG	C|0.990;G|0.010	0.010	strong		0.562	SLC26A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257281.1		
BUB1B	701	hgsc.bcm.edu	37	15	40498503	40498503	+	Missense_Mutation	SNP	T	T	C	rs1801528	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:40498503T>C	ENST00000287598.6	+	15	2048	c.1853T>C	c.(1852-1854)gTa>gCa	p.V618A	BUB1B_ENST00000412359.3_Missense_Mutation_p.V632A	NM_001211.5	NP_001202	O60566	BUB1B_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase B	618			V -> A (in colorectal cancer; dbSNP:rs1801528). {ECO:0000269|PubMed:10366450, ECO:0000269|PubMed:17344846}.		anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|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)|protein localization to chromosome, centromeric region (GO:0071459)|protein localization to kinetochore (GO:0034501)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|condensed chromosome kinetochore (GO:0000777)|condensed chromosome outer kinetochore (GO:0000940)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|perinuclear region of cytoplasm (GO:0048471)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(1)|stomach(2)|urinary_tract(2)	36		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)		GCTCGTTTTGTATCCACTCCT	0.448			"""Mis, N, F, S"""			rhabdomyosarcoma			Mosaic Variegated Aneuploidy Syndrome				T|||	465	0.0928514	0.3389	0.0245	5008	,	,		19876	0.0		0.0	False		,,,				2504	0.0				p.V618A		Atlas-SNP	.	yes	Rec		Mosaic variegated aneuploidy	15	15q15	701	BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast)		M	BUB1B,NS,carcinoma,+1,1	BUB1B	71	1	0			c.T1853C						PASS	.	T	ALA/VAL	1117,3289	402.2+/-332.3	135,847,1221	95.0	96.0	96.0		1853	-0.5	1.0	15	dbSNP_89	96	18,8582	13.3+/-46.6	0,18,4282	yes	missense	BUB1B	NM_001211.5	64	135,865,5503	CC,CT,TT		0.2093,25.3518,8.7267	benign	618/1051	40498503	1135,11871	2203	4300	6503	SO:0001583	missense	701	exon15	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	GTTTTGTATCCAC	AF107297	CCDS10053.1	15q15	2014-09-17	2013-01-17		ENSG00000156970	ENSG00000156970			1149	protein-coding gene	gene with protein product		602860	"""budding uninhibited by benzimidazoles 1 (yeast homolog), beta"", ""budding uninhibited by benzimidazoles 1 homolog beta (yeast)"""			9889005	Standard	NM_001211		Approved	BUBR1, MAD3L, Bub1A, SSK1	uc001zkx.4	O60566	OTTHUMG00000129877	ENST00000287598.6:c.1853T>C	15.37:g.40498503T>C	ENSP00000287598:p.Val618Ala	167.0	0.0	0		176.0	86.0	0.488636	NM_001211	B2R6U0|B4DL09|B4DLG3|O60501|O60627|O60758|O75389|Q59HH6|Q8WV50|Q96KM4	Missense_Mutation	SNP	ENST00000287598.6	37	CCDS10053.1	179	0.08195970695970696	169	0.3434959349593496	9	0.024861878453038673	0	0.0	1	0.0013192612137203166	T	5.086	0.201529	0.09652	0.253518	0.002093	ENSG00000156970	ENST00000287598;ENST00000412359	T;T	0.11277	2.79;2.8	5.51	-0.494	0.12034	.	0.391035	0.23252	N	0.050240	T	0.00012	0.0000	N	0.01874	-0.695	0.44409	P	0.0026760000000000117	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48490	-0.9031	9	0.02654	T	1	-0.8963	13.1761	0.59629	0.0:0.7666:0.0:0.2334	rs1801528;rs52836029	632;618	O60566-3;O60566	.;BUB1B_HUMAN	A	618;632	ENSP00000287598:V618A;ENSP00000398470:V632A	ENSP00000287598:V618A	V	+	2	0	BUB1B	38285795	0.999000	0.42202	0.961000	0.40146	0.990000	0.78478	0.726000	0.25984	-0.099000	0.12263	0.482000	0.46254	GTA	T|0.917;C|0.083	0.083	strong		0.448	BUB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252122.4		
MTFR2	113115	hgsc.bcm.edu	37	6	136570221	136570221	+	Missense_Mutation	SNP	T	T	C	rs147085272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:136570221T>C	ENST00000420702.1	-	2	406	c.17A>G	c.(16-18)aAt>aGt	p.N6S	MTFR2_ENST00000445767.2_5'UTR|MTFR2_ENST00000451457.2_Missense_Mutation_p.N6S	NM_001099286.1	NP_001092756.1	Q6P444	MTFR2_HUMAN	mitochondrial fission regulator 2	6					aerobic respiration (GO:0009060)|mitochondrial fission (GO:0000266)|mitochondrion organization (GO:0007005)	mitochondrion (GO:0005739)											TCTTAAGATATTCAGTATGAG	0.358													T|||	49	0.00978435	0.0356	0.0029	5008	,	,		19511	0.0		0.0	False		,,,				2504	0.0				p.N6S		Atlas-SNP	.											.	.	.	.	0			c.A17G						PASS	.	T	SER/ASN,SER/ASN	124,4282	91.6+/-130.3	5,114,2084	81.0	76.0	78.0		17,17	1.0	0.1	6	dbSNP_134	78	0,8600		0,0,4300	yes	missense,missense	FAM54A	NM_001099286.1,NM_138419.3	46,46	5,114,6384	CC,CT,TT		0.0,2.8143,0.9534	benign,benign	6/386,6/386	136570221	124,12882	2203	4300	6503	SO:0001583	missense	113115	exon2			AAGATATTCAGTA	BC011716	CCDS5176.1	6q23.2	2012-11-30	2012-11-29	2012-11-29	ENSG00000146410	ENSG00000146410			21115	protein-coding gene	gene with protein product			"""DUF729 domain containing 1"", ""family with sequence similarity 54, member A"""	DUFD1, FAM54A			Standard	NM_138419		Approved		uc003qgt.1	Q6P444	OTTHUMG00000015643	ENST00000420702.1:c.17A>G	6.37:g.136570221T>C	ENSP00000395232:p.Asn6Ser	47.0	0.0	0		42.0	16.0	0.380952	NM_138419	A8K8D8|E1P585|Q5JWR7|Q6ZUE8|Q7L3U6|Q9BZ39	Missense_Mutation	SNP	ENST00000420702.1	37	CCDS5176.1	31	0.014194139194139194	30	0.06097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	T	12.20	1.867291	0.32977	0.028143	0.0	ENSG00000146410	ENST00000451457;ENST00000420702	T;T	0.42900	0.96;0.96	4.85	0.955	0.19602	.	0.442859	0.25285	N	0.031765	T	0.11793	0.0287	L	0.36672	1.1	0.25226	N	0.989865	B	0.14438	0.01	B	0.12156	0.007	T	0.23226	-1.0194	10	0.87932	D	0	-9.0671	3.8762	0.09058	0.0:0.2276:0.1828:0.5896	.	6	Q6P444	FA54A_HUMAN	S	6	ENSP00000407010:N6S;ENSP00000395232:N6S	ENSP00000356758:N6S	N	-	2	0	FAM54A	136611914	0.991000	0.36638	0.053000	0.19242	0.995000	0.86356	0.177000	0.16801	-0.006000	0.14370	0.482000	0.46254	AAT	T|0.988;C|0.012	0.012	strong		0.358	MTFR2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042378.2	NM_138419	
NWD1	284434	hgsc.bcm.edu	37	19	16860087	16860087	+	Missense_Mutation	SNP	G	G	A	rs61750949	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16860087G>A	ENST00000552788.1	+	4	634	c.634G>A	c.(634-636)Gcg>Acg	p.A212T	NWD1_ENST00000379808.3_Missense_Mutation_p.A212T|NWD1_ENST00000523826.1_Missense_Mutation_p.A6T|NWD1_ENST00000339803.6_Missense_Mutation_p.A77T|NWD1_ENST00000524140.2_Missense_Mutation_p.A212T|NWD1_ENST00000549814.1_Missense_Mutation_p.A212T			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	212							ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GGACCGGCTCGCGGATGGCTG	0.592													G|||	120	0.0239617	0.0825	0.0101	5008	,	,		16617	0.0		0.001	False		,,,				2504	0.0031				p.A212T		Atlas-SNP	.											.	NWD1	303	.	0			c.G634A						PASS	.						74.0	56.0	62.0					19																	16860087		2203	4300	6503	SO:0001583	missense	284434	exon6			CGGCTCGCGGATG	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"""WD repeat domain containing"""	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.634G>A	19.37:g.16860087G>A	ENSP00000447224:p.Ala212Thr	87.0	0.0	0		101.0	51.0	0.504951	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		49	0.022435897435897436	42	0.08536585365853659	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	g	5.285	0.237974	0.10023	.	.	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.58940	1.72;1.72;1.72;0.3;1.72;0.44	4.52	-3.02	0.05446	.	0.678723	0.14068	N	0.343619	T	0.01287	0.0042	N	0.24115	0.695	0.09310	N	1	P;P;P	0.48230	0.716;0.907;0.85	B;B;B	0.31495	0.041;0.131;0.062	T	0.04946	-1.0916	10	0.17832	T	0.49	-0.4805	16.5319	0.84362	0.0:0.7256:0.2744:0.0	rs61750949	212;212;77	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	T	77;212;212;212;6;212;77	ENSP00000428579:A212T;ENSP00000447548:A212T;ENSP00000369136:A212T;ENSP00000428955:A6T;ENSP00000447224:A212T;ENSP00000340159:A77T	ENSP00000340159:A77T	A	+	1	0	NWD1	16721087	0.000000	0.05858	0.005000	0.12908	0.210000	0.24377	0.594000	0.24014	-0.722000	0.04922	-0.337000	0.08149	GCG	G|0.983;A|0.017	0.017	strong		0.592	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525	
DNAH10	196385	hgsc.bcm.edu	37	12	124360032	124360032	+	Silent	SNP	C	C	T	rs11834289	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124360032C>T	ENST00000409039.3	+	46	7864	c.7839C>T	c.(7837-7839)caC>caT	p.H2613H		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2613	AAA 3. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		TGAAAGGCCACACCTCGGTAA	0.438													T|||	462	0.0922524	0.2806	0.0418	5008	,	,		17889	0.0506		0.0089	False		,,,				2504	0.002				p.H2613H		Atlas-SNP	.											.	DNAH10	888	.	0			c.C7839T						PASS	.	T		909,2825		110,689,1068	108.0	100.0	103.0		7839	-6.8	0.4	12	dbSNP_120	103	88,8104		1,86,4009	no	coding-synonymous	DNAH10	NM_207437.3		111,775,5077	TT,TC,CC		1.0742,24.3439,8.3599		2613/4472	124360032	997,10929	1867	4096	5963	SO:0001819	synonymous_variant	196385	exon46			AGGCCACACCTCG	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.7839C>T	12.37:g.124360032C>T		91.0	0.0	0		101.0	48.0	0.475248	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																			C|0.924;T|0.076	0.076	strong		0.438	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
CRISP2	7180	hgsc.bcm.edu	37	6	49666100	49666100	+	Missense_Mutation	SNP	T	T	C	rs34457011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:49666100T>C	ENST00000339139.4	-	7	628	c.392A>G	c.(391-393)aAt>aGt	p.N131S		NM_001142407.2|NM_001142408.2|NM_001142417.2|NM_001142435.2|NM_001261822.1|NM_003296.3	NP_001135879.1|NP_001135880.1|NP_001135889.1|NP_001135907.1|NP_001248751.1|NP_003287.1	P16562	CRIS2_HUMAN	cysteine-rich secretory protein 2	131	SCP.		N -> S (in dbSNP:rs34457011).		single organismal cell-cell adhesion (GO:0016337)	extracellular space (GO:0005615)				kidney(1)|large_intestine(2)|lung(10)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	19	Lung NSC(77;0.0161)		KIRC - Kidney renal clear cell carcinoma(2;0.106)|Kidney(12;0.156)			AACAACTGCATTGGGACTCTT	0.408													T|||	35	0.00698882	0.0257	0.0014	5008	,	,		19608	0.0		0.0	False		,,,				2504	0.0				p.N131S		Atlas-SNP	.											.	CRISP2	53	.	0			c.A392G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN	102,4304	82.4+/-120.9	2,98,2103	124.0	114.0	117.0		392,392,392,392,392	-1.4	0.0	6	dbSNP_126	117	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense	CRISP2	NM_001142407.1,NM_001142408.1,NM_001142417.1,NM_001142435.1,NM_003296.2	46,46,46,46,46	2,98,6403	CC,CT,TT		0.0,2.315,0.7843	benign,benign,benign,benign,benign	131/244,131/244,131/244,131/244,131/244	49666100	102,12904	2203	4300	6503	SO:0001583	missense	7180	exon7			ACTGCATTGGGAC	X95239	CCDS4928.1	6p12.3	2009-03-12	2003-09-03	2003-09-05	ENSG00000124490	ENSG00000124490			12024	protein-coding gene	gene with protein product	"""cancer/testis antigen 36"""	187430	"""testis specific protein 1 (probe H4-1 p3-1)"""	GAPDL5, TPX1		2613236, 8665901	Standard	NM_003296		Approved	CRISP-2, CT36	uc003ozo.3	P16562	OTTHUMG00000014822	ENST00000339139.4:c.392A>G	6.37:g.49666100T>C	ENSP00000339155:p.Asn131Ser	113.0	0.0	0		137.0	59.0	0.430657	NM_001142408	A8K8M0|Q53FF2|Q5U8Z9|Q7Z7B2	Missense_Mutation	SNP	ENST00000339139.4	37	CCDS4928.1	11	0.005036630036630037	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	0	0.0	T	9.996	1.232230	0.22626	0.02315	0.0	ENSG00000124490	ENST00000339139;ENST00000211238	T	0.09630	2.96	5.26	-1.44	0.08856	CAP domain (3);	0.986209	0.08313	N	0.965097	T	0.02230	0.0069	L	0.33189	0.99	0.09310	N	1	B;B	0.20052	0.02;0.041	B;B	0.22152	0.038;0.038	T	0.47598	-0.9105	10	0.33940	T	0.23	.	5.0274	0.14393	0.0:0.3052:0.282:0.4128	rs34457011	131;131	Q7Z7B2;P16562	.;CRIS2_HUMAN	S	131	ENSP00000339155:N131S	ENSP00000211238:N131S	N	-	2	0	CRISP2	49774059	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.986000	0.03747	-0.396000	0.07703	-0.379000	0.06801	AAT	T|0.991;C|0.009	0.009	strong		0.408	CRISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040870.2	NM_003296	
USP44	84101	hgsc.bcm.edu	37	12	95927087	95927087	+	Missense_Mutation	SNP	C	C	G	rs7305024	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:95927087C>G	ENST00000258499.3	-	2	1234	c.946G>C	c.(946-948)Gag>Cag	p.E316Q	USP44_ENST00000537435.2_Missense_Mutation_p.E316Q|USP44_ENST00000552440.1_Missense_Mutation_p.E316Q|USP44_ENST00000393091.2_Missense_Mutation_p.E316Q	NM_001278393.1|NM_032147.2	NP_001265322.1|NP_115523.2	Q9H0E7	UBP44_HUMAN	ubiquitin specific peptidase 44	316	USP.		E -> Q (in dbSNP:rs7305024).		mitotic nuclear division (GO:0007067)|negative regulation of mitotic anaphase-promoting complex activity (GO:0060564)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deubiquitination (GO:0016579)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)|regulation of spindle checkpoint (GO:0090231)	nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(5)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	36						CTTGTCTTCTCGCTAGCAGTC	0.368													C|||	251	0.0501198	0.1808	0.0159	5008	,	,		21981	0.0		0.001	False		,,,				2504	0.0				p.E316Q		Atlas-SNP	.											.	USP44	83	.	0			c.G946C						PASS	.	C	GLN/GLU,GLN/GLU	667,3739	282.2+/-276.4	46,575,1582	59.0	56.0	57.0		946,946	5.0	0.5	12	dbSNP_116	57	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	USP44	NM_001042403.1,NM_032147.2	29,29	46,580,5877	GG,GC,CC		0.0581,15.1384,5.1668	benign,benign	316/713,316/713	95927087	672,12334	2203	4300	6503	SO:0001583	missense	84101	exon2			TCTTCTCGCTAGC	AK027434	CCDS9053.1	12q21.33	2005-08-08	2005-08-08			ENSG00000136014		"""Ubiquitin-specific peptidases"""	20064	protein-coding gene	gene with protein product		610993	"""ubiquitin specific protease 44"""			12838346	Standard	NM_001278393		Approved	FLJ14528	uc001teg.3	Q9H0E7		ENST00000258499.3:c.946G>C	12.37:g.95927087C>G	ENSP00000258499:p.Glu316Gln	60.0	0.0	0		64.0	31.0	0.484375	NM_032147	B2RDW3	Missense_Mutation	SNP	ENST00000258499.3	37	CCDS9053.1	103	0.04716117216117216	97	0.19715447154471544	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	C	3.204	-0.163026	0.06502	0.151384	5.81E-4	ENSG00000136014	ENST00000258499;ENST00000393091;ENST00000552440;ENST00000537435	T;T;T;T	0.29655	1.56;1.56;1.56;1.56	4.96	4.96	0.65561	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.473004	0.24200	N	0.040632	T	0.00039	0.0001	N	0.24115	0.695	0.44899	P	0.0020879999999999788	B	0.27264	0.173	B	0.35114	0.196	T	0.27054	-1.0085	9	0.16896	T	0.51	.	18.5826	0.91177	0.0:1.0:0.0:0.0	rs7305024;rs52829293;rs7305024	316	Q9H0E7	UBP44_HUMAN	Q	316	ENSP00000258499:E316Q;ENSP00000376806:E316Q;ENSP00000448670:E316Q;ENSP00000442629:E316Q	ENSP00000258499:E316Q	E	-	1	0	USP44	94451218	1.000000	0.71417	0.477000	0.27303	0.042000	0.13812	2.166000	0.42406	2.457000	0.83068	0.561000	0.74099	GAG	C|0.955;G|0.045	0.045	strong		0.368	USP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408312.1	NM_032147	
DNAH10	196385	hgsc.bcm.edu	37	12	124323011	124323011	+	Silent	SNP	T	T	C	rs116167096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124323011T>C	ENST00000409039.3	+	28	4582	c.4557T>C	c.(4555-4557)ggT>ggC	p.G1519G		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1519	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		AGATCATGGGTGAGACCTTAA	0.567													T|||	94	0.01877	0.0688	0.0043	5008	,	,		17334	0.0		0.0	False		,,,				2504	0.0				p.G1519G		Atlas-SNP	.											.	DNAH10	888	.	0			c.T4557C						PASS	.	T		189,3859		4,181,1839	33.0	34.0	34.0		4557	-10.4	0.0	12	dbSNP_132	34	1,8343		0,1,4171	no	coding-synonymous	DNAH10	NM_207437.3		4,182,6010	CC,CT,TT		0.012,4.669,1.5332		1519/4472	124323011	190,12202	2024	4172	6196	SO:0001819	synonymous_variant	196385	exon28			CATGGGTGAGACC	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.4557T>C	12.37:g.124323011T>C		51.0	0.0	0		72.0	35.0	0.486111	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																			T|0.983;C|0.017	0.017	strong		0.567	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
PCDHA2	56146	hgsc.bcm.edu	37	5	140176840	140176840	+	Missense_Mutation	SNP	C	C	T	rs6858913	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140176840C>T	ENST00000526136.1	+	1	2291	c.2291C>T	c.(2290-2292)cCc>cTc	p.P764L	PCDHA1_ENST00000394633.3_Intron|PCDHA2_ENST00000520672.2_Missense_Mutation_p.P764L|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000378132.1_Missense_Mutation_p.P764L	NM_018905.2	NP_061728.1	Q9Y5H9	PCDA2_HUMAN	protocadherin alpha 2	764	5 X 4 AA repeats of P-X-X-P.		P -> L (in dbSNP:rs6858913).		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(16)|lung(26)|ovary(4)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGGAGGACCCCCCCAAGACG	0.617													.|||	71	0.0141773	0.053	0.0014	5008	,	,		14850	0.0		0.0	False		,,,				2504	0.0				p.P764L		Atlas-SNP	.											.	PCDHA2	404	.	0			c.C2291T						PASS	.	C	,LEU/PRO,,LEU/PRO	225,4181	134.9+/-171.1	9,207,1987	47.0	51.0	49.0		,2291,,2291	1.0	0.7	5	dbSNP_116	49	1,8599	1.2+/-3.3	0,1,4299	yes	intron,missense,intron,missense	PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_031411.1,NM_031495.1	,98,,98	9,208,6286	TT,TC,CC		0.0116,5.1067,1.7377	,,,	,764/949,,764/825	140176840	226,12780	2203	4300	6503	SO:0001583	missense	56146	exon1			AGGACCCCCCCAA	AF152480	CCDS54914.1, CCDS64269.1	5q31	2010-11-26				ENSG00000204969		"""Cadherins / Protocadherins : Clustered"""	8668	other	complex locus constituent	"""KIAA0345-like 12"""	606308				10380929	Standard	NM_018905		Approved			Q9Y5H9		ENST00000526136.1:c.2291C>T	5.37:g.140176840C>T	ENSP00000431748:p.Pro764Leu	269.0	0.0	0		305.0	143.0	0.468852	NM_031495	O75287|Q9BTV3	Missense_Mutation	SNP	ENST00000526136.1	37	CCDS54914.1	23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	c	5.110	0.205978	0.09704	0.051067	1.16E-4	ENSG00000204969	ENST00000520672;ENST00000378132;ENST00000526136	T;T;T	0.11930	2.73;2.73;2.73	4.0	1.05	0.20165	.	2.011240	0.03846	N	0.271521	T	0.01940	0.0061	L	0.42487	1.325	0.09310	N	1	B;B;B	0.13594	0.008;0.001;0.007	B;B;B	0.15052	0.012;0.003;0.012	T	0.29792	-1.0000	10	0.35671	T	0.21	.	6.6028	0.22710	0.0:0.6237:0.131:0.2453	rs6858913;rs52809059;rs6858913	764;764;764	Q9Y5H9-3;Q9Y5H9;Q9Y5H9-2	.;PCDA2_HUMAN;.	L	764	ENSP00000430584:P764L;ENSP00000367372:P764L;ENSP00000431748:P764L	ENSP00000367372:P764L	P	+	2	0	PCDHA2	140157024	0.000000	0.05858	0.736000	0.30914	0.471000	0.32888	0.336000	0.19823	0.265000	0.21872	-0.225000	0.12378	CCC	C|0.982;T|0.018	0.018	strong		0.617	PCDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372877.3	NM_018905	
ZBTB22	9278	hgsc.bcm.edu	37	6	33283945	33283945	+	Missense_Mutation	SNP	C	C	G	rs35663442	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33283945C>G	ENST00000431845.2	-	2	900	c.749G>C	c.(748-750)gGa>gCa	p.G250A	TAPBP_ENST00000475304.1_5'Flank|TAPBP_ENST00000489157.1_5'Flank|TAPBP_ENST00000434618.2_5'Flank|TAPBP_ENST00000426633.2_5'Flank|TAPBP_ENST00000456592.2_5'Flank|ZBTB22_ENST00000418724.1_Missense_Mutation_p.G250A	NM_005453.4	NP_005444.4	O15209	ZBT22_HUMAN	zinc finger and BTB domain containing 22	250			G -> A (in dbSNP:rs35663442).		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						TGTGGCCCCTCCACTGCCAAC	0.627													C|||	54	0.0107827	0.0393	0.0029	5008	,	,		17213	0.0		0.0	False		,,,				2504	0.0				p.G250A		Atlas-SNP	.											.	ZBTB22	48	.	0			c.G749C						PASS	.	C	ALA/GLY,ALA/GLY	144,4262	101.2+/-139.8	5,134,2064	47.0	46.0	46.0		749,749	2.1	0.5	6	dbSNP_126	46	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	ZBTB22	NM_001145338.1,NM_005453.4	60,60	5,138,6360	GG,GC,CC		0.0465,3.2683,1.1379	benign,benign	250/635,250/635	33283945	148,12858	2203	4300	6503	SO:0001583	missense	9278	exon2			GCCCCTCCACTGC	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.749G>C	6.37:g.33283945C>G	ENSP00000407545:p.Gly250Ala	60.0	0.0	0		72.0	25.0	0.347222	NM_001145338	B0V007|Q5HYV4|Q5STL0|Q5STR7|Q8WV82	Missense_Mutation	SNP	ENST00000431845.2	37	CCDS4775.1	21	0.009615384615384616	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	0	0.0	C	2.540	-0.306538	0.05458	0.032683	4.65E-4	ENSG00000236104	ENST00000418724;ENST00000431845	T;T	0.07800	3.16;3.16	3.99	2.14	0.27477	.	0.253027	0.20824	N	0.085014	T	0.00875	0.0029	N	0.12182	0.205	0.28027	N	0.934308	B	0.06786	0.001	B	0.04013	0.001	T	0.46721	-0.9171	10	0.06757	T	0.87	.	4.0063	0.09603	0.0:0.5646:0.2105:0.2249	rs35663442	250	O15209	ZBT22_HUMAN	A	250	ENSP00000404403:G250A;ENSP00000407545:G250A	ENSP00000404403:G250A	G	-	2	0	ZBTB22	33391923	0.000000	0.05858	0.470000	0.27216	0.392000	0.30506	0.632000	0.24583	0.325000	0.23359	0.297000	0.19635	GGA	C|0.989;G|0.011	0.011	strong		0.627	ZBTB22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076183.2		
GJA4	2701	hgsc.bcm.edu	37	1	35260760	35260760	+	Missense_Mutation	SNP	G	G	A	rs140949366	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:35260760G>A	ENST00000342280.4	+	2	1034	c.946G>A	c.(946-948)Ggc>Agc	p.G316S		NM_002060.2	NP_002051.2	P35212	CXA4_HUMAN	gap junction protein, alpha 4, 37kDa	316					blood vessel development (GO:0001568)|calcium ion transport (GO:0006816)|cell-cell junction assembly (GO:0007043)|cell-cell signaling (GO:0007267)|endothelium development (GO:0003158)|response to pain (GO:0048265)|transport (GO:0006810)	connexon complex (GO:0005922)|gap junction (GO:0005921)|integral component of plasma membrane (GO:0005887)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(3)|prostate(4)|stomach(1)	14		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				CCCTCAGAATGGCCAAAAACC	0.577													G|||	40	0.00798722	0.0295	0.0014	5008	,	,		17399	0.0		0.0	False		,,,				2504	0.0				p.G316S		Atlas-SNP	.											.	GJA4	25	.	0			c.G946A						PASS	.	G	SER/GLY	121,4285	88.7+/-127.4	4,113,2086	42.0	40.0	41.0		946	3.4	0.0	1	dbSNP_134	41	0,8600		0,0,4300	yes	missense	GJA4	NM_002060.2	56	4,113,6386	AA,AG,GG		0.0,2.7463,0.9303	probably-damaging	316/334	35260760	121,12885	2203	4300	6503	SO:0001583	missense	2701	exon2			CAGAATGGCCAAA	M96789	CCDS30669.1	1p35.1	2008-02-05	2007-01-16		ENSG00000187513	ENSG00000187513		"""Ion channels / Gap junction proteins (connexins)"""	4278	protein-coding gene	gene with protein product	"""connexin 37"""	121012	"""gap junction protein, alpha 4, 37kD (connexin 37)"", ""gap junction protein, alpha 4, 37kDa (connexin 37)"""			9843209, 7680674	Standard	XM_005270750		Approved	CX37	uc001bya.3	P35212	OTTHUMG00000004050	ENST00000342280.4:c.946G>A	1.37:g.35260760G>A	ENSP00000343676:p.Gly316Ser	43.0	0.0	0		51.0	25.0	0.490196	NM_002060	A8K698|D3DPR4|Q9P106|Q9UBL1|Q9UNA9|Q9UNB0|Q9UNB1|Q9Y5N7	Missense_Mutation	SNP	ENST00000342280.4	37	CCDS30669.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	G	2.239	-0.374329	0.05034	0.027463	0.0	ENSG00000187513	ENST00000342280	D	0.97186	-4.28	5.25	3.39	0.38822	.	0.791228	0.11561	N	0.551774	D	0.85448	0.5699	L	0.44542	1.39	0.09310	N	0.999995	B	0.06786	0.001	B	0.04013	0.001	T	0.78170	-0.2308	10	0.11794	T	0.64	.	7.8674	0.29545	0.1462:0.1332:0.7206:0.0	.	316	P35212	CXA4_HUMAN	S	316	ENSP00000343676:G316S	ENSP00000343676:G316S	G	+	1	0	GJA4	35033347	0.002000	0.14202	0.009000	0.14445	0.026000	0.11368	0.960000	0.29253	0.603000	0.29913	0.561000	0.74099	GGC	G|0.989;A|0.011	0.011	strong		0.577	GJA4-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011556.1	NM_002060	
FRMPD1	22844	hgsc.bcm.edu	37	9	37745562	37745562	+	Missense_Mutation	SNP	C	C	T	rs62640016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:37745562C>T	ENST00000539465.1	+	16	4126	c.3533C>T	c.(3532-3534)cCt>cTt	p.P1178L	RP11-613M10.9_ENST00000540557.1_Intron|FRMPD1_ENST00000377765.3_Missense_Mutation_p.P1178L			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	1178						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)		p.P1178H(1)		NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		CCACATCCCCCTAGAGACCCT	0.483													C|||	81	0.0161741	0.0605	0.0014	5008	,	,		19697	0.0		0.0	False		,,,				2504	0.0				p.P1178L		Atlas-SNP	.											FRMPD1,scalp,carcinoma,+1,1	FRMPD1	237	1	1	Substitution - Missense(1)	lung(1)	c.C3533T						PASS	.	C	LEU/PRO	164,4242	104.7+/-143.2	3,158,2042	52.0	55.0	54.0		3533	3.2	0.0	9	dbSNP_129	54	0,8598		0,0,4299	yes	missense	FRMPD1	NM_014907.2	98	3,158,6341	TT,TC,CC		0.0,3.7222,1.2612	possibly-damaging	1178/1579	37745562	164,12840	2203	4299	6502	SO:0001583	missense	22844	exon16			ATCCCCCTAGAGA	AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.3533C>T	9.37:g.37745562C>T	ENSP00000444411:p.Pro1178Leu	75.0	0.0	0		78.0	41.0	0.525641	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	37	CCDS6612.1	23	0.010531135531135532	23	0.046747967479674794	0	0.0	0	0.0	0	0.0	C	11.39	1.625940	0.28889	0.037222	0.0	ENSG00000070601	ENST00000377765;ENST00000539465	T;T	0.06768	3.26;3.26	4.24	3.24	0.37175	.	1.039780	0.07531	N	0.912167	T	0.00998	0.0033	N	0.24115	0.695	0.19300	N	0.999977	B	0.06786	0.001	B	0.04013	0.001	T	0.15925	-1.0420	10	0.56958	D	0.05	-9.9948	8.5566	0.33485	0.2299:0.7701:0.0:0.0	rs62640016	1178	Q5SYB0	FRPD1_HUMAN	L	1178	ENSP00000366995:P1178L;ENSP00000444411:P1178L	ENSP00000366995:P1178L	P	+	2	0	FRMPD1	37735562	0.005000	0.15991	0.037000	0.18230	0.034000	0.12701	1.541000	0.36126	2.298000	0.77334	0.561000	0.74099	CCT	C|0.986;T|0.014	0.014	strong		0.483	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907	
MTERF3	51001	hgsc.bcm.edu	37	8	97263180	97263180	+	Missense_Mutation	SNP	T	T	G	rs112357919	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:97263180T>G	ENST00000287025.3	-	4	729	c.631A>C	c.(631-633)Aaa>Caa	p.K211Q	MTERFD1_ENST00000524341.1_Missense_Mutation_p.K21Q|MTERFD1_ENST00000522822.1_Missense_Mutation_p.K90Q|MTERFD1_ENST00000523821.1_Missense_Mutation_p.K211Q	NM_015942.3	NP_057026.3	Q96E29	MTEF3_HUMAN		211					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)	transcription regulatory region DNA binding (GO:0044212)			endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	24	Breast(36;5.16e-05)					GCATGATTTTTTGTCAGGAAT	0.363													T|||	215	0.0429313	0.1566	0.0101	5008	,	,		12111	0.0		0.001	False		,,,				2504	0.0				p.K211Q		Atlas-SNP	.											.	MTERFD1	50	.	0			c.A631C						PASS	.	T	GLN/LYS	602,3804	263.1+/-265.3	36,530,1637	113.0	116.0	115.0		631	6.0	1.0	8	dbSNP_132	115	3,8597	3.0+/-9.4	0,3,4297	yes	missense	MTERFD1	NM_015942.3	53	36,533,5934	GG,GT,TT		0.0349,13.6632,4.6517	probably-damaging	211/418	97263180	605,12401	2203	4300	6503	SO:0001583	missense	51001	exon4			GATTTTTTGTCAG																												ENST00000287025.3:c.631A>C	8.37:g.97263180T>G	ENSP00000287025:p.Lys211Gln	169.0	0.0	0		163.0	82.0	0.503067	NM_015942	B3KMG6|G3V130|Q9Y301	Missense_Mutation	SNP	ENST00000287025.3	37	CCDS6270.1	79	0.036172161172161175	76	0.15447154471544716	3	0.008287292817679558	0	0.0	0	0.0	T	22.3	4.273758	0.80580	0.136632	3.49E-4	ENSG00000156469	ENST00000523821;ENST00000522822;ENST00000524341;ENST00000287025	T;T;T;T	0.17213	2.73;2.73;2.29;2.73	5.98	5.98	0.97165	.	0.191366	0.51477	D	0.000091	T	0.00210	0.0006	M	0.69823	2.125	0.20821	P	0.999846152	D;D	0.65815	0.995;0.995	P;P	0.58820	0.846;0.799	T	0.01298	-1.1392	9	0.33940	T	0.23	-9.9875	15.0407	0.71788	0.0:0.0:0.0:1.0	.	211;211	E5RIK9;Q96E29	.;MTER1_HUMAN	Q	211;90;21;211	ENSP00000429400:K211Q;ENSP00000430138:K90Q;ENSP00000429267:K21Q;ENSP00000287025:K211Q	ENSP00000287025:K211Q	K	-	1	0	MTERFD1	97332356	1.000000	0.71417	0.963000	0.40424	0.946000	0.59487	4.381000	0.59587	2.289000	0.77006	0.482000	0.46254	AAA	T|0.958;G|0.042	0.042	strong		0.363	MTERFD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379876.1		
VN1R4	317703	hgsc.bcm.edu	37	19	53770846	53770846	+	Missense_Mutation	SNP	C	C	G	rs112743505	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53770846C>G	ENST00000311170.4	-	1	126	c.73G>C	c.(73-75)Gtt>Ctt	p.V25L	CTD-2245F17.9_ENST00000599803.1_lincRNA	NM_173857.2	NP_776256.2	Q7Z5H5	VN1R4_HUMAN	vomeronasal 1 receptor 4	25					response to pheromone (GO:0019236)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	pheromone receptor activity (GO:0016503)			central_nervous_system(1)|large_intestine(4)|lung(10)|ovary(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	22				GBM - Glioblastoma multiforme(134;0.00294)		TGGAGAAGAACAGAGAAGCTC	0.493										HNSCC(26;0.072)			G|||	256	0.0511182	0.1831	0.0159	5008	,	,		19164	0.002		0.001	False		,,,				2504	0.0				p.V25L		Atlas-SNP	.											.	VN1R4	65	.	0			c.G73C						PASS	.	G	LEU/VAL	706,3700	745.0+/-411.6	70,566,1567	57.0	63.0	61.0		73	1.2	0.0	19	dbSNP_134	61	8,8592	817.1+/-406.9	0,8,4292	yes	missense	VN1R4	NM_173857.2	32	70,574,5859	GG,GC,CC		0.093,16.0236,5.4898	benign	25/302	53770846	714,12292	2203	4300	6503	SO:0001583	missense	317703	exon1			GAAGAACAGAGAA	AY114733	CCDS33099.1	19q13.42	2012-08-22			ENSG00000228567	ENSG00000228567		"""Vomeronasal receptors / Type 1"", ""GPCR / Unclassified : Vomeronasal receptors, type 1"""	19871	protein-coding gene	gene with protein product						12123587	Standard	NM_173857		Approved	V1RL4	uc010ydu.2	Q7Z5H5		ENST00000311170.4:c.73G>C	19.37:g.53770846C>G	ENSP00000310856:p.Val25Leu	332.0	0.0	0		394.0	192.0	0.48731	NM_173857	Q2M3E2|Q7Z5H6|Q7Z5H7|Q8TDU2	Missense_Mutation	SNP	ENST00000311170.4	37	CCDS33099.1	93	0.042582417582417584	75	0.1524390243902439	8	0.022099447513812154	4	0.006993006993006993	6	0.0079155672823219	G	0.008	-1.870615	0.00542	0.160236	9.3E-4	ENSG00000228567	ENST00000311170	T	0.44482	0.92	2.26	1.19	0.21007	GPCR, rhodopsin-like superfamily (1);	0.610624	0.12496	N	0.463795	T	0.00073	0.0002	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.24905	-1.0147	9	0.02654	T	1	.	3.7996	0.08753	0.1549:0.2523:0.5928:0.0	.	25	Q7Z5H5	VN1R4_HUMAN	L	25	ENSP00000310856:V25L	ENSP00000310856:V25L	V	-	1	0	VN1R4	58462658	0.016000	0.18221	0.008000	0.14137	0.008000	0.06430	0.420000	0.21263	0.090000	0.17273	-0.275000	0.10095	GTT	C|0.953;G|0.047	0.047	strong		0.493	VN1R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464287.1	NM_173857	
ZNF813	126017	hgsc.bcm.edu	37	19	53994083	53994083	+	Silent	SNP	T	T	C	rs150664026	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53994083T>C	ENST00000396403.4	+	4	725	c.597T>C	c.(595-597)tcT>tcC	p.S199S	ZNF813_ENST00000396421.4_Intron	NM_001004301.3	NP_001004301.2	Q6ZN06	ZN813_HUMAN	zinc finger protein 813	199					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)		TCCGGAATTCTTCGTTACTCA	0.368													.|||	12	0.00239617	0.0083	0.0014	5008	,	,		20858	0.0		0.0	False		,,,				2504	0.0				p.S199S		Atlas-SNP	.											ZNF813_ENST00000396403,NS,carcinoma,+1,1	ZNF813	81	1	0			c.T597C						PASS	.	T		31,4353		0,31,2161	79.0	87.0	84.0		597	0.5	0.0	19	dbSNP_134	84	2,8584		0,2,4291	no	coding-synonymous	ZNF813	NM_001004301.3		0,33,6452	CC,CT,TT		0.0233,0.7071,0.2544		199/618	53994083	33,12937	2192	4293	6485	SO:0001819	synonymous_variant	126017	exon4			GAATTCTTCGTTA	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.597T>C	19.37:g.53994083T>C		249.0	0.0	0		248.0	119.0	0.479839	NM_001004301		Silent	SNP	ENST00000396403.4	37	CCDS46172.1																																																																																			T|0.999;C|0.001	0.001	strong		0.368	ZNF813-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350638.1	NM_001004301	
DPY19L1	23333	hgsc.bcm.edu	37	7	34978926	34978926	+	Silent	SNP	G	G	A	rs377307859		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:34978926G>A	ENST00000310974.4	-	20	1851	c.1707C>T	c.(1705-1707)ccC>ccT	p.P569P	MIR548N_ENST00000408742.1_RNA	NM_015283.1	NP_056098.1	Q2PZI1	D19L1_HUMAN	dpy-19-like 1 (C. elegans)	569						integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity, transferring glycosyl groups (GO:0016757)			endometrium(3)|kidney(5)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	31						GATTCACAATGGGCCGAAGTG	0.507																																					p.P569P		Atlas-SNP	.											.	DPY19L1	56	.	0			c.C1707T						PASS	.	G		1,4179		0,1,2089	120.0	112.0	115.0		1707	-0.4	0.0	7		115	0,8478		0,0,4239	no	coding-synonymous	DPY19L1	NM_015283.1		0,1,6328	AA,AG,GG		0.0,0.0239,0.0079		569/676	34978926	1,12657	2090	4239	6329	SO:0001819	synonymous_variant	23333	exon20			CACAATGGGCCGA	AB020684	CCDS43567.1	7p14.3-p14.2	2006-04-26			ENSG00000173852	ENSG00000173852			22205	protein-coding gene	gene with protein product		613892					Standard	NM_015283		Approved	KIAA0877	uc003tem.4	Q2PZI1	OTTHUMG00000154888	ENST00000310974.4:c.1707C>T	7.37:g.34978926G>A		113.0	0.0	0		138.0	71.0	0.514493	NM_015283	O94954|Q4G151	Silent	SNP	ENST00000310974.4	37	CCDS43567.1	.	.	.	.	.	.	.	.	.	.	G	9.689	1.151487	0.21371	2.39E-4	0.0	ENSG00000173852	ENST00000428054	.	.	.	5.9	-0.415	0.12355	.	.	.	.	.	T	0.41282	0.1152	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.21109	-1.0255	4	.	.	.	-12.4763	1.5429	0.02559	0.2774:0.217:0.3812:0.1244	.	.	.	.	Y	19	.	.	H	-	1	0	DPY19L1	34945451	0.075000	0.21258	0.018000	0.16275	0.856000	0.48823	0.068000	0.14531	-0.382000	0.07870	-0.150000	0.13652	CAT	.	.	weak		0.507	DPY19L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337506.1		
ALPK3	57538	hgsc.bcm.edu	37	15	85403104	85403104	+	Missense_Mutation	SNP	G	G	A	rs114686452	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:85403104G>A	ENST00000258888.5	+	8	4836	c.4669G>A	c.(4669-4671)Gcc>Acc	p.A1557T		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1557	Ig-like 2.		A -> D (in dbSNP:rs34775428). {ECO:0000269|PubMed:17344846}.		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)			GCACGGCTCGGCCTCCACCGA	0.687													G|||	11	0.00219649	0.0083	0.0	5008	,	,		16937	0.0		0.0	False		,,,				2504	0.0				p.A1557T		Atlas-SNP	.											.	ALPK3	289	.	0			c.G4669A						PASS	.	G	THR/ALA	17,4389	24.3+/-50.5	0,17,2186	57.0	55.0	55.0		4669	3.6	0.6	15	dbSNP_132	55	0,8598		0,0,4299	yes	missense	ALPK3	NM_020778.4	58	0,17,6485	AA,AG,GG		0.0,0.3858,0.1307	possibly-damaging	1557/1908	85403104	17,12987	2203	4299	6502	SO:0001583	missense	57538	exon8			GGCTCGGCCTCCA	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.4669G>A	15.37:g.85403104G>A	ENSP00000258888:p.Ala1557Thr	102.0	0.0	0		103.0	46.0	0.446602	NM_020778	Q9P2L6	Missense_Mutation	SNP	ENST00000258888.5	37	CCDS10333.1	4	0.0018315018315018315	3	0.006097560975609756	0	0.0	0	0.0	1	0.0013192612137203166	G	22.4	4.289118	0.80914	0.003858	0.0	ENSG00000136383	ENST00000258888	T	0.06687	3.27	5.52	3.62	0.41486	Immunoglobulin-like (1);Protein kinase-like domain (1);Immunoglobulin-like fold (1);	0.331817	0.30383	N	0.009744	T	0.07863	0.0197	L	0.34521	1.04	0.26266	N	0.978497	D	0.60575	0.988	P	0.54590	0.756	T	0.12344	-1.0551	10	0.27082	T	0.32	-10.6766	9.2405	0.37493	0.0811:0.1467:0.7721:0.0	.	1557	Q96L96	ALPK3_HUMAN	T	1557	ENSP00000258888:A1557T	ENSP00000258888:A1557T	A	+	1	0	ALPK3	83204108	1.000000	0.71417	0.556000	0.28293	0.972000	0.66771	3.919000	0.56439	0.680000	0.31366	0.563000	0.77884	GCC	G|0.998;A|0.002	0.002	strong		0.687	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778	
HDGFRP2	84717	hgsc.bcm.edu	37	19	4488718	4488718	+	Missense_Mutation	SNP	G	G	A	rs147061912	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4488718G>A	ENST00000301284.4	+	4	398	c.334G>A	c.(334-336)Gac>Aac	p.D112N	HDGFRP2_ENST00000586684.1_Missense_Mutation_p.D112N	NM_001001520.1|NM_032631.2	NP_001001520|NP_116020.1	Q7Z4V5	HDGR2_HUMAN		112					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										CAACCCCGCCGACGGCAGTGA	0.677													G|||	37	0.00738818	0.028	0.0	5008	,	,		14427	0.0		0.0	False		,,,				2504	0.0				p.D112N		Atlas-SNP	.											.	.	.	.	0			c.G334A						PASS	.	G	ASN/ASP,ASN/ASP	96,4038		1,94,1972	11.0	15.0	13.0		334,334	2.5	0.0	19	dbSNP_134	13	0,8302		0,0,4151	yes	missense,missense	HDGFRP2	NM_032631.2,NM_001001520.1	23,23	1,94,6123	AA,AG,GG		0.0,2.3222,0.772	benign,benign	112/676,112/677	4488718	96,12340	2067	4151	6218	SO:0001583	missense	0	exon4			CCCGCCGACGGCA																												ENST00000301284.4:c.334G>A	19.37:g.4488718G>A	ENSP00000301284:p.Asp112Asn	27.0	0.0	0		28.0	16.0	0.571429	NM_032631	I3L080|K7EQZ6|Q96GI5|Q9BW08	Missense_Mutation	SNP	ENST00000301284.4	37	CCDS42472.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	G	4.364	0.067010	0.08388	0.023222	0.0	ENSG00000167674	ENST00000301284;ENST00000398364	T	0.46451	0.87	4.86	2.5	0.30297	.	0.387710	0.23889	N	0.043579	T	0.10852	0.0265	L	0.38175	1.15	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.01281	0.0;0.0	T	0.08229	-1.0732	10	0.21014	T	0.42	.	8.9678	0.35887	0.0:0.1609:0.6729:0.1662	.	112;112	C9JEE1;Q7Z4V5	.;HDGR2_HUMAN	N	112;98	ENSP00000301284:D112N	ENSP00000301284:D112N	D	+	1	0	AC011498.1	4439718	0.052000	0.20516	0.003000	0.11579	0.006000	0.05464	2.427000	0.44740	1.143000	0.42306	0.555000	0.69702	GAC	G|0.994;A|0.006	0.006	strong		0.677	HDGFRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458642.1		
ZC3H4	23211	hgsc.bcm.edu	37	19	47575279	47575279	+	Silent	SNP	G	G	C	rs76187449	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:47575279G>C	ENST00000253048.5	-	13	1939	c.1902C>G	c.(1900-1902)ccC>ccG	p.P634P	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	634	Pro-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		ggtgcatgtcggggtgcatgt	0.672													g|||	134	0.0267572	0.0938	0.0115	5008	,	,		17976	0.0		0.002	False		,,,				2504	0.0				p.P634P		Atlas-SNP	.											.	ZC3H4	96	.	0			c.C1902G						PASS	.						31.0	36.0	35.0					19																	47575279		2097	4223	6320	SO:0001819	synonymous_variant	23211	exon13			CATGTCGGGGTGC	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"""Zinc fingers, CCCH-type domain containing"""	17808	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 7"""	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.1902C>G	19.37:g.47575279G>C		131.0	0.0	0		107.0	56.0	0.523364	NM_015168	Q9Y420	Silent	SNP	ENST00000253048.5	37	CCDS42582.1																																																																																			.	.	weak		0.672	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1		
TSKS	60385	hgsc.bcm.edu	37	19	50248556	50248556	+	Missense_Mutation	SNP	C	C	T	rs34082111	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50248556C>T	ENST00000246801.3	-	7	1172	c.1090G>A	c.(1090-1092)Ggc>Agc	p.G364S	TSKS_ENST00000358830.3_Missense_Mutation_p.G164S	NM_021733.1	NP_068379.1	Q9UJT2	TSKS_HUMAN	testis-specific serine kinase substrate	364					negative regulation of phosphatase activity (GO:0010923)	centriole (GO:0005814)	protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|prostate(3)|skin(3)	38		all_lung(116;3.24e-07)|Lung NSC(112;1.6e-06)|all_neural(266;0.0459)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00153)|GBM - Glioblastoma multiforme(134;0.0145)		CCTAGGAAGCCGTCGACCCTG	0.706													C|||	54	0.0107827	0.0401	0.0014	5008	,	,		13851	0.0		0.0	False		,,,				2504	0.0				p.G364S		Atlas-SNP	.											.	TSKS	97	.	0			c.G1090A						PASS	.	C	SER/GLY	120,4282		3,114,2084	23.0	23.0	23.0		1090	3.8	1.0	19	dbSNP_126	23	1,8595		0,1,4297	yes	missense	TSKS	NM_021733.1	56	3,115,6381	TT,TC,CC		0.0116,2.726,0.9309	probably-damaging	364/593	50248556	121,12877	2201	4298	6499	SO:0001583	missense	60385	exon7			GGAAGCCGTCGAC	BC058862	CCDS12780.1	19q13.3	2014-06-13							30719	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 161"""	608253				11444856, 18495105	Standard	NM_021733		Approved	TSSKS, PPP1R161	uc002ppm.3	Q9UJT2		ENST00000246801.3:c.1090G>A	19.37:g.50248556C>T	ENSP00000246801:p.Gly364Ser	26.0	0.0	0		61.0	38.0	0.622951	NM_021733	Q8WXJ0	Missense_Mutation	SNP	ENST00000246801.3	37	CCDS12780.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	C	25.2	4.614167	0.87359	0.02726	1.16E-4	ENSG00000126467	ENST00000246801;ENST00000358830	T;T	0.55588	0.51;0.51	4.89	3.84	0.44239	.	0.000000	0.53938	D	0.000058	T	0.14227	0.0344	L	0.29908	0.895	0.34627	D	0.719177	P	0.39964	0.697	B	0.32393	0.145	T	0.40403	-0.9565	10	0.35671	T	0.21	-19.1441	10.8376	0.46696	0.0:0.91:0.0:0.09	rs34082111	364	Q9UJT2	TSKS_HUMAN	S	364;164	ENSP00000246801:G364S;ENSP00000351691:G164S	ENSP00000246801:G364S	G	-	1	0	TSKS	54940368	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.050000	0.41297	1.273000	0.44346	0.561000	0.74099	GGC	C|0.991;T|0.009	0.009	strong		0.706	TSKS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465795.1	NM_021733	
MBOAT2	129642	hgsc.bcm.edu	37	2	8998971	8998971	+	Silent	SNP	T	T	C	rs35943010	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:8998971T>C	ENST00000305997.3	-	13	1599	c.1401A>G	c.(1399-1401)aaA>aaG	p.K467K	MBOAT2_ENST00000486484.1_5'Flank	NM_138799.2	NP_620154.2	Q6ZWT7	MBOA2_HUMAN	membrane bound O-acyltransferase domain containing 2	467					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)		MBOAT2/PRKCE(2)	endometrium(2)|kidney(1)|large_intestine(9)|lung(2)|skin(1)	15	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					TTCTTTGAGTTTTTTTCACTG	0.318													T|||	74	0.0147764	0.0227	0.0086	5008	,	,		17674	0.003		0.004	False		,,,				2504	0.0317				p.K467K	Ovarian(194;1699 3813 22401)	Atlas-SNP	.											.	MBOAT2	36	.	0			c.A1401G						PASS	.	T		69,4337	61.7+/-98.7	1,67,2135	77.0	79.0	78.0		1401	1.2	0.8	2	dbSNP_126	78	14,8586	9.8+/-36.6	0,14,4286	no	coding-synonymous	MBOAT2	NM_138799.2		1,81,6421	CC,CT,TT		0.1628,1.566,0.6382		467/521	8998971	83,12923	2203	4300	6503	SO:0001819	synonymous_variant	129642	exon13			TTGAGTTTTTTTC	BC016005	CCDS1660.1	2p25	2008-02-05	2006-06-29	2006-06-29	ENSG00000143797	ENSG00000143797			25193	protein-coding gene	gene with protein product		611949	"""O-acyltransferase (membrane bound) domain containing 2"""	OACT2			Standard	NM_138799		Approved	FLJ14415, FLJ90298	uc002qzg.1	Q6ZWT7	OTTHUMG00000090363	ENST00000305997.3:c.1401A>G	2.37:g.8998971T>C		130.0	0.0	0		106.0	45.0	0.424528	NM_138799	A9EDR2|Q8NCE7|Q96KY4	Silent	SNP	ENST00000305997.3	37	CCDS1660.1																																																																																			T|0.994;C|0.006	0.006	strong		0.318	MBOAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206735.1	NM_138799	
GBX1	2636	hgsc.bcm.edu	37	7	150846188	150846188	+	Missense_Mutation	SNP	C	C	T	rs11975799	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150846188C>T	ENST00000297537.4	-	2	579	c.580G>A	c.(580-582)Gca>Aca	p.A194T	GBX1_ENST00000475831.1_5'Flank	NM_001098834.1	NP_001092304.1	Q14549	GBX1_HUMAN	gastrulation brain homeobox 1	194			A -> T (in dbSNP:rs11975799).		adult walking behavior (GO:0007628)|neuron fate commitment (GO:0048663)|proprioception (GO:0019230)|regulation of transcription, DNA-templated (GO:0006355)|sensory neuron axon guidance (GO:0097374)|spinal cord motor neuron differentiation (GO:0021522)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			large_intestine(1)|lung(5)|skin(1)	7			OV - Ovarian serous cystadenocarcinoma(82;0.00989)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCTGCTGATGCCTCCAGCTTC	0.582													C|||	117	0.0233626	0.0764	0.0072	5008	,	,		16501	0.006		0.0	False		,,,				2504	0.0051				p.A194T		Atlas-SNP	.											.	GBX1	21	.	0			c.G580A						PASS	.	C	THR/ALA	219,3991		9,201,1895	204.0	220.0	215.0		580	0.8	0.8	7	dbSNP_120	215	4,8462		0,4,4229	yes	missense	GBX1	NM_001098834.1	58	9,205,6124	TT,TC,CC		0.0472,5.2019,1.7592	benign	194/364	150846188	223,12453	2105	4233	6338	SO:0001583	missense	2636	exon2			CTGATGCCTCCAG	L11239	CCDS43682.1	7q36.1	2012-03-09	2005-12-22		ENSG00000164900	ENSG00000164900		"""Homeoboxes / ANTP class : HOXL subclass"""	4185	protein-coding gene	gene with protein product		603354	"""gastrulation brain homeo box 1"""			7903253	Standard	NM_001098834		Approved		uc011kvg.2	Q14549	OTTHUMG00000158751	ENST00000297537.4:c.580G>A	7.37:g.150846188C>T	ENSP00000297537:p.Ala194Thr	21.0	0.0	0		24.0	15.0	0.625	NM_001098834		Missense_Mutation	SNP	ENST00000297537.4	37	CCDS43682.1	41	0.018772893772893772	33	0.06707317073170732	4	0.011049723756906077	4	0.006993006993006993	0	0.0	C	13.43	2.233908	0.39498	0.052019	4.72E-4	ENSG00000164900	ENST00000297537	D	0.91894	-2.93	4.95	0.769	0.18492	.	0.952841	0.08341	U	0.960876	T	0.27489	0.0675	N	0.08118	0	0.42774	D	0.993847	B	0.10296	0.003	B	0.06405	0.002	T	0.57165	-0.7858	10	0.19147	T	0.46	-4.7045	3.1719	0.06555	0.1248:0.4649:0.2571:0.1532	rs11975799;rs11975799	194	Q14549	GBX1_HUMAN	T	194	ENSP00000297537:A194T	ENSP00000297537:A194T	A	-	1	0	GBX1	150477121	0.997000	0.39634	0.847000	0.33407	0.987000	0.75469	1.560000	0.36331	0.141000	0.18875	-0.373000	0.07131	GCA	C|0.979;T|0.021	0.021	strong		0.582	GBX1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352029.1		
SHISA6	388336	hgsc.bcm.edu	37	17	11461483	11461483	+	Silent	SNP	C	C	T	rs148413919	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:11461483C>T	ENST00000409168.3	+	4	1365	c.1365C>T	c.(1363-1365)taC>taT	p.Y455Y	SHISA6_ENST00000441885.3_Silent_p.Y506Y|SHISA6_ENST00000432116.3_Silent_p.Y487Y	NM_001173461.1	NP_001166932.1	Q6ZSJ9	SHSA6_HUMAN	shisa family member 6	455						alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)				breast(1)|endometrium(4)	5						ATAACTCATACGCCACCCTGG	0.612													C|||	33	0.00658946	0.025	0.0	5008	,	,		16338	0.0		0.0	False		,,,				2504	0.0				p.Y506Y		Atlas-SNP	.											.	SHISA6	44	.	0			c.C1518T						PASS	.	C	,,	34,1350		0,34,658	65.0	62.0	63.0		1365,1461,1518	0.2	1.0	17	dbSNP_134	63	1,3181		0,1,1590	no	coding-synonymous,coding-synonymous,coding-synonymous	SHISA6	NM_001173461.1,NM_001173462.1,NM_207386.3	,,	0,35,2248	TT,TC,CC		0.0314,2.4566,0.7665	,,	455/501,487/533,506/552	11461483	35,4531	692	1591	2283	SO:0001819	synonymous_variant	388336	exon6			CTCATACGCCACC	AK127379, AK128003	CCDS45615.1, CCDS54089.1, CCDS54090.1	17p13.1-p12	2013-07-31	2013-07-31		ENSG00000188803	ENSG00000188803		"""Shisa homologs"""	34491	protein-coding gene	gene with protein product			"""shisa homolog 6 (Xenopus laevis)"""				Standard	NM_207386		Approved	FLJ45455	uc002gnc.2	Q6ZSJ9	OTTHUMG00000154121	ENST00000409168.3:c.1365C>T	17.37:g.11461483C>T		61.0	0.0	0		68.0	28.0	0.411765	NM_207386	B3KXV5|Q4PL63	Silent	SNP	ENST00000409168.3	37	CCDS54090.1																																																																																			C|0.994;T|0.006	0.006	strong		0.612	SHISA6-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000333970.2	NM_207386	
FBN2	2201	hgsc.bcm.edu	37	5	127624905	127624905	+	Missense_Mutation	SNP	T	T	A	rs149071226	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:127624905T>A	ENST00000508053.1	-	58	7525	c.6551A>T	c.(6550-6552)aAt>aTt	p.N2184I	FBN2_ENST00000262464.4_Missense_Mutation_p.N2184I			P35556	FBN2_HUMAN	fibrillin 2	2184	EGF-like 36; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		ACATTGACCATTTGAACAAAT	0.453													T|||	3	0.000599042	0.0023	0.0	5008	,	,		18157	0.0		0.0	False		,,,				2504	0.0				p.N2184I		Atlas-SNP	.											.	FBN2	858	.	0			c.A6551T						PASS	.	T	ILE/ASN	19,4387	26.2+/-53.5	0,19,2184	161.0	152.0	155.0		6551	5.8	1.0	5	dbSNP_134	155	0,8600		0,0,4300	yes	missense	FBN2	NM_001999.3	149	0,19,6484	AA,AT,TT		0.0,0.4312,0.1461	possibly-damaging	2184/2913	127624905	19,12987	2203	4300	6503	SO:0001583	missense	2201	exon52			TGACCATTTGAAC	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"""fibrillin 5"""	612570	"""congenital contractural arachnodactyly"""	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.6551A>T	5.37:g.127624905T>A	ENSP00000424571:p.Asn2184Ile	82.0	0.0	0		110.0	43.0	0.390909	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	37	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	T	23.2	4.385239	0.82792	0.004312	0.0	ENSG00000138829	ENST00000262464;ENST00000508053	D;D	0.92647	-3.08;-3.08	5.76	5.76	0.90799	Matrix fibril-associated (1);EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.000000	0.64402	D	0.000002	D	0.95768	0.8623	M	0.89030	3	0.58432	D	0.999995	D	0.58620	0.983	P	0.60012	0.867	D	0.96209	0.9151	10	0.87932	D	0	.	12.1851	0.54234	0.0:0.0683:0.0:0.9317	.	2184	P35556	FBN2_HUMAN	I	2184	ENSP00000262464:N2184I;ENSP00000424571:N2184I	ENSP00000262464:N2184I	N	-	2	0	FBN2	127652804	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	3.317000	0.51968	2.324000	0.78689	0.533000	0.62120	AAT	T|0.998;A|0.002	0.002	strong		0.453	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	
OBSCN	84033	hgsc.bcm.edu	37	1	228560181	228560181	+	Silent	SNP	G	G	A	rs62640372	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228560181G>A	ENST00000422127.1	+	94	21746	c.21702G>A	c.(21700-21702)tcG>tcA	p.S7234S	OBSCN_ENST00000366707.4_Silent_p.S4868S|OBSCN_ENST00000570156.2_Silent_p.S8191S	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	7234					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AGTCCCAGTCGGAGGAGCAGC	0.692													G|||	32	0.00638978	0.0227	0.0014	5008	,	,		15712	0.001		0.0	False		,,,				2504	0.0				p.S8191S		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G24573A						PASS	.	G		93,4067		0,93,1987	13.0	16.0	15.0		21702	-2.1	0.6	1	dbSNP_129	15	0,8404		0,0,4202	no	coding-synonymous	OBSCN	NM_001098623.1		0,93,6189	AA,AG,GG		0.0,2.2356,0.7402		7234/7969	228560181	93,12471	2080	4202	6282	SO:0001819	synonymous_variant	84033	exon105			CCAGTCGGAGGAG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.21702G>A	1.37:g.228560181G>A		94.0	0.0	0		92.0	44.0	0.478261	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1	7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	G	6.630	0.484618	0.12641	0.022356	0.0	ENSG00000154358	ENST00000441106	.	.	.	1.05	-2.1	0.07210	.	.	.	.	.	T	0.09774	0.0240	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.24835	-1.0149	4	.	.	.	.	2.4475	0.04509	0.0:0.253:0.2936:0.4534	rs62640372	.	.	.	R	1851	.	.	G	+	1	0	OBSCN	226626804	0.013000	0.17824	0.600000	0.28864	0.363000	0.29612	-0.971000	0.03806	0.119000	0.18210	0.121000	0.15741	GGA	G|0.996;A|0.004	0.004	strong		0.692	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
TCN2	6948	hgsc.bcm.edu	37	22	31011350	31011350	+	Missense_Mutation	SNP	C	C	T	rs35838082	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:31011350C>T	ENST00000215838.3	+	5	1137	c.643C>T	c.(643-645)Cgg>Tgg	p.R215W	TCN2_ENST00000407817.3_Missense_Mutation_p.R188W|TCN2_ENST00000405742.3_Missense_Mutation_p.R211W			P20062	TCO2_HUMAN	transcobalamin II	215			R -> W (in dbSNP:rs35838082).		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)	CAACCCTGGTCGGAGACAACG	0.557													C|||	365	0.0728834	0.2443	0.0159	5008	,	,		21382	0.001		0.006	False		,,,				2504	0.0245				p.R215W		Atlas-SNP	.											.	TCN2	44	.	0			c.C643T						PASS	.	C	TRP/ARG,TRP/ARG	1044,3362	382.1+/-324.3	124,796,1283	87.0	77.0	81.0		643,562	5.8	0.0	22	dbSNP_126	81	58,8542	35.9+/-90.5	0,58,4242	yes	missense,missense	TCN2	NM_000355.3,NM_001184726.1	101,101	124,854,5525	TT,TC,CC		0.6744,23.695,8.473	probably-damaging,probably-damaging	215/428,188/401	31011350	1102,11904	2203	4300	6503	SO:0001583	missense	6948	exon5			CCTGGTCGGAGAC		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.643C>T	22.37:g.31011350C>T	ENSP00000215838:p.Arg215Trp	183.0	0.0	0		208.0	208.0	1	NM_000355	Q96FD4|Q9BVI8|Q9UCI5|Q9UCI6|Q9UDM0	Missense_Mutation	SNP	ENST00000215838.3	37	CCDS13881.1	126	0.057692307692307696	115	0.23373983739837398	5	0.013812154696132596	0	0.0	6	0.0079155672823219	C	20.4	3.985921	0.74589	0.23695	0.006744	ENSG00000185339	ENST00000215838;ENST00000405742;ENST00000407817	T;T;T	0.15952	2.38;2.38;2.38	5.82	5.82	0.92795	.	0.978539	0.08426	N	0.947638	T	0.00012	0.0000	N	0.08118	0	0.09310	P	0.9999999999999691	D;D;D	0.60575	0.975;0.988;0.988	P;P;P	0.51229	0.663;0.559;0.559	T	0.48525	-0.9028	9	0.62326	D	0.03	-1.0E-4	17.0097	0.86403	0.0:1.0:0.0:0.0	rs35838082;rs61224137	188;211;215	Q96FD4;B5MBX2;P20062	.;.;TCO2_HUMAN	W	215;211;188	ENSP00000215838:R215W;ENSP00000385914:R211W;ENSP00000384914:R188W	ENSP00000215838:R215W	R	+	1	2	TCN2	29341350	0.001000	0.12720	0.009000	0.14445	0.013000	0.08279	1.271000	0.33098	2.756000	0.94617	0.561000	0.74099	CGG	C|0.925;T|0.075	0.075	strong		0.557	TCN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321282.2	NM_000355	
MUC17	140453	hgsc.bcm.edu	37	7	100683156	100683156	+	Missense_Mutation	SNP	C	C	T	rs79046921	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100683156C>T	ENST00000306151.4	+	3	8523	c.8459C>T	c.(8458-8460)aCg>aTg	p.T2820M		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2820	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					GTCAACCACACGCCAGTGGCC	0.493																																					p.T2820M		Atlas-SNP	.											MUC17,colon,carcinoma,-1,2	MUC17	804	2	0			c.C8459T						scavenged	.	C	MET/THR	620,3786	270.1+/-269.4	46,528,1629	241.0	247.0	245.0		8459	0.9	0.0	7	dbSNP_131	245	6,8594	3.0+/-9.4	0,6,4294	yes	missense	MUC17	NM_001040105.1	81	46,534,5923	TT,TC,CC		0.0698,14.0717,4.8132	probably-damaging	2820/4494	100683156	626,12380	2203	4300	6503	SO:0001583	missense	140453	exon3			ACCACACGCCAGT	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.8459C>T	7.37:g.100683156C>T	ENSP00000302716:p.Thr2820Met	117.0	1.0	0.00854701		143.0	77.0	0.538462	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	77	0.035256410256410256	74	0.15040650406504066	3	0.008287292817679558	0	0.0	0	0.0	C	6.722	0.501948	0.12822	0.140717	6.98E-4	ENSG00000169876	ENST00000306151	T	0.02015	4.5	0.911	0.911	0.19343	.	.	.	.	.	T	0.00039	0.0001	N	0.20986	0.625	0.80722	P	0.0	D	0.76494	0.999	D	0.64877	0.93	T	0.53265	-0.8463	8	0.62326	D	0.03	.	7.81	0.29226	0.0:1.0:0.0:0.0	.	2820	Q685J3	MUC17_HUMAN	M	2820	ENSP00000302716:T2820M	ENSP00000302716:T2820M	T	+	2	0	MUC17	100469876	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.791000	0.26915	0.801000	0.34066	0.134000	0.15878	ACG	A|0.000;C|0.960;T|0.040	0.040	strong		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
LPP	4026	hgsc.bcm.edu	37	3	188326955	188326955	+	Missense_Mutation	SNP	A	A	G	rs35417432	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:188326955A>G	ENST00000312675.4	+	6	682	c.436A>G	c.(436-438)Act>Gct	p.T146A	LPP_ENST00000448637.1_Missense_Mutation_p.T146A|LPP_ENST00000543006.1_Missense_Mutation_p.T146A|LPP_ENST00000471917.1_3'UTR	NM_001167672.1|NM_005578.3	NP_001161144.1|NP_005569.1	Q93052	LPP_HUMAN	LIM domain containing preferred translocation partner in lipoma	146	Pro-rich.		T -> A (in dbSNP:rs35417432).		cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)		HMGA2/LPP(161)	NS(1)|breast(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		TTAGAGCTCCACTGGTTCAAC	0.388			T	"""HMGA2, MLL, C12orf9"""	"""lipoma, leukemia"""								A|||	270	0.0539137	0.1899	0.0231	5008	,	,		16335	0.0		0.003	False		,,,				2504	0.0				p.T146A		Atlas-SNP	.		Dom	yes		3	3q28	4026	LIM domain containing preferred translocation partner in lipoma		"""L, M"""	.	LPP	72	.	0			c.A436G						PASS	.	A	ALA/THR,ALA/THR,ALA/THR	779,3627	315.2+/-294.0	66,647,1490	96.0	96.0	96.0		436,436,436	-2.5	0.2	3	dbSNP_126	96	10,8590	5.0+/-18.6	0,10,4290	yes	missense,missense,missense	LPP	NM_001167671.1,NM_001167672.1,NM_005578.3	58,58,58	66,657,5780	GG,GA,AA		0.1163,17.6804,6.0664	benign,benign,benign	146/613,146/466,146/613	188326955	789,12217	2203	4300	6503	SO:0001583	missense	4026	exon6			AGCTCCACTGGTT	AL833171	CCDS3291.1	3q27-q28	2004-03-02	2002-01-14		ENSG00000145012	ENSG00000145012			6679	protein-coding gene	gene with protein product		600700	"""LIM domain-containing preferred translocation partner in lipoma"""			8812423	Standard	XM_005247453		Approved		uc003frs.2	Q93052	OTTHUMG00000156387	ENST00000312675.4:c.436A>G	3.37:g.188326955A>G	ENSP00000318089:p.Thr146Ala	86.0	0.0	0		109.0	46.0	0.422018	NM_005578	A1L4L6|D3DNV6|Q8NFX5	Missense_Mutation	SNP	ENST00000312675.4	37	CCDS3291.1	99	0.04532967032967033	89	0.18089430894308944	9	0.024861878453038673	0	0.0	1	0.0013192612137203166	A	3.408	-0.120818	0.06838	0.176804	0.001163	ENSG00000145012	ENST00000448637;ENST00000416784;ENST00000312675;ENST00000543006	T;T;T;T	0.52057	2.06;1.09;0.68;0.68	5.64	-2.45	0.06481	.	0.868823	0.09583	N	0.782522	T	0.00039	0.0001	N	0.11560	0.145	0.80722	P	0.0	B;B;B	0.15930	0.015;0.0;0.0	B;B;B	0.10450	0.005;0.002;0.0	T	0.35001	-0.9806	9	0.07482	T	0.82	.	15.6517	0.77099	0.2645:0.0:0.7355:0.0	rs35417432	146;146;146	B7Z8W0;C9JUT4;Q93052	.;.;LPP_HUMAN	A	146	ENSP00000393602:T146A;ENSP00000410340:T146A;ENSP00000318089:T146A;ENSP00000438891:T146A	ENSP00000318089:T146A	T	+	1	0	LPP	189809649	0.000000	0.05858	0.211000	0.23655	0.179000	0.23085	-0.288000	0.08377	-0.925000	0.03775	0.533000	0.62120	ACT	A|0.939;G|0.061	0.061	strong		0.388	LPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344030.1	NM_005578	
C10orf12	26148	hgsc.bcm.edu	37	10	98742088	98742088	+	Missense_Mutation	SNP	T	T	C	rs7082522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:98742088T>C	ENST00000286067.2	+	1	1048	c.941T>C	c.(940-942)cTt>cCt	p.L314P		NM_015652.2	NP_056467.2	Q8N655	CJ012_HUMAN	chromosome 10 open reading frame 12	314			L -> P (in dbSNP:rs7082522).							NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(3)|prostate(2)|skin(2)|stomach(4)	45		Colorectal(252;0.172)		Epithelial(162;6.35e-09)|all cancers(201;3.21e-07)		CCTGCTCACCTTCCTGAAGAG	0.572													T|||	42	0.00838658	0.0234	0.0101	5008	,	,		19340	0.0		0.004	False		,,,				2504	0.0				p.L314P		Atlas-SNP	.											.	C10orf12	94	.	0			c.T941C						PASS	.	T	PRO/LEU	82,4324	69.8+/-107.6	0,82,2121	66.0	67.0	67.0		941	2.5	0.1	10	dbSNP_116	67	19,8581	12.6+/-44.7	0,19,4281	yes	missense	C10orf12	NM_015652.2	98	0,101,6402	CC,CT,TT		0.2209,1.8611,0.7766	benign	314/1248	98742088	101,12905	2203	4300	6503	SO:0001583	missense	26148	exon1			CTCACCTTCCTGA	BC024315	CCDS7452.1	10q24.2	2014-03-11			ENSG00000155640	ENSG00000155640			23420	protein-coding gene	gene with protein product						24550272	Standard	NM_015652		Approved	DKFZP564P1916, FLJ13022	uc001kmv.3	Q8N655	OTTHUMG00000018840	ENST00000286067.2:c.941T>C	10.37:g.98742088T>C	ENSP00000286067:p.Leu314Pro	96.0	0.0	0		82.0	36.0	0.439024	NM_015652	Q9H945|Q9Y457	Missense_Mutation	SNP	ENST00000286067.2	37	CCDS7452.1	9	0.004120879120879121	5	0.01016260162601626	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	T	6.674	0.492926	0.12702	0.018611	0.002209	ENSG00000155640	ENST00000286067;ENST00000539886	T	0.08720	3.06	6.05	2.49	0.30216	.	0.311072	0.22801	N	0.055461	T	0.02156	0.0067	N	0.14661	0.345	0.20638	N	0.999875	B;B	0.17038	0.006;0.02	B;B	0.16722	0.009;0.016	T	0.40850	-0.9541	10	0.33141	T	0.24	0.0135	8.0912	0.30801	0.0:0.3649:0.0:0.6351	rs7082522;rs7082522	148;314	A0PJI9;Q8N655	.;CJ012_HUMAN	P	314;148	ENSP00000286067:L314P	ENSP00000286067:L314P	L	+	2	0	C10orf12	98732078	0.000000	0.05858	0.055000	0.19348	0.931000	0.56810	-0.378000	0.07446	0.189000	0.20188	0.533000	0.62120	CTT	T|0.994;C|0.006	0.006	strong		0.572	C10orf12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049627.1	NM_015652	
PPP1R10	5514	hgsc.bcm.edu	37	6	30570374	30570374	+	Silent	SNP	G	G	A	rs35689098	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30570374G>A	ENST00000376511.2	-	19	2604	c.2052C>T	c.(2050-2052)ggC>ggT	p.G684G		NM_002714.3	NP_002705.2	Q96QC0	PP1RA_HUMAN	protein phosphatase 1, regulatory subunit 10	684	Gly-rich.				protein import into nucleus (GO:0006606)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|nucleus (GO:0005634)|PTW/PP1 phosphatase complex (GO:0072357)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein phosphatase inhibitor activity (GO:0004864)			cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(3)|skin(1)	25						GCATAGGGTCGCCCGGGCCAT	0.677													G|||	138	0.0275559	0.0915	0.0159	5008	,	,		15303	0.001		0.001	False		,,,				2504	0.0041				p.G684G		Atlas-SNP	.											.	PPP1R10	60	.	0			c.C2052T						PASS	.	G		164,2534		1,162,1186	7.0	10.0	9.0		2052	-0.1	0.9	6	dbSNP_126	9	11,5013		0,11,2501	no	coding-synonymous	PPP1R10	NM_002714.2		1,173,3687	AA,AG,GG		0.2189,6.0786,2.2663		684/941	30570374	175,7547	1349	2512	3861	SO:0001819	synonymous_variant	5514	exon19			AGGGTCGCCCGGG	Y13247	CCDS4681.1	6p21.3	2012-04-17	2011-10-04		ENSG00000204569	ENSG00000204569		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9284	protein-coding gene	gene with protein product	"""phosphatase 1 nuclear targeting subunit"", ""HLA-C associated transcript 53"""	603771	"""protein phosphatase 1, regulatory (inhibitor) subunit 10"""			9461602, 9784381	Standard	NM_002714		Approved	PNUTS, FB19, CAT53, p99	uc003nqn.2	Q96QC0	OTTHUMG00000031259	ENST00000376511.2:c.2052C>T	6.37:g.30570374G>A		20.0	0.0	0		26.0	13.0	0.5	NM_002714	O00405	Silent	SNP	ENST00000376511.2	37	CCDS4681.1																																																																																			G|0.970;A|0.030	0.030	strong		0.677	PPP1R10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076556.2	NM_002714	
KRTAP26-1	388818	hgsc.bcm.edu	37	21	31691993	31691993	+	Missense_Mutation	SNP	C	C	T	rs77018583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31691993C>T	ENST00000360542.3	-	1	614	c.361G>A	c.(361-363)Ggc>Agc	p.G121S		NM_203405.1	NP_981950.1	Q6PEX3	KR261_HUMAN	keratin associated protein 26-1	121						intermediate filament (GO:0005882)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16						GGACGACAGCCGCTGGACACA	0.547													C|||	50	0.00998403	0.0325	0.0029	5008	,	,		20333	0.004		0.0	False		,,,				2504	0.001				p.G121S		Atlas-SNP	.											KRTAP26-1,colon,carcinoma,+1,1	KRTAP26-1	58	1	0			c.G361A						PASS	.	C	SER/GLY	138,4268	98.9+/-137.6	0,138,2065	116.0	119.0	118.0		361	-5.4	0.0	21	dbSNP_131	118	0,8600		0,0,4300	yes	missense	KRTAP26-1	NM_203405.1	56	0,138,6365	TT,TC,CC		0.0,3.1321,1.061	benign	121/211	31691993	138,12868	2203	4300	6503	SO:0001583	missense	388818	exon1			GACAGCCGCTGGA	AB096936	CCDS13588.1	21q22.11	2007-11-23			ENSG00000197683	ENSG00000197683		"""Keratin associated proteins"""	33760	protein-coding gene	gene with protein product							Standard	NM_203405		Approved		uc002ynw.3	Q6PEX3	OTTHUMG00000057766	ENST00000360542.3:c.361G>A	21.37:g.31691993C>T	ENSP00000353742:p.Gly121Ser	106.0	0.0	0		150.0	77.0	0.513333	NM_203405	B0RZD3	Missense_Mutation	SNP	ENST00000360542.3	37	CCDS13588.1	20	0.009157509157509158	16	0.032520325203252036	2	0.0055248618784530384	2	0.0034965034965034965	0	0.0	C	0.014	-1.585008	0.00872	0.031321	0.0	ENSG00000197683	ENST00000360542	T	0.01902	4.57	5.21	-5.39	0.02664	.	1.102650	0.07134	N	0.846044	T	0.00356	0.0011	N	0.04132	-0.27	0.09310	N	1	B	0.14438	0.01	B	0.09377	0.004	T	0.48747	-0.9008	10	0.16896	T	0.51	0.1935	1.5488	0.02571	0.1297:0.3086:0.2657:0.2961	.	121	Q6PEX3	KR261_HUMAN	S	121	ENSP00000353742:G121S	ENSP00000353742:G121S	G	-	1	0	KRTAP26-1	30613864	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-1.339000	0.02652	-0.734000	0.04843	-0.290000	0.09829	GGC	C|0.989;T|0.011	0.011	strong		0.547	KRTAP26-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128218.1	NM_203405	
MUC4	4585	hgsc.bcm.edu	37	3	195515126	195515126	+	Missense_Mutation	SNP	C	C	A	rs529638482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195515126C>A	ENST00000463781.3	-	2	3784	c.3325G>T	c.(3325-3327)Gac>Tac	p.D1109Y	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D1109Y	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	540					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGAAGTGTCGGTGACAGGA	0.577													.|||	144	0.028754	0.0983	0.013	5008	,	,		17471	0.0		0.002	False		,,,				2504	0.0031				p.D1109Y		Atlas-SNP	.											.	MUC4	1505	.	0			c.G3325T						PASS	.						9.0	6.0	7.0					3																	195515126		654	1463	2117	SO:0001583	missense	4585	exon2			AAGTGTCGGTGAC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3325G>T	3.37:g.195515126C>A	ENSP00000417498:p.Asp1109Tyr	167.0	0.0	0		353.0	37.0	0.104816	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	.	.	.	.	.	.	.	.	.	.	-	3.781	-0.045714	0.07452	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33216	1.43;1.42	0.814	-1.63	0.08345	.	.	.	.	.	T	0.28863	0.0716	N	0.19112	0.55	0.09310	N	1	D	0.69078	0.997	P	0.62560	0.904	T	0.17837	-1.0356	8	.	.	.	.	5.2224	0.15375	0.0:0.4002:0.0:0.5998	.	1109	E7ESK3	.	Y	1109	ENSP00000417498:D1109Y;ENSP00000420243:D1109Y	.	D	-	1	0	MUC4	196999521	0.000000	0.05858	0.001000	0.08648	0.296000	0.27459	-0.592000	0.05747	-0.657000	0.05373	0.064000	0.15345	GAC	.	.	none		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
GRB10	2887	hgsc.bcm.edu	37	7	50672017	50672017	+	Silent	SNP	G	G	A	rs200886440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:50672017G>A	ENST00000401949.1	-	16	1916	c.1447C>T	c.(1447-1449)Cta>Tta	p.L483L	GRB10_ENST00000402578.1_Silent_p.L425L|GRB10_ENST00000335866.3_Silent_p.L425L|GRB10_ENST00000439599.1_Silent_p.L477L|GRB10_ENST00000402497.1_Silent_p.L425L|GRB10_ENST00000406641.1_Silent_p.L425L|GRB10_ENST00000403097.1_Silent_p.L477L|GRB10_ENST00000357271.5_Silent_p.L437L|GRB10_ENST00000398812.2_Silent_p.L483L|GRB10_ENST00000407526.1_Silent_p.L425L|GRB10_ENST00000398810.2_Silent_p.L425L			Q13322	GRB10_HUMAN	growth factor receptor-bound protein 10	483					insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of phosphorylation (GO:0042326)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of phosphorylation (GO:0042327)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|response to insulin (GO:0032868)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(19)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	41	Glioma(55;0.08)|all_neural(89;0.245)					CCTGTACTTAGGGTAGAAGGG	0.493									Russell-Silver syndrome				G|||	3	0.000599042	0.0023	0.0	5008	,	,		21445	0.0		0.0	False		,,,				2504	0.0				p.L483L		Atlas-SNP	.											.	GRB10	155	.	0			c.C1447T						PASS	.	G	,,,	2,4002		0,2,2000	140.0	141.0	141.0		1309,1273,1273,1447	1.1	0.3	7		141	0,8338		0,0,4169	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GRB10	NM_001001549.2,NM_001001550.2,NM_001001555.2,NM_005311.4	,,,	0,2,6169	AA,AG,GG		0.0,0.05,0.0162	,,,	437/549,425/537,425/537,483/595	50672017	2,12340	2002	4169	6171	SO:0001819	synonymous_variant	2887	exon13	Familial Cancer Database	Silver-Russell Dwarfism, Silver-Russell syndrome, SRS, Russel-Silver Dwarfism	TACTTAGGGTAGA		CCDS43582.1, CCDS43583.1, CCDS47586.1	7p12.2	2013-02-14			ENSG00000106070	ENSG00000106070		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	4564	protein-coding gene	gene with protein product		601523					Standard	NM_005311		Approved		uc003tpi.2	Q13322	OTTHUMG00000150622	ENST00000401949.1:c.1447C>T	7.37:g.50672017G>A		115.0	0.0	0		133.0	63.0	0.473684	NM_005311	A4D258|A7VJ95|A8K0E6|D3DVM9|O00427|O00701|O75222|Q92606|Q92907|Q92948	Silent	SNP	ENST00000401949.1	37	CCDS43582.1																																																																																			G|0.999;A|0.001	0.001	strong		0.493	GRB10-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319157.1		
GPR110	266977	hgsc.bcm.edu	37	6	46976924	46976924	+	Silent	SNP	G	G	A	rs45511696	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:46976924G>A	ENST00000371253.2	-	11	2462	c.2247C>T	c.(2245-2247)gtC>gtT	p.V749V	GPR110_ENST00000449332.2_5'UTR|GPR110_ENST00000283297.5_Silent_p.V552V	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	749					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)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	29						CCAGTGCAGGGACAACAAAAG	0.493													G|||	186	0.0371406	0.0787	0.0389	5008	,	,		22252	0.0		0.0447	False		,,,				2504	0.0102				p.V749V		Atlas-SNP	.											.	GPR110	102	.	0			c.C2247T						PASS	.	G		375,4031	188.5+/-214.9	14,347,1842	92.0	97.0	95.0		2247	1.2	0.5	6	dbSNP_127	95	328,8272	115.3+/-175.2	7,314,3979	no	coding-synonymous	GPR110	NM_153840.2		21,661,5821	AA,AG,GG		3.814,8.5111,5.4052		749/911	46976924	703,12303	2203	4300	6503	SO:0001819	synonymous_variant	266977	exon11			TGCAGGGACAACA	AB083618	CCDS4920.1, CCDS34471.1	6p21.1	2014-08-08			ENSG00000153292	ENSG00000153292		"""-"", ""GPCR / Class B : Orphans"""	18990	protein-coding gene	gene with protein product						12435584, 14623098	Standard	XM_005249006		Approved	hGPCR36, PGR19	uc003oyt.3	Q5T601	OTTHUMG00000014795	ENST00000371253.2:c.2247C>T	6.37:g.46976924G>A		126.0	0.0	0		135.0	69.0	0.511111	NM_153840	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Silent	SNP	ENST00000371253.2	37	CCDS34471.1																																																																																			G|0.952;A|0.048	0.048	strong		0.493	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840	
KANK2	25959	hgsc.bcm.edu	37	19	11289129	11289129	+	Intron	SNP	G	G	A	rs114414326	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11289129G>A	ENST00000586659.1	-	6	1732				KANK2_ENST00000355150.5_Intron|KANK2_ENST00000589894.1_Intron|KANK2_ENST00000432929.2_Missense_Mutation_p.P479L|KANK2_ENST00000589359.1_Missense_Mutation_p.P479L			Q63ZY3	KANK2_HUMAN	KN motif and ankyrin repeat domains 2						apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				endometrium(2)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						CCCGCCTGGAGGGGAGGACAG	0.677													G|||	79	0.0157748	0.0575	0.0043	5008	,	,		11402	0.0		0.0	False		,,,				2504	0.0				p.P479L		Atlas-SNP	.											.	KANK2	47	.	0			c.C1436T						PASS	.	G	,LEU/PRO	191,4215		4,183,2016	20.0	25.0	23.0		,1436	4.4	0.0	19	dbSNP_132	23	4,8590		0,4,4293	yes	intron,missense	KANK2	NM_001136191.2,NM_015493.6	,98	4,187,6309	AA,AG,GG		0.0465,4.335,1.5	,	,479/860	11289129	195,12805	2203	4297	6500	SO:0001627	intron_variant	25959	exon4			CCTGGAGGGGAGG	AK000011	CCDS12255.1, CCDS54219.1	19p13.2	2013-01-10	2008-01-29	2008-01-29		ENSG00000197256		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	29300	protein-coding gene	gene with protein product		614610	"""matrix-remodelling associated 3"", ""ankyrin repeat domain 25"""	MXRA3, ANKRD25		10819331, 17996375, 19554261	Standard	NM_015493		Approved	KIAA1518	uc002mqm.3	Q63ZY3		ENST00000586659.1:c.1418-6C>T	19.37:g.11289129G>A		64.0	0.0	0		80.0	39.0	0.4875	NM_015493	B0I1P4|Q3KQZ3|Q6GUF5|Q9H8S4|Q9NUP0|Q9P210	Missense_Mutation	SNP	ENST00000586659.1	37	CCDS12255.1	30	0.013736263736263736	26	0.052845528455284556	4	0.011049723756906077	0	0.0	0	0.0	G	15.34	2.803527	0.50315	0.04335	4.65E-4	ENSG00000197256	ENST00000432929	T	0.34472	1.36	5.45	4.39	0.52855	.	.	.	.	.	T	0.04092	0.0114	.	.	.	0.26307	N	0.977885	P	0.38827	0.649	B	0.32677	0.15	T	0.01776	-1.1276	8	0.31617	T	0.26	.	11.8895	0.52620	0.0841:0.0:0.9159:0.0	.	479	Q63ZY3-2	.	L	479	ENSP00000395650:P479L	ENSP00000395650:P479L	P	-	2	0	KANK2	11150129	0.745000	0.28261	0.002000	0.10522	0.180000	0.23129	1.956000	0.40382	1.283000	0.44513	0.655000	0.94253	CCT	G|0.990;A|0.010	0.010	strong		0.677	KANK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453066.2	NM_015493	
GAPVD1	26130	hgsc.bcm.edu	37	9	128099784	128099784	+	Missense_Mutation	SNP	C	C	T	rs62637637	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:128099784C>T	ENST00000495955.1	+	17	3081	c.2791C>T	c.(2791-2793)Cca>Tca	p.P931S	GAPVD1_ENST00000297933.6_Missense_Mutation_p.P931S|GAPVD1_ENST00000312123.9_Missense_Mutation_p.P910S|GAPVD1_ENST00000394105.2_Missense_Mutation_p.P958S|GAPVD1_ENST00000394104.2_Missense_Mutation_p.P931S|GAPVD1_ENST00000470056.1_Missense_Mutation_p.P931S|GAPVD1_ENST00000394083.2_Missense_Mutation_p.P910S|GAPVD1_ENST00000265956.4_Missense_Mutation_p.P905S			Q14C86	GAPD1_HUMAN	GTPase activating protein and VPS9 domains 1	931				P -> S (in Ref. 6; AAH13635). {ECO:0000305}.	endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of protein transport (GO:0051223)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)	cytosol (GO:0005829)|endosome (GO:0005768)|membrane (GO:0016020)	GTPase activating protein binding (GO:0032794)|GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44						AGAACTCCCTCCAGCTGCAGC	0.532													C|||	30	0.00599042	0.0219	0.0014	5008	,	,		18533	0.0		0.0	False		,,,				2504	0.0				p.P958S		Atlas-SNP	.											.	GAPVD1	124	.	0			c.C2872T						PASS	.	C	SER/PRO	68,4338	62.9+/-100.1	1,66,2136	70.0	69.0	70.0		2872	5.3	0.9	9	dbSNP_129	70	0,8600		0,0,4300	yes	missense	GAPVD1	NM_015635.2	74	1,66,6436	TT,TC,CC		0.0,1.5433,0.5228	benign	958/1488	128099784	68,12938	2203	4300	6503	SO:0001583	missense	26130	exon16			CTCCCTCCAGCTG		CCDS65130.1, CCDS65131.1, CCDS65132.1	9q34.11	2008-02-05			ENSG00000165219	ENSG00000165219			23375	protein-coding gene	gene with protein product		611714					Standard	XM_005251901		Approved	DKFZP434C212, KIAA1521	uc004bpr.3	Q14C86	OTTHUMG00000020678	ENST00000495955.1:c.2791C>T	9.37:g.128099784C>T	ENSP00000419063:p.Pro931Ser	119.0	0.0	0		136.0	33.0	0.242647	NM_015635	A8MYK3|B0QZ62|B0QZ63|B0QZ64|Q14C76|Q2Q1W1|Q8ND92|Q8WU86|Q96CZ4|Q9NXQ1|Q9P207|Q9Y4N0	Missense_Mutation	SNP	ENST00000495955.1	37		14|14	0.00641025641025641|0.00641025641025641	13|13	0.026422764227642278|0.026422764227642278	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	C|C	8.329|8.329	0.826071|0.826071	0.16749|0.16749	0.015433|0.015433	0.0|0.0	ENSG00000165219|ENSG00000165219	ENST00000470056;ENST00000394105;ENST00000394104;ENST00000265956;ENST00000394083;ENST00000495955;ENST00000467750;ENST00000297933;ENST00000312123|ENST00000436712	.|.	.|.	.|.	6.17|6.17	5.26|5.26	0.73747|0.73747	.|.	0.267957|.	0.43416|.	D|.	0.000568|.	T|T	0.15955|0.15955	0.0384|0.0384	N|N	0.19112|0.19112	0.55|0.55	0.32006|0.32006	N|N	0.602735|0.602735	B;B;B;B;B;B|.	0.15930|.	0.002;0.002;0.001;0.001;0.001;0.015|.	B;B;B;B;B;B|.	0.12837|.	0.006;0.004;0.004;0.004;0.004;0.008|.	T|T	0.35895|0.35895	-0.9770|-0.9770	9|5	0.15066|.	T|.	0.55|.	.|.	11.4079|11.4079	0.49908|0.49908	0.1307:0.6166:0.2527:0.0|0.1307:0.6166:0.2527:0.0	rs62637637|rs62637637	905;931;931;910;931;958|.	Q14C86-5;Q14C86;Q14C86-3;Q14C86-4;Q14C86-2;Q14C86-6|.	.;GAPD1_HUMAN;.;.;.;.|.	S|F	931;958;931;905;910;931;931;931;910|767	.|.	ENSP00000265956:P905S|.	P|S	+|+	1|2	0|0	GAPVD1|GAPVD1	127139605|127139605	0.914000|0.914000	0.31030|0.31030	0.948000|0.948000	0.38648|0.38648	0.162000|0.162000	0.22319|0.22319	2.148000|2.148000	0.42235|0.42235	1.586000|1.586000	0.49944|0.49944	0.655000|0.655000	0.94253|0.94253	CCA|TCC	C|0.993;T|0.007	0.007	strong		0.532	GAPVD1-014	KNOWN	alternative_5_UTR|basic	protein_coding	protein_coding	OTTHUMT00000355644.1		
NRIP1	8204	hgsc.bcm.edu	37	21	16338814	16338814	+	Missense_Mutation	SNP	T	T	C	rs9975169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:16338814T>C	ENST00000400202.1	-	3	2412	c.1700A>G	c.(1699-1701)aAt>aGt	p.N567S	AF127577.10_ENST00000446301.1_RNA|NRIP1_ENST00000318948.4_Missense_Mutation_p.N567S|NRIP1_ENST00000400199.1_Missense_Mutation_p.N567S			P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	567	Repression domain 2.		N -> S (in dbSNP:rs9975169).		androgen receptor signaling pathway (GO:0030521)|lipid storage (GO:0019915)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ovarian follicle rupture (GO:0001543)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|glucocorticoid receptor binding (GO:0035259)|nuclear hormone receptor binding (GO:0035257)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			cervix(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(13)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	39				Epithelial(23;1.19e-05)|all cancers(11;4.64e-05)|COAD - Colon adenocarcinoma(22;0.000232)|Colorectal(24;0.0006)|OV - Ovarian serous cystadenocarcinoma(11;0.00418)|Lung(58;0.199)|LUSC - Lung squamous cell carcinoma(23;0.24)		TTGAGAGAGATTGATGGGAGA	0.443													T|||	116	0.0231629	0.0809	0.013	5008	,	,		20094	0.0		0.0	False		,,,				2504	0.0				p.N567S		Atlas-SNP	.											.	NRIP1	103	.	0			c.A1700G						PASS	.	T	SER/ASN	356,4050	183.6+/-211.2	17,322,1864	240.0	238.0	238.0		1700	6.0	1.0	21	dbSNP_119	238	1,8599	1.2+/-3.3	0,1,4299	yes	missense	NRIP1	NM_003489.3	46	17,323,6163	CC,CT,TT		0.0116,8.0799,2.7449	probably-damaging	567/1159	16338814	357,12649	2203	4300	6503	SO:0001583	missense	8204	exon4			GAGAGATTGATGG	X84373	CCDS13568.1	21q11.2	2008-07-31			ENSG00000180530	ENSG00000180530			8001	protein-coding gene	gene with protein product	"""receptor interacting protein 140"", ""nuclear factor RIP140"""	602490				7641693, 9521594	Standard	NM_003489		Approved	RIP140	uc002yjx.2	P48552	OTTHUMG00000074323	ENST00000400202.1:c.1700A>G	21.37:g.16338814T>C	ENSP00000383063:p.Asn567Ser	223.0	1.0	0.00448431		232.0	118.0	0.508621	NM_003489	Q8IWE8	Missense_Mutation	SNP	ENST00000400202.1	37	CCDS13568.1	39	0.017857142857142856	35	0.07113821138211382	4	0.011049723756906077	0	0.0	0	0.0	T	17.23	3.337615	0.60963	0.080799	1.16E-4	ENSG00000180530	ENST00000400199;ENST00000400202;ENST00000318948	T;T;T	0.20200	2.09;2.09;2.09	6.02	6.02	0.97574	.	0.204155	0.42172	D	0.000750	T	0.02455	0.0075	L	0.53249	1.67	0.45490	D	0.998455	D	0.59767	0.986	P	0.58520	0.84	T	0.00019	-1.2359	10	0.62326	D	0.03	-19.3161	16.5446	0.84426	0.0:0.0:0.0:1.0	rs9975169;rs52814028;rs9975169	567	P48552	NRIP1_HUMAN	S	567	ENSP00000383060:N567S;ENSP00000383063:N567S;ENSP00000327213:N567S	ENSP00000327213:N567S	N	-	2	0	NRIP1	15260685	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.714000	0.61902	2.311000	0.77944	0.533000	0.62120	AAT	T|0.973;C|0.027	0.027	strong		0.443	NRIP1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157926.1	NM_003489	
PTPRN2	5799	hgsc.bcm.edu	37	7	157931151	157931151	+	Missense_Mutation	SNP	C	C	G	rs150508509	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:157931151C>G	ENST00000389418.4	-	7	976	c.967G>C	c.(967-969)Ggc>Cgc	p.G323R	PTPRN2_ENST00000409483.1_Missense_Mutation_p.G285R|PTPRN2_ENST00000389416.4_Missense_Mutation_p.G306R|PTPRN2_ENST00000404321.2_Missense_Mutation_p.G346R|PTPRN2_ENST00000389413.3_Missense_Mutation_p.G323R	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	323				G -> R (in Ref. 2; CAA69880). {ECO:0000305}.	negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		CCACTCAGGCCCCTCACCTCA	0.632													C|||	93	0.0185703	0.053	0.0058	5008	,	,		19317	0.0		0.0	False		,,,				2504	0.0194				p.G323R		Atlas-SNP	.											.	PTPRN2	243	.	0			c.G967C						PASS	.		ARG/GLY,ARG/GLY,ARG/GLY	217,4189	127.0+/-164.0	3,211,1989	62.0	64.0	64.0		967,916,967	-4.9	0.0	7	dbSNP_134	64	1,8599		0,1,4299	yes	missense,missense,missense	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	125,125,125	3,212,6288	GG,GC,CC		0.0116,4.9251,1.6761	benign,benign,benign	323/1016,306/999,323/987	157931151	218,12788	2203	4300	6503	SO:0001583	missense	5799	exon7			TCAGGCCCCTCAC	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.967G>C	7.37:g.157931151C>G	ENSP00000374069:p.Gly323Arg	93.0	0.0	0		101.0	35.0	0.346535	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	37	CCDS5947.1	29	0.013278388278388278	26	0.052845528455284556	3	0.008287292817679558	0	0.0	0	0.0	C	3.517	-0.098660	0.07010	0.049251	1.16E-4	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.02552	4.25;4.27;4.26;4.26;4.25	4.11	-4.94	0.03057	.	.	.	.	.	T	0.00271	0.0008	N	0.12746	0.255	0.09310	N	1	B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.001;0.0;0.001;0.0;0.0	T	0.48269	-0.9050	9	0.15499	T	0.54	.	5.6925	0.17837	0.0:0.3821:0.1927:0.4252	.	346;285;323;306;323	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	R	285;323;306;323;346	ENSP00000387114:G285R;ENSP00000374064:G323R;ENSP00000374067:G306R;ENSP00000374069:G323R;ENSP00000385464:G346R	ENSP00000374064:G323R	G	-	1	0	PTPRN2	157623912	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.128000	0.15810	-1.148000	0.02847	-0.312000	0.09012	GGC	C|0.981;G|0.019	0.019	strong		0.632	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
TTN	7273	hgsc.bcm.edu	37	2	179598399	179598399	+	Silent	SNP	C	C	T	rs72648932	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179598399C>T	ENST00000591111.1	-	51	14990	c.14766G>A	c.(14764-14766)acG>acA	p.T4922T	TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Silent_p.T3995T|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Silent_p.T5239T			Q8WZ42	TITIN_HUMAN	titin	12314	Ig-like 29.				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)			CAGCCAGGCACGTGTATTTGC	0.378													C|||	120	0.0239617	0.0877	0.0058	5008	,	,		20602	0.0		0.0	False		,,,				2504	0.0				p.T5239T		Atlas-SNP	.											.	TTN	18412	.	0			c.G15717A						PASS	.	C	,,,	223,3501		8,207,1647	136.0	130.0	132.0		,11985,,	-7.5	1.0	2	dbSNP_130	132	7,8189		0,7,4091	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	8,214,5738	TT,TC,CC		0.0854,5.9882,1.9295	,,,	,3995/33424,,	179598399	230,11690	1862	4098	5960	SO:0001819	synonymous_variant	7273	exon53			CAGGCACGTGTAT	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.14766G>A	2.37:g.179598399C>T		125.0	0.0	0		153.0	82.0	0.535948	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																																																																																				C|0.980;T|0.020	0.020	strong		0.378	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ZNF510	22869	hgsc.bcm.edu	37	9	99522508	99522508	+	Missense_Mutation	SNP	C	C	T	rs61731162	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:99522508C>T	ENST00000375231.1	-	6	1254	c.604G>A	c.(604-606)Ggt>Agt	p.G202S	ZNF510_ENST00000223428.4_Missense_Mutation_p.G202S|ZNF510_ENST00000472201.1_5'Flank			Q9Y2H8	ZN510_HUMAN	zinc finger protein 510	202					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|stomach(1)|urinary_tract(1)	21		Acute lymphoblastic leukemia(62;0.0527)				TTACCGCAACCTATTTTCTTT	0.294													C|||	172	0.034345	0.1263	0.0072	5008	,	,		17618	0.0		0.0	False		,,,				2504	0.0				p.G202S		Atlas-SNP	.											.	ZNF510	59	.	0			c.G604A						PASS	.	C	SER/GLY	441,3957	195.0+/-219.7	22,397,1780	39.0	44.0	42.0		604	0.0	0.0	9	dbSNP_129	42	2,8588	2.2+/-6.3	0,2,4293	yes	missense	ZNF510	NM_014930.1	56	22,399,6073	TT,TC,CC		0.0233,10.0273,3.4108	benign	202/684	99522508	443,12545	2199	4295	6494	SO:0001583	missense	22869	exon6			CGCAACCTATTTT	AB023189	CCDS35074.1	9q22.33	2013-01-08			ENSG00000081386	ENSG00000081386		"""Zinc fingers, C2H2-type"", ""-"""	29161	protein-coding gene	gene with protein product						10231032	Standard	XM_005251807		Approved	KIAA0972	uc004awn.1	Q9Y2H8	OTTHUMG00000020303	ENST00000375231.1:c.604G>A	9.37:g.99522508C>T	ENSP00000364379:p.Gly202Ser	116.0	0.0	0		108.0	67.0	0.62037	NM_014930	Q5SZP5	Missense_Mutation	SNP	ENST00000375231.1	37	CCDS35074.1	53	0.024267399267399268	50	0.1016260162601626	3	0.008287292817679558	0	0.0	0	0.0	c	10.85	1.467776	0.26335	0.100273	2.33E-4	ENSG00000081386	ENST00000375231;ENST00000223428	T;T	0.05139	3.49;3.49	3.02	0.0252	0.14144	.	.	.	.	.	T	0.00109	0.0003	N	0.12569	0.235	0.09310	N	1	B	0.26002	0.139	B	0.19946	0.027	T	0.48305	-0.9047	9	0.18710	T	0.47	.	2.8749	0.05628	0.3758:0.3954:0.0:0.2288	.	202	Q9Y2H8	ZN510_HUMAN	S	202	ENSP00000364379:G202S;ENSP00000223428:G202S	ENSP00000223428:G202S	G	-	1	0	ZNF510	98562329	0.000000	0.05858	0.001000	0.08648	0.318000	0.28184	0.101000	0.15251	0.012000	0.14892	0.655000	0.94253	GGT	C|0.973;T|0.027	0.027	strong		0.294	ZNF510-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053287.1	NM_014930	
LIPM	340654	hgsc.bcm.edu	37	10	90575251	90575251	+	Silent	SNP	T	T	C	rs61737049	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:90575251T>C	ENST00000404743.4	+	6	1016	c.849T>C	c.(847-849)aaT>aaC	p.N283N	LIPM_ENST00000539337.1_Silent_p.N243N	NM_001128215.1	NP_001121687.1	Q5VYY2	LIPM_HUMAN	lipase, family member M	283					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	hydrolase activity, acting on ester bonds (GO:0016788)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(2)|pancreas(1)|skin(1)	7						ACACCAACAATATGAACATGG	0.438													T|||	79	0.0157748	0.0575	0.0043	5008	,	,		19878	0.0		0.0	False		,,,				2504	0.0				p.N283N		Atlas-SNP	.											.	LIPM	17	.	0			c.T849C						PASS	.						145.0	117.0	125.0					10																	90575251		692	1591	2283	SO:0001819	synonymous_variant	340654	exon6			CAACAATATGAAC		CCDS44457.1	10q23.31	2008-02-04	2007-02-27	2007-02-27	ENSG00000173239	ENSG00000173239			23455	protein-coding gene	gene with protein product		613923	"""lipase-like, ab-hydrolase domain containing 3"""	LIPL3			Standard	NM_001128215		Approved	bA304I5.1	uc009xtm.1	Q5VYY2	OTTHUMG00000018698	ENST00000404743.4:c.849T>C	10.37:g.90575251T>C		98.0	0.0	0		115.0	46.0	0.4	NM_001128215	A6PVS3|B2RXK7|B5MCR3	Silent	SNP	ENST00000404743.4	37	CCDS44457.1																																																																																			T|0.985;C|0.015	0.015	strong		0.438	LIPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049261.3	XM_291663	
FLG	2312	hgsc.bcm.edu	37	1	152284576	152284576	+	Missense_Mutation	SNP	C	C	A	rs143382793	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152284576C>A	ENST00000368799.1	-	3	2821	c.2786G>T	c.(2785-2787)gGc>gTc	p.G929V	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	929	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TTGTCCCTGGCCTGCCTGTGA	0.557									Ichthyosis																												p.G929V		Atlas-SNP	.											.	FLG	900	.	0			c.G2786T						PASS	.						327.0	313.0	318.0					1																	152284576		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CCCTGGCCTGCCT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.2786G>T	1.37:g.152284576C>A	ENSP00000357789:p.Gly929Val	591.0	1.0	0.00169205		745.0	145.0	0.194631	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	-	1.719	-0.497190	0.04291	.	.	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.06528	3.29	1.17	0.0422	0.14216	.	.	.	.	.	T	0.06142	0.0159	M	0.77820	2.39	0.09310	N	1	D	0.67145	0.996	P	0.58970	0.849	T	0.24977	-1.0145	9	0.21014	T	0.42	.	4.8967	0.13753	0.0:0.6064:0.3936:0.0	.	929	P20930	FILA_HUMAN	V	929;136	ENSP00000357789:G929V	ENSP00000357789:G929V	G	-	2	0	FLG	150551200	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.167000	0.09940	0.033000	0.15463	0.479000	0.44913	GGC	C|0.993;A|0.007	0.007	strong		0.557	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
TINF2	26277	hgsc.bcm.edu	37	14	24709351	24709351	+	Silent	SNP	C	C	T	rs10141326	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24709351C>T	ENST00000267415.7	-	8	1481	c.1140G>A	c.(1138-1140)ccG>ccA	p.P380P	TINF2_ENST00000538777.1_3'UTR|TINF2_ENST00000558510.1_5'Flank|TINF2_ENST00000540705.1_Silent_p.P345P|TINF2_ENST00000558566.1_3'UTR|TINF2_ENST00000399423.4_3'UTR	NM_001099274.1	NP_001092744.1	Q9BSI4	TINF2_HUMAN	TERF1 (TRF1)-interacting nuclear factor 2	380					negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of protein ADP-ribosylation (GO:0010836)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of telomere maintenance (GO:0032206)|protein localization to chromosome (GO:0034502)|protein localization to chromosome, telomeric region (GO:0070198)|telomere assembly (GO:0032202)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)	chromosome, telomeric region (GO:0000781)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinucleolar chromocenter (GO:0010370)	telomeric DNA binding (GO:0042162)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|prostate(1)|urinary_tract(1)	7				GBM - Glioblastoma multiforme(265;0.0185)		TGCACAGAGACGGAGGACACA	0.502									Congenital Dyskeratosis;Ataxia Pancytopenia syndrome				T|||	299	0.0597045	0.2209	0.0101	5008	,	,		21880	0.0		0.0	False		,,,				2504	0.0				p.P380P		Atlas-SNP	.											.	TINF2	61	.	0			c.G1140A						PASS	.	T	,	753,3255		77,599,1328	164.0	172.0	169.0		1140,	1.7	0.0	14	dbSNP_119	169	10,8338		0,10,4164	no	coding-synonymous,utr-3	TINF2	NM_001099274.1,NM_012461.2	,	77,609,5492	TT,TC,CC		0.1198,18.7874,6.1751	,	380/452,	24709351	763,11593	2004	4174	6178	SO:0001819	synonymous_variant	26277	exon8	Familial Cancer Database	Zinsser-Engman-Cole syndrome, Dyskeratosis Congenita;Myelocerebellar disorder	CAGAGACGGAGGA	AF195512	CCDS41936.1, CCDS41937.1	14q12	2008-07-29				ENSG00000092330			11824	protein-coding gene	gene with protein product		604319				10581025, 18252230	Standard	NM_012461		Approved	TIN2	uc001woa.4	Q9BSI4		ENST00000267415.7:c.1140G>A	14.37:g.24709351C>T		125.0	0.0	0		123.0	64.0	0.520325	NM_001099274	B3W5Q7|Q9H904|Q9UHC2	Silent	SNP	ENST00000267415.7	37	CCDS41936.1																																																																																			C|0.944;T|0.056	0.056	strong		0.502	TINF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415406.2		
TIAM2	26230	hgsc.bcm.edu	37	6	155486535	155486535	+	Missense_Mutation	SNP	A	A	G	rs62621836	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:155486535A>G	ENST00000461783.3	+	11	3626	c.2353A>G	c.(2353-2355)Ata>Gta	p.I785V	TIAM2_ENST00000318981.5_Missense_Mutation_p.I785V|TIAM2_ENST00000529824.2_Missense_Mutation_p.I785V|TIAM2_ENST00000456144.1_Missense_Mutation_p.I785V|TIAM2_ENST00000456877.2_Missense_Mutation_p.I97V|TIAM2_ENST00000528391.2_Missense_Mutation_p.I97V|TIAM2_ENST00000367174.2_Missense_Mutation_p.I137V|TIAM2_ENST00000360366.4_Missense_Mutation_p.I785V			Q8IVF5	TIAM2_HUMAN	T-cell lymphoma invasion and metastasis 2	785					apoptotic signaling pathway (GO:0097190)|cellular lipid metabolic process (GO:0044255)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cell projection (GO:0042995)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(20)|lung(21)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	65		Ovarian(120;0.196)		OV - Ovarian serous cystadenocarcinoma(155;8.1e-13)|BRCA - Breast invasive adenocarcinoma(81;0.0053)		GAGACCTTCTATAACTCAGGT	0.448													A|||	100	0.0199681	0.0719	0.0072	5008	,	,		19834	0.0		0.0	False		,,,				2504	0.0				p.I785V		Atlas-SNP	.											.	TIAM2	161	.	0			c.A2353G						PASS	.	A	VAL/ILE	301,4105	165.4+/-196.9	7,287,1909	68.0	64.0	65.0		2353	-4.4	0.0	6	dbSNP_129	65	2,8598	1.2+/-3.3	0,2,4298	yes	missense	TIAM2	NM_012454.3	29	7,289,6207	GG,GA,AA		0.0233,6.8316,2.3297	benign	785/1702	155486535	303,12703	2203	4300	6503	SO:0001583	missense	26230	exon8			CCTTCTATAACTC		CCDS34558.1, CCDS34559.1	6q25	2013-01-10			ENSG00000146426	ENSG00000146426		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11806	protein-coding gene	gene with protein product		604709				10512681	Standard	NM_012454		Approved	STEF	uc003qqe.3	Q8IVF5	OTTHUMG00000015880	ENST00000461783.3:c.2353A>G	6.37:g.155486535A>G	ENSP00000437188:p.Ile785Val	96.0	0.0	0		114.0	59.0	0.517544	NM_012454	B2RP56|C9JZV2|Q6NXN9|Q6ZUP9|Q9UFG6|Q9UKV9|Q9UKW0	Missense_Mutation	SNP	ENST00000461783.3	37	CCDS34558.1	21	0.009615384615384616	20	0.04065040650406504	1	0.0027624309392265192	0	0.0	0	0.0	A	10.77	1.443893	0.25987	0.068316	2.33E-4	ENSG00000146426	ENST00000461783;ENST00000528928;ENST00000528535;ENST00000456144;ENST00000318981;ENST00000367174;ENST00000360366;ENST00000529824;ENST00000456877;ENST00000528391	T;T;T;T;T;T;T;T;T	0.06142	3.48;3.39;3.44;3.48;3.4;3.57;3.44;3.34;3.4	5.01	-4.42	0.03579	.	0.494314	0.23646	N	0.045965	T	0.01558	0.0050	M	0.61703	1.905	0.20196	N	0.999928	B;B;B;B	0.10296	0.0;0.003;0.003;0.002	B;B;B;B	0.12837	0.008;0.006;0.003;0.003	T	0.48670	-0.9015	10	0.17832	T	0.49	.	6.285	0.21029	0.3957:0.2475:0.3568:0.0	rs62621836	97;785;785;785	E9PKT1;Q8IVF5-2;Q8IVF5-5;Q8IVF5	.;.;.;TIAM2_HUMAN	V	785;1031;785;785;785;137;785;785;97;97	ENSP00000437188:I785V;ENSP00000434901:I785V;ENSP00000407746:I785V;ENSP00000327315:I785V;ENSP00000356142:I137V;ENSP00000353528:I785V;ENSP00000433348:I785V;ENSP00000407183:I97V;ENSP00000435335:I97V	ENSP00000327315:I785V	I	+	1	0	TIAM2	155528227	0.000000	0.05858	0.010000	0.14722	0.881000	0.50899	-0.215000	0.09279	-1.006000	0.03412	-0.274000	0.10170	ATA	A|0.979;G|0.021	0.021	strong		0.448	TIAM2-005	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000387980.2	NM_012454	
ECM2	1842	hgsc.bcm.edu	37	9	95267938	95267938	+	Silent	SNP	T	T	C	rs35161698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95267938T>C	ENST00000344604.5	-	7	1490	c.1341A>G	c.(1339-1341)ggA>ggG	p.G447G	CENPP_ENST00000375587.3_Intron|ECM2_ENST00000444490.2_Silent_p.G425G	NM_001197295.1|NM_001393.3	NP_001184224.1|NP_001384.1	O94769	ECM2_HUMAN	extracellular matrix protein 2, female organ and adipocyte specific	447					cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27						TGAGATTGTTTCCTTCCAATT	0.323													T|||	117	0.0233626	0.0802	0.0159	5008	,	,		15033	0.0		0.0	False		,,,				2504	0.0				p.G447G		Atlas-SNP	.											.	ECM2	147	.	0			c.A1341G						PASS	.	T	,,,	294,4112	144.2+/-179.2	6,282,1915	80.0	85.0	83.0		,1275,1275,1341	5.8	1.0	9	dbSNP_126	83	8,8592	5.7+/-21.5	0,8,4292	no	intron,coding-synonymous,coding-synonymous,coding-synonymous	ECM2,CENPP	NM_001012267.1,NM_001197295.1,NM_001197296.1,NM_001393.3	,,,	6,290,6207	CC,CT,TT		0.093,6.6727,2.322	,,,	,425/678,425/644,447/700	95267938	302,12704	2203	4300	6503	SO:0001819	synonymous_variant	1842	exon7			ATTGTTTCCTTCC	AB011792	CCDS6698.1, CCDS56578.1	9q22.3	2008-07-21			ENSG00000106823	ENSG00000106823			3154	protein-coding gene	gene with protein product	"""matrix glycoprotein SC1/ECM2"""	603479				9790758	Standard	NM_001393		Approved		uc011lty.2	O94769	OTTHUMG00000020226	ENST00000344604.5:c.1341A>G	9.37:g.95267938T>C		117.0	0.0	0		99.0	62.0	0.626263	NM_001393	B2R730|E2PU11|Q5T9F2|Q7Z3D0	Silent	SNP	ENST00000344604.5	37	CCDS6698.1																																																																																			T|0.978;C|0.022	0.022	strong		0.323	ECM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053091.1	NM_001393	
MED12L	116931	hgsc.bcm.edu	37	3	151127074	151127074	+	Missense_Mutation	SNP	G	G	A	rs78970280	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:151127074G>A	ENST00000474524.1	+	38	5797	c.5759G>A	c.(5758-5760)cGg>cAg	p.R1920Q	MED12L_ENST00000273432.4_Intron	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	1920	Gln-rich.					mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GCGCAAGCACGGCCCTCCCCT	0.527													G|||	36	0.0071885	0.0265	0.0014	5008	,	,		14258	0.0		0.0	False		,,,				2504	0.0				p.R1920Q		Atlas-SNP	.											MED12L,colon,carcinoma,-1,1	MED12L	271	1	0			c.G5759A						PASS	.	G	GLN/ARG	74,4332	66.4+/-103.9	1,72,2130	74.0	76.0	76.0		5759	5.8	1.0	3	dbSNP_132	76	0,8600		0,0,4300	yes	missense	MED12L	NM_053002.4	43	1,72,6430	AA,AG,GG		0.0,1.6795,0.569	probably-damaging	1920/2146	151127074	74,12932	2203	4300	6503	SO:0001583	missense	116931	exon38			AAGCACGGCCCTC	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"""			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.5759G>A	3.37:g.151127074G>A	ENSP00000417235:p.Arg1920Gln	81.0	0.0	0		71.0	32.0	0.450704	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Missense_Mutation	SNP	ENST00000474524.1	37	CCDS33876.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	G	15.65	2.896847	0.52121	0.016795	0.0	ENSG00000144893	ENST00000474524	T	0.55588	0.51	5.75	5.75	0.90469	Mediator complex, subunit Med12, catenin-binding (1);	0.133081	0.51477	D	0.000099	T	0.44582	0.1300	L	0.57536	1.79	0.80722	D	1	D	0.69078	0.997	D	0.70227	0.968	T	0.52734	-0.8536	10	0.23891	T	0.37	-27.2348	17.7294	0.88373	0.0:0.0:1.0:0.0	.	1920	Q86YW9	MD12L_HUMAN	Q	1920	ENSP00000417235:R1920Q	ENSP00000417235:R1920Q	R	+	2	0	MED12L	152609764	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	3.424000	0.52764	2.708000	0.92522	0.650000	0.86243	CGG	G|0.993;A|0.007	0.007	strong		0.527	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002	
MINPP1	9562	hgsc.bcm.edu	37	10	89312046	89312046	+	Silent	SNP	T	T	C	rs2233169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:89312046T>C	ENST00000371996.4	+	5	1316	c.1275T>C	c.(1273-1275)gcT>gcC	p.A425A	MINPP1_ENST00000536010.1_Silent_p.A224A|MINPP1_ENST00000472891.1_3'UTR|MINPP1_ENST00000371994.4_3'UTR	NM_004897.4	NP_004888.2	Q9UNW1	MINP1_HUMAN	multiple inositol-polyphosphate phosphatase 1	425					bone mineralization (GO:0030282)|dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|ossification (GO:0001503)|polyphosphate metabolic process (GO:0006797)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	acid phosphatase activity (GO:0003993)|bisphosphoglycerate 3-phosphatase activity (GO:0034417)|inositol hexakisphosphate 2-phosphatase activity (GO:0052826)|phosphohistidine phosphatase activity (GO:0008969)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|urinary_tract(2)	5		Colorectal(252;0.122)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00123)		GTGAAAATGCTAAGACTCCTA	0.368													T|||	142	0.0283546	0.0998	0.0086	5008	,	,		20648	0.0		0.002	False		,,,				2504	0.002				p.A425A		Atlas-SNP	.											.	MINPP1	22	.	0			c.T1275C						PASS	.	T	,,	354,4052	181.5+/-209.5	14,326,1863	126.0	123.0	124.0		,672,1275	-4.7	1.0	10	dbSNP_98	124	11,8589	7.7+/-29.5	0,11,4289	no	utr-3,coding-synonymous,coding-synonymous	MINPP1	NM_001178117.1,NM_001178118.1,NM_004897.4	,,	14,337,6152	CC,CT,TT		0.1279,8.0345,2.8064	,,	,224/287,425/488	89312046	365,12641	2203	4300	6503	SO:0001819	synonymous_variant	9562	exon5			AAATGCTAAGACT	AF046915	CCDS7384.1, CCDS53551.1, CCDS53552.1	10q23	2010-05-04	2010-05-04		ENSG00000107789	ENSG00000107789	3.1.3.62		7102	protein-coding gene	gene with protein product		605391	"""multiple inositol polyphosphate histidine phosphatase, 1"""			10087200	Standard	NM_004897		Approved	MIPP	uc001keu.3	Q9UNW1	OTTHUMG00000018678	ENST00000371996.4:c.1275T>C	10.37:g.89312046T>C		160.0	0.0	0		137.0	61.0	0.445255	NM_004897	F5H683|O95172|O95286|Q59EJ2|Q9UGA3	Silent	SNP	ENST00000371996.4	37	CCDS7384.1																																																																																			T|0.975;C|0.025	0.025	strong		0.368	MINPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049221.1		
COL17A1	1308	hgsc.bcm.edu	37	10	105824332	105824332	+	Silent	SNP	C	C	T	rs149012179	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:105824332C>T	ENST00000353479.5	-	10	920	c.630G>A	c.(628-630)acG>acA	p.T210T	COL17A1_ENST00000369733.3_Silent_p.T210T|COL17A1_ENST00000393211.3_Silent_p.T210T	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	210	Necessary for interaction with DST and for the recruitment of DST to hemidesmosome.|Nonhelical region (NC16).		T -> M (in dbSNP:rs805708). {ECO:0000269|PubMed:15489334}.		cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|hemidesmosome (GO:0030056)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				NS(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|liver(1)|lung(22)|ovary(5)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	62		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		CATCCAGGATCGTTGCATCGT	0.547													C|||	37	0.00738818	0.0272	0.0014	5008	,	,		15732	0.0		0.0	False		,,,				2504	0.0				p.T210T		Atlas-SNP	.											.	COL17A1	149	.	0			c.G630A						PASS	.	C		90,4316	74.7+/-112.8	0,90,2113	119.0	81.0	94.0		630	-8.0	0.1	10	dbSNP_134	94	0,8600		0,0,4300	no	coding-synonymous	COL17A1	NM_000494.3		0,90,6413	TT,TC,CC		0.0,2.0427,0.692		210/1498	105824332	90,12916	2203	4300	6503	SO:0001819	synonymous_variant	1308	exon10			CAGGATCGTTGCA	M91669	CCDS7554.1	10q24.3	2013-01-16			ENSG00000065618	ENSG00000065618		"""Collagens"""	2194	protein-coding gene	gene with protein product		113811		BPAG2		7916703	Standard	NM_000494		Approved	BP180	uc001kxr.3	Q9UMD9	OTTHUMG00000018998	ENST00000353479.5:c.630G>A	10.37:g.105824332C>T		141.0	0.0	0		156.0	79.0	0.50641	NM_000494	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Silent	SNP	ENST00000353479.5	37	CCDS7554.1																																																																																			C|0.993;T|0.007	0.007	strong		0.547	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494	
PLEKHG4B	153478	hgsc.bcm.edu	37	5	155059	155059	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:155059G>A	ENST00000283426.6	+	6	1044	c.994G>A	c.(994-996)Gac>Aac	p.D332N		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	332							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		CGCAGACCTCGACGGCTCCTT	0.577																																					p.D332N		Atlas-SNP	.											PLEKHG4B_ENST00000283426,NS,carcinoma,-2,2	PLEKHG4B	167	2	0			c.G994A						scavenged	.						86.0	77.0	80.0					5																	155059		2203	4300	6503	SO:0001583	missense	153478	exon6			GACCTCGACGGCT	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"""Pleckstrin homology (PH) domain containing"""	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.994G>A	5.37:g.155059G>A	ENSP00000283426:p.Asp332Asn	54.0	0.0	0		71.0	3.0	0.0422535	NM_052909		Missense_Mutation	SNP	ENST00000283426.6	37	CCDS34124.1	.	.	.	.	.	.	.	.	.	.	.	10.59	1.394085	0.25205	.	.	ENSG00000153404	ENST00000283426;ENST00000502646	T;T	0.59083	0.29;0.29	3.88	3.01	0.34805	.	.	.	.	.	T	0.66015	0.2747	L	0.60455	1.87	0.09310	N	1	D	0.76494	0.999	P	0.61275	0.886	T	0.53961	-0.8364	9	0.62326	D	0.03	.	7.3764	0.26831	0.126:0.0:0.874:0.0	.	332	Q96PX9	PKH4B_HUMAN	N	332;246	ENSP00000283426:D332N;ENSP00000422493:D246N	ENSP00000283426:D332N	D	+	1	0	PLEKHG4B	208059	1.000000	0.71417	0.000000	0.03702	0.106000	0.19336	4.161000	0.58170	0.623000	0.30267	0.460000	0.39030	GAC	.	.	none		0.577	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909	
STOM	2040	hgsc.bcm.edu	37	9	124110368	124110368	+	Silent	SNP	C	C	T	rs115702601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:124110368C>T	ENST00000286713.2	-	6	602	c.585G>A	c.(583-585)aaG>aaA	p.K195K	AL161784.1_ENST00000594963.1_Silent_p.S46S|STOM_ENST00000538954.1_Silent_p.K144K|STOM_ENST00000347359.2_Intron	NM_001270526.1|NM_004099.5	NP_001257455.1|NP_004090.4	P27105	STOM_HUMAN	stomatin	195					protein homooligomerization (GO:0051260)|regulation of acid-sensing ion channel activity (GO:1901585)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|vesicle (GO:0031982)				endometrium(1)|large_intestine(1)|lung(3)|urinary_tract(1)	6				OV - Ovarian serous cystadenocarcinoma(323;0.00107)|GBM - Glioblastoma multiforme(294;0.0137)		GTTTCACATCCTTAATTTCCA	0.493													C|||	19	0.00379393	0.0136	0.0	5008	,	,		16533	0.0		0.001	False		,,,				2504	0.0				p.K195K		Atlas-SNP	.											.	STOM	15	.	0			c.G585A						PASS	.	C	,	50,4356	52.3+/-87.9	0,50,2153	123.0	121.0	122.0		585,	1.5	1.0	9	dbSNP_132	122	1,8599	2.2+/-6.3	0,1,4299	no	coding-synonymous,intron	STOM	NM_004099.4,NM_198194.1	,	0,51,6452	TT,TC,CC		0.0116,1.1348,0.3921	,	195/289,	124110368	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	2040	exon6			CACATCCTTAATT		CCDS6830.1, CCDS6831.1, CCDS75892.1	9q34.1	2008-07-21	2002-11-11	2002-11-15	ENSG00000148175	ENSG00000148175			3383	protein-coding gene	gene with protein product		133090	"""erythrocyte membrane protein band 7.2 (stomatin)"""	EPB7, EPB72		1883838	Standard	NM_198194		Approved	BND7	uc004blh.4	P27105	OTTHUMG00000020590	ENST00000286713.2:c.585G>A	9.37:g.124110368C>T		123.0	0.0	0		100.0	55.0	0.55	NM_001270526	B1AM77|Q14087|Q15609|Q5VX96|Q96FK4	Silent	SNP	ENST00000286713.2	37	CCDS6830.1																																																																																			C|0.996;T|0.004	0.004	strong		0.493	STOM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053889.1	NM_004099	
TAF5L	27097	hgsc.bcm.edu	37	1	229750089	229750089	+	Splice_Site	SNP	T	T	C	rs144626601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229750089T>C	ENST00000366676.1	-	1	140	c.141A>G	c.(139-141)acA>acG	p.T47T	TAF5L_ENST00000477957.1_5'UTR|TAF5L_ENST00000258281.2_Splice_Site_p.T47T|TAF5L_ENST00000366675.3_Splice_Site_p.T47T|TAF5L_ENST00000366674.1_Silent_p.T47T			O75529	TAF5L_HUMAN	TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65kDa	47					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|transcription from RNA polymerase II promoter (GO:0006366)	STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)	11	Breast(184;0.193)|Ovarian(103;0.249)	Prostate(94;0.167)				CACCATTACCTGTTAGATTGG	0.557													T|||	17	0.00339457	0.0129	0.0	5008	,	,		20513	0.0		0.0	False		,,,				2504	0.0				p.T47T		Atlas-SNP	.											.	TAF5L	76	.	0			c.A141G						PASS	.	T	,	51,4355	53.6+/-89.4	0,51,2152	105.0	95.0	99.0		141,141	3.5	1.0	1	dbSNP_134	99	0,8600		0,0,4300	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	TAF5L	NM_001025247.1,NM_014409.3	,	0,51,6452	CC,CT,TT		0.0,1.1575,0.3921	,	47/326,47/590	229750089	51,12955	2203	4300	6503	SO:0001630	splice_region_variant	27097	exon2			ATTACCTGTTAGA	AF069736	CCDS1581.1, CCDS31051.1	1q42.11-q42.3	2013-01-10	2002-08-29		ENSG00000135801	ENSG00000135801		"""WD repeat domain containing"""	17304	protein-coding gene	gene with protein product	"""PCAF associated factor 65 beta"""		"""TAF5-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65 kD"""			9674425, 11124703	Standard	XM_005273100		Approved	PAF65B	uc001htq.3	O75529	OTTHUMG00000039463	ENST00000366676.1:c.142+1A>G	1.37:g.229750089T>C		136.0	0.0	0		156.0	65.0	0.416667	NM_001025247	Q5TDI5|Q5TDI6|Q8IW31	Silent	SNP	ENST00000366676.1	37	CCDS1581.1																																																																																			T|0.997;C|0.003	0.003	strong		0.557	TAF5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095229.1	NM_014409	Silent
MAATS1	89876	hgsc.bcm.edu	37	3	119445092	119445092	+	Missense_Mutation	SNP	T	T	A	rs9817771	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119445092T>A	ENST00000273390.5	+	7	834	c.757T>A	c.(757-759)Tct>Act	p.S253T		NM_033364.3	NP_203528	Q7Z4T9	MAAT1_HUMAN	MYCBP-associated, testis expressed 1	253			S -> T (in dbSNP:rs9817771).			mitochondrion (GO:0005739)											TTGGGAAGCCTCTCTCCCCGC	0.542													A|||	70	0.0139776	0.0514	0.0014	5008	,	,		19226	0.0		0.0	False		,,,				2504	0.001				p.S253T		Atlas-SNP	.											.	.	.	.	0			c.T757A						PASS	.	A	THR/SER	209,4197	807.3+/-415.9	3,203,1997	57.0	55.0	56.0		757	4.4	0.8	3	dbSNP_119	56	4,8596	819.2+/-406.8	1,2,4297	yes	missense	C3orf15	NM_033364.3	58	4,205,6294	AA,AT,TT		0.0465,4.7435,1.6377	benign	253/768	119445092	213,12793	2203	4300	6503	SO:0001583	missense	89876	exon7			GAAGCCTCTCTCC	AB063296	CCDS2994.1	3q12-q13.3	2014-07-31	2012-12-07	2012-09-26	ENSG00000183833	ENSG00000183833			24010	protein-coding gene	gene with protein product	"""AMY-1-associating protein expressed in testis 1"", ""MYCBP-binding protein"", ""spermatogenesis associated 26"""	609910	"""chromosome 3 open reading frame 15"", ""MYCBP/AMY-1-associated, testis expressed 1"""	C3orf15		12223483, 14551891, 17967944	Standard	NM_033364		Approved	AAT1, AAT1alpha, SPATA26, CaM-IP2	uc003ede.4	Q7Z4T9	OTTHUMG00000159422	ENST00000273390.5:c.757T>A	3.37:g.119445092T>A	ENSP00000273390:p.Ser253Thr	98.0	0.0	0		111.0	56.0	0.504505	NM_033364	A0AVK2|A8K1J9|B3KP23|B4DG52|B4DZ14|C9JUG4|Q68DX2|Q8TD41|Q96A45|Q96JE8	Missense_Mutation	SNP	ENST00000273390.5	37	CCDS2994.1	20	0.009157509157509158	20	0.04065040650406504	0	0.0	0	0.0	0	0.0	A	1.705	-0.500484	0.04291	0.047435	4.65E-4	ENSG00000183833	ENST00000273390	T	0.23147	1.92	5.62	4.44	0.53790	.	0.293168	0.41938	N	0.000789	T	0.00815	0.0027	N	0.00630	-1.315	0.80722	D	1	B;B;B;B;B	0.06786	0.0;0.001;0.0;0.0;0.0	B;B;B;B;B	0.06405	0.002;0.001;0.001;0.0;0.0	T	0.26430	-1.0103	10	0.02654	T	1	-7.7599	5.0067	0.14291	0.6979:0.1217:0.0641:0.1163	rs9817771;rs52835037;rs9817771	253;14;191;253;253	Q7Z4T9;Q9UFB4;Q7Z4T9-3;Q4G0Y0;Q7Z4T9-7	AAT1_HUMAN;.;.;.;.	T	253	ENSP00000273390:S253T	ENSP00000273390:S253T	S	+	1	0	C3orf15	120927782	1.000000	0.71417	0.839000	0.33178	0.385000	0.30292	3.898000	0.56281	0.484000	0.27630	-0.265000	0.10407	TCT	T|0.984;A|0.016	0.016	strong		0.542	MAATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355222.1	NM_033364	
RP11-93K22.13	0	hgsc.bcm.edu	37	3	129810973	129810973	+	lincRNA	SNP	G	G	A	rs114865400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:129810973G>A	ENST00000514010.1	-	0	157				ALG1L2_ENST00000507643.1_RNA																							GACACAGAGCGGTCGGCCTTC	0.632													N|||	155	0.0309505	0.1029	0.0086	5008	,	,		17255	0.0089		0.001	False		,,,				2504	0.0031				p.R54Q		Atlas-SNP	.											.	.	.	.	0			c.G161A						PASS	.	C	GLN/ARG	117,1267		4,109,579	18.0	20.0	19.0		161	-2.4	0.0	3	dbSNP_132	19	1,3181		0,1,1590	no	missense	ALG1L2	NM_001136152.1	43	4,110,2169	AA,AG,GG		0.0314,8.4538,2.5843	benign	54/216	129810973	118,4448	692	1591	2283			644974	exon3			CAGAGCGGTCGGC																													3.37:g.129810973G>A		493.0	0.0	0		556.0	273.0	0.491007	NM_001136152		Missense_Mutation	SNP	ENST00000514010.1	37																																																																																				G|0.968;A|0.032	0.032	strong		0.632	RP11-93K22.13-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000358040.1		
GKN2	200504	hgsc.bcm.edu	37	2	69172570	69172570	+	Missense_Mutation	SNP	G	G	A	rs73935451	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:69172570G>A	ENST00000328895.4	-	6	593	c.485C>T	c.(484-486)gCt>gTt	p.A162V	GKN2_ENST00000481498.1_3'UTR	NM_182536.2	NP_872342.2	Q86XP6	GKN2_HUMAN	gastrokine 2	162						extracellular region (GO:0005576)				autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|urinary_tract(1)	15						ACAGCCTCCAGCACCGACATT	0.343													G|||	95	0.0189696	0.0703	0.0029	5008	,	,		14842	0.0		0.0	False		,,,				2504	0.0				p.A162V		Atlas-SNP	.											.	GKN2	28	.	0			c.C485T						PASS	.	G	VAL/ALA	192,4214	117.5+/-155.4	5,182,2016	86.0	98.0	94.0		485	4.6	0.0	2	dbSNP_130	94	3,8597	3.0+/-9.4	0,3,4297	yes	missense	GKN2	NM_182536.2	64	5,185,6313	AA,AG,GG		0.0349,4.3577,1.4993	benign	162/185	69172570	195,12811	2203	4300	6503	SO:0001583	missense	200504	exon6			CCTCCAGCACCGA	AF494509	CCDS33215.1	2p14	2012-10-10			ENSG00000183607	ENSG00000183607		"""BRICHOS domain containing"""	24588	protein-coding gene	gene with protein product	"""down regulated in gastric cancer GDDR"", ""BRICHOS domain containing 1B"""					15774165, 15924415, 16888721	Standard	NM_182536		Approved	TFIZ1, PRO813, VLTI465, blottin, GDDR, BRICD1B	uc002sfa.3	Q86XP6	OTTHUMG00000152655	ENST00000328895.4:c.485C>T	2.37:g.69172570G>A	ENSP00000329292:p.Ala162Val	138.0	0.0	0		152.0	85.0	0.559211	NM_182536	Q6UWS6	Missense_Mutation	SNP	ENST00000328895.4	37	CCDS33215.1	36	0.016483516483516484	35	0.07113821138211382	1	0.0027624309392265192	0	0.0	0	0.0	G	16.09	3.023294	0.54683	0.043577	3.49E-4	ENSG00000183607	ENST00000328895	T	0.45668	0.89	5.48	4.61	0.57282	.	0.626420	0.16479	N	0.212605	T	0.02688	0.0081	L	0.50333	1.59	0.25024	N	0.991315	P	0.48294	0.908	B	0.34138	0.176	T	0.06075	-1.0847	10	0.66056	D	0.02	-5.4299	9.8712	0.41175	0.0908:0.0:0.9092:0.0	.	162	Q86XP6	GKN2_HUMAN	V	162	ENSP00000329292:A162V	ENSP00000329292:A162V	A	-	2	0	GKN2	69026074	0.014000	0.17966	0.006000	0.13384	0.410000	0.31052	1.135000	0.31454	1.562000	0.49601	0.650000	0.86243	GCT	G|0.983;A|0.017	0.017	strong		0.343	GKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327191.1	NM_182536	
MUC4	4585	hgsc.bcm.edu	37	3	195515257	195515257	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195515257G>T	ENST00000463781.3	-	2	3653	c.3194C>A	c.(3193-3195)gCa>gAa	p.A1065E	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A1065E	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	498					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.A1065E(3)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATGCTGAGGAAGT	0.562																																					p.A1065E		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	3	Substitution - Missense(3)	NS(2)|endometrium(1)	c.C3194A						PASS	.						24.0	18.0	20.0					3																	195515257		690	1590	2280	SO:0001583	missense	4585	exon2			GTGGATGCTGAGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3194C>A	3.37:g.195515257G>T	ENSP00000417498:p.Ala1065Glu	171.0	0.0	0		265.0	62.0	0.233962	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	.	.	.	.	.	.	.	.	.	.	-	6.830	0.522392	0.13066	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32753	1.44;1.44	0.573	-1.15	0.09709	.	.	.	.	.	T	0.14960	0.0361	N	0.19112	0.55	0.09310	N	1	B	0.19200	0.034	B	0.14023	0.01	T	0.28744	-1.0034	8	.	.	.	.	4.0999	0.10009	0.5176:0.0:0.4824:0.0	.	1065	E7ESK3	.	E	1065	ENSP00000417498:A1065E;ENSP00000420243:A1065E	.	A	-	2	0	MUC4	196999652	.	.	0.002000	0.10522	0.032000	0.12392	.	.	-0.302000	0.08869	-2.092000	0.00371	GCA	G|0.500;A|0.500	.	alt		0.562	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MYO7B	4648	hgsc.bcm.edu	37	2	128341904	128341904	+	Silent	SNP	G	G	A	rs61743462	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128341904G>A	ENST00000409816.2	+	12	1583	c.1551G>A	c.(1549-1551)ccG>ccA	p.P517P	MYO7B_ENST00000389524.4_Silent_p.P517P|MYO7B_ENST00000428314.1_Silent_p.P517P			Q6PIF6	MYO7B_HUMAN	myosin VIIB	517	Myosin motor.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		GCCGCTTCCCGCAGGTGTGTG	0.602													G|||	54	0.0107827	0.0393	0.0029	5008	,	,		18661	0.0		0.0	False		,,,				2504	0.0				p.P517P		Atlas-SNP	.											.	MYO7B	359	.	0			c.G1551A						PASS	.	G		144,3842		1,142,1850	55.0	59.0	57.0		1551	-6.6	0.9	2	dbSNP_129	57	1,8289		0,1,4144	no	coding-synonymous	MYO7B	NM_001080527.1		1,143,5994	AA,AG,GG		0.0121,3.6126,1.1812		517/2117	128341904	145,12131	1993	4145	6138	SO:0001819	synonymous_variant	4648	exon13			CTTCCCGCAGGTG		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"""Myosins / Myosin superfamily : Class VII"""	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.1551G>A	2.37:g.128341904G>A		92.0	0.0	0		119.0	53.0	0.445378	NM_001080527	Q14786|Q8TEE1	Silent	SNP	ENST00000409816.2	37	CCDS46405.1																																																																																			G|0.993;A|0.007	0.007	strong		0.602	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
SAMD15	161394	hgsc.bcm.edu	37	14	77843920	77843920	+	Silent	SNP	A	A	G	rs61729313	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:77843920A>G	ENST00000216471.4	+	1	445	c.159A>G	c.(157-159)caA>caG	p.Q53Q	TMED8_ENST00000216468.7_5'Flank|SAMD15_ENST00000533095.2_Intron	NM_001010860.1	NP_001010860.1	Q9P1V8	SAM15_HUMAN	sterile alpha motif domain containing 15	53										breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|pancreas(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						AGATTTACCAAGAGCCACAGC	0.532													A|||	324	0.0646965	0.2368	0.0159	5008	,	,		18476	0.0		0.0	False		,,,				2504	0.0				p.Q53Q		Atlas-SNP	.											.	SAMD15	60	.	0			c.A159G						PASS	.	A		744,3662	304.4+/-288.4	66,612,1525	68.0	69.0	69.0		159	0.9	0.0	14	dbSNP_129	69	5,8595	2.2+/-6.3	0,5,4295	no	coding-synonymous	SAMD15	NM_001010860.1		66,617,5820	GG,GA,AA		0.0581,16.8861,5.7589		53/675	77843920	749,12257	2203	4300	6503	SO:0001819	synonymous_variant	161394	exon1			TTACCAAGAGCCA	AK093282	CCDS32126.1	14q24.3	2013-01-10	2010-10-20	2010-10-20	ENSG00000100583	ENSG00000100583		"""Sterile alpha motif (SAM) domain containing"""	18631	protein-coding gene	gene with protein product			"""family with sequence similarity 15, member A"", ""chromosome 14 open reading frame 174"""	FAM15A, C14orf174			Standard	XM_006720069		Approved	FLJ35963	uc001xtq.1	Q9P1V8		ENST00000216471.4:c.159A>G	14.37:g.77843920A>G		97.0	0.0	0		102.0	54.0	0.529412	NM_001010860	Q2M3P3	Silent	SNP	ENST00000216471.4	37	CCDS32126.1																																																																																			A|0.932;G|0.068	0.068	strong		0.532	SAMD15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394587.2	NM_001010860	
MED7	9443	hgsc.bcm.edu	37	5	156565839	156565839	+	Missense_Mutation	SNP	C	C	T	rs151231455	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:156565839C>T	ENST00000286317.5	-	2	985	c.604G>A	c.(604-606)Gaa>Aaa	p.E202K	MED7_ENST00000420343.1_Missense_Mutation_p.E202K	NM_004270.4	NP_004261.1	O43513	MED7_HUMAN	mediator complex subunit 7	202					gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II transcription cofactor activity (GO:0001104)|transcription coactivator activity (GO:0003713)			kidney(1)|large_intestine(1)|lung(3)|urinary_tract(2)	7	Renal(175;0.00212)	Medulloblastoma(196;0.0354)|all_neural(177;0.0999)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CTTTGATGTTCATTCTGTCCA	0.388													C|||	37	0.00738818	0.0272	0.0014	5008	,	,		20059	0.0		0.0	False		,,,				2504	0.0				p.E202K		Atlas-SNP	.											.	MED7	18	.	0			c.G604A						PASS	.	C	LYS/GLU,LYS/GLU	127,4279	93.0+/-131.7	4,119,2080	178.0	165.0	170.0		604,604	4.0	1.0	5	dbSNP_134	170	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	MED7	NM_001100816.1,NM_004270.4	56,56	4,120,6379	TT,TC,CC		0.0116,2.8824,0.9842	benign,benign	202/234,202/234	156565839	128,12878	2203	4300	6503	SO:0001583	missense	9443	exon2			GATGTTCATTCTG	AF104251	CCDS4334.1	5q33.3	2008-02-05	2007-07-30	2007-07-30	ENSG00000155868	ENSG00000155868			2378	protein-coding gene	gene with protein product		605045	"""cofactor required for Sp1 transcriptional activation, subunit 9, 33kDa"""	CRSP9		9989412	Standard	NM_004270		Approved	CRSP33	uc003lwm.4	O43513	OTTHUMG00000130243	ENST00000286317.5:c.604G>A	5.37:g.156565839C>T	ENSP00000286317:p.Glu202Lys	348.0	1.0	0.00287356		319.0	149.0	0.467085	NM_001100816		Missense_Mutation	SNP	ENST00000286317.5	37	CCDS4334.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	C	8.966	0.971874	0.18736	0.028824	1.16E-4	ENSG00000155868	ENST00000286317;ENST00000420343	.	.	.	5.81	4.04	0.47022	.	0.530450	0.21352	N	0.075941	T	0.19005	0.0456	N	0.25647	0.755	0.35254	D	0.778968	B	0.06786	0.001	B	0.04013	0.001	T	0.29397	-1.0013	9	0.18710	T	0.47	-16.0444	11.7459	0.51819	0.0:0.8027:0.1305:0.0668	.	202	O43513	MED7_HUMAN	K	202	.	ENSP00000286317:E202K	E	-	1	0	MED7	156498417	0.986000	0.35501	0.999000	0.59377	0.951000	0.60555	1.750000	0.38329	0.791000	0.33826	-0.137000	0.14449	GAA	C|0.991;T|0.009	0.009	strong		0.388	MED7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252567.2	NM_004270	
THTPA	79178	hgsc.bcm.edu	37	14	24026174	24026174	+	Missense_Mutation	SNP	G	G	T	rs141465409	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24026174G>T	ENST00000288014.6	+	1	944	c.208G>T	c.(208-210)Gca>Tca	p.A70S	THTPA_ENST00000554789.1_Missense_Mutation_p.A70S|THTPA_ENST00000556015.1_Missense_Mutation_p.A70S|THTPA_ENST00000404535.3_Missense_Mutation_p.A70S|THTPA_ENST00000554970.1_Missense_Mutation_p.A70S|RP11-66N24.4_ENST00000555446.1_RNA|RP11-66N24.4_ENST00000556354.1_RNA|RP11-66N24.4_ENST00000553985.1_RNA			Q9BU02	THTPA_HUMAN	thiamine triphosphatase	70	CYTH. {ECO:0000255|PROSITE- ProRule:PRU01044}.				dephosphorylation (GO:0016311)|generation of precursor metabolites and energy (GO:0006091)|small molecule metabolic process (GO:0044281)|thiamine diphosphate metabolic process (GO:0042357)|thiamine metabolic process (GO:0006772)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	hydrolase activity (GO:0016787)|magnesium ion binding (GO:0000287)|thiamin-triphosphatase activity (GO:0050333)			large_intestine(1)|prostate(2)	3	all_cancers(95;0.000251)			GBM - Glioblastoma multiforme(265;0.00643)		TCCTGGAGCAGCAGGTGTCTT	0.582													G|||	6	0.00119808	0.0045	0.0	5008	,	,		18740	0.0		0.0	False		,,,				2504	0.0				p.A70S		Atlas-SNP	.											.	THTPA	11	.	0			c.G208T						PASS	.	G	SER/ALA,SER/ALA	5,4401	9.9+/-24.2	0,5,2198	84.0	71.0	75.0		208,208	-2.0	0.0	14	dbSNP_134	75	0,8600		0,0,4300	yes	missense,missense	THTPA	NM_001126339.1,NM_024328.3	99,99	0,5,6498	TT,TG,GG		0.0,0.1135,0.0384	benign,benign	70/231,70/231	24026174	5,13001	2203	4300	6503	SO:0001583	missense	79178	exon2			GGAGCAGCAGGTG	AF432862	CCDS32053.1, CCDS58306.1, CCDS58307.1	14q11.2	2011-04-28					3.6.1.28		18987	protein-coding gene	gene with protein product		611612				11827967	Standard	NR_046051		Approved	THTPASE	uc001wkh.5	Q9BU02		ENST00000288014.6:c.208G>T	14.37:g.24026174G>T	ENSP00000288014:p.Ala70Ser	201.0	0.0	0		215.0	115.0	0.534884	NM_001256321	D3DS50|G3V4J3	Missense_Mutation	SNP	ENST00000288014.6	37	CCDS32053.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	7.575	0.667592	0.14710	0.001135	0.0	ENSG00000157306	ENST00000404535;ENST00000288014;ENST00000557630;ENST00000556015;ENST00000554970;ENST00000554789	T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97	5.91	-1.95	0.07548	CYTH domain (2);CYTH-like domain (1);	1.127190	0.06371	N	0.713610	T	0.24431	0.0592	L	0.41573	1.285	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.12156	0.007;0.003	T	0.22452	-1.0216	10	0.05959	T	0.93	0.0017	1.2016	0.01886	0.2075:0.3314:0.2356:0.2254	.	70;70	G3V4J3;Q9BU02	.;THTPA_HUMAN	S	70	ENSP00000384580:A70S;ENSP00000288014:A70S;ENSP00000452281:A70S;ENSP00000451835:A70S;ENSP00000452465:A70S;ENSP00000450459:A70S	ENSP00000288014:A70S	A	+	1	0	THTPA	23096014	0.000000	0.05858	0.000000	0.03702	0.989000	0.77384	-0.268000	0.08607	-0.725000	0.04901	0.655000	0.94253	GCA	G|0.999;T|0.001	0.001	strong		0.582	THTPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413800.2		
PCSK7	9159	hgsc.bcm.edu	37	11	117079687	117079687	+	Silent	SNP	G	G	A	rs148329047	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117079687G>A	ENST00000320934.3	-	13	2247	c.1617C>T	c.(1615-1617)cgC>cgT	p.R539R	PCSK7_ENST00000540028.1_Silent_p.R180R|PCSK7_ENST00000529458.1_5'Flank	NM_004716.2	NP_004707.2	Q16549	PCSK7_HUMAN	proprotein convertase subtilisin/kexin type 7	539					peptide hormone processing (GO:0016486)|protein processing (GO:0016485)	integral component of Golgi membrane (GO:0030173)	peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|ovary(1)|skin(1)	16	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.72e-06)|Epithelial(105;6.71e-05)|all cancers(92;0.000537)		CCAAGCTGCCGCGCCGTGGGT	0.617			T	IGH@	MLCLS								G|||	44	0.00878594	0.031	0.0029	5008	,	,		24069	0.0		0.001	False		,,,				2504	0.0				p.R539R		Atlas-SNP	.		Dom	yes		11	11q23.3	9159	proprotein convertase subtilisin/kexin type 7		L	.	PCSK7	59	.	0			c.C1617T						PASS	.	G		81,4321	62.3+/-99.4	0,81,2120	41.0	42.0	41.0		1617	-9.1	0.2	11	dbSNP_134	41	0,8590		0,0,4295	no	coding-synonymous	PCSK7	NM_004716.2		0,81,6415	AA,AG,GG		0.0,1.8401,0.6235		539/786	117079687	81,12911	2201	4295	6496	SO:0001819	synonymous_variant	9159	exon13			GCTGCCGCGCCGT	U40623	CCDS8382.1	11q23-q24	2008-02-01			ENSG00000160613	ENSG00000160613			8748	protein-coding gene	gene with protein product		604872				8615762, 9820811	Standard	XM_006718938		Approved	PC7, PC8, LPC, SPC7	uc001pqr.3	Q16549	OTTHUMG00000165640	ENST00000320934.3:c.1617C>T	11.37:g.117079687G>A		393.0	0.0	0		246.0	92.0	0.373984	NM_004716	B0YJ60|Q3C1X1|Q53GM4|Q96FK8|Q9UL57	Silent	SNP	ENST00000320934.3	37	CCDS8382.1																																																																																			G|0.991;A|0.009	0.009	strong		0.617	PCSK7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385529.2	NM_004716	
PRSS41	360226	hgsc.bcm.edu	37	16	2849542	2849542	+	RNA	SNP	C	C	T	rs6500613	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2849542C>T	ENST00000399677.1	+	0	552							Q7RTY9	PRS41_HUMAN	protease, serine, 41							anchored component of membrane (GO:0031225)|intracellular organelle (GO:0043229)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)										GCTGGGTGACCGGCTGGGGGT	0.612													C|||	107	0.0213658	0.0809	0.0	5008	,	,		17014	0.0		0.0	False		,,,				2504	0.0				p.T184T		Atlas-SNP	.											.	.	.	.	0			c.C552T						PASS	.	C		65,1319		1,63,628	86.0	65.0	72.0		552	-9.1	0.8	16	dbSNP_116	72	0,3182		0,0,1591	no	coding-synonymous	PRSS41	NM_001135086.1		1,63,2219	TT,TC,CC		0.0,4.6965,1.4236		184/319	2849542	65,4501	692	1591	2283			360226	exon3			GGTGACCGGCTGG			16p13.3	2014-04-01			ENSG00000215148	ENSG00000215148		"""Serine peptidases / Serine peptidases"""	30715	other	unknown	"""testis serine protease 1"""					12838346	Standard	NM_001135086		Approved	TESSP1	uc010uwi.2	Q7RTY9	OTTHUMG00000128932		16.37:g.2849542C>T		77.0	0.0	0		80.0	35.0	0.4375	NM_001135086		Silent	SNP	ENST00000399677.1	37																																																																																				C|0.978;T|0.022	0.022	strong		0.612	PRSS41-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000436450.1	NM_183379	
ASB15	142685	hgsc.bcm.edu	37	7	123269280	123269280	+	Missense_Mutation	SNP	T	T	C	rs73718442	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:123269280T>C	ENST00000451558.1	+	12	1753	c.1232T>C	c.(1231-1233)aTg>aCg	p.M411T	ASB15_ENST00000451215.1_Missense_Mutation_p.M411T|ASB15_ENST00000540573.1_Missense_Mutation_p.M411T|ASB15_ENST00000275699.3_Missense_Mutation_p.M411T|ASB15_ENST00000434204.1_Missense_Mutation_p.M411T			Q8WXK1	ASB15_HUMAN	ankyrin repeat and SOCS box containing 15	411					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|kidney(1)|large_intestine(1)|lung(6)|skin(3)	12						TGTTATTTTATGCATGTGAAT	0.418													T|||	42	0.00838658	0.0303	0.0	5008	,	,		21984	0.001		0.001	False		,,,				2504	0.0				p.M411T		Atlas-SNP	.											.	ASB15	94	.	0			c.T1232C						PASS	.	T	THR/MET	102,4304	81.9+/-120.4	1,100,2102	151.0	134.0	140.0		1232	6.2	1.0	7	dbSNP_130	140	1,8599		0,1,4299	yes	missense	ASB15	NM_080928.3	81	1,101,6401	CC,CT,TT		0.0116,2.315,0.7919	benign	411/589	123269280	103,12903	2203	4300	6503	SO:0001583	missense	142685	exon8			ATTTTATGCATGT	AF403033	CCDS34742.1	7q31.31	2013-01-10	2011-01-25		ENSG00000146809	ENSG00000146809		"""Ankyrin repeat domain containing"""	19767	protein-coding gene	gene with protein product			"""ankyrin repeat and SOCS box-containing 15"""			12076535	Standard	XM_005250149		Approved	FLJ43370	uc003vkw.1	Q8WXK1	OTTHUMG00000157114	ENST00000451558.1:c.1232T>C	7.37:g.123269280T>C	ENSP00000397655:p.Met411Thr	129.0	0.0	0		129.0	66.0	0.511628	NM_080928	Q3ZCP3|Q3ZCP5|Q68D37	Missense_Mutation	SNP	ENST00000451558.1	37	CCDS34742.1	15	0.006868131868131868	15	0.03048780487804878	0	0.0	0	0.0	0	0.0	T	6.119	0.390139	0.11581	0.02315	1.16E-4	ENSG00000146809	ENST00000451558;ENST00000434204;ENST00000451215;ENST00000540573;ENST00000542545;ENST00000275699	T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2	6.17	6.17	0.99709	Ankyrin repeat-containing domain (2);	0.000000	0.85682	D	0.000000	T	0.25827	0.0629	L	0.43152	1.355	0.37857	D	0.929585	B	0.15473	0.013	B	0.09377	0.004	T	0.40739	-0.9547	10	0.06625	T	0.88	-21.3197	12.4321	0.55578	0.1256:0.0:0.0:0.8744	.	411	Q8WXK1	ASB15_HUMAN	T	411;411;411;411;200;411	ENSP00000397655:M411T;ENSP00000390963:M411T;ENSP00000416433:M411T;ENSP00000438643:M411T;ENSP00000275699:M411T	ENSP00000275699:M411T	M	+	2	0	ASB15	123056516	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	1.015000	0.29963	2.371000	0.80710	0.533000	0.62120	ATG	T|0.992;C|0.008	0.008	strong		0.418	ASB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347493.1		
CLRN3	119467	hgsc.bcm.edu	37	10	129676520	129676520	+	Missense_Mutation	SNP	T	T	C	rs34656572	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:129676520T>C	ENST00000368671.3	-	3	736	c.574A>G	c.(574-576)Ata>Gta	p.I192V		NM_152311.3	NP_689524.1	Q8NCR9	CLRN3_HUMAN	clarin 3	192						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	6		all_epithelial(44;0.00168)|all_lung(145;0.0586)|Lung NSC(174;0.0765)|all_neural(114;0.201)|Glioma(114;0.222)|Colorectal(57;0.235)				ACAGTGACTATATTTAGAAGA	0.458													T|||	45	0.00898562	0.0333	0.0014	5008	,	,		22782	0.0		0.0	False		,,,				2504	0.0				p.I192V		Atlas-SNP	.											.	CLRN3	27	.	0			c.A574G						PASS	.	T	VAL/ILE	169,4237	113.3+/-151.4	3,163,2037	220.0	190.0	200.0		574	-6.1	0.0	10	dbSNP_126	200	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CLRN3	NM_152311.3	29	3,165,6335	CC,CT,TT		0.0233,3.8357,1.3148	benign	192/227	129676520	171,12835	2203	4300	6503	SO:0001583	missense	119467	exon3			TGACTATATTTAG	BC029478	CCDS7656.1	10q26.2	2006-11-24	2006-11-23	2006-11-23	ENSG00000180745	ENSG00000180745			20795	protein-coding gene	gene with protein product			"""transmembrane protein 12"""	TMEM12		12145752, 12080385	Standard	NM_152311		Approved	MGC32871, USH3AL1	uc001lka.1	Q8NCR9	OTTHUMG00000019253	ENST00000368671.3:c.574A>G	10.37:g.129676520T>C	ENSP00000357660:p.Ile192Val	141.0	0.0	0		136.0	69.0	0.507353	NM_152311	Q6MZX8	Missense_Mutation	SNP	ENST00000368671.3	37	CCDS7656.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	T	4.071	0.010943	0.07912	0.038357	2.33E-4	ENSG00000180745	ENST00000368671	T	0.75154	-0.91	4.48	-6.08	0.02151	.	0.505264	0.18944	N	0.126863	T	0.21761	0.0524	N	0.21448	0.665	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.24941	-1.0146	10	0.10377	T	0.69	.	16.6501	0.85187	0.0:0.7096:0.0:0.2904	rs34656572	192;124	Q8NCR9;Q8NCR9-2	CLRN3_HUMAN;.	V	192	ENSP00000357660:I192V	ENSP00000357660:I192V	I	-	1	0	CLRN3	129566510	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-2.443000	0.01013	-1.177000	0.02744	-0.263000	0.10527	ATA	T|0.989;C|0.011	0.011	strong		0.458	CLRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050987.1	NM_152311	
MT-ND4	4538	hgsc.bcm.edu	37	M	11654	11654	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:11654A>G	ENST00000361381.2	+	1	895	c.895A>G	c.(895-897)Aca>Gca	p.T299A	MT-TR_ENST00000387439.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TH_ENST00000387441.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	299					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						CCCTCGTAGTAACAGCCATTC	0.468																																					p.T299A		Atlas-SNP	.											.	.	.	.	0			c.A895G						PASS	.																																			SO:0001583	missense	0	exon1			GTAGTAACAGCCA			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.895A>G	M.37:g.11654A>G	ENSP00000354961:p.Thr299Ala	7.0	0.0	0		12.0	12.0	1	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Missense_Mutation	SNP	ENST00000361381.2	37																																																																																				.	.	none		0.468	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
TNRC18	84629	hgsc.bcm.edu	37	7	5352731	5352731	+	Silent	SNP	G	G	A	rs114222264	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:5352731G>A	ENST00000430969.1	-	27	8139	c.7791C>T	c.(7789-7791)acC>acT	p.T2597T	TNRC18_ENST00000399537.4_Silent_p.T2597T	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2597	Ser-rich.						chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		TACGGCCCCCGGTGCCGCAGC	0.682													G|||	191	0.038139	0.1407	0.0029	5008	,	,		7259	0.0		0.003	False		,,,				2504	0.0				p.T2597T		Atlas-SNP	.											.	TNRC18	311	.	0			c.C7791T						PASS	.	G		243,2437		9,225,1106	7.0	12.0	11.0		7791	-3.8	0.0	7	dbSNP_132	11	2,6206		0,2,3102	no	coding-synonymous	TNRC18	NM_001080495.2		9,227,4208	AA,AG,GG		0.0322,9.0672,2.7565		2597/2969	5352731	245,8643	1340	3104	4444	SO:0001819	synonymous_variant	84629	exon27			GCCCCCGGTGCCG	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.7791C>T	7.37:g.5352731G>A		20.0	0.0	0		23.0	8.0	0.347826	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	37	CCDS47534.1																																																																																			G|0.964;A|0.036	0.036	strong		0.682	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
CUL9	23113	hgsc.bcm.edu	37	6	43154064	43154064	+	Silent	SNP	C	C	T	rs79828871	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43154064C>T	ENST00000252050.4	+	4	1206	c.1122C>T	c.(1120-1122)ggC>ggT	p.G374G	CUL9_ENST00000372647.2_Silent_p.G374G|CUL9_ENST00000354495.3_Silent_p.G374G	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	374					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						GCCGTAGTGGCTATGGAGAAT	0.577													C|||	187	0.0373403	0.1331	0.0144	5008	,	,		19600	0.0		0.001	False		,,,				2504	0.0				p.G374G		Atlas-SNP	.											.	CUL9	248	.	0			c.C1122T						PASS	.	C		441,3965	212.8+/-232.6	12,417,1774	74.0	73.0	73.0		1122	3.7	1.0	6	dbSNP_131	73	0,8600		0,0,4300	no	coding-synonymous	CUL9	NM_015089.2		12,417,6074	TT,TC,CC		0.0,10.0091,3.3907		374/2518	43154064	441,12565	2203	4300	6503	SO:0001819	synonymous_variant	23113	exon4			TAGTGGCTATGGA	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"""parkin-like cytoplasmic p53 binding protein"", ""p53-associated parkin-like cytoplasmic protein"""	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.1122C>T	6.37:g.43154064C>T		118.0	0.0	0		140.0	58.0	0.414286	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	37	CCDS4890.1																																																																																			C|0.967;T|0.033	0.033	strong		0.577	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	
THADA	63892	hgsc.bcm.edu	37	2	43518843	43518843	+	Missense_Mutation	SNP	A	A	G	rs17030648	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:43518843A>G	ENST00000405006.4	-	34	5353	c.5002T>C	c.(5002-5004)Tgt>Cgt	p.C1668R	THADA_ENST00000330266.7_Intron|THADA_ENST00000405975.2_Missense_Mutation_p.C1668R|THADA_ENST00000415080.2_Missense_Mutation_p.C1349R	NM_001083953.1|NM_001271643.1	NP_001077422.1|NP_001258572.1	Q6YHU6	THADA_HUMAN	thyroid adenoma associated	1668			C -> R (in dbSNP:rs17030648).							breast(1)|endometrium(9)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	66		Acute lymphoblastic leukemia(82;0.00361)|all_hematologic(82;0.00837)				ACCTCCACACATGTCTGCATG	0.393													A|||	159	0.0317492	0.1157	0.0086	5008	,	,		16790	0.0		0.0	False		,,,				2504	0.0				p.C1668R		Atlas-SNP	.											.	THADA	131	.	0			c.T5002C						PASS	.	A	ARG/CYS,ARG/CYS	351,3379		16,319,1530	62.0	58.0	59.0		5002,5002	-5.8	0.0	2	dbSNP_123	59	7,8131		0,7,4062	yes	missense,missense	THADA	NM_001083953.1,NM_022065.4	180,180	16,326,5592	GG,GA,AA		0.086,9.4102,3.0165	benign,benign	1668/1954,1668/1954	43518843	358,11510	1865	4069	5934	SO:0001583	missense	63892	exon34			CCACACATGTCTG	AY149629	CCDS46268.1, CCDS62901.1, CCDS62902.1	2p21	2008-02-05			ENSG00000115970	ENSG00000115970			19217	protein-coding gene	gene with protein product		611800				12063398, 11214970	Standard	NM_022065		Approved	FLJ21877, KIAA1767, GITA	uc002rsx.4	Q6YHU6	OTTHUMG00000152398	ENST00000405006.4:c.5002T>C	2.37:g.43518843A>G	ENSP00000385995:p.Cys1668Arg	204.0	1.0	0.00490196		213.0	118.0	0.553991	NM_001083953	A8K1V8|B7WNS6|Q3KR04|Q53RC6|Q53TB2|Q6YHU2|Q6ZU38|Q8IY32|Q8TAU8|Q96I88|Q9BZF7|Q9C096|Q9H6U0|Q9H6W7	Missense_Mutation	SNP	ENST00000405006.4	37	CCDS46268.1	62	0.028388278388278388	61	0.12398373983739837	1	0.0027624309392265192	0	0.0	0	0.0	A	0.081	-1.182910	0.01620	0.094102	8.6E-4	ENSG00000115970	ENST00000405975;ENST00000356975;ENST00000415080;ENST00000405006	T;T;T	0.67698	-0.28;-0.28;-0.28	4.52	-5.84	0.02318	.	1.778280	0.02439	N	0.084348	T	0.01092	0.0036	L	0.35723	1.085	0.58432	P	9.99999999995449E-6	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.15292	-1.0442	9	0.13108	T	0.6	-12.3615	13.0032	0.58687	0.3567:0.0:0.6433:0.0	rs17030648;rs52831994;rs17030648	1595;1668	B6ZDQ0;Q6YHU6	.;THADA_HUMAN	R	1668;1595;1349;1668	ENSP00000386088:C1668R;ENSP00000416048:C1349R;ENSP00000385995:C1668R	ENSP00000349464:C1595R	C	-	1	0	THADA	43372347	0.000000	0.05858	0.000000	0.03702	0.183000	0.23260	-2.041000	0.01415	-1.081000	0.03105	-0.384000	0.06662	TGT	A|0.958;G|0.042	0.042	strong		0.393	THADA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326070.3	NM_022065	
PLEC	5339	hgsc.bcm.edu	37	8	145006866	145006866	+	Silent	SNP	G	G	A	rs185978075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145006866G>A	ENST00000322810.4	-	15	2332	c.2163C>T	c.(2161-2163)ccC>ccT	p.P721P	PLEC_ENST00000398774.2_Silent_p.P552P|PLEC_ENST00000354958.2_Silent_p.P562P|PLEC_ENST00000345136.3_Silent_p.P584P|PLEC_ENST00000357649.2_Silent_p.P588P|PLEC_ENST00000354589.3_Silent_p.P584P|PLEC_ENST00000436759.2_Silent_p.P611P|PLEC_ENST00000527096.1_Silent_p.P607P|PLEC_ENST00000356346.3_Silent_p.P570P	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	721	Globular 1.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CCCGGGTGGCGGGGGAGAGCT	0.716													A|||	61	0.0121805	0.0424	0.0072	5008	,	,		14613	0.0		0.0	False		,,,				2504	0.0				p.P721P		Atlas-SNP	.											.	PLEC	1144	.	0			c.C2163T						PASS	.	A	,,,,,,,	99,3883		3,93,1895	10.0	14.0	13.0		1833,1710,1686,2163,1656,1752,1764,1752	-9.7	0.0	8		13	2,8238		0,2,4118	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	3,95,6013	AA,AG,GG		0.0243,2.4862,0.8264	,,,,,,,	611/4575,570/4534,562/4526,721/4685,552/4516,584/4548,588/4552,584/4548	145006866	101,12121	1991	4120	6111	SO:0001819	synonymous_variant	5339	exon15			GGTGGCGGGGGAG	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.2163C>T	8.37:g.145006866G>A		39.0	0.0	0		56.0	27.0	0.482143	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			G|0.994;A|0.006	0.006	strong		0.716	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
TNRC6A	27327	hgsc.bcm.edu	37	16	24802245	24802245	+	Missense_Mutation	SNP	T	T	G	rs112027699		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:24802245T>G	ENST00000395799.3	+	6	2411	c.2282T>G	c.(2281-2283)tTt>tGt	p.F761C	TNRC6A_ENST00000315183.7_Missense_Mutation_p.F761C	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	761	Interaction with argonaute family proteins.|Sufficient for interaction with AGO1 and AGO4.				cellular response to starvation (GO:0009267)|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)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		ACACAGACTTTTAACTCAGGG	0.488													T|||	1	0.000199681	0.0008	0.0	5008	,	,		19808	0.0		0.0	False		,,,				2504	0.0				p.F761C		Atlas-SNP	.											.	TNRC6A	171	.	0			c.T2282G						PASS	.	T	CYS/PHE	2,4390	2.1+/-5.4	0,2,2194	46.0	51.0	50.0		2282	4.7	1.0	16	dbSNP_132	50	0,8600		0,0,4300	no	missense	TNRC6A	NM_014494.2	205	0,2,6494	GG,GT,TT		0.0,0.0455,0.0154	benign	761/1963	24802245	2,12990	2196	4300	6496	SO:0001583	missense	27327	exon6			AGACTTTTAACTC	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"""Trinucleotide (CAG) repeat containing"""	11969	protein-coding gene	gene with protein product		610739	"""trinucleotide repeat containing 6"""	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.2282T>G	16.37:g.24802245T>G	ENSP00000379144:p.Phe761Cys	45.0	0.0	0		50.0	24.0	0.48	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Missense_Mutation	SNP	ENST00000395799.3	37	CCDS10624.2	.	.	.	.	.	.	.	.	.	.	T	9.930	1.214512	0.22289	4.55E-4	0.0	ENSG00000090905	ENST00000315183;ENST00000395799	T;T	0.11495	2.77;2.78	5.82	4.71	0.59529	.	0.329999	0.31859	N	0.006945	T	0.05410	0.0143	N	0.08118	0	0.80722	D	1	P;P;P	0.45078	0.687;0.681;0.85	B;B;B	0.42282	0.382;0.181;0.258	T	0.24440	-1.0160	10	0.56958	D	0.05	-1.2962	3.6846	0.08323	0.0:0.2795:0.0:0.7205	.	508;761;761	Q8NDV7-2;Q8NDV7-6;Q8NDV7	.;.;TNR6A_HUMAN	C	761	ENSP00000326900:F761C;ENSP00000379144:F761C	ENSP00000326900:F761C	F	+	2	0	TNRC6A	24709746	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.281000	0.33214	2.225000	0.72522	0.460000	0.39030	TTT	T|0.999;G|0.001	0.001	strong		0.488	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
SLC5A12	159963	hgsc.bcm.edu	37	11	26700344	26700344	+	Silent	SNP	G	G	C	rs150900623	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:26700344G>C	ENST00000396005.3	-	13	1803	c.1494C>G	c.(1492-1494)acC>acG	p.T498T		NM_178498.3	NP_848593.2	Q1EHB4	SC5AC_HUMAN	solute carrier family 5 (sodium/monocarboxylate cotransporter), member 12	498					sodium ion transport (GO:0006814)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	symporter activity (GO:0015293)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(1)	35						TCGAGTACCAGGTATCAGCTA	0.453													G|||	42	0.00838658	0.031	0.0014	5008	,	,		16935	0.0		0.0	False		,,,				2504	0.0				p.T498T		Atlas-SNP	.											.	SLC5A12	134	.	0			c.C1494G						PASS	.	G		75,3887		0,75,1906	116.0	114.0	115.0		1494	0.2	0.8	11	dbSNP_134	115	0,8338		0,0,4169	no	coding-synonymous	SLC5A12	NM_178498.3		0,75,6075	CC,CG,GG		0.0,1.893,0.6098		498/619	26700344	75,12225	1981	4169	6150	SO:0001819	synonymous_variant	159963	exon13			GTACCAGGTATCA	BC049207	CCDS7860.2	11p14.2	2013-07-19	2013-07-19		ENSG00000148942	ENSG00000148942		"""Solute carriers"""	28750	protein-coding gene	gene with protein product		612455	"""solute carrier family 5 (sodium/glucose cotransporter), member 12"""			12477932	Standard	NM_178498		Approved	MGC52019, SMCT2	uc001mra.2	Q1EHB4	OTTHUMG00000150706	ENST00000396005.3:c.1494C>G	11.37:g.26700344G>C		75.0	0.0	0		90.0	39.0	0.433333	NM_178498	Q86UC7	Silent	SNP	ENST00000396005.3	37	CCDS7860.2																																																																																			G|0.994;C|0.006	0.006	strong		0.453	SLC5A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319681.1	NM_178498	
UPF1	5976	hgsc.bcm.edu	37	19	18958562	18958562	+	Silent	SNP	A	A	T	rs73526913	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18958562A>T	ENST00000599848.1	+	3	590	c.381A>T	c.(379-381)ggA>ggT	p.G127G	UPF1_ENST00000262803.5_Silent_p.G127G			Q92900	RENT1_HUMAN	UPF1 regulator of nonsense transcripts homolog (yeast)	127	Sufficient for interaction with RENT2.				ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|dosage compensation by inactivation of X chromosome (GO:0009048)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of translational termination (GO:0006449)|RNA metabolic process (GO:0016070)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|exon-exon junction complex (GO:0035145)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	40						GTTACTGTGGAATACACGATC	0.428											OREG0025373	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	43	0.00858626	0.0318	0.0014	5008	,	,		19742	0.0		0.0	False		,,,				2504	0.0				p.G127G		Atlas-SNP	.											.	UPF1	88	.	0			c.A381T						PASS	.	A		130,4276	95.7+/-134.4	3,124,2076	128.0	120.0	123.0		381	-7.9	0.8	19	dbSNP_130	123	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	UPF1	NM_002911.3		3,125,6375	TT,TA,AA		0.0116,2.9505,1.0072		127/1119	18958562	131,12875	2203	4300	6503	SO:0001819	synonymous_variant	5976	exon3			CTGTGGAATACAC	AF074016	CCDS12386.1, CCDS74315.1	19p13.2-p13.11	2012-02-29	2006-02-07	2006-02-07	ENSG00000005007	ENSG00000005007			9962	protein-coding gene	gene with protein product	"""UP Frameshift 1"", ""smg-2 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	601430	"""regulator of nonsense transcripts 1"""	RENT1		8855285, 9064659	Standard	XM_005260015		Approved	HUPF1, KIAA0221, NORF1, pNORF1, smg-2	uc002nkf.3	Q92900		ENST00000599848.1:c.381A>T	19.37:g.18958562A>T		146.0	0.0	0	729	150.0	70.0	0.466667	NM_002911	O00239|O43343|Q86Z25|Q92842	Silent	SNP	ENST00000599848.1	37																																																																																				A|0.991;T|0.009	0.009	strong		0.428	UPF1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000464684.1	NM_002911	
XIRP2	129446	hgsc.bcm.edu	37	2	168100280	168100280	+	Missense_Mutation	SNP	G	G	A	rs201184820		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:168100280G>A	ENST00000409195.1	+	9	2467	c.2378G>A	c.(2377-2379)cGa>cAa	p.R793Q	XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.R793Q|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.R571Q|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409728.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	618					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						AAAGTTGTCCGAGGAATATCC	0.408													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18882	0.0		0.0	False		,,,				2504	0.0				p.R793Q		Atlas-SNP	.											XIRP2,larynx,carcinoma,+1,2	XIRP2	914	2	0			c.G2378A						PASS	.	G	GLN/ARG,GLN/ARG,,,	4,3694		0,4,1845	72.0	70.0	70.0		1712,2378,,,	5.9	1.0	2		70	0,8182		0,0,4091	yes	missense,missense,intron,intron,intron	XIRP2	NM_001199144.1,NM_152381.5,NM_001079810.3,NM_001199143.1,NM_001199145.1	43,43,,,	0,4,5936	AA,AG,GG		0.0,0.1082,0.0337	probably-damaging,probably-damaging,,,	571/3328,793/3550,,,	168100280	4,11876	1849	4091	5940	SO:0001583	missense	129446	exon9			TTGTCCGAGGAAT	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.2378G>A	2.37:g.168100280G>A	ENSP00000386840:p.Arg793Gln	199.0	0.0	0		140.0	83.0	0.592857	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	.	.	.	.	.	.	.	.	.	.	G	19.05	3.752177	0.69533	0.001082	0.0	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273	T;T;T	0.04234	3.68;3.68;3.67	5.92	5.92	0.95590	.	0.058183	0.64402	D	0.000001	T	0.24851	0.0603	M	0.80422	2.495	0.39027	D	0.959861	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.69479	0.92;0.964;0.964	T	0.00270	-1.1860	10	0.49607	T	0.09	-12.8648	20.3213	0.98679	0.0:0.0:1.0:0.0	.	618;618;571	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	Q	793;793;571	ENSP00000386840:R793Q;ENSP00000295237:R793Q;ENSP00000387255:R571Q	ENSP00000295237:R793Q	R	+	2	0	XIRP2	167808526	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.728000	0.54991	2.810000	0.96702	0.650000	0.86243	CGA	.	.	weak		0.408	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
RYR3	6263	hgsc.bcm.edu	37	15	34105084	34105084	+	Silent	SNP	A	A	G	rs16958093	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:34105084A>G	ENST00000389232.4	+	73	10348	c.10278A>G	c.(10276-10278)aaA>aaG	p.K3426K	RYR3_ENST00000415757.3_Silent_p.K3421K	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3426					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		CAGCTGTAAAATGGCAACTGA	0.428													A|||	198	0.0395367	0.1362	0.0101	5008	,	,		21062	0.006		0.0	False		,,,				2504	0.0051				p.K3426K		Atlas-SNP	.											.	RYR3	760	.	0			c.A10278G						PASS	.	A		360,3396		26,308,1544	88.0	85.0	86.0		10278	0.6	1.0	15	dbSNP_123	86	4,8238		0,4,4117	no	coding-synonymous	RYR3	NM_001036.3		26,312,5661	GG,GA,AA		0.0485,9.5847,3.0338		3426/4871	34105084	364,11634	1878	4121	5999	SO:0001819	synonymous_variant	6263	exon73			TGTAAAATGGCAA		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.10278A>G	15.37:g.34105084A>G		68.0	0.0	0		77.0	35.0	0.454545	NM_001036	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			A|0.955;G|0.045	0.045	strong		0.428	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
C15orf40	123207	hgsc.bcm.edu	37	15	83680313	83680313	+	Missense_Mutation	SNP	T	T	G	rs114478510	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:83680313T>G	ENST00000513601.2	-	1	54	c.47A>C	c.(46-48)aAt>aCt	p.N16T	C15orf40_ENST00000565712.1_Missense_Mutation_p.N16T|C15orf40_ENST00000304177.5_5'UTR|RP11-382A20.5_ENST00000566841.1_RNA|C15orf40_ENST00000451195.3_Missense_Mutation_p.N16T|C15orf40_ENST00000538348.2_Missense_Mutation_p.N16T|RP11-382A20.7_ENST00000570202.1_RNA			Q8WUR7	CO040_HUMAN	chromosome 15 open reading frame 40	16										large_intestine(3)|lung(2)|skin(1)	6						GCCCCGAGTATTGGGTGTTGC	0.692											OREG0023391	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	50	0.00998403	0.028	0.0144	5008	,	,		14631	0.0		0.003	False		,,,				2504	0.0				p.N16T		Atlas-SNP	.											.	C15orf40	18	.	0			c.A47C						PASS	.	T	THR/ASN,THR/ASN,THR/ASN,THR/ASN,THR/ASN	69,4335		0,69,2133	21.0	22.0	22.0		47,47,47,47,47	1.6	0.0	15	dbSNP_132	22	5,8595		0,5,4295	yes	missense,missense,missense,missense,missense	C15orf40	NM_144597.2,NM_001160116.1,NM_001160115.1,NM_001160114.1,NM_001160113.1	65,65,65,65,65	0,74,6428	GG,GT,TT		0.0581,1.5668,0.5691	benign,benign,benign,benign,benign	16/154,16/150,16/168,16/154,16/168	83680313	74,12930	2202	4300	6502	SO:0001583	missense	123207	exon1			CGAGTATTGGGTG	BC019820	CCDS32312.1, CCDS32312.2, CCDS53968.1, CCDS53969.1	15q25.2	2012-05-30			ENSG00000169609	ENSG00000169609			28443	protein-coding gene	gene with protein product							Standard	NM_144597		Approved	MGC29937	uc010uoo.1	Q8WUR7	OTTHUMG00000160473	ENST00000513601.2:c.47A>C	15.37:g.83680313T>G	ENSP00000424666:p.Asn16Thr	37.0	0.0	0	1223	30.0	9.0	0.3	NM_001160116	A6NIC9|B2R5E7|F5GX92|F8WD31|G5EA00	Missense_Mutation	SNP	ENST00000513601.2	37	CCDS32312.2	24	0.01098901098901099	16	0.032520325203252036	6	0.016574585635359115	0	0.0	2	0.002638522427440633	T	9.731	1.162258	0.21538	0.015668	5.81E-4	ENSG00000169609	ENST00000538348;ENST00000451195;ENST00000513601	.	.	.	3.61	1.58	0.23477	.	.	.	.	.	T	0.05823	0.0152	N	0.08118	0	0.20764	N	0.99985	B;B;B	0.17038	0.02;0.02;0.008	B;B;B	0.11329	0.006;0.006;0.006	T	0.15350	-1.0440	8	0.42905	T	0.14	.	5.5455	0.17061	0.0:0.7421:0.0:0.2579	.	16;16;16	F8WD31;F5GX92;G5EA00	.;.;.	T	16	.	ENSP00000403987:N16T	N	-	2	0	C15orf40	81471317	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.131000	0.10482	0.499000	0.27970	-0.624000	0.04008	AAT	T|0.992;G|0.008	0.008	strong		0.692	C15orf40-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360737.2	NM_144597	
WDR78	79819	hgsc.bcm.edu	37	1	67327986	67327986	+	Splice_Site	SNP	C	C	G	rs144890566		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:67327986C>G	ENST00000371026.3	-	7	996		c.e7-1		WDR78_ENST00000431318.1_Splice_Site|WDR78_ENST00000371023.3_Splice_Site|WDR78_ENST00000493572.1_5'UTR	NM_024763.4	NP_079039.4	Q5VTH9	WDR78_HUMAN	WD repeat domain 78						hematopoietic progenitor cell differentiation (GO:0002244)					NS(1)|endometrium(3)|kidney(6)|large_intestine(6)|lung(10)|ovary(3)|skin(3)	32						GACATTATGCCTAGATAAAGA	0.318																																					.		Atlas-SNP	.											.	WDR78	102	.	0			c.941-1G>C						PASS	.	C	,	2,4404	4.2+/-10.8	0,2,2201	65.0	65.0	65.0		,	4.8	0.6	1	dbSNP_134	65	0,8600		0,0,4300	no	splice-3,splice-3	WDR78	NM_024763.4,NM_207014.2	,	0,2,6501	GG,GC,CC		0.0,0.0454,0.0154	,	,	67327986	2,13004	2203	4300	6503	SO:0001630	splice_region_variant	79819	exon8			TTATGCCTAGATA	BX648840	CCDS635.1, CCDS44157.1	1p31.2	2014-02-21	2013-02-19	2013-02-19	ENSG00000152763	ENSG00000152763		"""WD repeat domain containing"""	26252	protein-coding gene	gene with protein product						21953912	Standard	NM_207014		Approved	DIC4, FLJ23129	uc001dcx.3	Q5VTH9	OTTHUMG00000009165	ENST00000371026.3:c.941-1G>C	1.37:g.67327986C>G		196.0	0.0	0		178.0	93.0	0.522472	NM_024763	A8K9W5|B5MDT3|H7BY80|Q5VTI0|Q8N5G5|Q9H5R9|Q9UF44	Splice_Site	SNP	ENST00000371026.3	37	CCDS635.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.64|17.64	3.440343|3.440343	0.63067|0.63067	4.54E-4|4.54E-4	0.0|0.0	ENSG00000152763|ENSG00000152763	ENST00000371026;ENST00000431318;ENST00000464352;ENST00000371023;ENST00000469450|ENST00000531552	.|T	.|0.55413	.|0.52	5.67|5.67	4.76|4.76	0.60689|0.60689	.|.	.|.	.|.	.|.	.|.	.|T	.|0.47544	.|0.1451	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.47262	.|-0.9131	.|5	.|.	.|.	.|.	.|.	12.3988|12.3988	0.55402|0.55402	0.0:0.9183:0.0:0.0817|0.0:0.9183:0.0:0.0817	.|.	.|.	.|.	.|.	.|R	-1|1	.|ENSP00000433037:G1R	.|.	.|G	-|-	.|1	.|0	WDR78|WDR78	67100574|67100574	1.000000|1.000000	0.71417|0.71417	0.631000|0.631000	0.29282|0.29282	0.826000|0.826000	0.46750|0.46750	4.397000|4.397000	0.59690|0.59690	1.393000|1.393000	0.46605|0.46605	0.591000|0.591000	0.81541|0.81541	.|GGC	C|1.000;G|0.000	0.000	weak		0.318	WDR78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025404.1	NM_024763	Intron
NPAP1	23742	hgsc.bcm.edu	37	15	24922407	24922407	+	Missense_Mutation	SNP	C	C	T	rs79339610	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:24922407C>T	ENST00000329468.2	+	1	1867	c.1393C>T	c.(1393-1395)Ctt>Ttt	p.L465F		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	465	Pro-rich.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											TCCTCTGGCTCTTCCTGCTGA	0.502													C|||	18	0.00359425	0.0121	0.0	5008	,	,		20216	0.0		0.002	False		,,,				2504	0.0				p.L465F		Atlas-SNP	.											C15orf2,colon,carcinoma,0,1	.	.	1	0			c.C1393T						PASS	.	C	PHE/LEU	56,4350		1,54,2148	191.0	185.0	187.0		1393	-4.1	0.0	15	dbSNP_131	187	1,8599		0,1,4299	yes	missense	C15orf2	NM_018958.2	22	1,55,6447	TT,TC,CC		0.0116,1.271,0.4383	probably-damaging	465/1157	24922407	57,12949	2203	4300	6503	SO:0001583	missense	23742	exon1			CTGGCTCTTCCTG	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"""chromosome 15 open reading frame 2"""	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.1393C>T	15.37:g.24922407C>T	ENSP00000333735:p.Leu465Phe	99.0	0.0	0		107.0	41.0	0.383178	NM_018958		Missense_Mutation	SNP	ENST00000329468.2	37	CCDS10015.1	6	0.0027472527472527475	5	0.01016260162601626	0	0.0	0	0.0	1	0.0013192612137203166	.	12.35	1.912039	0.33721	0.01271	1.16E-4	ENSG00000185823	ENST00000329468	T	0.10860	2.83	2.07	-4.13	0.03904	.	2.992630	0.01188	N	0.007259	T	0.04952	0.0133	L	0.29908	0.895	0.09310	N	1	B	0.31383	0.321	B	0.31614	0.133	T	0.14615	-1.0466	10	0.24483	T	0.36	.	2.191	0.03899	0.2812:0.1844:0.4144:0.12	.	465	Q9NZP6	CO002_HUMAN	F	465	ENSP00000333735:L465F	ENSP00000333735:L465F	L	+	1	0	C15orf2	22473500	0.000000	0.05858	0.000000	0.03702	0.366000	0.29705	-2.799000	0.00762	-2.586000	0.00459	0.313000	0.20887	CTT	C|0.996;T|0.004	0.004	strong		0.502	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958	
HDX	139324	hgsc.bcm.edu	37	X	83591879	83591879	+	Missense_Mutation	SNP	T	T	C	rs77791258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:83591879T>C	ENST00000297977.5	-	7	1781	c.1670A>G	c.(1669-1671)aAt>aGt	p.N557S	HDX_ENST00000506585.2_Missense_Mutation_p.N499S|HDX_ENST00000373177.2_Missense_Mutation_p.N557S	NM_001177479.1|NM_144657.4	NP_001170950.1|NP_653258.2	Q7Z353	HDX_HUMAN	highly divergent homeobox	557						nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(6)|kidney(2)|large_intestine(12)|liver(1)|lung(19)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	48						AACAACTTCATTGGGCTCTTC	0.333													t|||	172	0.0455629	0.1188	0.0216	3775	,	,		12736	0.0		0.0	False		,,,				2504	0.0				p.N557S	Pancreas(53;231 1169 36156 43751 51139)	Atlas-SNP	.											.	HDX	124	.	0			c.A1670G						PASS	.	C	SER/ASN,SER/ASN,SER/ASN	503,3330		35,338,95,1258,476	86.0	72.0	76.0		1496,1670,1670	-7.3	0.4	X	dbSNP_131	76	4,6720		0,4,0,2423,1870	yes	missense,missense,missense	HDX	NM_001177478.1,NM_001177479.1,NM_144657.4	46,46,46	35,342,95,3681,2346	CC,CT,C,TT,T		0.0595,13.1229,4.8025	benign,benign,benign	499/633,557/691,557/691	83591879	507,10050	2202	4297	6499	SO:0001583	missense	139324	exon7			ACTTCATTGGGCT	BX538112	CCDS35342.1, CCDS55456.1	Xq21.1	2012-03-09	2007-07-13	2007-07-13	ENSG00000165259	ENSG00000165259		"""Homeoboxes / POU class"""	26411	protein-coding gene	gene with protein product			"""chromosome X open reading frame 43"""	CXorf43			Standard	NM_144657		Approved	FLJ30678	uc004eek.2	Q7Z353	OTTHUMG00000021926	ENST00000297977.5:c.1670A>G	X.37:g.83591879T>C	ENSP00000297977:p.Asn557Ser	66.0	0.0	0		67.0	26.0	0.38806	NM_144657	A8K1Y5|B7ZL18|Q5JZB4|Q96NK7	Missense_Mutation	SNP	ENST00000297977.5	37	CCDS35342.1	60	0.03616636528028933	39	0.08369098712446352	4	0.011363636363636364	0	0.0	0	0.0	T	0.666	-0.803647	0.02841	0.131229	5.95E-4	ENSG00000165259	ENST00000297977;ENST00000373177;ENST00000506585	T;T;T	0.27557	1.66;1.66;1.66	5.33	-7.27	0.01461	.	0.753578	0.13237	N	0.403154	T	0.00144	0.0004	N	0.11560	0.145	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.04013	0.001	T	0.31888	-0.9927	9	0.06757	T	0.87	-14.8311	16.4567	0.84019	0.0:0.6124:0.0:0.3876	.	557	Q7Z353	HDX_HUMAN	S	557;499;557	ENSP00000297977:N557S;ENSP00000362272:N499S;ENSP00000423670:N557S	ENSP00000297977:N557S	N	-	2	0	HDX	83478535	0.008000	0.16893	0.432000	0.26747	0.605000	0.37080	-2.080000	0.01368	-1.696000	0.01421	0.409000	0.27619	AAT	T|0.950;C|0.050	0.050	strong		0.333	HDX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057379.2	NM_144657	
OGDHL	55753	hgsc.bcm.edu	37	10	50954850	50954850	+	Silent	SNP	G	G	A	rs75974530	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:50954850G>A	ENST00000374103.4	-	10	1327	c.1242C>T	c.(1240-1242)agC>agT	p.S414S	OGDHL_ENST00000419399.1_Silent_p.S357S|OGDHL_ENST00000432695.1_Silent_p.S205S	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	414					glycolytic process (GO:0006096)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	61						AGGGCAGGTCGCTCAGGTGGA	0.617													G|||	88	0.0175719	0.062	0.0072	5008	,	,		22610	0.0		0.001	False		,,,				2504	0.0				p.S414S		Atlas-SNP	.											.	OGDHL	149	.	0			c.C1242T						PASS	.	G	,,	299,4107	164.4+/-196.0	9,281,1913	151.0	102.0	119.0		1071,615,1242	-11.5	0.2	10	dbSNP_131	119	9,8591	6.4+/-24.3	0,9,4291	no	coding-synonymous,coding-synonymous,coding-synonymous	OGDHL	NM_001143996.1,NM_001143997.1,NM_018245.2	,,	9,290,6204	AA,AG,GG		0.1047,6.7862,2.3681	,,	357/954,205/802,414/1011	50954850	308,12698	2203	4300	6503	SO:0001819	synonymous_variant	55753	exon10			CAGGTCGCTCAGG	AK001713	CCDS7234.1, CCDS44390.1, CCDS44391.1	10q11.23	2013-09-20			ENSG00000197444	ENSG00000197444			25590	protein-coding gene	gene with protein product						10574462	Standard	NM_018245		Approved	FLJ10851	uc001jie.3	Q9ULD0	OTTHUMG00000018200	ENST00000374103.4:c.1242C>T	10.37:g.50954850G>A		114.0	0.0	0		126.0	66.0	0.52381	NM_018245	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Silent	SNP	ENST00000374103.4	37	CCDS7234.1																																																																																			G|0.976;A|0.024	0.024	strong		0.617	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245	
PTPRN	5798	hgsc.bcm.edu	37	2	220164886	220164886	+	Missense_Mutation	SNP	A	A	C	rs35314717	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220164886A>C	ENST00000295718.2	-	9	1497	c.1257T>G	c.(1255-1257)agT>agG	p.S419R	AC114803.3_ENST00000417355.1_RNA|PTPRN_ENST00000409251.3_Missense_Mutation_p.S419R|PTPRN_ENST00000423636.2_Missense_Mutation_p.S329R	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	419			S -> R (in dbSNP:rs35314717).		cytokine-mediated signaling pathway (GO:0019221)|peptidyl-tyrosine dephosphorylation (GO:0035335)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|response to reactive oxygen species (GO:0000302)	integral component of plasma membrane (GO:0005887)	spectrin binding (GO:0030507)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(3)|prostate(4)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		GCTGGACTTCACTGGAGGTAG	0.627													A|||	162	0.0323482	0.1172	0.0101	5008	,	,		16965	0.0		0.0	False		,,,				2504	0.0				p.S419R		Atlas-SNP	.											.	PTPRN	138	.	0			c.T1257G						PASS	.	A	ARG/SER,ARG/SER,ARG/SER	475,3931	223.9+/-240.3	29,417,1757	67.0	76.0	73.0		1257,987,1257	-2.4	0.0	2	dbSNP_126	73	6,8594	4.3+/-15.6	0,6,4294	yes	missense,missense,missense	PTPRN	NM_001199763.1,NM_001199764.1,NM_002846.3	110,110,110	29,423,6051	CC,CA,AA		0.0698,10.7808,3.6983	benign,benign,benign	419/951,329/890,419/980	220164886	481,12525	2203	4300	6503	SO:0001583	missense	5798	exon9			GACTTCACTGGAG		CCDS2440.1, CCDS56167.1, CCDS56168.1	2q35-q36.1	2011-06-09			ENSG00000054356	ENSG00000054356		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9676	protein-coding gene	gene with protein product		601773				8024693	Standard	NM_001199763		Approved	IA-2	uc002vkz.3	Q16849	OTTHUMG00000133129	ENST00000295718.2:c.1257T>G	2.37:g.220164886A>C	ENSP00000295718:p.Ser419Arg	73.0	0.0	0		89.0	53.0	0.595506	NM_002846	B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Missense_Mutation	SNP	ENST00000295718.2	37	CCDS2440.1	63	0.028846153846153848	61	0.12398373983739837	2	0.0055248618784530384	0	0.0	0	0.0	A	4.756	0.140493	0.09083	0.107808	6.98E-4	ENSG00000054356	ENST00000409251;ENST00000295718;ENST00000539342;ENST00000537666	T;T;T	0.27104	1.69;1.69;1.69	4.27	-2.38	0.06622	.	1.386960	0.04458	N	0.373874	T	0.00210	0.0006	N	0.24115	0.695	0.80722	P	0.0	B;B	0.23735	0.09;0.09	B;B	0.21360	0.034;0.015	T	0.23619	-1.0183	9	0.16420	T	0.52	.	7.6045	0.28095	0.276:0.1662:0.5578:0.0	rs35314717;rs60827710	419;419	Q6NSL1;Q16849	.;PTPRN_HUMAN	R	419;419;419;329	ENSP00000386638:S419R;ENSP00000295718:S419R;ENSP00000444244:S329R	ENSP00000295718:S419R	S	-	3	2	PTPRN	219873130	0.000000	0.05858	0.001000	0.08648	0.379000	0.30106	-0.764000	0.04735	-0.686000	0.05170	0.459000	0.35465	AGT	A|0.966;C|0.034	0.034	strong		0.627	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256819.2		
OC90	729330	hgsc.bcm.edu	37	8	133044172	133044172	+	Silent	SNP	G	G	A	rs6989686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133044172G>A	ENST00000443356.2	-	13	1121	c.1035C>T	c.(1033-1035)taC>taT	p.Y345Y	OC90_ENST00000603859.1_Silent_p.Y329Y|OC90_ENST00000254627.3_Silent_p.Y329Y|OC90_ENST00000262283.5_Silent_p.Y541Y			Q02509	OC90_HUMAN	otoconin 90	345	Phospholipase A2-like 2.				lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(23)|ovary(2)|prostate(1)|skin(1)	37	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)			CTTGTCCACAGTAACAGCCAT	0.542													G|||	45	0.00898562	0.0325	0.0029	5008	,	,		19082	0.0		0.0	False		,,,				2504	0.0				p.Y329Y		Atlas-SNP	.											.	OC90	163	.	0			c.C987T						PASS	.	G		111,3919		1,109,1905	57.0	60.0	59.0		987	4.1	1.0	8	dbSNP_116	59	1,8369		0,1,4184	no	coding-synonymous	OC90	NM_001080399.2		1,110,6089	AA,AG,GG		0.0119,2.7543,0.9032		329/478	133044172	112,12288	2015	4185	6200	SO:0001819	synonymous_variant	729330	exon12			TCCACAGTAACAG	Z14310	CCDS47919.1	8q24.22	2011-03-01			ENSG00000253117	ENSG00000253117			8100	protein-coding gene	gene with protein product		601658		PLA2L		10329003, 9860971	Standard	NM_001080399		Approved		uc011lix.1	Q02509	OTTHUMG00000164672	ENST00000443356.2:c.1035C>T	8.37:g.133044172G>A		130.0	0.0	0		144.0	65.0	0.451389	NM_001080399	B4DNG8	Silent	SNP	ENST00000443356.2	37																																																																																				G|0.994;A|0.006	0.006	strong		0.542	OC90-201	KNOWN	basic	protein_coding	protein_coding		NM_001080399	
PLXNB2	23654	hgsc.bcm.edu	37	22	50718941	50718941	+	Silent	SNP	C	C	T	rs73891209	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50718941C>T	ENST00000449103.1	-	25	4292	c.4152G>A	c.(4150-4152)aaG>aaA	p.K1384K	PLXNB2_ENST00000359337.4_Silent_p.K1384K|PLXNB2_ENST00000496720.1_5'Flank			O15031	PLXB2_HUMAN	plexin B2	1384					brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GCTTGGGGTTCTTGGCCACCA	0.692													C|||	222	0.0443291	0.1619	0.0115	5008	,	,		9618	0.0		0.0	False		,,,				2504	0.0				p.K1384K		Atlas-SNP	.											.	PLXNB2	172	.	0			c.G4152A						PASS	.	C		556,3828		45,466,1681	75.0	80.0	78.0		4152	4.3	1.0	22	dbSNP_130	78	1,8583		0,1,4291	no	coding-synonymous	PLXNB2	NM_012401.3		45,467,5972	TT,TC,CC		0.0116,12.6825,4.2952		1384/1839	50718941	557,12411	2192	4292	6484	SO:0001819	synonymous_variant	23654	exon25			GGGGTTCTTGGCC		CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"""Plexins"""	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.4152G>A	22.37:g.50718941C>T		22.0	0.0	0		29.0	11.0	0.37931	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Silent	SNP	ENST00000449103.1	37	CCDS43035.1																																																																																			C|0.976;G|0.000;T|0.024	0.024	strong		0.692	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401	
MUC17	140453	hgsc.bcm.edu	37	7	100675367	100675367	+	Missense_Mutation	SNP	A	A	G	rs116801454	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100675367A>G	ENST00000306151.4	+	3	734	c.670A>G	c.(670-672)Agc>Ggc	p.S224G		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	224	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					TATGCCTGCCAGCACCATGAA	0.473													A|||	67	0.0133786	0.0492	0.0029	5008	,	,		23907	0.0		0.0	False		,,,				2504	0.0				p.S224G		Atlas-SNP	.											.	MUC17	804	.	0			c.A670G						PASS	.	A	GLY/SER	208,4198	127.8+/-164.7	5,198,2000	175.0	178.0	177.0		670	-0.9	0.0	7	dbSNP_132	177	2,8598	1.2+/-3.3	0,2,4298	yes	missense	MUC17	NM_001040105.1	56	5,200,6298	GG,GA,AA		0.0233,4.7208,1.6146	possibly-damaging	224/4494	100675367	210,12796	2203	4300	6503	SO:0001583	missense	140453	exon3			CCTGCCAGCACCA	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.670A>G	7.37:g.100675367A>G	ENSP00000302716:p.Ser224Gly	99.0	0.0	0		107.0	46.0	0.429907	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	24	0.01098901098901099	24	0.04878048780487805	0	0.0	0	0.0	0	0.0	A	1.401	-0.578226	0.03854	0.047208	2.33E-4	ENSG00000169876	ENST00000306151	T	0.02552	4.25	0.801	-0.886	0.10590	.	.	.	.	.	T	0.00210	0.0006	N	0.08118	0	0.09310	N	1	P	0.51933	0.949	B	0.34138	0.176	T	0.46843	-0.9162	9	0.23302	T	0.38	.	2.6539	0.05007	0.5677:0.0:0.0:0.4323	.	224	Q685J3	MUC17_HUMAN	G	224	ENSP00000302716:S224G	ENSP00000302716:S224G	S	+	1	0	MUC17	100462087	0.006000	0.16342	0.000000	0.03702	0.006000	0.05464	0.201000	0.17276	-0.273000	0.09246	0.165000	0.16767	AGC	A|0.987;G|0.013	0.013	strong		0.473	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CFAP53	220136	hgsc.bcm.edu	37	18	47788535	47788535	+	Missense_Mutation	SNP	G	G	A	rs138060809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:47788535G>A	ENST00000398545.4	-	2	241	c.124C>T	c.(124-126)Cgc>Tgc	p.R42C		NM_145020.3	NP_659457.2														endometrium(1)|kidney(4)|large_intestine(6)|lung(6)|ovary(1)|pancreas(1)|skin(1)	20				STAD - Stomach adenocarcinoma(97;2.66e-05)|Colorectal(21;7.57e-05)|Lung(128;0.00932)|READ - Rectum adenocarcinoma(32;0.164)		TGATGGCTGCGTCGGATTCTT	0.433													G|||	5	0.000998403	0.0038	0.0	5008	,	,		18710	0.0		0.0	False		,,,				2504	0.0				p.R42C		Atlas-SNP	.											.	CCDC11	59	.	0			c.C124T						PASS	.	G	CYS/ARG	8,3834		0,8,1913	118.0	113.0	115.0		124	4.2	0.0	18	dbSNP_134	115	0,8250		0,0,4125	yes	missense	CCDC11	NM_145020.3	180	0,8,6038	AA,AG,GG		0.0,0.2082,0.0662	probably-damaging	42/515	47788535	8,12084	1921	4125	6046	SO:0001583	missense	220136	exon2			GGCTGCGTCGGAT																												ENST00000398545.4:c.124C>T	18.37:g.47788535G>A	ENSP00000381553:p.Arg42Cys	98.0	0.0	0		106.0	57.0	0.537736	NM_145020		Missense_Mutation	SNP	ENST00000398545.4	37	CCDS11940.2	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	6.779	0.512676	0.12944	0.002082	0.0	ENSG00000172361	ENST00000398545	T	0.35789	1.29	5.12	4.24	0.50183	.	0.138507	0.22268	U	0.062301	T	0.37237	0.0996	L	0.58101	1.795	0.09310	N	0.999996	D	0.64830	0.994	P	0.44477	0.451	T	0.35001	-0.9806	10	0.72032	D	0.01	0.0534	11.0958	0.48143	0.0:0.0:0.8151:0.1849	.	42	Q96M91	CCD11_HUMAN	C	42	ENSP00000381553:R42C	ENSP00000381553:R42C	R	-	1	0	CCDC11	46042533	0.058000	0.20735	0.003000	0.11579	0.110000	0.19582	3.065000	0.49994	1.503000	0.48686	-0.309000	0.09137	CGC	G|0.999;A|0.001	0.001	strong		0.433	CCDC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255922.3		
PLA2G4C	8605	hgsc.bcm.edu	37	19	48558159	48558159	+	Silent	SNP	G	G	A	rs2307280	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:48558159G>A	ENST00000599921.1	-	15	1762	c.1405C>T	c.(1405-1407)Ctg>Ttg	p.L469L	PLA2G4C_ENST00000596510.1_5'UTR|PLA2G4C_ENST00000599111.1_Silent_p.L479L|PLA2G4C_ENST00000413144.2_Silent_p.L469L|PLA2G4C_ENST00000354276.3_Silent_p.L469L			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	469	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				arachidonic acid metabolic process (GO:0019369)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|parturition (GO:0007567)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(12)|lung(13)|ovary(2)|prostate(1)|skin(3)	38		all_cancers(25;2.84e-05)|all_lung(116;4.62e-05)|Lung NSC(112;7.61e-05)|all_epithelial(76;0.000192)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;8.09e-05)|all cancers(93;0.000517)|Epithelial(262;0.0135)|GBM - Glioblastoma multiforme(486;0.0717)		ATGTTGAACAGGGGAAAATGC	0.517													g|||	408	0.0814696	0.2965	0.0231	5008	,	,		18425	0.0		0.0	False		,,,				2504	0.0				p.L479L		Atlas-SNP	.											.	PLA2G4C	76	.	0			c.C1435T						PASS	.	G	,,	996,3410	372.2+/-320.3	116,764,1323	110.0	102.0	105.0		1435,1405,1405	1.9	0.9	19	dbSNP_100	105	12,8588	7.7+/-29.5	0,12,4288	no	coding-synonymous,coding-synonymous,coding-synonymous	PLA2G4C	NM_001159322.1,NM_001159323.1,NM_003706.2	,,	116,776,5611	AA,AG,GG		0.1395,22.6055,7.7503	,,	479/552,469/528,469/542	48558159	1008,11998	2203	4300	6503	SO:0001819	synonymous_variant	8605	exon15			TGAACAGGGGAAA	AF065214	CCDS12710.1, CCDS54286.1, CCDS59403.1	19q13.3	2008-09-19					3.1.1.4		9037	protein-coding gene	gene with protein product		603602				9705332	Standard	NM_003706		Approved	cPLA2-gamma	uc002phx.3	Q9UP65		ENST00000599921.1:c.1405C>T	19.37:g.48558159G>A		121.0	0.0	0		130.0	66.0	0.507692	NM_001159322	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Silent	SNP	ENST00000599921.1	37	CCDS12710.1																																																																																			G|0.926;A|0.074	0.074	strong		0.517	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1		
C2CD3	26005	hgsc.bcm.edu	37	11	73759254	73759254	+	Missense_Mutation	SNP	C	C	A	rs1632245	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:73759254C>A	ENST00000334126.7	-	28	5717	c.5491G>T	c.(5491-5493)Ggg>Tgg	p.G1831W	C2CD3_ENST00000313663.7_Missense_Mutation_p.G1831W			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1831			G -> W (in dbSNP:rs1632245).		brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					ACTCACCTCCCAGGAGAGGAG	0.443													C|||	243	0.0485224	0.1778	0.0115	5008	,	,		19111	0.0		0.0	False		,,,				2504	0.0				p.G1831W		Atlas-SNP	.											C2CD3_ENST00000334126,NS,carcinoma,+2,2	C2CD3	288	2	0			c.G5491T						PASS	.						58.0	53.0	55.0					11																	73759254		2200	4293	6493	SO:0001583	missense	26005	exon28			ACCTCCCAGGAGA	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.5491G>T	11.37:g.73759254C>A	ENSP00000334379:p.Gly1831Trp	98.0	0.0	0		100.0	42.0	0.42	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	37		76|76	0.0347985347985348|0.0347985347985348	71|71	0.1443089430894309|0.1443089430894309	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	0|0	0.0|0.0	C|C	12.63|12.63	1.994257|1.994257	0.35226|0.35226	.|.	.|.	ENSG00000168014|ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681;ENST00000414160|ENST00000538361	T;T;T|.	0.14266|.	2.91;2.93;2.52|.	4.75|4.75	0.796|0.796	0.18648|0.18648	.|.	0.878366|.	0.10272|.	N|.	0.694613|.	T|T	0.00328|0.00328	0.0010|0.0010	L|L	0.47716|0.47716	1.5|1.5	0.42535|0.42535	P|P	0.006946000000000008|0.006946000000000008	D|.	0.60575|.	0.988|.	P|.	0.62089|.	0.898|.	T|T	0.09640|0.09640	-1.0665|-1.0665	9|4	0.72032|.	D|.	0.01|.	.|.	3.8081|3.8081	0.08786|0.08786	0.0:0.518:0.1836:0.2984|0.0:0.518:0.1836:0.2984	rs1632245;rs52791226;rs1632245|rs1632245;rs52791226;rs1632245	1831|.	Q4AC94-1|.	.|.	W|L	1831;1831;1812;639|64	ENSP00000334379:G1831W;ENSP00000323339:G1831W;ENSP00000388750:G639W|.	ENSP00000323339:G1831W|.	G|W	-|-	1|2	0|0	C2CD3|C2CD3	73436902|73436902	0.919000|0.919000	0.31177|0.31177	0.959000|0.959000	0.39883|0.39883	0.175000|0.175000	0.22909|0.22909	0.834000|0.834000	0.27518|0.27518	0.312000|0.312000	0.23038|0.23038	0.655000|0.655000	0.94253|0.94253	GGG|TGG	A|0.037;C|0.963	0.037	strong		0.443	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531	
P2RX7	5027	hgsc.bcm.edu	37	12	121622115	121622115	+	Missense_Mutation	SNP	C	C	T	rs28360459	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:121622115C>T	ENST00000546057.1	+	13	1441	c.1298C>T	c.(1297-1299)gCg>gTg	p.A433V	P2RX7_ENST00000443520.3_3'UTR|P2RX7_ENST00000328963.5_Missense_Mutation_p.A263V|P2RX7_ENST00000541446.1_Missense_Mutation_p.A144V|P2RX7_ENST00000535250.1_Missense_Mutation_p.A343V	NM_002562.5	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 7	433			A -> V (in dbSNP:rs28360459).		apoptotic signaling pathway (GO:0097190)|bleb assembly (GO:0032060)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|membrane depolarization (GO:0051899)|negative regulation of bone resorption (GO:0045779)|negative regulation of MAPK cascade (GO:0043409)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|pore complex assembly (GO:0046931)|positive regulation of bone mineralization (GO:0030501)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cytolysis (GO:0045919)|positive regulation of cytoskeleton organization (GO:0051495)|positive regulation of interleukin-1 beta secretion (GO:0050718)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of killing of cells of other organism (GO:0051709)|regulation of sodium ion transport (GO:0002028)|response to ATP (GO:0033198)|sensory perception of pain (GO:0019233)	bleb (GO:0032059)|cytoplasm (GO:0005737)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|lipopolysaccharide binding (GO:0001530)|protein homodimerization activity (GO:0042803)|purinergic nucleotide receptor activity (GO:0001614)|receptor binding (GO:0005102)			NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(9)|skin(1)|stomach(1)	19	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CAGAGACCTGCGATGGACTTC	0.453													C|||	177	0.0353435	0.1278	0.0115	5008	,	,		17958	0.0		0.0	False		,,,				2504	0.0				p.A433V		Atlas-SNP	.											.	P2RX7	53	.	0			c.C1298T						PASS	.	C	VAL/ALA	510,3896	235.5+/-248.0	29,452,1722	68.0	71.0	70.0		1298	-5.1	0.0	12	dbSNP_125	70	6,8594	3.7+/-12.6	0,6,4294	yes	missense	P2RX7	NM_002562.5	64	29,458,6016	TT,TC,CC		0.0698,11.5751,3.9674	benign	433/596	121622115	516,12490	2203	4300	6503	SO:0001583	missense	5027	exon13			GACCTGCGATGGA	Y09561	CCDS9213.1	12q24	2012-01-17			ENSG00000089041	ENSG00000089041		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8537	protein-coding gene	gene with protein product		602566				9038151, 9826911	Standard	NM_002562		Approved	P2X7, MGC20089	uc001tzm.3	Q99572	OTTHUMG00000169153	ENST00000546057.1:c.1298C>T	12.37:g.121622115C>T	ENSP00000442349:p.Ala433Val	37.0	0.0	0		28.0	11.0	0.392857	NM_002562	A8K2Z0|E7EMK6|F5H6P2|F5H7E8|F8W951|O14991|Q4VKH8|Q4VKH9|Q4VKI0|Q4VKI1|Q4VKI2|Q4VKI3|Q4VKI4|Q7Z771|Q96EV7	Missense_Mutation	SNP	ENST00000546057.1	37	CCDS9213.1	63	0.028846153846153848	58	0.11788617886178862	5	0.013812154696132596	0	0.0	0	0.0	C	2.926	-0.222035	0.06061	0.115751	6.98E-4	ENSG00000089041	ENST00000546057;ENST00000328963;ENST00000535250;ENST00000541446	T;T;T;T	0.05139	4.39;4.0;4.17;3.49	5.21	-5.06	0.02946	.	2.346980	0.01797	N	0.032678	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B;B;B;B	0.14805	0.011;0.001;0.011;0.003	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.42865	-0.9426	9	0.39692	T	0.17	0.4342	1.6799	0.02830	0.4149:0.2708:0.0915:0.2229	rs28360459	263;144;343;433	F8W951;F5H6P2;F5H7E8;Q99572	.;.;.;P2RX7_HUMAN	V	433;263;343;144	ENSP00000442349:A433V;ENSP00000330696:A263V;ENSP00000442572:A343V;ENSP00000437471:A144V	ENSP00000330696:A263V	A	+	2	0	P2RX7	120106498	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-0.486000	0.06513	-0.443000	0.07180	-0.218000	0.12543	GCG	C|0.965;T|0.035	0.035	strong		0.453	P2RX7-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402532.1	NM_002562	
TTN	7273	hgsc.bcm.edu	37	2	179435887	179435887	+	Missense_Mutation	SNP	A	A	G	rs744427	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179435887A>G	ENST00000591111.1	-	276	70273	c.70049T>C	c.(70048-70050)aTt>aCt	p.I23350T	TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.I16118T|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.I22423T|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.I16051T|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.I15926T|TTN_ENST00000589042.1_Missense_Mutation_p.I24991T			Q8WZ42	TITIN_HUMAN	titin	23350	Fibronectin type-III 69. {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)			CGGCTTGCCAATGCCCACGAT	0.438													A|||	82	0.0163738	0.0582	0.0072	5008	,	,		22831	0.0		0.0	False		,,,				2504	0.0				p.I24991T		Atlas-SNP	.											.	TTN	18412	.	0			c.T74972C						PASS	.	A	THR/ILE,THR/ILE,THR/ILE,THR/ILE	193,3777		5,183,1797	107.0	108.0	107.0		48353,48152,67268,47777	4.1	0.9	2	dbSNP_86	107	1,8337		0,1,4168	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	89,89,89,89	5,184,5965	GG,GA,AA		0.012,4.8615,1.5762	benign,benign,benign,benign	16118/27119,16051/27052,22423/33424,15926/26927	179435887	194,12114	1985	4169	6154	SO:0001583	missense	7273	exon326			TTGCCAATGCCCA	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.70049T>C	2.37:g.179435887A>G	ENSP00000465570:p.Ile23350Thr	53.0	0.0	0		70.0	37.0	0.528571	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		42	0.019230769230769232	39	0.07926829268292683	3	0.008287292817679558	0	0.0	0	0.0	A	9.233	1.036446	0.19669	0.048615	1.2E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.53206	0.63;0.63;0.63;0.63	5.28	4.13	0.48395	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.02418	0.0074	L	0.33093	0.98	0.25488	N	0.987672	B;B;B;B	0.09022	0.0;0.0;0.002;0.002	B;B;B;B	0.09377	0.001;0.001;0.004;0.004	T	0.05419	-1.0886	9	0.87932	D	0	.	11.1794	0.48618	0.9275:0.0:0.0725:0.0	rs744427;rs52837048;rs744427	15926;16051;16118;23350	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	T	22423;15926;16118;16051;15924	ENSP00000343764:I22423T;ENSP00000434586:I15926T;ENSP00000340554:I16118T;ENSP00000352154:I16051T	ENSP00000340554:I16118T	I	-	2	0	TTN	179144133	1.000000	0.71417	0.915000	0.36163	0.984000	0.73092	6.333000	0.72939	0.959000	0.37980	-0.256000	0.11100	ATT	A|0.984;G|0.016	0.016	strong		0.438	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
MT-ND5	4540	hgsc.bcm.edu	37	M	12477	12477	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:12477T>C	ENST00000361567.2	+	1	141	c.141T>C	c.(139-141)agT>agC	p.S47S	MT-TR_ENST00000387439.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	47					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						TTTATTATCAGTCTCTTCCCC	0.438																																					p.S47S		Atlas-SNP	.											.	.	.	.	0			c.T141C						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			TATCAGTCTCTTC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.141T>C	M.37:g.12477T>C		8.0	0.0	0		12.0	12.0	1	ENST00000361567	Q34773|Q8WCY3	Silent	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.438	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
NMRK2	27231	hgsc.bcm.edu	37	19	3942110	3942110	+	Missense_Mutation	SNP	G	G	A	rs16992131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3942110G>A	ENST00000168977.2	+	8	822	c.532G>A	c.(532-534)Gag>Aag	p.E178K	NMRK2_ENST00000593949.1_Missense_Mutation_p.E183K|NMRK2_ENST00000599576.1_Missense_Mutation_p.G109E	NM_170678.2	NP_733778.1	Q9NPI5	NRK2_HUMAN	nicotinamide riboside kinase 2	178			E -> K (in dbSNP:rs16992131).		NAD biosynthetic process (GO:0009435)|negative regulation of myoblast differentiation (GO:0045662)	intracellular (GO:0005622)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|ribosylnicotinamide kinase activity (GO:0050262)										GTCCCGAGAGGAGCTCTTCCG	0.642													G|||	117	0.0233626	0.084	0.0072	5008	,	,		15546	0.0		0.001	False		,,,				2504	0.0				p.E178K		Atlas-SNP	.											.	.	.	.	0			c.G532A						PASS	.	G	LYS/GLU	299,4107	154.4+/-187.8	9,281,1913	47.0	47.0	47.0		532	2.8	0.0	19	dbSNP_123	47	7,8593	5.0+/-18.6	0,7,4293	yes	missense	ITGB1BP3	NM_170678.2	56	9,288,6206	AA,AG,GG		0.0814,6.7862,2.3528	benign	178/231	3942110	306,12700	2203	4300	6503	SO:0001583	missense	27231	exon8			CGAGAGGAGCTCT	AF190819	CCDS12115.1, CCDS74259.1	19p13.3	2013-10-28	2012-05-31	2012-05-31	ENSG00000077009	ENSG00000077009			17871	protein-coding gene	gene with protein product	"""muscle-specific beta 1 integrin binding protein"", ""nicotinamide riboside kinase 2"""	608705	"""integrin beta 1 binding protein 3"""	ITGB1BP3		10613898, 15137942	Standard	NM_170678		Approved	MIBP, NRK2	uc002lyz.4	Q9NPI5	OTTHUMG00000181758	ENST00000168977.2:c.532G>A	19.37:g.3942110G>A	ENSP00000168977:p.Glu178Lys	64.0	0.0	0		81.0	38.0	0.469136	NM_170678	B7ZKR3|Q52M81|Q9NZK3	Missense_Mutation	SNP	ENST00000168977.2	37	CCDS12115.1	41	0.018772893772893772	39	0.07926829268292683	2	0.0055248618784530384	0	0.0	0	0.0	G	11.37	1.619506	0.28801	0.067862	8.14E-4	ENSG00000077009	ENST00000168977;ENST00000395034	T	0.59502	0.26	3.83	2.76	0.32466	.	0.214037	0.37437	U	0.002089	T	0.03959	0.0111	L	0.42245	1.32	0.31116	N	0.709375	B;P	0.37423	0.444;0.594	B;B	0.41412	0.356;0.231	T	0.08994	-1.0695	10	0.18710	T	0.47	-9.412	9.3096	0.37895	0.0:0.2212:0.7788:0.0	rs16992131;rs16992131	183;178	B7ZKR3;Q9NPI5	.;NRK2_HUMAN	K	178;134	ENSP00000168977:E178K	ENSP00000168977:E178K	E	+	1	0	ITGB1BP3	3893110	1.000000	0.71417	0.005000	0.12908	0.070000	0.16714	4.069000	0.57541	0.585000	0.29608	0.485000	0.47835	GAG	G|0.977;A|0.023	0.023	strong		0.642	NMRK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457492.1	NM_014446, NM_170678	
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39261717	39261717	+	Missense_Mutation	SNP	G	G	A	rs149483591	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39261717G>A	ENST00000391415.1	+	1	134	c.77G>A	c.(76-78)cGc>cAc	p.R26H		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	26	29 X 5 AA repeats of C-C-[RQVHIEK]- [SPTR]-[VSTQCRNP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						ACCTGCTGCCGCCCCAGCTGC	0.647													G|||	272	0.0543131	0.1959	0.0173	5008	,	,		18818	0.0		0.001	False		,,,				2504	0.0				p.R26H		Atlas-SNP	.											KRTAP4-9,NS,carcinoma,+1,1	KRTAP4-9	110	1	0			c.G77A						scavenged	.	G	HIS/ARG	218,1166		12,194,486	16.0	21.0	19.0		77	-0.7	1.0	17	dbSNP_134	19	2,3178		0,2,1588	no	missense	KRTAP4-9	NM_001146041.1	29	12,196,2074	AA,AG,GG		0.0629,15.7514,4.8203	benign	26/211	39261717	220,4344	692	1590	2282	SO:0001583	missense	100132386	exon1			GCTGCCGCCCCAG	AJ406941	CCDS54124.1	17q21.2	2013-06-25			ENSG00000212722	ENSG00000212722		"""Keratin associated proteins"""	18910	protein-coding gene	gene with protein product							Standard	NM_001146041		Approved	KAP4.9	uc010wfp.2	Q9BYQ8	OTTHUMG00000133584	ENST00000391415.1:c.77G>A	17.37:g.39261717G>A	ENSP00000375234:p.Arg26His	129.0	2.0	0.0155039		120.0	60.0	0.5	NM_001146041		Missense_Mutation	SNP	ENST00000391415.1	37	CCDS54124.1	95	0.043498168498168496	89	0.18089430894308944	6	0.016574585635359115	0	0.0	0	0.0	.	10.53	1.376288	0.24857	0.157514	6.29E-4	ENSG00000212722	ENST00000391415;ENST00000333994	T	0.32515	1.45	3.31	-0.714	0.11219	.	.	.	.	.	T	0.00073	0.0002	M	0.79614	2.46	0.52099	P	5.999999999994898E-5	B	0.25521	0.128	B	0.20767	0.031	T	0.08310	-1.0728	8	0.37606	T	0.19	.	6.5459	0.22406	0.5339:0.0:0.4661:0.0	.	26	Q9BYQ8	KRA49_HUMAN	H	26	ENSP00000375234:R26H	ENSP00000334461:R26H	R	+	2	0	KRTAP4-9	36515243	0.000000	0.05858	0.986000	0.45419	0.476000	0.33039	-1.656000	0.01980	-0.101000	0.12219	0.194000	0.17425	CGC	G|0.956;A|0.044	0.044	strong		0.647	KRTAP4-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257688.1	NM_001146041	
ITGA2B	3674	hgsc.bcm.edu	37	17	42457120	42457120	+	Silent	SNP	C	C	T	rs5912	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:42457120C>T	ENST00000262407.5	-	18	1846	c.1815G>A	c.(1813-1815)ccG>ccA	p.P605P	ITGA2B_ENST00000353281.4_Silent_p.P605P	NM_000419.3	NP_000410.2	P08514	ITA2B_HUMAN	integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41)	605					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of leukocyte migration (GO:0002687)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)	extracellular matrix binding (GO:0050840)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			biliary_tract(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.191)	Abciximab(DB00054)|Tirofiban(DB00775)	CCTCCGTGGGCGGTAGGGACA	0.617													C|||	59	0.0117812	0.0318	0.0159	5008	,	,		19144	0.0		0.006	False		,,,				2504	0.0				p.P605P		Atlas-SNP	.											ITGA2B,colon,carcinoma,-1,1	ITGA2B	88	1	0			c.G1815A						PASS	.	C		174,4232	111.6+/-149.8	4,166,2033	94.0	82.0	86.0		1815	-3.7	0.0	17	dbSNP_52	86	67,8533	39.8+/-96.3	0,67,4233	no	coding-synonymous	ITGA2B	NM_000419.3		4,233,6266	TT,TC,CC		0.7791,3.9492,1.853		605/1040	42457120	241,12765	2203	4300	6503	SO:0001819	synonymous_variant	3674	exon18			CGTGGGCGGTAGG		CCDS32665.1	17q21.32	2014-09-17	2006-02-22			ENSG00000005961		"""CD molecules"", ""Integrins"""	6138	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 93"""	607759	"""integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B)"""	GP2B			Standard	NM_000419		Approved	CD41B, CD41, PPP1R93	uc002igt.1	P08514		ENST00000262407.5:c.1815G>A	17.37:g.42457120C>T		81.0	0.0	0		100.0	52.0	0.52	NM_000419	B2RCY8|O95366|Q14443|Q17R67	Silent	SNP	ENST00000262407.5	37	CCDS32665.1																																																																																			C|0.982;T|0.018	0.018	strong		0.617	ITGA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439823.1		
ZHX1	11244	hgsc.bcm.edu	37	8	124265676	124265676	+	Silent	SNP	C	C	T	rs34145851	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:124265676C>T	ENST00000522655.1	-	3	3051	c.2511G>A	c.(2509-2511)gaG>gaA	p.E837E	ZHX1_ENST00000297857.2_Silent_p.E837E|ZHX1_ENST00000395571.3_Silent_p.E837E|ZHX1-C8ORF76_ENST00000357082.4_Intron|ZHX1_ENST00000522595.1_5'Flank			Q9UKY1	ZHX1_HUMAN	zinc fingers and homeoboxes 1	837	Required for repressor activity.				cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(37;1.25e-09)|Ovarian(258;0.0154)		STAD - Stomach adenocarcinoma(47;0.00527)			CTTCATCTTCCTCCTCATTTT	0.398													C|||	69	0.013778	0.0514	0.0014	5008	,	,		18508	0.0		0.0	False		,,,				2504	0.0				p.E837E		Atlas-SNP	.											ZHX1,NS,carcinoma,-2,1	ZHX1	89	1	0			c.G2511A						PASS	.	C	,,	194,4212	122.9+/-160.3	4,186,2013	210.0	202.0	205.0		2511,,2511	1.6	1.0	8	dbSNP_126	205	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,intron,coding-synonymous	ZHX1,ZHX1-C8ORF76	NM_001017926.2,NM_001204180.1,NM_007222.4	,,	4,187,6312	TT,TC,CC		0.0116,4.4031,1.4993	,,	837/874,,837/874	124265676	195,12811	2203	4300	6503	SO:0001819	synonymous_variant	11244	exon3			ATCTTCCTCCTCA	AF106862	CCDS6342.1	8q24.13	2012-03-09	2004-01-23		ENSG00000165156	ENSG00000165156		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	12871	protein-coding gene	gene with protein product		604764	"""zinc-fingers and homeoboxes 1"""			10441475	Standard	NM_001017926		Approved		uc003yqe.3	Q9UKY1	OTTHUMG00000165088	ENST00000522655.1:c.2511G>A	8.37:g.124265676C>T		325.0	0.0	0		311.0	149.0	0.4791	NM_007222	Q8IWD8	Silent	SNP	ENST00000522655.1	37	CCDS6342.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	C	5.662	0.306815	0.10733	0.044031	1.16E-4	ENSG00000165156	ENST00000520474	.	.	.	5.95	1.57	0.23409	.	.	.	.	.	T	0.20170	0.0485	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.09997	-1.0649	4	.	.	.	-14.7224	5.1468	0.14989	0.1123:0.5612:0.198:0.1285	rs34145851	.	.	.	K	522	.	.	R	-	2	0	ZHX1	124334857	0.995000	0.38212	0.997000	0.53966	0.983000	0.72400	0.381000	0.20619	0.384000	0.24942	0.491000	0.48974	AGG	C|0.986;T|0.014	0.014	strong		0.398	ZHX1-003	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000381759.1		
MED28	80306	hgsc.bcm.edu	37	4	17616349	17616349	+	Silent	SNP	G	G	A	rs146036794	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:17616349G>A	ENST00000237380.7	+	1	96	c.72G>A	c.(70-72)ccG>ccA	p.P24P	AC006160.5_ENST00000511010.1_RNA	NM_025205.3	NP_079481.2	Q9H204	MED28_HUMAN	mediator complex subunit 28	24					negative regulation of smooth muscle cell differentiation (GO:0051151)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	cortical actin cytoskeleton (GO:0030864)|mediator complex (GO:0016592)|membrane (GO:0016020)				lung(6)|skin(2)	8						CGGGCCTTCCGGGCCAAGCTT	0.587													G|||	27	0.00539137	0.0204	0.0	5008	,	,		14224	0.0		0.0	False		,,,				2504	0.0				p.P24P		Atlas-SNP	.											.	MED28	16	.	0			c.G72A						PASS	.	G		68,4338	54.9+/-90.9	1,66,2136	51.0	60.0	57.0		72	2.6	1.0	4	dbSNP_134	57	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	MED28	NM_025205.3		1,68,6434	AA,AG,GG		0.0233,1.5433,0.5382		24/179	17616349	70,12936	2203	4300	6503	SO:0001819	synonymous_variant	80306	exon1			CCTTCCGGGCCAA	AF317678	CCDS33963.1	4p16	2007-07-30	2007-07-30		ENSG00000118579	ENSG00000118579			24628	protein-coding gene	gene with protein product		610311	"""mediator of RNA polymerase II transcription, subunit 28 homolog (S. cerevisiae)"""			11779215, 15467741	Standard	NM_025205		Approved	EG1, DKFZP434N185, magicin	uc003gpi.1	Q9H204	OTTHUMG00000161980	ENST00000237380.7:c.72G>A	4.37:g.17616349G>A		101.0	0.0	0		156.0	72.0	0.461538	NM_025205	Q9BZJ5	Silent	SNP	ENST00000237380.7	37	CCDS33963.1																																																																																			G|0.996;A|0.004	0.004	strong		0.587	MED28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360055.3	NM_025205	
TGFBRAP1	9392	hgsc.bcm.edu	37	2	105924699	105924699	+	Silent	SNP	G	G	A	rs115690647	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:105924699G>A	ENST00000393359.2	-	2	486	c.60C>T	c.(58-60)ggC>ggT	p.G20G	TGFBRAP1_ENST00000258449.1_Silent_p.G20G			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	20					intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|membrane (GO:0016020)	SMAD binding (GO:0046332)|small GTPase regulator activity (GO:0005083)|transforming growth factor beta receptor binding (GO:0005160)			central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	31						GCTCCTTGTCGCCCATCAGCA	0.547													G|||	39	0.00778754	0.0295	0.0	5008	,	,		18930	0.0		0.0	False		,,,				2504	0.0				p.G20G	Esophageal Squamous(183;794 2019 9730 21801 48859)	Atlas-SNP	.											.	TGFBRAP1	70	.	0			c.C60T						PASS	.	G	,	101,4305	80.4+/-118.8	0,101,2102	42.0	41.0	42.0		60,60	-3.4	0.2	2	dbSNP_132	42	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	TGFBRAP1	NM_001142621.1,NM_004257.4	,	0,101,6402	AA,AG,GG		0.0,2.2923,0.7766	,	20/861,20/861	105924699	101,12905	2203	4300	6503	SO:0001819	synonymous_variant	9392	exon2			CTTGTCGCCCATC	AF022795	CCDS2067.1	2q12.1	2008-02-05			ENSG00000135966	ENSG00000135966			16836	protein-coding gene	gene with protein product		606237				9545258, 11278302	Standard	NM_001142621		Approved	TRAP-1, TRAP1	uc002tcr.4	Q8WUH2	OTTHUMG00000130809	ENST00000393359.2:c.60C>T	2.37:g.105924699G>A		76.0	0.0	0		88.0	50.0	0.568182	NM_004257	A8K5R7|D3DVJ8|O60466	Silent	SNP	ENST00000393359.2	37	CCDS2067.1																																																																																			G|0.990;A|0.010	0.010	strong		0.547	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2	NM_004257	
NUMA1	4926	hgsc.bcm.edu	37	11	71718413	71718413	+	Missense_Mutation	SNP	C	C	T	rs149588226	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71718413C>T	ENST00000393695.3	-	21	5616	c.5285G>A	c.(5284-5286)cGc>cAc	p.R1762H	NUMA1_ENST00000351960.6_Missense_Mutation_p.R626H|NUMA1_ENST00000358965.6_Missense_Mutation_p.R1748H	NM_006185.2	NP_006176.2			nuclear mitotic apparatus protein 1											central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(12)|lung(20)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	65						GGGGGGCAGGCGCTGGGAGAT	0.622			T	RARA	APL								C|||	14	0.00279553	0.0106	0.0	5008	,	,		17501	0.0		0.0	False		,,,				2504	0.0				p.R1762H		Atlas-SNP	.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1	142	.	0			c.G5285A						PASS	.	C	HIS/ARG	72,4328	63.5+/-100.7	1,70,2129	40.0	43.0	42.0		5285	4.6	1.0	11	dbSNP_134	42	0,8586		0,0,4293	yes	missense	NUMA1	NM_006185.2	29	1,70,6422	TT,TC,CC		0.0,1.6364,0.5544	probably-damaging	1762/2116	71718413	72,12914	2200	4293	6493	SO:0001583	missense	4926	exon21			GGCAGGCGCTGGG	Z11584	CCDS31633.1, CCDS66156.1	11q13	2008-02-05				ENSG00000137497			8059	protein-coding gene	gene with protein product		164009				8406455	Standard	NM_006185		Approved		uc001orl.1	Q14980		ENST00000393695.3:c.5285G>A	11.37:g.71718413C>T	ENSP00000377298:p.Arg1762His	79.0	0.0	0		85.0	28.0	0.329412	NM_006185		Missense_Mutation	SNP	ENST00000393695.3	37	CCDS31633.1	4|4	0.0018315018315018315|0.0018315018315018315	4|4	0.008130081300813009|0.008130081300813009	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	20.5|20.5	3.994037|3.994037	0.74703|0.74703	0.016364|0.016364	0.0|0.0	ENSG00000137497|ENSG00000137497	ENST00000541584|ENST00000351960;ENST00000358965;ENST00000393695;ENST00000359652;ENST00000536544	.|T;T;T	.|0.21543	.|2.0;2.46;2.46	4.58|4.58	4.58|4.58	0.56647|0.56647	.|.	.|0.000000	.|0.56097	.|D	.|0.000035	T|T	0.13329|0.13329	0.0323|0.0323	N|N	0.24115|0.24115	0.695|0.695	0.40559|0.40559	D|D	0.981196|0.981196	.|D;D;D;D	.|0.89917	.|0.999;0.999;0.999;1.0	.|P;D;P;D	.|0.67231	.|0.897;0.95;0.855;0.938	T|T	0.01587|0.01587	-1.1318|-1.1318	5|10	.|0.52906	.|T	.|0.07	.|.	6.077|6.077	0.19921|0.19921	0.0:0.7688:0.0:0.2312|0.0:0.7688:0.0:0.2312	.|.	.|1768;1748;1762;626	.|Q4LE64;Q14980-2;Q14980;Q9BTE9	.|.;.;NUMA1_HUMAN;.	T|H	611|626;1748;1762;1311;735	.|ENSP00000260051:R626H;ENSP00000351851:R1748H;ENSP00000377298:R1762H	.|ENSP00000260051:R626H	A|R	-|-	1|2	0|0	NUMA1|NUMA1	71396061|71396061	0.995000|0.995000	0.38212|0.38212	0.999000|0.999000	0.59377|0.59377	0.988000|0.988000	0.76386|0.76386	1.062000|1.062000	0.30555|0.30555	2.527000|2.527000	0.85204|0.85204	0.561000|0.561000	0.74099|0.74099	GCC|CGC	C|0.995;T|0.005	0.005	strong		0.622	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1		
EVPLL	645027	hgsc.bcm.edu	37	17	18284263	18284263	+	Silent	SNP	C	C	T	rs116412205|rs386795970	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18284263C>T	ENST00000399134.4	+	2	370	c.12C>T	c.(10-12)agC>agT	p.S4S	RP1-37N7.1_ENST00000579352.1_RNA	NM_001145127.1	NP_001138599.1	A8MZ36	EVPLL_HUMAN	envoplakin-like	4			S -> N (in dbSNP:rs570145). {ECO:0000269|PubMed:14702039}.							NS(1)|endometrium(1)|large_intestine(1)|lung(2)	5						TGCAAGCCAGCGCCGACCAGG	0.657													.|||	71	0.0141773	0.0507	0.0058	5008	,	,		17727	0.0		0.0	False		,,,				2504	0.0				p.S4S		Atlas-SNP	.											.	EVPLL	10	.	0			c.C12T						PASS	.	C		32,1352		3,26,663	99.0	101.0	100.0		12	-0.7	1.0	17	dbSNP_132	100	0,3182		0,0,1591	no	coding-synonymous	EVPLL	NM_001145127.1		3,26,2254	TT,TC,CC		0.0,2.3121,0.7008		4/302	18284263	32,4534	692	1591	2283	SO:0001819	synonymous_variant	645027	exon2			AGCCAGCGCCGAC		CCDS45626.1	17p11.2	2009-08-25			ENSG00000214860	ENSG00000214860			35236	protein-coding gene	gene with protein product							Standard	NM_001145127		Approved		uc002gte.3	A8MZ36	OTTHUMG00000059095	ENST00000399134.4:c.12C>T	17.37:g.18284263C>T		266.0	0.0	0		242.0	100.0	0.413223	NM_001145127	B4DPD4	Silent	SNP	ENST00000399134.4	37	CCDS45626.1																																																																																			C|0.993;T|0.007	0.007	strong		0.657	EVPLL-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130836.2	NM_001145127	
TMPRSS11B	132724	hgsc.bcm.edu	37	4	69094472	69094472	+	Silent	SNP	A	A	T	rs34044450	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:69094472A>T	ENST00000332644.5	-	9	1238	c.1077T>A	c.(1075-1077)gcT>gcA	p.A359A		NM_182502.3	NP_872308.2	Q86T26	TM11B_HUMAN	transmembrane protease, serine 11B	359	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)	p.A359A(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)	27						GACATGCATCAGCTTCTCCTG	0.323													A|||	48	0.00958466	0.0356	0.0014	5008	,	,		19437	0.0		0.0	False		,,,				2504	0.0				p.A359A		Atlas-SNP	.											TMPRSS11B,NS,carcinoma,0,1	TMPRSS11B	66	1	1	Substitution - coding silent(1)	lung(1)	c.T1077A						PASS	.	A		116,4290	88.2+/-126.9	2,112,2089	131.0	120.0	124.0		1077	-5.8	0.0	4	dbSNP_126	124	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	TMPRSS11B	NM_182502.3		2,120,6381	TT,TA,AA		0.093,2.6328,0.9534		359/417	69094472	124,12882	2203	4300	6503	SO:0001819	synonymous_variant	132724	exon9			TGCATCAGCTTCT	BX537945	CCDS3521.1	4q13.2	2010-04-13			ENSG00000185873	ENSG00000185873		"""Serine peptidases / Transmembrane"""	25398	protein-coding gene	gene with protein product							Standard	NM_182502		Approved		uc003hdw.4	Q86T26	OTTHUMG00000129301	ENST00000332644.5:c.1077T>A	4.37:g.69094472A>T		234.0	0.0	0		252.0	114.0	0.452381	NM_182502	A8K4D9	Silent	SNP	ENST00000332644.5	37	CCDS3521.1																																																																																			A|0.990;T|0.010	0.010	strong		0.323	TMPRSS11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251431.2	NM_182502	
SSPO	23145	hgsc.bcm.edu	37	7	149512267	149512267	+	RNA	SNP	C	C	T	rs142728666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149512267C>T	ENST00000378016.2	+	0	10587							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GCGTAGACTGCGGGGGTGGCC	0.667													C|||	46	0.0091853	0.0219	0.0029	5008	,	,		17602	0.0		0.002	False		,,,				2504	0.0133				p.C3529C		Atlas-SNP	.											.	.	.	.	0			c.C10587T						PASS	.	C		80,4040		1,78,1981	37.0	44.0	42.0		10597	-3.0	0.8	7	dbSNP_134	42	16,8358		0,16,4171	yes	coding-notMod3	SSPO	NM_198455.2		1,94,6152	TT,TC,CC		0.1911,1.9417,0.7684			149512267	96,12398	2060	4187	6247			23145	exon75			AGACTGCGGGGGT	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149512267C>T		81.0	0.0	0		75.0	33.0	0.44	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				C|0.996;T|0.004	0.004	strong		0.667	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
KDM4C	23081	hgsc.bcm.edu	37	9	7013874	7013874	+	Silent	SNP	C	C	T	rs35006356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:7013874C>T	ENST00000381309.3	+	14	2620	c.2055C>T	c.(2053-2055)ctC>ctT	p.L685L	KDM4C_ENST00000543771.1_Silent_p.L685L|KDM4C_ENST00000536108.1_Silent_p.L504L|KDM4C_ENST00000428870.2_Silent_p.L372L|KDM4C_ENST00000535193.1_Silent_p.L707L|KDM4C_ENST00000442236.2_Silent_p.L430L|KDM4C_ENST00000381306.3_Silent_p.L685L	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	685					histone H3-K9 demethylation (GO:0033169)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	androgen receptor binding (GO:0050681)|dioxygenase activity (GO:0051213)|enzyme binding (GO:0019899)|histone demethylase activity (H3-K9 specific) (GO:0032454)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43						CTAAGCCCCTCATACCAGAGA	0.388													C|||	36	0.0071885	0.0265	0.0	5008	,	,		19797	0.0		0.001	False		,,,				2504	0.0				p.L707L		Atlas-SNP	.											.	KDM4C	186	.	0			c.C2121T						PASS	.	C	,,,	96,4310	77.8+/-116.1	1,94,2108	118.0	114.0	115.0		2055,2055,2121,2055	1.3	1.0	9	dbSNP_126	115	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KDM4C	NM_001146694.1,NM_001146695.1,NM_001146696.1,NM_015061.3	,,,	1,94,6408	TT,TC,CC		0.0,2.1788,0.7381	,,,	685/1048,685/814,707/836,685/1057	7013874	96,12910	2203	4300	6503	SO:0001819	synonymous_variant	23081	exon14			GCCCCTCATACCA	AB018323	CCDS6471.1, CCDS55285.1, CCDS55286.1, CCDS55287.1	9p24-p23	2013-01-23	2009-04-06	2009-04-06	ENSG00000107077	ENSG00000107077		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	17071	protein-coding gene	gene with protein product	"""tudor domain containing 14C"""	605469	"""jumonji domain containing 2C"""	JMJD2C		9872452, 15138608	Standard	NM_015061		Approved	GASC1, KIAA0780, TDRD14C	uc003zkh.3	Q9H3R0	OTTHUMG00000019536	ENST00000381309.3:c.2055C>T	9.37:g.7013874C>T		76.0	0.0	0		67.0	35.0	0.522388	NM_001146696	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Silent	SNP	ENST00000381309.3	37	CCDS6471.1																																																																																			C|0.993;T|0.007	0.007	strong		0.388	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061	
C16orf82	162083	hgsc.bcm.edu	37	16	27078545	27078545	+	lincRNA	SNP	C	C	T	rs386790113|rs185409807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27078545C>T	ENST00000505035.1	+	0	518				RP11-673P17.2_ENST00000565783.1_RNA			Q7Z2V1	TNT_HUMAN	chromosome 16 open reading frame 82																		CGTGCAGCACCCGAGGCCAGA	0.652													C|||	96	0.0191693	0.0711	0.0014	5008	,	,		16664	0.0		0.001	False		,,,				2504	0.0				p.P77S		Atlas-SNP	.											.	.	.	.	0			c.C229T						PASS	.						23.0	31.0	28.0					16																	27078545		2188	4290	6478			162083	exon1			CAGCACCCGAGGC	BC031257		16p12.1	2013-01-24			ENSG00000234186	ENSG00000234186			30755	other	unknown						12477932	Standard	NM_001145545		Approved	TNT	uc010vcm.2	Q7Z2V1	OTTHUMG00000161986		16.37:g.27078545C>T		60.0	0.0	0		66.0	27.0	0.409091	NM_001145545	B9EGC2|Q8NEF0	Missense_Mutation	SNP	ENST00000505035.1	37																																																																																				C|0.982;T|0.018	0.018	strong		0.652	C16orf82-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000366634.1	NM_001145545	
IGJ	3512	hgsc.bcm.edu	37	4	71522999	71522999	+	Silent	SNP	C	C	T	rs75928327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:71522999C>T	ENST00000254801.4	-	3	367	c.198G>A	c.(196-198)ctG>ctA	p.L66L	IGJ_ENST00000543780.1_Silent_p.L82L|ENAM_ENST00000472903.1_Intron	NM_144646.3	NP_653247.1	P01591	IGJ_HUMAN	immunoglobulin J polypeptide, linker protein for immunoglobulin alpha and mu polypeptides	66					adaptive immune response (GO:0002250)|antibacterial humoral response (GO:0019731)|glomerular filtration (GO:0003094)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of respiratory burst (GO:0060267)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|dimeric IgA immunoglobulin complex (GO:0071750)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|monomeric IgA immunoglobulin complex (GO:0071748)|pentameric IgM immunoglobulin complex (GO:0071756)|secretory dimeric IgA immunoglobulin complex (GO:0071752)|secretory IgA immunoglobulin complex (GO:0071751)	antigen binding (GO:0003823)|IgA binding (GO:0019862)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)	7			Lung(101;0.235)			CCCTGTTGTTCAGAGGAACAC	0.328													C|||	45	0.00898562	0.034	0.0	5008	,	,		16873	0.0		0.0	False		,,,				2504	0.0				p.L66L		Atlas-SNP	.											.	IGJ	13	.	0			c.G198A						PASS	.	C		103,4303	82.9+/-121.4	0,103,2100	81.0	77.0	78.0		198	4.7	1.0	4	dbSNP_132	78	2,8594	2.2+/-6.3	0,2,4296	no	coding-synonymous	IGJ	NM_144646.3		0,105,6396	TT,TC,CC		0.0233,2.3377,0.8076		66/160	71522999	105,12897	2203	4298	6501	SO:0001819	synonymous_variant	3512	exon3			GTTGTTCAGAGGA	M12759	CCDS3545.1	4q21	2012-10-02			ENSG00000132465	ENSG00000132465		"""Immunoglobulins / IGJ linker"""	5713	protein-coding gene	gene with protein product	"""immunoglobulin J chain"", ""IgJ chain"""	147790				3016707, 2984306	Standard	NM_144646		Approved	IGCJ, JCH	uc003hfn.4	P01591	OTTHUMG00000129909	ENST00000254801.4:c.198G>A	4.37:g.71522999C>T		46.0	0.0	0		51.0	22.0	0.431373	NM_144646		Silent	SNP	ENST00000254801.4	37	CCDS3545.1																																																																																			C|0.990;T|0.010	0.010	strong		0.328	IGJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252160.1	NM_144646	
RANBP2	5903	hgsc.bcm.edu	37	2	109347314	109347314	+	Missense_Mutation	SNP	C	C	G	rs144278795	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:109347314C>G	ENST00000283195.6	+	3	351	c.225C>G	c.(223-225)aaC>aaG	p.N75K		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	75					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)|negative regulation of glucokinase activity (GO:0033132)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein sumoylation (GO:0016925)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)	ligase activity (GO:0016874)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|Ran GTPase binding (GO:0008536)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)		RANBP2/ALK(34)	NS(1)|biliary_tract(1)|breast(3)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(21)|large_intestine(19)|lung(51)|pancreas(1)|prostate(8)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	129						TGGAAGAAAACACAGACAAAG	0.353													C|||	16	0.00319489	0.0083	0.0058	5008	,	,		16939	0.0		0.001	False		,,,				2504	0.0				p.N75K		Atlas-SNP	.											.	RANBP2	488	.	0			c.C225G						PASS	.	C	LYS/ASN	19,2931		0,19,1456	102.0	123.0	115.0		225	-0.8	0.8	2	dbSNP_134	115	0,5138		0,0,2569	no	missense	RANBP2	NM_006267.4	94	0,19,4025	GG,GC,CC		0.0,0.6441,0.2349	probably-damaging	75/3225	109347314	19,8069	1475	2569	4044	SO:0001583	missense	5903	exon3			AGAAAACACAGAC	D42063	CCDS2079.1	2q13	2013-11-14			ENSG00000153201	ENSG00000153201		"""Tetratricopeptide (TTC) repeat domain containing"""	9848	protein-coding gene	gene with protein product		601181	"""acute necrotizing encephalopathy 1 (autosomal dominant)"""	ANE1		7724562, 19118815	Standard	NM_006267		Approved	NUP358, ADANE	uc002tem.4	P49792	OTTHUMG00000130981	ENST00000283195.6:c.225C>G	2.37:g.109347314C>G	ENSP00000283195:p.Asn75Lys	250.0	0.0	0		296.0	142.0	0.47973	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	C	15.44	2.833077	0.50951	0.006441	0.0	ENSG00000153201	ENST00000409491;ENST00000283195;ENST00000456637	T	0.61392	0.11	4.24	-0.825	0.10809	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	.	.	.	.	T	0.56645	0.1999	L	0.55103	1.725	0.27121	N	0.962148	D	0.61080	0.989	P	0.62435	0.902	T	0.55854	-0.8075	9	0.45353	T	0.12	-19.048	9.7309	0.40361	0.0:0.4107:0.0:0.5893	.	75	P49792	RBP2_HUMAN	K	75;75;49	ENSP00000283195:N75K	ENSP00000283195:N75K	N	+	3	2	RANBP2	108713746	0.342000	0.24809	0.759000	0.31340	0.848000	0.48234	-0.351000	0.07711	-0.299000	0.08909	-0.237000	0.12165	AAC	C|0.996;G|0.004	0.004	strong		0.353	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267	
DOCK8	81704	hgsc.bcm.edu	37	9	382646	382646	+	Silent	SNP	C	C	T	rs116523732	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:382646C>T	ENST00000453981.1	+	22	2851	c.2739C>T	c.(2737-2739)tcC>tcT	p.S913S	DOCK8_ENST00000382329.1_Silent_p.S380S|DOCK8_ENST00000382331.1_Silent_p.S215S|DOCK8_ENST00000469391.1_Silent_p.S845S|DOCK8_ENST00000432829.2_Silent_p.S845S			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	913					blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		GGACACACTCCGCAGCAGACG	0.507													C|||	56	0.0111821	0.0386	0.0072	5008	,	,		20060	0.0		0.0	False		,,,				2504	0.0				p.S913S		Atlas-SNP	.											.	DOCK8	401	.	0			c.C2739T						PASS	.	C	,,	139,4267	98.9+/-137.6	2,135,2066	61.0	53.0	56.0		2535,2535,2739	-6.7	0.0	9	dbSNP_132	56	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	,,	2,137,6364	TT,TC,CC		0.0233,3.1548,1.0841	,,	845/2000,845/2032,913/2100	382646	141,12865	2203	4300	6503	SO:0001819	synonymous_variant	81704	exon22			ACACTCCGCAGCA	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.2739C>T	9.37:g.382646C>T		96.0	0.0	0		118.0	62.0	0.525424	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Silent	SNP	ENST00000453981.1	37	CCDS6440.2																																																																																			C|0.991;T|0.009	0.009	strong		0.507	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	
HRNR	388697	hgsc.bcm.edu	37	1	152191052	152191052	+	Missense_Mutation	SNP	G	G	T	rs115232928	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152191052G>T	ENST00000368801.2	-	3	3128	c.3053C>A	c.(3052-3054)tCc>tAc	p.S1018Y	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	1018					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			AGACTGCCCGGAACCAGACCC	0.607													G|||	95	0.0189696	0.0696	0.0043	5008	,	,		21165	0.0		0.0	False		,,,				2504	0.0				p.S1018Y		Atlas-SNP	.											.	HRNR	403	.	0			c.C3053A						PASS	.	G	TYR/SER	190,4216	121.3+/-158.8	4,182,2017	135.0	149.0	145.0		3053	-0.1	0.0	1	dbSNP_132	145	0,8600		0,0,4300	no	missense	HRNR	NM_001009931.1	144	4,182,6317	TT,TG,GG		0.0,4.3123,1.4609	probably-damaging	1018/2851	152191052	190,12816	2203	4300	6503	SO:0001583	missense	388697	exon3			TGCCCGGAACCAG	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.3053C>A	1.37:g.152191052G>T	ENSP00000357791:p.Ser1018Tyr	224.0	0.0	0		264.0	122.0	0.462121	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	25	0.011446886446886446	22	0.044715447154471545	3	0.008287292817679558	0	0.0	0	0.0	G	4.651	0.121012	0.08881	0.043123	0.0	ENSG00000197915	ENST00000368801	T	0.02472	4.28	3.24	-0.0513	0.13827	.	.	.	.	.	T	0.01695	0.0054	L	0.29908	0.895	0.09310	N	1	D	0.69078	0.997	D	0.65987	0.94	T	0.44832	-0.9302	9	0.28530	T	0.3	.	3.0366	0.06124	0.2539:0.0:0.536:0.21	.	1018	Q86YZ3	HORN_HUMAN	Y	1018	ENSP00000357791:S1018Y	ENSP00000357791:S1018Y	S	-	2	0	HRNR	150457676	0.008000	0.16893	0.000000	0.03702	0.002000	0.02628	0.817000	0.27281	-0.110000	0.12022	0.558000	0.71614	TCC	G|0.985;T|0.015	0.015	strong		0.607	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
PSG2	5670	hgsc.bcm.edu	37	19	43585286	43585286	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43585286G>A	ENST00000406487.1	-	2	275	c.177C>T	c.(175-177)ccC>ccT	p.P59P	PSG2_ENST00000491995.1_5'Flank	NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	59	Ig-like V-type.				cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49		Prostate(69;0.00682)				TAAGATTCTGGGGCAAATTGT	0.458																																					p.P59P		Atlas-SNP	.											PSG2,colon,carcinoma,-2,4	PSG2	84	4	0			c.C177T						scavenged	.						113.0	116.0	115.0					19																	43585286		2203	4296	6499	SO:0001819	synonymous_variant	5670	exon2			ATTCTGGGGCAAA		CCDS12616.1	19q13.1-q13.2	2013-01-29			ENSG00000242221	ENSG00000242221		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9519	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1 glycoprotein"", ""pregnancy-specific beta-1-glycoprotein 7"", ""carcinoembryonic antigen SG8"""	176391		PSBG2		2377620	Standard	NM_031246		Approved	PSGGB, PSG1, CEA	uc002ovr.3	P11465	OTTHUMG00000151547	ENST00000406487.1:c.177C>T	19.37:g.43585286G>A		314.0	0.0	0		357.0	15.0	0.0420168	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Silent	SNP	ENST00000406487.1	37	CCDS12616.1																																																																																			.	.	none		0.458	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246	
TCEB3B	51224	hgsc.bcm.edu	37	18	44561069	44561069	+	Silent	SNP	G	G	T	rs139088020	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:44561069G>T	ENST00000332567.4	-	1	919	c.567C>A	c.(565-567)ccC>ccA	p.P189P	KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000245121.5_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	189					regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						GTTGCTTCCCGGGCGCAGCGG	0.701													G|||	8	0.00159744	0.0053	0.0014	5008	,	,		13286	0.0		0.0	False		,,,				2504	0.0				p.P189P		Atlas-SNP	.											.	TCEB3B	141	.	0			c.C567A						PASS	.	G	,	20,4348		0,20,2164	24.0	28.0	27.0		567,	-0.2	0.0	18	dbSNP_134	27	0,8562		0,0,4281	no	coding-synonymous,intron	TCEB3B,KATNAL2	NM_016427.2,NM_031303.2	,	0,20,6445	TT,TG,GG		0.0,0.4579,0.1547	,	189/754,	44561069	20,12910	2184	4281	6465	SO:0001819	synonymous_variant	51224	exon1			CTTCCCGGGCGCA	BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"""transcription elongation factor (SIII) elongin A2"", ""elongin A2"""	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.567C>A	18.37:g.44561069G>T		50.0	0.0	0		70.0	41.0	0.585714	NM_016427	Q9P2V9	Silent	SNP	ENST00000332567.4	37	CCDS11932.1																																																																																			G|0.998;T|0.002	0.002	strong		0.701	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427	
PRR21	643905	hgsc.bcm.edu	37	2	240981362	240981362	+	Silent	SNP	T	T	C	rs115420937	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:240981362T>C	ENST00000408934.1	-	1	1037	c.1038A>G	c.(1036-1038)ctA>ctG	p.L346L		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	346										NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(5)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	29						TGAAGAGGCGTAGATGAAGAG	0.562													t|||	43	0.00858626	0.031	0.0029	5008	,	,		22045	0.0		0.0	False		,,,				2504	0.0				p.L346L		Atlas-SNP	.											.	PRR21	53	.	0			c.A1038G						PASS	.	T		100,4306	80.4+/-118.8	3,94,2106	145.0	128.0	134.0		1038	-1.0	0.0	2	dbSNP_132	134	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	PRR21	NM_001080835.1		3,98,6402	CC,CT,TT		0.0465,2.2696,0.7996		346/390	240981362	104,12902	2203	4300	6503	SO:0001819	synonymous_variant	643905	exon1			GAGGCGTAGATGA	AF453950	CCDS33417.1	2q37.3	2009-04-20			ENSG00000221961	ENSG00000221961			33866	protein-coding gene	gene with protein product							Standard	NM_001080835		Approved		uc010zod.2	Q8WXC7	OTTHUMG00000159174	ENST00000408934.1:c.1038A>G	2.37:g.240981362T>C		144.0	0.0	0		133.0	57.0	0.428571	NM_001080835		Silent	SNP	ENST00000408934.1	37	CCDS33417.1																																																																																			T|0.992;C|0.008	0.008	strong		0.562	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
CACNA1F	778	hgsc.bcm.edu	37	X	49070329	49070329	+	Missense_Mutation	SNP	C	C	T	rs34308720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:49070329C>T	ENST00000376265.2	-	31	3836	c.3775G>A	c.(3775-3777)Gct>Act	p.A1259T	CACNA1F_ENST00000376251.1_Missense_Mutation_p.A1194T|CACNA1F_ENST00000323022.5_Missense_Mutation_p.A1248T	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	1259			A -> T (in dbSNP:rs34308720).		axonogenesis (GO:0007409)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|dendrite morphogenesis (GO:0048813)|detection of light stimulus involved in visual perception (GO:0050908)|membrane depolarization during action potential (GO:0086010)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|perikaryon (GO:0043204)|photoreceptor outer segment (GO:0001750)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			autonomic_ganglia(1)|breast(8)|central_nervous_system(3)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(4)|urinary_tract(1)	85					Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	ACAATAAGAGCGTCAAACGTG	0.512													c|||	16	0.00423841	0.0121	0.0	3775	,	,		15638	0.0		0.0	False		,,,				2504	0.0				p.A1259T		Atlas-SNP	.											.	CACNA1F	218	.	0			c.G3775A						PASS	.	C	THR/ALA	73,3762		0,64,9,1568,562	135.0	88.0	104.0		3775	5.0	1.0	X	dbSNP_126	104	0,6728		0,0,0,2428,1872	yes	missense	CACNA1F	NM_005183.2	58	0,64,9,3996,2434	TT,TC,T,CC,C		0.0,1.9035,0.6911	possibly-damaging	1259/1978	49070329	73,10490	2203	4300	6503	SO:0001583	missense	778	exon31			TAAGAGCGTCAAA	AA019975	CCDS35253.1, CCDS59166.1, CCDS59167.1	Xp11.23	2013-01-23	2007-02-16		ENSG00000102001	ENSG00000102001		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1393	protein-coding gene	gene with protein product		300110	"""Aland island eye disease (Forsius-Eriksson ocular albinism, ocular albinism type 2)"""	CSNB2, AIED		9344658, 9662400, 16382099, 12111638, 17525176	Standard	NM_005183		Approved	Cav1.4, JM8, JMC8, CSNBX2, CORDX3, CSNB2A, OA2	uc010nip.3	O60840	OTTHUMG00000022703	ENST00000376265.2:c.3775G>A	X.37:g.49070329C>T	ENSP00000365441:p.Ala1259Thr	116.0	0.0	0		117.0	55.0	0.470085	NM_005183	A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Missense_Mutation	SNP	ENST00000376265.2	37	CCDS35253.1	4	0.0024110910186859553	3	0.006122448979591836	0	0.0	0	0.0	0	0.0	C	22.4	4.288051	0.80803	0.019035	0.0	ENSG00000102001	ENST00000376251;ENST00000323022;ENST00000376265	D;D;D	0.98400	-4.91;-4.91;-4.91	4.97	4.97	0.65823	Ion transport (1);	0.053644	0.64402	D	0.000001	D	0.96002	0.8698	L	0.28014	0.82	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.87578	0.998;0.973	D	0.94804	0.7973	10	0.72032	D	0.01	.	16.1084	0.81241	0.0:1.0:0.0:0.0	rs34308720	1248;1259	F5CIQ9;O60840	.;CAC1F_HUMAN	T	1194;1248;1259	ENSP00000365427:A1194T;ENSP00000321618:A1248T;ENSP00000365441:A1259T	ENSP00000321618:A1248T	A	-	1	0	CACNA1F	48957273	0.995000	0.38212	1.000000	0.80357	0.634000	0.38068	1.260000	0.32968	2.053000	0.61076	0.529000	0.55759	GCT	C|0.993;T|0.007	0.007	strong		0.512	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183	
ZNF646	9726	hgsc.bcm.edu	37	16	31092629	31092629	+	Missense_Mutation	SNP	G	G	A	rs370035952		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31092629G>A	ENST00000394979.2	+	1	5407	c.4984G>A	c.(4984-4986)Gga>Aga	p.G1662R	ZNF646_ENST00000300850.5_Missense_Mutation_p.G1662R			O15015	ZN646_HUMAN	zinc finger protein 646	1662					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(4)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(1)|lung(21)|ovary(1)|prostate(4)|skin(3)	49						AGCCAGGGGAGGACAAGCGGT	0.662																																					p.G1662R		Atlas-SNP	.											.	ZNF646	133	.	0			c.G4984A						PASS	.	G	ARG/GLY	1,4393	2.1+/-5.4	0,1,2196	63.0	73.0	70.0		4984	2.8	0.0	16		70	0,8598		0,0,4299	no	missense	ZNF646	NM_014699.3	125	0,1,6495	AA,AG,GG		0.0,0.0228,0.0077	benign	1662/1833	31092629	1,12991	2197	4299	6496	SO:0001583	missense	9726	exon2			AGGGGAGGACAAG	AB002294	CCDS10702.1	16p11.2	2013-01-08			ENSG00000167395	ENSG00000167395		"""Zinc fingers, C2H2-type"""	29004	protein-coding gene	gene with protein product							Standard	NM_014699		Approved	KIAA0296	uc002eap.3	O15015	OTTHUMG00000047355	ENST00000394979.2:c.4984G>A	16.37:g.31092629G>A	ENSP00000378429:p.Gly1662Arg	141.0	0.0	0		144.0	83.0	0.576389	NM_014699	Q8IVD8	Missense_Mutation	SNP	ENST00000394979.2	37		.	.	.	.	.	.	.	.	.	.	G	5.858	0.342448	0.11069	2.28E-4	0.0	ENSG00000167395	ENST00000300850;ENST00000394979	T;T	0.09445	2.98;3.04	5.8	2.76	0.32466	.	.	.	.	.	T	0.07007	0.0178	L	0.29908	0.895	0.09310	N	1	B	0.15930	0.015	B	0.16289	0.015	T	0.40831	-0.9542	9	0.20519	T	0.43	-7.682	4.3737	0.11260	0.2498:0.1703:0.5798:0.0	.	1662	O15015-2	.	R	1662	ENSP00000300850:G1662R;ENSP00000378429:G1662R	ENSP00000300850:G1662R	G	+	1	0	ZNF646	31000130	0.133000	0.22466	0.003000	0.11579	0.061000	0.15899	1.546000	0.36179	0.783000	0.33636	0.655000	0.94253	GGA	.	.	weak		0.662	ZNF646-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000108510.2	NM_014699	
PCYOX1	51449	hgsc.bcm.edu	37	2	70485332	70485332	+	Silent	SNP	G	G	A	rs114523411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:70485332G>A	ENST00000433351.2	+	1	64	c.36G>A	c.(34-36)ctG>ctA	p.L12L	PCYOX1_ENST00000505044.2_Intron|PCYOX1_ENST00000545138.1_5'Flank|PCYOX1_ENST00000264441.5_Silent_p.L12L	NM_016297.3	NP_057381.3	Q9UHG3	PCYOX_HUMAN	prenylcysteine oxidase 1	12					prenylated protein catabolic process (GO:0030327)|prenylcysteine catabolic process (GO:0030328)|prenylcysteine metabolic process (GO:0030329)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	chloride-transporting ATPase activity (GO:0008555)|prenylcysteine oxidase activity (GO:0001735)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)	15						TCTCCTCGCTGCTGGGGTTGT	0.706													G|||	23	0.00459265	0.0174	0.0	5008	,	,		9844	0.0		0.0	False		,,,				2504	0.0				p.L12L		Atlas-SNP	.											.	PCYOX1	34	.	0			c.G36A						PASS	.	G		49,4355	50.9+/-86.3	0,49,2153	38.0	39.0	39.0		36	-3.9	0.0	2	dbSNP_132	39	0,8600		0,0,4300	no	coding-synonymous	PCYOX1	NM_016297.3		0,49,6453	AA,AG,GG		0.0,1.1126,0.3768		12/506	70485332	49,12955	2202	4300	6502	SO:0001819	synonymous_variant	51449	exon1			CTCGCTGCTGGGG	AB020715	CCDS1902.1	2p13.3	2008-02-05			ENSG00000116005	ENSG00000116005	1.8.3.5		20588	protein-coding gene	gene with protein product		610995				10585463, 12186880	Standard	NM_016297		Approved	KIAA0908, PCL1	uc002sgn.4	Q9UHG3	OTTHUMG00000129671	ENST00000433351.2:c.36G>A	2.37:g.70485332G>A		137.0	0.0	0		111.0	40.0	0.36036	NM_016297	B2RB14|B7Z9P8|O94982|Q8N4N5|Q96QM8	Silent	SNP	ENST00000433351.2	37	CCDS1902.1																																																																																			G|0.995;A|0.005	0.005	strong		0.706	PCYOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251872.3	NM_016297	
PLXNA4	91584	hgsc.bcm.edu	37	7	132193225	132193225	+	Silent	SNP	G	G	A	rs78248128	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:132193225G>A	ENST00000359827.3	-	2	1190	c.228C>T	c.(226-228)agC>agT	p.S76S	PLXNA4_ENST00000321063.4_Silent_p.S76S|PLXNA4_ENST00000378539.5_Silent_p.S76S|PLXNA4_ENST00000423507.2_Silent_p.S76S			Q9HCM2	PLXA4_HUMAN	plexin A4	76	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						CCTTCAGGTCGCTGGAGAGCT	0.587													G|||	189	0.0377396	0.1293	0.013	5008	,	,		18830	0.0		0.004	False		,,,				2504	0.0051				p.S76S		Atlas-SNP	.											.	PLXNA4	873	.	0			c.C228T						PASS	.	G	,,	450,3956	214.8+/-234.0	26,398,1779	57.0	60.0	59.0		228,228,228	-4.6	1.0	7	dbSNP_131	59	23,8577	16.0+/-53.3	1,21,4278	no	coding-synonymous,coding-synonymous,coding-synonymous	PLXNA4	NM_001105543.1,NM_020911.1,NM_181775.3	,,	27,419,6057	AA,AG,GG		0.2674,10.2133,3.6368	,,	76/493,76/1895,76/523	132193225	473,12533	2203	4300	6503	SO:0001819	synonymous_variant	91584	exon2			CAGGTCGCTGGAG	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.228C>T	7.37:g.132193225G>A		110.0	0.0	0		158.0	92.0	0.582278	NM_001105543	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Silent	SNP	ENST00000359827.3	37	CCDS43646.1																																																																																			G|0.966;A|0.034	0.034	strong		0.587	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
HDAC4	9759	hgsc.bcm.edu	37	2	240111556	240111556	+	Silent	SNP	G	G	A	rs6740794	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:240111556G>A	ENST00000345617.3	-	4	1103	c.312C>T	c.(310-312)caC>caT	p.H104H	HDAC4_ENST00000541256.1_Silent_p.H73H	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	104					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|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)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		GCTGCGCCTCGTGCTGCCGGG	0.677													g|||	239	0.0477236	0.171	0.0173	5008	,	,		14486	0.0		0.001	False		,,,				2504	0.0				p.H104H		Atlas-SNP	.											HDAC4,colon,carcinoma,0,1	HDAC4	127	1	0			c.C312T						PASS	.	A		671,3735	265.6+/-266.7	50,571,1582	30.0	27.0	28.0		312	-0.9	1.0	2	dbSNP_116	28	12,8588	7.1+/-27.0	0,12,4288	no	coding-synonymous	HDAC4	NM_006037.3		50,583,5870	AA,AG,GG		0.1395,15.2292,5.2514		104/1085	240111556	683,12323	2203	4300	6503	SO:0001819	synonymous_variant	9759	exon4			CGCCTCGTGCTGC	AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"""brachydactyly-mental retardation syndrome"""	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.312C>T	2.37:g.240111556G>A		83.0	0.0	0		115.0	54.0	0.469565	NM_006037	Q9UND6	Silent	SNP	ENST00000345617.3	37	CCDS2529.1																																																																																			G|0.938;A|0.062	0.062	strong		0.677	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037	
SNRPA1	6627	hgsc.bcm.edu	37	15	101835306	101835306	+	Silent	SNP	G	G	C	rs61738984	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:101835306G>C	ENST00000254193.6	-	1	150	c.78C>G	c.(76-78)ctC>ctG	p.L26L	SNRPA1_ENST00000560856.1_5'UTR|RP11-299G20.2_ENST00000558838.1_RNA	NM_003090.2	NP_003081.2	P09661	RU2A_HUMAN	small nuclear ribonucleoprotein polypeptide A'	26					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U2 snRNP (GO:0005686)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)	6	Lung NSC(78;0.00156)|all_lung(78;0.00195)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.00113)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			ACTCACCCCGGAGGTCCAGCT	0.721													G|||	442	0.0882588	0.2829	0.0749	5008	,	,		11636	0.001		0.007	False		,,,				2504	0.0082				p.L26L		Atlas-SNP	.											.	SNRPA1	11	.	0			c.C78G						PASS	.	G		774,3286		49,676,1305	5.0	5.0	5.0		78	-8.1	0.2	15	dbSNP_129	5	29,7973		1,27,3973	no	coding-synonymous	SNRPA1	NM_003090.2		50,703,5278	CC,CG,GG		0.3624,19.064,6.6573		26/256	101835306	803,11259	2030	4001	6031	SO:0001819	synonymous_variant	6627	exon1			ACCCCGGAGGTCC	AJ130971	CCDS10391.1	15q26.3	2011-10-11			ENSG00000131876	ENSG00000131876			11152	protein-coding gene	gene with protein product		603521				2928112	Standard	NM_003090		Approved	Lea1	uc002bww.3	P09661	OTTHUMG00000149871	ENST00000254193.6:c.78C>G	15.37:g.101835306G>C		36.0	0.0	0		47.0	21.0	0.446809	NM_003090	B2R5I6|Q8TBD2	Silent	SNP	ENST00000254193.6	37	CCDS10391.1																																																																																			G|0.906;C|0.094	0.094	strong		0.721	SNRPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313621.2	NM_003090	
PPP6R2	9701	hgsc.bcm.edu	37	22	50874851	50874851	+	Silent	SNP	G	G	A	rs78837601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50874851G>A	ENST00000216061.5	+	15	1942	c.1572G>A	c.(1570-1572)acG>acA	p.T524T	PPP6R2_ENST00000395744.3_Silent_p.T524T|PPP6R2_ENST00000395741.3_Silent_p.T525T|PPP6R2_ENST00000359139.3_Silent_p.T524T			O75170	PP6R2_HUMAN	protein phosphatase 6, regulatory subunit 2	524						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	22						AGACGCTGACGGAGACGAACC	0.687													G|||	105	0.0209665	0.0719	0.0086	5008	,	,		17157	0.004		0.0	False		,,,				2504	0.0				p.T525T		Atlas-SNP	.											.	PPP6R2	71	.	0			c.G1575A						PASS	.	G	,,,	322,4064		9,304,1880	53.0	34.0	41.0		1572,1575,1572,1572	-9.1	0.0	22	dbSNP_131	41	2,8584		0,2,4291	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PPP6R2	NM_001242898.1,NM_001242899.1,NM_001242900.1,NM_014678.4	,,,	9,306,6171	AA,AG,GG		0.0233,7.3415,2.4977	,,,	524/960,525/934,524/928,524/933	50874851	324,12648	2193	4293	6486	SO:0001819	synonymous_variant	9701	exon14			GCTGACGGAGACG	AB014585	CCDS33681.1, CCDS56235.1, CCDS56236.1, CCDS74881.1	22q13.33	2012-04-17	2010-06-28	2010-06-28	ENSG00000100239	ENSG00000100239		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	19253	protein-coding gene	gene with protein product		610877	"""KIAA0685"", ""SAPS domain family, member 2"""	KIAA0685, SAPS2		16769727	Standard	NM_014678		Approved	dJ579N16.1, SAP190	uc003blc.3	O75170	OTTHUMG00000150199	ENST00000216061.5:c.1572G>A	22.37:g.50874851G>A		314.0	0.0	0		342.0	166.0	0.48538	NM_001242899	A6PVG3|B7Z7T3|Q5U5P3|Q7Z2L2|Q7Z5G5|Q7Z731|Q9UGB9	Silent	SNP	ENST00000216061.5	37																																																																																				G|0.976;A|0.024	0.024	strong		0.687	PPP6R2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316809.1	NM_014678	
MYO5C	55930	hgsc.bcm.edu	37	15	52553259	52553259	+	Missense_Mutation	SNP	C	C	G	rs200784696		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:52553259C>G	ENST00000261839.7	-	10	1274	c.1113G>C	c.(1111-1113)caG>caC	p.Q371H	MYO5C_ENST00000541028.1_5'UTR|MYO5C_ENST00000443683.2_Missense_Mutation_p.Q314H	NM_018728.3	NP_061198.2	Q9NQX4	MYO5C_HUMAN	myosin VC	371	Myosin motor.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(8)|kidney(7)|large_intestine(15)|lung(12)|ovary(7)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	66				all cancers(107;0.0137)		TGCACAGCCACTGAGCAACTC	0.557													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19769	0.0		0.0	False		,,,				2504	0.0				p.Q371H		Atlas-SNP	.											.	MYO5C	162	.	0			c.G1113C						PASS	.	C	HIS/GLN	2,4080		0,2,2039	67.0	71.0	70.0		1113	4.6	1.0	15		70	0,8416		0,0,4208	yes	missense	MYO5C	NM_018728.3	24	0,2,6247	GG,GC,CC		0.0,0.049,0.016	benign	371/1743	52553259	2,12496	2041	4208	6249	SO:0001583	missense	55930	exon10			CAGCCACTGAGCA	AF272390	CCDS42036.1	15q21	2011-09-27				ENSG00000128833		"""Myosins / Myosin superfamily : Class V"""	7604	protein-coding gene	gene with protein product	"""myosin 5C"""	610022				11870218	Standard	NM_018728		Approved	MGC74969	uc010bff.3	Q9NQX4		ENST00000261839.7:c.1113G>C	15.37:g.52553259C>G	ENSP00000261839:p.Gln371His	56.0	0.0	0		66.0	29.0	0.439394	NM_018728	Q6P1W8	Missense_Mutation	SNP	ENST00000261839.7	37	CCDS42036.1	.	.	.	.	.	.	.	.	.	.	C	6.117	0.389752	0.11581	4.9E-4	0.0	ENSG00000128833	ENST00000261839;ENST00000443683	D;D	0.95238	-3.65;-2.21	5.51	4.59	0.56863	Myosin head, motor domain (2);	0.190704	0.47852	D	0.000217	D	0.87047	0.6080	N	0.05050	-0.12	0.47737	D	0.999502	B	0.09022	0.002	B	0.11329	0.006	T	0.81245	-0.1020	10	0.23302	T	0.38	.	16.3026	0.82830	0.0:0.8673:0.1327:0.0	.	371	Q9NQX4	MYO5C_HUMAN	H	371;314	ENSP00000261839:Q371H;ENSP00000410582:Q314H	ENSP00000261839:Q371H	Q	-	3	2	MYO5C	50340551	1.000000	0.71417	0.999000	0.59377	0.071000	0.16799	0.860000	0.27871	1.325000	0.45301	-0.175000	0.13238	CAG	.	.	weak		0.557	MYO5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419562.1	NM_018728	
RP3-470B24.5	0	hgsc.bcm.edu	37	6	168377054	168377054	+	lincRNA	SNP	G	G	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:168377054G>T	ENST00000538528.1	-	0	565																											CAGTGTGGGGGGAGGAGAAGA	0.642																																					p.S93S		Atlas-SNP	.											.	.	.	.	0			c.C279A						PASS	.						3.0	4.0	4.0					6																	168377054		618	1453	2071			0	exon1			GTGGGGGGAGGAG																													6.37:g.168377054G>T		309.0	0.0	0		331.0	52.0	0.1571	NM_001129895		Silent	SNP	ENST00000538528.1	37																																																																																				.	.	none		0.642	RP3-470B24.5-201	KNOWN	basic	lincRNA	lincRNA			
KRT71	112802	hgsc.bcm.edu	37	12	52946424	52946424	+	Silent	SNP	G	G	A	rs61729863	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52946424G>A	ENST00000267119.5	-	1	507	c.438C>T	c.(436-438)gaC>gaT	p.D146D		NM_033448.2	NP_258259.1	Q3SY84	K2C71_HUMAN	keratin 71	146	Coil 1A.|Rod.				hair follicle morphogenesis (GO:0031069)|intermediate filament organization (GO:0045109)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	22				BRCA - Breast invasive adenocarcinoma(357;0.194)		GACCCACCTTGTCGATGAAGG	0.537													G|||	187	0.0373403	0.1339	0.0144	5008	,	,		19941	0.0		0.0	False		,,,				2504	0.0				p.D146D		Atlas-SNP	.											.	KRT71	70	.	0			c.C438T						PASS	.	G		431,3975	208.5+/-229.5	28,375,1800	94.0	92.0	92.0		438	0.9	1.0	12	dbSNP_129	92	0,8600		0,0,4300	no	coding-synonymous	KRT71	NM_033448.2		28,375,6100	AA,AG,GG		0.0,9.7821,3.3139		146/524	52946424	431,12575	2203	4300	6503	SO:0001819	synonymous_variant	112802	exon1			CACCTTGTCGATG	AJ308600	CCDS8831.1	12q13.13	2013-01-16			ENSG00000139648	ENSG00000139648		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28927	protein-coding gene	gene with protein product		608245				11982755, 12648212, 16831889	Standard	NM_033448		Approved	KRT6IRS, KRT6IRS1, K6IRS1	uc001sao.3	Q3SY84	OTTHUMG00000167831	ENST00000267119.5:c.438C>T	12.37:g.52946424G>A		225.0	0.0	0		208.0	87.0	0.418269	NM_033448	B3KVC1|Q3SY85|Q96DU2	Silent	SNP	ENST00000267119.5	37	CCDS8831.1																																																																																			G|0.970;A|0.030	0.030	strong		0.537	KRT71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396487.1	NM_033448	
KRTAP26-1	388818	hgsc.bcm.edu	37	21	31692346	31692346	+	Missense_Mutation	SNP	C	C	T	rs115381362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31692346C>T	ENST00000360542.3	-	1	261	c.8G>A	c.(7-9)tGc>tAc	p.C3Y		NM_203405.1	NP_981950.1	Q6PEX3	KR261_HUMAN	keratin associated protein 26-1	3						intermediate filament (GO:0005882)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16						GTAGTTGGGGCAAGACATAGT	0.512													C|||	25	0.00499201	0.0182	0.0014	5008	,	,		17989	0.0		0.0	False		,,,				2504	0.0				p.C3Y		Atlas-SNP	.											.	KRTAP26-1	58	.	0			c.G8A						PASS	.	C	TYR/CYS	90,4308		0,90,2109	31.0	34.0	33.0		8	2.9	0.9	21	dbSNP_132	33	1,8591		0,1,4295	yes	missense	KRTAP26-1	NM_203405.1	194	0,91,6404	TT,TC,CC		0.0116,2.0464,0.7005	probably-damaging	3/211	31692346	91,12899	2199	4296	6495	SO:0001583	missense	388818	exon1			TTGGGGCAAGACA	AB096936	CCDS13588.1	21q22.11	2007-11-23			ENSG00000197683	ENSG00000197683		"""Keratin associated proteins"""	33760	protein-coding gene	gene with protein product							Standard	NM_203405		Approved		uc002ynw.3	Q6PEX3	OTTHUMG00000057766	ENST00000360542.3:c.8G>A	21.37:g.31692346C>T	ENSP00000353742:p.Cys3Tyr	111.0	0.0	0		141.0	65.0	0.460993	NM_203405	B0RZD3	Missense_Mutation	SNP	ENST00000360542.3	37	CCDS13588.1	15	0.006868131868131868	15	0.03048780487804878	0	0.0	0	0.0	0	0.0	C	15.21	2.765058	0.49574	0.020464	1.16E-4	ENSG00000197683	ENST00000360542	T	0.16073	2.37	4.95	2.91	0.33838	.	1.072940	0.07352	U	0.882550	T	0.07863	0.0197	N	0.08118	0	0.22975	N	0.998487	D	0.65815	0.995	D	0.66497	0.944	T	0.44081	-0.9351	10	0.72032	D	0.01	-3.9981	10.796	0.46461	0.0:0.6254:0.3746:0.0	.	3	Q6PEX3	KR261_HUMAN	Y	3	ENSP00000353742:C3Y	ENSP00000353742:C3Y	C	-	2	0	KRTAP26-1	30614217	0.953000	0.32496	0.911000	0.35937	0.718000	0.41266	0.656000	0.24948	1.347000	0.45714	0.655000	0.94253	TGC	C|0.993;T|0.007	0.007	strong		0.512	KRTAP26-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128218.1	NM_203405	
CCDC173	129881	hgsc.bcm.edu	37	2	170537661	170537661	+	Silent	SNP	A	A	G	rs145389999	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170537661A>G	ENST00000447353.1	-	2	255	c.150T>C	c.(148-150)atT>atC	p.I50I		NM_001085447.1	NP_001078916.1	Q0VFZ6	CC173_HUMAN	coiled-coil domain containing 173	50																	CATCGTGTGGAATTATGGTGA	0.393													A|||	52	0.0103834	0.0356	0.0072	5008	,	,		17148	0.0		0.0	False		,,,				2504	0.0				p.I50I		Atlas-SNP	.											.	.	.	.	0			c.T150C						PASS	.	A		89,3817		1,87,1865	161.0	153.0	156.0		150	3.2	1.0	2	dbSNP_134	156	0,8292		0,0,4146	no	coding-synonymous	C2orf77	NM_001085447.1		1,87,6011	GG,GA,AA		0.0,2.2785,0.7296		50/553	170537661	89,12109	1953	4146	6099	SO:0001819	synonymous_variant	129881	exon2			GTGTGGAATTATG	BC015980, BC117445	CCDS46445.1	2q31.1	2012-08-07	2012-08-07	2012-08-07	ENSG00000154479	ENSG00000154479			25064	protein-coding gene	gene with protein product	"""hypothetical LOC129881"""		"""chromosome 2 open reading frame 77"""	C2orf77		12477932	Standard	NM_001085447		Approved	LOC129881	uc002ufe.2	Q0VFZ6	OTTHUMG00000154116	ENST00000447353.1:c.150T>C	2.37:g.170537661A>G		203.0	1.0	0.00492611		202.0	108.0	0.534653	NM_001085447	Q6PJF6	Silent	SNP	ENST00000447353.1	37	CCDS46445.1																																																																																			A|0.993;G|0.007	0.007	strong		0.393	CCDC173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333954.2	NM_001085447	
CHRDL2	25884	hgsc.bcm.edu	37	11	74415606	74415606	+	Missense_Mutation	SNP	T	T	C	rs59876990	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:74415606T>C	ENST00000376332.3	-	7	1172	c.676A>G	c.(676-678)Atc>Gtc	p.I226V	CHRDL2_ENST00000534159.1_5'UTR|CHRDL2_ENST00000263671.5_Missense_Mutation_p.I226V	NM_001278473.1	NP_001265402.1	Q6WN34	CRDL2_HUMAN	chordin-like 2	226					cartilage development (GO:0051216)|cell differentiation (GO:0030154)|ossification (GO:0001503)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(6)|lung(4)|prostate(1)|skin(2)	15	Hepatocellular(1;0.098)					TGGCGAGGGATGAAGCTCAGA	0.582													T|||	102	0.0203674	0.0756	0.0029	5008	,	,		14376	0.0		0.0	False		,,,				2504	0.0				p.I226V		Atlas-SNP	.											.	CHRDL2	47	.	0			c.A676G						PASS	.	T	VAL/ILE	246,4154	144.6+/-179.5	7,232,1961	65.0	62.0	63.0		676	-1.4	1.0	11	dbSNP_129	63	0,8586		0,0,4293	yes	missense	CHRDL2	NM_015424.3	29	7,232,6254	CC,CT,TT		0.0,5.5909,1.8943	benign	226/452	74415606	246,12740	2200	4293	6493	SO:0001583	missense	25884	exon7			GAGGGATGAAGCT	AL110168	CCDS8234.1, CCDS60893.1	11q13.4	2013-09-20			ENSG00000054938	ENSG00000054938			24168	protein-coding gene	gene with protein product		613127				12853144, 12975309	Standard	NM_015424		Approved	BNF1	uc001ovh.3	Q6WN34	OTTHUMG00000165623	ENST00000376332.3:c.676A>G	11.37:g.74415606T>C	ENSP00000365510:p.Ile226Val	223.0	0.0	0		229.0	102.0	0.445415	NM_015424	A5PKU9|Q6WN30|Q6WN31|Q6WN32|Q7Z5J3	Missense_Mutation	SNP	ENST00000376332.3	37		42	0.019230769230769232	41	0.08333333333333333	1	0.0027624309392265192	0	0.0	0	0.0	T	12.53	1.964712	0.34659	0.055909	0.0	ENSG00000054938	ENST00000263671;ENST00000376332;ENST00000376323;ENST00000393519;ENST00000528789	T;T;T	0.62105	0.94;0.98;0.05	5.39	-1.36	0.09085	.	0.361824	0.31472	N	0.007600	T	0.03871	0.0109	L	0.56769	1.78	0.27110	N	0.962407	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.09377	0.001;0.002;0.004	T	0.06232	-1.0838	10	0.19147	T	0.46	-7.7366	6.1715	0.20421	0.0:0.1511:0.3979:0.451	rs59876990	226;226;226	E9PCG7;Q6WN34;Q6WN34-2	.;CRDL2_HUMAN;.	V	226;226;112;110;226	ENSP00000263671:I226V;ENSP00000365510:I226V;ENSP00000431380:I226V	ENSP00000263671:I226V	I	-	1	0	CHRDL2	74093254	0.983000	0.35010	0.996000	0.52242	0.980000	0.70556	-0.008000	0.12788	-0.250000	0.09555	0.379000	0.24179	ATC	T|0.978;C|0.022	0.022	strong		0.582	CHRDL2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000385391.1		
XIRP1	165904	hgsc.bcm.edu	37	3	39228514	39228514	+	Missense_Mutation	SNP	G	G	A	rs61736154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:39228514G>A	ENST00000340369.3	-	2	2651	c.2423C>T	c.(2422-2424)tCg>tTg	p.S808L	XIRP1_ENST00000396251.1_Missense_Mutation_p.S808L|XIRP1_ENST00000421646.1_Intron	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	808					cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		CCCTGTGCCCGAGAGCACATA	0.612													G|||	103	0.0205671	0.0719	0.0058	5008	,	,		19504	0.0		0.0	False		,,,				2504	0.0041				p.S808L		Atlas-SNP	.											.	XIRP1	173	.	0			c.C2423T						PASS	.	G	LEU/SER,LEU/SER	316,4090	169.1+/-199.8	13,290,1900	64.0	65.0	65.0		2423,2423	3.2	0.6	3	dbSNP_129	65	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	XIRP1	NM_001198621.1,NM_194293.2	145,145	13,293,6197	AA,AG,GG		0.0349,7.172,2.4527	benign,benign	808/1122,808/1844	39228514	319,12687	2203	4300	6503	SO:0001583	missense	165904	exon2			GTGCCCGAGAGCA	AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"""cardiomyopathy associated 1"""	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.2423C>T	3.37:g.39228514G>A	ENSP00000343140:p.Ser808Leu	149.0	0.0	0		158.0	73.0	0.462025	NM_001198621	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Missense_Mutation	SNP	ENST00000340369.3	37	CCDS2683.1	38	0.0173992673992674	36	0.07317073170731707	2	0.0055248618784530384	0	0.0	0	0.0	G	3.312	-0.140545	0.06669	0.07172	3.49E-4	ENSG00000168334	ENST00000396251;ENST00000340369	T;T	0.04862	3.54;3.95	4.11	3.23	0.37069	.	0.252041	0.37178	N	0.002208	T	0.00356	0.0011	N	0.14661	0.345	0.09310	N	0.999996	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41034	-0.9531	10	0.56958	D	0.05	.	10.0728	0.42343	0.1005:0.0:0.8995:0.0	.	808;808	Q702N8;Q702N8-2	XIRP1_HUMAN;.	L	808	ENSP00000379550:S808L;ENSP00000343140:S808L	ENSP00000343140:S808L	S	-	2	0	XIRP1	39203518	0.352000	0.24895	0.624000	0.29186	0.033000	0.12548	1.016000	0.29976	1.099000	0.41499	-0.244000	0.11960	TCG	G|0.977;A|0.023	0.023	strong		0.612	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522	
TET2	54790	hgsc.bcm.edu	37	4	106156983	106156983	+	Silent	SNP	G	G	A	rs35695427	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:106156983G>A	ENST00000540549.1	+	3	2744	c.1884G>A	c.(1882-1884)gaG>gaA	p.E628E	TET2_ENST00000513237.1_Silent_p.E649E|TET2_ENST00000413648.2_Silent_p.E628E|TET2_ENST00000380013.4_Silent_p.E628E|TET2_ENST00000394764.1_Silent_p.E628E|TET2_ENST00000305737.2_Silent_p.E628E|TET2_ENST00000545826.1_Silent_p.E628E			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	628	Gln-rich.				5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		CACAGCTGGAGCACAAGTCAC	0.478			"""Mis N, F"""		MDS								G|||	65	0.0129792	0.0484	0.0014	5008	,	,		20615	0.0		0.0	False		,,,				2504	0.0				p.E628E		Atlas-SNP	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	TET2_ENST00000305737,bladder,carcinoma,+2,2	TET2	1762	2	0			c.G1884A						PASS	.	G	,	225,4181	136.1+/-172.1	11,203,1989	70.0	71.0	71.0		1884,1884	0.0	0.1	4	dbSNP_126	71	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	TET2	NM_001127208.2,NM_017628.4	,	11,205,6287	AA,AG,GG		0.0233,5.1067,1.7453	,	628/2003,628/1166	106156983	227,12779	2203	4300	6503	SO:0001819	synonymous_variant	54790	exon3			GCTGGAGCACAAG	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.1884G>A	4.37:g.106156983G>A		132.0	0.0	0		136.0	71.0	0.522059	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Silent	SNP	ENST00000540549.1	37	CCDS47120.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	G	0.008	-1.911390	0.00508	0.051067	2.33E-4	ENSG00000168769	ENST00000535110	.	.	.	5.59	-0.00446	0.14022	.	.	.	.	.	T	0.02380	0.0073	.	.	.	0.48341	D	0.999636	.	.	.	.	.	.	T	0.27157	-1.0082	5	0.02654	T	1	.	1.5409	0.02555	0.3344:0.1288:0.389:0.1477	rs35695427	.	.	.	N	628	.	ENSP00000438851:S628N	S	+	2	0	TET2	106376432	0.996000	0.38824	0.083000	0.20561	0.103000	0.19146	0.236000	0.17967	0.243000	0.21327	-0.143000	0.13931	AGC	G|0.982;A|0.018	0.018	strong		0.478	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628	
CCDC142	84865	hgsc.bcm.edu	37	2	74708454	74708454	+	Missense_Mutation	SNP	A	A	C	rs142978072	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74708454A>C	ENST00000393965.3	-	3	1550	c.1154T>G	c.(1153-1155)cTt>cGt	p.L385R	TTC31_ENST00000442235.2_5'Flank|CCDC142_ENST00000290418.4_Missense_Mutation_p.L385R|TTC31_ENST00000410003.1_5'Flank|TTC31_ENST00000233623.5_5'Flank|CCDC142_ENST00000471713.1_5'UTR	NM_032779.3	NP_116168.3	Q17RM4	CC142_HUMAN	coiled-coil domain containing 142	385										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	16						GGATGTGGGAAGGCTGCTCTG	0.552													A|||	19	0.00379393	0.0144	0.0	5008	,	,		19474	0.0		0.0	False		,,,				2504	0.0				p.L385R		Atlas-SNP	.											.	CCDC142	40	.	0			c.T1154G						PASS	.	A	ARG/LEU	32,4374	37.6+/-69.7	0,32,2171	111.0	127.0	121.0		1154	-2.0	0.1	2	dbSNP_134	121	0,8600		0,0,4300	yes	missense	CCDC142	NM_032779.3	102	0,32,6471	CC,CA,AA		0.0,0.7263,0.246	possibly-damaging	385/744	74708454	32,12974	2203	4300	6503	SO:0001583	missense	84865	exon3			GTGGGAAGGCTGC	AK075543	CCDS1945.1	2p13.1	2008-02-05			ENSG00000135637	ENSG00000135637			25889	protein-coding gene	gene with protein product							Standard	NM_032779		Approved	FLJ14397	uc002slq.3	Q17RM4	OTTHUMG00000129962	ENST00000393965.3:c.1154T>G	2.37:g.74708454A>C	ENSP00000377537:p.Leu385Arg	175.0	0.0	0		145.0	56.0	0.386207	NM_032779	B7ZKV5|Q8NBJ3|Q8NBV2|Q96KA7	Missense_Mutation	SNP	ENST00000393965.3	37		6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	A	2.527	-0.309466	0.05458	0.007263	0.0	ENSG00000135637	ENST00000393965;ENST00000290418	T;T	0.43688	0.94;0.94	4.74	-2.0	0.07433	.	1.069320	0.07370	N	0.885599	T	0.32376	0.0827	L	0.41236	1.265	0.09310	N	1	P;P;P	0.47677	0.899;0.899;0.899	P;P;P	0.51355	0.466;0.466;0.667	T	0.36578	-0.9742	10	0.52906	T	0.07	0.0723	5.5768	0.17228	0.3761:0.1645:0.4594:0.0	.	385;385;385	Q17RM4;Q17RM4-2;Q17RM4-3	CC142_HUMAN;.;.	R	385	ENSP00000377537:L385R;ENSP00000290418:L385R	ENSP00000290418:L385R	L	-	2	0	CCDC142	74561962	0.003000	0.15002	0.052000	0.19188	0.399000	0.30720	0.052000	0.14163	-0.208000	0.10171	0.460000	0.39030	CTT	A|0.997;C|0.003	0.003	strong		0.552	CCDC142-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000328391.1	NM_032779	
TMPRSS9	360200	hgsc.bcm.edu	37	19	2413788	2413788	+	Missense_Mutation	SNP	G	G	A	rs147023760	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2413788G>A	ENST00000332578.3	+	9	1243	c.1243G>A	c.(1243-1245)Gcc>Acc	p.A415T		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	415	Peptidase S1 1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				plasminogen activation (GO:0031639)	integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				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)		GTGTGCGGAAGCCCGGCGTCC	0.652													G|||	78	0.0155751	0.0575	0.0029	5008	,	,		16111	0.0		0.0	False		,,,				2504	0.0				p.A415T		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.G1243A						PASS	.	G	THR/ALA	191,4215	119.2+/-156.9	7,177,2019	56.0	60.0	59.0		1243	2.9	0.0	19	dbSNP_134	59	0,8600		0,0,4300	yes	missense	TMPRSS9	NM_182973.1	58	7,177,6319	AA,AG,GG		0.0,4.335,1.4686	possibly-damaging	415/1060	2413788	191,12815	2203	4300	6503	SO:0001583	missense	360200	exon9			GCGGAAGCCCGGC	AJ488946	CCDS12088.1	19p13.3	2010-04-13						"""Serine peptidases / Transmembrane"""	30079	protein-coding gene	gene with protein product	"""polyserase 1"""	610477				12886014	Standard	NM_182973		Approved		uc010xgx.2	Q7Z410		ENST00000332578.3:c.1243G>A	19.37:g.2413788G>A	ENSP00000330264:p.Ala415Thr	107.0	0.0	0		99.0	46.0	0.464646	NM_182973	Q6ZND6|Q7Z411	Missense_Mutation	SNP	ENST00000332578.3	37	CCDS12088.1	31	0.014194139194139194	30	0.06097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	G	9.621	1.133714	0.21123	0.04335	0.0	ENSG00000178297	ENST00000395264;ENST00000332578	D	0.88664	-2.41	3.93	2.87	0.33458	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.157070	0.29806	N	0.011145	T	0.54711	0.1875	N	0.25647	0.755	0.09310	N	1	D;P	0.76494	0.999;0.587	D;P	0.79108	0.992;0.486	T	0.69367	-0.5164	10	0.15066	T	0.55	.	12.189	0.54257	0.0:0.1739:0.8261:0.0	.	415;449	Q7Z410;E7EMP4	TMPS9_HUMAN;.	T	449;415	ENSP00000330264:A415T	ENSP00000330264:A415T	A	+	1	0	TMPRSS9	2364788	0.674000	0.27549	0.004000	0.12327	0.000000	0.00434	2.621000	0.46418	0.637000	0.30526	-0.314000	0.08810	GCC	G|0.983;A|0.017	0.017	strong		0.652	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973	
INSRR	3645	hgsc.bcm.edu	37	1	156814884	156814884	+	Silent	SNP	C	C	T	rs149474857	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156814884C>T	ENST00000368195.3	-	12	2817	c.2421G>A	c.(2419-2421)gcG>gcA	p.A807A	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	807					actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GCATGGTGCGCGCAAAGACGA	0.617													C|||	36	0.0071885	0.0272	0.0	5008	,	,		16306	0.0		0.0	False		,,,				2504	0.0				p.A807A		Atlas-SNP	.											.	INSRR	309	.	0			c.G2421A						PASS	.	C	,	104,4302	78.3+/-116.7	0,104,2099	23.0	22.0	22.0		,2421	-4.1	0.9	1	dbSNP_134	22	1,8599		0,1,4299	no	intron,coding-synonymous	INSRR,NTRK1	NM_001007792.1,NM_014215.2	,	0,105,6398	TT,TC,CC		0.0116,2.3604,0.8073	,	,807/1298	156814884	105,12901	2203	4300	6503	SO:0001819	synonymous_variant	3645	exon12			GGTGCGCGCAAAG	J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"""Fibronectin type III domain containing"""	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.2421G>A	1.37:g.156814884C>T		83.0	0.0	0		115.0	56.0	0.486957	NM_014215	O60724|Q5VZS3	Silent	SNP	ENST00000368195.3	37	CCDS1160.1																																																																																			C|0.991;T|0.009	0.009	strong		0.617	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215	
ZNF157	7712	hgsc.bcm.edu	37	X	47272480	47272480	+	Silent	SNP	G	G	A	rs61736399	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:47272480G>A	ENST00000377073.3	+	4	1094	c.1008G>A	c.(1006-1008)ggG>ggA	p.G336G		NM_003446.3	NP_003437.2	P51786	ZN157_HUMAN	zinc finger protein 157	336					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	11						GTGAATGTGGGAAATTCTTCC	0.418													G|||	23	0.00609272	0.0144	0.0043	3775	,	,		15735	0.0		0.001	False		,,,				2504	0.0				p.G336G		Atlas-SNP	.											.	ZNF157	46	.	0			c.G1008A						PASS	.	G		119,3716		3,94,19,1535,552	39.0	37.0	38.0		1008	0.3	0.6	X	dbSNP_129	38	1,6726		0,1,0,2427,1871	no	coding-synonymous	ZNF157	NM_003446.3		3,95,19,3962,2423	AA,AG,A,GG,G		0.0149,3.103,1.1361		336/507	47272480	120,10442	2203	4299	6502	SO:0001819	synonymous_variant	7712	exon4			ATGTGGGAAATTC	U28687	CCDS14278.1	Xp11.2	2013-01-08	2006-08-22		ENSG00000147117	ENSG00000147117		"""Zinc fingers, C2H2-type"", ""-"""	12942	protein-coding gene	gene with protein product		300024	"""zinc finger protein 157 (HZF22)"""			8586441	Standard	NM_003446		Approved	HZF22	uc004dhr.1	P51786	OTTHUMG00000021443	ENST00000377073.3:c.1008G>A	X.37:g.47272480G>A		93.0	0.0	0		81.0	27.0	0.333333	NM_003446	Q96LE9	Silent	SNP	ENST00000377073.3	37	CCDS14278.1																																																																																			G|0.990;A|0.010	0.010	strong		0.418	ZNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056415.1	NM_003446	
TOM1L2	146691	hgsc.bcm.edu	37	17	17786042	17786042	+	Missense_Mutation	SNP	G	G	T	rs146710625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:17786042G>T	ENST00000379504.3	-	6	720	c.637C>A	c.(637-639)Ccc>Acc	p.P213T	TOM1L2_ENST00000318094.10_Missense_Mutation_p.P168T|TOM1L2_ENST00000395739.4_Missense_Mutation_p.P168T|TOM1L2_ENST00000535933.1_Intron|TOM1L2_ENST00000581396.1_Missense_Mutation_p.P163T|TOM1L2_ENST00000542206.1_Intron|TOM1L2_ENST00000540946.1_Intron	NM_001082968.1	NP_001076437.1	Q6ZVM7	TM1L2_HUMAN	target of myb1-like 2 (chicken)	213					intracellular protein transport (GO:0006886)|negative regulation of mitosis (GO:0045839)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	clathrin binding (GO:0030276)|protein kinase binding (GO:0019901)			endometrium(2)|kidney(2)|large_intestine(1)|lung(3)|prostate(2)	10	all_neural(463;0.228)					GCTGTGATGGGGCCAGTCACA	0.557																																					p.P213T	Melanoma(192;2505 2909 14455 25269)	Atlas-SNP	.											.	TOM1L2	54	.	0			c.C637A						PASS	.	G	THR/PRO,THR/PRO	11,4395	17.9+/-39.9	0,11,2192	96.0	89.0	91.0		487,637	4.7	1.0	17	dbSNP_134	91	0,8600		0,0,4300	yes	missense,missense	TOM1L2	NM_001033551.2,NM_001082968.1	38,38	0,11,6492	TT,TG,GG		0.0,0.2497,0.0846	benign,benign	163/458,213/508	17786042	11,12995	2203	4300	6503	SO:0001583	missense	146691	exon6			TGATGGGGCCAGT	AJ230803	CCDS32584.1, CCDS42270.1, CCDS74000.1, CCDS74001.1, CCDS74002.1, CCDS74003.1	17p11.2	2008-07-03	2001-11-28		ENSG00000175662	ENSG00000175662			11984	protein-coding gene	gene with protein product		615519	"""target of myb1 (chicken) homolog-like 1"""			10036180	Standard	NM_001082968		Approved		uc002grz.4	Q6ZVM7	OTTHUMG00000059353	ENST00000379504.3:c.637C>A	17.37:g.17786042G>T	ENSP00000368818:p.Pro213Thr	166.0	0.0	0		192.0	85.0	0.442708	NM_001082968	B7Z2L7|B7Z7F4|Q86V61|Q8TDE7|Q96M88	Missense_Mutation	SNP	ENST00000379504.3	37	CCDS42270.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.282146	0.80692	0.002497	0.0	ENSG00000175662	ENST00000379504;ENST00000318094;ENST00000395739;ENST00000537091	T;T	0.41065	1.01;1.01	5.7	4.73	0.59995	.	0.096186	0.85682	D	0.000000	T	0.56292	0.1975	M	0.79926	2.475	0.80722	D	1	B;P;B;B	0.50369	0.104;0.934;0.081;0.326	B;P;B;B	0.49361	0.059;0.608;0.067;0.142	T	0.61917	-0.6964	10	0.41790	T	0.15	-7.6658	16.772	0.85541	0.0:0.129:0.871:0.0	.	163;168;213;163	B7Z8F0;Q6ZVM7-3;Q6ZVM7;Q6ZVM7-2	.;.;TM1L2_HUMAN;.	T	213;163;168;163	ENSP00000368818:P213T;ENSP00000379088:P168T	ENSP00000312860:P163T	P	-	1	0	TOM1L2	17726767	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	5.571000	0.67404	1.388000	0.46506	0.655000	0.94253	CCC	G|0.999;T|0.001	0.001	strong		0.557	TOM1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131928.1		
DOCK1	1793	hgsc.bcm.edu	37	10	128795081	128795081	+	Silent	SNP	G	G	A	rs79043452	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:128795081G>A	ENST00000280333.6	+	7	652	c.543G>A	c.(541-543)acG>acA	p.T181T		NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	181					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		TAACTAGCACGATTAGTCTCT	0.368													G|||	19	0.00379393	0.0144	0.0	5008	,	,		20216	0.0		0.0	False		,,,				2504	0.0				p.T181T		Atlas-SNP	.											.	DOCK1	188	.	0			c.G543A						PASS	.	G		40,3640		0,40,1800	214.0	203.0	206.0		498	-10.2	0.0	10	dbSNP_133	206	1,8191		0,1,4095	no	coding-synonymous	DOCK1	NM_001380.3		0,41,5895	AA,AG,GG		0.0122,1.087,0.3454		166/1851	128795081	41,11831	1840	4096	5936	SO:0001819	synonymous_variant	1793	exon7			TAGCACGATTAGT	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"""DOwnstream of CrK"""	601403	"""dedicator of cyto-kinesis 1"""			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.543G>A	10.37:g.128795081G>A		130.0	0.0	0		159.0	79.0	0.496855	NM_001380	A9Z1Z5	Silent	SNP	ENST00000280333.6	37																																																																																				G|0.997;A|0.003	0.003	strong		0.368	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380	
CCDC8	83987	hgsc.bcm.edu	37	19	46915182	46915182	+	Missense_Mutation	SNP	C	C	T	rs11880658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:46915182C>T	ENST00000307522.3	-	1	1659	c.886G>A	c.(886-888)Ggg>Agg	p.G296R		NM_032040.4	NP_114429.2	Q9H0W5	CCDC8_HUMAN	coiled-coil domain containing 8	296			G -> R (in dbSNP:rs11880658).		microtubule cytoskeleton organization (GO:0000226)|negative regulation of phosphatase activity (GO:0010923)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(262;4.66e-05)|all cancers(93;0.000582)|Epithelial(262;0.00428)|GBM - Glioblastoma multiforme(486;0.0421)		GCCTCTCCCCCCTGATCAGCC	0.642													C|||	215	0.0429313	0.1558	0.0101	5008	,	,		16994	0.0		0.002	False		,,,				2504	0.0				p.G296R		Atlas-SNP	.											.	CCDC8	56	.	0			c.G886A						PASS	.	C	ARG/GLY	511,3895	229.4+/-244.0	26,459,1718	85.0	85.0	85.0		886	-0.9	0.2	19	dbSNP_120	85	4,8596	2.2+/-6.3	0,4,4296	yes	missense	CCDC8	NM_032040.3	125	26,463,6014	TT,TC,CC		0.0465,11.5978,3.9597	benign	296/539	46915182	515,12491	2203	4300	6503	SO:0001583	missense	83987	exon1			CTCCCCCCTGATC	BC025243	CCDS12685.1	19q13.33	2012-04-17			ENSG00000169515	ENSG00000169515		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25367	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 20"""	614145				11230166	Standard	NM_032040		Approved	DKFZp564K0322, 3M3, PPP1R20	uc002pep.3	Q9H0W5	OTTHUMG00000162348	ENST00000307522.3:c.886G>A	19.37:g.46915182C>T	ENSP00000303158:p.Gly296Arg	111.0	0.0	0		106.0	53.0	0.5	NM_032040	Q8TB26	Missense_Mutation	SNP	ENST00000307522.3	37	CCDS12685.1	80	0.03663003663003663	76	0.15447154471544716	4	0.011049723756906077	0	0.0	0	0.0	C	4.694	0.129001	0.08981	0.115978	4.65E-4	ENSG00000169515	ENST00000307522	T	0.10668	2.85	3.87	-0.89	0.10577	.	0.845492	0.09922	N	0.738356	T	0.00039	0.0001	N	0.02011	-0.69	0.29953	N	0.820099	B	0.06786	0.001	B	0.08055	0.003	T	0.48007	-0.9072	10	0.11485	T	0.65	-2.0588	8.1056	0.30883	0.0:0.5064:0.0:0.4936	rs11880658	296	Q9H0W5	CCDC8_HUMAN	R	296	ENSP00000303158:G296R	ENSP00000303158:G296R	G	-	1	0	CCDC8	51607022	0.000000	0.05858	0.194000	0.23346	0.165000	0.22458	-0.753000	0.04792	-0.122000	0.11766	0.655000	0.94253	GGG	C|0.962;T|0.038	0.038	strong		0.642	CCDC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368598.1	NM_032040	
THBS1	7057	hgsc.bcm.edu	37	15	39874092	39874092	+	Silent	SNP	C	C	T	rs35248254	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:39874092C>T	ENST00000260356.5	+	2	199	c.34C>T	c.(34-36)Ctg>Ttg	p.L12L		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	12					activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		CGTCCTGTTCCTGATGCATGT	0.592											OREG0023050	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	78	0.0155751	0.0552	0.0072	5008	,	,		18818	0.0		0.0	False		,,,				2504	0.0				p.L12L		Atlas-SNP	.											.	THBS1	106	.	0			c.C34T						PASS	.	C		165,4235	110.4+/-148.6	3,159,2038	121.0	101.0	108.0		34	4.0	1.0	15	dbSNP_126	108	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous	THBS1	NM_003246.2		3,160,6334	TT,TC,CC		0.0116,3.75,1.2775		12/1171	39874092	166,12828	2200	4297	6497	SO:0001819	synonymous_variant	7057	exon2			CTGTTCCTGATGC		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"""thrombospondin-1p180"""	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.34C>T	15.37:g.39874092C>T		128.0	0.0	0	889	125.0	57.0	0.456	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Silent	SNP	ENST00000260356.5	37	CCDS32194.1																																																																																			C|0.985;T|0.015	0.015	strong		0.592	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
SCG2	7857	hgsc.bcm.edu	37	2	224462714	224462714	+	Silent	SNP	G	G	A	rs721233	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:224462714G>A	ENST00000305409.2	-	2	1519	c.1287C>T	c.(1285-1287)gaC>gaT	p.D429D		NM_003469.4	NP_003460.2	O00255	MEN1_HUMAN	secretogranin II	0					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)			NS(1)|breast(1)|endometrium(1)|kidney(6)|large_intestine(10)|liver(1)|lung(16)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(4)	44		Renal(207;0.0112)|Lung NSC(271;0.0185)|all_lung(227;0.0271)		Epithelial(121;8.16e-11)|all cancers(144;4.66e-08)|Lung(261;0.00714)|LUSC - Lung squamous cell carcinoma(224;0.008)		CACTGAGCCCGTCTGGTAGGG	0.468													G|||	277	0.0553115	0.1604	0.0346	5008	,	,		19418	0.001		0.0189	False		,,,				2504	0.0215				p.D429D		Atlas-SNP	.											.	SCG2	99	.	0			c.C1287T						PASS	.	G		663,3743	279.3+/-274.7	49,565,1589	78.0	78.0	78.0		1287	-3.1	0.2	2	dbSNP_86	78	173,8427	78.6+/-141.3	3,167,4130	no	coding-synonymous	SCG2	NM_003469.4		52,732,5719	AA,AG,GG		2.0116,15.0477,6.4278		429/618	224462714	836,12170	2203	4300	6503	SO:0001819	synonymous_variant	7857	exon2			GAGCCCGTCTGGT	M25756	CCDS2457.1	2q35-q36	2010-04-27	2010-04-27		ENSG00000171951	ENSG00000171951			10575	protein-coding gene	gene with protein product	"""secretoneurin"", ""chromogranin C"""	118930				8617499, 16101435	Standard	NM_003469		Approved	CHGC, SgII, SN	uc002vnm.3	P13521	OTTHUMG00000133166	ENST00000305409.2:c.1287C>T	2.37:g.224462714G>A		86.0	0.0	0		79.0	44.0	0.556962	NM_003469	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Silent	SNP	ENST00000305409.2	37	CCDS2457.1																																																																																			G|0.932;A|0.068	0.068	strong		0.468	SCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256870.2	NM_003469	
OR10G7	390265	hgsc.bcm.edu	37	11	123909638	123909638	+	Missense_Mutation	SNP	G	G	A	rs148218442	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123909638G>A	ENST00000330487.5	-	1	79	c.71C>T	c.(70-72)cCc>cTc	p.P24L		NM_001004463.1	NP_001004463.1	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G, member 7	24						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(4)|kidney(7)|large_intestine(6)|lung(20)|ovary(2)|prostate(2)|stomach(3)|urinary_tract(1)	47		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		TCCAAAGAGGGGGGCGTCCAG	0.572													G|||	62	0.0123802	0.0416	0.0101	5008	,	,		16260	0.0		0.0	False		,,,				2504	0.0				p.P24L		Atlas-SNP	.											OR10G7,NS,carcinoma,+1,1	OR10G7	103	1	0			c.C71T						scavenged	.	G	LEU/PRO	70,4330	56.8+/-93.2	0,70,2130	96.0	92.0	94.0		71	-3.2	0.0	11	dbSNP_134	94	4,8594	3.0+/-9.4	0,4,4295	no	missense	OR10G7	NM_001004463.1	98	0,74,6425	AA,AG,GG		0.0465,1.5909,0.5693	benign	24/312	123909638	74,12924	2200	4299	6499	SO:0001583	missense	390265	exon1			AAGAGGGGGGCGT	AB065754	CCDS31705.1	11q24.1	2012-08-09			ENSG00000182634	ENSG00000182634		"""GPCR / Class A : Olfactory receptors"""	14842	protein-coding gene	gene with protein product							Standard	NM_001004463		Approved		uc001pzq.1	Q8NGN6	OTTHUMG00000165969	ENST00000330487.5:c.71C>T	11.37:g.123909638G>A	ENSP00000329689:p.Pro24Leu	408.0	2.0	0.00490196		229.0	109.0	0.475983	NM_001004463	Q6IFE8	Missense_Mutation	SNP	ENST00000330487.5	37	CCDS31705.1	20	0.009157509157509158	12	0.024390243902439025	4	0.011049723756906077	0	0.0	4	0.005277044854881266	G	0.023	-1.397240	0.01175	0.015909	4.65E-4	ENSG00000182634	ENST00000330487	T	0.00036	8.86	3.38	-3.23	0.05109	.	1.833280	0.02752	N	0.117583	T	0.00039	0.0001	N	0.01096	-1.015	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.33954	-0.9848	10	0.02654	T	1	.	10.6967	0.45903	0.7947:0.0:0.2053:0.0	.	24	Q8NGN6	O10G7_HUMAN	L	24	ENSP00000329689:P24L	ENSP00000329689:P24L	P	-	2	0	OR10G7	123414848	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.678000	0.05209	-0.661000	0.05345	-0.232000	0.12228	CCC	G|0.992;A|0.008	0.008	strong		0.572	OR10G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387271.1	NM_001004463	
RET	5979	hgsc.bcm.edu	37	10	43615094	43615094	+	Silent	SNP	C	C	T	rs1800862	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:43615094C>T	ENST00000355710.3	+	14	2740	c.2508C>T	c.(2506-2508)agC>agT	p.S836S	RET_ENST00000340058.5_Silent_p.S836S	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	836	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	GCAACTCCAGCTCCCTGGACC	0.642		1	"""T, Mis, N, F"""	"""H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma"""	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma				C|||	180	0.0359425	0.0129	0.0303	5008	,	,		15331	0.0		0.0586	False		,,,				2504	0.0849				p.S836S	Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	Atlas-SNP	.	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	"""E, O"""	.	RET	916	.	0			c.C2508T	GRCh37	CM012798	RET	M	rs1800862	PASS	.	C	,	117,4289	83.9+/-122.4	2,113,2088	36.0	35.0	35.0		2508,2508	2.5	1.0	10	dbSNP_89	35	435,8163	128.3+/-186.6	17,401,3881	no	coding-synonymous,coding-synonymous	RET	NM_020630.4,NM_020975.4	,	19,514,5969	TT,TC,CC		5.0593,2.6555,4.2448	,	836/1073,836/1115	43615094	552,12452	2203	4299	6502	SO:0001819	synonymous_variant	5979	exon14	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	CTCCAGCTCCCTG	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"""Cadherins / Cadherin-related"""	9967	protein-coding gene	gene with protein product	"""cadherin-related family member 16"""	164761	"""multiple endocrine neoplasia and medullary thyroid carcinoma 1"", ""Hirschsprung disease 1"""	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.2508C>T	10.37:g.43615094C>T		113.0	0.0	0		124.0	61.0	0.491935	NM_020630	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Silent	SNP	ENST00000355710.3	37	CCDS7200.1																																																																																			C|0.960;T|0.040	0.040	strong		0.642	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975	
ABCC10	89845	hgsc.bcm.edu	37	6	43411700	43411700	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43411700C>T	ENST00000372530.4	+	11	2661	c.2446C>T	c.(2446-2448)Caa>Taa	p.Q816*	ABCC10_ENST00000244533.3_Nonsense_Mutation_p.Q788*	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	816	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(8)|lung(21)|ovary(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)		Cyclosporine(DB00091)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Estradiol(DB00783)|Etoposide(DB00773)|Gemcitabine(DB00441)|Methotrexate(DB00563)|Paclitaxel(DB01229)|Sildenafil(DB00203)|Tenofovir(DB00300)|Verapamil(DB00661)|Vincristine(DB00541)	GCCACTGGTACAAGCTGTCCC	0.542																																					p.Q816X		Atlas-SNP	.											.	ABCC10	118	.	0			c.C2446T						PASS	.						150.0	145.0	147.0					6																	43411700		2203	4300	6503	SO:0001587	stop_gained	89845	exon11			CTGGTACAAGCTG	U66684	CCDS4896.1, CCDS56430.1	6p12.3	2012-03-14			ENSG00000124574	ENSG00000124574		"""ATP binding cassette transporters / subfamily C"""	52	protein-coding gene	gene with protein product		612509				8894702	Standard	NM_033450		Approved	EST182763, MRP7, SIMRP7	uc003ouy.1	Q5T3U5	OTTHUMG00000014733	ENST00000372530.4:c.2446C>T	6.37:g.43411700C>T	ENSP00000361608:p.Gln816*	91.0	0.0	0		83.0	45.0	0.542169	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Nonsense_Mutation	SNP	ENST00000372530.4	37	CCDS56430.1	.	.	.	.	.	.	.	.	.	.	C	42	9.524227	0.99195	.	.	ENSG00000124574	ENST00000372530;ENST00000244533	.	.	.	5.67	5.67	0.87782	.	0.128063	0.52532	D	0.000071	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06365	T	0.9	-28.5185	13.6285	0.62181	0.0:0.7989:0.2011:0.0	.	.	.	.	X	816;788	.	ENSP00000244533:Q788X	Q	+	1	0	ABCC10	43519678	0.921000	0.31238	0.981000	0.43875	0.798000	0.45092	3.288000	0.51739	2.673000	0.90976	0.655000	0.94253	CAA	.	.	none		0.542	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450	
FMO3	2328	hgsc.bcm.edu	37	1	171076888	171076888	+	Missense_Mutation	SNP	G	G	C	rs12072582	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:171076888G>C	ENST00000367755.4	+	4	505	c.394G>C	c.(394-396)Gat>Cat	p.D132H	FMO3_ENST00000542847.1_Missense_Mutation_p.D112H|FMO3_ENST00000538429.1_Missense_Mutation_p.D69H|FMO3_ENST00000392085.2_Missense_Mutation_p.D132H	NM_001002294.2	NP_001002294.1	P31513	FMO3_HUMAN	flavin containing monooxygenase 3	132			D -> H (in dbSNP:rs12072582). {ECO:0000269|PubMed:12527699, ECO:0000269|Ref.4}.		drug metabolic process (GO:0017144)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	amino acid binding (GO:0016597)|flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)|trimethylamine monooxygenase activity (GO:0034899)			endometrium(1)|kidney(1)|large_intestine(12)|lung(12)|skin(1)|stomach(2)|urinary_tract(2)	31	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Almotriptan(DB00918)|Cimetidine(DB00501)|Clozapine(DB00363)|Dapsone(DB00250)|Dasatinib(DB01254)|Olanzapine(DB00334)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	CACTGAAAGGGATGGTAAAAA	0.413													G|||	73	0.0145767	0.0522	0.0058	5008	,	,		15662	0.0		0.0	False		,,,				2504	0.0				p.D132H		Atlas-SNP	.											.	FMO3	73	.	0			c.G394C	GRCh37	CM033905	FMO3	M	rs12072582	PASS	.	G	HIS/ASP,HIS/ASP	176,4230	113.8+/-151.8	2,172,2029	132.0	133.0	133.0		394,394	-2.1	0.0	1	dbSNP_120	133	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	FMO3	NM_001002294.2,NM_006894.5	81,81	2,173,6328	CC,CG,GG		0.0116,3.9946,1.3609	benign,benign	132/533,132/533	171076888	177,12829	2203	4300	6503	SO:0001583	missense	2328	exon4			GAAAGGGATGGTA	BC032016	CCDS1292.1	1q24.3	2013-10-01			ENSG00000007933	ENSG00000007933	2.6.1.16		3771	protein-coding gene	gene with protein product		136132				8486388, 9417913	Standard	NM_001002294		Approved		uc001ghh.3	P31513	OTTHUMG00000035505	ENST00000367755.4:c.394G>C	1.37:g.171076888G>C	ENSP00000356729:p.Asp132His	176.0	0.0	0		189.0	73.0	0.386243	NM_006894	B2R816|Q14854|Q8N5N5	Missense_Mutation	SNP	ENST00000367755.4	37	CCDS1292.1	23	0.010531135531135532	20	0.04065040650406504	3	0.008287292817679558	0	0.0	0	0.0	G	8.560	0.877541	0.17395	0.039946	1.16E-4	ENSG00000007933	ENST00000367755;ENST00000392085;ENST00000542847;ENST00000538429	T;T;T;T	0.57436	0.4;0.4;0.4;0.4	4.84	-2.13	0.07144	.	0.100095	0.64402	N	0.000003	T	0.26085	0.0636	M	0.65677	2.01	0.34737	D	0.730401	B;B;B	0.26512	0.151;0.09;0.036	B;B;B	0.31245	0.126;0.069;0.078	T	0.02588	-1.1137	10	0.49607	T	0.09	-2.9075	3.4783	0.07593	0.1388:0.3402:0.4052:0.1158	rs12072582;rs52790216;rs58199544;rs12072582	69;112;132	F5H261;F5GZZ8;P31513	.;.;FMO3_HUMAN	H	132;132;112;69	ENSP00000356729:D132H;ENSP00000375935:D132H;ENSP00000444073:D112H;ENSP00000439500:D69H	ENSP00000356729:D132H	D	+	1	0	FMO3	169343512	0.005000	0.15991	0.035000	0.18076	0.054000	0.15201	0.421000	0.21280	-0.407000	0.07576	0.591000	0.81541	GAT	G|0.983;C|0.017	0.017	strong		0.413	FMO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086219.1	NM_006894	
IDS	3423	hgsc.bcm.edu	37	X	148579705	148579705	+	Missense_Mutation	SNP	G	G	A	rs61736892	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:148579705G>A	ENST00000340855.6	-	5	850	c.641C>T	c.(640-642)aCg>aTg	p.T214M	IDS_ENST00000541269.1_Missense_Mutation_p.T3M|IDS_ENST00000490775.1_5'UTR|IDS_ENST00000422081.2_Missense_Mutation_p.T3M|IDS_ENST00000370441.4_Missense_Mutation_p.T214M|IDS_ENST00000370443.4_Missense_Mutation_p.T214M	NM_000202.5|NM_001166550.1	NP_000193.1|NP_001160022.1	P22304	IDS_HUMAN	iduronate 2-sulfatase	214					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	lysosomal lumen (GO:0043202)	iduronate-2-sulfatase activity (GO:0004423)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(5)|large_intestine(2)|lung(8)|prostate(1)	20	Acute lymphoblastic leukemia(192;6.56e-05)|Colorectal(9;0.0662)					ACTGGCTGACGTTTTCATCTT	0.527													G|||	60	0.015894	0.0439	0.0029	3775	,	,		14709	0.0		0.0	False		,,,				2504	0.0				p.T214M		Atlas-SNP	.											.	IDS	46	.	0			c.C641T	GRCh37	CS961600	IDS	S	rs61736892	PASS	.	G	MET/THR,MET/THR,MET/THR	184,3651		7,143,27,1482,544	160.0	136.0	144.0		641,371,641	1.7	0.2	X	dbSNP_129	144	0,6728		0,0,0,2428,1872	yes	missense,missense,missense	IDS	NM_000202.5,NM_001166550.1,NM_006123.4	81,81,81	7,143,27,3910,2416	AA,AG,A,GG,G		0.0,4.7979,1.7419	benign,benign,benign	214/551,124/461,214/344	148579705	184,10379	2203	4300	6503	SO:0001583	missense	3423	exon5			GCTGACGTTTTCA	M58342	CCDS14685.1, CCDS14686.1	Xq27.3-q28	2012-10-02	2008-08-01		ENSG00000010404	ENSG00000010404	3.1.6.13		5389	protein-coding gene	gene with protein product	"""Hunter syndrome"""	300823		SIDS			Standard	NM_006123		Approved		uc011mxe.2	P22304	OTTHUMG00000022615	ENST00000340855.6:c.641C>T	X.37:g.148579705G>A	ENSP00000339801:p.Thr214Met	240.0	0.0	0		234.0	110.0	0.470085	NM_006123	D3DWT4|Q14604|Q9BRM3	Missense_Mutation	SNP	ENST00000340855.6	37	CCDS14685.1	24	0.014466546112115732	17	0.035416666666666666	1	0.0027624309392265192	0	0.0	0	0.0	G	13.84	2.358547	0.41801	0.047979	0.0	ENSG00000010404	ENST00000340855;ENST00000541269;ENST00000370441;ENST00000370443	D;D;D;D	0.99900	-7.62;-5.85;-7.62;-7.62	5.12	1.68	0.24146	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.624103	0.18240	N	0.147268	D	0.97676	0.9238	L	0.56340	1.77	0.80722	P	0.0	D;D;D	0.61697	0.987;0.973;0.99	P;P;P	0.59595	0.781;0.806;0.86	D	0.90347	0.4363	9	0.46703	T	0.11	.	3.6256	0.08112	0.0979:0.1075:0.4765:0.318	.	214;124;214	P22304-2;B4DGD7;P22304	.;.;IDS_HUMAN	M	214;3;214;214	ENSP00000339801:T214M;ENSP00000441261:T3M;ENSP00000359470:T214M;ENSP00000359472:T214M	ENSP00000339801:T214M	T	-	2	0	IDS	148387610	0.031000	0.19500	0.151000	0.22473	0.933000	0.57130	0.398000	0.20899	0.865000	0.35603	-0.395000	0.06472	ACG	G|0.982;A|0.018	0.018	strong		0.527	IDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058677.3		
SMCHD1	23347	hgsc.bcm.edu	37	18	2728559	2728559	+	Missense_Mutation	SNP	A	A	G	rs9961682	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:2728559A>G	ENST00000320876.6	+	23	3216	c.2878A>G	c.(2878-2880)Ata>Gta	p.I960V	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000609587.1_3'UTR|SMCHD1_ENST00000261598.8_Missense_Mutation_p.I960V	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	960			I -> V (in dbSNP:rs9961682).		chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						ATCAGACAACATAACAGCACA	0.358													A|||	154	0.0307508	0.1097	0.0101	5008	,	,		17853	0.001		0.001	False		,,,				2504	0.0				p.I960V		Atlas-SNP	.											.	SMCHD1	88	.	0			c.A2878G						PASS	.	A	VAL/ILE	409,3315		26,357,1479	104.0	100.0	101.0		2878	-3.5	0.9	18	dbSNP_119	101	7,8193		0,7,4093	yes	missense	SMCHD1	NM_015295.2	29	26,364,5572	GG,GA,AA		0.0854,10.9828,3.4888	benign	960/2006	2728559	416,11508	1862	4100	5962	SO:0001583	missense	23347	exon23			GACAACATAACAG	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.2878A>G	18.37:g.2728559A>G	ENSP00000326603:p.Ile960Val	65.0	0.0	0		58.0	36.0	0.62069	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Missense_Mutation	SNP	ENST00000320876.6	37	CCDS45822.1	52	0.023809523809523808	46	0.09349593495934959	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	A	10.45	1.352273	0.24512	0.109828	8.54E-4	ENSG00000101596	ENST00000320876;ENST00000261598	T;T	0.24908	1.83;1.84	5.84	-3.46	0.04767	.	0.509376	0.22250	N	0.062565	T	0.00241	0.0007	N	0.14661	0.345	0.26418	N	0.976158	B	0.02656	0.0	B	0.01281	0.0	T	0.16364	-1.0405	10	0.32370	T	0.25	-4.6572	9.6361	0.39809	0.3166:0.2087:0.4747:0.0	rs9961682;rs52802941;rs9961682	960	A6NHR9	SMHD1_HUMAN	V	960	ENSP00000326603:I960V;ENSP00000261598:I960V	ENSP00000261598:I960V	I	+	1	0	SMCHD1	2718559	0.830000	0.29337	0.936000	0.37596	0.999000	0.98932	-0.076000	0.11412	-0.889000	0.03950	0.528000	0.53228	ATA	A|0.969;G|0.031	0.031	strong		0.358	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2		
PDE6B	5158	hgsc.bcm.edu	37	4	660340	660340	+	Silent	SNP	G	G	A	rs61739716	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:660340G>A	ENST00000496514.1	+	20	2310	c.2289G>A	c.(2287-2289)aaG>aaA	p.K763K	PDE6B_ENST00000255622.6_Silent_p.K763K|PDE6B_ENST00000429163.2_Silent_p.K484K			P35913	PDE6B_HUMAN	phosphodiesterase 6B, cGMP-specific, rod, beta	763					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			NS(1)|breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(2)|prostate(2)|urinary_tract(1)	30					Caffeine(DB00201)	ACCGGAACAAGGCGGCCGAGC	0.652													.|||	53	0.0105831	0.0378	0.0014	5008	,	,		15996	0.0		0.001	False		,,,				2504	0.001				p.K763K	GBM(71;463 1194 9848 25922 46834)	Atlas-SNP	.											.	PDE6B	80	.	0			c.G2289A						PASS	.	G	,,	159,4247	108.2+/-146.6	2,155,2046	96.0	78.0	84.0		2289,2289,1452	1.0	1.0	4	dbSNP_129	84	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	PDE6B	NM_000283.3,NM_001145291.1,NM_001145292.1	,,	2,155,6346	AA,AG,GG		0.0,3.6087,1.2225	,,	763/855,763/854,484/576	660340	159,12847	2203	4300	6503	SO:0001819	synonymous_variant	5158	exon20			GAACAAGGCGGCC	BC000249	CCDS33932.1, CCDS46993.1, CCDS54703.1	4p16.3	2014-01-28	2008-07-31		ENSG00000133256	ENSG00000133256	3.1.4.17	"""Phosphodiesterases"""	8786	protein-coding gene	gene with protein product	"""congenital stationary night blindness 3, autosomal dominant"""	180072		PDEB		1313787	Standard	NM_001145292		Approved	CSNB3, rd1, RP40, CSNBAD2	uc003gap.3	P35913	OTTHUMG00000159909	ENST00000496514.1:c.2289G>A	4.37:g.660340G>A		79.0	0.0	0		85.0	34.0	0.4	NM_001145291	B7Z9T9|E7ETT3|Q53XN5|Q9BWH5|Q9UD49	Silent	SNP	ENST00000496514.1	37	CCDS33932.1	18	0.008241758241758242	18	0.036585365853658534	0	0.0	0	0.0	0	0.0	G	9.994	1.231604	0.22626	0.036087	0.0	ENSG00000133256	ENST00000461490	.	.	.	4.26	0.984	0.19773	.	.	.	.	.	T	0.22282	0.0537	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.13150	-1.0520	4	.	.	.	.	6.8943	0.24247	0.5241:0.0:0.4759:0.0	rs61739716	.	.	.	K	44	.	.	R	+	2	0	PDE6B	650340	1.000000	0.71417	0.999000	0.59377	0.990000	0.78478	1.242000	0.32755	0.120000	0.18254	0.650000	0.86243	AGG	G|0.990;A|0.010	0.010	strong		0.652	PDE6B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000358109.1	NM_000283	
ASTN1	460	hgsc.bcm.edu	37	1	176915087	176915087	+	Missense_Mutation	SNP	C	C	T	rs138686233	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:176915087C>T	ENST00000367654.3	-	13	2459	c.2248G>A	c.(2248-2250)Gga>Aga	p.G750R	ASTN1_ENST00000367657.3_Missense_Mutation_p.G742R|ASTN1_ENST00000424564.2_Missense_Mutation_p.G742R|ASTN1_ENST00000361833.2_Missense_Mutation_p.G742R|ASTN1_ENST00000281881.3_5'UTR	NM_004319.1	NP_004310.1	O14525	ASTN1_HUMAN	astrotactin 1	750					locomotory behavior (GO:0007626)|neuron cell-cell adhesion (GO:0007158)|neuron migration (GO:0001764)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)		p.G742*(1)		NS(4)|breast(5)|central_nervous_system(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(23)|liver(1)|lung(81)|ovary(6)|prostate(5)|skin(10)|urinary_tract(3)	153						AGCACCTGTCCGGCAGCCACT	0.463													C|||	8	0.00159744	0.0061	0.0	5008	,	,		19496	0.0		0.0	False		,,,				2504	0.0				p.G742R		Atlas-SNP	.											ASTN1,NS,carcinoma,0,1	ASTN1	314	1	1	Substitution - Nonsense(1)	lung(1)	c.G2224A						PASS	.	C	ARG/GLY,ARG/GLY	37,4369	41.6+/-74.8	0,37,2166	110.0	118.0	115.0		2224,2224	5.2	1.0	1	dbSNP_134	115	0,8600		0,0,4300	yes	missense,missense	ASTN1	NM_004319.1,NM_207108.1	125,125	0,37,6466	TT,TC,CC		0.0,0.8398,0.2845	possibly-damaging,possibly-damaging	742/1295,742/1217	176915087	37,12969	2203	4300	6503	SO:0001583	missense	460	exon13			CCTGTCCGGCAGC	AB006627	CCDS1319.1, CCDS44280.1, CCDS65732.1	1q25.2	2008-02-05	2006-08-24	2006-08-24	ENSG00000152092	ENSG00000152092			773	protein-coding gene	gene with protein product		600904	"""astrotactin"""	ASTN		9070947	Standard	NM_001286164		Approved		uc001glc.3	O14525	OTTHUMG00000035041	ENST00000367654.3:c.2248G>A	1.37:g.176915087C>T	ENSP00000356626:p.Gly750Arg	94.0	0.0	0		82.0	49.0	0.597561	NM_004319	A5PL12|B4DHI9|E9PFR8|O60799|Q5W0V7|Q5W0V8	Missense_Mutation	SNP	ENST00000367654.3	37		0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	25.9	4.687682	0.88639	0.008398	0.0	ENSG00000152092	ENST00000367657;ENST00000361833;ENST00000367654;ENST00000424564;ENST00000541808	T;T;T;T	0.17370	2.28;2.7;2.7;2.29	5.25	5.25	0.73442	.	0.107853	0.64402	D	0.000004	T	0.15478	0.0373	L	0.27053	0.805	0.58432	D	0.999998	D;D;D	0.67145	0.996;0.993;0.993	P;P;P	0.54856	0.762;0.762;0.762	T	0.00555	-1.1673	10	0.87932	D	0	-17.5766	11.9089	0.52727	0.0:0.9195:0.0:0.0805	.	750;742;742	O14525;O14525-2;B1AJS1	ASTN1_HUMAN;.;.	R	742;742;750;742;742	ENSP00000356629:G742R;ENSP00000354536:G742R;ENSP00000356626:G750R;ENSP00000395041:G742R	ENSP00000354536:G742R	G	-	1	0	ASTN1	175181710	1.000000	0.71417	0.951000	0.38953	0.992000	0.81027	5.539000	0.67199	2.467000	0.83353	0.655000	0.94253	GGA	C|0.998;T|0.002	0.002	strong		0.463	ASTN1-201	KNOWN	basic	protein_coding	protein_coding		NM_004319	
NRK	203447	hgsc.bcm.edu	37	X	105168689	105168689	+	Missense_Mutation	SNP	C	C	A	rs16984889	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:105168689C>A	ENST00000243300.9	+	19	3281	c.2978C>A	c.(2977-2979)gCa>gAa	p.A993E	NRK_ENST00000428173.2_Missense_Mutation_p.A994E	NM_198465.2	NP_940867.2	Q7Z2Y5	NRK_HUMAN	Nik related kinase	993			A -> E (in dbSNP:rs16984889).		activation of JNKK activity (GO:0007256)|negative regulation of cell proliferation (GO:0008285)|parturition (GO:0007567)|regulation of spongiotrophoblast cell proliferation (GO:0060721)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(8)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(14)|lung(36)|ovary(3)|prostate(1)|skin(2)	76						GTTGTCAGGGCAAGCTATGGC	0.408										HNSCC(51;0.14)			C|||	462	0.122384	0.3306	0.0331	3775	,	,		16586	0.0		0.002	False		,,,				2504	0.0				p.A993E		Atlas-SNP	.											.	NRK	321	.	0			c.C2978A						PASS	.	C	GLU/ALA	1205,2084		184,619,218,559,347	26.0	24.0	25.0		2978	1.8	0.1	X	dbSNP_123	25	9,6498		0,8,1,2351,1788	yes	missense	NRK	NM_198465.2	107	184,627,219,2910,2135	AA,AC,A,CC,C		0.1383,36.6373,12.3928	benign	993/1583	105168689	1214,8582	1927	4148	6075	SO:0001583	missense	203447	exon19			TCAGGGCAAGCTA	BX538345	CCDS65305.1	Xq22.3	2008-02-05			ENSG00000123572	ENSG00000123572			25391	protein-coding gene	gene with protein product		300791					Standard	NM_198465		Approved	DKFZp686A17109	uc004emd.3	Q7Z2Y5	OTTHUMG00000022143	ENST00000243300.9:c.2978C>A	X.37:g.105168689C>A	ENSP00000434830:p.Ala993Glu	254.0	0.0	0		267.0	163.0	0.610487	NM_198465	Q32ND6|Q5H9K2|Q6ZMP2	Missense_Mutation	SNP	ENST00000243300.9	37		168	0.10126582278481013	109	0.2794871794871795	4	0.011299435028248588	0	0.0	0	0.0	C	12.01	1.808484	0.31961	0.366373	0.001383	ENSG00000123572	ENST00000243300;ENST00000428173	T;T	0.79554	-1.27;-1.28	4.85	1.79	0.24919	.	0.766382	0.11121	N	0.597389	T	0.00012	0.0000	N	0.19112	0.55	0.58432	P	9.99999999995449E-6	B;B	0.30281	0.275;0.037	B;B	0.27796	0.083;0.011	T	0.14671	-1.0464	9	0.62326	D	0.03	.	1.9029	0.03271	0.212:0.4677:0.2021:0.1183	rs16984889;rs52799695;rs16984889	661;993	Q7Z2Y5-2;Q7Z2Y5	.;NRK_HUMAN	E	993;994	ENSP00000434830:A993E;ENSP00000438378:A994E	ENSP00000434830:A993E	A	+	2	0	NRK	105055345	0.038000	0.19896	0.138000	0.22173	0.767000	0.43475	-0.107000	0.10873	0.901000	0.36495	0.513000	0.50165	GCA	0|0.008;A|0.143	0.143	strong		0.408	NRK-001	KNOWN	non_canonical_conserved|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000106480.6	NM_198465	
C3orf30	152405	hgsc.bcm.edu	37	3	118865615	118865615	+	Missense_Mutation	SNP	G	G	C	rs9859242	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:118865615G>C	ENST00000295622.1	+	1	619	c.579G>C	c.(577-579)caG>caC	p.Q193H	IGSF11_ENST00000441144.2_5'Flank|IGSF11_ENST00000354673.2_5'Flank|IGSF11_ENST00000425327.2_5'Flank|RP11-484M3.5_ENST00000490594.1_5'Flank	NM_152539.2	NP_689752.2	Q96M34	CC030_HUMAN	chromosome 3 open reading frame 30	193			Q -> H (in dbSNP:rs9859242).							NS(1)|breast(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(20)|ovary(2)|prostate(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(114;0.222)		CTTCCGAGCAGATGGACCGCA	0.512													G|||	113	0.0225639	0.084	0.0029	5008	,	,		22926	0.0		0.0	False		,,,				2504	0.0				p.Q193H		Atlas-SNP	.											.	C3orf30	64	.	0			c.G579C						PASS	.	G	HIS/GLN	361,4045	184.3+/-211.7	17,327,1859	97.0	100.0	99.0		579	2.2	0.0	3	dbSNP_119	99	2,8598	2.2+/-6.3	0,2,4298	yes	missense	C3orf30	NM_152539.2	24	17,329,6157	CC,CG,GG		0.0233,8.1934,2.791	possibly-damaging	193/537	118865615	363,12643	2203	4300	6503	SO:0001583	missense	152405	exon1			CGAGCAGATGGAC	AK057421	CCDS2984.1	3q13.32	2011-08-09			ENSG00000163424	ENSG00000163424			26553	protein-coding gene	gene with protein product							Standard	NM_152539		Approved	FLJ32859	uc003ecb.1	Q96M34	OTTHUMG00000159349	ENST00000295622.1:c.579G>C	3.37:g.118865615G>C	ENSP00000295622:p.Gln193His	78.0	0.0	0		112.0	48.0	0.428571	NM_152539	A1L4B7	Missense_Mutation	SNP	ENST00000295622.1	37	CCDS2984.1	29|29	0.013278388278388278|0.013278388278388278	28|28	0.056910569105691054|0.056910569105691054	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	G|G	13.18|13.18	2.160413|2.160413	0.38119|0.38119	0.081934|0.081934	2.33E-4|2.33E-4	ENSG00000163424|ENSG00000163424	ENST00000460150|ENST00000295622;ENST00000470341	.|T	.|0.26223	.|1.75	4.09|4.09	2.24|2.24	0.28232|0.28232	.|.	.|1.043520	.|0.07559	.|N	.|0.916758	T|T	0.02767|0.02767	0.0083|0.0083	L|L	0.52573|0.52573	1.65|1.65	0.09310|0.09310	N|N	1|1	.|D;D	.|0.89917	.|1.0;0.999	.|D;D	.|0.74023	.|0.982;0.971	T|T	0.04128|0.04128	-1.0975|-1.0975	5|10	.|0.41790	.|T	.|0.15	0.0286|0.0286	6.1512|6.1512	0.20313|0.20313	0.1027:0.3712:0.5262:0.0|0.1027:0.3712:0.5262:0.0	rs9859242;rs9859242|rs9859242;rs9859242	.|193;193	.|E9PFE5;Q96M34	.|.;CC030_HUMAN	H|H	157|193	.|ENSP00000295622:Q193H	.|ENSP00000295622:Q193H	D|Q	+|+	1|3	0|2	C3orf30|C3orf30	120348305|120348305	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.003000|0.003000	0.03518|0.03518	-0.341000|-0.341000	0.07811|0.07811	0.661000|0.661000	0.30985|0.30985	0.514000|0.514000	0.50259|0.50259	GAT|CAG	G|0.977;C|0.023	0.023	strong		0.512	C3orf30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354838.1	NM_152539	
ZNF200	7752	hgsc.bcm.edu	37	16	3282468	3282468	+	Missense_Mutation	SNP	G	G	A	rs9302870	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3282468G>A	ENST00000431561.3	-	4	1031	c.419C>T	c.(418-420)aCg>aTg	p.T140M	ZNF200_ENST00000396871.4_Missense_Mutation_p.T140M|ZNF200_ENST00000396870.4_Missense_Mutation_p.T140M|ZNF200_ENST00000575948.1_Missense_Mutation_p.T140M|ZNF200_ENST00000414144.2_Missense_Mutation_p.T140M|ZNF200_ENST00000396868.3_Missense_Mutation_p.T139M	NM_001145447.1|NM_003454.3	NP_001138919.1|NP_003445.2	P98182	ZN200_HUMAN	zinc finger protein 200	140			T -> M (in dbSNP:rs9302870).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(2)|kidney(2)|large_intestine(4)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	17						CTTCTCTGACGTGAGTTGTTG	0.463													G|||	346	0.0690895	0.2504	0.0173	5008	,	,		21841	0.0		0.003	False		,,,				2504	0.0				p.T140M		Atlas-SNP	.											.	ZNF200	36	.	0			c.C419T						PASS	.	G	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	817,3577	326.7+/-299.7	77,663,1457	237.0	211.0	220.0		419,419,419,419,416,419	2.7	0.6	16	dbSNP_119	220	10,8590	7.1+/-27.0	0,10,4290	yes	missense,missense,missense,missense,missense,missense	ZNF200	NM_001145446.1,NM_001145447.1,NM_001145448.1,NM_003454.3,NM_198087.2,NM_198088.2	81,81,81,81,81,81	77,673,5747	AA,AG,GG		0.1163,18.5935,6.3645	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	140/395,140/395,140/395,140/396,139/395,140/396	3282468	827,12167	2197	4300	6497	SO:0001583	missense	7752	exon4			TCTGACGTGAGTT	AF060866	CCDS10497.1, CCDS42112.1, CCDS45395.1	16p13.3	2013-01-08			ENSG00000010539	ENSG00000010539		"""Zinc fingers, C2H2-type"""	12993	protein-coding gene	gene with protein product		603231				9288094, 9787081	Standard	NM_003454		Approved		uc002cuk.2	P98182	OTTHUMG00000129317	ENST00000431561.3:c.419C>T	16.37:g.3282468G>A	ENSP00000395723:p.Thr140Met	98.0	0.0	0		128.0	68.0	0.53125	NM_003454	D3DUB7|D3DUB8|O15361|Q5XKM5|Q7Z5V1	Missense_Mutation	SNP	ENST00000431561.3	37	CCDS10497.1	139	0.06364468864468864	133	0.2703252032520325	6	0.016574585635359115	0	0.0	0	0.0	G	12.60	1.986342	0.35036	0.185935	0.001163	ENSG00000010539	ENST00000396870;ENST00000396868;ENST00000396871;ENST00000414144;ENST00000431561	T;T;T;T;T	0.06449	3.3;3.33;3.3;3.39;3.39	4.84	2.73	0.32206	.	0.395014	0.18653	N	0.134956	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	P;P;P	0.42039	0.658;0.658;0.769	B;B;B	0.43082	0.23;0.23;0.407	T	0.49273	-0.8957	9	0.62326	D	0.03	-13.3741	8.5959	0.33714	0.2043:0.0:0.7957:0.0	rs9302870;rs9302870	140;140;139	D3DUB7;P98182;P98182-2	.;ZN200_HUMAN;.	M	140;139;140;140;140	ENSP00000380079:T140M;ENSP00000380077:T139M;ENSP00000380080:T140M;ENSP00000405786:T140M;ENSP00000395723:T140M	ENSP00000380077:T139M	T	-	2	0	ZNF200	3222469	0.179000	0.23135	0.574000	0.28523	0.226000	0.24999	0.021000	0.13489	1.257000	0.44085	0.555000	0.69702	ACG	G|0.914;A|0.086	0.086	strong		0.463	ZNF200-005	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000437545.1		
CLTA	1211	hgsc.bcm.edu	37	9	36197564	36197564	+	Silent	SNP	A	A	G	rs138682143	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:36197564A>G	ENST00000242285.6	+	2	354	c.234A>G	c.(232-234)gtA>gtG	p.V78V	CLTA_ENST00000540080.1_Intron|CLTA_ENST00000466396.1_Intron|CLTA_ENST00000345519.5_Silent_p.V78V|CLTA_ENST00000396603.2_Silent_p.V78V|CLTA_ENST00000470744.1_Silent_p.V78V|CLTA_ENST00000433436.2_Silent_p.V78V|CLTA_ENST00000538225.1_Silent_p.V78V			P09496	CLCA_HUMAN	clathrin, light chain A	78					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|post-Golgi vesicle-mediated transport (GO:0006892)	clathrin coat (GO:0030118)|clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin complex (GO:0071439)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	clathrin heavy chain binding (GO:0032050)|peptide binding (GO:0042277)|structural molecule activity (GO:0005198)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(1)	6			STAD - Stomach adenocarcinoma(86;0.228)			TTGATGGAGTAATGAATGGTG	0.383																																					p.V78V		Atlas-SNP	.											.	CLTA	18	.	0			c.A234G						PASS	.	A	,,,,,	10,4396	16.8+/-37.8	0,10,2193	254.0	237.0	243.0		234,234,234,,234,234	0.6	1.0	9	dbSNP_134	243	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous,coding-synonymous	CLTA	NM_001076677.2,NM_001184760.1,NM_001184761.1,NM_001184762.1,NM_001833.3,NM_007096.3	,,,,,	0,10,6493	GG,GA,AA		0.0,0.227,0.0769	,,,,,	78/237,78/231,78/169,,78/219,78/249	36197564	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	1211	exon2			TGGAGTAATGAAT		CCDS6600.1, CCDS6601.1, CCDS43802.1, CCDS55306.1, CCDS55307.1	9p13.3	2010-05-11	2010-05-11		ENSG00000122705	ENSG00000122705			2090	protein-coding gene	gene with protein product		118960	"""clathrin, light polypeptide (Lca)"""			7713494	Standard	NM_007096		Approved	Lca	uc003zzc.3	P09496	OTTHUMG00000019896	ENST00000242285.6:c.234A>G	9.37:g.36197564A>G		178.0	0.0	0		189.0	109.0	0.57672	NM_001184761	A8K4W3|B4DIN1|F5H6N3|Q2XPN5|Q53XZ1	Silent	SNP	ENST00000242285.6	37	CCDS6601.1																																																																																			A|0.998;G|0.002	0.002	strong		0.383	CLTA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052405.1	NM_007096	
ZNF28	7576	hgsc.bcm.edu	37	19	53304448	53304448	+	Missense_Mutation	SNP	C	C	T	rs143289804	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53304448C>T	ENST00000457749.2	-	4	769	c.650G>A	c.(649-651)tGt>tAt	p.C217Y	ZNF28_ENST00000438150.2_Missense_Mutation_p.C164Y|ZNF28_ENST00000360272.4_Missense_Mutation_p.C164Y|ZNF28_ENST00000414252.2_Missense_Mutation_p.C164Y	NM_006969.3	NP_008900.3	P17035	ZNF28_HUMAN	zinc finger protein 28	217					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|liver(1)|lung(10)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(134;0.0386)|Lung(386;0.145)		ACTCTCAATACATTGGAAAGA	0.328													-|||	6	0.00119808	0.0045	0.0	5008	,	,		21480	0.0		0.0	False		,,,				2504	0.0				p.C217Y		Atlas-SNP	.											.	ZNF28	191	.	0			c.G650A						PASS	.	C	TYR/CYS	22,4384		0,22,2181	118.0	121.0	120.0		650	-3.5	0.0	19	dbSNP_134	120	0,8600		0,0,4300	yes	missense	ZNF28	NM_006969.3	194	0,22,6481	TT,TC,CC		0.0,0.4993,0.1692	benign	217/719	53304448	22,12984	2203	4300	6503	SO:0001583	missense	7576	exon4			TCAATACATTGGA	X52355	CCDS33093.1, CCDS33093.2	19q13.41	2013-01-08	2006-05-10		ENSG00000198538	ENSG00000198538		"""Zinc fingers, C2H2-type"", ""-"""	13073	protein-coding gene	gene with protein product			"""zinc finger protein 28 (KOX 24)"""				Standard	NR_036599		Approved	KOX24, DKFZp781D0275	uc002qad.3	P17035	OTTHUMG00000154564	ENST00000457749.2:c.650G>A	19.37:g.53304448C>T	ENSP00000397693:p.Cys217Tyr	109.0	0.0	0		98.0	46.0	0.469388	NM_006969	A8KAK9|B4E3G0|B9EIK7|Q5H9V1|Q5HYM9|Q6ZML9|Q6ZN56	Missense_Mutation	SNP	ENST00000457749.2	37	CCDS33093.2	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	-	3.805	-0.040964	0.07452	0.004993	0.0	ENSG00000198538	ENST00000438150;ENST00000457749;ENST00000360272;ENST00000414252;ENST00000391783	T;T;T;T;T	0.58358	0.34;0.34;0.34;0.34;0.34	1.74	-3.48	0.04739	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.49236	0.1545	H	0.94183	3.505	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.55885	-0.8070	9	0.66056	D	0.02	.	5.4015	0.16299	0.0:0.5647:0.168:0.2673	.	217	P17035	ZNF28_HUMAN	Y	164;217;164;164;164	ENSP00000412143:C164Y;ENSP00000397693:C217Y;ENSP00000353410:C164Y;ENSP00000444965:C164Y;ENSP00000375661:C164Y	ENSP00000353410:C164Y	C	-	2	0	ZNF28	57996260	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	1.019000	0.30014	-1.136000	0.02892	-1.497000	0.00963	TGT	C|0.998;T|0.002	0.002	strong		0.328	ZNF28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336038.2	NM_006969	
FAM114A1	92689	hgsc.bcm.edu	37	4	38907222	38907222	+	Silent	SNP	A	A	G	rs17501308	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:38907222A>G	ENST00000358869.2	+	5	692	c.516A>G	c.(514-516)ggA>ggG	p.G172G	FAM114A1_ENST00000515037.1_5'UTR	NM_138389.2	NP_612398.2	Q8IWE2	NXP20_HUMAN	family with sequence similarity 114, member A1	172						cytoplasm (GO:0005737)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	20						CTTCTGAAGGAGCCCAACCAA	0.433													G|||	37	0.00738818	0.0257	0.0014	5008	,	,		17480	0.0		0.0	False		,,,				2504	0.002				p.G172G		Atlas-SNP	.											.	FAM114A1	42	.	0			c.A516G						PASS	.	G		110,4296	816.0+/-416.2	1,108,2094	100.0	102.0	101.0		516	2.0	0.2	4	dbSNP_123	101	1,8599	819.2+/-406.8	0,1,4299	no	coding-synonymous	FAM114A1	NM_138389.2		1,109,6393	GG,GA,AA		0.0116,2.4966,0.8535		172/564	38907222	111,12895	2203	4300	6503	SO:0001819	synonymous_variant	92689	exon5			TGAAGGAGCCCAA		CCDS3447.1	4p14	2006-09-21			ENSG00000197712	ENSG00000197712			25087	protein-coding gene	gene with protein product							Standard	NM_138389		Approved	Noxp20	uc003gtn.3	Q8IWE2	OTTHUMG00000128583	ENST00000358869.2:c.516A>G	4.37:g.38907222A>G		206.0	1.0	0.00485437		171.0	96.0	0.561404	NM_138389	A8K9W6|Q6MZV4|Q9BVL6	Silent	SNP	ENST00000358869.2	37	CCDS3447.1																																																																																			A|0.990;G|0.010	0.010	strong		0.433	FAM114A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250436.1	NM_138389	
NDUFAF2	91942	hgsc.bcm.edu	37	5	60448734	60448734	+	Silent	SNP	T	T	C	rs77878573	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:60448734T>C	ENST00000296597.5	+	4	589	c.462T>C	c.(460-462)ttT>ttC	p.F154F	NDUFAF2_ENST00000512623.1_3'UTR|NDUFAF2_ENST00000511107.1_3'UTR	NM_174889.4	NP_777549.1	Q8N183	MIMIT_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 2	154					negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)	mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|ovary(1)	6		Lung NSC(810;3.36e-05)|Prostate(74;0.0225)|Ovarian(174;0.17)|Breast(144;0.237)				GTAAAACCTTTCAGCCAGGAT	0.443													T|||	89	0.0177716	0.0658	0.0029	5008	,	,		13669	0.0		0.0	False		,,,				2504	0.0				p.F154F		Atlas-SNP	.											.	NDUFAF2	10	.	0			c.T462C						PASS	.	T		242,4162	130.2+/-166.9	6,230,1966	33.0	28.0	30.0		462	-4.8	1.0	5	dbSNP_131	30	4,8592	3.0+/-9.4	0,4,4294	no	coding-synonymous	NDUFAF2	NM_174889.4		6,234,6260	CC,CT,TT		0.0465,5.495,1.8923		154/170	60448734	246,12754	2202	4298	6500	SO:0001819	synonymous_variant	91942	exon4			AACCTTTCAGCCA	AB183433	CCDS3979.1	5q12.1	2012-10-12	2012-05-08	2008-02-15	ENSG00000164182	ENSG00000164182		"""Mitochondrial respiratory chain complex assembly factors"""	28086	protein-coding gene	gene with protein product	"""Myc-induced mitochondrial protein"""	609653	"""NDUFA12-like"", ""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, assembly factor 2"""	NDUFA12L		15774466, 16200211, 17383918	Standard	NM_174889		Approved	B17.2L, MMTN, mimitin	uc003jsp.4	Q8N183	OTTHUMG00000131221	ENST00000296597.5:c.462T>C	5.37:g.60448734T>C		147.0	0.0	0		143.0	71.0	0.496504	NM_174889	A8K5I1	Silent	SNP	ENST00000296597.5	37	CCDS3979.1																																																																																			T|0.981;C|0.019	0.019	strong		0.443	NDUFAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253965.1	NM_174889	
AGPAT2	10555	hgsc.bcm.edu	37	9	139571560	139571560	+	Silent	SNP	G	G	A	rs73668354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139571560G>A	ENST00000371696.2	-	3	410	c.345C>T	c.(343-345)tgC>tgT	p.C115C	AGPAT2_ENST00000371694.3_Silent_p.C115C|AGPAT2_ENST00000538402.1_Silent_p.C115C	NM_006412.3	NP_006403.2	O15120	PLCB_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 2	115					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|epidermis development (GO:0008544)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			endometrium(1)|large_intestine(1)|lung(2)|prostate(2)	6	all_cancers(76;0.0893)|all_epithelial(76;0.231)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.87e-06)|Epithelial(140;0.000123)		CGATCTGCACGCAGCGCTCCG	0.637													G|||	72	0.014377	0.0461	0.013	5008	,	,		15024	0.0		0.002	False		,,,				2504	0.0				p.C115C		Atlas-SNP	.											AGPAT2,NS,carcinoma,0,1	AGPAT2	17	1	0			c.C345T						PASS	.	A	,	183,4223	115.0+/-153.0	2,179,2022	50.0	57.0	54.0		345,345	-3.2	0.7	9	dbSNP_130	54	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous,coding-synonymous	AGPAT2	NM_001012727.1,NM_006412.3	,	2,185,6316	AA,AG,GG		0.0698,4.1534,1.4532	,	115/247,115/279	139571560	189,12817	2203	4300	6503	SO:0001819	synonymous_variant	10555	exon3			CTGCACGCAGCGC	AF000237	CCDS7003.1, CCDS35181.1	9q34.3	2013-02-05	2013-02-05		ENSG00000169692	ENSG00000169692	2.3.1.51	"""1-acylglycerol-3-phosphate O-acyltransferases"""	325	protein-coding gene	gene with protein product	"""LPAAT-beta"", ""lysophosphatidic acid acyltransferase, beta"""	603100	"""Berardinelli-Seip congenital lipodystrophy"", ""1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)"""	BSCL		9242711, 9212163	Standard	NM_006412		Approved		uc004cii.1	O15120	OTTHUMG00000020936	ENST00000371696.2:c.345C>T	9.37:g.139571560G>A		120.0	0.0	0		116.0	85.0	0.732759	NM_001012727	O00516|O15106|Q5VUD3|Q5VUD4|Q9BSV7|Q9BWR7	Silent	SNP	ENST00000371696.2	37	CCDS7003.1																																																																																			G|0.982;A|0.018	0.018	strong		0.637	AGPAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055090.1	NM_006412	
PLEKHG2	64857	hgsc.bcm.edu	37	19	39908215	39908215	+	Silent	SNP	G	G	A	rs142309421		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39908215G>A	ENST00000409794.3	+	8	1615	c.765G>A	c.(763-765)gcG>gcA	p.A255A	PLEKHG2_ENST00000458508.2_Silent_p.A196A|PLEKHG2_ENST00000409797.2_Silent_p.A255A|PLEKHG2_ENST00000425673.1_Silent_p.A255A|PLEKHG2_ENST00000378550.1_Silent_p.A255A	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	255	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			AGCACTGGGCGGAGGGCCCAG	0.572																																					p.A255A		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.G765A						PASS	.	G		4,4402	8.1+/-20.4	0,4,2199	56.0	50.0	52.0		765	-9.4	0.0	19	dbSNP_134	52	0,8600		0,0,4300	no	coding-synonymous	PLEKHG2	NM_022835.2		0,4,6499	AA,AG,GG		0.0,0.0908,0.0308		255/1387	39908215	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	64857	exon8			CTGGGCGGAGGGC	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.765G>A	19.37:g.39908215G>A		93.0	0.0	0		98.0	55.0	0.561224	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Silent	SNP	ENST00000409794.3	37	CCDS33022.2	.	.	.	.	.	.	.	.	.	.	G	0.870	-0.732282	0.03135	9.08E-4	0.0	ENSG00000090924	ENST00000205135	.	.	.	4.68	-9.36	0.00629	.	.	.	.	.	T	0.33760	0.0874	.	.	.	0.46901	D	0.999249	.	.	.	.	.	.	T	0.52064	-0.8625	4	.	.	.	.	1.5973	0.02666	0.2022:0.2901:0.2917:0.216	.	.	.	.	Q	152	.	.	R	+	2	0	PLEKHG2	44600055	0.000000	0.05858	0.019000	0.16419	0.184000	0.23303	-5.033000	0.00158	-4.337000	0.00055	-2.075000	0.00382	CGG	G|1.000;A|0.000	0.000	weak		0.572	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835	
SPNS3	201305	hgsc.bcm.edu	37	17	4351534	4351534	+	Missense_Mutation	SNP	G	G	C	rs61740736	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4351534G>C	ENST00000355530.2	+	6	986	c.706G>C	c.(706-708)Ggg>Cgg	p.G236R	SPNS3_ENST00000333476.2_Missense_Mutation_p.G109R|SPNS3_ENST00000576069.1_3'UTR	NM_182538.4	NP_872344.3	Q6ZMD2	SPNS3_HUMAN	spinster homolog 3 (Drosophila)	236					lipid transport (GO:0006869)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				NS(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(6)|stomach(2)	28						CGAGACACAGGGGGAGGGGGC	0.637													G|||	77	0.0153754	0.0552	0.0058	5008	,	,		17510	0.0		0.0	False		,,,				2504	0.0				p.G236R		Atlas-SNP	.											.	SPNS3	52	.	0			c.G706C						PASS	.	G	ARG/GLY	160,4246	104.3+/-142.8	3,154,2046	33.0	31.0	32.0		706	1.9	0.2	17	dbSNP_129	32	0,8600		0,0,4300	yes	missense	SPNS3	NM_182538.4	125	3,154,6346	CC,CG,GG		0.0,3.6314,1.2302	benign	236/513	4351534	160,12846	2203	4300	6503	SO:0001583	missense	201305	exon6			ACACAGGGGGAGG		CCDS11045.1	17p13.2	2014-08-12			ENSG00000182557	ENSG00000182557			28433	protein-coding gene	gene with protein product		611701					Standard	NM_182538		Approved	MGC29671	uc002fxt.3	Q6ZMD2	OTTHUMG00000177737	ENST00000355530.2:c.706G>C	17.37:g.4351534G>C	ENSP00000347721:p.Gly236Arg	95.0	0.0	0		103.0	43.0	0.417476	NM_182538	Q8IZ31	Missense_Mutation	SNP	ENST00000355530.2	37	CCDS11045.1	28	0.01282051282051282	25	0.0508130081300813	3	0.008287292817679558	0	0.0	0	0.0	G	3.051	-0.195356	0.06259	0.036314	0.0	ENSG00000182557	ENST00000355530;ENST00000333476	T;T	0.58797	0.31;0.31	5.42	1.9	0.25705	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.357041	0.32343	N	0.006225	T	0.05960	0.0155	N	0.17312	0.475	0.09310	N	0.999999	B;B	0.15141	0.001;0.012	B;B	0.23852	0.002;0.049	T	0.04153	-1.0973	10	0.11485	T	0.65	-3.8842	3.2294	0.06744	0.3204:0.0:0.4977:0.1819	rs61740736	109;236	Q6ZMD2-2;Q6ZMD2	.;SPNS3_HUMAN	R	236;109	ENSP00000347721:G236R;ENSP00000333207:G109R	ENSP00000333207:G109R	G	+	1	0	SPNS3	4298283	0.202000	0.23423	0.212000	0.23672	0.006000	0.05464	0.900000	0.28431	0.794000	0.33899	-0.217000	0.12591	GGG	G|0.989;C|0.011	0.011	strong		0.637	SPNS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438793.1	NM_182538	
OGFOD3	79701	hgsc.bcm.edu	37	17	80364341	80364341	+	Silent	SNP	C	C	T	rs34315006	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:80364341C>T	ENST00000313056.5	-	5	592	c.441G>A	c.(439-441)ttG>ttA	p.L147L	OGFOD3_ENST00000329197.5_Silent_p.L147L	NM_024648.2|NM_175902.4	NP_078924.1|NP_787098.3	Q6PK18	OGFD3_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 3	147						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)										CCCCTGAGTGCAAGTCCAGAA	0.532													C|||	8	0.00159744	0.0	0.0072	5008	,	,		18395	0.0		0.002	False		,,,				2504	0.001				p.L147L		Atlas-SNP	.											.	.	.	.	0			c.G441A						PASS	.	C	,	2,4404	4.2+/-10.8	0,2,2201	107.0	93.0	98.0		441,441	3.7	1.0	17	dbSNP_126	98	34,8566	23.4+/-69.3	0,34,4266	no	coding-synonymous,coding-synonymous	C17orf101	NM_024648.2,NM_175902.4	,	0,36,6467	TT,TC,CC		0.3953,0.0454,0.2768	,	147/320,147/332	80364341	36,12970	2203	4300	6503	SO:0001819	synonymous_variant	79701	exon5			TGAGTGCAAGTCC	BC023602	CCDS11811.1, CCDS11812.1	17q25.3	2012-10-23	2012-10-23	2012-10-23	ENSG00000181396	ENSG00000181396			26174	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 101"""	C17orf101		12477932	Standard	NM_175902		Approved	FLJ22222	uc002keu.2	Q6PK18		ENST00000313056.5:c.441G>A	17.37:g.80364341C>T		41.0	0.0	0		58.0	25.0	0.431034	NM_175902	C9JDC8|Q8IZ37|Q9H6J2	Silent	SNP	ENST00000313056.5	37	CCDS11811.1																																																																																			C|0.997;T|0.003	0.003	strong		0.532	OGFOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442895.1	NM_175902	
ZNF100	163227	hgsc.bcm.edu	37	19	21909548	21909548	+	Silent	SNP	A	A	G	rs371600049		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:21909548A>G	ENST00000358296.6	-	5	1764	c.1566T>C	c.(1564-1566)ttT>ttC	p.F522F	ZNF100_ENST00000305570.6_Silent_p.F458F	NM_173531.3	NP_775802.2	Q8IYN0	ZN100_HUMAN	zinc finger protein 100	522					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						GGGACTGGTTAAAGTCTTTAC	0.368													N|||	1	0.000199681	0.0008	0.0	5008	,	,		19310	0.0		0.0	False		,,,				2504	0.0				p.F522F		Atlas-SNP	.											.	ZNF100	62	.	0			c.T1566C						PASS	.	A		3,4315		0,3,2156	71.0	80.0	77.0		1566	-0.4	0.3	19		77	0,8552		0,0,4276	no	coding-synonymous	ZNF100	NM_173531.3		0,3,6432	GG,GA,AA		0.0,0.0695,0.0233		522/543	21909548	3,12867	2159	4276	6435	SO:0001819	synonymous_variant	163227	exon5			CTGGTTAAAGTCT	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.1566T>C	19.37:g.21909548A>G		43.0	0.0	0		36.0	27.0	0.75	NM_173531	Q7M4M0	Silent	SNP	ENST00000358296.6	37	CCDS42538.1																																																																																			.	.	weak		0.368	ZNF100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464087.1	NM_173531	
ADRB1	153	hgsc.bcm.edu	37	10	115804206	115804206	+	Silent	SNP	G	G	T	rs7921133	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:115804206G>T	ENST00000369295.2	+	1	401	c.315G>T	c.(313-315)ctG>ctT	p.L105L		NM_000684.2	NP_000675.1	P08588	ADRB1_HUMAN	adrenoceptor beta 1	105					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|aging (GO:0007568)|apoptotic process (GO:0006915)|brown fat cell differentiation (GO:0050873)|diet induced thermogenesis (GO:0002024)|fear response (GO:0042596)|glycogen catabolic process (GO:0005980)|heat generation (GO:0031649)|lipid homeostasis (GO:0055088)|memory (GO:0007613)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of smooth muscle contraction (GO:0045986)|negative regulation of urine volume (GO:0035811)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cation channel activity (GO:2001259)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of heart rate by epinephrine-norepinephrine (GO:0001996)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of renin secretion into blood stream (GO:1900135)|positive regulation of saliva secretion (GO:0046878)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of the force of heart contraction by norepinephrine (GO:0003061)|protein localization to organelle (GO:0033365)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|response to cold (GO:0009409)|Rho protein signal transduction (GO:0007266)|sensory perception of pain (GO:0019233)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)|wound healing (GO:0042060)	early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|beta-adrenergic receptor activity (GO:0004939)|beta1-adrenergic receptor activity (GO:0004940)|dopamine binding (GO:0035240)|drug binding (GO:0008144)|epinephrine binding (GO:0051379)|norepinephrine binding (GO:0051380)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|receptor signaling protein activity (GO:0005057)			large_intestine(4)|lung(1)|upper_aerodigestive_tract(1)	6		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0124)|all cancers(201;0.0298)	Acebutolol(DB01193)|Alprenolol(DB00866)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Asenapine(DB06216)|Atenolol(DB00335)|Betaxolol(DB00195)|Bethanidine(DB00217)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bopindolol(DB08807)|Bupranolol(DB08808)|Cabergoline(DB00248)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Dobutamine(DB00841)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Esmolol(DB00187)|Fenoterol(DB01288)|Isoetarine(DB00221)|Isoprenaline(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Loxapine(DB00408)|Mephentermine(DB01365)|Metipranolol(DB01214)|Metoprolol(DB00264)|Mirtazapine(DB00370)|Nadolol(DB01203)|Nebivolol(DB04861)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Phenylpropanolamine(DB00397)|Pindolol(DB00960)|Pirbuterol(DB01291)|Practolol(DB01297)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Salbutamol(DB01001)|Sotalol(DB00489)|Timolol(DB00373)|Trimipramine(DB00726)	GCGCCGACCTGGTCATGGGGC	0.662													G|||	144	0.028754	0.1044	0.0086	5008	,	,		15320	0.0		0.0	False		,,,				2504	0.0				p.L105L		Atlas-SNP	.											.	ADRB1	16	.	0			c.G315T						PASS	.	G		447,3959	205.8+/-227.6	24,399,1780	57.0	67.0	63.0		315	4.1	1.0	10	dbSNP_116	63	8,8590	6.4+/-24.3	0,8,4291	no	coding-synonymous	ADRB1	NM_000684.2		24,407,6071	TT,TG,GG		0.093,10.1453,3.4989		105/478	115804206	455,12549	2203	4299	6502	SO:0001819	synonymous_variant	153	exon1			CGACCTGGTCATG	J03019	CCDS7586.1	10q25.3	2012-08-08	2012-05-09		ENSG00000043591	ENSG00000043591		"""GPCR / Class A : Adrenoceptors : beta"""	285	protein-coding gene	gene with protein product		109630	"""adrenergic, beta-1-, receptor"""	ADRB1R			Standard	NM_000684		Approved		uc001lba.3	P08588	OTTHUMG00000019079	ENST00000369295.2:c.315G>T	10.37:g.115804206G>T		118.0	0.0	0		116.0	52.0	0.448276	NM_000684	B0LPE2|Q5T5Y4|Q9UKG7|Q9UKG8	Silent	SNP	ENST00000369295.2	37	CCDS7586.1																																																																																			G|0.963;T|0.037	0.037	strong		0.662	ADRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050448.1		
ADCK4	79934	hgsc.bcm.edu	37	19	41198210	41198210	+	Silent	SNP	A	A	G	rs17851001	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41198210A>G	ENST00000324464.3	-	15	1666	c.1365T>C	c.(1363-1365)taT>taC	p.Y455Y	ADCK4_ENST00000243583.6_Silent_p.Y414Y|NUMBL_ENST00000252891.4_5'Flank|NUMBL_ENST00000540131.1_5'Flank|NUMBL_ENST00000598779.1_5'Flank|NUMBL_ENST00000599594.1_5'Flank|ADCK4_ENST00000450541.1_Silent_p.Y414Y	NM_024876.3	NP_079152.3	Q96D53	ADCK4_HUMAN	aarF domain containing kinase 4	455						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(3)|large_intestine(3)|lung(6)|stomach(2)|urinary_tract(1)	17			Lung(22;9.49e-05)|LUSC - Lung squamous cell carcinoma(20;0.000219)			ACCCAAAGTCATAAGGGCCCT	0.672													A|||	68	0.0135783	0.0484	0.0058	5008	,	,		15061	0.0		0.0	False		,,,				2504	0.0				p.Y455Y		Atlas-SNP	.											.	ADCK4	92	.	0			c.T1365C						PASS	.	A	,	195,4211	116.3+/-154.2	5,185,2013	27.0	27.0	27.0		1242,1365	-10.1	0.4	19	dbSNP_123	27	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	ADCK4	NM_001142555.2,NM_024876.3	,	5,185,6312	GG,GA,AA		0.0,4.4258,1.4995	,	414/504,455/545	41198210	195,12809	2203	4299	6502	SO:0001819	synonymous_variant	79934	exon15			AAAGTCATAAGGG	AK022291	CCDS12562.1, CCDS46081.1	19q13.2	2008-02-05				ENSG00000123815			19041	protein-coding gene	gene with protein product		615567					Standard	NM_024876		Approved	FLJ12229, COQ8	uc002oor.2	Q96D53		ENST00000324464.3:c.1365T>C	19.37:g.41198210A>G		86.0	0.0	0		94.0	38.0	0.404255	NM_024876	Q8TAJ1|Q9HA52	Silent	SNP	ENST00000324464.3	37	CCDS12562.1																																																																																			A|0.986;G|0.014	0.014	strong		0.672	ADCK4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462731.1	NM_024876	
MAP3K9	4293	hgsc.bcm.edu	37	14	71202692	71202692	+	Silent	SNP	T	T	C	rs78155813	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:71202692T>C	ENST00000554752.2	-	9	1898	c.1899A>G	c.(1897-1899)ccA>ccG	p.P633P	MAP3K9_ENST00000553414.1_Intron|MAP3K9_ENST00000554146.1_Intron|MAP3K9_ENST00000381250.4_Intron|MAP3K9_ENST00000555993.2_Silent_p.P633P	NM_001284230.1	NP_001271159.1	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase 9	633					activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		ATP binding (GO:0005524)|JUN kinase kinase kinase activity (GO:0004706)|MAP kinase kinase activity (GO:0004708)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(1)|skin(3)|stomach(2)	46				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		AGTGGAAATGTGGAGATTCTG	0.453													T|||	59	0.0117812	0.0408	0.0072	5008	,	,		21579	0.0		0.0	False		,,,				2504	0.0				p.P633P	GBM(114;411 1587 13539 28235 50070)	Atlas-SNP	.											.	MAP3K9	109	.	0			c.A1899G						PASS	.	T		85,4321	72.0+/-110.0	1,83,2119	173.0	148.0	156.0		1899	3.2	1.0	14	dbSNP_132	156	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MAP3K9	NM_033141.2		1,84,6418	CC,CT,TT		0.0116,1.9292,0.6612		633/1119	71202692	86,12920	2203	4300	6503	SO:0001819	synonymous_variant	4293	exon9			GAAATGTGGAGAT	AF251442	CCDS32112.1, CCDS61485.1, CCDS61488.1, CCDS73650.1	14q24.2	2012-10-02			ENSG00000006432	ENSG00000006432		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6861	protein-coding gene	gene with protein product		600136		MLK1			Standard	NM_001284231		Approved	PRKE1, MEKK9	uc001xml.3	P80192	OTTHUMG00000171249	ENST00000554752.2:c.1899A>G	14.37:g.71202692T>C		85.0	0.0	0		81.0	44.0	0.54321	NM_033141	A3KN85|Q0D2G7|Q6EH31|Q9H2N5	Silent	SNP	ENST00000554752.2	37																																																																																				T|0.989;C|0.011	0.011	strong		0.453	MAP3K9-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412550.2		
RLBP1	6017	hgsc.bcm.edu	37	15	89762198	89762198	+	Missense_Mutation	SNP	T	T	G	rs146844731	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:89762198T>G	ENST00000268125.5	-	3	448	c.9A>C	c.(7-9)gaA>gaC	p.E3D		NM_000326.4	NP_000317.1	P12271	RLBP1_HUMAN	retinaldehyde binding protein 1	3					phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	cell body (GO:0044297)|cytosol (GO:0005829)	11-cis retinal binding (GO:0005502)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(1)|prostate(1)|skin(1)	18	Lung NSC(78;0.0472)|all_lung(78;0.089)				Vitamin A(DB00162)	TACTTACCCCTTCTGACATGT	0.542													T|||	10	0.00199681	0.0076	0.0	5008	,	,		19219	0.0		0.0	False		,,,				2504	0.0				p.E3D		Atlas-SNP	.											RLBP1,NS,carcinoma,-2,1	RLBP1	34	1	0			c.A9C						PASS	.	T	ASP/GLU	26,4374	32.6+/-62.9	0,26,2174	146.0	125.0	132.0		9	-3.2	1.0	15	dbSNP_134	132	0,8598		0,0,4299	yes	missense	RLBP1	NM_000326.4	45	0,26,6473	GG,GT,TT		0.0,0.5909,0.2	benign	3/318	89762198	26,12972	2200	4299	6499	SO:0001583	missense	6017	exon3			TACCCCTTCTGAC	BC004199	CCDS32324.1	15q26.1	2007-07-16	2001-11-28			ENSG00000140522			10024	protein-coding gene	gene with protein product		180090	"""retinaldehyde-binding protein 1"""			1733864, 9326942	Standard	NM_000326		Approved	CRALBP	uc002bnl.3	P12271		ENST00000268125.5:c.9A>C	15.37:g.89762198T>G	ENSP00000268125:p.Glu3Asp	76.0	0.0	0		63.0	38.0	0.603175	NM_000326	B2R667	Missense_Mutation	SNP	ENST00000268125.5	37	CCDS32324.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	T	9.490	1.100449	0.20552	0.005909	0.0	ENSG00000140522	ENST00000268125	T	0.79141	-1.24	5.17	-3.21	0.05140	.	0.467603	0.23298	N	0.049703	T	0.42359	0.1199	N	0.14661	0.345	0.26969	N	0.965636	B	0.02656	0.0	B	0.01281	0.0	T	0.30001	-0.9993	10	0.16420	T	0.52	-10.8678	5.1979	0.15249	0.0:0.2661:0.2778:0.4561	.	3	P12271	RLBP1_HUMAN	D	3	ENSP00000268125:E3D	ENSP00000268125:E3D	E	-	3	2	RLBP1	87563202	0.925000	0.31364	0.968000	0.41197	0.138000	0.21146	-0.148000	0.10219	-0.417000	0.07461	-1.276000	0.01395	GAA	T|0.998;G|0.002	0.002	strong		0.542	RLBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421135.1	NM_000326	
GPRASP2	114928	hgsc.bcm.edu	37	X	101970877	101970877	+	Silent	SNP	T	T	C	rs113906002	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:101970877T>C	ENST00000535209.1	+	4	1911	c.1080T>C	c.(1078-1080)acT>acC	p.T360T	GPRASP2_ENST00000332262.5_Silent_p.T360T|GPRASP2_ENST00000543253.1_Silent_p.T360T			Q96D09	GASP2_HUMAN	G protein-coupled receptor associated sorting protein 2	360						cytoplasm (GO:0005737)	beta-amyloid binding (GO:0001540)			breast(3)|endometrium(5)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	30						ATCCTAATACTGCCTTGAAAC	0.463													.|||	50	0.013245	0.0371	0.0014	3775	,	,		14732	0.0		0.0	False		,,,				2504	0.0				p.T360T		Atlas-SNP	.											.	GPRASP2	89	.	0			c.T1080C						PASS	.	C	,,,,,	148,3687		2,116,28,1514,543	90.0	84.0	86.0		1080,1080,1080,1080,1080,1080	0.1	0.0	X	dbSNP_132	86	0,6728		0,0,0,2428,1872	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GPRASP2,ARMCX5-GPRASP2	NM_001004051.3,NM_001184874.2,NM_001184875.2,NM_001184876.2,NM_001199818.1,NM_138437.5	,,,,,	2,116,28,3942,2415	CC,CT,C,TT,T		0.0,3.8592,1.4011	,,,,,	360/839,360/839,360/839,360/839,360/839,360/839	101970877	148,10415	2203	4300	6503	SO:0001819	synonymous_variant	114928	exon4			TAATACTGCCTTG	AK094646	CCDS14501.1	Xq22.1	2014-03-21			ENSG00000158301	ENSG00000158301		"""Armadillo repeat containing"""	25169	protein-coding gene	gene with protein product						15086532, 16221301	Standard	NM_138437		Approved	GASP2, FLJ37327		Q96D09	OTTHUMG00000022059	ENST00000535209.1:c.1080T>C	X.37:g.101970877T>C		104.0	0.0	0		113.0	38.0	0.336283	NM_138437	D3DXA0|Q8NAB4	Silent	SNP	ENST00000535209.1	37	CCDS14501.1																																																																																			T|0.986;C|0.014	0.014	strong		0.463	GPRASP2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057626.2	NM_138437	
DENND2A	27147	hgsc.bcm.edu	37	7	140221878	140221878	+	Silent	SNP	G	G	A	rs61737088	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140221878G>A	ENST00000275884.6	-	17	3105	c.2688C>T	c.(2686-2688)aaC>aaT	p.N896N	DENND2A_ENST00000537639.1_Silent_p.N896N|DENND2A_ENST00000496613.1_Silent_p.N896N			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	896	dDENN. {ECO:0000255|PROSITE- ProRule:PRU00306}.				positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(22)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49	Melanoma(164;0.00956)					ACACCACCTCGTTCAAGGGGC	0.582													G|||	62	0.0123802	0.0446	0.0029	5008	,	,		15621	0.0		0.001	False		,,,				2504	0.0				p.N896N		Atlas-SNP	.											.	DENND2A	132	.	0			c.C2688T						PASS	.	G		141,3909		3,135,1887	49.0	53.0	52.0		2688	-3.1	0.7	7	dbSNP_129	52	3,8365		0,3,4181	no	coding-synonymous	DENND2A	NM_015689.3		3,138,6068	AA,AG,GG		0.0359,3.4815,1.1596		896/1010	140221878	144,12274	2025	4184	6209	SO:0001819	synonymous_variant	27147	exon16			CACCTCGTTCAAG	AB033103	CCDS43659.1	7q34	2012-10-03	2005-08-17	2005-08-17	ENSG00000146966	ENSG00000146966		"""DENN/MADD domain containing"""	22212	protein-coding gene	gene with protein product			"""KIAA1277"""	KIAA1277			Standard	NM_015689		Approved	FAM31D	uc010lnj.3	Q9ULE3	OTTHUMG00000157411	ENST00000275884.6:c.2688C>T	7.37:g.140221878G>A		42.0	0.0	0		57.0	29.0	0.508772	NM_015689	C9JUI3|Q1RMD5|Q86XY0	Silent	SNP	ENST00000275884.6	37	CCDS43659.1																																																																																			G|0.993;A|0.007	0.007	strong		0.582	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	NM_015689	
MCMDC2	157777	hgsc.bcm.edu	37	8	67809160	67809160	+	Missense_Mutation	SNP	C	C	G	rs35595089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:67809160C>G	ENST00000422365.2	+	12	1763	c.1592C>G	c.(1591-1593)gCt>gGt	p.A531G	MCMDC2_ENST00000313616.5_Missense_Mutation_p.A531G|MCMDC2_ENST00000396592.3_Missense_Mutation_p.A531G|MCMDC2_ENST00000541540.1_Missense_Mutation_p.A468G	NM_173518.4	NP_775789.3	Q4G0Z9	MCMD2_HUMAN	minichromosome maintenance domain containing 2	531					DNA replication (GO:0006260)		ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(2)|kidney(2)|lung(5)	9						TTTTATGCGGCTTCTAGACAG	0.408													C|||	30	0.00599042	0.0227	0.0	5008	,	,		13579	0.0		0.0	False		,,,				2504	0.0				p.A531G		Atlas-SNP	.											.	MCMDC2	84	.	0			c.C1592G						PASS	.	C	GLY/ALA,GLY/ALA,GLY/ALA	93,4313	76.2+/-114.5	2,89,2112	100.0	100.0	100.0		1592,1592,1592	4.6	1.0	8	dbSNP_126	100	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	C8orf45	NM_001136160.1,NM_001136161.1,NM_173518.4	60,60,60	2,90,6411	GG,GC,CC		0.0116,2.1108,0.7227	possibly-damaging,possibly-damaging,possibly-damaging	531/633,531/591,531/682	67809160	94,12912	2203	4300	6503	SO:0001583	missense	157777	exon12			ATGCGGCTTCTAG	BC034576	CCDS6197.2, CCDS47868.1, CCDS47869.1	8q13.1	2012-04-13	2012-04-13	2012-04-13	ENSG00000178460	ENSG00000178460			26368	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 45"""	C8orf45			Standard	NM_173518		Approved	FLJ25692	uc003xwz.4	Q4G0Z9	OTTHUMG00000157068	ENST00000422365.2:c.1592C>G	8.37:g.67809160C>G	ENSP00000413632:p.Ala531Gly	146.0	0.0	0		119.0	59.0	0.495798	NM_173518	B4DYZ3|B4DZM4|B4E293|Q6P533|Q7Z3P4	Missense_Mutation	SNP	ENST00000422365.2	37	CCDS6197.2	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	10.04	1.240474	0.22711	0.021108	1.16E-4	ENSG00000178460	ENST00000396592;ENST00000422365;ENST00000313616;ENST00000541540	T;T;T;T	0.30182	1.54;1.54;1.54;1.54	5.51	4.57	0.56435	.	0.315894	0.33075	N	0.005315	T	0.12944	0.0314	L	0.40543	1.245	0.26863	N	0.967917	P;P;P	0.36354	0.493;0.549;0.549	B;B;B	0.41036	0.234;0.346;0.272	T	0.07233	-1.0783	10	0.22706	T	0.39	-9.108	6.8758	0.24147	0.1753:0.7144:0.0:0.1103	rs35595089;rs57404017	468;531;531	Q4G0Z9-4;Q4G0Z9;B4DXX4	.;CH045_HUMAN;.	G	531;531;531;468	ENSP00000379837:A531G;ENSP00000413632:A531G;ENSP00000317234:A531G;ENSP00000445629:A468G	ENSP00000317234:A531G	A	+	2	0	C8orf45	67971714	0.967000	0.33354	0.996000	0.52242	0.225000	0.24961	2.515000	0.45512	2.763000	0.94921	0.650000	0.86243	GCT	C|0.993;G|0.007	0.007	strong		0.408	MCMDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347350.1	NM_173518	
NWD1	284434	hgsc.bcm.edu	37	19	16918459	16918459	+	Missense_Mutation	SNP	C	C	T	rs78570914	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16918459C>T	ENST00000552788.1	+	16	3799	c.3799C>T	c.(3799-3801)Cgc>Tgc	p.R1267C	NWD1_ENST00000379808.3_Missense_Mutation_p.R1267C|NWD1_ENST00000523826.1_Missense_Mutation_p.R1061C|NWD1_ENST00000339803.6_Missense_Mutation_p.R1132C|NWD1_ENST00000524140.2_Missense_Mutation_p.R1267C|NWD1_ENST00000549814.1_Missense_Mutation_p.R1225C			Q149M9	NWD1_HUMAN	NACHT and WD repeat domain containing 1	1267							ATP binding (GO:0005524)			NS(3)|breast(2)|cervix(1)|endometrium(8)|large_intestine(17)|lung(18)|ovary(2)|pancreas(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						TGCTGAGCAGCGCAAGCTCCT	0.562													C|||	17	0.00339457	0.0121	0.0014	5008	,	,		18437	0.0		0.0	False		,,,				2504	0.0				p.R1267C		Atlas-SNP	.											NWD1_ENST00000524140,NS,carcinoma,-1,3	NWD1	303	3	0			c.C3799T						PASS	.	C	CYS/ARG	34,4372	40.0+/-72.8	1,32,2170	91.0	95.0	94.0		3799	-1.5	0.0	19	dbSNP_131	94	0,8600		0,0,4300	yes	missense	NWD1	NM_001007525.3	180	1,32,6470	TT,TC,CC		0.0,0.7717,0.2614	benign	1267/1433	16918459	34,12972	2203	4300	6503	SO:0001583	missense	284434	exon18			GAGCAGCGCAAGC	BX648940	CCDS32945.1, CCDS32945.2	19p13.11	2013-01-09				ENSG00000188039		"""WD repeat domain containing"""	27619	protein-coding gene	gene with protein product							Standard	NM_001007525		Approved		uc002neu.4	Q149M9		ENST00000552788.1:c.3799C>T	19.37:g.16918459C>T	ENSP00000447224:p.Arg1267Cys	125.0	0.0	0		123.0	54.0	0.439024	NM_001007525	C9J021|Q68CT3	Missense_Mutation	SNP	ENST00000552788.1	37		7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	C	7.773	0.707922	0.15239	0.007717	0.0	ENSG00000188039	ENST00000420818;ENST00000524140;ENST00000549814;ENST00000379808;ENST00000523826;ENST00000552788;ENST00000339803	T;T;T;T;T;T	0.70749	-0.19;-0.51;-0.19;2.21;1.55;2.21	5.27	-1.54	0.08584	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	1.389700	0.04604	N	0.399111	T	0.39436	0.1078	N	0.14661	0.345	0.09310	N	1	P;P;P	0.38922	0.519;0.651;0.519	B;B;B	0.34722	0.057;0.188;0.057	T	0.42716	-0.9435	10	0.72032	D	0.01	-0.223	1.2256	0.01932	0.3166:0.3553:0.1858:0.1423	.	1267;1267;1132	Q149M9;Q149M9-3;C9J2Y8	NWD1_HUMAN;.;.	C	1132;1267;1225;1267;1061;1267;1132	ENSP00000428579:R1267C;ENSP00000447548:R1225C;ENSP00000369136:R1267C;ENSP00000428955:R1061C;ENSP00000447224:R1267C;ENSP00000340159:R1132C	ENSP00000340159:R1132C	R	+	1	0	NWD1	16779459	0.911000	0.30947	0.011000	0.14972	0.055000	0.15305	1.787000	0.38704	-0.087000	0.12528	-0.140000	0.14226	CGC	C|0.997;T|0.003	0.003	strong		0.562	NWD1-005	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000403569.1	NM_001007525	
EPHB6	2051	hgsc.bcm.edu	37	7	142562011	142562011	+	Silent	SNP	C	C	T	rs8177141	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:142562011C>T	ENST00000392957.2	+	7	1240	c.453C>T	c.(451-453)cgC>cgT	p.R151R	EPHB6_ENST00000442129.1_Silent_p.R151R|EPHB6_ENST00000411471.2_Intron	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	151	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					ACCTCAAACGCTGGACCAAGG	0.627													C|||	122	0.024361	0.0847	0.0144	5008	,	,		17524	0.0		0.0	False		,,,				2504	0.0				p.R151R		Atlas-SNP	.											EPHB6,right_lower_lobe,carcinoma,-2,1	EPHB6	168	1	0			c.C453T						PASS	.	C		332,4074	168.3+/-199.2	19,294,1890	58.0	62.0	61.0		453	4.7	1.0	7	dbSNP_117	61	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	EPHB6	NM_004445.3		19,297,6187	TT,TC,CC		0.0349,7.5352,2.5757		151/1022	142562011	335,12671	2203	4300	6503	SO:0001819	synonymous_variant	2051	exon7			CAAACGCTGGACC	D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3396	protein-coding gene	gene with protein product		602757	"""EphB6"""				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.453C>T	7.37:g.142562011C>T		99.0	0.0	0		106.0	60.0	0.566038	NM_004445	A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Silent	SNP	ENST00000392957.2	37	CCDS5873.2																																																																																			C|0.970;T|0.030	0.030	strong		0.627	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1		
LONRF2	164832	hgsc.bcm.edu	37	2	100911980	100911980	+	Silent	SNP	C	C	T	rs116227203	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:100911980C>T	ENST00000393437.3	-	8	2151	c.1512G>A	c.(1510-1512)ctG>ctA	p.L504L	LONRF2_ENST00000409647.1_Silent_p.L261L	NM_198461.3	NP_940863.3	Q1L5Z9	LONF2_HUMAN	LON peptidase N-terminal domain and ring finger 2	504							ATP-dependent peptidase activity (GO:0004176)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	34						ATTCTTCGGCCAGAACAGTTA	0.343													C|||	73	0.0145767	0.0522	0.0043	5008	,	,		19323	0.0		0.001	False		,,,				2504	0.0				p.L504L		Atlas-SNP	.											.	LONRF2	62	.	0			c.G1512A						PASS	.	C		200,4206	124.5+/-161.8	1,198,2004	95.0	93.0	94.0		1512	3.3	0.2	2	dbSNP_132	94	0,8600		0,0,4300	no	coding-synonymous	LONRF2	NM_198461.3		1,198,6304	TT,TC,CC		0.0,4.5393,1.5378		504/755	100911980	200,12806	2203	4300	6503	SO:0001819	synonymous_variant	164832	exon8			TTCGGCCAGAACA	AK127206	CCDS2046.2	2q11.2	2013-01-09			ENSG00000170500	ENSG00000170500		"""RING-type (C3HC4) zinc fingers"""	24788	protein-coding gene	gene with protein product							Standard	NM_198461		Approved	FLJ45273, RNF192	uc002tal.4	Q1L5Z9	OTTHUMG00000130668	ENST00000393437.3:c.1512G>A	2.37:g.100911980C>T		80.0	0.0	0		90.0	41.0	0.455556	NM_198461	B9A006|Q6ZSR4	Silent	SNP	ENST00000393437.3	37	CCDS2046.2																																																																																			C|0.986;T|0.014	0.014	strong		0.343	LONRF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253161.2	NM_198461	
C9orf171	389799	hgsc.bcm.edu	37	9	135418389	135418389	+	Silent	SNP	G	G	A	rs61308567	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:135418389G>A	ENST00000343036.2	+	6	843	c.795G>A	c.(793-795)ccG>ccA	p.P265P	C9orf171_ENST00000393216.2_Silent_p.P229P	NM_207417.1	NP_997300.1	Q6ZQR2	CI171_HUMAN	chromosome 9 open reading frame 171	265										large_intestine(7)|lung(9)|ovary(4)|prostate(3)	23						AGTACAAGCCGCCCGTGAAGC	0.602													G|||	245	0.0489217	0.1762	0.0173	5008	,	,		16308	0.0		0.0	False		,,,				2504	0.0				p.P265P		Atlas-SNP	.											.	C9orf171	53	.	0			c.G795A						PASS	.	G		590,3816	262.2+/-264.8	37,516,1650	156.0	136.0	143.0		795	-5.2	0.9	9	dbSNP_129	143	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous	C9orf171	NM_207417.1		37,521,5945	AA,AG,GG		0.0581,13.3908,4.5748		265/321	135418389	595,12411	2203	4300	6503	SO:0001819	synonymous_variant	389799	exon6			CAAGCCGCCCGTG	AK128819	CCDS6949.1, CCDS65167.1	9q34.13	2012-04-03			ENSG00000188523	ENSG00000188523			33776	protein-coding gene	gene with protein product							Standard	NM_207417		Approved	FLJ46082	uc004cbn.3	Q6ZQR2	OTTHUMG00000131684	ENST00000343036.2:c.795G>A	9.37:g.135418389G>A		88.0	0.0	0		68.0	68.0	1	NM_207417	Q147X1	Silent	SNP	ENST00000343036.2	37	CCDS6949.1																																																																																			G|0.948;A|0.052	0.052	strong		0.602	C9orf171-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254589.1	NM_207417	
SLC4A1AP	22950	hgsc.bcm.edu	37	2	27886820	27886820	+	Silent	SNP	G	G	T	rs58106741	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27886820G>T	ENST00000326019.6	+	1	483	c.201G>T	c.(199-201)tcG>tcT	p.S67S	SUPT7L_ENST00000404798.2_5'Flank|SUPT7L_ENST00000464789.2_5'Flank|SUPT7L_ENST00000405491.1_5'Flank|SUPT7L_ENST00000406540.1_5'Flank|SUPT7L_ENST00000337768.5_5'Flank	NM_018158.2	NP_060628.2	Q9BWU0	NADAP_HUMAN	solute carrier family 4 (anion exchanger), member 1, adaptor protein	67						cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(9)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(172;0.155)					CCCTGGCGTCGCAAGACCTCA	0.592													G|||	334	0.0666933	0.2315	0.0187	5008	,	,		16985	0.0		0.0129	False		,,,				2504	0.002				p.S67S		Atlas-SNP	.											.	SLC4A1AP	63	.	0			c.G201T						PASS	.	G		771,3635	315.5+/-294.2	77,617,1509	77.0	76.0	76.0		201	-2.8	0.0	2	dbSNP_129	76	68,8532	40.3+/-97.0	0,68,4232	no	coding-synonymous	SLC4A1AP	NM_018158.2		77,685,5741	TT,TG,GG		0.7907,17.4989,6.4509		67/797	27886820	839,12167	2203	4300	6503	SO:0001819	synonymous_variant	22950	exon1			GGCGTCGCAAGAC		CCDS33166.1	2p23.3	2010-03-11	2001-11-28		ENSG00000163798	ENSG00000163798			13813	protein-coding gene	gene with protein product	"""lung cancer oncogene 3"""	602655	"""solute carrier family 4 (anion exchanger), member 1, adapter protein"""			9422766	Standard	NM_018158		Approved	kanadaptin, HLC3	uc002rlk.4	Q9BWU0	OTTHUMG00000151944	ENST00000326019.6:c.201G>T	2.37:g.27886820G>T		66.0	0.0	0		57.0	26.0	0.45614	NM_018158	A6NJ39|Q4KMT1|Q4KMX0|Q7Z5Q9|Q9NVN2	Silent	SNP	ENST00000326019.6	37	CCDS33166.1																																																																																			G|0.940;T|0.060	0.060	strong		0.592	SLC4A1AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324550.1	NM_018158	
AGO3	192669	hgsc.bcm.edu	37	1	36521340	36521340	+	Silent	SNP	C	C	T	rs61743816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:36521340C>T	ENST00000373191.4	+	19	2926	c.2577C>T	c.(2575-2577)ttC>ttT	p.F859F	AGO3_ENST00000246314.6_Silent_p.F625F	NM_024852.3	NP_079128.2	Q9H9G7	AGO3_HUMAN	argonaute RISC catalytic component 3	859					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)|mRNA catabolic process (GO:0006402)|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)|regulation of stem cell proliferation (GO:0072091)	cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)|poly(A) RNA binding (GO:0044822)										CAATGTACTTCGCTTAAATAG	0.428													C|||	48	0.00958466	0.034	0.0	5008	,	,		20951	0.0		0.003	False		,,,				2504	0.0				p.F859F		Atlas-SNP	.											.	.	.	.	0			c.C2577T						PASS	.	C	,	105,4301	81.9+/-120.4	2,101,2100	139.0	115.0	123.0		2577,1875	1.9	1.0	1	dbSNP_129	123	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	EIF2C3	NM_024852.3,NM_177422.2	,	2,106,6395	TT,TC,CC		0.0581,2.3831,0.8458	,	859/861,625/627	36521340	110,12896	2203	4300	6503	SO:0001819	synonymous_variant	192669	exon19			GTACTTCGCTTAA	AB046787	CCDS399.1, CCDS400.1	1p34	2013-06-03	2013-02-15	2013-02-15	ENSG00000126070	ENSG00000126070		"""Argonaute/PIWI family"""	18421	protein-coding gene	gene with protein product	"""argonaute 3"""	607355	"""eukaryotic translation initiation factor 2C, 3"""	EIF2C3		12906857	Standard	NM_024852		Approved	hAGO3, FLJ12765	uc001bzp.3	Q9H9G7	OTTHUMG00000184172	ENST00000373191.4:c.2577C>T	1.37:g.36521340C>T		122.0	0.0	0		90.0	43.0	0.477778	NM_024852	B1ALI0|Q5TA55|Q9H1U6	Silent	SNP	ENST00000373191.4	37	CCDS399.1																																																																																			C|0.992;T|0.008	0.008	strong		0.428	AGO3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019831.4	NM_024852	
GSAP	54103	hgsc.bcm.edu	37	7	77010661	77010661	+	Silent	SNP	T	T	C	rs17152629	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:77010661T>C	ENST00000257626.7	-	8	615	c.537A>G	c.(535-537)caA>caG	p.Q179Q		NM_017439.3	NP_059135.2	A4D1B5	GSAP_HUMAN	gamma-secretase activating protein	179					positive regulation of beta-amyloid formation (GO:1902004)|regulation of proteolysis (GO:0030162)	trans-Golgi network (GO:0005802)	beta-amyloid binding (GO:0001540)										GGATACGAAATTGTTCAATAT	0.284													T|||	157	0.0313498	0.1104	0.0144	5008	,	,		18372	0.001		0.0	False		,,,				2504	0.0				p.Q179Q		Atlas-SNP	.											.	PION	74	.	0			c.A537G						PASS	.	T		349,3271		20,309,1481	66.0	63.0	64.0		537	-1.6	0.2	7	dbSNP_123	64	3,8131		0,3,4064	no	coding-synonymous	PION	NM_017439.3		20,312,5545	CC,CT,TT		0.0369,9.6409,2.9947		179/855	77010661	352,11402	1810	4067	5877	SO:0001819	synonymous_variant	54103	exon8			ACGAAATTGTTCA		CCDS34672.2	7q11.23	2013-04-05	2013-04-05	2013-04-05	ENSG00000186088	ENSG00000186088			28042	protein-coding gene	gene with protein product		613552	"""pigeon homolog (Drosophila)"""	PION		20811458	Standard	NM_017439		Approved	LOC54103	uc003ugf.3	A4D1B5	OTTHUMG00000150504	ENST00000257626.7:c.537A>G	7.37:g.77010661T>C		43.0	0.0	0		37.0	15.0	0.405405	NM_017439	A4D1B6|Q3MJC0|Q8ND73|Q9UMH3|Q9Y4L9	Silent	SNP	ENST00000257626.7	37	CCDS34672.2																																																																																			T|0.965;C|0.035	0.035	strong		0.284	GSAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318672.2	NM_017439	
FYB	2533	hgsc.bcm.edu	37	5	39202911	39202911	+	Missense_Mutation	SNP	G	G	A	rs1642515	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:39202911G>A	ENST00000351578.6	-	2	342	c.152C>T	c.(151-153)cCc>cTc	p.P51L	FYB_ENST00000505428.1_Missense_Mutation_p.P51L|FYB_ENST00000540520.1_Missense_Mutation_p.P61L|FYB_ENST00000515010.1_Missense_Mutation_p.P51L|FYB_ENST00000512982.1_Missense_Mutation_p.P51L	NM_199335.3	NP_955367.1	O15117	FYB_HUMAN	FYN binding protein	51			P -> L (in dbSNP:rs1642515).		immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|NLS-bearing protein import into nucleus (GO:0006607)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	receptor binding (GO:0005102)			endometrium(2)|kidney(4)|large_intestine(6)|liver(1)|lung(29)|ovary(2)|upper_aerodigestive_tract(1)	45	all_lung(31;0.000343)		Epithelial(62;0.235)			TACATTGCTGGGTCCTGCAGG	0.502													G|||	182	0.0363419	0.1331	0.0086	5008	,	,		17552	0.0		0.0	False		,,,				2504	0.0				p.P61L		Atlas-SNP	.											.	FYB	354	.	0			c.C182T						PASS	.	G	LEU/PRO,LEU/PRO	449,3361		21,407,1477	60.0	58.0	58.0		152,152	3.4	0.5	5	dbSNP_89	58	5,8235		0,5,4115	yes	missense,missense	FYB	NM_001465.4,NM_199335.3	98,98	21,412,5592	AA,AG,GG		0.0607,11.7848,3.7676	benign,benign	51/830,51/784	39202911	454,11596	1905	4120	6025	SO:0001583	missense	2533	exon2			TTGCTGGGTCCTG	U93049	CCDS47200.1, CCDS54848.1	5p13.1	2012-05-04	2010-05-04		ENSG00000082074	ENSG00000082074			4036	protein-coding gene	gene with protein product		602731	"""FYN-binding protein (FYB-120/130)"""			9115214, 9207119	Standard	NM_001465		Approved	SLAP-130, FYB-120/130	uc011cpl.2	O15117	OTTHUMG00000162071	ENST00000351578.6:c.152C>T	5.37:g.39202911G>A	ENSP00000316460:p.Pro51Leu	121.0	0.0	0		120.0	57.0	0.475	NM_001243093	A8K2Y8|B4DLN2|E9PBV9|O00359|Q9NZI9	Missense_Mutation	SNP	ENST00000351578.6	37	CCDS47200.1	64	0.029304029304029304	60	0.12195121951219512	4	0.011049723756906077	0	0.0	0	0.0	G	12.15	1.852358	0.32699	0.117848	6.07E-4	ENSG00000082074	ENST00000351578;ENST00000515010;ENST00000512982;ENST00000505428;ENST00000540520;ENST00000542542;ENST00000510188;ENST00000512138	T;T;T;T;T;T;T	0.73897	0.51;0.51;0.57;0.57;0.56;-0.79;-0.14	6.17	3.39	0.38822	.	0.680112	0.15332	N	0.267922	T	0.01695	0.0054	L	0.43701	1.375	0.20403	P	0.9999089434	B;B	0.20887	0.049;0.007	B;B	0.15052	0.012;0.006	T	0.30504	-0.9976	9	0.56958	D	0.05	-0.0459	5.9531	0.19259	0.2021:0.0:0.6538:0.1441	rs1642515;rs1642515	61;51	B4DLN2;O15117	.;FYB_HUMAN	L	51;51;51;51;61;51;51;51	ENSP00000316460:P51L;ENSP00000426346:P51L;ENSP00000425845:P51L;ENSP00000427114:P51L;ENSP00000442840:P61L;ENSP00000426597:P51L;ENSP00000424919:P51L	ENSP00000316460:P51L	P	-	2	0	FYB	39238668	0.961000	0.32948	0.518000	0.27811	0.688000	0.40055	1.158000	0.31737	0.444000	0.26612	0.655000	0.94253	CCC	G|0.959;A|0.041	0.041	strong		0.502	FYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367098.1	NM_001465	
DAAM2	23500	hgsc.bcm.edu	37	6	39847153	39847153	+	Missense_Mutation	SNP	C	C	A	rs150676991	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:39847153C>A	ENST00000398904.2	+	14	1927	c.1745C>A	c.(1744-1746)cCt>cAt	p.P582H	DAAM2_ENST00000274867.4_Missense_Mutation_p.P582H|RP11-61I13.3_ENST00000607675.1_RNA|DAAM2_ENST00000538976.1_Missense_Mutation_p.P582H			Q86T65	DAAM2_HUMAN	dishevelled associated activator of morphogenesis 2	582	FH1.|Pro-rich.				actin cytoskeleton organization (GO:0030036)|determination of left/right symmetry (GO:0007368)					NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(18)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(5)	49	Ovarian(28;0.0355)|Colorectal(47;0.196)					CTGCCCCTCCCTCAGGACCCC	0.652													C|||	2	0.000399361	0.0015	0.0	5008	,	,		12540	0.0		0.0	False		,,,				2504	0.0				p.P582H		Atlas-SNP	.											.	DAAM2	101	.	0			c.C1745A						PASS	.	C	HIS/PRO,HIS/PRO	8,3826		0,8,1909	44.0	46.0	45.0		1745,1745	5.2	0.9	6	dbSNP_134	45	14,8208		0,14,4097	yes	missense,missense	DAAM2	NM_001201427.1,NM_015345.3	77,77	0,22,6006	AA,AC,CC		0.1703,0.2087,0.1825	benign,benign	582/1069,582/1068	39847153	22,12034	1917	4111	6028	SO:0001583	missense	23500	exon14			CCCTCCCTCAGGA	AB002379	CCDS54999.1, CCDS56426.1	6p21.1	2008-07-30			ENSG00000146122	ENSG00000146122			18143	protein-coding gene	gene with protein product		606627				11779461, 12632087	Standard	NM_015345		Approved	KIAA0381	uc003oow.3	Q86T65	OTTHUMG00000014653	ENST00000398904.2:c.1745C>A	6.37:g.39847153C>A	ENSP00000381876:p.Pro582His	216.0	0.0	0		250.0	110.0	0.44	NM_015345	G5EA45|Q5T4T8|Q5T4U0|Q9NQI5|Q9Y4G0	Missense_Mutation	SNP	ENST00000398904.2	37	CCDS56426.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	16.94	3.261074	0.59431	0.002087	0.001703	ENSG00000146122	ENST00000274867;ENST00000398904;ENST00000538976	D;D;D	0.84146	-1.81;-1.81;-1.79	5.15	5.15	0.70609	Actin-binding FH2 (1);	0.215647	0.39407	N	0.001370	T	0.65302	0.2678	N	0.08118	0	0.80722	D	1	P;B	0.40875	0.731;0.38	B;B	0.42555	0.391;0.159	T	0.73799	-0.3869	10	0.46703	T	0.11	.	13.0249	0.58808	0.0:0.9199:0.0:0.0801	.	582;582	G5EA45;Q86T65	.;DAAM2_HUMAN	H	582	ENSP00000274867:P582H;ENSP00000381876:P582H;ENSP00000437808:P582H	ENSP00000274867:P582H	P	+	2	0	DAAM2	39955131	0.989000	0.36119	0.881000	0.34555	0.838000	0.47535	3.359000	0.52292	2.383000	0.81215	0.650000	0.86243	CCT	C|0.998;A|0.002	0.002	strong		0.652	DAAM2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280648.1		
SYNE2	23224	hgsc.bcm.edu	37	14	64519053	64519053	+	Silent	SNP	C	C	T	rs35960129	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:64519053C>T	ENST00000344113.4	+	48	8634	c.8422C>T	c.(8422-8424)Cta>Tta	p.L2808L	SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Silent_p.L2841L|SYNE2_ENST00000358025.3_Silent_p.L2808L	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2808					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AAATAATACCCTAGAGGACTT	0.383													C|||	120	0.0239617	0.087	0.0072	5008	,	,		20674	0.0		0.0	False		,,,				2504	0.0				p.L2808L		Atlas-SNP	.											.	SYNE2	577	.	0			c.C8422T						PASS	.	C	,	260,3436		11,238,1599	73.0	68.0	70.0		8422,8422	4.0	0.9	14	dbSNP_126	70	0,8182		0,0,4091	no	coding-synonymous,coding-synonymous	SYNE2	NM_015180.4,NM_182914.2	,	11,238,5690	TT,TC,CC		0.0,7.0346,2.1889	,	2808/6886,2808/6908	64519053	260,11618	1848	4091	5939	SO:0001819	synonymous_variant	23224	exon48			AATACCCTAGAGG	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.8422C>T	14.37:g.64519053C>T		85.0	0.0	0		114.0	56.0	0.491228	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																			C|0.990;T|0.010	0.010	strong		0.383	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
UGT2B11	10720	hgsc.bcm.edu	37	4	70078393	70078393	+	Nonsense_Mutation	SNP	C	C	T	rs138593124	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:70078393C>T	ENST00000446444.1	-	2	776	c.768G>A	c.(766-768)tgG>tgA	p.W256*	RP11-704M14.1_ENST00000504301.1_RNA|RP11-704M14.1_ENST00000505646.1_RNA	NM_001073.1	NP_001064.1	O75310	UDB11_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B11	256					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						TTCGCATAAGCCATATGTCAG	0.388													.|||	22	0.00439297	0.0159	0.0014	5008	,	,		14009	0.0		0.0	False		,,,				2504	0.0				p.W256X		Atlas-SNP	.											.	UGT2B11	92	.	0			c.G768A						PASS	.	C	stop/TRP	83,4323		1,81,2121	141.0	147.0	145.0		768	2.0	0.2	4	dbSNP_134	145	0,8598		0,0,4299	no	stop-gained	UGT2B11	NM_001073.1		1,81,6420	TT,TC,CC		0.0,1.8838,0.6383		256/530	70078393	83,12921	2203	4299	6502	SO:0001587	stop_gained	10720	exon2			CATAAGCCATATG	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.768G>A	4.37:g.70078393C>T	ENSP00000387683:p.Trp256*	312.0	0.0	0		336.0	151.0	0.449405	NM_001073	Q3KNV9	Nonsense_Mutation	SNP	ENST00000446444.1	37	CCDS3527.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	-	12.43	1.936842	0.34189	0.018838	0.0	ENSG00000213759	ENST00000446444	.	.	.	1.96	1.96	0.26148	.	0.000000	0.64402	U	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	9.5515	0.39313	0.0:1.0:0.0:0.0	.	.	.	.	X	256	.	ENSP00000387683:W256X	W	-	3	0	UGT2B11	70112982	1.000000	0.71417	0.183000	0.23137	0.044000	0.14063	4.939000	0.63526	1.087000	0.41251	0.184000	0.17185	TGG	C|0.993;T|0.007	0.007	strong		0.388	UGT2B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251551.2	NM_001073	
TBX3	6926	hgsc.bcm.edu	37	12	115118722	115118722	+	Silent	SNP	G	G	A	rs35069811	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:115118722G>A	ENST00000257566.3	-	2	1008	c.619C>T	c.(619-621)Ctg>Ttg	p.L207L	TBX3_ENST00000349155.2_Silent_p.L207L	NM_016569.3	NP_057653.3	O15119	TBX3_HUMAN	T-box 3	207					anterior/posterior axis specification, embryo (GO:0008595)|atrioventricular bundle cell differentiation (GO:0003167)|blood vessel development (GO:0001568)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cardiac muscle cell fate commitment (GO:0060923)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|female genitalia development (GO:0030540)|follicle-stimulating hormone secretion (GO:0046884)|forelimb morphogenesis (GO:0035136)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|limbic system development (GO:0021761)|luteinizing hormone secretion (GO:0032275)|male genitalia development (GO:0030539)|mammary gland development (GO:0030879)|mammary placode formation (GO:0060596)|mesoderm morphogenesis (GO:0048332)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)|outflow tract morphogenesis (GO:0003151)|palate development (GO:0060021)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell proliferation (GO:0008284)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|sinoatrial node cell development (GO:0060931)|skeletal system development (GO:0001501)|specification of organ position (GO:0010159)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum morphogenesis (GO:0060412)	nucleus (GO:0005634)	RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|endometrium(1)|kidney(1)|large_intestine(6)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0574)		GTGAGTTTCAGTTTGTGGAAA	0.463													G|||	73	0.0145767	0.0537	0.0029	5008	,	,		19262	0.0		0.0	False		,,,				2504	0.0				p.L207L		Atlas-SNP	.											.	TBX3	106	.	0			c.C619T						PASS	.	G	,	256,4150	146.9+/-181.5	7,242,1954	147.0	139.0	142.0		619,619	4.9	1.0	12	dbSNP_126	142	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous,coding-synonymous	TBX3	NM_005996.3,NM_016569.3	,	7,246,6250	AA,AG,GG		0.0465,5.8103,1.9991	,	207/724,207/744	115118722	260,12746	2203	4300	6503	SO:0001819	synonymous_variant	6926	exon2			GTTTCAGTTTGTG	BC025258	CCDS9175.1, CCDS9176.1	12q24.21	2013-09-05	2008-07-31		ENSG00000135111	ENSG00000135111		"""T-boxes"""	11602	protein-coding gene	gene with protein product		601621	"""ulnar mammary syndrome"""	UMS		8988164	Standard	NM_005996		Approved	TBX3-ISO, XHL	uc001tvt.1	O15119	OTTHUMG00000169586	ENST00000257566.3:c.619C>T	12.37:g.115118722G>A		231.0	0.0	0		256.0	118.0	0.460938	NM_005996	Q8TB20|Q9UKF8	Silent	SNP	ENST00000257566.3	37	CCDS9176.1																																																																																			G|0.979;A|0.021	0.021	strong		0.463	TBX3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404947.2	NM_016569, NM_005996	
EXPH5	23086	hgsc.bcm.edu	37	11	108384857	108384857	+	Silent	SNP	T	T	C	rs116565594	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:108384857T>C	ENST00000265843.4	-	6	1487	c.1377A>G	c.(1375-1377)agA>agG	p.R459R	EXPH5_ENST00000524840.1_5'UTR|EXPH5_ENST00000428840.1_Silent_p.R383R|EXPH5_ENST00000525344.1_Silent_p.R452R|EXPH5_ENST00000443411.1_Silent_p.R271R	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	459					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		TGAAGAAAGATCTGGTAAATG	0.438													T|||	64	0.0127796	0.0477	0.0014	5008	,	,		22659	0.0		0.0	False		,,,				2504	0.0				p.R459R		Atlas-SNP	.											.	EXPH5	193	.	0			c.A1377G						PASS	.	T		168,4234	112.5+/-150.6	0,168,2033	158.0	150.0	152.0		1377	2.5	1.0	11	dbSNP_132	152	0,8596		0,0,4298	no	coding-synonymous	EXPH5	NM_015065.2		0,168,6331	CC,CT,TT		0.0,3.8164,1.2925		459/1990	108384857	168,12830	2201	4298	6499	SO:0001819	synonymous_variant	23086	exon6			GAAAGATCTGGTA		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.1377A>G	11.37:g.108384857T>C		136.0	0.0	0		116.0	55.0	0.474138	NM_015065	Q2KHM1|Q9Y4D6	Silent	SNP	ENST00000265843.4	37	CCDS8341.1																																																																																			T|0.987;C|0.013	0.013	strong		0.438	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
FASTKD1	79675	hgsc.bcm.edu	37	2	170428198	170428198	+	Silent	SNP	G	G	A	rs113959605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170428198G>A	ENST00000453153.2	-	2	688	c.342C>T	c.(340-342)gaC>gaT	p.D114D	FASTKD1_ENST00000453929.2_Silent_p.D114D	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	114					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(5)|large_intestine(10)|lung(9)|ovary(4)|prostate(3)	37						CCAGGGTATCGTCATTCATTA	0.279													G|||	37	0.00738818	0.0265	0.0014	5008	,	,		17370	0.0		0.001	False		,,,				2504	0.0				p.D114D		Atlas-SNP	.											.	FASTKD1	86	.	0			c.C342T						PASS	.	G		89,4315	68.7+/-106.4	2,85,2115	46.0	45.0	45.0		342	-5.3	0.0	2	dbSNP_132	45	1,8599		0,1,4299	no	coding-synonymous	FASTKD1	NM_024622.3		2,86,6414	AA,AG,GG		0.0116,2.0209,0.6921		114/848	170428198	90,12914	2202	4300	6502	SO:0001819	synonymous_variant	79675	exon2			GGTATCGTCATTC	AL832058	CCDS33318.1, CCDS63051.1	2q31.1	2008-02-05			ENSG00000138399	ENSG00000138399			26150	protein-coding gene	gene with protein product						11347906	Standard	NM_024622		Approved	FLJ21901	uc002uev.4	Q53R41	OTTHUMG00000154953	ENST00000453153.2:c.342C>T	2.37:g.170428198G>A		157.0	0.0	0		106.0	45.0	0.424528	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Silent	SNP	ENST00000453153.2	37	CCDS33318.1																																																																																			G|0.993;A|0.007	0.007	strong		0.279	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622	
RPL5	6125	hgsc.bcm.edu	37	1	93299193	93299193	+	Silent	SNP	G	G	A	rs58263806	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:93299193G>A	ENST00000370321.3	+	3	255	c.165G>A	c.(163-165)gtG>gtA	p.V55V		NM_000969.3	NP_000960.2	P46777	RL5_HUMAN	ribosomal protein L5	55					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal large subunit biogenesis (GO:0042273)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	5S rRNA binding (GO:0008097)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	9		all_lung(203;0.00265)|Lung NSC(277;0.0056)|all_neural(321;0.185)|Melanoma(281;0.192)|Glioma(108;0.203)		GBM - Glioblastoma multiforme(16;0.000305)|all cancers(265;0.000343)|Epithelial(280;0.0927)		TAGTTCGTGTGACAAACAGAG	0.368													A|||	121	0.0241613	0.0877	0.0058	5008	,	,		18734	0.0		0.001	False		,,,				2504	0.0				p.V55V		Atlas-SNP	.											.	RPL5	38	.	0			c.G165A						PASS	.	A		313,4093	796.5+/-415.4	11,291,1901	62.0	68.0	66.0		165	1.1	1.0	1	dbSNP_129	66	4,8596	818.7+/-406.8	0,4,4296	no	coding-synonymous	RPL5	NM_000969.3		11,295,6197	AA,AG,GG		0.0465,7.1039,2.4373		55/298	93299193	317,12689	2203	4300	6503	SO:0001819	synonymous_variant	6125	exon3			TCGTGTGACAAAC	U14966	CCDS741.1	1p22.1	2014-06-13			ENSG00000122406	ENSG00000122406		"""L ribosomal proteins"""	10360	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 135"""	603634				7937132, 7772601	Standard	NM_000969		Approved	L5, PPP1R135	uc001doz.3	P46777	OTTHUMG00000010899	ENST00000370321.3:c.165G>A	1.37:g.93299193G>A		67.0	0.0	0		70.0	25.0	0.357143	NM_000969	Q32LZ3|Q53HH6|Q9H3F4	Silent	SNP	ENST00000370321.3	37	CCDS741.1																																																																																			G|0.977;A|0.023	0.023	strong		0.368	RPL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030058.2	NM_000969	
CDK5R1	8851	hgsc.bcm.edu	37	17	30815208	30815208	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:30815208G>A	ENST00000313401.3	+	2	1259	c.570G>A	c.(568-570)tgG>tgA	p.W190*		NM_003885.2	NP_003876.1	Q15078	CD5R1_HUMAN	cyclin-dependent kinase 5, regulatory subunit 1 (p35)	190					axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|brain development (GO:0007420)|cell proliferation (GO:0008283)|cerebellum development (GO:0021549)|embryo development (GO:0009790)|ephrin receptor signaling pathway (GO:0048013)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|hippocampus development (GO:0021766)|ionotropic glutamate receptor signaling pathway (GO:0035235)|layer formation in cerebral cortex (GO:0021819)|negative regulation of axon extension (GO:0030517)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of protein targeting to membrane (GO:0090314)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of neuron differentiation (GO:0045664)|rhythmic process (GO:0048511)|serine phosphorylation of STAT3 protein (GO:0033136)|superior olivary nucleus maturation (GO:0021722)	axon (GO:0030424)|contractile fiber (GO:0043292)|cyclin-dependent protein kinase 5 holoenzyme complex (GO:0016533)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|growth cone (GO:0030426)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	cadherin binding (GO:0045296)|calcium ion binding (GO:0005509)|cyclin-dependent protein kinase 5 activator activity (GO:0016534)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activator activity (GO:0043539)			cervix(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)	8		Breast(31;0.159)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.0938)			TGCAGGGCTGGCAGGACCAGG	0.652																																					p.W190X		Atlas-SNP	.											.	CDK5R1	30	.	0			c.G570A						PASS	.						68.0	71.0	70.0					17																	30815208		2203	4300	6503	SO:0001587	stop_gained	8851	exon2			GGGCTGGCAGGAC	X80343	CCDS11273.1	17q12	2006-03-28			ENSG00000176749	ENSG00000176749			1775	protein-coding gene	gene with protein product		603460				8090221	Standard	NM_003885		Approved	p35nck5a, Nck5a	uc002hhn.3	Q15078	OTTHUMG00000132814	ENST00000313401.3:c.570G>A	17.37:g.30815208G>A	ENSP00000318486:p.Trp190*	107.0	0.0	0		131.0	20.0	0.152672	NM_003885	E1P664|Q5U0G3	Nonsense_Mutation	SNP	ENST00000313401.3	37	CCDS11273.1	.	.	.	.	.	.	.	.	.	.	G	43	10.067794	0.99329	.	.	ENSG00000176749	ENST00000313401	.	.	.	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-14.2883	16.9953	0.86366	0.0:0.0:1.0:0.0	.	.	.	.	X	190	.	ENSP00000318486:W190X	W	+	3	0	CDK5R1	27839321	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.759000	0.98931	2.609000	0.88269	0.557000	0.71058	TGG	.	.	none		0.652	CDK5R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256264.1	NM_003885	
CYTH4	27128	hgsc.bcm.edu	37	22	37693632	37693632	+	Silent	SNP	C	C	T	rs73887105	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:37693632C>T	ENST00000248901.6	+	5	449	c.262C>T	c.(262-264)Ctg>Ttg	p.L88L	CYTH4_ENST00000439667.1_3'UTR|CYTH4_ENST00000405206.3_Silent_p.L88L|CYTH4_ENST00000402997.1_Silent_p.L88L	NM_013385.3	NP_037517.1	Q9UIA0	CYH4_HUMAN	cytohesin 4	88	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)	plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|lipid binding (GO:0008289)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(2)|stomach(1)	15						TGAGCACAAGCTGCTGACCCC	0.572													C|||	31	0.0061901	0.0227	0.0014	5008	,	,		20239	0.0		0.0	False		,,,				2504	0.0				p.L88L		Atlas-SNP	.											.	CYTH4	51	.	0			c.C262T						PASS	.	C		102,4304	81.4+/-119.9	1,100,2102	74.0	68.0	70.0		262	4.0	1.0	22	dbSNP_130	70	0,8600		0,0,4300	no	coding-synonymous	CYTH4	NM_013385.3		1,100,6402	TT,TC,CC		0.0,2.315,0.7843		88/395	37693632	102,12904	2203	4300	6503	SO:0001819	synonymous_variant	27128	exon5			CACAAGCTGCTGA	AF075458	CCDS13946.1	22q12.3-q13.1	2014-05-02	2008-08-14	2008-08-14	ENSG00000100055	ENSG00000100055		"""Pleckstrin homology (PH) domain containing"""	9505	protein-coding gene	gene with protein product		606514	"""pleckstrin homology, Sec7 and coiled/coil domains 4"", ""pleckstrin homology, Sec7 and coiled-coil domains 4"""	PSCD4		10591208	Standard	NM_013385		Approved	CYT4, cytohesin-4	uc003arf.3	Q9UIA0	OTTHUMG00000150562	ENST00000248901.6:c.262C>T	22.37:g.37693632C>T		123.0	0.0	0		93.0	48.0	0.516129	NM_013385	Q5R3F9|Q9UGT6	Silent	SNP	ENST00000248901.6	37	CCDS13946.1																																																																																			C|0.992;T|0.008	0.008	strong		0.572	CYTH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318917.1		
FH	2271	hgsc.bcm.edu	37	1	241676972	241676972	+	Silent	SNP	G	G	A	rs10926501	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:241676972G>A	ENST00000366560.3	-	3	347	c.309C>T	c.(307-309)gcC>gcT	p.A103A	FH_ENST00000493477.1_5'Flank	NM_000143.3	NP_000134.2	P07954	FUMH_HUMAN	fumarate hydratase	103					cellular metabolic process (GO:0044237)|fumarate metabolic process (GO:0006106)|homeostasis of number of cells within a tissue (GO:0048873)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|tricarboxylic acid cycle enzyme complex (GO:0045239)	fumarate hydratase activity (GO:0004333)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|skin(2)	26	Ovarian(103;0.103)	all_cancers(173;2.37e-314)|all_epithelial(177;5.17e-286)|Breast(1374;1.06e-10)|Acute lymphoblastic leukemia(190;4.93e-10)|all_neural(198;0.00118)	OV - Ovarian serous cystadenocarcinoma(106;0.0214)	Colorectal(1306;2.33e-53)|COAD - Colon adenocarcinoma(196;1.05e-44)|KIRC - Kidney renal clear cell carcinoma(1967;0.000109)		TTACTTCAGCGGCCGCTCGCT	0.353			"""Mis, N, F"""			"""lieomyomatosis, renal"""			Hereditary Leiomyomatosis and Renal Cell Cancer				G|||	169	0.033746	0.1241	0.0072	5008	,	,		16468	0.0		0.0	False		,,,				2504	0.0				p.A103A	Melanoma(148;1573 2486 7381 46575)	Atlas-SNP	.	yes	Rec		hereditary leiomyomatosis and renal cell cancer	1	1q42.1	2271	fumarate hydratase		"""E, M"""	FH,NS,carcinoma,0,2	FH	64	2	0			c.C309T						PASS	.	G		386,4020	191.6+/-217.2	18,350,1835	121.0	123.0	122.0		309	0.9	1.0	1	dbSNP_120	122	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	FH	NM_000143.3		18,353,6132	AA,AG,GG		0.0349,8.7608,2.9909		103/511	241676972	389,12617	2203	4300	6503	SO:0001819	synonymous_variant	2271	exon3	Familial Cancer Database	HLRCC, Reed syndrome, Hereditary Multiple Leiomyomata of Skin and Uterus	TTCAGCGGCCGCT	BC003108	CCDS1617.1	1q42.1	2014-09-17			ENSG00000091483	ENSG00000091483	4.2.1.2		3700	protein-coding gene	gene with protein product		136850					Standard	NM_000143		Approved	fumarase	uc001hyx.3	P07954	OTTHUMG00000039597	ENST00000366560.3:c.309C>T	1.37:g.241676972G>A		282.0	0.0	0		273.0	141.0	0.516484	NM_000143	B1ANK7	Silent	SNP	ENST00000366560.3	37	CCDS1617.1																																																																																			G|0.975;A|0.025	0.025	strong		0.353	FH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095490.1	NM_000143	
PHAX	51808	hgsc.bcm.edu	37	5	125944131	125944131	+	Silent	SNP	G	G	C	rs61747690	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:125944131G>C	ENST00000297540.4	+	3	1481	c.786G>C	c.(784-786)ctG>ctC	p.L262L		NM_032177.3	NP_115553.2	Q9H814	PHAX_HUMAN	phosphorylated adaptor for RNA export	262	Necessary for interaction with CBP80. {ECO:0000250}.|Sufficient for poly U RNA-binding.				gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|protein transport (GO:0015031)|RNA metabolic process (GO:0016070)|snRNA export from nucleus (GO:0006408)|spliceosomal snRNP assembly (GO:0000387)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	RNA binding (GO:0003723)|toxic substance binding (GO:0015643)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)	8						TTGAACTTCTGATGGAAACCG	0.348													G|||	184	0.0367412	0.1324	0.0086	5008	,	,		18871	0.0		0.003	False		,,,				2504	0.0				p.L262L		Atlas-SNP	.											.	PHAX	20	.	0			c.G786C						PASS	.	G		471,3935	222.6+/-239.4	27,417,1759	159.0	167.0	164.0		786	0.7	1.0	5	dbSNP_129	164	12,8588	8.4+/-32.0	0,12,4288	no	coding-synonymous	PHAX	NM_032177.3		27,429,6047	CC,CG,GG		0.1395,10.69,3.7137		262/395	125944131	483,12523	2203	4300	6503	SO:0001819	synonymous_variant	51808	exon3			ACTTCTGATGGAA	AK023255	CCDS4138.1	5q23.2	2011-05-24	2008-10-01	2008-10-01	ENSG00000164902	ENSG00000164902			10241	protein-coding gene	gene with protein product		604924	"""RNA U, small nuclear RNA export adaptor (phosphorylation regulated)"""	RNUXA		10786834	Standard	NM_032177		Approved	FLJ13193	uc003kua.2	Q9H814	OTTHUMG00000163273	ENST00000297540.4:c.786G>C	5.37:g.125944131G>C		122.0	0.0	0		94.0	46.0	0.489362	NM_032177	Q9H8W1	Silent	SNP	ENST00000297540.4	37	CCDS4138.1																																																																																			G|0.963;C|0.037	0.037	strong		0.348	PHAX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250924.1	NM_032177	
DNAH12	201625	hgsc.bcm.edu	37	3	57469151	57469151	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:57469151T>C	ENST00000351747.2	-	13	1782	c.1602A>G	c.(1600-1602)gtA>gtG	p.V534V	DNAH12_ENST00000389536.4_Silent_p.V534V	NM_178504.4	NP_848599.3	Q6ZR08	DYH12_HUMAN	dynein, axonemal, heavy chain 12	534	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(7)|pancreas(1)|prostate(1)|skin(1)	25						GGGCTTTTTCTACATAAGATA	0.318																																					p.V534V		Atlas-SNP	.											.	DNAH12	182	.	0			c.A1602G						PASS	.						269.0	210.0	228.0					3																	57469151		692	1591	2283	SO:0001819	synonymous_variant	201625	exon13			TTTTTCTACATAA	U53532, AK126276	CCDS33771.1	3p21.1	2009-02-04	2006-09-04		ENSG00000174844	ENSG00000174844		"""Axonemal dyneins"""	2943	protein-coding gene	gene with protein product		603340	"""dynein, axonemal, heavy polypeptide 12"", ""dynein heavy chain domain 2"", ""dynein heavy domain 2"", ""dynein, axonemal, heavy chain 12-like"", ""dynein, axonemal, heavy chain 7-like"""	DNHD2, DNAH12L, DNAH7L		8812413, 8666668	Standard	NM_198564		Approved	DLP12, Dnahc3, HL-19, hdhc3, DHC3, FLJ40427, FLJ44290	uc003dit.2	Q6ZR08	OTTHUMG00000158598	ENST00000351747.2:c.1602A>G	3.37:g.57469151T>C		169.0	0.0	0		155.0	79.0	0.509677	NM_178504	A6NGI2|Q6ZTR8|Q8N7R9|Q8WXK2|Q92816	Silent	SNP	ENST00000351747.2	37																																																																																				.	.	none		0.318	DNAH12-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_178504	
NUMBL	9253	hgsc.bcm.edu	37	19	41190455	41190455	+	Missense_Mutation	SNP	G	G	T	rs143941883	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41190455G>T	ENST00000252891.4	-	3	283	c.116C>A	c.(115-117)gCg>gAg	p.A39E	NUMBL_ENST00000540131.1_5'UTR|NUMBL_ENST00000598779.1_5'UTR|NUMBL_ENST00000599594.1_5'UTR	NM_004756.3	NP_004747.1	Q9Y6R0	NUMBL_HUMAN	numb homolog (Drosophila)-like	39					adherens junction organization (GO:0034332)|axonogenesis (GO:0007409)|cytokine-mediated signaling pathway (GO:0019221)|lateral ventricle development (GO:0021670)|nervous system development (GO:0007399)|neuroblast division in subventricular zone (GO:0021849)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of neurogenesis (GO:0050769)|protein metabolic process (GO:0019538)	cytoplasm (GO:0005737)				NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(6)|ovary(2)	16			Lung(22;0.000393)|LUSC - Lung squamous cell carcinoma(20;0.00105)			CATGGTGCCCGCCCCGTCTGG	0.662													G|||	74	0.0147764	0.053	0.0058	5008	,	,		12097	0.0		0.0	False		,,,				2504	0.0				p.A39E		Atlas-SNP	.											.	NUMBL	49	.	0			c.C116A						PASS	.	G	GLU/ALA	198,4208	112.9+/-151.0	5,188,2010	20.0	20.0	20.0		116	4.1	1.0	19	dbSNP_134	20	0,8600		0,0,4300	yes	missense	NUMBL	NM_004756.3	107	5,188,6310	TT,TG,GG		0.0,4.4939,1.5224	benign	39/610	41190455	198,12808	2203	4300	6503	SO:0001583	missense	9253	exon3			GTGCCCGCCCCGT	AF015401	CCDS12561.1	19q13.13-q13.2	2008-07-17	2001-11-28			ENSG00000105245			8061	protein-coding gene	gene with protein product		604018	"""numb (Drosophila) homolog-like"""			9225980, 9303539	Standard	XM_006723471		Approved	NUMB-R, CTG3a, CAG3A, TNRC23, NUMBR, NUMBLIKE	uc002oon.3	Q9Y6R0		ENST00000252891.4:c.116C>A	19.37:g.41190455G>T	ENSP00000252891:p.Ala39Glu	145.0	0.0	0		147.0	58.0	0.394558	NM_004756	Q7Z4J9	Missense_Mutation	SNP	ENST00000252891.4	37	CCDS12561.1	15	0.006868131868131868	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	0	0.0	G	20.8	4.045316	0.75846	0.044939	0.0	ENSG00000105245	ENST00000252891	T	0.56776	0.44	5.17	4.14	0.48551	.	0.189579	0.32287	N	0.006318	T	0.08935	0.0221	N	0.08118	0	0.80722	D	1	B;B	0.09022	0.002;0.002	B;B	0.06405	0.002;0.002	T	0.04440	-1.0951	10	0.66056	D	0.02	-15.7799	11.0624	0.47955	0.0867:0.0:0.9133:0.0	.	39;39	A8K033;Q9Y6R0	.;NUMBL_HUMAN	E	39	ENSP00000252891:A39E	ENSP00000252891:A39E	A	-	2	0	NUMBL	45882295	0.627000	0.27129	0.999000	0.59377	0.995000	0.86356	1.270000	0.33086	1.423000	0.47198	0.591000	0.81541	GCG	G|0.987;T|0.013	0.013	strong		0.662	NUMBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462749.2	NM_004756	
NLRC3	197358	hgsc.bcm.edu	37	16	3599220	3599220	+	RNA	SNP	C	C	T	rs373104014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3599220C>T	ENST00000301749.7	-	0	2930				NLRC3_ENST00000603507.1_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000448023.2_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GGAGTTTTCTCGAAGGCTGAA	0.562													C|||	11	0.00219649	0.0083	0.0	5008	,	,		19418	0.0		0.0	False		,,,				2504	0.0				p.R842Q		Atlas-SNP	.											.	NLRC3	103	.	0			c.G2525A						PASS	.	C	GLN/ARG	10,3958		0,10,1974	36.0	37.0	37.0		2526	4.9	0.6	16		37	0,8318		0,0,4159	no	missense	NLRC3	NM_178844.2	43	0,10,6133	TT,TC,CC		0.0,0.252,0.0814	probably-damaging	842/1066	3599220	10,12276	1984	4159	6143			197358	exon14			TTTTCTCGAAGGC	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"""Nucleotide-binding domain and leucine rich repeat containing"""	29889	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3"", ""NOD-like receptor C3"""	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3599220C>T		103.0	0.0	0		99.0	43.0	0.434343	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	37		.	.	.	.	.	.	.	.	.	.	C	18.58	3.655008	0.67472	0.00252	0.0	ENSG00000167984	ENST00000301749;ENST00000359128;ENST00000448023	T;T;T	0.54071	0.59;0.6;0.59	4.95	4.95	0.65309	.	0.000000	0.64402	D	0.000001	T	0.52370	0.1730	N	0.13003	0.285	0.23227	N	0.998083	D;D	0.69078	0.997;0.961	D;P	0.76071	0.987;0.818	T	0.45542	-0.9254	10	0.15499	T	0.54	.	13.7484	0.62890	0.0:1.0:0.0:0.0	.	842;888	Q7RTR2;C9JLH9	NLRC3_HUMAN;.	Q	842;841;888	ENSP00000301749:R842Q;ENSP00000352039:R841Q;ENSP00000414415:R888Q	ENSP00000301749:R842Q	R	-	2	0	NLRC3	3539221	1.000000	0.71417	0.612000	0.29024	0.688000	0.40055	4.089000	0.57685	2.313000	0.78055	0.558000	0.71614	CGA	.	.	weak		0.562	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844	
CETP	1071	hgsc.bcm.edu	37	16	57017279	57017279	+	Missense_Mutation	SNP	G	G	A	rs2228667	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57017279G>A	ENST00000566128.1	+	15	1435	c.1168G>A	c.(1168-1170)Gtg>Atg	p.V390M	CETP_ENST00000200676.3_Missense_Mutation_p.V455M|CETP_ENST00000379780.2_Missense_Mutation_p.V395M					cholesteryl ester transfer protein, plasma											NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(4)|skin(3)	23						CAGCAAAGGCGTGAGCCTCTT	0.607																																					p.V455M		Atlas-SNP	.											CETP,NS,carcinoma,-1,1	CETP	50	1	0			c.G1363A						PASS	.		MET/VAL	3,4393		0,3,2195	103.0	95.0	98.0		1363	3.2	1.0	16	dbSNP_98	98	0,8600		0,0,4300	no	missense	CETP	NM_000078.2	21	0,3,6495	AA,AG,GG		0.0,0.0682,0.0231	benign	455/494	57017279	3,12993	2198	4300	6498	SO:0001583	missense	1071	exon15			AAAGGCGTGAGCC	M30185	CCDS10772.1, CCDS67032.1	16q13	2012-10-02			ENSG00000087237	ENSG00000087237		"""BPI fold containing"""	1869	protein-coding gene	gene with protein product	"""BPI fold containing family F"""	118470				3600759, 2334701	Standard	NM_000078		Approved	BPIFF	uc002eki.2	P11597	OTTHUMG00000133279	ENST00000566128.1:c.1168G>A	16.37:g.57017279G>A	ENSP00000456276:p.Val390Met	107.0	0.0	0		95.0	49.0	0.515789	NM_000078		Missense_Mutation	SNP	ENST00000566128.1	37		.	.	.	.	.	.	.	.	.	.	c	14.33	2.503998	0.44558	6.82E-4	0.0	ENSG00000087237	ENST00000200676;ENST00000379780	T;T	0.11712	2.75;2.75	3.16	3.16	0.36331	Lipid-binding serum glycoprotein, C-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	0.497607	0.16291	U	0.220905	T	0.04272	0.0118	N	0.08118	0	0.24408	N	0.994677	B;P	0.44380	0.049;0.834	B;B	0.30029	0.026;0.11	T	0.31833	-0.9929	10	0.66056	D	0.02	0.0425	8.4085	0.32629	0.0:0.7577:0.2423:0.0	rs2228667	395;455	P11597-2;P11597	.;CETP_HUMAN	M	455;395	ENSP00000200676:V455M;ENSP00000369106:V395M	ENSP00000200676:V455M	V	+	1	0	CETP	55574780	0.996000	0.38824	1.000000	0.80357	0.010000	0.07245	0.994000	0.29693	0.668000	0.31126	-0.225000	0.12378	GTG	A|0.002;G|0.998	0.002	strong		0.607	CETP-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432305.1	NM_000078	
SPINT4	391253	hgsc.bcm.edu	37	20	44351095	44351095	+	Missense_Mutation	SNP	C	C	A	rs16990631	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:44351095C>A	ENST00000279058.3	+	1	106	c.89C>A	c.(88-90)gCg>gAg	p.A30E		NM_178455.1	NP_848550.1	Q6UDR6	SPIT4_HUMAN	serine peptidase inhibitor, Kunitz type 4	30			A -> E (in dbSNP:rs16990631).			extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			lung(6)|ovary(1)|skin(1)	8		Myeloproliferative disorder(115;0.028)				AATAAAATTGCGGAGAAGATA	0.403													C|||	130	0.0259585	0.0212	0.0389	5008	,	,		22012	0.0		0.0398	False		,,,				2504	0.0358				p.A30E		Atlas-SNP	.											.	SPINT4	17	.	0			c.C89A						PASS	.	C	GLU/ALA	102,4304	80.4+/-118.8	1,100,2102	146.0	137.0	140.0		89	-3.5	0.0	20	dbSNP_123	140	406,8194	128.8+/-187.0	13,380,3907	yes	missense	SPINT4	NM_178455.1	107	14,480,6009	AA,AC,CC		4.7209,2.315,3.9059	benign	30/100	44351095	508,12498	2203	4300	6503	SO:0001583	missense	391253	exon1			AAATTGCGGAGAA	AY372174	CCDS33477.1	20q13.12	2012-08-20	2005-10-18	2005-10-25	ENSG00000149651	ENSG00000149651			16130	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 137"", ""serine peptidase inhibitor, Kunitz type 4"""	C20orf137		21988899	Standard	NM_178455		Approved	dJ601O1.1	uc002xpe.1	Q6UDR6	OTTHUMG00000130153	ENST00000279058.3:c.89C>A	20.37:g.44351095C>A	ENSP00000279058:p.Ala30Glu	197.0	0.0	0		192.0	99.0	0.515625	NM_178455	Q9BQN3	Missense_Mutation	SNP	ENST00000279058.3	37	CCDS33477.1	49	0.022435897435897436	12	0.024390243902439025	12	0.03314917127071823	0	0.0	25	0.032981530343007916	C	9.484	1.098836	0.20552	0.02315	0.047209	ENSG00000149651	ENST00000279058	T	0.54675	0.56	3.97	-3.46	0.04767	.	1.136080	0.06683	N	0.768367	T	0.05777	0.0151	.	.	.	0.09310	N	1	B	0.31077	0.307	B	0.23419	0.046	T	0.11690	-1.0577	9	0.66056	D	0.02	0.4807	0.4623	0.00518	0.2335:0.3326:0.1375:0.2964	rs16990631;rs16990631	30	Q6UDR6	SPIT4_HUMAN	E	30	ENSP00000279058:A30E	ENSP00000279058:A30E	A	+	2	0	SPINT4	43784509	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.705000	0.05052	-0.636000	0.05524	-0.143000	0.13931	GCG	C|0.963;A|0.037	0.037	strong		0.403	SPINT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252463.2	XM_372869	
SPATA13	221178	hgsc.bcm.edu	37	13	24797333	24797333	+	Intron	SNP	G	G	C	rs1220545	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:24797333G>C	ENST00000382095.4	+	2	185				SPATA13_ENST00000424834.2_Missense_Mutation_p.R89P|RP11-307N16.6_ENST00000382141.4_Missense_Mutation_p.R89P|SPATA13_ENST00000382108.3_Missense_Mutation_p.R89P	NM_153023.2	NP_694568.1	Q96N96	SPT13_HUMAN	spermatogenesis associated 13						cell migration (GO:0016477)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			breast(4)|endometrium(2)|large_intestine(9)|lung(4)|ovary(1)|prostate(1)|skin(2)	23		all_cancers(29;4.05e-15)|all_lung(29;2.77e-14)|all_epithelial(30;7.77e-13)|Lung SC(185;0.0279)		all cancers(112;0.00616)|Epithelial(112;0.0195)|OV - Ovarian serous cystadenocarcinoma(117;0.0705)|Lung(94;0.231)		CACCCCGAGCGGCCCCACTCC	0.607													.|||	15	0.00299521	0.0113	0.0	5008	,	,		18093	0.0		0.0	False		,,,				2504	0.0				p.R89P		Atlas-SNP	.											.	SPATA13	92	.	0			c.G266C						PASS	.	G	PRO/ARG,	25,1359		0,25,667	29.0	32.0	31.0		266,	5.2	1.0	13	dbSNP_87	31	0,3182		0,0,1591	no	missense,intron	SPATA13	NM_001166271.1,NM_153023.2	103,	0,25,2258	CC,CG,GG		0.0,1.8064,0.5475	benign,	89/1278,	24797333	25,4541	692	1591	2283	SO:0001627	intron_variant	221178	exon2			CCGAGCGGCCCCA	AK055770	CCDS9305.1, CCDS53857.1, CCDS66517.1, CCDS66518.1, CCDS73553.1	13q12.13	2013-01-10			ENSG00000182957	ENSG00000182957		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	23222	protein-coding gene	gene with protein product		613324					Standard	NM_001286795		Approved	FLJ31208, ARHGEF29	uc021rhg.1	Q96N96	OTTHUMG00000016578	ENST00000382095.4:c.-222-26282G>C	13.37:g.24797333G>C		60.0	0.0	0		79.0	50.0	0.632911	NM_001166271	A2VEA9|A6NF85|B4DQB1|B4DSZ0|B4DVM8|J3KPJ7|J3KQH2|Q5VX68|Q6ZML1|Q8N873|Q8TEK6	Missense_Mutation	SNP	ENST00000382095.4	37	CCDS9305.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	14.69	2.610495	0.46527	0.018064	0.0	ENSG00000182957	ENST00000382108	T	0.81330	-1.48	5.25	5.25	0.73442	.	0.000000	0.39475	U	0.001355	T	0.75280	0.3828	L	0.46157	1.445	0.80722	D	1	.	.	.	.	.	.	T	0.82309	-0.0521	8	0.87932	D	0	.	18.2627	0.90041	0.0:0.0:1.0:0.0	rs1220545	.	.	.	P	89	ENSP00000371542:R89P	ENSP00000371542:R89P	R	+	2	0	SPATA13	23695333	1.000000	0.71417	0.995000	0.50966	0.021000	0.10359	5.152000	0.64882	2.644000	0.89710	0.478000	0.44815	CGG	G|0.997;C|0.003	0.003	strong		0.607	SPATA13-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044180.2	NM_153023	
DDI1	414301	hgsc.bcm.edu	37	11	103908517	103908517	+	Missense_Mutation	SNP	G	G	A	rs116423827	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:103908517G>A	ENST00000302259.3	+	1	1210	c.967G>A	c.(967-969)Gat>Aat	p.D323N	PDGFD_ENST00000393158.2_Intron|PDGFD_ENST00000302251.5_Intron	NM_001001711.2	NP_001001711.1	Q8WTU0	DDI1_HUMAN	DNA-damage inducible 1 homolog 1 (S. cerevisiae)	323							aspartic-type endopeptidase activity (GO:0004190)			central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(12)|liver(2)|lung(21)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.00648)|Melanoma(852;0.055)|all_neural(303;0.164)		BRCA - Breast invasive adenocarcinoma(274;0.00128)|Epithelial(105;0.0631)|all cancers(92;0.169)		CATACTTGAGGATCAACCCAT	0.448													G|||	30	0.00599042	0.0219	0.0014	5008	,	,		19982	0.0		0.0	False		,,,				2504	0.0				p.D323N		Atlas-SNP	.											.	DDI1	222	.	0			c.G967A						PASS	.	G	ASN/ASP,,	55,4349	54.9+/-90.9	1,53,2148	139.0	129.0	133.0		967,,	5.2	1.0	11	dbSNP_132	133	1,8597	1.2+/-3.3	0,1,4298	yes	missense,intron,intron	PDGFD,DDI1	NM_001001711.2,NM_025208.4,NM_033135.3	23,,	1,54,6446	AA,AG,GG		0.0116,1.2489,0.4307	possibly-damaging,,	323/397,,	103908517	56,12946	2202	4299	6501	SO:0001583	missense	414301	exon1			CTTGAGGATCAAC		CCDS31660.1	11q22.3	2010-05-04	2010-05-04			ENSG00000170967			18961	protein-coding gene	gene with protein product			"""DDI1, DNA-damage inducible 1, homolog 1 (S. cerevisiae)"""				Standard	NM_001001711		Approved	FLJ36017	uc001phr.2	Q8WTU0		ENST00000302259.3:c.967G>A	11.37:g.103908517G>A	ENSP00000302805:p.Asp323Asn	105.0	0.0	0		117.0	41.0	0.350427	NM_001001711	Q7Z4U6|Q8WTS3	Missense_Mutation	SNP	ENST00000302259.3	37	CCDS31660.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	11.40	1.628901	0.28978	0.012489	1.16E-4	ENSG00000170967	ENST00000302259	T	0.43688	0.94	5.21	5.21	0.72293	Peptidase aspartic (1);Peptidase aspartic, eukaryotic predicted (1);Peptidase aspartic, catalytic (1);	0.165679	0.52532	D	0.000074	T	0.19765	0.0475	N	0.11364	0.135	0.47862	D	0.999536	B	0.26547	0.152	B	0.32090	0.14	T	0.06197	-1.0840	10	0.10636	T	0.68	-21.2941	16.6709	0.85266	0.0:0.0:1.0:0.0	.	323	Q8WTU0	DDI1_HUMAN	N	323	ENSP00000302805:D323N	ENSP00000302805:D323N	D	+	1	0	DDI1	103413727	1.000000	0.71417	0.954000	0.39281	0.097000	0.18754	9.016000	0.93645	2.884000	0.98904	0.655000	0.94253	GAT	G|0.995;A|0.005	0.005	strong		0.448	DDI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387326.1	NM_001001711	
RPS24	6229	hgsc.bcm.edu	37	10	79814747	79814747	+	Silent	SNP	C	C	T	rs76653255	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:79814747C>T	ENST00000440692.1	+	5	991	c.849C>T	c.(847-849)tgC>tgT	p.C283C		NM_001142285.1	NP_001135757.1	P62847	RS24_HUMAN	ribosomal protein S24	0					cellular protein metabolic process (GO:0044267)|erythrocyte homeostasis (GO:0034101)|gene expression (GO:0010467)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosomal small subunit biogenesis (GO:0042274)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic small ribosomal subunit (GO:0022627)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small ribosomal subunit (GO:0015935)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)|translation initiation factor binding (GO:0031369)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|ovary(2)|skin(1)	5	all_cancers(46;0.0343)|all_epithelial(25;0.000959)|Breast(12;0.00113)|Prostate(51;0.0095)		Epithelial(14;0.00128)|OV - Ovarian serous cystadenocarcinoma(4;0.00248)|all cancers(16;0.00428)			caccttcctgcctctctggtc	0.542													C|||	318	0.0634984	0.2231	0.0202	5008	,	,		17984	0.0		0.0089	False		,,,				2504	0.0				p.C283C		Atlas-SNP	.											.	RPS24	23	.	0			c.C849T						PASS	.	C		237,1147		17,203,472	37.0	35.0	35.0		849	-4.1	0.0	10	dbSNP_132	35	7,3175		0,7,1584	yes	coding-synonymous	RPS24	NM_001142285.1		17,210,2056	TT,TC,CC		0.22,17.1243,5.3438		283/290	79814747	244,4322	692	1591	2283	SO:0001819	synonymous_variant	6229	exon5			TTCCTGCCTCTCT	AB007159	CCDS7355.1, CCDS7356.1, CCDS44443.1	10q22	2011-04-06			ENSG00000138326	ENSG00000138326		"""S ribosomal proteins"""	10411	protein-coding gene	gene with protein product		602412				9027498, 9582194	Standard	NM_001142283		Approved	S24	uc001jzs.3	P62847	OTTHUMG00000018549	ENST00000440692.1:c.849C>T	10.37:g.79814747C>T		134.0	0.0	0		108.0	55.0	0.509259	NM_001142285	E7EPK6|P16632|Q5T0P7|Q5T0P8|Q7Z3D1	Silent	SNP	ENST00000440692.1	37	CCDS44443.1																																																																																			C|0.947;T|0.053	0.053	strong		0.542	RPS24-202	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_001026	
ZFAT	57623	hgsc.bcm.edu	37	8	135613947	135613947	+	Missense_Mutation	SNP	C	C	T	rs35003767	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:135613947C>T	ENST00000377838.3	-	6	2189	c.2015G>A	c.(2014-2016)aGg>aAg	p.R672K	ZFAT_ENST00000520356.1_Missense_Mutation_p.R660K|ZFAT-AS1_ENST00000505776.1_RNA|ZFAT_ENST00000520214.1_Missense_Mutation_p.R660K|ZFAT_ENST00000429442.2_Missense_Mutation_p.R660K|ZFAT_ENST00000523399.1_Missense_Mutation_p.R610K|ZFAT_ENST00000520727.1_Missense_Mutation_p.R660K	NM_001174157.1|NM_020863.3	NP_001167628.1|NP_065914.2	Q9P243	ZFAT_HUMAN	zinc finger and AT hook domain containing	672			R -> K (in dbSNP:rs35003767).		hematopoietic progenitor cell differentiation (GO:0002244)|spongiotrophoblast layer development (GO:0060712)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(10)|kidney(9)|large_intestine(8)|lung(16)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	all_epithelial(106;8.26e-19)|Lung NSC(106;3.47e-07)|all_lung(105;1.39e-06)|Ovarian(258;0.0102)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0432)			CCTGAGACACCTGCTGGGATC	0.602													C|||	119	0.023762	0.0855	0.0086	5008	,	,		19293	0.0		0.0	False		,,,				2504	0.0				p.R672K		Atlas-SNP	.											.	ZFAT	265	.	0			c.G2015A						PASS	.	C	LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG	224,3798		7,210,1794	60.0	66.0	64.0		1979,1979,1829,1979,2015	-2.1	0.0	8	dbSNP_126	64	2,8378		0,2,4188	yes	missense,missense,missense,missense,missense	ZFAT	NM_001029939.3,NM_001167583.2,NM_001174157.1,NM_001174158.1,NM_020863.3	26,26,26,26,26	7,212,5982	TT,TC,CC		0.0239,5.5694,1.8223	benign,benign,benign,benign,benign	660/1232,660/1232,610/1182,660/1146,672/1244	135613947	226,12176	2011	4190	6201	SO:0001583	missense	57623	exon6			AGACACCTGCTGG	BC025423	CCDS43768.1, CCDS47924.1, CCDS43768.2, CCDS55275.1, CCDS55276.1	8q24.23	2008-06-05	2008-01-25	2008-01-25	ENSG00000066827	ENSG00000066827		"""Zinc fingers, C2H2-type"""	19899	protein-coding gene	gene with protein product		610931	"""zinc finger protein 406"""	ZNF406, ZFAT1		10819331, 18329245	Standard	NM_020863		Approved	KIAA1485	uc003yup.3	Q9P243	OTTHUMG00000164321	ENST00000377838.3:c.2015G>A	8.37:g.135613947C>T	ENSP00000367069:p.Arg672Lys	83.0	0.0	0		82.0	39.0	0.47561	NM_020863	B7ZL15|E9PER3|Q3MIM5|Q6PJ01|Q75PJ6|Q75PJ7|Q75PJ9|Q86X64	Missense_Mutation	SNP	ENST00000377838.3	37	CCDS47924.1	59	0.027014652014652016	56	0.11382113821138211	3	0.008287292817679558	0	0.0	0	0.0	C	0.009	-1.816281	0.00595	0.055694	2.39E-4	ENSG00000066827	ENST00000520356;ENST00000520727;ENST00000429442;ENST00000377838;ENST00000520214;ENST00000318135;ENST00000523399;ENST00000398946	T;T;T;T;T;T	0.08282	3.18;3.12;3.13;3.11;3.12;3.12	4.76	-2.14	0.07123	.	1.175010	0.06093	N	0.663981	T	0.00109	0.0003	N	0.19112	0.55	0.09310	N	1	B;B;B;B	0.16396	0.001;0.017;0.002;0.001	B;B;B;B	0.15870	0.001;0.014;0.002;0.0	T	0.37731	-0.9693	10	0.05436	T	0.98	-1.7605	2.7057	0.05161	0.1238:0.3172:0.3665:0.1925	rs35003767	610;660;660;672	E9PER3;E9PBN4;Q9P243-3;Q9P243	.;.;.;ZFAT_HUMAN	K	660;660;660;672;660;559;610;660	ENSP00000427879:R660K;ENSP00000427831:R660K;ENSP00000394501:R660K;ENSP00000367069:R672K;ENSP00000428483:R660K;ENSP00000429091:R610K	ENSP00000326997:R559K	R	-	2	0	ZFAT	135683129	0.000000	0.05858	0.000000	0.03702	0.217000	0.24651	-2.263000	0.01174	-0.055000	0.13244	0.561000	0.74099	AGG	C|0.971;T|0.029	0.029	strong		0.602	ZFAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378272.1	NM_001029939	
LTF	4057	hgsc.bcm.edu	37	3	46496854	46496854	+	Missense_Mutation	SNP	G	G	A	rs60938611	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:46496854G>A	ENST00000231751.4	-	5	873	c.578C>T	c.(577-579)gCg>gTg	p.A193V	LTF_ENST00000417439.1_Missense_Mutation_p.A193V|LTF_ENST00000426532.2_Missense_Mutation_p.A149V	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	193	Transferrin-like 1. {ECO:0000255|PROSITE- ProRule:PRU00741}.				antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		CCCTGTCCCCGCACACAGGCG	0.552													G|||	324	0.0646965	0.2337	0.0216	5008	,	,		22455	0.0		0.0	False		,,,				2504	0.0				p.A193V		Atlas-SNP	.											.	LTF	98	.	0			c.C578T						PASS	.	G	VAL/ALA,VAL/ALA	726,3680	299.6+/-285.9	64,598,1541	140.0	115.0	124.0		446,578	-5.2	0.0	3	dbSNP_129	124	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	LTF	NM_001199149.1,NM_002343.3	64,64	64,603,5836	AA,AG,GG		0.0581,16.4775,5.6205	benign,benign	149/667,193/711	46496854	731,12275	2203	4300	6503	SO:0001583	missense	4057	exon5			GTCCCCGCACACA		CCDS33747.1, CCDS56251.1	3p21.31	2012-10-02			ENSG00000012223	ENSG00000012223			6720	protein-coding gene	gene with protein product		150210				17476971, 3356163	Standard	NM_001199149		Approved	HLF2	uc003cpq.3	P02788	OTTHUMG00000156325	ENST00000231751.4:c.578C>T	3.37:g.46496854G>A	ENSP00000231751:p.Ala193Val	132.0	0.0	0		141.0	68.0	0.482269	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Missense_Mutation	SNP	ENST00000231751.4	37	CCDS33747.1	102|102	0.046703296703296704|0.046703296703296704	92|92	0.18699186991869918|0.18699186991869918	7|7	0.019337016574585635|0.019337016574585635	0|0	0.0|0.0	3|3	0.00395778364116095|0.00395778364116095	G|G	7.510|7.510	0.654550|0.654550	0.14580|0.14580	0.164775|0.164775	5.81E-4|5.81E-4	ENSG00000012223|ENSG00000012223	ENST00000231751;ENST00000426532;ENST00000417439;ENST00000443496|ENST00000443743	T;T;T;T|.	0.34667|.	1.35;1.35;1.35;1.35|.	4.79|4.79	-5.21|-5.21	0.02815|0.02815	.|.	1.046820|.	0.07391|.	N|.	0.889107|.	T|T	0.00039|0.00039	0.0001|0.0001	N|N	0.25245|0.25245	0.725|0.725	0.80722|0.80722	P|P	0.0|0.0	B;B;B|.	0.15473|.	0.013;0.011;0.013|.	B;B;B|.	0.08055|.	0.002;0.003;0.002|.	T|T	0.29761|0.29761	-1.0001|-1.0001	9|5	0.10377|0.87932	T|D	0.69|0	0.3304|0.3304	5.6254|5.6254	0.17480|0.17480	0.3945:0.0:0.398:0.2075|0.3945:0.0:0.398:0.2075	rs60938611;rs61740469|rs60938611;rs61740469	193;180;193|.	E7ER44;E7EQB2;P02788|.	.;.;TRFL_HUMAN|.	V|W	193;149;193;180|126	ENSP00000231751:A193V;ENSP00000405719:A149V;ENSP00000405546:A193V;ENSP00000397427:A180V|.	ENSP00000231751:A193V|ENSP00000393737:R126W	A|R	-|-	2|1	0|2	LTF|LTF	46471858|46471858	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.023000|0.023000	0.10783|0.10783	-0.754000|-0.754000	0.04787|0.04787	-0.692000|-0.692000	0.05128|0.05128	-1.728000|-1.728000	0.00702|0.00702	GCG|CGG	G|0.949;A|0.051	0.051	strong		0.552	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343	
FOXD4L1	200350	hgsc.bcm.edu	37	2	114257381	114257381	+	Missense_Mutation	SNP	T	T	G	rs13428956	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:114257381T>G	ENST00000306507.5	+	1	721	c.548T>G	c.(547-549)cTg>cGg	p.L183R		NM_012184.4	NP_036316.1	Q9NU39	FX4L1_HUMAN	forkhead box D4-like 1	183					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						TACTGGAGCCTGGACCCCGCC	0.652													.|||	306	0.0611022	0.2216	0.0159	5008	,	,		10688	0.0		0.0	False		,,,				2504	0.002				p.L183R		Atlas-SNP	.											.	FOXD4L1	48	.	0			c.T548G						PASS	.	T	ARG/LEU	727,3503		131,465,1519	54.0	72.0	66.0		548	2.6	1.0	2	dbSNP_121	66	3,8201		0,3,4099	no	missense	FOXD4L1	NM_012184.4	102	131,468,5618	GG,GT,TT		0.0366,17.1868,5.871	probably-damaging	183/409	114257381	730,11704	2115	4102	6217	SO:0001583	missense	200350	exon1			GGAGCCTGGACCC	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.548T>G	2.37:g.114257381T>G	ENSP00000302756:p.Leu183Arg	148.0	0.0	0		174.0	82.0	0.471264	NM_012184	B3KWN1|B9EGF3	Missense_Mutation	SNP	ENST00000306507.5	37	CCDS2117.1	91	0.041666666666666664	90	0.18292682926829268	1	0.0027624309392265192	0	0.0	0	0.0	.	17.71	3.456701	0.63401	0.171868	3.66E-4	ENSG00000184492	ENST00000306507	D	0.97041	-4.22	2.57	2.57	0.30868	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.27841	U	0.017640	T	0.15219	0.0367	M	0.93854	3.465	0.09310	P	0.99999539299	D	0.76494	0.999	D	0.81914	0.995	T	0.05886	-1.0858	9	0.87932	D	0	.	8.6531	0.34046	0.0:0.0:0.0:1.0	rs13428956	183	Q9NU39	FX4L1_HUMAN	R	183	ENSP00000302756:L183R	ENSP00000302756:L183R	L	+	2	0	FOXD4L1	113973851	1.000000	0.71417	1.000000	0.80357	0.857000	0.48899	7.431000	0.80335	1.190000	0.43042	0.155000	0.16302	CTG	T|0.973;G|0.027	0.027	strong		0.652	FOXD4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254148.1	NM_012184	
ATAD2	29028	hgsc.bcm.edu	37	8	124357302	124357302	+	Missense_Mutation	SNP	C	C	T	rs78548009	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:124357302C>T	ENST00000287394.5	-	19	2647	c.2540G>A	c.(2539-2541)cGt>cAt	p.R847H	MIR548AA1_ENST00000384971.2_RNA|RNU6-875P_ENST00000516488.1_RNA|ATAD2_ENST00000521903.1_Missense_Mutation_p.R165H	NM_014109.3	NP_054828.2	Q6PL18	ATAD2_HUMAN	ATPase family, AAA domain containing 2	847					ATP catabolic process (GO:0006200)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.R847H(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|lung(16)|ovary(3)|prostate(3)|skin(1)|urinary_tract(2)	48	Lung NSC(37;1.25e-09)|Ovarian(258;0.00838)		STAD - Stomach adenocarcinoma(47;0.00288)			CTTAGCTTCACGAATCACCTA	0.398													C|||	7	0.00139776	0.0015	0.0	5008	,	,		17101	0.0		0.0	False		,,,				2504	0.0051				p.R847H		Atlas-SNP	.											ATAD2,NS,carcinoma,0,1	ATAD2	160	1	1	Substitution - Missense(1)	endometrium(1)	c.G2540A						PASS	.	C	HIS/ARG	8,4398	14.3+/-33.2	0,8,2195	175.0	150.0	159.0		2540	4.7	1.0	8	dbSNP_131	159	0,8600		0,0,4300	yes	missense	ATAD2	NM_014109.3	29	0,8,6495	TT,TC,CC		0.0,0.1816,0.0615	probably-damaging	847/1391	124357302	8,12998	2203	4300	6503	SO:0001583	missense	29028	exon19			GCTTCACGAATCA	BC019909	CCDS6343.1	8q24.13	2014-01-21		2007-02-08	ENSG00000156802	ENSG00000156802		"""ATPases / AAA-type"""	30123	protein-coding gene	gene with protein product		611941				12477932	Standard	NM_014109		Approved	PRO2000, DKFZp667N1320, MGC5254, MGC29843, CT137	uc003yqh.4	Q6PL18	OTTHUMG00000165090	ENST00000287394.5:c.2540G>A	8.37:g.124357302C>T	ENSP00000287394:p.Arg847His	61.0	0.0	0		76.0	44.0	0.578947	NM_014109	Q14CR1|Q658P2|Q68CQ0|Q6PJV6|Q8N890|Q9UHS5	Missense_Mutation	SNP	ENST00000287394.5	37	CCDS6343.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	C	19.10	3.761292	0.69763	0.001816	0.0	ENSG00000156802	ENST00000287394;ENST00000521903	D;D	0.82803	-1.65;-1.65	5.58	4.7	0.59300	.	0.888358	0.09837	N	0.749398	D	0.87783	0.6264	L	0.58101	1.795	0.37045	D	0.897316	D	0.63880	0.993	P	0.56514	0.8	D	0.85289	0.1066	10	0.46703	T	0.11	-4.8315	14.7146	0.69257	0.0:0.9301:0.0:0.0699	.	847	Q6PL18	ATAD2_HUMAN	H	847;165	ENSP00000287394:R847H;ENSP00000429213:R165H	ENSP00000287394:R847H	R	-	2	0	ATAD2	124426483	0.983000	0.35010	1.000000	0.80357	0.436000	0.31835	0.289000	0.18957	1.359000	0.45940	0.655000	0.94253	CGT	C|0.999;T|0.001	0.001	strong		0.398	ATAD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381766.2	NM_014109	
MCF2L2	23101	hgsc.bcm.edu	37	3	182994744	182994744	+	Splice_Site	SNP	C	C	T	rs61731401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:182994744C>T	ENST00000328913.3	-	15	2075	c.1778G>A	c.(1777-1779)aGt>aAt	p.S593N	MCF2L2_ENST00000473233.1_Splice_Site_p.S593N|MCF2L2_ENST00000447025.2_Splice_Site_p.S593N|MCF2L2_ENST00000414362.2_Splice_Site_p.S593N	NM_015078.2	NP_055893	Q86YR7	MF2L2_HUMAN	MCF.2 cell line derived transforming sequence-like 2	593							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(25)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	72	all_cancers(143;1.26e-12)|Ovarian(172;0.0355)		all cancers(12;3.35e-44)|Epithelial(37;6.48e-38)|LUSC - Lung squamous cell carcinoma(7;7.12e-25)|Lung(8;6.39e-23)|OV - Ovarian serous cystadenocarcinoma(80;6.75e-21)			GATTTCTTCACTCTGAAGTGA	0.443													T|||	136	0.0271565	0.0983	0.0072	5008	,	,		13396	0.0		0.001	False		,,,				2504	0.0				p.S593N		Atlas-SNP	.											MCF2L2,brain,glioma,0,1	MCF2L2	164	1	0			c.G1778A						PASS	.	T	ASN/SER	379,4027	769.4+/-413.7	24,331,1848	23.0	23.0	23.0		1778	3.7	1.0	3	dbSNP_129	23	2,8598	800.0+/-407.4	0,2,4298	yes	missense-near-splice	MCF2L2	NM_015078.2	46	24,333,6146	TT,TC,CC		0.0233,8.6019,2.9294	benign	593/1115	182994744	381,12625	2203	4300	6503	SO:0001630	splice_region_variant	23101	exon15			TCTTCACTCTGAA	AB020668	CCDS3243.1	3q27	2012-07-24			ENSG00000053524	ENSG00000053524		"""Rho guanine nucleotide exchange factors"""	30319	protein-coding gene	gene with protein product							Standard	NM_015078		Approved	KIAA0861, ARHGEF22	uc003fli.1	Q86YR7	OTTHUMG00000158388	ENST00000328913.3:c.1777-1G>A	3.37:g.182994744C>T		131.0	0.0	0		104.0	47.0	0.451923	NM_015078	O94942|Q6P2B8|Q6ZVJ5|Q8N318	Missense_Mutation	SNP	ENST00000328913.3	37	CCDS3243.1	46	0.021062271062271064	43	0.08739837398373984	3	0.008287292817679558	0	0.0	0	0.0	T	0.017	-1.489466	0.01018	0.086019	2.33E-4	ENSG00000053524	ENST00000328913;ENST00000473233;ENST00000447025;ENST00000437431;ENST00000414362	T;T;T;T	0.04603	4.59;4.6;3.71;3.59	4.9	3.66	0.41972	.	0.531863	0.17868	N	0.159298	T	0.00109	0.0003	N	0.08118	0	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.0	T	0.57394	-0.7819	10	0.31617	T	0.26	.	4.0278	0.09695	0.1805:0.097:0.0:0.7224	.	593;593	Q86YR7-2;Q86YR7	.;MF2L2_HUMAN	N	593;593;593;129;593	ENSP00000328118:S593N;ENSP00000420070:S593N;ENSP00000388190:S593N;ENSP00000414131:S593N	ENSP00000328118:S593N	S	-	2	0	MCF2L2	184477438	1.000000	0.71417	1.000000	0.80357	0.162000	0.22319	1.042000	0.30303	1.010000	0.39314	-0.360000	0.07572	AGT	C|0.975;T|0.025	0.025	strong		0.443	MCF2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350868.1	NM_015078	Missense_Mutation
NDUFA13	51079	hgsc.bcm.edu	37	19	19626087	19626087	+	5'Flank	SNP	C	C	T	rs150432013	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:19626087C>T	ENST00000507754.4	+	0	0				NDUFA13_ENST00000252576.5_5'Flank|NDUFA13_ENST00000503283.1_5'Flank|CTC-260F20.3_ENST00000555938.1_5'Flank|NDUFA13_ENST00000512771.3_5'Flank|NDUFA13_ENST00000428459.2_5'Flank|TSSK6_ENST00000585580.3_Silent_p.P50P|TSSK6_ENST00000360913.3_Silent_p.P50P|YJEFN3_ENST00000608404.1_5'Flank			Q9P0J0	NDUAD_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13						apoptotic signaling pathway (GO:0097190)|cellular metabolic process (GO:0044237)|cellular response to interferon-beta (GO:0035458)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell growth (GO:0030308)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of peptidase activity (GO:0010952)|positive regulation of protein catabolic process (GO:0045732)|protein import into mitochondrial inner membrane (GO:0045039)|reactive oxygen species metabolic process (GO:0072593)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain (GO:0005746)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)|NADH dehydrogenase activity (GO:0003954)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)	12						TGACGAAGTCCGGGGGCGCTC	0.617													C|||	18	0.00359425	0.0136	0.0	5008	,	,		15387	0.0		0.0	False		,,,				2504	0.0				p.P50P		Atlas-SNP	.											.	TSSK6	32	.	0			c.G150A						PASS	.	C		42,4364	44.6+/-78.6	0,42,2161	55.0	51.0	52.0		150	-9.9	0.9	19	dbSNP_134	52	0,8600		0,0,4300	no	coding-synonymous	TSSK6	NM_032037.2		0,42,6461	TT,TC,CC		0.0,0.9532,0.3229		50/274	19626087	42,12964	2203	4300	6503	SO:0001631	upstream_gene_variant	83983	exon1			GAAGTCCGGGGGC	AF261134	CCDS12404.1, CCDS12404.2	19p13.11	2011-07-04			ENSG00000186010	ENSG00000186010		"""Mitochondrial respiratory chain complex / Complex I"""	17194	protein-coding gene	gene with protein product	"""complex I B16.6 subunit"""	609435				12837546, 10924506, 15367666	Standard	NM_015965		Approved	CGI-39, CDA016, GRIM-19, GRIM19, B16.6		Q9P0J0	OTTHUMG00000162211		19.37:g.19626087C>T	Exception_encountered	50.0	0.0	0		72.0	38.0	0.527778	NM_032037	B4DF76|K7EK58|Q6PKI0|Q9H2L3|Q9Y327	Silent	SNP	ENST00000507754.4	37	CCDS12404.2																																																																																			C|0.996;T|0.004	0.004	strong		0.617	NDUFA13-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367916.6	NM_015965	
FAM136A	84908	hgsc.bcm.edu	37	2	70528092	70528092	+	Silent	SNP	G	G	A	rs72904358	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:70528092G>A	ENST00000037869.3	-	2	186	c.108C>T	c.(106-108)agC>agT	p.S36S	FAM136A_ENST00000430566.1_Silent_p.S143S|FAM136A_ENST00000450256.1_Missense_Mutation_p.R102C|AC022201.5_ENST00000445084.1_RNA	NM_032822.2	NP_116211.2	Q96C01	F136A_HUMAN	family with sequence similarity 136, member A	36						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				breast(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	6						AACAGCTGGCGCTGCACCGGA	0.577													G|||	492	0.0982428	0.3124	0.0202	5008	,	,		19465	0.001		0.003	False		,,,				2504	0.0624				p.S36S		Atlas-SNP	.											FAM136A,caecum,carcinoma,0,1	FAM136A	14	1	0			c.C108T						scavenged	.	G		1006,3400	373.9+/-321.0	116,774,1313	75.0	76.0	76.0		108	-1.5	1.0	2	dbSNP_130	76	25,8575	17.3+/-56.4	0,25,4275	no	coding-synonymous	FAM136A	NM_032822.2		116,799,5588	AA,AG,GG		0.2907,22.8325,7.9271		36/139	70528092	1031,11975	2203	4300	6503	SO:0001819	synonymous_variant	84908	exon2			GCTGGCGCTGCAC	BC014975	CCDS1904.1	2p14	2014-02-12	2007-07-10		ENSG00000035141	ENSG00000035141			25911	protein-coding gene	gene with protein product	"""hypothetical protein FLJ14668"""					12477932	Standard	NM_032822		Approved	FLJ14668	uc002sgq.4	Q96C01	OTTHUMG00000129668	ENST00000037869.3:c.108C>T	2.37:g.70528092G>A		217.0	2.0	0.00921659		225.0	113.0	0.502222	NM_032822	Q96SS3	Silent	SNP	ENST00000037869.3	37	CCDS1904.1	165	0.07554945054945054	151	0.30691056910569103	9	0.024861878453038673	1	0.0017482517482517483	4	0.005277044854881266	G	13.18	2.160192	0.38119	0.228325	0.002907	ENSG00000035141	ENST00000450256	.	.	.	5.01	-1.49	0.08718	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.34030	-0.9845	4	0.87932	D	0	.	10.957	0.47364	0.4179:0.0:0.5821:0.0	.	.	.	.	C	102	.	ENSP00000391468:R102C	R	-	1	0	FAM136A	70381596	0.992000	0.36948	0.966000	0.40874	0.969000	0.65631	0.199000	0.17237	-0.250000	0.09555	-0.263000	0.10527	CGC	G|0.921;A|0.079	0.079	strong		0.577	FAM136A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251869.2	NM_032822	
ZRANB3	84083	hgsc.bcm.edu	37	2	135988236	135988236	+	Nonsense_Mutation	SNP	G	G	A	rs200823309	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:135988236G>A	ENST00000264159.6	-	13	1917	c.1801C>T	c.(1801-1803)Cga>Tga	p.R601*	ZRANB3_ENST00000401392.1_Nonsense_Mutation_p.R601*|ZRANB3_ENST00000412849.1_5'UTR|ZRANB3_ENST00000536680.1_Nonsense_Mutation_p.R601*	NM_032143.2	NP_115519.2	Q5FWF4	ZRAB3_HUMAN	zinc finger, RAN-binding domain containing 3	601					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|DNA rewinding (GO:0036292)|DNA strand renaturation (GO:0000733)|negative regulation of DNA recombination (GO:0045910)|replication fork processing (GO:0031297)|replication fork protection (GO:0048478)|response to UV (GO:0009411)	nuclear replication fork (GO:0043596)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|endodeoxyribonuclease activity (GO:0004520)|helicase activity (GO:0004386)|K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|upper_aerodigestive_tract(1)	20				BRCA - Breast invasive adenocarcinoma(221;0.135)		AGTGGAGTTCGGATTTGCTTG	0.507													G|||	2	0.000399361	0.0015	0.0	5008	,	,		19706	0.0		0.0	False		,,,				2504	0.0				p.R601X		Atlas-SNP	.											.	ZRANB3	109	.	0			c.C1801T						PASS	.	G	stop/ARG	10,3932		0,10,1961	158.0	155.0	156.0		1801	-0.6	0.0	2		156	1,8297		0,1,4148	yes	stop-gained	ZRANB3	NM_032143.2		0,11,6109	AA,AG,GG		0.0121,0.2537,0.0899		601/1080	135988236	11,12229	1971	4149	6120	SO:0001587	stop_gained	84083	exon13			GAGTTCGGATTTG	AL136824	CCDS46419.1, CCDS67963.1, CCDS74580.1	2q21.3	2013-05-13			ENSG00000121988	ENSG00000121988		"""Zinc fingers, RAN-binding domain containing"""	25249	protein-coding gene	gene with protein product						11230166	Standard	XM_005263809		Approved	DKFZP434B1727	uc002tum.3	Q5FWF4	OTTHUMG00000150475	ENST00000264159.6:c.1801C>T	2.37:g.135988236G>A	ENSP00000264159:p.Arg601*	349.0	0.0	0		323.0	145.0	0.448916	NM_032143	B3KYA1|B4E375|B5MDI3|D3DP76|E9PBP0|Q53SM1|Q6P2C4|Q8N1P4|Q9H0E8	Nonsense_Mutation	SNP	ENST00000264159.6	37	CCDS46419.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	36	5.734207	0.96865	0.002537	1.21E-4	ENSG00000121988	ENST00000538542;ENST00000283060;ENST00000401392;ENST00000264159;ENST00000536680	.	.	.	4.8	-0.643	0.11482	.	1.959680	0.01762	N	0.030630	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.5281	2.7512	0.05281	0.137:0.0772:0.2876:0.4982	.	.	.	.	X	66;66;601;601;601	.	ENSP00000264159:R601X	R	-	1	2	ZRANB3	135704706	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.257000	0.18369	-0.270000	0.09285	-0.375000	0.07067	CGA	G|1.000;A|0.000	0.000	strong		0.507	ZRANB3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318254.1	NM_032143	
TESK1	7016	hgsc.bcm.edu	37	9	35608962	35608962	+	Silent	SNP	C	C	T	rs148341917	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35608962C>T	ENST00000336395.5	+	10	1354	c.1104C>T	c.(1102-1104)ccC>ccT	p.P368P	MIR4667_ENST00000578933.1_RNA|CD72_ENST00000490239.1_5'Flank|TESK1_ENST00000498522.1_3'UTR	NM_006285.2	NP_006276.2	Q15569	TESK1_HUMAN	testis-specific kinase 1	368					cell junction assembly (GO:0034329)|spermatogenesis (GO:0007283)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	27			Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			CAGAATCACCCCCCAACTGGG	0.607													C|||	30	0.00599042	0.0129	0.0014	5008	,	,		17980	0.001		0.002	False		,,,				2504	0.0092				p.P368P		Atlas-SNP	.											.	TESK1	46	.	0			c.C1104T						PASS	.	C		63,4343	58.7+/-95.3	0,63,2140	63.0	70.0	68.0		1104	3.4	1.0	9	dbSNP_134	68	25,8575	17.3+/-56.4	0,25,4275	no	coding-synonymous	TESK1	NM_006285.2		0,88,6415	TT,TC,CC		0.2907,1.4299,0.6766		368/627	35608962	88,12918	2203	4300	6503	SO:0001819	synonymous_variant	7016	exon10			ATCACCCCCCAAC	D50863	CCDS6580.1	9p13	2010-04-27			ENSG00000107140	ENSG00000107140	2.7.12.1		11731	protein-coding gene	gene with protein product	"""testis-specific kinase-1"", ""testis specific kinase-1"""	601782				8537404	Standard	NM_006285		Approved		uc003zxa.3	Q15569	OTTHUMG00000019863	ENST00000336395.5:c.1104C>T	9.37:g.35608962C>T		59.0	0.0	0		73.0	38.0	0.520548	NM_006285	Q8IXZ8	Silent	SNP	ENST00000336395.5	37	CCDS6580.1																																																																																			C|0.994;T|0.006	0.006	strong		0.607	TESK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052314.1	NM_006285	
SLC28A2	9153	hgsc.bcm.edu	37	15	45556163	45556163	+	Silent	SNP	T	T	C	rs8023604	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:45556163T>C	ENST00000347644.3	+	6	596	c.531T>C	c.(529-531)ttT>ttC	p.F177F	CTD-2651B20.3_ENST00000560344.1_RNA|CTD-2651B20.3_ENST00000561404.1_RNA	NM_004212.3	NP_004203.2	O43868	S28A2_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 2	177					nucleobase-containing compound metabolic process (GO:0006139)|purine nucleoside transmembrane transport (GO:0015860)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside:sodium symporter activity (GO:0005415)|purine nucleoside transmembrane transporter activity (GO:0015211)			NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|ovary(4)|skin(1)	26		all_cancers(109;8.53e-07)|all_epithelial(112;1.39e-05)|Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;3.77e-16)|GBM - Glioblastoma multiforme(94;2.71e-06)	Mercaptopurine(DB01033)	TGATCCCCTTTGCAGGAATCT	0.507													C|||	866	0.172923	0.5734	0.0533	5008	,	,		19479	0.0		0.002	False		,,,				2504	0.0706				p.F177F	NSCLC(92;493 1501 26361 28917 47116)	Atlas-SNP	.											.	SLC28A2	64	.	0			c.T531C						PASS	.	C		2273,2123	578.0+/-384.6	611,1051,536	196.0	159.0	171.0		531	-6.4	0.5	15	dbSNP_116	171	13,8583	818.5+/-406.9	0,13,4285	no	coding-synonymous	SLC28A2	NM_004212.3		611,1064,4821	CC,CT,TT		0.1512,48.2939,17.5954		177/659	45556163	2286,10706	2198	4298	6496	SO:0001819	synonymous_variant	9153	exon6			CCCCTTTGCAGGA	U84392	CCDS10121.1	15q15	2013-07-17	2013-07-17		ENSG00000137860	ENSG00000137860		"""Solute carriers"""	11002	protein-coding gene	gene with protein product		606208	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 2"""			9435697	Standard	NM_004212		Approved	CNT2, SPNT1, HCNT2, HsT17153	uc001zva.2	O43868	OTTHUMG00000131426	ENST00000347644.3:c.531T>C	15.37:g.45556163T>C		189.0	0.0	0		177.0	82.0	0.463277	NM_004212	A8K7F9|O43239|Q52LZ0	Silent	SNP	ENST00000347644.3	37	CCDS10121.1																																																																																			T|0.841;C|0.159	0.159	strong		0.507	SLC28A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254219.2	NM_004212	
C8orf74	203076	hgsc.bcm.edu	37	8	10555263	10555263	+	Missense_Mutation	SNP	C	C	G	rs147047803	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10555263C>G	ENST00000304519.5	+	3	425	c.396C>G	c.(394-396)gaC>gaG	p.D132E	RP1L1_ENST00000329335.3_Intron	NM_001040032.1	NP_001035121	Q6P047	CH074_HUMAN	chromosome 8 open reading frame 74	132										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	13				COAD - Colon adenocarcinoma(149;0.0811)		TGGGCCAGGACCAGCAGGTCG	0.622													C|||	11	0.00219649	0.0083	0.0	5008	,	,		17486	0.0		0.0	False		,,,				2504	0.0				p.D132E		Atlas-SNP	.											.	C8orf74	28	.	0			c.C396G						PASS	.	C	GLU/ASP	33,4233		0,33,2100	163.0	169.0	167.0		396	-3.2	0.2	8	dbSNP_134	167	0,8450		0,0,4225	yes	missense	C8orf74	NM_001040032.1	45	0,33,6325	GG,GC,CC		0.0,0.7736,0.2595	benign	132/295	10555263	33,12683	2133	4225	6358	SO:0001583	missense	203076	exon3			CCAGGACCAGCAG	BC038534	CCDS47800.1	8p23.1	2012-04-17			ENSG00000171060	ENSG00000171060			32296	protein-coding gene	gene with protein product							Standard	NM_001040032		Approved		uc003wtd.1	Q6P047	OTTHUMG00000163807	ENST00000304519.5:c.396C>G	8.37:g.10555263C>G	ENSP00000307129:p.Asp132Glu	79.0	0.0	0		97.0	44.0	0.453608	NM_001040032	A2RUD6	Missense_Mutation	SNP	ENST00000304519.5	37	CCDS47800.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	C	0.118	-1.129786	0.01756	0.007736	0.0	ENSG00000171060	ENST00000304519	T	0.28666	1.6	5.2	-3.25	0.05079	.	0.639609	0.15360	N	0.266446	T	0.08133	0.0203	N	0.16656	0.425	0.09310	N	1	B	0.14012	0.009	B	0.11329	0.006	T	0.22695	-1.0209	10	0.15499	T	0.54	.	2.1908	0.03898	0.1217:0.2888:0.3579:0.2316	.	132	Q6P047	CH074_HUMAN	E	132	ENSP00000307129:D132E	ENSP00000307129:D132E	D	+	3	2	C8orf74	10592673	0.006000	0.16342	0.207000	0.23584	0.043000	0.13939	-1.025000	0.03600	-0.299000	0.08909	-1.334000	0.01262	GAC	C|0.997;G|0.003	0.003	strong		0.622	C8orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375675.1	NM_001040032	
ASB16	92591	hgsc.bcm.edu	37	17	42254165	42254165	+	Missense_Mutation	SNP	A	A	G	rs146134954	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:42254165A>G	ENST00000293414.1	+	3	713	c.629A>G	c.(628-630)cAg>cGg	p.Q210R	ASB16-AS1_ENST00000588785.1_RNA|ASB16-AS1_ENST00000592897.1_RNA|ASB16-AS1_ENST00000591166.1_RNA|ASB16-AS1_ENST00000585457.1_RNA	NM_080863.4	NP_543139.4	Q96NS5	ASB16_HUMAN	ankyrin repeat and SOCS box containing 16	210					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|liver(2)|lung(2)|prostate(1)	14		Breast(137;0.00765)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.114)		GGCGAGAGCCAGGAGACGCCC	0.672													A|||	65	0.0129792	0.0477	0.0029	5008	,	,		13770	0.0		0.0	False		,,,				2504	0.0				p.Q210R		Atlas-SNP	.											.	ASB16	34	.	0			c.A629G						PASS	.	A	ARG/GLN,	154,4252	103.4+/-141.9	4,146,2053	52.0	51.0	52.0		629,456	4.7	0.1	17	dbSNP_134	52	2,8598	2.2+/-6.3	0,2,4298	yes	missense,coding-synonymous	ASB16,C17orf65	NM_080863.4,NM_178542.3	43,	4,148,6351	GG,GA,AA		0.0233,3.4952,1.1994	benign,	210/454,152/194	42254165	156,12850	2203	4300	6503	SO:0001583	missense	92591	exon3			AGAGCCAGGAGAC	AK054727	CCDS11478.1	17q21.31	2013-01-10	2011-01-25		ENSG00000161664	ENSG00000161664		"""Ankyrin repeat domain containing"""	19768	protein-coding gene	gene with protein product		615056	"""ankyrin repeat and SOCS box-containing 16"""			12076535	Standard	NM_080863		Approved	FLJ30165	uc002ifl.1	Q96NS5	OTTHUMG00000181809	ENST00000293414.1:c.629A>G	17.37:g.42254165A>G	ENSP00000293414:p.Gln210Arg	67.0	0.0	0		60.0	19.0	0.316667	NM_080863	B2RBC0|Q8WXK0	Missense_Mutation	SNP	ENST00000293414.1	37	CCDS11478.1	29	0.013278388278388278	28	0.056910569105691054	1	0.0027624309392265192	0	0.0	0	0.0	A	2.058	-0.416098	0.04766	0.034952	2.33E-4	ENSG00000161664	ENST00000293414	T	0.63913	-0.07	4.73	4.73	0.59995	Ankyrin repeat-containing domain (3);	0.305652	0.34067	N	0.004299	T	0.05456	0.0144	N	0.16602	0.42	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.04650	-1.0936	10	0.10902	T	0.67	-8.7467	5.8244	0.18546	0.8141:0.0:0.1859:0.0	.	210	Q96NS5	ASB16_HUMAN	R	210	ENSP00000293414:Q210R	ENSP00000293414:Q210R	Q	+	2	0	ASB16	39609691	0.009000	0.17119	0.120000	0.21714	0.087000	0.18053	1.072000	0.30678	1.985000	0.57927	0.374000	0.22700	CAG	A|0.987;G|0.013	0.013	strong		0.672	ASB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457703.1		
TTC21B	79809	hgsc.bcm.edu	37	2	166758389	166758389	+	Missense_Mutation	SNP	C	C	T	rs76726265	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:166758389C>T	ENST00000243344.7	-	20	2737	c.2600G>A	c.(2599-2601)cGt>cAt	p.R867H		NM_024753.4	NP_079029.3	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	867			R -> C (in JBTS11; functionally null mutation in vitro). {ECO:0000269|PubMed:21258341}.|R -> H (found in a patient with Meckel- Gruber syndrome also carrying a homozygous variant in CC2D2A; functionally null mutation in vitro; dbSNP:rs76726265). {ECO:0000269|PubMed:21258341}.		forebrain dorsal/ventral pattern formation (GO:0021798)|intraciliary retrograde transport (GO:0035721)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|protein localization to cilium (GO:0061512)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|nuclear chromatin (GO:0000790)				breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(9)|lung(28)|ovary(2)|pancreas(2)|skin(2)|urinary_tract(1)	58						CATCTGAACACGTTTTAGTAC	0.378													C|||	6	0.00119808	0.0038	0.0014	5008	,	,		14632	0.0		0.0	False		,,,				2504	0.0				p.R867H		Atlas-SNP	.											TTC21B,NS,carcinoma,-1,1	TTC21B	130	1	0			c.G2600A						PASS	.	C	HIS/ARG	25,4381	31.7+/-61.6	0,25,2178	59.0	55.0	56.0		2600	5.7	1.0	2	dbSNP_131	56	0,8600		0,0,4300	yes	missense	TTC21B	NM_024753.3	29	0,25,6478	TT,TC,CC		0.0,0.5674,0.1922	probably-damaging	867/1317	166758389	25,12981	2203	4300	6503	SO:0001583	missense	79809	exon20			TGAACACGTTTTA	AB082523	CCDS33315.1	2q24.3	2014-09-04			ENSG00000123607	ENSG00000123607		"""Tetratricopeptide (TTC) repeat domain containing"", ""Intraflagellar transport homologs"""	25660	protein-coding gene	gene with protein product		612014				12056414, 21258341	Standard	NM_024753		Approved	FLJ11457, JBTS11, NPHP12, IFT139, THM1	uc002udk.3	Q7Z4L5	OTTHUMG00000154083	ENST00000243344.7:c.2600G>A	2.37:g.166758389C>T	ENSP00000243344:p.Arg867His	178.0	0.0	0		181.0	80.0	0.441989	NM_024753	A8MUZ3|Q3LIE4|Q53T84|Q6P4A1|Q6PIF5|Q8NCN3|Q96MA4|Q9HAK8	Missense_Mutation	SNP	ENST00000243344.7	37	CCDS33315.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	34	5.320668	0.95682	0.005674	0.0	ENSG00000123607	ENST00000243344	T	0.55234	0.53	5.7	5.7	0.88788	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.68054	0.2959	M	0.75884	2.315	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.73297	-0.4027	10	0.62326	D	0.03	-13.8163	19.8381	0.96666	0.0:1.0:0.0:0.0	.	867	Q7Z4L5	TT21B_HUMAN	H	867	ENSP00000243344:R867H	ENSP00000243344:R867H	R	-	2	0	TTC21B	166466635	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.061000	0.71148	2.692000	0.91855	0.650000	0.86243	CGT	C|0.998;T|0.002	0.002	strong		0.378	TTC21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333770.1	NM_024753	
SLC35C1	55343	hgsc.bcm.edu	37	11	45827783	45827783	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:45827783A>G	ENST00000314134.3	+	1	1827	c.431A>G	c.(430-432)aAt>aGt	p.N144S	SLC35C1_ENST00000456334.1_Missense_Mutation_p.N131S|SLC35C1_ENST00000442528.2_Missense_Mutation_p.N131S	NM_018389.4	NP_060859.4	Q96A29	FUCT1_HUMAN	solute carrier family 35 (GDP-fucose transporter), member C1	144					carbohydrate transport (GO:0008643)|lipid glycosylation (GO:0030259)|negative regulation of Notch signaling pathway (GO:0045746)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)				endometrium(3)|kidney(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	10				GBM - Glioblastoma multiforme(35;0.227)		GCCTTCTACAATGTGGGCCGC	0.587																																					p.N144S		Atlas-SNP	.											.	SLC35C1	23	.	0			c.A431G						PASS	.						137.0	96.0	110.0					11																	45827783		2203	4299	6502	SO:0001583	missense	55343	exon1			TCTACAATGTGGG		CCDS7914.1, CCDS44575.1	11p11.2	2014-09-17	2013-07-17			ENSG00000181830		"""Solute carriers"""	20197	protein-coding gene	gene with protein product		605881	"""solute carrier family 35, member C1"""			11326279, 11326280	Standard	NM_018389		Approved	FUCT1, FLJ11320	uc010rgm.2	Q96A29		ENST00000314134.3:c.431A>G	11.37:g.45827783A>G	ENSP00000313318:p.Asn144Ser	63.0	0.0	0		77.0	4.0	0.0519481	NM_018389	B2RDB2|Q9BV76|Q9NUJ8	Missense_Mutation	SNP	ENST00000314134.3	37	CCDS7914.1	.	.	.	.	.	.	.	.	.	.	A	13.73	2.323167	0.41096	.	.	ENSG00000181830	ENST00000442528;ENST00000456334;ENST00000530670;ENST00000314134;ENST00000530471;ENST00000540685	T;T;T;T	0.37915	1.17;1.17;1.17;1.17	4.64	4.64	0.57946	Drug/metabolite transporter (1);	0.049836	0.85682	D	0.000000	T	0.28732	0.0712	L	0.39898	1.24	0.42596	D	0.993269	B	0.22909	0.077	B	0.26614	0.071	T	0.08289	-1.0729	10	0.23302	T	0.38	-24.5504	10.2877	0.43577	0.8343:0.1656:0.0:0.0	.	144	Q96A29	FUCT1_HUMAN	S	131;131;65;144;131;144	ENSP00000412408:N131S;ENSP00000399779:N131S;ENSP00000313318:N144S;ENSP00000432669:N131S	ENSP00000313318:N144S	N	+	2	0	SLC35C1	45784359	0.978000	0.34361	1.000000	0.80357	0.992000	0.81027	4.671000	0.61590	1.738000	0.51689	0.460000	0.39030	AAT	.	.	none		0.587	SLC35C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390139.1	NM_018389	
MUC4	4585	hgsc.bcm.edu	37	3	195508382	195508382	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195508382G>A	ENST00000463781.3	-	2	10528	c.10069C>T	c.(10069-10071)Cac>Tac	p.H3357Y	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H3357Y	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)		GGGGTGGCGTGACCTGTGGAT	0.602																																					p.H3357Y		Atlas-SNP	.											.	MUC4	1505	.	0			c.C10069T						PASS	.						38.0	30.0	32.0					3																	195508382		689	1583	2272	SO:0001583	missense	4585	exon2			TGGCGTGACCTGT	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.10069C>T	3.37:g.195508382G>A	ENSP00000417498:p.His3357Tyr	417.0	0.0	0		354.0	69.0	0.194915	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	0.904	-0.721432	0.03182	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31510	1.51;1.49	1.03	-2.05	0.07321	.	.	.	.	.	T	0.13884	0.0336	N	0.14661	0.345	0.09310	N	1	B	0.15141	0.012	B	0.01281	0.0	T	0.29518	-1.0009	8	.	.	.	.	5.4087	0.16336	0.0:0.0:0.5637:0.4363	.	3229	E7ESK3	.	Y	3357	ENSP00000417498:H3357Y;ENSP00000420243:H3357Y	.	H	-	1	0	MUC4	196993161	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	-2.033000	0.01425	-0.784000	0.04528	0.089000	0.15464	CAC	.	.	none		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
LRTOMT	220074	hgsc.bcm.edu	37	11	71806515	71806515	+	Silent	SNP	A	A	G	rs150245488	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71806515A>G	ENST00000289488.2	+	6	906	c.528A>G	c.(526-528)aaA>aaG	p.K176K	LRTOMT_ENST00000307198.7_Intron|LRTOMT_ENST00000419228.1_Intron|LRTOMT_ENST00000439209.1_Intron|LAMTOR1_ENST00000535107.1_Intron|LRTOMT_ENST00000541614.1_Intron|LRTOMT_ENST00000440313.2_Intron|LAMTOR1_ENST00000545249.1_Intron|LRTOMT_ENST00000423494.2_Silent_p.K158K|LRTOMT_ENST00000324866.7_3'UTR|LRTOMT_ENST00000539587.1_Missense_Mutation_p.N42S|LRTOMT_ENST00000447974.1_Intron|LRTOMT_ENST00000538478.1_Silent_p.K176K|LRTOMT_ENST00000435085.1_Intron|LAMTOR1_ENST00000539797.1_5'Flank|LRTOMT_ENST00000539271.1_Missense_Mutation_p.N42S	NM_001271471.2|NM_145309.5	NP_001258400.1|NP_660352.1	Q96E66	LRC51_HUMAN	leucine rich transmembrane and O-methyltransferase domain containing	176						cytoplasm (GO:0005737)				large_intestine(2)|lung(1)|ovary(1)	4						AAGTCTGGAAACGCATGAACA	0.537													A|||	14	0.00279553	0.0106	0.0	5008	,	,		20529	0.0		0.0	False		,,,				2504	0.0				p.K176K		Atlas-SNP	.											.	LRTOMT	20	.	0			c.A528G						PASS	.	A	,,,	72,4328	64.7+/-102.0	1,70,2129	96.0	69.0	78.0		,,474,528	0.6	1.0	11	dbSNP_134	78	0,8586		0,0,4293	no	intron,intron,coding-synonymous,coding-synonymous	LRTOMT	NM_001145307.2,NM_001145308.2,NM_001205138.1,NM_145309.3	,,,	1,70,6422	GG,GA,AA		0.0,1.6364,0.5544	,,,	,,158/175,176/193	71806515	72,12914	2200	4293	6493	SO:0001819	synonymous_variant	220074	exon6			CTGGAAACGCATG		CCDS8208.1, CCDS44667.1, CCDS44668.1, CCDS55778.1, CCDS59227.1	11q13.4	2014-09-05	2013-08-19	2008-11-27	ENSG00000184154	ENSG00000184154			25033	protein-coding gene	gene with protein product		612414	"""leucine rich repeat containing 51"", ""deafness, autosomal recessive 63"""	LRRC51, DFNB63		18794526, 18953341	Standard	NM_145309		Approved	COMT2, CFAP111	uc010rqw.2	Q8WZ04	OTTHUMG00000154887	ENST00000289488.2:c.528A>G	11.37:g.71806515A>G		160.0	0.0	0		149.0	81.0	0.543624	NM_145309	B2R7X1|B6CZ35|B6CZ36|B6CZ37|B6CZ38|B6CZ39|B7Z5I4	Silent	SNP	ENST00000289488.2	37	CCDS8208.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	14.26	2.483004	0.44147	0.016364	0.0	ENSG00000184154	ENST00000539271;ENST00000539587	.	.	.	5.9	0.652	0.17823	.	.	.	.	.	T	0.47395	0.1443	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58446	-0.7635	5	0.87932	D	0	-16.0144	8.9883	0.36008	0.4707:0.0:0.5292:0.0	.	.	.	.	S	42	.	ENSP00000442267:N42S	N	+	2	0	LRTOMT	71484163	0.998000	0.40836	1.000000	0.80357	0.998000	0.95712	0.340000	0.19892	0.072000	0.16694	0.496000	0.49642	AAC	A|0.995;G|0.005	0.005	strong		0.537	LRTOMT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337504.1	NM_145309	
CEP192	55125	hgsc.bcm.edu	37	18	13055915	13055915	+	Missense_Mutation	SNP	A	A	C	rs11080623	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:13055915A>C	ENST00000325971.8	+	17	3131	c.1538A>C	c.(1537-1539)cAg>cCg	p.Q513P	CEP192_ENST00000430049.2_Missense_Mutation_p.Q634P|CEP192_ENST00000506447.1_Missense_Mutation_p.Q1109P			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	513			Q -> P (in dbSNP:rs11080623).		centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						TCTATTATCCAGAATAACTCT	0.393													A|||	39	0.00778754	0.0008	0.0187	5008	,	,		21179	0.0		0.0239	False		,,,				2504	0.001				p.Q1109P		Atlas-SNP	.											.	CEP192	340	.	0			c.A3326C						PASS	.	A	PRO/GLN	22,4384	28.1+/-56.4	0,22,2181	60.0	59.0	59.0		3326	-0.5	0.1	18	dbSNP_120	59	276,8324	103.6+/-164.7	3,270,4027	yes	missense	CEP192	NM_032142.3	76	3,292,6208	CC,CA,AA		3.2093,0.4993,2.2913	benign	1109/2538	13055915	298,12708	2203	4300	6503	SO:0001583	missense	55125	exon19			TTATCCAGAATAA	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.1538A>C	18.37:g.13055915A>C	ENSP00000317156:p.Gln513Pro	125.0	0.0	0		107.0	50.0	0.46729	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	37		31	0.014194139194139194	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	22	0.029023746701846966	A	9.745	1.165868	0.21538	0.004993	0.032093	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049	T;T;T	0.24538	1.85;1.85;1.85	4.41	-0.462	0.12168	.	0.484808	0.17160	N	0.184713	T	0.06234	0.0161	L	0.47716	1.5	0.09310	N	1	B;B;B	0.17465	0.011;0.011;0.022	B;B;B	0.15484	0.007;0.007;0.013	T	0.19811	-1.0294	10	0.23891	T	0.37	-1.5367	7.8859	0.29651	0.5467:0.3343:0.0:0.119	rs11080623;rs52829180;rs11080623	634;1109;513	C9JT09;E9PF99;Q8TEP8	.;.;CE192_HUMAN	P	1109;513;513;634	ENSP00000427550:Q1109P;ENSP00000317156:Q513P;ENSP00000389190:Q634P	ENSP00000317156:Q513P	Q	+	2	0	CEP192	13045915	0.013000	0.17824	0.147000	0.22382	0.076000	0.17211	1.283000	0.33237	0.132000	0.18615	0.460000	0.39030	CAG	A|0.980;C|0.020	0.020	strong		0.393	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
TARS2	80222	hgsc.bcm.edu	37	1	150470182	150470182	+	Silent	SNP	A	A	G	rs115388015	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:150470182A>G	ENST00000369064.3	+	10	1231	c.1197A>G	c.(1195-1197)acA>acG	p.T399T	TARS2_ENST00000463555.1_3'UTR|TARS2_ENST00000606933.1_Silent_p.T317T|TARS2_ENST00000438568.2_3'UTR|TARS2_ENST00000369054.2_Silent_p.T269T	NM_025150.3	NP_079426.2	Q9BW92	SYTM_HUMAN	threonyl-tRNA synthetase 2, mitochondrial (putative)	399					gene expression (GO:0010467)|mitochondrial threonyl-tRNA aminoacylation (GO:0070159)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|threonine-tRNA ligase activity (GO:0004829)			cervix(1)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	35	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.51e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)		L-Threonine(DB00156)	GGCATATCACAGATACACTCG	0.512													A|||	83	0.0165735	0.059	0.0072	5008	,	,		16357	0.0		0.0	False		,,,				2504	0.0				p.T399T		Atlas-SNP	.											.	TARS2	91	.	0			c.A1197G						PASS	.	A		210,4196	128.6+/-165.4	9,192,2002	56.0	49.0	51.0		1197	-0.3	0.0	1	dbSNP_132	51	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	TARS2	NM_025150.3		9,195,6299	GG,GA,AA		0.0349,4.7662,1.6377		399/719	150470182	213,12793	2203	4300	6503	SO:0001819	synonymous_variant	80222	exon10			TATCACAGATACA	BC007824	CCDS952.1, CCDS60251.1, CCDS60252.1	1q21.2	2012-10-26	2007-02-23	2007-02-23	ENSG00000143374	ENSG00000143374	6.1.1.3	"""Aminoacyl tRNA synthetases / Class II"""	30740	protein-coding gene	gene with protein product	"""threonine tRNA ligase 2, mitochondrial"""	612805	"""threonyl-tRNA synthetase-like 1"""	TARSL1			Standard	NM_001271895		Approved	FLJ12528	uc001euq.4	Q9BW92	OTTHUMG00000012809	ENST00000369064.3:c.1197A>G	1.37:g.150470182A>G		67.0	0.0	0		60.0	28.0	0.466667	NM_025150	Q53GW7|Q96I50|Q9H9V2	Silent	SNP	ENST00000369064.3	37	CCDS952.1																																																																																			A|0.981;G|0.019	0.019	strong		0.512	TARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035847.1	NM_025150	
NEU2	4759	hgsc.bcm.edu	37	2	233899148	233899148	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:233899148T>C	ENST00000233840.3	+	2	524	c.524T>C	c.(523-525)gTg>gCg	p.V175A		NM_005383.2	NP_005374.2	Q9Y3R4	NEUR2_HUMAN	sialidase 2 (cytosolic sialidase)	175					ganglioside catabolic process (GO:0006689)|glycosphingolipid metabolic process (GO:0006687)|oligosaccharide catabolic process (GO:0009313)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	exo-alpha-(2->3)-sialidase activity (GO:0052794)|exo-alpha-(2->6)-sialidase activity (GO:0052795)|exo-alpha-(2->8)-sialidase activity (GO:0052796)			endometrium(3)|large_intestine(2)|lung(10)|skin(2)|urinary_tract(1)	18		Breast(86;0.00279)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0271)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0839)		Epithelial(121;7.17e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0488)	Oseltamivir(DB00198)|Zanamivir(DB00558)	CGGAGCCTGGTGGTGCCCGCC	0.657																																					p.V175A		Atlas-SNP	.											.	NEU2	42	.	0			c.T524C						PASS	.																																			SO:0001583	missense	4759	exon2			GCCTGGTGGTGCC	Y16535	CCDS2501.1	2q37	2008-05-27			ENSG00000115488	ENSG00000115488			7759	protein-coding gene	gene with protein product	"""N-acetyl-alpha-neuraminidase 2"""	605528				10191093, 14613940	Standard	NM_005383		Approved	SIAL2	uc010zmn.2	Q9Y3R4	OTTHUMG00000133274	ENST00000233840.3:c.524T>C	2.37:g.233899148T>C	ENSP00000233840:p.Val175Ala	98.0	0.0	0		104.0	48.0	0.461538	NM_005383	Q3KNW4|Q6NTB4	Missense_Mutation	SNP	ENST00000233840.3	37	CCDS2501.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.120495	0.77323	.	.	ENSG00000115488	ENST00000233840	D	0.85955	-2.05	4.88	4.88	0.63580	Neuraminidase (2);	0.234313	0.29707	N	0.011404	D	0.90113	0.6911	L	0.60455	1.87	0.38849	D	0.956227	D	0.65815	0.995	D	0.70487	0.969	D	0.91831	0.5475	10	0.87932	D	0	-13.5728	13.6972	0.62587	0.0:0.0:0.0:1.0	.	175	Q9Y3R4	NEUR2_HUMAN	A	175	ENSP00000233840:V175A	ENSP00000233840:V175A	V	+	2	0	NEU2	233607392	1.000000	0.71417	0.994000	0.49952	0.610000	0.37248	7.783000	0.85696	1.821000	0.53095	0.459000	0.35465	GTG	.	.	none		0.657	NEU2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257053.2	NM_005383	
FPGT	8790	hgsc.bcm.edu	37	1	74670277	74670277	+	Silent	SNP	G	G	A	rs139749795	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:74670277G>A	ENST00000609362.1	+	4	583	c.546G>A	c.(544-546)agG>agA	p.R182R	FPGT_ENST00000534056.1_Intron|FPGT-TNNI3K_ENST00000533006.1_Intron|FPGT_ENST00000370894.5_Intron|FPGT-TNNI3K_ENST00000370895.1_Intron|FPGT-TNNI3K_ENST00000557284.2_Intron|FPGT_ENST00000467578.2_3'UTR|FPGT_ENST00000524915.1_Intron|FPGT-TNNI3K_ENST00000370899.3_Intron|FPGT-TNNI3K_ENST00000370893.1_Intron|FPGT_ENST00000370898.3_Silent_p.R195R|TNNI3K_ENST00000370891.2_Intron	NM_003838.4	NP_003829.3	O14772	FPGT_HUMAN	fucose-1-phosphate guanylyltransferase	182					fucose metabolic process (GO:0006004)	cytoplasm (GO:0005737)	catalytic activity (GO:0003824)|fucose-1-phosphate guanylyltransferase activity (GO:0047341)|GTP binding (GO:0005525)	p.R182R(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(4)|skin(1)|urinary_tract(1)	39						AGTTTATTAGGTTTGACAAAC	0.353													G|||	15	0.00299521	0.0113	0.0	5008	,	,		17320	0.0		0.0	False		,,,				2504	0.0				p.R182R		Atlas-SNP	.											FPGT,NS,carcinoma,0,1	FPGT	77	1	1	Substitution - coding silent(1)	lung(1)	c.G546A						PASS	.	G	,,,,	49,4357	51.6+/-87.1	2,45,2156	113.0	111.0	111.0		,,,,546	-11.1	0.0	1	dbSNP_134	111	0,8600		0,0,4300	no	intron,intron,intron,intron,coding-synonymous	FPGT,FPGT-TNNI3K	NM_001112808.2,NM_001199327.1,NM_001199328.1,NM_001199329.1,NM_003838.3	,,,,	2,45,6456	AA,AG,GG		0.0,1.1121,0.3767	,,,,	,,,,182/595	74670277	49,12957	2203	4300	6503	SO:0001819	synonymous_variant	8790	exon4			TATTAGGTTTGAC	AF017445	CCDS663.1, CCDS663.2	1p31.1	2013-09-24			ENSG00000254685	ENSG00000254685	2.7.7.30		3825	protein-coding gene	gene with protein product		603609				9804772	Standard	NM_003838		Approved	GFPP		O14772	OTTHUMG00000009571	ENST00000609362.1:c.546G>A	1.37:g.74670277G>A		185.0	0.0	0		166.0	78.0	0.46988	NM_003838	A6NMH3|B4DRX2|B4E2Y7|E9PNQ2|Q8N5J7	Silent	SNP	ENST00000609362.1	37	CCDS663.1																																																																																			G|0.996;A|0.004	0.004	strong		0.353	FPGT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SMC2	10592	hgsc.bcm.edu	37	9	106888978	106888978	+	Silent	SNP	C	C	T	rs6479217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:106888978C>T	ENST00000286398.7	+	19	2796	c.2508C>T	c.(2506-2508)taC>taT	p.Y836Y	SMC2_ENST00000374793.3_Silent_p.Y836Y|SMC2_ENST00000303219.8_Silent_p.Y836Y|SMC2_ENST00000374787.3_Silent_p.Y836Y	NM_001042551.1|NM_001265602.1|NM_006444.2	NP_001036016.1|NP_001252531.1|NP_006435.2	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	836					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(14)|ovary(5)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	48						ATACATCTTACAAACAACAGC	0.348													C|||	326	0.0650958	0.2209	0.013	5008	,	,		16974	0.0129		0.007	False		,,,				2504	0.0051				p.Y836Y		Atlas-SNP	.											.	SMC2	127	.	0			c.C2508T						PASS	.	C	,,	745,3661	303.5+/-288.0	55,635,1513	82.0	83.0	83.0		2508,2508,2508	-0.1	0.0	9	dbSNP_116	83	62,8538	38.8+/-94.9	0,62,4238	no	coding-synonymous,coding-synonymous,coding-synonymous	SMC2	NM_001042550.1,NM_001042551.1,NM_006444.2	,,	55,697,5751	TT,TC,CC		0.7209,16.9088,6.2048	,,	836/1198,836/1198,836/1198	106888978	807,12199	2203	4300	6503	SO:0001819	synonymous_variant	10592	exon19			ATCTTACAAACAA	AF092563	CCDS35086.1	9q31.1	2008-05-14	2006-07-06	2006-07-06	ENSG00000136824	ENSG00000136824		"""Structural maintenance of chromosomes proteins"""	14011	protein-coding gene	gene with protein product		605576	"""SMC2 (structural maintenance of chromosomes 2, yeast)-like 1"", ""SMC2 structural maintenance of chromosomes 2-like 1 (yeast)"""	SMC2L1		9789013	Standard	NM_006444		Approved	hCAP-E, CAP-E	uc011lvl.2	O95347	OTTHUMG00000020401	ENST00000286398.7:c.2508C>T	9.37:g.106888978C>T		43.0	0.0	0		41.0	8.0	0.195122	NM_006444	Q6IEE0|Q9P1P2	Silent	SNP	ENST00000286398.7	37	CCDS35086.1																																																																																			C|0.935;T|0.065	0.065	strong		0.348	SMC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053470.1		
FZD1	8321	hgsc.bcm.edu	37	7	90895944	90895944	+	Silent	SNP	C	C	T	rs2232161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:90895944C>T	ENST00000287934.2	+	1	2162	c.1749C>T	c.(1747-1749)caC>caT	p.H583H		NM_003505.1	NP_003496.1	Q9UP38	FZD1_HUMAN	frizzled class receptor 1	583					autocrine signaling (GO:0035425)|axonogenesis (GO:0007409)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation (GO:0044338)|canonical Wnt signaling pathway involved in osteoblast differentiation (GO:0044339)|cell-cell signaling (GO:0007267)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hard palate development (GO:0060022)|lung alveolus development (GO:0048286)|membranous septum morphogenesis (GO:0003149)|muscular septum morphogenesis (GO:0003150)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron differentiation (GO:0030182)|outflow tract morphogenesis (GO:0003151)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|vasculature development (GO:0001944)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	apical part of cell (GO:0045177)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|neuron projection membrane (GO:0032589)|plasma membrane (GO:0005886)	frizzled binding (GO:0005109)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|receptor binding (GO:0005102)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24	all_cancers(62;3.1e-10)|all_epithelial(64;1.66e-08)|Breast(17;0.000635)|Lung NSC(181;0.153)|all_lung(186;0.154)|all_hematologic(106;0.215)		STAD - Stomach adenocarcinoma(171;0.0134)			CCTGCCCTCACCTCCAGGCGG	0.637													C|||	85	0.0169728	0.0605	0.0072	5008	,	,		13904	0.0		0.0	False		,,,				2504	0.0				p.H583H		Atlas-SNP	.											FZD1,NS,carcinoma,0,2	FZD1	64	2	0			c.C1749T						PASS	.	C		238,4168	130.2+/-166.9	9,220,1974	30.0	28.0	29.0		1749	2.9	1.0	7	dbSNP_98	29	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FZD1	NM_003505.1		9,221,6273	TT,TC,CC		0.0116,5.4017,1.8376		583/648	90895944	239,12767	2203	4300	6503	SO:0001819	synonymous_variant	8321	exon1			CCCTCACCTCCAG	AB017363	CCDS5620.1	7q21	2014-01-29	2014-01-29		ENSG00000157240	ENSG00000157240		"""GPCR / Class F : Frizzled receptors"""	4038	protein-coding gene	gene with protein product	"""Wnt receptor"", ""frizzled, Drosophila, homolog of, 1"""	603408	"""frizzled (Drosophila) homolog 1"", ""frizzled homolog 1 (Drosophila)"", ""frizzled 1, seven transmembrane spanning receptor"", ""frizzled family receptor 1"""			9813155	Standard	NM_003505		Approved	DKFZp564G072	uc003ula.3	Q9UP38	OTTHUMG00000023046	ENST00000287934.2:c.1749C>T	7.37:g.90895944C>T		70.0	0.0	0		76.0	36.0	0.473684	NM_003505	A4D1E8|O94815|Q549T8	Silent	SNP	ENST00000287934.2	37	CCDS5620.1																																																																																			C|0.983;T|0.017	0.017	strong		0.637	FZD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059367.2	NM_003505	
POM121L2	94026	hgsc.bcm.edu	37	6	27279185	27279185	+	Silent	SNP	A	A	T	rs16897553	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:27279185A>T	ENST00000444565.1	-	1	764	c.765T>A	c.(763-765)gcT>gcA	p.A255A	POM121L2_ENST00000377451.2_Silent_p.A255A	NM_033482.3	NP_258443.2	Q96KW2	P12L2_HUMAN	POM121 transmembrane nucleoporin-like 2	255										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1)	7						AGCTGCCAATAGCATTCCTTT	0.498													A|||	151	0.0301518	0.0983	0.0159	5008	,	,		18721	0.001		0.005	False		,,,				2504	0.0041				p.A255A		Atlas-SNP	.											.	POM121L2	61	.	0			c.T765A						PASS	.	A		118,1266		4,110,578	21.0	18.0	19.0		765	-8.0	0.0	6	dbSNP_123	19	38,3144		0,38,1553	no	coding-synonymous	POM121L2	NM_033482.3		4,148,2131	TT,TA,AA		1.1942,8.526,3.4166		255/1036	27279185	156,4410	692	1591	2283	SO:0001819	synonymous_variant	94026	exon1			GCCAATAGCATTC	AL021808	CCDS59497.1	6p21.3	2012-03-13	2012-03-13		ENSG00000158553	ENSG00000158553			13973	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 2 (rat)"", ""POM121 membrane glycoprotein-like 2"""				Standard	NM_033482		Approved	POM121-L	uc011dku.1	Q96KW2	OTTHUMG00000014475	ENST00000444565.1:c.765T>A	6.37:g.27279185A>T		81.0	0.0	0		94.0	51.0	0.542553	NM_033482	C9J1I7	Silent	SNP	ENST00000444565.1	37	CCDS59497.1																																																																																			A|0.953;T|0.047	0.047	strong		0.498	POM121L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040143.2	NM_033482	
ZNF594	84622	hgsc.bcm.edu	37	17	5085245	5085245	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5085245G>A	ENST00000399604.4	-	1	2447	c.2307C>T	c.(2305-2307)acC>acT	p.T769T	ZNF594_ENST00000575779.1_Silent_p.T769T			Q96JF6	ZN594_HUMAN	zinc finger protein 594	769					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						TGCCCTGGAAGGTCCTACTAC	0.413																																					p.T769T		Atlas-SNP	.											.	ZNF594	89	.	0			c.C2307T						PASS	.						205.0	206.0	206.0					17																	5085245		1989	4182	6171	SO:0001819	synonymous_variant	84622	exon2			CTGGAAGGTCCTA	AB058774	CCDS42241.1	17p13	2013-01-08			ENSG00000180626	ENSG00000180626		"""Zinc fingers, C2H2-type"""	29392	protein-coding gene	gene with protein product						11347906	Standard	NM_032530		Approved	KIAA1871	uc010cla.1	Q96JF6	OTTHUMG00000132059	ENST00000399604.4:c.2307C>T	17.37:g.5085245G>A		154.0	0.0	0		100.0	18.0	0.18	NM_032530	Q6RFS0	Silent	SNP	ENST00000399604.4	37	CCDS42241.1																																																																																			.	.	none		0.413	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737	
CDC42BPA	8476	hgsc.bcm.edu	37	1	227504745	227504745	+	Silent	SNP	A	A	G	rs144296174		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:227504745A>G	ENST00000366769.3	-	1	1430	c.139T>C	c.(139-141)Ttg>Ctg	p.L47L	CDC42BPA_ENST00000535525.1_Silent_p.L47L|CDC42BPA_ENST00000334218.5_Silent_p.L47L|CDC42BPA_ENST00000366764.2_Silent_p.L47L|CDC42BPA_ENST00000366767.3_Silent_p.L47L|CDC42BPA_ENST00000366765.3_Silent_p.L47L|CDC42BPA_ENST00000366766.2_Silent_p.L47L	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)											NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				TCTCTTCTCAATGGAGAATTA	0.378													a|||	1	0.000199681	0.0008	0.0	5008	,	,		18255	0.0		0.0	False		,,,				2504	0.0				p.L47L		Atlas-SNP	.											.	CDC42BPA	528	.	0			c.T139C						PASS	.	A	,	5,4401	9.9+/-24.2	0,5,2198	102.0	96.0	98.0		139,139	-1.5	0.8	1	dbSNP_134	98	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CDC42BPA	NM_003607.3,NM_014826.4	,	0,5,6498	GG,GA,AA		0.0,0.1135,0.0384	,	47/1720,47/1639	227504745	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	8476	exon1			TTCTCAATGGAGA	U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776			1737	protein-coding gene	gene with protein product	"""myotonic dystrophy kinase-related Cdc42-binding kinase"""	603412	"""CDC42-binding protein kinase alpha (DMPK-like)"""				Standard	NM_003607		Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.139T>C	1.37:g.227504745A>G		129.0	0.0	0		167.0	84.0	0.502994	NM_003607		Silent	SNP	ENST00000366769.3	37	CCDS1558.1																																																																																			A|1.000;G|0.000	0.000	strong		0.378	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826	
PLEC	5339	hgsc.bcm.edu	37	8	145007409	145007409	+	Silent	SNP	G	G	A	rs115081018	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145007409G>A	ENST00000322810.4	-	13	1954	c.1785C>T	c.(1783-1785)acC>acT	p.T595T	PLEC_ENST00000398774.2_Silent_p.T426T|PLEC_ENST00000354958.2_Silent_p.T436T|PLEC_ENST00000345136.3_Silent_p.T458T|PLEC_ENST00000357649.2_Silent_p.T462T|PLEC_ENST00000354589.3_Silent_p.T458T|PLEC_ENST00000436759.2_Silent_p.T485T|PLEC_ENST00000527096.1_Silent_p.T481T|PLEC_ENST00000356346.3_Silent_p.T444T	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	595	Globular 1.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						CATCCTTGAGGGTCTGCACGT	0.677													G|||	83	0.0165735	0.059	0.0072	5008	,	,		16349	0.0		0.0	False		,,,				2504	0.0				p.T595T		Atlas-SNP	.											.	PLEC	1144	.	0			c.C1785T						PASS	.	G	,,,,,,,	160,3982		4,152,1915	63.0	72.0	69.0		1455,1332,1308,1785,1278,1374,1386,1374	1.0	1.0	8	dbSNP_132	69	4,8358		0,4,4177	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	4,156,6092	AA,AG,GG		0.0478,3.8629,1.3116	,,,,,,,	485/4575,444/4534,436/4526,595/4685,426/4516,458/4548,462/4552,458/4548	145007409	164,12340	2071	4181	6252	SO:0001819	synonymous_variant	5339	exon13			CTTGAGGGTCTGC	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.1785C>T	8.37:g.145007409G>A		118.0	0.0	0		119.0	62.0	0.521008	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			G|0.988;A|0.012	0.012	strong		0.677	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
HMMR	3161	hgsc.bcm.edu	37	5	162910165	162910165	+	Missense_Mutation	SNP	G	G	C	rs2230362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:162910165G>C	ENST00000358715.3	+	14	1705	c.1669G>C	c.(1669-1671)Gat>Cat	p.D557H	HMMR_ENST00000353866.3_Missense_Mutation_p.D542H|RP11-80G7.1_ENST00000514724.2_RNA|RP11-80G7.1_ENST00000521666.1_RNA|HMMR_ENST00000393915.4_Missense_Mutation_p.D558H|HMMR_ENST00000432118.2_Missense_Mutation_p.D471H			O75330	HMMR_HUMAN	hyaluronan-mediated motility receptor (RHAMM)	557			D -> H (in dbSNP:rs2230362).		carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)			cervix(1)|kidney(3)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	23	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848)	Hyaluronan(DB08818)	ACAGCTGGAAGATGAAGAAGG	0.313													G|||	46	0.0091853	0.0287	0.0115	5008	,	,		17759	0.0		0.0	False		,,,				2504	0.0				p.D558H		Atlas-SNP	.											.	HMMR	64	.	0			c.G1672C						PASS	.	G	HIS/ASP,HIS/ASP,HIS/ASP,HIS/ASP	103,4303		1,101,2101	53.0	54.0	53.0		1672,1411,1669,1624	3.2	0.9	5	dbSNP_98	53	0,8598		0,0,4299	yes	missense,missense,missense,missense	HMMR	NM_001142556.1,NM_001142557.1,NM_012484.2,NM_012485.2	81,81,81,81	1,101,6400	CC,CG,GG		0.0,2.3377,0.7921	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	558/726,471/639,557/725,542/710	162910165	103,12901	2203	4299	6502	SO:0001583	missense	3161	exon14			CTGGAAGATGAAG	U29343	CCDS4362.1, CCDS4363.1, CCDS47334.1, CCDS47335.1	5q34	2013-09-19			ENSG00000072571	ENSG00000072571		"""CD molecules"""	5012	protein-coding gene	gene with protein product		600936					Standard	NM_001142556		Approved	RHAMM, CD168	uc003lzh.3	O75330	OTTHUMG00000130381	ENST00000358715.3:c.1669G>C	5.37:g.162910165G>C	ENSP00000351554:p.Asp557His	104.0	0.0	0		119.0	48.0	0.403361	NM_001142556	A8K3G2|B4E114|D3DQK9|D3DQL0|E9PCS0|Q32N02|Q92767	Missense_Mutation	SNP	ENST00000358715.3	37	CCDS4362.1	17	0.007783882783882784	12	0.024390243902439025	5	0.013812154696132596	0	0.0	0	0.0	G	9.635	1.137453	0.21123	0.023377	0.0	ENSG00000072571	ENST00000416990;ENST00000353866;ENST00000393915;ENST00000426586;ENST00000432118;ENST00000358715	T;T;T;T;T	0.07800	3.16;3.16;3.16;3.16;3.16	5.03	3.24	0.37175	.	0.678925	0.15280	N	0.270748	T	0.02304	0.0071	N	0.08118	0	0.09310	N	1	P;P;P;P	0.44380	0.697;0.755;0.834;0.834	B;B;B;B	0.41036	0.332;0.346;0.319;0.319	T	0.36553	-0.9743	10	0.49607	T	0.09	-4.1167	11.5254	0.50576	0.1543:0.0:0.8457:0.0	rs2230362;rs2230362	471;558;542;557	O75330-4;O75330-3;O75330-2;O75330	.;.;.;HMMR_HUMAN	H	443;542;558;534;471;557	ENSP00000400527:D443H;ENSP00000185942:D542H;ENSP00000377492:D558H;ENSP00000402673:D471H;ENSP00000351554:D557H	ENSP00000185942:D542H	D	+	1	0	HMMR	162842743	0.991000	0.36638	0.881000	0.34555	0.305000	0.27757	1.054000	0.30455	1.482000	0.48325	0.655000	0.94253	GAT	G|0.990;C|0.010	0.010	strong		0.313	HMMR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252752.1	NM_012484	
CPNE2	221184	hgsc.bcm.edu	37	16	57144689	57144689	+	Missense_Mutation	SNP	C	C	T	rs141954860		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57144689C>T	ENST00000535318.2	+	3	396	c.35C>T	c.(34-36)gCg>gTg	p.A12V	CPNE2_ENST00000290776.8_Missense_Mutation_p.A12V|CPNE2_ENST00000565874.1_Missense_Mutation_p.A12V|CPNE2_ENST00000537605.1_5'UTR			Q96FN4	CPNE2_HUMAN	copine II	12	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.					extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|endometrium(4)|large_intestine(4)|lung(5)|ovary(1)|skin(5)	21		all_neural(199;0.224)				GCCCCAGCAGCGGGGGCAGCC	0.642													c|||	1	0.000199681	0.0008	0.0	5008	,	,		13191	0.0		0.0	False		,,,				2504	0.0				p.A12V		Atlas-SNP	.											.	CPNE2	48	.	0			c.C35T						PASS	.	C	VAL/ALA	0,4394		0,0,2197	28.0	27.0	28.0		35	-2.0	0.0	16	dbSNP_134	28	6,8592		0,6,4293	no	missense	CPNE2	NM_152727.5	64	0,6,6490	TT,TC,CC		0.0698,0.0,0.0462	benign	12/549	57144689	6,12986	2197	4299	6496	SO:0001583	missense	221184	exon2			CAGCAGCGGGGGC		CCDS10774.1	16q13	2008-02-05			ENSG00000140848	ENSG00000140848			2315	protein-coding gene	gene with protein product		604206				9430674	Standard	NM_152727		Approved	CPN2	uc002eks.2	Q96FN4	OTTHUMG00000133471	ENST00000535318.2:c.35C>T	16.37:g.57144689C>T	ENSP00000439018:p.Ala12Val	114.0	0.0	0		123.0	66.0	0.536585	NM_152727	Q68D19|Q719H8|Q86XP9	Missense_Mutation	SNP	ENST00000535318.2	37	CCDS10774.1	.	.	.	.	.	.	.	.	.	.	C	13.92	2.381069	0.42207	0.0	6.98E-4	ENSG00000140848	ENST00000290776;ENST00000535318	T;T	0.05319	3.46;3.46	5.08	-1.97	0.07503	C2 calcium/lipid-binding domain, CaLB (1);	1.227400	0.05504	N	0.558977	T	0.04861	0.0131	N	0.24115	0.695	0.09310	N	0.999999	B;B	0.13145	0.007;0.001	B;B	0.04013	0.001;0.001	T	0.45056	-0.9287	10	0.33141	T	0.24	-14.5631	7.8677	0.29547	0.0:0.5348:0.2084:0.2568	.	12;12	A8K8A4;Q96FN4	.;CPNE2_HUMAN	V	12	ENSP00000290776:A12V;ENSP00000439018:A12V	ENSP00000290776:A12V	A	+	2	0	CPNE2	55702190	0.000000	0.05858	0.000000	0.03702	0.234000	0.25298	-0.045000	0.12003	-0.152000	0.11156	-0.201000	0.12746	GCG	C|0.999;T|0.001	0.001	strong		0.642	CPNE2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432986.2	NM_152727	
DNAH9	1770	hgsc.bcm.edu	37	17	11583192	11583192	+	Missense_Mutation	SNP	C	C	T	rs8070501	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:11583192C>T	ENST00000262442.4	+	18	3540	c.3472C>T	c.(3472-3474)Cgg>Tgg	p.R1158W	DNAH9_ENST00000454412.2_Missense_Mutation_p.R1158W	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	1158	Stem. {ECO:0000250}.		R -> W (in dbSNP:rs8070501).		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)		TGTTAAAGAACGGCAGAGTAA	0.408													C|||	57	0.0113818	0.0408	0.0029	5008	,	,		18781	0.001		0.0	False		,,,				2504	0.0				p.R1158W		Atlas-SNP	.											DNAH9,rectum,carcinoma,0,1	DNAH9	695	1	0			c.C3472T						PASS	.	C	TRP/ARG	164,4242	111.6+/-149.8	6,152,2045	136.0	129.0	132.0		3472	2.5	0.9	17	dbSNP_116	132	2,8598	1.2+/-3.3	0,2,4298	yes	missense	DNAH9	NM_001372.3	101	6,154,6343	TT,TC,CC		0.0233,3.7222,1.2763	probably-damaging	1158/4487	11583192	166,12840	2203	4300	6503	SO:0001583	missense	1770	exon18			AAAGAACGGCAGA	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.3472C>T	17.37:g.11583192C>T	ENSP00000262442:p.Arg1158Trp	90.0	0.0	0		99.0	50.0	0.50505	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	C	14.02	2.409862	0.42715	0.037222	2.33E-4	ENSG00000007174	ENST00000262442;ENST00000454412	T;T	0.25414	1.8;1.8	5.69	2.5	0.30297	.	0.257159	0.32343	N	0.006221	T	0.25717	0.0626	M	0.89840	3.065	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.60865	-0.7178	10	0.87932	D	0	.	16.2874	0.82727	0.6259:0.3741:0.0:0.0	rs8070501;rs52812603;rs56633662;rs8070501	1158	Q9NYC9	DYH9_HUMAN	W	1158	ENSP00000262442:R1158W;ENSP00000414874:R1158W	ENSP00000262442:R1158W	R	+	1	2	DNAH9	11523917	0.585000	0.26774	0.926000	0.36857	0.245000	0.25701	0.963000	0.29293	0.294000	0.22547	0.650000	0.86243	CGG	C|0.988;T|0.012	0.012	strong		0.408	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110539175	110539175	+	Missense_Mutation	SNP	T	T	A	rs141977750	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:110539175T>A	ENST00000378402.5	+	77	12751	c.12647T>A	c.(12646-12648)aTt>aAt	p.I4216N		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	4216					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			ACTGTAGTAATTAGCTGTCTG	0.418										HNSCC(38;0.096)			T|||	46	0.0091853	0.0325	0.0043	5008	,	,		17708	0.0		0.0	False		,,,				2504	0.0				p.I4216N		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.T12647A						PASS	.	T	ASN/ILE	77,3947		0,77,1935	93.0	98.0	96.0		12647	1.8	0.0	8	dbSNP_134	96	0,8418		0,0,4209	yes	missense	PKHD1L1	NM_177531.4	149	0,77,6144	AA,AT,TT		0.0,1.9135,0.6189	benign	4216/4244	110539175	77,12365	2012	4209	6221	SO:0001583	missense	93035	exon77			TAGTAATTAGCTG	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.12647T>A	8.37:g.110539175T>A	ENSP00000367655:p.Ile4216Asn	162.0	0.0	0		204.0	105.0	0.514706	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	16	0.007326007326007326	14	0.028455284552845527	2	0.0055248618784530384	0	0.0	0	0.0	T	7.650	0.682659	0.14907	0.019135	0.0	ENSG00000205038	ENST00000378402;ENST00000526472	D;D	0.87412	-2.25;-2.08	5.64	1.83	0.25207	.	0.492124	0.18017	N	0.154354	T	0.52933	0.1765	N	0.24115	0.695	0.09310	N	1	B	0.34015	0.435	B	0.27170	0.077	T	0.58312	-0.7658	10	0.72032	D	0.01	.	7.5255	0.27653	0.0:0.253:0.0:0.747	.	4216	Q86WI1	PKHL1_HUMAN	N	4216;1144	ENSP00000367655:I4216N;ENSP00000437376:I1144N	ENSP00000367655:I4216N	I	+	2	0	PKHD1L1	110608351	0.002000	0.14202	0.001000	0.08648	0.122000	0.20287	0.151000	0.16283	0.068000	0.16574	0.528000	0.53228	ATT	T|0.993;A|0.007	0.007	strong		0.418	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
CEACAM6	4680	hgsc.bcm.edu	37	19	42260697	42260697	+	Missense_Mutation	SNP	G	G	A	rs61736638	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42260697G>A	ENST00000199764.6	+	2	472	c.254G>A	c.(253-255)gGa>gAa	p.G85E	AC011513.4_ENST00000601409.1_RNA|CEA_ENST00000598976.1_Intron	NM_002483.4	NP_002474.3	P40199	CEAM6_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 6 (non-specific cross reacting antigen)	85	Ig-like V-type.				cell-cell signaling (GO:0007267)|signal transduction (GO:0007165)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|kidney(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	18				OV - Ovarian serous cystadenocarcinoma(3;0.00575)|all cancers(3;0.0352)|Epithelial(262;0.0797)		TATGTAATAGGAACTCAACAA	0.498													g|||	146	0.0291534	0.1074	0.0043	5008	,	,		18669	0.0		0.001	False		,,,				2504	0.0				p.G85E		Atlas-SNP	.											.	CEACAM6	52	.	0			c.G254A						PASS	.	G	GLU/GLY	359,4047	184.3+/-211.7	13,333,1857	246.0	230.0	235.0		254	-3.8	0.0	19	dbSNP_129	235	7,8589	5.0+/-18.6	0,7,4291	no	missense	CEACAM6	NM_002483.4	98	13,340,6148	AA,AG,GG		0.0814,8.148,2.815	benign	85/345	42260697	366,12636	2203	4298	6501	SO:0001583	missense	4680	exon2			TAATAGGAACTCA	M29541	CCDS12585.1	19q13.1-q13.2	2013-01-29			ENSG00000086548	ENSG00000086548		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1818	protein-coding gene	gene with protein product		163980		NCA			Standard	NM_002483		Approved	CD66c	uc002orm.2	P40199	OTTHUMG00000151064	ENST00000199764.6:c.254G>A	19.37:g.42260697G>A	ENSP00000199764:p.Gly85Glu	446.0	1.0	0.00224215		429.0	205.0	0.477855	NM_002483	Q13774|Q14920|Q53XP7	Missense_Mutation	SNP	ENST00000199764.6	37	CCDS12585.1	51	0.023351648351648352	47	0.09552845528455285	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	G	0.011	-1.703438	0.00719	0.08148	8.14E-4	ENSG00000086548	ENST00000199764	T	0.64085	-0.08	1.92	-3.84	0.04256	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.01189	0.0039	N	0.16903	0.455	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.02333	-1.1175	9	0.54805	T	0.06	.	5.4199	0.16394	0.2722:0.4787:0.2491:0.0	rs61736638	85	P40199	CEAM6_HUMAN	E	85	ENSP00000199764:G85E	ENSP00000199764:G85E	G	+	2	0	CEACAM6	46952537	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.930000	0.00689	-3.925000	0.00091	-3.948000	0.00015	GGA	G|0.974;A|0.026	0.026	strong		0.498	CEACAM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321147.1		
TMEM63A	9725	hgsc.bcm.edu	37	1	226034913	226034913	+	Splice_Site	SNP	G	G	A	rs58852301	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:226034913G>A	ENST00000366835.3	-	24	2522	c.2252C>T	c.(2251-2253)cCc>cTc	p.P751L	RP11-285F7.2_ENST00000424332.1_RNA	NM_014698.2	NP_055513.2	O94886	CSCL1_HUMAN	transmembrane protein 63A	751					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	nucleotide binding (GO:0000166)			breast(2)|endometrium(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	24	Breast(184;0.197)					AGGCACGTAGGGCTGTCAGCA	0.592													G|||	193	0.0385383	0.1346	0.0202	5008	,	,		20323	0.0		0.0	False		,,,				2504	0.001				p.P751L		Atlas-SNP	.											TMEM63A,colon,carcinoma,+1,1	TMEM63A	75	1	0			c.C2252T						PASS	.	G	LEU/PRO	562,3838	234.2+/-247.1	35,492,1673	65.0	56.0	59.0		2252	3.1	1.0	1	dbSNP_129	59	0,8598		0,0,4299	yes	missense-near-splice	TMEM63A	NM_014698.2	98	35,492,5972	AA,AG,GG		0.0,12.7727,4.3237	benign	751/808	226034913	562,12436	2200	4299	6499	SO:0001630	splice_region_variant	9725	exon24			ACGTAGGGCTGTC		CCDS31042.1	1q42.12	2008-02-05	2005-07-25	2005-07-25	ENSG00000196187	ENSG00000196187			29118	protein-coding gene	gene with protein product			"""KIAA0792"""	KIAA0792		9872452, 9455484	Standard	NM_014698		Approved		uc001hpm.2	O94886	OTTHUMG00000037442	ENST00000366835.3:c.2251-1C>T	1.37:g.226034913G>A		104.0	0.0	0		98.0	46.0	0.469388	NM_014698	Q53GI7|Q5TE96|Q8N2U2	Missense_Mutation	SNP	ENST00000366835.3	37	CCDS31042.1	78	0.03571428571428571	70	0.14227642276422764	8	0.022099447513812154	0	0.0	0	0.0	G	10.91	1.484973	0.26598	0.127727	0.0	ENSG00000196187	ENST00000366835	T	0.16597	2.33	4.11	3.1	0.35709	.	0.162225	0.53938	D	0.000053	T	0.00109	0.0003	L	0.57536	1.79	0.09310	P	0.99999999815609	B	0.06786	0.001	B	0.08055	0.003	T	0.05989	-1.0852	9	0.33940	T	0.23	-22.7721	5.9809	0.19407	0.1448:0.0:0.8552:0.0	rs58852301	751	O94886	TM63A_HUMAN	L	751	ENSP00000355800:P751L	ENSP00000355800:P751L	P	-	2	0	TMEM63A	224101536	1.000000	0.71417	0.999000	0.59377	0.909000	0.53808	1.585000	0.36600	2.146000	0.66826	0.448000	0.29417	CCC	G|0.956;A|0.044	0.044	strong		0.592	TMEM63A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091154.2	NM_014698	Missense_Mutation
FNDC1	84624	hgsc.bcm.edu	37	6	159654720	159654720	+	Missense_Mutation	SNP	G	G	C	rs115529940	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:159654720G>C	ENST00000297267.9	+	11	3376	c.3176G>C	c.(3175-3177)aGc>aCc	p.S1059T	FNDC1_ENST00000340366.6_Missense_Mutation_p.S996T	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	1059					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		TACACGGCGAGCTCCAGAGGG	0.701													G|||	62	0.0123802	0.0439	0.0058	5008	,	,		14068	0.0		0.0	False		,,,				2504	0.0				p.S1059T		Atlas-SNP	.											.	FNDC1	250	.	0			c.G3176C						PASS	.	G	THR/SER	102,3642		2,98,1772	9.0	12.0	11.0		3176	0.4	0.1	6	dbSNP_132	11	1,7791		0,1,3895	yes	missense	FNDC1	NM_032532.2	58	2,99,5667	CC,CG,GG		0.0128,2.7244,0.8929	benign	1059/1895	159654720	103,11433	1872	3896	5768	SO:0001583	missense	84624	exon11			CGGCGAGCTCCAG	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"""Fibronectin type III domain containing"""	21184	protein-coding gene	gene with protein product		609991	"""fibronectin type III domain containing 2"""	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.3176G>C	6.37:g.159654720G>C	ENSP00000297267:p.Ser1059Thr	37.0	0.0	0		45.0	9.0	0.2	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	25|25	0.011446886446886446|0.011446886446886446	23|23	0.046747967479674794|0.046747967479674794	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	G|G	12.73|12.73	2.026772|2.026772	0.35797|0.35797	0.027244|0.027244	1.28E-4|1.28E-4	ENSG00000164694|ENSG00000164694	ENST00000329629|ENST00000297267;ENST00000340366	.|T;T	.|0.09538	.|2.97;3.87	4.86|4.86	0.374|0.374	0.16183|0.16183	.|.	.|0.613338	.|0.15407	.|N	.|0.263994	T|T	0.01870|0.01870	0.0059|0.0059	L|L	0.27053|0.27053	0.805|0.805	0.09310|0.09310	N|N	1|1	.|P;P	.|0.40731	.|0.728;0.608	.|B;B	.|0.36092	.|0.217;0.115	T|T	0.42548|0.42548	-0.9445|-0.9445	5|10	.|0.51188	.|T	.|0.08	-5.582|-5.582	2.6419|2.6419	0.04973|0.04973	0.3758:0.0:0.4119:0.2123|0.3758:0.0:0.4119:0.2123	.|.	.|996;1059	.|Q4ZHG4-2;Q4ZHG4	.|.;FNDC1_HUMAN	D|T	954|1059;996	.|ENSP00000297267:S1059T;ENSP00000342460:S996T	.|ENSP00000297267:S1059T	E|S	+|+	3|2	2|0	FNDC1|FNDC1	159574710|159574710	0.096000|0.096000	0.21769|0.21769	0.052000|0.052000	0.19188|0.19188	0.053000|0.053000	0.15095|0.15095	0.113000|0.113000	0.15499|0.15499	0.445000|0.445000	0.26639|0.26639	0.561000|0.561000	0.74099|0.74099	GAG|AGC	G|0.986;C|0.014	0.014	strong		0.701	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
USP17L2	377630	hgsc.bcm.edu	37	8	11995004	11995004	+	Silent	SNP	C	C	T	rs186311075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11995004C>T	ENST00000333796.3	-	1	1582	c.1266G>A	c.(1264-1266)gaG>gaA	p.E422E	FAM66D_ENST00000434078.2_RNA	NM_001256869.1|NM_001256871.1|NM_001256872.1|NM_001256873.1|NM_001256874.1|NM_201402.2	NP_001243798.1|NP_001243800.1|NP_001243801.1|NP_001243802.1|NP_001243803.1|NP_958804.2	Q6R6M4	U17L2_HUMAN	ubiquitin specific peptidase 17-like family member 2	422	Mediates interaction with SUDS3.				apoptotic process (GO:0006915)|CAAX-box protein processing (GO:0071586)|cell cycle checkpoint (GO:0000075)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of histone deacetylation (GO:0031064)|negative regulation of protein processing (GO:0010955)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of Ras GTPase activity (GO:0034261)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of RIG-I signaling pathway (GO:1900246)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of apoptotic process (GO:0042981)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of defense response to virus by host (GO:0050691)|regulation of ruffle assembly (GO:1900027)|ubiquitin-dependent protein catabolic process (GO:0006511)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(1)|kidney(1)|large_intestine(11)|liver(1)|lung(8)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	29						CCACCAAGCGCTCGTCCAACT	0.562													C|||	51	0.0101837	0.0363	0.0043	5008	,	,		20092	0.0		0.0	False		,,,				2504	0.0				p.E422E		Atlas-SNP	.											.	USP17L2	47	.	0			c.G1266A						PASS	.	C		58,3128		3,52,1538	59.0	65.0	63.0		1266	0.7	0.0	8		63	5,7101		1,3,3549	no	coding-synonymous	USP17L2	NM_201402.2		4,55,5087	TT,TC,CC		0.0704,1.8205,0.6121		422/531	11995004	63,10229	1593	3553	5146	SO:0001819	synonymous_variant	377630	exon1			CAAGCGCTCGTCC	BC156290	CCDS43713.1	8p23.1	2012-10-09	2012-10-09		ENSG00000223443	ENSG00000223443			34434	protein-coding gene	gene with protein product	"""deubiquitinating enzyme 3"""	610186	"""ubiquitin specific peptidase 17-like 2"""				Standard	NM_201402		Approved	DUB3	uc003wvc.1	Q6R6M4	OTTHUMG00000165295	ENST00000333796.3:c.1266G>A	8.37:g.11995004C>T		95.0	0.0	0		131.0	27.0	0.206107	NM_201402		Silent	SNP	ENST00000333796.3	37	CCDS43713.1																																																																																			C|0.992;T|0.008	0.008	strong		0.562	USP17L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383303.2	NM_201402	
ATOH1	474	hgsc.bcm.edu	37	4	94750650	94750650	+	Silent	SNP	C	C	T	rs34543561	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:94750650C>T	ENST00000306011.3	+	1	609	c.573C>T	c.(571-573)aaC>aaT	p.N191N		NM_005172.1	NP_005163.1	Q92858	ATOH1_HUMAN	atonal homolog 1 (Drosophila)	191	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				auditory receptor cell fate determination (GO:0042668)|auditory receptor cell fate specification (GO:0042667)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|cerebral cortex development (GO:0021987)|inner ear morphogenesis (GO:0042472)|negative regulation of apoptotic process (GO:0043066)|neuron migration (GO:0001764)|positive regulation of auditory receptor cell differentiation (GO:0045609)|positive regulation of neuron differentiation (GO:0045666)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|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)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	11		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;3.57e-07)		CGTTCAACAACGACAAGAAGC	0.582													C|||	29	0.00579073	0.0219	0.0	5008	,	,		17596	0.0		0.0	False		,,,				2504	0.0				p.N191N		Atlas-SNP	.											ATOH1,NS,carcinoma,+2,1	ATOH1	40	1	0			c.C573T						PASS	.	C		97,4309	77.8+/-116.1	2,93,2108	53.0	54.0	53.0		573	4.4	1.0	4	dbSNP_126	53	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ATOH1	NM_005172.1		2,95,6406	TT,TC,CC		0.0233,2.2015,0.7612		191/355	94750650	99,12907	2203	4300	6503	SO:0001819	synonymous_variant	474	exon1			CAACAACGACAAG	U61148	CCDS3638.1	4q22	2013-05-21			ENSG00000172238	ENSG00000172238		"""Basic helix-loop-helix proteins"""	797	protein-coding gene	gene with protein product		601461				8872459	Standard	NM_005172		Approved	HATH1, MATH-1, Math1, bHLHa14	uc003hta.1	Q92858	OTTHUMG00000130972	ENST00000306011.3:c.573C>T	4.37:g.94750650C>T		139.0	0.0	0		192.0	98.0	0.510417	NM_005172	Q14CT9	Silent	SNP	ENST00000306011.3	37	CCDS3638.1																																																																																			C|0.992;T|0.008	0.008	strong		0.582	ATOH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253585.1	NM_005172	
FLG	2312	hgsc.bcm.edu	37	1	152277239	152277239	+	Missense_Mutation	SNP	G	G	A	rs111486002	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152277239G>A	ENST00000368799.1	-	3	10158	c.10123C>T	c.(10123-10125)Cgg>Tgg	p.R3375W	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3375	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCCCCTGACCGGTCACGTGCG	0.587									Ichthyosis				G|||	106	0.0211661	0.0756	0.0072	5008	,	,		19341	0.001		0.0	False		,,,				2504	0.0				p.R3375W		Atlas-SNP	.											.	FLG	900	.	0			c.C10123T						PASS	.	G	TRP/ARG	153,4253	93.4+/-132.2	4,145,2054	286.0	306.0	299.0		10123	1.8	0.0	1	dbSNP_132	299	2,8598	2.2+/-6.3	0,2,4298	no	missense	FLG	NM_002016.1	101	4,147,6352	AA,AG,GG		0.0233,3.4725,1.1918	probably-damaging	3375/4062	152277239	155,12851	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CTGACCGGTCACG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.10123C>T	1.37:g.152277239G>A	ENSP00000357789:p.Arg3375Trp	443.0	1.0	0.00225734		385.0	185.0	0.480519	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	23	0.010531135531135532	21	0.042682926829268296	2	0.0055248618784530384	0	0.0	0	0.0	G	9.323	1.058443	0.19987	0.034725	2.33E-4	ENSG00000143631	ENST00000368799;ENST00000368796	T	0.00966	5.49	1.82	1.82	0.25136	.	.	.	.	.	T	0.01454	0.0047	M	0.63428	1.95	0.09310	N	1	D	0.89917	1.0	D	0.71414	0.973	T	0.51529	-0.8694	9	0.72032	D	0.01	.	7.1799	0.25765	0.0:0.0:1.0:0.0	.	3375	P20930	FILA_HUMAN	W	3375;313	ENSP00000357789:R3375W	ENSP00000357786:R313W	R	-	1	2	FLG	150543863	.	.	0.001000	0.08648	0.001000	0.01503	.	.	1.327000	0.45338	0.454000	0.30748	CGG	G|0.986;A|0.014	0.014	strong		0.587	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
CELSR1	9620	hgsc.bcm.edu	37	22	46859701	46859701	+	Silent	SNP	C	C	T	rs140328042	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46859701C>T	ENST00000262738.3	-	2	4085	c.4086G>A	c.(4084-4086)acG>acA	p.T1362T	CELSR1_ENST00000395964.1_Silent_p.T1362T	NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	1362					anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		GGTCGATCTCCGTCTCGCAGT	0.692													C|||	11	0.00219649	0.0083	0.0	5008	,	,		13548	0.0		0.0	False		,,,				2504	0.0				p.T1362T		Atlas-SNP	.											.	CELSR1	242	.	0			c.G4086A						PASS	.	C		37,4357		0,37,2160	33.0	33.0	33.0		4086	-9.5	0.7	22	dbSNP_134	33	0,8594		0,0,4297	no	coding-synonymous	CELSR1	NM_014246.1		0,37,6457	TT,TC,CC		0.0,0.8421,0.2849		1362/3015	46859701	37,12951	2197	4297	6494	SO:0001819	synonymous_variant	9620	exon2			GATCTCCGTCTCG	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	1850	protein-coding gene	gene with protein product	"""flamingo homolog 2 (Drosophila)"""	604523	"""cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"""			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.4086G>A	22.37:g.46859701C>T		61.0	0.0	0		58.0	27.0	0.465517	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	37	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	C	8.918	0.960317	0.18507	0.008421	0.0	ENSG00000075275	ENST00000454637	.	.	.	4.75	-9.49	0.00587	.	.	.	.	.	T	0.25232	0.0613	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37911	-0.9685	4	.	.	.	.	1.2491	0.01978	0.1999:0.3436:0.1613:0.2952	.	.	.	.	Q	737	.	.	R	-	2	0	CELSR1	45238365	0.000000	0.05858	0.651000	0.29564	0.922000	0.55478	-3.266000	0.00534	-2.191000	0.00756	-0.892000	0.02923	CGG	C|0.997;T|0.003	0.003	strong		0.692	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
PARP4	143	hgsc.bcm.edu	37	13	25027745	25027745	+	Missense_Mutation	SNP	T	T	C	rs386769073|rs1130943	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:25027745T>C	ENST00000381989.3	-	23	2911	c.2806A>G	c.(2806-2808)Atg>Gtg	p.M936V	PARP4_ENST00000480576.1_5'Flank	NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	936	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.			M -> A (in Ref. 2; AAC62491 and 3; BAA11494). {ECO:0000305}.|M -> T (in Ref. 1; AAD47250). {ECO:0000305}.	cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		TCTGCTGCCATGGTATTGCTT	0.478													N|||	352	0.0702875	0.2262	0.0216	5008	,	,		15989	0.0298		0.001	False		,,,				2504	0.0072				p.M936V		Atlas-SNP	.											PARP4,NS,carcinoma,+2,1	PARP4	142	1	0			c.A2806G						PASS	.	C	VAL/MET	795,3611	743.2+/-411.4	86,623,1494	277.0	217.0	237.0		2806	-3.9	0.0	13	dbSNP_86	237	14,8586	818.4+/-406.9	0,14,4286	yes	missense	PARP4	NM_006437.3	21	86,637,5780	CC,CT,TT		0.1628,18.0436,6.2202	benign	936/1725	25027745	809,12197	2203	4300	6503	SO:0001583	missense	143	exon23			CTGCCATGGTATT	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.2806A>G	13.37:g.25027745T>C	ENSP00000371419:p.Met936Val	169.0	0.0	0		191.0	95.0	0.497382	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	37	CCDS9307.1	84	0.038461538461538464	71	0.1443089430894309	7	0.019337016574585635	6	0.01048951048951049	0	0.0	C	2.522	-0.310435	0.05458	0.180436	0.001628	ENSG00000102699	ENST00000381989	T	0.07567	3.18	4.29	-3.89	0.04193	von Willebrand factor, type A (3);	1.850880	0.02221	N	0.063999	T	0.00012	0.0000	L	0.36672	1.1	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.41538	-0.9503	9	0.16896	T	0.51	0.2561	6.1523	0.20318	0.1226:0.3669:0.0:0.5105	rs1130943;rs3190390;rs12323011;rs17413359	936	Q9UKK3	PARP4_HUMAN	V	936	ENSP00000371419:M936V	ENSP00000371419:M936V	M	-	1	0	PARP4	23925745	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.131000	0.03238	-1.328000	0.02261	-0.273000	0.10243	ATG	T|0.949;C|0.051	0.051	strong		0.478	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
CAPN12	147968	hgsc.bcm.edu	37	19	39226163	39226163	+	Silent	SNP	G	G	A	rs141009431	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39226163G>A	ENST00000328867.4	-	13	1913	c.1605C>T	c.(1603-1605)agC>agT	p.S535S	CAPN12_ENST00000601953.1_Silent_p.S386S|CTD-2540F13.2_ENST00000602255.1_RNA	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	535	Domain III.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(60;2.87e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)			GCAGGTCTGCGCTGATCACGT	0.647													G|||	11	0.00219649	0.0083	0.0	5008	,	,		8622	0.0		0.0	False		,,,				2504	0.0				p.S535S		Atlas-SNP	.											.	CAPN12	43	.	0			c.C1605T						PASS	.	G		27,4355	30.8+/-60.4	0,27,2164	38.0	37.0	37.0		1605	3.0	1.0	19	dbSNP_134	37	0,8590		0,0,4295	no	coding-synonymous	CAPN12	NM_144691.3		0,27,6459	AA,AG,GG		0.0,0.6162,0.2081		535/720	39226163	27,12945	2191	4295	6486	SO:0001819	synonymous_variant	147968	exon13			GTCTGCGCTGATC	BC014027	CCDS12519.1	19q13.2	2014-08-12			ENSG00000182472	ENSG00000182472		"""EF-hand domain containing"""	13249	protein-coding gene	gene with protein product		608839					Standard	NM_144691		Approved		uc002ojd.1	Q6ZSI9	OTTHUMG00000182525	ENST00000328867.4:c.1605C>T	19.37:g.39226163G>A		100.0	0.0	0		107.0	43.0	0.401869	NM_144691		Silent	SNP	ENST00000328867.4	37	CCDS12519.1																																																																																			G|0.998;A|0.002	0.002	strong		0.647	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1		
CEACAM20	125931	hgsc.bcm.edu	37	19	45017301	45017301	+	RNA	SNP	T	T	C	rs34921521	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45017301T>C	ENST00000454753.1	-	0	1635							Q6UY09	CEA20_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 20							integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)	15		Prostate(69;0.0352)				AGGATCCCGATGACAATACCA	0.567											OREG0025538	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	78	0.0155751	0.0575	0.0029	5008	,	,		15361	0.0		0.0	False		,,,				2504	0.0				p.I453V		Atlas-SNP	.											CEACAM20,NS,carcinoma,0,1	CEACAM20	31	1	0			c.A1357G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	166,3902		5,156,1873	76.0	76.0	76.0		1357,1078,1078,1357	-5.6	0.0	19	dbSNP_126	76	1,8347		0,1,4173	yes	missense,missense,missense,missense	CEACAM20	NM_001102597.1,NM_001102598.1,NM_001102599.1,NM_001102600.1	29,29,29,29	5,157,6046	CC,CT,TT		0.012,4.0806,1.345	benign,benign,benign,benign	453/597,360/492,360/504,453/585	45017301	167,12249	2034	4174	6208			125931	exon7			TCCCGATGACAAT	AY358129	CCDS74390.1, CCDS74391.1, CCDS74392.1, CCDS74393.1	19q13.31	2013-01-30			ENSG00000176395	ENSG00000273777		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	24879	protein-coding gene	gene with protein product						12975309	Standard	NM_001102600		Approved	UNQ9366	uc010ejo.1	Q6UY09	OTTHUMG00000151532		19.37:g.45017301T>C		67.0	0.0	0	928	81.0	37.0	0.45679	NM_001102600		Missense_Mutation	SNP	ENST00000454753.1	37																																																																																				T|0.986;C|0.014	0.014	strong		0.567	CEACAM20-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000323032.1	NM_198444	
HERC2	8924	hgsc.bcm.edu	37	15	28389880	28389880	+	Silent	SNP	G	G	A	rs1133496	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:28389880G>A	ENST00000261609.7	-	72	11187	c.11079C>T	c.(11077-11079)agC>agT	p.S3693S		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		CAGACCCATCGCTGATGAACT	0.592													G|||	434	0.0866613	0.3132	0.0274	5008	,	,		20257	0.0		0.001	False		,,,				2504	0.0				p.S3693S		Atlas-SNP	.											.	HERC2	501	.	0			c.C11079T						PASS	.	G		1171,3235	414.6+/-336.9	156,859,1188	106.0	86.0	93.0		11079	-2.7	1.0	15	dbSNP_86	93	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	HERC2	NM_004667.4		156,863,5484	AA,AG,GG		0.0465,26.5774,9.0343		3693/4835	28389880	1175,11831	2203	4300	6503	SO:0001819	synonymous_variant	8924	exon72			CCCATCGCTGATG	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.11079C>T	15.37:g.28389880G>A		129.0	0.0	0		145.0	73.0	0.503448	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			G|0.916;A|0.084	0.084	strong		0.592	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
NTRK3	4916	hgsc.bcm.edu	37	15	88576215	88576215	+	Silent	SNP	G	G	A	rs2229909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:88576215G>A	ENST00000360948.2	-	13	1619	c.1458C>T	c.(1456-1458)caC>caT	p.H486H	NTRK3_ENST00000557856.1_Silent_p.H478H|NTRK3_ENST00000542733.2_Silent_p.H388H|NTRK3_ENST00000558676.1_Silent_p.H478H|NTRK3_ENST00000317501.3_Silent_p.H486H|NTRK3_ENST00000558306.1_5'UTR|NTRK3_ENST00000357724.2_Silent_p.H478H|NTRK3_ENST00000355254.2_Silent_p.H486H|NTRK3_ENST00000540489.2_Silent_p.H486H|NTRK3_ENST00000394480.2_Silent_p.H486H	NM_001012338.2	NP_001012338.1	Q16288	NTRK3_HUMAN	neurotrophic tyrosine kinase, receptor, type 3	486					activation of MAPK activity (GO:0000187)|activation of protein kinase B activity (GO:0032148)|activation of Ras GTPase activity (GO:0032856)|cellular response to retinoic acid (GO:0071300)|circadian rhythm (GO:0007623)|cochlea development (GO:0090102)|lens fiber cell differentiation (GO:0070306)|mechanoreceptor differentiation (GO:0042490)|modulation by virus of host transcription (GO:0019056)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell death (GO:0060548)|negative regulation of protein phosphorylation (GO:0001933)|neuron fate specification (GO:0048665)|neuron migration (GO:0001764)|neurotrophin signaling pathway (GO:0038179)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of axon extension involved in regeneration (GO:0048691)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of positive chemotaxis (GO:0050927)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|response to corticosterone (GO:0051412)|response to ethanol (GO:0045471)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|neurotrophin binding (GO:0043121)|neurotrophin receptor activity (GO:0005030)|p53 binding (GO:0002039)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ETV6/NTRK3(238)	breast(3)|central_nervous_system(3)|endometrium(6)|kidney(1)|large_intestine(22)|lung(63)|ovary(6)|pancreas(3)|prostate(1)|skin(4)|stomach(5)|upper_aerodigestive_tract(2)	119			BRCA - Breast invasive adenocarcinoma(143;0.211)			TGGTGATGCCGTGGTTGATGT	0.607			T	ETV6	"""congenital fibrosarcoma, Secretory breast """					TSP Lung(13;0.10)			G|||	143	0.0285543	0.1051	0.0058	5008	,	,		10706	0.0		0.0	False		,,,				2504	0.0				p.H486H		Atlas-SNP	.		Dom	yes		15	15q25	4916	"""neurotrophic tyrosine kinase, receptor, type 3"""		"""E, M"""	NTRK3_ENST00000360948,NS,carcinoma,0,3	NTRK3	587	3	0			c.C1458T						PASS	.	G	,,	457,3945	216.4+/-235.1	27,403,1771	97.0	61.0	73.0		1458,1458,1458	-4.4	1.0	15	dbSNP_129	73	2,8596	3.0+/-9.4	0,2,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	NTRK3	NM_001007156.2,NM_001012338.2,NM_002530.3	,,	27,405,6068	AA,AG,GG		0.0233,10.3816,3.5308	,,	486/613,486/840,486/826	88576215	459,12541	2201	4299	6500	SO:0001819	synonymous_variant	4916	exon14			GATGCCGTGGTTG	U05012	CCDS10340.1, CCDS32322.1, CCDS32323.1, CCDS58399.1	15q24-q25	2013-01-11			ENSG00000140538	ENSG00000140538	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"""	8033	protein-coding gene	gene with protein product		191316				7806211	Standard	NM_001012338		Approved	TRKC	uc002bme.2	Q16288	OTTHUMG00000148677	ENST00000360948.2:c.1458C>T	15.37:g.88576215G>A		98.0	0.0	0		97.0	47.0	0.484536	NM_001012338	B7Z4C5|E9PG56|H0YND1|O75682|Q12827|Q16289	Silent	SNP	ENST00000360948.2	37	CCDS32322.1																																																																																			G|0.962;A|0.038	0.038	strong		0.607	NTRK3-204	KNOWN	basic|CCDS	protein_coding	protein_coding			
CAMKK1	84254	hgsc.bcm.edu	37	17	3786456	3786456	+	Silent	SNP	C	C	T	rs737362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3786456C>T	ENST00000348335.2	-	6	676	c.528G>A	c.(526-528)ccG>ccA	p.P176P	CAMKK1_ENST00000158166.5_Silent_p.P176P|CAMKK1_ENST00000381769.2_Silent_p.P203P|CAMKK1_ENST00000381771.2_Silent_p.P176P	NM_032294.2	NP_115670.1	Q8N5S9	KKCC1_HUMAN	calcium/calmodulin-dependent protein kinase kinase 1, alpha	176	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|RP domain.				synaptic transmission (GO:0007268)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)			NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)	11				LUAD - Lung adenocarcinoma(2;2.11e-05)|Lung(3;0.0176)		GGGACCCTCTCGGGGGAGGGC	0.627													C|||	289	0.0577077	0.2118	0.0101	5008	,	,		19719	0.0		0.002	False		,,,				2504	0.0				p.P176P		Atlas-SNP	.											.	CAMKK1	70	.	0			c.G528A						PASS	.	C	,,	836,3570	328.5+/-300.6	77,682,1444	61.0	60.0	60.0		528,528,528	-10.9	0.0	17	dbSNP_86	60	9,8591	6.4+/-24.3	0,9,4291	no	coding-synonymous,coding-synonymous,coding-synonymous	CAMKK1	NM_032294.2,NM_172206.1,NM_172207.2	,,	77,691,5735	TT,TC,CC		0.1047,18.9741,6.497	,,	176/506,176/506,176/521	3786456	845,12161	2203	4300	6503	SO:0001819	synonymous_variant	84254	exon6			CCCTCTCGGGGGA	AL136576	CCDS11038.1, CCDS11039.1	17p13.3	2004-02-18			ENSG00000004660	ENSG00000004660			1469	protein-coding gene	gene with protein product		611411				11230166	Standard	NM_172207		Approved	DKFZp761M0423, CAMKKA, MGC34095	uc002fwt.3	Q8N5S9	OTTHUMG00000090725	ENST00000348335.2:c.528G>A	17.37:g.3786456C>T		43.0	0.0	0		42.0	18.0	0.428571	NM_032294	Q9BQH3	Silent	SNP	ENST00000348335.2	37	CCDS11038.1																																																																																			C|0.934;T|0.066	0.066	strong		0.627	CAMKK1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207456.1	NM_032294, NM_172206, NM_172207	
AKAP10	11216	hgsc.bcm.edu	37	17	19835185	19835185	+	Missense_Mutation	SNP	G	G	C	rs141355495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:19835185G>C	ENST00000225737.6	-	10	1731	c.1574C>G	c.(1573-1575)aCt>aGt	p.T525S	RP11-209D14.4_ENST00000583067.1_RNA|AKAP10_ENST00000395536.3_Intron	NM_007202.3	NP_009133.2	O43572	AKA10_HUMAN	A kinase (PRKA) anchor protein 10	525					blood coagulation (GO:0007596)|protein localization (GO:0008104)|signal transduction (GO:0007165)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)				NS(1)|endometrium(3)|kidney(1)|large_intestine(4)|liver(1)|lung(3)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(2)	21	all_cancers(12;2.08e-05)|all_epithelial(12;0.00158)|Breast(13;0.165)					GCCAGGAGCAGTCAGCGACAC	0.488													G|||	3	0.000599042	0.0023	0.0	5008	,	,		14389	0.0		0.0	False		,,,				2504	0.0				p.T525S		Atlas-SNP	.											.	AKAP10	47	.	0			c.C1574G						PASS	.	G	SER/THR	6,4400	12.9+/-30.5	0,6,2197	85.0	83.0	84.0		1574	2.8	0.2	17	dbSNP_134	84	0,8600		0,0,4300	yes	missense	AKAP10	NM_007202.2	58	0,6,6497	CC,CG,GG		0.0,0.1362,0.0461	benign	525/663	19835185	6,13000	2203	4300	6503	SO:0001583	missense	11216	exon10			GGAGCAGTCAGCG	AF037439	CCDS11214.1	17p11.1	2008-07-18			ENSG00000108599	ENSG00000108599		"""A-kinase anchor proteins"""	368	protein-coding gene	gene with protein product	"""dual-specificity A-kinase anchoring protein 2"", ""protein kinase A anchoring protein 10"", ""mitochondrial A kinase PPKA anchor protein 10"""	604694				9326583	Standard	NM_007202		Approved	D-AKAP2, PRKA10, MGC9414	uc002gwo.4	O43572	OTTHUMG00000059515	ENST00000225737.6:c.1574C>G	17.37:g.19835185G>C	ENSP00000225737:p.Thr525Ser	55.0	0.0	0		64.0	36.0	0.5625	NM_007202	B2R650|Q96AJ7	Missense_Mutation	SNP	ENST00000225737.6	37	CCDS11214.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	5.299	0.240537	0.10023	0.001362	0.0	ENSG00000108599	ENST00000225737	T	0.28666	1.6	5.82	2.79	0.32731	.	0.783781	0.12491	N	0.464265	T	0.05914	0.0154	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33752	-0.9856	10	0.09084	T	0.74	0.4362	1.6078	0.02687	0.238:0.1522:0.4703:0.1395	.	525	O43572	AKA10_HUMAN	S	525	ENSP00000225737:T525S	ENSP00000225737:T525S	T	-	2	0	AKAP10	19775777	0.767000	0.28508	0.197000	0.23402	0.325000	0.28411	0.898000	0.28404	0.820000	0.34516	0.650000	0.86243	ACT	G|0.999;C|0.001	0.001	strong		0.488	AKAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132380.2	NM_007202	
ARHGAP32	9743	hgsc.bcm.edu	37	11	128994781	128994781	+	Silent	SNP	G	G	A	rs114955890	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:128994781G>A	ENST00000310343.9	-	3	233	c.234C>T	c.(232-234)ggC>ggT	p.G78G	ARHGAP32_ENST00000524655.1_Silent_p.G4G	NM_001142685.1	NP_001136157.1	A7KAX9	RHG32_HUMAN	Rho GTPase activating protein 32	78					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)|phosphatidylinositol binding (GO:0035091)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(28)|ovary(3)|prostate(6)|urinary_tract(3)	60						GAACATCTGCGCCTCTTGCCT	0.333													G|||	6	0.00119808	0.0045	0.0	5008	,	,		15533	0.0		0.0	False		,,,				2504	0.0				p.G78G		Atlas-SNP	.											.	ARHGAP32	307	.	0			c.C234T						PASS	.	G		17,3115		0,17,1549	108.0	98.0	101.0		234	2.2	1.0	11	dbSNP_132	101	0,7156		0,0,3578	no	coding-synonymous	ARHGAP32	NM_001142685.1		0,17,5127	AA,AG,GG		0.0,0.5428,0.1652		78/2088	128994781	17,10271	1566	3578	5144	SO:0001819	synonymous_variant	9743	exon3			ATCTGCGCCTCTT	AB018255	CCDS31718.1, CCDS44769.1	11q24.3	2011-06-29			ENSG00000134909	ENSG00000134909		"""Rho GTPase activating proteins"""	17399	protein-coding gene	gene with protein product		608541				12446789, 12819203, 17663722	Standard	NM_014715		Approved	GRIT, KIAA0712, MGC1892, RICS, GC-GAP	uc009zcp.3	A7KAX9	OTTHUMG00000165774	ENST00000310343.9:c.234C>T	11.37:g.128994781G>A		42.0	0.0	0		59.0	34.0	0.576271	NM_001142685	I7H0B0|O94820|Q86YL6|Q8IUG4|Q9BWG3	Silent	SNP	ENST00000310343.9	37	CCDS44769.1																																																																																			G|0.998;A|0.002	0.002	strong		0.333	ARHGAP32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386151.3	NM_014715	
ELK3	2004	hgsc.bcm.edu	37	12	96641344	96641344	+	Silent	SNP	G	G	A	rs115218295	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:96641344G>A	ENST00000228741.3	+	3	1160	c.834G>A	c.(832-834)tcG>tcA	p.S278S	ELK3_ENST00000552142.1_Intron	NM_005230.2	NP_005221.2	P41970	ELK3_HUMAN	ELK3, ETS-domain protein (SRF accessory protein 2)	278					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription from RNA polymerase II promoter (GO:0006366)|wound healing (GO:0042060)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	purine-rich negative regulatory element binding (GO:0032422)|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 RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)	p.S278S(1)		breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(5)|ovary(2)|prostate(1)|stomach(2)	20	all_cancers(2;0.00173)					ACCTGTCATCGGGCTCCAAGA	0.602													G|||	45	0.00898562	0.0333	0.0	5008	,	,		16138	0.0		0.001	False		,,,				2504	0.0				p.S278S		Atlas-SNP	.											.	ELK3	36	.	1	Substitution - coding silent(1)	lung(1)	c.G834A						PASS	.	G		125,4281	90.6+/-129.3	2,121,2080	67.0	75.0	72.0		834	-1.9	0.9	12	dbSNP_132	72	0,8600		0,0,4300	no	coding-synonymous	ELK3	NM_005230.2		2,121,6380	AA,AG,GG		0.0,2.837,0.9611		278/408	96641344	125,12881	2203	4300	6503	SO:0001819	synonymous_variant	2004	exon3			GTCATCGGGCTCC	BC017371	CCDS9060.1	12q23	2006-12-30				ENSG00000111145			3325	protein-coding gene	gene with protein product		600247				7851904	Standard	NM_005230		Approved	ERP, NET, SAP2	uc001teo.1	P41970		ENST00000228741.3:c.834G>A	12.37:g.96641344G>A		55.0	0.0	0		59.0	32.0	0.542373	NM_005230	B2R6S6|Q6FG57|Q6GU29|Q9UD17	Silent	SNP	ENST00000228741.3	37	CCDS9060.1																																																																																			G|0.990;A|0.010	0.010	strong		0.602	ELK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408694.1	NM_005230	
COG7	91949	hgsc.bcm.edu	37	16	23409440	23409440	+	Missense_Mutation	SNP	G	G	A	rs16940094	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:23409440G>A	ENST00000307149.5	-	14	1999	c.1814C>T	c.(1813-1815)aCg>aTg	p.T605M		NM_153603.3	NP_705831.1	P83436	COG7_HUMAN	component of oligomeric golgi complex 7	605			T -> M (in dbSNP:rs16940094).		intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to Golgi apparatus (GO:0034067)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(7)|large_intestine(9)|liver(1)|lung(7)|urinary_tract(1)	27				GBM - Glioblastoma multiforme(48;0.0401)		GATGCCAGCCGTATTCCAGCT	0.532													G|||	441	0.0880591	0.1861	0.1239	5008	,	,		19099	0.0169		0.0258	False		,,,				2504	0.0675				p.T605M		Atlas-SNP	.											.	COG7	62	.	0			c.C1814T						PASS	.	G	MET/THR	681,3713	286.9+/-279.0	50,581,1566	122.0	98.0	106.0		1814	3.7	0.7	16	dbSNP_123	106	257,8343	101.4+/-162.7	4,249,4047	yes	missense	COG7	NM_153603.3	81	54,830,5613	AA,AG,GG		2.9884,15.4984,7.2187	possibly-damaging	605/771	23409440	938,12056	2197	4300	6497	SO:0001583	missense	91949	exon14			CCAGCCGTATTCC	AF070568	CCDS10610.1	16p12.2	2008-02-05			ENSG00000168434	ENSG00000168434		"""Components of oligomeric golgi complex"""	18622	protein-coding gene	gene with protein product		606978				11980916	Standard	NM_153603		Approved		uc002dlo.3	P83436	OTTHUMG00000094807	ENST00000307149.5:c.1814C>T	16.37:g.23409440G>A	ENSP00000305442:p.Thr605Met	125.0	0.0	0		150.0	87.0	0.58	NM_153603	Q6UWU7	Missense_Mutation	SNP	ENST00000307149.5	37	CCDS10610.1	136	0.06227106227106227	79	0.16056910569105692	28	0.07734806629834254	11	0.019230769230769232	18	0.023746701846965697	G	13.05	2.121490	0.37436	0.154984	0.029884	ENSG00000168434	ENST00000307149	T	0.44881	0.91	5.6	3.67	0.42095	.	0.270197	0.42682	N	0.000671	T	0.00178	0.0005	N	0.24115	0.695	0.34894	P	0.254186	D	0.57571	0.98	P	0.52109	0.69	T	0.05632	-1.0873	9	0.42905	T	0.14	-15.5303	10.0248	0.42066	0.1547:0.0:0.8453:0.0	rs16940094;rs16940094	605	P83436	COG7_HUMAN	M	605	ENSP00000305442:T605M	ENSP00000305442:T605M	T	-	2	0	COG7	23316941	1.000000	0.71417	0.745000	0.31077	0.194000	0.23727	5.583000	0.67484	0.747000	0.32809	-0.742000	0.03525	ACG	G|0.931;A|0.069	0.069	strong		0.532	COG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211625.1		
TTLL11	158135	hgsc.bcm.edu	37	9	124855220	124855220	+	Missense_Mutation	SNP	G	G	A	rs61742325	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:124855220G>A	ENST00000373776.3	-	1	665	c.478C>T	c.(478-480)Ccc>Tcc	p.P160S	TTLL11_ENST00000474723.1_5'UTR|TTLL11_ENST00000321582.5_Missense_Mutation_p.P160S	NM_194252.2	NP_919228.2	Q8NHH1	TTL11_HUMAN	tubulin tyrosine ligase-like family, member 11	160					cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(3)|skin(1)	18						GCCGCACTGGGCTGCGCCGGG	0.766													G|||	247	0.0493211	0.1808	0.0115	5008	,	,		11208	0.0		0.0	False		,,,				2504	0.0				p.P160S		Atlas-SNP	.											.	TTLL11	67	.	0			c.C478T						PASS	.	G	SER/PRO,SER/PRO	440,3254		12,416,1419	5.0	6.0	6.0		478,478	0.4	0.2	9	dbSNP_129	6	1,7393		0,1,3696	no	missense,missense	TTLL11	NM_001139442.1,NM_194252.2	74,74	12,417,5115	AA,AG,GG		0.0135,11.9112,3.9773	possibly-damaging,possibly-damaging	160/801,160/539	124855220	441,10647	1847	3697	5544	SO:0001583	missense	158135	exon1			CACTGGGCTGCGC	AF521886	CCDS6834.2, CCDS48012.1	9q34.11	2013-02-14	2005-07-28	2005-07-28	ENSG00000175764	ENSG00000175764		"""Tubulin tyrosine ligase-like family"""	18113	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 20"""	C9orf20		15890843	Standard	NM_001139442		Approved	bA244O19.1	uc011lyl.2	Q8NHH1	OTTHUMG00000020597	ENST00000373776.3:c.478C>T	9.37:g.124855220G>A	ENSP00000362881:p.Pro160Ser	5.0	0.0	0		14.0	14.0	1	NM_001139442		Missense_Mutation	SNP	ENST00000373776.3	37	CCDS6834.2	98	0.04487179487179487	90	0.18292682926829268	8	0.022099447513812154	0	0.0	0	0.0	G	8.451	0.853131	0.17106	0.119112	1.35E-4	ENSG00000175764	ENST00000321582;ENST00000373776	T;T	0.08458	3.24;3.09	4.73	0.383	0.16239	.	8.202900	0.00520	U	0.000189	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.16396	0.017;0.01	B;B	0.10450	0.005;0.003	T	0.41360	-0.9513	8	.	.	.	.	3.3638	0.07196	0.0901:0.2587:0.426:0.2252	.	160;160	F8W6M1;Q8NHH1	.;TTL11_HUMAN	S	160	ENSP00000321346:P160S;ENSP00000362881:P160S	.	P	-	1	0	TTLL11	123895041	0.067000	0.21026	0.156000	0.22583	0.281000	0.26958	0.757000	0.26433	0.382000	0.24878	-0.379000	0.06801	CCC	G|0.955;A|0.045	0.045	strong		0.766	TTLL11-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053907.1	XM_088486	
UCK2	7371	hgsc.bcm.edu	37	1	165859482	165859482	+	Silent	SNP	T	T	C	rs145654595		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:165859482T>C	ENST00000367879.4	+	2	444	c.141T>C	c.(139-141)aaT>aaC	p.N47N	UCK2_ENST00000372212.4_Silent_p.N47N	NM_012474.4	NP_036606.2	Q9BZX2	UCK2_HUMAN	uridine-cytidine kinase 2	47					cellular response to oxygen levels (GO:0071453)|CTP salvage (GO:0044211)|feeding behavior (GO:0007631)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|response to axon injury (GO:0048678)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)	cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	ATP binding (GO:0005524)|nucleoside kinase activity (GO:0019206)|uridine kinase activity (GO:0004849)			breast(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	10	all_hematologic(923;0.048)|Acute lymphoblastic leukemia(8;0.155)					TGGGGCAGAATGAGGTGGACT	0.557																																					p.N47N		Atlas-SNP	.											.	UCK2	31	.	0			c.T141C						PASS	.	T		2,4404	4.2+/-10.8	0,2,2201	138.0	120.0	126.0		141	-3.1	1.0	1	dbSNP_134	126	0,8600		0,0,4300	no	coding-synonymous	UCK2	NM_012474.4		0,2,6501	CC,CT,TT		0.0,0.0454,0.0154		47/262	165859482	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	7371	exon2			GCAGAATGAGGTG	AF236637	CCDS1252.1	1p32	2012-10-02	2004-07-13	2004-07-14	ENSG00000143179	ENSG00000143179	2.7.1.48		12562	protein-coding gene	gene with protein product		609329	"""uridine monophosphate kinase"""	UMPK			Standard	NM_012474		Approved		uc001gdp.3	Q9BZX2	OTTHUMG00000040117	ENST00000367879.4:c.141T>C	1.37:g.165859482T>C		207.0	0.0	0		243.0	118.0	0.485597	NM_012474	Q5VV91|Q7KZV3|Q92528|Q96KG5|Q9BU42	Silent	SNP	ENST00000367879.4	37	CCDS1252.1																																																																																			T|1.000;C|0.000	0.000	weak		0.557	UCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096753.1	NM_012474	
MSH3	4437	hgsc.bcm.edu	37	5	79974885	79974885	+	Missense_Mutation	SNP	C	C	T	rs35121792	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:79974885C>T	ENST00000265081.6	+	8	1393	c.1313C>T	c.(1312-1314)gCg>gTg	p.A438V		NM_002439.4	NP_002430.3	P20585	MSH3_HUMAN	mutS homolog 3	438					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)		CAAACAGAGGCGCTCATCCAC	0.473								Mismatch excision repair (MMR)					C|||	5	0.000998403	0.0015	0.0	5008	,	,		15950	0.0		0.0	False		,,,				2504	0.0031				p.A438V	Melanoma(88;1010 1399 13793 26548 36275)	Atlas-SNP	.											.	MSH3	129	.	0			c.C1313T						PASS	.	C	VAL/ALA	14,4392	21.2+/-45.6	0,14,2189	133.0	129.0	130.0		1313	-11.0	0.0	5	dbSNP_126	130	0,8600		0,0,4300	yes	missense	MSH3	NM_002439.3	64	0,14,6489	TT,TC,CC		0.0,0.3177,0.1076	benign	438/1138	79974885	14,12992	2203	4300	6503	SO:0001583	missense	4437	exon8			CAGAGGCGCTCAT	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.1313C>T	5.37:g.79974885C>T	ENSP00000265081:p.Ala438Val	62.0	0.0	0		56.0	23.0	0.410714	NM_002439	A1L480|A1L482|A6NMM6|Q6PJT5|Q86UQ6|Q92867	Missense_Mutation	SNP	ENST00000265081.6	37	CCDS34195.1	.	.	.	.	.	.	.	.	.	.	C	14.36	2.513487	0.44660	0.003177	0.0	ENSG00000113318	ENST00000265081;ENST00000535995	D	0.86562	-2.14	5.51	-11.0	0.00169	DNA mismatch repair protein MutS, connector (2);	1.009680	0.07961	N	0.982372	T	0.70185	0.3195	N	0.14661	0.345	0.09310	N	1	B	0.22800	0.075	B	0.21546	0.035	T	0.55780	-0.8087	9	.	.	.	4.4871	11.55	0.50715	0.1018:0.6438:0.1479:0.1066	rs35121792	438	P20585	MSH3_HUMAN	V	438;429	ENSP00000265081:A438V	.	A	+	2	0	MSH3	80010641	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-1.700000	0.01905	-2.495000	0.00514	-1.181000	0.01715	GCG	C|0.999;T|0.001	0.001	strong		0.473	MSH3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369471.1	NM_002439	
TTN	7273	hgsc.bcm.edu	37	2	179447787	179447787	+	Missense_Mutation	SNP	G	G	T	rs62618736	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179447787G>T	ENST00000591111.1	-	263	61044	c.60820C>A	c.(60820-60822)Cag>Aag	p.Q20274K	TTN-AS1_ENST00000590743.1_RNA|RP11-171I2.2_ENST00000603521.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.Q13042K|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.Q19347K|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.Q12975K|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.Q12850K|TTN_ENST00000589042.1_Missense_Mutation_p.Q21915K			Q8WZ42	TITIN_HUMAN	titin	20274	Ig-like 111.				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)			AGATTCCGCTGCATGGCCATC	0.458													G|||	80	0.0159744	0.0575	0.0058	5008	,	,		18275	0.0		0.0	False		,,,				2504	0.0				p.Q21915K		Atlas-SNP	.											.	TTN	18412	.	0			c.C65743A						PASS	.	G	LYS/GLN,LYS/GLN,LYS/GLN,LYS/GLN	187,3793		5,177,1808	81.0	78.0	79.0		39124,38923,58039,38548	-1.6	1.0	2	dbSNP_129	79	1,8339		0,1,4169	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	53,53,53,53	5,178,5977	TT,TG,GG		0.012,4.6985,1.526	benign,benign,benign,benign	13042/27119,12975/27052,19347/33424,12850/26927	179447787	188,12132	1990	4170	6160	SO:0001583	missense	7273	exon313			TCCGCTGCATGGC	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.60820C>A	2.37:g.179447787G>T	ENSP00000465570:p.Gln20274Lys	182.0	0.0	0		228.0	122.0	0.535088	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		42	0.019230769230769232	39	0.07926829268292683	3	0.008287292817679558	0	0.0	0	0.0	G	14.68	2.608015	0.46527	0.046985	1.2E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.65178	-0.14;-0.14;-0.14;-0.14	5.82	-1.62	0.08372	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.02970	0.0088	N	0.04132	-0.27	0.23946	N	0.99638	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	0.03898	-1.0994	9	0.87932	D	0	.	18.5575	0.91090	0.0:0.0:0.6894:0.3106	rs62618736	12850;12975;13042;20274	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	K	19347;12850;13042;12975;12848	ENSP00000343764:Q19347K;ENSP00000434586:Q12850K;ENSP00000340554:Q13042K;ENSP00000352154:Q12975K	ENSP00000340554:Q13042K	Q	-	1	0	TTN	179156033	0.009000	0.17119	0.957000	0.39632	0.907000	0.53573	0.075000	0.14686	-0.544000	0.06232	-0.274000	0.10170	CAG	G|0.985;T|0.015	0.015	strong		0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ENGASE	64772	hgsc.bcm.edu	37	17	77082390	77082390	+	Missense_Mutation	SNP	G	G	A	rs11871357	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:77082390G>A	ENST00000579016.1	+	14	2191	c.2191G>A	c.(2191-2193)Gag>Aag	p.E731K		NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	731			E -> K (in dbSNP:rs11871357).			cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						ACCTCAGGCCGAGTGGGGCAG	0.652													G|||	226	0.0451278	0.1672	0.0072	5008	,	,		18045	0.0		0.0	False		,,,				2504	0.0				p.E731K		Atlas-SNP	.											ENGASE,NS,carcinoma,-1,1	ENGASE	55	1	0			c.G2191A						PASS	.	G	LYS/GLU	507,3419		28,451,1484	42.0	50.0	47.0		2191	3.7	0.9	17	dbSNP_120	47	12,8276		0,12,4132	yes	missense	ENGASE	NM_001042573.1	56	28,463,5616	AA,AG,GG		0.1448,12.9139,4.2492	possibly-damaging	731/744	77082390	519,11695	1963	4144	6107	SO:0001583	missense	64772	exon14			CAGGCCGAGTGGG	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"""Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase"", ""Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"""	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.2191G>A	17.37:g.77082390G>A	ENSP00000462333:p.Glu731Lys	105.0	0.0	0		76.0	33.0	0.434211	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Missense_Mutation	SNP	ENST00000579016.1	37	CCDS42394.1	62	0.028388278388278388	61	0.12398373983739837	1	0.0027624309392265192	0	0.0	0	0.0	G	9.605	1.129684	0.21041	0.129139	0.001448	ENSG00000167280	ENST00000545583	.	.	.	4.78	3.74	0.42951	.	0.425847	0.25291	N	0.031721	T	0.00328	0.0010	M	0.65975	2.015	0.42538	D	0.993067	P	0.45011	0.848	B	0.33960	0.173	T	0.06972	-1.0797	9	0.15066	T	0.55	-28.3266	3.1644	0.06530	0.0965:0.1746:0.5481:0.1808	rs11871357;rs11871357	731	Q8NFI3	ENASE_HUMAN	K	731	.	ENSP00000438577:E731K	E	+	1	0	ENGASE	74593985	0.563000	0.26594	0.919000	0.36401	0.056000	0.15407	1.450000	0.35134	2.193000	0.70182	0.591000	0.81541	GAG	G|0.965;A|0.035	0.035	strong		0.652	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759	
IFT140	9742	hgsc.bcm.edu	37	16	1618306	1618306	+	Missense_Mutation	SNP	C	C	T	rs8050974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1618306C>T	ENST00000426508.2	-	15	2045	c.1682G>A	c.(1681-1683)aGc>aAc	p.S561N	IFT140_ENST00000439987.2_5'UTR	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	561			S -> N (in dbSNP:rs8050974).		cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				CTCCGCCAGGCTCCTGCAGCT	0.662													C|||	128	0.0255591	0.0953	0.0029	5008	,	,		18208	0.0		0.0	False		,,,				2504	0.0				p.S561N		Atlas-SNP	.											.	IFT140	128	.	0			c.G1682A						PASS	.	C	ASN/SER	393,4005	193.0+/-218.2	17,359,1823	71.0	51.0	58.0		1682	-4.9	0.9	16	dbSNP_116	58	2,8598	1.2+/-3.3	0,2,4298	yes	missense	IFT140	NM_014714.3	46	17,361,6121	TT,TC,CC		0.0233,8.9359,3.0389	benign	561/1463	1618306	395,12603	2199	4300	6499	SO:0001583	missense	9742	exon15			GCCAGGCTCCTGC	AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	29077	protein-coding gene	gene with protein product		614620	"""WD and tetratricopeptide repeats 2"", ""intraflagellar transport 140 homolog (Chlamydomonas)"""	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.1682G>A	16.37:g.1618306C>T	ENSP00000406012:p.Ser561Asn	98.0	0.0	0		125.0	59.0	0.472	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Missense_Mutation	SNP	ENST00000426508.2	37	CCDS10439.1	55	0.025183150183150184	54	0.10975609756097561	1	0.0027624309392265192	0	0.0	0	0.0	C	0.085	-1.177507	0.01633	0.089359	2.33E-4	ENSG00000187535	ENST00000397417;ENST00000426508;ENST00000439987	T	0.70516	-0.49	5.79	-4.95	0.03048	.	0.370546	0.32357	N	0.006210	T	0.00724	0.0024	N	0.02854	-0.475	0.09310	N	0.999996	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.07947	-1.0746	10	0.10902	T	0.67	.	10.6786	0.45799	0.0:0.453:0.0951:0.4519	rs8050974;rs8050974	561;286	Q96RY7;B4DR58	IF140_HUMAN;.	N	561	ENSP00000406012:S561N	ENSP00000380562:S561N	S	-	2	0	IFT140	1558307	0.997000	0.39634	0.855000	0.33649	0.090000	0.18270	0.272000	0.18644	-1.081000	0.03105	-1.110000	0.02074	AGC	C|0.964;T|0.036	0.036	strong		0.662	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714	
TOP3A	7156	hgsc.bcm.edu	37	17	18217958	18217958	+	Silent	SNP	C	C	T	rs2230153	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18217958C>T	ENST00000321105.5	-	1	349	c.135G>A	c.(133-135)gcG>gcA	p.A45A	TOP3A_ENST00000582230.1_5'UTR|TOP3A_ENST00000542570.1_5'UTR|SMCR8_ENST00000406438.3_5'Flank	NM_004618.3	NP_004609.1	Q13472	TOP3A_HUMAN	topoisomerase (DNA) III alpha	45	Toprim. {ECO:0000255|PROSITE- ProRule:PRU00995}.				DNA topological change (GO:0006265)|meiotic nuclear division (GO:0007126)	chromosome (GO:0005694)|nucleus (GO:0005634)|PML body (GO:0016605)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(2)|urinary_tract(1)	36						TCCCCTTGGCCGCGTCGTTTT	0.657													C|||	231	0.0461262	0.1596	0.0259	5008	,	,		17522	0.0		0.002	False		,,,				2504	0.0				p.A45A		Atlas-SNP	.											.	TOP3A	85	.	0			c.G135A						PASS	.	C		552,3854	248.1+/-256.1	40,472,1691	55.0	43.0	47.0		135	1.0	1.0	17	dbSNP_116	47	48,8552	29.6+/-80.5	0,48,4252	no	coding-synonymous	TOP3A	NM_004618.3		40,520,5943	TT,TC,CC		0.5581,12.5284,4.6133		45/1002	18217958	600,12406	2203	4300	6503	SO:0001819	synonymous_variant	7156	exon1			CTTGGCCGCGTCG	U43431	CCDS11194.1	17p12-p11.2	2014-02-18			ENSG00000177302	ENSG00000177302			11992	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 7"""	601243		TOP3		9450867	Standard	NM_004618		Approved	ZGRF7	uc002gsx.1	Q13472	OTTHUMG00000059391	ENST00000321105.5:c.135G>A	17.37:g.18217958C>T		107.0	0.0	0		175.0	89.0	0.508571	NM_004618	A8KA61|B4DK80|D3DXC7|Q13473	Silent	SNP	ENST00000321105.5	37	CCDS11194.1	90	0.04120879120879121	78	0.15853658536585366	11	0.03038674033149171	0	0.0	1	0.0013192612137203166	C	14.01	2.407166	0.42715	0.125284	0.005581	ENSG00000177302	ENST00000412083	.	.	.	5.44	1.01	0.19927	.	.	.	.	.	T	0.00178	0.0005	.	.	.	0.09310	P	0.9999999999999994	.	.	.	.	.	.	T	0.11012	-1.0605	3	.	.	.	-26.1119	6.8195	0.23849	0.4676:0.3924:0.0:0.14	rs7212337	.	.	.	S	25	.	.	G	-	1	0	TOP3A	18158683	0.002000	0.14202	1.000000	0.80357	0.984000	0.73092	-1.659000	0.01975	0.367000	0.24454	0.655000	0.94253	GGC	C|0.948;T|0.052	0.052	strong		0.657	TOP3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132052.2		
DOK3	79930	hgsc.bcm.edu	37	5	176936822	176936822	+	Missense_Mutation	SNP	G	G	A	rs371788222		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:176936822G>A	ENST00000357198.4	-	1	36	c.32C>T	c.(31-33)gCg>gTg	p.A11V	DOK3_ENST00000377112.4_Intron|DOK3_ENST00000312943.6_Intron|DOK3_ENST00000501403.2_Intron	NM_024872.2	NP_079148.2	Q7L591	DOK3_HUMAN	docking protein 3	11					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)			CTGGGCACGCGCGTCTGATCG	0.711																																					p.A11V		Atlas-SNP	.											DOK3,NS,carcinoma,-1,1	DOK3	41	1	0			c.C32T						PASS	.	G	,,VAL/ALA	1,4403	2.1+/-5.4	0,1,2201	52.0	52.0	52.0		,,32	2.3	0.0	5		52	0,8600		0,0,4300	no	intron,intron,missense	DOK3	NM_001144875.1,NM_001144876.1,NM_024872.2	,,64	0,1,6501	AA,AG,GG		0.0,0.0227,0.0077	,,benign	,,11/497	176936822	1,13003	2202	4300	6502	SO:0001583	missense	79930	exon1			GCACGCGCGTCTG	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.32C>T	5.37:g.176936822G>A	ENSP00000349727:p.Ala11Val	253.0	1.0	0.00395257		310.0	144.0	0.464516	NM_024872	E9PAT0|H7BXS0|Q8N864|Q9BQB3|Q9H666	Missense_Mutation	SNP	ENST00000357198.4	37	CCDS4426.1	.	.	.	.	.	.	.	.	.	.	G	13.18	2.161465	0.38119	2.27E-4	0.0	ENSG00000146094	ENST00000357198	T	0.20200	2.09	3.22	2.34	0.29019	.	1.986640	0.03416	U	0.205582	T	0.12263	0.0298	N	0.08118	0	0.20563	N	0.999886	B	0.25955	0.138	B	0.11329	0.006	T	0.21381	-1.0247	10	0.87932	D	0	-23.7375	6.3296	0.21262	0.1376:0.0:0.8624:0.0	.	11	Q7L591	DOK3_HUMAN	V	11	ENSP00000349727:A11V	ENSP00000349727:A11V	A	-	2	0	DOK3	176869428	.	.	0.005000	0.12908	0.011000	0.07611	.	.	0.915000	0.36847	0.491000	0.48974	GCG	.	.	weak		0.711	DOK3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253420.4	NM_024872	
AKAP11	11215	hgsc.bcm.edu	37	13	42876996	42876996	+	Missense_Mutation	SNP	G	G	A	rs114980445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:42876996G>A	ENST00000025301.2	+	8	4289	c.4114G>A	c.(4114-4116)Gcc>Acc	p.A1372T		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	1372					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		CAATAGGCTTGCCTACCGATC	0.413													G|||	22	0.00439297	0.0144	0.0043	5008	,	,		21346	0.0		0.0	False		,,,				2504	0.0				p.A1372T		Atlas-SNP	.											.	AKAP11	146	.	0			c.G4114A						PASS	.	G	THR/ALA	79,4327	69.8+/-107.6	0,79,2124	88.0	82.0	84.0		4114	6.2	1.0	13	dbSNP_132	84	1,8599	1.2+/-3.3	0,1,4299	yes	missense	AKAP11	NM_016248.3	58	0,80,6423	AA,AG,GG		0.0116,1.793,0.6151	probably-damaging	1372/1902	42876996	80,12926	2203	4300	6503	SO:0001583	missense	11215	exon8			AGGCTTGCCTACC	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	369	protein-coding gene	gene with protein product	"""AKAP 220"", ""A-kinase anchoring protein, 220kDa"", ""protein kinase A anchoring protein 11"", ""protein phosphatase 1, regulatory subunit 44"""	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.4114G>A	13.37:g.42876996G>A	ENSP00000025301:p.Ala1372Thr	52.0	0.0	0		65.0	26.0	0.4	NM_016248	O75124|Q9NUK7	Missense_Mutation	SNP	ENST00000025301.2	37	CCDS9383.1	14	0.00641025641025641	12	0.024390243902439025	2	0.0055248618784530384	0	0.0	0	0.0	G	28.1	4.892258	0.91889	0.01793	1.16E-4	ENSG00000023516	ENST00000025301	T	0.56444	0.46	6.16	6.16	0.99307	.	0.065315	0.64402	D	0.000013	T	0.60287	0.2257	M	0.71581	2.175	0.54753	D	0.999989	D	0.89917	1.0	D	0.72982	0.979	T	0.69194	-0.5209	10	0.87932	D	0	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	1372	Q9UKA4	AKA11_HUMAN	T	1372	ENSP00000025301:A1372T	ENSP00000025301:A1372T	A	+	1	0	AKAP11	41774996	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.096000	0.94182	2.937000	0.99478	0.650000	0.86243	GCC	G|0.992;A|0.008	0.008	strong		0.413	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248	
PPEF2	5470	hgsc.bcm.edu	37	4	76797551	76797551	+	Missense_Mutation	SNP	C	C	G	rs370312706		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:76797551C>G	ENST00000286719.7	-	11	1565	c.1209G>C	c.(1207-1209)caG>caC	p.Q403H		NM_006239.2	NP_006230.2	O14830	PPE2_HUMAN	protein phosphatase, EF-hand calcium binding domain 2	403	Catalytic.				detection of stimulus involved in sensory perception (GO:0050906)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|protein dephosphorylation (GO:0006470)|regulation of JUN kinase activity (GO:0043506)|regulation of MAP kinase activity (GO:0043405)|visual perception (GO:0007601)	cilium (GO:0005929)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|Hsp70 protein binding (GO:0030544)|Hsp90 protein binding (GO:0051879)|iron ion binding (GO:0005506)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	50			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			GGCCTGCTTGCTGCCGGCACC	0.677																																					p.Q403H	NSCLC(105;1359 1603 15961 44567 47947)	Atlas-SNP	.											.	PPEF2	108	.	0			c.G1209C						PASS	.						29.0	32.0	31.0					4																	76797551		2203	4300	6503	SO:0001583	missense	5470	exon11			TGCTTGCTGCCGG	AF023456	CCDS34013.1	4q21.1	2013-01-10			ENSG00000156194	ENSG00000156194		"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"", ""EF-hand domain containing"""	9244	protein-coding gene	gene with protein product	"""protein phosphatase 7, catalytic subunit, beta isozyme"""	602256				9326663, 12051765	Standard	NM_006239		Approved	PPP7CB	uc003hix.3	O14830	OTTHUMG00000160915	ENST00000286719.7:c.1209G>C	4.37:g.76797551C>G	ENSP00000286719:p.Gln403His	98.0	0.0	0		86.0	40.0	0.465116	NM_006239	O14831	Missense_Mutation	SNP	ENST00000286719.7	37	CCDS34013.1	.	.	.	.	.	.	.	.	.	.	C	11.77	1.738539	0.30774	.	.	ENSG00000156194	ENST00000286719;ENST00000337500	T	0.41758	0.99	4.94	3.21	0.36854	Serine/threonine-specific protein phosphatase/bis(5-nucleosyl)-tetraphosphatase (1);Metallophosphoesterase domain (1);	1.466720	0.04609	N	0.399943	T	0.43100	0.1232	L	0.41236	1.265	0.25277	N	0.989465	P;P	0.41569	0.755;0.6	P;B	0.44946	0.465;0.382	T	0.29640	-1.0005	10	0.33940	T	0.23	0.0283	9.0738	0.36508	0.0:0.8174:0.0:0.1826	.	403;403	O14830-2;O14830	.;PPE2_HUMAN	H	403	ENSP00000286719:Q403H	ENSP00000286719:Q403H	Q	-	3	2	PPEF2	77016575	0.764000	0.28473	0.014000	0.15608	0.095000	0.18619	2.772000	0.47678	0.510000	0.28216	-0.339000	0.08088	CAG	.	.	alt		0.677	PPEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362929.1	NM_006239	
POFUT1	23509	hgsc.bcm.edu	37	20	30822455	30822455	+	Silent	SNP	C	C	T	rs7263390	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:30822455C>T	ENST00000375749.3	+	7	1220	c.1158C>T	c.(1156-1158)gaC>gaT	p.D386D	POFUT1_ENST00000539210.1_Silent_p.D175D	NM_015352.1	NP_056167.1	Q9H488	OFUT1_HUMAN	protein O-fucosyltransferase 1	386					angiogenesis (GO:0001525)|embryo development (GO:0009790)|fucose metabolic process (GO:0006004)|heart development (GO:0007507)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|O-glycan processing (GO:0016266)|protein O-linked fucosylation (GO:0036066)|protein O-linked glycosylation (GO:0006493)|regulation of transcription, DNA-templated (GO:0006355)|somitogenesis (GO:0001756)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	fucosyltransferase activity (GO:0008417)|peptide-O-fucosyltransferase activity (GO:0046922)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)|urinary_tract(1)	6			UCEC - Uterine corpus endometrioid carcinoma (5;0.0241)			AGCTGCGGGACGAGTTCTGAT	0.632													C|||	92	0.0183706	0.0651	0.0086	5008	,	,		18001	0.0		0.0	False		,,,				2504	0.0				p.D386D		Atlas-SNP	.											.	POFUT1	52	.	0			c.C1158T						PASS	.	C		233,4173	136.1+/-172.1	8,217,1978	54.0	54.0	54.0		1158	-3.8	1.0	20	dbSNP_116	54	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	POFUT1	NM_015352.1		8,224,6271	TT,TC,CC		0.0814,5.2882,1.8453		386/389	30822455	240,12766	2203	4300	6503	SO:0001819	synonymous_variant	23509	exon7			GCGGGACGAGTTC	AF375884	CCDS13198.1, CCDS13199.1	20q11	2013-03-06			ENSG00000101346	ENSG00000101346	2.4.1.221	"""Fucosyltransferases"""	14988	protein-coding gene	gene with protein product	"""peptide-O-fucosyltransferase"", ""GDP-fucose protein O-fucosyltransferase 1"""	607491				9023546, 9525914	Standard	NM_015352		Approved	O-FUT, O-Fuc-T, KIAA0180, FUT12	uc002wxp.3	Q9H488	OTTHUMG00000133268	ENST00000375749.3:c.1158C>T	20.37:g.30822455C>T		95.0	0.0	0		91.0	44.0	0.483516	NM_015352	A8K4R8|E1P5M4|Q14685|Q5W185|Q9BW76	Silent	SNP	ENST00000375749.3	37	CCDS13198.1																																																																																			C|0.973;T|0.027	0.027	strong		0.632	POFUT1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078613.1	NM_015352	
INTS5	80789	hgsc.bcm.edu	37	11	62415285	62415285	+	Missense_Mutation	SNP	C	C	T	rs149821915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:62415285C>T	ENST00000330574.2	-	2	2319	c.2267G>A	c.(2266-2268)cGt>cAt	p.R756H	GANAB_ENST00000346178.4_5'Flank|GANAB_ENST00000534779.1_5'Flank|GANAB_ENST00000540933.1_5'Flank|GANAB_ENST00000356638.3_5'Flank	NM_030628.1	NP_085131.1	Q6P9B9	INT5_HUMAN	integrator complex subunit 5	756					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|membrane (GO:0016020)				breast(1)|endometrium(4)|large_intestine(6)|lung(20)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	36						CTTTAAGCCACGGCCGATGAC	0.557																																					p.R756H		Atlas-SNP	.											.	INTS5	81	.	0			c.G2267A						PASS	.	C	HIS/ARG	6,4398	11.4+/-27.6	0,6,2196	51.0	57.0	55.0		2267	3.5	1.0	11	dbSNP_134	55	0,8598		0,0,4299	yes	missense	INTS5	NM_030628.1	29	0,6,6495	TT,TC,CC		0.0,0.1362,0.0461	benign	756/1020	62415285	6,12996	2202	4299	6501	SO:0001583	missense	80789	exon2			AAGCCACGGCCGA	AK123587	CCDS8027.1	11q12.3	2006-04-26	2006-03-15	2006-03-15	ENSG00000185085	ENSG00000185085			29352	protein-coding gene	gene with protein product		611349	"""KIAA1698"""	KIAA1698		16239144	Standard	NM_030628		Approved	INT5	uc001nud.3	Q6P9B9	OTTHUMG00000167605	ENST00000330574.2:c.2267G>A	11.37:g.62415285C>T	ENSP00000327889:p.Arg756His	118.0	0.0	0		143.0	75.0	0.524476	NM_030628	Q8N6W5|Q9C0G5	Missense_Mutation	SNP	ENST00000330574.2	37	CCDS8027.1	.	.	.	.	.	.	.	.	.	.	C	7.215	0.596297	0.13875	0.001362	0.0	ENSG00000185085	ENST00000330574	.	.	.	5.43	3.53	0.40419	.	0.200939	0.45867	D	0.000336	T	0.29126	0.0724	L	0.28115	0.83	0.30938	N	0.726113	B	0.10296	0.003	B	0.04013	0.001	T	0.14282	-1.0478	9	0.25106	T	0.35	.	6.0709	0.19889	0.0:0.6759:0.1555:0.1686	.	756	Q6P9B9	INT5_HUMAN	H	756	.	ENSP00000327889:R756H	R	-	2	0	INTS5	62171861	0.146000	0.22672	1.000000	0.80357	0.864000	0.49448	0.847000	0.27696	1.530000	0.49136	-0.145000	0.13849	CGT	C|1.000;T|0.000	0.000	strong		0.557	INTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395327.1	NM_030628	
KRT33B	3884	hgsc.bcm.edu	37	17	39521726	39521726	+	Missense_Mutation	SNP	T	T	C	rs61741663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39521726T>C	ENST00000251646.3	-	4	717	c.668A>G	c.(667-669)cAg>cGg	p.Q223R		NM_002279.4	NP_002270.1	Q14525	KT33B_HUMAN	keratin 33B	223	Coil 2.|Rod.				aging (GO:0007568)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(6)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)	21		Breast(137;0.000496)				GTTCAGGACCTGGTTCAGGTC	0.577													T|||	85	0.0169728	0.0635	0.0014	5008	,	,		18746	0.0		0.0	False		,,,				2504	0.0				p.Q223R		Atlas-SNP	.											KRT33B,NS,carcinoma,0,1	KRT33B	46	1	0			c.A668G						PASS	.	T	ARG/GLN	260,4120		25,210,1955	77.0	73.0	75.0		668	1.7	0.0	17	dbSNP_129	75	0,8600		0,0,4300	no	missense	KRT33B	NM_002279.3	43	25,210,6255	CC,CT,TT		0.0,5.9361,2.0031	benign	223/405	39521726	260,12720	2190	4300	6490	SO:0001583	missense	3884	exon4			AGGACCTGGTTCA	X82634	CCDS11389.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000131738	ENSG00000131738		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6451	protein-coding gene	gene with protein product	"""hard keratin type I 3II"""	602762	"""keratin, hair, acidic, 3B"""	KRTHA3B		7565656, 16831889	Standard	NM_002279		Approved	Ha-3II	uc002hwl.4	Q14525	OTTHUMG00000133429	ENST00000251646.3:c.668A>G	17.37:g.39521726T>C	ENSP00000251646:p.Gln223Arg	220.0	0.0	0		230.0	111.0	0.482609	NM_002279	O76010	Missense_Mutation	SNP	ENST00000251646.3	37	CCDS11389.1	39	0.017857142857142856	38	0.07723577235772358	1	0.0027624309392265192	0	0.0	0	0.0	t	0.004	-2.255496	0.00265	0.059361	0.0	ENSG00000131738	ENST00000251646	D	0.88818	-2.43	4.78	1.66	0.24008	Filament (1);	0.334269	0.24422	N	0.038665	T	0.08403	0.0209	N	0.01289	-0.905	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.42531	-0.9446	10	0.02654	T	1	.	7.0528	0.25083	0.0:0.524:0.0:0.476	rs61741663	223	Q14525	KT33B_HUMAN	R	223	ENSP00000251646:Q223R	ENSP00000251646:Q223R	Q	-	2	0	KRT33B	36775252	0.042000	0.20092	0.037000	0.18230	0.025000	0.11179	0.380000	0.20602	0.300000	0.22699	-0.911000	0.02809	CAG	T|0.976;C|0.024	0.024	strong		0.577	KRT33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257292.1	NM_002279	
TC2N	123036	hgsc.bcm.edu	37	14	92264736	92264736	+	Silent	SNP	A	A	G	rs147695092		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:92264736A>G	ENST00000435962.2	-	7	968	c.645T>C	c.(643-645)atT>atC	p.I215I	TC2N_ENST00000556018.1_Silent_p.I215I|TC2N_ENST00000360594.5_Silent_p.I215I|TC2N_ENST00000340892.5_Silent_p.I215I	NM_001128596.1	NP_001122068	Q8N9U0	TAC2N_HUMAN	tandem C2 domains, nuclear	215					regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(5)|skin(1)|upper_aerodigestive_tract(2)	18				COAD - Colon adenocarcinoma(157;0.218)		CTGATAGAGTAATTGTATCTG	0.328													A|||	1	0.000199681	0.0008	0.0	5008	,	,		15932	0.0		0.0	False		,,,				2504	0.0				p.I215I		Atlas-SNP	.											.	TC2N	49	.	0			c.T645C						PASS	.	A	,,	4,4392	8.1+/-20.4	0,4,2194	43.0	46.0	45.0		645,645,645	3.2	1.0	14	dbSNP_134	45	0,8570		0,0,4285	no	coding-synonymous,coding-synonymous,coding-synonymous	TC2N	NM_001128595.1,NM_001128596.1,NM_152332.4	,,	0,4,6479	GG,GA,AA		0.0,0.091,0.0308	,,	215/491,215/491,215/491	92264736	4,12962	2198	4285	6483	SO:0001819	synonymous_variant	123036	exon7			TAGAGTAATTGTA	AA243837	CCDS9897.1, CCDS73679.1	14q32.12	2007-10-17	2007-08-17	2007-08-17		ENSG00000165929			19859	protein-coding gene	gene with protein product	"""C2 calcium-dependent domain containing 1"""		"""chromosome 14 open reading frame 47"", ""membrane targeting (tandem) C2 domain containing 1"""	C14orf47, MTAC2D1		11526914	Standard	NM_001128596		Approved	FLJ36557, Tac2-N, C2CD1	uc001xzt.4	Q8N9U0		ENST00000435962.2:c.645T>C	14.37:g.92264736A>G		126.0	0.0	0		133.0	74.0	0.556391	NM_001128596		Silent	SNP	ENST00000435962.2	37	CCDS9897.1																																																																																			A|1.000;G|0.000	0.000	weak		0.328	TC2N-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411778.1	NM_152332	
TCF21	6943	hgsc.bcm.edu	37	6	134210600	134210600	+	Missense_Mutation	SNP	G	G	T	rs56412384	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:134210600G>T	ENST00000367882.4	+	1	325	c.65G>T	c.(64-66)gGg>gTg	p.G22V	RP3-323P13.2_ENST00000607033.1_RNA|RP3-323P13.2_ENST00000606544.1_RNA|TCF21_ENST00000237316.3_Missense_Mutation_p.G22V|RP3-323P13.2_ENST00000607641.1_RNA|RP3-323P13.2_ENST00000607573.1_RNA	NM_003206.3	NP_003197.2	O43680	TCF21_HUMAN	transcription factor 21	22					branching involved in ureteric bud morphogenesis (GO:0001658)|branchiomeric skeletal muscle development (GO:0014707)|bronchiole development (GO:0060435)|diaphragm development (GO:0060539)|embryonic digestive tract morphogenesis (GO:0048557)|epithelial cell differentiation (GO:0030855)|gland development (GO:0048732)|glomerulus development (GO:0032835)|kidney development (GO:0001822)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|lung vasculature development (GO:0060426)|metanephric glomerular capillary formation (GO:0072277)|metanephric mesenchymal cell differentiation (GO:0072162)|morphogenesis of a branching structure (GO:0001763)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|reproductive structure development (GO:0048608)|respiratory system development (GO:0060541)|Sertoli cell differentiation (GO:0060008)|sex determination (GO:0007530)|spleen development (GO:0048536)|ureteric bud development (GO:0001657)|vasculature development (GO:0001944)	nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|protein dimerization activity (GO:0046983)|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)			cervix(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	13	Colorectal(23;0.221)|Breast(56;0.247)			GBM - Glioblastoma multiforme(68;0.00518)|OV - Ovarian serous cystadenocarcinoma(155;0.00783)		GAATGTGACGGGTTGAAAATG	0.567													G|||	298	0.0595048	0.2057	0.0259	5008	,	,		17673	0.004		0.001	False		,,,				2504	0.0031				p.G22V		Atlas-SNP	.											TCF21,NS,carcinoma,+1,1	TCF21	30	1	0			c.G65T	GRCh37	HM050002	TCF21	M	rs56412384	scavenged	.	G	VAL/GLY,VAL/GLY	766,3640	311.6+/-292.2	84,598,1521	97.0	102.0	100.0		65,65	3.5	1.0	6	dbSNP_129	100	17,8583	11.9+/-42.8	0,17,4283	yes	missense,missense	TCF21	NM_003206.3,NM_198392.2	109,109	84,615,5804	TT,TG,GG		0.1977,17.3854,6.0203	benign,benign	22/180,22/180	134210600	783,12223	2203	4300	6503	SO:0001583	missense	6943	exon1			GTGACGGGTTGAA	AF047419	CCDS5167.1	6q23.2	2014-09-17			ENSG00000118526	ENSG00000118526		"""Basic helix-loop-helix proteins"""	11632	protein-coding gene	gene with protein product		603306				9507058	Standard	NM_198392		Approved	POD1, bHLHa23	uc003qei.4	O43680	OTTHUMG00000015608	ENST00000367882.4:c.65G>T	6.37:g.134210600G>T	ENSP00000356857:p.Gly22Val	93.0	1.0	0.0107527		107.0	106.0	0.990654	NM_003206	E1P581|O43545|Q6ICV0|Q9BZ14	Missense_Mutation	SNP	ENST00000367882.4	37	CCDS5167.1	108	0.04945054945054945	94	0.1910569105691057	10	0.027624309392265192	3	0.005244755244755245	1	0.0013192612137203166	G	10.95	1.496669	0.26861	0.173854	0.001977	ENSG00000118526	ENST00000367882;ENST00000237316	D;D	0.96200	-3.94;-3.94	4.43	3.53	0.40419	.	0.306082	0.28566	N	0.014896	D	0.85660	0.5748	L	0.36672	1.1	0.09310	P	0.99999762263	B	0.13594	0.008	B	0.11329	0.006	T	0.76484	-0.2942	9	0.15952	T	0.53	-15.4673	12.9612	0.58460	0.0:0.1708:0.8291:0.0	rs56412384;rs61729590	22	O43680	TCF21_HUMAN	V	22	ENSP00000356857:G22V;ENSP00000237316:G22V	ENSP00000237316:G22V	G	+	2	0	TCF21	134252293	1.000000	0.71417	0.997000	0.53966	0.798000	0.45092	5.440000	0.66563	0.797000	0.33971	0.313000	0.20887	GGG	G|0.944;T|0.056	0.056	strong		0.567	TCF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042292.1	NM_198392	
IFNL3	282617	hgsc.bcm.edu	37	19	39735535	39735535	+	Missense_Mutation	SNP	C	C	A	rs141536970	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39735535C>A	ENST00000413851.2	-	1	111	c.73G>T	c.(73-75)Gcc>Tcc	p.A25S	IFNL4_ENST00000606380.1_RNA	NM_172139.2	NP_742151.2	Q8IZI9	IFNL3_HUMAN	interferon, lambda 3	25					defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|negative regulation of viral genome replication (GO:0045071)|positive regulation of immune response (GO:0050778)	extracellular space (GO:0005615)											CGGAGCCTGGCGACAGGAACT	0.617													C|||	14	0.00279553	0.0098	0.0014	5008	,	,		20221	0.0		0.0	False		,,,				2504	0.0				p.A25S		Atlas-SNP	.											.	.	.	.	0			c.G73T						PASS	.	C	SER/ALA	29,4377	34.3+/-65.2	0,29,2174	61.0	58.0	59.0		73	-4.4	0.0	19	dbSNP_134	59	0,8600		0,0,4300	no	missense	IL28B	NM_172139.2	99	0,29,6474	AA,AC,CC		0.0,0.6582,0.223	benign	25/197	39735535	29,12977	2203	4300	6503	SO:0001583	missense	282617	exon1			GCCTGGCGACAGG	AY129149	CCDS12530.1	19q13.13	2014-05-22	2012-11-26	2012-11-26	ENSG00000197110	ENSG00000197110		"""Interferons"""	18365	protein-coding gene	gene with protein product		607402	"""interleukin 28B"", ""interleukin 28B (interferon, lambda 3)"""	IL28B			Standard	NM_172139		Approved	IL-28B, IL28C	uc010xut.2	Q8IZI9	OTTHUMG00000182805	ENST00000413851.2:c.73G>T	19.37:g.39735535C>A	ENSP00000409000:p.Ala25Ser	321.0	1.0	0.00311526		322.0	171.0	0.531056	NM_172139	A2BDE1|Q6VN56|Q7Z4J3|Q8IWL6	Missense_Mutation	SNP	ENST00000413851.2	37	CCDS12530.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	8.463	0.855868	0.17106	0.006582	0.0	ENSG00000197110	ENST00000413851	T	0.13657	2.57	3.14	-4.41	0.03590	.	0.976044	0.08385	N	0.953834	T	0.01156	0.0038	N	0.00347	-1.61	0.09310	N	1	B	0.14438	0.01	B	0.17433	0.018	T	0.40757	-0.9546	10	0.30854	T	0.27	-2.8121	1.9017	0.03269	0.1148:0.1693:0.2396:0.4763	.	25	Q8IZI9	IL28B_HUMAN	S	25	ENSP00000409000:A25S	ENSP00000409000:A25S	A	-	1	0	IL28B	44427375	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.104000	0.10923	-0.417000	0.07461	-1.495000	0.00966	GCC	A|0.003;C|0.997	0.003	strong		0.617	IFNL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463832.1	NM_172139	
ACSM4	341392	hgsc.bcm.edu	37	12	7477100	7477100	+	Missense_Mutation	SNP	G	G	A	rs61584783		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:7477100G>A	ENST00000399422.4	+	11	1490	c.1442G>A	c.(1441-1443)cGt>cAt	p.R481H		NM_001080454.1	NP_001073923.1	P0C7M7	ACSM4_HUMAN	acyl-CoA synthetase medium-chain family member 4	481			R -> H (in dbSNP:rs61584783).		acyl-CoA metabolic process (GO:0006637)|fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|fatty-acyl-CoA synthase activity (GO:0004321)|metal ion binding (GO:0046872)			endometrium(6)|kidney(1)|lung(14)	21						TTCAGGTACCGTATTGGGCCA	0.463													G|||	155	0.0309505	0.1127	0.0086	5008	,	,		-128	0.0		0.0	False		,,,				2504	0.0				p.R481H		Atlas-SNP	.											.	ACSM4	98	.	0			c.G1442A						PASS	.	G	HIS/ARG	395,3577		24,347,1615	139.0	128.0	132.0		1442	1.8	1.0	12	dbSNP_129	132	1,8369		0,1,4184	yes	missense	ACSM4	NM_001080454.1	29	24,348,5799	AA,AG,GG		0.0119,9.9446,3.2086	probably-damaging	481/581	7477100	396,11946	1986	4185	6171	SO:0001583	missense	341392	exon11			GGTACCGTATTGG		CCDS44825.1	12p13.31	2008-06-12			ENSG00000215009	ENSG00000215009		"""Acyl-CoA synthetase family"""	32016	protein-coding gene	gene with protein product	"""similar to olfactory specific medium-chain acyl CoA synthetase"""	614360				17762044	Standard	NM_001080454		Approved		uc001qsx.1	P0C7M7	OTTHUMG00000154975	ENST00000399422.4:c.1442G>A	12.37:g.7477100G>A	ENSP00000382349:p.Arg481His	174.0	0.0	0		157.0	76.0	0.484076	NM_001080454	A8MTI6	Missense_Mutation	SNP	ENST00000399422.4	37	CCDS44825.1	57	0.0260989010989011	54	0.10975609756097561	3	0.008287292817679558	0	0.0	0	0.0	G	17.40	3.379356	0.61845	0.099446	1.19E-4	ENSG00000215009	ENST00000399422	T	0.15256	2.44	2.74	1.84	0.25277	AMP-dependent synthetase/ligase (1);	0.000000	0.38959	U	0.001517	T	0.01061	0.0035	M	0.92122	3.275	0.40110	D	0.97647	D	0.89917	1.0	D	0.79108	0.992	T	0.00431	-1.1743	10	0.87932	D	0	-4.6674	7.7673	0.28986	0.1334:0.0:0.8666:0.0	rs61584783	481	P0C7M7	ACSM4_HUMAN	H	481	ENSP00000382349:R481H	ENSP00000382349:R481H	R	+	2	0	ACSM4	7368367	1.000000	0.71417	0.984000	0.44739	0.981000	0.71138	6.064000	0.71169	0.721000	0.32231	0.557000	0.71058	CGT	G|0.979;A|0.021	0.021	strong		0.463	ACSM4-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000337866.2	NM_001080454	
HLA-A	3105	hgsc.bcm.edu	37	6	29910660	29910660	+	Missense_Mutation	SNP	A	A	G	rs41559117	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29910660A>G	ENST00000396634.1	+	4	541	c.200A>G	c.(199-201)cAg>cGg	p.Q67R	HLA-A_ENST00000376809.5_Missense_Mutation_p.Q67R|HLA-A_ENST00000376806.5_Missense_Mutation_p.Q67R|HLA-A_ENST00000376802.2_Missense_Mutation_p.Q67R			P16189	1A31_HUMAN	major histocompatibility complex, class I, A	67	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	beta-2-microglobulin binding (GO:0030881)|peptide antigen binding (GO:0042605)|TAP binding (GO:0046977)			central_nervous_system(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	30						GCCGCGAGCCAGAGGATGGAG	0.682									Osteosarcoma, Familial Clustering of;Naso-/Oropharyngeal/Laryngeal Cancer, Familial Clustering of;Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of	Multiple Myeloma(9;0.094)			a|||	114	0.0227636	0.0575	0.0288	5008	,	,		14823	0.002		0.007	False		,,,				2504	0.0092				p.Q67R		Atlas-SNP	.											.	HLA-A	89	.	0			c.A200G						PASS	.	A	ARG/GLN	189,4215		2,185,2015	48.0	46.0	46.0		200	-0.8	0.2	6	dbSNP_127	46	76,8522		0,76,4223	no	missense	HLA-A	NM_002116.7	43	2,261,6238	GG,GA,AA		0.8839,4.2916,2.0381	possibly-damaging	67/366	29910660	265,12737	2202	4299	6501	SO:0001583	missense	3105	exon2	Familial Cancer Database	Familial Osteogenic Sarcoma;incl.: Familial Head and Neck Cancer; ;Lichen Sclerosis, Familial	CGAGCCAGAGGAT	D32129	CCDS34373.1	6p21.3	2013-01-11			ENSG00000206503	ENSG00000206503		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4931	protein-coding gene	gene with protein product		142800				8838351	Standard	NM_001242758		Approved		uc003nol.3	P01891	OTTHUMG00000130501	ENST00000396634.1:c.200A>G	6.37:g.29910660A>G	ENSP00000379873:p.Gln67Arg	134.0	0.0	0		219.0	54.0	0.246575	NM_001242758	O62924|O98009|O98137|Q8MHM1|Q9TPQ3|Q9TQ24|Q9UQU6|Q9UQU7	Missense_Mutation	SNP	ENST00000396634.1	37	CCDS34373.1	36	0.016483516483516484	22	0.044715447154471545	8	0.022099447513812154	2	0.0034965034965034965	4	0.005277044854881266	.	6.554	0.470589	0.12461	0.042916	0.008839	ENSG00000206503	ENST00000396634;ENST00000376806;ENST00000376809;ENST00000355767;ENST00000376802	T;T;T;T	0.00705	5.81;5.81;5.81;5.81	3.72	-0.813	0.10850	MHC class I, alpha chain, alpha1/alpha2 (3);MHC classes I/II-like antigen recognition protein (3);MHC class I-like antigen recognition (3);	.	.	.	.	T	0.00580	0.0019	N	0.21545	0.675	0.09310	N	1	B;D;B;D;B	0.54772	0.0;0.968;0.001;0.968;0.0	B;D;B;D;B	0.75484	0.006;0.986;0.006;0.986;0.006	T	0.55673	-0.8104	9	0.49607	T	0.09	.	5.0607	0.14555	0.5529:0.3361:0.0:0.1109	rs41559117	67;67;67;67;67	P13746;Q5SRN7;P16188;Q5SRN5;P04439	1A11_HUMAN;.;1A30_HUMAN;.;1A03_HUMAN	R	67	ENSP00000379873:Q67R;ENSP00000366002:Q67R;ENSP00000366005:Q67R;ENSP00000365998:Q67R	ENSP00000348012:Q67R	Q	+	2	0	HLA-A	30018639	0.000000	0.05858	0.192000	0.23308	0.357000	0.29423	-1.236000	0.02925	0.031000	0.15407	-1.821000	0.00599	CAG	A|0.977;C|0.002;G|0.021	0.021	strong		0.682	HLA-A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252909.1	NM_002116	
SPRR1A	6698	hgsc.bcm.edu	37	1	152957856	152957856	+	Missense_Mutation	SNP	C	C	G	rs143282605		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152957856C>G	ENST00000368762.1	+	1	150	c.150C>G	c.(148-150)caC>caG	p.H50Q	SPRR1A_ENST00000307122.2_Missense_Mutation_p.H50Q			P35321	SPR1A_HUMAN	small proline-rich protein 1A	50	6 X 8 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(2)|endometrium(1)|large_intestine(1)|liver(2)|lung(1)	7	Lung NSC(65;1.46e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			AGCCCTGCCACCCCAAAGTGC	0.647																																					p.H50Q		Atlas-SNP	.											.	SPRR1A	17	.	0			c.C150G						PASS	.																																			SO:0001583	missense	6698	exon2			CTGCCACCCCAAA	L05187	CCDS1032.1	1q21-q22	2008-02-05			ENSG00000169474	ENSG00000169474			11259	protein-coding gene	gene with protein product		182265				8325635	Standard	NM_005987		Approved		uc001faw.3	P35321	OTTHUMG00000014404	ENST00000368762.1:c.150C>G	1.37:g.152957856C>G	ENSP00000357751:p.His50Gln	158.0	0.0	0		125.0	24.0	0.192	NM_001199828	B1AN47|D3DV31|Q2M303|Q9UDG4	Missense_Mutation	SNP	ENST00000368762.1	37	CCDS1032.1	.	.	.	.	.	.	.	.	.	.	C	3.605	-0.080674	0.07141	.	.	ENSG00000169474	ENST00000307122;ENST00000368762	T;T	0.11169	2.8;2.8	5.64	-8.48	0.00935	.	0.637243	0.13026	N	0.419668	T	0.01222	0.0040	.	.	.	0.09310	N	0.999997	B	0.30326	0.276	B	0.32393	0.145	T	0.37009	-0.9724	9	0.29301	T	0.29	-0.4448	1.0644	0.01608	0.3555:0.2828:0.17:0.1916	.	50	P35321	SPR1A_HUMAN	Q	50	ENSP00000307340:H50Q;ENSP00000357751:H50Q	ENSP00000307340:H50Q	H	+	3	2	SPRR1A	151224480	0.020000	0.18652	0.125000	0.21846	0.298000	0.27526	-1.221000	0.02968	-1.749000	0.01330	-0.300000	0.09419	CAC	.	.	weak		0.647	SPRR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040062.1	NM_005987	
A2M	2	hgsc.bcm.edu	37	12	9251209	9251209	+	Silent	SNP	C	C	T	rs185750870		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:9251209C>T	ENST00000318602.7	-	15	2152	c.1845G>A	c.(1843-1845)gcG>gcA	p.A615A		NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	615					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)			breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	TCACCGAGGACGCCGAGAGCT	0.572													C|||	18	0.00359425	0.0129	0.0014	5008	,	,		-128	0.0		0.0	False		,,,				2504	0.0				p.A615A		Atlas-SNP	.											.	A2M	180	.	0			c.G1845A						PASS	.	C		41,4365		0,41,2162	28.0	28.0	28.0		1845	-11.1	0.0	12		28	1,8597		0,1,4298	no	coding-synonymous	A2M	NM_000014.4		0,42,6460	TT,TC,CC		0.0116,0.9305,0.323		615/1475	9251209	42,12962	2203	4299	6502	SO:0001819	synonymous_variant	2	exon15			CGAGGACGCCGAG	BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899			7	protein-coding gene	gene with protein product		103950					Standard	XM_006719056		Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.1845G>A	12.37:g.9251209C>T		59.0	0.0	0		77.0	42.0	0.545455	NM_000014	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Silent	SNP	ENST00000318602.7	37	CCDS44827.1																																																																																			C|0.998;T|0.002	0.002	strong		0.572	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014	
TADA2A	6871	hgsc.bcm.edu	37	17	35830554	35830554	+	Missense_Mutation	SNP	A	A	C	rs142392695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:35830554A>C	ENST00000394395.2	+	13	1119	c.946A>C	c.(946-948)Aaa>Caa	p.K316Q	TADA2A_ENST00000591992.1_3'UTR|TADA2A_ENST00000225396.6_Missense_Mutation_p.K316Q	NM_001166105.1	NP_001159577.1	O75478	TAD2A_HUMAN	transcriptional adaptor 2A	316					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|transcription from RNA polymerase II promoter (GO:0006366)	chromosome (GO:0005694)|nucleus (GO:0005634)|PCAF complex (GO:0000125)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)|zinc ion binding (GO:0008270)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|lung(3)|prostate(1)|skin(1)	13						AGAGCGCCTTAAACGCACTAT	0.507													A|||	16	0.00319489	0.0121	0.0	5008	,	,		16970	0.0		0.0	False		,,,				2504	0.0				p.K316Q		Atlas-SNP	.											.	TADA2A	91	.	0			c.A946C						PASS	.	A	GLN/LYS,GLN/LYS	52,4354	52.9+/-88.7	0,52,2151	143.0	135.0	138.0		946,946	5.6	1.0	17	dbSNP_134	138	0,8600		0,0,4300	yes	missense,missense	TADA2A	NM_001166105.1,NM_001488.3	53,53	0,52,6451	CC,CA,AA		0.0,1.1802,0.3998	possibly-damaging,possibly-damaging	316/444,316/444	35830554	52,12954	2203	4300	6503	SO:0001583	missense	6871	exon13			CGCCTTAAACGCA	AK022767	CCDS11319.1, CCDS45656.1	17q12-q21	2014-04-10	2009-10-02	2009-10-02	ENSG00000108264	ENSG00000276234			11531	protein-coding gene	gene with protein product		602276	"""transcriptional adaptor 2 (ADA2 homolog, yeast)-like"""	TADA2L		8552087	Standard	XM_006722043		Approved	ADA2, hADA2, ADA2A	uc002hnt.3	O75478	OTTHUMG00000188469	ENST00000394395.2:c.946A>C	17.37:g.35830554A>C	ENSP00000377918:p.Lys316Gln	71.0	0.0	0		71.0	33.0	0.464789	NM_001488	A8MVD0|B3KMU9|Q9BVJ0|Q9UCW2|Q9UP49	Missense_Mutation	SNP	ENST00000394395.2	37	CCDS11319.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	A	25.5	4.644355	0.87859	0.011802	0.0	ENSG00000108264	ENST00000394395;ENST00000428846;ENST00000225396	T;T	0.43294	0.95;0.95	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	T	0.18299	0.0439	N	0.14661	0.345	0.80722	D	1	P	0.47409	0.895	B	0.38056	0.264	T	0.05194	-1.0900	10	0.16420	T	0.52	-20.0499	15.8074	0.78524	1.0:0.0:0.0:0.0	.	316	O75478	TAD2A_HUMAN	Q	316;215;316	ENSP00000377918:K316Q;ENSP00000225396:K316Q	ENSP00000225396:K316Q	K	+	1	0	TADA2A	32904667	1.000000	0.71417	0.998000	0.56505	0.945000	0.59286	8.946000	0.92992	2.127000	0.65507	0.533000	0.62120	AAA	A|0.996;C|0.004	0.004	strong		0.507	TADA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256677.3	NM_001488	
LAMA2	3908	hgsc.bcm.edu	37	6	129824406	129824406	+	Missense_Mutation	SNP	A	A	G	rs73599293	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:129824406A>G	ENST00000421865.2	+	60	8577	c.8528A>G	c.(8527-8529)aAt>aGt	p.N2843S		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2843	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				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)		ACCAAAATCAATGATGGCCAG	0.493													A|||	96	0.0191693	0.0673	0.0086	5008	,	,		20534	0.0		0.001	False		,,,				2504	0.0				p.N2843S		Atlas-SNP	.											.	LAMA2	481	.	0			c.A8528G						PASS	.	A	SER/ASN,SER/ASN	305,4101	166.2+/-197.5	11,283,1909	81.0	76.0	78.0		8528,8516	5.9	1.0	6	dbSNP_130	78	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	LAMA2	NM_000426.3,NM_001079823.1	46,46	11,287,6205	GG,GA,AA		0.0465,6.9224,2.3758	probably-damaging,probably-damaging	2843/3123,2839/3119	129824406	309,12697	2203	4300	6503	SO:0001583	missense	3908	exon60			AAATCAATGATGG	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.8528A>G	6.37:g.129824406A>G	ENSP00000400365:p.Asn2843Ser	38.0	0.0	0		46.0	26.0	0.565217	NM_000426	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	23	0.010531135531135532	19	0.03861788617886179	4	0.011049723756906077	0	0.0	0	0.0	A	14.58	2.577584	0.45902	0.069224	4.65E-4	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865;ENST00000443169	T	0.71222	-0.55	5.86	5.86	0.93980	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 1 (1);	0.000000	0.85682	D	0.000000	T	0.76593	0.4009	L	0.54863	1.705	0.58432	D	0.999999	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.76329	-0.2999	9	.	.	.	.	16.2479	0.82454	1.0:0.0:0.0:0.0	.	2844;2843	A6NF00;P24043	.;LAMA2_HUMAN	S	2843;2842;2843;861	ENSP00000400365:N2843S	.	N	+	2	0	LAMA2	129866099	1.000000	0.71417	0.998000	0.56505	0.999000	0.98932	7.796000	0.85898	2.241000	0.73720	0.533000	0.62120	AAT	A|0.980;G|0.020	0.020	strong		0.493	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
TTN	7273	hgsc.bcm.edu	37	2	179621353	179621353	+	Intron	SNP	G	G	A	rs57389274	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179621353G>A	ENST00000591111.1	-	44	10528				TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.S3446F|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Intron|TTN_ENST00000360870.5_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.S3617F			Q8WZ42	TITIN_HUMAN	titin						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)			GGAACTTTGAGATACACTTTC	0.383													G|||	98	0.0195687	0.0726	0.0029	5008	,	,		22444	0.0		0.0	False		,,,				2504	0.0				p.S3617F		Atlas-SNP	.											.	TTN	18412	.	0			c.C10850T						PASS	.	G	,,,,PHE/SER	191,3647		6,179,1734	112.0	113.0	113.0		,,,,10337	3.3	0.8	2	dbSNP_129	113	6,8254		0,6,4124	yes	intron,intron,intron,intron,missense	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,155	6,185,5858	AA,AG,GG		0.0726,4.9766,1.6284	,,,,	,,,,3446/27119	179621353	197,11901	1919	4130	6049	SO:0001627	intron_variant	7273	exon46			CTTTGAGATACAC	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.10303+2357C>T	2.37:g.179621353G>A		122.0	0.0	0		135.0	58.0	0.42963	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		36	0.016483516483516484	35	0.07113821138211382	1	0.0027624309392265192	0	0.0	0	0.0	G	12.02	1.813296	0.32053	0.049766	7.26E-4	ENSG00000155657	ENST00000342175	T	0.60672	0.17	6.17	3.3	0.37823	.	.	.	.	.	T	0.06735	0.0172	.	.	.	0.80722	D	1	B	0.24092	0.097	B	0.23150	0.044	T	0.08249	-1.0731	8	0.87932	D	0	.	12.2661	0.54679	0.0:0.1167:0.6404:0.2429	rs57389274	3446	E7ET18	.	F	3446	ENSP00000340554:S3446F	ENSP00000340554:S3446F	S	-	2	0	TTN	179329598	1.000000	0.71417	0.783000	0.31826	0.997000	0.91878	2.776000	0.47709	0.422000	0.26005	0.655000	0.94253	TCT	G|0.982;A|0.018	0.018	strong		0.383	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
DIRC1	116093	hgsc.bcm.edu	37	2	189599373	189599373	+	Missense_Mutation	SNP	A	A	G	rs58846152	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:189599373A>G	ENST00000308100.4	-	2	545	c.275T>C	c.(274-276)tTg>tCg	p.L92S	AC079613.1_ENST00000431708.1_RNA	NM_052952.2	NP_443184.1	Q969H9	DIRC1_HUMAN	disrupted in renal carcinoma 1	92			L -> S (in dbSNP:rs58846152).							large_intestine(1)|lung(6)	7			OV - Ovarian serous cystadenocarcinoma(117;0.00842)|Epithelial(96;0.102)			CCACCCCCTCAATGAGTTAAG	0.383													A|||	167	0.0333466	0.121	0.0086	5008	,	,		18397	0.0		0.001	False		,,,				2504	0.0				p.L92S		Atlas-SNP	.											.	DIRC1	13	.	0			c.T275C						PASS	.	A	SER/LEU	350,4056	180.8+/-209.0	13,324,1866	155.0	160.0	158.0		275	1.2	0.0	2	dbSNP_129	158	2,8598	1.2+/-3.3	0,2,4298	yes	missense	DIRC1	NM_052952.2	145	13,326,6164	GG,GA,AA		0.0233,7.9437,2.7064	benign	92/105	189599373	352,12654	2203	4300	6503	SO:0001583	missense	116093	exon2			CCCCTCAATGAGT	AY039011	CCDS2296.1	2q33	2008-05-22			ENSG00000174325	ENSG00000174325			15760	protein-coding gene	gene with protein product		606423				11587072	Standard	NM_052952		Approved		uc002uqi.1	Q969H9	OTTHUMG00000132646	ENST00000308100.4:c.275T>C	2.37:g.189599373A>G	ENSP00000307860:p.Leu92Ser	214.0	0.0	0		186.0	79.0	0.424731	NM_052952	Q08AK1	Missense_Mutation	SNP	ENST00000308100.4	37	CCDS2296.1	53	0.024267399267399268	49	0.09959349593495935	4	0.011049723756906077	0	0.0	0	0.0	A	1.548	-0.540046	0.04053	0.079437	2.33E-4	ENSG00000174325	ENST00000308100	T	0.42131	0.98	2.38	1.21	0.21127	.	.	.	.	.	T	0.00524	0.0017	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.11251	-1.0595	9	0.87932	D	0	.	4.1545	0.10254	0.8279:0.0:0.1721:0.0	rs58846152	92	Q969H9	DIRC1_HUMAN	S	92	ENSP00000307860:L92S	ENSP00000307860:L92S	L	-	2	0	DIRC1	189307618	0.031000	0.19500	0.003000	0.11579	0.015000	0.08874	0.917000	0.28665	0.329000	0.23460	0.533000	0.62120	TTG	A|0.976;G|0.024	0.024	strong		0.383	DIRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255897.2	NM_052952	
ARMC12	221481	hgsc.bcm.edu	37	6	35716613	35716613	+	Missense_Mutation	SNP	A	A	G	rs73729781	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:35716613A>G	ENST00000373866.3	+	6	1011	c.989A>G	c.(988-990)cAg>cGg	p.Q330R	ARMC12_ENST00000373869.3_Missense_Mutation_p.Q320R|ARMC12_ENST00000288065.2_Missense_Mutation_p.Q357R			Q5T9G4	ARM12_HUMAN	armadillo repeat containing 12	330						nucleus (GO:0005634)											TCCTCCTGCCAGCCCAGTCGT	0.488													A|||	26	0.00519169	0.0189	0.0014	5008	,	,		17917	0.0		0.0	False		,,,				2504	0.0				p.Q357R		Atlas-SNP	.											.	.	.	.	0			c.A1070G						PASS	.	A	ARG/GLN	63,4343	57.4+/-93.9	0,63,2140	44.0	47.0	46.0		1070	-9.5	0.0	6	dbSNP_130	46	0,8600		0,0,4300	yes	missense	C6orf81	NM_145028.3	43	0,63,6440	GG,GA,AA		0.0,1.4299,0.4844	benign	357/368	35716613	63,12943	2203	4300	6503	SO:0001583	missense	221481	exon6			CCTGCCAGCCCAG	AK058119	CCDS4809.1, CCDS69093.1, CCDS69094.1	6p21.31	2013-02-14	2011-12-14	2011-12-14	ENSG00000157343	ENSG00000157343		"""Armadillo repeat containing"""	21099	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 81"""	C6orf81			Standard	XM_005248920		Approved	FLJ25390	uc003ola.3	Q5T9G4	OTTHUMG00000014577	ENST00000373866.3:c.989A>G	6.37:g.35716613A>G	ENSP00000362973:p.Gln330Arg	69.0	0.0	0		75.0	43.0	0.573333	NM_145028	Q8NEB2|Q96LL8	Missense_Mutation	SNP	ENST00000373866.3	37		10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	A	1.845	-0.466582	0.04476	0.014299	0.0	ENSG00000157343	ENST00000373869;ENST00000288065;ENST00000373866	T;T	0.39997	1.05;1.07	4.77	-9.54	0.00572	.	1.744990	0.03118	N	0.163415	T	0.02267	0.0070	N	0.01874	-0.695	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.07102	-1.0790	10	0.02654	T	1	.	1.28	0.02039	0.1771:0.3484:0.2459:0.2287	.	320;357	Q5T9G4-3;Q5T9G4-2	.;.	R	320;357;330	ENSP00000288065:Q357R;ENSP00000362973:Q330R	ENSP00000288065:Q357R	Q	+	2	0	C6orf81	35824591	0.000000	0.05858	0.001000	0.08648	0.269000	0.26545	-0.566000	0.05922	-1.836000	0.01190	-0.400000	0.06385	CAG	A|0.995;G|0.005	0.005	strong		0.488	ARMC12-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040311.2	NM_145028	
ZNF770	54989	hgsc.bcm.edu	37	15	35273867	35273867	+	Missense_Mutation	SNP	C	C	A	rs141323293	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:35273867C>A	ENST00000356321.4	-	3	2113	c.1769G>T	c.(1768-1770)gGt>gTt	p.G590V		NM_014106.3	NP_054825.2	Q6IQ21	ZN770_HUMAN	zinc finger protein 770	590					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)	29		Lung NSC(122;4.59e-10)|all_lung(180;8.78e-09)		all cancers(64;1.97e-18)|GBM - Glioblastoma multiforme(113;2.11e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0643)		CCCGGTGCTACCAGGAATAAA	0.438													C|||	3	0.000599042	0.0023	0.0	5008	,	,		19415	0.0		0.0	False		,,,				2504	0.0				p.G590V		Atlas-SNP	.											.	ZNF770	64	.	0			c.G1769T						PASS	.	C	VAL/GLY	45,4357	46.7+/-81.2	0,45,2156	117.0	119.0	118.0		1769	-0.4	0.0	15	dbSNP_134	118	0,8596		0,0,4298	no	missense	ZNF770	NM_014106.3	109	0,45,6454	AA,AC,CC		0.0,1.0223,0.3462	possibly-damaging	590/692	35273867	45,12953	2201	4298	6499	SO:0001583	missense	54989	exon3			GTGCTACCAGGAA	BC071603	CCDS10042.1	15q14	2013-01-08			ENSG00000198146	ENSG00000198146		"""Zinc fingers, C2H2-type"""	26061	protein-coding gene	gene with protein product							Standard	NM_014106		Approved	FLJ20582, PRO1914	uc001ziw.3	Q6IQ21	OTTHUMG00000129689	ENST00000356321.4:c.1769G>T	15.37:g.35273867C>A	ENSP00000348673:p.Gly590Val	60.0	0.0	0		48.0	22.0	0.458333	NM_014106	Q6ZMZ6|Q9NWV2	Missense_Mutation	SNP	ENST00000356321.4	37	CCDS10042.1	.	.	.	.	.	.	.	.	.	.	C	0.324	-0.960173	0.02267	0.010223	0.0	ENSG00000198146	ENST00000356321	T	0.10288	2.89	5.24	-0.357	0.12579	.	0.716901	0.12735	N	0.443539	T	0.03434	0.0099	N	0.14661	0.345	0.21020	N	0.999802	B	0.16396	0.017	B	0.15052	0.012	T	0.39014	-0.9634	10	0.33141	T	0.24	-0.2229	4.5334	0.12017	0.1656:0.3386:0.0:0.4958	.	590	Q6IQ21	ZN770_HUMAN	V	590	ENSP00000348673:G590V	ENSP00000348673:G590V	G	-	2	0	ZNF770	33061159	0.039000	0.19947	0.021000	0.16686	0.125000	0.20455	0.555000	0.23422	0.090000	0.17273	0.467000	0.42956	GGT	C|0.996;A|0.004	0.004	strong		0.438	ZNF770-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251896.2	NM_014106	
MGAM	8972	hgsc.bcm.edu	37	7	141736732	141736732	+	Missense_Mutation	SNP	G	G	A	rs116034282	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:141736732G>A	ENST00000549489.2	+	18	2281	c.2186G>A	c.(2185-2187)cGt>cAt	p.R729H	MGAM_ENST00000475668.2_Missense_Mutation_p.R729H	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	729	Maltase.				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)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	CTCTTCTTCCGTGCTCACAGC	0.493													G|||	56	0.0111821	0.0401	0.0043	5008	,	,		19313	0.0		0.0	False		,,,				2504	0.0				p.R729H		Atlas-SNP	.											.	MGAM	767	.	0			c.G2186A						PASS	.	G	HIS/ARG	129,3941		3,123,1909	199.0	203.0	202.0		2186	-1.0	0.0	7	dbSNP_132	202	0,8388		0,0,4194	yes	missense	MGAM	NM_004668.2	29	3,123,6103	AA,AG,GG		0.0,3.1695,1.0355	possibly-damaging	729/1858	141736732	129,12329	2035	4194	6229	SO:0001583	missense	8972	exon18			TCTTCCGTGCTCA	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.2186G>A	7.37:g.141736732G>A	ENSP00000447378:p.Arg729His	81.0	0.0	0		100.0	46.0	0.46	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	37	CCDS47727.1	28	0.01282051282051282	26	0.052845528455284556	2	0.0055248618784530384	0	0.0	0	0.0	G	12.77	2.038656	0.35989	0.031695	0.0	ENSG00000257335	ENST00000549489;ENST00000475668;ENST00000548812	D	0.91464	-2.85	5.81	-0.982	0.10266	Glycoside hydrolase, superfamily (1);	0.281671	0.23492	N	0.047582	T	0.44159	0.1280	N	0.20685	0.6	0.09310	N	1	B	0.30021	0.265	B	0.22753	0.041	T	0.54748	-0.8247	10	0.32370	T	0.25	.	11.754	0.51866	0.5808:0.0:0.4192:0.0	.	729	O43451	MGA_HUMAN	H	729;729;606	ENSP00000447378:R729H	ENSP00000316431:R606H	R	+	2	0	MGAM	141383201	0.034000	0.19679	0.000000	0.03702	0.991000	0.79684	0.534000	0.23098	-0.502000	0.06596	-0.145000	0.13849	CGT	G|0.986;A|0.014	0.014	strong		0.493	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
SLC9C2	284525	hgsc.bcm.edu	37	1	173516915	173516915	+	Silent	SNP	G	G	A	rs114115413	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:173516915G>A	ENST00000367714.3	-	13	1892	c.1470C>T	c.(1468-1470)caC>caT	p.H490H	SLC9C2_ENST00000536496.1_Silent_p.H388H|SLC9C2_ENST00000466087.1_5'UTR	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	490					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										TATGTGAAACGTGGGAAAACT	0.353													G|||	61	0.0121805	0.0454	0.0014	5008	,	,		18017	0.0		0.0	False		,,,				2504	0.0				p.H490H		Atlas-SNP	.											.	.	.	.	0			c.C1470T						PASS	.	G		125,4281	92.0+/-130.7	3,119,2081	134.0	119.0	124.0		1470	-8.2	0.0	1	dbSNP_132	124	0,8600		0,0,4300	no	coding-synonymous	SLC9A11	NM_178527.3		3,119,6381	AA,AG,GG		0.0,2.837,0.9611		490/1125	173516915	125,12881	2203	4300	6503	SO:0001819	synonymous_variant	284525	exon13			TGAAACGTGGGAA	AK128104	CCDS1308.1	1q25.1	2013-07-18	2013-07-18	2012-03-22	ENSG00000162753	ENSG00000162753		"""Solute carriers"""	28664	protein-coding gene	gene with protein product			"""solute carrier family 9, isoform 11"", ""solute carrier family 9, member 11"", ""solute carrier family 9, member C2"""	SLC9A11			Standard	NM_178527		Approved	MGC43026	uc001giz.2	Q5TAH2	OTTHUMG00000034800	ENST00000367714.3:c.1470C>T	1.37:g.173516915G>A		114.0	0.0	0		92.0	37.0	0.402174	NM_178527	Q86UF3	Silent	SNP	ENST00000367714.3	37	CCDS1308.1																																																																																			G|0.989;A|0.011	0.011	strong		0.353	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527	
TPGS1	91978	hgsc.bcm.edu	37	19	507560	507560	+	Silent	SNP	G	G	A	rs61746565	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:507560G>A	ENST00000359315.5	+	1	262	c.54G>A	c.(52-54)acG>acA	p.T18T	AC005775.2_ENST00000592413.1_RNA	NM_033513.2	NP_277048.2	Q6ZTW0	TPGS1_HUMAN	tubulin polyglutamylase complex subunit 1	18					adult behavior (GO:0030534)|multicellular organismal development (GO:0007275)|protein polyglutamylation (GO:0018095)|sperm axoneme assembly (GO:0007288)|synaptic transmission (GO:0007268)|vesicle localization (GO:0051648)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)	tubulin-glutamic acid ligase activity (GO:0070740)										CCGGTTTCACGGACAGCGGCC	0.706													G|||	35	0.00698882	0.025	0.0029	5008	,	,		11141	0.0		0.0	False		,,,				2504	0.0				p.T18T		Atlas-SNP	.											.	.	.	.	0			c.G54A						PASS	.						3.0	5.0	5.0					19																	507560		1241	3077	4318	SO:0001819	synonymous_variant	91978	exon1			TTTCACGGACAGC	BC009520	CCDS42454.1	19p13.3	2011-11-23	2011-11-23	2011-11-23	ENSG00000141933	ENSG00000141933			25058	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 20"""	C19orf20		11441184, 12972506	Standard	NM_033513		Approved	GTRGEO22, PGs1	uc002lou.3	Q6ZTW0		ENST00000359315.5:c.54G>A	19.37:g.507560G>A		18.0	0.0	0		24.0	23.0	0.958333	NM_033513	Q96GE2	Silent	SNP	ENST00000359315.5	37	CCDS42454.1																																																																																			G|0.991;A|0.009	0.009	strong		0.706	TPGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451887.2	NM_033513	
MT-ND5	4540	hgsc.bcm.edu	37	M	13789	13789	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:13789T>C	ENST00000361567.2	+	1	1453	c.1453T>C	c.(1453-1455)Tac>Cac	p.Y485H	MT-TT_ENST00000387460.2_RNA|MT-TE_ENST00000387459.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	485					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						CAATCCCCCTCTACCTAAAAC	0.463																																					p.Y485H		Atlas-SNP	.											.	.	.	.	0			c.T1453C						PASS	.																																			SO:0001583	missense	0	exon1			CCCCTCTACCTAA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1453T>C	M.37:g.13789T>C	ENSP00000354813:p.Tyr485His	11.0	0.0	0		5.0	5.0	1	ENST00000361567	Q34773|Q8WCY3	Missense_Mutation	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.463	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
ARHGAP28	79822	hgsc.bcm.edu	37	18	6908976	6908976	+	Missense_Mutation	SNP	G	G	A	rs116232392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:6908976G>A	ENST00000383472.4	+	17	2152	c.2048G>A	c.(2047-2049)tGt>tAt	p.C683Y	ARHGAP28_ENST00000419673.2_Missense_Mutation_p.C524Y|ARHGAP28_ENST00000314319.3_Missense_Mutation_p.C524Y|ARHGAP28_ENST00000531294.1_Missense_Mutation_p.C519Y			Q9P2N2	RHG28_HUMAN	Rho GTPase activating protein 28	683					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	37		Colorectal(10;0.168)				TCATCAGAATGTATTAAGATT	0.284													G|||	125	0.0249601	0.0877	0.0115	5008	,	,		16064	0.0		0.001	False		,,,				2504	0.0				p.C524Y		Atlas-SNP	.											.	ARHGAP28	181	.	0			c.G1571A						PASS	.	G	TYR/CYS	318,4064	152.9+/-186.6	7,304,1880	39.0	45.0	43.0		1571	3.0	0.9	18	dbSNP_132	43	8,8568	5.7+/-21.5	0,8,4280	yes	missense	ARHGAP28	NM_001010000.2	194	7,312,6160	AA,AG,GG		0.0933,7.257,2.5158	benign	524/571	6908976	326,12632	2191	4288	6479	SO:0001583	missense	79822	exon16			CAGAATGTATTAA	BC033668	CCDS32785.1	18p11.23	2011-06-29				ENSG00000088756		"""Rho GTPase activating proteins"""	25509	protein-coding gene	gene with protein product		610592				10718198	Standard	NM_001010000		Approved	KIAA1314, FLJ10312	uc002kne.3	Q9P2N2		ENST00000383472.4:c.2048G>A	18.37:g.6908976G>A	ENSP00000372964:p.Cys683Tyr	149.0	0.0	0		141.0	54.0	0.382979	NM_001010000	A8MQB7|A8MU88|Q6P160|Q8N4T3|Q9NW53	Missense_Mutation	SNP	ENST00000383472.4	37		53	0.024267399267399268	51	0.10365853658536585	2	0.0055248618784530384	0	0.0	0	0.0	G	7.913	0.736819	0.15574	0.07257	9.33E-4	ENSG00000088756	ENST00000419673;ENST00000531294;ENST00000314319	T;T;T	0.07327	3.2;3.21;3.2	5.8	2.98	0.34508	.	.	.	.	.	T	0.00144	0.0004	N	0.14661	0.345	0.25779	P	0.9847541	B	0.19073	0.033	B	0.16722	0.016	T	0.41270	-0.9518	8	0.05833	T	0.94	.	5.225	0.15389	0.2961:0.1403:0.5637:0.0	.	683	Q9P2N2	RHG28_HUMAN	Y	524;519;524	ENSP00000392660:C524Y;ENSP00000437262:C519Y;ENSP00000313506:C524Y	ENSP00000313506:C524Y	C	+	2	0	ARHGAP28	6898976	0.061000	0.20836	0.902000	0.35471	0.988000	0.76386	1.237000	0.32695	0.343000	0.23821	0.650000	0.86243	TGT	G|0.979;A|0.021	0.021	strong		0.284	ARHGAP28-006	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442123.3	XM_371108	
SVEP1	79987	hgsc.bcm.edu	37	9	113170323	113170323	+	Silent	SNP	G	G	A	rs111722103	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:113170323G>A	ENST00000401783.2	-	38	7893	c.7557C>T	c.(7555-7557)acC>acT	p.T2519T	SVEP1_ENST00000374469.1_Silent_p.T2496T|SVEP1_ENST00000297826.5_Silent_p.T445T	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2519	Sushi 19. {ECO:0000255|PROSITE- ProRule:PRU00302}.			T -> I (in Ref. 6; CAD97901). {ECO:0000305}.	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						AGTAGGTAACGGTCTGTCCAT	0.488													G|||	154	0.0307508	0.1097	0.013	5008	,	,		21854	0.0		0.0	False		,,,				2504	0.0				p.T2519T		Atlas-SNP	.											SVEP1,NS,carcinoma,0,1	SVEP1	326	1	0			c.C7557T						PASS	.	G		334,3532		13,308,1612	49.0	48.0	49.0		7557	-1.3	0.0	9	dbSNP_132	49	5,8261		0,5,4128	no	coding-synonymous	SVEP1	NM_153366.3		13,313,5740	AA,AG,GG		0.0605,8.6394,2.7943		2519/3572	113170323	339,11793	1933	4133	6066	SO:0001819	synonymous_variant	79987	exon38			GGTAACGGTCTGT	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.7557C>T	9.37:g.113170323G>A		90.0	0.0	0		90.0	66.0	0.733333	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	37	CCDS48004.1																																																																																			G|0.977;A|0.023	0.023	strong		0.488	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
COL27A1	85301	hgsc.bcm.edu	37	9	116930013	116930013	+	Missense_Mutation	SNP	G	G	A	rs74339956	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116930013G>A	ENST00000356083.3	+	3	569	c.178G>A	c.(178-180)Ggg>Agg	p.G60R		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	60					extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						GACGAAGGCCGGGAGCCCTGC	0.677													G|||	70	0.0139776	0.0522	0.0014	5008	,	,		16813	0.0		0.0	False		,,,				2504	0.0				p.G60R		Atlas-SNP	.											.	COL27A1	200	.	0			c.G178A						PASS	.	G	ARG/GLY	211,4195	122.5+/-159.9	6,199,1998	71.0	84.0	80.0		178	2.3	1.0	9	dbSNP_131	80	0,8598		0,0,4299	yes	missense	COL27A1	NM_032888.2	125	6,199,6297	AA,AG,GG		0.0,4.7889,1.6226	benign	60/1861	116930013	211,12793	2203	4299	6502	SO:0001583	missense	85301	exon3			AAGGCCGGGAGCC	AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"""Collagens"""	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.178G>A	9.37:g.116930013G>A	ENSP00000348385:p.Gly60Arg	84.0	0.0	0		102.0	37.0	0.362745	NM_032888	Q66K43|Q96JF7	Missense_Mutation	SNP	ENST00000356083.3	37	CCDS6802.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	G	9.795	1.179007	0.21787	0.047889	0.0	ENSG00000196739	ENST00000356083;ENST00000357257;ENST00000374106;ENST00000451716	T;T	0.03242	4.0;4.0	5.32	2.3	0.28687	Concanavalin A-like lectin/glucanase (1);Laminin G, thrombospondin-type, N-terminal (1);	.	.	.	.	T	0.00300	0.0009	N	0.01576	-0.805	0.24118	N	0.995813	B	0.02656	0.0	B	0.01281	0.0	T	0.48885	-0.8995	9	0.32370	T	0.25	.	6.932	0.24447	0.0:0.5451:0.36:0.095	.	60	Q8IZC6	CORA1_HUMAN	R	60;60;7;7	ENSP00000348385:G60R;ENSP00000391328:G7R	ENSP00000348385:G60R	G	+	1	0	COL27A1	115969834	0.010000	0.17322	1.000000	0.80357	0.271000	0.26615	1.569000	0.36428	0.627000	0.30340	-0.516000	0.04426	GGG	G|0.985;A|0.015	0.015	strong		0.677	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
HYDIN	54768	hgsc.bcm.edu	37	16	71009054	71009054	+	Missense_Mutation	SNP	C	C	T	rs201855097	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:71009054C>T	ENST00000393567.2	-	31	4907	c.4757G>A	c.(4756-4758)cGc>cAc	p.R1586H		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	1586					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				CAGTTTGCGGCGACTCCGATG	0.512													C|||	27	0.00539137	0.0144	0.0029	5008	,	,		20704	0.001		0.005	False		,,,				2504	0.0				p.R1586H		Atlas-SNP	.											LOC652153,NS,carcinoma,-1,2	HYDIN	788	2	0			c.G4757A						scavenged	.						2.0	2.0	2.0					16																	71009054		1187	2725	3912	SO:0001583	missense	54768	exon31			TTGCGGCGACTCC	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.4757G>A	16.37:g.71009054C>T	ENSP00000377197:p.Arg1586His	151.0	0.0	0		170.0	45.0	0.264706	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	C	10.57	1.388546	0.25118	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.00966	5.49	4.61	-0.89	0.10577	.	0.499604	0.14321	U	0.326982	T	0.01189	0.0039	M	0.66939	2.045	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.42344	-0.9457	10	0.42905	T	0.14	.	3.7169	0.08441	0.1643:0.4632:0.0:0.3725	.	1585	F8WD23	.	H	1586;1585	ENSP00000377197:R1586H	ENSP00000313052:R1585H	R	-	2	0	HYDIN	69566555	0.002000	0.14202	0.000000	0.03702	0.007000	0.05969	0.261000	0.18442	-0.186000	0.10533	-0.444000	0.05651	CGC	C|0.999;T|0.001	0.001	weak		0.512	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
MGAT1	4245	hgsc.bcm.edu	37	5	180219838	180219838	+	Missense_Mutation	SNP	C	C	T	rs61743256	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:180219838C>T	ENST00000446023.2	-	3	884	c.134G>A	c.(133-135)gGc>gAc	p.G45D	MGAT1_ENST00000307826.4_Missense_Mutation_p.G45D|MGAT1_ENST00000333055.3_Missense_Mutation_p.G45D|MGAT1_ENST00000427865.2_Missense_Mutation_p.G45D|MGAT1_ENST00000393340.3_Missense_Mutation_p.G45D	NM_001114617.1|NM_001114618.1	NP_001108089.1|NP_001108090.1	P26572	MGAT1_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase	45					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine catabolic process (GO:0006049)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	acetylglucosaminyltransferase activity (GO:0008375)|alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity (GO:0003827)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	13	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGCGGGGTCGCCATCGAGAGC	0.677													T|||	81	0.0161741	0.0333	0.0029	5008	,	,		13792	0.001		0.0	False		,,,				2504	0.0348				p.G45D		Atlas-SNP	.											.	MGAT1	48	.	0			c.G134A						PASS	.	T	ASP/GLY,ASP/GLY,ASP/GLY,ASP/GLY,ASP/GLY	77,4251		0,77,2087	9.0	10.0	10.0		134,134,134,134,134	3.4	0.0	5	dbSNP_129	10	1,8491		0,1,4245	yes	missense,missense,missense,missense,missense	MGAT1	NM_001114617.1,NM_001114618.1,NM_001114619.1,NM_001114620.1,NM_002406.3	94,94,94,94,94	0,78,6332	TT,TC,CC		0.0118,1.7791,0.6084	benign,benign,benign,benign,benign	45/446,45/446,45/446,45/446,45/446	180219838	78,12742	2164	4246	6410	SO:0001583	missense	4245	exon3			GGGTCGCCATCGA	M61829	CCDS4458.1	5q35.3	2013-02-25			ENSG00000131446	ENSG00000131446	2.4.1.101	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7044	protein-coding gene	gene with protein product		160995		MGAT, GLYT1		1827260	Standard	NM_002406		Approved	GNT-1, GLCNAC-TI	uc003mmg.4	P26572	OTTHUMG00000130937	ENST00000446023.2:c.134G>A	5.37:g.180219838C>T	ENSP00000404718:p.Gly45Asp	72.0	0.0	0		82.0	32.0	0.390244	NM_001114617	A8K404|B3KRU8|D3DWR1|Q6IBE3	Missense_Mutation	SNP	ENST00000446023.2	37	CCDS4458.1	15	0.006868131868131868	14	0.028455284552845527	1	0.0027624309392265192	0	0.0	0	0.0	T	0.001	-3.025352	0.00041	0.017791	1.18E-4	ENSG00000131446	ENST00000333055;ENST00000307826;ENST00000446023;ENST00000393340;ENST00000452920;ENST00000427865;ENST00000504671;ENST00000506889;ENST00000514283;ENST00000512695;ENST00000506269;ENST00000514438;ENST00000502678;ENST00000513431	D;D;D;D;D;D;D;D;D;D;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63;-1.63;-1.63;-1.63;-1.63;-1.63;-1.63;-1.63;-1.63;-1.63	4.71	3.41	0.39046	.	0.694372	0.14686	N	0.304491	T	0.44726	0.1307	L	0.34521	1.04	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.40346	-0.9568	10	0.08599	T	0.76	-8.3269	4.0209	0.09665	0.0:0.2398:0.1766:0.5835	.	45	P26572	MGAT1_HUMAN	D	45	ENSP00000332073:G45D;ENSP00000311888:G45D;ENSP00000404718:G45D;ENSP00000377010:G45D;ENSP00000402838:G45D;ENSP00000424891:G45D;ENSP00000425988:G45D;ENSP00000424382:G45D;ENSP00000427116:G45D;ENSP00000422906:G45D;ENSP00000421738:G45D;ENSP00000422588:G45D;ENSP00000423401:G45D	ENSP00000311888:G45D	G	-	2	0	MGAT1	180152444	0.000000	0.05858	0.020000	0.16555	0.026000	0.11368	0.260000	0.18424	0.282000	0.22254	-0.535000	0.04281	GGC	C|0.993;T|0.007	0.007	strong		0.677	MGAT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368189.1	NM_001114618	
SSPO	23145	hgsc.bcm.edu	37	7	149486420	149486420	+	RNA	SNP	C	C	G	rs855693	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149486420C>G	ENST00000378016.2	+	0	4396							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			ACGCTGCCTGCCGCCGGCCCT	0.677													C|||	135	0.0269569	0.0976	0.0086	5008	,	,		16567	0.0		0.0	False		,,,				2504	0.0				p.P1466A		Atlas-SNP	.											.	.	.	.	0			c.C4396G						PASS	.	C		238,4158		9,220,1969	20.0	24.0	22.0		4400	4.6	1.0	7	dbSNP_86	22	4,8582		0,4,4289	yes	coding-notMod3	SSPO	NM_198455.2		9,224,6258	GG,GC,CC		0.0466,5.414,1.8641			149486420	242,12740	2198	4293	6491			23145	exon30			TGCCTGCCGCCGG	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149486420C>G		87.0	0.0	0		92.0	46.0	0.5	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.979;G|0.021	0.021	strong		0.677	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
SMCO2	341346	hgsc.bcm.edu	37	12	27641465	27641465	+	Silent	SNP	A	A	G	rs76288777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:27641465A>G	ENST00000535986.1	+	5	585	c.585A>G	c.(583-585)caA>caG	p.Q195Q	SMCO2_ENST00000416383.1_Silent_p.Q195Q|SMCO2_ENST00000298876.4_Silent_p.Q145Q|SMCO2_ENST00000538647.1_Intron			A6NFE2	SMCO2_HUMAN	single-pass membrane protein with coiled-coil domains 2	195						integral component of membrane (GO:0016021)											ACCTTGATCAAGGGACAAGCA	0.453													A|||	31	0.0061901	0.0219	0.0029	5008	,	,		16660	0.0		0.0	False		,,,				2504	0.0				p.Q195Q		Atlas-SNP	.											.	.	.	.	0			c.A585G						PASS	.	A		46,1338		0,46,646	59.0	59.0	59.0		585	1.9	0.0	12	dbSNP_132	59	1,3181		0,1,1590	no	coding-synonymous	C12orf70	NM_001145010.1		0,47,2236	GG,GA,AA		0.0314,3.3237,1.0293		195/344	27641465	47,4519	692	1591	2283	SO:0001819	synonymous_variant	0	exon6			TGATCAAGGGACA		CCDS44852.1	12p11.23	2013-03-11	2013-03-11	2013-03-11	ENSG00000165935	ENSG00000165935			34448	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 70"""	C12orf70			Standard	NM_001145010		Approved	LOC341346	uc010sjq.2	A6NFE2	OTTHUMG00000169205	ENST00000535986.1:c.585A>G	12.37:g.27641465A>G		39.0	0.0	0		38.0	17.0	0.447368	NM_001145010		Silent	SNP	ENST00000535986.1	37	CCDS44852.1																																																																																			A|0.993;G|0.007	0.007	strong		0.453	SMCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402867.1	NM_001145010	
LRP1	4035	hgsc.bcm.edu	37	12	57603647	57603647	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:57603647C>T	ENST00000243077.3	+	80	12901	c.12435C>T	c.(12433-12435)ccC>ccT	p.P4145P		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	4145					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)	p.P4145P(1)		NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	ACAAGCAGCCCGAAGGTGGGG	0.632																																					p.P4145P		Atlas-SNP	.											LRP1,bladder,carcinoma,0,1	LRP1	428	1	1	Substitution - coding silent(1)	urinary_tract(1)	c.C12435T						PASS	.						35.0	37.0	36.0					12																	57603647		2203	4300	6503	SO:0001819	synonymous_variant	4035	exon80			GCAGCCCGAAGGT	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.12435C>T	12.37:g.57603647C>T		45.0	0.0	0		52.0	30.0	0.576923	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			.	.	none		0.632	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
ABCG4	64137	hgsc.bcm.edu	37	11	119027691	119027691	+	Missense_Mutation	SNP	C	C	G	rs12271907	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:119027691C>G	ENST00000449422.2	+	9	1223	c.1035C>G	c.(1033-1035)aaC>aaG	p.N345K	ABCG4_ENST00000307417.3_Missense_Mutation_p.N345K|AP002956.1_ENST00000599663.1_Intron|ABCG4_ENST00000531739.1_Missense_Mutation_p.N345K	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	345					cholesterol efflux (GO:0033344)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(28)|ovary(2)|prostate(1)|skin(1)	44	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		CTGAGAAGAACGAGGTCCCTG	0.607													C|||	379	0.0756789	0.2685	0.0331	5008	,	,		22013	0.0		0.001	False		,,,				2504	0.0				p.N345K		Atlas-SNP	.											.	ABCG4	77	.	0			c.C1035G						PASS	.	C	LYS/ASN,LYS/ASN	977,3423	367.3+/-318.2	117,743,1340	169.0	155.0	159.0		1035,1035	-11.3	0.0	11	dbSNP_120	159	7,8583	4.3+/-15.6	0,7,4288	yes	missense,missense	ABCG4	NM_001142505.1,NM_022169.4	94,94	117,750,5628	GG,GC,CC		0.0815,22.2045,7.5751	benign,benign	345/647,345/647	119027691	984,12006	2200	4295	6495	SO:0001583	missense	64137	exon9			GAAGAACGAGGTC	AJ300465	CCDS8415.1	11q23	2012-03-14			ENSG00000172350	ENSG00000172350		"""ATP binding cassette transporters / subfamily G"""	13884	protein-coding gene	gene with protein product	"""putative ABC transporter"", ""ATP-binding cassette, subfamily G, member 4"""	607784				11435397	Standard	NM_022169		Approved	WHITE2	uc001pvs.3	Q9H172	OTTHUMG00000166169	ENST00000449422.2:c.1035C>G	11.37:g.119027691C>G	ENSP00000406874:p.Asn345Lys	74.0	0.0	0		49.0	29.0	0.591837	NM_022169	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Missense_Mutation	SNP	ENST00000449422.2	37	CCDS8415.1	162	0.07417582417582418	154	0.3130081300813008	8	0.022099447513812154	0	0.0	0	0.0	C	9.694	1.152791	0.21371	0.222045	8.15E-4	ENSG00000172350	ENST00000307417;ENST00000449422;ENST00000531739;ENST00000534402	D;D;D;T	0.86562	-2.14;-2.14;-2.14;0.92	5.65	-11.3	0.00108	.	0.718923	0.14549	N	0.312774	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.22604	0.072	B	0.20577	0.03	T	0.08493	-1.0719	9	0.06365	T	0.9	-5.4059	11.0626	0.47957	0.0:0.2915:0.2915:0.4171	rs12271907;rs12271907	345	Q9H172	ABCG4_HUMAN	K	345;345;345;23	ENSP00000304111:N345K;ENSP00000406874:N345K;ENSP00000434318:N345K;ENSP00000434571:N23K	ENSP00000304111:N345K	N	+	3	2	ABCG4	118532901	0.002000	0.14202	0.001000	0.08648	0.350000	0.29205	-2.018000	0.01444	-3.564000	0.00140	-1.778000	0.00651	AAC	C|0.928;G|0.072;T|0.000	0.072	strong		0.607	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388215.1	NM_022169	
ROGDI	79641	hgsc.bcm.edu	37	16	4847976	4847976	+	Missense_Mutation	SNP	C	C	T	rs546063670	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4847976C>T	ENST00000322048.7	-	9	1036	c.658G>A	c.(658-660)Gct>Act	p.A220T	RP11-127I20.5_ENST00000592465.1_RNA|ROGDI_ENST00000586336.1_5'UTR	NM_024589.2	NP_078865.1	Q9GZN7	ROGDI_HUMAN	rogdi homolog (Drosophila)	220					hemopoiesis (GO:0030097)|positive regulation of cell proliferation (GO:0008284)	intracellular (GO:0005622)|nucleus (GO:0005634)				endometrium(2)|lung(1)|ovary(1)|skin(1)	5						GCGCCCCCAGCTGGGCGGAAG	0.701													C|||	2	0.000399361	0.0015	0.0	5008	,	,		17557	0.0		0.0	False		,,,				2504	0.0				p.A220T		Atlas-SNP	.											.	ROGDI	11	.	0			c.G658A						PASS	.						27.0	29.0	28.0					16																	4847976		2197	4299	6496	SO:0001583	missense	79641	exon9			CCCCAGCTGGGCG	AK026039	CCDS10523.1	16p13.3	2014-09-17			ENSG00000067836	ENSG00000067836			29478	protein-coding gene	gene with protein product		614574				11230166	Standard	NM_024589		Approved	FLJ22386	uc002cxv.4	Q9GZN7	OTTHUMG00000129479	ENST00000322048.7:c.658G>A	16.37:g.4847976C>T	ENSP00000322832:p.Ala220Thr	134.0	0.0	0		148.0	87.0	0.587838	NM_024589	Q6IA00	Missense_Mutation	SNP	ENST00000322048.7	37	CCDS10523.1	.	.	.	.	.	.	.	.	.	.	C	10.60	1.396518	0.25205	.	.	ENSG00000067836	ENST00000322048	T	0.42900	0.96	5.11	0.509	0.16977	.	0.114933	0.64402	D	0.000019	T	0.23249	0.0562	N	0.22421	0.69	0.28464	N	0.915729	B	0.13145	0.007	B	0.19148	0.024	T	0.18555	-1.0333	10	0.18276	T	0.48	-10.8216	7.925	0.29870	0.5389:0.3846:0.0:0.0765	.	220	Q9GZN7	ROGDI_HUMAN	T	220	ENSP00000322832:A220T	ENSP00000322832:A220T	A	-	1	0	ROGDI	4787977	0.000000	0.05858	0.178000	0.23040	0.322000	0.28314	-0.231000	0.09069	0.147000	0.19030	0.561000	0.74099	GCT	.	.	none		0.701	ROGDI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251643.3	NM_024589	
NDUFAF5	79133	hgsc.bcm.edu	37	20	13797179	13797179	+	Silent	SNP	G	G	A	rs34901599	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:13797179G>A	ENST00000378106.5	+	9	968	c.849G>A	c.(847-849)gcG>gcA	p.A283A	NDUFAF5_ENST00000463598.1_Silent_p.A255A|NDUFAF5_ENST00000475968.1_3'UTR	NM_024120.4	NP_077025.2	Q5TEU4	NDUF5_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 5	283					mitochondrial respiratory chain complex I assembly (GO:0032981)	extrinsic component of mitochondrial inner membrane (GO:0031314)	methyltransferase activity (GO:0008168)										TGGCAGCTGCGGCAGTGTACA	0.493													G|||	228	0.0455272	0.1619	0.0101	5008	,	,		17420	0.0		0.007	False		,,,				2504	0.0				p.A283A		Atlas-SNP	.											.	.	.	.	0			c.G849A						PASS	.	G	,	560,3846	249.0+/-256.6	25,510,1668	114.0	98.0	104.0		765,849	-11.2	0.0	20	dbSNP_126	104	10,8590	6.4+/-24.3	0,10,4290	no	coding-synonymous,coding-synonymous	C20orf7	NM_001039375.2,NM_024120.4	,	25,520,5958	AA,AG,GG		0.1163,12.7099,4.3826	,	255/318,283/346	13797179	570,12436	2203	4300	6503	SO:0001819	synonymous_variant	79133	exon9			AGCTGCGGCAGTG		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.849G>A	20.37:g.13797179G>A		108.0	0.0	0		94.0	45.0	0.478723	NM_024120	A8K166|Q6GPH3|Q9H6F4	Silent	SNP	ENST00000378106.5	37	CCDS13118.1																																																																																			G|0.960;A|0.040	0.040	strong		0.493	NDUFAF5-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078057.2	NM_001039375	
TSHZ2	128553	hgsc.bcm.edu	37	20	51872038	51872038	+	Missense_Mutation	SNP	G	G	A	rs6097319	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:51872038G>A	ENST00000371497.5	+	2	2928	c.2041G>A	c.(2041-2043)Gcc>Acc	p.A681T	RP4-678D15.1_ENST00000606932.1_RNA|TSHZ2_ENST00000603338.2_Missense_Mutation_p.A678T|TSHZ2_ENST00000329613.6_Missense_Mutation_p.A678T	NM_001193421.1|NM_173485.5	NP_001180350.1|NP_775756.3	Q9NRE2	TSH2_HUMAN	teashirt zinc finger homeobox 2	681			A -> T (in dbSNP:rs6097319).		multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(16)|lung(38)|ovary(5)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	84			STAD - Stomach adenocarcinoma(23;0.1)			CAATGGGTGCGCCCTCGCCAA	0.637													G|||	308	0.0615016	0.2231	0.013	5008	,	,		16470	0.0		0.004	False		,,,				2504	0.0				p.A681T		Atlas-SNP	.											.	TSHZ2	209	.	0			c.G2041A						PASS	.	G	THR/ALA,THR/ALA	827,3579	325.6+/-299.2	98,631,1474	50.0	46.0	48.0		2032,2041	-1.2	0.0	20	dbSNP_114	48	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense	TSHZ2	NM_001193421.1,NM_173485.5	58,58	98,637,5768	AA,AG,GG		0.0698,18.7699,6.4047	benign,benign	678/1032,681/1035	51872038	833,12173	2203	4300	6503	SO:0001583	missense	128553	exon2			GGGTGCGCCCTCG	AF230201	CCDS33490.1, CCDS54474.1	20q13.2	2013-11-20	2007-07-16	2006-03-14	ENSG00000182463	ENSG00000182463		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	13010	protein-coding gene	gene with protein product		614118	"""chromosome 20 open reading frame 17"", ""zinc finger protein 218"", ""teashirt family zinc finger 2"""	C20orf17, ZNF218		9671742	Standard	NM_173485		Approved	ZABC2, OVC10-2, TSH2	uc021wex.1	Q9NRE2	OTTHUMG00000033058	ENST00000371497.5:c.2041G>A	20.37:g.51872038G>A	ENSP00000360552:p.Ala681Thr	45.0	0.0	0		48.0	28.0	0.583333	NM_173485	B7Z7W1|J3KNQ0|Q4VXM4|Q6N003|Q8N260	Missense_Mutation	SNP	ENST00000371497.5	37	CCDS33490.1	122	0.055860805860805864	118	0.23983739837398374	4	0.011049723756906077	0	0.0	0	0.0	G	2.194	-0.384541	0.04966	0.187699	6.98E-4	ENSG00000182463	ENST00000371497;ENST00000329613;ENST00000450262	T;T	0.37752	1.18;1.18	5.53	-1.21	0.09524	.	0.276183	0.39020	N	0.001485	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.11235	0.004	B	0.04013	0.001	T	0.29579	-1.0007	9	0.10111	T	0.7	1.382	2.2477	0.04035	0.3252:0.1119:0.4479:0.115	rs6097319;rs6097319	681	Q9NRE2	TSH2_HUMAN	T	681;678;207	ENSP00000360552:A681T;ENSP00000333114:A678T	ENSP00000333114:A678T	A	+	1	0	TSHZ2	51305445	0.046000	0.20272	0.000000	0.03702	0.029000	0.11900	0.728000	0.26013	-0.174000	0.10743	0.643000	0.83706	GCC	G|0.935;A|0.065	0.065	strong		0.637	TSHZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080398.6	NM_173485	
F9	2158	hgsc.bcm.edu	37	X	138643939	138643939	+	Silent	SNP	A	A	G	rs112057482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:138643939A>G	ENST00000218099.2	+	8	1102	c.1095A>G	c.(1093-1095)tcA>tcG	p.S365S	F9_ENST00000394090.2_Silent_p.S327S	NM_000133.3	NP_000124.1	P00740	FA9_HUMAN	coagulation factor IX	365	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|blood coagulation, intrinsic pathway (GO:0007597)|cellular protein metabolic process (GO:0044267)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(7)|lung(19)|ovary(1)|skin(1)	35	Acute lymphoblastic leukemia(192;0.000127)				Antihemophilic Factor(DB00025)|Menadione(DB00170)	AAGGGAGATCAGCTTTAGTTC	0.438													A|||	42	0.0111258	0.0287	0.0058	3775	,	,		14652	0.0		0.0	False		,,,				2504	0.0				p.S365S		Atlas-SNP	.											.	F9	107	.	0			c.A1095G	GRCh37	CD010617	F9	D	rs112057482	PASS	.	A		127,3708		1,104,21,1527,550	141.0	117.0	125.0		1095	-9.5	0.0	X	dbSNP_132	125	1,6727		0,1,0,2427,1872	no	coding-synonymous	F9	NM_000133.3		1,105,21,3954,2422	GG,GA,G,AA,A		0.0149,3.3116,1.2118		365/462	138643939	128,10435	2203	4300	6503	SO:0001819	synonymous_variant	2158	exon8			GAGATCAGCTTTA	M11309	CCDS14666.1	Xq26.3-q27.1	2014-09-17	2008-08-01		ENSG00000101981	ENSG00000101981	3.4.21.22		3551	protein-coding gene	gene with protein product	"""Factor IX"", ""plasma thromboplastic component"", ""Christmas disease"", ""hemophilia B"""	300746					Standard	NM_000133		Approved	FIX	uc004fas.1	P00740	OTTHUMG00000022536	ENST00000218099.2:c.1095A>G	X.37:g.138643939A>G		140.0	0.0	0		136.0	85.0	0.625	NM_000133	A8K9N4|F2RM36|Q5FBE1|Q5JYJ8	Silent	SNP	ENST00000218099.2	37	CCDS14666.1																																																																																			A|0.989;G|0.011	0.011	strong		0.438	F9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058557.1		
CCDC40	55036	hgsc.bcm.edu	37	17	78069129	78069129	+	Missense_Mutation	SNP	G	G	T	rs61686936	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78069129G>T	ENST00000397545.4	+	18	2927	c.2900G>T	c.(2899-2901)cGc>cTc	p.R967L		NM_017950.3	NP_060420.2	Q4G0X9	CCD40_HUMAN	coiled-coil domain containing 40	967					axonemal dynein complex assembly (GO:0070286)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement (GO:0003351)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)|regulation of cilium beat frequency (GO:0003356)	cilium (GO:0005929)|cytoplasm (GO:0005737)				NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(7)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	38	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.149)			GCGGTTGCCCGCAGAGAGACC	0.667													G|||	137	0.0273562	0.0991	0.0072	5008	,	,		16509	0.0		0.001	False		,,,				2504	0.0				p.R967L		Atlas-SNP	.											CCDC40,colon,carcinoma,0,1	CCDC40	198	1	0			c.G2900T						PASS	.	G	LEU/ARG	367,3957		14,339,1809	54.0	66.0	62.0		2900	-0.6	1.0	17	dbSNP_129	62	2,8516		0,2,4257	yes	missense	CCDC40	NM_017950.3	102	14,341,6066	TT,TG,GG		0.0235,8.4875,2.8734	possibly-damaging	967/1143	78069129	369,12473	2162	4259	6421	SO:0001583	missense	55036	exon18			TTGCCCGCAGAGA	AB046860	CCDS42395.1, CCDS58604.1	17q25.3	2013-11-15			ENSG00000141519	ENSG00000141519			26090	protein-coding gene	gene with protein product		613799				21131974	Standard	NM_017950		Approved	FLJ20753, KIAA1640, FLJ32021, CILD15, FAP172	uc010dht.3	Q4G0X9	OTTHUMG00000132707	ENST00000397545.4:c.2900G>T	17.37:g.78069129G>T	ENSP00000380679:p.Arg967Leu	215.0	0.0	0		250.0	126.0	0.504	NM_017950	A8MTD2|C9JTI9|C9JTJ0|C9JXW1|Q6PE47|Q9HCD2|Q9NWL5	Missense_Mutation	SNP	ENST00000397545.4	37	CCDS42395.1	60	0.027472527472527472	58	0.11788617886178862	2	0.0055248618784530384	0	0.0	0	0.0	G	11.65	1.700481	0.30142	0.084875	2.35E-4	ENSG00000141519	ENST00000397545	T	0.57436	0.4	5.38	-0.582	0.11709	.	.	.	.	.	T	0.00666	0.0022	L	0.57536	1.79	0.09310	P	0.9999999999999583	P;B	0.40619	0.724;0.397	B;B	0.36289	0.202;0.221	T	0.06534	-1.0821	8	0.48119	T	0.1	-13.7927	6.9297	0.24434	0.3554:0.0:0.5288:0.1159	rs61686936;rs61749048	967;750	Q4G0X9;Q4G0X9-3	CCD40_HUMAN;.	L	967	ENSP00000380679:R967L	ENSP00000380679:R967L	R	+	2	0	CCDC40	75683724	0.797000	0.28877	0.997000	0.53966	0.125000	0.20455	0.916000	0.28651	0.263000	0.21812	0.563000	0.77884	CGC	A|0.000;G|0.981;T|0.019	0.019	strong		0.667	CCDC40-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256005.2	XM_371082	
MTMR9	66036	hgsc.bcm.edu	37	8	11142529	11142529	+	Silent	SNP	T	T	C	rs61752023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11142529T>C	ENST00000221086.3	+	1	605	c.132T>C	c.(130-132)aaT>aaC	p.N44N	MTMR9_ENST00000526292.1_5'Flank	NM_015458.3	NP_056273.2	Q96QG7	MTMR9_HUMAN	myotubularin related protein 9	44						cytoplasm (GO:0005737)	enzyme regulator activity (GO:0030234)|phosphatase activity (GO:0016791)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|skin(1)|urinary_tract(2)	16			STAD - Stomach adenocarcinoma(15;0.215)	COAD - Colon adenocarcinoma(149;0.0678)		GGCAGGACAATACGGAGGAGC	0.657													C|||	214	0.0427316	0.1573	0.0072	5008	,	,		12961	0.0		0.001	False		,,,				2504	0.0				p.N44N		Atlas-SNP	.											.	MTMR9	58	.	0			c.T132C						PASS	.	C		609,3797	765.8+/-413.4	36,537,1630	36.0	38.0	37.0		132	3.0	1.0	8	dbSNP_129	37	2,8598	817.5+/-406.9	0,2,4298	no	coding-synonymous	MTMR9	NM_015458.3		36,539,5928	CC,CT,TT		0.0233,13.8221,4.6978		44/550	11142529	611,12395	2203	4300	6503	SO:0001819	synonymous_variant	66036	exon1			GGACAATACGGAG	AJ297823	CCDS5979.1	8p23-p22	2011-06-09	2002-09-05	2002-09-06	ENSG00000104643	ENSG00000104643		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	14596	protein-coding gene	gene with protein product		606260	"""myotubularin related protein 8"""	C8orf9, MTMR8		11472061, 11896452, 12890864	Standard	NM_015458		Approved	DKFZp434K171, LIP-STYX	uc003wtm.3	Q96QG7	OTTHUMG00000090647	ENST00000221086.3:c.132T>C	8.37:g.11142529T>C		91.0	0.0	0		101.0	53.0	0.524752	NM_015458	B7Z291|Q52LU3|Q8WW11|Q96QG6|Q9NX50	Silent	SNP	ENST00000221086.3	37	CCDS5979.1																																																																																			T|0.958;C|0.042	0.042	strong		0.657	MTMR9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207307.2	NM_015458	
SIDT2	51092	hgsc.bcm.edu	37	11	117063020	117063020	+	Silent	SNP	C	C	T	rs12285062	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117063020C>T	ENST00000324225.4	+	20	2454	c.1923C>T	c.(1921-1923)caC>caT	p.H641H	SIDT2_ENST00000431081.2_Silent_p.H638H|SIDT2_ENST00000532062.1_5'Flank	NM_001040455.1	NP_001035545.1	Q8NBJ9	SIDT2_HUMAN	SID1 transmembrane family, member 2	641					cell morphogenesis (GO:0000902)|dsRNA transport (GO:0033227)|glucose homeostasis (GO:0042593)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to glucose (GO:0009749)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell proliferation (GO:0044342)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	RNA transmembrane transporter activity (GO:0051033)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	36	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000219)|all cancers(92;0.00144)		CCATCATTCACATCATCGCCA	0.632													C|||	40	0.00798722	0.0272	0.0058	5008	,	,		17690	0.0		0.0	False		,,,				2504	0.0				p.H641H		Atlas-SNP	.											.	SIDT2	82	.	0			c.C1923T						PASS	.	C		125,4277	92.0+/-130.7	2,121,2078	122.0	102.0	109.0		1923	0.0	1.0	11	dbSNP_120	109	2,8590	2.2+/-6.3	0,2,4294	no	coding-synonymous	SIDT2	NM_001040455.1		2,123,6372	TT,TC,CC		0.0233,2.8396,0.9774		641/833	117063020	127,12867	2201	4296	6497	SO:0001819	synonymous_variant	51092	exon20			CATTCACATCATC	AF151799	CCDS31682.1	11q23.3	2008-02-05			ENSG00000149577	ENSG00000149577			24272	protein-coding gene	gene with protein product						10810093, 12975309	Standard	NM_001040455		Approved	CGI-40	uc001pqh.1	Q8NBJ9	OTTHUMG00000167065	ENST00000324225.4:c.1923C>T	11.37:g.117063020C>T		106.0	0.0	0		94.0	49.0	0.521277	NM_001040455	Q8NBY7|Q9Y357	Silent	SNP	ENST00000324225.4	37	CCDS31682.1																																																																																			C|0.990;T|0.010	0.010	strong		0.632	SIDT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392836.1	NM_015996	
FAN1	22909	hgsc.bcm.edu	37	15	31196984	31196984	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:31196984G>A	ENST00000362065.4	+	2	409	c.118G>A	c.(118-120)Gct>Act	p.A40T	FAN1_ENST00000565466.1_Missense_Mutation_p.A40T|FAN1_ENST00000561607.1_Missense_Mutation_p.A40T|FAN1_ENST00000561594.1_Missense_Mutation_p.A40T	NM_014967.4	NP_055782.3	Q9Y2M0	FAN1_HUMAN	FANCD2/FANCI-associated nuclease 1	40					DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA incision (GO:0033683)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|5'-flap endonuclease activity (GO:0017108)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|phosphodiesterase I activity (GO:0004528)|ubiquitin binding (GO:0043130)			autonomic_ganglia(2)|breast(2)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(6)|lung(8)|skin(1)	29						TGCACCACCTGCTAAACTTGC	0.398								Direct reversal of damage																													p.A40T		Atlas-SNP	.											.	FAN1	77	.	0			c.G118A						PASS	.						74.0	76.0	75.0					15																	31196984		2202	4300	6502	SO:0001583	missense	22909	exon2			CCACCTGCTAAAC		CCDS32186.1, CCDS58344.1	15q13.2-q13.3	2010-08-04	2010-08-04	2010-08-04		ENSG00000198690			29170	protein-coding gene	gene with protein product		613534	"""KIAA1018"", ""myotubularin related protein 15"""	KIAA1018, MTMR15		20603015, 20603016, 20603073	Standard	NM_014967		Approved		uc001zff.3	Q9Y2M0		ENST00000362065.4:c.118G>A	15.37:g.31196984G>A	ENSP00000354497:p.Ala40Thr	134.0	0.0	0		135.0	67.0	0.496296	NM_001146095	A8K4M2|Q86WU8	Missense_Mutation	SNP	ENST00000362065.4	37	CCDS32186.1	.	.	.	.	.	.	.	.	.	.	g	21.9	4.222546	0.79464	.	.	ENSG00000198690	ENST00000362065	D	0.82711	-1.64	5.28	3.31	0.37934	.	0.247400	0.41097	D	0.000947	D	0.88749	0.6521	M	0.66939	2.045	0.39089	D	0.961052	D;D	0.89917	0.986;1.0	P;D	0.72982	0.738;0.979	D	0.89320	0.3639	10	0.72032	D	0.01	-9.7976	12.0726	0.53626	0.0:0.1314:0.7318:0.1368	.	40;40	Q9Y2M0;Q9Y2M0-2	FAN1_HUMAN;.	T	40	ENSP00000354497:A40T	ENSP00000354497:A40T	A	+	1	0	FAN1	28984276	0.538000	0.26394	0.288000	0.24862	0.886000	0.51366	2.025000	0.41059	0.662000	0.31006	0.555000	0.69702	GCT	.	.	none		0.398	FAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430740.1	NM_014967	
BCAS1	8537	hgsc.bcm.edu	37	20	52611552	52611552	+	Splice_Site	SNP	G	G	A	rs60878965	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:52611552G>A	ENST00000395961.3	-	6	1092	c.926C>T	c.(925-927)aCg>aTg	p.T309M	BCAS1_ENST00000434986.2_Splice_Site_p.T22M|BCAS1_ENST00000371440.3_Splice_Site_p.T309M|BCAS1_ENST00000371435.2_Splice_Site_p.T309M	NM_003657.2	NP_003648.2	O75363	BCAS1_HUMAN	breast carcinoma amplified sequence 1	309						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(23)|ovary(2)|skin(2)|stomach(1)|urinary_tract(1)	37	Breast(2;9.53e-15)|Lung NSC(4;5.57e-06)|all_lung(4;1.44e-05)		STAD - Stomach adenocarcinoma(23;0.116)|Colorectal(105;0.198)			ACTACCTACCGTGTCTTCTGG	0.343													G|||	449	0.0896565	0.3245	0.0274	5008	,	,		16173	0.0		0.001	False		,,,				2504	0.0				p.T309M		Atlas-SNP	.											.	BCAS1	77	.	0			c.C926T						PASS	.	G	MET/THR	1210,3196	421.1+/-339.2	174,862,1167	185.0	200.0	195.0		926	2.5	1.0	20	dbSNP_129	195	11,8589	8.4+/-32.0	0,11,4289	yes	missense-near-splice	BCAS1	NM_003657.2	81	174,873,5456	AA,AG,GG		0.1279,27.4626,9.388	possibly-damaging	309/585	52611552	1221,11785	2203	4300	6503	SO:0001630	splice_region_variant	8537	exon6			CCTACCGTGTCTT	AF041260	CCDS13444.1	20q13.2	2006-11-10			ENSG00000064787	ENSG00000064787			974	protein-coding gene	gene with protein product		602968				9671742	Standard	NM_003657		Approved	NABC1, AIBC1	uc002xws.2	O75363	OTTHUMG00000032772	ENST00000395961.3:c.927+1C>T	20.37:g.52611552G>A		55.0	0.0	0		63.0	24.0	0.380952	NM_003657	A0AVG5|Q68CZ3	Missense_Mutation	SNP	ENST00000395961.3	37	CCDS13444.1	163|163	0.07463369963369963|0.07463369963369963	155|155	0.3150406504065041|0.3150406504065041	8|8	0.022099447513812154|0.022099447513812154	0|0	0.0|0.0	0|0	0.0|0.0	G|G	16.69|16.69	3.194122|3.194122	0.58017|0.58017	0.274626|0.274626	0.001279|0.001279	ENSG00000064787|ENSG00000064787	ENST00000422805|ENST00000448484;ENST00000371440;ENST00000448710;ENST00000395961;ENST00000371435;ENST00000434986	.|T;T;T;T;T	.|0.08458	.|3.09;3.09;3.09;3.09;3.09	5.84|5.84	2.46|2.46	0.29980|0.29980	.|.	.|0.270974	.|0.35525	.|N	.|0.003141	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.61703|0.61703	1.905|1.905	0.09310|0.09310	P|P	0.9999999999996939|0.9999999999996939	.|D;P;D;P;D;D	.|0.89917	.|1.0;0.777;1.0;0.944;0.993;0.993	.|D;B;D;B;P;P	.|0.65773	.|0.938;0.1;0.938;0.332;0.596;0.596	T|T	0.40365|0.40365	-0.9567|-0.9567	4|9	.|0.54805	.|T	.|0.06	-4.1201|-4.1201	11.7384|11.7384	0.51778|0.51778	0.0:0.0:0.3884:0.6116|0.0:0.0:0.3884:0.6116	rs60878965;rs61731748|rs60878965;rs61731748	.|309;22;309;309;309;309	.|B2RCQ5;B4DFL4;O75363-2;G3XAF7;A0AVG7;O75363	.|.;.;.;.;.;BCAS1_HUMAN	W|M	28|171;309;187;309;309;22	.|ENSP00000396361:T171M;ENSP00000360495:T309M;ENSP00000379290:T309M;ENSP00000360490:T309M;ENSP00000409956:T22M	.|ENSP00000360490:T309M	R|T	-|-	1|2	2|0	BCAS1|BCAS1	52044959|52044959	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.929000|0.929000	0.56500|0.56500	1.044000|1.044000	0.30329|0.30329	0.727000|0.727000	0.32360|0.32360	0.655000|0.655000	0.94253|0.94253	CGG|ACG	G|0.916;A|0.084	0.084	strong		0.343	BCAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079766.2	NM_003657	Missense_Mutation
SEL1L	6400	hgsc.bcm.edu	37	14	81969158	81969158	+	Silent	SNP	A	A	G	rs35377988	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:81969158A>G	ENST00000336735.4	-	6	800	c.684T>C	c.(682-684)gcT>gcC	p.A228A	SEL1L_ENST00000555824.1_Silent_p.A228A	NM_005065.5	NP_005056.3	Q9UBV2	SE1L1_HUMAN	sel-1 suppressor of lin-12-like (C. elegans)	228	Interaction with ERLEC1, OS9 and SYVN1.				Notch signaling pathway (GO:0007219)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(3)	28				BRCA - Breast invasive adenocarcinoma(234;0.0299)		CAAATAAAAGAGCATATGACA	0.423													A|||	195	0.0389377	0.1437	0.0072	5008	,	,		1526	0.0		0.0	False		,,,				2504	0.0				p.A228A		Atlas-SNP	.											.	SEL1L	67	.	0			c.T684C						PASS	.	A		477,3929	224.6+/-240.7	21,435,1747	185.0	175.0	178.0		684	-1.6	1.0	14	dbSNP_126	178	0,8600		0,0,4300	no	coding-synonymous	SEL1L	NM_005065.4		21,435,6047	GG,GA,AA		0.0,10.8261,3.6675		228/795	81969158	477,12529	2203	4300	6503	SO:0001819	synonymous_variant	6400	exon6			TAAAAGAGCATAT		CCDS9876.1, CCDS58333.1	14q31	2011-03-31	2001-11-28		ENSG00000071537	ENSG00000071537			10717	protein-coding gene	gene with protein product	"""sel-1 suppressor of lin-12-like 1 (C. elegans)"""	602329	"""sel-1 (suppressor of lin-12, C.elegans)-like"""			9417916, 10051412, 16331677	Standard	NM_005065		Approved	IBD2, SEL1L1	uc010tvv.2	Q9UBV2		ENST00000336735.4:c.684T>C	14.37:g.81969158A>G		78.0	0.0	0		94.0	35.0	0.37234	NM_001244984	Q6UWT6|Q9P1T9|Q9UHK7	Silent	SNP	ENST00000336735.4	37	CCDS9876.1																																																																																			A|0.957;G|0.043	0.043	strong		0.423	SEL1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413325.1	NM_005065	
SALL4	57167	hgsc.bcm.edu	37	20	50408614	50408614	+	Silent	SNP	A	A	G	rs76870996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:50408614A>G	ENST00000217086.4	-	2	519	c.408T>C	c.(406-408)aaT>aaC	p.N136N	SALL4_ENST00000483130.1_5'UTR|SALL4_ENST00000371539.3_Intron|SALL4_ENST00000395997.3_Silent_p.N136N	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	136					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						AGCTGCCGCCATTCTCCCTGT	0.592													A|||	67	0.0133786	0.0469	0.0058	5008	,	,		16786	0.0		0.001	False		,,,				2504	0.0				p.N136N		Atlas-SNP	.											.	SALL4	168	.	0			c.T408C						PASS	.	A		172,4234	113.3+/-151.4	6,160,2037	128.0	134.0	132.0		408	-7.7	0.0	20	dbSNP_131	132	0,8600		0,0,4300	no	coding-synonymous	SALL4	NM_020436.3		6,160,6337	GG,GA,AA		0.0,3.9038,1.3225		136/1054	50408614	172,12834	2203	4300	6503	SO:0001819	synonymous_variant	57167	exon2			GCCGCCATTCTCC	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"""Zinc fingers, C2H2-type"""	15924	protein-coding gene	gene with protein product		607343	"""sal (Drosophila)-like 4"", ""sal-like 4 (Drosophila)"""				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.408T>C	20.37:g.50408614A>G		125.0	0.0	0		117.0	49.0	0.418803	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	37	CCDS13438.1																																																																																			A|0.988;G|0.012	0.012	strong		0.592	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
DSC1	1823	hgsc.bcm.edu	37	18	28710615	28710615	+	Silent	SNP	C	C	A	rs1816634	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:28710615C>A	ENST00000257198.5	-	16	2808	c.2547G>T	c.(2545-2547)tcG>tcT	p.S849S	RP11-408H20.2_ENST00000581836.1_RNA|RP11-408H20.3_ENST00000582307.1_RNA|DSC1_ENST00000257197.3_3'UTR	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	849					homophilic cell adhesion (GO:0007156)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			CATAGTTATACGAACAAACGT	0.418													C|||	465	0.0928514	0.2542	0.0533	5008	,	,		18467	0.0		0.0467	False		,,,				2504	0.046				p.S849S		Atlas-SNP	.											.	DSC1	240	.	0			c.G2547T						PASS	.	C	,	886,3520	344.1+/-307.9	88,710,1405	133.0	134.0	134.0		,2547	-12.3	0.0	18	dbSNP_92	134	344,8256	118.1+/-177.6	6,332,3962	no	utr-3,coding-synonymous	DSC1	NM_004948.3,NM_024421.2	,	94,1042,5367	AA,AC,CC		4.0,20.1089,9.4572	,	,849/895	28710615	1230,11776	2203	4300	6503	SO:0001819	synonymous_variant	1823	exon16			GTTATACGAACAA	AF293358	CCDS11894.1, CCDS11895.1	18q12.1	2010-01-26			ENSG00000134765	ENSG00000134765		"""Cadherins / Major cadherins"""	3035	protein-coding gene	gene with protein product		125643				8486729	Standard	NM_024421		Approved	CDHF1	uc002kwn.3	Q08554	OTTHUMG00000131982	ENST00000257198.5:c.2547G>T	18.37:g.28710615C>A		244.0	0.0	0		256.0	105.0	0.410156	NM_024421	Q9HB01	Silent	SNP	ENST00000257198.5	37	CCDS11894.1																																																																																			C|0.914;A|0.086	0.086	strong		0.418	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421	
CD109	135228	hgsc.bcm.edu	37	6	74407182	74407182	+	Missense_Mutation	SNP	G	G	T	rs9446983	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:74407182G>T	ENST00000287097.5	+	2	246	c.134G>T	c.(133-135)gGg>gTg	p.G45V	RP11-553A21.3_ENST00000428865.2_RNA|CD109_ENST00000437994.2_Missense_Mutation_p.G45V|CD109_ENST00000422508.2_Missense_Mutation_p.G45V			Q6YHK3	CD109_HUMAN	CD109 molecule	45			G -> V (in dbSNP:rs9446983).		negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GTGACTATTGGGGTGGAGCTT	0.522													G|||	75	0.014976	0.056	0.0014	5008	,	,		18228	0.0		0.0	False		,,,				2504	0.0				p.G45V		Atlas-SNP	.											CD109,NS,carcinoma,-1,1	CD109	170	1	0			c.G134T						PASS	.	G	VAL/GLY,VAL/GLY,VAL/GLY	158,4248	106.9+/-145.3	1,156,2046	118.0	118.0	118.0		134,134,134	5.3	1.0	6	dbSNP_119	118	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	CD109	NM_001159587.1,NM_001159588.1,NM_133493.3	109,109,109	1,157,6345	TT,TG,GG		0.0116,3.586,1.2225	possibly-damaging,possibly-damaging,possibly-damaging	45/1429,45/1369,45/1446	74407182	159,12847	2203	4300	6503	SO:0001583	missense	135228	exon2			CTATTGGGGTGGA	AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"""CD molecules"""	21685	protein-coding gene	gene with protein product		608859	"""CD109 antigen (Gov platelet alloantigens)"""			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.134G>T	6.37:g.74407182G>T	ENSP00000287097:p.Gly45Val	118.0	0.0	0		93.0	51.0	0.548387	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	37	CCDS4982.1	33	0.01510989010989011	32	0.06504065040650407	1	0.0027624309392265192	0	0.0	0	0.0	G	19.50	3.840234	0.71488	0.03586	1.16E-4	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.26810	1.98;1.71;1.98	5.31	5.31	0.75309	.	0.090017	0.44285	D	0.000473	T	0.26448	0.0646	N	0.19112	0.55	0.47778	D	0.99951	D;D;P;P	0.89917	1.0;0.999;0.508;0.938	D;D;B;P	0.97110	1.0;0.984;0.176;0.706	T	0.03077	-1.1075	10	0.38643	T	0.18	.	16.0095	0.80391	0.0:0.0:1.0:0.0	rs9446983;rs52825035;rs9446983	45;45;45;45	Q6YHK3-2;Q6YHK3-3;Q6YHK3-4;Q6YHK3	.;.;.;CD109_HUMAN	V	45	ENSP00000388062:G45V;ENSP00000404475:G45V;ENSP00000287097:G45V	ENSP00000287097:G45V	G	+	2	0	CD109	74463903	1.000000	0.71417	0.998000	0.56505	0.711000	0.40976	3.673000	0.54591	2.779000	0.95612	0.655000	0.94253	GGG	G|0.986;T|0.014	0.014	strong		0.522	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493	
SYNE2	23224	hgsc.bcm.edu	37	14	64688335	64688335	+	Silent	SNP	G	G	A	rs75079588	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:64688335G>A	ENST00000344113.4	+	111	20246	c.20034G>A	c.(20032-20034)gcG>gcA	p.A6678A	SYNE2_ENST00000394768.2_Silent_p.A3063A|SYNE2_ENST00000555022.1_Silent_p.A556A|SYNE2_ENST00000357395.3_Silent_p.A3063A|SYNE2_ENST00000554584.1_Silent_p.A6594A|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000441438.2_Silent_p.A223A|SYNE2_ENST00000555002.1_Silent_p.A3335A|SYNE2_ENST00000358025.3_Silent_p.A6701A|SYNE2_ENST00000554805.1_Silent_p.A461A|SYNE2_ENST00000458046.2_Silent_p.A349A	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	6678					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)	p.A6701A(1)		NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		TGTGGTTAGCGAGTGCCAAGA	0.547													G|||	30	0.00599042	0.0219	0.0014	5008	,	,		18920	0.0		0.0	False		,,,				2504	0.0				p.A6701A		Atlas-SNP	.											SYNE2,NS,carcinoma,0,1	SYNE2	577	1	1	Substitution - coding silent(1)	lung(1)	c.G20103A						PASS	.	G	,,,	88,4318	73.6+/-111.7	1,86,2116	179.0	174.0	175.0		20034,669,1047,20103	-9.2	0.0	14	dbSNP_131	175	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SYNE2	NM_015180.4,NM_182910.2,NM_182913.2,NM_182914.2	,,,	1,87,6415	AA,AG,GG		0.0116,1.9973,0.6843	,,,	6678/6886,223/430,349/557,6701/6908	64688335	89,12917	2203	4300	6503	SO:0001819	synonymous_variant	23224	exon112			GTTAGCGAGTGCC	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.20034G>A	14.37:g.64688335G>A		113.0	0.0	0		161.0	88.0	0.546584	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																			G|0.994;A|0.006	0.006	strong		0.547	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
MICU1	10367	hgsc.bcm.edu	37	10	74183034	74183034	+	Silent	SNP	G	G	A	rs186054834	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:74183034G>A	ENST00000361114.5	-	9	1125	c.1029C>T	c.(1027-1029)acC>acT	p.T343T	MICU1_ENST00000401998.3_Silent_p.T343T|MICU1_ENST00000418483.2_Silent_p.T145T|MICU1_ENST00000398761.4_Silent_p.T345T|MICU1_ENST00000398763.4_Silent_p.T145T	NM_001195518.1|NM_006077.3	NP_001182447.1|NP_006068.2	Q9BPX6	MICU1_HUMAN	mitochondrial calcium uptake 1	343					calcium ion import (GO:0070509)|calcium ion transmembrane import into mitochondrion (GO:0036444)|defense response (GO:0006952)|mitochondrial calcium ion homeostasis (GO:0051560)|mitochondrial calcium ion transport (GO:0006851)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|protein homooligomerization (GO:0051260)	calcium channel complex (GO:0034704)|integral component of mitochondrial membrane (GO:0032592)|intracellular (GO:0005622)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|uniplex complex (GO:1990246)	calcium ion binding (GO:0005509)|protein heterodimerization activity (GO:0046982)										TCTGCATGGCGGTCAGCTTCT	0.493													G|||	3	0.000599042	0.0023	0.0	5008	,	,		19951	0.0		0.0	False		,,,				2504	0.0				p.T343T		Atlas-SNP	.											.	.	.	.	0			c.C1029T						PASS	.	G	,,	5,3985		0,5,1990	106.0	100.0	102.0		1029,435,1035	-11.3	0.3	10		102	0,8342		0,0,4171	no	coding-synonymous,coding-synonymous,coding-synonymous	MICU1	NM_001195518.1,NM_001195519.1,NM_006077.3	,,	0,5,6161	AA,AG,GG		0.0,0.1253,0.0405	,,	343/477,145/279,345/479	74183034	5,12327	1995	4171	6166	SO:0001819	synonymous_variant	10367	exon9			CATGGCGGTCAGC	Y17711	CCDS55714.1, CCDS55715.1	10q22.1	2013-01-10	2011-06-23	2011-06-23	ENSG00000107745	ENSG00000107745		"""EF-hand domain containing"""	1530	protein-coding gene	gene with protein product		605084	"""calcium binding atopy-related autoantigen 1"""	CBARA1		9806765, 20693986	Standard	NM_006077		Approved	CALC, EFHA3, FLJ12684	uc001jtb.2	Q9BPX6	OTTHUMG00000018437	ENST00000361114.5:c.1029C>T	10.37:g.74183034G>A		164.0	0.0	0		160.0	69.0	0.43125	NM_001195518	A8MV96|B3KN20|B4DJH9|B4DPI1|B5MBY3|D3YTJ3|O75785|Q9H9N6|Q9UFX0	Silent	SNP	ENST00000361114.5	37	CCDS55715.1																																																																																			G|0.999;A|0.001	0.001	strong		0.493	MICU1-002	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048586.1	NM_006077	
ARHGAP30	257106	hgsc.bcm.edu	37	1	161022247	161022247	+	Missense_Mutation	SNP	C	C	T	rs149524176	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:161022247C>T	ENST00000368013.3	-	8	1243	c.923G>A	c.(922-924)cGg>cAg	p.R308Q	ARHGAP30_ENST00000368016.3_Missense_Mutation_p.R308Q|ARHGAP30_ENST00000368015.1_Missense_Mutation_p.R131Q	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	308					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)			breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			CTCAGCCCCCCGTGGAAGTTT	0.537													C|||	4	0.000798722	0.003	0.0	5008	,	,		16986	0.0		0.0	False		,,,				2504	0.0				p.R308Q		Atlas-SNP	.											LOC257106,NS,carcinoma,-1,2	ARHGAP30	105	2	0			c.G923A						PASS	.	C	GLN/ARG,GLN/ARG	5,4401	9.9+/-24.2	0,5,2198	198.0	211.0	207.0		923,923	3.8	0.5	1	dbSNP_134	207	0,8600		0,0,4300	no	missense,missense	ARHGAP30	NM_001025598.1,NM_181720.2	43,43	0,5,6498	TT,TC,CC		0.0,0.1135,0.0384	possibly-damaging,possibly-damaging	308/1102,308/891	161022247	5,13001	2203	4300	6503	SO:0001583	missense	257106	exon8			GCCCCCCGTGGAA	AL832852	CCDS1215.1, CCDS30918.1, CCDS72958.1	1q23.3	2011-06-29			ENSG00000186517	ENSG00000186517		"""Rho GTPase activating proteins"""	27414	protein-coding gene	gene with protein product		614264					Standard	NM_001287602		Approved	FLJ00267	uc001fxl.3	Q7Z6I6	OTTHUMG00000031477	ENST00000368013.3:c.923G>A	1.37:g.161022247C>T	ENSP00000356992:p.Arg308Gln	87.0	0.0	0		89.0	35.0	0.393258	NM_001025598	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	Missense_Mutation	SNP	ENST00000368013.3	37	CCDS30918.1	.	.	.	.	.	.	.	.	.	.	C	14.08	2.429037	0.43122	0.001135	0.0	ENSG00000186517	ENST00000368016;ENST00000368013;ENST00000368017;ENST00000368015	T;T;T	0.38401	2.84;2.76;1.14	4.72	3.77	0.43336	.	0.396100	0.21881	N	0.067728	T	0.28333	0.0700	L	0.56199	1.76	0.09310	N	1	D;D	0.65815	0.995;0.989	P;P	0.56788	0.716;0.806	T	0.11665	-1.0578	10	0.66056	D	0.02	.	5.6555	0.17640	0.2053:0.6933:0.0:0.1014	.	308;308	Q7Z6I6;Q7Z6I6-2	RHG30_HUMAN;.	Q	308;308;160;131	ENSP00000356995:R308Q;ENSP00000356992:R308Q;ENSP00000356994:R131Q	ENSP00000356992:R308Q	R	-	2	0	ARHGAP30	159288871	0.000000	0.05858	0.542000	0.28115	0.981000	0.71138	0.424000	0.21330	0.924000	0.37069	0.549000	0.68633	CGG	C|0.999;T|0.001	0.001	strong		0.537	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720	
DOC2B	8447	hgsc.bcm.edu	37	17	31199	31199	+	Silent	SNP	G	G	A	rs551529924	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:31199G>A	ENST00000343572.7	-	1	228	c.72C>T	c.(70-72)ccC>ccT	p.P24P	DOC2B_ENST00000609727.1_5'Flank|AC108004.2_ENST00000576171.1_lincRNA	NM_003585.3	NP_003576	Q14184	DOC2B_HUMAN	double C2-like domains, beta	24	Mediates interaction with DYNLT1.|Negatively regulates targeting to plasma membrane. {ECO:0000250}.				calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|positive regulation of insulin secretion (GO:0032024)|positive regulation of vesicle fusion (GO:0031340)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			endometrium(2)|ovary(1)	3						GGATGGGGCCGGGGCACACGT	0.751													G|||	8	0.00159744	0.0053	0.0014	5008	,	,		3708	0.0		0.0	False		,,,				2504	0.0				p.P24P		Atlas-SNP	.											.	DOC2B	6	.	0			c.C72T						PASS	.						3.0	3.0	3.0					17																	31199		571	1338	1909	SO:0001819	synonymous_variant	8447	exon1			GGGGCCGGGGCAC	D70830	CCDS73934.1	17p13.3	2014-07-16			ENSG00000272636	ENSG00000272636		"""Synaptotagmins"""	2986	protein-coding gene	gene with protein product		604568	"""double C2-like domains, beta-like"""	DOC2BL		7826360	Standard	NM_003585		Approved		uc010vpx.1	Q14184	OTTHUMG00000154415	ENST00000343572.7:c.72C>T	17.37:g.31199G>A		47.0	0.0	0		38.0	14.0	0.368421	NM_003585		Silent	SNP	ENST00000343572.7	37																																																																																				.	.	none		0.751	DOC2B-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000335122.3	NM_003585	
TTC4	7268	hgsc.bcm.edu	37	1	55188437	55188437	+	Missense_Mutation	SNP	C	C	T	rs62000412	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55188437C>T	ENST00000371281.3	+	5	646	c.559C>T	c.(559-561)Ctt>Ttt	p.L187F	MROH7-TTC4_ENST00000414150.2_3'UTR|TTC4_ENST00000371284.5_3'UTR	NM_004623.4	NP_004614.3	O95801	TTC4_HUMAN	tetratricopeptide repeat domain 4	187										breast(2)|endometrium(3)|kidney(1)|lung(2)|stomach(1)	9						AGAGAAGAAGCTTCTGGAAAT	0.463													C|||	65	0.0129792	0.0484	0.0014	5008	,	,		20967	0.0		0.0	False		,,,				2504	0.0				p.L187F		Atlas-SNP	.											.	TTC4	21	.	0			c.C559T						PASS	.	C	PHE/LEU	192,4214	121.7+/-159.2	4,184,2015	122.0	115.0	117.0		559	5.4	1.0	1	dbSNP_129	117	2,8598	2.2+/-6.3	0,2,4298	yes	missense	TTC4	NM_004623.4	22	4,186,6313	TT,TC,CC		0.0233,4.3577,1.4916	probably-damaging	187/388	55188437	194,12812	2203	4300	6503	SO:0001583	missense	7268	exon5			AAGAAGCTTCTGG		CCDS596.1	1p32	2013-01-11			ENSG00000243725	ENSG00000243725		"""Tetratricopeptide (TTC) repeat domain containing"""	12394	protein-coding gene	gene with protein product		606753				9933562	Standard	NM_004623		Approved	MGC5097, FLJ41930	uc001cxx.4	O95801	OTTHUMG00000009914	ENST00000371281.3:c.559C>T	1.37:g.55188437C>T	ENSP00000360329:p.Leu187Phe	102.0	0.0	0		85.0	46.0	0.541176	NM_004623	Q53Y95|Q5TA96|Q9H3I2	Missense_Mutation	SNP	ENST00000371281.3	37	CCDS596.1	21	0.009615384615384616	21	0.042682926829268296	0	0.0	0	0.0	0	0.0	C	21.3	4.125911	0.77436	0.043577	2.33E-4	ENSG00000243725	ENST00000371281;ENST00000371284	T	0.20200	2.09	5.42	5.42	0.78866	Tetratricopeptide-like helical (1);	.	.	.	.	T	0.13841	0.0335	M	0.82716	2.605	0.58432	D	0.999996	P;D	0.64830	0.908;0.994	P;P	0.51945	0.514;0.685	T	0.06320	-1.0833	9	0.48119	T	0.1	-11.5851	18.1602	0.89706	0.0:1.0:0.0:0.0	rs62000412	187;198	O95801;Q5TA95	TTC4_HUMAN;.	F	187;198	ENSP00000360329:L187F	ENSP00000360329:L187F	L	+	1	0	TTC4	54961025	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.354000	0.52254	2.703000	0.92315	0.460000	0.39030	CTT	C|0.986;T|0.014	0.014	strong		0.463	TTC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027432.1	NM_004623	
LILRB2	10288	hgsc.bcm.edu	37	19	54782165	54782165	+	Missense_Mutation	SNP	C	C	T	rs4993133	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54782165C>T	ENST00000391749.4	-	7	1478	c.1207G>A	c.(1207-1209)Gac>Aac	p.D403N	LILRB2_ENST00000471216.1_5'Flank|LILRB2_ENST00000391746.1_Missense_Mutation_p.D403N|LILRB2_ENST00000314446.5_Missense_Mutation_p.D403N|LILRB2_ENST00000434421.1_Missense_Mutation_p.D287N|LILRB2_ENST00000391748.1_Missense_Mutation_p.D403N	NM_001278406.1	NP_001265335.1	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2	403	Ig-like C2-type 4.		D -> N (in dbSNP:rs4993133).		cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|negative regulation of antigen processing and presentation (GO:0002578)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of dendritic cell differentiation (GO:2001198)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|inhibitory MHC class I receptor activity (GO:0032396)|MHC class I protein binding (GO:0042288)|MHC class Ib protein binding (GO:0023029)|protein phosphatase 1 binding (GO:0008157)|receptor activity (GO:0004872)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(30)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	44	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		AGGTAGGGGTCGGAGTTGAGT	0.592													.|||	31	0.0061901	0.0204	0.0014	5008	,	,		17568	0.0		0.002	False		,,,				2504	0.001				p.D403N		Atlas-SNP	.											.	LILRB2	94	.	0			c.G1207A						PASS	.	T	ASN/ASP,ASN/ASP	51,4355	821.0+/-416.4	1,49,2153	101.0	94.0	96.0		1207,1207	-2.2	0.0	19	dbSNP_113	96	5,8595	818.7+/-406.8	0,5,4295	no	missense,missense	LILRB2	NM_001080978.2,NM_005874.3	23,23	1,54,6448	TT,TC,CC		0.0581,1.1575,0.4306	benign,benign	403/598,403/599	54782165	56,12950	2203	4300	6503	SO:0001583	missense	10288	exon7			AGGGGTCGGAGTT	AF000574	CCDS12886.1, CCDS42612.1, CCDS62791.1, CCDS62792.1	19q13.4	2013-01-11			ENSG00000131042	ENSG00000131042		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6606	protein-coding gene	gene with protein product		604815				9151699, 9079806	Standard	XM_006722966		Approved	LIR-2, ILT4, MIR-10, LIR2, CD85d, MIR10	uc002qfb.3	Q8N423	OTTHUMG00000064896	ENST00000391749.4:c.1207G>A	19.37:g.54782165C>T	ENSP00000375629:p.Asp403Asn	190.0	0.0	0		142.0	61.0	0.429577	NM_005874	A8MU67|C9JF29|O75017|Q8NHJ7|Q8NHJ8	Missense_Mutation	SNP	ENST00000391749.4	37	CCDS12886.1	9	0.004120879120879121	7	0.014227642276422764	0	0.0	0	0.0	2	0.002638522427440633	T	1.465	-0.561273	0.03939	0.011575	5.81E-4	ENSG00000131042	ENST00000391748;ENST00000314446;ENST00000391749;ENST00000391746;ENST00000434421	T;T;T;T;T	0.00717	5.79;5.79;5.79;5.79;5.79	1.88	-2.23	0.06930	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	3.810930	0.01046	N	0.004391	T	0.00300	0.0009	N	0.03294	-0.36	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.001	B;B;B	0.06405	0.002;0.002;0.002	T	0.43653	-0.9378	10	0.06494	T	0.89	.	0.3448	0.00339	0.2691:0.185:0.1425:0.4034	rs4993133	403;420;403	A8MU67;E7EVY1;Q8N423	.;.;LIRB2_HUMAN	N	403;403;403;403;287	ENSP00000375628:D403N;ENSP00000319960:D403N;ENSP00000375629:D403N;ENSP00000375626:D403N;ENSP00000410117:D287N	ENSP00000319960:D403N	D	-	1	0	LILRB2	59473977	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-3.319000	0.00514	-1.728000	0.01366	-2.542000	0.00179	GAC	C|0.995;T|0.005	0.005	strong		0.592	LILRB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139510.1		
TTN	7273	hgsc.bcm.edu	37	2	179412452	179412452	+	Missense_Mutation	SNP	C	C	T	rs67665715	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179412452C>T	ENST00000591111.1	-	289	89202	c.88978G>A	c.(88978-88980)Gtc>Atc	p.V29660I	TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.V22428I|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592630.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V28733I|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.V22361I|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.V22236I|TTN_ENST00000589042.1_Missense_Mutation_p.V31301I			Q8WZ42	TITIN_HUMAN	titin	29660	Ig-like 135.				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)			ACAACTGTGACGCTAAATGTT	0.478													C|||	180	0.0359425	0.1271	0.0159	5008	,	,		20351	0.0		0.001	False		,,,				2504	0.0				p.V31301I		Atlas-SNP	.											.	TTN	18412	.	0			c.G93901A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	395,3517		24,347,1585	139.0	130.0	133.0		67282,67081,86197,66706	-2.3	0.9	2	dbSNP_130	133	8,8316		0,8,4154	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	29,29,29,29	24,355,5739	TT,TC,CC		0.0961,10.0971,3.2936	benign,benign,benign,benign	22428/27119,22361/27052,28733/33424,22236/26927	179412452	403,11833	1956	4162	6118	SO:0001583	missense	7273	exon339			CTGTGACGCTAAA	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.88978G>A	2.37:g.179412452C>T	ENSP00000465570:p.Val29660Ile	387.0	0.0	0		438.0	243.0	0.554795	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		86	0.039377289377289376	78	0.15853658536585366	8	0.022099447513812154	0	0.0	0	0.0	C	6.281	0.420045	0.11928	0.100971	9.61E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29	5.92	-2.32	0.06745	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Fibronectin, type III (1);Immunoglobulin-like (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00271	0.0008	N	0.17631	0.505	0.30962	P	0.723517	B;B;B;B	0.09022	0.002;0.002;0.002;0.002	B;B;B;B	0.08055	0.002;0.002;0.003;0.003	T	0.09618	-1.0666	8	0.87932	D	0	.	13.3122	0.60386	0.0:0.727:0.0:0.273	.	22236;22361;22428;29660	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	28733;22236;22428;22361;22233	ENSP00000343764:V28733I;ENSP00000434586:V22236I;ENSP00000340554:V22428I;ENSP00000352154:V22361I	ENSP00000340554:V22428I	V	-	1	0	TTN	179120698	0.965000	0.33210	0.865000	0.33974	0.314000	0.28054	0.991000	0.29654	-0.306000	0.08818	-1.934000	0.00508	GTC	C|0.967;T|0.033	0.033	strong		0.478	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
CRACR2A	84766	hgsc.bcm.edu	37	12	3747496	3747496	+	Missense_Mutation	SNP	G	G	C	rs58583720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:3747496G>C	ENST00000440314.2	-	14	1869	c.1396C>G	c.(1396-1398)Cgg>Ggg	p.R466G		NM_001144958.1	NP_001138430.1	Q9BSW2	EFC4B_HUMAN		0					activation of store-operated calcium channel activity (GO:0032237)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)			CGGAGCGGCCGGGGGTACGGA	0.612													G|||	59	0.0117812	0.0416	0.0058	5008	,	,		14651	0.0		0.0	False		,,,				2504	0.0				p.R466G		Atlas-SNP	.											.	EFCAB4B	100	.	0			c.C1396G						PASS	.	G	GLY/ARG	50,1334		1,48,643	20.0	24.0	23.0		1396	3.5	0.0	12	dbSNP_129	23	0,3182		0,0,1591	yes	missense	EFCAB4B	NM_001144958.1	125	1,48,2234	CC,CG,GG		0.0,3.6127,1.0951	benign	466/732	3747496	50,4516	692	1591	2283	SO:0001583	missense	84766	exon14			GCGGCCGGGGGTA																												ENST00000440314.2:c.1396C>G	12.37:g.3747496G>C	ENSP00000409382:p.Arg466Gly	72.0	0.0	0		81.0	46.0	0.567901	NM_001144958	B4E1X0|B9EK63	Missense_Mutation	SNP	ENST00000440314.2	37	CCDS44803.1	.	.	.	.	.	.	.	.	.	.	G	12.83	2.054114	0.36277	0.036127	0.0	ENSG00000130038	ENST00000440314	T	0.61274	0.12	4.4	3.51	0.40186	.	.	.	.	.	T	0.23926	0.0579	.	.	.	0.36197	D	0.85047	P	0.42620	0.785	P	0.45506	0.483	T	0.53479	-0.8433	8	0.45353	T	0.12	.	10.1568	0.42827	0.0984:0.0:0.9016:0.0	rs58583720	466	Q9BSW2-2	.	G	466	ENSP00000409382:R466G	ENSP00000409382:R466G	R	-	1	2	EFCAB4B	3617757	0.331000	0.24713	0.007000	0.13788	0.194000	0.23727	4.138000	0.58017	1.074000	0.40909	0.557000	0.71058	CGG	A|0.002;C|0.001;G|0.997	0.001	strong		0.612	EFCAB4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398640.2		
COMT	1312	hgsc.bcm.edu	37	22	19950268	19950268	+	Silent	SNP	G	G	A	rs740602	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:19950268G>A	ENST00000361682.6	+	3	601	c.219G>A	c.(217-219)caG>caA	p.Q73Q	MIR4761_ENST00000585066.1_RNA|COMT_ENST00000407537.1_Silent_p.Q23Q|COMT_ENST00000403710.1_Silent_p.Q73Q|COMT_ENST00000403184.1_Silent_p.Q73Q|COMT_ENST00000449653.1_Silent_p.Q23Q|COMT_ENST00000406520.3_Silent_p.Q73Q	NM_000754.3	NP_000745.1	P21964	COMT_HUMAN	catechol-O-methyltransferase	73					cellular response to phosphate starvation (GO:0016036)|dopamine catabolic process (GO:0042420)|estrogen metabolic process (GO:0008210)|female pregnancy (GO:0007565)|learning (GO:0007612)|methylation (GO:0032259)|multicellular organismal reproductive process (GO:0048609)|negative regulation of dopamine metabolic process (GO:0045963)|negative regulation of smooth muscle cell proliferation (GO:0048662)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter catabolic process (GO:0042135)|positive regulation of homocysteine metabolic process (GO:0050668)|response to drug (GO:0042493)|response to lipopolysaccharide (GO:0032496)|response to organic cyclic compound (GO:0014070)|response to pain (GO:0048265)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	catechol O-methyltransferase activity (GO:0016206)|magnesium ion binding (GO:0000287)|O-methyltransferase activity (GO:0008171)			kidney(1)|lung(1)|ovary(1)|prostate(1)|stomach(1)	5	Colorectal(54;0.0993)				Conjugated Estrogens(DB00286)|Diethylstilbestrol(DB00255)|Dobutamine(DB00841)|Dopamine(DB00988)|Entacapone(DB00494)|Methyldopa(DB00968)|Micafungin(DB01141)|S-Adenosylmethionine(DB00118)|Testosterone Propionate(DB01420)|Tolcapone(DB00323)	GGAACGCACAGAGCGTGCTGG	0.622													G|||	300	0.0599042	0.2005	0.0202	5008	,	,		18048	0.0		0.0089	False		,,,				2504	0.0123				p.Q73Q		Atlas-SNP	.											.	COMT	10	.	0			c.G219A						PASS	.	G	,,,	790,3616	314.4+/-293.6	72,646,1485	80.0	75.0	77.0		219,219,219,69	2.2	1.0	22	dbSNP_86	77	39,8561	25.7+/-73.6	0,39,4261	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	COMT	NM_000754.3,NM_001135161.1,NM_001135162.1,NM_007310.2	,,,	72,685,5746	AA,AG,GG		0.4535,17.9301,6.374	,,,	73/272,73/272,73/272,23/222	19950268	829,12177	2203	4300	6503	SO:0001819	synonymous_variant	1312	exon3			CGCACAGAGCGTG		CCDS13770.1, CCDS46663.1	22q11.21	2012-10-02			ENSG00000093010	ENSG00000093010	2.1.1.6		2228	protein-coding gene	gene with protein product		116790				1572656	Standard	NM_000754		Approved		uc002zqu.3	P21964	OTTHUMG00000150529	ENST00000361682.6:c.219G>A	22.37:g.19950268G>A		116.0	0.0	0		109.0	47.0	0.431193	NM_000754	A8MPV9|Q6IB07|Q6ICE6|Q9BWC7	Silent	SNP	ENST00000361682.6	37	CCDS13770.1																																																																																			A|0.059;C|0.007	0.059	strong		0.622	COMT-011	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318936.2	NM_000754	
PPL	5493	hgsc.bcm.edu	37	16	4935257	4935257	+	Silent	SNP	G	G	A	rs571194570	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4935257G>A	ENST00000345988.2	-	22	3488	c.3399C>T	c.(3397-3399)ctC>ctT	p.L1133L	PPL_ENST00000590782.2_Silent_p.L1131L	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1133					keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						ATTGGCGGGTGAGATCGCTGA	0.627													G|||	13	0.00259585	0.0091	0.0014	5008	,	,		12926	0.0		0.0	False		,,,				2504	0.0				p.L1133L		Atlas-SNP	.											.	PPL	168	.	0			c.C3399T						PASS	.						79.0	71.0	74.0					16																	4935257		2197	4300	6497	SO:0001819	synonymous_variant	5493	exon22			GCGGGTGAGATCG	AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.3399C>T	16.37:g.4935257G>A		152.0	0.0	0		135.0	48.0	0.355556	NM_002705	O60314|O60454|Q14C98	Silent	SNP	ENST00000345988.2	37	CCDS10526.1																																																																																			.	.	none		0.627	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
CEACAM21	90273	hgsc.bcm.edu	37	19	42092225	42092225	+	Splice_Site	SNP	G	G	A	rs62119455	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42092225G>A	ENST00000401445.2	+	6	908		c.e6+1		CEACAM21_ENST00000407170.2_Splice_Site|CEACAM21_ENST00000482870.2_Intron|CEACAM21_ENST00000187608.9_Splice_Site			Q3KPI0	CEA21_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 21							integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|urinary_tract(1)	13						CATCTCCTAGGTAAGACTGTC	0.592													g|||	124	0.0247604	0.0825	0.0072	5008	,	,		17365	0.0		0.0099	False		,,,				2504	0.0				.		Atlas-SNP	.											.	CEACAM21	52	.	0			c.882+1G>A						PASS	.	G	,	261,3973		8,245,1864	63.0	66.0	65.0		,	1.2	0.0	19	dbSNP_129	65	58,8460		1,56,4202	yes	splice-5,splice-5	CEACAM21	NM_001098506.1,NM_033543.3	,	9,301,6066	AA,AG,GG		0.6809,6.1644,2.5016	,	,	42092225	319,12433	2117	4259	6376	SO:0001630	splice_region_variant	90273	exon6			TCCTAGGTAAGAC	AK023602	CCDS46086.1, CCDS46087.1, CCDS74373.1	19q13.2	2013-01-29			ENSG00000007129	ENSG00000007129		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	28834	protein-coding gene	gene with protein product						12477932	Standard	XM_005278397		Approved	R29124_1, FLJ13540	uc002ore.4	Q3KPI0	OTTHUMG00000151062	ENST00000401445.2:c.879+1G>A	19.37:g.42092225G>A		140.0	1.0	0.00714286		158.0	158.0	1	NM_001098506	B7WNQ6|O75296|Q6UY47|Q96ER7	Splice_Site	SNP	ENST00000401445.2	37	CCDS46086.1																																																																																			G|0.981;A|0.019	0.019	strong		0.592	CEACAM21-005	KNOWN	non_canonical_polymorphism|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321140.1	NM_033543	Intron
WDR55	54853	hgsc.bcm.edu	37	5	140048792	140048792	+	Silent	SNP	C	C	A	rs35080423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140048792C>A	ENST00000358337.5	+	6	1026	c.789C>A	c.(787-789)acC>acA	p.T263T	WDR55_ENST00000520764.1_3'UTR	NM_017706.4	NP_060176	Q9H6Y2	WDR55_HUMAN	WD repeat domain 55	263					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)				NS(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)	9			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTCCAGTCACCGAGAGTCTGC	0.547													C|||	51	0.0101837	0.0378	0.0014	5008	,	,		21176	0.0		0.0	False		,,,				2504	0.0				p.T263T		Atlas-SNP	.											WDR55,NS,carcinoma,+2,1	WDR55	27	1	0			c.C789A						scavenged	.	C		113,4293	88.2+/-126.9	3,107,2093	84.0	77.0	79.0		789	-10.2	0.1	5	dbSNP_126	79	0,8600		0,0,4300	no	coding-synonymous	WDR55	NM_017706.4		3,107,6393	AA,AC,CC		0.0,2.5647,0.8688		263/384	140048792	113,12893	2203	4300	6503	SO:0001819	synonymous_variant	54853	exon6			AGTCACCGAGAGT	AK000202	CCDS4235.1	5q31.3	2013-01-09			ENSG00000120314	ENSG00000120314		"""WD repeat domain containing"""	25971	protein-coding gene	gene with protein product						12477932	Standard	NM_017706		Approved	FLJ20195, FLJ21702	uc003lgr.4	Q9H6Y2	OTTHUMG00000129506	ENST00000358337.5:c.789C>A	5.37:g.140048792C>A		70.0	1.0	0.0142857		61.0	32.0	0.52459	NM_017706	Q9NXK4	Silent	SNP	ENST00000358337.5	37	CCDS4235.1																																																																																			C|0.991;A|0.009	0.009	strong		0.547	WDR55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251680.3	NM_017706	
KIRREL2	84063	hgsc.bcm.edu	37	19	36351906	36351906	+	Silent	SNP	C	C	A	rs73928338	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36351906C>A	ENST00000360202.5	+	8	1222	c.1024C>A	c.(1024-1026)Cgg>Agg	p.R342R	KIRREL2_ENST00000592409.1_Silent_p.R342R|KIRREL2_ENST00000262625.7_Silent_p.R342R|NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000347900.6_Silent_p.R292R	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	342	Ig-like C2-type 4.				cell adhesion (GO:0007155)|negative regulation of protein phosphorylation (GO:0001933)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)				breast(2)|central_nervous_system(1)|endometrium(6)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	48	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CCCGCTTCCACGGGTAACCTG	0.662													C|||	35	0.00698882	0.0242	0.0043	5008	,	,		13850	0.0		0.0	False		,,,				2504	0.0				p.R342R		Atlas-SNP	.											.	KIRREL2	170	.	0			c.C1024A						PASS	.	C	,,	76,4284		0,76,2104	11.0	13.0	12.0		1024,874,1024	4.5	1.0	19	dbSNP_130	12	1,8531		0,1,4265	no	coding-synonymous,coding-synonymous,coding-synonymous	KIRREL2	NM_032123.5,NM_199179.2,NM_199180.2	,,	0,77,6369	AA,AC,CC		0.0117,1.7431,0.5973	,,	342/634,292/584,342/709	36351906	77,12815	2180	4266	6446	SO:0001819	synonymous_variant	84063	exon8			CTTCCACGGGTAA	AL136654	CCDS12479.1, CCDS12480.1, CCDS12481.1	19q13.13	2013-01-29				ENSG00000126259		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18816	protein-coding gene	gene with protein product		607762				12837264, 12504092	Standard	NM_199180		Approved	NLG1, NEPH3, FILTRIN, DKFZp564A1164, MGC15718	uc002ocb.4	Q6UWL6		ENST00000360202.5:c.1024C>A	19.37:g.36351906C>A		50.0	0.0	0		69.0	30.0	0.434783	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Silent	SNP	ENST00000360202.5	37	CCDS12481.1																																																																																			C|0.994;A|0.006	0.006	strong		0.662	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123	
CEP170	9859	hgsc.bcm.edu	37	1	243329093	243329093	+	Silent	SNP	G	G	C	rs2789194	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:243329093G>C	ENST00000366542.1	-	13	2220	c.2169C>G	c.(2167-2169)ggC>ggG	p.G723G	CEP170_ENST00000366543.1_Silent_p.G625G|RP11-261C10.4_ENST00000437499.1_RNA|CEP170_ENST00000366544.1_Silent_p.G625G|RP11-261C10.4_ENST00000422938.1_RNA|CEP170_ENST00000490813.1_5'Flank	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	723						centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)				NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			GAGCAGAGCTGCCTAAGTGAA	0.398													G|||	192	0.0383387	0.143	0.0043	5008	,	,		20676	0.0		0.0	False		,,,				2504	0.0				p.G723G		Atlas-SNP	.											.	CEP170	153	.	0			c.C2169G						PASS	.	G	,,	483,3189		39,405,1392	163.0	150.0	154.0		1875,1875,2169	1.0	0.0	1	dbSNP_100	154	3,8169		0,3,4083	no	coding-synonymous,coding-synonymous,coding-synonymous	CEP170	NM_001042404.1,NM_001042405.1,NM_014812.2	,,	39,408,5475	CC,CG,GG		0.0367,13.1536,4.1033	,,	625/1487,625/1461,723/1585	243329093	486,11358	1836	4086	5922	SO:0001819	synonymous_variant	9859	exon13			AGAGCTGCCTAAG	AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702			28920	protein-coding gene	gene with protein product	"""KARP 1 binding protein"", ""XRCC5 binding protein"""	613023	"""KIAA0470"""	KIAA0470		15616186	Standard	NM_014812		Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.2169C>G	1.37:g.243329093G>C		222.0	0.0	0		217.0	108.0	0.497696	NM_014812	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Silent	SNP	ENST00000366542.1	37	CCDS44339.1	64	0.029304029304029304	61	0.12398373983739837	3	0.008287292817679558	0	0.0	0	0.0	G	0.006	-2.025614	0.00414	0.131536	3.67E-4	ENSG00000143702	ENST00000336415	.	.	.	5.25	1.02	0.19986	.	.	.	.	.	T	0.00241	0.0007	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.15407	-1.0438	4	.	.	.	-3.8866	4.2033	0.10476	0.1806:0.0:0.4641:0.3553	rs2789194;rs2789194	.	.	.	G	687	.	.	A	-	2	0	CEP170	241395716	0.104000	0.21937	0.003000	0.11579	0.284000	0.27059	0.869000	0.27996	-0.080000	0.12685	-0.439000	0.05793	GCA	G|0.978;C|0.022	0.022	strong		0.398	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812	
C16orf62	57020	hgsc.bcm.edu	37	16	19590444	19590444	+	Silent	SNP	T	T	C	rs11866050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:19590444T>C	ENST00000251143.5	+	6	516	c.504T>C	c.(502-504)ttT>ttC	p.F168F	C16orf62_ENST00000448695.1_Silent_p.F46F|C16orf62_ENST00000543152.1_5'UTR|C16orf62_ENST00000542263.1_Silent_p.F257F|C16orf62_ENST00000438132.3_Silent_p.F257F|C16orf62_ENST00000417362.2_Silent_p.F168F|C16orf62_ENST00000538853.1_3'UTR			Q7Z3J2	CP062_HUMAN	chromosome 16 open reading frame 62	168				F -> S (in Ref. 3; CAH10399). {ECO:0000305}.		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						TGGATGACTTTGAGGAGGTGA	0.502													T|||	359	0.0716853	0.2057	0.0144	5008	,	,		18705	0.0337		0.0209	False		,,,				2504	0.0225				p.F257F		Atlas-SNP	.											.	C16orf62	164	.	0			c.T771C						PASS	.	T		633,3761	272.8+/-271.0	34,565,1598	94.0	83.0	87.0		771	-1.1	1.0	16	dbSNP_120	87	152,8448	72.3+/-134.9	0,152,4148	no	coding-synonymous	C16orf62	NM_020314.5		34,717,5746	CC,CT,TT		1.7674,14.406,6.0412		257/1053	19590444	785,12209	2197	4300	6497	SO:0001819	synonymous_variant	57020	exon6			TGACTTTGAGGAG		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.504T>C	16.37:g.19590444T>C		95.0	0.0	0		108.0	61.0	0.564815	NM_020314	A8K2M1|O43329|Q69YI1|Q6PDA0|Q7L371|Q86W66|Q8WXA5|Q9H0L7|Q9H7C8	Silent	SNP	ENST00000251143.5	37																																																																																				T|0.937;C|0.063	0.063	strong		0.502	C16orf62-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_020314	
EGLN2	112398	hgsc.bcm.edu	37	19	41306771	41306771	+	Silent	SNP	G	G	A	rs143206553	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41306771G>A	ENST00000593726.1	+	1	1322	c.294G>A	c.(292-294)gcG>gcA	p.A98A	EGLN2_ENST00000303961.4_Silent_p.A98A|RAB4B-EGLN2_ENST00000594136.1_3'UTR|CTC-490E21.12_ENST00000601627.1_5'Flank|EGLN2_ENST00000594140.1_5'Flank|EGLN2_ENST00000406058.2_Silent_p.A98A			Q96KS0	EGLN2_HUMAN	egl-9 family hypoxia-inducible factor 2	98	Bipartite nuclear localization signal.				cell redox homeostasis (GO:0045454)|cellular response to hypoxia (GO:0071456)|intracellular estrogen receptor signaling pathway (GO:0030520)|peptidyl-proline hydroxylation to 4-hydroxy-L-proline (GO:0018401)|positive regulation of protein catabolic process (GO:0045732)|regulation of cell growth (GO:0001558)|regulation of neuron apoptotic process (GO:0043523)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to hypoxia (GO:0001666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ferrous iron binding (GO:0008198)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|oxygen sensor activity (GO:0019826)|peptidyl-proline 4-dioxygenase activity (GO:0031545)			breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)	10			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Vitamin C(DB00126)	GCGCTGCAGCGCTGGTCACCA	0.677													G|||	18	0.00359425	0.0129	0.0014	5008	,	,		16000	0.0		0.0	False		,,,				2504	0.0				p.A98A		Atlas-SNP	.											.	EGLN2	31	.	0			c.G294A						PASS	.	G	,	77,4321		0,77,2122	14.0	16.0	15.0		294,294	-3.8	0.7	19	dbSNP_134	15	0,8582		0,0,4291	no	coding-synonymous,coding-synonymous	EGLN2	NM_053046.3,NM_080732.3	,	0,77,6413	AA,AG,GG		0.0,1.7508,0.5932	,	98/408,98/408	41306771	77,12903	2199	4291	6490	SO:0001819	synonymous_variant	112398	exon2			TGCAGCGCTGGTC	AJ310544	CCDS12567.1	19q13.2	2013-08-21	2013-08-21		ENSG00000269858	ENSG00000269858			14660	protein-coding gene	gene with protein product	"""HIF prolyl hydroxylase 1"""	606424	"""EGL nine (C.elegans) homolog 2"", ""egl nine homolog 2 (C. elegans)"""				Standard	NM_080732		Approved	PHD1, HIFPH1	uc002oph.3	Q96KS0		ENST00000593726.1:c.294G>A	19.37:g.41306771G>A		45.0	0.0	0		63.0	31.0	0.492063	NM_053046	A8K5S0|Q8WWY4|Q9BV14	Silent	SNP	ENST00000593726.1	37	CCDS12567.1																																																																																			G|0.993;A|0.007	0.007	strong		0.677	EGLN2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463218.1		
C17orf85	55421	hgsc.bcm.edu	37	17	3728315	3728315	+	Silent	SNP	C	C	T	rs218719	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3728315C>T	ENST00000389005.4	-	7	744	c.717G>A	c.(715-717)gaG>gaA	p.E239E	C17orf85_ENST00000577169.1_5'UTR|C17orf85_ENST00000158149.3_5'UTR	NM_001114118.2	NP_001107590.1	Q53F19	CQ085_HUMAN	chromosome 17 open reading frame 85	239							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(2)|lung(4)|skin(1)|urinary_tract(1)	10				UCEC - Uterine corpus endometrioid carcinoma (3;0.0725)		TTAACAAAGACTCCTCTTCTA	0.308													C|||	249	0.0497204	0.1808	0.0115	5008	,	,		17016	0.001		0.0	False		,,,				2504	0.001				p.E239E		Atlas-SNP	.											.	C17orf85	66	.	0			c.G717A						PASS	.	C	,	179,1205		16,147,529	120.0	94.0	102.0		717,	-1.8	1.0	17	dbSNP_79	102	2,3172		0,2,1585	no	coding-synonymous,utr-5	C17orf85	NM_001114118.1,NM_018553.3	,	16,149,2114	TT,TC,CC		0.063,12.9335,3.971	,	239/621,	3728315	181,4377	692	1587	2279	SO:0001819	synonymous_variant	55421	exon7			CAAAGACTCCTCT		CCDS45578.1	17p13.2	2012-10-23			ENSG00000074356	ENSG00000074356			24612	protein-coding gene	gene with protein product	"""ELG protein"""					11412301	Standard	NM_001114118		Approved	HSA277841, ELG	uc010ckl.2	Q53F19	OTTHUMG00000177672	ENST00000389005.4:c.717G>A	17.37:g.3728315C>T		30.0	0.0	0		27.0	11.0	0.407407	NM_001114118	B3KWG7|Q7L406|Q96FK1|Q9NXZ4	Silent	SNP	ENST00000389005.4	37	CCDS45578.1																																																																																			C|0.932;T|0.068	0.068	strong		0.308	C17orf85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438385.1	NM_018553	
VAV2	7410	hgsc.bcm.edu	37	9	136640122	136640122	+	Silent	SNP	G	G	A	rs7875953	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136640122G>A	ENST00000371850.3	-	25	2101	c.2070C>T	c.(2068-2070)caC>caT	p.H690H	VAV2_ENST00000371851.1_Silent_p.H680H|VAV2_ENST00000406606.3_Silent_p.H680H	NM_001134398.1	NP_001127870.1	P52735	VAV2_HUMAN	vav 2 guanine nucleotide exchange factor	690	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(3)|large_intestine(5)|lung(13)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|urinary_tract(1)	35				OV - Ovarian serous cystadenocarcinoma(145;3.9e-07)|Epithelial(140;2.07e-06)|all cancers(34;9.39e-06)		TCCCGCTGGCGTGGGACTTGA	0.617													G|||	132	0.0263578	0.0923	0.0115	5008	,	,		18617	0.0		0.002	False		,,,				2504	0.0				p.H690H		Atlas-SNP	.											VAV2_ENST00000371850,colon,carcinoma,0,2	VAV2	165	2	0			c.C2070T						PASS	.	G	,	426,3980	207.2+/-228.6	26,374,1803	71.0	64.0	66.0		2070,2040	-3.2	1.0	9	dbSNP_116	66	5,8593	3.0+/-9.4	0,5,4294	no	coding-synonymous,coding-synonymous	VAV2	NM_001134398.1,NM_003371.3	,	26,379,6097	AA,AG,GG		0.0582,9.6686,3.3144	,	690/879,680/840	136640122	431,12573	2203	4299	6502	SO:0001819	synonymous_variant	7410	exon25			GCTGGCGTGGGAC		CCDS6979.1, CCDS48053.1	9q34.1	2013-02-14	2007-07-25		ENSG00000160293	ENSG00000160293		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12658	protein-coding gene	gene with protein product		600428	"""vav 2 oncogene"""			7762982	Standard	NM_003371		Approved		uc004ces.3	P52735	OTTHUMG00000020882	ENST00000371850.3:c.2070C>T	9.37:g.136640122G>A		102.0	0.0	0		135.0	86.0	0.637037	NM_001134398	A2RUM4|A8MQ12|B6ZDF5|Q5SYV3|Q5SYV4|Q5SYV5|Q6N012|Q6PIJ9|Q6Q317	Silent	SNP	ENST00000371850.3	37	CCDS48053.1																																																																																			G|0.963;A|0.037	0.037	strong		0.617	VAV2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054939.1		
TGM6	343641	hgsc.bcm.edu	37	20	2377204	2377204	+	Silent	SNP	C	C	T	rs16984872	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:2377204C>T	ENST00000202625.2	+	4	538	c.477C>T	c.(475-477)agC>agT	p.S159S	TGM6_ENST00000381423.1_Silent_p.S159S|TGM6_ENST00000477505.1_Intron	NM_198994.2	NP_945345.2	O95932	TGM3L_HUMAN	transglutaminase 6	159					cell death (GO:0008219)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|endometrium(6)|kidney(2)|large_intestine(2)|lung(32)|ovary(4)|prostate(1)|skin(4)	52					L-Glutamine(DB00130)	ACGTGCTCAGCGACAGCGGCA	0.612													C|||	193	0.0385383	0.1225	0.0259	5008	,	,		19129	0.0		0.0099	False		,,,				2504	0.0031				p.S159S		Atlas-SNP	.											TGM6,NS,carcinoma,0,1	TGM6	126	1	0			c.C477T						PASS	.	C		447,3959	215.8+/-234.7	28,391,1784	96.0	85.0	89.0		477	-5.3	0.9	20	dbSNP_123	89	87,8513	49.4+/-109.1	0,87,4213	no	coding-synonymous	TGM6	NM_198994.2		28,478,5997	TT,TC,CC		1.0116,10.1453,4.1058		159/707	2377204	534,12472	2203	4300	6503	SO:0001819	synonymous_variant	343641	exon4			GCTCAGCGACAGC	AF540970	CCDS13025.1, CCDS58761.1	20p13	2010-12-19	2004-07-05	2004-07-07	ENSG00000166948	ENSG00000166948		"""Transglutaminases"""	16255	protein-coding gene	gene with protein product	"""spinocerebellar ataxia 35"""	613900	"""transglutaminase 3-like"""	TGM3L		11390390, 21106500	Standard	NM_198994		Approved	dJ734P14.3, TGY, SCA35	uc002wfy.1	O95932	OTTHUMG00000031692	ENST00000202625.2:c.477C>T	20.37:g.2377204C>T		252.0	0.0	0		266.0	124.0	0.466165	NM_198994	Q5JXU4|Q5JXU5|Q719M2|Q719M3|Q9Y4U8	Silent	SNP	ENST00000202625.2	37	CCDS13025.1																																																																																			C|0.960;T|0.040	0.040	strong		0.612	TGM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077581.2	NM_198994	
LUZP1	7798	hgsc.bcm.edu	37	1	23418576	23418576	+	Missense_Mutation	SNP	T	T	C	rs144862656	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:23418576T>C	ENST00000302291.4	-	4	2980	c.2179A>G	c.(2179-2181)Acc>Gcc	p.T727A	LUZP1_ENST00000314174.5_Missense_Mutation_p.T727A|LUZP1_ENST00000418342.1_Missense_Mutation_p.T727A|LUZP1_ENST00000374623.3_Missense_Mutation_p.T727A			Q86V48	LUZP1_HUMAN	leucine zipper protein 1	727					artery development (GO:0060840)|neural fold bending (GO:0021503)|ventricular septum development (GO:0003281)	membrane (GO:0016020)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(2)	31		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Ovarian(437;0.00373)|Breast(348;0.00815)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;4.88e-27)|Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;4.31e-06)|GBM - Glioblastoma multiforme(114;8.64e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00176)|STAD - Stomach adenocarcinoma(196;0.0146)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0967)|LUSC - Lung squamous cell carcinoma(448;0.199)		AGCTCCATGGTATTGGTGGAG	0.493													C|||	23	0.00459265	0.0159	0.0029	5008	,	,		20483	0.0		0.0	False		,,,				2504	0.0				p.T727A		Atlas-SNP	.											.	LUZP1	83	.	0			c.A2179G						PASS	.	C	ALA/THR,ALA/THR	41,4365	799.2+/-415.5	0,41,2162	182.0	199.0	193.0		2179,2179	3.8	0.4	1	dbSNP_134	193	1,8599	812.4+/-407.1	0,1,4299	yes	missense,missense	LUZP1	NM_001142546.1,NM_033631.3	58,58	0,42,6461	CC,CT,TT		0.0116,0.9305,0.3229	benign,benign	727/1077,727/1077	23418576	42,12964	2203	4300	6503	SO:0001583	missense	7798	exon4			CCATGGTATTGGT	BC051733	CCDS30628.1	1p36	2008-02-05			ENSG00000169641	ENSG00000169641			14985	protein-coding gene	gene with protein product		601422				8812416	Standard	NM_033631		Approved	LUZP	uc010odv.1	Q86V48	OTTHUMG00000003227	ENST00000302291.4:c.2179A>G	1.37:g.23418576T>C	ENSP00000303758:p.Thr727Ala	108.0	0.0	0		126.0	59.0	0.468254	NM_033631	Q5TH93|Q8N4X3|Q8TEH1	Missense_Mutation	SNP	ENST00000302291.4	37	CCDS30628.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	C	0.005	-2.197318	0.00299	0.009305	1.16E-4	ENSG00000169641	ENST00000418342;ENST00000374623;ENST00000302291;ENST00000314174	T;T;T;T	0.12039	2.94;2.94;2.94;2.72	4.74	3.81	0.43845	.	0.350958	0.20869	N	0.084207	T	0.01905	0.0060	N	0.00347	-1.61	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	0.23891	T	0.37	.	4.1464	0.10217	0.3497:0.476:0.0:0.1743	.	727;727	Q86V48-2;Q86V48	.;LUZP1_HUMAN	A	727	ENSP00000393460:T727A;ENSP00000363752:T727A;ENSP00000303758:T727A;ENSP00000313705:T727A	ENSP00000303758:T727A	T	-	1	0	LUZP1	23291163	0.087000	0.21565	0.421000	0.26609	0.137000	0.21094	0.043000	0.13971	0.605000	0.29947	-0.330000	0.08379	ACC	T|0.997;C|0.003	0.003	strong		0.493	LUZP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008900.3	NM_033631	
BTBD1	53339	hgsc.bcm.edu	37	15	83725291	83725291	+	Silent	SNP	T	T	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:83725291T>A	ENST00000261721.4	-	2	610	c.408A>T	c.(406-408)ctA>ctT	p.L136L	RP11-382A20.6_ENST00000568441.1_RNA|BTBD1_ENST00000379403.2_Silent_p.L136L|RP11-382A20.5_ENST00000566841.1_RNA|RP11-382A20.7_ENST00000570202.1_RNA	NM_001011885.1|NM_025238.3	NP_001011885.1|NP_079514.1	Q9H0C5	BTBD1_HUMAN	BTB (POZ) domain containing 1	136	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				protein ubiquitination (GO:0016567)|regulation of protein binding (GO:0043393)	cytoplasmic mRNA processing body (GO:0000932)|protein complex (GO:0043234)				central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(1)	10				all cancers(203;0.000186)		CATCTGAATATAGAAATCTGG	0.358																																					p.L136L		Atlas-SNP	.											BTBD1,NS,carcinoma,-2,1	BTBD1	32	1	0			c.A408T						PASS	.						87.0	83.0	84.0					15																	83725291		2203	4300	6503	SO:0001819	synonymous_variant	53339	exon2			TGAATATAGAAAT	AF355402	CCDS10322.1, CCDS32313.1	15q24	2013-01-08			ENSG00000064726	ENSG00000064726		"""BTB/POZ domain containing"""	1120	protein-coding gene	gene with protein product		608530					Standard	XM_006720573		Approved		uc002bjn.3	Q9H0C5	OTTHUMG00000147364	ENST00000261721.4:c.408A>T	15.37:g.83725291T>A		69.0	0.0	0		87.0	35.0	0.402299	NM_025238	A6NMI8|Q9BX71|Q9NWN4	Silent	SNP	ENST00000261721.4	37	CCDS10322.1																																																																																			.	.	none		0.358	BTBD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304008.1		
UGT3A1	133688	hgsc.bcm.edu	37	5	35957462	35957462	+	Silent	SNP	G	G	A	rs10428673	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:35957462G>A	ENST00000274278.3	-	5	1260	c.903C>T	c.(901-903)ggC>ggT	p.G301G	UGT3A1_ENST00000513233.1_5'UTR|UGT3A1_ENST00000507113.1_Silent_p.G267G|UGT3A1_ENST00000503189.1_Silent_p.G301G	NM_152404.3	NP_689617.3	Q6NUS8	UD3A1_HUMAN	UDP glycosyltransferase 3 family, polypeptide A1	301						integral component of membrane (GO:0016021)|UDP-N-acetylglucosamine transferase complex (GO:0043541)	glucuronosyltransferase activity (GO:0015020)|UDP-glycosyltransferase activity (GO:0008194)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|skin(4)	46	all_lung(31;0.000197)		Epithelial(62;0.107)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			TCAACATGGAGCCAAAGGCCA	0.488													G|||	40	0.00798722	0.028	0.0043	5008	,	,		20323	0.0		0.0	False		,,,				2504	0.0				p.G301G		Atlas-SNP	.											.	UGT3A1	95	.	0			c.C903T						PASS	.	G		109,4297		1,107,2095	104.0	90.0	95.0		903	1.4	1.0	5	dbSNP_119	95	2,8598		0,2,4298	no	coding-synonymous	UGT3A1	NM_152404.3		1,109,6393	AA,AG,GG		0.0233,2.4739,0.8535		301/524	35957462	111,12895	2203	4300	6503	SO:0001819	synonymous_variant	133688	exon5			CATGGAGCCAAAG		CCDS3913.1, CCDS54841.1	5p13.2	2014-05-20			ENSG00000145626	ENSG00000145626		"""UDP glucuronosyltransferases"""	26625	protein-coding gene	gene with protein product							Standard	NM_152404		Approved	FLJ34658	uc003jjv.2	Q6NUS8	OTTHUMG00000131107	ENST00000274278.3:c.903C>T	5.37:g.35957462G>A		110.0	0.0	0		135.0	69.0	0.511111	NM_152404	G5E961|Q8IYS9|Q8NAW4|Q96DM6	Silent	SNP	ENST00000274278.3	37	CCDS3913.1																																																																																			G|0.991;A|0.009	0.009	strong		0.488	UGT3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253770.2	NM_152404	
LRIG1	26018	hgsc.bcm.edu	37	3	66433458	66433458	+	Silent	SNP	G	G	A	rs34042409	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:66433458G>A	ENST00000273261.3	-	15	2963	c.2439C>T	c.(2437-2439)tgC>tgT	p.C813C	SLC25A26_ENST00000536651.1_Intron|LRIG1_ENST00000496559.2_5'UTR|LRIG1_ENST00000383703.3_Silent_p.C790C	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	813					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)		GGTAGATGATGCACACCCAGA	0.577													G|||	261	0.0521166	0.1906	0.013	5008	,	,		19695	0.0		0.0	False		,,,				2504	0.0				p.C813C		Atlas-SNP	.											.	LRIG1	138	.	0			c.C2439T						PASS	.	G		705,3701	294.7+/-283.3	56,593,1554	115.0	90.0	99.0		2439	5.9	1.0	3	dbSNP_126	99	7,8593	5.7+/-21.5	0,7,4293	yes	coding-synonymous	LRIG1	NM_015541.2		56,600,5847	AA,AG,GG		0.0814,16.0009,5.4744		813/1094	66433458	712,12294	2203	4300	6503	SO:0001819	synonymous_variant	26018	exon15			GATGATGCACACC	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.2439C>T	3.37:g.66433458G>A		95.0	0.0	0		89.0	41.0	0.460674	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Silent	SNP	ENST00000273261.3	37	CCDS33783.1																																																																																			G|0.941;A|0.059	0.059	strong		0.577	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541	
ZFP14	57677	hgsc.bcm.edu	37	19	36832427	36832427	+	Missense_Mutation	SNP	A	A	T	rs115297808	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36832427A>T	ENST00000270001.7	-	5	416	c.301T>A	c.(301-303)Ttt>Att	p.F101I		NM_020917.2	NP_065968.1	Q9HCL3	ZFP14_HUMAN	ZFP14 zinc finger protein	101					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	26	Esophageal squamous(110;0.162)					TCCCACTGAAATGAATATATT	0.343													A|||	69	0.013778	0.0507	0.0029	5008	,	,		17204	0.0		0.0	False		,,,				2504	0.0				p.F101I		Atlas-SNP	.											.	ZFP14	68	.	0			c.T301A						PASS	.	A	ILE/PHE	147,4259	94.8+/-133.5	4,139,2060	52.0	54.0	53.0		301	2.0	0.5	19	dbSNP_132	53	2,8586	1.2+/-3.3	0,2,4292	yes	missense	ZFP14	NM_020917.2	21	4,141,6352	TT,TA,AA		0.0233,3.3364,1.1467	benign	101/534	36832427	149,12845	2203	4294	6497	SO:0001583	missense	57677	exon5			ACTGAAATGAATA	AB046779	CCDS33002.1	19q13.13	2013-01-08	2012-11-27			ENSG00000142065		"""Zinc fingers, C2H2-type"", ""-"""	29312	protein-coding gene	gene with protein product			"""zinc finger protein 14 homolog (mouse)"""			10997877	Standard	NM_020917		Approved	KIAA1559, ZNF531	uc010eex.2	Q9HCL3		ENST00000270001.7:c.301T>A	19.37:g.36832427A>T	ENSP00000270001:p.Phe101Ile	136.0	0.0	0		118.0	61.0	0.516949	NM_020917	A7MD23	Missense_Mutation	SNP	ENST00000270001.7	37	CCDS33002.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	a	3.299	-0.143207	0.06669	0.033364	2.33E-4	ENSG00000142065	ENST00000270001;ENST00000392172	T	0.06528	3.29	4.2	2.05	0.26809	.	0.326738	0.22483	N	0.059470	T	0.00666	0.0022	L	0.38175	1.15	0.19775	N	0.999956	B;B	0.16603	0.018;0.005	B;B	0.12837	0.008;0.008	T	0.44907	-0.9297	10	0.21014	T	0.42	.	4.3827	0.11302	0.691:0.2011:0.1079:0.0	.	101;101	A8KAN8;Q9HCL3	.;ZFP14_HUMAN	I	101	ENSP00000270001:F101I	ENSP00000270001:F101I	F	-	1	0	ZFP14	41524267	0.005000	0.15991	0.453000	0.27007	0.613000	0.37349	1.042000	0.30303	0.240000	0.21263	0.523000	0.50628	TTT	A|0.990;T|0.010	0.010	strong		0.343	ZFP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452528.1	NM_020917	
TRPM6	140803	hgsc.bcm.edu	37	9	77418802	77418802	+	Splice_Site	SNP	G	G	A	rs115354606	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:77418802G>A	ENST00000360774.1	-	15	1876	c.1639C>T	c.(1639-1641)Cac>Tac	p.H547Y	TRPM6_ENST00000376871.3_Intron|TRPM6_ENST00000376864.4_Splice_Site_p.H547Y|TRPM6_ENST00000449912.2_Splice_Site_p.H542Y|TRPM6_ENST00000451710.3_Splice_Site_p.H547Y|TRPM6_ENST00000376872.3_Intron|TRPM6_ENST00000361255.3_Splice_Site_p.H542Y	NM_017662.4	NP_060132.3	Q9BX84	TRPM6_HUMAN	transient receptor potential cation channel, subfamily M, member 6	547					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|response to toxic substance (GO:0009636)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|liver(1)|lung(53)|ovary(1)|prostate(7)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	126						TGTCTCTGGTGCTGGGAAAGG	0.388													G|||	164	0.0327476	0.1127	0.0187	5008	,	,		17133	0.0		0.002	False		,,,				2504	0.0				p.H547Y		Atlas-SNP	.											.	TRPM6	377	.	0			c.C1639T						PASS	.	G	TYR/HIS,TYR/HIS,TYR/HIS	400,4006	201.1+/-224.2	18,364,1821	142.0	135.0	137.0		1624,1624,1639	2.7	0.7	9	dbSNP_132	137	9,8591	6.4+/-24.3	0,9,4291	yes	missense-near-splice,missense-near-splice,missense-near-splice	TRPM6	NM_001177310.1,NM_001177311.1,NM_017662.4	83,83,83	18,373,6112	AA,AG,GG		0.1047,9.0785,3.1447	benign,benign,benign	542/2018,542/2018,547/2023	77418802	409,12597	2203	4300	6503	SO:0001630	splice_region_variant	140803	exon15			TCTGGTGCTGGGA	AK026281	CCDS6647.1, CCDS55318.1, CCDS55319.1	9q21.13	2011-12-14	2003-12-02		ENSG00000119121	ENSG00000119121		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17995	protein-coding gene	gene with protein product		607009	"""hypomagnesemia, secondary hypocalcemia"""	HOMG, HSH		10021370, 12032570, 16382100	Standard	NM_017662		Approved	CHAK2, FLJ22628	uc004ajk.1	Q9BX84	OTTHUMG00000020027	ENST00000360774.1:c.1639-1C>T	9.37:g.77418802G>A		82.0	0.0	0		88.0	61.0	0.693182	NM_017662	Q6VPR8|Q6VPR9|Q6VPS0|Q6VPS1|Q6VPS2	Missense_Mutation	SNP	ENST00000360774.1	37	CCDS6647.1	67	0.030677655677655676	58	0.11788617886178862	8	0.022099447513812154	0	0.0	1	0.0013192612137203166	G	16.51	3.143177	0.57044	0.090785	0.001047	ENSG00000119121	ENST00000360774;ENST00000451710;ENST00000449912;ENST00000361255;ENST00000376864;ENST00000312449;ENST00000448641	T;T;T;T;T	0.73575	-0.76;-0.76;-0.76;-0.76;-0.76	5.51	2.69	0.31865	.	0.768746	0.12808	N	0.437439	T	0.03390	0.0098	M	0.67953	2.075	0.36472	P	0.132695	D;B	0.54397	0.966;0.402	P;B	0.49421	0.61;0.196	T	0.47799	-0.9089	9	0.62326	D	0.03	.	6.3637	0.21443	0.2288:0.1334:0.6379:0.0	.	547;542	Q9BX84;Q9BX84-3	TRPM6_HUMAN;.	Y	547;547;542;542;547;210;210	ENSP00000354006:H547Y;ENSP00000407341:H547Y;ENSP00000396672:H542Y;ENSP00000354962:H542Y;ENSP00000366060:H547Y	ENSP00000309693:H210Y	H	-	1	0	TRPM6	76608622	0.107000	0.21998	0.717000	0.30585	0.861000	0.49209	0.067000	0.14510	0.302000	0.22762	0.563000	0.77884	CAC	G|0.969;A|0.031	0.031	strong		0.388	TRPM6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052693.1	NM_017662	Missense_Mutation
RPAP3	79657	hgsc.bcm.edu	37	12	48075597	48075597	+	Silent	SNP	A	A	G	rs36123489	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:48075597A>G	ENST00000005386.3	-	10	1111	c.996T>C	c.(994-996)taT>taC	p.Y332Y	RPAP3_ENST00000432584.3_Silent_p.Y173Y|RPAP3_ENST00000380650.4_Silent_p.Y332Y	NM_024604.2	NP_078880.2	Q9H6T3	RPAP3_HUMAN	RNA polymerase II associated protein 3	332										endometrium(2)|large_intestine(4)|liver(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16	Lung SC(27;0.192)					CAGCTTCTTCATATCTATTGA	0.313													A|||	224	0.0447284	0.1566	0.0231	5008	,	,		18004	0.0		0.001	False		,,,				2504	0.0				p.Y332Y		Atlas-SNP	.											.	RPAP3	45	.	0			c.T996C						PASS	.	A	,,	647,3757	277.8+/-273.9	49,549,1604	61.0	59.0	59.0		996,519,996	1.9	1.0	12	dbSNP_126	59	12,8584	8.4+/-32.0	0,12,4286	no	coding-synonymous,coding-synonymous,coding-synonymous	RPAP3	NM_001146075.1,NM_001146076.1,NM_024604.2	,,	49,561,5890	GG,GA,AA		0.1396,14.6912,5.0692	,,	332/632,173/507,332/666	48075597	659,12341	2202	4298	6500	SO:0001819	synonymous_variant	79657	exon10			TTCTTCATATCTA	AK025561	CCDS8753.1, CCDS53782.1, CCDS53783.1	12q13.11	2013-01-10				ENSG00000005175		"""Tetratricopeptide (TTC) repeat domain containing"""	26151	protein-coding gene	gene with protein product		611477				17643375	Standard	NM_024604		Approved	FLJ21908, spag	uc001rpr.3	Q9H6T3	OTTHUMG00000169668	ENST00000005386.3:c.996T>C	12.37:g.48075597A>G		68.0	0.0	0		96.0	46.0	0.479167	NM_024604	B4DRW9|Q6PHR5	Silent	SNP	ENST00000005386.3	37	CCDS8753.1																																																																																			A|0.952;G|0.048	0.048	strong		0.313	RPAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405340.1	NM_024604	
MASP2	10747	hgsc.bcm.edu	37	1	11103408	11103408	+	Silent	SNP	G	G	A	rs7536030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11103408G>A	ENST00000400897.3	-	5	744	c.729C>T	c.(727-729)taC>taT	p.Y243Y		NM_006610.3	NP_006601.2	O00187	MASP2_HUMAN	mannan-binding lectin serine peptidase 2	243	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|complement component C4b binding (GO:0001855)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)	p.Y243Y(1)		biliary_tract(1)|endometrium(2)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	Ovarian(185;0.249)	Lung NSC(185;1.04e-05)|all_lung(284;1.31e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.071)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.12e-07)|COAD - Colon adenocarcinoma(227;7.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)|STAD - Stomach adenocarcinoma(313;0.192)		TGAGAAAGTCGTAGGGACACA	0.587													G|||	367	0.0732827	0.2648	0.0187	5008	,	,		19805	0.0		0.0	False		,,,				2504	0.0041				p.Y243Y	GBM(35;611 746 20780 22741 36496)	Atlas-SNP	.											MASP2,colon,carcinoma,0,1	MASP2	71	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C729T						PASS	.	G		1054,3346	365.4+/-317.4	125,804,1271	56.0	43.0	47.0		729	-1.1	1.0	1	dbSNP_116	47	21,8579	11.9+/-42.8	1,19,4280	no	coding-synonymous	MASP2	NM_006610.3		126,823,5551	AA,AG,GG		0.2442,23.9545,8.2692		243/687	11103408	1075,11925	2200	4300	6500	SO:0001819	synonymous_variant	10747	exon5			AAAGTCGTAGGGA	X98400	CCDS123.1, CCDS124.1	1p36.3-p36.2	2014-09-17	2005-08-17		ENSG00000009724	ENSG00000009724			6902	protein-coding gene	gene with protein product		605102	"""mannan-binding lectin serine protease 2"", ""mannan-binding lectin serine peptidase 1 pseudogene 1"", ""mannan-binding lectin serine protease 1 pseudogene 1"""	MASP1P1		9087411, 9777418	Standard	NM_006610		Approved		uc001aru.3	O00187	OTTHUMG00000002121	ENST00000400897.3:c.729C>T	1.37:g.11103408G>A		52.0	0.0	0		47.0	21.0	0.446809	NM_006610	A8K458|A8MWJ2|O75754|Q5TEQ5|Q5TER0|Q96QG4|Q9BZH0|Q9H498|Q9H499|Q9UBP3|Q9UC48|Q9ULC7|Q9UMV3|Q9Y270	Silent	SNP	ENST00000400897.3	37	CCDS123.1																																																																																			G|0.904;A|0.096	0.096	strong		0.587	MASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006072.1	NM_006610	
GPATCH4	54865	hgsc.bcm.edu	37	1	156567847	156567847	+	Missense_Mutation	SNP	G	G	C	rs141345590	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156567847G>C	ENST00000438976.2	-	5	358	c.328C>G	c.(328-330)Ctg>Gtg	p.L110V	GPATCH4_ENST00000368232.4_Missense_Mutation_p.L105V|GPATCH4_ENST00000334588.7_Missense_Mutation_p.L59V|GPATCH4_ENST00000497287.1_5'UTR			Q5T3I0	GPTC4_HUMAN	G patch domain containing 4	105							poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(3)|stomach(1)	17	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TTCTGATACAGCAAGTTGGGC	0.463													G|||	68	0.0135783	0.0499	0.0029	5008	,	,		21358	0.0		0.0	False		,,,				2504	0.0				p.L110V		Atlas-SNP	.											.	GPATCH4	34	.	0			c.C328G						PASS	.	G	VAL/LEU,VAL/LEU	171,4235	115.0+/-153.0	4,163,2036	145.0	141.0	142.0		328,313	2.3	1.0	1	dbSNP_134	142	0,8600		0,0,4300	yes	missense,missense	GPATCH4	NM_015590.3,NM_182679.2	32,32	4,163,6336	CC,CG,GG		0.0,3.8811,1.3148	probably-damaging,probably-damaging	110/376,105/371	156567847	171,12835	2203	4300	6503	SO:0001583	missense	54865	exon5			GATACAGCAAGTT	BC056904	CCDS1146.1, CCDS44245.1	1q22	2013-01-28		2006-12-13	ENSG00000160818	ENSG00000160818		"""G patch domain containing"""	25982	protein-coding gene	gene with protein product				GPATC4		12477932	Standard	NM_015590		Approved	FLJ20249, DKFZP434F1735	uc001fpl.3	Q5T3I0	OTTHUMG00000033203	ENST00000438976.2:c.328C>G	1.37:g.156567847G>C	ENSP00000396441:p.Leu110Val	175.0	0.0	0		182.0	91.0	0.5	NM_015590	Q5T3I1|Q6ZUE7|Q8IWG8|Q9NXH4	Missense_Mutation	SNP	ENST00000438976.2	37	CCDS44245.1	15	0.006868131868131868	14	0.028455284552845527	1	0.0027624309392265192	0	0.0	0	0.0	G	16.61	3.172437	0.57584	0.038811	0.0	ENSG00000160818	ENST00000368232;ENST00000368229;ENST00000438976;ENST00000334588	.	.	.	5.47	2.33	0.28932	.	0.073719	0.53938	D	0.000052	T	0.36496	0.0969	L	0.57130	1.785	0.41650	D	0.989123	D;D	0.58268	0.982;0.982	P;P	0.51266	0.664;0.664	T	0.31696	-0.9934	9	0.42905	T	0.14	-1.1016	3.0104	0.06043	0.2718:0.0:0.5275:0.2007	.	110;105	E9PAV9;Q5T3I0	.;GPTC4_HUMAN	V	105;105;110;59	.	ENSP00000334793:L59V	L	-	1	2	GPATCH4	154834471	1.000000	0.71417	0.994000	0.49952	0.998000	0.95712	1.145000	0.31577	0.837000	0.34925	0.655000	0.94253	CTG	G|0.988;C|0.012	0.012	strong		0.463	GPATCH4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386947.1	NM_017725	
MGA	23269	hgsc.bcm.edu	37	15	42019421	42019421	+	Silent	SNP	A	A	G	rs61736067	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42019421A>G	ENST00000570161.1	+	9	3474	c.3474A>G	c.(3472-3474)ccA>ccG	p.P1158P	MGA_ENST00000545763.1_Silent_p.P1158P|MGA_ENST00000219905.7_Silent_p.P1158P|MGA_ENST00000389936.4_Silent_p.P1158P|MGA_ENST00000566586.1_Silent_p.P1158P			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	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)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GACATTACCCATTATGGGTAA	0.408													A|||	80	0.0159744	0.0582	0.0029	5008	,	,		18915	0.0		0.001	False		,,,				2504	0.0				p.P1158P		Atlas-SNP	.											.	MGA	264	.	0			c.A3474G						PASS	.	A	,	166,3584		7,152,1716	86.0	79.0	81.0		3474,3474	0.6	1.0	15	dbSNP_129	81	3,8199		0,3,4098	no	coding-synonymous,coding-synonymous	MGA	NM_001080541.2,NM_001164273.1	,	7,155,5814	GG,GA,AA		0.0366,4.4267,1.414	,	1158/2857,1158/3066	42019421	169,11783	1875	4101	5976	SO:0001819	synonymous_variant	23269	exon10			TTACCCATTATGG	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"""MAX dimerization proteins"", ""T-boxes"""	14010	protein-coding gene	gene with protein product			"""MAX gene associated"""				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.3474A>G	15.37:g.42019421A>G		97.0	0.0	0		87.0	41.0	0.471264	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Silent	SNP	ENST00000570161.1	37	CCDS55959.1																																																																																			A|0.988;G|0.012	0.012	strong		0.408	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1	
ALDH1L1	10840	hgsc.bcm.edu	37	3	125855665	125855665	+	Missense_Mutation	SNP	T	T	G	rs9282691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:125855665T>G	ENST00000393434.2	-	11	1635	c.1286A>C	c.(1285-1287)gAg>gCg	p.E429A	ALDH1L1_ENST00000452905.2_Missense_Mutation_p.E328A|ALDH1L1_ENST00000472186.1_Missense_Mutation_p.E429A|ALDH1L1_ENST00000273450.3_Missense_Mutation_p.E439A|ALDH1L1_ENST00000393431.2_Missense_Mutation_p.E429A	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	429	Aldehyde dehydrogenase.		E -> A (in dbSNP:rs9282691).		10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	catalytic activity (GO:0003824)|formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(5)|large_intestine(10)|lung(22)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	52				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)	ATCCACGAACTCCCCCCCAAT	0.587													T|||	348	0.0694888	0.2368	0.0331	5008	,	,		19282	0.0		0.0	False		,,,				2504	0.0123				p.E439A		Atlas-SNP	.											.	ALDH1L1	138	.	0			c.A1316C						PASS	.	T	ALA/GLU	884,3522	318.8+/-295.8	95,694,1414	99.0	89.0	92.0		1286	-6.2	0.0	3	dbSNP_126	92	5,8595	3.0+/-9.4	0,5,4295	yes	missense	ALDH1L1	NM_012190.2	107	95,699,5709	GG,GT,TT		0.0581,20.0635,6.8353	benign	429/903	125855665	889,12117	2203	4300	6503	SO:0001583	missense	10840	exon11			ACGAACTCCCCCC	AF052732	CCDS3034.1, CCDS58850.1, CCDS58851.1	3q21.2	2010-07-19		2005-01-27	ENSG00000144908	ENSG00000144908	1.5.1.6	"""Aldehyde dehydrogenases"""	3978	protein-coding gene	gene with protein product	"""cytosolic 10-formyltetrahydrofolate dehydrogenase"""	600249	"""formyltetrahydrofolate dehydrogenase"""	FTHFD			Standard	NM_012190		Approved	10-fTHF	uc031sbp.1	O75891	OTTHUMG00000125551	ENST00000393434.2:c.1286A>C	3.37:g.125855665T>G	ENSP00000377083:p.Glu429Ala	79.0	0.0	0		93.0	49.0	0.526882	NM_001270364	B4DG36|E9PBX3|Q68CS1	Missense_Mutation	SNP	ENST00000393434.2	37	CCDS3034.1	118	0.05402930402930403	104	0.21138211382113822	14	0.03867403314917127	0	0.0	0	0.0	T	4.666	0.123895	0.08931	0.200635	5.81E-4	ENSG00000144908	ENST00000273450;ENST00000472186;ENST00000452905;ENST00000393434;ENST00000393431	T;T;T;T;T	0.09445	2.98;2.98;2.98;2.98;3.08	3.67	-6.25	0.02039	Acyl carrier protein-like (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	2.485370	0.02081	N	0.052371	T	0.00012	0.0000	L	0.49126	1.545	0.80722	P	0.0	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.35724	-0.9777	9	0.51188	T	0.08	.	3.3174	0.07038	0.1797:0.0968:0.1379:0.5855	rs9282691;rs52830184;rs60301528;rs9282691	328;481;429	E9PBX3;Q59G10;O75891	.;.;AL1L1_HUMAN	A	439;429;328;429;429	ENSP00000273450:E439A;ENSP00000420293:E429A;ENSP00000395881:E328A;ENSP00000377083:E429A;ENSP00000377081:E429A	ENSP00000273450:E439A	E	-	2	0	ALDH1L1	127338355	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.150000	0.16263	-1.451000	0.01933	-0.402000	0.06365	GAG	T|0.935;G|0.065	0.065	strong		0.587	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190	
PTPRN2	5799	hgsc.bcm.edu	37	7	157959888	157959888	+	Silent	SNP	G	G	A	rs73745197	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:157959888G>A	ENST00000389418.4	-	6	654	c.645C>T	c.(643-645)gaC>gaT	p.D215D	PTPRN2_ENST00000409483.1_Silent_p.D177D|PTPRN2_ENST00000389416.4_Silent_p.D198D|PTPRN2_ENST00000404321.2_Silent_p.D238D|PTPRN2_ENST00000389413.3_Silent_p.D215D	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	215					negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		GCGGCAGGAGGTCCTCGCGGA	0.652													G|||	100	0.0199681	0.0688	0.0086	5008	,	,		15889	0.0		0.003	False		,,,				2504	0.0				p.D215D		Atlas-SNP	.											.	PTPRN2	243	.	0			c.C645T						PASS	.		,,	303,4101	159.2+/-191.8	12,279,1911	42.0	42.0	42.0		645,594,645	2.3	0.0	7	dbSNP_130	42	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	,,	12,279,6211	AA,AG,GG		0.0,6.8801,2.3301	,,	215/1016,198/999,215/987	157959888	303,12701	2202	4300	6502	SO:0001819	synonymous_variant	5799	exon6			CAGGAGGTCCTCG	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.645C>T	7.37:g.157959888G>A		80.0	0.0	0		70.0	40.0	0.571429	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Silent	SNP	ENST00000389418.4	37	CCDS5947.1																																																																																			G|0.973;A|0.027	0.027	strong		0.652	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
PNMT	5409	hgsc.bcm.edu	37	17	37826249	37826249	+	Silent	SNP	A	A	G	rs5638	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:37826249A>G	ENST00000269582.2	+	3	774	c.456A>G	c.(454-456)aaA>aaG	p.K152K	PNMT_ENST00000581428.1_3'UTR|PNMT_ENST00000394246.1_Silent_p.K54K	NM_002686.3	NP_002677.1	P11086	PNMT_HUMAN	phenylethanolamine N-methyltransferase	152					catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|epinephrine biosynthetic process (GO:0042418)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	phenylethanolamine N-methyltransferase activity (GO:0004603)			NS(1)|breast(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8	all_cancers(6;6.59e-85)|all_epithelial(6;2.89e-103)|Breast(7;1.05e-86)|Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;3.87e-45)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			CCAGGGTGAAACGGGTCCTGC	0.657													A|||	317	0.0632987	0.1725	0.0317	5008	,	,		16981	0.004		0.0129	False		,,,				2504	0.0511				p.K152K		Atlas-SNP	.											.	PNMT	17	.	0			c.A456G						PASS	.	A		640,3766	252.4+/-258.8	45,550,1608	41.0	44.0	43.0		456	4.0	1.0	17	dbSNP_52	43	169,8429	74.5+/-137.1	1,167,4131	no	coding-synonymous	PNMT	NM_002686.3		46,717,5739	GG,GA,AA		1.9656,14.5256,6.2212		152/283	37826249	809,12195	2203	4299	6502	SO:0001819	synonymous_variant	5409	exon3			GGTGAAACGGGTC		CCDS11343.1	17q	2010-04-16			ENSG00000141744	ENSG00000141744	2.1.1.28		9160	protein-coding gene	gene with protein product		171190		PENT		3372503	Standard	NM_002686		Approved		uc002hsi.2	P11086	OTTHUMG00000133209	ENST00000269582.2:c.456A>G	17.37:g.37826249A>G		44.0	0.0	0		53.0	23.0	0.433962	NM_002686		Silent	SNP	ENST00000269582.2	37	CCDS11343.1																																																																																			A|0.933;G|0.067	0.067	strong		0.657	PNMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256923.2	NM_002686	
SLC7A4	6545	hgsc.bcm.edu	37	22	21385427	21385427	+	Missense_Mutation	SNP	G	G	C	rs80061703	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:21385427G>C	ENST00000382932.2	-	2	742	c.675C>G	c.(673-675)gaC>gaG	p.D225E	AC002472.11_ENST00000450652.1_RNA|SLC7A4_ENST00000403586.1_Missense_Mutation_p.D225E	NM_004173.2	NP_004164.2	O43246	CTR4_HUMAN	solute carrier family 7, member 4	225					basic amino acid transport (GO:0015802)|cellular amino acid metabolic process (GO:0006520)|transport (GO:0006810)	integral component of membrane (GO:0016021)	basic amino acid transmembrane transporter activity (GO:0015174)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(7)|ovary(1)|prostate(2)	18	all_cancers(11;2.85e-22)|Lung NSC(8;4.21e-14)|all_lung(8;6.08e-13)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0968)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)		L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	AGCCGCCTTCGTCAGCGCTCC	0.597													G|||	150	0.0299521	0.1104	0.0058	5008	,	,		20919	0.0		0.0	False		,,,				2504	0.0				p.D225E		Atlas-SNP	.											.	SLC7A4	50	.	0			c.C675G						PASS	.	G	GLU/ASP	446,3960	209.5+/-230.2	21,404,1778	55.0	56.0	56.0		675	0.6	0.2	22	dbSNP_131	56	5,8595	4.3+/-15.6	0,5,4295	yes	missense	SLC7A4	NM_004173.2	45	21,409,6073	CC,CG,GG		0.0581,10.1226,3.4676	benign	225/636	21385427	451,12555	2203	4300	6503	SO:0001583	missense	6545	exon2			GCCTTCGTCAGCG	AJ000730	CCDS33608.1	22q11.21	2013-07-19	2013-07-19		ENSG00000099960	ENSG00000099960		"""Solute carriers"""	11062	protein-coding gene	gene with protein product		603752	"""solute carrier family 7 (cationic amino acid transporter, y+ system), member 4"", ""solute carrier family 7 (orphan transporter), member 4"""			9598310, 11665818	Standard	NM_004173		Approved	HCAT3, CAT-4, VH	uc002zud.3	O43246	OTTHUMG00000150896	ENST00000382932.2:c.675C>G	22.37:g.21385427G>C	ENSP00000372390:p.Asp225Glu	39.0	0.0	0		54.0	34.0	0.62963	NM_004173	Q0P5U2|Q3KNQ6|Q4VC45|Q6IBY8|Q96H88	Missense_Mutation	SNP	ENST00000382932.2	37	CCDS33608.1	51	0.023351648351648352	47	0.09552845528455285	4	0.011049723756906077	0	0.0	0	0.0	G	0.007	-1.958563	0.00465	0.101226	5.81E-4	ENSG00000099960	ENST00000403586;ENST00000382932	D;D	0.89123	-2.47;-2.47	5.28	0.649	0.17806	Amino acid permease domain (1);	0.917457	0.09445	N	0.801263	T	0.03263	0.0095	N	0.00811	-1.165	0.20563	N	0.999887	B	0.02656	0.0	B	0.08055	0.003	T	0.40251	-0.9573	10	0.02654	T	1	.	2.2473	0.04034	0.1467:0.403:0.2873:0.1629	.	225	O43246	CTR4_HUMAN	E	225	ENSP00000384278:D225E;ENSP00000372390:D225E	ENSP00000372390:D225E	D	-	3	2	SLC7A4	19715427	0.085000	0.21516	0.212000	0.23672	0.016000	0.09150	0.308000	0.19314	0.022000	0.15160	-1.219000	0.01604	GAC	G|0.969;C|0.031	0.031	strong		0.597	SLC7A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320467.1	NM_004173	
HCN3	57657	hgsc.bcm.edu	37	1	155247408	155247408	+	Silent	SNP	G	G	T	rs184885598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:155247408G>T	ENST00000368358.3	+	1	35	c.27G>T	c.(25-27)gcG>gcT	p.A9A	CLK2_ENST00000536801.1_5'UTR	NM_020897.2	NP_065948.1	Q9P1Z3	HCN3_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 3	9					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)	cAMP binding (GO:0030552)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			GGCCGGCGGCGGGGGCCAGCG	0.726													G|||	109	0.0217652	0.0794	0.0058	5008	,	,		10168	0.0		0.0	False		,,,				2504	0.0				p.A9A		Atlas-SNP	.											.	HCN3	74	.	0			c.G27T						PASS	.			200,3496		3,194,1651	3.0	5.0	4.0		27	-1.1	0.0	1		4	0,7522		0,0,3761	no	coding-synonymous	HCN3	NM_020897.1		3,194,5412	TT,TG,GG		0.0,5.4113,1.7828		9/775	155247408	200,11018	1848	3761	5609	SO:0001819	synonymous_variant	57657	exon1			GGCGGCGGGGGCC	AB040968	CCDS1108.1	1q21.2	2011-07-05			ENSG00000143630	ENSG00000143630		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	19183	protein-coding gene	gene with protein product		609973				16382102	Standard	NM_020897		Approved	KIAA1535	uc001fjz.2	Q9P1Z3	OTTHUMG00000035872	ENST00000368358.3:c.27G>T	1.37:g.155247408G>T		2.0	0.0	0		13.0	8.0	0.615385	NM_020897	D3DV90|Q4VX12|Q8N6W6|Q9BWQ2	Silent	SNP	ENST00000368358.3	37	CCDS1108.1																																																																																			G|0.983;T|0.017	0.017	strong		0.726	HCN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087388.1	NM_020897	
LY75	4065	hgsc.bcm.edu	37	2	160690646	160690646	+	Silent	SNP	T	T	C	rs6722188	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160690646T>C	ENST00000263636.4	-	27	3777	c.3750A>G	c.(3748-3750)ccA>ccG	p.P1250P	LY75_ENST00000554112.1_Silent_p.P1250P|LY75-CD302_ENST00000505052.1_Silent_p.P1250P|LY75_ENST00000553424.1_Silent_p.P1250P|LY75-CD302_ENST00000504764.1_Silent_p.P1250P	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	1250					endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		AGTTCTGAAATGGTATCCACG	0.353													T|||	553	0.110423	0.4024	0.0288	5008	,	,		20151	0.0		0.001	False		,,,				2504	0.0				p.P1250P		Atlas-SNP	.											.	LY75	151	.	0			c.A3750G						PASS	.	T	,,	1532,2874	485.3+/-360.3	266,1000,937	145.0	134.0	138.0		3750,3750,3750	-4.4	1.0	2	dbSNP_116	138	18,8582	11.9+/-42.8	0,18,4282	no	coding-synonymous,coding-synonymous,coding-synonymous	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	,,	266,1018,5219	CC,CT,TT		0.2093,34.7708,11.9176	,,	1250/1874,1250/1818,1250/1723	160690646	1550,11456	2203	4300	6503	SO:0001819	synonymous_variant	4065	exon27			CTGAAATGGTATC	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.3750A>G	2.37:g.160690646T>C		182.0	0.0	0		150.0	86.0	0.573333	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Silent	SNP	ENST00000263636.4	37	CCDS2211.1																																																																																			T|0.880;C|0.120	0.120	strong		0.353	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
NCKAP1	10787	hgsc.bcm.edu	37	2	183817154	183817154	+	Silent	SNP	T	T	C	rs111993802	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:183817154T>C	ENST00000361354.4	-	23	2952	c.2580A>G	c.(2578-2580)tcA>tcG	p.S860S	NCKAP1_ENST00000360982.2_Silent_p.S866S	NM_013436.3	NP_038464.1	Q9Y2A7	NCKP1_HUMAN	NCK-associated protein 1	860					apical protein localization (GO:0045176)|apoptotic process (GO:0006915)|basal protein localization (GO:0045175)|central nervous system development (GO:0007417)|embryonic body morphogenesis (GO:0010172)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube development (GO:0035050)|endoderm development (GO:0007492)|establishment or maintenance of actin cytoskeleton polarity (GO:0030950)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|lamellipodium assembly (GO:0030032)|mesodermal cell migration (GO:0008078)|neural tube closure (GO:0001843)|notochord morphogenesis (GO:0048570)|paraxial mesoderm morphogenesis (GO:0048340)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|positive regulation of lamellipodium assembly (GO:0010592)|protein stabilization (GO:0050821)|Rac protein signal transduction (GO:0016601)|regulation of protein localization (GO:0032880)|somitogenesis (GO:0001756)|zygotic determination of anterior/posterior axis, embryo (GO:0007354)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|SCAR complex (GO:0031209)	protein complex binding (GO:0032403)			breast(3)|cervix(2)|endometrium(3)|kidney(4)|large_intestine(11)|lung(16)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)	45			OV - Ovarian serous cystadenocarcinoma(117;0.0942)|Epithelial(96;0.209)			CAACTTGTGATGAAATATGCC	0.313													t|||	50	0.00998403	0.0356	0.0043	5008	,	,		17373	0.0		0.0	False		,,,				2504	0.0				p.S866S		Atlas-SNP	.											.	NCKAP1	105	.	0			c.A2598G						PASS	.	C	,	133,4273	92.5+/-131.2	2,129,2072	68.0	73.0	71.0		2580,2598	3.2	1.0	2	dbSNP_132	71	6,8580	4.3+/-15.6	0,6,4287	no	coding-synonymous,coding-synonymous	NCKAP1	NM_013436.3,NM_205842.1	,	2,135,6359	CC,CT,TT		0.0699,3.0186,1.0699	,	860/1129,866/1135	183817154	139,12853	2203	4293	6496	SO:0001819	synonymous_variant	10787	exon24			TTGTGATGAAATA	AB014509	CCDS2287.1, CCDS2288.1	2q32	2009-08-14			ENSG00000061676	ENSG00000061676			7666	protein-coding gene	gene with protein product		604891				10673335, 12181570, 9344857	Standard	NM_013436		Approved	Nap1, HEM2, NAP125	uc002upb.4	Q9Y2A7	OTTHUMG00000132623	ENST00000361354.4:c.2580A>G	2.37:g.183817154T>C		193.0	0.0	0		188.0	97.0	0.515957	NM_205842	O60329|Q53QN5|Q53S94|Q53Y35	Silent	SNP	ENST00000361354.4	37	CCDS2287.1																																																																																			T|0.987;C|0.013	0.013	strong		0.313	NCKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255867.2	NM_205842	
ITGAD	3681	hgsc.bcm.edu	37	16	31429479	31429479	+	Silent	SNP	T	T	C	rs78517822	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31429479T>C	ENST00000389202.2	+	21	2632	c.2583T>C	c.(2581-2583)agT>agC	p.S861S		NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	861					activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						GCCGCTGCAGTGTCAACCACC	0.572													c|||	265	0.0529153	0.1906	0.0173	5008	,	,		17653	0.0		0.001	False		,,,				2504	0.0				p.S861S		Atlas-SNP	.											.	ITGAD	154	.	0			c.T2583C						PASS	.	C		752,3642	754.3+/-412.4	67,618,1512	140.0	132.0	135.0		2583	4.1	0.8	16	dbSNP_132	135	12,8588	818.8+/-406.8	0,12,4288	no	coding-synonymous	ITGAD	NM_005353.2		67,630,5800	CC,CT,TT		0.1395,17.1142,5.8796		861/1162	31429479	764,12230	2197	4300	6497	SO:0001819	synonymous_variant	3681	exon21			CTGCAGTGTCAAC	U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"""CD molecules"", ""Integrins"""	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.2583T>C	16.37:g.31429479T>C		225.0	0.0	0		205.0	96.0	0.468293	NM_005353	Q15575|Q15576	Silent	SNP	ENST00000389202.2	37	CCDS32438.1																																																																																			T|0.947;C|0.053	0.053	strong		0.572	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353	
OR2G2	81470	hgsc.bcm.edu	37	1	247751936	247751936	+	Missense_Mutation	SNP	T	T	G	rs146039934	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:247751936T>G	ENST00000320065.1	+	1	275	c.275T>G	c.(274-276)aTg>aGg	p.M92R	RP11-978I15.10_ENST00000446347.1_RNA|RP11-978I15.10_ENST00000435333.1_RNA	NM_001001915.1	NP_001001915.1	Q8NGZ5	OR2G2_HUMAN	olfactory receptor, family 2, subfamily G, member 2	92						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(4)|large_intestine(3)|lung(30)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	all_cancers(71;3.24e-05)|all_epithelial(71;1.3e-05)|Breast(184;0.0149)|Ovarian(71;0.0377)|all_lung(81;0.0662)|Lung NSC(105;0.0724)		OV - Ovarian serous cystadenocarcinoma(106;0.017)			TGGGAACCCATGAAAACTATC	0.527													t|||	30	0.00599042	0.0219	0.0014	5008	,	,		21752	0.0		0.0	False		,,,				2504	0.0				p.M92R		Atlas-SNP	.											.	OR2G2	88	.	0			c.T275G						PASS	.	C	ARG/MET	98,4308	79.9+/-118.3	1,96,2106	185.0	152.0	163.0		275	-6.5	0.0	1	dbSNP_134	163	0,8600		0,0,4300	yes	missense	OR2G2	NM_001001915.1	91	1,96,6406	GG,GT,TT		0.0,2.2242,0.7535	benign	92/318	247751936	98,12908	2203	4300	6503	SO:0001583	missense	81470	exon1			AACCCATGAAAAC	BK004472	CCDS31092.1	1q44	2012-08-09	2008-05-23		ENSG00000177489	ENSG00000177489		"""GPCR / Class A : Olfactory receptors"""	15007	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily G, member 2"", ""olfactory receptor, family 2, subfamily G, member 2 pseudogene"""				Standard	NM_001001915		Approved		uc010pyy.2	Q8NGZ5	OTTHUMG00000040575	ENST00000320065.1:c.275T>G	1.37:g.247751936T>G	ENSP00000326349:p.Met92Arg	354.0	0.0	0		347.0	176.0	0.507205	NM_001001915	Q5JQT2|Q6IEZ0	Missense_Mutation	SNP	ENST00000320065.1	37	CCDS31092.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	t	2.892	-0.229477	0.06022	0.022242	0.0	ENSG00000177489	ENST00000320065	T	0.01347	4.99	4.29	-6.53	0.01866	GPCR, rhodopsin-like superfamily (1);	2.209360	0.02699	U	0.111542	T	0.00271	0.0008	N	0.00408	-1.53	0.09310	N	1	B	0.16396	0.017	B	0.22753	0.041	T	0.49934	-0.8886	10	0.30078	T	0.28	.	1.2983	0.02074	0.4808:0.1651:0.1223:0.2318	.	92	Q8NGZ5	OR2G2_HUMAN	R	92	ENSP00000326349:M92R	ENSP00000326349:M92R	M	+	2	0	OR2G2	245818559	0.000000	0.05858	0.000000	0.03702	0.145000	0.21501	-0.280000	0.08468	-0.902000	0.03886	-0.332000	0.08345	ATG	T|0.994;G|0.006	0.006	strong		0.527	OR2G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097623.1		
GPR113	165082	hgsc.bcm.edu	37	2	26540951	26540951	+	Silent	SNP	G	G	A	rs116141676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:26540951G>A	ENST00000311519.1	-	2	218	c.219C>T	c.(217-219)agC>agT	p.S73S	GPR113_ENST00000421160.2_Intron|GPR113_ENST00000333478.6_Intron|GPR113_ENST00000459892.1_Intron|GPR113_ENST00000541401.1_Intron	NM_001145168.1	NP_001138640.1	Q8IZF5	GP113_HUMAN	G protein-coupled receptor 113	73					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)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(4)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ATCGGCCAAAGCTAGAAGATA	0.582													G|||	83	0.0165735	0.0605	0.0043	5008	,	,		19300	0.0		0.0	False		,,,				2504	0.0				p.S73S		Atlas-SNP	.											.	GPR113	134	.	0			c.C219T						PASS	.	G	,,	66,1318		3,60,629	58.0	64.0	62.0		219,,	0.0	0.0	2	dbSNP_132	62	0,3182		0,0,1591	no	coding-synonymous,intron,intron	GPR113	NM_001145168.1,NM_001145169.1,NM_153835.3	,,	3,60,2220	AA,AG,GG		0.0,4.7688,1.4455	,,	73/1080,,	26540951	66,4500	692	1591	2283	SO:0001819	synonymous_variant	165082	exon2			GCCAAAGCTAGAA	AB083619	CCDS33159.2, CCDS46238.1, CCDS46239.1	2p24.1	2014-08-08			ENSG00000173567	ENSG00000173567		"""-"", ""GPCR / Class B : Orphans"""	18989	protein-coding gene	gene with protein product						12435584	Standard	NM_153835		Approved	hGPCR37, PGR23	uc002rhe.4	Q8IZF5	OTTHUMG00000150225	ENST00000311519.1:c.219C>T	2.37:g.26540951G>A		125.0	0.0	0		145.0	59.0	0.406897	NM_001145168	B4DF15|E9PEV1|Q53TA5|Q6UXT7|Q6UXX3|Q86SL7|Q8IXD8|Q8TDT3	Silent	SNP	ENST00000311519.1	37	CCDS46239.1																																																																																			G|0.986;A|0.014	0.014	strong		0.582	GPR113-004	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316892.1	NM_153835	
ANKRD27	84079	hgsc.bcm.edu	37	19	33131227	33131227	+	Silent	SNP	C	C	T	rs10410241	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33131227C>T	ENST00000306065.4	-	11	1127	c.969G>A	c.(967-969)acG>acA	p.T323T	ANKRD27_ENST00000587352.1_Silent_p.T323T	NM_032139.2	NP_115515.2	Q96NW4	ANR27_HUMAN	ankyrin repeat domain 27 (VPS9 domain)	323	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				early endosome to late endosome transport (GO:0045022)|positive regulation of GTPase activity (GO:0043547)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|lysosome (GO:0005764)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			breast(3)|endometrium(7)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	42	Esophageal squamous(110;0.137)					TAGGGATCTCCGTTTTCACAA	0.458													C|||	375	0.0748802	0.2738	0.0173	5008	,	,		20964	0.0		0.001	False		,,,				2504	0.0				p.T323T		Atlas-SNP	.											ANKRD27,colon,carcinoma,-1,1	ANKRD27	86	1	0			c.G969A						PASS	.	C		963,3443	364.9+/-317.2	123,717,1363	114.0	106.0	109.0		969	1.7	1.0	19	dbSNP_119	109	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	ANKRD27	NM_032139.2		123,720,5660	TT,TC,CC		0.0349,21.8566,7.4273		323/1051	33131227	966,12040	2203	4300	6503	SO:0001819	synonymous_variant	84079	exon11			GATCTCCGTTTTC	AK054561	CCDS32986.1	19q13.12	2013-01-10				ENSG00000105186		"""Ankyrin repeat domain containing"""	25310	protein-coding gene	gene with protein product	"""Vps9 domain and ankyrin-repeat-containing protein"""					11230166, 16525121	Standard	NM_032139		Approved	FLJ00040, DKFZp434L0718, VARP	uc002ntn.1	Q96NW4		ENST00000306065.4:c.969G>A	19.37:g.33131227C>T		224.0	0.0	0		209.0	91.0	0.435407	NM_032139	Q71MF5|Q86UC3|Q8ND80|Q9H0I4	Silent	SNP	ENST00000306065.4	37	CCDS32986.1																																																																																			C|0.924;T|0.076	0.076	strong		0.458	ANKRD27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450329.1	NM_032139	
UPP2	151531	hgsc.bcm.edu	37	2	158971664	158971664	+	Missense_Mutation	SNP	A	A	C	rs7561584	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:158971664A>C	ENST00000005756.4	+	3	426	c.232A>C	c.(232-234)Atg>Ctg	p.M78L	UPP2_ENST00000460456.1_Intron|UPP2_ENST00000605860.1_Missense_Mutation_p.M135L|UPP2_ENST00000409859.4_Missense_Mutation_p.M135L	NM_173355.3	NP_775491.1	O95045	UPP2_HUMAN	uridine phosphorylase 2	78			M -> L (in dbSNP:rs7561584).		nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|nucleotide catabolic process (GO:0009166)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)|uridine metabolic process (GO:0046108)	cytosol (GO:0005829)|type III intermediate filament (GO:0045098)	uridine phosphorylase activity (GO:0004850)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31					Fluorouracil(DB00544)	TGCACTGTTTATGCACAAGGA	0.458													A|||	24	0.00479233	0.0166	0.0029	5008	,	,		14199	0.0		0.0	False		,,,				2504	0.0				p.M135L		Atlas-SNP	.											.	UPP2	60	.	0			c.A403C						PASS	.	A	LEU/MET,LEU/MET	83,4323	70.9+/-108.8	2,79,2122	104.0	104.0	104.0		232,403	4.5	0.9	2	dbSNP_116	104	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	UPP2	NM_173355.3,NM_001135098.1	15,15	2,82,6419	CC,CA,AA		0.0349,1.8838,0.6612	benign,benign	78/318,135/375	158971664	86,12920	2203	4300	6503	SO:0001583	missense	151531	exon5			CTGTTTATGCACA	AY225131	CCDS2207.1, CCDS46435.1	2q24.2	2008-02-05			ENSG00000007001	ENSG00000007001			23061	protein-coding gene	gene with protein product						12849978	Standard	NM_173355		Approved	UPASE2, UP2, UDRPASE2	uc002tzo.3	O95045	OTTHUMG00000131969	ENST00000005756.4:c.232A>C	2.37:g.158971664A>C	ENSP00000005756:p.Met78Leu	118.0	0.0	0		88.0	35.0	0.397727	NM_001135098	B3KV87	Missense_Mutation	SNP	ENST00000005756.4	37	CCDS2207.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	A	6.495	0.459468	0.12342	0.018838	3.49E-4	ENSG00000007001	ENST00000409859;ENST00000005756	T;T	0.35421	1.31;1.31	5.7	4.53	0.55603	Nucleoside phosphorylase domain (1);	0.153191	0.64402	D	0.000007	T	0.10294	0.0252	N	0.12961	0.28	0.46317	D	0.998983	B	0.06786	0.001	B	0.08055	0.003	T	0.04128	-1.0975	10	0.11794	T	0.64	.	11.9742	0.53081	0.8546:0.1454:0.0:0.0	rs7561584;rs7561584	78	O95045	UPP2_HUMAN	L	135;78	ENSP00000387230:M135L;ENSP00000005756:M78L	ENSP00000005756:M78L	M	+	1	0	UPP2	158679910	1.000000	0.71417	0.940000	0.37924	0.318000	0.28184	5.969000	0.70422	0.974000	0.38366	0.533000	0.62120	ATG	A|0.994;C|0.006	0.006	strong		0.458	UPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254929.2	NM_173355	
BPIFB2	80341	hgsc.bcm.edu	37	20	31598909	31598909	+	Silent	SNP	G	G	A	rs61734339	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31598909G>A	ENST00000170150.3	+	3	384	c.189G>A	c.(187-189)gcG>gcA	p.A63A		NM_025227.1	NP_079503.1	Q8N4F0	BPIB2_HUMAN	BPI fold containing family B, member 2	63			A -> V (in dbSNP:rs34128772).			extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										GTGGAGAGGCGCTTCAGCCCA	0.622													G|||	26	0.00519169	0.0159	0.0014	5008	,	,		18832	0.0		0.004	False		,,,				2504	0.0				p.A63A		Atlas-SNP	.											.	.	.	.	0			c.G189A						PASS	.	G		72,4334	65.3+/-102.7	1,70,2132	89.0	74.0	79.0		189	2.5	0.0	20	dbSNP_129	79	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	BPIFB2	NM_025227.1		1,75,6427	AA,AG,GG		0.0581,1.6341,0.592		63/459	31598909	77,12929	2203	4300	6503	SO:0001819	synonymous_variant	80341	exon3			AGAGGCGCTTCAG	AF465765	CCDS13210.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000078898	ENSG00000078898		"""BPI fold containing"""	16177	protein-coding gene	gene with protein product		614108	"""bactericidal/permeability-increasing protein-like 1"""	C20orf184, BPIL1		12185532, 21787333	Standard	NM_025227		Approved	dJ726C3.2, LPLUNC2	uc002wyj.4	Q8N4F0	OTTHUMG00000032232	ENST00000170150.3:c.189G>A	20.37:g.31598909G>A		116.0	0.0	0		93.0	42.0	0.451613	NM_025227	Q6UWN3|Q6ZME0|Q8NFQ7	Silent	SNP	ENST00000170150.3	37	CCDS13210.1																																																																																			G|0.992;A|0.008	0.008	strong		0.622	BPIFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078652.2	NM_025227	
PVRL1	5818	hgsc.bcm.edu	37	11	119509485	119509485	+	Missense_Mutation	SNP	G	G	A	rs73571271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:119509485G>A	ENST00000341398.2	-	7	1182	c.1183C>T	c.(1183-1185)Cct>Tct	p.P395S	RP11-196E1.3_ENST00000601999.1_RNA|RP11-196E1.3_ENST00000532153.1_RNA	NM_203285.1	NP_976030.1	Q15223	PVRL1_HUMAN	poliovirus receptor-related 1 (herpesvirus entry mediator C)	0					adherens junction organization (GO:0034332)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|desmosome organization (GO:0002934)|enamel mineralization (GO:0070166)|heterophilic cell-cell adhesion (GO:0007157)|homophilic cell adhesion (GO:0007156)|immune response (GO:0006955)|iron ion transport (GO:0006826)|lens morphogenesis in camera-type eye (GO:0002089)|regulation of synapse assembly (GO:0051963)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|viral entry into host cell (GO:0046718)	adherens junction (GO:0005912)|axon (GO:0030424)|cell-cell adherens junction (GO:0005913)|extracellular region (GO:0005576)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)|synapse (GO:0045202)	carbohydrate binding (GO:0030246)|cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|protein homodimerization activity (GO:0042803)|virion binding (GO:0046790)|virus receptor activity (GO:0001618)			breast(1)|endometrium(3)|kidney(2)|large_intestine(9)|liver(1)|lung(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Breast(348;0.037)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.29e-05)		CTGGGAGAAGGCTCCGGCTTC	0.617													G|||	94	0.01877	0.0643	0.013	5008	,	,		19246	0.0		0.0	False		,,,				2504	0.0				p.P395S		Atlas-SNP	.											.	PVRL1	133	.	0			c.C1183T						PASS	.	G	SER/PRO	274,4124	154.0+/-187.5	4,266,1929	48.0	46.0	46.0		1183	1.5	0.0	11	dbSNP_130	46	1,8589	1.2+/-3.3	0,1,4294	yes	missense	PVRL1	NM_203285.1	74	4,267,6223	AA,AG,GG		0.0116,6.2301,2.1173		395/459	119509485	275,12713	2199	4295	6494	SO:0001583	missense	5818	exon7			GAGAAGGCTCCGG	X76400	CCDS8425.1, CCDS8426.1, CCDS8427.1	11q23-q24	2013-01-29	2007-06-07		ENSG00000110400	ENSG00000110400		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9706	protein-coding gene	gene with protein product	"""nectin"""	600644		HVEC, ED4		7721102, 9616127	Standard	NM_203285		Approved	PRR, PRR1, PVRR1, SK-12, HIgR, CLPED1, CD111, OFC7	uc001pwv.3	Q15223	OTTHUMG00000166177	ENST00000341398.2:c.1183C>T	11.37:g.119509485G>A	ENSP00000344974:p.Pro395Ser	62.0	0.0	0		41.0	21.0	0.512195	NM_203285	O75465|Q2M3D3|Q9HBE6|Q9HBW2	Missense_Mutation	SNP	ENST00000341398.2	37	CCDS8425.1	41	0.018772893772893772	34	0.06910569105691057	7	0.019337016574585635	0	0.0	0	0.0	G	5.225	0.226965	0.09916	0.062301	1.16E-4	ENSG00000110400	ENST00000341398	T	0.77098	-1.07	3.39	1.49	0.22878	.	.	.	.	.	T	0.13072	0.0317	L	0.40543	1.245	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.14504	-1.0470	9	0.31617	T	0.26	.	5.6558	0.17642	0.257:0.0:0.743:0.0	.	395	Q15223-2	.	S	395	ENSP00000344974:P395S	ENSP00000344974:P395S	P	-	1	0	PVRL1	119014695	0.013000	0.17824	0.002000	0.10522	0.017000	0.09413	1.059000	0.30517	0.413000	0.25759	-0.448000	0.05591	CCT	G|0.978;A|0.022	0.022	strong		0.617	PVRL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388230.1		
FAM186B	84070	hgsc.bcm.edu	37	12	49994658	49994658	+	Missense_Mutation	SNP	C	C	G	rs74086906	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:49994658C>G	ENST00000257894.2	-	4	926	c.765G>C	c.(763-765)agG>agC	p.R255S	PRPF40B_ENST00000508736.1_3'UTR|FAM186B_ENST00000551047.1_Intron|FAM186B_ENST00000544141.1_Missense_Mutation_p.R165S	NM_032130.2	NP_115506.1	Q8IYM0	F186B_HUMAN	family with sequence similarity 186, member B	255						protein complex (GO:0043234)				breast(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						TCTCCAGGCTCCTGTTCTCCT	0.557													C|||	200	0.0399361	0.1445	0.0115	5008	,	,		20376	0.0		0.001	False		,,,				2504	0.0				p.R255S		Atlas-SNP	.											.	FAM186B	72	.	0			c.G765C						PASS	.	C	SER/ARG	471,3935	223.9+/-240.3	27,417,1759	118.0	107.0	111.0		765	-3.4	0.0	12	dbSNP_130	111	2,8598	1.2+/-3.3	0,2,4298	yes	missense	FAM186B	NM_032130.2	110	27,419,6057	GG,GC,CC		0.0233,10.69,3.6368	benign	255/894	49994658	473,12533	2203	4300	6503	SO:0001583	missense	84070	exon4			CAGGCTCCTGTTC	AL136748	CCDS8788.1	12q13.12	2008-09-17	2008-09-17	2008-09-17	ENSG00000135436	ENSG00000135436			25296	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 25"""	C12orf25		11230166	Standard	NM_032130		Approved	DKFZP434J0113	uc001ruo.3	Q8IYM0	OTTHUMG00000167427	ENST00000257894.2:c.765G>C	12.37:g.49994658C>G	ENSP00000257894:p.Arg255Ser	283.0	0.0	0		288.0	114.0	0.395833	NM_032130	B4DZ15|Q8TCP7|Q9H0L3	Missense_Mutation	SNP	ENST00000257894.2	37	CCDS8788.1	85	0.03891941391941392	77	0.1565040650406504	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	C	9.727	1.161124	0.21538	0.1069	2.33E-4	ENSG00000135436	ENST00000544141;ENST00000257894	T;T	0.13307	2.6;2.81	5.35	-3.38	0.04883	.	0.418099	0.20622	N	0.088744	T	0.00039	0.0001	L	0.29908	0.895	0.80722	P	0.0	B;B	0.28783	0.222;0.024	B;B	0.20955	0.032;0.015	T	0.37619	-0.9698	8	.	.	.	-11.8042	1.6749	0.02820	0.1249:0.2948:0.1626:0.4177	.	165;255	B4DZ15;Q8IYM0	.;F186B_HUMAN	S	165;255	ENSP00000438569:R165S;ENSP00000257894:R255S	.	R	-	3	2	FAM186B	48280925	0.000000	0.05858	0.019000	0.16419	0.986000	0.74619	-0.460000	0.06720	-0.364000	0.08088	-0.157000	0.13467	AGG	C|0.964;G|0.036	0.036	strong		0.557	FAM186B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394583.2	NM_032130	
ANKRD18B	441459	hgsc.bcm.edu	37	9	33572355	33572355	+	Silent	SNP	C	C	G	rs200701439		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:33572355C>G	ENST00000290943.6	+	16	3129	c.3033C>G	c.(3031-3033)ctC>ctG	p.L1011L		NM_001244752.1	NP_001231681.1	A2A2Z9	AN18B_HUMAN	ankyrin repeat domain 18B	1011										NS(1)|breast(1)|endometrium(2)|lung(1)|prostate(1)|stomach(1)	7						ACTTTCTTCTCTAGAATCCAC	0.328																																					p.L1010L		Atlas-SNP	.											.	ANKRD18B	46	.	0			c.C3030G						PASS	.																																			SO:0001819	synonymous_variant	441459	exon16			TCTTCTCTAGAAT			9p13.3	2013-01-10			ENSG00000230453	ENSG00000230453		"""Ankyrin repeat domain containing"""	23644	protein-coding gene	gene with protein product							Standard	NM_001244752		Approved	bA255A11.3	uc010mjw.2	A2A2Z9	OTTHUMG00000019776	ENST00000290943.6:c.3033C>G	9.37:g.33572355C>G		313.0	0.0	0		350.0	14.0	0.04	NM_001244752		Silent	SNP	ENST00000290943.6	37																																																																																				C|0.998;G|0.002	0.002	weak		0.328	ANKRD18B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000313729.2	XM_001718334	
C18orf32	497661	hgsc.bcm.edu	37	18	47008736	47008736	+	Silent	SNP	G	G	A	rs148432146	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:47008736G>A	ENST00000318240.3	-	3	421	c.210C>T	c.(208-210)atC>atT	p.I70I	C18orf32_ENST00000579820.1_Silent_p.I70I|RPL17-C18orf32_ENST00000332968.6_3'UTR|RPL17-C18orf32_ENST00000584895.1_3'UTR|RP11-110H1.4_ENST00000580150.1_RNA|C18orf32_ENST00000582392.1_Silent_p.I70I	NM_001035005.3	NP_001030177.1	Q8TCD1	CR032_HUMAN	chromosome 18 open reading frame 32	70					positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)		signal transducer activity (GO:0004871)			large_intestine(2)|lung(1)	3						TTTTATCACAGATTTCTGTTG	0.348													G|||	5	0.000998403	0.003	0.0014	5008	,	,		17984	0.0		0.0	False		,,,				2504	0.0				p.I70I		Atlas-SNP	.											.	C18orf32	8	.	0			c.C210T						PASS	.	G	,,,	21,4383	28.1+/-56.4	0,21,2181	112.0	118.0	116.0		210,210,,	2.8	0.8	18	dbSNP_134	116	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous,utr-3,utr-3	C18orf32,RPL17-C18ORF32	NM_001035005.3,NM_001199346.1,NM_001199355.1,NM_001199356.1	,,,	0,21,6479	AA,AG,GG		0.0,0.4768,0.1615	,,,	70/77,70/77,,	47008736	21,12979	2202	4298	6500	SO:0001819	synonymous_variant	497661	exon3			ATCACAGATTTCT	AK027111	CCDS32831.1	18q21.1	2012-10-24			ENSG00000177576	ENSG00000177576			31690	protein-coding gene	gene with protein product							Standard	NM_001035005		Approved	FLJ23458	uc002ldl.3	Q8TCD1	OTTHUMG00000179688	ENST00000318240.3:c.210C>T	18.37:g.47008736G>A		104.0	0.0	0		96.0	56.0	0.583333	NM_001199346		Silent	SNP	ENST00000318240.3	37	CCDS32831.1																																																																																			G|0.999;A|0.001	0.001	strong		0.348	C18orf32-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447656.1	NM_001035005	
CD8B	926	hgsc.bcm.edu	37	2	87073817	87073817	+	Missense_Mutation	SNP	G	G	C	rs1126874		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:87073817G>C	ENST00000390655.6	-	4	631	c.573C>G	c.(571-573)atC>atG	p.I191M	CD8B_ENST00000393761.2_Intron|CD8B_ENST00000331469.2_Missense_Mutation_p.I191M|CD8B_ENST00000393759.2_Missense_Mutation_p.I191M|CD8B_ENST00000349455.3_Intron|CD8B_ENST00000431506.2_Intron	NM_004931.4	NP_004922.1	P10966	CD8B_HUMAN	CD8b molecule	191					immune response (GO:0006955)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|viral process (GO:0016032)	early endosome membrane (GO:0031901)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	coreceptor activity (GO:0015026)|MHC class I protein binding (GO:0042288)	p.I191M(2)		NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	13						AGCACAGGTGGATGGCCACTC	0.552																																					p.I191M		Atlas-SNP	.											CD8B_ENST00000393759,NS,carcinoma,0,2	CD8B	37	2	2	Substitution - Missense(2)	kidney(2)	c.C573G						scavenged	.																																			SO:0001583	missense	926	exon4			CAGGTGGATGGCC		CCDS1994.1, CCDS1995.1, CCDS42708.1, CCDS1997.1, CCDS54376.1	2p12	2013-01-11	2006-03-28	2006-03-09	ENSG00000172116	ENSG00000172116		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1707	protein-coding gene	gene with protein product		186730	"""CD8 antigen, beta polypeptide 1 (p37)"""	CD8B1		1541829	Standard	NM_172213		Approved		uc002srw.3	P10966	OTTHUMG00000130264	ENST00000390655.6:c.573C>G	2.37:g.87073817G>C	ENSP00000375070:p.Ile191Met	402.0	0.0	0		413.0	29.0	0.0702179	NM_004931	P14860|P14861|Q15980|Q496E0|Q496E1|Q496E2|Q9UDB4|Q9UDB5|Q9UDB6|Q9UDB7|Q9UDB8|Q9UDB9|Q9UDC0|Q9UQ55	Missense_Mutation	SNP	ENST00000390655.6	37	CCDS1997.1	.	.	.	.	.	.	.	.	.	.	g	11.44	1.639958	0.29157	.	.	ENSG00000172116	ENST00000393759;ENST00000331469;ENST00000390655;ENST00000445248	.	.	.	4.91	0.92	0.19397	.	0.581228	0.17685	N	0.165462	T	0.30386	0.0763	.	.	.	0.09310	N	0.999999	B;B;B;B	0.33807	0.3;0.3;0.426;0.426	B;B;B;B	0.35278	0.098;0.098;0.199;0.199	T	0.17745	-1.0359	8	0.59425	D	0.04	-3.6541	5.5609	0.17144	0.1776:0.2773:0.545:0.0	.	191;191;191;191	Q53QL8;P10966;P10966-2;P10966-6	.;CD8B_HUMAN;.;.	M	191	.	ENSP00000331172:I191M	I	-	3	3	CD8B	86927328	0.916000	0.31088	0.002000	0.10522	0.678000	0.39670	0.548000	0.23314	0.063000	0.16370	0.655000	0.94253	ATC	.	.	weak		0.552	CD8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330402.1	NM_172099	
ATP10B	23120	hgsc.bcm.edu	37	5	160047491	160047491	+	Missense_Mutation	SNP	A	A	C	rs375262733		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:160047491A>C	ENST00000327245.5	-	15	3125	c.2279T>G	c.(2278-2280)cTc>cGc	p.L760R	CTC-348L5.1_ENST00000523598.1_RNA	NM_025153.2	NP_079429.2	O94823	AT10B_HUMAN	ATPase, class V, type 10B	760					phospholipid translocation (GO:0045332)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(37)|ovary(4)|pancreas(1)|prostate(5)|skin(3)|stomach(1)	75	Renal(175;0.00196)	Medulloblastoma(196;0.0377)|all_neural(177;0.121)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GGTGCAGAGGAGGCTGAAGGT	0.597																																					p.L760R		Atlas-SNP	.											.	ATP10B	201	.	0			c.T2279G						PASS	.	A	ARG/LEU	1,4181		0,1,2090	38.0	40.0	39.0		2279	5.4	0.9	5		39	0,8452		0,0,4226	no	missense	ATP10B	NM_025153.2	102	0,1,6316	CC,CA,AA		0.0,0.0239,0.0079	probably-damaging	760/1462	160047491	1,12633	2091	4226	6317	SO:0001583	missense	23120	exon15			CAGAGGAGGCTGA	AB018258	CCDS43394.1	5q34	2010-04-20	2007-09-19		ENSG00000118322	ENSG00000118322		"""ATPases / P-type"""	13543	protein-coding gene	gene with protein product			"""ATPase, Class V, type 10B"""			9872452, 11015572	Standard	NM_025153		Approved	ATPVB, KIAA0715, FLJ21477	uc003lym.1	O94823	OTTHUMG00000163551	ENST00000327245.5:c.2279T>G	5.37:g.160047491A>C	ENSP00000313600:p.Leu760Arg	199.0	0.0	0		241.0	100.0	0.414938	NM_025153	Q9H725	Missense_Mutation	SNP	ENST00000327245.5	37	CCDS43394.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.448539	0.84101	2.39E-4	0.0	ENSG00000118322	ENST00000327245;ENST00000520108	T;T	0.79033	-1.23;-1.23	5.36	5.36	0.76844	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.403835	0.25230	N	0.032170	T	0.82144	0.4973	L	0.49455	1.56	0.38198	D	0.940098	P;P	0.51933	0.949;0.949	P;P	0.57846	0.745;0.828	T	0.83105	-0.0126	9	.	.	.	.	14.5725	0.68220	1.0:0.0:0.0:0.0	.	368;760	Q2YDW8;O94823	.;AT10B_HUMAN	R	760;368	ENSP00000313600:L760R;ENSP00000431081:L368R	.	L	-	2	0	ATP10B	159980069	1.000000	0.71417	0.919000	0.36401	0.912000	0.54170	9.159000	0.94728	2.042000	0.60477	0.533000	0.62120	CTC	.	.	weak		0.597	ATP10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374127.1	NM_025153	
KRTAP13-4	284827	hgsc.bcm.edu	37	21	31802629	31802629	+	Silent	SNP	C	C	T	rs73356729	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31802629C>T	ENST00000334068.2	+	1	58	c.36C>T	c.(34-36)tcC>tcT	p.S12S		NM_181600.1	NP_853631.1	Q3LI77	KR134_HUMAN	keratin associated protein 13-4	12						intermediate filament (GO:0005882)				NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(9)|skin(1)	15						ACTTCTCCTCCCGCTCCTTTG	0.547													-|||	220	0.0439297	0.1581	0.0144	5008	,	,		18637	0.0		0.001	False		,,,				2504	0.0				p.S12S	NSCLC(196;2401 3038 18004 35753)	Atlas-SNP	.											.	KRTAP13-4	46	.	0			c.C36T						PASS	.	C		473,3933		25,423,1755	109.0	111.0	110.0		36	0.1	0.1	21	dbSNP_130	110	10,8590		0,10,4290	no	coding-synonymous	KRTAP13-4	NM_181600.1		25,433,6045	TT,TC,CC		0.1163,10.7354,3.7137		12/161	31802629	483,12523	2203	4300	6503	SO:0001819	synonymous_variant	284827	exon1			CTCCTCCCGCTCC	AP001708	CCDS13592.1	21q22.1	2006-03-13			ENSG00000186971	ENSG00000186971		"""Keratin associated proteins"""	18926	protein-coding gene	gene with protein product						12359730	Standard	NM_181600		Approved	KAP13.4	uc011acw.2	Q3LI77	OTTHUMG00000057770	ENST00000334068.2:c.36C>T	21.37:g.31802629C>T		208.0	0.0	0		242.0	104.0	0.429752	NM_181600	A2RRL3	Silent	SNP	ENST00000334068.2	37	CCDS13592.1																																																																																			C|0.963;T|0.037	0.037	strong		0.547	KRTAP13-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128222.1		
ZNF407	55628	hgsc.bcm.edu	37	18	72344202	72344202	+	Silent	SNP	T	T	C	rs374837339		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:72344202T>C	ENST00000299687.5	+	1	1227	c.1227T>C	c.(1225-1227)agT>agC	p.S409S	ZNF407_ENST00000309902.6_Silent_p.S409S|ZNF407_ENST00000582337.1_Silent_p.S409S|ZNF407_ENST00000577538.1_Silent_p.S409S	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	409					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		ACGGTAACAGTGTAACCTCGA	0.453																																					p.S409S		Atlas-SNP	.											.	ZNF407	231	.	0			c.T1227C						PASS	.	T	,,	1,3749		0,1,1874	57.0	59.0	58.0		1227,1227,1227	-3.8	0.0	18		58	0,8230		0,0,4115	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF407	NM_001146189.1,NM_001146190.1,NM_017757.2	,,	0,1,5989	CC,CT,TT		0.0,0.0267,0.0083	,,	409/1816,409/1661,409/2249	72344202	1,11979	1875	4115	5990	SO:0001819	synonymous_variant	55628	exon1			TAACAGTGTAACC	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.1227T>C	18.37:g.72344202T>C		112.0	0.0	0		119.0	66.0	0.554622	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Silent	SNP	ENST00000299687.5	37	CCDS45885.1																																																																																			.	.	weak		0.453	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	
IQCE	23288	hgsc.bcm.edu	37	7	2611908	2611908	+	Silent	SNP	G	G	C	rs147584030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:2611908G>C	ENST00000402050.2	+	5	526	c.342G>C	c.(340-342)ctG>ctC	p.L114L	IQCE_ENST00000438376.2_Silent_p.L98L|IQCE_ENST00000404984.1_Silent_p.L63L|IQCE_ENST00000325979.7_Silent_p.L49L	NM_001100390.1|NM_152558.3	NP_001093860.1|NP_689771.3	Q6IPM2	IQCE_HUMAN	IQ motif containing E	114						mitochondrion (GO:0005739)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.23e-13)		CTGACTGTCTGACAGACACCT	0.607													G|||	42	0.00838658	0.0303	0.0029	5008	,	,		18614	0.0		0.0	False		,,,				2504	0.0				p.L114L		Atlas-SNP	.											.	IQCE	66	.	0			c.G342C						PASS	.	G	,	116,3980		1,114,1933	51.0	55.0	54.0		294,342	3.3	0.0	7	dbSNP_134	54	4,8406		0,4,4201	no	coding-synonymous,coding-synonymous	IQCE	NM_001100390.1,NM_152558.3	,	1,118,6134	CC,CG,GG		0.0476,2.832,0.9595	,	98/680,114/696	2611908	120,12386	2048	4205	6253	SO:0001819	synonymous_variant	23288	exon5			CTGTCTGACAGAC	AL136792	CCDS43542.1, CCDS47527.1, CCDS47527.2, CCDS75559.1, CCDS75560.1	7p22.3	2006-04-12			ENSG00000106012	ENSG00000106012			29171	protein-coding gene	gene with protein product						10470851	Standard	XR_242067		Approved	KIAA1023	uc003smo.4	Q6IPM2	OTTHUMG00000152047	ENST00000402050.2:c.342G>C	7.37:g.2611908G>C		51.0	0.0	0		65.0	29.0	0.446154	NM_152558	Q4G0P7|Q6P7T4|Q9H0H7|Q9UPX7	Silent	SNP	ENST00000402050.2	37	CCDS43542.1																																																																																			G|0.994;C|0.006	0.006	strong		0.607	IQCE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325063.2	NM_152558	
FAT3	120114	hgsc.bcm.edu	37	11	92538422	92538422	+	Silent	SNP	C	C	T	rs59542280	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:92538422C>T	ENST00000298047.6	+	10	9017	c.9000C>T	c.(8998-9000)ctC>ctT	p.L3000L	FAT3_ENST00000525166.1_Silent_p.L2850L|FAT3_ENST00000409404.2_Silent_p.L3000L			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3000	Cadherin 27. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TTTACTTTCTCAATATCACTG	0.488										TCGA Ovarian(4;0.039)			C|||	78	0.0155751	0.0567	0.0043	5008	,	,		16467	0.0		0.0	False		,,,				2504	0.0				p.L3000L		Atlas-SNP	.											.	FAT3	1822	.	0			c.C9000T						PASS	.	C		199,3665		5,189,1738	82.0	84.0	83.0		9000	4.2	1.0	11	dbSNP_129	83	0,8304		0,0,4152	no	coding-synonymous	FAT3	NM_001008781.2		5,189,5890	TT,TC,CC		0.0,5.1501,1.6354		3000/4558	92538422	199,11969	1932	4152	6084	SO:0001819	synonymous_variant	120114	exon10			CTTTCTCAATATC	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.9000C>T	11.37:g.92538422C>T		150.0	0.0	0		140.0	65.0	0.464286	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				C|0.988;T|0.012	0.012	strong		0.488	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
ZSCAN2	54993	hgsc.bcm.edu	37	15	85164530	85164530	+	Silent	SNP	C	C	T	rs115131715	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:85164530C>T	ENST00000448803.2	+	3	1396	c.1104C>T	c.(1102-1104)ggC>ggT	p.G368G	ZSCAN2_ENST00000541040.1_Intron|ZSCAN2_ENST00000485222.2_Intron|ZSCAN2_ENST00000538076.1_Intron|ZSCAN2_ENST00000358472.3_Silent_p.G218G|ZSCAN2_ENST00000327179.6_Silent_p.G367G|ZSCAN2_ENST00000546148.1_Silent_p.G368G	NM_181877.3	NP_870992.2	Q7Z7L9	ZSCA2_HUMAN	zinc finger and SCAN domain containing 2	368					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|kidney(2)|large_intestine(7)|liver(2)|lung(4)|ovary(1)|pancreas(1)	19				UCEC - Uterine corpus endometrioid carcinoma (272;0.168)|all cancers(203;5.43e-22)		AAGAATGCGGCGAAAGCTTTA	0.502													C|||	49	0.00978435	0.0363	0.0014	5008	,	,		18077	0.0		0.0	False		,,,				2504	0.0				p.G368G		Atlas-SNP	.											.	ZSCAN2	43	.	0			c.C1104T						PASS	.	C		132,4274	96.2+/-134.9	3,126,2074	132.0	137.0	135.0		1104	-6.7	0.8	15	dbSNP_132	135	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	ZSCAN2	NM_181877.3		3,127,6372	TT,TC,CC		0.0116,2.9959,1.0228		368/615	85164530	133,12871	2203	4299	6502	SO:0001819	synonymous_variant	54993	exon3			ATGCGGCGAAAGC	BC041620	CCDS10329.2, CCDS32315.1, CCDS32316.1	15q25.2	2013-01-08	2004-11-01	2004-11-02	ENSG00000176371	ENSG00000176371		"""-"", ""Zinc fingers, C2H2-type"""	20994	protein-coding gene	gene with protein product			"""zinc finger protein 29"""	ZFP29		1937051	Standard	NM_017894		Approved	FLJ20595, ZNF854	uc002bkr.3	Q7Z7L9	OTTHUMG00000074027	ENST00000448803.2:c.1104C>T	15.37:g.85164530C>T		79.0	0.0	0		61.0	35.0	0.57377	NM_181877	A6NG83|B2RMQ9|Q6ZQY9|Q9NWU4	Silent	SNP	ENST00000448803.2	37	CCDS10329.2																																																																																			C|0.988;T|0.012	0.012	strong		0.502	ZSCAN2-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396956.1	NM_017894	
KIF7	374654	hgsc.bcm.edu	37	15	90192363	90192363	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90192363G>A	ENST00000394412.3	-	4	841	c.765C>T	c.(763-765)ggC>ggT	p.G255G		NM_198525.2	NP_940927.2	Q2M1P5	KIF7_HUMAN	kinesin family member 7	255	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|kinesin complex (GO:0005871)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	25	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.128)			CCCTCTCTGAGCCCGCCAGGT	0.711																																					p.G255G		Atlas-SNP	.											.	KIF7	130	.	0			c.C765T						PASS	.						9.0	13.0	12.0					15																	90192363		684	1585	2269	SO:0001819	synonymous_variant	374654	exon4			CTCTGAGCCCGCC	AY358384	CCDS32325.2	15q26.1	2011-06-02			ENSG00000166813	ENSG00000166813		"""Kinesins"""	30497	protein-coding gene	gene with protein product		611254				11416179, 15547730	Standard	NM_198525		Approved	JBTS12	uc002bof.2	Q2M1P5	OTTHUMG00000157177	ENST00000394412.3:c.765C>T	15.37:g.90192363G>A		48.0	0.0	0		57.0	32.0	0.561404	NM_198525	Q3SXY0|Q6UXE9|Q8IW72	Silent	SNP	ENST00000394412.3	37	CCDS32325.2																																																																																			.	.	none		0.711	KIF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347782.1	NM_198525	
FRMD7	90167	hgsc.bcm.edu	37	X	131212487	131212487	+	Missense_Mutation	SNP	G	G	C	rs61742429	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:131212487G>C	ENST00000298542.4	-	12	1733	c.1558C>G	c.(1558-1560)Cat>Gat	p.H520D	FRMD7_ENST00000464296.1_Missense_Mutation_p.H505D|FRMD7_ENST00000370879.1_Missense_Mutation_p.H400D	NM_194277.2	NP_919253.1	Q6ZUT3	FRMD7_HUMAN	FERM domain containing 7	520					regulation of neuron projection development (GO:0010975)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|growth cone (GO:0030426)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(12)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24	Acute lymphoblastic leukemia(192;0.000127)					ACATAGCTATGTGGACTTGTC	0.493													C|||	35	0.00927152	0.0257	0.0014	3775	,	,		13862	0.0		0.0	False		,,,				2504	0.0				p.H520D		Atlas-SNP	.											.	FRMD7	69	.	0			c.C1558G						PASS	.	C	ASP/HIS	75,3760		0,62,13,1570,558	164.0	160.0	162.0		1558	3.6	0.4	X	dbSNP_129	162	0,6728		0,0,0,2428,1872	yes	missense	FRMD7	NM_194277.2	81	0,62,13,3998,2430	CC,CG,C,GG,G		0.0,1.9557,0.71	benign	520/715	131212487	75,10488	2203	4300	6503	SO:0001583	missense	90167	exon12			AGCTATGTGGACT	AL161984	CCDS35397.1	Xq26.2	2014-09-17	2006-09-01	2006-09-01	ENSG00000165694	ENSG00000165694			8079	protein-coding gene	gene with protein product		300628	"""nystagmus 1, congenital"""	NYS, NYS1		2063919, 17013395	Standard	NM_194277		Approved	FLJ43346	uc004ewn.3	Q6ZUT3	OTTHUMG00000022421	ENST00000298542.4:c.1558C>G	X.37:g.131212487G>C	ENSP00000298542:p.His520Asp	204.0	0.0	0		215.0	84.0	0.390698	NM_194277	C0LLJ3|Q5JX99	Missense_Mutation	SNP	ENST00000298542.4	37	CCDS35397.1	3	0.0018083182640144665	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	0.001	-3.523968	0.00010	0.019557	0.0	ENSG00000165694	ENST00000370879;ENST00000298542;ENST00000464296	D;D;D	0.84800	-1.9;-1.55;-1.67	4.55	3.59	0.41128	.	0.259811	0.32041	N	0.006663	T	0.37461	0.1004	N	0.01168	-0.975	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.49244	-0.8960	10	0.02654	T	1	.	4.1382	0.10181	0.1501:0.4756:0.2878:0.0865	rs61742429	505;520	Q6ZUT3-2;Q6ZUT3	.;FRMD7_HUMAN	D	400;520;505	ENSP00000359916:H400D;ENSP00000298542:H520D;ENSP00000417996:H505D	ENSP00000298542:H520D	H	-	1	0	FRMD7	131040168	0.727000	0.28069	0.447000	0.26932	0.007000	0.05969	0.526000	0.22971	1.017000	0.39495	-0.170000	0.13304	CAT	G|0.982;C|0.018	0.018	strong		0.493	FRMD7-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355031.1	NM_194277	
SNED1	25992	hgsc.bcm.edu	37	2	242012729	242012729	+	Missense_Mutation	SNP	G	G	A	rs6721345	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242012729G>A	ENST00000310397.8	+	27	3866	c.3866G>A	c.(3865-3867)cGg>cAg	p.R1289Q	MTERFD2_ENST00000464344.2_5'UTR|SNED1_ENST00000401884.1_Missense_Mutation_p.R1289Q|SNED1_ENST00000405547.3_Intron|SNED1_ENST00000342631.6_Intron	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	1289			R -> Q (in dbSNP:rs6721345).		cell-matrix adhesion (GO:0007160)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(3)|prostate(3)|upper_aerodigestive_tract(1)	24		all_cancers(19;7.48e-31)|all_epithelial(40;1.35e-12)|Breast(86;0.000148)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;6.46e-32)|all cancers(36;6.23e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.1e-14)|Kidney(56;6.35e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.98e-08)|BRCA - Breast invasive adenocarcinoma(100;3.66e-06)|Lung(119;0.00072)|LUSC - Lung squamous cell carcinoma(224;0.00553)|Colorectal(34;0.0162)|COAD - Colon adenocarcinoma(134;0.109)		GCCCCCAAGCGGGTCAGCCTG	0.637													A|||	170	0.0339457	0.1218	0.013	5008	,	,		18018	0.0		0.0	False		,,,				2504	0.0				p.R1289Q		Atlas-SNP	.											.	SNED1	76	.	0			c.G3866A						PASS	.	A	GLN/ARG	389,3689		21,347,1671	23.0	30.0	27.0		3866	-1.4	0.0	2	dbSNP_116	27	1,8307		0,1,4153	yes	missense	SNED1	NM_001080437.1	43	21,348,5824	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	0.012,9.539,3.1487	benign	1289/1414	242012729	390,11996	2039	4154	6193	SO:0001583	missense	25992	exon27			CCAAGCGGGTCAG	AK074062	CCDS46562.1	2q37.3	2014-01-28			ENSG00000162804	ENSG00000162804		"""Fibronectin type III domain containing"""	24696	protein-coding gene	gene with protein product						12477932	Standard	NM_001080437		Approved	FLJ00133, SST3, Snep	uc002wah.1	Q8TER0	OTTHUMG00000151803	ENST00000310397.8:c.3866G>A	2.37:g.242012729G>A	ENSP00000308893:p.Arg1289Gln	150.0	0.0	0		161.0	72.0	0.447205	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Missense_Mutation	SNP	ENST00000310397.8	37	CCDS46562.1	55	0.025183150183150184	50	0.1016260162601626	5	0.013812154696132596	0	0.0	0	0.0	A	1.776	-0.483082	0.04383	0.09539	1.2E-4	ENSG00000162804	ENST00000401884;ENST00000310397	D;D	0.82433	-1.61;-1.58	4.46	-1.35	0.09114	.	0.544077	0.15478	N	0.260251	T	0.01627	0.0052	N	0.00583	-1.355	0.09310	N	1	B;B	0.12630	0.006;0.002	B;B	0.06405	0.002;0.001	T	0.20207	-1.0282	10	0.10111	T	0.7	.	6.6262	0.22830	0.1901:0.5219:0.288:0.0	rs6721345;rs6721345	1289;1289	Q8TER0-5;Q8TER0	.;SNED1_HUMAN	Q	1289	ENSP00000384871:R1289Q;ENSP00000308893:R1289Q	ENSP00000308893:R1289Q	R	+	2	0	SNED1	241661402	0.000000	0.05858	0.018000	0.16275	0.715000	0.41141	0.261000	0.18442	-0.370000	0.08016	-0.381000	0.06696	CGG	G|0.966;A|0.034	0.034	strong		0.637	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482	
CFAP46	54777	hgsc.bcm.edu	37	10	134628208	134628208	+	Missense_Mutation	SNP	C	C	T	rs61733298	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:134628208C>T	ENST00000368586.5	-	52	7331	c.7231G>A	c.(7231-7233)Gac>Aac	p.D2411N	TTC40_ENST00000263170.5_Missense_Mutation_p.D572N	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						TTGTCTGAGTCGACTATGATG	0.652													C|||	134	0.0267572	0.0923	0.013	5008	,	,		13521	0.0		0.001	False		,,,				2504	0.002				p.D2411N		Atlas-SNP	.											.	TTC40	100	.	0			c.G7231A						PASS	.	C	ASN/ASP	383,4021		14,355,1833	24.0	26.0	25.0		2167	4.3	0.0	10	dbSNP_129	25	8,8588		0,8,4290	yes	missense	C10orf92	NM_001200049.1	23	14,363,6123	TT,TC,CC		0.0931,8.6966,3.0077	probably-damaging	723/1028	134628208	391,12609	2202	4298	6500	SO:0001583	missense	54777	exon52			CTGAGTCGACTAT																												ENST00000368586.5:c.7231G>A	10.37:g.134628208C>T	ENSP00000357575:p.Asp2411Asn	99.0	0.0	0		79.0	37.0	0.468354	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	40	0.018315018315018316	36	0.07317073170731707	4	0.011049723756906077	0	0.0	0	0.0	C	15.33	2.802406	0.50315	0.086966	9.31E-4	ENSG00000171811	ENST00000368586;ENST00000263170	T;T	0.34275	1.37;1.37	4.32	4.32	0.51571	.	0.091107	0.39274	N	0.001412	T	0.01976	0.0062	L	0.51422	1.61	0.46336	D	0.998994	D	0.65815	0.995	P	0.52793	0.709	T	0.00115	-1.2039	10	0.33940	T	0.23	.	12.3296	0.55031	0.0:1.0:0.0:0.0	.	572	Q8IYW2	CJ092_HUMAN	N	2411;572	ENSP00000357575:D2411N;ENSP00000263170:D572N	ENSP00000263170:D572N	D	-	1	0	C10orf93	134478198	0.010000	0.17322	0.016000	0.15963	0.025000	0.11179	0.774000	0.26675	1.959000	0.56917	0.591000	0.81541	GAC	C|0.968;T|0.032	0.032	strong		0.652	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
AMDHD2	51005	hgsc.bcm.edu	37	16	2578131	2578131	+	Silent	SNP	C	C	G	rs35816046	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2578131C>G	ENST00000293971.6	+	6	793	c.699C>G	c.(697-699)ctC>ctG	p.L233L	AMDHD2_ENST00000565570.1_Intron|AMDHD2_ENST00000413459.3_Silent_p.L233L|CEMP1_ENST00000382350.1_Intron|AMDHD2_ENST00000302956.4_Silent_p.L233L	NM_015944.3	NP_057028.2	Q9Y303	NAGA_HUMAN	amidohydrolase domain containing 2	233					carbohydrate metabolic process (GO:0005975)|N-acetylglucosamine metabolic process (GO:0006044)|N-acetylneuraminate catabolic process (GO:0019262)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|N-acetylglucosamine-6-phosphate deacetylase activity (GO:0008448)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(3)|skin(2)|urinary_tract(2)	19						TCACCCACCTCTTCAACGCCA	0.667													C|||	109	0.0217652	0.0802	0.0043	5008	,	,		13645	0.0		0.0	False		,,,				2504	0.0				p.L233L		Atlas-SNP	.											.	AMDHD2	33	.	0			c.C699G						PASS	.	C	,	285,4111	155.5+/-188.7	9,267,1922	74.0	76.0	75.0		699,699	5.4	1.0	16	dbSNP_126	75	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	AMDHD2	NM_001145815.1,NM_015944.3	,	9,269,6220	GG,GC,CC		0.0233,6.4832,2.2084	,	233/595,233/440	2578131	287,12709	2198	4300	6498	SO:0001819	synonymous_variant	51005	exon6			CCACCTCTTCAAC	AF132948	CCDS10471.1, CCDS53984.1	16p13.3	2008-02-05			ENSG00000162066	ENSG00000162066			24262	protein-coding gene	gene with protein product						10810093	Standard	NM_001145815		Approved	CGI-14	uc010uwc.2	Q9Y303	OTTHUMG00000128866	ENST00000293971.6:c.699C>G	16.37:g.2578131C>G		84.0	0.0	0		98.0	37.0	0.377551	NM_001145815	B4DL77|Q8WV54	Silent	SNP	ENST00000293971.6	37																																																																																				G|0.019;C|0.981	0.019	strong		0.667	AMDHD2-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000435652.1	NM_015944	
TTC8	123016	hgsc.bcm.edu	37	14	89338786	89338786	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:89338786A>G	ENST00000345383.5	+	12	1391	c.1307A>G	c.(1306-1308)cAc>cGc	p.H436R	TTC8_ENST00000338104.6_Missense_Mutation_p.H462R|TTC8_ENST00000536576.1_Missense_Mutation_p.H207R|TTC8_ENST00000354441.6_Missense_Mutation_p.H181R|TTC8_ENST00000358622.5_Missense_Mutation_p.H248R|TTC8_ENST00000380656.2_Missense_Mutation_p.H446R|TTC8_ENST00000346301.4_Missense_Mutation_p.H406R	NM_198309.2	NP_938051.1	Q8TAM2	TTC8_HUMAN	tetratricopeptide repeat domain 8	472					axon guidance (GO:0007411)|camera-type eye photoreceptor cell differentiation (GO:0060219)|cilium assembly (GO:0042384)|establishment of anatomical structure orientation (GO:0048560)|fat cell differentiation (GO:0045444)|multicellular organism growth (GO:0035264)|nonmotile primary cilium assembly (GO:0035058)|olfactory bulb development (GO:0021772)|protein transport (GO:0015031)|regulation of protein localization (GO:0032880)|renal tubule development (GO:0061326)|sensory perception of smell (GO:0007608)|sensory processing (GO:0050893)	BBSome (GO:0034464)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|prostate(1)	15						CGGAAGGGCCACGTTGAACAG	0.517																																					p.H446R		Atlas-SNP	.											.	TTC8	42	.	0			c.A1337G						PASS	.						131.0	110.0	117.0					14																	89338786		2203	4300	6503	SO:0001583	missense	123016	exon13			AGGGCCACGTTGA	AK093891	CCDS9885.1, CCDS9886.1, CCDS32137.1, CCDS73674.1, CCDS73675.1	14q31.3	2013-02-14				ENSG00000165533		"""Tetratricopeptide (TTC) repeat domain containing"""	20087	protein-coding gene	gene with protein product		608132				14520415, 20451172	Standard	NM_144596		Approved	BBS8, RP51	uc001xxi.3	Q8TAM2		ENST00000345383.5:c.1307A>G	14.37:g.89338786A>G	ENSP00000339486:p.His436Arg	60.0	0.0	0		63.0	24.0	0.380952	NM_144596	A6NFG2|B3KWA5|Q67B97|Q86SY0|Q86TV9|Q86U26|Q8NDH9|Q96DG8	Missense_Mutation	SNP	ENST00000345383.5	37	CCDS9885.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	11.85|11.85	1.761724|1.761724	0.31228|0.31228	.|.	.|.	ENSG00000165533|ENSG00000165533	ENST00000345383;ENST00000536576;ENST00000346301;ENST00000338104;ENST00000354441;ENST00000380656;ENST00000358622|ENST00000554686	T;T;T;T;T;T;T|.	0.58797|.	1.0;0.31;1.0;1.0;0.31;1.0;1.0|.	5.59|5.59	5.59|5.59	0.84812|0.84812	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);|.	0.094735|.	0.64402|.	D|.	0.000001|.	T|T	0.30103|0.30103	0.0754|0.0754	N|N	0.02802|0.02802	-0.49|-0.49	0.49798|0.49798	D|D	0.999823|0.999823	B;B;B;B;B|.	0.12013|.	0.005;0.0;0.005;0.0;0.0|.	B;B;B;B;B|.	0.14578|.	0.004;0.004;0.011;0.002;0.002|.	T|T	0.27872|0.27872	-1.0061|-1.0061	10|5	0.27082|.	T|.	0.32|.	-24.1045|-24.1045	11.1717|11.1717	0.48575|0.48575	0.9283:0.0:0.0717:0.0|0.9283:0.0:0.0717:0.0	.|.	181;207;472;416;446|.	Q8TAM2-2;B3KSL8;Q8TAM2;Q8TAM2-3;Q8TAM2-4|.	.;.;TTC8_HUMAN;.;.|.	R|A	436;207;406;462;181;446;248|396	ENSP00000339486:H436R;ENSP00000445067:H207R;ENSP00000298324:H406R;ENSP00000337653:H462R;ENSP00000346427:H181R;ENSP00000370031:H446R;ENSP00000351439:H248R|.	ENSP00000337653:H462R|.	H|T	+|+	2|1	0|0	TTC8|TTC8	88408539|88408539	0.992000|0.992000	0.36948|0.36948	0.930000|0.930000	0.37139|0.37139	0.977000|0.977000	0.68977|0.68977	2.851000|2.851000	0.48302|0.48302	2.254000|2.254000	0.74563|0.74563	0.459000|0.459000	0.35465|0.35465	CAC|ACG	.	.	none		0.517	TTC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410861.1	NM_144596	
TTN	7273	hgsc.bcm.edu	37	2	179610477	179610477	+	Intron	SNP	A	A	G	rs16866488	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179610477A>G	ENST00000591111.1	-	46	10585				TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Intron|TTN_ENST00000360870.5_Silent_p.D5550D|TTN-AS1_ENST00000578746.1_RNA|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Intron			Q8WZ42	TITIN_HUMAN	titin						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)			CTAATTTTCCATCTTTGTACC	0.418													A|||	51	0.0101837	0.0371	0.0029	5008	,	,		20781	0.0		0.0	False		,,,				2504	0.0				p.D5550D		Atlas-SNP	.											.	TTN	18412	.	0			c.T16650C						PASS	.	A	,,,,	123,4283	93.0+/-131.7	2,119,2082	118.0	118.0	118.0		,,16650,,	-0.3	1.0	2	dbSNP_123	118	4,8594	3.0+/-9.4	0,4,4295	no	intron,intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	2,123,6377	GG,GA,AA		0.0465,2.7916,0.9766	,,,,	,,5550/5605,,	179610477	127,12877	2203	4299	6502	SO:0001627	intron_variant	7273	exon46			TTTTCCATCTTTG	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.10361-3829T>C	2.37:g.179610477A>G		163.0	0.0	0		168.0	88.0	0.52381	NM_133379	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|0.987;G|0.013	0.013	strong		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
DDIAS	220042	hgsc.bcm.edu	37	11	82644059	82644059	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:82644059G>C	ENST00000533655.1	+	6	1891	c.1679G>C	c.(1678-1680)aGa>aCa	p.R560T	C11orf82_ENST00000528759.1_3'UTR|C11orf82_ENST00000430323.2_Missense_Mutation_p.R560T|C11orf82_ENST00000525361.1_Intron|C11orf82_ENST00000329143.3_Missense_Mutation_p.R259T	NM_145018.3	NP_659455.3	Q8IXT1	DDIAS_HUMAN		560					apoptotic process (GO:0006915)|cellular response to cytokine stimulus (GO:0071345)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to hydroperoxide (GO:0071447)|cellular response to UV (GO:0034644)|hemopoiesis (GO:0030097)|mitotic cell cycle arrest (GO:0071850)|negative regulation of fibroblast apoptotic process (GO:2000270)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(17)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	33						AAGACTATCAGAATCTCACCA	0.333																																					p.R560T		Atlas-SNP	.											.	C11orf82	71	.	0			c.G1679C						PASS	.						39.0	40.0	40.0					11																	82644059		2203	4297	6500	SO:0001583	missense	220042	exon6			CTATCAGAATCTC																												ENST00000533655.1:c.1679G>C	11.37:g.82644059G>C	ENSP00000435421:p.Arg560Thr	42.0	0.0	0		33.0	17.0	0.515152	NM_145018	Q96LK6|Q9H856	Missense_Mutation	SNP	ENST00000533655.1	37	CCDS8263.1	.	.	.	.	.	.	.	.	.	.	G	3.431	-0.116076	0.06881	.	.	ENSG00000165490	ENST00000430323;ENST00000533655;ENST00000329143	T;T;T	0.18338	2.48;2.48;2.22	5.73	0.776	0.18532	.	0.891385	0.09988	N	0.730156	T	0.20901	0.0503	L	0.57536	1.79	0.09310	N	1	D	0.56521	0.976	P	0.46685	0.524	T	0.17167	-1.0378	9	.	.	.	.	8.4326	0.32766	0.3684:0.0:0.6316:0.0	.	560	Q8IXT1	NOXIN_HUMAN	T	560;560;259	ENSP00000414687:R560T;ENSP00000435421:R560T;ENSP00000329930:R259T	.	R	+	2	0	C11orf82	82321707	0.000000	0.05858	0.001000	0.08648	0.144000	0.21451	-0.075000	0.11431	0.102000	0.17638	0.655000	0.94253	AGA	.	.	none		0.333	C11orf82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391936.1		
MUC4	4585	hgsc.bcm.edu	37	3	195505893	195505893	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195505893G>A	ENST00000463781.3	-	2	13017	c.12558C>T	c.(12556-12558)tcC>tcT	p.S4186S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.S4186S	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)		TGTCACCTGTGGATGCTGAGG	0.592																																					p.S4186S		Atlas-SNP	.											.	MUC4	1505	.	0			c.C12558T						PASS	.						19.0	13.0	15.0					3																	195505893		691	1574	2265	SO:0001819	synonymous_variant	4585	exon2			ACCTGTGGATGCT	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.12558C>T	3.37:g.195505893G>A		167.0	0.0	0		240.0	14.0	0.0583333	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
LYPD3	27076	hgsc.bcm.edu	37	19	43967423	43967423	+	Silent	SNP	G	G	A	rs79420167	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43967423G>A	ENST00000244333.3	-	4	487	c.399C>T	c.(397-399)taC>taT	p.Y133Y		NM_014400.2	NP_055215.2	O95274	LYPD3_HUMAN	LY6/PLAUR domain containing 3	133					cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)	anchored component of plasma membrane (GO:0046658)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|pancreas(1)|upper_aerodigestive_tract(2)	11		Prostate(69;0.0153)				CGTTGGGCGGGTATGCACTCT	0.647													G|||	52	0.0103834	0.0378	0.0029	5008	,	,		15418	0.0		0.0	False		,,,				2504	0.0				p.Y133Y		Atlas-SNP	.											.	LYPD3	24	.	0			c.C399T						PASS	.	G		130,4276	94.8+/-133.5	4,122,2077	49.0	46.0	47.0		399	-2.9	0.0	19	dbSNP_132	47	0,8600		0,0,4300	no	coding-synonymous	LYPD3	NM_014400.2		4,122,6377	AA,AG,GG		0.0,2.9505,0.9995		133/347	43967423	130,12876	2203	4300	6503	SO:0001819	synonymous_variant	27076	exon4			GGGCGGGTATGCA	AF082889	CCDS12620.1	19q13.31	2008-02-05				ENSG00000124466			24880	protein-coding gene	gene with protein product		609484				11179665, 11245483	Standard	NM_014400		Approved	C4.4A	uc002owl.1	O95274		ENST00000244333.3:c.399C>T	19.37:g.43967423G>A		18.0	0.0	0		34.0	15.0	0.441176	NM_014400	Q9UJ74	Silent	SNP	ENST00000244333.3	37	CCDS12620.1																																																																																			G|0.987;A|0.013	0.013	strong		0.647	LYPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463177.1	NM_014400	
APOB	338	hgsc.bcm.edu	37	2	21224843	21224843	+	Missense_Mutation	SNP	G	G	A	rs12713450	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:21224843G>A	ENST00000233242.1	-	29	13578	c.13451C>T	c.(13450-13452)aCg>aTg	p.T4484M	RP11-116D2.1_ENST00000567376.2_lincRNA	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	4484			T -> M (in dbSNP:rs12713450).		artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TATTTTCTTCGTCGCAATGGC	0.378													G|||	192	0.0383387	0.1263	0.0259	5008	,	,		18757	0.0		0.006	False		,,,				2504	0.001				p.T4484M		Atlas-SNP	.											APOB,NS,carcinoma,+1,1	APOB	761	1	0			c.C13451T						scavenged	.	G	MET/THR	444,3962	204.8+/-226.9	20,404,1779	85.0	91.0	89.0		13451	2.2	0.0	2	dbSNP_126	89	43,8557	28.5+/-78.6	0,43,4257	yes	missense	APOB	NM_000384.2	81	20,447,6036	AA,AG,GG		0.5,10.0772,3.7444	benign	4484/4564	21224843	487,12519	2203	4300	6503	SO:0001583	missense	338	exon29			TTCTTCGTCGCAA	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.13451C>T	2.37:g.21224843G>A	ENSP00000233242:p.Thr4484Met	100.0	1.0	0.01		118.0	60.0	0.508475	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	72	0.03296703296703297	60	0.12195121951219512	8	0.022099447513812154	0	0.0	4	0.005277044854881266	G	0.008	-1.930298	0.00488	0.100772	0.005	ENSG00000084674	ENST00000233242	T	0.37915	1.17	5.9	2.22	0.28083	.	0.646971	0.15282	N	0.270656	T	0.00109	0.0003	N	0.00095	-2.16	0.22552	N	0.998995	B	0.06786	0.001	B	0.04013	0.001	T	0.33085	-0.9882	10	0.28530	T	0.3	.	6.3395	0.21314	0.4718:0.0:0.5282:0.0	rs12713450;rs17240965;rs52805962;rs60161843;rs12713450	4484	P04114	APOB_HUMAN	M	4484	ENSP00000233242:T4484M	ENSP00000233242:T4484M	T	-	2	0	APOB	21078348	0.907000	0.30839	0.005000	0.12908	0.008000	0.06430	1.767000	0.38501	0.490000	0.27771	-0.312000	0.09012	ACG	G|0.968;A|0.032	0.032	strong		0.378	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
CHAD	1101	hgsc.bcm.edu	37	17	48542690	48542690	+	Missense_Mutation	SNP	G	G	A	rs2231510	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48542690G>A	ENST00000508540.1	-	3	1201	c.1049C>T	c.(1048-1050)aCc>aTc	p.T350I	ACSF2_ENST00000502667.1_Intron|CHAD_ENST00000258969.4_Missense_Mutation_p.T350I|ACSF2_ENST00000541920.1_Intron|ACSF2_ENST00000300441.4_Intron|ACSF2_ENST00000504392.1_Intron|ACSF2_ENST00000427954.2_Intron	NM_001267.2	NP_001258.2	O15335	CHAD_HUMAN	chondroadherin	350			T -> I (in dbSNP:rs2231510).		bone development (GO:0060348)|cartilage condensation (GO:0001502)|negative regulation of bone trabecula formation (GO:1900155)	proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(2)|ovary(2)	15	Breast(11;1.93e-18)		BRCA - Breast invasive adenocarcinoma(22;1.55e-09)			GGACCTCTTGGTGGGGAACTT	0.597													G|||	100	0.0199681	0.0734	0.0043	5008	,	,		17381	0.0		0.0	False		,,,				2504	0.0				p.T350I		Atlas-SNP	.											.	CHAD	36	.	0			c.C1049T						PASS	.	G	ILE/THR,	338,4068	178.0+/-206.8	13,312,1878	56.0	52.0	53.0		1049,	5.1	1.0	17	dbSNP_98	53	1,8599	1.2+/-3.3	0,1,4299	yes	missense,intron	CHAD,ACSF2	NM_001267.2,NM_025149.4	89,	13,313,6177	AA,AG,GG		0.0116,7.6714,2.6065	benign,	350/360,	48542690	339,12667	2203	4300	6503	SO:0001583	missense	1101	exon3			CTCTTGGTGGGGA	U96767	CCDS11568.1	17q21.33	2008-02-05			ENSG00000136457	ENSG00000136457		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	1909	protein-coding gene	gene with protein product	"""chondroadherin proteoglycan"""	602178				9344663	Standard	NM_001267		Approved	SLRR4A	uc010dbr.3	O15335	OTTHUMG00000162129	ENST00000508540.1:c.1049C>T	17.37:g.48542690G>A	ENSP00000423812:p.Thr350Ile	105.0	0.0	0		109.0	50.0	0.458716	NM_001267	A8K812|Q6GTU0|Q96RJ5	Missense_Mutation	SNP	ENST00000508540.1	37	CCDS11568.1	39|39	0.017857142857142856|0.017857142857142856	38|38	0.07723577235772358|0.07723577235772358	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	G|G	17.86|17.86	3.492361|3.492361	0.64074|0.64074	0.076714|0.076714	1.16E-4|1.16E-4	ENSG00000136457|ENSG00000136457	ENST00000506187|ENST00000508540;ENST00000258969	.|T;T	.|0.56275	.|0.47;0.47	5.12|5.12	5.12|5.12	0.69794|0.69794	.|.	.|0.056342	.|0.64402	.|D	.|0.000001	T|T	0.05960|0.05960	0.0155|0.0155	L|L	0.45352|0.45352	1.415|1.415	0.58432|0.58432	D|D	0.999997|0.999997	.|D	.|0.64830	.|0.994	.|P	.|0.50314	.|0.637	T|T	0.03413|0.03413	-1.1039|-1.1039	5|10	.|0.37606	.|T	.|0.19	.|.	18.5806|18.5806	0.91170|0.91170	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs2231510;rs2231510|rs2231510;rs2231510	.|350	.|O15335	.|CHAD_HUMAN	S|I	33|350	.|ENSP00000423812:T350I;ENSP00000258969:T350I	.|ENSP00000258969:T350I	P|T	-|-	1|2	0|0	CHAD|CHAD	45897689|45897689	1.000000|1.000000	0.71417|0.71417	0.991000|0.991000	0.47740|0.47740	0.971000|0.971000	0.66376|0.66376	8.496000|8.496000	0.90485|0.90485	2.380000|2.380000	0.81148|0.81148	0.655000|0.655000	0.94253|0.94253	CCA|ACC	G|0.966;A|0.034	0.034	strong		0.597	CHAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367447.3	NM_001267	
PKN2	5586	hgsc.bcm.edu	37	1	89273241	89273241	+	Missense_Mutation	SNP	A	A	G	rs12085658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:89273241A>G	ENST00000370521.3	+	14	2323	c.1964A>G	c.(1963-1965)cAa>cGa	p.Q655R	PKN2_ENST00000370505.3_Missense_Mutation_p.Q498R|PKN2_ENST00000370513.5_Missense_Mutation_p.Q607R|PKN2_ENST00000544045.1_Missense_Mutation_p.Q329R	NM_006256.2	NP_006247.1	Q16513	PKN2_HUMAN	protein kinase N2	655			Q -> R (in dbSNP:rs12085658).		apical junction assembly (GO:0043297)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell division (GO:0051301)|epithelial cell migration (GO:0010631)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic cell cycle (GO:0045931)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	apical junction complex (GO:0043296)|centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium (GO:0030027)|membrane (GO:0016020)|midbody (GO:0030496)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(3)|kidney(3)|large_intestine(8)|lung(15)|prostate(1)|skin(1)	33		Lung NSC(277;0.123)		all cancers(265;0.0136)|Epithelial(280;0.0301)		TTTAATCTACAAGATTTCAGG	0.318													A|||	43	0.00858626	0.0295	0.0058	5008	,	,		16355	0.0		0.0	False		,,,				2504	0.0				p.Q655R		Atlas-SNP	.											.	PKN2	109	.	0			c.A1964G						PASS	.	A	ARG/GLN	90,3516		0,90,1713	150.0	145.0	146.0		1964	5.8	1.0	1	dbSNP_120	146	0,8134		0,0,4067	yes	missense	PKN2	NM_006256.2	43	0,90,5780	GG,GA,AA		0.0,2.4958,0.7666	benign	655/985	89273241	90,11650	1803	4067	5870	SO:0001583	missense	5586	exon14			ATCTACAAGATTT	U33052	CCDS714.1	1p22	2014-04-23	2004-07-01	2004-07-01	ENSG00000065243	ENSG00000065243			9406	protein-coding gene	gene with protein product	"""cardiolipin-activated protein kinase Pak2"""	602549	"""protein kinase C-like 2"""	PRKCL2		7988719, 7851406	Standard	NM_006256		Approved	PRK2, Pak-2, STK7	uc001dmn.3	Q16513	OTTHUMG00000010074	ENST00000370521.3:c.1964A>G	1.37:g.89273241A>G	ENSP00000359552:p.Gln655Arg	103.0	0.0	0		101.0	50.0	0.49505	NM_006256	B4DQ21|B4DTP5|B4DVG1|D3DT24|Q08AF4|Q9H1W4	Missense_Mutation	SNP	ENST00000370521.3	37	CCDS714.1	14	0.00641025641025641	12	0.024390243902439025	2	0.0055248618784530384	0	0.0	0	0.0	A	15.07	2.724560	0.48833	0.024958	0.0	ENSG00000065243	ENST00000370521;ENST00000370505;ENST00000370513;ENST00000544045	T;T;T;T	0.24538	1.85;1.85;1.85;1.85	5.75	5.75	0.90469	Protein kinase-like domain (1);	0.162237	0.28612	U	0.014721	T	0.07728	0.0194	N	0.08118	0	0.36654	D	0.877588	B;B;B	0.22683	0.073;0.073;0.025	B;B;B	0.17098	0.017;0.017;0.013	T	0.09773	-1.0659	10	0.54805	T	0.06	.	16.0549	0.80794	1.0:0.0:0.0:0.0	rs12085658;rs52814429;rs12085658	639;607;655	B4DTP5;E7ESL7;Q16513	.;.;PKN2_HUMAN	R	655;498;607;329	ENSP00000359552:Q655R;ENSP00000359536:Q498R;ENSP00000359544:Q607R;ENSP00000439643:Q329R	ENSP00000359536:Q498R	Q	+	2	0	PKN2	89045829	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.711000	0.61881	2.193000	0.70182	0.477000	0.44152	CAA	A|0.992;G|0.008	0.008	strong		0.318	PKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027828.3	NM_006256	
KIAA1211	57482	hgsc.bcm.edu	37	4	57180546	57180546	+	Missense_Mutation	SNP	G	G	A	rs145781098	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:57180546G>A	ENST00000504228.1	+	6	983	c.878G>A	c.(877-879)cGg>cAg	p.R293Q	KIAA1211_ENST00000541073.1_Missense_Mutation_p.R286Q|KIAA1211_ENST00000264229.6_Missense_Mutation_p.R293Q			Q6ZU35	K1211_HUMAN	KIAA1211	293	Glu-rich.									endometrium(7)|large_intestine(10)|lung(39)|ovary(2)|prostate(3)|skin(3)|stomach(1)	65	Glioma(25;0.08)|all_neural(26;0.101)					GAGCAGCAGCGGAGCCTGGAA	0.697													G|||	27	0.00539137	0.0197	0.0014	5008	,	,		13712	0.0		0.0	False		,,,				2504	0.0				p.R293Q		Atlas-SNP	.											.	KIAA1211	178	.	0			c.G878A						PASS	.	G	GLN/ARG	46,3696		0,46,1825	5.0	8.0	7.0		878	-2.7	0.0	4	dbSNP_134	7	6,7630		0,6,3812	no	missense	KIAA1211	NM_020722.1	43	0,52,5637	AA,AG,GG		0.0786,1.2293,0.457	benign	293/1234	57180546	52,11326	1871	3818	5689	SO:0001583	missense	57482	exon8			AGCAGCGGAGCCT	AB033037	CCDS43230.1	4q12	2012-08-03			ENSG00000109265	ENSG00000109265			29219	protein-coding gene	gene with protein product						10574462, 11230166	Standard	NM_020722		Approved		uc003hbk.2	Q6ZU35	OTTHUMG00000160749	ENST00000504228.1:c.878G>A	4.37:g.57180546G>A	ENSP00000423366:p.Arg293Gln	39.0	0.0	0		49.0	24.0	0.489796	NM_020722	Q9NTE2|Q9NTP8|Q9ULK9	Missense_Mutation	SNP	ENST00000504228.1	37	CCDS43230.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	G	12.98	2.100302	0.37048	0.012293	7.86E-4	ENSG00000109265	ENST00000264229;ENST00000504228;ENST00000541073;ENST00000546221	T;T;T	0.14391	2.51;2.51;2.52	4.88	-2.66	0.06077	.	.	.	.	.	T	0.00815	0.0027	N	0.00246	-1.78	0.09310	N	1	B;B;B	0.15930	0.015;0.015;0.015	B;B;B	0.11329	0.006;0.003;0.003	T	0.44159	-0.9346	9	0.11485	T	0.65	-0.6858	6.6117	0.22755	0.3545:0.2188:0.4268:0.0	.	286;286;293	B7ZVZ4;F5H1N7;Q6ZU35	.;.;K1211_HUMAN	Q	293;293;286;203	ENSP00000264229:R293Q;ENSP00000423366:R293Q;ENSP00000444006:R286Q	ENSP00000264229:R293Q	R	+	2	0	KIAA1211	56875303	0.000000	0.05858	0.000000	0.03702	0.143000	0.21401	-0.656000	0.05342	-0.778000	0.04566	0.462000	0.41574	CGG	G|0.994;A|0.006	0.006	strong		0.697	KIAA1211-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362097.2	NM_020722	
PRUNE2	158471	hgsc.bcm.edu	37	9	79319725	79319725	+	Missense_Mutation	SNP	T	T	C	rs375144440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:79319725T>C	ENST00000376718.3	-	8	7588	c.7465A>G	c.(7465-7467)Aca>Gca	p.T2489A	PRUNE2_ENST00000428286.1_Missense_Mutation_p.T2130A	NM_015225.2	NP_056040.2	Q8WUY3	PRUN2_HUMAN	prune homolog 2 (Drosophila)	2489					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|pyrophosphatase activity (GO:0016462)			endometrium(1)|kidney(4)|large_intestine(3)|lung(7)|prostate(1)	16						GAATTATCTGTTTCTACTTCC	0.448											OREG0019258	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	2	0.000399361	0.0015	0.0	5008	,	,		20535	0.0		0.0	False		,,,				2504	0.0				p.T2489A		Atlas-SNP	.											.	PRUNE2	331	.	0			c.A7465G						PASS	.	T	ALA/THR	5,3131		0,5,1563	72.0	60.0	64.0		7465	-1.6	0.2	9		64	0,7162		0,0,3581	no	missense	PRUNE2	NM_015225.2	58	0,5,5144	CC,CT,TT		0.0,0.1594,0.0486	benign	2489/3089	79319725	5,10293	1568	3581	5149	SO:0001583	missense	158471	exon8			TATCTGTTTCTAC	BC019095	CCDS47982.1	9q21.32	2013-04-29	2006-11-24	2006-11-24	ENSG00000106772	ENSG00000106772			25209	protein-coding gene	gene with protein product	"""olfaxin"""	610691	"""chromosome 9 open reading frame 65"", ""KIAA0367"""	C9orf65, KIAA0367		16288218	Standard	NM_015225		Approved	BMCC1, BNIPXL, A214N16.3, bA214N16.3	uc010mpk.3	Q8WUY3	OTTHUMG00000020047	ENST00000376718.3:c.7465A>G	9.37:g.79319725T>C	ENSP00000365908:p.Thr2489Ala	132.0	0.0	0	1190	149.0	104.0	0.697987	NM_015225	B3KYC4|B4DQH8|O15073|Q58A63|Q5JUB6|Q5T304|Q5T476|Q6T2V6|Q6T2V7|Q8N665	Missense_Mutation	SNP	ENST00000376718.3	37	CCDS47982.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	6.828|6.828	0.521980|0.521980	0.13005|0.13005	0.001594|0.001594	0.0|0.0	ENSG00000106772|ENSG00000106772	ENST00000426088|ENST00000376718;ENST00000428286;ENST00000422033	.|T;T	.|0.47869	.|0.83;0.83	5.66|5.66	-1.6|-1.6	0.08426|0.08426	.|.	.|0.512611	.|0.18219	.|N	.|0.147951	T|T	0.31295|0.31295	0.0792|0.0792	L|L	0.48362|0.48362	1.52|1.52	0.25662|0.25662	N|N	0.985999|0.985999	.|B	.|0.15141	.|0.012	.|B	.|0.11329	.|0.006	T|T	0.15235|0.15235	-1.0444|-1.0444	5|10	.|0.21540	.|T	.|0.41	-0.3544|-0.3544	4.9213|4.9213	0.13871|0.13871	0.3138:0.2585:0.0:0.4276|0.3138:0.2585:0.0:0.4276	.|.	.|2489	.|Q8WUY3	.|PRUN2_HUMAN	S|A	1810|2489;2130;2488	.|ENSP00000365908:T2489A;ENSP00000397425:T2130A	.|ENSP00000365908:T2489A	N|T	-|-	2|1	0|0	PRUNE2|PRUNE2	78509545|78509545	0.492000|0.492000	0.26027|0.26027	0.226000|0.226000	0.23910|0.23910	0.731000|0.731000	0.41821|0.41821	0.124000|0.124000	0.15728|0.15728	-0.097000|-0.097000	0.12307|0.12307	0.533000|0.533000	0.62120|0.62120	AAC|ACA	.	.	weak		0.448	PRUNE2-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052730.2	NM_138818	
BRWD1	54014	hgsc.bcm.edu	37	21	40570830	40570830	+	Missense_Mutation	SNP	G	G	C	rs2234547	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:40570830G>C	ENST00000333229.2	-	40	5839	c.5512C>G	c.(5512-5514)Cat>Gat	p.H1838D	BRWD1_ENST00000380800.3_Missense_Mutation_p.H1838D|BRWD1_ENST00000342449.3_Missense_Mutation_p.H1838D	NM_018963.4	NP_061836.2	Q9NSI6	BRWD1_HUMAN	bromodomain and WD repeat domain containing 1	1838					cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(2)|endometrium(6)|kidney(8)|large_intestine(14)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(2)	58		Prostate(19;8.44e-08)|all_epithelial(19;0.223)				TCCATTTTATGACATTTCCCA	0.373													G|||	17	0.00339457	0.0121	0.0014	5008	,	,		19409	0.0		0.0	False		,,,				2504	0.0				p.H1838D	Melanoma(170;988 1986 4794 16843 39731)	Atlas-SNP	.											.	BRWD1	325	.	0			c.C5512G						PASS	.	G	ASP/HIS,ASP/HIS	15,4389	22.3+/-47.3	0,15,2187	134.0	133.0	133.0		5512,5512	3.2	0.2	21	dbSNP_98	133	0,8600		0,0,4300	yes	missense,missense	BRWD1	NM_018963.4,NM_033656.3	81,81	0,15,6487	CC,CG,GG		0.0,0.3406,0.1153	benign,benign	1838/2321,1838/2270	40570830	15,12989	2202	4300	6502	SO:0001583	missense	54014	exon40			TTTTATGACATTT	AJ002572	CCDS13662.1, CCDS13663.1, CCDS33557.1	21q22.2	2013-05-21	2005-05-13	2005-05-13	ENSG00000185658	ENSG00000185658		"""WD repeat domain containing"""	12760	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 107"", ""WD repeat domain 9"""	C21orf107, WDR9			Standard	NM_033656		Approved	FLJ11315, N143	uc002yxk.2	Q9NSI6	OTTHUMG00000066030	ENST00000333229.2:c.5512C>G	21.37:g.40570830G>C	ENSP00000330753:p.His1838Asp	155.0	0.0	0		172.0	84.0	0.488372	NM_018963	C9JK25|O43721|Q5R2V0|Q5R2V1|Q6P2D1|Q8TCV3|Q96QG9|Q96QH0|Q9NUK1	Missense_Mutation	SNP	ENST00000333229.2	37	CCDS13662.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	G	11.80	1.746199	0.30955	0.003406	0.0	ENSG00000185658	ENST00000333229;ENST00000342449;ENST00000380800	T;T;T	0.44083	0.93;0.93;0.93	5.48	3.18	0.36537	.	0.908791	0.09391	N	0.808490	T	0.14098	0.0341	L	0.54323	1.7	0.09310	N	1	B;B	0.26775	0.095;0.159	B;B	0.24155	0.051;0.021	T	0.08534	-1.0717	10	0.35671	T	0.21	-2.3847	4.7666	0.13135	0.1553:0.4107:0.434:0.0	rs2234547;rs2234547	1838;1838	Q9NSI6-2;Q9NSI6	.;BRWD1_HUMAN	D	1838	ENSP00000330753:H1838D;ENSP00000344333:H1838D;ENSP00000370178:H1838D	ENSP00000330753:H1838D	H	-	1	0	BRWD1	39492700	0.000000	0.05858	0.203000	0.23512	0.374000	0.29953	0.674000	0.25218	2.576000	0.86940	0.655000	0.94253	CAT	G|0.997;C|0.003	0.003	strong		0.373	BRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141398.3	NM_033656	
LRRN3	54674	hgsc.bcm.edu	37	7	110763563	110763563	+	Silent	SNP	T	T	C	rs214865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:110763563T>C	ENST00000422987.3	+	2	1566	c.735T>C	c.(733-735)gaT>gaC	p.D245D	LRRN3_ENST00000451085.1_Silent_p.D245D|IMMP2L_ENST00000437687.1_Intron|IMMP2L_ENST00000452895.1_Intron|IMMP2L_ENST00000450877.1_Intron|IMMP2L_ENST00000415362.1_Intron|IMMP2L_ENST00000489381.1_Intron|IMMP2L_ENST00000447215.1_Intron|IMMP2L_ENST00000405709.2_Intron|LRRN3_ENST00000308478.5_Silent_p.D245D|IMMP2L_ENST00000331762.3_Intron	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	245					positive regulation of protein phosphorylation (GO:0001934)	clathrin adaptor complex (GO:0030131)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(15)|lung(20)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				UCEC - Uterine corpus endometrioid carcinoma (4;0.245)|LUSC - Lung squamous cell carcinoma(290;0.0715)|Lung(3;0.0864)|STAD - Stomach adenocarcinoma(3;0.125)		CTTTTTACGATAACAGGCTTA	0.358													C|||	472	0.0942492	0.3011	0.0418	5008	,	,		18738	0.002		0.0298	False		,,,				2504	0.0133				p.D245D		Atlas-SNP	.											.	LRRN3	132	.	0			c.T735C						PASS	.	C	,,,	1203,3203	693.7+/-405.7	159,885,1159	55.0	59.0	57.0		735,735,735,	3.2	1.0	7	dbSNP_79	57	236,8360	793.0+/-407.5	3,230,4065	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	LRRN3,IMMP2L	NM_001099658.1,NM_001099660.1,NM_018334.4,NM_032549.3	,,,	162,1115,5224	CC,CT,TT		2.7455,27.3037,11.0675	,,,	245/709,245/709,245/709,	110763563	1439,11563	2203	4298	6501	SO:0001819	synonymous_variant	54674	exon2			TTACGATAACAGG	AB060967	CCDS5754.1	7q31.1	2013-02-11			ENSG00000173114	ENSG00000173114		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17200	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 5"""					11549284	Standard	NM_001099660		Approved	NLRR3, FLJ11129, FIGLER5	uc003vfs.4	Q9H3W5	OTTHUMG00000155039	ENST00000422987.3:c.735T>C	7.37:g.110763563T>C		107.0	0.0	0		144.0	75.0	0.520833	NM_018334	O43377|Q6I9V8|Q8IYQ6	Silent	SNP	ENST00000422987.3	37	CCDS5754.1																																																																																			T|0.892;C|0.108	0.108	strong		0.358	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338171.2	NM_018334	
SLC9A9	285195	hgsc.bcm.edu	37	3	143185920	143185920	+	Silent	SNP	A	A	G	rs61734421	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:143185920A>G	ENST00000316549.6	-	12	1636	c.1428T>C	c.(1426-1428)ttT>ttC	p.F476F		NM_173653.3	NP_775924.1	Q8IVB4	SL9A9_HUMAN	solute carrier family 9, subfamily A (NHE9, cation proton antiporter 9), member 9	476					ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|recycling endosome (GO:0055037)	sodium:proton antiporter activity (GO:0015385)			breast(2)|endometrium(5)|kidney(2)|large_intestine(13)|lung(29)|ovary(2)|skin(3)|stomach(1)	57						TTCCTCCTCCAAATACCCAGA	0.473													A|||	23	0.00459265	0.0166	0.0014	5008	,	,		19226	0.0		0.0	False		,,,				2504	0.0				p.F476F		Atlas-SNP	.											.	SLC9A9	117	.	0			c.T1428C						PASS	.	A		91,4315	75.2+/-113.4	1,89,2113	141.0	116.0	124.0		1428	-3.0	0.9	3	dbSNP_129	124	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SLC9A9	NM_173653.3		1,91,6411	GG,GA,AA		0.0233,2.0654,0.7151		476/646	143185920	93,12913	2203	4300	6503	SO:0001819	synonymous_variant	285195	exon12			TCCTCCAAATACC	AY254100	CCDS33872.1	3q23-q24	2014-01-28	2012-03-22		ENSG00000181804	ENSG00000181804		"""Solute carriers"""	20653	protein-coding gene	gene with protein product		608396	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 9"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 9"""			14569117	Standard	NM_173653		Approved	FLJ35613, NHE9	uc003evn.3	Q8IVB4	OTTHUMG00000159373	ENST00000316549.6:c.1428T>C	3.37:g.143185920A>G		311.0	0.0	0		314.0	151.0	0.480892	NM_173653	A6NMQ9|Q3LIC2|Q5JPI6|Q5WA58|Q8NAB9	Silent	SNP	ENST00000316549.6	37	CCDS33872.1																																																																																			A|0.993;G|0.007	0.007	strong		0.473	SLC9A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354994.1	NM_173653	
BPIFA2	140683	hgsc.bcm.edu	37	20	31757078	31757078	+	Missense_Mutation	SNP	G	G	A	rs6059139	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31757078G>A	ENST00000253362.2	+	2	273	c.127G>A	c.(127-129)Gga>Aga	p.G43R	BPIFA2_ENST00000354932.5_Missense_Mutation_p.G43R			Q96DR5	BPIA2_HUMAN	BPI fold containing family A, member 2	43			G -> R (in dbSNP:rs6059139).			extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)										TCTTCACGAGGGACTTGAGAC	0.463													G|||	141	0.028155	0.0998	0.0058	5008	,	,		20844	0.0		0.005	False		,,,				2504	0.0				p.G43R		Atlas-SNP	.											.	.	.	.	0			c.G127A						PASS	.	G	ARG/GLY	408,3998	201.8+/-224.7	16,376,1811	145.0	120.0	128.0		127	2.2	0.0	20	dbSNP_114	128	17,8583	12.6+/-44.7	0,17,4283	yes	missense	BPIFA2	NM_080574.2	125	16,393,6094	AA,AG,GG		0.1977,9.2601,3.2677	possibly-damaging	43/250	31757078	425,12581	2203	4300	6503	SO:0001583	missense	140683	exon2			CACGAGGGACTTG	AF432917	CCDS13214.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131050	ENSG00000131050		"""BPI fold containing"""	16203	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 70"""	C20orf70		11971875	Standard	NM_080574		Approved	bA49G10.1, SPLUNC2, PSP	uc002wyo.1	Q96DR5	OTTHUMG00000032244	ENST00000253362.2:c.127G>A	20.37:g.31757078G>A	ENSP00000253362:p.Gly43Arg	91.0	0.0	0		95.0	31.0	0.326316	NM_080574	Q9BQQ0	Missense_Mutation	SNP	ENST00000253362.2	37	CCDS13214.1	59	0.027014652014652016	52	0.10569105691056911	3	0.008287292817679558	0	0.0	4	0.005277044854881266	G	2.971	-0.212453	0.06140	0.092601	0.001977	ENSG00000131050	ENST00000253362;ENST00000354932	T;T	0.13089	2.62;2.62	4.16	2.22	0.28083	.	0.708924	0.12096	N	0.499960	T	0.00241	0.0007	L	0.41824	1.3	0.80722	P	0.0	P	0.36010	0.532	B	0.36922	0.236	T	0.20075	-1.0286	9	0.51188	T	0.08	-10.3634	6.3866	0.21563	0.2201:0.0:0.7799:0.0	rs6059139;rs52815538;rs6059139	43	Q96DR5	BPIA2_HUMAN	R	43	ENSP00000253362:G43R;ENSP00000347012:G43R	ENSP00000253362:G43R	G	+	1	0	BPIFA2	31220739	0.001000	0.12720	0.002000	0.10522	0.009000	0.06853	0.736000	0.26130	0.707000	0.31934	0.655000	0.94253	GGA	G|0.962;A|0.038	0.038	strong		0.463	BPIFA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257117.1	NM_080574	
OGFR	11054	hgsc.bcm.edu	37	20	61443871	61443871	+	Missense_Mutation	SNP	C	C	T	rs77478162	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61443871C>T	ENST00000290291.6	+	7	929	c.904C>T	c.(904-906)Cat>Tat	p.H302Y	OGFR_ENST00000370461.1_Missense_Mutation_p.H250Y	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	302					opioid receptor signaling pathway (GO:0038003)|regulation of cell growth (GO:0001558)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	opioid receptor activity (GO:0004985)			endometrium(2)|kidney(1)|lung(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	17	Breast(26;3.65e-08)					CTCTCTGCCCCATCCGCTCGA	0.682													C|||	91	0.0181709	0.0666	0.0043	5008	,	,		13687	0.0		0.0	False		,,,				2504	0.0				p.H302Y		Atlas-SNP	.											.	OGFR	63	.	0			c.C904T						PASS	.	C	TYR/HIS	186,4136		0,186,1975	8.0	8.0	8.0		904	-1.5	0.0	20	dbSNP_131	8	2,8478		0,2,4238	yes	missense	OGFR	NM_007346.2	83	0,188,6213	TT,TC,CC		0.0236,4.3036,1.4685	benign	302/678	61443871	188,12614	2161	4240	6401	SO:0001583	missense	11054	exon7			CTGCCCCATCCGC	AF109134	CCDS13504.1	20q13.3	2008-05-02			ENSG00000060491	ENSG00000060491			15768	protein-coding gene	gene with protein product		606459				10677613	Standard	NM_007346		Approved	7-60	uc002ydj.3	Q9NZT2	OTTHUMG00000032937	ENST00000290291.6:c.904C>T	20.37:g.61443871C>T	ENSP00000290291:p.His302Tyr	60.0	0.0	0		65.0	32.0	0.492308	NM_007346	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Missense_Mutation	SNP	ENST00000290291.6	37	CCDS13504.1	31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	C	8.778	0.927439	0.18056	0.043036	2.36E-4	ENSG00000060491	ENST00000290291;ENST00000370468;ENST00000357163;ENST00000370469;ENST00000370461	T;T;T	0.43688	1.94;0.94;1.52	3.86	-1.55	0.08558	.	4.120900	0.01321	N	0.010938	T	0.02848	0.0085	N	0.22421	0.69	0.09310	N	1	B;B;B	0.24651	0.035;0.006;0.108	B;B;B	0.23018	0.031;0.001;0.043	T	0.06752	-1.0809	10	0.37606	T	0.19	0.1436	0.781	0.01041	0.2558:0.3046:0.1089:0.3306	.	302;285;302	B3KMQ6;Q05BV5;Q9NZT2	.;.;OGFR_HUMAN	Y	302;302;302;157;250	ENSP00000290291:H302Y;ENSP00000359499:H302Y;ENSP00000359491:H250Y	ENSP00000290291:H302Y	H	+	1	0	OGFR	60914316	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.754000	0.04787	-0.100000	0.12241	-0.254000	0.11334	CAT	C|0.984;T|0.016	0.016	strong		0.682	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1		
CLASP2	23122	hgsc.bcm.edu	37	3	33759474	33759474	+	Silent	SNP	C	C	T	rs112019256	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:33759474C>T	ENST00000468888.2	-	1	67	c.21G>A	c.(19-21)gaG>gaA	p.E7E	CLASP2_ENST00000307312.7_5'UTR|CLASP2_ENST00000399362.4_Silent_p.E7E|CLASP2_ENST00000359576.5_Silent_p.E7E			O75122	CLAP2_HUMAN	cytoplasmic linker associated protein 2	0					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						CGCAGAAGTACTCCATGCTGC	0.726													C|||	37	0.00738818	0.025	0.0014	5008	,	,		9762	0.002		0.0	False		,,,				2504	0.001				p.E7E		Atlas-SNP	.											.	CLASP2	138	.	0			c.G21A						PASS	.	C		54,3038		0,54,1492	3.0	4.0	3.0		21	1.0	1.0	3	dbSNP_132	3	2,7002		0,2,3500	no	coding-synonymous	CLASP2	NM_015097.2		0,56,4992	TT,TC,CC		0.0286,1.7464,0.5547		7/1516	33759474	56,10040	1546	3502	5048	SO:0001819	synonymous_variant	23122	exon1			GAAGTACTCCATG	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.21G>A	3.37:g.33759474C>T		23.0	0.0	0		14.0	5.0	0.357143	NM_015097	Q7L8F6|Q8N6R6|Q9BQT3|Q9BQT4|Q9H7A3|Q9NSZ2	Silent	SNP	ENST00000468888.2	37																																																																																				C|0.333;T|0.667	0.667	weak		0.726	CLASP2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000344320.4	NM_001207044	
SCN4A	6329	hgsc.bcm.edu	37	17	62018737	62018737	+	Silent	SNP	G	G	A	rs59081944	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:62018737G>A	ENST00000435607.1	-	24	4981	c.4905C>T	c.(4903-4905)atC>atT	p.I1635I	SCN4A_ENST00000578147.1_Silent_p.I1635I	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1635					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GGCTGTAGGCGATGAACTGGG	0.567													G|||	92	0.0183706	0.0681	0.0029	5008	,	,		18690	0.0		0.0	False		,,,				2504	0.0				p.I1635I		Atlas-SNP	.											.	SCN4A	205	.	0			c.C4905T						PASS	.	G		190,4046		4,182,1932	52.0	59.0	56.0		4905	-3.4	0.9	17	dbSNP_129	56	1,8481		0,1,4240	no	coding-synonymous	SCN4A	NM_000334.4		4,183,6172	AA,AG,GG		0.0118,4.4854,1.5018		1635/1837	62018737	191,12527	2118	4241	6359	SO:0001819	synonymous_variant	6329	exon24			GTAGGCGATGAAC	U24693		17q23.3	2012-02-26	2007-01-23					"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.4905C>T	17.37:g.62018737G>A		186.0	0.0	0		228.0	101.0	0.442982	NM_000334	Q15478|Q16447|Q7Z6B1	Silent	SNP	ENST00000435607.1	37	CCDS45761.1																																																																																			G|0.983;A|0.017	0.017	strong		0.567	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334	
CEP89	84902	hgsc.bcm.edu	37	19	33450806	33450806	+	Splice_Site	SNP	C	C	T	rs73926195	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33450806C>T	ENST00000305768.5	-	3	393	c.305G>A	c.(304-306)cGg>cAg	p.R102Q	CEP89_ENST00000590597.2_Splice_Site_p.R102Q	NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	102					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)		p.R102L(1)|p.R102Q(1)		breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						TGGTACCTACCGAGGCCTCAG	0.587													C|||	266	0.053115	0.1921	0.0173	5008	,	,		20668	0.0		0.0	False		,,,				2504	0.0				p.R102Q		Atlas-SNP	.											CEP89,colon,carcinoma,-1,4	CEP89	82	4	2	Substitution - Missense(2)	ovary(1)|prostate(1)	c.G305A						PASS	.	C	GLN/ARG	699,3707	291.5+/-281.6	54,591,1558	94.0	75.0	81.0		305	2.0	0.8	19	dbSNP_130	81	5,8595	3.7+/-12.6	0,5,4295	yes	missense-near-splice	CEP89	NM_032816.3	43	54,596,5853	TT,TC,CC		0.0581,15.8647,5.4129	benign	102/784	33450806	704,12302	2203	4300	6503	SO:0001630	splice_region_variant	84902	exon3			ACCTACCGAGGCC	AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"""coiled-coil domain containing 123"""	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.305+1G>A	19.37:g.33450806C>T		131.0	0.0	0		144.0	73.0	0.506944	NM_032816	B9EGA6|Q8N5J8	Missense_Mutation	SNP	ENST00000305768.5	37	CCDS32987.1	83	0.038003663003663	75	0.1524390243902439	8	0.022099447513812154	0	0.0	0	0.0	C	8.786	0.929433	0.18131	0.158647	5.81E-4	ENSG00000121289	ENST00000305768	T	0.30182	1.54	5.48	2.01	0.26516	.	0.317619	0.28382	N	0.015556	T	0.00039	0.0001	N	0.04203	-0.255	0.31021	P	0.718148	B;B	0.25235	0.017;0.121	B;B	0.14023	0.008;0.01	T	0.33929	-0.9849	8	.	.	.	-1.7133	10.2426	0.43321	0.0:0.7433:0.0:0.2567	.	102;102	Q96ST8-3;Q96ST8	.;CEP89_HUMAN	Q	102	ENSP00000306105:R102Q	.	R	-	2	0	CEP89	38142646	0.975000	0.34042	0.770000	0.31555	0.026000	0.11368	0.915000	0.28638	0.162000	0.19483	0.655000	0.94253	CGG	C|0.944;T|0.056	0.056	strong		0.587	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816	Missense_Mutation
SOX30	11063	hgsc.bcm.edu	37	5	157053365	157053365	+	Missense_Mutation	SNP	C	C	T	rs889057	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:157053365C>T	ENST00000265007.6	-	5	2586	c.2245G>A	c.(2245-2247)Gtg>Atg	p.V749M	SOX30_ENST00000519442.1_Missense_Mutation_p.V444M|SOX30_ENST00000311371.5_3'UTR	NM_178424.1	NP_848511.1	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30	749			V -> M (in dbSNP:rs889057).		regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to corticosteroid (GO:0031960)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	23	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			TCCCTGAGCACTTTTTCTTCT	0.373													C|||	5	0.000998403	0.0038	0.0	5008	,	,		17935	0.0		0.0	False		,,,				2504	0.0				p.V749M	Esophageal Squamous(31;525 799 19355 21125 41744)	Atlas-SNP	.											.	SOX30	67	.	0			c.G2245A						PASS	.	C	,MET/VAL	17,4389	11.4+/-27.6	0,17,2186	57.0	61.0	60.0		,2245	5.4	1.0	5	dbSNP_86	60	0,8600		0,0,4300	yes	utr-3,missense	SOX30	NM_007017.2,NM_178424.1	,21	0,17,6486	TT,TC,CC		0.0,0.3858,0.1307	,probably-damaging	,749/754	157053365	17,12989	2203	4300	6503	SO:0001583	missense	11063	exon5			TGAGCACTTTTTC	AB022083	CCDS4339.1, CCDS4340.1	5q33	2010-10-21			ENSG00000039600	ENSG00000039600		"""SRY (sex determining region Y)-boxes"""	30635	protein-coding gene	gene with protein product		606698				15019997, 11678506	Standard	NM_178424		Approved		uc003lxb.1	O94993	OTTHUMG00000130247	ENST00000265007.6:c.2245G>A	5.37:g.157053365C>T	ENSP00000265007:p.Val749Met	97.0	0.0	0		78.0	38.0	0.487179	NM_178424	O94995|Q8IYX6	Missense_Mutation	SNP	ENST00000265007.6	37	CCDS4339.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	17.31	3.357836	0.61403	0.003858	0.0	ENSG00000039600	ENST00000265007;ENST00000519442	D;D	0.98567	-4.82;-5.0	5.44	5.44	0.79542	.	0.000000	0.52532	D	0.000071	D	0.97676	0.9238	L	0.27053	0.805	0.37021	D	0.89618	D;D	0.76494	0.998;0.999	D;D	0.68765	0.915;0.96	D	0.99894	1.1141	10	0.87932	D	0	.	14.3095	0.66407	0.1478:0.8522:0.0:0.0	rs889057;rs52805214;rs889057	444;749	B4DXW7;O94993	.;SOX30_HUMAN	M	749;444	ENSP00000265007:V749M;ENSP00000427984:V444M	ENSP00000265007:V749M	V	-	1	0	SOX30	156985943	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.502000	0.53332	2.712000	0.92718	0.650000	0.86243	GTG	C|0.998;T|0.002	0.002	strong		0.373	SOX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252571.2	NM_007017	
MACF1	23499	hgsc.bcm.edu	37	1	39907949	39907949	+	Missense_Mutation	SNP	A	A	G	rs682351	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:39907949A>G	ENST00000372915.3	+	75	18689	c.18602A>G	c.(18601-18603)aAa>aGa	p.K6201R	MACF1_ENST00000564288.1_Missense_Mutation_p.K6302R|MACF1_ENST00000545844.1_Missense_Mutation_p.K4243R|MACF1_ENST00000539005.1_Missense_Mutation_p.K4113R|MACF1_ENST00000317713.7_Missense_Mutation_p.K4243R|MACF1_ENST00000289893.4_Missense_Mutation_p.K4745R|MACF1_ENST00000361689.2_Missense_Mutation_p.K4243R|MACF1_ENST00000567887.1_Missense_Mutation_p.K6339R			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	6201			K -> R (in dbSNP:rs682351).		ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			ACAGAACTCAAACACCTCTGG	0.453													A|||	60	0.0119808	0.0431	0.0043	5008	,	,		19820	0.0		0.0	False		,,,				2504	0.0				p.K4243R		Atlas-SNP	.											.	MACF1	909	.	0			c.A12728G						PASS	.	A	ARG/LYS,ARG/LYS	177,4229	114.6+/-152.6	3,171,2029	54.0	55.0	54.0		14234,12728	6.0	1.0	1	dbSNP_83	54	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense	MACF1	NM_033044.3,NM_012090.4	26,26	3,174,6326	GG,GA,AA		0.0349,4.0172,1.384	benign,benign	4745/5939,4243/5431	39907949	180,12826	2203	4300	6503	SO:0001583	missense	23499	exon73			AACTCAAACACCT	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"""EF-hand domain containing"""	13664	protein-coding gene	gene with protein product	"""actin cross-linking factor"", ""620 kDa actin binding protein"", ""macrophin 1"", ""trabeculin-alpha"", ""actin cross-linking family protein 7"""	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.18602A>G	1.37:g.39907949A>G	ENSP00000362006:p.Lys6201Arg	72.0	0.0	0		68.0	34.0	0.5	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	A	14.28	2.488881	0.44249	0.040172	3.49E-4	ENSG00000127603	ENST00000545844;ENST00000372915;ENST00000361689;ENST00000317713;ENST00000539005;ENST00000289893	T;T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82;0.82	6.03	6.03	0.97812	.	0.000000	0.64402	D	0.000002	T	0.06781	0.0173	N	0.12637	0.245	0.80722	D	1	B;B	0.31413	0.003;0.322	B;B	0.33454	0.014;0.164	T	0.04128	-1.0975	10	0.38643	T	0.18	.	16.5582	0.84512	1.0:0.0:0.0:0.0	rs682351;rs52811310;rs682351	6201;4243	Q9UPN3;F8W8Q1	MACF1_HUMAN;.	R	4243;6201;4243;4243;4113;4745	ENSP00000439537:K4243R;ENSP00000362006:K6201R;ENSP00000354573:K4243R;ENSP00000313438:K4243R;ENSP00000444364:K4113R;ENSP00000289893:K4745R	ENSP00000289893:K4745R	K	+	2	0	MACF1	39680536	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.094000	0.57721	2.308000	0.77769	0.533000	0.62120	AAA	A|0.986;G|0.014	0.014	strong		0.453	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
APBA3	9546	hgsc.bcm.edu	37	19	3759802	3759802	+	Missense_Mutation	SNP	C	C	A	rs35932323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3759802C>A	ENST00000316757.3	-	2	661	c.461G>T	c.(460-462)tGg>tTg	p.W154L	MRPL54_ENST00000330133.4_5'Flank	NM_004886.3	NP_004877.1	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 3	154			W -> L (in dbSNP:rs35932323).		in utero embryonic development (GO:0001701)|negative regulation of catalytic activity (GO:0043086)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	perinuclear region of cytoplasm (GO:0048471)	beta-amyloid binding (GO:0001540)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)			endometrium(1)|large_intestine(1)|skin(1)	3		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00467)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCCTCCACCCATTCTGGGGA	0.637													C|||	145	0.0289537	0.1067	0.0058	5008	,	,		15097	0.0		0.0	False		,,,				2504	0.0				p.W154L		Atlas-SNP	.											.	APBA3	28	.	0			c.G461T						PASS	.	C	LEU/TRP	361,4039		17,327,1856	22.0	26.0	25.0		461	2.4	0.2	19	dbSNP_126	25	4,8580		0,4,4288	yes	missense	APBA3	NM_004886.3	61	17,331,6144	AA,AC,CC		0.0466,8.2045,2.8112	possibly-damaging	154/576	3759802	365,12619	2200	4292	6492	SO:0001583	missense	9546	exon2			TCCACCCATTCTG	AB021638	CCDS12110.1	19p13.3	2008-07-18	2008-07-18			ENSG00000011132			580	protein-coding gene	gene with protein product	"""X11-like 2"""	604262				10049767	Standard	NM_004886		Approved	X11L2, mint3	uc002lyp.1	O96018		ENST00000316757.3:c.461G>T	19.37:g.3759802C>A	ENSP00000315136:p.Trp154Leu	71.0	0.0	0		59.0	32.0	0.542373	NM_004886	O60483|Q9UPZ2	Missense_Mutation	SNP	ENST00000316757.3	37	CCDS12110.1	53	0.024267399267399268	50	0.1016260162601626	3	0.008287292817679558	0	0.0	0	0.0	C	8.915	0.959726	0.18507	0.082045	4.66E-4	ENSG00000011132	ENST00000316757	T	0.06849	3.25	4.67	2.42	0.29668	.	0.166985	0.29040	N	0.013333	T	0.00178	0.0005	L	0.27053	0.805	0.22213	N	0.999285	B	0.22003	0.063	B	0.19666	0.026	T	0.45906	-0.9229	10	0.22109	T	0.4	.	6.1778	0.20453	0.1873:0.7142:0.0:0.0985	rs35932323	154	O96018	APBA3_HUMAN	L	154	ENSP00000315136:W154L	ENSP00000315136:W154L	W	-	2	0	APBA3	3710802	0.002000	0.14202	0.211000	0.23655	0.049000	0.14656	0.219000	0.17641	1.041000	0.40125	0.561000	0.74099	TGG	C|0.975;A|0.025	0.025	strong		0.637	APBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453634.2		
HRC	3270	hgsc.bcm.edu	37	19	49657754	49657754	+	Silent	SNP	G	G	A	rs567490515	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49657754G>A	ENST00000252825.4	-	1	927	c.741C>T	c.(739-741)gaC>gaT	p.D247D	HRC_ENST00000595625.1_Silent_p.D247D	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	247	4 X tandem repeats, acidic.|6 X approximate tandem repeats.|Asp-rich (acidic).				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		catcatcatcgtcatcttctt	0.507													G|||	238	0.047524	0.053	0.0476	5008	,	,		25432	0.0169		0.0417	False		,,,				2504	0.0777				p.D247D	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											.	HRC	85	.	0			c.C741T						PASS	.						127.0	92.0	104.0					19																	49657754		2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			ATCATCGTCATCT		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"""histidine-rich calcium-binding protein"""			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.741C>T	19.37:g.49657754G>A		117.0	0.0	0		136.0	6.0	0.0441176	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	37	CCDS12759.1																																																																																			.	.	none		0.507	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152	
CD180	4064	hgsc.bcm.edu	37	5	66479383	66479383	+	Missense_Mutation	SNP	T	T	C	rs2230523	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:66479383T>C	ENST00000256447.4	-	3	1445	c.1288A>G	c.(1288-1290)Acc>Gcc	p.T430A	CTD-2306M10.1_ENST00000602471.1_lincRNA	NM_005582.2	NP_005573.2	Q99467	CD180_HUMAN	CD180 molecule	430			T -> A (in dbSNP:rs2230523).		B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(2)|kidney(7)|large_intestine(12)|liver(1)|lung(8)|ovary(1)|stomach(2)	34		Lung NSC(167;4.94e-05)|Prostate(74;0.00601)|Ovarian(174;0.0654)|Breast(144;0.198)|Colorectal(97;0.234)		Lung(70;0.0046)		TGTAAGCGGGTAAATGCCAAA	0.458													T|||	93	0.0185703	0.0681	0.0043	5008	,	,		21421	0.0		0.0	False		,,,				2504	0.0				p.T430A		Atlas-SNP	.											CD180,NS,carcinoma,+1,2	CD180	78	2	0			c.A1288G						PASS	.	T	ALA/THR	254,4152	146.1+/-180.8	17,220,1966	175.0	181.0	179.0		1288	4.8	0.6	5	dbSNP_98	179	1,8599	1.2+/-3.3	0,1,4299	yes	missense	CD180	NM_005582.2	58	17,221,6265	CC,CT,TT		0.0116,5.7649,1.9606	probably-damaging	430/662	66479383	255,12751	2203	4300	6503	SO:0001583	missense	4064	exon3			AGCGGGTAAATGC	D83597	CCDS3992.1	5q12	2008-02-05	2006-03-28	2005-06-07	ENSG00000134061	ENSG00000134061		"""CD molecules"""	6726	protein-coding gene	gene with protein product		602226	"""lymphocyte antigen 64 (mouse) homolog, radioprotective, 105kD"", ""CD180 antigen"""	LY64		9763566, 8975706	Standard	NM_005582		Approved	RP105, Ly78	uc003juy.2	Q99467	OTTHUMG00000131229	ENST00000256447.4:c.1288A>G	5.37:g.66479383T>C	ENSP00000256447:p.Thr430Ala	174.0	0.0	0		146.0	66.0	0.452055	NM_005582	B2R7Z7|Q32MM5	Missense_Mutation	SNP	ENST00000256447.4	37	CCDS3992.1	20	0.009157509157509158	18	0.036585365853658534	2	0.0055248618784530384	0	0.0	0	0.0	T	12.29	1.894010	0.33442	0.057649	1.16E-4	ENSG00000134061	ENST00000256447	T	0.58060	0.36	4.81	4.81	0.61882	.	0.083576	0.50627	D	0.000118	T	0.14270	0.0345	M	0.83223	2.63	0.47441	D	0.99942	D	0.55605	0.972	P	0.46026	0.501	T	0.42599	-0.9442	10	0.33141	T	0.24	.	13.091	0.59167	0.0:0.0:0.0:1.0	rs2230523;rs52799097;rs2230523	430	Q99467	CD180_HUMAN	A	430	ENSP00000256447:T430A	ENSP00000256447:T430A	T	-	1	0	CD180	66515139	0.998000	0.40836	0.627000	0.29227	0.064000	0.16182	2.658000	0.46733	2.020000	0.59435	0.460000	0.39030	ACC	T|0.978;C|0.022	0.022	strong		0.458	CD180-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253973.2	NM_005582	
TNPO2	30000	hgsc.bcm.edu	37	19	12816559	12816559	+	Silent	SNP	G	G	T	rs7248726	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12816559G>T	ENST00000592287.1	-	15	1800	c.1692C>A	c.(1690-1692)ccC>ccA	p.P564P	TNPO2_ENST00000588216.1_Silent_p.P564P|TNPO2_ENST00000425528.1_Silent_p.P564P|TNPO2_ENST00000441499.1_Silent_p.P564P|TNPO2_ENST00000356861.5_Silent_p.P564P|SNORD41_ENST00000386967.1_RNA|TNPO2_ENST00000450764.2_Silent_p.P564P	NM_001136196.1	NP_001129668.1	O14787	TNPO2_HUMAN	transportin 2	564					intracellular protein transport (GO:0006886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						GGATCAGTGGGGGCATCAGCT	0.597													G|||	739	0.147564	0.5272	0.0461	5008	,	,		18127	0.0		0.0099	False		,,,				2504	0.0				p.P564P		Atlas-SNP	.											.	TNPO2	108	.	0			c.C1692A						PASS	.	G	,,	1656,2570		326,1004,783	32.0	32.0	32.0		1692,1692,1692	-10.9	0.2	19	dbSNP_116	32	119,8253		2,115,4069	no	coding-synonymous,coding-synonymous,coding-synonymous	TNPO2	NM_001136195.1,NM_001136196.1,NM_013433.4	,,	328,1119,4852	TT,TG,GG		1.4214,39.186,14.0895	,,	564/888,564/898,564/888	12816559	1775,10823	2113	4186	6299	SO:0001819	synonymous_variant	30000	exon15			CAGTGGGGGCATC	AF019039	CCDS45991.1, CCDS45992.1	19p13.13	2009-01-12	2009-01-12			ENSG00000105576		"""Importins"""	19998	protein-coding gene	gene with protein product	"""importin 3"", ""karyopherin beta 2b"""	603002				9298975, 12384575	Standard	NM_013433		Approved	IPO3, KPNB2B, FLJ12155, TRN2	uc002muo.3	O14787		ENST00000592287.1:c.1692C>A	19.37:g.12816559G>T		127.0	0.0	0		149.0	78.0	0.52349	NM_013433	O14655|Q6IN77	Silent	SNP	ENST00000592287.1	37	CCDS45991.1																																																																																			G|0.849;T|0.151	0.151	strong		0.597	TNPO2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450785.1	NM_013433	
KIRREL2	84063	hgsc.bcm.edu	37	19	36351545	36351545	+	Missense_Mutation	SNP	C	C	A	rs73928337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36351545C>A	ENST00000360202.5	+	7	1102	c.904C>A	c.(904-906)Cgc>Agc	p.R302S	KIRREL2_ENST00000592409.1_Missense_Mutation_p.R302S|KIRREL2_ENST00000262625.7_Missense_Mutation_p.R302S|NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000347900.6_Missense_Mutation_p.R252S	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	302	Ig-like C2-type 3.				cell adhesion (GO:0007155)|negative regulation of protein phosphorylation (GO:0001933)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)				breast(2)|central_nervous_system(1)|endometrium(6)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	48	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TAGCGCCAACCGCAGTACTGC	0.677													C|||	35	0.00698882	0.0242	0.0043	5008	,	,		16057	0.0		0.0	False		,,,				2504	0.0				p.R302S		Atlas-SNP	.											KIRREL2_ENST00000262625,NS,carcinoma,-1,2	KIRREL2	170	2	0			c.C904A						PASS	.	C	SER/ARG,SER/ARG,SER/ARG	87,4319	72.0+/-110.0	0,87,2116	63.0	69.0	67.0		904,754,904	4.0	1.0	19	dbSNP_130	67	0,8600		0,0,4300	yes	missense,missense,missense	KIRREL2	NM_032123.5,NM_199179.2,NM_199180.2	110,110,110	0,87,6416	AA,AC,CC		0.0,1.9746,0.6689	probably-damaging,probably-damaging,probably-damaging	302/634,252/584,302/709	36351545	87,12919	2203	4300	6503	SO:0001583	missense	84063	exon7			GCCAACCGCAGTA	AL136654	CCDS12479.1, CCDS12480.1, CCDS12481.1	19q13.13	2013-01-29				ENSG00000126259		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18816	protein-coding gene	gene with protein product		607762				12837264, 12504092	Standard	NM_199180		Approved	NLG1, NEPH3, FILTRIN, DKFZp564A1164, MGC15718	uc002ocb.4	Q6UWL6		ENST00000360202.5:c.904C>A	19.37:g.36351545C>A	ENSP00000353331:p.Arg302Ser	107.0	0.0	0		109.0	50.0	0.458716	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Missense_Mutation	SNP	ENST00000360202.5	37	CCDS12481.1	12	0.005494505494505495	8	0.016260162601626018	4	0.011049723756906077	0	0.0	0	0.0	c	21.8	4.203992	0.79127	0.019746	0.0	ENSG00000126259	ENST00000262625;ENST00000347900;ENST00000360202;ENST00000341658	T;T;T	0.14766	2.48;2.48;2.48	3.99	3.99	0.46301	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.42053	D	0.000769	T	0.10766	0.0263	N	0.22421	0.69	0.37484	D	0.916104	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.998;0.998	D;D;D;D;D	0.85130	0.993;0.988;0.997;0.994;0.994	T	0.04191	-1.0970	10	0.35671	T	0.21	-18.2581	11.8642	0.52484	0.0:1.0:0.0:0.0	.	302;282;302;252;302	F1T0I2;Q6UWL6-4;Q6UWL6;Q6UWL6-3;Q6UWL6-2	.;.;KIRR2_HUMAN;.;.	S	302;252;302;282	ENSP00000262625:R302S;ENSP00000345067:R252S;ENSP00000353331:R302S	ENSP00000262625:R302S	R	+	1	0	KIRREL2	41043385	1.000000	0.71417	1.000000	0.80357	0.852000	0.48524	2.485000	0.45250	2.257000	0.74773	0.444000	0.29173	CGC	C|0.994;A|0.006	0.006	strong		0.677	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123	
CLUAP1	23059	hgsc.bcm.edu	37	16	3554799	3554799	+	Silent	SNP	T	T	C	rs34672214	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3554799T>C	ENST00000576634.1	+	2	246	c.102T>C	c.(100-102)ctT>ctC	p.L34L	CLUAP1_ENST00000571025.1_Silent_p.L34L|CLUAP1_ENST00000341633.5_Silent_p.L34L|CLUAP1_ENST00000417763.2_5'UTR|LA16c-306E5.3_ENST00000574423.2_RNA	NM_015041.2	NP_055856.1	Q96AJ1	CLUA1_HUMAN	clusterin associated protein 1	34					cilium assembly (GO:0042384)	centrosome (GO:0005813)|cilium (GO:0005929)|intracellular membrane-bounded organelle (GO:0043231)|intraciliary transport particle B (GO:0030992)|nucleus (GO:0005634)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(2)	16						ATTTTGGACTTGTATCTGAAG	0.383													T|||	283	0.0565096	0.115	0.0331	5008	,	,		19316	0.0556		0.0159	False		,,,				2504	0.0368				p.L34L		Atlas-SNP	.											.	CLUAP1	32	.	0			c.T102C						PASS	.	T		427,3967	207.5+/-228.8	19,389,1789	111.0	109.0	110.0		102	3.1	1.0	16	dbSNP_126	110	138,8462	69.0+/-131.5	0,138,4162	no	coding-synonymous	CLUAP1	NM_015041.1		19,527,5951	CC,CT,TT		1.6047,9.7178,4.3482		34/414	3554799	565,12429	2197	4300	6497	SO:0001819	synonymous_variant	23059	exon2			TGGACTTGTATCT	BC017070	CCDS32381.1, CCDS45398.1	16p13.3	2014-07-18				ENSG00000103351		"""Intraflagellar transport homologs"""	19009	protein-coding gene	gene with protein product	"""flagellar associated protein 22, qilin-like protein, homolog (Chlamydomonas)"", ""cilia and flagella associated protein 22"""					15480429, 9734811, 19253336	Standard	NM_015041		Approved	FLJ13297, KIAA0643, FAP22, CFAP22	uc002cvk.2	Q96AJ1		ENST00000576634.1:c.102T>C	16.37:g.3554799T>C		243.0	0.0	0		192.0	84.0	0.4375	NM_015041	O75138|Q65ZA3|Q9H8R4|Q9H8T1	Silent	SNP	ENST00000576634.1	37	CCDS32381.1																																																																																			T|0.955;C|0.045	0.045	strong		0.383	CLUAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437883.2	NM_024793	
SPEM1	374768	hgsc.bcm.edu	37	17	7324588	7324588	+	Silent	SNP	G	G	A	rs78583740	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7324588G>A	ENST00000323675.3	+	3	619	c.594G>A	c.(592-594)ctG>ctA	p.L198L	RP11-104H15.7_ENST00000575310.1_RNA	NM_199339.2	NP_955371.2	Q8N4L4	SPEM1_HUMAN	spermatid maturation 1	198					sperm individualization (GO:0007291)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	12		Prostate(122;0.173)				GGTCCGAGCTGGGCCTAAGGG	0.632													G|||	241	0.048123	0.1762	0.0115	5008	,	,		17257	0.0		0.0	False		,,,				2504	0.0				p.L198L		Atlas-SNP	.											.	SPEM1	41	.	0			c.G594A						PASS	.	G		512,3372		36,440,1466	50.0	55.0	53.0		594	4.8	0.5	17	dbSNP_132	53	3,8221		0,3,4109	no	coding-synonymous	SPEM1	NM_199339.2		36,443,5575	AA,AG,GG		0.0365,13.1823,4.2534		198/310	7324588	515,11593	1942	4112	6054	SO:0001819	synonymous_variant	374768	exon3			CGAGCTGGGCCTA	AK097400	CCDS42254.1	17p13.1	2011-12-12	2008-02-04	2008-02-04	ENSG00000181323	ENSG00000181323			32429	protein-coding gene	gene with protein product		615116	"""chromosome 17 open reading frame 83"""	C17orf83		17426145, 20558241, 21184802	Standard	NM_199339		Approved	FLJ40081	uc002ggv.3	Q8N4L4		ENST00000323675.3:c.594G>A	17.37:g.7324588G>A		70.0	0.0	0		98.0	52.0	0.530612	NM_199339		Silent	SNP	ENST00000323675.3	37	CCDS42254.1																																																																																			G|0.961;A|0.039	0.039	strong		0.632	SPEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440932.1	NM_199339	
DUSP27	92235	hgsc.bcm.edu	37	1	167096770	167096770	+	Missense_Mutation	SNP	G	G	C	rs371850525		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:167096770G>C	ENST00000361200.2	+	6	2568	c.2402G>C	c.(2401-2403)tGc>tCc	p.C801S	DUSP27_ENST00000443333.1_Missense_Mutation_p.C801S|DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000271385.5_Missense_Mutation_p.C801S			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	801					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						GTGCTGTCCTGCAACACCACA	0.567																																					p.C801S		Atlas-SNP	.											.	DUSP27	235	.	0			c.G2402C						PASS	.	G	SER/CYS	1,4405	2.1+/-5.4	0,1,2202	83.0	74.0	77.0		2402	3.2	0.9	1		77	0,8600		0,0,4300	no	missense	DUSP27	NM_001080426.1	112	0,1,6502	CC,CG,GG		0.0,0.0227,0.0077	benign	801/1159	167096770	1,13005	2203	4300	6503	SO:0001583	missense	92235	exon5			TGTCCTGCAACAC	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.2402G>C	1.37:g.167096770G>C	ENSP00000354483:p.Cys801Ser	96.0	0.0	0		94.0	41.0	0.43617	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	37	CCDS30932.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.752901	0.00085	2.27E-4	0.0	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.03035	4.07;4.07;4.07	5.17	3.24	0.37175	.	1.061880	0.07353	N	0.882768	T	0.00412	0.0013	N	0.01352	-0.895	0.18873	N	0.999988	B	0.02656	0.0	B	0.04013	0.001	T	0.33033	-0.9884	10	0.05721	T	0.95	-3.5335	9.1613	0.37023	0.1176:0.3669:0.5156:0.0	.	801	Q5VZP5	DUS27_HUMAN	S	801	ENSP00000354483:C801S;ENSP00000271385:C801S;ENSP00000404874:C801S	ENSP00000271385:C801S	C	+	2	0	DUSP27	165363394	0.260000	0.24053	0.904000	0.35570	0.039000	0.13416	0.246000	0.18160	1.143000	0.42306	-0.371000	0.07208	TGC	.	.	none		0.567	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426	
SEC14L5	9717	hgsc.bcm.edu	37	16	5061191	5061191	+	Silent	SNP	C	C	T	rs8055468	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:5061191C>T	ENST00000251170.7	+	15	2076	c.1896C>T	c.(1894-1896)gaC>gaT	p.D632D	RP11-165E7.1_ENST00000588778.1_RNA	NM_014692.1	NP_055507.1	O43304	S14L5_HUMAN	SEC14-like 5 (S. cerevisiae)	632	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	transporter activity (GO:0005215)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|skin(1)	29						CGGGTGTGGACGATGTCCTGA	0.652													C|||	159	0.0317492	0.1135	0.0115	5008	,	,		16324	0.001		0.0	False		,,,				2504	0.0				p.D632D		Atlas-SNP	.											.	SEC14L5	79	.	0			c.C1896T						PASS	.	C		368,3642		19,330,1656	25.0	29.0	28.0		1896	-5.6	0.0	16	dbSNP_116	28	7,8319		0,7,4156	no	coding-synonymous	SEC14L5	NM_014692.1		19,337,5812	TT,TC,CC		0.0841,9.1771,3.0399		632/697	5061191	375,11961	2005	4163	6168	SO:0001819	synonymous_variant	9717	exon15			TGTGGACGATGTC	AB007880	CCDS45403.1	16p13.3	2008-02-05				ENSG00000103184			29032	protein-coding gene	gene with protein product						9455477	Standard	NM_014692		Approved	KIAA0420, PRELID4B	uc002cye.2	O43304		ENST00000251170.7:c.1896C>T	16.37:g.5061191C>T		140.0	0.0	0		146.0	69.0	0.472603	NM_014692		Silent	SNP	ENST00000251170.7	37	CCDS45403.1																																																																																			C|0.968;T|0.032	0.032	strong		0.652	SEC14L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434379.1		
KIF1C	10749	hgsc.bcm.edu	37	17	4925674	4925674	+	Silent	SNP	C	C	T	rs73345356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4925674C>T	ENST00000320785.5	+	22	2655	c.2298C>T	c.(2296-2298)caC>caT	p.H766H	AC109333.10_ENST00000438266.1_RNA	NM_006612.5	NP_006603.2	O43896	KIF1C_HUMAN	kinesin family member 1C	766					ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|skin(1)|urinary_tract(3)	30						ACTTCCGCCACGGGCGGGCTG	0.677													C|||	167	0.0333466	0.1188	0.0115	5008	,	,		17324	0.0		0.002	False		,,,				2504	0.0				p.H766H	Melanoma(96;1023 1447 10250 19259 33730)	Atlas-SNP	.											KIF1C,colon,carcinoma,0,1	KIF1C	70	1	0			c.C2298T						PASS	.	C		432,3962		26,380,1791	19.0	18.0	19.0		2298	-1.4	1.0	17	dbSNP_130	19	16,8566		0,16,4275	no	coding-synonymous	KIF1C	NM_006612.5		26,396,6066	TT,TC,CC		0.1864,9.8316,3.4525		766/1104	4925674	448,12528	2197	4291	6488	SO:0001819	synonymous_variant	10749	exon22			CCGCCACGGGCGG	U91329	CCDS11065.1	17p13.2	2014-03-03			ENSG00000129250	ENSG00000129250		"""Kinesins"""	6317	protein-coding gene	gene with protein product		603060	"""spastic ataxia 2 (autosomal recessive)"""	SAX2		9685376, 24319291, 24482476	Standard	NM_006612		Approved	SPAX2, SPG58	uc002gan.2	O43896	OTTHUMG00000099451	ENST00000320785.5:c.2298C>T	17.37:g.4925674C>T		94.0	0.0	0		80.0	42.0	0.525	NM_006612	D3DTL6|O75186|Q5U618	Silent	SNP	ENST00000320785.5	37	CCDS11065.1																																																																																			C|0.964;T|0.036	0.036	strong		0.677	KIF1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216916.1		
CCDC88C	440193	hgsc.bcm.edu	37	14	91805804	91805804	+	Silent	SNP	C	C	T	rs61220159	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:91805804C>T	ENST00000389857.6	-	8	713	c.627G>A	c.(625-627)ctG>ctA	p.L209L		NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	209					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				GGTCCACGATCAGCTGCAGCC	0.602													C|||	166	0.033147	0.1188	0.013	5008	,	,		17173	0.0		0.0	False		,,,				2504	0.0				p.L209L		Atlas-SNP	.											.	CCDC88C	192	.	0			c.G627A						PASS	.	C		438,3852		17,404,1724	41.0	50.0	47.0		627	-0.9	1.0	14	dbSNP_129	47	4,8512		0,4,4254	yes	coding-synonymous	CCDC88C	NM_001080414.3		17,408,5978	TT,TC,CC		0.047,10.2098,3.4515		209/2029	91805804	442,12364	2145	4258	6403	SO:0001819	synonymous_variant	440193	exon8			CACGATCAGCTGC		CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"""Dvl-associating protein with a high frequency of leucine residues"", ""spinocerebellar ataxia 40"""	611204	"""KIAA1509"""	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.627G>A	14.37:g.91805804C>T		193.0	0.0	0		230.0	124.0	0.53913	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Silent	SNP	ENST00000389857.6	37	CCDS45151.1																																																																																			C|0.968;T|0.032	0.032	strong		0.602	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353	
CDNF	441549	hgsc.bcm.edu	37	10	14862140	14862140	+	Missense_Mutation	SNP	C	C	A	rs61740068	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:14862140C>A	ENST00000378442.1	-	6	600	c.97G>T	c.(97-99)Gca>Tca	p.A33S	CDNF_ENST00000378441.2_5'UTR			Q49AH0	CDNF_HUMAN	cerebral dopamine neurotrophic factor	135						extracellular region (GO:0005576)				breast(2)|large_intestine(2)|lung(1)	5						TCAACTGATGCCAAGTCCAGT	0.418													C|||	76	0.0151757	0.0522	0.0072	5008	,	,		19434	0.0		0.0	False		,,,				2504	0.002				p.A135S		Atlas-SNP	.											.	CDNF	19	.	0			c.G403T						PASS	.	C	SER/ALA	205,4201	127.4+/-164.3	3,199,2001	96.0	98.0	97.0		403	5.9	1.0	10	dbSNP_129	97	0,8600		0,0,4300	yes	missense	CDNF	NM_001029954.2	99	3,199,6301	AA,AC,CC		0.0,4.6527,1.5762	benign	135/188	14862140	205,12801	2203	4300	6503	SO:0001583	missense	441549	exon4			CTGATGCCAAGTC	BC037872	CCDS31148.1	10p13	2009-06-04	2009-06-04	2009-06-04	ENSG00000185267	ENSG00000185267			24913	protein-coding gene	gene with protein product	"""conserved dopamine neurotrophic factor"""	611233	"""arginine-rich, mutated in early stage tumors-like 1"""	ARMETL1		17611540	Standard	NM_001029954		Approved		uc001inb.1	Q49AH0	OTTHUMG00000017713	ENST00000378442.1:c.97G>T	10.37:g.14862140C>A	ENSP00000367703:p.Ala33Ser	166.0	0.0	0		128.0	60.0	0.46875	NM_001029954	A2RUU0|B4DVW3	Missense_Mutation	SNP	ENST00000378442.1	37		27	0.012362637362637362	24	0.04878048780487805	3	0.008287292817679558	0	0.0	0	0.0	C	3.967	-0.009097	0.07727	0.046527	0.0	ENSG00000185267	ENST00000378442;ENST00000465530	.	.	.	5.9	5.9	0.94986	.	0.284770	0.36519	N	0.002549	T	0.03783	0.0107	N	0.04994	-0.135	0.34379	D	0.692882	B	0.22983	0.078	B	0.21360	0.034	T	0.09185	-1.0686	9	0.02654	T	1	-13.8964	13.0686	0.59048	0.0:0.9231:0.0:0.0769	.	135	Q49AH0	CDNF_HUMAN	S	33;135	.	ENSP00000367703:A33S	A	-	1	0	CDNF	14902146	1.000000	0.71417	0.997000	0.53966	0.555000	0.35460	3.795000	0.55499	2.806000	0.96561	0.655000	0.94253	GCA	C|0.985;A|0.015	0.015	strong		0.418	CDNF-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000046919.1	NM_001029954	
NCOR2	9612	hgsc.bcm.edu	37	12	124841276	124841276	+	Silent	SNP	G	G	A	rs200441401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124841276G>A	ENST00000405201.1	-	23	3153	c.3153C>T	c.(3151-3153)tcC>tcT	p.S1051S	NCOR2_ENST00000397355.1_Silent_p.S1042S|NCOR2_ENST00000404621.1_Silent_p.S1041S|NCOR2_ENST00000429285.2_Silent_p.S1041S|NCOR2_ENST00000356219.3_Silent_p.S1058S|NCOR2_ENST00000404121.2_Silent_p.S612S			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1059					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|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)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		AGGGCAGGCCGGAAGTCCAGC	0.677													G|||	5	0.000998403	0.003	0.0	5008	,	,		14484	0.0		0.0	False		,,,				2504	0.001				p.S1051S		Atlas-SNP	.											.	NCOR2	475	.	0			c.C3153T						PASS	.	G	,,	10,3816		0,10,1903	12.0	17.0	15.0		3123,3123,3153	-4.4	0.3	12		15	1,8229		0,1,4114	no	coding-synonymous,coding-synonymous,coding-synonymous	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	,,	0,11,6017	AA,AG,GG		0.0122,0.2614,0.0912	,,	1041/2459,1041/2505,1051/2515	124841276	11,12045	1913	4115	6028	SO:0001819	synonymous_variant	9612	exon25			CAGGCCGGAAGTC	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"""nuclear receptor co-repressor 2"""			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.3153C>T	12.37:g.124841276G>A		182.0	0.0	0		192.0	94.0	0.489583	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Silent	SNP	ENST00000405201.1	37	CCDS41858.2																																																																																			G|1.000;A|0.000	0.000	strong		0.677	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
TLDC1	57707	hgsc.bcm.edu	37	16	84520496	84520496	+	Missense_Mutation	SNP	C	C	G	rs34244563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84520496C>G	ENST00000343629.6	-	5	881	c.699G>C	c.(697-699)gaG>gaC	p.E233D	TLDC1_ENST00000561807.1_5'Flank|TLDC1_ENST00000535580.1_Missense_Mutation_p.E206D	NM_020947.3	NP_065998.3	Q6P9B6	TLDC1_HUMAN	TBC/LysM-associated domain containing 1	233			E -> D (in dbSNP:rs34244563).			lysosomal membrane (GO:0005765)											CCACTTGACGCTCAGGGACCA	0.572													C|||	55	0.0109824	0.0401	0.0014	5008	,	,		21248	0.0		0.001	False		,,,				2504	0.0				p.E233D		Atlas-SNP	.											.	KIAA1609	39	.	0			c.G699C						PASS	.	C	ASP/GLU	128,4272	91.6+/-130.3	3,122,2075	45.0	44.0	44.0		699	5.0	0.4	16	dbSNP_126	44	3,8597	3.0+/-9.4	0,3,4297	yes	missense	KIAA1609	NM_020947.3	45	3,125,6372	GG,GC,CC		0.0349,2.9091,1.0077	possibly-damaging	233/457	84520496	131,12869	2200	4300	6500	SO:0001583	missense	57707	exon5			TTGACGCTCAGGG	AB046829	CCDS32498.1	16q24.1	2013-03-14	2013-03-14	2013-03-14	ENSG00000140950	ENSG00000140950			29325	protein-coding gene	gene with protein product	"""TLD domain containing 1"""		"""KIAA1609"""	KIAA1609		10997877	Standard	NM_020947		Approved		uc002fib.3	Q6P9B6	OTTHUMG00000176739	ENST00000343629.6:c.699G>C	16.37:g.84520496C>G	ENSP00000343635:p.Glu233Asp	149.0	0.0	0		145.0	72.0	0.496552	NM_020947	Q8IZ64|Q9HCG3|Q9NTE8	Missense_Mutation	SNP	ENST00000343629.6	37	CCDS32498.1	27	0.012362637362637362	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	9.308	1.054856	0.19907	0.029091	3.49E-4	ENSG00000140950	ENST00000343629;ENST00000535580	T;T	0.10668	3.03;2.85	4.98	4.98	0.66077	.	0.749691	0.13046	N	0.418157	T	0.01905	0.0060	M	0.67953	2.075	0.25363	N	0.988763	P;B	0.51933	0.949;0.251	B;B	0.43301	0.415;0.051	T	0.19128	-1.0315	10	0.22706	T	0.39	-28.8132	7.464	0.27312	0.0:0.725:0.1841:0.0909	rs34244563	206;233	F5GWS3;Q6P9B6	.;K1609_HUMAN	D	233;206	ENSP00000343635:E233D;ENSP00000441997:E206D	ENSP00000343635:E233D	E	-	3	2	KIAA1609	83077997	0.971000	0.33674	0.403000	0.26384	0.015000	0.08874	1.112000	0.31172	2.295000	0.77249	0.563000	0.77884	GAG	C|0.989;G|0.011	0.011	strong		0.572	TLDC1-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433421.1	NM_020947	
SVEP1	79987	hgsc.bcm.edu	37	9	113233738	113233738	+	Silent	SNP	T	T	C	rs61732942	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:113233738T>C	ENST00000401783.2	-	16	3240	c.2904A>G	c.(2902-2904)gcA>gcG	p.A968A	SVEP1_ENST00000302728.8_Silent_p.A968A|SVEP1_ENST00000467821.1_5'UTR|SVEP1_ENST00000374469.1_Silent_p.A945A	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	968					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						GTATTTCTGATGCAAGCTGAA	0.428													T|||	210	0.0419329	0.1513	0.0144	5008	,	,		16743	0.0		0.0	False		,,,				2504	0.0				p.A968A		Atlas-SNP	.											.	SVEP1	326	.	0			c.A2904G						PASS	.	T		458,3258		27,404,1427	122.0	112.0	115.0		2904	-11.0	0.2	9	dbSNP_129	115	5,8209		0,5,4102	no	coding-synonymous	SVEP1	NM_153366.3		27,409,5529	CC,CT,TT		0.0609,12.3251,3.881		968/3572	113233738	463,11467	1858	4107	5965	SO:0001819	synonymous_variant	79987	exon16			TTCTGATGCAAGC	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.2904A>G	9.37:g.113233738T>C		249.0	1.0	0.00401606		267.0	181.0	0.677903	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Silent	SNP	ENST00000401783.2	37	CCDS48004.1																																																																																			T|0.963;C|0.037	0.037	strong		0.428	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
LILRB3	11025	hgsc.bcm.edu	37	19	54720967	54720967	+	Missense_Mutation	SNP	G	G	A	rs114510580	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54720967G>A	ENST00000391750.1	-	14	2027	c.1891C>T	c.(1891-1893)Cac>Tac	p.H631Y	LILRA6_ENST00000440558.2_Missense_Mutation_p.H631Y|LILRB3_ENST00000346401.6_Missense_Mutation_p.H643Y|LILRB3_ENST00000245620.9_Missense_Mutation_p.H632Y|LILRA6_ENST00000391735.3_3'UTR|LILRA6_ENST00000419410.2_Missense_Mutation_p.H632Y|LILRB3_ENST00000469273.1_5'Flank|LILRB3_ENST00000407860.2_Missense_Mutation_p.H648Y|LILRA6_ENST00000270464.5_Missense_Mutation_p.H632Y|LILRB3_ENST00000424807.1_Missense_Mutation_p.H631Y			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	631					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)		CCGGGCTAGTGGATGGCCAGA	0.627													.|||	171	0.0341454	0.1271	0.0043	5008	,	,		17170	0.0		0.0	False		,,,				2504	0.0				p.H632Y		Atlas-SNP	.											.	LILRB3	67	.	0			c.C1894T						PASS	.	G	TYR/HIS,TYR/HIS	442,3964	213.5+/-233.1	18,406,1779	90.0	84.0	86.0		1894,1891	0.7	0.0	19	dbSNP_132	86	3,8597	3.0+/-9.4	0,3,4297	no	missense,missense	LILRB3	NM_001081450.1,NM_006864.2	83,83	18,409,6076	AA,AG,GG		0.0349,10.0318,3.4215	probably-damaging,probably-damaging	632/633,631/632	54720967	445,12561	2203	4300	6503	SO:0001583	missense	11025	exon13			GCTAGTGGATGGC	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.1891C>T	19.37:g.54720967G>A	ENSP00000375630:p.His631Tyr	280.0	0.0	0		333.0	140.0	0.42042	NM_001081450	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	60	0.027472527472527472	57	0.11585365853658537	1	0.0027624309392265192	2	0.0034965034965034965	0	0.0	G	13.16	2.154570	0.38021	0.100318	3.49E-4	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410	T;T;T;T;T;T;T;T	0.00630	6.11;6.11;6.17;6.13;6.16;6.1;6.11;6.14	2.92	0.672	0.17935	.	.	.	.	.	T	0.00039	0.0001	M	0.73598	2.24	0.09310	N	1	D;P;B;P;P;P;P	0.71674	0.998;0.644;0.226;0.956;0.791;0.721;0.849	D;B;B;P;B;B;P	0.79784	0.993;0.425;0.064;0.61;0.324;0.056;0.555	T	0.52845	-0.8521	9	0.87932	D	0	.	2.9682	0.05915	0.1554:0.0:0.5739:0.2707	.	648;631;632;643;648;631;632	B5MCX0;F8WCY4;D3YTC4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;.;LIRB3_HUMAN;.	Y	631;631;643;632;648;631;632;632	ENSP00000375630:H631Y;ENSP00000412771:H631Y;ENSP00000345184:H643Y;ENSP00000245620:H632Y;ENSP00000384274:H648Y;ENSP00000390120:H631Y;ENSP00000270464:H632Y;ENSP00000411227:H632Y	ENSP00000270464:H632Y	H	-	1	0	LILRB3;LILRA6	59412779	0.015000	0.18098	0.004000	0.12327	0.059000	0.15707	2.746000	0.47467	0.274000	0.22072	0.472000	0.43445	CAC	G|0.962;A|0.038	0.038	strong		0.627	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
MAML3	55534	hgsc.bcm.edu	37	4	140811131	140811131	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:140811131G>T	ENST00000509479.2	-	2	2315	c.1459C>A	c.(1459-1461)Caa>Aaa	p.Q487K	MAML3_ENST00000398940.1_Missense_Mutation_p.Q26K|MAML3_ENST00000327122.5_Missense_Mutation_p.Q331K	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					tgttgctgttgctgtttctgc	0.557																																					p.Q487K		Atlas-SNP	.											.	MAML3	192	.	0			c.C1459A						PASS	.						19.0	21.0	20.0					4																	140811131		2198	4294	6492	SO:0001583	missense	55534	exon2			GCTGTTGCTGTTT	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"""mastermind (drosophila)-like 3"""	608991	"""trinucleotide repeat containing 3"""	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1459C>A	4.37:g.140811131G>T	ENSP00000421180:p.Gln487Lys	74.0	0.0	0		93.0	7.0	0.0752688	NM_018717		Missense_Mutation	SNP	ENST00000509479.2	37	CCDS54805.1	.	.	.	.	.	.	.	.	.	.	G	1.344	-0.593356	0.03771	.	.	ENSG00000196782	ENST00000509479;ENST00000327122;ENST00000398940	T;T	0.66460	0.85;-0.21	4.28	4.28	0.50868	.	0.000000	0.85682	D	0.000000	T	0.40570	0.1122	N	0.08118	0	0.46499	D	0.999073	B	0.19200	0.034	B	0.18871	0.023	T	0.36359	-0.9751	10	0.02654	T	1	.	12.5248	0.56079	0.0:0.0:1.0:0.0	.	487	Q96JK9	MAML3_HUMAN	K	487;331;26	ENSP00000421180:Q487K;ENSP00000313316:Q331K	ENSP00000313316:Q331K	Q	-	1	0	MAML3	141030581	1.000000	0.71417	1.000000	0.80357	0.599000	0.36880	6.453000	0.73488	2.671000	0.90904	0.650000	0.86243	CAA	.	.	none		0.557	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2		
TBX15	6913	hgsc.bcm.edu	37	1	119427937	119427937	+	Silent	SNP	G	G	A	rs145938710	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:119427937G>A	ENST00000369429.3	-	8	1236	c.1227C>T	c.(1225-1227)gcC>gcT	p.A409A	TBX15_ENST00000207157.3_Silent_p.A303A			Q96SF7	TBX15_HUMAN	T-box 15	409					embryonic cranial skeleton morphogenesis (GO:0048701)	Tle3-Aes complex (GO:0070722)	RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(19)|ovary(1)|pancreas(1)|skin(5)	37	all_neural(166;0.117)	all_cancers(81;0.000692)|all_lung(203;3.05e-06)|Lung NSC(69;2.13e-05)|all_epithelial(167;0.000237)		Lung(183;0.044)|LUSC - Lung squamous cell carcinoma(189;0.141)		AGCTCTGCAAGGCAGCCATGT	0.542													G|||	8	0.00159744	0.0061	0.0	5008	,	,		20115	0.0		0.0	False		,,,				2504	0.0				p.A303A		Atlas-SNP	.											.	TBX15	95	.	0			c.C909T						PASS	.	G		18,4388	23.3+/-48.9	0,18,2185	47.0	45.0	46.0		909	2.3	1.0	1	dbSNP_134	46	0,8600		0,0,4300	no	coding-synonymous	TBX15	NM_152380.2		0,18,6485	AA,AG,GG		0.0,0.4085,0.1384		303/497	119427937	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	6913	exon8			CTGCAAGGCAGCC	AK127536	CCDS30816.1	1p11.1	2008-02-05	2004-10-05		ENSG00000092607	ENSG00000092607		"""T-boxes"""	11594	protein-coding gene	gene with protein product		604127	"""T-box 14"""	TBX14		9693034	Standard	XM_005271162		Approved		uc001ehl.1	Q96SF7	OTTHUMG00000012263	ENST00000369429.3:c.1227C>T	1.37:g.119427937G>A		67.0	0.0	0		70.0	36.0	0.514286	NM_152380	Q08E76|Q5JT54|Q5T9S7	Silent	SNP	ENST00000369429.3	37																																																																																				G|0.998;A|0.002	0.002	strong		0.542	TBX15-002	PUTATIVE	not_organism_supported|upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000034351.1	NM_152380	
FLG	2312	hgsc.bcm.edu	37	1	152276474	152276474	+	Missense_Mutation	SNP	G	G	A	rs76019722		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152276474G>A	ENST00000368799.1	-	3	10923	c.10888C>T	c.(10888-10890)Cac>Tac	p.H3630Y	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3630	Ser-rich.		H -> Y (in dbSNP:rs9436065).		establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GACTGCTGGTGGTGGGATCCA	0.542									Ichthyosis																												p.H3630Y		Atlas-SNP	.											.	FLG	900	.	0			c.C10888T						PASS	.	G	TYR/HIS	1203,3199		0,1203,998	203.0	163.0	176.0		10888	2.2	0.0	1	dbSNP_131	176	14,8576		0,14,4281	no	missense	FLG	NM_002016.1	83	0,1217,5279	AA,AG,GG		0.163,27.3285,9.3673	probably-damaging	3630/4062	152276474	1217,11775	2201	4295	6496	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GCTGGTGGTGGGA	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.10888C>T	1.37:g.152276474G>A	ENSP00000357789:p.His3630Tyr	367.0	0.0	0		572.0	364.0	0.636364	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	157	0.07188644688644688	146	0.2967479674796748	11	0.03038674033149171	0	0.0	0	0.0	G	9.840	1.190882	0.21954	0.273285	0.00163	ENSG00000143631	ENST00000368799	T	0.01665	4.7	4.11	2.18	0.27775	.	.	.	.	.	T	0.01627	0.0052	M	0.63428	1.95	0.09310	N	1	D	0.67145	0.996	D	0.75020	0.985	T	0.24728	-1.0152	9	0.02654	T	1	.	6.2399	0.20785	0.2304:0.0:0.7696:0.0	rs9436065;rs52822444;rs9436065	3630	P20930	FILA_HUMAN	Y	3630	ENSP00000357789:H3630Y	ENSP00000357789:H3630Y	H	-	1	0	FLG	150543098	0.000000	0.05858	0.001000	0.08648	0.027000	0.11550	0.464000	0.21988	1.051000	0.40369	0.502000	0.49764	CAC	G|0.997;A|0.003	0.003	weak		0.542	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
GAA	2548	hgsc.bcm.edu	37	17	78092081	78092081	+	Silent	SNP	G	G	T	rs17853996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78092081G>T	ENST00000302262.3	+	18	2790	c.2571G>T	c.(2569-2571)ctG>ctT	p.L857L	GAA_ENST00000390015.3_Silent_p.L857L	NM_000152.3	NP_000143.2	P10253	LYAG_HUMAN	glucosidase, alpha; acid	857					cardiac muscle contraction (GO:0060048)|diaphragm contraction (GO:0002086)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|heart morphogenesis (GO:0003007)|locomotory behavior (GO:0007626)|lysosome organization (GO:0007040)|maltose metabolic process (GO:0000023)|muscle cell cellular homeostasis (GO:0046716)|neuromuscular process controlling balance (GO:0050885)|neuromuscular process controlling posture (GO:0050884)|regulation of the force of heart contraction (GO:0002026)|sucrose metabolic process (GO:0005985)|tissue development (GO:0009888)|vacuolar sequestering (GO:0043181)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|maltose alpha-glucosidase activity (GO:0032450)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|lung(6)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	21	all_neural(118;0.117)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.139)		Acarbose(DB00284)|Miglitol(DB00491)	GAGGGGAGCTGTTCTGGGACG	0.657													G|||	11	0.00219649	0.0083	0.0	5008	,	,		17228	0.0		0.0	False		,,,				2504	0.0				p.L857L		Atlas-SNP	.											.	GAA	66	.	0			c.G2571T						PASS	.	G	,,	48,4358	50.2+/-85.5	0,48,2155	65.0	74.0	71.0		2571,2571,2571	-1.4	1.0	17	dbSNP_123	71	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	GAA	NM_000152.3,NM_001079803.1,NM_001079804.1	,,	0,48,6455	TT,TG,GG		0.0,1.0894,0.3691	,,	857/953,857/953,857/953	78092081	48,12958	2203	4300	6503	SO:0001819	synonymous_variant	2548	exon19			GGAGCTGTTCTGG		CCDS32760.1	17q25.2-q25.3	2014-09-17	2008-08-01				3.2.1.20		4065	protein-coding gene	gene with protein product	"""Pompe disease"", ""glycogen storage disease type II"""	606800					Standard	NM_000152		Approved		uc002jxq.3	P10253		ENST00000302262.3:c.2571G>T	17.37:g.78092081G>T		148.0	0.0	0		134.0	67.0	0.5	NM_001079803	Q09GN4|Q14351|Q16302|Q8IWE7	Silent	SNP	ENST00000302262.3	37	CCDS32760.1																																																																																			G|0.997;T|0.003	0.003	strong		0.657	GAA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437441.1		
OR2A5	393046	hgsc.bcm.edu	37	7	143747796	143747796	+	Missense_Mutation	SNP	C	C	A	rs61741408	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:143747796C>A	ENST00000408906.2	+	1	336	c.302C>A	c.(301-303)aCc>aAc	p.T101N		NM_012365.1	NP_036497.1	Q96R48	OR2A5_HUMAN	olfactory receptor, family 2, subfamily A, member 5	101						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L103fs*14(1)		cervix(1)|endometrium(3)|large_intestine(5)|lung(23)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	38	Melanoma(164;0.0783)					ACAATGCAGACCTTTTTATAC	0.428													C|||	16	0.00319489	0.0121	0.0	5008	,	,		24203	0.0		0.0	False		,,,				2504	0.0				p.T101N		Atlas-SNP	.											OR2A5,colon,carcinoma,+1,5	OR2A5	78	5	1	Deletion - Frameshift(1)	lung(1)	c.C302A						PASS	.	C	ASN/THR	58,4162		0,58,2052	151.0	149.0	150.0		302	4.5	1.0	7	dbSNP_129	150	1,8505		0,1,4252	yes	missense	OR2A5	NM_012365.1	65	0,59,6304	AA,AC,CC		0.0118,1.3744,0.4636	benign	101/312	143747796	59,12667	2110	4253	6363	SO:0001583	missense	393046	exon1			TGCAGACCTTTTT	U86278	CCDS43668.1	7q35	2013-09-20	2003-11-24		ENSG00000221836	ENSG00000221836		"""GPCR / Class A : Olfactory receptors"""	8232	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily A, member 5"""	OR2A8, OR2A26		9500546	Standard	NM_012365		Approved	OR7-138, OR7-141	uc011ktw.2	Q96R48	OTTHUMG00000158006	ENST00000408906.2:c.302C>A	7.37:g.143747796C>A	ENSP00000386208:p.Thr101Asn	159.0	0.0	0		165.0	85.0	0.515152	NM_012365	B9EGX2|O43885|O43888	Missense_Mutation	SNP	ENST00000408906.2	37	CCDS43668.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	C	10.44	1.350249	0.24512	0.013744	1.18E-4	ENSG00000221836	ENST00000408906	T	0.02974	4.09	5.37	4.47	0.54385	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.03390	0.0098	M	0.71036	2.16	0.31492	N	0.665835	B	0.27932	0.194	B	0.27262	0.078	T	0.00896	-1.1523	9	0.66056	D	0.02	.	8.4796	0.33034	0.0:0.8307:0.0:0.1693	rs61741408	101	Q96R48	OR2A5_HUMAN	N	101	ENSP00000386208:T101N	ENSP00000386208:T101N	T	+	2	0	OR2A5	143378729	0.000000	0.05858	0.994000	0.49952	0.301000	0.27625	0.546000	0.23284	2.797000	0.96272	0.650000	0.86243	ACC	C|0.997;A|0.003	0.003	strong		0.428	OR2A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349986.1		
ZFYVE9	9372	hgsc.bcm.edu	37	1	52705174	52705174	+	Silent	SNP	A	A	G	rs34437486	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:52705174A>G	ENST00000371591.1	+	3	2216	c.2085A>G	c.(2083-2085)gtA>gtG	p.V695V	ZFYVE9_ENST00000357206.2_Silent_p.V695V|ZFYVE9_ENST00000287727.3_Silent_p.V695V	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9	695					endocytosis (GO:0006897)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome (GO:0005769)|early endosome membrane (GO:0031901)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|serine-type peptidase activity (GO:0008236)			breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	53						TGGCTCCAGTATGGGTACCGG	0.478													A|||	30	0.00599042	0.0227	0.0	5008	,	,		18368	0.0		0.0	False		,,,				2504	0.0				p.V695V		Atlas-SNP	.											.	ZFYVE9	131	.	0			c.A2085G						PASS	.	A	,,	126,4280	93.0+/-131.7	1,124,2078	71.0	69.0	70.0		2085,2085,2085	-7.1	0.7	1	dbSNP_126	70	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	ZFYVE9	NM_004799.2,NM_007323.1,NM_007324.2	,,	1,125,6377	GG,GA,AA		0.0116,2.8597,0.9765	,,	695/1426,695/763,695/1367	52705174	127,12879	2203	4300	6503	SO:0001819	synonymous_variant	9372	exon4			TCCAGTATGGGTA	AF104304	CCDS563.1, CCDS564.1	1p32.3	2014-06-13	2004-05-21	2004-05-26	ENSG00000157077	ENSG00000157077		"""Zinc fingers, FYVE domain containing"""	6775	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 173"""	603755	"""MAD, mothers against decapentaplegic homolog (Drosophila) interacting protein, receptor activation anchor"""	MADHIP		9865696	Standard	NM_007324		Approved	SMADIP, SARA, PPP1R173	uc001cto.4	O95405	OTTHUMG00000008061	ENST00000371591.1:c.2085A>G	1.37:g.52705174A>G		140.0	0.0	0		154.0	70.0	0.454545	NM_007323	Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Silent	SNP	ENST00000371591.1	37	CCDS563.1																																																																																			A|0.991;G|0.009	0.009	strong		0.478	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324	
MC1R	4157	hgsc.bcm.edu	37	16	89986566	89986566	+	Silent	SNP	C	C	T	rs3212367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89986566C>T	ENST00000555147.1	+	1	2280	c.900C>T	c.(898-900)ttC>ttT	p.F300F	RP11-566K11.4_ENST00000554623.1_RNA|MC1R_ENST00000555427.1_Silent_p.F300F|TUBB3_ENST00000556922.1_Silent_p.F300F|RP11-566K11.7_ENST00000570217.1_RNA|TUBB3_ENST00000554444.1_5'Flank	NM_002386.3	NP_002377.4	Q01726	MSHR_HUMAN	melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor)	300					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|intracellular signal transduction (GO:0035556)|melanin biosynthetic process (GO:0042438)|multicellular organismal development (GO:0007275)|negative regulation of tumor necrosis factor production (GO:0032720)|pigmentation (GO:0043473)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sensory perception of pain (GO:0019233)|UV protection (GO:0009650)|UV-damage excision repair (GO:0070914)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled peptide receptor activity (GO:0008528)|melanocortin receptor activity (GO:0004977)|melanocyte-stimulating hormone receptor activity (GO:0004980)|ubiquitin protein ligase binding (GO:0031625)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	11		all_cancers(9;1.69e-11)|Lung NSC(15;8.94e-06)|all_lung(18;1.39e-05)|all_neural(9;0.00581)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0273)		TCTACGCCTTCCACAGCCAGG	0.612									Melanoma, Familial Clustering of				C|||	98	0.0195687	0.0711	0.0058	5008	,	,		20124	0.0		0.0	False		,,,				2504	0.0				p.F300F		Atlas-SNP	.											.	MC1R	20	.	0			c.C900T						PASS	.	C		201,3963		2,197,1883	62.0	66.0	64.0		900	3.3	1.0	16	dbSNP_106	64	5,8459		0,5,4227	no	coding-synonymous	MC1R	NM_002386.3		2,202,6110	TT,TC,CC		0.0591,4.8271,1.6313		300/318	89986566	206,12422	2082	4232	6314	SO:0001819	synonymous_variant	4157	exon1	Familial Cancer Database		CGCCTTCCACAGC		CCDS56011.1	16q24.3	2012-10-05			ENSG00000258839	ENSG00000258839		"""GPCR / Class A : Melanocortin receptors"""	6929	protein-coding gene	gene with protein product		155555				8458079	Standard	NM_002386		Approved	MSH-R		Q01726		ENST00000555147.1:c.900C>T	16.37:g.89986566C>T		163.0	0.0	0		162.0	75.0	0.462963	NM_002386	Q66K38|Q6UR93|Q8WWX6|Q8WWX7|Q96I33|Q96RU4|Q9UBF7|Q9UN58|Q9UN59|Q9UN60|Q9UN61|Q9UN62	Silent	SNP	ENST00000555147.1	37	CCDS56011.1																																																																																			C|0.978;T|0.022	0.022	strong		0.612	MC1R-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412014.1	NM_002386	
ABCC10	89845	hgsc.bcm.edu	37	6	43413669	43413669	+	Silent	SNP	G	G	A	rs112977568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43413669G>A	ENST00000372530.4	+	15	3578	c.3363G>A	c.(3361-3363)ggG>ggA	p.G1121G	ABCC10_ENST00000244533.3_Silent_p.G1093G	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	1121	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(8)|lung(21)|ovary(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)		Cyclosporine(DB00091)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Estradiol(DB00783)|Etoposide(DB00773)|Gemcitabine(DB00441)|Methotrexate(DB00563)|Paclitaxel(DB01229)|Sildenafil(DB00203)|Tenofovir(DB00300)|Verapamil(DB00661)|Vincristine(DB00541)	GGGCCACAGGGGCCACCTACA	0.622													G|||	37	0.00738818	0.0272	0.0	5008	,	,		18669	0.0		0.001	False		,,,				2504	0.0				p.G1121G		Atlas-SNP	.											.	ABCC10	118	.	0			c.G3363A						PASS	.	G	,	106,4248		1,104,2072	21.0	23.0	22.0		3363,3279	3.4	1.0	6	dbSNP_132	22	0,8536		0,0,4268	no	coding-synonymous,coding-synonymous	ABCC10	NM_001198934.1,NM_033450.2	,	1,104,6340	AA,AG,GG		0.0,2.4345,0.8223	,	1121/1493,1093/1465	43413669	106,12784	2177	4268	6445	SO:0001819	synonymous_variant	89845	exon15			CACAGGGGCCACC	U66684	CCDS4896.1, CCDS56430.1	6p12.3	2012-03-14			ENSG00000124574	ENSG00000124574		"""ATP binding cassette transporters / subfamily C"""	52	protein-coding gene	gene with protein product		612509				8894702	Standard	NM_033450		Approved	EST182763, MRP7, SIMRP7	uc003ouy.1	Q5T3U5	OTTHUMG00000014733	ENST00000372530.4:c.3363G>A	6.37:g.43413669G>A		104.0	0.0	0		87.0	45.0	0.517241	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Silent	SNP	ENST00000372530.4	37	CCDS56430.1																																																																																			G|0.992;A|0.008	0.008	strong		0.622	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450	
TMEM176A	55365	hgsc.bcm.edu	37	7	150498773	150498773	+	Silent	SNP	C	C	T	rs10239586	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150498773C>T	ENST00000484928.1	+	2	716	c.135C>T	c.(133-135)acC>acT	p.T45T	TMEM176A_ENST00000461345.1_Intron|TMEM176B_ENST00000450753.2_5'Flank|TMEM176A_ENST00000004103.3_Silent_p.T45T|TMEM176B_ENST00000447204.2_5'Flank|TMEM176B_ENST00000492607.1_5'Flank|TMEM176B_ENST00000434545.1_5'Flank|TMEM176B_ENST00000326442.5_5'Flank			Q96HP8	T176A_HUMAN	transmembrane protein 176A	45					negative regulation of dendritic cell differentiation (GO:2001199)	integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|lung(7)|ovary(2)|stomach(1)	12			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CCCGGGCCACCCAGGCCAGGG	0.711													C|||	33	0.00658946	0.025	0.0	5008	,	,		12886	0.0		0.0	False		,,,				2504	0.0				p.T45T		Atlas-SNP	.											.	TMEM176A	35	.	0			c.C135T						PASS	.	C		60,4254		0,60,2097	8.0	9.0	8.0		135	3.0	0.0	7	dbSNP_119	8	0,8462		0,0,4231	no	coding-synonymous	TMEM176A	NM_018487.2		0,60,6328	TT,TC,CC		0.0,1.3908,0.4696		45/236	150498773	60,12716	2157	4231	6388	SO:0001819	synonymous_variant	55365	exon2			GGCCACCCAGGCC	AF258340	CCDS5909.1	7q36.1	2006-09-04			ENSG00000002933	ENSG00000002933			24930	protein-coding gene	gene with protein product		610334				12097419, 8889548	Standard	NM_018487		Approved	HCA112	uc003whx.1	Q96HP8	OTTHUMG00000158114	ENST00000484928.1:c.135C>T	7.37:g.150498773C>T		28.0	0.0	0		30.0	17.0	0.566667	NM_018487	D3DX00|Q9NYC7	Silent	SNP	ENST00000484928.1	37	CCDS5909.1																																																																																			C|0.993;T|0.007	0.007	strong		0.711	TMEM176A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350222.1	NM_018487	
SMCHD1	23347	hgsc.bcm.edu	37	18	2740798	2740798	+	Silent	SNP	A	A	T	rs115632137	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:2740798A>T	ENST00000320876.6	+	28	3950	c.3612A>T	c.(3610-3612)tcA>tcT	p.S1204S	RP11-703M24.5_ENST00000583546.1_RNA|SMCHD1_ENST00000261598.8_Silent_p.S1204S	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	1204					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						TTGATAGCTCAAATTTGAAAA	0.313													A|||	154	0.0307508	0.1104	0.0101	5008	,	,		14819	0.0		0.001	False		,,,				2504	0.0				p.S1204S		Atlas-SNP	.											.	SMCHD1	88	.	0			c.A3612T						PASS	.	A		399,3233		26,347,1443	108.0	110.0	109.0		3612	-0.6	1.0	18	dbSNP_132	109	7,8115		0,7,4054	no	coding-synonymous	SMCHD1	NM_015295.2		26,354,5497	TT,TA,AA		0.0862,10.9857,3.4541		1204/2006	2740798	406,11348	1816	4061	5877	SO:0001819	synonymous_variant	23347	exon28			TAGCTCAAATTTG	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.3612A>T	18.37:g.2740798A>T		129.0	0.0	0		129.0	74.0	0.573643	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Silent	SNP	ENST00000320876.6	37	CCDS45822.1																																																																																			A|0.973;T|0.027	0.027	strong		0.313	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2		
SPINK14	408187	hgsc.bcm.edu	37	5	147553829	147553829	+	Silent	SNP	C	C	T	rs79779038	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:147553829C>T	ENST00000356972.1	+	3	144	c.144C>T	c.(142-144)agC>agT	p.S48S	SPINK14_ENST00000562793.1_Intron	NM_001001325.1	NP_001001325.1	Q6IE38	ISK14_HUMAN	serine peptidase inhibitor, Kazal type 14 (putative)	48	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.					extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|large_intestine(1)|lung(1)	3						TAAACTTGAGCTGGTACAATG	0.413													T|||	536	0.107029	0.388	0.0303	5008	,	,		9611	0.001		0.001	False		,,,				2504	0.0				p.S48S		Atlas-SNP	.											.	SPINK14	9	.	0			c.C144T						PASS	.	T		841,2147		340,161,993	107.0	107.0	107.0		144	0.1	1.0	5	dbSNP_131	107	13,6231		1,11,3110	no	coding-synonymous	SPINK14	NM_001001325.1		341,172,4103	TT,TC,CC		0.2082,28.1459,9.2504		48/98	147553829	854,8378	1494	3122	4616	SO:0001819	synonymous_variant	408187	exon3			CTTGAGCTGGTAC		CCDS4288.1	5q32	2011-08-31			ENSG00000196800	ENSG00000196800		"""Serine peptidase inhibitors, Kazal type"""	33825	protein-coding gene	gene with protein product							Standard	NM_001001325		Approved	SPINK5L2	uc031sls.1	Q6IE38	OTTHUMG00000129732	ENST00000356972.1:c.144C>T	5.37:g.147553829C>T		135.0	0.0	0		55.0	55.0	1	NM_001001325		Silent	SNP	ENST00000356972.1	37	CCDS4288.1																																																																																			C|0.919;T|0.081	0.081	strong		0.413	SPINK14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251943.2	NM_001001325	
CCDC157	550631	hgsc.bcm.edu	37	22	30761995	30761995	+	Silent	SNP	G	G	A	rs61732271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30761995G>A	ENST00000405659.1	+	3	715	c.6G>A	c.(4-6)gcG>gcA	p.A2A	CCDC157_ENST00000338306.3_Silent_p.A2A|CCDC157_ENST00000399824.2_Silent_p.A2A			Q569K6	CC157_HUMAN	coiled-coil domain containing 157	2										central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(1)	15						TGAGGATGGCGCACCTGCTGG	0.657													G|||	89	0.0177716	0.0651	0.0029	5008	,	,		18741	0.0		0.001	False		,,,				2504	0.0				p.A2A		Atlas-SNP	.											.	CCDC157	86	.	0			c.G6A						PASS	.	G		69,1315		1,67,624	21.0	27.0	25.0		6	-10.5	0.8	22	dbSNP_129	25	0,3182		0,0,1591	no	coding-synonymous	CCDC157	NM_001017437.2		1,67,2215	AA,AG,GG		0.0,4.9855,1.5112		2/753	30761995	69,4497	692	1591	2283	SO:0001819	synonymous_variant	550631	exon3			GATGGCGCACCTG	BC018040	CCDS33632.2	22q12.2	2009-03-05			ENSG00000187860	ENSG00000187860			33854	protein-coding gene	gene with protein product							Standard	NM_001017437		Approved		uc011aku.2	Q569K6	OTTHUMG00000151007	ENST00000405659.1:c.6G>A	22.37:g.30761995G>A		21.0	0.0	0		20.0	5.0	0.25	NM_001017437	Q0VD76|Q9BYA4	Silent	SNP	ENST00000405659.1	37	CCDS33632.2																																																																																			G|0.990;A|0.010	0.010	strong		0.657	CCDC157-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320936.1	NM_001017437	
NEIL3	55247	hgsc.bcm.edu	37	4	178231219	178231219	+	Missense_Mutation	SNP	C	C	T	rs34007209	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:178231219C>T	ENST00000264596.3	+	1	230	c.112C>T	c.(112-114)Cgc>Tgc	p.R38C		NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	38			R -> C (in dbSNP:rs34007209). {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)			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)		TCTGCAGGGCCGCGCCTTGCG	0.652								Base excision repair (BER), DNA glycosylases					C|||	530	0.105831	0.3623	0.0447	5008	,	,		12349	0.0		0.0149	False		,,,				2504	0.0051				p.R38C		Atlas-SNP	.											NEIL3,NS,carcinoma,0,2	NEIL3	89	2	0			c.C112T						PASS	.	C	CYS/ARG	1374,3022		237,900,1061	14.0	16.0	15.0		112	-0.4	0.0	4	dbSNP_126	15	159,8417		4,151,4133	no	missense	NEIL3	NM_018248.2	180	241,1051,5194	TT,TC,CC		1.854,31.2557,11.8178	possibly-damaging	38/606	178231219	1533,11439	2198	4288	6486	SO:0001583	missense	55247	exon1			CAGGGCCGCGCCT	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.112C>T	4.37:g.178231219C>T	ENSP00000264596:p.Arg38Cys	32.0	0.0	0		57.0	33.0	0.578947	NM_018248	Q2PPJ3|Q8NG51|Q9NV95	Missense_Mutation	SNP	ENST00000264596.3	37	CCDS3828.1	198	0.09065934065934066	170	0.34552845528455284	16	0.04419889502762431	0	0.0	12	0.0158311345646438	C	13.86	2.362325	0.41902	0.312557	0.01854	ENSG00000109674	ENST00000264596	T	0.23552	1.9	4.59	-0.355	0.12587	DNA glycosylase/AP lyase, catalytic domain (1);	1.002150	0.08041	N	0.995170	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	P	0.48640	0.913	B	0.35312	0.2	T	0.41893	-0.9483	9	0.59425	D	0.04	-0.0398	4.619	0.12440	0.0:0.4873:0.155:0.3576	rs34007209	38	Q8TAT5	NEIL3_HUMAN	C	38	ENSP00000264596:R38C	ENSP00000264596:R38C	R	+	1	0	NEIL3	178468213	0.000000	0.05858	0.000000	0.03702	0.060000	0.15804	-0.600000	0.05693	-0.228000	0.09869	0.561000	0.74099	CGC	C|0.884;T|0.116	0.116	strong		0.652	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248	
HNRNPA2B1	3181	hgsc.bcm.edu	37	7	26236235	26236235	+	Silent	SNP	T	T	C	rs34317198	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:26236235T>C	ENST00000354667.4	-	6	723	c.555A>G	c.(553-555)agA>agG	p.R185R	HNRNPA2B1_ENST00000356674.7_Silent_p.R173R	NM_031243.2	NP_112533.1	P22626	ROA2_HUMAN	heterogeneous nuclear ribonucleoprotein A2/B1	185	RRM 2. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|RNA splicing (GO:0008380)|RNA transport (GO:0050658)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|pre-mRNA intronic binding (GO:0097157)|RNA binding (GO:0003723)|single-stranded telomeric DNA binding (GO:0043047)		HNRNPA2B1/ETV1(8)	breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	22						ACAAAGCCTTTCTTACTTCTG	0.323			T	ETV1	prostate								T|||	259	0.0517173	0.1861	0.0173	5008	,	,		19739	0.0		0.001	False		,,,				2504	0.0				p.R185R		Atlas-SNP	.		Dom	yes		7	7p15	3181	heterogeneous nuclear ribonucleoprotein A2/B1		E	.	HNRNPA2B1	70	.	0			c.A555G						PASS	.	T	,	677,3729	285.5+/-278.2	40,597,1566	168.0	179.0	176.0		519,555	4.9	1.0	7	dbSNP_126	176	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous,coding-synonymous	HNRNPA2B1	NM_002137.3,NM_031243.2	,	40,603,5860	CC,CT,TT		0.0698,15.3654,5.2514	,	173/342,185/354	26236235	683,12323	2203	4300	6503	SO:0001819	synonymous_variant	3181	exon6			AGCCTTTCTTACT	D28877	CCDS5397.1, CCDS43557.1	7p15	2013-02-12		2007-08-16	ENSG00000122566	ENSG00000122566		"""RNA binding motif (RRM) containing"""	5033	protein-coding gene	gene with protein product		600124		HNRPA2B1		8029005	Standard	NM_002137		Approved		uc003sxr.4	P22626	OTTHUMG00000023471	ENST00000354667.4:c.555A>G	7.37:g.26236235T>C		195.0	0.0	0		170.0	78.0	0.458824	NM_031243	A8K064|P22627|Q9UC98|Q9UDJ2	Silent	SNP	ENST00000354667.4	37	CCDS43557.1																																																																																			T|0.935;C|0.065	0.065	strong		0.323	HNRNPA2B1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214109.1	NM_002137	
MFSD6L	162387	hgsc.bcm.edu	37	17	8701701	8701701	+	Silent	SNP	A	A	G	rs16957601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:8701701A>G	ENST00000329805.4	-	1	966	c.738T>C	c.(736-738)ttT>ttC	p.F246F		NM_152599.3	NP_689812.3	Q8IWD5	MFS6L_HUMAN	major facilitator superfamily domain containing 6-like	246						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(7)|skin(4)	17						AGGAGAGGATAAAAGTCCGCC	0.582													G|||	141	0.028155	0.1021	0.0072	5008	,	,		17572	0.0		0.001	False		,,,				2504	0.0				p.F246F		Atlas-SNP	.											.	MFSD6L	46	.	0			c.T738C						PASS	.	G		349,4057	788.5+/-414.9	14,321,1868	56.0	63.0	60.0		738	2.8	1.0	17	dbSNP_123	60	2,8598	812.0+/-407.1	0,2,4298	no	coding-synonymous	MFSD6L	NM_152599.3		14,323,6166	GG,GA,AA		0.0233,7.921,2.6988		246/587	8701701	351,12655	2203	4300	6503	SO:0001819	synonymous_variant	162387	exon1			GAGGATAAAAGTC	AK093092	CCDS11146.1	17p13.1	2014-05-30			ENSG00000185156	ENSG00000185156			26656	protein-coding gene	gene with protein product							Standard	NM_152599		Approved	FLJ35773	uc002glp.2	Q8IWD5	OTTHUMG00000178584	ENST00000329805.4:c.738T>C	17.37:g.8701701A>G		15.0	0.0	0		12.0	9.0	0.75	NM_152599	Q6YL34|Q8NA76	Silent	SNP	ENST00000329805.4	37	CCDS11146.1																																																																																			A|0.974;G|0.026	0.026	strong		0.582	MFSD6L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442554.1	NM_152599	
BAI1	575	hgsc.bcm.edu	37	8	143599594	143599594	+	Silent	SNP	C	C	T	rs75573695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:143599594C>T	ENST00000517894.1	+	19	3807	c.2913C>T	c.(2911-2913)tcC>tcT	p.S971S	BAI1_ENST00000323289.5_Silent_p.S971S			O14514	BAI1_HUMAN	brain-specific angiogenesis inhibitor 1	971					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|neuropeptide signaling pathway (GO:0007218)|peripheral nervous system development (GO:0007422)|signal transduction (GO:0007165)	cell-cell junction (GO:0005911)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(28)|ovary(4)|pancreas(1)|prostate(7)	57	all_cancers(97;2.84e-12)|all_epithelial(106;5.91e-09)|Lung NSC(106;0.000322)|all_lung(105;0.000616)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0315)|Acute lymphoblastic leukemia(118;0.155)					TCTACGTGTCCGTGTGGAGGT	0.632													C|||	247	0.0493211	0.1142	0.0187	5008	,	,		14503	0.0258		0.002	False		,,,				2504	0.0562				p.S971S		Atlas-SNP	.											.	BAI1	146	.	0			c.C2913T						PASS	.	C		384,4012	181.2+/-209.3	15,354,1829	148.0	152.0	151.0		2913	-3.8	1.0	8	dbSNP_132	151	9,8573	6.4+/-24.3	0,9,4282	no	coding-synonymous	BAI1	NM_001702.2		15,363,6111	TT,TC,CC		0.1049,8.7352,3.0282		971/1585	143599594	393,12585	2198	4291	6489	SO:0001819	synonymous_variant	575	exon18			CGTGTCCGTGTGG	AB005297	CCDS64985.1	8q24.3	2014-08-08			ENSG00000181790	ENSG00000181790		"""-"", ""GPCR / Class B : Orphans"""	943	protein-coding gene	gene with protein product		602682				9533023	Standard	NM_001702		Approved		uc003ywm.3	O14514	OTTHUMG00000164732	ENST00000517894.1:c.2913C>T	8.37:g.143599594C>T		160.0	0.0	0		145.0	67.0	0.462069	NM_001702		Silent	SNP	ENST00000517894.1	37																																																																																				C|0.964;T|0.036	0.036	strong		0.632	BAI1-001	KNOWN	non_canonical_conserved|not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379963.3	NM_001702	
GPC2	221914	hgsc.bcm.edu	37	7	99773879	99773879	+	Silent	SNP	G	G	A	rs74662631	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99773879G>A	ENST00000292377.2	-	2	443	c.276C>T	c.(274-276)agC>agT	p.S92S	STAG3_ENST00000426455.1_5'Flank|STAG3_ENST00000394018.2_5'Flank|GPC2_ENST00000471050.1_5'Flank|STAG3_ENST00000317296.5_5'Flank	NM_152742.1	NP_689955.1	Q8N158	GPC2_HUMAN	glypican 2	92					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuron differentiation (GO:0030182)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|smoothened signaling pathway (GO:0007224)	anchored component of membrane (GO:0031225)|endoplasmic reticulum (GO:0005783)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(3)	18	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					GAAAGGAGCCGCTGTCCTCCA	0.587													G|||	87	0.0173722	0.0628	0.0058	5008	,	,		14063	0.0		0.0	False		,,,				2504	0.0				p.S92S		Atlas-SNP	.											.	GPC2	49	.	0			c.C276T						PASS	.	G		233,4173	138.4+/-174.2	6,221,1976	54.0	45.0	48.0		276	-4.0	0.4	7	dbSNP_132	48	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GPC2	NM_152742.1		6,222,6275	AA,AG,GG		0.0116,5.2882,1.7992		92/580	99773879	234,12772	2203	4300	6503	SO:0001819	synonymous_variant	221914	exon2			GGAGCCGCTGTCC	BX375153	CCDS5689.1	7q22.1	2007-02-16	2007-02-15		ENSG00000213420	ENSG00000213420		"""Proteoglycans / Cell Surface : Glypicans"""	4450	protein-coding gene	gene with protein product	"""glypican proteoglycan 2, cerebroglycan proteoglycan"""		"""glypican 2 (cerebroglycan)"""			8294498	Standard	NM_152742		Approved	cerebroglycan, FLJ38962, DKFZp547M109	uc003utv.3	Q8N158	OTTHUMG00000154894	ENST00000292377.2:c.276C>T	7.37:g.99773879G>A		231.0	0.0	0		276.0	136.0	0.492754	NM_152742	A4D2A7	Silent	SNP	ENST00000292377.2	37	CCDS5689.1																																																																																			G|0.985;A|0.015	0.015	strong		0.587	GPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337556.1	NM_152742	
EHMT1	79813	hgsc.bcm.edu	37	9	140707590	140707590	+	Silent	SNP	C	C	T	rs35943616	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140707590C>T	ENST00000460843.1	+	20	3027	c.3000C>T	c.(2998-3000)ccC>ccT	p.P1000P		NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	1000					chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|embryo development (GO:0009790)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|methyltransferase activity (GO:0008168)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		ACTCGGCCCCCGACAGGCCCA	0.622													C|||	555	0.110823	0.4017	0.0274	5008	,	,		17819	0.005		0.0	False		,,,				2504	0.0				p.P1000P		Atlas-SNP	.											.	EHMT1	196	.	0			c.C3000T						PASS	.	C		1428,2978	446.9+/-348.2	236,956,1011	34.0	40.0	38.0		3000	-9.4	0.0	9	dbSNP_126	38	12,8588	7.7+/-29.5	1,10,4289	no	coding-synonymous	EHMT1	NM_024757.4		237,966,5300	TT,TC,CC		0.1395,32.4103,11.0718		1000/1299	140707590	1440,11566	2203	4300	6503	SO:0001819	synonymous_variant	79813	exon20			GGCCCCCGACAGG	AY083210	CCDS7050.1, CCDS7050.2, CCDS56595.1	9q34.3	2013-09-20			ENSG00000181090	ENSG00000181090	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"", ""Ankyrin repeat domain containing"""	24650	protein-coding gene	gene with protein product		607001	"""euchromatic histone methyltransferase 1"""			11347906, 12004135	Standard	NM_024757		Approved	Eu-HMTase1, FLJ12879, KIAA1876, bA188C12.1, KMT1D	uc011mfc.2	Q9H9B1	OTTHUMG00000020995	ENST00000460843.1:c.3000C>T	9.37:g.140707590C>T		47.0	0.0	0		64.0	64.0	1	NM_024757	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Silent	SNP	ENST00000460843.1	37	CCDS7050.2																																																																																			C|0.899;T|0.101	0.101	strong		0.622	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757	
CCDC66	285331	hgsc.bcm.edu	37	3	56650054	56650054	+	Missense_Mutation	SNP	T	T	C	rs112267342|rs111934125	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:56650054T>C	ENST00000394672.3	+	13	1886	c.1816T>C	c.(1816-1818)Tct>Cct	p.S606P	CCDC66_ENST00000436465.2_Missense_Mutation_p.S606P|CCDC66_ENST00000326595.7_Missense_Mutation_p.S572P	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	606					post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|retinal rod cell development (GO:0046548)					breast(1)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		TTCTACGACTTCTAAGAAGGA	0.289																																					p.S606P		Atlas-SNP	.											CCDC66_ENST00000394672,caecum,carcinoma,0,2	CCDC66	145	2	0			c.T1816C						PASS	.						86.0	99.0	94.0					3																	56650054		2203	4291	6494	SO:0001583	missense	285331	exon13			ACGACTTCTAAGA	AL832692	CCDS33770.2, CCDS46852.1	3p14.3	2006-03-27			ENSG00000180376	ENSG00000180376			27709	protein-coding gene	gene with protein product						14702039	Standard	NR_024460		Approved	DKFZp686C0433	uc003dhz.3	A2RUB6	OTTHUMG00000155748	ENST00000394672.3:c.1816T>C	3.37:g.56650054T>C	ENSP00000378167:p.Ser606Pro	86.0	0.0	0		84.0	8.0	0.0952381	NM_001141947	B3KWL8|Q4VC34|Q8N949	Missense_Mutation	SNP	ENST00000394672.3	37	CCDS46852.1	.	.	.	.	.	.	.	.	.	.	T	11.57	1.676847	0.29783	.	.	ENSG00000180376	ENST00000422222;ENST00000394672;ENST00000326595;ENST00000436465	T;T;T;T	0.19105	2.17;2.28;2.28;2.28	5.5	4.32	0.51571	.	0.000000	0.85682	D	0.000000	T	0.32376	0.0827	M	0.72894	2.215	0.80722	D	1	D	0.58268	0.982	P	0.57911	0.829	T	0.40924	-0.9537	10	0.02654	T	1	-4.7355	10.7191	0.46030	0.0:0.0:0.1601:0.8399	.	606	A2RUB6	CCD66_HUMAN	P	562;606;572;606	ENSP00000401451:S562P;ENSP00000378167:S606P;ENSP00000326050:S572P;ENSP00000404320:S606P	ENSP00000326050:S572P	S	+	1	0	CCDC66	56625094	0.993000	0.37304	0.582000	0.28627	0.363000	0.29612	2.520000	0.45554	1.007000	0.39238	0.482000	0.46254	TCT	C|1.000;|0.000	1.000	weak		0.289	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506	
CBFB	865	hgsc.bcm.edu	37	16	67116169	67116169	+	Silent	SNP	C	C	T	rs78053453	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67116169C>T	ENST00000290858.6	+	5	714	c.453C>T	c.(451-453)cgC>cgT	p.R151R	CBFB_ENST00000561924.2_Silent_p.R51R|CBFB_ENST00000412916.2_Silent_p.R151R	NM_001755.2|NM_022845.2	NP_001746.1|NP_074036.1	Q13951	PEBB_HUMAN	core-binding factor, beta subunit	151					cell maturation (GO:0048469)|definitive hemopoiesis (GO:0060216)|lymphocyte differentiation (GO:0030098)|myeloid cell differentiation (GO:0030099)|osteoblast differentiation (GO:0001649)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			breast(3)|large_intestine(1)	4		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00189)|Epithelial(162;0.00755)|all cancers(182;0.066)		GAAGGACACGCGAATTTGAAG	0.433			T	MYH11	AML								C|||	358	0.0714856	0.1853	0.0115	5008	,	,		12709	0.0377		0.002	False		,,,				2504	0.0665				p.R151R		Atlas-SNP	.		Dom	yes		16	16q22	865	"""core-binding factor, beta subunit"""		L	CBFB_ENST00000412916,NS,carcinoma,+1,2	CBFB	52	2	0			c.C453T						PASS	.	C	,	664,3736	281.9+/-276.2	46,572,1582	98.0	90.0	93.0		453,453	0.1	1.0	16	dbSNP_132	93	10,8590	5.7+/-21.5	0,10,4290	no	coding-synonymous,coding-synonymous	CBFB	NM_001755.2,NM_022845.2	,	46,582,5872	TT,TC,CC		0.1163,15.0909,5.1846	,	151/183,151/188	67116169	674,12326	2200	4300	6500	SO:0001819	synonymous_variant	865	exon5			GACACGCGAATTT	BC018509	CCDS10827.1, CCDS45508.1	16q22.1	2008-02-05			ENSG00000067955	ENSG00000067955			1539	protein-coding gene	gene with protein product		121360				8351518, 7587111	Standard	NM_001755		Approved	PEBP2B	uc002erb.3	Q13951	OTTHUMG00000137520	ENST00000290858.6:c.453C>T	16.37:g.67116169C>T		80.0	0.0	0		88.0	38.0	0.431818	NM_022845	A8K347|Q13124|Q9HCT2	Silent	SNP	ENST00000290858.6	37	CCDS10827.1																																																																																			C|0.951;T|0.049	0.049	strong		0.433	CBFB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268843.2	NM_001755	
LNX2	222484	hgsc.bcm.edu	37	13	28130473	28130473	+	Silent	SNP	G	G	A	rs115119970	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:28130473G>A	ENST00000316334.3	-	7	1575	c.1446C>T	c.(1444-1446)acC>acT	p.T482T		NM_153371.3	NP_699202.1	Q8N448	LNX2_HUMAN	ligand of numb-protein X 2	482	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				protein homooligomerization (GO:0051260)		zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(7)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	31		Lung SC(185;0.0156)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.113)|all cancers(112;0.127)|Epithelial(112;0.248)		CCCCAGCAACGGTCATGCCAA	0.468													G|||	67	0.0133786	0.0446	0.0043	5008	,	,		15881	0.0		0.005	False		,,,				2504	0.0				p.T482T		Atlas-SNP	.											.	LNX2	70	.	0			c.C1446T						PASS	.	G		138,4268	98.9+/-137.6	0,138,2065	114.0	100.0	105.0		1446	-5.4	0.7	13	dbSNP_132	105	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	LNX2	NM_153371.3		0,146,6357	AA,AG,GG		0.093,3.1321,1.1226		482/691	28130473	146,12860	2203	4300	6503	SO:0001819	synonymous_variant	222484	exon7			AGCAACGGTCATG	AL138699	CCDS9323.1	13q12.2	2013-01-09	2004-01-22	2004-01-23	ENSG00000139517	ENSG00000139517		"""RING-type (C3HC4) zinc fingers"""	20421	protein-coding gene	gene with protein product		609733	"""PDZ domain containing ring finger 1"""	PDZRN1			Standard	NM_153371		Approved	MGC46315	uc001url.4	Q8N448	OTTHUMG00000016634	ENST00000316334.3:c.1446C>T	13.37:g.28130473G>A		73.0	0.0	0		85.0	29.0	0.341176	NM_153371	Q5W0P0|Q6ZMH2|Q96SH4	Silent	SNP	ENST00000316334.3	37	CCDS9323.1																																																																																			G|0.988;A|0.012	0.012	strong		0.468	LNX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044302.2		
FBF1	85302	hgsc.bcm.edu	37	17	73929118	73929118	+	Missense_Mutation	SNP	G	G	A	rs149283443	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73929118G>A	ENST00000586717.1	-	4	356	c.83C>T	c.(82-84)aCa>aTa	p.T28I	FBF1_ENST00000319129.5_Missense_Mutation_p.T28I|FBF1_ENST00000389570.4_Missense_Mutation_p.T28I			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	28					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	4						AGATACACCTGTGGTGTCTCT	0.448													G|||	17	0.00339457	0.0129	0.0	5008	,	,		17472	0.0		0.0	False		,,,				2504	0.0				p.T28I		Atlas-SNP	.											.	FBF1	48	.	0			c.C83T						PASS	.	G	ILE/THR	33,3797		0,33,1882	71.0	69.0	70.0		83	0.6	0.0	17	dbSNP_134	70	1,8275		0,1,4137	yes	missense	FBF1	NM_001080542.1	89	0,34,6019	AA,AG,GG		0.0121,0.8616,0.2809	benign	28/1134	73929118	34,12072	1915	4138	6053	SO:0001583	missense	85302	exon4			ACACCTGTGGTGT	AK074045	CCDS45779.1	17q25.3	2011-04-21			ENSG00000188878	ENSG00000188878			24674	protein-coding gene	gene with protein product	"""albatross"""					11347906	Standard	NM_001080542		Approved	FLJ00103, FBF-1, KIAA1863, ALB	uc002jqc.3	Q8TES7		ENST00000586717.1:c.83C>T	17.37:g.73929118G>A	ENSP00000465132:p.Thr28Ile	61.0	0.0	0		55.0	35.0	0.636364	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Missense_Mutation	SNP	ENST00000586717.1	37		7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	10.15	1.271825	0.23221	0.008616	1.21E-4	ENSG00000188878	ENST00000337792;ENST00000389570;ENST00000319129;ENST00000427433	T;T	0.20332	2.08;2.08	3.74	0.562	0.17290	.	.	.	.	.	T	0.09512	0.0234	L	0.36672	1.1	0.09310	N	1	B;B;B	0.33583	0.418;0.418;0.418	B;B;B	0.31101	0.124;0.058;0.058	T	0.21655	-1.0239	9	0.59425	D	0.04	6.5178	3.4486	0.07490	0.2201:0.0:0.5802:0.1997	.	42;28;28	Q8TES7-6;Q8TES7;A6NLR5	.;FBF1_HUMAN;.	I	28;28;28;41	ENSP00000374221:T28I;ENSP00000324292:T28I	ENSP00000324292:T28I	T	-	2	0	FBF1	71440713	0.000000	0.05858	0.000000	0.03702	0.167000	0.22549	0.333000	0.19768	0.162000	0.19483	0.557000	0.71058	ACA	G|0.997;A|0.003	0.003	strong		0.448	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542	
ABCC4	10257	hgsc.bcm.edu	37	13	95696540	95696540	+	Silent	SNP	C	C	T	rs11568695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:95696540C>T	ENST00000376887.4	-	28	3723	c.3609G>A	c.(3607-3609)gcG>gcA	p.A1203A	ABCC4_ENST00000412704.1_Silent_p.A1156A	NM_005845.3	NP_005836.2	O15439	MRP4_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 4	1203	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				blood coagulation (GO:0007596)|oxidation-reduction process (GO:0055114)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of smooth muscle cell proliferation (GO:0048661)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|response to organonitrogen compound (GO:0010243)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(1)|central_nervous_system(4)|endometrium(5)|kidney(4)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	43	all_neural(89;0.0878)|Medulloblastoma(90;0.163)				Adefovir Dipivoxil(DB00718)|Alprostadil(DB00770)|Atorvastatin(DB01076)|Cefazolin(DB01327)|Celecoxib(DB00482)|Conjugated Estrogens(DB00286)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Dipyridamole(DB00975)|Fluorouracil(DB00544)|Flurbiprofen(DB00712)|Folic Acid(DB00158)|Gadoxetate(DB08884)|Glutathione(DB00143)|Ibuprofen(DB01050)|Indomethacin(DB00328)|Ketoprofen(DB01009)|Lamivudine(DB00709)|Leucovorin(DB00650)|Meloxicam(DB00814)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Probenecid(DB01032)|Rosuvastatin(DB01098)|Sildenafil(DB00203)|Sorafenib(DB00398)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tenofovir(DB00300)|Tioguanine(DB00352)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Zidovudine(DB00495)	CATTTGCCGTCGCTTCATCAA	0.398													C|||	225	0.0449281	0.1604	0.013	5008	,	,		19815	0.001		0.002	False		,,,				2504	0.001				p.A1203A		Atlas-SNP	.											ABCC4_ENST00000376887,colon,carcinoma,-1,2	ABCC4	248	2	0			c.G3609A						PASS	.	C		644,3762	270.4+/-269.6	52,540,1611	72.0	64.0	66.0		3609	-6.7	0.9	13	dbSNP_126	66	10,8590	7.1+/-27.0	0,10,4290	no	coding-synonymous	ABCC4	NM_005845.3		52,550,5901	TT,TC,CC		0.1163,14.6164,5.0284		1203/1326	95696540	654,12352	2203	4300	6503	SO:0001819	synonymous_variant	10257	exon28			TGCCGTCGCTTCA	U66682	CCDS9474.1	13q31	2012-03-14			ENSG00000125257	ENSG00000125257		"""ATP binding cassette transporters / subfamily C"""	55	protein-coding gene	gene with protein product	"""canalicular multispecific organic anion transporter (ABC superfamily)"", ""bA464I2.1 (ATP-binding cassette, sub-family C (CFTR/MRP), member 4)"", ""multidrug resistance-associated protein 4"", ""multispecific organic anion transporter B"""	605250				8894702, 9661885	Standard	NM_005845		Approved	MRP4, EST170205, MOAT-B, MOATB	uc001vmd.4	O15439	OTTHUMG00000017216	ENST00000376887.4:c.3609G>A	13.37:g.95696540C>T		127.0	0.0	0		111.0	54.0	0.486486	NM_005845	A9Z1Z7|Q8IVZ4|Q8IZN6|Q8NEW8|Q9Y6J2	Silent	SNP	ENST00000376887.4	37	CCDS9474.1																																																																																			C|0.950;T|0.050	0.050	strong		0.398	ABCC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045478.2	NM_005845	
ITPR2	3709	hgsc.bcm.edu	37	12	26834833	26834833	+	Silent	SNP	G	G	A	rs35412320	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:26834833G>A	ENST00000381340.3	-	13	1799	c.1383C>T	c.(1381-1383)aaC>aaT	p.N461N		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	461					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	TTATTGTGCCGTTTTCTAGCT	0.378													G|||	47	0.00938498	0.0348	0.0014	5008	,	,		19655	0.0		0.0	False		,,,				2504	0.0				p.N461N		Atlas-SNP	.											ITPR2,colon,carcinoma,-2,1	ITPR2	270	1	0			c.C1383T						PASS	.	G		94,3584		1,92,1746	196.0	185.0	189.0		1383	-10.2	0.4	12	dbSNP_126	189	1,8193		0,1,4096	no	coding-synonymous	ITPR2	NM_002223.2		1,93,5842	AA,AG,GG		0.0122,2.5557,0.8002		461/2702	26834833	95,11777	1839	4097	5936	SO:0001819	synonymous_variant	3709	exon13			TGTGCCGTTTTCT	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.1383C>T	12.37:g.26834833G>A		101.0	0.0	0		119.0	44.0	0.369748	NM_002223	O94773	Silent	SNP	ENST00000381340.3	37	CCDS41764.1																																																																																			G|0.991;A|0.009	0.009	strong		0.378	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	
CALM3	808	hgsc.bcm.edu	37	19	47112207	47112207	+	Silent	SNP	C	C	T	rs35617141	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:47112207C>T	ENST00000291295.9	+	5	589	c.390C>T	c.(388-390)gaC>gaT	p.D130D	CALM3_ENST00000477244.1_3'UTR|CALM3_ENST00000594523.1_Silent_p.D94D|CTB-12A17.3_ENST00000597609.1_RNA|CALM3_ENST00000599839.1_Silent_p.D94D|CALM3_ENST00000596362.1_Silent_p.D130D|CALM3_ENST00000391918.2_Silent_p.D94D|CALM3_ENST00000597743.1_Silent_p.D64D|CALM3_ENST00000598871.1_Silent_p.D94D	NM_005184.2	NP_005175.2	P62158	CALM_HUMAN	calmodulin 3 (phosphorylase kinase, delta)	130	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|carbohydrate metabolic process (GO:0005975)|detection of calcium ion (GO:0005513)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nitric oxide metabolic process (GO:0046209)|phototransduction, visible light (GO:0007603)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cyclic nucleotide metabolic process (GO:0030801)|positive regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051343)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein autophosphorylation (GO:0031954)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of cytokinesis (GO:0032465)|regulation of heart rate (GO:0002027)|regulation of high voltage-gated calcium channel activity (GO:1901841)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|response to amphetamine (GO:0001975)|response to calcium ion (GO:0051592)|response to corticosterone (GO:0051412)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcomere (GO:0030017)|spindle microtubule (GO:0005876)|spindle pole (GO:0000922)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|N-terminal myristoylation domain binding (GO:0031997)|nitric-oxide synthase regulator activity (GO:0030235)|phospholipase binding (GO:0043274)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)|protein phosphatase activator activity (GO:0072542)|protein serine/threonine kinase activator activity (GO:0043539)|thioesterase binding (GO:0031996)|titin binding (GO:0031432)			breast(1)|cervix(2)|endometrium(1)|lung(1)|ovary(1)	6		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000338)|all cancers(93;0.000683)|Epithelial(262;0.0181)|GBM - Glioblastoma multiforme(486;0.0341)	Aprindine(DB01429)|Bepridil(DB01244)|Chlorpromazine(DB00477)|Cinchocaine(DB00527)|Felodipine(DB01023)|Flunarizine(DB04841)|Fluphenazine(DB00623)|Isoflurane(DB00753)|Loperamide(DB00836)|Melatonin(DB01065)|Nicardipine(DB00622)|Nifedipine(DB01115)|Perphenazine(DB00850)|Phenoxybenzamine(DB00925)|Pimozide(DB01100)|Promethazine(DB01069)|Trifluoperazine(DB00831)	GGGAGGCTGACATCGATGGAG	0.542													C|||	37	0.00738818	0.0265	0.0029	5008	,	,		21757	0.0		0.0	False		,,,				2504	0.0				p.D130D		Atlas-SNP	.											.	CALM3	9	.	0			c.C390T						PASS	.	C		98,4308	79.9+/-118.3	0,98,2105	93.0	71.0	79.0		390	4.8	1.0	19	dbSNP_126	79	0,8600		0,0,4300	no	coding-synonymous	CALM3	NM_005184.2		0,98,6405	TT,TC,CC		0.0,2.2242,0.7535		130/150	47112207	98,12908	2203	4300	6503	SO:0001819	synonymous_variant	808	exon5			GGCTGACATCGAT		CCDS33061.1	19q13.2-q13.3	2013-02-25			ENSG00000160014	ENSG00000160014		"""EF-hand domain containing"", ""Endogenous ligands"""	1449	protein-coding gene	gene with protein product	"""prepro-calmodulin 3"""	114183					Standard	NM_005184		Approved	PHKD	uc002pew.3	P62158	OTTHUMG00000133517	ENST00000291295.9:c.390C>T	19.37:g.47112207C>T		86.0	0.0	0		83.0	47.0	0.566265	NM_005184	P02593|P70667|P99014|Q13942|Q53S29|Q61379|Q61380|Q96HK3	Silent	SNP	ENST00000291295.9	37	CCDS33061.1																																																																																			C|0.990;T|0.010	0.010	strong		0.542	CALM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257483.2		
OR4D2	124538	hgsc.bcm.edu	37	17	56247794	56247794	+	Missense_Mutation	SNP	C	C	T	rs148697791	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:56247794C>T	ENST00000545221.1	+	1	778	c.778C>T	c.(778-780)Cgg>Tgg	p.R260W		NM_001004707.3	NP_001004707.1	P58180	OR4D2_HUMAN	olfactory receptor, family 4, subfamily D, member 2	260						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(1)|large_intestine(1)|lung(19)|ovary(1)|skin(2)|stomach(1)	26						CCTCTATGCCCGGCCCTTCAC	0.542													C|||	23	0.00459265	0.0166	0.0014	5008	,	,		21719	0.0		0.0	False		,,,				2504	0.0				p.R260W		Atlas-SNP	.											.	OR4D2	48	.	0			c.C778T						PASS	.	C	TRP/ARG	59,4347	57.4+/-93.9	0,59,2144	167.0	129.0	142.0		778	5.7	1.0	17	dbSNP_134	142	0,8600		0,0,4300	yes	missense	OR4D2	NM_001004707.3	101	0,59,6444	TT,TC,CC		0.0,1.3391,0.4536	benign	260/308	56247794	59,12947	2203	4300	6503	SO:0001583	missense	124538	exon1			TATGCCCGGCCCT		CCDS32688.1	17q22	2013-09-23			ENSG00000255713	ENSG00000255713		"""GPCR / Class A : Olfactory receptors"""	8294	protein-coding gene	gene with protein product							Standard	NM_001004707		Approved		uc010wnp.2	P58180	OTTHUMG00000178801	ENST00000545221.1:c.778C>T	17.37:g.56247794C>T	ENSP00000441354:p.Arg260Trp	361.0	1.0	0.00277008		362.0	191.0	0.527624	NM_001004707	Q6IFN8|Q96R75	Missense_Mutation	SNP	ENST00000545221.1	37	CCDS32688.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	12.16	1.854682	0.32791	0.013391	0.0	ENSG00000255713	ENST00000545221	T	0.37915	1.17	5.71	5.71	0.89125	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	D	0.000115	T	0.25082	0.0609	M	0.81341	2.54	0.30651	N	0.755458	B	0.33345	0.409	B	0.34931	0.192	T	0.40887	-0.9539	10	0.30854	T	0.27	-13.8261	11.0572	0.47925	0.0:0.9155:0.0:0.0845	.	260	P58180	OR4D2_HUMAN	W	260	ENSP00000441354:R260W	ENSP00000441354:R260W	R	+	1	2	OR4D2	53602793	0.003000	0.15002	0.994000	0.49952	0.678000	0.39670	1.764000	0.38471	2.860000	0.98153	0.609000	0.83330	CGG	C|0.995;T|0.005	0.005	strong		0.542	OR4D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443366.1		
RINT1	60561	hgsc.bcm.edu	37	7	105182995	105182995	+	Silent	SNP	G	G	A	rs7805216	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:105182995G>A	ENST00000257700.2	+	4	645	c.414G>A	c.(412-414)gcG>gcA	p.A138A	RINT1_ENST00000477285.1_3'UTR	NM_021930.4	NP_068749.3	Q6NUQ1	RINT1_HUMAN	RAD50 interactor 1	138					G2 DNA damage checkpoint (GO:0031572)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						TGCTGACTGCGCAACCTTGGA	0.403													G|||	307	0.0613019	0.2209	0.0187	5008	,	,		16144	0.0		0.002	False		,,,				2504	0.0				p.A138A		Atlas-SNP	.											.	RINT1	65	.	0			c.G414A						PASS	.	G		770,3636	312.7+/-292.7	65,640,1498	120.0	112.0	115.0		414	-10.0	0.1	7	dbSNP_116	115	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	RINT1	NM_021930.4		65,646,5792	AA,AG,GG		0.0698,17.4762,5.9665		138/793	105182995	776,12230	2203	4300	6503	SO:0001819	synonymous_variant	60561	exon4			GACTGCGCAACCT	AF317622	CCDS34726.1	7q22.2	2007-05-03			ENSG00000135249	ENSG00000135249			21876	protein-coding gene	gene with protein product		610089				11096100, 15029241	Standard	NM_021930		Approved	FLJ11785, RINT-1	uc003vda.1	Q6NUQ1	OTTHUMG00000157400	ENST00000257700.2:c.414G>A	7.37:g.105182995G>A		180.0	0.0	0		218.0	106.0	0.486239	NM_021930	Q75MG9|Q75MH0|Q96IW8|Q9H229|Q9HAD9	Silent	SNP	ENST00000257700.2	37	CCDS34726.1																																																																																			G|0.939;A|0.061	0.061	strong		0.403	RINT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348686.1	NM_021930	
RNASE4	6038	hgsc.bcm.edu	37	14	21167837	21167837	+	Missense_Mutation	SNP	G	G	A	rs59543367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:21167837G>A	ENST00000555835.1	+	2	983	c.307G>A	c.(307-309)Gta>Ata	p.V103I	RNASE4_ENST00000304704.4_Missense_Mutation_p.V103I|AL163636.6_ENST00000553909.1_3'UTR|RNASE4_ENST00000555597.1_Missense_Mutation_p.V103I|RNASE4_ENST00000397995.2_Missense_Mutation_p.V103I|RP11-903H12.3_ENST00000554286.1_RNA	NM_002937.3	NP_002928.1	P34096	RNAS4_HUMAN	ribonuclease, RNase A family, 4	103					cellular response to starvation (GO:0009267)|mRNA cleavage (GO:0006379)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	nucleic acid binding (GO:0003676)|pancreatic ribonuclease activity (GO:0004522)			central_nervous_system(1)|large_intestine(1)|lung(3)|skin(1)	6	all_cancers(95;0.00304)		Epithelial(56;5.13e-07)|all cancers(55;4.73e-06)	GBM - Glioblastoma multiforme(265;0.0133)		CCATGAGGGTGTAGTGAAGGT	0.493													G|||	22	0.00439297	0.0151	0.0029	5008	,	,		22587	0.0		0.0	False		,,,				2504	0.0				p.V103I	Esophageal Squamous(59;1059 1362 26290 51151)	Atlas-SNP	.											.	RNASE4	18	.	0			c.G307A						PASS	.	G	ILE/VAL,ILE/VAL	58,4348	57.4+/-93.9	0,58,2145	154.0	127.0	136.0		307,307	2.9	1.0	14	dbSNP_129	136	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense	RNASE4	NM_002937.3,NM_194431.1	29,29	0,61,6442	AA,AG,GG		0.0349,1.3164,0.469	benign,benign	103/148,103/148	21167837	61,12945	2203	4300	6503	SO:0001583	missense	6038	exon2			GAGGGTGTAGTGA	U36775	CCDS9555.1	14q11	2014-07-16			ENSG00000258818	ENSG00000258818		"""Ribonucleases, RNase A"""	10047	protein-coding gene	gene with protein product		601030				7501448	Standard	NM_002937		Approved		uc001vxy.4	P34096	OTTHUMG00000029575	ENST00000555835.1:c.307G>A	14.37:g.21167837G>A	ENSP00000452245:p.Val103Ile	36.0	0.0	0		30.0	22.0	0.733333	NM_002937		Missense_Mutation	SNP	ENST00000555835.1	37	CCDS9555.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	G	15.78	2.935052	0.52866	0.013164	3.49E-4	ENSG00000258818;ENSG00000258818;ENSG00000258818;ENSG00000181784;ENSG00000181784;ENSG00000181784	ENST00000555835;ENST00000397995;ENST00000555597;ENST00000398001;ENST00000304704;ENST00000397999	T;T;T;T;T;T	0.72615	-0.67;-0.67;-0.67;-0.67;-0.67;-0.67	5.8	2.92	0.33932	Ribonuclease A, domain (4);	0.325719	0.26453	N	0.024288	T	0.39572	0.1083	L	0.29908	0.895	0.28449	N	0.916432	B	0.06786	0.001	B	0.11329	0.006	T	0.47711	-0.9096	10	0.52906	T	0.07	-2.5954	8.6786	0.34194	0.2536:0.0:0.7464:0.0	rs59543367	103	P34096	RNAS4_HUMAN	I	103	ENSP00000452245:V103I;ENSP00000381081:V103I;ENSP00000451624:V103I;ENSP00000381087:V103I;ENSP00000307096:V103I;ENSP00000381085:V103I	ENSP00000307096:V103I	V	+	1	0	AL163636.2;RNASE4	20237677	0.769000	0.28531	0.998000	0.56505	0.957000	0.61999	1.259000	0.32956	0.886000	0.36113	0.650000	0.86243	GTA	G|0.994;A|0.006	0.006	strong		0.493	RNASE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073729.3		
AKAP8L	26993	hgsc.bcm.edu	37	19	15512393	15512393	+	Silent	SNP	G	G	A	rs61739315	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15512393G>A	ENST00000397410.5	-	5	514	c.384C>T	c.(382-384)tgC>tgT	p.C128C	AKAP8L_ENST00000595879.1_5'Flank|AKAP8L_ENST00000595465.2_Silent_p.C67C	NM_014371.2	NP_055186.2	Q9ULX6	AKP8L_HUMAN	A kinase (PRKA) anchor protein 8-like	128						cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	DEAD/H-box RNA helicase binding (GO:0017151)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(4)|kidney(2)|lung(1)|ovary(1)|prostate(1)|urinary_tract(1)	11						CCCTCGAGTCGCAGGACTCAT	0.597													G|||	43	0.00858626	0.0295	0.0058	5008	,	,		17723	0.0		0.0	False		,,,				2504	0.0				p.C128C		Atlas-SNP	.											.	AKAP8L	64	.	0			c.C384T						PASS	.	G		118,4112		2,114,1999	29.0	28.0	29.0		384	2.4	1.0	19	dbSNP_129	29	2,8440		0,2,4219	no	coding-synonymous	AKAP8L	NM_014371.2		2,116,6218	AA,AG,GG		0.0237,2.7896,0.947		128/647	15512393	120,12552	2115	4221	6336	SO:0001819	synonymous_variant	26993	exon5			CGAGTCGCAGGAC	BC000713	CCDS46005.1	19p13.12	2013-10-16			ENSG00000011243	ENSG00000011243			29857	protein-coding gene	gene with protein product	"""neighbor of A kinase anchoring protein 95"""	609475				10748171, 10761695	Standard	XM_005259854		Approved	NAKAP95, HAP95	uc002naw.1	Q9ULX6	OTTHUMG00000182446	ENST00000397410.5:c.384C>T	19.37:g.15512393G>A		42.0	0.0	0		48.0	19.0	0.395833	NM_014371	B4DJ74|B5BU90|O94792|Q96J58|Q9NRQ0|Q9UGM0	Silent	SNP	ENST00000397410.5	37	CCDS46005.1																																																																																			G|0.991;A|0.009	0.009	strong		0.597	AKAP8L-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461301.2	NM_014371	
GPNMB	10457	hgsc.bcm.edu	37	7	23300352	23300352	+	Silent	SNP	G	G	T	rs35115002	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:23300352G>T	ENST00000381990.2	+	6	1139	c.978G>T	c.(976-978)ccG>ccT	p.P326P	GPNMB_ENST00000539136.1_Silent_p.P227P|GPNMB_ENST00000258733.4_Silent_p.P326P|GPNMB_ENST00000453162.2_Silent_p.P268P	NM_001005340.1|NM_002510.2	NP_001005340.1|NP_002501.1	Q14956	GPNMB_HUMAN	glycoprotein (transmembrane) nmb	326	PKD. {ECO:0000255|PROSITE- ProRule:PRU00151}.|Poly-Pro.				bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|negative regulation of cell proliferation (GO:0008285)|osteoblast differentiation (GO:0001649)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)			breast(5)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(3)|stomach(2)	41			GBM - Glioblastoma multiforme(13;0.154)			GTCCGCCACCGCCACCACCAC	0.493													G|||	11	0.00219649	0.0083	0.0	5008	,	,		18491	0.0		0.0	False		,,,				2504	0.0				p.P326P		Atlas-SNP	.											.	GPNMB	88	.	0			c.G978T						PASS	.	G	,	58,4348	56.2+/-92.4	0,58,2145	119.0	128.0	125.0		978,978	-0.3	0.0	7	dbSNP_126	125	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	GPNMB	NM_001005340.1,NM_002510.2	,	0,58,6445	TT,TG,GG		0.0,1.3164,0.4459	,	326/573,326/561	23300352	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	10457	exon6			GCCACCGCCACCA	X76534	CCDS5380.1, CCDS34610.1	7p	2008-07-18			ENSG00000136235	ENSG00000136235			4462	protein-coding gene	gene with protein product	"""transmembrane glycoprotein"", ""glycoprotein NMB"", ""glycoprotein nmb-like protein"", ""osteoactivin"""	604368				7814155	Standard	NM_002510		Approved	NMB, HGFIN	uc003swc.3	Q14956	OTTHUMG00000022811	ENST00000381990.2:c.978G>T	7.37:g.23300352G>T		83.0	0.0	0		73.0	40.0	0.547945	NM_002510	A4D155|Q6UVX1|Q8N1A1	Silent	SNP	ENST00000381990.2	37	CCDS34610.1																																																																																			G|0.995;T|0.005	0.005	strong		0.493	GPNMB-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327152.1	NM_001005340	
ZNF446	55663	hgsc.bcm.edu	37	19	58991075	58991075	+	Silent	SNP	C	C	T	rs140158663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58991075C>T	ENST00000594369.1	+	5	1074	c.693C>T	c.(691-693)taC>taT	p.Y231Y	ZNF446_ENST00000596341.1_Silent_p.Y231Y|ZNF446_ENST00000335841.4_Intron	NM_017908.2	NP_060378.1	Q9NWS9	ZN446_HUMAN	zinc finger protein 446	231	KRAB.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	extracellular space (GO:0005615)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	8		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)		TGGAGAAGTACGGCACAGTGG	0.667													C|||	8	0.00159744	0.0061	0.0	5008	,	,		13917	0.0		0.0	False		,,,				2504	0.0				p.Y231Y		Atlas-SNP	.											.	ZNF446	22	.	0			c.C693T						PASS	.	C		19,4387	25.3+/-52.1	0,19,2184	106.0	93.0	97.0		693	-0.8	0.5	19	dbSNP_134	97	0,8600		0,0,4300	no	coding-synonymous	ZNF446	NM_017908.2		0,19,6484	TT,TC,CC		0.0,0.4312,0.1461		231/451	58991075	19,12987	2203	4300	6503	SO:0001819	synonymous_variant	55663	exon5			GAAGTACGGCACA		CCDS12982.1	19q13.43	2013-01-09				ENSG00000083838		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	21036	protein-coding gene	gene with protein product							Standard	NM_017908		Approved	ZKSCAN20, FLJ20626, ZSCAN52	uc002qsz.3	Q9NWS9		ENST00000594369.1:c.693C>T	19.37:g.58991075C>T		87.0	0.0	0		99.0	43.0	0.434343	NM_017908		Silent	SNP	ENST00000594369.1	37	CCDS12982.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	18.25	3.582969	0.65992	0.004312	0.0	ENSG00000083838	ENST00000391694	.	.	.	4.99	-0.83	0.10792	.	.	.	.	.	T	0.24122	0.0584	.	.	.	0.21675	N	0.999593	.	.	.	.	.	.	T	0.37126	-0.9719	5	0.87932	D	0	-20.9173	7.3852	0.26878	0.0:0.4473:0.0:0.5527	.	.	.	.	M	61	.	ENSP00000375576:T61M	T	+	2	0	ZNF446	63682887	0.000000	0.05858	0.518000	0.27811	0.871000	0.50021	-0.566000	0.05922	0.062000	0.16340	0.655000	0.94253	ACG	C|0.998;T|0.002	0.002	strong		0.667	ZNF446-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467052.1	NM_017908	
HDAC9	9734	hgsc.bcm.edu	37	7	18914209	18914209	+	Silent	SNP	G	G	T	rs17140166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:18914209G>T	ENST00000432645.2	+	21	2784	c.2784G>T	c.(2782-2784)gtG>gtT	p.V928V	HDAC9_ENST00000401921.1_Silent_p.V887V|HDAC9_ENST00000441542.2_Silent_p.V931V|HDAC9_ENST00000406451.4_Silent_p.V928V	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	928	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	GGTACAAAGTGACGGCAAAAT	0.443													G|||	94	0.01877	0.0681	0.0029	5008	,	,		18680	0.0		0.002	False		,,,				2504	0.0				p.V931V		Atlas-SNP	.											.	HDAC9	560	.	0			c.G2793T						PASS	.	G	,,	258,3528		7,244,1642	67.0	62.0	64.0		2784,2784,2793	1.4	1.0	7	dbSNP_123	64	4,8238		0,4,4117	no	coding-synonymous,coding-synonymous,coding-synonymous	HDAC9	NM_058176.2,NM_178423.1,NM_178425.2	,,	7,248,5759	TT,TG,GG		0.0485,6.8146,2.1783	,,	928/1012,928/1067,931/1070	18914209	262,11766	1893	4121	6014	SO:0001819	synonymous_variant	9734	exon21			CAAAGTGACGGCA	AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.2784G>T	7.37:g.18914209G>T		64.0	0.0	0		80.0	35.0	0.4375	NM_178425	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Silent	SNP	ENST00000432645.2	37	CCDS47555.1																																																																																			G|0.975;T|0.025	0.025	strong		0.443	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1		
ZSCAN25	221785	hgsc.bcm.edu	37	7	99227027	99227027	+	Missense_Mutation	SNP	C	C	T	rs142120776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99227027C>T	ENST00000394152.2	+	8	1346	c.1019C>T	c.(1018-1020)aCc>aTc	p.T340I	ZSCAN25_ENST00000466948.1_Intron|ZSCAN25_ENST00000262941.6_Missense_Mutation_p.T268I|ZSCAN25_ENST00000334715.3_Missense_Mutation_p.T340I	NM_145115.2	NP_660090.2	Q6NSZ9	ZSC25_HUMAN	zinc finger and SCAN domain containing 25	340					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)										GAAGTCAAAACCCACAGCTCC	0.617													C|||	14	0.00279553	0.0106	0.0	5008	,	,		18729	0.0		0.0	False		,,,				2504	0.0				p.T340I		Atlas-SNP	.											.	.	.	.	0			c.C1019T						PASS	.	C	ILE/THR	48,4358	47.5+/-82.1	0,48,2155	57.0	50.0	52.0		1019	3.9	0.0	7	dbSNP_134	52	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ZNF498	NM_145115.2	89	0,49,6454	TT,TC,CC		0.0116,1.0894,0.3767	possibly-damaging	340/545	99227027	49,12957	2203	4300	6503	SO:0001583	missense	221785	exon8			TCAAAACCCACAG	AK057030	CCDS5671.2	7q22.1	2013-01-09	2013-01-09	2013-01-09	ENSG00000197037	ENSG00000197037		"""-"", ""Zinc fingers, C2H2-type"""	21961	protein-coding gene	gene with protein product			"""zinc finger protein 498"""	ZNF498		11179890	Standard	XM_005250194		Approved	FLJ32468	uc003url.1	Q6NSZ9	OTTHUMG00000074055	ENST00000394152.2:c.1019C>T	7.37:g.99227027C>T	ENSP00000377708:p.Thr340Ile	57.0	0.0	0		59.0	28.0	0.474576	NM_145115	A4D290|D6W5T5|Q14C82|Q14C99|Q5EBM9|Q6DJZ0|Q6N032|Q6ZML3	Missense_Mutation	SNP	ENST00000394152.2	37	CCDS5671.2	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	8.033	0.762232	0.15914	0.010894	1.16E-4	ENSG00000197037	ENST00000394152;ENST00000334715;ENST00000262941	T;T;T	0.09073	3.03;3.03;3.02	3.89	3.89	0.44902	.	0.669254	0.13160	N	0.409125	T	0.03520	0.0101	N	0.11364	0.135	0.09310	N	1	B;B	0.26195	0.144;0.089	B;B	0.21546	0.025;0.035	T	0.35724	-0.9777	10	0.23891	T	0.37	-2.1444	14.1776	0.65552	0.0:1.0:0.0:0.0	.	268;340	Q6NSZ9-2;Q6NSZ9	.;ZN498_HUMAN	I	340;340;268	ENSP00000377708:T340I;ENSP00000334800:T340I;ENSP00000262941:T268I	ENSP00000262941:T268I	T	+	2	0	ZNF498	99064963	0.017000	0.18338	0.018000	0.16275	0.514000	0.34195	1.627000	0.37050	2.454000	0.82982	0.561000	0.74099	ACC	C|0.998;T|0.002	0.002	strong		0.617	ZSCAN25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157203.4	NM_145115	
THRSP	7069	hgsc.bcm.edu	37	11	77775157	77775157	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:77775157G>A	ENST00000281030.2	+	1	251	c.230G>A	c.(229-231)cGg>cAg	p.R77Q	NDUFC2-KCTD14_ENST00000530054.1_Intron|NDUFC2-KCTD14_ENST00000528251.1_Intron	NM_003251.3	NP_003242.1	Q92748	THRSP_HUMAN	thyroid hormone responsive	77					lipid metabolic process (GO:0006629)|regulation of lipid biosynthetic process (GO:0046890)|regulation of transcription, DNA-templated (GO:0006355)|regulation of triglyceride biosynthetic process (GO:0010866)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)				breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	7	all_cancers(14;2.23e-19)|all_epithelial(13;7.49e-22)|Breast(9;6.38e-17)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;2.15e-25)			CTGCTGCCGCGGGAGGAGTGG	0.632																																					p.R77Q		Atlas-SNP	.											.	THRSP	18	.	0			c.G230A						PASS	.						66.0	70.0	68.0					11																	77775157		2200	4292	6492	SO:0001583	missense	7069	exon1			TGCCGCGGGAGGA	Y08409	CCDS8256.1	11q14.1	2012-06-19	2010-06-25		ENSG00000151365	ENSG00000151365			11800	protein-coding gene	gene with protein product	"""SPOT14 homolog (rat)"""	601926	"""thyroid hormone responsive SPOT14 (rat) homolog"", ""lipogenic protein 1"""	LPGP1		9003802	Standard	NM_003251		Approved	SPOT14, Lpgp, S14, THRP	uc001oyx.3	Q92748	OTTHUMG00000166632	ENST00000281030.2:c.230G>A	11.37:g.77775157G>A	ENSP00000281030:p.Arg77Gln	128.0	0.0	0		120.0	62.0	0.516667	NM_003251	B2R4W7	Missense_Mutation	SNP	ENST00000281030.2	37	CCDS8256.1	.	.	.	.	.	.	.	.	.	.	G	9.274	1.046346	0.19748	.	.	ENSG00000151365	ENST00000281030	.	.	.	4.96	1.88	0.25563	.	0.320599	0.29328	N	0.012474	T	0.18045	0.0433	.	.	.	0.09310	N	1	B	0.25169	0.119	B	0.17722	0.019	T	0.09684	-1.0663	8	0.26408	T	0.33	-4.5778	3.7206	0.08454	0.3124:0.1858:0.5018:0.0	.	77	Q92748	THRSP_HUMAN	Q	77	.	ENSP00000281030:R77Q	R	+	2	0	THRSP	77452805	0.582000	0.26749	0.195000	0.23364	0.730000	0.41778	0.188000	0.17018	0.700000	0.31782	0.561000	0.74099	CGG	.	.	none		0.632	THRSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390939.1	NM_003251	
CBLN3	643866	hgsc.bcm.edu	37	14	24898135	24898135	+	Silent	SNP	C	C	T	rs57646536	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24898135C>T	ENST00000267406.6	-	1	596	c.126G>A	c.(124-126)gaG>gaA	p.E42E	CBLN3_ENST00000555436.1_Intron|KHNYN_ENST00000556842.1_5'Flank|KHNYN_ENST00000251343.5_5'Flank|KHNYN_ENST00000553935.1_5'Flank	NM_001039771.2	NP_001034860.1	Q6UW01	CBLN3_HUMAN	cerebellin 3 precursor	42						cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|synapse (GO:0045202)				central_nervous_system(1)|lung(3)	4				GBM - Glioblastoma multiforme(265;0.00159)		GGCACTCCCCCTCCAGCAGGA	0.716													C|||	296	0.0591054	0.2088	0.0274	5008	,	,		13699	0.0		0.001	False		,,,				2504	0.0				p.E42E		Atlas-SNP	.											.	CBLN3	21	.	0			c.G126A						PASS	.	C		554,3752		31,492,1630	9.0	11.0	10.0		126	1.0	1.0	14	dbSNP_129	10	5,8401		0,5,4198	no	coding-synonymous	CBLN3	NM_001039771.2		31,497,5828	TT,TC,CC		0.0595,12.8658,4.3974		42/206	24898135	559,12153	2153	4203	6356	SO:0001819	synonymous_variant	643866	exon1			CTCCCCCTCCAGC	AY359070	CCDS32057.1	14q12	2006-12-13				ENSG00000139899			20146	protein-coding gene	gene with protein product		612978				12975309	Standard	NM_001039771		Approved		uc001wpg.4	Q6UW01		ENST00000267406.6:c.126G>A	14.37:g.24898135C>T		121.0	0.0	0		99.0	50.0	0.50505	NM_001039771		Silent	SNP	ENST00000267406.6	37	CCDS32057.1																																																																																			C|0.963;T|0.037	0.037	strong		0.716	CBLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412943.1	XM_115232	
RGAG4	340526	hgsc.bcm.edu	37	X	71350294	71350294	+	Missense_Mutation	SNP	A	A	G	rs146618350		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:71350294A>G	ENST00000545866.1	-	1	1464	c.1097T>C	c.(1096-1098)aTg>aCg	p.M366T	RGAG4_ENST00000609883.1_Missense_Mutation_p.M366T|NHSL2_ENST00000540800.1_Intron	NM_001024455.3	NP_001019626.1	Q5HYW3	RGAG4_HUMAN	retrotransposon gag domain containing 4	366										cervix(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|skin(1)	24	Renal(35;0.156)					AAAAGCCCTCATGCGCTTCCT	0.498													A|||	19	0.00503311	0.0144	0.0	3775	,	,		14735	0.0		0.0	False		,,,				2504	0.0				p.M366T		Atlas-SNP	.											.	RGAG4	63	.	0			c.T1097C						PASS	.	A	,THR/MET	57,3395		0,49,8,1392,562	43.0	36.0	39.0		,1097	2.9	0.0	X	dbSNP_134	39	0,6522		0,0,0,2358,1806	yes	intron,missense	RGAG4,NHSL2	NM_001013627.2,NM_001024455.3	,81	0,49,8,3750,2368	GG,GA,G,AA,A		0.0,1.6512,0.5715	,benign	,366/570	71350294	57,9917	2011	4164	6175	SO:0001583	missense	340526	exon1			GCCCTCATGCGCT	AB082532	CCDS55446.1	Xq13.1	2008-02-05			ENSG00000242732	ENSG00000242732			29430	protein-coding gene	gene with protein product						12056414, 15716091, 16093683	Standard	NM_001024455		Approved	KIAA2001, Mar5, Mart5	uc004eaj.2	Q5HYW3	OTTHUMG00000021808	ENST00000545866.1:c.1097T>C	X.37:g.71350294A>G	ENSP00000441366:p.Met366Thr	205.0	0.0	0		238.0	237.0	0.995798	NM_001024455	A7E2W7|Q8NCM4|Q9NPX1	Missense_Mutation	SNP	ENST00000545866.1	37	CCDS55446.1	10	0.006027727546714889	7	0.01440329218106996	0	0.0	0	0.0	0	0.0	A	9.812	1.183556	0.21870	0.016512	0.0	ENSG00000242732	ENST00000545866;ENST00000479991	T;T	0.12984	2.63;2.63	4.13	2.94	0.34122	.	.	.	.	.	T	0.03305	0.0096	N	0.14661	0.345	0.09310	N	1	B	0.22276	0.067	B	0.15052	0.012	T	0.39742	-0.9599	8	.	.	.	-2.2205	8.3218	0.32134	0.8026:0.1974:0.0:0.0	.	366	Q5HYW3	RGAG4_HUMAN	T	366	ENSP00000441366:M366T;ENSP00000418667:M366T	.	M	-	2	0	RGAG4	71267019	0.000000	0.05858	0.001000	0.08648	0.122000	0.20287	0.748000	0.26305	0.701000	0.31803	0.486000	0.48141	ATG	A|0.994;G|0.006	0.006	strong		0.498	RGAG4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057171.1	NM_001024455	
ANKRD36B	57730	hgsc.bcm.edu	37	2	98201527	98201527	+	RNA	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:98201527G>A	ENST00000443455.1	-	0	508							Q8N2N9	AN36B_HUMAN	ankyrin repeat domain 36B																		TATTTGGATCGGCGCCATTTT	0.413																																					p.A110A		Atlas-SNP	.											.	.	.	.	0			c.C330T						PASS	.						22.0	18.0	19.0					2																	98201527		692	1578	2270			57730	exon3			TGGATCGGCGCCA	AK024934	CCDS74543.1	2q11.2	2013-01-11	2008-03-25	2008-03-25	ENSG00000196912	ENSG00000196912		"""Ankyrin repeat domain containing"""	29333	protein-coding gene	gene with protein product	"""melanoma-associated antigen"", ""CLL-associated antigen KW-1"""		"""KIAA1641"""	KIAA1641		10997877	Standard	NM_025190		Approved	FLJ21281	uc010yvc.1	Q8N2N9	OTTHUMG00000130547		2.37:g.98201527G>A		1252.0	1.0	0.000798722		1172.0	406.0	0.346416	NM_025190	Q08AK5|Q6IPR0|Q6PI49|Q8IZM7|Q8TDH6|Q96N30|Q9H759	Silent	SNP	ENST00000443455.1	37																																																																																				.	.	none		0.413	ANKRD36B-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000328967.2	NM_025190	
PRSS36	146547	hgsc.bcm.edu	37	16	31151927	31151927	+	Silent	SNP	G	G	A	rs61976958	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31151927G>A	ENST00000268281.4	-	13	2111	c.2053C>T	c.(2053-2055)Ctg>Ttg	p.L685L	PRSS36_ENST00000418068.2_Intron|PRSS36_ENST00000569305.1_Silent_p.L680L	NM_001258290.1|NM_173502.4	NP_001245219.1|NP_775773.2	Q5K4E3	POLS2_HUMAN	protease, serine, 36	685	Peptidase S1 3. {ECO:0000255|PROSITE- ProRule:PRU00274}.					cytoplasm (GO:0005737)|proteinaceous extracellular matrix (GO:0005578)	serine-type endopeptidase activity (GO:0004252)			kidney(2)|large_intestine(4)|lung(8)|ovary(3)	17						CGGGAGCTCAGCTCCAGGAGG	0.706													G|||	78	0.0155751	0.0545	0.0086	5008	,	,		15742	0.0		0.0	False		,,,				2504	0.0				p.L685L		Atlas-SNP	.											.	PRSS36	50	.	0			c.C2053T						PASS	.	G		227,4155		8,211,1972	14.0	19.0	17.0		2053	2.7	1.0	16	dbSNP_129	17	1,8573		0,1,4286	no	coding-synonymous	PRSS36	NM_173502.3		8,212,6258	AA,AG,GG		0.0117,5.1803,1.7598		685/856	31151927	228,12728	2191	4287	6478	SO:0001819	synonymous_variant	146547	exon13			AGCTCAGCTCCAG	AK075142	CCDS32436.1, CCDS58452.1, CCDS58453.1	16p11.2	2014-09-04			ENSG00000178226			"""Serine peptidases / Serine peptidases"""	26906	protein-coding gene	gene with protein product	"""polyserase 2"""	610560				15536082	Standard	NM_173502		Approved	FLJ90661	uc002ebd.4	Q5K4E3	OTTHUMG00000176751	ENST00000268281.4:c.2053C>T	16.37:g.31151927G>A		75.0	0.0	0		69.0	28.0	0.405797	NM_173502	A8K2P5|B4DW80|B7ZMK8|E7EX56|Q8NBY4	Silent	SNP	ENST00000268281.4	37	CCDS32436.1																																																																																			G|0.983;A|0.017	0.017	strong		0.706	PRSS36-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000433542.1	NM_173502	
ROBO4	54538	hgsc.bcm.edu	37	11	124764176	124764176	+	Silent	SNP	T	T	C	rs11820142	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124764176T>C	ENST00000306534.3	-	8	1724	c.1239A>G	c.(1237-1239)ccA>ccG	p.P413P	ROBO4_ENST00000526899.1_5'Flank|ROBO4_ENST00000533054.1_Silent_p.P268P	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	413	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		AGTAGGAGCCTGGCATATGGG	0.597													T|||	125	0.0249601	0.0893	0.0086	5008	,	,		3618	0.0		0.001	False		,,,				2504	0.0				p.P413P		Atlas-SNP	.											.	ROBO4	130	.	0			c.A1239G						PASS	.	T		344,4058	179.4+/-207.9	9,326,1866	111.0	87.0	95.0		1239	1.1	1.0	11	dbSNP_120	95	2,8596	1.2+/-3.3	0,2,4297	no	coding-synonymous	ROBO4	NM_019055.5		9,328,6163	CC,CT,TT		0.0233,7.8146,2.6615		413/1008	124764176	346,12654	2201	4299	6500	SO:0001819	synonymous_variant	54538	exon8			GGAGCCTGGCATA	AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17985	protein-coding gene	gene with protein product	"""magic roundabout"""	607528	"""roundabout homolog 4 (Drosophila)"""			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.1239A>G	11.37:g.124764176T>C		97.0	0.0	0		90.0	38.0	0.422222	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Silent	SNP	ENST00000306534.3	37	CCDS8455.1																																																																																			T|0.971;C|0.029	0.029	strong		0.597	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055	
ROR2	4920	hgsc.bcm.edu	37	9	94499797	94499797	+	Silent	SNP	A	A	G	rs16907720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:94499797A>G	ENST00000375708.3	-	5	696	c.498T>C	c.(496-498)gaT>gaC	p.D166D	ROR2_ENST00000550066.1_5'UTR|ROR2_ENST00000375715.1_Silent_p.D26D	NM_004560.3	NP_004551.2	Q01974	ROR2_HUMAN	receptor tyrosine kinase-like orphan receptor 2	166					cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|embryonic genitalia morphogenesis (GO:0030538)|inner ear morphogenesis (GO:0042472)|JNK cascade (GO:0007254)|multicellular organismal development (GO:0007275)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|somitogenesis (GO:0001756)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	clathrin-coated endocytic vesicle membrane (GO:0030669)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						CGTGGTAATCATCCCTGGTAA	0.512													A|||	361	0.0720847	0.1959	0.0504	5008	,	,		16550	0.0		0.0537	False		,,,				2504	0.0133				p.D166D		Atlas-SNP	.											.	ROR2	167	.	0			c.T498C						PASS	.	A		757,3649	309.1+/-290.9	63,631,1509	80.0	73.0	75.0		498	-4.9	0.8	9	dbSNP_123	75	573,8027	153.7+/-208.1	19,535,3746	no	coding-synonymous	ROR2	NM_004560.3		82,1166,5255	GG,GA,AA		6.6628,17.1811,10.226		166/944	94499797	1330,11676	2203	4300	6503	SO:0001819	synonymous_variant	4920	exon5			GTAATCATCCCTG	M97639	CCDS6691.1	9q22	2013-01-11			ENSG00000169071	ENSG00000169071		"""Immunoglobulin superfamily / I-set domain containing"""	10257	protein-coding gene	gene with protein product		602337		NTRKR2, BDB, BDB1		1334494, 10700182	Standard	NM_004560		Approved		uc004arj.2	Q01974	OTTHUMG00000020211	ENST00000375708.3:c.498T>C	9.37:g.94499797A>G		50.0	0.0	0		38.0	26.0	0.684211	NM_004560	Q59GF5|Q5SPI5|Q9HAY7|Q9HB61	Silent	SNP	ENST00000375708.3	37	CCDS6691.1																																																																																			A|0.902;G|0.098	0.098	strong		0.512	ROR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053040.1		
BEST1	7439	hgsc.bcm.edu	37	11	61730427	61730427	+	Intron	SNP	G	G	T	rs115979721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61730427G>T	ENST00000378043.4	+	10	2382				FTH1_ENST00000529631.1_Intron|BEST1_ENST00000301774.9_Missense_Mutation_p.A229S|FTH1_ENST00000529191.1_Intron|BEST1_ENST00000449131.2_Missense_Mutation_p.A541S|BEST1_ENST00000378042.3_Intron|BEST1_ENST00000534553.1_3'UTR	NM_004183.3	NP_004174.1	O76090	BEST1_HUMAN	bestrophin 1						chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|detection of light stimulus involved in visual perception (GO:0050908)|ion transmembrane transport (GO:0034220)|regulation of calcium ion transport (GO:0051924)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	basolateral plasma membrane (GO:0016323)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(2)|urinary_tract(2)	25						AGCTTCCCTTGCTCTGAGCCT	0.562													G|||	107	0.0213658	0.0764	0.0086	5008	,	,		19855	0.0		0.0	False		,,,				2504	0.0				p.A541S		Atlas-SNP	.											.	BEST1	85	.	0			c.G1621T						PASS	.	G	SER/ALA,	74,1310		2,70,620	123.0	114.0	116.0		1621,	-5.3	0.0	11	dbSNP_132	116	0,3182		0,0,1591	yes	missense,intron	BEST1	NM_001139443.1,NM_004183.3	99,	2,70,2211	TT,TG,GG		0.0,5.3468,1.6207	,	541/605,	61730427	74,4492	692	1591	2283	SO:0001627	intron_variant	7439	exon9			TCCCTTGCTCTGA	AF057170	CCDS31580.1, CCDS44623.1	11q12	2013-02-14	2006-10-18	2006-10-18	ENSG00000167995	ENSG00000167995		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	12703	protein-coding gene	gene with protein product	"""Best disease"""	607854	"""vitelliform macular dystrophy 2"""	VMD2		1302019, 17003041	Standard	NM_004183		Approved	BMD, BEST, RP50	uc001nsr.2	O76090	OTTHUMG00000167469	ENST00000378043.4:c.1739+62G>T	11.37:g.61730427G>T		193.0	0.0	0		165.0	81.0	0.490909	NM_001139443	A8K0W6|B7Z3J8|B7Z736|O75904|Q53YQ9|Q8IUR9|Q8IZ80	Missense_Mutation	SNP	ENST00000378043.4	37	CCDS31580.1	40	0.018315018315018316	38	0.07723577235772358	2	0.0055248618784530384	0	0.0	0	0.0	G	12.96	2.094835	0.36952	0.053468	0.0	ENSG00000167995	ENST00000301774;ENST00000449131	T;D	0.97089	-0.32;-4.24	4.13	-5.35	0.02697	.	.	.	.	.	T	0.35098	0.0920	N	0.08118	0	0.09310	N	0.999995	B	0.17268	0.021	B	0.14023	0.01	T	0.73116	-0.4084	8	.	.	.	.	0.3641	0.00369	0.2188:0.2264:0.2454:0.3094	.	541	O76090-3	.	S	229;541	ENSP00000301774:A229S;ENSP00000399709:A541S	.	A	+	1	0	BEST1	61487003	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.419000	0.07071	-1.297000	0.02351	-0.311000	0.09066	GCT	G|0.977;T|0.023	0.023	strong		0.562	BEST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394715.1	NM_004183	
ANKUB1	389161	hgsc.bcm.edu	37	3	149485581	149485581	+	Missense_Mutation	SNP	C	C	T	rs75855073	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:149485581C>T	ENST00000383050.3	-	5	1324	c.868G>A	c.(868-870)Gta>Ata	p.V290I	ANKUB1_ENST00000462519.2_Missense_Mutation_p.V290I|ANKUB1_ENST00000446160.1_Missense_Mutation_p.V290I			A6NFN9	ANKUB_HUMAN	ankyrin repeat and ubiquitin domain containing 1	290										breast(1)|kidney(1)|lung(1)|skin(1)	4						AAATATAATACACAGTCTTTA	0.388													C|||	112	0.0223642	0.0794	0.0101	5008	,	,		21007	0.0		0.0	False		,,,				2504	0.0				p.V290I		Atlas-SNP	.											.	ANKUB1	27	.	0			c.G868A						PASS	.	C	ILE/VAL	73,1311		1,71,620	89.0	74.0	79.0		868	5.2	0.3	3	dbSNP_132	79	0,3182		0,0,1591	yes	missense	ANKUB1	NM_001144960.1	29	1,71,2211	TT,TC,CC		0.0,5.2746,1.5988	benign	290/545	149485581	73,4493	692	1591	2283	SO:0001583	missense	389161	exon5			ATAATACACAGTC	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	ENST00000383050.3:c.868G>A	3.37:g.149485581C>T	ENSP00000372522:p.Val290Ile	76.0	0.0	0		77.0	38.0	0.493506	NM_001144960	B4E2N8	Missense_Mutation	SNP	ENST00000383050.3	37		49	0.022435897435897436	45	0.09146341463414634	4	0.011049723756906077	0	0.0	0	0.0	C	15.33	2.800905	0.50315	0.052746	0.0	ENSG00000206199	ENST00000446160;ENST00000383050;ENST00000462519	T;T;T	0.71698	-0.59;-0.59;-0.59	5.16	5.16	0.70880	Ankyrin repeat-containing domain (3);	.	.	.	.	T	0.12135	0.0295	L	0.35723	1.085	0.26889	N	0.967365	D;D	0.61697	0.99;0.979	P;P	0.60789	0.879;0.879	T	0.42327	-0.9458	9	0.44086	T	0.13	.	17.4257	0.87525	0.0:1.0:0.0:0.0	.	290;290	A6NFN9;E9PHT4	ANKUB_HUMAN;.	I	290	ENSP00000387907:V290I;ENSP00000372522:V290I;ENSP00000417635:V290I	ENSP00000372522:V290I	V	-	1	0	ANKUB1	150968271	0.977000	0.34250	0.346000	0.25655	0.995000	0.86356	3.945000	0.56637	2.401000	0.81631	0.591000	0.81541	GTA	C|0.974;T|0.026	0.026	strong		0.388	ANKUB1-201	KNOWN	basic	protein_coding	protein_coding		NM_001144960	
MED13	9969	hgsc.bcm.edu	37	17	60087932	60087932	+	Missense_Mutation	SNP	T	T	C	rs114223275	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:60087932T>C	ENST00000397786.2	-	9	2022	c.1946A>G	c.(1945-1947)gAa>gGa	p.E649G		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	649					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						TGTTACACTTTCCTGTCCAAA	0.333													T|||	7	0.00139776	0.0053	0.0	5008	,	,		20038	0.0		0.0	False		,,,				2504	0.0				p.E649G		Atlas-SNP	.											.	MED13	181	.	0			c.A1946G						PASS	.	T	GLY/GLU	11,3675		0,11,1832	67.0	60.0	62.0		1946	5.6	1.0	17	dbSNP_132	62	0,8172		0,0,4086	yes	missense	MED13	NM_005121.2	98	0,11,5918	CC,CT,TT		0.0,0.2984,0.0928	probably-damaging	649/2175	60087932	11,11847	1843	4086	5929	SO:0001583	missense	9969	exon9			ACACTTTCCTGTC	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"""thyroid hormone receptor associated protein 1"""	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.1946A>G	17.37:g.60087932T>C	ENSP00000380888:p.Glu649Gly	121.0	0.0	0		102.0	45.0	0.441176	NM_005121	B2RU05|O60334	Missense_Mutation	SNP	ENST00000397786.2	37	CCDS42366.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	T	12.76	2.033391	0.35893	0.002984	0.0	ENSG00000108510	ENST00000397786;ENST00000262436	T	0.75367	-0.93	5.62	5.62	0.85841	.	0.156711	0.44483	D	0.000448	T	0.74604	0.3738	L	0.46157	1.445	0.58432	D	0.999998	P;B	0.44139	0.827;0.181	P;B	0.46758	0.526;0.014	T	0.75639	-0.3248	10	0.46703	T	0.11	-17.8348	15.804	0.78477	0.0:0.0:0.0:1.0	.	162;649	Q9P0Q5;Q9UHV7	.;MED13_HUMAN	G	649;648	ENSP00000380888:E649G	ENSP00000262436:E648G	E	-	2	0	MED13	57442714	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.998000	0.63927	2.131000	0.65755	0.477000	0.44152	GAA	T|0.999;C|0.001	0.001	strong		0.333	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121	
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377120	49377120	+	Silent	SNP	C	C	T	rs34899467	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49377120C>T	ENST00000200453.5	+	2	899	c.630C>T	c.(628-630)gcC>gcT	p.A210A		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	210	Glu-rich.				apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		CTACTTCTGCCTTGTCTCCAG	0.512													C|||	82	0.0163738	0.0545	0.0014	5008	,	,		18999	0.002		0.0	False		,,,				2504	0.0072				p.A210A		Atlas-SNP	.											.	PPP1R15A	48	.	0			c.C630T						PASS	.	C		201,4205	124.9+/-162.1	2,197,2004	128.0	141.0	137.0		630	-0.7	0.0	19	dbSNP_126	137	0,8600		0,0,4300	no	coding-synonymous	PPP1R15A	NM_014330.3		2,197,6304	TT,TC,CC		0.0,4.562,1.5454		210/675	49377120	201,12805	2203	4300	6503	SO:0001819	synonymous_variant	23645	exon2			TTCTGCCTTGTCT	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14375	protein-coding gene	gene with protein product	"""growth arrest and DNA-damage-inducible 34"""	611048	"""protein phosphatase 1, regulatory (inhibitor) subunit 15A"""			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.630C>T	19.37:g.49377120C>T		93.0	0.0	0		76.0	35.0	0.460526	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Silent	SNP	ENST00000200453.5	37	CCDS12738.1																																																																																			C|0.984;T|0.016	0.016	strong		0.512	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
MAP10	54627	hgsc.bcm.edu	37	1	232942276	232942276	+	Missense_Mutation	SNP	G	G	A	rs61735495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:232942276G>A	ENST00000418460.1	+	1	1634	c.1507G>A	c.(1507-1509)Gaa>Aaa	p.E503K		NM_019090.2	NP_061963.2	Q9P2G4	MAP10_HUMAN	microtubule-associated protein 10	361					cytoplasmic microtubule organization (GO:0031122)|positive regulation of cytokinesis (GO:0032467)|regulation of microtubule-based process (GO:0032886)|spindle midzone assembly involved in mitosis (GO:0051256)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)	microtubule binding (GO:0008017)										TGCAGCACACGAACATCCTCC	0.403													G|||	107	0.0213658	0.0794	0.0029	5008	,	,		20484	0.0		0.0	False		,,,				2504	0.0				p.E503K		Atlas-SNP	.											.	.	.	.	0			c.G1507A						PASS	.	G	LYS/GLU	242,3624		6,230,1697	71.0	69.0	70.0		1507	2.5	0.0	1	dbSNP_129	70	0,8278		0,0,4139	yes	missense	KIAA1383	NM_019090.2	56	6,230,5836	AA,AG,GG		0.0,6.2597,1.9928	possibly-damaging	503/1048	232942276	242,11902	1933	4139	6072	SO:0001583	missense	54627	exon1			GCACACGAACATC	AB037804	CCDS44334.1	1q42.2	2013-02-12	2013-02-12	2013-02-12	ENSG00000212916	ENSG00000212916			29265	protein-coding gene	gene with protein product	"""microtubule regulator 120 KDa"""		"""KIAA1383"""	KIAA1383		23264731	Standard	NM_019090		Approved	MTR120	uc001hvh.2	Q9P2G4	OTTHUMG00000037819	ENST00000418460.1:c.1507G>A	1.37:g.232942276G>A	ENSP00000403208:p.Glu503Lys	67.0	0.0	0		90.0	50.0	0.555556	NM_019090	A8K2F1|Q32MI1|Q58EZ9|Q5VV83	Missense_Mutation	SNP	ENST00000418460.1	37	CCDS44334.1	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	G	17.33	3.362324	0.61403	0.062597	0.0	ENSG00000212916	ENST00000418460	.	.	.	4.69	2.48	0.30137	.	.	.	.	.	T	0.04679	0.0127	M	0.67953	2.075	0.09310	N	1	P	0.49559	0.925	B	0.43052	0.406	T	0.02774	-1.1112	8	0.37606	T	0.19	-11.7864	6.2799	0.21001	0.1287:0.1763:0.695:0.0	rs61735495	361	Q9P2G4	K1383_HUMAN	K	503	.	ENSP00000403208:E503K	E	+	1	0	KIAA1383	231008899	0.003000	0.15002	0.008000	0.14137	0.002000	0.02628	0.383000	0.20651	0.673000	0.31224	0.655000	0.94253	GAA	G|0.988;A|0.012	0.012	strong		0.403	MAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092317.3	NM_019090	
URI1	8725	hgsc.bcm.edu	37	19	30500195	30500195	+	Missense_Mutation	SNP	G	G	C	rs151025990	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:30500195G>C	ENST00000542441.2	+	8	1267	c.970G>C	c.(970-972)Gct>Cct	p.A324P	URI1_ENST00000360605.4_Missense_Mutation_p.A306P|URI1_ENST00000392271.1_Missense_Mutation_p.A248P|URI1_ENST00000312051.6_Missense_Mutation_p.A284P			O94763	RMP_HUMAN	URI1, prefoldin-like chaperone	324					cellular response to growth factor stimulus (GO:0071363)|cellular response to steroid hormone stimulus (GO:0071383)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of phosphatase activity (GO:0010923)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein folding (GO:0006457)|regulation of cell growth (GO:0001558)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to virus (GO:0009615)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, core complex (GO:0005665)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|prefoldin complex (GO:0016272)	chromatin binding (GO:0003682)|protein phosphatase inhibitor activity (GO:0004864)|RNA polymerase II transcription corepressor activity (GO:0001106)										cgaCCATGAGGCTTTAGGGGT	0.378													G|||	2	0.000399361	0.0015	0.0	5008	,	,		21705	0.0		0.0	False		,,,				2504	0.0				p.A324P		Atlas-SNP	.											.	.	.	.	0			c.G970C						PASS	.	G	PRO/ALA,PRO/ALA	13,4393	20.2+/-43.8	0,13,2190	95.0	82.0	86.0		970,850	-3.2	0.0	19	dbSNP_134	86	0,8600		0,0,4300	yes	missense,missense	C19orf2	NM_003796.2,NM_134447.1	27,27	0,13,6490	CC,CG,GG		0.0,0.2951,0.1	benign,benign	324/536,284/496	30500195	13,12993	2203	4300	6503	SO:0001583	missense	8725	exon8			CATGAGGCTTTAG	AF091095	CCDS12420.1, CCDS58658.1	19q12	2012-04-17	2011-11-21	2011-11-21	ENSG00000105176	ENSG00000105176		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	13236	protein-coding gene	gene with protein product	"""unconventional prefoldin RPB5 interactor"", ""RPB5-mediating protein"", ""protein phosphatase 1, regulatory subunit 19"""	603494	"""chromosome 19 open reading frame 2"""	C19orf2		9878255, 9819440	Standard	NM_003796		Approved	RMP, NNX3, FLJ10575, URI, PPP1R19	uc002nsr.3	O94763		ENST00000542441.2:c.970G>C	19.37:g.30500195G>C	ENSP00000442436:p.Ala324Pro	88.0	0.0	0		95.0	47.0	0.494737	NM_003796	A8K805|H7BY42|Q8TC23|Q9UNU3	Missense_Mutation	SNP	ENST00000542441.2	37	CCDS12420.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	15.04	2.714683	0.48622	0.002951	0.0	ENSG00000105176	ENST00000360605;ENST00000392271;ENST00000542441;ENST00000312051	T	0.50001	0.76	5.03	-3.22	0.05125	.	1.234740	0.05290	N	0.520817	T	0.22003	0.0530	N	0.08118	0	0.09310	N	1	P;B;P	0.38642	0.545;0.41;0.641	B;B;B	0.32864	0.147;0.11;0.154	T	0.13019	-1.0525	10	0.37606	T	0.19	-1.217	5.6351	0.17532	0.3821:0.0:0.4983:0.1197	.	284;324;321	F8W9T0;O94763;Q8TC23	.;RMP_HUMAN;.	P	322;248;324;284	ENSP00000442436:A324P	ENSP00000312530:A284P	A	+	1	0	C19orf2	35192035	0.042000	0.20092	0.000000	0.03702	0.248000	0.25809	0.075000	0.14686	-0.488000	0.06726	0.491000	0.48974	GCT	G|0.998;C|0.002	0.002	strong		0.378	URI1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439756.1	NM_134447	
ZBTB4	57659	hgsc.bcm.edu	37	17	7365289	7365289	+	Silent	SNP	A	A	T	rs114898274	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7365289A>T	ENST00000311403.4	-	4	3351	c.3012T>A	c.(3010-3012)gtT>gtA	p.V1004V	ZBTB4_ENST00000380599.4_Silent_p.V1004V	NM_020899.3	NP_065950.2	Q9P1Z0	ZBTB4_HUMAN	zinc finger and BTB domain containing 4	1004					cellular response to DNA damage stimulus (GO:0006974)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)|methyl-CpNpG binding (GO:0010428)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)|prostate(3)|skin(6)	36		Colorectal(1115;3.46e-05)|Myeloproliferative disorder(207;0.0255)		COAD - Colon adenocarcinoma(228;4.1e-06)|READ - Rectum adenocarcinoma(115;0.0642)		GGGTTCTCTCAACCCCTGCCC	0.617													A|||	41	0.0081869	0.0287	0.0043	5008	,	,		14891	0.0		0.0	False		,,,				2504	0.0				p.V1004V		Atlas-SNP	.											.	ZBTB4	163	.	0			c.T3012A						PASS	.	A	,	88,4318	74.1+/-112.3	1,86,2116	58.0	64.0	62.0		3012,3012	0.3	1.0	17	dbSNP_132	62	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous,coding-synonymous	ZBTB4	NM_001128833.1,NM_020899.3	,	1,92,6410	TT,TA,AA		0.0698,1.9973,0.7227	,	1004/1014,1004/1014	7365289	94,12912	2203	4300	6503	SO:0001819	synonymous_variant	57659	exon4			TCTCTCAACCCCT	AB040971	CCDS11107.1	17p13.2	2013-01-09			ENSG00000174282	ENSG00000174282		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	23847	protein-coding gene	gene with protein product		612308				12477932	Standard	NM_020899		Approved	KIAA1538, KAISO-L1, ZNF903	uc002ghd.4	Q9P1Z0	OTTHUMG00000108137	ENST00000311403.4:c.3012T>A	17.37:g.7365289A>T		110.0	0.0	0		93.0	40.0	0.430108	NM_001128833	B3KVL6|Q7Z697|Q86XJ4|Q8N4V8	Silent	SNP	ENST00000311403.4	37	CCDS11107.1																																																																																			A|0.992;T|0.008	0.008	strong		0.617	ZBTB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226940.2	NM_020899	
TACC2	10579	hgsc.bcm.edu	37	10	123970513	123970513	+	Silent	SNP	G	G	A	rs35913854	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:123970513G>A	ENST00000369005.1	+	9	6913	c.6573G>A	c.(6571-6573)acG>acA	p.T2191T	TACC2_ENST00000360561.3_Silent_p.T269T|TACC2_ENST00000369004.3_Silent_p.T269T|TACC2_ENST00000368999.1_Silent_p.T269T|TACC2_ENST00000453444.2_Silent_p.T2195T|TACC2_ENST00000369001.1_5'UTR|TACC2_ENST00000358010.1_Silent_p.T337T|TACC2_ENST00000515603.1_Silent_p.T2146T|TACC2_ENST00000515273.1_Silent_p.T2195T|TACC2_ENST00000513429.1_Silent_p.T337T|TACC2_ENST00000260733.3_Silent_p.T269T|TACC2_ENST00000369000.1_5'UTR|TACC2_ENST00000334433.3_Silent_p.T2191T	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	2191					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				TGGAGGAGACGCCCCTTGAGC	0.597													G|||	369	0.0736821	0.2648	0.0259	5008	,	,		15618	0.0		0.001	False		,,,				2504	0.0				p.T2191T		Atlas-SNP	.											.	TACC2	271	.	0			c.G6573A						PASS	.	G	,,,	913,3491	324.5+/-298.6	109,695,1398	54.0	66.0	62.0		807,807,1011,6573	-11.1	0.0	10	dbSNP_126	62	14,8586	9.8+/-36.6	0,14,4286	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TACC2	NM_006997.2,NM_206860.1,NM_206861.1,NM_206862.2	,,,	109,709,5684	AA,AG,GG		0.1628,20.7312,7.1286	,,,	269/1027,269/997,337/1095,2191/2949	123970513	927,12077	2202	4300	6502	SO:0001819	synonymous_variant	10579	exon9			GGAGACGCCCCTT	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.6573G>A	10.37:g.123970513G>A		54.0	0.0	0		52.0	23.0	0.442308	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Silent	SNP	ENST00000369005.1	37	CCDS7626.1																																																																																			G|0.936;A|0.064	0.064	strong		0.597	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
NOS2	4843	hgsc.bcm.edu	37	17	26085931	26085931	+	Silent	SNP	G	G	A	rs3729662	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:26085931G>A	ENST00000313735.6	-	26	3563	c.3330C>T	c.(3328-3330)gtC>gtT	p.V1110V		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	1110					arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	AATAGTCCTCGACCTGCTCCT	0.607													.|||	73	0.0145767	0.0537	0.0029	5008	,	,		20547	0.0		0.0	False		,,,				2504	0.0				p.V1110V		Atlas-SNP	.											.	NOS2	113	.	0			c.C3330T						PASS	.	G		158,4248	102.5+/-141.1	1,156,2046	30.0	28.0	29.0		3330	-9.7	0.2	17	dbSNP_107	29	1,8591	1.2+/-3.3	0,1,4295	no	coding-synonymous	NOS2	NM_000625.4		1,157,6341	AA,AG,GG		0.0116,3.586,1.2233		1110/1154	26085931	159,12839	2203	4296	6499	SO:0001819	synonymous_variant	4843	exon26			GTCCTCGACCTGC	U20141	CCDS11223.1	17q11.2	2014-06-12	2008-09-16	2008-09-16	ENSG00000007171	ENSG00000007171	1.14.13.39		7873	protein-coding gene	gene with protein product		163730	"""nitric oxide synthase 2A (inducible, hepatocytes)"""	NOS2A		7682706	Standard	NM_000625		Approved	iNOS, NOS, HEP-NOS	uc002gzu.3	P35228	OTTHUMG00000132445	ENST00000313735.6:c.3330C>T	17.37:g.26085931G>A		422.0	0.0	0		451.0	212.0	0.470067	NM_000625	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Silent	SNP	ENST00000313735.6	37	CCDS11223.1																																																																																			.	.	weak		0.607	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625	
ARHGEF4	50649	hgsc.bcm.edu	37	2	131803624	131803624	+	Silent	SNP	C	C	T	rs114004756	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:131803624C>T	ENST00000326016.5	+	14	2454	c.1935C>T	c.(1933-1935)ccC>ccT	p.P645P	ARHGEF4_ENST00000525839.1_3'UTR|ARHGEF4_ENST00000428230.2_Silent_p.P147P|ARHGEF4_ENST00000392953.3_3'UTR|ARHGEF4_ENST00000355771.3_Silent_p.P574P|ARHGEF4_ENST00000409303.1_Silent_p.P585P	NM_015320.2	NP_056135.2	Q9NR80	ARHG4_HUMAN	Rho guanine nucleotide exchange factor (GEF) 4	645					apoptotic signaling pathway (GO:0097190)|filopodium assembly (GO:0046847)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|protein domain specific binding (GO:0019904)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(5)|lung(7)|ovary(3)|pancreas(1)|prostate(1)|skin(4)	29		Prostate(154;0.055)		BRCA - Breast invasive adenocarcinoma(221;0.097)		TTGGCCGGCCCTGCTACCTGA	0.677													C|||	20	0.00399361	0.0151	0.0	5008	,	,		16752	0.0		0.0	False		,,,				2504	0.0				p.P645P		Atlas-SNP	.											.	ARHGEF4	89	.	0			c.C1935T						PASS	.	C	,	66,4340	61.1+/-98.1	3,60,2140	61.0	72.0	68.0		1935,	-1.7	1.0	2	dbSNP_132	68	0,8600		0,0,4300	no	coding-synonymous,utr-3	ARHGEF4	NM_015320.2,NM_032995.1	,	3,60,6440	TT,TC,CC		0.0,1.498,0.5075	,	645/691,	131803624	66,12940	2203	4300	6503	SO:0001819	synonymous_variant	50649	exon14			CCGGCCCTGCTAC	AL137289	CCDS2165.1, CCDS42754.1	2q22	2013-01-10			ENSG00000136002	ENSG00000136002		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	684	protein-coding gene	gene with protein product	"""APC-stimulated guanine nucleotide exchange factor"""	605216				10873612	Standard	NM_015320		Approved	STM6, KIAA1112, ASEF	uc002tsa.1	Q9NR80	OTTHUMG00000131657	ENST00000326016.5:c.1935C>T	2.37:g.131803624C>T		166.0	0.0	0		180.0	73.0	0.405556	NM_015320	Q9HDC6|Q9UPP0	Silent	SNP	ENST00000326016.5	37	CCDS2165.1																																																																																			C|0.996;T|0.004	0.004	strong		0.677	ARHGEF4-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254554.4		
HIST1H2BD	3017	hgsc.bcm.edu	37	6	26158456	26158456	+	Missense_Mutation	SNP	C	C	T	rs62623440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:26158456C>T	ENST00000289316.2	+	1	83	c.59C>T	c.(58-60)aCt>aTt	p.T20I	HIST1H2BD_ENST00000377777.4_Missense_Mutation_p.T20I	NM_138720.2	NP_619790.1	P58876	H2B1D_HUMAN	histone cluster 1, H2bd	20					chromatin organization (GO:0006325)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	24						AAGGCGGTGACTAAGGCTCAG	0.527													C|||	47	0.00938498	0.0348	0.0014	5008	,	,		19251	0.0		0.0	False		,,,				2504	0.0				p.T20I		Atlas-SNP	.											.	HIST1H2BD	45	.	0			c.C59T						PASS	.	C	ILE/THR,ILE/THR	128,4278		1,126,2076	126.0	124.0	124.0		59,59	4.1	1.0	6	dbSNP_129	124	1,8599		0,1,4299	yes	missense,missense	HIST1H2BD	NM_021063.3,NM_138720.2	89,89	1,127,6375	TT,TC,CC		0.0116,2.9051,0.9918	probably-damaging,probably-damaging	20/127,20/127	26158456	129,12877	2203	4300	6503	SO:0001583	missense	3017	exon1			CGGTGACTAAGGC	M60751	CCDS4587.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000158373	ENSG00000158373		"""Histones / Replication-dependent"""	4747	protein-coding gene	gene with protein product		602799	"""H2B histone family, member B"", ""histone 1, H2bd"""	H2BFB		1916825, 12408966	Standard	NM_021063		Approved	H2B/b	uc003ngr.3	P58876	OTTHUMG00000014426	ENST00000289316.2:c.59C>T	6.37:g.26158456C>T	ENSP00000289316:p.Thr20Ile	174.0	0.0	0		145.0	61.0	0.42069	NM_021063		Missense_Mutation	SNP	ENST00000289316.2	37	CCDS4587.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	.	15.37	2.814326	0.50527	0.029051	1.16E-4	ENSG00000158373	ENST00000377777;ENST00000289316	T;T	0.23754	1.89;1.89	4.95	4.07	0.47477	Histone-fold (2);	0.000000	0.42821	D	0.000655	T	0.19604	0.0471	M	0.79805	2.47	0.36491	D	0.868429	P	0.39216	0.664	B	0.39935	0.314	T	0.08554	-1.0716	10	0.72032	D	0.01	.	9.0973	0.36647	0.0:0.7713:0.147:0.0817	rs62623440	20	P58876	H2B1D_HUMAN	I	20	ENSP00000367008:T20I;ENSP00000289316:T20I	ENSP00000289316:T20I	T	+	2	0	HIST1H2BD	26266435	1.000000	0.71417	1.000000	0.80357	0.480000	0.33159	3.805000	0.55575	1.392000	0.46585	0.644000	0.83932	ACT	C|0.990;T|0.010	0.010	strong		0.527	HIST1H2BD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040088.1	NM_021063	
PSG3	5671	hgsc.bcm.edu	37	19	43237080	43237080	+	Missense_Mutation	SNP	T	T	C	rs76931703	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43237080T>C	ENST00000327495.5	-	3	749	c.565A>G	c.(565-567)Atg>Gtg	p.M189V	PSG3_ENST00000490592.1_5'Flank|PSG3_ENST00000595140.1_Missense_Mutation_p.M189V	NM_021016.3	NP_066296.2	Q16557	PSG3_HUMAN	pregnancy specific beta-1-glycoprotein 3	189	Ig-like C2-type 1.				defense response (GO:0006952)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36		Prostate(69;0.00682)				CTGTGAGTCATAGGGAGGCTC	0.498													.|||	53	0.0105831	0.0378	0.0043	5008	,	,		20000	0.0		0.0	False		,,,				2504	0.0				p.M189V		Atlas-SNP	.											.	PSG3	82	.	0			c.A565G						PASS	.	T	VAL/MET	167,4239		4,159,2040	240.0	239.0	239.0		565	-1.4	0.0	19	dbSNP_131	239	1,8599		0,1,4299	yes	missense	PSG3	NM_021016.3	21	4,160,6339	CC,CT,TT		0.0116,3.7903,1.2917	benign	189/429	43237080	168,12838	2203	4300	6503	SO:0001583	missense	5671	exon3			GAGTCATAGGGAG		CCDS12611.1	19q13.2	2013-01-29			ENSG00000221826	ENSG00000221826		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9520	protein-coding gene	gene with protein product		176392				2341148	Standard	NM_021016		Approved		uc002oue.3	Q16557	OTTHUMG00000151120	ENST00000327495.5:c.565A>G	19.37:g.43237080T>C	ENSP00000332215:p.Met189Val	237.0	0.0	0		235.0	116.0	0.493617	NM_021016	Q08265|Q9BRW2|Q9UPL4|Q9UQ77	Missense_Mutation	SNP	ENST00000327495.5	37	CCDS12611.1	20	0.009157509157509158	19	0.03861788617886179	1	0.0027624309392265192	0	0.0	0	0.0	-	0.003	-2.475018	0.00167	0.037903	1.16E-4	ENSG00000221826	ENST00000327495	T	0.08458	3.09	1.59	-1.36	0.09085	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00524	0.0017	N	0.02275	-0.615	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.41752	-0.9491	9	0.02654	T	1	.	4.1694	0.10322	0.0:0.5437:0.0:0.4563	.	167;189	Q08266;Q16557	.;PSG3_HUMAN	V	189	ENSP00000332215:M189V	ENSP00000332215:M189V	M	-	1	0	PSG3	47928920	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.084000	0.03393	-0.464000	0.06963	-0.562000	0.04174	ATG	T|0.988;C|0.012	0.012	strong		0.498	PSG3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321423.2	NM_021016	
CXCR6	10663	hgsc.bcm.edu	37	3	45987980	45987980	+	Missense_Mutation	SNP	G	G	A	rs2234355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:45987980G>A	ENST00000458629.1	+	1	1470	c.7G>A	c.(7-9)Gag>Aag	p.E3K	FYCO1_ENST00000535325.1_Intron|FYCO1_ENST00000438446.1_Intron|CXCR6_ENST00000304552.4_Missense_Mutation_p.E3K|CXCR6_ENST00000457814.1_Missense_Mutation_p.E3K|FYCO1_ENST00000296137.2_Intron|CXCR6_ENST00000438735.1_Missense_Mutation_p.E3K			O00574	CXCR6_HUMAN	chemokine (C-X-C motif) receptor 6	3			E -> K (in dbSNP:rs2234355). {ECO:0000269|Ref.4}.		chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|viral genome replication (GO:0019079)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(1)|kidney(3)|lung(1)|prostate(1)|skin(1)	8				BRCA - Breast invasive adenocarcinoma(193;0.00113)|KIRC - Kidney renal clear cell carcinoma(197;0.0172)|Kidney(197;0.0203)		CACCATGGCAGAGCATGATTA	0.483													G|||	702	0.140176	0.4909	0.0677	5008	,	,		22359	0.0		0.005	False		,,,				2504	0.001				p.E3K	Esophageal Squamous(63;1005 1117 15521 45762 47089)	Atlas-SNP	.											.	CXCR6	17	.	0			c.G7A						PASS	.	G	LYS/GLU,	1842,2564	534.4+/-373.9	402,1038,763	139.0	141.0	140.0		7,	3.8	0.2	3	dbSNP_98	140	23,8577	16.0+/-53.3	0,23,4277	yes	missense,intron	CXCR6,FYCO1	NM_006564.1,NM_024513.2	56,	402,1061,5040	AA,AG,GG		0.2674,41.8066,14.3395	benign,	3/343,	45987980	1865,11141	2203	4300	6503	SO:0001583	missense	10663	exon2			ATGGCAGAGCATG	AF007545	CCDS2735.1	3p21	2012-08-08			ENSG00000172215	ENSG00000172215		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : C-X-C motif"""	16647	protein-coding gene	gene with protein product		605163				9166430, 9230441	Standard	XM_005264809		Approved	TYMSTR, STRL33, BONZO, CD186	uc003cpc.1	O00574	OTTHUMG00000133448	ENST00000458629.1:c.7G>A	3.37:g.45987980G>A	ENSP00000395704:p.Glu3Lys	171.0	0.0	0		137.0	67.0	0.489051	NM_006564	O00575|Q9HCA5	Missense_Mutation	SNP	ENST00000458629.1	37	CCDS2735.1	255	0.11675824175824176	230	0.46747967479674796	24	0.06629834254143646	0	0.0	1	0.0013192612137203166	G	17.55	3.418151	0.62622	0.418066	0.002674	ENSG00000172215	ENST00000438735;ENST00000304552;ENST00000458629;ENST00000457814	T;T;T;T	0.66460	-0.21;-0.21;-0.21;-0.21	5.57	3.8	0.43715	.	3.673050	0.00622	N	0.000453	T	0.00012	0.0000	N	0.19112	0.55	0.35184	P	0.227213	P	0.39665	0.682	B	0.30401	0.115	T	0.29882	-0.9997	9	0.46703	T	0.11	.	9.5395	0.39242	0.1649:0.0:0.8351:0.0	rs2234355;rs52808267;rs56447809;rs2234355	3	O00574	CXCR6_HUMAN	K	3	ENSP00000396218:E3K;ENSP00000304414:E3K;ENSP00000395704:E3K;ENSP00000396886:E3K	ENSP00000304414:E3K	E	+	1	0	CXCR6	45962984	0.000000	0.05858	0.206000	0.23566	0.198000	0.23893	0.391000	0.20784	0.729000	0.32403	0.655000	0.94253	GAG	G|0.857;A|0.143	0.143	strong		0.483	CXCR6-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344395.1		
GNA12	2768	hgsc.bcm.edu	37	7	2834754	2834754	+	Silent	SNP	T	T	C	rs2230877	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:2834754T>C	ENST00000275364.3	-	2	495	c.333A>G	c.(331-333)gcA>gcG	p.A111A	GNA12_ENST00000544127.1_Silent_p.A35A|GNA12_ENST00000407904.3_Silent_p.A52A	NM_007353.2	NP_031379.2	Q03113	GNA12_HUMAN	guanine nucleotide binding protein (G protein) alpha 12	111					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|embryonic digit morphogenesis (GO:0042733)|G-protein coupled receptor signaling pathway (GO:0007186)|in utero embryonic development (GO:0001701)|platelet activation (GO:0030168)|regulation of cell shape (GO:0008360)|regulation of fibroblast migration (GO:0010762)|regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032434)|regulation of TOR signaling (GO:0032006)|response to drug (GO:0042493)|Rho protein signal transduction (GO:0007266)	brush border membrane (GO:0031526)|focal adhesion (GO:0005925)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	D5 dopamine receptor binding (GO:0031752)|G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			endometrium(1)|large_intestine(5)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13		Ovarian(82;0.0112)		OV - Ovarian serous cystadenocarcinoma(56;1.02e-13)		GCTTATCTCGTGCATCAACAA	0.468													T|||	99	0.0197684	0.0514	0.0101	5008	,	,		21010	0.0		0.0159	False		,,,				2504	0.0082				p.A111A		Atlas-SNP	.											.	GNA12	35	.	0			c.A333G						PASS	.	T		207,4199	127.8+/-164.7	6,195,2002	131.0	128.0	129.0		333	-11.2	0.5	7	dbSNP_123	129	77,8523	45.8+/-104.6	1,75,4224	no	coding-synonymous	GNA12	NM_007353.2		7,270,6226	CC,CT,TT		0.8953,4.6981,2.1836		111/382	2834754	284,12722	2203	4300	6503	SO:0001819	synonymous_variant	2768	exon2			ATCTCGTGCATCA	L01694	CCDS5335.1, CCDS64584.1, CCDS64583.1	7p22.3	2006-07-08			ENSG00000146535	ENSG00000146535			4380	protein-coding gene	gene with protein product		604394				8423800, 16247467	Standard	NM_007353		Approved	gep	uc003smu.3	Q03113	OTTHUMG00000023064	ENST00000275364.3:c.333A>G	7.37:g.2834754T>C		70.0	0.0	0		90.0	47.0	0.522222	NM_007353	A4D204|B3KXS2|B7Z3F7|Q2T9L1|Q5PPR5|Q86UM8|Q8TD71|Q9UDU9	Silent	SNP	ENST00000275364.3	37	CCDS5335.1																																																																																			T|0.980;C|0.020	0.020	strong		0.468	GNA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241608.1	NM_007353	
XRCC4	7518	hgsc.bcm.edu	37	5	82400773	82400773	+	Missense_Mutation	SNP	C	C	G	rs28383138	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:82400773C>G	ENST00000511817.1	+	2	115	c.35C>G	c.(34-36)tCt>tGt	p.S12C	XRCC4_ENST00000509268.1_3'UTR|XRCC4_ENST00000396027.4_Missense_Mutation_p.S12C|XRCC4_ENST00000282268.3_Missense_Mutation_p.S12C|XRCC4_ENST00000338635.6_Missense_Mutation_p.S12C			Q13426	XRCC4_HUMAN	X-ray repair complementing defective repair in Chinese hamster cells 4	12			S -> C (in dbSNP:rs28383138). {ECO:0000269|Ref.6}.		cellular response to lithium ion (GO:0071285)|central nervous system development (GO:0007417)|DNA ligation involved in DNA repair (GO:0051103)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via nonhomologous end joining (GO:0006303)|establishment of integrated proviral latency (GO:0075713)|immunoglobulin V(D)J recombination (GO:0033152)|in utero embryonic development (GO:0001701)|isotype switching (GO:0045190)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of ligase activity (GO:0051351)|positive regulation of neurogenesis (GO:0050769)|pro-B cell differentiation (GO:0002328)|response to gamma radiation (GO:0010332)|response to X-ray (GO:0010165)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytosol (GO:0005829)|DNA ligase IV complex (GO:0032807)|DNA-dependent protein kinase-DNA ligase 4 complex (GO:0005958)|nonhomologous end joining complex (GO:0070419)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein C-terminus binding (GO:0008022)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|prostate(2)|skin(3)	17		Lung NSC(167;0.00132)|all_lung(232;0.00154)|Ovarian(174;0.034)		OV - Ovarian serous cystadenocarcinoma(54;1.44e-38)|Epithelial(54;3.72e-33)|all cancers(79;9.22e-28)		CACCTTGTTTCTGAACCCAGT	0.333								Non-homologous end-joining					C|||	39	0.00778754	0.0287	0.0014	5008	,	,		14902	0.0		0.0	False		,,,				2504	0.0				p.S12C		Atlas-SNP	.											.	XRCC4	37	.	0			c.C35G						PASS	.	C	CYS/SER,CYS/SER,CYS/SER	104,4302	81.9+/-120.4	4,96,2103	90.0	94.0	93.0		35,35,35	4.8	1.0	5	dbSNP_125	93	0,8596		0,0,4298	yes	missense,missense,missense	XRCC4	NM_003401.3,NM_022406.2,NM_022550.2	112,112,112	4,96,6401	GG,GC,CC		0.0,2.3604,0.7999	probably-damaging,probably-damaging,probably-damaging	12/335,12/337,12/335	82400773	104,12898	2203	4298	6501	SO:0001583	missense	7518	exon2			TTGTTTCTGAACC	AB017445	CCDS4058.1, CCDS4059.1	5q14.2	2008-02-05			ENSG00000152422	ENSG00000152422			12831	protein-coding gene	gene with protein product	"""X-ray repair, complementing defective, repair in Chinese hamster"", ""DNA repair protein XRCC4"""	194363				1697445, 7665175	Standard	NM_022406		Approved		uc003kib.3	Q13426	OTTHUMG00000131319	ENST00000511817.1:c.35C>G	5.37:g.82400773C>G	ENSP00000421491:p.Ser12Cys	136.0	0.0	0		144.0	69.0	0.479167	NM_003401	A8K3X4|Q9BS72|Q9UP94	Missense_Mutation	SNP	ENST00000511817.1	37	CCDS4059.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	C	14.29	2.491902	0.44352	0.023604	0.0	ENSG00000152422	ENST00000282268;ENST00000338635;ENST00000396027;ENST00000511817	T;T;T;T	0.21031	2.03;2.03;2.03;2.03	5.67	4.8	0.61643	DNA double-strand break repair and VJ recombination XRCC4, N-terminal (2);	0.132928	0.51477	D	0.000085	T	0.23330	0.0564	M	0.74258	2.255	0.49687	D	0.99981	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	T	0.34378	-0.9831	10	0.87932	D	0	-5.2753	14.8049	0.69945	0.0:0.9305:0.0:0.0695	rs28383138	12;12;12	Q13426-2;Q13426;Q13426-3	.;XRCC4_HUMAN;.	C	12	ENSP00000282268:S12C;ENSP00000342011:S12C;ENSP00000379344:S12C;ENSP00000421491:S12C	ENSP00000282268:S12C	S	+	2	0	XRCC4	82436529	1.000000	0.71417	0.994000	0.49952	0.199000	0.23934	3.483000	0.53194	1.524000	0.49035	0.591000	0.81541	TCT	C|0.993;G|0.007	0.007	strong		0.333	XRCC4-003	NOVEL	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000369624.1	NM_022550	
VPS13A	23230	hgsc.bcm.edu	37	9	79875104	79875104	+	Silent	SNP	A	A	G	rs73466058	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:79875104A>G	ENST00000360280.3	+	23	2651	c.2391A>G	c.(2389-2391)ccA>ccG	p.P797P	VPS13A_ENST00000376636.3_Silent_p.P797P|VPS13A_ENST00000376634.4_Silent_p.P797P|VPS13A_ENST00000357409.5_Silent_p.P797P	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	797					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						AACCTGAACCAGTAACTGAAG	0.313													A|||	72	0.014377	0.0537	0.0014	5008	,	,		13428	0.0		0.0	False		,,,				2504	0.0				p.P797P		Atlas-SNP	.											.	VPS13A	735	.	0			c.A2391G						PASS	.	A	,,,	182,4224	118.0+/-155.7	3,176,2024	72.0	73.0	73.0		2391,2391,2391,2391	1.9	0.0	9	dbSNP_130	73	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	VPS13A	NM_001018037.1,NM_001018038.2,NM_015186.3,NM_033305.2	,,,	3,177,6322	GG,GA,AA		0.0116,4.1307,1.4073	,,,	797/3136,797/3070,797/3096,797/3175	79875104	183,12821	2203	4299	6502	SO:0001819	synonymous_variant	23230	exon23			TGAACCAGTAACT	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"""chorein"""	605978	"""chorea acanthocytosis"", ""vacuolar protein sorting 13A (yeast)"""	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.2391A>G	9.37:g.79875104A>G		145.0	0.0	0		150.0	93.0	0.62	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Silent	SNP	ENST00000360280.3	37	CCDS6655.1																																																																																			A|0.987;G|0.013	0.013	strong		0.313	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	
ITIH6	347365	hgsc.bcm.edu	37	X	54783952	54783952	+	Missense_Mutation	SNP	A	A	G	rs150850201	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:54783952A>G	ENST00000218436.6	-	8	2584	c.2555T>C	c.(2554-2556)aTc>aCc	p.I852T		NM_198510.2	NP_940912.1	Q6UXX5	ITIH6_HUMAN	inter-alpha-trypsin inhibitor heavy chain family, member 6	852	Pro-rich.				hyaluronan metabolic process (GO:0030212)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										AGATAATAAGATTTTAGGGGT	0.507													A|||	43	0.0113907	0.0303	0.0043	3775	,	,		13466	0.0		0.0	False		,,,				2504	0.0				p.I852T		Atlas-SNP	.											.	.	.	.	0			c.T2555C						PASS	.	-	THR/ILE	166,3669		3,134,26,1495,545	74.0	71.0	72.0		2555	1.4	0.0	X	dbSNP_134	72	2,6726		0,1,1,2427,1871	yes	missense	ITIH5L	NM_198510.2	89	3,135,27,3922,2416	GG,GA,G,AA,A		0.0297,4.3286,1.5905	possibly-damaging	852/1314	54783952	168,10395	2203	4300	6503	SO:0001583	missense	347365	exon8			AATAAGATTTTAG	AY358170	CCDS14361.1	Xp11.22-p11.21	2011-10-26	2011-10-26	2011-10-26	ENSG00000102313	ENSG00000102313			28907	protein-coding gene	gene with protein product			"""inter-alpha (globulin) inhibitor H5-like"""	ITIH5L		12975309	Standard	NM_198510		Approved	UNQ6369	uc004dtj.2	Q6UXX5	OTTHUMG00000021634	ENST00000218436.6:c.2555T>C	X.37:g.54783952A>G	ENSP00000218436:p.Ile852Thr	153.0	0.0	0		227.0	115.0	0.506608	NM_198510	A6NN03	Missense_Mutation	SNP	ENST00000218436.6	37	CCDS14361.1	20	0.012055455093429777	8	0.01694915254237288	0	0.0	0	0.0	0	0.0	A	9.484	1.098979	0.20552	0.043286	2.97E-4	ENSG00000102313	ENST00000218436	T	0.02863	4.13	3.91	1.43	0.22495	.	14.783200	0.01116	U	0.005696	T	0.00608	0.0020	N	0.14661	0.345	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.42032	-0.9475	9	0.72032	D	0.01	.	5.1877	0.15193	0.4176:0.0:0.5824:0.0	.	852	Q6UXX5	ITH5L_HUMAN	T	852	ENSP00000218436:I852T	ENSP00000218436:I852T	I	-	2	0	ITIH5L	54800677	0.003000	0.15002	0.007000	0.13788	0.008000	0.06430	0.571000	0.23669	0.275000	0.22094	0.380000	0.24917	ATC	A|0.982;G|0.018	0.018	strong		0.507	ITIH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056814.2	NM_198510	
CPNE7	27132	hgsc.bcm.edu	37	16	89645360	89645360	+	Silent	SNP	G	G	A	rs149812493	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89645360G>A	ENST00000268720.5	+	3	583	c.453G>A	c.(451-453)acG>acA	p.T151T	CPNE7_ENST00000319518.8_Intron	NM_014427.4	NP_055242.1	Q9UBL6	CPNE7_HUMAN	copine VII	151					lipid metabolic process (GO:0006629)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(2)	17		all_hematologic(23;0.0748)		all cancers(4;3.63e-08)|OV - Ovarian serous cystadenocarcinoma(4;1.7e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0147)		TGTGCTGCACGGAATCCTCAC	0.542													G|||	42	0.00838658	0.031	0.0014	5008	,	,		16677	0.0		0.0	False		,,,				2504	0.0				p.T151T		Atlas-SNP	.											.	CPNE7	56	.	0			c.G453A						PASS	.	G	,	132,4264	95.3+/-134.0	2,128,2068	115.0	98.0	104.0		453,	-0.3	0.0	16	dbSNP_134	104	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,intron	CPNE7	NM_014427.4,NM_153636.2	,	2,129,6367	AA,AG,GG		0.0116,3.0027,1.0234	,	151/634,	89645360	133,12863	2198	4300	6498	SO:0001819	synonymous_variant	27132	exon3			CTGCACGGAATCC	AJ133798	CCDS10980.1, CCDS10981.1	16q24.3	2008-07-03			ENSG00000178773	ENSG00000178773			2320	protein-coding gene	gene with protein product		605689					Standard	NM_014427		Approved		uc002fnq.3	Q9UBL6	OTTHUMG00000138051	ENST00000268720.5:c.453G>A	16.37:g.89645360G>A		72.0	0.0	0		86.0	37.0	0.430233	NM_014427		Silent	SNP	ENST00000268720.5	37	CCDS10980.1																																																																																			G|0.988;A|0.012	0.012	strong		0.542	CPNE7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269929.2		
KRT32	3882	hgsc.bcm.edu	37	17	39623496	39623496	+	Missense_Mutation	SNP	C	C	T	rs115680799	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39623496C>T	ENST00000225899.3	-	1	185	c.82G>A	c.(82-84)Ggc>Agc	p.G28S	RNU2-32P_ENST00000411193.1_RNA	NM_002278.3	NP_002269.3	Q14532	K1H2_HUMAN	keratin 32	28	Head.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(137;0.000812)				CAGTTCACGCCGCTGGAACAG	0.637													C|||	89	0.0177716	0.0658	0.0029	5008	,	,		17468	0.0		0.0	False		,,,				2504	0.0				p.G28S		Atlas-SNP	.											.	KRT32	57	.	0			c.G82A						PASS	.	C	SER/GLY	211,4193		4,203,1995	31.0	34.0	33.0		82	-0.2	0.0	17	dbSNP_132	33	6,8594		0,6,4294	yes	missense	KRT32	NM_002278.3	56	4,209,6289	TT,TC,CC		0.0698,4.7911,1.6687	benign	28/449	39623496	217,12787	2202	4300	6502	SO:0001583	missense	3882	exon1			TCACGCCGCTGGA	X90761	CCDS11393.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000108759	ENSG00000108759		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6449	protein-coding gene	gene with protein product	"""hard keratin type I"""	602760	"""keratin, hair, acidic, 2"""	KRTHA2		7556444, 8823373, 16831889	Standard	NM_002278		Approved	Ha-2	uc002hwr.3	Q14532	OTTHUMG00000133430	ENST00000225899.3:c.82G>A	17.37:g.39623496C>T	ENSP00000225899:p.Gly28Ser	80.0	0.0	0		95.0	47.0	0.494737	NM_002278		Missense_Mutation	SNP	ENST00000225899.3	37	CCDS11393.1	31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	C	0.012	-1.657918	0.00779	0.047911	6.98E-4	ENSG00000108759	ENST00000225899	D	0.86164	-2.08	5.16	-0.18	0.13295	.	0.662243	0.13290	N	0.399058	T	0.14917	0.0360	N	0.01874	-0.695	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.35599	-0.9782	10	0.10377	T	0.69	.	2.9903	0.05981	0.3289:0.3218:0.0:0.3493	.	28	Q14532	K1H2_HUMAN	S	28	ENSP00000225899:G28S	ENSP00000225899:G28S	G	-	1	0	KRT32	36877022	0.000000	0.05858	0.020000	0.16555	0.005000	0.04900	-0.360000	0.07622	0.060000	0.16281	-0.339000	0.08088	GGC	C|0.981;T|0.019	0.019	strong		0.637	KRT32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257293.1	NM_002278	
HEXIM2	124790	hgsc.bcm.edu	37	17	43246456	43246456	+	Silent	SNP	G	G	A	rs34207107	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:43246456G>A	ENST00000307275.3	+	4	577	c.141G>A	c.(139-141)ccG>ccA	p.P47P	HEXIM2_ENST00000592695.1_Silent_p.P47P|RP13-890H12.2_ENST00000589451.1_RNA|HEXIM2_ENST00000591576.1_Silent_p.P47P|RP13-890H12.2_ENST00000589796.1_RNA	NM_144608.1	NP_653209.1	Q96MH2	HEXI2_HUMAN	hexamethylene bis-acetamide inducible 2	47					negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|snRNA binding (GO:0017069)			endometrium(1)|large_intestine(3)|lung(1)	5						CCCTGACACCGCGGATGGAGA	0.642													G|||	209	0.0417332	0.143	0.0159	5008	,	,		15993	0.0		0.003	False		,,,				2504	0.0061				p.P47P		Atlas-SNP	.											.	HEXIM2	19	.	0			c.G141A						PASS	.	G		546,3860	240.6+/-251.3	31,484,1688	110.0	125.0	120.0		141	-7.9	0.0	17	dbSNP_126	120	32,8568	21.6+/-65.8	0,32,4268	no	coding-synonymous	HEXIM2	NM_144608.1		31,516,5956	AA,AG,GG		0.3721,12.3922,4.4441		47/287	43246456	578,12428	2203	4300	6503	SO:0001819	synonymous_variant	124790	exon4			GACACCGCGGATG	AK056946	CCDS11496.1	17q21.31	2011-07-29	2011-07-29			ENSG00000168517			28591	protein-coding gene	gene with protein product		615695				12832472	Standard	NM_144608		Approved	FLJ32384	uc002iih.1	Q96MH2		ENST00000307275.3:c.141G>A	17.37:g.43246456G>A		101.0	1.0	0.00990099		100.0	100.0	1	NM_144608	D3DX66	Silent	SNP	ENST00000307275.3	37	CCDS11496.1																																																																																			G|0.962;A|0.038	0.038	strong		0.642	HEXIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450181.1	NM_144608	
TSPEAR	54084	hgsc.bcm.edu	37	21	45953576	45953576	+	Silent	SNP	C	C	T	rs148713881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45953576C>T	ENST00000323084.4	-	3	599	c.534G>A	c.(532-534)ccG>ccA	p.P178P	TSPEAR_ENST00000397916.1_Silent_p.P110P	NM_001272037.1|NM_144991.2	NP_001258966.1|NP_659428.2	Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	178	Laminin G-like.				sensory perception of sound (GO:0007605)	cell surface (GO:0009986)|ciliary membrane (GO:0060170)|extracellular region (GO:0005576)|stereocilium (GO:0032420)				breast(1)|central_nervous_system(6)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	37						ACATGTCCACCGGGAGGCCGC	0.677													C|||	31	0.0061901	0.0227	0.0014	5008	,	,		13631	0.0		0.0	False		,,,				2504	0.0				p.P178P		Atlas-SNP	.											TSPEAR,caecum,carcinoma,0,1	TSPEAR	110	1	0			c.G534A						PASS	.	C		104,4254		5,94,2080	19.0	19.0	19.0		534	-0.2	0.7	21	dbSNP_134	19	0,8526		0,0,4263	no	coding-synonymous	TSPEAR	NM_144991.2		5,94,6343	TT,TC,CC		0.0,2.3864,0.8072		178/670	45953576	104,12780	2179	4263	6442	SO:0001819	synonymous_variant	54084	exon3			GTCCACCGGGAGG	AJ487962	CCDS13712.1, CCDS74801.1	21q22.3	2012-10-30	2011-01-25	2011-01-25	ENSG00000175894	ENSG00000175894			1268	protein-coding gene	gene with protein product		612920	"""chromosome 21 open reading frame 29"", ""deafness, autosomal recessive 98"""	C21orf29, DFNB98		12095917, 22678063	Standard	NM_144991		Approved	MGC11251, TSP-EAR	uc002zfe.1	Q8WU66	OTTHUMG00000041215	ENST00000323084.4:c.534G>A	21.37:g.45953576C>T		85.0	0.0	0		101.0	44.0	0.435644	NM_144991		Silent	SNP	ENST00000323084.4	37	CCDS13712.1																																																																																			C|0.990;T|0.010	0.010	strong		0.677	TSPEAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098761.1	NM_144991	
PENK	5179	hgsc.bcm.edu	37	8	57354380	57354380	+	Silent	SNP	T	T	C	rs76702938	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:57354380T>C	ENST00000314922.3	-	2	331	c.255A>G	c.(253-255)agA>agG	p.R85R	PENK_ENST00000523274.1_5'UTR|PENK_ENST00000451791.2_Silent_p.R85R	NM_006211.3	NP_006202.1	P01210	PENK_HUMAN	proenkephalin	85					aggressive behavior (GO:0002118)|behavioral fear response (GO:0001662)|locomotory behavior (GO:0007626)|neuropeptide signaling pathway (GO:0007218)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|startle response (GO:0001964)	extracellular region (GO:0005576)	neuropeptide hormone activity (GO:0005184)			central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(1)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	21		all_lung(136;0.229)	Epithelial(17;0.000873)|all cancers(17;0.0069)			TGCTATTTTCTCTGAGGGTGC	0.468													T|||	12	0.00239617	0.0091	0.0	5008	,	,		17675	0.0		0.0	False		,,,				2504	0.0				p.R85R		Atlas-SNP	.											.	PENK	59	.	0			c.A255G						PASS	.	T	,	15,4391	21.2+/-45.6	0,15,2188	98.0	100.0	99.0		255,255	1.5	0.0	8	dbSNP_132	99	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PENK	NM_001135690.1,NM_006211.3	,	0,15,6488	CC,CT,TT		0.0,0.3404,0.1153	,	85/268,85/268	57354380	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	5179	exon4			ATTTTCTCTGAGG		CCDS6168.1	8q23-q24	2013-02-26				ENSG00000181195		"""Endogenous ligands"""	8831	protein-coding gene	gene with protein product	"""preproenkephalin"""	131330				6281660	Standard	NM_006211		Approved		uc003xsz.2	P01210		ENST00000314922.3:c.255A>G	8.37:g.57354380T>C		115.0	0.0	0		107.0	58.0	0.542056	NM_001135690	B2RC23|Q6FHC6|Q6FHE6	Silent	SNP	ENST00000314922.3	37	CCDS6168.1																																																																																			T|0.999;C|0.001	0.001	strong		0.468	PENK-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378645.1		
RUFY4	285180	hgsc.bcm.edu	37	2	218954716	218954716	+	Missense_Mutation	SNP	A	A	G	rs116710266	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:218954716A>G	ENST00000344321.7	+	13	2173	c.1655A>G	c.(1654-1656)tAc>tGc	p.Y552C	RUFY4_ENST00000374155.3_3'UTR|RUFY4_ENST00000441828.2_3'UTR	NM_198483.3	NP_940885.2	Q6ZNE9	RUFY4_HUMAN	RUN and FYVE domain containing 4	552							metal ion binding (GO:0046872)			endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(1)	10		Renal(207;0.0915)		Epithelial(149;4.11e-06)|all cancers(144;0.000519)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		TCCATGGATTACAAGAAGAGA	0.632													A|||	70	0.0139776	0.0499	0.0058	5008	,	,		17641	0.0		0.0	False		,,,				2504	0.0				p.Y552C		Atlas-SNP	.											.	RUFY4	59	.	0			c.A1655G						PASS	.	A	CYS/TYR	158,3840		3,152,1844	37.0	44.0	42.0		1655	0.7	0.7	2	dbSNP_132	42	0,8322		0,0,4161	yes	missense	RUFY4	NM_198483.3	194	3,152,6005	GG,GA,AA		0.0,3.952,1.2825	probably-damaging	552/572	218954716	158,12162	1999	4161	6160	SO:0001583	missense	285180	exon13			TGGATTACAAGAA	AK128393		2q35	2007-01-29			ENSG00000188282	ENSG00000188282		"""Zinc fingers, FYVE domain containing"""	24804	protein-coding gene	gene with protein product							Standard	NM_198483		Approved	FLJ46536	uc010fvl.2	Q6ZNE9	OTTHUMG00000155235	ENST00000344321.7:c.1655A>G	2.37:g.218954716A>G	ENSP00000345900:p.Tyr552Cys	214.0	0.0	0		280.0	153.0	0.546429	NM_198483	Q6ZR96	Missense_Mutation	SNP	ENST00000344321.7	37		35	0.016025641025641024	31	0.06300813008130081	4	0.011049723756906077	0	0.0	0	0.0	A	11.43	1.636570	0.29068	0.03952	0.0	ENSG00000188282	ENST00000344321	T	0.76709	-1.04	4.6	0.663	0.17885	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, FYVE-related (1);Zinc finger, FYVE/PHD-type (1);	.	.	.	.	T	0.17238	0.0414	M	0.68952	2.095	0.80722	D	1	P	0.46784	0.884	B	0.32342	0.144	T	0.47182	-0.9137	9	0.59425	D	0.04	.	1.8069	0.03082	0.5702:0.1707:0.0947:0.1644	.	552	Q6ZNE9	RUFY4_HUMAN	C	552	ENSP00000345900:Y552C	ENSP00000345900:Y552C	Y	+	2	0	RUFY4	218662961	0.997000	0.39634	0.740000	0.30986	0.070000	0.16714	0.369000	0.20416	0.249000	0.21456	-0.488000	0.04728	TAC	A|0.982;G|0.018	0.018	strong		0.632	RUFY4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_198483	
MUC1	4582	hgsc.bcm.edu	37	1	155161714	155161714	+	Missense_Mutation	SNP	G	G	A	rs544579074	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:155161714G>A	ENST00000368395.1	-	2	490	c.419C>T	c.(418-420)tCg>tTg	p.S140L	MUC1_ENST00000343256.5_Intron|MUC1_ENST00000368392.3_Intron|RP11-201K10.3_ENST00000473363.2_5'Flank|MUC1_ENST00000337604.5_Intron|MUC1_ENST00000368389.2_Intron|MUC1_ENST00000368390.3_Intron|MUC1_ENST00000368393.3_Intron|MUC1_ENST00000457295.2_Intron|MUC1_ENST00000368396.4_Intron|MUC1_ENST00000342482.4_Intron|MUC1_ENST00000462215.1_Intron|MUC1_ENST00000368398.3_Intron|MUC1_ENST00000338684.5_Intron|MUC1_ENST00000438413.1_Intron	NM_001204285.1|NM_001204286.1	NP_001191214.1|NP_001191215.1	P15941	MUC1_HUMAN	mucin 1, cell surface associated	920	42 X 20 AA approximate tandem repeats of P-A-P-G-S-T-A-P-P-A-H-G-V-T-S-A-P-D-T-R.				cellular protein metabolic process (GO:0044267)|cellular response to retinoic acid (GO:0071300)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|epithelial cell differentiation (GO:0030855)|female pregnancy (GO:0007565)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of transcription by competitive promoter binding (GO:0010944)|O-glycan processing (GO:0016266)|positive regulation of histone H4 acetylation (GO:0090240)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|post-translational protein modification (GO:0043687)|regulation of transcription from RNA polymerase II promoter in response to stress (GO:0043618)|response to hypoxia (GO:0001666)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|nuclear chromatin (GO:0000790)|vesicle (GO:0031982)	p53 binding (GO:0002039)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|transcription cofactor activity (GO:0003712)			breast(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|skin(2)	10	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;5.31e-10)|all cancers(21;2.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			GTCCGGGGCCGAGGTGACACC	0.776			T	IGH@	B-NHL								G|||	100	0.0199681	0.0726	0.0058	5008	,	,		6075	0.0		0.0	False		,,,				2504	0.0				p.S149L		Atlas-SNP	.		Dom	yes		1	1q21	4582	"""mucin 1, transmembrane"""		L	.	MUC1	94	.	0			c.C446T						PASS	.																																			SO:0001583	missense	4582	exon2			GGGGCCGAGGTGA	J05581	CCDS1098.1, CCDS30882.1, CCDS30883.1, CCDS41408.1, CCDS41409.1, CCDS55640.1, CCDS55641.1, CCDS55642.1, CCDS55640.2, CCDS72933.1, CCDS72934.1, CCDS72935.1, CCDS72936.1	1q22	2014-01-31	2006-03-14		ENSG00000185499	ENSG00000185499		"""CD molecules"", ""Mucins"""	7508	protein-coding gene	gene with protein product		158340	"""mucin 1, transmembrane"", ""medullary cystic kidney disease 1 (autosomal dominant)"""	PUM, MCKD1		1697589, 23396133	Standard	NM_002456		Approved	CD227, PEM, ADMCKD, ADMCKD1, MCKD, MCD	uc031ppv.1	P15941	OTTHUMG00000035681	ENST00000368395.1:c.419C>T	1.37:g.155161714G>A	ENSP00000357380:p.Ser140Leu	5.0	0.0	0		6.0	4.0	0.666667	NM_001204286	A5YRV1|A6ZID9|A6ZIE0|B1AVQ8|B1AVR0|B6ECA1|E7ESE5|E7EUG9|P13931|P15942|P17626|Q0VAP5|Q0VAP6|Q14128|Q14876|Q16437|Q16442|Q16615|Q6S4Y3|Q7Z547|Q7Z548|Q7Z550|Q7Z552|Q9BXA4|Q9UE75|Q9UE76|Q9UQL1|Q9Y4J2	Missense_Mutation	SNP	ENST00000368395.1	37	CCDS55640.1	.	.	.	.	.	.	.	.	.	.	G	15.60	2.880738	0.51801	.	.	ENSG00000185499	ENST00000368395	T	0.50277	0.75	2.94	2.94	0.34122	.	1.042050	0.07734	N	0.945652	T	0.46756	0.1409	L	0.41492	1.28	0.44261	D	0.997118	D	0.61697	0.99	D	0.63957	0.92	T	0.45585	-0.9251	10	0.37606	T	0.19	0.7388	12.1668	0.54135	0.0:0.0:1.0:0.0	.	140	P15941	MUC1_HUMAN	L	140	ENSP00000357380:S140L	ENSP00000357380:S140L	S	-	2	0	MUC1	153428338	0.000000	0.05858	0.015000	0.15790	0.005000	0.04900	0.439000	0.21575	1.981000	0.57761	0.485000	0.47835	TCG	.	.	none		0.776	MUC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086735.1	NM_002456	
SIDT2	51092	hgsc.bcm.edu	37	11	117050007	117050007	+	Missense_Mutation	SNP	G	G	A	rs61729992	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117050007G>A	ENST00000324225.4	+	1	559	c.28G>A	c.(28-30)Gtg>Atg	p.V10M	SIDT2_ENST00000431081.2_Missense_Mutation_p.V10M	NM_001040455.1	NP_001035545.1	Q8NBJ9	SIDT2_HUMAN	SID1 transmembrane family, member 2	10					cell morphogenesis (GO:0000902)|dsRNA transport (GO:0033227)|glucose homeostasis (GO:0042593)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to glucose (GO:0009749)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell proliferation (GO:0044342)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	RNA transmembrane transporter activity (GO:0051033)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	36	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000219)|all cancers(92;0.00144)		GCCCTTCTTGGTGCTCTTGGT	0.677													G|||	43	0.00858626	0.0303	0.0029	5008	,	,		11337	0.0		0.001	False		,,,				2504	0.0				p.V10M		Atlas-SNP	.											.	SIDT2	82	.	0			c.G28A						PASS	.	G	MET/VAL	83,4319	70.3+/-108.2	0,83,2118	72.0	66.0	68.0		28	2.3	0.1	11	dbSNP_129	68	0,8592		0,0,4296	yes	missense	SIDT2	NM_001040455.1	21	0,83,6414	AA,AG,GG		0.0,1.8855,0.6388	benign	10/833	117050007	83,12911	2201	4296	6497	SO:0001583	missense	51092	exon1			TTCTTGGTGCTCT	AF151799	CCDS31682.1	11q23.3	2008-02-05			ENSG00000149577	ENSG00000149577			24272	protein-coding gene	gene with protein product						10810093, 12975309	Standard	NM_001040455		Approved	CGI-40	uc001pqh.1	Q8NBJ9	OTTHUMG00000167065	ENST00000324225.4:c.28G>A	11.37:g.117050007G>A	ENSP00000314023:p.Val10Met	43.0	0.0	0		44.0	15.0	0.340909	NM_001040455	Q8NBY7|Q9Y357	Missense_Mutation	SNP	ENST00000324225.4	37	CCDS31682.1	19	0.0086996336996337	16	0.032520325203252036	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	11.97	1.798338	0.31777	0.018855	0.0	ENSG00000149577	ENST00000324225;ENST00000532960;ENST00000525347;ENST00000278951;ENST00000431081;ENST00000392956	T;T;T;T	0.50548	2.12;0.74;2.1;2.12	4.19	2.28	0.28536	.	1.095770	0.07106	N	0.841382	T	0.19644	0.0472	L	0.44542	1.39	0.25313	N	0.989181	B;P;P;B	0.43701	0.126;0.815;0.718;0.232	B;B;B;B	0.43251	0.206;0.413;0.235;0.07	T	0.17806	-1.0357	10	0.62326	D	0.03	-4.7017	5.5137	0.16894	0.1108:0.2032:0.6859:0.0	rs61729992	10;10;10;10	Q8NBJ9-2;F5H8L4;Q8NBJ9;C9JBG5	.;.;SIDT2_HUMAN;.	M	10	ENSP00000314023:V10M;ENSP00000431176:V10M;ENSP00000278951:V10M;ENSP00000399635:V10M	ENSP00000278951:V10M	V	+	1	0	SIDT2	116555217	1.000000	0.71417	0.081000	0.20488	0.384000	0.30261	3.334000	0.52097	0.393000	0.25203	0.561000	0.74099	GTG	G|0.991;A|0.009	0.009	strong		0.677	SIDT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392836.1	NM_015996	
RAB19	401409	hgsc.bcm.edu	37	7	140125878	140125878	+	Silent	SNP	C	C	T	rs4585665	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140125878C>T	ENST00000356407.3	+	3	650	c.582C>T	c.(580-582)aaC>aaT	p.N194N	RAB19_ENST00000537763.1_Silent_p.N194N|RAB19_ENST00000275874.5_Silent_p.N241N			A4D1S5	RAB19_HUMAN	RAB19, member RAS oncogene family	194					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			breast(3)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)	9	Melanoma(164;0.0142)					GTGCCCTGAACGGCCTCCCCC	0.562													C|||	61	0.0121805	0.0439	0.0043	5008	,	,		18656	0.0		0.0	False		,,,				2504	0.0				p.N194N		Atlas-SNP	.											.	RAB19	21	.	0			c.C582T						PASS	.	C		126,4280	93.0+/-131.7	2,122,2079	77.0	72.0	74.0		582	0.4	0.0	7	dbSNP_111	74	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	RAB19	NM_001008749.2		2,124,6377	TT,TC,CC		0.0233,2.8597,0.9842		194/218	140125878	128,12878	2203	4300	6503	SO:0001819	synonymous_variant	401409	exon4			CCTGAACGGCCTC		CCDS34762.1, CCDS34762.2	7q34	2014-05-09			ENSG00000146955	ENSG00000146955		"""RAB, member RAS oncogene"""	19982	protein-coding gene	gene with protein product							Standard	NM_001008749		Approved	RAB19B	uc010lni.2	A4D1S5	OTTHUMG00000157410	ENST00000356407.3:c.582C>T	7.37:g.140125878C>T		81.0	0.0	0		91.0	41.0	0.450549	NM_001008749	A4D1S6|B2RTS6|B5MDR2|Q9UL27	Silent	SNP	ENST00000356407.3	37	CCDS34762.2																																																																																			C|0.989;T|0.011	0.011	strong		0.562	RAB19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348740.1		
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274212	39274212	+	Missense_Mutation	SNP	C	C	T	rs187464255	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39274212C>T	ENST00000391413.2	-	1	394	c.356G>A	c.(355-357)tGc>tAc	p.C119Y		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	119	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)			gggtctgcagcagctggacac	0.652													c|||	125	0.0249601	0.0923	0.0029	5008	,	,		17401	0.0		0.001	False		,,,				2504	0.0				p.C119Y		Atlas-SNP	.											.	KRTAP4-11	94	.	0			c.G356A						PASS	.						4.0	8.0	7.0					17																	39274212		643	1521	2164	SO:0001583	missense	653240	exon1			CTGCAGCAGCTGG	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.356G>A	17.37:g.39274212C>T	ENSP00000375232:p.Cys119Tyr	120.0	0.0	0		118.0	37.0	0.313559	NM_033059	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	CCDS45675.1	39	0.017857142857142856	36	0.07317073170731707	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	.	13.97	2.395614	0.42512	.	.	ENSG00000212721	ENST00000391413	T	0.03717	3.83	3.63	3.63	0.41609	.	.	.	.	.	T	0.01489	0.0048	H	0.95365	3.66	0.34837	D	0.740315	P	0.46395	0.877	P	0.54544	0.755	T	0.19063	-1.0317	9	0.72032	D	0.01	.	13.1597	0.59537	0.0:1.0:0.0:0.0	.	119	Q9BYQ6	KR411_HUMAN	Y	119	ENSP00000375232:C119Y	ENSP00000375232:C119Y	C	-	2	0	KRTAP4-11	36527738	0.060000	0.20803	0.929000	0.37066	0.073000	0.16967	0.773000	0.26661	1.757000	0.51966	0.514000	0.50259	TGC	C|0.982;T|0.018	0.018	strong		0.652	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
ZNF213	7760	hgsc.bcm.edu	37	16	3188789	3188789	+	Silent	SNP	G	G	A	rs35931391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3188789G>A	ENST00000396878.3	+	4	1042	c.567G>A	c.(565-567)acG>acA	p.T189T	ZNF213_ENST00000574902.1_Silent_p.T189T|ZNF213_ENST00000576416.1_Silent_p.T189T|ZNF213_ENST00000416391.2_Intron	NM_001134655.1|NM_004220.2	NP_001128127.1|NP_004211.1	O14771	ZN213_HUMAN	zinc finger protein 213	189					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)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	16						CCGGAGAGACGACGGACACCT	0.542													G|||	274	0.0547125	0.2012	0.0101	5008	,	,		19201	0.0		0.001	False		,,,				2504	0.0				p.T189T		Atlas-SNP	.											.	ZNF213	36	.	0			c.G567A						PASS	.	G	,	709,3685	297.6+/-284.8	61,587,1549	66.0	63.0	64.0		567,567	-10.3	0.0	16	dbSNP_126	64	9,8591	6.4+/-24.3	0,9,4291	no	coding-synonymous,coding-synonymous	ZNF213	NM_001134655.1,NM_004220.2	,	61,596,5840	AA,AG,GG		0.1047,16.1356,5.5256	,	189/460,189/460	3188789	718,12276	2197	4300	6497	SO:0001819	synonymous_variant	7760	exon4			AGAGACGACGGAC	AF017433	CCDS10495.1	16p13.3	2014-05-13	2007-02-20	2007-02-20	ENSG00000085644	ENSG00000085644		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13005	protein-coding gene	gene with protein product		608387				9653642, 10023065	Standard	NM_004220		Approved	CR53, ZKSCAN21, ZSCAN53	uc010uws.2	O14771	OTTHUMG00000177519	ENST00000396878.3:c.567G>A	16.37:g.3188789G>A		95.0	0.0	0		112.0	62.0	0.553571	NM_004220	A8K1B9|B4DMG6|Q96IS1	Silent	SNP	ENST00000396878.3	37	CCDS10495.1																																																																																			G|0.949;A|0.051	0.051	strong		0.542	ZNF213-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437334.1	NM_004220	
DNAH14	127602	hgsc.bcm.edu	37	1	225339732	225339732	+	Missense_Mutation	SNP	C	C	T	rs115743416	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:225339732C>T	ENST00000445597.2	+	19	3685	c.3685C>T	c.(3685-3687)Cgt>Tgt	p.R1229C	DNAH14_ENST00000439375.2_Missense_Mutation_p.R1639C|DNAH14_ENST00000430092.1_Missense_Mutation_p.R1639C			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	1229					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						AAAAGAAATTCGTATCAATAT	0.333													C|||	28	0.00559105	0.0204	0.0014	5008	,	,		21528	0.0		0.0	False		,,,				2504	0.0				p.R1639C		Atlas-SNP	.											DNAH14_ENST00000430092,colon,carcinoma,-1,2	DNAH14	300	2	0			c.C4915T						PASS	.	C	CYS/ARG	41,1343		0,41,651	279.0	248.0	257.0		4915	5.1	1.0	1	dbSNP_132	257	0,3182		0,0,1591	no	missense	DNAH14	NM_001373.1	180	0,41,2242	TT,TC,CC		0.0,2.9624,0.8979	probably-damaging	1639/4516	225339732	41,4525	692	1591	2283	SO:0001583	missense	127602	exon31			GAAATTCGTATCA	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.3685C>T	1.37:g.225339732C>T	ENSP00000409472:p.Arg1229Cys	138.0	0.0	0		126.0	62.0	0.492063	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	C	19.94	3.920296	0.73098	0.029624	0.0	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375;ENST00000328556	T;T;T;T	0.09538	2.97;2.97;2.97;2.97	6.03	5.13	0.70059	.	0.110231	0.34460	U	0.003951	T	0.14527	0.0351	M	0.84082	2.675	0.80722	D	1	D	0.89917	1.0	D	0.71414	0.973	T	0.03034	-1.1080	10	0.59425	D	0.04	.	14.0411	0.64676	0.0:0.9269:0.0:0.0731	.	1639	Q0VDD8-4	.	C	1229;1639;1639;736	ENSP00000409472:R1229C;ENSP00000414402:R1639C;ENSP00000392061:R1639C;ENSP00000332424:R736C	ENSP00000332424:R736C	R	+	1	0	DNAH14	223406355	0.000000	0.05858	0.998000	0.56505	0.924000	0.55760	0.521000	0.22893	1.568000	0.49683	0.603000	0.83216	CGT	C|0.993;T|0.007	0.007	strong		0.333	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
ELMO2	63916	hgsc.bcm.edu	37	20	45014804	45014804	+	Silent	SNP	G	G	A	rs201990540	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:45014804G>A	ENST00000290246.6	-	9	830	c.636C>T	c.(634-636)gcC>gcT	p.A212A	ELMO2_ENST00000439931.2_Silent_p.A212A|ELMO2_ENST00000445496.2_Silent_p.A29A|ELMO2_ENST00000352077.2_Silent_p.A210A|ELMO2_ENST00000372176.1_Silent_p.A124A|ELMO2_ENST00000396391.1_Silent_p.A212A|ELMO2_ENST00000488853.1_5'UTR	NM_133171.3	NP_573403.1	Q96JJ3	ELMO2_HUMAN	engulfment and cell motility 2	212					apoptotic process (GO:0006915)|cell chemotaxis (GO:0060326)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|urinary_tract(1)	16		Myeloproliferative disorder(115;0.0122)				TGATTTCCTCGGCTATCTTCT	0.527													g|||	3	0.000599042	0.0015	0.0014	5008	,	,		19968	0.0		0.0	False		,,,				2504	0.0				p.A212A		Atlas-SNP	.											ELMO2,NS,carcinoma,-1,1	ELMO2	51	1	0			c.C636T						scavenged	.						135.0	124.0	128.0					20																	45014804		2203	4300	6503	SO:0001819	synonymous_variant	63916	exon8			TTCCTCGGCTATC	AF398886	CCDS13398.1	20q13	2010-03-18	2006-01-20		ENSG00000062598	ENSG00000062598		"""Engulfment and cell motility proteins"""	17233	protein-coding gene	gene with protein product		606421	"""engulfment and cell motility 2 (ced-12 homolog, C. elegans)"""			11595183	Standard	NM_133171		Approved	CED12, ELMO-2, CED-12, KIAA1834, FLJ11656	uc002xru.1	Q96JJ3	OTTHUMG00000033070	ENST00000290246.6:c.636C>T	20.37:g.45014804G>A		95.0	1.0	0.0105263		111.0	5.0	0.045045	NM_182764	E1P5T3|Q5JVZ6|Q7Z5G9|Q96CJ2|Q96ME5|Q96PA9|Q9H938|Q9H9L5|Q9HAH0|Q9NQQ6	Silent	SNP	ENST00000290246.6	37	CCDS13398.1																																																																																			G|0.998;A|0.002	0.002	strong		0.527	ELMO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080466.1	NM_022086	
TEAD2	8463	hgsc.bcm.edu	37	19	49852070	49852070	+	Missense_Mutation	SNP	G	G	A	rs201393859	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49852070G>A	ENST00000311227.2	-	8	715	c.625C>T	c.(625-627)Ccc>Tcc	p.P209S	TEAD2_ENST00000598810.1_Missense_Mutation_p.P213S|TEAD2_ENST00000598397.1_5'UTR|TEAD2_ENST00000593945.1_Missense_Mutation_p.P213S|TEAD2_ENST00000601519.1_Missense_Mutation_p.P212S|TEAD2_ENST00000377214.4_Missense_Mutation_p.P212S|TEAD2_ENST00000539846.1_Missense_Mutation_p.P81S	NM_001256659.1|NM_003598.1	NP_001243588.1|NP_003589.1	Q15562	TEAD2_HUMAN	TEA domain family member 2	209	Pro-rich.|Transcriptional activation. {ECO:0000255}.				gene expression (GO:0010467)|hippo signaling (GO:0035329)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)	29		all_lung(116;7.65e-05)|Lung NSC(112;0.000132)|all_neural(266;0.0506)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00093)|GBM - Glioblastoma multiforme(486;0.0467)		GTAGGTGGGGGCAGGGGTGAG	0.577													G|||	35	0.00698882	0.0265	0.0	5008	,	,		9950	0.0		0.0	False		,,,				2504	0.0				p.P213S		Atlas-SNP	.											.	TEAD2	70	.	0			c.C637T						PASS	.	G	SER/PRO	94,4128		2,90,2019	11.0	14.0	13.0		625	3.6	1.0	19		13	2,8324		0,2,4161	yes	missense	TEAD2	NM_003598.1	74	2,92,6180	AA,AG,GG		0.024,2.2264,0.7651	benign	209/448	49852070	96,12452	2111	4163	6274	SO:0001583	missense	8463	exon9			GTGGGGGCAGGGG	X94440	CCDS12761.1, CCDS58670.1, CCDS58671.1, CCDS59406.1	19q13.3	2008-07-22							11715	protein-coding gene	gene with protein product		601729				9889009, 8702974	Standard	NM_003598		Approved	TEF-4, ETF, TEF4	uc031rls.1	Q15562		ENST00000311227.2:c.625C>T	19.37:g.49852070G>A	ENSP00000310701:p.Pro209Ser	114.0	0.0	0		127.0	57.0	0.448819	NM_001256660	B4DTJ6|M0R1T9|Q8NA25|Q96IG3	Missense_Mutation	SNP	ENST00000311227.2	37	CCDS12761.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	G	5.217	0.225622	0.09916	0.022264	2.4E-4	ENSG00000074219	ENST00000311227;ENST00000377214;ENST00000539846	T;T;T	0.34275	1.37;1.37;1.37	5.73	3.58	0.41010	.	0.229512	0.31031	N	0.008399	T	0.08980	0.0222	N	0.04148	-0.265	0.48975	D	0.999734	B;B;B	0.16166	0.01;0.016;0.006	B;B;B	0.22753	0.018;0.041;0.018	T	0.04930	-1.0917	10	0.30854	T	0.27	-21.1627	11.4865	0.50356	0.1569:0.0:0.8431:0.0	.	81;209;212	B4DTJ6;Q15562;Q8NA25	.;TEAD2_HUMAN;.	S	209;212;81	ENSP00000310701:P209S;ENSP00000366419:P212S;ENSP00000437928:P81S	ENSP00000310701:P209S	P	-	1	0	TEAD2	54543882	1.000000	0.71417	1.000000	0.80357	0.072000	0.16883	5.441000	0.66569	1.577000	0.49804	-0.150000	0.13652	CCC	G|0.995;A|0.005	0.005	strong		0.577	TEAD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465465.1	NM_003598	
GPRIN3	285513	hgsc.bcm.edu	37	4	90168945	90168945	+	Missense_Mutation	SNP	A	A	C	rs34322172	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:90168945A>C	ENST00000609438.1	-	2	2835	c.2317T>G	c.(2317-2319)Tct>Gct	p.S773A	GPRIN3_ENST00000333209.4_Missense_Mutation_p.S773A	NM_198281.2	NP_938022.2	Q6ZVF9	GRIN3_HUMAN	GPRIN family member 3	773										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|prostate(2)|skin(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;5.67e-05)		TCTAACACAGAAGACGGGGCA	0.463													A|||	34	0.00678914	0.025	0.0014	5008	,	,		17083	0.0		0.0	False		,,,				2504	0.0				p.S773A		Atlas-SNP	.											.	GPRIN3	90	.	0			c.T2317G						PASS	.	A	ALA/SER	121,4285	90.2+/-128.9	3,115,2085	91.0	97.0	95.0		2317	4.2	0.0	4	dbSNP_126	95	0,8600		0,0,4300	yes	missense	GPRIN3	NM_198281.2	99	3,115,6385	CC,CA,AA		0.0,2.7463,0.9303	probably-damaging	773/777	90168945	121,12885	2203	4300	6503	SO:0001583	missense	285513	exon2			ACACAGAAGACGG	AK124616	CCDS34030.1	4q22.1	2006-08-24				ENSG00000185477			27733	protein-coding gene	gene with protein product		611241				15488195	Standard	NM_198281		Approved	GRIN3, FLJ42625	uc003hsm.1	Q6ZVF9		ENST00000609438.1:c.2317T>G	4.37:g.90168945A>C	ENSP00000476603:p.Ser773Ala	173.0	0.0	0		183.0	93.0	0.508197	NM_198281	Q8IVE4	Missense_Mutation	SNP	ENST00000609438.1	37	CCDS34030.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	A	7.014	0.557400	0.13436	0.027463	0.0	ENSG00000185477	ENST00000333209	T	0.15256	2.44	5.45	4.24	0.50183	.	0.261257	0.20448	N	0.092147	T	0.04543	0.0124	N	0.22421	0.69	0.31631	N	0.649051	B	0.27997	0.197	B	0.31812	0.136	T	0.05616	-1.0874	10	0.87932	D	0	-8.6401	11.9204	0.52789	0.7247:0.2753:0.0:0.0	rs34322172	773	Q6ZVF9	GRIN3_HUMAN	A	773	ENSP00000328672:S773A	ENSP00000328672:S773A	S	-	1	0	GPRIN3	90387968	1.000000	0.71417	0.032000	0.17829	0.031000	0.12232	4.535000	0.60629	1.051000	0.40369	0.533000	0.62120	TCT	A|0.992;C|0.008	0.008	strong		0.463	GPRIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363540.2	NM_198281	
MLKL	197259	hgsc.bcm.edu	37	16	74709233	74709233	+	Missense_Mutation	SNP	C	C	A	rs144526386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:74709233C>A	ENST00000306247.7	-	4	944	c.605G>T	c.(604-606)gGc>gTc	p.G202V	MLKL_ENST00000308807.7_Intron	NM_001142497.1	NP_001135969.1			mixed lineage kinase domain-like											breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(2)|lung(6)|skin(1)|stomach(2)	19						ACTGGCTGAGCCAGTCTTCAC	0.493													C|||	51	0.0101837	0.0023	0.0144	5008	,	,		19105	0.0		0.0209	False		,,,				2504	0.0174				p.G202V		Atlas-SNP	.											.	MLKL	51	.	0			c.G605T						PASS	.	C	VAL/GLY,	17,4379	23.3+/-48.9	0,17,2181	113.0	108.0	110.0		605,	-1.0	0.0	16	dbSNP_134	110	162,8438	76.3+/-139.0	2,158,4140	yes	missense,intron	MLKL	NM_001142497.1,NM_152649.2	109,	2,175,6321	AA,AC,CC		1.8837,0.3867,1.3773	,	202/264,	74709233	179,12817	2198	4300	6498	SO:0001583	missense	197259	exon4			GCTGAGCCAGTCT	AK091708	CCDS32487.1, CCDS45528.1	16q22.3	2008-02-05				ENSG00000168404			26617	protein-coding gene	gene with protein product		615153				12477932	Standard	NM_152649		Approved	FLJ34389	uc002fdb.2	Q8NB16		ENST00000306247.7:c.605G>T	16.37:g.74709233C>A	ENSP00000303118:p.Gly202Val	103.0	0.0	0		93.0	49.0	0.526882	NM_001142497		Missense_Mutation	SNP	ENST00000306247.7	37	CCDS45528.1	23	0.010531135531135532	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	15	0.01978891820580475	C	8.923	0.961462	0.18583	0.003867	0.018837	ENSG00000168404	ENST00000306247	T	0.12147	2.71	4.96	-1.05	0.10036	.	.	.	.	.	T	0.14313	0.0346	.	.	.	0.09310	N	1	D	0.67145	0.996	D	0.65573	0.936	T	0.07501	-1.0769	8	0.48119	T	0.1	.	8.2986	0.32001	0.0:0.4852:0.0:0.5148	.	202	Q8NB16-2	.	V	202	ENSP00000303118:G202V	ENSP00000303118:G202V	G	-	2	0	MLKL	73266734	0.000000	0.05858	0.001000	0.08648	0.016000	0.09150	-0.620000	0.05565	-0.228000	0.09869	-0.374000	0.07098	GGC	C|0.986;A|0.014	0.014	strong		0.493	MLKL-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000436402.1	NM_152649	
TMEM201	199953	hgsc.bcm.edu	37	1	9671935	9671935	+	Silent	SNP	C	C	T	rs4073292	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:9671935C>T	ENST00000340381.6	+	10	1899	c.1890C>T	c.(1888-1890)gcC>gcT	p.A630A	TMEM201_ENST00000377376.4_Silent_p.A606A	NM_001130924.2	NP_001124396.2	Q5SNT2	TM201_HUMAN	transmembrane protein 201	630					fibroblast migration (GO:0010761)|nuclear migration (GO:0007097)	integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)				lung(3)|upper_aerodigestive_tract(1)	4	all_lung(157;0.222)	all_epithelial(116;2.09e-14)|Renal(390;0.000469)|all_lung(118;0.000521)|Lung NSC(185;0.000744)|Colorectal(325;0.0062)|Breast(348;0.0157)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.5e-08)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|STAD - Stomach adenocarcinoma(132;0.00345)|READ - Rectum adenocarcinoma(331;0.0419)		CGGAGGAGGCCGCCACCTGGA	0.642													C|||	355	0.0708866	0.2564	0.0202	5008	,	,		15597	0.0		0.002	False		,,,				2504	0.0				p.A630A		Atlas-SNP	.											.	TMEM201	63	.	0			c.C1890T						PASS	.	C		298,1086		35,228,429	21.0	21.0	21.0		1890	-2.5	0.0	1	dbSNP_108	21	4,3178		0,4,1587	no	coding-synonymous	TMEM201	NM_001130924.2		35,232,2016	TT,TC,CC		0.1257,21.5318,6.6141		630/667	9671935	302,4264	692	1591	2283	SO:0001819	synonymous_variant	199953	exon10			GGAGGCCGCCACC		CCDS30579.1, CCDS44055.1, CCDS44055.2	1p36.22	2009-11-06			ENSG00000188807	ENSG00000188807			33719	protein-coding gene	gene with protein product							Standard	NM_001130924		Approved	RP13-15M17.2, NET5	uc021ofy.1	Q5SNT2	OTTHUMG00000057457	ENST00000340381.6:c.1890C>T	1.37:g.9671935C>T		82.0	0.0	0		86.0	44.0	0.511628	NM_001130924	B9EH90|Q5SNT3	Silent	SNP	ENST00000340381.6	37	CCDS44055.2	154	0.07051282051282051	145	0.29471544715447157	8	0.022099447513812154	0	0.0	1	0.0013192612137203166	C	0.113	-1.136063	0.01742	0.215318	0.001257	ENSG00000188807	ENST00000416541	.	.	.	5.28	-2.46	0.06461	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.34304	-0.9834	3	.	.	.	-6.4317	7.9697	0.30119	0.0:0.4376:0.1547:0.4077	rs4073292;rs17034220;rs4073292	.	.	.	C	516	.	.	R	+	1	0	TMEM201	9594522	0.000000	0.05858	0.011000	0.14972	0.058000	0.15608	-0.270000	0.08584	-0.319000	0.08652	-1.134000	0.01955	CGC	C|0.934;T|0.066	0.066	strong		0.642	TMEM201-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127672.1	NM_001010866	
ZNF195	7748	hgsc.bcm.edu	37	11	3383015	3383015	+	Missense_Mutation	SNP	G	G	A	rs7125523	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:3383015G>A	ENST00000399602.4	-	4	457	c.331C>T	c.(331-333)Cgt>Tgt	p.R111C	ZNF195_ENST00000354599.6_Intron|ZNF195_ENST00000526601.1_Missense_Mutation_p.R115C|ZNF195_ENST00000438262.2_Intron|ZNF195_ENST00000005082.9_Missense_Mutation_p.R111C|ZNF195_ENST00000528796.1_Intron|ZNF195_ENST00000343338.7_Intron|ZNF195_ENST00000429541.2_Intron	NM_001130520.2	NP_001123992.1	O14628	ZN195_HUMAN	zinc finger protein 195	111	Spacer.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)	17		Medulloblastoma(188;0.00106)|Breast(177;0.00328)|all_neural(188;0.00681)|Ovarian(85;0.00965)		BRCA - Breast invasive adenocarcinoma(625;0.0361)|LUSC - Lung squamous cell carcinoma(625;0.2)		ggctgggcacggtggttcaca	0.502													g|||	110	0.0219649	0.0794	0.0072	5008	,	,		18477	0.0		0.0	False		,,,				2504	0.0				p.R115C		Atlas-SNP	.											.	ZNF195	77	.	0			c.C343T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG,,,	87,1297		0,87,605	184.0	176.0	179.0		331,331,343,,,	-0.4	0.0	11	dbSNP_116	179	4,3178		0,4,1587	yes	missense,missense,missense,intron,intron,intron	ZNF195	NM_001130519.2,NM_001130520.2,NM_001242841.1,NM_001242842.1,NM_001242843.1,NM_007152.4	180,180,180,,,	0,91,2192	AA,AG,GG		0.1257,6.2861,1.993	possibly-damaging,possibly-damaging,possibly-damaging,,,	111/607,111/630,115/611,,,	3383015	91,4475	692	1591	2283	SO:0001583	missense	7748	exon5			GGGCACGGTGGTT		CCDS41604.1, CCDS44521.1, CCDS44522.1, CCDS55736.1, CCDS55737.1, CCDS58111.1	11p15.5	2013-01-08			ENSG00000005801	ENSG00000005801		"""Zinc fingers, C2H2-type"", ""-"""	12986	protein-coding gene	gene with protein product		602187				9344677	Standard	NM_001130520		Approved		uc001lxt.3	O14628	OTTHUMG00000011694	ENST00000399602.4:c.331C>T	11.37:g.3383015G>A	ENSP00000382511:p.Arg111Cys	39.0	0.0	0		50.0	29.0	0.58	NM_001242841	A8K234|B3KTK2|B4DEL0|C9JLY9|L7MNK2|Q0VAJ6|Q658N8|Q6ZNA9	Missense_Mutation	SNP	ENST00000399602.4	37	CCDS44522.1	43	0.019688644688644688	39	0.07926829268292683	4	0.011049723756906077	0	0.0	0	0.0	g	0.950	-0.706656	0.03230	0.062861	0.001257	ENSG00000005801	ENST00000399602;ENST00000005082;ENST00000526601;ENST00000533036;ENST00000534569	T;T;T;T;T	0.14766	5.12;5.12;5.12;5.12;2.48	0.225	-0.451	0.12214	.	.	.	.	.	T	0.00271	0.0008	N	0.25992	0.78	0.09310	N	1	B;B;P	0.50710	0.0;0.0;0.938	B;B;B	0.22753	0.0;0.0;0.041	T	0.33727	-0.9857	8	0.56958	D	0.05	.	.	.	.	rs7125523	115;111;111	O14628-6;O14628-5;O14628	.;.;ZN195_HUMAN	C	111;111;115;130;115	ENSP00000382511:R111C;ENSP00000005082:R111C;ENSP00000435828:R115C;ENSP00000433911:R130C;ENSP00000437265:R115C	ENSP00000005082:R111C	R	-	1	0	ZNF195	3339591	0.001000	0.12720	0.002000	0.10522	0.002000	0.02628	-0.653000	0.05360	-1.864000	0.01148	-1.842000	0.00583	CGT	G|0.980;A|0.020	0.020	strong		0.502	ZNF195-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032321.2		
RAB11FIP5	26056	hgsc.bcm.edu	37	2	73339675	73339675	+	Silent	SNP	C	C	T	rs143108301	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:73339675C>T	ENST00000258098.6	-	1	471	c.231G>A	c.(229-231)ctG>ctA	p.L77L	RP11-44N22.3_ENST00000608612.1_RNA	NM_015470.2	NP_056285.1	Q9BXF6	RFIP5_HUMAN	RAB11 family interacting protein 5 (class I)	77	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				cellular response to acidic pH (GO:0071468)|insulin secretion involved in cellular response to glucose stimulus (GO:0035773)|protein transport (GO:0015031)|regulated secretory pathway (GO:0045055)|regulation of protein localization to cell surface (GO:2000008)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|microtubule organizing center (GO:0005815)|mitochondrial outer membrane (GO:0005741)|recycling endosome (GO:0055037)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)			biliary_tract(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	23						CCCCCGGCGGCAGCTCGAAGG	0.736													C|||	2	0.000399361	0.0008	0.0	5008	,	,		10052	0.001		0.0	False		,,,				2504	0.0				p.L77L		Atlas-SNP	.											.	RAB11FIP5	66	.	0			c.G231A						PASS	.	C		4,4354		0,4,2175	11.0	10.0	10.0		231	1.9	1.0	2	dbSNP_134	10	0,8504		0,0,4252	no	coding-synonymous	RAB11FIP5	NM_015470.2		0,4,6427	TT,TC,CC		0.0,0.0918,0.0311		77/654	73339675	4,12858	2179	4252	6431	SO:0001819	synonymous_variant	26056	exon1			CGGCGGCAGCTCG	AF334812	CCDS1923.1	2p13	2008-02-05			ENSG00000135631	ENSG00000135631			24845	protein-coding gene	gene with protein product		605536				10048485, 11163216	Standard	NM_015470		Approved	GAF1, KIAA0857, RIP11, pp75	uc002sis.4	Q9BXF6	OTTHUMG00000129779	ENST00000258098.6:c.231G>A	2.37:g.73339675C>T		44.0	0.0	0		69.0	30.0	0.434783	NM_015470	O94939|Q9P0M1	Silent	SNP	ENST00000258098.6	37	CCDS1923.1																																																																																			C|1.000;T|0.000	0.000	weak		0.736	RAB11FIP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251995.1	NM_015470	
FNDC1	84624	hgsc.bcm.edu	37	6	159654408	159654408	+	Missense_Mutation	SNP	G	G	A	rs73799344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:159654408G>A	ENST00000297267.9	+	11	3064	c.2864G>A	c.(2863-2865)aGc>aAc	p.S955N	FNDC1_ENST00000340366.6_Missense_Mutation_p.S892N	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	955					cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		GTTCAACAGAGCACAGACGCG	0.617													G|||	259	0.0517173	0.1846	0.0216	5008	,	,		18211	0.0		0.0	False		,,,				2504	0.0				p.S955N		Atlas-SNP	.											.	FNDC1	250	.	0			c.G2864A						PASS	.	G	ASN/SER	784,3552		68,648,1452	57.0	68.0	64.0		2864	3.8	0.1	6	dbSNP_130	64	8,8520		0,8,4256	yes	missense	FNDC1	NM_032532.2	46	68,656,5708	AA,AG,GG		0.0938,18.0812,6.1567	benign	955/1895	159654408	792,12072	2168	4264	6432	SO:0001583	missense	84624	exon11			AACAGAGCACAGA	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"""Fibronectin type III domain containing"""	21184	protein-coding gene	gene with protein product		609991	"""fibronectin type III domain containing 2"""	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.2864G>A	6.37:g.159654408G>A	ENSP00000297267:p.Ser955Asn	50.0	0.0	0		55.0	25.0	0.454545	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Missense_Mutation	SNP	ENST00000297267.9	37	CCDS47512.1	107	0.04899267399267399	99	0.20121951219512196	8	0.022099447513812154	0	0.0	0	0.0	G	16.37	3.104157	0.56291	0.180812	9.38E-4	ENSG00000164694	ENST00000297267;ENST00000340366	T;T	0.10005	2.92;3.77	3.81	3.81	0.43845	.	0.352689	0.24945	N	0.034358	T	0.06735	0.0172	L	0.29908	0.895	0.58432	P	1.999999999946489E-6	D;P	0.57257	0.979;0.734	P;B	0.56563	0.801;0.398	T	0.27839	-1.0062	9	0.13108	T	0.6	-19.0686	11.4852	0.50350	0.0:0.0:1.0:0.0	.	892;955	Q4ZHG4-2;Q4ZHG4	.;FNDC1_HUMAN	N	955;892	ENSP00000297267:S955N;ENSP00000342460:S892N	ENSP00000297267:S955N	S	+	2	0	FNDC1	159574398	0.523000	0.26274	0.140000	0.22221	0.635000	0.38103	1.701000	0.37825	2.423000	0.82170	0.561000	0.74099	AGC	G|0.959;A|0.041	0.041	strong		0.617	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
CXCR2	3579	hgsc.bcm.edu	37	2	219000193	219000193	+	Silent	SNP	A	A	G	rs2228414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:219000193A>G	ENST00000318507.2	+	3	1096	c.669A>G	c.(667-669)ccA>ccG	p.P223P		NM_001557.3	NP_001548.1	P25025	CXCR2_HUMAN	chemokine (C-X-C motif) receptor 2	223					cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|dendritic cell chemotaxis (GO:0002407)|inflammatory response (GO:0006954)|interleukin-8-mediated signaling pathway (GO:0038112)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cell proliferation (GO:0008284)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|mast cell granule (GO:0042629)|membrane (GO:0016020)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|interleukin-8 binding (GO:0019959)|interleukin-8 receptor activity (GO:0004918)|signal transducer activity (GO:0004871)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(11)|skin(1)|stomach(1)	22						TCATCGTGCCACTGCTGATCA	0.562													G|||	66	0.0131789	0.0469	0.0058	5008	,	,		21834	0.0		0.0	False		,,,				2504	0.0				p.P223P		Atlas-SNP	.											.	CXCR2	54	.	0			c.A669G						PASS	.	G	,	167,4239	111.2+/-149.4	3,161,2039	174.0	159.0	164.0		669,669	-10.8	0.0	2	dbSNP_98	164	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CXCR2	NM_001168298.1,NM_001557.3	,	3,161,6339	GG,GA,AA		0.0,3.7903,1.284	,	223/361,223/361	219000193	167,12839	2203	4300	6503	SO:0001819	synonymous_variant	3579	exon4			CGTGCCACTGCTG	U11869	CCDS2408.1	2q35	2012-08-08	2009-11-25	2009-11-25	ENSG00000180871	ENSG00000180871		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : C-X-C motif"", ""Interleukins and interleukin receptors"""	6027	protein-coding gene	gene with protein product		146928	"""interleukin 8 receptor, beta"""	IL8RB		1427896	Standard	NM_001557		Approved	CMKAR2, CD182	uc002vha.2	P25025	OTTHUMG00000133107	ENST00000318507.2:c.669A>G	2.37:g.219000193A>G		253.0	0.0	0		214.0	124.0	0.579439	NM_001168298	Q8IUZ1|Q9P2T6|Q9P2T7	Silent	SNP	ENST00000318507.2	37	CCDS2408.1																																																																																			A|0.985;G|0.015	0.015	strong		0.562	CXCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256772.2	NM_001557	
MT-ND3	4537	hgsc.bcm.edu	37	M	10321	10321	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:10321T>C	ENST00000361227.2	+	1	263	c.263T>C	c.(262-264)gTt>gCt	p.V88A	MT-TR_ENST00000387439.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-TS1_ENST00000387416.2_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-ND4_ENST00000361381.2_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-TK_ENST00000387421.1_RNA			P03897	NU3M_HUMAN	mitochondrially encoded NADH dehydrogenase 3	88					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)										GCCACTAATAGTTATGTCATC	0.373																																					p.V88A		Atlas-SNP	.											.	.	.	.	0			c.T263C						PASS	.																																			SO:0001583	missense	0	exon1			TAATAGTTATGTC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198840	ENSG00000198840	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7458	protein-coding gene	gene with protein product	"""complex I ND3 subunit"", ""NADH-ubiquinone oxidoreductase chain 3"""	516002	"""NADH dehydrogenase 3"""	MTND3			Standard			Approved	ND3, NAD3		P03897		ENST00000361227.2:c.263T>C	M.37:g.10321T>C	ENSP00000355206:p.Val88Ala	8.0	0.0	0		8.0	8.0	1	ENST00000361227		Missense_Mutation	SNP	ENST00000361227.2	37																																																																																				.	.	none		0.373	MT-ND3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024033	
CEP85L	387119	hgsc.bcm.edu	37	6	118803091	118803091	+	Missense_Mutation	SNP	C	C	G	rs9489410	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:118803091C>G	ENST00000368491.3	-	8	2217	c.1596G>C	c.(1594-1596)caG>caC	p.Q532H	CEP85L_ENST00000368488.5_Missense_Mutation_p.Q535H	NM_001042475.2	NP_001035940.1	Q5SZL2	CE85L_HUMAN	centrosomal protein 85kDa-like	532			Q -> H (in dbSNP:rs9489410).			centrosome (GO:0005813)|cytoplasm (GO:0005737)											CTTCCAGAATCTGCAGCTAAG	0.318													C|||	166	0.033147	0.059	0.0173	5008	,	,		11959	0.0		0.0189	False		,,,				2504	0.0583				p.Q535H		Atlas-SNP	.											.	CEP85L	26	.	0			c.G1605C						PASS	.	C	HIS/GLN,HIS/GLN	194,3380		4,186,1597	67.0	57.0	60.0		1596,1605	2.3	1.0	6	dbSNP_119	60	164,7956		1,162,3897	yes	missense,missense	C6orf204	NM_001042475.2,NM_001178035.1	24,24	5,348,5494	GG,GC,CC		2.0197,5.4281,3.0614	probably-damaging,probably-damaging	532/806,535/809	118803091	358,11336	1787	4060	5847	SO:0001583	missense	387119	exon9			CAGAATCTGCAGC	AF308284	CCDS5119.2, CCDS43498.1, CCDS55052.1	6q22.31	2011-11-25	2011-11-25	2011-11-25	ENSG00000111860	ENSG00000111860			21638	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 204"""	C6orf204			Standard	NM_206921		Approved	NY-BR-15, bA57K17.2	uc003pya.2	Q5SZL2	OTTHUMG00000015465	ENST00000368491.3:c.1596G>C	6.37:g.118803091C>G	ENSP00000357477:p.Gln532His	59.0	0.0	0		72.0	32.0	0.444444	NM_001178035	A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289	Missense_Mutation	SNP	ENST00000368491.3	37	CCDS43498.1	46	0.021062271062271064	26	0.052845528455284556	6	0.016574585635359115	0	0.0	14	0.018469656992084433	C	16.03	3.005806	0.54254	0.054281	0.020197	ENSG00000111860	ENST00000368491;ENST00000368488;ENST00000434604	T;T;T	0.11821	2.74;2.74;2.74	5.24	2.29	0.28610	.	0.061562	0.64402	D	0.000004	T	0.16642	0.0400	L	0.56769	1.78	0.34826	D	0.73918	D;D	0.76494	0.999;0.999	D;D	0.69479	0.964;0.964	T	0.02588	-1.1137	10	0.72032	D	0.01	-5.1646	9.1618	0.37028	0.0:0.6637:0.0:0.3363	rs9489410;rs52802289;rs9489410	535;532	F8W6J2;Q5SZL2	.;CF204_HUMAN	H	532;535;535	ENSP00000357477:Q532H;ENSP00000357474:Q535H;ENSP00000392131:Q535H	ENSP00000357474:Q535H	Q	-	3	2	C6orf204	118909784	1.000000	0.71417	0.999000	0.59377	0.937000	0.57800	0.983000	0.29552	0.219000	0.20840	0.561000	0.74099	CAG	C|0.982;G|0.018	0.018	strong		0.318	CEP85L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041996.2	NM_001042475	
PPP1R26	9858	hgsc.bcm.edu	37	9	138379608	138379608	+	Silent	SNP	C	C	T	rs139160467	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:138379608C>T	ENST00000356818.2	+	4	3801	c.3252C>T	c.(3250-3252)acC>acT	p.T1084T	PPP1R26_ENST00000604351.1_Silent_p.T1084T|PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000605660.1_Silent_p.T1084T|PPP1R26_ENST00000401470.3_Silent_p.T1084T|PPP1R26_ENST00000605286.1_Silent_p.T1084T	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	1084					negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										TGCTGTCCACCCAGCTCTTCC	0.726													C|||	57	0.0113818	0.0424	0.0014	5008	,	,		14055	0.0		0.0	False		,,,				2504	0.0				p.T1084T		Atlas-SNP	.											.	.	.	.	0			c.C3252T						PASS	.	C		72,3236		0,72,1582	4.0	5.0	5.0		3252	-7.1	0.1	9	dbSNP_134	5	2,7236		0,2,3617	no	coding-synonymous	KIAA0649	NM_014811.3		0,74,5199	TT,TC,CC		0.0276,2.1765,0.7017		1084/1210	138379608	74,10472	1654	3619	5273	SO:0001819	synonymous_variant	9858	exon4			GTCCACCCAGCTC	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.3252C>T	9.37:g.138379608C>T		24.0	0.0	0		22.0	8.0	0.363636	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Silent	SNP	ENST00000356818.2	37	CCDS6988.1																																																																																			C|0.989;T|0.011	0.011	strong		0.726	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811	
OR3A1	4994	hgsc.bcm.edu	37	17	3195603	3195603	+	Nonsense_Mutation	SNP	T	T	A	rs7218125	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3195603T>A	ENST00000323404.1	-	1	273	c.274A>T	c.(274-276)Aag>Tag	p.K92*	RP11-64J4.2_ENST00000573491.1_RNA	NM_002550.2	NP_002541.2	P47881	OR3A1_HUMAN	olfactory receptor, family 3, subfamily A, member 1	92					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|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)|kidney(4)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	20						ACTGCACGCTTGCGGGACAGG	0.567													.|||	111	0.0221645	0.0779	0.0101	5008	,	,		18657	0.0		0.001	False		,,,				2504	0.0				p.K92X	GBM(20;287 516 18743 28660 36594)	Atlas-SNP	.											.	OR3A1	46	.	0			c.A274T						PASS	.	T	stop/LYS	278,4128	155.5+/-188.7	10,258,1935	82.0	67.0	72.0		274	3.0	0.1	17	dbSNP_116	72	3,8597	2.2+/-6.3	0,3,4297	yes	stop-gained	OR3A1	NM_002550.2		10,261,6232	AA,AT,TT		0.0349,6.3096,2.1605		92/316	3195603	281,12725	2203	4300	6503	SO:0001587	stop_gained	4994	exon1			CACGCTTGCGGGA	X80391	CCDS11023.1	17p13.3	2012-08-09			ENSG00000180090	ENSG00000180090		"""GPCR / Class A : Olfactory receptors"""	8282	protein-coding gene	gene with protein product						8921386, 8647456	Standard	NM_002550		Approved	OLFRA03, OR40, OR17-40	uc002fvh.1	P47881	OTTHUMG00000090642	ENST00000323404.1:c.274A>T	17.37:g.3195603T>A	ENSP00000313803:p.Lys92*	254.0	0.0	0		277.0	148.0	0.534296	NM_002550	Q4VB06|Q6IFM4	Nonsense_Mutation	SNP	ENST00000323404.1	37	CCDS11023.1	37	0.01694139194139194	31	0.06300813008130081	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	T	10.77	1.444920	0.25987	0.063096	3.49E-4	ENSG00000180090	ENST00000323404	.	.	.	5.31	3.01	0.34805	.	0.663946	0.13864	N	0.357451	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.6046	7.6409	0.28292	0.0:0.0758:0.1405:0.7836	rs7218125;rs16952824;rs7218125	.	.	.	X	92	.	ENSP00000313803:K92X	K	-	1	0	OR3A1	3142353	0.000000	0.05858	0.097000	0.21041	0.002000	0.02628	0.063000	0.14410	1.003000	0.39130	0.528000	0.53228	AAG	T|0.972;A|0.028	0.028	strong		0.567	OR3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207302.2		
CYBA	1535	hgsc.bcm.edu	37	16	88713213	88713213	+	Silent	SNP	C	C	G	rs2228472	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88713213C>G	ENST00000261623.3	-	4	375	c.237G>C	c.(235-237)ctG>ctC	p.L79L	CYBA_ENST00000567174.1_Silent_p.L79L|CYBA_ENST00000561972.1_5'Flank|CYBA_ENST00000569359.1_Silent_p.L79L	NM_000101.3	NP_000092.2	P13498	CY24A_HUMAN	cytochrome b-245, alpha polypeptide	79					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)|cellular response to amino acid stimulus (GO:0071230)|cellular response to gamma radiation (GO:0071480)|cellular response to glucose stimulus (GO:0071333)|cellular response to mechanical stimulus (GO:0071260)|cellular response to organic cyclic compound (GO:0071407)|cellular response to tumor necrosis factor (GO:0071356)|cytochrome complex assembly (GO:0017004)|hydrogen peroxide biosynthetic process (GO:0050665)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|negative regulation of glomerular filtration by angiotensin (GO:0003106)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|positive regulation of cell growth (GO:0030307)|positive regulation of endothelial cell proliferation (GO:0001938)|respiratory burst (GO:0045730)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|response to nutrient levels (GO:0031667)|smooth muscle hypertrophy (GO:0014895)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	apical plasma membrane (GO:0016324)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|neuronal cell body (GO:0043025)|phagocytic vesicle membrane (GO:0030670)|secretory granule (GO:0030141)	electron carrier activity (GO:0009055)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|SH3 domain binding (GO:0017124)|superoxide-generating NADPH oxidase activity (GO:0016175)			endometrium(1)|liver(1)	2				BRCA - Breast invasive adenocarcinoma(80;0.0478)	Dextromethorphan(DB00514)	AGGGCCCGAACAGCTTCACCA	0.652													C|||	227	0.0453275	0.1672	0.0086	5008	,	,		15785	0.0		0.0	False		,,,				2504	0.0				p.L79L		Atlas-SNP	.											.	CYBA	12	.	0			c.G237C						PASS	.	C		627,3769	269.8+/-269.2	48,531,1619	81.0	91.0	87.0		237	0.7	0.3	16	dbSNP_98	87	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	CYBA	NM_000101.2		48,536,5914	GG,GC,CC		0.0581,14.263,4.863		79/196	88713213	632,12364	2198	4300	6498	SO:0001819	synonymous_variant	1535	exon4			CCCGAACAGCTTC		CCDS32504.1	16q24	2014-09-17				ENSG00000051523		"""Cytochrome b genes"""	2577	protein-coding gene	gene with protein product	"""flavocytochrome b-558 alpha polypeptide"""	608508				2243141	Standard	NM_000101		Approved	p22-PHOX	uc002flb.4	P13498		ENST00000261623.3:c.237G>C	16.37:g.88713213C>G		65.0	0.0	0		67.0	36.0	0.537313	NM_000101	Q14090|Q9BR72	Silent	SNP	ENST00000261623.3	37	CCDS32504.1																																																																																			C|0.949;G|0.051	0.051	strong		0.652	CYBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422765.1	NM_000101	
IFNA10	3446	hgsc.bcm.edu	37	9	21206724	21206724	+	Nonsense_Mutation	SNP	G	G	A	rs145785282	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21206724G>A	ENST00000357374.2	-	1	418	c.373C>T	c.(373-375)Cag>Tag	p.Q125*		NM_002171.1	NP_002162.1	P01566	IFN10_HUMAN	interferon, alpha 10	125					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)|type I interferon receptor binding (GO:0005132)			endometrium(1)|large_intestine(3)|liver(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	16				Lung(24;1.26e-23)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.17)		CCAACCTCCTGTATCACACAT	0.463													g|||	48	0.00958466	0.0325	0.0043	5008	,	,		19993	0.0		0.002	False		,,,				2504	0.0				p.Q125X		Atlas-SNP	.											.	IFNA10	29	.	0			c.C373T						PASS	.	G	stop/GLN	104,4300		2,100,2100	69.0	76.0	73.0		373	0.4	0.0	9	dbSNP_134	73	4,8556		0,4,4276	no	stop-gained	IFNA10	NM_002171.1		2,104,6376	AA,AG,GG		0.0467,2.3615,0.8331		125/190	21206724	108,12856	2202	4280	6482	SO:0001587	stop_gained	3446	exon1			CCTCCTGTATCAC		CCDS6499.1	9p22	2010-08-24			ENSG00000186803	ENSG00000186803		"""Interferons"""	5418	protein-coding gene	gene with protein product		147577				1385305	Standard	NM_002171		Approved	IFN-alphaC	uc003zoq.1	P01566	OTTHUMG00000019658	ENST00000357374.2:c.373C>T	9.37:g.21206724G>A	ENSP00000369566:p.Gln125*	599.0	0.0	0		702.0	210.0	0.299145	NM_002171	Q5VV13	Nonsense_Mutation	SNP	ENST00000357374.2	37	CCDS6499.1	.	.	.	.	.	.	.	.	.	.	-	12.34	1.908152	0.33721	0.023615	4.67E-4	ENSG00000186803	ENST00000357374	.	.	.	3.75	0.383	0.16239	.	0.485956	0.22193	N	0.063355	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.59425	D	0.04	.	7.857	0.29489	0.0:0.3253:0.508:0.1667	.	.	.	.	X	125	.	ENSP00000369566:Q125X	Q	-	1	0	IFNA10	21196724	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.002000	0.13061	0.171000	0.19730	-0.667000	0.03836	CAG	G|0.996;A|0.004	0.004	strong		0.463	IFNA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051887.1	NM_002171	
MUC4	4585	hgsc.bcm.edu	37	3	195507227	195507227	+	Missense_Mutation	SNP	C	C	T	rs569772156|rs74187968	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195507227C>T	ENST00000463781.3	-	2	11683	c.11224G>A	c.(11224-11226)Gtc>Atc	p.V3742I	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.V3742I	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)		AGAGGGGTGACGTGACCTGTG	0.582													.|||	4	0.000798722	0.0015	0.0	5008	,	,		9263	0.001		0.0	False		,,,				2504	0.001				p.V3742I		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	0			c.G11224A						PASS	.						26.0	26.0	26.0					3																	195507227		670	1583	2253	SO:0001583	missense	4585	exon2			GGGTGACGTGACC	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.11224G>A	3.37:g.195507227C>T	ENSP00000417498:p.Val3742Ile	283.0	0.0	0		70.0	46.0	0.657143	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	2.258	-0.369947	0.05069	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.43294	1.2;0.95	0.885	-1.77	0.07982	.	0.000000	0.25514	U	0.030158	T	0.16041	0.0386	N	0.14661	0.345	0.09310	N	1	B	0.12013	0.005	B	0.01281	0.0	T	0.10753	-1.0616	9	.	.	.	.	0.1331	0.00076	0.2533:0.2479:0.2524:0.2464	.	3614	E7ESK3	.	I	3742	ENSP00000417498:V3742I;ENSP00000420243:V3742I	.	V	-	1	0	MUC4	196992006	0.000000	0.05858	0.023000	0.16930	0.045000	0.14185	-2.139000	0.01302	-0.948000	0.03668	0.064000	0.15345	GTC	.	.	none		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PNPLA1	285848	hgsc.bcm.edu	37	6	36269946	36269946	+	Missense_Mutation	SNP	A	A	G	rs145856102	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36269946A>G	ENST00000394571.2	+	6	1084	c.1084A>G	c.(1084-1086)Act>Gct	p.T362A	PNPLA1_ENST00000312917.5_Missense_Mutation_p.T276A|PNPLA1_ENST00000388715.3_Missense_Mutation_p.T267A	NM_001145717.1	NP_001139189.2	Q8N8W4	PLPL1_HUMAN	patatin-like phospholipase domain containing 1	362	Pro-rich.				lipid catabolic process (GO:0016042)	cytoplasm (GO:0005737)	hydrolase activity (GO:0016787)			breast(1)|kidney(1)|large_intestine(4)|lung(9)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)	22						GGCCTCTTCAACTCCACTTTC	0.562											OREG0017382	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.T362A		Atlas-SNP	.											.	PNPLA1	92	.	0			c.A1084G						PASS	.	A	ALA/THR,ALA/THR,ALA/THR	18,4388	25.3+/-52.1	0,18,2185	130.0	125.0	127.0		826,1084,799	0.2	0.0	6	dbSNP_134	127	0,8600		0,0,4300	yes	missense,missense,missense	PNPLA1	NM_001145716.1,NM_001145717.1,NM_173676.2	58,58,58	0,18,6485	GG,GA,AA		0.0,0.4085,0.1384	benign,benign,benign	276/447,362/533,267/438	36269946	18,12988	2203	4300	6503	SO:0001583	missense	285848	exon6			TCTTCAACTCCAC		CCDS34438.1, CCDS47416.1, CCDS54997.1	6p21.31	2009-01-12			ENSG00000180316	ENSG00000180316		"""Patatin-like phospholipase domain containing"""	21246	protein-coding gene	gene with protein product		612121				16799181, 19029121	Standard	NM_001145717		Approved	FLJ38755, dJ50J22.1	uc010jwf.2	Q8N8W4	OTTHUMG00000014590	ENST00000394571.2:c.1084A>G	6.37:g.36269946A>G	ENSP00000378072:p.Thr362Ala	132.0	0.0	0	861	133.0	63.0	0.473684	NM_001145717	A3RMU3|J3JS20|Q2A6N1|Q3SY95|Q3SY96|Q5R3L2	Missense_Mutation	SNP	ENST00000394571.2	37	CCDS54997.1	.	.	.	.	.	.	.	.	.	.	A	0.635	-0.815820	0.02776	0.004085	0.0	ENSG00000180316	ENST00000388715;ENST00000312917;ENST00000457797;ENST00000394571	T;T;T;T	0.27256	1.91;1.91;1.68;1.68	5.4	0.208	0.15221	.	2.180320	0.02285	N	0.069728	T	0.03136	0.0092	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.25641	-1.0126	10	0.18710	T	0.47	0.729	2.0907	0.03656	0.1506:0.4124:0.2712:0.1658	.	362;276	Q8N8W4;Q8N8W4-3	PLPL1_HUMAN;.	A	267;276;363;362	ENSP00000373367:T267A;ENSP00000321116:T276A;ENSP00000391868:T363A;ENSP00000378072:T362A	ENSP00000321116:T276A	T	+	1	0	PNPLA1	36377924	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.120000	0.15647	0.002000	0.14630	-1.513000	0.00942	ACT	A|0.998;G|0.002	0.002	strong		0.562	PNPLA1-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_173676	
BRAF	673	hgsc.bcm.edu	37	7	140481425	140481425	+	Silent	SNP	T	T	C	rs56216404	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140481425T>C	ENST00000288602.6	-	11	1443	c.1383A>G	c.(1381-1383)caA>caG	p.Q461Q		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	461	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	ATCCAATTCTTTGTCCCACTG	0.393		61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome				T|||	27	0.00539137	0.0204	0.0	5008	,	,		15131	0.0		0.0	False		,,,				2504	0.0				p.Q461Q	Colon(40;35 892 2973 5743 27438)	Atlas-SNP	.		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	.	BRAF	36346	.	0			c.A1383G						PASS	.	T		41,4365	43.1+/-76.7	0,41,2162	170.0	145.0	154.0		1383	-3.9	1.0	7	dbSNP_129	154	0,8596		0,0,4298	no	coding-synonymous	BRAF	NM_004333.4		0,41,6460	CC,CT,TT		0.0,0.9305,0.3153		461/767	140481425	41,12961	2203	4298	6501	SO:0001819	synonymous_variant	673	exon11	Familial Cancer Database	CFC, CFCS	AATTCTTTGTCCC	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1383A>G	7.37:g.140481425T>C		103.0	0.0	0		112.0	59.0	0.526786	NM_004333	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Silent	SNP	ENST00000288602.6	37	CCDS5863.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	T	9.986	1.229394	0.22542	0.009305	0.0	ENSG00000157764	ENST00000496384	.	.	.	5.62	-3.94	0.04130	.	.	.	.	.	T	0.26593	0.0650	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40887	-0.9539	4	.	.	.	.	7.9193	0.29837	0.1332:0.5351:0.0:0.3317	rs56216404;rs61730028	.	.	.	R	69	.	.	K	-	2	0	BRAF	140127894	0.871000	0.30034	0.970000	0.41538	0.993000	0.82548	-0.010000	0.12743	-0.751000	0.04734	-0.481000	0.04817	AAA	T|0.995;C|0.005	0.005	strong		0.393	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333	
NPL	80896	hgsc.bcm.edu	37	1	182787797	182787797	+	Silent	SNP	G	G	A	rs58343016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:182787797G>A	ENST00000367553.1	+	8	623	c.579G>A	c.(577-579)caG>caA	p.Q193Q	NPL_ENST00000367554.3_Silent_p.Q174Q|NPL_ENST00000367555.1_Silent_p.Q193Q|NPL_ENST00000258317.2_Silent_p.Q193Q|NPL_ENST00000367552.2_Silent_p.Q193Q|NPL_ENST00000463899.1_3'UTR	NM_001200056.1|NM_030769.2	NP_001186985.1|NP_110396.1	Q9BXD5	NPL_HUMAN	N-acetylneuraminate pyruvate lyase (dihydrodipicolinate synthase)	193					carbohydrate metabolic process (GO:0005975)|N-acetylneuraminate catabolic process (GO:0019262)	cytoplasm (GO:0005737)	N-acetylneuraminate lyase activity (GO:0008747)			breast(1)|central_nervous_system(1)|large_intestine(5)|liver(1)|lung(4)|ovary(1)|skin(1)|stomach(1)	15						GCCAGCAACAGTTTGCTTTCC	0.458													G|||	83	0.0165735	0.0605	0.0043	5008	,	,		20020	0.0		0.0	False		,,,				2504	0.0				p.Q193Q		Atlas-SNP	.											.	NPL	55	.	0			c.G579A						PASS	.	G	,,,,	222,4184	133.7+/-170.0	5,212,1986	73.0	73.0	73.0		522,579,579,579,579	-0.5	1.0	1	dbSNP_129	73	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NPL	NM_001200050.1,NM_001200051.1,NM_001200052.1,NM_001200056.1,NM_030769.2	,,,,	5,212,6286	AA,AG,GG		0.0,5.0386,1.7069	,,,,	174/302,193/241,193/231,193/285,193/321	182787797	222,12784	2203	4300	6503	SO:0001819	synonymous_variant	80896	exon9			GCAACAGTTTGCT	AF338436	CCDS1350.1, CCDS55666.1, CCDS55667.1, CCDS72990.1	1q25	2010-11-25	2003-09-16	2003-09-17	ENSG00000135838	ENSG00000135838	4.1.3.3		16781	protein-coding gene	gene with protein product	"""dihydrodipicolinate synthetase homolog 1 (E. coli)"""	611412	"""chromosome 1 open reading frame 13"""	C1orf13		11318611	Standard	NM_001200056		Approved	NPL1, DHDPS1	uc009wyb.3	Q9BXD5	OTTHUMG00000035321	ENST00000367553.1:c.579G>A	1.37:g.182787797G>A		59.0	0.0	0		60.0	30.0	0.5	NM_001200052	B2R839|Q4G0Q8|Q4G0Z2|Q64L88|Q6PEL0	Silent	SNP	ENST00000367553.1	37	CCDS1350.1																																																																																			G|0.983;A|0.017	0.017	strong		0.458	NPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085463.1	NM_030769	
DGUOK	1716	hgsc.bcm.edu	37	2	74174013	74174013	+	Silent	SNP	G	G	A	rs1804599	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74174013G>A	ENST00000264093.4	+	3	508	c.423G>A	c.(421-423)gaG>gaA	p.E141E	DGUOK_ENST00000462685.1_3'UTR|DGUOK_ENST00000348222.1_Silent_p.E141E|DGUOK_ENST00000356837.6_Silent_p.E119E|DGUOK-AS1_ENST00000453103.1_RNA	NM_080916.2	NP_550438.1	Q16854	DGUOK_HUMAN	deoxyguanosine kinase	141					deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|dGTP metabolic process (GO:0046070)|guanosine metabolic process (GO:0008617)|negative regulation of neuron projection development (GO:0010977)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide biosynthetic process (GO:0009165)|protein phosphorylation (GO:0006468)|purine deoxyribonucleoside metabolic process (GO:0046122)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|deoxyguanosine kinase activity (GO:0004138)|nucleoside kinase activity (GO:0019206)			endometrium(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	8					Nelarabine(DB01280)	AGATCTTTGAGAGGTCTGTGT	0.507													G|||	89	0.0177716	0.0613	0.0115	5008	,	,		17020	0.0		0.0	False		,,,				2504	0.0				p.E141E		Atlas-SNP	.											.	DGUOK	16	.	0			c.G423A						PASS	.	G	,	197,4209	124.1+/-161.4	6,185,2012	49.0	43.0	45.0		423,423	4.8	1.0	2	dbSNP_89	45	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	DGUOK	NM_080916.1,NM_080918.1	,	6,187,6310	AA,AG,GG		0.0233,4.4712,1.5301	,	141/278,141/190	74174013	199,12807	2203	4300	6503	SO:0001819	synonymous_variant	1716	exon3			CTTTGAGAGGTCT	U41668	CCDS1931.1, CCDS1932.1	2p13	2008-02-05			ENSG00000114956	ENSG00000114956	2.7.1.113		2858	protein-coding gene	gene with protein product		601465					Standard	NM_080916		Approved	dGK	uc002sjx.3	Q16854	OTTHUMG00000129819	ENST00000264093.4:c.423G>A	2.37:g.74174013G>A		64.0	0.0	0		70.0	38.0	0.542857	NM_080918	P78532|Q16759|Q4ZG09|Q7L1W9|Q96BC1	Silent	SNP	ENST00000264093.4	37	CCDS1931.1																																																																																			G|0.986;A|0.014	0.014	strong		0.507	DGUOK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252050.1		
PRMT9	90826	hgsc.bcm.edu	37	4	148594177	148594177	+	Missense_Mutation	SNP	C	C	T	rs73853975	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:148594177C>T	ENST00000322396.6	-	4	918	c.676G>A	c.(676-678)Gaa>Aaa	p.E226K	PRMT10_ENST00000541232.1_Missense_Mutation_p.E113K	NM_138364.2	NP_612373.2	Q6P2P2	ANM9_HUMAN		226	SAM-dependent MTase PRMT-type 1. {ECO:0000255|PROSITE-ProRule:PRU01015}.					cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28						ATCCCTGCTTCCATCTTGTTT	0.388													C|||	229	0.0457268	0.1702	0.0058	5008	,	,		14532	0.0		0.0	False		,,,				2504	0.0				p.E226K		Atlas-SNP	.											.	PRMT10	68	.	0			c.G676A						PASS	.	C	LYS/GLU	610,3796	267.1+/-267.6	41,528,1634	160.0	150.0	154.0		676	4.6	1.0	4	dbSNP_130	154	3,8597	3.0+/-9.4	0,3,4297	yes	missense	PRMT10	NM_138364.2	56	41,531,5931	TT,TC,CC		0.0349,13.8448,4.7132	benign	226/846	148594177	613,12393	2203	4300	6503	SO:0001583	missense	90826	exon4			CTGCTTCCATCTT																												ENST00000322396.6:c.676G>A	4.37:g.148594177C>T	ENSP00000314396:p.Glu226Lys	114.0	0.0	0		151.0	77.0	0.509934	NM_138364	A8KA39|B3KU92|Q6ZR58|Q8N383|Q9BT55|Q9NT98	Missense_Mutation	SNP	ENST00000322396.6	37	CCDS3771.1	106	0.048534798534798536	105	0.21341463414634146	1	0.0027624309392265192	0	0.0	0	0.0	C	18.24	3.579466	0.65878	0.138448	3.49E-4	ENSG00000164169	ENST00000322396;ENST00000541232	T;T	0.23348	1.91;1.91	5.44	4.58	0.56647	.	0.210963	0.49305	D	0.000159	T	0.00012	0.0000	L	0.38733	1.17	0.24656	P	0.99349699	B	0.24675	0.109	B	0.30943	0.122	T	0.21211	-1.0252	9	0.41790	T	0.15	-7.5111	10.3867	0.44145	0.0:0.791:0.1363:0.0727	.	226	Q6P2P2	ANM10_HUMAN	K	226;113	ENSP00000314396:E226K;ENSP00000439508:E113K	ENSP00000314396:E226K	E	-	1	0	PRMT10	148813627	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	3.053000	0.49901	1.242000	0.43836	0.655000	0.94253	GAA	C|0.946;T|0.054	0.054	strong		0.388	PRMT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364650.1		
AGAP7P	653268	hgsc.bcm.edu	37	10	51465429	51465429	+	Missense_Mutation	SNP	C	C	T	rs183573385	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:51465429C>T	ENST00000374095.5	-	7	1152	c.1027G>A	c.(1027-1029)Gac>Aac	p.D343N		NM_001077685.1	NP_001071153.1	Q5VUJ5	AGAP7_HUMAN		343	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)	11						GTGTCCATGTCCTTGGATAGG	0.562													-|||	17	0.00339457	0.0	0.0043	5008	,	,		17858	0.0		0.0139	False		,,,				2504	0.0				p.D343N		Atlas-SNP	.											.	AGAP7	33	.	0			c.G1027A						PASS	.	C	ASN/ASP	8,4396		0,8,2194	116.0	137.0	130.0		1027		0.0	10		130	44,8556		0,44,4256	no	missense	AGAP7	NM_001077685.1	23	0,52,6450	TT,TC,CC		0.5116,0.1817,0.3999	benign	343/664	51465429	52,12952	2202	4300	6502	SO:0001583	missense	653268	exon7			CCATGTCCTTGGA																												ENST00000374095.5:c.1027G>A	10.37:g.51465429C>T	ENSP00000363208:p.Asp343Asn	591.0	0.0	0		650.0	348.0	0.535385	NM_001077685	A6NGH4	Missense_Mutation	SNP	ENST00000374095.5	37	CCDS41524.1	12	0.005494505494505495	0	0.0	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	.	4.603	0.112029	0.08831	0.001817	0.005116	ENSG00000204169	ENST00000374095	T	0.56103	0.48	.	.	.	Pleckstrin homology domain (3);	0.720818	0.12823	N	0.436252	T	0.35393	0.0930	M	0.74647	2.275	0.25300	N	0.98928	B	0.06786	0.001	B	0.15052	0.012	T	0.30937	-0.9961	9	0.27082	T	0.32	.	4.5676	0.12195	0.0:0.6819:0.0:0.3181	.	343	Q5VUJ5	AGAP7_HUMAN	N	343	ENSP00000363208:D343N	ENSP00000363208:D343N	D	-	1	0	AGAP7	51135435	0.999000	0.42202	0.016000	0.15963	0.016000	0.09150	2.917000	0.48821	-1.351000	0.02197	-1.360000	0.01215	GAC	C|0.996;T|0.004	0.004	strong		0.562	AGAP7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048033.1		
CARD14	79092	hgsc.bcm.edu	37	17	78177668	78177668	+	Missense_Mutation	SNP	G	G	A	rs34822755	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78177668G>A	ENST00000573882.1	+	18	2803	c.2267G>A	c.(2266-2268)tGc>tAc	p.C756Y	RP11-334C17.5_ENST00000576824.1_RNA|CARD14_ENST00000392434.2_3'UTR|RP11-334C17.5_ENST00000573935.1_RNA|RP11-334C17.5_ENST00000572730.1_RNA|RP11-334C17.5_ENST00000573346.1_RNA|RP11-334C17.5_ENST00000570309.1_RNA|CARD14_ENST00000344227.2_Missense_Mutation_p.C756Y			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	756					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)			NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(5)|prostate(1)|skin(1)	23	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.017)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			ACTCAGCAGTGCACCGTGACC	0.672													G|||	38	0.00758786	0.0272	0.0029	5008	,	,		16016	0.0		0.0	False		,,,				2504	0.0				p.C756Y		Atlas-SNP	.											.	CARD14	98	.	0			c.G2267A						PASS	.	G	TYR/CYS	127,4273		2,123,2075	27.0	24.0	25.0		2267	3.1	0.2	17	dbSNP_126	25	4,8592		0,4,4294	yes	missense	CARD14	NM_024110.3	194	2,127,6369	AA,AG,GG		0.0465,2.8864,1.008	benign	756/1005	78177668	131,12865	2200	4298	6498	SO:0001583	missense	79092	exon16			AGCAGTGCACCGT	AF322642	CCDS11768.1, CCDS58605.1	17q25.3	2014-09-04			ENSG00000141527	ENSG00000141527			16446	protein-coding gene	gene with protein product		607211	"""psoriasis susceptibility 2"""	PSORS2		11278692, 11356195, 22521418	Standard	NM_052819		Approved	CARMA2, BIMP2	uc031res.1	Q9BXL6	OTTHUMG00000177549	ENST00000573882.1:c.2267G>A	17.37:g.78177668G>A	ENSP00000458715:p.Cys756Tyr	287.0	0.0	0		283.0	139.0	0.491166	NM_024110	B8QQJ3|Q9BVB5	Missense_Mutation	SNP	ENST00000573882.1	37	CCDS11768.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	G	7.289	0.610773	0.14066	0.028864	4.65E-4	ENSG00000141527	ENST00000344227	T	0.05258	3.47	4.12	3.12	0.35913	.	0.712962	0.13426	N	0.388808	T	0.01320	0.0043	N	0.14661	0.345	0.33297	D	0.5643	B	0.15141	0.012	B	0.18871	0.023	T	0.17837	-1.0356	10	0.59425	D	0.04	-4.1501	6.7425	0.23443	0.1003:0.1828:0.7169:0.0	rs34822755	756	Q9BXL6	CAR14_HUMAN	Y	756	ENSP00000344549:C756Y	ENSP00000344549:C756Y	C	+	2	0	CARD14	75792263	0.870000	0.30015	0.159000	0.22649	0.311000	0.27955	1.320000	0.33666	0.706000	0.31912	0.485000	0.47835	TGC	G|0.991;A|0.009	0.009	strong		0.672	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1		
USP24	23358	hgsc.bcm.edu	37	1	55545240	55545240	+	Missense_Mutation	SNP	T	T	C	rs116203669	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55545240T>C	ENST00000294383.6	-	60	7170	c.7171A>G	c.(7171-7173)Atg>Gtg	p.M2391V	USP24_ENST00000407756.1_Missense_Mutation_p.M2231V	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	2391					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						CCTTCAGACATGAACAACAAG	0.433													T|||	23	0.00459265	0.0174	0.0	5008	,	,		20623	0.0		0.0	False		,,,				2504	0.0				p.M2391V		Atlas-SNP	.											.	USP24	323	.	0			c.A7171G						PASS	.	T	VAL/MET	33,3727		0,33,1847	159.0	154.0	156.0		7171	-2.0	1.0	1	dbSNP_132	156	0,8242		0,0,4121	yes	missense	USP24	NM_015306.2	21	0,33,5968	CC,CT,TT		0.0,0.8777,0.275	benign	2391/2621	55545240	33,11969	1880	4121	6001	SO:0001583	missense	23358	exon60			CAGACATGAACAA	AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"""Ubiquitin-specific peptidases"""	12623	protein-coding gene	gene with protein product		610569	"""ubiquitin specific protease 24"""			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.7171A>G	1.37:g.55545240T>C	ENSP00000294383:p.Met2391Val	81.0	0.0	0		89.0	41.0	0.460674	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Missense_Mutation	SNP	ENST00000294383.6	37	CCDS44154.2	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	T	0.334	-0.954398	0.02285	0.008777	0.0	ENSG00000162402	ENST00000294383;ENST00000407756	T;T	0.01887	4.58;4.58	4.8	-1.97	0.07503	.	0.295167	0.28544	N	0.014980	T	0.00468	0.0015	N	0.02539	-0.55	0.20764	N	0.999858	B	0.02656	0.0	B	0.01281	0.0	T	0.46707	-0.9172	10	0.28530	T	0.3	.	5.8291	0.18570	0.3638:0.0:0.4105:0.2258	.	2231	B7WPF4	.	V	2391;2231	ENSP00000294383:M2391V;ENSP00000385700:M2231V	ENSP00000294383:M2391V	M	-	1	0	USP24	55317828	0.985000	0.35326	0.995000	0.50966	0.984000	0.73092	0.139000	0.16036	-0.284000	0.09102	-0.691000	0.03719	ATG	T|0.996;C|0.004	0.004	strong		0.433	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2		
GEMIN4	50628	hgsc.bcm.edu	37	17	650371	650371	+	Silent	SNP	C	C	T	rs61735317	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:650371C>T	ENST00000319004.5	-	2	1030	c.912G>A	c.(910-912)tcG>tcA	p.S304S	GEMIN4_ENST00000437269.1_3'UTR|GEMIN4_ENST00000576778.1_Silent_p.S293S	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	304					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		GTTTGGCCAGCGAGGTCAGGC	0.627													C|||	116	0.0231629	0.0832	0.0058	5008	,	,		20285	0.0		0.002	False		,,,				2504	0.0				p.S304S		Atlas-SNP	.											.	GEMIN4	116	.	0			c.G912A						PASS	.	C		280,3980		7,266,1857	116.0	127.0	124.0		912	-11.3	0.1	17	dbSNP_129	124	4,8464		0,4,4230	no	coding-synonymous	GEMIN4	NM_015721.2		7,270,6087	TT,TC,CC		0.0472,6.5728,2.2313		304/1059	650371	284,12444	2130	4234	6364	SO:0001819	synonymous_variant	50628	exon2			GGCCAGCGAGGTC	AF177341	CCDS45559.1	17p13.3	2008-07-18				ENSG00000179409			15717	protein-coding gene	gene with protein product	"""HCC-associated protein 1"", ""component of gems 4"""	606969				10725331	Standard	NM_015721		Approved	HHRF-1, DKFZP434B131, p97, DKFZP434D174, HC56, HCAP1	uc002frs.1	P57678		ENST00000319004.5:c.912G>A	17.37:g.650371C>T		100.0	0.0	0		118.0	66.0	0.559322	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Silent	SNP	ENST00000319004.5	37	CCDS45559.1																																																																																			C|0.978;T|0.022	0.022	strong		0.627	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721	
C1orf61	10485	hgsc.bcm.edu	37	1	156377720	156377720	+	Silent	SNP	G	G	A	rs141938076	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156377720G>A	ENST00000368243.1	-	5	335	c.219C>T	c.(217-219)tcC>tcT	p.S73S	C1orf61_ENST00000488498.2_5'UTR	NM_006365.1	NP_006356.1	Q13536	CROC4_HUMAN	chromosome 1 open reading frame 61	73						nucleus (GO:0005634)				large_intestine(2)|lung(2)|skin(1)	5	Hepatocellular(266;0.158)					TACACCTGGTGGAGATTCCAC	0.582													G|||	12	0.00239617	0.0083	0.0014	5008	,	,		19992	0.0		0.0	False		,,,				2504	0.0				p.S73S		Atlas-SNP	.											.	C1orf61	15	.	0			c.C219T						PASS	.	G		24,4382		0,24,2179	114.0	86.0	96.0		219	-0.4	0.0	1	dbSNP_134	96	0,8594		0,0,4297	no	coding-synonymous	C1orf61	NM_006365.1		0,24,6476	AA,AG,GG		0.0,0.5447,0.1846		73/157	156377720	24,12976	2203	4297	6500	SO:0001819	synonymous_variant	10485	exon5			CCTGGTGGAGATT		CCDS1142.1	1q22	2014-03-17			ENSG00000125462	ENSG00000125462			30780	protein-coding gene	gene with protein product	"""contingent replication of cDNA-4"", ""transcriptional activator of the c fos promoter"""					10995546, 23012322	Standard	XM_005244832		Approved	CROC4	uc001fou.1	Q13536	OTTHUMG00000031022	ENST00000368243.1:c.219C>T	1.37:g.156377720G>A		106.0	0.0	0		124.0	53.0	0.427419	NM_006365	B1ALL5|B1ALL8	Silent	SNP	ENST00000368243.1	37	CCDS1142.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	3.575	-0.086754	0.07097	0.005447	0.0	ENSG00000125462	ENST00000368242	.	.	.	3.36	-0.454	0.12197	.	.	.	.	.	T	0.12305	0.0299	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.32719	-0.9896	4	.	.	.	.	5.8054	0.18438	0.5029:0.0:0.4971:0.0	.	.	.	.	L	105	.	.	P	-	2	0	C1orf61	154644344	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.003000	0.13083	-0.069000	0.12931	0.542000	0.68232	CCA	G|0.998;A|0.002	0.002	strong		0.582	C1orf61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075988.1	NM_006365	
LSM4	25804	hgsc.bcm.edu	37	19	18420501	18420501	+	Silent	SNP	G	G	A	rs148380214	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18420501G>A	ENST00000593829.1	-	4	568	c.315C>T	c.(313-315)ggC>ggT	p.G105G	LSM4_ENST00000252816.6_Silent_p.G91G	NM_001252129.1|NM_012321.4	NP_001239058.1|NP_036453.1	Q9Y4Z0	LSM4_HUMAN	LSM4 homolog, U6 small nuclear RNA associated (S. cerevisiae)	105					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)	cytosol (GO:0005829)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)|U6 snRNP (GO:0005688)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(2)|lung(3)	6						GGCCAGCGCCGCCCATGCCGC	0.682													g|||	9	0.00179712	0.0068	0.0	5008	,	,		16325	0.0		0.0	False		,,,				2504	0.0				p.G105G		Atlas-SNP	.											.	LSM4	15	.	0			c.C315T						PASS	.			37,4365		0,37,2164	29.0	28.0	28.0		315	-3.1	1.0	19	dbSNP_134	28	0,8596		0,0,4298	no	coding-synonymous	LSM4	NM_012321.3		0,37,6462	AA,AG,GG		0.0,0.8405,0.2847		105/140	18420501	37,12961	2201	4298	6499	SO:0001819	synonymous_variant	25804	exon4			AGCGCCGCCCATG	AF117235	CCDS12374.1, CCDS62601.1	19p13.1	2008-02-05				ENSG00000130520			17259	protein-coding gene	gene with protein product		607284				10369684, 10523320	Standard	NM_012321		Approved	YER112W	uc002niq.3	Q9Y4Z0		ENST00000593829.1:c.315C>T	19.37:g.18420501G>A		17.0	0.0	0		35.0	26.0	0.742857	NM_012321		Silent	SNP	ENST00000593829.1	37	CCDS12374.1																																																																																			G|0.997;A|0.003	0.003	strong		0.682	LSM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466321.1		
RFWD3	55159	hgsc.bcm.edu	37	16	74664698	74664698	+	Silent	SNP	A	A	G	rs78796563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:74664698A>G	ENST00000361070.4	-	10	1832	c.1735T>C	c.(1735-1737)Tta>Cta	p.L579L	RFWD3_ENST00000571750.1_Silent_p.L579L	NM_018124.3	NP_060594.3	Q6PCD5	RFWD3_HUMAN	ring finger and WD repeat domain 3	579					DNA repair (GO:0006281)|mitotic G1 DNA damage checkpoint (GO:0031571)|protein ubiquitination (GO:0016567)|regulation of DNA damage checkpoint (GO:2000001)|response to ionizing radiation (GO:0010212)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|MDM2/MDM4 family protein binding (GO:0097371)|p53 binding (GO:0002039)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.L579L(1)		NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	26						TGAGCTACTAACTCCTGCACA	0.473													A|||	67	0.0133786	0.0023	0.0259	5008	,	,		18719	0.0		0.0288	False		,,,				2504	0.0174				p.L579L		Atlas-SNP	.											RFWD3,NS,carcinoma,0,1	RFWD3	49	1	1	Substitution - coding silent(1)	lung(1)	c.T1735C						scavenged	.	A		28,4368	32.6+/-62.9	1,26,2171	94.0	70.0	78.0		1735	3.5	0.3	16	dbSNP_132	78	267,8333	102.3+/-163.5	4,259,4037	no	coding-synonymous	RFWD3	NM_018124.3		5,285,6208	GG,GA,AA		3.1047,0.6369,2.2699		579/775	74664698	295,12701	2198	4300	6498	SO:0001819	synonymous_variant	55159	exon10			CTACTAACTCCTG	AK001382	CCDS32486.1	16q22.3	2013-01-09						"""WD repeat domain containing"", ""RING-type (C3HC4) zinc fingers"""	25539	protein-coding gene	gene with protein product		614151				21504906	Standard	XM_005256021		Approved	FLJ10520, RNF201	uc002fda.3	Q6PCD5		ENST00000361070.4:c.1735T>C	16.37:g.74664698A>G		86.0	1.0	0.0116279		75.0	44.0	0.586667	NM_018124	A8K585|B2RE35|D3DUJ8|Q5XKR3|Q9H9Q3|Q9NVT4	Silent	SNP	ENST00000361070.4	37	CCDS32486.1																																																																																			A|0.981;G|0.019	0.019	strong		0.473	RFWD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436506.2	NM_018124	
SENP7	57337	hgsc.bcm.edu	37	3	101090924	101090924	+	Missense_Mutation	SNP	T	T	A	rs116197973	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:101090924T>A	ENST00000394095.2	-	7	777	c.724A>T	c.(724-726)Act>Tct	p.T242S	SENP7_ENST00000394091.1_Missense_Mutation_p.T78S|SENP7_ENST00000314261.7_Missense_Mutation_p.T176S|SENP7_ENST00000348610.3_Missense_Mutation_p.T209S|SENP7_ENST00000394094.2_Missense_Mutation_p.T177S|SENP7_ENST00000358203.3_Missense_Mutation_p.T78S	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	242						intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			breast(2)|endometrium(1)|kidney(1)|large_intestine(16)|lung(15)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						TTGTGCGCAGTCTGCTTTGCA	0.368													C|||	50	0.00998403	0.0371	0.0014	5008	,	,		13274	0.0		0.0	False		,,,				2504	0.0				p.T242S		Atlas-SNP	.											.	SENP7	170	.	0			c.A724T						PASS	.	C	SER/THR,SER/THR	156,4250		4,148,2051	135.0	126.0	129.0		529,724	1.3	0.0	3	dbSNP_132	129	0,8600		0,0,4300	yes	missense,missense	SENP7	NM_001077203.1,NM_020654.3	58,58	4,148,6351	AA,AT,TT		0.0,3.5406,1.1994	benign,benign	177/986,242/1051	101090924	156,12850	2203	4300	6503	SO:0001583	missense	57337	exon7			GCGCAGTCTGCTT		CCDS2941.2, CCDS43121.1, CCDS63704.1, CCDS63705.1, CCDS63706.1	3q12	2008-02-05	2005-08-17		ENSG00000138468	ENSG00000138468			30402	protein-coding gene	gene with protein product		612846	"""SUMO1/sentrin specific protease 7"""			11214970, 11230166	Standard	NM_001282802		Approved		uc003dut.3	Q9BQF6	OTTHUMG00000149927	ENST00000394095.2:c.724A>T	3.37:g.101090924T>A	ENSP00000377655:p.Thr242Ser	145.0	0.0	0		158.0	73.0	0.462025	NM_020654	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Missense_Mutation	SNP	ENST00000394095.2	37	CCDS2941.2	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	3.708	-0.060054	0.07317	0.035406	0.0	ENSG00000138468	ENST00000394095;ENST00000394094;ENST00000314261;ENST00000394091;ENST00000358203;ENST00000348610	T;T;T;T;T;T	0.16743	2.32;2.33;2.32;2.32;2.32;2.32	5.1	1.33	0.21861	.	1.879190	0.02560	N	0.096662	T	0.01940	0.0061	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	0.04013	0.0;0.0;0.001;0.0	T	0.29792	-1.0000	10	0.32370	T	0.25	-0.178	7.9128	0.29800	0.0:0.565:0.0:0.435	.	78;176;209;242	Q9BQF6-4;Q9BQF6-5;Q9BQF6-2;Q9BQF6	.;.;.;SENP7_HUMAN	S	242;177;176;78;78;209	ENSP00000377655:T242S;ENSP00000377654:T177S;ENSP00000313624:T176S;ENSP00000377651:T78S;ENSP00000350936:T78S;ENSP00000342159:T209S	ENSP00000313624:T176S	T	-	1	0	SENP7	102573614	0.029000	0.19370	0.027000	0.17364	0.001000	0.01503	-0.162000	0.10012	-0.170000	0.10816	-0.927000	0.02713	ACT	T|0.988;A|0.012	0.012	strong		0.368	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654	
PRSS38	339501	hgsc.bcm.edu	37	1	228003879	228003879	+	Silent	SNP	C	C	T	rs112241411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228003879C>T	ENST00000366757.3	+	2	261	c.237C>T	c.(235-237)taC>taT	p.Y79Y		NM_183062.2	NP_898885.1	A1L453	PRS38_HUMAN	protease, serine, 38	79	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						GCGTGCACTACGCAGGCCTCC	0.662													C|||	73	0.0145767	0.0537	0.0029	5008	,	,		13078	0.0		0.0	False		,,,				2504	0.0				p.Y79Y		Atlas-SNP	.											PRSS38,colon,carcinoma,0,1	PRSS38	55	1	0			c.C237T						PASS	.	C		279,4127	150.3+/-184.3	4,271,1928	60.0	68.0	65.0		237	-0.7	0.0	1	dbSNP_132	65	1,8597		0,1,4298	no	coding-synonymous	PRSS38	NM_183062.2		4,272,6226	TT,TC,CC		0.0116,6.3323,2.1532		79/327	228003879	280,12724	2203	4299	6502	SO:0001819	synonymous_variant	339501	exon2			GCACTACGCAGGC		CCDS1563.1	1q42.13	2010-05-07			ENSG00000185888	ENSG00000185888		"""Serine peptidases / Serine peptidases"""	29625	protein-coding gene	gene with protein product	"""marapsin 2"""					12838346	Standard	NM_183062		Approved	MPN2	uc001hrh.3	A1L453	OTTHUMG00000037701	ENST00000366757.3:c.237C>T	1.37:g.228003879C>T		190.0	0.0	0		254.0	131.0	0.515748	NM_183062	Q7RTY6	Silent	SNP	ENST00000366757.3	37	CCDS1563.1																																																																																			C|0.982;T|0.018	0.018	strong		0.662	PRSS38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091981.1	NM_183062	
DSG1	1828	hgsc.bcm.edu	37	18	28908178	28908178	+	Missense_Mutation	SNP	G	G	C	rs74368609	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:28908178G>C	ENST00000257192.4	+	4	455	c.243G>C	c.(241-243)caG>caC	p.Q81H		NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	81	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell-cell junction assembly (GO:0007043)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|protein stabilization (GO:0050821)|response to progesterone (GO:0032570)|single organismal cell-cell adhesion (GO:0016337)	apical plasma membrane (GO:0016324)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)|toxic substance binding (GO:0015643)			NS(2)|central_nervous_system(2)|endometrium(5)|kidney(7)|large_intestine(11)|lung(36)|ovary(3)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	76			OV - Ovarian serous cystadenocarcinoma(10;0.00559)			CTGCAAACCAGCAAGTTACAT	0.368													G|||	26	0.00519169	0.0189	0.0014	5008	,	,		19822	0.0		0.0	False		,,,				2504	0.0				p.Q81H		Atlas-SNP	.											.	DSG1	176	.	0			c.G243C						PASS	.	G	HIS/GLN	97,4309	78.8+/-117.2	0,97,2106	92.0	89.0	90.0		243	2.8	1.0	18	dbSNP_131	90	0,8598		0,0,4299	yes	missense	DSG1	NM_001942.2	24	0,97,6405	CC,CG,GG		0.0,2.2015,0.7459	probably-damaging	81/1050	28908178	97,12907	2203	4299	6502	SO:0001583	missense	1828	exon4			AAACCAGCAAGTT	X56654	CCDS11896.1	18q12.1	2014-05-13			ENSG00000134760	ENSG00000134760		"""Cadherins / Major cadherins"""	3048	protein-coding gene	gene with protein product		125670		DSG		1889810	Standard	NM_001942		Approved	CDHF4	uc002kwp.3	Q02413	OTTHUMG00000131983	ENST00000257192.4:c.243G>C	18.37:g.28908178G>C	ENSP00000257192:p.Gln81His	81.0	0.0	0		104.0	56.0	0.538462	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	G	17.26	3.343886	0.61073	0.022015	0.0	ENSG00000134760	ENST00000257192	T	0.61158	0.13	5.59	2.78	0.32641	Cadherin (4);Cadherin-like (1);	0.315599	0.27526	N	0.018975	T	0.47021	0.1423	L	0.59436	1.845	0.80722	D	1	D	0.60575	0.988	D	0.66196	0.942	T	0.54275	-0.8318	10	0.26408	T	0.33	.	4.6815	0.12738	0.3769:0.0:0.4739:0.1491	.	81	Q02413	DSG1_HUMAN	H	81	ENSP00000257192:Q81H	ENSP00000257192:Q81H	Q	+	3	2	DSG1	27162176	0.896000	0.30565	1.000000	0.80357	0.992000	0.81027	0.009000	0.13219	0.705000	0.31890	0.563000	0.77884	CAG	G|0.992;C|0.008	0.008	strong		0.368	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
KRTAP4-2	85291	hgsc.bcm.edu	37	17	39334314	39334314	+	Missense_Mutation	SNP	A	A	T	rs200720939		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39334314A>T	ENST00000377726.2	-	1	146	c.103T>A	c.(103-105)Tgc>Agc	p.C35S		NM_033062.3	NP_149051	Q9BYR5	KRA42_HUMAN	keratin associated protein 4-2	35	20 X 5 AA repeats OF C-C-[GRQVS]-[SPT]- [VSTQ].					keratin filament (GO:0045095)				kidney(2)|lung(4)|upper_aerodigestive_tract(1)	7		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			GGGCGGCAGCAGGTGGTCCTG	0.657																																					p.C35S		Atlas-SNP	.											KRTAP4-2_ENST00000458321,NS,haematopoietic_neoplasm,0,4	KRTAP4-2	93	4	0			c.T103A						scavenged	.						48.0	52.0	50.0					17																	39334314		2199	4289	6488	SO:0001583	missense	85291	exon1			GGCAGCAGGTGGT	AJ406934	CCDS11384.1	17q21.2	2013-06-25			ENSG00000244537	ENSG00000244537		"""Keratin associated proteins"""	18900	protein-coding gene	gene with protein product						11279113	Standard	NM_033062		Approved	KAP4.2	uc002hwd.3	Q9BYR5	OTTHUMG00000133437	ENST00000377726.2:c.103T>A	17.37:g.39334314A>T	ENSP00000366955:p.Cys35Ser	179.0	0.0	0		246.0	26.0	0.105691	NM_033062	A0JP64	Missense_Mutation	SNP	ENST00000377726.2	37	CCDS11384.1	.	.	.	.	.	.	.	.	.	.	.	9.002	0.980423	0.18812	.	.	ENSG00000244537	ENST00000377726;ENST00000458321	T	0.02085	4.46	4.24	4.24	0.50183	.	0.212644	0.23275	U	0.049980	T	0.10035	0.0246	H	0.95402	3.665	0.32423	N	0.54916	B	0.33883	0.43	B	0.40602	0.334	T	0.00912	-1.1517	10	0.49607	T	0.09	.	11.5905	0.50943	1.0:0.0:0.0:0.0	.	35	Q9BYR5	KRA42_HUMAN	S	35;152	ENSP00000366955:C35S	ENSP00000366955:C35S	C	-	1	0	KRTAP4-2	36587840	0.997000	0.39634	0.987000	0.45799	0.045000	0.14185	4.092000	0.57707	1.667000	0.50832	0.421000	0.28195	TGC	.	.	weak		0.657	KRTAP4-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257305.1		
ARHGAP25	9938	hgsc.bcm.edu	37	2	69049916	69049916	+	Missense_Mutation	SNP	G	G	A	rs61734450	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:69049916G>A	ENST00000295381.3	+	10	2061	c.1642G>A	c.(1642-1644)Gag>Aag	p.E548K	ARHGAP25_ENST00000409030.3_Missense_Mutation_p.E541K|ARHGAP25_ENST00000409220.1_Missense_Mutation_p.E542K|ARHGAP25_ENST00000467265.1_Missense_Mutation_p.E509K|ARHGAP25_ENST00000409202.3_Missense_Mutation_p.E549K|ARHGAP25_ENST00000479844.1_Missense_Mutation_p.E242K	NM_001007231.2	NP_001007232.2	P42331	RHG25_HUMAN	Rho GTPase activating protein 25	548					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(20)|ovary(3)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	52						CTCTGGAGAAGAGGAAATTGA	0.443													G|||	9	0.00179712	0.0068	0.0	5008	,	,		20738	0.0		0.0	False		,,,				2504	0.0				p.E549K		Atlas-SNP	.											ARHGAP25,NS,carcinoma,0,1	ARHGAP25	175	1	0			c.G1645A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	15,4389	21.2+/-45.6	0,15,2187	70.0	79.0	76.0		1645,1624,1525,1621	4.5	1.0	2	dbSNP_129	76	0,8598		0,0,4299	yes	missense,missense,missense,missense	ARHGAP25	NM_001007231.2,NM_001166276.1,NM_001166277.1,NM_014882.2	56,56,56,56	0,15,6486	AA,AG,GG		0.0,0.3406,0.1154	benign,benign,benign,benign	549/647,542/640,509/607,541/639	69049916	15,12987	2202	4299	6501	SO:0001583	missense	9938	exon10			GGAGAAGAGGAAA	D29642	CCDS33214.1, CCDS46312.1, CCDS33214.2, CCDS54363.1, CCDS54364.1	2p13.3	2013-01-10			ENSG00000163219	ENSG00000163219		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	28951	protein-coding gene	gene with protein product		610587				7584044	Standard	NM_001007231		Approved	KIAA0053	uc010fdg.3	P42331	OTTHUMG00000152621	ENST00000295381.3:c.1642G>A	2.37:g.69049916G>A	ENSP00000295381:p.Glu548Lys	69.0	0.0	0		68.0	31.0	0.455882	NM_001007231	A8K2Y1|B7Z498|E9PFQ7|G5E9G2|Q8IXQ2	Missense_Mutation	SNP	ENST00000295381.3	37		2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	11.43	1.637568	0.29157	0.003406	0.0	ENSG00000163219	ENST00000295381;ENST00000409202;ENST00000467265;ENST00000409030;ENST00000409220;ENST00000482106;ENST00000543533;ENST00000479844	T;T;T;T;T;T	0.41400	2.82;2.82;2.56;1.0;1.0;1.0	5.42	4.53	0.55603	.	0.709828	0.14852	N	0.294619	T	0.26412	0.0645	N	0.19112	0.55	0.80722	D	1	B;P;P;B;B	0.39480	0.361;0.675;0.675;0.355;0.015	B;B;B;B;B	0.36666	0.054;0.154;0.23;0.165;0.011	T	0.02728	-1.1118	10	0.08381	T	0.77	.	13.8458	0.63466	0.0:0.153:0.847:0.0	rs61734450	509;549;542;541;548	E9PFQ7;P42331-4;G5E9G2;P42331-3;P42331	.;.;.;.;RHG25_HUMAN	K	548;549;509;541;542;542;533;242	ENSP00000295381:E548K;ENSP00000386911:E549K;ENSP00000420583:E509K;ENSP00000386863:E541K;ENSP00000386241:E542K;ENSP00000417467:E242K	ENSP00000295381:E548K	E	+	1	0	ARHGAP25	68903420	0.641000	0.27251	0.975000	0.42487	0.790000	0.44656	1.904000	0.39868	1.399000	0.46721	0.557000	0.71058	GAG	G|0.998;A|0.002	0.002	strong		0.443	ARHGAP25-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014882	
PLEKHM1	9842	hgsc.bcm.edu	37	17	43552942	43552942	+	Silent	SNP	G	G	A	rs71373588	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:43552942G>A	ENST00000430334.3	-	4	580	c.447C>T	c.(445-447)taC>taT	p.Y149Y	PLEKHM1_ENST00000421073.2_Silent_p.Y60Y	NM_014798.2	NP_055613.1	Q9Y4G2	PKHM1_HUMAN	pleckstrin homology domain containing, family M (with RUN domain) member 1	149	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.				intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(6)|large_intestine(1)|lung(10)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26	Renal(3;0.0405)					CGGTGGGCTGGTAGTACTCAT	0.637													G|||	20	0.00399361	0.0136	0.0029	5008	,	,		18295	0.0		0.0	False		,,,				2504	0.0				p.Y149Y		Atlas-SNP	.											.	PLEKHM1	69	.	0			c.C447T						PASS	.	G		76,4328	63.5+/-100.7	2,72,2128	41.0	39.0	40.0		447	-2.8	1.0	17	dbSNP_130	40	0,8600		0,0,4300	no	coding-synonymous	PLEKHM1	NM_014798.2		2,72,6428	AA,AG,GG		0.0,1.7257,0.5844		149/1057	43552942	76,12928	2202	4300	6502	SO:0001819	synonymous_variant	9842	exon4			GGGCTGGTAGTAC	X85792	CCDS32671.1	17q21.31	2013-01-11				ENSG00000225190		"""Pleckstrin homology (PH) domain containing"""	29017	protein-coding gene	gene with protein product		611466				9205841, 12820725	Standard	NM_014798		Approved	KIAA0356	uc002ija.3	Q9Y4G2		ENST00000430334.3:c.447C>T	17.37:g.43552942G>A		247.0	1.0	0.00404858		281.0	131.0	0.466192	NM_014798	Q6P2R5|Q8TEL9|Q9NPP5|Q9NYA0	Silent	SNP	ENST00000430334.3	37	CCDS32671.1																																																																																			G|0.993;A|0.007	0.007	strong		0.637	PLEKHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444659.1	NM_014798	
C20orf27	54976	hgsc.bcm.edu	37	20	3736160	3736160	+	Missense_Mutation	SNP	G	G	A	rs140915844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:3736160G>A	ENST00000379772.3	-	4	1067	c.257C>T	c.(256-258)cCc>cTc	p.P86L	C20orf27_ENST00000217195.8_Missense_Mutation_p.P111L	NM_001258429.1	NP_001245358.1	Q9GZN8	CT027_HUMAN	chromosome 20 open reading frame 27	86										central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)|urinary_tract(1)	7						GTGCAGGCTGGGGACAGGTGC	0.617													G|||	7	0.00139776	0.0053	0.0	5008	,	,		20807	0.0		0.0	False		,,,				2504	0.0				p.P111L		Atlas-SNP	.											.	C20orf27	17	.	0			c.C332T						PASS	.	G	LEU/PRO	20,4386	27.2+/-55.0	0,20,2183	80.0	64.0	69.0		332	3.2	1.0	20	dbSNP_134	69	0,8600		0,0,4300	yes	missense	C20orf27	NM_001039140.1	98	0,20,6483	AA,AG,GG		0.0,0.4539,0.1538	benign	111/200	3736160	20,12986	2203	4300	6503	SO:0001583	missense	54976	exon4			AGGCTGGGGACAG	AK000557	CCDS33436.1, CCDS58763.1	20p13	2011-01-25			ENSG00000101220	ENSG00000101220			15873	protein-coding gene	gene with protein product	"""hypothetical protein LOC54976"""					11780052	Standard	NM_001258429		Approved	FLJ20550	uc002wjh.2	Q9GZN8	OTTHUMG00000031753	ENST00000379772.3:c.257C>T	20.37:g.3736160G>A	ENSP00000369097:p.Pro86Leu	48.0	0.0	0		65.0	27.0	0.415385	NM_001039140	A8K4J0|D3DVX8|Q5JX81|Q9NWX3	Missense_Mutation	SNP	ENST00000379772.3	37	CCDS58763.1	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	16.38|16.38	3.108437|3.108437	0.56291|0.56291	0.004539|0.004539	0.0|0.0	ENSG00000101220|ENSG00000101220	ENST00000379772;ENST00000217195;ENST00000399672;ENST00000379765|ENST00000399683	.|.	.|.	.|.	4.15|4.15	3.17|3.17	0.36434|0.36434	.|.	0.139643|0.139643	0.48286|0.48286	U|N	0.000198|0.000198	T|T	0.67915|0.67915	0.2944|0.2944	M|M	0.74881|0.74881	2.28|2.28	0.80722|0.80722	D|D	1|1	B;B;D|.	0.57257|.	0.001;0.435;0.979|.	B;B;P|.	0.59487|.	0.003;0.215;0.858|.	T|T	0.64179|0.64179	-0.6468|-0.6468	9|7	0.72032|0.19147	D|T	0.01|0.46	-3.9217|-3.9217	11.1696|11.1696	0.48563|0.48563	0.0:0.0:0.8075:0.1925|0.0:0.0:0.8075:0.1925	.|.	86;111;86|.	Q9GZN8;Q9GZN8-2;E9PAL2|.	CT027_HUMAN;.;.|.	L|S	86;111;86;86|80	.|.	ENSP00000217195:P111L|ENSP00000382591:P80S	P|P	-|-	2|1	0|0	C20orf27|C20orf27	3684160|3684160	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.901000|0.901000	0.52897|0.52897	4.963000|4.963000	0.63694|0.63694	1.297000|1.297000	0.44761|0.44761	0.561000|0.561000	0.74099|0.74099	CCC|CCA	G|0.999;A|0.001	0.001	strong		0.617	C20orf27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077750.2	NM_001039140	
MAATS1	89876	hgsc.bcm.edu	37	3	119466025	119466025	+	Missense_Mutation	SNP	G	G	A	rs9853426	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119466025G>A	ENST00000273390.5	+	15	2043	c.1966G>A	c.(1966-1968)Gcg>Acg	p.A656T	RP11-169N13.4_ENST00000489428.2_RNA	NM_033364.3	NP_203528	Q7Z4T9	MAAT1_HUMAN	MYCBP-associated, testis expressed 1	492						mitochondrion (GO:0005739)											GAATACCGAAGCGAATACTGC	0.388													G|||	71	0.0141773	0.0522	0.0014	5008	,	,		20049	0.0		0.0	False		,,,				2504	0.001				p.A656T		Atlas-SNP	.											.	.	.	.	0			c.G1966A						PASS	.	G	THR/ALA	210,4196	129.8+/-166.5	3,204,1996	112.0	105.0	107.0		1966	5.5	1.0	3	dbSNP_119	107	4,8596	1.2+/-3.3	1,2,4297	yes	missense	C3orf15	NM_033364.3	58	4,206,6293	AA,AG,GG		0.0465,4.7662,1.6454	benign	656/768	119466025	214,12792	2203	4300	6503	SO:0001583	missense	89876	exon15			ACCGAAGCGAATA	AB063296	CCDS2994.1	3q12-q13.3	2014-07-31	2012-12-07	2012-09-26	ENSG00000183833	ENSG00000183833			24010	protein-coding gene	gene with protein product	"""AMY-1-associating protein expressed in testis 1"", ""MYCBP-binding protein"", ""spermatogenesis associated 26"""	609910	"""chromosome 3 open reading frame 15"", ""MYCBP/AMY-1-associated, testis expressed 1"""	C3orf15		12223483, 14551891, 17967944	Standard	NM_033364		Approved	AAT1, AAT1alpha, SPATA26, CaM-IP2	uc003ede.4	Q7Z4T9	OTTHUMG00000159422	ENST00000273390.5:c.1966G>A	3.37:g.119466025G>A	ENSP00000273390:p.Ala656Thr	134.0	0.0	0		146.0	75.0	0.513699	NM_033364	A0AVK2|A8K1J9|B3KP23|B4DG52|B4DZ14|C9JUG4|Q68DX2|Q8TD41|Q96A45|Q96JE8	Missense_Mutation	SNP	ENST00000273390.5	37	CCDS2994.1	20	0.009157509157509158	20	0.04065040650406504	0	0.0	0	0.0	0	0.0	G	14.23	2.472805	0.43942	0.047662	4.65E-4	ENSG00000183833	ENST00000273390	T	0.22743	1.94	5.47	5.47	0.80525	.	0.170071	0.51477	D	0.000100	T	0.03136	0.0092	L	0.29908	0.895	0.80722	D	1	B;B;B	0.23990	0.095;0.055;0.095	B;B;B	0.26416	0.051;0.048;0.069	T	0.02519	-1.1147	10	0.42905	T	0.14	-11.3258	19.3267	0.94265	0.0:0.0:1.0:0.0	rs9853426;rs52829415;rs9853426	492;594;656	Q7Z4T9;Q7Z4T9-3;Q7Z4T9-7	AAT1_HUMAN;.;.	T	656	ENSP00000273390:A656T	ENSP00000273390:A656T	A	+	1	0	C3orf15	120948715	1.000000	0.71417	0.999000	0.59377	0.271000	0.26615	7.014000	0.76380	2.565000	0.86533	0.591000	0.81541	GCG	G|0.983;A|0.017	0.017	strong		0.388	MAATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355222.1	NM_033364	
TEX13A	56157	hgsc.bcm.edu	37	X	104464674	104464674	+	Silent	SNP	G	G	A	rs183606927		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:104464674G>A	ENST00000413579.1	-	2	519	c.408C>T	c.(406-408)ctC>ctT	p.L136L	IL1RAPL2_ENST00000344799.4_Intron|TEX13A_ENST00000372575.1_Silent_p.L136L|IL1RAPL2_ENST00000372582.1_Intron|TEX13A_ENST00000372578.3_Silent_p.L136L			Q9BXU3	TX13A_HUMAN	testis expressed 13A	136							zinc ion binding (GO:0008270)			large_intestine(5)|ovary(2)|upper_aerodigestive_tract(1)	8						GCACCTCCACGAGGCTGGTCT	0.607													G|||	61	0.0161589	0.0363	0.0072	3775	,	,		11953	0.0		0.003	False		,,,				2504	0.0051				p.L136L		Atlas-SNP	.											.	TEX13A	55	.	0			c.C408T						PASS	.	G	,	245,3427		5,188,47,1358,523	36.0	36.0	36.0		,408	-0.1	0.0	X		36	4,6586		0,1,3,2385,1815	no	intron,coding-synonymous	IL1RAPL2,TEX13A	NM_017416.1,NM_031274.3	,	5,189,50,3743,2338	AA,AG,A,GG,G		0.0607,6.6721,2.4264	,	,136/410	104464674	249,10013	2121	4204	6325	SO:0001819	synonymous_variant	56157	exon2			CTCCACGAGGCTG	AF285597	CCDS76005.1	Xq28	2012-04-20	2007-03-13		ENSG00000133149	ENSG00000268629			11735	protein-coding gene	gene with protein product		300312	"""testis expressed sequence 13A"""			11279525	Standard	NM_031274		Approved		uc004ema.3	Q9BXU3	OTTHUMG00000022133	ENST00000413579.1:c.408C>T	X.37:g.104464674G>A		71.0	0.0	0		80.0	25.0	0.3125	NM_031274	B1B1G8|Q32NB6	Silent	SNP	ENST00000413579.1	37																																																																																				G|0.992;A|0.008	0.008	strong		0.607	TEX13A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_031274	
PIF1	80119	hgsc.bcm.edu	37	15	65112116	65112116	+	Silent	SNP	C	C	T	rs145376177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:65112116C>T	ENST00000268043.4	-	8	1357	c.1263G>A	c.(1261-1263)gtG>gtA	p.V421V	PIF1_ENST00000333425.6_Silent_p.V421V|PIF1_ENST00000559239.1_Silent_p.V421V					PIF1 5'-to-3' DNA helicase											kidney(1)|lung(1)	2						GCCTCGTGGCCACAATCCCAT	0.652													C|||	2	0.000399361	0.0	0.0	5008	,	,		18557	0.002		0.0	False		,,,				2504	0.0				p.V421V		Atlas-SNP	.											.	PIF1	43	.	0			c.G1263A						PASS	.	C		1,4403	2.1+/-5.4	0,1,2201	81.0	72.0	75.0		1263	4.7	1.0	15	dbSNP_134	75	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	PIF1	NM_025049.2		0,2,6499	TT,TC,CC		0.0116,0.0227,0.0154		421/642	65112116	2,13000	2202	4299	6501	SO:0001819	synonymous_variant	80119	exon8			CGTGGCCACAATC	AK026345	CCDS10195.2, CCDS66797.1	15q22.1	2013-05-13	2013-05-13	2006-11-24	ENSG00000140451	ENSG00000140451	3.6.4.12		26220	protein-coding gene	gene with protein product		610953	"""chromosome 15 open reading frame 20"", ""PIF1 5'-to-3' DNA helicase homolog (S. cerevisiae)"""	C15orf20		10926538, 16522649	Standard	NM_025049		Approved	FLJ22692	uc002ant.2	Q9H611	OTTHUMG00000132974	ENST00000268043.4:c.1263G>A	15.37:g.65112116C>T		71.0	0.0	0		90.0	45.0	0.5	NM_025049		Silent	SNP	ENST00000268043.4	37	CCDS10195.2																																																																																			C|1.000;T|0.000	0.000	weak		0.652	PIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256533.1	NM_025049	
IGFALS	3483	hgsc.bcm.edu	37	16	1842454	1842454	+	Intron	SNP	G	G	A	rs34680334	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1842454G>A	ENST00000215539.3	-	2	127				IGFALS_ENST00000415638.3_Missense_Mutation_p.H27Y|IGFALS_ENST00000568221.1_Intron			P35858	ALS_HUMAN	insulin-like growth factor binding protein, acid labile subunit						cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin-like growth factor binding (GO:0005520)			endometrium(2)|lung(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	8						CTGCCCGAGTGAGCCTGATAC	0.701													G|||	347	0.0692891	0.2511	0.0187	5008	,	,		12605	0.0		0.002	False		,,,				2504	0.0				p.H27Y		Atlas-SNP	.											.	IGFALS	29	.	0			c.C79T						PASS	.	G	,TYR/HIS	325,1837		9,307,765	2.0	4.0	3.0		,79	-1.3	0.0	16	dbSNP_126	3	3,3869		0,3,1933	yes	intron,missense	IGFALS	NM_004970.2,NM_001146006.1	,83	9,310,2698	AA,AG,GG		0.0775,15.0324,5.4359	,benign	,27/644	1842454	328,5706	1081	1936	3017	SO:0001627	intron_variant	3483	exon2			CCGAGTGAGCCTG	M86826	CCDS10446.1, CCDS53982.1	16p13.3	2008-07-28			ENSG00000099769	ENSG00000099769			5468	protein-coding gene	gene with protein product		601489				1379671, 16114275	Standard	NM_004970		Approved	ALS	uc010uvn.2	P35858	OTTHUMG00000128638	ENST00000215539.3:c.17-52C>T	16.37:g.1842454G>A		11.0	0.0	0		13.0	9.0	0.692308	NM_001146006	B4DZY8|E9PGU3	Missense_Mutation	SNP	ENST00000215539.3	37	CCDS10446.1	114	0.0521978021978022	105	0.21341463414634146	7	0.019337016574585635	2	0.0034965034965034965	0	0.0	G	8.995	0.978678	0.18812	0.150324	7.75E-4	ENSG00000099769	ENST00000415638	T	0.54071	0.59	1.11	-1.27	0.09347	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.33266	0.404	B	0.18263	0.021	T	0.11717	-1.0576	8	0.66056	D	0.02	.	1.1011	0.01684	0.1624:0.2175:0.4:0.22	rs34680334	27	E9PGU3	.	Y	27	ENSP00000416683:H27Y	ENSP00000416683:H27Y	H	-	1	0	IGFALS	1782455	0.002000	0.14202	0.000000	0.03702	0.043000	0.13939	0.803000	0.27083	-0.428000	0.07339	0.549000	0.68633	CAC	G|0.947;A|0.053	0.053	strong		0.701	IGFALS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250509.2		
C5AR2	27202	hgsc.bcm.edu	37	19	47844899	47844899	+	Silent	SNP	C	C	T	rs34085015	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:47844899C>T	ENST00000595464.1	+	2	1061	c.843C>T	c.(841-843)ctC>ctT	p.L281L	C5AR2_ENST00000600626.1_Silent_p.L281L|C5AR2_ENST00000257267.2_Silent_p.L281L	NM_001271749.1	NP_001258678.1	Q9P296	C5AR2_HUMAN	complement component 5a receptor 2	281					chemotaxis (GO:0006935)|inflammatory response (GO:0006954)|negative regulation of interleukin-6 secretion (GO:1900165)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of tumor necrosis factor production (GO:0032720)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of interleukin-8 secretion (GO:2000482)	apical part of cell (GO:0045177)|basal plasma membrane (GO:0009925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C5a anaphylatoxin receptor activity (GO:0004944)										GCCTTGCCCTCGCTCACAGCT	0.667													C|||	27	0.00539137	0.0174	0.0043	5008	,	,		16697	0.0		0.001	False		,,,				2504	0.0				p.L281L		Atlas-SNP	.											.	.	.	.	0			c.C843T						PASS	.	C		92,4314	75.2+/-113.4	1,90,2112	59.0	59.0	59.0		843	-7.9	0.0	19	dbSNP_126	59	0,8600		0,0,4300	no	coding-synonymous	GPR77	NM_018485.1		1,90,6412	TT,TC,CC		0.0,2.0881,0.7074		281/338	47844899	92,12914	2203	4300	6503	SO:0001819	synonymous_variant	27202	exon2			TGCCCTCGCTCAC	AB038237	CCDS12699.1	19q13.33	2013-01-28	2013-01-28	2013-01-28		ENSG00000134830		"""GPCR / Class A : Complement component receptors"""	4527	protein-coding gene	gene with protein product		609949	"""G protein-coupled receptor 77"""	GPR77		11165367	Standard	NM_018485		Approved	C5L2	uc010ela.1	Q9P296		ENST00000595464.1:c.843C>T	19.37:g.47844899C>T		107.0	0.0	0		86.0	48.0	0.55814	NM_001271750	B2RA09	Silent	SNP	ENST00000595464.1	37	CCDS12699.1																																																																																			C|0.992;T|0.008	0.008	strong		0.667	C5AR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466926.1	NM_018485	
MST1L	11223	hgsc.bcm.edu	37	1	17087474	17087474	+	RNA	SNP	C	C	T	rs60783416		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17087474C>T	ENST00000455405.2	-	0	0							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										GGGCCCACAGCGACCAGCACA	0.632																																					p.R64H		Atlas-SNP	.											.	.	.	.	0			c.G191A						PASS	.																																					11223	exon2			CCACAGCGACCAG	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.17087474C>T		684.0	0.0	0		868.0	93.0	0.107143	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	6.967	0.548403	0.13312	.	.	ENSG00000186715	ENST00000389184;ENST00000334998;ENST00000442552	.	.	.	.	.	.	.	0.849673	0.09888	N	0.742825	T	0.33089	0.0851	.	.	.	.	.	.	B	0.19706	0.038	B	0.15870	0.014	T	0.32534	-0.9903	5	0.56958	D	0.05	.	.	.	.	rs60783416	64	Q2TV78-2	.	H	34;64;64	.	ENSP00000439273:R64H	R	-	2	0	MST1P9	16960061	0.458000	0.25760	0.000000	0.03702	0.000000	0.00434	-0.046000	0.11983	-0.000000	0.14550	0.000000	0.15137	CGC	C|0.500;T|0.500	0.500	weak		0.632	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
KRT31	3881	hgsc.bcm.edu	37	17	39551533	39551533	+	Silent	SNP	G	G	A	rs6503626	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39551533G>A	ENST00000251645.2	-	5	892	c.840C>T	c.(838-840)aaC>aaT	p.N280N		NM_002277.2	NP_002268.2	Q15323	K1H1_HUMAN	keratin 31	280	Coil 2.|Rod.				epidermis development (GO:0008544)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	31		Breast(137;0.000496)				TCTCCAGGGCGTTGACTGTGC	0.597													G|||	67	0.0133786	0.0469	0.0	5008	,	,		20660	0.0		0.0	False		,,,				2504	0.0051				p.N280N		Atlas-SNP	.											.	KRT31	158	.	0			c.C840T						PASS	.	G		123,4283	80.9+/-119.3	6,111,2086	98.0	90.0	93.0		840	-4.3	0.9	17	dbSNP_116	93	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	KRT31	NM_002277.2		6,113,6384	AA,AG,GG		0.0233,2.7916,0.9611		280/417	39551533	125,12881	2203	4300	6503	SO:0001819	synonymous_variant	3881	exon5			CAGGGCGTTGACT	X86570	CCDS11391.1	17q21.2	2014-05-20	2006-07-17	2006-07-17	ENSG00000094796	ENSG00000094796		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6448	protein-coding gene	gene with protein product	"""hard keratin type I 1"""	601077	"""keratin, hair, acidic, 1"""	KRTHA1		7578244, 16831889	Standard	NM_002277		Approved	Ha-1	uc002hwn.3	Q15323	OTTHUMG00000133423	ENST00000251645.2:c.840C>T	17.37:g.39551533G>A		236.0	0.0	0		210.0	101.0	0.480952	NM_002277	Q9UE12	Silent	SNP	ENST00000251645.2	37	CCDS11391.1																																																																																			G|0.988;A|0.012	0.012	strong		0.597	KRT31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257286.1	NM_002277	
FAM135A	57579	hgsc.bcm.edu	37	6	71235647	71235647	+	Missense_Mutation	SNP	C	C	T	rs16869301	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:71235647C>T	ENST00000418814.2	+	15	3474	c.2860C>T	c.(2860-2862)Cct>Tct	p.P954S	FAM135A_ENST00000457062.2_Missense_Mutation_p.P741S|FAM135A_ENST00000505868.1_Missense_Mutation_p.P954S|FAM135A_ENST00000370479.3_Missense_Mutation_p.P741S|FAM135A_ENST00000505769.1_Missense_Mutation_p.P534S|FAM135A_ENST00000361499.3_Missense_Mutation_p.P758S	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	954			P -> S (in dbSNP:rs16869301).							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						CTTCCAGAGTCCTGATAAATC	0.353													C|||	102	0.0203674	0.0726	0.0058	5008	,	,		19255	0.0		0.002	False		,,,				2504	0.0				p.P954S		Atlas-SNP	.											.	FAM135A	181	.	0			c.C2860T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO	296,4110	158.9+/-191.5	7,282,1914	52.0	55.0	54.0		2272,2860,2221	0.9	1.0	6	dbSNP_123	54	4,8590	3.7+/-12.6	0,4,4293	yes	missense,missense,missense	FAM135A	NM_001105531.2,NM_001162529.1,NM_020819.4	74,74,74	7,286,6207	TT,TC,CC		0.0465,6.7181,2.3077	benign,benign,benign	758/1320,954/1516,741/1303	71235647	300,12700	2203	4297	6500	SO:0001583	missense	57579	exon13			CAGAGTCCTGATA	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.2860C>T	6.37:g.71235647C>T	ENSP00000410768:p.Pro954Ser	96.0	0.0	0		99.0	41.0	0.414141	NM_001162529	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Missense_Mutation	SNP	ENST00000418814.2	37	CCDS55028.1	46	0.021062271062271064	43	0.08739837398373984	3	0.008287292817679558	0	0.0	0	0.0	C	0.006	-2.070499	0.00379	0.067181	4.65E-4	ENSG00000082269	ENST00000418814;ENST00000370479;ENST00000505769;ENST00000457062;ENST00000361499;ENST00000505868	T;T;T;T;T;T	0.21031	2.35;2.35;2.03;2.35;2.34;2.34	5.96	0.852	0.18995	.	0.426506	0.24048	N	0.042035	T	0.04907	0.0132	L	0.38531	1.155	0.20703	N	0.999861	B;B;B;B	0.21821	0.061;0.002;0.003;0.009	B;B;B;B	0.16289	0.015;0.004;0.011;0.01	T	0.35624	-0.9781	10	0.36615	T	0.2	.	7.0338	0.24983	0.0:0.5415:0.2138:0.2447	rs16869301;rs52792378;rs16869301	954;954;758;741	Q9P2D6-4;Q9P2D6;Q9P2D6-2;Q9P2D6-3	.;F135A_HUMAN;.;.	S	954;741;534;741;758;954	ENSP00000410768:P954S;ENSP00000359510:P741S;ENSP00000423785:P534S;ENSP00000409201:P741S;ENSP00000354913:P758S;ENSP00000423307:P954S	ENSP00000354913:P758S	P	+	1	0	FAM135A	71292368	0.903000	0.30736	0.997000	0.53966	0.055000	0.15305	0.715000	0.25822	0.405000	0.25532	-0.136000	0.14681	CCT	C|0.974;T|0.026	0.026	strong		0.353	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819	
BAD	572	hgsc.bcm.edu	37	11	64051853	64051853	+	5'UTR	SNP	G	G	A	rs75052600	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:64051853G>A	ENST00000394532.3	-	0	258				GPR137_ENST00000377702.4_5'Flank|GPR137_ENST00000438980.2_5'Flank|GPR137_ENST00000539851.1_5'Flank|BAD_ENST00000309032.3_Intron|BAD_ENST00000544785.1_5'Flank|GPR137_ENST00000313074.3_5'Flank|GPR137_ENST00000411458.1_Silent_p.V5V|BAD_ENST00000394531.3_Intron	NM_004322.3	NP_004313.1	Q92934	BAD_HUMAN	BCL2-associated agonist of cell death						activation of cysteine-type endopeptidase activity (GO:0097202)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|ADP metabolic process (GO:0046031)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|ATP metabolic process (GO:0046034)|cellular process regulating host cell cycle in response to virus (GO:0060154)|cellular response to chromate (GO:0071247)|cellular response to hypoxia (GO:0071456)|cellular response to lipid (GO:0071396)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose catabolic process (GO:0006007)|glucose homeostasis (GO:0042593)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|pore complex assembly (GO:0046931)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic process by virus (GO:0060139)|positive regulation of autophagy (GO:0010508)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of glucokinase activity (GO:0033133)|positive regulation of insulin secretion (GO:0032024)|positive regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0035774)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane potential (GO:0010918)|positive regulation of neuron death (GO:1901216)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of proteolysis (GO:0045862)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of T cell differentiation (GO:0045582)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of mitochondrial membrane permeability (GO:0046902)|release of cytochrome c from mitochondria (GO:0001836)|response to amino acid (GO:0043200)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to hydrogen peroxide (GO:0042542)|response to oleic acid (GO:0034201)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|suppression by virus of host apoptotic process (GO:0019050)|type B pancreatic cell proliferation (GO:0044342)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|lipid binding (GO:0008289)|phospholipid binding (GO:0005543)|protein kinase binding (GO:0019901)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(1)	4						TCTGGGCTGTGAGGACAAGAT	0.647													G|||	95	0.0189696	0.0658	0.0101	5008	,	,		18548	0.0		0.001	False		,,,				2504	0.0				p.V5V		Atlas-SNP	.											.	GPR137	52	.	0			c.G15A						PASS	.	G	,,	193,4209	120.8+/-158.4	8,177,2016	59.0	64.0	62.0		15,,	0.8	0.0	11	dbSNP_131	62	3,8591	3.0+/-9.4	0,3,4294	no	coding-synonymous,utr-5,intron	BAD,GPR137	NM_001170726.1,NM_004322.3,NM_032989.2	,,	8,180,6310	AA,AG,GG		0.0349,4.3844,1.5082	,,	5/476,,	64051853	196,12800	2201	4297	6498	SO:0001623	5_prime_UTR_variant	56834	exon1			GGCTGTGAGGACA	AF021792	CCDS8065.1	11q13.1	2014-03-07	2008-08-19		ENSG00000002330	ENSG00000002330			936	protein-coding gene	gene with protein product		603167				8929532	Standard	NM_004322		Approved	BCL2L8, BBC2	uc001nzd.3	Q92934	OTTHUMG00000134302	ENST00000394532.3:c.-13C>T	11.37:g.64051853G>A		38.0	0.0	0		48.0	26.0	0.541667	NM_001170726	O14803|Q6FH21	Silent	SNP	ENST00000394532.3	37	CCDS8065.1																																																																																			G|0.986;A|0.014	0.014	strong		0.647	BAD-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259180.2	NM_032989	
FAM159A	348378	hgsc.bcm.edu	37	1	53099242	53099242	+	Missense_Mutation	SNP	G	G	A	rs182623287	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:53099242G>A	ENST00000517870.1	+	1	227	c.77G>A	c.(76-78)gGc>gAc	p.G26D	FAM159A_ENST00000401050.3_3'UTR	NM_001042693.1	NP_001036158.1	Q6UWV7	F159A_HUMAN	family with sequence similarity 159, member A	26						integral component of membrane (GO:0016021)				endometrium(3)|lung(6)|upper_aerodigestive_tract(1)	10						cggccggggggcgaggcggcc	0.716													G|||	5	0.000998403	0.0008	0.0058	5008	,	,		9747	0.0		0.0	False		,,,				2504	0.0				p.G26D		Atlas-SNP	.											.	FAM159A	22	.	0			c.G77A						PASS	.						14.0	16.0	16.0					1																	53099242		1869	4059	5928	SO:0001583	missense	348378	exon1			CGGGGGGCGAGGC		CCDS41336.1	1p32.3	2008-08-08			ENSG00000182183	ENSG00000182183			28757	protein-coding gene	gene with protein product						12477932	Standard	NM_001042693		Approved	MGC52498	uc001cuf.3	Q6UWV7	OTTHUMG00000008330	ENST00000517870.1:c.77G>A	1.37:g.53099242G>A	ENSP00000429726:p.Gly26Asp	41.0	0.0	0		46.0	23.0	0.5	NM_001042693	Q6ZRG4	Missense_Mutation	SNP	ENST00000517870.1	37	CCDS41336.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	G	12.99	2.103714	0.37145	.	.	ENSG00000182183	ENST00000517870	.	.	.	3.44	3.44	0.39384	.	0.253016	0.29876	U	0.010972	T	0.22666	0.0547	N	0.03608	-0.345	0.36963	D	0.893453	P	0.34639	0.461	B	0.39562	0.303	T	0.23511	-1.0186	9	0.06625	T	0.88	.	15.773	0.78187	0.0:0.0:1.0:0.0	.	26	Q6UWV7	F159A_HUMAN	D	26	.	ENSP00000429726:G26D	G	+	2	0	FAM159A	52871830	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.263000	0.43293	1.860000	0.53959	0.455000	0.32223	GGC	G|0.999;A|0.001	0.001	strong		0.716	FAM159A-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022934.2	NM_001042693	
C15orf40	123207	hgsc.bcm.edu	37	15	83673653	83673653	+	3'UTR	SNP	A	A	C	rs74028206	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:83673653A>C	ENST00000513601.2	-	0	1165				C15orf40_ENST00000304177.5_3'UTR|RP11-382A20.5_ENST00000566841.1_RNA|C15orf40_ENST00000451195.3_Intron|C15orf40_ENST00000538348.2_Intron			Q8WUR7	CO040_HUMAN	chromosome 15 open reading frame 40											large_intestine(3)|lung(2)|skin(1)	6						AACTGCATTCAACAAGTagtc	0.393													A|||	66	0.0131789	0.0386	0.0173	5008	,	,		15049	0.0		0.003	False		,,,				2504	0.0				p.V146V		Atlas-SNP	.											.	C15orf40	18	.	0			c.T438G						PASS	.	A	,,,	38,1346		1,36,655	112.0	100.0	104.0		438,,,	1.1	0.0	15	dbSNP_130	104	0,3182		0,0,1591	no	coding-synonymous,intron,intron,utr-3	C15orf40	NM_001160114.1,NM_001160115.1,NM_001160116.1,NM_144597.2	,,,	1,36,2246	CC,CA,AA		0.0,2.7457,0.8322	,,,	146/154,,,	83673653	38,4528	692	1591	2283	SO:0001624	3_prime_UTR_variant	123207	exon4			GCATTCAACAAGT	BC019820	CCDS32312.1, CCDS32312.2, CCDS53968.1, CCDS53969.1	15q25.2	2012-05-30			ENSG00000169609	ENSG00000169609			28443	protein-coding gene	gene with protein product							Standard	NM_144597		Approved	MGC29937	uc010uoo.1	Q8WUR7	OTTHUMG00000160473	ENST00000513601.2:c.*696T>G	15.37:g.83673653A>C		122.0	0.0	0		101.0	53.0	0.524752	NM_001160114	A6NIC9|B2R5E7|F5GX92|F8WD31|G5EA00	Silent	SNP	ENST00000513601.2	37	CCDS32312.2																																																																																			A|0.985;C|0.015	0.015	strong		0.393	C15orf40-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360737.2	NM_144597	
KRT33B	3884	hgsc.bcm.edu	37	17	39521752	39521752	+	Silent	SNP	G	G	A	rs61741664	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39521752G>A	ENST00000251646.3	-	4	691	c.642C>T	c.(640-642)gaC>gaT	p.D214D		NM_002279.4	NP_002270.1	Q14525	KT33B_HUMAN	keratin 33B	214	Linker 12.|Rod.				aging (GO:0007568)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(6)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)	21		Breast(137;0.000496)				CGGGAGCAGCGTCCACCTCCA	0.542													G|||	72	0.014377	0.0537	0.0014	5008	,	,		19114	0.0		0.0	False		,,,				2504	0.0				p.D214D		Atlas-SNP	.											.	KRT33B	46	.	0			c.C642T						PASS	.	G		204,4178		19,166,2006	66.0	64.0	64.0		642	-4.8	0.7	17	dbSNP_129	64	1,8599		0,1,4299	no	coding-synonymous	KRT33B	NM_002279.3		19,167,6305	AA,AG,GG		0.0116,4.6554,1.5791		214/405	39521752	205,12777	2191	4300	6491	SO:0001819	synonymous_variant	3884	exon4			AGCAGCGTCCACC	X82634	CCDS11389.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000131738	ENSG00000131738		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6451	protein-coding gene	gene with protein product	"""hard keratin type I 3II"""	602762	"""keratin, hair, acidic, 3B"""	KRTHA3B		7565656, 16831889	Standard	NM_002279		Approved	Ha-3II	uc002hwl.4	Q14525	OTTHUMG00000133429	ENST00000251646.3:c.642C>T	17.37:g.39521752G>A		168.0	0.0	0		200.0	100.0	0.5	NM_002279	O76010	Silent	SNP	ENST00000251646.3	37	CCDS11389.1																																																																																			G|0.981;A|0.019	0.019	strong		0.542	KRT33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257292.1	NM_002279	
TMEM255B	348013	hgsc.bcm.edu	37	13	114507956	114507956	+	Silent	SNP	G	G	A	rs56032548	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:114507956G>A	ENST00000375353.3	+	8	795	c.768G>A	c.(766-768)acG>acA	p.T256T	TMEM255B_ENST00000467169.1_3'UTR	NM_182614.2	NP_872420.1	Q8WV15	T255B_HUMAN	transmembrane protein 255B	256						integral component of membrane (GO:0016021)											TCCGCCTGACGCCCGAGCCCG	0.672													G|||	355	0.0708866	0.2534	0.0288	5008	,	,		14726	0.0		0.0	False		,,,				2504	0.0				p.T256T		Atlas-SNP	.											.	.	.	.	0			c.G768A						PASS	.	G		962,3442	354.4+/-312.6	113,736,1353	62.0	60.0	60.0		768	-5.7	0.0	13	dbSNP_129	60	17,8583	12.6+/-44.7	0,17,4283	no	coding-synonymous	FAM70B	NM_182614.2		113,753,5636	AA,AG,GG		0.1977,21.8438,7.5285		256/327	114507956	979,12025	2202	4300	6502	SO:0001819	synonymous_variant	348013	exon8			CCTGACGCCCGAG	BC018995	CCDS45071.1	13q34	2012-11-30	2012-11-30	2012-11-30	ENSG00000184497	ENSG00000184497			28297	protein-coding gene	gene with protein product			"""family with sequence similarity 70, member B"""	FAM70B		12477932	Standard	NM_182614		Approved	MGC20579	uc001vuh.3	Q8WV15	OTTHUMG00000017398	ENST00000375353.3:c.768G>A	13.37:g.114507956G>A		54.0	0.0	0		60.0	29.0	0.483333	NM_182614		Silent	SNP	ENST00000375353.3	37	CCDS45071.1																																																																																			G|0.922;A|0.078	0.078	strong		0.672	TMEM255B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045953.4	NM_182614	
HUS1	3364	hgsc.bcm.edu	37	7	48008869	48008869	+	Missense_Mutation	SNP	G	G	C	rs138848570	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:48008869G>C	ENST00000258774.5	-	6	610	c.587C>G	c.(586-588)aCt>aGt	p.T196S	HUS1_ENST00000432325.1_Missense_Mutation_p.T175S	NM_004507.3	NP_004498.1	O60921	HUS1_HUMAN	HUS1 checkpoint homolog (S. pombe)	196					cellular response to DNA damage stimulus (GO:0006974)|cellular response to ionizing radiation (GO:0071479)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|embryo development (GO:0009790)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of DNA replication (GO:0008156)|protein phosphorylation (GO:0006468)|regulation of protein phosphorylation (GO:0001932)|response to UV (GO:0009411)	checkpoint clamp complex (GO:0030896)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(3)|ovary(2)|prostate(1)	13		Breast(660;0.00139)				TACTAATTCAGTTTCTATTTT	0.294								Direct reversal of damage;Other conserved DNA damage response genes			OREG0018063	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	21	0.00419329	0.0159	0.0	5008	,	,		20315	0.0		0.0	False		,,,				2504	0.0				p.T196S	Ovarian(103;466 1517 21788 34610 43890)	Atlas-SNP	.											.	HUS1	36	.	0			c.C587G						PASS	.	G	SER/THR	20,4378	28.1+/-56.4	1,18,2180	95.0	99.0	98.0		587	5.2	1.0	7	dbSNP_134	98	0,8600		0,0,4300	yes	missense	HUS1	NM_004507.3	58	1,18,6480	CC,CG,GG		0.0,0.4548,0.1539	benign	196/281	48008869	20,12978	2199	4300	6499	SO:0001583	missense	3364	exon6			AATTCAGTTTCTA	Y16893	CCDS34635.1	7p13-p12	2008-08-08	2001-11-28		ENSG00000136273	ENSG00000136273			5309	protein-coding gene	gene with protein product	"""hus1+-like protein"""	603760	"""HUS1 (S. pombe) checkpoint homolog"""			9878245, 9524127	Standard	NM_004507		Approved		uc003tod.2	O60921	OTTHUMG00000155645	ENST00000258774.5:c.587C>G	7.37:g.48008869G>C	ENSP00000258774:p.Thr196Ser	51.0	0.0	0	951	53.0	21.0	0.396226	NM_004507	B4DFI9	Missense_Mutation	SNP	ENST00000258774.5	37	CCDS34635.1	23	0.010531135531135532	23	0.046747967479674794	0	0.0	0	0.0	0	0.0	G	16.67	3.187502	0.57909	0.004548	0.0	ENSG00000136273	ENST00000258774;ENST00000432325;ENST00000432627	T;T;T	0.13196	2.61;2.61;2.61	5.19	5.19	0.71726	.	0.052227	0.85682	N	0.000000	T	0.02888	0.0086	L	0.46567	1.45	0.54753	D	0.999987	B	0.30033	0.266	B	0.40228	0.323	T	0.07829	-1.0752	10	0.22109	T	0.4	-12.6777	16.5638	0.84573	0.0:0.0:1.0:0.0	.	196	O60921	HUS1_HUMAN	S	196;175;175	ENSP00000258774:T196S;ENSP00000416588:T175S;ENSP00000404855:T175S	ENSP00000258774:T196S	T	-	2	0	HUS1	47975394	1.000000	0.71417	0.951000	0.38953	0.999000	0.98932	7.975000	0.88055	2.563000	0.86464	0.655000	0.94253	ACT	G|0.996;C|0.004	0.004	strong		0.294	HUS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340952.1	NM_004507	
OR5D18	219438	hgsc.bcm.edu	37	11	55587591	55587591	+	Silent	SNP	C	C	T	rs142792552	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55587591C>T	ENST00000333976.4	+	1	506	c.486C>T	c.(484-486)tgC>tgT	p.C162C		NM_001001952.1	NP_001001952.1	Q8NGL1	OR5DI_HUMAN	olfactory receptor, family 5, subfamily D, member 18	162						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			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)				AACTGACGTGCTCTGCTTTAA	0.453													N|||	7	0.00139776	0.0053	0.0	5008	,	,		18790	0.0		0.0	False		,,,				2504	0.0				p.C162C		Atlas-SNP	.											.	OR5D18	121	.	0			c.C486T						PASS	.	C		43,4357		0,43,2157	203.0	189.0	193.0		486	-0.8	0.2	11	dbSNP_134	193	0,8592		0,0,4296	no	coding-synonymous	OR5D18	NM_001001952.1		0,43,6453	TT,TC,CC		0.0,0.9773,0.331		162/314	55587591	43,12949	2200	4296	6496	SO:0001819	synonymous_variant	219438	exon1			GACGTGCTCTGCT	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.486C>T	11.37:g.55587591C>T		309.0	1.0	0.00323625		345.0	163.0	0.472464	NM_001001952	Q6IF67|Q6IFD3|Q96RB3	Silent	SNP	ENST00000333976.4	37	CCDS31510.1																																																																																			C|0.997;T|0.003	0.003	strong		0.453	OR5D18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391515.1	NM_001001952	
VPS33B	26276	hgsc.bcm.edu	37	15	91550232	91550232	+	Silent	SNP	G	G	A	rs59648701	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:91550232G>A	ENST00000333371.3	-	9	1001	c.648C>T	c.(646-648)ggC>ggT	p.G216G	VPS33B_ENST00000535906.1_Silent_p.G189G|VPS33B_ENST00000535843.1_Silent_p.G125G	NM_018668.3	NP_061138.3	Q9H267	VP33B_HUMAN	vacuolar protein sorting 33 homolog B (yeast)	216					lysosome localization (GO:0032418)|melanosome localization (GO:0032400)|membrane fusion (GO:0061025)|platelet alpha granule organization (GO:0070889)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule (GO:0031091)				central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|stomach(2)	16	Lung NSC(78;0.0987)|all_lung(78;0.175)					CCTTGGTTTCGCCATCCTCCT	0.527													G|||	120	0.0239617	0.0809	0.0144	5008	,	,		19376	0.0		0.003	False		,,,				2504	0.0				p.G216G		Atlas-SNP	.											.	VPS33B	42	.	0			c.C648T						PASS	.	G		294,4102	161.4+/-193.6	7,280,1911	114.0	118.0	117.0		648	-1.7	1.0	15	dbSNP_129	117	8,8588	7.1+/-27.0	0,8,4290	no	coding-synonymous	VPS33B	NM_018668.3		7,288,6201	AA,AG,GG		0.0931,6.6879,2.3245		216/618	91550232	302,12690	2198	4298	6496	SO:0001819	synonymous_variant	26276	exon9			GGTTTCGCCATCC	AF201694	CCDS10369.1, CCDS73783.1	15q26.1	2006-12-19	2006-12-19		ENSG00000184056	ENSG00000184056			12712	protein-coding gene	gene with protein product		608552	"""vacuolar protein sorting 33B (yeast homolog)"""			8996080	Standard	XM_005254887		Approved	FLJ14848	uc002bqp.1	Q9H267	OTTHUMG00000149835	ENST00000333371.3:c.648C>T	15.37:g.91550232G>A		14.0	0.0	0		33.0	32.0	0.969697	NM_018668	B3KQF6|Q96K14|Q9NRP6|Q9NSF3	Silent	SNP	ENST00000333371.3	37	CCDS10369.1																																																																																			G|0.978;A|0.022	0.022	strong		0.527	VPS33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313496.1	NM_018668	
LRIG1	26018	hgsc.bcm.edu	37	3	66431280	66431280	+	Missense_Mutation	SNP	C	C	T	rs9877201	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:66431280C>T	ENST00000273261.3	-	18	3300	c.2776G>A	c.(2776-2778)Ggt>Agt	p.G926S	SLC25A26_ENST00000536651.1_3'UTR|LRIG1_ENST00000496559.2_5'UTR|LRIG1_ENST00000383703.3_Missense_Mutation_p.G903S	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	926			G -> S (in dbSNP:rs9877201).		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)		ACCCGGCCACCGTGTTCTGAA	0.597													C|||	554	0.110623	0.3873	0.0346	5008	,	,		18811	0.0		0.0179	False		,,,				2504	0.0				p.G926S		Atlas-SNP	.											LRIG1,NS,carcinoma,0,1	LRIG1	138	1	0			c.G2776A						PASS	.	C	SER/GLY	1492,2914	473.5+/-356.7	259,974,970	49.0	52.0	51.0		2776	-3.4	0.0	3	dbSNP_119	51	84,8516	48.9+/-108.6	1,82,4217	yes	missense	LRIG1	NM_015541.2	56	260,1056,5187	TT,TC,CC		0.9767,33.8629,12.1175	benign	926/1094	66431280	1576,11430	2203	4300	6503	SO:0001583	missense	26018	exon18			GGCCACCGTGTTC	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.2776G>A	3.37:g.66431280C>T	ENSP00000273261:p.Gly926Ser	73.0	0.0	0		85.0	36.0	0.423529	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Missense_Mutation	SNP	ENST00000273261.3	37	CCDS33783.1	210	0.09615384615384616	187	0.3800813008130081	8	0.022099447513812154	0	0.0	15	0.01978891820580475	C	10.82	1.457361	0.26161	0.338629	0.009767	ENSG00000144749	ENST00000273261;ENST00000383703;ENST00000383702	T;T	0.69040	-0.18;-0.37	5.34	-3.41	0.04839	.	0.402609	0.28016	N	0.016939	T	0.00012	0.0000	N	0.02315	-0.6	0.80722	P	0.0	B;B;B	0.24651	0.012;0.108;0.007	B;B;B	0.15870	0.014;0.014;0.002	T	0.38908	-0.9639	9	0.18710	T	0.47	.	8.9885	0.36008	0.145:0.5962:0.0:0.2587	rs9877201;rs52813156;rs59347115;rs9877201	903;926;926	Q96JA1-2;Q5XWD3;Q96JA1	.;.;LRIG1_HUMAN	S	926;903;829	ENSP00000273261:G926S;ENSP00000373208:G903S	ENSP00000273261:G926S	G	-	1	0	LRIG1	66513970	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	-0.284000	0.08422	-0.442000	0.07190	-0.794000	0.03295	GGT	C|0.879;T|0.121	0.121	strong		0.597	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541	
VASN	114990	hgsc.bcm.edu	37	16	4431880	4431880	+	Silent	SNP	C	C	T	rs13333950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4431880C>T	ENST00000304735.3	+	2	1157	c.1002C>T	c.(1000-1002)aaC>aaT	p.N334N	CORO7_ENST00000423908.2_Intron|CORO7_ENST00000539968.1_Intron|CORO7_ENST00000251166.4_Intron|CORO7-PAM16_ENST00000572467.1_Intron|CORO7_ENST00000537233.2_Intron|CORO7_ENST00000574025.1_Intron	NM_138440.2	NP_612449.2	Q6EMK4	VASN_HUMAN	vasorin	334	LRRCT.				cellular response to hypoxia (GO:0071456)|cellular response to redox state (GO:0071461)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	transforming growth factor beta binding (GO:0050431)			breast(1)|lung(3)|prostate(1)|skin(1)	6						CGCCCAAGAACGCTGGCCGGC	0.692													C|||	177	0.0353435	0.1309	0.0058	5008	,	,		14062	0.0		0.0	False		,,,				2504	0.0				p.N334N		Atlas-SNP	.											.	VASN	21	.	0			c.C1002T						PASS	.	C	,,,,	532,3842		38,456,1693	19.0	22.0	21.0		,,,,1002	-11.3	0.1	16	dbSNP_121	21	1,8583		0,1,4291	no	intron,intron,intron,intron,coding-synonymous	CORO7,VASN,CORO7-PAM16	NM_001201472.1,NM_001201473.1,NM_001201479.1,NM_024535.4,NM_138440.2	,,,,	38,457,5984	TT,TC,CC		0.0116,12.1628,4.1133	,,,,	,,,,334/674	4431880	533,12425	2187	4292	6479	SO:0001819	synonymous_variant	114990	exon2			CAAGAACGCTGGC	AY358299	CCDS10514.1	16p13.3	2008-02-05	2006-03-30	2006-03-30	ENSG00000168140	ENSG00000168140			18517	protein-coding gene	gene with protein product		608843	"""slit-like 2 (Drosophila)"""	SLITL2		15247411	Standard	NM_138440		Approved		uc002cwj.1	Q6EMK4	OTTHUMG00000129469	ENST00000304735.3:c.1002C>T	16.37:g.4431880C>T		45.0	0.0	0		58.0	31.0	0.534483	NM_138440	Q6UXL4|Q6UXL5|Q96CX1	Silent	SNP	ENST00000304735.3	37	CCDS10514.1																																																																																			C|0.962;T|0.038	0.038	strong		0.692	VASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251632.1	NM_138440	
CDH13	1012	hgsc.bcm.edu	37	16	83378487	83378487	+	Silent	SNP	T	T	C	rs145120824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:83378487T>C	ENST00000566620.1	+	6	947	c.657T>C	c.(655-657)gaT>gaC	p.D219D	CDH13_ENST00000428848.3_Silent_p.D180D|CDH13_ENST00000268613.10_Silent_p.D266D|CDH13_ENST00000569454.1_3'UTR	NM_001220488.1|NM_001220489.1|NM_001220490.1|NM_001257.4	NP_001207417.1|NP_001207418.1|NP_001207419.1|NP_001248.1	P55290	CAD13_HUMAN	cadherin 13	219	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|endothelial cell migration (GO:0043542)|homophilic cell adhesion (GO:0007156)|keratinocyte proliferation (GO:0043616)|lamellipodium assembly (GO:0030032)|localization within membrane (GO:0051668)|low-density lipoprotein particle mediated signaling (GO:0055096)|mitotic cell cycle (GO:0000278)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell proliferation (GO:0008285)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Rac protein signal transduction (GO:0016601)|regulation of cell growth (GO:0001558)|regulation of endocytosis (GO:0030100)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|Rho protein signal transduction (GO:0007266)|sprouting angiogenesis (GO:0002040)	anchored component of membrane (GO:0031225)|caveola (GO:0005901)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	adiponectin binding (GO:0055100)|cadherin binding (GO:0045296)|calcium ion binding (GO:0005509)|lipoprotein particle binding (GO:0071813)|low-density lipoprotein particle binding (GO:0030169)			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		AGACCACTGATGTCAATGGCA	0.438													T|||	21	0.00419329	0.0144	0.0029	5008	,	,		19418	0.0		0.0	False		,,,				2504	0.0				p.D266D		Atlas-SNP	.											.	CDH13	97	.	0			c.T798C						PASS	.	T	,,,	47,3655		0,47,1804	78.0	80.0	79.0		798,540,,657	3.5	0.8	16	dbSNP_134	79	0,8178		0,0,4089	no	coding-synonymous,coding-synonymous,utr-5,coding-synonymous	CDH13	NM_001220488.1,NM_001220489.1,NM_001220490.1,NM_001257.4	,,,	0,47,5893	CC,CT,TT		0.0,1.2696,0.3956	,,,	266/761,180/675,,219/714	83378487	47,11833	1851	4089	5940	SO:0001819	synonymous_variant	1012	exon7			CACTGATGTCAAT	U59288	CCDS56009.1, CCDS56010.1, CCDS58485.1, CCDS58486.1, CCDS58487.1	16q23.3	2013-08-27	2013-08-27			ENSG00000140945		"""Cadherins / Major cadherins"""	1753	protein-coding gene	gene with protein product	"""T-cadherin"", ""H-cadherin (heart)"""	601364				8673923, 9468307	Standard	NM_001257		Approved	CDHH	uc010vns.2	P55290		ENST00000566620.1:c.657T>C	16.37:g.83378487T>C		126.0	0.0	0		120.0	48.0	0.4	NM_001220488	A8W476|A8W477|B7Z590|C9JRI6|J3KN62|Q6GTW4|Q8TBX3	Silent	SNP	ENST00000566620.1	37	CCDS58486.1																																																																																			T|0.996;C|0.004	0.004	strong		0.438	CDH13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432917.1	NM_001257	
UQCRH	7388	hgsc.bcm.edu	37	1	46775856	46775856	+	Nonsense_Mutation	SNP	C	C	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:46775856C>A	ENST00000311672.5	+	3	247	c.111C>A	c.(109-111)tgC>tgA	p.C37*		NM_001089591.1|NM_006004.2	NP_001083060.1|NP_005995.2	P07919	QCR6_HUMAN	ubiquinol-cytochrome c reductase hinge protein	37					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|oxidation-reduction process (GO:0055114)|oxidative phosphorylation (GO:0006119)|protein heterooligomerization (GO:0051291)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain (GO:0005746)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	ubiquinol-cytochrome-c reductase activity (GO:0008121)			large_intestine(1)|lung(1)|skin(1)|urinary_tract(1)	4	Acute lymphoblastic leukemia(166;0.155)					GAGAGCAATGCGAGCAGTTGG	0.468																																					p.C37X		Atlas-SNP	.											.	UQCRH	4	.	0			c.C111A						PASS	.						84.0	85.0	85.0					1																	46775856		2203	4300	6503	SO:0001587	stop_gained	7388	exon3			GCAATGCGAGCAG	BC001934	CCDS30704.1	1p34.1	2011-07-04			ENSG00000173660	ENSG00000173660	1.10.2.2	"""Mitochondrial respiratory chain complex / Complex III"""	12590	protein-coding gene	gene with protein product	"""ubiquinol-cytochrome c reductase, complex III subunit VIII"""	613844				2826252	Standard	XM_005271167		Approved	QCR6, UQCR8	uc001cpp.3	P07919	OTTHUMG00000007813	ENST00000311672.5:c.111C>A	1.37:g.46775856C>A	ENSP00000309565:p.Cys37*	182.0	0.0	0		193.0	100.0	0.518135	NM_006004	B2R4V9|D3DQ18|Q5TDF6|Q6LDB8|Q9BQ91	Nonsense_Mutation	SNP	ENST00000311672.5	37	CCDS30704.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.424984	0.83667	.	.	ENSG00000173660	ENST00000311672	.	.	.	5.23	0.0755	0.14399	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.1407	9.4087	0.38477	0.0:0.3877:0.0:0.6123	.	.	.	.	X	37	.	ENSP00000309565:C37X	C	+	3	2	UQCRH	46548443	0.816000	0.29132	0.998000	0.56505	0.997000	0.91878	-0.075000	0.11431	0.135000	0.18707	0.655000	0.94253	TGC	.	.	none		0.468	UQCRH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021451.1	NM_006004	
GGTLC1	92086	hgsc.bcm.edu	37	20	23966316	23966316	+	Silent	SNP	T	T	C	rs111546926	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:23966316T>C	ENST00000335694.4	-	5	723	c.519A>G	c.(517-519)agA>agG	p.R173R	GGTLC1_ENST00000278765.4_Silent_p.R173R|GGTLC1_ENST00000286890.4_Silent_p.R173R	NM_178311.2	NP_842563.1	Q9BX51	GGTL1_HUMAN	gamma-glutamyltransferase light chain 1	173					glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)	gamma-glutamyltransferase activity (GO:0003840)			NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	15						GGTCAATGTTTCTCTCCACTG	0.597													.|||	337	0.0672923	0.2239	0.0274	5008	,	,		16839	0.002		0.0089	False		,,,				2504	0.0112				p.R173R		Atlas-SNP	.											.	GGTLC1	37	.	0			c.A519G						PASS	.	T	,	856,3550	316.3+/-294.6	75,706,1422	52.0	54.0	53.0		519,519	0.8	0.4	20	dbSNP_132	53	103,8489	51.9+/-112.3	1,101,4194	no	coding-synonymous,coding-synonymous	GGTLC1	NM_178311.2,NM_178312.2	,	76,807,5616	CC,CT,TT		1.1988,19.4281,7.3781	,	173/226,173/226	23966316	959,12039	2203	4296	6499	SO:0001819	synonymous_variant	92086	exon5			AATGTTTCTCTCC	AL133466	CCDS13163.1	20p11.21	2010-07-14	2008-03-10	2008-03-10	ENSG00000149435	ENSG00000149435		"""Gamma-glutamyltransferases"""	16437	protein-coding gene	gene with protein product		612338	"""gamma-glutamyltransferase-like activity 4"", ""gamma-glutamyltransferase-like activity 3"""	GGTLA4, GGTLA3		10843999, 18357469	Standard	NM_178311		Approved	dJ831C21.2, dJ831C21.1	uc002wtu.3	Q9BX51	OTTHUMG00000032095	ENST00000335694.4:c.519A>G	20.37:g.23966316T>C		73.0	0.0	0		87.0	45.0	0.517241	NM_178311	D3DW43|Q08246	Silent	SNP	ENST00000335694.4	37	CCDS13163.1																																																																																			T|0.937;C|0.063	0.063	strong		0.597	GGTLC1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078366.2	NM_178311.2	
GIMAP8	155038	hgsc.bcm.edu	37	7	150164189	150164189	+	Silent	SNP	C	C	A	rs143212982	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150164189C>A	ENST00000307271.3	+	2	977	c.403C>A	c.(403-405)Cgg>Agg	p.R135R		NM_175571.2	NP_783161.1	Q8ND71	GIMA8_HUMAN	GTPase, IMAP family member 8	135	AIG1-type G 1.					cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(11)|lung(26)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(82;0.0218)	UCEC - Uterine corpus endometrioid carcinoma (81;0.17)		TGTCTTCACTCGGAAGGATGA	0.463																																					p.R135R		Atlas-SNP	.											GIMAP8,NS,carcinoma,-1,1	GIMAP8	136	1	0			c.C403A						PASS	.	C		37,4369	41.6+/-74.8	0,37,2166	79.0	75.0	76.0		403	-4.4	0.0	7	dbSNP_134	76	1,8599	1.2+/-3.3	0,1,4299	yes	coding-synonymous	GIMAP8	NM_175571.2		0,38,6465	AA,AC,CC		0.0116,0.8398,0.2922		135/666	150164189	38,12968	2203	4300	6503	SO:0001819	synonymous_variant	155038	exon2			TTCACTCGGAAGG	AL834361	CCDS34777.1	7q36.1	2014-04-04			ENSG00000171115	ENSG00000171115		"""GTPases, IMAP"""	21792	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 9"""					15474311	Standard	XM_005249951		Approved	DKFZp667I133, hIAN6, IAN9	uc003whj.3	Q8ND71	OTTHUMG00000158327	ENST00000307271.3:c.403C>A	7.37:g.150164189C>A		180.0	0.0	0		201.0	104.0	0.517413	NM_175571		Silent	SNP	ENST00000307271.3	37	CCDS34777.1																																																																																			A|0.002;C|0.998;G|0.001	0.002	strong		0.463	GIMAP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350701.1	NM_175571	
PCNT	5116	hgsc.bcm.edu	37	21	47766113	47766113	+	Missense_Mutation	SNP	T	T	G	rs34500739	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:47766113T>G	ENST00000359568.5	+	4	818	c.711T>G	c.(709-711)caT>caG	p.H237Q	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	237	Glu-rich.				brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					CTGGCCTGCATCAGAGTCAGG	0.602													G|||	128	0.0255591	0.028	0.0303	5008	,	,		16755	0.001		0.0646	False		,,,				2504	0.0041				p.H237Q		Atlas-SNP	.											.	PCNT	283	.	0			c.T711G						PASS	.	G	GLN/HIS	192,4214	807.9+/-415.9	5,182,2016	83.0	74.0	77.0		711	3.3	1.0	21	dbSNP_126	77	528,8072	795.4+/-407.5	11,506,3783	yes	missense	PCNT	NM_006031.5	24	16,688,5799	GG,GT,TT		6.1395,4.3577,5.5359	benign	237/3337	47766113	720,12286	2203	4300	6503	SO:0001583	missense	5116	exon4			CCTGCATCAGAGT	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.711T>G	21.37:g.47766113T>G	ENSP00000352572:p.His237Gln	100.0	0.0	0		129.0	71.0	0.550388	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	92	0.04212454212454213	21	0.042682926829268296	16	0.04419889502762431	1	0.0017482517482517483	54	0.0712401055408971	G	2.436	-0.329782	0.05314	0.043577	0.061395	ENSG00000160299	ENST00000359568;ENST00000337772	T	0.01279	5.06	3.27	3.27	0.37495	.	.	.	.	.	T	0.00073	0.0002	N	0.00926	-1.1	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45145	-0.9281	9	0.09084	T	0.74	.	8.0049	0.30319	0.0:0.0:0.7564:0.2436	rs34500739	119;237	O95613-2;O95613	.;PCNT_HUMAN	Q	237;224	ENSP00000352572:H237Q	ENSP00000338675:H224Q	H	+	3	2	PCNT	46590541	0.057000	0.20700	0.965000	0.40720	0.171000	0.22731	0.660000	0.25009	0.988000	0.38734	-0.648000	0.03929	CAT	T|0.949;G|0.051	0.051	strong		0.602	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
MUC4	4585	hgsc.bcm.edu	37	3	195508692	195508692	+	Missense_Mutation	SNP	G	G	C	rs528841424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195508692G>C	ENST00000463781.3	-	2	10218	c.9759C>G	c.(9757-9759)gaC>gaG	p.D3253E	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D3253E	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)		CTGAGGAAGTGTCGGTGACAG	0.562													.|||	426	0.0850639	0.3109	0.0216	5008	,	,		10371	0.0		0.0	False		,,,				2504	0.0				p.D3253E		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.C9759G						scavenged	.						3.0	2.0	3.0					3																	195508692		528	1216	1744	SO:0001583	missense	4585	exon2			GGAAGTGTCGGTG	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.9759C>G	3.37:g.195508692G>C	ENSP00000417498:p.Asp3253Glu	154.0	1.0	0.00649351		115.0	74.0	0.643478	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	7.901	0.734401	0.15574	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29142	1.58;1.58	1.03	-1.18	0.09617	.	.	.	.	.	T	0.26268	0.0641	N	0.08118	0	0.09310	N	1	D	0.61080	0.989	D	0.71656	0.974	T	0.26052	-1.0114	8	.	.	.	.	5.5419	0.17043	0.0:0.0:0.6865:0.3135	.	3125	E7ESK3	.	E	3253	ENSP00000417498:D3253E;ENSP00000420243:D3253E	.	D	-	3	2	MUC4	196993471	0.000000	0.05858	0.014000	0.15608	0.048000	0.14542	-0.521000	0.06245	0.494000	0.27859	0.089000	0.15464	GAC	.	.	none		0.562	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PSG2	5670	hgsc.bcm.edu	37	19	43576029	43576029	+	Missense_Mutation	SNP	C	C	T	rs112235686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43576029C>T	ENST00000406487.1	-	4	885	c.787G>A	c.(787-789)Gcg>Acg	p.A263T		NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	263	Ig-like C2-type 2.				cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(24)|ovary(1)|pancreas(2)|prostate(6)|stomach(2)|urinary_tract(2)	49		Prostate(69;0.00682)				TTAGAGTTCGCGAAGCAAGAC	0.438													C|||	8	0.00159744	0.0061	0.0	5008	,	,		20011	0.0		0.0	False		,,,				2504	0.0				p.A263T		Atlas-SNP	.											PSG2,colon,carcinoma,+1,2	PSG2	84	2	0			c.G787A						PASS	.	C	THR/ALA	27,4377	33.5+/-64.1	2,23,2177	180.0	191.0	187.0		787	-0.0	0.0	19	dbSNP_132	187	10,8588	7.7+/-29.5	0,10,4289	yes	missense	PSG2	NM_031246.3	58	2,33,6466	TT,TC,CC		0.1163,0.6131,0.2846		263/336	43576029	37,12965	2202	4299	6501	SO:0001583	missense	5670	exon4			AGTTCGCGAAGCA		CCDS12616.1	19q13.1-q13.2	2013-01-29			ENSG00000242221	ENSG00000242221		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9519	protein-coding gene	gene with protein product	"""pregnancy-specific beta-1 glycoprotein"", ""pregnancy-specific beta-1-glycoprotein 7"", ""carcinoembryonic antigen SG8"""	176391		PSBG2		2377620	Standard	NM_031246		Approved	PSGGB, PSG1, CEA	uc002ovr.3	P11465	OTTHUMG00000151547	ENST00000406487.1:c.787G>A	19.37:g.43576029C>T	ENSP00000385706:p.Ala263Thr	194.0	0.0	0		195.0	89.0	0.45641	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Missense_Mutation	SNP	ENST00000406487.1	37	CCDS12616.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	c	1.983	-0.433771	0.04669	0.006131	0.001163	ENSG00000242221	ENST00000406487;ENST00000329509;ENST00000401942;ENST00000406917	T	0.15603	2.41	1.26	-0.0241	0.13940	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.10981	0.0268	M	0.73372	2.23	0.09310	N	1	B;B	0.22414	0.069;0.003	B;B	0.20767	0.031;0.022	T	0.35400	-0.9790	9	0.20519	T	0.43	.	3.758	0.08593	0.0:0.7179:0.0:0.2821	.	263;263	B5MCM8;P11465	.;PSG2_HUMAN	T	263	ENSP00000385706:A263T	ENSP00000332984:A263T	A	-	1	0	PSG2	48267869	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.248000	0.08854	-0.149000	0.11215	0.398000	0.26397	GCG	C|0.998;T|0.002	0.002	strong		0.438	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246	
TRPC4	7223	hgsc.bcm.edu	37	13	38211046	38211046	+	Silent	SNP	T	T	C	rs731860	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:38211046T>C	ENST00000379705.3	-	11	3785	c.2928A>G	c.(2926-2928)agA>agG	p.R976R	TRPC4_ENST00000358477.2_Silent_p.R892R|TRPC4_ENST00000379681.3_Silent_p.R981R|TRPC4_ENST00000447043.1_Silent_p.R835R|TRPC4_ENST00000379679.1_Silent_p.R803R|TRPC4_ENST00000355779.2_Silent_p.R835R|TRPC4_ENST00000379673.2_Silent_p.R827R|TRPC4_ENST00000338947.5_Silent_p.R803R|TRPC4_ENST00000426868.2_3'UTR			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	976	Binds to ITPR1, ITPR2 and ITPR3.|PDZ-binding domain.				axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		AGTATCACAATCTTGTGGTCA	0.403													T|||	154	0.0307508	0.1112	0.0086	5008	,	,		19821	0.0		0.001	False		,,,				2504	0.0				p.R981R		Atlas-SNP	.											.	TRPC4	389	.	0			c.A2943G						PASS	.	T	,,,,,	428,3978	208.5+/-229.5	24,380,1799	118.0	111.0	114.0		2676,2481,2505,2409,2943,2928	-1.3	0.2	13	dbSNP_86	114	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRPC4	NM_001135955.1,NM_001135956.1,NM_001135957.1,NM_001135958.1,NM_003306.1,NM_016179.2	,,,,,	24,387,6092	CC,CT,TT		0.0814,9.714,3.3446	,,,,,	892/894,827/829,835/837,803/805,981/983,976/978	38211046	435,12571	2203	4300	6503	SO:0001819	synonymous_variant	7223	exon11			TCACAATCTTGTG	U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.2928A>G	13.37:g.38211046T>C		102.0	0.0	0		112.0	63.0	0.5625	NM_003306	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Silent	SNP	ENST00000379705.3	37	CCDS9365.1																																																																																			T|0.959;C|0.041	0.041	strong		0.403	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306	
TEX33	339669	hgsc.bcm.edu	37	22	37397876	37397876	+	Splice_Site	SNP	A	A	G	rs148258673	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:37397876A>G	ENST00000405091.2	-	4	741		c.e4+1		TEX33_ENST00000402860.3_Splice_Site|TEX33_ENST00000381821.1_Splice_Site			O43247	TEX33_HUMAN	testis expressed 33																		CTGCTATGACACCTGCTCCTC	0.493													A|||	11	0.00219649	0.0076	0.0014	5008	,	,		21381	0.0		0.0	False		,,,				2504	0.0				.		Atlas-SNP	.											.	TEX33	25	.	0			c.489+2T>C						PASS	.	A	,	62,4344		0,62,2141	86.0	58.0	68.0		,	4.6	1.0	22	dbSNP_134	68	0,8600		0,0,4300	yes	splice-5,splice-5	C22orf33	NM_001163857.1,NM_178552.3	,	0,62,6441	GG,GA,AA		0.0,1.4072,0.4767	,	,	37397876	62,12944	2203	4300	6503	SO:0001630	splice_region_variant	339669	exon4			TATGACACCTGCT	BC042635	CCDS13937.1, CCDS54524.1	22q12.3	2013-10-11	2012-02-16	2012-02-16	ENSG00000185264	ENSG00000185264			28568	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 33"""	C22orf33		22332119	Standard	NM_178552		Approved	MGC35206, EAN57	uc003aqf.3	O43247	OTTHUMG00000150531	ENST00000405091.2:c.489+1T>C	22.37:g.37397876A>G		107.0	0.0	0		101.0	44.0	0.435644	NM_001163857	B1AH46|Q6ICF2|Q8IVQ2|Q9Y4V8	Splice_Site	SNP	ENST00000405091.2	37	CCDS54524.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	A	15.90	2.968886	0.53614	0.014072	0.0	ENSG00000185264	ENST00000402860;ENST00000405091;ENST00000381821	.	.	.	5.68	4.64	0.57946	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.1587	0.37009	0.9146:0.0:0.0854:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C22orf33	35727822	0.995000	0.38212	0.992000	0.48379	0.817000	0.46193	3.503000	0.53340	2.159000	0.67721	0.533000	0.62120	.	A|0.997;G|0.003	0.003	strong		0.493	TEX33-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318778.2	NM_178552	Intron
WDR93	56964	hgsc.bcm.edu	37	15	90281381	90281381	+	Silent	SNP	T	T	C	rs35017767	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90281381T>C	ENST00000268130.7	+	16	1976	c.1875T>C	c.(1873-1875)tgT>tgC	p.C625C	WDR93_ENST00000560294.1_Silent_p.C597C|WDR93_ENST00000444934.2_Silent_p.C342C	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	625					electron transport chain (GO:0022900)		oxidoreductase activity, acting on NAD(P)H (GO:0016651)			NS(1)|breast(3)|endometrium(2)|kidney(4)|large_intestine(5)|liver(2)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	33	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			CAAAAAATTGTACCATTCCTC	0.453													C|||	235	0.0469249	0.1755	0.0043	5008	,	,		17775	0.0		0.0	False		,,,				2504	0.0				p.C625C		Atlas-SNP	.											.	WDR93	63	.	0			c.T1875C						PASS	.	C		662,3738	763.7+/-413.2	44,574,1582	232.0	238.0	236.0		1875	-1.2	0.0	15	dbSNP_126	236	6,8592	818.8+/-406.8	0,6,4293	no	coding-synonymous	WDR93	NM_020212.1		44,580,5875	CC,CT,TT		0.0698,15.0455,5.1393		625/687	90281381	668,12330	2200	4299	6499	SO:0001819	synonymous_variant	56964	exon16			AAATTGTACCATT		CCDS32326.1, CCDS66862.1, CCDS73779.1	15q26.1	2012-11-02						"""WD repeat domain containing"""	26924	protein-coding gene	gene with protein product							Standard	NM_020212		Approved		uc002boj.3	Q6P2C0		ENST00000268130.7:c.1875T>C	15.37:g.90281381T>C		151.0	0.0	0		153.0	90.0	0.588235	NM_020212	Q8N7Y8|Q9NP89	Silent	SNP	ENST00000268130.7	37	CCDS32326.1																																																																																			T|0.955;C|0.045	0.045	strong		0.453	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212	
DOCK8	81704	hgsc.bcm.edu	37	9	328144	328144	+	Silent	SNP	G	G	A	rs35746964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:328144G>A	ENST00000453981.1	+	9	1129	c.1017G>A	c.(1015-1017)ccG>ccA	p.P339P	DOCK8_ENST00000469391.1_Silent_p.P271P|DOCK8_ENST00000432829.2_Silent_p.P271P			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	339					blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		TCACCTACCCGTCCTCAGACA	0.493													G|||	11	0.00219649	0.0083	0.0	5008	,	,		20591	0.0		0.0	False		,,,				2504	0.0				p.P339P		Atlas-SNP	.											DOCK8_ENST00000453981,colon,carcinoma,0,2	DOCK8	401	2	0			c.G1017A						PASS	.	G	,,	41,4365	44.6+/-78.6	0,41,2162	100.0	82.0	88.0		813,813,1017	-8.7	0.6	9	dbSNP_126	88	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	DOCK8	NM_001190458.1,NM_001193536.1,NM_203447.3	,,	0,42,6461	AA,AG,GG		0.0116,0.9305,0.3229	,,	271/2000,271/2032,339/2100	328144	42,12964	2203	4300	6503	SO:0001819	synonymous_variant	81704	exon9			CTACCCGTCCTCA	AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.1017G>A	9.37:g.328144G>A		157.0	0.0	0		146.0	80.0	0.547945	NM_203447	A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Silent	SNP	ENST00000453981.1	37	CCDS6440.2																																																																																			G|0.996;A|0.004	0.004	strong		0.493	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5	XM_036307	
SPATA6L	55064	hgsc.bcm.edu	37	9	4625546	4625546	+	Silent	SNP	C	C	T	rs12338523	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:4625546C>T	ENST00000454239.2	-	7	695	c.450G>A	c.(448-450)cgG>cgA	p.R150R	SPATA6L_ENST00000381890.5_Silent_p.R164R|SPATA6L_ENST00000475086.1_Silent_p.R92R|SPATA6L_ENST00000223517.5_5'UTR|SPATA6L_ENST00000381895.5_Silent_p.R27R			Q8N4H0	SPA6L_HUMAN	spermatogenesis associated 6-like	150																	ATAAAGGCCTCCGTGACTCAT	0.294													T|||	73	0.0145767	0.0499	0.0101	5008	,	,		15547	0.0		0.0	False		,,,				2504	0.0				p.R92R		Atlas-SNP	.											.	SPATA6L	3	.	0			c.G276A						PASS	.	T		130,3480		1,128,1676	62.0	63.0	63.0		276	-1.8	0.0	9	dbSNP_120	63	2,8128		0,2,4063	no	coding-synonymous	C9orf68	NM_001039395.3		1,130,5739	TT,TC,CC		0.0246,3.6011,1.1244		92/335	4625546	132,11608	1805	4065	5870	SO:0001819	synonymous_variant	55064	exon5			AGGCCTCCGTGAC	AK000920	CCDS43785.1, CCDS43785.2	9p24.2	2012-03-15	2012-03-15	2012-03-15	ENSG00000106686	ENSG00000106686			25472	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 68"""	C9orf68			Standard	NM_001039395		Approved	FLJ10058	uc011llz.2	Q8N4H0	OTTHUMG00000019469	ENST00000454239.2:c.450G>A	9.37:g.4625546C>T		78.0	0.0	0		98.0	52.0	0.530612	NM_001039395	B4DIY4|Q5JVJ5|Q8IY90	Silent	SNP	ENST00000454239.2	37																																																																																				C|0.994;T|0.006	0.006	strong		0.294	SPATA6L-202	KNOWN	basic	protein_coding	protein_coding		NM_017985	
CD1B	910	hgsc.bcm.edu	37	1	158299299	158299299	+	Silent	SNP	C	C	T	rs11806249	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158299299C>T	ENST00000368168.3	-	4	854	c.747G>A	c.(745-747)caG>caA	p.Q249Q		NM_001764.2	NP_001755.1	P29016	CD1B_HUMAN	CD1b molecule	249	Ig-like.				antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	cell surface (GO:0009986)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)				breast(2)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	30	all_hematologic(112;0.0378)					TGTCCCCTAGCTGAGTGCCCT	0.612													.|||	67	0.0133786	0.0499	0.0014	5008	,	,		18986	0.0		0.0	False		,,,				2504	0.0				p.Q249Q		Atlas-SNP	.											.	CD1B	78	.	0			c.G747A						PASS	.	C		188,4218	120.0+/-157.7	5,178,2020	140.0	124.0	129.0		747	2.3	0.0	1	dbSNP_120	129	0,8600		0,0,4300	no	coding-synonymous	CD1B	NM_001764.2		5,178,6320	TT,TC,CC		0.0,4.2669,1.4455		249/334	158299299	188,12818	2203	4300	6503	SO:0001819	synonymous_variant	910	exon4			CCCTAGCTGAGTG	M28826	CCDS1176.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158485	ENSG00000158485		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1635	protein-coding gene	gene with protein product		188360	"""CD1B antigen, b polypeptide"", ""CD1b antigen"""	CD1		2447586	Standard	NM_001764		Approved		uc001frx.3	P29016	OTTHUMG00000017513	ENST00000368168.3:c.747G>A	1.37:g.158299299C>T		286.0	0.0	0		325.0	151.0	0.464615	NM_001764	Q5TDK9|Q5TDL0|Q9UMM2	Silent	SNP	ENST00000368168.3	37	CCDS1176.1																																																																																			C|0.984;T|0.016	0.016	strong		0.612	CD1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046350.2	NM_001764	
ZFYVE19	84936	hgsc.bcm.edu	37	15	41105979	41105979	+	Silent	SNP	C	C	G	rs116749518	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:41105979C>G	ENST00000355341.4	+	9	1680	c.1179C>G	c.(1177-1179)ccC>ccG	p.P393P	ZFYVE19_ENST00000570108.1_Silent_p.P370P|ZFYVE19_ENST00000299173.10_Silent_p.P325P|ZFYVE19_ENST00000564258.1_Silent_p.P218P|ZFYVE19_ENST00000336455.5_Silent_p.P383P	NM_001077268.1	NP_001070736.1	Q96K21	ANCHR_HUMAN	zinc finger, FYVE domain containing 19	393					abscission (GO:0009838)|cell division (GO:0051301)|cytokinesis checkpoint (GO:0031565)|negative regulation of cytokinesis (GO:0032466)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|midbody (GO:0030496)	phosphatidylinositol-3-phosphate binding (GO:0032266)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	9		all_cancers(109;3.31e-18)|all_epithelial(112;2.33e-15)|Lung NSC(122;5.34e-11)|all_lung(180;1.33e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;2.76e-05)|COAD - Colon adenocarcinoma(120;0.151)|BRCA - Breast invasive adenocarcinoma(123;0.164)		CTTCTCGACCCTGGACGCAAC	0.612													C|||	18	0.00359425	0.0136	0.0	5008	,	,		18843	0.0		0.0	False		,,,				2504	0.0				p.P393P		Atlas-SNP	.											.	ZFYVE19	31	.	0			c.C1179G						PASS	.	C		33,3971		1,31,1970	49.0	54.0	52.0		1179	1.1	0.0	15	dbSNP_132	52	1,8315		0,1,4157	no	coding-synonymous	ZFYVE19	NM_001077268.1		1,32,6127	GG,GC,CC		0.012,0.8242,0.276		393/472	41105979	34,12286	2002	4158	6160	SO:0001819	synonymous_variant	84936	exon9			TCGACCCTGGACG	AK027746	CCDS42025.1, CCDS58353.1, CCDS58354.1, CCDS58355.1	15q14	2008-05-02				ENSG00000166140		"""Zinc fingers, FYVE domain containing"""	20758	protein-coding gene	gene with protein product							Standard	NM_001077268		Approved	FLJ14840	uc031qrk.1	Q96K21		ENST00000355341.4:c.1179C>G	15.37:g.41105979C>G		90.0	0.0	0		100.0	51.0	0.51	NM_001077268	B3KVB2|C9JNF4|H3BUF9|Q86WC2|Q8WU96	Silent	SNP	ENST00000355341.4	37	CCDS42025.1																																																																																			C|0.997;G|0.003	0.003	strong		0.612	ZFYVE19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418996.1	NM_032850	
BBS9	27241	hgsc.bcm.edu	37	7	33545253	33545253	+	Missense_Mutation	SNP	A	A	G	rs140882212		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:33545253A>G	ENST00000242067.6	+	20	2815	c.2294A>G	c.(2293-2295)gAa>gGa	p.E765G	BBS9_ENST00000354265.4_Missense_Mutation_p.E730G|BBS9_ENST00000396127.2_Missense_Mutation_p.E730G|BBS9_ENST00000355070.2_Missense_Mutation_p.E760G|BBS9_ENST00000350941.3_Missense_Mutation_p.E725G	NM_198428.2	NP_940820.1	Q3SYG4	PTHB1_HUMAN	Bardet-Biedl syndrome 9	765	Interaction with LZTL1.				cilium assembly (GO:0042384)|fat cell differentiation (GO:0045444)|protein transport (GO:0015031)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	BBSome (GO:0034464)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)			BBS9/PKD1L1(2)	NS(1)|autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	50			GBM - Glioblastoma multiforme(11;0.0894)			GACACTCAAGAATTGGTAAGG	0.468									Bardet-Biedl syndrome				A|||	1	0.000199681	0.0008	0.0	5008	,	,		17434	0.0		0.0	False		,,,				2504	0.0				p.E765G		Atlas-SNP	.											.	BBS9	194	.	0			c.A2294G						PASS	.	A	GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU	4,4402	6.2+/-15.9	0,4,2199	38.0	38.0	38.0		2189,2279,2174,2294	5.6	1.0	7	dbSNP_134	38	0,8600		0,0,4300	yes	missense,missense,missense,missense	BBS9	NM_001033604.1,NM_001033605.1,NM_014451.3,NM_198428.2	98,98,98,98	0,4,6499	GG,GA,AA		0.0,0.0908,0.0308	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	730/853,760/883,725/848,765/888	33545253	4,13002	2203	4300	6503	SO:0001583	missense	27241	exon20	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	CTCAAGAATTGGT		CCDS5441.1, CCDS34618.1, CCDS43566.1, CCDS47572.1	7p14	2014-06-17			ENSG00000122507	ENSG00000122507			30000	protein-coding gene	gene with protein product	"""parathyroid hormone responsive B1 gene"""	607968				16380913, 10221542	Standard	XM_005249701		Approved	B1, PTHB1	uc003tdn.1	Q3SYG4	OTTHUMG00000128659	ENST00000242067.6:c.2294A>G	7.37:g.33545253A>G	ENSP00000242067:p.Glu765Gly	41.0	0.0	0		59.0	34.0	0.576271	NM_198428	E9PDC9|P78514|Q7KYS6|Q7KYS7|Q8N570|Q99844|Q99854|Q9Y699|Q9Y6A0	Missense_Mutation	SNP	ENST00000242067.6	37	CCDS43566.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	16.89	3.246980	0.59103	9.08E-4	0.0	ENSG00000122507	ENST00000242067;ENST00000350941;ENST00000396127;ENST00000355070;ENST00000354265;ENST00000396132	T;T;T;T;T	0.15952	2.38;2.38;2.38;2.38;2.38	5.61	5.61	0.85477	.	0.060219	0.64402	D	0.000004	T	0.24198	0.0586	L	0.46741	1.465	0.80722	D	1	P;P;D;P;P	0.54601	0.877;0.929;0.967;0.929;0.923	P;P;P;P;P	0.49252	0.501;0.501;0.604;0.501;0.501	T	0.00684	-1.1611	10	0.45353	T	0.12	-25.845	15.0016	0.71476	1.0:0.0:0.0:0.0	.	765;725;760;730;765	Q3SYG4-3;Q3SYG4-2;E9PDC9;Q3SYG4-4;Q3SYG4	.;.;.;.;PTHB1_HUMAN	G	765;725;730;760;730;765	ENSP00000242067:E765G;ENSP00000313122:E725G;ENSP00000379433:E730G;ENSP00000347182:E760G;ENSP00000346214:E730G	ENSP00000242067:E765G	E	+	2	0	BBS9	33511778	1.000000	0.71417	0.990000	0.47175	0.956000	0.61745	7.327000	0.79147	2.146000	0.66826	0.459000	0.35465	GAA	A|1.000;G|0.000	0.000	strong		0.468	BBS9-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329064.1		
XYLT2	64132	hgsc.bcm.edu	37	17	48434008	48434008	+	Missense_Mutation	SNP	C	C	T	rs151294421	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48434008C>T	ENST00000017003.2	+	8	1668	c.1619C>T	c.(1618-1620)aCc>aTc	p.T540I	XYLT2_ENST00000507602.1_Missense_Mutation_p.T540I	NM_022167.2	NP_071450.2	Q9H1B5	XYLT2_HUMAN	xylosyltransferase II	540					chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			endometrium(2)|kidney(2)|large_intestine(4)|pancreas(1)|prostate(2)|urinary_tract(1)	12	Breast(11;7.18e-19)					TGGGAGAACACCTACGACGCG	0.627													C|||	21	0.00419329	0.0129	0.0043	5008	,	,		16601	0.0		0.0	False		,,,				2504	0.001				p.T540I		Atlas-SNP	.											.	XYLT2	51	.	0			c.C1619T						PASS	.	C	ILE/THR	52,4354	51.6+/-87.1	0,52,2151	67.0	71.0	70.0		1619	-0.0	0.6	17	dbSNP_134	70	0,8600		0,0,4300	yes	missense	XYLT2	NM_022167.2	89	0,52,6451	TT,TC,CC		0.0,1.1802,0.3998	benign	540/866	48434008	52,12954	2203	4300	6503	SO:0001583	missense	64132	exon8			AGAACACCTACGA	AJ277442	CCDS11563.1	17q21.33	2013-02-25			ENSG00000015532	ENSG00000015532	2.4.2.26		15517	protein-coding gene	gene with protein product	"""protein xylosyltransferase 2"""	608125				11099377	Standard	NM_022167		Approved	XT-II, PXYLT2	uc002iqo.3	Q9H1B5	OTTHUMG00000162057	ENST00000017003.2:c.1619C>T	17.37:g.48434008C>T	ENSP00000017003:p.Thr540Ile	35.0	0.0	0		21.0	9.0	0.428571	NM_022167	Q6UY41|Q86V00	Missense_Mutation	SNP	ENST00000017003.2	37	CCDS11563.1	4	0.0018315018315018315	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	C	1.807	-0.475727	0.04414	0.011802	0.0	ENSG00000015532	ENST00000017003;ENST00000507602	T;T	0.38077	1.16;1.16	4.89	-0.0431	0.13861	.	0.659654	0.15078	N	0.281852	T	0.09730	0.0239	N	0.03608	-0.345	0.24112	N	0.995837	B	0.02656	0.0	B	0.04013	0.001	T	0.29792	-1.0000	10	0.15952	T	0.53	-8.2731	9.014	0.36159	0.0:0.3312:0.0:0.6688	.	540	Q9H1B5	XYLT2_HUMAN	I	540	ENSP00000017003:T540I;ENSP00000426501:T540I	ENSP00000017003:T540I	T	+	2	0	XYLT2	45789007	0.101000	0.21875	0.586000	0.28679	0.021000	0.10359	1.227000	0.32576	0.116000	0.18110	-0.253000	0.11424	ACC	C|0.996;T|0.004	0.004	strong		0.627	XYLT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367046.1	NM_022167	
ITPRIPL2	162073	hgsc.bcm.edu	37	16	19126578	19126578	+	Silent	SNP	T	T	C	rs114869688	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:19126578T>C	ENST00000381440.3	+	1	1325	c.795T>C	c.(793-795)acT>acC	p.T265T	CTD-2349B8.1_ENST00000564808.2_Intron	NM_001034841.3	NP_001030013.1	Q3MIP1	IPIL2_HUMAN	inositol 1,4,5-trisphosphate receptor interacting protein-like 2	265						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						CCTTGGCCACTGTGCGTTACA	0.642											OREG0023657	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	16	0.00319489	0.0121	0.0	5008	,	,		17325	0.0		0.0	False		,,,				2504	0.0				p.T265T		Atlas-SNP	.											ITPRIPL2,colon,carcinoma,+1,1	ITPRIPL2	40	1	0			c.T795C						PASS	.	T		72,4322	63.5+/-100.7	0,72,2125	94.0	95.0	95.0		795	-9.6	0.3	16	dbSNP_132	95	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ITPRIPL2	NM_001034841.3		0,73,6424	CC,CT,TT		0.0116,1.6386,0.5618		265/536	19126578	73,12921	2197	4300	6497	SO:0001819	synonymous_variant	162073	exon1			GGCCACTGTGCGT		CCDS32395.1	16p12.3	2011-04-28	2011-04-28		ENSG00000205730	ENSG00000205730			27257	protein-coding gene	gene with protein product			"""inositol 1,4,5-triphosphate receptor interacting protein-like 2"""				Standard	NM_001034841		Approved	FLJ22994, MGC126798, MGC126800, LOC162073	uc002dfu.4	Q3MIP1		ENST00000381440.3:c.795T>C	16.37:g.19126578T>C		106.0	0.0	0	730	88.0	38.0	0.431818	NM_001034841		Silent	SNP	ENST00000381440.3	37	CCDS32395.1																																																																																			T|0.995;C|0.005	0.005	strong		0.642	ITPRIPL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435827.3	NM_001034841	
VRK2	7444	hgsc.bcm.edu	37	2	58350340	58350340	+	Silent	SNP	T	T	C	rs17049354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:58350340T>C	ENST00000435505.2	+	11	1393	c.648T>C	c.(646-648)ttT>ttC	p.F216F	VRK2_ENST00000417641.2_Silent_p.F216F|VRK2_ENST00000340157.4_Silent_p.F216F|VRK2_ENST00000412104.2_Silent_p.F216F|VRK2_ENST00000440705.2_Silent_p.F193F			Q86Y07	VRK2_HUMAN	vaccinia related kinase 2	216	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to oxidative stress (GO:0034599)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interleukin-1-mediated signaling pathway (GO:2000659)|regulation of MAPK cascade (GO:0043408)|viral process (GO:0016032)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(4)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	24						CAATAGAGTTTACCAGCTTGG	0.388													T|||	210	0.0419329	0.152	0.0115	5008	,	,		18926	0.0		0.001	False		,,,				2504	0.0				p.F216F		Atlas-SNP	.											.	VRK2	46	.	0			c.T648C						PASS	.	T	,,,,	501,3905	232.3+/-245.9	34,433,1736	108.0	105.0	106.0		648,648,579,648,648	1.8	1.0	2	dbSNP_123	106	8,8592	4.3+/-15.6	0,8,4292	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	VRK2	NM_001130480.2,NM_001130481.2,NM_001130482.2,NM_001130483.2,NM_006296.5	,,,,	34,441,6028	CC,CT,TT		0.093,11.3709,3.9136	,,,,	216/509,216/509,193/486,216/397,216/509	58350340	509,12497	2203	4300	6503	SO:0001819	synonymous_variant	7444	exon8			AGAGTTTACCAGC	AK058199	CCDS1859.1, CCDS46291.1, CCDS46292.1	2p16.1	2008-05-15			ENSG00000028116	ENSG00000028116			12719	protein-coding gene	gene with protein product		602169					Standard	NM_001130480		Approved		uc002rzv.3	Q86Y07	OTTHUMG00000129348	ENST00000435505.2:c.648T>C	2.37:g.58350340T>C		76.0	0.0	0		72.0	38.0	0.527778	NM_001130480	B4DKL0|D6W5D4|D6W5D6|Q49AK9|Q53EU9|Q53S39|Q53S77|Q53TU1|Q86Y08|Q86Y09|Q86Y10|Q86Y11|Q86Y12|Q8IXI5|Q99987	Silent	SNP	ENST00000435505.2	37	CCDS1859.1																																																																																			T|0.962;C|0.038	0.038	strong		0.388	VRK2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325304.2	NM_006296	
FGF12	2257	hgsc.bcm.edu	37	3	192078253	192078253	+	Missense_Mutation	SNP	T	T	C	rs142373936		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:192078253T>C	ENST00000454309.2	-	2	1099	c.274A>G	c.(274-276)Acc>Gcc	p.T92A	FGF12_ENST00000430714.1_Intron|FGF12_ENST00000450716.1_Missense_Mutation_p.T30A|FGF12_ENST00000264730.3_Missense_Mutation_p.T30A|FGF12_ENST00000445105.2_Missense_Mutation_p.T30A	NM_021032.4	NP_066360.1	P61328	FGF12_HUMAN	fibroblast growth factor 12	92					adult locomotory behavior (GO:0008344)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell-cell signaling (GO:0007267)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|JNK cascade (GO:0007254)|negative regulation of cation channel activity (GO:2001258)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|positive regulation of sodium ion transport (GO:0010765)|regulation of membrane depolarization (GO:0003254)|regulation of sodium ion transmembrane transport (GO:1902305)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	extracellular space (GO:0005615)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|heparin binding (GO:0008201)|ion channel binding (GO:0044325)|sodium channel regulator activity (GO:0017080)			endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	30	all_cancers(143;1.72e-08)|Ovarian(172;0.0634)|Breast(254;0.247)	Lung NSC(153;0.21)	LUSC - Lung squamous cell carcinoma(58;5.45e-06)|Lung(62;6.17e-06)	GBM - Glioblastoma multiforme(46;0.00032)		CCATCAATGGTACCATCTGGG	0.408													T|||	1	0.000199681	0.0008	0.0	5008	,	,		19416	0.0		0.0	False		,,,				2504	0.0				p.T92A		Atlas-SNP	.											.	FGF12	88	.	0			c.A274G						PASS	.	T	ALA/THR,ALA/THR	1,4405	2.1+/-5.4	0,1,2202	176.0	150.0	159.0		88,274	3.0	1.0	3	dbSNP_134	159	0,8600		0,0,4300	no	missense,missense	FGF12	NM_004113.5,NM_021032.4	58,58	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	benign,benign	30/182,92/244	192078253	1,13005	2203	4300	6503	SO:0001583	missense	2257	exon2			CAATGGTACCATC	U66197	CCDS3301.1, CCDS46983.1	3q28	2008-07-18			ENSG00000114279	ENSG00000114279			3668	protein-coding gene	gene with protein product	"""fibroblast growth factor 12B"", ""fibroblast growth factor homologous factor 1"", ""myocyte-activating factor"", ""fibroblast growth factor FGF-12b"""	601513		FGF12B		8790420, 9345906	Standard	NM_021032		Approved	FHF1	uc003fsx.3	P61328	OTTHUMG00000156132	ENST00000454309.2:c.274A>G	3.37:g.192078253T>C	ENSP00000413496:p.Thr92Ala	214.0	0.0	0		213.0	92.0	0.431925	NM_021032	B2R6B7|B2R976|O35339|P70376|Q8TBG5|Q92912|Q93001	Missense_Mutation	SNP	ENST00000454309.2	37	CCDS3301.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	13.05	2.121112	0.37436	2.27E-4	0.0	ENSG00000114279	ENST00000264730;ENST00000392454;ENST00000445105;ENST00000454309;ENST00000450716;ENST00000448795;ENST00000418610	D;D;D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53;-1.53;-1.53	5.53	3.03	0.35002	.	0.136032	0.64402	N	0.000002	T	0.70657	0.3249	L	0.48935	1.535	0.47441	D	0.999428	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.64846	-0.6311	10	0.42905	T	0.14	.	6.4797	0.22055	0.1389:0.0758:0.0:0.7853	.	30;92	P61328-2;P61328	.;FGF12_HUMAN	A	30;30;30;92;30;6;30	ENSP00000264730:T30A;ENSP00000393686:T30A;ENSP00000413496:T92A;ENSP00000397635:T30A;ENSP00000412904:T6A;ENSP00000395517:T30A	ENSP00000264730:T30A	T	-	1	0	FGF12	193560947	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.860000	0.39428	0.953000	0.37825	0.482000	0.46254	ACC	T|1.000;C|0.000	0.000	strong		0.408	FGF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343160.1	NM_021032	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110491801	110491801	+	Silent	SNP	T	T	C	rs116618272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:110491801T>C	ENST00000378402.5	+	54	9215	c.9111T>C	c.(9109-9111)ttT>ttC	p.F3037F		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3037	G8 2. {ECO:0000255|PROSITE- ProRule:PRU00817}.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			ATGATTCTTTTTGGCAATCAT	0.328										HNSCC(38;0.096)			T|||	39	0.00778754	0.0287	0.0014	5008	,	,		20916	0.0		0.0	False		,,,				2504	0.0				p.F3037F		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.T9111C						PASS	.	T		56,3594		1,54,1770	127.0	111.0	116.0		9111	-2.1	1.0	8	dbSNP_132	116	0,8152		0,0,4076	no	coding-synonymous	PKHD1L1	NM_177531.4		1,54,5846	CC,CT,TT		0.0,1.5342,0.4745		3037/4244	110491801	56,11746	1825	4076	5901	SO:0001819	synonymous_variant	93035	exon54			TTCTTTTTGGCAA	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.9111T>C	8.37:g.110491801T>C		89.0	0.0	0		87.0	40.0	0.45977	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	37	CCDS47911.1																																																																																			T|0.993;C|0.007	0.007	strong		0.328	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
KRTAP9-2	83899	hgsc.bcm.edu	37	17	39383351	39383351	+	Missense_Mutation	SNP	T	T	C	rs146532415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39383351T>C	ENST00000377721.3	+	1	452	c.445T>C	c.(445-447)Tgc>Cgc	p.C149R	KRTAP9-2_ENST00000455970.2_Missense_Mutation_p.C133R	NM_031961.2	NP_114167.2	Q9BYQ4	KRA92_HUMAN	keratin associated protein 9-2	149	17 X 5 AA repeats of C-C-[RQVSGE]-[SPTQ]- [TASP].					keratin filament (GO:0045095)				large_intestine(1)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			CCGCCCAGCCTGCTGTGAGAC	0.607													.|||	58	0.0115815	0.0424	0.0029	5008	,	,		19288	0.0		0.0	False		,,,				2504	0.0				p.C149R		Atlas-SNP	.											.	KRTAP9-2	24	.	0			c.T445C						PASS	.	T	ARG/CYS	126,4166		3,120,2023	19.0	21.0	20.0		445	1.8	0.0	17	dbSNP_134	20	0,8406		0,0,4203	no	missense	KRTAP9-2	NM_031961.2	180	3,120,6226	CC,CT,TT		0.0,2.9357,0.9923	probably-damaging	149/175	39383351	126,12572	2146	4203	6349	SO:0001583	missense	83899	exon1			CCAGCCTGCTGTG	AJ406946	CCDS32651.1	17q21.2	2013-06-25			ENSG00000239886	ENSG00000239886		"""Keratin associated proteins"""	16926	protein-coding gene	gene with protein product						11279113	Standard	NM_031961		Approved	KAP9.2	uc002hwf.3	Q9BYQ4	OTTHUMG00000133609	ENST00000377721.3:c.445T>C	17.37:g.39383351T>C	ENSP00000366950:p.Cys149Arg	336.0	1.0	0.00297619		400.0	149.0	0.3725	NM_031961	Q17RK8|Q2TB15|Q6ISF6	Missense_Mutation	SNP	ENST00000377721.3	37	CCDS32651.1	.	.	.	.	.	.	.	.	.	.	.	19.02	3.746233	0.69418	0.029357	0.0	ENSG00000239886	ENST00000377721;ENST00000455970	T;T	0.05139	4.92;3.49	2.89	1.78	0.24846	.	.	.	.	.	T	0.02649	0.0080	M	0.74389	2.26	0.52501	D	0.999959	B	0.25904	0.137	B	0.23852	0.049	T	0.08806	-1.0704	9	0.87932	D	0	.	6.5335	0.22339	0.0:0.1318:0.0:0.8682	.	149	Q9BYQ4	KRA92_HUMAN	R	149;133	ENSP00000366950:C149R;ENSP00000398325:C133R	ENSP00000366950:C149R	C	+	1	0	KRTAP9-2	36636877	0.403000	0.25319	0.010000	0.14722	0.911000	0.54048	0.513000	0.22770	0.325000	0.23359	0.248000	0.18094	TGC	T|0.993;C|0.007	0.007	strong		0.607	KRTAP9-2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257717.1		
CRYZ	1429	hgsc.bcm.edu	37	1	75175865	75175865	+	Missense_Mutation	SNP	C	C	T	rs17095822	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:75175865C>T	ENST00000340866.5	-	6	634	c.547G>A	c.(547-549)Gag>Aag	p.E183K	CRYZ_ENST00000492102.1_5'Flank|CRYZ_ENST00000370871.3_Missense_Mutation_p.E183K|CRYZ_ENST00000370872.3_Missense_Mutation_p.E46K|CRYZ_ENST00000417775.1_Missense_Mutation_p.E183K	NM_001889.3	NP_001880.2	Q08257	QOR_HUMAN	crystallin, zeta (quinone reductase)	183			E -> K (in dbSNP:rs17095822).		protein homotetramerization (GO:0051289)|visual perception (GO:0007601)|xenobiotic catabolic process (GO:0042178)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	mRNA 3'-UTR binding (GO:0003730)|NADPH binding (GO:0070402)|NADPH:quinone reductase activity (GO:0003960)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)	10					Dicoumarol(DB00266)	TGTCCTTCCTCAGTACCAGCA	0.353													C|||	105	0.0209665	0.0756	0.0043	5008	,	,		15672	0.001		0.0	False		,,,				2504	0.001				p.E183K		Atlas-SNP	.											.	CRYZ	28	.	0			c.G547A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	244,4162	141.9+/-177.2	7,230,1966	78.0	79.0	79.0		547,547,136,547	4.6	1.0	1	dbSNP_123	79	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense,missense	CRYZ	NM_001130042.1,NM_001130043.1,NM_001134759.1,NM_001889.3	56,56,56,56	7,233,6263	TT,TC,CC		0.0349,5.5379,1.8991	benign,benign,benign,benign	183/330,183/296,46/193,183/330	75175865	247,12759	2203	4300	6503	SO:0001583	missense	1429	exon6			CTTCCTCAGTACC		CCDS665.1, CCDS44162.1, CCDS44163.1	1p31.1	2013-02-14			ENSG00000116791	ENSG00000116791			2419	protein-coding gene	gene with protein product		123691					Standard	NM_001889		Approved		uc001dgj.3	Q08257	OTTHUMG00000009620	ENST00000340866.5:c.547G>A	1.37:g.75175865C>T	ENSP00000339399:p.Glu183Lys	229.0	0.0	0		303.0	145.0	0.478548	NM_001130043	A6NN60|D3DQ76|Q53FT0|Q59EU7|Q5HYE7|Q6NSK9	Missense_Mutation	SNP	ENST00000340866.5	37	CCDS665.1	38	0.0173992673992674	37	0.07520325203252033	1	0.0027624309392265192	0	0.0	0	0.0	C	7.833	0.720290	0.15372	0.055379	3.49E-4	ENSG00000116791	ENST00000340866;ENST00000370872;ENST00000417775;ENST00000370871;ENST00000370870;ENST00000441120	T;T;T;T;T;T	0.32272	3.43;3.43;3.43;1.46;3.43;3.43	5.54	4.63	0.57726	Alcohol dehydrogenase, C-terminal (1);NAD(P)-binding domain (1);	0.170547	0.48767	D	0.000162	T	0.18173	0.0436	L	0.54863	1.705	0.42476	D	0.992842	B;B;B	0.27068	0.141;0.167;0.029	B;B;B	0.35114	0.051;0.196;0.027	T	0.05084	-1.0907	10	0.39692	T	0.17	.	9.917	0.41442	0.0:0.7871:0.1388:0.074	rs17095822;rs56573849;rs17095822	46;183;183	Q5HYE7;A6NN60;Q08257	.;.;QOR_HUMAN	K	183;46;183;183;183;183	ENSP00000339399:E183K;ENSP00000359909:E46K;ENSP00000399805:E183K;ENSP00000359908:E183K;ENSP00000359907:E183K;ENSP00000404289:E183K	ENSP00000339399:E183K	E	-	1	0	CRYZ	74948453	0.995000	0.38212	0.965000	0.40720	0.170000	0.22686	2.685000	0.46959	1.464000	0.47987	0.563000	0.77884	GAG	C|0.979;T|0.021	0.021	strong		0.353	CRYZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026514.1		
CYP4F12	66002	hgsc.bcm.edu	37	19	15794411	15794411	+	Silent	SNP	C	C	T	rs61731191	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15794411C>T	ENST00000550308.1	+	7	1136	c.756C>T	c.(754-756)gaC>gaT	p.D252D	CYP4F12_ENST00000324632.10_Silent_p.D252D	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	252					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	TCTCCCATGACGGGCGGCGCT	0.557													.|||	88	0.0175719	0.0635	0.0043	5008	,	,		21374	0.0		0.001	False		,,,				2504	0.0				p.D252D		Atlas-SNP	.											.	CYP4F12	89	.	0			c.C756T						PASS	.	C		286,4104		0,286,1909	76.0	78.0	77.0		756	-4.9	0.0	19	dbSNP_129	77	4,8584		0,4,4290	yes	coding-synonymous	CYP4F12	NM_023944.3		0,290,6199	TT,TC,CC		0.0466,6.5148,2.2346		252/525	15794411	290,12688	2195	4294	6489	SO:0001819	synonymous_variant	66002	exon7			CCATGACGGGCGG	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.756C>T	19.37:g.15794411C>T		140.0	0.0	0		210.0	58.0	0.27619	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Silent	SNP	ENST00000550308.1	37	CCDS42517.1																																																																																			C|0.985;T|0.015	0.015	strong		0.557	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
SEL1L3	23231	hgsc.bcm.edu	37	4	25849329	25849329	+	Missense_Mutation	SNP	T	T	C	rs16877661	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:25849329T>C	ENST00000399878.3	-	2	442	c.320A>G	c.(319-321)cAg>cGg	p.Q107R	SEL1L3_ENST00000502949.1_5'UTR|SEL1L3_ENST00000513364.1_Intron|SEL1L3_ENST00000264868.5_Missense_Mutation_p.Q72R	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	107			Q -> R (in dbSNP:rs16877661).			integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						AACACAAGGCTGAGAGCATAA	0.408													T|||	106	0.0211661	0.0779	0.0043	5008	,	,		20619	0.0		0.0	False		,,,				2504	0.0				p.Q107R		Atlas-SNP	.											.	SEL1L3	62	.	0			c.A320G						PASS	.	T	ARG/GLN	216,3516		6,204,1656	116.0	105.0	108.0		320	5.2	1.0	4	dbSNP_123	108	2,8224		0,2,4111	yes	missense	SEL1L3	NM_015187.3	43	6,206,5767	CC,CT,TT		0.0243,5.7878,1.823	benign	107/1133	25849329	218,11740	1866	4113	5979	SO:0001583	missense	23231	exon2			CAAGGCTGAGAGC	BC009945	CCDS47037.1, CCDS75113.1	4p15.2	2009-09-24			ENSG00000091490	ENSG00000091490			29108	protein-coding gene	gene with protein product	"""KIAA0746 protein"""					9872452	Standard	XM_005248143		Approved	KIAA0746	uc003gru.4	Q68CR1	OTTHUMG00000160331	ENST00000399878.3:c.320A>G	4.37:g.25849329T>C	ENSP00000382767:p.Gln107Arg	107.0	0.0	0		103.0	52.0	0.504854	NM_015187	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Missense_Mutation	SNP	ENST00000399878.3	37	CCDS47037.1	35	0.016025641025641024	32	0.06504065040650407	3	0.008287292817679558	0	0.0	0	0.0	T	12.92	2.082924	0.36758	0.057878	2.43E-4	ENSG00000091490	ENST00000399878;ENST00000264868	T;T	0.11712	2.75;2.76	5.25	5.25	0.73442	.	0.355245	0.29980	N	0.010710	T	0.00666	0.0022	L	0.38531	1.155	0.80722	D	1	B	0.16396	0.017	B	0.15870	0.014	T	0.18745	-1.0327	10	0.59425	D	0.04	-16.01	9.7021	0.40194	0.0:0.0776:0.0:0.9224	rs16877661;rs52796481;rs16877661	107	Q68CR1	SE1L3_HUMAN	R	107;72	ENSP00000382767:Q107R;ENSP00000264868:Q72R	ENSP00000264868:Q72R	Q	-	2	0	SEL1L3	25458427	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	3.246000	0.51414	1.995000	0.58328	0.449000	0.29647	CAG	T|0.984;C|0.016	0.016	strong		0.408	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187	
HELT	391723	hgsc.bcm.edu	37	4	185940196	185940196	+	Intron	SNP	A	A	T	rs370662812		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:185940196A>T	ENST00000515777.1	+	1	115				HELT_ENST00000505610.1_Intron|HELT_ENST00000338875.4_Silent_p.A38A			A6NFD8	HELT_HUMAN	helt bHLH transcription factor						central nervous system development (GO:0007417)|GABAergic neuron differentiation in basal ganglia (GO:0021858)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|suckling behavior (GO:0001967)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(3)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(2)	14		all_lung(41;9.65e-12)|Lung NSC(41;1.64e-11)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;8.92e-26)|Epithelial(43;3.02e-23)|OV - Ovarian serous cystadenocarcinoma(60;2.59e-11)|Colorectal(24;4.79e-05)|BRCA - Breast invasive adenocarcinoma(30;7.72e-05)|GBM - Glioblastoma multiforme(59;0.000274)|COAD - Colon adenocarcinoma(29;0.000362)|STAD - Stomach adenocarcinoma(60;0.000756)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.155)		GACCGATGGCAGGGAAGTGCC	0.602																																					p.A38A		Atlas-SNP	.											.	HELT	34	.	0			c.A114T						PASS	.	A		0,4406		0,0,2203	75.0	70.0	72.0		114	-2.8	0.0	4		72	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	HELT	NM_001029887.1		0,1,6502	TT,TA,AA		0.0116,0.0,0.0077		38/328	185940196	1,13005	2203	4300	6503	SO:0001627	intron_variant	391723	exon1			GATGGCAGGGAAG	BC144567	CCDS75214.1, CCDS75215.1	4q35.1	2014-07-17	2011-09-12		ENSG00000187821	ENSG00000187821		"""Basic helix-loop-helix proteins"""	33783	protein-coding gene	gene with protein product	"""megane bHLH factor"", ""HES-like"""		"""Hey-like transcription factor (zebrafish)"", ""HES/HEY-like transcription factor"""			14764602, 17611227	Standard	XM_005262989		Approved	HESL, HCM1228, Mgn, bHLHb44, MEGANE	uc011ckq.2	A6NFD8	OTTHUMG00000160484	ENST00000515777.1:c.27+87A>T	4.37:g.185940196A>T		112.0	0.0	0		114.0	60.0	0.526316	NM_001029887	B2RTS5|B7ZMI7|B7ZMI8	Silent	SNP	ENST00000515777.1	37																																																																																				.	.	weak		0.602	HELT-002	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000360792.1	NM_001300781	
MPZL3	196264	hgsc.bcm.edu	37	11	118100634	118100634	+	Splice_Site	SNP	T	T	A	rs7105729	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:118100634T>A	ENST00000278949.4	-	6	738	c.683A>T	c.(682-684)gAt>gTt	p.D228V	MPZL3_ENST00000527472.1_Splice_Site_p.D216V|MPZL3_ENST00000525386.1_Splice_Site_p.I47F			Q6UWV2	MPZL3_HUMAN	myelin protein zero-like 3	228			D -> V (in dbSNP:rs7105729).		cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|hair cycle (GO:0042633)	integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(1)|large_intestine(1)|lung(2)|stomach(2)|upper_aerodigestive_tract(1)	8	all_hematologic(175;0.046)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;3.28e-05)		ATAGTCTGAATCCTGGAGGGA	0.453													T|||	223	0.0445288	0.1528	0.0274	5008	,	,		19501	0.0		0.002	False		,,,				2504	0.0				p.D228V		Atlas-SNP	.											.	MPZL3	22	.	0			c.A683T						PASS	.	T	VAL/ASP	613,3787	268.6+/-268.5	54,505,1641	101.0	93.0	96.0		683	5.8	1.0	11	dbSNP_116	96	7,8585	6.4+/-24.3	0,7,4289	yes	missense-near-splice	MPZL3	NM_198275.1	152	54,512,5930	AA,AT,TT		0.0815,13.9318,4.7722	benign	228/236	118100634	620,12372	2200	4296	6496	SO:0001630	splice_region_variant	196264	exon6			TCTGAATCCTGGA	AK095399	CCDS8392.1, CCDS66241.1	11q23.3	2013-01-11			ENSG00000160588	ENSG00000160588		"""Immunoglobulin superfamily / V-set domain containing"""	27279	protein-coding gene	gene with protein product		611707				17273165	Standard	NM_198275		Approved		uc001psm.3	Q6UWV2	OTTHUMG00000166966	ENST00000278949.4:c.682-1A>T	11.37:g.118100634T>A		69.0	0.0	0		74.0	49.0	0.662162	NM_198275	A8K025|B4DLD5|B4E2I8	Missense_Mutation	SNP	ENST00000278949.4	37	CCDS8392.1	92|92	0.04212454212454213|0.04212454212454213	81|81	0.16463414634146342|0.16463414634146342	11|11	0.03038674033149171|0.03038674033149171	0|0	0.0|0.0	0|0	0.0|0.0	T|T	19.48|19.48	3.834812|3.834812	0.71373|0.71373	0.139318|0.139318	8.15E-4|8.15E-4	ENSG00000160588|ENSG00000160588	ENST00000278949;ENST00000527472|ENST00000525386	D;D|.	0.96651|.	-3.93;-4.08|.	5.78|5.78	5.78|5.78	0.91487|0.91487	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.00271|0.00271	0.0008|0.0008	L|L	0.34521|0.34521	1.04|1.04	0.09310|0.09310	P|P	0.9999999999999915|0.9999999999999915	P;P|.	0.47191|.	0.693;0.891|.	P;P|.	0.45681|.	0.49;0.49|.	T|T	0.11792|0.11792	-1.0573|-1.0573	9|5	0.87932|0.41790	D|T	0|0.15	.|.	12.5017|12.5017	0.55960|0.55960	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs7105729;rs52792812;rs7105729|rs7105729;rs52792812;rs7105729	216;228|.	B4E2I8;Q6UWV2|.	.;MPZL3_HUMAN|.	V|F	228;216|47	ENSP00000278949:D228V;ENSP00000432106:D216V|.	ENSP00000278949:D228V|ENSP00000434636:I47F	D|I	-|-	2|1	0|0	MPZL3|MPZL3	117605844|117605844	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.873000|0.873000	0.50193|0.50193	4.093000|4.093000	0.57714|0.57714	2.215000|2.215000	0.71742|0.71742	0.460000|0.460000	0.39030|0.39030	GAT|ATT	T|0.954;A|0.046	0.046	strong		0.453	MPZL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392109.1	NM_198275	Missense_Mutation
NCOR1	9611	hgsc.bcm.edu	37	17	15968887	15968887	+	Silent	SNP	T	T	C	rs7210057	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:15968887T>C	ENST00000268712.3	-	33	5120	c.4863A>G	c.(4861-4863)caA>caG	p.Q1621Q	NCOR1_ENST00000395857.3_Silent_p.Q205Q|NCOR1_ENST00000395851.1_Silent_p.Q1637Q	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	1621	Interaction with C1D. {ECO:0000250}.|Interaction with ETO.				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)			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)		CTTGCATCTGTTGTGAGGTAA	0.483													T|||	96	0.0191693	0.0666	0.0115	5008	,	,		19833	0.0		0.0	False		,,,				2504	0.0				p.Q1637Q		Atlas-SNP	.											.	NCOR1	240	.	0			c.A4911G						PASS	.	T	,	229,4177	137.3+/-173.1	5,219,1979	192.0	167.0	175.0		4911,4863	0.8	1.0	17	dbSNP_116	175	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous	NCOR1	NM_001190440.1,NM_006311.3	,	5,222,6276	CC,CT,TT		0.0349,5.1975,1.7838	,	1637/2338,1621/2441	15968887	232,12774	2203	4300	6503	SO:0001819	synonymous_variant	9611	exon32			CATCTGTTGTGAG	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.4863A>G	17.37:g.15968887T>C		299.0	1.0	0.00334448		314.0	150.0	0.477707	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Silent	SNP	ENST00000268712.3	37	CCDS11175.1																																																																																			T|0.979;C|0.021	0.021	strong		0.483	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311	
C5orf47	133491	hgsc.bcm.edu	37	5	173416508	173416508	+	Missense_Mutation	SNP	C	C	T	rs115473626	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:173416508C>T	ENST00000340147.6	+	1	347	c.242C>T	c.(241-243)cCt>cTt	p.P81L	C5orf47_ENST00000522195.1_Intron	NM_001144954.1	NP_001138426.1	Q569G3	CE047_HUMAN	chromosome 5 open reading frame 47	81										kidney(1)|prostate(1)	2						CCCACGACCCCTGGTGTGGAG	0.706													C|||	30	0.00599042	0.0144	0.0058	5008	,	,		10710	0.0		0.007	False		,,,				2504	0.0				p.P81L		Atlas-SNP	.											.	C5orf47	14	.	0			c.C242T						PASS	.						9.0	15.0	13.0					5																	173416508		686	1587	2273	SO:0001583	missense	133491	exon1			CGACCCCTGGTGT		CCDS47343.1	5q35.2	2012-02-24			ENSG00000185056	ENSG00000185056			27026	protein-coding gene	gene with protein product						12477932	Standard	NM_001144954		Approved	LOC133491	uc003mcw.4	Q569G3	OTTHUMG00000163349	ENST00000340147.6:c.242C>T	5.37:g.173416508C>T	ENSP00000340887:p.Pro81Leu	55.0	0.0	0		49.0	21.0	0.428571	NM_001144954	Q8IYU7	Missense_Mutation	SNP	ENST00000340147.6	37	CCDS47343.1	37	0.01694139194139194	18	0.036585365853658534	3	0.008287292817679558	0	0.0	16	0.021108179419525065	C	0.329	-0.957101	0.02267	.	.	ENSG00000185056	ENST00000340147	.	.	.	1.16	0.0674	0.14366	.	.	.	.	.	T	0.05227	0.0139	N	0.17082	0.46	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22243	-1.0222	8	0.14252	T	0.57	-0.6825	6.6571	0.22994	0.0:0.778:0.0:0.222	.	81	Q569G3	CE047_HUMAN	L	81	.	ENSP00000340887:P81L	P	+	2	0	C5orf47	173349114	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.573000	0.05874	-1.553000	0.01702	-1.786000	0.00637	CCT	C|0.984;T|0.016	0.016	strong		0.706	C5orf47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372926.1	NM_001144954	
C10orf95	79946	hgsc.bcm.edu	37	10	104210861	104210861	+	Missense_Mutation	SNP	C	C	A	rs73349055	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:104210861C>A	ENST00000239125.1	-	2	201	c.127G>T	c.(127-129)Ggg>Tgg	p.G43W	RP11-18I14.10_ENST00000494270.2_RNA|RP11-18I14.10_ENST00000473970.2_RNA|RP11-18I14.10_ENST00000596045.1_RNA|RP11-18I14.10_ENST00000596366.1_RNA|RP11-18I14.10_ENST00000492465.2_RNA|RP11-18I14.10_ENST00000594818.1_RNA	NM_024886.1	NP_079162.1	Q9H7T3	CJ095_HUMAN	chromosome 10 open reading frame 95	43										liver(1)	1		Colorectal(252;0.207)		Epithelial(162;8.34e-09)|all cancers(201;1.95e-07)|BRCA - Breast invasive adenocarcinoma(275;0.213)		GGTCGGCCCCCCAGGCGGCTG	0.657													C|||	318	0.0634984	0.2315	0.0144	5008	,	,		11331	0.0		0.002	False		,,,				2504	0.0				p.G43W		Atlas-SNP	.											.	C10orf95	5	.	0			c.G127T						PASS	.	C	TRP/GLY	452,2752		21,410,1171	9.0	11.0	10.0		127	-0.7	0.0	10	dbSNP_130	10	11,6951		0,11,3470	yes	missense	C10orf95	NM_024886.1	184	21,421,4641	AA,AC,CC		0.158,14.1074,4.5544	probably-damaging	43/258	104210861	463,9703	1602	3481	5083	SO:0001583	missense	79946	exon2			GGCCCCCCAGGCG	AK024342	CCDS7534.1	10q24.32	2014-02-19	2014-02-19	2014-02-19	ENSG00000120055	ENSG00000120055			25880	protein-coding gene	gene with protein product							Standard	NM_024886		Approved	FLJ14280	uc001kvo.1	Q9H7T3	OTTHUMG00000018959	ENST00000239125.1:c.127G>T	10.37:g.104210861C>A	ENSP00000239125:p.Gly43Trp	27.0	0.0	0		16.0	7.0	0.4375	NM_024886	A0AVQ7	Missense_Mutation	SNP	ENST00000239125.1	37	CCDS7534.1	121	0.0554029304029304	115	0.23373983739837398	6	0.016574585635359115	0	0.0	0	0.0	C	12.67	2.007558	0.35415	0.141074	0.00158	ENSG00000120055	ENST00000239125	.	.	.	4.67	-0.695	0.11291	.	1.984030	0.02659	N	0.107299	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	D	0.63046	0.992	P	0.56751	0.805	T	0.04281	-1.0963	8	0.87932	D	0	-26.9089	1.7389	0.02948	0.1583:0.0984:0.3263:0.417	.	43	Q9H7T3	CJ095_HUMAN	W	43	.	ENSP00000239125:G43W	G	-	1	0	C10orf95	104200851	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.146000	0.16180	-0.211000	0.10124	-0.350000	0.07774	GGG	C|0.954;A|0.046	0.046	strong		0.657	C10orf95-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050065.1	NM_024886	
LAMA1	284217	hgsc.bcm.edu	37	18	6961950	6961950	+	Silent	SNP	T	T	C	rs145257845	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:6961950T>C	ENST00000389658.3	-	52	7539	c.7446A>G	c.(7444-7446)ttA>ttG	p.L2482L		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2482					axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				CTACCTCCAGTAAACAGCCTT	0.378													T|||	15	0.00299521	0.0106	0.0014	5008	,	,		20021	0.0		0.0	False		,,,				2504	0.0				p.L2482L		Atlas-SNP	.											.	LAMA1	458	.	0			c.A7446G						PASS	.	T		15,4391	22.3+/-47.3	0,15,2188	130.0	131.0	131.0		7446	-9.1	0.0	18	dbSNP_134	131	0,8600		0,0,4300	no	coding-synonymous	LAMA1	NM_005559.3		0,15,6488	CC,CT,TT		0.0,0.3404,0.1153		2482/3076	6961950	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	284217	exon52			CTCCAGTAAACAG	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.7446A>G	18.37:g.6961950T>C		310.0	0.0	0		300.0	163.0	0.543333	NM_005559		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																			T|0.998;C|0.002	0.002	strong		0.378	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
IL16	3603	hgsc.bcm.edu	37	15	81592384	81592384	+	Missense_Mutation	SNP	C	C	T	rs17875513	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:81592384C>T	ENST00000302987.4	+	13	2717	c.2717C>T	c.(2716-2718)tCg>tTg	p.S906L	IL16_ENST00000560230.1_3'UTR|IL16_ENST00000394652.2_Missense_Mutation_p.S205L|IL16_ENST00000394660.2_Missense_Mutation_p.S906L			Q14005	IL16_HUMAN	interleukin 16	906			S -> L (in dbSNP:rs17875513). {ECO:0000269|Ref.8}.		immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						GTACTGTCCTCGGGGTCCCCT	0.642													C|||	215	0.0429313	0.1536	0.0115	5008	,	,		11772	0.0		0.004	False		,,,				2504	0.0				p.S906L		Atlas-SNP	.											.	IL16	254	.	0			c.C2717T						PASS	.	C	LEU/SER,LEU/SER,LEU/SER	558,3836		38,482,1677	44.0	49.0	47.0		2717,614,2717	-9.7	0.0	15	dbSNP_124	47	28,8572		0,28,4272	yes	missense,missense,missense	IL16	NM_001172128.1,NM_004513.5,NM_172217.3	145,145,145	38,510,5949	TT,TC,CC		0.3256,12.6991,4.5098	benign,benign,benign	906/1332,205/632,906/1333	81592384	586,12408	2197	4300	6497	SO:0001583	missense	3603	exon14			TGTCCTCGGGGTC	U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"""Interleukins and interleukin receptors"""	5980	protein-coding gene	gene with protein product	"""prointerleukin 16"", ""lymphocyte chemoattractant factor"""	603035	"""interleukin 16 (lymphocyte chemoattractant factor)"""			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.2717C>T	15.37:g.81592384C>T	ENSP00000302935:p.Ser906Leu	58.0	0.0	0		50.0	21.0	0.42	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Missense_Mutation	SNP	ENST00000302987.4	37	CCDS42069.1	82	0.037545787545787544	76	0.15447154471544716	4	0.011049723756906077	0	0.0	2	0.002638522427440633	C	8.558	0.877168	0.17395	0.126991	0.003256	ENSG00000172349	ENST00000394660;ENST00000355368;ENST00000302987;ENST00000329842;ENST00000394653;ENST00000394652;ENST00000394656	T;T;T	0.10763	2.84;2.84;3.43	4.85	-9.71	0.00518	.	1.594110	0.03725	N	0.252561	T	0.00039	0.0001	N	0.14661	0.345	0.80722	P	0.0	B;B;B;B;B;B	0.14438	0.001;0.01;0.0;0.001;0.0;0.001	B;B;B;B;B;B	0.04013	0.001;0.001;0.0;0.001;0.001;0.001	T	0.30208	-0.9986	9	0.30078	T	0.28	.	8.1212	0.30971	0.0709:0.1747:0.5288:0.2256	rs17875513	738;399;443;296;906;906	F8W7Z5;Q6ZTT5;B7Z8M3;B3KY62;Q14005;Q14005-2	.;.;.;.;IL16_HUMAN;.	L	906;738;906;443;296;205;205	ENSP00000378155:S906L;ENSP00000302935:S906L;ENSP00000378147:S205L	ENSP00000302935:S906L	S	+	2	0	IL16	79379439	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.830000	0.00744	-1.944000	0.01038	-1.710000	0.00715	TCG	C|0.955;T|0.045	0.045	strong		0.642	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217	
ZYG11B	79699	hgsc.bcm.edu	37	1	53262456	53262456	+	Splice_Site	SNP	G	G	A	rs11206020	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:53262456G>A	ENST00000294353.6	+	8	1630	c.1485G>A	c.(1483-1485)agG>agA	p.R495R	ZYG11B_ENST00000545132.1_Splice_Site_p.R495R|ZYG11B_ENST00000443756.2_Splice_Site_p.R495R	NM_024646.2	NP_078922.1	Q9C0D3	ZY11B_HUMAN	zyg-11 family member B, cell cycle regulator	495										breast(1)|endometrium(1)|kidney(6)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	30						TCATTGTCAGGGTAAGTCTAT	0.328													G|||	201	0.0401358	0.1452	0.0115	5008	,	,		10687	0.0		0.001	False		,,,				2504	0.0				p.R495R		Atlas-SNP	.											.	ZYG11B	61	.	0			c.G1485A						PASS	.	G		532,3874	238.7+/-250.0	28,476,1699	136.0	126.0	130.0		1485	2.2	1.0	1	dbSNP_120	130	6,8594	3.7+/-12.6	0,6,4294	yes	coding-synonymous-near-splice	ZYG11B	NM_024646.2		28,482,5993	AA,AG,GG		0.0698,12.0744,4.1366		495/745	53262456	538,12468	2203	4300	6503	SO:0001630	splice_region_variant	79699	exon8			TGTCAGGGTAAGT	AB051517	CCDS30717.1	1p32.3	2013-01-17	2012-12-10	2005-07-11	ENSG00000162378	ENSG00000162378		"""ZYG11 cell cycle regulator family"""	25820	protein-coding gene	gene with protein product			"""zyg-11 homolog (C. elegans)"", ""zyg-11 homolog B (C. elegans)"""	ZYG11		11214970	Standard	NM_024646		Approved	FLJ13456	uc001cuj.3	Q9C0D3	OTTHUMG00000008938	ENST00000294353.6:c.1485+1G>A	1.37:g.53262456G>A		126.0	0.0	0		131.0	55.0	0.419847	NM_024646	Q8N2X3|Q9H8L8	Silent	SNP	ENST00000294353.6	37	CCDS30717.1																																																																																			G|0.962;A|0.038	0.038	strong		0.328	ZYG11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024749.1	NM_024646	Silent
CLTCL1	8218	hgsc.bcm.edu	37	22	19196449	19196449	+	Missense_Mutation	SNP	T	T	C	rs182543131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:19196449T>C	ENST00000263200.10	-	21	3497	c.3425A>G	c.(3424-3426)cAg>cGg	p.Q1142R	CLTCL1_ENST00000427926.1_Missense_Mutation_p.Q1142R|CLTCL1_ENST00000442042.2_5'Flank|CLTCL1_ENST00000353891.5_Missense_Mutation_p.Q1142R	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	1142	Heavy chain arm.|Proximal segment.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					GCTGGCTGACTGAACAACTTC	0.517			T	?	ALCL								T|||	3	0.000599042	0.0023	0.0	5008	,	,		19417	0.0		0.0	False		,,,				2504	0.0				p.Q1142R		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"""clathrin, heavy polypeptide-like 1"""		L	.	CLTCL1	115	.	0			c.A3425G						PASS	.	T	ARG/GLN,ARG/GLN	5,3951		0,5,1973	58.0	59.0	59.0		3425,3425	2.8	1.0	22		59	0,8310		0,0,4155	yes	missense,missense	CLTCL1	NM_001835.3,NM_007098.3	43,43	0,5,6128	CC,CT,TT		0.0,0.1264,0.0408	benign,benign	1142/1584,1142/1641	19196449	5,12261	1978	4155	6133	SO:0001583	missense	8218	exon21			GCTGACTGAACAA		CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"""clathrin, heavy polypeptide-like 1"""	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.3425A>G	22.37:g.19196449T>C	ENSP00000445677:p.Gln1142Arg	103.0	0.0	0		96.0	53.0	0.552083	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	37	CCDS46662.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	T	12.81	2.050304	0.36181	0.001264	0.0	ENSG00000070371	ENST00000353891;ENST00000263200;ENST00000427926	T;T;T	0.19532	2.14;2.14;2.14	3.85	2.82	0.32997	Tetratricopeptide-like helical (1);Armadillo-type fold (1);	0.229394	0.37577	N	0.002026	T	0.15565	0.0375	N	0.26042	0.785	0.35290	D	0.782104	B;B	0.22541	0.003;0.071	B;B	0.31390	0.02;0.129	T	0.13899	-1.0492	10	0.39692	T	0.17	-8.2343	8.8849	0.35398	0.0:0.0903:0.0:0.9097	.	1142;1142	P53675-2;P53675	.;CLH2_HUMAN	R	1142	ENSP00000439662:Q1142R;ENSP00000445677:Q1142R;ENSP00000441158:Q1142R	ENSP00000445677:Q1142R	Q	-	2	0	CLTCL1	17576449	1.000000	0.71417	0.975000	0.42487	0.916000	0.54674	5.366000	0.66122	0.537000	0.28751	0.533000	0.62120	CAG	T|0.999;C|0.001	0.001	strong		0.517	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098	
BCO2	83875	hgsc.bcm.edu	37	11	112071464	112071464	+	Missense_Mutation	SNP	C	C	T	rs115780398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:112071464C>T	ENST00000357685.5	+	7	1129	c.994C>T	c.(994-996)Cgg>Tgg	p.R332W	BCO2_ENST00000526088.1_Missense_Mutation_p.R298W|BCO2_ENST00000393032.2_Missense_Mutation_p.R298W|BCO2_ENST00000532593.1_Missense_Mutation_p.R227W|BCO2_ENST00000531169.1_Missense_Mutation_p.R298W|BCO2_ENST00000361053.4_Missense_Mutation_p.R259W|BCO2_ENST00000438022.1_Missense_Mutation_p.R298W			Q9BYV7	BCDO2_HUMAN	beta-carotene oxygenase 2	332					carotene catabolic process (GO:0016121)|carotene metabolic process (GO:0016119)|carotenoid metabolic process (GO:0016116)|oxidation-reduction process (GO:0055114)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of reactive oxygen species metabolic process (GO:2000377)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)	intracellular (GO:0005622)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen (GO:0016702)			NS(1)|breast(1)|kidney(3)|large_intestine(1)|lung(9)|skin(1)	16						GTGTAATACGCGGTTTCATGT	0.398													C|||	31	0.0061901	0.0212	0.0014	5008	,	,		18093	0.002		0.0	False		,,,				2504	0.0				p.R332W	GBM(177;1916 2099 21049 29541 39946)	Atlas-SNP	.											BCO2,colon,carcinoma,0,1	BCO2	44	1	0			c.C994T						PASS	.	C	TRP/ARG,TRP/ARG	81,4321	69.8+/-107.6	0,81,2120	120.0	123.0	122.0		892,994	0.0	0.0	11	dbSNP_132	122	1,8593	1.2+/-3.3	0,1,4296	yes	missense,missense	BCO2	NM_001037290.1,NM_031938.4	101,101	0,82,6416	TT,TC,CC		0.0116,1.8401,0.631	probably-damaging,probably-damaging	298/546,332/580	112071464	82,12914	2201	4297	6498	SO:0001583	missense	83875	exon7			AATACGCGGTTTC	AJ290393	CCDS8358.2, CCDS41716.1, CCDS58181.1, CCDS58182.1, CCDS58183.1	11q23.1	2014-05-12	2008-04-15	2008-04-15	ENSG00000197580	ENSG00000197580	1.13.11.71		18503	protein-coding gene	gene with protein product	"""beta-carotene 9',10' oxygenase"", ""carotenoid-9',10'-cleaving dioxygenase"""	611740	"""beta-carotene dioxygenase 2"""	BCDO2		11278918, 15983114, 15949678	Standard	NM_031938		Approved	FLJ34464, B-DIOX-II	uc001pnf.3	Q9BYV7	OTTHUMG00000167155	ENST00000357685.5:c.994C>T	11.37:g.112071464C>T	ENSP00000350314:p.Arg332Trp	78.0	0.0	0		64.0	35.0	0.546875	NM_031938	B0YIX5|B4DNC3|E9PBI8|E9PJJ1|Q8IUS0|Q96JC8|Q96JY5	Missense_Mutation	SNP	ENST00000357685.5	37	CCDS8358.2	16	0.007326007326007326	13	0.026422764227642278	1	0.0027624309392265192	2	0.0034965034965034965	0	0.0	C	5.058	0.196301	0.09599	0.018401	1.16E-4	ENSG00000197580	ENST00000357685;ENST00000393032;ENST00000361053;ENST00000438022;ENST00000526088;ENST00000532593;ENST00000531169	D;D;D;D;D;D;D	0.95885	-3.84;-3.84;-3.84;-3.84;-3.84;-3.84;-3.84	5.45	0.0177	0.14113	.	0.629740	0.16560	N	0.209094	D	0.85120	0.5624	L	0.39566	1.225	0.09310	N	1	D;D;D;D	0.63046	0.965;0.99;0.965;0.992	P;P;P;P	0.58970	0.788;0.659;0.788;0.849	T	0.81052	-0.1107	10	0.37606	T	0.19	-11.5438	1.2953	0.02068	0.2227:0.4126:0.1085:0.2562	.	309;259;332;159	C9JEZ9;E9PBI8;Q9BYV7;Q8NAZ7	.;.;BCDO2_HUMAN;.	W	332;298;259;298;298;227;298	ENSP00000350314:R332W;ENSP00000376752:R298W;ENSP00000354338:R259W;ENSP00000414843:R298W;ENSP00000436615:R298W;ENSP00000431802:R227W;ENSP00000437053:R298W	ENSP00000350314:R332W	R	+	1	2	BCO2	111576674	0.000000	0.05858	0.010000	0.14722	0.089000	0.18198	0.047000	0.14056	0.024000	0.15214	-0.203000	0.12734	CGG	C|0.994;T|0.006	0.006	strong		0.398	BCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256570.3	NM_001037290	
KNDC1	85442	hgsc.bcm.edu	37	10	135012583	135012583	+	Missense_Mutation	SNP	C	C	A	rs111276772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:135012583C>A	ENST00000304613.3	+	14	2592	c.2571C>A	c.(2569-2571)gaC>gaA	p.D857E	KNDC1_ENST00000368571.2_Missense_Mutation_p.D792E|KNDC1_ENST00000368572.2_Missense_Mutation_p.D857E			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	857	Pro-rich.				cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		AACGTGATGACCAGAGTCCAG	0.741													C|||	102	0.0203674	0.0749	0.0029	5008	,	,		10501	0.0		0.001	False		,,,				2504	0.0				p.D857E		Atlas-SNP	.											.	KNDC1	155	.	0			c.C2571A						PASS	.		GLU/ASP	232,4062		3,226,1918	10.0	12.0	11.0		2571	-3.8	0.0	10	dbSNP_132	11	5,8501		0,5,4248	yes	missense	KNDC1	NM_152643.6	45	3,231,6166	AA,AC,CC		0.0588,5.4029,1.8516	benign	857/1750	135012583	237,12563	2147	4253	6400	SO:0001583	missense	85442	exon14			TGATGACCAGAGT	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"""RasGEF domain family, member 2"""	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.2571C>A	10.37:g.135012583C>A	ENSP00000304437:p.Asp857Glu	23.0	0.0	0		55.0	28.0	0.509091	NM_152643	B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Missense_Mutation	SNP	ENST00000304613.3	37	CCDS7674.1	35	0.016025641025641024	34	0.06910569105691057	1	0.0027624309392265192	0	0.0	0	0.0	C	7.348	0.622286	0.14193	0.054029	5.88E-4	ENSG00000171798	ENST00000304613;ENST00000368572;ENST00000368571	T;T;T	0.18502	2.69;2.69;2.21	1.93	-3.85	0.04243	.	13.355300	0.01309	U	0.010560	T	0.00552	0.0018	N	0.08118	0	0.09310	N	1	B;B;B	0.26195	0.144;0.002;0.106	B;B;B	0.19666	0.026;0.003;0.018	T	0.19614	-1.0300	10	0.22109	T	0.4	.	6.2917	0.21063	0.192:0.2336:0.5744:0.0	.	857;792;857	Q76NI1-4;Q76NI1-2;Q76NI1	.;.;VKIND_HUMAN	E	857;857;792	ENSP00000304437:D857E;ENSP00000357561:D857E;ENSP00000357560:D792E	ENSP00000304437:D857E	D	+	3	2	KNDC1	134862573	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.062000	0.14389	-0.906000	0.03866	-0.828000	0.03084	GAC	C|0.983;A|0.017	0.017	strong		0.741	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643	
SCN9A	6335	hgsc.bcm.edu	37	2	167145106	167145106	+	Silent	SNP	C	C	A	rs58465962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:167145106C>A	ENST00000409435.1	-	9	1154	c.1155G>T	c.(1153-1155)gtG>gtT	p.V385V	AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Silent_p.V386V|SCN9A_ENST00000409672.1_Silent_p.V385V|SCN9A_ENST00000375387.4_Silent_p.V386V			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	385					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CCAGGAAAATCACTACGACAA	0.383													C|||	229	0.0457268	0.1551	0.0187	5008	,	,		15943	0.0		0.003	False		,,,				2504	0.0082				p.V385V		Atlas-SNP	.											.	SCN9A	296	.	0			c.G1155T						PASS	.	C		457,3229		28,401,1414	79.0	76.0	77.0		1155	1.8	1.0	2	dbSNP_129	77	45,8183		3,39,4072	no	coding-synonymous	SCN9A	NM_002977.3		31,440,5486	AA,AC,CC		0.5469,12.3983,4.2135		385/1978	167145106	502,11412	1843	4114	5957	SO:0001819	synonymous_variant	6335	exon10			GAAAATCACTACG	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10597	protein-coding gene	gene with protein product		603415	"""sodium channel, voltage-gated, type IX, alpha polypeptide"""			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.1155G>T	2.37:g.167145106C>A		89.0	0.0	0		50.0	50.0	1	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Silent	SNP	ENST00000409435.1	37	CCDS46441.1																																																																																			C|0.964;A|0.036	0.036	strong		0.383	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	
NOTCH2	4853	hgsc.bcm.edu	37	1	120480583	120480583	+	Silent	SNP	G	G	A	rs7543643	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:120480583G>A	ENST00000256646.2	-	20	3453	c.3234C>T	c.(3232-3234)tgC>tgT	p.C1078C		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	1078	EGF-like 28. {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)		TTTTCTGAACGCAAGTACCTT	0.468			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome				G|||	356	0.0710863	0.2458	0.0202	5008	,	,		18636	0.002		0.001	False		,,,				2504	0.0143				p.C1078C		Atlas-SNP	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2	348	.	0			c.C3234T						PASS	.	G	,	906,3500	350.5+/-310.9	88,730,1385	133.0	122.0	125.0		3234,3234	-1.8	0.0	1	dbSNP_116	125	24,8576	16.6+/-54.9	0,24,4276	yes	coding-synonymous,coding-synonymous	NOTCH2	NM_001200001.1,NM_024408.3	,	88,754,5661	AA,AG,GG		0.2791,20.5629,7.1505	,	1078/1236,1078/2472	120480583	930,12076	2203	4300	6503	SO:0001819	synonymous_variant	4853	exon20	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	CTGAACGCAAGTA	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.3234C>T	1.37:g.120480583G>A		135.0	0.0	0		123.0	62.0	0.504065	NM_001200001	Q5T3X7|Q99734|Q9H240	Silent	SNP	ENST00000256646.2	37	CCDS908.1																																																																																			G|0.925;A|0.075	0.075	strong		0.468	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408	
CNGA2	1260	hgsc.bcm.edu	37	X	150912171	150912171	+	Missense_Mutation	SNP	G	G	A	rs150539917	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:150912171G>A	ENST00000329903.4	+	6	1229	c.1196G>A	c.(1195-1197)cGa>cAa	p.R399Q		NM_005140.1	NP_005131.1	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	399			R -> Q (in a breast cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)	p.R399Q(1)		breast(4)|endometrium(4)|large_intestine(5)|lung(34)|prostate(2)	49	Acute lymphoblastic leukemia(192;6.56e-05)					ATGCAGTTCCGAAAGGTCAGC	0.493													G|||	104	0.0275497	0.0726	0.0072	3775	,	,		18285	0.0		0.003	False		,,,				2504	0.0				p.R399Q		Atlas-SNP	.											.	CNGA2	136	.	1	Substitution - Missense(1)	breast(1)	c.G1196A						PASS	.	G	GLN/ARG	355,3480		19,261,56,1352,515	93.0	82.0	86.0		1196	3.2	1.0	X	dbSNP_134	86	2,6726		0,1,1,2427,1871	yes	missense	CNGA2	NM_005140.1	43	19,262,57,3779,2386	AA,AG,A,GG,G		0.0297,9.2568,3.3797	probably-damaging	399/665	150912171	357,10206	2203	4300	6503	SO:0001583	missense	1260	exon7			AGTTCCGAAAGGT	S76067	CCDS14701.1	Xq27	2011-07-05			ENSG00000183862	ENSG00000183862		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2149	protein-coding gene	gene with protein product		300338		CNCA1, CNCA		7532814, 16382102	Standard	NM_005140		Approved	CNG2, OCNC1, OCNCa, OCNCALPHA, OCNCalpha, FLJ46312	uc004fey.1	Q16280	OTTHUMG00000024173	ENST00000329903.4:c.1196G>A	X.37:g.150912171G>A	ENSP00000328478:p.Arg399Gln	91.0	0.0	0		80.0	34.0	0.425	NM_005140	A0AVD0	Missense_Mutation	SNP	ENST00000329903.4	37	CCDS14701.1	48	0.028933092224231464	33	0.07051282051282051	2	0.005555555555555556	0	0.0	1	0.0013192612137203166	G	15.92	2.975018	0.53720	0.092568	2.97E-4	ENSG00000183862	ENST00000329903	D	0.97066	-4.23	4.96	3.18	0.36537	Cyclic nucleotide-binding-like (1);	0.057024	0.64402	D	0.000001	T	0.77745	0.4176	M	0.88450	2.955	0.20764	P	0.999856176	D	0.89917	1.0	D	0.79108	0.992	T	0.79874	-0.1619	9	0.46703	T	0.11	.	9.1566	0.36996	0.1872:0.0:0.8128:0.0	.	399	Q16280	CNGA2_HUMAN	Q	399	ENSP00000328478:R399Q	ENSP00000328478:R399Q	R	+	2	0	CNGA2	150662827	1.000000	0.71417	0.996000	0.52242	0.974000	0.67602	5.415000	0.66411	0.437000	0.26423	-0.344000	0.07964	CGA	G|0.964;A|0.036	0.036	strong		0.493	CNGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060888.1	NM_005140	
CYP4F12	66002	hgsc.bcm.edu	37	19	15791074	15791074	+	Missense_Mutation	SNP	A	A	G	rs114254919	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15791074A>G	ENST00000550308.1	+	4	744	c.364A>G	c.(364-366)Aat>Gat	p.N122D	CYP4F12_ENST00000324632.10_Missense_Mutation_p.N122D	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	122					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	ACCCAAGGATAATCTCTTCAT	0.567													.|||	103	0.0205671	0.0734	0.0072	5008	,	,		20731	0.0		0.001	False		,,,				2504	0.0				p.N122D		Atlas-SNP	.											CYP4F12,colon,carcinoma,-1,1	CYP4F12	89	1	0			c.A364G						PASS	.	G	ASP/ASN	190,4188		1,188,2000	139.0	143.0	142.0		364	-5.8	0.0	19	dbSNP_132	142	3,8585		0,3,4291	yes	missense	CYP4F12	NM_023944.3	23	1,191,6291	GG,GA,AA		0.0349,4.3399,1.4885	benign	122/525	15791074	193,12773	2189	4294	6483	SO:0001583	missense	66002	exon4			AAGGATAATCTCT	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.364A>G	19.37:g.15791074A>G	ENSP00000448998:p.Asn122Asp	266.0	0.0	0		372.0	95.0	0.255376	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	38	0.0173992673992674	35	0.07113821138211382	3	0.008287292817679558	0	0.0	0	0.0	.	1.398	-0.578943	0.03854	0.043399	3.49E-4	ENSG00000186204	ENST00000550308;ENST00000324632	T;T	0.78707	-1.2;-1.2	2.92	-5.84	0.02318	.	1.494030	0.04917	N	0.454288	T	0.07458	0.0188	N	0.16567	0.415	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	0.22836	-1.0205	10	0.11794	T	0.64	.	1.4308	0.02333	0.4684:0.1455:0.2397:0.1465	.	122;122;122	B4E2R2;B4E270;Q9HCS2	.;.;CP4FC_HUMAN	D	122	ENSP00000448998:N122D;ENSP00000321821:N122D	ENSP00000321821:N122D	N	+	1	0	CYP4F12	15652074	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.894000	0.00707	-2.136000	0.00810	-1.140000	0.01884	AAT	A|0.989;G|0.011	0.011	strong		0.567	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
CNGB1	1258	hgsc.bcm.edu	37	16	57935443	57935443	+	Missense_Mutation	SNP	C	C	A	rs16942445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57935443C>A	ENST00000251102.8	-	28	2941	c.2881G>T	c.(2881-2883)Gca>Tca	p.A961S	CNGB1_ENST00000564448.1_Missense_Mutation_p.A955S	NM_001297.4	NP_001288.3	Q14028	CNGB1_HUMAN	cyclic nucleotide gated channel beta 1	961			A -> S (in dbSNP:rs16942445).		cation transport (GO:0006812)|cytosolic calcium ion homeostasis (GO:0051480)|detection of light stimulus involved in visual perception (GO:0050908)|phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|protein heterotetramerization (GO:0051290)|regulation of membrane potential (GO:0042391)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina homeostasis (GO:0001895)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of smell (GO:0007608)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|intracellular cyclic nucleotide activated cation channel complex (GO:0017071)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)|transmembrane transporter complex (GO:1902495)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cAMP activated cation channel activity (GO:0005222)|intracellular cGMP activated cation channel activity (GO:0005223)|ligand-gated ion channel activity (GO:0015276)|voltage-gated potassium channel activity (GO:0005249)			breast(7)|cervix(2)|endometrium(4)|kidney(2)|large_intestine(11)|liver(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	54						TGAAAGAGTGCGACTTTGCTA	0.537													C|||	193	0.0385383	0.1384	0.0086	5008	,	,		22586	0.0		0.004	False		,,,				2504	0.0				p.A961S	Colon(156;1293 1853 16336 28962 38659)	Atlas-SNP	.											.	CNGB1	105	.	0			c.G2881T						PASS	.	C	SER/ALA	387,3743		19,349,1697	111.0	114.0	113.0		2881	3.9	1.0	16	dbSNP_123	113	5,8409		0,5,4202	yes	missense	CNGB1	NM_001297.4	99	19,354,5899	AA,AC,CC		0.0594,9.3705,3.125	benign	961/1252	57935443	392,12152	2065	4207	6272	SO:0001583	missense	1258	exon28			AGAGTGCGACTTT	AF042498	CCDS42169.1, CCDS45495.1, CCDS67042.1	16q13	2013-02-14			ENSG00000070729	ENSG00000070729		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2151	protein-coding gene	gene with protein product	"""glutamic acid-rich protein"""	600724		CNCG2, CNCG3L		8766832, 7590744, 16382102	Standard	NM_001297		Approved	RCNC2, RCNCb, GARP, GAR1, CNGB1B, RP45	uc002emt.2	Q14028	OTTHUMG00000154810	ENST00000251102.8:c.2881G>T	16.37:g.57935443C>A	ENSP00000251102:p.Ala961Ser	97.0	0.0	0		93.0	46.0	0.494624	NM_001297	H3BN09|O43636|Q13059|Q14029|Q9UMG2	Missense_Mutation	SNP	ENST00000251102.8	37	CCDS42169.1	63	0.028846153846153848	59	0.11991869918699187	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	8.424	0.846959	0.17034	0.093705	5.94E-4	ENSG00000070729	ENST00000251102	D	0.96427	-4.01	4.8	3.86	0.44501	Cyclic nucleotide-binding-like (1);RmlC-like jelly roll fold (1);	0.070612	0.56097	D	0.000026	T	0.17450	0.0419	L	0.28556	0.865	0.80722	D	1	B;B	0.23540	0.087;0.082	B;B	0.28784	0.041;0.094	T	0.62955	-0.6744	10	0.14252	T	0.57	.	8.8322	0.35091	0.0:0.8291:0.0:0.1709	rs16942445;rs52812859;rs16942445	333;961	Q14028-2;Q14028	.;CNGB1_HUMAN	S	961	ENSP00000251102:A961S	ENSP00000251102:A961S	A	-	1	0	CNGB1	56492944	1.000000	0.71417	0.996000	0.52242	0.031000	0.12232	2.124000	0.42006	1.028000	0.39785	-0.215000	0.12644	GCA	C|0.957;A|0.043	0.043	strong		0.537	CNGB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337167.2	NM_001297	
SSPO	23145	hgsc.bcm.edu	37	7	149489037	149489037	+	RNA	SNP	T	T	C	rs1635802	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149489037T>C	ENST00000378016.2	+	0	5378							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CCCGGAGGCCTGCACAGCACC	0.652													C|||	202	0.0403355	0.1029	0.0144	5008	,	,		16636	0.004		0.003	False		,,,				2504	0.0501				p.L1793P		Atlas-SNP	.											.	.	.	.	0			c.T5378C						PASS	.	C		308,3816		12,284,1766	25.0	30.0	28.0		5382	3.9	0.0	7	dbSNP_89	28	19,8349		0,19,4165	no	coding-notMod3	SSPO	NM_198455.2		12,303,5931	CC,CT,TT		0.2271,7.4685,2.6177			149489037	327,12165	2062	4184	6246			23145	exon35			GAGGCCTGCACAG	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149489037T>C		60.0	0.0	0		75.0	38.0	0.506667	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				T|0.977;C|0.023	0.023	strong		0.652	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
MT-ND4	4538	hgsc.bcm.edu	37	M	12049	12049	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:12049C>T	ENST00000361381.2	+	1	1290	c.1290C>T	c.(1288-1290)ttC>ttT	p.F430F	MT-TR_ENST00000387439.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	430					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						AAACCCTCATTCACACGAGAA	0.448																																					p.F430F		Atlas-SNP	.											.	.	.	.	0			c.C1290T						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			CTCATTCACACGA			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.1290C>T	M.37:g.12049C>T		5.0	0.0	0		10.0	10.0	1	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Silent	SNP	ENST00000361381.2	37																																																																																				.	.	none		0.448	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
ZNF362	149076	hgsc.bcm.edu	37	1	33745781	33745781	+	Missense_Mutation	SNP	G	G	A	rs143005937	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:33745781G>A	ENST00000539719.1	+	5	576	c.406G>A	c.(406-408)Gcg>Acg	p.A136T	ZNF362_ENST00000373428.5_Missense_Mutation_p.A136T	NM_152493.2	NP_689706.2	Q5T0B9	ZN362_HUMAN	zinc finger protein 362	136					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)|kidney(1)|large_intestine(4)|lung(2)	10		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				AAGCGCGGGCGCGGGCACGGG	0.697													G|||	40	0.00798722	0.0272	0.0058	5008	,	,		11977	0.0		0.0	False		,,,				2504	0.0				p.A136T	Pancreas(162;1431 2676 35353 38425)	Atlas-SNP	.											.	ZNF362	31	.	0			c.G406A						PASS	.	G	THR/ALA	138,4266	98.5+/-137.1	6,126,2070	53.0	59.0	57.0		406	1.2	0.0	1	dbSNP_134	57	0,8596		0,0,4298	yes	missense	ZNF362	NM_152493.2	58	6,126,6368	AA,AG,GG		0.0,3.1335,1.0615	benign	136/421	33745781	138,12862	2202	4298	6500	SO:0001583	missense	149076	exon5			GCGGGCGCGGGCA		CCDS377.1	1p35.1	2013-01-08			ENSG00000160094	ENSG00000160094		"""Zinc fingers, C2H2-type"""	18079	protein-coding gene	gene with protein product	"""rotund homolog (Drosophila)"""						Standard	NM_152493		Approved	FLJ25476, lin-29, RN	uc001bxc.1	Q5T0B9	OTTHUMG00000004124	ENST00000539719.1:c.406G>A	1.37:g.33745781G>A	ENSP00000446335:p.Ala136Thr	103.0	0.0	0		137.0	81.0	0.591241	NM_152493	Q8WYU4	Missense_Mutation	SNP	ENST00000539719.1	37	CCDS377.1	9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	G	0.389	-0.924363	0.02377	0.031335	0.0	ENSG00000160094	ENST00000483388;ENST00000539719;ENST00000373428	T;T	0.07567	3.18;3.18	2.39	1.17	0.20885	.	1.192330	0.06286	N	0.698320	T	0.01222	0.0040	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.45687	-0.9244	10	0.12766	T	0.61	.	4.807	0.13325	0.8237:0.0:0.1763:0.0	.	136	Q5T0B9	ZN362_HUMAN	T	123;136;136	ENSP00000446335:A136T;ENSP00000362527:A136T	ENSP00000362527:A136T	A	+	1	0	ZNF362	33518368	0.998000	0.40836	0.007000	0.13788	0.438000	0.31896	0.857000	0.27831	0.111000	0.17947	-0.839000	0.03059	GCG	G|0.989;A|0.011	0.011	strong		0.697	ZNF362-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011857.2	NM_152493	
MYO5B	4645	hgsc.bcm.edu	37	18	47506874	47506874	+	Silent	SNP	G	G	T	rs16951352	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:47506874G>T	ENST00000285039.7	-	9	1295	c.996C>A	c.(994-996)atC>atA	p.I332I		NM_001080467.2	NP_001073936.1	Q9ULV0	MYO5B_HUMAN	myosin VB	332	Myosin motor.				endosome localization (GO:0032439)|metabolic process (GO:0008152)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)|vesicle-mediated transport (GO:0016192)|water transport (GO:0006833)	apical cortex (GO:0045179)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|protein complex (GO:0043234)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|Rab GTPase binding (GO:0017137)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(4)	87				READ - Rectum adenocarcinoma(32;0.103)		CAAGGTGCAAGATAGAAGCAA	0.418													G|||	61	0.0121805	0.0431	0.0043	5008	,	,		18907	0.0		0.001	False		,,,				2504	0.0				p.I332I		Atlas-SNP	.											.	MYO5B	178	.	0			c.C996A						PASS	.	G		125,3877		0,125,1876	117.0	113.0	114.0		996	4.3	1.0	18	dbSNP_123	114	11,8301		0,11,4145	no	coding-synonymous	MYO5B	NM_001080467.2		0,136,6021	TT,TG,GG		0.1323,3.1234,1.1044		332/1849	47506874	136,12178	2001	4156	6157	SO:0001819	synonymous_variant	4645	exon9			GTGCAAGATAGAA	AB032945	CCDS42436.1	18q	2011-09-27			ENSG00000167306	ENSG00000167306		"""Myosins / Myosin superfamily : Class V"""	7603	protein-coding gene	gene with protein product		606540				8884266, 17462998	Standard	NM_001080467		Approved	KIAA1119	uc002leb.2	Q9ULV0		ENST00000285039.7:c.996C>A	18.37:g.47506874G>T		139.0	0.0	0		134.0	60.0	0.447761	NM_001080467	B0I1R3|Q0P656|Q9H6Y6	Silent	SNP	ENST00000285039.7	37	CCDS42436.1																																																																																			G|0.993;T|0.007	0.007	strong		0.418	MYO5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448515.2		
KRTAP10-12	386685	hgsc.bcm.edu	37	21	46117553	46117553	+	Missense_Mutation	SNP	C	C	A	rs35076450	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46117553C>A	ENST00000400365.3	+	1	467	c.437C>A	c.(436-438)cCg>cAg	p.P146Q	TSPEAR_ENST00000323084.4_Intron	NM_198699.1	NP_941972.1	P60413	KR10C_HUMAN	keratin associated protein 10-12	146	19 X 5 AA repeats of C-C-X(3).		P -> Q (in dbSNP:rs35076450).			keratin filament (GO:0045095)				large_intestine(1)|lung(8)	9						ATCTCCTCCCCGTGTCAACAG	0.612													C|||	19	0.00379393	0.0136	0.0014	5008	,	,		19291	0.0		0.0	False		,,,				2504	0.0				p.P146Q		Atlas-SNP	.											.	KRTAP10-12	21	.	0			c.C437A						PASS	.	C	GLN/PRO,	66,4340	61.7+/-98.7	1,64,2138	161.0	165.0	164.0		437,	0.9	0.1	21	dbSNP_126	164	0,8600		0,0,4300	no	missense,intron	TSPEAR,KRTAP10-12	NM_198699.1,NM_144991.2	76,	1,64,6438	AA,AC,CC		0.0,1.498,0.5075	possibly-damaging,	146/246,	46117553	66,12940	2203	4300	6503	SO:0001583	missense	386685	exon1			CCTCCCCGTGTCA	AB076364	CCDS42967.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000189169	ENSG00000189169		"""Keratin associated proteins"""	20533	protein-coding gene	gene with protein product			"""keratin associated protein 18-12"""	KRTAP18-12			Standard	NM_198699		Approved	KRTAP18.12, KAP10.12	uc002zfw.1	P60413	OTTHUMG00000057629	ENST00000400365.3:c.437C>A	21.37:g.46117553C>A	ENSP00000383216:p.Pro146Gln	221.0	1.0	0.00452489		265.0	136.0	0.513208	NM_198699	B2RPA3	Missense_Mutation	SNP	ENST00000400365.3	37	CCDS42967.1	7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	c	0.797	-0.756781	0.03019	0.01498	0.0	ENSG00000189169	ENST00000400365;ENST00000452870	T	0.00644	6.01	2.19	0.906	0.19314	.	.	.	.	.	T	0.00552	0.0018	L	0.56280	1.765	0.09310	N	1	P	0.36660	0.564	B	0.32149	0.141	T	0.48536	-0.9027	9	0.54805	T	0.06	.	5.9287	0.19126	0.0:0.5224:0.4776:0.0	rs35076450	146	P60413	KR10C_HUMAN	Q	146;54	ENSP00000383216:P146Q	ENSP00000383216:P146Q	P	+	2	0	KRTAP10-12	44941981	0.001000	0.12720	0.088000	0.20740	0.003000	0.03518	0.160000	0.16462	0.881000	0.35993	0.305000	0.20034	CCG	C|0.995;A|0.005	0.005	strong		0.612	KRTAP10-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128032.1	NM_198699	
POLRMT	5442	hgsc.bcm.edu	37	19	617573	617573	+	Missense_Mutation	SNP	G	G	A	rs142850300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:617573G>A	ENST00000588649.2	-	19	3662	c.3578C>T	c.(3577-3579)tCt>tTt	p.S1193F	AC005559.2_ENST00000591847.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	1193	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)			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)		GCCTTACTCAGAGCAGAACCG	0.637													g|||	29	0.00579073	0.0197	0.0043	5008	,	,		11732	0.0		0.0	False		,,,				2504	0.0				p.S1193F		Atlas-SNP	.											.	POLRMT	91	.	0			c.C3578T						PASS	.	G	PHE/SER	73,4333		1,71,2131	42.0	41.0	41.0		3578	2.1	0.0	19	dbSNP_134	41	0,8600		0,0,4300	yes	missense	POLRMT	NM_005035.3	155	1,71,6431	AA,AG,GG		0.0,1.6568,0.5613	benign	1193/1231	617573	73,12933	2203	4300	6503	SO:0001583	missense	5442	exon19			TACTCAGAGCAGA		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.3578C>T	19.37:g.617573G>A	ENSP00000465759:p.Ser1193Phe	37.0	0.0	0		38.0	25.0	0.657895	NM_005035	O60370	Missense_Mutation	SNP	ENST00000588649.2	37	CCDS12036.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	.	0.192	-1.052853	0.01965	0.016568	0.0	ENSG00000099821	ENST00000215591	T	0.47528	0.84	3.21	2.12	0.27331	.	1.125910	0.06566	N	0.747594	T	0.31638	0.0803	M	0.68317	2.08	0.09310	N	1	B	0.14805	0.011	B	0.26310	0.068	T	0.36529	-0.9744	10	0.37606	T	0.19	.	7.4584	0.27280	0.0:0.0:0.7418:0.2582	.	1193	O00411	RPOM_HUMAN	F	1193	ENSP00000215591:S1193F	ENSP00000215591:S1193F	S	-	2	0	POLRMT	568573	0.086000	0.21541	0.007000	0.13788	0.002000	0.02628	1.811000	0.38942	0.645000	0.30675	0.431000	0.28591	TCT	G|0.995;A|0.005	0.005	strong		0.637	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035	
C2orf43	60526	hgsc.bcm.edu	37	2	20886706	20886706	+	Missense_Mutation	SNP	T	T	C	rs147773589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:20886706T>C	ENST00000237822.3	-	7	1014	c.935A>G	c.(934-936)gAc>gGc	p.D312G	C2orf43_ENST00000435420.2_Missense_Mutation_p.D264G|C2orf43_ENST00000403006.2_Missense_Mutation_p.D182G|C2orf43_ENST00000440866.2_3'UTR|C2orf43_ENST00000541941.1_Missense_Mutation_p.D182G|C2orf43_ENST00000381090.3_Missense_Mutation_p.D312G	NM_001282721.1|NM_021925.2	NP_001269650.1|NP_068744.1	Q9H6V9	CB043_HUMAN	chromosome 2 open reading frame 43	312										endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGCAATCATGTCTGCCATTTC	0.433													T|||	7	0.00139776	0.0053	0.0	5008	,	,		18458	0.0		0.0	False		,,,				2504	0.0				p.D312G		Atlas-SNP	.											.	C2orf43	28	.	0			c.A935G						PASS	.	T	GLY/ASP	30,4376	37.6+/-69.7	0,30,2173	159.0	141.0	147.0		935	-4.0	0.0	2	dbSNP_134	147	0,8600		0,0,4300	yes	missense	C2orf43	NM_021925.2	94	0,30,6473	CC,CT,TT		0.0,0.6809,0.2307	benign	312/326	20886706	30,12976	2203	4300	6503	SO:0001583	missense	60526	exon7			ATCATGTCTGCCA	AK025473	CCDS1702.1, CCDS62864.1, CCDS74488.1, CCDS74489.1	2p24.1	2014-02-07			ENSG00000118961	ENSG00000118961			26145	protein-coding gene	gene with protein product		613570				17135363, 24357060	Standard	NM_001282723		Approved	FLJ21820	uc002rec.3	Q9H6V9	OTTHUMG00000122097	ENST00000237822.3:c.935A>G	2.37:g.20886706T>C	ENSP00000237822:p.Asp312Gly	191.0	0.0	0		167.0	89.0	0.532934	NM_021925	B7ZA47|B7ZAJ5|D6W530|E7ESN0|Q53T37|Q53T58	Missense_Mutation	SNP	ENST00000237822.3	37	CCDS1702.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	4.392	0.072364	0.08436	0.006809	0.0	ENSG00000118961	ENST00000403006;ENST00000381090;ENST00000237822;ENST00000435420;ENST00000541941	T;T;T	0.46063	0.88;1.49;0.88	5.93	-4.01	0.04045	.	2.110680	0.01630	N	0.023469	T	0.20740	0.0499	L	0.28274	0.84	0.09310	N	1	B;B;B;B	0.11235	0.001;0.001;0.002;0.004	B;B;B;B	0.09377	0.001;0.001;0.003;0.004	T	0.12451	-1.0547	10	0.24483	T	0.36	0.2807	7.2059	0.25907	0.0808:0.0673:0.4763:0.3756	.	270;264;312;312	B4DS38;B7ZAJ5;Q9H6V9;B5MDU6	.;.;CB043_HUMAN;.	G	182;312;312;264;182	ENSP00000384267:D182G;ENSP00000388635:D264G;ENSP00000440570:D182G	ENSP00000237822:D312G	D	-	2	0	C2orf43	20750187	0.000000	0.05858	0.000000	0.03702	0.088000	0.18126	-0.087000	0.11215	-0.401000	0.07644	0.533000	0.62120	GAC	T|0.998;C|0.002	0.002	strong		0.433	C2orf43-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242861.1	NM_021925	
KIF1C	10749	hgsc.bcm.edu	37	17	4918122	4918122	+	Silent	SNP	A	A	G	rs57144955	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4918122A>G	ENST00000320785.5	+	18	2013	c.1656A>G	c.(1654-1656)ccA>ccG	p.P552P	KIF1C_ENST00000573815.1_3'UTR	NM_006612.5	NP_006603.2	O43896	KIF1C_HUMAN	kinesin family member 1C	552	FHA.				ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|endometrium(4)|kidney(2)|large_intestine(8)|lung(6)|skin(1)|urinary_tract(3)	30						TCCCCCAGCCAGATGGAGAAG	0.587													A|||	170	0.0339457	0.1225	0.0101	5008	,	,		19813	0.0		0.001	False		,,,				2504	0.0				p.P552P	Melanoma(96;1023 1447 10250 19259 33730)	Atlas-SNP	.											.	KIF1C	70	.	0			c.A1656G						PASS	.	A		454,3952		26,402,1775	41.0	29.0	33.0		1656	-9.6	0.1	17	dbSNP_129	33	4,8594		0,4,4295	no	coding-synonymous	KIF1C	NM_006612.5		26,406,6070	GG,GA,AA		0.0465,10.3041,3.522		552/1104	4918122	458,12546	2203	4299	6502	SO:0001819	synonymous_variant	10749	exon18			CCAGCCAGATGGA	U91329	CCDS11065.1	17p13.2	2014-03-03			ENSG00000129250	ENSG00000129250		"""Kinesins"""	6317	protein-coding gene	gene with protein product		603060	"""spastic ataxia 2 (autosomal recessive)"""	SAX2		9685376, 24319291, 24482476	Standard	NM_006612		Approved	SPAX2, SPG58	uc002gan.2	O43896	OTTHUMG00000099451	ENST00000320785.5:c.1656A>G	17.37:g.4918122A>G		76.0	0.0	0		63.0	30.0	0.47619	NM_006612	D3DTL6|O75186|Q5U618	Silent	SNP	ENST00000320785.5	37	CCDS11065.1																																																																																			A|0.964;G|0.036	0.036	strong		0.587	KIF1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216916.1		
PDE4DIP	9659	hgsc.bcm.edu	37	1	144852477	144852477	+	Missense_Mutation	SNP	G	G	A	rs148370554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:144852477G>A	ENST00000369354.3	-	44	7211	c.7022C>T	c.(7021-7023)cCa>cTa	p.P2341L	PDE4DIP_ENST00000313382.9_Missense_Mutation_p.P2235L|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.P2477L|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.P2426L|PDE4DIP_ENST00000369356.4_Intron|PDE4DIP_ENST00000524974.1_5'UTR			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2341					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TGGAGTACATGGCAGAGCCCT	0.512			T	PDGFRB	MPD								.|||	165	0.0329473	0.1203	0.0072	5008	,	,		45392	0.0		0.001	False		,,,				2504	0.0				p.P2341L		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C7022T						PASS	.						50.0	49.0	49.0					1																	144852477		2203	4293	6496	SO:0001583	missense	9659	exon44			GTACATGGCAGAG	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.7022C>T	1.37:g.144852477G>A	ENSP00000358360:p.Pro2341Leu	83.0	0.0	0		118.0	6.0	0.0508475	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	.	4.717	0.133299	0.09032	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000530740;ENST00000369359	T;T;T;T	0.01787	4.64;4.74;4.74;4.75	4.47	0.476	0.16779	.	.	.	.	.	T	0.00845	0.0028	M	0.64404	1.975	0.09310	N	1	B;B	0.12630	0.0;0.006	B;B	0.08055	0.0;0.003	T	0.40961	-0.9535	9	0.54805	T	0.06	.	7.4413	0.27185	0.3516:0.0:0.6483:0.0	.	2235;2341	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	L	2235;2341;2426;2477	ENSP00000327209:P2235L;ENSP00000358360:P2341L;ENSP00000435654:P2426L;ENSP00000358366:P2477L	ENSP00000327209:P2235L	P	-	2	0	PDE4DIP	143563834	0.000000	0.05858	0.001000	0.08648	0.174000	0.22865	0.216000	0.17585	-0.094000	0.12374	-0.274000	0.10170	CCA	.	.	weak		0.512	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
SHROOM3	57619	hgsc.bcm.edu	37	4	77476809	77476809	+	Silent	SNP	T	T	C	rs75039400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:77476809T>C	ENST00000296043.6	+	2	1169	c.216T>C	c.(214-216)gcT>gcC	p.A72A		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	72	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			AACTGCAGGCTGGGGATGAGG	0.577													C|||	84	0.0167732	0.0628	0.0014	5008	,	,		18555	0.0		0.0	False		,,,				2504	0.0				p.A72A		Atlas-SNP	.											.	SHROOM3	134	.	0			c.T216C						PASS	.	C		219,4187	806.1+/-415.8	4,211,1988	110.0	105.0	107.0		216	-7.1	0.0	4	dbSNP_131	107	3,8597	819.2+/-406.8	0,3,4297	no	coding-synonymous	SHROOM3	NM_020859.3		4,214,6285	CC,CT,TT		0.0349,4.9705,1.7069		72/1997	77476809	222,12784	2203	4300	6503	SO:0001819	synonymous_variant	57619	exon2			GCAGGCTGGGGAT	AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.216T>C	4.37:g.77476809T>C		64.0	0.0	0		95.0	40.0	0.421053	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Silent	SNP	ENST00000296043.6	37	CCDS3579.2																																																																																			T|0.980;C|0.020	0.020	strong		0.577	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859	
ADD2	119	hgsc.bcm.edu	37	2	70933494	70933494	+	Missense_Mutation	SNP	T	T	C	rs201443444	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:70933494T>C	ENST00000264436.4	-	3	491	c.47A>G	c.(46-48)cAg>cGg	p.Q16R	ADD2_ENST00000413157.2_Missense_Mutation_p.Q16R|ADD2_ENST00000355733.3_Missense_Mutation_p.Q16R|ADD2_ENST00000473232.1_5'Flank|ADD2_ENST00000430656.1_Missense_Mutation_p.Q32R|ADD2_ENST00000407644.2_Missense_Mutation_p.Q16R	NM_001617.3	NP_001608.1	P35612	ADDB_HUMAN	adducin 2 (beta)	16					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|barbed-end actin filament capping (GO:0051016)|hemopoiesis (GO:0030097)|positive regulation of protein binding (GO:0032092)|protein complex assembly (GO:0006461)	cytoplasmic membrane-bounded vesicle (GO:0016023)|F-actin capping protein complex (GO:0008290)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|spectrin binding (GO:0030507)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(11)|lung(13)|ovary(3)|pancreas(1)|skin(2)	36						AGGCTGCCCCTGCGGGGGCGG	0.642													T|||	73	0.0145767	0.0204	0.0144	5008	,	,		17067	0.0169		0.0189	False		,,,				2504	0.0				p.Q32R		Atlas-SNP	.											.	ADD2	261	.	0			c.A95G						PASS	.	T	ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN	67,4337	58.1+/-94.6	1,65,2136	43.0	48.0	46.0		47,95,47,47,47	5.1	1.0	2	dbSNP_134	46	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense	ADD2	NM_001185054.1,NM_001185055.1,NM_001617.3,NM_017482.3,NM_017488.3	43,43,43,43,43	1,65,6436	CC,CT,TT		0.0,1.5213,0.5152	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	16/727,32/576,16/727,16/560,16/644	70933494	67,12937	2202	4300	6502	SO:0001583	missense	119	exon2			TGCCCCTGCGGGG	X58199	CCDS1906.1, CCDS1909.1, CCDS46318.1, CCDS54365.1	2p13.3	2008-02-05			ENSG00000075340	ENSG00000075340			244	protein-coding gene	gene with protein product		102681				1840603	Standard	NM_001617		Approved	ADDB	uc021vjc.1	P35612	OTTHUMG00000129710	ENST00000264436.4:c.47A>G	2.37:g.70933494T>C	ENSP00000264436:p.Gln16Arg	111.0	0.0	0		111.0	54.0	0.486486	NM_001185055	A8K4P2|B4DM17|D6W5G7|D6W5G8|Q13482|Q16412|Q59G82|Q5U5P4|Q6P0P2|Q6PGQ4|Q7Z688|Q7Z689|Q7Z690|Q7Z691	Missense_Mutation	SNP	ENST00000264436.4	37	CCDS1906.1	48	0.02197802197802198	27	0.054878048780487805	6	0.016574585635359115	6	0.01048951048951049	9	0.011873350923482849	T	13.89	2.372523	0.42003	0.015213	0.0	ENSG00000075340	ENST00000264436;ENST00000407644;ENST00000456320;ENST00000355733;ENST00000522886;ENST00000264439;ENST00000356565;ENST00000517596;ENST00000413157;ENST00000430656;ENST00000415348;ENST00000425976;ENST00000447731	T;T;T;T;T;T;T;T	0.30448	1.58;1.58;1.58;1.58;1.58;1.53;1.58;1.58	5.11	5.11	0.69529	.	0.367672	0.26875	N	0.022043	T	0.03520	0.0101	L	0.29908	0.895	0.32494	N	0.539867	B;B;D;B;B;P	0.55385	0.138;0.058;0.971;0.215;0.18;0.867	B;B;B;B;B;B	0.39217	0.065;0.098;0.294;0.065;0.109;0.269	T	0.09400	-1.0676	10	0.52906	T	0.07	-11.8187	13.1749	0.59621	0.0:0.0:0.0:1.0	.	32;16;16;16;16;16	B4DM17;P35612-4;E9PAN1;Q05DK5;P35612;P35612-3	.;.;.;.;ADDB_HUMAN;.	R	16;16;16;16;16;16;16;16;16;32;16;16;16	ENSP00000264436:Q16R;ENSP00000384677:Q16R;ENSP00000347972:Q16R;ENSP00000430243:Q16R;ENSP00000388072:Q16R;ENSP00000398112:Q32R;ENSP00000412357:Q16R;ENSP00000412681:Q16R	ENSP00000264436:Q16R	Q	-	2	0	ADD2	70787002	0.024000	0.19004	0.998000	0.56505	0.919000	0.55068	0.633000	0.24598	2.265000	0.75225	0.482000	0.46254	CAG	T|0.978;C|0.022	0.022	strong		0.642	ADD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251918.4	NM_001617	
NLRP6	171389	hgsc.bcm.edu	37	11	284477	284477	+	Missense_Mutation	SNP	T	T	C	rs74044411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:284477T>C	ENST00000312165.5	+	7	2375	c.2375T>C	c.(2374-2376)gTa>gCa	p.V792A	NLRP6_ENST00000534750.1_Missense_Mutation_p.V791A|RP11-326C3.2_ENST00000533924.1_RNA	NM_138329.1	NP_612202.2	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	792					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|regulation of inflammatory response (GO:0050727)|response to bacterium (GO:0009617)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|vasopressin receptor activity (GO:0005000)			breast(1)|skin(1)|upper_aerodigestive_tract(2)	4		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)		TCCCACAGGGTACAGCTGCCT	0.697													T|||	324	0.0646965	0.2337	0.0202	5008	,	,		14829	0.0		0.001	False		,,,				2504	0.0				p.V792A		Atlas-SNP	.											.	NLRP6	4	.	0			c.T2375C						PASS	.	T	ALA/VAL	832,3574	301.5+/-286.9	87,658,1458	26.0	28.0	27.0		2375	1.9	0.1	11	dbSNP_130	27	11,8589	7.1+/-27.0	0,11,4289	yes	missense	NLRP6	NM_138329.1	64	87,669,5747	CC,CT,TT		0.1279,18.8833,6.4816	benign	792/893	284477	843,12163	2203	4300	6503	SO:0001583	missense	171389	exon7			ACAGGGTACAGCT	AF479748	CCDS7693.1, CCDS60680.1	11p15	2006-12-08	2006-12-08	2006-12-08	ENSG00000174885	ENSG00000174885		"""Nucleotide-binding domain and leucine rich repeat containing"""	22944	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 6"""	609650	"""NACHT, leucine rich repeat and PYD containing 6"""	NALP6		12563287, 12019269	Standard	NM_138329		Approved	PYPAF5, PAN3, CLR11.4	uc010qvs.3	P59044	OTTHUMG00000119070	ENST00000312165.5:c.2375T>C	11.37:g.284477T>C	ENSP00000309767:p.Val792Ala	87.0	0.0	0		79.0	30.0	0.379747	NM_138329	A8K9F3|E9PJZ8	Missense_Mutation	SNP	ENST00000312165.5	37	CCDS7693.1	99	0.04532967032967033	90	0.18292682926829268	8	0.022099447513812154	0	0.0	1	0.0013192612137203166	T	10.94	1.491727	0.26774	0.188833	0.001279	ENSG00000174885	ENST00000534750;ENST00000312165	T;T	0.54675	0.56;0.56	3.06	1.93	0.25924	.	1.705140	0.04569	U	0.393007	T	0.00073	0.0002	L	0.40543	1.245	0.09310	N	1	B;B	0.29037	0.006;0.231	B;B	0.22386	0.008;0.039	T	0.07927	-1.0747	10	0.87932	D	0	.	6.1513	0.20313	0.0:0.1362:0.0:0.8638	.	791;792	E9PJZ8;P59044	.;NALP6_HUMAN	A	791;792	ENSP00000433617:V791A;ENSP00000309767:V792A	ENSP00000309767:V792A	V	+	2	0	NLRP6	274477	0.524000	0.26282	0.112000	0.21494	0.161000	0.22273	1.453000	0.35167	1.414000	0.47017	0.374000	0.22700	GTA	T|0.940;C|0.060	0.060	strong		0.697	NLRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239283.1	NM_138329	
TMEFF2	23671	hgsc.bcm.edu	37	2	192922499	192922499	+	Missense_Mutation	SNP	G	G	A	rs61744272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:192922499G>A	ENST00000272771.5	-	5	1626	c.442C>T	c.(442-444)Cat>Tat	p.H148Y	TMEFF2_ENST00000392314.1_Missense_Mutation_p.H148Y	NM_016192.2	NP_057276.2	Q9UIK5	TEFF2_HUMAN	transmembrane protein with EGF-like and two follistatin-like domains 2	148						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)				breast(2)|cervix(1)|kidney(2)|large_intestine(4)|liver(1)|lung(12)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(117;0.0835)			GAGCCTTCATGGACTGTAGGA	0.403													G|||	92	0.0183706	0.0635	0.0086	5008	,	,		18753	0.0		0.002	False		,,,				2504	0.0				p.H148Y	Pancreas(50;1277 1381 28487 47072)	Atlas-SNP	.											.	TMEFF2	54	.	0			c.C442T						PASS	.	G	TYR/HIS	282,4124	158.5+/-191.2	10,262,1931	95.0	86.0	89.0		442	4.0	0.9	2	dbSNP_129	89	2,8598	2.2+/-6.3	0,2,4298	yes	missense	TMEFF2	NM_016192.2	83	10,264,6229	AA,AG,GG		0.0233,6.4004,2.1836	possibly-damaging	148/375	192922499	284,12722	2203	4300	6503	SO:0001583	missense	23671	exon5			CTTCATGGACTGT	AB017269	CCDS2314.1	2q32.3	2010-05-04			ENSG00000144339	ENSG00000144339			11867	protein-coding gene	gene with protein product	"""transmembrane protein TENB2"", ""tomoregulin"", ""cancer/testis antigen family 120, member 2"""	605734				10903839	Standard	NM_016192		Approved	TENB2, HPP1, TR, TPEF, CT120.2	uc002utc.3	Q9UIK5	OTTHUMG00000132723	ENST00000272771.5:c.442C>T	2.37:g.192922499G>A	ENSP00000272771:p.His148Tyr	130.0	0.0	0		128.0	68.0	0.53125	NM_016192	Q2FA44|Q4ZFW4|Q53H90|Q53RE1|Q8N2R5|Q9NR15|Q9NSS5|Q9P2Y9|Q9UK65	Missense_Mutation	SNP	ENST00000272771.5	37	CCDS2314.1	31	0.014194139194139194	27	0.054878048780487805	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	G	1.594	-0.528334	0.04112	0.064004	2.33E-4	ENSG00000144339	ENST00000392314;ENST00000272771	T;T	0.58797	0.31;0.31	4.93	3.99	0.46301	.	0.338199	0.31335	N	0.007834	T	0.03827	0.0108	N	0.03608	-0.345	0.80722	D	1	B	0.02656	0.0	B	0.06405	0.002	T	0.03043	-1.1079	10	0.15499	T	0.54	-18.1134	13.1246	0.59346	0.0:0.0:0.78:0.2199	.	148	Q9UIK5	TEFF2_HUMAN	Y	148	ENSP00000376128:H148Y;ENSP00000272771:H148Y	ENSP00000272771:H148Y	H	-	1	0	TMEFF2	192630744	1.000000	0.71417	0.949000	0.38748	0.824000	0.46624	3.823000	0.55715	2.713000	0.92767	0.655000	0.94253	CAT	G|0.982;A|0.018	0.018	strong		0.403	TMEFF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256065.2	NM_016192	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057343	46057343	+	Silent	SNP	C	C	A	rs76468958	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46057343C>A	ENST00000380095.1	+	1	71	c.9C>A	c.(7-9)gcC>gcA	p.A3A	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	3						keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						GCATGGCCGCCTCCACCATGT	0.647													A|||	197	0.0393371	0.1362	0.0043	5008	,	,		18834	0.002		0.001	False		,,,				2504	0.0112				p.A3A		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.C9A						PASS	.	A	,	601,3805	770.0+/-413.7	46,509,1648	107.0	115.0	112.0		,9	-4.6	0.0	21	dbSNP_131	112	5,8595	818.7+/-406.8	0,5,4295	no	intron,coding-synonymous	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,	46,514,5943	AA,AC,CC		0.0581,13.6405,4.6594	,	,3/252	46057343	606,12400	2203	4300	6503	SO:0001819	synonymous_variant	353333	exon1			GGCCGCCTCCACC	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.9C>A	21.37:g.46057343C>A		192.0	0.0	0		219.0	103.0	0.47032	NM_181688		Silent	SNP	ENST00000380095.1	37	CCDS33585.1																																																																																			C|0.960;A|0.040	0.040	strong		0.647	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
PARP15	165631	hgsc.bcm.edu	37	3	122354796	122354796	+	Missense_Mutation	SNP	G	G	C	rs145474072	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122354796G>C	ENST00000464300.2	+	12	1952	c.1886G>C	c.(1885-1887)cGt>cCt	p.R629P	PARP15_ENST00000483793.1_Missense_Mutation_p.R434P|PARP15_ENST00000493645.1_Missense_Mutation_p.R326P|PARP15_ENST00000465304.1_3'UTR|PARP15_ENST00000310366.4_Missense_Mutation_p.R395P	NM_001113523.1	NP_001106995.1	Q460N3	PAR15_HUMAN	poly (ADP-ribose) polymerase family, member 15	629	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(114;0.0531)		ACAAAGGGACGTGCAGGATTA	0.478													G|||	29	0.00579073	0.0219	0.0	5008	,	,		19916	0.0		0.0	False		,,,				2504	0.0				p.R629P		Atlas-SNP	.											.	PARP15	115	.	0			c.G1886C						PASS	.	G	PRO/ARG,PRO/ARG	66,4340	62.3+/-99.4	2,62,2139	162.0	132.0	142.0		1184,1886	-4.6	0.0	3	dbSNP_134	142	0,8600		0,0,4300	yes	missense,missense	PARP15	NM_152615.1,NM_001113523.1	103,103	2,62,6439	CC,CG,GG		0.0,1.498,0.5075	benign,benign	395/445,629/679	122354796	66,12940	2203	4300	6503	SO:0001583	missense	165631	exon12			AGGGACGTGCAGG	AK097916	CCDS3016.1, CCDS46893.1	3q21	2010-02-16			ENSG00000173200	ENSG00000173200		"""Poly (ADP-ribose) polymerases"""	26876	protein-coding gene	gene with protein product		612066				15273990	Standard	NM_001113523		Approved	FLJ40597, pART7	uc003efm.2	Q460N3	OTTHUMG00000159523	ENST00000464300.2:c.1886G>C	3.37:g.122354796G>C	ENSP00000417214:p.Arg629Pro	127.0	0.0	0		115.0	58.0	0.504348	NM_001113523	J3KR47|Q8N1K3	Missense_Mutation	SNP	ENST00000464300.2	37	CCDS46893.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	G	8.506	0.865423	0.17250	0.01498	0.0	ENSG00000173200	ENST00000464300;ENST00000483793;ENST00000542823;ENST00000310366;ENST00000493645	T;T;T;T	0.13657	2.57;2.57;2.57;2.57	3.99	-4.55	0.03441	Poly(ADP-ribose) polymerase, catalytic domain (2);	.	.	.	.	T	0.05686	0.0149	N	0.26162	0.8	0.09310	N	1	P;B;B;D;B	0.56521	0.566;0.246;0.427;0.976;0.124	B;B;B;B;B	0.43386	0.348;0.222;0.119;0.418;0.162	T	0.14504	-1.0470	9	0.45353	T	0.12	.	5.9187	0.19070	0.3756:0.2583:0.3661:0.0	.	326;395;376;434;607	B7ZL48;Q460N3-2;F5H8I1;C9J7L3;Q460N3	.;.;.;.;PAR15_HUMAN	P	629;434;376;395;326	ENSP00000417214:R629P;ENSP00000417785:R434P;ENSP00000308436:R395P;ENSP00000419488:R326P	ENSP00000308436:R395P	R	+	2	0	PARP15	123837486	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.511000	0.06321	-1.056000	0.03205	-1.043000	0.02367	CGT	G|0.995;C|0.005	0.005	strong		0.478	PARP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355964.2	NM_152615	
OR5AK2	390181	hgsc.bcm.edu	37	11	56756565	56756565	+	Silent	SNP	G	G	A	rs62001001	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:56756565G>A	ENST00000326855.2	+	1	219	c.177G>A	c.(175-177)acG>acA	p.T59T		NM_001005323.1	NP_001005323.1	Q8NH90	O5AK2_HUMAN	olfactory receptor, family 5, subfamily AK, member 2	59						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.T59T(1)		breast(3)|endometrium(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21						AAACACTCACGTACTTTTTTC	0.363													.|||	58	0.0115815	0.0431	0.0014	5008	,	,		21424	0.0		0.0	False		,,,				2504	0.0				p.T59T		Atlas-SNP	.											OR5AK2,NS,carcinoma,0,1	OR5AK2	45	1	1	Substitution - coding silent(1)	prostate(1)	c.G177A						PASS	.	G		174,4228	113.8+/-151.8	2,170,2029	118.0	104.0	109.0		177	0.4	0.9	11	dbSNP_129	109	3,8589	2.2+/-6.3	0,3,4293	no	coding-synonymous	OR5AK2	NM_001005323.1		2,173,6322	AA,AG,GG		0.0349,3.9527,1.3622		59/310	56756565	177,12817	2201	4296	6497	SO:0001819	synonymous_variant	390181	exon1			ACTCACGTACTTT	AB065496	CCDS31538.1	11q11	2012-08-09			ENSG00000181273	ENSG00000181273		"""GPCR / Class A : Olfactory receptors"""	15251	protein-coding gene	gene with protein product							Standard	NM_001005323		Approved		uc010rjp.2	Q8NH90	OTTHUMG00000167019	ENST00000326855.2:c.177G>A	11.37:g.56756565G>A		247.0	0.0	0		251.0	116.0	0.462151	NM_001005323	B2RNZ9	Silent	SNP	ENST00000326855.2	37	CCDS31538.1																																																																																			G|0.987;A|0.013	0.013	strong		0.363	OR5AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392446.1	NM_001005323	
CUL5	8065	hgsc.bcm.edu	37	11	107943124	107943124	+	Silent	SNP	T	T	C	rs111339569	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:107943124T>C	ENST00000393094.2	+	9	1556	c.940T>C	c.(940-942)Ttg>Ctg	p.L314L		NM_003478.3	NP_003469.2	Q93034	CUL5_HUMAN	cullin 5	314					calcium ion transmembrane transport (GO:0070588)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cytosolic calcium ion homeostasis (GO:0051480)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|response to osmotic stress (GO:0006970)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	Cul5-RING ubiquitin ligase complex (GO:0031466)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|receptor activity (GO:0004872)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(1)|prostate(1)|skin(1)	23		all_cancers(61;7.09e-10)|all_epithelial(67;2.97e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|Melanoma(852;4.48e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;3.58e-05)|Epithelial(105;4.68e-05)|all cancers(92;0.00122)|OV - Ovarian serous cystadenocarcinoma(223;0.217)		GTTGAAAGACTTGGAGGAACA	0.348													T|||	72	0.014377	0.053	0.0029	5008	,	,		19109	0.0		0.0	False		,,,				2504	0.0				p.L314L		Atlas-SNP	.											.	CUL5	71	.	0			c.T940C						PASS	.	T		204,4198	127.0+/-164.0	4,196,2001	113.0	111.0	112.0		940	3.9	1.0	11	dbSNP_132	112	1,8595		0,1,4297	no	coding-synonymous	CUL5	NM_003478.3		4,197,6298	CC,CT,TT		0.0116,4.6343,1.5772		314/781	107943124	205,12793	2201	4298	6499	SO:0001819	synonymous_variant	8065	exon9			AAAGACTTGGAGG	X81882	CCDS31668.1	11q22.3	2011-05-24			ENSG00000166266	ENSG00000166266			2556	protein-coding gene	gene with protein product		601741				8681378, 9037604	Standard	XM_005271682		Approved	VACM-1	uc001pjv.3	Q93034	OTTHUMG00000166369	ENST00000393094.2:c.940T>C	11.37:g.107943124T>C		81.0	0.0	0		62.0	28.0	0.451613	NM_003478	A8K960|O14766|Q9BZC6	Silent	SNP	ENST00000393094.2	37	CCDS31668.1																																																																																			T|0.987;C|0.013	0.013	strong		0.348	CUL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389429.1		
SPEG	10290	hgsc.bcm.edu	37	2	220347907	220347907	+	Missense_Mutation	SNP	A	A	G	rs200747365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220347907A>G	ENST00000312358.7	+	30	5854	c.5722A>G	c.(5722-5724)Atg>Gtg	p.M1908V	SPEG_ENST00000485813.1_3'UTR|AC053503.11_ENST00000429882.1_RNA	NM_005876.4	NP_005867.3	Q15772	SPEG_HUMAN	SPEG complex locus	1908					cardiac muscle cell development (GO:0055013)|in utero embryonic development (GO:0001701)|muscle organ development (GO:0007517)|negative regulation of cell proliferation (GO:0008285)|respiratory system development (GO:0060541)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(3)|endometrium(10)|kidney(2)|large_intestine(9)|lung(42)|ovary(5)|pancreas(1)|prostate(8)|skin(1)|stomach(9)|upper_aerodigestive_tract(4)|urinary_tract(4)	100		Renal(207;0.0183)		Epithelial(149;4.5e-10)|all cancers(144;7.93e-08)|Lung(261;0.00639)|LUSC - Lung squamous cell carcinoma(224;0.00829)|READ - Rectum adenocarcinoma(5;0.163)		GTGGGTGACCATGCCCAGAAG	0.672													A|||	9	0.00179712	0.0053	0.0029	5008	,	,		14834	0.0		0.0	False		,,,				2504	0.0				p.M1908V		Atlas-SNP	.											.	SPEG	272	.	0			c.A5722G						PASS	.	A	VAL/MET	26,3634		0,26,1804	8.0	10.0	9.0		5722	2.7	1.0	2		9	0,8058		0,0,4029	no	missense	SPEG	NM_005876.4	21	0,26,5833	GG,GA,AA		0.0,0.7104,0.2219	benign	1908/3268	220347907	26,11692	1830	4029	5859	SO:0001583	missense	10290	exon30			GTGACCATGCCCA	BC006346	CCDS42824.1, CCDS54432.1	2q35	2013-01-11	2006-04-27	2006-04-27	ENSG00000072195	ENSG00000072195		"""Immunoglobulin superfamily / I-set domain containing"""	16901	protein-coding gene	gene with protein product		615950	"""aortic preferentially expressed gene 1"""	APEG1		8663449, 10973969	Standard	NM_005876		Approved	MGC12676, KIAA1297, SPEGalpha, SPEGbeta, BPEG	uc010fwg.3	Q15772	OTTHUMG00000058925	ENST00000312358.7:c.5722A>G	2.37:g.220347907A>G	ENSP00000311684:p.Met1908Val	88.0	0.0	0		84.0	42.0	0.5	NM_005876	A8K0G6|A8MRU0|Q27J74|Q695L1|Q6FGA6|Q6ZQW1|Q6ZTL8|Q9P2P9	Missense_Mutation	SNP	ENST00000312358.7	37	CCDS42824.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	A	8.935	0.964345	0.18583	0.007104	0.0	ENSG00000072195	ENST00000312358;ENST00000265327	T	0.59772	0.24	4.75	2.74	0.32292	Protein kinase-like domain (1);	0.410582	0.17489	N	0.172415	T	0.11367	0.0277	N	0.00377	-1.585	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.26018	-1.0115	10	0.02654	T	1	.	5.4349	0.16476	0.3428:0.0:0.6572:0.0	.	1908	Q15772	SPEG_HUMAN	V	1908	ENSP00000311684:M1908V	ENSP00000265327:M1908V	M	+	1	0	SPEG	220056151	0.991000	0.36638	0.999000	0.59377	0.966000	0.64601	2.141000	0.42168	0.456000	0.26937	0.374000	0.22700	ATG	A|1.000;G|0.000	0.000	strong		0.672	SPEG-004	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130252.2	NM_005876	
C21orf2	755	hgsc.bcm.edu	37	21	45755646	45755646	+	Silent	SNP	C	C	T	rs146104157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45755646C>T	ENST00000339818.4	-	3	345	c.138G>A	c.(136-138)acG>acA	p.T46T	C21orf2_ENST00000325223.7_Silent_p.T46T|C21orf2_ENST00000397956.3_Silent_p.T46T|AP001062.7_ENST00000448927.1_RNA|C21orf2_ENST00000496321.1_5'UTR	NM_001271440.1|NM_004928.2	NP_001258369.1|NP_004919.1	O43822	CU002_HUMAN	chromosome 21 open reading frame 2	46					cilium morphogenesis (GO:0060271)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				endometrium(2)	2				Colorectal(79;0.0806)		GGTACCTGAGCGTGATCACCT	0.607													C|||	13	0.00259585	0.0091	0.0	5008	,	,		20080	0.0		0.0	False		,,,				2504	0.001				p.T46T		Atlas-SNP	.											.	C21orf2	10	.	0			c.G138A						PASS	.	C		35,4369		0,35,2167	65.0	42.0	50.0		138	-3.1	1.0	21	dbSNP_134	50	1,8587		0,1,4293	no	coding-synonymous	C21orf2	NM_004928.2		0,36,6460	TT,TC,CC		0.0116,0.7947,0.2771		46/257	45755646	36,12956	2202	4294	6496	SO:0001819	synonymous_variant	755	exon3			CCTGAGCGTGATC	Y11392	CCDS13709.1, CCDS59444.1, CCDS59445.1	21q22.3	2014-03-24			ENSG00000160226	ENSG00000160226			1260	protein-coding gene	gene with protein product	"""nuclear encoded mitochondrial protein"", ""leucine rich repeat containing 76"""	603191				9465297	Standard	NM_004928		Approved	YF5, A2, LRRC76	uc002zeq.2	O43822	OTTHUMG00000086909	ENST00000339818.4:c.138G>A	21.37:g.45755646C>T		140.0	0.0	0		178.0	79.0	0.44382	NM_004928	A8MPS9|O14993|Q8N5X6|Q99837|Q99838	Silent	SNP	ENST00000339818.4	37	CCDS13709.1																																																																																			C|0.997;T|0.003	0.003	strong		0.607	C21orf2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195799.1	NM_004928	
ZMIZ2	83637	hgsc.bcm.edu	37	7	44804989	44804989	+	Missense_Mutation	SNP	G	G	A	rs114574038	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:44804989G>A	ENST00000309315.4	+	16	2176	c.2053G>A	c.(2053-2055)Gtg>Atg	p.V685M	ZMIZ2_ENST00000441627.1_Missense_Mutation_p.V685M|ZMIZ2_ENST00000413916.1_Missense_Mutation_p.V627M|ZMIZ2_ENST00000265346.7_Missense_Mutation_p.V659M|ZMIZ2_ENST00000433667.1_Missense_Mutation_p.V653M	NM_031449.3	NP_113637.3	Q8NF64	ZMIZ2_HUMAN	zinc finger, MIZ-type containing 2	685					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	mitochondrion (GO:0005739)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|zinc ion binding (GO:0008270)			breast(3)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	35						GCCAGTGCCCGTGAAGCCTGA	0.637													G|||	47	0.00938498	0.0333	0.0043	5008	,	,		15398	0.0		0.0	False		,,,				2504	0.0				p.V685M	NSCLC(20;604 852 1948 16908 50522)	Atlas-SNP	.											.	ZMIZ2	82	.	0			c.G2053A						PASS	.	G	MET/VAL,MET/VAL	122,4158		1,120,2019	37.0	40.0	39.0		2053,1975	3.2	0.9	7	dbSNP_132	39	2,8500		0,2,4249	yes	missense,missense	ZMIZ2	NM_031449.3,NM_174929.2	21,21	1,122,6268	AA,AG,GG		0.0235,2.8505,0.9701	possibly-damaging,possibly-damaging	685/921,659/895	44804989	124,12658	2140	4251	6391	SO:0001583	missense	83637	exon16			GTGCCCGTGAAGC	AK090415	CCDS43576.1, CCDS43577.1, CCDS75591.1	7p13	2009-11-06			ENSG00000122515	ENSG00000122515		"""Zinc fingers, MIZ-type"""	22229	protein-coding gene	gene with protein product		611196					Standard	XM_005249866		Approved	KIAA1886, hZIMP7, ZIMP7, DKFZp761I2123, NET27	uc003tlr.3	Q8NF64	OTTHUMG00000155817	ENST00000309315.4:c.2053G>A	7.37:g.44804989G>A	ENSP00000311778:p.Val685Met	68.0	0.0	0		77.0	34.0	0.441558	NM_031449	A4D2K7|D3DVL1|O94790|Q0VGB4|Q659A8|Q6JKL5|Q8WTX8|Q96Q01|Q9BQH7	Missense_Mutation	SNP	ENST00000309315.4	37	CCDS43576.1	20	0.009157509157509158	16	0.032520325203252036	2	0.0055248618784530384	2	0.0034965034965034965	0	0.0	G	19.81	3.896626	0.72639	0.028505	2.35E-4	ENSG00000122515	ENST00000413916;ENST00000309315;ENST00000441627;ENST00000433667;ENST00000265346;ENST00000414051	T;T;T;T;T	0.32753	1.44;1.45;1.45;1.45;1.44	5.14	3.18	0.36537	.	0.277121	0.24642	N	0.036798	T	0.19446	0.0467	M	0.73598	2.24	0.52501	D	0.999953	P;P;P	0.50156	0.932;0.888;0.932	P;P;P	0.54100	0.656;0.557;0.742	T	0.06463	-1.0825	10	0.45353	T	0.12	-7.8333	7.1482	0.25595	0.284:0.0:0.716:0.0	.	659;685;627	Q8NF64-2;Q8NF64;Q8NF64-3	.;ZMIZ2_HUMAN;.	M	627;685;685;653;659;688	ENSP00000409648:V627M;ENSP00000311778:V685M;ENSP00000414723:V685M;ENSP00000396601:V653M;ENSP00000265346:V659M	ENSP00000265346:V659M	V	+	1	0	ZMIZ2	44771514	0.800000	0.28916	0.881000	0.34555	0.984000	0.73092	1.202000	0.32271	1.398000	0.46701	0.561000	0.74099	GTG	G|0.990;A|0.010	0.010	strong		0.637	ZMIZ2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341790.1	NM_031449	
ARHGEF2	9181	hgsc.bcm.edu	37	1	155935158	155935158	+	Silent	SNP	T	T	C	rs149517516	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:155935158T>C	ENST00000361247.4	-	6	615	c.516A>G	c.(514-516)tcA>tcG	p.S172S	ARHGEF2_ENST00000313695.7_Silent_p.S145S|ARHGEF2_ENST00000462460.2_Silent_p.S217S|ARHGEF2_ENST00000368315.4_Silent_p.S173S|ARHGEF2_ENST00000368316.1_Silent_p.S145S|ARHGEF2_ENST00000313667.4_Silent_p.S172S|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	172					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)					CTGTGGACTGTGAGAGGATCC	0.587													T|||	17	0.00339457	0.0129	0.0	5008	,	,		19917	0.0		0.0	False		,,,				2504	0.0				p.S172S	Melanoma(178;35 2768 6610 28839)	Atlas-SNP	.											.	ARHGEF2	81	.	0			c.A516G						PASS	.	T	,,	90,4316	73.6+/-111.7	1,88,2114	72.0	72.0	72.0		516,516,435	-11.3	0.3	1	dbSNP_134	72	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	ARHGEF2	NM_001162383.1,NM_001162384.1,NM_004723.3	,,	1,88,6414	CC,CT,TT		0.0,2.0427,0.692	,,	172/987,172/986,145/959	155935158	90,12916	2203	4300	6503	SO:0001819	synonymous_variant	9181	exon6			GGACTGTGAGAGG	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.516A>G	1.37:g.155935158T>C		158.0	0.0	0		170.0	87.0	0.511765	NM_001162383	D3DVA6|O75142|Q15079|Q5VY92|Q8TDA3|Q8WUG4|Q9H023	Silent	SNP	ENST00000361247.4	37	CCDS53376.1																																																																																			T|0.995;C|0.005	0.005	strong		0.587	ARHGEF2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046204.2	NM_004723	
STK32C	282974	hgsc.bcm.edu	37	10	134038817	134038817	+	Missense_Mutation	SNP	C	C	T	rs148669059	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:134038817C>T	ENST00000368622.1	-	7	826	c.445G>A	c.(445-447)Gtc>Atc	p.V149I	STK32C_ENST00000368625.4_Missense_Mutation_p.V279I					serine/threonine kinase 32C											breast(1)|endometrium(2)|large_intestine(2)|lung(15)|ovary(2)|skin(1)	23		all_cancers(35;2.72e-11)|all_epithelial(44;2.33e-08)|Lung NSC(174;0.000855)|all_lung(145;0.00146)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.112)|Melanoma(40;0.124)|Glioma(114;0.203)		Epithelial(32;3.99e-05)|all cancers(32;5.58e-05)|OV - Ovarian serous cystadenocarcinoma(35;9.96e-05)|BRCA - Breast invasive adenocarcinoma(275;0.222)		CCGCCGTTGACAAAAGAGTGG	0.627													C|||	10	0.00199681	0.0068	0.0014	5008	,	,		18797	0.0		0.0	False		,,,				2504	0.0				p.V266I		Atlas-SNP	.											.	STK32C	61	.	0			c.G796A						PASS	.	C	ILE/VAL	38,4360	40.8+/-73.8	0,38,2161	27.0	30.0	29.0		796	4.5	1.0	10	dbSNP_134	29	2,8592	2.2+/-6.3	0,2,4295	yes	missense	STK32C	NM_173575.2	29	0,40,6456	TT,TC,CC		0.0233,0.864,0.3079	benign	266/487	134038817	40,12952	2199	4297	6496	SO:0001583	missense	282974	exon7			CGTTGACAAAAGA	AK057849	CCDS7666.1	10q26.3	2004-07-22			ENSG00000165752	ENSG00000165752			21332	protein-coding gene	gene with protein product							Standard	NM_173575		Approved	PKE, MGC23665, YANK3	uc001lle.1	Q86UX6	OTTHUMG00000019285	ENST00000368622.1:c.445G>A	10.37:g.134038817C>T	ENSP00000357611:p.Val149Ile	137.0	0.0	0		102.0	54.0	0.529412	NM_173575		Missense_Mutation	SNP	ENST00000368622.1	37		.	.	.	.	.	.	.	.	.	.	C	18.26	3.583708	0.65992	0.00864	2.33E-4	ENSG00000165752	ENST00000368622;ENST00000298630;ENST00000368625	T;T;T	0.62364	0.03;0.03;0.03	4.49	4.49	0.54785	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.264823	0.24443	N	0.038493	T	0.47655	0.1457	N	0.14661	0.345	0.42125	D	0.991448	P;P;P	0.39376	0.67;0.629;0.577	P;B;B	0.50537	0.643;0.439;0.179	T	0.56962	-0.7892	10	0.46703	T	0.11	.	11.5206	0.50549	0.0:0.7538:0.2461:0.0	.	279;266;149	B7Z7J1;Q86UX6;Q86UX6-2	.;ST32C_HUMAN;.	I	149;266;279	ENSP00000357611:V149I;ENSP00000298630:V266I;ENSP00000357614:V279I	ENSP00000298630:V266I	V	-	1	0	STK32C	133888807	0.991000	0.36638	0.998000	0.56505	0.753000	0.42808	2.948000	0.49066	2.059000	0.61396	0.585000	0.79938	GTC	C|0.996;T|0.004	0.004	strong		0.627	STK32C-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000051068.2	NM_173575	
CST4	1472	hgsc.bcm.edu	37	20	23669598	23669598	+	Silent	SNP	C	C	T	rs73902132	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:23669598C>T	ENST00000217423.3	-	1	79	c.9G>A	c.(7-9)cgG>cgA	p.R3R		NM_001899.2	NP_001890.1	P01036	CYTS_HUMAN	cystatin S	3					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	16	Lung NSC(19;0.0789)|Colorectal(13;0.0993)|all_lung(19;0.169)					TACACAGAGGCCGGGCCATGG	0.617													.|||	170	0.0339457	0.1225	0.0115	5008	,	,		15350	0.0		0.0	False		,,,				2504	0.0				p.R3R		Atlas-SNP	.											.	CST4	37	.	0			c.G9A						PASS	.	C		418,3988	202.5+/-225.2	18,382,1803	44.0	44.0	44.0		9	-0.2	0.0	20	dbSNP_130	44	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	CST4	NM_001899.2		18,385,6100	TT,TC,CC		0.0349,9.4871,3.237		3/142	23669598	421,12585	2203	4300	6503	SO:0001819	synonymous_variant	1472	exon1			CAGAGGCCGGGCC		CCDS13159.1	20p11.2	2008-04-15			ENSG00000101441	ENSG00000101441			2476	protein-coding gene	gene with protein product		123857				1801729	Standard	NM_001899		Approved		uc002wto.1	P01036	OTTHUMG00000032083	ENST00000217423.3:c.9G>A	20.37:g.23669598C>T		93.0	0.0	0		109.0	40.0	0.366972	NM_001899	Q9UBI5|Q9UCS9	Silent	SNP	ENST00000217423.3	37	CCDS13159.1																																																																																			C|0.964;T|0.036	0.036	strong		0.617	CST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078349.2	NM_001899	
MTPN	136319	hgsc.bcm.edu	37	7	135612057	135612057	+	3'UTR	SNP	G	G	C	rs78834486	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:135612057G>C	ENST00000393085.3	-	0	3189				LUZP6_ENST00000589735.1_Missense_Mutation_p.P48A|AC015987.1_ENST00000419211.1_RNA|AC015987.2_ENST00000416501.1_5'UTR	NM_001128619.2|NM_145808.3	NP_001122091.2|NP_665807.1	P58546	MTPN_HUMAN	myotrophin						catecholamine metabolic process (GO:0006584)|cell growth (GO:0016049)|cerebellar granule cell differentiation (GO:0021707)|neuron differentiation (GO:0030182)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell growth (GO:0030307)|positive regulation of macromolecule biosynthetic process (GO:0010557)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein metabolic process (GO:0051247)|regulation of barbed-end actin filament capping (GO:2000812)|regulation of striated muscle tissue development (GO:0016202)|regulation of translation (GO:0006417)|skeletal muscle tissue regeneration (GO:0043403)|striated muscle cell differentiation (GO:0051146)	axon (GO:0030424)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|nucleus (GO:0005634)				endometrium(1)|lung(4)|prostate(1)	6						GAACTACTTGGGATATTCAAG	0.418													G|||	27	0.00539137	0.0197	0.0014	5008	,	,		19246	0.0		0.0	False		,,,				2504	0.0				p.P48A		Atlas-SNP	.											.	.	.	.	0			c.C142G						PASS	.	G	ALA/PRO,	20,1364		0,20,672	172.0	145.0	153.0		142,	-2.5	0.0	7	dbSNP_132	153	0,3182		0,0,1591	no	missense,utr-3	MTPN,LUZP6	NM_001128619.1,NM_145808.3	27,	0,20,2263	CC,CG,GG		0.0,1.4451,0.438	,	48/59,	135612057	20,4546	692	1591	2283	SO:0001624	3_prime_UTR_variant	767558	exon4			TACTTGGGATATT	AC015987	CCDS5842.1	7q33-q35	2013-01-10			ENSG00000105887	ENSG00000105887		"""Ankyrin repeat domain containing"""	15667	protein-coding gene	gene with protein product	"""granule cell differentiation protein"""	606484				11474205	Standard	NM_145808		Approved	MYOTROPHIN, GCDP, V-1		P58546	OTTHUMG00000155627	ENST00000393085.3:c.*2617C>G	7.37:g.135612057G>C		80.0	0.0	0		61.0	33.0	0.540984	NM_001128619		Missense_Mutation	SNP	ENST00000393085.3	37	CCDS5842.1																																																																																			G|0.993;C|0.007	0.007	strong		0.418	MTPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340921.1	NM_145808	
ZNF93	81931	hgsc.bcm.edu	37	19	20044886	20044886	+	Silent	SNP	T	T	C	rs10401345	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:20044886T>C	ENST00000343769.5	+	4	1150	c.1122T>C	c.(1120-1122)tgT>tgC	p.C374C	AC007204.2_ENST00000592245.1_lincRNA	NM_031218.3	NP_112495.2	P35789	ZNF93_HUMAN	zinc finger protein 93	374					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)	p.C374C(1)		endometrium(6)|kidney(2)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	24						GTGAAGAATGTGGCAAAGCCT	0.388													t|||	601	0.120008	0.2534	0.0447	5008	,	,		22657	0.0506		0.0437	False		,,,				2504	0.1431				p.C374C		Atlas-SNP	.											ZNF93,NS,carcinoma,0,1	ZNF93	81	1	1	Substitution - coding silent(1)	stomach(1)	c.T1122C						PASS	.	T		928,3478	355.1+/-312.9	98,732,1373	89.0	89.0	89.0		1122	0.9	0.5	19	dbSNP_119	89	281,8319	105.4+/-166.3	2,277,4021	no	coding-synonymous	ZNF93	NM_031218.3		100,1009,5394	CC,CT,TT		3.2674,21.0622,9.2957		374/621	20044886	1209,11797	2203	4300	6503	SO:0001819	synonymous_variant	81931	exon4			AGAATGTGGCAAA	M61873	CCDS32973.1	19p12	2014-02-12	2006-05-12		ENSG00000184635	ENSG00000184635		"""Zinc fingers, C2H2-type"", ""-"""	13169	protein-coding gene	gene with protein product		603975	"""zinc finger protein 505"", ""zinc finger protein 93 (HTF34)"""	ZNF505		8467795, 2023909	Standard	NM_031218		Approved	HPF34, TF34, FLJ12488	uc002non.3	P35789	OTTHUMG00000182371	ENST00000343769.5:c.1122T>C	19.37:g.20044886T>C		65.0	0.0	0		81.0	81.0	1	NM_031218	A6NMY2|B9EGT2|Q8N8Q4|Q9H9X5|Q9Y2N8	Silent	SNP	ENST00000343769.5	37	CCDS32973.1																																																																																			T|0.908;C|0.092	0.092	strong		0.388	ZNF93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460808.2	NM_031218	
CEP68	23177	hgsc.bcm.edu	37	2	65298657	65298657	+	Missense_Mutation	SNP	A	A	G	rs13389745	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:65298657A>G	ENST00000377990.2	+	3	630	c.427A>G	c.(427-429)Att>Gtt	p.I143V	CEP68_ENST00000537589.1_5'UTR|CEP68_ENST00000260569.4_Missense_Mutation_p.I143V|CEP68_ENST00000497039.1_3'UTR|CEP68_ENST00000546106.1_Missense_Mutation_p.I143V|RAB1A_ENST00000494188.1_Intron	NM_015147.2	NP_055962.2	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	143					centriole-centriole cohesion (GO:0010457)|centrosome organization (GO:0051297)|protein localization to organelle (GO:0033365)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(8)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32						AACAACAACTATTTGCTCAGG	0.517													A|||	358	0.0714856	0.261	0.0187	5008	,	,		22452	0.0		0.0	False		,,,				2504	0.0				p.I143V		Atlas-SNP	.											.	CEP68	69	.	0			c.A427G						PASS	.	A	VAL/ILE	853,3553	336.3+/-304.3	84,685,1434	104.0	99.0	101.0		427	-0.6	0.0	2	dbSNP_121	101	3,8597	3.7+/-12.6	0,3,4297	yes	missense	CEP68	NM_015147.2	29	84,688,5731	GG,GA,AA		0.0349,19.36,6.5816	benign	143/758	65298657	856,12150	2203	4300	6503	SO:0001583	missense	23177	exon3			ACAACTATTTGCT	BC004873	CCDS1880.2	2p14	2014-02-20	2005-12-01	2005-12-01	ENSG00000011523	ENSG00000011523			29076	protein-coding gene	gene with protein product			"""KIAA0582"""	KIAA0582		9628581, 9847074, 14654843	Standard	NM_015147		Approved		uc002sdl.4	Q76N32	OTTHUMG00000129538	ENST00000377990.2:c.427A>G	2.37:g.65298657A>G	ENSP00000367229:p.Ile143Val	163.0	0.0	0		202.0	101.0	0.5	NM_015147	B4DRQ1|D6W5F1|D6W5F2|O60326|Q9BQ18|Q9UDM9	Missense_Mutation	SNP	ENST00000377990.2	37	CCDS1880.2	148	0.06776556776556776	143	0.29065040650406504	5	0.013812154696132596	0	0.0	0	0.0	A	5.245	0.230663	0.09969	0.1936	3.49E-4	ENSG00000011523	ENST00000377990;ENST00000546106;ENST00000260569;ENST00000545501	T;T;T	0.28255	1.62;1.62;1.62	6.07	-0.64	0.11493	.	0.631703	0.14683	N	0.304637	T	0.00012	0.0000	N	0.04508	-0.205	0.58432	P	1.0000000000287557E-6	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	0.42015	-0.9476	9	0.02654	T	1	-1.7066	11.1914	0.48687	0.317:0.2513:0.4316:0.0	rs13389745;rs52830313;rs57922580;rs13389745	131;143;143;143;143	F5H3N9;F5H2Y2;Q76N32;Q76N32-2;Q05C09	.;.;CEP68_HUMAN;.;.	V	143;143;143;131	ENSP00000367229:I143V;ENSP00000438306:I143V;ENSP00000260569:I143V	ENSP00000260569:I143V	I	+	1	0	CEP68	65152161	0.000000	0.05858	0.001000	0.08648	0.027000	0.11550	-0.938000	0.03938	-0.309000	0.08779	-1.959000	0.00480	ATT	A|0.929;G|0.071	0.071	strong		0.517	CEP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251727.2	NM_015147	
APBA2	321	hgsc.bcm.edu	37	15	29398914	29398914	+	Silent	SNP	C	C	T	rs8032178	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:29398914C>T	ENST00000558402.1	+	13	2408	c.1809C>T	c.(1807-1809)ggC>ggT	p.G603G	APBA2_ENST00000558259.1_Silent_p.G603G|APBA2_ENST00000561069.1_Silent_p.G603G|APBA2_ENST00000558330.1_Silent_p.G591G|APBA2_ENST00000411764.1_Silent_p.G591G			Q99767	APBA2_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 2	603	PDZ 1. {ECO:0000255|PROSITE- ProRule:PRU00143}.				in utero embryonic development (GO:0001701)|locomotory behavior (GO:0007626)|multicellular organism growth (GO:0035264)|nervous system development (GO:0007399)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)	beta-amyloid binding (GO:0001540)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(7)|liver(2)|lung(33)|stomach(1)|urinary_tract(1)	59		all_lung(180;1.73e-12)|Breast(32;2.89e-05)|Colorectal(260;0.234)		all cancers(64;7.44e-11)|Epithelial(43;5.74e-10)|GBM - Glioblastoma multiforme(186;0.026)|BRCA - Breast invasive adenocarcinoma(123;0.0286)|Lung(196;0.24)		TGATGAATGGCGGCCCGGCTG	0.662													C|||	295	0.0589058	0.2118	0.0202	5008	,	,		13171	0.001		0.0	False		,,,				2504	0.0				p.G603G		Atlas-SNP	.											.	APBA2	132	.	0			c.C1809T						PASS	.	C	,	801,3605	312.2+/-292.5	71,659,1473	48.0	49.0	49.0		1773,1809	-8.4	0.4	15	dbSNP_116	49	3,8593	3.0+/-9.4	0,3,4295	no	coding-synonymous,coding-synonymous	APBA2	NM_001130414.1,NM_005503.3	,	71,662,5768	TT,TC,CC		0.0349,18.1798,6.1837	,	591/738,603/750	29398914	804,12198	2203	4298	6501	SO:0001819	synonymous_variant	321	exon11			GAATGGCGGCCCG	AB014719	CCDS10022.1, CCDS45197.1	15q11-q12	2008-07-18	2008-07-18		ENSG00000034053	ENSG00000034053			579	protein-coding gene	gene with protein product		602712	"""X11-like"", ""amyloid beta (A4) precursor protein-binding, family A, member 2 (X11-like)"""	X11L, MINT2		8955346	Standard	NM_005503		Approved	D15S1518E, LIN-10, MGC:14091, HsT16821	uc001zck.3	Q99767	OTTHUMG00000129255	ENST00000558402.1:c.1809C>T	15.37:g.29398914C>T		231.0	0.0	0		222.0	107.0	0.481982	NM_005503	E9PGI4|O60571|Q5XKC0	Silent	SNP	ENST00000558402.1	37	CCDS10022.1																																																																																			C|0.932;T|0.068	0.068	strong		0.662	APBA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251362.3	NM_005503	
ABHD12	26090	hgsc.bcm.edu	37	20	25319977	25319977	+	Missense_Mutation	SNP	C	C	T	rs11904930	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:25319977C>T	ENST00000339157.5	-	2	474	c.202G>A	c.(202-204)Gtg>Atg	p.V68M	ABHD12_ENST00000376542.3_Missense_Mutation_p.V68M	NM_001042472.2	NP_001035937.1	Q8N2K0	ABD12_HUMAN	abhydrolase domain containing 12	68					adult walking behavior (GO:0007628)|phosphatidylserine catabolic process (GO:0006660)|response to auditory stimulus (GO:0010996)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)	acylglycerol lipase activity (GO:0047372)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|liver(1)|lung(1)|skin(1)|urinary_tract(1)	12						CGCAACCACACGCCCTTTCGC	0.423													C|||	23	0.00459265	0.0166	0.0014	5008	,	,		17996	0.0		0.0	False		,,,				2504	0.0				p.V68M		Atlas-SNP	.											.	ABHD12	46	.	0			c.G202A						PASS	.	C	MET/VAL,MET/VAL	88,4318	74.1+/-112.3	1,86,2116	102.0	92.0	95.0		202,202	2.1	1.0	20	dbSNP_120	95	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	ABHD12	NM_001042472.2,NM_015600.4	21,21	1,88,6414	TT,TC,CC		0.0233,1.9973,0.692	benign,benign	68/399,68/405	25319977	90,12916	2203	4300	6503	SO:0001583	missense	26090	exon2			ACCACACGCCCTT	AL117442	CCDS13172.1, CCDS42857.1	20p11.21	2007-04-24	2006-03-10	2006-03-10	ENSG00000100997	ENSG00000100997		"""Abhydrolase domain containing"""	15868	protein-coding gene	gene with protein product		613599	"""chromosome 20 open reading frame 22"""	C20orf22			Standard	NM_015600		Approved	DKFZP434P106, dJ965G21.2, BEM46L2, ABHD12A	uc002wuq.3	Q8N2K0	OTTHUMG00000032121	ENST00000339157.5:c.202G>A	20.37:g.25319977C>T	ENSP00000341408:p.Val68Met	126.0	0.0	0		108.0	48.0	0.444444	NM_001042472	A6NED4|A6NJ90|A8K450|B4DE71|Q5T710|Q5T711|Q96CR1|Q9BX05|Q9NPX7|Q9UFV6	Missense_Mutation	SNP	ENST00000339157.5	37	CCDS42857.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	10.04	1.241327	0.22711	0.019973	2.33E-4	ENSG00000100997	ENST00000376542;ENST00000339157;ENST00000526543;ENST00000450393	T;T;T	0.25749	1.78;1.78;1.78	5.51	2.13	0.27403	.	0.327344	0.28409	N	0.015448	T	0.04452	0.0122	N	0.08118	0	0.19300	N	0.999971	B;B;B	0.12013	0.001;0.001;0.005	B;B;B	0.06405	0.002;0.001;0.002	T	0.15464	-1.0436	10	0.44086	T	0.13	0.0354	1.0324	0.01541	0.1484:0.1871:0.2866:0.378	rs11904930	23;68;68	Q5T712;Q8N2K0;Q8N2K0-2	.;ABD12_HUMAN;.	M	68;68;30;23	ENSP00000365725:V68M;ENSP00000341408:V68M;ENSP00000413311:V23M	ENSP00000341408:V68M	V	-	1	0	ABHD12	25267977	0.214000	0.23563	0.996000	0.52242	0.608000	0.37181	0.149000	0.16243	0.676000	0.31285	-0.226000	0.12346	GTG	C|0.993;T|0.007	0.007	strong		0.423	ABHD12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078423.2	NM_015600	
EVPL	2125	hgsc.bcm.edu	37	17	74006079	74006079	+	Silent	SNP	G	G	A	rs79450818	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74006079G>A	ENST00000301607.3	-	22	3460	c.3207C>T	c.(3205-3207)gaC>gaT	p.D1069D	EVPL_ENST00000586740.1_Silent_p.D1091D	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	1069	Central fibrous rod domain.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						TCTCCTTCACGTCCACCTCCC	0.592													G|||	58	0.0115815	0.0431	0.0014	5008	,	,		21848	0.0		0.0	False		,,,				2504	0.0				p.D1069D		Atlas-SNP	.											.	EVPL	155	.	0			c.C3207T						PASS	.	G		141,4265	101.2+/-139.8	2,137,2064	149.0	140.0	143.0		3207	-3.6	0.0	17	dbSNP_132	143	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	EVPL	NM_001988.2		2,138,6363	AA,AG,GG		0.0116,3.2002,1.0918		1069/2034	74006079	142,12864	2203	4300	6503	SO:0001819	synonymous_variant	2125	exon22			CTTCACGTCCACC	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.3207C>T	17.37:g.74006079G>A		107.0	0.0	0		115.0	70.0	0.608696	NM_001988	A0AUV5	Silent	SNP	ENST00000301607.3	37	CCDS11737.1																																																																																			G|0.987;A|0.013	0.013	strong		0.592	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988	
TENM3	55714	hgsc.bcm.edu	37	4	183720831	183720831	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:183720831G>A	ENST00000511685.1	+	28	7550	c.7427G>A	c.(7426-7428)aGc>aAc	p.S2476N	TENM3_ENST00000406950.2_Missense_Mutation_p.S2476N			Q9P273	TEN3_HUMAN	teneurin transmembrane protein 3	2476					camera-type eye morphogenesis (GO:0048593)|homophilic cell adhesion (GO:0007156)|positive regulation of neuron projection development (GO:0010976)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										GTGCAGGTGAgccggcgccgg	0.697																																					p.S2476N		Atlas-SNP	.											.	.	.	.	0			c.G7427A						PASS	.						5.0	7.0	7.0					4																	183720831		1716	3423	5139	SO:0001583	missense	55714	exon27			AGGTGAGCCGGCG	AF195420	CCDS47165.1	4q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000218336	ENSG00000218336			29944	protein-coding gene	gene with protein product		610083	"""odz, odd Oz/ten-m homolog 3 (Drosophila)"""	ODZ3		10331952, 10625539	Standard	NM_001080477		Approved	Ten-M3, KIAA1455	uc003ivd.1	Q9P273	OTTHUMG00000160682	ENST00000511685.1:c.7427G>A	4.37:g.183720831G>A	ENSP00000424226:p.Ser2476Asn	3.0	0.0	0		10.0	8.0	0.8	NM_001080477	Q5XUL9|Q96SY2|Q9NV77|Q9NVW1|Q9NZJ2	Missense_Mutation	SNP	ENST00000511685.1	37	CCDS47165.1	.	.	.	.	.	.	.	.	.	.	G	12.83	2.054373	0.36277	.	.	ENSG00000218336	ENST00000511685;ENST00000406950	D;D	0.86627	-2.15;-2.15	4.79	3.94	0.45596	.	.	.	.	.	T	0.79505	0.4457	L	0.32530	0.975	0.53005	D	0.999968	B	0.27498	0.18	B	0.18871	0.023	T	0.74352	-0.3693	9	0.18276	T	0.48	.	15.4632	0.75377	0.0:0.1392:0.8608:0.0	.	2476	Q9P273	TEN3_HUMAN	N	2476	ENSP00000424226:S2476N;ENSP00000385276:S2476N	ENSP00000385276:S2476N	S	+	2	0	ODZ3	183957825	1.000000	0.71417	0.997000	0.53966	0.764000	0.43329	6.546000	0.73887	1.357000	0.45904	0.557000	0.71058	AGC	.	.	none		0.697	TENM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361734.1		
SLC2A7	155184	hgsc.bcm.edu	37	1	9083094	9083094	+	Missense_Mutation	SNP	G	G	T	rs61744620	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:9083094G>T	ENST00000400906.1	-	3	193	c.194C>A	c.(193-195)gCa>gAa	p.A65E		NM_207420.2	NP_997303.2	Q6PXP3	GTR7_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 7	65					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			NS(1)|breast(1)|endometrium(4)|large_intestine(10)|lung(4)|prostate(2)|skin(2)	24	Ovarian(185;0.112)|all_lung(157;0.185)	all_epithelial(116;1.34e-15)|all_lung(118;9.46e-05)|Lung NSC(185;0.000172)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.00715)|Hepatocellular(190;0.0228)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.04e-07)|COAD - Colon adenocarcinoma(227;7.66e-05)|Kidney(185;0.000249)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|STAD - Stomach adenocarcinoma(132;0.00177)|BRCA - Breast invasive adenocarcinoma(304;0.00185)|READ - Rectum adenocarcinoma(331;0.0642)		CATGAATGTTGCGTGTCGCTC	0.502													G|||	118	0.0235623	0.0847	0.0086	5008	,	,		20374	0.0		0.0	False		,,,				2504	0.0				p.A65E		Atlas-SNP	.											SLC2A7,rectum,carcinoma,-1,2	SLC2A7	56	2	0			c.C194A						PASS	.	G	GLU/ALA	324,4082	172.3+/-202.3	18,288,1897	171.0	158.0	162.0		194	1.6	0.0	1	dbSNP_129	162	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SLC2A7	NM_207420.2	107	18,289,6196	TT,TG,GG		0.0116,7.3536,2.4988	benign	65/513	9083094	325,12681	2203	4300	6503	SO:0001583	missense	155184	exon3			AATGTTGCGTGTC	AL356306	CCDS98.2	1p36.2	2013-05-22			ENSG00000197241	ENSG00000197241		"""Solute carriers"""	13445	protein-coding gene	gene with protein product	"""intestinal facilitative glucose transporter 7"""	610371				11780753	Standard	NM_207420		Approved	GLUT7	uc009vmo.1	Q6PXP3	OTTHUMG00000057499	ENST00000400906.1:c.194C>A	1.37:g.9083094G>T	ENSP00000383698:p.Ala65Glu	77.0	0.0	0		83.0	45.0	0.542169	NM_207420	A2A333	Missense_Mutation	SNP	ENST00000400906.1	37	CCDS98.2	56	0.02564102564102564	52	0.10569105691056911	4	0.011049723756906077	0	0.0	0	0.0	G	13.62	2.292105	0.40594	0.073536	1.16E-4	ENSG00000197241	ENST00000400906	T	0.73047	-0.71	4.68	1.57	0.23409	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.305652	0.30210	N	0.010158	T	0.01287	0.0042	N	0.04994	-0.135	0.09310	N	1	B	0.10296	0.003	B	0.14578	0.011	T	0.03086	-1.1074	10	0.44086	T	0.13	.	15.0439	0.71813	0.0:0.5434:0.4566:0.0	.	65	Q6PXP3	GTR7_HUMAN	E	65	ENSP00000383698:A65E	ENSP00000383698:A65E	A	-	2	0	SLC2A7	9005681	0.000000	0.05858	0.002000	0.10522	0.305000	0.27757	1.115000	0.31209	0.567000	0.29293	0.556000	0.70494	GCA	G|0.974;T|0.026	0.026	strong		0.502	SLC2A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127768.3	NM_207420	
GABRG3	2567	hgsc.bcm.edu	37	15	27777751	27777751	+	Silent	SNP	T	T	C	rs16950126	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:27777751T>C	ENST00000333743.6	+	10	1382	c.1128T>C	c.(1126-1128)taT>taC	p.Y376Y	RP11-100M12.3_ENST00000556642.1_RNA	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	376					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(23)|skin(1)|upper_aerodigestive_tract(4)	42		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TGCAGAACTATTCCCTCCTGG	0.423													T|||	316	0.063099	0.2216	0.0274	5008	,	,		19532	0.0		0.004	False		,,,				2504	0.0				p.Y376Y	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											.	GABRG3	115	.	0			c.T1128C						PASS	.	T		648,3304		48,552,1376	91.0	88.0	89.0		1128	-7.8	0.7	15	dbSNP_123	89	8,8332		0,8,4162	no	coding-synonymous	GABRG3	NM_033223.4		48,560,5538	CC,CT,TT		0.0959,16.3968,5.3368		376/468	27777751	656,11636	1976	4170	6146	SO:0001819	synonymous_variant	2567	exon10			GAACTATTCCCTC		CCDS45195.1, CCDS59251.1	15q12	2012-06-22			ENSG00000182256	ENSG00000182256		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4088	protein-coding gene	gene with protein product	"""GABA(G) receptor, gamma 3"""	600233				7601451	Standard	NM_033223		Approved		uc001zbg.2	Q99928	OTTHUMG00000044462	ENST00000333743.6:c.1128T>C	15.37:g.27777751T>C		99.0	0.0	0		147.0	75.0	0.510204	NM_033223	G3V594|Q9HD46|Q9NYT2	Silent	SNP	ENST00000333743.6	37	CCDS45195.1																																																																																			T|0.932;C|0.068	0.068	strong		0.423	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2		
IPO13	9670	hgsc.bcm.edu	37	1	44433055	44433055	+	Silent	SNP	G	G	A	rs34392712	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:44433055G>A	ENST00000372343.3	+	19	3344	c.2682G>A	c.(2680-2682)aaG>aaA	p.K894K	DPH2_ENST00000255108.3_5'Flank|IPO13_ENST00000372339.3_Silent_p.K112K|DPH2_ENST00000396758.2_5'Flank|DPH2_ENST00000412950.2_5'Flank	NM_014652.3	NP_055467.3	O94829	IPO13_HUMAN	importin 13	894					protein import into nucleus (GO:0006606)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(6)|lung(13)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0821)				CCCTGAACAAGCACTGCTTCA	0.617													g|||	67	0.0133786	0.0499	0.0014	5008	,	,		18701	0.0		0.0	False		,,,				2504	0.0				p.K894K		Atlas-SNP	.											.	IPO13	86	.	0			c.G2682A						PASS	.			173,4233	110.4+/-148.6	3,167,2033	72.0	70.0	71.0		2682	-0.2	1.0	1	dbSNP_126	71	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	IPO13	NM_014652.3		3,168,6332	AA,AG,GG		0.0116,3.9265,1.3378		894/964	44433055	174,12832	2203	4300	6503	SO:0001819	synonymous_variant	9670	exon19			GAACAAGCACTGC	AB018267	CCDS503.1	1p34.1	2008-02-05			ENSG00000117408	ENSG00000117408		"""Importins"""	16853	protein-coding gene	gene with protein product		610411				9872452, 11447110	Standard	NM_014652		Approved	IMP13, KIAA0724, RANBP13	uc001ckx.3	O94829	OTTHUMG00000008297	ENST00000372343.3:c.2682G>A	1.37:g.44433055G>A		98.0	0.0	0		117.0	59.0	0.504274	NM_014652	D3DPY4|Q5T4X3|Q7LC04|Q96HS3|Q9H8N3|Q9UFR1	Silent	SNP	ENST00000372343.3	37	CCDS503.1																																																																																			G|0.989;A|0.011	0.011	strong		0.617	IPO13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022846.1	NM_014652	
AHNAK2	113146	hgsc.bcm.edu	37	14	105411096	105411096	+	Missense_Mutation	SNP	T	T	G	rs146355838	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105411096T>G	ENST00000333244.5	-	7	10811	c.10692A>C	c.(10690-10692)ttA>ttC	p.L3564F	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3564						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TGGGCGTCTTTAAACTGGGCA	0.612													.|||	364	0.0726837	0.2648	0.0173	5008	,	,		17395	0.0		0.002	False		,,,				2504	0.0				p.L3564F		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A10692C						PASS	.	T	PHE/LEU	745,2943		103,539,1202	98.0	113.0	108.0		10692	-0.5	0.1	14	dbSNP_134	108	9,8157		0,9,4074	no	missense	AHNAK2	NM_138420.2	22	103,548,5276	GG,GT,TT		0.1102,20.2007,6.3607	possibly-damaging	3564/5796	105411096	754,11100	1844	4083	5927	SO:0001583	missense	113146	exon7			CGTCTTTAAACTG	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.10692A>C	14.37:g.105411096T>G	ENSP00000353114:p.Leu3564Phe	238.0	2.0	0.00840336		254.0	252.0	0.992126	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	79	0.036172161172161175	74	0.15040650406504066	5	0.013812154696132596	0	0.0	0	0.0	t	0.125	-1.120104	0.01785	0.202007	0.001102	ENSG00000185567	ENST00000333244	T	0.01034	5.42	3.75	-0.46	0.12175	.	.	.	.	.	T	0.00012	0.0000	N	0.01086	-1.025	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.38373	-0.9664	8	0.39692	T	0.17	.	3.0553	0.06182	0.0902:0.143:0.3249:0.4419	.	3564	Q8IVF2	AHNK2_HUMAN	F	3564	ENSP00000353114:L3564F	ENSP00000353114:L3564F	L	-	3	2	AHNAK2	104482141	0.002000	0.14202	0.063000	0.19743	0.003000	0.03518	-0.991000	0.03728	-0.179000	0.10654	-3.555000	0.00030	TTA	T|0.971;G|0.029	0.029	strong		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
MUC4	4585	hgsc.bcm.edu	37	3	195511781	195511781	+	Missense_Mutation	SNP	G	G	A	rs71291863		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195511781G>A	ENST00000463781.3	-	2	7129	c.6670C>T	c.(6670-6672)Cct>Tct	p.P2224S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P2224S	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)		ACAAGAAGAGGGATGGCGTGA	0.597																																					p.P2224S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,+1,3	MUC4	1505	3	0			c.C6670T						PASS	.						34.0	32.0	33.0					3																	195511781		653	1583	2236	SO:0001583	missense	4585	exon2			GAAGAGGGATGGC	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.6670C>T	3.37:g.195511781G>A	ENSP00000417498:p.Pro2224Ser	404.0	1.0	0.00247525		187.0	47.0	0.251337	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	A	4.909	0.168944	0.09339	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.28255	1.76;1.62	.	.	.	.	.	.	.	.	T	0.13030	0.0316	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.24440	-1.0160	6	.	.	.	.	.	.	.	.	2224	E7ESK3	.	S	2224	ENSP00000417498:P2224S;ENSP00000420243:P2224S	.	P	-	1	0	MUC4	196996176	0.235000	0.23794	0.000000	0.03702	0.001000	0.01503	1.269000	0.33074	-1.833000	0.01195	-2.092000	0.00371	CCT	.	.	none		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SLC22A24	283238	hgsc.bcm.edu	37	11	62886706	62886706	+	Missense_Mutation	SNP	C	C	T	rs116063135	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:62886706C>T	ENST00000417740.1	-	3	1049	c.608G>A	c.(607-609)cGc>cAc	p.R203H	SLC22A24_ENST00000326192.5_Missense_Mutation_p.R203H	NM_001136506.2	NP_001129978.2	Q8N4F4	S22AO_HUMAN	solute carrier family 22, member 24	203					ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				kidney(1)|stomach(1)	2						TGCCAAGAAGCGCAGTATGCA	0.438													C|||	58	0.0115815	0.0439	0.0	5008	,	,		21113	0.0		0.0	False		,,,				2504	0.0				p.R203H		Atlas-SNP	.											.	SLC22A24	31	.	0			c.G608A						PASS	.	C	HIS/ARG	59,1325		0,59,633	136.0	120.0	125.0		608	1.8	0.0	11	dbSNP_132	125	1,3181		0,1,1590	yes	missense	SLC22A24	NM_001136506.2	29	0,60,2223	TT,TC,CC		0.0314,4.263,1.3141	probably-damaging	203/553	62886706	60,4506	692	1591	2283	SO:0001583	missense	283238	exon3			AAGAAGCGCAGTA		CCDS73308.1	11q12.3	2013-05-22			ENSG00000197658	ENSG00000197658		"""Solute carriers"""	28542	protein-coding gene	gene with protein product		611698				17714910	Standard	NM_001136506		Approved	MGC34821, NET46	uc021qkp.1	Q8N4F4	OTTHUMG00000165372	ENST00000417740.1:c.608G>A	11.37:g.62886706C>T	ENSP00000396586:p.Arg203His	165.0	0.0	0		162.0	84.0	0.518519	NM_001136506		Missense_Mutation	SNP	ENST00000417740.1	37		23	0.010531135531135532	23	0.046747967479674794	0	0.0	0	0.0	0	0.0	C	19.33	3.807587	0.70797	0.04263	3.14E-4	ENSG00000197658	ENST00000417740;ENST00000531535;ENST00000326192	D;T	0.90197	-2.63;-0.51	3.77	1.79	0.24919	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	U	0.000000	D	0.83353	0.5236	H	0.96365	3.81	0.09310	N	1	D;D	0.76494	0.999;0.995	D;P	0.66602	0.945;0.843	T	0.80094	-0.1526	10	0.87932	D	0	.	8.3277	0.32167	0.0:0.7891:0.0:0.2109	.	203;203	Q8N4F4;C9JC66	S22AO_HUMAN;.	H	203	ENSP00000396586:R203H;ENSP00000321549:R203H	ENSP00000321549:R203H	R	-	2	0	SLC22A24	62643282	0.007000	0.16637	0.002000	0.10522	0.505000	0.33919	1.812000	0.38952	0.801000	0.34066	0.501000	0.49751	CGC	C|0.988;T|0.012	0.012	strong		0.438	SLC22A24-003	PUTATIVE	non_canonical_polymorphism|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000383747.1	NM_173586	
NEIL3	55247	hgsc.bcm.edu	37	4	178257364	178257364	+	Missense_Mutation	SNP	G	G	C	rs17064658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:178257364G>C	ENST00000264596.3	+	4	634	c.516G>C	c.(514-516)caG>caC	p.Q172H		NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	172			Q -> H (in dbSNP:rs17064658). {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)			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)		TTAAAAAACAGAAAGGCCGGA	0.398								Base excision repair (BER), DNA glycosylases					G|||	123	0.0245607	0.0741	0.0144	5008	,	,		16964	0.0		0.0099	False		,,,				2504	0.0051				p.Q172H		Atlas-SNP	.											.	NEIL3	89	.	0			c.G516C						PASS	.	G	HIS/GLN	255,4151	147.3+/-181.8	12,231,1960	138.0	142.0	141.0		516	2.3	0.7	4	dbSNP_123	141	99,8501	54.0+/-114.7	1,97,4202	yes	missense	NEIL3	NM_018248.2	24	13,328,6162	CC,CG,GG		1.1512,5.7876,2.7218	possibly-damaging	172/606	178257364	354,12652	2203	4300	6503	SO:0001583	missense	55247	exon4			AAAACAGAAAGGC	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.516G>C	4.37:g.178257364G>C	ENSP00000264596:p.Gln172His	95.0	0.0	0		88.0	41.0	0.465909	NM_018248	Q2PPJ3|Q8NG51|Q9NV95	Missense_Mutation	SNP	ENST00000264596.3	37	CCDS3828.1	44	0.020146520146520148	29	0.05894308943089431	7	0.019337016574585635	0	0.0	8	0.010554089709762533	G	11.19	1.566029	0.27915	0.057876	0.011512	ENSG00000109674	ENST00000264596	T	0.14516	2.5	4.93	2.28	0.28536	DNA glycosylase/AP lyase, H2TH DNA-binding (1);Ribosomal protein S13-like, H2TH (1);	0.118971	0.64402	D	0.000017	T	0.01454	0.0047	L	0.31207	0.915	0.40999	D	0.984912	D	0.53312	0.959	P	0.53760	0.734	T	0.07195	-1.0785	10	0.37606	T	0.19	-13.2033	7.8072	0.29209	0.3219:0.0:0.6781:0.0	rs17064658;rs52811923;rs17064658	172	Q8TAT5	NEIL3_HUMAN	H	172	ENSP00000264596:Q172H	ENSP00000264596:Q172H	Q	+	3	2	NEIL3	178494358	0.987000	0.35691	0.674000	0.29902	0.558000	0.35554	1.962000	0.40442	0.367000	0.24454	0.655000	0.94253	CAG	G|0.975;C|0.025	0.025	strong		0.398	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248	
DNMT3B	1789	hgsc.bcm.edu	37	20	31388080	31388080	+	Silent	SNP	C	C	T	rs17123657	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31388080C>T	ENST00000328111.2	+	17	2202	c.1881C>T	c.(1879-1881)gaC>gaT	p.D627D	DNMT3B_ENST00000201963.3_Silent_p.D619D|DNMT3B_ENST00000375623.4_3'UTR|DNMT3B_ENST00000344505.4_Silent_p.D607D|DNMT3B_ENST00000353855.2_Silent_p.D607D|DNMT3B_ENST00000348286.2_Silent_p.D607D|DNMT3B_ENST00000443239.3_Silent_p.D565D|DNMT3B_ENST00000456297.2_Silent_p.D531D	NM_006892.3	NP_008823.1	Q9UBC3	DNM3B_HUMAN	DNA (cytosine-5-)-methyltransferase 3 beta	627	S-adenosyl-L-methionine binding. {ECO:0000250}.|SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation on cytosine within a CG sequence (GO:0010424)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of gene expression (GO:0010628)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of neuron differentiation (GO:0045666)|protein complex localization (GO:0031503)|regulation of gene expression by genetic imprinting (GO:0006349)|response to drug (GO:0042493)|response to ionizing radiation (GO:0010212)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA-methyltransferase activity (GO:0009008)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)|unmethylated CpG binding (GO:0045322)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(16)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						ACGTGAACGACGTGAGGAACA	0.498													C|||	277	0.0553115	0.1944	0.0144	5008	,	,		21823	0.0		0.007	False		,,,				2504	0.0031				p.D627D		Atlas-SNP	.											DNMT3B_ENST00000201963,NS,carcinoma,+2,4	DNMT3B	196	4	0			c.C1881T						PASS	.	C	,,,,,	762,3644	312.7+/-292.7	71,620,1512	198.0	170.0	180.0		1695,1593,1881,1821,1821,1857	-1.8	0.9	20	dbSNP_123	180	30,8570	21.0+/-64.5	0,30,4270	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DNMT3B	NM_001207055.1,NM_001207056.1,NM_006892.3,NM_175848.1,NM_175849.1,NM_175850.2	,,,,,	71,650,5782	TT,TC,CC		0.3488,17.2946,6.0895	,,,,,	565/729,531/695,627/854,607/834,607/771,619/846	31388080	792,12214	2203	4300	6503	SO:0001819	synonymous_variant	1789	exon17			GAACGACGTGAGG		CCDS13204.1, CCDS13205.1, CCDS13206.1, CCDS13207.1, CCDS56183.1, CCDS56184.1	20q11.2	2014-09-17			ENSG00000088305	ENSG00000088305			2979	protein-coding gene	gene with protein product		602900				9662389, 10433969	Standard	NM_006892		Approved		uc002wyc.3	Q9UBC3	OTTHUMG00000032226	ENST00000328111.2:c.1881C>T	20.37:g.31388080C>T		94.0	0.0	0		106.0	56.0	0.528302	NM_006892	A2A2E2|B4DSM8|B4DSU1|E1P5M6|E1P5M7|E7EN63|E9PBF2|Q9UBD4|Q9UJQ5|Q9UKA6|Q9UNE5|Q9Y5R9|Q9Y5S0	Silent	SNP	ENST00000328111.2	37	CCDS13205.1																																																																																			C|0.944;T|0.056	0.056	strong		0.498	DNMT3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078643.2	NM_006892	
TNFRSF25	8718	hgsc.bcm.edu	37	1	6525257	6525257	+	Silent	SNP	C	C	T	rs45438594	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:6525257C>T	ENST00000356876.3	-	3	273	c.186G>A	c.(184-186)acG>acA	p.T62T	TNFRSF25_ENST00000348333.3_Intron|TNFRSF25_ENST00000461703.2_5'UTR|TNFRSF25_ENST00000377782.3_Silent_p.T62T|TNFRSF25_ENST00000351748.3_Intron|TNFRSF25_ENST00000351959.5_Silent_p.T62T	NM_003790.2|NM_148967.1	NP_003781.1|NP_683868.1	Q93038	TNR25_HUMAN	tumor necrosis factor receptor superfamily, member 25	62					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell surface receptor signaling pathway (GO:0007166)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|tumor necrosis factor-activated receptor activity (GO:0005031)			breast(1)|central_nervous_system(2)|endometrium(1)|lung(4)|prostate(1)|stomach(1)	10	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Acute lymphoblastic leukemia(12;0.00157)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;4.58e-35)|GBM - Glioblastoma multiforme(13;3.06e-27)|Colorectal(212;6.01e-08)|COAD - Colon adenocarcinoma(227;1.3e-05)|Kidney(185;4.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000871)|BRCA - Breast invasive adenocarcinoma(365;0.00105)|STAD - Stomach adenocarcinoma(132;0.00158)|READ - Rectum adenocarcinoma(331;0.0419)		CGCAGGGCTCCGTGCAAGGGG	0.647													c|||	186	0.0371406	0.1135	0.0115	5008	,	,		16887	0.0		0.004	False		,,,				2504	0.0245				p.T62T		Atlas-SNP	.											.	TNFRSF25	22	.	0			c.G186A						PASS	.		,,,,,	397,4009	194.0+/-219.0	16,365,1822	45.0	43.0	44.0		186,186,186,186,,	-3.9	0.5	1	dbSNP_127	44	11,8589	7.1+/-27.0	0,11,4289	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron,intron	TNFRSF25	NM_001039664.1,NM_003790.2,NM_148965.1,NM_148966.1,NM_148967.1,NM_148970.1	,,,,,	16,376,6111	TT,TC,CC		0.1279,9.0104,3.137	,,,,,	62/182,62/418,62/427,62/381,,	6525257	408,12598	2203	4300	6503	SO:0001819	synonymous_variant	8718	exon3			GGGCTCCGTGCAA	U72763	CCDS71.1, CCDS72.1, CCDS73.1, CCDS74.1, CCDS75.1	1p36.2	2008-02-05	2002-12-20	2002-12-20	ENSG00000215788	ENSG00000215788		"""Tumor necrosis factor receptor superfamily"""	11910	protein-coding gene	gene with protein product		603366	"""tumor necrosis factor receptor superfamily, member 12 (translocating chain-association membrane protein)"""	TNFRSF12		9052839, 8934525	Standard	NM_003790		Approved	DR3, TRAMP, WSL-1, LARD, WSL-LR, DDR3, TR3, APO-3	uc001anh.3	Q93038	OTTHUMG00000000831	ENST00000356876.3:c.186G>A	1.37:g.6525257C>T		115.0	0.0	0		88.0	49.0	0.556818	NM_148966	B1ALX2|B1ALX3|B7ZLL7|O00275|O00276|O00277|O00278|O00279|O00280|O14865|O14866|P78507|P78515|Q17RU4|Q92983|Q93036|Q93037|Q99722|Q99830|Q99831|Q9BY86|Q9UME0|Q9UME1|Q9UME5	Silent	SNP	ENST00000356876.3	37	CCDS71.1																																																																																			C|0.965;T|0.035	0.035	strong		0.647	TNFRSF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002259.1	NM_148965	
SLMAP	7871	hgsc.bcm.edu	37	3	57743531	57743531	+	Silent	SNP	A	A	G	rs147270008		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:57743531A>G	ENST00000428312.1	+	1	247	c.153A>G	c.(151-153)ctA>ctG	p.L51L	SLMAP_ENST00000416870.1_5'UTR|SLMAP_ENST00000449503.2_Silent_p.L51L|SLMAP_ENST00000383718.3_Silent_p.L51L|SLMAP_ENST00000295952.3_Silent_p.L51L|SLMAP_ENST00000295951.3_Silent_p.L51L			Q14BN4	SLMAP_HUMAN	sarcolemma associated protein	51	FHA. {ECO:0000255|PROSITE- ProRule:PRU00086}.|Necessary for targeting to centrosomes. {ECO:0000250}.				muscle contraction (GO:0006936)	cytoskeleton (GO:0005856)|integral component of plasma membrane (GO:0005887)|smooth endoplasmic reticulum (GO:0005790)				endometrium(5)|kidney(1)|large_intestine(3)|lung(7)|urinary_tract(2)	18				BRCA - Breast invasive adenocarcinoma(55;0.000271)|KIRC - Kidney renal clear cell carcinoma(284;0.0602)|Kidney(284;0.0754)|OV - Ovarian serous cystadenocarcinoma(275;0.182)		GCAAAGTGCTATCAAGGAACC	0.498																																					p.L51L		Atlas-SNP	.											.	SLMAP	46	.	0			c.A153G						PASS	.	A		1,4405		0,1,2202	78.0	70.0	73.0		153	1.8	1.0	3	dbSNP_134	73	0,8600		0,0,4300	no	coding-synonymous	SLMAP	NM_007159.2		0,1,6502	GG,GA,AA		0.0,0.0227,0.0077		51/812	57743531	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	7871	exon1			AGTGCTATCAAGG	AF100750	CCDS33774.1	3p21.2-p14.3	2008-07-18			ENSG00000163681	ENSG00000163681			16643	protein-coding gene	gene with protein product	"""Sarcolemmal-associated protein"""	602701				9405447, 11042152	Standard	NM_007159		Approved	SLAP, KIAA1601	uc003djd.1	Q14BN4	OTTHUMG00000133764	ENST00000428312.1:c.153A>G	3.37:g.57743531A>G		224.0	0.0	0		223.0	106.0	0.475336	NM_007159	Q14C95|Q6AI54|Q6UXC9|Q6ZVQ8|Q8NCW9|Q9H297|Q9HCH1|Q9Y681	Silent	SNP	ENST00000428312.1	37																																																																																				A|1.000;G|0.000	0.000	weak		0.498	SLMAP-013	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351584.1	NM_007159	
AURKC	6795	hgsc.bcm.edu	37	19	57743518	57743518	+	Silent	SNP	C	C	T	rs142351971	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:57743518C>T	ENST00000302804.7	+	3	408	c.222C>T	c.(220-222)ctC>ctT	p.L74L	AURKC_ENST00000599062.1_Silent_p.L71L|AURKC_ENST00000598785.1_Silent_p.L40L|AURKC_ENST00000415300.2_Silent_p.L55L|AURKC_ENST00000448930.1_Silent_p.L40L	NM_001015878.1	NP_001015878.1	Q9UQB9	AURKC_HUMAN	aurora kinase C	74	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				attachment of spindle microtubules to kinetochore (GO:0008608)|cytokinesis (GO:0000910)|histone modification (GO:0016570)|meiotic nuclear division (GO:0007126)|positive regulation of cytokinesis (GO:0032467)|protein phosphorylation (GO:0006468)|spindle midzone assembly involved in mitosis (GO:0051256)	chromosome passenger complex (GO:0032133)|chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			breast(1)|endometrium(1)|large_intestine(9)|lung(9)|ovary(3)|prostate(1)|stomach(1)	25		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0122)		TGAAGGTTCTCTTCAAGTCGC	0.517													c|||	7	0.00139776	0.0053	0.0	5008	,	,		18570	0.0		0.0	False		,,,				2504	0.0				p.L74L		Atlas-SNP	.											AURKC_ENST00000302804,colon,carcinoma,+2,2	AURKC	97	2	0			c.C222T						PASS	.	C	,,	20,4386	28.1+/-56.4	1,18,2184	61.0	52.0	55.0		222,165,120	-4.8	1.0	19	dbSNP_134	55	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	AURKC	NM_001015878.1,NM_001015879.1,NM_003160.2	,,	1,18,6484	TT,TC,CC		0.0,0.4539,0.1538	,,	74/310,55/291,40/276	57743518	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	6795	exon3			GGTTCTCTTCAAG		CCDS33128.1, CCDS46205.1, CCDS46206.1	19q13.43	2013-09-19	2003-07-21	2003-07-23	ENSG00000105146	ENSG00000105146			11391	protein-coding gene	gene with protein product		603495	"""serine/threonine kinase 13 (aurora/IPL1-like)"""	STK13		9799611	Standard	XR_430209		Approved	AurC, ARK3	uc002qoe.3	Q9UQB9	OTTHUMG00000183106	ENST00000302804.7:c.222C>T	19.37:g.57743518C>T		68.0	0.0	0		66.0	19.0	0.287879	NM_001015878	O60681|O75442|Q6AZY8|Q6DLZ0|Q9UPK5	Silent	SNP	ENST00000302804.7	37	CCDS33128.1																																																																																			C|0.999;T|0.001	0.001	strong		0.517	AURKC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465089.1	NM_003160	
KIAA1755	85449	hgsc.bcm.edu	37	20	36841536	36841536	+	Missense_Mutation	SNP	G	G	A	rs142596886	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:36841536G>A	ENST00000279024.4	-	14	3782	c.3511C>T	c.(3511-3513)Cgc>Tgc	p.R1171C		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	1171										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				CCAGTGAGGCGAGGGACCTGG	0.637													G|||	6	0.00119808	0.0045	0.0	5008	,	,		17653	0.0		0.0	False		,,,				2504	0.0				p.R1171C		Atlas-SNP	.											.	KIAA1755	145	.	0			c.C3511T						PASS	.	G	CYS/ARG	23,4383	30.8+/-60.4	0,23,2180	38.0	40.0	40.0		3511	2.9	0.1	20	dbSNP_134	40	0,8600		0,0,4300	yes	missense	KIAA1755	NM_001029864.1	180	0,23,6480	AA,AG,GG		0.0,0.522,0.1768	possibly-damaging	1171/1201	36841536	23,12983	2203	4300	6503	SO:0001583	missense	85449	exon14			TGAGGCGAGGGAC	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.3511C>T	20.37:g.36841536G>A	ENSP00000279024:p.Arg1171Cys	72.0	0.0	0		56.0	23.0	0.410714	NM_001029864	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	37	CCDS33467.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	10.17	1.275548	0.23307	0.00522	0.0	ENSG00000149633	ENST00000279024	T	0.05855	3.38	4.88	2.94	0.34122	.	1.496300	0.03995	N	0.295521	T	0.04227	0.0117	N	0.24115	0.695	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36089	-0.9762	10	0.72032	D	0.01	.	6.9683	0.24635	0.2031:0.0:0.7969:0.0	.	1171	Q5JYT7	K1755_HUMAN	C	1171	ENSP00000279024:R1171C	ENSP00000279024:R1171C	R	-	1	0	KIAA1755	36274950	0.139000	0.22563	0.060000	0.19600	0.030000	0.12068	1.048000	0.30379	0.660000	0.30964	0.561000	0.74099	CGC	G|0.999;A|0.001	0.001	strong		0.637	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
FANCA	2175	hgsc.bcm.edu	37	16	89839752	89839752	+	Silent	SNP	C	C	T	rs17232917	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89839752C>T	ENST00000389301.3	-	22	1971	c.1941G>A	c.(1939-1941)gaG>gaA	p.E647E	FANCA_ENST00000568369.1_Silent_p.E647E|FANCA_ENST00000567284.2_5'UTR	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	647					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)		CCAGGGGCTCCTCAGCAGAGT	0.562			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				C|||	191	0.038139	0.1407	0.0072	5008	,	,		17401	0.0		0.0	False		,,,				2504	0.0				p.E647E		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	.	FANCA	99	.	0			c.G1941A						PASS	.	C		425,3647		19,387,1630	32.0	27.0	29.0		1941	-9.1	0.0	16	dbSNP_123	29	1,7893		0,1,3946	no	coding-synonymous	FANCA	NM_000135.2		19,388,5576	TT,TC,CC		0.0127,10.4371,3.5601		647/1456	89839752	426,11540	2036	3947	5983	SO:0001819	synonymous_variant	2175	exon22	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GGGCTCCTCAGCA	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.1941G>A	16.37:g.89839752C>T		90.0	0.0	0		94.0	52.0	0.553191	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Silent	SNP	ENST00000389301.3	37	CCDS32515.1																																																																																			C|0.960;T|0.040	0.040	strong		0.562	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
EFCAB13	124989	hgsc.bcm.edu	37	17	45471443	45471443	+	Silent	SNP	G	G	A	rs7217678	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:45471443G>A	ENST00000331493.2	+	16	2190	c.1779G>A	c.(1777-1779)acG>acA	p.T593T	EFCAB13_ENST00000517484.1_Silent_p.T497T	NM_152347.4	NP_689560.3	Q8IY85	EFC13_HUMAN	EF-hand calcium binding domain 13	593						cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)										TGAGCAACACGGAATGCTTCT	0.299													g|||	87	0.0173722	0.0628	0.0029	5008	,	,		14107	0.0		0.002	False		,,,				2504	0.0				p.T593T		Atlas-SNP	.											C17orf57,NS,carcinoma,+1,1	.	.	1	0			c.G1779A						PASS	.	G	,	238,4168	138.0+/-173.8	7,224,1972	106.0	119.0	114.0		1491,1779	-2.9	0.2	17	dbSNP_116	114	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous	C17orf57	NM_001195192.1,NM_152347.4	,	7,228,6268	AA,AG,GG		0.0465,5.4017,1.8607	,	497/785,593/974	45471443	242,12764	2203	4300	6503	SO:0001819	synonymous_variant	124989	exon16			CAACACGGAATGC	BC036407	CCDS11512.1, CCDS56034.1	17q21.32	2013-01-11	2012-07-20	2012-07-20	ENSG00000178852	ENSG00000178852		"""EF-hand domain containing"""	26864	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 57"""	C17orf57			Standard	NM_152347		Approved	FLJ40342	uc002iln.3	Q8IY85	OTTHUMG00000164767	ENST00000331493.2:c.1779G>A	17.37:g.45471443G>A		162.0	0.0	0		159.0	68.0	0.427673	NM_152347	G3V128|Q49AG9	Silent	SNP	ENST00000331493.2	37	CCDS11512.1																																																																																			G|0.977;A|0.023	0.023	strong		0.299	EFCAB13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380147.4	NM_152347	
ZC3H4	23211	hgsc.bcm.edu	37	19	47575291	47575291	+	Silent	SNP	A	A	G	rs144210335|rs79459609	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:47575291A>G	ENST00000253048.5	-	13	1927	c.1890T>C	c.(1888-1890)ccT>ccC	p.P630P	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	630	Pro-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		ggtgcatgtcaggatgcatTG	0.647													A|||	130	0.0259585	0.0908	0.0115	5008	,	,		17612	0.0		0.002	False		,,,				2504	0.0				p.P630P		Atlas-SNP	.											.	ZC3H4	96	.	0			c.T1890C						PASS	.	A		211,3961		8,195,1883	29.0	34.0	32.0		1890	-9.0	0.7	19	dbSNP_131	32	18,8402		0,18,4192	no	coding-synonymous	ZC3H4	NM_015168.1		8,213,6075	GG,GA,AA		0.2138,5.0575,1.8186		630/1304	47575291	229,12363	2086	4210	6296	SO:0001819	synonymous_variant	23211	exon13			CATGTCAGGATGC	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"""Zinc fingers, CCCH-type domain containing"""	17808	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 7"""	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.1890T>C	19.37:g.47575291A>G		117.0	0.0	0		97.0	50.0	0.515464	NM_015168	Q9Y420	Silent	SNP	ENST00000253048.5	37	CCDS42582.1																																																																																			A|0.983;G|0.017	0.017	strong		0.647	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1		
RAD21	5885	hgsc.bcm.edu	37	8	117864867	117864867	+	Missense_Mutation	SNP	A	A	C	rs75160167	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:117864867A>C	ENST00000297338.2	-	10	1529	c.1242T>G	c.(1240-1242)gaT>gaG	p.D414E	RAD21_ENST00000518055.1_5'Flank|RAD21_ENST00000523986.1_5'Flank	NM_006265.2	NP_006256.1	O60216	RAD21_HUMAN	RAD21 homolog (S. pombe)	414					apoptotic process (GO:0006915)|chromosome segregation (GO:0007059)|DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|protein localization to chromatin (GO:0071168)|reciprocal meiotic recombination (GO:0007131)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cytosol (GO:0005829)|membrane (GO:0016020)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(1)|stomach(1)	32	all_cancers(13;1.21e-21)|Lung NSC(37;0.000134)|Ovarian(258;0.0172)					TGAGGAATTCATCCAAATTAT	0.403													A|||	36	0.0071885	0.0265	0.0014	5008	,	,		15827	0.0		0.0	False		,,,				2504	0.0				p.D414E		Atlas-SNP	.											.	RAD21	95	.	0			c.T1242G						PASS	.	A	GLU/ASP	88,4318	74.1+/-112.3	0,88,2115	115.0	112.0	113.0		1242	5.5	1.0	8	dbSNP_131	113	0,8600		0,0,4300	yes	missense	RAD21	NM_006265.2	45	0,88,6415	CC,CA,AA		0.0,1.9973,0.6766	benign	414/632	117864867	88,12918	2203	4300	6503	SO:0001583	missense	5885	exon10			GAATTCATCCAAA	BC050381	CCDS6321.1	8q24.11	2014-09-17	2001-11-28		ENSG00000164754	ENSG00000164754			9811	protein-coding gene	gene with protein product	"""sister chromatid cohesion 1"""	606462	"""RAD21 (S. pombe) homolog"""			8812457	Standard	NM_006265		Approved	KIAA0078, hHR21, SCC1	uc003yod.3	O60216	OTTHUMG00000164959	ENST00000297338.2:c.1242T>G	8.37:g.117864867A>C	ENSP00000297338:p.Asp414Glu	197.0	0.0	0		203.0	86.0	0.423645	NM_006265	A8K0E0|Q15001|Q99568	Missense_Mutation	SNP	ENST00000297338.2	37	CCDS6321.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	A	13.90	2.373790	0.42105	0.019973	0.0	ENSG00000164754	ENST00000297338	T	0.50277	0.75	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.18341	0.0440	L	0.32530	0.975	0.80722	D	1	B	0.28900	0.227	B	0.21360	0.034	T	0.12967	-1.0527	10	0.02654	T	1	-14.1824	15.669	0.77258	1.0:0.0:0.0:0.0	.	414	O60216	RAD21_HUMAN	E	414	ENSP00000297338:D414E	ENSP00000297338:D414E	D	-	3	2	RAD21	117934048	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.009000	0.57110	2.092000	0.63282	0.460000	0.39030	GAT	A|0.992;C|0.008	0.008	strong		0.403	RAD21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381184.1	NM_006265	
CXXC1	30827	hgsc.bcm.edu	37	18	47809710	47809710	+	Silent	SNP	A	A	G	rs150530383	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:47809710A>G	ENST00000285106.6	-	13	2310	c.1596T>C	c.(1594-1596)gaT>gaC	p.D532D	MBD1_ENST00000591416.1_5'Flank|CXXC1_ENST00000412036.2_Silent_p.D536D|MBD1_ENST00000585672.1_5'Flank|MBD1_ENST00000585595.1_5'Flank|MBD1_ENST00000424334.2_5'Flank|MBD1_ENST00000347968.3_5'Flank|MBD1_ENST00000457839.2_5'Flank|MBD1_ENST00000436910.1_5'Flank|MBD1_ENST00000587605.1_5'Flank|MBD1_ENST00000382948.5_5'Flank|MBD1_ENST00000269471.5_5'Flank|MBD1_ENST00000353909.3_5'Flank|MBD1_ENST00000349085.2_5'Flank|MBD1_ENST00000269468.5_5'Flank|MBD1_ENST00000398493.1_5'Flank|MBD1_ENST00000590208.1_5'Flank|CXXC1_ENST00000589940.1_Intron|MBD1_ENST00000339998.6_5'Flank|CXXC1_ENST00000587396.1_5'Flank	NM_001101654.1|NM_014593.3	NP_001095124.1|NP_055408.2	Q9P0U4	CXXC1_HUMAN	CXXC finger protein 1	532					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|histone H3-K4 methylation (GO:0051568)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	24						GATTATACACATCACAGAAGA	0.572													A|||	11	0.00219649	0.0083	0.0	5008	,	,		18925	0.0		0.0	False		,,,				2504	0.0				p.D536D		Atlas-SNP	.											.	CXXC1	50	.	0			c.T1608C						PASS	.	A	,	12,4394	19.1+/-41.9	0,12,2191	133.0	139.0	137.0		1608,1596	1.9	1.0	18	dbSNP_134	137	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CXXC1	NM_001101654.1,NM_014593.3	,	0,12,6491	GG,GA,AA		0.0,0.2724,0.0923	,	536/661,532/657	47809710	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	30827	exon13			ATACACATCACAG	BC014940	CCDS11945.1, CCDS45866.1	18q12	2014-02-20	2014-02-20		ENSG00000154832	ENSG00000154832		"""Zinc fingers, PHD-type"""	24343	protein-coding gene	gene with protein product	"""CpG binding protein"", ""DNA-binding protein with PHD finger and CXXC domain"", ""zinc finger, CpG binding-type containing 1"""	609150	"""CXXC finger 1 (PHD domain)"""			10799292, 10688657	Standard	NM_014593		Approved	HsT2645, PCCX1, hCGBP, PHF18, CGBP, SPP1, CFP1, ZCGPC1	uc002ler.4	Q9P0U4	OTTHUMG00000132670	ENST00000285106.6:c.1596T>C	18.37:g.47809710A>G		108.0	0.0	0		147.0	74.0	0.503401	NM_001101654	B2RC03|Q8N2W4|Q96BC8|Q9P2V7	Silent	SNP	ENST00000285106.6	37	CCDS11945.1																																																																																			A|0.999;G|0.001	0.001	strong		0.572	CXXC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255927.2	NM_014593	
ARHGAP20	57569	hgsc.bcm.edu	37	11	110451470	110451470	+	Missense_Mutation	SNP	T	T	C	rs151169911	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:110451470T>C	ENST00000260283.4	-	16	2484	c.2200A>G	c.(2200-2202)Att>Gtt	p.I734V	ARHGAP20_ENST00000357139.3_Missense_Mutation_p.I708V|ARHGAP20_ENST00000529591.1_Missense_Mutation_p.I277V|ARHGAP20_ENST00000527598.1_Missense_Mutation_p.I698V|ARHGAP20_ENST00000528829.1_Missense_Mutation_p.I698V|ARHGAP20_ENST00000533353.1_Missense_Mutation_p.I708V|ARHGAP20_ENST00000524756.1_Missense_Mutation_p.I711V	NM_020809.3	NP_065860.2	Q9P2F6	RHG20_HUMAN	Rho GTPase activating protein 20	734					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(18)|lung(13)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	60		all_cancers(61;3.26e-12)|all_epithelial(67;6.09e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;0.000484)|Acute lymphoblastic leukemia(157;0.000967)|all_neural(223;0.0199)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;3.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|all cancers(92;0.000147)|OV - Ovarian serous cystadenocarcinoma(223;0.0475)		TGAGAAAGAATTGCATCACAG	0.448													T|||	3	0.000599042	0.0023	0.0	5008	,	,		21606	0.0		0.0	False		,,,				2504	0.0				p.I734V		Atlas-SNP	.											.	ARHGAP20	150	.	0			c.A2200G						PASS	.	T	VAL/ILE	10,4392	15.5+/-35.6	0,10,2191	66.0	69.0	68.0		2200	-1.6	0.0	11	dbSNP_134	68	0,8596		0,0,4298	yes	missense	ARHGAP20	NM_020809.2	29	0,10,6489	CC,CT,TT		0.0,0.2272,0.0769	benign	734/1192	110451470	10,12988	2201	4298	6499	SO:0001583	missense	57569	exon16			AAAGAATTGCATC	AB037812	CCDS31673.1, CCDS58175.1, CCDS58176.1, CCDS58177.1	11q23.2	2011-06-29			ENSG00000137727	ENSG00000137727		"""Rho GTPase activating proteins"""	18357	protein-coding gene	gene with protein product		609568				14532992	Standard	NM_020809		Approved	KIAA1391	uc001pkz.2	Q9P2F6	OTTHUMG00000166590	ENST00000260283.4:c.2200A>G	11.37:g.110451470T>C	ENSP00000260283:p.Ile734Val	164.0	0.0	0		127.0	58.0	0.456693	NM_020809	A8K8C5|B0YIW7|B0YIW8|Q6RJU1|Q6RJU2|Q6RJU3|Q6RJU5|Q8IXS1	Missense_Mutation	SNP	ENST00000260283.4	37	CCDS31673.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	T	4.295	0.054024	0.08291	0.002272	0.0	ENSG00000137727	ENST00000260283;ENST00000357139;ENST00000529591;ENST00000524756;ENST00000528829;ENST00000533353;ENST00000527598	T;T;T;T;T;T;T	0.07908	3.15;3.15;3.18;3.15;3.15;3.15;3.15	5.93	-1.65	0.08291	.	0.430046	0.22922	N	0.054011	T	0.03220	0.0094	N	0.25647	0.755	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.09377	0.004;0.001;0.002	T	0.44205	-0.9343	10	0.06365	T	0.9	.	13.7174	0.62705	0.0:0.7298:0.0:0.2702	.	708;734;711	Q9P2F6-2;Q9P2F6;Q9P2F6-3	.;RHG20_HUMAN;.	V	734;708;277;711;698;708;698	ENSP00000260283:I734V;ENSP00000349660:I708V;ENSP00000437905:I277V;ENSP00000432076:I711V;ENSP00000436319:I698V;ENSP00000436522:I708V;ENSP00000431399:I698V	ENSP00000260283:I734V	I	-	1	0	ARHGAP20	109956680	0.028000	0.19301	0.033000	0.17914	0.860000	0.49131	0.237000	0.17985	-0.263000	0.09378	-0.408000	0.06270	ATT	T|0.999;C|0.001	0.001	strong		0.448	ARHGAP20-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390628.1	NM_020809	
OTOF	9381	hgsc.bcm.edu	37	2	26699033	26699033	+	Silent	SNP	G	G	A	rs73920285	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:26699033G>A	ENST00000272371.2	-	23	2955	c.2829C>T	c.(2827-2829)ggC>ggT	p.G943G	OTOF_ENST00000403946.3_Silent_p.G943G|OTOF_ENST00000402415.3_Silent_p.G253G|OTOF_ENST00000338581.6_Silent_p.G196G|OTOF_ENST00000339598.3_Silent_p.G196G	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	943					membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					AGGCATGCAGGCCCAGGCCCT	0.667													G|||	218	0.0435304	0.1566	0.013	5008	,	,		13310	0.0		0.002	False		,,,				2504	0.0				p.G943G	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											OTOF_ENST00000402415,NS,carcinoma,0,3	OTOF	524	3	0			c.C2829T						PASS	.	G	,,,	542,3860	235.2+/-247.8	27,488,1686	34.0	35.0	35.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	588,2829,759,588	3.6	1.0	2	dbSNP_130	35	3,8593	2.2+/-6.3	0,3,4295	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OTOF	NM_004802.3,NM_194248.2,NM_194322.2,NM_194323.2	,,,	27,491,5981	AA,AG,GG		0.0349,12.3126,4.193	,,,	196/1231,943/1998,253/1308,196/1231	26699033	545,12453	2201	4298	6499	SO:0001819	synonymous_variant	9381	exon23			ATGCAGGCCCAGG	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.2829C>T	2.37:g.26699033G>A		85.0	0.0	0		91.0	38.0	0.417582	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Silent	SNP	ENST00000272371.2	37	CCDS1725.1																																																																																			G|0.953;A|0.047	0.047	strong		0.667	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
CASP5	838	hgsc.bcm.edu	37	11	104871193	104871193	+	Silent	SNP	A	A	G	rs45501691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:104871193A>G	ENST00000260315.3	-	6	746	c.747T>C	c.(745-747)gcT>gcC	p.A249A	CASP5_ENST00000444749.2_Silent_p.A191A|CASP5_ENST00000393141.2_Silent_p.A262A|CASP5_ENST00000393139.2_3'UTR|CASP5_ENST00000526056.1_Silent_p.A262A|CASP5_ENST00000531367.1_Silent_p.A107A|CASP5_ENST00000418434.1_Silent_p.A107A			P51878	CASP5_HUMAN	caspase 5, apoptosis-related cysteine peptidase	249					apoptotic process (GO:0006915)|cellular response to mechanical stimulus (GO:0071260)|execution phase of apoptosis (GO:0097194)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of inflammatory response (GO:0050727)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|NLRP1 inflammasome complex (GO:0072558)	cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|ovary(3)|skin(1)|urinary_tract(1)	35		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000943)|Epithelial(105;0.0104)|all cancers(92;0.042)		CTGGTCTGGCAGCAAATGCCC	0.448													A|||	212	0.0423323	0.1543	0.0115	5008	,	,		17767	0.0		0.0	False		,,,				2504	0.0				p.A262A		Atlas-SNP	.											.	CASP5	213	.	0			c.T786C						PASS	.	A	,,,	601,3803		51,499,1652	98.0	89.0	92.0		573,321,786,747	1.9	0.2	11	dbSNP_127	92	5,8593		0,5,4294	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CASP5	NM_001136109.1,NM_001136110.1,NM_001136112.1,NM_004347.3	,,,	51,504,5946	GG,GA,AA		0.0582,13.6467,4.6608	,,,	191/377,107/293,262/448,249/435	104871193	606,12396	2202	4299	6501	SO:0001819	synonymous_variant	838	exon6			TCTGGCAGCAAAT		CCDS8328.2, CCDS44718.1, CCDS44719.1, CCDS44720.1	11q22.2-q22.3	2006-02-17	2005-08-17		ENSG00000137757	ENSG00000137757		"""Caspases"""	1506	protein-coding gene	gene with protein product		602665	"""caspase 5, apoptosis-related cysteine protease"""			7797592, 9250871	Standard	NM_004347		Approved	ICE(rel)III	uc010ruz.1	P51878	OTTHUMG00000048073	ENST00000260315.3:c.747T>C	11.37:g.104871193A>G		139.0	0.0	0		118.0	68.0	0.576271	NM_001136112	B4DKP5|Q0QVY7|Q0QVY8|Q0QVZ0|Q0QVZ1|Q0QVZ2|Q14DD6|Q1HBJ3|Q6DJV7	Silent	SNP	ENST00000260315.3	37	CCDS8328.2																																																																																			A|0.954;G|0.046	0.046	strong		0.448	CASP5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109397.2	NM_004347	
NLRC5	84166	hgsc.bcm.edu	37	16	57060136	57060136	+	Missense_Mutation	SNP	G	G	T	rs149735722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57060136G>T	ENST00000262510.6	+	6	1506	c.1281G>T	c.(1279-1281)caG>caT	p.Q427H	NLRC5_ENST00000436936.1_Missense_Mutation_p.Q427H|NLRC5_ENST00000539144.1_Missense_Mutation_p.Q427H|NLRC5_ENST00000308149.7_Missense_Mutation_p.Q427H	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	427	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				CCCCAGGCCAGTCTGTGGCCC	0.632													G|||	13	0.00259585	0.0098	0.0	5008	,	,		19350	0.0		0.0	False		,,,				2504	0.0				p.Q427H		Atlas-SNP	.											NLRC5,NS,carcinoma,+1,1	NLRC5	186	1	0			c.G1281T						scavenged	.	G	HIS/GLN	16,4380	22.3+/-47.3	0,16,2182	67.0	67.0	67.0		1281	1.6	0.8	16	dbSNP_134	67	0,8600		0,0,4300	yes	missense	NLRC5	NM_032206.3	24	0,16,6482	TT,TG,GG		0.0,0.364,0.1231	probably-damaging	427/1867	57060136	16,12980	2198	4300	6498	SO:0001583	missense	84166	exon5			AGGCCAGTCTGTG	AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"""Nucleotide-binding domain and leucine rich repeat containing"""	29933	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5"", ""NOD-like receptor C5"""	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.1281G>T	16.37:g.57060136G>T	ENSP00000262510:p.Gln427His	44.0	1.0	0.0227273		46.0	19.0	0.413043	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Missense_Mutation	SNP	ENST00000262510.6	37	CCDS10773.1	3|3	0.0013736263736263737|0.0013736263736263737	3|3	0.006097560975609756|0.006097560975609756	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	8.532|8.532	0.871284|0.871284	0.17322|0.17322	0.00364|0.00364	0.0|0.0	ENSG00000140853|ENSG00000140853	ENST00000262510;ENST00000308149;ENST00000436936;ENST00000539144|ENST00000538805	T;T;T;T|.	0.75477|.	-0.75;-0.77;-0.94;-0.77|.	5.21|5.21	1.62|1.62	0.23740|0.23740	.|.	0.000000|.	0.32819|.	N|.	0.005615|.	T|T	0.42832|0.42832	0.1220|0.1220	L|L	0.60455|0.60455	1.87|1.87	0.09310|0.09310	N|N	1|1	P;B;B;B|.	0.42518|.	0.782;0.204;0.191;0.157|.	B;B;B;B|.	0.39339|.	0.297;0.056;0.112;0.122|.	T|T	0.37686|0.37686	-0.9695|-0.9695	10|5	0.44086|.	T|.	0.13|.	.|.	11.318|11.318	0.49403|0.49403	0.2425:0.0:0.7575:0.0|0.2425:0.0:0.7575:0.0	.|.	427;427;427;427|.	Q86WI3-5;Q86WI3-4;Q86WI3-6;Q86WI3|.	.;.;.;NLRC5_HUMAN|.	H|F	427|180	ENSP00000262510:Q427H;ENSP00000308886:Q427H;ENSP00000389739:Q427H;ENSP00000441727:Q427H|.	ENSP00000262510:Q427H|.	Q|V	+|+	3|1	2|0	NLRC5|NLRC5	55617637|55617637	0.142000|0.142000	0.22610|0.22610	0.826000|0.826000	0.32828|0.32828	0.189000|0.189000	0.23516|0.23516	0.756000|0.756000	0.26419|0.26419	0.568000|0.568000	0.29311|0.29311	0.561000|0.561000	0.74099|0.74099	CAG|GTC	G|0.998;T|0.002	0.002	strong		0.632	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206	
ZNF559	84527	hgsc.bcm.edu	37	19	9453160	9453160	+	Nonsense_Mutation	SNP	C	C	T	rs150358404	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9453160C>T	ENST00000393883.2	+	6	1681	c.1033C>T	c.(1033-1035)Cga>Tga	p.R345*	ZNF559_ENST00000586255.1_Intron|CTC-325H20.2_ENST00000592371.1_lincRNA|ZNF177_ENST00000602856.1_Intron|ZNF559_ENST00000317221.7_3'UTR|ZNF559_ENST00000603380.1_Nonsense_Mutation_p.R345*|ZNF559_ENST00000587557.1_Nonsense_Mutation_p.R409*|ZNF177_ENST00000605471.1_Intron|ZNF177_ENST00000541595.2_Intron|ZNF177_ENST00000602738.1_Intron|ZNF559_ENST00000538743.1_Nonsense_Mutation_p.R265*|ZNF177_ENST00000446085.4_Intron	NM_001202412.1	NP_001189341.1	Q9BR84	ZN559_HUMAN	zinc finger protein 559	345					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(2)|large_intestine(7)|lung(15)|ovary(1)|urinary_tract(1)	26						AAAACACAGGCGAACTCACAC	0.408													C|||	5	0.000998403	0.0038	0.0	5008	,	,		20978	0.0		0.0	False		,,,				2504	0.0				p.R409X		Atlas-SNP	.											ZNF559,NS,carcinoma,-1,4	ZNF559	77	4	0			c.C1225T						PASS	.	C	,stop/ARG,stop/ARG,,,,,,,stop/ARG	9,4397	15.5+/-35.6	0,9,2194	62.0	58.0	60.0		,1225,907,,,,,,,1033	-3.7	0.0	19	dbSNP_134	60	2,8598	2.2+/-6.3	0,2,4298	yes	intron,stop-gained,stop-gained,utr-3,utr-3,utr-3,utr-3,utr-3,intron,stop-gained	ZNF559,ZNF559-ZNF177	NM_001172650.2,NM_001202406.1,NM_001202407.1,NM_001202408.1,NM_001202409.1,NM_001202410.1,NM_001202411.1,NM_001202412.1,NM_001202425.1,NM_032497.2	,,,,,,,,,	0,11,6492	TT,TC,CC		0.0233,0.2043,0.0846	,,,,,,,,,	,409/603,303/497,,,,,,,345/539	9453160	11,12995	2203	4300	6503	SO:0001587	stop_gained	84527	exon6			CACAGGCGAACTC	AL389937	CCDS12211.1, CCDS59349.1, CCDS62531.1, CCDS62532.1	19p13.2	2013-09-20			ENSG00000188321	ENSG00000188321		"""Zinc fingers, C2H2-type"", ""-"""	28197	protein-coding gene	gene with protein product						12477932	Standard	NM_001202406		Approved	MGC13105	uc002mle.4	Q9BR84	OTTHUMG00000179942	ENST00000393883.2:c.1033C>T	19.37:g.9453160C>T	ENSP00000377461:p.Arg345*	49.0	0.0	0		59.0	33.0	0.559322	NM_001202406	K7EMG6	Nonsense_Mutation	SNP	ENST00000393883.2	37	CCDS12211.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	24.8	4.571286	0.86542	0.002043	2.33E-4	ENSG00000188321	ENST00000317221;ENST00000538743;ENST00000393883	.	.	.	1.87	-3.74	0.04385	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.8332	0.18593	0.3663:0.5052:0.1284:0.0	.	.	.	.	X	345;265;345	.	ENSP00000325393:R345X	R	+	1	2	ZNF559	9314160	0.000000	0.05858	0.000000	0.03702	0.493000	0.33554	-2.312000	0.01127	-1.360000	0.02172	0.313000	0.20887	CGA	C|0.999;T|0.001	0.001	strong		0.408	ZNF559-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449021.1	NM_032497	
ZNF330	27309	hgsc.bcm.edu	37	4	142155072	142155072	+	Missense_Mutation	SNP	T	T	A	rs34631212	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:142155072T>A	ENST00000262990.4	+	10	1120	c.892T>A	c.(892-894)Ttg>Atg	p.L298M	ZNF330_ENST00000421169.2_Missense_Mutation_p.L238M	NM_014487.4	NP_055302.1	Q9Y3S2	ZN330_HUMAN	zinc finger protein 330	298			L -> M (in dbSNP:rs34631212).			chromosome, centromeric region (GO:0000775)|midbody (GO:0030496)|nucleolus (GO:0005730)	metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	14	all_hematologic(180;0.162)					GTCATCAGATTTGTTTACTAA	0.453													T|||	199	0.0397364	0.1437	0.0115	5008	,	,		20408	0.0		0.001	False		,,,				2504	0.0				p.L298M		Atlas-SNP	.											.	ZNF330	31	.	0			c.T892A						PASS	.	T	MET/LEU	459,3947	218.4+/-236.5	16,427,1760	127.0	133.0	131.0		892	2.1	1.0	4	dbSNP_126	131	3,8597	3.0+/-9.4	0,3,4297	yes	missense	ZNF330	NM_014487.4	15	16,430,6057	AA,AT,TT		0.0349,10.4176,3.5522	benign	298/321	142155072	462,12544	2203	4300	6503	SO:0001583	missense	27309	exon10			TCAGATTTGTTTA	AJ006591	CCDS3754.1	4q31.21	2008-05-15			ENSG00000109445	ENSG00000109445		"""Zinc fingers, C2H2-type"""	15462	protein-coding gene	gene with protein product		609550				11528117, 10593942	Standard	NM_001292002		Approved	NOA36, HSA6591	uc003iiq.4	Q9Y3S2	OTTHUMG00000133413	ENST00000262990.4:c.892T>A	4.37:g.142155072T>A	ENSP00000262990:p.Leu298Met	131.0	0.0	0		164.0	74.0	0.451219	NM_014487	B2RDA3	Missense_Mutation	SNP	ENST00000262990.4	37	CCDS3754.1	73	0.033424908424908424	68	0.13821138211382114	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	T	13.71	2.318489	0.40996	0.104176	3.49E-4	ENSG00000109445	ENST00000262990;ENST00000421169	T;T	0.31510	1.49;1.49	6.17	2.08	0.27032	.	0.358122	0.29212	N	0.012804	T	0.00144	0.0004	N	0.14661	0.345	0.28660	N	0.906172	B;B	0.29716	0.255;0.225	B;B	0.39771	0.146;0.309	T	0.15378	-1.0439	10	0.36615	T	0.2	-31.7734	6.1183	0.20139	0.0:0.456:0.2274:0.3166	rs34631212;rs57194793	238;298	E9PDK6;Q9Y3S2	.;ZN330_HUMAN	M	298;238	ENSP00000262990:L298M;ENSP00000397397:L238M	ENSP00000262990:L298M	L	+	1	2	ZNF330	142374522	0.504000	0.26123	1.000000	0.80357	0.990000	0.78478	0.442000	0.21628	0.416000	0.25844	0.533000	0.62120	TTG	T|0.968;A|0.032	0.032	strong		0.453	ZNF330-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257271.2	NM_014487	
SLCO1B1	10599	hgsc.bcm.edu	37	12	21358933	21358933	+	Missense_Mutation	SNP	G	G	C	rs59502379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:21358933G>C	ENST00000256958.2	+	11	1559	c.1463G>C	c.(1462-1464)gGt>gCt	p.G488A		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	488	Kazal-like. {ECO:0000255|PROSITE- ProRule:PRU00798}.		G -> A (in dbSNP:rs59502379). {ECO:0000269|PubMed:11477075}.		bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|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)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	70					Acetylcysteine(DB06151)|Aminohippurate(DB00345)|Atorvastatin(DB01076)|Axitinib(DB06626)|Benzylpenicillin(DB01053)|Bezafibrate(DB01393)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Eltrombopag(DB06210)|Estradiol(DB00783)|Estrone(DB00655)|Ezetimibe(DB00973)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Gemfibrozil(DB01241)|Indinavir(DB00224)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Olmesartan(DB00275)|Ouabain(DB01092)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Penicillamine(DB00859)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Quinidine(DB00908)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sumatriptan(DB00669)|Valsartan(DB00177)|Verapamil(DB00661)	TGTCTAGCAGGTTGCAAATCT	0.363													G|||	56	0.0111821	0.0408	0.0029	5008	,	,		17184	0.0		0.0	False		,,,				2504	0.0				p.G488A		Atlas-SNP	.											.	SLCO1B1	151	.	0			c.G1463C	GRCh37	CM016147	SLCO1B1	M	rs59502379	PASS	.	G	ALA/GLY	155,4251	104.3+/-142.8	3,149,2051	127.0	125.0	126.0		1463	4.1	1.0	12	dbSNP_129	126	1,8597	1.2+/-3.3	0,1,4298	yes	missense	SLCO1B1	NM_006446.4	60	3,150,6349	CC,CG,GG		0.0116,3.5179,1.1996	probably-damaging	488/692	21358933	156,12848	2203	4299	6502	SO:0001583	missense	10599	exon11			TAGCAGGTTGCAA		CCDS8685.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000134538	ENSG00000134538		"""Solute carriers"""	10959	protein-coding gene	gene with protein product		604843	"""solute carrier family 21 (organic anion transporter), member 6"""	SLC21A6		10358072	Standard	NM_006446		Approved	OATP-C, LST-1, OATP1B1	uc001req.4	Q9Y6L6	OTTHUMG00000169047	ENST00000256958.2:c.1463G>C	12.37:g.21358933G>C	ENSP00000256958:p.Gly488Ala	156.0	0.0	0		150.0	55.0	0.366667	NM_006446	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Missense_Mutation	SNP	ENST00000256958.2	37	CCDS8685.1	22	0.010073260073260074	22	0.044715447154471545	0	0.0	0	0.0	0	0.0	G	14.57	2.574305	0.45902	0.035179	1.16E-4	ENSG00000134538	ENST00000256958	T	0.04862	3.54	4.06	4.06	0.47325	Proteinase inhibitor I1, Kazal (1);Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);Protease inhibitor, Kazal-type (1);	0.000000	0.85682	D	0.000000	T	0.11067	0.0270	H	0.96805	3.885	0.48632	D	0.999686	D	0.89917	1.0	D	0.97110	1.0	T	0.44421	-0.9329	10	0.87932	D	0	.	13.1306	0.59380	0.0:0.0:1.0:0.0	rs59502379	488	Q9Y6L6	SO1B1_HUMAN	A	488	ENSP00000256958:G488A	ENSP00000256958:G488A	G	+	2	0	SLCO1B1	21250200	1.000000	0.71417	1.000000	0.80357	0.335000	0.28730	7.474000	0.81024	1.783000	0.52377	0.484000	0.47621	GGT	G|0.988;C|0.012	0.012	strong		0.363	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446	
KITLG	4254	hgsc.bcm.edu	37	12	88912624	88912624	+	Silent	SNP	G	G	A	rs17015782	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:88912624G>A	ENST00000228280.5	-	4	395	c.213C>T	c.(211-213)agC>agT	p.S71S	KITLG_ENST00000378535.4_5'UTR|KITLG_ENST00000347404.5_Silent_p.S71S|KITLG_ENST00000357116.4_Intron	NM_000899.4	NP_000890.1	P21583	SCF_HUMAN	KIT ligand	71					cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|negative regulation of mast cell apoptotic process (GO:0033026)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of myeloid leukocyte differentiation (GO:0002763)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Ras protein signal transduction (GO:0046579)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	stem cell factor receptor binding (GO:0005173)			kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|stomach(1)	9						CTACCATCTCGCTTATCCAAC	0.353									Testicular Cancer, Familial Clustering of				G|||	52	0.0103834	0.0378	0.0029	5008	,	,		20000	0.0		0.0	False		,,,				2504	0.0				p.S71S		Atlas-SNP	.											.	KITLG	26	.	0			c.C213T						PASS	.	G	,	154,4252	106.0+/-144.5	2,150,2051	76.0	74.0	75.0		213,213	-10.1	0.0	12	dbSNP_123	75	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	KITLG	NM_000899.4,NM_003994.5	,	2,150,6351	AA,AG,GG		0.0,3.4952,1.1841	,	71/274,71/246	88912624	154,12852	2203	4300	6503	SO:0001819	synonymous_variant	4254	exon4	Familial Cancer Database		CATCTCGCTTATC	M59964	CCDS31867.1, CCDS31868.1	12q22	2010-11-23			ENSG00000049130	ENSG00000049130			6343	protein-coding gene	gene with protein product	"""mast cell growth factor"", ""stem cell factor"", ""steel factor"", ""familial progressive hyperpigmentation 2"""	184745		MGF		2208279, 1707188, 19375057	Standard	NM_003994		Approved	SCF, SF, Kitl, KL-1, FPH2	uc001tav.3	P21583	OTTHUMG00000169888	ENST00000228280.5:c.213C>T	12.37:g.88912624G>A		83.0	0.0	0		94.0	41.0	0.43617	NM_003994	A0AV09|A8K2Q4|B7ZLM4|Q16487|Q68DZ2|Q7M4N8|Q9UQK7	Silent	SNP	ENST00000228280.5	37	CCDS31868.1																																																																																			G|0.988;A|0.012	0.012	strong		0.353	KITLG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406424.2	NM_003994	
HGF	3082	hgsc.bcm.edu	37	7	81388042	81388042	+	Silent	SNP	T	T	C	rs5745635	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:81388042T>C	ENST00000222390.5	-	3	559	c.333A>G	c.(331-333)gaA>gaG	p.E111E	HGF_ENST00000423064.2_Silent_p.E111E|HGF_ENST00000457544.2_Silent_p.E111E|HGF_ENST00000354224.6_Silent_p.E111E|HGF_ENST00000444829.2_Silent_p.E111E|HGF_ENST00000453411.1_Silent_p.E111E|HGF_ENST00000453018.1_Silent_p.E8E	NM_000601.4	NP_000592.3	P14210	HGF_HUMAN	hepatocyte growth factor (hepapoietin A; scatter factor)	111	PAN. {ECO:0000255|PROSITE- ProRule:PRU00315}.				activation of MAPK activity (GO:0000187)|blood coagulation (GO:0007596)|cell chemotaxis (GO:0060326)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epithelial to mesenchymal transition (GO:0001837)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|hyaluronan metabolic process (GO:0030212)|liver development (GO:0001889)|mitotic nuclear division (GO:0007067)|myoblast proliferation (GO:0051450)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of hydrogen peroxide-mediated programmed cell death (GO:1901299)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|organ regeneration (GO:0031100)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive chemotaxis (GO:0050918)|positive regulation of cell migration (GO:0030335)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling (GO:0060665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)|platelet alpha granule lumen (GO:0031093)	catalytic activity (GO:0003824)|chemoattractant activity (GO:0042056)|growth factor activity (GO:0008083)|identical protein binding (GO:0042802)			NS(2)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(41)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	75						CATGGCCAAATTCTTTTTTCA	0.313													C|||	518	0.103435	0.3139	0.0317	5008	,	,		14939	0.0079		0.006	False		,,,				2504	0.0685				p.E111E		Atlas-SNP	.											HGF,spleen,lymphoid_neoplasm,-2,1	HGF	171	1	0			c.A333G						PASS	.	C	,,,,	1261,3145	702.0+/-406.8	174,913,1116	108.0	107.0	107.0		333,333,333,333,333	-3.0	0.1	7	dbSNP_114	107	92,8504	814.1+/-407.0	1,90,4207	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HGF	NM_000601.4,NM_001010931.1,NM_001010932.1,NM_001010933.1,NM_001010934.1	,,,,	175,1003,5323	CC,CT,TT		1.0703,28.6201,10.4061	,,,,	111/729,111/291,111/724,111/286,111/211	81388042	1353,11649	2203	4298	6501	SO:0001819	synonymous_variant	3082	exon3			GCCAAATTCTTTT		CCDS5597.1, CCDS47626.1, CCDS47627.1, CCDS47628.1, CCDS47629.1	7q21.1	2009-09-11			ENSG00000019991	ENSG00000019991			4893	protein-coding gene	gene with protein product	"""hepatopoietin A"", ""fibroblast-derived tumor cytotoxic factor"", ""scatter factor"", ""lung fibroblast-derived mitogen"""	142409	"""deafness, autosomal recessive 39"""	DFNB39		1837206, 19576567	Standard	XM_006715956		Approved	SF, F-TCF, HGFB, HPTA	uc003uhl.3	P14210	OTTHUMG00000023804	ENST00000222390.5:c.333A>G	7.37:g.81388042T>C		159.0	0.0	0		148.0	148.0	1	NM_000601	A1L3U6|Q02935|Q13494|Q14519|Q3KRB2|Q8TCE2|Q9BYL9|Q9BYM0|Q9UDU6	Silent	SNP	ENST00000222390.5	37	CCDS5597.1																																																																																			T|0.896;C|0.104	0.104	strong		0.313	HGF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253315.2	NM_000601	
HSD17B11	51170	hgsc.bcm.edu	37	4	88278484	88278484	+	Silent	SNP	T	T	G	rs34025653	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88278484T>G	ENST00000358290.4	-	5	957	c.642A>C	c.(640-642)acA>acC	p.T214T	HSD17B11_ENST00000507286.1_Silent_p.T170T|HSD17B11_ENST00000507518.1_5'UTR	NM_016245.3	NP_057329.2	Q8NBQ5	DHB11_HUMAN	hydroxysteroid (17-beta) dehydrogenase 11	214					androgen catabolic process (GO:0006710)|steroid biosynthetic process (GO:0006694)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|lipid particle (GO:0005811)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|steroid dehydrogenase activity (GO:0016229)			cervix(1)|endometrium(4)|kidney(2)|lung(2)|ovary(2)	11		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000339)		GACACAGACATGTTGTTTTGA	0.368													T|||	288	0.057508	0.2095	0.0159	5008	,	,		19416	0.0		0.0	False		,,,				2504	0.0				p.T214T		Atlas-SNP	.											.	HSD17B11	28	.	0			c.A642C						PASS	.	T		732,3672	301.5+/-286.9	69,594,1539	134.0	115.0	122.0		642	-11.3	0.6	4	dbSNP_126	122	7,8593	4.3+/-15.6	0,7,4293	no	coding-synonymous	HSD17B11	NM_016245.3		69,601,5832	GG,GT,TT		0.0814,16.6213,5.6829		214/301	88278484	739,12265	2202	4300	6502	SO:0001819	synonymous_variant	51170	exon5			CAGACATGTTGTT	AF126780	CCDS3619.1	4q22.1	2011-09-20	2006-11-22	2006-11-22	ENSG00000198189	ENSG00000198189	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	22960	protein-coding gene	gene with protein product	"""retinal short-chain dehydrogenase/reductase 2"", ""short chain dehydrogenase/reductase family 16C, member 2"""	612831	"""dehydrogenase/reductase (SDR family) member 8"""	DHRS8		11165019, 12697717, 19027726	Standard	XM_006714232		Approved	RetSDR2, 17-BETA-HSD11, 17-BETA-HSDXI, PAN1B, SDR16C2	uc003hqp.2	Q8NBQ5	OTTHUMG00000130594	ENST00000358290.4:c.642A>C	4.37:g.88278484T>G		179.0	0.0	0		176.0	68.0	0.386364	NM_016245	Q96HF6|Q9UKU4	Silent	SNP	ENST00000358290.4	37	CCDS3619.1																																																																																			T|0.938;G|0.062	0.062	strong		0.368	HSD17B11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253041.1	NM_016245	
SMTNL2	342527	hgsc.bcm.edu	37	17	4497137	4497137	+	Missense_Mutation	SNP	T	T	C	rs9916524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4497137T>C	ENST00000389313.4	+	4	818	c.751T>C	c.(751-753)Tgg>Cgg	p.W251R	SMTNL2_ENST00000338859.4_Missense_Mutation_p.W107R	NM_001114974.1	NP_001108446.1	Q2TAL5	SMTL2_HUMAN	smoothelin-like 2	251			W -> R (in dbSNP:rs9916524).							breast(1)|endometrium(9)|kidney(1)|lung(1)|skin(1)	13				READ - Rectum adenocarcinoma(115;0.0325)		CTCTTTCACGTGGTCTGTGCC	0.592													C|||	229	0.0457268	0.1399	0.0159	5008	,	,		18798	0.0		0.008	False		,,,				2504	0.0256				p.W251R		Atlas-SNP	.											.	SMTNL2	57	.	0			c.T751C						PASS	.	C	ARG/TRP,ARG/TRP	520,3886	776.1+/-414.1	26,468,1709	76.0	69.0	72.0		751,319	-0.1	0.0	17	dbSNP_119	72	10,8590	818.7+/-406.8	0,10,4290	yes	missense,missense	SMTNL2	NM_001114974.1,NM_198501.2	101,101	26,478,5999	CC,CT,TT		0.1163,11.8021,4.075	benign,benign	251/462,107/318	4497137	530,12476	2203	4300	6503	SO:0001583	missense	342527	exon4			TTCACGTGGTCTG	AK124452	CCDS11048.1, CCDS45583.1	17p13.2	2006-04-26			ENSG00000188176	ENSG00000188176			24764	protein-coding gene	gene with protein product							Standard	NM_001114974		Approved	FLJ42461	uc002fyf.1	Q2TAL5	OTTHUMG00000132938	ENST00000389313.4:c.751T>C	17.37:g.4497137T>C	ENSP00000373964:p.Trp251Arg	129.0	0.0	0		118.0	45.0	0.381356	NM_001114974	Q6ZVK6	Missense_Mutation	SNP	ENST00000389313.4	37	CCDS45583.1	93	0.042582417582417584	84	0.17073170731707318	4	0.011049723756906077	0	0.0	5	0.006596306068601583	C	0.021	-1.428801	0.01117	0.118021	0.001163	ENSG00000188176	ENST00000338859;ENST00000389313	T;T	0.80994	-1.41;-1.44	4.45	-0.126	0.13515	.	.	.	.	.	T	0.00178	0.0005	N	0.02142	-0.665	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.01814	-1.1268	9	0.02654	T	1	-20.7736	3.6672	0.08260	0.4915:0.3015:0.0:0.207	rs9916524;rs52797495;rs56667747;rs9916524	251	Q2TAL5	SMTL2_HUMAN	R	107;251	ENSP00000345143:W107R;ENSP00000373964:W251R	ENSP00000345143:W107R	W	+	1	0	SMTNL2	4443886	0.000000	0.05858	0.018000	0.16275	0.001000	0.01503	-2.881000	0.00715	-0.161000	0.10983	-1.043000	0.02367	TGG	T|0.951;C|0.049	0.049	strong		0.592	SMTNL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439129.1	NM_198501	
LDB3	11155	hgsc.bcm.edu	37	10	88476458	88476458	+	Missense_Mutation	SNP	G	G	A	rs113817827		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:88476458G>A	ENST00000361373.4	+	9	1627	c.1606G>A	c.(1606-1608)Gtc>Atc	p.V536I	LDB3_ENST00000458213.2_Missense_Mutation_p.V426I|LDB3_ENST00000429277.2_Missense_Mutation_p.V541I|LDB3_ENST00000352360.5_Missense_Mutation_p.V279I|LDB3_ENST00000263066.6_Missense_Mutation_p.V426I	NM_007078.2	NP_009009.1			LIM domain binding 3											breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|soft_tissue(1)	25						CAGGGGGACCGTCCAGAGGGC	0.667													G|||	1	0.000199681	0.0	0.0	5008	,	,		13034	0.001		0.0	False		,,,				2504	0.0				p.V541I		Atlas-SNP	.											.	LDB3	164	.	0			c.G1621A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL	2,4404	4.2+/-10.8	0,2,2201	33.0	33.0	33.0		1276,1621,1606	-0.3	0.9	10	dbSNP_132	33	0,8600		0,0,4300	no	missense,missense,missense	LDB3	NM_001080114.1,NM_001171610.1,NM_007078.2	29,29,29	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	benign,benign,benign	426/618,541/733,536/728	88476458	2,13004	2203	4300	6503	SO:0001583	missense	11155	exon10			GGGACCGTCCAGA	AB014513	CCDS7377.1, CCDS41544.1, CCDS41545.1, CCDS53549.1, CCDS53550.1	10q22.3-q23.2	2014-09-17			ENSG00000122367	ENSG00000122367			15710	protein-coding gene	gene with protein product	"""cypher"", ""oracle"", ""Z-band alternatively spliced PDZ motif protein"""	605906	"""cardiomyopathy, dilated 1C (autosomal dominant)"""	CMD1C		10427098, 23271734, 23996002, 14662268	Standard	NM_001080114		Approved	PDLIM6, KIAA0613, ZASP	uc001kdv.3	O75112	OTTHUMG00000018655	ENST00000361373.4:c.1606G>A	10.37:g.88476458G>A	ENSP00000355296:p.Val536Ile	251.0	0.0	0		235.0	105.0	0.446809	NM_001171610		Missense_Mutation	SNP	ENST00000361373.4	37	CCDS7377.1	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	G	13.41	2.227523	0.39399	4.54E-4	0.0	ENSG00000122367	ENST00000539402;ENST00000429277;ENST00000458213;ENST00000352360;ENST00000263066;ENST00000361373	T;T;T;T;T	0.54279	0.82;0.67;0.61;0.67;0.58	4.85	-0.331	0.12679	.	0.302757	0.18155	N	0.149948	T	0.21509	0.0518	N	0.05124	-0.11	0.80722	D	1	B;B;B;P;B	0.38729	0.001;0.003;0.0;0.644;0.0	B;B;B;B;B	0.32805	0.001;0.004;0.001;0.153;0.0	T	0.02852	-1.1102	10	0.35671	T	0.21	.	4.289	0.10869	0.1864:0.0:0.2957:0.5179	.	541;457;279;536;426	B4E3K3;F5H0C2;O75112-3;O75112;O75112-2	.;.;.;LDB3_HUMAN;.	I	457;541;426;279;426;536	ENSP00000401437:V541I;ENSP00000409148:V426I;ENSP00000263067:V279I;ENSP00000263066:V426I;ENSP00000355296:V536I	ENSP00000263066:V426I	V	+	1	0	LDB3	88466438	0.975000	0.34042	0.879000	0.34478	0.874000	0.50279	1.816000	0.38992	0.095000	0.17434	0.555000	0.69702	GTC	G|0.998;A|0.002	0.002	strong		0.667	LDB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049160.2		
B4GALNT4	338707	hgsc.bcm.edu	37	11	380390	380390	+	Silent	SNP	C	C	T	rs115057328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:380390C>T	ENST00000329962.6	+	18	2814	c.2814C>T	c.(2812-2814)gcC>gcT	p.A938A		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	938					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			endometrium(2)|kidney(4)|large_intestine(1)|liver(2)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GCAGGCTGGCCTTCGCGCCCG	0.682													.|||	22	0.00439297	0.0151	0.0029	5008	,	,		13932	0.0		0.0	False		,,,				2504	0.0				p.A938A		Atlas-SNP	.											.	B4GALNT4	83	.	0			c.C2814T						PASS	.	C		57,4349	51.6+/-87.1	0,57,2146	60.0	43.0	49.0		2814	3.8	1.0	11	dbSNP_132	49	0,8598		0,0,4299	no	coding-synonymous	B4GALNT4	NM_178537.4		0,57,6445	TT,TC,CC		0.0,1.2937,0.4383		938/1040	380390	57,12947	2203	4299	6502	SO:0001819	synonymous_variant	338707	exon18			GCTGGCCTTCGCG	AB089939	CCDS7694.1	11p15.5	2013-02-19			ENSG00000182272	ENSG00000182272	2.4.1.-	"""Beta 4-glycosyltransferases"""	26315	protein-coding gene	gene with protein product						15044014	Standard	NM_178537		Approved	FLJ25045, NGalNAc-T1	uc001lpb.3	Q76KP1	OTTHUMG00000119075	ENST00000329962.6:c.2814C>T	11.37:g.380390C>T		73.0	0.0	0		104.0	64.0	0.615385	NM_178537	Q96LV2	Silent	SNP	ENST00000329962.6	37	CCDS7694.1																																																																																			C|0.995;T|0.005	0.005	strong		0.682	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2	NM_178537	
NSUN2	54888	hgsc.bcm.edu	37	5	6622139	6622139	+	Silent	SNP	G	G	T	rs148924682	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:6622139G>T	ENST00000264670.6	-	6	923	c.612C>A	c.(610-612)gtC>gtA	p.V204V	NSUN2_ENST00000505264.1_Intron|NSUN2_ENST00000539938.1_Intron|NSUN2_ENST00000506139.1_Silent_p.V169V	NM_017755.5	NP_060225.4	Q08J23	NSUN2_HUMAN	NOP2/Sun RNA methyltransferase family, member 2	204					mitotic nuclear division (GO:0007067)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|tRNA (cytosine-5-)-methyltransferase activity (GO:0016428)|tRNA binding (GO:0000049)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(23)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	41						CTGGAAAGGGGACATTCATGT	0.408													G|||	51	0.0101837	0.0348	0.0058	5008	,	,		18768	0.0		0.001	False		,,,				2504	0.0				p.V204V		Atlas-SNP	.											NSUN2,NS,carcinoma,-1,1	NSUN2	82	1	0			c.C612A						PASS	.	G	,	150,4256	103.8+/-142.4	3,144,2056	180.0	150.0	161.0		507,612	-1.7	0.3	5	dbSNP_134	161	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	NSUN2	NM_001193455.1,NM_017755.5	,	3,144,6356	TT,TG,GG		0.0,3.4044,1.1533	,	169/733,204/768	6622139	150,12856	2203	4300	6503	SO:0001819	synonymous_variant	54888	exon6			AAAGGGGACATTC	AK000310	CCDS3869.1, CCDS54832.1	5p15.32	2014-01-31	2012-06-12		ENSG00000037474	ENSG00000037474		"""NOP2/Sun domain containing"""	25994	protein-coding gene	gene with protein product	"""tRNA methyltransferase 4 homolog (S. cerevisiae)"", ""Myc-induced SUN-domain-containing protein"""	610916	"""NOL1/NOP2/Sun domain family, member 2"", ""NOP2/Sun domain family, member 2"", ""mental retardation, non-syndromic, autosomal recessive, 5"""	MRT5		17071714, 22541559	Standard	NM_017755		Approved	FLJ20303, TRM4, Misu	uc003jdu.3	Q08J23	OTTHUMG00000090455	ENST00000264670.6:c.612C>A	5.37:g.6622139G>T		118.0	0.0	0		109.0	48.0	0.440367	NM_017755	A8K529|B2RNR4|B3KP09|B4DQW2|G3V1R4|Q9BVN4|Q9H858|Q9NXD9	Silent	SNP	ENST00000264670.6	37	CCDS3869.1																																																																																			G|0.990;T|0.010	0.010	strong		0.408	NSUN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206902.1	NM_017755	
UPK3A	7380	hgsc.bcm.edu	37	22	45683309	45683309	+	Silent	SNP	C	C	T	rs62001037	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:45683309C>T	ENST00000216211.4	+	3	497	c.465C>T	c.(463-465)ccC>ccT	p.P155P	UPK3A_ENST00000396082.2_Intron	NM_006953.3	NP_008884.1	O75631	UPK3A_HUMAN	uroplakin 3A	155					cell morphogenesis (GO:0000902)|epithelial cell differentiation (GO:0030855)|kidney development (GO:0001822)|potassium ion homeostasis (GO:0055075)|sodium ion homeostasis (GO:0055078)|urea transport (GO:0015840)|urinary bladder development (GO:0060157)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)|lung(2)|skin(1)	5		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		GTAACGCACCCCTGTCGGCAG	0.607													C|||	116	0.0231629	0.084	0.0058	5008	,	,		16168	0.0		0.001	False		,,,				2504	0.0				p.P155P		Atlas-SNP	.											.	UPK3A	14	.	0			c.C465T						PASS	.	C	,	338,4066		14,310,1878	28.0	27.0	28.0		,465	0.4	1.0	22	dbSNP_129	28	1,8599		0,1,4299	no	intron,coding-synonymous	UPK3A	NM_001167574.1,NM_006953.3	,	14,311,6177	TT,TC,CC		0.0116,7.6748,2.6069	,	,155/288	45683309	339,12665	2202	4300	6502	SO:0001819	synonymous_variant	7380	exon3			CGCACCCCTGTCG	AB010637	CCDS14064.1, CCDS54539.1	22q13.31	2005-11-14	2003-07-29	2003-07-30	ENSG00000100373	ENSG00000100373			12580	protein-coding gene	gene with protein product		611559	"""uroplakin 3"""	UPK3		9818021	Standard	NM_006953		Approved		uc003bfy.3	O75631	OTTHUMG00000151339	ENST00000216211.4:c.465C>T	22.37:g.45683309C>T		67.0	0.0	0		67.0	30.0	0.447761	NM_006953	B0QY25|O60261|Q32N05|Q5TII6	Silent	SNP	ENST00000216211.4	37	CCDS14064.1																																																																																			C|0.973;T|0.027	0.027	strong		0.607	UPK3A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000322276.1	NM_006953	
LRRC24	441381	hgsc.bcm.edu	37	8	145748075	145748075	+	Silent	SNP	T	T	G	rs112652028	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145748075T>G	ENST00000529415.2	-	5	1443	c.1326A>C	c.(1324-1326)ggA>ggC	p.G442G	LRRC14_ENST00000528528.1_3'UTR|LRRC24_ENST00000533758.1_Silent_p.G439G|LRRC14_ENST00000292524.1_3'UTR			Q50LG9	LRC24_HUMAN	leucine rich repeat containing 24	442						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(1)|lung(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			CGAACAGCGCTCCCTCCCCCG	0.682													G|||	75	0.014976	0.0522	0.0072	5008	,	,		9844	0.0		0.0	False		,,,				2504	0.001				p.G442G		Atlas-SNP	.											.	LRRC24	11	.	0			c.A1326C						PASS	.	G	,	155,4189		3,149,2020	13.0	14.0	14.0		1326,	3.1	1.0	8	dbSNP_132	14	2,8570		0,2,4284	no	coding-synonymous,utr-3	LRRC14,LRRC24	NM_001024678.3,NM_014665.2	,	3,151,6304	GG,GT,TT		0.0233,3.5681,1.2155	,	442/514,	145748075	157,12759	2172	4286	6458	SO:0001819	synonymous_variant	441381	exon5			CAGCGCTCCCTCC	AB178281	CCDS34969.1	8q24.3	2013-01-11			ENSG00000254402	ENSG00000254402		"""Immunoglobulin superfamily / I-set domain containing"""	28947	protein-coding gene	gene with protein product						7584026	Standard	NM_001024678		Approved	LRRC14OS	uc003zdm.3	Q50LG9	OTTHUMG00000165180	ENST00000529415.2:c.1326A>C	8.37:g.145748075T>G		49.0	0.0	0		53.0	21.0	0.396226	NM_001024678		Silent	SNP	ENST00000529415.2	37	CCDS34969.1																																																																																			T|0.986;G|0.014	0.014	strong		0.682	LRRC24-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382501.2	NM_001024678	
OR2K2	26248	hgsc.bcm.edu	37	9	114090277	114090277	+	Missense_Mutation	SNP	G	G	A	rs73656223	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:114090277G>A	ENST00000374428.1	-	1	523	c.524C>T	c.(523-525)aCg>aTg	p.T175M	OR2K2_ENST00000302681.1_Missense_Mutation_p.T146M			Q8NGT1	OR2K2_HUMAN	olfactory receptor, family 2, subfamily K, member 2	175						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(2)	20						CCAGGAGACCGTAGCCATCCG	0.547													G|||	74	0.0147764	0.053	0.0058	5008	,	,		21286	0.0		0.0	False		,,,				2504	0.0				p.T146M		Atlas-SNP	.											.	OR2K2	77	.	0			c.C437T						PASS	.	G	MET/THR	226,4180	116.7+/-154.6	5,216,1982	99.0	80.0	86.0		437	1.1	0.0	9	dbSNP_130	86	1,8599	1.2+/-3.3	0,1,4299	yes	missense	OR2K2	NM_205859.1	81	5,217,6281	AA,AG,GG		0.0116,5.1294,1.7453	benign	146/317	114090277	227,12779	2203	4300	6503	SO:0001583	missense	26248	exon1			GAGACCGTAGCCA	X64977	CCDS6778.1	9q31.3	2012-08-09			ENSG00000171133	ENSG00000171133		"""GPCR / Class A : Olfactory receptors"""	8264	protein-coding gene	gene with protein product				OR2AR1P		1370859, 17010214	Standard	NM_205859		Approved	HTPCRH06, HSHTPCRH06	uc011lwp.2	Q8NGT1	OTTHUMG00000020488	ENST00000374428.1:c.524C>T	9.37:g.114090277G>A	ENSP00000363550:p.Thr175Met	85.0	0.0	0		78.0	44.0	0.564103	NM_205859	Q2TA61|Q5VYK4|Q6IFI5	Missense_Mutation	SNP	ENST00000374428.1	37		25	0.011446886446886446	22	0.044715447154471545	3	0.008287292817679558	0	0.0	0	0.0	G	4.460	0.085171	0.08583	0.051294	1.16E-4	ENSG00000171133	ENST00000302681;ENST00000374428	T;T	0.37752	1.18;1.18	4.92	1.09	0.20402	GPCR, rhodopsin-like superfamily (1);	1.107710	0.07088	U	0.838300	T	0.04092	0.0114	N	0.20986	0.625	0.09310	N	1	B	0.18461	0.028	B	0.14578	0.011	T	0.20371	-1.0277	10	0.72032	D	0.01	.	6.3971	0.21618	0.1168:0.2929:0.5903:0.0	.	175	Q8NGT1	OR2K2_HUMAN	M	146;175	ENSP00000305055:T146M;ENSP00000363550:T175M	ENSP00000305055:T146M	T	-	2	0	OR2K2	113130098	0.000000	0.05858	0.000000	0.03702	0.242000	0.25591	0.116000	0.15561	0.150000	0.19136	-0.423000	0.05987	ACG	G|0.982;A|0.018	0.018	strong		0.547	OR2K2-201	KNOWN	basic	protein_coding	protein_coding		NM_205859	
ACP7	390928	hgsc.bcm.edu	37	19	39575987	39575987	+	Silent	SNP	G	G	A	rs544041	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39575987G>A	ENST00000331256.5	+	2	352	c.78G>A	c.(76-78)ggG>ggA	p.G26G	PAPL_ENST00000594229.1_Silent_p.G26G	NM_001004318.2	NP_001004318.2	Q6ZNF0	PAPL_HUMAN		26						extracellular region (GO:0005576)	acid phosphatase activity (GO:0003993)|metal ion binding (GO:0046872)										GGTCCCTGGGGGCTCCCAGCG	0.592													g|||	691	0.137979	0.4962	0.0447	5008	,	,		19220	0.0		0.004	False		,,,				2504	0.0				p.G26G		Atlas-SNP	.											.	.	.	.	0			c.G78A						PASS	.	G		1854,2552	538.2+/-374.9	377,1100,726	124.0	113.0	117.0		78	-0.7	0.0	19	dbSNP_83	117	29,8571	19.8+/-62.0	0,29,4271	no	coding-synonymous	PAPL	NM_001004318.2		377,1129,4997	AA,AG,GG		0.3372,42.079,14.4779		26/439	39575987	1883,11123	2203	4300	6503	SO:0001819	synonymous_variant	0	exon2			CCTGGGGGCTCCC																												ENST00000331256.5:c.78G>A	19.37:g.39575987G>A		126.0	0.0	0		122.0	121.0	0.991803	NM_001004318	B2RN68	Silent	SNP	ENST00000331256.5	37	CCDS33018.1																																																																																			G|0.870;A|0.130	0.130	strong		0.592	PAPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463810.1		
GMPPA	29926	hgsc.bcm.edu	37	2	220370746	220370746	+	Silent	SNP	G	G	A	rs13428617	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220370746G>A	ENST00000358215.3	+	11	1314	c.945G>A	c.(943-945)gaG>gaA	p.E315E	GMPPA_ENST00000341142.3_Silent_p.E315E|GMPPA_ENST00000373917.3_Silent_p.E368E|GMPPA_ENST00000313597.5_Silent_p.E315E|AC053503.11_ENST00000429882.1_RNA|GMPPA_ENST00000373908.1_Silent_p.E315E	NM_205847.2	NP_995319.1	Q96IJ6	GMPPA_HUMAN	GDP-mannose pyrophosphorylase A	315					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|GDP-mannose biosynthetic process (GO:0009298)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	nucleotidyltransferase activity (GO:0016779)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	20		Renal(207;0.0183)		Epithelial(149;3.82e-10)|all cancers(144;6.25e-08)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00807)|READ - Rectum adenocarcinoma(5;0.148)		CCGTGGGTGAGGGTGTGCGGC	0.622													G|||	101	0.0201677	0.0726	0.0058	5008	,	,		17609	0.001		0.0	False		,,,				2504	0.0				p.E315E		Atlas-SNP	.											.	GMPPA	50	.	0			c.G945A						PASS	.	G	,	286,4116		10,266,1925	40.0	33.0	36.0		945,945	3.0	1.0	2	dbSNP_121	36	3,8591		0,3,4294	no	coding-synonymous,coding-synonymous	GMPPA	NM_013335.3,NM_205847.2	,	10,269,6219	AA,AG,GG		0.0349,6.497,2.2238	,	315/421,315/421	220370746	289,12707	2201	4297	6498	SO:0001819	synonymous_variant	29926	exon11			GGGTGAGGGTGTG	AF135422	CCDS2441.1	2q36.1	2008-02-05			ENSG00000144591	ENSG00000144591			22923	protein-coding gene	gene with protein product		615495					Standard	NM_205847		Approved		uc002vlr.3	Q96IJ6	OTTHUMG00000058922	ENST00000358215.3:c.945G>A	2.37:g.220370746G>A		57.0	0.0	0		72.0	32.0	0.444444	NM_205847	A6NJ74|A8K3Q6|B3KMT4|Q53GI0|Q9NWC3|Q9Y5P5	Silent	SNP	ENST00000358215.3	37	CCDS2441.1																																																																																			G|0.979;A|0.021	0.021	strong		0.622	GMPPA-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130230.1	NM_013335	
C21orf2	755	hgsc.bcm.edu	37	21	45750713	45750713	+	Missense_Mutation	SNP	C	C	T	rs62000360	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45750713C>T	ENST00000339818.4	-	6	842	c.635G>A	c.(634-636)aGg>aAg	p.R212K	C21orf2_ENST00000325223.7_Missense_Mutation_p.R211K|AP001062.8_ENST00000422357.1_RNA|C21orf2_ENST00000397956.3_Missense_Mutation_p.R211K|AP001062.7_ENST00000448927.1_RNA|C21orf2_ENST00000496321.1_5'UTR	NM_001271440.1|NM_004928.2	NP_001258369.1|NP_004919.1	O43822	CU002_HUMAN	chromosome 21 open reading frame 2	212					cilium morphogenesis (GO:0060271)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				endometrium(2)	2				Colorectal(79;0.0806)		CACCCTGCCCCTGTGGCTGCT	0.697													C|||	126	0.0251597	0.0855	0.0159	5008	,	,		13869	0.0		0.002	False		,,,				2504	0.0				p.R212K		Atlas-SNP	.											.	C21orf2	10	.	0			c.G635A						PASS	.	C	LYS/ARG	228,4128		4,220,1954	11.0	13.0	12.0		635	-5.5	0.0	21	dbSNP_129	12	0,8504		0,0,4252	yes	missense	C21orf2	NM_004928.2	26	4,220,6206	TT,TC,CC		0.0,5.2342,1.7729	benign	212/257	45750713	228,12632	2178	4252	6430	SO:0001583	missense	755	exon6			CTGCCCCTGTGGC	Y11392	CCDS13709.1, CCDS59444.1, CCDS59445.1	21q22.3	2014-03-24			ENSG00000160226	ENSG00000160226			1260	protein-coding gene	gene with protein product	"""nuclear encoded mitochondrial protein"", ""leucine rich repeat containing 76"""	603191				9465297	Standard	NM_004928		Approved	YF5, A2, LRRC76	uc002zeq.2	O43822	OTTHUMG00000086909	ENST00000339818.4:c.635G>A	21.37:g.45750713C>T	ENSP00000344566:p.Arg212Lys	157.0	0.0	0		155.0	80.0	0.516129	NM_004928	A8MPS9|O14993|Q8N5X6|Q99837|Q99838	Missense_Mutation	SNP	ENST00000339818.4	37	CCDS13709.1	39	0.017857142857142856	34	0.06910569105691057	5	0.013812154696132596	0	0.0	0	0.0	C	1.956	-0.440014	0.04636	0.052342	0.0	ENSG00000160226	ENST00000339818;ENST00000397956;ENST00000325223	T;T;T	0.30448	1.65;1.53;1.61	4.25	-5.48	0.02592	.	0.521247	0.22438	N	0.060048	T	0.00608	0.0020	N	0.08118	0	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	0.17410	-1.0370	10	0.02654	T	1	-26.1772	5.5943	0.17319	0.0:0.3756:0.2867:0.3377	.	211;211;212;171	G5E952;Q8N5X6;O43822;O43822-2	.;.;CU002_HUMAN;.	K	212;211;211	ENSP00000344566:R212K;ENSP00000381047:R211K;ENSP00000317302:R211K	ENSP00000317302:R211K	R	-	2	0	C21orf2	44575141	0.000000	0.05858	0.029000	0.17559	0.002000	0.02628	-1.437000	0.02419	-1.158000	0.02811	-0.768000	0.03414	AGG	C|0.976;T|0.024	0.024	strong		0.697	C21orf2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195799.1	NM_004928	
POFUT2	23275	hgsc.bcm.edu	37	21	46685550	46685550	+	Splice_Site	SNP	C	C	T	rs112907087	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46685550C>T	ENST00000349485.5	-	9	1163	c.1137G>A	c.(1135-1137)agG>agA	p.R379R	POFUT2_ENST00000331343.7_3'UTR|POFUT2_ENST00000471540.1_5'UTR	NM_133635.4	NP_598368.2	Q9Y2G5	OFUT2_HUMAN	protein O-fucosyltransferase 2	379					fucose metabolic process (GO:0006004)|mesoderm formation (GO:0001707)|protein O-linked fucosylation (GO:0036066)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of gene expression (GO:0010468)|regulation of secretion (GO:0051046)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)	peptide-O-fucosyltransferase activity (GO:0046922)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	20				Colorectal(79;0.243)		CAATAAAAAACCTGCAAAGGA	0.493													C|||	27	0.00539137	0.0204	0.0	5008	,	,		16487	0.0		0.0	False		,,,				2504	0.0				p.R379R		Atlas-SNP	.											.	POFUT2	77	.	0			c.G1137A						PASS	.	C	,	86,4320	74.1+/-112.3	1,84,2118	52.0	57.0	56.0		,1137	3.9	1.0	21	dbSNP_132	56	0,8600		0,0,4300	yes	utr-3,coding-synonymous-near-splice	POFUT2	NM_015227.4,NM_133635.4	,	1,84,6418	TT,TC,CC		0.0,1.9519,0.6612	,	,379/430	46685550	86,12920	2203	4300	6503	SO:0001630	splice_region_variant	23275	exon9			AAAAAACCTGCAA	AJ203079	CCDS13719.1, CCDS13721.1	21q22.3	2013-03-06	2004-06-07	2004-06-09	ENSG00000186866	ENSG00000186866	2.4.1.221	"""Fucosyltransferases"""	14683	protein-coding gene	gene with protein product	"""peptide-O-fucosyltransferase"", ""GDP-fucose protein O-fucosyltransferase 2"""	610249	"""chromosome 21 open reading frame 80"""	C21orf80			Standard	NM_133635		Approved	KIAA0958, FUT13	uc002zhc.3	Q9Y2G5	OTTHUMG00000084874	ENST00000349485.5:c.1137-1G>A	21.37:g.46685550C>T		62.0	0.0	0		48.0	23.0	0.479167	NM_133635	Q6PJV1|Q7Z4N0|Q8WWU6|Q9BQS4|Q9BQS5|Q9UFY3	Silent	SNP	ENST00000349485.5	37	CCDS13719.1																																																																																			C|0.992;T|0.008	0.008	strong		0.493	POFUT2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192573.2	NM_015227	Silent
KIAA1683	80726	hgsc.bcm.edu	37	19	18368524	18368524	+	Silent	SNP	C	C	T	rs61740686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18368524C>T	ENST00000600328.3	-	4	3202	c.3009G>A	c.(3007-3009)acG>acA	p.T1003T	KIAA1683_ENST00000600359.3_Silent_p.T957T|PDE4C_ENST00000596647.1_5'Flank|KIAA1683_ENST00000392413.4_Silent_p.T1190T|PDE4C_ENST00000355502.3_5'Flank			Q9H0B3	K1683_HUMAN	KIAA1683	1003						mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						GCTCCACCCACGTGACGGGGT	0.662													C|||	170	0.0339457	0.1248	0.0072	5008	,	,		15480	0.0		0.0	False		,,,				2504	0.0				p.T1190T		Atlas-SNP	.											.	KIAA1683	190	.	0			c.G3570A						PASS	.	C	,,	427,3903		12,403,1750	23.0	30.0	28.0		3570,2871,3009	-2.8	0.0	19	dbSNP_129	28	0,8468		0,0,4234	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	,,	12,403,5984	TT,TC,CC		0.0,9.8614,3.3365	,,	1190/1368,957/1135,1003/1181	18368524	427,12371	2165	4234	6399	SO:0001819	synonymous_variant	80726	exon4			CACCCACGTGACG	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.3009G>A	19.37:g.18368524C>T		56.0	0.0	0		95.0	93.0	0.978947	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Silent	SNP	ENST00000600328.3	37	CCDS32958.1																																																																																			C|0.964;T|0.036	0.036	strong		0.662	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
DNAJC21	134218	hgsc.bcm.edu	37	5	34937649	34937649	+	Silent	SNP	G	G	A	rs77480286	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:34937649G>A	ENST00000342382.4	+	5	884	c.657G>A	c.(655-657)gcG>gcA	p.A219A	DNAJC21_ENST00000382021.2_Silent_p.A219A|DNAJC21_ENST00000303525.7_Silent_p.A219A			Q5F1R6	DJC21_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 21	219					protein folding (GO:0006457)	ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.A219A(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(10)|skin(2)|upper_aerodigestive_tract(1)	21	all_lung(31;7.08e-05)		COAD - Colon adenocarcinoma(61;0.174)|Colorectal(62;0.229)			GAGTGCAGGCGCATCGAAAAC	0.478													G|||	41	0.0081869	0.0303	0.0014	5008	,	,		18843	0.0		0.0	False		,,,				2504	0.0				p.A219A		Atlas-SNP	.											DNAJC21,caecum,carcinoma,0,1	DNAJC21	54	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G657A						PASS	.	G	,	68,4338	61.1+/-98.1	1,66,2136	77.0	85.0	82.0		657,657	-11.1	0.0	5	dbSNP_132	82	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	DNAJC21	NM_001012339.2,NM_194283.3	,	1,68,6434	AA,AG,GG		0.0233,1.5433,0.5382	,	219/532,219/577	34937649	70,12936	2203	4300	6503	SO:0001819	synonymous_variant	134218	exon5			GCAGGCGCATCGA		CCDS3907.2, CCDS34144.1	5p13-p12	2012-10-05			ENSG00000168724	ENSG00000168724		"""Heat shock proteins / DNAJ (HSP40)"""	27030	protein-coding gene	gene with protein product	"""JJJ1 DnaJ domain protein homolog (S. cerevisiae)"""					15067379	Standard	XM_005248250		Approved	GS3, DNAJA5, JJJ1	uc003jjc.3	Q5F1R6	OTTHUMG00000074103	ENST00000342382.4:c.657G>A	5.37:g.34937649G>A		257.0	1.0	0.00389105		228.0	108.0	0.473684	NM_001012339	Q3B7J9|Q6P086|Q6ZS43|Q86VC6	Silent	SNP	ENST00000342382.4	37	CCDS34144.1																																																																																			G|0.992;A|0.008	0.008	strong		0.478	DNAJC21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157337.1	NM_194283	
GPR182	11318	hgsc.bcm.edu	37	12	57389536	57389536	+	Silent	SNP	G	G	A	rs61740222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:57389536G>A	ENST00000300098.1	+	2	762	c.543G>A	c.(541-543)tcG>tcA	p.S181S	RP11-474N8.5_ENST00000556850.1_RNA|HBCBP_ENST00000600202.1_5'Flank	NM_007264.3	NP_009195.1	O15218	GP182_HUMAN	G protein-coupled receptor 182	181					cell surface receptor signaling pathway (GO:0007166)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)			endometrium(3)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	15						GGGTCCTCTCGGCCATCATCC	0.642													G|||	65	0.0129792	0.0492	0.0	5008	,	,		19981	0.0		0.0	False		,,,				2504	0.0				p.S181S		Atlas-SNP	.											.	GPR182	35	.	0			c.G543A						PASS	.	G		158,4248	106.5+/-144.9	2,154,2047	61.0	53.0	56.0		543	-8.9	0.1	12	dbSNP_129	56	2,8598		0,2,4298	no	coding-synonymous	GPR182	NM_007264.3		2,156,6345	AA,AG,GG		0.0233,3.586,1.2302		181/405	57389536	160,12846	2203	4300	6503	SO:0001819	synonymous_variant	11318	exon2			CCTCTCGGCCATC	Y13583	CCDS8927.1	12q13.3	2012-08-21	2007-09-24	2007-09-24		ENSG00000166856		"""GPCR / Class A : Orphans"""	13708	protein-coding gene	gene with protein product		605307	"""adrenomedullin receptor"""	ADMR		9367907, 9535752	Standard	NM_007264		Approved	hrhAMR, G10D, AM-R	uc001smk.3	O15218		ENST00000300098.1:c.543G>A	12.37:g.57389536G>A		88.0	0.0	0		103.0	53.0	0.514563	NM_007264		Silent	SNP	ENST00000300098.1	37	CCDS8927.1																																																																																			G|0.987;A|0.013	0.013	strong		0.642	GPR182-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411212.1	NM_007264	
FNDC3B	64778	hgsc.bcm.edu	37	3	171969312	171969312	+	Silent	SNP	G	G	C	rs34553291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:171969312G>C	ENST00000336824.4	+	6	870	c.771G>C	c.(769-771)tcG>tcC	p.S257S	FNDC3B_ENST00000415807.2_Silent_p.S257S|FNDC3B_ENST00000416957.1_Silent_p.S257S	NM_001135095.1	NP_001128567.1	Q53EP0	FND3B_HUMAN	fibronectin type III domain containing 3B	257					cell migration (GO:0016477)|negative regulation of osteoblast differentiation (GO:0045668)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of fibroblast proliferation (GO:0048146)|substrate adhesion-dependent cell spreading (GO:0034446)|Type II pneumocyte differentiation (GO:0060510)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(26)|ovary(3)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	69	all_cancers(22;1.01e-18)|Ovarian(172;0.00167)|Breast(254;0.165)		LUSC - Lung squamous cell carcinoma(14;3.57e-14)|Lung(28;9.39e-14)	GBM - Glioblastoma multiforme(1;0.0494)		GCCCAAAGTCGAATGATTCAG	0.468													G|||	28	0.00559105	0.0212	0.0	5008	,	,		17937	0.0		0.0	False		,,,				2504	0.0				p.S257S		Atlas-SNP	.											FNDC3B,rectum,carcinoma,+1,1	FNDC3B	118	1	0			c.G771C						PASS	.	G	,	92,4314	75.7+/-113.9	0,92,2111	69.0	71.0	70.0		771,771	-7.6	0.1	3	dbSNP_126	70	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	FNDC3B	NM_001135095.1,NM_022763.3	,	0,92,6411	CC,CG,GG		0.0,2.0881,0.7074	,	257/1205,257/1205	171969312	92,12914	2203	4300	6503	SO:0001819	synonymous_variant	64778	exon6			AAAGTCGAATGAT	AF543840	CCDS3217.1	3q26.31	2013-11-06			ENSG00000075420	ENSG00000075420		"""Fibronectin type III domain containing"""	24670	protein-coding gene	gene with protein product		611909				15527760	Standard	NM_022763		Approved	FAD104, DKFZp762K137, FLJ23399, PRO4979, YVTM2421	uc003fhy.3	Q53EP0	OTTHUMG00000156761	ENST00000336824.4:c.771G>C	3.37:g.171969312G>C		29.0	0.0	0		39.0	17.0	0.435897	NM_001135095	B2RB36|B3KXR8|D3DNQ7|Q5U5T8|Q6PIJ3|Q6UXG1|Q6UXZ5|Q8IXB2|Q8NBU7|Q96D78|Q9H5I7|Q9NSQ8	Silent	SNP	ENST00000336824.4	37	CCDS3217.1																																																																																			G|0.993;C|0.007	0.007	strong		0.468	FNDC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345618.2	NM_022763	
INSL4	3641	hgsc.bcm.edu	37	9	5233664	5233664	+	Silent	SNP	A	A	G	rs7030463	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:5233664A>G	ENST00000239316.4	+	2	312	c.207A>G	c.(205-207)tcA>tcG	p.S69S		NM_002195.1	NP_002186.1	Q14641	INSL4_HUMAN	insulin-like 4 (placenta)	69					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	insulin-like growth factor receptor binding (GO:0005159)|receptor binding (GO:0005102)			endometrium(2)|lung(2)|skin(1)|urinary_tract(1)	6	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.0201)|Lung(218;0.14)		AAATGGTGTCAACCTCCAACA	0.398													A|||	163	0.0325479	0.121	0.0043	5008	,	,		21594	0.0		0.0	False		,,,				2504	0.0				p.S69S		Atlas-SNP	.											INSL4,right_upper_lobe,carcinoma,+2,1	INSL4	20	1	0			c.A207G						PASS	.	A		394,4012	197.4+/-221.5	15,364,1824	62.0	58.0	59.0		207	1.8	0.3	9	dbSNP_116	59	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	INSL4	NM_002195.1		15,366,6122	GG,GA,AA		0.0233,8.9424,3.0447		69/140	5233664	396,12610	2203	4300	6503	SO:0001819	synonymous_variant	3641	exon2			GGTGTCAACCTCC		CCDS6459.1	9p24	2008-02-05			ENSG00000120211	ENSG00000120211			6087	protein-coding gene	gene with protein product		600910				8666396, 9730618	Standard	NM_002195		Approved	EPIL	uc003ziy.3	Q14641	OTTHUMG00000019494	ENST00000239316.4:c.207A>G	9.37:g.5233664A>G		55.0	0.0	0		61.0	33.0	0.540984	NM_002195	A8K678|Q5W127	Silent	SNP	ENST00000239316.4	37	CCDS6459.1																																																																																			A|0.967;G|0.033	0.033	strong		0.398	INSL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051616.2	NM_002195	
NXN	64359	hgsc.bcm.edu	37	17	706933	706933	+	Missense_Mutation	SNP	C	C	T	rs61731770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:706933C>T	ENST00000336868.3	-	7	1205	c.1114G>A	c.(1114-1116)Gta>Ata	p.V372I	NXN_ENST00000575801.1_Missense_Mutation_p.V264I|NXN_ENST00000538650.1_Missense_Mutation_p.V63I|NXN_ENST00000537628.2_Missense_Mutation_p.V123I	NM_022463.4	NP_071908.2	Q6DKJ4	NXN_HUMAN	nucleoredoxin	372				V -> I (in Ref. 4; AAH73845). {ECO:0000305}.	cardiovascular system development (GO:0072358)|cell differentiation (GO:0030154)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of Wnt signaling pathway (GO:0030178)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein-disulfide reductase activity (GO:0047134)|thioredoxin-disulfide reductase activity (GO:0004791)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|ovary(2)|pancreas(1)|prostate(1)	13				UCEC - Uterine corpus endometrioid carcinoma (25;0.0237)		TCCCCGGCTACGAAGAACAGA	0.602													c|||	110	0.0219649	0.0787	0.0043	5008	,	,		17906	0.0		0.003	False		,,,				2504	0.0				p.V372I		Atlas-SNP	.											.	NXN	32	.	0			c.G1114A						PASS	.	C	ILE/VAL,ILE/VAL	328,4078	173.4+/-203.2	20,288,1895	102.0	100.0	101.0		790,1114	5.3	1.0	17	dbSNP_129	101	11,8589	8.4+/-32.0	0,11,4289	yes	missense,missense	NXN	NM_001205319.1,NM_022463.4	29,29	20,299,6184	TT,TC,CC		0.1279,7.4444,2.6065	benign,benign	264/328,372/436	706933	339,12667	2203	4300	6503	SO:0001583	missense	64359	exon7			CGGCTACGAAGAA		CCDS10998.1, CCDS56013.1	17p13	2007-08-10			ENSG00000167693	ENSG00000167693			18008	protein-coding gene	gene with protein product		612895					Standard	NM_022463		Approved	FLJ12614, NRX	uc002fsa.3	Q6DKJ4	OTTHUMG00000090307	ENST00000336868.3:c.1114G>A	17.37:g.706933C>T	ENSP00000337443:p.Val372Ile	93.0	0.0	0		88.0	52.0	0.590909	NM_022463	B4DXQ0|D3DTH2|Q3SWW6|Q6P3U6|Q7L4C6|Q9H9Q1	Missense_Mutation	SNP	ENST00000336868.3	37	CCDS10998.1	42	0.019230769230769232	39	0.07926829268292683	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	C	13.45	2.239485	0.39598	0.074444	0.001279	ENSG00000167693	ENST00000336868;ENST00000538650;ENST00000537628	T;T	0.28454	1.61;2.57	5.26	5.26	0.73747	Thioredoxin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.02727	0.0082	L	0.28274	0.84	0.58432	D	0.999996	D;D;D	0.76494	0.999;0.981;0.992	D;P;P	0.74674	0.984;0.899;0.834	T	0.00883	-1.1528	10	0.15952	T	0.53	-19.0247	17.8205	0.88649	0.0:1.0:0.0:0.0	.	264;63;372	B4DXQ0;B4DNN6;Q6DKJ4	.;.;NXN_HUMAN	I	372;63;264	ENSP00000337443:V372I;ENSP00000445087:V63I	ENSP00000337443:V372I	V	-	1	0	NXN	653683	1.000000	0.71417	0.983000	0.44433	0.246000	0.25737	4.470000	0.60175	2.635000	0.89317	0.655000	0.94253	GTA	C|0.977;T|0.023	0.023	strong		0.602	NXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206669.1		
PTX4	390667	hgsc.bcm.edu	37	16	1536357	1536357	+	Silent	SNP	G	G	A	rs112226694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1536357G>A	ENST00000447419.2	-	3	1045	c.1020C>T	c.(1018-1020)ttC>ttT	p.F340F	PTX4_ENST00000293922.1_Silent_p.F335F|PTX4_ENST00000440447.2_Missense_Mutation_p.S192L			Q96A99	PTX4_HUMAN	pentraxin 4, long	340	Pentaxin.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						CCCCGATCACGAAGTGGATGG	0.662													G|||	88	0.0175719	0.0651	0.0029	5008	,	,		16575	0.0		0.0	False		,,,				2504	0.0				p.F335F		Atlas-SNP	.											.	PTX4	46	.	0			c.C1005T						PASS	.	G		251,4147	138.8+/-174.5	4,243,1952	42.0	50.0	47.0		1005	-11.2	0.2	16	dbSNP_132	47	0,8600		0,0,4300	no	coding-synonymous	PTX4	NM_001013658.1		4,243,6252	AA,AG,GG		0.0,5.7071,1.9311		335/474	1536357	251,12747	2199	4300	6499	SO:0001819	synonymous_variant	390667	exon3			GATCACGAAGTGG		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"""chromosome 16 open reading frame 38"""	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.1020C>T	16.37:g.1536357G>A		99.0	0.0	0		76.0	37.0	0.486842	NM_001013658		Silent	SNP	ENST00000447419.2	37																																																																																				G|0.979;A|0.021	0.021	strong		0.662	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
CALHM2	51063	hgsc.bcm.edu	37	10	105207176	105207176	+	Silent	SNP	G	G	A	rs2232663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:105207176G>A	ENST00000260743.5	-	4	1228	c.705C>T	c.(703-705)gcC>gcT	p.A235A	CALHM2_ENST00000494180.1_5'Flank|CALHM2_ENST00000369788.3_Silent_p.A235A|RP11-225H22.7_ENST00000608063.1_RNA	NM_015916.4	NP_057000.2	Q9HA72	CAHM2_HUMAN	calcium homeostasis modulator 2	235					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)|skin(1)	11						AGTGCACCTCGGCCGTGCGCT	0.597													G|||	370	0.0738818	0.2663	0.0216	5008	,	,		20251	0.0		0.003	False		,,,				2504	0.0				p.A235A		Atlas-SNP	.											.	CALHM2	30	.	0			c.C705T						PASS	.	G		896,3510	345.7+/-308.6	84,728,1391	67.0	61.0	63.0		705	-8.1	0.7	10	dbSNP_98	63	27,8573	19.2+/-60.6	0,27,4273	no	coding-synonymous	CALHM2	NM_015916.4		84,755,5664	AA,AG,GG		0.314,20.3359,7.0967		235/324	105207176	923,12083	2203	4300	6503	SO:0001819	synonymous_variant	51063	exon4			CACCTCGGCCGTG	BC000039	CCDS7549.1	10q24.33	2008-07-02	2008-07-02	2008-07-02	ENSG00000138172	ENSG00000138172			23493	protein-coding gene	gene with protein product		612235	"""family with sequence similarity 26, member B"""	FAM26B		18585350	Standard	NM_015916		Approved		uc001kxa.3	Q9HA72	OTTHUMG00000018990	ENST00000260743.5:c.705C>T	10.37:g.105207176G>A		77.0	0.0	0		85.0	85.0	1	NM_015916	D3DR94|O95893|Q6ZUV9	Silent	SNP	ENST00000260743.5	37	CCDS7549.1																																																																																			G|0.925;A|0.075	0.075	strong		0.597	CALHM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050159.1	NM_015916	
NUMA1	4926	hgsc.bcm.edu	37	11	71725612	71725612	+	Silent	SNP	A	A	G	rs142372284	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71725612A>G	ENST00000393695.3	-	15	3268	c.2937T>C	c.(2935-2937)aaT>aaC	p.N979N	NUMA1_ENST00000351960.6_Intron|RP11-849H4.4_ENST00000502284.1_RNA|NUMA1_ENST00000358965.6_Silent_p.N979N	NM_006185.2	NP_006176.2			nuclear mitotic apparatus protein 1											central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(12)|lung(20)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	65						GTTCCAGCTCATTGCCCATCT	0.672			T	RARA	APL								A|||	14	0.00279553	0.0106	0.0	5008	,	,		17846	0.0		0.0	False		,,,				2504	0.0				p.N979N		Atlas-SNP	.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1	142	.	0			c.T2937C						PASS	.	A		71,4329	59.3+/-96.0	1,69,2130	66.0	73.0	71.0		2937	-6.0	0.9	11	dbSNP_134	71	0,8586		0,0,4293	no	coding-synonymous	NUMA1	NM_006185.2		1,69,6423	GG,GA,AA		0.0,1.6136,0.5467		979/2116	71725612	71,12915	2200	4293	6493	SO:0001819	synonymous_variant	4926	exon15			CAGCTCATTGCCC	Z11584	CCDS31633.1, CCDS66156.1	11q13	2008-02-05				ENSG00000137497			8059	protein-coding gene	gene with protein product		164009				8406455	Standard	NM_006185		Approved		uc001orl.1	Q14980		ENST00000393695.3:c.2937T>C	11.37:g.71725612A>G		54.0	0.0	0		87.0	39.0	0.448276	NM_006185		Silent	SNP	ENST00000393695.3	37	CCDS31633.1																																																																																			A|0.995;G|0.005	0.005	strong		0.672	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1		
SERPINB12	89777	hgsc.bcm.edu	37	18	61234091	61234091	+	Silent	SNP	C	C	T	rs35623491	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61234091C>T	ENST00000269491.1	+	7	1065	c.1065C>T	c.(1063-1065)aaC>aaT	p.N355N	SERPINB12_ENST00000382768.1_Silent_p.N375N	NM_080474.1	NP_536722.1	Q96P63	SPB12_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 12	355					hematopoietic progenitor cell differentiation (GO:0002244)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of protein catabolic process (GO:0042177)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	enzyme binding (GO:0019899)|serine-type endopeptidase inhibitor activity (GO:0004867)			kidney(1)|large_intestine(5)|lung(19)|skin(1)	26						TGGATGAAAACGGTACCCAGG	0.453													C|||	184	0.0367412	0.1316	0.0101	5008	,	,		20333	0.0		0.003	False		,,,				2504	0.0				p.N355N		Atlas-SNP	.											.	SERPINB12	55	.	0			c.C1065T						PASS	.	C		482,3924	226.2+/-241.8	30,422,1751	78.0	82.0	80.0		1065	-4.4	0.1	18	dbSNP_126	80	1,8599		0,1,4299	no	coding-synonymous	SERPINB12	NM_080474.1		30,423,6050	TT,TC,CC		0.0116,10.9396,3.7137		355/406	61234091	483,12523	2203	4300	6503	SO:0001819	synonymous_variant	89777	exon7			TGAAAACGGTACC	AF411191	CCDS11984.1	18q21.33	2014-02-18	2005-08-18		ENSG00000166634	ENSG00000166634		"""Serine (or cysteine) peptidase inhibitors"""	14220	protein-coding gene	gene with protein product		615662	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 12"""			24172014	Standard	NM_080474		Approved	YUKOPIN	uc010xen.2	Q96P63	OTTHUMG00000132789	ENST00000269491.1:c.1065C>T	18.37:g.61234091C>T		88.0	0.0	0		74.0	35.0	0.472973	NM_080474	Q3SYB4	Silent	SNP	ENST00000269491.1	37	CCDS11984.1																																																																																			C|0.962;T|0.038	0.038	strong		0.453	SERPINB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256197.1	NM_080474	
DNAH2	146754	hgsc.bcm.edu	37	17	7722048	7722048	+	Missense_Mutation	SNP	G	G	A	rs61743907	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7722048G>A	ENST00000572933.1	+	70	12084	c.10624G>A	c.(10624-10626)Gcg>Acg	p.A3542T	DNAH2_ENST00000389173.2_Missense_Mutation_p.A3542T			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	3542	AAA 5. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				CATCAACATCGCGGCTGGTAA	0.642													G|||	52	0.0103834	0.0363	0.0058	5008	,	,		20147	0.0		0.0	False		,,,				2504	0.0				p.A3542T		Atlas-SNP	.											.	DNAH2	498	.	0			c.G10624A						PASS	.	G	THR/ALA	146,4260	102.5+/-141.1	2,142,2059	119.0	107.0	111.0		10624	3.4	0.1	17	dbSNP_129	111	0,8600		0,0,4300	yes	missense	DNAH2	NM_020877.2	58	2,142,6359	AA,AG,GG		0.0,3.3137,1.1226	probably-damaging	3542/4428	7722048	146,12860	2203	4300	6503	SO:0001583	missense	146754	exon69			AACATCGCGGCTG	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"""Axonemal dyneins"""	2948	protein-coding gene	gene with protein product		603333	"""dynein, axonemal, heavy polypeptide 2"", ""dynein heavy chain domain 3"""	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.10624G>A	17.37:g.7722048G>A	ENSP00000458355:p.Ala3542Thr	92.0	0.0	0		101.0	50.0	0.49505	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Missense_Mutation	SNP	ENST00000572933.1	37	CCDS32551.1	16	0.007326007326007326	14	0.028455284552845527	2	0.0055248618784530384	0	0.0	0	0.0	G	21.0	4.082529	0.76528	0.033137	0.0	ENSG00000183914	ENST00000360606;ENST00000389173	T	0.22134	1.97	4.34	3.38	0.38709	.	0.000000	0.85682	D	0.000000	T	0.09468	0.0233	M	0.65498	2.005	0.80722	D	1	P;P	0.42735	0.749;0.788	B;P	0.44422	0.321;0.449	T	0.01702	-1.1292	10	0.22706	T	0.39	.	11.1468	0.48434	0.0914:0.0:0.9086:0.0	rs61743907	3503;3542	Q9P225-2;Q9P225	.;DYH2_HUMAN	T	3503;3542	ENSP00000373825:A3542T	ENSP00000353818:A3503T	A	+	1	0	DNAH2	7662773	1.000000	0.71417	0.117000	0.21633	0.933000	0.57130	5.115000	0.64655	1.045000	0.40225	0.563000	0.77884	GCG	G|0.989;A|0.011	0.011	strong		0.642	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
ZACN	353174	hgsc.bcm.edu	37	17	74076504	74076504	+	Splice_Site	SNP	G	G	A	rs8066946	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74076504G>A	ENST00000334586.5	+	5	626	c.543G>A	c.(541-543)acG>acA	p.T181T	ZACN_ENST00000392503.2_Intron|EXOC7_ENST00000591724.1_5'Flank	NM_180990.3	NP_851321.2	Q401N2	ZACN_HUMAN	zinc activated ligand-gated ion channel	181					ion transmembrane transport (GO:0034220)|response to zinc ion (GO:0010043)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)|ligand-gated ion channel activity (GO:0015276)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|large_intestine(1)|lung(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	11						TCAGCAACACGGGTGCTGACA	0.657													G|||	424	0.0846645	0.3033	0.0331	5008	,	,		16820	0.0		0.0	False		,,,				2504	0.0				p.T181T		Atlas-SNP	.											.	ZACN	29	.	0			c.G543A						PASS	.	G		1144,3262	398.3+/-330.8	151,842,1210	61.0	56.0	58.0		543	-5.2	0.9	17	dbSNP_116	58	20,8580	11.9+/-42.8	0,20,4280	yes	coding-synonymous-near-splice	ZACN	NM_180990.3		151,862,5490	AA,AG,GG		0.2326,25.9646,8.9497		181/413	74076504	1164,11842	2203	4300	6503	SO:0001630	splice_region_variant	353174	exon5			CAACACGGGTGCT	AK122638	CCDS11740.2	17q25.3	2012-01-18	2008-04-17	2008-04-17	ENSG00000186919	ENSG00000186919		"""Ligand-gated ion channels / Zinc activated channels"""	29504	protein-coding gene	gene with protein product		610935	"""ligand-gated ion channel, zinc activated 1"""	LGICZ1		12381728, 16083862	Standard	NM_180990		Approved	LGICZ, L2, ZAC, ZAC1	uc002jqn.2	Q401N2	OTTHUMG00000157186	ENST00000334586.5:c.544+1G>A	17.37:g.74076504G>A		74.0	0.0	0		79.0	45.0	0.56962	NM_180990	Q2TB29|Q6ZWK3|Q86YW4	Silent	SNP	ENST00000334586.5	37	CCDS11740.2																																																																																			G|0.913;A|0.087	0.087	strong		0.657	ZACN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347827.2	NM_180990	Silent
CENPL	91687	hgsc.bcm.edu	37	1	173772506	173772506	+	Silent	SNP	T	T	G	rs16846420	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:173772506T>G	ENST00000345664.6	-	4	771	c.558A>C	c.(556-558)gcA>gcC	p.A186A	CENPL_ENST00000367710.3_Silent_p.A186A|CENPL_ENST00000356198.2_Silent_p.A232A	NM_001171182.1	NP_001164653.1	Q8N0S6	CENPL_HUMAN	centromere protein L	186					mitotic cell cycle (GO:0000278)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(3)	11						CTGCTCCATTTGCAAGGAATA	0.408													T|||	564	0.11262	0.4032	0.0346	5008	,	,		19168	0.0		0.007	False		,,,				2504	0.0				p.A232A		Atlas-SNP	.											.	CENPL	26	.	0			c.A696C						PASS	.	T	,,	1339,3067	438.4+/-345.3	198,943,1062	104.0	114.0	111.0		696,558,558	5.0	1.0	1	dbSNP_123	111	31,8569	18.5+/-59.3	0,31,4269	no	coding-synonymous,coding-synonymous,coding-synonymous	CENPL	NM_001127181.2,NM_001171182.1,NM_033319.3	,,	198,974,5331	GG,GT,TT		0.3605,30.3904,10.5336	,,	232/391,186/345,186/345	173772506	1370,11636	2203	4300	6503	SO:0001819	synonymous_variant	91687	exon6			TCCATTTGCAAGG	BC033154, BC019022, AK055606	CCDS30938.1, CCDS44277.1	1q25.1	2013-11-05	2006-06-15	2006-06-15	ENSG00000120334	ENSG00000120334			17879	protein-coding gene	gene with protein product		611503	"""chromosome 1 open reading frame 155"""	C1orf155		16622420, 16622419	Standard	NM_033319		Approved	dJ383J4.3, FLJ31044	uc001gje.4	Q8N0S6	OTTHUMG00000034802	ENST00000345664.6:c.558A>C	1.37:g.173772506T>G		176.0	0.0	0		171.0	85.0	0.497076	NM_001127181	Q5TEL5|Q96ND4	Silent	SNP	ENST00000345664.6	37	CCDS30938.1																																																																																			T|0.876;G|0.124	0.124	strong		0.408	CENPL-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084213.1	NM_033319	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110413806	110413806	+	Silent	SNP	G	G	A	rs200316129	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:110413806G>A	ENST00000378402.5	+	14	1466	c.1362G>A	c.(1360-1362)caG>caA	p.Q454Q		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	454					immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)	p.Q456Q(1)		NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			TTCATCTGCAGAAAGGAAAAG	0.313										HNSCC(38;0.096)			G|||	2	0.000399361	0.0015	0.0	5008	,	,		13925	0.0		0.0	False		,,,				2504	0.0				p.Q454Q		Atlas-SNP	.											PKHD1L1,NS,carcinoma,0,1	PKHD1L1	522	1	1	Substitution - coding silent(1)	breast(1)	c.G1362A						PASS	.	G		2,3624		0,2,1811	76.0	69.0	71.0		1362	3.4	1.0	8		71	0,8154		0,0,4077	no	coding-synonymous	PKHD1L1	NM_177531.4		0,2,5888	AA,AG,GG		0.0,0.0552,0.017		454/4244	110413806	2,11778	1813	4077	5890	SO:0001819	synonymous_variant	93035	exon14			TCTGCAGAAAGGA	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.1362G>A	8.37:g.110413806G>A		136.0	0.0	0		107.0	56.0	0.523364	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	37	CCDS47911.1																																																																																			G|1.000;A|0.000	0.000	strong		0.313	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
PDE6A	5145	hgsc.bcm.edu	37	5	149323781	149323781	+	Silent	SNP	G	G	A	rs149256612	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149323781G>A	ENST00000255266.5	-	1	575	c.456C>T	c.(454-456)aaC>aaT	p.N152N		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	152	GAF 1.				cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	TGTTGGGGACGTTAGCAATCT	0.562																																					p.N152N		Atlas-SNP	.											.	PDE6A	98	.	0			c.C456T						PASS	.	G		3,4403	6.2+/-15.9	0,3,2200	160.0	137.0	144.0		456	2.4	1.0	5	dbSNP_134	144	0,8600		0,0,4300	no	coding-synonymous	PDE6A	NM_000440.2		0,3,6500	AA,AG,GG		0.0,0.0681,0.0231		152/861	149323781	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	5145	exon1			GGGGACGTTAGCA		CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"""Phosphodiesterases"""	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.456C>T	5.37:g.149323781G>A		67.0	0.0	0		66.0	24.0	0.363636	NM_000440	Q0P638	Silent	SNP	ENST00000255266.5	37	CCDS4299.1																																																																																			G|1.000;A|0.000	0.000	strong		0.562	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2		
MEGF8	1954	hgsc.bcm.edu	37	19	42874900	42874900	+	Silent	SNP	C	C	T	rs28483598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42874900C>T	ENST00000251268.6	+	40	7053	c.7053C>T	c.(7051-7053)tgC>tgT	p.C2351C	MEGF8_ENST00000334370.4_Silent_p.C2284C|MEGF8_ENST00000378073.4_5'UTR	NM_001271938.1	NP_001258867.1	Q7Z7M0	MEGF8_HUMAN	multiple EGF-like-domains 8	2351					BMP signaling pathway (GO:0030509)|cell migration involved in gastrulation (GO:0042074)|craniofacial suture morphogenesis (GO:0097094)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of heart left/right asymmetry (GO:0061371)|embryonic heart tube left/right pattern formation (GO:0060971)|embryonic heart tube morphogenesis (GO:0003143)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|epiboly involved in gastrulation with mouth forming second (GO:0055113)|fasciculation of sensory neuron axon (GO:0097155)|left/right pattern formation (GO:0060972)|limb morphogenesis (GO:0035108)|positive regulation of axon extension involved in axon guidance (GO:0048842)|regulation of gene expression (GO:0010468)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|receptor activity (GO:0004872)			breast(2)|cervix(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	50		Prostate(69;0.00682)				AGGCCGTGTGCGTGAACTGCC	0.562													C|||	92	0.0183706	0.0635	0.0072	5008	,	,		10552	0.001		0.002	False		,,,				2504	0.0				p.C2351C		Atlas-SNP	.											.	MEGF8	358	.	0			c.C7053T						PASS	.	C		213,4191		7,199,1996	65.0	56.0	59.0		6852	-2.4	1.0	19	dbSNP_125	59	10,8586		0,10,4288	no	coding-synonymous	MEGF8	NM_001410.2		7,209,6284	TT,TC,CC		0.1163,4.8365,1.7154		2284/2779	42874900	223,12777	2202	4298	6500	SO:0001819	synonymous_variant	1954	exon40			CGTGTGCGTGAAC	AB011541	CCDS12604.2, CCDS62693.1	19q13.2	2011-11-24	2006-03-31	2006-03-31	ENSG00000105429	ENSG00000105429			3233	protein-coding gene	gene with protein product	"""HBV pre s2 binding protein 1"""	604267	"""EGF-like-domain, multiple 4"", ""chromosome 19 open reading frame 49"""	EGFL4, C19orf49		9693030	Standard	NM_001410		Approved	SBP1, FLJ22365	uc002otm.5	Q7Z7M0	OTTHUMG00000150342	ENST00000251268.6:c.7053C>T	19.37:g.42874900C>T		108.0	0.0	0		144.0	82.0	0.569444	NM_001271938	A8KAY0|O75097	Silent	SNP	ENST00000251268.6	37																																																																																				C|0.981;T|0.019	0.019	strong		0.562	MEGF8-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000463854.1	NM_001410	
ZNF697	90874	hgsc.bcm.edu	37	1	120165412	120165412	+	Silent	SNP	G	G	A	rs61734323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:120165412G>A	ENST00000421812.2	-	3	1673	c.1554C>T	c.(1552-1554)aaC>aaT	p.N518N		NM_001080470.1	NP_001073939.1	Q5TEC3	ZN697_HUMAN	zinc finger protein 697	518					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			ovary(2)	2	all_neural(166;0.219)	all_lung(203;3.66e-05)|Lung NSC(69;0.000202)|all_epithelial(167;0.0266)		Lung(183;0.011)|LUSC - Lung squamous cell carcinoma(189;0.0577)		TGTGCGGCTTGTTGCCCGTGT	0.642													G|||	60	0.0119808	0.0431	0.0029	5008	,	,		16736	0.0		0.001	False		,,,				2504	0.0				p.N518N		Atlas-SNP	.											.	ZNF697	26	.	0			c.C1554T						PASS	.	G		129,4179		2,125,2027	12.0	17.0	15.0		1554	4.1	1.0	1	dbSNP_129	15	1,8545		0,1,4272	no	coding-synonymous	ZNF697	NM_001080470.1		2,126,6299	AA,AG,GG		0.0117,2.9944,1.0114		518/546	120165412	130,12724	2154	4273	6427	SO:0001819	synonymous_variant	90874	exon3			CGGCTTGTTGCCC	AK027019, BC033126	CCDS44202.1	1p12	2013-01-08			ENSG00000143067	ENSG00000143067		"""Zinc fingers, C2H2-type"""	32034	protein-coding gene	gene with protein product							Standard	NM_001080470		Approved	MGC45731	uc001ehy.1	Q5TEC3	OTTHUMG00000012962	ENST00000421812.2:c.1554C>T	1.37:g.120165412G>A		154.0	0.0	0		153.0	72.0	0.470588	NM_001080470	Q96IT2	Silent	SNP	ENST00000421812.2	37	CCDS44202.1																																																																																			G|0.994;A|0.006	0.006	strong		0.642	ZNF697-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036349.3	XM_371286	
FBXO16	157574	hgsc.bcm.edu	37	8	28321153	28321153	+	Silent	SNP	A	A	G	rs7822086	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:28321153A>G	ENST00000380254.2	-	4	466	c.318T>C	c.(316-318)ccT>ccC	p.P106P	FBXO16_ENST00000518734.1_Silent_p.P94P|FBXO16_ENST00000517436.1_5'UTR|FBXO16_ENST00000346498.2_Silent_p.P94P	NM_001258211.1|NM_172366.3	NP_001245140.1|NP_758954.1	Q8IX29	FBX16_HUMAN	F-box protein 16	106	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.									large_intestine(2)|ovary(1)	3		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.121)|Kidney(114;0.144)|Colorectal(74;0.249)		AAAGGCTCCGAGGGTCCAGGA	0.443													G|||	308	0.0615016	0.2194	0.0101	5008	,	,		20959	0.005		0.001	False		,,,				2504	0.0051				p.P106P		Atlas-SNP	.											.	FBXO16	29	.	0			c.T318C						PASS	.	G		735,3671	720.3+/-409.0	73,589,1541	55.0	53.0	54.0		318	2.7	1.0	8	dbSNP_116	54	8,8592	818.7+/-406.8	0,8,4292	no	coding-synonymous	FBXO16	NM_172366.2		73,597,5833	GG,GA,AA		0.093,16.6818,5.7127		106/293	28321153	743,12263	2203	4300	6503	SO:0001819	synonymous_variant	157574	exon4			GCTCCGAGGGTCC	AF453435	CCDS6068.1, CCDS59099.1	8p21.1	2008-02-05	2004-06-15		ENSG00000214050	ENSG00000214050		"""F-boxes /  ""other"""""	13618	protein-coding gene	gene with protein product		608519	"""F-box only protein 16"""			12243353	Standard	NM_172366		Approved	FBX16	uc003xgu.4	Q8IX29	OTTHUMG00000102147	ENST00000380254.2:c.318T>C	8.37:g.28321153A>G		172.0	0.0	0		133.0	58.0	0.43609	NM_172366	Q3T1B2|Q3T1B3|Q3T1B4	Silent	SNP	ENST00000380254.2	37	CCDS6068.1																																																																																			A|0.932;G|0.068	0.068	strong		0.443	FBXO16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000219988.2	NM_172366	
ZNF684	127396	hgsc.bcm.edu	37	1	41006341	41006341	+	Silent	SNP	T	T	C	rs74575870	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:41006341T>C	ENST00000372699.3	+	3	350	c.99T>C	c.(97-99)taT>taC	p.Y33Y	ZNF684_ENST00000493756.1_Intron|ZNF684_ENST00000372697.3_Silent_p.Y33Y|ZNF684_ENST00000372696.3_Silent_p.Y33Y	NM_152373.3	NP_689586.3	Q5T5D7	ZN684_HUMAN	zinc finger protein 684	33	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(2)|endometrium(2)|kidney(2)|lung(3)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	13	Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;5.42e-18)			GAACCCTGTATTGGGATGTGA	0.433													T|||	176	0.0351438	0.1278	0.0086	5008	,	,		18203	0.0		0.001	False		,,,				2504	0.0				p.Y33Y		Atlas-SNP	.											.	ZNF684	37	.	0			c.T99C						PASS	.	T		384,4022	194.3+/-219.2	13,358,1832	198.0	172.0	181.0		99	2.7	1.0	1	dbSNP_132	181	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	ZNF684	NM_152373.3		13,365,6125	CC,CT,TT		0.0814,8.7154,3.0063		33/379	41006341	391,12615	2203	4300	6503	SO:0001819	synonymous_variant	127396	exon3			CCTGTATTGGGAT		CCDS454.1	1p34.2	2013-01-08			ENSG00000117010	ENSG00000117010		"""Zinc fingers, C2H2-type"", ""-"""	28418	protein-coding gene	gene with protein product	"""hypothetical protein MGC27466"""					12477932	Standard	NM_152373		Approved	MGC27466	uc001cft.2	Q5T5D7	OTTHUMG00000007359	ENST00000372699.3:c.99T>C	1.37:g.41006341T>C		287.0	0.0	0		311.0	133.0	0.427653	NM_152373	Q2NKY4	Silent	SNP	ENST00000372699.3	37	CCDS454.1																																																																																			T|0.973;C|0.027	0.027	strong		0.433	ZNF684-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019260.3	NM_152373	
CHSY3	337876	hgsc.bcm.edu	37	5	129520932	129520932	+	Silent	SNP	T	T	G	rs73788438	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:129520932T>G	ENST00000305031.4	+	3	2455	c.2097T>G	c.(2095-2097)ctT>ctG	p.L699L		NM_175856.4	NP_787052.3	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3	699					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)		CCAGAGGTCTTGGTCTTGAAA	0.433													T|||	191	0.038139	0.1271	0.0245	5008	,	,		20200	0.0		0.001	False		,,,				2504	0.0051				p.L699L		Atlas-SNP	.											CHSY3,colon,carcinoma,+2,2	CHSY3	92	2	0			c.T2097G						PASS	.	T		466,3940	217.1+/-235.6	21,424,1758	88.0	83.0	85.0		2097	-1.4	1.0	5	dbSNP_130	85	13,8587	10.5+/-38.8	0,13,4287	no	coding-synonymous	CHSY3	NM_175856.4		21,437,6045	GG,GT,TT		0.1512,10.5765,3.6829		699/883	129520932	479,12527	2203	4300	6503	SO:0001819	synonymous_variant	337876	exon3			AGGTCTTGGTCTT	AB086062	CCDS34223.1	5q13	2013-02-19			ENSG00000198108	ENSG00000198108	2.4.1.175, 2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	24293	protein-coding gene	gene with protein product		609963				12907687	Standard	XM_005271982		Approved	CSS3, CHSY-2	uc003kvd.3	Q70JA7	OTTHUMG00000163043	ENST00000305031.4:c.2097T>G	5.37:g.129520932T>G		122.0	0.0	0		119.0	55.0	0.462185	NM_175856	B2RP97|Q76L22|Q86Y52	Silent	SNP	ENST00000305031.4	37	CCDS34223.1																																																																																			T|0.966;G|0.034	0.034	strong		0.433	CHSY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371453.1	NM_175856	
ARFGEF2	10564	hgsc.bcm.edu	37	20	47588949	47588949	+	Silent	SNP	G	G	A	rs116550473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:47588949G>A	ENST00000371917.4	+	11	1512	c.1512G>A	c.(1510-1512)acG>acA	p.T504T		NM_006420.2	NP_006411.2	Q9Y6D5	BIG2_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 2 (brefeldin A-inhibited)	504					endomembrane system organization (GO:0010256)|endosome organization (GO:0007032)|exocytosis (GO:0006887)|Golgi to plasma membrane transport (GO:0006893)|intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of tumor necrosis factor production (GO:0032760)|protein transport (GO:0015031)|receptor recycling (GO:0001881)|regulation of ARF protein signal transduction (GO:0032012)|vesicle-mediated transport (GO:0016192)	asymmetric synapse (GO:0032279)|axonemal microtubule (GO:0005879)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|recycling endosome (GO:0055037)|symmetric synapse (GO:0032280)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|GABA receptor binding (GO:0050811)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein kinase A regulatory subunit binding (GO:0034237)			breast(7)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	63			BRCA - Breast invasive adenocarcinoma(12;0.00148)|Colorectal(8;0.198)			AGACTCTGACGAGGATCTGTG	0.408													G|||	17	0.00339457	0.0121	0.0014	5008	,	,		20979	0.0		0.0	False		,,,				2504	0.0				p.T504T	Esophageal Squamous(176;1738 1974 26285 33069 35354)	Atlas-SNP	.											.	ARFGEF2	160	.	0			c.G1512A						PASS	.	G		56,4350	56.2+/-92.4	0,56,2147	84.0	81.0	82.0		1512	-6.9	0.9	20	dbSNP_132	82	0,8600		0,0,4300	no	coding-synonymous	ARFGEF2	NM_006420.2		0,56,6447	AA,AG,GG		0.0,1.271,0.4306		504/1786	47588949	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	10564	exon11			TCTGACGAGGATC	AF084521	CCDS13411.1	20q13.13	2010-08-20			ENSG00000124198	ENSG00000124198		"""A-kinase anchor proteins"""	15853	protein-coding gene	gene with protein product	"""Brefeldin A-inhibited guanine nucleotide-exchange protein 2"""	605371				10212200	Standard	NM_006420		Approved	BIG2	uc002xtx.4	Q9Y6D5	OTTHUMG00000032687	ENST00000371917.4:c.1512G>A	20.37:g.47588949G>A		64.0	0.0	0		67.0	32.0	0.477612	NM_006420	Q5TFT9|Q9NTS1	Silent	SNP	ENST00000371917.4	37	CCDS13411.1																																																																																			G|0.996;A|0.004	0.004	strong		0.408	ARFGEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079627.1	NM_006420	
PRKAG2	51422	hgsc.bcm.edu	37	7	151257665	151257665	+	Silent	SNP	A	A	G	rs28763998	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:151257665A>G	ENST00000287878.4	-	15	2127	c.1623T>C	c.(1621-1623)atT>atC	p.I541I	PRKAG2_ENST00000418337.2_Silent_p.I300I|PRKAG2_ENST00000392801.2_Silent_p.I497I|PRKAG2_ENST00000433631.2_Silent_p.I416I|PRKAG2_ENST00000492843.1_Silent_p.I417I	NM_016203.3	NP_057287.2	Q9UGJ0	AAKG2_HUMAN	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	541	CBS 4. {ECO:0000255|PROSITE- ProRule:PRU00703}.				ATP biosynthetic process (GO:0006754)|carnitine shuttle (GO:0006853)|cell cycle arrest (GO:0007050)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|glycogen metabolic process (GO:0005977)|insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|membrane organization (GO:0061024)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase activity (GO:0045860)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid metabolic process (GO:0019217)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose import (GO:0046324)|regulation of glycolytic process (GO:0006110)|small molecule metabolic process (GO:0044281)|sterol biosynthetic process (GO:0016126)	AMP-activated protein kinase complex (GO:0031588)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|ATP binding (GO:0005524)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|phosphorylase kinase regulator activity (GO:0008607)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|upper_aerodigestive_tract(1)	26	all_neural(206;0.187)	all_hematologic(28;0.0605)	OV - Ovarian serous cystadenocarcinoma(82;0.00252)	UCEC - Uterine corpus endometrioid carcinoma (81;0.185)	Acetylsalicylic acid(DB00945)	TAATACCCACAATACTATCTG	0.448													A|||	220	0.0439297	0.1596	0.013	5008	,	,		18994	0.0		0.0	False		,,,				2504	0.0				p.I541I		Atlas-SNP	.											.	PRKAG2	86	.	0			c.T1623C						PASS	.	A	,,	526,3880	242.1+/-252.3	28,470,1705	126.0	122.0	123.0		1491,1623,900	-5.7	0.2	7	dbSNP_125	123	2,8598	2.2+/-6.3	0,2,4298	yes	coding-synonymous,coding-synonymous,coding-synonymous	PRKAG2	NM_001040633.1,NM_016203.3,NM_024429.1	,,	28,472,6003	GG,GA,AA		0.0233,11.9383,4.0597	,,	497/526,541/570,300/329	151257665	528,12478	2203	4300	6503	SO:0001819	synonymous_variant	51422	exon15			ACCCACAATACTA	AF087875	CCDS5928.1, CCDS43683.1, CCDS47752.1	7q35-q36	2014-09-17			ENSG00000106617	ENSG00000106617			9386	protein-coding gene	gene with protein product	"""AMPK gamma2"""	602743				8557660, 8621499	Standard	NM_024429		Approved	AAKG, AAKG2, H91620p, WPWS, CMH6	uc003wkk.3	Q9UGJ0	OTTHUMG00000157324	ENST00000287878.4:c.1623T>C	7.37:g.151257665A>G		119.0	0.0	0		100.0	45.0	0.45	NM_016203	Q53Y07|Q6NUI0|Q75MP4|Q9NUZ9|Q9UDN8|Q9ULX8	Silent	SNP	ENST00000287878.4	37	CCDS5928.1																																																																																			A|0.955;G|0.045	0.045	strong		0.448	PRKAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348440.2	NM_016203	
NBPF7	343505	hgsc.bcm.edu	37	1	120384162	120384162	+	IGR	SNP	G	G	A	rs78204967	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:120384162G>A								REG4 (29879 upstream) : ADAM30 (51993 downstream)																							CTCCCTTCCCGTAACTTCTCC	0.493													g|||	119	0.023762	0.0802	0.0115	5008	,	,		21233	0.0		0.004	False		,,,				2504	0.001				p.R134W		Atlas-SNP	.											NBPF7,NS,carcinoma,0,1	NBPF7	46	1	0			c.C400T						scavenged	.	G	TRP/ARG	282,4124	147.6+/-182.1	8,266,1929	137.0	154.0	148.0		400	-0.1	0.0	1	dbSNP_131	148	49,8551	29.6+/-80.5	1,47,4252	no	missense	NBPF7	NM_001047980.1	101	9,313,6181	AA,AG,GG		0.5698,6.4004,2.545	probably-damaging	134/422	120384162	331,12675	2203	4300	6503	SO:0001628	intergenic_variant	343505	exon3			CTTCCCGTAACTT																													1.37:g.120384162G>A		245.0	2.0	0.00816326		204.0	99.0	0.485294	NM_001047980		Missense_Mutation	SNP		37																																																																																				G|0.983;A|0.017	0.017	strong	0	0.493								
OR2H1	26716	hgsc.bcm.edu	37	6	29430356	29430356	+	Missense_Mutation	SNP	G	G	C	rs371076908|rs148433584	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29430356G>C	ENST00000377136.1	+	4	1275	c.810G>C	c.(808-810)aaG>aaC	p.K270N	OR2H1_ENST00000396792.2_Missense_Mutation_p.K270N|OR2H1_ENST00000442615.1_Missense_Mutation_p.K270N|OR2H1_ENST00000377132.1_Missense_Mutation_p.K270N|OR2H1_ENST00000377133.1_Missense_Mutation_p.K270N|OR2H1_ENST00000473369.1_3'UTR			Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H, member 1	270						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(5)|lung(12)	17						GGAGGGGCAAGTTCTTTGGTC	0.522													G|||	22	0.00439297	0.0159	0.0014	5008	,	,		21364	0.0		0.0	False		,,,				2504	0.0				p.K270N		Atlas-SNP	.											.	OR2H1	38	.	0			c.G810C						PASS	.	G	ASN/LYS	42,2980		0,42,1469	113.0	115.0	114.0		810	2.2	0.9	6	dbSNP_134	114	0,5418		0,0,2709	no	missense	OR2H1	NM_030883.3	94	0,42,4178	CC,CG,GG		0.0,1.3898,0.4976	probably-damaging	270/317	29430356	42,8398	1511	2709	4220	SO:0001583	missense	26716	exon3			GGGCAAGTTCTTT	AF044491	CCDS4660.1	6p22.1	2014-02-19	2002-02-28		ENSG00000204688	ENSG00000204688		"""GPCR / Class A : Olfactory receptors"""	8252	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily H, member 8"""	OR2H6, OR2H8			Standard	NM_030883		Approved	OR6-2	uc003nmi.3	Q9GZK4	OTTHUMG00000031050	ENST00000377136.1:c.810G>C	6.37:g.29430356G>C	ENSP00000366340:p.Lys270Asn	464.0	0.0	0		453.0	227.0	0.501104	NM_030883	B0S7T4|O43629|O43661|O43662|Q5SUN6|Q9GZK9	Missense_Mutation	SNP	ENST00000377136.1	37	CCDS4660.1	7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	G	10.39	1.335640	0.24253	0.013898	0.0	ENSG00000204688	ENST00000377136;ENST00000377133;ENST00000442615;ENST00000377132;ENST00000396792	T;T;T;T;T	0.00207	8.55;8.55;8.55;8.55;8.55	3.09	2.22	0.28083	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42682	D	0.000675	T	0.00241	0.0007	M	0.87617	2.895	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.32824	-0.9892	10	0.87932	D	0	.	6.4805	0.22060	0.322:0.0:0.678:0.0	.	270	Q9GZK4	OR2H1_HUMAN	N	270	ENSP00000366340:K270N;ENSP00000366337:K270N;ENSP00000393254:K270N;ENSP00000366336:K270N;ENSP00000380010:K270N	ENSP00000366336:K270N	K	+	3	2	OR2H1	29538335	0.000000	0.05858	0.935000	0.37517	0.315000	0.28087	-1.183000	0.03079	0.870000	0.35726	-0.199000	0.12753	AAG	G|0.995;C|0.005	0.005	strong		0.522	OR2H1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194014.3		
HYDIN	54768	hgsc.bcm.edu	37	16	71101206	71101206	+	Silent	SNP	A	A	G	rs11866903	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:71101206A>G	ENST00000393567.2	-	15	2212	c.2062T>C	c.(2062-2064)Tta>Cta	p.L688L	HYDIN_ENST00000288168.10_Silent_p.L705L|HYDIN_ENST00000393550.2_Silent_p.L703L|HYDIN_ENST00000448089.2_Silent_p.L688L|HYDIN_ENST00000541601.1_Silent_p.L705L|HYDIN_ENST00000538248.1_Silent_p.L715L|HYDIN_ENST00000321489.5_Silent_p.L688L|HYDIN_ENST00000448691.1_Silent_p.L688L|HYDIN_ENST00000543639.1_5'Flank	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	688					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				GCTGTAATTAAGAGCGCCAGC	0.562													A|||	378	0.0754792	0.2769	0.013	5008	,	,		18119	0.001		0.001	False		,,,				2504	0.001				p.L715L		Atlas-SNP	.											.	HYDIN	788	.	0			c.T2143C						PASS	.	A	,,,	969,3427	361.6+/-315.8	118,733,1347	68.0	59.0	62.0		2143,2113,2062,2062	-0.0	1.0	16	dbSNP_120	62	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HYDIN	NM_001198542.1,NM_001198543.1,NM_017558.3,NM_032821.2	,,,	118,737,5643	GG,GA,AA		0.0465,22.0428,7.4869	,,,	715/951,705/941,688/1018,688/5121	71101206	973,12023	2198	4300	6498	SO:0001819	synonymous_variant	54768	exon15			TAATTAAGAGCGC	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.2062T>C	16.37:g.71101206A>G		70.0	0.0	0		54.0	22.0	0.407407	NM_001198542	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Silent	SNP	ENST00000393567.2	37	CCDS59269.1																																																																																			A|0.919;G|0.081	0.081	strong		0.562	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
SSFA2	6744	hgsc.bcm.edu	37	2	182780817	182780817	+	Missense_Mutation	SNP	C	C	T	rs16867510	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:182780817C>T	ENST00000431877.2	+	11	2629	c.2450C>T	c.(2449-2451)gCg>gTg	p.A817V	SSFA2_ENST00000409001.1_Missense_Mutation_p.A817V|SSFA2_ENST00000428267.2_Missense_Mutation_p.A664V|SSFA2_ENST00000320370.7_Missense_Mutation_p.A817V|SSFA2_ENST00000409136.1_Missense_Mutation_p.A326V	NM_001130445.1	NP_001123917.1	P28290	SSFA2_HUMAN	sperm specific antigen 2	817			A -> V (in dbSNP:rs16867510).			cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(5)|lung(18)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	38			OV - Ovarian serous cystadenocarcinoma(117;0.0856)			CAGAGTGAGGCGCCGCGGGTG	0.507													C|||	172	0.034345	0.1263	0.0072	5008	,	,		20029	0.0		0.0	False		,,,				2504	0.0				p.A817V		Atlas-SNP	.											SSFA2,colon,carcinoma,0,1	SSFA2	130	1	0			c.C2450T						scavenged	.	C	VAL/ALA,VAL/ALA	438,3968	210.2+/-230.7	29,380,1794	66.0	73.0	71.0		2450,2450	-9.2	0.0	2	dbSNP_123	71	7,8593	5.7+/-21.5	0,7,4293	yes	missense,missense	SSFA2	NM_001130445.1,NM_006751.5	64,64	29,387,6087	TT,TC,CC		0.0814,9.941,3.4215	benign,benign	817/1260,817/1257	182780817	445,12561	2203	4300	6503	SO:0001583	missense	6744	exon11			GTGAGGCGCCGCG	M61199	CCDS2284.1, CCDS46467.1, CCDS74611.1	2q32.1	2012-02-01			ENSG00000138434	ENSG00000138434			11319	protein-coding gene	gene with protein product	"""cleavage signal-1 protein"", ""KRAS-induced actin-interacting protein"", ""sperm associated antigen 13"""	118990				1555770	Standard	XM_005246812		Approved	CS-1, SPAG13, KRAP, KIAA1927	uc002uoh.3	P28290	OTTHUMG00000132584	ENST00000431877.2:c.2450C>T	2.37:g.182780817C>T	ENSP00000388731:p.Ala817Val	191.0	1.0	0.0052356		188.0	92.0	0.489362	NM_001130445	A8K6T0|Q68DA6|Q7Z7L2|Q8N1L3|Q8N263|Q8N7H2|Q8NEN5|Q96E36|Q96PW1	Missense_Mutation	SNP	ENST00000431877.2	37	CCDS46467.1	52	0.023809523809523808	51	0.10365853658536585	1	0.0027624309392265192	0	0.0	0	0.0	C	2.957	-0.215497	0.06101	0.09941	8.14E-4	ENSG00000138434	ENST00000431877;ENST00000320370;ENST00000409001;ENST00000428267;ENST00000409136	T;T;T;T;T	0.14391	2.74;2.51;2.74;2.73;2.52	5.95	-9.19	0.00685	.	1.558920	0.02820	N	0.125417	T	0.00144	0.0004	N	0.03115	-0.41	0.80722	P	0.0	B;B;B;B;B	0.13594	0.003;0.008;0.002;0.002;0.002	B;B;B;B;B	0.06405	0.002;0.001;0.0;0.0;0.0	T	0.27123	-1.0083	9	0.20046	T	0.44	3.6137	7.4998	0.27511	0.0819:0.4875:0.2579:0.1727	rs16867510	664;326;817;817;817	E7END2;E7EUL7;E9PHV5;P28290;P28290-3	.;.;.;SSFA2_HUMAN;.	V	817;817;817;664;326	ENSP00000388731:A817V;ENSP00000314669:A817V;ENSP00000387319:A817V;ENSP00000409867:A664V;ENSP00000386916:A326V	ENSP00000314669:A817V	A	+	2	0	SSFA2	182489062	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-1.387000	0.02535	-1.938000	0.01046	-0.793000	0.03317	GCG	C|0.965;T|0.035	0.035	strong		0.507	SSFA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255793.2	NM_006751	
TCEB3B	51224	hgsc.bcm.edu	37	18	44559578	44559578	+	Silent	SNP	G	G	A	rs149717505	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:44559578G>A	ENST00000332567.4	-	1	2410	c.2058C>T	c.(2056-2058)tcC>tcT	p.S686S	KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000245121.5_Intron	NM_016427.2	NP_057511.2	Q8IYF1	ELOA2_HUMAN	transcription elongation factor B polypeptide 3B (elongin A2)	686					regulation of DNA-templated transcription, elongation (GO:0032784)|transcription from RNA polymerase II promoter (GO:0006366)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|lung(24)|ovary(2)|pancreas(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						tgctCTGGCTGGAGGGAGTGT	0.627													G|||	9	0.00179712	0.0053	0.0029	5008	,	,		14981	0.0		0.0	False		,,,				2504	0.0				p.S686S		Atlas-SNP	.											.	TCEB3B	141	.	0			c.C2058T						PASS	.	G	,	25,4377		0,25,2176	38.0	43.0	41.0		2058,	1.1	0.0	18	dbSNP_134	41	0,8598		0,0,4299	no	coding-synonymous,intron	TCEB3B,KATNAL2	NM_016427.2,NM_031303.2	,	0,25,6475	AA,AG,GG		0.0,0.5679,0.1923	,	686/754,	44559578	25,12975	2201	4299	6500	SO:0001819	synonymous_variant	51224	exon1			CTGGCTGGAGGGA	BC036022	CCDS11932.1	18q21.1	2009-08-04			ENSG00000206181	ENSG00000206181			30771	protein-coding gene	gene with protein product	"""transcription elongation factor (SIII) elongin A2"", ""elongin A2"""	609522				7660129, 8244996	Standard	NM_016427		Approved	HsT832, TCEB3L	uc002lcr.1	Q8IYF1	OTTHUMG00000132649	ENST00000332567.4:c.2058C>T	18.37:g.44559578G>A		170.0	0.0	0		154.0	77.0	0.5	NM_016427	Q9P2V9	Silent	SNP	ENST00000332567.4	37	CCDS11932.1																																																																																			G|0.998;A|0.002	0.002	strong		0.627	TCEB3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255900.1	NM_016427	
TTC21A	199223	hgsc.bcm.edu	37	3	39180100	39180100	+	Missense_Mutation	SNP	G	G	A	rs80238762	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:39180100G>A	ENST00000431162.2	+	28	4005	c.3871G>A	c.(3871-3873)Gaa>Aaa	p.E1291K	TTC21A_ENST00000493856.1_3'UTR|TTC21A_ENST00000301819.6_Missense_Mutation_p.E1292K|TTC21A_ENST00000440121.1_Missense_Mutation_p.E1243K			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	1291				E -> K (in Ref. 2; BAG63755). {ECO:0000305}.						NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(23)|ovary(1)|prostate(1)|skin(3)	50				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		GGAGGCCATTGAAATCTGCAA	0.522													G|||	29	0.00579073	0.0008	0.0173	5008	,	,		20962	0.0		0.0159	False		,,,				2504	0.0				p.E1291K		Atlas-SNP	.											.	TTC21A	96	.	0			c.G3871A						PASS	.	G	LYS/GLU,LYS/GLU	8,3990		0,8,1991	113.0	110.0	111.0		3727,3871	5.1	0.9	3	dbSNP_132	111	91,8241		1,89,4076	yes	missense,missense	TTC21A	NM_001105513.2,NM_145755.2	56,56	1,97,6067	AA,AG,GG		1.0922,0.2001,0.8029	possibly-damaging,possibly-damaging	1243/1273,1291/1321	39180100	99,12231	1999	4166	6165	SO:0001583	missense	199223	exon28			GCCATTGAAATCT	AJ487015	CCDS43068.1, CCDS46800.1, CCDS43068.2	3p22.2	2014-09-04			ENSG00000168026	ENSG00000168026		"""Tetratricopeptide (TTC) repeat domain containing"""	30761	protein-coding gene	gene with protein product		611430					Standard	NM_145755		Approved	STI2	uc003cjc.2	Q8NDW8	OTTHUMG00000155973	ENST00000431162.2:c.3871G>A	3.37:g.39180100G>A	ENSP00000398211:p.Glu1291Lys	236.0	1.0	0.00423729		236.0	111.0	0.470339	NM_145755	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	37	CCDS46800.1	15	0.006868131868131868	0	0.0	7	0.019337016574585635	0	0.0	8	0.010554089709762533	G	22.7	4.325101	0.81580	0.002001	0.010922	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.78481	-1.18;-1.18;-1.18	5.14	5.14	0.70334	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.151938	0.42682	D	0.000679	T	0.72486	0.3466	M	0.64170	1.965	0.58432	D	0.999999	P;D;P	0.55605	0.921;0.972;0.953	P;P;P	0.53912	0.497;0.737;0.551	T	0.78620	-0.2133	10	0.41790	T	0.15	-2.9838	17.3579	0.87342	0.0:0.0:1.0:0.0	.	1243;1292;1291	Q8NDW8-6;Q8NDW8-7;Q8NDW8	.;.;TT21A_HUMAN	K	1292;1274;1291;1243	ENSP00000301819:E1292K;ENSP00000398211:E1291K;ENSP00000410882:E1243K	ENSP00000301819:E1292K	E	+	1	0	TTC21A	39155104	1.000000	0.71417	0.918000	0.36340	0.278000	0.26855	7.431000	0.80335	2.377000	0.81083	0.561000	0.74099	GAA	G|0.989;A|0.011	0.011	strong		0.522	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755	
ARVCF	421	hgsc.bcm.edu	37	22	19960666	19960666	+	Missense_Mutation	SNP	G	G	A	rs115736959	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:19960666G>A	ENST00000263207.3	-	14	2705	c.2414C>T	c.(2413-2415)gCg>gTg	p.A805V	ARVCF_ENST00000406259.1_Missense_Mutation_p.A799V|ARVCF_ENST00000401994.1_Missense_Mutation_p.A742V|ARVCF_ENST00000406522.1_Missense_Mutation_p.A736V|ARVCF_ENST00000344269.3_Missense_Mutation_p.A742V	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	805					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|liver(1)|lung(4)|prostate(1)|urinary_tract(2)	13	Colorectal(54;0.0993)					AGCCACCAACGCTGGCACCCC	0.711													G|||	64	0.0127796	0.0446	0.0072	5008	,	,		10944	0.0		0.0	False		,,,				2504	0.0				p.A805V		Atlas-SNP	.											.	ARVCF	54	.	0			c.C2414T						PASS	.	G	VAL/ALA	188,4196		0,188,2004	19.0	18.0	18.0		2414	3.2	0.1	22	dbSNP_132	18	2,8574		0,2,4286	yes	missense	ARVCF	NM_001670.2	64	0,190,6290	AA,AG,GG		0.0233,4.2883,1.466	benign	805/963	19960666	190,12770	2192	4288	6480	SO:0001583	missense	421	exon14			ACCAACGCTGGCA		CCDS13771.1	22q11.21	2013-02-14	2010-04-28		ENSG00000099889	ENSG00000099889		"""Armadillo repeat containing"""	728	protein-coding gene	gene with protein product		602269				9126485, 15456900	Standard	NM_001670		Approved		uc002zqz.3	O00192	OTTHUMG00000030426	ENST00000263207.3:c.2414C>T	22.37:g.19960666G>A	ENSP00000263207:p.Ala805Val	24.0	0.0	0		38.0	19.0	0.5	NM_001670	B7WNV2	Missense_Mutation	SNP	ENST00000263207.3	37	CCDS13771.1	25	0.011446886446886446	22	0.044715447154471545	3	0.008287292817679558	0	0.0	0	0.0	G	15.10	2.734386	0.48939	0.042883	2.33E-4	ENSG00000099889	ENST00000263207;ENST00000344269;ENST00000401994;ENST00000406522;ENST00000406259	T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83	4.34	3.24	0.37175	Armadillo-like helical (1);Armadillo-type fold (1);	0.113654	0.56097	D	0.000025	T	0.06325	0.0163	N	0.22421	0.69	0.36590	D	0.874035	P;D	0.54601	0.782;0.967	B;B	0.34779	0.189;0.163	T	0.07986	-1.0744	9	.	.	.	-12.0845	9.633	0.39791	0.0:0.0:0.6411:0.3589	.	805;321	O00192;E7EV58	ARVC_HUMAN;.	V	805;742;742;736;799	ENSP00000263207:A805V;ENSP00000342042:A742V;ENSP00000384341:A742V;ENSP00000384732:A736V;ENSP00000385444:A799V	.	A	-	2	0	ARVCF	18340666	0.895000	0.30542	0.102000	0.21198	0.078000	0.17371	3.057000	0.49931	2.416000	0.81992	0.561000	0.74099	GCG	G|0.985;A|0.015	0.015	strong		0.711	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670	
GSG2	83903	hgsc.bcm.edu	37	17	3627619	3627619	+	Silent	SNP	C	C	T	rs1185511	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3627619C>T	ENST00000325418.4	+	1	409	c.390C>T	c.(388-390)tgC>tgT	p.C130C	CTD-3195I5.3_ENST00000571741.1_RNA|ITGAE_ENST00000571185.1_5'UTR|ITGAE_ENST00000263087.4_Intron	NM_031965.2	NP_114171.2	Q8TF76	HASP_HUMAN	germ cell associated 2 (haspin)	130					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)										GCACACCCTGCGGCCCGCTCC	0.731													C|||	804	0.160543	0.587	0.0403	5008	,	,		12752	0.0		0.0	False		,,,				2504	0.0				p.C130C		Atlas-SNP	.											.	GSG2	48	.	0			c.C390T						PASS	.	C	,	1822,2460		390,1042,709	6.0	8.0	8.0		,390	4.4	0.7	17	dbSNP_87	8	25,8313		0,25,4144	no	intron,coding-synonymous	ITGAE,GSG2	NM_002208.4,NM_031965.2	,	390,1067,4853	TT,TC,CC		0.2998,42.5502,14.6355	,	,130/799	3627619	1847,10773	2141	4169	6310	SO:0001819	synonymous_variant	83903	exon1			ACCCTGCGGCCCG	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.390C>T	17.37:g.3627619C>T		0.0	0.0	.		7.0	5.0	0.714286	NM_031965	Q5U5K3|Q96MN1|Q9BXS7	Silent	SNP	ENST00000325418.4	37	CCDS11036.1																																																																																			C|0.779;T|0.221	0.221	strong		0.731	GSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207391.1	NM_031965	
TMEM64	169200	hgsc.bcm.edu	37	8	91637929	91637929	+	Silent	SNP	T	T	C	rs75193995	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:91637929T>C	ENST00000458549.2	-	3	1290	c.1113A>G	c.(1111-1113)acA>acG	p.T371T	TMEM64_ENST00000519519.1_Silent_p.T110T|TMEM64_ENST00000418210.2_Silent_p.T319T	NM_001008495.3	NP_001008495.2	Q6YI46	TMM64_HUMAN	transmembrane protein 64	371					cytosolic calcium ion homeostasis (GO:0051480)|positive regulation of bone resorption (GO:0045780)|positive regulation of osteoclast differentiation (GO:0045672)|regulation of ATPase activity (GO:0043462)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)	2			BRCA - Breast invasive adenocarcinoma(11;0.0598)			CTCCAGAAAATGTTAGGGTCC	0.408													T|||	27	0.00539137	0.0197	0.0014	5008	,	,		16021	0.0		0.0	False		,,,				2504	0.0				p.T371T		Atlas-SNP	.											.	TMEM64	31	.	0			c.A1113G						PASS	.	T	,	60,4346	57.4+/-93.9	2,56,2145	101.0	92.0	95.0		1113,957	-2.3	1.0	8	dbSNP_132	95	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	TMEM64	NM_001008495.3,NM_001146273.1	,	2,57,6444	CC,CT,TT		0.0116,1.3618,0.469	,	371/381,319/329	91637929	61,12945	2203	4300	6503	SO:0001819	synonymous_variant	169200	exon3			AGAAAATGTTAGG	AL834364	CCDS34920.2, CCDS55260.1	8q21.3	2005-08-09			ENSG00000180694	ENSG00000180694			25441	protein-coding gene	gene with protein product							Standard	NM_001008495		Approved	DKFZp762C1112	uc003yen.2	Q6YI46	OTTHUMG00000157185	ENST00000458549.2:c.1113A>G	8.37:g.91637929T>C		207.0	0.0	0		174.0	77.0	0.442529	NM_001008495	B4DUC0|F5GXM4|Q2HIZ7|Q8N3G6	Silent	SNP	ENST00000458549.2	37	CCDS34920.2																																																																																			T|0.995;C|0.005	0.005	strong		0.408	TMEM64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347825.1	NM_001008495	
SEZ6L	23544	hgsc.bcm.edu	37	22	26688401	26688401	+	Silent	SNP	T	T	C	rs16981666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:26688401T>C	ENST00000248933.6	+	2	219	c.124T>C	c.(124-126)Ttg>Ctg	p.L42L	SEZ6L_ENST00000529632.2_Silent_p.L42L|SEZ6L_ENST00000402979.1_5'UTR|SEZ6L_ENST00000343706.4_Silent_p.L42L|SEZ6L_ENST00000404234.3_Silent_p.L42L|SEZ6L_ENST00000360929.3_Silent_p.L42L|SEZ6L_ENST00000403121.1_5'UTR			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	42					adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)				breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						TGCTAGCCCTTTGGGTCCTTA	0.562													T|||	452	0.0902556	0.2322	0.0216	5008	,	,		18973	0.1012		0.0	False		,,,				2504	0.0286				p.L42L		Atlas-SNP	.											.	SEZ6L	174	.	0			c.T124C						PASS	.	T	,,,,,	955,3451	354.1+/-312.5	100,755,1348	47.0	39.0	42.0		124,124,124,124,124,124	-1.8	0.0	22	dbSNP_123	42	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SEZ6L	NM_001184773.1,NM_001184774.1,NM_001184775.1,NM_001184776.1,NM_001184777.1,NM_021115.4	,,,,,	100,762,5641	CC,CT,TT		0.0814,21.675,7.3966	,,,,,	42/1024,42/1014,42/1012,42/950,42/949,42/1025	26688401	962,12044	2203	4300	6503	SO:0001819	synonymous_variant	23544	exon2			AGCCCTTTGGGTC	AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"""seizure related gene 6 (mouse)-like"""				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.124T>C	22.37:g.26688401T>C		62.0	0.0	0		60.0	32.0	0.533333	NM_001184777	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Silent	SNP	ENST00000248933.6	37	CCDS13833.1																																																																																			T|0.927;C|0.073	0.073	strong		0.562	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3		
FAM66D	100132923	hgsc.bcm.edu	37	8	11991328	11991328	+	RNA	SNP	G	G	A	rs144333235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11991328G>A	ENST00000434078.2	+	0	608					NR_027425.1				family with sequence similarity 66, member D																		CTTCTCCCTGGGAGCAAGCTG	0.537													G|||	105	0.0209665	0.0749	0.0072	5008	,	,		22364	0.0		0.001	False		,,,				2504	0.0				p.P64L		Atlas-SNP	.											.	.	.	.	0			c.C191T						PASS	.																																					392197	exon1			TCCCTGGGAGCAA			8p23.1	2013-07-05			ENSG00000255052	ENSG00000255052		"""Long non-coding RNAs"""	24159	non-coding RNA	RNA, long non-coding							Standard	NR_027425		Approved				OTTHUMG00000165269		8.37:g.11991328G>A		51.0	0.0	0		65.0	18.0	0.276923	NM_001256869		Missense_Mutation	SNP	ENST00000434078.2	37																																																																																				G|0.983;A|0.017	0.017	strong		0.537	FAM66D-201	KNOWN	basic	antisense	antisense		NR_027425	
UGGT2	55757	hgsc.bcm.edu	37	13	96648384	96648384	+	Missense_Mutation	SNP	T	T	C	rs73562939	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:96648384T>C	ENST00000376747.3	-	7	833	c.763A>G	c.(763-765)Act>Gct	p.T255A	UGGT2_ENST00000376714.3_Missense_Mutation_p.T255A|UGGT2_ENST00000467305.1_5'UTR|UGGT2_ENST00000376712.4_Missense_Mutation_p.T255A|UGGT2_ENST00000397618.3_Missense_Mutation_p.T255A	NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	255					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						GTAGTATTAGTCACAGCTACA	0.328													T|||	102	0.0203674	0.0749	0.0029	5008	,	,		18668	0.0		0.001	False		,,,				2504	0.0				p.T255A		Atlas-SNP	.											.	UGGT2	127	.	0			c.A763G						PASS	.	T	ALA/THR	288,4116	158.1+/-190.9	10,268,1924	117.0	127.0	124.0		763	5.8	0.9	13	dbSNP_130	124	0,8598		0,0,4299	yes	missense	UGGT2	NM_020121.3	58	10,268,6223	CC,CT,TT		0.0,6.5395,2.215	benign	255/1517	96648384	288,12714	2202	4299	6501	SO:0001583	missense	55757	exon7			TATTAGTCACAGC	AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"""UDP-glucose:glycoprotein glucosyltransferase 2"""	605898	"""UDP-glucose ceramide glucosyltransferase-like 2"""	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.763A>G	13.37:g.96648384T>C	ENSP00000365938:p.Thr255Ala	212.0	0.0	0		215.0	98.0	0.455814	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	37	CCDS9480.1	35	0.016025641025641024	34	0.06910569105691057	1	0.0027624309392265192	0	0.0	0	0.0	T	13.13	2.145554	0.37923	0.065395	0.0	ENSG00000102595	ENST00000376747;ENST00000376714;ENST00000397618;ENST00000376712	T;T	0.29397	1.57;1.57	5.84	5.84	0.93424	.	0.872316	0.10306	N	0.690619	T	0.02970	0.0088	L	0.60845	1.875	0.31130	N	0.707877	P;P;B	0.42692	0.787;0.787;0.004	B;B;B	0.36567	0.228;0.228;0.004	T	0.11966	-1.0566	10	0.87932	D	0	-2.0224	15.19	0.73035	0.0:0.0:0.0:1.0	.	255;255;255	Q2TAA6;E7EMU6;Q9NYU1	.;.;UGGG2_HUMAN	A	255	ENSP00000365938:T255A;ENSP00000380743:T255A	ENSP00000365902:T255A	T	-	1	0	UGGT2	95446385	0.651000	0.27340	0.866000	0.34008	0.846000	0.48090	2.811000	0.47986	2.231000	0.72958	0.397000	0.26171	ACT	T|0.976;C|0.024	0.024	strong		0.328	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121	
ORM2	5005	hgsc.bcm.edu	37	9	117094119	117094119	+	Silent	SNP	G	G	A	rs148394636	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117094119G>A	ENST00000431067.2	+	5	486	c.450G>A	c.(448-450)gaG>gaA	p.E150E	ORM2_ENST00000412657.1_3'UTR	NM_000608.2	NP_000599.1	P19652	A1AG2_HUMAN	orosomucoid 2	150					acute-phase response (GO:0006953)|regulation of immune system process (GO:0002682)|transport (GO:0006810)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(1)	7		Myeloproliferative disorder(63;0.163)			Chlorpromazine(DB00477)|Oxycodone(DB00497)|Thalidomide(DB01041)	ACAAGCCAGAGACGACCAAGG	0.602													G|||	399	0.0796725	0.2943	0.0144	5008	,	,		17341	0.0		0.0	False		,,,				2504	0.0				p.E150E	NSCLC(65;867 1308 1814 2391 12508)	Atlas-SNP	.											.	ORM2	13	.	0			c.G450A						PASS	.	G		955,3451	347.2+/-309.4	112,731,1360	59.0	63.0	62.0		450	-2.4	0.0	9	dbSNP_134	62	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous	ORM2	NM_000608.2		112,732,5656	AA,AG,GG		0.0116,21.675,7.3538		150/202	117094119	956,12044	2203	4297	6500	SO:0001819	synonymous_variant	5005	exon5			GCCAGAGACGACC		CCDS6804.1	9q32	2013-09-19			ENSG00000228278	ENSG00000228278		"""Lipocalins"""	8499	protein-coding gene	gene with protein product	"""alpha-1-acid glycoprotein, type 2"""	138610				4711474, 2970990	Standard	NM_000608		Approved	AGP-B, AGP-B', AGP2		P19652	OTTHUMG00000021014	ENST00000431067.2:c.450G>A	9.37:g.117094119G>A		176.0	0.0	0		182.0	46.0	0.252747	NM_000608	B2R5L2|Q16571|Q5T538|Q6IB74	Silent	SNP	ENST00000431067.2	37	CCDS6804.1																																																																																			G|0.931;A|0.069	0.069	strong		0.602	ORM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055432.1	NM_000608	
EIF4G2	1982	hgsc.bcm.edu	37	11	10821185	10821185	+	Silent	SNP	G	G	A	rs11542384	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:10821185G>A	ENST00000526148.1	-	19	2748	c.2238C>T	c.(2236-2238)tcC>tcT	p.S746S	EIF4G2_ENST00000339995.5_Silent_p.S746S|EIF4G2_ENST00000396525.2_Silent_p.S708S|SNORD97_ENST00000459187.1_RNA|RP11-685M7.5_ENST00000532365.1_RNA|EIF4G2_ENST00000525681.1_Silent_p.S746S	NM_001172705.1	NP_001166176			eukaryotic translation initiation factor 4 gamma, 2											NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(6)	43				all cancers(16;2.8e-07)|Epithelial(150;4.18e-07)|BRCA - Breast invasive adenocarcinoma(625;0.111)		TGGTTTGAGGGGATGGATCCA	0.378													G|||	614	0.122604	0.4342	0.0504	5008	,	,		20172	0.0		0.005	False		,,,				2504	0.0				p.S746S		Atlas-SNP	.											.	EIF4G2	89	.	0			c.C2238T						PASS	.	G	,,	1686,2716	512.4+/-368.1	337,1012,852	148.0	145.0	146.0		2124,2238,2238	4.6	1.0	11	dbSNP_120	146	27,8561	17.3+/-56.4	0,27,4267	no	coding-synonymous,coding-synonymous,coding-synonymous	EIF4G2	NM_001042559.2,NM_001172705.1,NM_001418.3	,,	337,1039,5119	AA,AG,GG		0.3144,38.3008,13.1871	,,	708/870,746/908,746/908	10821185	1713,11277	2201	4294	6495	SO:0001819	synonymous_variant	1982	exon19			TTGAGGGGATGGA	U73824	CCDS31428.1, CCDS41618.1	11p15	2005-09-29			ENSG00000110321	ENSG00000110321			3297	protein-coding gene	gene with protein product		602325				9030685, 9032289	Standard	NM_001042559		Approved	DAP5, NAT1, p97	uc001mjc.3	P78344	OTTHUMG00000165823	ENST00000526148.1:c.2238C>T	11.37:g.10821185G>A		191.0	0.0	0		198.0	86.0	0.434343	NM_001172705		Silent	SNP	ENST00000526148.1	37	CCDS31428.1																																																																																			T|0.000;G|0.885;C|0.000;A|0.115	0.115	strong		0.378	EIF4G2-006	KNOWN	alternative_5_UTR|non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000386603.1	NM_001418	
PVR	5817	hgsc.bcm.edu	37	19	45150763	45150763	+	Silent	SNP	G	G	A	rs10421291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45150763G>A	ENST00000425690.3	+	2	647	c.348G>A	c.(346-348)gaG>gaA	p.E116E	PVR_ENST00000403059.4_Silent_p.E116E|PVR_ENST00000406449.4_Silent_p.E116E|PVR_ENST00000344956.4_Silent_p.E116E|CTB-171A8.1_ENST00000590796.1_RNA	NM_006505.3	NP_006496.3	P15151	PVR_HUMAN	poliovirus receptor	116	Ig-like V-type.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|receptor activity (GO:0004872)			large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	6	Lung NSC(12;0.00608)|all_lung(12;0.0148)	Medulloblastoma(540;0.0425)|Ovarian(192;0.0728)|Prostate(69;0.081)|all_neural(266;0.112)		Epithelial(262;0.000601)		TGCGCGTAGAGGATGAAGGCA	0.617													G|||	250	0.0499201	0.1755	0.0259	5008	,	,		10654	0.0		0.0	False		,,,				2504	0.0				p.E116E		Atlas-SNP	.											.	PVR	23	.	0			c.G348A						PASS	.	G	,,,	658,3748	275.2+/-272.4	60,538,1605	59.0	53.0	55.0		348,348,348,348	-5.9	0.0	19	dbSNP_119	55	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PVR	NM_001135768.1,NM_001135769.1,NM_001135770.1,NM_006505.3	,,,	60,544,5899	AA,AG,GG		0.0698,14.9342,5.1053	,,,	116/373,116/365,116/393,116/418	45150763	664,12342	2203	4300	6503	SO:0001819	synonymous_variant	5817	exon2			CGTAGAGGATGAA	BC015542	CCDS12640.1, CCDS46105.1, CCDS46106.1, CCDS46107.1	19q13.2	2013-01-29			ENSG00000073008	ENSG00000073008		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9705	protein-coding gene	gene with protein product	"""nectin-like 5"""	173850		PVS		2170108	Standard	XM_005259120		Approved	CD155, HVED, Necl-5, NECL5, Tage4	uc002ozm.3	P15151	OTTHUMG00000151527	ENST00000425690.3:c.348G>A	19.37:g.45150763G>A		86.0	0.0	0		94.0	41.0	0.43617	NM_001135769	B4DTS9|P15152|Q15267|Q15268|Q96BJ1	Silent	SNP	ENST00000425690.3	37	CCDS12640.1																																																																																			G|0.937;A|0.063	0.063	strong		0.617	PVR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323017.2	NM_006505	
CYLD	1540	hgsc.bcm.edu	37	16	50783696	50783696	+	Silent	SNP	C	C	T	rs34564491	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:50783696C>T	ENST00000427738.3	+	2	292	c.87C>T	c.(85-87)agC>agT	p.S29S	CYLD_ENST00000566206.1_Silent_p.S29S|CYLD_ENST00000569418.1_Silent_p.S29S|CYLD_ENST00000398568.2_Silent_p.S29S|CYLD_ENST00000564326.1_Silent_p.S29S|CYLD_ENST00000540145.1_Silent_p.S29S|CYLD_ENST00000311559.9_Silent_p.S29S|CYLD_ENST00000568704.2_Silent_p.S29S			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	29					cell cycle (GO:0007049)|innate immune response (GO:0045087)|necroptotic process (GO:0070266)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein K63-linked deubiquitination (GO:0070536)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of mitotic cell cycle (GO:0007346)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|microtubule (GO:0005874)|nucleus (GO:0005634)	Lys63-specific deubiquitinase activity (GO:0061578)|proline-rich region binding (GO:0070064)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(9)|lung(17)|pancreas(1)|skin(22)|upper_aerodigestive_tract(1)	62		all_cancers(37;0.0156)				AAGAATGCAGCGTTACAGACA	0.408			"""Mis, N, F, S"""		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis				C|||	63	0.0125799	0.0446	0.0058	5008	,	,		18761	0.0		0.0	False		,,,				2504	0.0				p.S29S		Atlas-SNP	.	yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	.	CYLD	150	.	0			c.C87T						PASS	.	C	,,	145,3565		2,141,1712	83.0	79.0	80.0		87,87,87	2.0	1.0	16	dbSNP_126	80	1,8179		0,1,4089	no	coding-synonymous,coding-synonymous,coding-synonymous	CYLD	NM_001042355.1,NM_001042412.1,NM_015247.2	,,	2,142,5801	TT,TC,CC		0.0122,3.9084,1.2279	,,	29/954,29/954,29/957	50783696	146,11744	1855	4090	5945	SO:0001819	synonymous_variant	1540	exon3	Familial Cancer Database	;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s.	ATGCAGCGTTACA	AB020656	CCDS42164.1, CCDS45482.1	16q12-q13	2014-09-17							2584	protein-coding gene	gene with protein product	"""ubiquitin specific peptidase like 2"""	605018		CYLD1		7493027	Standard	NM_015247		Approved	KIAA0849, USPL2	uc002egq.1	Q9NQC7		ENST00000427738.3:c.87C>T	16.37:g.50783696C>T		50.0	0.0	0		60.0	26.0	0.433333	NM_001042355	O94934|Q7L3N6|Q96EH0|Q9NZX9	Silent	SNP	ENST00000427738.3	37	CCDS45482.1																																																																																			C|0.991;T|0.009	0.009	strong		0.408	CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2		
VCAN	1462	hgsc.bcm.edu	37	5	82835852	82835852	+	Missense_Mutation	SNP	C	C	T	rs61733401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:82835852C>T	ENST00000265077.3	+	8	7595	c.7030C>T	c.(7030-7032)Ccc>Tcc	p.P2344S	VCAN_ENST00000513016.1_3'UTR|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000512590.2_Intron|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000343200.5_Missense_Mutation_p.P1357S	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2344	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	AGCAGAAGGACCCACGGTGGC	0.468													C|||	165	0.0329473	0.1172	0.0101	5008	,	,		19057	0.0		0.003	False		,,,				2504	0.0				p.P2344S		Atlas-SNP	.											.	VCAN	498	.	0			c.C7030T						PASS	.	C	,SER/PRO,,SER/PRO	417,3989	203.8+/-226.2	21,375,1807	90.0	85.0	87.0		,4069,,7030	2.0	0.0	5	dbSNP_129	87	4,8596	3.7+/-12.6	0,4,4296	yes	intron,missense,intron,missense	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,74,,74	21,379,6103	TT,TC,CC		0.0465,9.4644,3.237	,benign,,benign	,1357/2410,,2344/3397	82835852	421,12585	2203	4300	6503	SO:0001583	missense	1462	exon8			GAAGGACCCACGG	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.7030C>T	5.37:g.82835852C>T	ENSP00000265077:p.Pro2344Ser	166.0	0.0	0		175.0	80.0	0.457143	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	64	0.029304029304029304	61	0.12398373983739837	3	0.008287292817679558	0	0.0	0	0.0	C	2.456	-0.325144	0.05350	0.094644	4.65E-4	ENSG00000038427	ENST00000265077;ENST00000343200	T;T	0.37235	1.21;1.21	6.07	2.02	0.26589	.	0.557747	0.17822	N	0.160824	T	0.00271	0.0008	L	0.41824	1.3	0.09310	N	1	P;P	0.38597	0.639;0.506	B;B	0.30029	0.11;0.051	T	0.07539	-1.0767	10	0.09843	T	0.71	.	6.8445	0.23980	0.3387:0.5251:0.0:0.1362	rs61733401	1357;2344	P13611-2;P13611	.;CSPG2_HUMAN	S	2344;1357	ENSP00000265077:P2344S;ENSP00000340062:P1357S	ENSP00000265077:P2344S	P	+	1	0	VCAN	82871608	0.000000	0.05858	0.007000	0.13788	0.153000	0.21895	-0.086000	0.11233	0.839000	0.34971	0.650000	0.86243	CCC	C|0.965;T|0.035	0.035	strong		0.468	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
ITGA9	3680	hgsc.bcm.edu	37	3	37536020	37536020	+	Silent	SNP	C	C	T	rs62001860	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:37536020C>T	ENST00000264741.5	+	5	829	c.573C>T	c.(571-573)caC>caT	p.H191H	ITGA9_ENST00000422441.1_Silent_p.H191H	NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	191					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		GAGAGGAACACGGCTCCTGCC	0.532													C|||	36	0.0071885	0.0272	0.0	5008	,	,		20312	0.0		0.0	False		,,,				2504	0.0				p.H191H		Atlas-SNP	.											.	ITGA9	98	.	0			c.C573T						PASS	.	C		68,4338	64.1+/-101.4	0,68,2135	152.0	152.0	152.0		573	-0.1	1.0	3	dbSNP_129	152	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ITGA9	NM_002207.2		0,69,6434	TT,TC,CC		0.0116,1.5433,0.5305		191/1036	37536020	69,12937	2203	4300	6503	SO:0001819	synonymous_variant	3680	exon5			GGAACACGGCTCC	L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"""Integrins"""	6145	protein-coding gene	gene with protein product	"""integrin, alpha 4-like"""	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.573C>T	3.37:g.37536020C>T		326.0	1.0	0.00306748		312.0	150.0	0.480769	NM_002207	Q14638	Silent	SNP	ENST00000264741.5	37	CCDS2669.1																																																																																			C|0.994;T|0.006	0.006	strong		0.532	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207	
GPSM2	29899	hgsc.bcm.edu	37	1	109465084	109465084	+	Missense_Mutation	SNP	T	T	A	rs61758992		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:109465084T>A	ENST00000406462.2	+	14	2259	c.1486T>A	c.(1486-1488)Tta>Ata	p.L496I	GPSM2_ENST00000264126.3_Missense_Mutation_p.L496I|AKNAD1_ENST00000357393.4_Intron			P81274	GPSM2_HUMAN	G-protein signaling modulator 2	496	GoLoco 1. {ECO:0000255|PROSITE- ProRule:PRU00097}.				establishment of mitotic spindle orientation (GO:0000132)|G-protein coupled receptor signaling pathway (GO:0007186)|lung epithelial cell differentiation (GO:0060487)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTPase regulator activity (GO:0030695)|identical protein binding (GO:0042802)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)	14		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0353)|Lung(183;0.0984)|COAD - Colon adenocarcinoma(174;0.129)|Epithelial(280;0.175)|all cancers(265;0.209)		CTTTGACTTATTAAGCCGATT	0.353													T|||	1	0.000199681	0.0008	0.0	5008	,	,		17405	0.0		0.0	False		,,,				2504	0.0				p.L496I		Atlas-SNP	.											.	GPSM2	56	.	0			c.T1486A						PASS	.	T	ILE/LEU	6,4400	9.9+/-24.2	0,6,2197	124.0	124.0	124.0		1486	-3.6	0.0	1	dbSNP_129	124	0,8600		0,0,4300	yes	missense	GPSM2	NM_013296.4	5	0,6,6497	AA,AT,TT		0.0,0.1362,0.0461	possibly-damaging	496/685	109465084	6,13000	2203	4300	6503	SO:0001583	missense	29899	exon13			GACTTATTAAGCC	AY136740	CCDS792.2	1p13.3	2013-10-11	2010-06-24		ENSG00000121957	ENSG00000121957		"""Tetratricopeptide (TTC) repeat domain containing"""	29501	protein-coding gene	gene with protein product		609245	"""G-protein signalling modulator 2 (AGS3-like, C. elegans)"", ""deafness, autosomal recessive 82"""	DFNB82		11832491, 8973305, 19888295, 20602914, 21348867	Standard	NM_013296		Approved	LGN, Pins	uc010ovc.2	P81274	OTTHUMG00000011730	ENST00000406462.2:c.1486T>A	1.37:g.109465084T>A	ENSP00000385510:p.Leu496Ile	197.0	0.0	0		178.0	78.0	0.438202	NM_013296	Q5T1N8|Q6IBL7|Q8N0Z5	Missense_Mutation	SNP	ENST00000406462.2	37	CCDS792.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	21.6|21.6	4.170507|4.170507	0.78452|0.78452	0.001362|0.001362	0.0|0.0	ENSG00000121957|ENSG00000121957	ENST00000406462;ENST00000264126|ENST00000441735	D;D|.	0.97941|.	-4.62;-4.62|.	6.17|6.17	-3.58|-3.58	0.04597|0.04597	GoLoco motif (3);|.	0.076404|.	0.53938|.	D|.	0.000049|.	T|.	0.26846|.	0.0657|.	L|L	0.53249|0.53249	1.67|1.67	0.25458|0.25458	N|N	0.987941|0.987941	B|.	0.22276|.	0.067|.	B|.	0.25291|.	0.059|.	T|.	0.40794|.	-0.9544|.	10|.	0.54805|.	T|.	0.06|.	-5.8623|-5.8623	11.0483|11.0483	0.47872|0.47872	0.0:0.5338:0.1124:0.3538|0.0:0.5338:0.1124:0.3538	rs61758992|rs61758992	496|.	P81274|.	GPSM2_HUMAN|.	I|X	496|85	ENSP00000385510:L496I;ENSP00000264126:L496I|.	ENSP00000264126:L496I|.	L|Y	+|+	1|3	2|2	GPSM2|GPSM2	109266607|109266607	0.073000|0.073000	0.21202|0.21202	0.000000|0.000000	0.03702|0.03702	0.983000|0.983000	0.72400|0.72400	0.418000|0.418000	0.21230|0.21230	-0.938000|-0.938000	0.03714|0.03714	0.533000|0.533000	0.62120|0.62120	TTA|TAT	T|1.000;A|0.000	0.000	weak		0.353	GPSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032400.3	NM_013296	
WFIKKN2	124857	hgsc.bcm.edu	37	17	48913352	48913352	+	Silent	SNP	G	G	A	rs117494161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48913352G>A	ENST00000311378.4	+	1	582	c.54G>A	c.(52-54)gcG>gcA	p.A18A	WFIKKN2_ENST00000426127.1_Intron	NM_175575.5	NP_783165.1	Q8TEU8	WFKN2_HUMAN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2	18					muscle fiber development (GO:0048747)|negative regulation of DNA binding (GO:0043392)|negative regulation of protein binding (GO:0032091)|palate development (GO:0060021)|skeletal system development (GO:0001501)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)	metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(13)|ovary(4)|skin(1)	29			BRCA - Breast invasive adenocarcinoma(22;1.09e-08)			AGGTGGCAGCgctgctgctgc	0.682													G|||	94	0.01877	0.0477	0.0101	5008	,	,		18532	0.0218		0.0	False		,,,				2504	0.002				p.A18A		Atlas-SNP	.											.	WFIKKN2	69	.	0			c.G54A						PASS	.	G		190,4206		4,182,2012	14.0	14.0	14.0		54	0.4	1.0	17	dbSNP_132	14	8,8576		0,8,4284	no	coding-synonymous	WFIKKN2	NM_175575.5		4,190,6296	AA,AG,GG		0.0932,4.3221,1.5254		18/577	48913352	198,12782	2198	4292	6490	SO:0001819	synonymous_variant	124857	exon1			GGCAGCGCTGCTG	AY358142	CCDS11575.1	17q21.33	2013-01-21			ENSG00000173714	ENSG00000173714		"""Immunoglobulin superfamily / I-set domain containing"", ""WAP four-disulfide core domain containing"""	30916	protein-coding gene	gene with protein product	"""WAP four-disulfide core domain 20B"""	610895				11928817, 12709070	Standard	NM_175575		Approved	WFIKKNRP, WFDC20B	uc002isv.4	Q8TEU8	OTTHUMG00000162274	ENST00000311378.4:c.54G>A	17.37:g.48913352G>A		110.0	0.0	0		107.0	63.0	0.588785	NM_175575	Q6UXZ9	Silent	SNP	ENST00000311378.4	37	CCDS11575.1																																																																																			G|0.982;A|0.018	0.018	strong		0.682	WFIKKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368358.1	NM_175575	
NOTCH4	4855	hgsc.bcm.edu	37	6	32184785	32184785	+	Missense_Mutation	SNP	C	C	G	rs11963697	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32184785C>G	ENST00000375023.3	-	11	1936	c.1798G>C	c.(1798-1800)Gtt>Ctt	p.V600L	NOTCH4_ENST00000465528.1_5'Flank	NM_004557.3	NP_004548.3	Q99466	NOTC4_HUMAN	notch 4	600	EGF-like 15; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				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						CTGGCTCCAACGGGACATGGG	0.567													C|||	14	0.00279553	0.0098	0.0014	5008	,	,		19616	0.0		0.0	False		,,,				2504	0.0				p.V600L		Atlas-SNP	.											.	NOTCH4	201	.	0			c.G1798C						PASS	.	C	LEU/VAL	14,3008		0,14,1497	120.0	92.0	102.0		1798	-7.7	0.0	6	dbSNP_120	102	0,5418		0,0,2709	yes	missense	NOTCH4	NM_004557.3	32	0,14,4206	GG,GC,CC		0.0,0.4633,0.1659	benign	600/2004	32184785	14,8426	1511	2709	4220	SO:0001583	missense	4855	exon11			CTCCAACGGGACA		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.1798G>C	6.37:g.32184785C>G	ENSP00000364163:p.Val600Leu	178.0	0.0	0		210.0	95.0	0.452381	NM_004557	B0V183|B0V1X5|O00306|Q5SSY7|Q99458|Q99940|Q9H3S8|Q9UII9|Q9UIJ0	Missense_Mutation	SNP	ENST00000375023.3	37	CCDS34420.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	5.110	0.205944	0.09704	0.004633	0.0	ENSG00000204301	ENST00000375023	D	0.92299	-3.01	4.07	-7.74	0.01241	EGF-like calcium-binding, conserved site (1);EGF (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	1.351570	0.05567	N	0.570461	T	0.75324	0.3834	L	0.29908	0.895	0.09310	N	1	B;B	0.21606	0.058;0.006	B;B	0.31191	0.125;0.003	T	0.72168	-0.4372	10	0.72032	D	0.01	.	7.0248	0.24934	0.0:0.3431:0.3629:0.294	rs11963697;rs11963697	600;600	Q6P3V5;Q99466	.;NOTC4_HUMAN	L	600	ENSP00000364163:V600L	ENSP00000364163:V600L	V	-	1	0	NOTCH4	32292763	0.000000	0.05858	0.001000	0.08648	0.070000	0.16714	-2.805000	0.00758	-1.167000	0.02779	-0.251000	0.11542	GTT	C|0.989;G|0.011;T|0.000	0.011	strong		0.567	NOTCH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076045.2		
PREB	10113	hgsc.bcm.edu	37	2	27354306	27354306	+	Silent	SNP	C	C	T	rs61276776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27354306C>T	ENST00000260643.2	-	9	1483	c.1230G>A	c.(1228-1230)caG>caA	p.Q410Q	PREB_ENST00000406567.3_Silent_p.Q352Q|PREB_ENST00000416802.1_5'Flank	NM_013388.4	NP_037520.1	Q9HCU5	PREB_HUMAN	prolactin regulatory element binding	410					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER to Golgi vesicle-mediated transport (GO:0006888)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)	14	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GAAAGGCACTCTGGAGCAGCA	0.577													C|||	48	0.00958466	0.0325	0.0072	5008	,	,		19726	0.0		0.0	False		,,,				2504	0.0				p.Q410Q		Atlas-SNP	.											.	PREB	37	.	0			c.G1230A						PASS	.	C		113,4285		3,107,2089	61.0	57.0	58.0		1230	5.1	1.0	2	dbSNP_129	58	1,8563		0,1,4281	no	coding-synonymous	PREB	NM_013388.4		3,108,6370	TT,TC,CC		0.0117,2.5693,0.8795		410/418	27354306	114,12848	2199	4282	6481	SO:0001819	synonymous_variant	10113	exon9			GGCACTCTGGAGC		CCDS1738.1	2p23	2013-01-10			ENSG00000138073	ENSG00000138073		"""WD repeat domain containing"""	9356	protein-coding gene	gene with protein product		606395				10194769, 12735795	Standard	NM_013388		Approved	SEC12	uc002rix.1	Q9HCU5	OTTHUMG00000097076	ENST00000260643.2:c.1230G>A	2.37:g.27354306C>T		96.0	0.0	0		87.0	38.0	0.436782	NM_013388	Q53SZ8|Q9UH94	Silent	SNP	ENST00000260643.2	37	CCDS1738.1	17	0.007783882783882784	13	0.026422764227642278	4	0.011049723756906077	0	0.0	0	0.0	C	14.76	2.630999	0.46944	0.025693	1.17E-4	ENSG00000138073	ENST00000456259	.	.	.	5.05	5.05	0.67936	.	.	.	.	.	T	0.45796	0.1360	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58521	-0.7622	4	.	.	.	-19.6044	13.7879	0.63121	0.0:1.0:0.0:0.0	rs61276776	.	.	.	K	153	.	.	R	-	2	0	PREB	27207810	0.977000	0.34250	1.000000	0.80357	0.997000	0.91878	1.333000	0.33816	2.611000	0.88343	0.655000	0.94253	AGA	C|0.989;T|0.011	0.011	strong		0.577	PREB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214195.1	NM_013388	
DCAF15	90379	hgsc.bcm.edu	37	19	14066772	14066772	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14066772T>C	ENST00000254337.6	+	4	436	c.415T>C	c.(415-417)Tac>Cac	p.Y139H	PODNL1_ENST00000538517.2_5'Flank|PODNL1_ENST00000588317.1_5'Flank|PODNL1_ENST00000538371.2_5'Flank	NM_138353.2	NP_612362.2	Q66K64	DCA15_HUMAN	DDB1 and CUL4 associated factor 15	139					protein ubiquitination (GO:0016567)					breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)	11						CAGCGACCTGTACCTGACCGT	0.642																																					p.Y139H		Atlas-SNP	.											.	DCAF15	30	.	0			c.T415C						PASS	.						110.0	101.0	104.0					19																	14066772		2203	4300	6503	SO:0001583	missense	90379	exon4			GACCTGTACCTGA	BC002926	CCDS32926.1	19p13.12	2009-07-17	2009-07-17	2009-07-17	ENSG00000132017	ENSG00000132017		"""DDB1 and CUL4 associated factors"""	25095	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 72"""	C19orf72			Standard	NM_138353		Approved	MGC99481	uc002mxt.3	Q66K64		ENST00000254337.6:c.415T>C	19.37:g.14066772T>C	ENSP00000254337:p.Tyr139His	87.0	0.0	0		113.0	5.0	0.0442478	NM_138353	B3KS86|Q96DW0|Q9BU31	Missense_Mutation	SNP	ENST00000254337.6	37	CCDS32926.1	.	.	.	.	.	.	.	.	.	.	t	13.68	2.309631	0.40895	.	.	ENSG00000132017	ENST00000254337	.	.	.	4.02	4.02	0.46733	.	0.000000	0.64402	D	0.000006	T	0.40247	0.1109	L	0.43152	1.355	0.47276	D	0.999373	P	0.42456	0.78	B	0.35353	0.201	T	0.28522	-1.0041	9	0.28530	T	0.3	-18.254	12.2557	0.54623	0.0:0.0:0.0:1.0	.	139	Q66K64	DCA15_HUMAN	H	139	.	ENSP00000254337:Y139H	Y	+	1	0	DCAF15	13927772	1.000000	0.71417	1.000000	0.80357	0.385000	0.30292	7.528000	0.81941	1.610000	0.50200	0.459000	0.35465	TAC	.	.	none		0.642	DCAF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458099.1	NM_138353	
HBS1L	10767	hgsc.bcm.edu	37	6	135359073	135359073	+	Intron	SNP	G	G	A	rs115458424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:135359073G>A	ENST00000367837.5	-	4	637				HBS1L_ENST00000445176.2_Intron|HBS1L_ENST00000367824.4_Intron|HBS1L_ENST00000367820.2_Intron|HBS1L_ENST00000367826.2_Intron|HBS1L_ENST00000415177.2_Intron|HBS1L_ENST00000367822.5_Silent_p.P174P|HBS1L_ENST00000525067.1_Missense_Mutation_p.P112L|HBS1L_ENST00000314674.3_Silent_p.P174P	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase						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)		CAAAATCAAAGGGTTTGCTAC	0.343													G|||	91	0.0181709	0.0628	0.0072	5008	,	,		21502	0.0		0.001	False		,,,				2504	0.002				p.P174P		Atlas-SNP	.											.	HBS1L	75	.	0			c.C522T						PASS	.						100.0	73.0	81.0					6																	135359073		692	1590	2282	SO:0001627	intron_variant	10767	exon5			ATCAAAGGGTTTG	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.430+1637C>T	6.37:g.135359073G>A		115.0	0.0	0		126.0	70.0	0.555556	NM_001145207	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Silent	SNP	ENST00000367837.5	37	CCDS5173.1	38	0.0173992673992674	33	0.06707317073170732	5	0.013812154696132596	0	0.0	0	0.0	G	1.871	-0.460307	0.04508	.	.	ENSG00000112339	ENST00000525067	.	.	.	5.23	-0.875	0.10628	.	.	.	.	.	T	0.18257	0.0438	.	.	.	0.09310	N	0.999995	.	.	.	.	.	.	T	0.33059	-0.9883	5	0.87932	D	0	.	3.928	0.09272	0.3333:0.0:0.2811:0.3855	.	.	.	.	L	112	.	ENSP00000435608:P112L	P	-	2	0	HBS1L	135400766	0.568000	0.26635	0.283000	0.24790	0.501000	0.33797	0.566000	0.23593	-0.076000	0.12775	0.650000	0.86243	CCT	G|0.979;A|0.021	0.021	strong		0.343	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2		
PCNT	5116	hgsc.bcm.edu	37	21	47754576	47754576	+	Missense_Mutation	SNP	A	A	C	rs200285580		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:47754576A>C	ENST00000359568.5	+	3	640	c.533A>C	c.(532-534)cAa>cCa	p.Q178P	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	178					brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					AGTGACCACCAACCGGAACAG	0.537																																					p.Q178P		Atlas-SNP	.											.	PCNT	283	.	0			c.A533C						PASS	.						205.0	139.0	161.0					21																	47754576		2203	4300	6503	SO:0001583	missense	5116	exon3			ACCACCAACCGGA	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.533A>C	21.37:g.47754576A>C	ENSP00000352572:p.Gln178Pro	293.0	0.0	0		333.0	48.0	0.144144	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	.	.	.	.	.	.	.	.	.	.	C	3.018	-0.202461	0.06219	.	.	ENSG00000160299	ENST00000359568;ENST00000337772	T	0.01258	5.09	0.235	0.235	0.15431	.	.	.	.	.	T	0.00754	0.0025	N	0.03608	-0.345	0.09310	N	1	B;B	0.20368	0.044;0.026	B;B	0.13407	0.009;0.004	T	0.47849	-0.9085	8	0.30854	T	0.27	.	.	.	.	.	60;178	O95613-2;O95613	.;PCNT_HUMAN	P	178;165	ENSP00000352572:Q178P	ENSP00000338675:Q165P	Q	+	2	0	PCNT	46579004	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	-2.630000	0.00871	0.263000	0.21812	0.260000	0.18958	CAA	A|0.999;G|0.001	.	alt		0.537	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
GPR150	285601	hgsc.bcm.edu	37	5	94957071	94957071	+	Silent	SNP	A	A	T	rs375018988	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:94957071A>T	ENST00000380007.2	+	1	1290	c.1092A>T	c.(1090-1092)cgA>cgT	p.R364R		NM_199243.1	NP_954713.1	Q8NGU9	GP150_HUMAN	G protein-coupled receptor 150	364						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			lung(2)	2		all_cancers(142;0.000462)|all_epithelial(76;2.44e-06)|all_lung(232;0.0318)|Lung NSC(167;0.041)|Ovarian(225;0.051)		all cancers(79;1.82e-16)		GGCTCCGGCGACAGCTGCGGA	0.726													A|||	3	0.000599042	0.0023	0.0	5008	,	,		12900	0.0		0.0	False		,,,				2504	0.0				p.R364R		Atlas-SNP	.											.	GPR150	7	.	0			c.A1092T						PASS	.	A		12,3928		0,12,1958	4.0	6.0	5.0		1092	2.7	0.3	5		5	0,7982		0,0,3991	no	coding-synonymous	GPR150	NM_199243.1		0,12,5949	TT,TA,AA		0.0,0.3046,0.1007		364/435	94957071	12,11910	1970	3991	5961	SO:0001819	synonymous_variant	285601	exon1			CCGGCGACAGCTG	BC030197	CCDS4074.1	5q15	2012-08-21			ENSG00000178015	ENSG00000178015		"""GPCR / Class A : Orphans"""	23628	protein-coding gene	gene with protein product						12679517	Standard	NM_199243		Approved	PGR11	uc003kle.1	Q8NGU9	OTTHUMG00000121170	ENST00000380007.2:c.1092A>T	5.37:g.94957071A>T		21.0	0.0	0		21.0	14.0	0.666667	NM_199243		Silent	SNP	ENST00000380007.2	37	CCDS4074.1																																																																																			.	.	weak		0.726	GPR150-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241657.2		
GCAT	23464	hgsc.bcm.edu	37	22	38211728	38211728	+	Silent	SNP	A	A	G	rs34340481	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:38211728A>G	ENST00000248924.6	+	7	929	c.873A>G	c.(871-873)ccA>ccG	p.P291P	GCAT_ENST00000323205.6_Silent_p.P317P	NM_014291.3	NP_055106.1	O75600	KBL_HUMAN	glycine C-acetyltransferase	291					biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)|L-threonine catabolic process to glycine (GO:0019518)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	glycine C-acetyltransferase activity (GO:0008890)|pyridoxal phosphate binding (GO:0030170)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	12	Melanoma(58;0.045)				Glycine(DB00145)	GCGCCCGGCCATACCTCTTCT	0.642													A|||	228	0.0455272	0.1649	0.0115	5008	,	,		17865	0.0		0.002	False		,,,				2504	0.0				p.P317P		Atlas-SNP	.											.	GCAT	27	.	0			c.A951G						PASS	.	A	,	584,3822	255.5+/-260.7	37,510,1656	88.0	97.0	94.0		951,873	-0.2	1.0	22	dbSNP_126	94	24,8576	15.3+/-51.7	0,24,4276	no	coding-synonymous,coding-synonymous	GCAT	NM_001171690.1,NM_014291.3	,	37,534,5932	GG,GA,AA		0.2791,13.2547,4.6748	,	317/446,291/420	38211728	608,12398	2203	4300	6503	SO:0001819	synonymous_variant	23464	exon7			CCGGCCATACCTC	AF077740	CCDS13957.1, CCDS54527.1	22q13.1	2010-01-19	2010-01-19		ENSG00000100116	ENSG00000100116	2.3.1.29		4188	protein-coding gene	gene with protein product	"""2-amino-3-ketobutyrate coenzyme A ligase"""	607422	"""glycine C-acetyltransferase (2-amino-3-ketobutyrate coenzyme A ligase)"""				Standard	NM_014291		Approved	KBL	uc003aua.2	O75600	OTTHUMG00000150664	ENST00000248924.6:c.873A>G	22.37:g.38211728A>G		214.0	0.0	0		263.0	119.0	0.452471	NM_001171690	E2QC23|Q6ZWF1|Q96CA9	Silent	SNP	ENST00000248924.6	37	CCDS13957.1																																																																																			A|0.958;G|0.042	0.042	strong		0.642	GCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319506.1	NM_014291.2	
LY75	4065	hgsc.bcm.edu	37	2	160738803	160738803	+	Missense_Mutation	SNP	G	G	A	rs35675007	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160738803G>A	ENST00000263636.4	-	7	1105	c.1078C>T	c.(1078-1080)Cgc>Tgc	p.R360C	LY75_ENST00000554112.1_Missense_Mutation_p.R360C|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.R360C|LY75_ENST00000553424.1_Missense_Mutation_p.R360C|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.R360C	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	360					endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		GCATCACAGCGGGTATCTGAG	0.398													G|||	19	0.00379393	0.0121	0.0	5008	,	,		22106	0.001		0.0	False		,,,				2504	0.002				p.R360C		Atlas-SNP	.											LY75,NS,carcinoma,+1,1	LY75	151	1	0			c.C1078T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG	44,4362	48.2+/-83.0	0,44,2159	114.0	111.0	112.0		1078,1078,1078	5.6	0.9	2	dbSNP_126	112	16,8584	11.9+/-42.8	0,16,4284	yes	missense,missense,missense	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	180,180,180	0,60,6443	AA,AG,GG		0.186,0.9986,0.4613	possibly-damaging,possibly-damaging,possibly-damaging	360/1874,360/1818,360/1723	160738803	60,12946	2203	4300	6503	SO:0001583	missense	4065	exon7			CACAGCGGGTATC	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.1078C>T	2.37:g.160738803G>A	ENSP00000263636:p.Arg360Cys	77.0	0.0	0		77.0	27.0	0.350649	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	17.54	3.416115	0.62511	0.009986	0.00186	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.07444	3.19;3.19;3.19;3.19;3.19	5.57	5.57	0.84162	C-type lectin-like (1);	1.087950	0.07314	U	0.876324	T	0.14399	0.0348	L	0.43152	1.355	0.19300	N	0.99998	B;D;D	0.76494	0.272;0.999;0.999	B;P;P	0.56278	0.072;0.724;0.795	T	0.29912	-0.9996	10	0.54805	T	0.06	0.0491	14.2185	0.65809	0.0:0.2692:0.7308:0.0	rs35675007	360;360;360	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	C	360	ENSP00000451511:R360C;ENSP00000451446:R360C;ENSP00000263636:R360C;ENSP00000423463:R360C;ENSP00000421035:R360C	ENSP00000423463:R360C	R	-	1	0	LY75;LY75-CD302	160447049	0.995000	0.38212	0.857000	0.33713	0.986000	0.74619	2.505000	0.45424	2.632000	0.89209	0.650000	0.86243	CGC	G|0.996;A|0.004	0.004	strong		0.398	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
PPARGC1B	133522	hgsc.bcm.edu	37	5	149200008	149200008	+	Missense_Mutation	SNP	G	G	A	rs45518035	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149200008G>A	ENST00000309241.5	+	2	123	c.91G>A	c.(91-93)Ggg>Agg	p.G31R	PPARGC1B_ENST00000394320.3_Missense_Mutation_p.G31R|PPARGC1B_ENST00000360453.4_Missense_Mutation_p.G31R|PPARGC1B_ENST00000403750.1_Missense_Mutation_p.G6R	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	31	Abolishes DNA transcriptional activity when missing.				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)			TGGAGGGTCCGGGGAGGAGCA	0.572													G|||	41	0.0081869	0.0295	0.0029	5008	,	,		17247	0.0		0.0	False		,,,				2504	0.0				p.G31R		Atlas-SNP	.											.	PPARGC1B	74	.	0			c.G91A						PASS	.	G	ARG/GLY,ARG/GLY,ARG/GLY	96,4310	78.3+/-116.7	3,90,2110	83.0	90.0	88.0		91,16,91	5.8	0.9	5	dbSNP_127	88	2,8598	1.2+/-3.3	0,2,4298	yes	missense,missense,missense	PPARGC1B	NM_001172698.1,NM_001172699.1,NM_133263.3	125,125,125	3,92,6408	AA,AG,GG		0.0233,2.1788,0.7535	probably-damaging,probably-damaging,probably-damaging	31/985,6/960,31/1024	149200008	98,12908	2203	4300	6503	SO:0001583	missense	133522	exon2			GGGTCCGGGGAGG	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.91G>A	5.37:g.149200008G>A	ENSP00000312649:p.Gly31Arg	30.0	0.0	0		45.0	28.0	0.622222	NM_133263	A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Missense_Mutation	SNP	ENST00000309241.5	37	CCDS4298.1	8	0.003663003663003663	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	g	22.2	4.254416	0.80135	0.021788	2.33E-4	ENSG00000155846	ENST00000360453;ENST00000394320;ENST00000309241;ENST00000403750	T;T;T;T	0.16073	2.37;2.46;2.49;2.75	5.76	5.76	0.90799	.	0.096989	0.64402	D	0.000001	T	0.27594	0.0678	M	0.73217	2.22	0.50632	D	0.999885	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.987;0.999	P;P;P;P;D	0.67548	0.875;0.905;0.875;0.558;0.952	T	0.07888	-1.0749	10	0.87932	D	0	-33.0089	19.9678	0.97275	0.0:0.0:1.0:0.0	rs45518035	10;10;31;31;31	Q86YN6-2;Q86YN6-4;Q86YN6-5;Q86YN6;Q86YN6-3	.;.;.;PRGC2_HUMAN;.	R	31;31;31;6	ENSP00000353638:G31R;ENSP00000377855:G31R;ENSP00000312649:G31R;ENSP00000384403:G6R	ENSP00000312649:G31R	G	+	1	0	PPARGC1B	149180201	1.000000	0.71417	0.930000	0.37139	0.301000	0.27625	7.339000	0.79282	2.724000	0.93272	0.651000	0.88453	GGG	G|0.994;A|0.006	0.006	strong		0.572	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263	
ERBB2	2064	hgsc.bcm.edu	37	17	37863268	37863268	+	Silent	SNP	G	G	A	rs4252610	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:37863268G>A	ENST00000269571.5	+	2	258	c.99G>A	c.(97-99)ctG>ctA	p.L33L	ERBB2_ENST00000406381.2_Silent_p.L3L|ERBB2_ENST00000541774.1_Silent_p.L18L|ERBB2_ENST00000445658.2_Intron|ERBB2_ENST00000540042.1_Silent_p.L3L|ERBB2_ENST00000584450.1_Silent_p.L33L|ERBB2_ENST00000578199.1_Silent_p.L3L|ERBB2_ENST00000584601.1_Silent_p.L3L|ERBB2_ENST00000540147.1_Silent_p.L3L			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	33					axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	ACATGAAGCTGCGGCTCCCTG	0.637		1	"""A, Mis, O"""		"""breast, ovarian, other tumour types, NSCLC, gastric"""					TCGA GBM(5;<1E-08)			G|||	90	0.0179712	0.0673	0.0014	5008	,	,		17261	0.0		0.0	False		,,,				2504	0.0				p.L33L		Atlas-SNP	.		Dom	yes		17	17q21.1	2064	"""v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"""		E	.	ERBB2	429	.	0			c.G99A						PASS	.	G	,	206,4192		5,196,1998	40.0	35.0	37.0		9,99	2.0	1.0	17	dbSNP_111	37	0,8584		0,0,4292	no	coding-synonymous,coding-synonymous	ERBB2	NM_001005862.1,NM_004448.2	,	5,196,6290	AA,AG,GG		0.0,4.6839,1.5868	,	3/1226,33/1256	37863268	206,12776	2199	4292	6491	SO:0001819	synonymous_variant	2064	exon2			GAAGCTGCGGCTC	X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"""CD molecules"""	3430	protein-coding gene	gene with protein product	"""neuro/glioblastoma derived oncogene homolog"""	164870	"""v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"""	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.99G>A	17.37:g.37863268G>A		128.0	0.0	0		137.0	63.0	0.459854	NM_004448	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Silent	SNP	ENST00000269571.5	37	CCDS32642.1																																																																																			G|0.982;A|0.018	0.018	strong		0.637	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2		
PCDHAC2	56134	hgsc.bcm.edu	37	5	140346670	140346670	+	Silent	SNP	C	C	A	rs155809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140346670C>A	ENST00000289269.5	+	1	851	c.319C>A	c.(319-321)Cgg>Agg	p.R107R	PCDHA11_ENST00000398640.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHAC1_ENST00000253807.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA13_ENST00000409494.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA3_ENST00000522353.2_Intron	NM_018899.5|NM_031883.2	NP_061722.1|NP_114089.1	Q9Y5I4	PCDC2_HUMAN	protocadherin alpha subfamily C, 2	107	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|liver(2)|lung(9)|ovary(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	45			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGCATTGATCGGGAGGCGCT	0.642													C|||	79	0.0157748	0.0567	0.0058	5008	,	,		18549	0.0		0.0	False		,,,				2504	0.0				p.R107R	Melanoma(190;638 2083 3390 11909 52360)	Atlas-SNP	.											.	PCDHAC2	142	.	0			c.C319A						PASS	.	C	,,,,,,,,,,,,,,,,,,	252,4154	137.7+/-173.5	5,242,1956	34.0	35.0	35.0		,319,,,,,,,,,,,,,,,,,319	5.7	1.0	5	dbSNP_79	35	1,8599	1.2+/-3.3	0,1,4299	no	intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHAC2,PCDHAC1,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018898.3,NM_018899.5,NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018904.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031883.2	,,,,,,,,,,,,,,,,,,	5,243,6255	AA,AC,CC		0.0116,5.7195,1.9453	,,,,,,,,,,,,,,,,,,	,107/1008,,,,,,,,,,,,,,,,,107/885	140346670	253,12753	2203	4300	6503	SO:0001819	synonymous_variant	56134	exon1			ATTGATCGGGAGG	AF152474	CCDS4242.1	5q31	2010-11-26			ENSG00000243232	ENSG00000243232		"""Cadherins / Protocadherins : Clustered"""	8677	other	complex locus constituent		606321				10380929	Standard	NM_031883		Approved	PCDH-ALPHA-C2		Q9Y5I4	OTTHUMG00000129607	ENST00000289269.5:c.319C>A	5.37:g.140346670C>A		28.0	0.0	0		28.0	11.0	0.392857	NM_031883	Q2M3V1|Q9Y5F4	Silent	SNP	ENST00000289269.5	37	CCDS4242.1																																																																																			C|0.979;A|0.021	0.021	strong		0.642	PCDHAC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251802.2	NM_018899	
OAS2	4939	hgsc.bcm.edu	37	12	113444285	113444285	+	Silent	SNP	C	C	T	rs16942424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:113444285C>T	ENST00000342315.4	+	8	1750	c.1536C>T	c.(1534-1536)tcC>tcT	p.S512S	RP1-71H24.1_ENST00000552784.1_RNA|OAS2_ENST00000392583.2_Silent_p.S512S	NM_016817.2	NP_058197.2	P29728	OAS2_HUMAN	2'-5'-oligoadenylate synthetase 2, 69/71kDa	512	OAS domain 2.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|nucleobase-containing compound metabolic process (GO:0006139)|protein glycosylation (GO:0006486)|protein myristoylation (GO:0018377)|purine nucleotide biosynthetic process (GO:0006164)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						TGTATAAATCCTCGGACCTCC	0.522													C|||	172	0.034345	0.1203	0.0173	5008	,	,		16629	0.0		0.001	False		,,,				2504	0.0				p.S512S	Pancreas(199;709 2232 18410 33584 35052)	Atlas-SNP	.											.	OAS2	86	.	0			c.C1536T						PASS	.	C	,	399,4007		18,363,1822	88.0	88.0	88.0		1536,1536	-0.6	0.0	12	dbSNP_123	88	19,8581		0,19,4281	no	coding-synonymous,coding-synonymous	OAS2	NM_002535.2,NM_016817.2	,	18,382,6103	TT,TC,CC		0.2209,9.0558,3.2139	,	512/688,512/720	113444285	418,12588	2203	4300	6503	SO:0001819	synonymous_variant	4939	exon8			TAAATCCTCGGAC	M87284	CCDS31906.1, CCDS41839.1, CCDS44982.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111335			8087	protein-coding gene	gene with protein product		603350	"""2'-5'-oligoadenylate synthetase 2 (69-71 kD)"""			9790745	Standard	NM_002535		Approved		uc001tuj.3	P29728	OTTHUMG00000169802	ENST00000342315.4:c.1536C>T	12.37:g.113444285C>T		70.0	0.0	0		106.0	54.0	0.509434	NM_002535	A8K9T1|Q6PJ33|Q86XX8	Silent	SNP	ENST00000342315.4	37	CCDS31906.1																																																																																			C|0.957;T|0.043	0.043	strong		0.522	OAS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000405937.1		
MT-ND4	4538	hgsc.bcm.edu	37	M	11252	11252	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:11252A>G	ENST00000361381.2	+	1	493	c.493A>G	c.(493-495)Att>Gtt	p.I165V	MT-TR_ENST00000387439.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-TK_ENST00000387421.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	165					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						TCATCGCACTAATTTACACTC	0.473																																					p.I165V		Atlas-SNP	.											.	.	.	.	0			c.A493G						PASS	.																																			SO:0001583	missense	0	exon1			GCACTAATTTACA			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.493A>G	M.37:g.11252A>G	ENSP00000354961:p.Ile165Val	12.0	0.0	0		13.0	13.0	1	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Missense_Mutation	SNP	ENST00000361381.2	37																																																																																				A|0.936;G|0.064	0.064	strong		0.473	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
SLC25A37	51312	hgsc.bcm.edu	37	8	23429093	23429093	+	Missense_Mutation	SNP	G	G	T	rs116050502	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:23429093G>T	ENST00000519973.1	+	4	940	c.742G>T	c.(742-744)Gcc>Tcc	p.A248S	FP15737_ENST00000399967.3_5'Flank	NM_016612.2	NP_057696.2	Q9NYZ2	MFRN1_HUMAN	solute carrier family 25 (mitochondrial iron transporter), member 37	248					iron ion homeostasis (GO:0055072)|mitochondrial iron ion transport (GO:0048250)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	iron ion transmembrane transporter activity (GO:0005381)			NS(1)|endometrium(3)|large_intestine(2)|lung(8)|urinary_tract(1)	15		Prostate(55;0.114)		Colorectal(74;0.0198)|COAD - Colon adenocarcinoma(73;0.0751)		CGGGGCCCTCGCCGCGGCCGC	0.662													G|||	33	0.00658946	0.025	0.0	5008	,	,		12709	0.0		0.0	False		,,,				2504	0.0				p.A248S		Atlas-SNP	.											.	SLC25A37	27	.	0			c.G742T						PASS	.	G	SER/ALA	93,3715		1,91,1812	22.0	26.0	25.0		742	5.8	0.2	8	dbSNP_132	25	1,8197		0,1,4098	yes	missense	SLC25A37	NM_016612.2	99	1,92,5910	TT,TG,GG		0.0122,2.4422,0.7829	possibly-damaging	248/339	23429093	94,11912	1904	4099	6003	SO:0001583	missense	51312	exon4			GCCCTCGCCGCGG	AF495725	CCDS47828.1	8p21.2	2013-05-22	2012-03-29		ENSG00000147454	ENSG00000147454		"""Solute carriers"""	29786	protein-coding gene	gene with protein product	"""mitoferrin"""	610387	"""solute carrier family 25, member 37"""			16511496	Standard	XM_006716352		Approved	MSCP, MFRN, MFRN1	uc003xdo.3	Q9NYZ2	OTTHUMG00000163865	ENST00000519973.1:c.742G>T	8.37:g.23429093G>T	ENSP00000429200:p.Ala248Ser	50.0	0.0	0		65.0	40.0	0.615385	NM_016612	A2RU93|Q53FT7|Q69YJ8|Q969S1|Q9P0J2	Missense_Mutation	SNP	ENST00000519973.1	37	CCDS47828.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	20.5	3.994188	0.74703	0.024422	1.22E-4	ENSG00000147454	ENST00000519973	T	0.79653	-1.29	5.8	5.8	0.92144	Mitochondrial carrier domain (2);	0.049561	0.85682	D	0.000000	T	0.80149	0.4570	L	0.54965	1.715	0.58432	D	0.999999	D	0.58970	0.984	D	0.69479	0.964	D	0.84394	0.0556	10	0.66056	D	0.02	-8.3551	18.6148	0.91299	0.0:0.0:1.0:0.0	.	248	Q9NYZ2	MFRN1_HUMAN	S	248	ENSP00000429200:A248S	ENSP00000429200:A248S	A	+	1	0	SLC25A37	23485038	1.000000	0.71417	0.214000	0.23707	0.949000	0.60115	5.096000	0.64535	2.740000	0.93945	0.650000	0.86243	GCC	G|0.994;T|0.006	0.006	strong		0.662	SLC25A37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376039.1	NM_016612	
SP100	6672	hgsc.bcm.edu	37	2	231380146	231380146	+	Missense_Mutation	SNP	G	G	A	rs61733089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:231380146G>A	ENST00000264052.5	+	25	2786	c.2431G>A	c.(2431-2433)Gct>Act	p.A811T	SP100_ENST00000340126.4_Intron	NM_003113.3	NP_003104.2	P23497	SP100_HUMAN	SP100 nuclear antigen	811					cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cellular component movement (GO:0051271)|negative regulation of DNA binding (GO:0043392)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of protein export from nucleus (GO:0046826)|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 viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of angiogenesis (GO:0045765)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of Fas signaling pathway (GO:1902044)|response to cytokine (GO:0034097)|response to interferon-gamma (GO:0034341)|response to retinoic acid (GO:0032526)|response to type I interferon (GO:0034340)|retinoic acid receptor signaling pathway (GO:0048384)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear periphery (GO:0034399)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(4)|upper_aerodigestive_tract(1)	25		Renal(207;0.0112)|all_lung(227;0.0335)|all_hematologic(139;0.0749)|Lung NSC(271;0.142)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		GAATAACACCGCTGCAGCTGA	0.433													G|||	41	0.0081869	0.0287	0.0043	5008	,	,		19980	0.0		0.0	False		,,,				2504	0.0				p.A811T		Atlas-SNP	.											.	SP100	167	.	0			c.G2431A						PASS	.	G	,THR/ALA	125,4281	89.2+/-127.9	1,123,2079	47.0	49.0	49.0		,2431	0.2	0.1	2	dbSNP_129	49	0,8600		0,0,4300	yes	intron,missense	SP100	NM_001080391.1,NM_003113.3	,58	1,123,6379	AA,AG,GG		0.0,2.837,0.9611	,	,811/880	231380146	125,12881	2203	4300	6503	SO:0001583	missense	6672	exon25			AACACCGCTGCAG	AF056322	CCDS2477.1, CCDS42832.1, CCDS56170.1, CCDS56171.1, CCDS56172.1, CCDS56173.1	2q37.1	2013-01-28	2005-11-30		ENSG00000067066	ENSG00000067066		"""Zinc fingers, PHD-type"""	11206	protein-coding gene	gene with protein product		604585	"""nuclear antigen Sp100"""			2258622, 8695863	Standard	NM_001080391		Approved		uc002vqu.1	P23497	OTTHUMG00000133203	ENST00000264052.5:c.2431G>A	2.37:g.231380146G>A	ENSP00000264052:p.Ala811Thr	80.0	0.0	0		78.0	40.0	0.512821	NM_003113	B4DDX5|B8ZZD8|E7EUA7|E9PH61|F8WFE2|O75450|Q13343|Q8TE34|Q96F70|Q96T24|Q96T95|Q9NP33|Q9UE32	Missense_Mutation	SNP	ENST00000264052.5	37	CCDS2477.1	13	0.005952380952380952	11	0.022357723577235773	2	0.0055248618784530384	0	0.0	0	0.0	G	9.783	1.175944	0.21704	0.02837	0.0	ENSG00000067066	ENST00000264052	D	0.93189	-3.18	0.158	0.158	0.14942	High mobility group, HMG1/HMG2, subgroup (1);High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	.	.	.	.	T	0.69949	0.3168	L	0.33485	1.01	0.43347	D	0.995409	P	0.42078	0.77	B	0.34346	0.18	T	0.73636	-0.3920	9	0.87932	D	0	.	6.0348	0.19702	5.0E-4:0.0:0.9995:0.0	rs61733089	811	P23497	SP100_HUMAN	T	811	ENSP00000264052:A811T	ENSP00000264052:A811T	A	+	1	0	SP100	231088390	0.000000	0.05858	0.057000	0.19452	0.058000	0.15608	-0.122000	0.10627	0.202000	0.20498	0.205000	0.17691	GCT	G|0.991;A|0.009	0.009	strong		0.433	SP100-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256914.2	NM_003113	
RELN	5649	hgsc.bcm.edu	37	7	103205949	103205949	+	Silent	SNP	G	G	C	rs78221963	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:103205949G>C	ENST00000428762.1	-	34	5145	c.4986C>G	c.(4984-4986)acC>acG	p.T1662T	RELN_ENST00000424685.2_Silent_p.T1662T|RELN_ENST00000343529.5_Silent_p.T1662T	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	1662					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)		ACTGCAAAAAGGTAGATGCTG	0.423													G|||	41	0.0081869	0.0303	0.0014	5008	,	,		18251	0.0		0.0	False		,,,				2504	0.0				p.T1662T	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.C4986G						PASS	.	G	,	65,4341	59.9+/-96.7	0,65,2138	77.0	70.0	72.0		4986,4986	4.0	1.0	7	dbSNP_132	72	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	RELN	NM_005045.3,NM_173054.2	,	0,66,6437	CC,CG,GG		0.0116,1.4753,0.5075	,	1662/3461,1662/3459	103205949	66,12940	2203	4300	6503	SO:0001819	synonymous_variant	5649	exon34			CAAAAAGGTAGAT		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.4986C>G	7.37:g.103205949G>C		70.0	0.0	0		65.0	31.0	0.476923	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Silent	SNP	ENST00000428762.1	37	CCDS47680.1																																																																																			G|0.993;C|0.007	0.007	strong		0.423	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
CLUAP1	23059	hgsc.bcm.edu	37	16	3576475	3576475	+	Missense_Mutation	SNP	A	A	C	rs35603863	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3576475A>C	ENST00000576634.1	+	9	1063	c.919A>C	c.(919-921)Aag>Cag	p.K307Q	CLUAP1_ENST00000572600.1_Missense_Mutation_p.K141Q|CLUAP1_ENST00000571025.1_Missense_Mutation_p.K307Q|CLUAP1_ENST00000341633.5_Missense_Mutation_p.K307Q|CLUAP1_ENST00000417763.2_Missense_Mutation_p.K141Q|CLUAP1_ENST00000445795.2_Missense_Mutation_p.K66Q	NM_015041.2	NP_055856.1	Q96AJ1	CLUA1_HUMAN	clusterin associated protein 1	307					cilium assembly (GO:0042384)	centrosome (GO:0005813)|cilium (GO:0005929)|intracellular membrane-bounded organelle (GO:0043231)|intraciliary transport particle B (GO:0030992)|nucleus (GO:0005634)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(2)	16						GCGCCTGCTCAAGAGTGGAAG	0.418													A|||	78	0.0155751	0.056	0.0058	5008	,	,		15679	0.0		0.0	False		,,,				2504	0.0				p.K307Q		Atlas-SNP	.											.	CLUAP1	32	.	0			c.A919C						PASS	.	A	GLN/LYS,GLN/LYS	223,4171	127.0+/-164.0	5,213,1979	53.0	52.0	52.0		919,421	4.3	1.0	16	dbSNP_126	52	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	CLUAP1	NM_015041.1,NM_024793.1	53,53	5,214,6278	CC,CA,AA		0.0116,5.0751,1.7239	benign,benign	307/414,141/248	3576475	224,12770	2197	4300	6497	SO:0001583	missense	23059	exon9			CTGCTCAAGAGTG	BC017070	CCDS32381.1, CCDS45398.1	16p13.3	2014-07-18				ENSG00000103351		"""Intraflagellar transport homologs"""	19009	protein-coding gene	gene with protein product	"""flagellar associated protein 22, qilin-like protein, homolog (Chlamydomonas)"", ""cilia and flagella associated protein 22"""					15480429, 9734811, 19253336	Standard	NM_015041		Approved	FLJ13297, KIAA0643, FAP22, CFAP22	uc002cvk.2	Q96AJ1		ENST00000576634.1:c.919A>C	16.37:g.3576475A>C	ENSP00000460850:p.Lys307Gln	97.0	0.0	0		107.0	55.0	0.514019	NM_015041	O75138|Q65ZA3|Q9H8R4|Q9H8T1	Missense_Mutation	SNP	ENST00000576634.1	37	CCDS32381.1	27	0.012362637362637362	26	0.052845528455284556	1	0.0027624309392265192	0	0.0	0	0.0	A	11.85	1.761898	0.31228	0.050751	1.16E-4	ENSG00000103351	ENST00000341633;ENST00000417763;ENST00000445795	T;T;T	0.47869	1.55;0.83;0.84	5.41	4.3	0.51218	.	0.180820	0.64402	D	0.000017	T	0.09905	0.0243	M	0.64997	1.995	0.42629	D	0.993376	P;P;P	0.46706	0.813;0.498;0.883	B;B;B	0.41860	0.368;0.202;0.255	T	0.05683	-1.0870	10	0.14252	T	0.57	-26.918	10.7228	0.46050	0.8398:0.1602:0.0:0.0	rs35603863	141;307;66	Q96AJ1-2;Q96AJ1;B4DFY1	.;CLUA1_HUMAN;.	Q	307;141;66	ENSP00000344392:K307Q;ENSP00000388642:K141Q;ENSP00000397710:K66Q	ENSP00000344392:K307Q	K	+	1	0	CLUAP1	3516476	1.000000	0.71417	0.972000	0.41901	0.260000	0.26232	5.607000	0.67648	0.877000	0.35895	0.523000	0.50628	AAG	A|0.981;C|0.019	0.019	strong		0.418	CLUAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437883.2	NM_024793	
WHSC1L1	54904	hgsc.bcm.edu	37	8	38205133	38205133	+	Missense_Mutation	SNP	G	G	A	rs13034	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:38205133G>A	ENST00000317025.8	-	2	1074	c.557C>T	c.(556-558)aCg>aTg	p.T186M	WHSC1L1_ENST00000433384.2_Missense_Mutation_p.T186M|WHSC1L1_ENST00000527502.1_Missense_Mutation_p.T186M|WHSC1L1_ENST00000316985.3_Missense_Mutation_p.T186M	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1	186			T -> M (in dbSNP:rs13034).		histone lysine methylation (GO:0034968)|histone methylation (GO:0016571)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			CTTTGATTTCGTGTGCTCACT	0.373			T	NUP98	AML								G|||	74	0.0147764	0.0552	0.0014	5008	,	,		19666	0.0		0.0	False		,,,				2504	0.0				p.T186M		Atlas-SNP	.		Dom	yes		8	8p12	54904	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)		L	.	WHSC1L1	137	.	0			c.C557T						PASS	.	G	MET/THR,MET/THR	236,4170	139.6+/-175.2	5,226,1972	179.0	163.0	168.0		557,557	3.0	1.0	8	dbSNP_52	168	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	WHSC1L1	NM_017778.2,NM_023034.1	81,81	5,228,6270	AA,AG,GG		0.0233,5.3563,1.8299	benign,benign	186/646,186/1438	38205133	238,12768	2203	4300	6503	SO:0001583	missense	54904	exon2			GATTTCGTGTGCT	AF332469	CCDS6105.1, CCDS43729.1	8p11.2	2013-05-20			ENSG00000147548	ENSG00000147548			12767	protein-coding gene	gene with protein product		607083				10802047, 23269674	Standard	NM_023034		Approved	FLJ20353, NSD3	uc003xli.3	Q9BZ95		ENST00000317025.8:c.557C>T	8.37:g.38205133G>A	ENSP00000313983:p.Thr186Met	224.0	0.0	0		189.0	86.0	0.455026	NM_017778	B7ZL11|D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	Missense_Mutation	SNP	ENST00000317025.8	37	CCDS43729.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	G	10.27	1.303287	0.23736	0.053563	2.33E-4	ENSG00000147548	ENST00000433384;ENST00000317025;ENST00000446459;ENST00000527502;ENST00000316985;ENST00000529223	D;D;D;T;T	0.95238	-3.64;-3.65;-3.65;-0.15;0.87	5.7	2.96	0.34315	.	0.453371	0.17834	U	0.160431	T	0.65719	0.2718	L	0.29908	0.895	0.33540	D	0.594756	B;B;B;B	0.25390	0.125;0.079;0.078;0.06	B;B;B;B	0.18561	0.008;0.009;0.022;0.005	T	0.79662	-0.1710	10	0.66056	D	0.02	.	11.7413	0.51794	0.1932:0.0:0.8068:0.0	rs13034	186;186;186;186	B7ZL11;Q9BZ95-2;Q9BZ95-3;Q9BZ95	.;.;.;NSD3_HUMAN	M	186;186;123;186;186;186	ENSP00000393284:T186M;ENSP00000313983:T186M;ENSP00000434730:T186M;ENSP00000313410:T186M;ENSP00000435422:T186M	ENSP00000313410:T186M	T	-	2	0	WHSC1L1	38324290	0.999000	0.42202	0.997000	0.53966	0.896000	0.52359	1.040000	0.30278	0.348000	0.23949	-0.916000	0.02749	ACG	G|0.983;A|0.017	0.017	strong		0.373	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381924.3	NM_023034	
RGPD3	653489	hgsc.bcm.edu	37	2	107084716	107084716	+	Missense_Mutation	SNP	C	C	T	rs190902687	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:107084716C>T	ENST00000409886.3	-	1	116	c.29G>A	c.(28-30)cGg>cAg	p.R10Q	RGPD3_ENST00000304514.7_Missense_Mutation_p.R10Q	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	10					protein targeting to Golgi (GO:0000042)					breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						GGCGACGTACCGCTCCCCGTA	0.692													.|||	45	0.00898562	0.0318	0.0043	5008	,	,		11990	0.0		0.0	False		,,,				2504	0.0				p.R10Q		Atlas-SNP	.											.	RGPD3	316	.	0			c.G29A						PASS	.	C	GLN/ARG	26,1358		0,26,666	63.0	92.0	84.0		29	1.8	1.0	2		84	0,3182		0,0,1591	no	missense	RGPD3	NM_001144013.1	43	0,26,2257	TT,TC,CC		0.0,1.8786,0.5694	probably-damaging	10/1759	107084716	26,4540	692	1591	2283	SO:0001583	missense	653489	exon1			ACGTACCGCTCCC		CCDS46379.1	2q12.2	2013-01-10			ENSG00000153165	ENSG00000153165		"""Tetratricopeptide (TTC) repeat domain containing"""	32416	protein-coding gene	gene with protein product		612706				15710750, 15815621	Standard	NM_001144013		Approved	RGP3	uc010ywi.1	A6NKT7	OTTHUMG00000153182	ENST00000409886.3:c.29G>A	2.37:g.107084716C>T	ENSP00000386588:p.Arg10Gln	341.0	0.0	0		437.0	193.0	0.441648	NM_001144013	B8ZZM4	Missense_Mutation	SNP	ENST00000409886.3	37	CCDS46379.1	18	0.008241758241758242	16	0.032520325203252036	2	0.0055248618784530384	0	0.0	0	0.0	.	12.78	2.039118	0.35989	0.018786	0.0	ENSG00000153165	ENST00000409886;ENST00000304514	T;T	0.53857	0.6;0.6	1.8	1.8	0.24995	.	.	.	.	.	T	0.27313	0.0670	L	0.54323	1.7	0.23685	N	0.997116	D	0.58620	0.983	P	0.49192	0.602	T	0.18429	-1.0337	9	0.59425	D	0.04	-11.0149	7.0248	0.24934	0.0:1.0:0.0:0.0	.	10	A6NKT7	RGPD3_HUMAN	Q	10	ENSP00000386588:R10Q;ENSP00000303659:R10Q	ENSP00000303659:R10Q	R	-	2	0	RGPD3	106451148	1.000000	0.71417	0.989000	0.46669	0.038000	0.13279	3.375000	0.52410	0.984000	0.38629	0.186000	0.17326	CGG	C|0.992;T|0.008	0.008	strong		0.692	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931	
ITGAD	3681	hgsc.bcm.edu	37	16	31422531	31422531	+	Silent	SNP	T	T	C	rs368058587		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31422531T>C	ENST00000389202.2	+	13	1540	c.1491T>C	c.(1489-1491)ccT>ccC	p.P497P		NM_005353.2	NP_005344.2	Q13349	ITAD_HUMAN	integrin, alpha D	497					activated T cell proliferation (GO:0050798)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|integrin-mediated signaling pathway (GO:0007229)	cell surface (GO:0009986)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(2)|lung(43)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	71						GTCCCTTGCCTAGGGGGGTGA	0.627													t|||	1	0.000199681	0.0008	0.0	5008	,	,		15986	0.0		0.0	False		,,,				2504	0.0				p.P497P		Atlas-SNP	.											.	ITGAD	154	.	0			c.T1491C						PASS	.	T		2,4392	4.2+/-10.8	0,2,2195	82.0	79.0	80.0		1491	0.8	0.1	16		80	0,8600		0,0,4300	no	coding-synonymous	ITGAD	NM_005353.2		0,2,6495	CC,CT,TT		0.0,0.0455,0.0154		497/1162	31422531	2,12992	2197	4300	6497	SO:0001819	synonymous_variant	3681	exon13			CTTGCCTAGGGGG	U40274	CCDS32438.1	16p13.1-p11	2010-03-23				ENSG00000156886		"""CD molecules"", ""Integrins"""	6146	protein-coding gene	gene with protein product		602453				8666289, 9598326	Standard	NM_005353		Approved	CD11d, ADB2	uc002ebv.1	Q13349		ENST00000389202.2:c.1491T>C	16.37:g.31422531T>C		179.0	0.0	0		229.0	104.0	0.454148	NM_005353	Q15575|Q15576	Silent	SNP	ENST00000389202.2	37	CCDS32438.1																																																																																			.	.	weak		0.627	ITGAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432836.1	NM_005353	
SSPO	23145	hgsc.bcm.edu	37	7	149522163	149522163	+	RNA	SNP	C	C	G	rs73727642	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149522163C>G	ENST00000378016.2	+	0	13950							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GAGGAGGCTGCCGGGAGCCAT	0.652													C|||	192	0.0383387	0.1354	0.0187	5008	,	,		15887	0.0		0.0	False		,,,				2504	0.0				p.C4650W		Atlas-SNP	.											.	.	.	.	0			c.C13950G						PASS	.	C		374,3424		21,332,1546	19.0	25.0	23.0		13964	3.5	0.4	7	dbSNP_130	23	7,8195		0,7,4094	yes	coding-notMod3	SSPO	NM_198455.2		21,339,5640	GG,GC,CC		0.0853,9.8473,3.175			149522163	381,11619	1899	4101	6000			23145	exon96			AGGCTGCCGGGAG	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149522163C>G		85.0	0.0	0		66.0	23.0	0.348485	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.974;G|0.026	0.026	strong		0.652	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
CEP162	22832	hgsc.bcm.edu	37	6	84925636	84925636	+	Silent	SNP	A	A	C	rs9449840	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:84925636A>C	ENST00000403245.3	-	4	291	c.177T>G	c.(175-177)ctT>ctG	p.L59L	KIAA1009_ENST00000257766.4_5'UTR	NM_014895.2	NP_055710.2														breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	43		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)		TTGTTCCAAGAAGTCCTAGGT	0.328													C|||	366	0.0730831	0.2602	0.0245	5008	,	,		16242	0.002		0.001	False		,,,				2504	0.002				p.L59L		Atlas-SNP	.											.	KIAA1009	119	.	0			c.T177G						PASS	.	C		1020,3368		119,782,1293	37.0	36.0	36.0		177	-3.0	0.0	6	dbSNP_119	36	6,8568		0,6,4281	no	coding-synonymous	KIAA1009	NM_014895.2		119,788,5574	CC,CA,AA		0.07,23.2452,7.9154		59/1404	84925636	1026,11936	2194	4287	6481	SO:0001819	synonymous_variant	22832	exon4			TCCAAGAAGTCCT																												ENST00000403245.3:c.177T>G	6.37:g.84925636A>C		74.0	0.0	0		62.0	31.0	0.5	NM_014895		Silent	SNP	ENST00000403245.3	37	CCDS34494.2																																																																																			A|0.936;C|0.064	0.064	strong		0.328	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1		
C2orf43	60526	hgsc.bcm.edu	37	2	21001192	21001192	+	Missense_Mutation	SNP	A	A	G	rs139472393	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:21001192A>G	ENST00000237822.3	-	2	111	c.32T>C	c.(31-33)gTg>gCg	p.V11A	C2orf43_ENST00000435420.2_Missense_Mutation_p.V11A|C2orf43_ENST00000403006.2_Intron|C2orf43_ENST00000419825.2_Missense_Mutation_p.V11A|C2orf43_ENST00000440866.2_Missense_Mutation_p.V11A|C2orf43_ENST00000541941.1_Intron|C2orf43_ENST00000381090.3_Missense_Mutation_p.V11A	NM_001282721.1|NM_021925.2	NP_001269650.1|NP_068744.1	Q9H6V9	CB043_HUMAN	chromosome 2 open reading frame 43	11										endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|stomach(1)	6	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTCCTCATGCACAGGAATTTC	0.408													A|||	7	0.00139776	0.0053	0.0	5008	,	,		17655	0.0		0.0	False		,,,				2504	0.0				p.V11A		Atlas-SNP	.											.	C2orf43	28	.	0			c.T32C						PASS	.	A	ALA/VAL	21,4385	29.0+/-57.7	0,21,2182	82.0	84.0	84.0		32	5.9	1.0	2	dbSNP_134	84	0,8600		0,0,4300	yes	missense	C2orf43	NM_021925.2	64	0,21,6482	GG,GA,AA		0.0,0.4766,0.1615	possibly-damaging	11/326	21001192	21,12985	2203	4300	6503	SO:0001583	missense	60526	exon2			TCATGCACAGGAA	AK025473	CCDS1702.1, CCDS62864.1, CCDS74488.1, CCDS74489.1	2p24.1	2014-02-07			ENSG00000118961	ENSG00000118961			26145	protein-coding gene	gene with protein product		613570				17135363, 24357060	Standard	NM_001282723		Approved	FLJ21820	uc002rec.3	Q9H6V9	OTTHUMG00000122097	ENST00000237822.3:c.32T>C	2.37:g.21001192A>G	ENSP00000237822:p.Val11Ala	112.0	0.0	0		91.0	34.0	0.373626	NM_021925	B7ZA47|B7ZAJ5|D6W530|E7ESN0|Q53T37|Q53T58	Missense_Mutation	SNP	ENST00000237822.3	37	CCDS1702.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	A	16.00	2.998870	0.54147	0.004766	0.0	ENSG00000118961	ENST00000381090;ENST00000237822;ENST00000435420;ENST00000440866;ENST00000412261;ENST00000402479;ENST00000419825	.	.	.	5.94	5.94	0.96194	.	0.514514	0.19627	N	0.109780	T	0.50497	0.1619	L	0.44542	1.39	0.32473	N	0.54249	B;P;P;D;P;P	0.60575	0.349;0.852;0.952;0.988;0.852;0.852	B;B;P;P;B;B	0.49085	0.091;0.177;0.452;0.6;0.177;0.177	T	0.63567	-0.6608	9	0.62326	D	0.03	-8.1279	15.3805	0.74651	1.0:0.0:0.0:0.0	.	11;11;11;11;11;11	B4DS38;B4DRG3;B7ZAJ5;B4DWE2;Q9H6V9;B5MDU6	.;.;.;.;CB043_HUMAN;.	A	11	.	ENSP00000237822:V11A	V	-	2	0	C2orf43	20864673	0.996000	0.38824	0.992000	0.48379	0.114000	0.19823	5.670000	0.68088	2.279000	0.76181	0.459000	0.35465	GTG	A|0.999;G|0.001	0.001	strong		0.408	C2orf43-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242861.1	NM_021925	
GPR85	54329	hgsc.bcm.edu	37	7	112724147	112724147	+	Silent	SNP	G	G	A	rs28392728	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:112724147G>A	ENST00000297146.3	-	3	1233	c.630C>T	c.(628-630)caC>caT	p.H210H	GPR85_ENST00000449591.1_Silent_p.H210H|GPR85_ENST00000501255.2_Silent_p.H210H|GPR85_ENST00000487573.1_5'Flank|GPR85_ENST00000424100.1_Silent_p.H210H	NM_001146266.1	NP_001139738.1	P60893	GPR85_HUMAN	G protein-coupled receptor 85	210					signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	17						TTCTTCGATCGTGGACGAAAA	0.498													G|||	97	0.019369	0.0703	0.0058	5008	,	,		19678	0.0		0.0	False		,,,				2504	0.0				p.H210H		Atlas-SNP	.											.	GPR85	49	.	0			c.C630T						PASS	.	G	,,,	296,4110	162.2+/-194.2	11,274,1918	56.0	55.0	55.0		630,630,630,630	-1.6	0.9	7	dbSNP_125	55	3,8597	1.2+/-3.3	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GPR85	NM_001146265.1,NM_001146266.1,NM_001146267.1,NM_018970.6	,,,	11,277,6215	AA,AG,GG		0.0349,6.7181,2.2989	,,,	210/371,210/371,210/371,210/371	112724147	299,12707	2203	4300	6503	SO:0001819	synonymous_variant	54329	exon3			TCGATCGTGGACG	AF250237	CCDS5758.1	7q31	2012-08-21			ENSG00000164604	ENSG00000164604		"""GPCR / Class A : Orphans"""	4536	protein-coding gene	gene with protein product		605188				10978537, 10833454	Standard	NM_018970		Approved	SREB2	uc003vgp.1	P60893	OTTHUMG00000156933	ENST00000297146.3:c.630C>T	7.37:g.112724147G>A		91.0	0.0	0		94.0	39.0	0.414894	NM_001146265	Q9JHI6|Q9NPD1	Silent	SNP	ENST00000297146.3	37	CCDS5758.1																																																																																			G|0.978;A|0.022	0.022	strong		0.498	GPR85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346650.2		
HAS1	3036	hgsc.bcm.edu	37	19	52223026	52223026	+	Silent	SNP	C	C	A	rs61736497	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52223026C>A	ENST00000222115.1	-	2	169	c.135G>T	c.(133-135)ccG>ccT	p.P45P	HAS1_ENST00000540069.2_Silent_p.P44P|HAS1_ENST00000601714.1_Silent_p.P52P|HAS1_ENST00000594621.1_5'Flank	NM_001523.2	NP_001514.2	Q92839	HYAS1_HUMAN	hyaluronan synthase 1	45					carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan biosynthetic process (GO:0030213)|hyaluronan metabolic process (GO:0030212)|negative regulation of fibroblast migration (GO:0010764)|small molecule metabolic process (GO:0044281)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronan synthase activity (GO:0050501)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(4)	40		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00102)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		CGGAGGCCAGCGGCACCCCGG	0.711													c|||	271	0.0541134	0.1891	0.0202	5008	,	,		12432	0.0		0.003	False		,,,				2504	0.0041				p.P45P	NSCLC(132;636 2450 45807 47979)	Atlas-SNP	.											.	HAS1	61	.	0			c.G135T						PASS	.	C		634,3594		36,562,1516	5.0	7.0	6.0		135	-6.3	1.0	19	dbSNP_129	6	8,8282		0,8,4137	no	coding-synonymous	HAS1	NM_001523.2		36,570,5653	AA,AC,CC		0.0965,14.9953,5.1286		45/579	52223026	642,11876	2114	4145	6259	SO:0001819	synonymous_variant	3036	exon2			GGCCAGCGGCACC	U59269	CCDS12838.1, CCDS74436.1	19q13.3-q13.4	2013-02-22			ENSG00000105509	ENSG00000105509	2.4.1.212	"""Glycosyltransferase family 2 domain containing"""	4818	protein-coding gene	gene with protein product		601463		HAS		9169154	Standard	XM_005258834		Approved		uc002pxo.1	Q92839		ENST00000222115.1:c.135G>T	19.37:g.52223026C>A		20.0	0.0	0		27.0	16.0	0.592593	NM_001523	Q14470|Q9NS49	Silent	SNP	ENST00000222115.1	37	CCDS12838.1																																																																																			C|0.947;A|0.053	0.053	strong		0.711	HAS1-005	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466953.1	NM_001523	
UBE4B	10277	hgsc.bcm.edu	37	1	10211588	10211588	+	Silent	SNP	G	G	A	rs149899336	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:10211588G>A	ENST00000253251.8	+	20	3347	c.2508G>A	c.(2506-2508)ttG>ttA	p.L836L	UBE4B_ENST00000377157.3_Silent_p.L720L|UBE4B_ENST00000343090.6_Silent_p.L965L					ubiquitination factor E4B											NS(3)|breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(14)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	48		all_lung(284;1.13e-05)|Lung NSC(185;1.74e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0268)|Colorectal(212;1.42e-07)|COAD - Colon adenocarcinoma(227;2.77e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000435)|Kidney(185;0.000482)|KIRC - Kidney renal clear cell carcinoma(229;0.00164)|STAD - Stomach adenocarcinoma(132;0.0117)|READ - Rectum adenocarcinoma(331;0.046)		CCACCAAGTTGTTGGTACCTT	0.453													G|||	3	0.000599042	0.0023	0.0	5008	,	,		22768	0.0		0.0	False		,,,				2504	0.0				p.L965L		Atlas-SNP	.											.	UBE4B	233	.	0			c.G2895A						PASS	.	G	,	15,4391	22.3+/-47.3	0,15,2188	166.0	152.0	157.0		2895,2508	4.2	0.9	1	dbSNP_134	157	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	UBE4B	NM_001105562.2,NM_006048.4	,	0,15,6488	AA,AG,GG		0.0,0.3404,0.1153	,	965/1303,836/1174	10211588	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	10277	exon21			CAAGTTGTTGGTA	AF091093	CCDS110.1, CCDS41245.1	1p36.1	2013-01-28	2011-05-19		ENSG00000130939	ENSG00000130939		"""U-box domain containing"""	12500	protein-coding gene	gene with protein product		613565	"""ubiquitination factor E4B (homologous to yeast UFD2)"", ""ubiquitination factor E4B (UFD2 homolog, yeast)"""			9734811, 10089879	Standard	NM_006048		Approved	UBOX3, E4, UFD2, KIAA0684	uc001aqs.4	O95155	OTTHUMG00000001797	ENST00000253251.8:c.2508G>A	1.37:g.10211588G>A		179.0	0.0	0		179.0	86.0	0.480447	NM_001105562		Silent	SNP	ENST00000253251.8	37	CCDS110.1																																																																																			G|0.999;A|0.001	0.001	strong		0.453	UBE4B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005017.1	NM_006048	
FNDC3A	22862	hgsc.bcm.edu	37	13	49775997	49775997	+	Missense_Mutation	SNP	A	A	G	rs45604939	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:49775997A>G	ENST00000492622.2	+	24	3354	c.3049A>G	c.(3049-3051)Aca>Gca	p.T1017A	FNDC3A_ENST00000398316.3_Missense_Mutation_p.T961A|FNDC3A_ENST00000541916.1_Missense_Mutation_p.T1017A	NM_001079673.1	NP_001073141.1	Q9Y2H6	FND3A_HUMAN	fibronectin type III domain containing 3A	1017	Fibronectin type-III 8. {ECO:0000255|PROSITE-ProRule:PRU00316}.				fertilization (GO:0009566)|Sertoli cell development (GO:0060009)|single organismal cell-cell adhesion (GO:0016337)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle membrane (GO:0012506)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(3)|large_intestine(10)|lung(15)|prostate(5)|skin(2)|urinary_tract(1)	41		all_lung(13;7.44e-08)|Lung NSC(96;4.08e-06)|Breast(56;0.000111)|Prostate(109;0.00174)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;2.94e-09)		TAATGAGTCAACATCCTATAA	0.368													A|||	127	0.0253594	0.0008	0.0476	5008	,	,		15155	0.0		0.0676	False		,,,				2504	0.0256				p.T1017A		Atlas-SNP	.											.	FNDC3A	93	.	0			c.A3049G						PASS	.	A	ALA/THR,ALA/THR	52,4354	50.9+/-86.3	0,52,2151	94.0	95.0	94.0		3049,2881	3.7	1.0	13	dbSNP_127	94	602,7996	158.2+/-211.7	19,564,3716	yes	missense,missense	FNDC3A	NM_001079673.1,NM_014923.3	58,58	19,616,5867	GG,GA,AA		7.0016,1.1802,5.0292	possibly-damaging,possibly-damaging	1017/1199,961/1143	49775997	654,12350	2203	4299	6502	SO:0001583	missense	22862	exon24			GAGTCAACATCCT	AB023187	CCDS9413.2, CCDS41886.1	13q14.12	2013-02-11	2005-01-20	2005-01-22	ENSG00000102531	ENSG00000102531		"""Fibronectin type III domain containing"""	20296	protein-coding gene	gene with protein product		615794	"""fibronectin type III domain containing 3"""	FNDC3			Standard	NM_001079673		Approved	bA203I16.5, KIAA0970	uc001vcm.3	Q9Y2H6	OTTHUMG00000016911	ENST00000492622.2:c.3049A>G	13.37:g.49775997A>G	ENSP00000417257:p.Thr1017Ala	116.0	0.0	0		149.0	77.0	0.516779	NM_001079673	B4DYG1|Q5HYC9|Q5JVF8|Q5JVF9|Q6EVH3|Q6EVH4|Q6N020|Q6P9D5|Q6ZME4|Q9H1W1	Missense_Mutation	SNP	ENST00000492622.2	37	CCDS41886.1	68	0.031135531135531136	1	0.0020325203252032522	18	0.049723756906077346	0	0.0	49	0.06464379947229551	A	22.8	4.334633	0.81801	0.011802	0.070016	ENSG00000102531	ENST00000492622;ENST00000337156;ENST00000541916;ENST00000398316	T;T;T	0.61627	0.09;0.09;0.09	6.16	3.66	0.41972	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.079122	0.52532	D	0.000074	T	0.21509	0.0518	M	0.87547	2.89	0.80722	D	1	D;P	0.64830	0.994;0.597	D;P	0.68765	0.96;0.531	T	0.54794	-0.8240	10	0.48119	T	0.1	-24.27	9.0647	0.36455	0.7455:0.1304:0.0:0.1241	rs45604939	961;1017	Q9Y2H6-2;Q9Y2H6	.;FND3A_HUMAN	A	1017;953;1017;961	ENSP00000417257:T1017A;ENSP00000441831:T1017A;ENSP00000381362:T961A	ENSP00000338579:T953A	T	+	1	0	FNDC3A	48673998	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	8.904000	0.92590	0.515000	0.28320	0.528000	0.53228	ACA	A|0.954;G|0.046	0.046	strong		0.368	FNDC3A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354845.2	NM_014923	
PPL	5493	hgsc.bcm.edu	37	16	4935258	4935258	+	Missense_Mutation	SNP	A	A	T	rs145318499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4935258A>T	ENST00000345988.2	-	22	3487	c.3398T>A	c.(3397-3399)cTc>cAc	p.L1133H	PPL_ENST00000590782.2_Missense_Mutation_p.L1131H	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1133					keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						TTGGCGGGTGAGATCGCTGAC	0.627													A|||	13	0.00259585	0.0091	0.0014	5008	,	,		12714	0.0		0.0	False		,,,				2504	0.0				p.L1133H		Atlas-SNP	.											.	PPL	168	.	0			c.T3398A						PASS	.						79.0	71.0	74.0					16																	4935258		2197	4300	6497	SO:0001583	missense	5493	exon22			CGGGTGAGATCGC	AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.3398T>A	16.37:g.4935258A>T	ENSP00000340510:p.Leu1133His	151.0	0.0	0		149.0	54.0	0.362416	NM_002705	O60314|O60454|Q14C98	Missense_Mutation	SNP	ENST00000345988.2	37	CCDS10526.1	.	.	.	.	.	.	.	.	.	.	A	15.98	2.992856	0.54041	.	.	ENSG00000118898	ENST00000345988	T	0.43688	0.94	5.17	5.17	0.71159	.	0.000000	0.64402	D	0.000001	T	0.66626	0.2808	M	0.80746	2.51	0.49130	D	0.99975	D	0.89917	1.0	D	0.91635	0.999	T	0.72327	-0.4327	10	0.87932	D	0	.	15.0069	0.71519	1.0:0.0:0.0:0.0	.	1133	O60437	PEPL_HUMAN	H	1133	ENSP00000340510:L1133H	ENSP00000340510:L1133H	L	-	2	0	PPL	4875259	1.000000	0.71417	0.064000	0.19789	0.868000	0.49771	9.292000	0.96076	1.967000	0.57214	0.459000	0.35465	CTC	.	.	weak		0.627	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
CIZ1	25792	hgsc.bcm.edu	37	9	130938650	130938650	+	Silent	SNP	G	G	A	rs45475893	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:130938650G>A	ENST00000393608.1	-	11	2125	c.1923C>T	c.(1921-1923)gaC>gaT	p.D641D	CIZ1_ENST00000476727.2_Intron|CIZ1_ENST00000538431.1_Silent_p.D641D|CIZ1_ENST00000325721.8_Silent_p.D612D|CIZ1_ENST00000357558.5_Silent_p.D613D|CIZ1_ENST00000372948.3_Silent_p.D585D|CIZ1_ENST00000372954.1_Silent_p.D561D|CIZ1_ENST00000372938.5_Silent_p.D641D|CIZ1_ENST00000541172.1_Silent_p.D540D|CIZ1_ENST00000277465.4_Silent_p.D613D	NM_012127.2	NP_036259.2	Q9ULV3	CIZ1_HUMAN	CDKN1A interacting zinc finger protein 1	641					maintenance of protein location in nucleus (GO:0051457)|positive regulation of DNA-dependent DNA replication initiation (GO:0032298)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|liver(1)|lung(9)|ovary(3)|prostate(2)|urinary_tract(2)	35						TCTCCAGGACGTCCCGGGGCA	0.637													G|||	22	0.00439297	0.0151	0.0029	5008	,	,		19335	0.0		0.0	False		,,,				2504	0.0				p.D671D		Atlas-SNP	.											.	CIZ1	75	.	0			c.C2013T						PASS	.	G	,,,,	75,4331	67.0+/-104.6	0,75,2128	98.0	103.0	101.0		1755,1923,1740,1683,1923	-8.3	0.0	9	dbSNP_127	101	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CIZ1	NM_001131015.1,NM_001131016.1,NM_001131017.1,NM_001131018.1,NM_012127.2	,,,,	0,76,6427	AA,AG,GG		0.0116,1.7022,0.5843	,,,,	585/843,641/899,580/838,561/819,641/899	130938650	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	25792	exon11			CAGGACGTCCCGG	AB030835	CCDS6894.1, CCDS48033.1, CCDS48034.1, CCDS75910.1	9q34.1	2012-10-05			ENSG00000148337	ENSG00000148337			16744	protein-coding gene	gene with protein product		611420				10529385	Standard	NM_001131015		Approved	LSFR1, ZNF356	uc011mas.2	Q9ULV3	OTTHUMG00000020735	ENST00000393608.1:c.1923C>T	9.37:g.130938650G>A		102.0	0.0	0		119.0	86.0	0.722689	NM_001257975	A8K9J8|B4E131|B7ZAS8|Q5SYW3|Q5SYW5|Q8WU72|Q9H868|Q9NYM8|Q9UHK4|Q9Y3F9|Q9Y3G0	Silent	SNP	ENST00000393608.1	37	CCDS6894.1																																																																																			G|0.994;A|0.006	0.006	strong		0.637	CIZ1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054399.1	NM_012127	
OR51S1	119692	hgsc.bcm.edu	37	11	4869792	4869792	+	Missense_Mutation	SNP	A	A	G	rs57238061	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:4869792A>G	ENST00000322101.2	-	1	722	c.647T>C	c.(646-648)tTg>tCg	p.L216S	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004758.1	NP_001004758.1	Q8NGJ8	O51S1_HUMAN	olfactory receptor, family 51, subfamily S, member 1	216						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(15)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		CAGGGGGTCCAAACCCATGGC	0.527													A|||	307	0.0613019	0.2209	0.0202	5008	,	,		18029	0.0		0.001	False		,,,				2504	0.0				p.L216S		Atlas-SNP	.											.	OR51S1	83	.	0			c.T647C						PASS	.	A	SER/LEU	791,3611	318.8+/-295.8	72,647,1482	78.0	82.0	80.0		647	4.1	1.0	11	dbSNP_129	80	11,8585	8.4+/-32.0	0,11,4287	yes	missense	OR51S1	NM_001004758.1	145	72,658,5769	GG,GA,AA		0.128,17.9691,6.1702	probably-damaging	216/324	4869792	802,12196	2201	4298	6499	SO:0001583	missense	119692	exon1			GGGTCCAAACCCA	AB065796	CCDS31362.1	11p15.4	2012-08-09			ENSG00000176922	ENSG00000176922		"""GPCR / Class A : Olfactory receptors"""	15204	protein-coding gene	gene with protein product							Standard	NM_001004758		Approved		uc010qyo.2	Q8NGJ8	OTTHUMG00000066506	ENST00000322101.2:c.647T>C	11.37:g.4869792A>G	ENSP00000322754:p.Leu216Ser	77.0	0.0	0		83.0	45.0	0.542169	NM_001004758	B9EGZ1|Q6IFI2	Missense_Mutation	SNP	ENST00000322101.2	37	CCDS31362.1	113	0.051739926739926737	105	0.21341463414634146	8	0.022099447513812154	0	0.0	0	0.0	A	16.28	3.079144	0.55753	0.179691	0.00128	ENSG00000176922	ENST00000322101	T	0.44482	0.92	5.25	4.09	0.47781	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36002	N	0.002844	T	0.00039	0.0001	L	0.43923	1.385	0.54753	P	1.799999999996249E-5	P	0.39535	0.677	B	0.39419	0.299	T	0.11567	-1.0582	9	0.51188	T	0.08	-6.8936	10.3194	0.43756	0.9202:0.0:0.0798:0.0	rs57238061;rs61746907	216	Q8NGJ8	O51S1_HUMAN	S	216	ENSP00000322754:L216S	ENSP00000322754:L216S	L	-	2	0	OR51S1	4826368	0.007000	0.16637	0.966000	0.40874	0.681000	0.39784	2.118000	0.41949	2.203000	0.70933	0.533000	0.62120	TTG	A|0.944;G|0.056	0.056	strong		0.527	OR51S1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142179.1	NM_001004758	
OR8U1	219417	hgsc.bcm.edu	37	11	56143113	56143113	+	Missense_Mutation	SNP	A	A	G	rs116344671	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:56143113A>G	ENST00000302270.1	+	1	14	c.14A>G	c.(13-15)aAt>aGt	p.N5S		NM_001005204.1	NP_001005204.1	Q8NH10	OR8U1_HUMAN	olfactory receptor, family 8, subfamily U, member 1	5						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(23)|ovary(4)|skin(1)|stomach(1)	39	Esophageal squamous(21;0.00448)					GCTCACATCAATTGCACCCAG	0.403													A|||	234	0.0467252	0.1649	0.0216	5008	,	,		15937	0.0		0.001	False		,,,				2504	0.0				p.N5S		Atlas-SNP	.											.	OR8U1	59	.	0			c.A14G						PASS	.	A	SER/ASN	496,3212		36,424,1394	93.0	85.0	88.0		14	5.9	0.4	11	dbSNP_132	88	8,8180		0,8,4086	yes	missense	OR8U1	NM_001005204.1	46	36,432,5480	GG,GA,AA		0.0977,13.3765,4.2367	probably-damaging	5/310	56143113	504,11392	1854	4094	5948	SO:0001583	missense	219417	exon1			ACATCAATTGCAC	AB065603	CCDS41647.1	11q11	2012-08-09			ENSG00000172199	ENSG00000172199		"""GPCR / Class A : Olfactory receptors"""	19611	protein-coding gene	gene with protein product							Standard	NM_001005204		Approved			Q8NH10	OTTHUMG00000166860	ENST00000302270.1:c.14A>G	11.37:g.56143113A>G	ENSP00000304188:p.Asn5Ser	156.0	0.0	0		197.0	99.0	0.502538	NM_001005204		Missense_Mutation	SNP	ENST00000302270.1	37	CCDS41647.1	89	0.04075091575091575	79	0.16056910569105692	9	0.024861878453038673	0	0.0	1	0.0013192612137203166	A	8.024	0.760291	0.15914	0.133765	9.77E-4	ENSG00000172199	ENST00000302270	T	0.14640	2.49	5.87	5.87	0.94306	.	0.000000	0.51477	D	0.000094	T	0.00109	0.0003	M	0.87269	2.87	0.50632	P	1.1200000000000099E-4	B	0.32051	0.354	B	0.35114	0.196	T	0.11792	-1.0573	9	0.87932	D	0	.	8.66	0.34086	0.8549:0.0:0.1451:0.0	.	5	Q8NH10	OR8U1_HUMAN	S	5	ENSP00000304188:N5S	ENSP00000304188:N5S	N	+	2	0	OR8U1	55899689	0.994000	0.37717	0.396000	0.26296	0.042000	0.13812	3.480000	0.53172	2.247000	0.74100	0.523000	0.50628	AAT	A|0.974;G|0.026	0.026	strong		0.403	OR8U1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391607.1	NM_001005204	
MOB3A	126308	hgsc.bcm.edu	37	19	2078424	2078424	+	Silent	SNP	G	G	T	rs34059622	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2078424G>T	ENST00000357066.3	-	3	515	c.136C>A	c.(136-138)Cgg>Agg	p.R46R	MOB3A_ENST00000592143.1_Intron|MOB3A_ENST00000592280.1_Silent_p.R46R	NM_130807.2	NP_570719.1	Q96BX8	MOB3A_HUMAN	MOB kinase activator 3A	46						intracellular (GO:0005622)	metal ion binding (GO:0046872)										ACGGCCAGCCGCAGGTCCAGC	0.637													G|||	64	0.0127796	0.0461	0.0043	5008	,	,		15140	0.0		0.0	False		,,,				2504	0.0				p.R46R		Atlas-SNP	.											.	.	.	.	0			c.C136A						PASS	.	G		170,4236	112.5+/-150.6	4,162,2037	51.0	54.0	53.0		136	-2.5	0.3	19	dbSNP_126	53	2,8596	2.2+/-6.3	0,2,4297	no	coding-synonymous	MOB3A	NM_130807.2		4,164,6334	TT,TG,GG		0.0233,3.8584,1.3227		46/218	2078424	172,12832	2203	4299	6502	SO:0001819	synonymous_variant	126308	exon3			CCAGCCGCAGGTC	AK095471	CCDS12081.1	19p13.3	2011-09-28	2011-09-28	2011-09-28	ENSG00000172081	ENSG00000172081		"""MOB kinase activators"""	29802	protein-coding gene	gene with protein product	"""MOB LAK"""		"""MOB1, Mps One Binder kinase activator-like 2A (yeast)"""	MOBKL2A		12477932	Standard	NM_130807		Approved	MOB1C, MOB-LAK, moblak	uc002luv.3	Q96BX8		ENST00000357066.3:c.136C>A	19.37:g.2078424G>T		65.0	0.0	0		55.0	28.0	0.509091	NM_130807	B3KTF1|O75249|Q8TF69	Silent	SNP	ENST00000357066.3	37	CCDS12081.1																																																																																			G|0.982;T|0.018	0.018	strong		0.637	MOB3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450893.1	NM_130807	
TTN	7273	hgsc.bcm.edu	37	2	179611680	179611680	+	Intron	SNP	G	G	A	rs72648911	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179611680G>A	ENST00000591111.1	-	46	10585				TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Intron|TTN_ENST00000360870.5_Silent_p.Y5149Y|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Intron			Q8WZ42	TITIN_HUMAN	titin						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)			CTGTAGGTGTGTAGAAATGCT	0.413													A|||	235	0.0469249	0.1725	0.0101	5008	,	,		19409	0.0		0.0	False		,,,				2504	0.0				p.Y5149Y		Atlas-SNP	.											.	TTN	18412	.	0			c.C15447T						PASS	.	A	,,,,	667,3739	763.1+/-413.2	50,567,1586	138.0	134.0	135.0		,,15447,,	-2.6	0.9	2	dbSNP_130	135	8,8590	818.5+/-406.9	0,8,4291	no	intron,intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	50,575,5877	AA,AG,GG		0.093,15.1384,5.1907	,,,,	,,5149/5605,,	179611680	675,12329	2203	4299	6502	SO:0001627	intron_variant	7273	exon46			AGGTGTGTAGAAA	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.10361-5032C>T	2.37:g.179611680G>A		181.0	0.0	0		190.0	99.0	0.521053	NM_133379	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																																																																																				G|0.954;A|0.046	0.046	strong		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
PKD1L1	168507	hgsc.bcm.edu	37	7	47955167	47955167	+	Silent	SNP	A	A	G	rs17131941	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:47955167A>G	ENST00000289672.2	-	8	1140	c.1090T>C	c.(1090-1092)Ttg>Ctg	p.L364L		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	364					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						GACATAtccaactgaaaatgt	0.323													A|||	90	0.0179712	0.0658	0.0043	5008	,	,		16011	0.0		0.0	False		,,,				2504	0.0				p.L364L		Atlas-SNP	.											.	PKD1L1	328	.	0			c.T1090C						PASS	.	A		173,4233	113.3+/-151.4	3,167,2033	78.0	76.0	77.0		1090	0.4	0.0	7	dbSNP_123	77	0,8600		0,0,4300	no	coding-synonymous	PKD1L1	NM_138295.3		3,167,6333	GG,GA,AA		0.0,3.9265,1.3302		364/2850	47955167	173,12833	2203	4300	6503	SO:0001819	synonymous_variant	168507	exon8			TATCCAACTGAAA	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.1090T>C	7.37:g.47955167A>G		46.0	0.0	0		43.0	24.0	0.55814	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	37	CCDS34633.1																																																																																			A|0.981;G|0.019	0.019	strong		0.323	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
HIP1	3092	hgsc.bcm.edu	37	7	75221693	75221693	+	Silent	SNP	C	C	T	rs144446822	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:75221693C>T	ENST00000336926.6	-	3	350	c.324G>A	c.(322-324)ccG>ccA	p.P108P	HIP1_ENST00000434438.2_Silent_p.P108P	NM_005338.5	NP_005329.3	O00291	HIP1_HUMAN	huntingtin interacting protein 1	108	ENTH. {ECO:0000255|PROSITE- ProRule:PRU00243}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|positive regulation of receptor-mediated endocytosis (GO:0048260)|regulation of apoptotic process (GO:0042981)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	clathrin-coated vesicle (GO:0030136)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	clathrin binding (GO:0030276)|phosphatidylinositol binding (GO:0035091)|structural constituent of cytoskeleton (GO:0005200)			breast(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						AACTCACGTTCGGGTGTCCAT	0.597			T	PDGFRB	CMML								C|||	6	0.00119808	0.0045	0.0	5008	,	,		20231	0.0		0.0	False		,,,				2504	0.0				p.P108P		Atlas-SNP	.		Dom	yes		7	7q11.23	3092	huntingtin interacting protein 1		L	.	HIP1	91	.	0			c.G324A						PASS	.	C		15,4391	22.3+/-47.3	0,15,2188	59.0	50.0	53.0		324	-11.6	0.0	7	dbSNP_134	53	0,8600		0,0,4300	no	coding-synonymous	HIP1	NM_005338.5		0,15,6488	TT,TC,CC		0.0,0.3404,0.1153		108/1038	75221693	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	3092	exon3			CACGTTCGGGTGT	AF052288	CCDS34669.1, CCDS59060.1	7q11.23	2008-07-18			ENSG00000127946	ENSG00000127946			4913	protein-coding gene	gene with protein product		601767				9140394, 9147654	Standard	NM_005338		Approved	ILWEQ	uc003uds.2	O00291	OTTHUMG00000156050	ENST00000336926.6:c.324G>A	7.37:g.75221693C>T		49.0	0.0	0		54.0	35.0	0.648148	NM_005338	B4E3I7|E7ES17|O00328|Q2TB58|Q8TDL4	Silent	SNP	ENST00000336926.6	37	CCDS34669.1																																																																																			C|0.999;T|0.001	0.001	strong		0.597	HIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342863.2	NM_005338	
TMEM41B	440026	hgsc.bcm.edu	37	11	9305136	9305136	+	Silent	SNP	G	G	A	rs77349011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:9305136G>A	ENST00000528080.1	-	7	1049	c.711C>T	c.(709-711)gtC>gtT	p.V237V	TMEM41B_ENST00000527813.1_Missense_Mutation_p.S191L	NM_015012.3	NP_055827.1	Q5BJD5	TM41B_HUMAN	transmembrane protein 41B	237					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(1)|prostate(1)|urinary_tract(2)	7				all cancers(16;9.96e-08)|Epithelial(150;4.89e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0972)		AAGGAGGTGCGACACCTGAAA	0.333													G|||	356	0.0710863	0.2557	0.0231	5008	,	,		14041	0.0		0.002	False		,,,				2504	0.0				p.V237V		Atlas-SNP	.											TMEM41B,NS,haematopoietic_neoplasm,0,1	TMEM41B	22	1	0			c.C711T						PASS	.	G		876,3526	335.5+/-303.9	87,702,1412	45.0	43.0	44.0		711	0.6	1.0	11	dbSNP_131	44	9,8583	7.1+/-27.0	0,9,4287	no	coding-synonymous	TMEM41B	NM_015012.3		87,711,5699	AA,AG,GG		0.1047,19.9,6.8108		237/292	9305136	885,12109	2201	4296	6497	SO:0001819	synonymous_variant	440026	exon7			AGGTGCGACACCT	D26067	CCDS31424.1, CCDS53600.1	11p15.3	2008-02-05			ENSG00000166471	ENSG00000166471			28948	protein-coding gene	gene with protein product						7584026, 7584028	Standard	NM_015012		Approved	KIAA0033	uc001mhn.2	Q5BJD5	OTTHUMG00000165719	ENST00000528080.1:c.711C>T	11.37:g.9305136G>A		58.0	0.0	0		33.0	33.0	1	NM_015012	D3DQU9|E9PP29|Q15055|Q4G0P0	Silent	SNP	ENST00000528080.1	37	CCDS31424.1	109	0.04990842490842491	102	0.2073170731707317	7	0.019337016574585635	0	0.0	0	0.0	G	11.73	1.724415	0.30593	0.199	0.001047	ENSG00000166471	ENST00000527813	.	.	.	5.55	0.652	0.17823	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.17137	-1.0379	4	0.59425	D	0.04	-12.5515	1.822	0.03112	0.415:0.2125:0.2657:0.1069	.	.	.	.	L	191	.	ENSP00000435685:S191L	S	-	2	0	TMEM41B	9261712	0.806000	0.28996	0.997000	0.53966	0.830000	0.47004	0.020000	0.13466	-0.132000	0.11557	-1.004000	0.02495	TCG	G|0.941;A|0.059	0.059	strong		0.333	TMEM41B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385940.2		
CASP4	837	hgsc.bcm.edu	37	11	104825597	104825597	+	Missense_Mutation	SNP	C	C	T	rs56226603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:104825597C>T	ENST00000444739.2	-	2	1049	c.139G>A	c.(139-141)Gat>Aat	p.D47N	CASP4_ENST00000531333.1_5'UTR|CASP4_ENST00000393150.3_5'UTR	NM_001225.3	NP_001216.1	P49662	CASP4_HUMAN	caspase 4, apoptosis-related cysteine peptidase	47	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.		D -> N (in dbSNP:rs56226603).		apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|proteolysis (GO:0006508)|regulation of apoptotic process (GO:0042981)|regulation of inflammatory response (GO:0050727)	AIM2 inflammasome complex (GO:0097169)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|IPAF inflammasome complex (GO:0072557)|membrane (GO:0016020)|mitochondrion (GO:0005739)|NLRP3 inflammasome complex (GO:0072559)	cysteine-type endopeptidase activity (GO:0004197)			central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(1)|skin(1)|urinary_tract(2)	23		Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Melanoma(852;0.0047)		BRCA - Breast invasive adenocarcinoma(274;0.000854)|Epithelial(105;0.00879)|all cancers(92;0.0357)		GTTTTAGCATCGTAATATTTC	0.398													C|||	136	0.0271565	0.0946	0.0159	5008	,	,		19636	0.0		0.0	False		,,,				2504	0.0				p.D47N		Atlas-SNP	.											.	CASP4	57	.	0			c.G139A						PASS	.	C	ASN/ASP,	361,4043	185.0+/-212.2	22,317,1863	226.0	209.0	215.0		139,	0.0	0.0	11	dbSNP_129	215	1,8597	1.2+/-3.3	0,1,4298	yes	missense,utr-5	CASP4	NM_001225.3,NM_033306.2	23,	22,318,6161	TT,TC,CC		0.0116,8.1971,2.7842	benign,	47/378,	104825597	362,12640	2202	4299	6501	SO:0001583	missense	837	exon2			TAGCATCGTAATA	U25804	CCDS8327.1, CCDS41704.1	11q22.2-q22.3	2006-02-17	2005-08-17		ENSG00000196954	ENSG00000196954		"""Caspases"""	1505	protein-coding gene	gene with protein product		602664	"""caspase 4, apoptosis-related cysteine protease"""			7797510, 9250871	Standard	NM_001225		Approved	ICE(rel)II, ICH-2, TX	uc001pid.1	P49662	OTTHUMG00000166078	ENST00000444739.2:c.139G>A	11.37:g.104825597C>T	ENSP00000388566:p.Asp47Asn	181.0	0.0	0		180.0	60.0	0.333333	NM_001225	A2NHL8|A2NHM0	Missense_Mutation	SNP	ENST00000444739.2	37	CCDS8327.1	65	0.02976190476190476	57	0.11585365853658537	8	0.022099447513812154	0	0.0	0	0.0	C	0.022	-1.408830	0.01155	0.081971	1.16E-4	ENSG00000196954	ENST00000444739;ENST00000417440	T;T	0.19394	2.15;2.15	3.04	0.0232	0.14136	DEATH-like (2);Caspase Recruitment (3);	0.704837	0.13761	N	0.364575	T	0.00073	0.0002	N	0.02357	-0.585	0.09310	N	0.999999	B;B;B	0.33288	0.406;0.007;0.002	B;B;B	0.26969	0.075;0.006;0.006	T	0.27123	-1.0083	10	0.02654	T	1	.	6.0472	0.19766	0.0:0.469:0.0:0.531	rs56226603;rs61751520	47;47;47	B4DJH5;B4E2D2;P49662	.;.;CASP4_HUMAN	N	47	ENSP00000388566:D47N;ENSP00000401673:D47N	ENSP00000401673:D47N	D	-	1	0	CASP4	104330807	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.945000	0.03909	0.002000	0.14630	-0.140000	0.14226	GAT	C|0.969;T|0.031	0.031	strong		0.398	CASP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387751.1	NM_001225	
GRB10	2887	hgsc.bcm.edu	37	7	50742326	50742326	+	Missense_Mutation	SNP	T	T	C	rs185094083	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:50742326T>C	ENST00000401949.1	-	6	638	c.169A>G	c.(169-171)Aac>Gac	p.N57D	GRB10_ENST00000402578.1_5'UTR|GRB10_ENST00000335866.3_5'UTR|GRB10_ENST00000439599.1_Missense_Mutation_p.N51D|GRB10_ENST00000402497.1_5'UTR|GRB10_ENST00000406641.1_5'UTR|GRB10_ENST00000403097.1_Missense_Mutation_p.N51D|GRB10_ENST00000357271.5_Missense_Mutation_p.N57D|GRB10_ENST00000398812.2_Missense_Mutation_p.N57D|GRB10_ENST00000407526.1_5'UTR|GRB10_ENST00000398810.2_5'UTR			Q13322	GRB10_HUMAN	growth factor receptor-bound protein 10	57					insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of glucose import (GO:0046325)|negative regulation of glycogen biosynthetic process (GO:0045719)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of phosphorylation (GO:0042326)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of phosphorylation (GO:0042327)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|response to insulin (GO:0032868)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	insulin receptor binding (GO:0005158)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(19)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	41	Glioma(55;0.08)|all_neural(89;0.245)					TTCATATCGTTCACCAGGGCT	0.522									Russell-Silver syndrome				T|||	14	0.00279553	0.0106	0.0	5008	,	,		21544	0.0		0.0	False		,,,				2504	0.0				p.N57D		Atlas-SNP	.											.	GRB10	155	.	0			c.A169G						PASS	.	T	ASP/ASN,,,ASP/ASN	21,4061		0,21,2020	57.0	59.0	59.0		169,,,169	4.5	1.0	7		59	1,8411		0,1,4205	yes	missense,utr-5,utr-5,missense	GRB10	NM_001001549.2,NM_001001550.2,NM_001001555.2,NM_005311.4	23,,,23	0,22,6225	CC,CT,TT		0.0119,0.5145,0.1761	probably-damaging,,,probably-damaging	57/549,,,57/595	50742326	22,12472	2041	4206	6247	SO:0001583	missense	2887	exon3	Familial Cancer Database	Silver-Russell Dwarfism, Silver-Russell syndrome, SRS, Russel-Silver Dwarfism	TATCGTTCACCAG		CCDS43582.1, CCDS43583.1, CCDS47586.1	7p12.2	2013-02-14			ENSG00000106070	ENSG00000106070		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	4564	protein-coding gene	gene with protein product		601523					Standard	NM_005311		Approved		uc003tpi.2	Q13322	OTTHUMG00000150622	ENST00000401949.1:c.169A>G	7.37:g.50742326T>C	ENSP00000385770:p.Asn57Asp	66.0	0.0	0		67.0	26.0	0.38806	NM_005311	A4D258|A7VJ95|A8K0E6|D3DVM9|O00427|O00701|O75222|Q92606|Q92907|Q92948	Missense_Mutation	SNP	ENST00000401949.1	37	CCDS43582.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	T	25.0	4.597321	0.87055	0.005145	1.19E-4	ENSG00000106070	ENST00000398812;ENST00000439599;ENST00000403097;ENST00000357271;ENST00000401949;ENST00000439044	D;D;D;D;D;T	0.87571	-1.97;-1.97;-1.97;-2.27;-1.97;-1.14	5.67	4.53	0.55603	.	0.083534	0.85682	N	0.000000	T	0.78194	0.4245	L	0.55481	1.735	0.80722	D	1	B;B;B	0.28933	0.228;0.027;0.074	B;B;B	0.24006	0.05;0.024;0.025	T	0.76653	-0.2880	10	0.37606	T	0.19	-25.4018	11.6266	0.51149	0.0:0.0693:0.0:0.9307	.	51;57;57	Q13322-4;Q13322-2;Q13322	.;.;GRB10_HUMAN	D	57;51;51;57;57;51	ENSP00000381793:N57D;ENSP00000406716:N51D;ENSP00000385544:N51D;ENSP00000349818:N57D;ENSP00000385770:N57D;ENSP00000413023:N51D	ENSP00000349818:N57D	N	-	1	0	GRB10	50709820	1.000000	0.71417	0.990000	0.47175	0.689000	0.40095	5.866000	0.69590	1.097000	0.41459	0.533000	0.62120	AAC	T|0.999;C|0.001	0.001	strong		0.522	GRB10-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319157.1		
TMEM45B	120224	hgsc.bcm.edu	37	11	129722512	129722512	+	Silent	SNP	C	C	T	rs115605173	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:129722512C>T	ENST00000524567.1	+	2	416	c.135C>T	c.(133-135)ctC>ctT	p.L45L	TMEM45B_ENST00000281441.3_Silent_p.L45L			Q96B21	TM45B_HUMAN	transmembrane protein 45B	45						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	12	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.012)|Lung(977;0.179)|LUSC - Lung squamous cell carcinoma(976;0.189)		ATCAGCGTCTCGAGATCGTCG	0.483													C|||	40	0.00798722	0.0272	0.0058	5008	,	,		19521	0.0		0.0	False		,,,				2504	0.0				p.L45L		Atlas-SNP	.											.	TMEM45B	25	.	0			c.C135T						PASS	.	C		118,4284	89.2+/-127.9	1,116,2084	144.0	133.0	136.0		135	-11.3	0.0	11	dbSNP_132	136	10,8584	7.1+/-27.0	0,10,4287	no	coding-synonymous	TMEM45B	NM_138788.3		1,126,6371	TT,TC,CC		0.1164,2.6806,0.9849		45/276	129722512	128,12868	2201	4297	6498	SO:0001819	synonymous_variant	120224	exon2			GCGTCTCGAGATC	AK098106	CCDS8482.1	11q24.3	2008-02-05				ENSG00000151715			25194	protein-coding gene	gene with protein product						12477932	Standard	NM_138788		Approved	BC016153, FLJ40787	uc001qfe.1	Q96B21		ENST00000524567.1:c.135C>T	11.37:g.129722512C>T		235.0	0.0	0		248.0	132.0	0.532258	NM_138788	A8K2L8	Silent	SNP	ENST00000524567.1	37	CCDS8482.1																																																																																			C|0.991;T|0.009	0.009	strong		0.483	TMEM45B-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386062.1	NM_138788	
ANK1	286	hgsc.bcm.edu	37	8	41552840	41552840	+	Silent	SNP	G	G	A	rs34969689	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:41552840G>A	ENST00000347528.4	-	27	3053	c.2970C>T	c.(2968-2970)atC>atT	p.I990I	ANK1_ENST00000396945.1_Silent_p.I990I|ANK1_ENST00000352337.4_Silent_p.I990I|ANK1_ENST00000265709.8_Silent_p.I1031I|ANK1_ENST00000379758.2_Silent_p.I990I|ANK1_ENST00000289734.7_Silent_p.I990I|ANK1_ENST00000396942.1_Silent_p.I990I	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic	990	ZU5 1. {ECO:0000255|PROSITE- ProRule:PRU00485}.				axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			GGATCTCCACGATTACAGGGC	0.642													G|||	71	0.0141773	0.0522	0.0014	5008	,	,		20368	0.0		0.0	False		,,,				2504	0.001				p.I1031I		Atlas-SNP	.											.	ANK1	497	.	0			c.C3093T						PASS	.	G	,,,,	167,4239	109.9+/-148.2	2,163,2038	94.0	79.0	84.0		2970,3093,2970,2970,2970	-4.0	1.0	8	dbSNP_126	84	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ANK1	NM_000037.3,NM_001142446.1,NM_020475.2,NM_020476.2,NM_020477.2	,,,,	2,166,6335	AA,AG,GG		0.0349,3.7903,1.3071	,,,,	990/1881,1031/1898,990/1857,990/1882,990/1720	41552840	170,12836	2203	4300	6503	SO:0001819	synonymous_variant	286	exon28			CTCCACGATTACA	M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"""Ankyrin repeat domain containing"""	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.2970C>T	8.37:g.41552840G>A		173.0	0.0	0		180.0	85.0	0.472222	NM_001142446	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Silent	SNP	ENST00000347528.4	37	CCDS6119.1	22	0.010073260073260074	21	0.042682926829268296	1	0.0027624309392265192	0	0.0	0	0.0	G	8.916	0.959980	0.18507	0.037903	3.49E-4	ENSG00000029534	ENST00000520299	.	.	.	4.99	-4.02	0.04034	.	.	.	.	.	T	0.21674	0.0522	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43734	-0.9373	4	.	.	.	.	9.6086	0.39648	0.649:0.1048:0.2461:0.0	rs34969689	.	.	.	C	312	.	.	R	-	1	0	ANK1	41671997	0.000000	0.05858	0.956000	0.39512	0.803000	0.45373	-2.206000	0.01231	-0.779000	0.04560	-0.251000	0.11542	CGT	G|0.987;A|0.013	0.013	strong		0.642	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475	
ZNF217	7764	hgsc.bcm.edu	37	20	52198619	52198619	+	Silent	SNP	C	C	A	rs78786003	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:52198619C>A	ENST00000371471.2	-	2	1172	c.747G>T	c.(745-747)gcG>gcT	p.A249A	ZNF217_ENST00000540425.1_5'Flank|ZNF217_ENST00000302342.3_Silent_p.A249A			O75362	ZN217_HUMAN	zinc finger protein 217	249					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			AGTCTGTCTGCGCGCTGCTGG	0.488													C|||	50	0.00998403	0.0348	0.0058	5008	,	,		21092	0.0		0.0	False		,,,				2504	0.0				p.A249A		Atlas-SNP	.											.	ZNF217	227	.	0			c.G747T						PASS	.	C		187,4219	118.4+/-156.1	1,185,2017	101.0	98.0	99.0		747	-8.0	0.0	20	dbSNP_131	99	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ZNF217	NM_006526.2		1,187,6315	AA,AC,CC		0.0233,4.2442,1.4532		249/1049	52198619	189,12817	2203	4300	6503	SO:0001819	synonymous_variant	7764	exon1			TGTCTGCGCGCTG	AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"""Zinc fingers, C2H2-type"""	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.747G>T	20.37:g.52198619C>A		118.0	0.0	0		111.0	52.0	0.468468	NM_006526	E1P5Y6|Q14DB8	Silent	SNP	ENST00000371471.2	37	CCDS13443.1																																																																																			C|0.985;A|0.015	0.015	strong		0.488	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526	
MGAT4A	11320	hgsc.bcm.edu	37	2	99256447	99256447	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:99256447T>A	ENST00000264968.3	-	11	1509	c.1146A>T	c.(1144-1146)aaA>aaT	p.K382N	MGAT4A_ENST00000414521.2_Missense_Mutation_p.K254N|MGAT4A_ENST00000409391.1_Missense_Mutation_p.K382N|MGAT4A_ENST00000393487.1_Missense_Mutation_p.K382N			Q9UM21	MGT4A_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme A	382					cellular protein metabolic process (GO:0044267)|N-glycan processing (GO:0006491)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|stomach(1)	19						GAAGTAATGGTTTCATATAAT	0.343																																					p.K382N		Atlas-SNP	.											.	MGAT4A	51	.	0			c.A1146T						PASS	.						63.0	67.0	66.0					2																	99256447		2203	4300	6503	SO:0001583	missense	11320	exon12			TAATGGTTTCATA	AB000616	CCDS2036.1, CCDS54380.1	2q12	2013-02-25	2005-11-16		ENSG00000071073	ENSG00000071073	2.4.1.145	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7047	protein-coding gene	gene with protein product		604623	"""mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isoenzyme A"""			10024668	Standard	NM_001160154		Approved	GnT-Iva, GnT-4a	uc002sze.3	Q9UM21	OTTHUMG00000130563	ENST00000264968.3:c.1146A>T	2.37:g.99256447T>A	ENSP00000264968:p.Lys382Asn	78.0	0.0	0		82.0	42.0	0.512195	NM_012214	B4E2R6|D3DVH6|E9PEN2|Q53S97|Q86Z15	Missense_Mutation	SNP	ENST00000264968.3	37	CCDS2036.1	.	.	.	.	.	.	.	.	.	.	T	17.73	3.462708	0.63513	.	.	ENSG00000071073	ENST00000393487;ENST00000414521;ENST00000264968;ENST00000409391	T;T;T;T	0.26957	1.7;1.75;1.7;1.7	5.64	1.45	0.22620	.	0.000000	0.85682	D	0.000000	T	0.49762	0.1576	M	0.85777	2.775	0.54753	D	0.999987	D;D	0.76494	0.988;0.999	P;D	0.78314	0.815;0.991	T	0.50792	-0.8786	10	0.52906	T	0.07	-5.7696	10.1002	0.42499	0.0:0.2309:0.0:0.7691	.	254;382	E9PEN2;Q9UM21	.;MGT4A_HUMAN	N	382;254;382;382	ENSP00000377127:K382N;ENSP00000404889:K254N;ENSP00000264968:K382N;ENSP00000386841:K382N	ENSP00000264968:K382N	K	-	3	2	MGAT4A	98622879	1.000000	0.71417	1.000000	0.80357	0.916000	0.54674	0.644000	0.24766	0.394000	0.25230	0.455000	0.32223	AAA	.	.	none		0.343	MGAT4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252988.2	NM_012214	
HDC	3067	hgsc.bcm.edu	37	15	50534789	50534789	+	Missense_Mutation	SNP	A	A	G	rs16963486	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:50534789A>G	ENST00000267845.3	-	12	2059	c.1657T>C	c.(1657-1659)Ttt>Ctt	p.F553L	HDC_ENST00000543581.1_Missense_Mutation_p.F520L|RN7SL494P_ENST00000461517.2_RNA	NM_002112.3	NP_002103.2	Q9UBI9	HDC_HUMAN	histidine decarboxylase	0					respiratory tube development (GO:0030323)	membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		all_lung(180;0.0138)		all cancers(107;1.12e-06)|GBM - Glioblastoma multiforme(94;9.95e-05)		TCTTCTGAAAAGCAGTCATCA	0.537													A|||	105	0.0209665	0.0764	0.0058	5008	,	,		20285	0.0		0.0	False		,,,				2504	0.0				p.F553L	GBM(95;1627 1936 6910 9570)	Atlas-SNP	.											.	HDC	86	.	0			c.T1657C						PASS	.	A	LEU/PHE	319,4073	168.3+/-199.2	11,297,1888	87.0	88.0	88.0		1657	5.7	1.0	15	dbSNP_123	88	1,8589	1.2+/-3.3	0,1,4294	yes	missense	HDC	NM_002112.3	22	11,298,6182	GG,GA,AA		0.0116,7.2632,2.465	probably-damaging	553/663	50534789	320,12662	2196	4295	6491	SO:0001583	missense	3067	exon12			CTGAAAAGCAGTC		CCDS10134.1	15q21.2	2013-09-20			ENSG00000140287	ENSG00000140287	4.1.1.22		4855	protein-coding gene	gene with protein product		142704				1487235	Standard	NM_002112		Approved		uc001zxz.3	P19113	OTTHUMG00000131644	ENST00000267845.3:c.1657T>C	15.37:g.50534789A>G	ENSP00000267845:p.Phe553Leu	135.0	0.0	0		123.0	65.0	0.528455	NM_002112		Missense_Mutation	SNP	ENST00000267845.3	37	CCDS10134.1	44	0.020146520146520148	41	0.08333333333333333	3	0.008287292817679558	0	0.0	0	0.0	A	17.30	3.353885	0.61293	0.072632	1.16E-4	ENSG00000140287	ENST00000267845;ENST00000543581	T;T	0.14144	2.92;2.53	5.73	5.73	0.89815	.	0.365309	0.23805	N	0.044383	T	0.01061	0.0035	L	0.34521	1.04	0.43444	D	0.99562	D;D	0.67145	0.996;0.976	P;B	0.54759	0.76;0.446	T	0.00294	-1.1840	10	0.54805	T	0.06	-19.7657	16.0115	0.80406	1.0:0.0:0.0:0.0	rs16963486;rs52824591;rs16963486	520;553	B7ZM01;P19113	.;DCHS_HUMAN	L	553;520	ENSP00000267845:F553L;ENSP00000440252:F520L	ENSP00000267845:F553L	F	-	1	0	HDC	48322081	1.000000	0.71417	0.999000	0.59377	0.039000	0.13416	6.778000	0.75043	2.187000	0.69744	0.460000	0.39030	TTT	A|0.975;G|0.025	0.025	strong		0.537	HDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254540.1		
MDH2	4191	hgsc.bcm.edu	37	7	75684273	75684273	+	Silent	SNP	G	G	A	rs77424348	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:75684273G>A	ENST00000315758.5	+	2	286	c.192G>A	c.(190-192)gtG>gtA	p.V64V	MDH2_ENST00000432020.2_Silent_p.V64V|MDH2_ENST00000443006.1_Intron|MDH2_ENST00000490105.1_3'UTR	NM_005918.2	NP_005909.2	P40926	MDHM_HUMAN	malate dehydrogenase 2, NAD (mitochondrial)	64					carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|internal protein amino acid acetylation (GO:0006475)|malate metabolic process (GO:0006108)|NADH metabolic process (GO:0006734)|oxaloacetate metabolic process (GO:0006107)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	L-malate dehydrogenase activity (GO:0030060)|malate dehydrogenase (NADP+) activity (GO:0046554)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(2)	14						CACCCGGAGTGGCCGCAGATC	0.612													g|||	28	0.00559105	0.0204	0.0014	5008	,	,		14182	0.0		0.0	False		,,,				2504	0.0				p.V64V		Atlas-SNP	.											.	MDH2	35	.	0			c.G192A						PASS	.	G		112,4294	86.8+/-125.4	3,106,2094	77.0	78.0	78.0		192	2.3	1.0	7	dbSNP_132	78	1,8599		0,1,4299	no	coding-synonymous	MDH2	NM_005918.2		3,107,6393	AA,AG,GG		0.0116,2.542,0.8688		64/339	75684273	113,12893	2203	4300	6503	SO:0001819	synonymous_variant	4191	exon2			CGGAGTGGCCGCA		CCDS5581.1, CCDS64691.1, CCDS75622.1	7q11.23	2013-09-20			ENSG00000146701	ENSG00000146701	1.1.1.37		6971	protein-coding gene	gene with protein product		154100					Standard	NM_005918		Approved		uc003ueo.3	P40926	OTTHUMG00000023827	ENST00000315758.5:c.192G>A	7.37:g.75684273G>A		69.0	0.0	0		77.0	54.0	0.701299	NM_005918	A8K414|B2RE78|B4DE44|E9PDB2|O43682	Silent	SNP	ENST00000315758.5	37	CCDS5581.1																																																																																			G|0.984;A|0.016	0.016	strong		0.612	MDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252851.1		
FAT1	2195	hgsc.bcm.edu	37	4	187524176	187524176	+	Missense_Mutation	SNP	G	G	A	rs200262460	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:187524176G>A	ENST00000441802.2	-	20	11572	c.11363C>T	c.(11362-11364)cCa>cTa	p.P3788L		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	3788					actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						GTGGACAGGTGGGCACCTTCC	0.493										HNSCC(5;0.00058)			G|||	4	0.000798722	0.003	0.0	5008	,	,		18565	0.0		0.0	False		,,,				2504	0.0				p.P3788L	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C11363T						PASS	.	G	LEU/PRO	4,3954		0,4,1975	88.0	88.0	88.0		11363	5.3	1.0	4	dbSNP_134	88	0,8326		0,0,4163	yes	missense	FAT1	NM_005245.3	98	0,4,6138	AA,AG,GG		0.0,0.1011,0.0326	benign	3788/4589	187524176	4,12280	1979	4163	6142	SO:0001583	missense	2195	exon20			ACAGGTGGGCACC	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.11363C>T	4.37:g.187524176G>A	ENSP00000406229:p.Pro3788Leu	122.0	0.0	0		123.0	71.0	0.577236	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	13.22	2.170718	0.38315	0.001011	0.0	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.32023	1.47	5.26	5.26	0.73747	.	0.056195	0.64402	D	0.000001	T	0.32823	0.0842	L	0.58428	1.81	0.80722	D	1	B	0.30686	0.29	B	0.25759	0.063	T	0.07252	-1.0782	10	0.32370	T	0.25	.	19.2203	0.93793	0.0:0.0:1.0:0.0	.	3788	Q14517	FAT1_HUMAN	L	3788;3790	ENSP00000406229:P3788L	ENSP00000260147:P3790L	P	-	2	0	FAT1	187761170	1.000000	0.71417	0.956000	0.39512	0.080000	0.17528	9.111000	0.94308	2.614000	0.88457	0.557000	0.71058	CCA	G|1.000;A|0.000	0.000	strong		0.493	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
PCDHB12	56124	hgsc.bcm.edu	37	5	140589334	140589334	+	Silent	SNP	A	A	G	rs149716951	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140589334A>G	ENST00000239450.2	+	1	1044	c.855A>G	c.(853-855)tcA>tcG	p.S285S	PCDHB12_ENST00000541609.1_Intron	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	285	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(10)|large_intestine(17)|lung(38)|ovary(3)|pancreas(1)|prostate(2)|skin(7)|stomach(1)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCCATGCCTCAGAAGATATTC	0.403													A|||	27	0.00539137	0.0204	0.0	5008	,	,		20813	0.0		0.0	False		,,,				2504	0.0				p.S285S		Atlas-SNP	.											.	PCDHB12	179	.	0			c.A855G						PASS	.	A		70,4336	63.5+/-100.7	1,68,2134	99.0	105.0	103.0		855	-4.1	1.0	5	dbSNP_134	103	0,8600		0,0,4300	no	coding-synonymous	PCDHB12	NM_018932.3		1,68,6434	GG,GA,AA		0.0,1.5887,0.5382		285/796	140589334	70,12936	2203	4300	6503	SO:0001819	synonymous_variant	56124	exon1			TGCCTCAGAAGAT	AF152491	CCDS4254.1	5q31	2010-01-26			ENSG00000120328	ENSG00000120328		"""Cadherins / Protocadherins : Clustered"""	8683	other	protocadherin		606338				10380929	Standard	NM_018932		Approved	PCDH-BETA12	uc003liz.3	Q9Y5F1	OTTHUMG00000129620	ENST00000239450.2:c.855A>G	5.37:g.140589334A>G		138.0	0.0	0		121.0	64.0	0.528926	NM_018932	B4DDU1	Silent	SNP	ENST00000239450.2	37	CCDS4254.1																																																																																			A|0.994;G|0.006	0.006	strong		0.403	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932	
ATP2A3	489	hgsc.bcm.edu	37	17	3850910	3850910	+	Silent	SNP	A	A	G	rs55837933	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3850910A>G	ENST00000352011.3	-	8	924	c.870T>C	c.(868-870)cgT>cgC	p.R290R	ATP2A3_ENST00000397035.3_Silent_p.R290R|ATP2A3_ENST00000397041.3_Silent_p.R290R|ATP2A3_ENST00000397043.3_Silent_p.R290R|ATP2A3_ENST00000309890.7_Silent_p.R290R|ATP2A3_ENST00000397039.1_5'UTR|ATP2A3_ENST00000359983.3_Silent_p.R290R			Q93084	AT2A3_HUMAN	ATPase, Ca++ transporting, ubiquitous	290					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	36				LUAD - Lung adenocarcinoma(1115;0.000692)|Lung(3;0.0766)		AGACAGCGCCACGCAGCCAGG	0.677													G|||	356	0.0710863	0.2564	0.0245	5008	,	,		16011	0.0		0.0	False		,,,				2504	0.0				p.R290R	GBM(32;29 774 15719 37967)	Atlas-SNP	.											.	ATP2A3	148	.	0			c.T870C						PASS	.	G	,,,,,,	1054,3350		133,788,1281	28.0	31.0	30.0		870,870,870,870,870,870,870	-7.5	0.1	17	dbSNP_129	30	5,8591		0,5,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ATP2A3	NM_005173.3,NM_174953.2,NM_174954.2,NM_174955.2,NM_174956.2,NM_174957.2,NM_174958.2	,,,,,,	133,793,5574	GG,GA,AA		0.0582,23.9328,8.1462	,,,,,,	290/1000,290/1053,290/1045,290/1044,290/1030,290/999,290/1030	3850910	1059,11941	2202	4298	6500	SO:0001819	synonymous_variant	489	exon8			AGCGCCACGCAGC		CCDS11041.1, CCDS11042.1, CCDS42234.1, CCDS45579.1, CCDS45580.1	17p13.3	2012-10-22			ENSG00000074370	ENSG00000074370	3.6.3.8	"""ATPases / P-type"""	813	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 3"", ""calcium pump 3"""	601929				8809064	Standard	NM_005173		Approved	SERCA3	uc002fwy.2	Q93084		ENST00000352011.3:c.870T>C	17.37:g.3850910A>G		38.0	0.0	0		43.0	26.0	0.604651	NM_174956	A8MZG0|D3DTJ8|O60900|O60901|O75501|O75502|Q16115|Q6JHX1|Q8TEX5|Q8TEX6	Silent	SNP	ENST00000352011.3	37	CCDS11041.1																																																																																			A|0.928;G|0.072	0.072	strong		0.677	ATP2A3-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000438401.1	NM_174953	
AHCTF1	25909	hgsc.bcm.edu	37	1	247013733	247013733	+	Missense_Mutation	SNP	T	T	C	rs139763225	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:247013733T>C	ENST00000391829.2	-	33	5698	c.5575A>G	c.(5575-5577)Aaa>Gaa	p.K1859E	AHCTF1_ENST00000470300.1_5'UTR|AHCTF1_ENST00000366508.1_Missense_Mutation_p.K1894E|AHCTF1_ENST00000326225.3_Missense_Mutation_p.K1868E			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	1859	Disordered. {ECO:0000250}.|Necessary for nuclear localization. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			ACTTCTTTTTTAGTAGTTTCT	0.328													T|||	222	0.0443291	0.1657	0.0043	5008	,	,		19442	0.0		0.0	False		,,,				2504	0.0				p.K1868E	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.A5602G						PASS	.	T	GLU/LYS	482,3810		21,440,1685	23.0	25.0	24.0		5602	5.2	0.4	1	dbSNP_134	24	6,8524		0,6,4259	no	missense	AHCTF1	NM_015446.4	56	21,446,5944	CC,CT,TT		0.0703,11.2302,3.806	benign	1868/2276	247013733	488,12334	2146	4265	6411	SO:0001583	missense	25909	exon33			CTTTTTTAGTAGT		CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"""ELYS transcription factor like protein TMBS62"""	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.5575A>G	1.37:g.247013733T>C	ENSP00000375705:p.Lys1859Glu	406.0	0.0	0		408.0	167.0	0.409314	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Missense_Mutation	SNP	ENST00000391829.2	37		75	0.034340659340659344	74	0.15040650406504066	1	0.0027624309392265192	0	0.0	0	0.0	T	0	-2.799134	0.00076	0.112302	7.03E-4	ENSG00000153207	ENST00000366508;ENST00000326225;ENST00000391829	T;T;T	0.29917	1.55;1.55;1.55	5.15	5.15	0.70609	.	2.053990	0.02125	N	0.055937	T	0.00109	0.0003	N	0.22421	0.69	0.09310	N	1	B;B;B	0.17667	0.014;0.016;0.023	B;B;B	0.14023	0.004;0.01;0.007	T	0.37979	-0.9682	10	0.05959	T	0.93	-0.8216	4.3077	0.10955	0.1767:0.097:0.0:0.7263	.	720;1894;1859	B3KTD2;Q8WYP5-2;Q8WYP5	.;.;ELYS_HUMAN	E	1894;1868;1859	ENSP00000355464:K1894E;ENSP00000355465:K1868E;ENSP00000375705:K1859E	ENSP00000355465:K1868E	K	-	1	0	AHCTF1	245080356	0.010000	0.17322	0.450000	0.26969	0.205000	0.24178	1.124000	0.31320	1.927000	0.55829	0.533000	0.62120	AAA	.	.	weak		0.328	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446	
CEACAM1	634	hgsc.bcm.edu	37	19	43031514	43031514	+	Missense_Mutation	SNP	G	G	T	rs8111171	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43031514G>T	ENST00000161559.6	-	2	237	c.103C>A	c.(103-105)Cag>Aag	p.Q35K	CEACAM1_ENST00000358394.3_Missense_Mutation_p.Q35K|LIPE-AS1_ENST00000457234.2_RNA|CEACAM1_ENST00000403461.1_Missense_Mutation_p.Q35K|LIPE-AS1_ENST00000594624.2_RNA|CEACAM1_ENST00000308072.4_5'UTR|CEACAM1_ENST00000599389.1_Missense_Mutation_p.Q35K|CEACAM1_ENST00000352591.5_Missense_Mutation_p.Q35K|CEACAM1_ENST00000403444.3_Missense_Mutation_p.Q35K|LIPE-AS1_ENST00000594688.1_RNA|CEACAM1_ENST00000351134.3_Missense_Mutation_p.Q35K	NM_001712.4	NP_001703.2	P13688	CEAM1_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein)	35	Ig-like V-type.		Q -> K (in dbSNP:rs8111171). {ECO:0000269|Ref.9}.		angiogenesis (GO:0001525)|cell migration (GO:0016477)|homophilic cell adhesion (GO:0007156)|integrin-mediated signaling pathway (GO:0007229)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	17		Prostate(69;0.00682)		GBM - Glioblastoma multiforme(486;0.00148)	Arcitumomab(DB00113)	GTAGTGAGCTGGGCAGTGGTG	0.502													g|||	596	0.11901	0.4228	0.0461	5008	,	,		19075	0.0		0.005	False		,,,				2504	0.0				p.Q35K		Atlas-SNP	.											.	CEACAM1	43	.	0			c.C103A						PASS	.	G	LYS/GLN,LYS/GLN,LYS/GLN,LYS/GLN,LYS/GLN,LYS/GLN	1556,2850	488.5+/-361.2	290,976,937	140.0	134.0	136.0		103,103,103,103,103,103	-0.2	0.0	19	dbSNP_116	136	22,8578	12.6+/-44.7	0,22,4278	yes	missense,missense,missense,missense,missense,missense	CEACAM1	NM_001024912.2,NM_001184813.1,NM_001184815.1,NM_001184816.1,NM_001205344.1,NM_001712.4	53,53,53,53,53,53	290,998,5215	TT,TG,GG		0.2558,35.3155,12.1329	benign,benign,benign,benign,benign,benign	35/465,35/431,35/462,35/369,35/469,35/527	43031514	1578,11428	2203	4300	6503	SO:0001583	missense	634	exon2			TGAGCTGGGCAGT	M72238	CCDS12609.1, CCDS46089.1, CCDS54272.1, CCDS54273.1, CCDS54274.1	19q13.2	2014-05-16			ENSG00000079385	ENSG00000079385		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1814	protein-coding gene	gene with protein product		109770		BGP		2457922, 2025273	Standard	NM_001712		Approved	BGP1, CD66a	uc002otv.3	P13688	OTTHUMG00000151078	ENST00000161559.6:c.103C>A	19.37:g.43031514G>T	ENSP00000161559:p.Gln35Lys	214.0	0.0	0		219.0	124.0	0.56621	NM_001184816	A6NE38|A8MY49|O60430|Q069I7|Q13854|Q13857|Q13858|Q13859|Q13860|Q15600|Q15601|Q16170|Q5UB49|Q7KYP5|Q96CA7|Q9UQV9	Missense_Mutation	SNP	ENST00000161559.6	37	CCDS12609.1	220	0.10073260073260074	196	0.3983739837398374	19	0.052486187845303865	0	0.0	5	0.006596306068601583	g	11.90	1.776621	0.31411	0.353155	0.002558	ENSG00000079385	ENST00000161559;ENST00000358394;ENST00000351134;ENST00000446434;ENST00000352591;ENST00000403444;ENST00000403461;ENST00000377806;ENST00000344391;ENST00000403136	T;T;T;T;T;T	0.01647	4.71;4.71;4.71;4.71;4.71;4.71	3.6	-0.184	0.13280	Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.49778	1.585	0.58432	P	2.9999999999752447E-6	B;B;B;B;B;B;B;B;B;B	0.22983	0.004;0.009;0.001;0.001;0.002;0.001;0.039;0.009;0.078;0.047	B;B;B;B;B;B;B;B;B;B	0.20184	0.006;0.003;0.005;0.003;0.002;0.004;0.028;0.008;0.015;0.027	T	0.36065	-0.9763	8	0.38643	T	0.18	.	6.2066	0.20606	0.0:0.3764:0.4131:0.2105	rs8111171;rs59246809	35;35;35;35;35;35;35;35;35;35	P13688-7;P13688-10;P13688-3;P13688-4;P13688-2;P13688-11;P13688-6;P13688-5;P13688-8;P13688	.;.;.;.;.;.;.;.;.;CEAM1_HUMAN	K	35;35;35;62;35;35;35;35;35;35	ENSP00000161559:Q35K;ENSP00000351165:Q35K;ENSP00000325946:Q35K;ENSP00000244291:Q35K;ENSP00000384709:Q35K;ENSP00000384083:Q35K	ENSP00000161559:Q35K	Q	-	1	0	CEACAM1	47723354	0.691000	0.27709	0.001000	0.08648	0.306000	0.27790	0.186000	0.16978	0.061000	0.16311	0.491000	0.48974	CAG	G|0.888;T|0.112	0.112	strong		0.502	CEACAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321190.2	NM_001712	
SACS	26278	hgsc.bcm.edu	37	13	23915089	23915089	+	Missense_Mutation	SNP	G	G	T	rs139993038	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:23915089G>T	ENST00000382292.3	-	9	3199	c.2926C>A	c.(2926-2928)Cgt>Agt	p.R976S	SACS_ENST00000382298.3_Missense_Mutation_p.R976S|SACS_ENST00000402364.1_Missense_Mutation_p.R226S			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	976					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TTTGCCAGACGAATAGTAGCT	0.348													G|||	8	0.00159744	0.0061	0.0	5008	,	,		20828	0.0		0.0	False		,,,				2504	0.0				p.R976S		Atlas-SNP	.											SACS_ENST00000382298,NS,carcinoma,0,2	SACS	871	2	0			c.C2926A						scavenged	.	G	SER/ARG	27,4379	33.5+/-64.1	0,27,2176	71.0	70.0	71.0		2926	6.1	1.0	13	dbSNP_134	71	0,8600		0,0,4300	no	missense	SACS	NM_014363.4	110	0,27,6476	TT,TG,GG		0.0,0.6128,0.2076	probably-damaging	976/4580	23915089	27,12979	2203	4300	6503	SO:0001583	missense	26278	exon10			CCAGACGAATAGT	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.2926C>A	13.37:g.23915089G>T	ENSP00000371729:p.Arg976Ser	190.0	1.0	0.00526316		183.0	71.0	0.387978	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	.	.	.	.	.	.	.	.	.	.	G	32	5.112212	0.94339	0.006128	0.0	ENSG00000151835	ENST00000382292;ENST00000402364;ENST00000382298	D;D;D	0.87809	-2.14;-2.3;-2.14	6.05	6.05	0.98169	.	0.000000	0.85682	D	0.000000	D	0.82486	0.5047	L	0.34521	1.04	0.80722	D	1	D	0.53312	0.959	P	0.47528	0.549	D	0.85013	0.0907	10	0.56958	D	0.05	.	20.6013	0.99457	0.0:0.0:1.0:0.0	.	976	Q9NZJ4	SACS_HUMAN	S	976;226;976	ENSP00000371729:R976S;ENSP00000385844:R226S;ENSP00000371735:R976S	ENSP00000371729:R976S	R	-	1	0	SACS	22813089	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	9.476000	0.97823	2.878000	0.98634	0.650000	0.86243	CGT	A|0.000;G|0.999;T|0.001	0.001	strong		0.348	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
LRFN2	57497	hgsc.bcm.edu	37	6	40400823	40400823	+	Silent	SNP	C	C	T	rs61731039	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:40400823C>T	ENST00000338305.6	-	2	572	c.30G>A	c.(28-30)gcG>gcA	p.A10A		NM_020737.1	NP_065788.1	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III domain containing 2	10						cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	58	Ovarian(28;0.0418)|Colorectal(47;0.196)					CCATGCCAAACGCTAGCAGGC	0.597													c|||	248	0.0495208	0.1785	0.0144	5008	,	,		18737	0.0		0.002	False		,,,				2504	0.0				p.A10A		Atlas-SNP	.											LRFN2,NS,carcinoma,-1,1	LRFN2	133	1	0			c.G30A						PASS	.	T		702,3704	266.8+/-267.5	63,576,1564	36.0	38.0	37.0		30	-1.2	1.0	6	dbSNP_129	37	13,8587	9.1+/-34.3	0,13,4287	no	coding-synonymous	LRFN2	NM_020737.1		63,589,5851	TT,TC,CC		0.1512,15.9328,5.4975		10/790	40400823	715,12291	2203	4300	6503	SO:0001819	synonymous_variant	57497	exon2			GCCAAACGCTAGC	AB033072	CCDS34443.1	6p21.2-p21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000156564	ENSG00000156564		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	21226	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 2"""	612808	"""KIAA1246"""	KIAA1246, SALM1		16495444, 16828986	Standard	NM_020737		Approved	FIGLER2	uc003oph.1	Q9ULH4	OTTHUMG00000014662	ENST00000338305.6:c.30G>A	6.37:g.40400823C>T		69.0	0.0	0		69.0	35.0	0.507246	NM_020737	A5PKU3|Q5SYP9	Silent	SNP	ENST00000338305.6	37	CCDS34443.1																																																																																			C|0.950;T|0.050	0.050	strong		0.597	LRFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040488.1	XM_166372	
MAP1B	4131	hgsc.bcm.edu	37	5	71495320	71495320	+	Silent	SNP	G	G	A	rs115914542	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:71495320G>A	ENST00000296755.7	+	5	6436	c.6138G>A	c.(6136-6138)gaG>gaA	p.E2046E		NM_005909.3	NP_005900.2	P46821	MAP1B_HUMAN	microtubule-associated protein 1B	2046					axon extension (GO:0048675)|cellular process (GO:0009987)|dendrite development (GO:0016358)|establishment of monopolar cell polarity (GO:0061162)|microtubule bundle formation (GO:0001578)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|positive regulation of axon extension (GO:0045773)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|plasma membrane (GO:0005886)|synapse (GO:0045202)	structural molecule activity (GO:0005198)	p.E2046D(2)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(42)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	104		Lung NSC(167;0.00202)|Ovarian(174;0.0175)|Prostate(461;0.142)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;7.99e-54)		AGACTGCAGAGAAAATCACTA	0.458													G|||	7	0.00139776	0.0053	0.0	5008	,	,		19505	0.0		0.0	False		,,,				2504	0.0				p.E2046E	Melanoma(17;367 822 11631 31730 47712)	Atlas-SNP	.											MAP1B,rectum,carcinoma,0,2	MAP1B	243	2	2	Substitution - Missense(2)	large_intestine(2)	c.G6138A						PASS	.	G		10,4396	15.5+/-35.6	0,10,2193	117.0	129.0	125.0		6138	3.9	0.9	5	dbSNP_133	125	0,8600		0,0,4300	no	coding-synonymous	MAP1B	NM_005909.3		0,10,6493	AA,AG,GG		0.0,0.227,0.0769		2046/2469	71495320	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	4131	exon5			TGCAGAGAAAATC	L06237	CCDS4012.1	5q13	2014-06-12			ENSG00000131711	ENSG00000131711			6836	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 102"""	157129				1881920	Standard	NM_005909		Approved	MAP5, PPP1R102	uc003kbw.4	P46821	OTTHUMG00000100952	ENST00000296755.7:c.6138G>A	5.37:g.71495320G>A		122.0	0.0	0		163.0	87.0	0.533742	NM_005909	A2BDK5	Silent	SNP	ENST00000296755.7	37	CCDS4012.1																																																																																			G|0.999;A|0.001	0.001	strong		0.458	MAP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218561.6	NM_005909	
HSD3B2	3284	hgsc.bcm.edu	37	1	119962118	119962118	+	Missense_Mutation	SNP	G	G	A	rs4986954	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:119962118G>A	ENST00000543831.1	+	3	469	c.220G>A	c.(220-222)Gac>Aac	p.D74N	HSD3B2_ENST00000471656.1_3'UTR|HSD3B2_ENST00000369416.3_Missense_Mutation_p.D74N	NM_001166120.1	NP_001159592.1	P26439	3BHS2_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 2	74			D -> N (in dbSNP:rs4986954).		androgen biosynthetic process (GO:0006702)|glucocorticoid biosynthetic process (GO:0006704)|mineralocorticoid biosynthetic process (GO:0006705)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial membrane (GO:0031966)|smooth endoplasmic reticulum membrane (GO:0030868)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|steroid delta-isomerase activity (GO:0004769)			breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(19)|ovary(2)|skin(1)	27	all_neural(166;0.187)	all_lung(203;1.06e-06)|Lung NSC(69;7.5e-06)|all_epithelial(167;0.000284)		Lung(183;0.015)|LUSC - Lung squamous cell carcinoma(189;0.0836)	Corticotropin(DB01285)|Medroxyprogesterone Acetate(DB00603)|Trilostane(DB01108)	AGCCTGCCAGGACGTCTCGGT	0.498													G|||	15	0.00299521	0.0113	0.0	5008	,	,		20071	0.0		0.0	False		,,,				2504	0.0				p.D74N		Atlas-SNP	.											.	HSD3B2	48	.	0			c.G220A						PASS	.	G	ASN/ASP,ASN/ASP	39,4367		1,37,2165	112.0	89.0	97.0		220,220	3.9	0.9	1	dbSNP_111	97	0,8600		0,0,4300	no	missense,missense	HSD3B2	NM_000198.3,NM_001166120.1	23,23	1,37,6465	AA,AG,GG		0.0,0.8852,0.2999	benign,benign	74/373,74/373	119962118	39,12967	2203	4300	6503	SO:0001583	missense	3284	exon3			TGCCAGGACGTCT	BC038419	CCDS902.1	1p12	2014-06-03			ENSG00000203859	ENSG00000203859	1.1.1.145, 5.3.3.1	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	5218	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 11E, member 2"""	613890				1363812, 19027726	Standard	NM_000198		Approved	SDR11E2	uc001eht.3	P26439	OTTHUMG00000012526	ENST00000543831.1:c.220G>A	1.37:g.119962118G>A	ENSP00000445122:p.Asp74Asn	161.0	0.0	0		196.0	88.0	0.44898	NM_001166120	A2RRA5|Q16010|Q53GD4|Q6AI10|Q6LDB9|Q99890|Q9UD08	Missense_Mutation	SNP	ENST00000543831.1	37	CCDS902.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	-	14.37	2.514988	0.44763	0.008852	0.0	ENSG00000203859	ENST00000543831;ENST00000433745;ENST00000369416	D;D;D	0.88509	-2.39;-2.39;-2.39	3.93	3.93	0.45458	3-beta hydroxysteroid dehydrogenase/isomerase (1);NAD(P)-binding domain (1);	0.054278	0.64402	D	0.000001	T	0.81969	0.4935	L	0.41906	1.305	0.30554	N	0.765177	P;P	0.36874	0.572;0.464	B;P	0.45913	0.173;0.497	T	0.77305	-0.2637	9	.	.	.	-17.182	13.5239	0.61584	0.0:0.0:1.0:0.0	rs4986954;rs52821087;rs4986954	74;74	P26439-2;P26439	.;3BHS2_HUMAN	N	74	ENSP00000445122:D74N;ENSP00000388292:D74N;ENSP00000358424:D74N	.	D	+	1	0	HSD3B2	119763641	1.000000	0.71417	0.934000	0.37439	0.009000	0.06853	7.003000	0.76310	1.943000	0.56356	0.298000	0.19748	GAC	G|0.996;A|0.004	0.004	strong		0.498	HSD3B2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034994.1	NM_000198	
PROKR2	128674	hgsc.bcm.edu	37	20	5283051	5283051	+	Missense_Mutation	SNP	G	G	A	rs148868355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:5283051G>A	ENST00000217270.3	-	2	789	c.790C>T	c.(790-792)Cgc>Tgc	p.R264C	PROKR2_ENST00000546004.1_Missense_Mutation_p.R264C	NM_144773.2	NP_658986.1	Q8NFJ6	PKR2_HUMAN	prokineticin receptor 2	264					circadian rhythm (GO:0007623)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide Y receptor activity (GO:0004983)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(3)|lung(22)|ovary(5)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	53						AGCCGCTTGCGAATCTGCTCC	0.612										HNSCC(71;0.22)			G|||	4	0.000798722	0.003	0.0	5008	,	,		20081	0.0		0.0	False		,,,				2504	0.0				p.R264C		Atlas-SNP	.											.	PROKR2	90	.	0			c.C790T						PASS	.	G	CYS/ARG	8,4398	14.3+/-33.2	0,8,2195	53.0	49.0	50.0		790	5.1	1.0	20	dbSNP_134	50	0,8600		0,0,4300	yes	missense	PROKR2	NM_144773.2	180	0,8,6495	AA,AG,GG		0.0,0.1816,0.0615	probably-damaging	264/385	5283051	8,12998	2203	4300	6503	SO:0001583	missense	128674	exon2			GCTTGCGAATCTG	AL121755	CCDS13089.1	20p12.3	2012-08-08	2006-02-15	2006-02-15	ENSG00000101292	ENSG00000101292		"""GPCR / Class A : Prokineticin receptors"""	15836	protein-coding gene	gene with protein product		607123	"""G protein-coupled receptor 73-like 1"", ""Kallmann syndrome 3 (autosomal dominant)"""	GPR73L1, KAL3		11886876, 17054399	Standard	NM_144773		Approved	GPR73b, PKR2, GPRg2, dJ680N4.3	uc010zqw.2	Q8NFJ6	OTTHUMG00000031800	ENST00000217270.3:c.790C>T	20.37:g.5283051G>A	ENSP00000217270:p.Arg264Cys	74.0	0.0	0		78.0	37.0	0.474359	NM_144773	A5JUU1|Q2M3C0|Q5TDY1|Q9NTT0	Missense_Mutation	SNP	ENST00000217270.3	37	CCDS13089.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	17.99	3.522846	0.64747	0.001816	0.0	ENSG00000101292	ENST00000546004;ENST00000217270	T;T	0.38401	1.14;1.14	5.05	5.05	0.67936	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.64713	0.2623	M	0.84585	2.705	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.71069	-0.4699	10	0.72032	D	0.01	.	15.9064	0.79433	0.0:0.0:1.0:0.0	.	264	Q8NFJ6	PKR2_HUMAN	C	264	ENSP00000440790:R264C;ENSP00000217270:R264C	ENSP00000217270:R264C	R	-	1	0	PROKR2	5231051	1.000000	0.71417	1.000000	0.80357	0.804000	0.45430	2.754000	0.47532	2.370000	0.80446	0.655000	0.94253	CGC	G|0.999;A|0.001	0.001	strong		0.612	PROKR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077854.1	NM_144773	
AKR1C2	1646	hgsc.bcm.edu	37	10	5043749	5043749	+	Missense_Mutation	SNP	G	G	A	rs147648222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:5043749G>A	ENST00000380753.4	-	2	396	c.209C>T	c.(208-210)gCa>gTa	p.A70V	AKR1C2_ENST00000407674.1_Missense_Mutation_p.A70V|AKR1C2_ENST00000455190.1_Missense_Mutation_p.A70V|AKR1C2_ENST00000421196.3_Missense_Mutation_p.A70V	NM_205845.2	NP_995317.1	P52895	AK1C2_HUMAN	aldo-keto reductase family 1, member C2	70					cellular response to jasmonic acid stimulus (GO:0071395)|daunorubicin metabolic process (GO:0044597)|digestion (GO:0007586)|doxorubicin metabolic process (GO:0044598)|epithelial cell differentiation (GO:0030855)|G-protein coupled receptor signaling pathway (GO:0007186)|oxidation-reduction process (GO:0055114)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|response to prostaglandin (GO:0034694)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)	alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|bile acid binding (GO:0032052)|carboxylic acid binding (GO:0031406)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin F receptor activity (GO:0004958)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(1)|large_intestine(5)|lung(3)|skin(1)	10					Ursodeoxycholic acid(DB01586)	ACTGCCATCTGCAATCTTGCT	0.443													G|||	17	0.00339457	0.0121	0.0	5008	,	,		21154	0.0		0.001	False		,,,				2504	0.0				p.A70V		Atlas-SNP	.											.	AKR1C2	68	.	0			c.C209T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA	44,4362	48.2+/-83.0	1,42,2160	132.0	114.0	120.0		209,209,209	-1.2	0.9	10	dbSNP_134	120	0,8596		0,0,4298	no	missense,missense,missense	AKR1C2	NM_001135241.1,NM_001354.4,NM_205845.1	64,64,64	1,42,6458	AA,AG,GG		0.0,0.9986,0.3384	benign,benign,benign	70/140,70/324,70/324	5043749	44,12958	2203	4298	6501	SO:0001583	missense	1646	exon4			CCATCTGCAATCT	L32592	CCDS7062.1, CCDS44350.1	10p15-p14	2014-01-29	2012-12-04		ENSG00000151632	ENSG00000151632	1.3.1.20, 1.1.1.213	"""Aldo-keto reductases"""	385	protein-coding gene	gene with protein product	"""dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III"""	600450	"""aldo-keto reductase family 1, member C2 (dihydrodiol dehydrogenase 2; bile acid binding protein; 3-alpha hydroxysteroid dehydrogenase, type III)"", ""testicular 17,20-desmolase deficiency"""	DDH2, TDD		9716498, 21802064	Standard	NM_001354		Approved	DD, BABP, DD2, HAKRD, MCDR2	uc001iht.3	P52895	OTTHUMG00000017584	ENST00000380753.4:c.209C>T	10.37:g.5043749G>A	ENSP00000370129:p.Ala70Val	297.0	0.0	0		328.0	172.0	0.52439	NM_001354	A8K2N9|B4DKR9|Q14133|Q5SR16|Q7M4N1|Q96A71	Missense_Mutation	SNP	ENST00000380753.4	37	CCDS7062.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	G	8.905	0.957221	0.18507	0.009986	0.0	ENSG00000151632	ENST00000380753;ENST00000421196;ENST00000407674;ENST00000455190	T;T;T;T	0.52526	0.66;0.66;0.66;0.66	2.35	-1.18	0.09617	NADP-dependent oxidoreductase domain (3);	0.225703	0.28730	N	0.014335	T	0.33177	0.0854	M	0.65498	2.005	0.20821	N	0.999846	B;B;B	0.30526	0.283;0.128;0.063	B;B;B	0.30646	0.118;0.071;0.057	T	0.36744	-0.9735	10	0.62326	D	0.03	.	9.2164	0.37351	0.0:0.0:0.4586:0.5414	.	70;70;70	B4DKR9;B4DK69;P52895	.;.;AK1C2_HUMAN	V	70	ENSP00000370129:A70V;ENSP00000392694:A70V;ENSP00000385221:A70V;ENSP00000408440:A70V	ENSP00000370129:A70V	A	-	2	0	AKR1C2	5033749	0.876000	0.30132	0.896000	0.35187	0.326000	0.28443	3.023000	0.49666	-0.272000	0.09259	0.205000	0.17691	GCA	G|0.998;A|0.002	0.002	strong		0.443	AKR1C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046531.1	NM_001354	
HIP1R	9026	hgsc.bcm.edu	37	12	123341199	123341199	+	Missense_Mutation	SNP	A	A	C	rs7972242	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:123341199A>C	ENST00000253083.4	+	17	1671	c.1546A>C	c.(1546-1548)Aag>Cag	p.K516Q		NM_003959.1	NP_003950.1	O75146	HIP1R_HUMAN	huntingtin interacting protein 1 related	516			K -> Q (in dbSNP:rs7972242).		receptor-mediated endocytosis (GO:0006898)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)	phosphatidylinositol binding (GO:0035091)			breast(1)|endometrium(5)|kidney(6)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	26	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;4.6e-05)|Epithelial(86;0.000119)|BRCA - Breast invasive adenocarcinoma(302;0.2)		CCAGCTGGAGAAGCTCAAGAG	0.662													A|||	203	0.0405351	0.146	0.013	5008	,	,		15928	0.0		0.001	False		,,,				2504	0.0				p.K516Q		Atlas-SNP	.											.	HIP1R	68	.	0			c.A1546C						PASS	.	A	GLN/LYS	542,3854		30,482,1686	29.0	33.0	32.0		1546	2.2	1.0	12	dbSNP_116	32	7,8587		0,7,4290	yes	missense	HIP1R	NM_003959.1	53	30,489,5976	CC,CA,AA		0.0815,12.3294,4.2263	benign	516/1069	123341199	549,12441	2198	4297	6495	SO:0001583	missense	9026	exon17			CTGGAGAAGCTCA	AB013384	CCDS31922.1	12q24	2007-12-07			ENSG00000130787	ENSG00000130787			18415	protein-coding gene	gene with protein product		605613				16415883	Standard	NM_003959		Approved	KIAA0655, HIP3, HIP12, FLJ14000, ILWEQ	uc001udj.1	O75146	OTTHUMG00000168765	ENST00000253083.4:c.1546A>C	12.37:g.123341199A>C	ENSP00000253083:p.Lys516Gln	108.0	0.0	0		88.0	42.0	0.477273	NM_003959	A6NHQ6|Q6NXG8|Q9UED9	Missense_Mutation	SNP	ENST00000253083.4	37	CCDS31922.1	69	0.03159340659340659	64	0.13008130081300814	5	0.013812154696132596	0	0.0	0	0.0	A	9.125	1.009956	0.19277	0.123294	8.15E-4	ENSG00000130787	ENST00000253083	T	0.14766	2.48	4.77	2.24	0.28232	.	0.103731	0.64402	D	0.000003	T	0.00073	0.0002	N	0.20483	0.58	0.32676	P	0.516181	B;B;B	0.14012	0.0;0.0;0.009	B;B;B	0.09377	0.001;0.004;0.004	T	0.38436	-0.9661	9	0.16420	T	0.52	-44.0738	5.6228	0.17467	0.5893:0.3098:0.101:0.0	rs7972242;rs7972242	516;516;504	O75146;Q6NXG8;B3KQW8	HIP1R_HUMAN;.;.	Q	516	ENSP00000253083:K516Q	ENSP00000253083:K516Q	K	+	1	0	HIP1R	121907152	0.990000	0.36364	0.998000	0.56505	0.681000	0.39784	0.484000	0.22308	0.682000	0.31407	0.459000	0.35465	AAG	A|0.954;C|0.046	0.046	strong		0.662	HIP1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400935.1	NM_003959	
FILIP1	27145	hgsc.bcm.edu	37	6	76022541	76022541	+	Missense_Mutation	SNP	G	G	A	rs34807169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:76022541G>A	ENST00000237172.7	-	5	3337	c.3007C>T	c.(3007-3009)Ccc>Tcc	p.P1003S	FILIP1_ENST00000498523.1_5'UTR|FILIP1_ENST00000393004.2_Missense_Mutation_p.P1003S|FILIP1_ENST00000370020.1_Missense_Mutation_p.P904S	NM_015687.2	NP_056502.1	Q7Z7B0	FLIP1_HUMAN	filamin A interacting protein 1	1003			P -> S (in dbSNP:rs34807169).							breast(3)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(28)|ovary(1)|pancreas(1)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)	80						GGGGATGTGGGCCTGTCTGCA	0.502													G|||	151	0.0301518	0.1112	0.0058	5008	,	,		19431	0.0		0.0	False		,,,				2504	0.0				p.P1003S		Atlas-SNP	.											.	FILIP1	173	.	0			c.C3007T						PASS	.	G	SER/PRO	365,4041	187.1+/-213.8	15,335,1853	117.0	111.0	113.0		3007	5.1	1.0	6	dbSNP_126	113	5,8595	4.3+/-15.6	0,5,4295	yes	missense	FILIP1	NM_015687.2	74	15,340,6148	AA,AG,GG		0.0581,8.2842,2.8448	probably-damaging	1003/1214	76022541	370,12636	2203	4300	6503	SO:0001583	missense	27145	exon5			ATGTGGGCCTGTC	AB033101	CCDS4984.1, CCDS75480.1	6q14.1	2008-02-05			ENSG00000118407	ENSG00000118407			21015	protein-coding gene	gene with protein product		607307				10574462	Standard	XM_005248713		Approved	FILIP, KIAA1275	uc003pia.3	Q7Z7B0	OTTHUMG00000015056	ENST00000237172.7:c.3007C>T	6.37:g.76022541G>A	ENSP00000237172:p.Pro1003Ser	241.0	1.0	0.00414938		237.0	109.0	0.459916	NM_015687	B2RMU6|Q5VUL6|Q86TC3|Q8N8B9|Q96SK6|Q9NVI8|Q9ULE5	Missense_Mutation	SNP	ENST00000237172.7	37	CCDS4984.1	60	0.027472527472527472	57	0.11585365853658537	3	0.008287292817679558	0	0.0	0	0.0	G	15.74	2.922149	0.52653	0.082842	5.81E-4	ENSG00000118407	ENST00000393004;ENST00000237172;ENST00000370020	T;T;T	0.19532	2.14;2.14;2.15	6.03	5.14	0.70334	.	0.273243	0.42548	D	0.000686	T	0.11452	0.0279	L	0.53249	1.67	0.53688	D	0.999977	B;B;B	0.31680	0.335;0.073;0.12	B;B;B	0.32624	0.058;0.103;0.149	T	0.05115	-1.0905	10	0.16420	T	0.52	-8.9487	17.2101	0.86928	0.0:0.1259:0.8741:0.0	rs34807169	1003;1003;1003	A8K2G7;Q7Z7B0;Q7Z7B0-2	.;FLIP1_HUMAN;.	S	1003;1003;904	ENSP00000376728:P1003S;ENSP00000237172:P1003S;ENSP00000359037:P904S	ENSP00000237172:P1003S	P	-	1	0	FILIP1	76079261	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	4.086000	0.57664	1.518000	0.48934	0.655000	0.94253	CCC	G|0.973;A|0.027	0.027	strong		0.502	FILIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041263.1	XM_029179	
NID2	22795	hgsc.bcm.edu	37	14	52486850	52486850	+	Silent	SNP	G	G	A	rs8007166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:52486850G>A	ENST00000216286.5	-	13	2720	c.2721C>T	c.(2719-2721)tgC>tgT	p.C907C	NID2_ENST00000541773.1_Silent_p.C806C	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	907	EGF-like 5; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					GAGTATTGTAGCAGGTAGCTG	0.463													g|||	144	0.028754	0.1051	0.0072	5008	,	,		18243	0.0		0.0	False		,,,				2504	0.0				p.C907C		Atlas-SNP	.											.	NID2	201	.	0			c.C2721T						PASS	.	G		345,4061	181.2+/-209.3	15,315,1873	127.0	110.0	115.0		2721	4.6	1.0	14	dbSNP_116	115	6,8594	3.7+/-12.6	0,6,4294	no	coding-synonymous	NID2	NM_007361.3		15,321,6167	AA,AG,GG		0.0698,7.8302,2.6988		907/1376	52486850	351,12655	2203	4300	6503	SO:0001819	synonymous_variant	22795	exon13			ATTGTAGCAGGTA	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.2721C>T	14.37:g.52486850G>A		111.0	0.0	0		115.0	60.0	0.521739	NM_007361	A8K6I7|B4DU19|O43710	Silent	SNP	ENST00000216286.5	37	CCDS9706.1																																																																																			G|0.971;A|0.029	0.029	strong		0.463	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1		
PKHD1L1	93035	hgsc.bcm.edu	37	8	110492328	110492328	+	Missense_Mutation	SNP	A	A	C	rs140472257	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:110492328A>C	ENST00000378402.5	+	55	9391	c.9287A>C	c.(9286-9288)tAc>tCc	p.Y3096S		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	3096	G8 2. {ECO:0000255|PROSITE- ProRule:PRU00817}.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			GAATCTTCTTACAGAGAAGTT	0.348										HNSCC(38;0.096)			A|||	43	0.00858626	0.0303	0.0043	5008	,	,		17254	0.0		0.0	False		,,,				2504	0.0				p.Y3096S		Atlas-SNP	.											.	PKHD1L1	522	.	0			c.A9287C						PASS	.	A	SER/TYR	59,3605		0,59,1773	51.0	52.0	52.0		9287	3.8	0.2	8	dbSNP_134	52	0,8158		0,0,4079	yes	missense	PKHD1L1	NM_177531.4	144	0,59,5852	CC,CA,AA		0.0,1.6103,0.4991	benign	3096/4244	110492328	59,11763	1832	4079	5911	SO:0001583	missense	93035	exon55			CTTCTTACAGAGA	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.9287A>C	8.37:g.110492328A>C	ENSP00000367655:p.Tyr3096Ser	149.0	0.0	0		138.0	58.0	0.42029	NM_177531	Q567P2|Q9UF27	Missense_Mutation	SNP	ENST00000378402.5	37	CCDS47911.1	15	0.006868131868131868	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	0	0.0	A	8.551	0.875589	0.17395	0.016103	0.0	ENSG00000205038	ENST00000378402	D	0.85411	-1.98	5.01	3.83	0.44106	G8 domain (2);	0.589185	0.17371	N	0.176674	T	0.69557	0.3124	M	0.76574	2.34	0.22213	N	0.999281	B	0.20164	0.042	B	0.32022	0.139	T	0.69176	-0.5214	10	0.36615	T	0.2	.	10.3982	0.44214	0.8352:0.1648:0.0:0.0	.	3096	Q86WI1	PKHL1_HUMAN	S	3096	ENSP00000367655:Y3096S	ENSP00000367655:Y3096S	Y	+	2	0	PKHD1L1	110561504	0.951000	0.32395	0.236000	0.24074	0.176000	0.22953	3.178000	0.50879	0.840000	0.34995	-0.323000	0.08544	TAC	A|0.993;C|0.007	0.007	strong		0.348	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
N4BP2L2	10443	hgsc.bcm.edu	37	13	33110831	33110831	+	Missense_Mutation	SNP	C	C	T	rs149614093	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:33110831C>T	ENST00000267068.3	-	2	498	c.334G>A	c.(334-336)Gca>Aca	p.A112T	N4BP2L2_ENST00000399396.3_Intron|N4BP2L2_ENST00000357505.6_Intron|N4BP2L2_ENST00000504114.1_Intron|N4BP2L2_ENST00000446957.2_Missense_Mutation_p.A112T	NM_014887.2	NP_055702.1	Q92802	N42L2_HUMAN	NEDD4 binding protein 2-like 2	112					negative regulation of hematopoietic stem cell differentiation (GO:1902037)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hematopoietic stem cell proliferation (GO:1902035)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)|RNA polymerase II transcription corepressor activity (GO:0001106)			kidney(4)|large_intestine(3)|liver(1)|lung(6)|skin(1)|urinary_tract(1)	16		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)		TCATCGTCTGCGGATACTAAT	0.413													T|||	8	0.00159744	0.0053	0.0014	5008	,	,		19703	0.0		0.0	False		,,,				2504	0.0				p.A112T		Atlas-SNP	.											.	N4BP2L2	90	.	0			c.G334A						PASS	.	T	THR/ALA,	35,4371	822.9+/-416.5	0,35,2168	194.0	193.0	193.0		334,	-0.4	0.0	13	dbSNP_134	193	0,8600		0,0,4300	yes	missense,intron	N4BP2L2	NM_014887.2,NM_033111.3	58,	0,35,6468	TT,TC,CC		0.0,0.7944,0.2691	,	112/584,	33110831	35,12971	2203	4300	6503	SO:0001583	missense	10443	exon2			CGTCTGCGGATAC	U50532	CCDS9346.1, CCDS45024.1, CCDS61307.1	13q13.1	2010-12-02			ENSG00000244754	ENSG00000244754			26916	protein-coding gene	gene with protein product	"""phosphonoformate immuno-associated protein 5"""	615788				8812419	Standard	NM_014887		Approved	CG005, PFAAP5	uc010abe.1	Q92802	OTTHUMG00000016700	ENST00000267068.3:c.334G>A	13.37:g.33110831C>T	ENSP00000267068:p.Ala112Thr	184.0	0.0	0		192.0	85.0	0.442708	NM_014887	A3KME8	Missense_Mutation	SNP	ENST00000267068.3	37	CCDS9346.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	0.982	-0.696861	0.03279	0.007944	0.0	ENSG00000244754	ENST00000446957;ENST00000505213;ENST00000267068	T;T;T	0.41400	1.0;1.0;1.0	5.09	-0.355	0.12587	.	.	.	.	.	T	0.07818	0.0196	N	0.00707	-1.245	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.30297	-0.9983	9	0.15499	T	0.54	-16.1287	5.0255	0.14383	0.1598:0.4478:0.0:0.3924	.	112;112	D6R968;Q92802	.;N42L2_HUMAN	T	112	ENSP00000394239:A112T;ENSP00000423362:A112T;ENSP00000267068:A112T	ENSP00000267068:A112T	A	-	1	0	N4BP2L2	32008831	0.005000	0.15991	0.000000	0.03702	0.071000	0.16799	-0.142000	0.10311	-0.249000	0.09569	-0.360000	0.07572	GCA	C|0.998;T|0.002	0.002	strong		0.413	N4BP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044421.1	NM_014887	
DSCR3	10311	hgsc.bcm.edu	37	21	38605694	38605694	+	Missense_Mutation	SNP	G	G	A	rs145630556	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:38605694G>A	ENST00000309117.6	-	4	638	c.401C>T	c.(400-402)aCa>aTa	p.T134I	DSCR3_ENST00000539844.1_Intron|DSCR3_ENST00000398998.1_Missense_Mutation_p.T86I|DSCR3_ENST00000399000.3_5'UTR|AP001432.14_ENST00000440629.1_lincRNA|DSCR3_ENST00000399001.1_Intron|DSCR3_ENST00000476950.1_Intron|DSCR3_ENST00000288304.5_Missense_Mutation_p.T92I	NM_006052.1	NP_006043.1	O14972	DSCR3_HUMAN	Down syndrome critical region gene 3	134						nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(3)|lung(3)	9						ACAGGTCTTTGTCAAGTCCTT	0.463													G|||	11	0.00219649	0.0083	0.0	5008	,	,		17905	0.0		0.0	False		,,,				2504	0.0				p.T134I		Atlas-SNP	.											.	DSCR3	21	.	0			c.C401T						PASS	.	G	ILE/THR	26,4380	31.7+/-61.6	0,26,2177	112.0	98.0	103.0		401	5.0	0.9	21	dbSNP_134	103	0,8600		0,0,4300	yes	missense	DSCR3	NM_006052.1	89	0,26,6477	AA,AG,GG		0.0,0.5901,0.1999	benign	134/298	38605694	26,12980	2203	4300	6503	SO:0001583	missense	10311	exon4			GTCTTTGTCAAGT	D87343	CCDS33553.1	21q22.2	2008-05-22			ENSG00000157538	ENSG00000157538			3044	protein-coding gene	gene with protein product		605298				9399594	Standard	NM_006052		Approved	DCRA	uc002ywf.1	O14972	OTTHUMG00000086659	ENST00000309117.6:c.401C>T	21.37:g.38605694G>A	ENSP00000311399:p.Thr134Ile	73.0	0.0	0		74.0	33.0	0.445946	NM_006052	B2R6T8|B7Z6B1|D3DSH4|Q2TAY6	Missense_Mutation	SNP	ENST00000309117.6	37	CCDS33553.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	G	17.52	3.411061	0.62399	0.005901	0.0	ENSG00000157538	ENST00000309117;ENST00000288304;ENST00000398998	T	0.06933	3.24	5.0	5.0	0.66597	.	0.051278	0.85682	D	0.000000	T	0.11707	0.0285	M	0.72894	2.215	0.48288	D	0.99962	P	0.40834	0.73	B	0.42361	0.385	T	0.01504	-1.1338	10	0.38643	T	0.18	-0.2541	18.6523	0.91435	0.0:0.0:1.0:0.0	.	134	O14972	DSCR3_HUMAN	I	134;92;86	ENSP00000311399:T134I	ENSP00000288304:T92I	T	-	2	0	DSCR3	37527564	1.000000	0.71417	0.939000	0.37840	0.996000	0.88848	5.652000	0.67959	2.462000	0.83206	0.455000	0.32223	ACA	G|0.998;A|0.002	0.002	strong		0.463	DSCR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194807.1		
KRTAP10-1	386677	hgsc.bcm.edu	37	21	45959279	45959279	+	Missense_Mutation	SNP	C	C	T	rs28644341	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45959279C>T	ENST00000400375.1	-	1	799	c.755G>A	c.(754-756)tGt>tAt	p.C252Y	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198691.2	NP_941964.2	P60331	KR101_HUMAN	keratin associated protein 10-1	252	24 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				breast(1)|central_nervous_system(1)|endometrium(1)|lung(3)|prostate(4)|skin(1)	11						GGCAGGGGCACAGCAGGAGGA	0.726													C|||	48	0.00958466	0.0356	0.0014	5008	,	,		14804	0.0		0.0	False		,,,				2504	0.0				p.C252Y		Atlas-SNP	.											.	KRTAP10-1	34	.	0			c.G755A						PASS	.	C	TYR/CYS,	119,4287	82.4+/-120.9	6,107,2090	43.0	50.0	48.0		755,	2.0	0.0	21	dbSNP_125	48	0,8600		0,0,4300	no	missense,intron	TSPEAR,KRTAP10-1	NM_198691.2,NM_144991.2	194,	6,107,6390	TT,TC,CC		0.0,2.7009,0.915	probably-damaging,	252/283,	45959279	119,12887	2203	4300	6503	SO:0001583	missense	386677	exon1			GGGGCACAGCAGG	AJ566380	CCDS42954.1	21q22.3	2007-10-05			ENSG00000215455	ENSG00000215455		"""Keratin associated proteins"""	22966	protein-coding gene	gene with protein product				KRTAP18-1			Standard	NM_198691		Approved	KAP10.1, KAP18.1	uc002zfh.1	P60331	OTTHUMG00000057627	ENST00000400375.1:c.755G>A	21.37:g.45959279C>T	ENSP00000383226:p.Cys252Tyr	89.0	0.0	0		81.0	42.0	0.518519	NM_198691	Q0VAR0|Q0VAR1	Missense_Mutation	SNP	ENST00000400375.1	37	CCDS42954.1	18	0.008241758241758242	17	0.034552845528455285	1	0.0027624309392265192	0	0.0	0	0.0	c	0.012	-1.682141	0.00745	0.027009	0.0	ENSG00000215455	ENST00000400375	T	0.02345	4.33	2.93	2.0	0.26442	.	.	.	.	.	T	0.05090	0.0136	M	0.90922	3.16	0.09310	N	1	D	0.59357	0.985	D	0.63488	0.915	T	0.02313	-1.1178	9	0.46703	T	0.11	.	8.9015	0.35497	0.0:0.5471:0.4529:0.0	rs28644341	252	P60331	KR101_HUMAN	Y	252	ENSP00000383226:C252Y	ENSP00000383226:C252Y	C	-	2	0	KRTAP10-1	44783707	0.050000	0.20438	0.003000	0.11579	0.018000	0.09664	0.887000	0.28254	0.532000	0.28657	-0.499000	0.04595	TGT	C|0.991;T|0.009	0.009	strong		0.726	KRTAP10-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128030.1		
PPP1R12C	54776	hgsc.bcm.edu	37	19	55606944	55606944	+	Missense_Mutation	SNP	G	G	A	rs35849605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55606944G>A	ENST00000263433.3	-	10	1270	c.1255C>T	c.(1255-1257)Cgc>Tgc	p.R419C	PPP1R12C_ENST00000435544.2_Missense_Mutation_p.R345C|PPP1R12C_ENST00000376393.2_Missense_Mutation_p.R419C	NM_001271618.1|NM_017607.2	NP_001258547.1|NP_060077.1			protein phosphatase 1, regulatory subunit 12C											central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	22			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0449)		AGGCCAAAGCGCCTGGAGAAG	0.627													G|||	126	0.0251597	0.0923	0.0058	5008	,	,		14816	0.0		0.0	False		,,,				2504	0.0				p.R419C		Atlas-SNP	.											.	PPP1R12C	46	.	0			c.C1255T						PASS	.	G	CYS/ARG	353,4039		9,335,1852	10.0	12.0	11.0		1255	2.9	1.0	19	dbSNP_126	11	3,8557		0,3,4277	yes	missense	PPP1R12C	NM_017607.2	180	9,338,6129	AA,AG,GG		0.035,8.0373,2.7486	probably-damaging	419/783	55606944	356,12596	2196	4280	6476	SO:0001583	missense	54776	exon10			CAAAGCGCCTGGA	AF312028	CCDS12916.1	19q13.42	2013-01-10	2011-10-04		ENSG00000125503	ENSG00000125503		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	14947	protein-coding gene	gene with protein product	"""myosin-binding subunit 85"""	613245	"""leukocyte receptor cluster (LRC) member 3"", ""protein phosphatase 1, regulatory (inhibitor) subunit 12C"""	LENG3		11399775	Standard	NM_017607		Approved	DKFZP434D0412, p84, MBS85, p85	uc002qix.4	Q9BZL4		ENST00000263433.3:c.1255C>T	19.37:g.55606944G>A	ENSP00000263433:p.Arg419Cys	56.0	0.0	0		76.0	39.0	0.513158	NM_017607		Missense_Mutation	SNP	ENST00000263433.3	37	CCDS12916.1	51	0.023351648351648352	49	0.09959349593495935	2	0.0055248618784530384	0	0.0	0	0.0	G	18.24	3.580072	0.65992	0.080373	3.5E-4	ENSG00000125503	ENST00000263433;ENST00000376393;ENST00000435544	T;T;T	0.70045	-0.3;-0.32;-0.45	3.95	2.91	0.33838	.	0.302492	0.23868	N	0.043762	T	0.05044	0.0135	M	0.72353	2.195	0.43703	D	0.99616	D;D;D	0.61697	0.99;0.987;0.978	P;P;P	0.50896	0.556;0.653;0.451	T	0.36672	-0.9738	10	0.87932	D	0	.	6.5557	0.22460	0.1281:0.0:0.8719:0.0	rs35849605	345;418;419	B4DME2;Q9BZL4-3;Q9BZL4	.;.;PP12C_HUMAN	C	419;419;345	ENSP00000263433:R419C;ENSP00000365573:R419C;ENSP00000387833:R345C	ENSP00000263433:R419C	R	-	1	0	PPP1R12C	60298756	0.719000	0.27986	0.986000	0.45419	0.973000	0.67179	0.866000	0.27954	2.147000	0.66899	0.549000	0.68633	CGC	G|0.958;A|0.042	0.042	strong		0.627	PPP1R12C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451814.2	NM_017607	
PTPRZ1	5803	hgsc.bcm.edu	37	7	121652964	121652964	+	Silent	SNP	T	T	C	rs139671030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:121652964T>C	ENST00000393386.2	+	12	4275	c.3864T>C	c.(3862-3864)agT>agC	p.S1288S	PTPRZ1_ENST00000483028.1_3'UTR|PTPRZ1_ENST00000449182.1_Intron	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	1288					axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						CTTTGTACAGTAATGATGAGT	0.398													T|||	22	0.00439297	0.0166	0.0	5008	,	,		20087	0.0		0.0	False		,,,				2504	0.0				p.S1288S		Atlas-SNP	.											.	PTPRZ1	605	.	0			c.T3864C						PASS	.	T	,,	46,4360	45.3+/-79.5	0,46,2157	74.0	69.0	70.0		,,3864	-1.6	0.0	7	dbSNP_134	70	0,8600		0,0,4300	yes	intron,intron,coding-synonymous	PTPRZ1	NM_001206838.1,NM_001206839.1,NM_002851.2	,,	0,46,6457	CC,CT,TT		0.0,1.044,0.3537	,,	,,1288/2316	121652964	46,12960	2203	4300	6503	SO:0001819	synonymous_variant	5803	exon12			GTACAGTAATGAT	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.3864T>C	7.37:g.121652964T>C		116.0	0.0	0		114.0	52.0	0.45614	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Silent	SNP	ENST00000393386.2	37	CCDS34740.1																																																																																			T|0.997;C|0.003	0.003	strong		0.398	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	
METTL15	196074	hgsc.bcm.edu	37	11	28351963	28351963	+	Missense_Mutation	SNP	A	A	T	rs11030280	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:28351963A>T	ENST00000407364.3	+	7	1151	c.799A>T	c.(799-801)Att>Ttt	p.I267F	METTL15_ENST00000406787.3_Missense_Mutation_p.Y252F|METTL15_ENST00000342303.5_3'UTR|METTL15_ENST00000303459.6_3'UTR			A6NJ78	MET15_HUMAN	methyltransferase like 15	267			I -> F (in dbSNP:rs11030280).				methyltransferase activity (GO:0008168)			NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(2)|ovary(2)|skin(1)|urinary_tract(1)	14						TCCCTCTGCTATTTATACACG	0.368													a|||	66	0.0131789	0.0484	0.0029	5008	,	,		18196	0.0		0.0	False		,,,				2504	0.0				p.I267F		Atlas-SNP	.											.	METTL15	63	.	0			c.A799T						PASS	.						26.0	20.0	22.0					11																	28351963		692	1591	2283	SO:0001583	missense	196074	exon7			TCTGCTATTTATA	AL832668	CCDS31450.1, CCDS44559.1, CCDS73269.1	11p14.1	2011-03-02	2011-03-02	2011-03-02	ENSG00000169519	ENSG00000169519			26606	protein-coding gene	gene with protein product			"""methyltransferase 5 domain containing 1"""	METT5D1		12477932	Standard	NM_152636		Approved	FLJ33979	uc001msh.2	A6NJ78	OTTHUMG00000150448	ENST00000407364.3:c.799A>T	11.37:g.28351963A>T	ENSP00000384369:p.Ile267Phe	229.0	1.0	0.00436681		242.0	117.0	0.483471	NM_001113528	A8MRS5|B7WNU2|Q3MHD3|Q8N601|Q8NBA7	Missense_Mutation	SNP	ENST00000407364.3	37	CCDS44559.1	16|16	0.007326007326007326|0.007326007326007326	16|16	0.032520325203252036|0.032520325203252036	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	a|a	6.700|6.700	0.497771|0.497771	0.12762|0.12762	.|.	.|.	ENSG00000169519|ENSG00000169519	ENST00000407364|ENST00000406787	T|T	0.22743|0.42513	1.94|0.97	5.32|5.32	-8.55|-8.55	0.00908|0.00908	S-adenosyl-L-methionine-dependent methyltransferase, MraW, recognition domain (2);|.	1.236540|.	0.05563|.	N|.	0.569607|.	T|T	0.04497|0.04497	0.0123|0.0123	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	0.999999|0.999999	B|B	0.15473|0.02656	0.013|0.0	B|B	0.17979|0.04013	0.02|0.001	T|T	0.14227|0.14227	-1.0480|-1.0480	9|8	.|.	.|.	.|.	.|.	1.7987|1.7987	0.03067|0.03067	0.2726:0.3206:0.2653:0.1414|0.2726:0.3206:0.2653:0.1414	rs11030280|rs11030280	267|252	A6NJ78|A6NJ78-4	MET15_HUMAN|.	F|F	267|252	ENSP00000384369:I267F|ENSP00000385507:Y252F	.|.	I|Y	+|+	1|2	0|0	METTL15|METTL15	28308539|28308539	0.002000|0.002000	0.14202|0.14202	0.010000|0.010000	0.14722|0.14722	0.688000|0.688000	0.40055|0.40055	-0.377000|-0.377000	0.07456|0.07456	-0.966000|-0.966000	0.03587|0.03587	-1.125000|-1.125000	0.01998|0.01998	ATT|TAT	A|0.993;T|0.007	0.007	strong		0.368	METTL15-003	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318135.2	NM_152636	
FAM26F	441168	hgsc.bcm.edu	37	6	116783585	116783585	+	Missense_Mutation	SNP	G	G	C	rs76716752	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:116783585G>C	ENST00000368605.1	+	2	588	c.493G>C	c.(493-495)Gac>Cac	p.D165H	RP1-93H18.6_ENST00000476099.1_RNA|FAM26F_ENST00000368606.3_Intron	NM_001010919.1	NP_001010919.1	Q5R3K3	FA26F_HUMAN	family with sequence similarity 26, member F	165					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				large_intestine(2)|lung(1)	3				GBM - Glioblastoma multiforme(226;0.0402)|all cancers(137;0.0627)|OV - Ovarian serous cystadenocarcinoma(136;0.0655)|Epithelial(106;0.231)		GGACGTGCAGGACCTCCTGAA	0.716													G|||	243	0.0485224	0.1747	0.0086	5008	,	,		12495	0.0		0.006	False		,,,				2504	0.0				p.S165P		Atlas-SNP	.											.	FAM26F	12	.	0			c.T493C						PASS	.	G	HIS/ASP	207,1869		8,191,839	3.0	2.0	2.0		493	0.7	0.0	6	dbSNP_131	2	9,2855		0,9,1423	yes	missense	FAM26F	NM_001010919.1	81	8,200,2262	CC,CG,GG		0.3142,9.9711,4.3725	possibly-damaging	165/316	116783585	216,4724	1038	1432	2470	SO:0001583	missense	441168	exon2			GTGCAGGACCTCC	AF086130	CCDS34519.1, CCDS64506.1	6q22.1	2007-06-20			ENSG00000188820	ENSG00000188820			33391	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 187"""	C6orf187			Standard	NM_001010919		Approved	RP1-93H18.5, OTTHUMP00000017061, OTTHUMP00000017062, dJ93H18.5	uc003pwv.4	Q5R3K3	OTTHUMG00000015438	ENST00000368605.1:c.493G>C	6.37:g.116783585G>C	ENSP00000357594:p.Asp165His	15.0	0.0	0		33.0	33.0	1	NM_001010919	B9EJB0|Q5R3K4	Missense_Mutation	SNP	ENST00000368605.1	37	CCDS34519.1	91	0.041666666666666664	84	0.17073170731707318	3	0.008287292817679558	0	0.0	4	0.005277044854881266	G	22.3	4.278004	0.80692	0.099711	0.003142	ENSG00000188820	ENST00000368605	T	0.17528	2.27	4.82	0.664	0.17890	.	1.210450	0.05680	N	0.590259	T	0.09598	0.0236	L	0.46157	1.445	0.09310	N	1	D	0.57257	0.979	P	0.47915	0.561	T	0.33189	-0.9878	10	0.48119	T	0.1	-3.4085	9.6311	0.39780	0.4247:0.0:0.5753:0.0	.	165	Q5R3K3	FA26F_HUMAN	H	165	ENSP00000357594:D165H	ENSP00000357594:D165H	D	+	1	0	FAM26F	116890278	0.017000	0.18338	0.001000	0.08648	0.784000	0.44337	1.686000	0.37669	-0.058000	0.13177	0.313000	0.20887	GAC	G|0.954;C|0.046	0.046	strong		0.716	FAM26F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041946.1	NM_001010919	
TMPRSS11F	389208	hgsc.bcm.edu	37	4	68934515	68934515	+	Silent	SNP	A	A	G	rs35687346	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:68934515A>G	ENST00000356291.2	-	7	635	c.576T>C	c.(574-576)tcT>tcC	p.S192S	UBA6-AS1_ENST00000500538.2_RNA|UBA6-AS1_ENST00000511571.1_RNA|UBA6-AS1_ENST00000499180.2_RNA	NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	192						extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(4)	39						GCATGTTTGAAGATGTCATCC	0.423													A|||	232	0.0463259	0.1619	0.0216	5008	,	,		21406	0.0		0.003	False		,,,				2504	0.0				p.S192S		Atlas-SNP	.											.	TMPRSS11F	79	.	0			c.T576C						PASS	.	A		551,3855	245.3+/-254.3	37,477,1689	88.0	83.0	85.0		576	-1.1	1.0	4	dbSNP_126	85	39,8561	25.1+/-72.6	0,39,4261	no	coding-synonymous	TMPRSS11F	NM_207407.2		37,516,5950	GG,GA,AA		0.4535,12.5057,4.5364		192/439	68934515	590,12416	2203	4300	6503	SO:0001819	synonymous_variant	389208	exon7			GTTTGAAGATGTC	AK122625	CCDS3520.1	4q13.2	2010-04-13			ENSG00000198092	ENSG00000198092		"""Serine peptidases / Transmembrane"""	29994	protein-coding gene	gene with protein product							Standard	NM_207407		Approved	FLJ16046	uc003hdt.1	Q6ZWK6	OTTHUMG00000129307	ENST00000356291.2:c.576T>C	4.37:g.68934515A>G		129.0	0.0	0		132.0	61.0	0.462121	NM_207407	A8MXX2	Silent	SNP	ENST00000356291.2	37	CCDS3520.1																																																																																			A|0.955;G|0.045	0.045	strong		0.423	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407	
BCL9L	283149	hgsc.bcm.edu	37	11	118770054	118770054	+	Silent	SNP	G	G	A	rs12277303	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:118770054G>A	ENST00000334801.3	-	8	4534	c.3570C>T	c.(3568-3570)aaC>aaT	p.N1190N	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	1190	Pro-rich.				canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		TCCCCTGTGCGTTGGGATGCA	0.692													G|||	262	0.0523163	0.1921	0.0101	5008	,	,		11201	0.0		0.001	False		,,,				2504	0.0				p.N1190N		Atlas-SNP	.											.	BCL9L	254	.	0			c.C3570T						PASS	.	G		401,3799		5,391,1704	5.0	6.0	6.0		3570	-0.1	0.9	11	dbSNP_120	6	6,8276		0,6,4135	no	coding-synonymous	BCL9L	NM_182557.2		5,397,5839	AA,AG,GG		0.0724,9.5476,3.2607		1190/1500	118770054	407,12075	2100	4141	6241	SO:0001819	synonymous_variant	283149	exon8			CTGTGCGTTGGGA	AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.3570C>T	11.37:g.118770054G>A		112.0	0.0	0		95.0	55.0	0.578947	NM_182557	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Silent	SNP	ENST00000334801.3	37	CCDS8403.1																																																																																			G|0.948;A|0.052	0.052	strong		0.692	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557	
ZNF540	163255	hgsc.bcm.edu	37	19	38102955	38102955	+	Silent	SNP	T	T	C	rs115588579	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38102955T>C	ENST00000592533.1	+	5	1106	c.774T>C	c.(772-774)ctT>ctC	p.L258L	ZNF540_ENST00000589117.1_Silent_p.L226L|ZNF540_ENST00000316433.4_Silent_p.L258L|ZNF540_ENST00000343599.5_Silent_p.L258L	NM_152606.4	NP_689819.1	Q8NDQ6	ZN540_HUMAN	zinc finger protein 540	258					negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of translation (GO:0017148)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|translation repressor activity, nucleic acid binding (GO:0000900)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(13)|lung(8)|skin(1)	28			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			ACCCACAACTTAATCGACATC	0.343													T|||	33	0.00658946	0.0227	0.0043	5008	,	,		18475	0.0		0.0	False		,,,				2504	0.0				p.L258L		Atlas-SNP	.											.	ZNF540	75	.	0			c.T774C						PASS	.	T	,,	77,4329	64.7+/-102.0	1,75,2127	33.0	35.0	35.0		774,678,774	1.3	0.0	19	dbSNP_132	35	1,8595		0,1,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF540	NM_001172225.1,NM_001172226.1,NM_152606.3	,,	1,76,6424	CC,CT,TT		0.0116,1.7476,0.5999	,,	258/661,226/629,258/661	38102955	78,12924	2203	4298	6501	SO:0001819	synonymous_variant	163255	exon5			ACAACTTAATCGA	AL832315	CCDS12506.1, CCDS54258.1	19q13.13	2013-01-08				ENSG00000171817		"""Zinc fingers, C2H2-type"", ""-"""	25331	protein-coding gene	gene with protein product		613903					Standard	NM_152606		Approved	DKFZp547B0714	uc002ogq.4	Q8NDQ6		ENST00000592533.1:c.774T>C	19.37:g.38102955T>C		68.0	0.0	0		51.0	26.0	0.509804	NM_152606	A0AVS5|A8K371|Q05D58|Q3LIC5|Q6ZN36|Q7Z3C8|Q86T31	Silent	SNP	ENST00000592533.1	37	CCDS12506.1																																																																																			T|0.992;C|0.008	0.008	strong		0.343	ZNF540-009	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000459481.1	NM_152606	
CHD3	1107	hgsc.bcm.edu	37	17	7792326	7792326	+	Missense_Mutation	SNP	C	C	T	rs931543	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7792326C>T	ENST00000330494.7	+	1	158	c.8C>T	c.(7-9)gCg>gTg	p.A3V	CHD3_ENST00000380358.4_Intron|CHD3_ENST00000358181.4_Missense_Mutation_p.A3V	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	3			A -> V (in dbSNP:rs931543).		centrosome organization (GO:0051297)|chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|spindle organization (GO:0007051)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(11)|kidney(6)|large_intestine(13)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	65		Prostate(122;0.202)				GTGATGAAGGCGGCAGACACT	0.468													T|||	392	0.0782748	0.2179	0.062	5008	,	,		18301	0.0278		0.0239	False		,,,				2504	0.0092				p.A3V		Atlas-SNP	.											.	CHD3	169	.	0			c.C8T						PASS	.	T	,VAL/ALA,VAL/ALA	865,3541		76,713,1414	151.0	155.0	154.0		,8,8	1.3	0.4	17	dbSNP_86	154	223,8377		4,215,4081	yes	intron,missense,missense	CHD3	NM_001005271.2,NM_001005273.2,NM_005852.3	,64,64	80,928,5495	TT,TC,CC		2.593,19.6323,8.3654	,,	,3/2001,3/1967	7792326	1088,11918	2203	4300	6503	SO:0001583	missense	1107	exon1			TGAAGGCGGCAGA	U08379	CCDS32553.2, CCDS32554.1, CCDS32555.1	17p13	2013-01-28			ENSG00000170004	ENSG00000170004		"""Zinc fingers, PHD-type"""	1918	protein-coding gene	gene with protein product		602120				9326634, 7560064	Standard	NM_001005271		Approved	Mi-2a, ZFH, Mi2-ALPHA	uc002gjd.2	Q12873	OTTHUMG00000150427	ENST00000330494.7:c.8C>T	17.37:g.7792326C>T	ENSP00000332628:p.Ala3Val	102.0	0.0	0		100.0	47.0	0.47	NM_001005273	D3DTQ9|E9PG89|Q9Y4I0	Missense_Mutation	SNP	ENST00000330494.7	37	CCDS32554.1	167	0.07646520146520147	105	0.21341463414634146	21	0.058011049723756904	23	0.04020979020979021	18	0.023746701846965697	N	14.54	2.564799	0.45694	0.196323	0.02593	ENSG00000170004	ENST00000358181;ENST00000330494	D;D	0.89552	-2.53;-2.53	3.7	1.29	0.21616	.	.	.	.	.	T	0.00144	0.0004	N	0.08118	0	0.80722	P	0.0	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.03394	-1.1041	8	0.16896	T	0.51	.	5.2159	0.15342	0.3615:0.5187:0.1197:0.0	rs931543;rs58342197;rs931543	3;3	Q12873-2;Q12873	.;CHD3_HUMAN	V	3	ENSP00000350907:A3V;ENSP00000332628:A3V	ENSP00000332628:A3V	A	+	2	0	CHD3	7733051	0.033000	0.19621	0.446000	0.26920	0.797000	0.45037	0.104000	0.15313	0.096000	0.17463	-0.398000	0.06409	GCG	C|0.915;T|0.085	0.085	strong		0.468	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273	
GPR26	2849	hgsc.bcm.edu	37	10	125447511	125447511	+	Silent	SNP	G	G	A	rs62640899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:125447511G>A	ENST00000284674.1	+	3	902	c.849G>A	c.(847-849)gcG>gcA	p.A283A		NM_153442.3	NP_703143.1	Q8NDV2	GPR26_HUMAN	G protein-coupled receptor 26	283					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(3)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	20		Colorectal(57;0.178)|Glioma(114;0.222)|all_neural(114;0.226)				AGTGCTTGGCGTACAGCAAGG	0.577													G|||	139	0.0277556	0.1006	0.0072	5008	,	,		17997	0.0		0.001	False		,,,				2504	0.0				p.A283A		Atlas-SNP	.											.	GPR26	47	.	0			c.G849A						PASS	.	G		363,4043	186.4+/-213.3	16,331,1856	91.0	80.0	84.0		849	2.3	1.0	10	dbSNP_129	84	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	GPR26	NM_153442.3		16,338,6149	AA,AG,GG		0.0814,8.2388,2.8448		283/338	125447511	370,12636	2203	4300	6503	SO:0001819	synonymous_variant	2849	exon3			CTTGGCGTACAGC		CCDS7636.1	10q26.2-q26.3	2012-08-21			ENSG00000154478	ENSG00000154478		"""GPCR / Class A : Orphans"""	4481	protein-coding gene	gene with protein product		604847					Standard	NM_153442		Approved		uc001lhh.3	Q8NDV2	OTTHUMG00000019204	ENST00000284674.1:c.849G>A	10.37:g.125447511G>A		58.0	0.0	0		67.0	31.0	0.462687	NM_153442	Q2M2E2	Silent	SNP	ENST00000284674.1	37	CCDS7636.1																																																																																			G|0.970;A|0.030	0.030	strong		0.577	GPR26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050850.1		
PFAS	5198	hgsc.bcm.edu	37	17	8172141	8172141	+	Missense_Mutation	SNP	G	G	A	rs73975814	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:8172141G>A	ENST00000314666.6	+	27	3806	c.3673G>A	c.(3673-3675)Gcc>Acc	p.A1225T	PFAS_ENST00000545834.1_Missense_Mutation_p.A801T	NM_012393.2	NP_036525.1	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	1225	Glutamine amidotransferase type-1.				'de novo' IMP biosynthetic process (GO:0006189)|glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|phosphoribosylformylglycinamidine synthase activity (GO:0004642)			central_nervous_system(3)|endometrium(8)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	35					L-Glutamine(DB00130)	GATGGAGGGCGCCGTGCTGCC	0.697													G|||	46	0.0091853	0.0333	0.0	5008	,	,		14129	0.001		0.0	False		,,,				2504	0.001				p.A1225T		Atlas-SNP	.											.	PFAS	91	.	0			c.G3673A						PASS	.	G	THR/ALA	73,4329		0,73,2128	33.0	37.0	36.0		3673	4.4	0.0	17	dbSNP_130	36	0,8592		0,0,4296	no	missense	PFAS	NM_012393.2	58	0,73,6424	AA,AG,GG		0.0,1.6583,0.5618	benign	1225/1339	8172141	73,12921	2201	4296	6497	SO:0001583	missense	5198	exon27			GAGGGCGCCGTGC	AB002359	CCDS11136.1	17p13.1	2008-07-31	2008-07-31		ENSG00000178921	ENSG00000178921	6.3.5.3		8863	protein-coding gene	gene with protein product	"""FGAR amidotransferase"""	602133				8110788	Standard	NM_012393		Approved	PURL, FGARAT, KIAA0361	uc002gkr.3	O15067	OTTHUMG00000108188	ENST00000314666.6:c.3673G>A	17.37:g.8172141G>A	ENSP00000313490:p.Ala1225Thr	17.0	0.0	0		18.0	10.0	0.555556	NM_012393	A6H8V8	Missense_Mutation	SNP	ENST00000314666.6	37	CCDS11136.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	G	13.30	2.195407	0.38806	0.016583	0.0	ENSG00000178921	ENST00000545834;ENST00000314666;ENST00000546020	T;T	0.29397	1.57;2.3	5.41	4.41	0.53225	Glutamine amidotransferase type 1 (1);	0.192639	0.45606	D	0.000358	T	0.08670	0.0215	N	0.10685	0.025	0.09310	N	1	B;B	0.30439	0.279;0.279	B;B	0.31390	0.129;0.129	T	0.14504	-1.0470	10	0.87932	D	0	-12.0495	10.9394	0.47264	0.0:0.0:0.6471:0.3529	.	1225;1225	A8K8N7;O15067	.;PUR4_HUMAN	T	801;1225;634	ENSP00000441706:A801T;ENSP00000313490:A1225T	ENSP00000313490:A1225T	A	+	1	0	PFAS	8112866	0.998000	0.40836	0.033000	0.17914	0.848000	0.48234	3.977000	0.56874	1.220000	0.43490	0.563000	0.77884	GCC	G|0.994;A|0.006	0.006	strong		0.697	PFAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226994.2		
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39262091	39262091	+	Missense_Mutation	SNP	C	C	T	rs571292694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39262091C>T	ENST00000391415.1	+	1	508	c.451C>T	c.(451-453)Cgc>Tgc	p.R151C		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	151	29 X 5 AA repeats of C-C-[RQVHIEK]- [SPTR]-[VSTQCRNP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						caactgctgccgccccagctg	0.662													C|||	26	0.00519169	0.0197	0.0	5008	,	,		18753	0.0		0.0	False		,,,				2504	0.0				p.R151C		Atlas-SNP	.											.	KRTAP4-9	110	.	0			c.C451T						PASS	.						5.0	8.0	7.0					17																	39262091		667	1548	2215	SO:0001583	missense	100132386	exon1			TGCTGCCGCCCCA	AJ406941	CCDS54124.1	17q21.2	2013-06-25			ENSG00000212722	ENSG00000212722		"""Keratin associated proteins"""	18910	protein-coding gene	gene with protein product							Standard	NM_001146041		Approved	KAP4.9	uc010wfp.2	Q9BYQ8	OTTHUMG00000133584	ENST00000391415.1:c.451C>T	17.37:g.39262091C>T	ENSP00000375234:p.Arg151Cys	126.0	0.0	0		186.0	64.0	0.344086	NM_001146041		Missense_Mutation	SNP	ENST00000391415.1	37	CCDS54124.1	.	.	.	.	.	.	.	.	.	.	.	11.75	1.733214	0.30684	.	.	ENSG00000212722	ENST00000377734;ENST00000391415;ENST00000333994	T	0.00609	6.24	3.18	-6.36	0.01969	.	1.407670	0.05656	U	0.586011	T	0.00695	0.0023	M	0.69358	2.11	0.09310	N	0.999995	B	0.13594	0.008	B	0.06405	0.002	T	0.37033	-0.9723	10	0.54805	T	0.06	.	3.1538	0.06497	0.4027:0.2953:0.2179:0.0841	.	151	Q9BYQ8	KRA49_HUMAN	C	139;151;142	ENSP00000375234:R151C	ENSP00000334461:R142C	R	+	1	0	KRTAP4-9	36515617	0.000000	0.05858	0.000000	0.03702	0.674000	0.39518	-0.828000	0.04419	-3.015000	0.00271	-0.443000	0.05667	CGC	.	.	none		0.662	KRTAP4-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257688.1	NM_001146041	
MAATS1	89876	hgsc.bcm.edu	37	3	119449159	119449159	+	Missense_Mutation	SNP	G	G	A	rs61742290	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119449159G>A	ENST00000273390.5	+	8	1030	c.953G>A	c.(952-954)cGg>cAg	p.R318Q		NM_033364.3	NP_203528	Q7Z4T9	MAAT1_HUMAN	MYCBP-associated, testis expressed 1	318						mitochondrion (GO:0005739)											TTGAATGCCCGGTGGTCTAAA	0.438													G|||	23	0.00459265	0.0151	0.0043	5008	,	,		19286	0.0		0.0	False		,,,				2504	0.0				p.R318Q		Atlas-SNP	.											C3orf15,NS,carcinoma,+1,2	.	.	2	0			c.G953A						PASS	.	G	GLN/ARG	62,4344	58.7+/-95.3	0,62,2141	193.0	196.0	195.0		953	1.5	1.0	3	dbSNP_129	195	0,8600		0,0,4300	yes	missense	C3orf15	NM_033364.3	43	0,62,6441	AA,AG,GG		0.0,1.4072,0.4767	benign	318/768	119449159	62,12944	2203	4300	6503	SO:0001583	missense	89876	exon8			ATGCCCGGTGGTC	AB063296	CCDS2994.1	3q12-q13.3	2014-07-31	2012-12-07	2012-09-26	ENSG00000183833	ENSG00000183833			24010	protein-coding gene	gene with protein product	"""AMY-1-associating protein expressed in testis 1"", ""MYCBP-binding protein"", ""spermatogenesis associated 26"""	609910	"""chromosome 3 open reading frame 15"", ""MYCBP/AMY-1-associated, testis expressed 1"""	C3orf15		12223483, 14551891, 17967944	Standard	NM_033364		Approved	AAT1, AAT1alpha, SPATA26, CaM-IP2	uc003ede.4	Q7Z4T9	OTTHUMG00000159422	ENST00000273390.5:c.953G>A	3.37:g.119449159G>A	ENSP00000273390:p.Arg318Gln	108.0	0.0	0		131.0	69.0	0.526718	NM_033364	A0AVK2|A8K1J9|B3KP23|B4DG52|B4DZ14|C9JUG4|Q68DX2|Q8TD41|Q96A45|Q96JE8	Missense_Mutation	SNP	ENST00000273390.5	37	CCDS2994.1	8	0.003663003663003663	6	0.012195121951219513	2	0.0055248618784530384	0	0.0	0	0.0	G	6.250	0.414169	0.11870	0.014072	0.0	ENSG00000183833	ENST00000273390	T	0.21734	1.99	5.2	1.55	0.23275	.	0.711873	0.14769	N	0.299528	T	0.05410	0.0143	N	0.04636	-0.2	0.80722	D	1	B;B;B;B;B	0.19935	0.008;0.04;0.012;0.019;0.005	B;B;B;B;B	0.12156	0.004;0.003;0.007;0.005;0.003	T	0.27297	-1.0078	10	0.12430	T	0.62	-20.1193	8.0697	0.30682	0.6841:0.0:0.3159:0.0	rs61742290	318;79;256;318;318	Q7Z4T9;Q9UFB4;Q7Z4T9-3;Q4G0Y0;Q7Z4T9-7	AAT1_HUMAN;.;.;.;.	Q	318	ENSP00000273390:R318Q	ENSP00000273390:R318Q	R	+	2	0	C3orf15	120931849	0.005000	0.15991	0.967000	0.41034	0.762000	0.43233	0.707000	0.25704	0.382000	0.24878	-0.484000	0.04775	CGG	G|0.995;A|0.005	0.005	strong		0.438	MAATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355222.1	NM_033364	
PDZD2	23037	hgsc.bcm.edu	37	5	32077653	32077653	+	Missense_Mutation	SNP	G	G	A	rs61745726	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:32077653G>A	ENST00000438447.1	+	19	4011	c.3623G>A	c.(3622-3624)aGc>aAc	p.S1208N	PDZD2_ENST00000282493.3_Missense_Mutation_p.S1208N			O15018	PDZD2_HUMAN	PDZ domain containing 2	1208					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						CTGGATGCCAGCCACCTCACA	0.498													G|||	454	0.090655	0.3298	0.0231	5008	,	,		18720	0.0		0.002	False		,,,				2504	0.0				p.S1208N		Atlas-SNP	.											.	PDZD2	306	.	0			c.G3623A						PASS	.	G	ASN/SER	1252,3154	430.6+/-342.6	174,904,1125	105.0	101.0	102.0		3623	4.1	0.0	5	dbSNP_129	102	4,8596	3.7+/-12.6	0,4,4296	yes	missense	PDZD2	NM_178140.2	46	174,908,5421	AA,AG,GG		0.0465,28.4158,9.6571	benign	1208/2840	32077653	1256,11750	2203	4300	6503	SO:0001583	missense	23037	exon18			ATGCCAGCCACCT	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"""PDZ domain containing 3"""	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.3623G>A	5.37:g.32077653G>A	ENSP00000402033:p.Ser1208Asn	106.0	0.0	0		121.0	121.0	1	NM_178140	Q9BXD4	Missense_Mutation	SNP	ENST00000438447.1	37	CCDS34137.1	178	0.0815018315018315	172	0.34959349593495936	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	G	5.804	0.332658	0.10956	0.284158	4.65E-4	ENSG00000133401	ENST00000438447;ENST00000382161;ENST00000282493	T;T	0.06449	3.3;3.3	4.98	4.08	0.47627	.	0.800186	0.10630	N	0.652231	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B;B	0.24823	0.112;0.063	B;B	0.22386	0.026;0.039	T	0.41161	-0.9524	9	0.10636	T	0.68	.	10.343	0.43891	0.1022:0.0:0.8977:0.0	rs61745726	1034;1208	B4E3P2;O15018	.;PDZD2_HUMAN	N	1208;1013;1208	ENSP00000402033:S1208N;ENSP00000282493:S1208N	ENSP00000282493:S1208N	S	+	2	0	PDZD2	32113410	0.543000	0.26434	0.014000	0.15608	0.054000	0.15201	3.444000	0.52914	1.049000	0.40321	0.563000	0.77884	AGC	G|0.913;A|0.087	0.087	strong		0.498	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1		
PDE9A	5152	hgsc.bcm.edu	37	21	44179112	44179112	+	Missense_Mutation	SNP	C	C	G	rs146382324	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:44179112C>G	ENST00000291539.6	+	11	874	c.814C>G	c.(814-816)Ctg>Gtg	p.L272V	PDE9A_ENST00000335440.6_Missense_Mutation_p.L170V|PDE9A_ENST00000470987.1_3'UTR|PDE9A_ENST00000349112.3_Missense_Mutation_p.L144V|PDE9A_ENST00000398224.3_Missense_Mutation_p.L145V|PDE9A_ENST00000398236.3_Missense_Mutation_p.L186V|PDE9A_ENST00000398225.3_Missense_Mutation_p.L231V|PDE9A_ENST00000398227.3_Missense_Mutation_p.L112V|PDE9A_ENST00000328862.6_Missense_Mutation_p.L246V|PDE9A_ENST00000539837.1_Missense_Mutation_p.L144V|PDE9A_ENST00000398234.3_Missense_Mutation_p.L171V|PDE9A_ENST00000398232.3_Missense_Mutation_p.L205V|PDE9A_ENST00000335512.4_Missense_Mutation_p.L212V|PDE9A_ENST00000398229.3_Missense_Mutation_p.L138V|PDE9A_ENST00000380328.2_Missense_Mutation_p.L219V	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A	272					blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|metabolic process (GO:0008152)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|large_intestine(6)|lung(8)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Caffeine(DB00201)	CCCACAGATGCTGAGCTGCCT	0.637													C|||	2	0.000399361	0.0015	0.0	5008	,	,		19507	0.0		0.0	False		,,,				2504	0.0				p.L272V		Atlas-SNP	.											.	PDE9A	69	.	0			c.C814G						PASS	.	C	VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU	11,4395	17.9+/-39.9	0,11,2192	81.0	65.0	71.0		634,433,430,655,511,193,193,556,334,163,412,508,193,163,613,691,736,193,193,814	5.1	1.0	21	dbSNP_134	71	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	PDE9A	NM_001001567.1,NM_001001568.1,NM_001001569.1,NM_001001570.1,NM_001001571.1,NM_001001572.1,NM_001001573.1,NM_001001574.1,NM_001001575.1,NM_001001576.1,NM_001001577.1,NM_001001578.1,NM_001001579.1,NM_001001580.1,NM_001001581.1,NM_001001582.1,NM_001001583.1,NM_001001584.2,NM_001001585.1,NM_002606.2	32,32,32,32,32,32,32,32,32,32,32,32,32,32,32,32,32,32,32,32	0,11,6492	GG,GC,CC		0.0,0.2497,0.0846	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	212/534,145/467,144/466,219/541,171/493,65/387,65/387,186/508,112/434,55/377,138/460,170/492,65/387,55/377,205/527,231/553,246/568,65/387,65/387,272/594	44179112	11,12995	2203	4300	6503	SO:0001583	missense	5152	exon11			CAGATGCTGAGCT	AF048837	CCDS13690.1, CCDS33567.1, CCDS33568.1, CCDS33569.1, CCDS33570.1, CCDS33571.1, CCDS42941.1, CCDS42942.1, CCDS42943.1, CCDS42944.1, CCDS42945.1, CCDS42946.1, CCDS42947.1	21q22.3	2005-11-29			ENSG00000160191	ENSG00000160191	3.1.4.17	"""Phosphodiesterases"""	8795	protein-coding gene	gene with protein product		602973				9624146	Standard	NM_001001584		Approved		uc002zbm.3	O76083	OTTHUMG00000086825	ENST00000291539.6:c.814C>G	21.37:g.44179112C>G	ENSP00000291539:p.Leu272Val	99.0	0.0	0		133.0	71.0	0.533835	NM_002606	B2RBI5|B4DFI5|D3DSJ8|D3DSJ9|O75490|O75491|O95225|Q53Y40|Q5QD39|Q86SF7|Q86SI6|Q86SJ3|Q86WN3|Q86WN4|Q86WN5|Q86WN6|Q86WN7|Q86WN8|Q86WN9|Q86WP0	Missense_Mutation	SNP	ENST00000291539.6	37	CCDS13690.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	18.52	3.641532	0.67244	0.002497	0.0	ENSG00000160191	ENST00000335512;ENST00000539837;ENST00000291539;ENST00000380328;ENST00000398232;ENST00000398234;ENST00000398236;ENST00000328862;ENST00000335440;ENST00000398225;ENST00000398229;ENST00000398227;ENST00000349112;ENST00000398224	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.75938	-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98;-0.98	5.1	5.1	0.69264	5&apos (1);-cyclic nucleotide phosphodiesterase, catalytic domain (1);3&apos (1);	0.000000	0.85682	D	0.000000	T	0.79387	0.4437	L	0.53780	1.695	0.52099	D	0.999942	B;B;B;B;B;B;P;B;B;B;B;B;P;B;B;B	0.38597	0.079;0.101;0.101;0.237;0.101;0.161;0.639;0.237;0.101;0.101;0.237;0.11;0.579;0.441;0.101;0.027	B;B;B;B;B;B;P;B;B;B;B;B;B;B;B;B	0.48030	0.092;0.064;0.102;0.092;0.162;0.319;0.564;0.216;0.064;0.064;0.092;0.158;0.442;0.216;0.102;0.048	T	0.81147	-0.1065	10	0.66056	D	0.02	.	18.5908	0.91212	0.0:1.0:0.0:0.0	.	144;205;186;171;246;231;164;212;55;112;138;144;170;219;145;272	F5GWD0;O76083-13;O76083-8;O76083-6;O76083-15;O76083-14;O76083-16;O76083-2;O76083-10;O76083-9;O76083-11;O76083-4;O76083-12;O76083-5;O76083-3;O76083	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;PDE9A_HUMAN	V	212;144;272;219;205;171;186;246;170;231;138;112;144;145	ENSP00000335242:L212V;ENSP00000441899:L144V;ENSP00000291539:L272V;ENSP00000369685:L219V;ENSP00000381287:L205V;ENSP00000381289:L171V;ENSP00000381291:L186V;ENSP00000328699:L246V;ENSP00000335365:L170V;ENSP00000381281:L231V;ENSP00000381285:L138V;ENSP00000381283:L112V;ENSP00000344730:L144V;ENSP00000381280:L145V	ENSP00000291539:L272V	L	+	1	2	PDE9A	43052181	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.526000	0.60566	2.388000	0.81334	0.650000	0.86243	CTG	C|0.999;G|0.001	0.001	strong		0.637	PDE9A-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195466.1		
TRPC5	7224	hgsc.bcm.edu	37	X	111020096	111020096	+	Silent	SNP	C	C	A	rs141761268	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:111020096C>A	ENST00000262839.2	-	11	3285	c.2367G>T	c.(2365-2367)ggG>ggT	p.G789G		NM_012471.2	NP_036603.1	Q9UL62	TRPC5_HUMAN	transient receptor potential cation channel, subfamily C, member 5	789					axon guidance (GO:0007411)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|nervous system development (GO:0007399)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			biliary_tract(1)|breast(4)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(38)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	62						TGGCCCGAGCCCCACCACTGC	0.478													C|||	5	0.0013245	0.0038	0.0	3775	,	,		12501	0.0		0.0	False		,,,				2504	0.0				p.G789G		Atlas-SNP	.											.	TRPC5	142	.	0			c.G2367T						PASS	.	C		13,3822		0,9,4,1623,567	137.0	143.0	141.0		2367	2.8	1.0	X	dbSNP_134	141	0,6728		0,0,0,2428,1872	no	coding-synonymous	TRPC5	NM_012471.2		0,9,4,4051,2439	AA,AC,A,CC,C		0.0,0.339,0.1231		789/974	111020096	13,10550	2203	4300	6503	SO:0001819	synonymous_variant	7224	exon11			CCGAGCCCCACCA	AF054568	CCDS14561.1	Xq23	2014-06-13			ENSG00000072315	ENSG00000072315		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12337	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 159"""	300334				10493832, 16382100	Standard	NM_012471		Approved	PPP1R159	uc004epl.1	Q9UL62	OTTHUMG00000022212	ENST00000262839.2:c.2367G>T	X.37:g.111020096C>A		177.0	0.0	0		160.0	101.0	0.63125	NM_012471	B2RP53|O75233|Q5JXY8|Q9Y514	Silent	SNP	ENST00000262839.2	37	CCDS14561.1																																																																																			C|0.998;A|0.002	0.002	strong		0.478	TRPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057945.1	NM_012471	
TNRC18	84629	hgsc.bcm.edu	37	7	5417093	5417093	+	Silent	SNP	G	G	T	rs60530083	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:5417093G>T	ENST00000430969.1	-	7	2718	c.2370C>A	c.(2368-2370)cgC>cgA	p.R790R	TNRC18_ENST00000399537.4_Silent_p.R790R	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	790							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		CGGCAGACCAGCGACCTGAGC	0.701													G|||	138	0.0275559	0.0514	0.0058	5008	,	,		11884	0.0139		0.002	False		,,,				2504	0.0511				p.R790R		Atlas-SNP	.											.	TNRC18	311	.	0			c.C2370A						PASS	.	G		181,3615		4,173,1721	8.0	11.0	10.0		2370	-0.9	0.9	7	dbSNP_129	10	21,8133		0,21,4056	no	coding-synonymous	TNRC18	NM_001080495.2		4,194,5777	TT,TG,GG		0.2575,4.7682,1.6904		790/2969	5417093	202,11748	1898	4077	5975	SO:0001819	synonymous_variant	84629	exon7			AGACCAGCGACCT	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.2370C>A	7.37:g.5417093G>T		28.0	0.0	0		53.0	32.0	0.603774	NM_001080495	A8MX41|Q96JH1|Q96K91	Silent	SNP	ENST00000430969.1	37	CCDS47534.1																																																																																			G|0.985;T|0.015	0.015	strong		0.701	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
TMEM232	642987	hgsc.bcm.edu	37	5	109941887	109941887	+	Missense_Mutation	SNP	C	C	T	rs73224392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:109941887C>T	ENST00000455884.2	-	9	1054	c.1004G>A	c.(1003-1005)aGc>aAc	p.S335N	TMEM232_ENST00000515518.2_5'UTR|TMEM232_ENST00000429839.2_Missense_Mutation_p.S335N			C9JQI7	TM232_HUMAN	transmembrane protein 232	335						integral component of membrane (GO:0016021)				breast(1)|kidney(2)	3						AGACATAATGCTTGAAACAAA	0.353													C|||	234	0.0467252	0.1694	0.0101	5008	,	,		12131	0.0		0.003	False		,,,				2504	0.0				p.S335N		Atlas-SNP	.											.	TMEM232	57	.	0			c.G1004A						PASS	.	C	ASN/SER	195,1189		17,161,514	70.0	59.0	62.0		1004	-2.9	0.3	5	dbSNP_130	62	5,3177		0,5,1586	yes	missense	TMEM232	NM_001039763.3	46	17,166,2100	TT,TC,CC		0.1571,14.0896,4.3802	benign	335/658	109941887	200,4366	692	1591	2283	SO:0001583	missense	642987	exon9			ATAATGCTTGAAA	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.1004G>A	5.37:g.109941887C>T	ENSP00000401477:p.Ser335Asn	238.0	0.0	0		217.0	98.0	0.451613	NM_001039763	B4DKF4	Missense_Mutation	SNP	ENST00000455884.2	37	CCDS47253.2	91	0.041666666666666664	86	0.17479674796747968	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	C	9.441	1.088145	0.20390	0.140896	0.001571	ENSG00000186952	ENST00000429839;ENST00000455884	.	.	.	5.45	-2.92	0.05615	.	0.756414	0.13148	N	0.410099	T	0.00073	0.0002	L	0.27053	0.805	0.80722	P	0.0	B;B;B	0.24186	0.099;0.004;0.037	B;B;B	0.19148	0.024;0.009;0.024	T	0.21724	-1.0237	7	.	.	.	-1.5952	5.9581	0.19286	0.0:0.3106:0.3588:0.3306	.	335;335;217	C9JQI7;C9JQI7-2;E9PFK0	TM232_HUMAN;.;.	N	335	.	.	S	-	2	0	TMEM232	109969786	0.000000	0.05858	0.319000	0.25293	0.578000	0.36192	-0.228000	0.09114	-0.134000	0.11516	-0.315000	0.08773	AGC	C|0.965;T|0.035	0.035	strong		0.353	TMEM232-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372488.2	NM_001039763	
BRD1	23774	hgsc.bcm.edu	37	22	50217387	50217387	+	Silent	SNP	G	G	A	rs11912787	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50217387G>A	ENST00000216267.8	-	1	1065	c.579C>T	c.(577-579)ttC>ttT	p.F193F	BRD1_ENST00000342989.5_5'Flank|BRD1_ENST00000457780.2_Silent_p.F193F|BRD1_ENST00000404760.1_Silent_p.F193F|BRD1_ENST00000459821.1_5'Flank|BRD1_ENST00000404034.1_Silent_p.F193F|BRD1_ENST00000542442.1_5'Flank	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	193					histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	37		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)		ACTCCTTCTCGAAGCGGTCCA	0.602													G|||	508	0.101438	0.1664	0.0432	5008	,	,		21111	0.003		0.0746	False		,,,				2504	0.184				p.F193F		Atlas-SNP	.											.	BRD1	144	.	0			c.C579T						PASS	.	G		801,3605	322.9+/-297.8	69,663,1471	72.0	61.0	65.0		579	-5.2	1.0	22	dbSNP_120	65	702,7898	172.6+/-223.3	31,640,3629	no	coding-synonymous	BRD1	NM_014577.1		100,1303,5100	AA,AG,GG		8.1628,18.1798,11.5562		193/1059	50217387	1503,11503	2203	4300	6503	SO:0001819	synonymous_variant	23774	exon1			CTTCTCGAAGCGG	AF005067	CCDS14080.1	22q13.33	2008-07-01	2002-01-14		ENSG00000100425	ENSG00000100425			1102	protein-coding gene	gene with protein product	"""BR140-like"""	604589	"""bromodomain-containing 1"""			10591208, 10602503	Standard	NM_014577		Approved	BRL, BRPF2	uc003biv.3	O95696	OTTHUMG00000150288	ENST00000216267.8:c.579C>T	22.37:g.50217387G>A		105.0	0.0	0		104.0	50.0	0.480769	NM_014577	A6ZJA4	Silent	SNP	ENST00000216267.8	37	CCDS14080.1																																																																																			G|0.899;A|0.101	0.101	strong		0.602	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577	
OR10K1	391109	hgsc.bcm.edu	37	1	158436201	158436201	+	Silent	SNP	T	T	C	rs76117330	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158436201T>C	ENST00000289451.2	+	1	930	c.850T>C	c.(850-852)Ttg>Ctg	p.L284L		NM_001004473.1	NP_001004473.1	Q8NGX5	O10K1_HUMAN	olfactory receptor, family 10, subfamily K, member 1	284						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)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	27	all_hematologic(112;0.0378)					CCTTACCCCATTGTTCAATCC	0.388													T|||	189	0.0377396	0.1354	0.013	5008	,	,		21238	0.0		0.001	False		,,,				2504	0.0				p.L284L		Atlas-SNP	.											.	OR10K1	80	.	0			c.T850C						PASS	.	T		513,3893	235.2+/-247.8	29,455,1719	146.0	140.0	142.0		850	-7.0	0.0	1	dbSNP_131	142	8,8592	7.1+/-27.0	0,8,4292	no	coding-synonymous	OR10K1	NM_001004473.1		29,463,6011	CC,CT,TT		0.093,11.6432,4.0058		284/314	158436201	521,12485	2203	4300	6503	SO:0001819	synonymous_variant	391109	exon1			ACCCCATTGTTCA	AP002532	CCDS30897.1	1q23.1	2012-08-09			ENSG00000173285	ENSG00000173285		"""GPCR / Class A : Olfactory receptors"""	14693	protein-coding gene	gene with protein product							Standard	NM_001004473		Approved		uc010pij.2	Q8NGX5	OTTHUMG00000017517	ENST00000289451.2:c.850T>C	1.37:g.158436201T>C		131.0	0.0	0		139.0	62.0	0.446043	NM_001004473	Q6IFS2	Silent	SNP	ENST00000289451.2	37	CCDS30897.1																																																																																			T|0.963;C|0.037	0.037	strong		0.388	OR10K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046367.1		
PLOD2	5352	hgsc.bcm.edu	37	3	145809622	145809622	+	Missense_Mutation	SNP	A	A	G	rs138948307	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:145809622A>G	ENST00000360060.3	-	8	1021	c.844T>C	c.(844-846)Tgt>Cgt	p.C282R	PLOD2_ENST00000282903.5_Missense_Mutation_p.C282R|PLOD2_ENST00000494950.1_Missense_Mutation_p.C227R|RP11-274H2.2_ENST00000480247.1_RNA	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	282					cellular protein modification process (GO:0006464)|extracellular matrix organization (GO:0030198)|response to hypoxia (GO:0001666)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-lysine 5-dioxygenase activity (GO:0008475)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29					Vitamin C(DB00126)	TCGAATTCACAAAGAGTGCAG	0.343													A|||	3	0.000599042	0.0015	0.0014	5008	,	,		17493	0.0		0.0	False		,,,				2504	0.0				p.C282R		Atlas-SNP	.											.	PLOD2	81	.	0			c.T844C						PASS	.	A	ARG/CYS,ARG/CYS	9,4397	15.5+/-35.6	0,9,2194	104.0	92.0	96.0		844,844	6.1	0.7	3	dbSNP_134	96	0,8600		0,0,4300	yes	missense,missense	PLOD2	NM_000935.2,NM_182943.2	180,180	0,9,6494	GG,GA,AA		0.0,0.2043,0.0692	probably-damaging,probably-damaging	282/738,282/759	145809622	9,12997	2203	4300	6503	SO:0001583	missense	5352	exon8			ATTCACAAAGAGT	U84573	CCDS3131.1, CCDS3132.1	3q24	2011-08-24	2005-01-04		ENSG00000152952	ENSG00000152952			9082	protein-coding gene	gene with protein product	"""lysyl hydroxlase 2"""	601865	"""procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2"""			9054364	Standard	XM_005247535		Approved	LH2	uc003evr.1	O00469	OTTHUMG00000159417	ENST00000360060.3:c.844T>C	3.37:g.145809622A>G	ENSP00000353170:p.Cys282Arg	115.0	0.0	0		136.0	53.0	0.389706	NM_182943	B3KWS3|Q59ED2|Q8N170	Missense_Mutation	SNP	ENST00000360060.3	37	CCDS3131.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.172440	0.78452	0.002043	0.0	ENSG00000152952	ENST00000282903;ENST00000360060;ENST00000494950	T;T;T	0.69306	-0.39;-0.37;-0.35	6.06	6.06	0.98353	.	0.000000	0.85682	D	0.000000	D	0.84651	0.5519	M	0.89353	3.025	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.996	D;D;P	0.91635	0.997;0.999;0.903	D	0.87463	0.2409	10	0.87932	D	0	-32.5497	15.6071	0.76682	1.0:0.0:0.0:0.0	.	227;282;282	E7ETU9;O00469;O00469-2	.;PLOD2_HUMAN;.	R	282;282;227	ENSP00000282903:C282R;ENSP00000353170:C282R;ENSP00000420094:C227R	ENSP00000282903:C282R	C	-	1	0	PLOD2	147292312	1.000000	0.71417	0.726000	0.30738	0.917000	0.54804	7.900000	0.87376	2.323000	0.78572	0.528000	0.53228	TGT	A|0.999;G|0.001	0.001	strong		0.343	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935	
KIAA0141	9812	hgsc.bcm.edu	37	5	141313888	141313888	+	Silent	SNP	A	A	C	rs115183657	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:141313888A>C	ENST00000432126.2	+	9	1115	c.981A>C	c.(979-981)ccA>ccC	p.P327P	KIAA0141_ENST00000194118.4_Silent_p.P327P	NM_001142603.1|NM_014773.3	NP_001136075.1|NP_055588.3	Q14154	DELE_HUMAN	KIAA0141	327					extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	mitochondrion (GO:0005739)				endometrium(3)|large_intestine(4)|lung(5)|skin(1)|urinary_tract(3)	16		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TACGAGACCCAGCCTCTTCGT	0.597													A|||	44	0.00878594	0.0318	0.0029	5008	,	,		14901	0.0		0.0	False		,,,				2504	0.0				p.P327P		Atlas-SNP	.											.	KIAA0141	44	.	0			c.A981C						PASS	.	A	,	104,4302	79.9+/-118.3	0,104,2099	49.0	47.0	48.0		981,981	-7.0	0.0	5	dbSNP_132	48	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	KIAA0141	NM_001142603.1,NM_014773.3	,	0,104,6399	CC,CA,AA		0.0,2.3604,0.7996	,	327/516,327/516	141313888	104,12902	2203	4300	6503	SO:0001819	synonymous_variant	9812	exon9			AGACCCAGCCTCT	BC011269	CCDS4268.1	5q31	2011-05-05			ENSG00000081791	ENSG00000081791			28969	protein-coding gene	gene with protein product	"""death ligand signal enhancer"""	615741				20563667	Standard	XM_005268549		Approved	DELE	uc003llt.3	Q14154	OTTHUMG00000129662	ENST00000432126.2:c.981A>C	5.37:g.141313888A>C		88.0	0.0	0		129.0	61.0	0.472868	NM_001142603	Q969R4|Q96EU9	Silent	SNP	ENST00000432126.2	37	CCDS4268.1	16	0.007326007326007326	14	0.028455284552845527	2	0.0055248618784530384	0	0.0	0	0.0	A	0.525	-0.860231	0.02610	0.023604	0.0	ENSG00000081791	ENST00000507481	.	.	.	5.55	-6.96	0.01622	.	.	.	.	.	T	0.06371	0.0164	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.24657	-1.0154	4	.	.	.	-1.6157	4.7459	0.13036	0.1625:0.5451:0.1777:0.1147	.	.	.	.	P	29	.	.	Q	+	2	0	KIAA0141	141294072	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.619000	0.05572	-1.086000	0.03084	-0.290000	0.09829	CAG	A|0.991;C|0.009	0.009	strong		0.597	KIAA0141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251863.2	NM_014773	
PEX16	9409	hgsc.bcm.edu	37	11	45932458	45932458	+	Silent	SNP	G	G	A	rs150774189	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:45932458G>A	ENST00000378750.5	-	10	1186	c.943C>T	c.(943-945)Ctg>Ttg	p.L315L	PEX16_ENST00000532681.1_Silent_p.L220L|PEX16_ENST00000241041.3_Silent_p.L315L			Q9Y5Y5	PEX16_HUMAN	peroxisomal biogenesis factor 16	315	Interaction with PEX19.				ER-dependent peroxisome organization (GO:0032581)|peroxisome membrane biogenesis (GO:0016557)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome membrane (GO:0045046)|protein localization to endoplasmic reticulum (GO:0070972)|protein targeting to peroxisome (GO:0006625)|protein to membrane docking (GO:0022615)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	protein C-terminus binding (GO:0008022)			large_intestine(2)|lung(2)|ovary(2)|skin(1)	7				GBM - Glioblastoma multiforme(35;0.223)		CTTGTGACCAGGCCAACGCCA	0.597													G|||	19	0.00379393	0.0136	0.0014	5008	,	,		18792	0.0		0.0	False		,,,				2504	0.0				p.L315L		Atlas-SNP	.											.	PEX16	24	.	0			c.C943T						PASS	.	G	,	68,4338	62.3+/-99.4	2,64,2137	118.0	102.0	108.0		943,943	3.4	1.0	11	dbSNP_134	108	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	PEX16	NM_004813.2,NM_057174.2	,	2,64,6436	AA,AG,GG		0.0,1.5433,0.5229	,	315/337,315/347	45932458	68,12936	2203	4299	6502	SO:0001819	synonymous_variant	9409	exon10			TGACCAGGCCAAC	AF118240	CCDS7917.1, CCDS31472.1	11p	2007-12-14			ENSG00000121680	ENSG00000121680			8857	protein-coding gene	gene with protein product		603360				9922452	Standard	NM_057174		Approved		uc001nbt.3	Q9Y5Y5	OTTHUMG00000167005	ENST00000378750.5:c.943C>T	11.37:g.45932458G>A		91.0	0.0	0		111.0	60.0	0.540541	NM_004813	Q9BWB9	Silent	SNP	ENST00000378750.5	37	CCDS31472.1																																																																																			G|0.995;A|0.005	0.005	strong		0.597	PEX16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392398.1	NM_057174	
ERN1	2081	hgsc.bcm.edu	37	17	62149423	62149423	+	Silent	SNP	G	G	A	rs374999844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:62149423G>A	ENST00000433197.3	-	6	491	c.396C>T	c.(394-396)acC>acT	p.T132T	ERN1_ENST00000577567.1_5'UTR	NM_001433.3	NP_001424.3			endoplasmic reticulum to nucleus signaling 1											central_nervous_system(4)|kidney(1)|lung(2)|ovary(1)|stomach(1)	9						GCTTCTCTCCGGTCAGGAGGT	0.448													G|||	2	0.000399361	0.0015	0.0	5008	,	,		20164	0.0		0.0	False		,,,				2504	0.0				p.T132T		Atlas-SNP	.											.	ERN1	102	.	0			c.C396T						PASS	.	G		5,3827		0,5,1911	51.0	50.0	51.0		396	-2.8	1.0	17		51	1,8269		0,1,4134	no	coding-synonymous	ERN1	NM_001433.3		0,6,6045	AA,AG,GG		0.0121,0.1305,0.0496		132/978	62149423	6,12096	1916	4135	6051	SO:0001819	synonymous_variant	2081	exon6			CTCTCCGGTCAGG	AF059198	CCDS45762.1	17q23	2011-08-12	2007-08-14			ENSG00000178607			3449	protein-coding gene	gene with protein product	"""inositol-requiring enzyme 1"""	604033	"""ER to nucleus signalling 1"""			9637683	Standard	NM_001433		Approved	IRE1, IRE1P	uc002jdz.2	O75460		ENST00000433197.3:c.396C>T	17.37:g.62149423G>A		72.0	0.0	0		64.0	29.0	0.453125	NM_001433		Silent	SNP	ENST00000433197.3	37	CCDS45762.1																																																																																			.	.	weak		0.448	ERN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443734.2	NM_001433	
LILRA2	11027	hgsc.bcm.edu	37	19	55098736	55098736	+	Missense_Mutation	SNP	G	G	C	rs73939007	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55098736G>C	ENST00000251377.3	+	9	1508	c.1375G>C	c.(1375-1377)Gtc>Ctc	p.V459L	LILRA2_ENST00000391737.1_Missense_Mutation_p.V430L|LILRA2_ENST00000251376.3_Missense_Mutation_p.V442L|CTB-83J4.2_ENST00000596330.1_lincRNA|LILRA2_ENST00000391738.3_Missense_Mutation_p.V459L|LILRB1_ENST00000448689.1_Intron|LILRB1_ENST00000418536.2_Intron|LILRB1_ENST00000396321.2_Intron			Q8N149	LIRA2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 2	459					defense response (GO:0006952)|immune system process (GO:0002376)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(33)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	50				GBM - Glioblastoma multiforme(193;0.0963)		GGCTGGCTTGGTCCTGGTGGT	0.567													g|||	51	0.0101837	0.0378	0.0014	5008	,	,		17382	0.0		0.0	False		,,,				2504	0.0				p.V459L		Atlas-SNP	.											.	LILRA2	99	.	0			c.G1375C						PASS	.	G	LEU/VAL,LEU/VAL	100,4306	79.3+/-117.8	0,100,2103	111.0	96.0	101.0		1375,1324	-5.5	0.0	19	dbSNP_130	101	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense	LILRA2	NM_001130917.1,NM_006866.2	32,32	0,102,6401	CC,CG,GG		0.0233,2.2696,0.7843	,	459/484,442/467	55098736	102,12904	2203	4300	6503	SO:0001583	missense	11027	exon8			GGCTTGGTCCTGG	U82275	CCDS12900.1, CCDS46179.1, CCDS74453.1	19q13.4	2013-01-11			ENSG00000239998	ENSG00000239998		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6603	protein-coding gene	gene with protein product		604812				9079806, 9548455	Standard	XM_005258452		Approved	LIR-7, ILT1, CD85h, LIR7		Q8N149	OTTHUMG00000065703	ENST00000251377.3:c.1375G>C	19.37:g.55098736G>C	ENSP00000251377:p.Val459Leu	228.0	1.0	0.00438596		257.0	115.0	0.447471	NM_001130917	O75020	Missense_Mutation	SNP	ENST00000251377.3	37	CCDS46179.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	G	9.895	1.205412	0.22205	0.022696	2.33E-4	ENSG00000239998	ENST00000251377;ENST00000391738;ENST00000251376;ENST00000391737	T;T;T;T	0.00617	6.41;6.41;6.35;6.19	2.74	-5.49	0.02584	.	30.411000	0.00832	N	0.001664	T	0.00241	0.0007	L	0.43923	1.385	0.09310	N	0.999998	B;B;B	0.24258	0.098;0.1;0.024	B;B;B	0.25614	0.051;0.062;0.028	T	0.42965	-0.9420	10	0.49607	T	0.09	.	7.5721	0.27913	0.1909:0.1704:0.6387:0.0	.	430;459;442	A8MZH0;Q8N149;Q8N149-2	.;LIRA2_HUMAN;.	L	459;459;442;430	ENSP00000251377:V459L;ENSP00000375618:V459L;ENSP00000251376:V442L;ENSP00000375617:V430L	ENSP00000251376:V442L	V	+	1	0	LILRA2	59790548	0.005000	0.15991	0.002000	0.10522	0.162000	0.22319	-0.202000	0.09451	-1.128000	0.02922	-0.320000	0.08662	GTC	G|0.991;C|0.009	0.009	strong		0.567	LILRA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140813.2		
STAB2	55576	hgsc.bcm.edu	37	12	104014294	104014294	+	Missense_Mutation	SNP	C	C	T	rs150189813	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:104014294C>T	ENST00000388887.2	+	4	584	c.380C>T	c.(379-381)gCt>gTt	p.A127V		NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						GGCAGTTGTGCTGAAGGCATG	0.493													C|||	2	0.000399361	0.0008	0.0014	5008	,	,		19345	0.0		0.0	False		,,,				2504	0.0				p.A127V		Atlas-SNP	.											.	STAB2	370	.	0			c.C380T						PASS	.	C	VAL/ALA	5,4399		0,5,2197	115.0	93.0	100.0		380	1.8	0.1	12	dbSNP_134	100	0,8594		0,0,4297	yes	missense	STAB2	NM_017564.9	64	0,5,6494	TT,TC,CC		0.0,0.1135,0.0385	possibly-damaging	127/2552	104014294	5,12993	2202	4297	6499	SO:0001583	missense	55576	exon4			GTTGTGCTGAAGG	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"""hyaluronic acid receptor for endocytosis"""	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.380C>T	12.37:g.104014294C>T	ENSP00000373539:p.Ala127Val	195.0	0.0	0		209.0	107.0	0.511962	NM_017564		Missense_Mutation	SNP	ENST00000388887.2	37	CCDS31888.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	13.25	2.179669	0.38511	0.001135	0.0	ENSG00000136011	ENST00000388887	D	0.83673	-1.75	4.98	1.84	0.25277	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.200082	0.43919	D	0.000512	T	0.71221	0.3314	L	0.33485	1.01	0.18873	N	0.999987	P	0.41041	0.736	B	0.38803	0.282	T	0.59762	-0.7393	10	0.18710	T	0.47	.	11.2145	0.48819	0.5338:0.4662:0.0:0.0	.	127	Q8WWQ8	STAB2_HUMAN	V	127	ENSP00000373539:A127V	ENSP00000373539:A127V	A	+	2	0	STAB2	102538424	0.227000	0.23707	0.136000	0.22124	0.997000	0.91878	0.357000	0.20199	0.122000	0.18314	0.549000	0.68633	GCT	C|1.000;T|0.000	0.000	strong		0.493	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
FBN3	84467	hgsc.bcm.edu	37	19	8150428	8150428	+	Silent	SNP	G	G	A	rs34514496	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8150428G>A	ENST00000600128.1	-	56	7320	c.6906C>T	c.(6904-6906)gcC>gcT	p.A2302A	FBN3_ENST00000601739.1_Silent_p.A2302A|FBN3_ENST00000270509.2_Silent_p.A2302A			Q75N90	FBN3_HUMAN	fibrillin 3	2302	TB 9.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						GCAGCACCTCGGCAAAGCAGG	0.647													G|||	228	0.0455272	0.1619	0.0202	5008	,	,		15702	0.0		0.0	False		,,,				2504	0.0				p.A2302A		Atlas-SNP	.											.	FBN3	300	.	0			c.C6906T						PASS	.	G		536,3858		22,492,1683	11.0	12.0	12.0		6906	-6.9	0.9	19	dbSNP_126	12	13,8555		0,13,4271	no	coding-synonymous	FBN3	NM_032447.3		22,505,5954	AA,AG,GG		0.1517,12.1985,4.2355		2302/2810	8150428	549,12413	2197	4284	6481	SO:0001819	synonymous_variant	84467	exon55			CACCTCGGCAAAG		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.6906C>T	19.37:g.8150428G>A		40.0	0.0	0		53.0	26.0	0.490566	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																			G|0.956;A|0.044	0.044	strong		0.647	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
C10orf71	118461	hgsc.bcm.edu	37	10	50531907	50531907	+	Silent	SNP	C	C	T	rs74528495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:50531907C>T	ENST00000374144.3	+	3	1605	c.1317C>T	c.(1315-1317)ccC>ccT	p.P439P	C10orf71_ENST00000323868.4_Silent_p.P439P			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	439										endometrium(1)	1						ATTATGATCCCCCCTTTAACA	0.522													C|||	27	0.00539137	0.0182	0.0043	5008	,	,		17686	0.0		0.0	False		,,,				2504	0.0				p.P439P		Atlas-SNP	.											.	C10orf71	179	.	0			c.C1317T						PASS	.	C	,	53,3975		0,53,1961	84.0	88.0	87.0		1317,1317	-2.9	0.4	10	dbSNP_133	87	1,8371		0,1,4185	no	coding-synonymous,coding-synonymous	C10orf71	NM_001135196.1,NM_199459.3	,	0,54,6146	TT,TC,CC		0.0119,1.3158,0.4355	,	439/1436,439/720	50531907	54,12346	2014	4186	6200	SO:0001819	synonymous_variant	118461	exon3			TGATCCCCCCTTT	AL833265	CCDS44387.1	10q11.23	2012-05-31			ENSG00000177354	ENSG00000177354			26973	protein-coding gene	gene with protein product							Standard	NM_001135196		Approved	FLJ45913	uc021pqa.2	Q711Q0	OTTHUMG00000018190	ENST00000374144.3:c.1317C>T	10.37:g.50531907C>T		97.0	0.0	0		98.0	42.0	0.428571	NM_001135196	A0AVL8	Silent	SNP	ENST00000374144.3	37	CCDS44387.1																																																																																			C|0.994;T|0.006	0.006	strong		0.522	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
VARS	7407	hgsc.bcm.edu	37	6	31747833	31747833	+	Missense_Mutation	SNP	G	G	A	rs1076827	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31747833G>A	ENST00000375663.3	-	26	3463	c.3023C>T	c.(3022-3024)cCg>cTg	p.P1008L	VWA7_ENST00000467576.1_5'Flank|VWA7_ENST00000375688.4_5'Flank|Y_RNA_ENST00000364685.1_RNA|VARS_ENST00000482996.1_5'Flank|VWA7_ENST00000375686.3_5'Flank|VWA7_ENST00000447450.1_5'Flank	NM_006295.2	NP_006286.1	P26640	SYVC_HUMAN	valyl-tRNA synthetase	1008			P -> L (in dbSNP:rs1076827).		gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)|valyl-tRNA aminoacylation (GO:0006438)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|valine-tRNA ligase activity (GO:0004832)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(18)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	30					L-Valine(DB00161)	GGTGACGGCCGGGAAGTCGTA	0.627													G|||	95	0.0189696	0.0658	0.0101	5008	,	,		17107	0.0		0.0	False		,,,				2504	0.001				p.P1008L		Atlas-SNP	.											.	VARS	76	.	0			c.C3023T						PASS	.	G	LEU/PRO	261,4145	150.3+/-184.3	5,251,1947	59.0	61.0	61.0		3023	5.2	1.0	6	dbSNP_86	61	5,8595	4.3+/-15.6	0,5,4295	yes	missense	VARS	NM_006295.2	98	5,256,6242	AA,AG,GG		0.0581,5.9237,2.0452	possibly-damaging	1008/1265	31747833	266,12740	2203	4300	6503	SO:0001583	missense	7407	exon26			ACGGCCGGGAAGT	BC012808	CCDS34412.1	6p21.3	2011-07-01		2005-07-05	ENSG00000204394	ENSG00000204394	6.1.1.9	"""Aminoacyl tRNA synthetases / Class I"""	12651	protein-coding gene	gene with protein product	"""valine tRNA ligase 1, cytoplasmic"""	192150	"""valyl-tRNA synthetase 2"""	VARS2		15779907	Standard	XM_005249362		Approved		uc003nxe.3	P26640	OTTHUMG00000031286	ENST00000375663.3:c.3023C>T	6.37:g.31747833G>A	ENSP00000364815:p.Pro1008Leu	82.0	0.0	0		74.0	37.0	0.5	NM_006295	B0V1N1|B4DZ61|Q5JQ90|Q96E77|Q9UQM2	Missense_Mutation	SNP	ENST00000375663.3	37	CCDS34412.1	43	0.019688644688644688	40	0.08130081300813008	3	0.008287292817679558	0	0.0	0	0.0	G	12.66	2.003411	0.35320	0.059237	5.81E-4	ENSG00000204394	ENST00000375663	T	0.13420	2.59	5.23	5.23	0.72850	Valyl/Leucyl/Isoleucyl-tRNA synthetase, class I, anticodon-binding (1);Aminoacyl-tRNA synthetase, class 1a, anticodon-binding (1);	0.000000	0.85682	D	0.000000	T	0.14270	0.0345	L	0.48260	1.515	0.80722	D	1	D	0.58268	0.982	P	0.55667	0.781	T	0.05178	-1.0901	10	0.21014	T	0.42	-11.0663	16.2949	0.82765	0.0:0.0:1.0:0.0	rs1076827;rs4368836;rs16867555;rs1076827	1008	P26640	SYVC_HUMAN	L	1008	ENSP00000364815:P1008L	ENSP00000364815:P1008L	P	-	2	0	VARS	31855812	1.000000	0.71417	0.975000	0.42487	0.423000	0.31445	5.547000	0.67249	2.445000	0.82738	0.650000	0.86243	CCG	G|0.978;A|0.022	0.022	strong		0.627	VARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076619.2	NM_006295	
NOM1	64434	hgsc.bcm.edu	37	7	156745224	156745224	+	Silent	SNP	G	G	A	rs59371845	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:156745224G>A	ENST00000275820.3	+	2	1059	c.1044G>A	c.(1042-1044)gaG>gaA	p.E348E		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	348						nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(4)|large_intestine(9)|lung(7)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31	Ovarian(565;0.218)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		AAGCTGAGGAGACAGTGGACT	0.393													G|||	267	0.0533147	0.1906	0.0202	5008	,	,		21925	0.0		0.001	False		,,,				2504	0.0				p.E348E		Atlas-SNP	.											.	NOM1	73	.	0			c.G1044A						PASS	.	G		715,3691	298.1+/-285.1	53,609,1541	104.0	94.0	98.0		1044	1.0	0.0	7	dbSNP_129	98	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	NOM1	NM_138400.1		53,613,5837	AA,AG,GG		0.0465,16.2279,5.5282		348/861	156745224	719,12287	2203	4300	6503	SO:0001819	synonymous_variant	64434	exon2			TGAGGAGACAGTG	AF107455	CCDS34787.1	7q36.3	2014-06-13	2005-03-30	2005-03-30	ENSG00000146909	ENSG00000146909			13244	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 113"""	611269	"""chromosome 7 open reading frame 3"""	C7orf3		10329000	Standard	XM_005249560		Approved	SGD1, PPP1R113	uc003wmy.3	Q5C9Z4	OTTHUMG00000152639	ENST00000275820.3:c.1044G>A	7.37:g.156745224G>A		170.0	0.0	0		166.0	81.0	0.487952	NM_138400	Q96I08	Silent	SNP	ENST00000275820.3	37	CCDS34787.1																																																																																			G|0.950;A|0.050	0.050	strong		0.393	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1	NM_138400	
ARID3C	138715	hgsc.bcm.edu	37	9	34625800	34625800	+	Silent	SNP	G	G	A	rs144207435	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:34625800G>A	ENST00000378909.2	-	2	422	c.330C>T	c.(328-330)ctC>ctT	p.L110L		NM_001017363.1	NP_001017363.1	A6NKF2	ARI3C_HUMAN	AT rich interactive domain 3C (BRIGHT-like)	110					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane raft (GO:0045121)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)	14	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.175)		GGTCTGCATCGAGCTCATACA	0.547													G|||	12	0.00239617	0.0083	0.0	5008	,	,		17241	0.0		0.001	False		,,,				2504	0.0				p.L110L		Atlas-SNP	.											ARID3C,NS,carcinoma,0,2	ARID3C	33	2	0			c.C330T						PASS	.	G		40,4366	44.6+/-78.6	0,40,2163	175.0	136.0	149.0		330	-2.9	1.0	9	dbSNP_134	149	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous	ARID3C	NM_001017363.1		0,50,6453	AA,AG,GG		0.1163,0.9079,0.3844		110/413	34625800	50,12956	2203	4300	6503	SO:0001819	synonymous_variant	138715	exon2			TGCATCGAGCTCA		CCDS35006.1	9p13.2	2013-02-07	2006-11-08		ENSG00000205143	ENSG00000205143		"""-"""	21209	protein-coding gene	gene with protein product			"""AT rich interactive domain 3C (BRIGHT- like)"""				Standard	NM_001017363		Approved		uc011lon.2	A6NKF2	OTTHUMG00000000445	ENST00000378909.2:c.330C>T	9.37:g.34625800G>A		142.0	0.0	0		146.0	80.0	0.547945	NM_001017363		Silent	SNP	ENST00000378909.2	37	CCDS35006.1																																																																																			G|0.997;A|0.003	0.003	strong		0.547	ARID3C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348265.1	XM_071061	
ZNF236	7776	hgsc.bcm.edu	37	18	74640002	74640002	+	Missense_Mutation	SNP	G	G	A	rs76679748	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:74640002G>A	ENST00000253159.8	+	25	4726	c.4528G>A	c.(4528-4530)Gct>Act	p.A1510T	ZNF236_ENST00000320610.9_Missense_Mutation_p.A1512T	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	1510					cellular response to glucose stimulus (GO:0071333)|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)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(43)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	94		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)		GGCACAGGCCGCTGGGCCCAC	0.542													G|||	28	0.00559105	0.0204	0.0014	5008	,	,		13599	0.0		0.0	False		,,,				2504	0.0				p.A1510T		Atlas-SNP	.											.	ZNF236	325	.	0			c.G4528A						PASS	.	G	THR/ALA	32,3768		0,32,1868	45.0	49.0	48.0		4528	2.3	0.0	18	dbSNP_131	48	0,8234		0,0,4117	yes	missense	ZNF236	NM_007345.3	58	0,32,5985	AA,AG,GG		0.0,0.8421,0.2659	benign	1510/1846	74640002	32,12002	1900	4117	6017	SO:0001583	missense	7776	exon25			CAGGCCGCTGGGC	AF085243	CCDS42447.1	18q22-q23	2013-01-08				ENSG00000130856		"""Zinc fingers, C2H2-type"""	13028	protein-coding gene	gene with protein product		604760				10458916	Standard	NM_007345		Approved		uc002lmi.3	Q9UL36		ENST00000253159.8:c.4528G>A	18.37:g.74640002G>A	ENSP00000253159:p.Ala1510Thr	180.0	0.0	0		200.0	99.0	0.495	NM_007345	B2RTX9|Q9UL37	Missense_Mutation	SNP	ENST00000253159.8	37	CCDS42447.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	0.098	-1.156936	0.01686	0.008421	0.0	ENSG00000130856	ENST00000253159;ENST00000543926;ENST00000320610	T;T	0.10192	2.9;3.06	5.07	2.3	0.28687	.	0.166139	0.45126	D	0.000391	T	0.02688	0.0081	N	0.04880	-0.145	0.09310	N	1	B	0.13145	0.007	B	0.08055	0.003	T	0.39461	-0.9613	10	0.25751	T	0.34	.	4.3857	0.11316	0.298:0.0:0.4852:0.2168	.	1510	Q9UL36	ZN236_HUMAN	T	1510	ENSP00000253159:A1510T;ENSP00000444524:A1510T	ENSP00000253159:A1510T	A	+	1	0	ZNF236	72768990	0.088000	0.21588	0.015000	0.15790	0.230000	0.25150	0.368000	0.20399	0.660000	0.30964	-1.276000	0.01395	GCT	G|0.996;A|0.004	0.004	strong		0.542	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1		
MYH7B	57644	hgsc.bcm.edu	37	20	33574784	33574784	+	Missense_Mutation	SNP	G	G	A	rs115275866	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33574784G>A	ENST00000262873.7	+	13	1218	c.1126G>A	c.(1126-1128)Gcc>Acc	p.A376T		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	334	Myosin motor.					membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			GGAGCTCATCGCCACCGACGT	0.607													G|||	16	0.00319489	0.0121	0.0	5008	,	,		18635	0.0		0.0	False		,,,				2504	0.0				p.A376T		Atlas-SNP	.											MYH7B,colon,carcinoma,0,1	MYH7B	145	1	0			c.G1126A						PASS	.	G	THR/ALA	57,4197		0,57,2070	77.0	76.0	76.0		1126	3.7	1.0	20	dbSNP_132	76	1,8471		0,1,4235	yes	missense	MYH7B	NM_020884.3	58	0,58,6305	AA,AG,GG		0.0118,1.3399,0.4558	possibly-damaging	376/1984	33574784	58,12668	2127	4236	6363	SO:0001583	missense	57644	exon15			CTCATCGCCACCG	AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"""Myosins / Myosin superfamily : Class II"""	15906	protein-coding gene	gene with protein product		609928	"""myosin, heavy polypeptide 7B, cardiac muscle, beta"""			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.1126G>A	20.37:g.33574784G>A	ENSP00000262873:p.Ala376Thr	66.0	0.0	0		93.0	50.0	0.537634	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Missense_Mutation	SNP	ENST00000262873.7	37	CCDS42869.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	G	19.22	3.786240	0.70337	0.013399	1.18E-4	ENSG00000078814	ENST00000262873	D	0.87491	-2.26	3.66	3.66	0.41972	Myosin head, motor domain (2);	0.000000	0.35708	N	0.003040	T	0.81612	0.4859	M	0.80847	2.515	0.39394	D	0.966466	P	0.51240	0.943	P	0.47299	0.543	D	0.87287	0.2296	10	0.72032	D	0.01	.	12.3325	0.55048	0.0878:0.0:0.9122:0.0	.	334	A7E2Y1	MYH7B_HUMAN	T	376	ENSP00000262873:A376T	ENSP00000262873:A376T	A	+	1	0	MYH7B	33038445	0.861000	0.29849	1.000000	0.80357	0.538000	0.34931	2.633000	0.46519	2.356000	0.79943	0.655000	0.94253	GCC	G|0.993;A|0.007	0.007	strong		0.607	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884	
KLHL2	11275	hgsc.bcm.edu	37	4	166149999	166149999	+	Missense_Mutation	SNP	A	A	G	rs80341433	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:166149999A>G	ENST00000226725.6	+	3	452	c.193A>G	c.(193-195)Atg>Gtg	p.M65V	KLHL2_ENST00000538127.1_Intron|KLHL2_ENST00000421009.2_Silent_p.T8T|KLHL2_ENST00000514860.1_Missense_Mutation_p.M69V	NM_007246.3	NP_009177.3	O95198	KLHL2_HUMAN	kelch-like family member 2	65	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				protein ubiquitination (GO:0016567)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)	actin binding (GO:0003779)			endometrium(3)|large_intestine(5)|lung(4)|prostate(1)|urinary_tract(1)	14	all_hematologic(180;0.221)			GBM - Glioblastoma multiforme(119;2.94e-27)|COAD - Colon adenocarcinoma(41;1.4e-05)|Kidney(143;4.95e-05)|KIRC - Kidney renal clear cell carcinoma(143;0.000927)		GGCAGAAGACATGGAAATTTC	0.348													A|||	32	0.00638978	0.0234	0.0014	5008	,	,		20934	0.0		0.0	False		,,,				2504	0.0				p.M69V		Atlas-SNP	.											.	KLHL2	42	.	0			c.A205G						PASS	.	A	VAL/MET,,VAL/MET	77,4329	65.3+/-102.7	1,75,2127	68.0	65.0	66.0		205,,193	4.2	1.0	4	dbSNP_131	66	1,8599		0,1,4299	no	missense,intron,missense	KLHL2	NM_001161521.1,NM_001161522.1,NM_007246.3	21,,21	1,76,6426	GG,GA,AA		0.0116,1.7476,0.5997	benign,,benign	69/598,,65/594	166149999	78,12928	2203	4300	6503	SO:0001583	missense	11275	exon3			GAAGACATGGAAA	AF059569	CCDS34094.1, CCDS54815.1, CCDS54816.1	4q21.2	2013-01-30	2013-01-30		ENSG00000109466	ENSG00000109466		"""Kelch-like"", ""BTB/POZ domain containing"""	6353	protein-coding gene	gene with protein product	"""mayven"""	605774	"""kelch (Drosophila)-like 2 (Mayven)"", ""kelch-like 2, Mayven (Drosophila)"""			10397770, 16035103	Standard	NM_007246		Approved	MAV	uc011cjm.2	O95198	OTTHUMG00000161294	ENST00000226725.6:c.193A>G	4.37:g.166149999A>G	ENSP00000226725:p.Met65Val	736.0	0.0	0		576.0	285.0	0.494792	NM_001161521	A6NCM7|B2RD18|B4DFH7|F5H6M3|Q8N484|Q8TBH5	Missense_Mutation	SNP	ENST00000226725.6	37	CCDS34094.1	.	.	.	.	.	.	.	.	.	.	A	8.320	0.824018	0.16678	0.017476	1.16E-4	ENSG00000109466	ENST00000226725;ENST00000511305;ENST00000509704;ENST00000514860	T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19	4.16	4.16	0.48862	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.104953	0.64402	D	0.000003	T	0.10121	0.0248	N	0.00157	-1.96	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.10847	-1.0612	10	0.13470	T	0.59	.	8.1516	0.31143	0.9087:0.0:0.0913:0.0	.	69;65	B4DFH7;O95198	.;KLHL2_HUMAN	V	65;105;27;69	ENSP00000226725:M65V;ENSP00000422113:M105V;ENSP00000421324:M27V;ENSP00000424198:M69V	ENSP00000226725:M65V	M	+	1	0	KLHL2	166369449	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	4.885000	0.63142	1.750000	0.51863	0.383000	0.25322	ATG	A|0.994;G|0.006	0.006	strong		0.348	KLHL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364439.1		
C14orf159	80017	hgsc.bcm.edu	37	14	91666248	91666248	+	Splice_Site	SNP	T	T	C	rs28715808	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:91666248T>C	ENST00000523771.1	+	11	2031	c.1428T>C	c.(1426-1428)acT>acC	p.T476T	C14orf159_ENST00000518868.1_Splice_Site_p.T481T|C14orf159_ENST00000522322.1_Splice_Site_p.T476T|C14orf159_ENST00000521077.2_Splice_Site_p.T481T|C14orf159_ENST00000428926.2_Splice_Site_p.T476T|C14orf159_ENST00000520328.1_Splice_Site_p.T464T|C14orf159_ENST00000523816.1_Splice_Site_p.T476T|C14orf159_ENST00000412671.2_Splice_Site_p.T481T|C14orf159_ENST00000256324.10_Splice_Site_p.T481T|C14orf159_ENST00000525393.2_Splice_Site_p.T352T			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	476						mitochondrion (GO:0005739)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		TCTCATCAACTGGTAAGTATG	0.458													T|||	181	0.0361422	0.1067	0.0346	5008	,	,		22154	0.0		0.0109	False		,,,				2504	0.0051				p.T481T		Atlas-SNP	.											.	C14orf159	57	.	0			c.T1443C						PASS	.	T	,,,,	337,4069	176.9+/-206.0	16,305,1882	151.0	142.0	145.0		1428,1428,1443,1392,1428	-2.7	0.1	14	dbSNP_125	145	117,8483	61.0+/-122.8	0,117,4183	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	C14orf159	NM_001102366.1,NM_001102367.1,NM_001102368.1,NM_001102369.1,NM_024952.6	,,,,	16,422,6065	CC,CT,TT		1.3605,7.6487,3.4907	,,,,	476/617,476/617,481/622,464/565,476/617	91666248	454,12552	2203	4300	6503	SO:0001630	splice_region_variant	80017	exon11			ATCAACTGGTAAG	AK097294	CCDS32141.1, CCDS41979.1, CCDS45150.1, CCDS66693.1, CCDS73677.1	14q32.11	2012-09-26			ENSG00000133943	ENSG00000133943			20498	protein-coding gene	gene with protein product							Standard	NM_001102367		Approved	FLJ39975	uc001xze.2	Q7Z3D6	OTTHUMG00000164980	ENST00000523771.1:c.1429+1T>C	14.37:g.91666248T>C		135.0	0.0	0		155.0	86.0	0.554839	NM_001102368	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Silent	SNP	ENST00000523771.1	37	CCDS32141.1	60	0.027472527472527472	41	0.08333333333333333	12	0.03314917127071823	0	0.0	7	0.009234828496042216	T	0.894	-0.724442	0.03158	0.076487	0.013605	ENSG00000133943	ENST00000522816	.	.	.	5.1	-2.71	0.05986	.	.	.	.	.	T	0.00967	0.0032	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.22173	-1.0224	3	.	.	.	.	2.29	0.04136	0.3649:0.0777:0.3565:0.2009	rs28715808	.	.	.	P	77	.	.	L	+	2	0	C14orf159	90736001	0.990000	0.36364	0.051000	0.19133	0.053000	0.15095	0.237000	0.17985	-0.360000	0.08138	-0.461000	0.05368	CTG	T|0.967;C|0.033	0.033	strong		0.458	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952	Silent
NAT8	9027	hgsc.bcm.edu	37	2	73868446	73868446	+	Missense_Mutation	SNP	C	C	T	rs13424561	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:73868446C>T	ENST00000272425.3	-	2	459	c.310G>A	c.(310-312)Gag>Aag	p.E104K		NM_003960.3|NM_016347.2	NP_003951.3|NP_057431.2			N-acetyltransferase 8 (GCN5-related, putative)											breast(1)|endometrium(2)|kidney(2)|lung(2)|ovary(1)|prostate(1)	9						GAGCCACGCTCACTCAGGTAG	0.537													.|||	179	0.0357428	0.1286	0.013	5008	,	,		22094	0.0		0.0	False		,,,				2504	0.0				p.E104K		Atlas-SNP	.											.	NAT8	26	.	0			c.G310A						PASS	.	C	LYS/GLU	505,3901	235.2+/-247.8	38,429,1736	118.0	112.0	114.0		310	-0.2	0.0	2	dbSNP_121	114	3,8597	3.7+/-12.6	0,3,4297	yes	missense	NAT8	NM_003960.3	56	38,432,6033	TT,TC,CC		0.0349,11.4616,3.9059	possibly-damaging	104/228	73868446	508,12498	2203	4300	6503	SO:0001583	missense	9027	exon2			CACGCTCACTCAG	AB013094	CCDS1926.1	2p13.2	2012-03-20	2008-09-24		ENSG00000144035	ENSG00000144035			18069	protein-coding gene	gene with protein product		606716	"""N-acetyltransferase 8"""			11397015, 9852678, 19011241	Standard	NM_003960		Approved	Hcml1, TSC501, GLA, ATase2	uc002sji.1	Q9UHE5	OTTHUMG00000129818	ENST00000272425.3:c.310G>A	2.37:g.73868446C>T	ENSP00000272425:p.Glu104Lys	139.0	0.0	0		164.0	83.0	0.506098	NM_003960		Missense_Mutation	SNP	ENST00000272425.3	37	CCDS1926.1	75	0.034340659340659344	71	0.1443089430894309	4	0.011049723756906077	0	0.0	0	0.0	C	2.671	-0.277447	0.05679	0.114616	3.49E-4	ENSG00000144035	ENST00000272425	T	0.29397	1.57	3.86	-0.22	0.13130	GCN5-related N-acetyltransferase (GNAT) domain (1);Acyl-CoA N-acyltransferase (2);	1.343440	0.05236	N	0.511242	T	0.00144	0.0004	L	0.31752	0.955	0.80722	P	0.0	B	0.24426	0.103	B	0.17722	0.019	T	0.20739	-1.0266	9	0.08179	T	0.78	-1.1728	7.9371	0.29935	0.0:0.5069:0.0:0.4931	rs13424561;rs13424561	104	Q9UHE5	NAT8_HUMAN	K	104	ENSP00000272425:E104K	ENSP00000272425:E104K	E	-	1	0	NAT8	73721954	0.000000	0.05858	0.000000	0.03702	0.058000	0.15608	-0.648000	0.05391	-0.174000	0.10743	-0.151000	0.13558	GAG	C|0.956;T|0.044	0.044	strong		0.537	NAT8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327854.1	NM_003960	
SERPINB3	6317	hgsc.bcm.edu	37	18	61322998	61322998	+	Missense_Mutation	SNP	G	G	A	rs73962331	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61322998G>A	ENST00000283752.5	-	8	1209	c.1066C>T	c.(1066-1068)Cct>Tct	p.P356S	SERPINB11_ENST00000489748.1_RNA|SERPINB3_ENST00000332821.8_Missense_Mutation_p.P304S	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	356					negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						GTTGAAGTAGGTGATGATCCG	0.463													G|||	286	0.0571086	0.205	0.0144	5008	,	,		20255	0.0		0.004	False		,,,				2504	0.001				p.P356S		Atlas-SNP	.											.	SERPINB3	90	.	0			c.C1066T						PASS	.	G	SER/PRO	674,3732	277.2+/-273.6	53,568,1582	145.0	147.0	147.0		1066	0.5	0.0	18	dbSNP_130	147	15,8585	9.8+/-36.6	0,15,4285	yes	missense	SERPINB3	NM_006919.2	74	53,583,5867	AA,AG,GG		0.1744,15.2973,5.2976	benign	356/391	61322998	689,12317	2203	4300	6503	SO:0001583	missense	6317	exon8			AAGTAGGTGATGA	U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"""Serine (or cysteine) peptidase inhibitors"""	10569	protein-coding gene	gene with protein product		600517	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"""	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.1066C>T	18.37:g.61322998G>A	ENSP00000283752:p.Pro356Ser	215.0	0.0	0		203.0	71.0	0.349754	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	Missense_Mutation	SNP	ENST00000283752.5	37	CCDS11987.1	99	0.04532967032967033	91	0.18495934959349594	6	0.016574585635359115	0	0.0	2	0.002638522427440633	G	1.994	-0.431080	0.04669	0.152973	0.001744	ENSG00000057149	ENST00000283752;ENST00000332821	D;D	0.83673	-1.75;-1.75	2.96	0.496	0.16896	Serpin domain (3);	3.431400	0.01103	N	0.005437	T	0.00178	0.0005	N	0.02181	-0.65	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.45483	-0.9258	9	0.02654	T	1	.	2.8087	0.05435	0.6154:0.1428:0.1014:0.1403	.	304;356	P29508-2;P29508	.;SPB3_HUMAN	S	356;304	ENSP00000283752:P356S;ENSP00000329498:P304S	ENSP00000283752:P356S	P	-	1	0	SERPINB3	59473978	0.018000	0.18449	0.004000	0.12327	0.000000	0.00434	0.503000	0.22610	0.107000	0.17824	-1.316000	0.01300	CCT	G|0.948;A|0.052	0.052	strong		0.463	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919	
COG5	10466	hgsc.bcm.edu	37	7	107204371	107204371	+	Missense_Mutation	SNP	C	C	T	rs73419464	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:107204371C>T	ENST00000347053.3	-	1	114	c.64G>A	c.(64-66)Gct>Act	p.A22T	DUS4L_ENST00000498786.1_Intron|DUS4L_ENST00000265720.3_5'Flank|COG5_ENST00000297135.3_Missense_Mutation_p.A22T|DUS4L_ENST00000402620.1_5'Flank|COG5_ENST00000393603.2_Missense_Mutation_p.A22T	NM_181733.2	NP_859422.2	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5	22					intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|skin(4)|stomach(1)	40						ATGTCGTCAGCAGCAGAACGG	0.697													C|||	152	0.0303514	0.1089	0.0101	5008	,	,		12302	0.0		0.0	False		,,,				2504	0.001				p.A22T		Atlas-SNP	.											.	COG5	78	.	0			c.G64A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	347,4057		15,317,1870	18.0	18.0	18.0		64,64,64	1.7	0.4	7	dbSNP_130	18	7,8587		0,7,4290	yes	missense,missense,missense	COG5	NM_181733.2,NM_006348.3,NM_001161520.1	58,58,58	15,324,6160	TT,TC,CC		0.0815,7.8792,2.7235	benign,benign,benign	22/840,22/861,22/824	107204371	354,12644	2202	4297	6499	SO:0001583	missense	10466	exon1			CGTCAGCAGCAGA	AF058718	CCDS5742.1, CCDS5743.1, CCDS55152.1	7q31	2010-06-24	2001-12-07	2002-05-10	ENSG00000164597	ENSG00000164597		"""Components of oligomeric golgi complex"""	14857	protein-coding gene	gene with protein product		606821	"""golgi transport complex 1 (90 kDa subunit)"""	GOLTC1		9792665, 11980916	Standard	NM_006348		Approved	GTC90	uc003vec.2	Q9UP83	OTTHUMG00000023895	ENST00000347053.3:c.64G>A	7.37:g.107204371C>T	ENSP00000334703:p.Ala22Thr	93.0	0.0	0		112.0	64.0	0.571429	NM_006348	A4D0R6|A4D0R7|O14555|O95008|Q6NUL5	Missense_Mutation	SNP	ENST00000347053.3	37	CCDS5743.1	62	0.028388278388278388	57	0.11585365853658537	5	0.013812154696132596	0	0.0	0	0.0	C	14.15	2.449883	0.43531	0.078792	8.15E-4	ENSG00000164597	ENST00000347053;ENST00000297135;ENST00000393603	T;T;T	0.18502	2.22;2.21;2.21	4.76	1.72	0.24424	.	0.904518	0.09273	N	0.824937	T	0.00144	0.0004	N	0.08118	0	0.21355	N	0.999718	B;B	0.21905	0.037;0.062	B;B	0.20184	0.013;0.028	T	0.38067	-0.9678	10	0.28530	T	0.3	-1.6692	12.2534	0.54611	0.0:0.4485:0.5515:0.0	.	22;22	Q9UP83;Q9UP83-2	COG5_HUMAN;.	T	22	ENSP00000334703:A22T;ENSP00000297135:A22T;ENSP00000377228:A22T	ENSP00000297135:A22T	A	-	1	0	COG5	106991607	0.002000	0.14202	0.354000	0.25760	0.206000	0.24218	0.304000	0.19228	0.574000	0.29417	0.591000	0.81541	GCT	C|0.970;T|0.030	0.030	strong		0.697	COG5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060216.4		
MMP17	4326	hgsc.bcm.edu	37	12	132329666	132329666	+	Silent	SNP	C	C	T	rs36031288	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132329666C>T	ENST00000360564.1	+	7	1074	c.972C>T	c.(970-972)ccC>ccT	p.P324P	MMP17_ENST00000535291.1_Silent_p.P240P|MMP17_ENST00000535004.1_5'Flank|MMP17_ENST00000535182.1_3'UTR	NM_016155.4	NP_057239.4	Q9ULZ9	MMP17_HUMAN	matrix metallopeptidase 17 (membrane-inserted)	324					positive regulation of catalytic activity (GO:0043085)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(1)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.82e-07)|Epithelial(86;1.51e-06)|all cancers(50;2.35e-05)	Marimastat(DB00786)	CCTGCAGGCCCAGGAAGGACG	0.667													C|||	191	0.038139	0.1377	0.0101	5008	,	,		15735	0.0		0.002	False		,,,				2504	0.0				p.P324P		Atlas-SNP	.											.	MMP17	77	.	0			c.C972T						PASS	.	C		485,3921	225.9+/-241.6	31,423,1749	73.0	70.0	71.0		972	-2.7	0.1	12	dbSNP_126	71	6,8594	3.7+/-12.6	0,6,4294	no	coding-synonymous	MMP17	NM_016155.4		31,429,6043	TT,TC,CC		0.0698,11.0077,3.7752		324/604	132329666	491,12515	2203	4300	6503	SO:0001819	synonymous_variant	4326	exon7			CAGGCCCAGGAAG	X89576	CCDS31927.1	12q24.3	2005-08-08	2005-08-08		ENSG00000198598	ENSG00000198598			7163	protein-coding gene	gene with protein product		602285	"""matrix metalloproteinase 17 (membrane-inserted)"""			9878265	Standard	NM_016155		Approved	MT4-MMP	uc001ujc.1	Q9ULZ9	OTTHUMG00000168050	ENST00000360564.1:c.972C>T	12.37:g.132329666C>T		102.0	0.0	0		118.0	58.0	0.491525	NM_016155	Q14850	Silent	SNP	ENST00000360564.1	37	CCDS31927.1																																																																																			C|0.961;T|0.039	0.039	strong		0.667	MMP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397757.1	NM_016155	
CD44	960	hgsc.bcm.edu	37	11	35223303	35223303	+	Silent	SNP	G	G	A	rs11033026	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:35223303G>A	ENST00000428726.2	+	9	1245	c.1122G>A	c.(1120-1122)gaG>gaA	p.E374E	CD44_ENST00000360158.4_Intron|CD44_ENST00000433892.2_Intron|CD44_ENST00000415148.2_Silent_p.E331E|CD44_ENST00000526669.2_Intron|CD44_ENST00000352818.4_Intron|CD44_ENST00000449691.2_Silent_p.E374E|CD44_ENST00000437706.2_Silent_p.E374E|CD44_ENST00000278386.6_Intron|CD44_ENST00000433354.2_Silent_p.E375E|CD44_ENST00000434472.2_Intron|CD44_ENST00000263398.6_Intron	NM_000610.3	NP_000601.3	P16070	CD44_HUMAN	CD44 molecule (Indian blood group)	374	Stem.				blood coagulation (GO:0007596)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|monocyte aggregation (GO:0070487)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|Wnt signaling pathway (GO:0016055)|wound healing involved in inflammatory response (GO:0002246)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|skin(1)	23	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronan(DB08818)	AGCATCATGAGGAAGAAGAGA	0.473													G|||	473	0.0944489	0.3449	0.0245	5008	,	,		18781	0.0		0.0	False		,,,				2504	0.0				p.E374E		Atlas-SNP	.											.	CD44	48	.	0			c.G1122A						PASS	.	G	,,,,,,,	1185,3219	417.2+/-337.8	174,837,1191	153.0	129.0	137.0		1122,993,,,,,,	-10.3	0.1	11	dbSNP_120	137	12,8584	5.7+/-21.5	0,12,4286	no	coding-synonymous,coding-synonymous,intron,intron,intron,intron,intron,intron	CD44	NM_000610.3,NM_001001389.1,NM_001001390.1,NM_001001391.1,NM_001001392.1,NM_001202555.1,NM_001202556.1,NM_001202557.1	,,,,,,,	174,849,5477	AA,AG,GG		0.1396,26.9074,9.2077	,,,,,,,	374/743,331/700,,,,,,	35223303	1197,11803	2202	4298	6500	SO:0001819	synonymous_variant	960	exon9			TCATGAGGAAGAA	M59040	CCDS7897.1, CCDS31455.1, CCDS31456.1, CCDS31457.1, CCDS31458.1, CCDS55754.1, CCDS55755.1	11p13	2014-07-18	2006-03-28		ENSG00000026508	ENSG00000026508		"""CD molecules"", ""Blood group antigens"", ""Proteoglycans / Cell surface : Other"""	1681	protein-coding gene	gene with protein product	"""hematopoietic cell E- and L-selectin ligand"", ""chondroitin sulfate proteoglycan 8"""	107269	"""CD44 antigen (homing function and Indian blood group system)"""	MIC4, MDU2, MDU3		2454887	Standard	NM_001202555		Approved	IN, MC56, Pgp1, CD44R, HCELL, CSPG8	uc001mvu.3	P16070	OTTHUMG00000044388	ENST00000428726.2:c.1122G>A	11.37:g.35223303G>A		170.0	0.0	0		161.0	160.0	0.993789	NM_000610	A5YRN9|B6EAT9|D3DR12|D3DR13|O95370|P22511|Q04858|Q13419|Q13957|Q13958|Q13959|Q13960|Q13961|Q13967|Q13968|Q13980|Q15861|Q16064|Q16065|Q16066|Q16208|Q16522|Q86T72|Q86Z27|Q8N694|Q92493|Q96J24|Q9H5A5|Q9UC28|Q9UC29|Q9UC30|Q9UCB0|Q9UJ36	Silent	SNP	ENST00000428726.2	37	CCDS7897.1	176	0.08058608058608059	170	0.34552845528455284	6	0.016574585635359115	0	0.0	0	0.0	G	0.022	-1.413724	0.01145	0.269074	0.001396	ENSG00000026508	ENST00000528455	.	.	.	5.14	-10.3	0.00346	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	.	.	.	.	.	.	T	0.35450	-0.9788	3	.	.	.	-9.2826	1.2309	0.01943	0.2577:0.2623:0.3217:0.1583	rs11033026;rs11033026	.	.	.	R	226	.	.	G	+	1	0	CD44	35179879	0.000000	0.05858	0.068000	0.19968	0.002000	0.02628	-2.933000	0.00687	-1.585000	0.01634	-1.108000	0.02087	GGA	G|0.883;A|0.117	0.117	strong		0.473	CD44-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388927.1	NM_000610	
PASD1	139135	hgsc.bcm.edu	37	X	150840690	150840690	+	Missense_Mutation	SNP	G	G	T	rs370395923		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:150840690G>T	ENST00000370357.4	+	14	1718	c.1473G>T	c.(1471-1473)gaG>gaT	p.E491D		NM_173493.2	NP_775764.2	Q8IV76	PASD1_HUMAN	PAS domain containing 1	491						nucleus (GO:0005634)	signal transducer activity (GO:0004871)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(3)|liver(1)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	48	Acute lymphoblastic leukemia(192;6.56e-05)					acctgaaggagcagcagcggc	0.527													G|||	16	0.00423841	0.0121	0.0	3775	,	,		14023	0.0		0.0	False		,,,				2504	0.0				p.E491D		Atlas-SNP	.											.	PASD1	286	.	0			c.G1473T						PASS	.	G	ASP/GLU	35,3366		0,33,2,1472,389	10.0	10.0	10.0		1473	1.0	0.0	X		10	1,5850		0,0,1,2208,1434	yes	missense	PASD1	NM_173493.2	45	0,33,3,3680,1823	TT,TG,T,GG,G		0.0171,1.0291,0.3891	possibly-damaging	491/774	150840690	36,9216	1896	3643	5539	SO:0001583	missense	139135	exon14			GAAGGAGCAGCAG	AY270020	CCDS35431.1	Xq28	2009-08-06			ENSG00000166049	ENSG00000166049			20686	protein-coding gene	gene with protein product	"""cancer/testis antigen 63"""					15122589, 15162151	Standard	NM_173493		Approved	CT63	uc004fev.4	Q8IV76	OTTHUMG00000024169	ENST00000370357.4:c.1473G>T	X.37:g.150840690G>T	ENSP00000359382:p.Glu491Asp	84.0	0.0	0		115.0	48.0	0.417391	NM_173493	Q3MNE0|Q69HD7|Q8N7X9	Missense_Mutation	SNP	ENST00000370357.4	37	CCDS35431.1	.	.	.	.	.	.	.	.	.	.	G	9.223	1.033777	0.19590	0.010291	1.71E-4	ENSG00000166049	ENST00000370357	T	0.17691	2.26	2.03	1.04	0.20106	.	.	.	.	.	T	0.03871	0.0109	N	0.08118	0	0.09310	N	1	P	0.50710	0.938	B	0.37387	0.248	T	0.23904	-1.0175	9	0.15066	T	0.55	.	4.9456	0.13987	0.0:0.0:0.6449:0.355	.	491	Q8IV76	PASD1_HUMAN	D	491	ENSP00000359382:E491D	ENSP00000359382:E491D	E	+	3	2	PASD1	150591346	0.001000	0.12720	0.004000	0.12327	0.251000	0.25915	-0.444000	0.06854	0.252000	0.21531	0.462000	0.41574	GAG	.	.	weak		0.527	PASD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060879.2	NM_173493	
IL25	64806	hgsc.bcm.edu	37	14	23845061	23845061	+	Missense_Mutation	SNP	T	T	C	rs149802556	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:23845061T>C	ENST00000329715.2	+	2	764	c.506T>C	c.(505-507)gTg>gCg	p.V169A	CMTM5_ENST00000339180.4_5'Flank|CMTM5_ENST00000342473.4_5'Flank|CMTM5_ENST00000397227.3_5'Flank|CMTM5_ENST00000382809.2_5'Flank|CMTM5_ENST00000359320.3_5'Flank|CMTM5_ENST00000555731.1_5'Flank|IL25_ENST00000397242.2_Missense_Mutation_p.V153A	NM_022789.3	NP_073626.1	Q9H293	IL25_HUMAN	interleukin 25	169					eosinophil differentiation (GO:0030222)|inflammatory response to antigenic stimulus (GO:0002437)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to fungus (GO:0009620)|response to nematode (GO:0009624)	extracellular space (GO:0005615)	interleukin-17E receptor binding (GO:0030380)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	9	all_cancers(95;2e-05)			GBM - Glioblastoma multiforme(265;0.00665)|READ - Rectum adenocarcinoma(4;0.0276)|Colorectal(4;0.0396)		TTAGCTTGTGTGTGTGTGCGG	0.607																																					p.V169A		Atlas-SNP	.											.	IL25	21	.	0			c.T506C						PASS	.	T	ALA/VAL,ALA/VAL	2,4404	4.2+/-10.8	0,2,2201	150.0	137.0	141.0		506,458	4.6	1.0	14	dbSNP_134	141	0,8600		0,0,4300	no	missense,missense	IL25	NM_022789.3,NM_172314.1	64,64	0,2,6501	CC,CT,TT		0.0,0.0454,0.0154	probably-damaging,probably-damaging	169/178,153/162	23845061	2,13004	2203	4300	6503	SO:0001583	missense	64806	exon2			CTTGTGTGTGTGT	AF305200	CCDS9597.1, CCDS45086.1	14q11.2	2008-01-07	2006-05-17	2006-05-17	ENSG00000166090	ENSG00000166090		"""Interleukins and interleukin receptors"""	13765	protein-coding gene	gene with protein product		605658	"""interleukin 17E"""	IL17E		11058597, 11754819	Standard	NM_172314		Approved	IL-25, IL-17E	uc001wjq.3	Q9H293	OTTHUMG00000028749	ENST00000329715.2:c.506T>C	14.37:g.23845061T>C	ENSP00000328111:p.Val169Ala	254.0	1.0	0.00393701		262.0	105.0	0.400763	NM_022789	Q2M3F0|Q8IZV3|Q8WXB0	Missense_Mutation	SNP	ENST00000329715.2	37	CCDS9597.1	.	.	.	.	.	.	.	.	.	.	T	20.8	4.049273	0.75846	4.54E-4	0.0	ENSG00000166090	ENST00000397242;ENST00000329715	T;T	0.55234	0.53;0.53	4.58	4.58	0.56647	.	0.145674	0.33023	N	0.005361	T	0.57636	0.2067	L	0.44542	1.39	0.30135	N	0.804464	P;D	0.64830	0.64;0.994	B;P	0.59056	0.334;0.851	T	0.58634	-0.7602	10	0.48119	T	0.1	-26.6522	10.2614	0.43430	0.0:0.0:0.0:1.0	.	169;153	Q9H293;Q9H293-2	IL25_HUMAN;.	A	153;169	ENSP00000380417:V153A;ENSP00000328111:V169A	ENSP00000328111:V169A	V	+	2	0	IL25	22914901	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.712000	0.54875	1.947000	0.56498	0.459000	0.35465	GTG	T|1.000;C|0.000	0.000	strong		0.607	IL25-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000071789.2		
PTCD2	79810	hgsc.bcm.edu	37	5	71618069	71618069	+	Silent	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:71618069A>G	ENST00000380639.5	+	2	214	c.198A>G	c.(196-198)gcA>gcG	p.A66A	PTCD2_ENST00000543322.1_Silent_p.A66A|MRPS27_ENST00000513900.1_5'Flank|MRPS27_ENST00000522095.1_5'Flank|PTCD2_ENST00000536805.1_5'UTR|PTCD2_ENST00000503868.1_Silent_p.A66A|MRPS27_ENST00000457646.4_5'Flank|MRPS27_ENST00000515404.1_5'Flank|MRPS27_ENST00000261413.5_5'Flank	NM_024754.3	NP_079030.3	Q8WV60	PTCD2_HUMAN	pentatricopeptide repeat domain 2	66					kidney development (GO:0001822)|liver development (GO:0001889)|mitochondrion organization (GO:0007005)|mRNA processing (GO:0006397)|muscle fiber development (GO:0048747)|regulation of mRNA processing (GO:0050684)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(6)|lung(1)|skin(1)	11		Lung NSC(167;0.00237)|Ovarian(174;0.0175)|Prostate(461;0.141)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.73e-53)		TGGCTGTTGCATGTAATCTTT	0.299																																					p.A66A		Atlas-SNP	.											.	PTCD2	31	.	0			c.A198G						PASS	.						107.0	119.0	115.0					5																	71618069		1815	4077	5892	SO:0001819	synonymous_variant	79810	exon2			TGTTGCATGTAAT	BC018720	CCDS4014.2, CCDS68891.1, CCDS68892.1, CCDS75258.1	5q13.2	2008-02-05			ENSG00000049883	ENSG00000049883			25734	protein-coding gene	gene with protein product		615484				12477932	Standard	XM_005248601		Approved	FLJ12598	uc003kcb.3	Q8WV60	OTTHUMG00000100953	ENST00000380639.5:c.198A>G	5.37:g.71618069A>G		86.0	0.0	0		75.0	24.0	0.32	NM_024754	B7Z5D0|B7Z8L7|E9PFV7|Q6IA65|Q9H9R0	Silent	SNP	ENST00000380639.5	37	CCDS4014.2																																																																																			.	.	none		0.299	PTCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218562.6	NM_024754	
FLG	2312	hgsc.bcm.edu	37	1	152283367	152283367	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152283367T>C	ENST00000368799.1	-	3	4030	c.3995A>G	c.(3994-3996)cAt>cGt	p.H1332R	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1332	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTCTGTGTGATGAGTGCCTGA	0.552									Ichthyosis																												p.H1332R		Atlas-SNP	.											.	FLG	900	.	0			c.A3995G						PASS	.						304.0	292.0	296.0					1																	152283367		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GTGTGATGAGTGC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.3995A>G	1.37:g.152283367T>C	ENSP00000357789:p.His1332Arg	509.0	0.0	0		622.0	48.0	0.0771704	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	2.821	-0.244841	0.05906	.	.	ENSG00000143631	ENST00000368799	T	0.03951	3.75	2.24	-3.75	0.04372	.	.	.	.	.	T	0.00580	0.0019	N	0.05383	-0.06	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.45673	-0.9245	9	0.11182	T	0.66	.	8.4062	0.32616	0.0:0.3846:0.0:0.6154	.	1332	P20930	FILA_HUMAN	R	1332	ENSP00000357789:H1332R	ENSP00000357789:H1332R	H	-	2	0	FLG	150549991	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-3.669000	0.00398	-1.560000	0.01686	-1.470000	0.01010	CAT	.	.	none		0.552	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
LARS2	23395	hgsc.bcm.edu	37	3	45459030	45459030	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:45459030C>T	ENST00000415258.1	+	4	561	c.420C>T	c.(418-420)gtC>gtT	p.V140V	LARS2_ENST00000265537.3_Silent_p.V140V|LARS2_ENST00000414984.1_Silent_p.V97V			Q15031	SYLM_HUMAN	leucyl-tRNA synthetase 2, mitochondrial	140					gene expression (GO:0010467)|leucyl-tRNA aminoacylation (GO:0006429)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	aminoacyl-tRNA editing activity (GO:0002161)|ATP binding (GO:0005524)|leucine-tRNA ligase activity (GO:0004823)			endometrium(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	18				BRCA - Breast invasive adenocarcinoma(193;0.0122)|KIRC - Kidney renal clear cell carcinoma(197;0.0313)|Kidney(197;0.0372)	L-Leucine(DB00149)	ATGCCGCAGTCGAGAGGAATC	0.398																																					p.V140V		Atlas-SNP	.											.	LARS2	48	.	0			c.C420T						PASS	.						123.0	116.0	118.0					3																	45459030		2203	4300	6503	SO:0001819	synonymous_variant	23395	exon5			CGCAGTCGAGAGG	AJ312685	CCDS2728.1	3p21.3	2012-10-26			ENSG00000011376	ENSG00000011376	6.1.1.4	"""Aminoacyl tRNA synthetases / Class I"""	17095	protein-coding gene	gene with protein product	"""leucine tRNA ligase 2, mitochondrial"""	604544				20194621, 15123417	Standard	NM_015340		Approved	KIAA0028, LEURS, MGC26121	uc003cop.1	Q15031	OTTHUMG00000133177	ENST00000415258.1:c.420C>T	3.37:g.45459030C>T		143.0	0.0	0		100.0	29.0	0.29	NM_015340		Silent	SNP	ENST00000415258.1	37	CCDS2728.1																																																																																			.	.	none		0.398	LARS2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345001.1	NM_015340	
TTN	7273	hgsc.bcm.edu	37	2	179441917	179441917	+	Missense_Mutation	SNP	T	T	C	rs72646881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179441917T>C	ENST00000591111.1	-	274	64446	c.64222A>G	c.(64222-64224)Atc>Gtc	p.I21408V	RP11-171I2.2_ENST00000603521.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.I14176V|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.I20481V|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.I14109V|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|RP11-171I2.5_ENST00000604215.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.I13984V|TTN_ENST00000589042.1_Missense_Mutation_p.I23049V			Q8WZ42	TITIN_HUMAN	titin	21408	Fibronectin type-III 55. {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)			ACATTACTGATTTCAACAGGA	0.448													T|||	182	0.0363419	0.1278	0.0173	5008	,	,		21850	0.0		0.001	False		,,,				2504	0.0				p.I23049V		Atlas-SNP	.											TTN_ENST00000359218,NS,carcinoma,+2,5	TTN	18412	5	0			c.A69145G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	402,3490		24,354,1568	60.0	59.0	59.0		42526,42325,61441,41950	3.2	1.0	2	dbSNP_130	59	8,8272		0,8,4132	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	29,29,29,29	24,362,5700	CC,CT,TT		0.0966,10.3289,3.3684	benign,benign,benign,benign	14176/27119,14109/27052,20481/33424,13984/26927	179441917	410,11762	1946	4140	6086	SO:0001583	missense	7273	exon324			TACTGATTTCAAC	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.64222A>G	2.37:g.179441917T>C	ENSP00000465570:p.Ile21408Val	112.0	0.0	0		116.0	56.0	0.482759	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		86	0.039377289377289376	78	0.15853658536585366	8	0.022099447513812154	0	0.0	0	0.0	T	10.04	1.241565	0.22711	0.103289	9.66E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.53423	0.62;0.62;0.62;0.62	5.62	3.18	0.36537	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00073	0.0002	N	0.02368	-0.58	0.40312	P	0.02127100000000004	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.002;0.002;0.002	T	0.07616	-1.0763	8	0.87932	D	0	.	4.7345	0.12981	0.129:0.2044:0.0:0.6665	.	13984;14109;14176;21408	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	V	20481;13984;14176;14109;13982	ENSP00000343764:I20481V;ENSP00000434586:I13984V;ENSP00000340554:I14176V;ENSP00000352154:I14109V	ENSP00000340554:I14176V	I	-	1	0	TTN	179150163	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.225000	0.32551	0.466000	0.27193	0.533000	0.62120	ATC	T|0.967;C|0.033	0.033	strong		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
CSH2	1443	hgsc.bcm.edu	37	17	61950694	61950694	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:61950694G>A	ENST00000392886.2	-	2	167	c.16C>T	c.(16-18)Cgg>Tgg	p.R6W	CSH2_ENST00000336844.5_Missense_Mutation_p.R6W|CSH2_ENST00000345366.7_Missense_Mutation_p.R6W|CSH2_ENST00000560142.1_Missense_Mutation_p.R6W	NM_020991.3	NP_066271.1	P0DML3	CSH2_HUMAN	chorionic somatomammotropin hormone 2	6						extracellular region (GO:0005576)	metal ion binding (GO:0046872)			endometrium(2)|large_intestine(1)|lung(3)	6						AGGGACGTCCGGGAGCCTGGG	0.607																																					p.R6W		Atlas-SNP	.											.	CSH2	37	.	0			c.C16T						PASS	.						12.0	12.0	12.0					17																	61950694		2179	4248	6427	SO:0001583	missense	1443	exon2			ACGTCCGGGAGCC	V00573	CCDS11646.1, CCDS42368.1, CCDS42369.1	17q22-q24	2012-10-02							2441	protein-coding gene	gene with protein product	"""placental lactogen"", ""chorionic somatomammotropin B"""	118820				593368, 6208192	Standard	NM_020991		Approved	hCS-B, CSB, CS-2	uc002jch.3	P0DML3		ENST00000392886.2:c.16C>T	17.37:g.61950694G>A	ENSP00000376623:p.Arg6Trp	248.0	0.0	0		235.0	55.0	0.234043	NM_022645	P01243|Q0VDB1|Q14407	Missense_Mutation	SNP	ENST00000392886.2	37	CCDS42369.1	.	.	.	.	.	.	.	.	.	.	g	9.767	1.171702	0.21704	.	.	ENSG00000213218	ENST00000345366;ENST00000336844;ENST00000392886	D;D;D	0.91407	-2.84;-2.17;-2.36	4.1	3.12	0.35913	.	0.628574	0.16367	N	0.217506	D	0.83175	0.5197	L	0.39397	1.21	0.09310	N	1	D;B;D;B	0.54397	0.966;0.035;0.966;0.003	B;B;B;B	0.39660	0.306;0.006;0.306;0.005	T	0.72577	-0.4251	10	0.27082	T	0.32	.	7.9049	0.29757	0.1194:0.0:0.8806:0.0	.	6;6;6;6	P01243;A6NIT4;A8K6C2;B1A4H9	CSH_HUMAN;.;.;.	W	6	ENSP00000308396:R6W;ENSP00000338816:R6W;ENSP00000376623:R6W	ENSP00000338816:R6W	R	-	1	2	CSH2	59304426	0.001000	0.12720	0.003000	0.11579	0.011000	0.07611	0.623000	0.24447	0.839000	0.34971	0.561000	0.74099	CGG	G|0.980;A|0.020	0.020	strong		0.607	CSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417657.1	NM_020991	
GRIK4	2900	hgsc.bcm.edu	37	11	120811161	120811161	+	Missense_Mutation	SNP	G	G	A	rs2230298	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:120811161G>A	ENST00000527524.2	+	14	1869	c.1582G>A	c.(1582-1584)Gtt>Att	p.V528I	GRIK4_ENST00000438375.2_Missense_Mutation_p.V528I	NM_001282470.1	NP_001269399.1	Q16099	GRIK4_HUMAN	glutamate receptor, ionotropic, kainate 4	528			V -> I (in dbSNP:rs35599906). {ECO:0000269|PubMed:8263508}.		glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|response to corticosteroid (GO:0031960)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|nucleus (GO:0005634)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)|terminal bouton (GO:0043195)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(20)|liver(1)|lung(29)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	69		Breast(109;0.000868)|Medulloblastoma(222;0.0453)|all_neural(223;0.116)|all_hematologic(192;0.21)		BRCA - Breast invasive adenocarcinoma(274;1.24e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.116)		TCTTTACCGCGTTCATATGGT	0.388													G|||	151	0.0301518	0.1104	0.0072	5008	,	,		22695	0.0		0.0	False		,,,				2504	0.0				p.V528I		Atlas-SNP	.											.	GRIK4	149	.	0			c.G1582A						PASS	.	G	ILE/VAL	396,4010	195.7+/-220.2	25,346,1832	82.0	84.0	83.0		1582	5.5	1.0	11	dbSNP_126	83	7,8591	6.4+/-24.3	0,7,4292	yes	missense	GRIK4	NM_014619.2	29	25,353,6124	AA,AG,GG		0.0814,8.9877,3.099	probably-damaging	528/957	120811161	403,12601	2203	4299	6502	SO:0001583	missense	2900	exon12			TACCGCGTTCATA	S67803	CCDS8433.1	11q23.3	2012-08-29			ENSG00000149403	ENSG00000149403		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4582	protein-coding gene	gene with protein product		600282		GRIK			Standard	NM_001282470		Approved	GluK4, KA1	uc009zax.1	Q16099	OTTHUMG00000048255	ENST00000527524.2:c.1582G>A	11.37:g.120811161G>A	ENSP00000435648:p.Val528Ile	103.0	0.0	0		65.0	30.0	0.461538	NM_014619	A8K9L1	Missense_Mutation	SNP	ENST00000527524.2	37	CCDS8433.1	61	0.027930402930402932	59	0.11991869918699187	2	0.0055248618784530384	0	0.0	0	0.0	G	21.3	4.125095	0.77436	0.089877	8.14E-4	ENSG00000149403	ENST00000527524;ENST00000438375	T;T	0.11385	2.78;2.78	5.47	5.47	0.80525	Ionotropic glutamate receptor (1);	0.121890	0.56097	D	0.000035	T	0.00356	0.0011	L	0.39147	1.195	0.80722	D	1	D;D	0.89917	1.0;0.995	D;P	0.68353	0.957;0.871	T	0.00812	-1.1556	10	0.34782	T	0.22	.	18.9072	0.92467	0.0:0.0:1.0:0.0	rs35599906	528;528	A6H8K8;Q16099	.;GRIK4_HUMAN	I	528	ENSP00000435648:V528I;ENSP00000404063:V528I	ENSP00000404063:V528I	V	+	1	0	GRIK4	120316371	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.384000	0.97219	2.579000	0.87056	0.591000	0.81541	GTT	G|0.964;A|0.036	0.036	strong		0.388	GRIK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109760.4	NM_014619	
INADL	10207	hgsc.bcm.edu	37	1	62288730	62288730	+	Missense_Mutation	SNP	G	G	C	rs1286812	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:62288730G>C	ENST00000371158.2	+	15	1911	c.1797G>C	c.(1795-1797)caG>caC	p.Q599H	INADL_ENST00000316485.6_Missense_Mutation_p.Q599H	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	599	PDZ 4. {ECO:0000255|PROSITE- ProRule:PRU00143}.		Q -> H (in dbSNP:rs1286812).		cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						GTCTCCTACAGCCAGAAGATG	0.428													G|||	61	0.0121805	0.0454	0.0014	5008	,	,		18625	0.0		0.0	False		,,,				2504	0.0				p.Q599H		Atlas-SNP	.											.	INADL	179	.	0			c.G1797C						PASS	.	G	HIS/GLN	95,4311	76.8+/-115.0	0,95,2108	154.0	140.0	145.0		1797	4.0	1.0	1	dbSNP_87	145	0,8600		0,0,4300	yes	missense	INADL	NM_176877.2	24	0,95,6408	CC,CG,GG		0.0,2.1562,0.7304	possibly-damaging	599/1802	62288730	95,12911	2203	4300	6503	SO:0001583	missense	10207	exon15			CCTACAGCCAGAA	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.1797G>C	1.37:g.62288730G>C	ENSP00000360200:p.Gln599His	223.0	0.0	0		219.0	111.0	0.506849	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	37	CCDS617.2	17	0.007783882783882784	17	0.034552845528455285	0	0.0	0	0.0	0	0.0	G	12.64	1.998539	0.35226	0.021562	0.0	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513;ENST00000255202	T;T	0.27720	1.65;1.65	4.99	4.02	0.46733	PDZ/DHR/GLGF (4);	0.205916	0.32868	N	0.005548	T	0.16041	0.0386	L	0.35644	1.08	0.80722	D	1	D;D;P	0.65815	0.995;0.995;0.808	P;D;B	0.66716	0.894;0.946;0.442	T	0.01496	-1.1340	10	0.39692	T	0.17	.	6.7972	0.23732	0.1259:0.1743:0.6997:0.0	rs1286812;rs1286812	599;599;599	F8W8T2;Q8NI35;Q8NI35-4	.;INADL_HUMAN;.	H	599	ENSP00000360200:Q599H;ENSP00000326199:Q599H	ENSP00000255202:Q599H	Q	+	3	2	INADL	62061318	0.999000	0.42202	1.000000	0.80357	0.416000	0.31233	0.561000	0.23515	2.322000	0.78497	0.561000	0.74099	CAG	G|0.992;C|0.008	0.008	strong		0.428	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
TNR	7143	hgsc.bcm.edu	37	1	175335162	175335162	+	Silent	SNP	T	T	C	rs7516376	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:175335162T>C	ENST00000367674.2	-	11	2874	c.2166A>G	c.(2164-2166)ccA>ccG	p.P722P	TNR_ENST00000263525.2_Silent_p.P722P			Q92752	TENR_HUMAN	tenascin R	722	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					TCCCAGAGGATGGGGTAAAGG	0.552													T|||	277	0.0553115	0.1989	0.0202	5008	,	,		21185	0.0		0.0	False		,,,				2504	0.0				p.P722P		Atlas-SNP	.											TNR,NS,carcinoma,-1,2	TNR	399	2	0			c.A2166G						PASS	.	T		774,3632	314.1+/-293.5	71,632,1500	169.0	158.0	162.0		2166	-11.8	0.2	1	dbSNP_116	162	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	TNR	NM_003285.2		71,637,5795	CC,CT,TT		0.0581,17.567,5.9895		722/1359	175335162	779,12227	2203	4300	6503	SO:0001819	synonymous_variant	7143	exon11			AGAGGATGGGGTA	X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11953	protein-coding gene	gene with protein product	"""restrictin"", ""janusin"""	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.2166A>G	1.37:g.175335162T>C		228.0	0.0	0		241.0	114.0	0.473029	NM_003285	C9J563|Q15568|Q5R3G0	Silent	SNP	ENST00000367674.2	37	CCDS1318.1																																																																																			T|0.929;C|0.071	0.071	strong		0.552	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285	
SRGAP2	23380	hgsc.bcm.edu	37	1	206566947	206566947	+	Missense_Mutation	SNP	C	C	T	rs375845037		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:206566947C>T	ENST00000414007.1	+	3	328	c.328C>T	c.(328-330)Cgg>Tgg	p.R110W	SRGAP2_ENST00000419187.2_5'UTR			O75044	SRGP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2	250	F-BAR domain.				actin filament severing (GO:0051014)|axon guidance (GO:0007411)|dendritic spine development (GO:0060996)|extension of a leading process involved in cell motility in cerebral cortex radial glia guided migration (GO:0021816)|filopodium assembly (GO:0046847)|lamellipodium assembly involved in ameboidal cell migration (GO:0003363)|negative regulation of neuron migration (GO:2001223)|neuron projection morphogenesis (GO:0048812)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic spine head (GO:0044327)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	protein homodimerization activity (GO:0042803)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)			NS(1)|breast(1)|kidney(1)|lung(1)	4	Breast(84;0.137)					CATCAAAGCCCGGAATGAGTA	0.428																																					p.Q97X		Atlas-SNP	.											.	.	.	.	0			c.C289T						PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG	13,3921		0,13,1954	127.0	110.0	115.0		491,491,491	5.7	1.0	1		115	0,8334		0,0,4167	yes	missense,missense,missense	SRGAP2	NM_001042758.1,NM_001170637.1,NM_015326.2	101,101,101	0,13,6121	TT,TC,CC		0.0,0.3305,0.106	probably-damaging,probably-damaging,probably-damaging	250/837,250/1071,250/1072	206566947	13,12255	1967	4167	6134	SO:0001583	missense	100996712	exon3			AAAGCCCGGAATG	AB007925	CCDS73017.1	1q32.1	2014-08-13	2004-11-12	2004-11-12	ENSG00000163486	ENSG00000266028		"""Rho GTPase activating proteins"""	19751	protein-coding gene	gene with protein product		606524	"""formin binding protein 2"""	FNBP2		15046868, 11672528	Standard	XM_005277510		Approved	KIAA0456, ARHGAP34, SRGAP2A	uc001hdy.3	O75044	OTTHUMG00000184381	ENST00000414007.1:c.328C>T	1.37:g.206566947C>T	ENSP00000390898:p.Arg110Trp	553.0	0.0	0		647.0	99.0	0.153014	NM_001271887		Nonsense_Mutation	SNP	ENST00000414007.1	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	21.4|21.4	4.139626|4.139626	0.77775|0.77775	0.003305|0.003305	0.0|0.0	ENSG00000163486|ENSG00000163486	ENST00000295713|ENST00000414359;ENST00000414007	.|T	.|0.16457	.|2.34	5.73|5.73	5.73|5.73	0.89815|0.89815	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.42899|0.42899	0.1223|0.1223	.|.	.|.	.|.	.|0.30974	.|N	.|0.7227589999999999	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.91635	.|0.998;0.999;0.999	T|T	0.48927|0.48927	-0.8991|-0.8991	3|8	.|0.87932	.|D	.|0	.|.	14.6067|14.6067	0.68483|0.68483	0.1807:0.8193:0.0:0.0|0.1807:0.8193:0.0:0.0	.|.	.|97;250;250	.|B4DDU0;O75044;B7Z3G4	.|.;FNBP2_HUMAN;.	L|W	163|164;110	.|ENSP00000390898:R110W	.|ENSP00000390898:R110W	P|R	+|+	2|1	0|2	SRGAP2|SRGAP2	204633570|204633570	0.998000|0.998000	0.40836|0.40836	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	2.909000|2.909000	0.48758|0.48758	2.705000|2.705000	0.92388|0.92388	0.555000|0.555000	0.69702|0.69702	CCG|CGG	.	.	none		0.428	SRGAP2-201	KNOWN	basic	protein_coding	protein_coding		NM_015326	
KRBA2	124751	hgsc.bcm.edu	37	17	8273246	8273246	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:8273246C>T	ENST00000331336.2	-	2	690	c.685G>A	c.(685-687)Gtc>Atc	p.V229I	RP11-849F2.5_ENST00000583963.1_RNA|RP11-849F2.7_ENST00000582471.1_3'UTR|RP11-849F2.5_ENST00000580537.1_RNA|KRBA2_ENST00000396267.1_Missense_Mutation_p.V147I	NM_213597.2	NP_998762.1	Q6ZNG9	KRBA2_HUMAN	KRAB-A domain containing 2	229					DNA integration (GO:0015074)|regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	nucleic acid binding (GO:0003676)			endometrium(2)|kidney(2)|large_intestine(7)|lung(5)|stomach(1)|urinary_tract(1)	18						AGATATAAGACAATAACTTCT	0.453																																					p.V229I		Atlas-SNP	.											.	KRBA2	34	.	0			c.G685A						PASS	.						126.0	121.0	123.0					17																	8273246		2203	4300	6503	SO:0001583	missense	124751	exon2			ATAAGACAATAAC	BC024723	CCDS11141.1	17p13.1	2013-01-08	2006-08-15		ENSG00000184619	ENSG00000184619		"""-"""	26989	protein-coding gene	gene with protein product			"""KRAB A domain containing 2"""			12477932	Standard	NM_213597		Approved		uc002glf.1	Q6ZNG9	OTTHUMG00000132864	ENST00000331336.2:c.685G>A	17.37:g.8273246C>T	ENSP00000328017:p.Val229Ile	259.0	0.0	0		225.0	61.0	0.271111	NM_213597	Q8IYY0	Missense_Mutation	SNP	ENST00000331336.2	37	CCDS11141.1	.	.	.	.	.	.	.	.	.	.	C	12.40	1.926066	0.34002	.	.	ENSG00000184619	ENST00000396267;ENST00000331336	T;T	0.23348	1.93;1.91	2.64	2.64	0.31445	.	.	.	.	.	T	0.13329	0.0323	N	0.08118	0	0.22982	N	0.998471	B	0.23490	0.086	B	0.22601	0.04	T	0.15350	-1.0440	9	0.48119	T	0.1	.	8.9489	0.35776	0.0:1.0:0.0:0.0	.	229	Q6ZNG9	KRBA2_HUMAN	I	147;229	ENSP00000379565:V147I;ENSP00000328017:V229I	ENSP00000328017:V229I	V	-	1	0	KRBA2	8213971	0.997000	0.39634	1.000000	0.80357	0.992000	0.81027	1.587000	0.36622	1.804000	0.52760	0.650000	0.86243	GTC	.	.	none		0.453	KRBA2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256338.1	NM_213597	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39253819	39253819	+	Missense_Mutation	SNP	G	G	C	rs201814486	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39253819G>C	ENST00000333822.4	-	1	574	c.518C>G	c.(517-519)aCc>aGc	p.T173S		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	173					aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						GCGGGGGCAGGTGGAGATGAC	0.632													G|||	264	0.0527157	0.1778	0.0231	5008	,	,		16542	0.0099		0.001	False		,,,				2504	0.002				p.T173S		Atlas-SNP	.											.	KRTAP4-8	57	.	0			c.C518G						PASS	.						53.0	64.0	61.0					17																	39253819		691	1591	2282	SO:0001583	missense	728224	exon1			GGGCAGGTGGAGA	AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"""Keratin associated proteins"""	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.518C>G	17.37:g.39253819G>C	ENSP00000328444:p.Thr173Ser	240.0	0.0	0		167.0	46.0	0.275449	NM_031960	A8MSH3	Missense_Mutation	SNP	ENST00000333822.4	37	CCDS45674.1	.	.	.	.	.	.	.	.	.	.	.	5.072	0.198925	0.09652	.	.	ENSG00000204880	ENST00000333822;ENST00000332991	T	0.00590	6.36	3.73	2.73	0.32206	.	0.227898	0.21667	U	0.070931	T	0.00815	0.0027	L	0.35854	1.095	0.26449	N	0.975649	D	0.63046	0.992	P	0.57244	0.816	T	0.49597	-0.8923	10	0.07813	T	0.8	.	6.5126	0.22230	0.1366:0.0:0.8634:0.0	.	173	Q9BYQ9	KRA48_HUMAN	S	173;143	ENSP00000328444:T173S	ENSP00000414561:T143S	T	-	2	0	KRTAP4-8	36507345	1.000000	0.71417	1.000000	0.80357	0.560000	0.35617	2.706000	0.47135	1.794000	0.52575	0.449000	0.29647	ACC	.	.	weak		0.632	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
RBM11	54033	hgsc.bcm.edu	37	21	15591968	15591968	+	Missense_Mutation	SNP	G	G	A	rs141942958	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:15591968G>A	ENST00000400577.3	+	2	190	c.181G>A	c.(181-183)Gaa>Aaa	p.E61K	RBM11_ENST00000468643.1_3'UTR	NM_144770.3	NP_658983.3	P57052	RBM11_HUMAN	RNA binding motif protein 11	61	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cell differentiation (GO:0030154)|cellular response to oxidative stress (GO:0034599)|mRNA processing (GO:0006397)|multicellular organismal development (GO:0007275)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(U) RNA binding (GO:0008266)|protein homodimerization activity (GO:0042803)			endometrium(3)|kidney(3)|lung(7)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16				Epithelial(23;0.000314)|COAD - Colon adenocarcinoma(22;0.00242)|Colorectal(24;0.0129)|Lung(58;0.141)		TAAACACCCAGAATCGGTGTC	0.398													.|||	17	0.00339457	0.0106	0.0043	5008	,	,		16689	0.0		0.0	False		,,,				2504	0.0				p.E61K		Atlas-SNP	.											RBM11,NS,neuroblastoma,-1,1	RBM11	41	1	0			c.G181A						PASS	.	G	LYS/GLU	44,3092		0,44,1524	86.0	80.0	82.0		181	5.3	1.0	21	dbSNP_134	82	0,7162		0,0,3581	yes	missense	RBM11	NM_144770.3	56	0,44,5105	AA,AG,GG		0.0,1.4031,0.4273	possibly-damaging	61/282	15591968	44,10254	1568	3581	5149	SO:0001583	missense	54033	exon2			CACCCAGAATCGG	AF130358	CCDS46635.1	21q11	2013-02-12			ENSG00000185272	ENSG00000185272		"""RNA binding motif (RRM) containing"""	9897	protein-coding gene	gene with protein product						12036298	Standard	NM_144770		Approved		uc002yjo.4	P57052	OTTHUMG00000074263	ENST00000400577.3:c.181G>A	21.37:g.15591968G>A	ENSP00000383421:p.Glu61Lys	143.0	0.0	0		146.0	88.0	0.60274	NM_144770	Q6YNC2|Q8NBA1|Q8NFF6	Missense_Mutation	SNP	ENST00000400577.3	37	CCDS46635.1	10	0.004578754578754579	8	0.016260162601626018	2	0.0055248618784530384	0	0.0	0	0.0	G	29.4	5.004735	0.93287	0.014031	0.0	ENSG00000185272	ENST00000400577	T	0.78364	-1.17	5.29	5.29	0.74685	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.64402	D	0.000009	T	0.72220	0.3433	M	0.66378	2.025	0.58432	D	0.999994	P	0.41420	0.749	P	0.48189	0.57	T	0.78703	-0.2101	10	0.48119	T	0.1	-20.9416	18.9174	0.92512	0.0:0.0:1.0:0.0	.	61	P57052	RBM11_HUMAN	K	61	ENSP00000383421:E61K	ENSP00000383421:E61K	E	+	1	0	RBM11	14513839	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.772000	0.85439	2.661000	0.90470	0.655000	0.94253	GAA	G|0.995;A|0.005	0.005	strong		0.398	RBM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157818.1	NM_144770	
SMG8	55181	hgsc.bcm.edu	37	17	57288251	57288251	+	Missense_Mutation	SNP	C	C	T	rs8068240	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:57288251C>T	ENST00000543872.2	+	2	1103	c.839C>T	c.(838-840)cCt>cTt	p.P280L	SMG8_ENST00000300917.5_Missense_Mutation_p.P280L|SMG8_ENST00000578922.1_Missense_Mutation_p.P280L|SMG8_ENST00000580498.1_Intron|CTD-2510F5.6_ENST00000577660.1_Intron			Q8ND04	SMG8_HUMAN	SMG8 nonsense mediated mRNA decay factor	280			P -> L (in dbSNP:rs8068240).		gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of protein kinase activity (GO:0045859)|RNA metabolic process (GO:0016070)	cytosol (GO:0005829)				NS(1)|breast(5)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(9)|ovary(3)|prostate(1)|skin(1)	33						GTAGAACCTCCTCGGAACCAA	0.517													C|||	134	0.0267572	0.093	0.0159	5008	,	,		20461	0.0		0.0	False		,,,				2504	0.0				p.P280L		Atlas-SNP	.											.	SMG8	79	.	0			c.C839T						PASS	.	C	LEU/PRO	414,3992	199.4+/-223.0	25,364,1814	69.0	77.0	74.0		839	5.9	1.0	17	dbSNP_116	74	9,8591	7.1+/-27.0	0,9,4291	yes	missense	SMG8	NM_018149.6	98	25,373,6105	TT,TC,CC		0.1047,9.3963,3.2523	benign	280/992	57288251	423,12583	2203	4300	6503	SO:0001583	missense	55181	exon1			AACCTCCTCGGAA	AL834490	CCDS11615.1	17q23.2	2013-07-02	2013-07-02	2011-06-21					25551	protein-coding gene	gene with protein product		613175	"""chromosome 17 open reading frame 71"", ""smg-8 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C17orf71		19417104	Standard	NM_018149		Approved	FLJ10587, FLJ23205	uc002ixi.3	Q8ND04		ENST00000543872.2:c.839C>T	17.37:g.57288251C>T	ENSP00000438748:p.Pro280Leu	88.0	0.0	0		104.0	44.0	0.423077	NM_018149	Q8N5U5|Q8TDN0|Q9H5P5|Q9NVQ1	Missense_Mutation	SNP	ENST00000543872.2	37	CCDS11615.1	45	0.020604395604395604	44	0.08943089430894309	1	0.0027624309392265192	0	0.0	0	0.0	C	11.98	1.801825	0.31869	0.093963	0.001047	ENSG00000167447	ENST00000300917;ENST00000543872	T;T	0.44881	0.91;0.91	5.88	5.88	0.94601	.	0.385695	0.31210	N	0.008044	T	0.01029	0.0034	N	0.14661	0.345	0.41054	D	0.985328	B	0.09022	0.002	B	0.12156	0.007	T	0.01235	-1.1410	10	0.66056	D	0.02	-9.762	12.6648	0.56835	0.0:0.9223:0.0:0.0777	rs8068240;rs52805280;rs56931279;rs8068240	280	Q8ND04	SMG8_HUMAN	L	280	ENSP00000300917:P280L;ENSP00000438748:P280L	ENSP00000300917:P280L	P	+	2	0	SMG8	54643033	0.003000	0.15002	1.000000	0.80357	0.939000	0.58152	0.955000	0.29188	2.769000	0.95229	0.655000	0.94253	CCT	C|0.967;T|0.033	0.033	strong		0.517	SMG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445960.2	NM_018149	
SRL	6345	hgsc.bcm.edu	37	16	4245656	4245656	+	Silent	SNP	G	G	A	rs76988584	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4245656G>A	ENST00000399609.3	-	5	520	c.508C>T	c.(508-510)Cta>Tta	p.L170L	SRL_ENST00000537996.1_Silent_p.L128L	NM_001098814.1	NP_001092284.1	Q86TD4	SRCA_HUMAN	sarcalumenin	629	Acidic domain, probably binds calcium. {ECO:0000250}.					sarcoplasmic reticulum (GO:0016529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(8)|ovary(3)|skin(3)	21						AGCTTCTCTAGGAAATTCTGG	0.522													G|||	95	0.0189696	0.0703	0.0029	5008	,	,		18443	0.0		0.0	False		,,,				2504	0.0				p.L170L		Atlas-SNP	.											.	SRL	56	.	0			c.C508T						PASS	.	G		177,3613		5,167,1723	102.0	102.0	102.0		508	4.1	1.0	16	dbSNP_131	102	1,8253		0,1,4126	no	coding-synonymous	SRL	NM_001098814.1		5,168,5849	AA,AG,GG		0.0121,4.6702,1.4779		170/474	4245656	178,11866	1895	4127	6022	SO:0001819	synonymous_variant	6345	exon5			TCTCTAGGAAATT	AK056588	CCDS42113.1	16p13.3	2008-02-05				ENSG00000185739			11295	protein-coding gene	gene with protein product		604992				2762314	Standard	NM_001098814		Approved		uc002cvz.4	Q86TD4		ENST00000399609.3:c.508C>T	16.37:g.4245656G>A		220.0	0.0	0		248.0	118.0	0.475806	NM_001098814		Silent	SNP	ENST00000399609.3	37	CCDS42113.1																																																																																			G|0.992;A|0.008	0.008	strong		0.522	SRL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438087.1	XM_064152	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39253797	39253797	+	Silent	SNP	G	G	A	rs142150852	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39253797G>A	ENST00000333822.4	-	1	596	c.540C>T	c.(538-540)tgC>tgT	p.C180C		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	180					aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						AAGAGGAGGCGCAGCACACGG	0.602													g|||	249	0.0497204	0.1778	0.0159	5008	,	,		17550	0.002		0.001	False		,,,				2504	0.0				p.C180C		Atlas-SNP	.											KRTAP4-8,colon,carcinoma,-2,1	KRTAP4-8	57	1	0			c.C540T						PASS	.						69.0	80.0	76.0					17																	39253797		692	1591	2283	SO:0001819	synonymous_variant	728224	exon1			GGAGGCGCAGCAC	AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"""Keratin associated proteins"""	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.540C>T	17.37:g.39253797G>A		274.0	0.0	0		227.0	81.0	0.356828	NM_031960	A8MSH3	Silent	SNP	ENST00000333822.4	37	CCDS45674.1																																																																																			G|0.982;A|0.018	0.018	strong		0.602	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
DEFB110	245913	hgsc.bcm.edu	37	6	49989622	49989622	+	Silent	SNP	A	A	G	rs9473719	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:49989622A>G	ENST00000371148.2	-	1	72	c.27T>C	c.(25-27)atT>atC	p.I9I	DEFB110_ENST00000393660.2_Silent_p.I9I	NM_001037497.1	NP_001032586.1	Q30KQ9	DB110_HUMAN	defensin, beta 110 locus	9					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(1)|lung(1)|ovary(1)	3	Lung NSC(77;0.042)					AAAAGTGCAGAATAAAGAAAA	0.313													A|||	75	0.014976	0.056	0.0014	5008	,	,		16040	0.0		0.0	False		,,,				2504	0.0				p.I9I		Atlas-SNP	.											.	DEFB110	5	.	0			c.T27C						PASS	.	A	,	200,4202	113.8+/-151.8	5,190,2006	32.0	36.0	35.0		27,27	3.5	1.0	6	dbSNP_119	35	1,8591	1.2+/-3.3	0,1,4295	no	coding-synonymous,coding-synonymous	DEFB110	NM_001037497.1,NM_001037728.2	,	5,191,6301	GG,GA,AA		0.0116,4.5434,1.5469	,	9/68,9/63	49989622	201,12793	2201	4296	6497	SO:0001819	synonymous_variant	245913	exon1			GTGCAGAATAAAG	DQ012014, BC148541	CCDS43473.1, CCDS34475.1	6p12.3	2010-11-26	2010-11-26		ENSG00000203970	ENSG00000203970		"""Defensins, beta"""	18091	protein-coding gene	gene with protein product			"""defensin, beta 110"""			11854508, 16033865	Standard	NM_001037728		Approved	DEFB-10, DEFB-11, DEFB111	uc003pac.3	Q30KQ9	OTTHUMG00000160208	ENST00000371148.2:c.27T>C	6.37:g.49989622A>G		86.0	0.0	0		89.0	46.0	0.516854	NM_001037728	Q30KR0	Silent	SNP	ENST00000371148.2	37	CCDS34475.1																																																																																			A|0.986;G|0.014	0.014	strong		0.313	DEFB110-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359664.1	NM_001037728	
DLG5	9231	hgsc.bcm.edu	37	10	79603423	79603423	+	Silent	SNP	C	C	T	rs12257229	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:79603423C>T	ENST00000372391.2	-	6	911	c.906G>A	c.(904-906)ctG>ctA	p.L302L	DLG5_ENST00000372388.2_Silent_p.L302L	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	302					apical protein localization (GO:0045176)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|intracellular signal transduction (GO:0035556)|metanephric collecting duct development (GO:0072205)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|polarized epithelial cell differentiation (GO:0030859)|protein complex assembly (GO:0006461)|protein localization to adherens junction (GO:0071896)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|zonula adherens assembly (GO:0045186)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cytoskeletal protein binding (GO:0008092)|receptor signaling complex scaffold activity (GO:0030159)			breast(9)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(17)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	60	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)			CCGTGTCATACAGTTTGTTGA	0.532													C|||	497	0.0992412	0.3593	0.0274	5008	,	,		21222	0.0		0.003	False		,,,				2504	0.0				p.L302L		Atlas-SNP	.											.	DLG5	154	.	0			c.G906A						PASS	.	C		1351,3055	449.4+/-349.0	200,951,1052	180.0	162.0	168.0		906	2.6	1.0	10	dbSNP_120	168	21,8579	14.0+/-48.4	0,21,4279	no	coding-synonymous	DLG5	NM_004747.3		200,972,5331	TT,TC,CC		0.2442,30.6627,10.549		302/1920	79603423	1372,11634	2203	4300	6503	SO:0001819	synonymous_variant	9231	exon6			GTCATACAGTTTG	U61843	CCDS7353.2	10q23	2008-07-09	2001-11-28		ENSG00000151208	ENSG00000151208			2904	protein-coding gene	gene with protein product		604090	"""discs, large (Drosophila) homolog 5"""			9738934	Standard	XM_005270276		Approved	P-dlg, KIAA0583	uc001jzk.3	Q8TDM6	OTTHUMG00000018548	ENST00000372391.2:c.906G>A	10.37:g.79603423C>T		195.0	0.0	0		201.0	94.0	0.467662	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Silent	SNP	ENST00000372391.2	37	CCDS7353.2																																																																																			C|0.888;T|0.112	0.112	strong		0.532	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2		
PLA1A	51365	hgsc.bcm.edu	37	3	119336962	119336962	+	Missense_Mutation	SNP	G	G	A	rs2692622	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119336962G>A	ENST00000273371.4	+	7	923	c.851G>A	c.(850-852)aGc>aAc	p.S284N	PLA1A_ENST00000494440.1_Missense_Mutation_p.S268N|PLA1A_ENST00000495992.1_Missense_Mutation_p.S268N|PLA1A_ENST00000488919.1_Missense_Mutation_p.S111N	NM_015900.3	NP_056984.1	Q53H76	PLA1A_HUMAN	phospholipase A1 member A	284			S -> N (in dbSNP:rs2692622).		lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|phosphatidylserine metabolic process (GO:0006658)	extracellular vesicular exosome (GO:0070062)	phosphatidylcholine 1-acylhydrolase activity (GO:0008970)			NS(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						CCCTGTGCCAGCTACAAGGCC	0.502													G|||	238	0.047524	0.1725	0.0144	5008	,	,		20613	0.0		0.0	False		,,,				2504	0.0				p.S284N		Atlas-SNP	.											.	PLA1A	65	.	0			c.G851A						PASS	.	G	ASN/SER,ASN/SER,ASN/SER	611,3795	267.1+/-267.6	36,539,1628	323.0	307.0	313.0		803,332,851	0.3	0.7	3	dbSNP_100	313	6,8594	4.3+/-15.6	0,6,4294	yes	missense,missense,missense	PLA1A	NM_001206960.1,NM_001206961.1,NM_015900.3	46,46,46	36,545,5922	AA,AG,GG		0.0698,13.8675,4.744	benign,benign,benign	268/441,111/284,284/457	119336962	617,12389	2203	4300	6503	SO:0001583	missense	51365	exon7			GTGCCAGCTACAA	AF035268	CCDS2991.1, CCDS56268.1, CCDS56269.1	3q13.13-q13.2	2002-11-28			ENSG00000144837	ENSG00000144837			17661	protein-coding gene	gene with protein product		607460				10196188	Standard	NM_015900		Approved	ps-PLA1	uc003ecu.3	Q53H76	OTTHUMG00000159425	ENST00000273371.4:c.851G>A	3.37:g.119336962G>A	ENSP00000273371:p.Ser284Asn	177.0	0.0	0		239.0	132.0	0.552301	NM_015900	B2R8V2|B4DXA2|O95991|Q86WX6|Q9UPD2	Missense_Mutation	SNP	ENST00000273371.4	37	CCDS2991.1	71	0.03250915750915751	68	0.13821138211382114	3	0.008287292817679558	0	0.0	0	0.0	G	11.49	1.653192	0.29425	0.138675	6.98E-4	ENSG00000144837	ENST00000273371;ENST00000488919;ENST00000495992;ENST00000494440;ENST00000475963	D;D;D;D;D	0.93247	-3.19;-3.19;-3.19;-3.19;-3.19	5.26	0.275	0.15659	Lipase, N-terminal (1);	0.427416	0.31268	N	0.007943	T	0.04679	0.0127	L	0.41492	1.28	0.46011	P	0.0011889999999999956	B;B	0.18013	0.005;0.025	B;B	0.20184	0.009;0.028	T	0.55611	-0.8114	9	0.56958	D	0.05	-5.9575	5.7584	0.18186	0.2197:0.2586:0.5217:0.0	rs2692622;rs52825291;rs2692622	268;284	Q53H76-3;Q53H76	.;PLA1A_HUMAN	N	284;111;268;268;150	ENSP00000273371:S284N;ENSP00000420625:S111N;ENSP00000417326:S268N;ENSP00000418793:S268N;ENSP00000417295:S150N	ENSP00000273371:S284N	S	+	2	0	PLA1A	120819652	0.995000	0.38212	0.688000	0.30117	0.454000	0.32378	0.833000	0.27504	-0.255000	0.09486	0.555000	0.69702	AGC	G|0.946;A|0.054	0.054	strong		0.502	PLA1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355252.2		
SCN1A	6323	hgsc.bcm.edu	37	2	166868775	166868775	+	Silent	SNP	A	A	G	rs36031496	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:166868775A>G	ENST00000303395.4	-	19	3722	c.3723T>C	c.(3721-3723)taT>taC	p.Y1241Y	AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000597623.1_RNA|SCN1A_ENST00000423058.2_Silent_p.Y1241Y|SCN1A_ENST00000409050.1_Silent_p.Y1213Y|SCN1A_ENST00000375405.3_Silent_p.Y1230Y			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1241					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	GCTGATCAATATATATATCTT	0.284													A|||	179	0.0357428	0.1316	0.0072	5008	,	,		18217	0.0		0.0	False		,,,				2504	0.0				p.Y1241Y		Atlas-SNP	.											.	SCN1A	641	.	0			c.T3723C						PASS	.	A	,,,	554,3852	240.3+/-251.1	48,458,1697	51.0	49.0	50.0		3723,3639,3723,3690	3.2	1.0	2	dbSNP_126	50	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SCN1A	NM_001165963.1,NM_001165964.1,NM_001202435.1,NM_006920.4	,,,	48,458,5995	GG,GA,AA		0.0,12.5738,4.2609	,,,	1241/2010,1213/1982,1241/2010,1230/1999	166868775	554,12448	2203	4298	6501	SO:0001819	synonymous_variant	6323	exon19			ATCAATATATATA	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10585	protein-coding gene	gene with protein product		182389	"""febrile convulsions 3"""	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.3723T>C	2.37:g.166868775A>G		179.0	0.0	0		190.0	119.0	0.626316	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Silent	SNP	ENST00000303395.4	37	CCDS54413.1																																																																																			.	.	none		0.284	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920	
ATP13A1	57130	hgsc.bcm.edu	37	19	19766365	19766365	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:19766365G>A	ENST00000357324.6	-	10	1394	c.1368C>T	c.(1366-1368)atC>atT	p.I456I	ATP13A1_ENST00000291503.5_Silent_p.I338I|ATP13A1_ENST00000496082.1_5'UTR	NM_020410.2	NP_065143.2	Q9HD20	AT131_HUMAN	ATPase type 13A1	456	Poly-Ala.					endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|liver(2)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	29						CAGCTGCAGCGATGGCAAACA	0.607																																					p.I456I	Esophageal Squamous(142;920 1789 9047 14684 24777)	Atlas-SNP	.											.	ATP13A1	82	.	0			c.C1368T						PASS	.						75.0	68.0	70.0					19																	19766365		2203	4300	6503	SO:0001819	synonymous_variant	57130	exon10			TGCAGCGATGGCA	AK056420	CCDS32970.2	19p13.11	2010-04-20	2005-01-12	2005-01-12	ENSG00000105726	ENSG00000105726		"""ATPases / P-type"""	24215	protein-coding gene	gene with protein product	"""cation transporting ATPase"""		"""ATPase type 13A"""	ATP13A		11347906	Standard	NM_020410		Approved	KIAA1825, FLJ31858, CGI-152	uc002nnh.4	Q9HD20	OTTHUMG00000153016	ENST00000357324.6:c.1368C>T	19.37:g.19766365G>A		134.0	0.0	0		147.0	79.0	0.537415	NM_020410	B3KPJ2|B3KTA7|Q6NT90|Q6ZMG7|Q9H6C6	Silent	SNP	ENST00000357324.6	37	CCDS32970.2																																																																																			.	.	none		0.607	ATP13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329005.1	NM_020410	
HPSE	10855	hgsc.bcm.edu	37	4	84222208	84222208	+	Silent	SNP	A	A	G	rs11031	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:84222208A>G	ENST00000405413.2	-	12	1513	c.1377T>C	c.(1375-1377)aaT>aaC	p.N459N	HPSE_ENST00000512196.1_Silent_p.N385N|HPSE_ENST00000311412.5_Silent_p.N459N|HPSE_ENST00000513463.1_Silent_p.N401N	NM_006665.5	NP_006656.2	Q9Y251	HPSE_HUMAN	heparanase	459					carbohydrate metabolic process (GO:0005975)|cell-matrix adhesion (GO:0007160)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|positive regulation of blood coagulation (GO:0030194)|positive regulation of hair follicle development (GO:0051798)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation vascular endothelial growth factor production (GO:0010575)|proteoglycan metabolic process (GO:0006029)|regulation of hair follicle development (GO:0051797)|small molecule metabolic process (GO:0044281)|vascular wound healing (GO:0061042)	extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)	beta-glucuronidase activity (GO:0004566)|heparanase activity (GO:0030305)|protein dimerization activity (GO:0046983)|syndecan binding (GO:0045545)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	20		Hepatocellular(203;0.114)		COAD - Colon adenocarcinoma(81;0.141)	Dalteparin(DB06779)|Heparin(DB01109)	ACTTGGTGACATTATGGAGGT	0.353													A|||	426	0.0850639	0.3064	0.0259	5008	,	,		18825	0.0		0.003	False		,,,				2504	0.0				p.N459N		Atlas-SNP	.											.	HPSE	55	.	0			c.T1377C						PASS	.	A	,,,	1123,3283	402.2+/-332.3	156,811,1236	119.0	126.0	123.0		1377,1155,1203,1377	-3.8	1.0	4	dbSNP_52	123	18,8582	11.9+/-42.8	0,18,4282	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HPSE	NM_001098540.2,NM_001166498.2,NM_001199830.1,NM_006665.5	,,,	156,829,5518	GG,GA,AA		0.2093,25.488,8.7729	,,,	459/544,385/470,401/486,459/544	84222208	1141,11865	2203	4300	6503	SO:0001819	synonymous_variant	10855	exon11			GGTGACATTATGG	AF144325	CCDS3602.1, CCDS54774.1, CCDS56337.1	4q21.3	2008-02-05			ENSG00000173083	ENSG00000173083			5164	protein-coding gene	gene with protein product		604724				10395325, 10395326	Standard	NM_006665		Approved	HPA, HSE1, HPSE1	uc003hoj.4	Q9Y251	OTTHUMG00000130425	ENST00000405413.2:c.1377T>C	4.37:g.84222208A>G		121.0	0.0	0		134.0	66.0	0.492537	NM_001098540	A9JIG7|C7F7I3|C7F7I4|E9PCA9|E9PGR1|Q53GE5|Q9UL39	Silent	SNP	ENST00000405413.2	37	CCDS3602.1																																																																																			A|0.911;G|0.089	0.089	strong		0.353	HPSE-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252812.2	NM_006665	
VWDE	221806	hgsc.bcm.edu	37	7	12381687	12381687	+	Missense_Mutation	SNP	G	G	A	rs116125922	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:12381687G>A	ENST00000275358.3	-	23	4456	c.4268C>T	c.(4267-4269)aCa>aTa	p.T1423I		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	1423	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.					extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						AATTTTACCTGTACTACAGGT	0.403													G|||	69	0.013778	0.0492	0.0014	5008	,	,		17679	0.0		0.0	False		,,,				2504	0.0031				p.T1423I		Atlas-SNP	.											.	VWDE	123	.	0			c.C4268T						PASS	.	G	ILE/THR	56,1328		1,54,637	83.0	76.0	78.0		4268	2.4	1.0	7	dbSNP_132	78	1,3181		0,1,1590	yes	missense	VWDE	NM_001135924.1	89	1,55,2227	AA,AG,GG		0.0314,4.0462,1.2484	possibly-damaging	1423/1591	12381687	57,4509	692	1591	2283	SO:0001583	missense	221806	exon23			TTACCTGTACTAC		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.4268C>T	7.37:g.12381687G>A	ENSP00000275358:p.Thr1423Ile	76.0	0.0	0		89.0	44.0	0.494382	NM_001135924	B7ZM77|Q96SQ3	Missense_Mutation	SNP	ENST00000275358.3	37	CCDS47544.1	20	0.009157509157509158	19	0.03861788617886179	1	0.0027624309392265192	0	0.0	0	0.0	G	16.79	3.220210	0.58560	0.040462	3.14E-4	ENSG00000146530	ENST00000275358;ENST00000536307	T	0.42131	0.98	4.38	2.42	0.29668	Epidermal growth factor-like, type 3 (1);	0.445804	0.23112	N	0.051794	T	0.15825	0.0381	L	0.35414	1.06	0.25456	N	0.987962	D	0.89917	1.0	D	0.69307	0.963	T	0.04915	-1.0918	10	0.23302	T	0.38	.	9.3739	0.38270	0.0799:0.0:0.7769:0.1432	.	1423	Q8N2E2	VWDE_HUMAN	I	1423;877	ENSP00000275358:T1423I	ENSP00000275358:T1423I	T	-	2	0	VWDE	12348212	1.000000	0.71417	0.996000	0.52242	0.638000	0.38207	4.130000	0.57964	1.193000	0.43086	0.650000	0.86243	ACA	G|0.990;A|0.010	0.010	strong		0.403	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
RRM2B	50484	hgsc.bcm.edu	37	8	103251034	103251034	+	Intron	SNP	A	A	C	rs72554092	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:103251034A>C	ENST00000251810.3	-	1	292				KB-431C1.4_ENST00000520820.1_RNA|RRM2B_ENST00000519317.1_Intron|RRM2B_ENST00000395912.2_Intron|RRM2B_ENST00000519962.1_Intron	NM_001172478.1|NM_015713.4	NP_001165949.1|NP_056528.2	Q7LG56	RIR2B_HUMAN	ribonucleotide reductase M2 B (TP53 inducible)						deoxyribonucleoside diphosphate metabolic process (GO:0009186)|deoxyribonucleoside triphosphate metabolic process (GO:0009200)|deoxyribonucleotide biosynthetic process (GO:0009263)|DNA repair (GO:0006281)|kidney development (GO:0001822)|mitochondrial DNA replication (GO:0006264)|negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator (GO:1902254)|nucleobase-containing small molecule interconversion (GO:0015949)|nucleobase-containing small molecule metabolic process (GO:0055086)|renal system process (GO:0003014)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor (GO:0004748)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|ovary(2)|upper_aerodigestive_tract(1)	9	all_cancers(14;8e-07)|all_epithelial(15;2.18e-08)|Lung NSC(17;2.55e-05)|all_lung(17;8.85e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000728)		Cladribine(DB00242)	GTGAGGGGGAAGACGCAACAG	0.637								Modulation of nucleotide pools					A|||	104	0.0207668	0.0764	0.0029	5008	,	,		13321	0.0		0.0	False		,,,				2504	0.001				p.L6R		Atlas-SNP	.											.	RRM2B	31	.	0			c.T17G						PASS	.	A	ARG/LEU,,	414,3992	200.4+/-223.7	20,374,1809	63.0	62.0	62.0		17,,	-4.6	0.0	8	dbSNP_130	62	2,8598	2.2+/-6.3	0,2,4298	yes	missense,intron,intron	RRM2B	NM_001172477.1,NM_001172478.1,NM_015713.4	102,,	20,376,6107	CC,CA,AA		0.0233,9.3963,3.1985	,,	6/424,,	103251034	416,12590	2203	4300	6503	SO:0001627	intron_variant	50484	exon1			GGGGGAAGACGCA	AB036532	CCDS34932.1, CCDS55267.1	8q23.1	2014-09-17			ENSG00000048392	ENSG00000048392			17296	protein-coding gene	gene with protein product		604712				10716435, 10980602, 17486094	Standard	NM_015713		Approved	p53R2	uc022azl.1	Q7LG56	OTTHUMG00000164776	ENST00000251810.3:c.48+20T>G	8.37:g.103251034A>C		28.0	0.0	0		26.0	15.0	0.576923	NM_001172477	B4E2N4|Q17R22|Q75PQ6|Q75PQ7|Q75PY8|Q75PY9|Q86YE3|Q9NPD6|Q9NTD8|Q9NUW3	Missense_Mutation	SNP	ENST00000251810.3	37	CCDS34932.1																																																																																			A|0.975;C|0.025	0.025	strong		0.637	RRM2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380191.3		
CNKSR1	10256	hgsc.bcm.edu	37	1	26508997	26508997	+	Silent	SNP	C	C	T	rs2802347	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:26508997C>T	ENST00000374253.5	+	6	585	c.546C>T	c.(544-546)caC>caT	p.H182H	CNKSR1_ENST00000480348.2_3'UTR|CNKSR1_ENST00000361530.6_Silent_p.H182H|CNKSR1_ENST00000531191.1_5'UTR	NM_006314.2	NP_006305.2	Q969H4	CNKR1_HUMAN	connector enhancer of kinase suppressor of Ras 1	182					Ras protein signal transduction (GO:0007265)|Rho protein signal transduction (GO:0007266)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|plasma membrane (GO:0005886)	protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	28		Colorectal(325;3.46e-05)|all_lung(284;0.000116)|Lung NSC(340;0.000154)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.72e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|BRCA - Breast invasive adenocarcinoma(304;0.000959)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00823)|READ - Rectum adenocarcinoma(331;0.0649)		GGATCTGCCACAACATCCTGG	0.652													C|||	259	0.0517173	0.1846	0.0202	5008	,	,		17396	0.0		0.001	False		,,,				2504	0.0				p.H182H	NSCLC(180;1396 2109 28270 30756 34275)	Atlas-SNP	.											.	CNKSR1	66	.	0			c.C546T						PASS	.	C		702,3704	293.3+/-282.5	64,574,1565	65.0	65.0	65.0		546	2.4	1.0	1	dbSNP_100	65	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	CNKSR1	NM_006314.2		64,578,5861	TT,TC,CC		0.0465,15.9328,5.4283		182/714	26508997	706,12300	2203	4300	6503	SO:0001819	synonymous_variant	10256	exon6			CTGCCACAACATC	AF100153	CCDS276.1, CCDS72732.1	1p35.3	2013-01-10			ENSG00000142675	ENSG00000142675		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	19700	protein-coding gene	gene with protein product		603272				9814705	Standard	NM_006314		Approved	CNK1, KSR, CNK	uc001blm.4	Q969H4	OTTHUMG00000007541	ENST00000374253.5:c.546C>T	1.37:g.26508997C>T		156.0	0.0	0		182.0	93.0	0.510989	NM_006314	B1AMW9|O95381	Silent	SNP	ENST00000374253.5	37		108	0.04945054945054945	98	0.1991869918699187	10	0.027624309392265192	0	0.0	0	0.0	C	13.82	2.352119	0.41700	0.159328	4.65E-4	ENSG00000142675	ENST00000422547	.	.	.	4.47	2.37	0.29283	.	.	.	.	.	.	.	.	.	.	.	0.09310	P	0.999999889351	.	.	.	.	.	.	.	.	.	.	0.28530	T	0.3	-2.2956	5.5452	0.17059	0.0:0.4831:0.4021:0.1148	rs2802347	.	.	.	X	170	.	ENSP00000390945:Q170X	Q	+	1	0	CNKSR1	26381584	0.230000	0.23740	0.998000	0.56505	0.271000	0.26615	0.419000	0.21247	1.068000	0.40764	0.650000	0.86243	CAA	C|0.940;T|0.060	0.060	strong		0.652	CNKSR1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000089943.2	NM_006314	
GPR35	2859	hgsc.bcm.edu	37	2	241569535	241569535	+	Missense_Mutation	SNP	C	C	T	rs115880579	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:241569535C>T	ENST00000319838.5	+	6	1108	c.166C>T	c.(166-168)Cgc>Tgc	p.R56C	GPR35_ENST00000407714.1_Missense_Mutation_p.R56C|GPR35_ENST00000430267.1_Missense_Mutation_p.R56C|GPR35_ENST00000403859.1_Missense_Mutation_p.R56C|GPR35_ENST00000438013.2_Missense_Mutation_p.R87C	NM_001195381.1	NP_001182310.1	Q9HC97	GPR35_HUMAN	G protein-coupled receptor 35	56					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			NS(2)|breast(1)|cervix(1)|endometrium(1)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	17		all_epithelial(40;7.49e-12)|Breast(86;0.000148)|Renal(207;0.00571)|Ovarian(221;0.104)|all_neural(83;0.107)|all_hematologic(139;0.182)|all_lung(227;0.186)|Melanoma(123;0.238)		Epithelial(32;5.29e-32)|all cancers(36;1.38e-29)|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;5.02e-06)|Lung(119;0.00163)|Colorectal(34;0.00463)|LUSC - Lung squamous cell carcinoma(224;0.008)|COAD - Colon adenocarcinoma(134;0.031)		GACGGAGACCCGCATCTACAT	0.642													C|||	29	0.00579073	0.0204	0.0029	5008	,	,		18411	0.0		0.0	False		,,,				2504	0.0				p.R87C		Atlas-SNP	.											GPR35,NS,malignant_melanoma,-1,1	GPR35	43	1	0			c.C259T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG	72,4334	65.3+/-102.7	1,70,2132	103.0	89.0	94.0		259,259,166	3.1	0.2	2	dbSNP_132	94	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense,missense	GPR35	NM_001195381.1,NM_001195382.1,NM_005301.3	180,180,180	1,74,6428	TT,TC,CC		0.0465,1.6341,0.5843	probably-damaging,probably-damaging,probably-damaging	87/341,87/341,56/310	241569535	76,12930	2203	4300	6503	SO:0001583	missense	2859	exon6			GAGACCCGCATCT		CCDS2541.1, CCDS56174.1	2q37.3	2012-08-21			ENSG00000178623	ENSG00000178623		"""GPCR / Class A : Orphans"""	4492	protein-coding gene	gene with protein product		602646				9479505	Standard	NM_005301		Approved		uc021vze.1	Q9HC97	OTTHUMG00000133356	ENST00000319838.5:c.166C>T	2.37:g.241569535C>T	ENSP00000322731:p.Arg56Cys	94.0	0.0	0		60.0	27.0	0.45	NM_001195382	J3KR30|O43495|Q17R58|Q4VBN5|Q4ZFV2|Q6FHI8|Q86UH4	Missense_Mutation	SNP	ENST00000319838.5	37	CCDS2541.1	16	0.007326007326007326	14	0.028455284552845527	2	0.0055248618784530384	0	0.0	0	0.0	C	15.47	2.843986	0.51164	0.016341	4.65E-4	ENSG00000178623	ENST00000319838;ENST00000403859;ENST00000438013;ENST00000407714;ENST00000430267	T;T;T;T;T	0.37915	1.17;1.17;1.17;1.17;1.17	4.02	3.06	0.35304	GPCR, rhodopsin-like superfamily (1);	0.640810	0.14659	N	0.306078	T	0.33614	0.0869	M	0.79693	2.465	0.09310	N	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79108	0.992;0.991;0.991	T	0.14980	-1.0453	10	0.54805	T	0.06	-20.0686	9.7984	0.40748	0.0:0.6693:0.3307:0.0	.	141;87;56	Q6ZMP9;A8K2J1;Q9HC97	.;.;GPR35_HUMAN	C	56;56;87;56;56	ENSP00000322731:R56C;ENSP00000385140:R56C;ENSP00000415890:R87C;ENSP00000384263:R56C;ENSP00000411788:R56C	ENSP00000322731:R56C	R	+	1	0	GPR35	241218208	0.000000	0.05858	0.235000	0.24058	0.783000	0.44284	-0.829000	0.04415	2.250000	0.74265	0.462000	0.41574	CGC	C|0.993;T|0.007	0.007	strong		0.642	GPR35-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325631.1	NM_001195382	
GOLGA6L1	283767	hgsc.bcm.edu	37	15	22743130	22743130	+	Silent	SNP	C	C	T	rs376169003		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:22743130C>T	ENST00000560659.2	+	8	1365	c.1365C>T	c.(1363-1365)caC>caT	p.H455H	GOLGA6L1_ENST00000316397.3_Silent_p.H505H			Q8N7Z2	GG6L1_HUMAN	golgin A6 family-like 1	499										NS(1)|breast(2)|endometrium(5)|large_intestine(1)|lung(1)|skin(1)	11						agaagatgcacgaccaggagg	0.557																																					p.H505H		Atlas-SNP	.											.	GOLGA6L1	20	.	0			c.C1515T						PASS	.						3.0	2.0	3.0					15																	22743130		901	1302	2203	SO:0001819	synonymous_variant	283767	exon8			GATGCACGACCAG	AK097517	CCDS73699.1	15q11.2	2012-10-05	2010-02-12		ENSG00000197414	ENSG00000277865			37444	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 6-like 1"""				Standard	NM_001001413		Approved		uc010tzx.1	Q8N7Z2	OTTHUMG00000171883	ENST00000560659.2:c.1365C>T	15.37:g.22743130C>T		169.0	0.0	0		256.0	45.0	0.175781	NM_001001413		Silent	SNP	ENST00000560659.2	37																																																																																				.	.	weak		0.557	GOLGA6L1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000415616.2	NM_001001413	
CLSTN2	64084	hgsc.bcm.edu	37	3	140281768	140281768	+	Silent	SNP	G	G	A	rs35951028	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:140281768G>A	ENST00000458420.3	+	14	2518	c.2328G>A	c.(2326-2328)ggG>ggA	p.G776G		NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	776					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						AACTCAATGGGCGCTACACTA	0.542										HNSCC(16;0.037)			G|||	111	0.0221645	0.0779	0.0115	5008	,	,		21673	0.0		0.0	False		,,,				2504	0.0				p.G776G	GBM(45;858 913 3709 36904 37282)	Atlas-SNP	.											.	CLSTN2	190	.	0			c.G2328A						PASS	.	G		331,4075	175.5+/-204.9	8,315,1880	60.0	58.0	59.0		2328	3.8	1.0	3	dbSNP_126	59	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	CLSTN2	NM_022131.2		8,319,6176	AA,AG,GG		0.0465,7.5125,2.5757		776/956	140281768	335,12671	2203	4300	6503	SO:0001819	synonymous_variant	64084	exon14			CAATGGGCGCTAC	AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"""Cadherins / Cadherin-related"""	17448	protein-coding gene	gene with protein product	"""cadherin-related family member 13"""	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.2328G>A	3.37:g.140281768G>A		114.0	0.0	0		128.0	127.0	0.992188	NM_022131	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Silent	SNP	ENST00000458420.3	37	CCDS3112.1																																																																																			G|0.973;A|0.027	0.027	strong		0.542	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131	
MACF1	23499	hgsc.bcm.edu	37	1	39853163	39853163	+	Silent	SNP	T	T	C	rs79901102	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:39853163T>C	ENST00000372915.3	+	57	14751	c.14664T>C	c.(14662-14664)caT>caC	p.H4888H	MACF1_ENST00000564288.1_Silent_p.H4883H|MACF1_ENST00000545844.1_Silent_p.H2821H|MACF1_ENST00000539005.1_Silent_p.H2800H|MACF1_ENST00000317713.7_Silent_p.H2821H|MACF1_ENST00000289893.4_Silent_p.H3323H|MACF1_ENST00000361689.2_Silent_p.H2821H|MACF1_ENST00000567887.1_Silent_p.H4920H			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	4888					ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			TCAAAAACCATTGGGAAGAGC	0.438													T|||	125	0.0249601	0.0885	0.0086	5008	,	,		19483	0.0		0.001	False		,,,				2504	0.001				p.H2821H		Atlas-SNP	.											.	MACF1	909	.	0			c.T8463C						PASS	.	T	,	308,4096	161.1+/-193.3	8,292,1902	73.0	82.0	79.0		8463,9969	-12.3	0.0	1	dbSNP_131	79	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	MACF1	NM_012090.4,NM_033044.3	,	8,295,6199	CC,CT,TT		0.0349,6.9936,2.3916	,	2821/5431,3323/5939	39853163	311,12693	2202	4300	6502	SO:0001819	synonymous_variant	23499	exon54			AAACCATTGGGAA	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"""EF-hand domain containing"""	13664	protein-coding gene	gene with protein product	"""actin cross-linking factor"", ""620 kDa actin binding protein"", ""macrophin 1"", ""trabeculin-alpha"", ""actin cross-linking family protein 7"""	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.14664T>C	1.37:g.39853163T>C		74.0	0.0	0		66.0	36.0	0.545455	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Silent	SNP	ENST00000372915.3	37																																																																																				T|0.975;C|0.025	0.025	strong		0.438	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
HEG1	57493	hgsc.bcm.edu	37	3	124732426	124732426	+	Missense_Mutation	SNP	G	G	A	rs113838848	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:124732426G>A	ENST00000311127.4	-	6	2064	c.1997C>T	c.(1996-1998)tCc>tTc	p.S666F	HEG1_ENST00000477536.1_5'UTR	NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	666	Ser-rich.				cardiac atrium morphogenesis (GO:0003209)|cell-cell junction assembly (GO:0007043)|endothelial cell morphogenesis (GO:0001886)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|lymph circulation (GO:0003017)|lymph vessel development (GO:0001945)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|post-embryonic development (GO:0009791)|regulation of body fluid levels (GO:0050878)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(24)|ovary(2)|urinary_tract(4)	47						agaagaggaggaggaggaaga	0.493													G|||	86	0.0171725	0.0598	0.0101	5008	,	,		20835	0.0		0.0	False		,,,				2504	0.0				p.S666F		Atlas-SNP	.											.	HEG1	109	.	0			c.C1997T						PASS	.	G	PHE/SER	183,4127		5,173,1977	55.0	61.0	59.0		1997	0.6	0.0	3	dbSNP_132	59	1,8509		0,1,4254	yes	missense	HEG1	NM_020733.1	155	5,174,6231	AA,AG,GG		0.0118,4.2459,1.4353	probably-damaging	666/1382	124732426	184,12636	2155	4255	6410	SO:0001583	missense	57493	exon6			GAGGAGGAGGAGG	AK074987	CCDS46898.1	3q21.2	2013-03-08	2013-03-08		ENSG00000173706	ENSG00000173706			29227	protein-coding gene	gene with protein product	"""heart of glass"""	614182	"""HEG homolog 1 (zebrafish)"""			10574462, 19151727, 23007647	Standard	NM_020733		Approved	KIAA1237, HEG	uc003ehs.4	Q9ULI3	OTTHUMG00000159486	ENST00000311127.4:c.1997C>T	3.37:g.124732426G>A	ENSP00000311502:p.Ser666Phe	123.0	0.0	0		130.0	72.0	0.553846	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Missense_Mutation	SNP	ENST00000311127.4	37	CCDS46898.1	28	0.01282051282051282	24	0.04878048780487805	4	0.011049723756906077	0	0.0	0	0.0	G	6.371	0.436495	0.12104	0.042459	1.18E-4	ENSG00000173706	ENST00000311127	D	0.89617	-2.54	0.635	0.635	0.17723	.	22.921900	0.01454	U	0.015599	T	0.57359	0.2048	N	0.08118	0	0.09310	N	1	D;D	0.58268	0.982;0.972	P;P	0.58013	0.452;0.831	T	0.72865	-0.4163	9	0.66056	D	0.02	.	.	.	.	.	666;666	Q9ULI3-2;Q9ULI3	.;HEG1_HUMAN	F	666	ENSP00000311502:S666F	ENSP00000311502:S666F	S	-	2	0	HEG1	126215116	0.001000	0.12720	0.004000	0.12327	0.003000	0.03518	0.345000	0.19979	0.619000	0.30197	0.313000	0.20887	TCC	G|0.986;A|0.014	0.014	strong		0.493	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386	
ANKRD36B	57730	hgsc.bcm.edu	37	2	98206013	98206013	+	RNA	SNP	C	C	T	rs188661236	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:98206013C>T	ENST00000443455.1	-	0	314							Q8N2N9	AN36B_HUMAN	ankyrin repeat domain 36B																		CTCTTATTGGCGTCATAATAC	0.522													.|||	73	0.0145767	0.0469	0.0043	5008	,	,		11667	0.006		0.001	False		,,,				2504	0.001				p.A46T		Atlas-SNP	.											.	.	.	.	0			c.G136A						PASS	.	C	THR/ALA	41,1343		2,37,653	107.0	83.0	90.0		136	-1.5	0.0	2		90	0,3182		0,0,1591	no	missense	ANKRD36B	NM_025190.3	58	2,37,2244	TT,TC,CC		0.0,2.9624,0.8979	benign	46/1354	98206013	41,4525	692	1591	2283			57730	exon1			TATTGGCGTCATA	AK024934	CCDS74543.1	2q11.2	2013-01-11	2008-03-25	2008-03-25	ENSG00000196912	ENSG00000196912		"""Ankyrin repeat domain containing"""	29333	protein-coding gene	gene with protein product	"""melanoma-associated antigen"", ""CLL-associated antigen KW-1"""		"""KIAA1641"""	KIAA1641		10997877	Standard	NM_025190		Approved	FLJ21281	uc010yvc.1	Q8N2N9	OTTHUMG00000130547		2.37:g.98206013C>T		295.0	1.0	0.00338983		262.0	127.0	0.484733	NM_025190	Q08AK5|Q6IPR0|Q6PI49|Q8IZM7|Q8TDH6|Q96N30|Q9H759	Missense_Mutation	SNP	ENST00000443455.1	37																																																																																				C|0.989;T|0.011	0.011	strong		0.522	ANKRD36B-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000328967.2	NM_025190	
LRRC16A	55604	hgsc.bcm.edu	37	6	25606442	25606442	+	Missense_Mutation	SNP	A	A	G	rs201300946	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:25606442A>G	ENST00000329474.6	+	35	4156	c.3788A>G	c.(3787-3789)aAa>aGa	p.K1263R		NM_001173977.1|NM_017640.5	NP_001167448.1|NP_060110.4	Q5VZK9	LR16A_HUMAN	leucine rich repeat containing 16A	1263					actin filament organization (GO:0007015)|barbed-end actin filament uncapping (GO:0051638)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|lamellipodium assembly (GO:0030032)|negative regulation of barbed-end actin filament capping (GO:2000813)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of lamellipodium organization (GO:1902745)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|ruffle organization (GO:0031529)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|lamellipodium (GO:0030027)|nucleus (GO:0005634)	protein complex binding (GO:0032403)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	50						CAGTCCCCCAAACCCAGTCTG	0.582													A|||	5	0.000998403	0.0038	0.0	5008	,	,		16648	0.0		0.0	False		,,,				2504	0.0				p.K1263R		Atlas-SNP	.											.	LRRC16A	168	.	0			c.A3788G						PASS	.	A	ARG/LYS,ARG/LYS	10,3848		0,10,1919	42.0	50.0	47.0		3770,3788	5.8	1.0	6		47	0,8290		0,0,4145	yes	missense,missense	LRRC16A	NM_001173977.1,NM_017640.5	26,26	0,10,6064	GG,GA,AA		0.0,0.2592,0.0823	probably-damaging,probably-damaging	1257/1366,1263/1372	25606442	10,12138	1929	4145	6074	SO:0001583	missense	55604	exon35			CCCCCAAACCCAG	AK000055	CCDS54973.1	6p22.1	2010-09-10	2008-02-12	2008-02-12	ENSG00000079691	ENSG00000079691			21581	protein-coding gene	gene with protein product	"""capping protein, Arp2/3, and Myosin-I Linker homolog 1 (Dictyostelium)"""	609593	"""leucine rich repeat containing 16"""	LRRC16		19846667	Standard	NM_017640		Approved	dJ501N12.1, FLJ20048, CARMIL, CARMIL1	uc011djw.2	Q5VZK9	OTTHUMG00000014393	ENST00000329474.6:c.3788A>G	6.37:g.25606442A>G	ENSP00000331983:p.Lys1263Arg	99.0	0.0	0		116.0	53.0	0.456897	NM_017640	B8X1J0|Q6ZUH5|Q6ZW07|Q9NXU7	Missense_Mutation	SNP	ENST00000329474.6	37	CCDS54973.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.846082	0.91277	0.002592	0.0	ENSG00000079691	ENST00000329474;ENST00000399313	T	0.18657	2.2	5.85	5.85	0.93711	.	0.000000	0.85682	D	0.000000	T	0.35422	0.0931	M	0.65975	2.015	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.999	D;D;D	0.80764	0.993;0.993;0.994	T	0.05257	-1.0896	10	0.38643	T	0.18	-24.4349	16.2375	0.82384	1.0:0.0:0.0:0.0	.	1263;1257;1218	Q5VZK9;B2RTQ5;Q5VZK9-2	LR16A_HUMAN;.;.	R	1263;1218	ENSP00000331983:K1263R	ENSP00000331983:K1263R	K	+	2	0	LRRC16A	25714421	1.000000	0.71417	0.997000	0.53966	0.878000	0.50629	6.167000	0.71902	2.222000	0.72286	0.533000	0.62120	AAA	.	.	weak		0.582	LRRC16A-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040045.2	NM_017640	
COL6A2	1292	hgsc.bcm.edu	37	21	47535816	47535816	+	Missense_Mutation	SNP	G	G	A	rs61735835	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:47535816G>A	ENST00000300527.4	+	6	936	c.832G>A	c.(832-834)Gag>Aag	p.E278K	COL6A2_ENST00000409416.1_Missense_Mutation_p.E278K|COL6A2_ENST00000357838.4_Missense_Mutation_p.E278K|COL6A2_ENST00000310645.5_Missense_Mutation_p.E278K|COL6A2_ENST00000397763.1_Missense_Mutation_p.E278K	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	278	Triple-helical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		TGAGCCGGGAGAGCCTGGCCA	0.657													G|||	41	0.0081869	0.028	0.0014	5008	,	,		15727	0.003		0.0	False		,,,				2504	0.0				p.E278K		Atlas-SNP	.											.	COL6A2	351	.	0			c.G832A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU	105,4295	83.4+/-121.9	2,101,2097	63.0	57.0	59.0		832,832,832	4.0	1.0	21	dbSNP_129	59	2,8596	1.2+/-3.3	0,2,4297	yes	missense,missense,missense	COL6A2	NM_001849.3,NM_058174.2,NM_058175.2	56,56,56	2,103,6394	AA,AG,GG		0.0233,2.3864,0.8232	possibly-damaging,possibly-damaging,possibly-damaging	278/1020,278/919,278/829	47535816	107,12891	2200	4299	6499	SO:0001583	missense	1292	exon6			CCGGGAGAGCCTG	M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"""Collagens"""	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.832G>A	21.37:g.47535816G>A	ENSP00000300527:p.Glu278Lys	42.0	0.0	0		58.0	32.0	0.551724	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Missense_Mutation	SNP	ENST00000300527.4	37	CCDS13728.1	20	0.009157509157509158	20	0.04065040650406504	0	0.0	0	0.0	0	0.0	G	12.81	2.050127	0.36181	0.023864	2.33E-4	ENSG00000142173	ENST00000300527;ENST00000357838;ENST00000310645;ENST00000409416;ENST00000397763	D;D;D;D;D	0.94184	-3.37;-3.37;-3.37;-3.37;-3.37	3.98	3.98	0.46160	.	1.534500	0.03661	N	0.242608	T	0.77418	0.4127	N	0.22421	0.69	0.25510	N	0.987462	P;P;P	0.49090	0.897;0.919;0.55	P;P;B	0.51615	0.675;0.514;0.198	T	0.78476	-0.2189	10	0.11485	T	0.65	-9.2802	11.7636	0.51918	0.0:0.0:0.7742:0.2258	rs61735835	278;278;278	P12110;P12110-2;P12110-3	CO6A2_HUMAN;.;.	K	278	ENSP00000300527:E278K;ENSP00000350497:E278K;ENSP00000312529:E278K;ENSP00000387115:E278K;ENSP00000380870:E278K	ENSP00000300527:E278K	E	+	1	0	COL6A2	46360244	0.075000	0.21258	1.000000	0.80357	0.787000	0.44495	0.977000	0.29475	1.956000	0.56807	0.555000	0.69702	GAG	G|0.991;A|0.009	0.009	strong		0.657	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		
DTNBP1	84062	hgsc.bcm.edu	37	6	15523388	15523388	+	Missense_Mutation	SNP	T	T	C	rs73369534	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:15523388T>C	ENST00000344537.5	-	10	1046	c.874A>G	c.(874-876)Aga>Gga	p.R292G	DTNBP1_ENST00000462989.2_Missense_Mutation_p.R136G|DTNBP1_ENST00000355917.3_Missense_Mutation_p.R293G	NM_032122.4	NP_115498.2	Q96EV8	DTBP1_HUMAN	dystrobrevin binding protein 1	292	Dysbindin.				actin cytoskeleton reorganization (GO:0031532)|anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|blood coagulation (GO:0007596)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|neuron projection development (GO:0031175)|neuron projection morphogenesis (GO:0048812)|platelet dense granule organization (GO:0060155)|positive regulation of gene expression (GO:0010628)|positive regulation of neurotransmitter secretion (GO:0001956)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of dopamine secretion (GO:0014059)	axon (GO:0030424)|BLOC-1 complex (GO:0031083)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|growth cone (GO:0030426)|neuron projection (GO:0043005)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)|synaptic vesicle membrane (GO:0030672)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|skin(2)	14	Breast(50;0.0289)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.211)			GGCTTGGCTCTTAATTCTGAG	0.532									Hermansky-Pudlak syndrome				t|||	140	0.0279553	0.0998	0.0086	5008	,	,		19166	0.0		0.002	False		,,,				2504	0.0				p.R292G		Atlas-SNP	.											.	DTNBP1	56	.	0			c.A874G						PASS	.	T	GLY/ARG	400,4006	196.4+/-220.7	18,364,1821	154.0	163.0	160.0		874	2.4	0.0	6	dbSNP_130	160	5,8595	4.3+/-15.6	0,5,4295	yes	missense	DTNBP1	NM_032122.4	125	18,369,6116	CC,CT,TT		0.0581,9.0785,3.1139	possibly-damaging	292/352	15523388	405,12601	2203	4300	6503	SO:0001583	missense	84062	exon10	Familial Cancer Database	HPS, HPS1-8	TGGCTCTTAATTC	AF394226	CCDS4534.1, CCDS4535.1, CCDS75404.1, CCDS75405.1	6p22.3	2013-09-27			ENSG00000047579	ENSG00000047579		"""Biogenesis of lysosomal organelles complex-1 subunits"""	17328	protein-coding gene	gene with protein product	"""dysbindin-1"", ""biogenesis of lysosomal organelles complex-1, subunit 8"""	607145				11316798	Standard	NM_032122		Approved	Dysbindin, My031, HPS7, DBND, BLOC1S8	uc003nbm.3	Q96EV8	OTTHUMG00000014295	ENST00000344537.5:c.874A>G	6.37:g.15523388T>C	ENSP00000341680:p.Arg292Gly	136.0	0.0	0		133.0	55.0	0.413534	NM_032122	A8K3V3|Q5THY3|Q5THY4|Q96NV2|Q9H0U2|Q9H3J5	Missense_Mutation	SNP	ENST00000344537.5	37	CCDS4534.1	37	0.01694139194139194	33	0.06707317073170732	4	0.011049723756906077	0	0.0	0	0.0	t	12.91	2.078161	0.36662	0.090785	5.81E-4	ENSG00000047579	ENST00000344537;ENST00000462989;ENST00000355917;ENST00000397306;ENST00000509674	T;T;T;T	0.33438	1.41;1.41;1.41;1.41	5.42	2.43	0.29744	.	1.442950	0.04672	N	0.410792	T	0.21387	0.0515	M	0.75447	2.3	0.09310	N	1	B	0.25390	0.125	B	0.31390	0.129	T	0.44081	-0.9351	10	0.49607	T	0.09	.	10.1887	0.43013	0.0:0.118:0.41:0.472	.	292	Q96EV8	DTBP1_HUMAN	G	292;136;293;211;109	ENSP00000341680:R292G;ENSP00000427239:R136G;ENSP00000348183:R293G;ENSP00000421797:R109G	ENSP00000341680:R292G	R	-	1	2	DTNBP1	15631367	0.149000	0.22717	0.000000	0.03702	0.104000	0.19210	2.937000	0.48979	0.621000	0.30232	-0.224000	0.12420	AGA	T|0.967;C|0.033	0.033	strong		0.532	DTNBP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000039933.2	NM_032122	
KIAA2018	205717	hgsc.bcm.edu	37	3	113379720	113379720	+	Missense_Mutation	SNP	G	G	A	rs114838141	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:113379720G>A	ENST00000478658.1	-	5	826	c.809C>T	c.(808-810)tCt>tTt	p.S270F	KIAA2018_ENST00000491165.1_Intron|KIAA2018_ENST00000316407.4_Missense_Mutation_p.S270F			Q68DE3	K2018_HUMAN	KIAA2018	270						membrane (GO:0016020)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|mannosyl-oligosaccharide 1,2-alpha-mannosidase activity (GO:0004571)			NS(1)|breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|liver(1)|lung(30)|ovary(8)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	80						TGTGTGCAAAGAATGATGTTG	0.413													G|||	22	0.00439297	0.0166	0.0	5008	,	,		22506	0.0		0.0	False		,,,				2504	0.0				p.S270F		Atlas-SNP	.											.	KIAA2018	180	.	0			c.C809T						PASS	.	G	PHE/SER	49,3769		0,49,1860	60.0	57.0	58.0		809	5.4	0.1	3	dbSNP_132	58	0,8260		0,0,4130	yes	missense	KIAA2018	NM_001009899.2	155	0,49,5990	AA,AG,GG		0.0,1.2834,0.4057	possibly-damaging	270/2246	113379720	49,12029	1909	4130	6039	SO:0001583	missense	205717	exon7			TGCAAAGAATGAT	AB095938	CCDS43133.1	3q13.2	2014-01-02			ENSG00000176542	ENSG00000176542			30494	protein-coding gene	gene with protein product							Standard	XM_005247208		Approved		uc003eam.3	Q68DE3	OTTHUMG00000159322	ENST00000478658.1:c.809C>T	3.37:g.113379720G>A	ENSP00000420721:p.Ser270Phe	173.0	0.0	0		200.0	78.0	0.39	NM_001009899	Q7Z3L9|Q8IVF3|Q9H8T4	Missense_Mutation	SNP	ENST00000478658.1	37	CCDS43133.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	G	12.32	1.903297	0.33628	0.012834	0.0	ENSG00000176542	ENST00000316407;ENST00000478658	T;T	0.17691	2.26;2.26	5.36	5.36	0.76844	.	0.360582	0.24061	N	0.041908	T	0.11281	0.0275	N	0.08118	0	0.30845	N	0.735209	D	0.76494	0.999	D	0.67231	0.95	T	0.04333	-1.0959	10	0.72032	D	0.01	-4.2876	14.9458	0.71029	0.0:0.0:0.8566:0.1433	.	270	Q68DE3	K2018_HUMAN	F	270	ENSP00000320794:S270F;ENSP00000420721:S270F	ENSP00000320794:S270F	S	-	2	0	KIAA2018	114862410	0.990000	0.36364	0.073000	0.20177	0.608000	0.37181	4.214000	0.58527	2.789000	0.95967	0.655000	0.94253	TCT	G|0.996;A|0.004	0.004	strong		0.413	KIAA2018-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354591.1	NM_001009899	
KIAA0754	643314	hgsc.bcm.edu	37	1	39879517	39879517	+	Missense_Mutation	SNP	G	G	A	rs587523	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:39879517G>A	ENST00000530275.1	+	1	3367	c.3172G>A	c.(3172-3174)Gaa>Aaa	p.E1058K	MACF1_ENST00000564288.1_Intron|MACF1_ENST00000545844.1_Intron|MACF1_ENST00000372915.3_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000289893.4_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000567887.1_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	1058	Ala-rich.		E -> K (in dbSNP:rs587523).							central_nervous_system(1)|large_intestine(6)|skin(1)	8	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			CACCCTGGAGGAACCCACTTC	0.637													N|||	206	0.0411342	0.1392	0.0187	5008	,	,		13391	0.002		0.004	False		,,,				2504	0.0031				p.E1194K		Atlas-SNP	.											.	KIAA0754	93	.	0			c.G3580A						PASS	.	G	,,LYS/GLU	469,3435		31,407,1514	18.0	21.0	20.0		,,3580	0.1	0.0	1	dbSNP_83	20	47,8247		0,47,4100	yes	intron,intron,missense	MACF1,KIAA0754	NM_012090.4,NM_033044.3,NM_015038.1	,,56	31,454,5614	AA,AG,GG		0.5667,12.0133,4.2302	,,benign	,,1194/1428	39879517	516,11682	1952	4147	6099	SO:0001583	missense	643314	exon1			CTGGAGGAACCCA			1p34.2	2009-07-09				ENSG00000255103			29111	protein-coding gene	gene with protein product						9872452	Standard	NM_015038		Approved		uc009vvt.1	O94854		ENST00000530275.1:c.3172G>A	1.37:g.39879517G>A	ENSP00000431179:p.Glu1058Lys	179.0	0.0	0		191.0	96.0	0.502618	NM_015038	E9PMC2|Q6ZSB2	Missense_Mutation	SNP	ENST00000530275.1	37		81	0.03708791208791209	73	0.1483739837398374	6	0.016574585635359115	0	0.0	2	0.002638522427440633	N	13.03	2.116599	0.37339	0.120133	0.005667	ENSG00000255103	ENST00000530275	T	0.26223	1.75	3.58	0.0671	0.14364	.	.	.	.	.	T	0.00073	0.0002	N	0.14661	0.345	0.09310	N	1	B	0.27351	0.176	B	0.17433	0.018	T	0.32929	-0.9888	9	0.28530	T	0.3	.	7.1222	0.25450	0.0:0.1645:0.4977:0.3378	rs587523;rs587523	1058	O94854	K0754_HUMAN	K	1058	ENSP00000431179:E1058K	ENSP00000431179:E1058K	E	+	1	0	RP4-562N20.1	39652104	0.089000	0.21612	0.001000	0.08648	0.083000	0.17756	2.290000	0.43531	0.013000	0.14918	0.205000	0.17691	GAA	G|0.932;A|0.068	0.068	strong		0.637	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038	
OR10X1	128367	hgsc.bcm.edu	37	1	158549082	158549082	+	Missense_Mutation	SNP	A	A	T	rs61755876	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158549082A>T	ENST00000368150.1	-	1	607	c.608T>A	c.(607-609)cTg>cAg	p.L203Q		NM_001004477.1	NP_001004477.1	Q8NGY0	O10X1_HUMAN	olfactory receptor, family 10, subfamily X, member 1 (gene/pseudogene)	203						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(22)|ovary(2)|skin(2)|urinary_tract(1)	37	all_hematologic(112;0.0378)					TATACAAGACAGCCTAATAAC	0.433													A|||	79	0.0157748	0.0582	0.0029	5008	,	,		22248	0.0		0.0	False		,,,				2504	0.0				p.L203Q		Atlas-SNP	.											.	OR10X1	96	.	0			c.T608A						PASS	.	A	GLN/LEU	227,4179	134.9+/-171.1	6,215,1982	85.0	85.0	85.0		608	4.8	0.0	1	dbSNP_129	85	3,8597	2.2+/-6.3	0,3,4297	yes	missense	OR10X1	NM_001004477.1	113	6,218,6279	TT,TA,AA		0.0349,5.1521,1.7684	probably-damaging	203/327	158549082	230,12776	2203	4300	6503	SO:0001583	missense	128367	exon1			CAAGACAGCCTAA	BK004194	CCDS30900.1	1q23.1	2013-10-10	2013-10-10	2004-03-10	ENSG00000186400	ENSG00000186400		"""GPCR / Class A : Olfactory receptors"""	14995	protein-coding gene	gene with protein product			"""olfactory receptor, family 10, subfamily X, member 1"""	OR10X1P			Standard	NM_001004477		Approved		uc010pin.2	Q8NGY0	OTTHUMG00000019635	ENST00000368150.1:c.608T>A	1.37:g.158549082A>T	ENSP00000357132:p.Leu203Gln	185.0	0.0	0		207.0	100.0	0.483092	NM_001004477	Q6IFR8	Missense_Mutation	SNP	ENST00000368150.1	37	CCDS30900.1	26	0.011904761904761904	26	0.052845528455284556	0	0.0	0	0.0	0	0.0	A	13.52	2.261476	0.39995	0.051521	3.49E-4	ENSG00000186400	ENST00000368150	T	0.00411	7.53	4.8	4.8	0.61643	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37393	N	0.002120	T	0.01124	0.0037	H	0.97390	3.995	0.22684	N	0.998857	D	0.89917	1.0	D	0.97110	1.0	T	0.29701	-1.0003	10	0.87932	D	0	.	13.4538	0.61187	1.0:0.0:0.0:0.0	rs61755876	203	Q8NGY0	O10X1_HUMAN	Q	203	ENSP00000357132:L203Q	ENSP00000357132:L203Q	L	-	2	0	OR10X1	156815706	0.944000	0.32072	0.042000	0.18584	0.176000	0.22953	8.331000	0.90022	1.998000	0.58463	0.455000	0.32223	CTG	A|0.972;T|0.028	0.028	strong		0.433	OR10X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051850.2	NM_001004477	
GIMAP6	474344	hgsc.bcm.edu	37	7	150325177	150325177	+	Missense_Mutation	SNP	C	C	T	rs11974345	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150325177C>T	ENST00000328902.5	-	3	725	c.509G>A	c.(508-510)gGc>gAc	p.G170D	GIMAP6_ENST00000493969.1_3'UTR	NM_001244072.1|NM_024711.5	NP_001231001.1|NP_078987.3	Q6P9H5	GIMA6_HUMAN	GTPase, IMAP family member 6	170	AIG1-type G.		G -> D (in dbSNP:rs11974345).			cytosol (GO:0005829)	GTP binding (GO:0005525)			endometrium(4)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	29			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CAGGGAGCCGCCAGCCAGGTC	0.612													C|||	163	0.0325479	0.1203	0.0058	5008	,	,		16861	0.0		0.0	False		,,,				2504	0.0				p.G240D		Atlas-SNP	.											GIMAP6,NS,carcinoma,+1,1	GIMAP6	60	1	0			c.G719A						PASS	.	C	ASP/GLY	480,3926	224.6+/-240.7	28,424,1751	110.0	112.0	112.0		509	-1.6	0.0	7	dbSNP_120	112	4,8596	3.7+/-12.6	0,4,4296	yes	missense	GIMAP6	NM_024711.5	94	28,428,6047	TT,TC,CC		0.0465,10.8942,3.7214	benign	170/293	150325177	484,12522	2203	4300	6503	SO:0001583	missense	474344	exon3			GAGCCGCCAGCCA	AK026343	CCDS34778.1, CCDS59087.1, CCDS75676.1	7q36.1	2014-04-04			ENSG00000133561	ENSG00000133561		"""GTPases, IMAP"""	21918	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 6"""					15474311	Standard	NM_001244072		Approved	FLJ22690, IAN6	uc022apv.1	Q6P9H5	OTTHUMG00000159137	ENST00000328902.5:c.509G>A	7.37:g.150325177C>T	ENSP00000330374:p.Gly170Asp	47.0	0.0	0		52.0	23.0	0.442308	NM_001244072	C9J7B6|D3DWZ4|Q5ZPR6|Q9H612	Missense_Mutation	SNP	ENST00000328902.5	37	CCDS34778.1	47	0.02152014652014652	44	0.08943089430894309	3	0.008287292817679558	0	0.0	0	0.0	C	10.17	1.277158	0.23307	0.108942	4.65E-4	ENSG00000133561	ENST00000328902;ENST00000392862	T	0.32272	1.46	4.29	-1.56	0.08532	AIG1 (1);	0.323921	0.26719	N	0.022855	T	0.00241	0.0007	N	0.16708	0.43	0.09310	N	1	B;B	0.18863	0.003;0.031	B;B	0.17433	0.018;0.011	T	0.20240	-1.0281	10	0.12766	T	0.61	.	3.9744	0.09468	0.0:0.2878:0.3552:0.357	rs11974345;rs52826484;rs60915768;rs11974345	170;90	Q6P9H5;Q6P9H5-2	GIMA6_HUMAN;.	D	170;231	ENSP00000330374:G170D	ENSP00000330374:G170D	G	-	2	0	GIMAP6	149956110	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.081000	0.03403	-0.159000	0.11021	-0.304000	0.09214	GGC	C|0.960;T|0.040	0.040	strong		0.612	GIMAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353457.1	NM_024711	
RBM19	9904	hgsc.bcm.edu	37	12	114386723	114386723	+	Silent	SNP	G	G	A	rs7979406	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:114386723G>A	ENST00000545145.2	-	10	1269	c.1191C>T	c.(1189-1191)gaC>gaT	p.D397D	RBM19_ENST00000392561.3_Silent_p.D397D|RBM19_ENST00000261741.5_Silent_p.D397D	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	397					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)					ATTCGGCCAGGTCCTCCTCCT	0.562													G|||	156	0.0311502	0.1104	0.013	5008	,	,		19228	0.0		0.001	False		,,,				2504	0.0				p.D397D		Atlas-SNP	.											.	RBM19	117	.	0			c.C1191T						PASS	.	G	,,	389,4017	194.0+/-219.0	16,357,1830	180.0	170.0	173.0		1191,1191,1191	4.3	1.0	12	dbSNP_116	173	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	,,	16,360,6127	AA,AG,GG		0.0349,8.8289,3.014	,,	397/961,397/961,397/961	114386723	392,12614	2203	4300	6503	SO:0001819	synonymous_variant	9904	exon10			GGCCAGGTCCTCC	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.1191C>T	12.37:g.114386723G>A		216.0	0.0	0		247.0	121.0	0.489879	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Silent	SNP	ENST00000545145.2	37	CCDS9172.1																																																																																			G|0.971;A|0.029	0.029	strong		0.562	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
POLR3A	11128	hgsc.bcm.edu	37	10	79781326	79781326	+	Missense_Mutation	SNP	T	T	C	rs550436426		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:79781326T>C	ENST00000372371.3	-	8	1300	c.1163A>G	c.(1162-1164)aAa>aGa	p.K388R	POLR3A_ENST00000484760.1_5'Flank	NM_007055.3	NP_008986.2	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide A, 155kDa	388					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|ribonucleoside binding (GO:0032549)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)			AGTTAGAATTTTGGCCACATG	0.423													T|||	1	0.000199681	0.0008	0.0	5008	,	,		18712	0.0		0.0	False		,,,				2504	0.0				p.K388R		Atlas-SNP	.											.	POLR3A	104	.	0			c.A1163G						PASS	.						74.0	71.0	72.0					10																	79781326		2203	4300	6503	SO:0001583	missense	11128	exon8			AGAATTTTGGCCA	AF021351	CCDS7354.1	10q22-q23	2013-01-21			ENSG00000148606	ENSG00000148606		"""RNA polymerase subunits"""	30074	protein-coding gene	gene with protein product		614258				9331371, 12391170	Standard	NM_007055		Approved	RPC1, RPC155, hRPC155	uc001jzn.3	O14802	OTTHUMG00000018550	ENST00000372371.3:c.1163A>G	10.37:g.79781326T>C	ENSP00000361446:p.Lys388Arg	77.0	0.0	0		69.0	29.0	0.42029	NM_007055	Q8IW34|Q8TCW5	Missense_Mutation	SNP	ENST00000372371.3	37	CCDS7354.1	.	.	.	.	.	.	.	.	.	.	T	27.6	4.845255	0.91197	.	.	ENSG00000148606	ENST00000372371;ENST00000540842	T	0.68331	-0.32	5.58	5.58	0.84498	RNA polymerase, alpha subunit (1);RNA polymerase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.62258	0.2413	L	0.41906	1.305	0.80722	D	1	P	0.46578	0.88	B	0.44133	0.442	T	0.61705	-0.7008	9	.	.	.	-24.6898	16.0507	0.80760	0.0:0.0:0.0:1.0	.	388	O14802	RPC1_HUMAN	R	388	ENSP00000361446:K388R	.	K	-	2	0	POLR3A	79451332	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.646000	0.83445	2.243000	0.73865	0.528000	0.53228	AAA	.	.	none		0.423	POLR3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048923.1	NM_007055	
C5orf60	285679	hgsc.bcm.edu	37	5	179069413	179069413	+	Missense_Mutation	SNP	A	A	G	rs374415765	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:179069413A>G	ENST00000448248.2	-	5	786	c.761T>C	c.(760-762)aTa>aCa	p.I254T	C5orf60_ENST00000506142.1_5'Flank	NM_001142306.1	NP_001135778.1	A6NFR6	CE060_HUMAN	chromosome 5 open reading frame 60	143						integral component of membrane (GO:0016021)				NS(1)|breast(1)|kidney(5)	7						TTGGTGTCTTATGCGTCCAGC	0.562													a|||	117	0.0233626	0.0832	0.0072	5008	,	,		18498	0.0		0.002	False		,,,				2504	0.0				p.I254T		Atlas-SNP	.											.	C5orf60	24	.	0			c.T761C						PASS	.						200.0	171.0	180.0					5																	179069413		692	1591	2283	SO:0001583	missense	285679	exon5			TGTCTTATGCGTC	BC043435	CCDS47353.1	5q35.3	2010-08-19			ENSG00000204661	ENSG00000204661			27753	protein-coding gene	gene with protein product						12477932	Standard	NM_001142306		Approved		uc003mki.3	A6NFR6	OTTHUMG00000163221	ENST00000448248.2:c.761T>C	5.37:g.179069413A>G	ENSP00000404583:p.Ile254Thr	134.0	0.0	0		111.0	35.0	0.315315	NM_001142306	A1L488|B7ZM52|B7ZM53	Missense_Mutation	SNP	ENST00000448248.2	37	CCDS47353.1	.	.	.	.	.	.	.	.	.	.	N	0.018	-1.471398	0.01044	.	.	ENSG00000204661	ENST00000448248	T	0.23147	1.92	0.226	0.226	0.15353	.	.	.	.	.	T	0.11580	0.0282	.	.	.	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36890	-0.9729	7	0.15499	T	0.54	.	.	.	.	.	258;254	A6NFR6-2;A6NFR6-4	.;.	T	254	ENSP00000404583:I254T	ENSP00000404583:I254T	I	-	2	0	C5orf60	179002019	0.079000	0.21365	0.036000	0.18154	0.053000	0.15095	-0.873000	0.04214	-0.682000	0.05197	-0.674000	0.03794	ATA	.	.	weak		0.562	C5orf60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372148.2	NM_001142306	
SORCS2	57537	hgsc.bcm.edu	37	4	7741941	7741941	+	Missense_Mutation	SNP	G	G	A	rs189272447		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:7741941G>A	ENST00000507866.2	+	27	3539	c.3430G>A	c.(3430-3432)Gtg>Atg	p.V1144M	SORCS2_ENST00000329016.9_Missense_Mutation_p.V987M	NM_020777.2	NP_065828.2	Q96PQ0	SORC2_HUMAN	sortilin-related VPS10 domain containing receptor 2	1144					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(8)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	42						CCACTCAGGCGTGGTCCTGAG	0.617													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16669	0.0		0.0	False		,,,				2504	0.0				p.V1144M		Atlas-SNP	.											.	SORCS2	98	.	0			c.G3430A						PASS	.	G	MET/VAL	4,4138		0,4,2067	44.0	48.0	47.0		3430	3.8	0.9	4		47	1,8397		0,1,4198	yes	missense	SORCS2	NM_020777.2	21	0,5,6265	AA,AG,GG		0.0119,0.0966,0.0399	probably-damaging	1144/1160	7741941	5,12535	2071	4199	6270	SO:0001583	missense	57537	exon27			TCAGGCGTGGTCC	AB037750	CCDS47008.1	4p16.1	2008-02-05			ENSG00000184985	ENSG00000184985			16698	protein-coding gene	gene with protein product		606284				11499680	Standard	NM_020777		Approved	KIAA1329	uc003gkb.4	Q96PQ0	OTTHUMG00000159981	ENST00000507866.2:c.3430G>A	4.37:g.7741941G>A	ENSP00000422185:p.Val1144Met	20.0	0.0	0		19.0	8.0	0.421053	NM_020777	Q9P2L7	Missense_Mutation	SNP	ENST00000507866.2	37	CCDS47008.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	21.3	4.122447	0.77436	9.66E-4	1.19E-4	ENSG00000184985	ENST00000507866;ENST00000329016;ENST00000505529	T;T	0.19394	2.17;2.15	3.78	3.78	0.43462	.	0.167836	0.25948	U	0.027280	T	0.38295	0.1035	L	0.60455	1.87	0.58432	D	0.999996	D;D	0.76494	0.999;0.958	P;B	0.58970	0.849;0.13	T	0.39375	-0.9617	10	0.87932	D	0	.	15.8127	0.78576	0.0:0.0:1.0:0.0	.	987;1144	B5MED8;Q96PQ0	.;SORC2_HUMAN	M	1144;987;86	ENSP00000422185:V1144M;ENSP00000329124:V987M	ENSP00000329124:V987M	V	+	1	0	SORCS2	7792841	1.000000	0.71417	0.893000	0.35052	0.845000	0.48019	7.974000	0.88039	1.935000	0.56089	0.561000	0.74099	GTG	G|0.999;A|0.001	0.001	strong		0.617	SORCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358685.4	NM_020777	
CCS	9973	hgsc.bcm.edu	37	11	66366682	66366682	+	Missense_Mutation	SNP	G	G	A	rs61731812	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:66366682G>A	ENST00000533244.1	+	3	649	c.208G>A	c.(208-210)Ggg>Agg	p.G70R	CCS_ENST00000310190.4_Missense_Mutation_p.G51R	NM_005125.1	NP_005116.1	O14618	CCS_HUMAN	copper chaperone for superoxide dismutase	70	HMA. {ECO:0000255|PROSITE- ProRule:PRU00280}.				copper ion transmembrane transport (GO:0035434)|intracellular copper ion transport (GO:0015680)|positive regulation of oxidoreductase activity (GO:0051353)|removal of superoxide radicals (GO:0019430)|superoxide metabolic process (GO:0006801)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|protein disulfide oxidoreductase activity (GO:0015035)|superoxide dismutase activity (GO:0004784)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|large_intestine(2)|lung(3)|stomach(1)	9						GGAAGGCACGGGGCGGCAGGC	0.642													G|||	21	0.00419329	0.0144	0.0029	5008	,	,		18662	0.0		0.0	False		,,,				2504	0.0				p.G70R		Atlas-SNP	.											.	CCS	22	.	0			c.G208A						PASS	.	G	ARG/GLY	48,4352	50.9+/-86.3	0,48,2152	68.0	59.0	62.0		208	4.9	1.0	11	dbSNP_129	62	0,8590		0,0,4295	yes	missense	CCS	NM_005125.1	125	0,48,6447	AA,AG,GG		0.0,1.0909,0.3695	probably-damaging	70/275	66366682	48,12942	2200	4295	6495	SO:0001583	missense	9973	exon3			GGCACGGGGCGGC	AF002210	CCDS8146.1	11q13.2	2012-09-20			ENSG00000173992	ENSG00000173992			1613	protein-coding gene	gene with protein product		603864				9295278	Standard	NM_005125		Approved		uc001oir.3	O14618	OTTHUMG00000167238	ENST00000533244.1:c.208G>A	11.37:g.66366682G>A	ENSP00000436318:p.Gly70Arg	80.0	0.0	0		91.0	57.0	0.626374	NM_005125	Q2M366|Q8NEV0	Missense_Mutation	SNP	ENST00000533244.1	37	CCDS8146.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	G	27.6	4.842813	0.91197	0.010909	0.0	ENSG00000173992	ENST00000533244;ENST00000310190	D;D	0.94092	-3.35;-2.58	4.87	4.87	0.63330	Heavy metal-associated domain, HMA (3);	0.000000	0.85682	D	0.000000	D	0.97417	0.9155	H	0.99261	4.49	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96137	0.9097	10	0.87932	D	0	.	13.3773	0.60747	0.0:0.0:1.0:0.0	rs61731812	70	O14618	CCS_HUMAN	R	70;51	ENSP00000436318:G70R;ENSP00000307870:G51R	ENSP00000307870:G51R	G	+	1	0	CCS	66123258	1.000000	0.71417	0.955000	0.39395	0.970000	0.65996	7.533000	0.81994	2.546000	0.85860	0.561000	0.74099	GGG	G|0.996;A|0.004	0.004	strong		0.642	CCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393826.1	NM_005125	
SNX4	8723	hgsc.bcm.edu	37	3	125179676	125179676	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:125179676C>T	ENST00000251775.4	-	10	907	c.883G>A	c.(883-885)Gaa>Aaa	p.E295K	SNX4_ENST00000536067.1_Missense_Mutation_p.E150K	NM_003794.2	NP_003785.1	O95219	SNX4_HUMAN	sorting nexin 4	295					endocytic recycling (GO:0032456)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|early endosome membrane (GO:0031901)|membrane (GO:0016020)|protein complex (GO:0043234)	epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|leptin receptor binding (GO:1990460)|phosphatidylinositol binding (GO:0035091)|transferrin receptor binding (GO:1990459)			breast(2)|central_nervous_system(1)|lung(6)|ovary(1)|skin(1)	11						TCTTCATCTTCCAAAATATCA	0.333																																					p.E295K		Atlas-SNP	.											.	SNX4	29	.	0			c.G883A						PASS	.						85.0	82.0	83.0					3																	125179676		2202	4298	6500	SO:0001583	missense	8723	exon10			CATCTTCCAAAAT	AF065485	CCDS3032.1	3q21.2	2014-02-12			ENSG00000114520	ENSG00000114520		"""Sorting nexins"""	11175	protein-coding gene	gene with protein product		605931				9819414	Standard	NM_003794		Approved	ATG24B	uc003eib.4	O95219	OTTHUMG00000159575	ENST00000251775.4:c.883G>A	3.37:g.125179676C>T	ENSP00000251775:p.Glu295Lys	203.0	0.0	0		196.0	94.0	0.479592	NM_003794	B3KMH0|B4DQV4|D3DNA3	Missense_Mutation	SNP	ENST00000251775.4	37	CCDS3032.1	.	.	.	.	.	.	.	.	.	.	C	30	5.053128	0.93793	.	.	ENSG00000114520	ENST00000251775;ENST00000536067	T;T	0.76578	-1.03;-1.03	5.34	5.34	0.76211	.	0.513245	0.21868	N	0.067933	D	0.86451	0.5936	M	0.72894	2.215	0.80722	D	1	D	0.76494	0.999	D	0.68353	0.957	D	0.83631	0.0145	10	0.29301	T	0.29	-16.9581	17.4034	0.87467	0.0:1.0:0.0:0.0	.	295	O95219	SNX4_HUMAN	K	295;150	ENSP00000251775:E295K;ENSP00000440824:E150K	ENSP00000251775:E295K	E	-	1	0	SNX4	126662366	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.541000	0.73865	2.776000	0.95493	0.650000	0.86243	GAA	.	.	none		0.333	SNX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356299.1	NM_003794	
OR4N2	390429	hgsc.bcm.edu	37	14	20295972	20295972	+	Missense_Mutation	SNP	G	G	A	rs76952476	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20295972G>A	ENST00000315947.1	+	1	365	c.365G>A	c.(364-366)cGc>cAc	p.R122H	OR4N2_ENST00000568211.1_Missense_Mutation_p.R122H	NM_001004723.1	NP_001004723.1	Q8NGD1	OR4N2_HUMAN	olfactory receptor, family 4, subfamily N, member 2	122						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(32)|ovary(2)|prostate(1)|skin(2)|stomach(2)	52	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;2.95e-06)	GBM - Glioblastoma multiforme(265;0.00327)		GCCTTTGACCGCTACATCGCC	0.507													.|||	121	0.0241613	0.09	0.0029	5008	,	,		28676	0.0		0.0	False		,,,				2504	0.0				p.R122H		Atlas-SNP	.											OR4N2,NS,carcinoma,+1,5	OR4N2	125	5	0			c.G365A						PASS	.	G	HIS/ARG	333,4073		8,317,1878	158.0	168.0	165.0		365	4.5	1.0	14	dbSNP_131	165	3,8597		0,3,4297	no	missense	OR4N2	NM_001004723.1	29	8,320,6175	AA,AG,GG		0.0349,7.5579,2.5834	probably-damaging	122/308	20295972	336,12670	2203	4300	6503	SO:0001583	missense	390429	exon1			TTGACCGCTACAT		CCDS32022.1	14q11.2	2013-09-23				ENSG00000176294		"""GPCR / Class A : Olfactory receptors"""	14742	protein-coding gene	gene with protein product							Standard	NM_001004723		Approved		uc010tkv.2	Q8NGD1		ENST00000315947.1:c.365G>A	14.37:g.20295972G>A	ENSP00000319601:p.Arg122His	486.0	0.0	0		383.0	171.0	0.446475	NM_001004723	Q6IEY9|Q6IFA2	Missense_Mutation	SNP	ENST00000315947.1	37	CCDS32022.1	46	0.021062271062271064	44	0.08943089430894309	2	0.0055248618784530384	0	0.0	0	0.0	.	18.31	3.594861	0.66219	0.075579	3.49E-4	ENSG00000176294	ENST00000557677;ENST00000315947	D;T	0.97161	-4.27;-1.1	4.53	4.53	0.55603	GPCR, rhodopsin-like superfamily (1);	0.000000	0.50627	D	0.000113	T	0.66665	0.2812	M	0.90252	3.1	0.36488	D	0.868276	B	0.34103	0.437	B	0.30782	0.12	T	0.83054	-0.0151	10	0.72032	D	0.01	-14.9923	15.1112	0.72359	0.0:0.0:1.0:0.0	.	122	Q8NGD1	OR4N2_HUMAN	H	122	ENSP00000452022:R122H;ENSP00000319601:R122H	ENSP00000319601:R122H	R	+	2	0	OR4N2	19365812	0.992000	0.36948	1.000000	0.80357	0.999000	0.98932	5.956000	0.70315	2.488000	0.83962	0.591000	0.81541	CGC	G|0.977;A|0.023	0.023	strong		0.507	OR4N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409821.2		
ROBO2	6092	hgsc.bcm.edu	37	3	77614215	77614215	+	Missense_Mutation	SNP	T	T	C	rs185792666	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:77614215T>C	ENST00000461745.1	+	12	2693	c.1793T>C	c.(1792-1794)aTc>aCc	p.I598T	ROBO2_ENST00000487694.3_Missense_Mutation_p.I614T|ROBO2_ENST00000332191.8_Missense_Mutation_p.I598T	NM_002942.4	NP_002933.1	Q9HCK4	ROBO2_HUMAN	roundabout, axon guidance receptor, homolog 2 (Drosophila)	598	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic process involved in luteolysis (GO:0061364)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|brain development (GO:0007420)|cellular response to hormone stimulus (GO:0032870)|central nervous system development (GO:0007417)|homophilic cell adhesion (GO:0007156)|metanephros development (GO:0001656)|negative regulation of negative chemotaxis (GO:0050925)|negative regulation of synapse assembly (GO:0051964)|olfactory bulb interneuron development (GO:0021891)|positive regulation of axonogenesis (GO:0050772)|retinal ganglion cell axon guidance (GO:0031290)|ureteric bud development (GO:0001657)	axolemma (GO:0030673)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)			NS(1)|biliary_tract(5)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(23)|liver(1)|lung(52)|ovary(2)|pancreas(2)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	117				Epithelial(33;0.00199)|LUSC - Lung squamous cell carcinoma(21;0.008)|BRCA - Breast invasive adenocarcinoma(55;0.00884)|Lung(72;0.0183)|KIRC - Kidney renal clear cell carcinoma(39;0.0832)|Kidney(39;0.103)		GTCAGAGCGATCAACCCCCAA	0.498													T|||	10	0.00199681	0.0	0.0086	5008	,	,		17327	0.0		0.004	False		,,,				2504	0.0				p.I598T		Atlas-SNP	.											.	ROBO2	527	.	0			c.T1793C						PASS	.	T	THR/ILE,THR/ILE	2,3978		0,2,1988	131.0	129.0	130.0		1841,1793	6.0	1.0	3		130	43,8283		0,43,4120	yes	missense,missense	ROBO2	NM_001128929.2,NM_002942.4	89,89	0,45,6108	CC,CT,TT		0.5165,0.0503,0.3657	possibly-damaging,possibly-damaging	614/1395,598/1379	77614215	45,12261	1990	4163	6153	SO:0001583	missense	6092	exon12			GAGCGATCAACCC	AF040991	CCDS43109.1, CCDS54609.1	3p12.3	2013-02-11	2001-11-28		ENSG00000185008	ENSG00000185008		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	10250	protein-coding gene	gene with protein product		602431	"""roundabout (axon guidance receptor, Drosophila) homolog 2"""			9458045	Standard	NM_002942		Approved	KIAA1568	uc003dpy.4	Q9HCK4	OTTHUMG00000158935	ENST00000461745.1:c.1793T>C	3.37:g.77614215T>C	ENSP00000417164:p.Ile598Thr	61.0	0.0	0		82.0	44.0	0.536585	NM_002942	O43608|Q19AB4|Q19AB5	Missense_Mutation	SNP	ENST00000461745.1	37	CCDS43109.1	5	0.0022893772893772895	0	0.0	5	0.013812154696132596	0	0.0	0	0.0	T	17.82	3.482426	0.63962	5.03E-4	0.005165	ENSG00000185008	ENST00000487694;ENST00000403211;ENST00000343019;ENST00000461745;ENST00000332191;ENST00000398467	T;T;T	0.57595	0.39;0.39;0.39	6.02	6.02	0.97574	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.46758	D	0.000269	T	0.47135	0.1429	N	0.25890	0.77	0.39849	D	0.973215	P;P;B	0.35411	0.486;0.5;0.296	P;P;P	0.50825	0.651;0.588;0.651	T	0.51340	-0.8718	9	0.20519	T	0.43	.	16.542	0.84395	0.0:0.0:0.0:1.0	.	614;598;598	Q19AB5;F8W703;Q9HCK4	.;.;ROBO2_HUMAN	T	614;614;618;598;598;319	ENSP00000417335:I614T;ENSP00000417164:I598T;ENSP00000327536:I598T	ENSP00000327536:I598T	I	+	2	0	ROBO2	77696905	1.000000	0.71417	0.995000	0.50966	0.962000	0.63368	5.141000	0.64814	2.304000	0.77564	0.528000	0.53228	ATC	T|0.996;C|0.004	0.004	strong		0.498	ROBO2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352600.2	XM_031246	
RPP40	10799	hgsc.bcm.edu	37	6	4996611	4996611	+	Missense_Mutation	SNP	T	T	G	rs61730291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:4996611T>G	ENST00000380051.2	-	6	647	c.603A>C	c.(601-603)caA>caC	p.Q201H	RPP40_ENST00000464646.1_Missense_Mutation_p.Q141H|RPP40_ENST00000319533.5_Missense_Mutation_p.Q178H	NM_006638.2	NP_006629.2	O75818	RPP40_HUMAN	ribonuclease P/MRP 40kDa subunit	201					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA processing (GO:0008033)	nucleolar ribonuclease P complex (GO:0005655)|nucleus (GO:0005634)	ribonuclease P activity (GO:0004526)			NS(1)|breast(1)|large_intestine(4)|lung(4)|ovary(1)|skin(2)|urinary_tract(1)	14	Ovarian(93;0.11)	all_hematologic(90;0.0895)				GCTCCTGAATTTGGTACTTGG	0.473													T|||	158	0.0315495	0.115	0.0086	5008	,	,		19568	0.0		0.0	False		,,,				2504	0.0				p.Q201H		Atlas-SNP	.											.	RPP40	36	.	0			c.A603C						PASS	.	T	HIS/GLN	431,3975	209.8+/-230.5	23,385,1795	105.0	101.0	103.0		603	-5.1	0.6	6	dbSNP_129	103	0,8600		0,0,4300	yes	missense	RPP40	NM_006638.2	24	23,385,6095	GG,GT,TT		0.0,9.7821,3.3139	benign	201/364	4996611	431,12575	2203	4300	6503	SO:0001583	missense	10799	exon6			CTGAATTTGGTAC	U94317	CCDS34333.1, CCDS69040.1, CCDS75391.1	6p25.1	2012-05-21	2007-06-26	2004-03-19	ENSG00000124787	ENSG00000124787			20992	protein-coding gene	gene with protein product		606117	"""ribonuclease P1"", ""ribonuclease P 40kDa subunit"""	RNASEP1		9630247	Standard	NM_006638		Approved	bA428J1.3	uc003mwl.3	O75818	OTTHUMG00000014168	ENST00000380051.2:c.603A>C	6.37:g.4996611T>G	ENSP00000369391:p.Gln201His	132.0	0.0	0		98.0	47.0	0.479592	NM_006638	Q5VX97|Q8WVK8	Missense_Mutation	SNP	ENST00000380051.2	37	CCDS34333.1	61	0.027930402930402932	58	0.11788617886178862	3	0.008287292817679558	0	0.0	0	0.0	T	13.36	2.213743	0.39102	0.097821	0.0	ENSG00000124787	ENST00000380051;ENST00000319533;ENST00000464646	T;T;T	0.44083	0.93;0.93;0.93	5.23	-5.06	0.02946	.	0.748127	0.13823	N	0.360291	T	0.13841	0.0335	M	0.67953	2.075	0.29984	N	0.817458	B;B	0.09022	0.001;0.002	B;B	0.12156	0.003;0.007	T	0.12016	-1.0564	10	0.44086	T	0.13	-1.8359	2.4943	0.04618	0.1158:0.3526:0.2381:0.2936	.	178;201	O75818-2;O75818	.;RPP40_HUMAN	H	201;178;141	ENSP00000369391:Q201H;ENSP00000317998:Q178H;ENSP00000419431:Q141H	ENSP00000317998:Q178H	Q	-	3	2	RPP40	4941610	0.466000	0.25823	0.631000	0.29282	0.902000	0.53008	-0.492000	0.06467	-0.982000	0.03515	-0.321000	0.08615	CAA	T|0.971;G|0.029	0.029	strong		0.473	RPP40-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039733.2	NM_006638	
SERPINA5	5104	hgsc.bcm.edu	37	14	95058477	95058477	+	Silent	SNP	G	G	A	rs6117	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:95058477G>A	ENST00000554866.1	+	5	1236	c.1122G>A	c.(1120-1122)tcG>tcA	p.S374S	RP11-986E7.7_ENST00000553947.1_Intron|SERPINA5_ENST00000329597.7_Silent_p.S374S|SERPINA5_ENST00000554276.1_Silent_p.S374S|SERPINA5_ENST00000553780.1_Silent_p.S374S			P05154	IPSP_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5	374		Reactive bond.			fusion of sperm to egg plasma membrane (GO:0007342)|lipid transport (GO:0006869)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|spermatogenesis (GO:0007283)	acrosomal membrane (GO:0002080)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|platelet alpha granule (GO:0031091)|platelet dense tubular network (GO:0031094)|protein C inhibitor-coagulation factor V complex (GO:0097181)|protein C inhibitor-coagulation factor Xa complex (GO:0097182)|protein C inhibitor-coagulation factor XI complex (GO:0097183)|protein C inhibitor-KLK3 complex (GO:0036029)|protein C inhibitor-plasma kallikrein complex (GO:0036030)|protein C inhibitor-PLAT complex (GO:0036026)|protein C inhibitor-PLAU complex (GO:0036027)|protein C inhibitor-thrombin complex (GO:0036028)|protein C inhibitor-TMPRSS11E complex (GO:0036025)|protein C inhibitor-TMPRSS7 complex (GO:0036024)|protein complex (GO:0043234)	acrosin binding (GO:0032190)|glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|phosphatidylcholine binding (GO:0031210)|protease binding (GO:0002020)|retinoic acid binding (GO:0001972)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(3)|large_intestine(5)|lung(18)|ovary(2)|skin(5)|upper_aerodigestive_tract(3)	36				COAD - Colon adenocarcinoma(157;0.21)	Drotrecogin alfa(DB00055)|Urokinase(DB00013)	CTTTCAGGTCGGCCCGCCTGA	0.557													G|||	199	0.0397364	0.1399	0.0202	5008	,	,		18216	0.0		0.0	False		,,,				2504	0.0				p.S374S		Atlas-SNP	.											.	SERPINA5	69	.	0			c.G1122A						PASS	.	G		562,3844	251.8+/-258.4	41,480,1682	208.0	214.0	212.0		1122	-6.8	0.0	14	dbSNP_52	212	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	SERPINA5	NM_000624.4		41,487,5975	AA,AG,GG		0.0814,12.7553,4.3749		374/407	95058477	569,12437	2203	4300	6503	SO:0001819	synonymous_variant	5104	exon6			CAGGTCGGCCCGC	M68516	CCDS9928.1	14q32.1	2014-02-18	2005-08-18		ENSG00000188488	ENSG00000188488		"""Serine (or cysteine) peptidase inhibitors"""	8723	protein-coding gene	gene with protein product		601841	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5"""	PLANH3, PCI		1714450, 8381582, 24172014	Standard	NM_000624		Approved	PAI3, PROCI	uc001ydm.3	P05154	OTTHUMG00000170860	ENST00000554866.1:c.1122G>A	14.37:g.95058477G>A		126.0	0.0	0		124.0	77.0	0.620968	NM_000624	Q07616|Q9UG30	Silent	SNP	ENST00000554866.1	37	CCDS9928.1																																																																																			G|0.956;A|0.044	0.044	strong		0.557	SERPINA5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410726.1	NM_000624	
OBSCN	84033	hgsc.bcm.edu	37	1	228559225	228559225	+	Missense_Mutation	SNP	G	G	A	rs200269110	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228559225G>A	ENST00000422127.1	+	94	20790	c.20746G>A	c.(20746-20748)Gag>Aag	p.E6916K	OBSCN_ENST00000366707.4_Missense_Mutation_p.E4550K|OBSCN_ENST00000570156.2_Missense_Mutation_p.E7873K	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	6916					apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AGGCCTGCGCGAGCCACTGAT	0.746													G|||	34	0.00678914	0.0257	0.0	5008	,	,		12917	0.0		0.0	False		,,,				2504	0.0				p.E7873K		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G23617A						PASS	.	G	LYS/GLU	70,3774		0,70,1852	5.0	9.0	8.0		20746	4.4	0.9	1		8	0,8116		0,0,4058	yes	missense	OBSCN	NM_001098623.1	56	0,70,5910	AA,AG,GG		0.0,1.821,0.5853	benign	6916/7969	228559225	70,11890	1922	4058	5980	SO:0001583	missense	84033	exon105			CTGCGCGAGCCAC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.20746G>A	1.37:g.228559225G>A	ENSP00000409493:p.Glu6916Lys	12.0	0.0	0		20.0	8.0	0.4	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	17.35|17.35	3.368034|3.368034	0.61513|0.61513	0.01821|0.01821	0.0|0.0	ENSG00000154358|ENSG00000154358	ENST00000422127;ENST00000366707|ENST00000441106	T;T|T	0.65549|0.72394	-0.16;-0.1|-0.65	4.41|4.41	4.41|4.41	0.53225|0.53225	.|.	.|.	.|.	.|.	.|.	T|T	0.64068|0.64068	0.2565|0.2565	L|L	0.53249|0.53249	1.67|1.67	0.80722|0.80722	D|D	1|1	D|.	0.89917|.	1.0|.	D|.	0.83275|.	0.996|.	T|T	0.72301|0.72301	-0.4334|-0.4334	9|7	0.40728|0.41790	T|T	0.16|0.15	.|.	17.2084|17.2084	0.86924|0.86924	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	6916|.	Q5VST9|.	OBSCN_HUMAN|.	K|Q	6916;4550|1532	ENSP00000409493:E6916K;ENSP00000355668:E4550K|ENSP00000388554:R1532Q	ENSP00000355668:E4550K|ENSP00000388554:R1532Q	E|R	+|+	1|2	0|0	OBSCN|OBSCN	226625848|226625848	0.999000|0.999000	0.42202|0.42202	0.931000|0.931000	0.37212|0.37212	0.040000|0.040000	0.13550|0.13550	2.926000|2.926000	0.48892|0.48892	2.300000|2.300000	0.77407|0.77407	0.555000|0.555000	0.69702|0.69702	GAG|CGA	.	.	weak		0.746	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
LYPD4	147719	hgsc.bcm.edu	37	19	42343355	42343355	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42343355C>G	ENST00000330743.3	-	2	1216	c.5G>C	c.(4-6)gGa>gCa	p.G2A	LYPD4_ENST00000601246.1_Missense_Mutation_p.G2A|LYPD4_ENST00000343055.4_Missense_Mutation_p.G2A	NM_173506.4	NP_775777.3	Q6UWN0	LYPD4_HUMAN	LY6/PLAUR domain containing 4	2						anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				breast(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(2)	12						ATGCTGGGGTCCCATGGCCCT	0.542																																					p.G2A		Atlas-SNP	.											.	LYPD4	30	.	0			c.G5C						PASS	.						123.0	117.0	119.0					19																	42343355		2203	4300	6503	SO:0001583	missense	147719	exon2			TGGGGTCCCATGG	AY358726	CCDS12587.1	19q13.2	2008-02-05				ENSG00000273111			28659	protein-coding gene	gene with protein product						12975309	Standard	XM_005278383		Approved	MGC42718	uc002orp.1	Q6UWN0		ENST00000330743.3:c.5G>C	19.37:g.42343355C>G	ENSP00000328737:p.Gly2Ala	112.0	0.0	0		102.0	49.0	0.480392	NM_173506	Q8IYW0	Missense_Mutation	SNP	ENST00000330743.3	37	CCDS12587.1	.	.	.	.	.	.	.	.	.	.	C	13.50	2.255112	0.39896	.	.	ENSG00000183103	ENST00000330743;ENST00000343055	T;T	0.13657	3.41;2.57	3.9	2.83	0.33086	.	0.430475	0.17224	N	0.182217	T	0.13030	0.0316	L	0.46157	1.445	0.23827	N	0.996738	P;P	0.49961	0.93;0.793	P;B	0.44477	0.451;0.264	T	0.12708	-1.0537	10	0.23302	T	0.38	-2.1155	8.5663	0.33543	0.241:0.759:0.0:0.0	.	2;2	Q6UWN0-2;Q6UWN0	.;LYPD4_HUMAN	A	2	ENSP00000328737:G2A;ENSP00000339568:G2A	ENSP00000328737:G2A	G	-	2	0	LYPD4	47035195	0.988000	0.35896	0.975000	0.42487	0.942000	0.58702	0.660000	0.25009	1.156000	0.42514	0.551000	0.68910	GGA	.	.	none		0.542	LYPD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463039.1	NM_173506	
ANK2	287	hgsc.bcm.edu	37	4	114279770	114279770	+	Silent	SNP	T	T	C	rs145557320	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:114279770T>C	ENST00000357077.4	+	38	10049	c.9996T>C	c.(9994-9996)agT>agC	p.S3332S	ANK2_ENST00000510275.2_Intron|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000506722.1_Intron|ANK2_ENST00000264366.6_Silent_p.S3299S|ANK2_ENST00000509550.1_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	3332					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		TTCTATCCAGTGTAGATGAGG	0.443													T|||	39	0.00778754	0.0272	0.0029	5008	,	,		18580	0.0		0.001	False		,,,				2504	0.0				p.S3332S		Atlas-SNP	.											.	ANK2	576	.	0			c.T9996C						PASS	.	T	,,	114,4292	85.8+/-124.5	0,114,2089	110.0	113.0	112.0		,9996,	-2.8	0.2	4	dbSNP_134	112	1,8599	1.2+/-3.3	0,1,4299	no	intron,coding-synonymous,intron	ANK2	NM_001127493.1,NM_001148.4,NM_020977.3	,,	0,115,6388	CC,CT,TT		0.0116,2.5874,0.8842	,,	,3332/3958,	114279770	115,12891	2203	4300	6503	SO:0001819	synonymous_variant	287	exon38			ATCCAGTGTAGAT	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"""Ankyrin repeat domain containing"""	493	protein-coding gene	gene with protein product		106410	"""long (electrocardiographic) QT syndrome 4"""	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.9996T>C	4.37:g.114279770T>C		74.0	0.0	0		93.0	45.0	0.483871	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Silent	SNP	ENST00000357077.4	37	CCDS3702.1																																																																																			T|0.992;C|0.008	0.008	strong		0.443	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148	
UBR2	23304	hgsc.bcm.edu	37	6	42562027	42562027	+	Missense_Mutation	SNP	A	A	T	rs6905054	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42562027A>T	ENST00000372899.1	+	4	774	c.516A>T	c.(514-516)gaA>gaT	p.E172D	UBR2_ENST00000372901.1_Missense_Mutation_p.E172D|UBR2_ENST00000372903.2_Missense_Mutation_p.E172D	NM_015255.2	NP_056070.1	Q8IWV8	UBR2_HUMAN	ubiquitin protein ligase E3 component n-recognin 2	172			E -> D (in dbSNP:rs6905054).		cellular response to leucine (GO:0071233)|chromatin silencing (GO:0006342)|histone H2A ubiquitination (GO:0033522)|male meiosis I (GO:0007141)|negative regulation of TOR signaling (GO:0032007)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(10)|kidney(7)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|skin(5)	64	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.004)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.196)			ACACCTCTGAAATTGAGGAAG	0.363													A|||	166	0.033147	0.1089	0.0072	5008	,	,		17588	0.0099		0.0	False		,,,				2504	0.0072				p.E172D		Atlas-SNP	.											.	UBR2	134	.	0			c.A516T						PASS	.	A	ASP/GLU,ASP/GLU	360,4046	185.0+/-212.2	14,332,1857	113.0	110.0	111.0		516,516	5.2	1.0	6	dbSNP_116	111	2,8598	1.2+/-3.3	0,2,4298	yes	missense,missense	UBR2	NM_001184801.1,NM_015255.2	45,45	14,334,6155	TT,TA,AA		0.0233,8.1707,2.7833	benign,benign	172/440,172/1756	42562027	362,12644	2203	4300	6503	SO:0001583	missense	23304	exon4			CTCTGAAATTGAG	BC024217	CCDS4870.1, CCDS55001.1	6p21.1	2008-06-23	2005-01-10	2005-01-12	ENSG00000024048	ENSG00000024048		"""Ubiquitin protein ligase E3 component n-recognins"""	21289	protein-coding gene	gene with protein product		609134	"""chromosome 6 open reading frame 133"""	C6orf133			Standard	NM_015255		Approved	bA49A4.1, dJ392M17.3, KIAA0349	uc011dur.2	Q8IWV8	OTTHUMG00000014703	ENST00000372899.1:c.516A>T	6.37:g.42562027A>T	ENSP00000361990:p.Glu172Asp	64.0	0.0	0		66.0	22.0	0.333333	NM_001184801	O15057|Q4VXK2|Q5TFH6|Q6P2I2|Q6ZUD0	Missense_Mutation	SNP	ENST00000372899.1	37	CCDS4870.1	58	0.026556776556776556	50	0.1016260162601626	0	0.0	8	0.013986013986013986	0	0.0	A	11.03	1.518060	0.27211	0.081707	2.33E-4	ENSG00000024048	ENST00000372903;ENST00000372899;ENST00000372901	T;T;T	0.73152	-0.72;0.27;0.27	5.17	5.17	0.71159	.	0.218116	0.47093	D	0.000242	T	0.34571	0.0902	N	0.22421	0.69	0.09310	P	0.9999999999999195	B;B	0.09022	0.001;0.002	B;B	0.12837	0.001;0.008	T	0.13415	-1.0510	9	0.11485	T	0.65	-28.0504	11.0648	0.47968	0.9248:0.0:0.0752:0.0	rs6905054;rs52816446;rs61683407;rs6905054	172;172	Q8IWV8;Q8IWV8-2	UBR2_HUMAN;.	D	172	ENSP00000361994:E172D;ENSP00000361990:E172D;ENSP00000361992:E172D	ENSP00000361990:E172D	E	+	3	2	UBR2	42670005	1.000000	0.71417	0.995000	0.50966	0.998000	0.95712	1.373000	0.34272	1.953000	0.56701	0.459000	0.35465	GAA	A|0.966;T|0.034	0.034	strong		0.363	UBR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040558.2	NM_015255	
ASTN2	23245	hgsc.bcm.edu	37	9	119249690	119249690	+	Missense_Mutation	SNP	C	C	T	rs16933591	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:119249690C>T	ENST00000313400.4	-	20	3545	c.3445G>A	c.(3445-3447)Gtc>Atc	p.V1149I	ASTN2_ENST00000361209.2_Missense_Mutation_p.V1098I|ASTN2_ENST00000288520.5_Missense_Mutation_p.V250I|ASTN2_ENST00000361477.3_Missense_Mutation_p.V201I|ASTN2_ENST00000341734.4_Missense_Mutation_p.V201I|ASTN2_ENST00000373996.3_Missense_Mutation_p.V1145I			O75129	ASTN2_HUMAN	astrotactin 2	1149	Fibronectin type-III.		V -> I (in dbSNP:rs16933591).		negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)		p.V1098F(1)|p.V201F(1)		breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						TAGATACTGACTTCAGGGACC	0.507													C|||	101	0.0201677	0.0741	0.0043	5008	,	,		17865	0.0		0.0	False		,,,				2504	0.0				p.V1098I		Atlas-SNP	.											ASTN2_ENST00000361477,NS,carcinoma,0,1	ASTN2	307	1	2	Substitution - Missense(2)	lung(2)	c.G3292A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	262,4144	150.7+/-184.7	5,252,1946	118.0	106.0	110.0		601,3292,748,601,601	3.6	1.0	9	dbSNP_123	110	2,8598	1.2+/-3.3	0,2,4298	yes	missense,missense,missense,missense,missense	ASTN2	NM_001184734.1,NM_014010.4,NM_198186.3,NM_198187.3,NM_198188.2	29,29,29,29,29	5,254,6244	TT,TC,CC		0.0233,5.9464,2.0298	benign,benign,benign,benign,benign	201/376,1098/1289,250/441,201/403,201/396	119249690	264,12742	2203	4300	6503	SO:0001583	missense	23245	exon19			TACTGACTTCAGG	AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.3445G>A	9.37:g.119249690C>T	ENSP00000314038:p.Val1149Ile	70.0	0.0	0		79.0	50.0	0.632911	NM_014010	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Missense_Mutation	SNP	ENST00000313400.4	37		38	0.0173992673992674	36	0.07317073170731707	2	0.0055248618784530384	0	0.0	0	0.0	C	12.97	2.096981	0.37048	0.059464	2.33E-4	ENSG00000148219	ENST00000313400;ENST00000373996;ENST00000288520;ENST00000341734;ENST00000373986;ENST00000361209;ENST00000361477	T;T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95;0.95	5.49	3.6	0.41247	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.383922	0.28225	N	0.016137	T	0.01320	0.0043	N	0.08118	0	0.29275	N	0.870436	B;B;B;B;B;B;B	0.15473	0.013;0.0;0.006;0.0;0.01;0.0;0.0	B;B;B;B;B;B;B	0.11329	0.006;0.0;0.001;0.001;0.005;0.0;0.0	T	0.06338	-1.0832	10	0.20519	T	0.43	-28.4103	5.7264	0.18015	0.0:0.6328:0.0:0.3672	rs16933591;rs52796427;rs16933591	201;201;1098;1149;1145;201;250	B7ZKP4;B7ZKP5;O75129-2;O75129;O75129-3;O75129-6;O75129-4	.;.;.;ASTN2_HUMAN;.;.;.	I	1149;1145;250;201;872;1098;201	ENSP00000314038:V1149I;ENSP00000363108:V1145I;ENSP00000288520:V250I;ENSP00000339925:V201I;ENSP00000363098:V872I;ENSP00000354504:V1098I;ENSP00000355116:V201I	ENSP00000288520:V250I	V	-	1	0	ASTN2	118289511	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.748000	0.47483	1.436000	0.47453	0.655000	0.94253	GTC	C|0.979;T|0.021	0.021	strong		0.507	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010	
PLA1A	51365	hgsc.bcm.edu	37	3	119347623	119347623	+	Missense_Mutation	SNP	C	C	A	rs115172544	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119347623C>A	ENST00000273371.4	+	10	1269	c.1197C>A	c.(1195-1197)ttC>ttA	p.F399L	PLA1A_ENST00000494440.1_Missense_Mutation_p.F383L|PLA1A_ENST00000495992.1_Missense_Mutation_p.F383L|PLA1A_ENST00000488919.1_Missense_Mutation_p.F226L	NM_015900.3	NP_056984.1	Q53H76	PLA1A_HUMAN	phospholipase A1 member A	399	Involved in the recognition of diacyl- phospholipids.				lipid catabolic process (GO:0016042)|lipid metabolic process (GO:0006629)|phosphatidylserine metabolic process (GO:0006658)	extracellular vesicular exosome (GO:0070062)	phosphatidylcholine 1-acylhydrolase activity (GO:0008970)			NS(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						AAGTGAAATTCAAGTTTCAGT	0.468													C|||	78	0.0155751	0.0545	0.0086	5008	,	,		21512	0.0		0.0	False		,,,				2504	0.0				p.F399L		Atlas-SNP	.											.	PLA1A	65	.	0			c.C1197A						PASS	.	C	LEU/PHE,LEU/PHE,LEU/PHE	161,4245	108.2+/-146.6	4,153,2046	141.0	134.0	136.0		1149,678,1197	2.2	0.9	3	dbSNP_132	136	0,8600		0,0,4300	yes	missense,missense,missense	PLA1A	NM_001206960.1,NM_001206961.1,NM_015900.3	22,22,22	4,153,6346	AA,AC,CC		0.0,3.6541,1.2379	benign,benign,benign	383/441,226/284,399/457	119347623	161,12845	2203	4300	6503	SO:0001583	missense	51365	exon10			GAAATTCAAGTTT	AF035268	CCDS2991.1, CCDS56268.1, CCDS56269.1	3q13.13-q13.2	2002-11-28			ENSG00000144837	ENSG00000144837			17661	protein-coding gene	gene with protein product		607460				10196188	Standard	NM_015900		Approved	ps-PLA1	uc003ecu.3	Q53H76	OTTHUMG00000159425	ENST00000273371.4:c.1197C>A	3.37:g.119347623C>A	ENSP00000273371:p.Phe399Leu	156.0	0.0	0		141.0	65.0	0.460993	NM_015900	B2R8V2|B4DXA2|O95991|Q86WX6|Q9UPD2	Missense_Mutation	SNP	ENST00000273371.4	37	CCDS2991.1	26	0.011904761904761904	24	0.04878048780487805	2	0.0055248618784530384	0	0.0	0	0.0	C	0.008	-1.883913	0.00532	0.036541	0.0	ENSG00000144837	ENST00000273371;ENST00000488919;ENST00000495992;ENST00000494440	D;D;D;D	0.90004	-2.0;-2.6;-2.04;-2.12	5.29	2.23	0.28157	.	1.028510	0.07692	N	0.938840	T	0.34687	0.0906	N	0.04508	-0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.45234	-0.9275	10	0.02654	T	1	-0.7164	9.9541	0.41655	0.1251:0.5238:0.3511:0.0	.	383;399	Q53H76-3;Q53H76	.;PLA1A_HUMAN	L	399;226;383;383	ENSP00000273371:F399L;ENSP00000420625:F226L;ENSP00000417326:F383L;ENSP00000418793:F383L	ENSP00000273371:F399L	F	+	3	2	PLA1A	120830313	0.945000	0.32115	0.862000	0.33874	0.035000	0.12851	0.606000	0.24194	0.590000	0.29694	-0.304000	0.09214	TTC	C|0.984;A|0.016	0.016	strong		0.468	PLA1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355252.2		
FXR1	8087	hgsc.bcm.edu	37	3	180630500	180630500	+	Silent	SNP	C	C	T	rs1805578	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:180630500C>T	ENST00000357559.4	+	1	411	c.27C>T	c.(25-27)cgC>cgT	p.R9R	FXR1_ENST00000305586.7_5'UTR|FXR1_ENST00000468861.1_5'UTR|FXR1_ENST00000491674.1_Silent_p.R9R|FXR1_ENST00000480918.1_5'Flank|FXR1_ENST00000491062.1_Silent_p.R9R|FXR1_ENST00000445140.2_Silent_p.R9R	NM_001013438.2|NM_005087.3	NP_001013456.1|NP_005078.2	P51114	FXR1_HUMAN	fragile X mental retardation, autosomal homolog 1	9	Agenet-like 1.				apoptotic process (GO:0006915)|cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|negative regulation of translation (GO:0017148)	costamere (GO:0043034)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|polysome (GO:0005844)	G-quadruplex RNA binding (GO:0002151)|mRNA 3'-UTR binding (GO:0003730)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(3)|endometrium(4)|large_intestine(5)|lung(12)|skin(2)	26	all_cancers(143;6.07e-14)|Ovarian(172;0.0212)		Epithelial(37;3.05e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.4e-22)			TGGAGGTTCGCGGCTCTAACG	0.592											OREG0015934	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	179	0.0357428	0.1263	0.0159	5008	,	,		11846	0.0		0.001	False		,,,				2504	0.0				p.R9R		Atlas-SNP	.											.	FXR1	75	.	0			c.C27T						PASS	.	C	,,	444,3962	214.1+/-233.5	22,400,1781	146.0	145.0	145.0		27,,27	0.7	1.0	3	dbSNP_92	145	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,utr-5,coding-synonymous	FXR1	NM_001013438.2,NM_001013439.2,NM_005087.3	,,	22,405,6076	TT,TC,CC		0.0581,10.0772,3.4523	,,	9/540,,9/622	180630500	449,12557	2203	4300	6503	SO:0001819	synonymous_variant	8087	exon1			GGTTCGCGGCTCT	M67468	CCDS3238.1, CCDS33894.1, CCDS46965.1	3q28	2014-01-28			ENSG00000114416	ENSG00000114416			4023	protein-coding gene	gene with protein product		600819				7781595, 9642279	Standard	NM_005087		Approved		uc003fkq.3	P51114	OTTHUMG00000158138	ENST00000357559.4:c.27C>T	3.37:g.180630500C>T		312.0	1.0	0.00320513	1963	304.0	168.0	0.552632	NM_001013438	A8K9B8|Q7Z450|Q8N6R8	Silent	SNP	ENST00000357559.4	37	CCDS3238.1																																																																																			C|0.961;T|0.039	0.039	strong		0.592	FXR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350265.5		
TRIP10	9322	hgsc.bcm.edu	37	19	6751103	6751103	+	Missense_Mutation	SNP	G	G	A	rs139253875	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6751103G>A	ENST00000313244.9	+	15	1722	c.1687G>A	c.(1687-1689)Gag>Aag	p.E563K	TRIP10_ENST00000596758.1_Silent_p.P516P|TRIP10_ENST00000313285.8_Missense_Mutation_p.E507K|TRIP10_ENST00000600428.1_Missense_Mutation_p.E399K|CTD-3128G10.6_ENST00000594056.1_RNA			Q15642	CIP4_HUMAN	thyroid hormone receptor interactor 10	563	Interaction with ARHGAP17, DAAM1, DIAPH1 and DIAPH2.|Interaction with DNM1 and WASL.|Interaction with PDE6G. {ECO:0000250}.|Interaction with WAS.|Required for interaction with FASLG and localization to lysosomes.|Required for podosome formation.|SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin cytoskeleton organization (GO:0030036)|cell communication (GO:0007154)|endocytosis (GO:0006897)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)|lipid binding (GO:0008289)	p.E507Q(1)|p.E563Q(1)		NS(1)|breast(1)|endometrium(1)|large_intestine(1)|liver(2)|lung(7)|ovary(1)|prostate(1)|urinary_tract(1)	16						CTCTATGGCCGAGGGTGAAGA	0.532													G|||	7	0.00139776	0.0053	0.0	5008	,	,		15820	0.0		0.0	False		,,,				2504	0.0				p.E507K		Atlas-SNP	.											TRIP10_ENST00000313244,NS,carcinoma,0,2	TRIP10	104	2	2	Substitution - Missense(2)	lung(2)	c.G1519A						PASS	.	G	LYS/GLU	13,4393	20.2+/-43.8	0,13,2190	52.0	59.0	57.0		1519	4.7	1.0	19	dbSNP_134	57	0,8600		0,0,4300	yes	missense	TRIP10	NM_004240.2	56	0,13,6490	AA,AG,GG		0.0,0.2951,0.1	possibly-damaging	507/546	6751103	13,12993	2203	4300	6503	SO:0001583	missense	9322	exon14			ATGGCCGAGGGTG	AB072596	CCDS12172.1, CCDS74271.1, CCDS74272.1	19p13.3	2008-02-05			ENSG00000125733	ENSG00000125733			12304	protein-coding gene	gene with protein product	"""Cdc42-interacting protein"""	604504	"""salt tolerator"""	STOT		7776974, 9210375, 11294612	Standard	XM_005259683		Approved	STP, HSTP, CIP4	uc002mfr.3	Q15642	OTTHUMG00000150255	ENST00000313244.9:c.1687G>A	19.37:g.6751103G>A	ENSP00000320117:p.Glu563Lys	118.0	0.0	0		146.0	65.0	0.445205	NM_004240	B2R8A6|B7WP22|D6W645|O15184|Q53G22|Q5TZN1|Q6FI24|Q8NFL1|Q8TCY1|Q8TDX3|Q96RJ1	Missense_Mutation	SNP	ENST00000313244.9	37		1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	27.1	4.800102	0.90538	0.002951	0.0	ENSG00000125733	ENST00000313285;ENST00000313244	T;T	0.40756	1.02;1.02	4.66	4.66	0.58398	Src homology-3 domain (4);	0.349695	0.29822	N	0.011119	T	0.60894	0.2304	L	0.59912	1.85	0.80722	D	1	D;D	0.89917	0.996;1.0	D;D	0.85130	0.983;0.997	T	0.63739	-0.6569	10	0.87932	D	0	-32.2852	15.4165	0.74974	0.0:0.0:1.0:0.0	.	563;507	Q15642;Q15642-2	CIP4_HUMAN;.	K	507;563	ENSP00000320493:E507K;ENSP00000320117:E563K	ENSP00000320117:E563K	E	+	1	0	TRIP10	6702103	1.000000	0.71417	0.992000	0.48379	0.699000	0.40488	8.973000	0.93428	2.580000	0.87095	0.305000	0.20034	GAG	G|0.999;A|0.001	0.001	strong		0.532	TRIP10-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000317129.2		
FBN3	84467	hgsc.bcm.edu	37	19	8150353	8150353	+	Silent	SNP	C	C	T	rs61729617	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8150353C>T	ENST00000600128.1	-	56	7395	c.6981G>A	c.(6979-6981)ggG>ggA	p.G2327G	FBN3_ENST00000601739.1_Silent_p.G2327G|FBN3_ENST00000270509.2_Silent_p.G2327G			Q75N90	FBN3_HUMAN	fibrillin 3	2327	TB 9.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						CCCGGCCACCCCCACAGCAGC	0.692													C|||	204	0.0407348	0.1445	0.0187	5008	,	,		14856	0.0		0.0	False		,,,				2504	0.0				p.G2327G		Atlas-SNP	.											.	FBN3	300	.	0			c.G6981A						PASS	.	C		418,3948		15,388,1780	9.0	11.0	10.0		6981	3.6	0.8	19	dbSNP_129	10	8,8498		0,8,4245	no	coding-synonymous	FBN3	NM_032447.3		15,396,6025	TT,TC,CC		0.0941,9.574,3.3095		2327/2810	8150353	426,12446	2183	4253	6436	SO:0001819	synonymous_variant	84467	exon55			GCCACCCCCACAG		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.6981G>A	19.37:g.8150353C>T		36.0	0.0	0		47.0	21.0	0.446809	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																			C|0.967;T|0.033	0.033	strong		0.692	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
HDHD2	84064	hgsc.bcm.edu	37	18	44660923	44660923	+	Missense_Mutation	SNP	C	C	T	rs7230131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:44660923C>T	ENST00000300605.6	-	3	406	c.254G>A	c.(253-255)cGg>cAg	p.R85Q	HDHD2_ENST00000587841.1_Intron	NM_032124.4	NP_115500.1	Q9H0R4	HDHD2_HUMAN	haloacid dehalogenase-like hydrolase domain containing 2	85			R -> Q (in dbSNP:rs7230131).			extracellular vesicular exosome (GO:0070062)	enzyme binding (GO:0019899)|metal ion binding (GO:0046872)			kidney(2)|large_intestine(2)|lung(1)|skin(1)	6						GACTTGTTTCCGCTCTAGTAA	0.378													c|||	182	0.0363419	0.1293	0.0101	5008	,	,		18140	0.001		0.001	False		,,,				2504	0.002				p.R85Q		Atlas-SNP	.											.	HDHD2	12	.	0			c.G254A						PASS	.	C	GLN/ARG	435,3971	210.5+/-231.0	13,409,1781	110.0	108.0	109.0		254	3.6	1.0	18	dbSNP_116	109	4,8596	3.7+/-12.6	0,4,4296	yes	missense	HDHD2	NM_032124.4	43	13,413,6077	TT,TC,CC		0.0465,9.8729,3.3754	benign	85/260	44660923	439,12567	2203	4300	6503	SO:0001583	missense	84064	exon3			TGTTTCCGCTCTA	AL136681	CCDS32829.1	18q21.1	2008-02-05				ENSG00000167220			25364	protein-coding gene	gene with protein product						11230166	Standard	NM_032124		Approved	DKFZP564D1378	uc002lcs.3	Q9H0R4		ENST00000300605.6:c.254G>A	18.37:g.44660923C>T	ENSP00000300605:p.Arg85Gln	128.0	0.0	0		93.0	46.0	0.494624	NM_032124	A8K7T3|Q96NV4	Missense_Mutation	SNP	ENST00000300605.6	37	CCDS32829.1	55	0.025183150183150184	52	0.10569105691056911	3	0.008287292817679558	0	0.0	0	0.0	c	8.194	0.796607	0.16327	0.098729	4.65E-4	ENSG00000167220	ENST00000300605	T	0.29917	1.55	5.97	3.57	0.40892	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);	0.197776	0.44688	N	0.000433	T	0.00210	0.0006	N	0.02539	-0.55	0.26525	N	0.974354	B	0.02656	0.0	B	0.01281	0.0	T	0.26292	-1.0107	10	0.02654	T	1	2.3857	10.9093	0.47099	0.0:0.1293:0.0:0.8707	rs7230131;rs52803001;rs7230131	85	Q9H0R4	HDHD2_HUMAN	Q	85	ENSP00000300605:R85Q	ENSP00000300605:R85Q	R	-	2	0	HDHD2	42914921	1.000000	0.71417	1.000000	0.80357	0.921000	0.55340	4.293000	0.59037	1.077000	0.40990	-0.285000	0.09966	CGG	C|0.966;T|0.034	0.034	strong		0.378	HDHD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450668.2	NM_032124	
MBOAT4	619373	hgsc.bcm.edu	37	8	29994923	29994923	+	Intron	SNP	G	G	A	rs77053651	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:29994923G>A	ENST00000320542.3	-	2	429				LEPROTL1_ENST00000523116.1_Missense_Mutation_p.V139M|LEPROTL1_ENST00000442880.2_3'UTR	NM_001100916.1	NP_001094386.1	Q96T53	MBOA4_HUMAN	membrane bound O-acyltransferase domain containing 4						cellular protein metabolic process (GO:0044267)|peptidyl-serine octanoylation (GO:0018191)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	serine O-acyltransferase activity (GO:0016412)			endometrium(1)	1						CACTCAACCCGTGCTGAGGCT	0.562													G|||	82	0.0163738	0.056	0.0101	5008	,	,		19995	0.0		0.001	False		,,,				2504	0.0				p.V139M		Atlas-SNP	.											.	LEPROTL1	16	.	0			c.G415A						PASS	.	G	,MET/VAL	82,1302		3,76,613	51.0	44.0	46.0		,415	-1.1	0.0	8	dbSNP_132	46	1,3181		0,1,1590	yes	intron,missense	LEPROTL1,MBOAT4	NM_001100916.1,NM_001128208.1	,21	3,77,2203	AA,AG,GG		0.0314,5.9249,1.8178	,benign	,139/170	29994923	83,4483	692	1591	2283	SO:0001627	intron_variant	23484	exon4			CAACCCGTGCTGA	AF359269	CCDS47835.1	8p12	2008-08-04	2006-06-29	2006-06-29	ENSG00000177669	ENSG00000177669			32311	protein-coding gene	gene with protein product	"""ghrelin O-acyltransferase"""	611940	"""O-acyltransferase (membrane bound) domain containing 4"""	OACT4		18443287	Standard	NM_001100916		Approved	FKSG89, GOAT	uc010lvg.3	Q96T53	OTTHUMG00000163824	ENST00000320542.3:c.344+1124C>T	8.37:g.29994923G>A		118.0	0.0	0		135.0	56.0	0.414815	NM_001128208	B1Q003	Missense_Mutation	SNP	ENST00000320542.3	37	CCDS47835.1	33	0.01510989010989011	29	0.05894308943089431	4	0.011049723756906077	0	0.0	0	0.0	G	13.55	2.271741	0.40194	0.059249	3.14E-4	ENSG00000104660	ENST00000523116	.	.	.	3.84	-1.13	0.09775	.	.	.	.	.	T	0.01523	0.0049	N	0.08118	0	0.09310	N	0.999999	B	0.16396	0.017	B	0.08055	0.003	T	0.23297	-1.0192	7	.	.	.	.	7.2794	0.26302	0.5248:0.0:0.4752:0.0	.	139	E9PHP8	.	M	139	.	.	V	+	1	0	LEPROTL1	30114465	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-0.030000	0.12308	-0.204000	0.10235	-0.469000	0.05056	GTG	G|0.984;A|0.016	0.016	strong		0.562	MBOAT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375795.1		
AMZ1	155185	hgsc.bcm.edu	37	7	2752026	2752026	+	Silent	SNP	G	G	A	rs61743920	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:2752026G>A	ENST00000312371.4	+	7	1379	c.1011G>A	c.(1009-1011)ccG>ccA	p.P337P	AMZ1_ENST00000489665.1_Intron|AMZ1_ENST00000407112.1_Missense_Mutation_p.V281I	NM_133463.1	NP_597720.1	Q400G9	AMZ1_HUMAN	archaelysin family metallopeptidase 1	337							metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|kidney(1)|large_intestine(4)|lung(8)|skin(1)	16		Ovarian(82;0.0779)		OV - Ovarian serous cystadenocarcinoma(56;5.03e-14)		CGGGGGAGCCGTCAGTGTGGG	0.672													G|||	54	0.0107827	0.0386	0.0029	5008	,	,		15627	0.001		0.0	False		,,,				2504	0.0				p.P337P		Atlas-SNP	.											.	AMZ1	41	.	0			c.G1011A						PASS	.	G		160,4240	98.5+/-137.1	4,152,2044	23.0	28.0	26.0		1011	3.0	0.0	7	dbSNP_129	26	7,8591	5.7+/-21.5	0,7,4292	no	coding-synonymous	AMZ1	NM_133463.1		4,159,6336	AA,AG,GG		0.0814,3.6364,1.2848		337/499	2752026	167,12831	2200	4299	6499	SO:0001819	synonymous_variant	155185	exon7			GGAGCCGTCAGTG	AB075830	CCDS34589.1, CCDS64582.1	7p22.3	2008-01-17			ENSG00000174945	ENSG00000174945			22231	protein-coding gene	gene with protein product	"""archaemetzincin-1"""	615168				15972818	Standard	NM_133463		Approved	KIAA1950	uc003smr.1	Q400G9	OTTHUMG00000152111	ENST00000312371.4:c.1011G>A	7.37:g.2752026G>A		55.0	0.0	0		40.0	22.0	0.55	NM_133463	B3KRS0|Q8TF51	Silent	SNP	ENST00000312371.4	37	CCDS34589.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	G	5.330	0.246159	0.10130	0.036364	8.14E-4	ENSG00000174945	ENST00000407112	T	0.35421	1.31	4.85	2.96	0.34315	.	.	.	.	.	T	0.05273	0.0140	.	.	.	0.09310	N	0.999999	B	0.20459	0.045	B	0.13407	0.009	T	0.16808	-1.0390	8	0.23302	T	0.38	-30.2079	7.4751	0.27371	0.0927:0.1681:0.7392:0.0	rs61743920	281	B3KRS0	.	I	281	ENSP00000386020:V281I	ENSP00000386020:V281I	V	+	1	0	AMZ1	2718552	0.000000	0.05858	0.027000	0.17364	0.064000	0.16182	-0.564000	0.05936	0.412000	0.25729	0.462000	0.41574	GTC	G|0.988;A|0.012	0.012	strong		0.672	AMZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325244.1	NM_133463	
ZNF93	81931	hgsc.bcm.edu	37	19	20044810	20044810	+	Missense_Mutation	SNP	C	C	T	rs75974774	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:20044810C>T	ENST00000343769.5	+	4	1074	c.1046C>T	c.(1045-1047)gCc>gTc	p.A349V	AC007204.2_ENST00000592245.1_lincRNA	NM_031218.3	NP_112495.2	P35789	ZNF93_HUMAN	zinc finger protein 93	349					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(2)|large_intestine(4)|lung(8)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	24						TGTGGCAAAGCCTTTATTGCA	0.383													c|||	7	0.00139776	0.0053	0.0	5008	,	,		23005	0.0		0.0	False		,,,				2504	0.0				p.A349V		Atlas-SNP	.											.	ZNF93	81	.	0			c.C1046T						PASS	.	C	VAL/ALA	13,4393	20.2+/-43.8	0,13,2190	88.0	86.0	87.0		1046	0.9	0.8	19	dbSNP_131	87	0,8600		0,0,4300	yes	missense	ZNF93	NM_031218.3	64	0,13,6490	TT,TC,CC		0.0,0.2951,0.1	benign	349/621	20044810	13,12993	2203	4300	6503	SO:0001583	missense	81931	exon4			GCAAAGCCTTTAT	M61873	CCDS32973.1	19p12	2014-02-12	2006-05-12		ENSG00000184635	ENSG00000184635		"""Zinc fingers, C2H2-type"", ""-"""	13169	protein-coding gene	gene with protein product		603975	"""zinc finger protein 505"", ""zinc finger protein 93 (HTF34)"""	ZNF505		8467795, 2023909	Standard	NM_031218		Approved	HPF34, TF34, FLJ12488	uc002non.3	P35789	OTTHUMG00000182371	ENST00000343769.5:c.1046C>T	19.37:g.20044810C>T	ENSP00000342002:p.Ala349Val	70.0	0.0	0		92.0	47.0	0.51087	NM_031218	A6NMY2|B9EGT2|Q8N8Q4|Q9H9X5|Q9Y2N8	Missense_Mutation	SNP	ENST00000343769.5	37	CCDS32973.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	c	16.93	3.258220	0.59321	0.002951	0.0	ENSG00000184635	ENST00000343769;ENST00000427325	T	0.13778	2.56	0.85	0.85	0.18980	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12305	0.0299	L	0.28458	0.855	0.09310	N	0.999998	D	0.56035	0.974	P	0.60068	0.868	T	0.12760	-1.0535	9	0.52906	T	0.07	.	4.6298	0.12496	0.0:0.5889:0.4111:0.0	.	349	P35789	ZNF93_HUMAN	V	349	ENSP00000342002:A349V	ENSP00000342002:A349V	A	+	2	0	ZNF93	19905810	0.001000	0.12720	0.767000	0.31495	0.766000	0.43426	0.320000	0.19540	0.192000	0.20272	0.195000	0.17529	GCC	C|0.998;T|0.002	0.002	strong		0.383	ZNF93-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460808.2	NM_031218	
IGSF9	57549	hgsc.bcm.edu	37	1	159898437	159898437	+	Missense_Mutation	SNP	G	G	A	rs35574000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:159898437G>A	ENST00000368094.1	-	19	2938	c.2741C>T	c.(2740-2742)cCc>cTc	p.P914L	TAGLN2_ENST00000368097.4_5'Flank|IGSF9_ENST00000361509.3_Missense_Mutation_p.P898L|IGSF9_ENST00000493195.1_5'UTR	NM_001135050.1	NP_001128522.1	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9	914	Pro-rich.		P -> L (in dbSNP:rs35574000).		dendrite development (GO:0016358)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(17)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)			CAAGGGACTGGGTGGGGCTGC	0.657													G|||	74	0.0147764	0.0522	0.0072	5008	,	,		14684	0.0		0.0	False		,,,				2504	0.0				p.P914L		Atlas-SNP	.											.	IGSF9	123	.	0			c.C2741T						PASS	.	G	LEU/PRO,LEU/PRO	267,4113		7,253,1930	9.0	9.0	9.0		2741,2693	4.6	0.1	1	dbSNP_126	9	4,8536		0,4,4266	yes	missense,missense	IGSF9	NM_001135050.1,NM_020789.3	98,98	7,257,6196	AA,AG,GG		0.0468,6.0959,2.0975	probably-damaging,probably-damaging	914/1180,898/1164	159898437	271,12649	2190	4270	6460	SO:0001583	missense	57549	exon19			GGACTGGGTGGGG	AB037776	CCDS1190.1, CCDS44254.1	1q22-q23	2013-02-11			ENSG00000085552	ENSG00000085552		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	18132	protein-coding gene	gene with protein product		609738				11991715	Standard	NM_020789		Approved	KIAA1355, Nrt1, IGSF9A	uc001fur.2	Q9P2J2	OTTHUMG00000022794	ENST00000368094.1:c.2741C>T	1.37:g.159898437G>A	ENSP00000357073:p.Pro914Leu	96.0	0.0	0		104.0	56.0	0.538462	NM_001135050		Missense_Mutation	SNP	ENST00000368094.1	37	CCDS44254.1	27	0.012362637362637362	26	0.052845528455284556	1	0.0027624309392265192	0	0.0	0	0.0	G	14.74	2.625456	0.46840	0.060959	4.68E-4	ENSG00000085552	ENST00000361509;ENST00000368094;ENST00000198587	T;T	0.66815	-0.23;-0.14	4.63	4.63	0.57726	.	0.000000	0.37906	N	0.001887	T	0.58694	0.2140	N	0.24115	0.695	0.21697	N	0.999586	D;B	0.89917	1.0;0.19	D;B	0.83275	0.996;0.081	T	0.53704	-0.8401	9	.	.	.	-10.2414	12.8357	0.57771	0.0:0.0:1.0:0.0	rs35574000	914;452	Q9P2J2;C9JI81	TUTLA_HUMAN;.	L	898;914;452	ENSP00000355049:P898L;ENSP00000357073:P914L	.	P	-	2	0	IGSF9	158165061	0.579000	0.26725	0.117000	0.21633	0.543000	0.35085	4.142000	0.58044	2.378000	0.81104	0.655000	0.94253	CCC	G|0.987;A|0.013	0.013	strong		0.657	IGSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059115.1	NM_020789	
KLHL32	114792	hgsc.bcm.edu	37	6	97533193	97533193	+	Silent	SNP	C	C	A	rs551403903		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:97533193C>A	ENST00000369261.4	+	6	966	c.603C>A	c.(601-603)tcC>tcA	p.S201S	KLHL32_ENST00000536676.1_Silent_p.S165S|KLHL32_ENST00000544166.1_Intron|KLHL32_ENST00000539200.1_Silent_p.S132S	NM_052904.3	NP_443136.2	Q96NJ5	KLH32_HUMAN	kelch-like family member 32	201										breast(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(13)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)		GCCTGACCTCCCTGAGTGAAG	0.527																																					p.S201S		Atlas-SNP	.											KLHL32,mouth,carcinoma,+1,1	KLHL32	85	1	0			c.C603A						PASS	.						57.0	57.0	57.0					6																	97533193		2203	4300	6503	SO:0001819	synonymous_variant	114792	exon6			GACCTCCCTGAGT	AB067487	CCDS5038.1, CCDS69154.1, CCDS69155.1, CCDS75495.1	6q16.3	2013-02-22	2013-02-22	2007-01-09	ENSG00000186231	ENSG00000186231		"""Kelch-like"", ""BTB/POZ domain containing"""	21221	protein-coding gene	gene with protein product			"""BTB and kelch domain containing 5"", ""KIAA1900"", ""kelch-like 32 (Drosophila)"""	BKLHD5, KIAA1900			Standard	NM_052904		Approved		uc010kcm.1	Q96NJ5	OTTHUMG00000015247	ENST00000369261.4:c.603C>A	6.37:g.97533193C>A		52.0	0.0	0		83.0	4.0	0.0481928	NM_052904	B7Z346|B7Z4E2|E1P528|Q5THT0|Q96PY7	Silent	SNP	ENST00000369261.4	37	CCDS5038.1																																																																																			.	.	none		0.527	KLHL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041570.1	NM_052904	
TMCO4	255104	hgsc.bcm.edu	37	1	20009837	20009837	+	Missense_Mutation	SNP	G	G	C	rs116650784	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:20009837G>C	ENST00000294543.6	-	16	1842	c.1601C>G	c.(1600-1602)gCc>gGc	p.A534G	TMCO4_ENST00000375122.2_Missense_Mutation_p.A494G|TMCO4_ENST00000489814.1_5'UTR|TMCO4_ENST00000375127.1_Missense_Mutation_p.A534G	NM_181719.4	NP_859070.3	Q5TGY1	TMCO4_HUMAN	transmembrane and coiled-coil domains 4	534						integral component of membrane (GO:0016021)				biliary_tract(1)|breast(2)|endometrium(2)|kidney(1)|lung(11)|skin(1)|upper_aerodigestive_tract(1)	19		Colorectal(325;0.000147)|Renal(390;0.000469)|all_lung(284;0.00519)|Breast(348;0.00526)|Lung NSC(340;0.00544)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0439)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00708)|COAD - Colon adenocarcinoma(152;2.28e-05)|BRCA - Breast invasive adenocarcinoma(304;5.8e-05)|Kidney(64;0.000367)|GBM - Glioblastoma multiforme(114;0.000377)|KIRC - Kidney renal clear cell carcinoma(64;0.00459)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0862)|Lung(427;0.223)		GCAGCCTGGGGCCAGCAAGAG	0.672													G|||	115	0.0229633	0.0802	0.013	5008	,	,		16781	0.0		0.0	False		,,,				2504	0.0				p.A534G		Atlas-SNP	.											.	TMCO4	46	.	0			c.C1601G						PASS	.	G	GLY/ALA	310,4096	135.3+/-171.4	14,282,1907	30.0	33.0	32.0		1601	5.1	1.0	1	dbSNP_132	32	6,8594	5.0+/-18.6	0,6,4294	no	missense	TMCO4	NM_181719.4	60	14,288,6201	CC,CG,GG		0.0698,7.0359,2.4296	possibly-damaging	534/635	20009837	316,12690	2203	4300	6503	SO:0001583	missense	255104	exon16			CCTGGGGCCAGCA		CCDS198.1	1p36.13	2008-02-05			ENSG00000162542	ENSG00000162542			27393	protein-coding gene	gene with protein product							Standard	NM_181719		Approved	DKFZp686C23231	uc001bcn.3	Q5TGY1	OTTHUMG00000002697	ENST00000294543.6:c.1601C>G	1.37:g.20009837G>C	ENSP00000294543:p.Ala534Gly	175.0	0.0	0		201.0	95.0	0.472637	NM_181719	Q5TGY2|Q6MZN5|Q7Z6K6|Q9UQP4|Q9Y3K1	Missense_Mutation	SNP	ENST00000294543.6	37	CCDS198.1	41	0.018772893772893772	36	0.07317073170731707	5	0.013812154696132596	0	0.0	0	0.0	G	14.56	2.573196	0.45902	0.070359	6.98E-4	ENSG00000162542	ENST00000294543;ENST00000375127;ENST00000375122	T;T;T	0.34275	1.39;1.41;1.37	5.11	5.11	0.69529	.	0.134780	0.33959	N	0.004400	T	0.02047	0.0064	L	0.32530	0.975	0.31140	N	0.706765	P;P;B	0.43231	0.473;0.801;0.42	B;B;B	0.35353	0.056;0.201;0.061	T	0.02070	-1.1219	10	0.39692	T	0.17	-0.7187	15.6348	0.76944	0.0:0.0:1.0:0.0	.	118;534;494	Q6ZSC6;Q5TGY1;Q5TGY1-2	.;TMCO4_HUMAN;.	G	534;534;494	ENSP00000294543:A534G;ENSP00000364269:A534G;ENSP00000364264:A494G	ENSP00000294543:A534G	A	-	2	0	TMCO4	19882424	1.000000	0.71417	1.000000	0.80357	0.792000	0.44763	2.016000	0.40971	2.532000	0.85374	0.563000	0.77884	GCC	G|0.975;C|0.025	0.025	strong		0.672	TMCO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007658.1	NM_181719	
IGF2R	3482	hgsc.bcm.edu	37	6	160469542	160469542	+	Silent	SNP	A	A	G	rs8191809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:160469542A>G	ENST00000356956.1	+	18	2629	c.2481A>G	c.(2479-2481)gcA>gcG	p.A827A		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	827					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	ACCGATATGCATCGGCTTGCC	0.493													A|||	48	0.00958466	0.0348	0.0029	5008	,	,		21284	0.0		0.0	False		,,,				2504	0.0				p.A827A		Atlas-SNP	.											.	IGF2R	251	.	0			c.A2481G						PASS	.	A		112,4294	85.8+/-124.5	0,112,2091	98.0	82.0	87.0		2481	-7.3	0.0	6	dbSNP_117	87	0,8600		0,0,4300	no	coding-synonymous	IGF2R	NM_000876.2		0,112,6391	GG,GA,AA		0.0,2.542,0.8611		827/2492	160469542	112,12894	2203	4300	6503	SO:0001819	synonymous_variant	3482	exon18			ATATGCATCGGCT	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"""CD molecules"""	5467	protein-coding gene	gene with protein product	"""cation-independent mannose-6 phosphate receptor"""	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.2481A>G	6.37:g.160469542A>G		65.0	0.0	0		68.0	33.0	0.485294	NM_000876	Q7Z7G9|Q96PT5	Silent	SNP	ENST00000356956.1	37	CCDS5273.1																																																																																			A|0.988;G|0.012	0.012	strong		0.493	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
OR13C4	138804	hgsc.bcm.edu	37	9	107289352	107289352	+	Missense_Mutation	SNP	T	T	C	rs61738891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107289352T>C	ENST00000277216.3	-	1	138	c.139A>G	c.(139-141)Ata>Gta	p.I47V		NM_001001919.1	NP_001001919.1	Q8NGS5	O13C4_HUMAN	olfactory receptor, family 13, subfamily C, member 4	47						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|large_intestine(2)|lung(14)|skin(1)	18						ATGCTTGCTATGATCAGAACA	0.438													T|||	43	0.00858626	0.0318	0.0014	5008	,	,		22015	0.0		0.0	False		,,,				2504	0.0				p.I47V		Atlas-SNP	.											.	OR13C4	55	.	0			c.A139G						PASS	.	T	VAL/ILE	119,4287	89.2+/-127.9	1,117,2085	149.0	127.0	134.0		139	1.9	0.6	9	dbSNP_129	134	0,8600		0,0,4300	yes	missense	OR13C4	NM_001001919.1	29	1,117,6385	CC,CT,TT		0.0,2.7009,0.915	benign	47/319	107289352	119,12887	2203	4300	6503	SO:0001583	missense	138804	exon1			TTGCTATGATCAG		CCDS35088.1	9q31.1	2013-09-24			ENSG00000148136	ENSG00000148136		"""GPCR / Class A : Olfactory receptors"""	14722	protein-coding gene	gene with protein product							Standard	NM_001001919		Approved		uc011lvn.2	Q8NGS5	OTTHUMG00000020407	ENST00000277216.3:c.139A>G	9.37:g.107289352T>C	ENSP00000277216:p.Ile47Val	86.0	0.0	0		82.0	32.0	0.390244	NM_001001919	Q6IF51|Q96R41	Missense_Mutation	SNP	ENST00000277216.3	37	CCDS35088.1	13	0.005952380952380952	12	0.024390243902439025	1	0.0027624309392265192	0	0.0	0	0.0	T	4.428	0.079162	0.08533	0.027009	0.0	ENSG00000148136	ENST00000277216;ENST00000545903	T	0.03889	3.77	4.45	1.9	0.25705	GPCR, rhodopsin-like superfamily (1);	0.410669	0.20335	U	0.094356	T	0.00815	0.0027	N	0.10782	0.045	0.09310	N	1	B	0.14805	0.011	B	0.15052	0.012	T	0.44772	-0.9306	10	0.40728	T	0.16	.	3.6631	0.08246	0.3365:0.0958:0.0:0.5676	.	47	Q8NGS5	O13C4_HUMAN	V	47;76	ENSP00000277216:I47V	ENSP00000277216:I47V	I	-	1	0	OR13C4	106329173	0.000000	0.05858	0.607000	0.28956	0.763000	0.43281	-0.351000	0.07711	0.256000	0.21614	0.482000	0.46254	ATA	T|0.992;C|0.008	0.008	strong		0.438	OR13C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053478.1		
CCDC125	202243	hgsc.bcm.edu	37	5	68588029	68588029	+	Missense_Mutation	SNP	T	T	C	rs112794294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:68588029T>C	ENST00000396496.2	-	10	1192	c.1085A>G	c.(1084-1086)cAc>cGc	p.H362R	CCDC125_ENST00000383374.2_Intron|CCDC125_ENST00000460090.1_Intron|CCDC125_ENST00000511257.1_Missense_Mutation_p.H237R|CCDC125_ENST00000396499.1_Missense_Mutation_p.H362R			Q86Z20	CC125_HUMAN	coiled-coil domain containing 125	362						cytoplasm (GO:0005737)				breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(7)|urinary_tract(1)	19		Lung NSC(167;7.26e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.2e-56)|Epithelial(20;2.31e-52)|all cancers(19;5.85e-48)|Lung(70;0.0183)		CTCTTTAAGGTGCTTCCAATT	0.318													T|||	58	0.0115815	0.0408	0.0058	5008	,	,		20797	0.0		0.0	False		,,,				2504	0.0				p.H362R		Atlas-SNP	.											.	CCDC125	41	.	0			c.A1085G						PASS	.	T	ARG/HIS	173,4231	113.3+/-151.4	1,171,2030	273.0	236.0	248.0		1085	-0.1	1.0	5	dbSNP_132	248	0,8600		0,0,4300	yes	missense	CCDC125	NM_176816.3	29	1,171,6330	CC,CT,TT		0.0,3.9282,1.3304	benign	362/512	68588029	173,12831	2202	4300	6502	SO:0001583	missense	202243	exon9			TTAAGGTGCTTCC	AB024691	CCDS4000.1, CCDS75255.1	5q13.2	2008-02-05			ENSG00000183323	ENSG00000183323			28924	protein-coding gene	gene with protein product		613781					Standard	XM_005248461		Approved	KENAE	uc003jvv.1	Q86Z20	OTTHUMG00000131259	ENST00000396496.2:c.1085A>G	5.37:g.68588029T>C	ENSP00000379754:p.His362Arg	240.0	0.0	0		180.0	79.0	0.438889	NM_176816	Q86Z19	Missense_Mutation	SNP	ENST00000396496.2	37	CCDS4000.1	19	0.0086996336996337	15	0.03048780487804878	4	0.011049723756906077	0	0.0	0	0.0	T	0.922	-0.715564	0.03206	0.039282	0.0	ENSG00000183323	ENST00000396496;ENST00000396499;ENST00000511257	T;T;T	0.44482	0.92;0.92;0.92	4.28	-0.0527	0.13821	.	0.770151	0.12698	N	0.446592	T	0.06325	0.0163	L	0.41710	1.295	0.24112	N	0.995833	B	0.06786	0.001	B	0.09377	0.004	T	0.15206	-1.0445	10	0.17832	T	0.49	0.0174	2.3018	0.04164	0.1438:0.086:0.2964:0.4739	.	362	Q86Z20	CC125_HUMAN	R	362;362;237	ENSP00000379754:H362R;ENSP00000379756:H362R;ENSP00000426795:H237R	ENSP00000379754:H362R	H	-	2	0	CCDC125	68623785	0.832000	0.29368	0.951000	0.38953	0.996000	0.88848	0.157000	0.16402	-0.073000	0.12842	0.459000	0.35465	CAC	T|0.986;C|0.014	0.014	strong		0.318	CCDC125-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254027.4	NM_176816	
BDP1	55814	hgsc.bcm.edu	37	5	70818150	70818150	+	Missense_Mutation	SNP	C	C	G	rs12187098	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:70818150C>G	ENST00000358731.4	+	23	5289	c.5026C>G	c.(5026-5028)Caa>Gaa	p.Q1676E	BDP1_ENST00000380675.2_5'UTR	NM_018429.2	NP_060899.2	A6H8Y1	BDP1_HUMAN	B double prime 1, subunit of RNA polymerase III transcription initiation factor IIIB	1676			Q -> E (in dbSNP:rs12187098).		gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(34)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		Lung NSC(167;0.000422)|Prostate(74;0.00815)|Ovarian(174;0.0176)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;5.28e-56)|Epithelial(20;2.31e-50)		TAGTTCAGCACAAATGACAAG	0.348													C|||	101	0.0201677	0.0454	0.013	5008	,	,		17087	0.0		0.0298	False		,,,				2504	0.002				p.Q1676E		Atlas-SNP	.											.	BDP1	204	.	0			c.C5026G						PASS	.	C	GLU/GLN	182,3514		3,176,1669	130.0	127.0	128.0		5026	4.5	0.1	5	dbSNP_120	128	196,7988		6,184,3902	yes	missense	BDP1	NM_018429.2	29	9,360,5571	GG,GC,CC		2.3949,4.9242,3.1818	possibly-damaging	1676/2625	70818150	378,11502	1848	4092	5940	SO:0001583	missense	55814	exon23			TCAGCACAAATGA	AF298151	CCDS43328.1	5q12-q13	2008-02-05	2001-11-29	2001-11-30	ENSG00000145734	ENSG00000145734			13652	protein-coding gene	gene with protein product		607012	"""TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 1"""	TFNR, TAF3B1		11214970, 11040218	Standard	NM_018429		Approved	TFIIIB150, TFC5, TFIIIB90, KIAA1689, HSA238520, KIAA1241	uc003kbp.1	A6H8Y1	OTTHUMG00000162506	ENST00000358731.4:c.5026C>G	5.37:g.70818150C>G	ENSP00000351575:p.Gln1676Glu	165.0	0.0	0		173.0	76.0	0.439306	NM_018429	Q68DS6|Q68DY5|Q6MZL9|Q6PIM7|Q86W98|Q96LR8|Q9C0H4|Q9H197|Q9H1A1|Q9HAW1|Q9HAW2|Q9HCY0|Q9ULH9	Missense_Mutation	SNP	ENST00000358731.4	37	CCDS43328.1	41	0.018772893772893772	19	0.03861788617886179	5	0.013812154696132596	0	0.0	17	0.022427440633245383	C	8.668	0.902198	0.17760	0.049242	0.023949	ENSG00000145734	ENST00000358731;ENST00000451951	T	0.10477	2.87	5.35	4.48	0.54585	.	1.312210	0.05133	N	0.493011	T	0.01489	0.0048	L	0.47716	1.5	0.49687	D	0.999812	P;P	0.42871	0.557;0.792	B;B	0.37601	0.116;0.254	T	0.48514	-0.9029	10	0.02654	T	1	.	11.1063	0.48205	0.0:0.9126:0.0:0.0874	rs12187098;rs13169583;rs52833258;rs56647603;rs12187098	1676;1676	A6H8Y1;A6H8Y1-2	BDP1_HUMAN;.	E	1676;1256	ENSP00000351575:Q1676E	ENSP00000351575:Q1676E	Q	+	1	0	BDP1	70853906	0.019000	0.18553	0.098000	0.21074	0.052000	0.14988	2.086000	0.41643	1.251000	0.43983	0.555000	0.69702	CAA	C|0.971;G|0.029	0.029	strong		0.348	BDP1-016	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374681.2	NM_018429	
VPS54	51542	hgsc.bcm.edu	37	2	64160864	64160864	+	Missense_Mutation	SNP	G	G	C	rs34015596	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:64160864G>C	ENST00000272322.4	-	12	1836	c.1682C>G	c.(1681-1683)tCt>tGt	p.S561C	VPS54_ENST00000354504.3_Missense_Mutation_p.S408C|VPS54_ENST00000409558.4_Missense_Mutation_p.S549C			Q9P1Q0	VPS54_HUMAN	vacuolar protein sorting 54 homolog (S. cerevisiae)	561			S -> C (in dbSNP:rs34015596).		growth (GO:0040007)|homeostasis of number of cells within a tissue (GO:0048873)|musculoskeletal movement (GO:0050881)|neurofilament cytoskeleton organization (GO:0060052)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	GARP complex (GO:0000938)				endometrium(3)|kidney(4)|large_intestine(8)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	27						GCTGGATGAAGAATCAGTAGT	0.428													G|||	139	0.0277556	0.0998	0.0101	5008	,	,		17370	0.0		0.0	False		,,,				2504	0.0				p.S561C		Atlas-SNP	.											.	VPS54	57	.	0			c.C1682G						PASS	.	G	CYS/SER,CYS/SER	358,4048	185.0+/-212.2	14,330,1859	123.0	119.0	120.0		1646,1682	5.5	1.0	2	dbSNP_126	120	0,8600		0,0,4300	yes	missense,missense	VPS54	NM_001005739.1,NM_016516.2	112,112	14,330,6159	CC,CG,GG		0.0,8.1253,2.7526	probably-damaging,probably-damaging	549/966,561/978	64160864	358,12648	2203	4300	6503	SO:0001583	missense	51542	exon12			GATGAAGAATCAG	AF102177	CCDS33208.1, CCDS46302.1	2p15-p14	2014-06-13	2006-12-19		ENSG00000143952	ENSG00000143952			18652	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 164"""	614633	"""vacuolar protein sorting 54 (yeast)"""			12039048	Standard	NM_016516		Approved	HCC8, PPP1R164	uc002scq.3	Q9P1Q0	OTTHUMG00000152627	ENST00000272322.4:c.1682C>G	2.37:g.64160864G>C	ENSP00000272322:p.Ser561Cys	88.0	0.0	0		88.0	50.0	0.568182	NM_016516	Q5VIR5|Q86YF7|Q8N6G3|Q9NPV0|Q9NT07|Q9NUJ0	Missense_Mutation	SNP	ENST00000272322.4	37	CCDS33208.1	38	0.0173992673992674	34	0.06910569105691057	4	0.011049723756906077	0	0.0	0	0.0	G	22.3	4.266853	0.80469	0.081253	0.0	ENSG00000143952	ENST00000354504;ENST00000272322;ENST00000409558;ENST00000483277;ENST00000394400	T;T;T	0.34859	1.34;1.37;1.37	5.47	5.47	0.80525	.	0.218968	0.49305	D	0.000159	T	0.03220	0.0094	N	0.22421	0.69	0.80722	D	1	D;D;D	0.63880	0.992;0.989;0.993	P;P;P	0.58660	0.794;0.701;0.843	T	0.01182	-1.1426	10	0.48119	T	0.1	.	19.3282	0.94273	0.0:0.0:1.0:0.0	rs34015596	408;561;549	Q9P1Q0-3;Q9P1Q0;Q9P1Q0-4	.;VPS54_HUMAN;.	C	408;561;549;549;561	ENSP00000346499:S408C;ENSP00000272322:S561C;ENSP00000386980:S549C	ENSP00000272322:S561C	S	-	2	0	VPS54	64014368	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.562000	0.82300	2.566000	0.86566	0.563000	0.77884	TCT	G|0.970;C|0.030	0.030	strong		0.428	VPS54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327062.2	NM_016516	
TJP3	27134	hgsc.bcm.edu	37	19	3747890	3747890	+	Silent	SNP	C	C	T	rs10409928	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3747890C>T	ENST00000541714.2	+	19	2883	c.2421C>T	c.(2419-2421)taC>taT	p.Y807Y	TJP3_ENST00000589378.1_Silent_p.Y816Y|TJP3_ENST00000262968.9_Silent_p.Y840Y|TJP3_ENST00000539908.2_Silent_p.Y771Y|TJP3_ENST00000587686.1_Silent_p.Y826Y|TJP3_ENST00000382008.3_Silent_p.Y821Y	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	807					regulation of G1/S transition of mitotic cell cycle (GO:2000045)	apical plasma membrane (GO:0016324)|nucleus (GO:0005634)|tight junction (GO:0005923)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0118)|STAD - Stomach adenocarcinoma(1328;0.18)		ACAGCGACTACGAGACGGACG	0.672													C|||	286	0.0571086	0.177	0.0187	5008	,	,		16934	0.0		0.0	False		,,,				2504	0.0399				p.Y816Y		Atlas-SNP	.											.	TJP3	79	.	0			c.C2448T						PASS	.	C		652,3752	261.0+/-264.0	45,562,1595	35.0	31.0	32.0		2520	-6.7	0.8	19	dbSNP_119	32	4,8592	3.0+/-9.4	0,4,4294	no	coding-synonymous	TJP3	NM_014428.1		45,566,5889	TT,TC,CC		0.0465,14.8047,5.0462		840/953	3747890	656,12344	2202	4298	6500	SO:0001819	synonymous_variant	27134	exon19			CGACTACGAGACG	AC005954	CCDS32873.1, CCDS32873.2, CCDS59332.1	19p13.3	2012-07-12	2012-07-12			ENSG00000105289			11829	protein-coding gene	gene with protein product	"""zona occludens 3"""	612689					Standard	NM_001267560		Approved	ZO-3	uc010xhu.3	O95049		ENST00000541714.2:c.2421C>T	19.37:g.3747890C>T		91.0	0.0	0		132.0	76.0	0.575758	NM_001267561	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Silent	SNP	ENST00000541714.2	37	CCDS32873.2																																																																																			C|0.946;T|0.054	0.054	strong		0.672	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1		
USP17L2	377630	hgsc.bcm.edu	37	8	11996074	11996074	+	Missense_Mutation	SNP	T	T	C	rs142023572	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11996074T>C	ENST00000333796.3	-	1	512	c.196A>G	c.(196-198)Aag>Gag	p.K66E	FAM66D_ENST00000434078.2_RNA	NM_001256869.1|NM_001256871.1|NM_001256872.1|NM_001256873.1|NM_001256874.1|NM_201402.2	NP_001243798.1|NP_001243800.1|NP_001243801.1|NP_001243802.1|NP_001243803.1|NP_958804.2	Q6R6M4	U17L2_HUMAN	ubiquitin specific peptidase 17-like family member 2	66				K -> E (in Ref. 1; AAR91701). {ECO:0000305}.	apoptotic process (GO:0006915)|CAAX-box protein processing (GO:0071586)|cell cycle checkpoint (GO:0000075)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of histone deacetylation (GO:0031064)|negative regulation of protein processing (GO:0010955)|negative regulation of protein targeting to membrane (GO:0090315)|negative regulation of Ras GTPase activity (GO:0034261)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of RIG-I signaling pathway (GO:1900246)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|regulation of apoptotic process (GO:0042981)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of defense response to virus by host (GO:0050691)|regulation of ruffle assembly (GO:1900027)|ubiquitin-dependent protein catabolic process (GO:0006511)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			central_nervous_system(1)|kidney(1)|large_intestine(11)|liver(1)|lung(8)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	29						GGAAGCTTCTTCCTGGGAGCA	0.577													t|||	237	0.0473243	0.1679	0.0173	5008	,	,		18470	0.0		0.001	False		,,,				2504	0.002				p.K66E		Atlas-SNP	.											USP17L2,bladder,carcinoma,+2,1	USP17L2	47	1	0			c.A196G						scavenged	.						43.0	58.0	53.0					8																	11996074		1243	2766	4009	SO:0001583	missense	377630	exon1			GCTTCTTCCTGGG	BC156290	CCDS43713.1	8p23.1	2012-10-09	2012-10-09		ENSG00000223443	ENSG00000223443			34434	protein-coding gene	gene with protein product	"""deubiquitinating enzyme 3"""	610186	"""ubiquitin specific peptidase 17-like 2"""				Standard	NM_201402		Approved	DUB3	uc003wvc.1	Q6R6M4	OTTHUMG00000165295	ENST00000333796.3:c.196A>G	8.37:g.11996074T>C	ENSP00000333329:p.Lys66Glu	120.0	0.0	0		124.0	50.0	0.403226	NM_201402		Missense_Mutation	SNP	ENST00000333796.3	37	CCDS43713.1	135	0.061813186813186816	73	0.1483739837398374	17	0.04696132596685083	21	0.03671328671328671	24	0.0316622691292876	t	4.441	0.081611	0.08533	.	.	ENSG00000223443	ENST00000333796	T	0.11169	2.8	0.36	0.36	0.16097	.	0.863387	0.09306	N	0.820218	T	0.00039	0.0001	.	.	.	0.58432	P	1.999999999946489E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.41413	-0.9510	8	0.02654	T	1	.	2.3221	0.04213	0.0:0.39:0.3289:0.2811	.	66	Q6R6M4	U17L2_HUMAN	E	66	ENSP00000333329:K66E	ENSP00000333329:K66E	K	-	1	0	USP17L2	12033483	0.166000	0.22962	0.015000	0.15790	0.015000	0.08874	0.848000	0.27710	-0.366000	0.08064	-0.368000	0.07277	AAG	T|0.955;C|0.045	0.045	strong		0.577	USP17L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383303.2	NM_201402	
CLCC1	23155	hgsc.bcm.edu	37	1	109479953	109479953	+	Missense_Mutation	SNP	G	G	A	rs150665002		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:109479953G>A	ENST00000369971.2	-	10	1258	c.1129C>T	c.(1129-1131)Cgg>Tgg	p.R377W	CLCC1_ENST00000482889.1_Intron|CLCC1_ENST00000369970.3_Missense_Mutation_p.R327W|AKNAD1_ENST00000357393.4_Intron|CLCC1_ENST00000369976.1_Intron|CLCC1_ENST00000302500.4_Missense_Mutation_p.R256W|CLCC1_ENST00000415331.1_Missense_Mutation_p.R327W|CLCC1_ENST00000369968.2_Missense_Mutation_p.R192W|CLCC1_ENST00000356970.2_Missense_Mutation_p.R377W|CLCC1_ENST00000348264.2_Missense_Mutation_p.R192W|CLCC1_ENST00000369969.2_Missense_Mutation_p.R256W	NM_001048210.1	NP_001041675.1	Q96S66	CLCC1_HUMAN	chloride channel CLIC-like 1	377						chloride channel complex (GO:0034707)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	chloride channel activity (GO:0005254)			autonomic_ganglia(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|liver(1)|skin(1)	14		all_epithelial(167;0.000114)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.231)		CTTCTATCCCGTGGCCGAAGT	0.517													g|||	1	0.000199681	0.0008	0.0	5008	,	,		15244	0.0		0.0	False		,,,				2504	0.0				p.R377W		Atlas-SNP	.											.	CLCC1	55	.	0			c.C1129T						PASS	.	A	TRP/ARG,TRP/ARG	7,4399	11.4+/-27.6	0,7,2196	67.0	69.0	68.0		1129,979	2.7	0.0	1	dbSNP_134	68	0,8600		0,0,4300	yes	missense,missense	CLCC1	NM_001048210.1,NM_015127.3	101,101	0,7,6496	AA,AG,GG		0.0,0.1589,0.0538	probably-damaging,probably-damaging	377/552,327/502	109479953	7,12999	2203	4300	6503	SO:0001583	missense	23155	exon10			TATCCCGTGGCCG	AB018304	CCDS793.1, CCDS41362.1, CCDS60214.1, CCDS60215.1	1p13.3	2008-02-05			ENSG00000121940	ENSG00000121940			29675	protein-coding gene	gene with protein product	"""Mid1-related chloride channel (yeast)"""					9872452, 11279057	Standard	NM_001048210		Approved	MCLC	uc001dwf.2	Q96S66	OTTHUMG00000011732	ENST00000369971.2:c.1129C>T	1.37:g.109479953G>A	ENSP00000358988:p.Arg377Trp	97.0	0.0	0		106.0	54.0	0.509434	NM_001048210	O94861|Q8WYP8|Q8WYP9|Q9BU25	Missense_Mutation	SNP	ENST00000369971.2	37	CCDS41362.1	.	.	.	.	.	.	.	.	.	.	g	6.512	0.462630	0.12402	0.001589	0.0	ENSG00000121940	ENST00000356970;ENST00000369971;ENST00000415331;ENST00000369969;ENST00000369968;ENST00000369970;ENST00000348264;ENST00000302500	T;T;T;T;T;T;T;T	0.49720	0.77;0.77;0.77;0.77;0.77;0.77;0.77;0.77	5.57	2.72	0.32119	.	0.690178	0.15514	N	0.258371	T	0.08670	0.0215	N	0.08118	0	0.09310	N	1	B;B;B;B	0.22851	0.008;0.076;0.008;0.0	B;B;B;B	0.17433	0.006;0.018;0.006;0.001	T	0.24261	-1.0165	10	0.36615	T	0.2	-3.3681	4.209	0.10502	0.2394:0.4109:0.2766:0.0731	.	192;256;327;377	Q96S66-4;Q96S66-3;Q96S66-2;Q96S66	.;.;.;CLCC1_HUMAN	W	377;377;327;256;192;327;192;256	ENSP00000349456:R377W;ENSP00000358988:R377W;ENSP00000411591:R327W;ENSP00000358986:R256W;ENSP00000358985:R192W;ENSP00000358987:R327W;ENSP00000337243:R192W;ENSP00000306552:R256W	ENSP00000306552:R256W	R	-	1	2	CLCC1	109281476	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	0.037000	0.13840	0.422000	0.26005	-0.820000	0.03113	CGG	G|1.000;A|0.000	0.000	strong		0.517	CLCC1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032405.1	NM_015127	
OR2AE1	81392	hgsc.bcm.edu	37	7	99474007	99474007	+	Missense_Mutation	SNP	T	T	C	rs60737583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99474007T>C	ENST00000316368.2	-	1	673	c.650A>G	c.(649-651)tAt>tGt	p.Y217C		NM_001005276.1	NP_001005276.1	Q8NHA4	O2AE1_HUMAN	olfactory receptor, family 2, subfamily AE, member 1	217			Y -> C (in dbSNP:rs60737583).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(2)	11	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					GATGAAGACATAGGATGTAGA	0.488													T|||	372	0.0742812	0.2557	0.0288	5008	,	,		23905	0.001		0.002	False		,,,				2504	0.0112				p.Y217C		Atlas-SNP	.											.	OR2AE1	32	.	0			c.A650G						PASS	.	T	CYS/TYR	953,3453	361.1+/-315.5	103,747,1353	113.0	95.0	101.0		650	3.6	0.1	7	dbSNP_129	101	22,8578	14.0+/-48.4	0,22,4278	yes	missense	OR2AE1	NM_001005276.1	194	103,769,5631	CC,CT,TT		0.2558,21.6296,7.4965	probably-damaging	217/324	99474007	975,12031	2203	4300	6503	SO:0001583	missense	81392	exon1			AAGACATAGGATG	AC011904	CCDS34696.1	7q22.1	2014-02-19	2002-02-28		ENSG00000244623	ENSG00000244623		"""GPCR / Class A : Olfactory receptors"""	15087	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily AE, member 2"""	OR2AE2			Standard	NM_001005276		Approved		uc003usc.1	Q8NHA4	OTTHUMG00000156650	ENST00000316368.2:c.650A>G	7.37:g.99474007T>C	ENSP00000313936:p.Tyr217Cys	91.0	0.0	0		91.0	42.0	0.461538	NM_001005276	B2RPD2	Missense_Mutation	SNP	ENST00000316368.2	37	CCDS34696.1	140	0.0641025641025641	127	0.258130081300813	12	0.03314917127071823	0	0.0	1	0.0013192612137203166	T	13.17	2.158510	0.38119	0.216296	0.002558	ENSG00000244623	ENST00000316368	T	0.00520	6.85	3.62	3.62	0.41486	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36444	N	0.002597	T	0.00012	0.0000	H	0.95611	3.695	0.26077	P	0.9811449	D	0.89917	1.0	D	0.91635	0.999	T	0.23261	-1.0193	9	0.72032	D	0.01	.	10.8339	0.46675	0.0:0.0:0.0:1.0	rs60737583	217	Q8NHA4	O2AE1_HUMAN	C	217	ENSP00000313936:Y217C	ENSP00000313936:Y217C	Y	-	2	0	OR2AE1	99311943	1.000000	0.71417	0.058000	0.19502	0.189000	0.23516	5.082000	0.64450	1.877000	0.54381	0.405000	0.27470	TAT	T|0.932;C|0.068	0.068	strong		0.488	OR2AE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345053.1		
FSCN2	25794	hgsc.bcm.edu	37	17	79495890	79495890	+	Silent	SNP	C	C	T	rs117946784	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:79495890C>T	ENST00000417245.2	+	1	469	c.333C>T	c.(331-333)ttC>ttT	p.F111F	RP13-766D20.2_ENST00000442532.1_RNA|RP13-766D20.2_ENST00000430912.1_RNA|FSCN2_ENST00000334850.7_Silent_p.F111F	NM_001077182.2|NM_012418.3	NP_001070650.1|NP_036550.1	O14926	FSCN2_HUMAN	fascin actin-bundling protein 2, retinal	111					actin cytoskeleton organization (GO:0030036)|actin filament bundle assembly (GO:0051017)|anatomical structure morphogenesis (GO:0009653)|eye photoreceptor cell development (GO:0042462)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|stereocilium (GO:0032420)	actin binding (GO:0003779)|actin filament binding (GO:0051015)			endometrium(1)|lung(1)|prostate(1)|urinary_tract(1)	4	all_neural(118;0.0878)|Melanoma(429;0.242)		BRCA - Breast invasive adenocarcinoma(99;0.0282)|OV - Ovarian serous cystadenocarcinoma(97;0.0371)			GCCGCTTCTTCGGAGGCACCG	0.711													C|||	51	0.0101837	0.0023	0.0173	5008	,	,		15165	0.0		0.0209	False		,,,				2504	0.0153				p.F111F		Atlas-SNP	.											.	FSCN2	35	.	0			c.C333T						PASS	.	C	,	16,4090		0,16,2037	5.0	6.0	6.0		333,333	-1.7	0.9	17	dbSNP_132	6	130,8106		0,130,3988	no	coding-synonymous,coding-synonymous	FSCN2	NM_001077182.2,NM_012418.3	,	0,146,6025	TT,TC,CC		1.5784,0.3897,1.183	,	111/517,111/493	79495890	146,12196	2053	4118	6171	SO:0001819	synonymous_variant	25794	exon1			CTTCTTCGGAGGC	AF030165	CCDS45810.1, CCDS45811.1	17q25	2014-02-03	2014-02-03		ENSG00000186765	ENSG00000186765		"""Fascins"""	3960	protein-coding gene	gene with protein product		607643	"""fascin (Strongylocentrotus purpuratus) homolog 2 (actin-bundling protein, retinal)"", ""fascin homolog 2, actin-bundling protein, retinal (Strongylocentrotus purpuratus)"""			10234509	Standard	NM_012418		Approved	RP30, RFSN	uc010wuo.2	O14926	OTTHUMG00000167477	ENST00000417245.2:c.333C>T	17.37:g.79495890C>T		9.0	0.0	0		10.0	5.0	0.5	NM_001077182	A0AVC4|A8MRA6	Silent	SNP	ENST00000417245.2	37	CCDS45811.1																																																																																			C|0.990;T|0.010	0.010	strong		0.711	FSCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394746.1	NM_012418	
TRERF1	55809	hgsc.bcm.edu	37	6	42233529	42233529	+	Silent	SNP	G	G	A	rs79466811	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42233529G>A	ENST00000372922.4	-	6	2006	c.1444C>T	c.(1444-1446)Cta>Tta	p.L482L	TRERF1_ENST00000541110.1_Silent_p.L482L|TRERF1_ENST00000354325.2_Silent_p.L482L|TRERF1_ENST00000372917.4_Silent_p.L482L|TRERF1_ENST00000340840.2_Silent_p.L482L	NM_033502.2	NP_277037.1	Q96PN7	TREF1_HUMAN	transcriptional regulating factor 1	482	Interacts with CREBBP.				cholesterol catabolic process (GO:0006707)|homeostatic process (GO:0042592)|multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of hormone biosynthetic process (GO:0046885)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|steroid biosynthetic process (GO:0006694)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|RNA polymerase II transcription cofactor activity (GO:0001104)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(2)|endometrium(7)|kidney(1)|large_intestine(12)|lung(13)|ovary(3)|pancreas(1)|skin(3)|urinary_tract(2)	45	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			CCATCAGGTAGGTGCATCTAA	0.502													G|||	84	0.0167732	0.0605	0.0058	5008	,	,		18570	0.0		0.0	False		,,,				2504	0.0				p.L482L		Atlas-SNP	.											.	TRERF1	124	.	0			c.C1444T						PASS	.	G		239,4167	140.8+/-176.2	6,227,1970	56.0	54.0	55.0		1444	1.8	1.0	6	dbSNP_132	55	3,8597	3.7+/-12.6	0,3,4297	no	coding-synonymous	TRERF1	NM_033502.2		6,230,6267	AA,AG,GG		0.0349,5.4244,1.8607		482/1201	42233529	242,12764	2203	4300	6503	SO:0001819	synonymous_variant	55809	exon6			CAGGTAGGTGCAT	AF297872	CCDS4867.1, CCDS75455.1	6p21.1-p12.1	2012-09-25			ENSG00000124496	ENSG00000124496			18273	protein-coding gene	gene with protein product		610322	"""breast cancer anti-estrogen resistance 2"""	BCAR2		11349124	Standard	XM_005249223		Approved	TReP-132, HSA277276, RAPA, dJ139D8.5	uc003osd.2	Q96PN7	OTTHUMG00000014698	ENST00000372922.4:c.1444C>T	6.37:g.42233529G>A		87.0	0.0	0		96.0	42.0	0.4375	NM_033502	Q05GC6|Q7Z6T2|Q7Z6T3|Q9NQ72|Q9NQ73|Q9NUN9	Silent	SNP	ENST00000372922.4	37	CCDS4867.1																																																																																			G|0.981;A|0.019	0.019	strong		0.502	TRERF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040551.2	NM_033502	
SLC16A5	9121	hgsc.bcm.edu	37	17	73096199	73096199	+	Silent	SNP	C	C	T	rs142993518	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73096199C>T	ENST00000450736.2	+	4	856	c.441C>T	c.(439-441)ggC>ggT	p.G147G	SLC16A5_ENST00000329783.4_Silent_p.G147G|SLC16A5_ENST00000538213.2_Silent_p.G187G|SLC16A5_ENST00000580123.1_Silent_p.G147G			O15375	MOT6_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 5	147					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	22	all_lung(278;0.226)		LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235)		Pyruvic acid(DB00119)	CCTCGATGGGCGTCTCCCTGG	0.642													C|||	6	0.00119808	0.0045	0.0	5008	,	,		16275	0.0		0.0	False		,,,				2504	0.0				p.G147G		Atlas-SNP	.											.	SLC16A5	80	.	0			c.C441T						PASS	.	C		24,4382	30.8+/-60.4	0,24,2179	41.0	39.0	40.0		441	-7.9	0.0	17	dbSNP_134	40	0,8600		0,0,4300	no	coding-synonymous	SLC16A5	NM_004695.2		0,24,6479	TT,TC,CC		0.0,0.5447,0.1845		147/506	73096199	24,12982	2203	4300	6503	SO:0001819	synonymous_variant	9121	exon5			GATGGGCGTCTCC	U59299	CCDS11713.1	17q25.1	2013-07-18	2013-07-18		ENSG00000170190	ENSG00000170190		"""Solute carriers"""	10926	protein-coding gene	gene with protein product		603879	"""solute carrier family 16 (monocarboxylic acid transporters), member 5"", ""solute carrier family 16, member 5 (monocarboxylic acid transporter 6)"""			9425115	Standard	NM_004695		Approved	MCT5, MCT6	uc002jmr.4	O15375	OTTHUMG00000179277	ENST00000450736.2:c.441C>T	17.37:g.73096199C>T		130.0	0.0	0		123.0	52.0	0.422764	NM_001271765	B4E288	Silent	SNP	ENST00000450736.2	37	CCDS11713.1																																																																																			C|0.998;T|0.002	0.002	strong		0.642	SLC16A5-004	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445547.1	NM_004695	
HLA-DOA	3111	hgsc.bcm.edu	37	6	32976013	32976013	+	Silent	SNP	G	G	A	rs78635760|rs41541116|rs538455361	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32976013G>A	ENST00000229829.5	-	2	183	c.108C>T	c.(106-108)ccC>ccT	p.P36P	HLA-DOA_ENST00000450833.2_Silent_p.P6P|HLA-DOA_ENST00000495532.1_5'Flank	NM_002119.3	NP_002110.1	P06340	DOA_HUMAN	major histocompatibility complex, class II, DO alpha	36	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|immune response (GO:0006955)|negative regulation of antigen processing and presentation of peptide antigen via MHC class II (GO:0002587)|regulation of T cell differentiation (GO:0045580)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)	MHC class II protein complex binding (GO:0023026)|MHC class II receptor activity (GO:0032395)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(1)	9						GGTAGAAGGCGGGTCCGTAGG	0.522													G|||	65	0.0129792	0.0454	0.0072	5008	,	,		19086	0.0		0.0	False		,,,				2504	0.0				p.P36P		Atlas-SNP	.											HLA-DOA,colon,carcinoma,0,1	HLA-DOA	22	1	0			c.C108T						PASS	.	G		140,2880		7,126,1377	47.0	49.0	48.0		108	0.4	1.0	6	dbSNP_131	48	3,5411		0,3,2704	no	coding-synonymous	HLA-DOA	NM_002119.3		7,129,4081	AA,AG,GG		0.0554,4.6358,1.6955		36/251	32976013	143,8291	1510	2707	4217	SO:0001819	synonymous_variant	3111	exon2			GAAGGCGGGTCCG	M31525	CCDS4763.1	6p21.3	2013-01-11		2001-10-05	ENSG00000204252	ENSG00000204252		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4936	protein-coding gene	gene with protein product		142930		HLA-DZA, HLA-DNA		2370084	Standard	XM_005272804		Approved	HLA-D0-alpha	uc003ocr.3	P06340	OTTHUMG00000031211	ENST00000229829.5:c.108C>T	6.37:g.32976013G>A		66.0	0.0	0		89.0	60.0	0.674157	NM_002119	Q58HU0|Q58HU1|Q5STC7|Q9TQC6|Q9TQC7|Q9TQC8|Q9TQC9|Q9TQD0|Q9TQD1|Q9TQD2|Q9TQD3	Silent	SNP	ENST00000229829.5	37	CCDS4763.1	24	0.01098901098901099	21	0.042682926829268296	3	0.008287292817679558	0	0.0	0	0.0	G	11.11	1.541489	0.27563	0.046358	5.54E-4	ENSG00000204252	ENST00000432150	.	.	.	4.4	0.402	0.16344	.	0.265318	0.38720	N	0.001589	T	0.45577	0.1349	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48875	-0.8996	6	0.87932	D	0	.	5.2858	0.15700	0.0:0.0992:0.3715:0.5293	.	.	.	.	L	36	.	ENSP00000412819:P36L	P	-	2	0	HLA-DOA	33083991	0.970000	0.33590	0.999000	0.59377	0.977000	0.68977	-0.448000	0.06820	-0.008000	0.14320	-0.271000	0.10264	CCG	G|0.984;A|0.016	0.016	strong		0.522	HLA-DOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076426.2	NM_002119	
KMT2C	58508	hgsc.bcm.edu	37	7	151859495	151859495	+	Missense_Mutation	SNP	C	C	G	rs115580901	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:151859495C>G	ENST00000262189.6	-	43	11385	c.11167G>C	c.(11167-11169)Gct>Cct	p.A3723P	KMT2C_ENST00000355193.2_Missense_Mutation_p.A3723P	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	3723					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TCTGTCTCAGCCTTTTCCAGT	0.478													C|||	9	0.00179712	0.0061	0.0014	5008	,	,		19613	0.0		0.0	False		,,,				2504	0.0				p.A3723P		Atlas-SNP	.											.	MLL3	1564	.	0			c.G11167C						PASS	.	C	PRO/ALA	19,4387	26.2+/-53.5	0,19,2184	177.0	181.0	180.0		11167	-2.0	0.0	7	dbSNP_133	180	0,8600		0,0,4300	yes	missense	MLL3	NM_170606.2	27	0,19,6484	GG,GC,CC		0.0,0.4312,0.1461	benign	3723/4912	151859495	19,12987	2203	4300	6503	SO:0001583	missense	58508	exon43			TCTCAGCCTTTTC	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.11167G>C	7.37:g.151859495C>G	ENSP00000262189:p.Ala3723Pro	158.0	0.0	0		176.0	93.0	0.528409	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	3|3	0.0013736263736263737|0.0013736263736263737	3|3	0.006097560975609756|0.006097560975609756	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	5.391|5.391	0.257270|0.257270	0.10239|0.10239	0.004312|0.004312	0.0|0.0	ENSG00000055609|ENSG00000055609	ENST00000262189;ENST00000355193;ENST00000424877|ENST00000360104	D;D;D|.	0.89415|.	-1.83;-1.81;-2.51|.	5.51|5.51	-2.01|-2.01	0.07410|0.07410	.|.	0.151901|.	0.29660|.	U|.	0.011527|.	T|T	0.18341|0.18341	0.0440|0.0440	L|L	0.29908|0.29908	0.895|0.895	0.29679|0.29679	N|N	0.841841|0.841841	B;B;B|.	0.10296|.	0.002;0.001;0.003|.	B;B;B|.	0.09377|.	0.003;0.003;0.004|.	T|T	0.24440|0.24440	-1.0160|-1.0160	10|5	0.37606|.	T|.	0.19|.	.|.	2.0729|2.0729	0.03618|0.03618	0.1792:0.4224:0.1773:0.2212|0.1792:0.4224:0.1773:0.2212	.|.	3723;2784;3723|.	Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3|.	MLL3_HUMAN;.;.|.	P|A	3723;3723;309|1228	ENSP00000262189:A3723P;ENSP00000347325:A3723P;ENSP00000410411:A309P|.	ENSP00000262189:A3723P|.	A|G	-|-	1|2	0|0	MLL3|MLL3	151490428|151490428	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.471000|0.471000	0.32888|0.32888	-0.542000|-0.542000	0.06091|0.06091	-1.225000|-1.225000	0.02578|0.02578	-1.938000|-1.938000	0.00498|0.00498	GCT|GGC	C|0.998;G|0.002	0.002	strong		0.478	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
TMEM200B	399474	hgsc.bcm.edu	37	1	29447765	29447765	+	Silent	SNP	G	G	T	rs115927590	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:29447765G>T	ENST00000420504.2	-	2	733	c.576C>A	c.(574-576)tcC>tcA	p.S192S	TMEM200B_ENST00000521452.1_Silent_p.S192S	NM_001171868.1	NP_001165339.1	Q69YZ2	T200B_HUMAN	transmembrane protein 200B	192	Pro-rich.					integral component of membrane (GO:0016021)				ovary(1)	1		Colorectal(325;3.46e-05)|Breast(348;0.00765)|Lung NSC(340;0.0153)|all_lung(284;0.0173)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;7.32e-08)|COAD - Colon adenocarcinoma(152;4.92e-06)|STAD - Stomach adenocarcinoma(196;0.00618)|BRCA - Breast invasive adenocarcinoma(304;0.0501)|READ - Rectum adenocarcinoma(331;0.0649)|KIRC - Kidney renal clear cell carcinoma(1967;0.126)		CCCGACGCGGGGACGGGTCCC	0.692													G|||	46	0.0091853	0.0325	0.0043	5008	,	,		14044	0.0		0.0	False		,,,				2504	0.0				p.S192S		Atlas-SNP	.											.	TMEM200B	9	.	0			c.C576A						PASS	.	G	,	98,4306		2,94,2106	16.0	17.0	17.0		576,576	1.4	1.0	1	dbSNP_132	17	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous	TMEM200B	NM_001003682.3,NM_001171868.1	,	2,94,6404	TT,TG,GG		0.0,2.2252,0.7538	,	192/308,192/308	29447765	98,12902	2202	4298	6500	SO:0001819	synonymous_variant	399474	exon2			ACGCGGGGACGGG		CCDS30658.1	1p35	2007-12-18			ENSG00000253304	ENSG00000253304			33785	protein-coding gene	gene with protein product						15722956	Standard	NM_001003682		Approved	TTMB	uc001brn.2	Q69YZ2	OTTHUMG00000003658	ENST00000420504.2:c.576C>A	1.37:g.29447765G>T		72.0	0.0	0		56.0	23.0	0.410714	NM_001171868	Q6P2G8|Q6P2Q5	Silent	SNP	ENST00000420504.2	37	CCDS30658.1																																																																																			G|0.990;T|0.010	0.010	strong		0.692	TMEM200B-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010377.2	NM_001003682	
NOS3	4846	hgsc.bcm.edu	37	7	150710392	150710392	+	Silent	SNP	G	G	A	rs3730011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150710392G>A	ENST00000297494.3	+	25	3537	c.3180G>A	c.(3178-3180)gaG>gaA	p.E1060E	ATG9B_ENST00000377974.2_3'UTR|NOS3_ENST00000461406.1_Silent_p.E854E|NOS3_ENST00000477227.1_3'UTR|ATG9B_ENST00000444312.1_3'UTR|ATG9B_ENST00000494791.1_5'UTR|ATG9B_ENST00000605938.1_3'UTR	NM_000603.4	NP_000594.2	P60323	NANO3_HUMAN	nitric oxide synthase 3 (endothelial cell)	0					germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic signaling pathway (GO:2001234)|oogenesis (GO:0048477)|regulation of cell cycle (GO:0051726)|regulation of translation (GO:0006417)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytoplasmic stress granule (GO:0010494)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(6)|liver(2)|lung(11)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	50	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ACCGCGACGAGGTGCAGAACG	0.642											OREG0018443	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	18	0.00359425	0.0136	0.0	5008	,	,		13957	0.0		0.0	False		,,,				2504	0.0				p.E1060E		Atlas-SNP	.											NOS3,NS,carcinoma,+2,1	NOS3	131	1	0			c.G3180A						PASS	.	G	,	49,4357	50.2+/-85.5	1,47,2155	77.0	72.0	74.0		3180,	4.2	1.0	7	dbSNP_107	74	0,8600		0,0,4300	no	coding-synonymous,utr-3	NOS3,ATG9B	NM_000603.4,NM_173681.5	,	1,47,6455	AA,AG,GG		0.0,1.1121,0.3767	,	1060/1204,	150710392	49,12957	2203	4300	6503	SO:0001819	synonymous_variant	4846	exon25			CGACGAGGTGCAG		CCDS5912.1, CCDS55182.1, CCDS55183.1	7q36	2007-02-15			ENSG00000164867	ENSG00000164867	1.14.13.39		7876	protein-coding gene	gene with protein product	"""endothelial nitric oxide synthase"""	163729				1379542	Standard	NM_000603		Approved	ECNOS, eNOS	uc003wif.3	P29474	OTTHUMG00000158343	ENST00000297494.3:c.3180G>A	7.37:g.150710392G>A		68.0	0.0	0	1734	75.0	41.0	0.546667	NM_000603	Q495E5	Silent	SNP	ENST00000297494.3	37	CCDS5912.1																																																																																			G|0.995;A|0.005	0.005	strong		0.642	NOS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350750.2	NM_000603	
CACNA1S	779	hgsc.bcm.edu	37	1	201046164	201046164	+	Missense_Mutation	SNP	C	C	T	rs114191482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:201046164C>T	ENST00000362061.3	-	12	1937	c.1711G>A	c.(1711-1713)Gtc>Atc	p.V571I	CACNA1S_ENST00000367338.3_Missense_Mutation_p.V571I	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	571					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	GCGAAGATGACGATGAAGAGG	0.557													C|||	8	0.00159744	0.0053	0.0	5008	,	,		23357	0.001		0.0	False		,,,				2504	0.0				p.V571I		Atlas-SNP	.											.	CACNA1S	249	.	0			c.G1711A						PASS	.	C	ILE/VAL	29,4377	37.6+/-69.7	0,29,2174	152.0	135.0	141.0		1711	-2.8	1.0	1	dbSNP_132	141	0,8600		0,0,4300	yes	missense	CACNA1S	NM_000069.2	29	0,29,6474	TT,TC,CC		0.0,0.6582,0.223	benign	571/1874	201046164	29,12977	2203	4300	6503	SO:0001583	missense	779	exon12			AGATGACGATGAA	L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.1711G>A	1.37:g.201046164C>T	ENSP00000355192:p.Val571Ile	311.0	0.0	0		368.0	187.0	0.508152	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Missense_Mutation	SNP	ENST00000362061.3	37	CCDS1407.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	0	0.0	C	4.708	0.131666	0.08981	0.006582	0.0	ENSG00000081248	ENST00000362061;ENST00000367338	D;D	0.98381	-4.9;-4.9	4.45	-2.76	0.05896	Ion transport (1);	0.302241	0.36034	N	0.002837	D	0.87888	0.6291	N	0.11201	0.11	0.24428	N	0.994582	B	0.06786	0.001	B	0.08055	0.003	T	0.82733	-0.0311	10	0.02654	T	1	.	8.3162	0.32102	0.1089:0.1105:0.0:0.7805	.	571	Q13698	CAC1S_HUMAN	I	571	ENSP00000355192:V571I;ENSP00000356307:V571I	ENSP00000355192:V571I	V	-	1	0	CACNA1S	199312787	0.896000	0.30565	0.989000	0.46669	0.995000	0.86356	-0.005000	0.12855	-0.570000	0.06022	0.549000	0.68633	GTC	C|0.997;T|0.003	0.003	strong		0.557	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
NLRC3	197358	hgsc.bcm.edu	37	16	3606947	3606947	+	RNA	SNP	G	G	T	rs116349864	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3606947G>T	ENST00000301749.7	-	0	2553				NLRC3_ENST00000603507.1_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000448023.2_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TCTTCAAAGCGTCTGCCAGCG	0.582													g|||	78	0.0155751	0.056	0.0058	5008	,	,		18998	0.0		0.0	False		,,,				2504	0.0				p.D716E		Atlas-SNP	.											.	NLRC3	103	.	0			c.C2148A						PASS	.	A	GLU/ASP	187,3749		5,177,1786	78.0	87.0	84.0		2148	-7.0	0.6	16	dbSNP_132	84	1,8305		0,1,4152	yes	missense	NLRC3	NM_178844.2	45	5,178,5938	TT,TG,GG		0.012,4.751,1.5357	benign	716/1066	3606947	188,12054	1968	4153	6121			197358	exon8			CAAAGCGTCTGCC	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"""Nucleotide-binding domain and leucine rich repeat containing"""	29889	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3"", ""NOD-like receptor C3"""	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3606947G>T		108.0	0.0	0		90.0	46.0	0.511111	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	37		26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	g	13.03	2.114951	0.37339	0.04751	1.2E-4	ENSG00000167984	ENST00000419350;ENST00000301749;ENST00000359128;ENST00000448023	T;T;T	0.50548	0.74;0.74;0.74	5.37	-6.97	0.01616	.	0.127878	0.52532	N	0.000077	T	0.04318	0.0119	.	.	.	0.20563	N	0.999887	B	0.28026	0.198	B	0.34138	0.176	T	0.15780	-1.0425	9	0.18276	T	0.48	.	7.4907	0.27460	0.6283:0.0:0.1808:0.1909	.	763	C9JLH9	.	E	716;716;716;763	ENSP00000301749:D716E;ENSP00000352039:D716E;ENSP00000414415:D763E	ENSP00000301749:D716E	D	-	3	2	NLRC3	3546948	0.002000	0.14202	0.606000	0.28943	0.419000	0.31324	-1.356000	0.02609	-1.733000	0.01357	-2.239000	0.00288	GAC	G|0.985;T|0.015	0.015	strong		0.582	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844	
CHST12	55501	hgsc.bcm.edu	37	7	2472599	2472599	+	Missense_Mutation	SNP	C	C	A	rs17132395	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:2472599C>A	ENST00000258711.6	+	2	460	c.325C>A	c.(325-327)Cgc>Agc	p.R109S		NM_001243794.1|NM_001243795.1|NM_018641.4	NP_001230723.1|NP_001230724.1|NP_061111.1	Q9NRB3	CHSTC_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 12	109			R -> S (in dbSNP:rs17132395).		carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|chondroitin 4-sulfotransferase activity (GO:0047756)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	21		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0847)|OV - Ovarian serous cystadenocarcinoma(56;2.25e-13)		CTGGTCCCCGCGCGACGCCCG	0.711													C|||	141	0.028155	0.0976	0.0159	5008	,	,		13900	0.0		0.001	False		,,,				2504	0.0				p.R109S		Atlas-SNP	.											.	CHST12	39	.	0			c.C325A						PASS	.	C	SER/ARG	357,4031		15,327,1852	19.0	25.0	23.0		325	5.0	0.0	7	dbSNP_123	23	2,8568		0,2,4283	no	missense	CHST12	NM_018641.4	110	15,329,6135	AA,AC,CC		0.0233,8.1358,2.7705	benign	109/415	2472599	359,12599	2194	4285	6479	SO:0001583	missense	55501	exon2			TCCCCGCGCGACG	AF239822	CCDS5333.1	7p22	2007-03-14			ENSG00000136213	ENSG00000136213	2.8.2.5	"""Sulfotransferases, membrane-bound"""	17423	protein-coding gene	gene with protein product		610129				10781601	Standard	NM_018641		Approved	C4S-2, C4ST2	uc021zyu.1	Q9NRB3	OTTHUMG00000023849	ENST00000258711.6:c.325C>A	7.37:g.2472599C>A	ENSP00000258711:p.Arg109Ser	10.0	0.0	0		10.0	8.0	0.8	NM_018641	A4D1Z9|Q502W3|Q9NXY7	Missense_Mutation	SNP	ENST00000258711.6	37	CCDS5333.1	53	0.024267399267399268	48	0.0975609756097561	5	0.013812154696132596	0	0.0	0	0.0	C	4.045	0.006027	0.07866	0.081358	2.33E-4	ENSG00000136213	ENST00000258711;ENST00000432336	T;T	0.61742	0.08;0.92	4.98	4.98	0.66077	.	0.798952	0.11372	N	0.570741	T	0.01029	0.0034	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.06405	0.002	T	0.00870	-1.1533	10	0.08837	T	0.75	1.0898	13.2418	0.60002	0.1591:0.8409:0.0:0.0	rs17132395;rs17132395	109	Q9NRB3	CHSTC_HUMAN	S	109	ENSP00000258711:R109S;ENSP00000411207:R109S	ENSP00000258711:R109S	R	+	1	0	CHST12	2439125	0.002000	0.14202	0.022000	0.16811	0.456000	0.32438	1.538000	0.36094	2.304000	0.77564	0.561000	0.74099	CGC	C|0.976;A|0.024	0.024	strong		0.711	CHST12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060170.3	NM_018641	
PTGFRN	5738	hgsc.bcm.edu	37	1	117452869	117452869	+	Missense_Mutation	SNP	C	C	G	rs77292583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:117452869C>G	ENST00000393203.2	+	1	191	c.44C>G	c.(43-45)tCg>tGg	p.S15W	RP4-753F5.1_ENST00000610171.1_lincRNA	NM_020440.2	NP_065173.2	Q9P2B2	FPRP_HUMAN	prostaglandin F2 receptor inhibitor	15					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)		GCGCTCCTGTCGTTGGGTGAG	0.786													C|||	146	0.0291534	0.1074	0.0058	5008	,	,		7813	0.0		0.0	False		,,,				2504	0.0				p.S15W		Atlas-SNP	.											PTGFRN,NS,carcinoma,0,1	PTGFRN	91	1	0			c.C44G						PASS	.	C	TRP/SER	237,3861		2,233,1814	4.0	6.0	5.0		44	0.3	0.1	1	dbSNP_132	5	3,8095		0,3,4046	no	missense	PTGFRN	NM_020440.2	177	2,236,5860	GG,GC,CC		0.037,5.7833,1.9679	benign	15/880	117452869	240,11956	2049	4049	6098	SO:0001583	missense	5738	exon1			TCCTGTCGTTGGG	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.44C>G	1.37:g.117452869C>G	ENSP00000376899:p.Ser15Trp	16.0	0.0	0		8.0	4.0	0.5	NM_020440	Q5VVU9|Q8N2K6	Missense_Mutation	SNP	ENST00000393203.2	37	CCDS890.1	47	0.02152014652014652	45	0.09146341463414634	2	0.0055248618784530384	0	0.0	0	0.0	C	5.911	0.352168	0.11182	0.057833	3.7E-4	ENSG00000134247	ENST00000393203	T	0.03982	3.74	3.41	0.296	0.15757	Immunoglobulin-like (1);	6.098340	0.00166	N	0.000011	T	0.01156	0.0038	N	0.14661	0.345	0.44214	D	0.997042	B	0.02656	0.0	B	0.01281	0.0	T	0.33394	-0.9870	10	0.66056	D	0.02	0.1948	3.6279	0.08120	0.0:0.498:0.2382:0.2638	.	15	Q9P2B2	FPRP_HUMAN	W	15	ENSP00000376899:S15W	ENSP00000376899:S15W	S	+	2	0	PTGFRN	117254392	0.444000	0.25649	0.089000	0.20774	0.001000	0.01503	-0.612000	0.05616	-0.140000	0.11394	-0.481000	0.04817	TCG	C|0.978;G|0.022	0.022	strong		0.786	PTGFRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033271.1	NM_020440	
TMEM156	80008	hgsc.bcm.edu	37	4	39033851	39033851	+	Missense_Mutation	SNP	G	G	A	rs61732938	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:39033851G>A	ENST00000381938.3	-	1	190	c.83C>T	c.(82-84)cCg>cTg	p.P28L	TMEM156_ENST00000372489.2_5'UTR	NM_024943.1	NP_079219.1	Q8N614	TM156_HUMAN	transmembrane protein 156	28						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(3)|lung(3)|ovary(1)|skin(1)|stomach(1)	10						CTCACCTTTCGGTGTCTTGAA	0.333													G|||	9	0.00179712	0.0061	0.0014	5008	,	,		16764	0.0		0.0	False		,,,				2504	0.0				p.P28L		Atlas-SNP	.											.	TMEM156	31	.	0			c.C83T						PASS	.	G	LEU/PRO	28,4376	31.7+/-61.6	0,28,2174	50.0	47.0	48.0		83	3.7	1.0	4	dbSNP_129	48	0,8600		0,0,4300	yes	missense	TMEM156	NM_024943.1	98	0,28,6474	AA,AG,GG		0.0,0.6358,0.2153	benign	28/297	39033851	28,12976	2202	4300	6502	SO:0001583	missense	80008	exon1			CCTTTCGGTGTCT	AK026888	CCDS3448.1	4p14	2008-02-05			ENSG00000121895	ENSG00000121895			26260	protein-coding gene	gene with protein product						12477932	Standard	NM_024943		Approved	FLJ23235	uc003gto.3	Q8N614	OTTHUMG00000128582	ENST00000381938.3:c.83C>T	4.37:g.39033851G>A	ENSP00000371364:p.Pro28Leu	79.0	0.0	0		75.0	37.0	0.493333	NM_024943	Q9H5N9	Missense_Mutation	SNP	ENST00000381938.3	37	CCDS3448.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	0.012	-1.665798	0.00765	0.006358	0.0	ENSG00000121895	ENST00000381938;ENST00000344606	T;T	0.42513	1.98;0.97	5.39	3.65	0.41850	.	0.637311	0.14864	N	0.293940	T	0.19485	0.0468	L	0.34521	1.04	0.40731	D	0.982742	B	0.26902	0.163	B	0.22880	0.042	T	0.03384	-1.1042	10	0.09590	T	0.72	-3.7493	7.8212	0.29288	0.1868:0.0:0.8132:0.0	.	28	Q8N614	TM156_HUMAN	L	28	ENSP00000371364:P28L;ENSP00000343758:P28L	ENSP00000343758:P28L	P	-	2	0	TMEM156	38710246	0.962000	0.33011	0.992000	0.48379	0.081000	0.17604	1.670000	0.37502	1.404000	0.46819	-0.216000	0.12614	CCG	G|0.998;A|0.002	0.002	strong		0.333	TMEM156-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250435.3	NM_024943	
OR4S2	219431	hgsc.bcm.edu	37	11	55419147	55419147	+	Silent	SNP	C	C	T	rs74538149	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55419147C>T	ENST00000312422.2	+	1	768	c.768C>T	c.(766-768)taC>taT	p.Y256Y		NM_001004059.2	NP_001004059.2	Q8NH73	OR4S2_HUMAN	olfactory receptor, family 4, subfamily S, member 2	256						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(4)|lung(28)|ovary(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_epithelial(135;0.0748)				CTTTTATGTACATGCGCCCTG	0.463													c|||	56	0.0111821	0.0416	0.0014	5008	,	,		14395	0.0		0.0	False		,,,				2504	0.0				p.Y256Y		Atlas-SNP	.											.	OR4S2	89	.	0			c.C768T						PASS	.	C		169,4189		21,127,2031	161.0	136.0	145.0		768	0.1	1.0	11	dbSNP_132	145	3,8047		0,3,4022	yes	coding-synonymous	OR4S2	NM_001004059.2		21,130,6053	TT,TC,CC		0.0373,3.8779,1.3862		256/312	55419147	172,12236	2179	4025	6204	SO:0001819	synonymous_variant	219431	exon1			TATGTACATGCGC	BK004390	CCDS31505.1	11q11	2012-08-09	2002-11-13	2002-11-15	ENSG00000174982	ENSG00000174982		"""GPCR / Class A : Olfactory receptors"""	15183	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily S, member 2 pseudogene"""	OR4S2P			Standard	NM_001004059		Approved	OST725	uc001nhs.1	Q8NH73	OTTHUMG00000166799	ENST00000312422.2:c.768C>T	11.37:g.55419147C>T		111.0	1.0	0.00900901		73.0	72.0	0.986301	NM_001004059	Q6IF72	Silent	SNP	ENST00000312422.2	37	CCDS31505.1																																																																																			C|0.988;T|0.012	0.012	strong		0.463	OR4S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391503.1	NM_001004059	
MYO10	4651	hgsc.bcm.edu	37	5	16682062	16682062	+	Silent	SNP	C	C	T	rs16868979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:16682062C>T	ENST00000513610.1	-	31	4561	c.4107G>A	c.(4105-4107)ccG>ccA	p.P1369P	MYO10_ENST00000515803.1_Silent_p.P708P|MYO10_ENST00000427430.2_Silent_p.P726P|MYO10_ENST00000505695.1_Silent_p.P708P|MYO10_ENST00000274203.9_Silent_p.P726P	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	1369					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						GCATCTCCTCCGGCGTGTCGG	0.587													C|||	141	0.028155	0.0998	0.0058	5008	,	,		17271	0.0		0.0	False		,,,				2504	0.0051				p.P1369P		Atlas-SNP	.											MYO10,NS,carcinoma,0,1	MYO10	198	1	0			c.G4107A						PASS	.	C		367,3887		21,325,1781	112.0	113.0	113.0		4107	-11.6	0.4	5	dbSNP_123	113	2,8458		0,2,4228	no	coding-synonymous	MYO10	NM_012334.2		21,327,6009	TT,TC,CC		0.0236,8.6272,2.9023		1369/2059	16682062	369,12345	2127	4230	6357	SO:0001819	synonymous_variant	4651	exon31			CTCCTCCGGCGTG	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"""Myosins / Myosin superfamily : Class X"", ""Pleckstrin homology (PH) domain containing"""	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.4107G>A	5.37:g.16682062C>T		111.0	0.0	0		127.0	64.0	0.503937	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	37	CCDS54834.1																																																																																			C|0.960;T|0.040	0.040	strong		0.587	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
CIZ1	25792	hgsc.bcm.edu	37	9	130948018	130948018	+	Silent	SNP	G	G	A	rs45545033	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:130948018G>A	ENST00000393608.1	-	5	598	c.396C>T	c.(394-396)ctC>ctT	p.L132L	CIZ1_ENST00000476727.2_5'UTR|CIZ1_ENST00000538431.1_Silent_p.L132L|CIZ1_ENST00000372948.3_Silent_p.L132L|CIZ1_ENST00000372954.1_Silent_p.L108L|CIZ1_ENST00000372938.5_Silent_p.L132L|CIZ1_ENST00000541172.1_Silent_p.L31L|CIZ1_ENST00000277465.4_Silent_p.L132L|CIZ1_ENST00000357558.5_Silent_p.L132L|CIZ1_ENST00000325721.8_Silent_p.L108L	NM_012127.2	NP_036259.2	Q9ULV3	CIZ1_HUMAN	CDKN1A interacting zinc finger protein 1	132					maintenance of protein location in nucleus (GO:0051457)|positive regulation of DNA-dependent DNA replication initiation (GO:0032298)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|liver(1)|lung(9)|ovary(3)|prostate(2)|urinary_tract(2)	35						TGGGGGCTGCGAGGCCTGGGG	0.602													G|||	162	0.0323482	0.1165	0.0115	5008	,	,		16972	0.0		0.0	False		,,,				2504	0.0				p.L162L		Atlas-SNP	.											.	CIZ1	75	.	0			c.C486T						PASS	.	G	,,,,	520,3886	238.4+/-249.8	36,448,1719	38.0	38.0	38.0		396,396,396,324,396	0.2	0.0	9	dbSNP_127	38	8,8592	3.7+/-12.6	0,8,4292	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CIZ1	NM_001131015.1,NM_001131016.1,NM_001131017.1,NM_001131018.1,NM_012127.2	,,,,	36,456,6011	AA,AG,GG		0.093,11.8021,4.0597	,,,,	132/843,132/899,132/838,108/819,132/899	130948018	528,12478	2203	4300	6503	SO:0001819	synonymous_variant	25792	exon5			GGCTGCGAGGCCT	AB030835	CCDS6894.1, CCDS48033.1, CCDS48034.1, CCDS75910.1	9q34.1	2012-10-05			ENSG00000148337	ENSG00000148337			16744	protein-coding gene	gene with protein product		611420				10529385	Standard	NM_001131015		Approved	LSFR1, ZNF356	uc011mas.2	Q9ULV3	OTTHUMG00000020735	ENST00000393608.1:c.396C>T	9.37:g.130948018G>A		49.0	0.0	0		63.0	43.0	0.68254	NM_001257975	A8K9J8|B4E131|B7ZAS8|Q5SYW3|Q5SYW5|Q8WU72|Q9H868|Q9NYM8|Q9UHK4|Q9Y3F9|Q9Y3G0	Silent	SNP	ENST00000393608.1	37	CCDS6894.1																																																																																			G|0.962;A|0.038	0.038	strong		0.602	CIZ1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054399.1	NM_012127	
ALDH8A1	64577	hgsc.bcm.edu	37	6	135271178	135271178	+	Missense_Mutation	SNP	T	T	C	rs56954234	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:135271178T>C	ENST00000265605.2	-	1	82	c.14A>G	c.(13-15)aAc>aGc	p.N5S	ALDH8A1_ENST00000367845.2_Missense_Mutation_p.N5S|ALDH8A1_ENST00000367847.2_Missense_Mutation_p.N5S	NM_022568.3	NP_072090.1	Q9H2A2	AL8A1_HUMAN	aldehyde dehydrogenase 8 family, member A1	5					9-cis-retinoic acid biosynthetic process (GO:0042904)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	retinal dehydrogenase activity (GO:0001758)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	36	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00401)|GBM - Glioblastoma multiforme(68;0.0058)		CAAAAGTGCGTTTGTTCCAGC	0.453													T|||	71	0.0141773	0.0514	0.0043	5008	,	,		19775	0.0		0.0	False		,,,				2504	0.0				p.N5S		Atlas-SNP	.											.	ALDH8A1	68	.	0			c.A14G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN	141,4265	98.9+/-137.6	3,135,2065	102.0	102.0	102.0		14,14,14	-1.8	0.0	6	dbSNP_129	102	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense	ALDH8A1	NM_001193480.1,NM_022568.3,NM_170771.2	46,46,46	3,138,6362	CC,CT,TT		0.0349,3.2002,1.1072	benign,benign,benign	5/438,5/488,5/434	135271178	144,12862	2203	4300	6503	SO:0001583	missense	64577	exon1			AGTGCGTTTGTTC	AL021939	CCDS5171.1, CCDS5172.1, CCDS55057.1	6q24.1-q25.1	2008-07-03			ENSG00000118514	ENSG00000118514		"""Aldehyde dehydrogenases"""	15471	protein-coding gene	gene with protein product		606467				11007799	Standard	NM_001193480		Approved	ALDH12	uc003qew.3	Q9H2A2	OTTHUMG00000015623	ENST00000265605.2:c.14A>G	6.37:g.135271178T>C	ENSP00000265605:p.Asn5Ser	87.0	0.0	0		110.0	43.0	0.390909	NM_022568	B7Z521|O60793|Q24JS9|Q53GT3|Q5TI80	Missense_Mutation	SNP	ENST00000265605.2	37	CCDS5171.1	33	0.01510989010989011	30	0.06097560975609756	3	0.008287292817679558	0	0.0	0	0.0	T	14.25	2.479974	0.44044	0.032002	3.49E-4	ENSG00000118514	ENST00000265605;ENST00000367845;ENST00000367847	T;T;T	0.75154	-0.91;-0.88;-0.87	6.14	-1.83	0.07833	.	1.633190	0.02930	N	0.139121	T	0.28699	0.0711	N	0.11560	0.145	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.07121	-1.0789	10	0.21014	T	0.42	.	6.0545	0.19804	0.1131:0.3306:0.0:0.5563	rs56954234;rs61731728	5;5;5	B7Z521;Q9H2A2-2;Q9H2A2	.;.;AL8A1_HUMAN	S	5	ENSP00000265605:N5S;ENSP00000356819:N5S;ENSP00000356821:N5S	ENSP00000265605:N5S	N	-	2	0	ALDH8A1	135312871	0.000000	0.05858	0.000000	0.03702	0.932000	0.56968	0.157000	0.16402	-0.524000	0.06400	0.529000	0.55759	AAC	T|0.985;C|0.015	0.015	strong		0.453	ALDH8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042334.2		
LIPE	3991	hgsc.bcm.edu	37	19	42906914	42906914	+	Missense_Mutation	SNP	G	G	T	rs7246232	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42906914G>T	ENST00000244289.4	-	9	3088	c.2812C>A	c.(2812-2814)Cgt>Agt	p.R938S	LIPE-AS1_ENST00000594624.2_RNA|LIPE-AS1_ENST00000597203.1_RNA|LIPE-AS1_ENST00000599276.1_RNA|LIPE-AS1_ENST00000593491.2_RNA	NM_005357.2	NP_005348.2	Q05469	LIPS_HUMAN	lipase, hormone-sensitive	938			R -> S (in dbSNP:rs7246232). {ECO:0000269|Ref.3}.		cholesterol metabolic process (GO:0008203)|diacylglycerol catabolic process (GO:0046340)|lipid catabolic process (GO:0016042)|long-chain fatty acid catabolic process (GO:0042758)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)	hormone-sensitive lipase activity (GO:0033878)|triglyceride lipase activity (GO:0004806)			breast(2)|endometrium(4)|kidney(7)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		Prostate(69;0.00682)				AAGGCGGCACGGACGCCCAGG	0.602													G|||	101	0.0201677	0.0711	0.0072	5008	,	,		16054	0.0		0.002	False		,,,				2504	0.0				p.R938S		Atlas-SNP	.											.	LIPE	83	.	0			c.C2812A						PASS	.	G	SER/ARG	227,4179	135.7+/-171.8	6,215,1982	72.0	61.0	64.0		2812	-10.8	0.0	19	dbSNP_116	64	11,8589	8.4+/-32.0	0,11,4289	yes	missense	LIPE	NM_005357.2	110	6,226,6271	TT,TG,GG		0.1279,5.1521,1.8299	benign	938/1077	42906914	238,12768	2203	4300	6503	SO:0001583	missense	3991	exon9			CGGCACGGACGCC	L11706	CCDS12607.1	19q13.1-q13.2	2014-03-14			ENSG00000079435	ENSG00000079435	3.1.1.3		6621	protein-coding gene	gene with protein product		151750				8506334	Standard	NM_005357		Approved	HSL	uc002otr.3	Q05469	OTTHUMG00000182814	ENST00000244289.4:c.2812C>A	19.37:g.42906914G>T	ENSP00000244289:p.Arg938Ser	115.0	0.0	0		122.0	57.0	0.467213	NM_005357	Q3LRT2|Q6NSL7	Missense_Mutation	SNP	ENST00000244289.4	37	CCDS12607.1	49	0.022435897435897436	44	0.08943089430894309	3	0.008287292817679558	0	0.0	2	0.002638522427440633	G	6.053	0.378025	0.11466	0.051521	0.001279	ENSG00000079435	ENST00000244289	T	0.03272	3.99	5.38	-10.8	0.00216	.	1.425700	0.04445	N	0.371619	T	0.00109	0.0003	N	0.19112	0.55	0.09310	N	1	B	0.09022	0.002	B	0.15870	0.014	T	0.33727	-0.9857	10	0.26408	T	0.33	5.9579	9.2186	0.37362	0.0796:0.1474:0.6138:0.1592	rs7246232;rs56962270;rs7246232	938	Q05469	LIPS_HUMAN	S	938	ENSP00000244289:R938S	ENSP00000244289:R938S	R	-	1	0	LIPE	47598754	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.465000	0.00995	-3.013000	0.00272	-1.669000	0.00746	CGT	G|0.970;T|0.030	0.030	strong		0.602	LIPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463861.1	NM_005357	
FAM114A1	92689	hgsc.bcm.edu	37	4	38933869	38933869	+	Missense_Mutation	SNP	C	C	T	rs36058104	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:38933869C>T	ENST00000358869.2	+	12	1513	c.1337C>T	c.(1336-1338)tCg>tTg	p.S446L	FAM114A1_ENST00000515037.1_Missense_Mutation_p.S239L	NM_138389.2	NP_612398.2	Q8IWE2	NXP20_HUMAN	family with sequence similarity 114, member A1	446			S -> L (in dbSNP:rs36058104).			cytoplasm (GO:0005737)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	20						GTATACATGTCGTCCATTGAA	0.368													T|||	146	0.0291534	0.0734	0.0058	5008	,	,		17511	0.005		0.002	False		,,,				2504	0.0389				p.S446L		Atlas-SNP	.											.	FAM114A1	42	.	0			c.C1337T						PASS	.	T	LEU/SER	267,4139	799.7+/-415.5	6,255,1942	63.0	62.0	62.0		1337	4.4	0.7	4	dbSNP_126	62	53,8547	816.7+/-406.9	2,49,4249	yes	missense	FAM114A1	NM_138389.2	145	8,304,6191	TT,TC,CC		0.6163,6.0599,2.4604	benign	446/564	38933869	320,12686	2203	4300	6503	SO:0001583	missense	92689	exon12			ACATGTCGTCCAT		CCDS3447.1	4p14	2006-09-21			ENSG00000197712	ENSG00000197712			25087	protein-coding gene	gene with protein product							Standard	NM_138389		Approved	Noxp20	uc003gtn.3	Q8IWE2	OTTHUMG00000128583	ENST00000358869.2:c.1337C>T	4.37:g.38933869C>T	ENSP00000351740:p.Ser446Leu	257.0	0.0	0		261.0	106.0	0.40613	NM_138389	A8K9W6|Q6MZV4|Q9BVL6	Missense_Mutation	SNP	ENST00000358869.2	37	CCDS3447.1	27	0.012362637362637362	22	0.044715447154471545	2	0.0055248618784530384	2	0.0034965034965034965	1	0.0013192612137203166	T	0.057	-1.233148	0.01505	0.060599	0.006163	ENSG00000197712	ENST00000515037;ENST00000358869;ENST00000355404	T;T	0.22539	1.95;2.98	5.62	4.43	0.53597	.	0.312620	0.32231	N	0.006386	T	0.00468	0.0015	N	0.00446	-1.495	0.09310	N	0.999992	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36841	-0.9731	10	0.12103	T	0.63	-1.327	4.0001	0.09576	0.1273:0.068:0.1332:0.6715	rs36058104	239;446	Q6MZV4;Q8IWE2	.;NXP20_HUMAN	L	239;446;239	ENSP00000424115:S239L;ENSP00000351740:S446L	ENSP00000347569:S239L	S	+	2	0	FAM114A1	38610264	1.000000	0.71417	0.736000	0.30914	0.196000	0.23810	3.031000	0.49728	0.411000	0.25702	-0.516000	0.04426	TCG	C|0.979;T|0.021	0.021	strong		0.368	FAM114A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250436.1	NM_138389	
TTN	7273	hgsc.bcm.edu	37	2	179614059	179614059	+	Intron	SNP	T	T	C	rs16866490	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179614059T>C	ENST00000591111.1	-	45	10585				TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Intron|TTN_ENST00000360870.5_Silent_p.Q4356Q|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Intron			Q8WZ42	TITIN_HUMAN	titin						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)			CAGCCTGACATTGTATGAATT	0.413													T|||	29	0.00579073	0.0204	0.0029	5008	,	,		18368	0.0		0.0	False		,,,				2504	0.0				p.Q4356Q		Atlas-SNP	.											.	TTN	18412	.	0			c.A13068G						PASS	.	T	,,,,	78,4328	62.9+/-100.1	0,78,2125	87.0	93.0	91.0		,,13068,,	-3.6	0.0	2	dbSNP_123	91	2,8594	1.2+/-3.3	0,2,4296	no	intron,intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	0,80,6421	CC,CT,TT		0.0233,1.7703,0.6153	,,,,	,,4356/5605,,	179614059	80,12922	2203	4298	6501	SO:0001627	intron_variant	7273	exon46			CTGACATTGTATG	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.10360+3791A>G	2.37:g.179614059T>C		74.0	0.0	0		58.0	29.0	0.5	NM_133379	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|0.991;C|0.009	0.009	strong		0.413	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
DNAH9	1770	hgsc.bcm.edu	37	17	11532787	11532787	+	Silent	SNP	C	C	T	rs73290804	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:11532787C>T	ENST00000262442.4	+	7	1472	c.1404C>T	c.(1402-1404)agC>agT	p.S468S	DNAH9_ENST00000454412.2_Silent_p.S468S	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	468	Stem. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		TGGAGTTCAGCGGCGTCAGAG	0.478													C|||	100	0.0199681	0.0726	0.0043	5008	,	,		15848	0.001		0.0	False		,,,				2504	0.0				p.S468S		Atlas-SNP	.											.	DNAH9	695	.	0			c.C1404T						PASS	.	C		272,4134	155.2+/-188.4	10,252,1941	100.0	98.0	99.0		1404	-0.7	1.0	17	dbSNP_130	99	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	DNAH9	NM_001372.3		10,254,6239	TT,TC,CC		0.0233,6.1734,2.1067		468/4487	11532787	274,12732	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon7			GTTCAGCGGCGTC	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.1404C>T	17.37:g.11532787C>T		132.0	0.0	0		159.0	78.0	0.490566	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			C|0.978;T|0.022	0.022	strong		0.478	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
PCDHA4	56144	hgsc.bcm.edu	37	5	140188392	140188392	+	Silent	SNP	C	C	G	rs7707144	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140188392C>G	ENST00000530339.1	+	1	1620	c.1620C>G	c.(1618-1620)gcC>gcG	p.A540A	PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000356878.4_Silent_p.A540A|PCDHA4_ENST00000512229.2_Silent_p.A540A|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	540	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTCGCGATGCCGGCGTGCCAC	0.657													.|||	286	0.0571086	0.208	0.013	5008	,	,		17478	0.001		0.001	False		,,,				2504	0.0				p.A540A		Atlas-SNP	.											PCDHA4_ENST00000530339,NS,carcinoma,0,2	PCDHA4	419	2	0			c.C1620G						PASS	.	G	,,,,,	748,3658		64,620,1519	60.0	68.0	65.0		,,,1620,,1620	-0.6	1.0	5	dbSNP_116	65	2,8596		0,2,4297	no	intron,intron,intron,coding-synonymous,intron,coding-synonymous	PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_031411.1,NM_031500.1	,,,,,	64,622,5816	GG,GC,CC		0.0233,16.9768,5.7675	,,,,,	,,,540/948,,540/799	140188392	750,12254	2203	4299	6502	SO:0001819	synonymous_variant	56144	exon1			CGATGCCGGCGTG	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.1620C>G	5.37:g.140188392C>G		83.0	0.0	0		92.0	29.0	0.315217	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			C|0.937;G|0.063	0.063	strong		0.657	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
ZNF276	92822	hgsc.bcm.edu	37	16	89790020	89790020	+	Silent	SNP	C	C	T	rs34629175	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89790020C>T	ENST00000443381.2	+	4	1006	c.909C>T	c.(907-909)ccC>ccT	p.P303P	ZNF276_ENST00000568064.1_Missense_Mutation_p.P222L|ZNF276_ENST00000446326.2_Missense_Mutation_p.P100L|ZNF276_ENST00000289816.5_Silent_p.P228P|VPS9D1_ENST00000389386.3_5'Flank	NM_001113525.1	NP_001106997.1	Q8N554	ZN276_HUMAN	zinc finger protein 276	303					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)		AGACCCTGCCCAGCACGGATG	0.697													C|||	131	0.0261581	0.0968	0.0043	5008	,	,		17634	0.0		0.0	False		,,,				2504	0.0				p.P303P		Atlas-SNP	.											.	ZNF276	70	.	0			c.C909T						PASS	.	C	,	354,4038		12,330,1854	30.0	37.0	34.0		909,684	2.4	0.1	16	dbSNP_126	34	1,8587		0,1,4293	no	coding-synonymous,coding-synonymous	ZNF276	NM_001113525.1,NM_152287.3	,	12,331,6147	TT,TC,CC		0.0116,8.0601,2.735	,	303/615,228/540	89790020	355,12625	2196	4294	6490	SO:0001819	synonymous_variant	92822	exon4			CCTGCCCAGCACG	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.909C>T	16.37:g.89790020C>T		107.0	0.0	0		123.0	66.0	0.536585	NM_001113525	Q0VGA1|Q2TBE8|Q3B7H7	Silent	SNP	ENST00000443381.2	37	CCDS45554.1	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	C	2.587	-0.296169	0.05532	0.080601	1.16E-4	ENSG00000158805	ENST00000446326	T	0.13307	2.6	5.66	2.44	0.29823	.	0.247400	0.40818	N	0.001014	T	0.00468	0.0015	.	.	.	0.24132	N	0.995761	B	0.11235	0.004	B	0.08055	0.003	T	0.30765	-0.9967	9	0.56958	D	0.05	-22.5813	5.0473	0.14490	0.0:0.5552:0.1597:0.2851	rs34629175	100	A8K186	.	L	100	ENSP00000415999:P100L	ENSP00000415999:P100L	P	+	2	0	ZNF276	88317521	0.001000	0.12720	0.110000	0.21437	0.015000	0.08874	0.109000	0.15417	0.240000	0.21263	-0.367000	0.07326	CCA	C|0.976;T|0.024	0.024	strong		0.697	ZNF276-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422517.1	NM_152287	
ST7L	54879	hgsc.bcm.edu	37	1	113153536	113153536	+	Silent	SNP	T	T	C	rs35364712	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:113153536T>C	ENST00000358039.4	-	3	682	c.378A>G	c.(376-378)acA>acG	p.T126T	ST7L_ENST00000543570.1_Silent_p.T109T|ST7L_ENST00000343210.7_Silent_p.T126T|ST7L_ENST00000369668.2_Silent_p.T126T|ST7L_ENST00000369666.1_Silent_p.T109T|ST7L_ENST00000369669.1_5'UTR|ST7L_ENST00000490067.1_Silent_p.T109T|ST7L_ENST00000538187.1_Silent_p.T70T|ST7L_ENST00000360743.4_Silent_p.T126T|ST7L_ENST00000463235.1_5'UTR|ST7L_ENST00000544629.1_Silent_p.T126T	NM_017744.4|NM_138727.3	NP_060214.2|NP_620055.1	Q8TDW4	ST7L_HUMAN	suppression of tumorigenicity 7 like	126					negative regulation of cell growth (GO:0030308)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(4)|large_intestine(3)|lung(1)|prostate(2)|stomach(1)|urinary_tract(3)	15	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGCTGCTCTCTGTTCCTCCCA	0.408													T|||	59	0.0117812	0.0431	0.0029	5008	,	,		21004	0.0		0.0	False		,,,				2504	0.0				p.T126T		Atlas-SNP	.											.	ST7L	31	.	0			c.A378G						PASS	.	T	,,,	197,4209	124.5+/-161.8	5,187,2011	156.0	150.0	152.0		378,327,378,378	4.9	1.0	1	dbSNP_126	152	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ST7L	NM_017744.4,NM_138727.3,NM_138728.2,NM_138729.3	,,,	5,188,6310	CC,CT,TT		0.0116,4.4712,1.5224	,,,	126/576,109/559,126/545,126/556	113153536	198,12808	2203	4300	6503	SO:0001819	synonymous_variant	54879	exon3			GCTCTCTGTTCCT	AB081317	CCDS848.1, CCDS849.1, CCDS850.1, CCDS852.1	1p13.1	2008-06-06			ENSG00000007341	ENSG00000007341			18441	protein-coding gene	gene with protein product						12012006	Standard	NM_138729		Approved	FLJ20284, STLR, ST7R, FAM4B	uc001ecd.3	Q8TDW4	OTTHUMG00000011753	ENST00000358039.4:c.378A>G	1.37:g.113153536T>C		254.0	0.0	0		268.0	134.0	0.5	NM_138729	A8K4S7|Q49AH6|Q5TEI4|Q5U5K6|Q6N067|Q7Z2Z0|Q7Z3C2|Q8N7P8|Q8TDW1|Q8TDW2|Q8TDW3|Q9NXF3	Silent	SNP	ENST00000358039.4	37	CCDS848.1																																																																																			T|0.984;C|0.016	0.016	strong		0.408	ST7L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032504.3		
DGKI	9162	hgsc.bcm.edu	37	7	137150665	137150665	+	Silent	SNP	T	T	C	rs35245703	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:137150665T>C	ENST00000288490.5	-	27	2625	c.2625A>G	c.(2623-2625)gaA>gaG	p.E875E	DGKI_ENST00000446122.1_Silent_p.E857E|DGKI_ENST00000424189.2_Silent_p.E888E|DGKI_ENST00000453654.2_Silent_p.E585E	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	875					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|positive regulation of Ras protein signal transduction (GO:0046579)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of Rap GTPase activity (GO:0032317)	cytoplasm (GO:0005737)|guanyl-nucleotide exchange factor complex (GO:0032045)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(46)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	84						CCGAGGCTTGTTCCACCACCA	0.542													C|||	480	0.0958466	0.3555	0.013	5008	,	,		17525	0.0		0.001	False		,,,				2504	0.0				p.E875E		Atlas-SNP	.											.	DGKI	335	.	0			c.A2625G						PASS	.	C		1335,3071	695.8+/-406.0	210,915,1078	64.0	62.0	63.0		2625	2.9	1.0	7	dbSNP_126	63	5,8595	819.0+/-406.8	0,5,4295	no	coding-synonymous	DGKI	NM_004717.2		210,920,5373	CC,CT,TT		0.0581,30.2996,10.3029		875/1066	137150665	1340,11666	2203	4300	6503	SO:0001819	synonymous_variant	9162	exon27			GGCTTGTTCCACC	AF061936	CCDS5845.1	7q32.3-q33	2013-01-10			ENSG00000157680	ENSG00000157680		"""Ankyrin repeat domain containing"""	2855	protein-coding gene	gene with protein product		604072				9830018	Standard	NM_004717		Approved	DGK-IOTA	uc003vtt.3	O75912	OTTHUMG00000155697	ENST00000288490.5:c.2625A>G	7.37:g.137150665T>C		92.0	0.0	0		76.0	28.0	0.368421	NM_004717	A4D1Q9|Q9NZ49	Silent	SNP	ENST00000288490.5	37	CCDS5845.1																																																																																			T|0.910;C|0.090	0.090	strong		0.542	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717	
HAO1	54363	hgsc.bcm.edu	37	20	7920986	7920986	+	Silent	SNP	C	C	T	rs33931524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:7920986C>T	ENST00000378789.3	-	1	135	c.84G>A	c.(82-84)agG>agA	p.R28R		NM_017545.2	NP_060015.1	Q9UJM8	HAOX1_HUMAN	hydroxyacid oxidase (glycolate oxidase) 1	28	FMN hydroxy acid dehydrogenase. {ECO:0000255|PROSITE-ProRule:PRU00683}.				cellular nitrogen compound metabolic process (GO:0034641)|fatty acid alpha-oxidation (GO:0001561)|glycolate catabolic process (GO:0046296)|glyoxylate metabolic process (GO:0046487)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	(S)-2-hydroxy-acid oxidase activity (GO:0003973)|FMN binding (GO:0010181)|glycolate oxidase activity (GO:0008891)|glyoxylate oxidase activity (GO:0047969)|long-chain-(S)-2-hydroxy-long-chain-acid oxidase activity (GO:0052853)|medium-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052854)|receptor binding (GO:0005102)|very-long-chain-(S)-2-hydroxy-acid oxidase activity (GO:0052852)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(19)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						TTGCCCCAGACCTGTAATAGT	0.318													C|||	161	0.0321486	0.1082	0.0187	5008	,	,		17203	0.0		0.003	False		,,,				2504	0.002				p.R28R		Atlas-SNP	.											.	HAO1	71	.	0			c.G84A						PASS	.	C		456,3950	215.1+/-234.2	17,422,1764	70.0	70.0	70.0		84	-3.4	0.8	20	dbSNP_126	70	41,8559	25.7+/-73.6	0,41,4259	no	coding-synonymous	HAO1	NM_017545.2		17,463,6023	TT,TC,CC		0.4767,10.3495,3.8213		28/371	7920986	497,12509	2203	4300	6503	SO:0001819	synonymous_variant	54363	exon1			CCCAGACCTGTAA	AL021879	CCDS13100.1	20p12	2005-01-10			ENSG00000101323	ENSG00000101323	1.1.3.15		4809	protein-coding gene	gene with protein product		605023		GOX1		9891009	Standard	NM_017545		Approved	GOX	uc002wmw.1	Q9UJM8	OTTHUMG00000031841	ENST00000378789.3:c.84G>A	20.37:g.7920986C>T		100.0	0.0	0		98.0	53.0	0.540816	NM_017545	Q14CQ0|Q9UPZ0|Q9Y3I7	Silent	SNP	ENST00000378789.3	37	CCDS13100.1																																																																																			C|0.966;T|0.034	0.034	strong		0.318	HAO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077926.2		
DCAF8L2	347442	hgsc.bcm.edu	37	X	27765405	27765405	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:27765405G>A	ENST00000451261.2	+	5	792	c.393G>A	c.(391-393)gaG>gaA	p.E131E		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	131	Glu-rich.									central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						aggaagaggaggaggaggagg	0.562																																					p.E131E		Atlas-SNP	.											.	DCAF8L2	79	.	0			c.G393A						PASS	.						20.0	18.0	18.0					X																	27765405		692	1587	2279	SO:0001819	synonymous_variant	347442	exon1			AGAGGAGGAGGAG		CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"""WD repeat domain containing"""	31811	protein-coding gene	gene with protein product			"""WD repeat domain 42C"""	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.393G>A	X.37:g.27765405G>A		45.0	0.0	0		56.0	7.0	0.125	NM_001136533	B2RXH9|J3KT06	Silent	SNP	ENST00000451261.2	37	CCDS59162.1																																																																																			.	.	none		0.562	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354	
EFCAB3	146779	hgsc.bcm.edu	37	17	60451185	60451185	+	Missense_Mutation	SNP	G	G	C	rs6504103	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:60451185G>C	ENST00000450662.2	+	2	116	c.45G>C	c.(43-45)aaG>aaC	p.K15N		NM_001144933.1	NP_001138405.1	Q8N7B9	EFCB3_HUMAN	EF-hand calcium binding domain 3	0							calcium ion binding (GO:0005509)			cervix(1)|endometrium(2)|large_intestine(5)|lung(6)|skin(3)	17			BRCA - Breast invasive adenocarcinoma(2;2.27e-11)			GAAATGGAAAGATTAATGTTA	0.254													G|||	123	0.0245607	0.0908	0.0029	5008	,	,		14237	0.0		0.001	False		,,,				2504	0.0				p.K15N		Atlas-SNP	.											.	EFCAB3	71	.	0			c.G45C						PASS	.						46.0	41.0	43.0					17																	60451185		692	1584	2276	SO:0001583	missense	146779	exon2			TGGAAAGATTAAT	AK098684	CCDS11632.1, CCDS45751.1	17q23.3	2013-01-10			ENSG00000172421	ENSG00000172421		"""EF-hand domain containing"""	26379	protein-coding gene	gene with protein product						12477932	Standard	NM_173503		Approved	FLJ25818	uc010wpc.2	Q8N7B9	OTTHUMG00000179175	ENST00000450662.2:c.45G>C	17.37:g.60451185G>C	ENSP00000403932:p.Lys15Asn	145.0	0.0	0		145.0	71.0	0.489655	NM_001144933	J3KQM8	Missense_Mutation	SNP	ENST00000450662.2	37	CCDS45751.1	38	0.0173992673992674	37	0.07520325203252033	0	0.0	0	0.0	1	0.0013192612137203166	.	8.466	0.856348	0.17106	.	.	ENSG00000172421	ENST00000450662	T	0.10668	2.85	4.0	0.787	0.18596	.	.	.	.	.	T	0.00440	0.0014	.	.	.	0.18873	N	0.999986	.	.	.	.	.	.	T	0.42155	-0.9468	6	0.32370	T	0.25	.	5.523	0.16943	0.3862:0.0:0.6138:0.0	rs6504103;rs6504103	.	.	.	N	15	ENSP00000403932:K15N	ENSP00000403932:K15N	K	+	3	2	EFCAB3	57804917	0.869000	0.29996	0.031000	0.17742	0.003000	0.03518	0.480000	0.22244	0.396000	0.25283	0.591000	0.81541	AAG	G|0.983;C|0.017	0.017	strong		0.254	EFCAB3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000379315.1	NM_173503	
MYO7B	4648	hgsc.bcm.edu	37	2	128381861	128381861	+	Missense_Mutation	SNP	G	G	A	rs61743523	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128381861G>A	ENST00000409816.2	+	28	3967	c.3935G>A	c.(3934-3936)cGa>cAa	p.R1312Q	RP11-286H15.1_ENST00000609697.1_RNA|MYO7B_ENST00000389524.4_Missense_Mutation_p.R1312Q|MYO7B_ENST00000409090.1_Missense_Mutation_p.R165Q|MYO7B_ENST00000428314.1_Missense_Mutation_p.R1312Q			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1312	FERM 1. {ECO:0000255|PROSITE- ProRule:PRU00084}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		CAAGTCCTCCGAGGAGTCTGG	0.592													A|||	36	0.0071885	0.0234	0.0072	5008	,	,		19505	0.0		0.0	False		,,,				2504	0.0				p.R1312Q		Atlas-SNP	.											.	MYO7B	359	.	0			c.G3935A						PASS	.	A	GLN/ARG	82,3886		2,78,1904	15.0	16.0	16.0		3935	-0.1	0.1	2	dbSNP_129	16	2,8290		0,2,4144	yes	missense	MYO7B	NM_001080527.1	43	2,80,6048	AA,AG,GG		0.0241,2.0665,0.6852	benign	1312/2117	128381861	84,12176	1984	4146	6130	SO:0001583	missense	4648	exon29			TCCTCCGAGGAGT		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"""Myosins / Myosin superfamily : Class VII"""	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.3935G>A	2.37:g.128381861G>A	ENSP00000386461:p.Arg1312Gln	69.0	0.0	0		74.0	40.0	0.540541	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	37	CCDS46405.1	12	0.005494505494505495	9	0.018292682926829267	3	0.008287292817679558	0	0.0	0	0.0	.	13.32	2.200829	0.38905	0.020665	2.41E-4	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000272666;ENST00000409816;ENST00000437387;ENST00000409090	T;T;T;T;T	0.74947	-0.89;-0.89;-0.89;-0.6;-0.89	3.68	-0.0642	0.13773	FERM central domain (1);Band 4.1 domain (1);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	0.715826	0.13724	N	0.367181	T	0.49236	0.1545	M	0.79258	2.445	0.21579	N	0.999633	P	0.42337	0.776	B	0.32465	0.146	T	0.49995	-0.8879	10	0.38643	T	0.18	.	5.7748	0.18273	0.2859:0.0:0.5394:0.1747	rs61743523	1312	Q6PIF6	MYO7B_HUMAN	Q	1312;1312;165;1312;165;165	ENSP00000374175:R1312Q;ENSP00000415090:R1312Q;ENSP00000386461:R1312Q;ENSP00000404927:R165Q;ENSP00000386850:R165Q	ENSP00000272666:R165Q	R	+	2	0	MYO7B	128098331	0.985000	0.35326	0.083000	0.20561	0.098000	0.18820	2.232000	0.43018	-0.259000	0.09432	-0.361000	0.07541	CGA	G|0.993;A|0.007	0.007	strong		0.592	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
STK40	83931	hgsc.bcm.edu	37	1	36820015	36820015	+	Silent	SNP	T	T	C	rs115120808	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:36820015T>C	ENST00000373129.3	-	7	979	c.573A>G	c.(571-573)aaA>aaG	p.K191K	STK40_ENST00000482458.1_5'Flank|STK40_ENST00000359297.2_Silent_p.K191K|STK40_ENST00000373132.3_Silent_p.K191K|STK40_ENST00000373130.3_Silent_p.K196K	NM_032017.1	NP_114406.1	Q8N2I9	STK40_HUMAN	serine/threonine kinase 40	191	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.			Missing (in Ref. 2; BAC11371). {ECO:0000305}.	glycogen metabolic process (GO:0005977)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|regulation of gene expression (GO:0010468)|regulation of MAPK cascade (GO:0043408)|respiratory system process (GO:0003016)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(1)|skin(1)|stomach(1)	13		Myeloproliferative disorder(586;0.0393)				GCACGATATTTTTCTGTAAAA	0.527													T|||	55	0.0109824	0.0401	0.0029	5008	,	,		20477	0.0		0.0	False		,,,				2504	0.0				p.K191K		Atlas-SNP	.											.	STK40	53	.	0			c.A573G						PASS	.	T		162,4244	109.1+/-147.4	5,152,2046	189.0	177.0	181.0		573	3.0	1.0	1	dbSNP_132	181	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	STK40	NM_032017.1		5,153,6345	CC,CT,TT		0.0116,3.6768,1.2533		191/436	36820015	163,12843	2203	4300	6503	SO:0001819	synonymous_variant	83931	exon7			GATATTTTTCTGT	BC008344	CCDS407.1, CCDS60089.1	1p34.3	2008-02-05			ENSG00000196182	ENSG00000196182			21373	protein-coding gene	gene with protein product		609437					Standard	NM_032017		Approved	MGC4796, SgK495	uc001cak.1	Q8N2I9	OTTHUMG00000008238	ENST00000373129.3:c.573A>G	1.37:g.36820015T>C		184.0	0.0	0		173.0	81.0	0.468208	NM_032017	D3DPS8|Q5VTK8|Q5VTK9|Q6ZMN1|Q8N2J8|Q8N3I6|Q96HN6|Q96I44|Q9BSA3|Q9H7H6	Silent	SNP	ENST00000373129.3	37	CCDS407.1																																																																																			T|0.990;C|0.010	0.010	strong		0.527	STK40-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022592.1	NM_032017	
SSBP4	170463	hgsc.bcm.edu	37	19	18542201	18542201	+	Silent	SNP	C	C	T	rs113198578	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18542201C>T	ENST00000270061.7	+	6	702	c.408C>T	c.(406-408)aaC>aaT	p.N136N	SSBP4_ENST00000598159.2_Intron|SSBP4_ENST00000599699.2_5'Flank|SSBP4_ENST00000348495.6_Intron	NM_032627.4	NP_116016.1	Q9BWG4	SSBP4_HUMAN	single stranded DNA binding protein 4	136	Pro-rich.					nucleus (GO:0005634)	single-stranded DNA binding (GO:0003697)			endometrium(2)|kidney(1)|skin(1)	4						ACAACCCCAACGCCCCCATGA	0.697													C|||	148	0.0295527	0.0968	0.0159	5008	,	,		7118	0.0		0.0089	False		,,,				2504	0.0				p.N136N		Atlas-SNP	.											SSBP4,NS,neuroblastoma,0,1	SSBP4	19	1	0			c.C408T						PASS	.	C	,	349,3959		14,321,1819	10.0	10.0	10.0		,408	1.0	0.0	19	dbSNP_132	10	52,8436		0,52,4192	no	intron,coding-synonymous	SSBP4	NM_001009998.3,NM_032627.4	,	14,373,6011	TT,TC,CC		0.6126,8.1012,3.1338	,	,136/386	18542201	401,12395	2154	4244	6398	SO:0001819	synonymous_variant	170463	exon6			CCCCAACGCCCCC		CCDS12378.1, CCDS32960.1	19p13.1	2008-02-05				ENSG00000130511			15676	protein-coding gene	gene with protein product		607391				12079286	Standard	NM_032627		Approved		uc002niy.3	Q9BWG4		ENST00000270061.7:c.408C>T	19.37:g.18542201C>T		367.0	0.0	0		425.0	236.0	0.555294	NM_032627	Q9BWW5	Silent	SNP	ENST00000270061.7	37	CCDS12378.1																																																																																			C|0.976;T|0.024	0.024	strong		0.697	SSBP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000466348.3	NM_032627	
GLRA4	441509	hgsc.bcm.edu	37	X	102979184	102979184	+	Missense_Mutation	SNP	G	G	A	rs16984014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102979184G>A	ENST00000372617.4	-	4	736	c.316C>T	c.(316-318)Cgc>Tgc	p.R106C	GLRA4_ENST00000469567.1_5'Flank	NM_001024452.2	NP_001019623.2	Q5JXX5	GLRA4_HUMAN	glycine receptor, alpha 4	106						cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|glycine binding (GO:0016594)|transmitter-gated ion channel activity (GO:0022824)			cervix(1)|endometrium(2)|large_intestine(2)|lung(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	21						TAGGACAGGCGTGGGTCATTC	0.542													G|||	280	0.0741722	0.2065	0.0101	3775	,	,		14747	0.0		0.0	False		,,,				2504	0.0				p.R106C		Atlas-SNP	.											.	GLRA4	86	.	0			c.C316T						PASS	.	G	CYS/ARG,CYS/ARG	690,2992		49,480,112,1027,458	109.0	107.0	108.0		316,316	5.4	1.0	X	dbSNP_123	108	4,6663		0,4,0,2404,1851	yes	missense,missense	GLRA4	NM_001024452.2,NM_001172285.1	180,180	49,484,112,3431,2309	AA,AG,A,GG,G		0.06,18.7398,6.706	probably-damaging,probably-damaging	106/418,106/343	102979184	694,9655	2126	4259	6385	SO:0001583	missense	441509	exon4			ACAGGCGTGGGTC	Z93848	CCDS43980.2	Xq22.2	2012-01-16			ENSG00000188828	ENSG00000188828		"""Ligand-gated ion channels / Glycine receptors"""	31715	protein-coding gene	gene with protein product							Standard	NM_001024452		Approved		uc011mse.2	Q5JXX5	OTTHUMG00000022110	ENST00000372617.4:c.316C>T	X.37:g.102979184G>A	ENSP00000361700:p.Arg106Cys	144.0	0.0	0		150.0	98.0	0.653333	NM_001024452		Missense_Mutation	SNP	ENST00000372617.4	37	CCDS43980.2	105	0.06329113924050633	66	0.15865384615384615	1	0.0027624309392265192	0	0.0	0	0.0	G	24.1	4.494287	0.85069	0.187398	6.0E-4	ENSG00000188828	ENST00000372617	D	0.82344	-1.6	5.37	5.37	0.77165	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	T	0.01905	0.0060	H	0.95917	3.74	0.09310	P	0.99999999821083	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.17349	-1.0372	9	0.87932	D	0	.	15.3872	0.74711	0.0:0.0:1.0:0.0	rs16984014;rs56514211;rs16984014	106;65	Q5JXX5;B9WSA6	GLRA4_HUMAN;.	C	106	ENSP00000361700:R106C	ENSP00000361700:R106C	R	-	1	0	GLRA4	102865840	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.903000	0.87398	2.224000	0.72417	0.513000	0.50165	CGC	0|0.009;A|0.067	0.067	strong		0.542	GLRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057742.2	NM_001024452	
LAMB1	3912	hgsc.bcm.edu	37	7	107591720	107591720	+	Silent	SNP	G	G	A	rs25660	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:107591720G>A	ENST00000222399.6	-	24	3572	c.3342C>T	c.(3340-3342)tgC>tgT	p.C1114C	LAMB1_ENST00000393561.1_Silent_p.C1138C	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	1114	Laminin EGF-like 12. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)			NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						GGCACTCGCTGCAGGTGCGGC	0.607													G|||	229	0.0457268	0.1694	0.0043	5008	,	,		16184	0.0		0.002	False		,,,				2504	0.0				p.C1114C		Atlas-SNP	.											.	LAMB1	185	.	0			c.C3342T						PASS	.	G		632,3774	269.2+/-268.9	40,552,1611	54.0	50.0	51.0		3342	4.1	1.0	7	dbSNP_72	51	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous	LAMB1	NM_002291.2		40,557,5906	AA,AG,GG		0.0581,14.3441,4.8977		1114/1787	107591720	637,12369	2203	4300	6503	SO:0001819	synonymous_variant	3912	exon24			CTCGCTGCAGGTG	M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136		"""Laminins"""	6486	protein-coding gene	gene with protein product		150240	"""cutis laxa with marfanoid phenotype"""	CLM		2563160, 2704655, 1864606	Standard	NM_002291		Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.3342C>T	7.37:g.107591720G>A		152.0	0.0	0		150.0	150.0	1	NM_002291	Q14D91	Silent	SNP	ENST00000222399.6	37	CCDS5750.1																																																																																			G|0.957;A|0.043	0.043	strong		0.607	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291	
CRB2	286204	hgsc.bcm.edu	37	9	126133252	126133252	+	Silent	SNP	C	C	T	rs55965026	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:126133252C>T	ENST00000373631.3	+	7	1921	c.1920C>T	c.(1918-1920)tgC>tgT	p.C640C	CRB2_ENST00000373629.2_Silent_p.C308C|CRB2_ENST00000359999.3_Silent_p.C640C	NM_173689.5	NP_775960.4	Q5IJ48	CRUM2_HUMAN	crumbs family member 2	640	EGF-like 10. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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						GTCCCACGTGCGCTGATGGTG	0.617													C|||	160	0.0319489	0.0893	0.0159	5008	,	,		19920	0.0		0.0229	False		,,,				2504	0.0082				p.C640C		Atlas-SNP	.											.	CRB2	86	.	0			c.C1920T						PASS	.	C		332,4074	168.3+/-199.2	12,308,1883	56.0	61.0	59.0		1920	-3.2	0.1	9	dbSNP_129	59	257,8343	97.9+/-159.5	8,241,4051	no	coding-synonymous	CRB2	NM_173689.5		20,549,5934	TT,TC,CC		2.9884,7.5352,4.5287		640/1286	126133252	589,12417	2203	4300	6503	SO:0001819	synonymous_variant	286204	exon7			CACGTGCGCTGAT	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.1920C>T	9.37:g.126133252C>T		59.0	0.0	0		51.0	33.0	0.647059	NM_173689	A2A3N4|Q0QD46|Q5JS41|Q5JS43|Q6ZTA9|Q6ZWI6	Silent	SNP	ENST00000373631.3	37	CCDS6852.2																																																																																			C|0.962;T|0.038	0.038	strong		0.617	CRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053990.3	NM_173689	
SYNE4	163183	hgsc.bcm.edu	37	19	36497747	36497747	+	Missense_Mutation	SNP	C	C	G	rs77925409	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36497747C>G	ENST00000324444.3	-	4	634	c.523G>C	c.(523-525)Gcc>Ccc	p.A175P	AC002116.8_ENST00000473572.2_RNA|ALKBH6_ENST00000495116.2_5'Flank|SYNE4_ENST00000340477.5_Intron	NM_001039876.1	NP_001034965.1	Q8N205	SYNE4_HUMAN	spectrin repeat containing, nuclear envelope family member 4	175					establishment of epithelial cell apical/basal polarity (GO:0045198)	integral component of nuclear outer membrane (GO:0031309)											TGCTCCAGGGCTGCCCAGGCC	0.687													C|||	140	0.0279553	0.1006	0.0101	5008	,	,		14555	0.0		0.0	False		,,,				2504	0.0				p.A175P		Atlas-SNP	.											.	.	.	.	0			c.G523C						PASS	.	C	PRO/ALA	304,3792		11,282,1755	14.0	21.0	19.0		523	-1.4	0.0	19	dbSNP_131	19	6,8318		0,6,4156	yes	missense	C19orf46	NM_001039876.1	27	11,288,5911	GG,GC,CC		0.0721,7.4219,2.496	possibly-damaging	175/405	36497747	310,12110	2048	4162	6210	SO:0001583	missense	163183	exon4			CCAGGGCTGCCCA	BC038360	CCDS42553.1	19q13.12	2014-01-28	2012-05-31	2012-05-31	ENSG00000181392	ENSG00000181392			26703	protein-coding gene	gene with protein product		615535	"""chromosome 19 open reading frame 46"", ""deafness, autosomal recessive 76"""	C19orf46, DFNB76		23348741	Standard	XM_005258597		Approved	FLJ36445, Nesprin-4, Nesp4	uc002ocq.1	Q8N205	OTTHUMG00000048135	ENST00000324444.3:c.523G>C	19.37:g.36497747C>G	ENSP00000316130:p.Ala175Pro	81.0	0.0	0		85.0	36.0	0.423529	NM_001039876	A8MRS0|A8MYE3|Q7Z7L3	Missense_Mutation	SNP	ENST00000324444.3	37	CCDS42553.1	40	0.018315018315018316	34	0.06910569105691057	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	C	13.03	2.114112	0.37339	0.074219	7.21E-4	ENSG00000181392	ENST00000324444;ENST00000490730	T;T	0.53206	0.63;0.63	5.95	-1.44	0.08856	.	0.656922	0.16361	N	0.217750	T	0.02380	0.0073	L	0.40543	1.245	0.09310	N	1	B;B	0.21381	0.055;0.001	B;B	0.20577	0.03;0.002	T	0.07046	-1.0793	10	0.48119	T	0.1	-12.2768	2.0383	0.03545	0.2949:0.4044:0.1655:0.1353	.	175;175	D6RAE3;Q8N205	.;SYNE4_HUMAN	P	175	ENSP00000316130:A175P;ENSP00000422716:A175P	ENSP00000316130:A175P	A	-	1	0	C19orf46	41189587	0.002000	0.14202	0.030000	0.17652	0.956000	0.61745	-0.333000	0.07894	-0.067000	0.12976	-0.262000	0.10625	GCC	C|0.979;G|0.021	0.021	strong		0.687	SYNE4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109525.3	NM_001039876	
PCYOX1	51449	hgsc.bcm.edu	37	2	70503954	70503954	+	Silent	SNP	G	G	T	rs36012096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:70503954G>T	ENST00000433351.2	+	6	976	c.948G>T	c.(946-948)ccG>ccT	p.P316P	PCYOX1_ENST00000505044.2_Silent_p.P239P|PCYOX1_ENST00000545138.1_Silent_p.P238P|PCYOX1_ENST00000264441.5_Intron	NM_016297.3	NP_057381.3	Q9UHG3	PCYOX_HUMAN	prenylcysteine oxidase 1	316					prenylated protein catabolic process (GO:0030327)|prenylcysteine catabolic process (GO:0030328)|prenylcysteine metabolic process (GO:0030329)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	chloride-transporting ATPase activity (GO:0008555)|prenylcysteine oxidase activity (GO:0001735)			breast(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)	15						TGGCCACTCCGTTGAATCGAA	0.368													G|||	464	0.0926518	0.3048	0.0187	5008	,	,		18461	0.001		0.003	False		,,,				2504	0.045				p.P316P		Atlas-SNP	.											.	PCYOX1	34	.	0			c.G948T						PASS	.	G		987,3419	365.1+/-317.3	112,763,1328	54.0	57.0	56.0		948	-5.4	0.9	2	dbSNP_126	56	25,8575	17.3+/-56.4	0,25,4275	no	coding-synonymous	PCYOX1	NM_016297.3		112,788,5603	TT,TG,GG		0.2907,22.4013,7.781		316/506	70503954	1012,11994	2203	4300	6503	SO:0001819	synonymous_variant	51449	exon6			CACTCCGTTGAAT	AB020715	CCDS1902.1	2p13.3	2008-02-05			ENSG00000116005	ENSG00000116005	1.8.3.5		20588	protein-coding gene	gene with protein product		610995				10585463, 12186880	Standard	NM_016297		Approved	KIAA0908, PCL1	uc002sgn.4	Q9UHG3	OTTHUMG00000129671	ENST00000433351.2:c.948G>T	2.37:g.70503954G>T		197.0	0.0	0		199.0	89.0	0.447236	NM_016297	B2RB14|B7Z9P8|O94982|Q8N4N5|Q96QM8	Silent	SNP	ENST00000433351.2	37	CCDS1902.1																																																																																			G|0.926;T|0.074	0.074	strong		0.368	PCYOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251872.3	NM_016297	
SDK1	221935	hgsc.bcm.edu	37	7	4308360	4308360	+	3'UTR	SNP	C	C	T	rs11981816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:4308360C>T	ENST00000404826.2	+	0	10125					NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1						cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		AGTGTGGCTCCCCGTGGGTCA	0.542													C|||	303	0.0605032	0.2201	0.0144	5008	,	,		17837	0.0		0.002	False		,,,				2504	0.0				p.P673L		Atlas-SNP	.											.	SDK1	361	.	0			c.C2018T						PASS	.	C		758,3648	299.3+/-285.7	79,600,1524	184.0	193.0	190.0			0.2	0.0	7	dbSNP_120	190	3,8591	2.2+/-6.3	0,3,4294	no	utr-3	SDK1	NM_152744.3		79,603,5818	TT,TC,CC		0.0349,17.2038,5.8538			4308360	761,12239	2203	4297	6500	SO:0001624	3_prime_UTR_variant	221935	exon20			TGGCTCCCCGTGG	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19307	protein-coding gene	gene with protein product		607216	"""sidekick homolog 1 (chicken)"", ""sidekick homolog 1, cell adhesion molecule (chicken)"""			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.*3344C>T	7.37:g.4308360C>T		153.0	0.0	0		148.0	72.0	0.486486	NM_001079653	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	37	CCDS34590.1																																																																																			C|0.967;T|0.033	0.033	strong		0.542	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
PKHD1L1	93035	hgsc.bcm.edu	37	8	110408347	110408347	+	Silent	SNP	C	C	T	rs6469258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:110408347C>T	ENST00000378402.5	+	11	1007	c.903C>T	c.(901-903)ccC>ccT	p.P301P		NM_177531.4	NP_803875.2	Q86WI1	PKHL1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)-like 1	301	IPT/TIG 3.				immune response (GO:0006955)	cytosol (GO:0005829)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(4)|breast(13)|central_nervous_system(6)|cervix(1)|endometrium(19)|kidney(17)|large_intestine(34)|lung(122)|ovary(11)|pancreas(3)|prostate(9)|skin(3)|stomach(4)|upper_aerodigestive_tract(13)|urinary_tract(4)	263			OV - Ovarian serous cystadenocarcinoma(57;9.88e-13)			CAGATTTCCCCGTCAGAGTTC	0.393										HNSCC(38;0.096)			C|||	138	0.0275559	0.1006	0.0072	5008	,	,		17027	0.0		0.0	False		,,,				2504	0.0				p.P301P		Atlas-SNP	.											PKHD1L1,NS,carcinoma,+2,1	PKHD1L1	522	1	0			c.C903T						PASS	.	C		335,3603		16,303,1650	74.0	64.0	67.0		903	2.1	0.8	8	dbSNP_116	67	1,8335		0,1,4167	no	coding-synonymous	PKHD1L1	NM_177531.4		16,304,5817	TT,TC,CC		0.012,8.5069,2.7375		301/4244	110408347	336,11938	1969	4168	6137	SO:0001819	synonymous_variant	93035	exon11			TTTCCCCGTCAGA	AY219181	CCDS47911.1	8q23	2003-03-28			ENSG00000205038	ENSG00000205038			20313	protein-coding gene	gene with protein product		607843				12620974	Standard	NM_177531		Approved		uc003yne.3	Q86WI1	OTTHUMG00000164934	ENST00000378402.5:c.903C>T	8.37:g.110408347C>T		61.0	0.0	0		49.0	25.0	0.510204	NM_177531	Q567P2|Q9UF27	Silent	SNP	ENST00000378402.5	37	CCDS47911.1																																																																																			C|0.975;T|0.025	0.025	strong		0.393	PKHD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381017.1	NM_177531	
COL6A6	131873	hgsc.bcm.edu	37	3	130287096	130287096	+	Silent	SNP	C	C	T	rs61730501	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:130287096C>T	ENST00000358511.6	+	5	2080	c.2049C>T	c.(2047-2049)agC>agT	p.S683S	COL6A6_ENST00000453409.2_Silent_p.S683S	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	683	Nonhelical region.|VWFA 4. {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 matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						TGTCCCAAAGCGACATTTCAA	0.478													C|||	67	0.0133786	0.0477	0.0029	5008	,	,		20256	0.0		0.001	False		,,,				2504	0.001				p.S683S		Atlas-SNP	.											.	COL6A6	497	.	0			c.C2049T						PASS	.	C		128,3762		1,126,1818	153.0	152.0	152.0		2049	-11.5	0.0	3	dbSNP_129	152	1,8267		0,1,4133	no	coding-synonymous	COL6A6	NM_001102608.1		1,127,5951	TT,TC,CC		0.0121,3.2905,1.061		683/2264	130287096	129,12029	1945	4134	6079	SO:0001819	synonymous_variant	131873	exon5			CCAAAGCGACATT	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"""Collagens"""	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.2049C>T	3.37:g.130287096C>T		243.0	0.0	0		247.0	126.0	0.510121	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Silent	SNP	ENST00000358511.6	37	CCDS46911.1																																																																																			C|0.993;T|0.007	0.007	strong		0.478	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608	
TTN	7273	hgsc.bcm.edu	37	2	179401015	179401015	+	Missense_Mutation	SNP	G	G	A	rs72629779	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179401015G>A	ENST00000591111.1	-	307	95760	c.95536C>T	c.(95536-95538)Ccc>Tcc	p.P31846S	TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.P24614S|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.P30919S|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000415561.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.P24547S|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.P24422S|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.P33487S			Q8WZ42	TITIN_HUMAN	titin	31846	Fibronectin type-III 131. {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)			TCAGATTTGGGAGTGATGGGT	0.403													G|||	69	0.013778	0.0499	0.0043	5008	,	,		21952	0.0		0.0	False		,,,				2504	0.0				p.P33487S		Atlas-SNP	.											.	TTN	18412	.	0			c.C100459T						PASS	.	G	SER/PRO,SER/PRO,SER/PRO,SER/PRO	127,3629		1,125,1752	87.0	80.0	83.0		73264,92755,73639,73840	5.8	1.0	2	dbSNP_130	83	2,8222		0,2,4110	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	74,74,74,74	1,127,5862	AA,AG,GG		0.0243,3.3813,1.0768	probably-damaging,probably-damaging,probably-damaging,probably-damaging	24422/26927,30919/33424,24547/27052,24614/27119	179401015	129,11851	1878	4112	5990	SO:0001583	missense	7273	exon357			ATTTGGGAGTGAT	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.95536C>T	2.37:g.179401015G>A	ENSP00000465570:p.Pro31846Ser	178.0	0.0	0		179.0	85.0	0.47486	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		22	0.010073260073260074	20	0.04065040650406504	2	0.0055248618784530384	0	0.0	0	0.0	G	20.0	3.930466	0.73327	0.033813	2.43E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.54675	0.56;0.56;0.56;0.56	5.76	5.76	0.90799	Fibronectin, type III (2);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.46927	0.1418	M	0.80183	2.485	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.83275	0.996;0.996;0.996;0.996	T	0.69327	-0.5174	9	0.87932	D	0	.	19.9595	0.97236	0.0:0.0:1.0:0.0	.	24422;24547;24614;31846	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	S	30919;24422;24614;24547;24419	ENSP00000343764:P30919S;ENSP00000434586:P24422S;ENSP00000340554:P24614S;ENSP00000352154:P24547S	ENSP00000340554:P24614S	P	-	1	0	TTN	179109261	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	7.997000	0.88414	2.706000	0.92434	0.563000	0.77884	CCC	G|0.990;A|0.010	0.010	strong		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
PTX4	390667	hgsc.bcm.edu	37	16	1536047	1536047	+	Missense_Mutation	SNP	T	T	C	rs59554810	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1536047T>C	ENST00000447419.2	-	3	1355	c.1330A>G	c.(1330-1332)Atc>Gtc	p.I444V	PTX4_ENST00000293922.1_Missense_Mutation_p.I439V|PTX4_ENST00000440447.2_3'UTR			Q96A99	PTX4_HUMAN	pentraxin 4, long	444	Pentaxin.		I -> V (in dbSNP:rs59554810).			extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						TCTTTCCCGATGGCAAGGTTT	0.632													T|||	277	0.0553115	0.1974	0.0231	5008	,	,		16980	0.0		0.0	False		,,,				2504	0.0				p.I439V		Atlas-SNP	.											.	PTX4	46	.	0			c.A1315G						PASS	.	T	VAL/ILE	834,3564	328.8+/-300.7	75,684,1440	69.0	68.0	68.0		1315	1.5	0.0	16	dbSNP_129	68	3,8597	2.2+/-6.3	0,3,4297	yes	missense	PTX4	NM_001013658.1	29	75,687,5737	CC,CT,TT		0.0349,18.9632,6.4395	benign	439/474	1536047	837,12161	2199	4300	6499	SO:0001583	missense	390667	exon3			TCCCGATGGCAAG		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"""chromosome 16 open reading frame 38"""	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.1330A>G	16.37:g.1536047T>C	ENSP00000445277:p.Ile444Val	56.0	0.0	0		46.0	23.0	0.5	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		110	0.05036630036630037	99	0.20121951219512196	11	0.03038674033149171	0	0.0	0	0.0	T	10.44	1.351103	0.24512	0.189632	3.49E-4	ENSG00000251692	ENST00000447419;ENST00000293922	T;T	0.62788	0.0;0.0	5.21	1.54	0.23209	.	3.825800	0.00481	N	0.000131	T	0.00073	0.0002	N	0.22421	0.69	0.80722	P	0.0	B	0.17465	0.022	B	0.21917	0.037	T	0.03354	-1.1045	9	0.29301	T	0.29	.	2.6395	0.04967	0.1515:0.0841:0.1477:0.6167	rs59554810	439	Q96A99-2	.	V	444;439	ENSP00000445277:I444V;ENSP00000293922:I439V	ENSP00000293922:I439V	I	-	1	0	PTX4	1476048	0.001000	0.12720	0.002000	0.10522	0.006000	0.05464	0.387000	0.20718	-0.013000	0.14199	-0.376000	0.06991	ATC	T|0.942;C|0.058	0.058	strong		0.632	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
SLC27A3	11000	hgsc.bcm.edu	37	1	153750650	153750650	+	Missense_Mutation	SNP	G	G	A	rs35102232	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:153750650G>A	ENST00000368661.3	+	5	1381	c.1316G>A	c.(1315-1317)cGt>cAt	p.R439H	SLC27A3_ENST00000271857.2_Missense_Mutation_p.R520H|SLC27A3_ENST00000484014.1_3'UTR	NM_024330.1	NP_077306.1	Q5K4L6	S27A3_HUMAN	solute carrier family 27 (fatty acid transporter), member 3	439			R -> H (in dbSNP:rs35102232).		fatty acid metabolic process (GO:0006631)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)	fatty-acyl-CoA synthase activity (GO:0004321)|ligase activity (GO:0016874)|nucleotide binding (GO:0000166)			NS(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)	14	all_lung(78;6.47e-32)|Lung NSC(65;2.52e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			AAGGCAGAACGTGGCCATAAG	0.627													G|||	89	0.0177716	0.0628	0.0072	5008	,	,		17430	0.0		0.001	False		,,,				2504	0.0				p.R439H		Atlas-SNP	.											.	SLC27A3	42	.	0			c.G1316A						PASS	.	G	HIS/ARG	257,4147		5,247,1950	32.0	38.0	36.0		1316	-2.7	0.0	1	dbSNP_126	36	2,8598		0,2,4298	yes	missense	SLC27A3	NM_024330.1	29	5,249,6248	AA,AG,GG		0.0233,5.8356,1.9917	possibly-damaging	439/731	153750650	259,12745	2202	4300	6502	SO:0001583	missense	11000	exon5			CAGAACGTGGCCA	BC009916	CCDS1053.1	1q21.1	2013-05-22			ENSG00000143554	ENSG00000143554		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10997	protein-coding gene	gene with protein product		604193				9671728	Standard	NM_024330		Approved	FATP3, MGC4365, ACSVL3	uc001fcz.3	Q5K4L6	OTTHUMG00000037155	ENST00000368661.3:c.1316G>A	1.37:g.153750650G>A	ENSP00000357650:p.Arg439His	37.0	0.0	0		36.0	16.0	0.444444	NM_024330	Q5VUQ7|Q5VUQ8|Q5VUR3|Q6ZV16|Q8N2X7|Q8TEJ0|Q96SW5|Q9BTJ5|Q9BTY5	Missense_Mutation	SNP	ENST00000368661.3	37	CCDS1053.1	39|39	0.017857142857142856|0.017857142857142856	34|34	0.06910569105691057|0.06910569105691057	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	G|G	13.72|13.72	2.320062|2.320062	0.41096|0.41096	0.058356|0.058356	2.33E-4|2.33E-4	ENSG00000143554|ENSG00000143554	ENST00000271857;ENST00000368661|ENST00000458027	T;T|.	0.41758|.	0.99;0.99|.	5.03|5.03	-2.66|-2.66	0.06077|0.06077	AMP-dependent synthetase/ligase (1);|.	0.933680|.	0.09084|.	N|.	0.850843|.	T|T	0.37812|0.37812	0.1017|0.1017	M|M	0.83312|0.83312	2.635|2.635	0.09310|0.09310	N|N	1|1	B|.	0.19073|.	0.033|.	B|.	0.21546|.	0.035|.	T|T	0.49303|0.49303	-0.8954|-0.8954	10|5	0.42905|.	T|.	0.14|.	1.8444|1.8444	7.2084|7.2084	0.25919|0.25919	0.4489:0.1139:0.4372:0.0|0.4489:0.1139:0.4372:0.0	rs35102232|rs35102232	439|.	Q5K4L6|.	S27A3_HUMAN|.	H|M	520;439|144	ENSP00000271857:R520H;ENSP00000357650:R439H|.	ENSP00000271857:R520H|.	R|V	+|+	2|1	0|0	SLC27A3|SLC27A3	152017274|152017274	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.193000|0.193000	0.23685|0.23685	-1.444000|-1.444000	0.02403|0.02403	-0.720000|-0.720000	0.04935|0.04935	-0.605000|-0.605000	0.04089|0.04089	CGT|GTG	G|0.979;A|0.021	0.021	strong		0.627	SLC27A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_024330	
IGFALS	3483	hgsc.bcm.edu	37	16	1838050	1838050	+	IGR	SNP	A	A	G	rs57822546	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1838050A>G	ENST00000215539.3	-	0	2116				NUBP2_ENST00000565134.1_Missense_Mutation_p.T200A|NUBP2_ENST00000565987.1_Missense_Mutation_p.T140A|NUBP2_ENST00000568706.1_Missense_Mutation_p.T59A|NUBP2_ENST00000262302.9_Missense_Mutation_p.T200A|NUBP2_ENST00000543305.1_Missense_Mutation_p.T59A			P35858	ALS_HUMAN	insulin-like growth factor binding protein, acid labile subunit						cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin-like growth factor binding (GO:0005520)			endometrium(2)|lung(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	8						CCCACACTGCACGGTGAGTCC	0.662													A|||	461	0.0920527	0.3359	0.0216	5008	,	,		15389	0.0		0.002	False		,,,				2504	0.0				p.T200A		Atlas-SNP	.											.	NUBP2	25	.	0			c.A598G						PASS	.	G	ALA/THR	1287,3109	430.4+/-342.5	179,929,1090	64.0	66.0	65.0		598	-9.0	0.0	16	dbSNP_129	65	8,8592	5.7+/-21.5	0,8,4292	yes	missense	NUBP2	NM_012225.2	58	179,937,5382	GG,GA,AA		0.093,29.2766,9.9646	benign	200/272	1838050	1295,11701	2198	4300	6498	SO:0001628	intergenic_variant	10101	exon5			CACTGCACGGTGA	M86826	CCDS10446.1, CCDS53982.1	16p13.3	2008-07-28			ENSG00000099769	ENSG00000099769			5468	protein-coding gene	gene with protein product		601489				1379671, 16114275	Standard	NM_004970		Approved	ALS	uc010uvn.2	P35858	OTTHUMG00000128638		16.37:g.1838050A>G		78.0	0.0	0		80.0	36.0	0.45	NM_012225	B4DZY8|E9PGU3	Missense_Mutation	SNP	ENST00000215539.3	37	CCDS10446.1	165	0.07554945054945054	156	0.3170731707317073	9	0.024861878453038673	0	0.0	0	0.0	A	7.896	0.733364	0.15574	0.292766	9.3E-4	ENSG00000095906	ENST00000262302;ENST00000543305	T;T	0.40476	1.03;1.61	4.6	-9.03	0.00737	.	0.551776	0.20420	N	0.092691	T	0.00012	0.0000	N	0.03253	-0.375	0.80722	P	0.0	B	0.02656	0.0	B	0.09377	0.004	T	0.22941	-1.0202	9	0.14252	T	0.57	-10.367	2.1262	0.03739	0.2373:0.079:0.3155:0.3683	rs57822546;rs61739604	200	Q9Y5Y2	NUBP2_HUMAN	A	200;59	ENSP00000262302:T200A;ENSP00000437763:T59A	ENSP00000262302:T200A	T	+	1	0	NUBP2	1778051	0.000000	0.05858	0.004000	0.12327	0.013000	0.08279	-0.292000	0.08332	-1.796000	0.01253	-2.629000	0.00154	ACG	A|0.895;G|0.105	0.105	strong		0.662	IGFALS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250509.2		
ADRA2A	150	hgsc.bcm.edu	37	10	112838135	112838135	+	Silent	SNP	C	C	G	rs142434876	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:112838135C>G	ENST00000280155.2	+	1	1346	c.381C>G	c.(379-381)ctC>ctG	p.L127L		NM_000681.3	NP_000672.3	P08913	ADA2A_HUMAN	adrenoceptor alpha 2A	112					actin cytoskeleton organization (GO:0030036)|activation of MAPK activity by adrenergic receptor signaling pathway (GO:0071883)|activation of protein kinase activity (GO:0032147)|activation of protein kinase B activity (GO:0032148)|acute inflammatory response (GO:0002526)|adenylate cyclase-inhibiting adrenergic receptor signaling pathway (GO:0071881)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|cellular response to hormone stimulus (GO:0032870)|DNA replication (GO:0006260)|energy reserve metabolic process (GO:0006112)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|fear response (GO:0042596)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|intestinal absorption (GO:0050892)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of adrenergic receptor signaling pathway (GO:0071878)|negative regulation of calcium ion transmembrane transporter activity (GO:1901020)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of insulin secretion (GO:0046676)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of norepinephrine secretion (GO:0010700)|negative regulation of uterine smooth muscle contraction (GO:0070473)|phospholipase C-activating adrenergic receptor signaling pathway (GO:0071882)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokine production (GO:0001819)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|positive regulation of potassium ion transport (GO:0043268)|positive regulation of vasodilation (GO:0045909)|positive regulation of wound healing (GO:0090303)|Ras protein signal transduction (GO:0007265)|regulation of insulin secretion (GO:0050796)|regulation of vasoconstriction (GO:0019229)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|thermoception (GO:0050955)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	alpha-1B adrenergic receptor binding (GO:0031692)|alpha-2C adrenergic receptor binding (GO:0031696)|alpha2-adrenergic receptor activity (GO:0004938)|epinephrine binding (GO:0051379)|heterotrimeric G-protein binding (GO:0032795)|norepinephrine binding (GO:0051380)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|thioesterase binding (GO:0031996)			breast(1)|cervix(3)|endometrium(6)|large_intestine(3)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Breast(234;0.0735)|Lung NSC(174;0.238)		Epithelial(162;0.000316)|all cancers(201;0.00501)|BRCA - Breast invasive adenocarcinoma(275;0.118)	Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Apraclonidine(DB00964)|Aripiprazole(DB01238)|Asenapine(DB06216)|Benzphetamine(DB00865)|Bethanidine(DB00217)|Brimonidine(DB00484)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Desipramine(DB01151)|Dexmedetomidine(DB00633)|Dihydroergotamine(DB00320)|Dipivefrin(DB00449)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinastine(DB00751)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Flupirtine(DB06623)|Guanabenz(DB00629)|Guanfacine(DB01018)|Lisuride(DB00589)|Lofexidine(DB04948)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Methyldopa(DB00968)|Mianserin(DB06148)|Mirtazapine(DB00370)|Naphazoline(DB06711)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Phentolamine(DB00692)|Phenylpropanolamine(DB00397)|Pramipexole(DB00413)|Prazosin(DB00457)|Propericiazine(DB01608)|Pseudoephedrine(DB00852)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Tizanidine(DB00697)|Tolazoline(DB00797)|Trazodone(DB00656)|Trimipramine(DB00726)|Xylometazoline(DB06694)|Yohimbine(DB01392)|Ziprasidone(DB00246)	ACCTGGCGCTCGACGTGCTCT	0.602													C|||	4	0.000798722	0.0023	0.0014	5008	,	,		15105	0.0		0.0	False		,,,				2504	0.0				p.L127L	Esophageal Squamous(173;605 2658 7278 49362)	Atlas-SNP	.											.	ADRA2A	38	.	0			c.C381G						PASS	.	C		32,4374	36.8+/-68.6	0,32,2171	94.0	75.0	82.0		381	2.3	1.0	10	dbSNP_134	82	0,8600		0,0,4300	no	coding-synonymous	ADRA2A	NM_000681.3		0,32,6471	GG,GC,CC		0.0,0.7263,0.246		127/466	112838135	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	150	exon1			GGCGCTCGACGTG	AF284095	CCDS7569.2	10q25.2	2012-08-08	2012-05-09		ENSG00000150594	ENSG00000150594		"""GPCR / Class A : Adrenoceptors : alpha"""	281	protein-coding gene	gene with protein product	"""alpha-2AAR subtype C10"", "" alpha-2A-adrenergic receptor"""	104210	"""adrenergic, alpha-2A-, receptor"""	ADRA2, ADRA2R			Standard	NM_000681		Approved	ADRAR	uc001kzo.3	P08913	OTTHUMG00000019050	ENST00000280155.2:c.381C>G	10.37:g.112838135C>G		145.0	0.0	0		172.0	97.0	0.563953	NM_000681	B0LPF6|Q2I8G2|Q2XN99|Q86TH8|Q9BZK1	Silent	SNP	ENST00000280155.2	37	CCDS7569.2																																																																																			C|0.998;G|0.002	0.002	strong		0.602	ADRA2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050372.2	NM_000681	
MAPKAP1	79109	hgsc.bcm.edu	37	9	128206855	128206855	+	Silent	SNP	C	C	T	rs35549826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:128206855C>T	ENST00000373498.1	-	10	1436	c.1368G>A	c.(1366-1368)acG>acA	p.T456T	MAPKAP1_ENST00000394063.1_Silent_p.T264T|MAPKAP1_ENST00000373511.2_Silent_p.T409T|MAPKAP1_ENST00000265960.3_Silent_p.T456T|MAPKAP1_ENST00000373497.5_Silent_p.T169T|MAPKAP1_ENST00000373503.3_Silent_p.T264T|MAPKAP1_ENST00000350766.3_Silent_p.T420T|MAPKAP1_ENST00000483937.1_5'UTR			Q9BPZ7	SIN1_HUMAN	mitogen-activated protein kinase associated protein 1	456					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|negative regulation of Ras protein signal transduction (GO:0046580)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|substantia nigra development (GO:0021762)|T cell costimulation (GO:0031295)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|protein kinase binding (GO:0019901)|Ras GTPase binding (GO:0017016)			endometrium(2)|kidney(1)|large_intestine(2)|lung(15)|ovary(3)	23						TGCTTAGATACGTGAGTTTAA	0.453													c|||	29	0.00579073	0.0212	0.0014	5008	,	,		20762	0.0		0.0	False		,,,				2504	0.0				p.T456T		Atlas-SNP	.											MAPKAP1_ENST00000265960,NS,carcinoma,-1,4	MAPKAP1	68	4	0			c.G1368A						scavenged	.	T	,,,,	63,4343	59.9+/-96.7	1,61,2141	167.0	147.0	154.0		1368,1227,792,792,1260	-6.7	0.7	9	dbSNP_126	154	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MAPKAP1	NM_001006617.1,NM_001006619.1,NM_001006620.1,NM_001006621.1,NM_024117.3	,,,,	1,62,6440	TT,TC,CC		0.0116,1.4299,0.4921	,,,,	456/523,409/476,264/331,264/331,420/487	128206855	64,12942	2203	4300	6503	SO:0001819	synonymous_variant	79109	exon11			TAGATACGTGAGT	M37191	CCDS6864.1, CCDS35139.1, CCDS35140.1, CCDS35141.1, CCDS48020.1	9q34.11	2008-02-05			ENSG00000119487	ENSG00000119487			18752	protein-coding gene	gene with protein product	"""stress-activated protein kinase-interacting 1"""	610558				15363842	Standard	NM_001006620		Approved	MGC2745, SIN1, MIP1	uc004bpv.3	Q9BPZ7	OTTHUMG00000020683	ENST00000373498.1:c.1368G>A	9.37:g.128206855C>T		112.0	1.0	0.00892857		166.0	67.0	0.403614	NM_001006617	A8K1Z5|B1AMA4|B7Z309|Q00426|Q5JSV5|Q5JSV6|Q5JSV9|Q658R0|Q699U1|Q699U2|Q699U3|Q699U4|Q6GVJ0|Q6GVJ1|Q6GVJ2	Silent	SNP	ENST00000373498.1	37	CCDS35140.1	13	0.005952380952380952	12	0.024390243902439025	1	0.0027624309392265192	0	0.0	0	0.0	c	4.720	0.133973	0.09032	0.014299	1.16E-4	ENSG00000119487	ENST00000444226	.	.	.	5.91	-6.66	0.01789	.	.	.	.	.	T	0.34948	0.0915	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53457	-0.8436	4	.	.	.	-6.8579	10.2871	0.43573	0.0:0.2969:0.167:0.5361	rs35549826	.	.	.	I	28	.	.	V	-	1	0	MAPKAP1	127246676	0.012000	0.17670	0.657000	0.29651	0.643000	0.38383	-1.022000	0.03611	-1.316000	0.02295	-4.302000	0.00007	GTA	C|0.994;T|0.006	0.006	strong		0.453	MAPKAP1-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054092.1		
SARDH	1757	hgsc.bcm.edu	37	9	136577770	136577770	+	Silent	SNP	C	C	T	rs147188337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136577770C>T	ENST00000371872.4	-	10	1556	c.1299G>A	c.(1297-1299)ccG>ccA	p.P433P	SARDH_ENST00000439388.1_Silent_p.P433P|SARDH_ENST00000422262.2_Silent_p.P265P	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	433					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		TGTCCTTCTCCGGGCGCCCAT	0.642													C|||	12	0.00239617	0.0091	0.0	5008	,	,		16347	0.0		0.0	False		,,,				2504	0.0				p.P433P		Atlas-SNP	.											.	SARDH	112	.	0			c.G1299A						PASS	.	C	,	54,4352	54.9+/-90.9	0,54,2149	69.0	68.0	69.0		1299,1299	-9.4	0.5	9	dbSNP_134	69	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	SARDH	NM_001134707.1,NM_007101.3	,	0,55,6448	TT,TC,CC		0.0116,1.2256,0.4229	,	433/919,433/919	136577770	55,12951	2203	4300	6503	SO:0001819	synonymous_variant	1757	exon10			CTTCTCCGGGCGC		CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.1299G>A	9.37:g.136577770C>T		59.0	0.0	0		58.0	42.0	0.724138	NM_007101	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Silent	SNP	ENST00000371872.4	37	CCDS6978.1																																																																																			C|0.996;T|0.004	0.004	strong		0.642	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1		
FAM83G	644815	hgsc.bcm.edu	37	17	18881225	18881225	+	Missense_Mutation	SNP	T	T	A	rs200348726	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18881225T>A	ENST00000388995.6	-	5	1977	c.1754A>T	c.(1753-1755)gAc>gTc	p.D585V	SLC5A10_ENST00000417251.2_Intron|FAM83G_ENST00000345041.4_Missense_Mutation_p.D585V|SLC5A10_ENST00000395647.2_Intron|SLC5A10_ENST00000395643.2_Intron|SLC5A10_ENST00000395642.1_Intron|SLC5A10_ENST00000317977.6_Intron|FAM83G_ENST00000585154.2_Missense_Mutation_p.D585V|SLC5A10_ENST00000395645.3_Intron			A6ND36	FA83G_HUMAN	family with sequence similarity 83, member G	585	Poly-Asp.				BMP signaling pathway (GO:0030509)	cytosol (GO:0005829)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(3)|stomach(1)	22						TACGTAGTCGTCATCATCTTC	0.652													T|||	4	0.000798722	0.003	0.0	5008	,	,		16212	0.0		0.0	False		,,,				2504	0.0				p.D585V		Atlas-SNP	.											.	FAM83G	51	.	0			c.A1754T						PASS	.	T	VAL/ASP,,	12,4022		0,12,2005	45.0	52.0	50.0		1754,,	5.9	0.5	17		50	0,8316		0,0,4158	yes	missense,intron,intron	SLC5A10,FAM83G	NM_001039999.2,NM_001042450.1,NM_152351.3	152,,	0,12,6163	AA,AT,TT		0.0,0.2975,0.0972	probably-damaging,,	585/824,,	18881225	12,12338	2017	4158	6175	SO:0001583	missense	644815	exon5			TAGTCGTCATCAT	AK123558	CCDS42276.1	17p11.2	2014-05-01	2006-03-22		ENSG00000188522	ENSG00000188522			32554	protein-coding gene	gene with protein product	"""protein associated with SMAD1"""	615886				24554596	Standard	NM_001039999		Approved	FLJ41564, PAWS1	uc002guw.3	A6ND36	OTTHUMG00000059411	ENST00000388995.6:c.1754A>T	17.37:g.18881225T>A	ENSP00000373647:p.Asp585Val	54.0	0.0	0		59.0	35.0	0.59322	NM_001039999	Q3KQZ4|Q6ZW60	Missense_Mutation	SNP	ENST00000388995.6	37	CCDS42276.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	20.7	4.038233	0.75617	0.002975	0.0	ENSG00000188522	ENST00000388995;ENST00000345041	T;T	0.15139	2.45;2.45	5.91	5.91	0.95273	.	0.446831	0.22573	N	0.058301	T	0.41119	0.1145	M	0.67953	2.075	0.80722	D	1	D	0.71674	0.998	D	0.68353	0.957	T	0.20974	-1.0259	10	0.87932	D	0	-28.3264	16.0171	0.80450	0.0:0.0:0.0:1.0	.	585	A6ND36	FA83G_HUMAN	V	585	ENSP00000373647:D585V;ENSP00000343279:D585V	ENSP00000343279:D585V	D	-	2	0	FAM83G	18821950	0.972000	0.33761	0.512000	0.27736	0.887000	0.51463	2.926000	0.48892	2.269000	0.75478	0.533000	0.62120	GAC	T|1.000;A|0.000	0.000	strong		0.652	FAM83G-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253108.4		
AHNAK2	113146	hgsc.bcm.edu	37	14	105417738	105417738	+	Silent	SNP	G	G	C	rs536679222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105417738G>C	ENST00000333244.5	-	7	4169	c.4050C>G	c.(4048-4050)tcC>tcG	p.S1350S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1350						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			ACAGGTCCACGGAGGCCTCAA	0.592													.|||	371	0.0740815	0.0136	0.1398	5008	,	,		14224	0.0119		0.1571	False		,,,				2504	0.0879				p.S1350S		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C4050G						PASS	.						129.0	111.0	118.0					14																	105417738		1816	2913	4729	SO:0001819	synonymous_variant	113146	exon7			GTCCACGGAGGCC	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.4050C>G	14.37:g.105417738G>C		371.0	0.0	0		265.0	107.0	0.403774	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			.	.	none		0.592	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
HIST1H2BH	8345	hgsc.bcm.edu	37	6	26252148	26252148	+	Silent	SNP	C	C	T	rs61746493	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:26252148C>T	ENST00000356350.2	+	1	270	c.270C>T	c.(268-270)atC>atT	p.I90I	HIST1H3F_ENST00000446824.2_5'Flank	NM_003524.2	NP_003515.1	Q93079	H2B1H_HUMAN	histone cluster 1, H2bh	90					chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(3)|breast(2)|large_intestine(1)|lung(3)|ovary(3)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	17						GTTCGACCATCACCTCCAGGG	0.597													C|||	185	0.0369409	0.1309	0.0144	5008	,	,		18322	0.0		0.002	False		,,,				2504	0.0				p.I90I		Atlas-SNP	.											.	HIST1H2BH	36	.	0			c.C270T						PASS	.	C		426,3980		22,382,1799	85.0	89.0	88.0		270	3.7	1.0	6	dbSNP_129	88	27,8573		0,27,4273	no	coding-synonymous	HIST1H2BH	NM_003524.2		22,409,6072	TT,TC,CC		0.314,9.6686,3.483		90/127	26252148	453,12553	2203	4300	6503	SO:0001819	synonymous_variant	8345	exon1			GACCATCACCTCC	Z80781	CCDS4601.1	6p21.3	2011-01-27	2006-10-11	2003-02-14	ENSG00000197459	ENSG00000275713		"""Histones / Replication-dependent"""	4755	protein-coding gene	gene with protein product		602806	"""H2B histone family, member J"", ""histone 1, H2bh"""	H2BFJ		9119399, 12408966	Standard	NM_003524		Approved	H2B/j	uc003nhh.3	Q93079	OTTHUMG00000014447	ENST00000356350.2:c.270C>T	6.37:g.26252148C>T		136.0	0.0	0		171.0	91.0	0.532164	NM_003524	B2R541|Q4VB74	Silent	SNP	ENST00000356350.2	37	CCDS4601.1																																																																																			C|0.968;T|0.032	0.032	strong		0.597	HIST1H2BH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040110.1	NM_003524	
PLEKHG2	64857	hgsc.bcm.edu	37	19	39915677	39915677	+	Missense_Mutation	SNP	G	G	A	rs34603507		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39915677G>A	ENST00000409794.3	+	19	4754	c.3904G>A	c.(3904-3906)Gca>Aca	p.A1302T	PLEKHG2_ENST00000458508.2_Intron|PLEKHG2_ENST00000409797.2_Intron|PLEKHG2_ENST00000425673.1_Missense_Mutation_p.A1273T|CTB-60E11.4_ENST00000601124.1_lincRNA|PLEKHG2_ENST00000378550.1_Intron	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	1302			A -> T (in dbSNP:rs34603507).		apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			AGGGGCCCCCGCAGCCTCCCG	0.721													G|||	1	0.000199681	0.0008	0.0	5008	,	,		11603	0.0		0.0	False		,,,				2504	0.0				p.A1302T		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.G3904A						PASS	.	G	THR/ALA	5,4237		0,5,2116	13.0	16.0	15.0		3904	-7.2	0.0	19	dbSNP_126	15	0,8448		0,0,4224	no	missense	PLEKHG2	NM_022835.2	58	0,5,6340	AA,AG,GG		0.0,0.1179,0.0394	benign	1302/1387	39915677	5,12685	2121	4224	6345	SO:0001583	missense	64857	exon19			GCCCCCGCAGCCT	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.3904G>A	19.37:g.39915677G>A	ENSP00000386733:p.Ala1302Thr	27.0	0.0	0		26.0	17.0	0.653846	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Missense_Mutation	SNP	ENST00000409794.3	37	CCDS33022.2	.	.	.	.	.	.	.	.	.	.	G	10.97	1.500290	0.26861	0.001179	0.0	ENSG00000090924	ENST00000409794;ENST00000425673	T;T	0.67171	-0.24;-0.25	4.35	-7.16	0.01516	.	1.186420	0.06463	N	0.729685	T	0.34513	0.0900	N	0.05383	-0.06	0.09310	N	1	B;B	0.12013	0.005;0.003	B;B	0.06405	0.002;0.001	T	0.13602	-1.0503	9	.	.	.	.	2.4588	0.04536	0.1357:0.2896:0.4002:0.1745	rs34603507	1273;1302	Q9H7P9-3;Q9H7P9	.;PKHG2_HUMAN	T	1302;1273	ENSP00000386733:A1302T;ENSP00000392906:A1273T	.	A	+	1	0	PLEKHG2	44607517	0.000000	0.05858	0.000000	0.03702	0.833000	0.47200	-0.923000	0.04000	-1.368000	0.02149	-1.305000	0.01319	GCA	G|0.970;A|0.030	0.030	strong		0.721	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835	
TATDN3	128387	hgsc.bcm.edu	37	1	212969889	212969889	+	Missense_Mutation	SNP	G	G	A	rs55709122	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:212969889G>A	ENST00000366974.4	+	3	224	c.130G>A	c.(130-132)Gaa>Aaa	p.E44K	TATDN3_ENST00000525569.1_3'UTR|TATDN3_ENST00000531963.1_Missense_Mutation_p.E44K|TATDN3_ENST00000366973.4_Missense_Mutation_p.E44K|TATDN3_ENST00000532324.1_Missense_Mutation_p.E44K|TATDN3_ENST00000530441.1_Missense_Mutation_p.E44K|TATDN3_ENST00000526641.1_Missense_Mutation_p.E44K|TATDN3_ENST00000526997.1_Missense_Mutation_p.E44K	NM_001042552.2|NM_001042553.2|NM_001146169.1|NM_001146171.1	NP_001036017.1|NP_001036018.1|NP_001139641.1|NP_001139643.1	Q17R31	TATD3_HUMAN	TatD DNase domain containing 3	44					DNA catabolic process (GO:0006308)	intracellular organelle (GO:0043229)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(6)	9				OV - Ovarian serous cystadenocarcinoma(81;0.00699)|all cancers(67;0.0118)|GBM - Glioblastoma multiforme(131;0.0801)|Epithelial(68;0.104)		GGCAGTTGCCGAACATTCAGG	0.289													G|||	8	0.00159744	0.0061	0.0	5008	,	,		13128	0.0		0.0	False		,,,				2504	0.0				p.E44K		Atlas-SNP	.											.	TATDN3	23	.	0			c.G130A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	43,4363	41.6+/-74.8	0,43,2160	38.0	41.0	40.0		130,130,130,130,130	5.8	1.0	1	dbSNP_129	40	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense	TATDN3	NM_001042552.2,NM_001042553.2,NM_001146169.1,NM_001146170.1,NM_001146171.1	56,56,56,56,56	0,43,6460	AA,AG,GG		0.0,0.9759,0.3306	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	44/275,44/274,44/241,44/254,44/282	212969889	43,12963	2203	4300	6503	SO:0001583	missense	128387	exon3			GTTGCCGAACATT	AL832248	CCDS31019.1, CCDS41465.1, CCDS53475.1, CCDS53476.1, CCDS53477.1	1q32.3	2008-02-05			ENSG00000203705	ENSG00000203705			27010	protein-coding gene	gene with protein product							Standard	NM_001042552		Approved		uc001hjo.2	Q17R31	OTTHUMG00000036805	ENST00000366974.4:c.130G>A	1.37:g.212969889G>A	ENSP00000355941:p.Glu44Lys	78.0	0.0	0		99.0	52.0	0.525253	NM_001146170	A6NGS3|B7Z1C1|B7Z978|B7ZLQ6|E9PJE5|E9PNH3|G3V151|Q4G0L1	Missense_Mutation	SNP	ENST00000366974.4	37	CCDS31019.1	5|5	0.0022893772893772895|0.0022893772893772895	5|5	0.01016260162601626|0.01016260162601626	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	29.3|29.3	4.990408|4.990408	0.93106|0.93106	0.009759|0.009759	0.0|0.0	ENSG00000203705|ENSG00000203705	ENST00000532324;ENST00000366974;ENST00000530441;ENST00000526641;ENST00000531963;ENST00000366973;ENST00000526997;ENST00000530399|ENST00000488246	.|.	.|.	.|.	5.75|5.75	5.75|5.75	0.90469|0.90469	.|.	0.046199|.	0.85682|.	D|.	0.000000|.	T|T	0.69904|0.69904	0.3163|0.3163	M|M	0.72118|0.72118	2.19|2.19	0.80722|0.80722	D|D	1|1	D;D;D;D;D|.	0.67145|.	0.995;0.996;0.995;0.989;0.992|.	P;P;P;P;P|.	0.61275|.	0.836;0.836;0.886;0.658;0.769|.	T|T	0.71938|0.71938	-0.4441|-0.4441	9|5	0.29301|.	T|.	0.29|.	-8.3766|-8.3766	18.7217|18.7217	0.91697|0.91697	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs55709122|rs55709122	44;44;44;44;44|.	E9PNH3;G3V151;E9PJE5;Q17R31-2;Q17R31|.	.;.;.;.;TATD3_HUMAN|.	K|Q	44;44;44;44;44;44;44;43|43	.|.	ENSP00000355940:E44K|.	E|R	+|+	1|2	0|0	TATDN3|TATDN3	211036512|211036512	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.952000|0.952000	0.60782|0.60782	4.428000|4.428000	0.59894|0.59894	2.731000|2.731000	0.93534|0.93534	0.555000|0.555000	0.69702|0.69702	GAA|CGA	G|0.997;A|0.003	0.003	strong		0.289	TATDN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089396.2	XM_375838	
ULK1	8408	hgsc.bcm.edu	37	12	132404101	132404101	+	Silent	SNP	C	C	T	rs143340589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132404101C>T	ENST00000321867.4	+	25	3120	c.2769C>T	c.(2767-2769)gcC>gcT	p.A923A	ULK1_ENST00000540647.1_Silent_p.A168A	NM_003565.2	NP_003556	O75385	ULK1_HUMAN	unc-51 like autophagy activating kinase 1	923					autophagic vacuole assembly (GO:0000045)|axon extension (GO:0048675)|cellular response to nutrient levels (GO:0031669)|cerebellar granule cell differentiation (GO:0021707)|negative regulation of collateral sprouting (GO:0048671)|neuron projection development (GO:0031175)|neuron projection regeneration (GO:0031102)|positive regulation of autophagy (GO:0010508)|positive regulation of macroautophagy (GO:0016239)|protein autophosphorylation (GO:0046777)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|radial glia guided migration of cerebellar granule cell (GO:0021933)|Ras protein signal transduction (GO:0007265)|receptor internalization (GO:0031623)|regulation of autophagy (GO:0010506)|regulation of neurotrophin TRK receptor signaling pathway (GO:0051386)|response to starvation (GO:0042594)	ATG1/UKL1 signaling complex (GO:0034273)|autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extrinsic component of autophagic vacuole membrane (GO:0097635)|extrinsic component of omegasome membrane (GO:0097629)|extrinsic component of pre-autophagosomal structure membrane (GO:0097632)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)	ATP binding (GO:0005524)|protein complex binding (GO:0032403)|protein serine/threonine kinase activity (GO:0004674)|Rab GTPase binding (GO:0017137)			breast(1)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	29	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;2.07e-08)|Epithelial(86;2.56e-07)|all cancers(50;3.01e-07)		AGATCCGGGCCGGCAAGCTCT	0.662													C|||	7	0.00139776	0.0053	0.0	5008	,	,		16277	0.0		0.0	False		,,,				2504	0.0				p.A923A		Atlas-SNP	.											.	ULK1	92	.	0			c.C2769T						PASS	.	C		29,4377	34.3+/-65.2	0,29,2174	62.0	66.0	65.0		2769	-4.8	0.9	12	dbSNP_134	65	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	ULK1	NM_003565.2		0,30,6472	TT,TC,CC		0.0116,0.6582,0.2307		923/1051	132404101	30,12974	2203	4299	6502	SO:0001819	synonymous_variant	8408	exon25			CCGGGCCGGCAAG	AF045458	CCDS9274.1	12q24.3	2014-02-12	2013-07-02		ENSG00000177169	ENSG00000177169			12558	protein-coding gene	gene with protein product	"""ATG1 autophagy related 1 homolog (S. cerevisiae)"""	603168	"""unc-51 (C. elegans)-like kinase 1"", ""unc-51-like kinase 1 (C. elegans)"""			9693035	Standard	NM_003565		Approved	ATG1, ATG1A	uc001uje.3	O75385	OTTHUMG00000168052	ENST00000321867.4:c.2769C>T	12.37:g.132404101C>T		102.0	0.0	0		77.0	28.0	0.363636	NM_003565	Q9UQ28	Silent	SNP	ENST00000321867.4	37	CCDS9274.1																																																																																			C|0.998;T|0.002	0.002	strong		0.662	ULK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397769.3		
FAM179B	23116	hgsc.bcm.edu	37	14	45473265	45473265	+	Splice_Site	SNP	G	G	A	rs17092470	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:45473265G>A	ENST00000361577.3	+	4	2554	c.2340G>A	c.(2338-2340)gtG>gtA	p.V780V	FAM179B_ENST00000361462.2_Splice_Site_p.V780V|KLHL28_ENST00000553817.1_Intron|FAM179B_ENST00000382233.2_Splice_Site_p.V780V	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	780										endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						TTATTACAGTGTATGCTAGCC	0.338													G|||	262	0.0523163	0.1899	0.0159	5008	,	,		17095	0.0		0.0	False		,,,				2504	0.0				p.V780V		Atlas-SNP	.											.	FAM179B	115	.	0			c.G2340A						PASS	.	G		688,3718	284.6+/-277.7	50,588,1565	47.0	43.0	44.0		2340	-0.8	0.1	14	dbSNP_123	44	7,8593	5.0+/-18.6	0,7,4293	yes	coding-synonymous-near-splice	FAM179B	NM_015091.2		50,595,5858	AA,AG,GG		0.0814,15.6151,5.3437		780/1721	45473265	695,12311	2203	4300	6503	SO:0001630	splice_region_variant	23116	exon4			TACAGTGTATGCT	AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"""KIAA0423"""	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.2339-1G>A	14.37:g.45473265G>A		27.0	0.0	0		37.0	16.0	0.432432	NM_015091	Q68D66|Q6PG27	Silent	SNP	ENST00000361577.3	37	CCDS9681.1																																																																																			G|0.948;A|0.052	0.052	strong		0.338	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781	Silent
GPR17	2840	hgsc.bcm.edu	37	2	128408747	128408747	+	Silent	SNP	C	C	A	rs34722685	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128408747C>A	ENST00000272644.3	+	3	596	c.522C>A	c.(520-522)ctC>ctA	p.L174L	LIMS2_ENST00000410038.1_5'Flank|LIMS2_ENST00000545738.2_Intron|GPR17_ENST00000544369.1_Silent_p.L174L|LIMS2_ENST00000410011.1_Intron|LIMS2_ENST00000324938.5_Intron|LIMS2_ENST00000409254.1_5'Flank|LIMS2_ENST00000409455.1_Intron|LIMS2_ENST00000355119.4_Intron|LIMS2_ENST00000409808.2_Intron|GPR17_ENST00000393018.3_Silent_p.L174L|GPR17_ENST00000486700.1_3'UTR	NM_001161416.1|NM_001161417.1|NM_005291.2	NP_001154888.1|NP_001154889.1|NP_005282.1	Q13304	GPR17_HUMAN	G protein-coupled receptor 17	174					chemokine-mediated signaling pathway (GO:0070098)|G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	chemokine receptor activity (GO:0004950)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(11)|prostate(2)|urinary_tract(1)	19	Colorectal(110;0.1)	Ovarian(717;0.15)		BRCA - Breast invasive adenocarcinoma(221;0.0677)		GCAGGCCCCTCTACGCACACC	0.637													C|||	70	0.0139776	0.0499	0.0058	5008	,	,		18872	0.0		0.0	False		,,,				2504	0.0				p.L174L		Atlas-SNP	.											.	GPR17	56	.	0			c.C522A						PASS	.	C	,,,,,,,	158,4248	106.5+/-144.9	2,154,2047	112.0	99.0	103.0		,,,522,438,438,522,	3.6	1.0	2	dbSNP_126	103	1,8599		0,1,4299	no	intron,intron,intron,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron	GPR17,LIMS2	NM_001136037.2,NM_001161403.1,NM_001161404.1,NM_001161415.1,NM_001161416.1,NM_001161417.1,NM_005291.2,NM_017980.4	,,,,,,,	2,155,6346	AA,AC,CC		0.0116,3.586,1.2225	,,,,,,,	,,,174/368,146/340,146/340,174/368,	128408747	159,12847	2203	4300	6503	SO:0001819	synonymous_variant	2840	exon3			GCCCCTCTACGCA		CCDS2148.1	2q21	2014-01-30			ENSG00000144230	ENSG00000144230		"""GPCR / Class A : Orphans"""	4471	protein-coding gene	gene with protein product		603071				8558062	Standard	NM_001161415		Approved		uc002tpc.3	Q13304	OTTHUMG00000131533	ENST00000272644.3:c.522C>A	2.37:g.128408747C>A		84.0	0.0	0		88.0	44.0	0.5	NM_005291	A8K9L0|B2R9X0|Q8N5S7|Q9UDZ6|Q9UE21	Silent	SNP	ENST00000272644.3	37	CCDS2148.1																																																																																			C|0.985;A|0.015	0.015	strong		0.637	GPR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254390.1		
WDR66	144406	hgsc.bcm.edu	37	12	122396424	122396424	+	Silent	SNP	C	C	A	rs73415652	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:122396424C>A	ENST00000288912.4	+	12	2831	c.1977C>A	c.(1975-1977)ccC>ccA	p.P659P	WDR66_ENST00000397454.2_Silent_p.P659P	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	659							calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(13)|ovary(2)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		CCTACAACCCCGAAGGTATTT	0.488													G|||	372	0.0742812	0.2572	0.0202	5008	,	,		19706	0.0		0.0	False		,,,				2504	0.0184				p.P659P	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											.	WDR66	143	.	0			c.C1977A						PASS	.	G	,	729,3035		71,587,1224	182.0	178.0	180.0		1977,1977	-10.6	0.0	12	dbSNP_130	180	8,8194		0,8,4093	no	coding-synonymous,coding-synonymous	WDR66	NM_001178003.1,NM_144668.5	,	71,595,5317	AA,AC,CC		0.0975,19.3677,6.1591	,	659/942,659/1150	122396424	737,11229	1882	4101	5983	SO:0001819	synonymous_variant	144406	exon12			CAACCCCGAAGGT	AL833930	CCDS41853.1, CCDS53840.1	12q24.31	2014-07-31			ENSG00000158023	ENSG00000158023		"""WD repeat domain containing"""	28506	protein-coding gene	gene with protein product						17967944	Standard	NM_001178003		Approved	MGC33630, CaM-IP4	uc009zxk.3	Q8TBY9	OTTHUMG00000168948	ENST00000288912.4:c.1977C>A	12.37:g.122396424C>A		119.0	0.0	0		123.0	68.0	0.552846	NM_001178003	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Silent	SNP	ENST00000288912.4	37	CCDS41853.1																																																																																			C|0.963;A|0.037	0.037	strong		0.488	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668	
ZFP36	7538	hgsc.bcm.edu	37	19	39898521	39898521	+	Missense_Mutation	SNP	C	C	T	rs2229272		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39898521C>T	ENST00000248673.3	+	2	221	c.163C>T	c.(163-165)Cct>Tct	p.P55S	ZFP36_ENST00000594045.1_3'UTR|ZFP36_ENST00000597629.1_Missense_Mutation_p.P61S|MIR4530_ENST00000581459.1_RNA	NM_003407.3	NP_003398.2	P26651	TTP_HUMAN	ZFP36 ring finger protein	55			P -> S (in dbSNP:rs2229272).		3'-UTR-mediated mRNA stabilization (GO:0070935)|gene expression (GO:0010467)|intracellular signal transduction (GO:0035556)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|negative regulation of inflammatory response (GO:0050728)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of tumor necrosis factor production (GO:0032680)|response to starvation (GO:0042594)|RNA destabilization (GO:0050779)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|AU-rich element binding (GO:0017091)|C-C chemokine binding (GO:0019957)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|single-stranded RNA binding (GO:0003727)			large_intestine(1)|lung(5)|pancreas(1)	7	all_cancers(60;6.54e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;1.53e-06)|Ovarian(47;0.0512)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CTCCCGCCTGCCTGGCCGCTC	0.736													C|||	1	0.000199681	0.0008	0.0	5008	,	,		11689	0.0		0.0	False		,,,				2504	0.0				p.P61S	NSCLC(67;1164 1324 12056 21056 30097)	Atlas-SNP	.											.	ZFP36	19	.	0			c.C181T						PASS	.	C	SER/PRO	3,4271		0,3,2134	15.0	19.0	18.0		163	2.8	1.0	19	dbSNP_98	18	0,8330		0,0,4165	no	missense	ZFP36	NM_003407.2	74	0,3,6299	TT,TC,CC		0.0,0.0702,0.0238	benign	55/327	39898521	3,12601	2137	4165	6302	SO:0001583	missense	7538	exon2			CGCCTGCCTGGCC	M63625	CCDS12534.1, CCDS12534.2	19q13.1	2012-11-27	2012-11-27			ENSG00000128016		"""RING-type (C3HC4) zinc fingers"""	12862	protein-coding gene	gene with protein product		190700	"""zinc finger protein 36, C3H type, homolog (mouse)"""			1699942	Standard	NM_003407		Approved	RNF162A, TIS11, G0S24, TTP, NUP475, tristetraprolin	uc002olh.2	P26651		ENST00000248673.3:c.163C>T	19.37:g.39898521C>T	ENSP00000248673:p.Pro55Ser	25.0	0.0	0		32.0	18.0	0.5625	NM_003407	B2RA54	Missense_Mutation	SNP	ENST00000248673.3	37		2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	11.91	1.779652	0.31502	7.02E-4	0.0	ENSG00000128016	ENST00000248673	T	0.18174	2.23	3.91	2.84	0.33178	.	0.070080	0.56097	D	0.000022	T	0.10809	0.0264	N	0.24115	0.695	0.26691	N	0.971344	B	0.20052	0.041	B	0.18871	0.023	T	0.22347	-1.0219	10	0.29301	T	0.29	-3.1484	10.0703	0.42328	0.2111:0.7889:0.0:0.0	rs2229272	55	P26651	TTP_HUMAN	S	55	ENSP00000248673:P55S	ENSP00000248673:P55S	P	+	1	0	ZFP36	44590361	0.842000	0.29525	1.000000	0.80357	0.750000	0.42670	1.235000	0.32671	0.799000	0.34018	0.549000	0.68633	CCT	C|0.998;T|0.002	0.002	strong		0.736	ZFP36-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding			
CEP170	9859	hgsc.bcm.edu	37	1	243328226	243328226	+	Silent	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:243328226A>G	ENST00000366542.1	-	13	3087	c.3036T>C	c.(3034-3036)agT>agC	p.S1012S	CEP170_ENST00000366543.1_Silent_p.S914S|RP11-261C10.4_ENST00000437499.1_RNA|CEP170_ENST00000366544.1_Silent_p.S914S|RP11-261C10.4_ENST00000422938.1_RNA|CEP170_ENST00000490813.1_5'Flank	NM_014812.2	NP_055627.2	Q5SW79	CE170_HUMAN	centrosomal protein 170kDa	1012	Targeting to microtubules.					centriole (GO:0005814)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nuclear membrane (GO:0031965)				NS(1)|breast(2)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(14)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	62	all_neural(11;0.101)	all_cancers(173;0.003)	all cancers(7;5.81e-06)|GBM - Glioblastoma multiforme(7;0.000443)|OV - Ovarian serous cystadenocarcinoma(106;0.0101)			TTATTCTCCCACTGGACTGAA	0.408																																					p.S1012S		Atlas-SNP	.											.	CEP170	153	.	0			c.T3036C						PASS	.						157.0	139.0	145.0					1																	243328226		1909	4120	6029	SO:0001819	synonymous_variant	9859	exon13			TCTCCCACTGGAC	AB022657	CCDS44337.1, CCDS44338.1, CCDS44339.1	1q44	2014-02-20	2006-01-12	2006-01-12	ENSG00000143702	ENSG00000143702			28920	protein-coding gene	gene with protein product	"""KARP 1 binding protein"", ""XRCC5 binding protein"""	613023	"""KIAA0470"""	KIAA0470		15616186	Standard	NM_014812		Approved	KAB, FAM68A	uc021plo.1	Q5SW79	OTTHUMG00000039862	ENST00000366542.1:c.3036T>C	1.37:g.243328226A>G		527.0	0.0	0		616.0	236.0	0.383117	NM_014812	O75058|Q5SW77|Q5SW78|Q7LGA9|Q86W31|Q9UQ08|Q9UQ09	Silent	SNP	ENST00000366542.1	37	CCDS44339.1	.	.	.	.	.	.	.	.	.	.	A	1.317	-0.600452	0.03744	.	.	ENSG00000143702	ENST00000336415	.	.	.	4.37	4.37	0.52481	.	.	.	.	.	T	0.64125	0.2570	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63567	-0.6608	4	.	.	.	-11.7439	12.8963	0.58101	1.0:0.0:0.0:0.0	.	.	.	.	A	976	.	.	V	-	2	0	CEP170	241394849	1.000000	0.71417	1.000000	0.80357	0.588000	0.36517	1.938000	0.40203	1.823000	0.53134	0.454000	0.30748	GTG	.	.	none		0.408	CEP170-003	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096178.2	NM_014812	
LRRC55	219527	hgsc.bcm.edu	37	11	56949529	56949529	+	Silent	SNP	C	C	T	rs80306837	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:56949529C>T	ENST00000497933.1	+	1	309	c.162C>T	c.(160-162)ccC>ccT	p.P54P		NM_001005210.2	NP_001005210.1	Q6ZSA7	LRC55_HUMAN	leucine rich repeat containing 55	24	LRRNT.				ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|skin(2)	25						TTCCCTGGCCCGGGCCACCCC	0.632													C|||	184	0.0367412	0.1339	0.0101	5008	,	,		18733	0.0		0.0	False		,,,				2504	0.0				p.P54P		Atlas-SNP	.											.	LRRC55	52	.	0			c.C162T						PASS	.	C		516,3886	234.9+/-247.6	28,460,1713	43.0	38.0	40.0		162	-11.3	0.8	11	dbSNP_131	40	4,8588	3.7+/-12.6	0,4,4292	no	coding-synonymous	LRRC55	NM_001005210.2		28,464,6005	TT,TC,CC		0.0466,11.7219,4.0018		54/342	56949529	520,12474	2201	4296	6497	SO:0001819	synonymous_variant	219527	exon1			CTGGCCCGGGCCA		CCDS31539.1	11q12.1	2008-02-05			ENSG00000183908	ENSG00000183908			32324	protein-coding gene	gene with protein product		615213					Standard	NM_001005210		Approved	FLJ45686	uc001njl.2	Q6ZSA7	OTTHUMG00000159309	ENST00000497933.1:c.162C>T	11.37:g.56949529C>T		185.0	0.0	0		142.0	66.0	0.464789	NM_001005210	A7E2U7|B2RN81	Silent	SNP	ENST00000497933.1	37	CCDS31539.1																																																																																			C|0.952;T|0.048	0.048	strong		0.632	LRRC55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354503.2	NM_001005210	
S1PR1	1901	hgsc.bcm.edu	37	1	101704772	101704772	+	Silent	SNP	C	C	A	rs150493209	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:101704772C>A	ENST00000305352.6	+	2	607	c.232C>A	c.(232-234)Cga>Aga	p.R78R	S1PR1_ENST00000475821.1_3'UTR|RP4-575N6.4_ENST00000432195.1_RNA	NM_001400.4	NP_001391.2	P21453	S1PR1_HUMAN	sphingosine-1-phosphate receptor 1	78					actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|angiogenesis (GO:0001525)|blood vessel maturation (GO:0001955)|brain development (GO:0007420)|cardiac muscle tissue growth involved in heart morphogenesis (GO:0003245)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|chemotaxis (GO:0006935)|endothelial cell differentiation (GO:0045446)|G-protein coupled receptor signaling pathway (GO:0007186)|heart trabecula morphogenesis (GO:0061384)|lamellipodium assembly (GO:0030032)|negative regulation of stress fiber assembly (GO:0051497)|neuron differentiation (GO:0030182)|positive regulation of cell migration (GO:0030335)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of bone mineralization (GO:0030500)|regulation of bone resorption (GO:0045124)|regulation of cell adhesion (GO:0030155)|sphingosine-1-phosphate signaling pathway (GO:0003376)|T cell migration (GO:0072678)|transmission of nerve impulse (GO:0019226)	endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|G-protein coupled receptor binding (GO:0001664)|sphingolipid binding (GO:0046625)|sphingosine-1-phosphate receptor activity (GO:0038036)			NS(1)|autonomic_ganglia(1)|breast(1)|large_intestine(7)|lung(23)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	43						GAAATTCCACCGACCCATGTA	0.473											OREG0013620	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	3	0.000599042	0.0023	0.0	5008	,	,		20524	0.0		0.0	False		,,,				2504	0.0				p.R78R		Atlas-SNP	.											.	S1PR1	87	.	0			c.C232A						PASS	.	C		5,4401	9.9+/-24.2	0,5,2198	113.0	115.0	114.0		232	5.0	1.0	1	dbSNP_134	114	0,8600		0,0,4300	no	coding-synonymous	S1PR1	NM_001400.4		0,5,6498	AA,AC,CC		0.0,0.1135,0.0384		78/383	101704772	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	1901	exon2			TTCCACCGACCCA	M31210	CCDS777.1	1p21	2012-08-08	2008-04-30	2008-04-30	ENSG00000170989	ENSG00000170989		"""GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"", ""CD molecules"""	3165	protein-coding gene	gene with protein product		601974	"""endothelial differentiation, sphingolipid G-protein-coupled receptor, 1"""	EDG1		2160972, 9488656	Standard	NM_001400		Approved	edg-1, D1S3362, CD363	uc001dud.2	P21453	OTTHUMG00000010835	ENST00000305352.6:c.232C>A	1.37:g.101704772C>A		164.0	0.0	0	1360	139.0	62.0	0.446043	NM_001400	D3DT66|Q9BYY4|Q9NYN8	Silent	SNP	ENST00000305352.6	37	CCDS777.1																																																																																			C|1.000;A|0.000	0.000	strong		0.473	S1PR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029908.1	NM_001400	
ZBED2	79413	hgsc.bcm.edu	37	3	111312965	111312965	+	Silent	SNP	A	A	T	rs34083626	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:111312965A>T	ENST00000317012.4	-	2	1092	c.84T>A	c.(82-84)atT>atA	p.I28I	CD96_ENST00000283285.5_Intron|CD96_ENST00000352690.4_Intron|CD96_ENST00000438817.2_Intron	NM_024508.4	NP_078784.2	Q9BTP6	ZBED2_HUMAN	zinc finger, BED-type containing 2	28							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(3)|lung(1)|skin(2)	6						CTGTCTCACTAATCTCTTCCT	0.517													A|||	266	0.053115	0.1891	0.0187	5008	,	,		14454	0.0		0.003	False		,,,				2504	0.0				p.I28I		Atlas-SNP	.											.	ZBED2	22	.	0			c.T84A						PASS	.	A	,,	642,3764	274.6+/-272.0	38,566,1599	268.0	221.0	237.0		,84,	0.4	0.0	3	dbSNP_126	237	9,8591	5.7+/-21.5	0,9,4291	no	intron,coding-synonymous,intron	CD96,ZBED2	NM_005816.4,NM_024508.4,NM_198196.2	,,	38,575,5890	TT,TA,AA		0.1047,14.571,5.0054	,,	,28/219,	111312965	651,12355	2203	4300	6503	SO:0001819	synonymous_variant	79413	exon2			CTCACTAATCTCT	BC003536	CCDS2960.2	3p13-q13.2	2013-05-03			ENSG00000177494	ENSG00000177494		"""Zinc fingers, BED-type"""	20710	protein-coding gene	gene with protein product		615246				23533661	Standard	NM_024508		Approved	MGC10796	uc003dxy.3	Q9BTP6	OTTHUMG00000074061	ENST00000317012.4:c.84T>A	3.37:g.111312965A>T		265.0	1.0	0.00377358		304.0	136.0	0.447368	NM_024508	D3DN62	Silent	SNP	ENST00000317012.4	37	CCDS2960.2																																																																																			A|0.950;T|0.050	0.050	strong		0.517	ZBED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157228.2	NM_024508	
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25266547	25266547	+	Missense_Mutation	SNP	C	C	A	rs113273135	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:25266547C>A	ENST00000328086.7	-	2	1369	c.566G>T	c.(565-567)cGt>cTt	p.R189L		NM_001012981.4	NP_001012999.3	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	189					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	36				GBM - Glioblastoma multiforme(48;0.0378)		TAAGGGCCGACGTTCTCGCTT	0.602													C|||	70	0.0139776	0.0477	0.0072	5008	,	,		17212	0.0		0.002	False		,,,				2504	0.0				p.R189L		Atlas-SNP	.											ZKSCAN2,NS,carcinoma,-1,1	ZKSCAN2	90	1	0			c.G566T						PASS	.	C	LEU/ARG	136,4258	98.0+/-136.7	2,132,2063	114.0	99.0	104.0		566	-5.2	0.0	16	dbSNP_132	104	8,8592	5.0+/-18.6	1,6,4293	yes	missense	ZKSCAN2	NM_001012981.4	102	3,138,6356	AA,AC,CC		0.093,3.0951,1.1082	benign	189/968	25266547	144,12850	2197	4300	6497	SO:0001583	missense	342357	exon2			GGCCGACGTTCTC	AK026852	CCDS32410.1	16p12.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000155592		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	25677	protein-coding gene	gene with protein product			"""zinc finger protein 694"""	ZNF694			Standard	NM_001012981		Approved	FLJ23199, ZSCAN34	uc002dod.4	Q63HK3		ENST00000328086.7:c.566G>T	16.37:g.25266547C>A	ENSP00000331626:p.Arg189Leu	92.0	0.0	0		101.0	58.0	0.574257	NM_001012981	A1L3B4|Q6ZN77	Missense_Mutation	SNP	ENST00000328086.7	37	CCDS32410.1	24	0.01098901098901099	19	0.03861788617886179	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	C	0.541	-0.853648	0.02630	0.030951	9.3E-4	ENSG00000155592	ENST00000328086;ENST00000536768	T	0.14144	2.53	5.3	-5.17	0.02849	.	1.318600	0.04683	N	0.412758	T	0.00608	0.0020	N	0.00621	-1.32	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.36456	-0.9747	10	0.12766	T	0.61	0.0	0.7766	0.01033	0.3527:0.1598:0.1131:0.3743	.	189;189	Q63HK3-2;Q63HK3	.;ZKSC2_HUMAN	L	189	ENSP00000331626:R189L	ENSP00000331626:R189L	R	-	2	0	ZKSCAN2	25174048	0.000000	0.05858	0.000000	0.03702	0.100000	0.18952	-0.679000	0.05203	-0.480000	0.06803	-1.467000	0.01014	CGT	C|0.991;A|0.009	0.009	strong		0.602	ZKSCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435739.1	NM_001012981	
ITGA4	3676	hgsc.bcm.edu	37	2	182376480	182376480	+	Missense_Mutation	SNP	T	T	A	rs35322532	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:182376480T>A	ENST00000397033.2	+	17	2330	c.1900T>A	c.(1900-1902)Tct>Act	p.S634T		NM_000885.4	NP_000876.3	P13612	ITA4_HUMAN	integrin, alpha 4 (antigen CD49D, alpha 4 subunit of VLA-4 receptor)	634			S -> T (in dbSNP:rs35322532).		B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cell-matrix adhesion (GO:0007160)|cell-matrix adhesion involved in ameboidal cell migration (GO:0003366)|chorio-allantoic fusion (GO:0060710)|endodermal cell differentiation (GO:0035987)|extracellular matrix organization (GO:0030198)|face development (GO:0060324)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte tethering or rolling (GO:0050901)|negative regulation of protein homodimerization activity (GO:0090074)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|substrate adhesion-dependent cell spreading (GO:0034446)|T cell migration (GO:0072678)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integrin alpha4-beta7 complex (GO:0034669)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(27)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.0593)		Natalizumab(DB00108)|Tinzaparin(DB06822)	TTTACAGGTTTCTGCAAAGAT	0.338													T|||	86	0.0171725	0.0605	0.0072	5008	,	,		16437	0.0		0.001	False		,,,				2504	0.0				p.S634T		Atlas-SNP	.											.	ITGA4	142	.	0			c.T1900A						PASS	.	T	THR/SER	206,3446		6,194,1626	148.0	144.0	145.0		1900	4.7	1.0	2	dbSNP_126	145	9,8139		0,9,4065	yes	missense	ITGA4	NM_000885.4	58	6,203,5691	AA,AT,TT		0.1105,5.6407,1.822	possibly-damaging	634/1033	182376480	215,11585	1826	4074	5900	SO:0001583	missense	3676	exon17			CAGGTTTCTGCAA		CCDS42788.1	2q31-q32	2010-03-23			ENSG00000115232	ENSG00000115232		"""CD molecules"", ""Integrins"""	6140	protein-coding gene	gene with protein product		192975		CD49D		1537388	Standard	NM_000885		Approved	CD49d	uc002unu.3	P13612	OTTHUMG00000154212	ENST00000397033.2:c.1900T>A	2.37:g.182376480T>A	ENSP00000380227:p.Ser634Thr	192.0	0.0	0		149.0	149.0	1	NM_000885	D3DPG4|Q7Z4L6	Missense_Mutation	SNP	ENST00000397033.2	37	CCDS42788.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	T	18.59	3.657151	0.67586	0.056407	0.001105	ENSG00000115232	ENST00000397033	T	0.50001	0.76	5.87	4.68	0.58851	Integrin alpha-2 (1);	0.170160	0.53938	D	0.000050	T	0.09949	0.0244	L	0.41710	1.295	0.48185	D	0.999603	D;P	0.54397	0.966;0.906	P;P	0.55999	0.646;0.789	T	0.02385	-1.1167	10	0.42905	T	0.14	.	10.2631	0.43438	0.2642:0.0:0.0:0.7358	rs35322532	456;634	Q59H74;P13612	.;ITA4_HUMAN	T	634	ENSP00000380227:S634T	ENSP00000380227:S634T	S	+	1	0	ITGA4	182084725	1.000000	0.71417	0.989000	0.46669	0.992000	0.81027	2.791000	0.47829	1.004000	0.39156	0.529000	0.55759	TCT	T|0.987;A|0.013	0.013	strong		0.338	ITGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334427.1		
SMCO2	341346	hgsc.bcm.edu	37	12	27628521	27628521	+	Silent	SNP	G	G	C	rs77197438	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:27628521G>C	ENST00000535986.1	+	4	369	c.369G>C	c.(367-369)ctG>ctC	p.L123L	SMCO2_ENST00000416383.1_Silent_p.L123L|SMCO2_ENST00000298876.4_Intron|SMCO2_ENST00000538647.1_3'UTR			A6NFE2	SMCO2_HUMAN	single-pass membrane protein with coiled-coil domains 2	123						integral component of membrane (GO:0016021)											GCAGGTGTCTGAAGGGCATGT	0.408													G|||	31	0.0061901	0.0219	0.0029	5008	,	,		17088	0.0		0.0	False		,,,				2504	0.0				p.L123L		Atlas-SNP	.											.	.	.	.	0			c.G369C						PASS	.	G		46,1338		0,46,646	77.0	65.0	68.0		369	-0.8	0.0	12	dbSNP_132	68	1,3181		0,1,1590	no	coding-synonymous	C12orf70	NM_001145010.1		0,47,2236	CC,CG,GG		0.0314,3.3237,1.0293		123/344	27628521	47,4519	692	1591	2283	SO:0001819	synonymous_variant	0	exon5			GTGTCTGAAGGGC		CCDS44852.1	12p11.23	2013-03-11	2013-03-11	2013-03-11	ENSG00000165935	ENSG00000165935			34448	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 70"""	C12orf70			Standard	NM_001145010		Approved	LOC341346	uc010sjq.2	A6NFE2	OTTHUMG00000169205	ENST00000535986.1:c.369G>C	12.37:g.27628521G>C		65.0	0.0	0		62.0	30.0	0.483871	NM_001145010		Silent	SNP	ENST00000535986.1	37	CCDS44852.1																																																																																			G|0.993;C|0.007	0.007	strong		0.408	SMCO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402867.1	NM_001145010	
DIABLO	56616	hgsc.bcm.edu	37	12	122692958	122692958	+	Silent	SNP	C	C	T	rs35426428	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:122692958C>T	ENST00000443649.3	-	7	1507	c.690G>A	c.(688-690)tcG>tcA	p.S230S	RP11-512M8.5_ENST00000535844.1_3'UTR|DIABLO_ENST00000267169.6_Silent_p.S177S|B3GNT4_ENST00000546192.1_3'UTR|B3GNT4_ENST00000545141.1_Intron|DIABLO_ENST00000353548.6_Silent_p.S186S|DIABLO_ENST00000464942.2_Silent_p.S177S|DIABLO_ENST00000413918.1_Silent_p.S186S	NM_019887.4	NP_063940.1	Q9NR28	DBLOH_HUMAN	diablo, IAP-binding mitochondrial protein	230					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c (GO:0008635)|apoptotic process (GO:0006915)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|neuron apoptotic process (GO:0051402)|positive regulation of apoptotic process (GO:0043065)	CD40 receptor complex (GO:0035631)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|mitochondrial intermembrane space (GO:0005758)|mitochondrion (GO:0005739)				breast(1)|endometrium(3)|large_intestine(1)|lung(1)|ovary(1)	7	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000302)|Epithelial(86;0.00051)|BRCA - Breast invasive adenocarcinoma(302;0.223)		CCTCCTGCTCCGACTCAGCCC	0.617													C|||	454	0.090655	0.3283	0.0274	5008	,	,		20976	0.0		0.001	False		,,,				2504	0.0				p.S230S		Atlas-SNP	.											DIABLO,NS,carcinoma,-2,1	DIABLO	16	1	0			c.G690A						PASS	.	C	,	1365,3041	452.8+/-350.1	219,927,1057	113.0	107.0	109.0		690,558	-6.1	0.0	12	dbSNP_126	109	23,8577	16.0+/-53.3	0,23,4277	no	coding-synonymous,coding-synonymous	DIABLO	NM_019887.4,NM_138929.3	,	219,950,5334	TT,TC,CC		0.2674,30.9805,10.672	,	230/240,186/196	122692958	1388,11618	2203	4300	6503	SO:0001819	synonymous_variant	56616	exon7			CTGCTCCGACTCA	AF262240	CCDS9228.1, CCDS9229.1, CCDS73541.1	12q24.31	2011-08-02	2011-03-11		ENSG00000184047	ENSG00000184047			21528	protein-coding gene	gene with protein product	"""second mitochondria-derived activator of caspase"""	605219				12749848, 17237824, 21722859	Standard	NM_019887		Approved	SMAC, DIABLO-S, FLJ25049, FLJ10537, DFNA64	uc010tab.2	Q9NR28	OTTHUMG00000157014	ENST00000443649.3:c.690G>A	12.37:g.122692958C>T		130.0	1.0	0.00769231		168.0	168.0	1	NM_019887	B2RDQ0|Q6W3F3|Q96LV0|Q9BT11|Q9HAV6	Silent	SNP	ENST00000443649.3	37	CCDS9228.1																																																																																			C|0.906;T|0.094	0.094	strong		0.617	DIABLO-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347102.2	NM_019887	
SLURP1	57152	hgsc.bcm.edu	37	8	143822612	143822612	+	Silent	SNP	G	G	A	rs62636564	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:143822612G>A	ENST00000246515.1	-	3	286	c.261C>T	c.(259-261)gcC>gcT	p.A87A		NM_020427.2	NP_065160.1	P55000	SLUR1_HUMAN	secreted LY6/PLAUR domain containing 1	87					cell activation (GO:0001775)|cell adhesion (GO:0007155)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cytokine activity (GO:0005125)			breast(1)|lung(7)|ovary(1)	9	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					TCAGGTGGGCGGCCCCGATGC	0.662													G|||	111	0.0221645	0.0802	0.0072	5008	,	,		15680	0.0		0.0	False		,,,				2504	0.0				p.A87A		Atlas-SNP	.											.	SLURP1	16	.	0			c.C261T						PASS	.	G		250,4156	143.5+/-178.5	7,236,1960	43.0	45.0	45.0		261	-7.5	0.0	8	dbSNP_129	45	5,8593	4.3+/-15.6	0,5,4294	no	coding-synonymous	SLURP1	NM_020427.2		7,241,6254	AA,AG,GG		0.0582,5.6741,1.9609		87/104	143822612	255,12749	2203	4299	6502	SO:0001819	synonymous_variant	57152	exon3			GTGGGCGGCCCCG	AY579080	CCDS6387.1	8q24.3	2004-11-16			ENSG00000126233	ENSG00000126233			18746	protein-coding gene	gene with protein product	"""lymphocyte antigen 6-like secreted"", ""ARS component B"""	606119				11285253, 10211827	Standard	NM_020427		Approved	ARS, ANUP, MDM, ArsB, LY6LS	uc003ywy.3	P55000	OTTHUMG00000164685	ENST00000246515.1:c.261C>T	8.37:g.143822612G>A		74.0	0.0	0		79.0	41.0	0.518987	NM_020427	Q53YJ6|Q6PUA6|Q92483	Silent	SNP	ENST00000246515.1	37	CCDS6387.1																																																																																			G|0.979;A|0.021	0.021	strong		0.662	SLURP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379741.1	NM_020427	
MRC2	9902	hgsc.bcm.edu	37	17	60767303	60767303	+	Missense_Mutation	SNP	G	G	A	rs77299955	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:60767303G>A	ENST00000303375.5	+	25	4024	c.3622G>A	c.(3622-3624)Ggc>Agc	p.G1208S	MRC2_ENST00000446119.2_Missense_Mutation_p.G74S	NM_006039.4	NP_006030.2	Q9UBG0	MRC2_HUMAN	mannose receptor, C type 2	1208	C-type lectin 7. {ECO:0000255|PROSITE- ProRule:PRU00040}.				collagen catabolic process (GO:0030574)|endocytosis (GO:0006897)|osteoblast differentiation (GO:0001649)	focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|collagen binding (GO:0005518)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(11)|lung(28)|ovary(2)|prostate(1)|skin(3)	53						GAACTACGTGGGCTGGCAGGA	0.677													G|||	39	0.00778754	0.0287	0.0014	5008	,	,		12596	0.0		0.0	False		,,,				2504	0.0				p.G1208S		Atlas-SNP	.											.	MRC2	126	.	0			c.G3622A						PASS	.	G	SER/GLY	95,4295		0,95,2100	13.0	16.0	15.0		3622	1.8	0.2	17	dbSNP_131	15	1,8567		0,1,4283	yes	missense	MRC2	NM_006039.3	56	0,96,6383	AA,AG,GG		0.0117,2.164,0.7409	benign	1208/1480	60767303	96,12862	2195	4284	6479	SO:0001583	missense	9902	exon25			TACGTGGGCTGGC	AB014609	CCDS11634.1	17q23	2011-08-30				ENSG00000011028		"""CD molecules"", ""C-type lectin domain containing"""	16875	protein-coding gene	gene with protein product		612264				9734811, 8702911	Standard	NM_006039		Approved	KIAA0709, ENDO180, CLEC13E, CD280	uc002jad.4	Q9UBG0		ENST00000303375.5:c.3622G>A	17.37:g.60767303G>A	ENSP00000307513:p.Gly1208Ser	75.0	0.0	0		84.0	38.0	0.452381	NM_006039	A6H8K4|D3DU08|Q7LGE7|Q9Y5P9	Missense_Mutation	SNP	ENST00000303375.5	37	CCDS11634.1	17	0.007783882783882784	17	0.034552845528455285	0	0.0	0	0.0	0	0.0	G	11.35	1.614242	0.28712	0.02164	1.17E-4	ENSG00000011028	ENST00000303375;ENST00000446119	T;T	0.53423	0.62;0.62	5.16	1.8	0.24995	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.232107	0.49916	N	0.000124	T	0.08133	0.0203	N	0.08118	0	0.23478	N	0.997599	B;B	0.09022	0.002;0.0	B;B	0.06405	0.002;0.001	T	0.13072	-1.0523	10	0.18276	T	0.48	-17.6713	8.5553	0.33478	0.7771:0.0:0.2229:0.0	.	74;1208	E7EME3;Q9UBG0	.;MRC2_HUMAN	S	1208;74	ENSP00000307513:G1208S;ENSP00000400445:G74S	ENSP00000307513:G1208S	G	+	1	0	MRC2	58121035	0.920000	0.31207	0.177000	0.23020	0.707000	0.40811	1.980000	0.40618	0.124000	0.18369	-0.367000	0.07326	GGC	G|0.991;A|0.009	0.009	strong		0.677	MRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445152.1		
PGLYRP2	114770	hgsc.bcm.edu	37	19	15587103	15587103	+	Silent	SNP	C	C	T	rs35973013	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15587103C>T	ENST00000340880.4	-	2	858	c.378G>A	c.(376-378)gcG>gcA	p.A126A	PGLYRP2_ENST00000292609.4_Silent_p.A126A	NM_052890.3	NP_443122.3	Q96PD5	PGRP2_HUMAN	peptidoglycan recognition protein 2	126					defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|growth of symbiont in host (GO:0044117)|innate immune response (GO:0045087)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of natural killer cell differentiation involved in immune response (GO:0032827)|pattern recognition receptor signaling pathway (GO:0002221)|peptide amidation (GO:0001519)|peptidoglycan catabolic process (GO:0009253)|regulation of inflammatory response (GO:0050727)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	N-acetylmuramoyl-L-alanine amidase activity (GO:0008745)|peptidoglycan binding (GO:0042834)|peptidoglycan receptor activity (GO:0016019)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(3)|prostate(2)|skin(3)|stomach(2)|urinary_tract(1)	28						CCTCCAGCCCCGCCAGCAGAG	0.607													C|||	123	0.0245607	0.0477	0.0058	5008	,	,		19723	0.006		0.008	False		,,,				2504	0.0429				p.A126A		Atlas-SNP	.											.	PGLYRP2	116	.	0			c.G378A						PASS	.	C		193,4213	120.4+/-158.0	3,187,2013	100.0	86.0	91.0		378	-10.3	0.1	19	dbSNP_126	91	75,8525	44.0+/-102.2	0,75,4225	no	coding-synonymous	PGLYRP2	NM_052890.3		3,262,6238	TT,TC,CC		0.8721,4.3804,2.0606		126/577	15587103	268,12738	2203	4300	6503	SO:0001819	synonymous_variant	114770	exon2			CAGCCCCGCCAGC	AY358156	CCDS12330.2	19p13.12	2010-04-27			ENSG00000161031	ENSG00000161031	3.5.1.28		30013	protein-coding gene	gene with protein product	"""peptidoglycan recognition protein L precursor"", ""peptidoglycan recognition protein-like"", ""N-acetylmuramoyl-L-alanine amidase"""	608199				11461926, 12669421, 14506276	Standard	NM_052890		Approved	PGRP-L, PGLYRPL, TAGL-like, tagL, tagL-alpha, tagl-beta, PGRPL	uc002nbf.4	Q96PD5	OTTHUMG00000150690	ENST00000340880.4:c.378G>A	19.37:g.15587103C>T		125.0	0.0	0		136.0	76.0	0.558824	NM_052890	A8K050|A8K8C7|B2RMZ2|B7ZM33|Q68CK1|Q96N74|Q9UC60	Silent	SNP	ENST00000340880.4	37	CCDS12330.2																																																																																			C|0.981;T|0.019	0.019	strong		0.607	PGLYRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319626.1	NM_052890	
ZNF678	339500	hgsc.bcm.edu	37	1	227842561	227842561	+	Missense_Mutation	SNP	A	A	G	rs116552491	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:227842561A>G	ENST00000343776.5	+	4	955	c.610A>G	c.(610-612)Agt>Ggt	p.S204G	ZNF678_ENST00000608949.1_Intron|ZNF678_ENST00000397097.3_Missense_Mutation_p.S259G	NM_178549.3	NP_848644.2	Q5SXM1	ZN678_HUMAN	zinc finger protein 678	204					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|pancreas(1)|prostate(1)	24		Prostate(94;0.0885)				GAAAATTCATAGTGGAGAGAA	0.373													A|||	30	0.00599042	0.0212	0.0014	5008	,	,		19312	0.0		0.001	False		,,,				2504	0.0				p.S259G		Atlas-SNP	.											.	ZNF678	137	.	0			c.A775G						PASS	.	A	GLY/SER	77,4327	64.1+/-101.4	0,77,2125	100.0	115.0	110.0		775	0.3	0.0	1	dbSNP_132	110	0,8594		0,0,4297	no	missense	ZNF678	NM_178549.3	56	0,77,6422	GG,GA,AA		0.0,1.7484,0.5924	possibly-damaging	259/581	227842561	77,12921	2202	4297	6499	SO:0001583	missense	339500	exon4			ATTCATAGTGGAG	BC042500		1q42.13	2013-01-08			ENSG00000181450	ENSG00000181450		"""Zinc fingers, C2H2-type"", ""-"""	28652	protein-coding gene	gene with protein product	"""hypothetical protein MGC42493"""					12477932	Standard	NM_178549		Approved	MGC42493	uc021pjy.1	Q5SXM1	OTTHUMG00000037700	ENST00000343776.5:c.610A>G	1.37:g.227842561A>G	ENSP00000344828:p.Ser204Gly	49.0	0.0	0		46.0	23.0	0.5	NM_178549	Q8IVQ9	Missense_Mutation	SNP	ENST00000343776.5	37		10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	A	13.99	2.401576	0.42613	0.017484	0.0	ENSG00000181450	ENST00000343776;ENST00000397097	T;T	0.19669	2.13;2.13	1.49	0.308	0.15815	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.10937	0.0267	L	0.58354	1.805	0.24788	N	0.992776	P	0.43938	0.822	B	0.44044	0.439	T	0.13926	-1.0491	9	0.87932	D	0	.	4.1011	0.10014	0.7609:0.0:0.2391:0.0	.	204	Q5SXM1	ZN678_HUMAN	G	204;259	ENSP00000344828:S204G;ENSP00000440403:S259G	ENSP00000344828:S204G	S	+	1	0	ZNF678	225909184	0.232000	0.23762	0.004000	0.12327	0.027000	0.11550	1.213000	0.32407	0.587000	0.29643	0.413000	0.27773	AGT	A|0.996;G|0.004	0.004	strong		0.373	ZNF678-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000091976.2	NM_178549	
C7orf71	285941	hgsc.bcm.edu	37	7	26678910	26678910	+	Silent	SNP	C	C	T	rs111516571	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:26678910C>T	ENST00000409974.3	+	2	863	c.147C>T	c.(145-147)ctC>ctT	p.L49L		NM_001145531.1	NP_001139003.1	A4D174	CG071_HUMAN	chromosome 7 open reading frame 71	49																	agaggggcctcggggaagcca	0.527													C|||	474	0.0946486	0.3381	0.0288	5008	,	,		17598	0.004		0.003	False		,,,				2504	0.0				p.L49L		Atlas-SNP	.											.	C7orf71	6	.	0			c.C147T						PASS	.						48.0	63.0	59.0					7																	26678910		692	1591	2283	SO:0001819	synonymous_variant	285941	exon2			GGGCCTCGGGGAA		CCDS47565.1	7p15.2	2009-09-11			ENSG00000222004	ENSG00000222004			22364	protein-coding gene	gene with protein product							Standard	NM_001145531		Approved		uc003syb.3	A4D174	OTTHUMG00000152860	ENST00000409974.3:c.147C>T	7.37:g.26678910C>T		38.0	0.0	0		21.0	20.0	0.952381	NM_001145531		Silent	SNP	ENST00000409974.3	37	CCDS47565.1																																																																																			C|0.925;T|0.075	0.075	strong		0.527	C7orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328272.1	NM_001145531	
TNC	3371	hgsc.bcm.edu	37	9	117848368	117848368	+	Missense_Mutation	SNP	C	C	T	rs61729478	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117848368C>T	ENST00000350763.4	-	3	2053	c.1642G>A	c.(1642-1644)Gtg>Atg	p.V548M	TNC_ENST00000535648.1_Missense_Mutation_p.V548M|TNC_ENST00000537320.1_Missense_Mutation_p.V548M|TNC_ENST00000345230.3_Missense_Mutation_p.V548M|TNC_ENST00000341037.4_Missense_Mutation_p.V548M|TNC_ENST00000340094.3_Missense_Mutation_p.V548M|TNC_ENST00000423613.2_Missense_Mutation_p.V548M|TNC_ENST00000346706.3_Missense_Mutation_p.V548M|TNC_ENST00000542877.1_Missense_Mutation_p.V548M	NM_002160.3	NP_002151.2	P24821	TENA_HUMAN	tenascin C	548	EGF-like 13. {ECO:0000255|PROSITE- ProRule:PRU00076}.				bud outgrowth involved in lung branching (GO:0060447)|cell adhesion (GO:0007155)|cellular response to prostaglandin D stimulus (GO:0071799)|cellular response to retinoic acid (GO:0071300)|cellular response to vitamin D (GO:0071305)|extracellular matrix organization (GO:0030198)|mesenchymal-epithelial cell signaling involved in prostate gland development (GO:0060739)|negative regulation of cell adhesion (GO:0007162)|neuromuscular junction development (GO:0007528)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|peripheral nervous system axon regeneration (GO:0014012)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|prostate gland epithelium morphogenesis (GO:0060740)|response to ethanol (GO:0045471)|response to fibroblast growth factor (GO:0071774)|response to mechanical stimulus (GO:0009612)|response to wounding (GO:0009611)|wound healing (GO:0042060)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|interstitial matrix (GO:0005614)|membrane (GO:0016020)	syndecan binding (GO:0045545)			NS(3)|breast(5)|central_nervous_system(4)|endometrium(8)|kidney(6)|large_intestine(32)|liver(1)|lung(39)|ovary(1)|pancreas(2)|prostate(5)|skin(5)|stomach(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	120						TCATGGCACACGCACTGCCCA	0.587													C|||	32	0.00638978	0.0038	0.0072	5008	,	,		21065	0.0		0.0119	False		,,,				2504	0.0102				p.V548M		Atlas-SNP	.											.	TNC	282	.	0			c.G1642A						PASS	.	C	MET/VAL	41,4365	44.6+/-78.6	0,41,2162	106.0	76.0	86.0		1642	4.1	0.9	9	dbSNP_129	86	123,8477	63.1+/-125.2	1,121,4178	yes	missense	TNC	NM_002160.3	21	1,162,6340	TT,TC,CC		1.4302,0.9305,1.261	benign	548/2202	117848368	164,12842	2203	4300	6503	SO:0001583	missense	3371	exon3			GGCACACGCACTG		CCDS6811.1	9q33.1	2014-01-28	2008-07-31	2002-06-07	ENSG00000041982	ENSG00000041982		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	5318	protein-coding gene	gene with protein product	"""hexabrachion (tenascin)"""	187380	"""hexabrachion (tenascin C, cytotactin)"", ""deafness, autosomal dominant 56"""	HXB, DFNA56		1704365, 1707164, 23936043	Standard	NM_002160		Approved	TN, MGC167029	uc004bjj.4	P24821	OTTHUMG00000021010	ENST00000350763.4:c.1642G>A	9.37:g.117848368C>T	ENSP00000265131:p.Val548Met	181.0	0.0	0		165.0	108.0	0.654545	NM_002160	C9IYT7|C9J575|C9J6D9|C9J848|Q14583|Q15567|Q5T7S3	Missense_Mutation	SNP	ENST00000350763.4	37	CCDS6811.1	15	0.006868131868131868	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	10	0.013192612137203167	C	9.105	1.005034	0.19199	0.009305	0.014302	ENSG00000041982	ENST00000340094;ENST00000535648;ENST00000346706;ENST00000345230;ENST00000350763;ENST00000442945;ENST00000341037;ENST00000423613;ENST00000537320;ENST00000542877	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	5.95	4.13	0.48395	EGF, extracellular (1);Epidermal growth factor-like (1);EGF-like region, conserved site (2);	0.111211	0.64402	N	0.000008	T	0.16471	0.0396	M	0.79614	2.46	0.51767	D	0.999938	D;P	0.55385	0.971;0.52	P;B	0.49953	0.627;0.223	T	0.01245	-1.1407	10	0.59425	D	0.04	.	12.6844	0.56940	0.0:0.8672:0.0:0.1328	.	548;548	E9PC84;P24821	.;TENA_HUMAN	M	548	ENSP00000344400:V548M;ENSP00000438152:V548M;ENSP00000344555:V548M;ENSP00000345861:V548M;ENSP00000265131:V548M;ENSP00000339553:V548M;ENSP00000411406:V548M;ENSP00000443478:V548M;ENSP00000442242:V548M	ENSP00000344400:V548M	V	-	1	0	TNC	116888189	0.008000	0.16893	0.874000	0.34290	0.117000	0.20001	0.248000	0.18198	0.867000	0.35654	-0.222000	0.12452	GTG	C|0.990;T|0.010	0.010	strong		0.587	TNC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055418.2	NM_002160	
C17orf50	146853	hgsc.bcm.edu	37	17	34091130	34091130	+	Missense_Mutation	SNP	C	C	A	rs140052043	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34091130C>A	ENST00000285023.4	+	2	150	c.118C>A	c.(118-120)Cag>Aag	p.Q40K	C17orf50_ENST00000586491.1_Missense_Mutation_p.Q40K|C17orf50_ENST00000588628.1_Missense_Mutation_p.P47Q	NM_145272.3	NP_660315.2	Q8WW18	CQ050_HUMAN	chromosome 17 open reading frame 50	40													Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		cgaggaCAACCAGAGGCCGCT	0.692													C|||	43	0.00858626	0.0318	0.0014	5008	,	,		9618	0.0		0.0	False		,,,				2504	0.0				p.Q40K		Atlas-SNP	.											.	C17orf50	4	.	0			c.C118A						PASS	.	C	LYS/GLN	73,3255		1,71,1592	8.0	13.0	11.0		118	-3.7	0.0	17	dbSNP_134	11	2,6858		0,2,3428	yes	missense	C17orf50	NM_145272.3	53	1,73,5020	AA,AC,CC		0.0292,2.1935,0.7362	benign	40/175	34091130	75,10113	1664	3430	5094	SO:0001583	missense	146853	exon2			GACAACCAGAGGC	BC021727	CCDS42298.1	17q12	2014-05-06			ENSG00000154768	ENSG00000270806			29581	protein-coding gene	gene with protein product							Standard	NM_145272		Approved		uc002hjx.3	Q8WW18	OTTHUMG00000188389	ENST00000285023.4:c.118C>A	17.37:g.34091130C>A	ENSP00000285023:p.Gln40Lys	71.0	0.0	0		76.0	34.0	0.447368	NM_145272	Q6Q621	Missense_Mutation	SNP	ENST00000285023.4	37	CCDS42298.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	C	6.499	0.460290	0.12342	0.021935	2.92E-4	ENSG00000154768	ENST00000285023	T	0.42513	0.97	1.86	-3.72	0.04411	.	.	.	.	.	T	0.07052	0.0179	N	0.19112	0.55	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.20571	-1.0271	9	0.54805	T	0.06	-3.6237	0.4196	0.00454	0.216:0.2495:0.3138:0.2207	.	40	Q8WW18	CQ050_HUMAN	K	40	ENSP00000285023:Q40K	ENSP00000285023:Q40K	Q	+	1	0	C17orf50	31115243	0.000000	0.05858	0.016000	0.15963	0.022000	0.10575	-0.033000	0.12246	-0.319000	0.08652	-0.502000	0.04539	CAG	C|0.993;A|0.007	0.007	strong		0.692	C17orf50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449132.1	NM_145272	
TNS3	64759	hgsc.bcm.edu	37	7	47343079	47343079	+	Missense_Mutation	SNP	A	A	G	rs61731305	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:47343079A>G	ENST00000398879.1	-	22	3292	c.2926T>C	c.(2926-2928)Tcc>Ccc	p.S976P	TNS3_ENST00000355730.3_Missense_Mutation_p.S736P|TNS3_ENST00000311160.9_Missense_Mutation_p.S976P			Q68CZ2	TENS3_HUMAN	tensin 3	976					cell migration (GO:0016477)|lung alveolus development (GO:0048286)|positive regulation of cell proliferation (GO:0008284)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				NS(1)|autonomic_ganglia(1)|breast(17)|endometrium(5)|kidney(4)|large_intestine(7)|liver(1)|lung(16)|ovary(4)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	64						CTGGTACCGGAGAACTCAGCG	0.652													A|||	50	0.00998403	0.0371	0.0014	5008	,	,		16308	0.0		0.0	False		,,,				2504	0.0				p.S976P		Atlas-SNP	.											.	TNS3	140	.	0			c.T2926C						PASS	.	A	PRO/SER	110,3944		1,108,1918	24.0	30.0	28.0		2926	-4.5	0.0	7	dbSNP_129	28	1,8365		0,1,4182	yes	missense	TNS3	NM_022748.11	74	1,109,6100	GG,GA,AA		0.012,2.7134,0.8937	benign	976/1446	47343079	111,12309	2027	4183	6210	SO:0001583	missense	64759	exon22			TACCGGAGAACTC	AF378756	CCDS5506.2	7p12.3	2013-02-14	2005-05-13	2005-05-13	ENSG00000136205	ENSG00000136205		"""SH2 domain containing"""	21616	protein-coding gene	gene with protein product	"""tumor endothelial marker 6"""	606825	"""tensin-like SH2 domain-containing 1"""	TENS1		11559528	Standard	NM_022748		Approved	TEM6, H_NH0549I23.2, FLJ13732	uc003tnw.3	Q68CZ2	OTTHUMG00000074075	ENST00000398879.1:c.2926T>C	7.37:g.47343079A>G	ENSP00000381854:p.Ser976Pro	73.0	0.0	0		94.0	55.0	0.585106	NM_022748	B2RNV1|Q6IPQ2|Q8IZW7|Q8NAD0|Q96PE0|Q96S48	Missense_Mutation	SNP	ENST00000398879.1	37	CCDS5506.2	23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	A	7.817	0.717014	0.15372	0.027134	1.2E-4	ENSG00000136205	ENST00000311160;ENST00000538633;ENST00000398879;ENST00000355730;ENST00000545849;ENST00000457718	D;D;D;D	0.94828	-3.07;-3.07;-3.53;-3.23	5.34	-4.47	0.03525	.	1.008340	0.07998	N	0.988200	T	0.56891	0.2016	N	0.08118	0	0.24069	N	0.995984	B	0.02656	0.0	B	0.04013	0.001	T	0.65516	-0.6149	10	0.25751	T	0.34	-5.9377	1.8322	0.03132	0.4155:0.1339:0.3198:0.1308	.	976	Q68CZ2	TENS3_HUMAN	P	976;1086;976;736;432;1079	ENSP00000312143:S976P;ENSP00000381854:S976P;ENSP00000347968:S736P;ENSP00000414358:S1079P	ENSP00000312143:S976P	S	-	1	0	TNS3	47309604	0.942000	0.31987	0.002000	0.10522	0.058000	0.15608	0.267000	0.18552	-0.660000	0.05352	0.528000	0.53228	TCC	A|0.989;G|0.011	0.011	strong		0.652	TNS3-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157253.1	NM_022748	
PCDHB10	56126	hgsc.bcm.edu	37	5	140573759	140573759	+	Missense_Mutation	SNP	C	C	T	rs17844584	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140573759C>T	ENST00000239446.4	+	1	1818	c.1634C>T	c.(1633-1635)gCg>gTg	p.A545V		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	545	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.A545V(1)		breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGCAGAGAGGCGCTGGTGCGC	0.706													C|||	27	0.00539137	0.0204	0.0	5008	,	,		16480	0.0		0.0	False		,,,				2504	0.0				p.A545V		Atlas-SNP	.											PCDHB10,colon,carcinoma,0,1	PCDHB10	177	1	1	Substitution - Missense(1)	large_intestine(1)	c.C1634T						scavenged	.	C	VAL/ALA	66,4300		0,66,2117	34.0	48.0	43.0		1634	3.5	1.0	5	dbSNP_123	43	0,8560		0,0,4280	no	missense	PCDHB10	NM_018930.3	64	0,66,6397	TT,TC,CC		0.0,1.5117,0.5106	benign	545/801	140573759	66,12860	2183	4280	6463	SO:0001583	missense	56126	exon1			GAGAGGCGCTGGT	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"""Cadherins / Protocadherins : Clustered"""	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.1634C>T	5.37:g.140573759C>T	ENSP00000239446:p.Ala545Val	147.0	1.0	0.00680272		145.0	68.0	0.468966	NM_018930	Q96T99	Missense_Mutation	SNP	ENST00000239446.4	37	CCDS4252.1	.	.	.	.	.	.	.	.	.	.	c	14.35	2.508907	0.44660	0.015117	0.0	ENSG00000120324	ENST00000239446	T	0.01787	4.64	3.53	3.53	0.40419	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.00875	0.0029	N	0.16266	0.395	0.09310	N	1	D	0.54047	0.964	P	0.48921	0.595	T	0.53136	-0.8481	9	0.14252	T	0.57	.	7.8479	0.29437	0.0:0.8331:0.0:0.1669	rs17844584	545	Q9UN67	PCDBA_HUMAN	V	545	ENSP00000239446:A545V	ENSP00000239446:A545V	A	+	2	0	PCDHB10	140553943	0.000000	0.05858	0.998000	0.56505	0.980000	0.70556	-0.423000	0.07034	1.994000	0.58287	0.549000	0.68633	GCG	C|0.993;T|0.007	0.007	strong		0.706	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930	
TIGD7	91151	hgsc.bcm.edu	37	16	3349300	3349300	+	Missense_Mutation	SNP	C	C	G	rs151295470		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3349300C>G	ENST00000396862.1	-	2	3143	c.1315G>C	c.(1315-1317)Gtg>Ctg	p.V439L	TIGD7_ENST00000574598.1_5'Flank|TIGD7_ENST00000268674.2_Missense_Mutation_p.V439L	NM_033208.3	NP_149985.2	Q6NT04	TIGD7_HUMAN	tigger transposable element derived 7	439						nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|upper_aerodigestive_tract(1)	12						TTTAACCACACCCTATCATCA	0.383																																					p.V439L		Atlas-SNP	.											.	TIGD7	41	.	0			c.G1315C						PASS	.	C	LEU/VAL	3,4391	6.2+/-15.9	0,3,2194	162.0	174.0	170.0		1315	-0.7	0.0	16	dbSNP_134	170	0,8600		0,0,4300	yes	missense	TIGD7	NM_033208.3	32	0,3,6494	GG,GC,CC		0.0,0.0683,0.0231	possibly-damaging	439/550	3349300	3,12991	2197	4300	6497	SO:0001583	missense	91151	exon2			ACCACACCCTATC	AF251050	CCDS10500.1	16p13.11	2008-02-05			ENSG00000140993	ENSG00000140993			18331	protein-coding gene	gene with protein product		612969					Standard	NM_033208		Approved	Sancho	uc002cus.3	Q6NT04	OTTHUMG00000129325	ENST00000396862.1:c.1315G>C	16.37:g.3349300C>G	ENSP00000380071:p.Val439Leu	264.0	0.0	0		300.0	142.0	0.473333	NM_033208	Q9BXZ0	Missense_Mutation	SNP	ENST00000396862.1	37	CCDS10500.1	.	.	.	.	.	.	.	.	.	.	C	0.050	-1.253366	0.01457	6.83E-4	0.0	ENSG00000140993	ENST00000426381;ENST00000396862;ENST00000268674	T;T	0.31510	1.49;1.49	4.88	-0.699	0.11277	.	1.396770	0.05259	U	0.515337	T	0.19327	0.0464	N	0.19112	0.55	0.09310	N	1	B	0.13145	0.007	B	0.09377	0.004	T	0.26503	-1.0101	10	0.26408	T	0.33	.	7.8653	0.29533	0.0:0.5056:0.0:0.4944	.	439	Q6NT04	TIGD7_HUMAN	L	439	ENSP00000380071:V439L;ENSP00000268674:V439L	ENSP00000268674:V439L	V	-	1	0	TIGD7	3289301	0.005000	0.15991	0.001000	0.08648	0.291000	0.27294	-0.189000	0.09629	-0.110000	0.12022	-0.150000	0.13652	GTG	C|1.000;G|0.000	0.000	weak		0.383	TIGD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251465.1	NM_033208	
WDR26	80232	hgsc.bcm.edu	37	1	224607296	224607296	+	Silent	SNP	T	T	C	rs142827296	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:224607296T>C	ENST00000414423.2	-	5	979	c.786A>G	c.(784-786)gcA>gcG	p.A262A	WDR26_ENST00000295024.6_Silent_p.A115A|WDR26_ENST00000366852.2_3'UTR	NM_001115113.2|NM_025160.6	NP_001108585.2|NP_079436.4	Q9H7D7	WDR26_HUMAN	WD repeat domain 26	262						cytoplasm (GO:0005737)|nucleus (GO:0005634)				biliary_tract(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)	18				GBM - Glioblastoma multiforme(131;0.0104)		GTAGGTCTTCTGCATGGCTAC	0.353													T|||	6	0.00119808	0.0038	0.0	5008	,	,		17617	0.001		0.0	False		,,,				2504	0.0				p.A262A		Atlas-SNP	.											WDR26_ENST00000414423,NS,carcinoma,0,2	WDR26	104	2	0			c.A786G						PASS	.	T	,	8,4398	14.3+/-33.2	0,8,2195	126.0	112.0	117.0		738,786	-1.0	1.0	1	dbSNP_134	117	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	WDR26	NM_001115113.2,NM_025160.6	,	0,8,6495	CC,CT,TT		0.0,0.1816,0.0615	,	246/646,262/662	224607296	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	80232	exon5			GTCTTCTGCATGG	AK024669	CCDS31037.1, CCDS31037.2	1q42.13	2013-01-09			ENSG00000162923	ENSG00000162923		"""WD repeat domain containing"""	21208	protein-coding gene	gene with protein product	"""GID complex subunit 7 homolog (S. cerevisiae)"""						Standard	NM_001115113		Approved	FLJ21016, GID7	uc001hop.4	Q9H7D7	OTTHUMG00000037636	ENST00000414423.2:c.786A>G	1.37:g.224607296T>C		77.0	0.0	0		100.0	46.0	0.46	NM_025160	A0MNN3|Q4G100|Q59EC4|Q5GLZ9|Q86UY4|Q9H3C2	Silent	SNP	ENST00000414423.2	37	CCDS31037.2																																																																																			T|0.999;C|0.001	0.001	strong		0.353	WDR26-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000091760.2	NM_025160	
SCAF1	58506	hgsc.bcm.edu	37	19	50157980	50157980	+	Silent	SNP	G	G	A	rs61741228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50157980G>A	ENST00000360565.3	+	9	3595	c.3471G>A	c.(3469-3471)ctG>ctA	p.L1157L		NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	1157					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	20		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)		CTTTGGGTCTGCCCCCTGGCC	0.672													g|||	32	0.00638978	0.0234	0.0014	5008	,	,		15138	0.0		0.0	False		,,,				2504	0.0				p.L1157L		Atlas-SNP	.											.	SCAF1	78	.	0			c.G3471A						PASS	.			84,4322	71.4+/-109.4	2,80,2121	85.0	77.0	80.0		3471	-1.0	1.0	19	dbSNP_129	80	0,8600		0,0,4300	no	coding-synonymous	SCAF1	NM_021228.2		2,80,6421	AA,AG,GG		0.0,1.9065,0.6459		1157/1313	50157980	84,12922	2203	4300	6503	SO:0001819	synonymous_variant	58506	exon9			GGGTCTGCCCCCT	AK024444	CCDS33074.1	19q13.3-q13.4	2011-01-10			ENSG00000126461	ENSG00000126461			30403	protein-coding gene	gene with protein product						11461075	Standard	NM_021228		Approved	SR-A1, FLJ00034	uc002poq.3	Q9H7N4		ENST00000360565.3:c.3471G>A	19.37:g.50157980G>A		53.0	0.0	0		66.0	29.0	0.439394	NM_021228	Q7Z5V7|Q8WVA1|Q9NR59	Silent	SNP	ENST00000360565.3	37	CCDS33074.1																																																																																			G|0.993;A|0.007	0.007	strong		0.672	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1	NM_021228	
PINK1	65018	hgsc.bcm.edu	37	1	20975047	20975047	+	Silent	SNP	T	T	C	rs45499398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:20975047T>C	ENST00000321556.4	+	6	1267	c.1173T>C	c.(1171-1173)gaT>gaC	p.D391D	PINK1-AS_ENST00000451424.1_RNA|PINK1_ENST00000492302.1_3'UTR	NM_032409.2	NP_115785.1	Q9BXM7	PINK1_HUMAN	PTEN induced putative kinase 1	391	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.				activation of protein kinase B activity (GO:0032148)|cell death (GO:0008219)|cellular response to hypoxia (GO:0071456)|cellular response to toxic substance (GO:0097237)|intracellular signal transduction (GO:0035556)|mitochondrion degradation (GO:0000422)|mitochondrion organization (GO:0007005)|negative regulation of gene expression (GO:0010629)|negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway (GO:1903384)|negative regulation of JNK cascade (GO:0046329)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|peptidyl-serine autophosphorylation (GO:0036289)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial electron transport, NADH to ubiquinone (GO:1902958)|positive regulation of peptidase activity (GO:0010952)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of mitochondrion degradation (GO:1903146)|regulation of protein complex assembly (GO:0043254)|regulation of protein ubiquitination (GO:0031396)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|TORC2 signaling (GO:0038203)|ubiquitin-dependent protein catabolic process (GO:0006511)	astrocyte projection (GO:0097449)|axon (GO:0030424)|cell body (GO:0044297)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of mitochondrial outer membrane (GO:0031307)|Lewy body (GO:0097413)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|C3HC4-type RING finger domain binding (GO:0055131)|calcium-dependent protein kinase activity (GO:0010857)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)|protein kinase B binding (GO:0043422)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)	14		all_lung(284;2.72e-05)|Lung NSC(340;2.94e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.21e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000146)|Kidney(64;0.000182)|GBM - Glioblastoma multiforme(114;0.000497)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GCCTGGCTGATGAGAGCATCG	0.607													T|||	50	0.00998403	0.0356	0.0043	5008	,	,		19352	0.0		0.0	False		,,,				2504	0.0				p.D391D	Esophageal Squamous(145;853 1803 8146 34412 35011)	Atlas-SNP	.											.	PINK1	37	.	0			c.T1173C						PASS	.	T		157,4249	107.8+/-146.2	6,145,2052	65.0	57.0	60.0		1173	-5.2	0.0	1	dbSNP_127	60	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	PINK1	NM_032409.2		6,147,6350	CC,CT,TT		0.0233,3.5633,1.2225		391/582	20975047	159,12847	2203	4300	6503	SO:0001819	synonymous_variant	65018	exon6			GGCTGATGAGAGC	AB053323	CCDS211.1	1p36.12	2011-07-21			ENSG00000158828	ENSG00000158828		"""Parkinson disease"""	14581	protein-coding gene	gene with protein product		608309	"""Parkinson disease (autosomal recessive) 6"""	PARK6		11494141, 15349860	Standard	NM_032409		Approved		uc001bdm.3	Q9BXM7	OTTHUMG00000002841	ENST00000321556.4:c.1173T>C	1.37:g.20975047T>C		81.0	0.0	0		101.0	52.0	0.514852	NM_032409	Q8N6T9|Q8NBU3|Q96DE4	Silent	SNP	ENST00000321556.4	37	CCDS211.1																																																																																			T|0.989;C|0.011	0.011	strong		0.607	PINK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007954.1	NM_032409	
FAM101A	144347	hgsc.bcm.edu	37	12	124798797	124798797	+	Missense_Mutation	SNP	C	C	T	rs116090335	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124798797C>T	ENST00000389727.3	+	3	377	c.377C>T	c.(376-378)gCg>gTg	p.A126V	FAM101A_ENST00000324038.3_Missense_Mutation_p.A45V|FAM101A_ENST00000546355.1_Missense_Mutation_p.A45V|FAM101A_ENST00000338359.4_Missense_Mutation_p.A45V			Q6ZTI6	F101A_HUMAN	family with sequence similarity 101, member A	126										endometrium(1)|kidney(1)|lung(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;2.38e-05)|OV - Ovarian serous cystadenocarcinoma(86;6.95e-05)|all cancers(50;0.000361)|BRCA - Breast invasive adenocarcinoma(302;0.059)		GTCTTCTATGCGCCCGTACCC	0.622													C|||	9	0.00179712	0.0068	0.0	5008	,	,		18557	0.0		0.0	False		,,,				2504	0.0				p.A45V		Atlas-SNP	.											.	FAM101A	10	.	0			c.C134T						PASS	.	C	VAL/ALA,VAL/ALA	31,4375	37.6+/-69.7	0,31,2172	84.0	72.0	76.0		134,134	0.0	0.1	12	dbSNP_132	76	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	FAM101A,ZNF664-FAM101A	NM_001204299.1,NM_181709.4	64,64	0,32,6471	TT,TC,CC		0.0116,0.7036,0.246	benign,benign	45/136,45/136	124798797	32,12974	2203	4300	6503	SO:0001583	missense	144347	exon3			TCTATGCGCCCGT		CCDS9258.1	12q24.31	2012-11-30			ENSG00000178882	ENSG00000178882			27051	protein-coding gene	gene with protein product		615927				12477932	Standard	NM_181709		Approved	FLJ44614	uc001ugd.2	Q6ZTI6	OTTHUMG00000168609	ENST00000389727.3:c.377C>T	12.37:g.124798797C>T	ENSP00000374377:p.Ala126Val	114.0	0.0	0		144.0	80.0	0.555556	NM_181709	A5D8T5	Missense_Mutation	SNP	ENST00000389727.3	37		3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	2.675	-0.276668	0.05679	0.007036	1.16E-4	ENSG00000178882	ENST00000324038;ENST00000541200;ENST00000389727;ENST00000546355;ENST00000338359	.	.	.	4.69	0.0271	0.14153	.	0.566604	0.18703	N	0.133527	T	0.13243	0.0321	N	0.10874	0.06	0.28756	N	0.901148	B	0.13145	0.007	B	0.08055	0.003	T	0.10683	-1.0619	9	0.29301	T	0.29	-0.5442	5.5434	0.17051	0.0:0.3925:0.1872:0.4203	.	126	Q6ZTI6	F101A_HUMAN	V	45;45;126;45;45	.	ENSP00000315626:A45V	A	+	2	0	FAM101A	123364750	0.126000	0.22350	0.078000	0.20375	0.034000	0.12701	0.293000	0.19029	0.085000	0.17107	-1.175000	0.01729	GCG	C|0.998;T|0.002	0.002	strong		0.622	FAM101A-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_181709	
COL6A3	1293	hgsc.bcm.edu	37	2	238243369	238243369	+	Silent	SNP	G	G	A	rs10201909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:238243369G>A	ENST00000295550.4	-	41	9581	c.9129C>T	c.(9127-9129)cgC>cgT	p.R3043R	COL6A3_ENST00000346358.4_Silent_p.R2843R|COL6A3_ENST00000353578.4_Silent_p.R2837R|COL6A3_ENST00000347401.3_Silent_p.R2842R|COL6A3_ENST00000472056.1_Silent_p.R2436R|COL6A3_ENST00000409809.1_Silent_p.R2837R	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	3043	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Nonhelical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		CTCCAATGACGCGGTCCGTGA	0.572													G|||	355	0.0708866	0.2194	0.0375	5008	,	,		17549	0.005		0.0179	False		,,,				2504	0.0164				p.R3043R		Atlas-SNP	.											COL6A3,colon,carcinoma,-1,2	COL6A3	608	2	0			c.C9129T						scavenged	.	G	,,	810,3596	323.7+/-298.2	58,694,1451	72.0	66.0	68.0		9129,7308,8511	-9.8	0.0	2	dbSNP_119	68	169,8431	78.1+/-140.7	1,167,4132	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A3	NM_004369.3,NM_057166.4,NM_057167.3	,,	59,861,5583	AA,AG,GG		1.9651,18.384,7.5273	,,	3043/3178,2436/2571,2837/2972	238243369	979,12027	2203	4300	6503	SO:0001819	synonymous_variant	1293	exon41			AATGACGCGGTCC	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.9129C>T	2.37:g.238243369G>A		128.0	1.0	0.0078125		149.0	72.0	0.483221	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Silent	SNP	ENST00000295550.4	37	CCDS33412.1																																																																																			G|0.933;A|0.067	0.067	strong		0.572	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
CYLC1	1538	hgsc.bcm.edu	37	X	83128911	83128911	+	Missense_Mutation	SNP	G	G	C	rs12008888	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:83128911G>C	ENST00000329312.4	+	4	1232	c.1195G>C	c.(1195-1197)Gat>Cat	p.D399H		NM_021118.1	NP_066941.1	P35663	CYLC1_HUMAN	cylicin, basic protein of sperm head cytoskeleton 1	399			D -> H (in dbSNP:rs12008888).		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	acrosomal matrix (GO:0043159)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			NS(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	58						CAAGAAAAAGGATGCAAAGAA	0.343													G|||	200	0.0529801	0.1384	0.0231	3775	,	,		14297	0.0		0.001	False		,,,				2504	0.0				p.D399H		Atlas-SNP	.											.	CYLC1	272	.	0			c.G1195C						PASS	.	G	HIS/ASP	581,3240		41,402,97,1184,470	30.0	24.0	26.0		1195	3.2	0.0	X	dbSNP_120	26	5,6711		0,5,0,2421,1864	yes	missense	CYLC1	NM_021118.1	81	41,407,97,3605,2334	CC,CG,C,GG,G		0.0744,15.2054,5.5614	probably-damaging	399/652	83128911	586,9951	2194	4290	6484	SO:0001583	missense	1538	exon4			AAAAAGGATGCAA	Z22780	CCDS35341.1, CCDS75998.1	Xq21.1	2008-07-31			ENSG00000183035	ENSG00000183035			2582	protein-coding gene	gene with protein product	"""cylicin 1"""	300768				7737358, 8354692	Standard	NM_021118		Approved		uc004eei.2	P35663	OTTHUMG00000021922	ENST00000329312.4:c.1195G>C	X.37:g.83128911G>C	ENSP00000331556:p.Asp399His	106.0	0.0	0		91.0	44.0	0.483516	NM_021118	A0AVQ8|Q5JQQ9	Missense_Mutation	SNP	ENST00000329312.4	37	CCDS35341.1	75	0.045207956600361664	41	0.09234234234234234	5	0.014204545454545454	0	0.0	0	0.0	g	2.122	-0.401166	0.04865	0.152054	7.44E-4	ENSG00000183035	ENST00000329312;ENST00000544771	T	0.28895	1.59	4.12	3.24	0.37175	.	.	.	.	.	T	0.00271	0.0008	L	0.49126	1.545	0.80722	P	0.0	D;D	0.89917	1.0;1.0	D;D	0.73380	0.98;0.98	T	0.06588	-1.0818	8	0.66056	D	0.02	-7.8087	6.0759	0.19915	0.1403:0.0:0.8597:0.0	rs12008888;rs52819056;rs12008888	399;399	P35663;F5H4V5	CYLC1_HUMAN;.	H	399	ENSP00000331556:D399H	ENSP00000331556:D399H	D	+	1	0	CYLC1	83015567	0.979000	0.34478	0.008000	0.14137	0.011000	0.07611	3.108000	0.50337	2.026000	0.59711	0.600000	0.82982	GAT	0|0.017;C|0.055	0.055	strong		0.343	CYLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057371.1	NM_021118	
SCML4	256380	hgsc.bcm.edu	37	6	108029133	108029133	+	Silent	SNP	C	C	T	rs61742583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:108029133C>T	ENST00000369020.3	-	7	1301	c.1056G>A	c.(1054-1056)gtG>gtA	p.V352V	SCML4_ENST00000369022.2_Silent_p.V294V|SCML4_ENST00000369025.2_Silent_p.V110V	NM_198081.3	NP_932347.2	Q8N228	SCML4_HUMAN	sex comb on midleg-like 4 (Drosophila)	352	SAM.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(2)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(1)	25		all_cancers(87;3.26e-06)|Acute lymphoblastic leukemia(125;3.08e-08)|all_hematologic(75;1.15e-06)|all_epithelial(87;0.00142)|Colorectal(196;0.0316)		BRCA - Breast invasive adenocarcinoma(108;0.01)|Epithelial(106;0.0509)|all cancers(137;0.0586)|OV - Ovarian serous cystadenocarcinoma(136;0.0758)		TCACAAACCACACCACGTCCT	0.627													C|||	64	0.0127796	0.0477	0.0014	5008	,	,		18965	0.0		0.0	False		,,,				2504	0.0				p.V352V		Atlas-SNP	.											.	SCML4	65	.	0			c.G1056A						PASS	.	C		75,1309		0,75,617	54.0	63.0	60.0		1056	2.7	0.9	6	dbSNP_129	60	0,3182		0,0,1591	no	coding-synonymous	SCML4	NM_198081.3		0,75,2208	TT,TC,CC		0.0,5.4191,1.6426		352/415	108029133	75,4491	692	1591	2283	SO:0001819	synonymous_variant	256380	exon7			AAACCACACCACG		CCDS5060.2, CCDS69163.1, CCDS75500.1	6q21	2013-01-10			ENSG00000146285	ENSG00000146285		"""Sterile alpha motif (SAM) domain containing"""	21397	protein-coding gene	gene with protein product							Standard	NM_001286409		Approved	dJ47M23.1	uc010kdf.3	Q8N228	OTTHUMG00000015313	ENST00000369020.3:c.1056G>A	6.37:g.108029133C>T		138.0	0.0	0		171.0	78.0	0.45614	NM_198081	B0QZ10|B0QZ11|B7ZBX3|Q5JXD0|Q5T0T6|Q8IYY6	Silent	SNP	ENST00000369020.3	37	CCDS5060.2																																																																																			C|0.991;T|0.009	0.009	strong		0.627	SCML4-005	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000041700.3	XM_171128	
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305760	39305760	+	Missense_Mutation	SNP	C	C	T	rs427961	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39305760C>T	ENST00000343246.4	-	1	294	c.260G>A	c.(259-261)aGg>aAg	p.R87K		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	87	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			gcaggtggtcctgcagcaggt	0.657													T|||	184	0.0367412	0.1256	0.0086	5008	,	,		15710	0.001		0.001	False		,,,				2504	0.0102				p.R87K		Atlas-SNP	.											.	KRTAP4-5	34	.	0			c.G260A						PASS	.						17.0	23.0	21.0					17																	39305760		2133	4241	6374	SO:0001583	missense	85289	exon1			GTGGTCCTGCAGC	AJ406937	CCDS32650.1	17q21.2	2013-06-25			ENSG00000198271	ENSG00000198271		"""Keratin associated proteins"""	18899	protein-coding gene	gene with protein product						11279113	Standard	NM_033188		Approved	KAP4.5	uc002hwb.3	Q9BYR2	OTTHUMG00000133638	ENST00000343246.4:c.260G>A	17.37:g.39305760C>T	ENSP00000340546:p.Arg87Lys	150.0	0.0	0		90.0	44.0	0.488889	NM_033188		Missense_Mutation	SNP	ENST00000343246.4	37	CCDS32650.1	.	.	.	.	.	.	.	.	.	.	.	6.445	0.450231	0.12223	.	.	ENSG00000198271	ENST00000343246	T	0.00568	6.53	2.87	-5.75	0.02384	.	.	.	.	.	T	0.00468	0.0015	L	0.56769	1.78	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.43893	-0.9363	9	0.10111	T	0.7	.	5.8578	0.18730	0.1977:0.5979:0.0:0.2045	rs427961	92	Q9BYR2	KRA45_HUMAN	K	87	ENSP00000340546:R87K	ENSP00000340546:R87K	R	-	2	0	KRTAP4-5	36559286	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.772000	0.04694	-2.052000	0.00902	-1.408000	0.01128	AGG	T|1.000;|0.000	1.000	weak		0.657	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1		
FAM71E2	284418	hgsc.bcm.edu	37	19	55870319	55870319	+	Silent	SNP	C	C	T	rs143731075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55870319C>T	ENST00000424985.3	-	9	2110	c.1917G>A	c.(1915-1917)caG>caA	p.Q639Q	CTD-2105E13.6_ENST00000591954.3_Missense_Mutation_p.R189K	NM_001145402.1	NP_001138874.1	Q8N5Q1	F71E2_HUMAN	family with sequence similarity 71, member E2	639										NS(1)|breast(3)|endometrium(2)|kidney(1)|skin(1)	8						CCAACTTCCCCTGGCCCCTGA	0.617													c|||	91	0.0181709	0.0666	0.0043	5008	,	,		17639	0.0		0.0	False		,,,				2504	0.0				p.Q639Q		Atlas-SNP	.											.	FAM71E2	41	.	0			c.G1917A						PASS	.	C		100,1284		4,92,596	48.0	47.0	48.0		1917	1.8	0.0	19	dbSNP_134	48	0,3182		0,0,1591	no	coding-synonymous	FAM71E2	NM_001145402.1		4,92,2187	TT,TC,CC		0.0,7.2254,2.1901		639/923	55870319	100,4466	692	1591	2283	SO:0001819	synonymous_variant	284418	exon9			CTTCCCCTGGCCC	AL834316		19q13.42	2014-04-02	2007-11-20	2007-11-20	ENSG00000180043	ENSG00000180043			25278	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 16"""	C19orf16			Standard	NM_001145402		Approved	DKFZp434G1729	uc002qkr.2	Q8N5Q1	OTTHUMG00000170357	ENST00000424985.3:c.1917G>A	19.37:g.55870319C>T		83.0	0.0	0		66.0	30.0	0.454545	NM_001145402	Q8ND99	Silent	SNP	ENST00000424985.3	37																																																																																				C|0.983;T|0.017	0.017	strong		0.617	FAM71E2-010	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000409063.4	NM_001145402	
SCARF1	8578	hgsc.bcm.edu	37	17	1538561	1538561	+	Missense_Mutation	SNP	G	G	A	rs8072430	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:1538561G>A	ENST00000263071.4	-	11	2033	c.1984C>T	c.(1984-1986)Cgg>Tgg	p.R662W	SCARF1_ENST00000348987.3_Missense_Mutation_p.R576W|SCARF1_ENST00000571272.1_3'UTR	NM_003693.2|NM_145350.1	NP_003684.2|NP_663325.1	Q14162	SREC_HUMAN	scavenger receptor class F, member 1	662	Gly-rich.		R -> W (in dbSNP:rs8072430). {ECO:0000269|PubMed:8590280, ECO:0000269|PubMed:9395444}.		cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|dendrite development (GO:0016358)|neuron remodeling (GO:0016322)|positive regulation of axon regeneration (GO:0048680)|positive regulation of neuron projection development (GO:0010976)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(3)|kidney(2)|lung(9)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		AGTGGGGGCCGCCGGTGGCCA	0.682													G|||	105	0.0209665	0.0764	0.0058	5008	,	,		13011	0.0		0.0	False		,,,				2504	0.0				p.R662W		Atlas-SNP	.											.	SCARF1	46	.	0			c.C1984T						PASS	.	G	TRP/ARG,,TRP/ARG	237,3973		10,217,1878	15.0	17.0	17.0		1984,,1726	1.2	0.0	17	dbSNP_116	17	3,8223		0,3,4110	yes	missense,utr-3,missense	SCARF1	NM_003693.2,NM_145350.1,NM_145352.2	101,,101	10,220,5988	AA,AG,GG		0.0365,5.6295,1.9299	probably-damaging,,probably-damaging	662/831,,576/745	1538561	240,12196	2105	4113	6218	SO:0001583	missense	8578	exon11			GGGGCCGCCGGTG	D63483	CCDS11007.1, CCDS45564.1	17p13.3	2008-07-18			ENSG00000074660	ENSG00000074660			16820	protein-coding gene	gene with protein product	"""scavenger receptor expressed by endothelial cells"", ""acetyl LDL receptor"""	607873				9395444, 8590280	Standard	NM_003693		Approved	SREC, KIAA0149	uc002fsz.2	Q14162	OTTHUMG00000090555	ENST00000263071.4:c.1984C>T	17.37:g.1538561G>A	ENSP00000263071:p.Arg662Trp	53.0	0.0	0		68.0	25.0	0.367647	NM_003693	A8MQ05|O43701|Q8NHD2|Q8NHD3|Q8NHD4|Q8NHD5	Missense_Mutation	SNP	ENST00000263071.4	37	CCDS11007.1	36	0.016483516483516484	34	0.06910569105691057	2	0.0055248618784530384	0	0.0	0	0.0	G	11.44	1.639770	0.29157	0.056295	3.65E-4	ENSG00000074660	ENST00000263071;ENST00000348987	T;T	0.35973	1.28;1.28	5.0	1.23	0.21249	.	1.186410	0.06503	N	0.736688	T	0.07908	0.0198	M	0.62723	1.935	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.72075	0.942;0.976	T	0.04930	-1.0917	10	0.72032	D	0.01	-0.2214	6.3298	0.21264	0.1799:0.0:0.5964:0.2237	rs8072430;rs8072430	576;662	Q14162-2;Q14162	.;SREC_HUMAN	W	662;576	ENSP00000263071:R662W;ENSP00000323964:R576W	ENSP00000263071:R662W	R	-	1	2	SCARF1	1485311	0.001000	0.12720	0.008000	0.14137	0.014000	0.08584	0.529000	0.23019	0.433000	0.26313	-0.377000	0.06932	CGG	G|0.979;A|0.021	0.021	strong		0.682	SCARF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207081.4	NM_003693	
PRKG1	5592	hgsc.bcm.edu	37	10	53822344	53822344	+	Silent	SNP	T	T	C	rs113994747	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:53822344T>C	ENST00000401604.2	+	7	1037	c.843T>C	c.(841-843)ctT>ctC	p.L281L	PRKG1_ENST00000373975.2_5'UTR|PRKG1_ENST00000373985.1_Silent_p.L269L|PRKG1_ENST00000373980.4_Silent_p.L296L			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	281	cGMP-binding, low affinity.				actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		CAGTCTTTCTTAGAACTTTAG	0.403													T|||	106	0.0211661	0.0764	0.0058	5008	,	,		15835	0.0		0.001	False		,,,				2504	0.0				p.L296L		Atlas-SNP	.											.	PRKG1	167	.	0			c.T888C						PASS	.	T	,	299,4107	162.9+/-194.8	15,269,1919	65.0	67.0	66.0		843,888	0.8	1.0	10	dbSNP_132	66	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PRKG1	NM_001098512.2,NM_006258.3	,	15,269,6219	CC,CT,TT		0.0,6.7862,2.2989	,	281/672,296/687	53822344	299,12707	2203	4300	6503	SO:0001819	synonymous_variant	5592	exon7			CTTTCTTAGAACT		CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B		2792381, 1544322	Standard	NM_001098512		Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000401604.2:c.843T>C	10.37:g.53822344T>C		121.0	0.0	0		119.0	68.0	0.571429	NM_006258	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Silent	SNP	ENST00000401604.2	37	CCDS44399.1																																																																																			T|0.976;C|0.024	0.024	strong		0.403	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
ESYT3	83850	hgsc.bcm.edu	37	3	138176436	138176436	+	Silent	SNP	A	A	G	rs35605373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:138176436A>G	ENST00000389567.4	+	4	717	c.531A>G	c.(529-531)gcA>gcG	p.A177A	ESYT3_ENST00000289135.4_Silent_p.A177A	NM_031913.3	NP_114119.2	A0FGR9	ESYT3_HUMAN	extended synaptotagmin-like protein 3	177	Glycerophospholipid-binding barrel-like domain. {ECO:0000250}.				lipid transport (GO:0006869)	extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|integral component of plasma membrane (GO:0005887)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|organelle membrane contact site (GO:0044232)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)			breast(1)|endometrium(5)|large_intestine(7)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	25						GTGTCAAGGCACACACTAATA	0.587													A|||	118	0.0235623	0.0825	0.013	5008	,	,		20302	0.0		0.0	False		,,,				2504	0.0				p.A177A		Atlas-SNP	.											.	ESYT3	64	.	0			c.A531G						PASS	.	A		310,4096	166.5+/-197.7	5,300,1898	182.0	160.0	168.0		531	-10.9	0.0	3	dbSNP_126	168	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	ESYT3	NM_031913.3		5,304,6194	GG,GA,AA		0.0465,7.0359,2.4143		177/887	138176436	314,12692	2203	4300	6503	SO:0001819	synonymous_variant	83850	exon4			CAAGGCACACACT	AJ303366	CCDS3101.2	3q22.3	2014-07-02	2009-06-23	2009-06-23	ENSG00000158220	ENSG00000158220		"""Synaptotagmins"""	24295	protein-coding gene	gene with protein product			"""family with sequence similarity 62 (C2 domain containing), member C"""	FAM62C		11543631, 17672888	Standard	NM_031913		Approved	CHR3SYT	uc003esk.3	A0FGR9	OTTHUMG00000147354	ENST00000389567.4:c.531A>G	3.37:g.138176436A>G		130.0	0.0	0		154.0	75.0	0.487013	NM_031913	A8K0G5|Q6ZV21|Q8NDZ5|Q9BQR9	Silent	SNP	ENST00000389567.4	37	CCDS3101.2																																																																																			A|0.975;G|0.025	0.025	strong		0.587	ESYT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303993.1	NM_031913	
FBXW9	84261	hgsc.bcm.edu	37	19	12807187	12807187	+	Missense_Mutation	SNP	C	C	T	rs6511833	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12807187C>T	ENST00000380339.3	-	1	245	c.209G>A	c.(208-210)aGg>aAg	p.R70K	FBXW9_ENST00000544494.1_5'UTR|FBXW9_ENST00000393261.3_Missense_Mutation_p.R70K|FBXW9_ENST00000587955.1_Missense_Mutation_p.R70K			Q5XUX1	FBXW9_HUMAN	F-box and WD repeat domain containing 9	70			R -> K (in dbSNP:rs6511833).		SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)					cervix(1)|lung(4)|ovary(1)|prostate(1)	7						GGCCGAAACCCTGGACGCGGC	0.692													T|||	748	0.149361	0.5333	0.0461	5008	,	,		12421	0.0		0.0109	False		,,,				2504	0.0				p.R70K		Atlas-SNP	.											.	FBXW9	30	.	0			c.G209A						PASS	.	T	LYS/ARG	1544,2262		327,890,686	14.0	18.0	17.0		209	-0.2	0.0	19	dbSNP_116	17	128,8068		4,120,3974	yes	missense	FBXW9	NM_032301.2	26	331,1010,4660	TT,TC,CC		1.5617,40.5675,13.931	benign	70/459	12807187	1672,10330	1903	4098	6001	SO:0001583	missense	84261	exon1			GAAACCCTGGACG	BC004290	CCDS12278.2	19p13.2	2013-01-09	2007-02-08		ENSG00000132004	ENSG00000132004		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	28136	protein-coding gene	gene with protein product		609074	"""F-box and WD-40 domain protein 9"""			12477932	Standard	NM_032301		Approved	MGC10870, Fbw9	uc002mum.1	Q5XUX1	OTTHUMG00000150152	ENST00000380339.3:c.209G>A	19.37:g.12807187C>T	ENSP00000369696:p.Arg70Lys	44.0	0.0	0		69.0	33.0	0.478261	NM_032301	B3KVP7|Q9BT89	Missense_Mutation	SNP	ENST00000380339.3	37		244	0.11172161172161173	220	0.44715447154471544	17	0.04696132596685083	0	0.0	7	0.009234828496042216	T	7.621	0.676786	0.14841	0.405675	0.015617	ENSG00000132004	ENST00000393261;ENST00000380339	T;T	0.53857	0.6;0.6	5.0	-0.247	0.13019	.	0.338458	0.20979	N	0.082254	T	0.00012	0.0000	N	0.02916	-0.46	0.46849	P	7.759999999999989E-4	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.41998	-0.9477	9	0.02654	T	1	-7.7148	10.6828	0.45823	0.0:0.4314:0.0:0.5686	rs6511833;rs61227291;rs6511833	70;70	Q5XUX1-2;Q5XUX1-3	.;.	K	70	ENSP00000376945:R70K;ENSP00000369696:R70K	ENSP00000369696:R70K	R	-	2	0	FBXW9	12668187	0.063000	0.20901	0.023000	0.16930	0.194000	0.23727	-0.092000	0.11129	-0.309000	0.08779	-0.521000	0.04368	AGG	C|0.880;T|0.120	0.120	strong		0.692	FBXW9-201	KNOWN	basic	protein_coding	protein_coding		NM_032301	
HMMR	3161	hgsc.bcm.edu	37	5	162910136	162910136	+	Missense_Mutation	SNP	A	A	G	rs112257004	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:162910136A>G	ENST00000358715.3	+	14	1676	c.1640A>G	c.(1639-1641)cAg>cGg	p.Q547R	HMMR_ENST00000353866.3_Missense_Mutation_p.Q532R|RP11-80G7.1_ENST00000514724.2_RNA|RP11-80G7.1_ENST00000521666.1_RNA|HMMR_ENST00000393915.4_Missense_Mutation_p.Q548R|HMMR_ENST00000432118.2_Missense_Mutation_p.Q461R			O75330	HMMR_HUMAN	hyaluronan-mediated motility receptor (RHAMM)	547				Q -> R (in Ref. 3; BAF83266). {ECO:0000305}.	carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)			cervix(1)|kidney(3)|large_intestine(6)|lung(9)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	23	Renal(175;0.000281)	Medulloblastoma(196;0.00853)|all_neural(177;0.0408)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0296)|OV - Ovarian serous cystadenocarcinoma(192;0.0423)|Epithelial(171;0.0848)	Hyaluronan(DB08818)	CTCAAGCAACAGGAGGAAGAC	0.358													A|||	46	0.0091853	0.0287	0.0115	5008	,	,		17094	0.0		0.0	False		,,,				2504	0.0				p.Q548R		Atlas-SNP	.											.	HMMR	64	.	0			c.A1643G						PASS	.	A	ARG/GLN,ARG/GLN,ARG/GLN,ARG/GLN	101,4305		1,99,2103	55.0	57.0	57.0		1643,1382,1640,1595	5.3	0.9	5	dbSNP_132	57	0,8594		0,0,4297	yes	missense,missense,missense,missense	HMMR	NM_001142556.1,NM_001142557.1,NM_012484.2,NM_012485.2	43,43,43,43	1,99,6400	GG,GA,AA		0.0,2.2923,0.7769	benign,benign,benign,benign	548/726,461/639,547/725,532/710	162910136	101,12899	2203	4297	6500	SO:0001583	missense	3161	exon14			AGCAACAGGAGGA	U29343	CCDS4362.1, CCDS4363.1, CCDS47334.1, CCDS47335.1	5q34	2013-09-19			ENSG00000072571	ENSG00000072571		"""CD molecules"""	5012	protein-coding gene	gene with protein product		600936					Standard	NM_001142556		Approved	RHAMM, CD168	uc003lzh.3	O75330	OTTHUMG00000130381	ENST00000358715.3:c.1640A>G	5.37:g.162910136A>G	ENSP00000351554:p.Gln547Arg	121.0	0.0	0		128.0	53.0	0.414062	NM_001142556	A8K3G2|B4E114|D3DQK9|D3DQL0|E9PCS0|Q32N02|Q92767	Missense_Mutation	SNP	ENST00000358715.3	37	CCDS4362.1	17	0.007783882783882784	12	0.024390243902439025	5	0.013812154696132596	0	0.0	0	0.0	A	13.18	2.159585	0.38119	0.022923	0.0	ENSG00000072571	ENST00000416990;ENST00000353866;ENST00000393915;ENST00000426586;ENST00000432118;ENST00000358715	T;T;T;T;T	0.08282	3.11;3.11;3.11;3.11;3.11	5.33	5.33	0.75918	.	0.292472	0.38326	N	0.001730	T	0.06050	0.0157	L	0.60455	1.87	0.27255	N	0.958781	B;P;P;P	0.36959	0.383;0.51;0.575;0.575	B;B;B;P	0.45232	0.165;0.273;0.394;0.474	T	0.12319	-1.0552	10	0.14656	T	0.56	-11.8252	9.8283	0.40925	0.8474:0.0:0.0:0.1526	.	461;548;532;547	O75330-4;O75330-3;O75330-2;O75330	.;.;.;HMMR_HUMAN	R	433;532;548;524;461;547	ENSP00000400527:Q433R;ENSP00000185942:Q532R;ENSP00000377492:Q548R;ENSP00000402673:Q461R;ENSP00000351554:Q547R	ENSP00000185942:Q532R	Q	+	2	0	HMMR	162842714	0.998000	0.40836	0.903000	0.35520	0.684000	0.39900	2.194000	0.42668	2.234000	0.73211	0.533000	0.62120	CAG	A|0.990;G|0.010	0.010	strong		0.358	HMMR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252752.1	NM_012484	
MMP15	4324	hgsc.bcm.edu	37	16	58079268	58079268	+	Missense_Mutation	SNP	C	C	T	rs141377329	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:58079268C>T	ENST00000219271.3	+	10	2713	c.1928C>T	c.(1927-1929)aCc>aTc	p.T643I		NM_002428.2	NP_002419.1	P51511	MMP15_HUMAN	matrix metallopeptidase 15 (membrane-inserted)	643					cellular protein modification process (GO:0006464)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)|response to estradiol (GO:0032355)	extracellular matrix (GO:0031012)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	18					Marimastat(DB00786)	CTGGGCCTCACCTACGCGCTG	0.662													C|||	14	0.00279553	0.0098	0.0014	5008	,	,		14760	0.0		0.0	False		,,,				2504	0.0				p.T643I		Atlas-SNP	.											.	MMP15	58	.	0			c.C1928T						PASS	.	C	ILE/THR	39,4355		0,39,2158	124.0	127.0	126.0		1928	3.6	0.0	16	dbSNP_134	126	1,8595		0,1,4297	yes	missense	MMP15	NM_002428.2	89	0,40,6455	TT,TC,CC		0.0116,0.8876,0.3079	benign	643/670	58079268	40,12950	2197	4298	6495	SO:0001583	missense	4324	exon10			GCCTCACCTACGC	Z48482	CCDS10792.1	16q13	2008-05-14	2005-08-08		ENSG00000102996	ENSG00000102996			7161	protein-coding gene	gene with protein product		602261	"""matrix metalloproteinase 15 (membrane-inserted)"""			9070935, 9119382	Standard	NM_002428		Approved	MT2-MMP, MTMMP2, SMCP-2	uc002ena.3	P51511	OTTHUMG00000133466	ENST00000219271.3:c.1928C>T	16.37:g.58079268C>T	ENSP00000219271:p.Thr643Ile	77.0	0.0	0		90.0	51.0	0.566667	NM_002428	A0A2U6|Q14111	Missense_Mutation	SNP	ENST00000219271.3	37	CCDS10792.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	C	2.732	-0.264139	0.05754	0.008876	1.16E-4	ENSG00000102996	ENST00000219271	T	0.25579	1.79	4.65	3.62	0.41486	Peptidase M10A, matrix metallopeptidase, C-terminal (1);	0.337903	0.33772	N	0.004578	T	0.02970	0.0088	N	0.00186	-1.895	0.26149	N	0.980165	B	0.06786	0.001	B	0.06405	0.002	T	0.40194	-0.9576	10	0.10902	T	0.67	.	5.4497	0.16556	0.0:0.7809:0.0:0.2191	.	643	P51511	MMP15_HUMAN	I	643	ENSP00000219271:T643I	ENSP00000219271:T643I	T	+	2	0	MMP15	56636769	0.999000	0.42202	0.018000	0.16275	0.093000	0.18481	2.919000	0.48836	2.418000	0.82041	0.555000	0.69702	ACC	C|0.997;T|0.003	0.003	strong		0.662	MMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257342.1	NM_002428	
INPP5B	3633	hgsc.bcm.edu	37	1	38411444	38411444	+	Missense_Mutation	SNP	C	C	T	rs56993041	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:38411444C>T	ENST00000373026.1	-	2	136	c.136G>A	c.(136-138)Ggc>Agc	p.G46S	INPP5B_ENST00000373023.2_Missense_Mutation_p.G46S|INPP5B_ENST00000373021.1_Missense_Mutation_p.G46S|INPP5B_ENST00000373024.3_Missense_Mutation_p.G46S			P32019	I5P2_HUMAN	inositol polyphosphate-5-phosphatase, 75kDa	46	PH.		G -> S (in dbSNP:rs56993041).		in utero embryonic development (GO:0001701)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol dephosphorylation (GO:0046856)|regulation of protein processing (GO:0070613)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	inositol-1,4,5-trisphosphate 5-phosphatase activity (GO:0052658)|metal ion binding (GO:0046872)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)			breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(9)|urinary_tract(1)	15	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				TCCTGGCCGCCGTGCTCCAGG	0.652													C|||	143	0.0285543	0.1021	0.0115	5008	,	,		15864	0.0		0.0	False		,,,				2504	0.0				p.G46S		Atlas-SNP	.											.	INPP5B	76	.	0			c.G136A						PASS	.	C	SER/GLY	341,3813		12,317,1748	54.0	65.0	61.0		136	4.4	0.0	1	dbSNP_129	61	0,8390		0,0,4195	yes	missense	INPP5B	NM_005540.2	56	12,317,5943	TT,TC,CC		0.0,8.209,2.7184	possibly-damaging	46/914	38411444	341,12203	2077	4195	6272	SO:0001583	missense	3633	exon3			GGCCGCCGTGCTC	M74161	CCDS41306.1, CCDS72760.1	1p34	2008-02-05	2002-08-29		ENSG00000204084	ENSG00000204084	3.1.3.56		6077	protein-coding gene	gene with protein product		147264	"""inositol polyphosphate-5-phosphatase, 75kD"""			1718960	Standard	NM_005540		Approved		uc001ccg.1	P32019	OTTHUMG00000004436	ENST00000373026.1:c.136G>A	1.37:g.38411444C>T	ENSP00000362117:p.Gly46Ser	191.0	1.0	0.0052356		215.0	118.0	0.548837	NM_005540	C9J6U5|Q5VSG9|Q5VSH0|Q5VSH1|Q658Q5|Q6P6D4|Q6PD53|Q86YE1	Missense_Mutation	SNP	ENST00000373026.1	37		47	0.02152014652014652	44	0.08943089430894309	3	0.008287292817679558	0	0.0	0	0.0	C	15.32	2.799766	0.50208	0.08209	0.0	ENSG00000204084	ENST00000373023;ENST00000373029;ENST00000373026;ENST00000373024;ENST00000373021	D;D;D;T	0.91945	-2.93;-2.93;-2.94;0.96	4.43	4.43	0.53597	.	0.993232	0.08181	N	0.985409	T	0.32763	0.0840	L	0.54323	1.7	0.80722	D	1	P	0.39920	0.695	B	0.32149	0.141	T	0.68047	-0.5512	10	0.51188	T	0.08	.	13.2598	0.60098	0.0:1.0:0.0:0.0	rs56993041;rs61744649	46	P32019-2	.	S	46	ENSP00000362114:G46S;ENSP00000362117:G46S;ENSP00000362115:G46S;ENSP00000362112:G46S	ENSP00000362112:G46S	G	-	1	0	INPP5B	38184031	0.009000	0.17119	0.018000	0.16275	0.185000	0.23345	2.347000	0.44036	2.411000	0.81874	0.563000	0.77884	GGC	C|0.978;T|0.022	0.022	strong		0.652	INPP5B-003	KNOWN	non_canonical_conserved|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000012968.1	NM_005540	
TNXB	7148	hgsc.bcm.edu	37	6	32023903	32023903	+	Missense_Mutation	SNP	G	G	C	rs440160	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32023903G>C	ENST00000375244.3	-	24	8393	c.8192C>G	c.(8191-8193)cCg>cGg	p.P2731R	TNXB_ENST00000375247.2_Missense_Mutation_p.P2731R			P22105	TENX_HUMAN	tenascin XB	2789	Fibronectin type-III 19. {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						AGGGGGCTCCGGGGCCTCAGT	0.642													G|||	223	0.0445288	0.1036	0.0605	5008	,	,		14531	0.001		0.0427	False		,,,				2504	0.0				p.P2731R		Atlas-SNP	.											.	TNXB	553	.	0			c.C8192G						PASS	.	G	ARG/PRO	201,2183		10,181,1001	40.0	47.0	45.0		8192	4.5	1.0	6	dbSNP_80	45	209,4793		4,201,2296	no	missense	TNXB	NM_019105.6	103	14,382,3297	CC,CG,GG		4.1783,8.4312,5.551	probably-damaging	2731/4243	32023903	410,6976	1192	2501	3693	SO:0001583	missense	7148	exon24			GGCTCCGGGGCCT	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.8192C>G	6.37:g.32023903G>C	ENSP00000364393:p.Pro2731Arg	101.0	0.0	0		126.0	63.0	0.5	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		94	0.04304029304029304	42	0.08536585365853659	22	0.06077348066298342	1	0.0017482517482517483	29	0.03825857519788918	G	15.03	2.713296	0.48517	0.084312	0.041783	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.61510	0.47;0.1	4.48	4.48	0.54585	.	.	.	.	.	T	0.65974	0.2743	M	0.82923	2.615	0.28078	N	0.932303	D	0.61080	0.989	P	0.61070	0.883	T	0.60722	-0.7207	9	0.62326	D	0.03	.	12.0664	0.53590	0.0:0.1746:0.8254:0.0	rs440160;rs3948802	2731	P22105-3	.	R	2731	ENSP00000364393:P2731R;ENSP00000364396:P2731R	ENSP00000364393:P2731R	P	-	2	0	TNXB	32131881	0.037000	0.19845	0.989000	0.46669	0.396000	0.30629	0.607000	0.24209	2.317000	0.78254	0.456000	0.33151	CCG	G|0.931;C|0.069	0.069	strong		0.642	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
ZNF668	79759	hgsc.bcm.edu	37	16	31075364	31075364	+	Silent	SNP	G	G	A	rs34889904	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31075364G>A	ENST00000538906.1	-	2	1201	c.417C>T	c.(415-417)ccC>ccT	p.P139P	ZNF668_ENST00000539836.3_Silent_p.P162P|ZNF668_ENST00000564456.1_5'Flank|ZNF668_ENST00000535577.1_Silent_p.P139P|ZNF668_ENST00000426488.2_Silent_p.P162P|ZNF668_ENST00000300849.4_Silent_p.P139P|AC135050.5_ENST00000568708.1_RNA|ZNF668_ENST00000394983.2_Silent_p.P139P	NM_001172668.1	NP_001166139	Q96K58	ZN668_HUMAN	zinc finger protein 668	139					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	27						CACAGCGGAAGGGCAGTTCGC	0.697													G|||	38	0.00758786	0.0257	0.0058	5008	,	,		17086	0.0		0.0	False		,,,				2504	0.0				p.P162P	Colon(181;1111 1980 5060 10512 25785)	Atlas-SNP	.											.	ZNF668	121	.	0			c.C486T						PASS	.	G	,,,	135,4259	84.8+/-123.5	4,127,2066	26.0	23.0	24.0		417,486,417,417	-0.6	1.0	16	dbSNP_126	24	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF668	NM_001172668.1,NM_001172669.1,NM_001172670.1,NM_024706.4	,,,	4,128,6363	AA,AG,GG		0.0116,3.0724,1.047	,,,	139/620,162/643,139/620,139/620	31075364	136,12854	2197	4298	6495	SO:0001819	synonymous_variant	79759	exon3			GCGGAAGGGCAGT		CCDS10701.1, CCDS54003.1	16p11.2	2013-01-08			ENSG00000167394	ENSG00000167394		"""Zinc fingers, C2H2-type"""	25821	protein-coding gene	gene with protein product						12477932	Standard	NM_024706		Approved	FLJ13479	uc021tgt.1	Q96K58	OTTHUMG00000047357	ENST00000538906.1:c.417C>T	16.37:g.31075364G>A		38.0	0.0	0		60.0	29.0	0.483333	NM_001172669	C9JHH8|F5H7E7|Q59EV1|Q8N669|Q9H8L4	Silent	SNP	ENST00000538906.1	37	CCDS10701.1																																																																																			G|0.990;A|0.010	0.010	strong		0.697	ZNF668-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108516.2	NM_024706	
CEP135	9662	hgsc.bcm.edu	37	4	56837458	56837458	+	Missense_Mutation	SNP	A	A	G	rs141602415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:56837458A>G	ENST00000257287.4	+	10	1257	c.1133A>G	c.(1132-1134)gAa>gGa	p.E378G		NM_025009.4	NP_079285.2	Q66GS9	CP135_HUMAN	centrosomal protein 135kDa	378					centriole replication (GO:0007099)|centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centriole (GO:0005814)|centrosome (GO:0005813)|cytosol (GO:0005829)	protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(26)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	50	Glioma(25;0.08)|all_neural(26;0.101)					TGCCAGAAAGAAAAGGAGAGA	0.294													A|||	4	0.000798722	0.003	0.0	5008	,	,		15338	0.0		0.0	False		,,,				2504	0.0				p.E378G		Atlas-SNP	.											CEP135,NS,carcinoma,+1,1	CEP135	115	1	0			c.A1133G						PASS	.	A	GLY/GLU	25,4381	26.2+/-53.5	0,25,2178	42.0	43.0	43.0		1133	6.0	1.0	4	dbSNP_134	43	0,8600		0,0,4300	yes	missense	CEP135	NM_025009.3	98	0,25,6478	GG,GA,AA		0.0,0.5674,0.1922	probably-damaging	378/1141	56837458	25,12981	2203	4300	6503	SO:0001583	missense	9662	exon10			AGAAAGAAAAGGA	AB014535	CCDS33986.1	4q12	2014-02-20	2005-12-02	2005-12-02	ENSG00000174799	ENSG00000174799			29086	protein-coding gene	gene with protein product		611423	"""KIAA0635"", ""centrosomal protein 4"""	KIAA0635, CEP4		9734811, 14654843	Standard	NM_025009		Approved	FLJ13621	uc003hbi.4	Q66GS9	OTTHUMG00000160748	ENST00000257287.4:c.1133A>G	4.37:g.56837458A>G	ENSP00000257287:p.Glu378Gly	141.0	0.0	0		122.0	57.0	0.467213	NM_025009	B2RMY0|O75130|Q58F25|Q9H8H7	Missense_Mutation	SNP	ENST00000257287.4	37	CCDS33986.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	A	25.9	4.681724	0.88542	0.005674	0.0	ENSG00000174799	ENST00000257287	T	0.53640	0.61	6.04	6.04	0.98038	.	0.091491	0.64402	D	0.000001	T	0.56920	0.2018	M	0.63428	1.95	0.42620	D	0.993343	D	0.69078	0.997	P	0.62885	0.908	T	0.63404	-0.6645	10	0.52906	T	0.07	.	16.5763	0.84648	1.0:0.0:0.0:0.0	.	378	Q66GS9	CP135_HUMAN	G	378	ENSP00000257287:E378G	ENSP00000257287:E378G	E	+	2	0	CEP135	56532215	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.387000	0.73191	2.317000	0.78254	0.459000	0.35465	GAA	A|0.998;G|0.002	0.002	strong		0.294	CEP135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362092.2	NM_025009	
POF1B	79983	hgsc.bcm.edu	37	X	84600948	84600948	+	Missense_Mutation	SNP	T	T	C	rs60768249	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:84600948T>C	ENST00000262753.4	-	6	786	c.641A>G	c.(640-642)cAa>cGa	p.Q214R	POF1B_ENST00000373145.3_Missense_Mutation_p.Q214R	NM_024921.3	NP_079197.3	Q8WVV4	POF1B_HUMAN	premature ovarian failure, 1B	214						tight junction (GO:0005923)				central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|liver(2)|lung(17)|ovary(1)|prostate(1)	35						TGTGATGGCTTGGATTTGCTG	0.463													T|||	135	0.0357616	0.0946	0.0144	3775	,	,		12542	0.0		0.0	False		,,,				2504	0.0				p.Q214R		Atlas-SNP	.											.	POF1B	77	.	0			c.A641G						PASS	.	T	ARG/GLN	462,3373		16,338,92,1278,479	234.0	189.0	204.0		641	4.6	0.0	X	dbSNP_129	204	2,6726		0,1,1,2427,1871	yes	missense	POF1B	NM_024921.3	43	16,339,93,3705,2350	CC,CT,C,TT,T		0.0297,12.0469,4.3927	possibly-damaging	214/590	84600948	464,10099	2203	4300	6503	SO:0001583	missense	79983	exon6			ATGGCTTGGATTT	BC017500	CCDS14452.1	Xq21.2	2008-02-05			ENSG00000124429	ENSG00000124429			13711	protein-coding gene	gene with protein product		300603				11299520	Standard	NM_024921		Approved	POF, FLJ22792	uc004eer.2	Q8WVV4	OTTHUMG00000021934	ENST00000262753.4:c.641A>G	X.37:g.84600948T>C	ENSP00000262753:p.Gln214Arg	228.0	0.0	0		202.0	106.0	0.524752	NM_024921	A8K2U5|Q5H9E9|Q5H9F0|Q8NG12|Q9H5Y2|Q9H738|Q9H744	Missense_Mutation	SNP	ENST00000262753.4	37	CCDS14452.1	53	0.031946955997588906	32	0.06926406926406926	3	0.008426966292134831	0	0.0	0	0.0	T	6.220	0.408732	0.11812	0.120469	2.97E-4	ENSG00000124429	ENST00000262753;ENST00000373145;ENST00000276124	T;T	0.10763	2.84;2.84	4.56	4.56	0.56223	.	0.364164	0.23070	N	0.052276	T	0.00178	0.0005	L	0.53249	1.67	0.80722	P	0.0	B;B	0.25272	0.058;0.122	B;B	0.25291	0.059;0.04	T	0.05801	-1.0863	9	0.66056	D	0.02	.	9.2182	0.37360	0.0:0.0:0.0:1.0	rs60768249	214;214	Q8WVV4-1;Q8WVV4	.;POF1B_HUMAN	R	214	ENSP00000262753:Q214R;ENSP00000362238:Q214R	ENSP00000262753:Q214R	Q	-	2	0	POF1B	84487604	0.828000	0.29307	0.049000	0.19019	0.045000	0.14185	3.232000	0.51302	1.775000	0.52247	0.481000	0.45027	CAA	T|0.958;C|0.042	0.042	strong		0.463	POF1B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057391.2	NM_024921	
PLEC	5339	hgsc.bcm.edu	37	8	144991428	144991428	+	Silent	SNP	G	G	A	rs11998271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144991428G>A	ENST00000322810.4	-	32	13141	c.12972C>T	c.(12970-12972)gaC>gaT	p.D4324D	PLEC_ENST00000398774.2_Silent_p.D4155D|PLEC_ENST00000354958.2_Silent_p.D4165D|PLEC_ENST00000345136.3_Silent_p.D4187D|PLEC_ENST00000357649.2_Silent_p.D4191D|PLEC_ENST00000354589.3_Silent_p.D4187D|PLEC_ENST00000436759.2_Silent_p.D4214D|PLEC_ENST00000527096.1_Silent_p.D4210D|PLEC_ENST00000356346.3_Silent_p.D4173D	NM_201380.2	NP_958782.1	Q15149	PLEC_HUMAN	plectin	4324	Globular 2.				apoptotic process (GO:0006915)|cell junction assembly (GO:0034329)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)	ankyrin binding (GO:0030506)|poly(A) RNA binding (GO:0044822)|structural constituent of muscle (GO:0008307)			NS(1)|breast(3)|central_nervous_system(4)|cervix(7)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(8)|lung(57)|ovary(4)|pancreas(2)|prostate(11)|skin(9)|stomach(2)|upper_aerodigestive_tract(10)	137						TGACCACGCCGTCCGAGGAGG	0.622													G|||	419	0.0836661	0.3011	0.0173	5008	,	,		18486	0.001		0.002	False		,,,				2504	0.0061				p.D4324D		Atlas-SNP	.											.	PLEC	1144	.	0			c.C12972T						PASS	.	G	,,,,,,,	1134,3084		148,838,1123	56.0	63.0	61.0		12642,12519,12495,12972,12465,12561,12573,12561	-4.4	0.9	8	dbSNP_120	61	5,8413		0,5,4204	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEC	NM_000445.3,NM_201378.2,NM_201379.1,NM_201380.2,NM_201381.1,NM_201382.2,NM_201383.1,NM_201384.1	,,,,,,,	148,843,5327	AA,AG,GG		0.0594,26.8848,9.0139	,,,,,,,	4214/4575,4173/4534,4165/4526,4324/4685,4155/4516,4187/4548,4191/4552,4187/4548	144991428	1139,11497	2109	4209	6318	SO:0001819	synonymous_variant	5339	exon32			CACGCCGTCCGAG	U53204	CCDS43769.1, CCDS43770.1, CCDS43771.1, CCDS43772.1, CCDS43773.1, CCDS43774.1, CCDS43775.1, CCDS47936.1	8q24	2010-02-04	2010-02-04	2010-02-04	ENSG00000178209	ENSG00000178209			9069	protein-coding gene	gene with protein product		601282	"""plectin 1, intermediate filament binding protein, 500kD"", ""epidermolysis bullosa simplex 1 (Ogna)"", ""plectin 1, intermediate filament binding protein 500kDa"""	EBS1, PLEC1		8633055, 8696340	Standard	XM_005250976		Approved	PCN, PLTN	uc003zaf.1	Q15149	OTTHUMG00000165291	ENST00000322810.4:c.12972C>T	8.37:g.144991428G>A		40.0	0.0	0		42.0	22.0	0.52381	NM_201380	Q15148|Q16640|Q6S376|Q6S377|Q6S378|Q6S379|Q6S380|Q6S381|Q6S382|Q6S383	Silent	SNP	ENST00000322810.4	37	CCDS43772.1																																																																																			G|0.957;A|0.043	0.043	strong		0.622	PLEC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383281.1	NM_000445	
SEMA5B	54437	hgsc.bcm.edu	37	3	122634665	122634665	+	Missense_Mutation	SNP	G	G	C	rs34037493	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122634665G>C	ENST00000357599.3	-	13	2147	c.1761C>G	c.(1759-1761)gaC>gaG	p.D587E	SEMA5B_ENST00000195173.4_Missense_Mutation_p.D587E|SEMA5B_ENST00000451055.2_Missense_Mutation_p.D641E	NM_001031702.3|NM_001256348.1	NP_001026872.2|NP_001243277.1	Q9P283	SEM5B_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5B	587					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(13)|lung(26)|ovary(2)|pancreas(3)|skin(2)|upper_aerodigestive_tract(3)	55				GBM - Glioblastoma multiforme(114;0.0367)		TGTTGGAGCTGTCCTCGAGTG	0.597													G|||	161	0.0321486	0.1089	0.0216	5008	,	,		18045	0.0		0.002	False		,,,				2504	0.0				p.D641E		Atlas-SNP	.											.	SEMA5B	303	.	0			c.C1923G						PASS	.	G	GLU/ASP	369,4037	187.4+/-214.1	18,333,1852	142.0	134.0	137.0		1761	4.6	1.0	3	dbSNP_126	137	4,8596	3.7+/-12.6	0,4,4296	yes	missense	SEMA5B	NM_001031702.2	45	18,337,6148	CC,CG,GG		0.0465,8.3749,2.8679	benign	587/1152	122634665	373,12633	2203	4300	6503	SO:0001583	missense	54437	exon13			GGAGCTGTCCTCG	AB040878	CCDS35491.1, CCDS58848.1, CCDS74995.1	3q21.1	2008-07-18			ENSG00000082684	ENSG00000082684		"""Semaphorins"""	10737	protein-coding gene	gene with protein product		609298		SEMAG		8817451	Standard	NM_001256346		Approved	SemG, KIAA1445, FLJ10372	uc031sbm.1	Q9P283	OTTHUMG00000140392	ENST00000357599.3:c.1761C>G	3.37:g.122634665G>C	ENSP00000350215:p.Asp587Glu	255.0	0.0	0		280.0	144.0	0.514286	NM_001256347	A8K5U2|B7Z393|F8W9U8|Q6DD89|Q6UY12|Q9NW17	Missense_Mutation	SNP	ENST00000357599.3	37	CCDS35491.1	62	0.028388278388278388	51	0.10365853658536585	9	0.024861878453038673	0	0.0	2	0.002638522427440633	G	12.03	1.817110	0.32145	0.083749	4.65E-4	ENSG00000082684	ENST00000357599;ENST00000195173;ENST00000418793;ENST00000451055;ENST00000393583	T;T;T;T	0.21361	2.01;2.01;2.01;2.01	4.64	4.64	0.57946	.	0.000000	0.85682	D	0.000000	T	0.00271	0.0008	N	0.11284	0.12	0.54753	D	0.999981	B;B;B	0.27559	0.086;0.181;0.181	B;B;B	0.27500	0.048;0.08;0.08	T	0.11108	-1.0601	10	0.05525	T	0.97	.	14.3689	0.66826	0.0:0.0:1.0:0.0	rs34037493;rs59368219	529;587;587	D3YTI7;B5ME80;Q9P283	.;.;SEM5B_HUMAN	E	587;587;529;641;587	ENSP00000350215:D587E;ENSP00000195173:D587E;ENSP00000389588:D641E;ENSP00000377208:D587E	ENSP00000195173:D587E	D	-	3	2	SEMA5B	124117355	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.083000	0.41615	2.404000	0.81709	0.561000	0.74099	GAC	G|0.970;C|0.030	0.030	strong		0.597	SEMA5B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000277165.1	NM_001031702	
GNA13	10672	hgsc.bcm.edu	37	17	63049709	63049709	+	Missense_Mutation	SNP	C	C	T	rs116700192	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:63049709C>T	ENST00000439174.2	-	2	666	c.421G>A	c.(421-423)Gtt>Att	p.V141I	RP11-583F2.5_ENST00000581796.1_RNA|GNA13_ENST00000541118.1_Missense_Mutation_p.V46I	NM_006572.4	NP_006563.2	Q14344	GNA13_HUMAN	guanine nucleotide binding protein (G protein), alpha 13	141					activation of phospholipase D activity (GO:0031584)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|in utero embryonic development (GO:0001701)|patterning of blood vessels (GO:0001569)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of cell migration (GO:0030334)|regulation of cell shape (GO:0008360)|Rho protein signal transduction (GO:0007266)|signal transduction (GO:0007165)	brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|heterotrimeric G-protein complex (GO:0005834)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	D5 dopamine receptor binding (GO:0031752)|G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 1 angiotensin receptor binding (GO:0031702)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(14)|kidney(2)|large_intestine(4)|lung(6)|urinary_tract(1)	34						TGTAAGAAAACCCTTGTTTCC	0.468													C|||	55	0.0109824	0.0408	0.0014	5008	,	,		16418	0.0		0.0	False		,,,				2504	0.0				p.V141I		Atlas-SNP	.											.	GNA13	69	.	0			c.G421A						PASS	.	C	ILE/VAL	193,4213	121.3+/-158.8	4,185,2014	126.0	127.0	127.0		421	3.4	0.0	17	dbSNP_132	127	1,8599	1.2+/-3.3	0,1,4299	yes	missense	GNA13	NM_006572.4	29	4,186,6313	TT,TC,CC		0.0116,4.3804,1.4916	benign	141/378	63049709	194,12812	2203	4300	6503	SO:0001583	missense	10672	exon2			AGAAAACCCTTGT	L22075	CCDS11661.1, CCDS62302.1	17q24.1	2014-09-04			ENSG00000120063	ENSG00000120063			4381	protein-coding gene	gene with protein product		604406				7791744	Standard	NM_006572		Approved	G13, MGC46138	uc002jfc.3	Q14344	OTTHUMG00000179316	ENST00000439174.2:c.421G>A	17.37:g.63049709C>T	ENSP00000400717:p.Val141Ile	104.0	0.0	0		105.0	102.0	0.971429	NM_006572	B2R977|B7Z7R0|F5H1G8|Q8TD70	Missense_Mutation	SNP	ENST00000439174.2	37	CCDS11661.1	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	C	13.82	2.351213	0.41700	0.043804	1.16E-4	ENSG00000120063	ENST00000439174;ENST00000541118;ENST00000239138	D;D	0.88818	-2.43;-2.43	5.42	3.44	0.39384	G protein alpha subunit, helical insertion (2);	0.125987	0.30630	N	0.009208	T	0.54431	0.1858	L	0.45470	1.425	0.34370	D	0.691943	B	0.27594	0.182	B	0.31337	0.128	T	0.75269	-0.3377	10	0.37606	T	0.19	.	11.6014	0.51006	0.0:0.8574:0.0:0.1426	.	141	Q14344	GNA13_HUMAN	I	141;46;116	ENSP00000400717:V141I;ENSP00000439647:V46I	ENSP00000239138:V116I	V	-	1	0	GNA13	60480171	0.972000	0.33761	0.014000	0.15608	0.975000	0.68041	2.447000	0.44917	0.664000	0.31047	0.655000	0.94253	GTT	C|0.988;T|0.012	0.012	strong		0.468	GNA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445720.1	NM_006572	
UBR4	23352	hgsc.bcm.edu	37	1	19403331	19403331	+	Silent	SNP	G	G	A	rs142064832	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19403331G>A	ENST00000375254.3	-	105	15417	c.15390C>T	c.(15388-15390)aaC>aaT	p.N5130N	UBR4_ENST00000375217.2_Silent_p.N5123N|UBR4_ENST00000543981.1_Silent_p.N794N|UBR4_ENST00000375226.2_Silent_p.N5106N|UBR4_ENST00000429347.2_Silent_p.N653N|UBR4_ENST00000375224.1_Silent_p.N837N|UBR4_ENST00000375225.3_Silent_p.N205N|RP5-1126H10.2_ENST00000606379.1_RNA|UBR4_ENST00000375267.2_Silent_p.N5151N	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	5130					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)		TGGGCATGTCGTTGTGGCGGA	0.552													G|||	14	0.00279553	0.0106	0.0	5008	,	,		19899	0.0		0.0	False		,,,				2504	0.0				p.N5130N		Atlas-SNP	.											.	UBR4	415	.	0			c.C15390T						PASS	.	G		14,4392	22.3+/-47.3	0,14,2189	199.0	172.0	181.0		15390	-4.1	1.0	1	dbSNP_134	181	0,8600		0,0,4300	no	coding-synonymous	UBR4	NM_020765.2		0,14,6489	AA,AG,GG		0.0,0.3177,0.1076		5130/5184	19403331	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	23352	exon105			CATGTCGTTGTGG	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.15390C>T	1.37:g.19403331G>A		195.0	0.0	0		193.0	88.0	0.455959	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Silent	SNP	ENST00000375254.3	37	CCDS189.1																																																																																			G|0.999;A|0.001	0.001	strong		0.552	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
TPRX1	284355	hgsc.bcm.edu	37	19	48305731	48305731	+	Silent	SNP	G	G	T	rs79291962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:48305731G>T	ENST00000322175.3	-	2	692	c.537C>A	c.(535-537)atC>atA	p.I179I	TPRX1_ENST00000535759.1_Silent_p.I276I|TPRX1_ENST00000543508.1_Silent_p.I169I	NM_198479.2	NP_940881.2	Q8N7U7	TPRX1_HUMAN	tetra-peptide repeat homeobox 1	179	Gly-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(2)|skin(1)	18		all_cancers(25;3.02e-09)|all_epithelial(76;7e-07)|all_lung(116;2.48e-06)|Lung NSC(112;5.15e-06)|Ovarian(192;0.0139)|all_neural(266;0.0146)|Breast(70;0.133)		OV - Ovarian serous cystadenocarcinoma(262;0.000241)|all cancers(93;0.00036)|Epithelial(262;0.0127)|GBM - Glioblastoma multiforme(486;0.048)		ttgggcctgggatcgggcctg	0.662													G|||	40	0.00798722	0.0295	0.0014	5008	,	,		13670	0.0		0.0	False		,,,				2504	0.0				p.I179I	Esophageal Squamous(123;175 2281 3051 32395)	Atlas-SNP	.											.	TPRX1	46	.	0			c.C537A						PASS	.	G		80,3372		0,80,1646	15.0	13.0	14.0		537	0.3	0.1	19	dbSNP_131	14	1,6371		0,1,3185	no	coding-synonymous	TPRX1	NM_198479.2		0,81,4831	TT,TG,GG		0.0157,2.3175,0.8245		179/412	48305731	81,9743	1726	3186	4912	SO:0001819	synonymous_variant	284355	exon2			GCCTGGGATCGGG		CCDS33066.1	19q13.33	2011-07-08			ENSG00000178928	ENSG00000178928		"""Homeoboxes / PRD class"""	32174	protein-coding gene	gene with protein product		611166					Standard	XM_005258788		Approved	FLJ40321	uc002php.2	Q8N7U7		ENST00000322175.3:c.537C>A	19.37:g.48305731G>T		111.0	0.0	0		129.0	60.0	0.465116	NM_198479	A5D8Y3|B2RPL5	Silent	SNP	ENST00000322175.3	37	CCDS33066.1																																																																																			G|0.993;T|0.007	0.007	strong		0.662	TPRX1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409868.1	NM_198479	
PADI2	11240	hgsc.bcm.edu	37	1	17413127	17413127	+	Silent	SNP	G	G	A	rs35184728	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17413127G>A	ENST00000375486.4	-	7	786	c.723C>T	c.(721-723)taC>taT	p.Y241Y	PADI2_ENST00000444885.2_Missense_Mutation_p.T160I|PADI2_ENST00000375481.1_Silent_p.Y241Y	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	241					chromatin-mediated maintenance of transcription (GO:0048096)|histone H3-R26 citrullination (GO:0036413)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of lymphocyte chemotaxis (GO:1901624)|protein citrullination (GO:0018101)|regulation of chromatin disassembly (GO:0010848)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptionally active chromatin (GO:0035327)	calcium ion binding (GO:0005509)|estrogen receptor binding (GO:0030331)|protein-arginine deiminase activity (GO:0004668)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)	AGCCACCCGTGTACTTGACCA	0.602													G|||	105	0.0209665	0.0635	0.0072	5008	,	,		17470	0.0159		0.0	False		,,,				2504	0.0				p.Y241Y		Atlas-SNP	.											PADI2,NS,malignant_melanoma,-1,1	PADI2	72	1	0			c.C723T						PASS	.	G		290,4116	159.2+/-191.8	8,274,1921	81.0	85.0	84.0		723	2.6	1.0	1	dbSNP_126	84	0,8600		0,0,4300	no	coding-synonymous	PADI2	NM_007365.2		8,274,6221	AA,AG,GG		0.0,6.5819,2.2297		241/666	17413127	290,12716	2203	4300	6503	SO:0001819	synonymous_variant	11240	exon7			ACCCGTGTACTTG	AB030176	CCDS177.1	1p35.2-p35.1	2008-02-05			ENSG00000117115	ENSG00000117115	3.5.3.15	"""Peptidyl arginine deiminases"""	18341	protein-coding gene	gene with protein product		607935				2768262	Standard	NM_007365		Approved	KIAA0994, PDI2	uc001baf.3	Q9Y2J8	OTTHUMG00000002295	ENST00000375486.4:c.723C>T	1.37:g.17413127G>A		84.0	0.0	0		110.0	62.0	0.563636	NM_007365	Q96DA7|Q9UPN2	Silent	SNP	ENST00000375486.4	37	CCDS177.1	42	0.019230769230769232	28	0.056910569105691054	2	0.0055248618784530384	12	0.02097902097902098	0	0.0	G	11.73	1.726689	0.30593	0.065819	0.0	ENSG00000117115	ENST00000444885	T	0.05258	3.47	4.56	2.62	0.31277	.	.	.	.	.	T	0.00328	0.0010	.	.	.	0.24587	N	0.993841	B	0.02656	0.0	B	0.06405	0.002	T	0.45818	-0.9235	8	0.20519	T	0.43	-30.2651	8.7762	0.34762	0.2513:0.0:0.7487:0.0	rs35184728	160	B4DIU3	.	I	160	ENSP00000405894:T160I	ENSP00000405894:T160I	T	-	2	0	PADI2	17285714	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	3.058000	0.49939	1.124000	0.41980	0.460000	0.39030	ACA	G|0.976;A|0.024	0.024	strong		0.602	PADI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006624.1		
URB2	9816	hgsc.bcm.edu	37	1	229772285	229772285	+	Missense_Mutation	SNP	C	C	T	rs115230066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229772285C>T	ENST00000258243.2	+	4	2061	c.1925C>T	c.(1924-1926)tCg>tTg	p.S642L		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	642						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						CTGGAGATCTCGAACCTCCCT	0.468													C|||	6	0.00119808	0.0045	0.0	5008	,	,		21056	0.0		0.0	False		,,,				2504	0.0				p.S642L		Atlas-SNP	.											.	URB2	152	.	0			c.C1925T						PASS	.	C	LEU/SER	10,4396	16.8+/-37.8	0,10,2193	206.0	212.0	210.0		1925	2.9	0.0	1	dbSNP_132	210	0,8600		0,0,4300	yes	missense	URB2	NM_014777.2	145	0,10,6493	TT,TC,CC		0.0,0.227,0.0769	possibly-damaging	642/1525	229772285	10,12996	2203	4300	6503	SO:0001583	missense	9816	exon4			AGATCTCGAACCT	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.1925C>T	1.37:g.229772285C>T	ENSP00000258243:p.Ser642Leu	215.0	0.0	0		253.0	130.0	0.513834	NM_014777	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	37	CCDS31052.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	6.986	0.551949	0.13374	0.00227	0.0	ENSG00000135763	ENST00000258243	T	0.31769	1.48	4.79	2.91	0.33838	.	1.112010	0.06634	N	0.759866	T	0.26593	0.0650	L	0.51422	1.61	0.09310	N	1	B	0.18968	0.032	B	0.08055	0.003	T	0.21895	-1.0232	9	.	.	.	-2.6001	4.7928	0.13257	0.0:0.4546:0.297:0.2483	.	642	Q14146	URB2_HUMAN	L	642	ENSP00000258243:S642L	.	S	+	2	0	URB2	227838908	0.001000	0.12720	0.002000	0.10522	0.001000	0.01503	1.070000	0.30653	1.391000	0.46566	-0.157000	0.13467	TCG	C|0.999;T|0.001	0.001	strong		0.468	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777	
MYBBP1A	10514	hgsc.bcm.edu	37	17	4458536	4458536	+	Silent	SNP	T	T	C	rs144321472	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4458536T>C	ENST00000254718.4	-	1	390	c.84A>G	c.(82-84)ctA>ctG	p.L28L	MYBBP1A_ENST00000381556.2_Silent_p.L28L			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	28	Interaction with MYB. {ECO:0000250}.				cellular response to glucose starvation (GO:0042149)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|osteoblast differentiation (GO:0001649)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|NLS-dependent protein nuclear import complex (GO:0042564)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)	24						TGTGCTTCAATAGGCCATAGC	0.637													C|||	34	0.00678914	0.0234	0.0043	5008	,	,		16162	0.0		0.0	False		,,,				2504	0.0				p.L28L		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.A84G						PASS	.	C	,	77,4327	780.9+/-414.5	1,75,2126	24.0	25.0	25.0		84,84	0.6	0.1	17	dbSNP_134	25	2,8596	790.5+/-407.6	0,2,4297	no	coding-synonymous,coding-synonymous	MYBBP1A	NM_001105538.1,NM_014520.3	,	1,77,6423	CC,CT,TT		0.0233,1.7484,0.6076	,	28/1333,28/1329	4458536	79,12923	2202	4299	6501	SO:0001819	synonymous_variant	10514	exon1			CTTCAATAGGCCA	AF147709	CCDS11046.1, CCDS42238.1	17p13.3	2008-07-18			ENSG00000132382	ENSG00000132382			7546	protein-coding gene	gene with protein product	"""p53-activated protein-2"""	604885				10644447	Standard	NM_014520		Approved	P160, PAP2, FLJ37886	uc002fxz.4	Q9BQG0	OTTHUMG00000090747	ENST00000254718.4:c.84A>G	17.37:g.4458536T>C		59.0	0.0	0		64.0	39.0	0.609375	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Silent	SNP	ENST00000254718.4	37	CCDS11046.1																																																																																			T|0.995;C|0.005	0.005	strong		0.637	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520	
TCEB3	6924	hgsc.bcm.edu	37	1	24078234	24078234	+	Missense_Mutation	SNP	T	T	C	rs34394004	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:24078234T>C	ENST00000418390.2	+	4	1488	c.1217T>C	c.(1216-1218)tTg>tCg	p.L406S	TCEB3_ENST00000609199.1_Missense_Mutation_p.L380S	NM_003198.2	NP_003189.2	Q14241	ELOA1_HUMAN	transcription elongation factor B (SIII), polypeptide 3 (110kDa, elongin A)	406					gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	19		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.42e-24)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;4.74e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|KIRC - Kidney renal clear cell carcinoma(1967;0.00334)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		AAAACTAATTTGGATAGAAAG	0.448											OREG0013232	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	279	0.0557109	0.202	0.0144	5008	,	,		18505	0.0		0.001	False		,,,				2504	0.001				p.L406S		Atlas-SNP	.											.	TCEB3	61	.	0			c.T1217C						PASS	.	C	SER/LEU	741,3665	746.0+/-411.7	66,609,1528	97.0	109.0	105.0		1217	-2.6	0.0	1	dbSNP_126	105	16,8584	812.1+/-407.1	0,16,4284	yes	missense	TCEB3	NM_003198.2	145	66,625,5812	CC,CT,TT		0.186,16.818,5.8204	benign	406/799	24078234	757,12249	2203	4300	6503	SO:0001583	missense	6924	exon4			CTAATTTGGATAG	L47345	CCDS239.2	1p36.1	2010-06-22	2002-08-29		ENSG00000011007	ENSG00000011007			11620	protein-coding gene	gene with protein product		600786	"""transcription elongation factor B (SIII), polypeptide 3 (110kD, elongin A)"""			8586449, 7660129	Standard	NM_003198		Approved	SIII, TCEB3A	uc001bho.3	Q14241	OTTHUMG00000002957	ENST00000418390.2:c.1217T>C	1.37:g.24078234T>C	ENSP00000395574:p.Leu406Ser	63.0	0.0	0	768	74.0	36.0	0.486486	NM_003198	B2R7Q8|Q8IXH1	Missense_Mutation	SNP	ENST00000418390.2	37	CCDS239.2	102	0.046703296703296704	94	0.1910569105691057	8	0.022099447513812154	0	0.0	0	0.0	C	0.011	-1.697264	0.00725	0.16818	0.00186	ENSG00000011007	ENST00000418390	T	0.06768	3.26	5.85	-2.64	0.06114	.	1.391920	0.04481	N	0.377838	T	0.00012	0.0000	N	0.01003	-1.06	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45116	-0.9283	9	0.11794	T	0.64	2.5335	6.9989	0.24799	0.1849:0.3127:0.0:0.5025	rs34394004	406	Q14241	ELOA1_HUMAN	S	406	ENSP00000395574:L406S	ENSP00000395574:L406S	L	+	2	0	TCEB3	23950821	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.017000	0.01445	-1.183000	0.02723	-1.073000	0.02249	TTG	T|0.935;C|0.065	0.065	strong		0.448	TCEB3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000008230.2	NM_003198	
KLF4	9314	hgsc.bcm.edu	37	9	110249415	110249415	+	Silent	SNP	T	T	C	rs45596731	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:110249415T>C	ENST00000374672.4	-	4	1631	c.1158A>G	c.(1156-1158)cgA>cgG	p.R386R		NM_004235.4	NP_004226.3	O43474	KLF4_HUMAN	Kruppel-like factor 4 (gut)	420	Pro-rich.				cellular response to cycloheximide (GO:0071409)|cellular response to growth factor stimulus (GO:0071363)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to peptide (GO:1901653)|epidermal cell differentiation (GO:0009913)|epidermis morphogenesis (GO:0048730)|fat cell differentiation (GO:0045444)|mesodermal cell fate determination (GO:0007500)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine (C-X-C motif) ligand 2 production (GO:2000342)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of heterotypic cell-cell adhesion (GO:0034115)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of muscle hyperplasia (GO:0014740)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of response to cytokine stimulus (GO:0060761)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of hemoglobin biosynthetic process (GO:0046985)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic camera-type eye development (GO:0031077)|post-embryonic hemopoiesis (GO:0035166)|regulation of cell differentiation (GO:0045595)|response to retinoic acid (GO:0032526)|stem cell maintenance (GO:0019827)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter proximal region sequence-specific DNA binding (GO:0000987)|double-stranded DNA binding (GO:0003690)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding transcription factor activity (GO:0003700)|sequence-specific DNA binding transcription factor recruiting transcription factor activity (GO:0001010)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(5)|large_intestine(1)|lung(3)|pancreas(1)|prostate(2)	16						GGGGCCACGATCGTCTTCCCC	0.597													T|||	18	0.00359425	0.0129	0.0014	5008	,	,		17148	0.0		0.0	False		,,,				2504	0.0				p.R386R		Atlas-SNP	.											.	KLF4	106	.	0			c.A1158G						PASS	.	T		51,4355	52.3+/-87.9	0,51,2152	192.0	175.0	180.0		1158	4.4	1.0	9	dbSNP_127	180	0,8600		0,0,4300	no	coding-synonymous	KLF4	NM_004235.4		0,51,6452	CC,CT,TT		0.0,1.1575,0.3921		386/480	110249415	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	9314	exon4			CCACGATCGTCTT	AF022184	CCDS6770.2	9q31	2013-01-08			ENSG00000136826	ENSG00000136826		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	6348	protein-coding gene	gene with protein product		602253				9422764, 16372018	Standard	NM_004235		Approved	EZF, GKLF	uc004bdg.3	O43474	OTTHUMG00000020449	ENST00000374672.4:c.1158A>G	9.37:g.110249415T>C		270.0	1.0	0.0037037		269.0	171.0	0.635688	NM_004235	B2R8S4|B3KT79|L0R3I6|L0R4N5|P78338|Q5T3J8|Q5T3J9|Q8N717|Q9UNP3	Silent	SNP	ENST00000374672.4	37	CCDS6770.2																																																																																			T|0.996;C|0.004	0.004	strong		0.597	KLF4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053556.2	NM_004235	
HYDIN	54768	hgsc.bcm.edu	37	16	70841703	70841703	+	Missense_Mutation	SNP	A	A	G	rs116730273	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:70841703A>G	ENST00000393567.2	-	86	15296	c.15146T>C	c.(15145-15147)aTg>aCg	p.M5049T		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	5049					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				GAAGGTCACCATGTGATAGAA	0.527													A|||	27	0.00539137	0.0197	0.0014	5008	,	,		21437	0.0		0.0	False		,,,				2504	0.0				p.M5049T		Atlas-SNP	.											.	HYDIN	788	.	0			c.T15146C						PASS	.	A	THR/MET	39,4047		0,39,2004	124.0	127.0	126.0		15143	3.1	0.0	16	dbSNP_132	126	0,8402		0,0,4201	yes	missense	HYDIN	NM_032821.2	81	0,39,6205	GG,GA,AA		0.0,0.9545,0.3123	benign	5048/5121	70841703	39,12449	2043	4201	6244	SO:0001583	missense	54768	exon86			GTCACCATGTGAT	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.15146T>C	16.37:g.70841703A>G	ENSP00000377197:p.Met5049Thr	273.0	0.0	0		310.0	142.0	0.458065	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	A	0.004	-2.378729	0.00205	0.009545	0.0	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.00705	5.81	6.16	3.06	0.35304	.	7.165540	0.02602	N	0.101146	T	0.00178	0.0005	N	0.00142	-2.005	0.23645	N	0.997212	B	0.09022	0.002	B	0.01281	0.0	T	0.41875	-0.9484	10	0.02654	T	1	.	8.741	0.34558	0.1238:0.0:0.7538:0.1223	.	5048	F8WD23	.	T	5049;5048	ENSP00000377197:M5049T	ENSP00000313052:M5048T	M	-	2	0	HYDIN	69399204	0.030000	0.19436	0.001000	0.08648	0.002000	0.02628	2.046000	0.41260	0.921000	0.36994	-0.924000	0.02725	ATG	A|0.994;G|0.006	0.006	strong		0.527	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
CLTCL1	8218	hgsc.bcm.edu	37	22	19178854	19178854	+	Missense_Mutation	SNP	G	G	A	rs190366603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:19178854G>A	ENST00000263200.10	-	27	4357	c.4285C>T	c.(4285-4287)Cgg>Tgg	p.R1429W	CLTCL1_ENST00000427926.1_Missense_Mutation_p.R1429W|CLTCL1_ENST00000442042.2_5'UTR|CLTCL1_ENST00000353891.5_Missense_Mutation_p.R1429W	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	1429	Heavy chain arm.|Involved in binding clathrin light chain. {ECO:0000250}.|Proximal segment.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					TGGTCCAGCCGGGGTGAAAGC	0.493			T	?	ALCL								G|||	3	0.000599042	0.0023	0.0	5008	,	,		16783	0.0		0.0	False		,,,				2504	0.0				p.R1429W		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"""clathrin, heavy polypeptide-like 1"""		L	CLTCL1,NS,carcinoma,0,1	CLTCL1	115	1	0			c.C4285T						PASS	.	G	TRP/ARG,TRP/ARG	5,3907		0,5,1951	80.0	84.0	83.0		4285,4285	3.6	1.0	22		83	0,8286		0,0,4143	yes	missense,missense	CLTCL1	NM_007098.3,NM_001835.3	101,101	0,5,6094	AA,AG,GG		0.0,0.1278,0.041	benign,benign	1429/1641,1429/1584	19178854	5,12193	1956	4143	6099	SO:0001583	missense	8218	exon27			CCAGCCGGGGTGA		CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"""clathrin, heavy polypeptide-like 1"""	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.4285C>T	22.37:g.19178854G>A	ENSP00000445677:p.Arg1429Trp	91.0	0.0	0		88.0	51.0	0.579545	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	37	CCDS46662.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	18.39	3.613700	0.66672	0.001278	0.0	ENSG00000070371	ENST00000353891;ENST00000263200;ENST00000427926	T;T;T	0.20332	2.08;2.08;2.08	3.61	3.61	0.41365	Tetratricopeptide-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000002	T	0.40956	0.1138	M	0.92649	3.33	0.80722	D	1	B;B;B	0.33171	0.4;0.318;0.266	B;B;B	0.39217	0.283;0.256;0.294	T	0.57888	-0.7733	10	0.87932	D	0	-17.9135	15.4348	0.75137	0.0:0.0:1.0:0.0	.	1429;252;1429	P53675-2;B7Z1Z7;P53675	.;.;CLH2_HUMAN	W	1429	ENSP00000439662:R1429W;ENSP00000445677:R1429W;ENSP00000441158:R1429W	ENSP00000445677:R1429W	R	-	1	2	CLTCL1	17558854	1.000000	0.71417	0.998000	0.56505	0.787000	0.44495	2.973000	0.49264	1.868000	0.54150	0.585000	0.79938	CGG	G|0.999;A|0.001	0.001	strong		0.493	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098	
SLC25A13	10165	hgsc.bcm.edu	37	7	95820500	95820500	+	Silent	SNP	C	C	T	rs78247004	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:95820500C>T	ENST00000265631.5	-	7	811	c.675G>A	c.(673-675)tcG>tcA	p.S225S	SLC25A13_ENST00000416240.2_Silent_p.S225S|SLC25A13_ENST00000542654.1_Silent_p.S117S			Q9UJS0	CMC2_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 13	225					aspartate transport (GO:0015810)|ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular respiration (GO:0045333)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)|transporter activity (GO:0005215)			breast(4)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(8)|liver(2)|lung(14)|prostate(1)|skin(4)	42	all_cancers(62;7.75e-08)|all_epithelial(64;1.16e-07)		STAD - Stomach adenocarcinoma(171;0.194)		L-Aspartic Acid(DB00128)	TGTTAAGGAGCGAATTAAATC	0.368													C|||	58	0.0115815	0.0439	0.0	5008	,	,		16454	0.0		0.0	False		,,,				2504	0.0				p.S225S		Atlas-SNP	.											SLC25A13,NS,carcinoma,-1,2	SLC25A13	131	2	0			c.G675A						PASS	.	C	,	161,4245	108.6+/-147.0	4,153,2046	147.0	145.0	146.0		675,675	-10.4	0.1	7	dbSNP_132	146	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SLC25A13	NM_001160210.1,NM_014251.2	,	4,153,6346	TT,TC,CC		0.0,3.6541,1.2379	,	225/677,225/676	95820500	161,12845	2203	4300	6503	SO:0001819	synonymous_variant	10165	exon7			AAGGAGCGAATTA	AF118838	CCDS5645.1, CCDS55130.1	7q21.3	2013-05-22	2012-03-29		ENSG00000004864	ENSG00000004864		"""Solute carriers"", ""EF-hand domain containing"""	10983	protein-coding gene	gene with protein product	"""mitochondrial aspartate glutamate carrier 2"""	603859	"""solute carrier family 25, member 13 (citrin)"""	CTLN2		10369257	Standard	NM_014251		Approved	CITRIN, ARALAR2	uc003uog.4	Q9UJS0	OTTHUMG00000023074	ENST00000265631.5:c.675G>A	7.37:g.95820500C>T		77.0	0.0	0		67.0	34.0	0.507463	NM_001160210	O14566|O14575|Q546F9|Q9NZW1|Q9UNI7	Silent	SNP	ENST00000265631.5	37	CCDS5645.1																																																																																			C|0.985;T|0.015	0.015	strong		0.368	SLC25A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059395.2	NM_014251	
NFRKB	4798	hgsc.bcm.edu	37	11	129752426	129752426	+	Silent	SNP	G	G	A	rs76967949	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:129752426G>A	ENST00000446488.3	-	9	1105	c.1002C>T	c.(1000-1002)gcC>gcT	p.A334A	NFRKB_ENST00000524746.1_Silent_p.A334A|NFRKB_ENST00000304521.5_Silent_p.A334A|NFRKB_ENST00000524794.1_Silent_p.A359A	NM_001143835.1	NP_001137307.1	Q6P4R8	NFRKB_HUMAN	nuclear factor related to kappaB binding protein	334					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	Ino80 complex (GO:0031011)|nucleus (GO:0005634)	DNA binding (GO:0003677)|protease binding (GO:0002020)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(13)|ovary(4)|skin(3)|urinary_tract(1)	32	all_hematologic(175;0.0537)	Breast(109;0.00526)|Lung NSC(97;0.00901)|all_lung(97;0.018)|Medulloblastoma(222;0.0523)|all_neural(223;0.186)		OV - Ovarian serous cystadenocarcinoma(99;0.0167)|Lung(977;0.171)|LUSC - Lung squamous cell carcinoma(976;0.184)		TTAGCGGCTCGGCCAGGTCCT	0.463													G|||	42	0.00838658	0.0295	0.0043	5008	,	,		17616	0.0		0.0	False		,,,				2504	0.0				p.A359A		Atlas-SNP	.											.	NFRKB	101	.	0			c.C1077T						PASS	.	G	,	177,4225	116.3+/-154.2	5,167,2029	95.0	99.0	98.0		1002,1077	-0.8	0.6	11	dbSNP_131	98	5,8589	4.3+/-15.6	0,5,4292	no	coding-synonymous,coding-synonymous	NFRKB	NM_001143835.1,NM_006165.3	,	5,172,6321	AA,AG,GG		0.0582,4.0209,1.4004	,	334/1300,359/1325	129752426	182,12814	2201	4297	6498	SO:0001819	synonymous_variant	4798	exon8			CGGCTCGGCCAGG		CCDS8483.1, CCDS44770.1	11q24-q25	2011-07-06			ENSG00000170322	ENSG00000170322		"""INO80 complex subunits"""	7802	protein-coding gene	gene with protein product	"""nuclear factor related to kappa B binding protein"", ""DNA-binding protein R kappa B"", ""INO80 complex subunit G"""	164013				1427843	Standard	NM_006165		Approved	DKFZp547B2013, INO80G	uc001qfg.3	Q6P4R8	OTTHUMG00000165761	ENST00000446488.3:c.1002C>T	11.37:g.129752426G>A		89.0	0.0	0		85.0	51.0	0.6	NM_006165	Q12869|Q15312|Q9H048	Silent	SNP	ENST00000446488.3	37	CCDS44770.1																																																																																			G|0.985;A|0.015	0.015	strong		0.463	NFRKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386063.2	NM_006165	
RAB25	57111	hgsc.bcm.edu	37	1	156039960	156039960	+	Missense_Mutation	SNP	C	C	T	rs115837676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156039960C>T	ENST00000361084.5	+	5	765	c.524C>T	c.(523-525)gCg>gTg	p.A175V		NM_020387.2	NP_065120.2	P57735	RAB25_HUMAN	RAB25, member RAS oncogene family	175					positive regulation of cell proliferation (GO:0008284)|protein transport (GO:0015031)|pseudopodium organization (GO:0031268)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	GTP binding (GO:0005525)|myosin V binding (GO:0031489)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)	5	Hepatocellular(266;0.158)|all_neural(408;0.195)					GAAATCTTTGCGAAGGTGTCC	0.597													C|||	29	0.00579073	0.0212	0.0014	5008	,	,		18839	0.0		0.0	False		,,,				2504	0.0				p.A175V		Atlas-SNP	.											RAB25,NS,carcinoma,-1,1	RAB25	18	1	0			c.C524T						PASS	.	C	VAL/ALA	100,3904		2,96,1904	65.0	69.0	68.0		524	4.9	0.1	1	dbSNP_132	68	0,8350		0,0,4175	no	missense	RAB25	NM_020387.2	64	2,96,6079	TT,TC,CC		0.0,2.4975,0.8095	benign	175/214	156039960	100,12254	2002	4175	6177	SO:0001583	missense	57111	exon5			TCTTTGCGAAGGT	AF083124	CCDS41413.1	1q22	2008-07-03			ENSG00000132698	ENSG00000132698		"""RAB, member RAS oncogene"""	18238	protein-coding gene	gene with protein product		612942				11697911	Standard	NM_020387		Approved	CATX-8	uc001fnc.3	P57735	OTTHUMG00000017457	ENST00000361084.5:c.524C>T	1.37:g.156039960C>T	ENSP00000354376:p.Ala175Val	331.0	1.0	0.00302115		317.0	157.0	0.495268	NM_020387	Q5VYA2|Q8NG24|Q96GB1|Q9BT12	Missense_Mutation	SNP	ENST00000361084.5	37	CCDS41413.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	C	13.90	2.375470	0.42105	0.024975	0.0	ENSG00000132698	ENST00000361084	T	0.80033	-1.33	5.85	4.94	0.65067	.	0.395029	0.26800	N	0.022433	T	0.48370	0.1496	N	0.11560	0.145	0.09310	N	1	B	0.17465	0.022	B	0.09377	0.004	T	0.50533	-0.8817	10	0.87932	D	0	.	12.4852	0.55868	0.1671:0.8329:0.0:0.0	.	175	P57735	RAB25_HUMAN	V	175	ENSP00000354376:A175V	ENSP00000354376:A175V	A	+	2	0	RAB25	154306584	0.001000	0.12720	0.130000	0.21974	0.895000	0.52256	0.961000	0.29267	1.475000	0.48197	-0.152000	0.13540	GCG	C|0.996;T|0.004	0.004	strong		0.597	RAB25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046185.1		
GRAMD3	65983	hgsc.bcm.edu	37	5	125696127	125696127	+	Missense_Mutation	SNP	A	A	G	rs78682130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:125696127A>G	ENST00000513040.1	+	1	304	c.104A>G	c.(103-105)aAg>aGg	p.K35R		NM_001146319.1	NP_001139791.1	Q96HH9	GRAM3_HUMAN	GRAM domain containing 3	0						cytoplasmic microtubule (GO:0005881)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0401)|OV - Ovarian serous cystadenocarcinoma(64;0.0604)|all cancers(49;0.108)		AGAGAAGTGAAGCCAGTGGGT	0.488													A|||	118	0.0235623	0.087	0.0043	5008	,	,		21319	0.0		0.0	False		,,,				2504	0.0				p.K35R		Atlas-SNP	.											.	GRAMD3	30	.	0			c.A104G						PASS	.	A	ARG/LYS	87,1297		2,83,607	119.0	112.0	114.0		104	4.2	0.0	5	dbSNP_132	114	0,3182		0,0,1591	yes	missense	GRAMD3	NM_001146319.1	26	2,83,2198	GG,GA,AA		0.0,6.2861,1.9054	benign	35/448	125696127	87,4479	692	1591	2283	SO:0001583	missense	65983	exon1			AAGTGAAGCCAGT	BC008590	CCDS4136.1, CCDS54891.1, CCDS54892.1, CCDS54893.1, CCDS54894.1	5q23.2	2014-02-12	2005-11-03		ENSG00000155324	ENSG00000155324			24911	protein-coding gene	gene with protein product	"""HCV NS3 transactivated protein 2"""					12477932	Standard	NM_023927		Approved	NS3TP2, FLJ21313	uc011cwt.2	Q96HH9	OTTHUMG00000128943	ENST00000513040.1:c.104A>G	5.37:g.125696127A>G	ENSP00000426120:p.Lys35Arg	181.0	0.0	0		210.0	80.0	0.380952	NM_001146319	B7Z1F2|B7Z3R1|B7Z6D8|B7Z8T2|D3DSZ3|Q9H753	Missense_Mutation	SNP	ENST00000513040.1	37	CCDS54891.1	43	0.019688644688644688	41	0.08333333333333333	2	0.0055248618784530384	0	0.0	0	0.0	A	12.15	1.852185	0.32699	0.062861	0.0	ENSG00000155324	ENST00000513040	T	0.35048	1.33	4.15	4.15	0.48705	.	.	.	.	.	T	0.01061	0.0035	.	.	.	0.34252	D	0.678883	B	0.24186	0.099	B	0.22753	0.041	T	0.12682	-1.0538	8	0.16896	T	0.51	.	9.8683	0.41157	1.0:0.0:0.0:0.0	.	35	B7Z6D8	.	R	35	ENSP00000426120:K35R	ENSP00000426120:K35R	K	+	2	0	GRAMD3	125724026	0.158000	0.22850	0.005000	0.12908	0.006000	0.05464	1.900000	0.39828	2.107000	0.64212	0.460000	0.39030	AAG	A|0.975;G|0.025	0.025	strong		0.488	GRAMD3-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000371350.1	NM_023927	
CCDC142	84865	hgsc.bcm.edu	37	2	74708453	74708453	+	Silent	SNP	A	A	T	rs115125840	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74708453A>T	ENST00000393965.3	-	3	1551	c.1155T>A	c.(1153-1155)ctT>ctA	p.L385L	TTC31_ENST00000442235.2_5'Flank|CCDC142_ENST00000290418.4_Silent_p.L385L|TTC31_ENST00000410003.1_5'Flank|TTC31_ENST00000233623.5_5'Flank|CCDC142_ENST00000471713.1_5'UTR	NM_032779.3	NP_116168.3	Q17RM4	CC142_HUMAN	coiled-coil domain containing 142	385										central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	16						AGGATGTGGGAAGGCTGCTCT	0.557													A|||	19	0.00379393	0.0144	0.0	5008	,	,		19536	0.0		0.0	False		,,,				2504	0.0				p.L385L		Atlas-SNP	.											.	CCDC142	40	.	0			c.T1155A						PASS	.	A		32,4374	37.6+/-69.7	0,32,2171	111.0	126.0	121.0		1155	-2.6	0.0	2	dbSNP_132	121	0,8600		0,0,4300	no	coding-synonymous	CCDC142	NM_032779.3		0,32,6471	TT,TA,AA		0.0,0.7263,0.246		385/744	74708453	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	84865	exon3			TGTGGGAAGGCTG	AK075543	CCDS1945.1	2p13.1	2008-02-05			ENSG00000135637	ENSG00000135637			25889	protein-coding gene	gene with protein product							Standard	NM_032779		Approved	FLJ14397	uc002slq.3	Q17RM4	OTTHUMG00000129962	ENST00000393965.3:c.1155T>A	2.37:g.74708453A>T		173.0	0.0	0		144.0	56.0	0.388889	NM_032779	B7ZKV5|Q8NBJ3|Q8NBV2|Q96KA7	Silent	SNP	ENST00000393965.3	37																																																																																				A|0.997;T|0.003	0.003	strong		0.557	CCDC142-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000328391.1	NM_032779	
TANC1	85461	hgsc.bcm.edu	37	2	160087410	160087410	+	Missense_Mutation	SNP	C	C	T	rs77049231	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160087410C>T	ENST00000263635.6	+	27	5710	c.5473C>T	c.(5473-5475)Cat>Tat	p.H1825Y	TANC1_ENST00000454300.1_Missense_Mutation_p.H1719Y	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	1825					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						GACTGTTTCTCATCTGTACCA	0.453													C|||	220	0.0439297	0.1611	0.0086	5008	,	,		18665	0.0		0.001	False		,,,				2504	0.0				p.H1825Y		Atlas-SNP	.											.	TANC1	157	.	0			c.C5473T						PASS	.	C	,TYR/HIS	476,3394		31,414,1490	76.0	77.0	77.0		,5473	5.2	0.0	2	dbSNP_131	77	2,8310		0,2,4154	yes	utr-3,missense	TANC1	NM_001145909.1,NM_033394.2	,83	31,416,5644	TT,TC,CC		0.0241,12.2997,3.9238	,possibly-damaging	,1825/1862	160087410	478,11704	1935	4156	6091	SO:0001583	missense	85461	exon27			GTTTCTCATCTGT	AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29364	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.5473C>T	2.37:g.160087410C>T	ENSP00000263635:p.His1825Tyr	193.0	0.0	0		165.0	94.0	0.569697	NM_033394	C9JD88|Q49AI8	Missense_Mutation	SNP	ENST00000263635.6	37	CCDS42766.1	66	0.03021978021978022	64	0.13008130081300814	2	0.0055248618784530384	0	0.0	0	0.0	C	13.58	2.280696	0.40294	0.122997	2.41E-4	ENSG00000115183	ENST00000454300;ENST00000263635	T;T	0.71817	-0.59;-0.6	6.06	5.18	0.71444	.	0.096342	0.64402	D	0.000001	T	0.01489	0.0048	L	0.56769	1.78	0.23003	P	0.99844134	D	0.56521	0.976	B	0.40636	0.335	T	0.33675	-0.9859	8	.	.	.	.	17.4939	0.87712	0.0:0.876:0.124:0.0	.	1825	Q9C0D5	TANC1_HUMAN	Y	1719;1825	ENSP00000396339:H1719Y;ENSP00000263635:H1825Y	.	H	+	1	0	TANC1	159795656	1.000000	0.71417	0.030000	0.17652	0.010000	0.07245	5.453000	0.66645	1.559000	0.49555	0.655000	0.94253	CAT	C|0.980;T|0.020	0.020	strong		0.453	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1		
DDX47	51202	hgsc.bcm.edu	37	12	12980305	12980305	+	Missense_Mutation	SNP	G	G	A	rs373273540		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:12980305G>A	ENST00000358007.3	+	11	1254	c.1232G>A	c.(1231-1233)cGa>cAa	p.R411Q	DDX47_ENST00000352940.4_Missense_Mutation_p.R362Q	NM_016355.3	NP_057439.2	Q9H0S4	DDX47_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 47	411					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)		AGGTTTGCCCGAATGGTATGC	0.423													G|||	1	0.000199681	0.0	0.0	5008	,	,		21240	0.001		0.0	False		,,,				2504	0.0				p.R411Q		Atlas-SNP	.											DDX47,colon,carcinoma,+1,1	DDX47	37	1	0			c.G1232A						PASS	.						218.0	216.0	217.0					12																	12980305		2203	4300	6503	SO:0001583	missense	51202	exon11			TTGCCCGAATGGT	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.1232G>A	12.37:g.12980305G>A	ENSP00000350698:p.Arg411Gln	118.0	0.0	0		116.0	73.0	0.62931	NM_016355	B3KXP4|G5E955|Q96GM0|Q96NV8|Q9UI98	Missense_Mutation	SNP	ENST00000358007.3	37	CCDS8655.1	.	.	.	.	.	.	.	.	.	.	G	13.60	2.284152	0.40394	.	.	ENSG00000213782	ENST00000352940;ENST00000358007	T;T	0.26957	2.5;1.7	5.75	3.89	0.44902	.	0.066087	0.64402	D	0.000015	T	0.17704	0.0425	L	0.28649	0.875	0.53688	D	0.999974	B;B	0.20887	0.036;0.049	B;B	0.16722	0.016;0.004	T	0.04203	-1.0969	10	0.13108	T	0.6	-5.9575	12.9654	0.58481	0.0:0.1243:0.7461:0.1296	.	362;411	G5E955;Q9H0S4	.;DDX47_HUMAN	Q	362;411	ENSP00000319578:R362Q;ENSP00000350698:R411Q	ENSP00000319578:R362Q	R	+	2	0	DDX47	12871572	1.000000	0.71417	0.983000	0.44433	0.988000	0.76386	7.657000	0.83745	0.746000	0.32786	0.655000	0.94253	CGA	.	.	weak		0.423	DDX47-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400674.1	NM_016355	
SALL4	57167	hgsc.bcm.edu	37	20	50406646	50406646	+	Silent	SNP	A	A	G	rs143601538	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:50406646A>G	ENST00000217086.4	-	2	2487	c.2376T>C	c.(2374-2376)aaT>aaC	p.N792N	SALL4_ENST00000483130.1_5'Flank|SALL4_ENST00000371539.3_Intron|SALL4_ENST00000395997.3_Intron	NM_020436.3	NP_065169.1	Q9UJQ4	SALL4_HUMAN	spalt-like transcription factor 4	792					embryonic limb morphogenesis (GO:0030326)|inner cell mass cell proliferation (GO:0001833)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(27)|ovary(5)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CGGCTTGACTATTGGCCGGGG	0.547													A|||	4	0.000798722	0.003	0.0	5008	,	,		17547	0.0		0.0	False		,,,				2504	0.0				p.N792N		Atlas-SNP	.											.	SALL4	168	.	0			c.T2376C						PASS	.	A		11,4395	17.9+/-39.9	0,11,2192	79.0	73.0	75.0		2376	2.2	1.0	20	dbSNP_134	75	0,8600		0,0,4300	no	coding-synonymous	SALL4	NM_020436.3		0,11,6492	GG,GA,AA		0.0,0.2497,0.0846		792/1054	50406646	11,12995	2203	4300	6503	SO:0001819	synonymous_variant	57167	exon2			TTGACTATTGGCC	AK001666	CCDS13438.1	20q13.2	2014-09-17	2013-10-17		ENSG00000101115	ENSG00000101115		"""Zinc fingers, C2H2-type"""	15924	protein-coding gene	gene with protein product		607343	"""sal (Drosophila)-like 4"", ""sal-like 4 (Drosophila)"""				Standard	NM_020436		Approved	dJ1112F19.1, ZNF797	uc002xwh.4	Q9UJQ4	OTTHUMG00000032752	ENST00000217086.4:c.2376T>C	20.37:g.50406646A>G		323.0	0.0	0		302.0	158.0	0.523179	NM_020436	A2A2D8|Q540H3|Q6Y8G6	Silent	SNP	ENST00000217086.4	37	CCDS13438.1																																																																																			A|0.999;G|0.001	0.001	strong		0.547	SALL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079738.3		
NXPE1	120400	hgsc.bcm.edu	37	11	114393066	114393066	+	Missense_Mutation	SNP	A	A	G	rs34993124	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:114393066A>G	ENST00000424269.1	-	5	1267	c.1268T>C	c.(1267-1269)aTt>aCt	p.I423T	NXPE1_ENST00000251921.2_Missense_Mutation_p.I281T|NXPE1_ENST00000536271.1_Missense_Mutation_p.I139T			Q8N323	NXPE1_HUMAN	neurexophilin and PC-esterase domain family, member 1	423			I -> T (in dbSNP:rs34993124).			extracellular region (GO:0005576)											TAGCCGGTCAATTTCCCGAGG	0.443													A|||	95	0.0189696	0.0651	0.013	5008	,	,		18652	0.0		0.0	False		,,,				2504	0.0				p.I281T		Atlas-SNP	.											.	NXPE1	8	.	0			c.T842C						PASS	.	A	THR/ILE	254,4148	146.1+/-180.8	4,246,1951	147.0	140.0	142.0		842	2.1	0.6	11	dbSNP_126	142	3,8589	3.0+/-9.4	0,3,4293	yes	missense	FAM55A	NM_152315.2	89	4,249,6244	GG,GA,AA		0.0349,5.7701,1.9778	probably-damaging	281/406	114393066	257,12737	2201	4296	6497	SO:0001583	missense	120400	exon6			CGGTCAATTTCCC	BC029049	CCDS8372.1	11q23.2	2012-06-14	2012-06-11	2012-06-11	ENSG00000095110	ENSG00000095110			28527	protein-coding gene	gene with protein product			"""family with sequence similarity 55, member A"""	FAM55A		12477932	Standard	NM_152315		Approved	MGC34290	uc001ppa.3	Q8N323	OTTHUMG00000168284	ENST00000424269.1:c.1268T>C	11.37:g.114393066A>G	ENSP00000411690:p.Ile423Thr	172.0	0.0	0		161.0	74.0	0.459627	NM_152315	B0YJ13	Missense_Mutation	SNP	ENST00000424269.1	37		38	0.0173992673992674	34	0.06910569105691057	4	0.011049723756906077	0	0.0	0	0.0	A	27.2	4.809928	0.90707	0.057701	3.49E-4	ENSG00000095110	ENST00000536271;ENST00000251921;ENST00000424269	T;T;T	0.27256	1.68;1.68;1.68	4.44	2.07	0.26955	.	0.082106	0.49916	D	0.000132	T	0.07503	0.0189	M	0.92367	3.3	0.28092	N	0.931779	D	0.76494	0.999	D	0.67382	0.951	T	0.10177	-1.0641	10	0.56958	D	0.05	.	8.0262	0.30438	0.8267:0.0:0.1733:0.0	rs34993124	423	Q8N323	FA55A_HUMAN	T	139;281;423	ENSP00000445200:I139T;ENSP00000251921:I281T;ENSP00000411690:I423T	ENSP00000251921:I281T	I	-	2	0	FAM55A	113898276	0.993000	0.37304	0.643000	0.29450	0.931000	0.56810	1.124000	0.31320	0.298000	0.22638	0.528000	0.53228	ATT	A|0.982;G|0.018	0.018	strong		0.443	NXPE1-201	KNOWN	basic	protein_coding	protein_coding		NM_152315	
SMC2	10592	hgsc.bcm.edu	37	9	106901506	106901506	+	Silent	SNP	A	A	G	rs16923746	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:106901506A>G	ENST00000286398.7	+	25	3792	c.3504A>G	c.(3502-3504)gtA>gtG	p.V1168V	SMC2_ENST00000374793.3_Silent_p.V1168V|SMC2_ENST00000374787.3_Silent_p.V1168V	NM_001042551.1|NM_001265602.1|NM_006444.2	NP_001036016.1|NP_001252531.1|NP_006435.2	O95347	SMC2_HUMAN	structural maintenance of chromosomes 2	1168					kinetochore organization (GO:0051383)|meiotic chromosome condensation (GO:0010032)|meiotic chromosome segregation (GO:0045132)|mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein heterodimerization activity (GO:0046982)			breast(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(14)|ovary(5)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	48						TTTCTACAGTAGCCAGATTTA	0.363													A|||	326	0.0650958	0.2209	0.013	5008	,	,		15837	0.0129		0.007	False		,,,				2504	0.0051				p.V1168V		Atlas-SNP	.											.	SMC2	127	.	0			c.A3504G						PASS	.	A	,,	742,3664	302.7+/-287.5	56,630,1517	89.0	89.0	89.0		3504,3504,3504	-3.0	1.0	9	dbSNP_123	89	62,8538	39.3+/-95.6	0,62,4238	no	coding-synonymous,coding-synonymous,coding-synonymous	SMC2	NM_001042550.1,NM_001042551.1,NM_006444.2	,,	56,692,5755	GG,GA,AA		0.7209,16.8407,6.1818	,,	1168/1198,1168/1198,1168/1198	106901506	804,12202	2203	4300	6503	SO:0001819	synonymous_variant	10592	exon25			TACAGTAGCCAGA	AF092563	CCDS35086.1	9q31.1	2008-05-14	2006-07-06	2006-07-06	ENSG00000136824	ENSG00000136824		"""Structural maintenance of chromosomes proteins"""	14011	protein-coding gene	gene with protein product		605576	"""SMC2 (structural maintenance of chromosomes 2, yeast)-like 1"", ""SMC2 structural maintenance of chromosomes 2-like 1 (yeast)"""	SMC2L1		9789013	Standard	NM_006444		Approved	hCAP-E, CAP-E	uc011lvl.2	O95347	OTTHUMG00000020401	ENST00000286398.7:c.3504A>G	9.37:g.106901506A>G		177.0	0.0	0		194.0	66.0	0.340206	NM_006444	Q6IEE0|Q9P1P2	Silent	SNP	ENST00000286398.7	37	CCDS35086.1																																																																																			A|0.935;G|0.065	0.065	strong		0.363	SMC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053470.1		
ZCCHC9	84240	hgsc.bcm.edu	37	5	80604427	80604427	+	Silent	SNP	C	C	T	rs149561750	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:80604427C>T	ENST00000254037.2	+	2	3587	c.432C>T	c.(430-432)ccC>ccT	p.P144P	ZCCHC9_ENST00000438268.2_Silent_p.P144P|ZCCHC9_ENST00000407610.3_Silent_p.P144P|ZCCHC9_ENST00000506458.1_3'UTR|ZCCHC9_ENST00000380199.5_Silent_p.P144P			Q8N567	ZCHC9_HUMAN	zinc finger, CCHC domain containing 9	144					negative regulation of phosphatase activity (GO:0010923)		poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)	13		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;8.18e-45)|Epithelial(54;2.72e-39)|all cancers(79;7.33e-34)		CAGATTGCCCCGCCGCCCTTG	0.473													C|||	2	0.000399361	0.0015	0.0	5008	,	,		14028	0.0		0.0	False		,,,				2504	0.0				p.P144P		Atlas-SNP	.											ZCCHC9,bladder,carcinoma,0,1	ZCCHC9	26	1	0			c.C432T						scavenged	.	C	,,	20,4386	28.1+/-56.4	1,18,2184	87.0	88.0	88.0		432,432,432	-11.9	0.6	5	dbSNP_134	88	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	ZCCHC9	NM_001131035.1,NM_001131036.1,NM_032280.2	,,	1,18,6484	TT,TC,CC		0.0,0.4539,0.1538	,,	144/272,144/272,144/272	80604427	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	84240	exon3			TTGCCCCGCCGCC	BC014841	CCDS4054.1	5q14.1	2013-01-09			ENSG00000131732	ENSG00000131732		"""Zinc fingers, CCHC domain containing"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25424	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 41"""					12477932	Standard	NM_032280		Approved	DKFZp761J139, PPP1R41	uc003khi.3	Q8N567	OTTHUMG00000119014	ENST00000254037.2:c.432C>T	5.37:g.80604427C>T		187.0	1.0	0.00534759		180.0	78.0	0.433333	NM_001131036	B2RAE7|Q9H027	Silent	SNP	ENST00000254037.2	37	CCDS4054.1																																																																																			C|0.998;T|0.002	0.002	strong		0.473	ZCCHC9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239213.1	NM_032280	
CDKN1A	1026	hgsc.bcm.edu	37	6	36652135	36652135	+	Missense_Mutation	SNP	G	G	A	rs566071526		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36652135G>A	ENST00000405375.1	+	2	492	c.257G>A	c.(256-258)cGg>cAg	p.R86Q	CDKN1A_ENST00000244741.5_Missense_Mutation_p.R86Q|CDKN1A_ENST00000478800.1_3'UTR|CDKN1A_ENST00000448526.2_Missense_Mutation_p.R120Q|CDKN1A_ENST00000373711.2_Missense_Mutation_p.R86Q	NM_001220778.1	NP_001207707.1	P38936	CDN1A_HUMAN	cyclin-dependent kinase inhibitor 1A (p21, Cip1)	86					cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to extracellular stimulus (GO:0031668)|cellular response to ionizing radiation (GO:0071479)|cellular senescence (GO:0090398)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|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)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle (GO:0000278)|mitotic cell cycle arrest (GO:0071850)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of gene expression (GO:0010629)|negative regulation of phosphorylation (GO:0042326)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ regeneration (GO:0031100)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of DNA biosynthetic process (GO:2000278)|regulation of protein import into nucleus, translocation (GO:0033158)|response to arsenic-containing substance (GO:0046685)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to hyperoxia (GO:0055093)|response to organonitrogen compound (GO:0010243)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|stress-induced premature senescence (GO:0090400)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCNA-p21 complex (GO:0070557)	cyclin-dependent protein kinase activating kinase activity (GO:0019912)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|urinary_tract(5)	15						CGGCGAGGCCGGGATGAGTTG	0.652													G|||	1	0.000199681	0.0	0.0	5008	,	,		18244	0.001		0.0	False		,,,				2504	0.0				p.R86Q		Atlas-SNP	.											CDKN1A,NS,carcinoma,+1,1	CDKN1A	27	1	0			c.G257A						PASS	.						25.0	25.0	25.0					6																	36652135		2203	4300	6503	SO:0001583	missense	1026	exon2			GAGGCCGGGATGA	U03106	CCDS4824.1	6p21.1	2009-01-21			ENSG00000124762	ENSG00000124762			1784	protein-coding gene	gene with protein product		116899		CDKN1			Standard	NM_000389		Approved	P21, CIP1, WAF1, SDI1, CAP20, p21CIP1, p21Cip1/Waf1	uc021yzb.1	P38936	OTTHUMG00000014603	ENST00000405375.1:c.257G>A	6.37:g.36652135G>A	ENSP00000384849:p.Arg86Gln	41.0	0.0	0		54.0	23.0	0.425926	NM_001220778	Q14010|Q6FI05|Q9BUT4	Missense_Mutation	SNP	ENST00000405375.1	37	CCDS4824.1	.	.	.	.	.	.	.	.	.	.	G	4.718	0.133545	0.09032	.	.	ENSG00000124762	ENST00000448526;ENST00000244741;ENST00000405375;ENST00000373711	T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05	5.16	0.313	0.15842	.	1.118360	0.06876	N	0.801660	T	0.25121	0.0610	L	0.34521	1.04	0.09310	N	1	B;B;B	0.24882	0.113;0.064;0.037	B;B;B	0.16289	0.015;0.006;0.006	T	0.21759	-1.0236	10	0.51188	T	0.08	-1.0186	4.3301	0.11059	0.3607:0.161:0.4783:0.0	.	120;86;86	B4DQP9;P38936;Q96LE1	.;CDN1A_HUMAN;.	Q	120;86;86;86	ENSP00000409259:R120Q;ENSP00000244741:R86Q;ENSP00000384849:R86Q;ENSP00000362815:R86Q	ENSP00000244741:R86Q	R	+	2	0	CDKN1A	36760113	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.096000	0.11059	-0.131000	0.11578	0.511000	0.50034	CGG	.	.	none		0.652	CDKN1A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040354.1	NM_078467	
GALNT4	8693	hgsc.bcm.edu	37	12	89916781	89916781	+	Missense_Mutation	SNP	G	G	T	rs139995124	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:89916781G>T	ENST00000529983.2	-	1	1802	c.1546C>A	c.(1546-1548)Caa>Aaa	p.Q516K	POC1B_ENST00000549035.1_Intron|POC1B-GALNT4_ENST00000547474.1_3'UTR|RP11-734K2.4_ENST00000605233.1_RNA|POC1B-GALNT4_ENST00000548729.1_Missense_Mutation_p.Q513K|POC1B_ENST00000393179.4_Intron|GALNT4_ENST00000413530.1_Missense_Mutation_p.Q344K|POC1B_ENST00000541909.1_Intron|POC1B_ENST00000549504.1_Intron|POC1B_ENST00000313546.3_Intron	NM_003774.4	NP_003765.2	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	516	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(4)|kidney(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)	14						GGACAATTTTGCATTCCCACA	0.358													G|||	11	0.00219649	0.0023	0.0	5008	,	,		19748	0.0		0.007	False		,,,				2504	0.001				p.Q516K		Atlas-SNP	.											.	GALNT4	38	.	0			c.C1546A						PASS	.	G	,LYS/GLN,LYS/GLN,LYS/GLN,	5,3649		0,5,1822	71.0	67.0	68.0		,1537,1030,1546,	5.0	1.0	12	dbSNP_134	68	65,8115		0,65,4025	yes	intron,missense,missense,missense,intron	GALNT4,POC1B,POC1B-GALNT4	NM_001199777.1,NM_001199781.1,NM_001199782.1,NM_003774.4,NM_172240.2	,53,53,53,	0,70,5847	TT,TG,GG		0.7946,0.1368,0.5915	,benign,benign,benign,	,513/576,344/407,516/579,	89916781	70,11764	1827	4090	5917	SO:0001583	missense	8693	exon1			AATTTTGCATTCC	Y08564	CCDS53817.1	12q21.33	2014-03-13	2014-03-13		ENSG00000257594	ENSG00000257594	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4126	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 4"""	603565	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 4 (GalNAc-T4)"""			9804815	Standard	NM_003774		Approved	GalNAc-T4	uc001tbd.3	Q8N4A0	OTTHUMG00000166292	ENST00000529983.2:c.1546C>A	12.37:g.89916781G>T	ENSP00000436604:p.Gln516Lys	82.0	0.0	0		84.0	46.0	0.547619	NM_003774	B2R775|B4DMX6|O00208	Missense_Mutation	SNP	ENST00000529983.2	37	CCDS53817.1	9	0.004120879120879121	3	0.006097560975609756	0	0.0	0	0.0	6	0.0079155672823219	G	11.35	1.612993	0.28712	0.001368	0.007946	ENSG00000259075;ENSG00000259075;ENSG00000257594	ENST00000548729;ENST00000413530;ENST00000529983	T;T;T	0.29397	1.57;1.57;1.57	5.93	4.99	0.66335	Ricin B-related lectin (1);Ricin B lectin (3);	.	.	.	.	T	0.11623	0.0283	N	0.10645	0.015	0.39363	D	0.965958	B;B	0.06786	0.0;0.001	B;B	0.09377	0.003;0.004	T	0.08638	-1.0712	9	0.27785	T	0.31	.	12.0779	0.53655	0.0:0.0:0.7004:0.2996	.	513;516	F8VUJ3;Q8N4A0	.;GALT4_HUMAN	K	513;344;516	ENSP00000447852:Q513K;ENSP00000389686:Q344K;ENSP00000436604:Q516K	ENSP00000436604:Q516K	Q	-	1	0	GALNT4;RP11-1109F11.4	88440912	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	6.469000	0.73555	2.814000	0.96858	0.591000	0.81541	CAA	G|0.996;T|0.004	0.004	strong		0.358	GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388973.2	NM_003774	
PTGIR	5739	hgsc.bcm.edu	37	19	47124579	47124579	+	Silent	SNP	C	C	T	rs2229130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:47124579C>T	ENST00000291294.2	-	3	1252	c.1119G>A	c.(1117-1119)acG>acA	p.T373T	PTGIR_ENST00000594275.1_Silent_p.T130T|PTGIR_ENST00000597185.1_Silent_p.T102T|PTGIR_ENST00000598865.1_Silent_p.T161T	NM_000960.3	NP_000951.1	P43119	PI2R_HUMAN	prostaglandin I2 (prostacyclin) receptor (IP)	373					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of GTPase activity (GO:0043547)|response to lipopolysaccharide (GO:0032496)	cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	13		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000327)|all cancers(93;0.000641)|Epithelial(262;0.0174)|GBM - Glioblastoma multiforme(486;0.0331)	Dinoprost Tromethamine(DB01160)|Epoprostenol(DB01240)|Iloprost(DB01088)|Treprostinil(DB00374)	CTTTGGACGACGTTCCCACGG	0.632													C|||	64	0.0127796	0.0446	0.0072	5008	,	,		16398	0.0		0.0	False		,,,				2504	0.0				p.T373T		Atlas-SNP	.											.	PTGIR	31	.	0			c.G1119A						PASS	.	C		207,4199	121.7+/-159.2	7,193,2003	44.0	47.0	46.0		1119	-9.5	0.0	19	dbSNP_98	46	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	PTGIR	NM_000960.3		7,196,6300	TT,TC,CC		0.0349,4.6981,1.6146		373/387	47124579	210,12796	2203	4300	6503	SO:0001819	synonymous_variant	5739	exon3			GGACGACGTTCCC		CCDS12686.1	19q13.3	2012-08-08				ENSG00000160013		"""GPCR / Class A : Prostanoid receptors"""	9602	protein-coding gene	gene with protein product		600022				7759114	Standard	NM_000960		Approved	IP	uc002pex.3	P43119		ENST00000291294.2:c.1119G>A	19.37:g.47124579C>T		136.0	0.0	0		124.0	62.0	0.5	NM_000960		Silent	SNP	ENST00000291294.2	37	CCDS12686.1																																																																																			C|0.984;T|0.016	0.016	strong		0.632	PTGIR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466581.1		
MYO7B	4648	hgsc.bcm.edu	37	2	128381717	128381717	+	Missense_Mutation	SNP	G	G	A	rs2245408	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128381717G>A	ENST00000409816.2	+	28	3823	c.3791G>A	c.(3790-3792)cGg>cAg	p.R1264Q	RP11-286H15.1_ENST00000609697.1_RNA|MYO7B_ENST00000389524.4_Missense_Mutation_p.R1264Q|MYO7B_ENST00000409090.1_Missense_Mutation_p.R117Q|MYO7B_ENST00000428314.1_Missense_Mutation_p.R1264Q			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1264	FERM 1. {ECO:0000255|PROSITE- ProRule:PRU00084}.		R -> Q (in dbSNP:rs2245408).			extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		GCCATCGCCCGGTGTGAGCAG	0.667													A|||	64	0.0127796	0.0439	0.0086	5008	,	,		17463	0.0		0.0	False		,,,				2504	0.0				p.R1264Q		Atlas-SNP	.											.	MYO7B	359	.	0			c.G3791A						PASS	.	A	GLN/ARG	141,3873		2,137,1868	21.0	26.0	25.0		3791	3.8	1.0	2	dbSNP_100	25	2,8324		0,2,4161	yes	missense	MYO7B	NM_001080527.1	43	2,139,6029	AA,AG,GG		0.024,3.5127,1.1588	benign	1264/2117	128381717	143,12197	2007	4163	6170	SO:0001583	missense	4648	exon29			TCGCCCGGTGTGA		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"""Myosins / Myosin superfamily : Class VII"""	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.3791G>A	2.37:g.128381717G>A	ENSP00000386461:p.Arg1264Gln	78.0	0.0	0		90.0	51.0	0.566667	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	37	CCDS46405.1	22	0.010073260073260074	19	0.03861788617886179	3	0.008287292817679558	0	0.0	0	0.0	.	9.528	1.110073	0.20714	0.035127	2.4E-4	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000272666;ENST00000409816;ENST00000437387;ENST00000409090	T;T;T;T;T	0.77229	-1.08;-1.08;-1.08;-1.08;-1.08	3.76	3.76	0.43208	Band 4.1 domain (1);FERM domain (1);	0.000000	0.85682	N	0.000000	T	0.09247	0.0228	N	0.00084	-2.21	0.22562	N	0.998982	B	0.02656	0.0	B	0.01281	0.0	T	0.38308	-0.9667	10	0.02654	T	1	.	9.5173	0.39113	0.9119:0.0:0.0881:0.0	rs2245408;rs2245408	1264	Q6PIF6	MYO7B_HUMAN	Q	1264;1264;117;1264;117;117	ENSP00000374175:R1264Q;ENSP00000415090:R1264Q;ENSP00000386461:R1264Q;ENSP00000404927:R117Q;ENSP00000386850:R117Q	ENSP00000272666:R117Q	R	+	2	0	MYO7B	128098187	1.000000	0.71417	0.998000	0.56505	0.832000	0.47134	4.758000	0.62220	0.809000	0.34255	-0.490000	0.04691	CGG	G|0.990;A|0.010	0.010	strong		0.667	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
PTCRA	171558	hgsc.bcm.edu	37	6	42893328	42893328	+	Missense_Mutation	SNP	T	T	C	rs115331994	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42893328T>C	ENST00000304672.1	+	4	835	c.754T>C	c.(754-756)Tgc>Cgc	p.C252R	PTCRA_ENST00000446507.1_Missense_Mutation_p.C145R|PTCRA_ENST00000441198.1_Missense_Mutation_p.C227R	NM_001243168.1|NM_138296.2	NP_001230097.1|NP_612153.2	Q6ISU1	PTCRA_HUMAN	pre T-cell antigen receptor alpha	252					negative regulation of thymocyte apoptotic process (GO:0070244)	integral component of membrane (GO:0016021)				large_intestine(2)|lung(4)|ovary(2)	8	Colorectal(47;0.196)		all cancers(41;0.000731)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|OV - Ovarian serous cystadenocarcinoma(102;0.0218)|Kidney(15;0.0388)			ACAGGCCTGGTGCTCAAGATC	0.642													T|||	44	0.00878594	0.0257	0.0	5008	,	,		2807	0.0		0.0	False		,,,				2504	0.0102				p.C267R		Atlas-SNP	.											.	PTCRA	24	.	0			c.T799C						PASS	.	T	ARG/CYS	60,4338		0,60,2139	36.0	30.0	32.0		754	-8.4	0.0	6	dbSNP_132	32	2,8594		0,2,4296	yes	missense	PTCRA	NM_138296.2	180	0,62,6435	CC,CT,TT		0.0233,1.3643,0.4771	possibly-damaging	252/282	42893328	62,12932	2199	4298	6497	SO:0001583	missense	171558	exon4			GCCTGGTGCTCAA	AF084941	CCDS4874.1, CCDS59019.1, CCDS59020.1, CCDS75457.1	6p21.3	2008-02-05			ENSG00000171611	ENSG00000171611			21290	protein-coding gene	gene with protein product		606817				8618853, 9842925	Standard	NM_138296		Approved	PTA, PT-ALPHA	uc021yzp.1	Q6ISU1	OTTHUMG00000014709	ENST00000304672.1:c.754T>C	6.37:g.42893328T>C	ENSP00000304447:p.Cys252Arg	62.0	0.0	0		85.0	50.0	0.588235	NM_001243168	Q5TFZ7	Missense_Mutation	SNP	ENST00000304672.1	37	CCDS4874.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	T	12.26	1.885331	0.33255	0.013643	2.33E-4	ENSG00000171611	ENST00000304672;ENST00000441198;ENST00000446507;ENST00000418903	T;T;T	0.55413	1.23;1.19;0.52	4.17	-8.35	0.00984	.	2.132630	0.02556	N	0.096213	T	0.09774	0.0240	N	0.14661	0.345	0.09310	N	0.999999	B;B;B	0.23806	0.091;0.005;0.005	B;B;B	0.22152	0.038;0.008;0.003	T	0.03166	-1.1065	10	0.72032	D	0.01	.	1.2025	0.01888	0.3397:0.3089:0.1915:0.1599	.	145;227;252	Q6ISU1-2;Q6ISU1-3;Q6ISU1	.;.;PTCRA_HUMAN	R	252;227;145;98	ENSP00000304447:C252R;ENSP00000409550:C227R;ENSP00000392288:C145R	ENSP00000304447:C252R	C	+	1	0	PTCRA	43001306	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-4.585000	0.00212	-3.458000	0.00159	0.533000	0.62120	TGC	T|0.994;C|0.006	0.006	strong		0.642	PTCRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040565.2	NM_138296	
SEMA3D	223117	hgsc.bcm.edu	37	7	84697540	84697540	+	Missense_Mutation	SNP	C	C	T	rs148351346	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:84697540C>T	ENST00000284136.6	-	5	599	c.556G>A	c.(556-558)Gat>Aat	p.D186N	SEMA3D_ENST00000444867.1_Missense_Mutation_p.D186N	NM_152754.2	NP_689967.2	O95025	SEM3D_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D	186	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|membrane (GO:0016020)	receptor activity (GO:0004872)			NS(1)|breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(19)|lung(29)|ovary(3)|pancreas(1)|prostate(4)|skin(2)	73						TGCTGAGGATCGAAAGGACAT	0.343													C|||	2	0.000399361	0.0015	0.0	5008	,	,		17192	0.0		0.0	False		,,,				2504	0.0				p.D186N	Ovarian(63;442 1191 17318 29975 31528)	Atlas-SNP	.											.	SEMA3D	177	.	0			c.G556A						PASS	.	C	ASN/ASP	13,4393	20.2+/-43.8	0,13,2190	103.0	102.0	102.0		556	5.5	1.0	7	dbSNP_134	102	0,8600		0,0,4300	yes	missense	SEMA3D	NM_152754.2	23	0,13,6490	TT,TC,CC		0.0,0.2951,0.1	probably-damaging	186/778	84697540	13,12993	2203	4300	6503	SO:0001583	missense	223117	exon5			GAGGATCGAAAGG	BC029590	CCDS34676.1	7q21.11	2013-01-11			ENSG00000153993	ENSG00000153993		"""Semaphorins"", ""Immunoglobulin superfamily / V-set domain containing"""	10726	protein-coding gene	gene with protein product		609907					Standard	NM_152754		Approved	coll-2, Sema-Z2	uc003uic.3	O95025	OTTHUMG00000154569	ENST00000284136.6:c.556G>A	7.37:g.84697540C>T	ENSP00000284136:p.Asp186Asn	99.0	0.0	0		98.0	46.0	0.469388	NM_152754	A6NK46|Q6UW77|Q8NCQ1	Missense_Mutation	SNP	ENST00000284136.6	37	CCDS34676.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	33	5.213062	0.95069	0.002951	0.0	ENSG00000153993	ENST00000284136;ENST00000444867	T;T	0.15017	2.46;2.46	5.49	5.49	0.81192	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.000000	0.85682	D	0.000000	T	0.28499	0.0705	M	0.72479	2.2	0.80722	D	1	D;P	0.59357	0.985;0.769	P;B	0.54238	0.746;0.404	T	0.01276	-1.1398	10	0.40728	T	0.16	.	19.7307	0.96181	0.0:1.0:0.0:0.0	.	186;186	C9JYT6;O95025	.;SEM3D_HUMAN	N	186	ENSP00000284136:D186N;ENSP00000401366:D186N	ENSP00000284136:D186N	D	-	1	0	SEMA3D	84535476	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.435000	0.80391	2.707000	0.92482	0.655000	0.94253	GAT	C|0.999;T|0.001	0.001	strong		0.343	SEMA3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336084.2	NM_152754	
SOWAHD	347454	hgsc.bcm.edu	37	X	118893390	118893390	+	Missense_Mutation	SNP	A	A	G	rs12841259		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:118893390A>G	ENST00000343905.3	+	1	815	c.760A>G	c.(760-762)Acc>Gcc	p.T254A		NM_001105576.2	NP_001099046.1	A6NJG2	SWAHD_HUMAN	sosondowah ankyrin repeat domain family member D	254			T -> A (in dbSNP:rs12841259).														CAGCGGGTGCACCAACCTGAA	0.697													A|||	174	0.0460927	0.0764	0.0072	3775	,	,		10862	0.0377		0.002	False		,,,				2504	0.0286				p.T254A		Atlas-SNP	.											.	.	.	.	0			c.A760G						PASS	.	A	ALA/THR	249,3366		5,194,45,1337,498	7.0	10.0	9.0		760	-7.0	0.0	X	dbSNP_121	9	19,6433		0,15,4,2340,1738	yes	missense	ANKRD58	NM_001105576.2	58	5,209,49,3677,2236	GG,GA,G,AA,A		0.2945,6.888,2.6622	benign	254/316	118893390	268,9799	2079	4097	6176	SO:0001583	missense	347454	exon1			GGGTGCACCAACC		CCDS43984.1	Xq24	2013-01-10	2012-01-12	2012-01-12	ENSG00000187808	ENSG00000187808		"""Ankyrin repeat domain containing"""	32960	protein-coding gene	gene with protein product			"""ankyrin repeat domain 58"""	ANKRD58		22234889	Standard	NM_001105576		Approved		uc010nql.3	A6NJG2	OTTHUMG00000159606	ENST00000343905.3:c.760A>G	X.37:g.118893390A>G	ENSP00000340975:p.Thr254Ala	100.0	0.0	0		97.0	59.0	0.608247	NM_001105576		Missense_Mutation	SNP	ENST00000343905.3	37	CCDS43984.1	67	0.04038577456298975	23	0.04893617021276596	4	0.011111111111111112	20	0.03597122302158273	0	0.0	A	5.179	0.218585	0.09810	0.06888	0.002945	ENSG00000187808	ENST00000343905	T	0.13420	2.59	4.24	-7.04	0.01578	.	.	.	.	.	T	0.00412	0.0013	N	0.08118	0	0.80722	P	0.0	B	0.10296	0.003	B	0.08055	0.003	T	0.47005	-0.9150	8	0.09084	T	0.74	1.5969	11.8996	0.52675	0.1977:0.1212:0.681:0.0	rs12841259	254	A6NJG2	ANR58_HUMAN	A	254	ENSP00000340975:T254A	ENSP00000340975:T254A	T	+	1	0	ANKRD58	118777418	0.000000	0.05858	0.000000	0.03702	0.077000	0.17291	-1.267000	0.02839	-1.676000	0.01457	0.314000	0.21332	ACC	A|0.958;G|0.042	0.042	strong		0.697	SOWAHD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356469.1	NM_001105576	
HECA	51696	hgsc.bcm.edu	37	6	139488364	139488364	+	Silent	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:139488364C>G	ENST00000367658.2	+	2	1500	c.1215C>G	c.(1213-1215)ctC>ctG	p.L405L	RP1-225E12.2_ENST00000588638.1_RNA|RP1-225E12.2_ENST00000587577.1_RNA|RP1-225E12.2_ENST00000591102.1_RNA|RP1-225E12.2_ENST00000586229.1_RNA|RP1-225E12.2_ENST00000585447.1_RNA|RP1-225E12.2_ENST00000588529.1_RNA|RP1-225E12.2_ENST00000415194.2_RNA|RP1-225E12.3_ENST00000585874.1_RNA|RP1-225E12.2_ENST00000586266.1_RNA|RP1-225E12.2_ENST00000590679.1_RNA|RP1-225E12.2_ENST00000589192.1_RNA	NM_016217.2	NP_057301.1	Q9UBI9	HDC_HUMAN	headcase homolog (Drosophila)	405					respiratory tube development (GO:0030323)	membrane (GO:0016020)				endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)|skin(1)	15				GBM - Glioblastoma multiforme(68;0.000252)|OV - Ovarian serous cystadenocarcinoma(155;0.000387)		ACCGGGCGCTCCCGGTGTTCG	0.557																																					p.L405L		Atlas-SNP	.											.	HECA	45	.	0			c.C1215G						PASS	.						62.0	57.0	59.0					6																	139488364		2203	4300	6503	SO:0001819	synonymous_variant	51696	exon2			GGCGCTCCCGGTG	AB033492	CCDS5194.1	6q23-q24	2010-11-25			ENSG00000112406	ENSG00000112406			21041	protein-coding gene	gene with protein product		607977				11696983, 19643820	Standard	NM_016217		Approved	HDCL, hHDC, HDC, dJ225E12.1	uc003qin.3	Q9UBI9	OTTHUMG00000015686	ENST00000367658.2:c.1215C>G	6.37:g.139488364C>G		95.0	0.0	0		96.0	59.0	0.614583	NM_016217		Silent	SNP	ENST00000367658.2	37	CCDS5194.1																																																																																			.	.	none		0.557	HECA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042456.1	NM_016217	
FLII	2314	hgsc.bcm.edu	37	17	18148944	18148944	+	Silent	SNP	C	C	G	rs113208618	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18148944C>G	ENST00000327031.4	-	28	3759	c.3534G>C	c.(3532-3534)gtG>gtC	p.V1178V	FLII_ENST00000578558.1_Intron|FLII_ENST00000379450.4_Silent_p.V1092V|FLII_ENST00000579294.1_Silent_p.V1167V|FLII_ENST00000545457.2_Silent_p.V1123V	NM_002018.3	NP_002009.1	Q13045	FLII_HUMAN	flightless I homolog (Drosophila)	1178					multicellular organismal development (GO:0007275)|muscle contraction (GO:0006936)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)			central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32	all_neural(463;0.228)					ATTTCTCAGTCACTGCAAAGT	0.542													C|||	209	0.0417332	0.1301	0.0259	5008	,	,		22593	0.0079		0.004	False		,,,				2504	0.0072				p.V1178V		Atlas-SNP	.											.	FLII	79	.	0			c.G3534C						PASS	.	C		455,3951	217.1+/-235.6	31,393,1779	221.0	195.0	204.0		3534	3.4	1.0	17	dbSNP_132	204	46,8554	30.1+/-81.4	0,46,4254	no	coding-synonymous	FLII	NM_002018.2		31,439,6033	GG,GC,CC		0.5349,10.3268,3.8521		1178/1270	18148944	501,12505	2203	4300	6503	SO:0001819	synonymous_variant	2314	exon28			CTCAGTCACTGCA	U01184	CCDS11192.1, CCDS58521.1, CCDS58522.1	17p11.2	2008-07-18	2001-11-28		ENSG00000177731	ENSG00000177731			3750	protein-coding gene	gene with protein product		600362	"""flightless I (Drosophila) homolog"""			7825574	Standard	NM_002018		Approved	FLI, FLIL, Fli1, MGC39265	uc002gsr.2	Q13045	OTTHUMG00000059389	ENST00000327031.4:c.3534G>C	17.37:g.18148944C>G		76.0	0.0	0		92.0	42.0	0.456522	NM_002018	B4DIL0|F5H407|J3QLG3	Silent	SNP	ENST00000327031.4	37	CCDS11192.1																																																																																			C|0.964;G|0.036	0.036	strong		0.542	FLII-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132032.2	NM_002018	
TBC1D16	125058	hgsc.bcm.edu	37	17	77984168	77984168	+	Silent	SNP	G	G	A	rs35393459	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:77984168G>A	ENST00000310924.2	-	3	685	c.570C>T	c.(568-570)gtC>gtT	p.V190V		NM_001271844.1|NM_001271845.1|NM_019020.2	NP_001258773.1|NP_001258774.1|NP_061893.2	Q8TBP0	TBC16_HUMAN	TBC1 domain family, member 16	190							Rab GTPase activator activity (GO:0005097)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(3)	28	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.00739)|BRCA - Breast invasive adenocarcinoma(99;0.0819)			CCTGCGGACTGACCGTCGACA	0.687													G|||	141	0.028155	0.0983	0.0159	5008	,	,		16011	0.0		0.0	False		,,,				2504	0.0				p.V190V	Ovarian(14;397 562 4850 31922 49378)	Atlas-SNP	.											.	TBC1D16	48	.	0			c.C570T						PASS	.	G		397,4003	178.3+/-207.1	23,351,1826	29.0	33.0	31.0		570	3.5	0.1	17	dbSNP_126	31	3,8589	3.0+/-9.4	0,3,4293	no	coding-synonymous	TBC1D16	NM_019020.2		23,354,6119	AA,AG,GG		0.0349,9.0227,3.0788		190/768	77984168	400,12592	2200	4296	6496	SO:0001819	synonymous_variant	125058	exon3			CGGACTGACCGTC	AL157485	CCDS11766.1, CCDS62351.1, CCDS62352.1, CCDS62353.1	17q25.3	2013-07-10				ENSG00000167291			28356	protein-coding gene	gene with protein product						23019362	Standard	NM_019020		Approved	MGC25062, FLJ20748	uc002jxj.4	Q8TBP0		ENST00000310924.2:c.570C>T	17.37:g.77984168G>A		141.0	0.0	0		112.0	64.0	0.571429	NM_019020	B9A6L7|I3L1E0|I3L4U2|Q8N3Z4|Q96DH7	Silent	SNP	ENST00000310924.2	37	CCDS11766.1																																																																																			G|0.967;A|0.033	0.033	strong		0.687	TBC1D16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437145.1	NM_019020	
KRT79	338785	hgsc.bcm.edu	37	12	53215684	53215684	+	Missense_Mutation	SNP	G	G	A	rs73303800	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53215684G>A	ENST00000330553.5	-	9	1614	c.1580C>T	c.(1579-1581)aCg>aTg	p.T527M		NM_175834.2	NP_787028.1	Q5XKE5	K2C79_HUMAN	keratin 79	527	Tail.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	enzyme binding (GO:0019899)|structural molecule activity (GO:0005198)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CGTCTTGACCGTAGTGGTCTT	0.622													G|||	44	0.00878594	0.0318	0.0029	5008	,	,		17021	0.0		0.0	False		,,,				2504	0.0				p.T527M		Atlas-SNP	.											.	KRT79	78	.	0			c.C1580T						PASS	.	G	MET/THR	121,4285	90.6+/-129.3	3,115,2085	58.0	44.0	48.0		1580	4.0	1.0	12	dbSNP_130	48	2,8598	1.2+/-3.3	0,2,4298	yes	missense	KRT79	NM_175834.2	81	3,117,6383	AA,AG,GG		0.0233,2.7463,0.9457	probably-damaging	527/536	53215684	123,12883	2203	4300	6503	SO:0001583	missense	338785	exon9			TTGACCGTAGTGG	AJ564105	CCDS8839.1	12q13.13	2014-02-12	2007-07-03		ENSG00000185640	ENSG00000185640		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28930	protein-coding gene	gene with protein product	"""keratin 6-like"""	611160				11683385	Standard	NM_175834		Approved	K6L, KRT6L	uc001sbb.3	Q5XKE5	OTTHUMG00000169878	ENST00000330553.5:c.1580C>T	12.37:g.53215684G>A	ENSP00000328358:p.Thr527Met	64.0	0.0	0		73.0	40.0	0.547945	NM_175834	Q6P465|Q7Z793	Missense_Mutation	SNP	ENST00000330553.5	37	CCDS8839.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	G	18.23	3.578041	0.65878	0.027463	2.33E-4	ENSG00000185640	ENST00000330553	D	0.83075	-1.68	3.97	3.97	0.46021	.	0.000000	0.47852	D	0.000213	T	0.75824	0.3902	M	0.61703	1.905	0.37441	D	0.914404	D	0.89917	1.0	D	0.78314	0.991	D	0.85029	0.0916	10	0.72032	D	0.01	.	11.8409	0.52353	0.0:0.0:1.0:0.0	.	527	Q5XKE5	K2C79_HUMAN	M	527	ENSP00000328358:T527M	ENSP00000328358:T527M	T	-	2	0	KRT79	51501951	0.969000	0.33509	1.000000	0.80357	0.997000	0.91878	1.735000	0.38176	2.516000	0.84829	0.655000	0.94253	ACG	G|0.990;A|0.010	0.010	strong		0.622	KRT79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406376.1	NM_175834	
AQP12B	653437	hgsc.bcm.edu	37	2	241622008	241622008	+	Missense_Mutation	SNP	G	G	A	rs187845451	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:241622008G>A	ENST00000407834.3	-	1	309	c.247C>T	c.(247-249)Cac>Tac	p.H83Y		NM_001102467.1	NP_001095937.1	A6NM10	AQ12B_HUMAN	aquaporin 12B	71						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)		GTGACCCCGTGCGCCAGGAAG	0.672													N|||	54	0.0107827	0.0408	0.0	5008	,	,		18265	0.0		0.0	False		,,,				2504	0.0				p.H83Y		Atlas-SNP	.											AQP12B,colon,carcinoma,+2,1	AQP12B	33	1	0			c.C247T						PASS	.		TYR/HIS	141,4265		1,139,2063	50.0	51.0	50.0		247	2.5	0.5	2		50	0,8598		0,0,4299	no	missense	AQP12B	NM_001102467.1	83	1,139,6362	AA,AG,GG		0.0,3.2002,1.0843	probably-damaging	83/308	241622008	141,12863	2203	4299	6502	SO:0001583	missense	653437	exon1			CCCCGTGCGCCAG	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.247C>T	2.37:g.241622008G>A	ENSP00000384894:p.His83Tyr	165.0	0.0	0		245.0	98.0	0.4	NM_001102467	A4QPB9	Missense_Mutation	SNP	ENST00000407834.3	37	CCDS46560.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	.	13.39	2.223741	0.39300	0.032002	0.0	ENSG00000185176	ENST00000407834	T	0.14516	2.5	2.53	2.53	0.30540	.	0.000000	0.85682	D	0.000000	T	0.10380	0.0254	M	0.80982	2.52	0.44547	D	0.997501	D	0.89917	1.0	D	0.87578	0.998	T	0.02053	-1.1222	9	.	.	.	-1.4545	11.1973	0.48719	0.0:0.0:1.0:0.0	.	83	A6NM10-2	.	Y	83	ENSP00000384894:H83Y	.	H	-	1	0	AQP12B	241270681	1.000000	0.71417	0.528000	0.27938	0.035000	0.12851	8.195000	0.89723	1.720000	0.51447	0.479000	0.44913	CAC	G|0.991;A|0.009	0.009	strong		0.672	AQP12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325625.1		
MUC4	4585	hgsc.bcm.edu	37	3	195506483	195506483	+	Missense_Mutation	SNP	T	T	C	rs201375109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195506483T>C	ENST00000463781.3	-	2	12427	c.11968A>G	c.(11968-11970)Act>Gct	p.T3990A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T3990A	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.T3990P(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)		ACTGAGGAAGTGTCGGTGACA	0.592																																					p.T3990A		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	endometrium(1)	c.A11968G						scavenged	.						10.0	7.0	8.0					3																	195506483		622	1355	1977	SO:0001583	missense	4585	exon2			AGGAAGTGTCGGT	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.11968A>G	3.37:g.195506483T>C	ENSP00000417498:p.Thr3990Ala	72.0	0.0	0		47.0	6.0	0.12766	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	8.956	0.969412	0.18659	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33438	1.41;1.5	0.481	-0.864	0.10666	.	0.562686	0.09843	U	0.748557	T	0.21718	0.0523	N	0.14661	0.345	0.09310	N	1	B	0.31790	0.34	B	0.43274	0.414	T	0.40478	-0.9561	9	.	.	.	.	5.8902	0.18909	0.0:0.618:0.0:0.382	.	3862	E7ESK3	.	A	3990	ENSP00000417498:T3990A;ENSP00000420243:T3990A	.	T	-	1	0	MUC4	196991262	0.000000	0.05858	0.001000	0.08648	0.052000	0.14988	-2.288000	0.01150	-2.052000	0.00902	-2.075000	0.00382	ACT	C|0.002;G|0.002;T|0.996	0.002	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
NUP133	55746	hgsc.bcm.edu	37	1	229622236	229622236	+	Missense_Mutation	SNP	G	G	A	rs35442997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229622236G>A	ENST00000261396.3	-	11	1473	c.1382C>T	c.(1381-1383)cCt>cTt	p.P461L	NUP133_ENST00000537506.1_Missense_Mutation_p.P445L	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	461					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 export from nucleus (GO:0006406)|nuclear pore organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				AAAAATGATAGGAACACCACC	0.368													G|||	50	0.00998403	0.0325	0.0043	5008	,	,		17685	0.0		0.002	False		,,,				2504	0.002				p.P461L		Atlas-SNP	.											.	NUP133	111	.	0			c.C1382T						PASS	.	G	LEU/PRO	141,4265	99.8+/-138.5	4,133,2066	92.0	93.0	93.0		1382	4.3	0.5	1	dbSNP_126	93	4,8596	4.3+/-15.6	0,4,4296	yes	missense	NUP133	NM_018230.2	98	4,137,6362	AA,AG,GG		0.0465,3.2002,1.1149	benign	461/1157	229622236	145,12861	2203	4300	6503	SO:0001583	missense	55746	exon11			ATGATAGGAACAC		CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"""nucleoporin 133kD"""			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.1382C>T	1.37:g.229622236G>A	ENSP00000261396:p.Pro461Leu	146.0	0.0	0		176.0	74.0	0.420455	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Missense_Mutation	SNP	ENST00000261396.3	37	CCDS1579.1	23	0.010531135531135532	22	0.044715447154471545	0	0.0	0	0.0	1	0.0013192612137203166	G	18.11	3.549917	0.65311	0.032002	4.65E-4	ENSG00000069248	ENST00000366681;ENST00000261396;ENST00000366679;ENST00000537506	T;T;T	0.40225	1.04;1.04;1.04	5.21	4.3	0.51218	WD40/YVTN repeat-like-containing domain (1);	0.251116	0.47093	N	0.000247	T	0.14442	0.0349	M	0.65975	2.015	0.80722	D	1	P	0.47841	0.901	P	0.45276	0.475	T	0.15435	-1.0437	10	0.11485	T	0.65	-6.4934	13.9867	0.64339	0.0737:0.0:0.9263:0.0	rs35442997	461	Q8WUM0	NU133_HUMAN	L	461;461;461;445	ENSP00000261396:P461L;ENSP00000355640:P461L;ENSP00000443496:P445L	ENSP00000261396:P461L	P	-	2	0	NUP133	227688859	1.000000	0.71417	0.535000	0.28026	0.989000	0.77384	6.520000	0.73773	1.321000	0.45227	0.467000	0.42956	CCT	G|0.990;A|0.010	0.010	strong		0.368	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230	
AAED1	195827	hgsc.bcm.edu	37	9	99417000	99417000	+	Missense_Mutation	SNP	C	C	T	rs9886834|rs77297714	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:99417000C>T	ENST00000375234.3	-	2	247	c.248G>A	c.(247-249)aGg>aAg	p.R83K	AAED1_ENST00000464512.1_5'UTR	NM_153698.1	NP_714542.1	Q7RTV5	AAED1_HUMAN	AhpC/TSA antioxidant enzyme domain containing 1	83			R -> K (in dbSNP:rs9886834).														TAAGAAACTCCTGGGGATTTT	0.572													T|||	410	0.081869	0.2912	0.0259	5008	,	,		16276	0.0		0.002	False		,,,				2504	0.0051				p.R83K		Atlas-SNP	.											.	.	.	.	0			c.G248A						PASS	.	T	LYS/ARG	1109,3283		125,859,1212	59.0	58.0	58.0		248	-1.6	0.8	9	dbSNP_119	58	16,8558		0,16,4271	yes	missense	C9orf21	NM_153698.1	26	125,875,5483	TT,TC,CC		0.1866,25.2505,8.6765	benign	83/227	99417000	1125,11841	2196	4287	6483	SO:0001583	missense	195827	exon2			AAACTCCTGGGGA	BK000255	CCDS35073.1	9q22.32	2013-01-07	2012-03-06	2012-03-06	ENSG00000158122	ENSG00000158122			16881	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 21"""	C9orf21			Standard	XM_005251783		Approved		uc004awm.3	Q7RTV5	OTTHUMG00000020299	ENST00000375234.3:c.248G>A	9.37:g.99417000C>T	ENSP00000364382:p.Arg83Lys	90.0	0.0	0		69.0	41.0	0.594203	NM_153698	B2RMW4|Q5JU02	Missense_Mutation	SNP	ENST00000375234.3	37	CCDS35073.1	132|132	0.06043956043956044|0.06043956043956044	124|124	0.25203252032520324|0.25203252032520324	8|8	0.022099447513812154|0.022099447513812154	0|0	0.0|0.0	0|0	0.0|0.0	T|T	0.325|0.325	-0.959491|-0.959491	0.02267|0.02267	0.252505|0.252505	0.001866|0.001866	ENSG00000158122|ENSG00000158122	ENST00000411939|ENST00000375234;ENST00000375233	.|T	.|0.39592	.|1.07	4.79|4.79	-1.64|-1.64	0.08318|0.08318	.|Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant (1);Thioredoxin-like fold (2);	.|0.514983	.|0.21661	.|N	.|0.071010	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02539|0.02539	-0.55|-0.55	0.80722|0.80722	P|P	0.0|0.0	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	T|T	0.20240|0.20240	-1.0281|-1.0281	4|9	.|0.02654	.|T	.|1	-1.013|-1.013	5.5316|5.5316	0.16987|0.16987	0.1376:0.4036:0.0:0.4588|0.1376:0.4036:0.0:0.4588	rs9886834;rs11538195;rs57315001;rs9886834|rs9886834;rs11538195;rs57315001;rs9886834	.|83	.|Q7RTV5	.|CI021_HUMAN	R|K	11|83	.|ENSP00000364382:R83K	.|ENSP00000364381:R83K	G|R	-|-	1|2	0|0	C9orf21|C9orf21	98456821|98456821	0.175000|0.175000	0.23083|0.23083	0.814000|0.814000	0.32528|0.32528	0.098000|0.098000	0.18820|0.18820	-0.008000|-0.008000	0.12788|0.12788	-0.858000|-0.858000	0.04110|0.04110	-1.916000|-1.916000	0.00518|0.00518	GGA|AGG	C|0.901;T|0.099	0.099	strong		0.572	AAED1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053273.1	NM_153698	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057766	46057766	+	Missense_Mutation	SNP	G	G	C	rs142146787	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46057766G>C	ENST00000380095.1	+	1	494	c.432G>C	c.(430-432)caG>caC	p.Q144H	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	144	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						CATGCCAGCAGGCCTGCTGTG	0.602													G|||	3	0.000599042	0.0015	0.0	5008	,	,		23205	0.0		0.0	False		,,,				2504	0.001				p.Q144H		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.G432C						PASS	.	G	,HIS/GLN	7,4399	12.9+/-30.5	0,7,2196	293.0	265.0	274.0		,432	-0.5	0.1	21	dbSNP_134	274	0,8600		0,0,4300	yes	intron,missense	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,24	0,7,6496	CC,CG,GG		0.0,0.1589,0.0538	,probably-damaging	,144/252	46057766	7,12999	2203	4300	6503	SO:0001583	missense	353333	exon1			CCAGCAGGCCTGC	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.432G>C	21.37:g.46057766G>C	ENSP00000369438:p.Gln144His	155.0	0.0	0		172.0	53.0	0.30814	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	.	.	.	.	.	.	.	.	.	.	g	8.829	0.939468	0.18281	0.001589	0.0	ENSG00000221859	ENST00000380095	T	0.01178	5.22	3.27	-0.456	0.12190	.	.	.	.	.	T	0.05273	0.0140	M	0.91300	3.195	0.09310	N	1	D	0.56746	0.977	P	0.56343	0.796	T	0.12760	-1.0535	9	0.87932	D	0	.	5.8436	0.18647	0.632:0.0:0.368:0.0	.	144	P60014	KR10A_HUMAN	H	144	ENSP00000369438:Q144H	ENSP00000369438:Q144H	Q	+	3	2	KRTAP10-10	44882194	0.000000	0.05858	0.109000	0.21407	0.190000	0.23558	-1.200000	0.03029	0.065000	0.16485	0.461000	0.40582	CAG	G|1.000;C|0.000	0.000	weak		0.602	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
GABRA4	2557	hgsc.bcm.edu	37	4	46995387	46995387	+	Missense_Mutation	SNP	C	C	T	rs16859837	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:46995387C>T	ENST00000264318.3	-	1	1037	c.55G>A	c.(55-57)Gcc>Acc	p.A19T	GABRA4_ENST00000509316.1_5'UTR	NM_000809.3|NM_001204266.1|NM_001204267.1	NP_000800.2|NP_001191195.1|NP_001191196.1	P48169	GBRA4_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 4	19			A -> T (in dbSNP:rs16859837).		central nervous system development (GO:0007417)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|regulation of response to drug (GO:2001023)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45					Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	CGCAGGAGGGCGAAACTGACC	0.582													C|||	59	0.0117812	0.0439	0.0014	5008	,	,		16882	0.0		0.0	False		,,,				2504	0.0				p.A19T	Ovarian(6;283 369 8234 12290 33402)	Atlas-SNP	.											.	GABRA4	129	.	0			c.G55A						PASS	.	C	THR/ALA,,	164,4242	109.9+/-148.2	5,154,2044	115.0	109.0	111.0		55,,	1.8	1.0	4	dbSNP_123	111	2,8598	1.2+/-3.3	0,2,4298	yes	missense,intron,intron	GABRA4	NM_000809.3,NM_001204266.1,NM_001204267.1	58,,	5,156,6342	TT,TC,CC		0.0233,3.7222,1.2763	benign,,	19/555,,	46995387	166,12840	2203	4300	6503	SO:0001583	missense	2557	exon1			GGAGGGCGAAACT		CCDS3473.1	4p12	2012-06-22			ENSG00000109158	ENSG00000109158		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4078	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 4"""	137141				7607683	Standard	NM_000809		Approved		uc021xnz.1	P48169	OTTHUMG00000099431	ENST00000264318.3:c.55G>A	4.37:g.46995387C>T	ENSP00000264318:p.Ala19Thr	185.0	0.0	0		194.0	192.0	0.989691	NM_000809	Q8IYR7	Missense_Mutation	SNP	ENST00000264318.3	37	CCDS3473.1	27	0.012362637362637362	27	0.054878048780487805	0	0.0	0	0.0	0	0.0	C	15.70	2.911015	0.52439	0.037222	2.33E-4	ENSG00000109158	ENST00000264318	T	0.79845	-1.31	4.72	1.79	0.24919	.	0.494117	0.20686	N	0.087559	T	0.17789	0.0427	N	0.08118	0	0.28598	N	0.909322	B	0.06786	0.001	B	0.04013	0.001	T	0.13980	-1.0489	10	0.20519	T	0.43	.	5.9264	0.19114	0.0:0.6558:0.0:0.3442	rs16859837;rs52821342;rs16859837	19	P48169	GBRA4_HUMAN	T	19	ENSP00000264318:A19T	ENSP00000264318:A19T	A	-	1	0	GABRA4	46690144	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	1.961000	0.40432	0.595000	0.29777	-0.237000	0.12165	GCC	C|0.984;T|0.016	0.016	strong		0.582	GABRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216893.1		
ZNF618	114991	hgsc.bcm.edu	37	9	116811184	116811184	+	Silent	SNP	G	G	A	rs7852282	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116811184G>A	ENST00000374126.5	+	15	1701	c.1602G>A	c.(1600-1602)aaG>aaA	p.K534K	ZNF618_ENST00000470105.1_3'UTR|ZNF618_ENST00000288466.7_Silent_p.K441K			Q5T7W0	ZN618_HUMAN	zinc finger protein 618	534					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|lung(10)|urinary_tract(1)	16						ACCAGGTGAAGGTGAAAGTGA	0.587													G|||	338	0.067492	0.2375	0.0303	5008	,	,		21657	0.0		0.0	False		,,,				2504	0.0031				p.K441K		Atlas-SNP	.											.	ZNF618	184	.	0			c.G1323A						PASS	.	G		796,3538		77,642,1448	27.0	30.0	29.0		1323	3.5	1.0	9	dbSNP_116	29	18,8520		0,18,4251	no	coding-synonymous	ZNF618	NM_133374.2		77,660,5699	AA,AG,GG		0.2108,18.3664,6.3238		441/862	116811184	814,12058	2167	4269	6436	SO:0001819	synonymous_variant	114991	exon14			GGTGAAGGTGAAA	BC012922	CCDS48008.1	9q33.1	2010-04-21			ENSG00000157657	ENSG00000157657		"""Zinc fingers, C2H2-type"""	29416	protein-coding gene	gene with protein product	"""neural precursor cell expressed, developmentally down-regulated 10"""					11853319	Standard	NM_133374		Approved	KIAA1952, NEDD10	uc004bic.3	Q5T7W0	OTTHUMG00000020532	ENST00000374126.5:c.1602G>A	9.37:g.116811184G>A		55.0	0.0	0		60.0	38.0	0.633333	NM_133374	B9EG82|Q4G0X6|Q5T7W1|Q6ZT53|Q7Z6B9|Q8TF49|Q96E49	Silent	SNP	ENST00000374126.5	37																																																																																				G|0.921;A|0.079	0.079	strong		0.587	ZNF618-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000053749.1	XM_054983	
DOCK2	1794	hgsc.bcm.edu	37	5	169469088	169469088	+	Silent	SNP	G	G	C	rs6555882	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:169469088G>C	ENST00000256935.8	+	38	3908	c.3828G>C	c.(3826-3828)ctG>ctC	p.L1276L	DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000540750.1_Silent_p.L337L|DOCK2_ENST00000520908.1_Silent_p.L768L	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	1276	DHR-2.|Interaction with CRKL.				actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ACCGGCAGCTGAAGGAGACGC	0.577													C|||	461	0.0920527	0.2837	0.0317	5008	,	,		19097	0.0		0.0189	False		,,,				2504	0.046				p.L1276L		Atlas-SNP	.											.	DOCK2	389	.	0			c.G3828C						PASS	.	C		1166,3240	713.1+/-408.2	139,888,1176	61.0	54.0	57.0		3828	3.4	1.0	5	dbSNP_116	57	164,8436	811.3+/-407.1	3,158,4139	no	coding-synonymous	DOCK2	NM_004946.2		142,1046,5315	CC,CG,GG		1.907,26.4639,10.226		1276/1831	169469088	1330,11676	2203	4300	6503	SO:0001819	synonymous_variant	1794	exon38			GCAGCTGAAGGAG	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"""dedicator of cyto-kinesis 2"""				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.3828G>C	5.37:g.169469088G>C		225.0	0.0	0		242.0	242.0	1	NM_004946	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	37	CCDS4371.1																																																																																			G|0.867;C|0.133	0.133	strong		0.577	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	
DUOX1	53905	hgsc.bcm.edu	37	15	45427345	45427345	+	Silent	SNP	C	C	T	rs78022423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:45427345C>T	ENST00000321429.4	+	6	758	c.351C>T	c.(349-351)ggC>ggT	p.G117G	DUOX1_ENST00000389037.3_Silent_p.G117G	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	117	Peroxidase-like; mediates peroxidase activity.				cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		AAACTCCCGGCTGCCCCGCCG	0.647													C|||	111	0.0221645	0.0809	0.0058	5008	,	,		15061	0.0		0.0	False		,,,				2504	0.0				p.G117G		Atlas-SNP	.											.	DUOX1	125	.	0			c.C351T						PASS	.	C	,	295,4099	160.0+/-192.4	11,273,1913	48.0	48.0	48.0		351,351	2.1	1.0	15	dbSNP_131	48	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous	DUOX1	NM_017434.3,NM_175940.1	,	11,273,6211	TT,TC,CC		0.0,6.7137,2.271	,	117/1552,117/1552	45427345	295,12695	2197	4298	6495	SO:0001819	synonymous_variant	53905	exon6			TCCCGGCTGCCCC	AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"""EF-hand domain containing"""	3062	protein-coding gene	gene with protein product	"""NADPH thyroid oxidase 1"", ""flavoprotein NADPH oxidase"", ""nicotinamide adenine dinucleotide phosphate oxidase"""	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		ENST00000321429.4:c.351C>T	15.37:g.45427345C>T		170.0	0.0	0		206.0	95.0	0.461165	NM_017434	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Silent	SNP	ENST00000321429.4	37	CCDS32221.1																																																																																			C|0.976;T|0.024	0.024	strong		0.647	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434	
OR7G2	390882	hgsc.bcm.edu	37	19	9213396	9213396	+	Missense_Mutation	SNP	G	G	A	rs7247751	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9213396G>A	ENST00000305456.2	-	1	586	c.587C>T	c.(586-588)cCg>cTg	p.P196L		NM_001005193.1	NP_001005193.1	Q8NG99	OR7G2_HUMAN	olfactory receptor, family 7, subfamily G, member 2	175						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|skin(3)	16						GAAGAAGAGCGGGATTTCCAG	0.478													-|||	155	0.0309505	0.1127	0.0086	5008	,	,		21697	0.0		0.0	False		,,,				2504	0.0				p.P196L	Esophageal Squamous(67;143 1448 28637 40648)	Atlas-SNP	.											OR7G2,NS,carcinoma,+1,1	OR7G2	48	1	0			c.C587T						PASS	.	G	LEU/PRO	380,4026	190.9+/-216.7	16,348,1839	98.0	86.0	90.0		587	2.2	0.0	19	dbSNP_116	90	4,8596	3.0+/-9.4	0,4,4296	yes	missense	OR7G2	NM_001005193.1	98	16,352,6135	AA,AG,GG		0.0465,8.6246,2.9525	possibly-damaging	196/346	9213396	384,12622	2203	4300	6503	SO:0001583	missense	390882	exon1			AAGAGCGGGATTT		CCDS32897.1	19p13.2	2013-09-24			ENSG00000170923	ENSG00000170923		"""GPCR / Class A : Olfactory receptors"""	8466	protein-coding gene	gene with protein product							Standard	NM_001005193		Approved	OST260	uc010xkk.2	Q8NG99	OTTHUMG00000179931	ENST00000305456.2:c.587C>T	19.37:g.9213396G>A	ENSP00000303822:p.Pro196Leu	207.0	0.0	0		216.0	102.0	0.472222	NM_001005193	Q6IFJ4|Q96RA0	Missense_Mutation	SNP	ENST00000305456.2	37	CCDS32897.1	55	0.025183150183150184	54	0.10975609756097561	1	0.0027624309392265192	0	0.0	0	0.0	g	8.801	0.932843	0.18131	0.086246	4.65E-4	ENSG00000170923	ENST00000305456	T	0.37752	1.18	3.27	2.19	0.27852	GPCR, rhodopsin-like superfamily (1);	0.212960	0.23524	U	0.047241	T	0.00637	0.0021	L	0.58583	1.82	0.09310	N	1	P	0.45672	0.864	B	0.40825	0.341	T	0.01262	-1.1402	10	0.66056	D	0.02	.	9.1271	0.36821	0.0:0.0:0.4786:0.5214	rs7247751;rs52817351;rs7247751	175	Q8NG99	OR7G2_HUMAN	L	196	ENSP00000303822:P196L	ENSP00000303822:P196L	P	-	2	0	OR7G2	9074396	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	-0.621000	0.05559	0.954000	0.37851	0.545000	0.68477	CCG	G|0.968;A|0.032	0.032	strong		0.478	OR7G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448994.1		
MERTK	10461	hgsc.bcm.edu	37	2	112722854	112722854	+	Splice_Site	SNP	G	G	A	rs7588635	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:112722854G>A	ENST00000295408.4	+	5	1101	c.844G>A	c.(844-846)Gca>Aca	p.A282T	MERTK_ENST00000421804.2_Splice_Site_p.A282T|MERTK_ENST00000409780.1_Splice_Site_p.A106T			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	282			A -> T (in dbSNP:rs7588635). {ECO:0000269|PubMed:11062461, ECO:0000269|PubMed:17344846}.		apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|leukocyte migration (GO:0050900)|natural killer cell differentiation (GO:0001779)|negative regulation of lymphocyte activation (GO:0051250)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of phagocytosis (GO:0050766)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|secretion by cell (GO:0032940)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|rhabdomere (GO:0016028)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(10)	46						CAACATCAAAGGTAAGCAGCA	0.567													G|||	233	0.0465256	0.171	0.0086	5008	,	,		19523	0.0		0.001	False		,,,				2504	0.0				p.A282T		Atlas-SNP	.											.	MERTK	112	.	0			c.G844A						PASS	.	G	THR/ALA	598,3808	255.2+/-260.5	47,504,1652	102.0	80.0	88.0		844	5.8	1.0	2	dbSNP_116	88	6,8594	4.3+/-15.6	0,6,4294	yes	missense-near-splice	MERTK	NM_006343.2	58	47,510,5946	AA,AG,GG		0.0698,13.5724,4.644	benign	282/1000	112722854	604,12402	2203	4300	6503	SO:0001630	splice_region_variant	10461	exon5			ATCAAAGGTAAGC	U08023	CCDS2094.1	2q14.1	2014-06-26	2014-06-26		ENSG00000153208	ENSG00000153208		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7027	protein-coding gene	gene with protein product		604705	"""c-mer proto-oncogene tyrosine kinase"""			8086340, 10343112	Standard	XM_005263565		Approved	mer, RP38	uc002thk.1	Q12866	OTTHUMG00000131278	ENST00000295408.4:c.844+1G>A	2.37:g.112722854G>A		219.0	1.0	0.00456621		201.0	94.0	0.467662	NM_006343	Q9HBB4	Missense_Mutation	SNP	ENST00000295408.4	37	CCDS2094.1	90	0.04120879120879121	87	0.17682926829268292	3	0.008287292817679558	0	0.0	0	0.0	G	17.78	3.474628	0.63737	0.135724	6.98E-4	ENSG00000153208	ENST00000295408;ENST00000421804;ENST00000409780	T;T;T	0.36520	1.25;1.25;1.25	5.75	5.75	0.90469	Immunoglobulin-like fold (1);	0.534882	0.13857	U	0.357982	T	0.00109	0.0003	L	0.58101	1.795	0.30039	P	0.8128029999999999	B	0.32245	0.361	B	0.25140	0.058	T	0.05084	-1.0907	9	0.72032	D	0.01	-0.4319	19.5333	0.95239	0.0:0.0:1.0:0.0	rs7588635;rs17838486;rs7588635	282	Q12866	MERTK_HUMAN	T	282;282;106	ENSP00000295408:A282T;ENSP00000389152:A282T;ENSP00000387277:A106T	ENSP00000295408:A282T	A	+	1	0	MERTK	112439325	1.000000	0.71417	1.000000	0.80357	0.579000	0.36224	4.652000	0.61454	2.720000	0.93068	0.563000	0.77884	GCA	G|0.947;A|0.053	0.053	strong		0.567	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2		Missense_Mutation
MAN2B2	23324	hgsc.bcm.edu	37	4	6602378	6602378	+	Silent	SNP	G	G	A	rs73796294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:6602378G>A	ENST00000285599.3	+	10	1470	c.1434G>A	c.(1432-1434)tcG>tcA	p.S478S	MAN2B2_ENST00000504248.1_Silent_p.S427S	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	478					mannose metabolic process (GO:0006013)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	30						ATTTTGCCTCGGTCTACAACC	0.597													G|||	186	0.0371406	0.1331	0.013	5008	,	,		19561	0.0		0.001	False		,,,				2504	0.0				p.S478S		Atlas-SNP	.											.	MAN2B2	80	.	0			c.G1434A						PASS	.	G		515,3891	236.8+/-248.8	34,447,1722	155.0	122.0	133.0		1434	-7.5	0.0	4	dbSNP_130	133	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	MAN2B2	NM_015274.1		34,453,6016	AA,AG,GG		0.0698,11.6886,4.0058		478/1010	6602378	521,12485	2203	4300	6503	SO:0001819	synonymous_variant	23324	exon10			TGCCTCGGTCTAC	BC033307	CCDS33951.1	4p16.2	2005-11-09			ENSG00000013288	ENSG00000013288			29623	protein-coding gene	gene with protein product	"""core-specific lysosomal alpha-1,6-Mannosidase"""					10231032, 16115860	Standard	XR_241647		Approved	KIAA0935	uc003gjf.1	Q9Y2E5	OTTHUMG00000160073	ENST00000285599.3:c.1434G>A	4.37:g.6602378G>A		80.0	0.0	0		79.0	40.0	0.506329	NM_015274	Q66MP2|Q86T67	Silent	SNP	ENST00000285599.3	37	CCDS33951.1	65	0.02976190476190476	62	0.12601626016260162	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	4.539	0.100114	0.08731	0.116886	6.98E-4	ENSG00000013288	ENST00000505907	.	.	.	4.67	-7.52	0.01341	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.42109	P	0.008626000000000023	.	.	.	.	.	.	T	0.26744	-1.0094	3	.	.	.	-3.5583	0.9855	0.01445	0.1784:0.1741:0.2587:0.3887	.	.	.	.	Q	477	.	.	R	+	2	0	MAN2B2	6653279	0.014000	0.17966	0.003000	0.11579	0.008000	0.06430	-0.480000	0.06559	-1.075000	0.03129	-1.224000	0.01588	CGG	G|0.959;A|0.041	0.041	strong		0.597	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274	
BRPF3	27154	hgsc.bcm.edu	37	6	36177597	36177597	+	Silent	SNP	C	C	T	rs73730485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36177597C>T	ENST00000357641.6	+	5	2024	c.1771C>T	c.(1771-1773)Ctg>Ttg	p.L591L	BRPF3_ENST00000534694.1_Silent_p.L591L|BRPF3_ENST00000534400.1_Silent_p.L591L|BRPF3_ENST00000543502.1_Silent_p.L591L|BRPF3_ENST00000339717.7_Silent_p.L591L|BRPF3_ENST00000443324.2_Silent_p.L591L	NM_015695.2	NP_056510.2	Q9ULD4	BRPF3_HUMAN	bromodomain and PHD finger containing, 3	591					blood coagulation (GO:0007596)|histone H3 acetylation (GO:0043966)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	cytosol (GO:0005829)|extracellular region (GO:0005576)|MOZ/MORF histone acetyltransferase complex (GO:0070776)	zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(1)|skin(4)|urinary_tract(2)	40						GGAGCTGGAGCTGATGCCATT	0.507													C|||	53	0.0105831	0.0393	0.0014	5008	,	,		20080	0.0		0.0	False		,,,				2504	0.0				p.L591L		Atlas-SNP	.											.	BRPF3	93	.	0			c.C1771T						PASS	.	C		186,4220	118.8+/-156.5	4,178,2021	96.0	84.0	88.0		1771	3.2	1.0	6	dbSNP_130	88	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	BRPF3	NM_015695.2		4,179,6320	TT,TC,CC		0.0116,4.2215,1.4378		591/1206	36177597	187,12819	2203	4300	6503	SO:0001819	synonymous_variant	27154	exon5			CTGGAGCTGATGC	AB033112	CCDS34437.1	6p21.31	2008-02-05			ENSG00000096070	ENSG00000096070			14256	protein-coding gene	gene with protein product						10574462	Standard	NM_015695		Approved	KIAA1286	uc003olv.4	Q9ULD4	OTTHUMG00000014589	ENST00000357641.6:c.1771C>T	6.37:g.36177597C>T		88.0	0.0	0		114.0	53.0	0.464912	NM_015695	A6ND56|A6NJE2|B7ZLN5|E7EX85|Q17RB6|Q5R3K8	Silent	SNP	ENST00000357641.6	37	CCDS34437.1																																																																																			C|0.987;T|0.013	0.013	strong		0.507	BRPF3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000040335.3	NM_015695	
GFI1B	8328	hgsc.bcm.edu	37	9	135864547	135864547	+	Missense_Mutation	SNP	G	G	A	rs62638686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:135864547G>A	ENST00000339463.3	+	9	1429	c.610G>A	c.(610-612)Gct>Act	p.A204T	GFI1B_ENST00000372124.1_Intron|GFI1B_ENST00000450530.1_Missense_Mutation_p.A204T|GFI1B_ENST00000372123.1_Intron|GFI1B_ENST00000534944.1_Intron|GFI1B_ENST00000372122.1_Missense_Mutation_p.A204T			Q5VTD9	GFI1B_HUMAN	growth factor independent 1B transcription repressor	204	Interaction with ARIH2.|Mediates interaction with GATA1.				cell proliferation (GO:0008283)|chromatin modification (GO:0016568)|multicellular organismal development (GO:0007275)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of histone H3-K9 methylation (GO:0051574)|regulation of erythrocyte differentiation (GO:0045646)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II transcription factor binding (GO:0001085)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)	21				OV - Ovarian serous cystadenocarcinoma(145;9.04e-07)|Epithelial(140;1.17e-05)		CTTCGGCCACGCTGTGAGCCT	0.662													G|||	75	0.014976	0.0537	0.0043	5008	,	,		19398	0.0		0.001	False		,,,				2504	0.0				p.A204T		Atlas-SNP	.											.	GFI1B	37	.	0			c.G610A						PASS	.	G	,THR/ALA	228,4178	134.5+/-170.7	6,216,1981	63.0	50.0	55.0		,610	2.5	0.3	9	dbSNP_129	55	3,8597	2.2+/-6.3	0,3,4297	yes	intron,missense	GFI1B	NM_001135031.1,NM_004188.4	,58	6,219,6278	AA,AG,GG		0.0349,5.1748,1.7761	,benign	,204/331	135864547	231,12775	2203	4300	6503	SO:0001583	missense	8328	exon5			GGCCACGCTGTGA	AF081946	CCDS6957.1, CCDS48049.1	9q34.13	2014-09-17	2007-10-04		ENSG00000165702	ENSG00000165702		"""Zinc fingers, C2H2-type"""	4238	protein-coding gene	gene with protein product		604383	"""growth factor independent 1B (potential regulator of CDKN1A, translocated in CML)"""			9878267	Standard	NM_001135031		Approved		uc004ccg.3	Q5VTD9	OTTHUMG00000020848	ENST00000339463.3:c.610G>A	9.37:g.135864547G>A	ENSP00000344782:p.Ala204Thr	112.0	0.0	0		121.0	41.0	0.338843	NM_004188	O95270|Q5VTD8|Q6FHZ2|Q6T888	Missense_Mutation	SNP	ENST00000339463.3	37	CCDS6957.1	38	0.0173992673992674	34	0.06910569105691057	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	G	13.62	2.290120	0.40494	0.051748	3.49E-4	ENSG00000165702	ENST00000339463;ENST00000450530;ENST00000372122	T;T;T	0.07800	3.16;3.16;3.16	5.42	2.45	0.29901	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.129163	0.51477	D	0.000098	T	0.00524	0.0017	N	0.21142	0.635	0.47245	D	0.99936	B	0.30727	0.292	B	0.31812	0.136	T	0.44877	-0.9299	10	0.72032	D	0.01	-23.2176	14.0232	0.64571	0.0:0.0:0.6057:0.3943	rs62638686	204	Q5VTD9	GFI1B_HUMAN	T	204	ENSP00000344782:A204T;ENSP00000409546:A204T;ENSP00000361195:A204T	ENSP00000344782:A204T	A	+	1	0	GFI1B	134854368	1.000000	0.71417	0.338000	0.25549	0.016000	0.09150	4.773000	0.62331	0.649000	0.30751	-0.122000	0.15005	GCT	A|0.017;G|0.983;T|0.000	0.017	strong		0.662	GFI1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393840.1	NM_004188	
B9D1	27077	hgsc.bcm.edu	37	17	19246667	19246667	+	Silent	SNP	A	A	G	rs7212549	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:19246667A>G	ENST00000261499.4	-	7	723	c.580T>C	c.(580-582)Ttg>Ctg	p.L194L	B9D1_ENST00000461069.2_Intron|B9D1_ENST00000395615.1_3'UTR|MIR1180_ENST00000408613.1_RNA|B9D1_ENST00000477478.2_3'UTR|B9D1_ENST00000575403.1_Intron	NM_015681.3	NP_056496.1	Q9UPM9	B9D1_HUMAN	B9 protein domain 1	194					camera-type eye development (GO:0043010)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|embryonic digit morphogenesis (GO:0042733)|in utero embryonic development (GO:0001701)|neuroepithelial cell differentiation (GO:0060563)|regulation of protein localization (GO:0032880)|smoothened signaling pathway (GO:0007224)|vasculature development (GO:0001944)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|membrane (GO:0016020)|TCTN-B9D complex (GO:0036038)	hedgehog receptor activity (GO:0008158)			large_intestine(3)|urinary_tract(1)	4	all_cancers(12;2.04e-05)|all_epithelial(12;0.000806)|Hepatocellular(7;0.00345)|Breast(13;0.143)					CTGGGCCCCAACACACCCTGT	0.587													A|||	153	0.0305511	0.0514	0.0029	5008	,	,		18629	0.0079		0.0	False		,,,				2504	0.0767				p.L194L		Atlas-SNP	.											.	B9D1	8	.	0			c.T580C						PASS	.	A		172,4234	113.8+/-151.8	1,170,2032	75.0	68.0	70.0		580	-2.2	0.0	17	dbSNP_116	70	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	B9D1	NM_015681.3		1,171,6331	GG,GA,AA		0.0116,3.9038,1.3302		194/205	19246667	173,12833	2203	4300	6503	SO:0001819	synonymous_variant	27077	exon7			GCCCCAACACACC	BC002944	CCDS11205.1, CCDS58528.1	17p11.2	2014-09-17			ENSG00000108641	ENSG00000108641			24123	protein-coding gene	gene with protein product	"""endothelial precursor protein B9"""	614144				21493627	Standard	NM_015681		Approved	B9, EPPB9, MKS9	uc010vyr.2	Q9UPM9	OTTHUMG00000059586	ENST00000261499.4:c.580T>C	17.37:g.19246667A>G		59.0	0.0	0		82.0	40.0	0.487805	NM_015681	Q9BU22	Silent	SNP	ENST00000261499.4	37	CCDS11205.1																																																																																			A|0.980;G|0.020	0.020	strong		0.587	B9D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132494.1	NM_015681	
KRTAP4-9	100132386	hgsc.bcm.edu	37	17	39261793	39261793	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39261793G>A	ENST00000391415.1	+	1	210	c.153G>A	c.(151-153)agG>agA	p.R51R		NM_001146041.1	NP_001139513.1	Q9BYQ8	KRA49_HUMAN	keratin associated protein 4-9	51	29 X 5 AA repeats of C-C-[RQVHIEK]- [SPTR]-[VSTQCRNP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|urinary_tract(3)	14						GCTGCTGCAGGCCCCAGTGCT	0.647																																					p.R51R		Atlas-SNP	.											.	KRTAP4-9	110	.	0			c.G153A						PASS	.						16.0	23.0	21.0					17																	39261793		686	1591	2277	SO:0001819	synonymous_variant	100132386	exon1			CTGCAGGCCCCAG	AJ406941	CCDS54124.1	17q21.2	2013-06-25			ENSG00000212722	ENSG00000212722		"""Keratin associated proteins"""	18910	protein-coding gene	gene with protein product							Standard	NM_001146041		Approved	KAP4.9	uc010wfp.2	Q9BYQ8	OTTHUMG00000133584	ENST00000391415.1:c.153G>A	17.37:g.39261793G>A		115.0	0.0	0		76.0	14.0	0.184211	NM_001146041		Silent	SNP	ENST00000391415.1	37	CCDS54124.1																																																																																			.	.	none		0.647	KRTAP4-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257688.1	NM_001146041	
ZNF157	7712	hgsc.bcm.edu	37	X	47272970	47272970	+	Missense_Mutation	SNP	A	A	G	rs61736398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:47272970A>G	ENST00000377073.3	+	4	1584	c.1498A>G	c.(1498-1500)Aca>Gca	p.T500A		NM_003446.3	NP_003437.2	P51786	ZN157_HUMAN	zinc finger protein 157	500					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	11						CTGGCGTTGTACAATGAAGAA	0.493													A|||	37	0.00980132	0.025	0.0043	3775	,	,		14772	0.0		0.001	False		,,,				2504	0.0				p.T500A		Atlas-SNP	.											.	ZNF157	46	.	0			c.A1498G						PASS	.	A	ALA/THR	191,3644		3,153,32,1476,539	71.0	60.0	64.0		1498	-2.0	0.0	X	dbSNP_129	64	5,6723		0,4,1,2424,1871	yes	missense	ZNF157	NM_003446.3	58	3,157,33,3900,2410	GG,GA,G,AA,A		0.0743,4.9804,1.8555	benign	500/507	47272970	196,10367	2203	4300	6503	SO:0001583	missense	7712	exon4			CGTTGTACAATGA	U28687	CCDS14278.1	Xp11.2	2013-01-08	2006-08-22		ENSG00000147117	ENSG00000147117		"""Zinc fingers, C2H2-type"", ""-"""	12942	protein-coding gene	gene with protein product		300024	"""zinc finger protein 157 (HZF22)"""			8586441	Standard	NM_003446		Approved	HZF22	uc004dhr.1	P51786	OTTHUMG00000021443	ENST00000377073.3:c.1498A>G	X.37:g.47272970A>G	ENSP00000366273:p.Thr500Ala	150.0	0.0	0		139.0	53.0	0.381295	NM_003446	Q96LE9	Missense_Mutation	SNP	ENST00000377073.3	37	CCDS14278.1	12	0.007233273056057866	4	0.008264462809917356	2	0.005555555555555556	0	0.0	1	0.0013192612137203166	A	2.829	-0.243005	0.05906	0.049804	7.43E-4	ENSG00000147117	ENST00000377073	T	0.06068	3.35	2.85	-1.99	0.07457	.	.	.	.	.	T	0.00637	0.0021	N	0.16790	0.44	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.28808	-1.0032	8	0.59425	D	0.04	.	9.8782	0.41216	0.2684:0.0:0.7316:0.0	rs61736398	500	P51786	ZN157_HUMAN	A	500	ENSP00000366273:T500A	ENSP00000366273:T500A	T	+	1	0	ZNF157	47157914	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.258000	0.08733	-0.564000	0.06070	-0.466000	0.05196	ACA	A|0.984;G|0.016	0.016	strong		0.493	ZNF157-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056415.1	NM_003446	
TRPM5	29850	hgsc.bcm.edu	37	11	2428434	2428434	+	Silent	SNP	G	G	A	rs369339407		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:2428434G>A	ENST00000155858.6	-	20	3041	c.3033C>T	c.(3031-3033)gcC>gcT	p.A1011A	AC124057.5_ENST00000433035.1_RNA|TRPM5_ENST00000533060.1_Silent_p.A1011A|TRPM5_ENST00000452833.1_Silent_p.A1013A|TRPM5_ENST00000528453.1_Silent_p.A1011A	NM_014555.3	NP_055370.1			transient receptor potential cation channel, subfamily M, member 5											breast(1)|central_nervous_system(1)|endometrium(4)|liver(1)|lung(8)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	23		Medulloblastoma(188;0.0049)|Breast(177;0.00586)|all_epithelial(84;0.0075)|Ovarian(85;0.0256)|all_neural(188;0.0311)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|LUSC - Lung squamous cell carcinoma(625;0.191)		TGAAGGGCGGGGCCAGGGCGG	0.637																																					p.A1011A	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.C3033T						PASS	.						35.0	34.0	34.0					11																	2428434		2198	4299	6497	SO:0001819	synonymous_variant	29850	exon20			GGGCGGGGCCAGG	AF177473	CCDS31340.1	11p15.5	2011-12-14			ENSG00000070985	ENSG00000070985		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	14323	protein-coding gene	gene with protein product		604600				10607831, 16382100	Standard	NM_014555		Approved	LTRPC5, MTR1	uc001lwm.4	Q9NZQ8	OTTHUMG00000009896	ENST00000155858.6:c.3033C>T	11.37:g.2428434G>A		101.0	0.0	0		123.0	70.0	0.569106	NM_014555		Silent	SNP	ENST00000155858.6	37	CCDS31340.1																																																																																			.	.	weak		0.637	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555	
OR2S2	56656	hgsc.bcm.edu	37	9	35957728	35957728	+	Missense_Mutation	SNP	C	C	T	rs2233563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35957728C>T	ENST00000341959.2	-	1	423	c.368G>A	c.(367-369)cGc>cAc	p.R123H		NM_019897.2	NP_063950.2	Q9NQN1	OR2S1_HUMAN	olfactory receptor, family 2, subfamily S, member 2	123			R -> H (in dbSNP:rs2233563).		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(2)|endometrium(2)|large_intestine(2)|lung(8)|ovary(1)|skin(1)|stomach(1)	17			LUSC - Lung squamous cell carcinoma(32;0.00613)|STAD - Stomach adenocarcinoma(86;0.194)			GGCCACATAGCGATCAAATGC	0.557													C|||	122	0.024361	0.0915	0.0014	5008	,	,		24963	0.0		0.0	False		,,,				2504	0.0				p.R123H	Pancreas(172;293 2036 17878 24427 30946)	Atlas-SNP	.											.	OR2S2	46	.	0			c.G368A						PASS	.	C	HIS/ARG	351,4055	182.9+/-210.6	14,323,1866	94.0	80.0	85.0		368	0.8	0.2	9	dbSNP_98	85	3,8597	3.0+/-9.4	0,3,4297	yes	missense	OR2S2	NM_019897.2	29	14,326,6163	TT,TC,CC		0.0349,7.9664,2.7218	possibly-damaging	123/320	35957728	354,12652	2203	4300	6503	SO:0001583	missense	56656	exon1			ACATAGCGATCAA	AL135841	CCDS6596.2	9p13.3	2012-08-09			ENSG00000122718	ENSG00000122718		"""GPCR / Class A : Olfactory receptors"""	8276	protein-coding gene	gene with protein product							Standard	NM_019897		Approved		uc011lpi.2	Q9NQN1	OTTHUMG00000019891	ENST00000341959.2:c.368G>A	9.37:g.35957728C>T	ENSP00000344040:p.Arg123His	103.0	0.0	0		100.0	57.0	0.57	NM_019897	Q2M3L0|Q6IF19|Q96R42	Missense_Mutation	SNP	ENST00000341959.2	37	CCDS6596.2	45	0.020604395604395604	45	0.09146341463414634	0	0.0	0	0.0	0	0.0	C	10.24	1.295956	0.23650	0.079664	3.49E-4	ENSG00000122718	ENST00000341959	T	0.77489	-1.1	4.32	0.775	0.18527	GPCR, rhodopsin-like superfamily (1);	0.388525	0.22144	N	0.064012	T	0.11110	0.0271	M	0.88310	2.945	0.25060	N	0.991077	P	0.47034	0.889	B	0.36504	0.226	T	0.48747	-0.9008	10	0.72032	D	0.01	.	8.045	0.30545	0.0:0.6808:0.0:0.3192	rs2233563;rs2233563	123	Q9NQN1	OR2S1_HUMAN	H	123	ENSP00000344040:R123H	ENSP00000344040:R123H	R	-	2	0	OR2S2	35947728	0.990000	0.36364	0.195000	0.23364	0.101000	0.19017	1.416000	0.34759	0.125000	0.18397	0.655000	0.94253	CGC	C|0.975;T|0.025	0.025	strong		0.557	OR2S2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052400.2	NM_019897	
OR14A16	284532	hgsc.bcm.edu	37	1	247978768	247978768	+	Silent	SNP	G	G	A	rs61740923	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:247978768G>A	ENST00000357627.1	-	1	263	c.264C>T	c.(262-264)aaC>aaT	p.N88N		NM_001001966.1	NP_001001966.1	Q8NHC5	O14AG_HUMAN	olfactory receptor, family 14, subfamily A, member 16	88						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(5)|kidney(1)|large_intestine(3)|lung(32)|skin(2)|stomach(1)	45						ATGAAATGGAGTTGTTGTGTA	0.448													g|||	78	0.0155751	0.053	0.0029	5008	,	,		19549	0.0		0.003	False		,,,				2504	0.0031				p.N88N	Ovarian(112;180 1586 15073 21914 33526)	Atlas-SNP	.											.	OR14A16	90	.	0			c.C264T						PASS	.	T		187,4219	120.4+/-158.0	7,173,2023	91.0	91.0	91.0		264	-0.9	0.0	1	dbSNP_129	91	19,8581	14.0+/-48.4	0,19,4281	no	coding-synonymous	OR14A16	NM_001001966.1		7,192,6304	AA,AG,GG		0.2209,4.2442,1.5839		88/310	247978768	206,12800	2203	4300	6503	SO:0001819	synonymous_variant	284532	exon1			AATGGAGTTGTTG	BK004366	CCDS31097.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000196772	ENSG00000196772		"""GPCR / Class A : Olfactory receptors"""	15022	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily AT, member 1"""	OR5AT1			Standard	NM_001001966		Approved		uc001idm.1	Q8NHC5	OTTHUMG00000040199	ENST00000357627.1:c.264C>T	1.37:g.247978768G>A		191.0	0.0	0		203.0	84.0	0.413793	NM_001001966	Q6IF96	Silent	SNP	ENST00000357627.1	37	CCDS31097.1																																																																																			G|0.986;A|0.014	0.014	strong		0.448	OR14A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096856.1	NM_001001966	
GDF5	8200	hgsc.bcm.edu	37	20	34022344	34022344	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34022344C>T	ENST00000374372.1	-	4	1372	c.869G>A	c.(868-870)gGc>gAc	p.G290D	GDF5OS_ENST00000374375.1_Missense_Mutation_p.P130S|GDF5_ENST00000374369.3_Missense_Mutation_p.G290D			P43026	GDF5_HUMAN	growth differentiation factor 5	290					cell-cell signaling (GO:0007267)|chondrocyte differentiation (GO:0002062)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix organization (GO:0030198)|forelimb morphogenesis (GO:0035136)|growth (GO:0040007)|hindlimb morphogenesis (GO:0035137)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mesenchymal cell apoptotic process (GO:2001054)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuron differentiation (GO:0045666)|regulation of multicellular organism growth (GO:0040014)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	growth factor activity (GO:0008083)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(3)|lung(9)|skin(3)	26	Lung NSC(9;0.00642)|all_lung(11;0.0094)		BRCA - Breast invasive adenocarcinoma(18;0.00663)			CACCTCCCAGCCAGATCCGTC	0.682																																					p.G290D		Atlas-SNP	.											.	GDF5	66	.	0			c.G869A						PASS	.						17.0	19.0	18.0					20																	34022344		2197	4298	6495	SO:0001583	missense	8200	exon2			TCCCAGCCAGATC	X80915	CCDS13254.1	20q11.2	2008-05-22	2007-04-12		ENSG00000125965	ENSG00000125965			4220	protein-coding gene	gene with protein product	"""cartilage-derived morphogenetic protein-1"""	601146				9288091, 9288098	Standard	NM_000557		Approved	CDMP1, BMP14	uc002xck.1	P43026	OTTHUMG00000032341	ENST00000374372.1:c.869G>A	20.37:g.34022344C>T	ENSP00000363492:p.Gly290Asp	97.0	0.0	0		88.0	4.0	0.0454545	NM_000557	E1P5Q2|Q96SB1	Missense_Mutation	SNP	ENST00000374372.1	37	CCDS13254.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.00|14.00	2.403881|2.403881	0.42613|0.42613	.|.	.|.	ENSG00000125965|ENSG00000204183	ENST00000374369;ENST00000374372|ENST00000374375	T;T|.	0.69806|.	-0.43;-0.43|.	4.56|4.56	4.56|4.56	0.56223|0.56223	Transforming growth factor-beta, N-terminal (1);|.	0.494665|.	0.18574|.	N|.	0.137222|.	T|T	0.41834|0.41834	0.1176|0.1176	L|L	0.47190|0.47190	1.495|1.495	0.29135|0.29135	N|N	0.87936|0.87936	B;P|.	0.34615|.	0.316;0.459|.	B;B|.	0.39465|.	0.3;0.245|.	T|T	0.46693|0.46693	-0.9173|-0.9173	10|6	0.17832|0.87932	T|D	0.49|0	.|.	5.4132|5.4132	0.16360|0.16360	0.0:0.7525:0.0:0.2475|0.0:0.7525:0.0:0.2475	.|.	290;290|.	F1T0J1;P43026|.	.;GDF5_HUMAN|.	D|S	290|130	ENSP00000363489:G290D;ENSP00000363492:G290D|.	ENSP00000363489:G290D|ENSP00000363495:P130S	G|P	-|+	2|1	0|0	GDF5|GDF5OS	33485758|33485758	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	2.633000|2.633000	0.46519|0.46519	2.353000|2.353000	0.79882|0.79882	0.491000|0.491000	0.48974|0.48974	GGC|CCA	.	.	none		0.682	GDF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078875.2		
PMS2	5395	hgsc.bcm.edu	37	7	6026787	6026787	+	Missense_Mutation	SNP	C	C	T	rs115052399	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:6026787C>T	ENST00000265849.7	-	11	1714	c.1609G>A	c.(1609-1611)Gag>Aag	p.E537K	PMS2_ENST00000406569.3_Missense_Mutation_p.E537K|PMS2_ENST00000441476.2_Missense_Mutation_p.E431K|PMS2_ENST00000382321.4_Intron|PMS2_ENST00000469652.1_Intron	NM_000535.5	NP_000526	P54278	PMS2_HUMAN	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)	537					ATP catabolic process (GO:0006200)|mismatch repair (GO:0006298)|response to drug (GO:0042493)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|single base insertion or deletion binding (GO:0032138)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(11)|lung(13)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Ovarian(82;0.0694)		UCEC - Uterine corpus endometrioid carcinoma (126;0.101)|OV - Ovarian serous cystadenocarcinoma(56;4.39e-15)		GGCGCTTTCTCCTGAGAGTCC	0.537			"""Mis, N, F"""			"""colorectal, endometrial, ovarian, medulloblastoma, glioma"""		Direct reversal of damage;Mismatch excision repair (MMR)	Turcot syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				C|||	28	0.00559105	0.0204	0.0014	5008	,	,		15948	0.0		0.0	False		,,,				2504	0.0				p.E537K		Atlas-SNP	.	yes	Rec		"""Hereditary non-polyposis colorectal cancer, Turcot syndrome"""	7	7p22	5395	PMS2 postmeiotic segregation increased 2 (S. cerevisiae)		E	.	PMS2	88	.	0			c.G1609A						PASS	.	C	LYS/GLU	55,4351		0,55,2148	78.0	85.0	83.0		1609	3.7	0.0	7	dbSNP_132	83	0,8596		0,0,4298	no	missense	PMS2	NM_000535.5	56	0,55,6446	TT,TC,CC		0.0,1.2483,0.423	benign	537/863	6026787	55,12947	2203	4298	6501	SO:0001583	missense	5395	exon11	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	CTTTCTCCTGAGA		CCDS5343.1	7p22.1	2014-09-17	2001-11-28		ENSG00000122512	ENSG00000122512			9122	protein-coding gene	gene with protein product		600259	"""postmeiotic segregation increased (S. cerevisiae) 2"""	PMSL2		8072530	Standard	NM_000535		Approved	H_DJ0042M02.9, HNPCC4	uc003spl.3	P54278	OTTHUMG00000023135	ENST00000265849.7:c.1609G>A	7.37:g.6026787C>T	ENSP00000265849:p.Glu537Lys	89.0	0.0	0		102.0	48.0	0.470588	NM_000535	B2R610|Q52LH6|Q5FBW9|Q5FBX1|Q5FBX2|Q75MR2	Missense_Mutation	SNP	ENST00000265849.7	37	CCDS5343.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	c	11.03	1.519693	0.27211	0.012483	0.0	ENSG00000122512	ENST00000265849;ENST00000382322;ENST00000441476;ENST00000406569	T;T;D	0.87179	1.1;1.1;-2.22	5.85	3.72	0.42706	.	0.843000	0.10493	N	0.668254	T	0.67449	0.2894	L	0.38838	1.175	0.09310	N	0.999999	B;B;B	0.21071	0.023;0.001;0.051	B;B;B	0.19391	0.011;0.003;0.025	T	0.58086	-0.7698	10	0.09338	T	0.73	-16.5088	10.2582	0.43410	0.0:0.7388:0.1388:0.1224	.	537;537;431	P54278-3;P54278;C9J167	.;PMS2_HUMAN;.	K	537;490;431;537	ENSP00000265849:E537K;ENSP00000392843:E431K;ENSP00000384308:E537K	ENSP00000265849:E537K	E	-	1	0	PMS2	5993313	0.001000	0.12720	0.016000	0.15963	0.016000	0.09150	0.250000	0.18235	1.474000	0.48178	0.650000	0.86243	GAG	C|0.995;T|0.005	0.005	strong		0.537	PMS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207353.3	NM_000535	
PRR27	401137	hgsc.bcm.edu	37	4	71024552	71024552	+	Missense_Mutation	SNP	C	C	G	rs143985138	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:71024552C>G	ENST00000344526.5	+	3	772	c.583C>G	c.(583-585)Cca>Gca	p.P195A	C4orf40_ENST00000502294.1_Missense_Mutation_p.P195A	NM_214711.3	NP_999876.2	Q6MZM9	PRR27_HUMAN		195	Ala/Pro-rich.					extracellular vesicular exosome (GO:0070062)				breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						GGAACCTTCACCAGCTGAGCC	0.557													C|||	48	0.00958466	0.0348	0.0029	5008	,	,		16492	0.0		0.0	False		,,,				2504	0.0				p.P195A		Atlas-SNP	.											.	C4orf40	19	.	0			c.C583G						PASS	.	C	ALA/PRO	172,4234		1,170,2032	57.0	52.0	54.0		583	-7.9	0.0	4	dbSNP_134	54	1,8599		0,1,4299	yes	missense	C4orf40	NM_214711.3	27	1,171,6331	GG,GC,CC		0.0116,3.9038,1.3302	benign	195/220	71024552	173,12833	2203	4300	6503	SO:0001583	missense	401137	exon3			CCTTCACCAGCTG																												ENST00000344526.5:c.583C>G	4.37:g.71024552C>G	ENSP00000343172:p.Pro195Ala	325.0	0.0	0		303.0	136.0	0.448845	NM_214711	A8MXP0|Q6MZR6	Missense_Mutation	SNP	ENST00000344526.5	37	CCDS3535.1	11	0.005036630036630037	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	0	0.0	C	5.440	0.266257	0.10294	0.039038	1.16E-4	ENSG00000187533	ENST00000502294;ENST00000344526	T;T	0.28454	1.61;1.61	3.97	-7.94	0.01152	.	.	.	.	.	T	0.02047	0.0064	N	0.14661	0.345	0.09310	N	1	B	0.14438	0.01	B	0.12837	0.008	T	0.26538	-1.0100	9	0.02654	T	1	5.212	3.7914	0.08722	0.2107:0.3878:0.3086:0.0929	.	195	Q6MZM9	CD040_HUMAN	A	195	ENSP00000426249:P195A;ENSP00000343172:P195A	ENSP00000343172:P195A	P	+	1	0	C4orf40	71059141	0.001000	0.12720	0.000000	0.03702	0.012000	0.07955	0.133000	0.15912	-1.914000	0.01078	0.411000	0.27672	CCA	C|0.987;G|0.013	0.013	strong		0.557	C4orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251558.1		
PARK2	5071	hgsc.bcm.edu	37	6	162475167	162475167	+	Missense_Mutation	SNP	T	T	G	rs9456735	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:162475167T>G	ENST00000366898.1	-	5	676	c.574A>C	c.(574-576)Atg>Ctg	p.M192L	PARK2_ENST00000366892.1_Missense_Mutation_p.M192L|PARK2_ENST00000366894.1_Start_Codon_SNP_p.M1L|PARK2_ENST00000366897.1_Intron|PARK2_ENST00000338468.3_Start_Codon_SNP_p.M1L|PARK2_ENST00000366896.1_Intron	NM_004562.2	NP_004553.2	O60260	PRKN2_HUMAN	parkin RBR E3 ubiquitin protein ligase	192			M -> L (in PARK2; unknown pathological significance; dbSNP:rs9456735). {ECO:0000269|PubMed:11971093}.|M -> V (in PARK2; unknown pathological significance; dbSNP:rs9456735). {ECO:0000269|PubMed:12629236}.		adult locomotory behavior (GO:0008344)|aggresome assembly (GO:0070842)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|cellular response to dopamine (GO:1903351)|cellular response to manganese ion (GO:0071287)|cellular response to toxic substance (GO:0097237)|cellular response to unfolded protein (GO:0034620)|central nervous system development (GO:0007417)|dopamine metabolic process (GO:0042417)|dopamine uptake involved in synaptic transmission (GO:0051583)|learning (GO:0007612)|mitochondrion degradation (GO:0000422)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell death (GO:0060548)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|negative regulation of glucokinase activity (GO:0033132)|negative regulation of insulin secretion (GO:0046676)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway (GO:1903377)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|norepinephrine metabolic process (GO:0042415)|positive regulation of DNA binding (GO:0043388)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial fusion (GO:0010636)|positive regulation of proteasomal protein catabolic process (GO:1901800)|positive regulation of protein linear polyubiquitination (GO:1902530)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor-mediated signaling pathway (GO:1903265)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|protein K27-linked ubiquitination (GO:0044314)|protein K29-linked ubiquitination (GO:0035519)|protein K48-linked ubiquitination (GO:0070936)|protein K6-linked ubiquitination (GO:0085020)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of autophagy (GO:0010506)|regulation of dopamine secretion (GO:0014059)|regulation of glucose metabolic process (GO:0010906)|regulation of lipid transport (GO:0032368)|regulation of mitochondrion degradation (GO:1903146)|regulation of mitochondrion organization (GO:0010821)|regulation of neurotransmitter secretion (GO:0046928)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to endoplasmic reticulum stress (GO:0034976)|startle response (GO:0001964)|synaptic transmission, glutamatergic (GO:0035249)|transcription, DNA-templated (GO:0006351)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Lewy body (GO:0097413)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|Parkin-FBXW7-Cul1 ubiquitin ligase complex (GO:1990452)|perinuclear region of cytoplasm (GO:0048471)|ubiquitin ligase complex (GO:0000151)	chaperone binding (GO:0051087)|cullin family protein binding (GO:0097602)|F-box domain binding (GO:1990444)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|Hsp70 protein binding (GO:0030544)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|ligase activity (GO:0016874)|PDZ domain binding (GO:0030165)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)|ubiquitin binding (GO:0043130)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease binding (GO:1990381)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(21)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	39		all_cancers(1;8.13e-65)|all_epithelial(1;5.77e-64)|Colorectal(1;9.65e-15)|all_lung(1;1.66e-13)|Lung NSC(1;7.54e-11)|Melanoma(1;1.75e-09)|Breast(66;7.81e-05)|Ovarian(120;0.000981)|Prostate(117;0.0288)|Esophageal squamous(34;0.102)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0663)|all cancers(1;1.9e-63)|Epithelial(1;1.5e-59)|Colorectal(1;2.16e-23)|OV - Ovarian serous cystadenocarcinoma(65;3.53e-20)|COAD - Colon adenocarcinoma(1;2.11e-15)|STAD - Stomach adenocarcinoma(1;4.64e-07)|BRCA - Breast invasive adenocarcinoma(81;1.49e-06)|READ - Rectum adenocarcinoma(1;2.95e-06)|GBM - Glioblastoma multiforme(2;7.23e-06)|Lung(1;0.00163)|KIRC - Kidney renal clear cell carcinoma(4;0.00371)|LUSC - Lung squamous cell carcinoma(1;0.00442)|Kidney(4;0.0046)		TCACCACTCATCCGGTTTGGA	0.398													T|||	95	0.0189696	0.0681	0.0029	5008	,	,		18248	0.0		0.003	False		,,,				2504	0.0				p.M192L		Atlas-SNP	.											.	PARK2	96	.	0			c.A574C	GRCh37	CM024241|CM030925	PARK2	M	rs9456735	PASS	.	T	LEU/MET,,	252,4154	146.1+/-180.8	8,236,1959	141.0	123.0	129.0		574,,	5.4	1.0	6	dbSNP_119	129	1,8599	1.2+/-3.3	0,1,4299	yes	missense,intron,intron	PARK2	NM_004562.2,NM_013987.2,NM_013988.2	15,,	8,237,6258	GG,GT,TT		0.0116,5.7195,1.9453	benign,,	192/466,,	162475167	253,12753	2203	4300	6503	SO:0001583	missense	5071	exon5			CACTCATCCGGTT		CCDS5281.1, CCDS5282.1, CCDS5283.1	6q25.2-q27	2013-10-03	2013-10-03		ENSG00000185345	ENSG00000185345		"""Parkinson disease"""	8607	protein-coding gene	gene with protein product	"""E3 ubiquitin ligase"""	602544	"""Parkinson disease (autosomal recessive, juvenile) 2, parkin"", ""parkinson protein 2, E3 ubiquitin protein ligase (parkin)"""			9560156, 9570960	Standard	NM_004562		Approved	PDJ, AR-JP, parkin	uc003qtx.4	O60260	OTTHUMG00000015970	ENST00000366898.1:c.574A>C	6.37:g.162475167T>G	ENSP00000355865:p.Met192Leu	98.0	0.0	0		97.0	53.0	0.546392	NM_004562	A3FG77|A8K975|D3JZW7|D3K2X0|Q5TFV8|Q5VVX4|Q6Q2I6|Q8NI41|Q8NI43|Q8NI44|Q8WW07	Missense_Mutation	SNP	ENST00000366898.1	37	CCDS5281.1	43	0.019688644688644688	40	0.08130081300813008	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	T	14.04	2.416234	0.42918	0.057195	1.16E-4	ENSG00000185345	ENST00000366898;ENST00000366894;ENST00000338468;ENST00000392134;ENST00000366892;ENST00000366895	D;D;D;D	0.90385	-2.58;-2.33;-2.33;-2.66	5.39	5.39	0.77823	.	0.199863	0.45867	D	0.000329	T	0.79364	0.4433	L	0.41236	1.265	0.29921	N	0.822717	B;B;B	0.17268	0.021;0.001;0.016	B;B;B	0.17722	0.019;0.001;0.003	T	0.74583	-0.3617	10	0.54805	T	0.06	.	11.8193	0.52228	0.0:0.0:0.0:1.0	rs9456735;rs52822498;rs9456735	192;192;1	O60260-5;O60260;Q8NI42	.;PRKN2_HUMAN;.	L	192;1;1;1;192;113	ENSP00000355865:M192L;ENSP00000355860:M1L;ENSP00000343589:M1L;ENSP00000355858:M192L	ENSP00000343589:M1L	M	-	1	0	PARK2	162395157	0.984000	0.35163	0.997000	0.53966	0.944000	0.59088	2.591000	0.46163	2.043000	0.60533	0.533000	0.62120	ATG	T|0.977;G|0.023	0.023	strong		0.398	PARK2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042995.1		
REL	5966	hgsc.bcm.edu	37	2	61148988	61148988	+	Missense_Mutation	SNP	C	C	G	rs34661029	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:61148988C>G	ENST00000295025.8	+	11	1498	c.1178C>G	c.(1177-1179)cCc>cGc	p.P393R	REL_ENST00000394479.3_Missense_Mutation_p.P361R	NM_002908.2	NP_002899.1	Q04864	REL_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog	393					cytokine production (GO:0001816)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of neuron death (GO:1901215)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|large_intestine(5)|lung(3)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	16	all_hematologic(2;0.0797)	Ovarian(717;0.0728)	LUSC - Lung squamous cell carcinoma(5;6.2e-08)|Lung(5;1.65e-06)|Epithelial(17;0.064)|all cancers(80;0.221)			TCACCTGGGCCCATCTCAAGT	0.512			A		Hodgkin Lymphoma								C|||	34	0.00678914	0.025	0.0014	5008	,	,		16212	0.0		0.0	False		,,,				2504	0.0				p.P393R		Atlas-SNP	.		Dom	yes		2	2p13-p12	5966	v-rel reticuloendotheliosis viral oncogene homolog (avian)		L	.	REL	48	.	0			c.C1178G						PASS	.	C	ARG/PRO	93,4313	74.1+/-112.3	0,93,2110	100.0	98.0	99.0		1178	3.6	0.9	2	dbSNP_126	99	1,8599	1.2+/-3.3	0,1,4299	yes	missense	REL	NM_002908.2	103	0,94,6409	GG,GC,CC		0.0116,2.1108,0.7227	benign	393/620	61148988	94,12912	2203	4300	6503	SO:0001583	missense	5966	exon11			CTGGGCCCATCTC	M11595	CCDS1864.1, CCDS74515.1	2p13-p12	2013-07-09	2013-07-09		ENSG00000162924	ENSG00000162924			9954	protein-coding gene	gene with protein product		164910				1577270	Standard	XM_005264470		Approved	I-Rel, c-Rel	uc002sam.1	Q04864	OTTHUMG00000129418	ENST00000295025.8:c.1178C>G	2.37:g.61148988C>G	ENSP00000295025:p.Pro393Arg	105.0	0.0	0		132.0	132.0	1	NM_002908	Q17RU2|Q2PNZ7|Q6LDY0	Missense_Mutation	SNP	ENST00000295025.8	37	CCDS1864.1	7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	C	10.88	1.476325	0.26511	0.021108	1.16E-4	ENSG00000162924	ENST00000295025;ENST00000394479	T;T	0.42131	0.98;0.98	5.54	3.63	0.41609	.	0.859295	0.10279	N	0.693783	T	0.12135	0.0295	N	0.08118	0	0.09310	N	1	B;B	0.28128	0.201;0.181	B;B	0.20577	0.014;0.03	T	0.09314	-1.0680	10	0.52906	T	0.07	-22.6802	9.6826	0.40078	0.159:0.6877:0.1533:0.0	rs34661029	361;393	Q17RU2;Q04864	.;REL_HUMAN	R	393;361	ENSP00000295025:P393R;ENSP00000377989:P361R	ENSP00000295025:P393R	P	+	2	0	REL	61002492	0.771000	0.28555	0.926000	0.36857	0.866000	0.49608	1.214000	0.32419	1.345000	0.45676	-0.158000	0.13435	CCC	C|0.993;G|0.007	0.007	strong		0.512	REL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251576.3	NM_002908	
LMNTD1	160492	hgsc.bcm.edu	37	12	25672955	25672955	+	Missense_Mutation	SNP	C	C	T	rs35450203	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:25672955C>T	ENST00000282881.6	-	6	939	c.790G>A	c.(790-792)Gct>Act	p.A264T	IFLTD1_ENST00000539744.1_Missense_Mutation_p.A167T|IFLTD1_ENST00000458174.2_Missense_Mutation_p.A285T|IFLTD1_ENST00000413632.2_Missense_Mutation_p.A245T|IFLTD1_ENST00000445693.1_Missense_Mutation_p.A201T	NM_152590.3	NP_689803.2	Q8N9Z9	LMTD1_HUMAN		264			A -> T (in dbSNP:rs35450203).		cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22	all_lung(3;2.75e-22)|Lung NSC(3;1.77e-21)|all_hematologic(7;0.00656)|Colorectal(261;0.0847)					TCAACGTCAGCATCTAATTTT	0.383													T|||	88	0.0175719	0.0628	0.0072	5008	,	,		13163	0.0		0.0	False		,,,				2504	0.0				p.A285T		Atlas-SNP	.											.	IFLTD1	121	.	0			c.G853A						PASS	.	T	THR/ALA,THR/ALA,THR/ALA,THR/ALA	252,4154	803.0+/-415.7	5,242,1956	123.0	107.0	112.0		601,853,733,790	2.6	1.0	12	dbSNP_126	112	1,8599	818.9+/-406.8	0,1,4299	yes	missense,missense,missense,missense	IFLTD1	NM_001145727.1,NM_001145728.1,NM_001145729.1,NM_152590.2	58,58,58,58	5,243,6255	TT,TC,CC		0.0116,5.7195,1.9453	benign,benign,benign,benign	201/326,285/410,245/370,264/389	25672955	253,12753	2203	4300	6503	SO:0001583	missense	160492	exon7			CGTCAGCATCTAA																												ENST00000282881.6:c.790G>A	12.37:g.25672955C>T	ENSP00000282881:p.Ala264Thr	158.0	0.0	0		159.0	89.0	0.559748	NM_001145728	B4DL27|B4DY70|Q8IY38	Missense_Mutation	SNP	ENST00000282881.6	37	CCDS8704.1	20|20	0.009157509157509158|0.009157509157509158	17|17	0.034552845528455285|0.034552845528455285	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	T|T	2.163|2.163	-0.391668|-0.391668	0.04932|0.04932	0.057195|0.057195	1.16E-4|1.16E-4	ENSG00000152936|ENSG00000152936	ENST00000282881;ENST00000539744;ENST00000458174;ENST00000445693;ENST00000413632;ENST00000545543|ENST00000543629	T;T;T;T;T;T|.	0.12569|.	2.92;2.9;2.94;2.89;2.67;2.69|.	5.05|5.05	2.61|2.61	0.31194|0.31194	.|.	.|.	.|.	.|.	.|.	T|T	0.00815|0.00815	0.0027|0.0027	N|N	0.01048|0.01048	-1.04|-1.04	0.19300|0.19300	N|N	0.999978|0.999978	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	0.32188|0.32188	-0.9916|-0.9916	9|5	0.02654|.	T|.	1|.	-2.2559|-2.2559	4.0577|4.0577	0.09824|0.09824	0.3165:0.0877:0.0:0.5958|0.3165:0.0877:0.0:0.5958	rs35450203|rs35450203	201;285;245;264|.	Q8N9Z9-3;Q8N9Z9-5;Q8N9Z9-4;Q8N9Z9|.	.;.;.;ILFT1_HUMAN|.	T|Y	264;167;285;201;245;94|38	ENSP00000282881:A264T;ENSP00000443132:A167T;ENSP00000407353:A285T;ENSP00000407043:A201T;ENSP00000393150:A245T;ENSP00000443596:A94T|.	ENSP00000282881:A264T|.	A|C	-|-	1|2	0|0	IFLTD1|IFLTD1	25564222|25564222	0.160000|0.160000	0.22878|0.22878	0.953000|0.953000	0.39169|0.39169	0.671000|0.671000	0.39405|0.39405	0.141000|0.141000	0.16076|0.16076	0.050000|0.050000	0.15949|0.15949	-0.352000|-0.352000	0.07741|0.07741	GCT|TGC	C|0.980;T|0.020	0.020	strong		0.383	IFLTD1-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402279.1		
IGSF9B	22997	hgsc.bcm.edu	37	11	133789790	133789790	+	Missense_Mutation	SNP	G	G	C	rs200373794	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:133789790G>C	ENST00000321016.8	-	18	4060	c.3830C>G	c.(3829-3831)aCt>aGt	p.T1277S	IGSF9B_ENST00000533871.2_Missense_Mutation_p.T1277S			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	1277	Pro-rich.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		GGTGGCCAGAGTGGTGAAGCC	0.677													G|||	20	0.00399361	0.0151	0.0	5008	,	,		12387	0.0		0.0	False		,,,				2504	0.0				p.T1277S		Atlas-SNP	.											.	IGSF9B	290	.	0			c.C3830G						PASS	.	G	SER/THR	55,3777		1,53,1862	24.0	32.0	30.0		3830	4.8	0.9	11	dbSNP_132	30	1,8223		0,1,4111	yes	missense	IGSF9B	NM_014987.1	58	1,54,5973	CC,CG,GG		0.0122,1.4353,0.4645	benign	1277/1350	133789790	56,12000	1916	4112	6028	SO:0001583	missense	22997	exon18			GCCAGAGTGGTGA	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.3830C>G	11.37:g.133789790G>C	ENSP00000317980:p.Thr1277Ser	92.0	0.0	0		91.0	46.0	0.505495	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	37		.	.	.	.	.	.	.	.	.	.	G	12.95	2.091421	0.36952	0.014353	1.22E-4	ENSG00000080854	ENST00000321016;ENST00000533871	T;T	0.65916	0.15;-0.18	4.76	4.76	0.60689	.	0.000000	0.44688	D	0.000431	T	0.37320	0.0999	N	0.12182	0.205	0.38308	D	0.943176	B	0.06786	0.001	B	0.04013	0.001	T	0.35301	-0.9794	10	0.28530	T	0.3	.	17.5598	0.87902	0.0:0.0:1.0:0.0	.	1277	Q9UPX0	TUTLB_HUMAN	S	1277;1119	ENSP00000317980:T1277S;ENSP00000436552:T1119S	ENSP00000317980:T1277S	T	-	2	0	IGSF9B	133295000	1.000000	0.71417	0.926000	0.36857	0.814000	0.46013	8.633000	0.90999	2.484000	0.83849	0.555000	0.69702	ACT	.	.	weak		0.677	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	
ZNF280B	140883	hgsc.bcm.edu	37	22	22842484	22842484	+	Missense_Mutation	SNP	C	C	T	rs57235089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:22842484C>T	ENST00000406426.1	-	4	1982	c.1240G>A	c.(1240-1242)Gtc>Atc	p.V414I	ZNF280B_ENST00000360412.2_Missense_Mutation_p.V414I			Q86YH2	Z280B_HUMAN	zinc finger protein 280B	414					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(9)|ovary(2)	22	all_hematologic(9;0.0135)|Acute lymphoblastic leukemia(84;0.17)	all_hematologic(6;1.74e-30)|Acute lymphoblastic leukemia(6;7.75e-22)		READ - Rectum adenocarcinoma(21;0.145)		TCAGCAAAGACCGACGATCTA	0.403													C|||	151	0.0301518	0.0877	0.0072	5008	,	,		19574	0.0		0.0099	False		,,,				2504	0.0204				p.V414I		Atlas-SNP	.											.	ZNF280B	67	.	0			c.G1240A						PASS	.	C	ILE/VAL	339,4067	176.9+/-206.0	15,309,1879	131.0	122.0	125.0		1240	-1.6	0.0	22	dbSNP_129	125	106,8494	56.0+/-117.1	2,102,4196	no	missense	ZNF280B	NM_080764.2	29	17,411,6075	TT,TC,CC		1.2326,7.6941,3.4215	benign	414/544	22842484	445,12561	2203	4300	6503	SO:0001583	missense	140883	exon4			CAAAGACCGACGA	AK097608	CCDS13799.1	22q11.2	2007-09-20	2007-09-20	2007-09-20	ENSG00000198477	ENSG00000275004			23022	protein-coding gene	gene with protein product			"""zinc finger protein 279"", ""suppressor of hairy wing homolog 2 (Drosophila)"""	ZNF279, SUHW2		9074928	Standard	NM_080764		Approved	5'OY11.1, ZNF632	uc002zwc.1	Q86YH2	OTTHUMG00000151066	ENST00000406426.1:c.1240G>A	22.37:g.22842484C>T	ENSP00000385998:p.Val414Ile	286.0	0.0	0		266.0	110.0	0.413534	NM_080764		Missense_Mutation	SNP	ENST00000406426.1	37	CCDS13799.1	38	0.0173992673992674	26	0.052845528455284556	3	0.008287292817679558	0	0.0	9	0.011873350923482849	C	0.005	-2.182245	0.00308	0.076941	0.012326	ENSG00000198477	ENST00000406426;ENST00000360412	T;T	0.28069	1.63;1.63	4.32	-1.63	0.08345	Zinc finger, C2H2-like (1);	.	.	.	.	T	0.00695	0.0023	N	0.25890	0.77	0.09310	N	1	B	0.21905	0.062	B	0.18871	0.023	T	0.24764	-1.0151	9	0.06625	T	0.88	5.8306	4.7941	0.13263	0.4233:0.4085:0.0:0.1682	rs57235089;rs61910698	414	Q86YH2	Z280B_HUMAN	I	414	ENSP00000385998:V414I;ENSP00000353586:V414I	ENSP00000353586:V414I	V	-	1	0	ZNF280B	21172484	0.945000	0.32115	0.000000	0.03702	0.099000	0.18886	2.087000	0.41653	-0.168000	0.10853	-0.152000	0.13540	GTC	C|0.973;T|0.027	0.027	strong		0.403	ZNF280B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321170.2	NM_080764	
FLG2	388698	hgsc.bcm.edu	37	1	152325456	152325456	+	Silent	SNP	G	G	A	rs73007787	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152325456G>A	ENST00000388718.5	-	3	4878	c.4806C>T	c.(4804-4806)gcC>gcT	p.A1602A	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1602					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)			GTTGAGATCCGGCTTGGCCGT	0.512													g|||	341	0.0680911	0.2421	0.0231	5008	,	,		26525	0.0		0.005	False		,,,				2504	0.0				p.A1602A		Atlas-SNP	.											.	FLG2	431	.	0			c.C4806T						PASS	.	G		841,3565	331.8+/-302.1	70,701,1432	353.0	305.0	321.0		4806	-7.5	0.0	1	dbSNP_130	321	25,8575	17.9+/-57.8	0,25,4275	no	coding-synonymous	FLG2	NM_001014342.2		70,726,5707	AA,AG,GG		0.2907,19.0876,6.6585		1602/2392	152325456	866,12140	2203	4300	6503	SO:0001819	synonymous_variant	388698	exon3			AGATCCGGCTTGG	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.4806C>T	1.37:g.152325456G>A		404.0	1.0	0.00247525		399.0	226.0	0.566416	NM_001014342	Q9H4U1	Silent	SNP	ENST00000388718.5	37	CCDS30861.1																																																																																			G|0.940;A|0.060	0.060	strong		0.512	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
KMT2C	58508	hgsc.bcm.edu	37	7	151970811	151970811	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:151970811T>C	ENST00000262189.6	-	7	1209	c.991A>G	c.(991-993)Att>Gtt	p.I331V	KMT2C_ENST00000355193.2_Missense_Mutation_p.I331V	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	331					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										GCTTGGTCAATGTGTTCTGGA	0.393																																					p.I331V		Atlas-SNP	.											.	MLL3	1564	.	0			c.A991G						PASS	.																																			SO:0001583	missense	58508	exon7			GGTCAATGTGTTC	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.991A>G	7.37:g.151970811T>C	ENSP00000262189:p.Ile331Val	725.0	0.0	0		801.0	39.0	0.0486891	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	T	14.18	2.458970	0.43634	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.83992	-1.79;-1.79	4.78	4.78	0.61160	Zinc finger, PHD-type (1);Protein kinase C-like, phorbol ester/diacylglycerol binding (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.44097	U	0.000493	T	0.72993	0.3530	L	0.34521	1.04	0.80722	D	1	P	0.39094	0.659	B	0.34873	0.191	T	0.71537	-0.4563	10	0.21014	T	0.42	.	14.599	0.68427	0.0:0.0:0.0:1.0	.	331	Q8NEZ4	MLL3_HUMAN	V	331	ENSP00000262189:I331V;ENSP00000347325:I331V	ENSP00000262189:I331V	I	-	1	0	MLL3	151601744	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.185000	0.58330	1.924000	0.55735	0.477000	0.44152	ATT	.	.	none		0.393	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
PITRM1	10531	hgsc.bcm.edu	37	10	3214939	3214939	+	Missense_Mutation	SNP	C	C	A	rs199766052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:3214939C>A	ENST00000224949.4	-	1	60	c.26G>T	c.(25-27)gGc>gTc	p.G9V	PITRM1_ENST00000451104.2_Silent_p.G11G|PITRM1_ENST00000380989.2_Missense_Mutation_p.G9V			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	9					positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						CACACACAGGCCCTGCCGCCC	0.751													C|||	58	0.0115815	0.0416	0.0029	5008	,	,		8716	0.0		0.0	False		,,,				2504	0.001				p.G9V		Atlas-SNP	.											.	PITRM1	109	.	0			c.G26T						PASS	.	C	VAL/GLY,,VAL/GLY	125,3595		1,123,1736	4.0	7.0	6.0		26,33,26	-4.6	0.0	10		6	3,7519		0,3,3758	no	missense,coding-synonymous,missense	PITRM1	NM_001242307.1,NM_001242309.1,NM_014889.3	109,,109	1,126,5494	AA,AC,CC		0.0399,3.3602,1.1386	benign,,benign	9/1039,11/940,9/1038	3214939	128,11114	1860	3761	5621	SO:0001583	missense	10531	exon1			CACAGGCCCTGCC	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.26G>T	10.37:g.3214939C>A	ENSP00000224949:p.Gly9Val	22.0	0.0	0		58.0	29.0	0.5	NM_014889	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	37	CCDS59208.1	.	.	.	.	.	.	.	.	.	.	C	11.07	1.530296	0.27387	0.033602	3.99E-4	ENSG00000107959	ENST00000224949;ENST00000380989	T;T	0.03920	3.76;3.76	3.31	-4.59	0.03400	.	2.102200	0.01907	N	0.039579	T	0.01092	0.0036	.	.	.	0.09310	N	0.999998	B;B	0.18968	0.032;0.019	B;B	0.19391	0.025;0.011	T	0.42699	-0.9436	9	0.30078	T	0.28	.	7.0117	0.24865	0.2341:0.5702:0.1957:0.0	.	9;9	Q5JRX3-2;Q5JRX3	.;PREP_HUMAN	V	9	ENSP00000224949:G9V;ENSP00000370377:G9V	ENSP00000224949:G9V	G	-	2	0	PITRM1	3204939	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.319000	0.08039	-0.576000	0.05974	0.313000	0.20887	GGC	.	.	weak		0.751	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
NBPF7	343505	hgsc.bcm.edu	37	1	120386922	120386922	+	IGR	SNP	A	A	T	rs12068863	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:120386922A>T								REG4 (32639 upstream) : ADAM30 (49233 downstream)																							TATAGATCTTACTGTATTTGT	0.428											OREG0013730	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	a|||	371	0.0740815	0.27	0.0202	5008	,	,		20192	0.0		0.0	False		,,,				2504	0.0				.		Atlas-SNP	.											.	NBPF7	46	.	0			c.235+2T>A						PASS	.	A		829,3303		91,647,1328	78.0	86.0	83.0			0.7	0.0	1	dbSNP_120	83	22,8414		0,22,4196	no	splice-5	NBPF7	NM_001047980.1		91,669,5524	TT,TA,AA		0.2608,20.0629,6.7712			120386922	851,11717	2066	4218	6284	SO:0001628	intergenic_variant	343505	exon2			GATCTTACTGTAT																													1.37:g.120386922A>T		83.0	0.0	0	1503	109.0	40.0	0.366972	NM_001047980		Splice_Site	SNP		37																																																																																				A|0.957;T|0.043	0.043	strong	0	0.428								
TET3	200424	hgsc.bcm.edu	37	2	74275174	74275174	+	Silent	SNP	C	C	T	rs73951129	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74275174C>T	ENST00000409262.3	+	1	1725	c.1725C>T	c.(1723-1725)ctC>ctT	p.L575L		NM_144993.1	NP_659430.1	O43151	TET3_HUMAN	tet methylcytosine dioxygenase 3	575					DNA demethylation (GO:0080111)|DNA demethylation of male pronucleus (GO:0044727)|histone H3-K4 trimethylation (GO:0080182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methylcytosine dioxygenase activity (GO:0070579)			NS(1)|breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TGGAAGAGCTCATCCGGCAGT	0.602													C|||	79	0.0157748	0.0582	0.0	5008	,	,		17465	0.001		0.001	False		,,,				2504	0.0				p.L575L		Atlas-SNP	.											.	TET3	101	.	0			c.C1725T						PASS	.	C		157,3687		4,149,1769	41.0	45.0	43.0		1725	4.5	1.0	2	dbSNP_130	43	1,8255		0,1,4127	no	coding-synonymous	TET3	NM_144993.1		4,150,5896	TT,TC,CC		0.0121,4.0843,1.3058		575/1661	74275174	158,11942	1922	4128	6050	SO:0001819	synonymous_variant	200424	exon1			AGAGCTCATCCGG		CCDS46339.1, CCDS46339.2	2p13.1	2011-09-30	2011-09-30		ENSG00000187605	ENSG00000187605			28313	protein-coding gene	gene with protein product		613555	"""tet oncogene family member 3"""			9455477	Standard	XM_005264187		Approved	MGC22014, hCG_40738	uc031roi.1	O43151	OTTHUMG00000152823	ENST00000409262.3:c.1725C>T	2.37:g.74275174C>T		121.0	0.0	0		121.0	65.0	0.53719	NM_144993	A6NEI3|Q86Z24|Q8TBM9	Silent	SNP	ENST00000409262.3	37	CCDS46339.1																																																																																			C|0.984;T|0.016	0.016	strong		0.602	TET3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328141.4		
RELA	5970	hgsc.bcm.edu	37	11	65422374	65422374	+	Silent	SNP	C	C	T	rs7116571	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:65422374C>T	ENST00000406246.3	-	11	1392	c.1131G>A	c.(1129-1131)tcG>tcA	p.S377S	RELA_ENST00000525693.1_3'UTR|RELA_ENST00000308639.9_Silent_p.S374S	NM_001243984.1|NM_001243985.1|NM_021975.3	NP_001230913.1|NP_001230914.1|NP_068810.3	Q04206	TF65_HUMAN	v-rel avian reticuloendotheliosis viral oncogene homolog A	377				QISQASALA -> RSARPRLG (in Ref. 2; CAA80524). {ECO:0000305}.	acetaldehyde metabolic process (GO:0006117)|aging (GO:0007568)|cellular defense response (GO:0006968)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|Fc-epsilon receptor signaling pathway (GO:0038095)|hair follicle development (GO:0001942)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|liver development (GO:0001889)|membrane protein intracellular domain proteolysis (GO:0031293)|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 extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|organ morphogenesis (GO:0009887)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of Schwann cell differentiation (GO:0014040)|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)|regulation of inflammatory response (GO:0050727)|response to amino acid (GO:0043200)|response to cAMP (GO:0051591)|response to cobalamin (GO:0033590)|response to drug (GO:0042493)|response to insulin (GO:0032868)|response to interleukin-1 (GO:0070555)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to muramyl dipeptide (GO:0032495)|response to organic substance (GO:0010033)|response to progesterone (GO:0032570)|response to UV-B (GO:0010224)|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)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|phosphate ion binding (GO:0042301)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|repressing transcription factor binding (GO:0070491)|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 distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(11)|ovary(1)|urinary_tract(1)	19						gggccaaggccgaggcCTGGC	0.647													C|||	153	0.0305511	0.1074	0.0159	5008	,	,		14470	0.0		0.0	False		,,,				2504	0.0				p.S377S		Atlas-SNP	.											.	RELA	44	.	0			c.G1131A						PASS	.	C	,	346,4040		7,332,1854	10.0	10.0	10.0		1122,1131	-7.6	0.2	11	dbSNP_116	10	6,8576		0,6,4285	no	coding-synonymous,coding-synonymous	RELA	NM_001145138.1,NM_021975.3	,	7,338,6139	TT,TC,CC		0.0699,7.8887,2.7144	,	374/549,377/552	65422374	352,12616	2193	4291	6484	SO:0001819	synonymous_variant	5970	exon11			CAAGGCCGAGGCC	Z22951	CCDS31609.1, CCDS44651.1, CCDS73322.1	11q13	2013-07-09	2013-07-09		ENSG00000173039	ENSG00000173039			9955	protein-coding gene	gene with protein product		164014	"""nuclear factor of kappa light polypeptide gene enhancer in B-cells 3"""	NFKB3		2001591	Standard	NM_021975		Approved	p65	uc001ofg.3	Q04206	OTTHUMG00000166566	ENST00000406246.3:c.1131G>A	11.37:g.65422374C>T		131.0	0.0	0		149.0	69.0	0.463087	NM_021975	Q6GTV1|Q6SLK1	Silent	SNP	ENST00000406246.3	37	CCDS31609.1																																																																																			C|0.965;T|0.035	0.035	strong		0.647	RELA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390457.2	NM_021975	
CHST5	23563	hgsc.bcm.edu	37	16	75563352	75563352	+	Missense_Mutation	SNP	C	C	T	rs7206332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:75563352C>T	ENST00000336257.3	-	3	2325	c.931G>A	c.(931-933)Gcc>Acc	p.A311T	CHST5_ENST00000541075.1_Missense_Mutation_p.A317T|RP11-77K12.7_ENST00000460606.1_3'UTR	NM_024533.4	NP_078809.2	Q9GZS9	CHST5_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 5	311			A -> T (in dbSNP:rs7206332).		carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|N-acetylglucosamine metabolic process (GO:0006044)|protein sulfation (GO:0006477)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)	24						CCGGTGAAGGCGTAGAGTGCG	0.677													C|||	124	0.0247604	0.0908	0.0058	5008	,	,		15530	0.0		0.0	False		,,,				2504	0.0				p.A311T		Atlas-SNP	.											CHST5,middle_lobe,carcinoma,+1,1	CHST5	47	1	0			c.G931A						PASS	.	C	THR/ALA	322,4070	164.0+/-195.7	15,292,1889	67.0	68.0	67.0		931	2.8	1.0	16	dbSNP_116	67	13,8587	7.7+/-29.5	0,13,4287	yes	missense	CHST5	NM_024533.4	58	15,305,6176	TT,TC,CC		0.1512,7.3315,2.5785	benign	311/412	75563352	335,12657	2196	4300	6496	SO:0001583	missense	23563	exon3			TGAAGGCGTAGAG	AF176839	CCDS10919.1	16q23.1	2008-02-05			ENSG00000135702	ENSG00000135702		"""Sulfotransferases, membrane-bound"""	1973	protein-coding gene	gene with protein product		604817				10491328, 11017086	Standard	NM_024533		Approved	I-GLCNAC-6-ST, FLJ22167	uc002fei.3	Q9GZS9	OTTHUMG00000137610	ENST00000336257.3:c.931G>A	16.37:g.75563352C>T	ENSP00000338783:p.Ala311Thr	58.0	0.0	0		55.0	27.0	0.490909	NM_024533	B2RV23|Q7LCN3|Q9UBY3	Missense_Mutation	SNP	ENST00000336257.3	37	CCDS10919.1	36	0.016483516483516484	32	0.06504065040650407	4	0.011049723756906077	0	0.0	0	0.0	C	6.674	0.492920	0.12702	0.073315	0.001512	ENSG00000135702	ENST00000336257;ENST00000541075	T;T	0.23950	1.88;1.88	2.84	2.84	0.33178	Sulfotransferase domain (1);	0.322809	0.31495	N	0.007547	T	0.01092	0.0036	L	0.29908	0.895	0.26382	N	0.976729	B;B	0.22851	0.062;0.076	B;B	0.22753	0.024;0.041	T	0.11567	-1.0582	10	0.25751	T	0.34	.	7.8661	0.29539	0.0:0.8684:0.0:0.1316	rs7206332;rs57580922;rs7206332	317;311	Q9GZS9-2;Q9GZS9	.;CHST5_HUMAN	T	311;317	ENSP00000338783:A311T;ENSP00000441220:A317T	ENSP00000338783:A311T	A	-	1	0	CHST5	74120853	0.000000	0.05858	0.995000	0.50966	0.142000	0.21351	0.279000	0.18771	1.583000	0.49898	0.313000	0.20887	GCC	C|0.974;T|0.026	0.026	strong		0.677	CHST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269025.2	NM_012126	
ATM	472	hgsc.bcm.edu	37	11	108143299	108143299	+	Missense_Mutation	SNP	A	A	G	rs3092857	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:108143299A>G	ENST00000452508.2	+	22	3307	c.3118A>G	c.(3118-3120)Atg>Gtg	p.M1040V	ATM_ENST00000278616.4_Missense_Mutation_p.M1040V			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1040			M -> V (in B-cell non-Hodgkin lymphoma; dbSNP:rs3092857). {ECO:0000269|PubMed:9288106}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.M1040V(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	CTCTGTAAGAATGGCCCTAGT	0.303			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)			A|||	71	0.0141773	0.053	0.0014	5008	,	,		17666	0.0		0.0	False		,,,				2504	0.0				p.M1040V		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	ATM_ENST00000278616,colon,carcinoma,-1,7	ATM	1657	7	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.A3118G						PASS	.	A	VAL/MET	177,4225	112.5+/-150.6	1,175,2025	112.0	117.0	115.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3118	-1.1	1.0	11	dbSNP_103	115	0,8596		0,0,4298	yes	missense	ATM	NM_000051.3	21	1,175,6323	GG,GA,AA		0.0,4.0209,1.3617	benign	1040/3057	108143299	177,12821	2201	4298	6499	SO:0001583	missense	472	exon21	Familial Cancer Database	AT, Louis-Bar syndrome	GTAAGAATGGCCC	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"""TEL1, telomere maintenance 1, homolog (S. cerevisiae)"""	607585	"""ataxia telangiectasia mutated (includes complementation groups A, C and D)"", ""ataxia telangiectasia mutated"""	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.3118A>G	11.37:g.108143299A>G	ENSP00000388058:p.Met1040Val	203.0	0.0	0		142.0	51.0	0.359155	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	A	0.185	-1.058171	0.01950	0.040209	0.0	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.68624	-0.34;-0.34;-0.34	5.43	-1.09	0.09904	Armadillo-type fold (1);	0.532223	0.22706	N	0.056633	T	0.10380	0.0254	L	0.35723	1.085	0.20926	N	0.999827	B	0.02656	0.0	B	0.01281	0.0	T	0.14531	-1.0469	10	0.02654	T	1	.	6.8803	0.24168	0.4453:0.1325:0.4222:0.0	rs3092857;rs17107892;rs52804880;rs3092857	1040	Q13315	ATM_HUMAN	V	1040	ENSP00000435747:M1040V;ENSP00000278616:M1040V;ENSP00000388058:M1040V	ENSP00000278616:M1040V	M	+	1	0	ATM	107648509	0.995000	0.38212	0.990000	0.47175	0.533000	0.34776	0.324000	0.19610	-0.134000	0.11516	0.533000	0.62120	ATG	A|0.985;G|0.015	0.015	strong		0.303	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
TGFBI	7045	hgsc.bcm.edu	37	5	135392482	135392482	+	Missense_Mutation	SNP	T	T	G	rs200219644		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:135392482T>G	ENST00000442011.2	+	12	1837	c.1676T>G	c.(1675-1677)tTg>tGg	p.L559W	TGFBI_ENST00000305126.8_Missense_Mutation_p.L559W|TGFBI_ENST00000508076.1_5'Flank	NM_000358.2	NP_000349.1	Q15582	BGH3_HUMAN	transforming growth factor, beta-induced, 68kDa	559	FAS1 4. {ECO:0000255|PROSITE- ProRule:PRU00082}.				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|chondrocyte differentiation (GO:0002062)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)|integrin binding (GO:0005178)			breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AGCAGACTCTTGGGTAAAGAC	0.512													T|||	1	0.000199681	0.0	0.0	5008	,	,		19392	0.0		0.001	False		,,,				2504	0.0				p.L559W		Atlas-SNP	.											.	TGFBI	76	.	0			c.T1676G						PASS	.	T	TRP/LEU	3,3871		0,3,1934	43.0	45.0	45.0		1676	5.8	1.0	5		45	0,8266		0,0,4133	yes	missense	TGFBI	NM_000358.2	61	0,3,6067	GG,GT,TT		0.0,0.0774,0.0247	probably-damaging	559/684	135392482	3,12137	1937	4133	6070	SO:0001583	missense	7045	exon12			GACTCTTGGGTAA	M77349	CCDS47266.1	5q31	2008-02-05	2002-08-29		ENSG00000120708	ENSG00000120708			11771	protein-coding gene	gene with protein product		601692	"""transforming growth factor, beta-induced, 68kD"""	CSD3, LCD1, CSD1, CSD2		9463327	Standard	NM_000358		Approved	BIGH3, CDB1, CDGG1	uc003lbf.4	Q15582	OTTHUMG00000163213	ENST00000442011.2:c.1676T>G	5.37:g.135392482T>G	ENSP00000416330:p.Leu559Trp	178.0	0.0	0		216.0	117.0	0.541667	NM_000358	D3DQB1|O14471|O14472|O14476|O43216|O43217|O43218|O43219|Q53XM1	Missense_Mutation	SNP	ENST00000442011.2	37	CCDS47266.1	.	.	.	.	.	.	.	.	.	.	T	22.9	4.344323	0.82022	7.74E-4	0.0	ENSG00000120708	ENST00000442011;ENST00000398813;ENST00000305126	D;D	0.92495	-3.05;-3.05	5.75	5.75	0.90469	FAS1 domain (5);	0.345979	0.31636	N	0.007304	D	0.97012	0.9024	M	0.93854	3.465	0.58432	D	0.999999	D;D	0.67145	0.992;0.996	D;D	0.70487	0.969;0.969	D	0.97996	1.0357	10	0.87932	D	0	-1.0597	16.0502	0.80755	0.0:0.0:0.0:1.0	.	292;559	B9ZVW9;Q15582	.;BGH3_HUMAN	W	559;292;559	ENSP00000416330:L559W;ENSP00000306306:L559W	ENSP00000306306:L559W	L	+	2	0	TGFBI	135420381	1.000000	0.71417	1.000000	0.80357	0.737000	0.42083	5.538000	0.67193	2.201000	0.70794	0.496000	0.49642	TTG	.	.	weak		0.512	TGFBI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372108.1		
C2orf44	80304	hgsc.bcm.edu	37	2	24260862	24260862	+	Silent	SNP	A	A	G	rs115270382	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:24260862A>G	ENST00000295148.4	-	2	1560	c.1503T>C	c.(1501-1503)agT>agC	p.S501S	C2orf44_ENST00000406895.3_Silent_p.S501S	NM_025203.2	NP_079479.1	Q9H6R7	CB044_HUMAN	chromosome 2 open reading frame 44	501									C2orf44/ALK(2)	breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TAGACAGAGGACTCTGGATTT	0.488			T	ALK	NSCLC								A|||	27	0.00539137	0.0204	0.0	5008	,	,		17626	0.0		0.0	False		,,,				2504	0.0				p.S501S		Atlas-SNP	.		Dom	yes		2	2p23.3	80304	chromosome 2 open reading frame 44		E	.	C2orf44	56	.	0			c.T1503C						PASS	.	A	,	136,4270	94.4+/-133.1	2,132,2069	65.0	69.0	68.0		1503,1503	-3.5	0.1	2	dbSNP_132	68	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	C2orf44	NM_001142319.1,NM_025203.2	,	2,133,6368	GG,GA,AA		0.0116,3.0867,1.0534	,	501/623,501/722	24260862	137,12869	2203	4300	6503	SO:0001819	synonymous_variant	80304	exon2			CAGAGGACTCTGG	AK025598	CCDS1705.1, CCDS46229.1	2p23.3	2012-07-30			ENSG00000163026	ENSG00000163026			26157	protein-coding gene	gene with protein product						22327622	Standard	NM_025203		Approved	FLJ21945	uc002rep.2	Q9H6R7	OTTHUMG00000125498	ENST00000295148.4:c.1503T>C	2.37:g.24260862A>G		126.0	0.0	0		156.0	72.0	0.461538	NM_025203	D6W532|Q8IYK0|Q9HBP5	Silent	SNP	ENST00000295148.4	37	CCDS1705.1																																																																																			A|0.992;G|0.008	0.008	strong		0.488	C2orf44-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246825.1	NM_025203	
GRIN3A	116443	hgsc.bcm.edu	37	9	104385646	104385646	+	Silent	SNP	A	A	G	rs138253972	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:104385646A>G	ENST00000361820.3	-	5	3168	c.2568T>C	c.(2566-2568)gaT>gaC	p.D856D		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	856					calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	TGCAGTCAGCATCTATTGACA	0.413													A|||	5	0.000998403	0.0023	0.0029	5008	,	,		18756	0.0		0.0	False		,,,				2504	0.0				p.D856D		Atlas-SNP	.											.	GRIN3A	186	.	0			c.T2568C						PASS	.	A		7,4399	12.9+/-30.5	0,7,2196	165.0	149.0	154.0		2568	1.7	1.0	9	dbSNP_134	154	0,8600		0,0,4300	no	coding-synonymous	GRIN3A	NM_133445.2		0,7,6496	GG,GA,AA		0.0,0.1589,0.0538		856/1116	104385646	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	116443	exon5			GTCAGCATCTATT		CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.2568T>C	9.37:g.104385646A>G		169.0	0.0	0		183.0	121.0	0.661202	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Silent	SNP	ENST00000361820.3	37	CCDS6758.1																																																																																			A|1.000;G|0.000	0.000	strong		0.413	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
C2CD3	26005	hgsc.bcm.edu	37	11	73796683	73796683	+	Missense_Mutation	SNP	T	T	C	rs1095423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:73796683T>C	ENST00000334126.7	-	21	4116	c.3890A>G	c.(3889-3891)tAt>tGt	p.Y1297C	C2CD3_ENST00000313663.7_Missense_Mutation_p.Y1297C			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1297			Y -> C (in dbSNP:rs1095423).		brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					ATTTTCATGATAGACAGCAAA	0.413													T|||	239	0.0477236	0.1747	0.0115	5008	,	,		19547	0.0		0.0	False		,,,				2504	0.0				p.Y1297C		Atlas-SNP	.											.	C2CD3	288	.	0			c.A3890G						PASS	.	T	CYS/TYR	554,3846	248.7+/-256.4	40,474,1686	64.0	62.0	63.0		3890	5.9	1.0	11	dbSNP_86	63	15,8571	11.2+/-40.8	0,15,4278	yes	missense	C2CD3	NM_015531.4	194	40,489,5964	CC,CT,TT		0.1747,12.5909,4.3816	probably-damaging	1297/1964	73796683	569,12417	2200	4293	6493	SO:0001583	missense	26005	exon21			TCATGATAGACAG	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.3890A>G	11.37:g.73796683T>C	ENSP00000334379:p.Tyr1297Cys	97.0	0.0	0		101.0	47.0	0.465347	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	37		75	0.034340659340659344	70	0.14227642276422764	5	0.013812154696132596	0	0.0	0	0.0	T	18.08	3.542983	0.65198	0.125909	0.001747	ENSG00000168014	ENST00000334126;ENST00000313663;ENST00000313681;ENST00000414160	T;T;T	0.46063	0.88;0.88;0.88	5.95	5.95	0.96441	.	0.188748	0.48767	D	0.000167	T	0.00754	0.0025	M	0.68317	2.08	0.29764	P	0.835337	D	0.89917	1.0	D	0.91635	0.999	T	0.29427	-1.0012	9	0.72032	D	0.01	-12.7519	11.7864	0.52045	0.1316:0.0:0.0:0.8684	rs1095423;rs1790396;rs52807296;rs61681570;rs1095423	1297	Q4AC94-1	.	C	1297;1297;1297;105	ENSP00000334379:Y1297C;ENSP00000323339:Y1297C;ENSP00000388750:Y105C	ENSP00000323339:Y1297C	Y	-	2	0	C2CD3	73474331	1.000000	0.71417	1.000000	0.80357	0.936000	0.57629	3.834000	0.55798	2.268000	0.75426	0.533000	0.62120	TAT	T|0.951;C|0.049	0.049	strong		0.413	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531	
ZNF284	342909	hgsc.bcm.edu	37	19	44590753	44590753	+	Silent	SNP	T	T	C	rs114253786	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44590753T>C	ENST00000421176.3	+	5	1338	c.1122T>C	c.(1120-1122)aaT>aaC	p.N374N	ZNF223_ENST00000591793.1_3'UTR|RNU6-902P_ENST00000517212.1_RNA	NM_001037813.2	NP_001032902.1	Q2VY69	ZN284_HUMAN	zinc finger protein 284	374					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|upper_aerodigestive_tract(1)	15		Prostate(69;0.0435)				ATAATTGTAATGTATGTGGGA	0.433													T|||	24	0.00479233	0.0166	0.0029	5008	,	,		21791	0.0		0.0	False		,,,				2504	0.0				p.N374N		Atlas-SNP	.											.	ZNF284	38	.	0			c.T1122C						PASS	.	T		65,4171		0,65,2053	93.0	100.0	98.0		1122	-4.8	0.0	19	dbSNP_132	98	0,8480		0,0,4240	no	coding-synonymous	ZNF284	NM_001037813.2		0,65,6293	CC,CT,TT		0.0,1.5345,0.5112		374/594	44590753	65,12651	2118	4240	6358	SO:0001819	synonymous_variant	342909	exon5			TTGTAATGTATGT	AY166789	CCDS46099.1	19q13.32	2013-01-08				ENSG00000186026		"""Zinc fingers, C2H2-type"", ""-"""	13078	protein-coding gene	gene with protein product						12743021	Standard	NM_001037813		Approved	DKFZp781F1775	uc002oyg.1	Q2VY69		ENST00000421176.3:c.1122T>C	19.37:g.44590753T>C		196.0	0.0	0		149.0	74.0	0.496644	NM_001037813	Q86WM1	Silent	SNP	ENST00000421176.3	37	CCDS46099.1																																																																																			T|0.995;C|0.005	0.005	strong		0.433	ZNF284-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460473.1	NM_001037813	
ALOX15	246	hgsc.bcm.edu	37	17	4539171	4539171	+	Silent	SNP	G	G	T	rs11568113	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4539171G>T	ENST00000570836.1	-	9	1140	c.1044C>A	c.(1042-1044)cgC>cgA	p.R348R	ALOX15_ENST00000574640.1_Silent_p.R309R|ALOX15_ENST00000545513.1_Silent_p.R370R|ALOX15_ENST00000293761.3_Silent_p.R348R			P16050	LOX15_HUMAN	arachidonate 15-lipoxygenase	348	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				apoptotic cell clearance (GO:0043277)|arachidonic acid metabolic process (GO:0019369)|bone mineralization (GO:0030282)|cellular response to calcium ion (GO:0071277)|cellular response to interleukin-13 (GO:0035963)|hepoxilin biosynthetic process (GO:0051122)|inflammatory response (GO:0006954)|leukotriene metabolic process (GO:0006691)|lipoxin A4 biosynthetic process (GO:2001303)|lipoxygenase pathway (GO:0019372)|negative regulation of adaptive immune response (GO:0002820)|ossification (GO:0001503)|phosphatidylethanolamine biosynthetic process (GO:0006646)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of engulfment of apoptotic cell (GO:1901074)|regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035358)|response to endoplasmic reticulum stress (GO:0034976)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|lipid particle (GO:0005811)|membrane (GO:0016020)|plasma membrane (GO:0005886)	arachidonate 12-lipoxygenase activity (GO:0004052)|arachidonate 15-lipoxygenase activity (GO:0050473)|eoxin A4 synthase activity (GO:0097260)|iron ion binding (GO:0005506)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(5)	20				READ - Rectum adenocarcinoma(115;0.0327)		AGTCAGAGCTGCGCACCCAGC	0.602													G|||	93	0.0185703	0.0681	0.0043	5008	,	,		20183	0.0		0.0	False		,,,				2504	0.0				p.R348R		Atlas-SNP	.											.	ALOX15	70	.	0			c.C1044A						PASS	.	G		314,4092	169.1+/-199.8	15,284,1904	68.0	70.0	69.0		1044	-7.4	0.6	17	dbSNP_120	69	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	ALOX15	NM_001140.3		15,286,6202	TT,TG,GG		0.0233,7.1266,2.4296		348/663	4539171	316,12690	2203	4300	6503	SO:0001819	synonymous_variant	246	exon8			AGAGCTGCGCACC	M23892	CCDS11049.1	17p13.3	2010-09-24			ENSG00000161905	ENSG00000161905	1.13.11.33	"""Arachidonate lipoxygenases"""	433	protein-coding gene	gene with protein product		152392				1570320	Standard	NM_001140		Approved	15-LOX-1	uc002fyh.3	P16050	OTTHUMG00000090746	ENST00000570836.1:c.1044C>A	17.37:g.4539171G>T		160.0	0.0	0		150.0	77.0	0.513333	NM_001140	A8K2P4|B7ZA11|Q8N6R7|Q99657	Silent	SNP	ENST00000570836.1	37	CCDS11049.1																																																																																			G|0.973;T|0.027	0.027	strong		0.602	ALOX15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207487.2		
ACACA	31	hgsc.bcm.edu	37	17	35470031	35470031	+	Silent	SNP	T	T	G	rs55811414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:35470031T>G	ENST00000394406.2	-	51	6523	c.6333A>C	c.(6331-6333)cgA>cgC	p.R2111R	ACACA_ENST00000335166.5_Silent_p.R2033R|ACACA_ENST00000360679.3_Silent_p.R2053R|ACACA_ENST00000361253.5_Silent_p.R237R|ACACA_ENST00000353139.5_Silent_p.R2148R	NM_198836.1	NP_942133.1	Q13085	ACACA_HUMAN	acetyl-CoA carboxylase alpha	2111	Carboxyltransferase.				acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|lipid homeostasis (GO:0055088)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|malonyl-CoA biosynthetic process (GO:2001295)|multicellular organismal protein metabolic process (GO:0044268)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|small molecule metabolic process (GO:0044281)|tissue homeostasis (GO:0001894)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(2)|breast(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(24)|lung(23)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	83		Breast(25;0.00157)|Ovarian(249;0.15)			Biotin(DB00121)	ACCTGCTTTCTCGGTCAGCAT	0.552													T|||	221	0.0441294	0.149	0.0274	5008	,	,		19920	0.0		0.004	False		,,,				2504	0.001				p.R2148R	Colon(23;82 258 739 2117 10493 24037 27661 34815 35438 36249)	Atlas-SNP	.											.	ACACA	395	.	0			c.A6444C						PASS	.	T	,,,,	461,3945	218.4+/-236.5	26,409,1768	82.0	71.0	75.0		6444,6333,6159,6099,6333	-1.6	1.0	17	dbSNP_129	75	32,8568	21.6+/-65.8	0,32,4268	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ACACA	NM_198834.1,NM_198836.1,NM_198837.1,NM_198838.1,NM_198839.1	,,,,	26,441,6036	GG,GT,TT		0.3721,10.463,3.7906	,,,,	2148/2384,2111/2347,2053/2289,2033/2269,2111/2347	35470031	493,12513	2203	4300	6503	SO:0001819	synonymous_variant	31	exon51			GCTTTCTCGGTCA	U19822	CCDS11317.1, CCDS11318.1, CCDS42302.1, CCDS42303.1	17q21	2014-05-06	2010-04-30		ENSG00000132142	ENSG00000278540	6.4.1.2		84	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 1"""	200350	"""acetyl-Coenzyme A carboxylase alpha"""	ACAC, ACC			Standard	NM_198837		Approved	ACC1	uc002hno.3	Q13085	OTTHUMG00000188463	ENST00000394406.2:c.6333A>C	17.37:g.35470031T>G		126.0	0.0	0		124.0	57.0	0.459677	NM_198834	B2RP68|Q6KEV6|Q6XDA8|Q7Z2G8|Q7Z561|Q7Z563|Q7Z564|Q86WB2|Q86WB3	Silent	SNP	ENST00000394406.2	37	CCDS11317.1																																																																																			G|0.034;T|0.966	0.034	strong		0.552	ACACA-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256696.1	NM_198836	
GIMAP2	26157	hgsc.bcm.edu	37	7	150390255	150390255	+	Missense_Mutation	SNP	T	T	C	rs115945256	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150390255T>C	ENST00000223293.5	+	3	975	c.881T>C	c.(880-882)aTg>aCg	p.M294T		NM_015660.2	NP_056475.1	Q9UG22	GIMA2_HUMAN	GTPase, IMAP family member 2	294						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)	GTP binding (GO:0005525)			kidney(1)|large_intestine(1)|lung(8)|skin(2)|urinary_tract(1)	13			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CTGCACAGCATGTGCAATTTG	0.323													T|||	24	0.00479233	0.0098	0.0014	5008	,	,		22226	0.004		0.0	False		,,,				2504	0.0061				p.M294T		Atlas-SNP	.											.	GIMAP2	39	.	0			c.T881C						PASS	.	T	THR/MET	58,4348	57.4+/-93.9	1,56,2146	117.0	108.0	111.0		881	2.1	0.0	7	dbSNP_132	111	0,8600		0,0,4300	yes	missense	GIMAP2	NM_015660.2	81	1,56,6446	CC,CT,TT		0.0,1.3164,0.4459	possibly-damaging	294/338	150390255	58,12948	2203	4300	6503	SO:0001583	missense	26157	exon3			ACAGCATGTGCAA	AL110151	CCDS5905.1	7q36.1	2014-04-04			ENSG00000106560	ENSG00000106560		"""GTPases, IMAP"""	21789	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 12"""	608085				15474311	Standard	NM_015660		Approved	DKFZp586D0824, HIMAP2, IMAP2, IAN12	uc003who.3	Q9UG22	OTTHUMG00000157488	ENST00000223293.5:c.881T>C	7.37:g.150390255T>C	ENSP00000223293:p.Met294Thr	119.0	0.0	0		126.0	55.0	0.436508	NM_015660	Q96L25	Missense_Mutation	SNP	ENST00000223293.5	37	CCDS5905.1	7	0.003205128205128205	4	0.008130081300813009	0	0.0	3	0.005244755244755245	0	0.0	T	3.694	-0.062952	0.07273	0.013164	0.0	ENSG00000106560	ENST00000223293	T	0.05382	3.45	3.32	2.14	0.27477	.	1.629670	0.03647	N	0.240382	T	0.03739	0.0106	N	0.19112	0.55	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.37663	-0.9696	10	0.87932	D	0	.	5.2908	0.15725	0.0:0.1378:0.0:0.8622	.	294	Q9UG22	GIMA2_HUMAN	T	294	ENSP00000223293:M294T	ENSP00000223293:M294T	M	+	2	0	GIMAP2	150021188	0.004000	0.15560	0.005000	0.12908	0.008000	0.06430	0.560000	0.23500	0.491000	0.27793	0.533000	0.62120	ATG	T|0.995;C|0.005	0.005	strong		0.323	GIMAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348948.1	NM_015660	
FBN2	2201	hgsc.bcm.edu	37	5	127670412	127670412	+	Splice_Site	SNP	T	T	G	rs28763943	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:127670412T>G	ENST00000508053.1	-	37	5072	c.4098A>C	c.(4096-4098)acA>acC	p.T1366T	FBN2_ENST00000508989.1_Splice_Site_p.T1333T|FBN2_ENST00000507835.1_Splice_Site_p.T216T|FBN2_ENST00000262464.4_Splice_Site_p.T1366T			P35556	FBN2_HUMAN	fibrillin 2	1366	EGF-like 21; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		GAAACCTACCTGTACATCCTG	0.443													T|||	98	0.0195687	0.0726	0.0029	5008	,	,		21065	0.0		0.0	False		,,,				2504	0.0				p.T1366T		Atlas-SNP	.											.	FBN2	858	.	0			c.A4098C						PASS	.	T		331,4075	174.4+/-204.0	15,301,1887	131.0	117.0	122.0		4098	5.0	1.0	5	dbSNP_125	122	3,8597	3.0+/-9.4	0,3,4297	yes	coding-synonymous-near-splice	FBN2	NM_001999.3		15,304,6184	GG,GT,TT		0.0349,7.5125,2.568		1366/2913	127670412	334,12672	2203	4300	6503	SO:0001630	splice_region_variant	2201	exon31			CCTACCTGTACAT	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"""fibrillin 5"""	612570	"""congenital contractural arachnodactyly"""	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.4099+1A>C	5.37:g.127670412T>G		62.0	0.0	0		68.0	30.0	0.441176	NM_001999	B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	37	CCDS34222.1																																																																																			T|0.975;G|0.025	0.025	strong		0.443	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	Silent
COL6A2	1292	hgsc.bcm.edu	37	21	47545889	47545889	+	Silent	SNP	C	C	G	rs61735829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:47545889C>G	ENST00000300527.4	+	26	2264	c.2160C>G	c.(2158-2160)cgC>cgG	p.R720R	COL6A2_ENST00000409416.1_Silent_p.R720R|COL6A2_ENST00000357838.4_Silent_p.R720R|COL6A2_ENST00000310645.5_Silent_p.R720R|COL6A2_ENST00000397763.1_Silent_p.R720R	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	720	Nonhelical region.|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		AGAGCCGGCGCCAGAAGACAC	0.637													C|||	82	0.0163738	0.059	0.0058	5008	,	,		14676	0.0		0.0	False		,,,				2504	0.0				p.R720R		Atlas-SNP	.											COL6A2_ENST00000357838,NS,carcinoma,+2,3	COL6A2	351	3	0			c.C2160G						PASS	.	C	,,	227,4179	135.3+/-171.4	6,215,1982	68.0	67.0	67.0		2160,2160,2160	0.1	1.0	21	dbSNP_129	67	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	COL6A2	NM_001849.3,NM_058174.2,NM_058175.2	,,	6,218,6279	GG,GC,CC		0.0349,5.1521,1.7684	,,	720/1020,720/919,720/829	47545889	230,12776	2203	4300	6503	SO:0001819	synonymous_variant	1292	exon26			CCGGCGCCAGAAG	M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"""Collagens"""	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.2160C>G	21.37:g.47545889C>G		148.0	0.0	0		166.0	86.0	0.518072	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Silent	SNP	ENST00000300527.4	37	CCDS13728.1																																																																																			C|0.982;G|0.018	0.018	strong		0.637	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		
ZNF841	284371	hgsc.bcm.edu	37	19	52569479	52569479	+	Silent	SNP	G	G	A	rs61738706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52569479G>A	ENST00000426391.2	-	5	1859	c.1308C>T	c.(1306-1308)taC>taT	p.Y436Y	ZNF841_ENST00000594295.1_Silent_p.Y552Y|ZNF432_ENST00000598446.1_Intron|ZNF841_ENST00000359973.2_Intron|CTC-471J1.2_ENST00000569091.1_RNA|ZNF841_ENST00000389534.4_Silent_p.Y552Y			Q6ZN19	ZN841_HUMAN	zinc finger protein 841	436					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(3)|lung(3)	11						GGTATCCACCGTAATTAAAGA	0.403													g|||	110	0.0219649	0.0772	0.0101	5008	,	,		22430	0.0		0.001	False		,,,				2504	0.0				p.Y552Y		Atlas-SNP	.											.	ZNF841	183	.	0			c.C1656T						PASS	.	A		87,1297		3,81,608	93.0	81.0	85.0		1656	-4.5	0.0	19	dbSNP_129	85	0,3182		0,0,1591	no	coding-synonymous	ZNF841	NM_001136499.1		3,81,2199	AA,AG,GG		0.0,6.2861,1.9054		552/925	52569479	87,4479	692	1591	2283	SO:0001819	synonymous_variant	284371	exon7			TCCACCGTAATTA	AK131409	CCDS46161.1	19q13.41	2013-01-08			ENSG00000197608	ENSG00000197608		"""Zinc fingers, C2H2-type"", ""-"""	27611	protein-coding gene	gene with protein product							Standard	NM_001136499		Approved	LOC284371	uc010ydh.1	Q6ZN19		ENST00000426391.2:c.1308C>T	19.37:g.52569479G>A		48.0	0.0	0		53.0	21.0	0.396226	NM_001136499	B9EG58|Q6ZN82|Q6ZP71|Q8N9U7	Silent	SNP	ENST00000426391.2	37																																																																																				G|0.979;A|0.021	0.021	strong		0.403	ZNF841-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000462435.1	XM_209155	
TH	7054	hgsc.bcm.edu	37	11	2190982	2190982	+	Silent	SNP	A	A	G	rs7950050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:2190982A>G	ENST00000381178.1	-	3	321	c.303T>C	c.(301-303)gcT>gcC	p.A101A	TH_ENST00000333684.5_Silent_p.A74A|TH_ENST00000381175.1_Silent_p.A97A|TH_ENST00000352909.3_Silent_p.A70A	NM_199292.2	NP_954986.2	P07101	TY3H_HUMAN	tyrosine hydroxylase	101					anatomical structure morphogenesis (GO:0009653)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth factor stimulus (GO:0071363)|cellular response to manganese ion (GO:0071287)|cellular response to nicotine (GO:0071316)|cerebral cortex development (GO:0021987)|circadian sleep/wake cycle (GO:0042745)|dopamine biosynthetic process (GO:0042416)|dopamine biosynthetic process from tyrosine (GO:0006585)|eating behavior (GO:0042755)|embryonic camera-type eye morphogenesis (GO:0048596)|epinephrine biosynthetic process (GO:0042418)|eye photoreceptor cell development (GO:0042462)|fatty acid metabolic process (GO:0006631)|glycoside metabolic process (GO:0016137)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|isoquinoline alkaloid metabolic process (GO:0033076)|learning (GO:0007612)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|memory (GO:0007613)|multicellular organismal aging (GO:0010259)|neurotransmitter biosynthetic process (GO:0042136)|norepinephrine biosynthetic process (GO:0042421)|organ morphogenesis (GO:0009887)|phthalate metabolic process (GO:0018963)|phytoalexin metabolic process (GO:0052314)|pigmentation (GO:0043473)|regulation of heart contraction (GO:0008016)|response to activity (GO:0014823)|response to amphetamine (GO:0001975)|response to corticosterone (GO:0051412)|response to electrical stimulus (GO:0051602)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to ether (GO:0045472)|response to herbicide (GO:0009635)|response to hypoxia (GO:0001666)|response to light stimulus (GO:0009416)|response to lipopolysaccharide (GO:0032496)|response to nutrient levels (GO:0031667)|response to peptide hormone (GO:0043434)|response to pyrethroid (GO:0046684)|response to salt stress (GO:0009651)|response to water deprivation (GO:0009414)|response to zinc ion (GO:0010043)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|sphingolipid metabolic process (GO:0006665)|synaptic transmission, dopaminergic (GO:0001963)|synaptic vesicle amine transport (GO:0015842)|terpene metabolic process (GO:0042214)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|melanosome membrane (GO:0033162)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perikaryon (GO:0043204)|smooth endoplasmic reticulum (GO:0005790)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	amino acid binding (GO:0016597)|dopamine binding (GO:0035240)|enzyme binding (GO:0019899)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)|oxygen binding (GO:0019825)|tetrahydrobiopterin binding (GO:0034617)|tyrosine 3-monooxygenase activity (GO:0004511)			NS(1)|endometrium(1)|large_intestine(1)|lung(7)|skin(1)	11		all_epithelial(84;1.46e-23)|Lung NSC(207;4.44e-11)|all_lung(207;1.11e-09)|Ovarian(85;1.78e-06)|Breast(177;1.78e-05)|Medulloblastoma(188;0.0208)|all_neural(188;0.0416)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;8.45e-09)|Lung(200;0.000152)|LUSC - Lung squamous cell carcinoma(625;0.00154)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)|Metyrosine(DB00765)|Tetrahydrobiopterin(DB00360)	CAAAGGCCACAGCCTCCAGGG	0.697													G|||	168	0.0335463	0.1233	0.0058	5008	,	,		14629	0.0		0.001	False		,,,				2504	0.0				p.A101A		Atlas-SNP	.											.	TH	43	.	0			c.T303C						PASS	.	G	,,	522,3882	744.0+/-411.5	23,476,1703	32.0	34.0	34.0		210,303,291	-1.3	0.1	11	dbSNP_116	34	13,8583	796.2+/-407.5	0,13,4285	no	coding-synonymous,coding-synonymous,coding-synonymous	TH	NM_000360.3,NM_199292.2,NM_199293.2	,,	23,489,5988	GG,GA,AA		0.1512,11.8529,4.1154	,,	70/498,101/529,97/525	2190982	535,12465	2202	4298	6500	SO:0001819	synonymous_variant	7054	exon3			GGCCACAGCCTCC	X05290	CCDS7730.1, CCDS7731.1, CCDS31338.1	11p15.5	2013-06-03			ENSG00000180176	ENSG00000180176	1.14.16.2		11782	protein-coding gene	gene with protein product	"""tyrosine 3-monooxygenase"""	191290					Standard	NM_199292		Approved	DYT5b	uc001lvq.3	P07101	OTTHUMG00000009559	ENST00000381178.1:c.303T>C	11.37:g.2190982A>G		121.0	0.0	0		116.0	62.0	0.534483	NM_199292	B7ZL70|B7ZL73|Q0PWM2|Q0PWM3|Q15585|Q15588|Q15589|Q2M3B4	Silent	SNP	ENST00000381178.1	37	CCDS7731.1																																																																																			A|0.952;G|0.048	0.048	strong		0.697	TH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026597.1	NM_000360	
POLR3D	661	hgsc.bcm.edu	37	8	22107707	22107707	+	Silent	SNP	C	C	T	rs34435413	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22107707C>T	ENST00000397802.4	+	7	1256	c.1041C>T	c.(1039-1041)gaC>gaT	p.D347D	POLR3D_ENST00000306433.4_Silent_p.D347D			P05423	RPC4_HUMAN	polymerase (RNA) III (DNA directed) polypeptide D, 44kDa	347					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|prostate(1)|stomach(1)	13				Colorectal(74;0.0146)|COAD - Colon adenocarcinoma(73;0.061)		TGACTCTGGACGTGACCATGG	0.567													C|||	19	0.00379393	0.0144	0.0	5008	,	,		19108	0.0		0.0	False		,,,				2504	0.0				p.D347D		Atlas-SNP	.											.	POLR3D	26	.	0			c.C1041T						PASS	.	C		78,4328	68.1+/-105.8	0,78,2125	82.0	73.0	76.0		1041	-10.8	0.5	8	dbSNP_126	76	0,8600		0,0,4300	no	coding-synonymous	POLR3D	NM_001722.2		0,78,6425	TT,TC,CC		0.0,1.7703,0.5997		347/399	22107707	78,12928	2203	4300	6503	SO:0001819	synonymous_variant	661	exon8			TCTGGACGTGACC	M17754	CCDS34858.1	8q21	2013-01-21	2003-04-01	2003-04-04	ENSG00000168495	ENSG00000168495		"""RNA polymerase subunits"""	1080	protein-coding gene	gene with protein product		187280	"""BN51 (BHK21) temperature sensitivity complementing"""	BN51T		12391170, 11279001	Standard	NM_001722		Approved	TSBN51, RPC4	uc003xbl.3	P05423	OTTHUMG00000163778	ENST00000397802.4:c.1041C>T	8.37:g.22107707C>T		97.0	0.0	0		112.0	52.0	0.464286	NM_001722	Q6FI28|Q9BPV7|Q9BPZ1|Q9BXB3	Silent	SNP	ENST00000397802.4	37	CCDS34858.1																																																																																			C|0.993;T|0.007	0.007	strong		0.567	POLR3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375434.2	NM_001722	
NECAB3	63941	hgsc.bcm.edu	37	20	32248088	32248088	+	Silent	SNP	C	C	T	rs146604647	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:32248088C>T	ENST00000246190.6	-	6	556	c.501G>A	c.(499-501)ctG>ctA	p.L167L	RP1-63M2.6_ENST00000607224.1_RNA|C20orf144_ENST00000375222.3_5'Flank|NECAB3_ENST00000375238.4_Silent_p.L167L|NECAB3_ENST00000606525.1_5'UTR	NM_031232.3	NP_112509.3	Q96P71	NECA3_HUMAN	N-terminal EF-hand calcium binding protein 3	167					protein metabolic process (GO:0019538)|protein secretion (GO:0009306)|regulation of amyloid precursor protein biosynthetic process (GO:0042984)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|Golgi cis cisterna (GO:0000137)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			large_intestine(3)|lung(5)|skin(2)	10						CCTGGGCCTCCAGGGTATCTG	0.622													C|||	10	0.00199681	0.0076	0.0	5008	,	,		18803	0.0		0.0	False		,,,				2504	0.0				p.L167L		Atlas-SNP	.											.	NECAB3	27	.	0			c.G501A						PASS	.	C	,	24,4058		0,24,2017	48.0	54.0	52.0		501,501	3.9	1.0	20	dbSNP_134	52	0,8376		0,0,4188	no	coding-synonymous,coding-synonymous	NECAB3	NM_031231.3,NM_031232.3	,	0,24,6205	TT,TC,CC		0.0,0.5879,0.1926	,	167/363,167/397	32248088	24,12434	2041	4188	6229	SO:0001819	synonymous_variant	63941	exon6			GGCCTCCAGGGTA	AB039947	CCDS42866.1, CCDS42867.1	20q11.21	2013-01-10	2007-12-06	2007-12-06	ENSG00000125967	ENSG00000125967		"""N-terminal EF-hand calcium binding proteins"", ""EF-hand domain containing"""	15851	protein-coding gene	gene with protein product	"""EF-hand calcium binding protein 3"""	612478	"""amyloid beta (A4) precursor protein-binding, family A, member 2 binding protein"""	SYTIP2, APBA2BP		10833507	Standard	NM_031232		Approved	XB51, dJ63M2.4, NIP1, dJ63M2.5, EFCBP3	uc002wzn.4	Q96P71	OTTHUMG00000032264	ENST00000246190.6:c.501G>A	20.37:g.32248088C>T		69.0	0.0	0		54.0	23.0	0.425926	NM_031232	A8K780|E1P5N2|Q5JWF5|Q5JWF6|Q5JWF7|Q86VV1|Q9H433|Q9H8G8|Q9HBW7|Q9HCQ9	Silent	SNP	ENST00000246190.6	37	CCDS42866.1																																																																																			C|0.996;T|0.004	0.004	strong		0.622	NECAB3-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078724.2		
TICRR	90381	hgsc.bcm.edu	37	15	90145118	90145118	+	Silent	SNP	T	T	A	rs202042800		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90145118T>A	ENST00000268138.7	+	12	2583	c.2478T>A	c.(2476-2478)ccT>ccA	p.P826P	TICRR_ENST00000560985.1_Silent_p.P825P			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	826					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|formation of translation preinitiation complex (GO:0001731)|mitotic DNA replication checkpoint (GO:0033314)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	chromatin binding (GO:0003682)										TTTCTGTGCCTTTTTTGTCAA	0.458													T|||	1	0.000199681	0.0008	0.0	5008	,	,		19991	0.0		0.0	False		,,,				2504	0.0				p.P826P		Atlas-SNP	.											.	.	.	.	0			c.T2478A						PASS	.	T		5,3841		0,5,1918	137.0	125.0	129.0		2478	0.3	0.1	15		129	0,8276		0,0,4138	no	coding-synonymous	C15orf42	NM_152259.3		0,5,6056	AA,AT,TT		0.0,0.13,0.0412		826/1911	90145118	5,12117	1923	4138	6061	SO:0001819	synonymous_variant	90381	exon12			TGTGCCTTTTTTG	AK123612	CCDS10352.2	15q26.1	2012-07-11	2012-07-11	2012-07-11	ENSG00000140534	ENSG00000140534			28704	protein-coding gene	gene with protein product	"""TOPBP1-interacting replication-stimulating protein"", ""SLD3 homolog (S. cerevisiae)"""	613298	"""chromosome 15 open reading frame 42"""	C15orf42		20116089, 20080954	Standard	NM_152259		Approved	MGC45866, FLJ41618, Treslin, SLD3	uc002boe.3	Q7Z2Z1	OTTHUMG00000149648	ENST00000268138.7:c.2478T>A	15.37:g.90145118T>A		80.0	0.0	0		74.0	36.0	0.486486	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Silent	SNP	ENST00000268138.7	37	CCDS10352.2																																																																																			T|1.000;A|0.000	0.000	strong		0.458	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259	
DNAH9	1770	hgsc.bcm.edu	37	17	11550413	11550413	+	Silent	SNP	T	T	C	rs61745426	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:11550413T>C	ENST00000262442.4	+	12	2063	c.1995T>C	c.(1993-1995)gaT>gaC	p.D665D	DNAH9_ENST00000454412.2_Silent_p.D665D	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	665	Stem. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		TTTATGAGGATTGGTGCCGGA	0.488													T|||	59	0.0117812	0.0431	0.0029	5008	,	,		16804	0.0		0.0	False		,,,				2504	0.0				p.D665D		Atlas-SNP	.											.	DNAH9	695	.	0			c.T1995C						PASS	.	T		162,4244	110.8+/-149.0	6,150,2047	151.0	128.0	136.0		1995	-0.4	1.0	17	dbSNP_129	136	1,8599		0,1,4299	no	coding-synonymous	DNAH9	NM_001372.3		6,151,6346	CC,CT,TT		0.0116,3.6768,1.2533		665/4487	11550413	163,12843	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon12			TGAGGATTGGTGC	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.1995T>C	17.37:g.11550413T>C		129.0	0.0	0		131.0	59.0	0.450382	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			T|0.988;C|0.012	0.012	strong		0.488	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
IGSF9	57549	hgsc.bcm.edu	37	1	159900655	159900655	+	Missense_Mutation	SNP	G	G	A	rs140306211	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:159900655G>A	ENST00000368094.1	-	14	1837	c.1640C>T	c.(1639-1641)gCc>gTc	p.A547V	IGSF9_ENST00000361509.3_Missense_Mutation_p.A531V|IGSF9_ENST00000493195.1_5'UTR	NM_001135050.1	NP_001128522.1	Q9P2J2	TUTLA_HUMAN	immunoglobulin superfamily, member 9	547	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				dendrite development (GO:0016358)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synapse (GO:0045202)				central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(13)|lung(17)|ovary(3)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_hematologic(112;0.0597)	Breast(1374;0.000126)	BRCA - Breast invasive adenocarcinoma(70;0.111)			AGGACGCTTGGCCCTGGGAGA	0.617													G|||	17	0.00339457	0.0129	0.0	5008	,	,		19874	0.0		0.0	False		,,,				2504	0.0				p.A547V		Atlas-SNP	.											.	IGSF9	123	.	0			c.C1640T						PASS	.	G	VAL/ALA,VAL/ALA	78,4328	67.0+/-104.6	0,78,2125	34.0	35.0	35.0		1640,1592	4.7	1.0	1	dbSNP_134	35	0,8600		0,0,4300	yes	missense,missense	IGSF9	NM_001135050.1,NM_020789.3	64,64	0,78,6425	AA,AG,GG		0.0,1.7703,0.5997	benign,benign	547/1180,531/1164	159900655	78,12928	2203	4300	6503	SO:0001583	missense	57549	exon14			CGCTTGGCCCTGG	AB037776	CCDS1190.1, CCDS44254.1	1q22-q23	2013-02-11			ENSG00000085552	ENSG00000085552		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	18132	protein-coding gene	gene with protein product		609738				11991715	Standard	NM_020789		Approved	KIAA1355, Nrt1, IGSF9A	uc001fur.2	Q9P2J2	OTTHUMG00000022794	ENST00000368094.1:c.1640C>T	1.37:g.159900655G>A	ENSP00000357073:p.Ala547Val	152.0	0.0	0		146.0	71.0	0.486301	NM_001135050		Missense_Mutation	SNP	ENST00000368094.1	37	CCDS44254.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	G	8.888	0.953376	0.18431	0.017703	0.0	ENSG00000085552	ENST00000361509;ENST00000368094	T;T	0.56776	0.44;0.44	4.65	4.65	0.58169	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.165414	0.28700	N	0.014421	T	0.13670	0.0331	N	0.05510	-0.035	0.33488	D	0.588349	B	0.13145	0.007	B	0.20384	0.029	T	0.10337	-1.0634	9	.	.	.	-14.7856	8.6122	0.33808	0.1024:0.0:0.8976:0.0	.	547	Q9P2J2	TUTLA_HUMAN	V	531;547	ENSP00000355049:A531V;ENSP00000357073:A547V	.	A	-	2	0	IGSF9	158167279	1.000000	0.71417	1.000000	0.80357	0.856000	0.48823	3.744000	0.55112	2.400000	0.81607	0.462000	0.41574	GCC	G|0.994;A|0.006	0.006	strong		0.617	IGSF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059115.1	NM_020789	
SLC13A1	6561	hgsc.bcm.edu	37	7	122787306	122787306	+	Missense_Mutation	SNP	G	G	A	rs10231144	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:122787306G>A	ENST00000194130.2	-	7	758	c.719C>T	c.(718-720)aCg>aTg	p.T240M	SLC13A1_ENST00000539873.1_3'UTR	NM_022444.3	NP_071889.2	Q9BZW2	S13A1_HUMAN	solute carrier family 13 (sodium/sulfate symporter), member 1	240			T -> M (in dbSNP:rs10231144).		transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:sulfate symporter activity (GO:0015382)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(20)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	45					Succinic acid(DB00139)	GCACAAACACGTAAGTTTACG	0.413													A|||	31	0.0061901	0.0227	0.0014	5008	,	,		20613	0.0		0.0	False		,,,				2504	0.0				p.T240M		Atlas-SNP	.											.	SLC13A1	110	.	0			c.C719T						PASS	.	A	MET/THR	92,4314	818.0+/-416.3	0,92,2111	236.0	180.0	199.0		719	5.0	1.0	7	dbSNP_119	199	1,8599		0,1,4299	yes	missense	SLC13A1	NM_022444.3	81	0,93,6410	AA,AG,GG		0.0116,2.0881,0.7151	benign	240/596	122787306	93,12913	2203	4300	6503	SO:0001583	missense	6561	exon7			AAACACGTAAGTT		CCDS5786.1	7q31.32	2013-07-18	2013-07-18		ENSG00000081800	ENSG00000081800		"""Solute carriers"""	10916	protein-coding gene	gene with protein product		606193	"""solute carrier family 13 (sodium/sulphate symporters), member 1"""			11161786	Standard	NM_022444		Approved	NaSi-1, NAS1	uc003vkm.3	Q9BZW2	OTTHUMG00000157087	ENST00000194130.2:c.719C>T	7.37:g.122787306G>A	ENSP00000194130:p.Thr240Met	95.0	0.0	0		136.0	79.0	0.580882	NM_022444	Q9H5Z0	Missense_Mutation	SNP	ENST00000194130.2	37	CCDS5786.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	A	3.455	-0.111112	0.06881	0.020881	1.16E-4	ENSG00000081800	ENST00000194130	T	0.63913	-0.07	5.0	5.0	0.66597	.	0.085242	0.85682	N	0.000000	T	0.05914	0.0154	N	0.00030	-2.605	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.04946	-1.0916	10	0.13108	T	0.6	.	9.0284	0.36243	0.9119:0.0:0.0881:0.0	rs10231144;rs52791983;rs57837984;rs10231144	240;240	A4D0X1;Q9BZW2	.;S13A1_HUMAN	M	240	ENSP00000194130:T240M	ENSP00000194130:T240M	T	-	2	0	SLC13A1	122574542	1.000000	0.71417	0.997000	0.53966	0.706000	0.40770	6.172000	0.71932	0.772000	0.33382	-0.360000	0.07572	ACG	G|0.989;A|0.011	0.011	strong		0.413	SLC13A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347404.1	NM_022444	
SGCD	6444	hgsc.bcm.edu	37	5	156184786	156184786	+	Intron	SNP	G	G	A	rs187204080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:156184786G>A	ENST00000435422.3	+	7	1183				SGCD_ENST00000447401.1_Silent_p.*257*|SGCD_ENST00000517913.1_Silent_p.*257*|SGCD_ENST00000337851.4_Intron	NM_001128209.1	NP_001121681.1	Q92629	SGCD_HUMAN	sarcoglycan, delta (35kDa dystrophin-associated glycoprotein)						muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)				breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(16)|prostate(1)	24	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ATAACTGGTTGACCTCGGAGT	0.448													G|||	14	0.00279553	0.0106	0.0	5008	,	,		17960	0.0		0.0	False		,,,				2504	0.0				p.X257X		Atlas-SNP	.											.	SGCD	52	.	0			c.G770A						PASS	.	G	,,	33,3799		0,33,1883	64.0	63.0	63.0		,,770	0.0	0.0	5		63	0,8268		0,0,4134	no	intron,intron,coding-synonymous	SGCD	NM_000337.5,NM_001128209.1,NM_172244.2	,,	0,33,6017	AA,AG,GG		0.0,0.8612,0.2727	,,	,,257/257	156184786	33,12067	1916	4134	6050	SO:0001627	intron_variant	6444	exon8			CTGGTTGACCTCG	BX537948	CCDS47325.1, CCDS47326.1, CCDS47327.1	5q33-q34	2014-09-17	2002-08-29						10807	protein-coding gene	gene with protein product		601411	"""sarcoglycan, delta (35kD dystrophin-associated glycoprotein)"""			8776597, 8841194, 10974018	Standard	NM_000337		Approved	DAGD, LGMD2F, CMD1L	uc003lwd.4	Q92629		ENST00000435422.3:c.696+71G>A	5.37:g.156184786G>A		201.0	0.0	0		217.0	98.0	0.451613	NM_172244	A8K9S9|Q53XA5|Q99644	Silent	SNP	ENST00000435422.3	37	CCDS47327.1																																																																																			G|0.998;A|0.002	0.002	strong		0.448	SGCD-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000373469.3		
CPNE7	27132	hgsc.bcm.edu	37	16	89645345	89645345	+	Missense_Mutation	SNP	C	C	A	rs9944362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89645345C>A	ENST00000268720.5	+	3	568	c.438C>A	c.(436-438)caC>caA	p.H146Q	CPNE7_ENST00000319518.8_Intron	NM_014427.4	NP_055242.1	Q9UBL6	CPNE7_HUMAN	copine VII	146					lipid metabolic process (GO:0006629)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(2)	17		all_hematologic(23;0.0748)		all cancers(4;3.63e-08)|OV - Ovarian serous cystadenocarcinoma(4;1.7e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0147)		GCGCTAAGCACTTCCTGTGCT	0.552													C|||	24	0.00479233	0.0174	0.0014	5008	,	,		16713	0.0		0.0	False		,,,				2504	0.0				p.H146Q		Atlas-SNP	.											.	CPNE7	56	.	0			c.C438A						PASS	.	C	GLN/HIS,	41,4355	46.0+/-80.4	1,39,2158	133.0	112.0	119.0		438,	-0.7	0.0	16	dbSNP_119	119	1,8599	1.2+/-3.3	0,1,4299	yes	missense,intron	CPNE7	NM_014427.4,NM_153636.2	24,	1,40,6457	AA,AC,CC		0.0116,0.9327,0.3232	,	146/634,	89645345	42,12954	2198	4300	6498	SO:0001583	missense	27132	exon3			TAAGCACTTCCTG	AJ133798	CCDS10980.1, CCDS10981.1	16q24.3	2008-07-03			ENSG00000178773	ENSG00000178773			2320	protein-coding gene	gene with protein product		605689					Standard	NM_014427		Approved		uc002fnq.3	Q9UBL6	OTTHUMG00000138051	ENST00000268720.5:c.438C>A	16.37:g.89645345C>A	ENSP00000268720:p.His146Gln	78.0	0.0	0		100.0	58.0	0.58	NM_014427		Missense_Mutation	SNP	ENST00000268720.5	37	CCDS10980.1	4	0.0018315018315018315	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	C	0.672	-0.801433	0.02841	0.009327	1.16E-4	ENSG00000178773	ENST00000268720	T	0.13089	2.62	0.471	-0.661	0.11417	C2 calcium/lipid-binding domain, CaLB (1);	432.516000	0.00520	U	0.000184	T	0.07324	0.0185	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21965	-1.0230	9	0.15066	T	0.55	.	.	.	.	rs9944362	146	Q9UBL6	CPNE7_HUMAN	Q	146	ENSP00000268720:H146Q	ENSP00000268720:H146Q	H	+	3	2	CPNE7	88172846	0.003000	0.15002	0.001000	0.08648	0.006000	0.05464	0.396000	0.20867	-0.368000	0.08040	0.205000	0.17691	CAC	C|0.998;A|0.002	0.002	strong		0.552	CPNE7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269929.2		
KIRREL2	84063	hgsc.bcm.edu	37	19	36353880	36353880	+	Missense_Mutation	SNP	G	G	A	rs35775934	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36353880G>A	ENST00000360202.5	+	13	1865	c.1667G>A	c.(1666-1668)aGc>aAc	p.S556N	KIRREL2_ENST00000592409.1_Missense_Mutation_p.S521N|KIRREL2_ENST00000262625.7_Missense_Mutation_p.S556N|NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000347900.6_Missense_Mutation_p.S506N	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	556			S -> N (in dbSNP:rs35775934).		cell adhesion (GO:0007155)|negative regulation of protein phosphorylation (GO:0001933)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)				breast(2)|central_nervous_system(1)|endometrium(6)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	48	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CCTGGCAGCAGCGACGGCTCC	0.607													G|||	165	0.0329473	0.121	0.0072	5008	,	,		16611	0.0		0.0	False		,,,				2504	0.0				p.S556N		Atlas-SNP	.											KIRREL2_ENST00000262625,NS,carcinoma,-1,2	KIRREL2	170	2	0			c.G1667A						PASS	.	G	ASN/SER,ASN/SER,ASN/SER	503,3901		19,465,1718	38.0	36.0	37.0		1667,1517,1667	3.9	0.9	19	dbSNP_126	37	4,8592		0,4,4294	yes	missense,missense,missense	KIRREL2	NM_032123.5,NM_199179.2,NM_199180.2	46,46,46	19,469,6012	AA,AG,GG		0.0465,11.4214,3.9	benign,benign,benign	556/634,506/584,556/709	36353880	507,12493	2202	4298	6500	SO:0001583	missense	84063	exon13			GCAGCAGCGACGG	AL136654	CCDS12479.1, CCDS12480.1, CCDS12481.1	19q13.13	2013-01-29				ENSG00000126259		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18816	protein-coding gene	gene with protein product		607762				12837264, 12504092	Standard	NM_199180		Approved	NLG1, NEPH3, FILTRIN, DKFZp564A1164, MGC15718	uc002ocb.4	Q6UWL6		ENST00000360202.5:c.1667G>A	19.37:g.36353880G>A	ENSP00000353331:p.Ser556Asn	65.0	0.0	0		65.0	65.0	1	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Missense_Mutation	SNP	ENST00000360202.5	37	CCDS12481.1	45	0.020604395604395604	39	0.07926829268292683	6	0.016574585635359115	0	0.0	0	0.0	G	13.69	2.311961	0.40895	0.114214	4.65E-4	ENSG00000126259	ENST00000262625;ENST00000347900;ENST00000360202;ENST00000341658;ENST00000270294	T;T;T	0.65178	-0.13;0.1;-0.14	4.98	3.94	0.45596	.	0.000000	0.45126	D	0.000386	T	0.03651	0.0104	L	0.56769	1.78	0.25267	N	0.989546	D;D;D;D;D	0.71674	0.993;0.998;0.993;0.996;0.996	D;D;D;D;D	0.80764	0.968;0.994;0.968;0.986;0.986	T	0.05451	-1.0884	10	0.21540	T	0.41	-13.9497	8.3131	0.32084	0.1065:0.0:0.8935:0.0	rs35775934	556;536;556;506;556	F1T0I2;Q6UWL6-4;Q6UWL6;Q6UWL6-3;Q6UWL6-2	.;.;KIRR2_HUMAN;.;.	N	556;506;556;536;67	ENSP00000262625:S556N;ENSP00000345067:S506N;ENSP00000353331:S556N	ENSP00000262625:S556N	S	+	2	0	KIRREL2	41045720	0.958000	0.32768	0.945000	0.38365	0.102000	0.19082	1.580000	0.36547	2.321000	0.78463	0.561000	0.74099	AGC	G|0.959;A|0.041	0.041	strong		0.607	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123	
S100A3	6274	hgsc.bcm.edu	37	1	153520203	153520203	+	Silent	SNP	G	G	A	rs41265164	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:153520203G>A	ENST00000368713.3	-	3	457	c.261C>T	c.(259-261)caC>caT	p.H87H	S100A4_ENST00000368715.1_5'Flank|S100A4_ENST00000368716.4_5'Flank|S100A4_ENST00000354332.4_5'Flank|S100A4_ENST00000481009.1_5'Flank|S100A4_ENST00000368714.1_Intron|S100A3_ENST00000368712.1_Silent_p.H87H	NM_002960.1	NP_002951.1	P33764	S10A3_HUMAN	S100 calcium binding protein A3	87						cytoplasm (GO:0005737)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(1)|liver(1)|lung(1)	3	all_lung(78;5.98e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			TGAAGTACTCGTGGCAGTAGA	0.592													G|||	760	0.151757	0.4228	0.1037	5008	,	,		19755	0.0149		0.0517	False		,,,				2504	0.0634				p.H87H		Atlas-SNP	.											.	S100A3	7	.	0			c.C261T						PASS	.	G		1633,2773	502.5+/-365.3	318,997,888	157.0	139.0	145.0		261	-2.6	1.0	1	dbSNP_127	145	466,8134	137.9+/-194.8	16,434,3850	no	coding-synonymous	S100A3	NM_002960.1		334,1431,4738	AA,AG,GG		5.4186,37.0631,16.1387		87/102	153520203	2099,10907	2203	4300	6503	SO:0001819	synonymous_variant	6274	exon3			GTACTCGTGGCAG	BC012893	CCDS1043.1	1q21	2008-02-05	2001-11-28		ENSG00000188015	ENSG00000188015		"""S100 calcium binding proteins"""	10493	protein-coding gene	gene with protein product		176992	"""S100 calcium-binding protein A3"""	S100E		8341667	Standard	NM_002960		Approved		uc001fca.1	P33764	OTTHUMG00000013550	ENST00000368713.3:c.261C>T	1.37:g.153520203G>A		156.0	0.0	0		146.0	74.0	0.506849	NM_002960	D3DV51|Q6FGE4	Silent	SNP	ENST00000368713.3	37	CCDS1043.1																																																																																			A|0.147;C|0.000;G|0.853;T|0.000	0.147	strong		0.592	S100A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037726.1	NM_002960	
ORM2	5005	hgsc.bcm.edu	37	9	117094159	117094159	+	Missense_Mutation	SNP	G	G	A	rs148221879	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117094159G>A	ENST00000431067.2	+	5	526	c.490G>A	c.(490-492)Gac>Aac	p.D164N	ORM2_ENST00000412657.1_3'UTR	NM_000608.2	NP_000599.1	P19652	A1AG2_HUMAN	orosomucoid 2	164					acute-phase response (GO:0006953)|regulation of immune system process (GO:0002682)|transport (GO:0006810)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(1)	7		Myeloproliferative disorder(63;0.163)			Chlorpromazine(DB00477)|Oxycodone(DB00497)|Thalidomide(DB01041)	CGAAGCTCTCGACTGCTTGTG	0.572													G|||	14	0.00279553	0.0083	0.0014	5008	,	,		18564	0.0		0.001	False		,,,				2504	0.001				p.D164N	NSCLC(65;867 1308 1814 2391 12508)	Atlas-SNP	.											.	ORM2	13	.	0			c.G490A						PASS	.	G	ASN/ASP	54,4352	53.6+/-89.4	1,52,2150	103.0	99.0	100.0		490	-5.1	0.0	9	dbSNP_134	100	0,8600		0,0,4300	yes	missense	ORM2	NM_000608.2	23	1,52,6450	AA,AG,GG		0.0,1.2256,0.4152		164/202	117094159	54,12952	2203	4300	6503	SO:0001583	missense	5005	exon5			GCTCTCGACTGCT		CCDS6804.1	9q32	2013-09-19			ENSG00000228278	ENSG00000228278		"""Lipocalins"""	8499	protein-coding gene	gene with protein product	"""alpha-1-acid glycoprotein, type 2"""	138610				4711474, 2970990	Standard	NM_000608		Approved	AGP-B, AGP-B', AGP2		P19652	OTTHUMG00000021014	ENST00000431067.2:c.490G>A	9.37:g.117094159G>A	ENSP00000394936:p.Asp164Asn	194.0	0.0	0		215.0	152.0	0.706977	NM_000608	B2R5L2|Q16571|Q5T538|Q6IB74	Missense_Mutation	SNP	ENST00000431067.2	37	CCDS6804.1	3	0.0013736263736263737	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	0	0.0	G	14.61	2.587382	0.46110	0.012256	0.0	ENSG00000228278	ENST00000431067	T	0.07567	3.18	3.83	-5.07	0.02938	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	1.832830	0.02642	N	0.105407	T	0.03827	0.0108	L	0.36672	1.1	0.09310	N	1	P	0.39748	0.686	B	0.27076	0.076	T	0.35822	-0.9773	10	0.24483	T	0.36	-2.7618	10.116	0.42591	0.3551:0.0:0.6449:0.0	.	164	P19652	A1AG2_HUMAN	N	164	ENSP00000394936:D164N	ENSP00000394936:D164N	D	+	1	0	ORM2	116133980	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-1.487000	0.02310	-1.079000	0.03113	0.544000	0.68410	GAC	G|0.997;A|0.003	0.003	strong		0.572	ORM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055432.1	NM_000608	
CLASRP	11129	hgsc.bcm.edu	37	19	45561014	45561014	+	Silent	SNP	A	A	G	rs76953457	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45561014A>G	ENST00000221455.3	+	7	569	c.471A>G	c.(469-471)gcA>gcG	p.A157A	CLASRP_ENST00000544944.2_Silent_p.A157A|CLASRP_ENST00000391953.4_Silent_p.A95A	NM_007056.2	NP_008987	Q8N2M8	CLASR_HUMAN	CLK4-associating serine/arginine rich protein	157					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|pancreas(2)|prostate(1)	16						TCAGGCTGGCAGAGAAGAAGG	0.637													A|||	50	0.00998403	0.034	0.0072	5008	,	,		19589	0.0		0.0	False		,,,				2504	0.0				p.A157A		Atlas-SNP	.											.	CLASRP	44	.	0			c.A471G						PASS	.	A		108,4298	85.3+/-124.0	1,106,2096	111.0	99.0	103.0		471	-5.3	0.9	19	dbSNP_131	103	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CLASRP	NM_007056.2		1,107,6395	GG,GA,AA		0.0116,2.4512,0.8381		157/675	45561014	109,12897	2203	4300	6503	SO:0001819	synonymous_variant	11129	exon7			GCTGGCAGAGAAG	AF042800	CCDS12652.2, CCDS62710.1	19q13.3	2010-09-21	2010-09-21	2010-09-21	ENSG00000104859	ENSG00000104859			17731	protein-coding gene	gene with protein product	"""Clk4 associating SR-related protein"""		"""splicing factor, arginine/serine-rich 16"""	SFRS16		12169693	Standard	NM_007056		Approved	SWAP2, CLASP	uc002pak.3	Q8N2M8	OTTHUMG00000150189	ENST00000221455.3:c.471A>G	19.37:g.45561014A>G		75.0	0.0	0		70.0	29.0	0.414286	NM_007056	B4DDT8|F8WAG9|O96026|Q6UW71|Q96DX2	Silent	SNP	ENST00000221455.3	37	CCDS12652.2																																																																																			A|0.990;G|0.010	0.010	strong		0.637	CLASRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316749.1	NM_007056	
SGK223	157285	hgsc.bcm.edu	37	8	8175868	8175868	+	Silent	SNP	C	C	T	rs114026601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:8175868C>T	ENST00000520004.1	-	6	4281	c.4017G>A	c.(4015-4017)tcG>tcA	p.S1339S	SGK223_ENST00000330777.4_Silent_p.S1339S			Q86YV5	SG223_HUMAN		1343							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										GCGCCTCCTCCGAGGTGCCCG	0.682													C|||	123	0.0245607	0.0885	0.0072	5008	,	,		13730	0.0		0.001	False		,,,				2504	0.0				p.S1339S	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.G4017A						PASS	.	C		318,3830		13,292,1769	64.0	73.0	70.0		4017	-6.6	0.1	8	dbSNP_132	70	1,8381		0,1,4190	no	coding-synonymous	SGK223	NM_001080826.1		13,293,5959	TT,TC,CC		0.0119,7.6663,2.5459		1339/1403	8175868	319,12211	2074	4191	6265	SO:0001819	synonymous_variant	0	exon5			CTCCTCCGAGGTG																												ENST00000520004.1:c.4017G>A	8.37:g.8175868C>T		91.0	0.0	0		109.0	68.0	0.623853	NM_001080826	Q8N3N5	Silent	SNP	ENST00000520004.1	37	CCDS43706.1																																																																																			C|0.988;T|0.012	0.012	strong		0.682	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
IGSF22	283284	hgsc.bcm.edu	37	11	18731905	18731905	+	Silent	SNP	T	T	A	rs114511413	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:18731905T>A	ENST00000513874.1	-	17	2809	c.2670A>T	c.(2668-2670)ccA>ccT	p.P890P	RP11-1081L13.4_ENST00000527285.1_RNA	NM_173588.3	NP_775859	Q8N9C0	IGS22_HUMAN	immunoglobulin superfamily, member 22	888	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.									NS(2)|autonomic_ganglia(1)|breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(20)|ovary(4)|prostate(4)|skin(3)	56						CTGAGCTGGATGGCACACTGG	0.493													T|||	67	0.0133786	0.0484	0.0043	5008	,	,		20918	0.0		0.0	False		,,,				2504	0.0				p.P890P		Atlas-SNP	.											.	IGSF22	211	.	0			c.A2670T						PASS	.	T		123,3791		3,117,1837	119.0	119.0	119.0		2670	-0.4	0.2	11	dbSNP_132	119	3,8295		0,3,4146	no	coding-synonymous	IGSF22	NM_173588.3		3,120,5983	AA,AT,TT		0.0362,3.1426,1.0318		890/1327	18731905	126,12086	1957	4149	6106	SO:0001819	synonymous_variant	283284	exon17			GCTGGATGGCACA	AK095113	CCDS41625.1, CCDS41625.2	11p15.1	2014-06-06			ENSG00000179057	ENSG00000179057		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26750	protein-coding gene	gene with protein product							Standard	NM_173588		Approved	FLJ37794	uc009yht.2	Q8N9C0	OTTHUMG00000160502	ENST00000513874.1:c.2670A>T	11.37:g.18731905T>A		133.0	0.0	0		110.0	53.0	0.481818	NM_173588	A6NNA0|D6RGV7	Silent	SNP	ENST00000513874.1	37	CCDS41625.2																																																																																			T|0.991;A|0.009	0.009	strong		0.493	IGSF22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360850.2	NM_173588	
ZFP28	140612	hgsc.bcm.edu	37	19	57050521	57050521	+	Missense_Mutation	SNP	G	G	A	rs199655023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:57050521G>A	ENST00000301318.3	+	1	205	c.134G>A	c.(133-135)gGa>gAa	p.G45E	AC005498.3_ENST00000593218.1_lincRNA|ZFP28_ENST00000594386.1_3'UTR|ZFP28_ENST00000591844.1_Missense_Mutation_p.G45E	NM_020828.1	NP_065879.1	Q8NHY6	ZFP28_HUMAN	ZFP28 zinc finger protein	45					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(1)|large_intestine(14)|lung(6)|ovary(1)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	35		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0302)		CCTGCCCGGGGAAGGCCGCGC	0.726													G|||	19	0.00379393	0.0144	0.0	5008	,	,		8689	0.0		0.0	False		,,,				2504	0.0				p.G45E	Ovarian(124;554 1662 19430 21141 52494)	Atlas-SNP	.											.	ZFP28	99	.	0			c.G134A						PASS	.	G	GLU/GLY	32,4078		0,32,2023	6.0	8.0	7.0		134	2.7	1.0	19		7	2,8204		0,2,4101	yes	missense	ZFP28	NM_020828.1	98	0,34,6124	AA,AG,GG		0.0244,0.7786,0.2761	probably-damaging	45/869	57050521	34,12282	2055	4103	6158	SO:0001583	missense	140612	exon1			CCCGGGGAAGGCC		CCDS12946.1	19q13.43	2013-01-08	2012-11-27			ENSG00000196867		"""Zinc fingers, C2H2-type"", ""-"""	17801	protein-coding gene	gene with protein product			"""zinc finger protein 28 homolog (mouse)"""				Standard	NM_020828		Approved	KIAA1431, mkr5	uc002qnj.3	Q8NHY6		ENST00000301318.3:c.134G>A	19.37:g.57050521G>A	ENSP00000301318:p.Gly45Glu	37.0	0.0	0		57.0	26.0	0.45614	NM_020828	A0JNV6|K7ES88|Q8NHU8|Q9BY30|Q9P2B6	Missense_Mutation	SNP	ENST00000301318.3	37	CCDS12946.1	.	.	.	.	.	.	.	.	.	.	G	14.82	2.650497	0.47362	0.007786	2.44E-4	ENSG00000196867	ENST00000301318	T	0.05717	3.4	2.74	2.74	0.32292	.	0.000000	0.31301	U	0.007892	T	0.06280	0.0162	N	0.24115	0.695	0.34331	D	0.687738	D;D	0.89917	0.999;1.0	D;D	0.87578	0.998;0.998	T	0.11227	-1.0596	10	0.06757	T	0.87	.	9.1377	0.36883	0.0:0.0:1.0:0.0	.	45;45	Q8NHY6;A8K0L8	ZFP28_HUMAN;.	E	45	ENSP00000301318:G45E	ENSP00000301318:G45E	G	+	2	0	ZFP28	61742333	0.909000	0.30893	0.986000	0.45419	0.823000	0.46562	0.683000	0.25349	1.817000	0.53016	0.462000	0.41574	GGA	.	.	weak		0.726	ZFP28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458409.1	NM_020828	
OR2A4	79541	hgsc.bcm.edu	37	6	132021722	132021722	+	Silent	SNP	G	G	A	rs145289654	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:132021722G>A	ENST00000315453.2	-	1	913	c.820C>T	c.(820-822)Ctg>Ttg	p.L274L	ENPP3_ENST00000357639.3_Intron|ENPP3_ENST00000414305.1_Intron|ENPP3_ENST00000358229.5_Intron	NM_030908.1	NP_112170.1	O95047	OR2A4_HUMAN	olfactory receptor, family 2, subfamily A, member 4	274					positive regulation of cytokinesis (GO:0032467)|regulation of actin cytoskeleton organization (GO:0032956)	cleavage furrow (GO:0032154)|Flemming body (GO:0090543)|integral component of membrane (GO:0016021)|mitotic spindle midzone (GO:1990023)|mitotic spindle pole (GO:0097431)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(1)|ovary(1)|skin(1)	3	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.018)|OV - Ovarian serous cystadenocarcinoma(155;0.041)		TGAAACAGCAGGAGATATTTC	0.453													g|||	76	0.0151757	0.0545	0.0058	5008	,	,		22576	0.0		0.0	False		,,,				2504	0.0				p.L274L		Atlas-SNP	.											.	OR2A4	17	.	0			c.C820T						PASS	.	G	,	198,3340		56,86,1627	20.0	30.0	27.0		,820	0.7	0.9	6	dbSNP_134	27	0,8486		0,0,4243	no	intron,coding-synonymous	ENPP3,OR2A4	NM_005021.3,NM_030908.1	,	56,86,5870	AA,AG,GG		0.0,5.5964,1.6467	,	,274/311	132021722	198,11826	1769	4243	6012	SO:0001819	synonymous_variant	79541	exon1			ACAGCAGGAGATA	AC005587	CCDS5149.1	6q23	2012-08-09	2003-05-22		ENSG00000180658	ENSG00000180658		"""GPCR / Class A : Olfactory receptors"""	14729	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily A, member 10"""	OR2A10			Standard	NM_030908		Approved		uc011ecd.2	O95047	OTTHUMG00000016316	ENST00000315453.2:c.820C>T	6.37:g.132021722G>A		770.0	2.0	0.0025974		935.0	254.0	0.271658	NM_030908	Q0VAR3|Q6IF18|Q9NQN0	Silent	SNP	ENST00000315453.2	37	CCDS5149.1																																																																																			G|0.995;A|0.005	0.005	strong		0.453	OR2A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109221.1	NM_030908	
ANAPC16	119504	hgsc.bcm.edu	37	10	73992862	73992862	+	Silent	SNP	C	C	G	rs9275	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73992862C>G	ENST00000299381.4	+	4	439	c.321C>G	c.(319-321)ccC>ccG	p.P107P	ANAPC16_ENST00000470481.2_3'UTR	NM_001242546.1|NM_001242547.1|NM_001242548.1|NM_173473.3	NP_001229475.1|NP_001229476.1|NP_001229477.1|NP_775744.1	Q96DE5	APC16_HUMAN	anaphase promoting complex subunit 16	107					mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	anaphase-promoting complex (GO:0005680)|cytoplasm (GO:0005737)				large_intestine(1)|ovary(1)	2						GATTCACCCCCTCTTCAGGTT	0.542													C|||	364	0.0726837	0.2595	0.0274	5008	,	,		14954	0.0		0.002	False		,,,				2504	0.0				p.P107P		Atlas-SNP	.											.	ANAPC16	10	.	0			c.C321G						PASS	.	C	,,,	919,3487	344.1+/-307.9	90,739,1374	66.0	64.0	65.0		321,321,246,321	-0.3	1.0	10	dbSNP_52	65	13,8587	9.1+/-34.3	0,13,4287	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ANAPC16	NM_001242546.1,NM_001242547.1,NM_001242548.1,NM_173473.3	,,,	90,752,5661	GG,GC,CC		0.1512,20.8579,7.1659	,,,	107/111,107/111,82/86,107/111	73992862	932,12074	2203	4300	6503	SO:0001819	synonymous_variant	119504	exon5			CACCCCCTCTTCA	BC009530	CCDS7314.1, CCDS73147.1	10q22.2	2011-08-12	2010-04-06	2010-04-06	ENSG00000166295	ENSG00000166295		"""Anaphase promoting complex subunits"""	26976	protein-coding gene	gene with protein product	"""centromere protein 27"""	613427	"""chromosome 10 open reading frame 104"""	C10orf104		14702039, 20360068	Standard	NM_001242546		Approved	bA570G20.3, FLJ33728, APC16, CENP-27	uc021psp.1	Q96DE5	OTTHUMG00000018433	ENST00000299381.4:c.321C>G	10.37:g.73992862C>G		40.0	0.0	0		45.0	26.0	0.577778	NM_001242546		Silent	SNP	ENST00000299381.4	37	CCDS7314.1																																																																																			G|0.064;C|0.936	0.064	strong		0.542	ANAPC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048565.2	NM_173473	
RAP1GAP	5909	hgsc.bcm.edu	37	1	21932598	21932598	+	Silent	SNP	G	G	A	rs150973141	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:21932598G>A	ENST00000374765.4	-	18	1589	c.1389C>T	c.(1387-1389)ttC>ttT	p.F463F	RAP1GAP_ENST00000290101.4_Silent_p.F527F|RAP1GAP_ENST00000374761.2_Silent_p.F494F|RAP1GAP_ENST00000374763.2_Silent_p.F463F|RAP1GAP_ENST00000542643.2_Silent_p.F463F	NM_002885.2	NP_002876.2	P47736	RPGP1_HUMAN	RAP1 GTPase activating protein	463					GTP catabolic process (GO:0006184)|positive regulation of Rap GTPase activity (GO:0032854)|regulation of Ras GTPase activity (GO:0032318)|signal transduction (GO:0007165)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|GTPase activity (GO:0003924)|protein homodimerization activity (GO:0042803)|Rap GTPase activator activity (GO:0046582)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	17		Colorectal(325;0.000147)|Renal(390;0.000734)|Lung NSC(340;0.000861)|all_lung(284;0.000901)|Breast(348;0.012)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0192)|OV - Ovarian serous cystadenocarcinoma(117;2.3e-26)|COAD - Colon adenocarcinoma(152;1.59e-05)|GBM - Glioblastoma multiforme(114;2.7e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000354)|STAD - Stomach adenocarcinoma(196;0.00645)|KIRC - Kidney renal clear cell carcinoma(1967;0.00862)|READ - Rectum adenocarcinoma(331;0.0625)|Lung(427;0.146)		TGTTGGGCGCGAAGCTCCCGC	0.682																																					p.F527F		Atlas-SNP	.											.	RAP1GAP	119	.	0			c.C1581T						PASS	.	G	,,	7,4383		0,7,2188	55.0	33.0	40.0		1389,1581,1389	-2.1	0.1	1	dbSNP_134	40	0,8592		0,0,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	RAP1GAP	NM_001145657.1,NM_001145658.1,NM_002885.2	,,	0,7,6484	AA,AG,GG		0.0,0.1595,0.0539	,,	463/682,527/728,463/664	21932598	7,12975	2195	4296	6491	SO:0001819	synonymous_variant	5909	exon18			GGGCGCGAAGCTC	BC054490	CCDS218.1, CCDS53276.1, CCDS53277.1	1p36.1-p35	2009-09-14	2006-04-12	2006-04-12	ENSG00000076864	ENSG00000076864			9858	protein-coding gene	gene with protein product		600278	"""RAP1, GTPase activating protein 1"""	RAP1GA1		1904317	Standard	NM_001145657		Approved	KIAA0474, RAP1GAP1, RAP1GAPII	uc001bew.3	P47736	OTTHUMG00000007513	ENST00000374765.4:c.1389C>T	1.37:g.21932598G>A		106.0	0.0	0		114.0	50.0	0.438596	NM_001145658	J3QSS6|O75062|Q5T3S9|Q5T3T4|Q7Z5S8|Q9UQ51	Silent	SNP	ENST00000374765.4	37	CCDS218.1																																																																																			G|0.999;A|0.001	0.001	strong		0.682	RAP1GAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019759.2	NM_002885	
MRPS9	64965	hgsc.bcm.edu	37	2	105708936	105708936	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:105708936G>C	ENST00000258455.3	+	8	839	c.729G>C	c.(727-729)agG>agC	p.R243S		NM_182640.2	NP_872578.1	P82933	RT09_HUMAN	mitochondrial ribosomal protein S9	243					DNA damage response, detection of DNA damage (GO:0042769)|peptide biosynthetic process (GO:0043043)|translation (GO:0006412)	mitochondrial small ribosomal subunit (GO:0005763)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	18						TTGTGCAGAGGTTTCGAAGAA	0.388																																					p.R243S		Atlas-SNP	.											.	MRPS9	32	.	0			c.G729C						PASS	.						140.0	143.0	142.0					2																	105708936		2203	4300	6503	SO:0001583	missense	64965	exon8			GCAGAGGTTTCGA		CCDS2065.1	2q12.1	2012-09-13			ENSG00000135972	ENSG00000135972		"""Mitochondrial ribosomal proteins / small subunits"""	14501	protein-coding gene	gene with protein product	"""28S ribosomal protein S9, mitochondrial"""	611975				11279123	Standard	NM_182640		Approved	RPMS9, MRP-S9, S9mt	uc002tcn.4	P82933	OTTHUMG00000130807	ENST00000258455.3:c.729G>C	2.37:g.105708936G>C	ENSP00000258455:p.Arg243Ser	81.0	0.0	0		90.0	46.0	0.511111	NM_182640	Q6PG40	Missense_Mutation	SNP	ENST00000258455.3	37	CCDS2065.1	.	.	.	.	.	.	.	.	.	.	G	11.24	1.580061	0.28180	.	.	ENSG00000135972	ENST00000258455	D	0.92099	-2.97	5.61	1.81	0.25067	.	0.318283	0.38111	N	0.001806	D	0.86896	0.6043	M	0.61703	1.905	0.42674	D	0.993529	B	0.16396	0.017	B	0.10450	0.005	T	0.76602	-0.2899	10	0.39692	T	0.17	-24.4138	2.1982	0.03916	0.2617:0.1209:0.4925:0.1249	.	243	P82933	RT09_HUMAN	S	243	ENSP00000258455:R243S	ENSP00000258455:R243S	R	+	3	2	MRPS9	105075368	0.997000	0.39634	0.988000	0.46212	0.789000	0.44602	0.322000	0.19576	0.115000	0.18071	0.655000	0.94253	AGG	.	.	none		0.388	MRPS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253352.1	NM_182640	
GAB4	128954	hgsc.bcm.edu	37	22	17445710	17445710	+	Silent	SNP	C	C	T	rs5992599	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:17445710C>T	ENST00000400588.1	-	8	1529	c.1422G>A	c.(1420-1422)acG>acA	p.T474T	GAB4_ENST00000523144.1_5'Flank	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	474										breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(24)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44		all_epithelial(15;0.112)|Lung NSC(13;0.248)				TGATGCTCTGCGTGGAGATGG	0.572													C|||	202	0.0403355	0.1498	0.0058	5008	,	,		19710	0.0		0.0	False		,,,				2504	0.0				p.T474T		Atlas-SNP	.											.	GAB4	95	.	0			c.G1422A						PASS	.	C		504,3876	213.5+/-233.1	31,442,1717	151.0	162.0	158.0		1422	-3.9	0.3	22	dbSNP_114	158	2,8580	2.2+/-6.3	0,2,4289	no	coding-synonymous	GAB4	NM_001037814.1		31,444,6006	TT,TC,CC		0.0233,11.5068,3.9037		474/575	17445710	506,12456	2190	4291	6481	SO:0001819	synonymous_variant	128954	exon8			GCTCTGCGTGGAG	AK057252	CCDS42976.1	22q11.2	2013-01-10			ENSG00000215568	ENSG00000215568		"""Pleckstrin homology (PH) domain containing"""	18325	protein-coding gene	gene with protein product							Standard	NM_001037814		Approved		uc002zlw.3	Q2WGN9	OTTHUMG00000149992	ENST00000400588.1:c.1422G>A	22.37:g.17445710C>T		208.0	1.0	0.00480769		259.0	127.0	0.490348	NM_001037814		Silent	SNP	ENST00000400588.1	37	CCDS42976.1																																																																																			C|0.954;T|0.046	0.046	strong		0.572	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882	
USP44	84101	hgsc.bcm.edu	37	12	95927172	95927172	+	Silent	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:95927172A>G	ENST00000258499.3	-	2	1149	c.861T>C	c.(859-861)gtT>gtC	p.V287V	USP44_ENST00000537435.2_Silent_p.V287V|USP44_ENST00000552440.1_Silent_p.V287V|USP44_ENST00000393091.2_Silent_p.V287V	NM_001278393.1|NM_032147.2	NP_001265322.1|NP_115523.2	Q9H0E7	UBP44_HUMAN	ubiquitin specific peptidase 44	287	USP.				mitotic nuclear division (GO:0007067)|negative regulation of mitotic anaphase-promoting complex activity (GO:0060564)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deubiquitination (GO:0016579)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)|regulation of spindle checkpoint (GO:0090231)	nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(5)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	36						ACACCTGAAGAACAGAATTCA	0.378																																					p.V287V		Atlas-SNP	.											.	USP44	83	.	0			c.T861C						PASS	.						77.0	79.0	78.0					12																	95927172		2203	4300	6503	SO:0001819	synonymous_variant	84101	exon2			CTGAAGAACAGAA	AK027434	CCDS9053.1	12q21.33	2005-08-08	2005-08-08			ENSG00000136014		"""Ubiquitin-specific peptidases"""	20064	protein-coding gene	gene with protein product		610993	"""ubiquitin specific protease 44"""			12838346	Standard	NM_001278393		Approved	FLJ14528	uc001teg.3	Q9H0E7		ENST00000258499.3:c.861T>C	12.37:g.95927172A>G		66.0	0.0	0		76.0	35.0	0.460526	NM_032147	B2RDW3	Silent	SNP	ENST00000258499.3	37	CCDS9053.1																																																																																			.	.	none		0.378	USP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408312.1	NM_032147	
SETD9	133383	hgsc.bcm.edu	37	5	56205559	56205559	+	Silent	SNP	C	C	T	rs80198735	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:56205559C>T	ENST00000285947.2	+	1	473	c.87C>T	c.(85-87)agC>agT	p.S29S	AC008937.3_ENST00000453721.1_RNA|SETD9_ENST00000475908.1_Intron|SETD9_ENST00000541720.1_Silent_p.S29S	NM_153706.3	NP_714917.2	Q8NE22	SETD9_HUMAN	SET domain containing 9	29							methyltransferase activity (GO:0008168)										TGAACCTAAGCCACAACCCGA	0.687													C|||	53	0.0105831	0.0386	0.0029	5008	,	,		9227	0.0		0.0	False		,,,				2504	0.0				p.S29S		Atlas-SNP	.											.	.	.	.	0			c.C87T						PASS	.	C	,	152,4254	98.9+/-137.6	5,142,2056	49.0	32.0	38.0		87,87	2.4	0.5	5	dbSNP_131	38	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	C5orf35	NM_001171990.1,NM_153706.3	,	5,143,6355	TT,TC,CC		0.0116,3.4498,1.1764	,	29/272,29/300	56205559	153,12853	2203	4300	6503	SO:0001819	synonymous_variant	133383	exon1			CCTAAGCCACAAC	BC036528	CCDS3972.1	5q11.2	2012-02-23	2012-02-23	2012-02-23	ENSG00000155542	ENSG00000155542			28508	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 35"""	C5orf35		20930037	Standard	NM_153706		Approved	MGC33648	uc003jqx.3	Q8NE22	OTTHUMG00000059485	ENST00000285947.2:c.87C>T	5.37:g.56205559C>T		75.0	0.0	0		98.0	34.0	0.346939	NM_153706	F5H713	Silent	SNP	ENST00000285947.2	37	CCDS3972.1																																																																																			C|0.987;T|0.013	0.013	strong		0.687	SETD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132304.2	NM_153706	
OR11A1	26531	hgsc.bcm.edu	37	6	29395180	29395180	+	Missense_Mutation	SNP	A	A	G	rs61978565	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29395180A>G	ENST00000377149.1	-	5	711	c.239T>C	c.(238-240)aTg>aCg	p.M80T	OR5V1_ENST00000377154.1_Intron|OR11A1_ENST00000377147.2_Missense_Mutation_p.M80T|OR11A1_ENST00000377148.1_Missense_Mutation_p.M80T			Q9GZK7	O11A1_HUMAN	olfactory receptor, family 11, subfamily A, member 1	80						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.M80T(1)		cervix(1)|large_intestine(1)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	19						CATTTTTGGCATCACTGCGGA	0.483													A|||	219	0.04373	0.1384	0.0115	5008	,	,		19957	0.0119		0.0129	False		,,,				2504	0.0031				p.M80T		Atlas-SNP	.											OR11A1,NS,carcinoma,0,1	OR11A1	30	1	1	Substitution - Missense(1)	pancreas(1)	c.T239C						PASS	.	A	THR/MET	369,2651		26,317,1167	70.0	63.0	66.0		239	3.8	0.9	6	dbSNP_129	66	34,5384		0,34,2675	yes	missense	OR11A1	NM_013937.2	81	26,351,3842	GG,GA,AA		0.6275,12.2185,4.776	benign	80/316	29395180	403,8035	1510	2709	4219	SO:0001583	missense	26531	exon1			TTTGGCATCACTG		CCDS34363.1	6p22.2-p21.31	2014-02-19	2002-02-28		ENSG00000204694	ENSG00000204694		"""GPCR / Class A : Olfactory receptors"""	8176	protein-coding gene	gene with protein product			"""olfactory receptor, family 11, subfamily A, member 2"""	OR11A2			Standard	XM_005249001		Approved	hs6M1-18	uc003nmg.3	Q9GZK7	OTTHUMG00000031225	ENST00000377149.1:c.239T>C	6.37:g.29395180A>G	ENSP00000366354:p.Met80Thr	60.0	0.0	0		75.0	44.0	0.586667	NM_013937	A2BF33|A6NFQ3|B0S7T2|Q5ST16|Q9GZK8	Missense_Mutation	SNP	ENST00000377149.1	37	CCDS34363.1	102	0.046703296703296704	74	0.15040650406504066	7	0.019337016574585635	10	0.017482517482517484	11	0.014511873350923483	A	8.985	0.976299	0.18736	0.122185	0.006275	ENSG00000204694	ENST00000377148;ENST00000377149;ENST00000377147	T;T;T	0.02974	4.09;4.09;4.09	3.78	3.78	0.43462	GPCR, rhodopsin-like superfamily (1);	0.297272	0.18047	U	0.153413	T	0.00524	0.0017	N	0.01209	-0.955	0.18873	N	0.999989	B	0.13594	0.008	B	0.14578	0.011	T	0.51028	-0.8757	10	0.56958	D	0.05	-9.2563	11.5265	0.50582	1.0:0.0:0.0:0.0	.	80	Q9GZK7	O11A1_HUMAN	T	80	ENSP00000366353:M80T;ENSP00000366354:M80T;ENSP00000366352:M80T	ENSP00000366352:M80T	M	-	2	0	OR11A1	29503159	0.000000	0.05858	0.925000	0.36789	0.702000	0.40608	0.971000	0.29396	1.569000	0.49696	0.333000	0.21579	ATG	A|0.957;G|0.043	0.043	strong		0.483	OR11A1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000193778.1		
HMCN1	83872	hgsc.bcm.edu	37	1	186043899	186043899	+	Silent	SNP	T	T	C	rs77026548	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:186043899T>C	ENST00000271588.4	+	53	8395	c.8166T>C	c.(8164-8166)aaT>aaC	p.N2722N	HMCN1_ENST00000367492.2_Silent_p.N2722N	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2722	Ig-like C2-type 25.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						ATCATGTTAATATTGCTGCGA	0.383													T|||	153	0.0305511	0.1104	0.0086	5008	,	,		14973	0.0		0.001	False		,,,				2504	0.0				p.N2722N		Atlas-SNP	.											.	HMCN1	797	.	0			c.T8166C						PASS	.	T		425,3981	208.2+/-229.3	24,377,1802	113.0	109.0	110.0		8166	-2.0	0.1	1	dbSNP_131	110	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	HMCN1	NM_031935.2		24,383,6096	CC,CT,TT		0.0698,9.6459,3.3139		2722/5636	186043899	431,12575	2203	4300	6503	SO:0001819	synonymous_variant	83872	exon53			TGTTAATATTGCT	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.8166T>C	1.37:g.186043899T>C		119.0	0.0	0		126.0	61.0	0.484127	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	37	CCDS30956.1																																																																																			T|0.967;C|0.033	0.033	strong		0.383	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
KLHL26	55295	hgsc.bcm.edu	37	19	18779728	18779728	+	Silent	SNP	C	C	T	rs73533829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18779728C>T	ENST00000300976.4	+	3	1611	c.1521C>T	c.(1519-1521)ggC>ggT	p.G507G	KLHL26_ENST00000599006.1_Intron	NM_018316.1	NP_060786.1	Q53HC5	KLH26_HUMAN	kelch-like family member 26	507										breast(1)|central_nervous_system(1)|kidney(1)|lung(10)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	17						TGGGTGCCGGCGGCCGCATCT	0.667													C|||	49	0.00978435	0.034	0.0043	5008	,	,		14368	0.0		0.001	False		,,,				2504	0.0				p.G507G		Atlas-SNP	.											.	KLHL26	43	.	0			c.C1521T						PASS	.	C		121,4283		1,119,2082	37.0	38.0	37.0		1521	-6.0	0.1	19	dbSNP_130	37	4,8576		0,4,4286	no	coding-synonymous	KLHL26	NM_018316.1		1,123,6368	TT,TC,CC		0.0466,2.7475,0.9627		507/616	18779728	125,12859	2202	4290	6492	SO:0001819	synonymous_variant	55295	exon3			TGCCGGCGGCCGC		CCDS12384.1	19p13.11	2013-10-15	2013-02-22		ENSG00000167487	ENSG00000167487		"""Kelch-like"", ""BTB/POZ domain containing"""	25623	protein-coding gene	gene with protein product			"""kelch-like 26 (Drosophila)"""				Standard	XM_006722785		Approved		uc002njz.1	Q53HC5	OTTHUMG00000183114	ENST00000300976.4:c.1521C>T	19.37:g.18779728C>T		24.0	0.0	0		36.0	18.0	0.5	NM_018316	Q8TAP0|Q9NUX3	Silent	SNP	ENST00000300976.4	37	CCDS12384.1																																																																																			C|0.988;T|0.012	0.012	strong		0.667	KLHL26-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465145.1	NM_018316	
TNFRSF1B	7133	hgsc.bcm.edu	37	1	12253003	12253003	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12253003G>A	ENST00000376259.3	+	6	724	c.635G>A	c.(634-636)gGg>gAg	p.G212E	MIR4632_ENST00000584158.1_RNA|TNFRSF1B_ENST00000492361.1_3'UTR	NM_001066.2	NP_001057.1	P20333	TNR1B_HUMAN	tumor necrosis factor receptor superfamily, member 1B	212					aging (GO:0007568)|cellular response to growth factor stimulus (GO:0071363)|cellular response to lipopolysaccharide (GO:0071222)|extrinsic apoptotic signaling pathway (GO:0097191)|immune response (GO:0006955)|inflammatory response (GO:0006954)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of inflammatory response (GO:0050728)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|RNA destabilization (GO:0050779)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|varicosity (GO:0043196)	tumor necrosis factor-activated receptor activity (GO:0005031)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|liver(1)|lung(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10	Ovarian(185;0.249)	Lung NSC(185;8.72e-05)|all_lung(284;9.92e-05)|Renal(390;0.000147)|Colorectal(325;0.000584)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0234)|Colorectal(212;5.52e-07)|COAD - Colon adenocarcinoma(227;0.000345)|BRCA - Breast invasive adenocarcinoma(304;0.000353)|Kidney(185;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00302)|STAD - Stomach adenocarcinoma(313;0.00815)|READ - Rectum adenocarcinoma(331;0.0284)	Etanercept(DB00005)	ATGGCCCCAGGGGCAGTACAC	0.617																																					p.G212E		Atlas-SNP	.											.	TNFRSF1B	28	.	0			c.G635A						PASS	.						165.0	121.0	136.0					1																	12253003		2203	4300	6503	SO:0001583	missense	7133	exon6			CCCCAGGGGCAGT	M32315	CCDS145.1	1p36.22	2008-02-05			ENSG00000028137	ENSG00000028137		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11917	protein-coding gene	gene with protein product		191191		TNFR2		2158863, 8702885	Standard	NM_001066		Approved	TNFBR, TNFR80, TNF-R75, TNF-R-II, p75, CD120b	uc001att.3	P20333	OTTHUMG00000001829	ENST00000376259.3:c.635G>A	1.37:g.12253003G>A	ENSP00000365435:p.Gly212Glu	76.0	0.0	0		110.0	58.0	0.527273	NM_001066	B1AJZ3|Q16042|Q6YI29|Q9UIH1	Missense_Mutation	SNP	ENST00000376259.3	37	CCDS145.1	.	.	.	.	.	.	.	.	.	.	G	3.321	-0.138774	0.06669	.	.	ENSG00000028137	ENST00000376259;ENST00000400863	D	0.86097	-2.07	3.31	-0.714	0.11219	.	2.871980	0.01167	N	0.006766	T	0.75273	0.3827	L	0.38953	1.18	0.09310	N	1	B	0.15473	0.013	B	0.12837	0.008	T	0.60840	-0.7183	10	0.02654	T	1	0.0033	6.2978	0.21095	0.4784:0.0:0.5216:0.0	.	212	P20333	TNR1B_HUMAN	E	212	ENSP00000365435:G212E	ENSP00000365435:G212E	G	+	2	0	TNFRSF1B	12175590	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.169000	0.09911	-0.138000	0.11434	-0.812000	0.03155	GGG	.	.	none		0.617	TNFRSF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005133.1	NM_001066	
FOXC1	2296	hgsc.bcm.edu	37	6	1612243	1612243	+	Silent	SNP	T	T	G	rs73406891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:1612243T>G	ENST00000380874.2	+	1	1563	c.1563T>G	c.(1561-1563)tcT>tcG	p.S521S		NM_001453.2	NP_001444.2	Q12948	FOXC1_HUMAN	forkhead box C1	521					artery morphogenesis (GO:0048844)|blood vessel remodeling (GO:0001974)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|cardiac muscle cell proliferation (GO:0060038)|collagen fibril organization (GO:0030199)|embryonic heart tube development (GO:0035050)|eye development (GO:0001654)|germ cell migration (GO:0008354)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|lacrimal gland development (GO:0032808)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process involved in outflow tract morphogenesis (GO:1902257)|negative regulation of mitotic cell cycle (GO:0045930)|neural crest cell development (GO:0014032)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|ovarian follicle development (GO:0001541)|paraxial mesoderm formation (GO:0048341)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood vessel size (GO:0050880)|regulation of organ growth (GO:0046620)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|somitogenesis (GO:0001756)|ureteric bud development (GO:0001657)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|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 regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	8	Ovarian(93;0.0733)	all_cancers(2;4.45e-07)|all_epithelial(2;4.33e-05)|all_lung(73;0.0713)|all_hematologic(90;0.0895)		Epithelial(2;0.0904)|OV - Ovarian serous cystadenocarcinoma(45;0.095)|all cancers(2;0.168)		TGAACAACTCTCCAGTGAACG	0.602													T|||	160	0.0319489	0.115	0.0101	5008	,	,		9192	0.0		0.001	False		,,,				2504	0.0				p.S521S	Pancreas(133;719 1821 3197 26645 35015)	Atlas-SNP	.											.	FOXC1	19	.	0			c.T1563G						PASS	.	T		452,3950	202.1+/-225.0	23,406,1772	64.0	47.0	52.0		1563	-4.6	1.0	6	dbSNP_130	52	4,8594	1.2+/-3.3	0,4,4295	no	coding-synonymous	FOXC1	NM_001453.2		23,410,6067	GG,GT,TT		0.0465,10.2681,3.5077		521/554	1612243	456,12544	2201	4299	6500	SO:0001819	synonymous_variant	2296	exon1			CAACTCTCCAGTG	AF048693	CCDS4473.1	6p25	2008-04-10			ENSG00000054598	ENSG00000054598		"""Forkhead boxes"""	3800	protein-coding gene	gene with protein product		601090		FKHL7, IRID1		7957066, 9620769	Standard	NM_001453		Approved	FREAC3, ARA, IGDA, IHG1	uc003mtp.3	Q12948	OTTHUMG00000016182	ENST00000380874.2:c.1563T>G	6.37:g.1612243T>G		43.0	0.0	0		61.0	24.0	0.393443	NM_001453	Q86UP7|Q9BYM1|Q9NUE5|Q9UDD0|Q9UP06	Silent	SNP	ENST00000380874.2	37	CCDS4473.1																																																																																			T|0.963;G|0.037	0.037	strong		0.602	FOXC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043450.1		
TBC1D8B	54885	hgsc.bcm.edu	37	X	106083304	106083304	+	Silent	SNP	A	A	G	rs56825776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:106083304A>G	ENST00000357242.5	+	9	1554	c.1380A>G	c.(1378-1380)tcA>tcG	p.S460S	TBC1D8B_ENST00000276175.3_Silent_p.S454S|TBC1D8B_ENST00000310452.2_Silent_p.S460S	NM_017752.2	NP_060222.2	Q0IIM8	TBC8B_HUMAN	TBC1 domain family, member 8B (with GRAM domain)	460							calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(6)|liver(4)|lung(15)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						AGGAACAGTCATGGAAAATAC	0.343													A|||	263	0.0696689	0.1876	0.0202	3775	,	,		13833	0.0		0.001	False		,,,				2504	0.0				p.S460S		Atlas-SNP	.											.	TBC1D8B	181	.	0			c.A1380G						PASS	.	A	,	857,2978		87,555,128,990,443	116.0	108.0	111.0		1380,1380	-3.8	1.0	X	dbSNP_129	111	2,6726		0,1,1,2427,1871	no	coding-synonymous,coding-synonymous	TBC1D8B	NM_017752.2,NM_198881.1	,	87,556,129,3417,2314	GG,GA,G,AA,A		0.0297,22.3468,8.1322	,	460/1121,460/633	106083304	859,9704	2203	4300	6503	SO:0001819	synonymous_variant	54885	exon9			ACAGTCATGGAAA	AK123957	CCDS14522.1, CCDS14523.1	Xq22.3	2013-01-10			ENSG00000133138	ENSG00000133138		"""EF-hand domain containing"""	24715	protein-coding gene	gene with protein product						8889548	Standard	NM_017752		Approved	FLJ20298, RP11-321G1.1	uc004emo.3	Q0IIM8	OTTHUMG00000022152	ENST00000357242.5:c.1380A>G	X.37:g.106083304A>G		338.0	1.0	0.00295858		318.0	318.0	1	NM_198881	B9A6K5|B9A6K6|Q5JRB7|Q6ZVX5|Q9NXE3	Silent	SNP	ENST00000357242.5	37	CCDS14522.1																																																																																			A|0.923;G|0.077	0.077	strong		0.343	TBC1D8B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057807.2	NM_017752	
GATA3	2625	hgsc.bcm.edu	37	10	8100632	8100632	+	Silent	SNP	T	T	C	rs2228254	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:8100632T>C	ENST00000346208.3	+	3	1061	c.606T>C	c.(604-606)cgT>cgC	p.R202R	GATA3_ENST00000461472.1_3'UTR|GATA3_ENST00000379328.3_Silent_p.R202R			P23771	GATA3_HUMAN	GATA binding protein 3	202					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						CCCACTCCCGTGGCAGCATGA	0.687			"""F, N, S"""		breast		"""HDR syndrome (HYPOPARATHYROIDISM, SENSORINEURAL DEAFNESS, AND RENAL DISEASE)"""						T|||	189	0.0377396	0.1392	0.0058	5008	,	,		14132	0.0		0.001	False		,,,				2504	0.0				p.R202R		Atlas-SNP	.		Rec	yes		10	10p15	2625	GATA binding protein 3	yes	E	.	GATA3	182	.	0			c.T606C						PASS	.	T	,	504,3902	227.8+/-242.9	31,442,1730	85.0	77.0	80.0		606,606	-11.1	0.4	10	dbSNP_98	80	2,8596	2.2+/-6.3	0,2,4297	no	coding-synonymous,coding-synonymous	GATA3	NM_001002295.1,NM_002051.2	,	31,444,6027	CC,CT,TT		0.0233,11.4389,3.8911	,	202/445,202/444	8100632	506,12498	2203	4299	6502	SO:0001819	synonymous_variant	2625	exon3			CTCCCGTGGCAGC	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.606T>C	10.37:g.8100632T>C		55.0	0.0	0		46.0	27.0	0.586957	NM_002051	Q5VWG7|Q5VWG8|Q96J16	Silent	SNP	ENST00000346208.3	37	CCDS7083.1																																																																																			T|0.959;C|0.041	0.041	strong		0.687	GATA3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046719.1	NM_001002295	
MYH11	4629	hgsc.bcm.edu	37	16	15931975	15931975	+	Silent	SNP	G	G	A	rs28570191|rs587781074	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:15931975G>A	ENST00000300036.5	-	2	244	c.135C>T	c.(133-135)ttC>ttT	p.F45F	MYH11_ENST00000452625.2_Silent_p.F45F|MYH11_ENST00000396324.3_Silent_p.F45F|MYH11_ENST00000576790.2_Silent_p.F45F	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	45					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						TGGCTGCCTCGAAGCCCTGCT	0.562			T	CBFB	AML								G|||	220	0.0439297	0.1543	0.0231	5008	,	,		18928	0.0		0.0	False		,,,				2504	0.0				p.F45F		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	MYH11	520	.	0			c.C135T						PASS	.	G	,,,	591,3803	261.9+/-264.6	42,507,1648	166.0	156.0	159.0		135,135,135,135	-0.4	1.0	16	dbSNP_125	159	17,8583	11.9+/-42.8	0,17,4283	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MYH11	NM_001040113.1,NM_001040114.1,NM_002474.2,NM_022844.2	,,,	42,524,5931	AA,AG,GG		0.1977,13.4502,4.6791	,,,	45/1946,45/1980,45/1973,45/1939	15931975	608,12386	2197	4300	6497	SO:0001819	synonymous_variant	4629	exon2			TGCCTCGAAGCCC	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.135C>T	16.37:g.15931975G>A		87.0	0.0	0		98.0	58.0	0.591837	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																			G|0.951;A|0.049	0.049	strong		0.562	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
SETD1A	9739	hgsc.bcm.edu	37	16	30978324	30978324	+	Silent	SNP	C	C	A	rs11866157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:30978324C>A	ENST00000262519.8	+	9	3311	c.2625C>A	c.(2623-2625)atC>atA	p.I875I		NM_014712.1	NP_055527.1	O15047	SET1A_HUMAN	SET domain containing 1A	875					histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone methyltransferase activity (H3-K4 specific) (GO:0042800)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(21)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	59						CTACGGGCATCGAGGCTTTCG	0.607													C|||	150	0.0299521	0.1104	0.0058	5008	,	,		14627	0.0		0.0	False		,,,				2504	0.0				p.I875I		Atlas-SNP	.											.	SETD1A	143	.	0			c.C2625A						PASS	.	C		357,4037		14,329,1854	30.0	27.0	28.0		2625	-7.1	0.9	16	dbSNP_120	28	4,8594		0,4,4295	no	coding-synonymous	SETD1A	NM_014712.1		14,333,6149	AA,AC,CC		0.0465,8.1247,2.7786		875/1708	30978324	361,12631	2197	4299	6496	SO:0001819	synonymous_variant	9739	exon9			GGGCATCGAGGCT	AB002337	CCDS32435.1	16p11.2	2013-02-12			ENSG00000099381	ENSG00000099381		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29010	protein-coding gene	gene with protein product		611052				9205841, 12670868	Standard	XM_005255723		Approved	KIAA0339, Set1, KMT2F	uc002ead.1	O15047	OTTHUMG00000150474	ENST00000262519.8:c.2625C>A	16.37:g.30978324C>A		81.0	0.0	0		100.0	54.0	0.54	NM_014712	A6NP62|Q6PIF3|Q8TAJ6	Silent	SNP	ENST00000262519.8	37	CCDS32435.1																																																																																			C|0.968;A|0.032	0.032	strong		0.607	SETD1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318244.2	NM_014712	
USP29	57663	hgsc.bcm.edu	37	19	57641887	57641887	+	Missense_Mutation	SNP	A	A	G	rs74511605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:57641887A>G	ENST00000254181.4	+	4	2298	c.1844A>G	c.(1843-1845)cAa>cGa	p.Q615R	USP29_ENST00000598197.1_Missense_Mutation_p.Q615R	NM_020903.2	NP_065954.1	Q9HBJ7	UBP29_HUMAN	ubiquitin specific peptidase 29	615	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			breast(3)|endometrium(4)|kidney(3)|large_intestine(15)|lung(47)|ovary(2)|pancreas(1)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		GATGCAAGCCAAGAGCAGCAT	0.493													A|||	12	0.00239617	0.0091	0.0	5008	,	,		20449	0.0		0.0	False		,,,				2504	0.0				p.Q615R		Atlas-SNP	.											.	USP29	186	.	0			c.A1844G						PASS	.	A	ARG/GLN	50,4356	51.6+/-87.1	0,50,2153	73.0	72.0	72.0		1844	1.4	0.0	19	dbSNP_131	72	0,8600		0,0,4300	yes	missense	USP29	NM_020903.2	43	0,50,6453	GG,GA,AA		0.0,1.1348,0.3844	benign	615/923	57641887	50,12956	2203	4300	6503	SO:0001583	missense	57663	exon4			CAAGCCAAGAGCA		CCDS33124.1	19q13.4	2008-06-23	2005-08-08			ENSG00000131864		"""Ubiquitin-specific peptidases"""	18563	protein-coding gene	gene with protein product		609546	"""ubiquitin specific protease 29"""			12838346	Standard	NM_020903		Approved		uc002qny.3	Q9HBJ7		ENST00000254181.4:c.1844A>G	19.37:g.57641887A>G	ENSP00000254181:p.Gln615Arg	132.0	0.0	0		120.0	74.0	0.616667	NM_020903		Missense_Mutation	SNP	ENST00000254181.4	37	CCDS33124.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	A	0.013	-1.643501	0.00792	0.011348	0.0	ENSG00000131864	ENST00000254181	T	0.74002	-0.8	2.43	1.4	0.22301	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	.	.	.	.	T	0.37571	0.1008	N	0.11313	0.125	0.09310	N	1	B	0.14805	0.011	B	0.14578	0.011	T	0.32402	-0.9908	9	0.02654	T	1	0.0203	4.2465	0.10674	0.8306:0.0:0.1694:0.0	.	615	Q9HBJ7	UBP29_HUMAN	R	615	ENSP00000254181:Q615R	ENSP00000254181:Q615R	Q	+	2	0	USP29	62333699	0.021000	0.18746	0.003000	0.11579	0.085000	0.17905	2.747000	0.47475	0.347000	0.23924	0.383000	0.25322	CAA	A|0.995;G|0.005	0.005	strong		0.493	USP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465075.1		
ZBED4	9889	hgsc.bcm.edu	37	22	50279749	50279749	+	Silent	SNP	C	C	T	rs61731524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50279749C>T	ENST00000216268.5	+	2	2916	c.2439C>T	c.(2437-2439)atC>atT	p.I813I		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	813						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		ACGCCAGCATCGGGAAGACGC	0.617													C|||	18	0.00359425	0.0083	0.0029	5008	,	,		19867	0.0		0.0	False		,,,				2504	0.0051				p.I813I		Atlas-SNP	.											.	ZBED4	102	.	0			c.C2439T						PASS	.	C		14,4392	20.2+/-43.8	0,14,2189	38.0	38.0	38.0		2439	-9.5	0.2	22	dbSNP_129	38	0,8598		0,0,4299	no	coding-synonymous	ZBED4	NM_014838.2		0,14,6488	TT,TC,CC		0.0,0.3177,0.1077		813/1172	50279749	14,12990	2203	4299	6502	SO:0001819	synonymous_variant	9889	exon2			CAGCATCGGGAAG	AB014537	CCDS33677.1	22q13.33	2013-05-03			ENSG00000100426	ENSG00000100426		"""Zinc fingers, BED-type"""	20721	protein-coding gene	gene with protein product		612552				23533661	Standard	NM_014838		Approved	KIAA0637	uc003bix.2	O75132	OTTHUMG00000150291	ENST00000216268.5:c.2439C>T	22.37:g.50279749C>T		61.0	0.0	0		72.0	28.0	0.388889	NM_014838	B2RZH1|Q1ECU0|Q9UGG8	Silent	SNP	ENST00000216268.5	37	CCDS33677.1																																																																																			C|0.998;T|0.002	0.002	strong		0.617	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	NM_014838	
SEMG2	6407	hgsc.bcm.edu	37	20	43851101	43851101	+	Silent	SNP	T	T	C	rs2233902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43851101T>C	ENST00000372769.3	+	2	918	c.828T>C	c.(826-828)gaT>gaC	p.D276D		NM_003008.2	NP_002999.1	Q02383	SEMG2_HUMAN	semenogelin II	276	4 X 60 AA tandem repeats, type I.|Repeat-rich region.				sexual reproduction (GO:0019953)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Myeloproliferative disorder(115;0.0122)				TCAGTCAAGATCAAGAGCATG	0.398													T|||	79	0.0157748	0.0484	0.0101	5008	,	,		22551	0.0		0.004	False		,,,				2504	0.0041				p.D276D		Atlas-SNP	.											.	SEMG2	92	.	0			c.T828C						PASS	.	T		177,4229	114.6+/-152.6	3,171,2029	93.0	90.0	91.0		828	-1.5	0.0	20	dbSNP_98	91	18,8582	12.6+/-44.7	0,18,4282	no	coding-synonymous	SEMG2	NM_003008.2		3,189,6311	CC,CT,TT		0.2093,4.0172,1.4993		276/583	43851101	195,12811	2203	4300	6503	SO:0001819	synonymous_variant	6407	exon2			TCAAGATCAAGAG		CCDS13346.1	20q12-q13.1	2008-07-02			ENSG00000124157	ENSG00000124157			10743	protein-coding gene	gene with protein product	"""Semenogelin 2"""	182141				1517240, 9523691	Standard	NM_003008		Approved	SGII	uc002xnk.3	Q02383	OTTHUMG00000032566	ENST00000372769.3:c.828T>C	20.37:g.43851101T>C		158.0	0.0	0		151.0	78.0	0.516556	NM_003008	Q53ZU2|Q6X2M5|Q6X2M6	Silent	SNP	ENST00000372769.3	37	CCDS13346.1																																																																																			T|0.985;C|0.015	0.015	strong		0.398	SEMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079417.1	NM_003008	
PWWP2B	170394	hgsc.bcm.edu	37	10	134218802	134218802	+	Silent	SNP	G	G	T	rs76160300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:134218802G>T	ENST00000305233.5	+	2	857	c.798G>T	c.(796-798)gtG>gtT	p.V266V	PWWP2B_ENST00000368609.4_Silent_p.V266V	NM_138499.3	NP_612508.3	Q6NUJ5	PWP2B_HUMAN	PWWP domain containing 2B	266										central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|urinary_tract(1)	9		all_cancers(35;6.69e-12)|all_epithelial(44;1.55e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.109)|Melanoma(40;0.123)|Glioma(114;0.203)|all_hematologic(284;0.224)		OV - Ovarian serous cystadenocarcinoma(35;7.49e-05)|Epithelial(32;0.00016)|all cancers(32;0.000186)		AGGGAGAGGTGGTCAAGATCC	0.701													G|||	36	0.0071885	0.0272	0.0	5008	,	,		12729	0.0		0.0	False		,,,				2504	0.0				p.V266V		Atlas-SNP	.											.	PWWP2B	33	.	0			c.G798T						PASS	.	G	,	107,4271		1,105,2083	15.0	20.0	19.0		798,798	-1.2	1.0	10	dbSNP_131	19	1,8565		0,1,4282	no	coding-synonymous,coding-synonymous	PWWP2B	NM_001098637.1,NM_138499.3	,	1,106,6365	TT,TG,GG		0.0117,2.444,0.8344	,	266/500,266/591	134218802	108,12836	2189	4283	6472	SO:0001819	synonymous_variant	170394	exon2			AGAGGTGGTCAAG	AK128663	CCDS7667.2	10q26.3	2009-06-03	2007-10-22	2007-10-22	ENSG00000171813	ENSG00000171813			25150	protein-coding gene	gene with protein product			"""PWWP domain containing 2"""	PWWP2			Standard	NM_001098637		Approved	bA432J24.1, FLJ46823	uc001lll.4	Q6NUJ5	OTTHUMG00000019286	ENST00000305233.5:c.798G>T	10.37:g.134218802G>T		116.0	0.0	0		93.0	52.0	0.55914	NM_001098637	A6NM90|B5MDQ1|H9KV61|Q5SZI0|Q6ZQX5|Q96F43	Silent	SNP	ENST00000305233.5	37	CCDS7667.2																																																																																			G|0.993;T|0.007	0.007	strong		0.701	PWWP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051075.3	NM_138499	
WDR87	83889	hgsc.bcm.edu	37	19	38376804	38376804	+	Missense_Mutation	SNP	T	T	C	rs78748271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38376804T>C	ENST00000303868.5	-	6	7614	c.7390A>G	c.(7390-7392)Acc>Gcc	p.T2464A	WDR87_ENST00000447313.2_Missense_Mutation_p.T2503A	NM_031951.3	NP_114157.3	Q6ZQQ6	WDR87_HUMAN	WD repeat domain 87	2464										NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|prostate(1)|skin(3)|stomach(1)	36						ATAAATGGGGTCTTTAAGTCC	0.463													T|||	144	0.028754	0.1051	0.0072	5008	,	,		19760	0.0		0.0	False		,,,				2504	0.0				p.T2464A		Atlas-SNP	.											.	WDR87	191	.	0			c.A7390G						PASS	.	T	ALA/THR	156,1228		13,130,549	123.0	107.0	112.0		7390	1.7	0.0	19	dbSNP_132	112	0,3182		0,0,1591	yes	missense	WDR87	NM_031951.3	58	13,130,2140	CC,CT,TT		0.0,11.2717,3.4166	benign	2464/2874	38376804	156,4410	692	1591	2283	SO:0001583	missense	83889	exon6			ATGGGGTCTTTAA	AK128826	CCDS46063.1, CCDS74356.1	19q13.13	2013-01-09			ENSG00000171804	ENSG00000171804		"""WD repeat domain containing"""	29934	protein-coding gene	gene with protein product							Standard	XM_005259304		Approved	NYD-SP11	uc010efu.2	Q6ZQQ6	OTTHUMG00000048187	ENST00000303868.5:c.7390A>G	19.37:g.38376804T>C	ENSP00000368025:p.Thr2464Ala	284.0	1.0	0.00352113		299.0	147.0	0.491639	NM_031951	Q9BWV9	Missense_Mutation	SNP	ENST00000303868.5	37	CCDS46063.1	38	0.0173992673992674	35	0.07113821138211382	3	0.008287292817679558	0	0.0	0	0.0	T	5.593	0.294248	0.10567	0.112717	0.0	ENSG00000171804	ENST00000447313;ENST00000303868	T;T	0.10573	2.86;2.86	3.84	1.68	0.24146	.	.	.	.	.	T	0.00144	0.0004	N	0.14661	0.345	0.09310	N	1	B;B	0.30793	0.295;0.088	B;B	0.32211	0.142;0.068	T	0.45026	-0.9289	9	0.45353	T	0.12	.	6.465	0.21977	0.3971:0.0:0.0:0.6029	.	2464;2503	Q6ZQQ6;E7ESW6	WDR87_HUMAN;.	A	2503;2464	ENSP00000405012:T2503A;ENSP00000368025:T2464A	ENSP00000368025:T2464A	T	-	1	0	WDR87	43068644	0.032000	0.19561	0.001000	0.08648	0.005000	0.04900	0.878000	0.28126	0.282000	0.22254	-0.341000	0.08007	ACC	T|0.979;C|0.021	0.021	strong		0.463	WDR87-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314628.2	XM_940478	
DNAH3	55567	hgsc.bcm.edu	37	16	21049286	21049286	+	Missense_Mutation	SNP	C	C	T	rs16970832	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:21049286C>T	ENST00000261383.3	-	34	4746	c.4747G>A	c.(4747-4749)Gtt>Att	p.V1583I	DNAH3_ENST00000415178.1_Missense_Mutation_p.V1583I	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1583	AAA 1. {ECO:0000250}.		V -> I (in dbSNP:rs16970832).		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)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		TAGGTCGCAACGATCTTCTGG	0.547													C|||	248	0.0495208	0.1808	0.0101	5008	,	,		21358	0.0		0.002	False		,,,				2504	0.0				p.V1583I		Atlas-SNP	.											.	DNAH3	1142	.	0			c.G4747A						PASS	.	C	ILE/VAL	675,3727	286.9+/-279.0	56,563,1582	88.0	66.0	74.0		4747	5.8	1.0	16	dbSNP_123	74	7,8593	3.7+/-12.6	0,7,4293	yes	missense	DNAH3	NM_017539.1	29	56,570,5875	TT,TC,CC		0.0814,15.3339,5.2453	probably-damaging	1583/4117	21049286	682,12320	2201	4300	6501	SO:0001583	missense	55567	exon34			TCGCAACGATCTT	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.4747G>A	16.37:g.21049286C>T	ENSP00000261383:p.Val1583Ile	88.0	0.0	0		96.0	60.0	0.625	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	79	0.036172161172161175	77	0.1565040650406504	2	0.0055248618784530384	0	0.0	0	0.0	C	32	5.164216	0.94727	0.153339	8.14E-4	ENSG00000158486	ENST00000261383;ENST00000415178	T;T	0.06608	3.28;3.28	5.76	5.76	0.90799	.	0.000000	0.64402	D	0.000001	T	0.00109	0.0003	M	0.82056	2.57	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.00076	-1.2118	10	0.36615	T	0.2	.	19.9616	0.97254	0.0:1.0:0.0:0.0	rs16970832;rs56565035;rs16970832	1583	Q8TD57	DYH3_HUMAN	I	1583	ENSP00000261383:V1583I;ENSP00000394245:V1583I	ENSP00000261383:V1583I	V	-	1	0	DNAH3	20956787	1.000000	0.71417	0.998000	0.56505	0.731000	0.41821	7.764000	0.85297	2.724000	0.93272	0.561000	0.74099	GTT	C|0.944;T|0.056	0.056	strong		0.547	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
ACVRL1	94	hgsc.bcm.edu	37	12	52306898	52306898	+	Missense_Mutation	SNP	C	C	T	rs199542304	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52306898C>T	ENST00000388922.4	+	3	360	c.77C>T	c.(76-78)cCg>cTg	p.P26L	ACVRL1_ENST00000550683.1_Missense_Mutation_p.P40L|ACVRL1_ENST00000419526.2_Intron	NM_000020.2	NP_000011.2	P37023	ACVL1_HUMAN	activin A receptor type II-like 1	26					activin receptor signaling pathway (GO:0032924)|angiogenesis (GO:0001525)|artery development (GO:0060840)|blood circulation (GO:0008015)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|blood vessel maturation (GO:0001955)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|cellular response to transforming growth factor beta stimulus (GO:0071560)|endothelial tube morphogenesis (GO:0061154)|in utero embryonic development (GO:0001701)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of focal adhesion assembly (GO:0051895)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of blood pressure (GO:0008217)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of DNA replication (GO:0006275)|regulation of endothelial cell proliferation (GO:0001936)|regulation of transcription, DNA-templated (GO:0006355)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|venous blood vessel development (GO:0060841)|wound healing, spreading of epidermal cells (GO:0035313)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	activin binding (GO:0048185)|activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|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 I (GO:0005025)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	20				BRCA - Breast invasive adenocarcinoma(357;0.0991)	Adenosine triphosphate(DB00171)	CCTGTGAAGCCGTCTCGGGGC	0.657													C|||	2	0.000399361	0.0	0.0	5008	,	,		14365	0.002		0.0	False		,,,				2504	0.0				p.P26L		Atlas-SNP	.											.	ACVRL1	60	.	0			c.C77T						PASS	.	C	LEU/PRO,LEU/PRO	1,4371		0,1,2185	13.0	15.0	14.0		77,77	5.8	0.9	12		14	1,8567		0,1,4283	yes	missense,missense	ACVRL1	NM_000020.2,NM_001077401.1	98,98	0,2,6468	TT,TC,CC		0.0117,0.0229,0.0155	possibly-damaging,possibly-damaging	26/504,26/504	52306898	2,12938	2186	4284	6470	SO:0001583	missense	94	exon3			TGAAGCCGTCTCG	L17075	CCDS31804.1	12q13.13	2014-09-17			ENSG00000139567	ENSG00000139567			175	protein-coding gene	gene with protein product		601284		ACVRLK1, ORW2		8397373, 8640225	Standard	NM_000020		Approved	HHT2, ALK1, HHT	uc001rzk.3	P37023	OTTHUMG00000169507	ENST00000388922.4:c.77C>T	12.37:g.52306898C>T	ENSP00000373574:p.Pro26Leu	24.0	0.0	0		42.0	12.0	0.285714	NM_000020	A6NGA8	Missense_Mutation	SNP	ENST00000388922.4	37	CCDS31804.1	.	.	.	.	.	.	.	.	.	.	C	17.59	3.427822	0.62733	2.29E-4	1.17E-4	ENSG00000139567	ENST00000388922;ENST00000267008;ENST00000547400;ENST00000550683	D;D;D	0.92149	-2.98;-2.98;-2.98	5.76	5.76	0.90799	.	0.343290	0.21467	N	0.074075	T	0.80649	0.4663	N	0.08118	0	0.80722	D	1	P	0.43750	0.816	B	0.27380	0.079	D	0.83667	0.0164	10	0.44086	T	0.13	.	15.4529	0.75290	0.0:1.0:0.0:0.0	.	26	P37023	ACVL1_HUMAN	L	26;26;40;40	ENSP00000373574:P26L;ENSP00000446724:P40L;ENSP00000447884:P40L	ENSP00000267008:P26L	P	+	2	0	ACVRL1	50593165	0.004000	0.15560	0.898000	0.35279	0.512000	0.34134	0.741000	0.26202	2.716000	0.92895	0.655000	0.94253	CCG	.	.	weak		0.657	ACVRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404520.2		
JRK	8629	hgsc.bcm.edu	37	8	143746399	143746399	+	RNA	SNP	T	T	C	rs73379623	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:143746399T>C	ENST00000507178.2	-	0	1411							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				tatggcatcgttcatgttgta	0.602													T|||	63	0.0125799	0.0469	0.0014	5008	,	,		18767	0.0		0.0	False		,,,				2504	0.0				p.N360S		Atlas-SNP	.											.	.	.	.	0			c.A1079G						PASS	.	T	SER/ASN,SER/ASN	137,3981		0,137,1922	9.0	10.0	10.0		1079,1079	1.4	0.0	8	dbSNP_130	10	1,8401		0,1,4200	yes	missense,missense	JRK	NM_001077527.1,NM_003724.2	46,46	0,138,6122	CC,CT,TT		0.0119,3.3269,1.1022	benign,benign	360/557,360/569	143746399	138,12382	2059	4201	6260			8629	exon2			GCATCGTTCATGT	AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"""jerky (mouse) homolog"", ""jerky homolog (mouse)"""			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			8.37:g.143746399T>C		89.0	0.0	0		91.0	43.0	0.472527	NM_003724	O75565	Missense_Mutation	SNP	ENST00000507178.2	37																																																																																				T|0.992;C|0.008	0.008	strong		0.602	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724	
FCGBP	8857	hgsc.bcm.edu	37	19	40384035	40384035	+	Missense_Mutation	SNP	G	G	A	rs367618328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40384035G>A	ENST00000221347.6	-	21	9582	c.9575C>T	c.(9574-9576)gCg>gTg	p.A3192V		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	3192	TIL 7.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CACGAAACCCGCGTCGCACTG	0.662													G|||	65	0.0129792	0.0446	0.0058	5008	,	,		24198	0.001		0.001	False		,,,				2504	0.0				p.A3192V		Atlas-SNP	.											FCGBP,NS,haematopoietic_neoplasm,-1,1	FCGBP	416	1	0			c.C9575T						scavenged	.	G	VAL/ALA	47,2527		0,47,1240	4.0	4.0	4.0		9575	-4.6	0.0	19		4	1,5829		0,1,2914	no	missense	FCGBP	NM_003890.2	64	0,48,4154	AA,AG,GG		0.0172,1.826,0.5712	possibly-damaging	3192/5406	40384035	48,8356	1287	2915	4202	SO:0001583	missense	8857	exon21			AAACCCGCGTCGC	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.9575C>T	19.37:g.40384035G>A	ENSP00000221347:p.Ala3192Val	585.0	1.0	0.0017094		639.0	130.0	0.203443	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	G	7.646	0.681900	0.14907	0.01826	1.72E-4	ENSG00000090920	ENST00000221347	T	0.30981	1.51	3.48	-4.63	0.03359	Protease inhibitor I8, cysteine-rich trypsin inhibitor-like (2);	.	.	.	.	T	0.18676	0.0448	L	0.49350	1.555	0.09310	N	1	D	0.56287	0.975	P	0.54372	0.75	T	0.25082	-1.0142	9	0.33141	T	0.24	.	7.6572	0.28381	0.0999:0.0:0.2726:0.6275	.	3192	Q9Y6R7	FCGBP_HUMAN	V	3192	ENSP00000221347:A3192V	ENSP00000221347:A3192V	A	-	2	0	FCGBP	45075875	0.000000	0.05858	0.001000	0.08648	0.033000	0.12548	-0.286000	0.08399	-0.448000	0.07128	-0.513000	0.04457	GCG	.	.	weak		0.662	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
ATP8A1	10396	hgsc.bcm.edu	37	4	42576646	42576646	+	Missense_Mutation	SNP	C	C	T	rs61755862	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:42576646C>T	ENST00000381668.5	-	14	1516	c.1285G>A	c.(1285-1287)Gtt>Att	p.V429I	ATP8A1_ENST00000264449.10_Missense_Mutation_p.V429I	NM_006095.2	NP_006086.1	Q9Y2Q0	AT8A1_HUMAN	ATPase, aminophospholipid transporter (APLT), class I, type 8A, member 1	429					cation transmembrane transport (GO:0098655)|ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|transmembrane transport (GO:0055085)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|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)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	51					Phosphatidylserine(DB00144)	CCATAAGCAACTCCCGCTATG	0.343													C|||	126	0.0251597	0.0923	0.0058	5008	,	,		17551	0.0		0.0	False		,,,				2504	0.0				p.V429I		Atlas-SNP	.											ATP8A1_ENST00000264449,NS,carcinoma,+1,2	ATP8A1	206	2	0			c.G1285A						PASS	.	C	ILE/VAL,ILE/VAL	297,4109	159.6+/-192.1	13,271,1919	55.0	56.0	56.0		1285,1285	3.4	1.0	4	dbSNP_129	56	2,8596	1.2+/-3.3	0,2,4297	yes	missense,missense	ATP8A1	NM_001105529.1,NM_006095.2	29,29	13,273,6216	TT,TC,CC		0.0233,6.7408,2.2993	benign,benign	429/1150,429/1165	42576646	299,12705	2203	4299	6502	SO:0001583	missense	10396	exon14			AAGCAACTCCCGC	AF067820	CCDS3466.1, CCDS47049.1	4p13	2010-04-20	2007-09-19		ENSG00000124406	ENSG00000124406		"""ATPases / P-type"""	13531	protein-coding gene	gene with protein product		609542	"""ATPase, aminophospholipid transporter (APLT), Class I, type 8A, member 1"""			10198212, 9548971	Standard	NM_006095		Approved	ATPIA	uc003gwr.2	Q9Y2Q0	OTTHUMG00000099403	ENST00000381668.5:c.1285G>A	4.37:g.42576646C>T	ENSP00000371084:p.Val429Ile	206.0	0.0	0		190.0	84.0	0.442105	NM_001105529	Q32M35|Q32M36|Q4W5J7|Q4W5P2	Missense_Mutation	SNP	ENST00000381668.5	37	CCDS3466.1	40	0.018315018315018316	38	0.07723577235772358	2	0.0055248618784530384	0	0.0	0	0.0	C	4.770	0.143139	0.09083	0.067408	2.33E-4	ENSG00000124406	ENST00000381668;ENST00000264449	T;T	0.74947	-0.89;-0.89	5.27	3.4	0.38934	ATPase, cation-transporting, domain N (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.068109	0.64402	D	0.000017	T	0.04137	0.0115	N	0.11845	0.185	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.001;0.003;0.001	T	0.03325	-1.1048	10	0.09338	T	0.73	.	6.9831	0.24713	0.0:0.6446:0.0:0.3554	.	429;429;429	B4DII6;Q32M35;Q9Y2Q0	.;.;AT8A1_HUMAN	I	429	ENSP00000371084:V429I;ENSP00000264449:V429I	ENSP00000264449:V429I	V	-	1	0	ATP8A1	42271403	0.999000	0.42202	1.000000	0.80357	0.986000	0.74619	0.657000	0.24963	1.459000	0.47892	0.591000	0.81541	GTT	C|0.975;T|0.025	0.025	strong		0.343	ATP8A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216861.2	NM_006095	
ZNF257	113835	hgsc.bcm.edu	37	19	22256347	22256347	+	Silent	SNP	G	G	A	rs10423157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22256347G>A	ENST00000594947.1	+	3	351	c.207G>A	c.(205-207)gaG>gaA	p.E69E	ZNF257_ENST00000600162.1_Silent_p.E69E	NM_033468.2	NP_258429.2	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	69	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|lung(4)	6		all_lung(12;0.0961)|Lung NSC(12;0.103)				AGAGACATGAGATGGTAGCCA	0.438													G|||	556	0.111022	0.4054	0.0274	5008	,	,		16022	0.0		0.0	False		,,,				2504	0.001				p.E69E		Atlas-SNP	.											.	ZNF257	156	.	0			c.G207A						PASS	.	G		1613,2793	496.2+/-363.5	291,1031,881	133.0	145.0	141.0		207	-1.7	0.0	19	dbSNP_119	141	17,8583	11.2+/-40.8	0,17,4283	no	coding-synonymous	ZNF257	NM_033468.2		291,1048,5164	AA,AG,GG		0.1977,36.6092,12.5327		69/564	22256347	1630,11376	2203	4300	6503	SO:0001819	synonymous_variant	113835	exon3			ACATGAGATGGTA	AF070651	CCDS46030.1	19p12	2014-02-14			ENSG00000197134	ENSG00000197134		"""Zinc fingers, C2H2-type"", ""-"""	13498	protein-coding gene	gene with protein product		606957				10585455	Standard	NM_033468		Approved	BMZF-4	uc010ecx.3	Q9Y2Q1	OTTHUMG00000182927	ENST00000594947.1:c.207G>A	19.37:g.22256347G>A		55.0	0.0	0		61.0	26.0	0.42623	NM_033468	B3KPS4|E9PG34|Q8NE34	Silent	SNP	ENST00000594947.1	37	CCDS46030.1																																																																																			G|0.927;A|0.073	0.073	strong		0.438	ZNF257-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464382.1		
KLHL20	27252	hgsc.bcm.edu	37	1	173735378	173735378	+	Silent	SNP	T	T	C	rs7536773	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:173735378T>C	ENST00000209884.4	+	8	1381	c.1245T>C	c.(1243-1245)ctT>ctC	p.L415L	KLHL20_ENST00000546011.1_Silent_p.L226L	NM_014458.3	NP_055273.2	Q9Y2M5	KLH20_HUMAN	kelch-like family member 20	415					cytoskeleton organization (GO:0007010)|Golgi to endosome transport (GO:0006895)|negative regulation of apoptotic process (GO:0043066)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K33-linked ubiquitination (GO:1990390)|protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|response to interferon-alpha (GO:0035455)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|PML body (GO:0016605)|trans-Golgi network (GO:0005802)	interferon-gamma binding (GO:0019964)|ubiquitin-protein transferase activity (GO:0004842)			breast(3)|endometrium(6)|kidney(1)|large_intestine(8)|lung(14)|ovary(1)|upper_aerodigestive_tract(1)	34						GAGGCTTTCTTTATGCTGTGG	0.433													C|||	555	0.110823	0.3971	0.0346	5008	,	,		15265	0.0		0.006	False		,,,				2504	0.0				p.L415L	GBM(159;862 2695 6559 23041)	Atlas-SNP	.											.	KLHL20	54	.	0			c.T1245C						PASS	.	C		1333,3073	695.2+/-405.9	197,939,1067	285.0	261.0	269.0		1245	0.1	1.0	1	dbSNP_116	269	31,8569	818.0+/-406.9	0,31,4269	no	coding-synonymous	KLHL20	NM_014458.3		197,970,5336	CC,CT,TT		0.3605,30.2542,10.4875		415/610	173735378	1364,11642	2203	4300	6503	SO:0001819	synonymous_variant	27252	exon8			CTTTCTTTATGCT	AB026190	CCDS1310.1	1q25.1	2013-01-30	2013-01-30		ENSG00000076321	ENSG00000076321		"""Kelch-like"", ""BTB/POZ domain containing"""	25056	protein-coding gene	gene with protein product			"""kelch-like 20 (Drosophila)"""			14668487, 20389280	Standard	NM_014458		Approved	KLEIP, KHLHX	uc001gjc.3	Q9Y2M5	OTTHUMG00000040548	ENST00000209884.4:c.1245T>C	1.37:g.173735378T>C		303.0	0.0	0		330.0	135.0	0.409091	NM_014458	B3KMA0|B4DUR0|Q5TZF2|Q5ZF45|Q9H457	Silent	SNP	ENST00000209884.4	37	CCDS1310.1																																																																																			T|0.875;C|0.125	0.125	strong		0.433	KLHL20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097582.1	NM_014458	
ADAMTS12	81792	hgsc.bcm.edu	37	5	33881385	33881385	+	Missense_Mutation	SNP	G	G	C	rs16891862	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:33881385G>C	ENST00000504830.1	-	2	663	c.328C>G	c.(328-330)Caa>Gaa	p.Q110E	ADAMTS12_ENST00000515401.1_Missense_Mutation_p.Q110E|ADAMTS12_ENST00000352040.3_Missense_Mutation_p.Q110E	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	110			Q -> E (in dbSNP:rs16891862).		cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						AGAAATCCTTGATTGACCGTC	0.478										HNSCC(64;0.19)			G|||	63	0.0125799	0.0446	0.0058	5008	,	,		20577	0.0		0.0	False		,,,				2504	0.0				p.Q110E		Atlas-SNP	.											.	ADAMTS12	464	.	0			c.C328G						PASS	.	G	GLU/GLN	137,4269	97.1+/-135.8	5,127,2071	118.0	113.0	115.0		328	2.2	0.0	5	dbSNP_123	115	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ADAMTS12	NM_030955.2	29	5,128,6370	CC,CG,GG		0.0116,3.1094,1.061	benign	110/1595	33881385	138,12868	2203	4300	6503	SO:0001583	missense	81792	exon2			ATCCTTGATTGAC	AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14605	protein-coding gene	gene with protein product		606184	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"""			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.328C>G	5.37:g.33881385G>C	ENSP00000422554:p.Gln110Glu	130.0	0.0	0		164.0	72.0	0.439024	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	15	0.006868131868131868	12	0.024390243902439025	3	0.008287292817679558	0	0.0	0	0.0	G	5.178	0.218364	0.09810	0.031094	1.16E-4	ENSG00000151388	ENST00000504830;ENST00000352040;ENST00000515401	T;T;T	0.05513	3.43;3.43;3.43	5.65	2.19	0.27852	Peptidase M12B, propeptide (1);	1.682860	0.03218	N	0.177161	T	0.01940	0.0061	L	0.42245	1.32	0.09310	N	1	B;B;B	0.21309	0.0;0.054;0.001	B;B;B	0.19666	0.001;0.026;0.02	T	0.42666	-0.9438	10	0.16420	T	0.52	.	2.8766	0.05632	0.1002:0.3354:0.3077:0.2567	rs16891862;rs52818503;rs16891862	110;110;110	P58397-3;D6REX0;P58397	.;.;ATS12_HUMAN	E	110	ENSP00000422554:Q110E;ENSP00000344847:Q110E;ENSP00000421638:Q110E	ENSP00000344847:Q110E	Q	-	1	0	ADAMTS12	33917142	0.018000	0.18449	0.001000	0.08648	0.807000	0.45602	0.455000	0.21843	0.100000	0.17581	0.467000	0.42956	CAA	C|0.011;G|0.989	0.011	strong		0.478	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955	
SLC5A8	160728	hgsc.bcm.edu	37	12	101551065	101551065	+	Missense_Mutation	SNP	G	G	A	rs113062899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:101551065G>A	ENST00000536262.2	-	15	2383	c.1825C>T	c.(1825-1827)Cgt>Tgt	p.R609C		NM_145913.3	NP_666018.3			solute carrier family 5 (sodium/monocarboxylate cotransporter), member 8											breast(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(29)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						CTTCACAAACGAGTCCCATTG	0.378													G|||	60	0.0119808	0.0446	0.0014	5008	,	,		19406	0.0		0.0	False		,,,				2504	0.0				p.R609C	GBM(60;420 1056 13605 22380 47675)	Atlas-SNP	.											.	SLC5A8	102	.	0			c.C1825T						PASS	.	G	CYS/ARG	145,4261	100.7+/-139.4	0,145,2058	136.0	119.0	125.0		1825	5.2	1.0	12	dbSNP_132	125	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SLC5A8	NM_145913.3	180	0,146,6357	AA,AG,GG		0.0116,3.291,1.1226	probably-damaging	609/611	101551065	146,12860	2203	4300	6503	SO:0001583	missense	160728	exon15			ACAAACGAGTCCC	AY081220	CCDS9080.1	12q23.1	2013-07-19	2013-07-19		ENSG00000256870	ENSG00000256870		"""Solute carriers"""	19119	protein-coding gene	gene with protein product		608044	"""solute carrier family 5 (iodide transporter), member 8"""			12107270, 12829793	Standard	NM_145913		Approved	AIT	uc001thz.4	Q8N695	OTTHUMG00000170499	ENST00000536262.2:c.1825C>T	12.37:g.101551065G>A	ENSP00000445340:p.Arg609Cys	128.0	0.0	0		118.0	67.0	0.567797	NM_145913		Missense_Mutation	SNP	ENST00000536262.2	37	CCDS9080.1	27	0.012362637362637362	26	0.052845528455284556	1	0.0027624309392265192	0	0.0	0	0.0	G	15.83	2.949451	0.53186	0.03291	1.16E-4	ENSG00000256870	ENST00000536262	D	0.86230	-2.09	5.15	5.15	0.70609	.	0.710763	0.13338	N	0.395349	T	0.55577	0.1929	L	0.47716	1.5	0.40861	D	0.983839	D	0.56968	0.978	B	0.43623	0.425	T	0.77590	-0.2531	10	0.87932	D	0	.	15.919	0.79544	0.0:0.0:1.0:0.0	.	609	Q8N695	SC5A8_HUMAN	C	609	ENSP00000445340:R609C	ENSP00000445340:R609C	R	-	1	0	SLC5A8	100075196	1.000000	0.71417	1.000000	0.80357	0.510000	0.34073	3.942000	0.56614	2.574000	0.86865	0.655000	0.94253	CGT	G|0.987;A|0.013	0.013	strong		0.378	SLC5A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409401.1	NM_145913	
THEG	51298	hgsc.bcm.edu	37	19	373531	373531	+	Splice_Site	SNP	C	C	T	rs73489977	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:373531C>T	ENST00000342640.4	-	4	546	c.504G>A	c.(502-504)tgG>tgA	p.W168*	THEG_ENST00000346878.2_Splice_Site_p.R144R	NM_016585.4	NP_057669.1	Q9P2T0	THEG_HUMAN	theg spermatid protein	168					cell differentiation (GO:0030154)|chaperone-mediated protein complex assembly (GO:0051131)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)				NS(1)|breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|skin(2)|soft_tissue(1)	29		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-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)		ACACAGAGGGCCTGGAATAAG	0.677													C|||	186	0.0371406	0.1339	0.0115	5008	,	,		15295	0.0		0.001	False		,,,				2504	0.0				p.W168X		Atlas-SNP	.											.	THEG	58	.	0			c.G504A						PASS	.	C	stop/TRP,	514,3892	229.4+/-244.0	23,468,1712	44.0	39.0	41.0		504,432	3.0	1.0	19	dbSNP_130	41	3,8597	3.0+/-9.4	0,3,4297	yes	stop-gained-near-splice,coding-synonymous-near-splice	THEG	NM_016585.3,NM_199202.1	,	23,471,6009	TT,TC,CC		0.0349,11.6659,3.9751	,	168/380,144/356	373531	517,12489	2203	4300	6503	SO:0001630	splice_region_variant	51298	exon4			AGAGGGCCTGGAA	AF268610	CCDS12025.1, CCDS12026.1	19p13.3	2012-02-24	2012-02-24		ENSG00000105549	ENSG00000105549			13706	protein-coding gene	gene with protein product	"""cancer/testis antigen 56"""	609503	"""Theg homolog (mouse)"""			11173852	Standard	NM_016585		Approved	CT56, THEG1	uc002lol.3	Q9P2T0	OTTHUMG00000165491	ENST00000342640.4:c.504-1G>A	19.37:g.373531C>T		134.0	0.0	0		166.0	86.0	0.518072	NM_016585	A6NMJ8	Nonsense_Mutation	SNP	ENST00000342640.4	37	CCDS12025.1	61	0.027930402930402932	56	0.11382113821138211	5	0.013812154696132596	0	0.0	0	0.0	C	16.59	3.166200	0.57476	0.116659	3.49E-4	ENSG00000105549	ENST00000342640	.	.	.	3.03	3.03	0.35002	.	0.466367	0.16510	N	0.211261	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	.	9.7902	0.40702	0.0:1.0:0.0:0.0	.	.	.	.	X	168	.	ENSP00000340088:W168X	W	-	3	0	THEG	324531	1.000000	0.71417	0.985000	0.45067	0.153000	0.21895	3.225000	0.51246	2.008000	0.58898	0.561000	0.74099	TGG	C|0.960;T|0.040	0.040	strong		0.677	THEG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384431.2		Nonsense_Mutation
HOMEZ	57594	hgsc.bcm.edu	37	14	23744844	23744844	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:23744844C>T	ENST00000357460.5	-	2	1757	c.1593G>A	c.(1591-1593)gaG>gaA	p.E531E	HOMEZ_ENST00000431326.2_Silent_p.E533E|HOMEZ_ENST00000561013.1_Silent_p.E533E	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	531	Glu-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|lung(7)	12	all_cancers(95;5.54e-06)			GBM - Glioblastoma multiforme(265;0.00643)		cctcctcctcctcttcctcat	0.493																																					p.E531E		Atlas-SNP	.											.	HOMEZ	80	.	0			c.G1593A						PASS	.						37.0	36.0	36.0					14																	23744844		2196	4286	6482	SO:0001819	synonymous_variant	57594	exon2			CTCCTCCTCTTCC	AB037864	CCDS45085.1	14q11.2	2011-06-20	2007-02-15	2007-02-15		ENSG00000215271		"""Homeoboxes / ZF class"""	20164	protein-coding gene	gene with protein product		608119	"""KIAA1443"""	KIAA1443		12925734	Standard	NM_020834		Approved		uc001wja.2	Q8IX15		ENST00000357460.5:c.1593G>A	14.37:g.23744844C>T		127.0	0.0	0		114.0	7.0	0.0614035	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	Silent	SNP	ENST00000357460.5	37	CCDS45085.1																																																																																			.	.	none		0.493	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834	
IL16	3603	hgsc.bcm.edu	37	15	81589340	81589340	+	Silent	SNP	C	C	T	rs201624502	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:81589340C>T	ENST00000302987.4	+	12	1974	c.1974C>T	c.(1972-1974)gcC>gcT	p.A658A	IL16_ENST00000560230.1_3'UTR|IL16_ENST00000394652.2_5'UTR|IL16_ENST00000394660.2_Silent_p.A658A			Q14005	IL16_HUMAN	interleukin 16	658					immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						GTGCCTCTGCCGGCTGCCCAG	0.592													C|||	6	0.00119808	0.0045	0.0	5008	,	,		18755	0.0		0.0	False		,,,				2504	0.0				p.A658A		Atlas-SNP	.											.	IL16	254	.	0			c.C1974T						PASS	.	C	,,	8,3906		0,8,1949	34.0	39.0	37.0		1974,,1974	-3.6	0.0	15		37	0,8326		0,0,4163	no	coding-synonymous,utr-5,coding-synonymous	IL16	NM_001172128.1,NM_004513.5,NM_172217.3	,,	0,8,6112	TT,TC,CC		0.0,0.2044,0.0654	,,	658/1332,,658/1333	81589340	8,12232	1957	4163	6120	SO:0001819	synonymous_variant	3603	exon13			CTCTGCCGGCTGC	U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"""Interleukins and interleukin receptors"""	5980	protein-coding gene	gene with protein product	"""prointerleukin 16"", ""lymphocyte chemoattractant factor"""	603035	"""interleukin 16 (lymphocyte chemoattractant factor)"""			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.1974C>T	15.37:g.81589340C>T		176.0	0.0	0		173.0	89.0	0.514451	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Silent	SNP	ENST00000302987.4	37	CCDS42069.1																																																																																			C|0.999;T|0.001	0.001	strong		0.592	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217	
PSAP	5660	hgsc.bcm.edu	37	10	73574948	73574948	+	IGR	SNP	C	C	T	rs73277900	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73574948C>T	ENST00000394936.3	-	0	2866				CDH23_ENST00000224721.6_Silent_p.N3331N|CDH23_ENST00000475158.1_3'UTR|CDH23_ENST00000398788.3_Silent_p.N1086N			P07602	SAP_HUMAN	prosaposin						blood coagulation (GO:0007596)|cellular response to organic substance (GO:0071310)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|glycosphingolipid metabolic process (GO:0006687)|lipid transport (GO:0006869)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catalytic activity (GO:0043085)|prostate gland growth (GO:0060736)|regulation of lipid metabolic process (GO:0019216)|regulation of MAPK cascade (GO:0043408)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|lipid binding (GO:0008289)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	13						TCGAGCGCAACGCCCGCACAG	0.637													C|||	106	0.0211661	0.0756	0.0072	5008	,	,		17511	0.0		0.001	False		,,,				2504	0.0				p.N3326N		Atlas-SNP	.											.	CDH23	365	.	0			c.C9978T						PASS	.	C	,,,,	260,4058		7,246,1906	21.0	28.0	26.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3258,3153,669,564,9978	-0.8	1.0	10	dbSNP_130	26	3,8497		0,3,4247	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CDH23	NM_001171933.1,NM_001171934.1,NM_001171935.1,NM_001171936.1,NM_022124.5	,,,,	7,249,6153	TT,TC,CC		0.0353,6.0213,2.0518	,,,,	1086/1115,1051/1080,223/252,188/217,3326/3355	73574948	263,12555	2159	4250	6409	SO:0001628	intergenic_variant	64072	exon68			GCGCAACGCCCGC	BC004275	CCDS7311.1	10q21-q22	2014-01-30	2008-07-31		ENSG00000197746	ENSG00000197746		"""Endogenous ligands"""	9498	protein-coding gene	gene with protein product	"""variant Gaucher disease and variant metachromatic leukodystrophy"""	176801	"""sphingolipid activator protein-1"""	SAP1, GLBA		2717620	Standard	NM_001042465		Approved		uc001jsm.3	P07602	OTTHUMG00000018429		10.37:g.73574948C>T		59.0	0.0	0		54.0	27.0	0.5	NM_022124	P07292|P15793|P78538|P78541|P78546|P78547|P78558|Q53Y86|Q6IBQ6|Q92739|Q92740|Q92741|Q92742	Silent	SNP	ENST00000394936.3	37	CCDS7311.1																																																																																			C|0.984;T|0.016	0.016	strong		0.637	PSAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048553.1	NM_002778	
POLQ	10721	hgsc.bcm.edu	37	3	121251924	121251924	+	Silent	SNP	C	C	T	rs41390550	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:121251924C>T	ENST00000264233.5	-	6	1001	c.873G>A	c.(871-873)ccG>ccA	p.P291P	POLQ_ENST00000488282.1_5'UTR	NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	291					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		ACTCCAAAAGCGGTACAGGGC	0.428								DNA polymerases (catalytic subunits)					C|||	107	0.0213658	0.0749	0.0115	5008	,	,		17115	0.0		0.0	False		,,,				2504	0.0				p.P291P	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.G873A						PASS	.	C		267,4139	152.5+/-186.2	7,253,1943	94.0	93.0	93.0		873	0.1	1.0	3	dbSNP_127	93	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	POLQ	NM_199420.3		7,257,6239	TT,TC,CC		0.0465,6.0599,2.0837		291/2591	121251924	271,12735	2203	4300	6503	SO:0001819	synonymous_variant	10721	exon6			CAAAAGCGGTACA	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.873G>A	3.37:g.121251924C>T		317.0	0.0	0		260.0	117.0	0.45	NM_199420	O95160|Q6VMB5	Silent	SNP	ENST00000264233.5	37	CCDS33833.1																																																																																			C|0.982;T|0.018	0.018	strong		0.428	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
MT-CO2	4513	hgsc.bcm.edu	37	M	8027	8027	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:8027G>A	ENST00000361739.1	+	1	442	c.442G>A	c.(442-444)Gcc>Acc	p.A148T	MT-TR_ENST00000387439.1_RNA|MT-ND3_ENST00000361227.2_5'Flank|MT-ATP6_ENST00000361899.2_5'Flank|MT-TD_ENST00000387419.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-CO3_ENST00000362079.2_5'Flank|MT-ND4L_ENST00000361335.1_5'Flank|MT-TA_ENST00000387392.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-ND4_ENST00000361381.2_5'Flank|MT-TY_ENST00000387409.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ATP8_ENST00000361851.1_5'Flank|MT-TN_ENST00000387400.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-TC_ENST00000387405.1_RNA			P00403	COX2_HUMAN	mitochondrially encoded cytochrome c oxidase II	148			A -> T. {ECO:0000269|PubMed:8277847}.		cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, cytochrome c to oxygen (GO:0006123)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|respiratory chain complex IV (GO:0045277)	copper ion binding (GO:0005507)|cytochrome-c oxidase activity (GO:0004129)			endometrium(5)|kidney(8)|lung(2)|pancreas(3)|prostate(1)	19						TCCCGATTGAAGCCCCCATTC	0.468																																					p.A148T		Atlas-SNP	.											.	.	.	.	0			c.G442A						PASS	.																																			SO:0001583	missense	5743	exon1			ATTGAAGCCCCCA			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198712	ENSG00000198712		"""Mitochondrial respiratory chain complex / Complex IV"""	7421	protein-coding gene	gene with protein product		516040	"""cytochrome c oxidase II"""	MTCO2		1712754, 1989603	Standard			Approved	COX2, CO2		P00403		ENST00000361739.1:c.442G>A	M.37:g.8027G>A	ENSP00000354876:p.Ala148Thr	5.0	0.0	0		14.0	13.0	0.928571	ENST00000361739	Q37526	Missense_Mutation	SNP	ENST00000361739.1	37																																																																																				.	.	none		0.468	MT-CO2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024029	
C7orf72	100130988	hgsc.bcm.edu	37	7	50173702	50173702	+	Splice_Site	SNP	A	A	G	rs78990563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:50173702A>G	ENST00000297001.6	+	4	778		c.e4-1			NM_001161834.2	NP_001155306	A4D263	CG072_HUMAN	chromosome 7 open reading frame 72											NS(1)|breast(1)|endometrium(2)|kidney(1)|lung(1)|ovary(1)|prostate(2)	9						ATAACTTCATAGAGCTTATGA	0.348													A|||	11	0.00219649	0.0083	0.0	5008	,	,		19208	0.0		0.0	False		,,,				2504	0.0				.		Atlas-SNP	.											.	C7orf72	26	.	0			c.729-2A>G						PASS	.						60.0	52.0	55.0					7																	50173702		692	1591	2283	SO:0001630	splice_region_variant	100130988	exon4			CTTCATAGAGCTT		CCDS47585.1	7p12.2	2009-10-15			ENSG00000164500	ENSG00000164500			22564	protein-coding gene	gene with protein product							Standard	NM_001161834		Approved		uc011kcj.2	A4D263	OTTHUMG00000155883	ENST00000297001.6:c.729-1A>G	7.37:g.50173702A>G		49.0	0.0	0		53.0	29.0	0.54717	NM_001161834	A6NDX9	Splice_Site	SNP	ENST00000297001.6	37	CCDS47585.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	A	16.77	3.215312	0.58452	.	.	ENSG00000164500	ENST00000297001	.	.	.	5.92	5.92	0.95590	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.7596	0.57356	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C7orf72	50144248	1.000000	0.71417	0.974000	0.42286	0.738000	0.42128	4.739000	0.62080	2.254000	0.74563	0.528000	0.53228	.	A|0.997;G|0.003	0.003	strong		0.348	C7orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342124.1	NM_001161834	Intron
TUBGCP2	10844	hgsc.bcm.edu	37	10	135106718	135106718	+	Silent	SNP	G	G	A	rs3008344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:135106718G>A	ENST00000252936.3	-	6	888	c.849C>T	c.(847-849)ttC>ttT	p.F283F	TUBGCP2_ENST00000417178.2_Silent_p.F153F|TUBGCP2_ENST00000543663.1_Silent_p.F311F|TUBGCP2_ENST00000368563.2_Silent_p.F283F|RP11-122K13.12_ENST00000424450.1_RNA|TUBGCP2_ENST00000368562.1_5'Flank			Q9BSJ2	GCP2_HUMAN	tubulin, gamma complex associated protein 2	283					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)|protein complex assembly (GO:0006461)	centrosome (GO:0005813)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(16)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)	35		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.87e-06)|all cancers(32;8.98e-06)|Epithelial(32;1.15e-05)		GCCCGTACTCGAAGGAAGACT	0.547													G|||	16	0.00319489	0.0106	0.0014	5008	,	,		20270	0.0		0.001	False		,,,				2504	0.0				p.F311F		Atlas-SNP	.											.	TUBGCP2	79	.	0			c.C933T						PASS	.	G		48,4358	50.2+/-85.5	0,48,2155	60.0	58.0	59.0		849	-6.7	0.8	10	dbSNP_101	59	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	TUBGCP2	NM_006659.2		0,51,6452	AA,AG,GG		0.0349,1.0894,0.3921		283/903	135106718	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	10844	exon8			GTACTCGAAGGAA	AF042379	CCDS7676.1, CCDS58104.1, CCDS58105.1	10q26.3	2008-07-28			ENSG00000130640	ENSG00000130640			18599	protein-coding gene	gene with protein product						9566967	Standard	NM_001256617		Approved	GCP2, Spc97p, SPBC97	uc010qvc.2	Q9BSJ2	OTTHUMG00000019319	ENST00000252936.3:c.849C>T	10.37:g.135106718G>A		60.0	0.0	0		58.0	26.0	0.448276	NM_001256617	B4DM18|B7ZKL8|F5H4E0|F5H4L0|O43632|Q5VWX7	Silent	SNP	ENST00000252936.3	37	CCDS7676.1																																																																																			G|0.996;A|0.004	0.004	strong		0.547	TUBGCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051148.1		
POLRMT	5442	hgsc.bcm.edu	37	19	622834	622834	+	Missense_Mutation	SNP	C	C	G	rs146178977	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:622834C>G	ENST00000588649.2	-	7	1526	c.1442G>C	c.(1441-1443)cGg>cCg	p.R481P	LLNLR-299G3.1_ENST00000607288.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	481					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)			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)		CAGGAGCATCCGCACCACCTC	0.716													c|||	17	0.00339457	0.0129	0.0	5008	,	,		14871	0.0		0.0	False		,,,				2504	0.0				p.R481P		Atlas-SNP	.											.	POLRMT	91	.	0			c.G1442C						PASS	.	C	PRO/ARG	33,4365		0,33,2166	23.0	22.0	22.0		1442	-8.0	0.0	19	dbSNP_134	22	0,8598		0,0,4299	no	missense	POLRMT	NM_005035.3	103	0,33,6465	GG,GC,CC		0.0,0.7503,0.2539	benign	481/1231	622834	33,12963	2199	4299	6498	SO:0001583	missense	5442	exon7			AGCATCCGCACCA		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.1442G>C	19.37:g.622834C>G	ENSP00000465759:p.Arg481Pro	66.0	0.0	0		56.0	36.0	0.642857	NM_005035	O60370	Missense_Mutation	SNP	ENST00000588649.2	37	CCDS12036.1	.	.	.	.	.	.	.	.	.	.	.	10.38	1.332902	0.24167	0.007503	0.0	ENSG00000099821	ENST00000215591	T	0.41758	0.99	4.01	-8.03	0.01114	.	0.937015	0.08876	N	0.880708	T	0.17577	0.0422	N	0.08118	0	0.09310	N	1	B	0.27594	0.182	B	0.32724	0.151	T	0.32295	-0.9912	10	0.30854	T	0.27	-0.4611	17.4545	0.87603	0.0:0.1116:0.0:0.8884	.	481	O00411	RPOM_HUMAN	P	481	ENSP00000215591:R481P	ENSP00000215591:R481P	R	-	2	0	POLRMT	573834	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.305000	0.08188	-2.543000	0.00484	-2.079000	0.00380	CGG	C|0.997;G|0.003	0.003	strong		0.716	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035	
HIST1H2AL	8332	hgsc.bcm.edu	37	6	27833342	27833342	+	Silent	SNP	C	C	T	rs11966705	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:27833342C>T	ENST00000357320.2	+	1	309	c.210C>T	c.(208-210)gcC>gcT	p.A70A		NM_003511.2	NP_003502.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2al	70						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)			breast(1)|endometrium(1)|large_intestine(2)|lung(3)|urinary_tract(2)	9						CGGGCAACGCCGCCCGCGACA	0.657													C|||	123	0.0245607	0.0703	0.0144	5008	,	,		15159	0.005		0.0119	False		,,,				2504	0.0031				p.A70A		Atlas-SNP	.											.	HIST1H2AL	14	.	0			c.C210T						PASS	.	C		329,4077		11,307,1885	78.0	83.0	81.0		210	1.8	1.0	6	dbSNP_120	81	48,8552		0,48,4252	no	coding-synonymous	HIST1H2AL	NM_003511.2		11,355,6137	TT,TC,CC		0.5581,7.4671,2.8987		70/131	27833342	377,12629	2203	4300	6503	SO:0001819	synonymous_variant	8332	exon1			CAACGCCGCCCGC	X83549	CCDS4634.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000198374	ENSG00000276903		"""Histones / Replication-dependent"""	4730	protein-coding gene	gene with protein product		602793	"""H2A histone family, member I"", ""histone 1, H2al"""	H2AFI		9439656, 9031620, 12408966	Standard	NM_003511		Approved	H2A/i, dJ193B12.9	uc003njw.3	P0C0S8	OTTHUMG00000014492	ENST00000357320.2:c.210C>T	6.37:g.27833342C>T		245.0	0.0	0		248.0	122.0	0.491935	NM_003511	P02261|Q2M1R2|Q76PA6	Silent	SNP	ENST00000357320.2	37	CCDS4634.1																																																																																			C|0.975;T|0.025	0.025	strong		0.657	HIST1H2AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040160.1	NM_003511	
SLC26A4	5172	hgsc.bcm.edu	37	7	107342294	107342294	+	Missense_Mutation	SNP	T	T	G	rs17154335	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:107342294T>G	ENST00000265715.3	+	17	2050	c.1826T>G	c.(1825-1827)gTt>gGt	p.V609G	SLC26A4_ENST00000544569.1_Missense_Mutation_p.V196G|SLC26A4_ENST00000480841.1_3'UTR|SLC26A4_ENST00000543100.1_Missense_Mutation_p.V178G|SLC26A4_ENST00000541474.1_Missense_Mutation_p.V170G	NM_000441.1	NP_000432.1	O43511	S26A4_HUMAN	solute carrier family 26 (anion exchanger), member 4	609	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.		V -> G (in dbSNP:rs17154335). {ECO:0000269|PubMed:15689455, ECO:0000269|PubMed:19204907}.		chloride transmembrane transport (GO:1902476)|inorganic anion transport (GO:0015698)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|regulation of protein localization (GO:0032880)|sensory perception of sound (GO:0007605)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	chloride transmembrane transporter activity (GO:0015108)|iodide transmembrane transporter activity (GO:0015111)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)			central_nervous_system(2)|endometrium(1)|kidney(5)|large_intestine(8)|lung(16)|ovary(3)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	46						AGTGATGCTGTTTCAACAAAT	0.343									Pendred syndrome				G|||	229	0.0457268	0.1657	0.0115	5008	,	,		21715	0.0		0.002	False		,,,				2504	0.0				p.V609G		Atlas-SNP	.											.	SLC26A4	117	.	0			c.T1826G	GRCh37	CM050323	SLC26A4	M	rs17154335	PASS	.	G	GLY/VAL	629,3777	767.8+/-413.5	43,543,1617	97.0	96.0	96.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1826	5.8	0.9	7	dbSNP_123	96	7,8593	818.9+/-406.8	0,7,4293	yes	missense	SLC26A4	NM_000441.1	109	43,550,5910	GG,GT,TT		0.0814,14.276,4.8901	benign	609/781	107342294	636,12370	2203	4300	6503	SO:0001583	missense	5172	exon17	Familial Cancer Database	Goiter-Deafness syndrome	ATGCTGTTTCAAC	AF030880	CCDS5746.1	7q31	2013-07-18	2013-07-18		ENSG00000091137	ENSG00000091137		"""Solute carriers"""	8818	protein-coding gene	gene with protein product	"""pendrin"""	605646	"""solute carrier family 26, member 4"""	DFNB4		9500541, 11087667	Standard	NM_000441		Approved	PDS	uc003vep.3	O43511	OTTHUMG00000154807	ENST00000265715.3:c.1826T>G	7.37:g.107342294T>G	ENSP00000265715:p.Val609Gly	89.0	0.0	0		92.0	43.0	0.467391	NM_000441	B7Z266|O43170	Missense_Mutation	SNP	ENST00000265715.3	37	CCDS5746.1	78	0.03571428571428571	71	0.1443089430894309	7	0.019337016574585635	0	0.0	0	0.0	G	14.16	2.453089	0.43531	0.14276	8.14E-4	ENSG00000091137	ENST00000265715;ENST00000541474;ENST00000544569;ENST00000543100	D;D;D;D	0.94793	-3.2;-3.47;-3.52;-3.51	5.83	5.83	0.93111	Sulphate transporter/antisigma-factor antagonist STAS (3);	0.120219	0.56097	N	0.000035	T	0.02304	0.0071	N	0.00237	-1.79	0.30149	P	0.80322	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.57493	-0.7802	9	0.20046	T	0.44	.	16.5365	0.84373	0.0:0.0:0.8681:0.1319	rs17154335;rs17154335	170;196;609	F5H104;B7Z6M6;O43511	.;.;S26A4_HUMAN	G	609;170;196;178	ENSP00000265715:V609G;ENSP00000439743:V170G;ENSP00000437427:V196G;ENSP00000441209:V178G	ENSP00000265715:V609G	V	+	2	0	SLC26A4	107129530	1.000000	0.71417	0.889000	0.34880	0.977000	0.68977	3.712000	0.54875	1.478000	0.48253	-0.121000	0.15023	GTT	T|0.952;G|0.048	0.048	strong		0.343	SLC26A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337148.1	NM_000441	
CELSR3	1951	hgsc.bcm.edu	37	3	48699134	48699134	+	Silent	SNP	G	G	T	rs76423828	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:48699134G>T	ENST00000164024.4	-	1	1214	c.934C>A	c.(934-936)Cgg>Agg	p.R312R	RP11-148G20.1_ENST00000421275.1_RNA|CELSR3_ENST00000544264.1_Silent_p.R312R	NM_001407.2	NP_001398.2	Q9NYQ7	CELR3_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 3	312					axonal fasciculation (GO:0007413)|cilium assembly (GO:0042384)|G-protein coupled receptor signaling pathway (GO:0007186)|homophilic cell adhesion (GO:0007156)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|regulation of protein localization (GO:0032880)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(23)|ovary(9)|prostate(6)|skin(7)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(5)	83				BRCA - Breast invasive adenocarcinoma(193;0.000292)|KIRC - Kidney renal clear cell carcinoma(197;0.00549)|Kidney(197;0.00619)		AAGCGTGCCCGGTTCGCCGAG	0.701													G|||	29	0.00579073	0.0212	0.0014	5008	,	,		14032	0.0		0.0	False		,,,				2504	0.0				p.R312R		Atlas-SNP	.											.	CELSR3	237	.	0			c.C934A						PASS	.	G		51,4315		0,51,2132	39.0	43.0	42.0		934	1.4	0.0	3	dbSNP_131	42	1,8499		0,1,4249	no	coding-synonymous	CELSR3	NM_001407.2		0,52,6381	TT,TG,GG		0.0118,1.1681,0.4042		312/3313	48699134	52,12814	2183	4250	6433	SO:0001819	synonymous_variant	1951	exon1			GTGCCCGGTTCGC	AF231023	CCDS2775.1	3p21.31	2014-08-08	2013-02-18		ENSG00000008300	ENSG00000008300		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	3230	protein-coding gene	gene with protein product	"""flamingo homolog 1 (Drosophila)"""	604264	"""cadherin EGF LAG seven-pass G-type receptor 3, flamingo (Drosophila) homolog"""	EGFL1		9693030	Standard	NM_001407		Approved	MEGF2, HFMI1, FMI1, CDHF11	uc003cuf.1	Q9NYQ7	OTTHUMG00000133544	ENST00000164024.4:c.934C>A	3.37:g.48699134G>T		46.0	0.0	0		68.0	33.0	0.485294	NM_001407	O75092	Silent	SNP	ENST00000164024.4	37	CCDS2775.1																																																																																			G|0.995;T|0.005	0.005	strong		0.701	CELSR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257523.1	NM_001407	
OR4K13	390433	hgsc.bcm.edu	37	14	20502779	20502779	+	Missense_Mutation	SNP	C	C	T	rs144683363	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20502779C>T	ENST00000315693.2	-	1	140	c.139G>A	c.(139-141)Gtg>Atg	p.V47M	AL359218.1_ENST00000580563.1_RNA	NM_001004714.1	NP_001004714.1	Q8NH42	OR4KD_HUMAN	olfactory receptor, family 4, subfamily K, member 13	47						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(3)|skin(4)	24	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		GTCACAGTCACCAAGATGAGC	0.423													C|||	55	0.0109824	0.0393	0.0043	5008	,	,		21594	0.0		0.0	False		,,,				2504	0.0				p.V47M		Atlas-SNP	.											.	OR4K13	68	.	0			c.G139A						PASS	.	C	MET/VAL	178,4228		4,170,2029	109.0	99.0	102.0		139	-1.9	0.0	14	dbSNP_134	102	1,8599		0,1,4299	yes	missense	OR4K13	NM_001004714.1	21	4,171,6328	TT,TC,CC		0.0116,4.0399,1.3763	possibly-damaging	47/305	20502779	179,12827	2203	4300	6503	SO:0001583	missense	390433	exon1			CAGTCACCAAGAT		CCDS32028.1	14q11.2	2013-09-23			ENSG00000176253	ENSG00000176253		"""GPCR / Class A : Olfactory receptors"""	15351	protein-coding gene	gene with protein product							Standard	NM_001004714		Approved		uc010tkz.2	Q8NH42	OTTHUMG00000170781	ENST00000315693.2:c.139G>A	14.37:g.20502779C>T	ENSP00000319322:p.Val47Met	107.0	0.0	0		86.0	39.0	0.453488	NM_001004714	Q6IF13	Missense_Mutation	SNP	ENST00000315693.2	37	CCDS32028.1	27	0.012362637362637362	27	0.054878048780487805	0	0.0	0	0.0	0	0.0	.	10.51	1.369413	0.24771	0.040399	1.16E-4	ENSG00000176253	ENST00000315693	T	0.01113	5.32	3.75	-1.86	0.07760	GPCR, rhodopsin-like superfamily (1);	0.760143	0.10674	U	0.647227	T	0.00241	0.0007	L	0.49571	1.57	0.09310	N	1	B	0.31077	0.307	B	0.22601	0.04	T	0.44682	-0.9312	10	0.52906	T	0.07	.	4.8534	0.13547	0.0:0.3611:0.2819:0.357	.	47	Q8NH42	OR4KD_HUMAN	M	47	ENSP00000319322:V47M	ENSP00000319322:V47M	V	-	1	0	OR4K13	19572619	0.000000	0.05858	0.011000	0.14972	0.005000	0.04900	-0.485000	0.06520	-0.020000	0.14032	-0.335000	0.08231	GTG	C|0.985;T|0.015	0.015	strong		0.423	OR4K13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410344.1		
SUN1	23353	hgsc.bcm.edu	37	7	883088	883088	+	Missense_Mutation	SNP	G	G	A	rs116520953	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:883088G>A	ENST00000405266.1	+	5	613	c.589G>A	c.(589-591)Gtg>Atg	p.V197M	SUN1_ENST00000401592.1_Missense_Mutation_p.V197M|SUN1_ENST00000389574.3_Missense_Mutation_p.V147M|SUN1_ENST00000456758.2_Missense_Mutation_p.V255M|SUN1_ENST00000425407.2_Missense_Mutation_p.V147M|SUN1_ENST00000457378.2_Missense_Mutation_p.V218M|SUN1_ENST00000403868.1_Missense_Mutation_p.V197M|SUN1_ENST00000452783.2_Intron			O94901	SUN1_HUMAN	Sad1 and UNC84 domain containing 1	197					cytoskeletal anchoring at nuclear membrane (GO:0090286)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)	acrosomal membrane (GO:0002080)|integral component of nuclear inner membrane (GO:0005639)|nuclear envelope (GO:0005635)|SUN-KASH complex (GO:0034993)				NS(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GCGCAAGGACGTGCTCACGGC	0.592													.|||	32	0.00638978	0.0234	0.0014	5008	,	,		13852	0.0		0.0	False		,,,				2504	0.0				p.V218M		Atlas-SNP	.											.	SUN1	157	.	0			c.G652A						PASS	.	G	MET/VAL,,MET/VAL,MET/VAL,MET/VAL	82,3924		2,78,1923	94.0	112.0	107.0		589,,652,589,439	-0.1	0.0	7	dbSNP_132	107	1,8309		0,1,4154	yes	missense,intron,missense,missense,missense	SUN1	NM_001130965.2,NM_001171944.1,NM_001171945.1,NM_001171946.1,NM_025154.5	21,,21,21,21	2,79,6077	AA,AG,GG		0.012,2.0469,0.6739	benign,,benign,benign,benign	197/786,,218/279,197/258,147/703	883088	83,12233	2003	4155	6158	SO:0001583	missense	23353	exon7			AAGGACGTGCTCA	AF202724	CCDS43533.1, CCDS47525.1, CCDS55078.1, CCDS55079.1, CCDS55080.1	7p22.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164828	ENSG00000164828			18587	protein-coding gene	gene with protein product	"""Sad1 unc-84 domain protein 1"""	607723	"""unc-84 homolog A (C. elegans)"""	UNC84A		11593002	Standard	NM_001130965		Approved	KIAA0810, FLJ12407	uc021zym.1	O94901	OTTHUMG00000151426	ENST00000405266.1:c.589G>A	7.37:g.883088G>A	ENSP00000384116:p.Val197Met	63.0	0.0	0		73.0	43.0	0.589041	NM_001171945	A5PL20|B3KMV7|B4DZF7|B7WNY4|B7WP53|E9PDU4|E9PF23|F8WD13|Q96CZ7|Q9HA14|Q9UH98	Missense_Mutation	SNP	ENST00000405266.1	37		7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	G	15.86	2.959220	0.53400	0.020469	1.2E-4	ENSG00000164828	ENST00000456758;ENST00000389574;ENST00000457378;ENST00000405266;ENST00000401592;ENST00000403868;ENST00000297445;ENST00000425407;ENST00000429178	T;T;T;T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89;0.89;0.89;0.89	4.4	-0.0819	0.13701	.	1.178380	0.05856	N	0.622191	T	0.11707	0.0285	N	0.19112	0.55	0.09310	N	1	B;P;P;B	0.37038	0.038;0.532;0.579;0.079	B;B;B;B	0.27380	0.035;0.079;0.045;0.024	T	0.09907	-1.0653	10	0.33141	T	0.24	-2.952	5.938	0.19177	0.2089:0.0:0.6586:0.1325	.	197;218;147;197	E9PF23;F8WD13;O94901-5;O94901-3	.;.;.;.	M	255;147;218;197;197;197;197;147;28	ENSP00000388743:V255M;ENSP00000374225:V147M;ENSP00000395952:V218M;ENSP00000384116:V197M;ENSP00000384015:V197M;ENSP00000383947:V197M;ENSP00000392309:V147M;ENSP00000409909:V28M	ENSP00000297445:V197M	V	+	1	0	SUN1	849614	0.003000	0.15002	0.000000	0.03702	0.084000	0.17831	0.577000	0.23758	-0.272000	0.09259	0.591000	0.81541	GTG	G|0.996;A|0.004	0.004	strong		0.592	SUN1-001	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000322566.1	NM_025154	
PSKH2	85481	hgsc.bcm.edu	37	8	87060793	87060793	+	Silent	SNP	T	T	A	rs28483271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:87060793T>A	ENST00000276616.2	-	3	1130	c.1056A>T	c.(1054-1056)ggA>ggT	p.G352G		NM_033126.1	NP_149117.1	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	352							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|kidney(11)|large_intestine(2)|lung(26)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(1)	47			STAD - Stomach adenocarcinoma(118;0.129)			ACTGTGCAGATCCAGGACTCT	0.498													T|||	124	0.0247604	0.0885	0.0101	5008	,	,		16173	0.0		0.0	False		,,,				2504	0.0				p.G352G		Atlas-SNP	.											.	PSKH2	79	.	0			c.A1056T						PASS	.	T		302,4104	164.0+/-195.7	9,284,1910	113.0	117.0	115.0		1056	-0.0	0.5	8	dbSNP_125	115	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PSKH2	NM_033126.1		9,285,6209	AA,AT,TT		0.0116,6.8543,2.3297		352/386	87060793	303,12703	2203	4300	6503	SO:0001819	synonymous_variant	85481	exon3			TGCAGATCCAGGA	AY037806	CCDS6240.1	8q21.13	2004-06-03				ENSG00000147613			18997	protein-coding gene	gene with protein product							Standard	NM_033126		Approved		uc011lfy.2	Q96QS6		ENST00000276616.2:c.1056A>T	8.37:g.87060793T>A		150.0	0.0	0		142.0	69.0	0.485915	NM_033126	A0AV22	Silent	SNP	ENST00000276616.2	37	CCDS6240.1																																																																																			T|0.966;A|0.034	0.034	strong		0.498	PSKH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374628.1	NM_033126	
ORM2	5005	hgsc.bcm.edu	37	9	117093856	117093856	+	Missense_Mutation	SNP	G	G	A	rs142633392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117093856G>A	ENST00000431067.2	+	4	374	c.338G>A	c.(337-339)cGa>cAa	p.R113Q	ORM2_ENST00000412657.1_3'UTR	NM_000608.2	NP_000599.1	P19652	A1AG2_HUMAN	orosomucoid 2	113					acute-phase response (GO:0006953)|regulation of immune system process (GO:0002682)|transport (GO:0006810)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(1)	7		Myeloproliferative disorder(63;0.163)			Chlorpromazine(DB00477)|Oxycodone(DB00497)|Thalidomide(DB01041)	GAGGGAGGCCGAGAACATGTT	0.537													-|||	29	0.00579073	0.0197	0.0029	5008	,	,		18793	0.0		0.001	False		,,,				2504	0.0				p.R113Q	NSCLC(65;867 1308 1814 2391 12508)	Atlas-SNP	.											.	ORM2	13	.	0			c.G338A						PASS	.	G	GLN/ARG	77,4329		1,75,2127	132.0	116.0	121.0		338	-5.9	0.0	9	dbSNP_134	121	0,8600		0,0,4300	yes	missense	ORM2	NM_000608.2	43	1,75,6427	AA,AG,GG		0.0,1.7476,0.592		113/202	117093856	77,12929	2203	4300	6503	SO:0001583	missense	5005	exon4			GAGGCCGAGAACA		CCDS6804.1	9q32	2013-09-19			ENSG00000228278	ENSG00000228278		"""Lipocalins"""	8499	protein-coding gene	gene with protein product	"""alpha-1-acid glycoprotein, type 2"""	138610				4711474, 2970990	Standard	NM_000608		Approved	AGP-B, AGP-B', AGP2		P19652	OTTHUMG00000021014	ENST00000431067.2:c.338G>A	9.37:g.117093856G>A	ENSP00000394936:p.Arg113Gln	208.0	0.0	0		216.0	135.0	0.625	NM_000608	B2R5L2|Q16571|Q5T538|Q6IB74	Missense_Mutation	SNP	ENST00000431067.2	37	CCDS6804.1	10	0.004578754578754579	8	0.016260162601626018	2	0.0055248618784530384	0	0.0	0	0.0	-	0.084	-1.178327	0.01633	0.017476	0.0	ENSG00000228278	ENST00000431067	T	0.08008	3.14	2.95	-5.9	0.02275	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	1.906400	0.02445	N	0.084964	T	0.03095	0.0091	L	0.37561	1.115	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.24476	-1.0159	10	0.20519	T	0.43	4.2497	6.8017	0.23754	0.121:0.0928:0.6382:0.148	.	113	P19652	A1AG2_HUMAN	Q	113	ENSP00000394936:R113Q	ENSP00000394936:R113Q	R	+	2	0	ORM2	116133677	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.988000	0.00319	-4.920000	0.00027	-2.326000	0.00250	CGA	G|0.995;A|0.005	0.005	strong		0.537	ORM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055432.1	NM_000608	
PCLO	27445	hgsc.bcm.edu	37	7	82785096	82785096	+	Silent	SNP	G	G	A	rs61744360	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:82785096G>A	ENST00000333891.9	-	2	1198	c.861C>T	c.(859-861)gaC>gaT	p.D287D	PCLO_ENST00000423517.2_Silent_p.D287D	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						CCCTTACTATGTCTGCCTGTT	0.512													G|||	12	0.00239617	0.0068	0.0029	5008	,	,		18830	0.0		0.0	False		,,,				2504	0.001				p.D287D		Atlas-SNP	.											.	PCLO	1506	.	0			c.C861T						PASS	.	G	,	25,4119		0,25,2047	122.0	111.0	114.0		861,861	-1.0	0.0	7	dbSNP_129	114	0,8422		0,0,4211	no	coding-synonymous,coding-synonymous	PCLO	NM_014510.2,NM_033026.5	,	0,25,6258	AA,AG,GG		0.0,0.6033,0.1989	,	287/4936,287/5143	82785096	25,12541	2072	4211	6283	SO:0001819	synonymous_variant	27445	exon2			TACTATGTCTGCC	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.861C>T	7.37:g.82785096G>A		264.0	1.0	0.00378788		270.0	125.0	0.462963	NM_014510		Silent	SNP	ENST00000333891.9	37	CCDS47630.1																																																																																			G|0.998;A|0.002	0.002	strong		0.512	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
GPR179	440435	hgsc.bcm.edu	37	17	36487412	36487412	+	Silent	SNP	G	G	A	rs111770829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:36487412G>A	ENST00000342292.4	-	11	2060	c.2040C>T	c.(2038-2040)gaC>gaT	p.D680D		NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	680					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				TCTTCAGCTCGTCCTGTGGGG	0.587													G|||	133	0.0265575	0.0998	0.0014	5008	,	,		18185	0.0		0.0	False		,,,				2504	0.0				p.D680D		Atlas-SNP	.											.	GPR179	170	.	0			c.C2040T						PASS	.	G		294,3810		10,274,1768	45.0	50.0	48.0		2040	-9.7	0.5	17	dbSNP_132	48	3,8383		0,3,4190	no	coding-synonymous	GPR179	NM_001004334.2		10,277,5958	AA,AG,GG		0.0358,7.1637,2.3779		680/2368	36487412	297,12193	2052	4193	6245	SO:0001819	synonymous_variant	440435	exon11			CAGCTCGTCCTGT		CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"""GPCR / Class C : Orphans"""	31371	protein-coding gene	gene with protein product		614515	"""GPR158-like 1"", ""GPR179"""	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.2040C>T	17.37:g.36487412G>A		168.0	0.0	0		205.0	92.0	0.44878	NM_001004334		Silent	SNP	ENST00000342292.4	37	CCDS42308.1																																																																																			G|0.981;A|0.019	0.019	strong		0.587	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2		
ABCC10	89845	hgsc.bcm.edu	37	6	43412935	43412935	+	Silent	SNP	T	T	C	rs2125740	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43412935T>C	ENST00000372530.4	+	14	3128	c.2913T>C	c.(2911-2913)taT>taC	p.Y971Y	ABCC10_ENST00000244533.3_Silent_p.Y943Y	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	971	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(8)|lung(21)|ovary(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)		Cyclosporine(DB00091)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Estradiol(DB00783)|Etoposide(DB00773)|Gemcitabine(DB00441)|Methotrexate(DB00563)|Paclitaxel(DB01229)|Sildenafil(DB00203)|Tenofovir(DB00300)|Verapamil(DB00661)|Vincristine(DB00541)	TCACCGTGTATGCGACCATTG	0.602													T|||	271	0.0541134	0.1974	0.0115	5008	,	,		17679	0.0		0.002	False		,,,				2504	0.0				p.Y971Y		Atlas-SNP	.											.	ABCC10	118	.	0			c.T2913C						PASS	.	T	,	845,3561	334.7+/-303.5	72,701,1430	132.0	102.0	112.0		2913,2829	-6.0	0.3	6	dbSNP_96	112	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous,coding-synonymous	ABCC10	NM_001198934.1,NM_033450.2	,	72,706,5725	CC,CT,TT		0.0581,19.1784,6.5354	,	971/1493,943/1465	43412935	850,12156	2203	4300	6503	SO:0001819	synonymous_variant	89845	exon14			CGTGTATGCGACC	U66684	CCDS4896.1, CCDS56430.1	6p12.3	2012-03-14			ENSG00000124574	ENSG00000124574		"""ATP binding cassette transporters / subfamily C"""	52	protein-coding gene	gene with protein product		612509				8894702	Standard	NM_033450		Approved	EST182763, MRP7, SIMRP7	uc003ouy.1	Q5T3U5	OTTHUMG00000014733	ENST00000372530.4:c.2913T>C	6.37:g.43412935T>C		225.0	0.0	0		234.0	103.0	0.440171	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Silent	SNP	ENST00000372530.4	37	CCDS56430.1																																																																																			T|0.940;C|0.060	0.060	strong		0.602	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450	
CCT3	7203	hgsc.bcm.edu	37	1	156281999	156281999	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156281999G>A	ENST00000295688.3	-	11	1268	c.988C>T	c.(988-990)Cgg>Tgg	p.R330W	CCT3_ENST00000368261.3_Missense_Mutation_p.R285W|CCT3_ENST00000472765.2_Missense_Mutation_p.R285W|CCT3_ENST00000368259.2_Missense_Mutation_p.R292W	NM_005998.4	NP_005989.3	P49368	TCPG_HUMAN	chaperonin containing TCP1, subunit 3 (gamma)	330					'de novo' posttranslational protein folding (GO:0051084)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	cell body (GO:0044297)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|unfolded protein binding (GO:0051082)			endometrium(4)|large_intestine(1)|liver(1)|lung(11)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	22	Hepatocellular(266;0.158)					CTGACTATCCGGGCCCCACAG	0.468																																					p.R330W		Atlas-SNP	.											.	CCT3	61	.	0			c.C988T						PASS	.						57.0	61.0	60.0					1																	156281999		2203	4300	6503	SO:0001583	missense	7203	exon11			CTATCCGGGCCCC	BC008019	CCDS1140.2, CCDS30888.1	1q23	2011-09-02			ENSG00000163468	ENSG00000163468		"""Heat Shock Proteins / Chaperonins"""	1616	protein-coding gene	gene with protein product		600114		TRIC5		8110840	Standard	NM_005998		Approved	Cctg	uc001fol.2	P49368	OTTHUMG00000024061	ENST00000295688.3:c.988C>T	1.37:g.156281999G>A	ENSP00000295688:p.Arg330Trp	86.0	0.0	0		92.0	48.0	0.521739	NM_005998	A6NE14|Q5SZY1|Q9BR64	Missense_Mutation	SNP	ENST00000295688.3	37	CCDS1140.2	.	.	.	.	.	.	.	.	.	.	G	27.7	4.856417	0.91355	.	.	ENSG00000163468	ENST00000295688;ENST00000368259;ENST00000368261;ENST00000472765	T;T;T;T	0.80214	-1.35;-1.35;-1.35;-1.35	6.15	5.24	0.73138	.	0.000000	0.85682	D	0.000000	D	0.88822	0.6541	M	0.88512	2.96	0.58432	D	0.999999	D;D;D	0.76494	0.999;0.997;0.997	D;D;D	0.69307	0.963;0.949;0.949	D	0.91190	0.4983	10	0.72032	D	0.01	-15.521	14.8519	0.70303	0.0:0.0:0.8555:0.1445	.	292;329;330	P49368-2;E9PAQ6;P49368	.;.;TCPG_HUMAN	W	330;292;285;285	ENSP00000295688:R330W;ENSP00000357242:R292W;ENSP00000357244:R285W;ENSP00000431543:R285W	ENSP00000295688:R330W	R	-	1	2	CCT3	154548623	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.908000	0.87438	1.610000	0.50200	0.643000	0.83706	CGG	.	.	none		0.468	CCT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060602.3	NM_005998	
PCDH12	51294	hgsc.bcm.edu	37	5	141331098	141331098	+	Missense_Mutation	SNP	G	G	A	rs115735066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:141331098G>A	ENST00000231484.3	-	2	4148	c.2938C>T	c.(2938-2940)Cac>Tac	p.H980Y	AC005740.6_ENST00000607378.1_RNA	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	980					calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTTCCTCGGTGGTTTGGTTTG	0.547											OREG0016877	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	44	0.00878594	0.0318	0.0029	5008	,	,		20762	0.0		0.0	False		,,,				2504	0.0				p.H980Y		Atlas-SNP	.											.	PCDH12	133	.	0			c.C2938T						PASS	.	G	TYR/HIS	104,4302	81.4+/-119.9	0,104,2099	113.0	103.0	106.0		2938	6.1	1.0	5	dbSNP_132	106	0,8600		0,0,4300	yes	missense	PCDH12	NM_016580.2	83	0,104,6399	AA,AG,GG		0.0,2.3604,0.7996	probably-damaging	980/1185	141331098	104,12902	2203	4300	6503	SO:0001583	missense	51294	exon2			CTCGGTGGTTTGG	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"""Cadherins / Protocadherins : Non-clustered"""	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.2938C>T	5.37:g.141331098G>A	ENSP00000231484:p.His980Tyr	106.0	0.0	0	1663	118.0	45.0	0.381356	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	37	CCDS4269.1	16	0.007326007326007326	14	0.028455284552845527	2	0.0055248618784530384	0	0.0	0	0.0	G	17.98	3.520092	0.64747	0.023604	0.0	ENSG00000113555	ENST00000231484	T	0.52754	0.65	6.08	6.08	0.98989	.	0.107907	0.64402	D	0.000003	T	0.21022	0.0506	M	0.62723	1.935	0.42331	D	0.992297	P	0.43788	0.817	B	0.39339	0.297	T	0.15809	-1.0424	10	0.36615	T	0.2	.	11.4227	0.49991	0.0811:0.0:0.9189:0.0	.	980	Q9NPG4	PCD12_HUMAN	Y	980	ENSP00000231484:H980Y	ENSP00000231484:H980Y	H	-	1	0	PCDH12	141311282	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.297000	0.65704	2.894000	0.99253	0.655000	0.94253	CAC	G|0.991;A|0.009	0.009	strong		0.547	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580	
SSPO	23145	hgsc.bcm.edu	37	7	149509048	149509048	+	RNA	SNP	C	C	T	rs115723456	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149509048C>T	ENST00000378016.2	+	0	9594							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GTTCAGCCTCCTGTGGCCCTG	0.697													C|||	70	0.0139776	0.053	0.0	5008	,	,		15590	0.0		0.0	False		,,,				2504	0.0				p.S3198S		Atlas-SNP	.											.	.	.	.	0			c.C9594T						PASS	.	C		162,3908		5,152,1878	30.0	35.0	34.0		9604	0.7	1.0	7	dbSNP_132	34	0,8344		0,0,4172	no	coding-notMod3	SSPO	NM_198455.2		5,152,6050	TT,TC,CC		0.0,3.9803,1.305			149509048	162,12252	2035	4172	6207			23145	exon68			AGCCTCCTGTGGC	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149509048C>T		83.0	0.0	0		104.0	52.0	0.5	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				C|0.989;T|0.011	0.011	strong		0.697	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
PCDHB10	56126	hgsc.bcm.edu	37	5	140573655	140573655	+	Silent	SNP	C	C	T	rs17844572	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140573655C>T	ENST00000239446.4	+	1	1714	c.1530C>T	c.(1528-1530)aaC>aaT	p.N510N		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	510	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACGCGGACAACGGCCACCTGT	0.692													C|||	79	0.0157748	0.0582	0.0029	5008	,	,		18416	0.0		0.0	False		,,,				2504	0.0				p.N510N		Atlas-SNP	.											.	PCDHB10	177	.	0			c.C1530T						PASS	.	C		182,4224	107.8+/-146.2	5,172,2026	102.0	119.0	113.0		1530	1.7	0.9	5	dbSNP_123	113	0,8594		0,0,4297	no	coding-synonymous	PCDHB10	NM_018930.3		5,172,6323	TT,TC,CC		0.0,4.1307,1.4		510/801	140573655	182,12818	2203	4297	6500	SO:0001819	synonymous_variant	56126	exon1			GGACAACGGCCAC	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"""Cadherins / Protocadherins : Clustered"""	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.1530C>T	5.37:g.140573655C>T		374.0	0.0	0		395.0	107.0	0.270886	NM_018930	Q96T99	Silent	SNP	ENST00000239446.4	37	CCDS4252.1																																																																																			C|0.986;T|0.014	0.014	strong		0.692	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930	
AIRE	326	hgsc.bcm.edu	37	21	45712983	45712983	+	Silent	SNP	T	T	C	rs61737072	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45712983T>C	ENST00000291582.5	+	10	1330	c.1203T>C	c.(1201-1203)ccT>ccC	p.P401P	AIRE_ENST00000355347.4_Silent_p.P194P|AIRE_ENST00000329347.4_Intron	NM_000383.3	NP_000374.1	O43918	AIRE_HUMAN	autoimmune regulator	401					humoral immune response (GO:0006959)|immune response (GO:0006955)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|transcription regulatory region DNA binding (GO:0044212)|translation regulator activity (GO:0045182)|zinc ion binding (GO:0008270)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|skin(2)|urinary_tract(1)	14				Colorectal(79;0.0806)		CGGCTCCGCCTTCTGCAGCCC	0.677									Autoimmune PolyEndocrinopathy Candidiasis Ectodermal Dystrophy				T|||	232	0.0463259	0.1649	0.0202	5008	,	,		10975	0.0		0.0	False		,,,				2504	0.0				p.P401P		Atlas-SNP	.											.	AIRE	61	.	0			c.T1203C						PASS	.	T	,	665,3717		60,545,1586	22.0	26.0	24.0		1203,612	-2.4	0.0	21	dbSNP_129	24	2,8586		0,2,4292	no	coding-synonymous,coding-synonymous	AIRE	NM_000383.2,NM_000658.2	,	60,547,5878	CC,CT,TT		0.0233,15.1757,5.1426	,	401/546,204/349	45712983	667,12303	2191	4294	6485	SO:0001819	synonymous_variant	326	exon10	Familial Cancer Database	APECED	TCCGCCTTCTGCA	AB006684	CCDS13706.1	21q22.3	2014-09-17	2007-06-20		ENSG00000160224	ENSG00000160224		"""Zinc fingers, PHD-type"""	360	protein-coding gene	gene with protein product	"""autoimmune polyendocrinopathy candidiasis ectodermal dystrophy"""	607358	"""autoimmune regulator (autoimmune polyendocrinopathy candidiasis ectodermal dystrophy)"""	APECED		9398840	Standard	NM_000383		Approved	PGA1, APS1	uc002zei.3	O43918	OTTHUMG00000086921	ENST00000291582.5:c.1203T>C	21.37:g.45712983T>C		32.0	0.0	0		46.0	20.0	0.434783	NM_000383	B2RP50|O43922|O43932|O75745	Silent	SNP	ENST00000291582.5	37	CCDS13706.1																																																																																			T|0.951;C|0.049	0.049	strong		0.677	AIRE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195842.2		
MSH2	4436	hgsc.bcm.edu	37	2	47637439	47637439	+	Silent	SNP	C	C	T	rs1800151	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:47637439C>T	ENST00000233146.2	+	3	796	c.573C>T	c.(571-573)ctC>ctT	p.L191L	MSH2_ENST00000406134.1_Silent_p.L191L|MSH2_ENST00000543555.1_Silent_p.L125L	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	191					ATP catabolic process (GO:0006200)|B cell differentiation (GO:0030183)|B cell mediated immunity (GO:0019724)|cell cycle arrest (GO:0007050)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|intra-S DNA damage checkpoint (GO:0031573)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|isotype switching (GO:0045190)|maintenance of DNA repeat elements (GO:0043570)|male gonad development (GO:0008584)|meiotic gene conversion (GO:0006311)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reciprocal meiotic recombination (GO:0045128)|oxidative phosphorylation (GO:0006119)|positive regulation of helicase activity (GO:0051096)|postreplication repair (GO:0006301)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSalpha complex (GO:0032301)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|guanine/thymine mispair binding (GO:0032137)|heteroduplex DNA loop binding (GO:0000404)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|Y-form DNA binding (GO:0000403)	p.0?(2)|p.?(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(5)|large_intestine(50)|lung(18)|ovary(5)|prostate(2)|skin(3)|small_intestine(1)|stomach(2)|urinary_tract(1)	112		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AGGCTCTCCTCATCCAGATTG	0.463			"""D, Mis, N, F, S"""		"""colorectal, endometrial, ovarian"""	"""colorectal, endometrial, ovarian"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				C|||	97	0.019369	0.0696	0.0072	5008	,	,		15087	0.0		0.0	False		,,,				2504	0.0				p.L191L		Atlas-SNP	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p22-p21	4436	mutS homolog 2 (E. coli)		E	.	MSH2	198	.	3	Whole gene deletion(2)|Unknown(1)	haematopoietic_and_lymphoid_tissue(3)	c.C573T						PASS	.	C		254,4152	146.9+/-181.5	4,246,1953	182.0	176.0	178.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	573	1.6	1.0	2	dbSNP_89	178	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	MSH2	NM_000251.1		4,250,6249	TT,TC,CC		0.0465,5.7649,1.9837		191/935	47637439	258,12748	2203	4300	6503	SO:0001819	synonymous_variant	4436	exon3	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	TCTCCTCATCCAG	U03911	CCDS1834.1, CCDS58709.1	2p21	2014-09-17	2013-09-12		ENSG00000095002	ENSG00000095002			7325	protein-coding gene	gene with protein product		609309	"""mutS (E. coli) homolog 2 (colon cancer, nonpolyposis type 1)"", ""mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)"""	COCA1		8484120, 9843200	Standard	NM_000251		Approved	HNPCC, HNPCC1	uc002rvy.2	P43246	OTTHUMG00000128861	ENST00000233146.2:c.573C>T	2.37:g.47637439C>T		106.0	0.0	0		129.0	55.0	0.426357	NM_000251	B4E2Z2|O75488	Silent	SNP	ENST00000233146.2	37	CCDS1834.1																																																																																			C|0.977;T|0.023	0.023	strong		0.463	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3		
IL10RA	3587	hgsc.bcm.edu	37	11	117870257	117870257	+	Silent	SNP	C	C	T	rs146193205	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117870257C>T	ENST00000227752.3	+	7	1758	c.1638C>T	c.(1636-1638)gcC>gcT	p.A546A	IL10RA_ENST00000545409.1_Silent_p.A397A|IL10RA_ENST00000541785.1_Silent_p.A526A|IL10RA_ENST00000533700.1_3'UTR	NM_001558.3	NP_001549.2	Q13651	I10R1_HUMAN	interleukin 10 receptor, alpha	546					cytokine-mediated signaling pathway (GO:0019221)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-10 receptor activity (GO:0004920)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(10)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.07e-05)|Epithelial(105;0.00108)		ATGACCTTGCCCCTCTAGGCT	0.592													C|||	3	0.000599042	0.0023	0.0	5008	,	,		19108	0.0		0.0	False		,,,				2504	0.0				p.A546A		Atlas-SNP	.											.	IL10RA	46	.	0			c.C1638T						PASS	.	C		6,4394	11.4+/-27.6	0,6,2194	51.0	48.0	49.0		1638	-0.1	0.0	11	dbSNP_134	49	0,8592		0,0,4296	no	coding-synonymous	IL10RA	NM_001558.3		0,6,6490	TT,TC,CC		0.0,0.1364,0.0462		546/579	117870257	6,12986	2200	4296	6496	SO:0001819	synonymous_variant	3587	exon7			CCTTGCCCCTCTA	U00672	CCDS8388.1	11q23	2014-09-17			ENSG00000110324	ENSG00000110324		"""Interleukins and interleukin receptors"", ""CD molecules"""	5964	protein-coding gene	gene with protein product		146933		IL10R		8120391	Standard	NR_026691		Approved	HIL-10R, CDW210A, CD210a, CD210	uc001prv.3	Q13651	OTTHUMG00000166523	ENST00000227752.3:c.1638C>T	11.37:g.117870257C>T		67.0	0.0	0		53.0	30.0	0.566038	NM_001558	A8K6I0|B0YJ27	Silent	SNP	ENST00000227752.3	37	CCDS8388.1																																																																																			C|0.999;T|0.001	0.001	strong		0.592	IL10RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390167.1		
IGSF10	285313	hgsc.bcm.edu	37	3	151165106	151165106	+	Missense_Mutation	SNP	T	T	G	rs35491609	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:151165106T>G	ENST00000282466.3	-	4	2662	c.2663A>C	c.(2662-2664)cAa>cCa	p.Q888P		NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	888					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GGATGAATGTTGATTGGTTGT	0.428													T|||	37	0.00738818	0.0272	0.0014	5008	,	,		22524	0.0		0.0	False		,,,				2504	0.0				p.Q888P		Atlas-SNP	.											IGSF10,NS,carcinoma,-1,1	IGSF10	279	1	0			c.A2663C						PASS	.	T	PRO/GLN	99,4307	79.3+/-117.8	0,99,2104	356.0	355.0	355.0		2663	-5.0	0.0	3	dbSNP_126	355	0,8600		0,0,4300	yes	missense	IGSF10	NM_178822.4	76	0,99,6404	GG,GT,TT		0.0,2.2469,0.7612	benign	888/2624	151165106	99,12907	2203	4300	6503	SO:0001583	missense	285313	exon4			GAATGTTGATTGG	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"""Immunoglobulin superfamily / I-set domain containing"""	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.2663A>C	3.37:g.151165106T>G	ENSP00000282466:p.Gln888Pro	324.0	0.0	0		348.0	156.0	0.448276	NM_178822	Q86YJ9|Q8N772|Q8NA84	Missense_Mutation	SNP	ENST00000282466.3	37	CCDS3160.1	11	0.005036630036630037	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	0	0.0	T	10.97	1.500447	0.26861	0.022469	0.0	ENSG00000152580	ENST00000282466	T	0.68903	-0.36	5.41	-5.03	0.02973	.	0.536026	0.15865	N	0.240805	T	0.20333	0.0489	N	0.08118	0	0.09310	N	1	B	0.12630	0.006	B	0.08055	0.003	T	0.16541	-1.0399	10	0.20519	T	0.43	.	7.7274	0.28767	0.0:0.217:0.3727:0.4103	rs35491609	888	Q6WRI0	IGS10_HUMAN	P	888	ENSP00000282466:Q888P	ENSP00000282466:Q888P	Q	-	2	0	IGSF10	152647796	0.000000	0.05858	0.000000	0.03702	0.347000	0.29111	-0.226000	0.09139	-0.598000	0.05806	0.482000	0.46254	CAA	T|0.992;G|0.008	0.008	strong		0.428	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
MTRR	4552	hgsc.bcm.edu	37	5	7885907	7885907	+	Missense_Mutation	SNP	C	C	G	rs10064631	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:7885907C>G	ENST00000264668.2	+	7	1108	c.1078C>G	c.(1078-1080)Ctt>Gtt	p.L360V	MTRR_ENST00000341013.6_3'UTR|MTRR_ENST00000440940.2_Missense_Mutation_p.L333V	NM_002454.2|NM_024010.2	NP_002445.2|NP_076915.2	Q9UBK8	MTRR_HUMAN	5-methyltetrahydrofolate-homocysteine methyltransferase reductase	360	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.		L -> V (in dbSNP:rs10064631). {ECO:0000269|PubMed:10484769}.		cellular nitrogen compound metabolic process (GO:0034641)|cobalamin metabolic process (GO:0009235)|DNA methylation (GO:0006306)|folic acid metabolic process (GO:0046655)|methionine biosynthetic process (GO:0009086)|methionine metabolic process (GO:0006555)|methylation (GO:0032259)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	[methionine synthase] reductase activity (GO:0030586)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|oxidoreductase activity, oxidizing metal ions, NAD or NADP as acceptor (GO:0016723)			NS(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(14)|ovary(1)|prostate(3)|stomach(1)	31					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)|L-Methionine(DB00134)	AAGACTGCAGCTTGAAGATAA	0.468													C|||	199	0.0397364	0.1445	0.0115	5008	,	,		17404	0.0		0.0	False		,,,				2504	0.0				p.L360V		Atlas-SNP	.											.	MTRR	74	.	0			c.C1078G	GRCh37	CM992646	MTRR	M	rs10064631	PASS	.	C	VAL/LEU,VAL/LEU	639,3767	275.4+/-272.5	46,547,1610	109.0	109.0	109.0		997,1078	5.8	1.0	5	dbSNP_119	109	8,8592	6.4+/-24.3	0,8,4292	yes	missense,missense	MTRR	NM_002454.2,NM_024010.2	32,32	46,555,5902	GG,GC,CC		0.093,14.503,4.9746	probably-damaging,probably-damaging	333/699,360/726	7885907	647,12359	2203	4300	6503	SO:0001583	missense	4552	exon7			CTGCAGCTTGAAG	AF025794	CCDS3874.1, CCDS47190.1	5p15.31	2011-05-12			ENSG00000124275	ENSG00000124275	1.16.1.8		7473	protein-coding gene	gene with protein product		602568				9501215	Standard	NM_024010		Approved	cblE	uc003jed.3	Q9UBK8	OTTHUMG00000090477	ENST00000264668.2:c.1078C>G	5.37:g.7885907C>G	ENSP00000264668:p.Leu360Val	176.0	0.0	0		197.0	92.0	0.467005	NM_024010	O60471|Q32MA9|Q7Z4M8	Missense_Mutation	SNP	ENST00000264668.2	37	CCDS3874.1	75	0.034340659340659344	71	0.1443089430894309	4	0.011049723756906077	0	0.0	0	0.0	C	15.42	2.826850	0.50739	0.14503	9.3E-4	ENSG00000124275	ENST00000264668;ENST00000440940	T;T	0.39406	1.08;1.08	5.83	5.83	0.93111	Riboflavin synthase-like beta-barrel (1);FAD-binding, type 1 (1);NADPH-cytochrome p450 reductase, FAD-binding, alpha-helical domain-3 (1);Ferredoxin reductase-type FAD-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.00524	0.0017	M	0.66378	2.025	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	T	0.00119	-1.2031	10	0.31617	T	0.26	-27.2783	13.3424	0.60553	0.0:0.9283:0.0:0.0717	rs10064631;rs10064631	360	Q9UBK8	MTRR_HUMAN	V	360;333	ENSP00000264668:L360V;ENSP00000402510:L333V	ENSP00000264668:L360V	L	+	1	0	MTRR	7938907	1.000000	0.71417	0.991000	0.47740	0.034000	0.12701	4.189000	0.58358	2.753000	0.94483	0.650000	0.86243	CTT	C|0.948;G|0.052	0.052	strong		0.468	MTRR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206931.1		
ABCA1	19	hgsc.bcm.edu	37	9	107578478	107578478	+	Silent	SNP	C	C	T	rs2230807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107578478C>T	ENST00000374736.3	-	25	4078	c.3684G>A	c.(3682-3684)cgG>cgA	p.R1228R		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	1228					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)			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)	GGTCTGAGAGCCGGTCATCAA	0.488													C|||	316	0.063099	0.2269	0.0231	5008	,	,		18611	0.0		0.0	False		,,,				2504	0.0				p.R1228R		Atlas-SNP	.											.	ABCA1	244	.	0			c.G3684A						PASS	.	C		778,3628	314.7+/-293.7	70,638,1495	159.0	165.0	163.0		3684	-2.1	1.0	9	dbSNP_98	163	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous	ABCA1	NM_005502.3		70,647,5786	TT,TC,CC		0.1047,17.6577,6.0511		1228/2262	107578478	787,12219	2203	4300	6503	SO:0001819	synonymous_variant	19	exon25			TGAGAGCCGGTCA	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.3684G>A	9.37:g.107578478C>T		148.0	0.0	0		158.0	87.0	0.550633	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Silent	SNP	ENST00000374736.3	37	CCDS6762.1																																																																																			T|0.049;G|0.134	0.049	strong		0.488	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502	
ARMCX2	9823	hgsc.bcm.edu	37	X	100912065	100912065	+	Silent	SNP	C	C	T	rs78189978	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:100912065C>T	ENST00000328766.5	-	5	963	c.510G>A	c.(508-510)gcG>gcA	p.A170A	ARMCX2_ENST00000356824.4_Silent_p.A170A|ARMCX2_ENST00000467416.1_5'Flank|ARMCX2_ENST00000330154.2_Silent_p.A170A	NM_014782.5	NP_055597.1	Q7L311	ARMX2_HUMAN	armadillo repeat containing, X-linked 2	170	Ala-rich.					integral component of membrane (GO:0016021)				NS(1)|breast(4)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(6)|prostate(1)|skin(1)	29						TGGAAGTCTCCGCTTCTCTGG	0.652													C|||	57	0.0150993	0.0416	0.0029	3775	,	,		11432	0.0		0.0	False		,,,				2504	0.0				p.A170A		Atlas-SNP	.											.	ARMCX2	75	.	0			c.G510A						PASS	.	C	,	213,3621		7,168,31,1457,539	28.0	29.0	28.0		510,510	-0.1	0.0	X	dbSNP_131	28	1,6713		0,1,0,2427,1858	no	coding-synonymous,coding-synonymous	ARMCX2	NM_014782.5,NM_177949.2	,	7,169,31,3884,2397	TT,TC,T,CC,C		0.0149,5.5556,2.0288	,	170/633,170/633	100912065	214,10334	2202	4286	6488	SO:0001819	synonymous_variant	9823	exon5			AGTCTCCGCTTCT	AB011084	CCDS14490.1	Xq21.33-q22.2	2014-03-21			ENSG00000184867	ENSG00000184867		"""Armadillo repeat containing"""	16869	protein-coding gene	gene with protein product		300363				9628581, 11162520, 16221301, 22569362	Standard	XM_005278109		Approved	ALEX2, KIAA0512, GASP9	uc004eif.3	Q7L311	OTTHUMG00000022038	ENST00000328766.5:c.510G>A	X.37:g.100912065C>T		116.0	0.0	0		74.0	46.0	0.621622	NM_014782	O60267|Q5H9D9	Silent	SNP	ENST00000328766.5	37	CCDS14490.1																																																																																			C|0.981;T|0.019	0.019	strong		0.652	ARMCX2-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057586.1	NM_014782	
MYO18B	84700	hgsc.bcm.edu	37	22	26423477	26423477	+	Missense_Mutation	SNP	G	G	A	rs7284177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:26423477G>A	ENST00000407587.2	+	43	7709	c.7540G>A	c.(7540-7542)Ggc>Agc	p.G2514S	MYO18B_ENST00000536101.1_Missense_Mutation_p.G2513S|MYO18B_ENST00000335473.7_Missense_Mutation_p.G2513S			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2513	Poly-Ser.					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						CTCATCCTCCGGCTCCATCGT	0.587													A|||	352	0.0702875	0.2005	0.0259	5008	,	,		18932	0.004		0.0179	False		,,,				2504	0.0481				p.G2513S		Atlas-SNP	.											.	MYO18B	322	.	0			c.G7537A						PASS	.	A	SER/GLY	695,3407		58,579,1414	53.0	55.0	55.0		7537	1.8	1.0	22	dbSNP_116	55	146,8242		1,144,4049	yes	missense	MYO18B	NM_032608.5	56	59,723,5463	AA,AG,GG		1.7406,16.943,6.7334	benign	2513/2568	26423477	841,11649	2051	4194	6245	SO:0001583	missense	84700	exon43			TCCTCCGGCTCCA	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.7540G>A	22.37:g.26423477G>A	ENSP00000386096:p.Gly2514Ser	61.0	0.0	0		56.0	21.0	0.375	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		123	0.05631868131868132	92	0.18699186991869918	13	0.03591160220994475	4	0.006993006993006993	14	0.018469656992084433	A	4.656	0.121893	0.08931	0.16943	0.017406	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.85088	-1.92;-1.92;-1.94	5.17	1.8	0.24995	.	0.170297	0.37437	N	0.002083	T	0.00109	0.0003	N	0.00729	-1.24	0.54753	P	1.0999999999983245E-5	B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.001	B;B;B;B;B	0.06405	0.002;0.001;0.001;0.002;0.002	T	0.12426	-1.0548	9	0.02654	T	1	.	4.0444	0.09766	0.4128:0.0:0.4136:0.1736	rs7284177;rs52837742;rs59696890;rs7284177	2026;2515;2513;2514;2513	Q8IUG5-2;B0QYF5;Q8IUG5;F5GXR6;F5GYU7	.;.;MY18B_HUMAN;.;.	S	2513;2513;2514	ENSP00000441229:G2513S;ENSP00000334563:G2513S;ENSP00000386096:G2514S	ENSP00000334563:G2513S	G	+	1	0	MYO18B	24753477	0.459000	0.25768	0.958000	0.39756	0.893000	0.52053	0.694000	0.25512	-0.007000	0.14345	-0.361000	0.07541	GGC	G|0.931;A|0.069	0.069	strong		0.587	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
NMU	10874	hgsc.bcm.edu	37	4	56466734	56466734	+	Missense_Mutation	SNP	G	G	T	rs12108463	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:56466734G>T	ENST00000264218.3	-	8	549	c.444C>A	c.(442-444)ttC>ttA	p.F148L	NMU_ENST00000507338.1_Missense_Mutation_p.F123L|NMU_ENST00000511469.1_Missense_Mutation_p.F132L|NMU_ENST00000515325.1_5'UTR|NMU_ENST00000505262.1_Missense_Mutation_p.F121L	NM_006681.2	NP_006672.1	P48645	NMU_HUMAN	neuromedin U	148			F -> L (in dbSNP:rs12108463).		digestion (GO:0007586)|eating behavior (GO:0042755)|G-protein coupled receptor signaling pathway (GO:0007186)|gastric acid secretion (GO:0001696)|neuropeptide signaling pathway (GO:0007218)|photoperiodism (GO:0009648)|positive regulation of hormone secretion (GO:0046887)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of synaptic transmission (GO:0050806)|regulation of smooth muscle contraction (GO:0006940)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|terminal bouton (GO:0043195)	receptor binding (GO:0005102)			lung(3)|ovary(1)|urinary_tract(1)	5	Lung NSC(11;0.00256)|all_epithelial(27;0.075)|Glioma(25;0.08)|all_neural(26;0.101)	all_hematologic(202;0.103)	LUSC - Lung squamous cell carcinoma(4;6.72e-08)|Lung(4;6.22e-07)|Epithelial(7;0.00559)	LUSC - Lung squamous cell carcinoma(721;0.0115)		AGGGACTTTGGAATTCTTCCT	0.299													G|||	209	0.0417332	0.1543	0.0072	5008	,	,		17523	0.0		0.0	False		,,,				2504	0.0				p.F148L		Atlas-SNP	.											.	NMU	17	.	0			c.C444A						PASS	.	G	LEU/PHE	585,3821	251.8+/-258.4	41,503,1659	54.0	59.0	57.0		444	-3.0	0.2	4	dbSNP_120	57	5,8585	3.7+/-12.6	0,5,4290	yes	missense	NMU	NM_006681.2	22	41,508,5949	TT,TG,GG		0.0582,13.2773,4.5399	benign	148/175	56466734	590,12406	2203	4295	6498	SO:0001583	missense	10874	exon8			ACTTTGGAATTCT	X76029	CCDS3501.1, CCDS75125.1	4q12	2013-02-26			ENSG00000109255	ENSG00000109255		"""Endogenous ligands"""	7859	protein-coding gene	gene with protein product	"""prepro-NMU"""	605103				7619205	Standard	XM_005265713		Approved		uc003hbc.3	P48645	OTTHUMG00000102161	ENST00000264218.3:c.444C>A	4.37:g.56466734G>T	ENSP00000264218:p.Phe148Leu	230.0	0.0	0		213.0	91.0	0.42723	NM_006681		Missense_Mutation	SNP	ENST00000264218.3	37	CCDS3501.1	64	0.029304029304029304	62	0.12601626016260162	2	0.0055248618784530384	0	0.0	0	0.0	G	4.096	0.015910	0.07959	0.132773	5.82E-4	ENSG00000109255	ENST00000511469;ENST00000264218;ENST00000505262;ENST00000541393;ENST00000507338	T;T;T;T	0.42900	0.96;0.96;0.96;0.96	4.72	-2.96	0.05547	.	0.703326	0.13471	N	0.385414	T	0.00144	0.0004	N	0.11064	0.09	0.09310	N	0.999996	B	0.09022	0.002	B	0.08055	0.003	T	0.13019	-1.0525	10	0.07813	T	0.8	-6.4377	2.1008	0.03679	0.3758:0.1231:0.3762:0.1249	rs12108463;rs52827993;rs12108463	148	P48645	NMU_HUMAN	L	132;148;121;131;123	ENSP00000422399:F132L;ENSP00000264218:F148L;ENSP00000424246:F121L;ENSP00000422870:F123L	ENSP00000264218:F148L	F	-	3	2	NMU	56161491	0.165000	0.22948	0.173000	0.22940	0.971000	0.66376	-1.188000	0.03064	-0.684000	0.05183	0.585000	0.79938	TTC	G|0.960;T|0.040	0.040	strong		0.299	NMU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220006.2		
TG	7038	hgsc.bcm.edu	37	8	133898949	133898949	+	Silent	SNP	C	C	T	rs61741629	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133898949C>T	ENST00000220616.4	+	9	1372	c.1332C>T	c.(1330-1332)atC>atT	p.I444I	TG_ENST00000377869.1_Silent_p.I444I	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	444					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		AAGAAGCCATCCGAGCAATTT	0.502													C|||	124	0.0247604	0.0923	0.0029	5008	,	,		18045	0.0		0.0	False		,,,				2504	0.0				p.I444I		Atlas-SNP	.											.	TG	416	.	0			c.C1332T						PASS	.	C		332,4074	169.1+/-199.8	19,294,1890	73.0	80.0	78.0		1332	-1.0	0.0	8	dbSNP_129	78	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TG	NM_003235.4		19,296,6188	TT,TC,CC		0.0233,7.5352,2.568		444/2769	133898949	334,12672	2203	4300	6503	SO:0001819	synonymous_variant	7038	exon9			AGCCATCCGAGCA	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.1332C>T	8.37:g.133898949C>T		48.0	0.0	0		68.0	42.0	0.617647	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1																																																																																			C|0.971;T|0.029	0.029	strong		0.502	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
ZNF746	155061	hgsc.bcm.edu	37	7	149174758	149174758	+	Silent	SNP	G	G	A	rs61746598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149174758G>A	ENST00000340622.3	-	5	889	c.609C>T	c.(607-609)ggC>ggT	p.G203G	ZNF746_ENST00000458143.2_Silent_p.G203G			Q6NUN9	ZN746_HUMAN	zinc finger protein 746	203					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of neuron death (GO:1901216)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34	Melanoma(164;0.165)		OV - Ovarian serous cystadenocarcinoma(82;0.00358)			ACGCCTCCACGCCCAGGGCCT	0.667													G|||	174	0.0347444	0.1248	0.013	5008	,	,		16240	0.0		0.0	False		,,,				2504	0.0				p.G203G		Atlas-SNP	.											.	ZNF746	68	.	0			c.C609T						PASS	.	G	,	528,3878	228.1+/-243.1	33,462,1708	27.0	30.0	29.0		609,609	-6.2	0.7	7	dbSNP_129	29	3,8597	3.0+/-9.4	0,3,4297	yes	coding-synonymous,coding-synonymous	ZNF746	NM_001163474.1,NM_152557.4	,	33,465,6005	AA,AG,GG		0.0349,11.9837,4.0827	,	203/646,203/645	149174758	531,12475	2203	4300	6503	SO:0001819	synonymous_variant	155061	exon5			CTCCACGCCCAGG	AK055975	CCDS5897.1, CCDS55180.1	7q36.1	2013-01-08			ENSG00000181220	ENSG00000181220		"""Zinc fingers, C2H2-type"", ""-"""	21948	protein-coding gene	gene with protein product		613914					Standard	NM_152557		Approved	FLJ31413	uc010lpi.2	Q6NUN9	OTTHUMG00000158972	ENST00000340622.3:c.609C>T	7.37:g.149174758G>A		69.0	0.0	0		85.0	47.0	0.552941	NM_001163474	A8K6Z9|Q6ZRF9	Silent	SNP	ENST00000340622.3	37	CCDS5897.1																																																																																			G|0.960;A|0.040	0.040	strong		0.667	ZNF746-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352730.1	NM_152557	
IL12RB2	3595	hgsc.bcm.edu	37	1	67787286	67787286	+	Splice_Site	SNP	T	T	C	rs2307147	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:67787286T>C	ENST00000262345.1	+	3	718	c.78T>C	c.(76-78)gaT>gaC	p.D26D	IL12RB2_ENST00000371000.1_Splice_Site_p.D26D|IL12RB2_ENST00000541374.1_Splice_Site_p.D26D|IL12RB2_ENST00000544434.1_Splice_Site_p.D26D	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	26					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma production (GO:0032609)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interferon-gamma production (GO:0032729)|response to lipopolysaccharide (GO:0032496)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(21)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	45						TTATTGCAGATGCGTGCAAGA	0.388													T|||	324	0.0646965	0.2383	0.013	5008	,	,		20536	0.0		0.0	False		,,,				2504	0.0				p.D26D		Atlas-SNP	.											.	IL12RB2	94	.	0			c.T78C						PASS	.	T		901,3505	347.5+/-309.5	88,725,1390	103.0	94.0	97.0		78	-1.2	1.0	1	dbSNP_100	97	9,8591	5.7+/-21.5	0,9,4291	yes	coding-synonymous-near-splice	IL12RB2	NM_001559.2		88,734,5681	CC,CT,TT		0.1047,20.4494,6.9968		26/863	67787286	910,12096	2203	4300	6503	SO:0001630	splice_region_variant	3595	exon3			TGCAGATGCGTGC	U64198	CCDS638.1, CCDS58006.1, CCDS58007.1, CCDS72805.1	1p31.3-p31.2	2014-07-15			ENSG00000081985	ENSG00000081985		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	5972	protein-coding gene	gene with protein product		601642				9284929, 8943050	Standard	NM_001559		Approved		uc001ddu.3	Q99665	OTTHUMG00000009094	ENST00000262345.1:c.77-1T>C	1.37:g.67787286T>C		56.0	0.0	0		78.0	35.0	0.448718	NM_001559	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Silent	SNP	ENST00000262345.1	37	CCDS638.1																																																																																			T|0.926;C|0.074	0.074	strong		0.388	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2	NM_001559	Silent
FLG2	388698	hgsc.bcm.edu	37	1	152326516	152326516	+	Missense_Mutation	SNP	T	T	C	rs16833974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152326516T>C	ENST00000388718.5	-	3	3818	c.3746A>G	c.(3745-3747)cAt>cGt	p.H1249R	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1249	Ser-rich.		H -> R (in dbSNP:rs16833974).		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)			AGACTGGCTATGTCTAGTGGT	0.478													T|||	341	0.0680911	0.2421	0.0231	5008	,	,		25196	0.0		0.005	False		,,,				2504	0.0				p.H1249R		Atlas-SNP	.											.	FLG2	431	.	0			c.A3746G						PASS	.	T	ARG/HIS	842,3564	332.0+/-302.3	71,700,1432	263.0	245.0	251.0		3746	2.5	0.0	1	dbSNP_123	251	25,8575	17.9+/-57.8	0,25,4275	yes	missense	FLG2	NM_001014342.2	29	71,725,5707	CC,CT,TT		0.2907,19.1103,6.6662	possibly-damaging	1249/2392	152326516	867,12139	2203	4300	6503	SO:0001583	missense	388698	exon3			TGGCTATGTCTAG	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.3746A>G	1.37:g.152326516T>C	ENSP00000373370:p.His1249Arg	271.0	0.0	0		349.0	175.0	0.501433	NM_001014342	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	CCDS30861.1	118	0.05402930402930403	112	0.22764227642276422	4	0.011049723756906077	0	0.0	2	0.002638522427440633	T	9.679	1.148853	0.21288	0.191103	0.002907	ENSG00000143520	ENST00000388718	T	0.37752	1.18	3.64	2.47	0.30058	.	.	.	.	.	T	0.09468	0.0233	L	0.52266	1.64	0.80722	P	0.0	P	0.39480	0.675	B	0.28638	0.092	T	0.17410	-1.0370	8	0.16420	T	0.52	-0.2453	7.1344	0.25521	0.0:0.0:0.2304:0.7696	rs16833974;rs16833974	1249	Q5D862	FILA2_HUMAN	R	1249	ENSP00000373370:H1249R	ENSP00000373370:H1249R	H	-	2	0	FLG2	150593140	0.000000	0.05858	0.001000	0.08648	0.076000	0.17211	-0.219000	0.09228	0.384000	0.24942	0.254000	0.18369	CAT	T|0.932;C|0.068	0.068	strong		0.478	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
C2orf16	84226	hgsc.bcm.edu	37	2	27802457	27802457	+	Silent	SNP	T	T	C	rs12329054	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27802457T>C	ENST00000408964.2	+	1	3069	c.3018T>C	c.(3016-3018)ggT>ggC	p.G1006G	AC074091.1_ENST00000408604.1_RNA	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1006						extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					CGTTCAATGGTATATCCCAAG	0.443													T|||	55	0.0109824	0.0378	0.0043	5008	,	,		20778	0.0		0.002	False		,,,				2504	0.0				p.G1006G		Atlas-SNP	.											.	C2orf16	357	.	0			c.T3018C						PASS	.	T		122,3976		3,116,1930	101.0	100.0	100.0		3018	-0.3	0.1	2	dbSNP_120	100	3,8421		0,3,4209	no	coding-synonymous	C2orf16	NM_032266.3		3,119,6139	CC,CT,TT		0.0356,2.9771,0.9982		1006/1985	27802457	125,12397	2049	4212	6261	SO:0001819	synonymous_variant	84226	exon1			CAATGGTATATCC	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.3018T>C	2.37:g.27802457T>C		96.0	0.0	0		102.0	59.0	0.578431	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Silent	SNP	ENST00000408964.2	37	CCDS42666.1																																																																																			T|0.986;C|0.014	0.014	strong		0.443	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
ABCC6	368	hgsc.bcm.edu	37	16	16259497	16259497	+	Missense_Mutation	SNP	G	G	T	rs60707953	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:16259497G>T	ENST00000205557.7	-	23	3318	c.3289C>A	c.(3289-3291)Ctc>Atc	p.L1097I		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	1097	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.		L -> I (in dbSNP:rs60707953).		response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	CCAGCGTAGAGGAGAAACAGT	0.612													G|||	38	0.00758786	0.0242	0.0058	5008	,	,		17411	0.0		0.002	False		,,,				2504	0.0				p.L1097I		Atlas-SNP	.											.	ABCC6	110	.	0			c.C3289A						PASS	.	G	ILE/LEU	94,4300	71.4+/-109.4	1,92,2104	58.0	51.0	54.0		3289	-0.2	0.9	16	dbSNP_129	54	7,8591	4.3+/-15.6	0,7,4292	yes	missense	ABCC6	NM_001171.5	5	1,99,6396	TT,TG,GG		0.0814,2.1393,0.7774	benign	1097/1504	16259497	101,12891	2197	4299	6496	SO:0001583	missense	368	exon23			CGTAGAGGAGAAA	AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"""ATP binding cassette transporters / subfamily C"""	57	protein-coding gene	gene with protein product		603234	"""pseudoxanthoma elasticum"""	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.3289C>A	16.37:g.16259497G>T	ENSP00000205557:p.Leu1097Ile	88.0	0.0	0		84.0	38.0	0.452381	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	37	CCDS10568.1	14	0.00641025641025641	13	0.026422764227642278	1	0.0027624309392265192	0	0.0	0	0.0	G	8.586	0.883526	0.17467	0.021393	8.14E-4	ENSG00000091262	ENST00000205557	D	0.89681	-2.55	5.38	-0.254	0.12992	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.180137	0.27482	U	0.019165	T	0.63367	0.2505	L	0.33710	1.025	0.80722	D	1	D	0.53619	0.961	P	0.48089	0.566	T	0.68205	-0.5470	10	0.20519	T	0.43	.	5.9149	0.19050	0.3303:0.2203:0.4494:0.0	rs60707953;rs61731991	1097	O95255	MRP6_HUMAN	I	1097	ENSP00000205557:L1097I	ENSP00000205557:L1097I	L	-	1	0	ABCC6	16166998	0.280000	0.24249	0.932000	0.37286	0.098000	0.18820	0.223000	0.17719	0.247000	0.21414	0.561000	0.74099	CTC	G|0.992;T|0.008	0.008	strong		0.612	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2		
DLK1	8788	hgsc.bcm.edu	37	14	101200514	101200514	+	Missense_Mutation	SNP	G	G	T	rs116078181	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:101200514G>T	ENST00000341267.4	+	5	675	c.433G>T	c.(433-435)Gtg>Ttg	p.V145L	DLK1_ENST00000331224.6_Missense_Mutation_p.V145L	NM_003836.5	NP_003827	P80370	DLK1_HUMAN	delta-like 1 homolog (Drosophila)	145	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell differentiation (GO:0030154)|embryonic skeletal system development (GO:0048706)|multicellular organismal development (GO:0007275)|negative regulation of Notch signaling pathway (GO:0045746)|Notch signaling pathway (GO:0007219)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)	external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(16)|ovary(2)|prostate(1)|skin(1)	29		Melanoma(154;0.155)				AGGCACCTGCGTGGATGATGA	0.652													G|||	93	0.0185703	0.0696	0.0014	5008	,	,		12961	0.0		0.0	False		,,,				2504	0.0				p.V145L		Atlas-SNP	.											.	DLK1	57	.	0			c.G433T						PASS	.	G	LEU/VAL	197,4207		7,183,2012	45.0	43.0	44.0		433	3.2	1.0	14	dbSNP_132	44	0,8598		0,0,4299	yes	missense	DLK1	NM_003836.5	32	7,183,6311	TT,TG,GG		0.0,4.4732,1.5152	possibly-damaging	145/384	101200514	197,12805	2202	4299	6501	SO:0001583	missense	8788	exon5			ACCTGCGTGGATG	U15979	CCDS9963.1	14q32	2011-12-05	2001-12-03			ENSG00000185559			2907	protein-coding gene	gene with protein product		176290	"""delta-like homolog (Drosophila)"""			8095043, 7925474	Standard	NM_003836		Approved	FA1, pG2, Pref-1, ZOG, Delta1	uc001yhs.4	P80370		ENST00000341267.4:c.433G>T	14.37:g.101200514G>T	ENSP00000340292:p.Val145Leu	126.0	0.0	0		89.0	54.0	0.606742	NM_003836	P15803|Q96DW5	Missense_Mutation	SNP	ENST00000341267.4	37	CCDS9963.1	37	0.01694139194139194	37	0.07520325203252033	0	0.0	0	0.0	0	0.0	G	15.51	2.856381	0.51376	0.044732	0.0	ENSG00000185559	ENST00000341267;ENST00000331224	T;T	0.71817	-0.6;-0.6	4.1	3.18	0.36537	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.432951	0.20458	N	0.091958	T	0.10981	0.0268	L	0.28776	0.89	0.80722	D	1	D;P	0.67145	0.996;0.926	D;P	0.64595	0.927;0.542	T	0.37820	-0.9689	10	0.30854	T	0.27	.	5.9295	0.19130	0.2969:0.0:0.7031:0.0	.	145;145	P80370-2;P80370	.;DLK1_HUMAN	L	145	ENSP00000340292:V145L;ENSP00000331081:V145L	ENSP00000331081:V145L	V	+	1	0	DLK1	100270267	0.812000	0.29077	0.997000	0.53966	0.813000	0.45954	1.136000	0.31467	1.981000	0.57761	0.491000	0.48974	GTG	G|0.981;T|0.019	0.019	strong		0.652	DLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414389.1		
DDX43	55510	hgsc.bcm.edu	37	6	74125283	74125283	+	Silent	SNP	T	T	C	rs138615882	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:74125283T>C	ENST00000370336.4	+	15	1967	c.1809T>C	c.(1807-1809)atT>atC	p.I603I	MB21D1_ENST00000370318.1_Intron	NM_018665.2	NP_061135.2	Q9NXZ2	DDX43_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 43	603	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)	intracellular (GO:0005622)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			NS(1)|breast(2)|central_nervous_system(1)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	24						CTGAATTGATTAATATTCTGG	0.383													T|||	13	0.00259585	0.0098	0.0	5008	,	,		16489	0.0		0.0	False		,,,				2504	0.0				p.I603I		Atlas-SNP	.											.	DDX43	69	.	0			c.T1809C						PASS	.	T		33,4373	37.6+/-69.7	1,31,2171	110.0	109.0	109.0		1809	0.9	1.0	6	dbSNP_134	109	0,8600		0,0,4300	no	coding-synonymous	DDX43	NM_018665.2		1,31,6471	CC,CT,TT		0.0,0.749,0.2537		603/649	74125283	33,12973	2203	4300	6503	SO:0001819	synonymous_variant	55510	exon15			ATTGATTAATATT		CCDS4977.1	6q13	2014-01-21			ENSG00000080007	ENSG00000080007		"""DEAD-boxes"""	18677	protein-coding gene	gene with protein product	"""cancer/testis antigen 13"""	606286				10919659	Standard	NM_018665		Approved	HAGE, DKFZp434H2114, CT13	uc003pgw.3	Q9NXZ2	OTTHUMG00000015033	ENST00000370336.4:c.1809T>C	6.37:g.74125283T>C		61.0	0.0	0		78.0	43.0	0.551282	NM_018665	B4E0C8|Q6NXR1	Silent	SNP	ENST00000370336.4	37	CCDS4977.1																																																																																			T|0.997;C|0.003	0.003	strong		0.383	DDX43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041219.3	NM_018665	
PLEKHH1	57475	hgsc.bcm.edu	37	14	68023989	68023989	+	Missense_Mutation	SNP	G	G	C	rs149253165	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:68023989G>C	ENST00000329153.5	+	4	325	c.193G>C	c.(193-195)Ggt>Cgt	p.G65R		NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	65						cytoskeleton (GO:0005856)				endometrium(2)|kidney(4)|lung(12)|urinary_tract(1)	19				all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011)		TTTTCAGGTGGGTGTCATGGA	0.507													G|||	40	0.00798722	0.028	0.0043	5008	,	,		19812	0.0		0.0	False		,,,				2504	0.0				p.G65R		Atlas-SNP	.											.	PLEKHH1	118	.	0			c.G193C						PASS	.	G	ARG/GLY	87,3815		0,87,1864	74.0	88.0	83.0		193	2.5	1.0	14	dbSNP_134	83	1,8305		0,1,4152	yes	missense	PLEKHH1	NM_020715.2	125	0,88,6016	CC,CG,GG		0.012,2.2296,0.7208	benign	65/1365	68023989	88,12120	1951	4153	6104	SO:0001583	missense	57475	exon4			CAGGTGGGTGTCA	AB033026	CCDS45128.1	14q24.1	2013-01-10				ENSG00000054690		"""Pleckstrin homology (PH) domain containing"""	17733	protein-coding gene	gene with protein product						10574462	Standard	NM_020715		Approved	KIAA1200	uc001xjl.1	Q9ULM0		ENST00000329153.5:c.193G>C	14.37:g.68023989G>C	ENSP00000330278:p.Gly65Arg	81.0	0.0	0		92.0	52.0	0.565217	NM_020715	A6H8X6|Q6PJL4|Q6ZWC7	Missense_Mutation	SNP	ENST00000329153.5	37	CCDS45128.1	16	0.007326007326007326	13	0.026422764227642278	3	0.008287292817679558	0	0.0	0	0.0	G	2.631	-0.286399	0.05605	0.022296	1.2E-4	ENSG00000054690	ENST00000329153	T	0.04083	3.71	5.41	2.47	0.30058	.	0.335067	0.36303	N	0.002673	T	0.00936	0.0031	L	0.28014	0.82	0.80722	D	1	B	0.09022	0.002	B	0.06405	0.002	T	0.42207	-0.9465	10	0.02654	T	1	.	7.9764	0.30157	0.2765:0.0:0.7235:0.0	.	65	Q9ULM0	PKHH1_HUMAN	R	65	ENSP00000330278:G65R	ENSP00000330278:G65R	G	+	1	0	PLEKHH1	67093742	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	0.637000	0.24659	0.349000	0.23975	-0.254000	0.11334	GGT	G|0.993;C|0.007	0.007	strong		0.507	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054	
PARP14	54625	hgsc.bcm.edu	37	3	122419151	122419151	+	Missense_Mutation	SNP	G	G	A	rs201474464		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122419151G>A	ENST00000474629.2	+	6	2016	c.1750G>A	c.(1750-1752)Gcc>Acc	p.A584T		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	584					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		TTCTTCTGAAGCCCTGTTAGA	0.398													G|||	1	0.000199681	0.0008	0.0	5008	,	,		21056	0.0		0.0	False		,,,				2504	0.0				p.A584T		Atlas-SNP	.											PARP14_ENST00000474629,caecum,carcinoma,-2,2	PARP14	242	2	0			c.G1750A						PASS	.	G	THR/ALA	10,3702		0,10,1846	38.0	35.0	36.0		1750	3.5	0.0	3		36	0,8178		0,0,4089	yes	missense	PARP14	NM_017554.2	58	0,10,5935	AA,AG,GG		0.0,0.2694,0.0841	benign	584/1802	122419151	10,11880	1856	4089	5945	SO:0001583	missense	54625	exon6			TCTGAAGCCCTGT	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"""Poly (ADP-ribose) polymerases"""	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.1750G>A	3.37:g.122419151G>A	ENSP00000418194:p.Ala584Thr	79.0	0.0	0		77.0	32.0	0.415584	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	37	CCDS46894.1	.	.	.	.	.	.	.	.	.	.	G	8.583	0.882878	0.17467	0.002694	0.0	ENSG00000173193	ENST00000474629;ENST00000398162	T	0.09817	2.94	5.34	3.52	0.40303	.	0.755868	0.11822	N	0.526062	T	0.06690	0.0171	N	0.22421	0.69	0.09310	N	1	B;B	0.15473	0.005;0.013	B;B	0.09377	0.002;0.004	T	0.33343	-0.9872	10	0.02654	T	1	.	11.1929	0.48696	0.1539:0.0:0.8461:0.0	.	584;584	Q460N5-4;Q460N5	.;PAR14_HUMAN	T	584;503	ENSP00000418194:A584T	ENSP00000381228:A503T	A	+	1	0	PARP14	123901841	0.558000	0.26554	0.005000	0.12908	0.634000	0.38068	2.752000	0.47516	1.494000	0.48533	-0.142000	0.14014	GCC	.	.	weak		0.398	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554	
TG	7038	hgsc.bcm.edu	37	8	134042164	134042164	+	Missense_Mutation	SNP	C	C	T	rs61742878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:134042164C>T	ENST00000220616.4	+	41	7175	c.7135C>T	c.(7135-7137)Cgc>Tgc	p.R2379C	TG_ENST00000542445.1_Missense_Mutation_p.R749C|TG_ENST00000377869.1_Missense_Mutation_p.R2322C|TG_ENST00000519543.1_Missense_Mutation_p.R512C	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	2379					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		GGACCCTCGGCGCGTGTCCCT	0.667													C|||	22	0.00439297	0.0166	0.0	5008	,	,		14003	0.0		0.0	False		,,,				2504	0.0				p.R2379C		Atlas-SNP	.											TG,NS,carcinoma,0,4	TG	416	4	0			c.C7135T						PASS	.	C	CYS/ARG	54,4352	54.2+/-90.2	0,54,2149	47.0	49.0	48.0		7135	4.2	0.6	8	dbSNP_129	48	0,8596		0,0,4298	yes	missense	TG	NM_003235.4	180	0,54,6447	TT,TC,CC		0.0,1.2256,0.4153	probably-damaging	2379/2769	134042164	54,12948	2203	4298	6501	SO:0001583	missense	7038	exon41			CCTCGGCGCGTGT	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.7135C>T	8.37:g.134042164C>T	ENSP00000220616:p.Arg2379Cys	106.0	0.0	0		124.0	49.0	0.395161	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	7|7	0.003205128205128205|0.003205128205128205	7|7	0.014227642276422764|0.014227642276422764	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	15.00|15.00	2.701863|2.701863	0.48307|0.48307	0.012256|0.012256	0.0|0.0	ENSG00000042832|ENSG00000042832	ENST00000519178;ENST00000518108|ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445;ENST00000519543	.|T;T;T;T	.|0.65364	.|-0.15;-0.15;-0.15;-0.15	5.13|5.13	4.22|4.22	0.49857|0.49857	.|Carboxylesterase, type B (1);	.|0.761860	.|0.12170	.|N	.|0.493098	T|T	0.69993|0.69993	0.3173|0.3173	M|M	0.72576|0.72576	2.205|2.205	0.09310|0.09310	N|N	0.999993|0.999993	.|D;D;D	.|0.89917	.|1.0;0.999;0.999	.|D;P;D	.|0.63192	.|0.912;0.899;0.912	T|T	0.63853|0.63853	-0.6543|-0.6543	5|10	.|0.87932	.|D	.|0	.|.	13.7454|13.7454	0.62872|0.62872	0.1544:0.8456:0.0:0.0|0.1544:0.8456:0.0:0.0	rs61742878|rs61742878	.|512;749;2379	.|E7EVM0;F5GWW5;P01266	.|.;.;THYG_HUMAN	V|C	834;174|2322;1185;2379;749;512	.|ENSP00000367100:R2322C;ENSP00000220616:R2379C;ENSP00000441693:R749C;ENSP00000430430:R512C	.|ENSP00000220616:R2379C	A|R	+|+	2|1	0|0	TG|TG	134111346|134111346	0.060000|0.060000	0.20803|0.20803	0.550000|0.550000	0.28217|0.28217	0.384000|0.384000	0.30261|0.30261	2.504000|2.504000	0.45416|0.45416	2.407000|2.407000	0.81776|0.81776	0.485000|0.485000	0.47835|0.47835	GCG|CGC	C|0.995;T|0.005	0.005	strong		0.667	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
TRPM2	7226	hgsc.bcm.edu	37	21	45786709	45786709	+	Missense_Mutation	SNP	G	G	A	rs45544142	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45786709G>A	ENST00000397928.1	+	4	941	c.496G>A	c.(496-498)Gtc>Atc	p.V166I	TRPM2_ENST00000300482.5_Missense_Mutation_p.V166I|TRPM2_ENST00000397932.2_Missense_Mutation_p.V166I|TRPM2_ENST00000300481.9_Missense_Mutation_p.V166I	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	166			V -> I (in dbSNP:rs45544142). {ECO:0000269|Ref.6}.		calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)			breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						GGGGCTGGACGTCCCCAATCT	0.612													G|||	148	0.0295527	0.1044	0.0101	5008	,	,		16186	0.003		0.0	False		,,,				2504	0.0				p.V166I		Atlas-SNP	.											.	TRPM2	196	.	0			c.G496A						PASS	.	G	ILE/VAL	454,3952	216.4+/-235.1	24,406,1773	61.0	57.0	58.0		496	2.3	0.1	21	dbSNP_127	58	6,8594	4.3+/-15.6	0,6,4294	yes	missense	TRPM2	NM_003307.3	29	24,412,6067	AA,AG,GG		0.0698,10.3041,3.5368	benign	166/1504	45786709	460,12546	2203	4300	6503	SO:0001583	missense	7226	exon4			CTGGACGTCCCCA	AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Nudix motif containing"""	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.496G>A	21.37:g.45786709G>A	ENSP00000381023:p.Val166Ile	51.0	0.0	0		65.0	33.0	0.507692	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	37	CCDS13710.1	60	0.027472527472527472	55	0.11178861788617886	3	0.008287292817679558	2	0.0034965034965034965	0	0.0	G	5.471	0.271913	0.10349	0.103041	6.98E-4	ENSG00000142185	ENST00000300482;ENST00000397928;ENST00000300481;ENST00000397932	T;T;T;T	0.55930	0.49;0.49;0.49;0.49	4.12	2.28	0.28536	.	0.459727	0.21621	U	0.071660	T	0.00754	0.0025	L	0.39397	1.21	0.09310	N	1	B;B	0.23377	0.084;0.039	B;B	0.17433	0.018;0.007	T	0.02821	-1.1106	10	0.22109	T	0.4	-28.3824	5.9165	0.19057	0.2468:0.1389:0.6143:0.0	rs45544142;rs61747092	166;166	E9PGK7;O94759	.;TRPM2_HUMAN	I	166	ENSP00000300482:V166I;ENSP00000381023:V166I;ENSP00000300481:V166I;ENSP00000381026:V166I	ENSP00000300481:V166I	V	+	1	0	TRPM2	44611137	0.000000	0.05858	0.110000	0.21437	0.394000	0.30568	0.164000	0.16542	0.314000	0.23086	0.297000	0.19635	GTC	G|0.962;A|0.038	0.038	strong		0.612	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307	
MBLAC1	255374	hgsc.bcm.edu	37	7	99725466	99725466	+	Missense_Mutation	SNP	G	G	T	rs78225840	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99725466G>T	ENST00000398075.2	+	2	847	c.448G>T	c.(448-450)Ggt>Tgt	p.G150C	RP11-506M12.1_ENST00000494221.1_RNA	NM_203397.1	NP_981942.1	A4D2B0	MBLC1_HUMAN	metallo-beta-lactamase domain containing 1	150							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|skin(1)	7						CCACGGGCTGGGTGAGGGGCA	0.746													G|||	125	0.0249601	0.09	0.0086	5008	,	,		12011	0.0		0.0	False		,,,				2504	0.0				p.G150C		Atlas-SNP	.											.	MBLAC1	13	.	0			c.G448T						PASS	.	G	CYS/GLY	289,3345		6,277,1534	9.0	11.0	10.0		448	-1.4	0.0	7	dbSNP_131	10	2,8064		0,2,4031	yes	missense	MBLAC1	NM_203397.1	159	6,279,5565	TT,TG,GG		0.0248,7.9527,2.4872	benign	150/267	99725466	291,11409	1817	4033	5850	SO:0001583	missense	255374	exon2			GGGCTGGGTGAGG	BC031288	CCDS43620.1	7q22	2014-02-12	2009-04-08		ENSG00000214309	ENSG00000214309			22180	protein-coding gene	gene with protein product							Standard	XM_005250250		Approved	MGC49416	uc003utp.3	A4D2B0	OTTHUMG00000154846	ENST00000398075.2:c.448G>T	7.37:g.99725466G>T	ENSP00000381150:p.Gly150Cys	32.0	0.0	0		49.0	27.0	0.55102	NM_203397	Q8N5X8	Missense_Mutation	SNP	ENST00000398075.2	37	CCDS43620.1	37	0.01694139194139194	31	0.06300813008130081	3	0.008287292817679558	3	0.005244755244755245	0	0.0	G	8.154	0.788075	0.16258	0.079527	2.48E-4	ENSG00000214309	ENST00000398075	T	0.30448	1.53	4.35	-1.38	0.09027	Beta-lactamase-like (2);	0.393038	0.20783	N	0.085752	T	0.00936	0.0031	L	0.46819	1.47	0.09310	N	1	B	0.10296	0.003	B	0.17979	0.02	T	0.11060	-1.0603	10	0.38643	T	0.18	.	1.2154	0.01913	0.4798:0.1516:0.204:0.1646	.	150	A4D2B0	MBLC1_HUMAN	C	150	ENSP00000381150:G150C	ENSP00000381150:G150C	G	+	1	0	MBLAC1	99563402	0.000000	0.05858	0.005000	0.12908	0.332000	0.28634	0.180000	0.16860	-0.294000	0.08973	0.561000	0.74099	GGT	G|0.980;T|0.020	0.020	strong		0.746	MBLAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337353.1	NM_203397	
TTLL11	158135	hgsc.bcm.edu	37	9	124633018	124633018	+	Silent	SNP	C	C	T	rs16911064	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:124633018C>T	ENST00000321582.5	-	7	1948	c.1761G>A	c.(1759-1761)caG>caA	p.Q587Q	TTLL11_ENST00000474723.1_5'UTR	NM_001139442.1	NP_001132914.1	Q8NHH1	TTL11_HUMAN	tubulin tyrosine ligase-like family, member 11	0					cellular protein modification process (GO:0006464)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	ligase activity (GO:0016874)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(3)|skin(1)	18						GTTTTTCAAGCTGCTGAGACC	0.488													C|||	88	0.0175719	0.0613	0.0058	5008	,	,		21797	0.0		0.003	False		,,,				2504	0.0				p.Q587Q		Atlas-SNP	.											.	TTLL11	67	.	0			c.G1761A						PASS	.	C		96,1288		2,92,598	142.0	125.0	130.0		1761	1.6	0.8	9	dbSNP_123	130	0,3182		0,0,1591	no	coding-synonymous	TTLL11	NM_001139442.1		2,92,2189	TT,TC,CC		0.0,6.9364,2.1025		587/801	124633018	96,4470	692	1591	2283	SO:0001819	synonymous_variant	158135	exon7			TTCAAGCTGCTGA	AF521886	CCDS6834.2, CCDS48012.1	9q34.11	2013-02-14	2005-07-28	2005-07-28	ENSG00000175764	ENSG00000175764		"""Tubulin tyrosine ligase-like family"""	18113	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 20"""	C9orf20		15890843	Standard	NM_001139442		Approved	bA244O19.1	uc011lyl.2	Q8NHH1	OTTHUMG00000020597	ENST00000321582.5:c.1761G>A	9.37:g.124633018C>T		159.0	0.0	0		132.0	67.0	0.507576	NM_001139442		Silent	SNP	ENST00000321582.5	37	CCDS48012.1																																																																																			C|0.983;T|0.017	0.017	strong		0.488	TTLL11-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_088486	
IL17RA	23765	hgsc.bcm.edu	37	22	17589983	17589983	+	Missense_Mutation	SNP	G	G	A	rs189025188		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:17589983G>A	ENST00000319363.6	+	13	2007	c.1874G>A	c.(1873-1875)cGc>cAc	p.R625H		NM_014339.5	NP_055154.3	Q96F46	I17RA_HUMAN	interleukin 17 receptor A	625					cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|fibroblast activation (GO:0072537)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)|positive regulation of interleukin-23 production (GO:0032747)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	interleukin-17 receptor activity (GO:0030368)			endometrium(2)|large_intestine(8)|lung(16)|ovary(1)|skin(2)|stomach(1)	30		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.241)		CCCCTGGTGCGCGAGCCTGGC	0.677													G|||	1	0.000199681	0.0008	0.0	5008	,	,		13392	0.0		0.0	False		,,,				2504	0.0				p.R625H		Atlas-SNP	.											.	IL17RA	62	.	0			c.G1874A						PASS	.	G	HIS/ARG	1,4309		0,1,2154	7.0	6.0	6.0		1874	-4.2	0.0	22		6	0,8498		0,0,4249	no	missense	IL17RA	NM_014339.5	29	0,1,6403	AA,AG,GG		0.0,0.0232,0.0078	benign	625/867	17589983	1,12807	2155	4249	6404	SO:0001583	missense	23765	exon13			TGGTGCGCGAGCC	U58917	CCDS13739.1	22q11.1	2014-09-17	2006-04-26	2006-04-26	ENSG00000177663	ENSG00000177663		"""Interleukins and interleukin receptors"", ""CD molecules"""	5985	protein-coding gene	gene with protein product		605461	"""interleukin 17 receptor"""	IL17R		9367539, 10591208	Standard	NM_014339		Approved	hIL-17R, IL-17RA, CDw217, CD217	uc002zly.4	Q96F46	OTTHUMG00000150026	ENST00000319363.6:c.1874G>A	22.37:g.17589983G>A	ENSP00000320936:p.Arg625His	10.0	0.0	0		16.0	12.0	0.75	NM_014339	O43844|Q20WK1	Missense_Mutation	SNP	ENST00000319363.6	37	CCDS13739.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	7.477	0.647869	0.14516	2.32E-4	0.0	ENSG00000177663	ENST00000425985;ENST00000319363	T	0.07800	3.16	5.1	-4.19	0.03835	.	0.588863	0.17907	N	0.157988	T	0.04363	0.0120	N	0.21583	0.68	0.09310	N	1	B;B	0.17038	0.01;0.02	B;B	0.10450	0.002;0.005	T	0.31475	-0.9942	10	0.37606	T	0.19	-15.8275	7.1335	0.25515	0.4871:0.0:0.4036:0.1092	.	573;625	D3YTB4;Q96F46	.;I17RA_HUMAN	H	573;625	ENSP00000320936:R625H	ENSP00000320936:R625H	R	+	2	0	IL17RA	15969983	0.000000	0.05858	0.016000	0.15963	0.002000	0.02628	-0.188000	0.09642	-0.559000	0.06110	-0.254000	0.11334	CGC	G|0.999;A|0.001	0.001	strong		0.677	IL17RA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315820.1	NM_014339	
ZNF594	84622	hgsc.bcm.edu	37	17	5085247	5085247	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5085247T>C	ENST00000399604.4	-	1	2445	c.2305A>G	c.(2305-2307)Acc>Gcc	p.T769A	ZNF594_ENST00000575779.1_Missense_Mutation_p.T769A			Q96JF6	ZN594_HUMAN	zinc finger protein 594	769					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						CCCTGGAAGGTCCTACTACAC	0.413																																					p.T769A		Atlas-SNP	.											.	ZNF594	89	.	0			c.A2305G						PASS	.						207.0	208.0	208.0					17																	5085247		1990	4182	6172	SO:0001583	missense	84622	exon2			GGAAGGTCCTACT	AB058774	CCDS42241.1	17p13	2013-01-08			ENSG00000180626	ENSG00000180626		"""Zinc fingers, C2H2-type"""	29392	protein-coding gene	gene with protein product						11347906	Standard	NM_032530		Approved	KIAA1871	uc010cla.1	Q96JF6	OTTHUMG00000132059	ENST00000399604.4:c.2305A>G	17.37:g.5085247T>C	ENSP00000382513:p.Thr769Ala	155.0	0.0	0		98.0	16.0	0.163265	NM_032530	Q6RFS0	Missense_Mutation	SNP	ENST00000399604.4	37	CCDS42241.1	.	.	.	.	.	.	.	.	.	.	T	0.005	-2.220840	0.00286	.	.	ENSG00000180626	ENST00000399604	T	0.14022	2.54	0.98	-0.251	0.13003	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04907	0.0132	N	0.12831	0.26	0.09310	N	1	B	0.18310	0.027	B	0.04013	0.001	T	0.42616	-0.9441	9	0.02654	T	1	.	4.0333	0.09719	0.0:0.2705:0.0:0.7295	.	769	Q96JF6	ZN594_HUMAN	A	769	ENSP00000382513:T769A	ENSP00000382513:T769A	T	-	1	0	ZNF594	5025971	0.000000	0.05858	0.002000	0.10522	0.239000	0.25481	-1.239000	0.02916	0.413000	0.25759	0.240000	0.17902	ACC	.	.	none		0.413	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737	
FAM46C	54855	hgsc.bcm.edu	37	1	118166195	118166195	+	Silent	SNP	C	C	T	rs10923359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:118166195C>T	ENST00000369448.3	+	2	952	c.705C>T	c.(703-705)aaC>aaT	p.N235N		NM_017709.3	NP_060179.2	Q5VWP2	FA46C_HUMAN	family with sequence similarity 46, member C	235										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)		CCACCAAGAACCCAGAAGAAA	0.527			"""Mis, F, O"""		MM					Multiple Myeloma(3;1.13e-06)			C|||	85	0.0169728	0.0613	0.0058	5008	,	,		18879	0.0		0.0	False		,,,				2504	0.0				p.N235N		Atlas-SNP	.		Rec	yes		1	1p12	54855	"""family with sequence similarity 46, member C"""		L	.	FAM46C	25	.	0			c.C705T						PASS	.	C		207,4199	127.4+/-164.3	6,195,2002	69.0	74.0	72.0		705	4.8	1.0	1	dbSNP_120	72	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	FAM46C	NM_017709.3		6,197,6300	TT,TC,CC		0.0233,4.6981,1.607		235/392	118166195	209,12797	2203	4300	6503	SO:0001819	synonymous_variant	54855	exon2			CAAGAACCCAGAA	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.705C>T	1.37:g.118166195C>T		135.0	0.0	0		128.0	56.0	0.4375	NM_017709	A3KMG2|Q8NE25|Q9NXK0	Silent	SNP	ENST00000369448.3	37	CCDS896.1																																																																																			C|0.979;T|0.021	0.021	strong		0.527	FAM46C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038424.1	NM_017709	
ERICH6B	220081	hgsc.bcm.edu	37	13	46170898	46170898	+	Silent	SNP	C	C	T	rs78950901	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:46170898C>T	ENST00000298738.2	-	3	407	c.243G>A	c.(241-243)aaG>aaA	p.K81K		NM_182542.2	NP_872348.2	Q5W0A0	ERI6B_HUMAN		81	Glu-rich.									breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)	5						actcttcctccttcAAGTATT	0.478													C|||	54	0.0107827	0.0386	0.0043	5008	,	,		22241	0.0		0.0	False		,,,				2504	0.0				p.K81K		Atlas-SNP	.											.	FAM194B	42	.	0			c.G243A						PASS	.	-		53,1331		0,53,639	243.0	195.0	210.0		243	-4.5	0.0	13	dbSNP_132	210	0,3182		0,0,1591	no	coding-synonymous	FAM194B	NM_182542.2		0,53,2230	TT,TC,CC		0.0,3.8295,1.1608		81/697	46170898	53,4513	692	1591	2283	SO:0001819	synonymous_variant	220081	exon3			TTCCTCCTTCAAG																												ENST00000298738.2:c.243G>A	13.37:g.46170898C>T		340.0	0.0	0		334.0	163.0	0.488024	NM_182542	Q96MB5	Silent	SNP	ENST00000298738.2	37	CCDS45045.1																																																																																			C|0.987;T|0.013	0.013	strong		0.478	FAM194B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044781.3		
PIF1	80119	hgsc.bcm.edu	37	15	65108939	65108939	+	Missense_Mutation	SNP	A	A	G	rs138069301		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:65108939A>G	ENST00000268043.4	-	12	1794	c.1700T>C	c.(1699-1701)aTt>aCt	p.I567T	PIF1_ENST00000333425.6_Missense_Mutation_p.I567T|PIF1_ENST00000559239.1_Missense_Mutation_p.I567T					PIF1 5'-to-3' DNA helicase											kidney(1)|lung(1)	2						GCCCAGAGAAATCTCCACACA	0.612																																					p.I567T		Atlas-SNP	.											.	PIF1	43	.	0			c.T1700C						PASS	.	A	THR/ILE	1,4399		0,1,2199	42.0	38.0	39.0		1700	5.7	1.0	15	dbSNP_134	39	0,8592		0,0,4296	no	missense	PIF1	NM_025049.2	89	0,1,6495	GG,GA,AA		0.0,0.0227,0.0077	possibly-damaging	567/642	65108939	1,12991	2200	4296	6496	SO:0001583	missense	80119	exon12			AGAGAAATCTCCA	AK026345	CCDS10195.2, CCDS66797.1	15q22.1	2013-05-13	2013-05-13	2006-11-24	ENSG00000140451	ENSG00000140451	3.6.4.12		26220	protein-coding gene	gene with protein product		610953	"""chromosome 15 open reading frame 20"", ""PIF1 5'-to-3' DNA helicase homolog (S. cerevisiae)"""	C15orf20		10926538, 16522649	Standard	NM_025049		Approved	FLJ22692	uc002ant.2	Q9H611	OTTHUMG00000132974	ENST00000268043.4:c.1700T>C	15.37:g.65108939A>G	ENSP00000268043:p.Ile567Thr	175.0	0.0	0		174.0	84.0	0.482759	NM_025049		Missense_Mutation	SNP	ENST00000268043.4	37	CCDS10195.2	.	.	.	.	.	.	.	.	.	.	A	19.18	3.777475	0.70107	2.27E-4	0.0	ENSG00000140451	ENST00000268043;ENST00000333425	T;T	0.48836	0.8;0.8	5.73	5.73	0.89815	.	0.045148	0.85682	D	0.000000	T	0.64000	0.2559	M	0.75085	2.285	0.80722	D	1	P	0.51653	0.947	P	0.56751	0.805	T	0.68573	-0.5373	10	0.87932	D	0	-13.5461	13.9753	0.64268	1.0:0.0:0.0:0.0	.	567	Q9H611	PIF1_HUMAN	T	567	ENSP00000268043:I567T;ENSP00000328174:I567T	ENSP00000268043:I567T	I	-	2	0	PIF1	62895992	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	9.272000	0.95707	2.186000	0.69663	0.533000	0.62120	ATT	A|1.000;G|0.000	0.000	weak		0.612	PIF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256533.1	NM_025049	
SLC35D3	340146	hgsc.bcm.edu	37	6	137245567	137245567	+	Missense_Mutation	SNP	C	C	A	rs116512494	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:137245567C>A	ENST00000331858.4	+	2	1149	c.984C>A	c.(982-984)gaC>gaA	p.D328E		NM_001008783.1	NP_001008783.1	Q5M8T2	S35D3_HUMAN	solute carrier family 35, member D3	328					carbohydrate transport (GO:0008643)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	13	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000136)|OV - Ovarian serous cystadenocarcinoma(155;0.00365)		TAAGTGGAGACCAGCTGCCGT	0.622													C|||	50	0.00998403	0.0371	0.0014	5008	,	,		17722	0.0		0.0	False		,,,				2504	0.0				p.D328E		Atlas-SNP	.											.	SLC35D3	33	.	0			c.C984A						PASS	.	C	GLU/ASP	110,4296	78.3+/-116.7	1,108,2094	28.0	30.0	29.0		984	0.3	1.0	6	dbSNP_132	29	0,8600		0,0,4300	yes	missense	SLC35D3	NM_001008783.1	45	1,108,6394	AA,AC,CC		0.0,2.4966,0.8458	benign	328/417	137245567	110,12896	2203	4300	6503	SO:0001583	missense	340146	exon2			TGGAGACCAGCTG		CCDS34544.1	6q23.2	2013-05-22			ENSG00000182747	ENSG00000182747		"""Solute carriers"""	15621	protein-coding gene	gene with protein product		612519		FRCL1			Standard	NM_001008783		Approved		uc003qhe.3	Q5M8T2	OTTHUMG00000015651	ENST00000331858.4:c.984C>A	6.37:g.137245567C>A	ENSP00000333591:p.Asp328Glu	88.0	0.0	0		105.0	59.0	0.561905	NM_001008783	B4DI58|Q5QNZ6|Q6NX71	Missense_Mutation	SNP	ENST00000331858.4	37	CCDS34544.1	34	0.015567765567765568	33	0.06707317073170732	1	0.0027624309392265192	0	0.0	0	0.0	C	12.85	2.061537	0.36373	0.024966	0.0	ENSG00000182747	ENST00000331858	T	0.54279	0.58	5.99	0.297	0.15762	.	0.219154	0.44902	D	0.000414	T	0.14141	0.0342	N	0.19112	0.55	0.35092	D	0.764393	B	0.06786	0.001	B	0.04013	0.001	T	0.03306	-1.1050	10	0.37606	T	0.19	-11.3298	5.2593	0.15563	0.134:0.399:0.0:0.467	.	328	Q5M8T2	S35D3_HUMAN	E	328	ENSP00000333591:D328E	ENSP00000333591:D328E	D	+	3	2	SLC35D3	137287260	0.998000	0.40836	0.996000	0.52242	0.699000	0.40488	0.450000	0.21762	0.106000	0.17784	0.609000	0.83330	GAC	C|0.988;A|0.012	0.012	strong		0.622	SLC35D3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042389.2	XM_294017	
EPOR	2057	hgsc.bcm.edu	37	19	11489049	11489049	+	Missense_Mutation	SNP	G	G	C	rs35423344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11489049G>C	ENST00000222139.6	-	8	1242	c.1138C>G	c.(1138-1140)Ccg>Gcg	p.P380A	EPOR_ENST00000592375.2_3'UTR	NM_000121.3	NP_000112.1	P19235	EPOR_HUMAN	erythropoietin receptor	380			P -> A (in dbSNP:rs35423344).		brain development (GO:0007420)|decidualization (GO:0046697)|erythropoietin-mediated signaling pathway (GO:0038162)|heart development (GO:0007507)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	erythropoietin receptor activity (GO:0004900)|identical protein binding (GO:0042802)			endometrium(1)|lung(2)|ovary(1)|urinary_tract(1)	5					Darbepoetin alfa(DB00012)|Epoetin alfa(DB00016)|Epoetin Zeta(DB08923)|Peginesatide(DB08894)	TCACTGGGCGGGTTCCGGGGC	0.617											OREG0025254	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	306	0.0611022	0.2231	0.0144	5008	,	,		17759	0.0		0.001	False		,,,				2504	0.0				p.P380A		Atlas-SNP	.											.	EPOR	26	.	0			c.C1138G						PASS	.	G	ALA/PRO	863,3543	335.5+/-303.9	79,705,1419	58.0	56.0	57.0		1138	4.5	0.2	19	dbSNP_126	57	11,8589	6.4+/-24.3	0,11,4289	yes	missense	EPOR	NM_000121.3	27	79,716,5708	CC,CG,GG		0.1279,19.5869,6.72	probably-damaging	380/509	11489049	874,12132	2203	4300	6503	SO:0001583	missense	2057	exon8			TGGGCGGGTTCCG	M34986	CCDS12260.1	19p13.3-p13.2	2013-02-11				ENSG00000187266		"""Fibronectin type III domain containing"""	3416	protein-coding gene	gene with protein product		133171					Standard	NM_000121		Approved		uc002mrj.2	P19235		ENST00000222139.6:c.1138C>G	19.37:g.11489049G>C	ENSP00000222139:p.Pro380Ala	32.0	0.0	0	672	34.0	19.0	0.558824	NM_000121	B2RCG4|Q15443|Q2M205	Missense_Mutation	SNP	ENST00000222139.6	37	CCDS12260.1	109	0.04990842490842491	105	0.21341463414634146	4	0.011049723756906077	0	0.0	0	0.0	G	10.08	1.251233	0.22880	0.195869	0.001279	ENSG00000187266	ENST00000222139	T	0.59364	0.27	4.51	4.51	0.55191	.	0.229422	0.36778	N	0.002409	T	0.00109	0.0003	M	0.67953	2.075	0.42246	P	0.008044000000000051	D	0.76494	0.999	P	0.60609	0.877	T	0.11591	-1.0581	9	0.14656	T	0.56	-28.7314	12.5811	0.56391	0.0:0.0:1.0:0.0	rs35423344;rs57359971	380	P19235	EPOR_HUMAN	A	380	ENSP00000222139:P380A	ENSP00000222139:P380A	P	-	1	0	EPOR	11350049	0.629000	0.27146	0.196000	0.23383	0.027000	0.11550	3.028000	0.49705	2.320000	0.78422	0.650000	0.86243	CCG	G|0.941;C|0.059	0.059	strong		0.617	EPOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458791.1		
PCDHA8	56140	hgsc.bcm.edu	37	5	140222534	140222534	+	Missense_Mutation	SNP	C	C	A	rs6889154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140222534C>A	ENST00000531613.1	+	1	1628	c.1628C>A	c.(1627-1629)cCg>cAg	p.P543Q	PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000378123.3_Missense_Mutation_p.P543Q|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	543	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(31)|ovary(2)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(6)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGGGCGTGCCGCCTCTGGGC	0.687													.|||	85	0.0169728	0.0635	0.0014	5008	,	,		15269	0.0		0.0	False		,,,				2504	0.0				p.P543Q		Atlas-SNP	.											PCDHA8_ENST00000531613,NS,carcinoma,-1,6	PCDHA8	366	6	0			c.C1628A						PASS	.	C	,,,,,,,GLN/PRO,,,GLN/PRO	287,4097		26,235,1931	52.0	61.0	58.0		,,,,,,,1628,,,1628	3.7	0.9	5	dbSNP_116	58	2,8524		0,2,4261	no	intron,intron,intron,intron,intron,intron,intron,missense,intron,intron,missense	PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031856.1	,,,,,,,76,,,76	26,237,6192	AA,AC,CC		0.0235,6.5465,2.2386	,,,,,,,,,,	,,,,,,,543/951,,,543/815	140222534	289,12621	2192	4263	6455	SO:0001583	missense	56140	exon1			GCGTGCCGCCTCT	AF152486	CCDS54919.1	5q31	2010-11-26				ENSG00000204962		"""Cadherins / Protocadherins : Clustered"""	8674	other	complex locus constituent	"""KIAA0345-like 6"""	606314				10380929	Standard	NM_018911		Approved			Q9Y5H6		ENST00000531613.1:c.1628C>A	5.37:g.140222534C>A	ENSP00000434655:p.Pro543Gln	55.0	0.0	0		57.0	29.0	0.508772	NM_031856	B9EGT7|O75281	Missense_Mutation	SNP	ENST00000531613.1	37	CCDS54919.1	31	0.014194139194139194	30	0.06097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	C	17.62	3.434270	0.62955	0.065465	2.35E-4	ENSG00000204962	ENST00000531613;ENST00000378123	T;T	0.55588	0.51;0.51	3.72	3.72	0.42706	Cadherin (4);Cadherin-like (1);	0.000000	0.36555	U	0.002521	T	0.22166	0.0534	M	0.87180	2.865	0.46376	D	0.999014	D;D	0.76494	0.999;0.999	D;D	0.80764	0.991;0.994	T	0.66396	-0.5934	10	0.87932	D	0	.	15.9202	0.79556	0.0:1.0:0.0:0.0	rs6889154	543;543	Q9Y5H6;Q9Y5H6-2	PCDA8_HUMAN;.	Q	543	ENSP00000434655:P543Q;ENSP00000367363:P543Q	ENSP00000367363:P543Q	P	+	2	0	PCDHA8	140202718	1.000000	0.71417	0.869000	0.34112	0.258000	0.26162	7.317000	0.79018	1.790000	0.52503	0.306000	0.20318	CCG	C|0.978;A|0.022	0.022	strong		0.687	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911	
CLUH	23277	hgsc.bcm.edu	37	17	2604698	2604698	+	Silent	SNP	G	G	A	rs115717445	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:2604698G>A	ENST00000570628.2	-	6	852	c.747C>T	c.(745-747)gtC>gtT	p.V249V	CLUH_ENST00000538975.1_Silent_p.V249V|CLUH_ENST00000435359.1_Silent_p.V249V			O75153	CLU_HUMAN	clustered mitochondria (cluA/CLU1) homolog	249					intracellular distribution of mitochondria (GO:0048312)	cytoplasm (GO:0005737)											CGGTGATGCTGACTTGCCGGT	0.632													G|||	21	0.00419329	0.0159	0.0	5008	,	,		14270	0.0		0.0	False		,,,				2504	0.0				p.V249V		Atlas-SNP	.											.	.	.	.	0			c.C747T						PASS	.	G		48,4218		0,48,2085	27.0	34.0	32.0		747	1.3	1.0	17	dbSNP_132	32	0,8468		0,0,4234	yes	coding-synonymous	KIAA0664	NM_015229.3		0,48,6319	AA,AG,GG		0.0,1.1252,0.3769		249/1310	2604698	48,12686	2133	4234	6367	SO:0001819	synonymous_variant	23277	exon6			GATGCTGACTTGC	AB014564	CCDS45572.1	17p13.3	2012-12-18	2012-11-30	2012-11-30	ENSG00000132361	ENSG00000132361			29094	protein-coding gene	gene with protein product			"""KIAA0664"""	KIAA0664			Standard	XM_005256567		Approved	CLU1	uc002fuy.1	O75153	OTTHUMG00000177575	ENST00000570628.2:c.747C>T	17.37:g.2604698G>A		95.0	0.0	0		87.0	53.0	0.609195	NM_015229	Q6AHY2|Q6P3X7|Q6ZUG8|Q8N4U7|Q9BTA3|Q9H979	Silent	SNP	ENST00000570628.2	37	CCDS45572.1																																																																																			G|0.993;A|0.007	0.007	strong		0.632	CLUH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437807.2	NM_015229	
MXRA8	54587	hgsc.bcm.edu	37	1	1290408	1290408	+	Silent	SNP	A	A	G	rs147996767	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1290408A>G	ENST00000309212.6	-	5	633	c.603T>C	c.(601-603)gcT>gcC	p.A201A	MXRA8_ENST00000477278.2_Silent_p.A192A|MXRA8_ENST00000342753.4_Silent_p.A100A|MXRA8_ENST00000445648.2_Silent_p.A201A	NM_001282582.1|NM_032348.2	NP_001269511.1|NP_115724.1	Q9BRK3	MXRA8_HUMAN	matrix-remodelling associated 8	201	Ig-like V-type 2.				establishment of glial blood-brain barrier (GO:0060857)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(3)	7	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;2.83e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.77e-21)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		CCACCTGTTGAGCCTCCTCCA	0.751													-|||	361	0.0720847	0.2579	0.0274	5008	,	,		8344	0.0		0.001	False		,,,				2504	0.0				p.A201A		Atlas-SNP	.											.	MXRA8	28	.	0			c.T603C						PASS	.			722,3238		65,592,1323	7.0	9.0	9.0		603	-0.7	1.0	1	dbSNP_134	9	6,7864		0,6,3929	no	coding-synonymous	MXRA8	NM_032348.2		65,598,5252	GG,GA,AA		0.0762,18.2323,6.1538		201/443	1290408	728,11102	1980	3935	5915	SO:0001819	synonymous_variant	54587	exon5			CTGTTGAGCCTCC	BC006213	CCDS24.1, CCDS59950.1, CCDS59951.1, CCDS59952.1	1p36.33	2013-01-11			ENSG00000162576	ENSG00000162576		"""Immunoglobulin superfamily / V-set domain containing"""	7542	protein-coding gene	gene with protein product	"""limitrin"""					14603461	Standard	XM_005244758		Approved	DKFZp586E2023	uc001aew.3	Q9BRK3	OTTHUMG00000002973	ENST00000309212.6:c.603T>C	1.37:g.1290408A>G		11.0	0.0	0		14.0	7.0	0.5	NM_032348	B3KTR6|B4DE34|Q5TA39|Q96KC3	Silent	SNP	ENST00000309212.6	37	CCDS24.1																																																																																			A|0.939;G|0.061	0.061	strong		0.751	MXRA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008282.2	NM_032348	
ZSCAN10	84891	hgsc.bcm.edu	37	16	3140601	3140601	+	Silent	SNP	C	C	T	rs140690870	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3140601C>T	ENST00000252463.2	-	5	756	c.669G>A	c.(667-669)gaG>gaA	p.E223E	ZSCAN10_ENST00000538082.2_Silent_p.E141E|ZSCAN10_ENST00000572548.1_3'UTR|ZSCAN10_ENST00000575108.1_5'UTR	NM_032805.1	NP_116194.1	Q96SZ4	ZSC10_HUMAN	zinc finger and SCAN domain containing 10	223					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(3)|endometrium(3)|kidney(1)|lung(8)|ovary(2)|prostate(1)|skin(4)|urinary_tract(1)	24						CCCCTTTGGGCTCTTCTTGTT	0.592													C|||	25	0.00499201	0.0182	0.0014	5008	,	,		15976	0.0		0.0	False		,,,				2504	0.0				p.E223E		Atlas-SNP	.											.	ZSCAN10	63	.	0			c.G669A						PASS	.	C		77,4279		1,75,2102	33.0	36.0	35.0		669	-6.0	0.0	16	dbSNP_134	35	0,8496		0,0,4248	no	coding-synonymous	ZSCAN10	NM_032805.1		1,75,6350	TT,TC,CC		0.0,1.7677,0.5991		223/726	3140601	77,12775	2178	4248	6426	SO:0001819	synonymous_variant	84891	exon5			TTTGGGCTCTTCT	AA206569	CCDS10493.1, CCDS61813.1, CCDS61814.1	16p13.3	2013-01-08	2007-02-20	2007-02-20		ENSG00000130182		"""-"", ""Zinc fingers, C2H2-type"""	12997	protein-coding gene	gene with protein product			"""zinc finger protein 206"""	ZNF206		9653642	Standard	NM_032805		Approved		uc002ctv.1	Q96SZ4		ENST00000252463.2:c.669G>A	16.37:g.3140601C>T		41.0	0.0	0		30.0	11.0	0.366667	NM_032805	B3KQD3|H0YFS6|Q1WWM2	Silent	SNP	ENST00000252463.2	37	CCDS10493.1																																																																																			C|0.991;T|0.009	0.009	strong		0.592	ZSCAN10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437124.2	NM_032805	
OR1L1	26737	hgsc.bcm.edu	37	9	125424164	125424164	+	Missense_Mutation	SNP	C	C	T	rs111803762	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:125424164C>T	ENST00000373686.1	+	1	320	c.320C>T	c.(319-321)aCg>aTg	p.T107M	OR1L1_ENST00000309623.1_Missense_Mutation_p.T57M			Q8NH94	OR1L1_HUMAN	olfactory receptor, family 1, subfamily L, member 1	107						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)	17						CGTCTCCAGACGCCCATGTAC	0.463													.|||	67	0.0133786	0.0477	0.0058	5008	,	,		21488	0.0		0.0	False		,,,				2504	0.0				p.T57M		Atlas-SNP	.											OR1L1,caecum,carcinoma,0,1	OR1L1	54	1	0			c.C170T						PASS	.	C	MET/THR	147,4259	102.1+/-140.7	3,141,2059	133.0	124.0	127.0		170	1.0	0.2	9	dbSNP_132	127	1,8599		0,1,4299	yes	missense	OR1L1	NM_001005236.3	81	3,142,6358	TT,TC,CC		0.0116,3.3364,1.1379	probably-damaging	57/311	125424164	148,12858	2203	4300	6503	SO:0001583	missense	26737	exon1			TCCAGACGCCCAT		CCDS35127.1, CCDS35127.2	9q33.2	2013-09-20			ENSG00000173679	ENSG00000173679		"""GPCR / Class A : Olfactory receptors"""	8213	protein-coding gene	gene with protein product				OR1L2			Standard	NM_001005236		Approved	OR9-C	uc022bmz.1	Q8NH94	OTTHUMG00000020618	ENST00000373686.1:c.320C>T	9.37:g.125424164C>T	ENSP00000362790:p.Thr107Met	155.0	0.0	0		226.0	151.0	0.668142	NM_001005236	Q5T7Z3|Q6IFN2	Missense_Mutation	SNP	ENST00000373686.1	37		27	0.012362637362637362	26	0.052845528455284556	1	0.0027624309392265192	0	0.0	0	0.0	C	14.01	2.408566	0.42715	0.033364	1.16E-4	ENSG00000173679	ENST00000373686;ENST00000309623	T;T	0.00481	7.11;7.11	3.11	1.01	0.19927	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00178	0.0005	L	0.58428	1.81	0.09310	N	0.999997	D	0.59357	0.985	P	0.55391	0.775	T	0.54077	-0.8347	9	0.72032	D	0.01	.	9.8389	0.40987	0.511:0.489:0.0:0.0	.	107	Q8NH94	OR1L1_HUMAN	M	107;57	ENSP00000362790:T107M;ENSP00000310773:T57M	ENSP00000310773:T57M	T	+	2	0	OR1L1	124463985	0.000000	0.05858	0.188000	0.23233	0.075000	0.17131	-1.376000	0.02561	0.095000	0.17434	0.313000	0.20887	ACG	C|0.987;T|0.013	0.013	strong		0.463	OR1L1-201	KNOWN	basic	protein_coding	protein_coding			
DNAH10	196385	hgsc.bcm.edu	37	12	124270467	124270467	+	Silent	SNP	C	C	T	rs116310078	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124270467C>T	ENST00000409039.3	+	9	1247	c.1222C>T	c.(1222-1224)Ctg>Ttg	p.L408L		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	408	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		AGTGGTCAACCTGCGGACTTT	0.438													C|||	28	0.00559105	0.0212	0.0	5008	,	,		19731	0.0		0.0	False		,,,				2504	0.0				p.L408L		Atlas-SNP	.											.	DNAH10	888	.	0			c.C1222T						PASS	.	C		76,4330	65.8+/-103.3	0,76,2127	86.0	77.0	80.0		1222	4.4	1.0	12	dbSNP_132	80	1,8599		0,1,4299	no	coding-synonymous	DNAH10	NM_207437.3		0,77,6426	TT,TC,CC		0.0116,1.7249,0.592		408/4472	124270467	77,12929	2203	4300	6503	SO:0001819	synonymous_variant	196385	exon9			GTCAACCTGCGGA	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.1222C>T	12.37:g.124270467C>T		27.0	0.0	0		60.0	30.0	0.5	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																			C|0.994;T|0.006	0.006	strong		0.438	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
PCDHA5	56143	hgsc.bcm.edu	37	5	140202821	140202821	+	Silent	SNP	C	C	G	rs80008076	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140202821C>G	ENST00000529859.1	+	1	1461	c.1461C>G	c.(1459-1461)gcC>gcG	p.A487A	PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000378126.3_Silent_p.A487A|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Silent_p.A487A	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	487	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.A487A(2)		NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(3)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGGAGAACGCCCTGGTGTCCT	0.667													.|||	72	0.014377	0.0537	0.0014	5008	,	,		18355	0.0		0.0	False		,,,				2504	0.0				p.A487A		Atlas-SNP	.											PCDHA5_ENST00000529859,NS,carcinoma,0,2	PCDHA5	361	2	2	Substitution - coding silent(2)	lung(2)	c.C1461G						PASS	.	G	,,,,,,	227,4179	797.7+/-415.4	9,209,1985	68.0	73.0	71.0		,,,,1461,,1461	2.0	1.0	5	dbSNP_131	71	1,8599	814.7+/-407.0	0,1,4299	no	intron,intron,intron,intron,coding-synonymous,intron,coding-synonymous	PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_031411.1,NM_031501.1	,,,,,,	9,210,6284	GG,GC,CC		0.0116,5.1521,1.753	,,,,,,	,,,,487/937,,487/817	140202821	228,12778	2203	4300	6503	SO:0001819	synonymous_variant	56143	exon1			GAACGCCCTGGTG	AF152483	CCDS54917.1	5q31	2010-11-26				ENSG00000204965		"""Cadherins / Protocadherins : Clustered"""	8671	other	complex locus constituent	"""ortholog of mouse CNR6"", ""KIAA0345-like 9"""	606311		CNRS6		10380929, 10662547	Standard	NM_018908		Approved	CNR6, CRNR6, CNRN6, PCDH-ALPHA5		Q9Y5H7		ENST00000529859.1:c.1461C>G	5.37:g.140202821C>G		258.0	0.0	0		276.0	145.0	0.525362	NM_018908	O75284|Q8N4R3	Silent	SNP	ENST00000529859.1	37	CCDS54917.1																																																																																			C|0.983;G|0.017	0.017	strong		0.667	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908	
ITGAX	3687	hgsc.bcm.edu	37	16	31382464	31382464	+	Silent	SNP	G	G	C	rs2230426	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31382464G>C	ENST00000268296.4	+	15	1891	c.1770G>C	c.(1768-1770)ggG>ggC	p.G590G	ITGAX_ENST00000562522.1_Silent_p.G590G	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	590					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						CACTGAGCGGGGGTCAAGACC	0.637													G|||	223	0.0445288	0.1619	0.0115	5008	,	,		17382	0.0		0.001	False		,,,				2504	0.0				p.G590G		Atlas-SNP	.											.	ITGAX	198	.	0			c.G1770C						PASS	.	G		552,3842	239.0+/-250.2	39,474,1684	60.0	66.0	64.0		1770	2.3	1.0	16	dbSNP_98	64	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	ITGAX	NM_000887.3		39,479,5979	CC,CG,GG		0.0581,12.5626,4.2866		590/1164	31382464	557,12437	2197	4300	6497	SO:0001819	synonymous_variant	3687	exon15			GAGCGGGGGTCAA	BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"""CD molecules"", ""Complement system"", ""Integrins"""	6152	protein-coding gene	gene with protein product		151510	"""integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"""	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.1770G>C	16.37:g.31382464G>C		68.0	0.0	0		77.0	36.0	0.467532	NM_000887	Q8IVA6	Silent	SNP	ENST00000268296.4	37	CCDS10711.1																																																																																			G|0.961;C|0.039	0.039	strong		0.637	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887	
COL12A1	1303	hgsc.bcm.edu	37	6	75899300	75899300	+	Missense_Mutation	SNP	T	T	G	rs75535959	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:75899300T>G	ENST00000322507.8	-	6	935	c.626A>C	c.(625-627)aAa>aCa	p.K209T	COL12A1_ENST00000483888.2_Missense_Mutation_p.K209T|COL12A1_ENST00000345356.6_Intron|COL12A1_ENST00000416123.2_Missense_Mutation_p.K209T	NM_004370.5	NP_004361.3	Q99715	COCA1_HUMAN	collagen, type XII, alpha 1	209	VWFA 1. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|skeletal system development (GO:0001501)	collagen type XII trimer (GO:0005595)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)			breast(7)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(5)|large_intestine(44)|liver(1)|lung(77)|ovary(7)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	169						ATATGGAATTTTTTTTATTGC	0.318													T|||	138	0.0275559	0.1006	0.0072	5008	,	,		18044	0.0		0.0	False		,,,				2504	0.0				p.K209T		Atlas-SNP	.											.	COL12A1	385	.	0			c.A626C						PASS	.	T	THR/LYS,	278,3348		12,254,1547	123.0	114.0	117.0		626,	0.4	1.0	6	dbSNP_131	117	2,8142		0,2,4070	yes	missense,intron	COL12A1	NM_004370.5,NM_080645.2	78,	12,256,5617	GG,GT,TT		0.0246,7.6669,2.3789	benign,	209/3064,	75899300	280,11490	1813	4072	5885	SO:0001583	missense	1303	exon6			GGAATTTTTTTTA	U73779	CCDS43481.1, CCDS43482.1	6q12-q13	2013-02-11	2003-07-24		ENSG00000111799	ENSG00000111799		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"", ""Fibronectin type III domain containing"""	2188	protein-coding gene	gene with protein product	"""collagen type XII proteoglycan"""	120320	"""collagen, type XII, alpha 1-like"""	COL12A1L		9143499	Standard	XM_006715334		Approved		uc003phs.3	Q99715	OTTHUMG00000015051	ENST00000322507.8:c.626A>C	6.37:g.75899300T>G	ENSP00000325146:p.Lys209Thr	74.0	0.0	0		91.0	50.0	0.549451	NM_004370	O43853|Q15955|Q5VYK1|Q5VYK2|Q71UR3|Q99716	Missense_Mutation	SNP	ENST00000322507.8	37	CCDS43482.1	53	0.024267399267399268	50	0.1016260162601626	3	0.008287292817679558	0	0.0	0	0.0	T	7.405	0.633502	0.14322	0.076669	2.46E-4	ENSG00000111799	ENST00000322507;ENST00000432784;ENST00000416123;ENST00000483888	T;T;T	0.78481	-1.18;-1.18;-1.18	5.65	0.435	0.16544	von Willebrand factor, type A (3);	0.422713	0.24285	N	0.039863	T	0.43433	0.1247	L	0.31926	0.97	0.25462	N	0.987905	B	0.14438	0.01	B	0.16289	0.015	T	0.38950	-0.9637	10	0.22706	T	0.39	.	10.6931	0.45884	0.0:0.4407:0.0:0.5593	.	209	Q99715	COCA1_HUMAN	T	209	ENSP00000325146:K209T;ENSP00000412864:K209T;ENSP00000421216:K209T	ENSP00000325146:K209T	K	-	2	0	COL12A1	75956020	0.989000	0.36119	0.995000	0.50966	0.916000	0.54674	0.615000	0.24329	-0.134000	0.11516	0.533000	0.62120	AAA	T|0.984;G|0.016	0.016	strong		0.318	COL12A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041249.3	NM_004370	
APC	324	hgsc.bcm.edu	37	5	112175240	112175240	+	Missense_Mutation	SNP	G	G	C	rs1801166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:112175240G>C	ENST00000457016.1	+	16	4329	c.3949G>C	c.(3949-3951)Gaa>Caa	p.E1317Q	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Missense_Mutation_p.E1317Q|APC_ENST00000508376.2_Missense_Mutation_p.E1317Q			P25054	APC_HUMAN	adenomatous polyposis coli	1317	Responsible for down-regulation through a process mediated by direct ubiquitination.|Ser-rich.		E -> Q (may contribute to colorectal tumor development; dbSNP:rs1801166). {ECO:0000269|PubMed:9724771}.		anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.E1317Q(5)|p.E1317*(3)|p.E1317fs*4(3)|p.?(1)|p.K1192fs*3(1)|p.A1316fs*9(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TAGGTCAGCTGAAGATCCTGT	0.438		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)			G|||	15	0.00299521	0.003	0.0029	5008	,	,		21730	0.0		0.006	False		,,,				2504	0.0031				p.E1317Q	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	APC,bladder,carcinoma,0,14	APC	4158	14	14	Substitution - Missense(5)|Deletion - Frameshift(5)|Substitution - Nonsense(3)|Unknown(1)	large_intestine(9)|stomach(1)|soft_tissue(1)|urinary_tract(1)|lung(1)|skin(1)	c.G3949C	GRCh37	CM980089	APC	M	rs1801166	PASS	.	G	GLN/GLU,GLN/GLU,GLN/GLU	28,4376	33.5+/-64.1	0,28,2174	60.0	61.0	61.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3949,3949,3895	5.2	0.7	5	dbSNP_89	61	80,8520	46.3+/-105.2	1,78,4221	yes	missense,missense,missense	APC	NM_000038.5,NM_001127510.2,NM_001127511.2	29,29,29	1,106,6395	CC,CG,GG		0.9302,0.6358,0.8305	benign,benign,benign	1317/2844,1317/2844,1299/2826	112175240	108,12896	2202	4300	6502	SO:0001583	missense	324	exon17	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	TCAGCTGAAGATC	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.3949G>C	5.37:g.112175240G>C	ENSP00000413133:p.Glu1317Gln	171.0	0.0	0		162.0	54.0	0.333333	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	8	0.003663003663003663	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	9.512	1.105897	0.20632	0.006358	0.009302	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.90324	-2.65;-2.65;-2.65	6.03	5.15	0.70609	.	0.502603	0.24048	N	0.042028	T	0.80325	0.4602	N	0.24115	0.695	0.37326	A	0.90977	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.003	T	0.79045	-0.1964	8	.	.	.	-16.8737	17.2207	0.86956	0.0:0.1257:0.8742:0.0	rs1801166;rs52811293	1319;1317	Q4LE70;P25054	.;APC_HUMAN	Q	1317	ENSP00000413133:E1317Q;ENSP00000257430:E1317Q;ENSP00000427089:E1317Q	.	E	+	1	0	APC	112203139	1.000000	0.71417	0.685000	0.30070	0.277000	0.26821	6.359000	0.73060	1.533000	0.49186	0.655000	0.94253	GAA	G|0.992;C|0.008	0.008	strong		0.438	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
KRTAP16-1	100505753	hgsc.bcm.edu	37	17	39464934	39464934	+	Missense_Mutation	SNP	G	G	A	rs150797223	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39464934G>A	ENST00000391352.1	-	1	571	c.572C>T	c.(571-573)cCt>cTt	p.P191L		NM_001146182.1	NP_001139654.1	A8MUX0	KR161_HUMAN	keratin associated protein 16-1	191	11 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				haematopoietic_and_lymphoid_tissue(1)	1						GCAGAGGACAGGCTGGCAGGA	0.587													G|||	32	0.00638978	0.0242	0.0	5008	,	,		23787	0.0		0.0	False		,,,				2504	0.0				p.P191L		Atlas-SNP	.											.	KRTAP16-1	12	.	0			c.C572T						PASS	.																																			SO:0001583	missense	100505753	exon1			AGGACAGGCTGGC	AP001708	CCDS56032.1	17q21.2	2012-07-04			ENSG00000212657	ENSG00000212657		"""Keratin associated proteins"""	18916	protein-coding gene	gene with protein product							Standard	NM_001146182		Approved	KAP16.1	uc021txi.1	A8MUX0	OTTHUMG00000133640	ENST00000391352.1:c.572C>T	17.37:g.39464934G>A	ENSP00000375147:p.Pro191Leu	162.0	0.0	0		190.0	86.0	0.452632	NM_001146182		Missense_Mutation	SNP	ENST00000391352.1	37	CCDS56032.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	G	13.44	2.236547	0.39498	.	.	ENSG00000212657	ENST00000391352	T	0.02158	4.42	4.22	4.22	0.49857	.	.	.	.	.	T	0.01870	0.0059	N	0.24115	0.695	0.45704	D	0.998617	.	.	.	.	.	.	T	0.57418	-0.7815	7	0.87932	D	0	.	14.8704	0.70453	0.0:0.0:1.0:0.0	.	.	.	.	L	191	ENSP00000375147:P191L	ENSP00000375147:P191L	P	-	2	0	KRTAP16-1	36718460	0.423000	0.25482	0.702000	0.30337	0.002000	0.02628	2.042000	0.41222	2.605000	0.88082	0.655000	0.94253	CCT	G|0.995;A|0.005	0.005	strong		0.587	KRTAP16-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257785.1	NM_001146182	
SNX5	27131	hgsc.bcm.edu	37	20	17923043	17923043	+	Silent	SNP	G	G	A	rs17349809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:17923043G>A	ENST00000377768.3	-	14	1485	c.1173C>T	c.(1171-1173)gtC>gtT	p.V391V	SNX5_ENST00000377759.4_Silent_p.V391V|SNX5_ENST00000483485.1_5'UTR	NM_152227.1	NP_689413.1	Q9Y5X3	SNX5_HUMAN	sorting nexin 5	391	BAR.				intracellular protein transport (GO:0006886)|pinocytosis (GO:0006907)	cytoplasmic vesicle (GO:0031410)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|extrinsic component of endosome membrane (GO:0031313)|macropinocytic cup (GO:0070685)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	11						GCAAAAGGGAGACATTGTTCT	0.408													G|||	148	0.0295527	0.1097	0.0014	5008	,	,		18450	0.0		0.001	False		,,,				2504	0.001				p.V391V		Atlas-SNP	.											.	SNX5	38	.	0			c.C1173T						PASS	.	G	,	452,3954	217.8+/-236.0	19,414,1770	111.0	101.0	105.0		1173,1173	1.0	1.0	20	dbSNP_123	105	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous	SNX5	NM_014426.2,NM_152227.1	,	19,418,6066	AA,AG,GG		0.0465,10.2587,3.5061	,	391/405,391/405	17923043	456,12550	2203	4300	6503	SO:0001819	synonymous_variant	27131	exon13			AAGGGAGACATTG	AF121855	CCDS13130.1	20p11	2008-05-22			ENSG00000089006	ENSG00000089006		"""Sorting nexins"""	14969	protein-coding gene	gene with protein product		605937				10600472, 17148574	Standard	NM_152227		Approved		uc002wqc.3	Q9Y5X3	OTTHUMG00000031953	ENST00000377768.3:c.1173C>T	20.37:g.17923043G>A		123.0	0.0	0		125.0	66.0	0.528	NM_014426	B7ZKN3|D3DW26|Q52LC4|Q7KZN0|Q9BWP0	Silent	SNP	ENST00000377768.3	37	CCDS13130.1																																																																																			G|1.000;|0.000	.	weak		0.408	SNX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078137.4		
DENND2A	27147	hgsc.bcm.edu	37	7	140227184	140227184	+	Silent	SNP	C	C	T	rs76760136	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140227184C>T	ENST00000275884.6	-	14	2856	c.2439G>A	c.(2437-2439)ccG>ccA	p.P813P	DENND2A_ENST00000537639.1_Silent_p.P813P|DENND2A_ENST00000496613.1_Silent_p.P813P			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	813	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(22)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49	Melanoma(164;0.00956)					GGAAGGGCGTCGGCGAGCACA	0.672													C|||	35	0.00698882	0.0257	0.0014	5008	,	,		17558	0.0		0.0	False		,,,				2504	0.0				p.P813P		Atlas-SNP	.											.	DENND2A	132	.	0			c.G2439A						PASS	.	C		59,4119		0,59,2030	12.0	18.0	16.0		2439	-2.2	0.4	7	dbSNP_132	16	0,8420		0,0,4210	no	coding-synonymous	DENND2A	NM_015689.3		0,59,6240	TT,TC,CC		0.0,1.4122,0.4683		813/1010	140227184	59,12539	2089	4210	6299	SO:0001819	synonymous_variant	27147	exon13			GGGCGTCGGCGAG	AB033103	CCDS43659.1	7q34	2012-10-03	2005-08-17	2005-08-17	ENSG00000146966	ENSG00000146966		"""DENN/MADD domain containing"""	22212	protein-coding gene	gene with protein product			"""KIAA1277"""	KIAA1277			Standard	NM_015689		Approved	FAM31D	uc010lnj.3	Q9ULE3	OTTHUMG00000157411	ENST00000275884.6:c.2439G>A	7.37:g.140227184C>T		243.0	0.0	0		209.0	113.0	0.54067	NM_015689	C9JUI3|Q1RMD5|Q86XY0	Silent	SNP	ENST00000275884.6	37	CCDS43659.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	C	10.80	1.452752	0.26074	0.014122	0.0	ENSG00000146966	ENST00000469373	T	0.36340	1.26	5.04	-2.21	0.06973	.	.	.	.	.	T	0.29458	0.0734	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43228	-0.9404	6	0.87932	D	0	-17.1724	10.9649	0.47406	0.0:0.2873:0.2046:0.5082	.	.	.	.	Q	141	ENSP00000420145:R141Q	ENSP00000417673:R794Q	R	-	2	0	DENND2A	139873653	0.155000	0.22806	0.413000	0.26509	0.012000	0.07955	-0.761000	0.04751	-0.836000	0.04229	-1.134000	0.01955	CGA	C|0.995;T|0.005	0.005	strong		0.672	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	NM_015689	
ATP2C1	27032	hgsc.bcm.edu	37	3	130698205	130698205	+	Silent	SNP	C	C	T	rs114319700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:130698205C>T	ENST00000510168.1	+	19	2233	c.1683C>T	c.(1681-1683)gcC>gcT	p.A561A	ATP2C1_ENST00000328560.8_Silent_p.A561A|ATP2C1_ENST00000507488.2_Silent_p.A545A|ATP2C1_ENST00000422190.2_Silent_p.A561A|ATP2C1_ENST00000504381.1_Silent_p.A506A|ATP2C1_ENST00000508532.1_Silent_p.A561A|ATP2C1_ENST00000393221.4_Silent_p.A595A|ATP2C1_ENST00000428331.2_Silent_p.A561A|ATP2C1_ENST00000505330.1_Silent_p.A545A|ATP2C1_ENST00000533801.2_Silent_p.A556A|ATP2C1_ENST00000513801.1_Silent_p.A545A|ATP2C1_ENST00000359644.3_Silent_p.A561A|ATP2C1_ENST00000504948.1_Silent_p.A545A			P98194	AT2C1_HUMAN	ATPase, Ca++ transporting, type 2C, member 1	561					actin cytoskeleton reorganization (GO:0031532)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cellular calcium ion homeostasis (GO:0006874)|cellular manganese ion homeostasis (GO:0030026)|epidermis development (GO:0008544)|Golgi calcium ion homeostasis (GO:0032468)|Golgi calcium ion transport (GO:0032472)|ion transmembrane transport (GO:0034220)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|manganese ion binding (GO:0030145)|manganese-transporting ATPase activity (GO:0015410)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|prostate(2)|skin(2)|urinary_tract(1)	39					Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	CACTCATTGCCTCAGGAGTAT	0.413									Hailey-Hailey disease				C|||	19	0.00379393	0.0129	0.0014	5008	,	,		17464	0.001		0.0	False		,,,				2504	0.0				p.A595A	Esophageal Squamous(99;456 1443 27647 34099 42636)	Atlas-SNP	.											.	ATP2C1	94	.	0			c.C1785T						PASS	.	C	,,,,,,,,,,	60,4346	57.4+/-93.9	0,60,2143	121.0	118.0	119.0		1683,1683,1683,1683,1785,1785,1668,1635,1635,1683,1683	4.8	1.0	3	dbSNP_132	119	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ATP2C1	NM_001001485.2,NM_001001486.1,NM_001001487.1,NM_001199179.1,NM_001199180.1,NM_001199181.1,NM_001199182.1,NM_001199183.1,NM_001199184.1,NM_001199185.1,NM_014382.3	,,,,,,,,,,	0,60,6443	TT,TC,CC		0.0,1.3618,0.4613	,,,,,,,,,,	561/889,561/950,561/940,561/920,595/974,595/954,556/945,545/924,545/904,561/889,561/920	130698205	60,12946	2203	4300	6503	SO:0001819	synonymous_variant	27032	exon18	Familial Cancer Database	HHD, Familial Benign Chronic Pemphigus, Benign Familial Pemphigus	CATTGCCTCAGGA	AF181120	CCDS33856.1, CCDS46912.1, CCDS46913.1, CCDS46914.1, CCDS56278.1, CCDS56279.1, CCDS56280.1, CCDS56281.1, CCDS75006.1	3q21.3	2012-10-22			ENSG00000017260	ENSG00000017260	3.6.3.8	"""ATPases / P-type"""	13211	protein-coding gene	gene with protein product	"""secretory pathway Ca2+/Mn2+ ATPase 1"", ""calcium-transporting ATPase type 2C member 1"""	604384	"""benign chronic pemphigus (Hailey-Hailey disease)"""	BCPM		10615129, 10767338	Standard	NM_001001485		Approved	KIAA1347, ATP2C1A, PMR1, SPCA1	uc011bli.2	P98194	OTTHUMG00000136802	ENST00000510168.1:c.1683C>T	3.37:g.130698205C>T		122.0	0.0	0		146.0	87.0	0.59589	NM_001199181	B2RAT7|B4DSW3|B7Z3X9|G3XAH8|G8JLN9|O76005|Q86V72|Q86V73|Q8N6V1|Q8NCJ7	Silent	SNP	ENST00000510168.1	37	CCDS46914.1	8	0.003663003663003663	7	0.014227642276422764	0	0.0	1	0.0017482517482517483	0	0.0	C	10.04	1.240288	0.22711	0.013618	0.0	ENSG00000017260	ENST00000504612	.	.	.	5.68	4.8	0.61643	.	.	.	.	.	T	0.49847	0.1581	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53549	-0.8423	4	.	.	.	.	7.3917	0.26913	0.1283:0.6805:0.1237:0.0676	.	.	.	.	L	515	.	.	P	+	2	0	ATP2C1	132180895	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.225000	0.32551	1.386000	0.46466	0.655000	0.94253	CCT	C|0.995;T|0.005	0.005	strong		0.413	ATP2C1-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356648.2	NM_001001486	
EPHA10	284656	hgsc.bcm.edu	37	1	38188736	38188736	+	Missense_Mutation	SNP	G	G	A	rs146568133	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:38188736G>A	ENST00000373048.4	-	10	1936	c.1937C>T	c.(1936-1938)aCg>aTg	p.T646M	EPHA10_ENST00000330210.7_Missense_Mutation_p.T141M|EPHA10_ENST00000427468.2_Missense_Mutation_p.T646M|EPHA10_ENST00000540011.1_Missense_Mutation_p.T141M|EPHA10_ENST00000446149.2_5'UTR	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	646	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)			NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CCTCTCCAGCGTGACGCTTTT	0.617													G|||	5	0.000998403	0.003	0.0	5008	,	,		19137	0.0		0.001	False		,,,				2504	0.0				p.T646M		Atlas-SNP	.											.	EPHA10	120	.	0			c.C1937T						PASS	.	G	MET/THR	16,4208		0,16,2096	53.0	59.0	57.0		1937	0.7	0.6	1	dbSNP_134	57	3,8429		0,3,4213	yes	missense	EPHA10	NM_001099439.1	81	0,19,6309	AA,AG,GG		0.0356,0.3788,0.1501	probably-damaging	646/1009	38188736	19,12637	2112	4216	6328	SO:0001583	missense	284656	exon10			TCCAGCGTGACGC	AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.1937C>T	1.37:g.38188736G>A	ENSP00000362139:p.Thr646Met	128.0	0.0	0		118.0	57.0	0.483051	NM_001099439	A4FU89|J3KPB5|Q6NW42	Missense_Mutation	SNP	ENST00000373048.4	37	CCDS41305.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	6.575	0.474435	0.12521	0.003788	3.56E-4	ENSG00000183317	ENST00000330210;ENST00000427468;ENST00000540011;ENST00000373048	D;D;T;D	0.83250	-1.7;-1.7;2.32;-1.7	3.96	0.672	0.17935	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.805996	0.10139	N	0.711048	T	0.66005	0.2746	L	0.41632	1.29	0.21579	N	0.99964	B	0.22851	0.076	B	0.17433	0.018	T	0.60321	-0.7286	10	0.66056	D	0.02	.	3.9999	0.09576	0.2121:0.0:0.4597:0.3283	.	646	Q5JZY3	EPHAA_HUMAN	M	141;646;141;646	ENSP00000330379:T141M;ENSP00000397746:T646M;ENSP00000441822:T141M;ENSP00000362139:T646M	ENSP00000330379:T141M	T	-	2	0	EPHA10	37961323	0.800000	0.28916	0.606000	0.28943	0.055000	0.15305	1.113000	0.31184	0.274000	0.22072	-0.657000	0.03884	ACG	G|0.999;A|0.001	0.001	strong		0.617	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641	
POM121L2	94026	hgsc.bcm.edu	37	6	27279877	27279877	+	Missense_Mutation	SNP	T	T	C	rs11965377	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:27279877T>C	ENST00000444565.1	-	1	72	c.73A>G	c.(73-75)Agg>Ggg	p.R25G	POM121L2_ENST00000377451.2_Missense_Mutation_p.R25G	NM_033482.3	NP_258443.2	Q96KW2	P12L2_HUMAN	POM121 transmembrane nucleoporin-like 2	25										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1)	7						TTCGTGGGCCTCTCGGGCAAG	0.637													T|||	101	0.0201677	0.053	0.0144	5008	,	,		14836	0.005		0.0129	False		,,,				2504	0.0031				p.R25G		Atlas-SNP	.											.	POM121L2	61	.	0			c.A73G						PASS	.	T	GLY/ARG	69,1315		1,67,624	16.0	23.0	21.0		73	-2.2	0.0	6	dbSNP_120	21	22,3160		0,22,1569	yes	missense	POM121L2	NM_033482.3	125	1,89,2193	CC,CT,TT		0.6914,4.9855,1.993	benign	25/1036	27279877	91,4475	692	1591	2283	SO:0001583	missense	94026	exon1			TGGGCCTCTCGGG	AL021808	CCDS59497.1	6p21.3	2012-03-13	2012-03-13		ENSG00000158553	ENSG00000158553			13973	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 2 (rat)"", ""POM121 membrane glycoprotein-like 2"""				Standard	NM_033482		Approved	POM121-L	uc011dku.1	Q96KW2	OTTHUMG00000014475	ENST00000444565.1:c.73A>G	6.37:g.27279877T>C	ENSP00000392726:p.Arg25Gly	93.0	0.0	0		95.0	39.0	0.410526	NM_033482	C9J1I7	Missense_Mutation	SNP	ENST00000444565.1	37	CCDS59497.1	58	0.026556776556776556	34	0.06910569105691057	8	0.022099447513812154	4	0.006993006993006993	12	0.0158311345646438	T	9.921	1.212259	0.22289	0.049855	0.006914	ENSG00000158553	ENST00000377451;ENST00000444565	T;T	0.16457	2.34;2.34	3.19	-2.24	0.06909	.	.	.	.	.	T	0.05135	0.0137	M	0.62723	1.935	0.09310	N	1	B	0.14012	0.009	B	0.13407	0.009	T	0.40021	-0.9585	9	0.39692	T	0.17	.	4.1196	0.10099	0.0:0.4172:0.2106:0.3722	rs11965377;rs11965377	25	C9J1I7	.	G	25	ENSP00000366671:R25G;ENSP00000392726:R25G	ENSP00000366671:R25G	R	-	1	2	POM121L2	27387856	0.004000	0.15560	0.000000	0.03702	0.001000	0.01503	0.165000	0.16564	-0.445000	0.07159	0.459000	0.35465	AGG	T|0.968;C|0.032	0.032	strong		0.637	POM121L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040143.2	NM_033482	
EVI5L	115704	hgsc.bcm.edu	37	19	7914022	7914022	+	Silent	SNP	C	C	T	rs554853	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7914022C>T	ENST00000270530.4	+	4	739	c.543C>T	c.(541-543)aaC>aaT	p.N181N	EVI5L_ENST00000538904.2_Silent_p.N181N	NM_145245.3	NP_660288.1	Q96CN4	EVI5L_HUMAN	ecotropic viral integration site 5-like	181	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				negative regulation of cilium assembly (GO:1902018)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)		Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			breast(1)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	12						TCCTCTTCAACGTCATGAAGG	0.647													C|||	83	0.0165735	0.0567	0.0101	5008	,	,		19132	0.0		0.001	False		,,,				2504	0.0				p.N181N		Atlas-SNP	.											.	EVI5L	43	.	0			c.C543T						PASS	.	C	,	232,4172	131.4+/-167.9	8,216,1978	34.0	30.0	32.0		543,543	-7.8	0.7	19	dbSNP_83	32	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous,coding-synonymous	EVI5L	NM_001159944.1,NM_145245.3	,	8,221,6273	TT,TC,CC		0.0581,5.2679,1.8225	,	181/806,181/795	7914022	237,12767	2202	4300	6502	SO:0001819	synonymous_variant	115704	exon3			CTTCAACGTCATG	BC014111	CCDS12188.1, CCDS54209.1	19p13	2013-07-09				ENSG00000142459			30464	protein-coding gene	gene with protein product						23669355	Standard	NM_001159944		Approved		uc010xjz.2	Q96CN4		ENST00000270530.4:c.543C>T	19.37:g.7914022C>T		65.0	0.0	0		73.0	34.0	0.465753	NM_001159944	B9A6I9	Silent	SNP	ENST00000270530.4	37	CCDS12188.1																																																																																			C|0.984;T|0.016	0.016	strong		0.647	EVI5L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000461347.1	NM_145245	
UBA1	7317	hgsc.bcm.edu	37	X	47070261	47070261	+	Silent	SNP	G	G	A	rs2230147	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:47070261G>A	ENST00000335972.6	+	19	2403	c.2220G>A	c.(2218-2220)ccG>ccA	p.P740P	UBA1_ENST00000377351.4_Silent_p.P740P|UBA1_ENST00000377269.3_Silent_p.P188P	NM_003334.3	NP_003325.2	P22314	UBA1_HUMAN	ubiquitin-like modifier activating enzyme 1	740					cell death (GO:0008219)|cellular response to DNA damage stimulus (GO:0006974)|modification-dependent protein catabolic process (GO:0019941)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						CAGGAGCGCCGTTCTGGTCTG	0.537													G|||	364	0.0964238	0.2648	0.0202	3775	,	,		14687	0.0		0.0	False		,,,				2504	0.0				p.P740P		Atlas-SNP	.											.	UBA1	89	.	0			c.G2220A						PASS	.	G	,	1067,2768		149,620,149,863,422	105.0	81.0	89.0		2220,2220	-9.5	0.0	X	dbSNP_98	89	14,6714		0,10,4,2418,1868	no	coding-synonymous,coding-synonymous	UBA1	NM_003334.3,NM_153280.2	,	149,630,153,3281,2290	AA,AG,A,GG,G		0.2081,27.8227,10.2338	,	740/1059,740/1059	47070261	1081,9482	2203	4300	6503	SO:0001819	synonymous_variant	7317	exon19			AGCGCCGTTCTGG	AF258566	CCDS14275.1	Xp11.23	2014-08-13	2007-11-30	2007-11-30	ENSG00000130985	ENSG00000130985	6.3.2.19	"""Ubiquitin-like modifier activating enzymes"""	12469	protein-coding gene	gene with protein product	"""UBA1, ubiquitin-activating enzyme E1 homolog (yeast)"", ""POC20 centriolar protein homolog (Chlamydomonas)"""	314370	"""ubiquitin-activating enzyme E1 (A1S9T and BN75 temperature sensitivity complementing)"", ""ubiquitin-activating enzyme E1"""	A1S9T, GXP1, UBE1		1845793	Standard	NM_153280		Approved	UBE1X, POC20, CFAP124	uc004dhj.4	P22314	OTTHUMG00000021436	ENST00000335972.6:c.2220G>A	X.37:g.47070261G>A		177.0	0.0	0		180.0	94.0	0.522222	NM_153280	Q5JRR8|Q96E13	Silent	SNP	ENST00000335972.6	37	CCDS14275.1																																																																																			0|0.004;A|0.126	0.126	strong		0.537	UBA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056389.1	NM_003334	
PCDHB4	56131	hgsc.bcm.edu	37	5	140503278	140503278	+	Silent	SNP	T	T	C	rs535776973	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140503278T>C	ENST00000194152.1	+	1	1698	c.1698T>C	c.(1696-1698)aaT>aaC	p.N566N	AC005754.8_ENST00000606030.1_lincRNA	NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	566					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	67			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGCTGCAGAATGGCTCCGCGC	0.701													C|||	29	0.00579073	0.0219	0.0	5008	,	,		15744	0.0		0.0	False		,,,				2504	0.0				p.N566N		Atlas-SNP	.											PCDHB4,NS,carcinoma,+1,1	PCDHB4	177	1	0			c.T1698C						scavenged	.						19.0	23.0	22.0					5																	140503278		2185	4269	6454	SO:0001819	synonymous_variant	56131	exon1			GCAGAATGGCTCC	AF152497	CCDS4246.1	5q31	2010-01-26			ENSG00000081818	ENSG00000081818		"""Cadherins / Protocadherins : Clustered"""	8689	other	protocadherin		606330				10380929	Standard	NM_018938		Approved	PCDH-BETA4	uc003lip.1	Q9Y5E5	OTTHUMG00000129617	ENST00000194152.1:c.1698T>C	5.37:g.140503278T>C		61.0	1.0	0.0163934		65.0	24.0	0.369231	NM_018938	Q4V761	Silent	SNP	ENST00000194152.1	37	CCDS4246.1																																																																																			.	.	none		0.701	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938	
FCGBP	8857	hgsc.bcm.edu	37	19	40364011	40364011	+	Silent	SNP	G	G	A	rs78835791	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40364011G>A	ENST00000221347.6	-	31	14638	c.14631C>T	c.(14629-14631)tcC>tcT	p.S4877S		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4877	VWFD 12. {ECO:0000255|PROSITE- ProRule:PRU00580}.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CATAGGAGCAGGAGCCATGCA	0.602													G|||	61	0.0121805	0.0439	0.0029	5008	,	,		20928	0.0		0.001	False		,,,				2504	0.0				p.S4877S		Atlas-SNP	.											.	FCGBP	416	.	0			c.C14631T						PASS	.	G		151,4255	103.8+/-142.4	1,149,2053	94.0	82.0	86.0		14631	4.0	1.0	19	dbSNP_131	86	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FCGBP	NM_003890.2		1,150,6352	AA,AG,GG		0.0116,3.4271,1.1687		4877/5406	40364011	152,12854	2203	4300	6503	SO:0001819	synonymous_variant	8857	exon31			GGAGCAGGAGCCA	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.14631C>T	19.37:g.40364011G>A		146.0	0.0	0		146.0	65.0	0.445205	NM_003890	O95784	Silent	SNP	ENST00000221347.6	37	CCDS12546.1																																																																																			G|0.988;A|0.012	0.012	strong		0.602	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
RGMA	56963	hgsc.bcm.edu	37	15	93588657	93588657	+	Silent	SNP	G	G	A	rs61733836	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:93588657G>A	ENST00000329082.7	-	4	1195	c.924C>T	c.(922-924)gaC>gaT	p.D308D	RGMA_ENST00000538818.1_Silent_p.D199D|RGMA_ENST00000557301.1_Silent_p.D316D|RGMA_ENST00000425933.2_Silent_p.D292D|RGMA_ENST00000542321.2_Silent_p.D292D|RGMA_ENST00000543599.1_Silent_p.D292D|RGMA_ENST00000557420.1_3'UTR|RGMA_ENST00000556658.1_Silent_p.D199D	NM_020211.2	NP_064596	Q96B86	RGMA_HUMAN	repulsive guidance molecule family member a	308					axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|neural tube closure (GO:0001843)|regulation of BMP signaling pathway (GO:0030510)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	9	Lung NSC(78;0.0542)|all_lung(78;0.0786)		BRCA - Breast invasive adenocarcinoma(143;0.0312)|OV - Ovarian serous cystadenocarcinoma(32;0.108)			GACCCTGGCTGTCCCAGTCCT	0.647													G|||	30	0.00599042	0.0212	0.0029	5008	,	,		18464	0.0		0.0	False		,,,				2504	0.0				p.D316D		Atlas-SNP	.											.	RGMA	49	.	0			c.C948T						PASS	.	G	,,,,,	93,4121		3,87,2017	27.0	34.0	32.0		948,876,876,876,876,924	4.8	1.0	15	dbSNP_129	32	0,8432		0,0,4216	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RGMA	NM_001166283.1,NM_001166286.1,NM_001166287.1,NM_001166288.1,NM_001166289.1,NM_020211.2	,,,,,	3,87,6233	AA,AG,GG		0.0,2.2069,0.7354	,,,,,	316/459,292/435,292/435,292/435,292/435,308/451	93588657	93,12553	2107	4216	6323	SO:0001819	synonymous_variant	56963	exon4			CTGGCTGTCCCAG	AL390083	CCDS45357.1, CCDS53973.1, CCDS53974.1	15q26.1	2013-11-06	2013-11-06			ENSG00000182175			30308	protein-coding gene	gene with protein product		607362	"""RGM domain family, member A"""			15975920	Standard	NM_020211		Approved	RGM, RGMa	uc010urc.2	Q96B86		ENST00000329082.7:c.924C>T	15.37:g.93588657G>A		77.0	0.0	0		84.0	38.0	0.452381	NM_001166283	B2RTW1|B7Z5S8|F5GXQ7|F5GZU6|G3V518|Q0JV97|Q8NC80|Q9H0E6|Q9NPM3	Silent	SNP	ENST00000329082.7	37	CCDS45357.1																																																																																			G|0.994;A|0.006	0.006	strong		0.647	RGMA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000415091.1	NM_020211	
SLC6A16	28968	hgsc.bcm.edu	37	19	49793620	49793620	+	Silent	SNP	C	C	T	rs34817563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49793620C>T	ENST00000335875.4	-	12	2212	c.1971G>A	c.(1969-1971)ccG>ccA	p.P657P	SLC6A16_ENST00000454748.3_3'UTR	NM_014037.2	NP_054756.2	Q9GZN6	S6A16_HUMAN	solute carrier family 6, member 16	657					neurotransmitter transport (GO:0006836)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)	neurotransmitter transporter activity (GO:0005326)|neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00099)|GBM - Glioblastoma multiforme(486;0.0336)		GCAGTGCCCACGGTGGGTATG	0.488													T|||	106	0.0211661	0.0711	0.0144	5008	,	,		20056	0.0		0.001	False		,,,				2504	0.001				p.P657P		Atlas-SNP	.											.	SLC6A16	62	.	0			c.G1971A						PASS	.	T		221,3697		6,209,1744	68.0	66.0	67.0		1971	-4.6	0.0	19	dbSNP_126	67	2,8306		0,2,4152	no	coding-synonymous	SLC6A16	NM_014037.2		6,211,5896	TT,TC,CC		0.0241,5.6406,1.824		657/737	49793620	223,12003	1959	4154	6113	SO:0001819	synonymous_variant	28968	exon12			TGCCCACGGTGGG	AF265578	CCDS42590.1	19q13.33	2013-05-22			ENSG00000063127	ENSG00000063127		"""Solute carriers"""	13622	protein-coding gene	gene with protein product	"""NTT5 protein"""	607972	"""solute carrier family 6 (neurotransmitter transporter), member 16"""			10471414, 11112352	Standard	XM_005258820		Approved	NTT5	uc002pmz.3	Q9GZN6		ENST00000335875.4:c.1971G>A	19.37:g.49793620C>T		134.0	0.0	0		133.0	68.0	0.511278	NM_014037	Q8IYV4|Q9Y5I9	Silent	SNP	ENST00000335875.4	37	CCDS42590.1																																																																																			C|0.989;T|0.011	0.011	strong		0.488	SLC6A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465503.2	NM_014037	
LYPLA1	10434	hgsc.bcm.edu	37	8	54967638	54967638	+	Missense_Mutation	SNP	A	A	C	rs76859468	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:54967638A>C	ENST00000316963.3	-	6	535	c.342T>G	c.(340-342)atT>atG	p.I114M	LYPLA1_ENST00000343231.6_Missense_Mutation_p.I98M|LYPLA1_ENST00000519926.1_5'UTR|LYPLA1_ENST00000522007.1_Intron	NM_001279360.1|NM_006330.2	NP_001266289.1|NP_006321.1	O75608	LYPA1_HUMAN	lysophospholipase I	114					fatty acid metabolic process (GO:0006631)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|nitric oxide metabolic process (GO:0046209)|protein depalmitoylation (GO:0002084)|regulation of nitric-oxide synthase activity (GO:0050999)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	lysophospholipase activity (GO:0004622)|palmitoyl-(protein) hydrolase activity (GO:0008474)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(3)	6		Lung NSC(129;0.109)|all_epithelial(80;0.11)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;8.48e-07)|Epithelial(17;9.29e-05)|all cancers(17;0.000689)			ACCCTCCCAAAATAATTCTGT	0.328													A|||	56	0.0111821	0.0401	0.0043	5008	,	,		16168	0.0		0.0	False		,,,				2504	0.0				p.I114M		Atlas-SNP	.											.	LYPLA1	15	.	0			c.T342G						PASS	.	A	MET/ILE	211,4195	127.4+/-164.3	6,199,1998	60.0	58.0	59.0		342	5.2	1.0	8	dbSNP_131	59	1,8591	1.2+/-3.3	0,1,4295	yes	missense	LYPLA1	NM_006330.2	10	6,200,6293	CC,CA,AA		0.0116,4.7889,1.631	benign	114/231	54967638	212,12786	2203	4296	6499	SO:0001583	missense	10434	exon6			TCCCAAAATAATT	AF081281	CCDS6157.1, CCDS64899.1, CCDS75738.1, CCDS75739.1	8q11.23-q12.1	2008-05-15			ENSG00000120992	ENSG00000120992	3.1.1.5		6737	protein-coding gene	gene with protein product		605599				10064899	Standard	NM_006330		Approved	LPL1	uc003xry.3	O75608	OTTHUMG00000164313	ENST00000316963.3:c.342T>G	8.37:g.54967638A>C	ENSP00000320043:p.Ile114Met	212.0	0.0	0		223.0	108.0	0.484305	NM_006330	O43202|Q9UQF9	Missense_Mutation	SNP	ENST00000316963.3	37	CCDS6157.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	A	12.13	1.846250	0.32606	0.047889	1.16E-4	ENSG00000120992	ENST00000316963;ENST00000523751;ENST00000343231;ENST00000521171;ENST00000518546;ENST00000521352;ENST00000519926;ENST00000521898	T;T;T;T;T	0.27720	1.65;1.65;1.65;1.65;1.65	5.23	5.23	0.72850	Phospholipase/carboxylesterase/thioesterase (1);	0.223460	0.46145	D	0.000313	T	0.05547	0.0146	L	0.45744	1.44	0.80722	D	1	B;B;B	0.33549	0.417;0.392;0.073	B;B;B	0.41666	0.363;0.259;0.105	T	0.05649	-1.0872	10	0.51188	T	0.08	-5.5049	5.7137	0.17948	0.7698:0.0:0.0798:0.1504	.	114;98;114	B4DP64;O75608-2;O75608	.;.;LYPA1_HUMAN	M	114;114;98;23;98;50;114;92	ENSP00000320043:I114M;ENSP00000344477:I98M;ENSP00000428729:I98M;ENSP00000428306:I50M;ENSP00000430791:I92M	ENSP00000320043:I114M	I	-	3	3	LYPLA1	55130191	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.404000	0.34623	2.103000	0.63969	0.528000	0.53228	ATT	A|0.983;C|0.017	0.017	strong		0.328	LYPLA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378238.1		
WWC3	55841	hgsc.bcm.edu	37	X	10106971	10106971	+	Missense_Mutation	SNP	C	C	T	rs377116582		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:10106971C>T	ENST00000380861.4	+	21	3470	c.3079C>T	c.(3079-3081)Cgg>Tgg	p.R1027W	WWC3_ENST00000454666.1_Missense_Mutation_p.R1027W	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	1027					negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						GGAGGCCGAGCGGCAGGTGGG	0.711																																					p.R1027W		Atlas-SNP	.											.	WWC3	142	.	0			c.C3079T						PASS	.	C	TRP/ARG	2,3724		0,1,1,1592,539	8.0	9.0	9.0		3079	-6.4	0.5	X		9	1,6500		0,1,0,2373,1753	no	missense	WWC3	NM_015691.3	101	0,2,1,3965,2292	TT,TC,T,CC,C		0.0154,0.0537,0.0293	probably-damaging	1027/1093	10106971	3,10224	2133	4127	6260	SO:0001583	missense	55841	exon21			GCCGAGCGGCAGG	AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"""WW, C2 and coiled-coil domain containing"""	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.3079C>T	X.37:g.10106971C>T	ENSP00000370242:p.Arg1027Trp	10.0	0.0	0		19.0	16.0	0.842105	NM_015691	A8KA96|Q659C1|Q9BTQ1	Missense_Mutation	SNP	ENST00000380861.4	37	CCDS14136.1	.	.	.	.	.	.	.	.	.	.	C	18.48	3.632188	0.67015	5.37E-4	1.54E-4	ENSG00000047644	ENST00000380861;ENST00000454666;ENST00000543412	T;T	0.44482	0.92;0.92	4.8	-6.37	0.01963	.	0.044151	0.85682	D	0.000000	T	0.56396	0.1982	M	0.67953	2.075	0.43032	D	0.994601	D	0.76494	0.999	D	0.74348	0.983	T	0.64748	-0.6334	9	.	.	.	-20.9116	18.8956	0.92421	0.2618:0.7382:0.0:0.0	.	1027	Q9ULE0	WWC3_HUMAN	W	1027;1027;522	ENSP00000370242:R1027W;ENSP00000399584:R1027W	.	R	+	1	2	WWC3	10066971	1.000000	0.71417	0.517000	0.27799	0.613000	0.37349	2.008000	0.40893	-1.390000	0.02087	-0.436000	0.05848	CGG	.	.	weak		0.711	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691	
TACSTD2	4070	hgsc.bcm.edu	37	1	59041940	59041940	+	Missense_Mutation	SNP	T	T	C	rs114373153	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:59041940T>C	ENST00000371225.2	-	1	1226	c.889A>G	c.(889-891)Atc>Gtc	p.I297V		NM_002353.2	NP_002344.2	P09758	TACD2_HUMAN	tumor-associated calcium signal transducer 2	297					cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of branching involved in ureteric bud morphogenesis (GO:0090191)|negative regulation of cell motility (GO:2000146)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of stress fiber assembly (GO:0051497)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of stem cell differentiation (GO:2000738)|regulation of epithelial cell proliferation (GO:0050678)|ureteric bud morphogenesis (GO:0060675)|visual perception (GO:0007601)	basal plasma membrane (GO:0009925)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|nucleus (GO:0005634)	receptor activity (GO:0004872)					all_cancers(7;6.54e-05)					CGGTTGGTGATCACCAGgacg	0.622													T|||	149	0.0297524	0.1082	0.0043	5008	,	,		14669	0.0		0.003	False		,,,				2504	0.0				p.I297V		Atlas-SNP	.											.	TACSTD2	6	.	0			c.A889G						PASS	.	T	VAL/ILE	398,4008	195.0+/-219.7	18,362,1823	50.0	46.0	47.0		889	1.0	0.8	1	dbSNP_132	47	6,8594	4.3+/-15.6	0,6,4294	yes	missense	TACSTD2	NM_002353.2	29	18,368,6117	CC,CT,TT		0.0698,9.0331,3.1063	benign	297/324	59041940	404,12602	2203	4300	6503	SO:0001583	missense	4070	exon1			TGGTGATCACCAG	X77753	CCDS609.1	1p32	2008-02-05			ENSG00000184292	ENSG00000184292			11530	protein-coding gene	gene with protein product		137290		M1S1		8382772, 11306819	Standard	NM_002353		Approved	TROP2, GA733-1, EGP-1	uc001cyz.4	P09758	OTTHUMG00000010067	ENST00000371225.2:c.889A>G	1.37:g.59041940T>C	ENSP00000360269:p.Ile297Val	103.0	0.0	0		105.0	61.0	0.580952	NM_002353	Q15658|Q6FG48|Q7Z7Q4|Q96QD2	Missense_Mutation	SNP	ENST00000371225.2	37	CCDS609.1	61	0.027930402930402932	58	0.11788617886178862	3	0.008287292817679558	0	0.0	0	0.0	T	3.973	-0.008046	0.07773	0.090331	6.98E-4	ENSG00000184292	ENST00000371225	T	0.76448	-1.02	4.59	0.995	0.19838	.	0.178739	0.48286	N	0.000189	T	0.00936	0.0031	N	0.12422	0.21	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.01071	-1.1461	10	0.11182	T	0.66	-9.0532	3.5124	0.07713	0.1616:0.2884:0.0:0.5501	.	297	P09758	TACD2_HUMAN	V	297	ENSP00000360269:I297V	ENSP00000360269:I297V	I	-	1	0	TACSTD2	58814528	0.005000	0.15991	0.797000	0.32132	0.803000	0.45373	-0.133000	0.10451	0.004000	0.14682	0.533000	0.62120	ATC	T|0.965;C|0.035	0.035	strong		0.622	TACSTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027818.1	NM_002353	
ASXL1	171023	hgsc.bcm.edu	37	20	31022480	31022480	+	Silent	SNP	C	C	T	rs79865730	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31022480C>T	ENST00000375687.4	+	13	2389	c.1965C>T	c.(1963-1965)acC>acT	p.T655T	ASXL1_ENST00000306058.5_Silent_p.T650T	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	655	Gly-rich.|Interaction with NCOA1. {ECO:0000250}.				bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.T639_G659>PPWD(1)|p.A640_S664>PCSGG(1)|p.T655fs*8(1)		NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						GCGGGGCCACCGATGAGGGAG	0.701			"""F, N, Mis"""		"""MDS, CMML"""								C|||	39	0.00778754	0.025	0.0043	5008	,	,		12008	0.0		0.003	False		,,,				2504	0.0				p.T655T		Atlas-SNP	.		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	.	ASXL1	1114	.	3	Complex - deletion inframe(2)|Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(3)	c.C1965T						PASS	.	C		53,4213		1,51,2081	8.0	9.0	9.0		1965	1.2	1.0	20	dbSNP_131	9	2,8376		0,2,4187	no	coding-synonymous	ASXL1	NM_015338.5		1,53,6268	TT,TC,CC		0.0239,1.2424,0.435		655/1542	31022480	55,12589	2133	4189	6322	SO:0001819	synonymous_variant	171023	exon12			GGCCACCGATGAG	AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"""additional sex combs like 1 (Drosophila)"""			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.1965C>T	20.37:g.31022480C>T		29.0	0.0	0		54.0	33.0	0.611111	NM_015338	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Silent	SNP	ENST00000375687.4	37	CCDS13201.1																																																																																			C|0.993;T|0.007	0.007	strong		0.701	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338	
GANC	2595	hgsc.bcm.edu	37	15	42585099	42585099	+	Missense_Mutation	SNP	A	A	G	rs16973015	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42585099A>G	ENST00000318010.8	+	5	736	c.496A>G	c.(496-498)Att>Gtt	p.I166V	GANC_ENST00000566442.1_Missense_Mutation_p.I166V	NM_198141.2	NP_937784.2	Q8TET4	GANC_HUMAN	glucosidase, alpha; neutral C	166			I -> V (in dbSNP:rs16973015).		carbohydrate metabolic process (GO:0005975)		alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|maltose alpha-glucosidase activity (GO:0032450)			breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		all_cancers(109;3.08e-16)|all_epithelial(112;7.48e-15)|Lung NSC(122;3.08e-09)|all_lung(180;1.48e-08)|Melanoma(134;0.0574)|Colorectal(260;0.153)		GBM - Glioblastoma multiforme(94;1.06e-06)	Miglitol(DB00491)	GCATCTACAGATTCTTCACAA	0.363													A|||	64	0.0127796	0.0212	0.0058	5008	,	,		20822	0.0		0.008	False		,,,				2504	0.0245				p.I166V		Atlas-SNP	.											.	GANC	57	.	0			c.A496G						PASS	.	A	VAL/ILE	63,4343	59.9+/-96.7	0,63,2140	128.0	123.0	125.0		496	0.4	0.9	15	dbSNP_123	125	39,8559	26.8+/-75.7	0,39,4260	yes	missense	GANC	NM_198141.2	29	0,102,6400	GG,GA,AA		0.4536,1.4299,0.7844	benign	166/915	42585099	102,12902	2203	4299	6502	SO:0001583	missense	2595	exon5			CTACAGATTCTTC	AF545045	CCDS10084.1	15q15.2	2012-10-02			ENSG00000214013	ENSG00000214013	3.2.1.20		4139	protein-coding gene	gene with protein product		104180				6995030, 12370436	Standard	NM_198141		Approved		uc001zpi.3	Q8TET4	OTTHUMG00000130487	ENST00000318010.8:c.496A>G	15.37:g.42585099A>G	ENSP00000326227:p.Ile166Val	177.0	0.0	0		170.0	99.0	0.582353	NM_198141	Q52LQ4|Q8IWZ0|Q8IZM4|Q8IZM5	Missense_Mutation	SNP	ENST00000318010.8	37	CCDS10084.1	22	0.010073260073260074	13	0.026422764227642278	4	0.011049723756906077	0	0.0	5	0.006596306068601583	A	2.471	-0.321955	0.05386	0.014299	0.004536	ENSG00000214013	ENST00000318010	T	0.15487	2.42	5.27	0.387	0.16259	Glycoside hydrolase-type carbohydrate-binding (1);	1.002620	0.08037	N	0.994447	T	0.02342	0.0072	N	0.08118	0	0.19575	N	0.999961	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40553	-0.9557	10	0.25106	T	0.35	-0.2169	5.5278	0.16967	0.4019:0.2069:0.3911:0.0	rs16973015;rs52796001;rs16973015	166;166	Q8TET4;Q2M2A3	GANC_HUMAN;.	V	166	ENSP00000326227:I166V	ENSP00000326227:I166V	I	+	1	0	GANC	40372391	0.078000	0.21339	0.939000	0.37840	0.098000	0.18820	0.247000	0.18179	-0.089000	0.12484	0.528000	0.53228	ATT	A|0.989;G|0.011	0.011	strong		0.363	GANC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252887.2	NM_198141	
SSPO	23145	hgsc.bcm.edu	37	7	149486367	149486367	+	RNA	SNP	C	C	A	rs855692	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149486367C>A	ENST00000378016.2	+	0	4343							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			ACGGATGAGCCGAGCTATCCG	0.687													A|||	158	0.0315495	0.1029	0.0115	5008	,	,		16290	0.004		0.0	False		,,,				2504	0.0102				p.P1448Q		Atlas-SNP	.											.	.	.	.	0			c.C4343A						PASS	.	A		317,4079		13,291,1894	24.0	28.0	27.0		4347	0.9	0.5	7	dbSNP_86	27	5,8583		0,5,4289	yes	coding-notMod3	SSPO	NM_198455.2		13,296,6183	AA,AC,CC		0.0582,7.2111,2.48			149486367	322,12662	2198	4294	6492			23145	exon30			ATGAGCCGAGCTA	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149486367C>A		81.0	0.0	0		87.0	47.0	0.54023	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.968;A|0.032	0.032	strong		0.687	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
AFP	174	hgsc.bcm.edu	37	4	74316461	74316461	+	Silent	SNP	C	C	T	rs115622472	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:74316461C>T	ENST00000395792.2	+	11	1519	c.1419C>T	c.(1417-1419)ggC>ggT	p.G473G	AFP_ENST00000226359.2_Silent_p.G473G	NM_001134.1	NP_001125.1	P02771	FETA_HUMAN	alpha-fetoprotein	473	Albumin 3. {ECO:0000255|PROSITE- ProRule:PRU00769}.				ovulation from ovarian follicle (GO:0001542)|progesterone metabolic process (GO:0042448)|SMAD protein signal transduction (GO:0060395)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(3)|lung(13)|ovary(1)|skin(1)|urinary_tract(1)	22	Breast(15;0.00102)		Epithelial(6;2.42e-05)|all cancers(17;0.000268)|OV - Ovarian serous cystadenocarcinoma(6;0.000324)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TGGCCTGTGGCGAGGGAGCGG	0.522									Alpha-Fetoprotein, Hereditary Persistence of				C|||	22	0.00439297	0.0159	0.0014	5008	,	,		18710	0.0		0.0	False		,,,				2504	0.0				p.G473G		Atlas-SNP	.											.	AFP	60	.	0			c.C1419T						PASS	.	C		76,4330	67.6+/-105.2	0,76,2127	156.0	134.0	142.0		1419	-9.9	0.1	4	dbSNP_132	142	3,8597		0,3,4297	no	coding-synonymous	AFP	NM_001134.1		0,79,6424	TT,TC,CC		0.0349,1.7249,0.6074		473/610	74316461	79,12927	2203	4300	6503	SO:0001819	synonymous_variant	174	exon11	Familial Cancer Database	HPAFP	CTGTGGCGAGGGA	V01514	CCDS3556.1	4q13.3	2012-05-16			ENSG00000081051	ENSG00000081051			317	protein-coding gene	gene with protein product		104150		HPAFP			Standard	NM_001134		Approved	FETA	uc003hgz.1	P02771	OTTHUMG00000130011	ENST00000395792.2:c.1419C>T	4.37:g.74316461C>T		145.0	0.0	0		161.0	70.0	0.434783	NM_001134	B2RBU3	Silent	SNP	ENST00000395792.2	37	CCDS3556.1																																																																																			C|0.994;T|0.006	0.006	strong		0.522	AFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252284.3		
FAM83B	222584	hgsc.bcm.edu	37	6	54805074	54805074	+	Missense_Mutation	SNP	C	C	G	rs9475076	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:54805074C>G	ENST00000306858.7	+	5	1421	c.1305C>G	c.(1303-1305)agC>agG	p.S435R	RP3-523K23.2_ENST00000562834.1_RNA	NM_001010872.1	NP_001010872.1	Q5T0W9	FA83B_HUMAN	family with sequence similarity 83, member B	435			S -> R (in dbSNP:rs9475076).							autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(6)|lung(28)|ovary(6)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	71	Lung NSC(77;0.0178)|Renal(3;0.122)					GCTATGTAAGCCACCACAACA	0.448													C|||	288	0.057508	0.2088	0.0144	5008	,	,		18486	0.0		0.002	False		,,,				2504	0.0				p.S435R		Atlas-SNP	.											.	FAM83B	186	.	0			c.C1305G						PASS	.	C	ARG/SER	795,3611	321.0+/-296.9	67,661,1475	65.0	69.0	67.0		1305	0.8	0.0	6	dbSNP_119	67	16,8584	10.5+/-38.8	0,16,4284	yes	missense	FAM83B	NM_001010872.1	110	67,677,5759	GG,GC,CC		0.186,18.0436,6.2356	benign	435/1012	54805074	811,12195	2203	4300	6503	SO:0001583	missense	222584	exon5			TGTAAGCCACCAC	AK055204	CCDS34479.1	6p12.1	2014-03-13	2006-03-23	2006-03-23	ENSG00000168143	ENSG00000168143			21357	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 143"""	C6orf143		22886302	Standard	NM_001010872		Approved	FLJ30642	uc003pck.4	Q5T0W9	OTTHUMG00000014899	ENST00000306858.7:c.1305C>G	6.37:g.54805074C>G	ENSP00000304078:p.Ser435Arg	80.0	0.0	0		110.0	54.0	0.490909	NM_001010872	Q2M1P3|Q96DQ2	Missense_Mutation	SNP	ENST00000306858.7	37	CCDS34479.1	112	0.05128205128205128	105	0.21341463414634146	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	C	1.045	-0.677640	0.03378	0.180436	0.00186	ENSG00000168143	ENST00000306858	T	0.08546	3.08	5.56	0.802	0.18686	.	1.270360	0.05003	N	0.469411	T	0.02807	0.0084	L	0.47716	1.5	0.80722	P	0.0	P	0.34780	0.468	B	0.27500	0.08	T	0.43572	-0.9383	9	0.42905	T	0.14	-0.061	9.8787	0.41220	0.0:0.4374:0.0:0.5626	rs9475076;rs52793316;rs9475076	435	Q5T0W9	FA83B_HUMAN	R	435	ENSP00000304078:S435R	ENSP00000304078:S435R	S	+	3	2	FAM83B	54913033	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.071000	0.14594	-0.074000	0.12820	-0.137000	0.14449	AGC	C|0.945;G|0.055	0.055	strong		0.448	FAM83B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040994.1	XM_294139	
PTX4	390667	hgsc.bcm.edu	37	16	1536114	1536114	+	Silent	SNP	C	C	A	rs79788206	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1536114C>A	ENST00000447419.2	-	3	1288	c.1263G>T	c.(1261-1263)gtG>gtT	p.V421V	PTX4_ENST00000293922.1_Silent_p.V416V|PTX4_ENST00000440447.2_3'UTR			Q96A99	PTX4_HUMAN	pentraxin 4, long	421	Pentaxin.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						ACATGCTCCCCACGAAGGCCT	0.637													C|||	88	0.0175719	0.0635	0.0058	5008	,	,		17747	0.0		0.0	False		,,,				2504	0.0				p.V416V		Atlas-SNP	.											.	PTX4	46	.	0			c.G1248T						PASS	.	C		286,4112	139.6+/-175.2	5,276,1918	67.0	65.0	66.0		1248	4.2	1.0	16	dbSNP_131	66	0,8600		0,0,4300	no	coding-synonymous	PTX4	NM_001013658.1		5,276,6218	AA,AC,CC		0.0,6.503,2.2003		416/474	1536114	286,12712	2199	4300	6499	SO:0001819	synonymous_variant	390667	exon3			GCTCCCCACGAAG		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"""chromosome 16 open reading frame 38"""	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.1263G>T	16.37:g.1536114C>A		76.0	0.0	0		83.0	37.0	0.445783	NM_001013658		Silent	SNP	ENST00000447419.2	37																																																																																				C|0.976;A|0.024	0.024	strong		0.637	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
NLRC5	84166	hgsc.bcm.edu	37	16	57071167	57071167	+	Silent	SNP	G	G	A	rs137919442	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57071167G>A	ENST00000262510.6	+	15	2997	c.2772G>A	c.(2770-2772)gcG>gcA	p.A924A	NLRC5_ENST00000436936.1_Silent_p.A924A|NLRC5_ENST00000539144.1_Silent_p.A924A|NLRC5_ENST00000308149.7_Silent_p.A924A	NM_032206.4	NP_115582.4	Q86WI3	NLRC5_HUMAN	NLR family, CARD domain containing 5	924					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|positive regulation of MHC class I biosynthetic process (GO:0045345)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)|regulation of kinase activity (GO:0043549)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)			NS(2)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(21)|ovary(8)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	75		all_neural(199;0.225)				CCGTGAGTGCGTGCTGGACCC	0.622													G|||	14	0.00279553	0.0106	0.0	5008	,	,		18115	0.0		0.0	False		,,,				2504	0.0				p.A924A		Atlas-SNP	.											.	NLRC5	186	.	0			c.G2772A						PASS	.	G		20,4376	26.2+/-53.5	0,20,2178	119.0	103.0	108.0		2772	-6.2	0.0	16	dbSNP_134	108	0,8600		0,0,4300	no	coding-synonymous	NLRC5	NM_032206.3		0,20,6478	AA,AG,GG		0.0,0.455,0.1539		924/1867	57071167	20,12976	2198	4300	6498	SO:0001819	synonymous_variant	84166	exon14			GAGTGCGTGCTGG	AF389420	CCDS10773.1	16q13	2008-02-05			ENSG00000140853	ENSG00000140853		"""Nucleotide-binding domain and leucine rich repeat containing"""	29933	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 5"", ""NOD-like receptor C5"""	613537				12615073	Standard	NM_032206		Approved	NOD27, CLR16.1, FLJ21709	uc021tiu.1	Q86WI3	OTTHUMG00000133470	ENST00000262510.6:c.2772G>A	16.37:g.57071167G>A		62.0	0.0	0		67.0	23.0	0.343284	NM_032206	B5MEF1|C9JMD8|Q6P4A6|Q86VM7|Q8NF42|Q8TEE2|Q8TEJ1|Q969L7	Silent	SNP	ENST00000262510.6	37	CCDS10773.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	g	3.650	-0.071627	0.07228	0.00455	0.0	ENSG00000140853	ENST00000538805	.	.	.	3.5	-6.21	0.02065	.	.	.	.	.	T	0.19685	0.0473	.	.	.	0.19300	N	0.99997	.	.	.	.	.	.	T	0.25950	-1.0117	4	.	.	.	.	7.5874	0.28002	0.4148:0.309:0.2761:0.0	.	.	.	.	M	677	.	.	V	+	1	0	NLRC5	55628668	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.843000	0.00736	-1.778000	0.01282	-1.694000	0.00725	GTG	G|0.998;A|0.002	0.002	strong		0.622	NLRC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257346.1	NM_032206	
WDR93	56964	hgsc.bcm.edu	37	15	90281452	90281452	+	Missense_Mutation	SNP	G	G	A	rs35389334	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90281452G>A	ENST00000268130.7	+	16	2047	c.1946G>A	c.(1945-1947)cGt>cAt	p.R649H	WDR93_ENST00000560294.1_Missense_Mutation_p.R621H|WDR93_ENST00000444934.2_Missense_Mutation_p.R366H	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	649					electron transport chain (GO:0022900)		oxidoreductase activity, acting on NAD(P)H (GO:0016651)			NS(1)|breast(3)|endometrium(2)|kidney(4)|large_intestine(5)|liver(2)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	33	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			AGATGTGAGCGTTTCCTCCAG	0.473													G|||	102	0.0203674	0.0756	0.0029	5008	,	,		17358	0.0		0.0	False		,,,				2504	0.0				p.R649H		Atlas-SNP	.											WDR93,colon,carcinoma,+1,1	WDR93	63	1	0			c.G1946A						PASS	.	G	HIS/ARG	251,4149	143.8+/-178.8	7,237,1956	165.0	167.0	166.0		1946	-10.5	0.0	15	dbSNP_126	166	2,8596	2.2+/-6.3	0,2,4297	yes	missense	WDR93	NM_020212.1	29	7,239,6253	AA,AG,GG		0.0233,5.7045,1.9465	possibly-damaging	649/687	90281452	253,12745	2200	4299	6499	SO:0001583	missense	56964	exon16			GTGAGCGTTTCCT		CCDS32326.1, CCDS66862.1, CCDS73779.1	15q26.1	2012-11-02						"""WD repeat domain containing"""	26924	protein-coding gene	gene with protein product							Standard	NM_020212		Approved		uc002boj.3	Q6P2C0		ENST00000268130.7:c.1946G>A	15.37:g.90281452G>A	ENSP00000268130:p.Arg649His	105.0	0.0	0		130.0	72.0	0.553846	NM_020212	Q8N7Y8|Q9NP89	Missense_Mutation	SNP	ENST00000268130.7	37	CCDS32326.1	52	0.023809523809523808	50	0.1016260162601626	2	0.0055248618784530384	0	0.0	0	0.0	G	11.54	1.670012	0.29693	0.057045	2.33E-4	ENSG00000140527	ENST00000268130;ENST00000444934	T;T	0.43294	1.95;0.95	5.27	-10.5	0.00291	.	3.609450	0.00520	N	0.000193	T	0.00608	0.0020	N	0.22421	0.69	0.09310	N	1	P;P	0.50943	0.859;0.94	B;B	0.41571	0.276;0.36	T	0.38520	-0.9657	10	0.40728	T	0.16	3.3554	5.7049	0.17903	0.3798:0.0:0.2483:0.3718	rs35389334	621;649	Q6P2C0-2;Q6P2C0	.;WDR93_HUMAN	H	649;366	ENSP00000268130:R649H;ENSP00000403871:R366H	ENSP00000268130:R649H	R	+	2	0	WDR93	88082456	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.725000	0.00808	-2.790000	0.00356	-0.156000	0.13503	CGT	G|0.977;A|0.023	0.023	strong		0.473	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212	
IL4I1	259307	hgsc.bcm.edu	37	19	50393743	50393743	+	Silent	SNP	A	A	G	rs61740372	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50393743A>G	ENST00000391826.2	-	8	1030	c.888T>C	c.(886-888)gaT>gaC	p.D296D	IL4I1_ENST00000595948.1_Silent_p.D318D|IL4I1_ENST00000341114.3_Silent_p.D318D|MIR4750_ENST00000584564.1_RNA	NM_152899.1	NP_690863.1	Q96RQ9	OXLA_HUMAN	interleukin 4 induced 1	296						extracellular region (GO:0005576)|lysosome (GO:0005764)	L-amino-acid oxidase activity (GO:0001716)			endometrium(3)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00245)|OV - Ovarian serous cystadenocarcinoma(262;0.0169)	Flavin adenine dinucleotide(DB03147)	GCACGTGCACATCGTGCGGTC	0.692											OREG0025629	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	83	0.0165735	0.059	0.0072	5008	,	,		12580	0.0		0.0	False		,,,				2504	0.0				p.D318D		Atlas-SNP	.											.	IL4I1	50	.	0			c.T954C						PASS	.	A	,	242,4162	131.8+/-168.3	9,224,1969	28.0	27.0	27.0		888,954	-7.9	0.0	19	dbSNP_129	27	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	IL4I1	NM_152899.1,NM_172374.1	,	9,225,6268	GG,GA,AA		0.0116,5.495,1.8687	,	296/568,318/590	50393743	243,12761	2202	4300	6502	SO:0001819	synonymous_variant	259307	exon10			GTGCACATCGTGC	AF293462	CCDS12786.1, CCDS12787.1	19q13.3-q13.4	2014-06-26				ENSG00000104951			19094	protein-coding gene	gene with protein product		609742				12031486	Standard	NM_152899		Approved	FIG1	uc002pqt.1	Q96RQ9		ENST00000391826.2:c.888T>C	19.37:g.50393743A>G		63.0	0.0	0	969	76.0	40.0	0.526316	NM_172374	Q1WMJ3|Q4GZN1|Q4GZN2|Q6P2Q3|Q8TEM5|Q96RQ8	Silent	SNP	ENST00000391826.2	37	CCDS12787.1																																																																																			A|0.982;G|0.018	0.018	strong		0.692	IL4I1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466413.1		
DDX5	1655	hgsc.bcm.edu	37	17	62499163	62499163	+	Silent	SNP	C	C	T	rs56025355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:62499163C>T	ENST00000225792.5	-	8	1265	c.864G>A	c.(862-864)caG>caA	p.Q288Q	DDX5_ENST00000580026.1_5'Flank|MIR3064_ENST00000581130.1_RNA|DDX5_ENST00000450599.2_Silent_p.Q209Q|MIR5047_ENST00000579212.1_RNA|DDX5_ENST00000578804.1_Silent_p.Q288Q	NM_004396.3	NP_004387.1	P17844	DDX5_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 5	288	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				cell growth (GO:0016049)|circadian rhythm (GO:0007623)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of osteoblast differentiation (GO:0045667)|regulation of skeletal muscle cell differentiation (GO:2001014)|regulation of viral genome replication (GO:0045069)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|pre-mRNA binding (GO:0036002)|RNA helicase activity (GO:0003724)|transcription coactivator activity (GO:0003713)			breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	19	Breast(5;2.15e-14)		BRCA - Breast invasive adenocarcinoma(8;8.6e-12)			CTTCAGCAAGCTGTCTTACTT	0.398			T	ETV4	prostate								C|||	19	0.00379393	0.0015	0.0029	5008	,	,		20101	0.0		0.0149	False		,,,				2504	0.0				p.Q288Q	NSCLC(22;406 813 4871 19580 40307)	Atlas-SNP	.		Dom	yes		17	17q21	1655	DEAD (Asp-Glu-Ala-Asp) box polypeptide 5		E	.	DDX5	101	.	0			c.G864A						PASS	.	C		10,4396	16.8+/-37.8	0,10,2193	180.0	174.0	176.0		864	3.9	1.0	17	dbSNP_129	176	83,8517	48.9+/-108.6	0,83,4217	no	coding-synonymous	DDX5	NM_004396.3		0,93,6410	TT,TC,CC		0.9651,0.227,0.7151		288/615	62499163	93,12913	2203	4300	6503	SO:0001819	synonymous_variant	1655	exon8			AGCAAGCTGTCTT	AF015812	CCDS11659.1	17q21	2012-07-27	2012-02-23		ENSG00000108654	ENSG00000108654		"""DEAD-boxes"""	2746	protein-coding gene	gene with protein product		180630	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 5 (RNA helicase, 68kD)"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 5"""	HLR1, G17P1		22156369, 18698352	Standard	NM_004396		Approved	p68	uc002jek.2	P17844	OTTHUMG00000178936	ENST00000225792.5:c.864G>A	17.37:g.62499163C>T		153.0	0.0	0		169.0	68.0	0.402367	NM_004396	B4DLW8|B5BU21|D3DU32|E7ETL9|O75681|Q53Y61	Silent	SNP	ENST00000225792.5	37	CCDS11659.1																																																																																			C|0.993;T|0.007	0.007	strong		0.398	DDX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444030.1	NM_004396	
TBCD	6904	hgsc.bcm.edu	37	17	80887123	80887123	+	Missense_Mutation	SNP	G	G	T	rs8072406	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:80887123G>T	ENST00000355528.4	+	31	2958	c.2828G>T	c.(2827-2829)gGa>gTa	p.G943V	TBCD_ENST00000539345.2_Missense_Mutation_p.G943V	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	943			G -> V (in dbSNP:rs8072406).		'de novo' posttranslational protein folding (GO:0051084)|adherens junction assembly (GO:0034333)|cellular protein metabolic process (GO:0044267)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of GTPase activity (GO:0043547)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|tight junction (GO:0005923)	beta-tubulin binding (GO:0048487)|chaperone binding (GO:0051087)|GTPase activator activity (GO:0005096)					Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			CCCCACCGAGGAGAACTGGAA	0.637													G|||	119	0.023762	0.084	0.0101	5008	,	,		19308	0.0		0.001	False		,,,				2504	0.0				p.G943V		Atlas-SNP	.											.	TBCD	94	.	0			c.G2828T						PASS	.	G	VAL/GLY	333,3793		15,303,1745	62.0	66.0	65.0		2828	-10.3	0.0	17	dbSNP_116	65	2,8418		0,2,4208	yes	missense	TBCD	NM_005993.4	109	15,305,5953	TT,TG,GG		0.0238,8.0708,2.6702	possibly-damaging	943/1193	80887123	335,12211	2063	4210	6273	SO:0001583	missense	6904	exon31			ACCGAGGAGAACT	BC003094	CCDS45818.1	17q25.3	2006-11-21	2006-11-21			ENSG00000141556			11581	protein-coding gene	gene with protein product		604649	"""tubulin-specific chaperone d"""				Standard	NM_005993		Approved		uc002kfz.3	Q9BTW9		ENST00000355528.4:c.2828G>T	17.37:g.80887123G>T	ENSP00000347719:p.Gly943Val	119.0	0.0	0		111.0	53.0	0.477477	NM_005993	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Missense_Mutation	SNP	ENST00000355528.4	37	CCDS45818.1	45	0.020604395604395604	42	0.08536585365853659	3	0.008287292817679558	0	0.0	0	0.0	G	8.712	0.912371	0.17907	0.080708	2.38E-4	ENSG00000141556	ENST00000355528;ENST00000334614	T	0.29917	1.55	5.13	-10.3	0.00346	Armadillo-type fold (1);Tubulin-specific chaperone D, C-terminal (1);	1.128570	0.06621	N	0.757363	T	0.00666	0.0022	L	0.40543	1.245	0.09310	N	1	B;B;B	0.32010	0.351;0.238;0.351	B;B;B	0.31101	0.076;0.124;0.108	T	0.02933	-1.1092	9	.	.	.	.	11.0645	0.47968	0.6996:0.1867:0.1137:0.0	rs8072406;rs8072406	694;943;943	F8WC00;Q9BTW9;Q9BTW9-4	.;TBCD_HUMAN;.	V	943;694	ENSP00000347719:G943V	.	G	+	2	0	TBCD	78480412	0.019000	0.18553	0.000000	0.03702	0.011000	0.07611	0.131000	0.15870	-2.089000	0.00860	-0.165000	0.13383	GGA	G|0.974;T|0.026	0.026	strong		0.637	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993	
PCDHA5	56143	hgsc.bcm.edu	37	5	140202132	140202132	+	Missense_Mutation	SNP	A	A	G	rs61730633	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140202132A>G	ENST00000529859.1	+	1	772	c.772A>G	c.(772-774)Aca>Gca	p.T258A	PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000378126.3_Missense_Mutation_p.T258A|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Missense_Mutation_p.T258A	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	258	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(3)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACCAAGTGGGACATTAGTTAT	0.353													.|||	28	0.00559105	0.0212	0.0	5008	,	,		19252	0.0		0.0	False		,,,				2504	0.0				p.T258A		Atlas-SNP	.											.	PCDHA5	361	.	0			c.A772G						PASS	.	A	,,,,ALA/THR,,ALA/THR	104,4302	76.8+/-115.0	0,104,2099	62.0	65.0	64.0		,,,,772,,772	4.1	0.1	5	dbSNP_129	64	0,8598		0,0,4299	yes	intron,intron,intron,intron,missense,intron,missense	PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_031411.1,NM_031501.1	,,,,58,,58	0,104,6398	GG,GA,AA		0.0,2.3604,0.7998	,,,,,,	,,,,258/937,,258/817	140202132	104,12900	2203	4299	6502	SO:0001583	missense	56143	exon1			AGTGGGACATTAG	AF152483	CCDS54917.1	5q31	2010-11-26				ENSG00000204965		"""Cadherins / Protocadherins : Clustered"""	8671	other	complex locus constituent	"""ortholog of mouse CNR6"", ""KIAA0345-like 9"""	606311		CNRS6		10380929, 10662547	Standard	NM_018908		Approved	CNR6, CRNR6, CNRN6, PCDH-ALPHA5		Q9Y5H7		ENST00000529859.1:c.772A>G	5.37:g.140202132A>G	ENSP00000436557:p.Thr258Ala	130.0	0.0	0		126.0	52.0	0.412698	NM_018908	O75284|Q8N4R3	Missense_Mutation	SNP	ENST00000529859.1	37	CCDS54917.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	A	15.50	2.851517	0.51270	0.023604	0.0	ENSG00000204965	ENST00000529619;ENST00000529859;ENST00000378126	T;T;T	0.57107	0.42;0.42;0.42	4.11	4.11	0.48088	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.46983	0.1421	M	0.82517	2.595	0.29191	N	0.875842	P;P;P	0.49862	0.929;0.913;0.913	P;P;B	0.62382	0.901;0.596;0.444	T	0.58042	-0.7706	9	0.62326	D	0.03	.	8.9776	0.35946	0.9105:0.0:0.0895:0.0	rs61730633	258;258;258	Q9Y5H7;Q9Y5H7-3;Q9Y5H7-2	PCDA5_HUMAN;.;.	A	258	ENSP00000433416:T258A;ENSP00000436557:T258A;ENSP00000367366:T258A	ENSP00000367366:T258A	T	+	1	0	PCDHA5	140182316	0.275000	0.24201	0.125000	0.21846	0.947000	0.59692	2.543000	0.45752	1.624000	0.50355	0.533000	0.62120	ACA	A|0.993;G|0.007	0.007	strong		0.353	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908	
TNFRSF25	8718	hgsc.bcm.edu	37	1	6524649	6524649	+	Silent	SNP	T	T	C	rs35137293	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:6524649T>C	ENST00000356876.3	-	4	513	c.426A>G	c.(424-426)ctA>ctG	p.L142L	TNFRSF25_ENST00000348333.3_Silent_p.L97L|TNFRSF25_ENST00000461703.2_5'UTR|TNFRSF25_ENST00000377782.3_Silent_p.L142L|TNFRSF25_ENST00000351748.3_Intron|TNFRSF25_ENST00000351959.5_Silent_p.L142L	NM_003790.2|NM_148967.1	NP_003781.1|NP_683868.1	Q93038	TNR25_HUMAN	tumor necrosis factor receptor superfamily, member 25	142					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell surface receptor signaling pathway (GO:0007166)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)|tumor necrosis factor-activated receptor activity (GO:0005031)			breast(1)|central_nervous_system(2)|endometrium(1)|lung(4)|prostate(1)|stomach(1)	10	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;1.7e-35)|all_epithelial(116;2.78e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|Colorectal(325;4.47e-05)|all_hematologic(16;0.00014)|Breast(487;0.000688)|Renal(390;0.0007)|Acute lymphoblastic leukemia(12;0.00157)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0448)		Epithelial(90;4.58e-35)|GBM - Glioblastoma multiforme(13;3.06e-27)|Colorectal(212;6.01e-08)|COAD - Colon adenocarcinoma(227;1.3e-05)|Kidney(185;4.88e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000871)|BRCA - Breast invasive adenocarcinoma(365;0.00105)|STAD - Stomach adenocarcinoma(132;0.00158)|READ - Rectum adenocarcinoma(331;0.0419)		CCCCGCAGTCTAGGCATGGTT	0.627													t|||	104	0.0207668	0.0734	0.0072	5008	,	,		16978	0.0		0.002	False		,,,				2504	0.0				p.L142L		Atlas-SNP	.											.	TNFRSF25	22	.	0			c.A426G						PASS	.	T	,,,,,	262,4144	147.6+/-182.1	5,252,1946	52.0	56.0	54.0		426,426,426,426,291,	-6.5	0.0	1	dbSNP_126	54	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron	TNFRSF25	NM_001039664.1,NM_003790.2,NM_148965.1,NM_148966.1,NM_148967.1,NM_148970.1	,,,,,	5,258,6240	CC,CT,TT		0.0698,5.9464,2.0606	,,,,,	142/182,142/418,142/427,142/381,97/373,	6524649	268,12738	2203	4300	6503	SO:0001819	synonymous_variant	8718	exon4			GCAGTCTAGGCAT	U72763	CCDS71.1, CCDS72.1, CCDS73.1, CCDS74.1, CCDS75.1	1p36.2	2008-02-05	2002-12-20	2002-12-20	ENSG00000215788	ENSG00000215788		"""Tumor necrosis factor receptor superfamily"""	11910	protein-coding gene	gene with protein product		603366	"""tumor necrosis factor receptor superfamily, member 12 (translocating chain-association membrane protein)"""	TNFRSF12		9052839, 8934525	Standard	NM_003790		Approved	DR3, TRAMP, WSL-1, LARD, WSL-LR, DDR3, TR3, APO-3	uc001anh.3	Q93038	OTTHUMG00000000831	ENST00000356876.3:c.426A>G	1.37:g.6524649T>C		131.0	0.0	0		110.0	50.0	0.454545	NM_148966	B1ALX2|B1ALX3|B7ZLL7|O00275|O00276|O00277|O00278|O00279|O00280|O14865|O14866|P78507|P78515|Q17RU4|Q92983|Q93036|Q93037|Q99722|Q99830|Q99831|Q9BY86|Q9UME0|Q9UME1|Q9UME5	Silent	SNP	ENST00000356876.3	37	CCDS71.1																																																																																			T|0.978;C|0.022	0.022	strong		0.627	TNFRSF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002259.1	NM_148965	
TNFRSF10C	8794	hgsc.bcm.edu	37	8	22960655	22960655	+	Silent	SNP	C	C	T	rs10107827|rs374790272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22960655C>T	ENST00000356864.3	+	1	553	c.21C>T	c.(19-21)acC>acT	p.T7T	TNFRSF10C_ENST00000397703.2_Silent_p.T47T|TNFRSF10C_ENST00000520607.1_Intron|TNFRSF10C_ENST00000540813.1_5'UTR	NM_003841.3	NP_003832	O14798	TR10C_HUMAN	tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain	7					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)			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)		TCCCCAAGACCCTAAAGTTCG	0.716													C|||	208	0.0415335	0.149	0.0101	5008	,	,		14742	0.0		0.004	False		,,,				2504	0.0				p.T7T		Atlas-SNP	.											.	TNFRSF10C	30	.	0			c.C21T						PASS	.	C		438,3966	169.8+/-200.3	25,388,1789	80.0	59.0	66.0		21	0.8	0.0	8	dbSNP_119	66	12,8586	5.0+/-18.6	0,12,4287	no	coding-synonymous	TNFRSF10C	NM_003841.3		25,400,6076	TT,TC,CC		0.1396,9.9455,3.461		7/260	22960655	450,12552	2202	4299	6501	SO:0001819	synonymous_variant	8794	exon1			CAAGACCCTAAAG	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.21C>T	8.37:g.22960655C>T		77.0	0.0	0		82.0	40.0	0.487805	NM_003841	O14755|Q08AS6|Q6FH98|Q6UXM5	Silent	SNP	ENST00000356864.3	37	CCDS6037.1																																																																																			.	.	alt		0.716	TNFRSF10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215134.3		
PAX8	7849	hgsc.bcm.edu	37	2	113994191	113994191	+	Silent	SNP	G	G	A	rs112872760	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:113994191G>A	ENST00000429538.3	-	8	1079	c.885C>T	c.(883-885)taC>taT	p.Y295Y	AC016683.6_ENST00000451179.1_RNA|AC016683.6_ENST00000556070.1_RNA|AC016683.6_ENST00000333145.5_RNA|PAX8_ENST00000348715.5_Silent_p.Y295Y|PAX8_ENST00000263334.5_Silent_p.Y295Y|AC016683.6_ENST00000422956.2_RNA|AC016683.6_ENST00000437551.1_RNA|PAX8_ENST00000397647.3_Intron|PAX8_ENST00000263335.7_Intron|AC016683.6_ENST00000553869.2_RNA|AC016683.6_ENST00000431844.2_RNA|AC016683.6_ENST00000456685.1_RNA|AC016683.6_ENST00000436293.2_RNA|AC016683.6_ENST00000445745.1_RNA	NM_003466.3	NP_003457.1	Q06710	PAX8_HUMAN	paired box 8	295					anatomical structure morphogenesis (GO:0009653)|branching involved in ureteric bud morphogenesis (GO:0001658)|cellular response to gonadotropin stimulus (GO:0071371)|central nervous system development (GO:0007417)|inner ear morphogenesis (GO:0042472)|kidney development (GO:0001822)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesonephros development (GO:0001823)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric distal convoluted tubule development (GO:0072221)|metanephric epithelium development (GO:0072207)|metanephric nephron tubule formation (GO:0072289)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process involved in metanephric collecting duct development (GO:1900215)|negative regulation of apoptotic process involved in metanephric nephron tubule development (GO:1900218)|negative regulation of mesenchymal cell apoptotic process involved in metanephric nephron morphogenesis (GO:0072305)|negative regulation of mesenchymal cell apoptotic process involved in metanephros development (GO:1900212)|otic vesicle development (GO:0071599)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of metanephric DCT cell differentiation (GO:2000594)|positive regulation of thyroid hormone generation (GO:2000611)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephric field specification (GO:0039003)|pronephros development (GO:0048793)|regulation of apoptotic process (GO:0042981)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of thyroid-stimulating hormone secretion (GO:2000612)|thyroid gland development (GO:0030878)|thyroid-stimulating hormone signaling pathway (GO:0038194)|transcription, DNA-templated (GO:0006351)|urogenital system development (GO:0001655)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding transcription factor activity (GO:0003700)|thyroid-stimulating hormone receptor activity (GO:0004996)|transcription regulatory region DNA binding (GO:0044212)		PAX8/PPARG(117)	breast(1)|endometrium(4)|kidney(2)|large_intestine(1)|liver(1)|lung(9)|ovary(1)|skin(1)	20						CCACCACGGGGTAGGTCTGGT	0.682			T	PPARG	follicular thyroid		Thyroid dysgenesis						G|||	8	0.00159744	0.0061	0.0	5008	,	,		14226	0.0		0.0	False		,,,				2504	0.0				p.Y295Y	Ovarian(188;7 2067 9084 29802 29892)	Atlas-SNP	.		Dom	yes		2	2q12-q14	7849	paired box gene 8	yes	E	.	PAX8	42	.	0			c.C885T						PASS	.	G	,,,	25,4077		0,25,2026	34.0	41.0	38.0		885,885,,	3.7	1.0	2	dbSNP_132	38	1,8367		0,1,4183	no	coding-synonymous,coding-synonymous,intron,intron	PAX8	NM_003466.3,NM_013952.3,NM_013953.3,NM_013992.3	,,,	0,26,6209	AA,AG,GG		0.012,0.6095,0.2085	,,,	295/451,295/399,,	113994191	26,12444	2051	4184	6235	SO:0001819	synonymous_variant	7849	exon8			CACGGGGTAGGTC	X69699	CCDS42735.1, CCDS42736.1, CCDS46398.1, CCDS46399.1	2q13	2011-06-20	2007-07-12		ENSG00000125618	ENSG00000125618		"""Paired boxes"", ""Homeoboxes / PRD class"""	8622	protein-coding gene	gene with protein product		167415	"""paired box gene 8"""			8431641, 7981748	Standard	NM_003466		Approved		uc010yxt.2	Q06710	OTTHUMG00000128529	ENST00000429538.3:c.885C>T	2.37:g.113994191G>A		52.0	0.0	0		69.0	35.0	0.507246	NM_013952	Q09155|Q16337|Q16338|Q16339|Q4ZG35|Q96J49	Silent	SNP	ENST00000429538.3	37	CCDS46398.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	16.70	3.196529	0.58126	0.006095	1.2E-4	ENSG00000125618	ENST00000468980	.	.	.	5.58	3.7	0.42460	.	.	.	.	.	T	0.51143	0.1657	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50566	-0.8813	4	.	.	.	.	9.3385	0.38065	0.1849:0.0:0.8151:0.0	.	.	.	.	S	81	.	.	P	-	1	0	PAX8	113710662	1.000000	0.71417	0.997000	0.53966	0.812000	0.45895	2.702000	0.47102	0.646000	0.30693	-0.345000	0.07892	CCC	G|0.999;A|0.001	0.001	strong		0.682	PAX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250353.5		
ADAM18	8749	hgsc.bcm.edu	37	8	39468128	39468128	+	Missense_Mutation	SNP	A	A	T	rs73605945	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:39468128A>T	ENST00000265707.5	+	6	470	c.425A>T	c.(424-426)cAa>cTa	p.Q142L	ADAM18_ENST00000520772.1_Missense_Mutation_p.Q142L|ADAM18_ENST00000379866.1_Missense_Mutation_p.Q142L|ADAM18_ENST00000541111.1_Intron	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	142					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(31)|ovary(1)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)	71		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)			ATAATTTATCAAATGAAAAAT	0.328													A|||	181	0.0361422	0.1203	0.0144	5008	,	,		15463	0.0		0.0089	False		,,,				2504	0.0031				p.Q142L		Atlas-SNP	.											.	ADAM18	169	.	0			c.A425T						PASS	.	A	LEU/GLN,LEU/GLN	505,3901	221.7+/-238.7	22,461,1720	47.0	49.0	48.0		425,425	4.1	1.0	8	dbSNP_130	48	49,8547	29.0+/-79.6	0,49,4249	yes	missense,missense	ADAM18	NM_001190956.1,NM_014237.2	113,113	22,510,5969	TT,TA,AA		0.57,11.4616,4.2609	probably-damaging,probably-damaging	142/183,142/740	39468128	554,12448	2203	4298	6501	SO:0001583	missense	8749	exon6			TTTATCAAATGAA	AJ133004	CCDS6113.1, CCDS55225.1	8p11.22	2008-08-07	2005-08-18		ENSG00000168619	ENSG00000168619		"""ADAM metallopeptidase domain containing"""	196	protein-coding gene	gene with protein product			"""a disintegrin and metalloproteinase domain 18"""			12200459	Standard	NM_014237		Approved	tMDCIII, ADAM27	uc003xni.3	Q9Y3Q7	OTTHUMG00000164040	ENST00000265707.5:c.425A>T	8.37:g.39468128A>T	ENSP00000265707:p.Gln142Leu	289.0	0.0	0		280.0	125.0	0.446429	NM_001190956	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Missense_Mutation	SNP	ENST00000265707.5	37	CCDS6113.1	75	0.034340659340659344	66	0.13414634146341464	6	0.016574585635359115	0	0.0	3	0.00395778364116095	A	15.82	2.946102	0.53079	0.114616	0.0057	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000520772;ENST00000522198	T;T;T	0.12465	5.29;4.82;2.68	5.25	4.07	0.47477	.	0.000000	0.47093	D	0.000245	T	0.00144	0.0004	N	0.08118	0	0.80722	D	1	D;D;D	0.63046	0.98;0.967;0.992	P;P;P	0.60286	0.872;0.749;0.84	T	0.34179	-0.9839	10	0.41790	T	0.15	.	7.8609	0.29509	0.9058:0.0:0.0942:0.0	.	142;142;142	Q9Y3Q7-2;Q9Y3Q7;Q6IRW9	.;ADA18_HUMAN;.	L	142;142;142;98	ENSP00000265707:Q142L;ENSP00000369195:Q142L;ENSP00000429908:Q142L	ENSP00000265707:Q142L	Q	+	2	0	ADAM18	39587285	1.000000	0.71417	1.000000	0.80357	0.291000	0.27294	2.766000	0.47629	2.206000	0.71126	0.533000	0.62120	CAA	A|0.964;T|0.036	0.036	strong		0.328	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237	
BSN	8927	hgsc.bcm.edu	37	3	49698695	49698695	+	Silent	SNP	T	T	C	rs149210839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:49698695T>C	ENST00000296452.4	+	6	9531	c.9417T>C	c.(9415-9417)cgT>cgC	p.R3139R		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	3139					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		CTGATAGCCGTGCCCCACTGC	0.602													T|||	14	0.00279553	0.0098	0.0014	5008	,	,		16801	0.0		0.0	False		,,,				2504	0.0				p.R3139R		Atlas-SNP	.											.	BSN	272	.	0			c.T9417C						PASS	.	T		26,4380	32.6+/-62.9	0,26,2177	67.0	53.0	58.0		9417	-2.3	0.0	3	dbSNP_134	58	0,8600		0,0,4300	no	coding-synonymous	BSN	NM_003458.3		0,26,6477	CC,CT,TT		0.0,0.5901,0.1999		3139/3927	49698695	26,12980	2203	4300	6503	SO:0001819	synonymous_variant	8927	exon6			TAGCCGTGCCCCA	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"""zinc finger protein 231"", ""neuronal double zinc finger protein"""	604020	"""bassoon (presynaptic cytomatrix protein)"""	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.9417T>C	3.37:g.49698695T>C		163.0	0.0	0		154.0	70.0	0.454545	NM_003458	O43161|Q7LGH3	Silent	SNP	ENST00000296452.4	37	CCDS2800.1																																																																																			T|0.998;C|0.002	0.002	strong		0.602	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458	
OR10K1	391109	hgsc.bcm.edu	37	1	158435573	158435573	+	Silent	SNP	C	C	G	rs76205582|rs386635902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158435573C>G	ENST00000289451.2	+	1	302	c.222C>G	c.(220-222)acC>acG	p.T74T		NM_001004473.1	NP_001004473.1	Q8NGX5	O10K1_HUMAN	olfactory receptor, family 10, subfamily K, member 1	74						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)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	27	all_hematologic(112;0.0378)					TTTGCTATACCTTTGTCATTG	0.458													C|||	189	0.0377396	0.1354	0.013	5008	,	,		24689	0.0		0.001	False		,,,				2504	0.0				p.T74T		Atlas-SNP	.											.	OR10K1	80	.	0			c.C222G						PASS	.	C		503,3903	214.8+/-234.0	27,449,1727	209.0	190.0	196.0		222	-0.3	1.0	1	dbSNP_131	196	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	OR10K1	NM_001004473.1		27,457,6019	GG,GC,CC		0.093,11.4163,3.929		74/314	158435573	511,12495	2203	4300	6503	SO:0001819	synonymous_variant	391109	exon1			CTATACCTTTGTC	AP002532	CCDS30897.1	1q23.1	2012-08-09			ENSG00000173285	ENSG00000173285		"""GPCR / Class A : Olfactory receptors"""	14693	protein-coding gene	gene with protein product							Standard	NM_001004473		Approved		uc010pij.2	Q8NGX5	OTTHUMG00000017517	ENST00000289451.2:c.222C>G	1.37:g.158435573C>G		489.0	1.0	0.00204499		474.0	205.0	0.432489	NM_001004473	Q6IFS2	Silent	SNP	ENST00000289451.2	37	CCDS30897.1																																																																																			C|0.966;G|0.034	0.034	strong		0.458	OR10K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046367.1		
AXDND1	126859	hgsc.bcm.edu	37	1	179363114	179363114	+	Missense_Mutation	SNP	G	G	C	rs139341288	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:179363114G>C	ENST00000367618.3	+	10	1327	c.940G>C	c.(940-942)Gtg>Ctg	p.V314L	AXDND1_ENST00000461179.2_3'UTR|AXDND1_ENST00000457238.2_Missense_Mutation_p.V314L	NM_144696.4	NP_653297.3	Q5T1B0	AXDN1_HUMAN	axonemal dynein light chain domain containing 1	314										NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(27)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	59						AACTCAGCGAGTGATGGACCA	0.378													G|||	21	0.00419329	0.0159	0.0	5008	,	,		17593	0.0		0.0	False		,,,				2504	0.0				p.V314L		Atlas-SNP	.											.	AXDND1	142	.	0			c.G940C						PASS	.	G	LEU/VAL	55,4351	55.5+/-91.7	1,53,2149	153.0	150.0	151.0		940	-8.5	0.4	1	dbSNP_134	151	0,8600		0,0,4300	yes	missense	AXDND1	NM_144696.4	32	1,53,6449	CC,CG,GG		0.0,1.2483,0.4229	benign	314/1013	179363114	55,12951	2203	4300	6503	SO:0001583	missense	126859	exon10			CAGCGAGTGATGG	BX647935	CCDS30948.1	1q25.2	2011-02-18	2011-02-18	2011-02-18	ENSG00000162779	ENSG00000162779			26564	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 125"""	C1orf125		14702039	Standard	NM_144696		Approved	FLJ32940	uc001gmo.3	Q5T1B0	OTTHUMG00000035266	ENST00000367618.3:c.940G>C	1.37:g.179363114G>C	ENSP00000356590:p.Val314Leu	75.0	0.0	0		79.0	33.0	0.417722	NM_144696	Q6AWB2|Q96LJ3|Q96M01	Missense_Mutation	SNP	ENST00000367618.3	37	CCDS30948.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	11.60	1.686179	0.29962	0.012483	0.0	ENSG00000162779	ENST00000367618;ENST00000360322;ENST00000457238;ENST00000434088	T;T;T	0.44083	2.23;0.93;2.25	5.33	-8.49	0.00931	.	1.179580	0.05606	N	0.577214	T	0.15609	0.0376	N	0.17474	0.49	0.09310	N	0.999999	B;B;B	0.11235	0.001;0.002;0.004	B;B;B	0.11329	0.005;0.005;0.006	T	0.16748	-1.0392	10	0.24483	T	0.36	-0.2882	8.4441	0.32833	0.3562:0.1866:0.4572:0.0	.	272;314;314	E9PCJ4;Q5T1B0;F5GWM2	.;AXDN1_HUMAN;.	L	314;272;314;248	ENSP00000356590:V314L;ENSP00000416712:V314L;ENSP00000391716:V248L	ENSP00000353471:V272L	V	+	1	0	AXDND1	177629737	0.041000	0.20044	0.412000	0.26496	0.994000	0.84299	-1.684000	0.01932	-1.766000	0.01302	-0.152000	0.13540	GTG	G|0.997;C|0.003	0.003	strong		0.378	AXDND1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085312.1	NM_144696	
CEACAM5	1048	hgsc.bcm.edu	37	19	42221418	42221418	+	Missense_Mutation	SNP	G	G	A	rs75927810	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42221418G>A	ENST00000221992.6	+	5	1117	c.1003G>A	c.(1003-1005)Gtg>Atg	p.V335M	CEACAM5_ENST00000398599.4_Missense_Mutation_p.V334M|CEACAM5_ENST00000405816.1_Missense_Mutation_p.V335M|CEA_ENST00000598976.1_Intron	NM_004363.2	NP_004354.2	P06731	CEAM5_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 5	335	Ig-like 4.				homotypic cell-cell adhesion (GO:0034109)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of myotube differentiation (GO:0010832)	anchored component of membrane (GO:0031225)|basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of external side of plasma membrane (GO:0071575)|integral component of plasma membrane (GO:0005887)	GPI anchor binding (GO:0034235)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(3)|kidney(5)|large_intestine(4)|lung(10)|ovary(2)|skin(7)|stomach(1)|urinary_tract(1)	34				OV - Ovarian serous cystadenocarcinoma(3;0.00278)|all cancers(3;0.00625)|Epithelial(262;0.0379)|GBM - Glioblastoma multiforme(1328;0.142)		CTCCAACCCCGTGGAGGATGA	0.532													g|||	97	0.019369	0.0688	0.0072	5008	,	,		21742	0.0		0.001	False		,,,				2504	0.0				p.V335M		Atlas-SNP	.											CEACAM5,NS,carcinoma,-2,1	CEACAM5	84	1	0			c.G1003A						PASS	.	G	MET/VAL	231,4175	135.7+/-171.8	6,219,1978	143.0	144.0	144.0		1003	-5.6	0.0	19	dbSNP_131	144	7,8593	5.7+/-21.5	0,7,4293	yes	missense	CEACAM5	NM_004363.2	21	6,226,6271	AA,AG,GG		0.0814,5.2429,1.8299	benign	335/703	42221418	238,12768	2203	4300	6503	SO:0001583	missense	1048	exon5			AACCCCGTGGAGG	M17303	CCDS12584.1	19q13.1-q13.2	2013-01-29			ENSG00000105388	ENSG00000105388		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1817	protein-coding gene	gene with protein product		114890		CEA			Standard	XM_005258413		Approved	CD66e	uc002orl.3	P06731	OTTHUMG00000151061	ENST00000221992.6:c.1003G>A	19.37:g.42221418G>A	ENSP00000221992:p.Val335Met	142.0	0.0	0		172.0	91.0	0.52907	NM_004363	H9KVA7	Missense_Mutation	SNP	ENST00000221992.6	37	CCDS12584.1	25|25	0.011446886446886446|0.011446886446886446	19|19	0.03861788617886179|0.03861788617886179	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	G|G	7.757|7.757	0.704676|0.704676	0.15172|0.15172	0.052429|0.052429	8.14E-4|8.14E-4	ENSG00000105388|ENSG00000105388	ENST00000398599|ENST00000221992;ENST00000405816	.|T;T	.|0.72167	.|-0.63;-0.63	2.77|2.77	-5.55|-5.55	0.02536|0.02536	.|Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.|.	.|.	.|.	.|.	T|T	0.38852|0.38852	0.1056|0.1056	M|M	0.83603|0.83603	2.65|2.65	0.09310|0.09310	N|N	1|1	.|P;D	.|0.63880	.|0.881;0.993	.|P;D	.|0.64042	.|0.572;0.921	T|T	0.60697|0.60697	-0.7212|-0.7212	5|9	.|0.56958	.|D	.|0.05	.|.	0.9149|0.9149	0.01302|0.01302	0.3457:0.1551:0.3423:0.1569|0.3457:0.1551:0.3423:0.1569	.|.	.|335;335	.|P06731;Q53G30	.|CEAM5_HUMAN;.	H|M	330|335	.|ENSP00000221992:V335M;ENSP00000385072:V335M	.|ENSP00000221992:V335M	R|V	+|+	2|1	0|0	CEACAM5|CEACAM5	46913258|46913258	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.009000|0.009000	0.06853|0.06853	-1.341000|-1.341000	0.02647|0.02647	-1.658000|-1.658000	0.01490|0.01490	-0.706000|-0.706000	0.03657|0.03657	CGT|GTG	G|0.985;A|0.015	0.015	strong		0.532	CEACAM5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321132.2	NM_004363	
MPRIP	23164	hgsc.bcm.edu	37	17	17030129	17030129	+	Silent	SNP	G	G	A	rs140002644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:17030129G>A	ENST00000341712.4	+	4	381	c.381G>A	c.(379-381)gaG>gaA	p.E127E	MPRIP_ENST00000395811.5_Silent_p.E127E|MPRIP_ENST00000444976.1_Silent_p.E127E|MPRIP_ENST00000395804.3_Silent_p.E127E			Q6WCQ1	MPRIP_HUMAN	myosin phosphatase Rho interacting protein	127	Interaction with F-actin. {ECO:0000250}.|PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.					actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)				biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	31						CTGAGAAGGAGCATTTCATCC	0.587													G|||	3	0.000599042	0.0023	0.0	5008	,	,		20330	0.0		0.0	False		,,,				2504	0.0				p.E127E		Atlas-SNP	.											.	MPRIP	87	.	0			c.G381A						PASS	.	G	,	21,4385	28.1+/-56.4	0,21,2182	92.0	89.0	90.0		381,381	3.4	1.0	17	dbSNP_134	90	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	MPRIP	NM_015134.3,NM_201274.3	,	0,21,6482	AA,AG,GG		0.0,0.4766,0.1615	,	127/1039,127/1026	17030129	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	23164	exon4			GAAGGAGCATTTC	BC014102	CCDS32578.1, CCDS42268.1	17p11.2	2013-01-10			ENSG00000133030	ENSG00000133030		"""Pleckstrin homology (PH) domain containing"""	30321	protein-coding gene	gene with protein product	"""Rho interacting protein 3"""	612935				10048485	Standard	NM_201274		Approved	RHOIP3, M-RIP, p116Rip	uc002gqy.2	Q6WCQ1	OTTHUMG00000059276	ENST00000341712.4:c.381G>A	17.37:g.17030129G>A		160.0	0.0	0		136.0	52.0	0.382353	NM_015134	Q3KQZ5|Q5FB94|Q6DHW2|Q7Z5Y2|Q8N390|Q96G40	Silent	SNP	ENST00000341712.4	37	CCDS32578.1																																																																																			G|0.998;A|0.002	0.002	strong		0.587	MPRIP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131587.1	NM_015134	
OPRL1	4987	hgsc.bcm.edu	37	20	62729843	62729843	+	Silent	SNP	A	A	G	rs34874539	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:62729843A>G	ENST00000349451.3	+	6	1216	c.804A>G	c.(802-804)gtA>gtG	p.V268V	OPRL1_ENST00000336866.2_Silent_p.V268V|OPRL1_ENST00000355631.4_Silent_p.V268V	NM_001200019.1	NP_001186948.1	P41146	OPRX_HUMAN	opiate receptor-like 1	268					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavior (GO:0007610)|opioid receptor signaling pathway (GO:0038003)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|nociceptin receptor activity (GO:0001626)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(2)|urinary_tract(1)	19	all_cancers(38;4.74e-11)|all_epithelial(29;1.33e-12)|Lung NSC(23;3.27e-09)|all_lung(23;1.02e-08)					TGCTGGTGGTAGTGGCTGTGT	0.672													G|||	99	0.0197684	0.0719	0.0058	5008	,	,		16073	0.0		0.0	False		,,,				2504	0.0				p.V268V		Atlas-SNP	.											.	OPRL1	47	.	0			c.A804G						PASS	.		,,	263,4139	793.7+/-415.2	9,245,1947	70.0	63.0	65.0		804,804,804	1.0	1.0	20	dbSNP_126	65	1,8593		0,1,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	OPRL1	NM_000913.4,NM_001200019.1,NM_182647.2	,,	9,246,6243	GG,GA,AA		0.0116,5.9746,2.0314	,,	268/371,268/371,268/371	62729843	264,12732	2201	4297	6498	SO:0001819	synonymous_variant	4987	exon4			GGTGGTAGTGGCT		CCDS13556.1	20q13.33	2012-08-08			ENSG00000125510	ENSG00000125510		"""GPCR / Class A : Opioid receptors"""	8155	protein-coding gene	gene with protein product	"""LC132 receptor-like"", ""orphanin FQ receptor"", ""kappa3-related opioid receptor"""	602548				8137918	Standard	NM_000913		Approved	NOCIR, ORL1, OOR, KOR-3	uc021wgs.1	P41146	OTTHUMG00000033027	ENST00000349451.3:c.804A>G	20.37:g.62729843A>G		190.0	0.0	0		224.0	114.0	0.508929	NM_000913	Q8TD34|Q8WYH9|Q9H4K4	Silent	SNP	ENST00000349451.3	37	CCDS13556.1																																																																																			A|0.979;G|0.021	0.021	strong		0.672	OPRL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080295.1	NM_182647	
NUP155	9631	hgsc.bcm.edu	37	5	37299007	37299007	+	Silent	SNP	G	G	A	rs216400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37299007G>A	ENST00000231498.3	-	32	3959	c.3756C>T	c.(3754-3756)ggC>ggT	p.G1252G	NUP155_ENST00000513532.1_Silent_p.G1188G|NUP155_ENST00000381843.2_Silent_p.G1193G|NUP155_ENST00000502533.1_5'UTR	NM_153485.1	NP_705618.1	O75694	NU155_HUMAN	nucleoporin 155kDa	1252					atrial cardiac muscle cell action potential (GO:0086014)|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 export from nucleus (GO:0006406)|nuclear envelope organization (GO:0006998)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)	structural constituent of nuclear pore (GO:0017056)|transporter activity (GO:0005215)			endometrium(1)|kidney(16)|large_intestine(5)|lung(29)|ovary(2)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	62	all_lung(31;0.000137)		COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CATAAATTTTGCCAAGGAGAA	0.408													G|||	150	0.0299521	0.1112	0.0043	5008	,	,		18740	0.0		0.0	False		,,,				2504	0.0				p.G1252G		Atlas-SNP	.											.	NUP155	116	.	0			c.C3756T						PASS	.	G	,	437,3969	210.5+/-231.0	24,389,1790	134.0	119.0	124.0		3579,3756	0.7	1.0	5	dbSNP_79	124	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	NUP155	NM_004298.2,NM_153485.1	,	24,390,6089	AA,AG,GG		0.0116,9.9183,3.3677	,	1193/1333,1252/1392	37299007	438,12568	2203	4300	6503	SO:0001819	synonymous_variant	9631	exon32			AATTTTGCCAAGG	AJ007558	CCDS3921.1, CCDS43310.1, CCDS64142.1	5p13.1	2008-02-05	2002-08-29		ENSG00000113569	ENSG00000113569			8063	protein-coding gene	gene with protein product		606694	"""nucleoporin 155kD"""			10191094	Standard	NM_153485		Approved	KIAA0791, N155	uc003jku.1	O75694	OTTHUMG00000090803	ENST00000231498.3:c.3756C>T	5.37:g.37299007G>A		87.0	0.0	0		108.0	40.0	0.37037	NM_153485	Q9UBE9|Q9UFL5	Silent	SNP	ENST00000231498.3	37	CCDS3921.1																																																																																			G|0.967;A|0.033	0.033	strong		0.408	NUP155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207593.2	NM_153485, NM_004298	
RIMS2	9699	hgsc.bcm.edu	37	8	104513156	104513156	+	Silent	SNP	C	C	A	rs78505067	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:104513156C>A	ENST00000406091.3	+	1	42	c.42C>A	c.(40-42)atC>atA	p.I14I	RP11-1C8.4_ENST00000517376.1_RNA|RP11-1C8.4_ENST00000523422.1_RNA	NM_001100117.2	NP_001093587.1	Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	14					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)			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)			TGGCTCCCATCCCGGCGGCCT	0.677										HNSCC(12;0.0054)			C|||	38	0.00758786	0.0257	0.0058	5008	,	,		10505	0.0		0.0	False		,,,				2504	0.0				p.I14I		Atlas-SNP	.											.	RIMS2	1357	.	0			c.C42A						PASS	.	C		67,3591		1,65,1763	14.0	17.0	16.0		42	1.2	1.0	8	dbSNP_132	16	0,8116		0,0,4058	no	coding-synonymous	RIMS2	NM_001100117.2		1,65,5821	AA,AC,CC		0.0,1.8316,0.5691		14/1350	104513156	67,11707	1829	4058	5887	SO:0001819	synonymous_variant	9699	exon1			TCCCATCCCGGCG	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		ENST00000406091.3:c.42C>A	8.37:g.104513156C>A		80.0	0.0	0		95.0	47.0	0.494737	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Silent	SNP	ENST00000406091.3	37	CCDS55269.1																																																																																			C|0.994;A|0.006	0.006	strong		0.677	RIMS2-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001100117	
GSDMD	79792	hgsc.bcm.edu	37	8	144641514	144641514	+	Silent	SNP	G	G	T	rs7840446	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144641514G>T	ENST00000526406.1	+	5	892	c.9G>T	c.(7-9)tcG>tcT	p.S3S	GSDMD_ENST00000533063.1_Silent_p.S51S|GSDMD_ENST00000262580.4_Silent_p.S3S	NM_001166237.1	NP_001159709.1	P57764	GSDMD_HUMAN	gasdermin D	3					cellular response to extracellular stimulus (GO:0031668)					breast(1)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	12						GCATGGGGTCGGCCTTTGAGC	0.627													G|||	165	0.0329473	0.121	0.0058	5008	,	,		10930	0.0		0.001	False		,,,				2504	0.0				p.S3S		Atlas-SNP	.											.	GSDMD	28	.	0			c.G9T						PASS	.	G	,	383,4023	190.2+/-216.2	15,353,1835	63.0	58.0	60.0		9,9	-9.4	0.0	8	dbSNP_116	60	4,8594	3.0+/-9.4	0,4,4295	no	coding-synonymous,coding-synonymous	GSDMD	NM_001166237.1,NM_024736.6	,	15,357,6130	TT,TG,GG		0.0465,8.6927,2.976	,	3/485,3/485	144641514	387,12617	2203	4299	6502	SO:0001819	synonymous_variant	79792	exon5			GGGGTCGGCCTTT	AK096216	CCDS34956.1	8q24.3	2008-07-31	2008-07-31	2008-07-31		ENSG00000104518			25697	protein-coding gene	gene with protein product			"""gasdermin domain containing 1"""	GSDMDC1		15289881, 17350798	Standard	NM_024736		Approved	FLJ12150, DF5L	uc003yyg.3	P57764		ENST00000526406.1:c.9G>T	8.37:g.144641514G>T		74.0	0.0	0		79.0	48.0	0.607595	NM_001166237	D3DWJ9|Q96Q98	Silent	SNP	ENST00000526406.1	37	CCDS34956.1																																																																																			G|0.971;T|0.029	0.029	strong		0.627	GSDMD-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382046.3	NM_024736	
C11orf53	341032	hgsc.bcm.edu	37	11	111156523	111156523	+	Missense_Mutation	SNP	G	G	T	rs74649813	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:111156523G>T	ENST00000280325.4	+	4	602	c.455G>T	c.(454-456)tGg>tTg	p.W152L		NM_198498.1	NP_940900.1	Q8IXP5	CK053_HUMAN	chromosome 11 open reading frame 53	152										endometrium(1)|large_intestine(2)|lung(3)|skin(2)	8		all_cancers(61;2.05e-09)|Melanoma(852;4.04e-05)|all_epithelial(67;6.15e-05)|all_hematologic(158;0.000826)|Acute lymphoblastic leukemia(157;0.000966)|all_neural(223;0.0332)|Medulloblastoma(222;0.0425)|Breast(348;0.147)		Epithelial(105;1.7e-06)|BRCA - Breast invasive adenocarcinoma(274;3.16e-06)|all cancers(92;2.88e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0507)		GGCTCAAGCTGGGGGTCATCC	0.642													G|||	223	0.0445288	0.1589	0.0187	5008	,	,		21186	0.0		0.0	False		,,,				2504	0.0				p.W152L		Atlas-SNP	.											C11orf53,NS,haematopoietic_neoplasm,-1,1	C11orf53	17	1	0			c.G455T						PASS	.	G	LEU/TRP	526,3876	237.4+/-249.2	36,454,1711	75.0	72.0	73.0		455	5.2	1.0	11	dbSNP_131	73	3,8591	2.2+/-6.3	0,3,4294	yes	missense	C11orf53	NM_198498.1	61	36,457,6005	TT,TG,GG		0.0349,11.9491,4.0705	probably-damaging	152/237	111156523	529,12467	2201	4297	6498	SO:0001583	missense	341032	exon4			CAAGCTGGGGGTC	BC039669	CCDS31674.1	11q23.1	2012-05-31			ENSG00000150750	ENSG00000150750			30527	protein-coding gene	gene with protein product						12477932	Standard	NM_198498		Approved	MGC50104	uc001plc.3	Q8IXP5	OTTHUMG00000166656	ENST00000280325.4:c.455G>T	11.37:g.111156523G>T	ENSP00000280325:p.Trp152Leu	75.0	0.0	0		56.0	34.0	0.607143	NM_198498		Missense_Mutation	SNP	ENST00000280325.4	37	CCDS31674.1	86	0.039377289377289376	77	0.1565040650406504	9	0.024861878453038673	0	0.0	0	0.0	G	18.56	3.650861	0.67472	0.119491	3.49E-4	ENSG00000150750	ENST00000280325	.	.	.	5.15	5.15	0.70609	.	0.069080	0.64402	D	0.000009	T	0.00754	0.0025	M	0.67953	2.075	0.24566	P	0.99394883	D	0.89917	1.0	D	0.87578	0.998	T	0.23833	-1.0177	8	0.12103	T	0.63	-12.1586	16.1285	0.81410	0.0:0.0:1.0:0.0	.	152	Q8IXP5	CK053_HUMAN	L	152	.	ENSP00000280325:W152L	W	+	2	0	C11orf53	110661733	1.000000	0.71417	0.995000	0.50966	0.655000	0.38815	6.849000	0.75414	2.402000	0.81655	0.561000	0.74099	TGG	G|0.961;T|0.039	0.039	strong		0.642	C11orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390989.1	NM_198498	
ZNF846	162993	hgsc.bcm.edu	37	19	9868764	9868764	+	Missense_Mutation	SNP	C	C	G	rs60387559	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9868764C>G	ENST00000397902.2	-	6	1402	c.989G>C	c.(988-990)cGa>cCa	p.R330P	ZNF846_ENST00000586293.1_3'UTR|ZNF846_ENST00000592859.1_Missense_Mutation_p.R201P|ZNF846_ENST00000588267.1_Missense_Mutation_p.R201P	NM_001077624.1	NP_001071092.1	Q147U1	ZN846_HUMAN	zinc finger protein 846	330					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.R330Q(1)		NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	22						AGTGTGAATTCGCATGTGTAA	0.388													N|||	64	0.0127796	0.0461	0.0043	5008	,	,		23084	0.0		0.0	False		,,,				2504	0.0				p.R330P		Atlas-SNP	.											ZNF846,NS,carcinoma,0,3	ZNF846	61	3	1	Substitution - Missense(1)	large_intestine(1)	c.G989C						PASS	.	C	PRO/ARG	247,4097		17,213,1942	63.0	68.0	66.0		989	-3.1	0.0	19	dbSNP_129	66	0,8586		0,0,4293	yes	missense	ZNF846	NM_001077624.1	103	17,213,6235	GG,GC,CC		0.0,5.686,1.9103	probably-damaging	330/534	9868764	247,12683	2172	4293	6465	SO:0001583	missense	162993	exon6			TGAATTCGCATGT	AK097652	CCDS42496.1	19p13.2	2013-01-08			ENSG00000196605	ENSG00000196605		"""Zinc fingers, C2H2-type"", ""-"""	27260	protein-coding gene	gene with protein product							Standard	NM_001077624		Approved		uc002mmb.1	Q147U1		ENST00000397902.2:c.989G>C	19.37:g.9868764C>G	ENSP00000380999:p.Arg330Pro	105.0	0.0	0		80.0	39.0	0.4875	NM_001077624	A8K0H1|B3KUP1	Missense_Mutation	SNP	ENST00000397902.2	37	CCDS42496.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	.	15.85	2.955405	0.53293	0.05686	0.0	ENSG00000196605	ENST00000397902	T	0.25749	1.78	2.01	-3.1	0.05315	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.07143	0.0181	M	0.89840	3.065	0.09310	N	1	D	0.71674	0.998	P	0.58013	0.831	T	0.08554	-1.0716	8	.	.	.	.	3.6327	0.08138	0.1949:0.251:0.0:0.5541	rs60387559	330	Q147U1	ZN846_HUMAN	P	330	ENSP00000380999:R330P	.	R	-	2	0	ZNF846	9729764	0.000000	0.05858	0.000000	0.03702	0.688000	0.40055	-1.594000	0.02094	-0.747000	0.04759	0.456000	0.33151	CGA	C|0.992;G|0.007;T|0.000	0.007	strong		0.388	ZNF846-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450253.1	NM_001077624	
GPRIN3	285513	hgsc.bcm.edu	37	4	90170015	90170015	+	Missense_Mutation	SNP	C	C	A	rs114960901	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:90170015C>A	ENST00000609438.1	-	2	1765	c.1247G>T	c.(1246-1248)gGg>gTg	p.G416V	GPRIN3_ENST00000333209.4_Missense_Mutation_p.G416V	NM_198281.2	NP_938022.2	Q6ZVF9	GRIN3_HUMAN	GPRIN family member 3	416										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(5)|prostate(2)|skin(1)	36		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;5.67e-05)		TTTAAGGACCCCACCTGGTAG	0.507													C|||	41	0.0081869	0.0295	0.0029	5008	,	,		19599	0.0		0.0	False		,,,				2504	0.0				p.G416V		Atlas-SNP	.											GPRIN3,colon,carcinoma,+1,1	GPRIN3	90	1	0			c.G1247T						PASS	.	C	VAL/GLY	114,4292	85.8+/-124.5	1,112,2090	108.0	112.0	110.0		1247	2.8	0.0	4	dbSNP_132	110	1,8599		0,1,4299	yes	missense	GPRIN3	NM_198281.2	109	1,113,6389	AA,AC,CC		0.0116,2.5874,0.8842	benign	416/777	90170015	115,12891	2203	4300	6503	SO:0001583	missense	285513	exon2			AGGACCCCACCTG	AK124616	CCDS34030.1	4q22.1	2006-08-24				ENSG00000185477			27733	protein-coding gene	gene with protein product		611241				15488195	Standard	NM_198281		Approved	GRIN3, FLJ42625	uc003hsm.1	Q6ZVF9		ENST00000609438.1:c.1247G>T	4.37:g.90170015C>A	ENSP00000476603:p.Gly416Val	172.0	0.0	0		190.0	95.0	0.5	NM_198281	Q8IVE4	Missense_Mutation	SNP	ENST00000609438.1	37	CCDS34030.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	C	10.41	1.341579	0.24339	0.025874	1.16E-4	ENSG00000185477	ENST00000333209	T	0.11385	2.78	5.38	2.81	0.32909	.	0.502634	0.14825	N	0.296209	T	0.01592	0.0051	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.34129	-0.9841	10	0.45353	T	0.12	-1.3894	1.9135	0.03292	0.1497:0.0899:0.2415:0.5188	.	416	Q6ZVF9	GRIN3_HUMAN	V	416	ENSP00000328672:G416V	ENSP00000328672:G416V	G	-	2	0	GPRIN3	90389038	0.000000	0.05858	0.014000	0.15608	0.026000	0.11368	-0.091000	0.11146	1.050000	0.40346	-0.290000	0.09829	GGG	C|0.991;A|0.009	0.009	strong		0.507	GPRIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363540.2	NM_198281	
SGK223	157285	hgsc.bcm.edu	37	8	8176770	8176770	+	Missense_Mutation	SNP	C	C	T	rs28533138	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:8176770C>T	ENST00000520004.1	-	6	3379	c.3115G>A	c.(3115-3117)Gtg>Atg	p.V1039M	SGK223_ENST00000330777.4_Missense_Mutation_p.V1039M			Q86YV5	SG223_HUMAN		1041	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										TGCACGGGCACGGACGGGCTG	0.617													C|||	160	0.0319489	0.115	0.0086	5008	,	,		14630	0.0		0.002	False		,,,				2504	0.0				p.V1039M	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.G3115A						PASS	.	C	MET/VAL	347,3795		11,325,1735	41.0	49.0	46.0		3115	5.3	1.0	8	dbSNP_125	46	14,8330		0,14,4158	yes	missense	SGK223	NM_001080826.1	21	11,339,5893	TT,TC,CC		0.1678,8.3776,2.8912	probably-damaging	1039/1403	8176770	361,12125	2071	4172	6243	SO:0001583	missense	0	exon5			CGGGCACGGACGG																												ENST00000520004.1:c.3115G>A	8.37:g.8176770C>T	ENSP00000428054:p.Val1039Met	93.0	0.0	0		96.0	44.0	0.458333	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	58	0.026556776556776556	55	0.11178861788617886	3	0.008287292817679558	0	0.0	0	0.0	C	18.72	3.684827	0.68157	0.083776	0.001678	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.32515	1.45;1.45	5.33	5.33	0.75918	Protein kinase, catalytic domain (1);	0.318706	0.31809	N	0.007027	T	0.00496	0.0016	L	0.27053	0.805	0.46028	D	0.998827	D	0.58268	0.982	P	0.45449	0.481	T	0.00225	-1.1901	10	0.72032	D	0.01	.	14.0559	0.64769	0.0:0.8492:0.1508:0.0	rs28533138	1039	Q86YV5	SG223_HUMAN	M	1039	ENSP00000330930:V1039M;ENSP00000428054:V1039M	ENSP00000330930:V1039M	V	-	1	0	AC068353.1	8214180	1.000000	0.71417	0.959000	0.39883	0.726000	0.41606	4.871000	0.63042	2.670000	0.90874	0.467000	0.42956	GTG	C|0.982;T|0.018	0.018	strong		0.617	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
TMEM57	55219	hgsc.bcm.edu	37	1	25757607	25757607	+	Silent	SNP	C	C	T	rs114403991	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:25757607C>T	ENST00000374343.4	+	1	197	c.18C>T	c.(16-18)gcC>gcT	p.A6A	TMEM57_ENST00000399763.3_Silent_p.A6A|TMEM57_ENST00000399766.3_Silent_p.A6A|RHCE_ENST00000349320.3_5'Flank	NM_018202.4	NP_060672.2	Q8N5G2	MACOI_HUMAN	transmembrane protein 57	6					brain development (GO:0007420)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuron projection terminus (GO:0044306)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|synapse (GO:0045202)				breast(3)|endometrium(2)|kidney(2)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	27		Colorectal(325;0.000147)|Renal(390;0.00211)|Lung NSC(340;0.00715)|all_lung(284;0.00989)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.051)|Breast(348;0.0675)|all_neural(195;0.201)		UCEC - Uterine corpus endometrioid carcinoma (279;0.042)|OV - Ovarian serous cystadenocarcinoma(117;1.85e-26)|Colorectal(126;2.99e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000751)|STAD - Stomach adenocarcinoma(196;0.000766)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|GBM - Glioblastoma multiforme(114;0.0191)|READ - Rectum adenocarcinoma(331;0.0649)		GGCGGAACGCCGACTGCAGTA	0.761													C|||	56	0.0111821	0.0371	0.0086	5008	,	,		5510	0.0		0.001	False		,,,				2504	0.0				p.A6A		Atlas-SNP	.											.	TMEM57	72	.	0			c.C18T						PASS	.	C		61,4291		0,61,2115	11.0	13.0	12.0		18	-0.5	1.0	1	dbSNP_132	12	1,8539		0,1,4269	no	coding-synonymous	TMEM57	NM_018202.4		0,62,6384	TT,TC,CC		0.0117,1.4017,0.4809		6/665	25757607	62,12830	2176	4270	6446	SO:0001819	synonymous_variant	55219	exon1			GAACGCCGACTGC	AK001609	CCDS30638.1, CCDS60034.1	1p36.11	2008-02-05			ENSG00000204178	ENSG00000204178			25572	protein-coding gene	gene with protein product		610301				12459264, 15255972	Standard	XM_005245931		Approved	FLJ10747	uc001bkk.3	Q8N5G2	OTTHUMG00000003473	ENST00000374343.4:c.18C>T	1.37:g.25757607C>T		36.0	0.0	0		55.0	34.0	0.618182	NM_018202	B1AK00|Q2TLX5|Q2TLX6|Q9NVG6	Silent	SNP	ENST00000374343.4	37	CCDS30638.1																																																																																			C|0.992;T|0.008	0.008	strong		0.761	TMEM57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009659.2	NM_018202	
OR10T2	128360	hgsc.bcm.edu	37	1	158368915	158368915	+	Silent	SNP	G	G	T	rs56704148	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158368915G>T	ENST00000334438.1	-	1	341	c.342C>A	c.(340-342)ctC>ctA	p.L114L		NM_001004475.1	NP_001004475.1	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T, member 2	114						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(4)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_hematologic(112;0.0378)					CAGCAATGAGGAGGCAGTTGG	0.498													G|||	46	0.0091853	0.034	0.0014	5008	,	,		21129	0.0		0.0	False		,,,				2504	0.0				p.L114L		Atlas-SNP	.											.	OR10T2	76	.	0			c.C342A						PASS	.	G		139,4267	98.0+/-136.7	5,129,2069	122.0	121.0	121.0		342	-1.0	1.0	1	dbSNP_129	121	0,8600		0,0,4300	no	coding-synonymous	OR10T2	NM_001004475.1		5,129,6369	TT,TG,GG		0.0,3.1548,1.0687		114/315	158368915	139,12867	2203	4300	6503	SO:0001819	synonymous_variant	128360	exon1			AATGAGGAGGCAG	AB065643	CCDS30895.1	1q23.1	2012-08-09			ENSG00000186306	ENSG00000186306		"""GPCR / Class A : Olfactory receptors"""	14816	protein-coding gene	gene with protein product							Standard	NM_001004475		Approved		uc010pih.2	Q8NGX3	OTTHUMG00000017521	ENST00000334438.1:c.342C>A	1.37:g.158368915G>T		134.0	0.0	0		147.0	74.0	0.503401	NM_001004475	Q6IF98	Silent	SNP	ENST00000334438.1	37	CCDS30895.1																																																																																			G|0.989;T|0.011	0.011	strong		0.498	OR10T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046371.1	NM_001004475	
SPATA17	128153	hgsc.bcm.edu	37	1	217824488	217824488	+	Silent	SNP	T	T	C	rs143446051		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:217824488T>C	ENST00000366933.4	+	3	263	c.208T>C	c.(208-210)Tta>Cta	p.L70L		NM_138796.2	NP_620151.1	Q96L03	SPT17_HUMAN	spermatogenesis associated 17	70	IQ 2. {ECO:0000255|PROSITE- ProRule:PRU00116}.					cytoplasm (GO:0005737)				endometrium(1)|kidney(1)|large_intestine(9)|lung(6)|pancreas(2)|prostate(1)|urinary_tract(1)	21				OV - Ovarian serous cystadenocarcinoma(81;0.0516)|all cancers(67;0.0891)|GBM - Glioblastoma multiforme(131;0.117)		GAGAAGTTTCTTAGGCAGAAA	0.299													T|||	1	0.000199681	0.0	0.0	5008	,	,		18465	0.0		0.001	False		,,,				2504	0.0				p.L70L		Atlas-SNP	.											.	SPATA17	59	.	0			c.T208C						PASS	.	T		1,4405	2.1+/-5.4	0,1,2202	84.0	94.0	91.0		208	2.5	1.0	1	dbSNP_134	91	15,8569	10.5+/-38.8	0,15,4277	no	coding-synonymous	SPATA17	NM_138796.2		0,16,6479	CC,CT,TT		0.1747,0.0227,0.1232		70/362	217824488	16,12974	2203	4292	6495	SO:0001819	synonymous_variant	128153	exon3			AGTTTCTTAGGCA	AK098591	CCDS1519.1	1q41	2008-02-05			ENSG00000162814	ENSG00000162814			25184	protein-coding gene	gene with protein product	"""IQ motif containing H"""	611032				16395525	Standard	NM_138796		Approved	IQCH	uc001hlh.1	Q96L03	OTTHUMG00000037875	ENST00000366933.4:c.208T>C	1.37:g.217824488T>C		191.0	0.0	0		217.0	104.0	0.479263	NM_138796	A5D6N2	Silent	SNP	ENST00000366933.4	37	CCDS1519.1																																																																																			T|0.998;C|0.002	0.002	strong		0.299	SPATA17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092433.2	NM_138796	
RRP7A	27341	hgsc.bcm.edu	37	22	42910142	42910142	+	Missense_Mutation	SNP	C	C	T	rs61731241	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:42910142C>T	ENST00000323013.6	-	6	742	c.727G>A	c.(727-729)Gcc>Acc	p.A243T	SERHL_ENST00000359906.2_RNA	NM_015703.4	NP_056518.2	Q9Y3A4	RRP7A_HUMAN	ribosomal RNA processing 7 homolog A (S. cerevisiae)	243							nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|liver(2)|lung(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	10						TGCTGCCAGGCGTAGAAGTTG	0.667													C|||	247	0.0493211	0.1793	0.013	5008	,	,		21135	0.0		0.001	False		,,,				2504	0.0				p.A243T		Atlas-SNP	.											.	RRP7A	25	.	0			c.G727A						PASS	.	C	THR/ALA	589,3817		31,527,1645	53.0	36.0	42.0		727	3.7	0.9	22	dbSNP_129	42	18,8582		0,18,4282	yes	missense	RRP7A	NM_015703.4	58	31,545,5927	TT,TC,CC		0.2093,13.3681,4.6671	benign	243/281	42910142	607,12399	2203	4300	6503	SO:0001583	missense	27341	exon6			GCCAGGCGTAGAA	BC035992	CCDS14036.1	22q13.2	2008-08-08			ENSG00000189306	ENSG00000189306			24286	protein-coding gene	gene with protein product						10810093, 12087473	Standard	NM_015703		Approved	CGI-96	uc003bcq.3	Q9Y3A4	OTTHUMG00000150891	ENST00000323013.6:c.727G>A	22.37:g.42910142C>T	ENSP00000321449:p.Ala243Thr	49.0	0.0	0		75.0	35.0	0.466667	NM_015703	A4FTX2|B2RBG4|Q0VAD0|Q5JZ94|Q6P4B5|Q8IVR9|Q8IVY0|Q8N5Q3|Q8NEY6|Q9Y3H5	Missense_Mutation	SNP	ENST00000323013.6	37	CCDS14036.1	84	0.038461538461538464	78	0.15853658536585366	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	.	6.304	0.424130	0.11928	0.133681	0.002093	ENSG00000189306	ENST00000323013	T	0.22539	1.95	3.66	3.66	0.41972	Winged helix-turn-helix transcription repressor DNA-binding (1);	0.164932	0.53938	D	0.000046	T	0.00039	0.0001	N	0.03999	-0.3	0.21967	P	0.999444231	P;B	0.45396	0.857;0.364	B;B	0.35510	0.204;0.121	T	0.42292	-0.9460	9	0.16420	T	0.52	-28.9794	15.7164	0.77672	0.0:1.0:0.0:0.0	.	243;66	Q9Y3A4;Q9NSQ0	RRP7A_HUMAN;RRP7B_HUMAN	T	243	ENSP00000321449:A243T	ENSP00000321449:A243T	A	-	1	0	RRP7A	41240086	0.995000	0.38212	0.922000	0.36590	0.018000	0.09664	3.198000	0.51035	1.747000	0.51819	0.205000	0.17691	GCC	C|0.958;T|0.042	0.042	strong		0.667	RRP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320451.1	NM_015703	
DDX55	57696	hgsc.bcm.edu	37	12	124090655	124090655	+	Silent	SNP	C	C	T	rs7973689	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124090655C>T	ENST00000238146.4	+	3	245	c.195C>T	c.(193-195)atC>atT	p.I65I	DDX55_ENST00000538744.1_Silent_p.I65I	NM_020936.1	NP_065987.1	Q8NHQ9	DDX55_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55	65	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					membrane (GO:0016020)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000142)|Epithelial(86;0.000637)|all cancers(50;0.00772)		CTTTTGTCATCCCCATCCTGG	0.428													C|||	364	0.0726837	0.2315	0.0202	5008	,	,		20720	0.0		0.0159	False		,,,				2504	0.0286				p.I65I		Atlas-SNP	.											.	DDX55	51	.	0			c.C195T						PASS	.	C		764,3642	308.0+/-290.3	67,630,1506	81.0	76.0	77.0		195	1.6	1.0	12	dbSNP_116	77	163,8437	74.2+/-136.8	0,163,4137	no	coding-synonymous	DDX55	NM_020936.1		67,793,5643	TT,TC,CC		1.8953,17.34,7.1275		65/601	124090655	927,12079	2203	4300	6503	SO:0001819	synonymous_variant	57696	exon3			TGTCATCCCCATC	AB046815	CCDS9251.1	12q24.31	2003-06-13			ENSG00000111364	ENSG00000111364		"""DEAD-boxes"""	20085	protein-coding gene	gene with protein product						10997877	Standard	NM_020936		Approved	KIAA1595	uc001ufi.3	Q8NHQ9	OTTHUMG00000168695	ENST00000238146.4:c.195C>T	12.37:g.124090655C>T		93.0	0.0	0		105.0	56.0	0.533333	NM_020936	Q658L6|Q8IYH0|Q9HCH7	Silent	SNP	ENST00000238146.4	37	CCDS9251.1																																																																																			C|0.929;T|0.071	0.071	strong		0.428	DDX55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400616.2		
LAMB4	22798	hgsc.bcm.edu	37	7	107756510	107756510	+	Missense_Mutation	SNP	A	A	G	rs35644375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:107756510A>G	ENST00000388781.3	-	3	214	c.131T>C	c.(130-132)aTg>aCg	p.M44T	LAMB4_ENST00000388780.3_Missense_Mutation_p.M44T|LAMB4_ENST00000205386.4_Missense_Mutation_p.M44T|LAMB4_ENST00000414450.2_Missense_Mutation_p.M44T|LAMB4_ENST00000418464.1_Missense_Mutation_p.M44T	NM_007356.2	NP_031382.2	A4D0S4	LAMB4_HUMAN	laminin, beta 4	44	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.		M -> T (in dbSNP:rs35644375).		cell adhesion (GO:0007155)	basement membrane (GO:0005604)				NS(1)|breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(22)|lung(40)|ovary(4)|prostate(5)|skin(4)	97						AGAAGAAGCCATAAGCTGCGT	0.512													G|||	503	0.100439	0.3631	0.0317	5008	,	,		19458	0.0		0.001	False		,,,				2504	0.0				p.M44T		Atlas-SNP	.											.	LAMB4	253	.	0			c.T131C						PASS	.	G	THR/MET	1279,3127	700.8+/-406.7	186,907,1110	105.0	106.0	106.0		131	2.8	0.0	7	dbSNP_126	106	32,8568	817.9+/-406.9	0,32,4268	yes	missense	LAMB4	NM_007356.2	81	186,939,5378	GG,GA,AA		0.3721,29.0286,10.08	benign	44/1762	107756510	1311,11695	2203	4300	6503	SO:0001583	missense	22798	exon3			GAAGCCATAAGCT	AF028816	CCDS34732.1	7q31	2013-03-01			ENSG00000091128	ENSG00000091128		"""Laminins"""	6491	protein-coding gene	gene with protein product							Standard	NM_007356		Approved		uc010ljo.1	A4D0S4	OTTHUMG00000154874	ENST00000388781.3:c.131T>C	7.37:g.107756510A>G	ENSP00000373433:p.Met44Thr	92.0	0.0	0		101.0	41.0	0.405941	NM_007356	A5PKU6|B2RTT3|B5MEB9|Q86TP7|Q86XN2|Q8NBX5	Missense_Mutation	SNP	ENST00000388781.3	37	CCDS34732.1	190	0.08699633699633699	177	0.3597560975609756	13	0.03591160220994475	0	0.0	0	0.0	G	0.019	-1.450644	0.01080	0.290286	0.003721	ENSG00000091128	ENST00000205386;ENST00000388781;ENST00000388780;ENST00000418464;ENST00000414450	T;T;T;T;T	0.73789	-0.78;-0.78;-0.78;-0.78;-0.78	5.6	2.81	0.32909	Laminin, N-terminal (3);	0.560407	0.16178	N	0.225961	T	0.00012	0.0000	N	0.00099	-2.14	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.26849	-1.0091	9	0.06625	T	0.88	.	6.7977	0.23734	0.2544:0.0:0.6319:0.1136	rs35644375;rs60836843	44	A4D0S4	LAMB4_HUMAN	T	44	ENSP00000205386:M44T;ENSP00000373433:M44T;ENSP00000373432:M44T;ENSP00000402353:M44T;ENSP00000402265:M44T	ENSP00000205386:M44T	M	-	2	0	LAMB4	107543746	0.000000	0.05858	0.003000	0.11579	0.082000	0.17680	0.434000	0.21494	0.049000	0.15920	-0.735000	0.03563	ATG	A|0.908;G|0.092	0.092	strong		0.512	LAMB4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337442.1	XM_209857	
FANCI	55215	hgsc.bcm.edu	37	15	89849413	89849413	+	Silent	SNP	C	C	A	rs114810692	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:89849413C>A	ENST00000310775.7	+	32	3611	c.3525C>A	c.(3523-3525)gcC>gcA	p.A1175A	FANCI_ENST00000300027.8_Silent_p.A1115A	NM_001113378.1	NP_001106849.1	Q9NVI1	FANCI_HUMAN	Fanconi anemia, complementation group I	1175					cell cycle (GO:0007049)|DNA repair (GO:0006281)|positive regulation of protein ubiquitination (GO:0031398)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA polymerase binding (GO:0070182)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	Lung NSC(78;0.0472)|all_lung(78;0.089)					CACTTACAGCCCTTGTCAGAT	0.512								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				C|||	33	0.00658946	0.0242	0.0014	5008	,	,		19687	0.0		0.0	False		,,,				2504	0.0				p.A1175A		Atlas-SNP	.											.	FANCI	129	.	0			c.C3525A						PASS	.	C	,	75,4325	66.4+/-103.9	0,75,2125	109.0	96.0	100.0		3525,3345	-10.8	0.6	15	dbSNP_132	100	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous,coding-synonymous	FANCI	NM_001113378.1,NM_018193.2	,	0,76,6423	AA,AC,CC		0.0116,1.7045,0.5847	,	1175/1329,1115/1269	89849413	76,12922	2200	4299	6499	SO:0001819	synonymous_variant	55215	exon32	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	TACAGCCCTTGTC	BC004277	CCDS10349.2, CCDS45346.1	15q26.1	2014-09-17	2007-05-03	2007-05-03	ENSG00000140525	ENSG00000140525		"""Fanconi anemia, complementation groups"""	25568	protein-coding gene	gene with protein product		611360	"""KIAA1794"""	KIAA1794		14630800, 17460694, 17412408	Standard	NM_001113378		Approved	FLJ10719	uc010bnp.1	Q9NVI1	OTTHUMG00000132993	ENST00000310775.7:c.3525C>A	15.37:g.89849413C>A		66.0	0.0	0		68.0	32.0	0.470588	NM_001113378	A4ZVE4|A5YMH4|A6NJZ0|Q96JN1|Q96ST0|Q9BT96	Silent	SNP	ENST00000310775.7	37	CCDS45346.1																																																																																			C|0.994;A|0.006	0.006	strong		0.512	FANCI-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421140.1	NM_018193	
SCN3B	55800	hgsc.bcm.edu	37	11	123516316	123516316	+	Silent	SNP	G	G	A	rs115752338	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123516316G>A	ENST00000392770.2	-	2	1000	c.198C>T	c.(196-198)ccC>ccT	p.P66P	SCN3B_ENST00000530277.1_Silent_p.P66P|SCN3B_ENST00000299333.3_Silent_p.P66P	NM_018400.3	NP_060870.1	Q9NY72	SCN3B_HUMAN	sodium channel, voltage-gated, type III, beta subunit	66	Ig-like C2-type.				atrial cardiac muscle cell action potential (GO:0086014)|axon guidance (GO:0007411)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cardiac muscle contraction (GO:0060048)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|positive regulation of heart rate (GO:0010460)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|ventricular cardiac muscle cell action potential (GO:0086005)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ion channel binding (GO:0044325)|sodium channel regulator activity (GO:0017080)|voltage-gated sodium channel activity (GO:0005248)|voltage-gated sodium channel activity involved in cardiac muscle cell action potential (GO:0086006)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(2)|skin(2)	26		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;5.37e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0227)	Valproic Acid(DB00313)|Zonisamide(DB00909)	TACCGCCCTCGGGCCTGTAGA	0.597													A|||	46	0.0091853	0.0325	0.0043	5008	,	,		19339	0.0		0.0	False		,,,				2504	0.0				p.P66P		Atlas-SNP	.											.	SCN3B	53	.	0			c.C198T						PASS	.	A	,	118,4286	815.4+/-416.2	2,114,2086	131.0	135.0	134.0		198,198	-11.9	0.0	11	dbSNP_132	134	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	SCN3B	NM_001040151.1,NM_018400.3	,	2,114,6385	AA,AG,GG		0.0,2.6794,0.9076	,	66/216,66/216	123516316	118,12884	2202	4299	6501	SO:0001819	synonymous_variant	55800	exon2			GCCCTCGGGCCTG	AJ243396	CCDS8442.1	11q24.1	2014-09-17	2012-02-28		ENSG00000166257	ENSG00000166257		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"", ""Immunoglobulin superfamily / V-set domain containing"""	20665	protein-coding gene	gene with protein product		608214	"""sodium channel, voltage-gated, type III, beta"""			10688874	Standard	XR_428980		Approved	HSA243396	uc001pzb.1	Q9NY72	OTTHUMG00000166006	ENST00000392770.2:c.198C>T	11.37:g.123516316G>A		145.0	0.0	0		112.0	68.0	0.607143	NM_018400	A5H1I5|Q17RL3|Q9ULR2	Silent	SNP	ENST00000392770.2	37	CCDS8442.1																																																																																			G|0.990;A|0.010	0.010	strong		0.597	SCN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387412.1	NM_018400	
TMEM218	219854	hgsc.bcm.edu	37	11	124972114	124972114	+	Silent	SNP	G	G	A	rs7114520	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124972114G>A	ENST00000279968.4	-	3	347	c.24C>T	c.(22-24)gtC>gtT	p.V8V	TMEM218_ENST00000531909.1_Silent_p.V8V|TMEM218_ENST00000532407.1_Silent_p.V8V|TMEM218_ENST00000527271.1_Silent_p.V8V|TMEM218_ENST00000531262.1_Intron|TMEM218_ENST00000455225.1_Silent_p.V8V|TMEM218_ENST00000526175.1_Silent_p.V8V|TMEM218_ENST00000529583.1_Silent_p.V8V|TMEM218_ENST00000529609.1_Silent_p.V8V|TMEM218_ENST00000532156.1_Silent_p.V8V|TMEM218_ENST00000527766.1_Silent_p.V8V|TMEM218_ENST00000528724.1_Silent_p.V8V			A2RU14	TM218_HUMAN	transmembrane protein 218	8						integral component of membrane (GO:0016021)				breast(1)|large_intestine(2)|lung(1)|prostate(1)	5						CGCCCGCACCGACTCCGAGCA	0.682													G|||	294	0.0587061	0.1861	0.0115	5008	,	,		12552	0.001		0.008	False		,,,				2504	0.0317				p.V43V		Atlas-SNP	.											.	TMEM218	14	.	0			c.C129T						PASS	.	G		735,3661	293.8+/-282.8	52,631,1515	42.0	43.0	43.0		24	0.9	1.0	11	dbSNP_116	43	70,8520	41.7+/-99.0	0,70,4225	no	coding-synonymous	TMEM218	NM_001080546.1		52,701,5740	AA,AG,GG		0.8149,16.7197,6.199		8/116	124972114	805,12181	2198	4295	6493	SO:0001819	synonymous_variant	219854	exon4			CGCACCGACTCCG		CCDS31715.1	11q24.2	2008-08-08			ENSG00000150433	ENSG00000150433			27344	protein-coding gene	gene with protein product							Standard	NM_001258238		Approved		uc031qeu.1	A2RU14		ENST00000279968.4:c.24C>T	11.37:g.124972114G>A		88.0	0.0	0		79.0	43.0	0.544304	NM_001258243	B7ZM48	Silent	SNP	ENST00000279968.4	37	CCDS31715.1																																																																																			G|0.946;A|0.054	0.054	strong		0.682	TMEM218-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386849.1	NM_001080546	
MED15	51586	hgsc.bcm.edu	37	22	20909389	20909389	+	Silent	SNP	G	G	A	rs147554746	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:20909389G>A	ENST00000263205.7	+	5	474	c.405G>A	c.(403-405)ggG>ggA	p.G135G	MED15_ENST00000406969.1_Silent_p.G109G|MED15_ENST00000292733.7_Silent_p.G135G|MED15_ENST00000425759.2_Intron|MED15_ENST00000382974.2_Intron|MED15_ENST00000541476.1_Silent_p.G109G|MED15_ENST00000542773.1_Intron	NM_001003891.1	NP_001003891.1	Q96RN5	MED15_HUMAN	mediator complex subunit 15	135					gene expression (GO:0010467)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	25	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)			GGACCTCGGGGATGGCCCCTC	0.612													G|||	2	0.000399361	0.0015	0.0	5008	,	,		17772	0.0		0.0	False		,,,				2504	0.0				p.G135G		Atlas-SNP	.											.	MED15	68	.	0			c.G405A						PASS	.	G	,	1,4405	2.1+/-5.4	0,1,2202	29.0	29.0	29.0		405,405	-2.0	1.0	22	dbSNP_134	29	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	MED15	NM_001003891.1,NM_015889.3	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	135/789,135/749	20909389	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	51586	exon5			CTCGGGGATGGCC	AF056191	CCDS13781.1, CCDS33602.1, CCDS74824.1	22q11.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000099917	ENSG00000099917			14248	protein-coding gene	gene with protein product		607372	"""trinucleotide repeat containing 7"", ""PC2 (positive cofactor 2, multiprotein complex) glutamine/Q-rich-associated protein"""	TNRC7, PCQAP		11024300, 11414760, 15175163	Standard	XM_005261632		Approved	TIG-1, CAG7A, Arc105	uc002zsp.3	Q96RN5	OTTHUMG00000150810	ENST00000263205.7:c.405G>A	22.37:g.20909389G>A		47.0	0.0	0		53.0	24.0	0.45283	NM_015889	D3DX31|D3DX32|O15413|Q6IC31|Q8NF16|Q96CT0|Q96IH7|Q9P1T3	Silent	SNP	ENST00000263205.7	37	CCDS33602.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	11.36	1.615678	0.28801	2.27E-4	0.0	ENSG00000099917	ENST00000423862	.	.	.	5.46	-2.03	0.07365	.	.	.	.	.	T	0.39279	0.1072	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.31724	-0.9933	4	.	.	.	.	1.4274	0.02326	0.2499:0.2738:0.3381:0.1381	.	.	.	.	N	76	.	.	D	+	1	0	MED15	19239389	0.446000	0.25665	0.981000	0.43875	0.986000	0.74619	-0.516000	0.06282	-0.109000	0.12044	-0.225000	0.12378	GAT	G|1.000;A|0.000	0.000	strong		0.612	MED15-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320177.2	NM_015889	
RBM19	9904	hgsc.bcm.edu	37	12	114358449	114358449	+	Silent	SNP	C	C	T	rs79120696	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:114358449C>T	ENST00000545145.2	-	19	2430	c.2352G>A	c.(2350-2352)ccG>ccA	p.P784P	RBM19_ENST00000392561.3_Silent_p.P784P|RBM19_ENST00000261741.5_Silent_p.P784P	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	784	RRM 5. {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)					GGGCTTGCTCCGGCTTCCTGT	0.562													C|||	384	0.0766773	0.2716	0.0317	5008	,	,		16543	0.0		0.003	False		,,,				2504	0.0				p.P784P		Atlas-SNP	.											.	RBM19	117	.	0			c.G2352A						PASS	.	C	,,	1093,3313	394.4+/-329.3	152,789,1262	237.0	239.0	238.0		2352,2352,2352	-10.0	0.3	12	dbSNP_131	238	10,8590	5.7+/-21.5	0,10,4290	no	coding-synonymous,coding-synonymous,coding-synonymous	RBM19	NM_001146698.1,NM_001146699.1,NM_016196.3	,,	152,799,5552	TT,TC,CC		0.1163,24.8071,8.4807	,,	784/961,784/961,784/961	114358449	1103,11903	2203	4300	6503	SO:0001819	synonymous_variant	9904	exon19			TTGCTCCGGCTTC	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.2352G>A	12.37:g.114358449C>T		102.0	0.0	0		108.0	58.0	0.537037	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Silent	SNP	ENST00000545145.2	37	CCDS9172.1																																																																																			C|0.917;T|0.083	0.083	strong		0.562	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
GPRC6A	222545	hgsc.bcm.edu	37	6	117127551	117127551	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:117127551G>A	ENST00000310357.3	-	3	1338	c.1317C>T	c.(1315-1317)aaC>aaT	p.N439N	GPRC6A_ENST00000368549.3_Silent_p.N439N|GPRC6A_ENST00000530250.1_Intron	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	439					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)		GTTGAAAGGCGTTGGGGTTCT	0.438																																					p.N439N		Atlas-SNP	.											.	GPRC6A	152	.	0			c.C1317T						PASS	.						96.0	85.0	88.0					6																	117127551		2203	4299	6502	SO:0001819	synonymous_variant	222545	exon3			AAAGGCGTTGGGG	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.1317C>T	6.37:g.117127551G>A		75.0	0.0	0		88.0	4.0	0.0454545	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Silent	SNP	ENST00000310357.3	37	CCDS5112.1																																																																																			.	.	none		0.438	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2		
GRAMD3	65983	hgsc.bcm.edu	37	5	125696124	125696124	+	Missense_Mutation	SNP	T	T	A	rs79046516	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:125696124T>A	ENST00000513040.1	+	1	301	c.101T>A	c.(100-102)gTg>gAg	p.V34E		NM_001146319.1	NP_001139791.1	Q96HH9	GRAM3_HUMAN	GRAM domain containing 3	0						cytoplasmic microtubule (GO:0005881)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	11		Prostate(80;0.0928)	KIRC - Kidney renal clear cell carcinoma(527;0.0584)|Kidney(363;0.0934)	Epithelial(69;0.0401)|OV - Ovarian serous cystadenocarcinoma(64;0.0604)|all cancers(49;0.108)		GGGAGAGAAGTGAAGCCAGTG	0.488													T|||	118	0.0235623	0.087	0.0043	5008	,	,		21249	0.0		0.0	False		,,,				2504	0.0				p.V34E		Atlas-SNP	.											.	GRAMD3	30	.	0			c.T101A						PASS	.						123.0	116.0	119.0					5																	125696124		692	1591	2283	SO:0001583	missense	65983	exon1			GAGAAGTGAAGCC	BC008590	CCDS4136.1, CCDS54891.1, CCDS54892.1, CCDS54893.1, CCDS54894.1	5q23.2	2014-02-12	2005-11-03		ENSG00000155324	ENSG00000155324			24911	protein-coding gene	gene with protein product	"""HCV NS3 transactivated protein 2"""					12477932	Standard	NM_023927		Approved	NS3TP2, FLJ21313	uc011cwt.2	Q96HH9	OTTHUMG00000128943	ENST00000513040.1:c.101T>A	5.37:g.125696124T>A	ENSP00000426120:p.Val34Glu	184.0	0.0	0		215.0	82.0	0.381395	NM_001146319	B7Z1F2|B7Z3R1|B7Z6D8|B7Z8T2|D3DSZ3|Q9H753	Missense_Mutation	SNP	ENST00000513040.1	37	CCDS54891.1	43	0.019688644688644688	41	0.08333333333333333	2	0.0055248618784530384	0	0.0	0	0.0	T	9.413	1.081098	0.20309	.	.	ENSG00000155324	ENST00000513040	T	0.36878	1.23	4.15	-5.51	0.02568	.	.	.	.	.	T	0.00496	0.0016	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.18429	-1.0337	8	0.02654	T	1	.	2.4366	0.04485	0.2542:0.0881:0.4343:0.2234	.	34	B7Z6D8	.	E	34	ENSP00000426120:V34E	ENSP00000426120:V34E	V	+	2	0	GRAMD3	125724023	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-0.306000	0.08178	-0.956000	0.03631	-1.304000	0.01323	GTG	T|0.975;A|0.025	0.025	strong		0.488	GRAMD3-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000371350.1	NM_023927	
NRCAM	4897	hgsc.bcm.edu	37	7	107790417	107790417	+	Missense_Mutation	SNP	C	C	T	rs74708699	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:107790417C>T	ENST00000425651.2	-	30	3852	c.3853G>A	c.(3853-3855)Gct>Act	p.A1285T	NRCAM_ENST00000351718.4_Missense_Mutation_p.A1164T|NRCAM_ENST00000379024.4_Missense_Mutation_p.A1173T|NRCAM_ENST00000379028.3_Missense_Mutation_p.A1285T|NRCAM_ENST00000413765.2_Missense_Mutation_p.A1161T|NRCAM_ENST00000522550.2_5'UTR	NM_001037132.2	NP_001032209.1	Q92823	NRCAM_HUMAN	neuronal cell adhesion molecule	1285					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|neuron migration (GO:0001764)|neuronal action potential propagation (GO:0019227)|positive regulation of neuron differentiation (GO:0045666)|protein localization (GO:0008104)|regulation of axon extension (GO:0030516)|retinal ganglion cell axon guidance (GO:0031290)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)	axon initial segment (GO:0043194)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|synapse (GO:0045202)	ankyrin binding (GO:0030506)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|liver(1)|lung(36)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)	65						TTTCCTTCAGCCGGCTCTTTC	0.428													C|||	36	0.0071885	0.0272	0.0	5008	,	,		15356	0.0		0.0	False		,,,				2504	0.0				p.A1285T		Atlas-SNP	.											.	NRCAM	267	.	0			c.G3853A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	115,4291	87.8+/-126.4	0,115,2088	161.0	150.0	154.0		3853,3574,3517,3481,3490	5.3	0.5	7	dbSNP_131	154	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense,missense,missense,missense	NRCAM	NM_001037132.2,NM_001193582.1,NM_001193583.1,NM_001193584.1,NM_005010.4	58,58,58,58,58	0,118,6385	TT,TC,CC		0.0349,2.6101,0.9073	benign,benign,benign,benign,benign	1285/1305,1192/1212,1173/1193,1161/1181,1164/1184	107790417	118,12888	2203	4300	6503	SO:0001583	missense	4897	exon30			CTTCAGCCGGCTC		CCDS5751.1, CCDS47686.1, CCDS55153.1, CCDS75652.1	7q31	2013-02-11			ENSG00000091129	ENSG00000091129		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7994	protein-coding gene	gene with protein product	"""NgCAM-related cell adhesion molecule"""	601581				8812479	Standard	NM_001037132		Approved	KIAA0343, Bravo	uc022aka.1	Q92823	OTTHUMG00000154973	ENST00000425651.2:c.3853G>A	7.37:g.107790417C>T	ENSP00000401244:p.Ala1285Thr	214.0	0.0	0		175.0	93.0	0.531429	NM_001037132	A4D0S3|E9PDA4|O15051|O15179|Q14BM2|Q9UHI3|Q9UHI4	Missense_Mutation	SNP	ENST00000425651.2	37	CCDS47686.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	12.19	1.863087	0.32884	0.026101	3.49E-4	ENSG00000091129	ENST00000379032;ENST00000379028;ENST00000413765;ENST00000437386;ENST00000351718;ENST00000379024;ENST00000425651	T;T;T;T;T	0.58940	0.34;0.57;0.3;0.35;0.34	6.17	5.3	0.74995	.	0.344041	0.33290	N	0.005080	T	0.15912	0.0383	N	0.14661	0.345	0.80722	D	1	B;B;B;B;B;B;P	0.47106	0.01;0.001;0.144;0.021;0.036;0.001;0.89	B;B;B;B;B;B;B	0.37833	0.021;0.002;0.17;0.011;0.016;0.004;0.259	T	0.09228	-1.0684	10	0.13108	T	0.6	.	15.699	0.77528	0.0:0.9348:0.0:0.0652	.	1289;131;1161;1173;1164;1285;68	Q92823-5;B4DFP9;Q92823-3;E9PDA4;Q92823-4;Q92823;Q6QRP2	.;.;.;.;.;NRCAM_HUMAN;.	T	1289;1285;1161;129;1164;1173;1285	ENSP00000368314:A1285T;ENSP00000407858:A1161T;ENSP00000325269:A1164T;ENSP00000368310:A1173T;ENSP00000401244:A1285T	ENSP00000325269:A1164T	A	-	1	0	NRCAM	107577653	1.000000	0.71417	0.514000	0.27761	0.983000	0.72400	5.115000	0.64655	1.630000	0.50440	0.655000	0.94253	GCT	C|0.990;T|0.010	0.010	strong		0.428	NRCAM-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337942.2	NM_001037132	
PTPRN2	5799	hgsc.bcm.edu	37	7	157959870	157959870	+	Silent	SNP	G	G	T	rs112343839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:157959870G>T	ENST00000389418.4	-	6	672	c.663C>A	c.(661-663)ctC>ctA	p.L221L	PTPRN2_ENST00000409483.1_Silent_p.L183L|PTPRN2_ENST00000389416.4_Silent_p.L204L|PTPRN2_ENST00000404321.2_Silent_p.L244L|PTPRN2_ENST00000389413.3_Silent_p.L221L	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	221					negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		GGAGCTGGCCGAGGGTCCGCG	0.667													G|||	49	0.00978435	0.034	0.0043	5008	,	,		16342	0.0		0.001	False		,,,				2504	0.0				p.L221L		Atlas-SNP	.											.	PTPRN2	243	.	0			c.C663A						PASS	.		,,	161,4245	105.6+/-144.1	5,151,2047	40.0	39.0	39.0		663,612,663	-1.8	0.0	7	dbSNP_132	39	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	,,	5,151,6347	TT,TG,GG		0.0,3.6541,1.2379	,,	221/1016,204/999,221/987	157959870	161,12845	2203	4300	6503	SO:0001819	synonymous_variant	5799	exon6			CTGGCCGAGGGTC	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.663C>A	7.37:g.157959870G>T		76.0	0.0	0		63.0	33.0	0.52381	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Silent	SNP	ENST00000389418.4	37	CCDS5947.1																																																																																			G|0.985;T|0.015	0.015	strong		0.667	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
PPP1R1B	84152	hgsc.bcm.edu	37	17	37791894	37791894	+	Silent	SNP	A	A	G	rs34257414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:37791894A>G	ENST00000254079.4	+	6	949	c.480A>G	c.(478-480)gaA>gaG	p.E160E	PPP1R1B_ENST00000394265.1_Silent_p.E124E|PPP1R1B_ENST00000394267.2_Silent_p.E124E|PPP1R1B_ENST00000580825.1_Silent_p.E160E|STARD3_ENST00000580611.1_5'Flank|STARD3_ENST00000544210.2_5'Flank|PPP1R1B_ENST00000579000.1_Silent_p.E127E|STARD3_ENST00000394250.4_5'Flank|STARD3_ENST00000336308.5_5'Flank	NM_032192.3	NP_115568.2	Q9UD71	PPR1B_HUMAN	protein phosphatase 1, regulatory (inhibitor) subunit 1B	160					intracellular signal transduction (GO:0035556)|negative regulation of catalytic activity (GO:0043086)|negative regulation of female receptivity (GO:0007621)|negative regulation of protein kinase activity (GO:0006469)|regulation of catalytic activity (GO:0050790)|response to amphetamine (GO:0001975)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytosol (GO:0005829)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	protein kinase inhibitor activity (GO:0004860)|protein phosphatase inhibitor activity (GO:0004864)|protein phosphatase type 1 regulator activity (GO:0008599)			kidney(1)|large_intestine(1)|liver(1)|lung(2)	5	Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;1.04e-44)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			AGGGTCTGGAAGGGCCCTGGG	0.587													G|||	94	0.01877	0.0711	0.0	5008	,	,		19292	0.0		0.0	False		,,,				2504	0.0				p.E160E		Atlas-SNP	.											.	PPP1R1B	9	.	0			c.A480G						PASS	.	G	,,	206,4200	784.3+/-414.7	3,200,2000	74.0	85.0	81.0		372,480,372	2.1	1.0	17	dbSNP_126	81	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	PPP1R1B	NM_001242464.1,NM_032192.3,NM_181505.3	,,	3,200,6300	GG,GA,AA		0.0,4.6754,1.5839	,,	124/169,160/205,124/169	37791894	206,12800	2203	4300	6503	SO:0001819	synonymous_variant	84152	exon6			TCTGGAAGGGCCC	AI124650	CCDS11339.1, CCDS11340.1	17q12	2012-04-17	2008-07-31		ENSG00000131771	ENSG00000131771	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9287	protein-coding gene	gene with protein product	"""dopamine and cAMP regulated phosphoprotein"""	604399				8120638	Standard	NM_032192		Approved	DARPP-32, FLJ20940	uc002hrz.3	Q9UD71	OTTHUMG00000133210	ENST00000254079.4:c.480A>G	17.37:g.37791894A>G		76.0	0.0	0		92.0	43.0	0.467391	NM_032192	Q547V9|Q547W0|Q9H7G1	Silent	SNP	ENST00000254079.4	37	CCDS11339.1																																																																																			A|0.979;G|0.021	0.021	strong		0.587	PPP1R1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256925.2	NM_032192	
SLC9A8	23315	hgsc.bcm.edu	37	20	48472098	48472098	+	Silent	SNP	A	A	G	rs35137210	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:48472098A>G	ENST00000361573.2	+	8	735	c.693A>G	c.(691-693)gcA>gcG	p.A231A	SLC9A8_ENST00000541138.1_5'UTR|SLC9A8_ENST00000417961.1_Silent_p.A247A|SLC9A8_ENST00000539601.1_Silent_p.A12A			Q9Y2E8	SL9A8_HUMAN	solute carrier family 9, subfamily A (NHE8, cation proton antiporter 8), member 8	231					ion transport (GO:0006811)|regulation of intracellular pH (GO:0051453)|transmembrane transport (GO:0055085)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	potassium:proton antiporter activity (GO:0015386)|sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	30			BRCA - Breast invasive adenocarcinoma(9;3.91e-07)			TCAACGATGCAGTCTCCATTG	0.463													A|||	18	0.00359425	0.0136	0.0	5008	,	,		22384	0.0		0.0	False		,,,				2504	0.0				p.A247A		Atlas-SNP	.											.	SLC9A8	63	.	0			c.A741G						PASS	.	A		60,4346	56.2+/-92.4	0,60,2143	107.0	92.0	97.0		693	-10.5	0.0	20	dbSNP_126	97	0,8600		0,0,4300	no	coding-synonymous	SLC9A8	NM_015266.1		0,60,6443	GG,GA,AA		0.0,1.3618,0.4613		231/582	48472098	60,12946	2203	4300	6503	SO:0001819	synonymous_variant	23315	exon8			CGATGCAGTCTCC	AB023156	CCDS13421.1, CCDS58774.1	20q13.13	2013-05-22	2012-03-22		ENSG00000197818	ENSG00000197818		"""Solute carriers"""	20728	protein-coding gene	gene with protein product		612730	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 8"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 8"""			12409279	Standard	NM_001260491		Approved	KIAA0939, NHE8	uc002xuv.2	Q9Y2E8	OTTHUMG00000032710	ENST00000361573.2:c.693A>G	20.37:g.48472098A>G		164.0	0.0	0		161.0	85.0	0.52795	NM_001260491	B4DTQ8|Q2M1U9|Q68CZ8|Q9BX15|Q9Y507	Silent	SNP	ENST00000361573.2	37	CCDS13421.1																																																																																			A|0.994;G|0.006	0.006	strong		0.463	SLC9A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106483.3	XM_030524	
SLC19A3	80704	hgsc.bcm.edu	37	2	228566993	228566993	+	Silent	SNP	G	G	A	rs34080459	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:228566993G>A	ENST00000258403.3	-	2	113	c.42C>T	c.(40-42)taC>taT	p.Y14Y	SLC19A3_ENST00000409287.1_Silent_p.Y14Y|SLC19A3_ENST00000541617.1_5'UTR	NM_025243.3	NP_079519.1	Q9BZV2	S19A3_HUMAN	solute carrier family 19 (thiamine transporter), member 3	14					small molecule metabolic process (GO:0044281)|thiamine transmembrane transport (GO:0071934)|thiamine-containing compound metabolic process (GO:0042723)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	thiamine uptake transmembrane transporter activity (GO:0015403)			breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|skin(3)	30		Renal(207;0.0112)|all_lung(227;0.0335)|Lung NSC(271;0.142)|all_hematologic(139;0.21)|Esophageal squamous(248;0.236)		Epithelial(121;1.58e-10)|all cancers(144;8.55e-08)|Lung(261;0.00948)|LUSC - Lung squamous cell carcinoma(224;0.0125)	L-Cysteine(DB00151)	TCACAGTGGGGTAAATCCAGG	0.383													G|||	79	0.0157748	0.0537	0.0086	5008	,	,		19039	0.001		0.001	False		,,,				2504	0.0				p.Y14Y		Atlas-SNP	.											.	SLC19A3	62	.	0			c.C42T						PASS	.	G		221,4185	134.9+/-171.1	6,209,1988	108.0	115.0	113.0		42	1.7	1.0	2	dbSNP_126	113	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SLC19A3	NM_025243.3		6,210,6287	AA,AG,GG		0.0116,5.0159,1.7069		14/497	228566993	222,12784	2203	4300	6503	SO:0001819	synonymous_variant	80704	exon2			AGTGGGGTAAATC	AF271633	CCDS2468.1	2q37	2013-07-18	2013-07-18		ENSG00000135917	ENSG00000135917		"""Solute carriers"""	16266	protein-coding gene	gene with protein product	"""thiamine transporter 2"""	606152	"""solute carrier family 19, member 3"""			11136550, 15871139	Standard	XM_005246871		Approved	THTR2	uc002vpi.3	Q9BZV2	OTTHUMG00000133185	ENST00000258403.3:c.42C>T	2.37:g.228566993G>A		78.0	0.0	0		71.0	34.0	0.478873	NM_025243		Silent	SNP	ENST00000258403.3	37	CCDS2468.1																																																																																			G|0.982;A|0.018	0.018	strong		0.383	SLC19A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256894.1		
ROBO1	6091	hgsc.bcm.edu	37	3	78676701	78676701	+	Silent	SNP	T	T	C	rs116125749	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:78676701T>C	ENST00000464233.1	-	26	3758	c.3645A>G	c.(3643-3645)ccA>ccG	p.P1215P	ROBO1_ENST00000495273.1_Silent_p.P1170P|ROBO1_ENST00000436010.2_Silent_p.P1176P|ROBO1_ENST00000467549.1_Silent_p.P1115P	NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	1215					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		GCACGGGACATGGCATTTCTT	0.413													T|||	52	0.0103834	0.0371	0.0043	5008	,	,		19868	0.0		0.0	False		,,,				2504	0.0				p.P1215P		Atlas-SNP	.											.	ROBO1	833	.	0			c.A3645G						PASS	.	T	,,	114,3892		1,112,1890	59.0	70.0	67.0		3345,3645,3510	-1.6	1.0	3	dbSNP_132	67	1,8321		0,1,4160	no	coding-synonymous,coding-synonymous,coding-synonymous	ROBO1	NM_001145845.1,NM_002941.3,NM_133631.3	,,	1,113,6050	CC,CT,TT		0.012,2.8457,0.9328	,,	1115/1552,1215/1652,1170/1607	78676701	115,12213	2003	4161	6164	SO:0001819	synonymous_variant	6091	exon26			GGGACATGGCATT	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	10249	protein-coding gene	gene with protein product		602430	"""roundabout (axon guidance receptor, Drosophila) homolog 1"""			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.3645A>G	3.37:g.78676701T>C		268.0	0.0	0		244.0	120.0	0.491803	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Silent	SNP	ENST00000464233.1	37	CCDS54611.1	17	0.007783882783882784	17	0.034552845528455285	0	0.0	0	0.0	0	0.0	T	5.980	0.364753	0.11296	0.028457	1.2E-4	ENSG00000169855	ENST00000472273	.	.	.	5.29	-1.6	0.08426	.	.	.	.	.	T	0.17152	0.0412	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.17137	-1.0379	4	.	.	.	.	1.2302	0.01942	0.174:0.1782:0.1809:0.4669	.	.	.	.	R	142	.	.	H	-	2	0	ROBO1	78759391	0.944000	0.32072	0.963000	0.40424	0.670000	0.39368	0.033000	0.13754	-0.468000	0.06922	-1.447000	0.01057	CAT	T|0.991;C|0.009	0.009	strong		0.413	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941	
PCDHA4	56144	hgsc.bcm.edu	37	5	140188023	140188023	+	Silent	SNP	C	C	T	rs7702779	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140188023C>T	ENST00000530339.1	+	1	1251	c.1251C>T	c.(1249-1251)agC>agT	p.S417S	PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000356878.4_Silent_p.S417S|PCDHA4_ENST00000512229.2_Silent_p.S417S|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	417	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACCGCGAGAGCGTGTCAGCCT	0.612													.|||	285	0.0569089	0.208	0.013	5008	,	,		19748	0.0		0.001	False		,,,				2504	0.0				p.S417S		Atlas-SNP	.											.	PCDHA4	419	.	0			c.C1251T						PASS	.	C	,,,,,	797,3609	321.8+/-297.3	66,665,1472	155.0	146.0	149.0		,,,1251,,1251	-9.0	0.0	5	dbSNP_116	149	2,8598	2.2+/-6.3	0,2,4298	no	intron,intron,intron,coding-synonymous,intron,coding-synonymous	PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_031411.1,NM_031500.1	,,,,,	66,667,5770	TT,TC,CC		0.0233,18.089,6.1433	,,,,,	,,,417/948,,417/799	140188023	799,12207	2203	4300	6503	SO:0001819	synonymous_variant	56144	exon1			CGAGAGCGTGTCA	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.1251C>T	5.37:g.140188023C>T		268.0	0.0	0		295.0	151.0	0.511864	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			C|0.944;T|0.056	0.056	strong		0.612	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
GATAD2B	57459	hgsc.bcm.edu	37	1	153788927	153788927	+	Silent	SNP	G	G	A	rs114813239	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:153788927G>A	ENST00000368655.4	-	7	1281	c.1038C>T	c.(1036-1038)gcC>gcT	p.A346A		NM_020699.2	NP_065750.1	Q8WXI9	P66B_HUMAN	GATA zinc finger domain containing 2B	346	CR2; histone tail-binding.				ATP-dependent chromatin remodeling (GO:0043044)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(5)|lung(12)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	38	all_lung(78;1.34e-32)|Lung NSC(65;1.04e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			CCTGTGAGTTGGCAGCATCAG	0.537													G|||	51	0.0101837	0.0371	0.0029	5008	,	,		19938	0.0		0.0	False		,,,				2504	0.0				p.A346A		Atlas-SNP	.											.	GATAD2B	62	.	0			c.C1038T						PASS	.	G		139,4267	99.4+/-138.0	2,135,2066	105.0	83.0	90.0		1038	4.2	1.0	1	dbSNP_132	90	0,8600		0,0,4300	no	coding-synonymous	GATAD2B	NM_020699.2		2,135,6366	AA,AG,GG		0.0,3.1548,1.0687		346/594	153788927	139,12867	2203	4300	6503	SO:0001819	synonymous_variant	57459	exon7			TGAGTTGGCAGCA	AF411836	CCDS1054.1	1q21.3	2013-01-25			ENSG00000143614	ENSG00000143614		"""GATA zinc finger domain containing"""	30778	protein-coding gene	gene with protein product	"""transcription repressor p66 beta component of the MeCP1 complex"""	614998				10574461, 11756549	Standard	NM_020699		Approved	P66beta	uc001fdb.4	Q8WXI9	OTTHUMG00000037162	ENST00000368655.4:c.1038C>T	1.37:g.153788927G>A		289.0	0.0	0		307.0	144.0	0.469055	NM_020699	D3DUZ2|Q5VUR2|Q7LG68|Q9ULS0	Silent	SNP	ENST00000368655.4	37	CCDS1054.1																																																																																			G|0.987;A|0.013	0.013	strong		0.537	GATAD2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090305.1	NM_020699	
MT-ND4L	4539	hgsc.bcm.edu	37	M	10586	10586	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:10586G>A	ENST00000361335.1	+	1	117	c.117G>A	c.(115-117)tcG>tcA	p.S39S	MT-TR_ENST00000387439.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-ND4_ENST00000361381.2_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-TK_ENST00000387421.1_RNA			P03901	NU4LM_HUMAN	mitochondrially encoded NADH dehydrogenase 4L	39					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(2)|kidney(2)	5						ATAATACTATCGCTGTTCATT	0.418																																					p.S39S		Atlas-SNP	.											.	.	.	.	0			c.G117A						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			ACTATCGCTGTTC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000212907	ENSG00000212907	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7460	protein-coding gene	gene with protein product	"""complex I ND4L subunit"", ""NADH-ubiquinone oxidoreductase chain 4L"""	516004	"""NADH dehydrogenase 4L"""	MTND4L			Standard			Approved	ND4L, NAD4L		P03901		ENST00000361335.1:c.117G>A	M.37:g.10586G>A		14.0	0.0	0		8.0	8.0	1	ENST00000361335		Silent	SNP	ENST00000361335.1	37																																																																																				.	.	none		0.418	MT-ND4L-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024034	
WDR34	89891	hgsc.bcm.edu	37	9	131398633	131398633	+	Silent	SNP	C	C	T	rs61744155	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131398633C>T	ENST00000372715.2	-	4	690	c.630G>A	c.(628-630)ccG>ccA	p.P210P	WDR34_ENST00000483181.1_5'Flank	NM_052844.3	NP_443076.2	Q96EX3	WDR34_HUMAN	WD repeat domain 34	210						axoneme (GO:0005930)|centriole (GO:0005814)|ciliary basal body (GO:0036064)				central_nervous_system(2)|lung(5)|skin(1)|urinary_tract(1)	9						CCACGGCCGACGGCTGCTGGG	0.682													C|||	77	0.0153754	0.056	0.0043	5008	,	,		16542	0.0		0.0	False		,,,				2504	0.0				p.P210P		Atlas-SNP	.											.	WDR34	29	.	0			c.G630A						PASS	.	C		252,4150	136.5+/-172.5	10,232,1959	56.0	49.0	51.0		630	-5.2	0.0	9	dbSNP_129	51	5,8589	3.7+/-12.6	0,5,4292	no	coding-synonymous	WDR34	NM_052844.3		10,237,6251	TT,TC,CC		0.0582,5.7247,1.9775		210/537	131398633	257,12739	2201	4297	6498	SO:0001819	synonymous_variant	89891	exon4			GGCCGACGGCTGC	BC011874	CCDS6906.2	9q34.11	2013-11-15	2013-02-19	2013-02-19	ENSG00000119333	ENSG00000119333		"""WD repeat domain containing"""	28296	protein-coding gene	gene with protein product		613363				19521662, 21953912, 24183451	Standard	NM_052844		Approved	DIC5, MGC20486, bA216B9.3, FAP133	uc004bvq.1	Q96EX3	OTTHUMG00000020750	ENST00000372715.2:c.630G>A	9.37:g.131398633C>T		92.0	0.0	0		110.0	30.0	0.272727	NM_052844	Q5VXV4|Q9BV46	Silent	SNP	ENST00000372715.2	37	CCDS6906.2																																																																																			C|0.978;T|0.022	0.022	strong		0.682	WDR34-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054463.1	NM_052844	
FUCA2	2519	hgsc.bcm.edu	37	6	143816869	143816869	+	Missense_Mutation	SNP	G	G	A	rs151156975		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:143816869G>A	ENST00000002165.6	-	7	1434	c.1379C>T	c.(1378-1380)gCt>gTt	p.A460V	RP1-20N2.6_ENST00000591892.1_RNA|RP1-20N2.6_ENST00000610068.1_RNA|RP1-20N2.6_ENST00000589563.1_RNA	NM_032020.4	NP_114409.2	Q9BTY2	FUCO2_HUMAN	fucosidase, alpha-L- 2, plasma	460					fucose metabolic process (GO:0006004)|glycoside catabolic process (GO:0016139)|regulation of entry of bacterium into host cell (GO:2000535)|response to bacterium (GO:0009617)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)			endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9				OV - Ovarian serous cystadenocarcinoma(155;7.45e-06)|GBM - Glioblastoma multiforme(68;0.0142)		CAGGGCTAGAGCCCAGCCCCA	0.453																																					p.A460V		Atlas-SNP	.											.	FUCA2	28	.	0			c.C1379T						PASS	.	G	VAL/ALA	0,4406		0,0,2203	98.0	82.0	87.0		1379	5.4	0.8	6	dbSNP_134	87	1,8599	1.2+/-3.3	0,1,4299	no	missense	FUCA2	NM_032020.4	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	460/468	143816869	1,13005	2203	4300	6503	SO:0001583	missense	2519	exon7			GCTAGAGCCCAGC	BC003060	CCDS5200.1	6q24	2012-10-02			ENSG00000001036	ENSG00000001036	3.2.1.51		4008	protein-coding gene	gene with protein product		136820				6590153	Standard	NM_032020		Approved	MGC1314, dJ20N2.5	uc003qjm.3	Q9BTY2	OTTHUMG00000015728	ENST00000002165.6:c.1379C>T	6.37:g.143816869G>A	ENSP00000002165:p.Ala460Val	109.0	0.0	0		120.0	66.0	0.55	NM_032020	E9PEB6|Q7Z6V1|Q7Z6Y2|Q8NBK4	Missense_Mutation	SNP	ENST00000002165.6	37	CCDS5200.1	.	.	.	.	.	.	.	.	.	.	G	2.438	-0.329383	0.05314	0.0	1.16E-4	ENSG00000001036	ENST00000002165	T	0.50001	0.76	5.44	5.44	0.79542	.	0.495248	0.23750	N	0.044936	T	0.10423	0.0255	N	0.05383	-0.06	0.80722	D	1	B	0.02656	0.0	B	0.08055	0.003	T	0.12041	-1.0563	10	0.02654	T	1	-0.6766	12.588	0.56428	0.0758:0.0:0.9242:0.0	.	460	Q9BTY2	FUCO2_HUMAN	V	460	ENSP00000002165:A460V	ENSP00000002165:A460V	A	-	2	0	FUCA2	143858562	0.998000	0.40836	0.842000	0.33263	0.068000	0.16541	6.197000	0.72100	2.575000	0.86900	0.650000	0.86243	GCT	G|1.000;A|0.000	0.000	weak		0.453	FUCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042521.2	NM_032020	
CSTB	1476	hgsc.bcm.edu	37	21	45196136	45196136	+	Silent	SNP	C	C	A	rs4533	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45196136C>A	ENST00000291568.5	-	1	190	c.15G>T	c.(13-15)gcG>gcT	p.A5A		NM_000100.3	NP_000091.1	P04080	CYTB_HUMAN	cystatin B (stefin B)	5					adult locomotory behavior (GO:0008344)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|endopeptidase inhibitor activity (GO:0004866)|poly(A) RNA binding (GO:0044822)|protease binding (GO:0002020)			lung(1)|prostate(1)	2				STAD - Stomach adenocarcinoma(101;0.168)		TGGCGGAGGGCGCCCCGCACA	0.746													C|||	86	0.0171725	0.062	0.0058	5008	,	,		9141	0.0		0.0	False		,,,				2504	0.0				p.A5A	Esophageal Squamous(58;831 1093 17019 29789 35147)	Atlas-SNP	.											.	CSTB	3	.	0			c.G15T						PASS	.	C		142,3048		0,142,1453	4.0	7.0	6.0		15	1.4	0.0	21	dbSNP_52	6	2,5900		0,2,2949	no	coding-synonymous	CSTB	NM_000100.2		0,144,4402	AA,AC,CC		0.0339,4.4514,1.5838		5/99	45196136	144,8948	1595	2951	4546	SO:0001819	synonymous_variant	1476	exon1			GGAGGGCGCCCCG	L03558	CCDS13701.1	21q22.3	2014-09-17			ENSG00000160213	ENSG00000160213			2482	protein-coding gene	gene with protein product		601145		EPM1, STFB		8596935	Standard	NM_000100		Approved	CST6, PME	uc002zdr.4	P04080	OTTHUMG00000086886	ENST00000291568.5:c.15G>T	21.37:g.45196136C>A		13.0	0.0	0		28.0	16.0	0.571429	NM_000100		Silent	SNP	ENST00000291568.5	37	CCDS13701.1																																																																																			C|0.988;A|0.012	0.012	strong		0.746	CSTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195689.1	NM_000100	
KRTAP10-3	386682	hgsc.bcm.edu	37	21	45978128	45978128	+	Silent	SNP	G	G	A	rs186210430	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45978128G>A	ENST00000391620.1	-	1	515	c.471C>T	c.(469-471)tcC>tcT	p.S157S	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198696.2	NP_941969.2	P60369	KR103_HUMAN	keratin associated protein 10-3	157	18 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				kidney(1)|lung(4)|prostate(1)|skin(1)	7						GGAGGGACACGGAGGAGGAGG	0.692													G|||	70	0.0139776	0.0484	0.0086	5008	,	,		16657	0.0		0.0	False		,,,				2504	0.0				p.S157S		Atlas-SNP	.											.	KRTAP10-3	17	.	0			c.C471T						PASS	.	G	,	263,4143	147.3+/-181.8	4,255,1944	90.0	98.0	95.0		,471	-5.3	0.0	21		95	0,8600		0,0,4300	no	intron,coding-synonymous	TSPEAR,KRTAP10-3	NM_144991.2,NM_198696.2	,	4,255,6244	AA,AG,GG		0.0,5.9691,2.0221	,	,157/222	45978128	263,12743	2203	4300	6503	SO:0001819	synonymous_variant	386682	exon1			GGACACGGAGGAG	AJ566383	CCDS42956.1	21q22.3	2007-10-05			ENSG00000212935	ENSG00000212935		"""Keratin associated proteins"""	22968	protein-coding gene	gene with protein product				KRTAP18-3			Standard	NM_198696		Approved	KAP10.3, KAP18.3	uc002zfj.1	P60369	OTTHUMG00000057628	ENST00000391620.1:c.471C>T	21.37:g.45978128G>A		149.0	0.0	0		189.0	99.0	0.52381	NM_198696	A3KN67|Q70LJ4	Silent	SNP	ENST00000391620.1	37	CCDS42956.1																																																																																			G|0.992;A|0.008	0.008	strong		0.692	KRTAP10-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128031.1		
TRIML1	339976	hgsc.bcm.edu	37	4	189061010	189061010	+	Missense_Mutation	SNP	A	A	G	rs111308948	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:189061010A>G	ENST00000332517.3	+	1	438	c.298A>G	c.(298-300)Acc>Gcc	p.T100A	RP11-366H4.3_ENST00000501322.2_RNA	NM_178556.3	NP_848651.2	Q8N9V2	TRIML_HUMAN	tripartite motif family-like 1	100					multicellular organismal development (GO:0007275)|protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	60		all_cancers(14;1.33e-43)|all_epithelial(14;7.86e-31)|all_lung(41;4.3e-13)|Lung NSC(41;9.69e-13)|Melanoma(20;7.86e-05)|Breast(6;0.000148)|Hepatocellular(41;0.0218)|Renal(120;0.0376)|Prostate(90;0.0513)|all_hematologic(60;0.062)		OV - Ovarian serous cystadenocarcinoma(60;1.52e-11)|BRCA - Breast invasive adenocarcinoma(30;4.19e-06)|GBM - Glioblastoma multiforme(59;0.000232)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.156)		GAGGATGCCCACCACTGCCAA	0.647													G|||	203	0.0405351	0.1445	0.0159	5008	,	,		18008	0.0		0.001	False		,,,				2504	0.0				p.T100A	Melanoma(31;213 1036 16579 23968 32372)	Atlas-SNP	.											.	TRIML1	126	.	0			c.A298G						PASS	.	G	ALA/THR	538,3868	767.9+/-413.5	40,458,1705	41.0	40.0	41.0		298	3.3	0.0	4	dbSNP_132	41	0,8600		0,0,4300	yes	missense	TRIML1	NM_178556.3	58	40,458,6005	GG,GA,AA		0.0,12.2106,4.1366	benign	100/469	189061010	538,12468	2203	4300	6503	SO:0001583	missense	339976	exon1			ATGCCCACCACTG	AK093499	CCDS3851.1	4q35.2	2013-01-09			ENSG00000184108	ENSG00000184108		"""RING-type (C3HC4) zinc fingers"""	26698	protein-coding gene	gene with protein product						12477932	Standard	NM_178556		Approved	FLJ36180, RNF209	uc003izm.1	Q8N9V2	OTTHUMG00000160237	ENST00000332517.3:c.298A>G	4.37:g.189061010A>G	ENSP00000327738:p.Thr100Ala	134.0	0.0	0		156.0	73.0	0.467949	NM_178556	Q96BE5	Missense_Mutation	SNP	ENST00000332517.3	37	CCDS3851.1	78	0.03571428571428571	71	0.1443089430894309	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	G	0.714	-0.786047	0.02907	0.122106	0.0	ENSG00000184108	ENST00000332517	T	0.61040	0.14	5.06	3.27	0.37495	.	0.559255	0.16346	N	0.218439	T	0.00144	0.0004	N	0.00347	-1.61	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.05649	-1.0872	9	0.42905	T	0.14	-6.5562	4.0011	0.09580	0.191:0.0:0.6206:0.1884	.	100	Q8N9V2	TRIML_HUMAN	A	100	ENSP00000327738:T100A	ENSP00000327738:T100A	T	+	1	0	TRIML1	189298004	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	0.371000	0.20450	0.776000	0.33473	-0.215000	0.12644	ACC	A|0.962;G|0.038	0.038	strong		0.647	TRIML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359813.1	NM_178556	
CPN2	1370	hgsc.bcm.edu	37	3	194062821	194062821	+	Missense_Mutation	SNP	G	G	A	rs146126834	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:194062821G>A	ENST00000323830.3	-	2	700	c.611C>T	c.(610-612)gCg>gTg	p.A204V	CPN2_ENST00000429275.1_Missense_Mutation_p.A204V	NM_001080513.2	NP_001073982	P22792	CPN2_HUMAN	carboxypeptidase N, polypeptide 2	204					protein stabilization (GO:0050821)|regulation of catalytic activity (GO:0050790)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	enzyme regulator activity (GO:0030234)	p.A204V(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(11)|ovary(5)|prostate(1)	27	all_cancers(143;5.31e-09)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;2.2e-17)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;4.65e-05)		ACCAGAGAGCGCGTTGTTGCT	0.617													G|||	13	0.00259585	0.0083	0.0014	5008	,	,		20075	0.0		0.001	False		,,,				2504	0.0				p.A204V		Atlas-SNP	.											CPN2,NS,carcinoma,0,1	CPN2	56	1	1	Substitution - Missense(1)	endometrium(1)	c.C611T						PASS	.	G	VAL/ALA	46,4360	48.2+/-83.0	0,46,2157	47.0	52.0	50.0		611	-3.7	0.0	3	dbSNP_134	50	1,8599	1.2+/-3.3	0,1,4299	yes	missense	CPN2	NM_001080513.2	64	0,47,6456	AA,AG,GG		0.0116,1.044,0.3614	benign	204/546	194062821	47,12959	2203	4300	6503	SO:0001583	missense	1370	exon2			GAGAGCGCGTTGT	J05158	CCDS33920.1	3q29	2012-02-10	2007-02-23		ENSG00000178772	ENSG00000178772	3.4.17.3		2313	protein-coding gene	gene with protein product		603104	"""carboxypeptidase N, polypeptide 2, 83kD"""	ACBP		2378615, 9628828	Standard	XM_005269280		Approved		uc003fts.3	P22792	OTTHUMG00000156047	ENST00000323830.3:c.611C>T	3.37:g.194062821G>A	ENSP00000319464:p.Ala204Val	124.0	0.0	0		142.0	77.0	0.542253	NM_001080513	B2RPE7|Q86SU4|Q8N5V4	Missense_Mutation	SNP	ENST00000323830.3	37	CCDS33920.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	5.618	0.298668	0.10622	0.01044	1.16E-4	ENSG00000178772	ENST00000323830;ENST00000429275	T;T	0.57907	0.37;0.37	4.77	-3.7	0.04437	.	1.593460	0.04366	N	0.358343	T	0.19127	0.0459	N	0.25031	0.7	0.09310	N	1	P	0.39520	0.676	B	0.25759	0.063	T	0.14531	-1.0469	10	0.29301	T	0.29	.	1.8943	0.03254	0.2691:0.1002:0.1357:0.495	.	204	P22792	CPN2_HUMAN	V	204	ENSP00000319464:A204V;ENSP00000402232:A204V	ENSP00000319464:A204V	A	-	2	0	CPN2	195544516	0.000000	0.05858	0.000000	0.03702	0.297000	0.27493	-2.161000	0.01278	-0.371000	0.08004	-0.305000	0.09177	GCG	G|0.996;A|0.004	0.004	strong		0.617	CPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342856.2	NM_001080513	
USP34	9736	hgsc.bcm.edu	37	2	61433919	61433919	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:61433919T>C	ENST00000398571.2	-	71	9098	c.9022A>G	c.(9022-9024)Aca>Gca	p.T3008A	USP34_ENST00000472689.1_5'Flank	NM_014709.3	NP_055524.3	Q70CQ2	UBP34_HUMAN	ubiquitin specific peptidase 34	3008					positive regulation of canonical Wnt signaling pathway (GO:0090263)|protein deubiquitination (GO:0016579)|protein K48-linked deubiquitination (GO:0071108)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)		cysteine-type endopeptidase activity (GO:0004197)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			autonomic_ganglia(1)|breast(14)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(24)|lung(52)|ovary(8)|prostate(10)|skin(6)|urinary_tract(2)	138			Epithelial(17;0.229)			TAAGGGCGTGTAGACTTCAAA	0.388																																					p.T3008A		Atlas-SNP	.											.	USP34	334	.	0			c.A9022G						PASS	.						69.0	64.0	66.0					2																	61433919		1842	4099	5941	SO:0001583	missense	9736	exon71			GGCGTGTAGACTT	AB011142	CCDS42686.1	2p16.1-p15	2005-08-08	2005-08-08		ENSG00000115464	ENSG00000115464		"""Ubiquitin-specific peptidases"""	20066	protein-coding gene	gene with protein product		615295	"""ubiquitin specific protease 34"""			12838346	Standard	NM_014709		Approved	KIAA0570, KIAA0729	uc002sbe.3	Q70CQ2	OTTHUMG00000152265	ENST00000398571.2:c.9022A>G	2.37:g.61433919T>C	ENSP00000381577:p.Thr3008Ala	101.0	0.0	0		89.0	40.0	0.449438	NM_014709	A8MWD0|B3KWU9|O60316|O94834|Q3B777|Q6P6C9|Q7L8P6|Q8N3T9|Q8TBW2|Q9UGA1	Missense_Mutation	SNP	ENST00000398571.2	37	CCDS42686.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.32|16.32	3.090012|3.090012	0.55968|0.55968	.|.	.|.	ENSG00000115464|ENSG00000115464	ENST00000263989;ENST00000398571|ENST00000411912	T|.	0.64438|.	-0.1|.	5.82|5.82	5.82|5.82	0.92795|0.92795	Armadillo-type fold (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.53351|0.53351	0.1791|0.1791	N|N	0.22421|0.22421	0.69|0.69	0.80722|0.80722	D|D	1|1	P|.	0.52842|.	0.956|.	D|.	0.65010|.	0.931|.	T|T	0.50074|0.50074	-0.8870|-0.8870	10|5	0.19590|.	T|.	0.45|.	.|.	16.19|16.19	0.81981|0.81981	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	3008|.	Q70CQ2|.	UBP34_HUMAN|.	A|C	2856;3008|767	ENSP00000381577:T3008A|.	ENSP00000263989:T2856A|.	T|Y	-|-	1|2	0|0	USP34|USP34	61287423|61287423	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	6.295000|6.295000	0.72744|0.72744	2.225000|2.225000	0.72522|0.72522	0.460000|0.460000	0.39030|0.39030	ACA|TAC	.	.	none		0.388	USP34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325650.4		
TRAM1L1	133022	hgsc.bcm.edu	37	4	118005458	118005458	+	Silent	SNP	C	C	T	rs35809332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:118005458C>T	ENST00000310754.4	-	1	1278	c.1092G>A	c.(1090-1092)agG>agA	p.R364R		NM_152402.2	NP_689615.2	Q8N609	TR1L1_HUMAN	translocation associated membrane protein 1-like 1	364					protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22						ATTTCTCTTTCCTCTTTGGCG	0.378													C|||	56	0.0111821	0.0401	0.0043	5008	,	,		18119	0.0		0.0	False		,,,				2504	0.0				p.R364R		Atlas-SNP	.											.	TRAM1L1	55	.	0			c.G1092A						PASS	.	C		161,4245	94.8+/-133.5	4,153,2046	135.0	140.0	138.0		1092	2.9	1.0	4	dbSNP_126	138	0,8600		0,0,4300	no	coding-synonymous	TRAM1L1	NM_152402.2		4,153,6346	TT,TC,CC		0.0,3.6541,1.2379		364/370	118005458	161,12845	2203	4300	6503	SO:0001819	synonymous_variant	133022	exon1			CTCTTTCCTCTTT	AK074617	CCDS3707.1	4q26	2008-02-05			ENSG00000174599	ENSG00000174599			28371	protein-coding gene	gene with protein product						12477932	Standard	NM_152402		Approved	MGC26568	uc003ibv.4	Q8N609	OTTHUMG00000132956	ENST00000310754.4:c.1092G>A	4.37:g.118005458C>T		205.0	0.0	0		199.0	94.0	0.472362	NM_152402	Q8N2L7	Silent	SNP	ENST00000310754.4	37	CCDS3707.1																																																																																			C|0.987;T|0.013	0.013	strong		0.378	TRAM1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256513.1	NM_152402	
EXT2	2132	hgsc.bcm.edu	37	11	44129386	44129386	+	Missense_Mutation	SNP	A	A	G	rs4755779	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:44129386A>G	ENST00000343631.3	+	2	253	c.124A>G	c.(124-126)Atg>Gtg	p.M42V	EXT2_ENST00000395673.3_Missense_Mutation_p.M75V|EXT2_ENST00000533608.1_Missense_Mutation_p.M42V|EXT2_ENST00000358681.4_Missense_Mutation_p.M42V			Q93063	EXT2_HUMAN	exostosin glycosyltransferase 2	42			M -> V (in dbSNP:rs4755779).		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						TGCCACTGGCATGTTTCAGTT	0.527			"""Mis, N, F, S"""			"""exostoses, osteosarcoma"""			Hereditary Multiple Exostoses				A|||	65	0.0129792	0.0492	0.0	5008	,	,		19628	0.0		0.0	False		,,,				2504	0.0				p.M75V		Atlas-SNP	.	yes	Rec		Multiple Exostoses Type 2	11	11p12-p11	2132	multiple exostoses type 2 gene		M	.	EXT2	129	.	0			c.A223G						PASS	.	A	VAL/MET,VAL/MET,VAL/MET	215,4191	132.1+/-168.6	3,209,1991	158.0	164.0	162.0		223,124,124	-1.5	1.0	11	dbSNP_111	162	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	EXT2	NM_000401.3,NM_001178083.1,NM_207122.1	21,21,21	3,210,6290	GG,GA,AA		0.0116,4.8797,1.6608	benign,benign,benign	75/752,42/729,42/719	44129386	216,12790	2203	4300	6503	SO:0001583	missense	2132	exon2	Familial Cancer Database	HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	ACTGGCATGTTTC		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.124A>G	11.37:g.44129386A>G	ENSP00000342656:p.Met42Val	188.0	0.0	0		204.0	98.0	0.480392	NM_000401	B2R5Z6|C9JU51|J3KPT2|O15288	Missense_Mutation	SNP	ENST00000343631.3	37	CCDS7908.1	24	0.01098901098901099	24	0.04878048780487805	0	0.0	0	0.0	0	0.0	A	9.644	1.139669	0.21205	0.048797	1.16E-4	ENSG00000151348	ENST00000533608;ENST00000532479;ENST00000527014;ENST00000358681;ENST00000395673;ENST00000343631	T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95	5.45	-1.52	0.08637	.	0.204155	0.64402	N	0.000019	T	0.03095	0.0091	N	0.24115	0.695	0.43814	D	0.996377	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	0.17018	-1.0383	10	0.07990	T	0.79	-5.2768	8.2837	0.31915	0.5707:0.1043:0.3249:0.0	rs4755779;rs52810595;rs4755779	42;42;42;42;55	Q6NUL1;C9JU51;Q93063-2;Q93063;D3DR24	.;.;.;EXT2_HUMAN;.	V	42;42;42;42;75;42	ENSP00000431173:M42V;ENSP00000433827:M42V;ENSP00000434716:M42V;ENSP00000351509:M42V;ENSP00000379032:M75V;ENSP00000342656:M42V	ENSP00000342656:M42V	M	+	1	0	EXT2	44085962	1.000000	0.71417	0.996000	0.52242	0.995000	0.86356	1.323000	0.33701	-0.161000	0.10983	0.528000	0.53228	ATG	A|0.981;G|0.019	0.019	strong		0.527	EXT2-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390074.1	NM_000401	
OBSCN	84033	hgsc.bcm.edu	37	1	228504486	228504486	+	Silent	SNP	G	G	A	rs372827129	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228504486G>A	ENST00000422127.1	+	51	13406	c.13362G>A	c.(13360-13362)acG>acA	p.T4454T	OBSCN_ENST00000366707.4_Silent_p.T2088T|OBSCN_ENST00000570156.2_Silent_p.T5411T|OBSCN_ENST00000366709.4_Silent_p.T1573T|OBSCN_ENST00000284548.11_Silent_p.T4454T	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4454	Ig-like 46.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TCACCTGCACGCTCAGCGAGG	0.672													g|||	36	0.0071885	0.0272	0.0	5008	,	,		15193	0.0		0.0	False		,,,				2504	0.0				p.T5411T		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G16233A						PASS	.		,	111,4087		0,111,1988	16.0	21.0	19.0		13362,13362	-0.1	0.1	1		19	0,8410		0,0,4205	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	0,111,6193	AA,AG,GG		0.0,2.6441,0.8804	,	4454/7969,4454/6621	228504486	111,12497	2099	4205	6304	SO:0001819	synonymous_variant	84033	exon62			CTGCACGCTCAGC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.13362G>A	1.37:g.228504486G>A		65.0	0.0	0		99.0	60.0	0.606061	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			.	.	none		0.672	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
BUB1B	701	hgsc.bcm.edu	37	15	40453430	40453430	+	Silent	SNP	G	G	T	rs7168394	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:40453430G>T	ENST00000287598.6	+	1	204	c.9G>T	c.(7-9)gcG>gcT	p.A3A	BUB1B_ENST00000560120.1_3'UTR|BUB1B_ENST00000412359.3_Silent_p.A3A	NM_001211.5	NP_001202	O60566	BUB1B_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase B	3					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|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)|protein localization to chromosome, centromeric region (GO:0071459)|protein localization to kinetochore (GO:0034501)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|condensed chromosome kinetochore (GO:0000777)|condensed chromosome outer kinetochore (GO:0000940)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|perinuclear region of cytoplasm (GO:0048471)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(1)|stomach(2)|urinary_tract(2)	36		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)		GGATGGCGGCGGTGAAGAAGG	0.637			"""Mis, N, F, S"""			rhabdomyosarcoma			Mosaic Variegated Aneuploidy Syndrome				G|||	335	0.066893	0.2458	0.0144	5008	,	,		17894	0.0		0.0	False		,,,				2504	0.0				p.A3A		Atlas-SNP	.	yes	Rec		Mosaic variegated aneuploidy	15	15q15	701	BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast)		M	.	BUB1B	71	.	0			c.G9T						PASS	.	G		761,3645	297.3+/-284.7	70,621,1512	66.0	54.0	58.0		9	1.1	0.0	15	dbSNP_116	58	18,8582	12.6+/-44.7	0,18,4282	no	coding-synonymous	BUB1B	NM_001211.5		70,639,5794	TT,TG,GG		0.2093,17.2719,5.9895		3/1051	40453430	779,12227	2203	4300	6503	SO:0001819	synonymous_variant	701	exon1	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	GGCGGCGGTGAAG	AF107297	CCDS10053.1	15q15	2014-09-17	2013-01-17		ENSG00000156970	ENSG00000156970			1149	protein-coding gene	gene with protein product		602860	"""budding uninhibited by benzimidazoles 1 (yeast homolog), beta"", ""budding uninhibited by benzimidazoles 1 homolog beta (yeast)"""			9889005	Standard	NM_001211		Approved	BUBR1, MAD3L, Bub1A, SSK1	uc001zkx.4	O60566	OTTHUMG00000129877	ENST00000287598.6:c.9G>T	15.37:g.40453430G>T		126.0	0.0	0		136.0	74.0	0.544118	NM_001211	B2R6U0|B4DL09|B4DLG3|O60501|O60627|O60758|O75389|Q59HH6|Q8WV50|Q96KM4	Silent	SNP	ENST00000287598.6	37	CCDS10053.1																																																																																			G|0.922;T|0.078	0.078	strong		0.637	BUB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252122.4		
NACA2	342538	hgsc.bcm.edu	37	17	59668275	59668275	+	Silent	SNP	T	T	A	rs61739271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:59668275T>A	ENST00000521764.1	-	1	288	c.267A>T	c.(265-267)acA>acT	p.T89T		NM_199290.3	NP_954984.1	Q9H009	NACA2_HUMAN	nascent polypeptide-associated complex alpha subunit 2	89	NAC-A/B. {ECO:0000255|PROSITE- ProRule:PRU00507}.				myoblast migration (GO:0051451)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			large_intestine(1)|lung(5)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	12	all_epithelial(1;3.12e-14)					TAGTAACTCCTGTAACCTGTA	0.443													T|||	198	0.0395367	0.1415	0.0144	5008	,	,		21980	0.0		0.001	False		,,,				2504	0.0				p.T89T		Atlas-SNP	.											.	NACA2	33	.	0			c.A267T						PASS	.	T		554,3852	249.6+/-257.0	38,478,1687	231.0	226.0	228.0		267	0.8	1.0	17	dbSNP_129	228	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	NACA2	NM_199290.3		38,480,5985	AA,AT,TT		0.0233,12.5738,4.275		89/216	59668275	556,12450	2203	4300	6503	SO:0001819	synonymous_variant	342538	exon1			AACTCCTGTAACC	BC062710	CCDS11630.1	17q23.3	2014-01-28	2007-04-20	2007-04-20		ENSG00000253506			23290	protein-coding gene	gene with protein product	"""alpha-NAC protein"""	609274	"""nascent-polypeptide-associated complex alpha polypeptide-like"""	NACAL		12406326	Standard	NM_199290		Approved	MGC71999	uc002izj.2	Q9H009		ENST00000521764.1:c.267A>T	17.37:g.59668275T>A		310.0	0.0	0		257.0	134.0	0.521401	NM_199290	Q2VIR9	Silent	SNP	ENST00000521764.1	37	CCDS11630.1																																																																																			T|0.957;A|0.043	0.043	strong		0.443	NACA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255437.2	NM_199290	
ZNF469	84627	hgsc.bcm.edu	37	16	88495021	88495021	+	Silent	SNP	C	C	A	rs74032864	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88495021C>A	ENST00000437464.1	+	1	1143	c.1143C>A	c.(1141-1143)ccC>ccA	p.P381P	ZNF469_ENST00000565624.1_Silent_p.P381P	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	381	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						AAATCCTTCCCGAAAGACCAC	0.617													C|||	256	0.0511182	0.1838	0.0187	5008	,	,		14646	0.0		0.0	False		,,,				2504	0.0				p.P381P		Atlas-SNP	.											.	ZNF469	121	.	0			c.C1143A						PASS	.						7.0	9.0	8.0					16																	88495021		683	1565	2248	SO:0001819	synonymous_variant	84627	exon1			CCTTCCCGAAAGA	AB058761	CCDS45544.1	16q24	2010-08-04				ENSG00000225614		"""Zinc fingers, C2H2-type"""	23216	protein-coding gene	gene with protein product		612078				11347906	Standard	NM_001127464		Approved	KIAA1858	uc002fku.2	Q96JG9		ENST00000437464.1:c.1143C>A	16.37:g.88495021C>A		32.0	0.0	0		53.0	53.0	1	NM_001127464		Silent	SNP	ENST00000437464.1	37	CCDS45544.1																																																																																			C|0.956;A|0.044	0.044	strong		0.617	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
TAS2R30	259293	hgsc.bcm.edu	37	12	11286688	11286688	+	Silent	SNP	C	C	T	rs375822837		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:11286688C>T	ENST00000539585.1	-	1	555	c.156G>A	c.(154-156)gcG>gcA	p.A52A	TAS2R14_ENST00000381852.4_Intron|PRR4_ENST00000536668.1_Intron	NM_001097643.1	NP_001091112.1	P59541	T2R30_HUMAN	taste receptor, type 2, member 30	52					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			autonomic_ganglia(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	13						CTCTGGAGACCGCCAGAGCAG	0.388																																					p.A52A		Atlas-SNP	.											.	TAS2R30	28	.	0			c.G156A						PASS	.	C		2,4110		0,2,2054	78.0	79.0	79.0		156	-5.4	0.0	12		79	0,8504		0,0,4252	no	coding-synonymous	TAS2R30	NM_001097643.1		0,2,6306	TT,TC,CC		0.0,0.0486,0.0159		52/320	11286688	2,12614	2056	4252	6308	SO:0001819	synonymous_variant	259293	exon1			GGAGACCGCCAGA	AX097746, AF494233	CCDS53750.1	12p13.2	2012-08-22				ENSG00000256188		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	19112	protein-coding gene	gene with protein product		613963	"""taste receptor, type 2, member 47"""	TAS2R47			Standard	NM_001097643		Approved	T2R30	uc009zhs.1	P59541		ENST00000539585.1:c.156G>A	12.37:g.11286688C>T		305.0	1.0	0.00327869		357.0	187.0	0.52381	NM_001097643	Q645X7	Silent	SNP	ENST00000539585.1	37	CCDS53750.1																																																																																			.	.	weak		0.388	TAS2R30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400238.1	NM_001097643	
SUPT16H	11198	hgsc.bcm.edu	37	14	21841524	21841524	+	Silent	SNP	A	A	G	rs75576875	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:21841524A>G	ENST00000216297.2	-	2	470	c.132T>C	c.(130-132)atT>atC	p.I44I		NM_007192.3	NP_009123.1	Q9Y5B9	SP16H_HUMAN	suppressor of Ty 16 homolog (S. cerevisiae)	44					DNA repair (GO:0006281)|DNA replication (GO:0006260)|gene expression (GO:0010467)|nucleosome disassembly (GO:0006337)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	chromosome (GO:0005694)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(4)|kidney(1)|large_intestine(9)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	27	all_cancers(95;0.00115)		Epithelial(56;1.62e-06)|all cancers(55;1.49e-05)	GBM - Glioblastoma multiforme(265;0.0159)		TGGCATAAACAATTTCTTCAT	0.378													A|||	80	0.0159744	0.059	0.0029	5008	,	,		18715	0.0		0.0	False		,,,				2504	0.0				p.I44I		Atlas-SNP	.											.	SUPT16H	84	.	0			c.T132C						PASS	.	A		224,4182	134.9+/-171.1	5,214,1984	179.0	159.0	166.0		132	1.9	1.0	14	dbSNP_132	166	0,8600	1.2+/-3.3	0,0,4300	no	coding-synonymous	SUPT16H	NM_007192.3		5,214,6284	GG,GA,AA		0.0,5.084,1.7223		44/1048	21841524	224,12782	2203	4300	6503	SO:0001819	synonymous_variant	11198	exon2			ATAAACAATTTCT	AF152961	CCDS9569.1	14q11.1	2008-08-13	2001-11-28		ENSG00000092201	ENSG00000092201			11465	protein-coding gene	gene with protein product	"""facilitates chromatin remodeling 140 kDa subunit"""	605012	"""suppressor of Ty (S.cerevisiae) 16 homolog"""			9489704, 11239457	Standard	NM_007192		Approved	FACT, FACTP140, SPT16/CDC68, FLJ14010, FLJ10857, CDC68	uc001wao.2	Q9Y5B9	OTTHUMG00000029685	ENST00000216297.2:c.132T>C	14.37:g.21841524A>G		126.0	0.0	0		170.0	84.0	0.494118	NM_007192	Q6GMT8|Q6P2F1|Q6PJM1|Q9NRX0	Silent	SNP	ENST00000216297.2	37	CCDS9569.1																																																																																			A|0.985;G|0.015	0.015	strong		0.378	SUPT16H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074025.2		
ZCCHC9	84240	hgsc.bcm.edu	37	5	80608363	80608363	+	Splice_Site	SNP	A	A	C	rs144053491	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:80608363A>C	ENST00000254037.2	+	5	3853	c.698A>C	c.(697-699)gAg>gCg	p.E233A	ZCCHC9_ENST00000380199.5_Splice_Site_p.E233A|ZCCHC9_ENST00000506458.1_3'UTR|ZCCHC9_ENST00000438268.2_Splice_Site_p.E233A|ZCCHC9_ENST00000407610.3_Splice_Site_p.E233A			Q8N567	ZCHC9_HUMAN	zinc finger, CCHC domain containing 9	233					negative regulation of phosphatase activity (GO:0010923)		poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)	13		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;8.18e-45)|Epithelial(54;2.72e-39)|all cancers(79;7.33e-34)		TCCTTTACAGAGCGAATGGTC	0.368													A|||	2	0.000399361	0.0015	0.0	5008	,	,		20172	0.0		0.0	False		,,,				2504	0.0				p.E233A		Atlas-SNP	.											.	ZCCHC9	26	.	0			c.A698C						PASS	.	A	ALA/GLU,ALA/GLU,ALA/GLU	19,4387	27.2+/-55.0	1,17,2185	75.0	73.0	74.0		698,698,698	5.9	0.9	5	dbSNP_134	74	0,8600		0,0,4300	yes	missense-near-splice,missense-near-splice,missense-near-splice	ZCCHC9	NM_001131035.1,NM_001131036.1,NM_032280.2	107,107,107	1,17,6485	CC,CA,AA		0.0,0.4312,0.1461	benign,benign,benign	233/272,233/272,233/272	80608363	19,12987	2203	4300	6503	SO:0001630	splice_region_variant	84240	exon6			TTACAGAGCGAAT	BC014841	CCDS4054.1	5q14.1	2013-01-09			ENSG00000131732	ENSG00000131732		"""Zinc fingers, CCHC domain containing"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25424	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 41"""					12477932	Standard	NM_032280		Approved	DKFZp761J139, PPP1R41	uc003khi.3	Q8N567	OTTHUMG00000119014	ENST00000254037.2:c.698-1A>C	5.37:g.80608363A>C		116.0	0.0	0		107.0	54.0	0.504673	NM_001131036	B2RAE7|Q9H027	Missense_Mutation	SNP	ENST00000254037.2	37	CCDS4054.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	A	10.88	1.474400	0.26423	0.004312	0.0	ENSG00000131732	ENST00000254037;ENST00000407610;ENST00000380199;ENST00000438268	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	5.89	5.89	0.94794	.	0.392038	0.30302	N	0.009933	T	0.20047	0.0482	N	0.03608	-0.345	0.29325	N	0.867064	B	0.06786	0.001	B	0.06405	0.002	T	0.13072	-1.0523	9	.	.	.	.	11.9071	0.52719	0.8547:0.1453:0.0:0.0	.	233	Q8N567	ZCHC9_HUMAN	A	233	ENSP00000254037:E233A;ENSP00000385047:E233A;ENSP00000369546:E233A;ENSP00000412637:E233A	.	E	+	2	0	ZCCHC9	80644119	0.991000	0.36638	0.942000	0.38095	0.749000	0.42624	2.913000	0.48790	2.246000	0.74042	0.533000	0.62120	GAG	A|0.998;C|0.002	0.002	strong		0.368	ZCCHC9-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239213.1	NM_032280	Missense_Mutation
MUC4	4585	hgsc.bcm.edu	37	3	195507851	195507851	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195507851C>G	ENST00000463781.3	-	2	11059	c.10600G>C	c.(10600-10602)Gcc>Ccc	p.A3534P	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A3534P	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)		AGAGGCGTGGCGTGACCGGTG	0.612																																					p.A3534P		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.G10600C						PASS	.						31.0	30.0	31.0					3																	195507851		674	1579	2253	SO:0001583	missense	4585	exon2			GCGTGGCGTGACC	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.10600G>C	3.37:g.195507851C>G	ENSP00000417498:p.Ala3534Pro	473.0	1.0	0.00211416		242.0	142.0	0.586777	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	8.586	0.883527	0.17467	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30448	1.53;1.55	0.743	-0.725	0.11174	.	0.326178	0.13539	U	0.380396	T	0.14098	0.0341	N	0.19112	0.55	0.09310	N	1	B	0.31581	0.329	B	0.28784	0.094	T	0.20371	-1.0277	9	.	.	.	.	4.4534	0.11631	0.0:0.67:0.0:0.33	.	3406	E7ESK3	.	P	3534	ENSP00000417498:A3534P;ENSP00000420243:A3534P	.	A	-	1	0	MUC4	196992630	0.000000	0.05858	0.019000	0.16419	0.019000	0.09904	-1.527000	0.02227	0.088000	0.17205	0.089000	0.15464	GCC	.	.	none		0.612	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CHD1L	9557	hgsc.bcm.edu	37	1	146757092	146757092	+	Missense_Mutation	SNP	A	A	C	rs13374920	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:146757092A>C	ENST00000369258.4	+	17	1966	c.1946A>C	c.(1945-1947)gAa>gCa	p.E649A	CHD1L_ENST00000467213.1_3'UTR|CHD1L_ENST00000369259.3_Missense_Mutation_p.E445A|CHD1L_ENST00000361293.5_Missense_Mutation_p.E368A|CHD1L_ENST00000431239.1_Missense_Mutation_p.E555A	NM_001256336.1|NM_004284.4|NM_024568.2	NP_001243265.1|NP_004275.4|NP_078844.2	Q86WJ1	CHD1L_HUMAN	chromodomain helicase DNA binding protein 1-like	649			E -> A (in dbSNP:rs13374920).		ATP catabolic process (GO:0006200)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA duplex unwinding (GO:0032508)|DNA repair (GO:0006281)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|nucleotide binding (GO:0000166)			breast(2)|endometrium(4)|kidney(1)|large_intestine(4)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(923;0.0487)					AAAAGACAAGAAGCAGCTGCC	0.493													A|||	114	0.0227636	0.0825	0.0058	5008	,	,		19571	0.0		0.0	False		,,,				2504	0.001				p.E649A		Atlas-SNP	.											CHD1L,right_upper_lobe,carcinoma,+1,1	CHD1L	72	1	0			c.A1946C						PASS	.	A	ALA/GLU	307,4099	165.8+/-197.2	8,291,1904	148.0	146.0	147.0		1946	3.4	1.0	1	dbSNP_121	147	5,8595	4.3+/-15.6	0,5,4295	yes	missense	CHD1L	NM_004284.3	107	8,296,6199	CC,CA,AA		0.0581,6.9678,2.3989	possibly-damaging	649/898	146757092	312,12694	2203	4300	6503	SO:0001583	missense	9557	exon17			GACAAGAAGCAGC	AF054177	CCDS927.1, CCDS58021.1, CCDS58022.1, CCDS72882.1	1q21.1	2008-02-05			ENSG00000131778	ENSG00000131778			1916	protein-coding gene	gene with protein product		613039				9653160	Standard	NM_004284		Approved	ALC1	uc001epm.5	Q86WJ1	OTTHUMG00000150271	ENST00000369258.4:c.1946A>C	1.37:g.146757092A>C	ENSP00000358262:p.Glu649Ala	176.0	0.0	0		183.0	95.0	0.519126	NM_004284	A5YM64|B4DDE1|B5MDZ7|Q53EZ3|Q5VXX7|Q6DD94|Q6PK83|Q86XH3|Q96HF7|Q96SP3|Q9BVJ1|Q9NVV8	Missense_Mutation	SNP	ENST00000369258.4	37	CCDS927.1	47	0.02152014652014652	46	0.09349593495934959	1	0.0027624309392265192	0	0.0	0	0.0	A	8.801	0.932825	0.18131	0.069678	5.81E-4	ENSG00000131778	ENST00000431239;ENST00000369259;ENST00000369258;ENST00000361293	D;T;D;D	0.89810	-2.57;-1.43;-2.45;-1.55	5.78	3.4	0.38934	.	0.337634	0.31809	N	0.007040	T	0.76765	0.4033	L	0.43152	1.355	0.44098	D	0.996861	P;B;B	0.39181	0.663;0.419;0.339	B;B;B	0.38921	0.285;0.151;0.04	T	0.74481	-0.3651	10	0.49607	T	0.09	.	10.1412	0.42736	0.6754:0.3246:0.0:0.0	rs13374920;rs52828089;rs13374920	555;445;649	Q86WJ1-2;Q86WJ1-3;Q86WJ1	.;.;CHD1L_HUMAN	A	555;445;649;368	ENSP00000389031:E555A;ENSP00000358263:E445A;ENSP00000358262:E649A;ENSP00000355100:E368A	ENSP00000355100:E368A	E	+	2	0	CHD1L	145223716	1.000000	0.71417	0.989000	0.46669	0.006000	0.05464	2.163000	0.42377	0.418000	0.25898	-0.446000	0.05623	GAA	A|0.976;C|0.024	0.024	strong		0.493	CHD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040377.1	NM_004284	
DENND6B	414918	hgsc.bcm.edu	37	22	50752258	50752258	+	Silent	SNP	G	G	A	rs115446109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50752258G>A	ENST00000413817.3	-	14	1259	c.1188C>T	c.(1186-1188)ctC>ctT	p.L396L	XX-C283C717.1_ENST00000453835.1_RNA	NM_001001794.3	NP_001001794.3	Q8NEG7	DEN6B_HUMAN	DENN/MADD domain containing 6B	396					positive regulation of Rab GTPase activity (GO:0032851)	endosome (GO:0005768)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)										GCAGCCGTTTGAGCAGCGCCT	0.677													G|||	61	0.0121805	0.0446	0.0029	5008	,	,		10156	0.0		0.0	False		,,,				2504	0.0				p.L396L		Atlas-SNP	.											.	.	.	.	0			c.C1188T						PASS	.	G		202,3980		3,196,1892	34.0	40.0	38.0		1188	1.0	1.0	22	dbSNP_132	38	2,8408		0,2,4203	no	coding-synonymous	FAM116B	NM_001001794.3		3,198,6095	AA,AG,GG		0.0238,4.8302,1.6201		396/586	50752258	204,12388	2091	4205	6296	SO:0001819	synonymous_variant	414918	exon14			CCGTTTGAGCAGC	AK054743	CCDS46732.1	22q13.33	2012-10-03	2012-10-03	2012-10-03	ENSG00000205593	ENSG00000205593		"""DENN/MADD domain containing"""	32690	protein-coding gene	gene with protein product			"""family with sequence similarity 116, member B"""	FAM116B		21330364	Standard	NM_001001794		Approved	MGC33692, AFI1B	uc011arv.1	Q8NEG7	OTTHUMG00000150210	ENST00000413817.3:c.1188C>T	22.37:g.50752258G>A		97.0	0.0	0		126.0	59.0	0.468254	NM_001001794	A6X8I5	Silent	SNP	ENST00000413817.3	37	CCDS46732.1																																																																																			G|0.984;A|0.016	0.016	strong		0.677	DENND6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316845.3	NM_001001794	
DUSP27	92235	hgsc.bcm.edu	37	1	167095768	167095768	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:167095768G>A	ENST00000361200.2	+	6	1566	c.1400G>A	c.(1399-1401)cGc>cAc	p.R467H	DUSP27_ENST00000443333.1_Missense_Mutation_p.R467H|DUSP27_ENST00000485151.1_Intron|DUSP27_ENST00000271385.5_Missense_Mutation_p.R467H			Q5VZP5	DUS27_HUMAN	dual specificity phosphatase 27 (putative)	467					protein dephosphorylation (GO:0006470)		protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.R467H(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(11)|liver(1)|lung(46)|ovary(5)|prostate(5)|skin(4)|upper_aerodigestive_tract(3)	89						AGGAGGCGCCGCGCAGACTCG	0.652																																					p.R467H		Atlas-SNP	.											DUSP27,NS,carcinoma,0,2	DUSP27	235	2	1	Substitution - Missense(1)	lung(1)	c.G1400A						PASS	.						21.0	21.0	21.0					1																	167095768		2202	4300	6502	SO:0001583	missense	92235	exon5			GGCGCCGCGCAGA	AF119045	CCDS30932.1	1q22-q24	2008-02-05			ENSG00000198842	ENSG00000198842			25034	protein-coding gene	gene with protein product							Standard	NM_001080426		Approved		uc001geb.1	Q5VZP5	OTTHUMG00000034434	ENST00000361200.2:c.1400G>A	1.37:g.167095768G>A	ENSP00000354483:p.Arg467His	83.0	0.0	0		98.0	13.0	0.132653	NM_001080426	A0AUM4|Q9C074	Missense_Mutation	SNP	ENST00000361200.2	37	CCDS30932.1	.	.	.	.	.	.	.	.	.	.	G	13.16	2.155451	0.38021	.	.	ENSG00000198842	ENST00000361200;ENST00000271385;ENST00000443333	T;T;T	0.03607	3.87;3.87;3.87	5.02	4.1	0.47936	.	0.086313	0.49305	D	0.000150	T	0.02649	0.0080	M	0.67953	2.075	0.30396	N	0.780517	B	0.19817	0.039	B	0.12156	0.007	T	0.12268	-1.0554	10	0.87932	D	0	-16.6929	13.7869	0.63115	0.076:0.0:0.924:0.0	.	467	Q5VZP5	DUS27_HUMAN	H	467	ENSP00000354483:R467H;ENSP00000271385:R467H;ENSP00000404874:R467H	ENSP00000271385:R467H	R	+	2	0	DUSP27	165362392	0.650000	0.27331	0.790000	0.31976	0.263000	0.26337	2.340000	0.43974	2.291000	0.77112	0.643000	0.83706	CGC	.	.	none		0.652	DUSP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083244.1	NM_001080426	
WWP1	11059	hgsc.bcm.edu	37	8	87414308	87414308	+	Silent	SNP	A	A	G	rs10106066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:87414308A>G	ENST00000517970.1	+	8	907	c.600A>G	c.(598-600)caA>caG	p.Q200Q	WWP1_ENST00000341922.2_Intron|WWP1_ENST00000265428.4_Silent_p.Q200Q|WWP1_ENST00000349423.2_Intron	NM_007013.3	NP_008944.1	Q9H0M0	WWP1_HUMAN	WW domain containing E3 ubiquitin protein ligase 1	200					central nervous system development (GO:0007417)|ion transmembrane transport (GO:0034220)|negative regulation of transcription, DNA-templated (GO:0045892)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(3)|kidney(2)|large_intestine(9)|liver(4)|lung(10)|prostate(2)|urinary_tract(1)	31						CTCTAGTCCAAAACTCATGCT	0.408													A|||	265	0.0529153	0.1921	0.013	5008	,	,		16493	0.0		0.001	False		,,,				2504	0.001				p.Q200Q		Atlas-SNP	.											.	WWP1	97	.	0			c.A600G						PASS	.	A		678,3728	286.0+/-278.5	47,584,1572	119.0	105.0	109.0		600	-4.8	0.0	8	dbSNP_119	109	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	WWP1	NM_007013.3		47,589,5867	GG,GA,AA		0.0581,15.3881,5.2514		200/923	87414308	683,12323	2203	4300	6503	SO:0001819	synonymous_variant	11059	exon8			AGTCCAAAACTCA	AY043361	CCDS6242.1	8q21.3	2013-07-22			ENSG00000123124	ENSG00000123124			17004	protein-coding gene	gene with protein product		602307				9169421, 9647693	Standard	NM_007013		Approved	AIP5, DKFZP434D2111	uc003ydt.3	Q9H0M0	OTTHUMG00000163690	ENST00000517970.1:c.600A>G	8.37:g.87414308A>G		216.0	1.0	0.00462963		196.0	104.0	0.530612	NM_007013	O00307|Q5YLC1|Q96BP4	Silent	SNP	ENST00000517970.1	37	CCDS6242.1																																																																																			.	.	weak		0.408	WWP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374755.1	NM_007013	
SLC9C2	284525	hgsc.bcm.edu	37	1	173552703	173552703	+	Silent	SNP	G	G	A	rs16828416	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:173552703G>A	ENST00000367714.3	-	6	1004	c.582C>T	c.(580-582)atC>atT	p.I194I	SLC9C2_ENST00000536496.1_Silent_p.I92I|RP3-436N22.3_ENST00000431459.1_RNA	NM_178527.3	NP_848622.2	Q5TAH2	SL9C2_HUMAN	solute carrier family 9, member C2 (putative)	194					sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	solute:proton antiporter activity (GO:0015299)										AAATTGATGCGATGCTACAAA	0.303													G|||	344	0.0686901	0.2466	0.0245	5008	,	,		16936	0.0		0.0	False		,,,				2504	0.001				p.I194I		Atlas-SNP	.											.	.	.	.	0			c.C582T						PASS	.	G		996,3410	357.6+/-314.0	113,770,1320	55.0	60.0	58.0		582	0.1	0.0	1	dbSNP_123	58	6,8590	5.0+/-18.6	0,6,4292	yes	coding-synonymous	SLC9A11	NM_178527.3		113,776,5612	AA,AG,GG		0.0698,22.6055,7.7065		194/1125	173552703	1002,12000	2203	4298	6501	SO:0001819	synonymous_variant	284525	exon6			TGATGCGATGCTA	AK128104	CCDS1308.1	1q25.1	2013-07-18	2013-07-18	2012-03-22	ENSG00000162753	ENSG00000162753		"""Solute carriers"""	28664	protein-coding gene	gene with protein product			"""solute carrier family 9, isoform 11"", ""solute carrier family 9, member 11"", ""solute carrier family 9, member C2"""	SLC9A11			Standard	NM_178527		Approved	MGC43026	uc001giz.2	Q5TAH2	OTTHUMG00000034800	ENST00000367714.3:c.582C>T	1.37:g.173552703G>A		212.0	0.0	0		202.0	98.0	0.485149	NM_178527	Q86UF3	Silent	SNP	ENST00000367714.3	37	CCDS1308.1																																																																																			G|0.910;A|0.090	0.090	strong		0.303	SLC9C2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084205.1	NM_178527	
ARMC5	79798	hgsc.bcm.edu	37	16	31477442	31477442	+	Silent	SNP	T	T	C	rs116201073	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31477442T>C	ENST00000563544.1	+	7	2586	c.2040T>C	c.(2038-2040)ggT>ggC	p.G680G	ARMC5_ENST00000412665.2_Silent_p.G324G|ARMC5_ENST00000457010.2_3'UTR|ARMC5_ENST00000268314.4_Silent_p.G680G|ARMC5_ENST00000538189.1_Silent_p.G712G|ARMC5_ENST00000408912.3_Silent_p.G775G			Q96C12	ARMC5_HUMAN	armadillo repeat containing 5	680										central_nervous_system(1)|endometrium(4)|large_intestine(3)|liver(2)|lung(12)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						AGCAGGGTGGTCTCCGGCTCC	0.647													C|||	122	0.024361	0.0893	0.0058	5008	,	,		15259	0.0		0.0	False		,,,				2504	0.0				p.G680G		Atlas-SNP	.											ARMC5,NS,carcinoma,0,1	ARMC5	94	1	0			c.T2040C						scavenged	.	C	,	253,3943		8,237,1853	31.0	36.0	34.0		2040,	3.0	1.0	16	dbSNP_132	34	1,8425		0,1,4212	no	coding-synonymous,utr-3	ARMC5	NM_001105247.1,NM_024742.2	,	8,238,6065	CC,CT,TT		0.0119,6.0296,2.0124	,	680/936,	31477442	254,12368	2098	4213	6311	SO:0001819	synonymous_variant	79798	exon6			GGGTGGTCTCCGG	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.2040T>C	16.37:g.31477442T>C		56.0	1.0	0.0178571		55.0	55.0	1	NM_001105247	Q86WM9|Q9H7P8|Q9H925	Silent	SNP	ENST00000563544.1	37	CCDS45472.1																																																																																			T|0.974;C|0.026	0.026	strong		0.647	ARMC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432847.1	NM_024742	
XAB2	56949	hgsc.bcm.edu	37	19	7692132	7692132	+	Silent	SNP	G	G	A	rs4134824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7692132G>A	ENST00000358368.4	-	4	556	c.519C>T	c.(517-519)ctC>ctT	p.L173L	XAB2_ENST00000534844.1_Silent_p.L170L|PET100_ENST00000601406.1_5'Flank|PET100_ENST00000594797.1_5'Flank|CTD-3214H19.4_ENST00000595866.1_5'Flank|PET100_ENST00000456958.3_5'Flank	NM_020196.2	NP_064581.2	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	173					blastocyst development (GO:0001824)|DNA repair (GO:0006281)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	26						GGCTCACCTTGAGGAAGCGCC	0.597								Direct reversal of damage;Nucleotide excision repair (NER)					G|||	32	0.00638978	0.0242	0.0	5008	,	,		18719	0.0		0.0	False		,,,				2504	0.0				p.L173L		Atlas-SNP	.											.	XAB2	69	.	0			c.C519T						PASS	.	G		115,4291	87.3+/-125.9	2,111,2090	54.0	56.0	56.0		519	4.0	1.0	19	dbSNP_108	56	0,8600		0,0,4300	no	coding-synonymous	XAB2	NM_020196.2		2,111,6390	AA,AG,GG		0.0,2.6101,0.8842		173/856	7692132	115,12891	2203	4300	6503	SO:0001819	synonymous_variant	56949	exon4			CACCTTGAGGAAG	AB026111	CCDS32892.1	19p13.3	2013-08-21				ENSG00000076924			14089	protein-coding gene	gene with protein product	"""SYF1 homolog, RNA splicing factor (S. cerevisiae)"", ""SYF1 pre-mRNA-splicing factor"""	610850				10944529	Standard	NM_020196		Approved	HCNP, HCRN, SYF1, NTC90	uc002mgx.3	Q9HCS7		ENST00000358368.4:c.519C>T	19.37:g.7692132G>A		29.0	0.0	0		39.0	24.0	0.615385	NM_020196	Q8TET6|Q96HB0|Q96IW0|Q9NRG6|Q9ULP3	Silent	SNP	ENST00000358368.4	37	CCDS32892.1																																																																																			G|0.990;A|0.010	0.010	strong		0.597	XAB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461021.1	NM_020196	
ZNF510	22869	hgsc.bcm.edu	37	9	99521150	99521150	+	Silent	SNP	T	T	C	rs61735521	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:99521150T>C	ENST00000375231.1	-	6	2612	c.1962A>G	c.(1960-1962)aaA>aaG	p.K654K	ZNF510_ENST00000223428.4_Silent_p.K654K			Q9Y2H8	ZN510_HUMAN	zinc finger protein 510	654					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|stomach(1)|urinary_tract(1)	21		Acute lymphoblastic leukemia(62;0.0527)				ATTCATAAGATTTCTCCCCAC	0.383													T|||	174	0.0347444	0.1278	0.0072	5008	,	,		18490	0.0		0.0	False		,,,				2504	0.0				p.K654K		Atlas-SNP	.											.	ZNF510	59	.	0			c.A1962G						PASS	.	T		448,3958	211.8+/-231.9	22,404,1777	101.0	107.0	105.0		1962	-0.6	0.0	9	dbSNP_129	105	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ZNF510	NM_014930.1		22,406,6075	CC,CT,TT		0.0233,10.168,3.4599		654/684	99521150	450,12556	2203	4300	6503	SO:0001819	synonymous_variant	22869	exon6			ATAAGATTTCTCC	AB023189	CCDS35074.1	9q22.33	2013-01-08			ENSG00000081386	ENSG00000081386		"""Zinc fingers, C2H2-type"", ""-"""	29161	protein-coding gene	gene with protein product						10231032	Standard	XM_005251807		Approved	KIAA0972	uc004awn.1	Q9Y2H8	OTTHUMG00000020303	ENST00000375231.1:c.1962A>G	9.37:g.99521150T>C		148.0	0.0	0		162.0	103.0	0.635802	NM_014930	Q5SZP5	Silent	SNP	ENST00000375231.1	37	CCDS35074.1																																																																																			T|0.970;C|0.030	0.030	strong		0.383	ZNF510-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053287.1	NM_014930	
KRT24	192666	hgsc.bcm.edu	37	17	38859664	38859664	+	Silent	SNP	G	G	A	rs61237409	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38859664G>A	ENST00000264651.2	-	1	338	c.282C>T	c.(280-282)ggC>ggT	p.G94G		NM_019016.2	NP_061889.2	Q2M2I5	K1C24_HUMAN	keratin 24	94	Gly-rich.|Head.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Breast(137;0.00526)				CAGAGACCCCGCCAAAGCTAG	0.572													G|||	192	0.0383387	0.1384	0.0115	5008	,	,		13481	0.0		0.001	False		,,,				2504	0.0				p.G94G	GBM(61;380 1051 14702 23642 31441)	Atlas-SNP	.											.	KRT24	60	.	0			c.C282T						PASS	.	G		416,3990	201.1+/-224.2	22,372,1809	95.0	118.0	110.0		282	-8.3	0.0	17	dbSNP_129	110	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	KRT24	NM_019016.2		22,375,6106	AA,AG,GG		0.0349,9.4417,3.2216		94/526	38859664	419,12587	2203	4300	6503	SO:0001819	synonymous_variant	192666	exon1			GACCCCGCCAAAG		CCDS11372.1	17q21.2	2013-06-25			ENSG00000167916	ENSG00000167916		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	18527	protein-coding gene	gene with protein product		607742				16831889	Standard	NM_019016		Approved	FLJ20261, MGC138169, MGC138173	uc002hvd.3	Q2M2I5	OTTHUMG00000133372	ENST00000264651.2:c.282C>T	17.37:g.38859664G>A		67.0	0.0	0		56.0	28.0	0.5	NM_019016	Q9NXG7	Silent	SNP	ENST00000264651.2	37	CCDS11372.1																																																																																			G|0.969;A|0.031	0.031	strong		0.572	KRT24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257217.1	NM_019016	
PTPN13	5783	hgsc.bcm.edu	37	4	87696623	87696623	+	Silent	SNP	C	C	T	rs148059206	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:87696623C>T	ENST00000411767.2	+	35	5772	c.5709C>T	c.(5707-5709)agC>agT	p.S1903S	PTPN13_ENST00000436978.1_Silent_p.S1908S|PTPN13_ENST00000511467.1_Silent_p.S1908S|PTPN13_ENST00000316707.6_Silent_p.S1712S|PTPN13_ENST00000427191.2_Silent_p.S1884S			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	1903	PDZ 5. {ECO:0000255|PROSITE- ProRule:PRU00143}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		GTCATGACAGCCTTTATCAAG	0.353													C|||	9	0.00179712	0.0068	0.0	5008	,	,		20073	0.0		0.0	False		,,,				2504	0.0				p.S1908S		Atlas-SNP	.											.	PTPN13	203	.	0			c.C5724T						PASS	.	C	,,,	20,3920		0,20,1950	94.0	89.0	90.0		5652,5709,5136,5724	1.0	0.3	4	dbSNP_134	90	1,8343		0,1,4171	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPN13	NM_006264.2,NM_080683.2,NM_080684.2,NM_080685.2	,,,	0,21,6121	TT,TC,CC		0.012,0.5076,0.171	,,,	1884/2467,1903/2486,1712/2295,1908/2491	87696623	21,12263	1970	4172	6142	SO:0001819	synonymous_variant	5783	exon35			TGACAGCCTTTAT		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.5709C>T	4.37:g.87696623C>T		141.0	0.0	0		143.0	69.0	0.482517	NM_080685	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Silent	SNP	ENST00000411767.2	37	CCDS47094.1																																																																																			C|0.999;T|0.001	0.001	strong		0.353	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1		
TCOF1	6949	hgsc.bcm.edu	37	5	149759201	149759201	+	Missense_Mutation	SNP	C	C	T	rs114689020	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149759201C>T	ENST00000504761.2	+	17	2765	c.2765C>T	c.(2764-2766)tCg>tTg	p.S922L	TCOF1_ENST00000323668.7_Missense_Mutation_p.S845L|TCOF1_ENST00000439160.2_Missense_Mutation_p.S922L|TCOF1_ENST00000513346.1_Missense_Mutation_p.S922L|TCOF1_ENST00000445265.2_Missense_Mutation_p.S845L|TCOF1_ENST00000451292.1_Missense_Mutation_p.S922L|TCOF1_ENST00000506063.1_3'UTR|TCOF1_ENST00000377797.3_Missense_Mutation_p.S922L|TCOF1_ENST00000394269.3_Missense_Mutation_p.S922L			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	922					skeletal system development (GO:0001501)|transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:0042790)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transporter activity (GO:0005215)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	35		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ACAGGGCCTTCGGCTGCCCAG	0.632													C|||	114	0.0227636	0.0787	0.0101	5008	,	,		19801	0.0		0.003	False		,,,				2504	0.0				p.S922L		Atlas-SNP	.											.	TCOF1	154	.	0			c.C2765T						PASS	.	C	LEU/SER,LEU/SER,LEU/SER,LEU/SER,LEU/SER,LEU/SER	281,4125	157.4+/-190.3	14,253,1936	54.0	60.0	58.0		2534,2765,2765,2765,2534,2765	0.4	0.0	5	dbSNP_132	58	11,8589	8.4+/-32.0	0,11,4289	yes	missense,missense,missense,missense,missense,missense	TCOF1	NM_000356.3,NM_001008657.2,NM_001135243.1,NM_001135244.1,NM_001135245.1,NM_001195141.1	145,145,145,145,145,145	14,264,6225	TT,TC,CC		0.1279,6.3777,2.2451	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	845/1412,922/959,922/1489,922/1452,845/1413,922/1451	149759201	292,12714	2203	4300	6503	SO:0001583	missense	6949	exon17			GGCCTTCGGCTGC		CCDS4306.1, CCDS47305.1, CCDS47306.1, CCDS47307.1, CCDS54936.1	5q32	2014-06-18			ENSG00000070814	ENSG00000070814			11654	protein-coding gene	gene with protein product		606847				1765376	Standard	NM_001008657		Approved	treacle, TCS	uc003lry.3	Q13428	OTTHUMG00000130081	ENST00000504761.2:c.2765C>T	5.37:g.149759201C>T	ENSP00000421655:p.Ser922Leu	170.0	0.0	0		142.0	75.0	0.528169	NM_001135243	A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	Missense_Mutation	SNP	ENST00000504761.2	37	CCDS54936.1	43	0.019688644688644688	39	0.07926829268292683	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	13.10	2.136775	0.37728	0.063777	0.001279	ENSG00000070814	ENST00000451292;ENST00000377797;ENST00000445265;ENST00000323668;ENST00000439160;ENST00000394269;ENST00000427724;ENST00000504761;ENST00000513346	T;T;T;T;T;T;T;T;T	0.74947	-0.01;-0.01;-0.01;-0.01;-0.02;-0.01;-0.89;-0.01;-0.87	5.63	0.389	0.16269	Treacher Collins syndrome, treacle (1);	1.572510	0.03797	N	0.263889	T	0.05823	0.0152	N	0.11560	0.145	0.09310	N	1	B;B;B;B;B;B;B	0.06786	0.0;0.001;0.001;0.001;0.001;0.001;0.001	B;B;B;B;B;B;B	0.04013	0.0;0.001;0.001;0.001;0.001;0.001;0.001	T	0.25293	-1.0136	10	0.66056	D	0.02	1.7592	4.6859	0.12757	0.1423:0.5093:0.0:0.3484	.	431;922;845;922;922;845;922	B4DRA2;Q13428-7;Q13428-2;Q13428-6;Q13428;Q13428-8;Q13428-5	.;.;.;.;TCOF_HUMAN;.;.	L	922;922;845;845;922;922;922;922;922	ENSP00000400939:S922L;ENSP00000367028:S922L;ENSP00000409944:S845L;ENSP00000325223:S845L;ENSP00000406888:S922L;ENSP00000377811:S922L;ENSP00000390717:S922L;ENSP00000421655:S922L;ENSP00000427484:S922L	ENSP00000325223:S845L	S	+	2	0	TCOF1	149739394	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.568000	0.05909	0.103000	0.17682	-0.254000	0.11334	TCG	C|0.979;T|0.021	0.021	strong		0.632	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380552.1	NM_001008656	
MVP	9961	hgsc.bcm.edu	37	16	29856082	29856082	+	Missense_Mutation	SNP	G	G	A	rs35916172	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:29856082G>A	ENST00000357402.5	+	11	2041	c.1903G>A	c.(1903-1905)Gtc>Atc	p.V635I	MVP_ENST00000395353.1_Missense_Mutation_p.V635I	NM_005115.4|NM_017458.3	NP_005106.2|NP_059447.2	Q14764	MVP_HUMAN	major vault protein	635			V -> I (in dbSNP:rs35916172).		cell proliferation (GO:0008283)|ERBB signaling pathway (GO:0038127)|mRNA transport (GO:0051028)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of protein tyrosine kinase activity (GO:0061099)|negative regulation of signaling (GO:0023057)|protein activation cascade (GO:0072376)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(7)|ovary(2)|skin(3)|soft_tissue(1)|stomach(1)	27						CGGGCTGGTGGTCAGCAGTGT	0.647													G|||	63	0.0125799	0.0439	0.0058	5008	,	,		16638	0.0		0.001	False		,,,				2504	0.0				p.V635I		Atlas-SNP	.											.	MVP	80	.	0			c.G1903A						PASS	.	G	ILE/VAL,ILE/VAL	151,4243	106.0+/-144.5	0,151,2046	80.0	81.0	81.0		1903,1903	5.0	1.0	16	dbSNP_126	81	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	MVP	NM_005115.4,NM_017458.3	29,29	0,152,6345	AA,AG,GG		0.0116,3.4365,1.1698	benign,benign	635/894,635/894	29856082	152,12842	2197	4300	6497	SO:0001583	missense	9961	exon11			CTGGTGGTCAGCA	X79882	CCDS10656.1	16p11.2	2012-04-25			ENSG00000013364	ENSG00000013364			7531	protein-coding gene	gene with protein product	"""lung resistance-related protein"""	605088				7585126	Standard	NM_005115		Approved	LRP, VAULT1	uc002dui.3	Q14764	OTTHUMG00000048227	ENST00000357402.5:c.1903G>A	16.37:g.29856082G>A	ENSP00000349977:p.Val635Ile	55.0	0.0	0		51.0	25.0	0.490196	NM_017458	Q96BG4|Q9BPW6|Q9BQT1|Q9UBD1	Missense_Mutation	SNP	ENST00000357402.5	37	CCDS10656.1	17	0.007783882783882784	16	0.032520325203252036	0	0.0	0	0.0	1	0.0013192612137203166	G	7.470	0.646386	0.14451	0.034365	1.16E-4	ENSG00000013364	ENST00000357402;ENST00000395353	T;T	0.39406	1.08;1.08	5.91	4.96	0.65561	Shoulder domain (1);	0.103708	0.64402	N	0.000003	T	0.08980	0.0222	N	0.20881	0.62	0.80722	D	1	B	0.18610	0.029	B	0.25140	0.058	T	0.04664	-1.0935	10	0.02654	T	1	-17.7157	9.1044	0.36689	0.1639:0.0:0.836:0.0	rs35916172;rs35916172	635	Q14764	MVP_HUMAN	I	635	ENSP00000349977:V635I;ENSP00000378760:V635I	ENSP00000349977:V635I	V	+	1	0	MVP	29763583	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	3.270000	0.51600	1.513000	0.48852	0.655000	0.94253	GTC	G|0.985;A|0.015	0.015	strong		0.647	MVP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109711.3	NM_005115	
RAB40AL	282808	hgsc.bcm.edu	37	X	102192885	102192885	+	Silent	SNP	G	G	A	rs7876193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102192885G>A	ENST00000218249.5	+	1	686	c.639G>A	c.(637-639)ccG>ccA	p.P213P	LL0XNC01-237H1.3_ENST00000413528.1_RNA	NM_001031834.1	NP_001027004.1	P0C0E4	RB40L_HUMAN	RAB40A, member RAS oncogene family-like	213	SOCS box. {ECO:0000255|PROSITE- ProRule:PRU00194}.				protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			endometrium(4)|large_intestine(2)|lung(3)|ovary(3)	12						ACAAGCTCCCGCTCCCCATTG	0.592													.|||	68	0.0180132	0.0477	0.0058	3775	,	,		13822	0.0		0.0	False		,,,				2504	0.001				p.P213P		Atlas-SNP	.											.	RAB40AL	33	.	0			c.G639A						PASS	.	G		213,3622		4,171,34,1457,537	145.0	117.0	127.0		639	-0.3	0.4	X	dbSNP_116	127	0,6728		0,0,0,2428,1872	no	coding-synonymous	RAB40AL	NM_001031834.1		4,171,34,3885,2409	AA,AG,A,GG,G		0.0,5.5541,2.0165		213/279	102192885	213,10350	2203	4300	6503	SO:0001819	synonymous_variant	282808	exon1			GCTCCCGCTCCCC	BC101169	CCDS35353.1	Xq22.2	2008-02-05			ENSG00000102128	ENSG00000102128			25410	protein-coding gene	gene with protein product	"""Ras like GTPase"""	300405					Standard	NM_001031834		Approved	RAR2, RLGP	uc004ejs.3	P0C0E4	OTTHUMG00000022084	ENST00000218249.5:c.639G>A	X.37:g.102192885G>A		266.0	0.0	0		310.0	111.0	0.358065	NM_001031834	Q495H3	Silent	SNP	ENST00000218249.5	37	CCDS35353.1																																																																																			G|0.981;A|0.019	0.019	strong		0.592	RAB40AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057679.1	NM_001031834	
TENM1	10178	hgsc.bcm.edu	37	X	123775824	123775824	+	Missense_Mutation	SNP	T	T	C	rs16999334	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:123775824T>C	ENST00000371130.3	-	11	1957	c.1894A>G	c.(1894-1896)Atg>Gtg	p.M632V	TENM1_ENST00000422452.2_Missense_Mutation_p.M632V	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	632	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.		M -> V (in dbSNP:rs16999334).		immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										TTGGAACACATTGGGTCTAGG	0.468													T|||	168	0.0445033	0.121	0.0086	3775	,	,		14477	0.0		0.001	False		,,,				2504	0.001				p.M632V		Atlas-SNP	.											.	.	.	.	0			c.A1894G						PASS	.	T	VAL/MET,VAL/MET,VAL/MET	562,3273		49,384,80,1199,491	196.0	175.0	182.0		1894,1891,1894	4.2	1.0	X	dbSNP_123	182	3,6725		0,3,0,2425,1872	yes	missense,missense,missense	ODZ1	NM_001163278.1,NM_001163279.1,NM_014253.3	21,21,21	49,387,80,3624,2363	CC,CT,C,TT,T		0.0446,14.6545,5.3489	benign,benign,benign	632/2733,631/2732,632/2726	123775824	565,9998	2203	4300	6503	SO:0001583	missense	10178	exon11			AACACATTGGGTC	AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"""tenascin M"", ""odz, odd Oz/ten-m homolog 1 (Drosophila)"""	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.1894A>G	X.37:g.123775824T>C	ENSP00000360171:p.Met632Val	155.0	0.0	0		159.0	56.0	0.352201	NM_001163278	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	59	0.03556359252561784	41	0.08836206896551724	3	0.008379888268156424	0	0.0	0	0.0	T	13.41	2.228398	0.39399	0.146545	4.46E-4	ENSG00000009694	ENST00000371130;ENST00000422452	T;T	0.03212	4.01;4.01	5.32	4.15	0.48705	Epidermal growth factor-like (1);	0.119478	0.56097	D	0.000024	T	0.00039	0.0001	N	0.21373	0.66	0.27607	P	0.9487963	B;B;B	0.27351	0.176;0.111;0.006	B;B;B	0.17098	0.016;0.017;0.005	T	0.48864	-0.8997	9	0.38643	T	0.18	.	10.3355	0.43847	0.0:0.0784:0.0:0.9216	rs16999334;rs52832334;rs58243564;rs16999334	631;632;632	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	V	632	ENSP00000360171:M632V;ENSP00000403954:M632V	ENSP00000360171:M632V	M	-	1	0	ODZ1	123603505	0.989000	0.36119	1.000000	0.80357	0.978000	0.69477	2.162000	0.42367	0.675000	0.31264	0.481000	0.45027	ATG	0|0.018;C|0.053	0.053	strong		0.468	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253	
AKAP7	9465	hgsc.bcm.edu	37	6	131490324	131490324	+	Missense_Mutation	SNP	C	C	T	rs115301121	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:131490324C>T	ENST00000431975.2	+	5	598	c.500C>T	c.(499-501)cCc>cTc	p.P167L	AKAP7_ENST00000366358.2_Intron|AKAP7_ENST00000541650.1_Missense_Mutation_p.P166L|AKAP7_ENST00000368123.4_Missense_Mutation_p.P145L	NM_016377.3	NP_057461.2	Q9P0M2	AKA7G_HUMAN	A kinase (PRKA) anchor protein 7	167						cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|nucleotide binding (GO:0000166)|protein kinase A binding (GO:0051018)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|stomach(1)	13	Breast(56;0.152)			GBM - Glioblastoma multiforme(226;0.0184)|OV - Ovarian serous cystadenocarcinoma(155;0.0345)		TTGACTTTGCCCTTTCAAGGG	0.373													C|||	26	0.00519169	0.0197	0.0	5008	,	,		17471	0.0		0.0	False		,,,				2504	0.0				p.P167L		Atlas-SNP	.											.	AKAP7	61	.	0			c.C500T						PASS	.	C	LEU/PRO	80,4326	68.7+/-106.4	3,74,2126	130.0	133.0	132.0		500	5.9	1.0	6	dbSNP_132	132	2,8598	1.2+/-3.3	0,2,4298	yes	missense	AKAP7	NM_016377.3	98	3,76,6424	TT,TC,CC		0.0233,1.8157,0.6305	benign	167/349	131490324	82,12924	2203	4300	6503	SO:0001583	missense	9465	exon5			CTTTGCCCTTTCA	AF047715	CCDS5142.1, CCDS5143.1, CCDS5144.1, CCDS5142.2	6q23.2	2012-10-24			ENSG00000118507	ENSG00000118507		"""A-kinase anchor proteins"""	377	protein-coding gene	gene with protein product		604693				9545239	Standard	NM_016377		Approved	AKAP18, AKAP15	uc003qck.4	O43687	OTTHUMG00000015563	ENST00000431975.2:c.500C>T	6.37:g.131490324C>T	ENSP00000405252:p.Pro167Leu	188.0	0.0	0		210.0	104.0	0.495238	NM_016377	B4DUC3|Q9HCZ8	Missense_Mutation	SNP	ENST00000431975.2	37	CCDS5142.2	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	C	25.2	4.613160	0.87359	0.018157	2.33E-4	ENSG00000118507	ENST00000431975;ENST00000541650;ENST00000368123	T;T;T	0.62941	-0.01;-0.01;-0.01	5.9	5.9	0.94986	RNA ligase/cyclic nucleotide phosphodiesterase (1);Protein kinase A anchor protein, nuclear localisation signal domain (1);	0.159801	0.56097	D	0.000021	T	0.63022	0.2476	M	0.73598	2.24	0.58432	D	0.999999	D;P	0.53312	0.959;0.945	P;P	0.50440	0.62;0.641	T	0.62077	-0.6930	10	0.33141	T	0.24	-11.449	15.779	0.78246	0.0:1.0:0.0:0.0	.	166;167	F5GXD1;Q9P0M2	.;AKA7G_HUMAN	L	167;166;145	ENSP00000405252:P167L;ENSP00000441048:P166L;ENSP00000357105:P145L	ENSP00000357105:P145L	P	+	2	0	AKAP7	131532017	0.998000	0.40836	1.000000	0.80357	0.984000	0.73092	4.775000	0.62346	2.788000	0.95919	0.650000	0.86243	CCC	C|0.993;T|0.007	0.007	strong		0.373	AKAP7-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042209.2	NM_004842	
STARD13	90627	hgsc.bcm.edu	37	13	33684221	33684221	+	Missense_Mutation	SNP	C	C	T	rs140868444	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:33684221C>T	ENST00000336934.5	-	12	2952	c.2836G>A	c.(2836-2838)Gac>Aac	p.D946N	STARD13_ENST00000399365.3_Missense_Mutation_p.D828N|STARD13_ENST00000255486.4_Missense_Mutation_p.D938N	NM_001243476.1|NM_178006.3	NP_001230405.1|NP_821074.1	Q9Y3M8	STA13_HUMAN	StAR-related lipid transfer (START) domain containing 13	946	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				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)		GGGTTCCCGTCGCCCACCTTG	0.547											OREG0022359	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	13	0.00259585	0.0098	0.0	5008	,	,		18177	0.0		0.0	False		,,,				2504	0.0				p.D946N		Atlas-SNP	.											.	STARD13	100	.	0			c.G2836A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP	51,4355	53.6+/-89.4	0,51,2152	36.0	35.0	35.0		2482,2836,2812	5.3	0.9	13	dbSNP_134	35	0,8600		0,0,4300	yes	missense,missense,missense	STARD13	NM_052851.2,NM_178006.3,NM_178007.2	23,23,23	0,51,6452	TT,TC,CC		0.0,1.1575,0.3921	probably-damaging,probably-damaging,probably-damaging	828/996,946/1114,938/1106	33684221	51,12955	2203	4300	6503	SO:0001583	missense	90627	exon12			TCCCGTCGCCCAC	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.2836G>A	13.37:g.33684221C>T	ENSP00000338785:p.Asp946Asn	64.0	0.0	0	841	48.0	14.0	0.291667	NM_178006	A2A309|A2A310|Q5HYH1|Q5TAE3|Q6UN61|Q86TP6|Q86WQ3|Q86XT1	Missense_Mutation	SNP	ENST00000336934.5	37	CCDS9348.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	35	5.458396	0.96240	0.011575	0.0	ENSG00000133121	ENST00000399365;ENST00000255486;ENST00000336934	T;T;T	0.34859	1.34;1.34;1.34	5.34	5.34	0.76211	Lipid-binding START (3);START-like domain (1);	0.000000	0.85682	D	0.000000	T	0.53690	0.1812	M	0.90650	3.135	0.80722	D	1	D;D;D	0.89917	0.998;1.0;1.0	D;D;D	0.77004	0.954;0.989;0.982	T	0.71573	-0.4552	10	0.87932	D	0	.	19.4036	0.94640	0.0:1.0:0.0:0.0	.	911;946;938	Q9Y3M8-4;Q9Y3M8;Q9Y3M8-2	.;STA13_HUMAN;.	N	828;938;946	ENSP00000382300:D828N;ENSP00000255486:D938N;ENSP00000338785:D946N	ENSP00000255486:D938N	D	-	1	0	STARD13	32582221	1.000000	0.71417	0.931000	0.37212	0.958000	0.62258	7.689000	0.84165	2.657000	0.90304	0.655000	0.94253	GAC	C|0.996;T|0.004	0.004	strong		0.547	STARD13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276118.2	NM_001243466	
ATP10A	57194	hgsc.bcm.edu	37	15	25959298	25959298	+	Missense_Mutation	SNP	T	T	C	rs141928852	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:25959298T>C	ENST00000356865.6	-	10	1978	c.1867A>G	c.(1867-1869)Agc>Ggc	p.S623G		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	623					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|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)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		CCGATGCTGCTGCAGCCTGAG	0.617													T|||	18	0.00359425	0.0136	0.0	5008	,	,		14466	0.0		0.0	False		,,,				2504	0.0				p.S623G		Atlas-SNP	.											.	ATP10A	270	.	0			c.A1867G						PASS	.	T	GLY/SER	50,4356	43.8+/-77.6	0,50,2153	44.0	49.0	47.0		1867	0.6	1.0	15	dbSNP_134	47	0,8600		0,0,4300	yes	missense	ATP10A	NM_024490.3	56	0,50,6453	CC,CT,TT		0.0,1.1348,0.3844	benign	623/1500	25959298	50,12956	2203	4300	6503	SO:0001583	missense	57194	exon10			TGCTGCTGCAGCC	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.1867A>G	15.37:g.25959298T>C	ENSP00000349325:p.Ser623Gly	58.0	0.0	0		70.0	30.0	0.428571	NM_024490	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	T	11.14	1.550168	0.27652	0.011348	0.0	ENSG00000206190	ENST00000356865	T	0.11604	2.76	4.21	0.576	0.17380	HAD-like domain (1);	0.310582	0.37761	N	0.001944	T	0.04907	0.0132	L	0.35723	1.085	0.41036	D	0.985193	B	0.17038	0.02	B	0.20384	0.029	T	0.34527	-0.9825	10	0.28530	T	0.3	-9.6357	5.3687	0.16127	0.0:0.1605:0.149:0.6905	.	623	O60312	AT10A_HUMAN	G	623	ENSP00000349325:S623G	ENSP00000349325:S623G	S	-	1	0	ATP10A	23510391	1.000000	0.71417	0.952000	0.39060	0.450000	0.32258	3.499000	0.53310	-0.061000	0.13110	0.533000	0.62120	AGC	T|0.997;C|0.003	0.003	strong		0.617	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	
ABCC12	94160	hgsc.bcm.edu	37	16	48180311	48180311	+	Missense_Mutation	SNP	T	T	G	rs16945901	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:48180311T>G	ENST00000311303.3	-	1	370	c.25A>C	c.(25-27)Atc>Ctc	p.I9L	ABCC12_ENST00000416054.1_Missense_Mutation_p.I9L|ABCC12_ENST00000448542.1_Missense_Mutation_p.I9L	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	9			I -> L (in dbSNP:rs16945901).			integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|liver(1)|lung(43)|ovary(2)|prostate(3)|skin(7)|urinary_tract(1)	90		all_cancers(37;0.0474)|all_lung(18;0.047)				AGATCTGAGATAAGGTAGGGT	0.552													T|||	189	0.0377396	0.1399	0.0058	5008	,	,		20637	0.0		0.0	False		,,,				2504	0.0				p.I9L		Atlas-SNP	.											.	ABCC12	190	.	0			c.A25C						PASS	.	T	LEU/ILE	477,3925	225.9+/-241.6	24,429,1748	108.0	96.0	100.0		25	5.4	1.0	16	dbSNP_123	100	7,8593	4.3+/-15.6	0,7,4293	yes	missense	ABCC12	NM_033226.2	5	24,436,6041	GG,GT,TT		0.0814,10.836,3.7225	possibly-damaging	9/1360	48180311	484,12518	2201	4300	6501	SO:0001583	missense	94160	exon1			CTGAGATAAGGTA	AY040220	CCDS10730.1	16q12.1	2012-03-14			ENSG00000140798	ENSG00000140798		"""ATP binding cassette transporters / subfamily C"""	14640	protein-coding gene	gene with protein product		607041				11435397, 11483364	Standard	NM_033226		Approved	MRP9	uc002efc.1	Q96J65	OTTHUMG00000133143	ENST00000311303.3:c.25A>C	16.37:g.48180311T>G	ENSP00000311030:p.Ile9Leu	133.0	0.0	0		128.0	63.0	0.492188	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Missense_Mutation	SNP	ENST00000311303.3	37	CCDS10730.1	74	0.03388278388278388	72	0.14634146341463414	2	0.0055248618784530384	0	0.0	0	0.0	T	17.20	3.327928	0.60743	0.10836	8.14E-4	ENSG00000140798	ENST00000311303;ENST00000448542;ENST00000449939;ENST00000416054;ENST00000527640	D;D;D;D	0.92911	-2.8;-3.04;-3.13;-2.66	5.41	5.41	0.78517	.	0.208161	0.39687	N	0.001292	T	0.01976	0.0062	N	0.25144	0.715	0.34860	P	0.257501	B;B	0.21821	0.061;0.007	B;B	0.16289	0.015;0.003	T	0.56914	-0.7900	9	0.02654	T	1	.	11.8356	0.52321	0.0:0.0:0.0:1.0	rs16945901;rs59437921;rs16945901	9;9	Q96J65-2;Q96J65	.;MRP9_HUMAN	L	9	ENSP00000311030:I9L;ENSP00000401855:I9L;ENSP00000413046:I9L;ENSP00000436647:I9L	ENSP00000311030:I9L	I	-	1	0	ABCC12	46737812	0.989000	0.36119	0.994000	0.49952	0.960000	0.62799	1.976000	0.40579	2.022000	0.59522	0.496000	0.49642	ATC	T|0.955;G|0.045	0.045	strong		0.552	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226	
PPEF2	5470	hgsc.bcm.edu	37	4	76788564	76788564	+	Missense_Mutation	SNP	C	C	T	rs34155925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:76788564C>T	ENST00000286719.7	-	14	2014	c.1658G>A	c.(1657-1659)aGa>aAa	p.R553K		NM_006239.2	NP_006230.2	O14830	PPE2_HUMAN	protein phosphatase, EF-hand calcium binding domain 2	553			R -> K (in dbSNP:rs34155925).		detection of stimulus involved in sensory perception (GO:0050906)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|protein dephosphorylation (GO:0006470)|regulation of JUN kinase activity (GO:0043506)|regulation of MAP kinase activity (GO:0043405)|visual perception (GO:0007601)	cilium (GO:0005929)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|Hsp70 protein binding (GO:0030544)|Hsp90 protein binding (GO:0051879)|iron ion binding (GO:0005506)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	50			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			CTCCTCCACTCTGCTAATCCT	0.403													C|||	639	0.127596	0.4531	0.0346	5008	,	,		19539	0.0079		0.002	False		,,,				2504	0.0061				p.R553K	NSCLC(105;1359 1603 15961 44567 47947)	Atlas-SNP	.											.	PPEF2	108	.	0			c.G1658A						PASS	.	C	LYS/ARG	1783,2623	524.1+/-371.2	357,1069,777	55.0	57.0	57.0		1658	4.3	1.0	4	dbSNP_126	57	21,8579	14.0+/-48.4	0,21,4279	yes	missense	PPEF2	NM_006239.2	26	357,1090,5056	TT,TC,CC		0.2442,40.4675,13.8705	benign	553/754	76788564	1804,11202	2203	4300	6503	SO:0001583	missense	5470	exon14			TCCACTCTGCTAA	AF023456	CCDS34013.1	4q21.1	2013-01-10			ENSG00000156194	ENSG00000156194		"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"", ""EF-hand domain containing"""	9244	protein-coding gene	gene with protein product	"""protein phosphatase 7, catalytic subunit, beta isozyme"""	602256				9326663, 12051765	Standard	NM_006239		Approved	PPP7CB	uc003hix.3	O14830	OTTHUMG00000160915	ENST00000286719.7:c.1658G>A	4.37:g.76788564C>T	ENSP00000286719:p.Arg553Lys	127.0	0.0	0		136.0	66.0	0.485294	NM_006239	O14831	Missense_Mutation	SNP	ENST00000286719.7	37	CCDS34013.1	251	0.11492673992673992	239	0.48577235772357724	9	0.024861878453038673	2	0.0034965034965034965	1	0.0013192612137203166	C	12.33	1.906038	0.33628	0.404675	0.002442	ENSG00000156194	ENST00000286719;ENST00000337500	T	0.05081	3.5	6.04	4.31	0.51392	.	4.318100	0.00508	N	0.000165	T	0.00012	0.0000	L	0.55990	1.75	0.21627	P	0.999610337	B;B	0.30146	0.27;0.031	B;B	0.41946	0.371;0.015	T	0.47611	-0.9104	9	0.46703	T	0.11	1.3252	5.7123	0.17941	0.0:0.6724:0.1619:0.1657	rs34155925;rs57342715	553;553	O14830-2;O14830	.;PPE2_HUMAN	K	553	ENSP00000286719:R553K	ENSP00000286719:R553K	R	-	2	0	PPEF2	77007588	0.978000	0.34361	1.000000	0.80357	0.979000	0.70002	1.205000	0.32308	1.571000	0.49722	0.561000	0.74099	AGA	C|0.877;T|0.123	0.123	strong		0.403	PPEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362929.1	NM_006239	
CAMK2D	817	hgsc.bcm.edu	37	4	114438740	114438740	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:114438740C>T	ENST00000342666.5	-	9	674	c.675G>A	c.(673-675)caG>caA	p.Q225Q	CAMK2D_ENST00000296402.5_Silent_p.Q225Q|CAMK2D_ENST00000394526.2_Silent_p.Q225Q|CAMK2D_ENST00000394524.3_Silent_p.Q225Q|CAMK2D_ENST00000429180.1_Silent_p.Q225Q|CAMK2D_ENST00000505990.1_Silent_p.Q225Q|CAMK2D_ENST00000508738.1_Silent_p.Q225Q|CAMK2D_ENST00000515496.1_Silent_p.Q225Q|CAMK2D_ENST00000511664.1_Silent_p.Q225Q|CAMK2D_ENST00000379773.2_Silent_p.Q225Q|CAMK2D_ENST00000394522.3_Silent_p.Q225Q|CAMK2D_ENST00000454265.2_Silent_p.Q225Q|CAMK2D_ENST00000418639.2_Silent_p.Q225Q|CAMK2D_ENST00000514328.1_Silent_p.Q225Q			Q13557	KCC2D_HUMAN	calcium/calmodulin-dependent protein kinase II delta	225	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				calcium ion transport (GO:0006816)|cardiac muscle cell contraction (GO:0086003)|cellular response to calcium ion (GO:0071277)|cytokine-mediated signaling pathway (GO:0019221)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|G1/S transition of mitotic cell cycle (GO:0000082)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of sodium ion transmembrane transport (GO:1902306)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|protein autophosphorylation (GO:0046777)|protein oligomerization (GO:0051259)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle cell action potential (GO:0098901)|regulation of cardiac muscle cell action potential involved in regulation of contraction (GO:0098909)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of cell growth (GO:0001558)|regulation of cellular localization (GO:0060341)|regulation of generation of L-type calcium current (GO:1902514)|regulation of heart contraction (GO:0008016)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of histone deacetylase activity (GO:1901725)|regulation of membrane depolarization (GO:0003254)|regulation of relaxation of cardiac muscle (GO:1901897)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of the force of heart contraction (GO:0002026)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|relaxation of cardiac muscle (GO:0055119)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|calcium channel complex (GO:0034704)|calcium- and calmodulin-dependent protein kinase complex (GO:0005954)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|intercalated disc (GO:0014704)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|ion channel binding (GO:0044325)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|sodium channel inhibitor activity (GO:0019871)|titin binding (GO:0031432)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	13		Ovarian(17;0.00369)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000271)		CAGCCTTGATCTGCTGATAGA	0.383																																					p.Q225Q		Atlas-SNP	.											.	CAMK2D	55	.	0			c.G675A						PASS	.						129.0	131.0	130.0					4																	114438740		2203	4300	6503	SO:0001819	synonymous_variant	817	exon9			CTTGATCTGCTGA	U50361	CCDS3703.1, CCDS3704.1, CCDS43263.1, CCDS47127.1, CCDS54797.1	4q26	2008-10-30	2008-10-30		ENSG00000145349	ENSG00000145349			1462	protein-coding gene	gene with protein product		607708	"""calcium/calmodulin-dependent protein kinase (CaM kinase) II delta"""	CAMKD			Standard	NM_001221		Approved		uc003ibi.3	Q13557	OTTHUMG00000132910	ENST00000342666.5:c.675G>A	4.37:g.114438740C>T		66.0	0.0	0		85.0	4.0	0.0470588	NM_172128	A8MVS8|Q52PK4|Q59G21|Q8N553|Q9UGH6|Q9UQE9	Silent	SNP	ENST00000342666.5	37	CCDS3703.1																																																																																			.	.	none		0.383	CAMK2D-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256420.2		
MUC4	4585	hgsc.bcm.edu	37	3	195511524	195511524	+	Silent	SNP	G	G	A	rs201351734	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195511524G>A	ENST00000463781.3	-	2	7386	c.6927C>T	c.(6925-6927)gaC>gaT	p.D2309D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.D2309D	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)		CTGAGGAAGCGTCGGTGACAT	0.582																																					p.D2309D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,5	MUC4	1505	5	0			c.C6927T						scavenged	.						4.0	5.0	5.0					3																	195511524		476	1230	1706	SO:0001819	synonymous_variant	4585	exon2			GGAAGCGTCGGTG	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.6927C>T	3.37:g.195511524G>A		126.0	0.0	0		114.0	20.0	0.175439	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			G|0.967;A|0.033	0.033	strong		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
C17orf53	78995	hgsc.bcm.edu	37	17	42225250	42225250	+	Missense_Mutation	SNP	G	G	A	rs35879996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:42225250G>A	ENST00000319977.4	+	3	316	c.79G>A	c.(79-81)Gca>Aca	p.A27T	C17orf53_ENST00000245382.6_Missense_Mutation_p.A27T|C17orf53_ENST00000585683.1_Missense_Mutation_p.A27T	NM_001171251.1|NM_024032.3	NP_001164722.1|NP_076937.2	Q8N3J3	CQ053_HUMAN	chromosome 17 open reading frame 53	27										NS(1)|breast(3)|cervix(1)|kidney(3)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	22		Breast(137;0.0364)|Prostate(33;0.0376)		BRCA - Breast invasive adenocarcinoma(366;0.114)		TGTGGAGGATGCAGAGAACCG	0.532													G|||	94	0.01877	0.0681	0.0058	5008	,	,		20182	0.0		0.0	False		,,,				2504	0.0				p.A27T		Atlas-SNP	.											.	C17orf53	59	.	0			c.G79A						PASS	.	G	THR/ALA,THR/ALA	223,4183	127.4+/-164.3	2,219,1982	57.0	58.0	58.0		79,79	2.0	1.0	17	dbSNP_126	58	5,8595	3.7+/-12.6	0,5,4295	yes	missense,missense	C17orf53	NM_001171251.1,NM_024032.3	58,58	2,224,6277	AA,AG,GG		0.0581,5.0613,1.753	probably-damaging,probably-damaging	27/647,27/648	42225250	228,12778	2203	4300	6503	SO:0001583	missense	78995	exon3			GAGGATGCAGAGA	AK021656	CCDS11477.1, CCDS59293.1	17q21.31	2012-10-11			ENSG00000125319	ENSG00000125319			28460	protein-coding gene	gene with protein product							Standard	NM_001171251		Approved	MGC3130	uc002ifi.2	Q8N3J3	OTTHUMG00000181808	ENST00000319977.4:c.79G>A	17.37:g.42225250G>A	ENSP00000313500:p.Ala27Thr	68.0	0.0	0		75.0	37.0	0.493333	NM_001171251	A8K7A9|Q9BWM9|Q9HAI1	Missense_Mutation	SNP	ENST00000319977.4	37	CCDS11477.1	34	0.015567765567765568	31	0.06300813008130081	3	0.008287292817679558	0	0.0	0	0.0	G	18.70	3.679486	0.68042	0.050613	5.81E-4	ENSG00000125319	ENST00000319977;ENST00000245382;ENST00000253405	T;T	0.52057	0.68;0.68	5.28	2.05	0.26809	.	0.355277	0.25487	N	0.030330	T	0.07098	0.0180	L	0.46157	1.445	0.27350	N	0.956269	P;B;P	0.51537	0.946;0.15;0.946	P;B;P	0.48677	0.586;0.044;0.586	T	0.01834	-1.1264	10	0.40728	T	0.16	-5.352	7.9308	0.29901	0.3513:0.0:0.6487:0.0	rs35879996	27;27;27	A8K7A9;Q8N3J3-3;Q8N3J3	.;.;CQ053_HUMAN	T	27	ENSP00000313500:A27T;ENSP00000245382:A27T	ENSP00000245382:A27T	A	+	1	0	C17orf53	39580776	0.992000	0.36948	1.000000	0.80357	0.960000	0.62799	2.005000	0.40864	0.797000	0.33971	0.561000	0.74099	GCA	G|0.983;A|0.017	0.017	strong		0.532	C17orf53-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457697.1	NM_024032	
PXDN	7837	hgsc.bcm.edu	37	2	1642736	1642736	+	Missense_Mutation	SNP	C	C	T	rs61747868	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:1642736C>T	ENST00000252804.4	-	21	4138	c.4088G>A	c.(4087-4089)gGg>gAg	p.G1363E		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	1363					extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		GAGATGTTCCCCCTGTCTCCC	0.527													C|||	49	0.00978435	0.034	0.0043	5008	,	,		20724	0.0		0.001	False		,,,				2504	0.0				p.G1363E		Atlas-SNP	.											.	PXDN	255	.	0			c.G4088A						PASS	.	C	GLU/GLY	96,4162		1,94,2034	103.0	106.0	105.0		4088	3.2	0.0	2	dbSNP_129	105	5,8489		0,5,4242	yes	missense	PXDN	NM_012293.1	98	1,99,6276	TT,TC,CC		0.0589,2.2546,0.792	benign	1363/1480	1642736	101,12651	2129	4247	6376	SO:0001583	missense	7837	exon21			TGTTCCCCCTGTC	AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"""Immunoglobulin superfamily / I-set domain containing"""	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.4088G>A	2.37:g.1642736C>T	ENSP00000252804:p.Gly1363Glu	105.0	0.0	0		107.0	47.0	0.439252	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Missense_Mutation	SNP	ENST00000252804.4	37	CCDS46221.1	17	0.007783882783882784	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	0	0.0	C	0.157	-1.085078	0.01888	0.022546	5.89E-4	ENSG00000130508	ENST00000252804	T	0.58652	0.32	5.07	3.21	0.36854	.	1.792660	0.02747	N	0.116942	T	0.22205	0.0535	L	0.36672	1.1	0.09310	N	1	B	0.16603	0.018	B	0.18263	0.021	T	0.24728	-1.0152	10	0.02654	T	1	-1.7644	7.7153	0.28700	0.0:0.7222:0.0:0.2778	.	1363	Q92626	PXDN_HUMAN	E	1363	ENSP00000252804:G1363E	ENSP00000252804:G1363E	G	-	2	0	PXDN	1621743	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.343000	0.19944	0.604000	0.29930	0.563000	0.77884	GGG	C|0.992;T|0.008	0.008	strong		0.527	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455	
OR7A10	390892	hgsc.bcm.edu	37	19	14952189	14952189	+	Silent	SNP	G	G	T	rs114596415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14952189G>T	ENST00000248058.1	-	1	500	c.501C>A	c.(499-501)ccC>ccA	p.P167P		NM_001005190.1	NP_001005190.1	O76100	OR7AA_HUMAN	olfactory receptor, family 7, subfamily A, member 10	167						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)					GTGTACAAAAGGGCAGTGGCA	0.418													.|||	115	0.0229633	0.0832	0.0058	5008	,	,		22672	0.0		0.001	False		,,,				2504	0.0				p.P167P		Atlas-SNP	.											OR7A10,NS,carcinoma,-2,1	OR7A10	33	1	0			c.C501A						PASS	.	G		235,4171	137.7+/-173.5	8,219,1976	81.0	79.0	80.0		501	-4.2	0.0	19	dbSNP_132	80	1,8599		0,1,4299	no	coding-synonymous	OR7A10	NM_001005190.1		8,220,6275	TT,TG,GG		0.0116,5.3336,1.8145		167/310	14952189	236,12770	2203	4300	6503	SO:0001819	synonymous_variant	390892	exon1			ACAAAAGGGCAGT		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.501C>A	19.37:g.14952189G>T		137.0	0.0	0		152.0	74.0	0.486842	NM_001005190	Q6IFP0|Q96R97	Silent	SNP	ENST00000248058.1	37	CCDS32936.1																																																																																			G|0.980;T|0.020	0.020	strong		0.418	OR7A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466520.1	NM_001005190	
ASMTL	8623	hgsc.bcm.edu	37	X	1531701	1531701	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:1531701C>T	ENST00000381317.3	-	12	1601	c.1569G>A	c.(1567-1569)ctG>ctA	p.L523L	ASMTL_ENST00000534940.1_Silent_p.L465L|ASMTL_ENST00000381333.4_Silent_p.L507L|ASMTL-AS1_ENST00000420411.2_RNA|ASMTL-AS1_ENST00000602357.1_RNA|ASMTL_ENST00000416733.2_Silent_p.L447L|ASMTL-AS1_ENST00000419737.2_RNA|ASMTL-AS1_ENST00000425740.2_RNA	NM_004192.3	NP_004183.2	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like	523	ASMT-like.					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)				GGATCCGGCACAGGACGTACA	0.562													c|||	95	0.0189696	0.0703	0.0014	5008	,	,		16507	0.0		0.001	False		,,,				2504	0.0				p.L523L		Atlas-SNP	.											.	ASMTL	56	.	0			c.G1569A						PASS	.		,,	280,3766		9,262,1752	160.0	174.0	169.0		1395,1521,1569	-1.9	0.0	X	dbSNP_134	169	2,8348		0,2,4173	no	coding-synonymous,coding-synonymous,coding-synonymous	ASMTL	NM_001173473.1,NM_001173474.1,NM_004192.3	,,	9,264,5925	TT,TC,CC		0.024,6.9204,2.2749	,,	465/564,507/606,523/622	1531701	282,12114	2023	4175	6198	SO:0001819	synonymous_variant	8623	exon12			CCGGCACAGGACG	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.1569G>A	X.37:g.1531701C>T		404.0	1.0	0.00247525		448.0	211.0	0.470982	NM_004192	B4DX75|F5GXH4|J3JS33|Q5JQ53|Q8NBH5|Q96G02|Q9BUL6	Silent	SNP	ENST00000381317.3	37	CCDS43917.1																																																																																			C|0.981;T|0.019	0.019	strong		0.562	ASMTL-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055595.1	NM_004192	
ATP1A4	480	hgsc.bcm.edu	37	1	160129273	160129273	+	Silent	SNP	G	G	A	rs61734686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:160129273G>A	ENST00000368081.4	+	6	1206	c.735G>A	c.(733-735)ctG>ctA	p.L245L		NM_144699.3	NP_653300.2	Q13733	AT1A4_HUMAN	ATPase, Na+/K+ transporting, alpha 4 polypeptide	245					ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|fertilization (GO:0009566)|ion transmembrane transport (GO:0034220)|potassium ion transport (GO:0006813)|regulation of cellular pH (GO:0030641)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(34)|ovary(2)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	75	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			AGAACCCTCTGGAGACCCGAA	0.507													G|||	53	0.0105831	0.0401	0.0	5008	,	,		17615	0.0		0.0	False		,,,				2504	0.0				p.L245L		Atlas-SNP	.											.	ATP1A4	167	.	0			c.G735A						PASS	.	G		96,4310	77.3+/-115.6	3,90,2110	97.0	100.0	99.0		735	2.6	1.0	1	dbSNP_129	99	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ATP1A4	NM_144699.3		3,91,6409	AA,AG,GG		0.0116,2.1788,0.7458		245/1030	160129273	97,12909	2203	4300	6503	SO:0001819	synonymous_variant	480	exon6			CCCTCTGGAGACC	BC028297	CCDS1197.1, CCDS44255.1	1q23.2	2012-10-22	2002-02-25		ENSG00000132681	ENSG00000132681		"""ATPases / P-type"""	14073	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-4"", ""sodium pump subunit alpha-4"", ""sodium-potassium ATPase catalytic subunit alpha-4"""	607321	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 2"""	ATP1AL2		1981991, 3035563	Standard	NM_144699		Approved		uc001fve.4	Q13733	OTTHUMG00000031609	ENST00000368081.4:c.735G>A	1.37:g.160129273G>A		176.0	0.0	0		150.0	72.0	0.48	NM_144699	Q504T2|Q7Z4I9|Q8TBN8|Q8WXA7|Q8WXH7|Q8WY13	Silent	SNP	ENST00000368081.4	37	CCDS1197.1																																																																																			G|0.992;A|0.008	0.008	strong		0.507	ATP1A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077415.1	NM_144699	
FLNA	2316	hgsc.bcm.edu	37	X	153581214	153581214	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:153581214C>A	ENST00000369850.3	-	39	6541	c.6305G>T	c.(6304-6306)tGc>tTc	p.C2102F	FLNA_ENST00000422373.1_Missense_Mutation_p.C2094F|FLNA_ENST00000369856.3_Missense_Mutation_p.C235F|FLNA_ENST00000344736.4_Missense_Mutation_p.C2062F|FLNA_ENST00000360319.4_Missense_Mutation_p.C2094F|FLNA_ENST00000498491.1_5'Flank	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	2102					actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GGTGACCCTGCACGTCCCGTC	0.607																																					p.C2102F		Atlas-SNP	.											.	FLNA	373	.	0			c.G6305T						PASS	.						108.0	109.0	109.0					X																	153581214		2157	4239	6396	SO:0001583	missense	2316	exon39			ACCCTGCACGTCC	X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924			3754	protein-coding gene	gene with protein product	"""actin binding protein 280"""	300017	"""filamin A, alpha (actin binding protein 280)"""	FLN1, FLN, OPD2, OPD1		8406501, 12612583	Standard	NM_001456		Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000369850.3:c.6305G>T	X.37:g.153581214C>A	ENSP00000358866:p.Cys2102Phe	167.0	0.0	0		182.0	41.0	0.225275	NM_001110556	E9KL45|Q5HY53|Q5HY55|Q8NF52	Missense_Mutation	SNP	ENST00000369850.3	37	CCDS48194.1	.	.	.	.	.	.	.	.	.	.	C	16.87	3.241318	0.58995	.	.	ENSG00000196924	ENST00000360319;ENST00000422373;ENST00000369850;ENST00000369856;ENST00000344736;ENST00000444578	D;D;D;D;D;D	0.83673	-1.75;-1.75;-1.75;-1.75;-1.75;-1.75	5.64	5.64	0.86602	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.90477	0.7017	M	0.73217	2.22	0.80722	D	1	D;D;B;B	0.71674	0.994;0.998;0.407;0.407	P;D;B;B	0.67900	0.89;0.954;0.356;0.356	D	0.91224	0.5009	10	0.72032	D	0.01	.	18.7428	0.91780	0.0:1.0:0.0:0.0	.	235;2094;2102;2102	E9PHF0;P21333-2;P21333;E9KL45	.;.;FLNA_HUMAN;.	F	2094;2094;2102;235;2062;83	ENSP00000353467:C2094F;ENSP00000416926:C2094F;ENSP00000358866:C2102F;ENSP00000358872:C235F;ENSP00000358863:C2062F;ENSP00000397824:C83F	ENSP00000358863:C2062F	C	-	2	0	FLNA	153234408	1.000000	0.71417	0.989000	0.46669	0.513000	0.34164	7.779000	0.85648	2.372000	0.80975	0.513000	0.50165	TGC	.	.	none		0.607	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3		
FBF1	85302	hgsc.bcm.edu	37	17	73913827	73913827	+	Silent	SNP	G	G	T	rs150139322	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73913827G>T	ENST00000586717.1	-	22	2722	c.2449C>A	c.(2449-2451)Cgg>Agg	p.R817R	FBF1_ENST00000319129.5_Silent_p.R816R|FBF1_ENST00000389570.4_Silent_p.R817R			Q8TES7	FBF1_HUMAN	Fas (TNFRSF6) binding factor 1	817					apical junction assembly (GO:0043297)|cilium assembly (GO:0042384)|establishment of epithelial cell polarity (GO:0090162)	cell junction (GO:0030054)|centriole (GO:0005814)|ciliary transition fiber (GO:0097539)|spindle pole (GO:0000922)				large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	4						TCCAGCAGCCGGCTCTGCTCA	0.697													G|||	17	0.00339457	0.0129	0.0	5008	,	,		17377	0.0		0.0	False		,,,				2504	0.0				p.R816R		Atlas-SNP	.											.	FBF1	48	.	0			c.C2446A						PASS	.	G		36,4118		0,36,2041	25.0	29.0	28.0		2446	3.9	1.0	17	dbSNP_134	28	1,8413		0,1,4206	no	coding-synonymous	FBF1	NM_001080542.1		0,37,6247	TT,TG,GG		0.0119,0.8666,0.2944		816/1134	73913827	37,12531	2077	4207	6284	SO:0001819	synonymous_variant	85302	exon22			GCAGCCGGCTCTG	AK074045	CCDS45779.1	17q25.3	2011-04-21			ENSG00000188878	ENSG00000188878			24674	protein-coding gene	gene with protein product	"""albatross"""					11347906	Standard	NM_001080542		Approved	FLJ00103, FBF-1, KIAA1863, ALB	uc002jqc.3	Q8TES7		ENST00000586717.1:c.2449C>A	17.37:g.73913827G>T		161.0	0.0	0		185.0	85.0	0.459459	NM_001080542	B5MEM5|Q96IF6|Q96JG4|Q96MA8	Silent	SNP	ENST00000586717.1	37																																																																																				G|0.997;T|0.003	0.003	strong		0.697	FBF1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000448945.2	NM_001080542	
OR4D9	390199	hgsc.bcm.edu	37	11	59283299	59283299	+	Missense_Mutation	SNP	T	T	C	rs79922105	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:59283299T>C	ENST00000329328.3	+	1	914	c.914T>C	c.(913-915)cTa>cCa	p.L305P		NM_001004711.1	NP_001004711.1	Q8NGE8	OR4D9_HUMAN	olfactory receptor, family 4, subfamily D, member 9	305						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(3)|lung(14)|prostate(5)|upper_aerodigestive_tract(1)	26						AAGAGACGGCTAGGACAATCA	0.383													T|||	108	0.0215655	0.0802	0.0029	5008	,	,		20633	0.0		0.0	False		,,,				2504	0.0				p.L305P		Atlas-SNP	.											.	OR4D9	47	.	0			c.T914C						PASS	.	T	PRO/LEU	260,4142	140.0+/-175.5	8,244,1949	54.0	56.0	55.0		914	2.3	0.0	11	dbSNP_132	55	1,8589		0,1,4294	yes	missense	OR4D9	NM_001004711.1	98	8,245,6243	CC,CT,TT		0.0116,5.9064,2.0089	possibly-damaging	305/315	59283299	261,12731	2201	4295	6496	SO:0001583	missense	390199	exon1			GACGGCTAGGACA	AB065861	CCDS31564.1	11q12.1	2012-08-09	2003-12-15		ENSG00000172742	ENSG00000172742		"""GPCR / Class A : Olfactory receptors"""	15178	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily D, member 9 pseudogene"""				Standard	NM_001004711		Approved		uc010rkv.2	Q8NGE8	OTTHUMG00000167343	ENST00000329328.3:c.914T>C	11.37:g.59283299T>C	ENSP00000328563:p.Leu305Pro	69.0	0.0	0		83.0	26.0	0.313253	NM_001004711	Q6IFF3	Missense_Mutation	SNP	ENST00000329328.3	37	CCDS31564.1	53	0.024267399267399268	52	0.10569105691056911	1	0.0027624309392265192	0	0.0	0	0.0	T	6.379	0.438092	0.12104	0.059064	1.16E-4	ENSG00000172742	ENST00000329328	T	0.38887	1.11	3.47	2.29	0.28610	.	0.257134	0.20056	U	0.100183	T	0.00356	0.0011	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.18263	0.021	T	0.09975	-1.0650	10	0.37606	T	0.19	.	4.1407	0.10191	0.208:0.0:0.2151:0.5769	.	305	Q8NGE8	OR4D9_HUMAN	P	305	ENSP00000328563:L305P	ENSP00000328563:L305P	L	+	2	0	OR4D9	59039875	0.003000	0.15002	0.001000	0.08648	0.002000	0.02628	1.303000	0.33470	0.480000	0.27534	-0.490000	0.04691	CTA	T|0.980;C|0.020	0.020	strong		0.383	OR4D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394237.1	NM_001004711	
ATP13A4	84239	hgsc.bcm.edu	37	3	193120627	193120627	+	Silent	SNP	C	C	T	rs61733355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:193120627C>T	ENST00000342695.4	-	30	3727	c.3405G>A	c.(3403-3405)ctG>ctA	p.L1135L	ATP13A4_ENST00000392443.3_Silent_p.L1116L|ATP13A4_ENST00000482964.1_5'UTR|ATP13A4_ENST00000400270.2_Silent_p.L151L	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	1135						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(27)|ovary(2)|prostate(3)|skin(11)|upper_aerodigestive_tract(2)	71	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		TCATCATCCACAGGGCTCGAT	0.448													C|||	72	0.014377	0.0522	0.0043	5008	,	,		18910	0.0		0.0	False		,,,				2504	0.0				p.L1135L		Atlas-SNP	.											.	ATP13A4	154	.	0			c.G3405A						PASS	.	C		237,4169	139.2+/-174.8	10,217,1976	74.0	71.0	72.0		3405	0.0	1.0	3	dbSNP_129	72	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	ATP13A4	NM_032279.2		10,220,6273	TT,TC,CC		0.0349,5.379,1.8453		1135/1197	193120627	240,12766	2203	4300	6503	SO:0001819	synonymous_variant	84239	exon30			CATCCACAGGGCT	AK095277	CCDS3304.2	3q29	2010-04-20			ENSG00000127249	ENSG00000127249		"""ATPases / P-type"""	25422	protein-coding gene	gene with protein product		609556				14702039, 12975309	Standard	XM_005247829		Approved	DKFZp761I1011, FLJ37958	uc003ftd.3	Q4VNC1	OTTHUMG00000074067	ENST00000342695.4:c.3405G>A	3.37:g.193120627C>T		128.0	0.0	0		146.0	63.0	0.431507	NM_032279	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Silent	SNP	ENST00000342695.4	37	CCDS3304.2																																																																																			C|0.982;T|0.018	0.018	strong		0.448	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279	
NOP9	161424	hgsc.bcm.edu	37	14	24772373	24772373	+	Missense_Mutation	SNP	C	C	T	rs147123517	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24772373C>T	ENST00000267425.3	+	6	1330	c.1237C>T	c.(1237-1239)Cgc>Tgc	p.R413C	NOP9_ENST00000396802.3_Missense_Mutation_p.R413C	NM_174913.1	NP_777573.1	Q86U38	NOP9_HUMAN	NOP9 nucleolar protein	413							poly(A) RNA binding (GO:0044822)										GGGGGCCTGTCGCAGAGTTGG	0.557													C|||	8	0.00159744	0.0	0.0014	5008	,	,		16884	0.0		0.007	False		,,,				2504	0.0				p.R413C		Atlas-SNP	.											.	.	.	.	0			c.C1237T						PASS	.	C	CYS/ARG	4,4402	6.2+/-15.9	0,4,2199	70.0	71.0	71.0		1237	4.2	1.0	14	dbSNP_134	71	45,8555	30.1+/-81.4	0,45,4255	yes	missense	C14orf21	NM_174913.1	180	0,49,6454	TT,TC,CC		0.5233,0.0908,0.3767	probably-damaging	413/637	24772373	49,12957	2203	4300	6503	SO:0001583	missense	161424	exon6			GCCTGTCGCAGAG		CCDS9624.1, CCDS66616.1	14q12	2012-12-10	2012-12-10	2012-06-06	ENSG00000196943	ENSG00000196943			19826	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 21"", ""NOP9 nucleolar protein homolog (yeast)"""	C14orf21		21653694	Standard	XM_005267385		Approved		uc001wol.1	Q86U38	OTTHUMG00000029342	ENST00000267425.3:c.1237C>T	14.37:g.24772373C>T	ENSP00000267425:p.Arg413Cys	148.0	0.0	0		150.0	70.0	0.466667	NM_174913	A8MY76|Q8IVF0|Q8TBS6	Missense_Mutation	SNP	ENST00000267425.3	37	CCDS9624.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	18.19	3.567896	0.65651	9.08E-4	0.005233	ENSG00000196943	ENST00000267425;ENST00000396802	T;T	0.32753	1.48;1.44	5.16	4.25	0.50352	.	0.224065	0.38897	N	0.001525	T	0.35189	0.0923	L	0.54323	1.7	0.43536	D	0.995829	D	0.76494	0.999	P	0.59288	0.855	T	0.23013	-1.0200	10	0.52906	T	0.07	-4.9362	11.1833	0.48642	0.4521:0.5479:0.0:0.0	.	413	Q86U38	CN021_HUMAN	C	413	ENSP00000267425:R413C;ENSP00000380020:R413C	ENSP00000267425:R413C	R	+	1	0	C14orf21	23842213	0.869000	0.29996	1.000000	0.80357	0.909000	0.53808	0.630000	0.24553	1.356000	0.45884	0.563000	0.77884	CGC	C|0.996;T|0.004	0.004	strong		0.557	NOP9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073186.2		
IRGQ	126298	hgsc.bcm.edu	37	19	44096772	44096772	+	Silent	SNP	C	C	T	rs114508854	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44096772C>T	ENST00000602269.1	-	2	1463	c.1278G>A	c.(1276-1278)gaG>gaA	p.E426E	IRGQ_ENST00000422989.1_Silent_p.E426E|L34079.2_ENST00000594374.1_Intron|IRGQ_ENST00000601520.1_Intron			Q8WZA9	IRGQ_HUMAN	immunity-related GTPase family, Q	426	IRG-type G.									endometrium(2)|large_intestine(4)|lung(6)|ovary(2)|pancreas(1)|prostate(3)	18		Prostate(69;0.0199)				GCGGCGGCGCCTCCTCCAGCA	0.687													C|||	128	0.0255591	0.0613	0.0029	5008	,	,		13730	0.0308		0.0	False		,,,				2504	0.0143				p.E426E		Atlas-SNP	.											.	IRGQ	40	.	0			c.G1278A						PASS	.	C		173,4233	106.5+/-144.9	4,165,2034	39.0	44.0	42.0		1278	2.0	0.9	19	dbSNP_132	42	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	IRGQ	NM_001007561.2		4,169,6330	TT,TC,CC		0.0465,3.9265,1.3609		426/624	44096772	177,12829	2203	4300	6503	SO:0001819	synonymous_variant	126298	exon3			CGGCGCCTCCTCC	AF322648	CCDS33040.1	19q13.31	2013-07-03	2005-10-31	2005-10-31		ENSG00000167378			24868	protein-coding gene	gene with protein product			"""immunity-related GTPase family, Q1"""	IRGQ1		16277747	Standard	NM_001007561		Approved	FKSG27	uc010eiv.2	Q8WZA9		ENST00000602269.1:c.1278G>A	19.37:g.44096772C>T		21.0	0.0	0		26.0	13.0	0.5	NM_001007561	B2RNP3	Silent	SNP	ENST00000602269.1	37	CCDS33040.1																																																																																			C|0.981;T|0.019	0.019	strong		0.687	IRGQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463205.1	NM_001007561	
NBPF7	343505	hgsc.bcm.edu	37	1	120378702	120378702	+	IGR	SNP	A	A	G	rs10158823	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:120378702A>G								REG4 (24419 upstream) : ADAM30 (57453 downstream)																							CTTTCTGTTCAACTAGTGCCA	0.488													a|||	405	0.0808706	0.295	0.0216	5008	,	,		21265	0.0		0.0	False		,,,				2504	0.0				p.V348V		Atlas-SNP	.											.	NBPF7	46	.	0			c.T1044C						PASS	.	A		848,3086		97,654,1216	107.0	106.0	107.0		1044	-0.1	0.0	1	dbSNP_119	107	21,8319		0,21,4149	no	coding-synonymous	NBPF7	NM_001047980.1		97,675,5365	GG,GA,AA		0.2518,21.5557,7.08		348/422	120378702	869,11405	1967	4170	6137	SO:0001628	intergenic_variant	343505	exon7			CTGTTCAACTAGT																													1.37:g.120378702A>G		152.0	0.0	0		203.0	105.0	0.517241	NM_001047980		Silent	SNP		37																																																																																				A|0.919;G|0.081	0.081	strong	0	0.488								
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324254	39324254	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39324254G>A	ENST00000391356.2	-	1	170	c.171C>T	c.(169-171)tcC>tcT	p.S57S		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	57	29 X 5 AA repeats of C-C-[GIKRQVH]-[SPT]- [STA].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			tgcagcagctggagatacagc	0.642																																					p.S57S		Atlas-SNP	.											.	KRTAP4-3	40	.	0			c.C171T						PASS	.						3.0	4.0	4.0					17																	39324254		1542	3395	4937	SO:0001819	synonymous_variant	85290	exon1			GCAGCTGGAGATA	AJ406935	CCDS42331.1	17q21.2	2013-06-25			ENSG00000196156	ENSG00000196156		"""Keratin associated proteins"""	18908	protein-coding gene	gene with protein product							Standard	NM_033187		Approved	KAP4.3	uc010cxl.3	Q9BYR4	OTTHUMG00000133639	ENST00000391356.2:c.171C>T	17.37:g.39324254G>A		434.0	0.0	0		210.0	33.0	0.157143	NM_033187		Silent	SNP	ENST00000391356.2	37	CCDS42331.1																																																																																			.	.	none		0.642	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1		
IQGAP3	128239	hgsc.bcm.edu	37	1	156539169	156539169	+	Splice_Site	SNP	G	G	A	rs370931618		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156539169G>A	ENST00000361170.2	-	2	134	c.124C>T	c.(124-126)Cgc>Tgc	p.R42C		NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	42	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TCCGCTCACCGCTTGGCCTCC	0.557													G|||	1	0.000199681	0.0008	0.0	5008	,	,		13122	0.0		0.0	False		,,,				2504	0.0				p.R42C		Atlas-SNP	.											.	IQGAP3	146	.	0			c.C124T						PASS	.	G	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	43.0	36.0	39.0		124	5.0	1.0	1		39	0,8600		0,0,4300	no	missense-near-splice	IQGAP3	NM_178229.4	180	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	42/1632	156539169	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	128239	exon2			CTCACCGCTTGGC	AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.125+1C>T	1.37:g.156539169G>A		153.0	0.0	0		107.0	43.0	0.401869	NM_178229	Q5T3H8	Missense_Mutation	SNP	ENST00000361170.2	37	CCDS1144.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.053545	0.75960	2.27E-4	0.0	ENSG00000183856	ENST00000361170	D	0.95554	-3.74	4.97	4.97	0.65823	Calponin homology domain (5);	0.000000	0.85682	D	0.000000	D	0.97139	0.9065	M	0.72353	2.195	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.97567	1.0102	10	0.72032	D	0.01	-13.4997	16.978	0.86319	0.0:0.0:1.0:0.0	.	42	Q86VI3	IQGA3_HUMAN	C	42	ENSP00000354451:R42C	ENSP00000354451:R42C	R	-	1	0	IQGAP3	154805793	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	2.887000	0.48586	2.592000	0.87571	0.467000	0.42956	CGC	.	.	none		0.557	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229	Missense_Mutation
DNAH6	1768	hgsc.bcm.edu	37	2	84752784	84752784	+	Silent	SNP	A	A	C	rs73945104	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:84752784A>C	ENST00000237449.6	+	2	329	c.321A>C	c.(319-321)ccA>ccC	p.P107P	DNAH6_ENST00000468661.1_3'UTR|DNAH6_ENST00000389394.3_Silent_p.P107P|DNAH6_ENST00000398278.2_Silent_p.P107P			Q9C0G6	DYH6_HUMAN	dynein, axonemal, heavy chain 6	107	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(9)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	57						TTAAACGTCCAGTAAGCATAG	0.348													A|||	65	0.0129792	0.0477	0.0029	5008	,	,		16979	0.0		0.0	False		,,,				2504	0.0				p.P107P		Atlas-SNP	.											.	DNAH6	194	.	0			c.A321C						PASS	.						114.0	92.0	98.0					2																	84752784		692	1591	2283	SO:0001819	synonymous_variant	1768	exon3			ACGTCCAGTAAGC	U61736	CCDS46348.1	2p11.2	2011-05-24	2006-09-04		ENSG00000115423	ENSG00000115423		"""Axonemal dyneins"""	2951	protein-coding gene	gene with protein product		603336	"""dynein, axonemal, heavy polypeptide 6"", ""dynein heavy chain-like 1"""	DNHL1		8812413	Standard	NM_001370		Approved	Dnahc6, HL-2, FLJ37357	uc010fgb.3	Q9C0G6	OTTHUMG00000128957	ENST00000237449.6:c.321A>C	2.37:g.84752784A>C		277.0	0.0	0		261.0	130.0	0.498084	NM_001370	A0PJN9|B5MEE0|B7ZL99|O95493|Q53QZ1|Q53TE5|Q8N1W6|Q92861|Q96BL6|Q9H030|Q9H5E1	Silent	SNP	ENST00000237449.6	37	CCDS46348.1																																																																																			A|0.989;C|0.011	0.011	strong		0.348	DNAH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328537.2	NM_001370	
THBS1	7057	hgsc.bcm.edu	37	15	39874396	39874396	+	Missense_Mutation	SNP	T	T	G	rs41515347	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:39874396T>G	ENST00000260356.5	+	3	235	c.70T>G	c.(70-72)Tct>Gct	p.S24A		NM_003246.2	NP_003237.2	P07996	TSP1_HUMAN	thrombospondin 1	24			S -> A (in dbSNP:rs41515347).		activation of MAPK activity (GO:0000187)|behavioral response to pain (GO:0048266)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular response to growth factor stimulus (GO:0071363)|cellular response to heat (GO:0034605)|cellular response to tumor necrosis factor (GO:0071356)|chronic inflammatory response (GO:0002544)|endocardial cushion development (GO:0003197)|engulfment of apoptotic cell (GO:0043652)|extracellular matrix organization (GO:0030198)|growth plate cartilage development (GO:0003417)|immune response (GO:0006955)|negative regulation of angiogenesis (GO:0016525)|negative regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II (GO:0002581)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cGMP-mediated signaling (GO:0010754)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of dendritic cell antigen processing and presentation (GO:0002605)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide mediated signal transduction (GO:0010751)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of plasminogen activation (GO:0010757)|outflow tract morphogenesis (GO:0003151)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of chemotaxis (GO:0050921)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of macrophage activation (GO:0043032)|positive regulation of macrophage chemotaxis (GO:0010759)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of translation (GO:0045727)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to endoplasmic reticulum stress (GO:0034976)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to magnesium ion (GO:0032026)|response to mechanical stimulus (GO:0009612)|response to progesterone (GO:0032570)|response to testosterone (GO:0033574)|response to unfolded protein (GO:0006986)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|sarcoplasmic reticulum (GO:0016529)|secretory granule (GO:0030141)	calcium ion binding (GO:0005509)|collagen V binding (GO:0070052)|fibrinogen binding (GO:0070051)|fibroblast growth factor binding (GO:0017134)|fibronectin binding (GO:0001968)|glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|laminin binding (GO:0043236)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|proteoglycan binding (GO:0043394)|transforming growth factor beta binding (GO:0050431)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(5)|large_intestine(15)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	53		all_cancers(109;1.35e-17)|all_epithelial(112;2.07e-15)|Lung NSC(122;4.44e-11)|all_lung(180;1.11e-09)|Melanoma(134;0.0574)|Colorectal(260;0.117)|Ovarian(310;0.223)		GBM - Glioblastoma multiforme(113;2.77e-06)|BRCA - Breast invasive adenocarcinoma(123;0.105)		TCTAACAGAGTCTGGCGGAGA	0.597													T|||	183	0.0365415	0.1241	0.0101	5008	,	,		18737	0.0099		0.001	False		,,,				2504	0.001				p.S24A		Atlas-SNP	.											.	THBS1	106	.	0			c.T70G						PASS	.	T	ALA/SER	457,3939	207.2+/-228.6	28,401,1769	36.0	39.0	38.0		70	4.0	1.0	15	dbSNP_127	38	7,8579	5.7+/-21.5	0,7,4286	yes	missense	THBS1	NM_003246.2	99	28,408,6055	GG,GT,TT		0.0815,10.3958,3.5742	benign	24/1171	39874396	464,12518	2198	4293	6491	SO:0001583	missense	7057	exon3			ACAGAGTCTGGCG		CCDS32194.1	15q15	2009-04-08			ENSG00000137801	ENSG00000137801			11785	protein-coding gene	gene with protein product	"""thrombospondin-1p180"""	188060				2341158, 2335352	Standard	NM_003246		Approved	TSP1, THBS, TSP, THBS-1, TSP-1	uc001zkh.3	P07996	OTTHUMG00000133665	ENST00000260356.5:c.70T>G	15.37:g.39874396T>G	ENSP00000260356:p.Ser24Ala	76.0	0.0	0		94.0	41.0	0.43617	NM_003246	A8K6H4|B4E3J7|B9EGH6|Q15667|Q59E99	Missense_Mutation	SNP	ENST00000260356.5	37	CCDS32194.1	73	0.033424908424908424	62	0.12601626016260162	5	0.013812154696132596	5	0.008741258741258742	1	0.0013192612137203166	T	17.25	3.342644	0.61073	0.103958	8.15E-4	ENSG00000137801	ENST00000260356;ENST00000397591	T;T	0.78003	-1.14;0.73	5.17	4.02	0.46733	Laminin G, thrombospondin-type, N-terminal (1);	0.000000	0.35708	N	0.003030	T	0.02727	0.0082	N	0.22421	0.69	0.32910	D	0.514417	D	0.58268	0.982	D	0.67548	0.952	T	0.52586	-0.8556	10	0.34782	T	0.22	-12.2229	11.4375	0.50076	0.0:0.0:0.1511:0.8489	rs41515347;rs61731227	24	P07996	TSP1_HUMAN	A	24	ENSP00000260356:S24A;ENSP00000380720:S24A	ENSP00000260356:S24A	S	+	1	0	THBS1	37661688	1.000000	0.71417	0.993000	0.49108	0.712000	0.41017	5.745000	0.68672	0.947000	0.37659	0.460000	0.39030	TCT	T|0.969;G|0.031	0.031	strong		0.597	THBS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257831.2	NM_003246	
LIPE	3991	hgsc.bcm.edu	37	19	42910416	42910416	+	Silent	SNP	C	C	T	rs28657829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42910416C>T	ENST00000244289.4	-	7	2538	c.2262G>A	c.(2260-2262)ccG>ccA	p.P754P	LIPE_ENST00000602000.1_5'Flank|LIPE-AS1_ENST00000594624.2_RNA|LIPE-AS1_ENST00000597203.1_RNA|LIPE-AS1_ENST00000599276.1_RNA|LIPE-AS1_ENST00000593491.2_RNA	NM_005357.2	NP_005348.2	Q05469	LIPS_HUMAN	lipase, hormone-sensitive	754					cholesterol metabolic process (GO:0008203)|diacylglycerol catabolic process (GO:0046340)|lipid catabolic process (GO:0016042)|long-chain fatty acid catabolic process (GO:0042758)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)	hormone-sensitive lipase activity (GO:0033878)|triglyceride lipase activity (GO:0004806)			breast(2)|endometrium(4)|kidney(7)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		Prostate(69;0.00682)				GCATTGTGGCCGGGTAGGCTG	0.662													C|||	103	0.0205671	0.0726	0.0072	5008	,	,		14500	0.0		0.002	False		,,,				2504	0.0				p.P754P		Atlas-SNP	.											LIPE,rectum,carcinoma,-1,1	LIPE	83	1	0			c.G2262A						PASS	.	C		229,4177	131.4+/-167.9	6,217,1980	47.0	45.0	45.0		2262	-10.2	0.1	19	dbSNP_125	45	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous	LIPE	NM_005357.2		6,227,6270	TT,TC,CC		0.1163,5.1975,1.8376		754/1077	42910416	239,12767	2203	4300	6503	SO:0001819	synonymous_variant	3991	exon7			TGTGGCCGGGTAG	L11706	CCDS12607.1	19q13.1-q13.2	2014-03-14			ENSG00000079435	ENSG00000079435	3.1.1.3		6621	protein-coding gene	gene with protein product		151750				8506334	Standard	NM_005357		Approved	HSL	uc002otr.3	Q05469	OTTHUMG00000182814	ENST00000244289.4:c.2262G>A	19.37:g.42910416C>T		92.0	0.0	0		124.0	56.0	0.451613	NM_005357	Q3LRT2|Q6NSL7	Silent	SNP	ENST00000244289.4	37	CCDS12607.1																																																																																			C|0.978;T|0.022	0.022	strong		0.662	LIPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463861.1	NM_005357	
ODF2	4957	hgsc.bcm.edu	37	9	131260808	131260808	+	Missense_Mutation	SNP	C	C	G	rs16930426	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131260808C>G	ENST00000434106.3	+	19	2492	c.2129C>G	c.(2128-2130)aCc>aGc	p.T710S	ODF2_ENST00000444119.2_Missense_Mutation_p.T686S|ODF2_ENST00000351030.3_Missense_Mutation_p.T705S|ODF2_ENST00000393527.3_Missense_Mutation_p.T686S|ODF2_ENST00000372807.5_Missense_Mutation_p.T705S|ODF2_ENST00000604420.1_Missense_Mutation_p.T710S	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	710			T -> S (in dbSNP:rs16930426).		G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|regulation of cilium assembly (GO:1902017)|spermatid development (GO:0007286)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)|primary cilium (GO:0072372)	Rab GTPase binding (GO:0017137)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(7)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	37						GAATGTGGGACCctggcaagg	0.542													C|||	106	0.0211661	0.0749	0.0086	5008	,	,		20036	0.0		0.001	False		,,,				2504	0.0				p.T774S		Atlas-SNP	.											.	ODF2	227	.	0			c.C2321G						PASS	.	C	SER/THR,SER/THR,SER/THR,SER/THR,SER/THR	330,4076	173.0+/-202.9	15,300,1888	73.0	62.0	66.0		2114,2129,2057,2129,2321	3.8	0.3	9	dbSNP_123	66	4,8596	3.0+/-9.4	0,4,4296	yes	missense,missense,missense,missense,missense	ODF2	NM_001242352.1,NM_001242353.1,NM_002540.4,NM_153433.1,NM_153435.1	58,58,58,58,58	15,304,6184	GG,GC,CC		0.0465,7.4898,2.568	benign,benign,benign,benign,benign	705/825,710/830,686/806,710/830,774/894	131260808	334,12672	2203	4300	6503	SO:0001583	missense	4957	exon19			GTGGGACCCTGGC	AF012549	CCDS6902.1, CCDS56585.1, CCDS56586.1, CCDS56587.1, CCDS56588.1, CCDS56589.1, CCDS56590.1	9q34	2010-04-23	2002-10-21		ENSG00000136811	ENSG00000136811			8114	protein-coding gene	gene with protein product	"""cancer/testis antigen 134"""	602015	"""outer dense fibre of sperm tails 2"""			9045620, 10072582	Standard	NM_153435		Approved	ODF84, CT134	uc004bvc.3	Q5BJF6	OTTHUMG00000020748	ENST00000434106.3:c.2129C>G	9.37:g.131260808C>G	ENSP00000403453:p.Thr710Ser	128.0	0.0	0		117.0	76.0	0.649573	NM_153435	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Missense_Mutation	SNP	ENST00000434106.3	37	CCDS56588.1	45	0.020604395604395604	41	0.08333333333333333	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	C	9.645	1.139924	0.21205	0.074898	4.65E-4	ENSG00000136811	ENST00000351030;ENST00000372796;ENST00000303890	T;T;T	0.20069	2.1;2.11;2.1	5.67	3.8	0.43715	.	1.035180	0.07583	N	0.920674	T	0.00468	0.0015	N	0.01576	-0.805	0.25699	N	0.985609	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	0.09997	-1.0649	10	0.05721	T	0.95	-0.0175	15.5266	0.75915	0.0:0.6681:0.3319:0.0	rs16930426;rs52827709;rs16930426	705;55;710;686	Q5BJF6-4;Q6PJQ8;Q5BJF6;Q5BJF6-3	.;.;ODFP2_HUMAN;.	S	705;710;686	ENSP00000342581:T705S;ENSP00000361882:T710S;ENSP00000307781:T686S	ENSP00000307781:T686S	T	+	2	0	ODF2	130300629	0.000000	0.05858	0.265000	0.24526	0.689000	0.40095	0.677000	0.25262	0.685000	0.31468	-0.211000	0.12701	ACC	C|0.971;G|0.029	0.029	strong		0.542	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3		
SPAG4	6676	hgsc.bcm.edu	37	20	34208869	34208869	+	Silent	SNP	G	G	A	rs34962502	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34208869G>A	ENST00000374273.3	+	12	1351	c.1239G>A	c.(1237-1239)acG>acA	p.T413T		NM_003116.1	NP_003107.1	Q9NPE6	SPAG4_HUMAN	sperm associated antigen 4	413	SUN. {ECO:0000255|PROSITE- ProRule:PRU00802}.				spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|motile cilium (GO:0031514)	structural molecule activity (GO:0005198)			NS(1)|cervix(5)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)	21	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.0127)			CCCGTTTCACGTGCTTGTATC	0.557													G|||	51	0.0101837	0.0378	0.0014	5008	,	,		15888	0.0		0.0	False		,,,				2504	0.0				p.T413T		Atlas-SNP	.											SPAG4,colon,carcinoma,+1,1	SPAG4	36	1	0			c.G1239A						PASS	.	G		183,4223	118.4+/-156.1	4,175,2024	82.0	83.0	83.0		1239	-11.1	0.2	20	dbSNP_126	83	2,8598	2.2+/-6.3	0,2,4298	yes	coding-synonymous	SPAG4	NM_003116.1		4,177,6322	AA,AG,GG		0.0233,4.1534,1.4224		413/438	34208869	185,12821	2203	4300	6503	SO:0001819	synonymous_variant	6676	exon12			TTTCACGTGCTTG	AF043344	CCDS13259.1	20q11.2	2010-04-23			ENSG00000061656	ENSG00000061656			11214	protein-coding gene	gene with protein product	"""acrosomal protein ACR55"", ""Sad1 and UNC84 domain containing 4"", ""cancer/testis antigen 127"""	603038				9691178, 10373309	Standard	NM_003116		Approved	SUN4, CT127	uc002xdb.1	Q9NPE6	OTTHUMG00000032352	ENST00000374273.3:c.1239G>A	20.37:g.34208869G>A		92.0	0.0	0		116.0	66.0	0.568965	NM_003116	O43648	Silent	SNP	ENST00000374273.3	37	CCDS13259.1																																																																																			G|0.986;A|0.014	0.014	strong		0.557	SPAG4-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078896.1	NM_003116	
OR10G4	390264	hgsc.bcm.edu	37	11	123886648	123886648	+	Silent	SNP	T	T	C	rs397832341	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123886648T>C	ENST00000320891.4	+	1	367	c.367T>C	c.(367-369)Ttg>Ctg	p.L123L		NM_001004462.1	NP_001004462.1	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G, member 4	123						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)|skin(4)|stomach(6)|upper_aerodigestive_tract(1)	48		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)		TGATCGCTACTTGGCCATCAG	0.567													t|||	2	0.000399361	0.0008	0.0	5008	,	,		23929	0.0		0.0	False		,,,				2504	0.001				p.L123L		Atlas-SNP	.											OR10G4,right_lower_lobe,carcinoma,-2,1	OR10G4	77	1	0			c.T367C						scavenged	.																																			SO:0001819	synonymous_variant	390264	exon1			CGCTACTTGGCCA	AB065757	CCDS31702.1	11q24.1	2012-08-09			ENSG00000254737	ENSG00000254737		"""GPCR / Class A : Olfactory receptors"""	14809	protein-coding gene	gene with protein product							Standard	NM_001004462		Approved		uc010sac.2	Q8NGN3	OTTHUMG00000165966	ENST00000320891.4:c.367T>C	11.37:g.123886648T>C		1243.0	0.0	0		939.0	202.0	0.215122	NM_001004462	Q6IEW0	Silent	SNP	ENST00000320891.4	37	CCDS31702.1																																																																																			.	.	none		0.567	OR10G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387268.1	NM_001004462	
MYH14	79784	hgsc.bcm.edu	37	19	50810405	50810405	+	Silent	SNP	C	C	T	rs201839634	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50810405C>T	ENST00000596571.1	+	38	5655	c.5655C>T	c.(5653-5655)ctC>ctT	p.L1885L	MYH14_ENST00000376970.2_Silent_p.L1918L|CTB-191K22.5_ENST00000595563.1_RNA|MYH14_ENST00000601313.1_Silent_p.L1926L|MYH14_ENST00000598205.1_Silent_p.L1893L|MYH14_ENST00000440075.2_Silent_p.L1926L|MYH14_ENST00000262269.8_Silent_p.L1926L|MYH14_ENST00000425460.1_Silent_p.L1893L			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1885					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		CTGACCAGCTCCGGGACCAGG	0.592													C|||	2	0.000399361	0.0015	0.0	5008	,	,		20297	0.0		0.0	False		,,,				2504	0.0				p.L1926L		Atlas-SNP	.											.	MYH14	261	.	0			c.C5778T						PASS	.	C	,,	2,3712		0,2,1855	39.0	49.0	46.0		5679,5778,5655	2.0	1.0	19		46	0,7216		0,0,3608	no	coding-synonymous,coding-synonymous,coding-synonymous	MYH14	NM_001077186.1,NM_001145809.1,NM_024729.3	,,	0,2,5463	TT,TC,CC		0.0,0.0539,0.0183	,,	1893/2004,1926/2037,1885/1996	50810405	2,10928	1857	3608	5465	SO:0001819	synonymous_variant	79784	exon41			CCAGCTCCGGGAC	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"""Myosins / Myosin superfamily : Class II"""	23212	protein-coding gene	gene with protein product		608568	"""myosin, heavy polypeptide 14"", ""myosin, heavy chain 14"""	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.5655C>T	19.37:g.50810405C>T		66.0	0.0	0		40.0	17.0	0.425	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Silent	SNP	ENST00000596571.1	37	CCDS59411.1																																																																																			C|0.999;T|0.001	0.001	strong		0.592	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011547	46011547	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46011547G>A	ENST00000400368.1	-	1	839	c.819C>T	c.(817-819)ccC>ccT	p.P273P	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	273	29 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(6)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23						CAGAGCAGACGGGCACACAGC	0.652																																					p.P273P		Atlas-SNP	.											.	KRTAP10-6	57	.	0			c.C819T						PASS	.						114.0	115.0	115.0					21																	46011547		2203	4300	6503	SO:0001819	synonymous_variant	386674	exon1			GCAGACGGGCACA	AB076353	CCDS42959.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000188155	ENSG00000188155		"""Keratin associated proteins"""	20523	protein-coding gene	gene with protein product			"""keratin associated protein 18-6"""	KRTAP18-6			Standard	NM_198688		Approved	KRTAP18.6, KAP18.6, KAP10.6	uc002zfm.3	P60371	OTTHUMG00000057634	ENST00000400368.1:c.819C>T	21.37:g.46011547G>A		254.0	0.0	0		330.0	34.0	0.10303	NM_198688		Silent	SNP	ENST00000400368.1	37	CCDS42959.1																																																																																			.	.	none		0.652	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688	
ATXN1	6310	hgsc.bcm.edu	37	6	16328115	16328115	+	Missense_Mutation	SNP	T	T	C	rs143125796	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:16328115T>C	ENST00000244769.4	-	8	1363	c.427A>G	c.(427-429)Atc>Gtc	p.I143V	ATXN1_ENST00000436367.1_Missense_Mutation_p.I143V	NM_000332.3	NP_000323.2	P54253	ATX1_HUMAN	ataxin 1	143					adult locomotory behavior (GO:0008344)|cell death (GO:0008219)|negative regulation of insulin-like growth factor receptor signaling pathway (GO:0043569)|negative regulation of phosphorylation (GO:0042326)|negative regulation of transcription, DNA-templated (GO:0045892)|nuclear export (GO:0051168)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|RNA processing (GO:0006396)|transcription, DNA-templated (GO:0006351)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear inclusion body (GO:0042405)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|poly(G) binding (GO:0034046)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|protein self-association (GO:0043621)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(11)|lung(12)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)	44	Breast(50;0.063)|Ovarian(93;0.0733)	all_hematologic(90;0.000682)|Ovarian(999;0.00973)				TGTGATGGGATGAAGCTGGCA	0.657													T|||	2	0.000399361	0.0015	0.0	5008	,	,		14675	0.0		0.0	False		,,,				2504	0.0				p.I143V		Atlas-SNP	.											.	ATXN1	117	.	0			c.A427G						PASS	.	T	VAL/ILE,VAL/ILE	4,4402	8.1+/-20.4	0,4,2199	73.0	79.0	77.0		427,427	1.0	1.0	6	dbSNP_134	77	0,8600		0,0,4300	no	missense,missense	ATXN1	NM_000332.3,NM_001128164.1	29,29	0,4,6499	CC,CT,TT		0.0,0.0908,0.0308	possibly-damaging,possibly-damaging	143/816,143/816	16328115	4,13002	2203	4300	6503	SO:0001583	missense	6310	exon7			ATGGGATGAAGCT	X79204	CCDS34342.1	6p23	2014-09-17	2004-08-12	2004-08-13	ENSG00000124788	ENSG00000124788		"""Ataxins"""	10548	protein-coding gene	gene with protein product		601556	"""spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1)"""	SCA1		1582256	Standard	NM_000332		Approved	D6S504E, ATX1	uc010jpi.3	P54253	OTTHUMG00000014303	ENST00000244769.4:c.427A>G	6.37:g.16328115T>C	ENSP00000244769:p.Ile143Val	42.0	0.0	0		51.0	24.0	0.470588	NM_001128164	Q17S02|Q9UJG2|Q9Y4J1	Missense_Mutation	SNP	ENST00000244769.4	37	CCDS34342.1	.	.	.	.	.	.	.	.	.	.	T	8.212	0.800596	0.16397	9.08E-4	0.0	ENSG00000124788	ENST00000244769;ENST00000450222;ENST00000436367	T;T	0.45276	0.9;0.9	5.11	1.04	0.20106	.	0.101815	0.64402	D	0.000004	T	0.14874	0.0359	L	0.46157	1.445	0.41711	D	0.989452	B	0.27229	0.172	B	0.18871	0.023	T	0.04635	-1.0937	10	0.38643	T	0.18	-15.4984	7.2098	0.25927	0.0:0.0733:0.2756:0.6511	.	143	P54253	ATX1_HUMAN	V	143	ENSP00000244769:I143V;ENSP00000416360:I143V	ENSP00000244769:I143V	I	-	1	0	ATXN1	16436094	1.000000	0.71417	1.000000	0.80357	0.147000	0.21601	3.031000	0.49728	0.264000	0.21851	-0.456000	0.05471	ATC	T|0.999;C|0.001	0.001	strong		0.657	ATXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039943.3	NM_000332	
SMCHD1	23347	hgsc.bcm.edu	37	18	2667005	2667005	+	Silent	SNP	T	T	C	rs7239096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:2667005T>C	ENST00000320876.6	+	3	737	c.399T>C	c.(397-399)taT>taC	p.Y133Y	SMCHD1_ENST00000261598.8_Silent_p.Y133Y	NM_015295.2	NP_056110.2	A6NHR9	SMHD1_HUMAN	structural maintenance of chromosomes flexible hinge domain containing 1	133					chromosome organization (GO:0051276)|inactivation of X chromosome by DNA methylation (GO:0060821)	Barr body (GO:0001740)	ATP binding (GO:0005524)			NS(3)|breast(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(16)|lung(15)|pancreas(1)	45						ATGAATATTATGCCAGTGAAG	0.378													T|||	159	0.0317492	0.1142	0.0101	5008	,	,		20279	0.0		0.001	False		,,,				2504	0.0				p.Y133Y		Atlas-SNP	.											.	SMCHD1	88	.	0			c.T399C						PASS	.	T		429,3325		30,369,1478	83.0	72.0	76.0		399	5.6	1.0	18	dbSNP_116	76	7,8219		0,7,4106	no	coding-synonymous	SMCHD1	NM_015295.2		30,376,5584	CC,CT,TT		0.0851,11.4278,3.6394		133/2006	2667005	436,11544	1877	4113	5990	SO:0001819	synonymous_variant	23347	exon3			ATATTATGCCAGT	AB014550	CCDS45822.1	18p11.32	2010-05-12			ENSG00000101596	ENSG00000101596			29090	protein-coding gene	gene with protein product		614982				9734811	Standard	NM_015295		Approved	KIAA0650	uc002klm.4	A6NHR9		ENST00000320876.6:c.399T>C	18.37:g.2667005T>C		97.0	0.0	0		98.0	54.0	0.55102	NM_015295	O75141|Q6AHX6|Q6ZTQ8|Q9H6Q2|Q9UG39	Silent	SNP	ENST00000320876.6	37	CCDS45822.1																																																																																			T|0.974;C|0.026	0.026	strong		0.378	SMCHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441082.2		
TSPAN9	10867	hgsc.bcm.edu	37	12	3389559	3389559	+	Silent	SNP	C	C	T	rs877089	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:3389559C>T	ENST00000011898.5	+	6	503	c.342C>T	c.(340-342)aaC>aaT	p.N114N	TSPAN9_ENST00000537971.1_Silent_p.N114N|TSPAN9_ENST00000407263.1_Silent_p.N114N|TSPAN9_ENST00000492305.1_3'UTR	NM_006675.4	NP_006666.1	O75954	TSN9_HUMAN	tetraspanin 9	114						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)				endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	11			OV - Ovarian serous cystadenocarcinoma(31;0.00153)|COAD - Colon adenocarcinoma(12;0.0831)			TGAACGAGAACGCCAAGAAGG	0.617													c|||	104	0.0207668	0.0598	0.0173	5008	,	,		18186	0.0		0.0099	False		,,,				2504	0.0031				p.N114N		Atlas-SNP	.											.	TSPAN9	20	.	0			c.C342T						PASS	.		,	237,4169	138.4+/-174.2	3,231,1969	136.0	92.0	107.0		342,342	-3.5	1.0	12	dbSNP_86	107	130,8470	65.6+/-127.9	1,128,4171	no	coding-synonymous,coding-synonymous	TSPAN9	NM_001168320.1,NM_006675.4	,	4,359,6140	TT,TC,CC		1.5116,5.379,2.8218	,	114/240,114/240	3389559	367,12639	2203	4300	6503	SO:0001819	synonymous_variant	10867	exon6			CGAGAACGCCAAG	AF089749	CCDS8520.1	12p13.33-p13.32	2013-02-14			ENSG00000011105	ENSG00000011105		"""Tetraspanins"""	21640	protein-coding gene	gene with protein product		613137				10719184, 11739647	Standard	NM_006675		Approved	NET-5	uc021qtd.1	O75954	OTTHUMG00000150333	ENST00000011898.5:c.342C>T	12.37:g.3389559C>T		38.0	0.0	0		38.0	13.0	0.342105	NM_006675	D3DUQ7|Q53FV2|Q6FGJ8	Silent	SNP	ENST00000011898.5	37	CCDS8520.1																																																																																			C|0.974;T|0.026	0.026	strong		0.617	TSPAN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317606.2	NM_006675	
TTN	7273	hgsc.bcm.edu	37	2	179613258	179613258	+	Intron	SNP	A	A	C	rs72648906	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179613258A>C	ENST00000591111.1	-	45	10585				TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Intron|TTN_ENST00000360870.5_Silent_p.S4623S|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Intron			Q8WZ42	TITIN_HUMAN	titin						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)			CTCCTATATGAGAATACATTT	0.368													A|||	104	0.0207668	0.0764	0.0043	5008	,	,		18443	0.0		0.0	False		,,,				2504	0.0				p.S4623S		Atlas-SNP	.											.	TTN	18412	.	0			c.T13869G						PASS	.	A	,,,,	244,4160	139.2+/-174.8	7,230,1965	99.0	109.0	106.0		,,13869,,	3.5	1.0	2	dbSNP_130	106	6,8590	3.7+/-12.6	0,6,4292	no	intron,intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	7,236,6257	CC,CA,AA		0.0698,5.5404,1.9231	,,,,	,,4623/5605,,	179613258	250,12750	2202	4298	6500	SO:0001627	intron_variant	7273	exon46			TATATGAGAATAC	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.10360+4592T>G	2.37:g.179613258A>C		190.0	0.0	0		202.0	97.0	0.480198	NM_133379	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|0.977;C|0.023	0.023	strong		0.368	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
WRN	7486	hgsc.bcm.edu	37	8	30954338	30954338	+	Silent	SNP	C	C	T	rs11574263	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:30954338C>T	ENST00000298139.5	+	17	2202	c.1953C>T	c.(1951-1953)ggC>ggT	p.G651G		NM_000553.4	NP_000544.2	Q14191	WRN_HUMAN	Werner syndrome, RecQ helicase-like	651	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				aging (GO:0007568)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|cell aging (GO:0007569)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|cellular response to starvation (GO:0009267)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|double-strand break repair (GO:0006302)|multicellular organismal aging (GO:0010259)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleolus to nucleoplasm transport (GO:0032066)|positive regulation of hydrolase activity (GO:0051345)|regulation of apoptotic process (GO:0042981)|regulation of growth rate (GO:0040009)|replication fork processing (GO:0031297)|replicative cell aging (GO:0001302)|response to oxidative stress (GO:0006979)|response to UV-C (GO:0010225)|telomere maintenance (GO:0000723)	centrosome (GO:0005813)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	3'-5' DNA helicase activity (GO:0043138)|3'-5' exonuclease activity (GO:0008408)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|ATPase activity (GO:0016887)|bubble DNA binding (GO:0000405)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|exonuclease activity (GO:0004527)|four-way junction helicase activity (GO:0009378)|G-quadruplex DNA binding (GO:0051880)|helicase activity (GO:0004386)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|Y-form DNA binding (GO:0000403)			central_nervous_system(2)|endometrium(4)|kidney(4)|large_intestine(13)|lung(28)|ovary(3)|skin(3)|upper_aerodigestive_tract(3)	60		Breast(100;0.195)		KIRC - Kidney renal clear cell carcinoma(542;0.147)|Kidney(114;0.176)|Colorectal(111;0.192)		GTAACATGGGCCTGCTCCAGC	0.338			"""Mis, N, F, S"""			"""osteosarcoma, meningioma, others"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Werner syndrome				C|||	20	0.00399361	0.0144	0.0014	5008	,	,		16879	0.0		0.0	False		,,,				2504	0.0				p.G651G	Ovarian(18;161 598 2706 14834 27543)	Atlas-SNP	.	yes	Rec		Werner Syndrome	8	8p12-p11.2	7486	Werner syndrome (RECQL2)		"""L, E, M, O"""	.	WRN	116	.	0			c.C1953T						PASS	.	C		78,4328	67.0+/-104.6	2,74,2127	92.0	91.0	91.0		1953	2.1	0.0	8	dbSNP_120	91	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	WRN	NM_000553.4		2,76,6425	TT,TC,CC		0.0233,1.7703,0.6151		651/1433	30954338	80,12926	2203	4300	6503	SO:0001819	synonymous_variant	7486	exon17	Familial Cancer Database	WS, Adult Progeria	CATGGGCCTGCTC		CCDS6082.1	8p12	2014-09-17	2009-03-19		ENSG00000165392	ENSG00000165392			12791	protein-coding gene	gene with protein product		604611	"""Werner syndrome"""			9288107	Standard	NM_000553		Approved	RECQL2, RECQ3	uc003xio.4	Q14191	OTTHUMG00000163894	ENST00000298139.5:c.1953C>T	8.37:g.30954338C>T		28.0	0.0	0		29.0	12.0	0.413793	NM_000553	A1KYY9	Silent	SNP	ENST00000298139.5	37	CCDS6082.1																																																																																			C|0.997;T|0.003	0.003	strong		0.338	WRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376248.1		
EPB41L1	2036	hgsc.bcm.edu	37	20	34782156	34782156	+	Silent	SNP	G	G	A	rs111865221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34782156G>A	ENST00000338074.2	+	12	1484	c.1323G>A	c.(1321-1323)tcG>tcA	p.S441S	EPB41L1_ENST00000441639.1_Silent_p.S379S|EPB41L1_ENST00000373950.2_Silent_p.S344S|EPB41L1_ENST00000202028.5_Silent_p.S379S|EPB41L1_ENST00000373946.3_Silent_p.S410S|EPB41L1_ENST00000373941.1_Silent_p.S441S	NM_001258329.1|NM_012156.2	NP_001245258.1|NP_036288.2	Q9H4G0	E41L1_HUMAN	erythrocyte membrane protein band 4.1-like 1	441					cortical actin cytoskeleton organization (GO:0030866)|synaptic transmission (GO:0007268)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(10)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	37	Breast(12;0.0239)					GCCCAGCCTCGGTCAGCGAGA	0.627													G|||	32	0.00638978	0.0234	0.0014	5008	,	,		20291	0.0		0.0	False		,,,				2504	0.0				p.S441S		Atlas-SNP	.											.	EPB41L1	111	.	0			c.G1323A						PASS	.	G	,	93,4313	77.8+/-116.1	2,89,2112	60.0	52.0	55.0		1323,1137	-10.4	0.0	20	dbSNP_132	55	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	EPB41L1	NM_012156.2,NM_177996.1	,	2,89,6412	AA,AG,GG		0.0,2.1108,0.7151	,	441/882,379/780	34782156	93,12913	2203	4300	6503	SO:0001819	synonymous_variant	2036	exon13			AGCCTCGGTCAGC	AB002336	CCDS13271.1, CCDS13272.1, CCDS58771.1	20q11.2-q12	2003-03-17			ENSG00000088367	ENSG00000088367			3378	protein-coding gene	gene with protein product		602879				9570967, 9828140	Standard	NM_012156		Approved	KIAA0338	uc002xfb.3	Q9H4G0	OTTHUMG00000032378	ENST00000338074.2:c.1323G>A	20.37:g.34782156G>A		137.0	0.0	0		170.0	77.0	0.452941	NM_001258329	O15046|Q4VXM6|Q4VXM7|Q4VXM8|Q4VXN4|Q6ZT61|Q8IUU7|Q96CV5|Q96L65	Silent	SNP	ENST00000338074.2	37	CCDS13271.1	16	0.007326007326007326	15	0.03048780487804878	1	0.0027624309392265192	0	0.0	0	0.0	G	1.735	-0.493136	0.04322	0.021108	0.0	ENSG00000088367	ENST00000451082	.	.	.	5.18	-10.4	0.00318	.	.	.	.	.	T	0.16514	0.0397	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.72204	-0.4361	4	.	.	.	.	1.9428	0.03350	0.0936:0.1922:0.346:0.3681	.	.	.	.	Q	19	.	.	R	+	2	0	EPB41L1	34245570	0.000000	0.05858	0.002000	0.10522	0.521000	0.34408	-9.217000	0.00013	-7.995000	0.00000	-3.875000	0.00017	CGG	G|0.991;A|0.009	0.009	strong		0.627	EPB41L1-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078978.3	NM_012156	
CELSR1	9620	hgsc.bcm.edu	37	22	46932079	46932079	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46932079G>A	ENST00000262738.3	-	1	988	c.989C>T	c.(988-990)aCg>aTg	p.T330M	CELSR1_ENST00000497509.1_5'Flank|CELSR1_ENST00000395964.1_Missense_Mutation_p.T330M	NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	330	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		GCGCGGCGGCGTACTGTAGTC	0.647																																					p.T330M		Atlas-SNP	.											.	CELSR1	242	.	0			c.C989T						PASS	.						116.0	95.0	102.0					22																	46932079		2201	4300	6501	SO:0001583	missense	9620	exon1			GGCGGCGTACTGT	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	1850	protein-coding gene	gene with protein product	"""flamingo homolog 2 (Drosophila)"""	604523	"""cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"""			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.989C>T	22.37:g.46932079G>A	ENSP00000262738:p.Thr330Met	95.0	0.0	0		89.0	45.0	0.505618	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	.	.	.	.	.	.	.	.	.	.	G	3.466	-0.109044	0.06924	.	.	ENSG00000075275	ENST00000262738;ENST00000395964	T;T	0.01838	4.61;4.61	4.32	-0.683	0.11335	Cadherin (4);Cadherin-like (1);	0.310145	0.26203	U	0.025732	T	0.01800	0.0057	L	0.35854	1.095	0.09310	N	0.999999	P	0.34522	0.455	B	0.32805	0.153	T	0.48305	-0.9047	10	0.32370	T	0.25	.	6.6282	0.22841	0.1613:0.2739:0.5649:0.0	.	330	Q9NYQ6	CELR1_HUMAN	M	330	ENSP00000262738:T330M;ENSP00000379293:T330M	ENSP00000262738:T330M	T	-	2	0	CELSR1	45310743	0.376000	0.25098	0.741000	0.31004	0.009000	0.06853	3.037000	0.49775	-0.001000	0.14495	-0.391000	0.06502	ACG	.	.	none		0.647	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
KIAA1407	57577	hgsc.bcm.edu	37	3	113699599	113699599	+	Missense_Mutation	SNP	C	C	G	rs35546981	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:113699599C>G	ENST00000295878.3	-	14	2351	c.2205G>C	c.(2203-2205)caG>caC	p.Q735H	KIAA1407_ENST00000545063.1_3'UTR	NM_020817.1	NP_065868.1	Q8NCU4	K1407_HUMAN	KIAA1407	735										endometrium(9)|large_intestine(7)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(1)	40						TTGCTTCCAGCTGCTGGTTCC	0.363													C|||	5	0.000998403	0.003	0.0014	5008	,	,		18688	0.0		0.0	False		,,,				2504	0.0				p.Q735H		Atlas-SNP	.											.	KIAA1407	80	.	0			c.G2205C						PASS	.	C	HIS/GLN	32,4374	37.6+/-69.7	0,32,2171	170.0	161.0	164.0		2205	3.8	1.0	3	dbSNP_126	164	0,8600		0,0,4300	yes	missense	KIAA1407	NM_020817.1	24	0,32,6471	GG,GC,CC		0.0,0.7263,0.246	probably-damaging	735/937	113699599	32,12974	2203	4300	6503	SO:0001583	missense	57577	exon14			TTCCAGCTGCTGG	AF509494	CCDS2977.1	3q13.31	2005-01-10			ENSG00000163617	ENSG00000163617			29272	protein-coding gene	gene with protein product						10718198	Standard	NM_020817		Approved		uc003eax.3	Q8NCU4	OTTHUMG00000159337	ENST00000295878.3:c.2205G>C	3.37:g.113699599C>G	ENSP00000295878:p.Gln735His	223.0	1.0	0.00448431		266.0	121.0	0.454887	NM_020817	B4DYL1|Q9P2E0	Missense_Mutation	SNP	ENST00000295878.3	37	CCDS2977.1	3	0.0013736263736263737	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	0	0.0	C	17.30	3.354777	0.61293	0.007263	0.0	ENSG00000163617	ENST00000295878	T	0.33216	1.42	5.57	3.75	0.43078	.	0.298923	0.36932	N	0.002326	T	0.24160	0.0585	L	0.59436	1.845	0.80722	D	1	B	0.21071	0.051	B	0.21917	0.037	T	0.07693	-1.0759	10	0.56958	D	0.05	.	12.7141	0.57105	0.2994:0.7006:0.0:0.0	rs35546981	735	Q8NCU4	K1407_HUMAN	H	735	ENSP00000295878:Q735H	ENSP00000295878:Q735H	Q	-	3	2	KIAA1407	115182289	0.988000	0.35896	1.000000	0.80357	0.940000	0.58332	0.569000	0.23638	0.797000	0.33971	0.591000	0.81541	CAG	C|0.997;G|0.003	0.003	strong		0.363	KIAA1407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354724.2	NM_020817	
CFAP57	149465	hgsc.bcm.edu	37	1	43638436	43638436	+	Silent	SNP	G	G	T	rs6695238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:43638436G>T	ENST00000372492.4	+	2	336	c.12G>T	c.(10-12)gtG>gtT	p.V4V	WDR65_ENST00000528956.1_Silent_p.V4V|EBNA1BP2_ENST00000472982.1_5'Flank|EBNA1BP2_ENST00000236051.2_5'Flank|EBNA1BP2_ENST00000431635.2_5'Flank	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		4										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)				TGTCAGCCGTGGTAGCTCAGA	0.547													G|||	341	0.0680911	0.1899	0.0576	5008	,	,		10442	0.001		0.0368	False		,,,				2504	0.0123				p.V4V		Atlas-SNP	.											.	WDR65	76	.	0			c.G12T						PASS	.	G	,,	714,3692	295.6+/-283.7	65,584,1554	116.0	104.0	108.0		12,12,12	2.1	1.0	1	dbSNP_116	108	354,8246	119.5+/-178.9	6,342,3952	no	coding-synonymous,coding-synonymous,coding-synonymous	WDR65	NM_001167965.1,NM_001167966.1,NM_152498.3	,,	71,926,5506	TT,TG,GG		4.1163,16.2052,8.2116	,,	4/699,4/699,4/699	43638436	1068,11938	2203	4300	6503	SO:0001819	synonymous_variant	149465	exon2			AGCCGTGGTAGCT																												ENST00000372492.4:c.12G>T	1.37:g.43638436G>T		95.0	0.0	0		129.0	66.0	0.511628	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Silent	SNP	ENST00000372492.4	37																																																																																				G|0.920;T|0.080	0.080	strong		0.547	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1		
OR10Z1	128368	hgsc.bcm.edu	37	1	158576472	158576472	+	Missense_Mutation	SNP	C	C	T	rs76424590	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158576472C>T	ENST00000361284.1	+	1	244	c.244C>T	c.(244-246)Ctc>Ttc	p.L82F		NM_001004478.1	NP_001004478.1	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z, member 1	82						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(6)|lung(21)|pancreas(1)|prostate(3)|skin(4)	37	all_hematologic(112;0.0378)					CCCTAGAATGCTCTCTGGCCT	0.542													C|||	190	0.0379393	0.1377	0.0086	5008	,	,		20262	0.0		0.002	False		,,,				2504	0.0				p.L82F		Atlas-SNP	.											OR10Z1,NS,carcinoma,-2,1	OR10Z1	99	1	0			c.C244T						PASS	.	C	PHE/LEU	525,3881	238.7+/-250.0	33,459,1711	203.0	209.0	207.0		244	5.4	1.0	1	dbSNP_131	207	12,8588	9.1+/-34.3	0,12,4288	yes	missense	OR10Z1	NM_001004478.1	22	33,471,5999	TT,TC,CC		0.1395,11.9156,4.1289	probably-damaging	82/314	158576472	537,12469	2203	4300	6503	SO:0001583	missense	128368	exon1			AGAATGCTCTCTG	AB065635	CCDS30901.1	1q23.1	2012-08-23			ENSG00000198967	ENSG00000198967		"""GPCR / Class A : Olfactory receptors"""	14996	protein-coding gene	gene with protein product							Standard	NM_001004478		Approved		uc010pio.2	Q8NGY1	OTTHUMG00000019637	ENST00000361284.1:c.244C>T	1.37:g.158576472C>T	ENSP00000354707:p.Leu82Phe	211.0	0.0	0		210.0	93.0	0.442857	NM_001004478	Q5VYL0|Q6IFR7	Missense_Mutation	SNP	ENST00000361284.1	37	CCDS30901.1	68	0.031135531135531136	66	0.13414634146341464	2	0.0055248618784530384	0	0.0	0	0.0	C	17.17	3.321840	0.60634	0.119156	0.001395	ENSG00000198967	ENST00000361284	T	0.00419	7.48	5.36	5.36	0.76844	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36778	N	0.002405	T	0.01222	0.0040	H	0.97077	3.935	0.26251	P	0.97873	D	0.89917	1.0	D	0.80764	0.994	T	0.03296	-1.1051	9	0.87932	D	0	.	13.5532	0.61745	0.1563:0.8437:0.0:0.0	.	82	Q8NGY1	O10Z1_HUMAN	F	82	ENSP00000354707:L82F	ENSP00000354707:L82F	L	+	1	0	OR10Z1	156843096	0.996000	0.38824	0.997000	0.53966	0.647000	0.38526	1.184000	0.32053	2.783000	0.95769	0.655000	0.94253	CTC	C|0.962;T|0.038	0.038	strong		0.542	OR10Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051853.1	NM_001004478	
RALGDS	5900	hgsc.bcm.edu	37	9	135974054	135974054	+	Missense_Mutation	SNP	C	C	T	rs143209866	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:135974054C>T	ENST00000372050.3	-	18	2686	c.2665G>A	c.(2665-2667)Gtg>Atg	p.V889M	RALGDS_ENST00000542690.1_Missense_Mutation_p.V960M|RALGDS_ENST00000393160.3_Missense_Mutation_p.V834M|RALGDS_ENST00000372047.3_Missense_Mutation_p.V877M|RALGDS_ENST00000372062.3_Missense_Mutation_p.V860M|RALGDS_ENST00000393157.3_Missense_Mutation_p.V888M|RALGDS_ENST00000469972.1_5'UTR	NM_006266.2	NP_006257.1	Q12967	GNDS_HUMAN	ral guanine nucleotide dissociation stimulator	889					neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|regulation of catalytic activity (GO:0050790)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|small GTPase regulator activity (GO:0005083)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10				OV - Ovarian serous cystadenocarcinoma(145;3.66e-06)|Epithelial(140;2.77e-05)		TTGACCTTCACTCCCTTGGTG	0.542			T	CIITA	"""PMBL, Hodgkin Lymphona, """								C|||	4	0.000798722	0.003	0.0	5008	,	,		21550	0.0		0.0	False		,,,				2504	0.0				p.V889M	Melanoma(189;762 2088 15384 21931 52515)	Atlas-SNP	.		Dom	yes		9	9q34.3	5900	ral guanine nucleotide dissociation stimulator		L	.	RALGDS	75	.	0			c.G2665A						PASS	.	C	MET/VAL,MET/VAL	19,4387	26.2+/-53.5	0,19,2184	116.0	93.0	100.0		2500,2665	2.5	0.8	9	dbSNP_134	100	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	RALGDS	NM_001042368.1,NM_006266.2	21,21	0,20,6483	TT,TC,CC		0.0116,0.4312,0.1538	possibly-damaging,possibly-damaging	834/860,889/915	135974054	20,12986	2203	4300	6503	SO:0001583	missense	5900	exon18			CCTTCACTCCCTT	AB037729	CCDS6959.1, CCDS43897.1, CCDS65172.1, CCDS65173.1, CCDS65174.1	9q34.3	2009-04-08			ENSG00000160271	ENSG00000160271			9842	protein-coding gene	gene with protein product		601619				7972015	Standard	NM_006266		Approved	RGF, RalGEF, RGDS	uc004ccr.3	Q12967	OTTHUMG00000020858	ENST00000372050.3:c.2665G>A	9.37:g.135974054C>T	ENSP00000361120:p.Val889Met	132.0	0.0	0		189.0	65.0	0.343915	NM_006266	B7Z753|E7ER93|E7ERZ0|Q5T7V4|Q6KH11|Q6PCE1|Q6ZSD5|Q9HAX7|Q9HAY1|Q9HCT1|Q9P2N8	Missense_Mutation	SNP	ENST00000372050.3	37	CCDS6959.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	10.20	1.285630	0.23478	0.004312	1.16E-4	ENSG00000160271	ENST00000372050;ENST00000372047;ENST00000393160;ENST00000393157;ENST00000542690;ENST00000372062	T;T;T;T;T;T	0.40476	1.52;1.04;1.52;1.5;1.68;1.03	5.37	2.55	0.30701	.	0.458064	0.20879	N	0.084033	T	0.34716	0.0907	L	0.46157	1.445	0.19945	N	0.999946	B;P;P;P;P;B	0.51240	0.349;0.943;0.694;0.758;0.943;0.35	B;B;B;B;B;B	0.41271	0.057;0.352;0.295;0.173;0.352;0.077	T	0.18053	-1.0349	10	0.72032	D	0.01	.	9.9724	0.41763	0.0:0.7793:0.0:0.2207	.	960;860;834;888;877;889	F5H6M6;E7ER93;Q6KH11;E7ERZ0;Q6PCE1;Q12967	.;.;.;.;.;GNDS_HUMAN	M	889;877;834;888;960;860	ENSP00000361120:V889M;ENSP00000361117:V877M;ENSP00000376867:V834M;ENSP00000376864:V888M;ENSP00000437518:V960M;ENSP00000361132:V860M	ENSP00000361117:V877M	V	-	1	0	RALGDS	134963875	0.000000	0.05858	0.797000	0.32132	0.292000	0.27327	0.038000	0.13862	0.259000	0.21709	0.561000	0.74099	GTG	C|0.998;T|0.002	0.002	strong		0.542	RALGDS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054837.1	NM_006266	
ATP6V0D2	245972	hgsc.bcm.edu	37	8	87162515	87162515	+	Missense_Mutation	SNP	G	G	A	rs10094744	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:87162515G>A	ENST00000285393.3	+	6	956	c.814G>A	c.(814-816)Gga>Aga	p.G272R	CTD-3118D11.2_ENST00000522679.1_RNA	NM_152565.1	NP_689778.1	Q8N8Y2	VA0D2_HUMAN	ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d2	272			G -> R (in dbSNP:rs10094744).		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)	apical plasma membrane (GO:0016324)|early endosome (GO:0005769)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|proton-transporting V-type ATPase, V0 domain (GO:0033179)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	hydrogen ion transmembrane transporter activity (GO:0015078)			breast(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(9)|prostate(1)	27						GGATCATTACGGAGTATGTGA	0.453													G|||	152	0.0303514	0.1089	0.0115	5008	,	,		18274	0.0		0.0	False		,,,				2504	0.0				p.G272R		Atlas-SNP	.											.	ATP6V0D2	61	.	0			c.G814A						PASS	.	G	ARG/GLY	421,3985	204.5+/-226.7	19,383,1801	100.0	90.0	94.0		814	5.3	0.1	8	dbSNP_119	94	5,8595	4.3+/-15.6	0,5,4295	yes	missense	ATP6V0D2	NM_152565.1	125	19,388,6096	AA,AG,GG		0.0581,9.5552,3.2754	benign	272/351	87162515	426,12580	2203	4300	6503	SO:0001583	missense	245972	exon6			CATTACGGAGTAT	AY079172	CCDS6241.1	8q21.3	2014-01-28	2006-01-20	2002-05-24	ENSG00000147614	ENSG00000147614		"""ATPases / V-type"""	18266	protein-coding gene	gene with protein product			"""ATPase, H+ transporting, lysosomal 38kD, V0 subunit d isoform 2"", ""ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d isoform 2"", ""ATPase, H+ transporting, lysosomal 38kDa, V0 subunit D2"""			12384298	Standard	NM_152565		Approved	FLJ38708, VMA6, ATP6D2	uc003ydp.1	Q8N8Y2	OTTHUMG00000163637	ENST00000285393.3:c.814G>A	8.37:g.87162515G>A	ENSP00000285393:p.Gly272Arg	107.0	0.0	0		101.0	45.0	0.445545	NM_152565		Missense_Mutation	SNP	ENST00000285393.3	37	CCDS6241.1	37	0.01694139194139194	35	0.07113821138211382	2	0.0055248618784530384	0	0.0	0	0.0	G	14.33	2.504335	0.44558	0.095552	5.81E-4	ENSG00000147614	ENST00000285393	T	0.29917	1.55	6.17	5.27	0.74061	.	0.585174	0.17628	N	0.167492	T	0.00724	0.0024	L	0.48642	1.525	0.23689	N	0.997107	D	0.53462	0.96	B	0.38194	0.267	T	0.01940	-1.1243	10	0.40728	T	0.16	-22.0686	16.0952	0.81114	0.0:0.0:0.8659:0.1341	rs10094744;rs52810720;rs10094744	272	Q8N8Y2	VA0D2_HUMAN	R	272	ENSP00000285393:G272R	ENSP00000285393:G272R	G	+	1	0	ATP6V0D2	87231631	0.153000	0.22777	0.096000	0.21009	0.040000	0.13550	3.075000	0.50073	2.941000	0.99782	0.655000	0.94253	GGA	G|0.970;A|0.030	0.030	strong		0.453	ATP6V0D2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374651.1	NM_152565	
ZP4	57829	hgsc.bcm.edu	37	1	238046056	238046056	+	Missense_Mutation	SNP	G	G	A	rs35187146	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:238046056G>A	ENST00000366570.4	-	11	1639	c.1481C>T	c.(1480-1482)cCt>cTt	p.P494L	RP11-193H5.1_ENST00000450451.1_RNA	NM_021186.3	NP_067009.1	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4	494					acrosomal vesicle exocytosis (GO:0060478)|binding of sperm to zona pellucida (GO:0007339)|intracellular signal transduction (GO:0035556)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of humoral immune response (GO:0002922)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of T cell proliferation (GO:0042102)|protein kinase A signaling (GO:0010737)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	acrosin binding (GO:0032190)|signal transducer activity (GO:0004871)			breast(6)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(42)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	73	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			CTTTTCTGGAGGGTCCTTAGT	0.418													G|||	98	0.0195687	0.0681	0.0101	5008	,	,		18510	0.0		0.001	False		,,,				2504	0.0				p.P494L	NSCLC(166;160 2029 11600 18754 19936)	Atlas-SNP	.											.	ZP4	161	.	0			c.C1481T						PASS	.	G	LEU/PRO	232,4174	136.1+/-172.1	4,224,1975	113.0	113.0	113.0		1481	3.3	0.0	1	dbSNP_126	113	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ZP4	NM_021186.3	98	4,225,6274	AA,AG,GG		0.0116,5.2655,1.7915	benign	494/541	238046056	233,12773	2203	4300	6503	SO:0001583	missense	57829	exon11			TCTGGAGGGTCCT	U05781	CCDS1615.1	1q43	2013-01-17			ENSG00000116996	ENSG00000116996		"""Zona pellucida glycoproteins"""	15770	protein-coding gene	gene with protein product		613514				7841460	Standard	NM_021186		Approved	ZPB	uc001hym.3	Q12836	OTTHUMG00000039586	ENST00000366570.4:c.1481C>T	1.37:g.238046056G>A	ENSP00000355529:p.Pro494Leu	103.0	0.0	0		107.0	44.0	0.411215	NM_021186	B2RAE1	Missense_Mutation	SNP	ENST00000366570.4	37	CCDS1615.1	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	G	13.86	2.362971	0.41902	0.052655	1.16E-4	ENSG00000116996	ENST00000366570	T	0.75154	-0.91	4.2	3.29	0.37713	.	1.113200	0.06962	N	0.816574	T	0.11750	0.0286	L	0.38175	1.15	0.09310	N	1	B	0.18741	0.03	B	0.12837	0.008	T	0.13737	-1.0498	10	0.11485	T	0.65	-6.9559	8.323	0.32140	0.1076:0.0:0.8924:0.0	rs35187146	494	Q12836	ZP4_HUMAN	L	494	ENSP00000355529:P494L	ENSP00000355529:P494L	P	-	2	0	ZP4	236112679	0.088000	0.21588	0.002000	0.10522	0.836000	0.47400	2.346000	0.44027	1.146000	0.42352	-0.126000	0.14955	CCT	G|0.985;A|0.015	0.015	strong		0.418	ZP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095476.1		
CES5A	221223	hgsc.bcm.edu	37	16	55883667	55883667	+	Missense_Mutation	SNP	T	T	C	rs545527146		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:55883667T>C	ENST00000290567.9	-	11	1413	c.1292A>G	c.(1291-1293)tAc>tGc	p.Y431C	CES5A_ENST00000319165.9_Intron|CES5A_ENST00000541580.1_5'UTR|CES5A_ENST00000520435.1_Missense_Mutation_p.Y401C|CES5A_ENST00000518005.1_Missense_Mutation_p.Y325C|CES5A_ENST00000521992.1_Missense_Mutation_p.Y460C	NM_001143685.1	NP_001137157.1	Q6NT32	EST5A_HUMAN	carboxylesterase 5A	431						extracellular region (GO:0005576)	carboxylic ester hydrolase activity (GO:0052689)			breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(13)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	39						CTCATAGAAGTAGACAGGTGC	0.557																																					p.Y460C		Atlas-SNP	.											.	CES5A	206	.	0			c.A1379G						PASS	.						77.0	68.0	71.0					16																	55883667		1568	3582	5150	SO:0001583	missense	221223	exon12			TAGAAGTAGACAG	AK090997	CCDS10755.1, CCDS45490.1, CCDS54012.1	16q13	2010-10-12	2010-10-12	2010-10-12	ENSG00000159398	ENSG00000159398	3.1.1.1	"""Carboxylesterases"""	26459	protein-coding gene	gene with protein product			"""carboxylesterase 7"""	CES7		20931200	Standard	NM_145024		Approved	FLJ31547, CES4C1, CES5, CAUXIN	uc021tir.1	Q6NT32	OTTHUMG00000133236	ENST00000290567.9:c.1292A>G	16.37:g.55883667T>C	ENSP00000290567:p.Tyr431Cys	58.0	0.0	0		54.0	31.0	0.574074	NM_001190158	B7Z252|B7ZLB6|Q8NBC8|Q96DN9	Missense_Mutation	SNP	ENST00000290567.9	37	CCDS45490.1	.	.	.	.	.	.	.	.	.	.	.	15.85	2.955162	0.53293	.	.	ENSG00000159398	ENST00000521992;ENST00000518005;ENST00000290567;ENST00000520435;ENST00000541580	T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07	5.03	5.03	0.67393	Carboxylesterase, type B (1);	0.181974	0.27084	N	0.021018	D	0.92665	0.7669	H	0.98802	4.335	0.49483	D	0.999795	D	0.89917	1.0	D	0.91635	0.999	D	0.95007	0.8148	10	0.87932	D	0	.	13.3257	0.60459	0.0:0.0:0.0:1.0	.	431	Q6NT32	EST5A_HUMAN	C	460;325;431;401;211	ENSP00000428864:Y460C;ENSP00000428571:Y325C;ENSP00000290567:Y431C;ENSP00000428887:Y401C	ENSP00000290567:Y431C	Y	-	2	0	CES5A	54441168	1.000000	0.71417	0.999000	0.59377	0.526000	0.34562	4.597000	0.61062	2.194000	0.70268	0.379000	0.24179	TAC	.	.	none		0.557	CES5A-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256975.3	NM_145024	
PRDM8	56978	hgsc.bcm.edu	37	4	81124299	81124299	+	Silent	SNP	C	C	T	rs150632206	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:81124299C>T	ENST00000504452.1	+	8	2522	c.1683C>T	c.(1681-1683)tcC>tcT	p.S561S	PRDM8_ENST00000339711.4_Silent_p.S561S|PRDM8_ENST00000415738.2_Silent_p.S561S			Q9NQV8	PRDM8_HUMAN	PR domain containing 8	561					corpus callosum morphogenesis (GO:0021540)|corticospinal tract morphogenesis (GO:0021957)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(2)|skin(2)	10						GTTGCGGGTCCCTGCCGAGCG	0.746													C|||	105	0.0209665	0.0764	0.0058	5008	,	,		7601	0.0		0.0	False		,,,				2504	0.0				p.S561S		Atlas-SNP	.											.	PRDM8	44	.	0			c.C1683T						PASS	.	C	,	100,2254		0,100,1077	2.0	3.0	3.0		1683,1683	-2.1	1.0	4	dbSNP_134	3	1,5715		0,1,2857	no	coding-synonymous,coding-synonymous	PRDM8	NM_001099403.1,NM_020226.3	,	0,101,3934	TT,TC,CC		0.0175,4.2481,1.2515	,	561/690,561/690	81124299	101,7969	1177	2858	4035	SO:0001819	synonymous_variant	56978	exon4			CGGGTCCCTGCCG	AF275815	CCDS43243.1	4q21	2008-08-21				ENSG00000152784			13993	protein-coding gene	gene with protein product							Standard	NM_020226		Approved		uc003hmc.4	Q9NQV8		ENST00000504452.1:c.1683C>T	4.37:g.81124299C>T		2.0	0.0	0		4.0	4.0	1	NM_001099403	A8K7X2|Q6IQ36	Silent	SNP	ENST00000504452.1	37	CCDS43243.1																																																																																			C|0.982;T|0.018	0.018	strong		0.746	PRDM8-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362793.1		
MUC4	4585	hgsc.bcm.edu	37	3	195510266	195510266	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195510266A>C	ENST00000463781.3	-	2	8644	c.8185T>G	c.(8185-8187)Tca>Gca	p.S2729A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S2729A	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)		CCTGTGGATGATGAGGAAGTG	0.552																																					p.S2729A		Atlas-SNP	.											MUC4_ENST00000463781,NS,lymphoid_neoplasm,0,1	MUC4	1505	1	0			c.T8185G						scavenged	.						2.0	2.0	2.0					3																	195510266		261	672	933	SO:0001583	missense	4585	exon2			TGGATGATGAGGA	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.8185T>G	3.37:g.195510266A>C	ENSP00000417498:p.Ser2729Ala	79.0	2.0	0.0253165		69.0	18.0	0.26087	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	.	.	.	.	.	.	.	.	.	.	-	1.325	-0.598449	0.03744	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30448	1.54;1.53	1.02	-0.144	0.13440	.	.	.	.	.	T	0.10594	0.0259	N	0.08118	0	0.80722	P	0.0	.	.	.	.	.	.	T	0.25293	-1.0136	5	.	.	.	.	0.3308	0.00318	0.2449:0.2997:0.2433:0.2122	.	.	.	.	A	2729	ENSP00000417498:S2729A;ENSP00000420243:S2729A	.	S	-	1	0	MUC4	196993365	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-2.757000	0.00788	-2.087000	0.00862	-2.380000	0.00233	TCA	.	.	none		0.552	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PDE9A	5152	hgsc.bcm.edu	37	21	44119120	44119120	+	Splice_Site	SNP	C	C	T	rs74697345	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:44119120C>T	ENST00000291539.6	+	4	321	c.261C>T	c.(259-261)tcC>tcT	p.S87S	PDE9A_ENST00000335440.6_Splice_Site_p.R64*|PDE9A_ENST00000470987.1_3'UTR|PDE9A_ENST00000349112.3_Splice_Site_p.R38*|PDE9A_ENST00000398224.3_Splice_Site_p.S20S|PDE9A_ENST00000398236.3_Splice_Site_p.S61S|PDE9A_ENST00000398225.3_Splice_Site_p.S46S|PDE9A_ENST00000398227.3_Intron|PDE9A_ENST00000328862.6_Splice_Site_p.S61S|PDE9A_ENST00000539837.1_Intron|PDE9A_ENST00000398234.3_Splice_Site_p.S46S|PDE9A_ENST00000398232.3_Splice_Site_p.S20S|PDE9A_ENST00000335512.4_Splice_Site_p.S87S|PDE9A_ENST00000398229.3_Intron|PDE9A_ENST00000380328.2_Splice_Site_p.R113*	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A	87					blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|metabolic process (GO:0008152)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)	p.S87S(1)		breast(1)|endometrium(4)|large_intestine(6)|lung(8)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Caffeine(DB00201)	AGCAACTCTCCGGTAAGGCCC	0.448													T|||	49	0.00978435	0.0348	0.0043	5008	,	,		14460	0.0		0.0	False		,,,				2504	0.0				p.R113X		Atlas-SNP	.											PDE9A,colon,carcinoma,0,1	PDE9A	69	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C337T						PASS	.	T	,,stop/ARG,stop/ARG,,,,,,,,stop/ARG,,,,,,,,	155,4251	812.6+/-416.1	1,153,2049	85.0	78.0	80.0		261,60,112,337,138,,,183,,,,190,,,60,138,183,,,261	-4.7	0.9	21	dbSNP_132	80	3,8597	819.0+/-406.8	0,3,4297	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,stop-gained-near-splice,stop-gained-near-splice,coding-synonymous-near-splice,intron,intron,coding-synonymous-near-splice,intron,utr-5,intron,stop-gained-near-splice,utr-5,intron,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,utr-5,utr-5,coding-synonymous-near-splice	PDE9A	NM_001001567.1,NM_001001568.1,NM_001001569.1,NM_001001570.1,NM_001001571.1,NM_001001572.1,NM_001001573.1,NM_001001574.1,NM_001001575.1,NM_001001576.1,NM_001001577.1,NM_001001578.1,NM_001001579.1,NM_001001580.1,NM_001001581.1,NM_001001582.1,NM_001001583.1,NM_001001584.2,NM_001001585.1,NM_002606.2	,,,,,,,,,,,,,,,,,,,	1,156,6346	TT,TC,CC		0.0349,3.5179,1.2148	,,,,,,,,,,,,,,,,,,,	87/534,20/467,38/466,113/541,46/493,,,61/508,,,,64/492,,,20/527,46/553,61/568,,,87/594	44119120	158,12848	2203	4300	6503	SO:0001630	splice_region_variant	5152	exon5			ACTCTCCGGTAAG	AF048837	CCDS13690.1, CCDS33567.1, CCDS33568.1, CCDS33569.1, CCDS33570.1, CCDS33571.1, CCDS42941.1, CCDS42942.1, CCDS42943.1, CCDS42944.1, CCDS42945.1, CCDS42946.1, CCDS42947.1	21q22.3	2005-11-29			ENSG00000160191	ENSG00000160191	3.1.4.17	"""Phosphodiesterases"""	8795	protein-coding gene	gene with protein product		602973				9624146	Standard	NM_001001584		Approved		uc002zbm.3	O76083	OTTHUMG00000086825	ENST00000291539.6:c.262+1C>T	21.37:g.44119120C>T		81.0	0.0	0		91.0	38.0	0.417582	NM_001001570	B2RBI5|B4DFI5|D3DSJ8|D3DSJ9|O75490|O75491|O95225|Q53Y40|Q5QD39|Q86SF7|Q86SI6|Q86SJ3|Q86WN3|Q86WN4|Q86WN5|Q86WN6|Q86WN7|Q86WN8|Q86WN9|Q86WP0	Nonsense_Mutation	SNP	ENST00000291539.6	37	CCDS13690.1	18	0.008241758241758242	18	0.036585365853658534	0	0.0	0	0.0	0	0.0	t	15.04	2.716118	0.48622	0.035179	3.49E-4	ENSG00000160191	ENST00000380328;ENST00000335440;ENST00000349112	.	.	.	4.19	-4.74	0.03249	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.8976	0.29715	0.1418:0.5569:0.0:0.3013	.	.	.	.	X	113;64;38	.	ENSP00000335365:R64X	R	+	1	2	PDE9A	42992189	0.847000	0.29606	0.876000	0.34364	0.886000	0.51366	-0.556000	0.05992	-1.122000	0.02945	-0.439000	0.05793	CGA	C|0.990;T|0.010	0.010	strong		0.448	PDE9A-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195466.1		Silent
CCDC105	126402	hgsc.bcm.edu	37	19	15122104	15122104	+	Missense_Mutation	SNP	G	G	T	rs199904661	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15122104G>T	ENST00000292574.3	+	1	549	c.467G>T	c.(466-468)cGc>cTc	p.R156L	SLC1A6_ENST00000430939.2_5'Flank	NM_173482.2	NP_775753.2	Q8IYK2	CC105_HUMAN	coiled-coil domain containing 105	156						extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|prostate(4)|skin(2)	23						CAGCTGCTGCGCCAGCGCGAG	0.692													G|||	66	0.0131789	0.0469	0.0058	5008	,	,		14563	0.0		0.0	False		,,,				2504	0.0				p.R156L		Atlas-SNP	.											.	CCDC105	53	.	0			c.G467T						PASS	.	G	LEU/ARG	163,3785		3,157,1814	7.0	8.0	7.0		467	2.8	1.0	19	dbSNP_134	7	3,8257		0,3,4127	yes	missense	CCDC105	NM_173482.2	102	3,160,5941	TT,TG,GG		0.0363,4.1287,1.3598	probably-damaging	156/500	15122104	166,12042	1974	4130	6104	SO:0001583	missense	126402	exon1			TGCTGCGCCAGCG	AK097684	CCDS12322.1	19p13.12	2008-02-05				ENSG00000160994			26866	protein-coding gene	gene with protein product						12477932	Standard	NM_173482		Approved	FLJ40365	uc002nae.2	Q8IYK2		ENST00000292574.3:c.467G>T	19.37:g.15122104G>T	ENSP00000292574:p.Arg156Leu	43.0	0.0	0		44.0	30.0	0.681818	NM_173482	Q8N7T5|Q8NDL5	Missense_Mutation	SNP	ENST00000292574.3	37	CCDS12322.1	15	0.006868131868131868	15	0.03048780487804878	0	0.0	0	0.0	0	0.0	G	17.67	3.446054	0.63178	0.041287	3.63E-4	ENSG00000160994	ENST00000292574	T	0.02579	4.24	3.82	2.78	0.32641	.	0.117336	0.34603	N	0.003821	T	0.01765	0.0056	M	0.67953	2.075	0.25682	N	0.985784	D	0.69078	0.997	D	0.63957	0.92	T	0.05517	-1.0880	10	0.49607	T	0.09	-17.7965	6.322	0.21223	0.1376:0.0:0.8624:0.0	.	156	Q8IYK2	CC105_HUMAN	L	156	ENSP00000292574:R156L	ENSP00000292574:R156L	R	+	2	0	CCDC105	14983104	0.402000	0.25311	0.998000	0.56505	0.645000	0.38454	1.363000	0.34159	1.678000	0.50952	0.462000	0.41574	CGC	G|0.993;T|0.007	0.007	strong		0.692	CCDC105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466293.1	NM_173482	
DOCK5	80005	hgsc.bcm.edu	37	8	25149590	25149590	+	Silent	SNP	G	G	A	rs35475676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:25149590G>A	ENST00000276440.7	+	6	416	c.372G>A	c.(370-372)ctG>ctA	p.L124L	DOCK5_ENST00000481100.1_Silent_p.L124L	NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	124					positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		CGTACAGCCTGATCGAGTGGC	0.483													G|||	59	0.0117812	0.0416	0.0058	5008	,	,		18104	0.0		0.0	False		,,,				2504	0.0				p.L124L	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											.	DOCK5	167	.	0			c.G372A						PASS	.	G		213,4193	121.7+/-159.2	8,197,1998	38.0	36.0	36.0		372	3.7	1.0	8	dbSNP_126	36	0,8600		0,0,4300	yes	coding-synonymous	DOCK5	NM_024940.6		8,197,6298	AA,AG,GG		0.0,4.8343,1.6377		124/1871	25149590	213,12793	2203	4300	6503	SO:0001819	synonymous_variant	80005	exon6			CAGCCTGATCGAG		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.372G>A	8.37:g.25149590G>A		96.0	0.0	0		111.0	51.0	0.459459	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Silent	SNP	ENST00000276440.7	37	CCDS6047.1																																																																																			G|0.983;A|0.017	0.017	strong		0.483	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	
CIAPIN1	57019	hgsc.bcm.edu	37	16	57474740	57474740	+	Missense_Mutation	SNP	G	G	T	rs11557672	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:57474740G>T	ENST00000569979.1	-	1	147	c.101C>A	c.(100-102)gCg>gAg	p.A34E	CIAPIN1_ENST00000568940.1_Missense_Mutation_p.A34E|CIAPIN1_ENST00000394391.4_Missense_Mutation_p.A34E|CIAPIN1_ENST00000569370.1_Missense_Mutation_p.A34E|CIAPIN1_ENST00000567518.1_Missense_Mutation_p.A34E|CIAPIN1_ENST00000569246.1_5'UTR|CIAPIN1_ENST00000565961.1_Missense_Mutation_p.A34E					cytokine induced apoptosis inhibitor 1											cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	10						GCCGGTTAACGCTTGAAGCTT	0.522													G|||	73	0.0145767	0.0499	0.0086	5008	,	,		18615	0.0		0.001	False		,,,				2504	0.0				p.A34E		Atlas-SNP	.											.	CIAPIN1	17	.	0			c.C101A						PASS	.	G	GLU/ALA	142,3808		2,138,1835	86.0	84.0	85.0		101	-10.0	0.0	16	dbSNP_120	85	3,8331		0,3,4164	no	missense	CIAPIN1	NM_020313.2	107	2,141,5999	TT,TG,GG		0.036,3.5949,1.1804	benign	34/313	57474740	145,12139	1975	4167	6142	SO:0001583	missense	57019	exon2			GTTAACGCTTGAA	AF248964	CCDS10781.2	16q21	2012-09-20			ENSG00000005194	ENSG00000005194			28050	protein-coding gene	gene with protein product		608943				10493829, 11230166	Standard	XM_005256061		Approved	Anamorsin	uc002ell.1	Q6FI81	OTTHUMG00000133457	ENST00000569979.1:c.101C>A	16.37:g.57474740G>T	ENSP00000458000:p.Ala34Glu	117.0	0.0	0		138.0	56.0	0.405797	NM_020313		Missense_Mutation	SNP	ENST00000569979.1	37		31	0.014194139194139194	26	0.052845528455284556	5	0.013812154696132596	0	0.0	0	0.0	G	4.538	0.099964	0.08681	0.035949	3.6E-4	ENSG00000005194	ENST00000394391	T	0.28666	1.6	4.98	-9.96	0.00443	.	1.395360	0.05048	N	0.477654	T	0.01976	0.0062	L	0.33753	1.03	0.09310	N	1	B;B;B	0.10296	0.001;0.003;0.0	B;B;B	0.08055	0.002;0.003;0.001	T	0.18935	-1.0321	10	0.05959	T	0.93	1.2775	3.7895	0.08715	0.0939:0.1347:0.3108:0.4606	rs11557672;rs16957069;rs11557672	34;34;34	B4DHB9;Q6FI81-3;Q6FI81	.;.;CPIN1_HUMAN	E	34	ENSP00000377914:A34E	ENSP00000377914:A34E	A	-	2	0	CIAPIN1	56032241	0.000000	0.05858	0.009000	0.14445	0.950000	0.60333	-1.034000	0.03567	-2.690000	0.00404	-0.295000	0.09555	GCG	G|0.975;T|0.025	0.025	strong		0.522	CIAPIN1-010	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432580.1	NM_020313	
TRAF3IP3	80342	hgsc.bcm.edu	37	1	209933659	209933659	+	Missense_Mutation	SNP	G	G	A	rs78296889	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:209933659G>A	ENST00000367024.1	+	3	791	c.275G>A	c.(274-276)cGg>cAg	p.R92Q	TRAF3IP3_ENST00000367025.3_Missense_Mutation_p.R92Q|TRAF3IP3_ENST00000367026.3_Missense_Mutation_p.R92Q|TRAF3IP3_ENST00000400959.3_Missense_Mutation_p.R92Q|TRAF3IP3_ENST00000010338.4_Missense_Mutation_p.R92Q			Q9Y228	T3JAM_HUMAN	TRAF3 interacting protein 3	92						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32				OV - Ovarian serous cystadenocarcinoma(81;0.045)		CCCTCCAGGCGGCCAGGACAG	0.597													G|||	87	0.0173722	0.0628	0.0058	5008	,	,		17422	0.0		0.0	False		,,,				2504	0.0				p.R92Q		Atlas-SNP	.											.	TRAF3IP3	68	.	0			c.G275A						PASS	.	G	GLN/ARG	220,4186	125.7+/-162.9	4,212,1987	25.0	26.0	25.0		275	1.8	0.0	1	dbSNP_132	25	3,8597	3.0+/-9.4	0,3,4297	yes	missense	TRAF3IP3	NM_025228.2	43	4,215,6284	AA,AG,GG		0.0349,4.9932,1.7146	possibly-damaging	92/552	209933659	223,12783	2203	4300	6503	SO:0001583	missense	80342	exon3			CCAGGCGGCCAGG		CCDS1490.1, CCDS1490.2, CCDS73023.1	1q32.3-q41	2008-02-05			ENSG00000009790	ENSG00000009790			30766	protein-coding gene	gene with protein product	"""TRAF3 interacting Jun N terminal kinase (JNK) activating modulator"""	608255				14572659	Standard	XR_247044		Approved	T3JAM	uc001hho.3	Q9Y228	OTTHUMG00000036480	ENST00000367024.1:c.275G>A	1.37:g.209933659G>A	ENSP00000355991:p.Arg92Gln	150.0	0.0	0		158.0	65.0	0.411392	NM_025228	A1L464|A6NIU9|Q2YDB5|Q4VY06|Q7Z706	Missense_Mutation	SNP	ENST00000367024.1	37	CCDS1490.2	38	0.0173992673992674	36	0.07317073170731707	2	0.0055248618784530384	0	0.0	0	0.0	G	11.69	1.712561	0.30322	0.049932	3.49E-4	ENSG00000009790	ENST00000400959;ENST00000367025;ENST00000458110;ENST00000367026;ENST00000367024;ENST00000010338	T;T;T;T;T	0.46819	0.86;0.87;0.91;0.87;0.91	4.69	1.75	0.24633	.	2.341960	0.02012	N	0.047071	T	0.05044	0.0135	L	0.44542	1.39	0.09310	N	1	B;D;B;P	0.56746	0.003;0.977;0.007;0.938	B;P;B;B	0.46718	0.003;0.525;0.007;0.308	T	0.12682	-1.0538	10	0.13108	T	0.6	-7.597	7.4585	0.27280	0.2986:0.0:0.7014:0.0	.	92;92;92;92	Q9Y228;Q9Y228-2;Q9Y228-3;E2QRE5	T3JAM_HUMAN;.;.;.	Q	92;92;75;92;92;92	ENSP00000383743:R92Q;ENSP00000355992:R92Q;ENSP00000355993:R92Q;ENSP00000355991:R92Q;ENSP00000010338:R92Q	ENSP00000010338:R92Q	R	+	2	0	TRAF3IP3	208000282	0.000000	0.05858	0.008000	0.14137	0.006000	0.05464	-0.029000	0.12329	0.523000	0.28482	-0.448000	0.05591	CGG	G|0.984;A|0.016	0.016	strong		0.597	TRAF3IP3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088734.2		
KCNG4	93107	hgsc.bcm.edu	37	16	84270650	84270650	+	Missense_Mutation	SNP	C	C	T	rs61743417	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84270650C>T	ENST00000308251.4	-	2	510	c.442G>A	c.(442-444)Gcc>Acc	p.A148T	KCNG4_ENST00000568181.1_Missense_Mutation_p.A148T	NM_172347.2	NP_758857.1	Q8TDN1	KCNG4_HUMAN	potassium voltage-gated channel, subfamily G, member 4	148					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	31						CCCCAGTAGGCCAGCTCCTCC	0.667													C|||	149	0.0297524	0.1097	0.0058	5008	,	,		16764	0.0		0.0	False		,,,				2504	0.0				p.A148T		Atlas-SNP	.											KCNG4,NS,carcinoma,0,1	KCNG4	71	1	0			c.G442A						PASS	.	C	THR/ALA	380,4020	191.6+/-217.2	19,342,1839	42.0	43.0	42.0		442	-1.0	0.6	16	dbSNP_129	42	0,8600		0,0,4300	yes	missense	KCNG4	NM_172347.2	58	19,342,6139	TT,TC,CC		0.0,8.6364,2.9231	benign	148/520	84270650	380,12620	2200	4300	6500	SO:0001583	missense	93107	exon2			AGTAGGCCAGCTC	AF348984	CCDS10945.1	16q24.1	2011-07-05			ENSG00000168418	ENSG00000168418		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	19697	protein-coding gene	gene with protein product		607603				12060745, 16382104	Standard	NM_172347		Approved	Kv6.4	uc010voc.2	Q8TDN1	OTTHUMG00000137638	ENST00000308251.4:c.442G>A	16.37:g.84270650C>T	ENSP00000312129:p.Ala148Thr	126.0	0.0	0		142.0	59.0	0.415493	NM_172347	Q96H24	Missense_Mutation	SNP	ENST00000308251.4	37	CCDS10945.1	48	0.02197802197802198	47	0.09552845528455285	1	0.0027624309392265192	0	0.0	0	0.0	C	4.103	0.017220	0.07959	0.086364	0.0	ENSG00000168418	ENST00000308251	T	0.76709	-1.04	5.11	-1.05	0.10036	BTB/POZ-like (1);BTB/POZ fold (2);Potassium channel, voltage dependent, Kv, tetramerisation (1);	0.951541	0.08816	N	0.889546	T	0.02727	0.0082	N	0.11818	0.18	0.09310	N	0.999999	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.001	T	0.01215	-1.1416	10	0.16896	T	0.51	.	9.62	0.39716	0.0:0.3441:0.0:0.6559	.	148;148	Q8TDN1;Q8TDN1-2	KCNG4_HUMAN;.	T	148	ENSP00000312129:A148T	ENSP00000312129:A148T	A	-	1	0	KCNG4	82828151	0.000000	0.05858	0.631000	0.29282	0.993000	0.82548	-0.583000	0.05807	-0.538000	0.06281	-0.275000	0.10095	GCC	C|0.971;T|0.029	0.029	strong		0.667	KCNG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269079.2	NM_172347	
NLRP7	199713	hgsc.bcm.edu	37	19	55441971	55441971	+	Silent	SNP	G	G	A	rs61746780	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55441971G>A	ENST00000590030.1	-	8	2746	c.2706C>T	c.(2704-2706)gcC>gcT	p.A902A	NLRP7_ENST00000340844.2_Silent_p.A902A|NLRP7_ENST00000328092.5_Silent_p.A874A|NLRP7_ENST00000448121.2_Silent_p.A874A|NLRP7_ENST00000588756.1_Silent_p.A902A|NLRP7_ENST00000446217.1_Silent_p.A930A|NLRP7_ENST00000592784.1_Silent_p.A902A			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	902							ATP binding (GO:0005524)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		TGAGGCTGCAGGCTTCTTGGA	0.463													.|||	128	0.0255591	0.09	0.0086	5008	,	,		17972	0.0		0.002	False		,,,				2504	0.001				p.A902A		Atlas-SNP	.											.	NLRP7	411	.	0			c.C2706T						PASS	.	G	,,	368,4038	187.4+/-214.1	15,338,1850	132.0	126.0	128.0		2706,2622,2706	-1.7	0.0	19	dbSNP_129	128	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	NLRP7	NM_001127255.1,NM_139176.3,NM_206828.3	,,	15,342,6146	AA,AG,GG		0.0465,8.3522,2.8602	,,	902/1038,874/1010,902/981	55441971	372,12634	2203	4300	6503	SO:0001819	synonymous_variant	199713	exon9			GCTGCAGGCTTCT	AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"""Nucleotide-binding domain and leucine rich repeat containing"""	22947	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"""	609661	"""NACHT, leucine rich repeat and PYD containing 7"""	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.2706C>T	19.37:g.55441971G>A		105.0	0.0	0		111.0	63.0	0.567568	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Silent	SNP	ENST00000590030.1	37	CCDS33109.1																																																																																			G|0.976;A|0.024	0.024	strong		0.463	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176	
ACSL5	51703	hgsc.bcm.edu	37	10	114181773	114181773	+	Missense_Mutation	SNP	A	A	G	rs12254915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:114181773A>G	ENST00000393081.1	+	16	1763	c.1456A>G	c.(1456-1458)Aca>Gca	p.T486A	ACSL5_ENST00000354273.4_Missense_Mutation_p.T486A|RP11-324O2.6_ENST00000424422.1_RNA|ACSL5_ENST00000433418.1_Missense_Mutation_p.T486A|ACSL5_ENST00000369410.3_Missense_Mutation_p.T268A|ACSL5_ENST00000354655.4_Missense_Mutation_p.T486A|ACSL5_ENST00000356116.1_Missense_Mutation_p.T542A	NM_203380.1	NP_976314.1	Q9ULC5	ACSL5_HUMAN	acyl-CoA synthetase long-chain family member 5	486			T -> A (in dbSNP:rs12254915).		cellular lipid metabolic process (GO:0044255)|long-chain fatty acid metabolic process (GO:0001676)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)			breast(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(6)|prostate(1)|skin(2)|stomach(1)	21		Colorectal(252;0.117)|Breast(234;0.222)		Epithelial(162;0.0343)|all cancers(201;0.137)		GAACTACTTTACAGTGAATAA	0.458													A|||	75	0.014976	0.0552	0.0029	5008	,	,		20705	0.0		0.0	False		,,,				2504	0.0				p.T542A		Atlas-SNP	.											.	ACSL5	51	.	0			c.A1624G						PASS	.	A	ALA/THR,ALA/THR,ALA/THR	193,4213	122.9+/-160.3	2,189,2012	135.0	132.0	133.0		1624,1456,1456	0.6	0.7	10	dbSNP_120	133	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	ACSL5	NM_016234.3,NM_203379.1,NM_203380.1	58,58,58	2,190,6311	GG,GA,AA		0.0116,4.3804,1.4916	benign,benign,benign	542/740,486/684,486/684	114181773	194,12812	2203	4300	6503	SO:0001583	missense	51703	exon16			TACTTTACAGTGA	AB033899	CCDS7572.1, CCDS7573.1	10q25.1-q25.2	2004-06-21	2004-02-19	2004-02-20	ENSG00000197142	ENSG00000197142		"""Acyl-CoA synthetase family"""	16526	protein-coding gene	gene with protein product	"""FACL5 for fatty acid coenzyme A ligase 5"", ""long-chain acyl-CoA synthetase 5"", ""long-chain fatty acid coenzyme A ligase 5"", ""fatty-acid-Coenzyme A ligase, long-chain 5"""	605677	"""fatty-acid-Coenzyme A ligase, long-chain 5"""	FACL5		11127823	Standard	NM_016234		Approved	ACS5, ACS2	uc001kzu.3	Q9ULC5	OTTHUMG00000019060	ENST00000393081.1:c.1456A>G	10.37:g.114181773A>G	ENSP00000376796:p.Thr486Ala	88.0	0.0	0		70.0	22.0	0.314286	NM_016234	A6GV77|D3DRB3|Q6UX44|Q9UIU4	Missense_Mutation	SNP	ENST00000393081.1	37	CCDS7573.1	25	0.011446886446886446	23	0.046747967479674794	2	0.0055248618784530384	0	0.0	0	0.0	A	2.991	-0.208102	0.06180	0.043804	1.16E-4	ENSG00000197142	ENST00000354655;ENST00000393081;ENST00000356116;ENST00000433418;ENST00000354273;ENST00000369410	T;T;T;T;T;T	0.09630	2.96;2.96;2.96;2.96;2.96;2.96	5.86	0.636	0.17729	AMP-dependent synthetase/ligase (1);	0.395320	0.28724	N	0.014342	T	0.00356	0.0011	N	0.00405	-1.535	0.09310	N	0.999999	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.0;0.0	T	0.44283	-0.9338	10	0.02654	T	1	-2.9242	8.9257	0.35639	0.2131:0.0:0.462:0.3249	rs12254915;rs52833907;rs12254915	268;486;542;486	B4DX30;A6GV77;Q9ULC5-3;Q9ULC5	.;.;.;ACSL5_HUMAN	A	486;486;542;486;486;268	ENSP00000346680:T486A;ENSP00000376796:T486A;ENSP00000348429:T542A;ENSP00000403647:T486A;ENSP00000346223:T486A;ENSP00000358418:T268A	ENSP00000346223:T486A	T	+	1	0	ACSL5	114171763	0.994000	0.37717	0.677000	0.29947	0.906000	0.53458	1.059000	0.30517	-0.131000	0.11578	-0.270000	0.10280	ACA	A|0.982;G|0.018	0.018	strong		0.458	ACSL5-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050386.1	NM_016234	
KRT78	196374	hgsc.bcm.edu	37	12	53242389	53242389	+	Missense_Mutation	SNP	G	G	A	rs116117459	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53242389G>A	ENST00000304620.4	-	1	389	c.326C>T	c.(325-327)aCg>aTg	p.T109M	KRT78_ENST00000359499.4_5'Flank	NM_173352.2	NP_775487.2	Q8N1N4	K2C78_HUMAN	keratin 78	109	Head.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	18						GGTCTCCTGCGTCCGCACCAC	0.567													G|||	67	0.0133786	0.0507	0.0	5008	,	,		16189	0.0		0.0	False		,,,				2504	0.0				p.T109M		Atlas-SNP	.											.	KRT78	41	.	0			c.C326T						PASS	.	G	MET/THR	254,4152	145.7+/-180.5	5,244,1954	106.0	88.0	94.0		326	4.2	1.0	12	dbSNP_132	94	1,8599	1.2+/-3.3	0,1,4299	yes	missense	KRT78	NM_173352.2	81	5,245,6253	AA,AG,GG		0.0116,5.7649,1.9606	probably-damaging	109/521	53242389	255,12751	2203	4300	6503	SO:0001583	missense	196374	exon1			TCCTGCGTCCGCA	AK096419	CCDS8840.1, CCDS73473.1	12q13.13	2013-06-25			ENSG00000170423	ENSG00000170423		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28926	protein-coding gene	gene with protein product		611159				16831889	Standard	XM_005268695		Approved	K5B	uc001sbc.1	Q8N1N4	OTTHUMG00000169880	ENST00000304620.4:c.326C>T	12.37:g.53242389G>A	ENSP00000306261:p.Thr109Met	142.0	0.0	0		187.0	89.0	0.475936	NM_173352	A8K4D6|Q5HYM7|Q7RTT2	Missense_Mutation	SNP	ENST00000304620.4	37	CCDS8840.1	31	0.014194139194139194	31	0.06300813008130081	0	0.0	0	0.0	0	0.0	G	20.4	3.978126	0.74360	0.057649	1.16E-4	ENSG00000170423	ENST00000304620	T	0.77877	-1.13	5.18	4.22	0.49857	.	.	.	.	.	T	0.56485	0.1988	M	0.90369	3.11	0.25830	N	0.984172	D	0.89917	1.0	D	0.65874	0.939	T	0.67364	-0.5689	9	0.72032	D	0.01	.	13.5578	0.61770	0.0:0.0:0.8437:0.1563	.	109	Q8N1N4	K2C78_HUMAN	M	109	ENSP00000306261:T109M	ENSP00000306261:T109M	T	-	2	0	KRT78	51528656	0.080000	0.21391	0.977000	0.42913	0.994000	0.84299	2.068000	0.41471	2.575000	0.86900	0.491000	0.48974	ACG	G|0.983;A|0.017	0.017	strong		0.567	KRT78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406380.1	NM_173352	
UACA	55075	hgsc.bcm.edu	37	15	70960422	70960422	+	Silent	SNP	C	C	T	rs61742861	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:70960422C>T	ENST00000322954.6	-	16	2786	c.2601G>A	c.(2599-2601)gaG>gaA	p.E867E	UACA_ENST00000379983.2_Silent_p.E854E|UACA_ENST00000560441.1_Silent_p.E852E|UACA_ENST00000539319.1_Silent_p.E758E	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	867					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						TCATTTTAACCTCTTCATGGG	0.333													C|||	75	0.014976	0.0552	0.0029	5008	,	,		19447	0.0		0.0	False		,,,				2504	0.0				p.E867E		Atlas-SNP	.											.	UACA	235	.	0			c.G2601A						PASS	.	C	,	195,4201	120.0+/-157.7	3,189,2006	96.0	90.0	92.0		2562,2601	2.6	0.6	15	dbSNP_129	92	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous,coding-synonymous	UACA	NM_001008224.1,NM_018003.2	,	3,190,6303	TT,TC,CC		0.0116,4.4359,1.5086	,	854/1404,867/1417	70960422	196,12796	2198	4298	6496	SO:0001819	synonymous_variant	55075	exon16			TTTAACCTCTTCA	AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"""Ankyrin repeat domain containing"""	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.2601G>A	15.37:g.70960422C>T		140.0	0.0	0		108.0	56.0	0.518519	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Silent	SNP	ENST00000322954.6	37	CCDS10235.1																																																																																			C|0.985;T|0.015	0.015	strong		0.333	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2		
PAPPA2	60676	hgsc.bcm.edu	37	1	176564092	176564092	+	Missense_Mutation	SNP	C	C	T	rs34698817	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:176564092C>T	ENST00000367662.3	+	3	2516	c.1352C>T	c.(1351-1353)gCg>gTg	p.A451V	PAPPA2_ENST00000367661.3_Missense_Mutation_p.A451V	NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	451	Metalloprotease.				bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						GAGGAGGAAGCGACTGACTTG	0.532													C|||	17	0.00339457	0.0113	0.0029	5008	,	,		21732	0.0		0.0	False		,,,				2504	0.0				p.A451V		Atlas-SNP	.											PAPPA2_ENST00000367661,NS,carcinoma,-1,1	PAPPA2	665	1	0			c.C1352T						PASS	.	C	VAL/ALA,VAL/ALA	29,4195		0,29,2083	99.0	105.0	103.0		1352,1352	2.4	0.0	1	dbSNP_126	103	0,8456		0,0,4228	yes	missense,missense	PAPPA2	NM_020318.2,NM_021936.2	64,64	0,29,6311	TT,TC,CC		0.0,0.6866,0.2287	benign,benign	451/1792,451/828	176564092	29,12651	2112	4228	6340	SO:0001583	missense	60676	exon3			AGGAAGCGACTGA	BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"""placenta-specific 3"""	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.1352C>T	1.37:g.176564092C>T	ENSP00000356634:p.Ala451Val	91.0	0.0	0		76.0	34.0	0.447368	NM_021936	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Missense_Mutation	SNP	ENST00000367662.3	37	CCDS41438.1	6	0.0027472527472527475	4	0.008130081300813009	2	0.0055248618784530384	0	0.0	0	0.0	C	0.118	-1.128701	0.01756	0.006866	0.0	ENSG00000116183	ENST00000367662;ENST00000367661	T;T	0.30448	4.78;1.53	4.87	2.4	0.29515	.	1.625110	0.03455	N	0.211229	T	0.12732	0.0309	N	0.14661	0.345	0.09310	N	1	B;B	0.15473	0.008;0.013	B;B	0.08055	0.003;0.001	T	0.18871	-1.0323	10	0.18276	T	0.48	0.1753	3.9845	0.09509	0.1568:0.3405:0.0:0.5026	rs34698817	451;451	Q9BXP8;A9Z1Y8	PAPP2_HUMAN;.	V	451	ENSP00000356634:A451V;ENSP00000356633:A451V	ENSP00000356633:A451V	A	+	2	0	PAPPA2	174830715	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.277000	0.18734	0.230000	0.21059	-0.300000	0.09419	GCG	C|0.997;T|0.003	0.003	strong		0.532	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1		
AARS2	57505	hgsc.bcm.edu	37	6	44270189	44270189	+	Missense_Mutation	SNP	A	A	T	rs35967387	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:44270189A>T	ENST00000244571.4	-	18	2428	c.2426T>A	c.(2425-2427)cTg>cAg	p.L809Q	AARS2_ENST00000491573.1_5'Flank|RP11-444E17.6_ENST00000505802.1_Intron|TMEM151B_ENST00000438774.2_Intron	NM_020745.3	NP_065796			alanyl-tRNA synthetase 2, mitochondrial											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(2)|stomach(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CCGGCTCCCCAGACTCAGCCG	0.632													T|||	114	0.0227636	0.0847	0.0029	5008	,	,		18406	0.0		0.0	False		,,,				2504	0.0				p.L809Q		Atlas-SNP	.											.	AARS2	77	.	0			c.T2426A						PASS	.	T	GLN/LEU	256,4150	795.4+/-415.3	5,246,1952	41.0	46.0	44.0		2426	0.2	1.0	6	dbSNP_126	44	1,8599		0,1,4299	yes	missense	AARS2	NM_020745.2	113	5,247,6251	TT,TA,AA		0.0116,5.8103,1.976	benign	809/986	44270189	257,12749	2203	4300	6503	SO:0001583	missense	57505	exon18			CTCCCCAGACTCA	AB033096	CCDS34464.1	6p21.1	2012-10-26	2012-10-26	2007-02-23	ENSG00000124608	ENSG00000124608	6.1.1.7	"""Aminoacyl tRNA synthetases / Class II"""	21022	protein-coding gene	gene with protein product	"""alanine tRNA ligase 2, mitochondrial"""	612035	"""alanyl-tRNA synthetase like"", ""alanyl-tRNA synthetase 2, mitochondrial (putative)"""	AARSL		15779907, 21549344	Standard	NM_020745		Approved	KIAA1270, bA444E17.1	uc010jza.1	Q5JTZ9	OTTHUMG00000014766	ENST00000244571.4:c.2426T>A	6.37:g.44270189A>T	ENSP00000244571:p.Leu809Gln	133.0	0.0	0		131.0	66.0	0.503817	NM_020745		Missense_Mutation	SNP	ENST00000244571.4	37	CCDS34464.1	48	0.02197802197802198	47	0.09552845528455285	1	0.0027624309392265192	0	0.0	0	0.0	T	1.128	-0.653372	0.03480	0.058103	1.16E-4	ENSG00000124608	ENST00000244571	T	0.63913	-0.07	5.32	0.155	0.14906	.	1.197330	0.05517	N	0.561479	T	0.09113	0.0225	N	0.01048	-1.04	0.22947	N	0.998524	B	0.02656	0.0	B	0.01281	0.0	T	0.09250	-1.0683	10	0.12103	T	0.63	-10.1928	4.7087	0.12861	0.2367:0.3061:0.0:0.4572	rs35967387	809	Q5JTZ9	SYAM_HUMAN	Q	809	ENSP00000244571:L809Q	ENSP00000244571:L809Q	L	-	2	0	AARS2	44378167	0.362000	0.24980	0.961000	0.40146	0.084000	0.17831	-0.656000	0.05342	-0.185000	0.10550	-0.983000	0.02560	CTG	A|0.977;T|0.023	0.023	strong		0.632	AARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040741.2	NM_020745	
LRIT3	345193	hgsc.bcm.edu	37	4	110791453	110791453	+	Silent	SNP	T	T	C	rs9994891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:110791453T>C	ENST00000594814.1	+	4	1548	c.1548T>C	c.(1546-1548)acT>acC	p.T516T	LRIT3_ENST00000327908.3_Silent_p.T333T|LRIT3_ENST00000379920.3_Silent_p.T471T|LRIT3_ENST00000409621.2_Silent_p.T333T	NM_198506.3	NP_940908.3	Q3SXY7	LRIT3_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 3	516	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				cervix(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(2)|skin(1)	16				OV - Ovarian serous cystadenocarcinoma(123;0.0011)		CTGCAGTGACTGTGTTGTATT	0.473													T|||	588	0.117412	0.4228	0.0346	5008	,	,		22015	0.001		0.004	False		,,,				2504	0.0				p.T516T		Atlas-SNP	.											.	LRIT3	107	.	0			c.T1548C						PASS	.	T		1599,2807	496.0+/-363.4	295,1009,899	152.0	139.0	144.0		1413	-6.0	0.0	4	dbSNP_119	144	61,8539	36.4+/-91.3	1,59,4240	no	coding-synonymous	LRIT3	NM_198506.2		296,1068,5139	CC,CT,TT		0.7093,36.2914,12.7633		471/635	110791453	1660,11346	2203	4300	6503	SO:0001819	synonymous_variant	345193	exon4			AGTGACTGTGTTG	AK126648	CCDS3688.2, CCDS3688.3	4q25	2014-01-28	2007-06-19		ENSG00000183423	ENSG00000183423		"""Immunoglobulin superfamily / I-set domain containing"""	24783	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 4"""	615004					Standard	NM_198506		Approved	FLJ44691, FIGLER4, CSNB1F	uc031sgv.1	Q3SXY7	OTTHUMG00000132043	ENST00000594814.1:c.1548T>C	4.37:g.110791453T>C		128.0	0.0	0		151.0	148.0	0.980132	NM_198506	C9J1C2|Q6ZTG1	Silent	SNP	ENST00000594814.1	37	CCDS3688.3																																																																																			T|0.866;C|0.134	0.134	strong		0.473	LRIT3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335270.2	NM_198506	
C5orf42	65250	hgsc.bcm.edu	37	5	37226888	37226888	+	Silent	SNP	A	A	G	rs115435816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37226888A>G	ENST00000508244.1	-	11	1902	c.1809T>C	c.(1807-1809)acT>acC	p.T603T	C5orf42_ENST00000274258.7_5'UTR|C5orf42_ENST00000425232.2_Silent_p.T603T			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	603						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			AAAAAAAATGAGTGATACAAA	0.284													A|||	92	0.0183706	0.0673	0.0043	5008	,	,		18803	0.0		0.0	False		,,,				2504	0.0				p.T603T		Atlas-SNP	.											.	C5orf42	422	.	0			c.T1809C						PASS	.	A		89,1295		5,79,608	46.0	38.0	40.0		1809	4.1	1.0	5	dbSNP_132	40	1,3175		0,1,1587	no	coding-synonymous	C5orf42	NM_023073.3		5,80,2195	GG,GA,AA		0.0315,6.4306,1.9737		603/3198	37226888	90,4470	692	1588	2280	SO:0001819	synonymous_variant	65250	exon12			AAAATGAGTGATA		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.1809T>C	5.37:g.37226888A>G		93.0	0.0	0		90.0	51.0	0.566667	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Silent	SNP	ENST00000508244.1	37	CCDS34146.2																																																																																			A|0.984;G|0.016	0.016	strong		0.284	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073	
HMGB1	3146	hgsc.bcm.edu	37	13	31037445	31037445	+	Silent	SNP	T	T	C	rs983723	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:31037445T>C	ENST00000405805.1	-	3	1135	c.195A>G	c.(193-195)aaA>aaG	p.K65K	HMGB1_ENST00000341423.5_Silent_p.K65K|HMGB1_ENST00000399489.1_Silent_p.K65K|HMGB1_ENST00000399494.1_Silent_p.K65K|HMGB1_ENST00000339872.4_Silent_p.K65K|HMGB1_ENST00000326004.4_Silent_p.K65K|HMGB1_ENST00000468384.1_5'Flank			P09429	HMGB1_HUMAN	high mobility group box 1	65					apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|base-excision repair, DNA ligation (GO:0006288)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|dendritic cell chemotaxis (GO:0002407)|DNA ligation involved in DNA repair (GO:0051103)|DNA recombination (GO:0006310)|DNA topological change (GO:0006265)|inflammatory response to antigenic stimulus (GO:0002437)|innate immune response (GO:0045087)|myeloid dendritic cell activation (GO:0001773)|negative regulation of apoptotic cell clearance (GO:2000426)|negative regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0017055)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron projection development (GO:0031175)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA binding (GO:0043388)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|V(D)J recombination (GO:0033151)	cell surface (GO:0009986)|condensed chromosome (GO:0000793)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chemoattractant activity (GO:0042056)|cytokine activity (GO:0005125)|damaged DNA binding (GO:0003684)|DNA binding, bending (GO:0008301)|double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)|RAGE receptor binding (GO:0050786)|repressing transcription factor binding (GO:0070491)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription factor binding (GO:0008134)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(1)|ovary(1)	8		Lung SC(185;0.0257)		all cancers(112;0.072)|OV - Ovarian serous cystadenocarcinoma(117;0.177)|Lung(94;0.216)|GBM - Glioblastoma multiforme(144;0.232)		CCTTGTCCGCTTTTGCCATAT	0.368													C|||	399	0.0796725	0.292	0.0159	5008	,	,		19065	0.0		0.002	False		,,,				2504	0.0				p.K65K		Atlas-SNP	.											.	HMGB1	21	.	0			c.A195G						PASS	.	C		996,3410	684.5+/-404.4	121,754,1328	57.0	64.0	62.0		195	3.4	1.0	13	dbSNP_86	62	7,8593	813.0+/-407.0	0,7,4293	no	coding-synonymous	HMGB1	NM_002128.4		121,761,5621	CC,CT,TT		0.0814,22.6055,7.7118		65/216	31037445	1003,12003	2203	4300	6503	SO:0001819	synonymous_variant	3146	exon3			GTCCGCTTTTGCC	D63874	CCDS9335.1	13q12	2011-07-01	2011-04-05	2002-08-16	ENSG00000189403	ENSG00000189403		"""High-mobility group / Canonical"""	4983	protein-coding gene	gene with protein product	"""high mobility group box 1"", ""Sulfoglucuronyl carbohydrate binding protein"", ""Amphoterin"", ""high mobility group protein 1"""	163905	"""high-mobility group (nonhistone chromosomal) protein 1"", ""high-mobility group box 1"""	HMG1		8661151, 11279268	Standard	NM_002128		Approved	HMG3, SBP-1, DKFZp686A04236	uc001usx.3	P09429	OTTHUMG00000016670	ENST00000405805.1:c.195A>G	13.37:g.31037445T>C		40.0	0.0	0		53.0	22.0	0.415094	NM_002128	A5D8W9|Q14321|Q5T7C3|Q6IBE1	Silent	SNP	ENST00000405805.1	37	CCDS9335.1																																																																																			T|0.941;C|0.059	0.059	strong		0.368	HMGB1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303998.2	NM_002128	
LRP4	4038	hgsc.bcm.edu	37	11	46918529	46918529	+	Silent	SNP	C	C	T	rs879721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:46918529C>T	ENST00000378623.1	-	8	1055	c.813G>A	c.(811-813)acG>acA	p.T271T		NM_002334.3	NP_002325.2	O75096	LRP4_HUMAN	low density lipoprotein receptor-related protein 4	271	LDL-receptor class A 7. {ECO:0000255|PROSITE-ProRule:PRU00124}.				dendrite morphogenesis (GO:0048813)|dorsal/ventral pattern formation (GO:0009953)|embryonic digit morphogenesis (GO:0042733)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|limb development (GO:0060173)|negative regulation of axonogenesis (GO:0050771)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ossification (GO:0030279)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of presynaptic membrane organization (GO:1901631)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|proximal/distal pattern formation (GO:0009954)|regulation of protein phosphorylation (GO:0001932)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|synapse organization (GO:0050808)|synaptic growth at neuromuscular junction (GO:0051124)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic density (GO:0014069)|synaptic membrane (GO:0097060)	calcium ion binding (GO:0005509)|receptor tyrosine kinase binding (GO:0030971)|scaffold protein binding (GO:0097110)			breast(7)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(13)|lung(24)|ovary(3)|pancreas(2)|prostate(5)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)	70				Lung(87;0.159)		ACTGTTCTGCCGTACACATGG	0.552													T|||	309	0.0617013	0.2239	0.0173	5008	,	,		17998	0.0		0.001	False		,,,				2504	0.0				p.T271T		Atlas-SNP	.											.	LRP4	160	.	0			c.G813A						PASS	.	T		770,3632	753.5+/-412.4	68,634,1499	113.0	100.0	104.0		813	-11.6	0.0	11	dbSNP_86	104	3,8595	819.0+/-406.8	0,3,4296	no	coding-synonymous	LRP4	NM_002334.3		68,637,5795	TT,TC,CC		0.0349,17.492,5.9462		271/1906	46918529	773,12227	2201	4299	6500	SO:0001819	synonymous_variant	4038	exon8			TTCTGCCGTACAC	AB011540	CCDS31478.1	11p11.2	2013-05-29			ENSG00000134569	ENSG00000134569		"""Low density lipoprotein receptors"""	6696	protein-coding gene	gene with protein product		604270				9693030	Standard	NM_002334		Approved	MEGF7, CLSS, LRP-4, SOST2	uc001ndn.4	O75096	OTTHUMG00000166700	ENST00000378623.1:c.813G>A	11.37:g.46918529C>T		86.0	0.0	0		76.0	35.0	0.460526	NM_002334	B2RN39|Q4AC85|Q5KTZ5	Silent	SNP	ENST00000378623.1	37	CCDS31478.1																																																																																			C|0.943;T|0.057	0.057	strong		0.552	LRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391133.1	NM_002334	
PRR3	80742	hgsc.bcm.edu	37	6	30529622	30529622	+	Missense_Mutation	SNP	G	G	A	rs3888778	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30529622G>A	ENST00000376560.3	+	3	640	c.181G>A	c.(181-183)Ggt>Agt	p.G61S	PRR3_ENST00000498336.1_3'UTR|PRR3_ENST00000376557.3_Missense_Mutation_p.G40S	NM_025263.3	NP_079539.2	P79522	PRR3_HUMAN	proline rich 3	61	Pro-rich.		G -> S (in dbSNP:rs3888778). {ECO:0000269|PubMed:15489334}.				metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			lung(1)|ovary(1)	2						TCTTCACAGAGGTCCTCCAGG	0.507													G|||	166	0.033147	0.0862	0.0259	5008	,	,		17768	0.0208		0.0109	False		,,,				2504	0.002				p.G61S		Atlas-SNP	.											.	PRR3	5	.	0			c.G181A						PASS	.	G	SER/GLY,SER/GLY	137,2249		3,131,1059	9.0	9.0	9.0		118,181	3.9	1.0	6	dbSNP_108	9	47,4983		0,47,2468	yes	missense,missense	PRR3	NM_001077497.2,NM_025263.3	56,56	3,178,3527	AA,AG,GG		0.9344,5.7418,2.4811	possibly-damaging,possibly-damaging	40/168,61/189	30529622	184,7232	1193	2515	3708	SO:0001583	missense	80742	exon3			CACAGAGGTCCTC	AK074531	CCDS43440.1, CCDS43441.1	6p21.32	2013-01-18	2004-05-27		ENSG00000204576	ENSG00000204576		"""Zinc fingers, CCCH-type domain containing"""	21149	protein-coding gene	gene with protein product			"""proline-rich polpeptide 3"""				Standard	NM_025263		Approved	CAT56, Em:AB014077.1, Em:AB023052.2	uc003nqi.2	P79522	OTTHUMG00000031037	ENST00000376560.3:c.181G>A	6.37:g.30529622G>A	ENSP00000365744:p.Gly61Ser	62.0	0.0	0		63.0	33.0	0.52381	NM_025263	A1A4H4|Q5RJB5|Q5STN6	Missense_Mutation	SNP	ENST00000376560.3	37	CCDS43440.1	75	0.034340659340659344	41	0.08333333333333333	10	0.027624309392265192	17	0.02972027972027972	7	0.009234828496042216	G	18.14	3.558222	0.65538	0.057418	0.009344	ENSG00000204576	ENST00000376560;ENST00000376555;ENST00000376557	T;T	0.61392	0.79;0.11	4.8	3.93	0.45458	.	0.000000	0.44097	D	0.000490	T	0.28665	0.0710	N	0.14661	0.345	0.35071	D	0.762444	D;P	0.55385	0.971;0.952	P;B	0.46585	0.521;0.322	T	0.33471	-0.9867	10	0.87932	D	0	-4.6812	8.9334	0.35684	0.1014:0.0:0.8986:0.0	rs3888778;rs4559118;rs3888778	40;61	P79522-2;P79522	.;PRR3_HUMAN	S	61;126;40	ENSP00000365744:G61S;ENSP00000365740:G40S	ENSP00000365738:G126S	G	+	1	0	PRR3	30637601	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.111000	0.57838	1.243000	0.43853	0.655000	0.94253	GGT	G|0.963;A|0.037	0.037	strong		0.507	PRR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076033.2	NM_025263	
SLC38A5	92745	hgsc.bcm.edu	37	X	48326270	48326270	+	Silent	SNP	C	C	T	rs34099520	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:48326270C>T	ENST00000376876.3	-	2	885	c.42G>A	c.(40-42)tcG>tcA	p.S14S	SLC38A5_ENST00000376875.1_5'Flank|SLC38A5_ENST00000317669.5_Silent_p.S14S			Q8WUX1	S38A5_HUMAN	solute carrier family 38, member 5	14					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine transmembrane transporter activity (GO:0015187)			breast(1)|cervix(1)|endometrium(6)|large_intestine(2)|lung(5)|ovary(3)|skin(1)	19						CCACAGCATCCGAAGGGAGGG	0.557													C|||	15	0.00397351	0.0113	0.0	3775	,	,		13307	0.0		0.0	False		,,,				2504	0.0				p.S14S		Atlas-SNP	.											.	SLC38A5	98	.	0			c.G42A						PASS	.	C		45,3790		1,34,9,1597,562	58.0	47.0	51.0		42	-2.4	0.0	X	dbSNP_126	51	1,6725		0,0,1,2428,1869	no	coding-synonymous	SLC38A5	NM_033518.2		1,34,10,4025,2431	TT,TC,T,CC,C		0.0149,1.1734,0.4356		14/473	48326270	46,10515	2203	4298	6501	SO:0001819	synonymous_variant	92745	exon3			AGCATCCGAAGGG	AF276889	CCDS14293.1	Xp11.23	2013-05-22			ENSG00000017483	ENSG00000017483		"""Solute carriers"""	18070	protein-coding gene	gene with protein product		300649				11243884	Standard	NM_033518		Approved	SN2, JM24	uc010nid.3	Q8WUX1	OTTHUMG00000024117	ENST00000376876.3:c.42G>A	X.37:g.48326270C>T		121.0	0.0	0		145.0	64.0	0.441379	NM_033518	B3KT20|B5MDE6|B7WPJ9|Q6PIW9|Q8WYU2|Q96PQ4	Silent	SNP	ENST00000376876.3	37	CCDS14293.1																																																																																			C|0.997;T|0.003	0.003	strong		0.557	SLC38A5-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060724.1	NM_033518	
ORC5	5001	hgsc.bcm.edu	37	7	103844599	103844599	+	Missense_Mutation	SNP	T	T	A	rs2307413	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:103844599T>A	ENST00000297431.4	-	2	298	c.156A>T	c.(154-156)aaA>aaT	p.K52N	ORC5_ENST00000545943.1_5'UTR|ORC5_ENST00000447452.2_Missense_Mutation_p.K52N|ORC5_ENST00000485726.1_5'UTR	NM_002553.3	NP_002544.1	O43913	ORC5_HUMAN	origin recognition complex, subunit 5	52			K -> N (in dbSNP:rs2307413).		DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)	cytoplasm (GO:0005737)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|origin recognition complex (GO:0000808)	ATP binding (GO:0005524)|DNA replication origin binding (GO:0003688)|nucleotide binding (GO:0000166)			kidney(1)|large_intestine(2)|lung(9)|pancreas(1)|upper_aerodigestive_tract(1)	14						CCTCTAAAGTTTTCAACAACG	0.299													T|||	72	0.014377	0.053	0.0029	5008	,	,		17463	0.0		0.0	False		,,,				2504	0.0				p.K52N		Atlas-SNP	.											.	ORC5	48	.	0			c.A156T						PASS	.	T	ASN/LYS,ASN/LYS	219,4183	128.6+/-165.4	8,203,1990	59.0	60.0	59.0		156,156	2.7	1.0	7	dbSNP_100	59	2,8594	1.2+/-3.3	0,2,4296	yes	missense,missense	ORC5	NM_002553.3,NM_181747.3	94,94	8,205,6286	AA,AT,TT		0.0233,4.975,1.7003	benign,benign	52/436,52/325	103844599	221,12777	2201	4298	6499	SO:0001583	missense	5001	exon2			TAAAGTTTTCAAC		CCDS5734.1, CCDS47681.1	7q22.1	2014-06-13	2010-10-12	2010-10-12	ENSG00000164815	ENSG00000164815			8491	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 117"""	602331	"""origin recognition complex, subunit 5 (yeast homolog)-like"", ""origin recognition complex, subunit 5-like (yeast)"", ""origin recognition complex, subunit 5 homolog (yeast)"""	ORC5L		9417919, 9829972	Standard	NM_002553		Approved	Orc5p, ORC5T, PPP1R117	uc003vcb.3	O43913	OTTHUMG00000157275	ENST00000297431.4:c.156A>T	7.37:g.103844599T>A	ENSP00000297431:p.Lys52Asn	123.0	0.0	0		115.0	58.0	0.504348	NM_002553	A4D0P8|O60590|O95268	Missense_Mutation	SNP	ENST00000297431.4	37	CCDS5734.1	33	0.01510989010989011	31	0.06300813008130081	2	0.0055248618784530384	0	0.0	0	0.0	T	10.43	1.347141	0.24426	0.04975	2.33E-4	ENSG00000164815	ENST00000297431;ENST00000447452	T;T	0.62941	-0.01;-0.01	5.16	2.74	0.32292	.	0.189382	0.56097	D	0.000033	T	0.05364	0.0142	N	0.17474	0.49	0.80722	D	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.08055	0.002;0.003;0.002	T	0.02431	-1.1160	10	0.23302	T	0.38	.	3.8148	0.08811	0.1211:0.0725:0.371:0.4354	rs2307413;rs16873425;rs52800217;rs2307413	52;52;52	A4D0P7;O43913-2;O43913	.;.;ORC5_HUMAN	N	52	ENSP00000297431:K52N;ENSP00000395747:K52N	ENSP00000297431:K52N	K	-	3	2	ORC5	103631835	0.995000	0.38212	1.000000	0.80357	0.913000	0.54294	0.264000	0.18497	0.294000	0.22547	-0.438000	0.05819	AAA	T|0.985;A|0.015	0.015	strong		0.299	ORC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348286.1	NM_002553	
AHNAK2	113146	hgsc.bcm.edu	37	14	105411091	105411091	+	Missense_Mutation	SNP	G	G	A	rs143814844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105411091G>A	ENST00000333244.5	-	7	10816	c.10697C>T	c.(10696-10698)aCg>aTg	p.T3566M	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	3566						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)		p.T3566M(1)		cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CACTTTGGGCGTCTTTAAACT	0.612													.|||	367	0.0732827	0.267	0.0173	5008	,	,		17318	0.0		0.002	False		,,,				2504	0.0				p.T3566M		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	1	1	Substitution - Missense(1)	prostate(1)	c.C10697T						PASS	.	A	MET/THR	783,2917		107,569,1174	98.0	113.0	108.0		10697	1.6	0.0	14	dbSNP_134	108	10,8158		0,10,4074	no	missense	AHNAK2	NM_138420.2	81	107,579,5248	AA,AG,GG		0.1224,21.1622,6.6818	benign	3566/5796	105411091	793,11075	1850	4084	5934	SO:0001583	missense	113146	exon7			TTGGGCGTCTTTA	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.10697C>T	14.37:g.105411091G>A	ENSP00000353114:p.Thr3566Met	241.0	2.0	0.00829876		257.0	254.0	0.988327	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	80	0.03663003663003663	75	0.1524390243902439	5	0.013812154696132596	0	0.0	0	0.0	a	2.924	-0.222471	0.06061	0.211622	0.001224	ENSG00000185567	ENST00000333244	T	0.00745	5.75	4.06	1.63	0.23807	.	1.601890	0.05251	U	0.513995	T	0.00012	0.0000	N	0.00086	-2.195	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39461	-0.9613	9	0.33940	T	0.23	.	4.4622	0.11671	0.5589:0.1614:0.2797:0.0	rs2819442	3566	Q8IVF2	AHNK2_HUMAN	M	3566	ENSP00000353114:T3566M	ENSP00000353114:T3566M	T	-	2	0	AHNAK2	104482136	0.000000	0.05858	0.042000	0.18584	0.008000	0.06430	-0.778000	0.04664	-0.237000	0.09739	-1.140000	0.01884	ACG	G|0.971;A|0.029	0.029	strong		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
HIRA	7290	hgsc.bcm.edu	37	22	19340928	19340928	+	Silent	SNP	G	G	A	rs34000365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:19340928G>A	ENST00000263208.5	-	23	3055	c.2799C>T	c.(2797-2799)caC>caT	p.H933H	HIRA_ENST00000340170.4_Silent_p.H726H|HIRA_ENST00000541063.1_Silent_p.H889H|HIRA_ENST00000546308.1_3'UTR	NM_003325.3	NP_003316.3	P54198	HIRA_HUMAN	histone cell cycle regulator	933	Interaction with histone H4.				anatomical structure morphogenesis (GO:0009653)|chromatin modification (GO:0016568)|DNA replication-independent nucleosome assembly (GO:0006336)|gastrulation (GO:0007369)|muscle cell differentiation (GO:0042692)|osteoblast differentiation (GO:0001649)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(14)|ovary(2)|prostate(1)|skin(1)	37	Colorectal(54;0.0993)					GGCGGTACTCGTGGCTGGACT	0.622													G|||	35	0.00698882	0.0257	0.0014	5008	,	,		20446	0.0		0.0	False		,,,				2504	0.0				p.H933H		Atlas-SNP	.											.	HIRA	100	.	0			c.C2799T						PASS	.	G		124,4282	91.1+/-129.8	3,118,2082	73.0	48.0	57.0		2799	-2.7	1.0	22	dbSNP_126	57	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	HIRA	NM_003325.3		3,126,6374	AA,AG,GG		0.093,2.8143,1.0149		933/1018	19340928	132,12874	2203	4300	6503	SO:0001819	synonymous_variant	7290	exon23			GTACTCGTGGCTG	X75296	CCDS13759.1	22q11.2	2013-05-03	2013-05-03		ENSG00000100084	ENSG00000100084		"""WD repeat domain containing"""	4916	protein-coding gene	gene with protein product	"""DiGeorge critical region gene 1"""	600237	"""HIR (histone cell cycle regulation defective) homolog A (S. cerevisiae)"", ""HIR histone cell cycle regulation defective homolog A (S. cerevisiae)"""	TUPLE1		8111380, 7633437, 9731536	Standard	NM_003325		Approved	DGCR1, TUP1	uc002zpf.1	P54198	OTTHUMG00000150134	ENST00000263208.5:c.2799C>T	22.37:g.19340928G>A		96.0	0.0	0		107.0	50.0	0.46729	NM_003325	Q05BU9|Q8IXN2	Silent	SNP	ENST00000263208.5	37	CCDS13759.1																																																																																			G|0.990;A|0.010	0.010	strong		0.622	HIRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316488.2	NM_003325	
RARS2	57038	hgsc.bcm.edu	37	6	88229953	88229953	+	Missense_Mutation	SNP	G	G	A	rs138460258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:88229953G>A	ENST00000369536.5	-	13	1102	c.1057C>T	c.(1057-1059)Cat>Tat	p.H353Y	RARS2_ENST00000497828.1_5'Flank	NM_020320.3	NP_064716.2	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	353					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	22		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0456)		TGCTGAAAATGCTTTTTTTGT	0.333													G|||	3	0.000599042	0.0015	0.0014	5008	,	,		17566	0.0		0.0	False		,,,				2504	0.0				p.H353Y		Atlas-SNP	.											.	RARS2	61	.	0			c.C1057T						PASS	.	G	TYR/HIS	1,4405	2.1+/-5.4	0,1,2202	203.0	194.0	197.0		1057	5.8	1.0	6	dbSNP_134	197	0,8600		0,0,4300	no	missense	RARS2	NM_020320.3	83	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	353/579	88229953	1,13005	2203	4300	6503	SO:0001583	missense	57038	exon13			GAAAATGCTTTTT	AK093934	CCDS5011.1	6q16.1	2011-07-01	2007-09-27	2007-02-23	ENSG00000146282	ENSG00000146282	6.1.1.19	"""Aminoacyl tRNA synthetases / Class I"""	21406	protein-coding gene	gene with protein product	"""arginine tRNA ligase 2, mitochondrial (putative)"""	611524	"""arginyl-tRNA synthetase-like"""	RARSL		17847012	Standard	NM_020320		Approved	MGC14993, MGC23778, PRO1992, dJ382I10.6, DALRD2	uc003pme.3	Q5T160	OTTHUMG00000015178	ENST00000369536.5:c.1057C>T	6.37:g.88229953G>A	ENSP00000358549:p.His353Tyr	78.0	0.0	0		52.0	27.0	0.519231	NM_020320	B2RDT7|Q96FU5|Q9H8K8	Missense_Mutation	SNP	ENST00000369536.5	37	CCDS5011.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	25.9	4.688534	0.88639	2.27E-4	0.0	ENSG00000146282	ENST00000369536	T	0.62232	0.04	5.76	5.76	0.90799	Arginyl-tRNA synthetase, class Ia, core (1);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.000000	0.85682	D	0.000000	T	0.79701	0.4491	M	0.84082	2.675	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.81291	-0.0999	10	0.72032	D	0.01	.	19.975	0.97300	0.0:0.0:1.0:0.0	.	353	Q5T160	SYRM_HUMAN	Y	353	ENSP00000358549:H353Y	ENSP00000358549:H353Y	H	-	1	0	RARS2	88286672	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.939000	0.92951	2.724000	0.93272	0.585000	0.79938	CAT	G|1.000;A|0.000	0.000	strong		0.333	RARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041448.1	NM_020320	
TM2D1	83941	hgsc.bcm.edu	37	1	62190780	62190780	+	Missense_Mutation	SNP	A	A	G	rs200054903	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:62190780A>G	ENST00000606498.1	-	1	33	c.13T>C	c.(13-15)Tgg>Cgg	p.W5R	TM2D1_ENST00000294613.5_Missense_Mutation_p.W5R|TM2D1_ENST00000371177.2_Missense_Mutation_p.W5R|TM2D1_ENST00000371180.2_Missense_Mutation_p.W67R			Q9BX74	TM2D1_HUMAN	TM2 domain containing 1	5					apoptotic signaling pathway (GO:0097190)	integral component of plasma membrane (GO:0005887)	beta-amyloid binding (GO:0001540)|G-protein coupled receptor activity (GO:0004930)			large_intestine(2)|lung(3)|ovary(1)	6						CCAGACGGCCAGGCGGCCGCC	0.652													A|||	31	0.0061901	0.0219	0.0029	5008	,	,		16840	0.0		0.0	False		,,,				2504	0.0				p.W5R		Atlas-SNP	.											TM2D1_ENST00000371177,right_upper_lobe,carcinoma,+1,3	TM2D1	37	3	0			c.T13C						PASS	.	A	ARG/TRP	54,3760		0,54,1853	35.0	41.0	39.0		13	-6.0	0.0	1		39	0,8178		0,0,4089	no	missense	TM2D1	NM_032027.2	101	0,54,5942	GG,GA,AA		0.0,1.4158,0.4503	benign	5/208	62190780	54,11938	1907	4089	5996	SO:0001583	missense	83941	exon1			ACGGCCAGGCGGC	AF353990	CCDS65554.1	1p32.1	2008-02-05			ENSG00000162604	ENSG00000162604			24142	protein-coding gene	gene with protein product		610080				11278849, 12553667	Standard	NM_032027		Approved	BBP	uc001czz.1	Q9BX74	OTTHUMG00000008466	ENST00000606498.1:c.13T>C	1.37:g.62190780A>G	ENSP00000475700:p.Trp5Arg	63.0	0.0	0		57.0	34.0	0.596491	NM_032027	A6NDA8	Missense_Mutation	SNP	ENST00000606498.1	37		.	.	.	.	.	.	.	.	.	.	A	13.04	2.117243	0.37339	0.014158	0.0	ENSG00000162604	ENST00000371180;ENST00000294613;ENST00000371178;ENST00000371177	.	.	.	4.69	-5.98	0.02220	.	1.041710	0.07590	N	0.921834	T	0.17789	0.0427	L	0.38531	1.155	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33292	-0.9874	9	0.72032	D	0.01	3.1902	0.4995	0.00577	0.1994:0.2683:0.1696:0.3628	.	5	Q9BX74	TM2D1_HUMAN	R	67;5;5;5	.	ENSP00000294613:W5R	W	-	1	0	TM2D1	61963368	0.061000	0.20836	0.000000	0.03702	0.034000	0.12701	-0.222000	0.09190	-0.981000	0.03520	0.379000	0.24179	TGG	.	.	weak		0.652	TM2D1-012	KNOWN	non_canonical_U12|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000470779.2	NM_032027	
FBRSL1	57666	hgsc.bcm.edu	37	12	133084874	133084874	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:133084874G>A	ENST00000434748.2	+	2	1447	c.427G>A	c.(427-429)Ggg>Agg	p.G143R	FBRSL1_ENST00000261673.6_Missense_Mutation_p.G70R|FBRSL1_ENST00000542061.1_3'UTR	NM_001142641.1	NP_001136113.1	Q9HCM7	FBSL_HUMAN	fibrosin-like 1	143							poly(A) RNA binding (GO:0044822)			central_nervous_system(2)|endometrium(1)|stomach(1)	4						AGGCAGCCCCGGGCAGGACCT	0.697																																					p.G143R		Atlas-SNP	.											.	FBRSL1	47	.	0			c.G427A						PASS	.						33.0	46.0	42.0					12																	133084874		692	1590	2282	SO:0001583	missense	57666	exon2			AGCCCCGGGCAGG		CCDS45010.1	12q24.33	2008-12-09			ENSG00000112787	ENSG00000112787			29308	protein-coding gene	gene with protein product						10997877	Standard	NM_001142641		Approved	KIAA1545	uc001ukf.3	Q9HCM7	OTTHUMG00000167991	ENST00000434748.2:c.427G>A	12.37:g.133084874G>A	ENSP00000396160:p.Gly143Arg	81.0	0.0	0		63.0	31.0	0.492063	NM_001142641	Q86XQ1	Missense_Mutation	SNP	ENST00000434748.2	37	CCDS45010.1	.	.	.	.	.	.	.	.	.	.	G	4.618	0.114914	0.08831	.	.	ENSG00000112787	ENST00000434748;ENST00000261673	T;T	0.28069	1.63;1.63	4.3	1.29	0.21616	.	.	.	.	.	T	0.10895	0.0266	N	0.11427	0.14	0.09310	N	1	B	0.32893	0.389	B	0.21546	0.035	T	0.26087	-1.0113	9	0.07325	T	0.83	.	6.0554	0.19809	0.184:0.156:0.66:0.0	.	143	Q9HCM7	FBSL_HUMAN	R	143;70	ENSP00000396160:G143R;ENSP00000261673:G70R	ENSP00000261673:G70R	G	+	1	0	FBRSL1	131594947	0.000000	0.05858	0.010000	0.14722	0.309000	0.27889	0.228000	0.17814	0.160000	0.19432	-0.275000	0.10095	GGG	.	.	none		0.697	FBRSL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397404.2		
LPIN3	64900	hgsc.bcm.edu	37	20	39977300	39977300	+	Missense_Mutation	SNP	G	G	C	rs150562240	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:39977300G>C	ENST00000373257.3	+	4	421	c.330G>C	c.(328-330)tgG>tgC	p.W110C		NM_022896.1	NP_075047.1	Q9BQK8	LPIN3_HUMAN	lipin 3	110					fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|liver(2)|lung(7)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		Myeloproliferative disorder(115;0.000739)				CCATCCCTTGGGGGGGTCTGT	0.662																																					p.W110C		Atlas-SNP	.											.	LPIN3	69	.	0			c.G330C						PASS	.	G	CYS/TRP	0,4406		0,0,2203	33.0	37.0	36.0		330	2.2	1.0	20	dbSNP_134	36	3,8597	1.2+/-3.3	0,3,4297	yes	missense	LPIN3	NM_022896.1	215	0,3,6500	CC,CG,GG		0.0349,0.0,0.0231	benign	110/852	39977300	3,13003	2203	4300	6503	SO:0001583	missense	64900	exon4			CCCTTGGGGGGGT	AL132654	CCDS33469.1	20q11.2-q12	2006-04-04	2002-05-23		ENSG00000132793	ENSG00000132793			14451	protein-coding gene	gene with protein product		605520	"""lipin 3-like"""	LIPN3L		11138012	Standard	XM_005260515		Approved	SMP2	uc002xjx.3	Q9BQK8	OTTHUMG00000033056	ENST00000373257.3:c.330G>C	20.37:g.39977300G>C	ENSP00000362354:p.Trp110Cys	44.0	0.0	0		44.0	17.0	0.386364	NM_022896	B2RTT5|Q5TDB9|Q9NPY8|Q9UJE5	Missense_Mutation	SNP	ENST00000373257.3	37	CCDS33469.1	.	.	.	.	.	.	.	.	.	.	G	11.33	1.606536	0.28623	0.0	3.49E-4	ENSG00000132793	ENST00000373257	T	0.76316	-1.01	4.22	2.19	0.27852	Lipin, N-terminal (1);	0.299857	0.26016	N	0.026860	T	0.53753	0.1816	N	0.08118	0	0.46874	D	0.999231	B;B	0.18968	0.002;0.032	B;B	0.19391	0.005;0.025	T	0.30592	-0.9973	9	.	.	.	-2.1502	8.2485	0.31704	0.0:0.1724:0.6488:0.1788	.	110;110	Q9BQK8-2;Q9BQK8	.;LPIN3_HUMAN	C	110	ENSP00000362354:W110C	.	W	+	3	0	LPIN3	39410714	1.000000	0.71417	0.971000	0.41717	0.955000	0.61496	2.688000	0.46984	0.488000	0.27723	0.557000	0.71058	TGG	G|0.999;C|0.001	0.001	strong		0.662	LPIN3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080393.1	NM_022896	
OSCAR	126014	hgsc.bcm.edu	37	19	54599119	54599119	+	Missense_Mutation	SNP	G	G	A	rs1110643	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54599119G>A	ENST00000284648.6	-	5	870	c.673C>T	c.(673-675)Cgg>Tgg	p.R225W	OSCAR_ENST00000391761.1_Missense_Mutation_p.R214W|OSCAR_ENST00000391760.1_3'UTR|OSCAR_ENST00000356532.3_Intron|OSCAR_ENST00000359649.4_Missense_Mutation_p.R229W|OSCAR_ENST00000358375.4_Intron|OSCAR_ENST00000351806.4_Intron			Q8IYS5	OSCAR_HUMAN	osteoclast associated, immunoglobulin-like receptor	225						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				large_intestine(1)|skin(1)	2	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)					gaggcgggccgggCCTCAGGG	0.697													G|||	37	0.00738818	0.0272	0.0014	5008	,	,		11125	0.0		0.0	False		,,,				2504	0.0				p.R229W		Atlas-SNP	.											.	OSCAR	22	.	0			c.C685T						PASS	.	G	,,,TRP/ARG	77,4115		0,77,2019	7.0	8.0	8.0		,,,685	-4.1	0.0	19	dbSNP_86	8	0,8172		0,0,4086	yes	intron,intron,intron,missense	OSCAR	NM_130771.3,NM_133168.3,NM_133169.3,NM_206818.1	,,,101	0,77,6105	AA,AG,GG		0.0,1.8368,0.6228	,,,benign	,,,229/287	54599119	77,12287	2096	4086	6182	SO:0001583	missense	126014	exon5			CGGGCCGGGCCTC	AK130199	CCDS12873.1, CCDS12874.1, CCDS12875.1, CCDS12876.1, CCDS62789.1, CCDS74444.1	19q13.42	2013-01-29			ENSG00000170909	ENSG00000170909		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29960	protein-coding gene	gene with protein product		606862				11805147	Standard	NM_206818		Approved		uc002qda.3	Q8IYS5	OTTHUMG00000064966	ENST00000284648.6:c.673C>T	19.37:g.54599119G>A	ENSP00000365808:p.Arg225Trp	61.0	0.0	0		96.0	53.0	0.552083	NM_206818	B7WNS2|Q5GRG5|Q8N763|Q8NHL4|Q8WXQ0|Q8WXQ1|Q8WXQ2	Missense_Mutation	SNP	ENST00000284648.6	37		12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	G	14.75	2.627173	0.46944	0.018368	0.0	ENSG00000170909	ENST00000391761;ENST00000359649;ENST00000284648	T;T;T	0.00524	6.82;6.85;6.83	2.03	-4.06	0.03986	.	.	.	.	.	T	0.00144	0.0004	N	0.08118	0	0.09310	N	0.999999	D;D;D	0.71674	0.997;0.998;0.996	B;P;P	0.50136	0.428;0.632;0.48	T	0.40664	-0.9551	9	0.02654	T	1	.	0.9438	0.01361	0.1669:0.2216:0.3875:0.2239	rs1110643	225;214;229	Q8IYS5;Q8IYS5-4;Q8IYS5-7	OSCAR_HUMAN;.;.	W	214;229;225	ENSP00000375641:R214W;ENSP00000352671:R229W;ENSP00000365808:R225W	ENSP00000365808:R225W	R	-	1	2	OSCAR	59290931	0.010000	0.17322	0.005000	0.12908	0.115000	0.19883	-0.599000	0.05700	-0.941000	0.03700	0.289000	0.19496	CGG	G|0.993;A|0.007	0.007	strong		0.697	OSCAR-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000139493.4	NM_133169	
SGCG	6445	hgsc.bcm.edu	37	13	23853547	23853547	+	Silent	SNP	C	C	T	rs35628352	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:23853547C>T	ENST00000218867.3	+	5	559	c.435C>T	c.(433-435)aaC>aaT	p.N145N	SGCG_ENST00000545013.1_Silent_p.N145N|SGCG_ENST00000537476.1_Silent_p.N145N	NM_000231.2	NP_000222	Q13326	SGCG_HUMAN	sarcoglycan, gamma (35kDa dystrophin-associated glycoprotein)	145					muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(29;4.34e-23)|all_epithelial(30;4.4e-19)|all_lung(29;2.45e-18)|Lung SC(185;0.0228)|Breast(139;0.188)		all cancers(112;0.00255)|Epithelial(112;0.0129)|OV - Ovarian serous cystadenocarcinoma(117;0.0365)|Lung(94;0.205)		TCAACTCCAACGACGGCAAGC	0.383													C|||	47	0.00938498	0.031	0.0072	5008	,	,		17239	0.0		0.001	False		,,,				2504	0.0				p.N145N		Atlas-SNP	.											.	SGCG	64	.	0			c.C435T						PASS	.	C		130,4276	93.9+/-132.6	2,126,2075	98.0	90.0	93.0		435	-3.5	0.4	13	dbSNP_126	93	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SGCG	NM_000231.2		2,127,6374	TT,TC,CC		0.0116,2.9505,1.0072		145/292	23853547	131,12875	2203	4300	6503	SO:0001819	synonymous_variant	6445	exon5			CTCCAACGACGGC	U34976	CCDS9299.1	13q12-q13	2014-09-17	2002-08-29		ENSG00000102683	ENSG00000102683			10809	protein-coding gene	gene with protein product	"""Maghrebian myopathy (autosomal recessive)"", ""35kD dystrophin-associated glycoprotein"", ""limb girdle muscular dystrophy 2C (Duchenne-like muscular dystrophy, autosomal recessive)"", ""gamma sarcoglycan"""	608896	"""sarcoglycan, gamma (35kD dystrophin-associated glycoprotein)"""	DMDA1, MAM, LGMD2C		8968757	Standard	NM_000231		Approved	SCARMD2, DAGA4, SCG3, DMDA, TYPE, A4, MGC130048	uc001uom.2	Q13326	OTTHUMG00000016563	ENST00000218867.3:c.435C>T	13.37:g.23853547C>T		117.0	0.0	0		109.0	59.0	0.541284	NM_000231	Q32M32|Q5T9J6	Silent	SNP	ENST00000218867.3	37	CCDS9299.1																																																																																			C|0.991;T|0.009	0.009	strong		0.383	SGCG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044151.1	NM_000231	
CPAMD8	27151	hgsc.bcm.edu	37	19	17081707	17081707	+	Missense_Mutation	SNP	G	G	T	rs9305083	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17081707G>T	ENST00000443236.1	-	18	2379	c.2348C>A	c.(2347-2349)cCc>cAc	p.P783H	CPAMD8_ENST00000388925.4_3'UTR	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	736						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						TTACCTGGGGGGGTGCCTGGA	0.572													G|||	520	0.103834	0.3608	0.036	5008	,	,		16421	0.0		0.0129	False		,,,				2504	0.0051				p.P783H		Atlas-SNP	.											.	CPAMD8	192	.	0			c.C2348A						PASS	.	G	HIS/PRO	1156,2704		169,818,943	26.0	29.0	28.0		2348	-3.2	0.2	19	dbSNP_119	28	180,8074		3,174,3950	yes	missense	CPAMD8	NM_015692.2	77	172,992,4893	TT,TG,GG		2.1808,29.9482,11.0286	possibly-damaging	783/1933	17081707	1336,10778	1930	4127	6057	SO:0001583	missense	27151	exon18			CTGGGGGGGTGCC	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.2348C>A	19.37:g.17081707G>T	ENSP00000402505:p.Pro783His	34.0	0.0	0		38.0	19.0	0.5	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	222|222	0.10164835164835165|0.10164835164835165	191|191	0.3882113821138211|0.3882113821138211	19|19	0.052486187845303865|0.052486187845303865	0|0	0.0|0.0	12|12	0.0158311345646438|0.0158311345646438	G|G	11.55|11.55	1.673598|1.673598	0.29693|0.29693	0.299482|0.299482	0.021808|0.021808	ENSG00000160111|ENSG00000160111	ENST00000291440|ENST00000443236	.|.	.|.	.|.	3.19|3.19	-3.22|-3.22	0.05125|0.05125	.|.	1.230310|1.230310	0.06279|0.06279	N|U	0.697038|0.697038	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.36672|0.36672	1.1|1.1	0.09310|0.09310	P|P	1.0|1.0	P|.	0.51653|.	0.947|.	B|.	0.40741|.	0.339|.	T|T	0.44329|0.44329	-0.9335|-0.9335	8|6	0.42905|0.14252	T|T	0.14|0.57	.|.	0.9563|0.9563	0.01386|0.01386	0.342:0.161:0.3358:0.1611|0.342:0.161:0.3358:0.1611	rs9305083;rs52812668;rs9305083|rs9305083;rs52812668;rs9305083	736|.	Q8IZJ3|.	CPMD8_HUMAN|.	H|T	783|794	.|.	ENSP00000291440:P783H|ENSP00000402505:P794T	P|P	-|-	2|1	0|0	CPAMD8|CPAMD8	16942707|16942707	0.013000|0.013000	0.17824|0.17824	0.179000|0.179000	0.23059|0.23059	0.258000|0.258000	0.26162|0.26162	0.758000|0.758000	0.26447|0.26447	-0.437000|-0.437000	0.07243|0.07243	-1.045000|-1.045000	0.02358|0.02358	CCC|CCC	G|0.914;T|0.086	0.086	strong		0.572	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
CYP3A5	1577	hgsc.bcm.edu	37	7	99262835	99262835	+	Silent	SNP	C	C	T	rs10264272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99262835C>T	ENST00000222982.4	-	7	723	c.624G>A	c.(622-624)aaG>aaA	p.K208K	CYP3A5_ENST00000339843.2_3'UTR|CYP3A5_ENST00000343703.5_Silent_p.K198K|CYP3A5_ENST00000480723.1_5'Flank	NM_000777.3	NP_000768.1	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 5	208					alkaloid catabolic process (GO:0009822)|drug catabolic process (GO:0042737)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_epithelial(64;2.77e-08)|Lung NSC(181;0.00396)|all_lung(186;0.00659)|Esophageal squamous(72;0.0166)				ado-trastuzumab emtansine(DB05773)|Alfentanil(DB00802)|Alprazolam(DB00404)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Apixaban(DB06605)|Aprepitant(DB00673)|Argatroban(DB00278)|Aripiprazole(DB01238)|Artemether(DB06697)|Astemizole(DB00637)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Beclomethasone(DB00394)|Boceprevir(DB08873)|Brentuximab vedotin(DB08870)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clonidine(DB00575)|Clopidogrel(DB00758)|Cocaine(DB00907)|Codeine(DB00318)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diltiazem(DB00343)|Disulfiram(DB00822)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Dutasteride(DB01126)|Enzalutamide(DB08899)|Eplerenone(DB00700)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Ethosuximide(DB00593)|Etoposide(DB00773)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluticasone Propionate(DB00588)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gestodene(DB06730)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Losartan(DB00678)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Modafinil(DB00745)|Mycophenolate mofetil(DB00688)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxcarbazepine(DB00776)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Pentamidine(DB00738)|Perampanel(DB08883)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Rosuvastatin(DB01098)|Salmeterol(DB00938)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Teniposide(DB00444)|Testosterone(DB00624)|Thalidomide(DB01041)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Troleandomycin(DB01361)|Udenafil(DB06267)|Valproic Acid(DB00313)|Vardenafil(DB00862)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	TTAGGAACTTCTTAGTGCTCT	0.378													C|||	223	0.0445288	0.1543	0.0231	5008	,	,		18786	0.0		0.003	False		,,,				2504	0.0				p.K208K		Atlas-SNP	.											.	CYP3A5	46	.	0			c.G624A	GRCh37	CS015291	CYP3A5	S	rs10264272	PASS	.	C		530,3876	238.4+/-249.8	43,444,1716	113.0	108.0	110.0		624	2.9	0.0	7	dbSNP_119	110	7,8593	3.7+/-12.6	0,7,4293	no	coding-synonymous	CYP3A5	NM_000777.3		43,451,6009	TT,TC,CC		0.0814,12.0291,4.1289		208/503	99262835	537,12469	2203	4300	6503	SO:0001819	synonymous_variant	1577	exon7			GAACTTCTTAGTG	L26985	CCDS5672.1, CCDS55134.1	7q21.1	2007-12-14	2003-01-14		ENSG00000106258	ENSG00000106258		"""Cytochrome P450s"""	2638	protein-coding gene	gene with protein product		605325	"""cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 5"""				Standard	NR_033808		Approved	PCN3, P450PCN3, CP35		P20815	OTTHUMG00000156724	ENST00000222982.4:c.624G>A	7.37:g.99262835C>T		136.0	0.0	0		160.0	72.0	0.45	NM_000777	A4D289|B7Z5I7|Q53WY8|Q75MV0|Q9HB56	Silent	SNP	ENST00000222982.4	37	CCDS5672.1																																																																																			C|0.952;T|0.048	0.048	strong		0.378	CYP3A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345469.1		
ABCC11	85320	hgsc.bcm.edu	37	16	48234381	48234381	+	Missense_Mutation	SNP	G	G	A	rs41282045	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:48234381G>A	ENST00000394747.1	-	14	2237	c.1888C>T	c.(1888-1890)Cgg>Tgg	p.R630W	ABCC11_ENST00000394748.1_Missense_Mutation_p.R630W|ABCC11_ENST00000356608.2_Missense_Mutation_p.R630W|ABCC11_ENST00000353782.5_Missense_Mutation_p.R630W|ABCC11_ENST00000537808.1_Missense_Mutation_p.R630W	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	630	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	TTGAGGCCCCGCTCTCCAATC	0.597													G|||	13	0.00259585	0.003	0.0043	5008	,	,		18082	0.0		0.004	False		,,,				2504	0.002				p.R630W		Atlas-SNP	.											.	ABCC11	177	.	0			c.C1888T						PASS	.	G	TRP/ARG,TRP/ARG,TRP/ARG	12,4390	19.1+/-41.9	0,12,2189	46.0	38.0	41.0		1888,1888,1888	1.2	1.0	16	dbSNP_127	41	61,8539	37.8+/-93.5	0,61,4239	yes	missense,missense,missense	ABCC11	NM_032583.3,NM_033151.3,NM_145186.2	101,101,101	0,73,6428	AA,AG,GG		0.7093,0.2726,0.5615	probably-damaging,probably-damaging,probably-damaging	630/1383,630/1383,630/1345	48234381	73,12929	2201	4300	6501	SO:0001583	missense	85320	exon14			GGCCCCGCTCTCC	AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"""ATP binding cassette transporters / subfamily C"""	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.1888C>T	16.37:g.48234381G>A	ENSP00000378230:p.Arg630Trp	50.0	0.0	0		48.0	24.0	0.5	NM_033151	Q8TDJ0|Q96JA6|Q9BX80	Missense_Mutation	SNP	ENST00000394747.1	37	CCDS10732.1	6	0.0027472527472527475	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	20.3	3.968770	0.74131	0.002726	0.007093	ENSG00000121270	ENST00000353782;ENST00000356608;ENST00000394748;ENST00000394747;ENST00000537808	D;D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53;-1.53	5.61	1.19	0.21007	ABC transporter, transmembrane domain, type 1 (1);ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.067924	0.64402	N	0.000016	D	0.85375	0.5682	M	0.91561	3.22	0.80722	D	1	B;D	0.89917	0.333;1.0	B;D	0.97110	0.061;1.0	D	0.83707	0.0185	10	0.87932	D	0	-11.3458	4.1375	0.10178	0.1727:0.0:0.5052:0.3221	rs41282045	630;630	Q96J66-2;Q96J66	.;ABCCB_HUMAN	W	630	ENSP00000311326:R630W;ENSP00000349017:R630W;ENSP00000378231:R630W;ENSP00000378230:R630W;ENSP00000438530:R630W	ENSP00000311326:R630W	R	-	1	2	ABCC11	46791882	0.945000	0.32115	0.999000	0.59377	0.784000	0.44337	0.691000	0.25467	0.316000	0.23135	0.655000	0.94253	CGG	G|0.996;A|0.004	0.004	strong		0.597	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583	
CACNG6	59285	hgsc.bcm.edu	37	19	54501540	54501540	+	Missense_Mutation	SNP	C	C	T	rs78495589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54501540C>T	ENST00000252729.2	+	2	969	c.379C>T	c.(379-381)Cgc>Tgc	p.R127C	CACNG6_ENST00000352529.1_Intron|CACNG6_ENST00000346968.2_Missense_Mutation_p.R127C	NM_145814.1	NP_665813.1	Q9BXT2	CCG6_HUMAN	calcium channel, voltage-dependent, gamma subunit 6	127					calcium ion transport (GO:0006816)	voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	15	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(134;0.168)		GGAGAATGCACGCATCTTTCA	0.502													C|||	79	0.0157748	0.0567	0.0058	5008	,	,		18465	0.0		0.0	False		,,,				2504	0.0				p.R127C		Atlas-SNP	.											.	CACNG6	42	.	0			c.C379T						PASS	.	C	,CYS/ARG,CYS/ARG	179,4227		5,169,2029	104.0	93.0	97.0		,379,379	5.4	0.2	19	dbSNP_131	97	1,8599		0,1,4299	yes	intron,missense,missense	CACNG6	NM_031897.2,NM_145814.1,NM_145815.1	,180,180	5,170,6328	TT,TC,CC		0.0116,4.0626,1.384	,possibly-damaging,possibly-damaging	,127/261,127/215	54501540	180,12826	2203	4300	6503	SO:0001583	missense	59285	exon2			AATGCACGCATCT	AF288386	CCDS12870.1, CCDS12871.1	19q13.4	2008-05-02			ENSG00000130433	ENSG00000130433		"""Calcium channel subunits"""	13625	protein-coding gene	gene with protein product		606898				11170751	Standard	NM_145814		Approved		uc002qct.3	Q9BXT2	OTTHUMG00000064907	ENST00000252729.2:c.379C>T	19.37:g.54501540C>T	ENSP00000252729:p.Arg127Cys	63.0	0.0	0		56.0	38.0	0.678571	NM_145815		Missense_Mutation	SNP	ENST00000252729.2	37	CCDS12870.1	30	0.013736263736263736	29	0.05894308943089431	1	0.0027624309392265192	0	0.0	0	0.0	.	16.01	3.000193	0.54147	0.040626	1.16E-4	ENSG00000130433	ENST00000252729;ENST00000346968	T;T	0.31769	1.48;1.48	5.36	5.36	0.76844	.	0.633990	0.14809	N	0.297160	T	0.03608	0.0103	N	0.22421	0.69	0.40471	D	0.980344	D;D	0.61697	0.987;0.99	P;P	0.48114	0.555;0.567	T	0.01039	-1.1472	10	0.62326	D	0.03	-13.2984	14.9705	0.71229	0.0:1.0:0.0:0.0	.	127;127	A6NFR2;Q9BXT2	.;CCG6_HUMAN	C	127	ENSP00000252729:R127C;ENSP00000319097:R127C	ENSP00000252729:R127C	R	+	1	0	CACNG6	59193352	0.024000	0.19004	0.244000	0.24202	0.499000	0.33736	2.549000	0.45803	2.685000	0.91497	0.655000	0.94253	CGC	C|0.986;T|0.014	0.014	strong		0.502	CACNG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139359.1		
CEP85L	387119	hgsc.bcm.edu	37	6	118953755	118953755	+	Silent	SNP	T	T	C	rs9320659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:118953755T>C	ENST00000368491.3	-	2	714	c.93A>G	c.(91-93)gcA>gcG	p.A31A	CEP85L_ENST00000368488.5_Silent_p.A34A|CEP85L_ENST00000392500.3_Silent_p.A34A|CEP85L_ENST00000419517.2_Silent_p.A31A|CEP85L_ENST00000360290.3_5'UTR	NM_001042475.2	NP_001035940.1	Q5SZL2	CE85L_HUMAN	centrosomal protein 85kDa-like	31						centrosome (GO:0005813)|cytoplasm (GO:0005737)											CAGGTAGCCATGCTGATGAAT	0.388													T|||	163	0.0325479	0.0582	0.0159	5008	,	,		17382	0.0		0.0179	False		,,,				2504	0.0583				p.A34A		Atlas-SNP	.											.	CEP85L	26	.	0			c.A102G						PASS	.	T	,,	199,3547		4,191,1678	79.0	74.0	76.0		93,102,93	1.9	1.0	6	dbSNP_119	76	163,8055		2,159,3948	no	coding-synonymous,coding-synonymous,coding-synonymous	C6orf204	NM_001042475.2,NM_001178035.1,NM_206921.2	,,	6,350,5626	CC,CT,TT		1.9835,5.3123,3.0257	,,	31/806,34/809,31/497	118953755	362,11602	1873	4109	5982	SO:0001819	synonymous_variant	387119	exon3			TAGCCATGCTGAT	AF308284	CCDS5119.2, CCDS43498.1, CCDS55052.1	6q22.31	2011-11-25	2011-11-25	2011-11-25	ENSG00000111860	ENSG00000111860			21638	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 204"""	C6orf204			Standard	NM_206921		Approved	NY-BR-15, bA57K17.2	uc003pya.2	Q5SZL2	OTTHUMG00000015465	ENST00000368491.3:c.93A>G	6.37:g.118953755T>C		83.0	0.0	0		57.0	31.0	0.54386	NM_001178035	A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289	Silent	SNP	ENST00000368491.3	37	CCDS43498.1																																																																																			T|0.980;C|0.020	0.020	strong		0.388	CEP85L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041996.2	NM_001042475	
SRGAP2-AS1	100873165	hgsc.bcm.edu	37	1	121116732	121116732	+	lincRNA	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:121116732C>T	ENST00000437515.1	-	0	329					NR_104189.1																						CATCAAAGCCCAGAATGAGTA	0.428																																					p.Q97X		Atlas-SNP	.											.	.	.	.	0			c.C289T						PASS	.																																					100996712	exon3			AAAGCCCAGAATG																													1.37:g.121116732C>T		288.0	0.0	0		272.0	11.0	0.0404412	NM_001271887		Nonsense_Mutation	SNP	ENST00000437515.1	37																																																																																				.	.	none		0.428	RP11-343N15.1-002	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000098477.2		
CST4	1472	hgsc.bcm.edu	37	20	23669584	23669584	+	Missense_Mutation	SNP	A	A	T	rs73902131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:23669584A>T	ENST00000217423.3	-	1	93	c.23T>A	c.(22-24)cTg>cAg	p.L8Q		NM_001899.2	NP_001890.1	P01036	CYTS_HUMAN	cystatin S	8					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|retina homeostasis (GO:0001895)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	cysteine-type endopeptidase inhibitor activity (GO:0004869)			breast(1)|endometrium(1)|large_intestine(2)|lung(10)|skin(1)|upper_aerodigestive_tract(1)	16	Lung NSC(19;0.0789)|Colorectal(13;0.0993)|all_lung(19;0.169)					CAGGAGTAGCAGGGTACACAG	0.602													.|||	170	0.0339457	0.1225	0.0115	5008	,	,		15657	0.0		0.0	False		,,,				2504	0.0				p.L8Q		Atlas-SNP	.											.	CST4	37	.	0			c.T23A						PASS	.	A	GLN/LEU	411,3995	201.5+/-224.5	18,375,1810	53.0	52.0	52.0		23	0.4	0.0	20	dbSNP_130	52	3,8597	2.2+/-6.3	0,3,4297	yes	missense	CST4	NM_001899.2	113	18,378,6107	TT,TA,AA		0.0349,9.3282,3.1831	possibly-damaging	8/142	23669584	414,12592	2203	4300	6503	SO:0001583	missense	1472	exon1			AGTAGCAGGGTAC		CCDS13159.1	20p11.2	2008-04-15			ENSG00000101441	ENSG00000101441			2476	protein-coding gene	gene with protein product		123857				1801729	Standard	NM_001899		Approved		uc002wto.1	P01036	OTTHUMG00000032083	ENST00000217423.3:c.23T>A	20.37:g.23669584A>T	ENSP00000217423:p.Leu8Gln	102.0	0.0	0		122.0	48.0	0.393443	NM_001899	Q9UBI5|Q9UCS9	Missense_Mutation	SNP	ENST00000217423.3	37	CCDS13159.1	58	0.026556776556776556	51	0.10365853658536585	7	0.019337016574585635	0	0.0	0	0.0	A	2.719	-0.266983	0.05754	0.093282	3.49E-4	ENSG00000101441	ENST00000217423	T	0.08458	3.09	1.45	0.431	0.16523	.	1.397050	0.04408	N	0.365592	T	0.00109	0.0003	N	0.08118	0	0.09310	N	1	P	0.50156	0.932	B	0.34991	0.193	T	0.28522	-1.0041	10	0.54805	T	0.06	.	3.6086	0.08052	0.2712:0.0:0.7288:0.0	.	8	P01036	CYTS_HUMAN	Q	8	ENSP00000217423:L8Q	ENSP00000217423:L8Q	L	-	2	0	CST4	23617584	0.005000	0.15991	0.001000	0.08648	0.003000	0.03518	1.018000	0.30002	0.157000	0.19338	-0.483000	0.04790	CTG	A|0.964;T|0.036	0.036	strong		0.602	CST4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078349.2	NM_001899	
MUC20	200958	hgsc.bcm.edu	37	3	195452679	195452679	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195452679C>T	ENST00000447234.2	+	2	1331	c.1205C>T	c.(1204-1206)cCg>cTg	p.P402L	MUC20_ENST00000436408.1_Missense_Mutation_p.P402L|MUC20_ENST00000445522.2_Missense_Mutation_p.P367L|MUC20_ENST00000320736.6_Missense_Mutation_p.P231L	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	402					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)		TCATGGTCCCCGGGATCTGAC	0.577																																					p.P231L		Atlas-SNP	.											.	MUC20	84	.	0			c.C692T						PASS	.						4.0	3.0	4.0					3																	195452679		1669	3676	5345	SO:0001583	missense	200958	exon3			GGTCCCCGGGATC	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.1205C>T	3.37:g.195452679C>T	ENSP00000414350:p.Pro402Leu	609.0	0.0	0		990.0	191.0	0.192929	NM_152673	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	37		.	.	.	.	.	.	.	.	.	.	c	0.869	-0.732706	0.03135	.	.	ENSG00000176945	ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	T;T;T;T	0.11169	3.13;3.17;3.42;2.8	3.26	-6.52	0.01872	.	0.588934	0.14297	N	0.328508	T	0.02848	0.0085	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30995	-0.9959	10	0.87932	D	0	10.2224	0.1188	0.00063	0.242:0.2215:0.2078:0.3286	.	231	E9PH32	.	L	402;231;402;367	ENSP00000414350:P402L;ENSP00000325431:P231L;ENSP00000396774:P402L;ENSP00000405629:P367L	ENSP00000325431:P231L	P	+	2	0	MUC20	196938350	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.247000	0.02893	-2.014000	0.00948	-0.972000	0.02603	CCG	.	.	none		0.577	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1	NM_152673	
PLIN4	729359	hgsc.bcm.edu	37	19	4511944	4511944	+	Silent	SNP	A	A	G	rs143131726	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4511944A>G	ENST00000301286.3	-	3	1985	c.1986T>C	c.(1984-1986)aaT>aaC	p.N662N		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	662	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						CTTTGGCCACATTCACAGCAC	0.577													A|||	40	0.00798722	0.0303	0.0	5008	,	,		25673	0.0		0.0	False		,,,				2504	0.0				p.N662N		Atlas-SNP	.											.	PLIN4	191	.	0			c.T1986C						PASS	.	A		115,4007		6,103,1952	96.0	106.0	103.0		1986	-10.3	0.0	19	dbSNP_134	103	1,8383		0,1,4191	no	coding-synonymous	PLIN4	NM_001080400.1		6,104,6143	GG,GA,AA		0.0119,2.7899,0.9276		662/1358	4511944	116,12390	2061	4192	6253	SO:0001819	synonymous_variant	729359	exon3			GGCCACATTCACA	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"""Perilipins"""	29393	protein-coding gene	gene with protein product		613247	"""KIAA1881"""	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.1986T>C	19.37:g.4511944A>G		321.0	0.0	0		306.0	134.0	0.437909	NM_001080400	A6NEI2	Silent	SNP	ENST00000301286.3	37	CCDS45927.1																																																																																			A|0.994;G|0.006	0.006	strong		0.577	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
P2RX7	5027	hgsc.bcm.edu	37	12	121622380	121622380	+	Missense_Mutation	SNP	C	C	G	rs2230913	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:121622380C>G	ENST00000546057.1	+	13	1706	c.1563C>G	c.(1561-1563)caC>caG	p.H521Q	P2RX7_ENST00000443520.3_3'UTR|P2RX7_ENST00000328963.5_Missense_Mutation_p.H351Q|P2RX7_ENST00000541446.1_Missense_Mutation_p.H232Q|P2RX7_ENST00000535250.1_Missense_Mutation_p.H431Q|RP11-340F14.5_ENST00000569999.1_RNA	NM_002562.5	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 7	521			H -> Q (in dbSNP:rs2230913).		apoptotic signaling pathway (GO:0097190)|bleb assembly (GO:0032060)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|membrane depolarization (GO:0051899)|negative regulation of bone resorption (GO:0045779)|negative regulation of MAPK cascade (GO:0043409)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|pore complex assembly (GO:0046931)|positive regulation of bone mineralization (GO:0030501)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cytolysis (GO:0045919)|positive regulation of cytoskeleton organization (GO:0051495)|positive regulation of interleukin-1 beta secretion (GO:0050718)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of killing of cells of other organism (GO:0051709)|regulation of sodium ion transport (GO:0002028)|response to ATP (GO:0033198)|sensory perception of pain (GO:0019233)	bleb (GO:0032059)|cytoplasm (GO:0005737)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|lipopolysaccharide binding (GO:0001530)|protein homodimerization activity (GO:0042803)|purinergic nucleotide receptor activity (GO:0001614)|receptor binding (GO:0005102)			NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(9)|skin(1)|stomach(1)	19	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TGTCCAGACACGTCCTGCAGT	0.627													C|||	223	0.0445288	0.1619	0.013	5008	,	,		17902	0.0		0.0	False		,,,				2504	0.0				p.H521Q		Atlas-SNP	.											.	P2RX7	53	.	0			c.C1563G						PASS	.	C	GLN/HIS	615,3791	246.2+/-254.9	43,529,1631	35.0	31.0	32.0		1563	-10.4	0.0	12	dbSNP_98	32	7,8593	4.3+/-15.6	0,7,4293	yes	missense	P2RX7	NM_002562.5	24	43,536,5924	GG,GC,CC		0.0814,13.9582,4.7824	benign	521/596	121622380	622,12384	2203	4300	6503	SO:0001583	missense	5027	exon13			CAGACACGTCCTG	Y09561	CCDS9213.1	12q24	2012-01-17			ENSG00000089041	ENSG00000089041		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8537	protein-coding gene	gene with protein product		602566				9038151, 9826911	Standard	NM_002562		Approved	P2X7, MGC20089	uc001tzm.3	Q99572	OTTHUMG00000169153	ENST00000546057.1:c.1563C>G	12.37:g.121622380C>G	ENSP00000442349:p.His521Gln	65.0	0.0	0		64.0	32.0	0.5	NM_002562	A8K2Z0|E7EMK6|F5H6P2|F5H7E8|F8W951|O14991|Q4VKH8|Q4VKH9|Q4VKI0|Q4VKI1|Q4VKI2|Q4VKI3|Q4VKI4|Q7Z771|Q96EV7	Missense_Mutation	SNP	ENST00000546057.1	37	CCDS9213.1	81	0.03708791208791209	75	0.1524390243902439	6	0.016574585635359115	0	0.0	0	0.0	C	0.024	-1.393088	0.01185	0.139582	8.14E-4	ENSG00000089041	ENST00000546057;ENST00000328963;ENST00000535250;ENST00000541446	T;T;T;T	0.04454	4.5;4.13;4.29;3.62	5.21	-10.4	0.00318	.	2.829390	0.01180	N	0.007078	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B;B;B;B	0.06786	0.001;0.001;0.001;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.40194	-0.9576	9	0.21540	T	0.41	.	3.5355	0.07793	0.0826:0.2354:0.3527:0.3294	rs2230913;rs2230913	351;232;431;521	F8W951;F5H6P2;F5H7E8;Q99572	.;.;.;P2RX7_HUMAN	Q	521;351;431;232	ENSP00000442349:H521Q;ENSP00000330696:H351Q;ENSP00000442572:H431Q;ENSP00000437471:H232Q	ENSP00000330696:H351Q	H	+	3	2	P2RX7	120106763	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-6.209000	0.00076	-4.138000	0.00070	-1.865000	0.00557	CAC	C|0.955;G|0.045;T|0.000	0.045	strong		0.627	P2RX7-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402532.1	NM_002562	
HRC	3270	hgsc.bcm.edu	37	19	49657526	49657526	+	Silent	SNP	G	G	A	rs150557795	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49657526G>A	ENST00000252825.4	-	1	1155	c.969C>T	c.(967-969)gaC>gaT	p.D323D	HRC_ENST00000595625.1_Silent_p.D323D	NM_002152.2	NP_002143.1	P23327	SRCH_HUMAN	histidine rich calcium binding protein	323	4 X tandem repeats, acidic.|6 X approximate tandem repeats.				cytosolic calcium ion homeostasis (GO:0051480)|muscle contraction (GO:0006936)|positive regulation of heart contraction (GO:0045823)|positive regulation of heart rate (GO:0010460)|positive regulation of relaxation of cardiac muscle (GO:1901899)|regulation of calcium ion transmembrane transport (GO:1903169)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901844)|regulation of heart rate (GO:0002027)|regulation of peptidyl-serine phosphorylation (GO:0033135)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(10)|lung(10)|ovary(1)|prostate(3)|urinary_tract(2)	34		all_lung(116;3.16e-06)|Lung NSC(112;6.25e-06)|all_neural(266;0.0189)|Ovarian(192;0.0392)		all cancers(93;2.01e-05)|OV - Ovarian serous cystadenocarcinoma(262;0.00019)|GBM - Glioblastoma multiforme(486;0.00279)|Epithelial(262;0.00622)		CCTTTCTGTGGTCTTGGTGCC	0.542													G|||	63	0.0125799	0.0401	0.0029	5008	,	,		27949	0.0		0.005	False		,,,				2504	0.0031				p.D323D	Melanoma(37;75 1097 24567 25669 30645)	Atlas-SNP	.											HRC,NS,carcinoma,0,1	HRC	85	1	0			c.C969T						scavenged	.						212.0	161.0	178.0					19																	49657526		2203	4300	6503	SO:0001819	synonymous_variant	3270	exon1			TCTGTGGTCTTGG		CCDS12759.1	19q13.3	2008-07-16	2001-11-28			ENSG00000130528			5178	protein-coding gene	gene with protein product		142705	"""histidine-rich calcium-binding protein"""			2037293	Standard	XR_243928		Approved	MGC133236	uc002pmv.3	P23327		ENST00000252825.4:c.969C>T	19.37:g.49657526G>A		253.0	1.0	0.00395257		283.0	36.0	0.127208	NM_002152	Q504Y6	Silent	SNP	ENST00000252825.4	37	CCDS12759.1																																																																																			G|0.999;A|0.001	0.001	weak		0.542	HRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465649.1	NM_002152	
CHPF2	54480	hgsc.bcm.edu	37	7	150935367	150935367	+	Missense_Mutation	SNP	C	C	T	rs76509585	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150935367C>T	ENST00000035307.2	+	4	3432	c.1919C>T	c.(1918-1920)cCg>cTg	p.P640L	CHPF2_ENST00000495645.1_Missense_Mutation_p.P632L|MIR671_ENST00000390183.1_RNA|RP4-548D19.3_ENST00000607902.1_RNA	NM_019015.1	NP_061888.1	Q9P2E5	CHPF2_HUMAN	chondroitin polymerizing factor 2	640	Gly/Pro-rich.				carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			breast(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(4)|prostate(1)|skin(3)	17						CCAGGGCCCCCGGGGGCTGGC	0.657													C|||	77	0.0153754	0.0545	0.0072	5008	,	,		13615	0.0		0.0	False		,,,				2504	0.0				p.P640L		Atlas-SNP	.											.	CHPF2	52	.	0			c.C1919T						PASS	.	C	LEU/PRO	169,4233		1,167,2033	19.0	22.0	21.0		1919	2.9	0.0	7	dbSNP_131	21	1,8597		0,1,4298	yes	missense	CHPF2	NM_019015.1	98	1,168,6331	TT,TC,CC		0.0116,3.8392,1.3077	probably-damaging	640/773	150935367	170,12830	2201	4299	6500	SO:0001583	missense	54480	exon4			GGCCCCCGGGGGC	AB037823	CCDS34779.1, CCDS64803.1	7q36.1	2013-02-19			ENSG00000033100	ENSG00000033100	2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	29270	protein-coding gene	gene with protein product		608037				10718198, 12145278, 18316376	Standard	NM_019015		Approved	KIAA1402, ChSy-3, CSGlcA-T	uc003wjr.1	Q9P2E5	OTTHUMG00000157380	ENST00000035307.2:c.1919C>T	7.37:g.150935367C>T	ENSP00000035307:p.Pro640Leu	36.0	0.0	0		38.0	10.0	0.263158	NM_019015	B2DBD8|Q6P2I4|Q6UXD2	Missense_Mutation	SNP	ENST00000035307.2	37	CCDS34779.1	23	0.010531135531135532	21	0.042682926829268296	2	0.0055248618784530384	0	0.0	0	0.0	C	10.20	1.283741	0.23392	0.038392	1.16E-4	ENSG00000033100	ENST00000495645;ENST00000035307	T;T	0.15372	2.43;2.43	4.81	2.92	0.33932	.	0.129772	0.36002	N	0.002859	T	0.01627	0.0052	N	0.08118	0	0.21147	N	0.999775	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.32214	-0.9915	10	0.30078	T	0.28	-5.8196	9.1096	0.36718	0.0:0.8523:0.0:0.1477	.	640;632	Q9P2E5;G5E9W2	CHPF2_HUMAN;.	L	632;640	ENSP00000418914:P632L;ENSP00000035307:P640L	ENSP00000035307:P640L	P	+	2	0	CHPF2	150566300	0.009000	0.17119	0.015000	0.15790	0.410000	0.31052	0.945000	0.29056	0.573000	0.29400	0.655000	0.94253	CCG	C|0.988;T|0.012	0.012	strong		0.657	CHPF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348648.2	NM_019015	
RNF145	153830	hgsc.bcm.edu	37	5	158596032	158596032	+	Silent	SNP	G	G	A	rs61732785	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:158596032G>A	ENST00000424310.2	-	8	1329	c.970C>T	c.(970-972)Ctg>Ttg	p.L324L	RNF145_ENST00000521606.2_Silent_p.L341L|RNF145_ENST00000519865.1_Silent_p.L324L|RNF145_ENST00000518802.1_Silent_p.L354L|RNF145_ENST00000520638.1_Silent_p.L338L|RNF145_ENST00000274542.2_Silent_p.L352L	NM_001199383.1	NP_001186312.1	Q96MT1	RN145_HUMAN	ring finger protein 145	324						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)			TGCACTGCCAGGATTAACAGC	0.373													G|||	71	0.0141773	0.053	0.0014	5008	,	,		17610	0.0		0.0	False		,,,				2504	0.0				p.L354L		Atlas-SNP	.											RNF145,right_upper_lobe,carcinoma,+2,1	RNF145	110	1	0			c.C1060T						PASS	.	G	,,,,	200,4206	124.1+/-161.4	2,196,2005	116.0	119.0	118.0		1060,1021,1012,970,1054	4.2	1.0	5	dbSNP_129	118	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RNF145	NM_001199380.1,NM_001199381.1,NM_001199382.1,NM_001199383.1,NM_144726.2	,,,,	2,199,6302	AA,AG,GG		0.0349,4.5393,1.5608	,,,,	354/694,341/681,338/678,324/664,352/692	158596032	203,12803	2203	4300	6503	SO:0001819	synonymous_variant	153830	exon8			CTGCCAGGATTAA	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.970C>T	5.37:g.158596032G>A		334.0	1.0	0.00299401		353.0	167.0	0.473088	NM_001199380	B7Z903|B7Z949|E7EVI7|Q8IVP7	Silent	SNP	ENST00000424310.2	37	CCDS56390.1																																																																																			G|0.985;A|0.015	0.015	strong		0.373	RNF145-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374048.1	NM_144726	
GYG1	2992	hgsc.bcm.edu	37	3	148714662	148714662	+	Missense_Mutation	SNP	A	A	T	rs35054019	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:148714662A>T	ENST00000345003.4	+	4	752	c.452A>T	c.(451-453)cAt>cTt	p.H151L	GYG1_ENST00000296048.6_Missense_Mutation_p.H151L|GYG1_ENST00000484197.1_Missense_Mutation_p.H151L|GYG1_ENST00000483267.1_Missense_Mutation_p.H151L	NM_004130.3	NP_004121.2	P46976	GLYG_HUMAN	glycogenin 1	151					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	glucose binding (GO:0005536)|glycogenin glucosyltransferase activity (GO:0008466)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(2)|lung(3)|ovary(1)	8			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			CAGCTGTTGCATCTTGCTTCT	0.433													A|||	46	0.0091853	0.0348	0.0	5008	,	,		19931	0.0		0.0	False		,,,				2504	0.0				p.H151L		Atlas-SNP	.											.	GYG1	29	.	0			c.A452T						PASS	.	A	LEU/HIS,LEU/HIS,LEU/HIS	137,4269	98.5+/-137.1	1,135,2067	76.0	70.0	72.0		452,452,452	1.1	0.1	3	dbSNP_126	72	0,8600		0,0,4300	yes	missense,missense,missense	GYG1	NM_001184720.1,NM_001184721.1,NM_004130.3	99,99,99	1,135,6367	TT,TA,AA		0.0,3.1094,1.0534	benign,benign,benign	151/334,151/280,151/351	148714662	137,12869	2203	4300	6503	SO:0001583	missense	2992	exon4			TGTTGCATCTTGC	AF087942	CCDS3139.1, CCDS54654.1, CCDS54655.1	3q24-q25.1	2013-02-22	2005-11-04	2005-11-04	ENSG00000163754	ENSG00000163754	2.4.1.186	"""Glycosyltransferase family 8 domain containing"""	4699	protein-coding gene	gene with protein product	"""glycogenin glucosyltransferase"""	603942	"""glycogenin"""	GYG		8602861	Standard	NM_004130		Approved		uc003ewn.3	P46976	OTTHUMG00000159533	ENST00000345003.4:c.452A>T	3.37:g.148714662A>T	ENSP00000340736:p.His151Leu	154.0	0.0	0		179.0	85.0	0.47486	NM_004130	D3DNH0|D3DNH1|D3DNH2|Q6FHZ1|Q9UNV0	Missense_Mutation	SNP	ENST00000345003.4	37	CCDS3139.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	A	11.23	1.576606	0.28092	0.031094	0.0	ENSG00000163754	ENST00000345003;ENST00000296048;ENST00000483267;ENST00000484197;ENST00000492285;ENST00000461191	T;T;T;T;T;T	0.63096	-0.02;-0.02;-0.02;-0.02;-0.02;-0.02	6.11	1.11	0.20524	.	0.519143	0.23943	N	0.043027	T	0.24431	0.0592	L	0.33339	1.005	0.20873	N	0.999833	B;B;B;B	0.13145	0.001;0.007;0.001;0.0	B;B;B;B	0.20184	0.004;0.028;0.01;0.005	T	0.31861	-0.9928	10	0.59425	D	0.04	-35.2266	9.9467	0.41613	0.7509:0.0:0.2491:0.0	rs35054019	151;151;151;151	G5E9W8;D3DNH0;P46976-2;P46976	.;.;.;GLYG_HUMAN	L	151;151;151;151;105;151	ENSP00000340736:H151L;ENSP00000296048:H151L;ENSP00000419499:H151L;ENSP00000420683:H151L;ENSP00000418297:H105L;ENSP00000420247:H151L	ENSP00000296048:H151L	H	+	2	0	GYG1	150197352	0.258000	0.24033	0.099000	0.21106	0.896000	0.52359	1.243000	0.32767	-0.028000	0.13850	-0.261000	0.10672	CAT	A|0.990;T|0.010	0.010	strong		0.433	GYG1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000356046.1	NM_004130	
ZNF385C	201181	hgsc.bcm.edu	37	17	40180910	40180910	+	Silent	SNP	G	G	A	rs7208473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:40180910G>A	ENST00000436535.3	-	5	861	c.861C>T	c.(859-861)gcC>gcT	p.A287A	ZNF385C_ENST00000461831.1_5'Flank			Q66K41	Z385C_HUMAN	zinc finger protein 385C	205						nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			lung(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	3		all_cancers(22;0.00127)|Breast(137;0.00104)|all_epithelial(22;0.0126)				TGCTTCCCACGGCAGCTGCCG	0.637													G|||	75	0.014976	0.0567	0.0	5008	,	,		19369	0.0		0.0	False		,,,				2504	0.0				p.A207A		Atlas-SNP	.											.	ZNF385C	7	.	0			c.C621T						PASS	.																																			SO:0001819	synonymous_variant	201181	exon5			TCCCACGGCAGCT	BC067901	CCDS74065.1	17q21.2	2012-10-05			ENSG00000187595	ENSG00000187595			33722	protein-coding gene	gene with protein product							Standard	NM_001242704		Approved		uc021txr.1	Q66K41	OTTHUMG00000132073	ENST00000436535.3:c.861C>T	17.37:g.40180910G>A		75.0	0.0	0		84.0	39.0	0.464286	NM_001242704	Q4G0J1	Silent	SNP	ENST00000436535.3	37																																																																																				G|0.989;A|0.011	0.011	strong		0.637	ZNF385C-001	NOVEL	not_organism_supported|mRNA_end_NF|cds_end_NF|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000347740.3	NM_001013624	
TRPM1	4308	hgsc.bcm.edu	37	15	31323360	31323360	+	Splice_Site	SNP	T	T	G	rs181499296	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:31323360T>G	ENST00000256552.6	-	23	3100	c.2953A>C	c.(2953-2955)Atg>Ctg	p.M985L	RP11-348B17.1_ENST00000561299.1_RNA|RP11-348B17.1_ENST00000558755.1_RNA|TRPM1_ENST00000542188.1_Splice_Site_p.M1002L|TRPM1_ENST00000397795.2_Splice_Site_p.M963L	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		ATGTCGATCATCTGAGTAAGG	0.493													T|||	4	0.000798722	0.0023	0.0014	5008	,	,		22528	0.0		0.0	False		,,,				2504	0.0				p.M1002L		Atlas-SNP	.											.	TRPM1	183	.	0			c.A3004C						PASS	.	T	LEU/MET	8,4150		0,8,2071	68.0	66.0	66.0		2887	5.9	1.0	15		66	0,8476		0,0,4238	yes	missense-near-splice	TRPM1	NM_002420.4	15	0,8,6309	GG,GT,TT		0.0,0.1924,0.0633	possibly-damaging	963/1604	31323360	8,12626	2079	4238	6317	SO:0001630	splice_region_variant	4308	exon22			CGATCATCTGAGT	AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	7146	protein-coding gene	gene with protein product		603576	"""melastatin 1"""	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.2953-1A>C	15.37:g.31323360T>G		74.0	0.0	0		126.0	46.0	0.365079	NM_001252020		Missense_Mutation	SNP	ENST00000256552.6	37	CCDS58346.1	2	9.157509157509158E-4	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	0	0.0	T	21.6	4.177858	0.78564	0.001924	0.0	ENSG00000134160	ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793	T;T;T	0.73363	-0.74;-0.74;-0.74	5.92	5.92	0.95590	Ion transport (1);	0.000000	0.85682	D	0.000000	T	0.79718	0.4494	L	0.33485	1.01	0.58432	D	0.999997	D;D	0.59767	0.986;0.983	P;D	0.64687	0.8;0.928	T	0.81803	-0.0765	10	0.72032	D	0.01	-46.9433	16.371	0.83361	0.0:0.0:0.0:1.0	.	957;963	Q7Z4N2-3;Q7Z4N2	.;TRPM1_HUMAN	L	963;1002;985;963	ENSP00000380897:M963L;ENSP00000437849:M1002L;ENSP00000256552:M985L	ENSP00000256552:M985L	M	-	1	0	TRPM1	29110652	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	6.296000	0.72751	2.267000	0.75376	0.477000	0.44152	ATG	T|0.999;G|0.001	0.001	strong		0.493	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420	Missense_Mutation
OR51F2	119694	hgsc.bcm.edu	37	11	4843119	4843119	+	Silent	SNP	C	C	T	rs142530902		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:4843119C>T	ENST00000322110.5	+	1	569	c.504C>T	c.(502-504)gcC>gcT	p.A168A	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron	NM_001004753.1	NP_001004753.1	Q8NH61	O51F2_HUMAN	olfactory receptor, family 51, subfamily F, member 2	168						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(4)|large_intestine(3)|lung(16)|ovary(1)|pancreas(1)|prostate(4)|skin(2)	33		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.0778)		Epithelial(150;5.06e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00438)|LUSC - Lung squamous cell carcinoma(625;0.19)		GAAATGTTGCCGTCATGTTGC	0.443																																					p.A168A		Atlas-SNP	.											.	OR51F2	72	.	0			c.C504T						PASS	.	C		2,4400	6.2+/-15.9	0,2,2199	336.0	287.0	303.0		504	-1.1	1.0	11	dbSNP_134	303	0,8596		0,0,4298	no	coding-synonymous	OR51F2	NM_001004753.1		0,2,6497	TT,TC,CC		0.0,0.0454,0.0154		168/343	4843119	2,12996	2201	4298	6499	SO:0001819	synonymous_variant	119694	exon1			TGTTGCCGTCATG	BK004281	CCDS31361.1	11p15.4	2012-08-09			ENSG00000176925	ENSG00000176925		"""GPCR / Class A : Olfactory receptors"""	15197	protein-coding gene	gene with protein product							Standard	NM_001004753		Approved		uc010qyn.2	Q8NH61	OTTHUMG00000066508	ENST00000322110.5:c.504C>T	11.37:g.4843119C>T		134.0	0.0	0		143.0	83.0	0.58042	NM_001004753	Q6IFI1	Silent	SNP	ENST00000322110.5	37	CCDS31361.1																																																																																			C|1.000;T|0.000	0.000	weak		0.443	OR51F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142181.1	NM_001004753	
ATP1A2	477	hgsc.bcm.edu	37	1	160090993	160090993	+	Silent	SNP	G	G	A	rs61734527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:160090993G>A	ENST00000361216.3	+	3	218	c.129G>A	c.(127-129)aaG>aaA	p.K43K	ATP1A2_ENST00000392233.3_Silent_p.K43K	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	43					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|locomotion (GO:0040011)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of heart contraction (GO:0045822)|negative regulation of striated muscle contraction (GO:0045988)|neurotransmitter uptake (GO:0001504)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of smooth muscle contraction (GO:0006940)|regulation of striated muscle contraction (GO:0006942)|regulation of the force of heart contraction (GO:0002026)|regulation of vasoconstriction (GO:0019229)|relaxation of cardiac muscle (GO:0055119)|response to nicotine (GO:0035094)|sodium ion export from cell (GO:0036376)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	caveola (GO:0005901)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|endosome (GO:0005768)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			ATGACCACAAGCTGTCCTTGG	0.537													G|||	33	0.00658946	0.0242	0.0014	5008	,	,		21718	0.0		0.0	False		,,,				2504	0.0				p.K43K		Atlas-SNP	.											.	ATP1A2	167	.	0			c.G129A						PASS	.	G		122,4284	90.2+/-128.9	2,118,2083	229.0	232.0	231.0		129	3.7	1.0	1	dbSNP_129	231	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ATP1A2	NM_000702.3		2,119,6382	AA,AG,GG		0.0116,2.769,0.9457		43/1021	160090993	123,12883	2203	4300	6503	SO:0001819	synonymous_variant	477	exon3			CCACAAGCTGTCC	AB018321	CCDS1196.1	1q23.2	2014-09-17	2010-04-20		ENSG00000018625	ENSG00000018625	3.6.3.9	"""ATPases / P-type"""	800	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-2"", ""sodium pump subunit alpha-2"", ""sodium-potassium ATPase catalytic subunit alpha-2"""	182340	"""migraine, hemiplegic 2"", ""ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide"""	MHP2		9403481	Standard	NM_000702		Approved	FHM2	uc001fvc.3	P50993	OTTHUMG00000024080	ENST00000361216.3:c.129G>A	1.37:g.160090993G>A		85.0	0.0	0		77.0	29.0	0.376623	NM_000702	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Silent	SNP	ENST00000361216.3	37	CCDS1196.1																																																																																			G|0.991;A|0.009	0.009	strong		0.537	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702	
GLRA1	2741	hgsc.bcm.edu	37	5	151231140	151231140	+	Silent	SNP	C	C	G	rs76872663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:151231140C>G	ENST00000455880.2	-	7	1009	c.723G>C	c.(721-723)cgG>cgC	p.R241R	GLRA1_ENST00000274576.4_Silent_p.R241R|GLRA1_ENST00000471351.2_5'UTR|GLRA1_ENST00000545569.1_Silent_p.R158R			P23415	GLRA1_HUMAN	glycine receptor, alpha 1	241					acrosome reaction (GO:0007340)|action potential (GO:0001508)|adult walking behavior (GO:0007628)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|muscle contraction (GO:0006936)|negative regulation of transmission of nerve impulse (GO:0051970)|neuromuscular process controlling posture (GO:0050884)|neuropeptide signaling pathway (GO:0007218)|positive regulation of acrosome reaction (GO:2000344)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of membrane potential (GO:0042391)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|righting reflex (GO:0060013)|startle response (GO:0001964)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|external side of plasma membrane (GO:0009897)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|glycine binding (GO:0016594)|taurine binding (GO:0030977)|transmitter-gated ion channel activity (GO:0022824)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	23		all_hematologic(541;0.0341)|Medulloblastoma(196;0.0912)	Kidney(363;0.000171)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)		Desflurane(DB01189)|Enflurane(DB00228)|Ethanol(DB00898)|Ginkgo biloba(DB01381)|Glycine(DB00145)|Halothane(DB01159)|Isoflurane(DB00753)|Lindane(DB00431)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	CCAGGTGGAACCGGGCCTCAA	0.483													C|||	25	0.00499201	0.0189	0.0	5008	,	,		22610	0.0		0.0	False		,,,				2504	0.0				p.R241R		Atlas-SNP	.											GLRA1,NS,carcinoma,-2,1	GLRA1	61	1	0			c.G723C						PASS	.	C	,	68,4338	60.5+/-97.4	0,68,2135	92.0	89.0	90.0		723,723	-1.0	1.0	5	dbSNP_132	90	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	GLRA1	NM_000171.3,NM_001146040.1	,	0,68,6435	GG,GC,CC		0.0,1.5433,0.5228	,	241/450,241/458	151231140	68,12938	2203	4300	6503	SO:0001819	synonymous_variant	2741	exon7			GTGGAACCGGGCC		CCDS4320.1, CCDS54942.1	5q33.1	2012-02-07	2008-01-24		ENSG00000145888	ENSG00000145888		"""Ligand-gated ion channels / Glycine receptors"""	4326	protein-coding gene	gene with protein product	"""startle disease/hyperekplexia"", ""stiff person syndrome"""	138491	"""glycine receptor, alpha 1 (startle disease/hyperekplexia)"""	STHE		1355335, 8298642	Standard	NM_000171		Approved		uc003lut.3	P23415	OTTHUMG00000130121	ENST00000455880.2:c.723G>C	5.37:g.151231140C>G		109.0	0.0	0		145.0	76.0	0.524138	NM_000171	B2R6T3|Q14C77|Q6DJV9	Silent	SNP	ENST00000455880.2	37	CCDS54942.1																																																																																			C|0.994;G|0.006	0.006	strong		0.483	GLRA1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373959.1		
NFATC3	4775	hgsc.bcm.edu	37	16	68224786	68224786	+	Missense_Mutation	SNP	C	C	G	rs77352556	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:68224786C>G	ENST00000346183.3	+	9	2238	c.2214C>G	c.(2212-2214)gaC>gaG	p.D738E	SNORA48_ENST00000391143.1_RNA|NFATC3_ENST00000329524.4_Missense_Mutation_p.D738E|NFATC3_ENST00000349223.5_Missense_Mutation_p.D738E|NFATC3_ENST00000535127.2_3'UTR|NFATC3_ENST00000575270.1_Missense_Mutation_p.D738E	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3	738					cellular respiration (GO:0045333)|cellular response to calcium ion (GO:0071277)|cellular response to lithium ion (GO:0071285)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	44		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)		GTTCACATGACAGTGTACTGT	0.478													C|||	46	0.0091853	0.0333	0.0029	5008	,	,		21238	0.0		0.0	False		,,,				2504	0.0				p.D738E		Atlas-SNP	.											.	NFATC3	190	.	0			c.C2214G						PASS	.	C	GLU/ASP,GLU/ASP,GLU/ASP	88,4308	74.1+/-112.3	2,84,2112	109.0	92.0	97.0		2214,2214,2214	-1.8	0.9	16	dbSNP_131	97	0,8600		0,0,4300	yes	missense,missense,missense	NFATC3	NM_004555.3,NM_173163.2,NM_173165.2	45,45,45	2,84,6412	GG,GC,CC		0.0,2.0018,0.6771	benign,benign,benign	738/1069,738/1066,738/1076	68224786	88,12908	2198	4300	6498	SO:0001583	missense	4775	exon9			ACATGACAGTGTA	L41067	CCDS10860.1, CCDS10861.1, CCDS10862.1	16q22	2009-11-24			ENSG00000072736	ENSG00000072736		"""Nuclear factor of activated T-cells"""	7777	protein-coding gene	gene with protein product		602698				7749981	Standard	NM_004555		Approved	NFAT4, NFATX	uc002evo.2	Q12968	OTTHUMG00000137555	ENST00000346183.3:c.2214C>G	16.37:g.68224786C>G	ENSP00000300659:p.Asp738Glu	200.0	0.0	0		231.0	128.0	0.554113	NM_173163	O75211|Q14516|Q99840|Q99841|Q99842	Missense_Mutation	SNP	ENST00000346183.3	37	CCDS10860.1	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	C	9.959	1.222209	0.22457	0.020018	0.0	ENSG00000072736	ENST00000349223;ENST00000346183;ENST00000329524;ENST00000535127	T;T;T	0.11604	2.76;2.76;2.76	5.55	-1.84	0.07809	.	1.004540	0.07995	N	0.987827	T	0.01353	0.0044	M	0.65975	2.015	0.38233	D	0.941091	B;B;B;B	0.13145	0.001;0.006;0.007;0.001	B;B;B;B	0.16289	0.004;0.015;0.007;0.004	T	0.46062	-0.9218	10	0.06099	T	0.92	-3.3363	6.3098	0.21159	0.0:0.2985:0.3225:0.379	.	738;738;738;738	Q12968;Q12968-3;B5B2S0;B5B2S2	NFAC3_HUMAN;.;.;.	E	738;738;738;259	ENSP00000264008:D738E;ENSP00000300659:D738E;ENSP00000331324:D738E	ENSP00000331324:D738E	D	+	3	2	NFATC3	66782287	0.992000	0.36948	0.876000	0.34364	0.316000	0.28119	0.366000	0.20365	-0.220000	0.09988	0.557000	0.71058	GAC	C|0.991;G|0.009	0.009	strong		0.478	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2	NM_004555	
H1FOO	132243	hgsc.bcm.edu	37	3	129267915	129267915	+	Silent	SNP	T	T	C	rs60616647	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:129267915T>C	ENST00000324382.2	+	3	455	c.450T>C	c.(448-450)ggT>ggC	p.G150G	H1FOO_ENST00000503977.1_Silent_p.G11G	NM_153833.1	NP_722575.1	Q8IZA3	H1FOO_HUMAN	H1 histone family, member O, oocyte-specific	150					meiotic nuclear division (GO:0007126)|negative regulation of stem cell differentiation (GO:2000737)|nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)|regulation of DNA methylation (GO:0044030)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|female germ cell nucleus (GO:0001674)|nucleosome (GO:0000786)|nucleus (GO:0005634)	nucleosomal DNA binding (GO:0031492)			endometrium(1)|lung(4)|skin(1)	6						GGAGAGCGGGTGAGGCCAAGG	0.607													C|||	315	0.0628994	0.2277	0.0202	5008	,	,		16740	0.0		0.0	False		,,,				2504	0.0				p.G150G		Atlas-SNP	.											.	H1FOO	20	.	0			c.T450C						PASS	.	C		795,3611	723.7+/-409.4	75,645,1483	30.0	30.0	30.0		450	-5.2	0.0	3	dbSNP_129	30	10,8590	800.0+/-407.4	0,10,4290	no	coding-synonymous	H1FOO	NM_153833.1		75,655,5773	CC,CT,TT		0.1163,18.0436,6.1895		150/347	129267915	805,12201	2203	4300	6503	SO:0001819	synonymous_variant	132243	exon3			AGCGGGTGAGGCC	AY158091	CCDS3064.1	3q21.3	2011-01-27			ENSG00000178804	ENSG00000178804		"""Histones / Replication-independent"""	18463	protein-coding gene	gene with protein product						12408966	Standard	NM_153833		Approved		uc003emu.3	Q8IZA3	OTTHUMG00000159541	ENST00000324382.2:c.450T>C	3.37:g.129267915T>C		127.0	0.0	0		134.0	134.0	1	NM_153833	Q86WT7	Silent	SNP	ENST00000324382.2	37	CCDS3064.1																																																																																			T|0.938;C|0.062	0.062	strong		0.607	H1FOO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356100.3	NM_153833	
ZC3H4	23211	hgsc.bcm.edu	37	19	47575170	47575170	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:47575170T>C	ENST00000253048.5	-	13	2048	c.2011A>G	c.(2011-2013)Atg>Gtg	p.M671V	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	671	Pro-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		TAGGGCATCATTGGAGGGCCG	0.617																																					p.M671V		Atlas-SNP	.											.	ZC3H4	96	.	0			c.A2011G						PASS	.						33.0	39.0	37.0					19																	47575170		2040	4187	6227	SO:0001583	missense	23211	exon13			GCATCATTGGAGG	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"""Zinc fingers, CCCH-type domain containing"""	17808	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 7"""	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.2011A>G	19.37:g.47575170T>C	ENSP00000253048:p.Met671Val	92.0	0.0	0		117.0	63.0	0.538462	NM_015168	Q9Y420	Missense_Mutation	SNP	ENST00000253048.5	37	CCDS42582.1	.	.	.	.	.	.	.	.	.	.	T	11.74	1.728939	0.30684	.	.	ENSG00000130749	ENST00000253048	T	0.18174	2.23	5.35	5.35	0.76521	.	0.784041	0.11696	N	0.538401	T	0.13415	0.0325	L	0.34521	1.04	0.46499	D	0.999079	B	0.31485	0.325	B	0.21917	0.037	T	0.12167	-1.0558	10	0.15499	T	0.54	.	14.3108	0.66415	0.0:0.0:0.0:1.0	.	671	Q9UPT8	ZC3H4_HUMAN	V	671	ENSP00000253048:M671V	ENSP00000253048:M671V	M	-	1	0	ZC3H4	52267010	1.000000	0.71417	0.982000	0.44146	0.507000	0.33981	6.886000	0.75611	2.028000	0.59812	0.523000	0.50628	ATG	.	.	none		0.617	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1		
BPIFB3	359710	hgsc.bcm.edu	37	20	31661399	31661399	+	Silent	SNP	C	C	T	rs114341725	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31661399C>T	ENST00000375494.3	+	15	1419	c.1419C>T	c.(1417-1419)acC>acT	p.T473T		NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	473					innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)	p.T473T(1)									TTGTGCTGACCGTGGCATCCT	0.552													C|||	27	0.00539137	0.0204	0.0	5008	,	,		19225	0.0		0.0	False		,,,				2504	0.0				p.T473T		Atlas-SNP	.											C20orf185,caecum,carcinoma,+2,1	.	.	1	1	Substitution - coding silent(1)	lung(1)	c.C1419T						scavenged	.	C		71,4335	65.3+/-102.7	0,71,2132	237.0	182.0	201.0		1419	-2.5	1.0	20	dbSNP_132	201	0,8600		0,0,4300	yes	coding-synonymous	BPIFB3	NM_182658.1		0,71,6432	TT,TC,CC		0.0,1.6114,0.5459		473/477	31661399	71,12935	2203	4300	6503	SO:0001819	synonymous_variant	359710	exon15			GCTGACCGTGGCA	AF549189	CCDS13212.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186190	ENSG00000186190		"""BPI fold containing"""	16178	protein-coding gene	gene with protein product		615717	"""chromosome 20 open reading frame 185"""	C20orf185		11971875, 21787333	Standard	NM_182658		Approved	dJ726C3.4, LPLUNC3, RYA3	uc002wym.1	P59826	OTTHUMG00000032234	ENST00000375494.3:c.1419C>T	20.37:g.31661399C>T		184.0	1.0	0.00543478		218.0	109.0	0.5	NM_182658	Q5TDX7	Silent	SNP	ENST00000375494.3	37	CCDS13212.1																																																																																			C|0.993;T|0.007	0.007	strong		0.552	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658	
PRPF4	9128	hgsc.bcm.edu	37	9	116053895	116053895	+	Silent	SNP	C	C	T	rs146201781	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116053895C>T	ENST00000374198.4	+	14	1626	c.1524C>T	c.(1522-1524)gcC>gcT	p.A508A	PRPF4_ENST00000374199.4_Silent_p.A507A	NM_001244926.1|NM_004697.4	NP_001231855.1|NP_004688.2	O43172	PRP4_HUMAN	pre-mRNA processing factor 4	508					gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U4/U6 snRNP (GO:0071001)				NS(1)|breast(2)|endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|prostate(2)	23						AGCTCATAGCCACTTGCTCAT	0.517													C|||	7	0.00139776	0.0045	0.0014	5008	,	,		19015	0.0		0.0	False		,,,				2504	0.0				p.A508A		Atlas-SNP	.											.	PRPF4	56	.	0			c.C1524T						PASS	.	C		14,4392	21.2+/-45.6	0,14,2189	88.0	80.0	83.0		1524	3.9	1.0	9	dbSNP_134	83	0,8600		0,0,4300	no	coding-synonymous	PRPF4	NM_004697.3		0,14,6489	TT,TC,CC		0.0,0.3177,0.1076		508/523	116053895	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	9128	exon14			CATAGCCACTTGC	AF001687	CCDS6791.1, CCDS59142.1	9q31-q33	2013-10-03	2013-10-03		ENSG00000136875	ENSG00000136875		"""WD repeat domain containing"""	17349	protein-coding gene	gene with protein product	"""PRP4/STK/WD splicing factor"", ""U4/U6 small nuclear ribonucleoprotein Prp4"""	607795	"""PRP4 pre-mRNA processing factor 4 homolog (yeast)"""			9257651, 9404889	Standard	NM_004697		Approved	Prp4p, HPRP4, HPRP4P, PRP4, SNRNP60	uc004bgx.3	O43172	OTTHUMG00000020517	ENST00000374198.4:c.1524C>T	9.37:g.116053895C>T		102.0	0.0	0		122.0	78.0	0.639344	NM_004697	O43445|O43864|Q5T1M8|Q96DG2|Q96IK4	Silent	SNP	ENST00000374198.4	37	CCDS6791.1																																																																																			C|0.999;T|0.001	0.001	strong		0.517	PRPF4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053708.2	NM_004697	
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011409	46011409	+	Silent	SNP	G	G	A	rs144363824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46011409G>A	ENST00000400368.1	-	1	977	c.957C>T	c.(955-957)ccC>ccT	p.P319P	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	319	29 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(6)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23						AGGAGGGGACGGGCACGCAGC	0.697													.|||	155	0.0309505	0.1127	0.0086	5008	,	,		18795	0.0		0.0	False		,,,				2504	0.0				p.P319P		Atlas-SNP	.											.	KRTAP10-6	57	.	0			c.C957T						PASS	.						70.0	85.0	80.0					21																	46011409		2201	4300	6501	SO:0001819	synonymous_variant	386674	exon1			GGGGACGGGCACG	AB076353	CCDS42959.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000188155	ENSG00000188155		"""Keratin associated proteins"""	20523	protein-coding gene	gene with protein product			"""keratin associated protein 18-6"""	KRTAP18-6			Standard	NM_198688		Approved	KRTAP18.6, KAP18.6, KAP10.6	uc002zfm.3	P60371	OTTHUMG00000057634	ENST00000400368.1:c.957C>T	21.37:g.46011409G>A		364.0	0.0	0		265.0	54.0	0.203774	NM_198688		Silent	SNP	ENST00000400368.1	37	CCDS42959.1																																																																																			G|0.975;A|0.025	0.025	strong		0.697	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688	
JRK	8629	hgsc.bcm.edu	37	8	143746414	143746414	+	RNA	SNP	G	G	A	rs115218091	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:143746414G>A	ENST00000507178.2	-	0	1396							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				gttgtagcgggcatgggggcc	0.617													G|||	63	0.0125799	0.0469	0.0014	5008	,	,		18410	0.0		0.0	False		,,,				2504	0.0				p.A355V		Atlas-SNP	.											.	.	.	.	0			c.C1064T						PASS	.	G	VAL/ALA,VAL/ALA	67,3943		0,67,1938	8.0	9.0	9.0		1064,1064	3.7	0.0	8	dbSNP_132	9	1,8323		0,1,4161	yes	missense,missense	JRK	NM_001077527.1,NM_003724.2	64,64	0,68,6099	AA,AG,GG		0.012,1.6708,0.5513	benign,benign	355/557,355/569	143746414	68,12266	2005	4162	6167			8629	exon2			TAGCGGGCATGGG	AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"""jerky (mouse) homolog"", ""jerky homolog (mouse)"""			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			8.37:g.143746414G>A		90.0	0.0	0		88.0	38.0	0.431818	NM_003724	O75565	Missense_Mutation	SNP	ENST00000507178.2	37																																																																																				G|0.991;A|0.009	0.009	strong		0.617	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724	
SSTR5	6755	hgsc.bcm.edu	37	16	1128901	1128901	+	Silent	SNP	C	C	T	rs35128939	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1128901C>T	ENST00000293897.4	+	1	121	c.33C>T	c.(31-33)agC>agT	p.S11S	SSTR5-AS1_ENST00000569832.1_RNA|SSTR5_ENST00000397547.2_Silent_p.S11S|SSTR5_ENST00000562758.1_Silent_p.S11S	NM_001053.3	NP_001044.1	P35346	SSR5_HUMAN	somatostatin receptor 5	11					G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cytokinesis (GO:0032467)|regulation of insulin secretion (GO:0050796)|somatostatin signaling pathway (GO:0038170)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			endometrium(2)|lung(5)|prostate(1)|skin(1)	9		Hepatocellular(780;0.00369)			Octreotide(DB00104)|Pasireotide(DB06663)|Vapreotide(DB04894)	CCACGCCCAGCTGGAACGCCT	0.731													C|||	17	0.00339457	0.0121	0.0014	5008	,	,		13446	0.0		0.0	False		,,,				2504	0.0				p.S11S		Atlas-SNP	.											.	SSTR5	36	.	0			c.C33T						PASS	.	C	,	44,4262		0,44,2109	10.0	11.0	11.0		33,33	3.8	1.0	16	dbSNP_126	11	0,8488		0,0,4244	no	coding-synonymous,coding-synonymous	SSTR5	NM_001053.3,NM_001172560.1	,	0,44,6353	TT,TC,CC		0.0,1.0218,0.3439	,	11/365,11/365	1128901	44,12750	2153	4244	6397	SO:0001819	synonymous_variant	6755	exon2			GCCCAGCTGGAAC	D16827	CCDS10429.1	16p13.3	2012-08-08			ENSG00000162009	ENSG00000162009		"""GPCR / Class A : Somatostatin receptors"""	11334	protein-coding gene	gene with protein product		182455				7607700	Standard	NM_001053		Approved		uc021taf.1	P35346	OTTHUMG00000047842	ENST00000293897.4:c.33C>T	16.37:g.1128901C>T		24.0	0.0	0		24.0	5.0	0.208333	NM_001172560	P34988|Q541E0|Q9UJI5	Silent	SNP	ENST00000293897.4	37	CCDS10429.1																																																																																			C|0.997;T|0.003	0.003	strong		0.731	SSTR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420836.1		
SLC3A2	6520	hgsc.bcm.edu	37	11	62648748	62648748	+	Silent	SNP	C	C	T	rs73487878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:62648748C>T	ENST00000377890.2	+	4	724	c.556C>T	c.(556-558)Ctg>Ttg	p.L186L	SLC3A2_ENST00000338663.7_Silent_p.L85L|SLC3A2_ENST00000377891.2_Silent_p.L187L|SLC3A2_ENST00000535296.1_Silent_p.L155L|SLC3A2_ENST00000377889.2_Silent_p.L124L|SLC3A2_ENST00000377892.1_Silent_p.L217L|SLC3A2_ENST00000536981.1_5'Flank	NM_002394.5	NP_002385.3	P08195	4F2_HUMAN	solute carrier family 3 (amino acid transporter heavy chain), member 2	186					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|carbohydrate metabolic process (GO:0005975)|cell growth (GO:0016049)|ion transport (GO:0006811)|leucine import (GO:0060356)|leukocyte migration (GO:0050900)|response to exogenous dsRNA (GO:0043330)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|tryptophan transport (GO:0015827)	cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium:sodium antiporter activity (GO:0005432)|catalytic activity (GO:0003824)|cation binding (GO:0043169)|double-stranded RNA binding (GO:0003725)|neutral amino acid transmembrane transporter activity (GO:0015175)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)	22						CTGGGCACTGCTGCTGCTCTT	0.687											OREG0021031	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	116	0.0231629	0.0809	0.0101	5008	,	,		13125	0.0		0.002	False		,,,				2504	0.0				p.L187L		Atlas-SNP	.											.	SLC3A2	55	.	0			c.C559T						PASS	.	C	,,,	239,4153		11,217,1968	15.0	16.0	16.0		559,370,253,556	5.0	1.0	11	dbSNP_130	16	1,8579		0,1,4289	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC3A2	NM_001012662.2,NM_001012664.2,NM_001013251.2,NM_002394.5	,,,	11,218,6257	TT,TC,CC		0.0117,5.4417,1.8501	,,,	187/632,124/569,85/530,186/631	62648748	240,12732	2196	4290	6486	SO:0001819	synonymous_variant	6520	exon4			GCACTGCTGCTGC		CCDS8039.2, CCDS31588.1, CCDS31589.1, CCDS31590.1	11q12-q22	2013-07-19	2013-07-19		ENSG00000168003	ENSG00000168003		"""Solute carriers"""	11026	protein-coding gene	gene with protein product	"""antigen identified by monoclonal antibodies 4F2, TRA1.10, TROP4, and T43"", ""antigen defined by monoclonal antibody 4F2"", ""heavy chain"", ""4F2 heavy chain"", ""CD98 heavy chain"", ""monoclonal antibody 44D7"", ""4F2 cell-surface antigen heavy chain"", ""lymphocyte activation antigen 4F2 large subunit"""	158070	"""solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2"""	MDU1		3036867	Standard	NM_001012662		Approved	4T2HC, 4F2, NACAE, CD98, CD98HC, 4F2HC	uc001nwd.3	P08195	OTTHUMG00000074091	ENST00000377890.2:c.556C>T	11.37:g.62648748C>T		57.0	0.0	0	1062	73.0	36.0	0.493151	NM_001012662	Q13543	Silent	SNP	ENST00000377890.2	37	CCDS8039.2																																																																																			C|0.975;T|0.025	0.025	strong		0.687	SLC3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000157306.1	NM_001012661	
TCP10L2	401285	hgsc.bcm.edu	37	6	167585652	167585652	+	Missense_Mutation	SNP	A	A	C	rs59203630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:167585652A>C	ENST00000366832.2	+	2	151	c.20A>C	c.(19-21)gAg>gCg	p.E7A		NM_001145121.1	NP_001138593.1	B9ZVM9	TCP2L_HUMAN	t-complex 10-like 2	7										endometrium(1)|kidney(2)|lung(3)	6						GGTCAGCTCGAGGCCAGGGAG	0.672													A|||	197	0.0393371	0.1422	0.013	5008	,	,		18107	0.0		0.0	False		,,,				2504	0.0				p.E7A		Atlas-SNP	.											.	TCP10L2	41	.	0			c.A20C						PASS	.	A	ALA/GLU	207,1177		20,167,505	21.0	31.0	28.0		20	-2.1	0.0	6	dbSNP_129	28	0,3182		0,0,1591	no	missense	TCP10L2	NM_001145121.1	107	20,167,2096	CC,CA,AA		0.0,14.9566,4.5335	possibly-damaging	7/354	167585652	207,4359	692	1591	2283	SO:0001583	missense	401285	exon2			AGCTCGAGGCCAG		CCDS47514.1	6q27	2012-09-20	2012-09-20		ENSG00000166984	ENSG00000166984			21254	protein-coding gene	gene with protein product			"""t-complex 10-like 2 (mouse)"""				Standard	NM_001145121		Approved	bA517H2.3	uc010kkp.3	B9ZVM9	OTTHUMG00000016014	ENST00000366832.2:c.20A>C	6.37:g.167585652A>C	ENSP00000355797:p.Glu7Ala	183.0	0.0	0		177.0	173.0	0.977401	NM_001145121		Missense_Mutation	SNP	ENST00000366832.2	37	CCDS47514.1	75	0.034340659340659344	73	0.1483739837398374	2	0.0055248618784530384	0	0.0	0	0.0	a	11.90	1.775977	0.31411	0.149566	0.0	ENSG00000166984	ENST00000486697;ENST00000366832	T	0.20200	2.09	2.61	-2.13	0.07144	.	.	.	.	.	T	0.10852	0.0265	L	0.51422	1.61	0.80722	P	0.0	D	0.58268	0.982	P	0.52554	0.702	T	0.04811	-1.0925	8	0.62326	D	0.03	.	3.0393	0.06133	0.4685:0.2327:0.2987:0.0	rs59203630	7	B9ZVM9	TCP2L_HUMAN	A	7	ENSP00000355797:E7A	ENSP00000283507:E7A	E	+	2	0	TCP10L2	167505642	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	0.176000	0.16782	-0.554000	0.06150	-0.863000	0.03009	GAG	A|0.966;C|0.034	0.034	strong		0.672	TCP10L2-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043112.5	XR_040749	
MUC4	4585	hgsc.bcm.edu	37	3	195508524	195508524	+	Silent	SNP	G	G	A	rs141064104	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195508524G>A	ENST00000463781.3	-	2	10386	c.9927C>T	c.(9925-9927)caC>caT	p.H3309H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.H3309H	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.V3305_S3320delVSTGHATPLLVTDASS(1)|p.V3305_S3336delVSTGHATPLLVTDASSASTGHATPLHVTSPSS(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGAGTGGCGTGACCTGTGG	0.567													.|||	179	0.0357428	0.1293	0.0101	5008	,	,		9468	0.0		0.001	False		,,,				2504	0.0				p.H3309H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-2,2	MUC4	1505	2	2	Deletion - In frame(2)	stomach(2)	c.C9927T						PASS	.						18.0	18.0	18.0					3																	195508524		659	1500	2159	SO:0001819	synonymous_variant	4585	exon2			AGTGGCGTGACCT	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.9927C>T	3.37:g.195508524G>A		197.0	0.0	0		119.0	57.0	0.478992	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			G|0.950;A|0.050	0.050	strong		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ADRB1	153	hgsc.bcm.edu	37	10	115804123	115804123	+	Silent	SNP	C	C	T	rs373125312		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:115804123C>T	ENST00000369295.2	+	1	318	c.232C>T	c.(232-234)Ctg>Ttg	p.L78L		NM_000684.2	NP_000675.1	P08588	ADRB1_HUMAN	adrenoceptor beta 1	78					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|aging (GO:0007568)|apoptotic process (GO:0006915)|brown fat cell differentiation (GO:0050873)|diet induced thermogenesis (GO:0002024)|fear response (GO:0042596)|glycogen catabolic process (GO:0005980)|heat generation (GO:0031649)|lipid homeostasis (GO:0055088)|memory (GO:0007613)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of smooth muscle contraction (GO:0045986)|negative regulation of urine volume (GO:0035811)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of cation channel activity (GO:2001259)|positive regulation of cell growth involved in cardiac muscle cell development (GO:0061051)|positive regulation of heart rate by epinephrine-norepinephrine (GO:0001996)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of renin secretion into blood stream (GO:1900135)|positive regulation of saliva secretion (GO:0046878)|positive regulation of systemic arterial blood pressure (GO:0003084)|positive regulation of the force of heart contraction by norepinephrine (GO:0003061)|protein localization to organelle (GO:0033365)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|response to cold (GO:0009409)|Rho protein signal transduction (GO:0007266)|sensory perception of pain (GO:0019233)|vasodilation by norepinephrine-epinephrine involved in regulation of systemic arterial blood pressure (GO:0002025)|wound healing (GO:0042060)	early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|beta-adrenergic receptor activity (GO:0004939)|beta1-adrenergic receptor activity (GO:0004940)|dopamine binding (GO:0035240)|drug binding (GO:0008144)|epinephrine binding (GO:0051379)|norepinephrine binding (GO:0051380)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|receptor signaling protein activity (GO:0005057)			large_intestine(4)|lung(1)|upper_aerodigestive_tract(1)	6		Colorectal(252;0.172)|Breast(234;0.188)		Epithelial(162;0.0124)|all cancers(201;0.0298)	Acebutolol(DB01193)|Alprenolol(DB00866)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amphetamine(DB00182)|Arbutamine(DB01102)|Asenapine(DB06216)|Atenolol(DB00335)|Betaxolol(DB00195)|Bethanidine(DB00217)|Bevantolol(DB01295)|Bisoprolol(DB00612)|Bopindolol(DB08807)|Bupranolol(DB08808)|Cabergoline(DB00248)|Carteolol(DB00521)|Carvedilol(DB01136)|Clenbuterol(DB01407)|Desipramine(DB01151)|Dobutamine(DB00841)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Esmolol(DB00187)|Fenoterol(DB01288)|Isoetarine(DB00221)|Isoprenaline(DB01064)|Labetalol(DB00598)|Levobunolol(DB01210)|Loxapine(DB00408)|Mephentermine(DB01365)|Metipranolol(DB01214)|Metoprolol(DB00264)|Mirtazapine(DB00370)|Nadolol(DB01203)|Nebivolol(DB04861)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxprenolol(DB01580)|Penbutolol(DB01359)|Phenylpropanolamine(DB00397)|Pindolol(DB00960)|Pirbuterol(DB01291)|Practolol(DB01297)|Propranolol(DB00571)|Pseudoephedrine(DB00852)|Salbutamol(DB01001)|Sotalol(DB00489)|Timolol(DB00373)|Trimipramine(DB00726)	GGGCAATGTGCTGGTGATCGT	0.657																																					p.L78L		Atlas-SNP	.											.	ADRB1	16	.	0			c.C232T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	43.0	39.0	40.0		232	2.1	1.0	10		40	0,8600		0,0,4300	no	coding-synonymous	ADRB1	NM_000684.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		78/478	115804123	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	153	exon1			AATGTGCTGGTGA	J03019	CCDS7586.1	10q25.3	2012-08-08	2012-05-09		ENSG00000043591	ENSG00000043591		"""GPCR / Class A : Adrenoceptors : beta"""	285	protein-coding gene	gene with protein product		109630	"""adrenergic, beta-1-, receptor"""	ADRB1R			Standard	NM_000684		Approved		uc001lba.3	P08588	OTTHUMG00000019079	ENST00000369295.2:c.232C>T	10.37:g.115804123C>T		89.0	0.0	0		80.0	42.0	0.525	NM_000684	B0LPE2|Q5T5Y4|Q9UKG7|Q9UKG8	Silent	SNP	ENST00000369295.2	37	CCDS7586.1																																																																																			.	.	none		0.657	ADRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050448.1		
NUDT6	11162	hgsc.bcm.edu	37	4	123814170	123814170	+	Missense_Mutation	SNP	G	G	A	rs138619142		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:123814170G>A	ENST00000304430.5	-	5	797	c.764C>T	c.(763-765)gCg>gTg	p.A255V	FGF2_ENST00000264498.3_3'UTR|NUDT6_ENST00000339154.2_Missense_Mutation_p.A86V|FGF2_ENST00000608478.1_3'UTR|NUDT6_ENST00000608639.1_5'Flank|NUDT6_ENST00000502270.1_Missense_Mutation_p.A86V	NM_007083.4	NP_009014.2	P53370	NUDT6_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 6	255	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.					mitochondrion (GO:0005739)|nucleus (GO:0005634)	growth factor activity (GO:0008083)|hydrolase activity (GO:0016787)			endometrium(2)|lung(1)|prostate(1)|skin(1)|stomach(1)	6						TTCAGTCTTCGCCAGGTCATT	0.433													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18368	0.0		0.0	False		,,,				2504	0.0				p.A255V		Atlas-SNP	.											.	NUDT6	50	.	0			c.C764T						PASS	.	G	,VAL/ALA,VAL/ALA	15,4391	22.3+/-47.3	0,15,2188	134.0	125.0	128.0		,764,257	-3.6	0.0	4	dbSNP_134	128	0,8600		0,0,4300	yes	utr-3,missense,missense	FGF2,NUDT6	NM_002006.4,NM_007083.3,NM_198041.1	,64,64	0,15,6488	AA,AG,GG		0.0,0.3404,0.1153	,benign,benign	,255/317,86/148	123814170	15,12991	2203	4300	6503	SO:0001583	missense	11162	exon5			GTCTTCGCCAGGT	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.764C>T	4.37:g.123814170G>A	ENSP00000306070:p.Ala255Val	212.0	0.0	0		231.0	114.0	0.493506	NM_007083	A8K756|O95097|Q9UQD9	Missense_Mutation	SNP	ENST00000304430.5	37	CCDS43268.1	.	.	.	.	.	.	.	.	.	.	G	0.014	-1.606796	0.00842	0.003404	0.0	ENSG00000170917	ENST00000304430;ENST00000339154;ENST00000502270	T;T;T	0.29397	1.57;1.57;1.57	5.11	-3.64	0.04515	NUDIX hydrolase domain (3);NUDIX hydrolase domain-like (1);	0.356862	0.31312	N	0.007867	T	0.14960	0.0361	L	0.41124	1.26	0.38646	D	0.951723	B	0.31241	0.315	B	0.24006	0.05	T	0.43410	-0.9393	10	0.02654	T	1	-8.3014	10.6191	0.45470	0.2019:0.0:0.6699:0.1282	.	255	P53370	NUDT6_HUMAN	V	255;86;86	ENSP00000306070:A255V;ENSP00000344011:A86V;ENSP00000424117:A86V	ENSP00000306070:A255V	A	-	2	0	NUDT6	124033620	0.857000	0.29778	0.016000	0.15963	0.203000	0.24098	1.354000	0.34056	-0.254000	0.09500	-0.312000	0.09012	GCG	G|0.998;A|0.002	0.002	strong		0.433	NUDT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095331.3	NM_007083	
FGD3	89846	hgsc.bcm.edu	37	9	95766336	95766336	+	Silent	SNP	C	C	T	rs201073654		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95766336C>T	ENST00000375482.3	+	5	1093	c.597C>T	c.(595-597)ggC>ggT	p.G199G	FGD3_ENST00000337352.6_Silent_p.G199G|FGD3_ENST00000416701.2_Silent_p.G199G	NM_001083536.1	NP_001077005.1	Q5JSP0	FGD3_HUMAN	FYVE, RhoGEF and PH domain containing 3	199	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|urinary_tract(1)	17						TCATCATGGGCATATTCTCTA	0.582											OREG0019318	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G199G		Atlas-SNP	.											.	FGD3	116	.	0			c.C597T						PASS	.	C	,	1,4183		0,1,2091	77.0	81.0	80.0		597,597	-0.6	1.0	9		80	0,8488		0,0,4244	no	coding-synonymous,coding-synonymous	FGD3	NM_001083536.1,NM_033086.2	,	0,1,6335	TT,TC,CC		0.0,0.0239,0.0079	,	199/726,199/726	95766336	1,12671	2092	4244	6336	SO:0001819	synonymous_variant	89846	exon5			CATGGGCATATTC	AK000004	CCDS43849.1, CCDS69619.1	9q22	2013-01-10	2004-08-24		ENSG00000127084	ENSG00000127084		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	16027	protein-coding gene	gene with protein product			"""FGD1 family, member 3"""			11214971	Standard	NM_001083536		Approved	FLJ00004, ZFYVE5	uc004asz.2	Q5JSP0	OTTHUMG00000021032	ENST00000375482.3:c.597C>T	9.37:g.95766336C>T		99.0	0.0	0	1315	93.0	60.0	0.645161	NM_001083536	F8W7P2|Q4VX84|Q7Z7D9|Q8N5G1	Silent	SNP	ENST00000375482.3	37	CCDS43849.1																																																																																			C|1.000;T|0.000	0.000	strong		0.582	FGD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055493.1	NM_033086	
ERCC5	2073	hgsc.bcm.edu	37	13	103519119	103519119	+	Silent	SNP	G	G	A	rs73573973	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:103519119G>A	ENST00000355739.4	+	11	3880	c.2457G>A	c.(2455-2457)cgG>cgA	p.R819R	BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.A1245T|ERCC5_ENST00000375954.1_Silent_p.R52R	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	819	I-domain.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|response to UV (GO:0009411)|response to UV-C (GO:0010225)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	51	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					TTGGAGCGCGGCATGTCTATA	0.423			"""Mis, N, F"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				G|||	35	0.00698882	0.0257	0.0014	5008	,	,		18124	0.0		0.0	False		,,,				2504	0.0				p.R1273R		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (G)	13	13q33	2073	"""excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))"""		E	ERCC5,NS,carcinoma,+2,1	.	.	1	0			c.G3819A						PASS	.	G	,	91,4315	75.2+/-113.4	2,87,2114	57.0	58.0	58.0		2457,3819	3.1	1.0	13	dbSNP_130	58	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ERCC5,BIVM-ERCC5	NM_000123.3,NM_001204425.1	,	2,87,6414	AA,AG,GG		0.0,2.0654,0.6997	,	819/1187,1273/1641	103519119	91,12915	2203	4300	6503	SO:0001819	synonymous_variant	0	exon19	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	AGCGCGGCATGTC	X71342	CCDS32004.1	13q22-q34	2014-09-17	2014-03-07		ENSG00000134899	ENSG00000134899			3437	protein-coding gene	gene with protein product	"""Cockayne syndrome"""	133530	"""xeroderma pigmentosum, complementation group G"", ""excision repair cross-complementing rodent repair deficiency, complementation group 5"""	ERCM2, XPGC		8088806	Standard	NM_000123		Approved			P28715	OTTHUMG00000017310	ENST00000355739.4:c.2457G>A	13.37:g.103519119G>A		48.0	0.0	0		74.0	35.0	0.472973	NM_001204425	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Silent	SNP	ENST00000355739.4	37	CCDS32004.1																																																																																			G|0.994;A|0.006	0.006	strong		0.423	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1		
PLEKHS1	79949	hgsc.bcm.edu	37	10	115531790	115531790	+	Missense_Mutation	SNP	C	C	T	rs143039412		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:115531790C>T	ENST00000369310.3	+	7	1158	c.596C>T	c.(595-597)gCc>gTc	p.A199V	PLEKHS1_ENST00000361048.1_Missense_Mutation_p.A205V|PLEKHS1_ENST00000369312.4_Missense_Mutation_p.A117V|PLEKHS1_ENST00000369309.1_Missense_Mutation_p.A19V|PLEKHS1_ENST00000354462.3_5'UTR	NM_182601.1	NP_872407.1	Q5SXH7	PKHS1_HUMAN	pleckstrin homology domain containing, family S member 1	199																	TTATCAGAAGCCACTCAAGAT	0.353													C|||	1	0.000199681	0.0008	0.0	5008	,	,		21165	0.0		0.0	False		,,,				2504	0.0				p.A205V		Atlas-SNP	.											.	PLEKHS1	19	.	0			c.C614T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	3,4403	4.2+/-10.8	0,3,2200	147.0	137.0	140.0		350,350,614,596	2.6	0.0	10	dbSNP_134	140	0,8600		0,0,4300	no	missense,missense,missense,missense	C10orf81	NM_001193434.1,NM_001193435.1,NM_024889.4,NM_182601.1	64,64,64,64	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	benign,benign,benign,benign	117/367,117/367,205/364,199/466	115531790	3,13003	2203	4300	6503	SO:0001583	missense	79949	exon8			CAGAAGCCACTCA	AK027190	CCDS7583.1, CCDS53580.1, CCDS53581.1	10q26.11	2013-01-11	2012-05-31	2012-05-31	ENSG00000148735	ENSG00000148735		"""Pleckstrin homology (PH) domain containing"""	26285	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 81"""	C10orf81		12477932	Standard	NM_024889		Approved	FLJ23537, bA211N11.2	uc001lat.2	Q5SXH7	OTTHUMG00000019074	ENST00000369310.3:c.596C>T	10.37:g.115531790C>T	ENSP00000358316:p.Ala199Val	141.0	0.0	0		126.0	56.0	0.444444	NM_024889	A8KA02|B3KX00|B6EDE1|Q5SXH8|Q5SXI0|Q6ZQR5|Q8NE42|Q9H5D9	Missense_Mutation	SNP	ENST00000369310.3	37	CCDS53580.1	.	.	.	.	.	.	.	.	.	.	C	12.12	1.843362	0.32606	6.81E-4	0.0	ENSG00000148735	ENST00000361048;ENST00000369312;ENST00000369310;ENST00000369309	T;T;T;T	0.30448	1.53;1.53;1.53;1.53	5.63	2.59	0.31030	.	1.116260	0.06460	N	0.729232	T	0.13970	0.0338	N	0.08118	0	0.09310	N	1	B;B;B;B	0.31077	0.307;0.009;0.049;0.043	B;B;B;B	0.23419	0.046;0.005;0.019;0.03	T	0.17198	-1.0377	10	0.36615	T	0.2	-21.7194	3.245	0.06794	0.1867:0.5589:0.1595:0.095	.	199;199;199;205	Q5SXH7;Q5SXH7-5;Q5SXH7-2;Q5SXH7-4	CJ081_HUMAN;.;.;.	V	205;117;199;19	ENSP00000354332:A205V;ENSP00000358318:A117V;ENSP00000358316:A199V;ENSP00000358315:A19V	ENSP00000354332:A205V	A	+	2	0	C10orf81	115521780	0.002000	0.14202	0.002000	0.10522	0.072000	0.16883	0.513000	0.22770	1.390000	0.46547	0.650000	0.86243	GCC	C|1.000;T|0.000	0.000	weak		0.353	PLEKHS1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050432.1	NM_024889	
ASL	435	hgsc.bcm.edu	37	7	65551782	65551782	+	Silent	SNP	G	G	A	rs115468878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:65551782G>A	ENST00000304874.9	+	8	678	c.576G>A	c.(574-576)aaG>aaA	p.K192K	ASL_ENST00000380839.4_Intron|AC068533.7_ENST00000450043.1_5'Flank|ASL_ENST00000395332.3_Silent_p.K192K|ASL_ENST00000395331.3_Silent_p.K192K	NM_000048.3	NP_000039.2	P04424	ARLY_HUMAN	argininosuccinate lyase	192					arginine biosynthetic process via ornithine (GO:0042450)|arginine catabolic process (GO:0006527)|cellular nitrogen compound metabolic process (GO:0034641)|internal protein amino acid acetylation (GO:0006475)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	argininosuccinate lyase activity (GO:0004056)			breast(3)|endometrium(3)|large_intestine(2)|lung(9)|upper_aerodigestive_tract(1)	18					L-Arginine(DB00125)	AGGTGCGGAAGCGGATCAATG	0.687													g|||	29	0.00579073	0.0212	0.0014	5008	,	,		17651	0.0		0.0	False		,,,				2504	0.0				p.K192K		Atlas-SNP	.											.	ASL	39	.	0			c.G576A						PASS	.	A	,,,	95,4307		1,93,2107	27.0	28.0	28.0		576,576,576,	1.8	1.0	7	dbSNP_132	28	0,8584		0,0,4292	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	ASL	NM_000048.3,NM_001024943.1,NM_001024944.1,NM_001024946.1	,,,	1,93,6399	AA,AG,GG		0.0,2.1581,0.7316	,,,	192/465,192/465,192/445,	65551782	95,12891	2201	4292	6493	SO:0001819	synonymous_variant	435	exon8			GCGGAAGCGGATC		CCDS5531.1, CCDS47597.1, CCDS47598.1	7q11.21	2012-10-02			ENSG00000126522	ENSG00000126522	4.3.2.1		746	protein-coding gene	gene with protein product		608310					Standard	NM_001024943		Approved		uc003tuo.3	P04424	OTTHUMG00000022876	ENST00000304874.9:c.576G>A	7.37:g.65551782G>A		90.0	0.0	0		74.0	35.0	0.472973	NM_000048	E7EMI0|E9PE48|Q6LDS5|Q96HS2	Silent	SNP	ENST00000304874.9	37	CCDS5531.1																																																																																			G|0.993;A|0.007	0.007	strong		0.687	ASL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251695.2	NM_000048	
PCLO	27445	hgsc.bcm.edu	37	7	82585803	82585803	+	Missense_Mutation	SNP	G	G	C	rs114445550	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:82585803G>C	ENST00000333891.9	-	5	4803	c.4466C>G	c.(4465-4467)tCc>tGc	p.S1489C	PCLO_ENST00000423517.2_Missense_Mutation_p.S1489C	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						GTCCTTGCTGGAAGGAATATC	0.358													G|||	19	0.00379393	0.0144	0.0	5008	,	,		21243	0.0		0.0	False		,,,				2504	0.0				p.S1489C		Atlas-SNP	.											.	PCLO	1506	.	0			c.C4466G						PASS	.	G	CYS/SER,CYS/SER	50,3644		0,50,1797	112.0	103.0	106.0		4466,4466	3.6	0.0	7	dbSNP_132	106	0,8172		0,0,4086	yes	missense,missense	PCLO	NM_014510.2,NM_033026.5	112,112	0,50,5883	CC,CG,GG		0.0,1.3535,0.4214	possibly-damaging,possibly-damaging	1489/4936,1489/5143	82585803	50,11816	1847	4086	5933	SO:0001583	missense	27445	exon5			TTGCTGGAAGGAA	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.4466C>G	7.37:g.82585803G>C	ENSP00000334319:p.Ser1489Cys	120.0	0.0	0		139.0	71.0	0.510791	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	0.586	-0.834971	0.02713	0.013535	0.0	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.17370	2.28;2.28	5.43	3.57	0.40892	.	.	.	.	.	T	0.17408	0.0418	L	0.47716	1.5	0.09310	N	0.999996	P;P	0.49253	0.921;0.921	P;P	0.50378	0.518;0.639	T	0.04041	-1.0982	9	0.87932	D	0	.	10.4646	0.44600	0.0726:0.1355:0.7919:0.0	.	1489;1489	Q9Y6V0-5;Q9Y6V0-6	.;.	C	1420;1489;1489	ENSP00000334319:S1489C;ENSP00000388393:S1489C	ENSP00000334319:S1489C	S	-	2	0	PCLO	82423739	0.976000	0.34144	0.012000	0.15200	0.080000	0.17528	3.139000	0.50577	1.265000	0.44215	0.650000	0.86243	TCC	G|0.997;C|0.003	0.003	strong		0.358	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
JAG2	3714	hgsc.bcm.edu	37	14	105622157	105622157	+	Silent	SNP	G	G	A	rs61750261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105622157G>A	ENST00000331782.3	-	4	1048	c.645C>T	c.(643-645)aaC>aaT	p.N215N	JAG2_ENST00000347004.2_Silent_p.N215N|RP11-44N21.4_ENST00000548203.1_RNA	NM_002226.4	NP_002217.3	Q9Y219	JAG2_HUMAN	jagged 2	215	DSL. {ECO:0000255|PROSITE- ProRule:PRU00377}.				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)			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)		CGAAAAAGTCGTTGCGGGGCC	0.637													G|||	147	0.029353	0.1074	0.0072	5008	,	,		16759	0.0		0.0	False		,,,				2504	0.0				p.N215N		Atlas-SNP	.											.	JAG2	69	.	0			c.C645T						PASS	.	G	,	361,4031	179.7+/-208.2	15,331,1850	85.0	62.0	70.0		645,645	-3.3	1.0	14	dbSNP_129	70	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous,coding-synonymous	JAG2	NM_002226.3,NM_145159.1	,	15,332,6146	AA,AG,GG		0.0116,8.2195,2.7876	,	215/1239,215/1201	105622157	362,12624	2196	4297	6493	SO:0001819	synonymous_variant	3714	exon4			AAAGTCGTTGCGG	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.645C>T	14.37:g.105622157G>A		161.0	0.0	0		153.0	68.0	0.444444	NM_145159	Q9UE17|Q9UE99|Q9UNK8|Q9Y6P9|Q9Y6Q0	Silent	SNP	ENST00000331782.3	37	CCDS9998.1																																																																																			G|0.974;A|0.026	0.026	strong		0.637	JAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276506.2		
PCDHA9	9752	hgsc.bcm.edu	37	5	140229925	140229925	+	Silent	SNP	G	G	C	rs58792000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140229925G>C	ENST00000532602.1	+	1	2878	c.1845G>C	c.(1843-1845)acG>acC	p.T615T	PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA9_ENST00000378122.3_Silent_p.T615T|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	615	Cadherin 6. {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(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGCCAGAAACGGCCAGCGCGA	0.687													.|||	325	0.0648962	0.2315	0.0187	5008	,	,		16120	0.0		0.006	False		,,,				2504	0.0				p.T615T	Melanoma(55;1800 1972 14909)	Atlas-SNP	.											.	PCDHA9	373	.	0			c.G1845C						PASS	.	G	,,,,,,,,,,,	892,3500		144,604,1448	61.0	66.0	64.0		1845,,,,,,,,,,,1845	2.4	0.0	5	dbSNP_129	64	19,8521		1,17,4252	no	coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_014005.3,NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1	,,,,,,,,,,,	145,621,5700	CC,CG,GG		0.2225,20.3097,7.0445	,,,,,,,,,,,	615/843,,,,,,,,,,,615/951	140229925	911,12021	2196	4270	6466	SO:0001819	synonymous_variant	9752	exon1			AGAAACGGCCAGC	AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"""Cadherins / Protocadherins : Clustered"""	8675	other	complex locus constituent	"""KIAA0345-like 5"""	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.1845G>C	5.37:g.140229925G>C		220.0	0.0	0		211.0	111.0	0.526066	NM_031857	O15053|Q2M3S5	Silent	SNP	ENST00000532602.1	37	CCDS54920.1																																																																																			G|0.937;C|0.063	0.063	strong		0.687	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857	
BPIFA2	140683	hgsc.bcm.edu	37	20	31756954	31756954	+	Start_Codon_SNP	SNP	G	G	A	rs17124277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31756954G>A	ENST00000253362.2	+	2	149	c.3G>A	c.(1-3)atG>atA	p.M1I	BPIFA2_ENST00000354932.5_Start_Codon_SNP_p.M1I			Q96DR5	BPIA2_HUMAN	BPI fold containing family A, member 2	1						extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)										GACAAAAGATGCTTCAGCTTT	0.473													G|||	140	0.0279553	0.0991	0.0058	5008	,	,		20080	0.0		0.005	False		,,,				2504	0.0				p.M1I		Atlas-SNP	.											.	.	.	.	0			c.G3A						PASS	.	G	ILE/MET	400,4006	199.1+/-222.7	14,372,1817	149.0	134.0	139.0		3	4.2	1.0	20	dbSNP_123	139	17,8583	12.6+/-44.7	0,17,4283	yes	missense	BPIFA2	NM_080574.2	10	14,389,6100	AA,AG,GG		0.1977,9.0785,3.2062	probably-damaging	1/250	31756954	417,12589	2203	4300	6503	SO:0001582	initiator_codon_variant	140683	exon2			AAAGATGCTTCAG	AF432917	CCDS13214.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131050	ENSG00000131050		"""BPI fold containing"""	16203	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 70"""	C20orf70		11971875	Standard	NM_080574		Approved	bA49G10.1, SPLUNC2, PSP	uc002wyo.1	Q96DR5	OTTHUMG00000032244	ENST00000253362.2:c.3G>A	20.37:g.31756954G>A	ENSP00000253362:p.Met1Ile	141.0	0.0	0		116.0	47.0	0.405172	NM_080574	Q9BQQ0	Missense_Mutation	SNP	ENST00000253362.2	37	CCDS13214.1	59	0.027014652014652016	52	0.10569105691056911	3	0.008287292817679558	0	0.0	4	0.005277044854881266	G	18.40	3.615032	0.66672	0.090785	0.001977	ENSG00000131050	ENST00000253362;ENST00000354932	T;T	0.33654	1.4;1.4	4.22	4.22	0.49857	.	0.093315	0.47455	D	0.000230	T	0.01905	0.0060	.	.	.	0.09310	P	0.9999999999804186	D	0.89917	1.0	D	0.80764	0.994	T	0.35001	-0.9806	8	0.87932	D	0	-13.9353	12.3777	0.55289	0.0:0.0:1.0:0.0	rs17124277;rs52823533;rs17124277	1	Q96DR5	BPIA2_HUMAN	I	1	ENSP00000253362:M1I;ENSP00000347012:M1I	ENSP00000253362:M1I	M	+	3	0	BPIFA2	31220615	1.000000	0.71417	0.998000	0.56505	0.876000	0.50452	3.596000	0.54024	2.633000	0.89246	0.591000	0.81541	ATG	G|0.963;A|0.037	0.037	strong		0.473	BPIFA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257117.1	NM_080574	Missense_Mutation
MVP	9961	hgsc.bcm.edu	37	16	29841950	29841950	+	Missense_Mutation	SNP	G	G	A	rs142997389	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:29841950G>A	ENST00000357402.5	+	2	218	c.80G>A	c.(79-81)cGt>cAt	p.R27H	MVP_ENST00000566554.1_3'UTR|MVP_ENST00000452209.2_Missense_Mutation_p.V11M|MVP_ENST00000395353.1_Missense_Mutation_p.R27H	NM_005115.4|NM_017458.3	NP_005106.2|NP_059447.2	Q14764	MVP_HUMAN	major vault protein	27					cell proliferation (GO:0008283)|ERBB signaling pathway (GO:0038127)|mRNA transport (GO:0051028)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of protein tyrosine kinase activity (GO:0061099)|negative regulation of signaling (GO:0023057)|protein activation cascade (GO:0072376)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(7)|ovary(2)|skin(3)|soft_tissue(1)|stomach(1)	27						AACGTGTCCCGTGTGGAGGTC	0.597													G|||	40	0.00798722	0.0287	0.0029	5008	,	,		15564	0.0		0.0	False		,,,				2504	0.0				p.R27H		Atlas-SNP	.											.	MVP	80	.	0			c.G80A						PASS	.	G	HIS/ARG,HIS/ARG	112,4282	88.2+/-126.9	0,112,2085	135.0	97.0	110.0		80,80	0.5	0.2	16	dbSNP_134	110	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	MVP	NM_005115.4,NM_017458.3	29,29	0,114,6383	AA,AG,GG		0.0233,2.5489,0.8773	benign,benign	27/894,27/894	29841950	114,12880	2197	4300	6497	SO:0001583	missense	9961	exon2			TGTCCCGTGTGGA	X79882	CCDS10656.1	16p11.2	2012-04-25			ENSG00000013364	ENSG00000013364			7531	protein-coding gene	gene with protein product	"""lung resistance-related protein"""	605088				7585126	Standard	NM_005115		Approved	LRP, VAULT1	uc002dui.3	Q14764	OTTHUMG00000048227	ENST00000357402.5:c.80G>A	16.37:g.29841950G>A	ENSP00000349977:p.Arg27His	132.0	0.0	0		123.0	52.0	0.422764	NM_017458	Q96BG4|Q9BPW6|Q9BQT1|Q9UBD1	Missense_Mutation	SNP	ENST00000357402.5	37	CCDS10656.1	12|12	0.005494505494505495|0.005494505494505495	12|12	0.024390243902439025|0.024390243902439025	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	14.62|14.62	2.588764|2.588764	0.46110|0.46110	0.025489|0.025489	2.33E-4|2.33E-4	ENSG00000013364|ENSG00000013364	ENST00000357402;ENST00000395353|ENST00000452209	T;T|.	0.33865|.	1.39;1.39|.	5.82|5.82	0.469|0.469	0.16741|0.16741	.|.	0.109460|.	0.64402|.	N|.	0.000005|.	T|T	0.35998|0.35998	0.0951|0.0951	M|M	0.85197|0.85197	2.74|2.74	0.21675|0.21675	N|N	0.999591|0.999591	B|.	0.28400|.	0.21|.	B|.	0.27500|.	0.08|.	T|T	0.47509|0.47509	-0.9112|-0.9112	10|6	0.48119|0.87932	T|D	0.1|0	-4.9453|-4.9453	9.041|9.041	0.36319|0.36319	0.3672:0.0:0.6328:0.0|0.3672:0.0:0.6328:0.0	.|.	27|.	Q14764|.	MVP_HUMAN|.	H|M	27|11	ENSP00000349977:R27H;ENSP00000378760:R27H|.	ENSP00000349977:R27H|ENSP00000387916:V11M	R|V	+|+	2|1	0|0	MVP|MVP	29749451|29749451	0.915000|0.915000	0.31059|0.31059	0.191000|0.191000	0.23289|0.23289	0.606000|0.606000	0.37113|0.37113	1.270000|1.270000	0.33086|0.33086	0.110000|0.110000	0.17919|0.17919	-0.224000|-0.224000	0.12420|0.12420	CGT|GTG	G|0.991;A|0.009	0.009	strong		0.597	MVP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109711.3	NM_005115	
CEP350	9857	hgsc.bcm.edu	37	1	179983153	179983153	+	Missense_Mutation	SNP	A	A	G	rs111349041	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:179983153A>G	ENST00000367607.3	+	10	1983	c.1565A>G	c.(1564-1566)gAc>gGc	p.D522G		NM_014810.4	NP_055625.4	Q5VT06	CE350_HUMAN	centrosomal protein 350kDa	522					microtubule anchoring (GO:0034453)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	66						TTAAATAAGGACTTTTTACCT	0.378													A|||	63	0.0125799	0.0461	0.0029	5008	,	,		19374	0.0		0.0	False		,,,				2504	0.0				p.D522G		Atlas-SNP	.											.	CEP350	418	.	0			c.A1565G						PASS	.	A	GLY/ASP	160,4246	106.0+/-144.5	4,152,2047	43.0	43.0	43.0		1565	5.6	1.0	1	dbSNP_132	43	2,8598	1.2+/-3.3	0,2,4298	yes	missense	CEP350	NM_014810.4	94	4,154,6345	GG,GA,AA		0.0233,3.6314,1.2456	possibly-damaging	522/3118	179983153	162,12844	2203	4300	6503	SO:0001583	missense	9857	exon10			ATAAGGACTTTTT	AF287356	CCDS1336.1	1q25.2	2014-02-20			ENSG00000135837	ENSG00000135837			24238	protein-coding gene	gene with protein product	"""centrosome associated protein 350"""					16314388, 15615782	Standard	NM_014810		Approved	KIAA0480, CAP350	uc001gnt.3	Q5VT06	OTTHUMG00000035269	ENST00000367607.3:c.1565A>G	1.37:g.179983153A>G	ENSP00000356579:p.Asp522Gly	75.0	0.0	0		75.0	46.0	0.613333	NM_014810	O75068|Q8TDK3|Q8WY20	Missense_Mutation	SNP	ENST00000367607.3	37	CCDS1336.1	23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	A	19.07	3.755539	0.69648	0.036314	2.33E-4	ENSG00000135837	ENST00000367607	D	0.89485	-2.52	5.6	5.6	0.85130	.	0.122043	0.36555	N	0.002523	T	0.73345	0.3575	M	0.65975	2.015	0.46901	D	0.999242	P;P	0.49635	0.78;0.926	B;P	0.47673	0.265;0.554	T	0.81703	-0.0812	9	.	.	.	.	15.7476	0.77958	1.0:0.0:0.0:0.0	.	522;522	E7EU22;Q5VT06	.;CE350_HUMAN	G	522	ENSP00000356579:D522G	.	D	+	2	0	CEP350	178249776	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.597000	0.74118	2.251000	0.74343	0.528000	0.53228	GAC	A|0.986;G|0.014	0.014	strong		0.378	CEP350-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085315.2	NM_014810	
STAU2	27067	hgsc.bcm.edu	37	8	74526081	74526081	+	Silent	SNP	G	G	A	rs28728027	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:74526081G>A	ENST00000521451.1	-	4	505	c.129C>T	c.(127-129)cgC>cgT	p.R43R	STAU2_ENST00000522509.1_Silent_p.R231R|STAU2_ENST00000521727.1_Silent_p.R243R|STAU2_ENST00000517542.1_Silent_p.R225R|STAU2_ENST00000522695.1_Silent_p.R231R|STAU2_ENST00000521210.1_Silent_p.R159R|STAU2_ENST00000519961.1_Silent_p.R263R|STAU2_ENST00000524300.1_Silent_p.R263R|STAU2_ENST00000523558.1_Silent_p.R91R|STAU2_ENST00000355780.5_Silent_p.R231R			Q9NUL3	STAU2_HUMAN	staufen double-stranded RNA binding protein 2	263	DRBM 1. {ECO:0000255|PROSITE- ProRule:PRU00266}.				transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|liver(1)|lung(6)|ovary(1)	19	Breast(64;0.0138)		Epithelial(68;0.026)|BRCA - Breast invasive adenocarcinoma(89;0.0483)|all cancers(69;0.0972)			TGGTCGCAGCGCGCTTCTTGG	0.418													G|||	28	0.00559105	0.0189	0.0043	5008	,	,		15334	0.0		0.0	False		,,,				2504	0.0				p.R263R		Atlas-SNP	.											STAU2_ENST00000524300,NS,carcinoma,-1,3	STAU2	148	3	0			c.C789T						PASS	.	G	,,,,,,	79,4327	68.1+/-105.8	1,77,2125	88.0	83.0	85.0		789,693,477,273,693,675,693	-11.9	0.3	8	dbSNP_125	85	3,8597	2.2+/-6.3	0,3,4297	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	STAU2	NM_001164380.1,NM_001164381.1,NM_001164382.1,NM_001164383.1,NM_001164384.1,NM_001164385.1,NM_014393.2	,,,,,,	1,80,6422	AA,AG,GG		0.0349,1.793,0.6305	,,,,,,	263/571,231/539,159/505,91/399,231/480,225/474,231/480	74526081	82,12924	2203	4300	6503	SO:0001819	synonymous_variant	27067	exon9			CGCAGCGCGCTTC	Y19062	CCDS6214.1, CCDS55244.1, CCDS55245.1, CCDS55246.1, CCDS55247.1, CCDS55248.1	8q21.11	2013-06-05	2013-06-05		ENSG00000040341	ENSG00000040341			11371	protein-coding gene	gene with protein product		605920	"""staufen (Drosophila, RNA-binding protein) homolog 2"", ""staufen, RNA binding protein, homolog 2 (Drosophila)"""			10585778	Standard	NM_014393		Approved	39K2	uc003xzm.3	Q9NUL3	OTTHUMG00000164499	ENST00000521451.1:c.129C>T	8.37:g.74526081G>A		79.0	0.0	0		56.0	26.0	0.464286	NM_001164380	B7Z1I6|B7Z292|B7Z8B4|E7ER74|E9PEI3|E9PF26|E9PF50|Q6AHY7|Q96HM0|Q96HM1|Q9NVI5|Q9UGG6	Silent	SNP	ENST00000521451.1	37																																																																																				G|0.995;A|0.005	0.005	strong		0.418	STAU2-006	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000379006.4	NM_001164380	
ROR1	4919	hgsc.bcm.edu	37	1	64643650	64643650	+	Silent	SNP	C	C	T	rs35586842	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:64643650C>T	ENST00000371079.1	+	9	2301	c.1926C>T	c.(1924-1926)tcC>tcT	p.S642S	ROR1_ENST00000545203.1_Silent_p.S93S	NM_005012.3	NP_005003.2	Q01973	ROR1_HUMAN	receptor tyrosine kinase-like orphan receptor 1	642	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				peptidyl-tyrosine phosphorylation (GO:0018108)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|Wnt-protein binding (GO:0017147)			breast(7)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(10)|ovary(6)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	51						AAATTTACTCCGCTGATTACT	0.448													C|||	122	0.024361	0.0885	0.0058	5008	,	,		18919	0.0		0.001	False		,,,				2504	0.0				p.S642S		Atlas-SNP	.											.	ROR1	113	.	0			c.C1926T						PASS	.	C		346,4060	177.3+/-206.3	12,322,1869	62.0	64.0	64.0		1926	-11.8	0.3	1	dbSNP_126	64	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	ROR1	NM_005012.2		12,326,6165	TT,TC,CC		0.0465,7.8529,2.6911		642/938	64643650	350,12656	2203	4300	6503	SO:0001819	synonymous_variant	4919	exon9			TTACTCCGCTGAT	M97675	CCDS626.1, CCDS41344.1	1p32-p31	2013-01-11			ENSG00000185483	ENSG00000185483		"""Immunoglobulin superfamily / I-set domain containing"""	10256	protein-coding gene	gene with protein product		602336		NTRKR1		1334494, 8875995	Standard	NM_001083592		Approved		uc001dbj.3	Q01973	OTTHUMG00000009022	ENST00000371079.1:c.1926C>T	1.37:g.64643650C>T		121.0	0.0	0		126.0	76.0	0.603175	NM_005012	Q5VVX6|Q66K77|Q92776	Silent	SNP	ENST00000371079.1	37	CCDS626.1																																																																																			C|0.972;T|0.028	0.028	strong		0.448	ROR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025002.1	NM_005012	
CLEC4F	165530	hgsc.bcm.edu	37	2	71044076	71044076	+	Missense_Mutation	SNP	T	T	C	rs61754946	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71044076T>C	ENST00000272367.2	-	4	513	c.437A>G	c.(436-438)aAt>aGt	p.N146S	CLEC4F_ENST00000426626.1_Missense_Mutation_p.N146S	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	146					endocytosis (GO:0006897)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			endometrium(1)|large_intestine(5)|lung(18)|ovary(5)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	37						GATGTCAGCATTGGTGTTTCC	0.473													C|||	95	0.0189696	0.0703	0.0029	5008	,	,		20407	0.0		0.0	False		,,,				2504	0.0				p.N146S	Colon(107;10 2157 6841 26035)	Atlas-SNP	.											.	CLEC4F	95	.	0			c.A437G						PASS	.	C	SER/ASN	282,4124	800.8+/-415.6	6,270,1927	142.0	120.0	127.0		437	-2.8	0.0	2	dbSNP_129	127	1,8599		0,1,4299	yes	missense	CLEC4F	NM_173535.2	46	6,271,6226	CC,CT,TT		0.0116,6.4004,2.1759	benign	146/590	71044076	283,12723	2203	4300	6503	SO:0001583	missense	165530	exon4			TCAGCATTGGTGT	AK096429	CCDS1910.1	2p13.3	2008-02-05	2005-02-09	2005-02-11	ENSG00000152672	ENSG00000152672		"""C-type lectin domain containing"""	25357	protein-coding gene	gene with protein product			"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 13"""	CLECSF13		8889548, 1846367	Standard	NM_001258027		Approved	FLJ39110, KCLR	uc002shf.3	Q8N1N0	OTTHUMG00000129713	ENST00000272367.2:c.437A>G	2.37:g.71044076T>C	ENSP00000272367:p.Asn146Ser	199.0	0.0	0		254.0	112.0	0.440945	NM_173535	A4QPA5	Missense_Mutation	SNP	ENST00000272367.2	37	CCDS1910.1	27	0.012362637362637362	27	0.054878048780487805	0	0.0	0	0.0	0	0.0	C	0.067	-1.210900	0.01555	0.064004	1.16E-4	ENSG00000152672	ENST00000272367;ENST00000426626	T;T	0.01854	4.6;4.63	5.15	-2.79	0.05841	.	0.560537	0.16319	N	0.219645	T	0.00109	0.0003	N	0.01352	-0.895	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.40346	-0.9568	10	0.02654	T	1	.	6.1052	0.20069	0.0:0.2149:0.2644:0.5207	.	146;146	B7ZMM1;Q8N1N0	.;CLC4F_HUMAN	S	146	ENSP00000272367:N146S;ENSP00000390581:N146S	ENSP00000272367:N146S	N	-	2	0	CLEC4F	70897584	0.066000	0.20996	0.001000	0.08648	0.003000	0.03518	0.005000	0.13129	-0.464000	0.06963	-1.201000	0.01664	AAT	T|0.979;C|0.021	0.021	strong		0.473	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535	
SSPO	23145	hgsc.bcm.edu	37	7	149489443	149489443	+	RNA	SNP	C	C	A	rs893603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149489443C>A	ENST00000378016.2	+	0	5596							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			TGTGTGGCCCCGGCAGTGCCC	0.697													C|||	202	0.0403355	0.1029	0.0144	5008	,	,		16052	0.004		0.003	False		,,,				2504	0.0501				p.R1866R		Atlas-SNP	.											.	.	.	.	0			c.C5596A						PASS	.	C		301,3865		12,277,1794	13.0	21.0	19.0		5600	-1.9	0.1	7	dbSNP_86	19	18,8382		0,18,4182	no	coding-notMod3	SSPO	NM_198455.2		12,295,5976	AA,AC,CC		0.2143,7.2252,2.5386			149489443	319,12247	2083	4200	6283			23145	exon37			TGGCCCCGGCAGT	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149489443C>A		81.0	0.0	0		112.0	37.0	0.330357	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				C|0.975;A|0.025	0.025	strong		0.697	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
ZNF76	7629	hgsc.bcm.edu	37	6	35263009	35263009	+	Missense_Mutation	SNP	C	C	T	rs73745177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:35263009C>T	ENST00000373953.3	+	14	1963	c.1697C>T	c.(1696-1698)tCg>tTg	p.S566L	ZNF76_ENST00000339411.5_Missense_Mutation_p.S511L|ZNF76_ENST00000440666.2_Missense_Mutation_p.S540L|DEF6_ENST00000542066.1_5'Flank|DEF6_ENST00000316637.5_5'Flank	NM_003427.3	NP_003418.2	P36508	ZNF76_HUMAN	zinc finger protein 76	566					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)	16						ACAACAGTGTCGGAGAGTGGC	0.627													C|||	27	0.00539137	0.0151	0.0086	5008	,	,		19071	0.0		0.0	False		,,,				2504	0.001				p.S566L	Esophageal Squamous(52;92 1039 20612 23956 34676)	Atlas-SNP	.											.	ZNF76	37	.	0			c.C1697T						PASS	.	C	LEU/SER	71,4333	62.9+/-100.1	0,71,2131	58.0	45.0	49.0		1697	5.9	0.3	6	dbSNP_130	49	4,8596	2.2+/-6.3	0,4,4296	yes	missense	ZNF76	NM_003427.3	145	0,75,6427	TT,TC,CC		0.0465,1.6122,0.5767	benign	566/571	35263009	75,12929	2202	4300	6502	SO:0001583	missense	7629	exon14			CAGTGTCGGAGAG	M91592	CCDS4801.1, CCDS75435.1	6p21.31	2013-01-08	2011-02-25		ENSG00000065029	ENSG00000065029		"""Zinc fingers, C2H2-type"""	13149	protein-coding gene	gene with protein product		194549	"""zinc finger protein 76 (expressed in testis)"""	D6S229E		1427894	Standard	XM_005249364		Approved	Zfp523, ZNF523	uc003oki.1	P36508	OTTHUMG00000014564	ENST00000373953.3:c.1697C>T	6.37:g.35263009C>T	ENSP00000363064:p.Ser566Leu	52.0	0.0	0		40.0	18.0	0.45	NM_003427	Q9BQB2	Missense_Mutation	SNP	ENST00000373953.3	37	CCDS4801.1	9	0.004120879120879121	6	0.012195121951219513	3	0.008287292817679558	0	0.0	0	0.0	C	16.72	3.202287	0.58234	0.016122	4.65E-4	ENSG00000065029	ENST00000373953;ENST00000440666;ENST00000339411	T;T;T	0.10005	2.95;2.95;2.92	5.91	5.91	0.95273	.	0.306088	0.18150	N	0.150126	T	0.04137	0.0115	N	0.22421	0.69	0.09310	N	1	B;B	0.23806	0.046;0.091	B;B	0.12837	0.008;0.007	T	0.24225	-1.0166	10	0.72032	D	0.01	.	17.0178	0.86424	0.0:1.0:0.0:0.0	.	511;566	P36508-2;P36508	.;ZNF76_HUMAN	L	566;540;511	ENSP00000363064:S566L;ENSP00000392243:S540L;ENSP00000344097:S511L	ENSP00000344097:S511L	S	+	2	0	ZNF76	35370987	0.090000	0.21635	0.330000	0.25442	0.994000	0.84299	2.471000	0.45127	2.793000	0.96121	0.655000	0.94253	TCG	C|0.994;T|0.006	0.006	strong		0.627	ZNF76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040279.2	NM_003427	
NPNT	255743	hgsc.bcm.edu	37	4	106819089	106819089	+	Silent	SNP	C	C	T	rs147630398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:106819089C>T	ENST00000379987.2	+	2	319	c.103C>T	c.(103-105)Cta>Tta	p.L35L	NPNT_ENST00000514622.1_Silent_p.L35L|NPNT_ENST00000427316.2_Silent_p.L35L|NPNT_ENST00000305572.8_Silent_p.L35L|NPNT_ENST00000453617.2_Silent_p.L35L|NPNT_ENST00000506666.1_Silent_p.L35L	NM_001033047.2	NP_001028219.1	Q6UXI9	NPNT_HUMAN	nephronectin	35					branching involved in ureteric bud morphogenesis (GO:0001658)|cell-cell adhesion mediated by integrin (GO:0033631)|cell-matrix adhesion (GO:0007160)|cellular response to tumor necrosis factor (GO:0071356)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|pilomotor reflex (GO:0097195)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription from RNA polymerase II promoter involved in smooth muscle cell differentiation (GO:2000721)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|ureteric bud development (GO:0001657)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integrin alpha8-beta1 complex (GO:0034678)|proteinaceous extracellular matrix (GO:0005578)|smooth muscle contractile fiber (GO:0030485)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)			kidney(5)|large_intestine(2)|lung(10)|prostate(2)|skin(1)|urinary_tract(1)	21		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.41e-07)		ATCGATTGGCCTATGTCGTTA	0.468													C|||	7	0.00139776	0.0	0.0029	5008	,	,		18023	0.0		0.002	False		,,,				2504	0.0031				p.L35L		Atlas-SNP	.											.	NPNT	69	.	0			c.C103T						PASS	.	C	,,,,	2,4404	4.2+/-10.8	0,2,2201	135.0	123.0	127.0		103,103,103,103,103	5.8	1.0	4	dbSNP_134	127	13,8587	9.8+/-36.6	0,13,4287	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NPNT	NM_001033047.2,NM_001184690.1,NM_001184691.1,NM_001184692.1,NM_001184693.1	,,,,	0,15,6488	TT,TC,CC		0.1512,0.0454,0.1153	,,,,	35/566,35/583,35/596,35/537,35/567	106819089	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	255743	exon2			ATTGGCCTATGTC		CCDS34046.1, CCDS54784.1, CCDS54785.1, CCDS54786.1, CCDS54787.1	4q25	2005-10-07							27405	protein-coding gene	gene with protein product		610306				15754038	Standard	NM_001033047		Approved	EGFL6L, POEM	uc011cfd.2	Q6UXI9		ENST00000379987.2:c.103C>T	4.37:g.106819089C>T		191.0	0.0	0		205.0	113.0	0.55122	NM_001184692	A6NFT9|A8K1W4|B4DIT4|B4DYK3|B4E2H7|B4E3H2|D6RCA1|E9PCK8|E9PCQ1|E9PE64|E9PF04	Silent	SNP	ENST00000379987.2	37	CCDS34046.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	C	6.225	0.409722	0.11812	4.54E-4	0.001512	ENSG00000168743	ENST00000514837	.	.	.	5.81	5.81	0.92471	.	.	.	.	.	T	0.57592	0.2064	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.59700	-0.7405	4	.	.	.	.	12.8916	0.58073	0.0:0.9222:0.0:0.0778	.	.	.	.	L	11	.	.	P	+	2	0	NPNT	107038538	1.000000	0.71417	1.000000	0.80357	0.488000	0.33401	1.277000	0.33167	2.746000	0.94184	0.655000	0.94253	CCT	C|0.999;T|0.001	0.001	strong		0.468	NPNT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364083.1	NM_198278	
DTX2	113878	hgsc.bcm.edu	37	7	76109877	76109877	+	Silent	SNP	G	G	A	rs149301449	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:76109877G>A	ENST00000324432.5	+	4	561	c.51G>A	c.(49-51)gcG>gcA	p.A17A	DTX2_ENST00000446600.1_Intron|DTX2_ENST00000446820.2_Silent_p.A17A|DTX2_ENST00000472426.1_3'UTR|AC007078.4_ENST00000479299.2_RNA|DTX2_ENST00000430490.2_Silent_p.A17A|DTX2_ENST00000307569.8_Silent_p.A17A|DTX2_ENST00000413936.2_Silent_p.A17A	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	17	WWE 1. {ECO:0000255|PROSITE- ProRule:PRU00248}.				Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(1)|skin(1)|stomach(2)	27						CCAGCCCCGCGGCTGTGGCCG	0.642													.|||	15	0.00299521	0.0083	0.0014	5008	,	,		18307	0.003		0.0	False		,,,				2504	0.0				p.A17A		Atlas-SNP	.											.	DTX2	64	.	0			c.G51A						PASS	.	G	,,,	16,4390		0,16,2187	28.0	29.0	29.0		51,51,51,51	4.2	1.0	7	dbSNP_134	29	0,8592		0,0,4296	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DTX2	NM_001102594.1,NM_001102595.1,NM_001102596.1,NM_020892.2	,,,	0,16,6483	AA,AG,GG		0.0,0.3631,0.1231	,,,	17/623,17/623,17/576,17/623	76109877	16,12982	2203	4296	6499	SO:0001819	synonymous_variant	113878	exon1			CCCCGCGGCTGTG		CCDS5587.1, CCDS43605.1	7q11.23	2014-01-28	2014-01-28		ENSG00000091073	ENSG00000091073		"""RING-type (C3HC4) zinc fingers"""	15973	protein-coding gene	gene with protein product		613141	"""deltex (Drosophila) homolog 2"", ""deltex homolog 2 (Drosophila)"""			12670957	Standard	NM_020892		Approved	RNF58, KIAA1528	uc003ufh.4	Q86UW9	OTTHUMG00000162594	ENST00000324432.5:c.51G>A	7.37:g.76109877G>A		214.0	0.0	0		238.0	135.0	0.567227	NM_001102596	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Silent	SNP	ENST00000324432.5	37	CCDS5587.1																																																																																			G|0.997;A|0.003	0.003	strong		0.642	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2		
AKNA	80709	hgsc.bcm.edu	37	9	117130838	117130838	+	Missense_Mutation	SNP	C	C	T	rs138188658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117130838C>T	ENST00000307564.4	-	5	1615	c.1454G>A	c.(1453-1455)aGc>aAc	p.S485N	AKNA_ENST00000374075.5_Missense_Mutation_p.S404N|AKNA_ENST00000374088.3_Missense_Mutation_p.S485N|AKNA_ENST00000312033.3_Missense_Mutation_p.S485N|AKNA_ENST00000223791.3_5'UTR	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	485					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						CGTGTGGATGCTGTGGTTGGG	0.652													C|||	18	0.00359425	0.0113	0.0029	5008	,	,		18213	0.0		0.001	False		,,,				2504	0.0				p.S485N		Atlas-SNP	.											.	AKNA	119	.	0			c.G1454A						PASS	.	C	ASN/SER	61,4345	56.8+/-93.2	0,61,2142	80.0	54.0	63.0		1454	4.0	0.6	9	dbSNP_134	63	0,8600		0,0,4300	yes	missense	AKNA	NM_030767.4	46	0,61,6442	TT,TC,CC		0.0,1.3845,0.469	probably-damaging	485/1440	117130838	61,12945	2203	4300	6503	SO:0001583	missense	80709	exon5			TGGATGCTGTGGT	AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.1454G>A	9.37:g.117130838C>T	ENSP00000303769:p.Ser485Asn	104.0	0.0	0		120.0	66.0	0.55	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	SNP	ENST00000307564.4	37	CCDS6805.1	5	0.0022893772893772895	3	0.006097560975609756	2	0.0055248618784530384	0	0.0	0	0.0	C	6.631	0.484937	0.12641	0.013845	0.0	ENSG00000106948	ENST00000307564;ENST00000394582;ENST00000374088;ENST00000374075;ENST00000312033	T;T;T;T	0.33654	2.63;2.63;2.63;1.4	4.87	3.97	0.46021	.	0.575422	0.18059	N	0.153006	T	0.23886	0.0578	L	0.56769	1.78	0.09310	N	0.999995	B;B	0.30937	0.079;0.301	B;B	0.27715	0.037;0.082	T	0.15780	-1.0425	10	0.41790	T	0.15	-10.4751	7.9366	0.29933	0.1595:0.755:0.0:0.0855	.	485;404	Q7Z591;Q7Z591-2	AKNA_HUMAN;.	N	485;326;485;404;485	ENSP00000303769:S485N;ENSP00000363201:S485N;ENSP00000363188:S404N;ENSP00000309222:S485N	ENSP00000303769:S485N	S	-	2	0	AKNA	116170659	0.924000	0.31332	0.604000	0.28916	0.007000	0.05969	0.647000	0.24812	1.279000	0.44446	-0.140000	0.14226	AGC	C|0.996;T|0.004	0.004	strong		0.652	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767	
CCDC37	348807	hgsc.bcm.edu	37	3	126137456	126137456	+	Silent	SNP	T	T	C	rs76764772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:126137456T>C	ENST00000352312.1	+	7	588	c.489T>C	c.(487-489)taT>taC	p.Y163Y	CCDC37_ENST00000505024.1_Silent_p.Y164Y|CCDC37_ENST00000393425.1_Silent_p.Y164Y	NM_182628.2	NP_872434.2	Q494V2	CCD37_HUMAN	coiled-coil domain containing 37	163										NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.166)		GCCCCCAGTATGCCCTGGATG	0.667													T|||	283	0.0565096	0.2057	0.0159	5008	,	,		14709	0.0		0.0	False		,,,				2504	0.0				p.Y163Y		Atlas-SNP	.											.	CCDC37	69	.	0			c.T489C						PASS	.	T		794,3608		80,634,1487	34.0	36.0	35.0		489	-6.4	0.0	3	dbSNP_131	35	10,8588		0,10,4289	no	coding-synonymous	CCDC37	NM_182628.2		80,644,5776	CC,CT,TT		0.1163,18.0373,6.1846		163/612	126137456	804,12196	2201	4299	6500	SO:0001819	synonymous_variant	348807	exon7			CCAGTATGCCCTG	AK097402	CCDS3037.1	3q21.2	2014-07-31			ENSG00000163885	ENSG00000163885			26842	protein-coding gene	gene with protein product						23569216	Standard	NM_182628		Approved	FLJ40083, MIA1	uc003eiu.1	Q494V2	OTTHUMG00000162691	ENST00000352312.1:c.489T>C	3.37:g.126137456T>C		67.0	0.0	0		66.0	29.0	0.439394	NM_182628	D3DNA8|Q494V1|Q494V4|Q8N838	Silent	SNP	ENST00000352312.1	37	CCDS3037.1																																																																																			T|0.941;C|0.059	0.059	strong		0.667	CCDC37-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000370099.4	NM_182628	
UHMK1	127933	hgsc.bcm.edu	37	1	162467927	162467927	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:162467927C>G	ENST00000489294.1	+	1	295	c.137C>G	c.(136-138)cCt>cGt	p.P46R	UHMK1_ENST00000538489.1_Missense_Mutation_p.P46R|UHMK1_ENST00000545294.1_Intron|UHMK1_ENST00000282169.8_3'UTR	NM_175866.4	NP_787062.1	Q8TAS1	UHMK1_HUMAN	U2AF homology motif (UHM) kinase 1	46	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.				cell cycle arrest (GO:0007050)|neuron projection development (GO:0031175)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of translational initiation (GO:0045948)|protein autophosphorylation (GO:0046777)|regulation of protein export from nucleus (GO:0046825)	axon (GO:0030424)|dendrite cytoplasm (GO:0032839)|neuronal ribonucleoprotein granule (GO:0071598)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|ribonucleoprotein complex binding (GO:0043021)|RNA binding (GO:0003723)|transferase activity (GO:0016740)			endometrium(1)|large_intestine(2)|lung(6)|prostate(2)	11	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			TGCGGCAACCCTGGCTCGCCC	0.697																																					p.P46R		Atlas-SNP	.											UHMK1_ENST00000489294,NS,carcinoma,0,2	UHMK1	65	2	0			c.C137G						PASS	.						11.0	14.0	13.0					1																	162467927		2186	4284	6470	SO:0001583	missense	127933	exon1			GCAACCCTGGCTC	BC026046	CCDS1239.1, CCDS53423.1, CCDS53424.1	1q23.1	2013-02-12			ENSG00000152332	ENSG00000152332		"""RNA binding motif (RRM) containing"""	19683	protein-coding gene	gene with protein product		608849				12093740, 12782393	Standard	NM_175866		Approved	KIS, Kist	uc001gcc.2	Q8TAS1	OTTHUMG00000031373	ENST00000489294.1:c.137C>G	1.37:g.162467927C>G	ENSP00000420270:p.Pro46Arg	115.0	0.0	0		122.0	57.0	0.467213	NM_175866	A8K8K4|G3V1M1|Q96C22	Missense_Mutation	SNP	ENST00000489294.1	37	CCDS1239.1	.	.	.	.	.	.	.	.	.	.	C	13.90	2.374293	0.42105	.	.	ENSG00000152332	ENST00000538489;ENST00000489294	T;T	0.19669	2.13;2.13	4.94	4.94	0.65067	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.064455	0.64402	D	0.000006	T	0.05044	0.0135	N	0.16166	0.38	.	.	.	P;B	0.35821	0.523;0.324	B;B	0.24541	0.054;0.053	T	0.23332	-1.0191	9	0.39692	T	0.17	-9.9211	13.8569	0.63534	0.0:1.0:0.0:0.0	.	46;46	Q8TAS1-2;Q8TAS1	.;UHMK1_HUMAN	R	46	ENSP00000446416:P46R;ENSP00000420270:P46R	ENSP00000420270:P46R	P	+	2	0	UHMK1	160734551	0.781000	0.28676	0.811000	0.32455	0.991000	0.79684	3.781000	0.55394	2.715000	0.92844	0.655000	0.94253	CCT	.	.	none		0.697	UHMK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076788.1	NM_175866	
ALK	238	hgsc.bcm.edu	37	2	30143259	30143259	+	Silent	SNP	G	G	T	rs192127241	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:30143259G>T	ENST00000389048.3	-	1	1173	c.267C>A	c.(265-267)ggC>ggA	p.G89G	ALK_ENST00000431873.1_Silent_p.G89G	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	89					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)		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)	GAGCTAGCGAGCCGCGGGCCT	0.721			"""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				G|||	16	0.00319489	0.0113	0.0014	5008	,	,		11936	0.0		0.0	False		,,,				2504	0.0				p.G89G		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	.	ALK	533	.	0			c.C267A						PASS	.	G		73,4275		0,73,2101	12.0	14.0	13.0		267	2.2	0.3	2		13	0,8484		0,0,4242	no	coding-synonymous	ALK	NM_004304.4		0,73,6343	TT,TG,GG		0.0,1.6789,0.5689		89/1621	30143259	73,12759	2174	4242	6416	SO:0001819	synonymous_variant	238	exon1	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	TAGCGAGCCGCGG	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.267C>A	2.37:g.30143259G>T		15.0	0.0	0		20.0	9.0	0.45	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			G|0.998;T|0.002	0.002	strong		0.721	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
CLEC4F	165530	hgsc.bcm.edu	37	2	71046536	71046536	+	Silent	SNP	G	G	A	rs17006361	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71046536G>A	ENST00000272367.2	-	3	295	c.219C>T	c.(217-219)gcC>gcT	p.A73A	CLEC4F_ENST00000426626.1_Silent_p.A73A	NM_001258027.1|NM_173535.2	NP_001244956.1|NP_775806.2	Q8N1N0	CLC4F_HUMAN	C-type lectin domain family 4, member F	73					endocytosis (GO:0006897)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			endometrium(1)|large_intestine(5)|lung(18)|ovary(5)|prostate(5)|skin(1)|upper_aerodigestive_tract(2)	37						CCAGAATTACGGCTTGCACAG	0.532													A|||	198	0.0395367	0.143	0.013	5008	,	,		18946	0.0		0.0	False		,,,				2504	0.0				p.A73A	Colon(107;10 2157 6841 26035)	Atlas-SNP	.											CLEC4F,NS,carcinoma,0,3	CLEC4F	95	3	0			c.C219T						PASS	.	A		584,3822	259.8+/-263.3	32,520,1651	124.0	107.0	112.0		219	-0.0	0.0	2	dbSNP_123	112	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	CLEC4F	NM_173535.2		32,523,5948	AA,AG,GG		0.0349,13.2547,4.5133		73/590	71046536	587,12419	2203	4300	6503	SO:0001819	synonymous_variant	165530	exon3			AATTACGGCTTGC	AK096429	CCDS1910.1	2p13.3	2008-02-05	2005-02-09	2005-02-11	ENSG00000152672	ENSG00000152672		"""C-type lectin domain containing"""	25357	protein-coding gene	gene with protein product			"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 13"""	CLECSF13		8889548, 1846367	Standard	NM_001258027		Approved	FLJ39110, KCLR	uc002shf.3	Q8N1N0	OTTHUMG00000129713	ENST00000272367.2:c.219C>T	2.37:g.71046536G>A		180.0	0.0	0		167.0	85.0	0.508982	NM_173535	A4QPA5	Silent	SNP	ENST00000272367.2	37	CCDS1910.1																																																																																			G|0.948;A|0.052	0.052	strong		0.532	CLEC4F-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251922.1	NM_173535	
OR8B12	219858	hgsc.bcm.edu	37	11	124413491	124413491	+	Silent	SNP	C	C	T	rs61746453	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124413491C>T	ENST00000306842.2	-	1	84	c.60G>A	c.(58-60)ccG>ccA	p.P20P		NM_001005195.1	NP_001005195.1	Q8NGG6	OR8BC_HUMAN	olfactory receptor, family 8, subfamily B, member 12	20						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		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;0.0213)		TCCGCAGTCCCGGCTGGTGGG	0.542													C|||	139	0.0277556	0.1021	0.0058	5008	,	,		18064	0.0		0.0	False		,,,				2504	0.0				p.P20P		Atlas-SNP	.											OR8B12,bladder,carcinoma,-1,1	OR8B12	66	1	0			c.G60A						PASS	.	C		321,4081	155.5+/-188.7	7,307,1887	47.0	51.0	49.0		60	-5.8	0.0	11	dbSNP_129	49	16,8582	10.5+/-38.8	0,16,4283	no	coding-synonymous	OR8B12	NM_001005195.1		7,323,6170	TT,TC,CC		0.1861,7.2921,2.5923		20/311	124413491	337,12663	2201	4299	6500	SO:0001819	synonymous_variant	219858	exon1			CAGTCCCGGCTGG		CCDS31711.1	11q24.2	2013-09-24			ENSG00000170953	ENSG00000170953		"""GPCR / Class A : Olfactory receptors"""	15307	protein-coding gene	gene with protein product							Standard	NM_001005195		Approved		uc010sam.2	Q8NGG6	OTTHUMG00000165922	ENST00000306842.2:c.60G>A	11.37:g.124413491C>T		60.0	0.0	0		51.0	27.0	0.529412	NM_001005195	B2RNF6|Q6IEW8|Q96RC7	Silent	SNP	ENST00000306842.2	37	CCDS31711.1																																																																																			C|0.974;T|0.026	0.026	strong		0.542	OR8B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387061.1		
PCNP	57092	hgsc.bcm.edu	37	3	101293097	101293097	+	Missense_Mutation	SNP	A	A	G	rs116752753	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:101293097A>G	ENST00000265260.3	+	1	159	c.38A>G	c.(37-39)aAg>aGg	p.K13R	PCNP_ENST00000469941.1_5'UTR|PCNP_ENST00000486406.1_3'UTR|PCNP_ENST00000296024.5_Missense_Mutation_p.K13R	NM_020357.1	NP_065090.1	Q8WW12	PCNP_HUMAN	PEST proteolytic signal containing nuclear protein	13					cell cycle (GO:0007049)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)	nucleus (GO:0005634)				large_intestine(1)|lung(1)	2						AAGCCTGAAAAGTCGCAGCGA	0.677													A|||	49	0.00978435	0.0363	0.0014	5008	,	,		12760	0.0		0.0	False		,,,				2504	0.0				p.K13R		Atlas-SNP	.											.	PCNP	8	.	0			c.A38G						PASS	.	A	ARG/LYS	87,3257		0,87,1585	23.0	27.0	26.0		38	2.6	0.9	3	dbSNP_132	26	1,6167		0,1,3083	yes	missense	PCNP	NM_020357.1	26	0,88,4668	GG,GA,AA		0.0162,2.6017,0.9251	benign	13/179	101293097	88,9424	1672	3084	4756	SO:0001583	missense	57092	exon1			CTGAAAAGTCGCA		CCDS2942.1	3q12.3	2006-03-09			ENSG00000081154	ENSG00000081154			30023	protein-coding gene	gene with protein product		615210				12176013	Standard	NM_020357		Approved		uc003dva.3	Q8WW12	OTTHUMG00000159108	ENST00000265260.3:c.38A>G	3.37:g.101293097A>G	ENSP00000265260:p.Lys13Arg	161.0	0.0	0		210.0	114.0	0.542857	NM_020357	B2RBE7|D3DN52|Q53GF3|Q6AI44|Q96CU3|Q9NS81	Missense_Mutation	SNP	ENST00000265260.3	37	CCDS2942.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	A	15.73	2.921230	0.52653	0.026017	1.62E-4	ENSG00000081154	ENST00000265260;ENST00000296024	.	.	.	5.08	2.59	0.31030	.	2.264980	0.01941	N	0.041900	T	0.06735	0.0172	N	0.08118	0	0.27175	N	0.960801	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.14868	-1.0457	9	0.27785	T	0.31	.	1.8535	0.03174	0.5685:0.1752:0.0887:0.1676	.	13;13	Q8WW12-2;Q8WW12	.;PCNP_HUMAN	R	13	.	ENSP00000265260:K13R	K	+	2	0	PCNP	102775787	1.000000	0.71417	0.891000	0.34965	0.933000	0.57130	1.646000	0.37249	0.366000	0.24427	-0.336000	0.08194	AAG	A|0.993;G|0.007	0.007	strong		0.677	PCNP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353338.2	NM_020357	
NCL	4691	hgsc.bcm.edu	37	2	232320281	232320281	+	Silent	SNP	G	G	A	rs78372304	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:232320281G>A	ENST00000322723.4	-	13	2127	c.1887C>T	c.(1885-1887)gcC>gcT	p.A629A	SNORA75_ENST00000384158.1_RNA|SNORD20_ENST00000384550.1_RNA	NM_005381.2	NP_005372.2	P19338	NUCL_HUMAN	nucleolin	629	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				angiogenesis (GO:0001525)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)	cell cortex (GO:0005938)|cytoplasmic ribonucleoprotein granule (GO:0036464)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)|RNA binding (GO:0003723)|telomeric DNA binding (GO:0042162)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(7)|ovary(2)|pancreas(2)|prostate(2)|skin(3)	35		Ovarian(221;1.34e-05)|Renal(207;0.0112)|Lung NSC(271;0.0339)|all_lung(227;0.0616)|all_hematologic(139;0.0748)|Hepatocellular(293;0.137)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.65e-111)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.014)|COAD - Colon adenocarcinoma(134;0.141)|STAD - Stomach adenocarcinoma(1183;0.18)		CGTCTTCCATGGCCTCCTTGG	0.488													.|||	26	0.00519169	0.0189	0.0014	5008	,	,		21137	0.0		0.0	False		,,,				2504	0.0				p.A629A		Atlas-SNP	.											.	NCL	80	.	0			c.C1887T						PASS	.	G		73,4333	65.3+/-102.7	2,69,2132	209.0	222.0	218.0		1887	2.1	1.0	2	dbSNP_131	218	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	NCL	NM_005381.2		2,71,6430	AA,AG,GG		0.0233,1.6568,0.5767		629/711	232320281	75,12931	2203	4300	6503	SO:0001819	synonymous_variant	4691	exon13			TTCCATGGCCTCC		CCDS33397.1	2q37.1	2013-09-19			ENSG00000115053	ENSG00000115053		"""RNA binding motif (RRM) containing"""	7667	protein-coding gene	gene with protein product		164035				2394707, 3409881	Standard	NM_005381		Approved	C23	uc002vru.3	P19338	OTTHUMG00000153866	ENST00000322723.4:c.1887C>T	2.37:g.232320281G>A		259.0	0.0	0		210.0	109.0	0.519048	NM_005381	Q53SK1|Q8NB06|Q9UCF0|Q9UDG1	Silent	SNP	ENST00000322723.4	37	CCDS33397.1																																																																																			G|0.994;A|0.006	0.006	strong		0.488	NCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332731.1	NM_005381	
LGI3	203190	hgsc.bcm.edu	37	8	22005939	22005939	+	Missense_Mutation	SNP	C	C	T	rs559732127		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22005939C>T	ENST00000306317.2	-	8	1670	c.1381G>A	c.(1381-1383)Gcc>Acc	p.A461T	LGI3_ENST00000424267.2_Missense_Mutation_p.A437T	NM_139278.2	NP_644807.1	Q8N145	LGI3_HUMAN	leucine-rich repeat LGI family, member 3	461					exocytosis (GO:0006887)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|extracellular region (GO:0005576)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	catalytic activity (GO:0003824)			endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	17				Colorectal(74;0.00189)|COAD - Colon adenocarcinoma(73;0.0612)|READ - Rectum adenocarcinoma(644;0.0999)		GAGGGCAGGGCCTGCACCTCC	0.657													C|||	1	0.000199681	0.0008	0.0	5008	,	,		15389	0.0		0.0	False		,,,				2504	0.0				p.A461T		Atlas-SNP	.											.	LGI3	44	.	0			c.G1381A						PASS	.						30.0	30.0	30.0					8																	22005939		2203	4300	6503	SO:0001583	missense	203190	exon8			GCAGGGCCTGCAC	AJ487518	CCDS6025.1	8p21.2	2008-07-28			ENSG00000168481	ENSG00000168481			18711	protein-coding gene	gene with protein product		608302				12023020, 18628660	Standard	NM_139278		Approved		uc003xav.3	Q8N145	OTTHUMG00000131599	ENST00000306317.2:c.1381G>A	8.37:g.22005939C>T	ENSP00000302297:p.Ala461Thr	48.0	0.0	0		46.0	21.0	0.456522	NM_139278	A5PLP2|Q86TL4|Q8N296	Missense_Mutation	SNP	ENST00000306317.2	37	CCDS6025.1	.	.	.	.	.	.	.	.	.	.	C	13.05	2.122032	0.37436	.	.	ENSG00000168481	ENST00000306317;ENST00000424267	T;T	0.78924	-1.22;-1.22	5.19	5.19	0.71726	Six-bladed beta-propeller, TolB-like (1);	0.062211	0.64402	D	0.000004	T	0.49372	0.1553	N	0.01686	-0.76	0.35162	D	0.770725	B;B	0.16396	0.017;0.008	B;B	0.18561	0.022;0.012	T	0.55970	-0.8056	10	0.12430	T	0.62	-31.0187	9.7807	0.40647	0.0:0.9063:0.0:0.0937	.	437;461	A5PLP2;Q8N145	.;LGI3_HUMAN	T	461;437	ENSP00000302297:A461T;ENSP00000399121:A437T	ENSP00000302297:A461T	A	-	1	0	LGI3	22061884	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.203000	0.51075	2.396000	0.81511	0.561000	0.74099	GCC	.	.	none		0.657	LGI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254482.1		
PRODH2	58510	hgsc.bcm.edu	37	19	36304143	36304143	+	Missense_Mutation	SNP	G	G	A	rs138605929	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36304143G>A	ENST00000301175.3	-	1	58	c.41C>T	c.(40-42)tCc>tTc	p.S14F		NM_021232.1	NP_067055.1	Q9UF12	PROD2_HUMAN	proline dehydrogenase (oxidase) 2	14					proline catabolic process to glutamate (GO:0010133)	mitochondrial inner membrane (GO:0005743)	proline dehydrogenase activity (GO:0004657)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(9)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	21	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			aacactttgggaggccaagac	0.423													G|||	30	0.00599042	0.0212	0.0029	5008	,	,		21126	0.0		0.0	False		,,,				2504	0.0				p.S14F		Atlas-SNP	.											.	PRODH2	68	.	0			c.C41T						PASS	.	G	PHE/SER	79,4327	54.9+/-90.9	0,79,2124	60.0	54.0	56.0		41	0.4	0.0	19	dbSNP_134	56	0,8600		0,0,4300	no	missense	PRODH2	NM_021232.1	155	0,79,6424	AA,AG,GG		0.0,1.793,0.6074	possibly-damaging	14/537	36304143	79,12927	2203	4300	6503	SO:0001583	missense	58510	exon1			CTTTGGGAGGCCA	U80018	CCDS12478.1	19q13.1	2014-07-11				ENSG00000250799			17325	protein-coding gene	gene with protein product							Standard	NM_021232		Approved	HSPOX1	uc002obx.1	Q9UF12		ENST00000301175.3:c.41C>T	19.37:g.36304143G>A	ENSP00000301175:p.Ser14Phe	50.0	0.0	0		43.0	28.0	0.651163	NM_021232		Missense_Mutation	SNP	ENST00000301175.3	37	CCDS12478.1	9	0.004120879120879121	7	0.014227642276422764	2	0.0055248618784530384	0	0.0	0	0.0	G	6.284	0.420467	0.11928	0.01793	0.0	ENSG00000250799	ENST00000301175	T	0.06849	3.25	0.36	0.36	0.16097	.	.	.	.	.	T	0.02571	0.0078	N	0.08118	0	0.09310	N	1	P	0.39520	0.676	P	0.45558	0.485	T	0.41034	-0.9531	8	0.56958	D	0.05	.	.	.	.	.	14	Q9UF12	PROD2_HUMAN	F	14	ENSP00000301175:S14F	ENSP00000301175:S14F	S	-	2	0	PRODH2	40995983	0.037000	0.19845	0.031000	0.17742	0.030000	0.12068	0.477000	0.22196	0.469000	0.27268	0.472000	0.43445	TCC	G|0.992;A|0.008	0.008	strong		0.423	PRODH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452552.2	NM_021232	
NLN	57486	hgsc.bcm.edu	37	5	65084101	65084101	+	Missense_Mutation	SNP	A	A	G	rs6863012	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:65084101A>G	ENST00000380985.5	+	8	1293	c.1115A>G	c.(1114-1116)aAg>aGg	p.K372R	NLN_ENST00000502464.1_Missense_Mutation_p.K268R	NM_020726.4	NP_065777.1	Q9BYT8	NEUL_HUMAN	neurolysin (metallopeptidase M3 family)	372			K -> R (in dbSNP:rs6863012).			mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0743)|Lung(70;0.00616)		GAGGAACTCAAGTATTCCATA	0.408													A|||	276	0.0551118	0.1944	0.0202	5008	,	,		20583	0.0		0.004	False		,,,				2504	0.001				p.K372R		Atlas-SNP	.											.	NLN	51	.	0			c.A1115G						PASS	.	A	ARG/LYS	803,3603	319.3+/-296.1	63,677,1463	131.0	135.0	133.0		1115	6.1	1.0	5	dbSNP_116	133	32,8568	22.8+/-68.1	0,32,4268	yes	missense	NLN	NM_020726.4	26	63,709,5731	GG,GA,AA		0.3721,18.2251,6.4201	benign	372/705	65084101	835,12171	2203	4300	6503	SO:0001583	missense	57486	exon8			AACTCAAGTATTC	AJ300837	CCDS3989.1	5q12.3	2008-02-05	2005-03-31		ENSG00000123213	ENSG00000123213	3.4.24.16		16058	protein-coding gene	gene with protein product		611530	"""angiotensin binding protein"""	AGTBP		10574462	Standard	NM_020726		Approved	KIAA1226	uc003juf.3	Q9BYT8	OTTHUMG00000097803	ENST00000380985.5:c.1115A>G	5.37:g.65084101A>G	ENSP00000370372:p.Lys372Arg	175.0	0.0	0		170.0	88.0	0.517647	NM_020726	Q9ULJ4	Missense_Mutation	SNP	ENST00000380985.5	37	CCDS3989.1	108	0.04945054945054945	101	0.20528455284552846	7	0.019337016574585635	0	0.0	0	0.0	A	10.38	1.333268	0.24167	0.182251	0.003721	ENSG00000123213	ENST00000380985;ENST00000502464;ENST00000340159;ENST00000511299	T;T;T	0.08458	3.09;3.09;3.09	6.07	6.07	0.98685	Neurolysin/Thimet oligopeptidase, domain 2 (1);	0.045838	0.85682	D	0.000000	T	0.00012	0.0000	N	0.12961	0.28	0.19575	P	0.9999611304	B;B;D	0.64830	0.001;0.004;0.994	B;B;D	0.73708	0.001;0.008;0.981	T	0.56366	-0.7991	9	0.12430	T	0.62	-22.309	16.6406	0.85098	1.0:0.0:0.0:0.0	rs6863012;rs6863012	67;372;372	Q96K48;Q9BYT8;Q9BQD0	.;NEUL_HUMAN;.	R	372;268;372;100	ENSP00000370372:K372R;ENSP00000423214:K268R;ENSP00000427417:K100R	ENSP00000339283:K372R	K	+	2	0	NLN	65119857	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.934000	0.70138	2.326000	0.78906	0.533000	0.62120	AAG	A|0.936;G|0.064	0.064	strong		0.408	NLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215060.1		
C4BPA	722	hgsc.bcm.edu	37	1	207305069	207305069	+	Silent	SNP	A	A	C	rs6663608	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:207305069A>C	ENST00000367070.3	+	8	1262	c.1068A>C	c.(1066-1068)ccA>ccC	p.P356P		NM_000715.3	NP_000706.1	P04003	C4BPA_HUMAN	complement component 4 binding protein, alpha	356	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|negative regulation of complement activation, classical pathway (GO:0045959)|positive regulation of protein catabolic process (GO:0045732)|regulation of complement activation (GO:0030449)|regulation of opsonization (GO:1903027)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|other organism cell (GO:0044216)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)|skin(1)|urinary_tract(2)	28						GATGGACCCCATACCAAGGAT	0.368													A|||	276	0.0551118	0.1967	0.0187	5008	,	,		20256	0.0		0.001	False		,,,				2504	0.002				p.P356P		Atlas-SNP	.											.	C4BPA	70	.	0			c.A1068C						PASS	.	A		733,3673	284.3+/-277.5	69,595,1539	117.0	101.0	106.0		1068	-8.7	0.0	1	dbSNP_116	106	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	C4BPA	NM_000715.3		69,601,5833	CC,CA,AA		0.0698,16.6364,5.682		356/598	207305069	739,12267	2203	4300	6503	SO:0001819	synonymous_variant	722	exon8			GACCCCATACCAA	M31452	CCDS1477.1	1q32	2010-09-24	2001-11-28		ENSG00000123838	ENSG00000123838			1325	protein-coding gene	gene with protein product		120830	"""complement component 4-binding protein, alpha"""	C4BP			Standard	XM_005273251		Approved		uc001hfo.3	P04003	OTTHUMG00000036173	ENST00000367070.3:c.1068A>C	1.37:g.207305069A>C		87.0	0.0	0		117.0	52.0	0.444444	NM_000715	Q5VVQ8	Silent	SNP	ENST00000367070.3	37	CCDS1477.1																																																																																			A|0.930;C|0.070	0.070	strong		0.368	C4BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088089.3		
COL6A5	256076	hgsc.bcm.edu	37	3	130188009	130188009	+	Silent	SNP	C	C	T	rs59160673	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:130188009C>T	ENST00000432398.2	+	38	7655	c.7161C>T	c.(7159-7161)ggC>ggT	p.G2387G	COL6A5_ENST00000265379.6_Silent_p.G2387G	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	2387	Nonhelical region.|VWFA 10. {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						TTTTTATTGGCCATGCCTTGC	0.388													C|||	67	0.0133786	0.0499	0.0014	5008	,	,		23052	0.0		0.0	False		,,,				2504	0.0				p.G2387G		Atlas-SNP	.											.	COL6A5	205	.	0			c.C7161T						PASS	.	C		164,3580		2,160,1710	118.0	106.0	110.0		7161	1.4	0.9	3	dbSNP_129	110	0,8222		0,0,4111	no	coding-synonymous	COL6A5	NM_153264.5		2,160,5821	TT,TC,CC		0.0,4.3803,1.3705		2387/2527	130188009	164,11802	1872	4111	5983	SO:0001819	synonymous_variant	256076	exon38			TATTGGCCATGCC	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.7161C>T	3.37:g.130188009C>T		103.0	0.0	0		108.0	49.0	0.453704	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Silent	SNP	ENST00000432398.2	37		19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	C	4.754	0.140218	0.09083	0.043803	0.0	ENSG00000172752	ENST00000512836	.	.	.	5.35	1.44	0.22558	.	.	.	.	.	T	0.22126	0.0533	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.10382	-1.0632	4	.	.	.	.	6.4978	0.22152	0.0:0.6424:0.1312:0.2264	rs59160673	.	.	.	S	639	.	.	P	+	1	0	COL6A5	131670699	0.738000	0.28186	0.950000	0.38849	0.667000	0.39255	-0.305000	0.08188	-0.018000	0.14079	-0.137000	0.14449	CCA	C|0.989;T|0.011	0.011	strong		0.388	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
LRRC8C	84230	hgsc.bcm.edu	37	1	90179470	90179470	+	Silent	SNP	A	A	G	rs34576461	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:90179470A>G	ENST00000370454.4	+	3	1596	c.1341A>G	c.(1339-1341)caA>caG	p.Q447Q	LRRC8C_ENST00000479252.1_Intron|RP11-302M6.4_ENST00000370453.5_Intron	NM_032270.4	NP_115646	Q8TDW0	LRC8C_HUMAN	leucine rich repeat containing 8 family, member C	447					fat cell differentiation (GO:0045444)|ion transport (GO:0006811)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|urinary_tract(1)	28		all_lung(203;0.126)		all cancers(265;0.00756)|Epithelial(280;0.0313)		CAGAGTTGCAATCTCTAAAAC	0.423													A|||	99	0.0197684	0.0703	0.0086	5008	,	,		19984	0.0		0.0	False		,,,				2504	0.0				p.Q447Q		Atlas-SNP	.											.	LRRC8C	73	.	0			c.A1341G						PASS	.	A		281,4125	158.5+/-191.2	11,259,1933	88.0	84.0	85.0		1341	-0.5	1.0	1	dbSNP_126	85	0,8600		0,0,4300	no	coding-synonymous	LRRC8C	NM_032270.4		11,259,6233	GG,GA,AA		0.0,6.3777,2.1605		447/804	90179470	281,12725	2203	4300	6503	SO:0001819	synonymous_variant	84230	exon3			GTTGCAATCTCTA		CCDS725.1	1p22.2	2011-02-10			ENSG00000171488	ENSG00000171488			25075	protein-coding gene	gene with protein product	"""hypothetical protein AD158"""	612889				11230166	Standard	NM_032270		Approved	AD158	uc001dnl.4	Q8TDW0	OTTHUMG00000010305	ENST00000370454.4:c.1341A>G	1.37:g.90179470A>G		81.0	0.0	0		68.0	35.0	0.514706	NM_032270	B3KXS9|Q29RV6|Q9H075	Silent	SNP	ENST00000370454.4	37	CCDS725.1																																																																																			A|0.979;G|0.021	0.021	strong		0.423	LRRC8C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028435.2	NM_032270	
MYO7B	4648	hgsc.bcm.edu	37	2	128364787	128364787	+	Missense_Mutation	SNP	G	G	C	rs201386852	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128364787G>C	ENST00000409816.2	+	20	2463	c.2431G>C	c.(2431-2433)Gtg>Ctg	p.V811L	MYO7B_ENST00000389524.4_Missense_Mutation_p.V811L|MYO7B_ENST00000428314.1_Missense_Mutation_p.V811L			Q6PIF6	MYO7B_HUMAN	myosin VIIB	811	IQ 3. {ECO:0000255|PROSITE- ProRule:PRU00116}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		GCAGATCCTCGTGGGCTTTGA	0.632													G|||	2	0.000399361	0.0015	0.0	5008	,	,		17201	0.0		0.0	False		,,,				2504	0.0				p.V811L		Atlas-SNP	.											.	MYO7B	359	.	0			c.G2431C						PASS	.	G	LEU/VAL	8,3810		0,8,1901	7.0	9.0	8.0		2431	-6.2	0.1	2		8	0,7854		0,0,3927	yes	missense	MYO7B	NM_001080527.1	32	0,8,5828	CC,CG,GG		0.0,0.2095,0.0685	benign	811/2117	128364787	8,11664	1909	3927	5836	SO:0001583	missense	4648	exon21			ATCCTCGTGGGCT		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"""Myosins / Myosin superfamily : Class VII"""	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.2431G>C	2.37:g.128364787G>C	ENSP00000386461:p.Val811Leu	192.0	0.0	0		180.0	93.0	0.516667	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	37	CCDS46405.1	.	.	.	.	.	.	.	.	.	.	G	4.550	0.102047	0.08731	0.002095	0.0	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000409816	D;D;D	0.86627	-2.15;-2.15;-2.15	5.6	-6.22	0.02058	.	0.757314	0.11581	N	0.549776	T	0.52901	0.1763	N	0.01352	-0.895	0.09310	N	0.999991	B	0.02656	0.0	B	0.04013	0.001	T	0.59177	-0.7503	10	0.07990	T	0.79	.	1.1174	0.01717	0.1671:0.2857:0.2377:0.3095	.	811	Q6PIF6	MYO7B_HUMAN	L	811	ENSP00000374175:V811L;ENSP00000415090:V811L;ENSP00000386461:V811L	ENSP00000374175:V811L	V	+	1	0	MYO7B	128081257	0.000000	0.05858	0.057000	0.19452	0.727000	0.41649	-0.731000	0.04909	-1.131000	0.02910	-0.344000	0.07964	GTG	.	.	weak		0.632	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
SBNO2	22904	hgsc.bcm.edu	37	19	1109577	1109577	+	Silent	SNP	C	C	T	rs200767766	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1109577C>T	ENST00000361757.3	-	28	3381	c.3144G>A	c.(3142-3144)ctG>ctA	p.L1048L	SBNO2_ENST00000587024.1_Silent_p.L1038L|SBNO2_ENST00000438103.2_Silent_p.L991L	NM_014963.2	NP_055778.2	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 (Drosophila)	1048					bone mineralization (GO:0030282)|bone trabecula morphogenesis (GO:0061430)|macrophage activation involved in immune response (GO:0002281)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoclast fusion (GO:0072675)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of inflammatory response (GO:0050727)|transcription, DNA-templated (GO:0006351)					NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|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)		CCTCCCACTTCAGGCCGCGGT	0.697													C|||	31	0.0061901	0.0234	0.0	5008	,	,		7099	0.0		0.0	False		,,,				2504	0.0				p.L1048L		Atlas-SNP	.											.	SBNO2	112	.	0			c.G3144A						PASS	.	C	,	57,3687		0,57,1815	7.0	9.0	8.0		2973,3144	2.3	1.0	19		8	0,8122		0,0,4061	no	coding-synonymous,coding-synonymous	SBNO2	NM_001100122.1,NM_014963.2	,	0,57,5876	TT,TC,CC		0.0,1.5224,0.4804	,	991/1310,1048/1367	1109577	57,11809	1872	4061	5933	SO:0001819	synonymous_variant	22904	exon28			CCACTTCAGGCCG	AK074102	CCDS45894.1, CCDS45895.1	19p13.3	2008-02-05	2006-10-06	2006-10-06		ENSG00000064932			29158	protein-coding gene	gene with protein product		615729	"""KIAA0963"""	KIAA0963		10231032	Standard	NM_014963		Approved	FLJ00173, Stno, Sno	uc002lrk.4	Q9Y2G9		ENST00000361757.3:c.3144G>A	19.37:g.1109577C>T		88.0	0.0	0		104.0	50.0	0.480769	NM_014963	A8K8P2|B3KWJ1|O75257|Q3KQX0|Q8TEM0	Silent	SNP	ENST00000361757.3	37	CCDS45894.1																																																																																			C|0.986;T|0.014	0.014	strong		0.697	SBNO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458065.2	NM_014963	
SGK223	157285	hgsc.bcm.edu	37	8	8176540	8176540	+	Silent	SNP	C	C	T	rs116402506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:8176540C>T	ENST00000520004.1	-	6	3609	c.3345G>A	c.(3343-3345)gcG>gcA	p.A1115A	SGK223_ENST00000330777.4_Silent_p.A1115A			Q86YV5	SG223_HUMAN		1117	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										GCCGCTCGTACGCCTCGGGCT	0.667													C|||	318	0.0634984	0.2231	0.0274	5008	,	,		10206	0.0		0.003	False		,,,				2504	0.001				p.A1115A	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.G3345A						PASS	.	C		726,3448		70,586,1431	77.0	86.0	83.0		3345	-11.0	0.0	8	dbSNP_132	83	13,8401		0,13,4194	no	coding-synonymous	SGK223	NM_001080826.1		70,599,5625	TT,TC,CC		0.1545,17.3934,5.8707		1115/1403	8176540	739,11849	2087	4207	6294	SO:0001819	synonymous_variant	0	exon5			CTCGTACGCCTCG																												ENST00000520004.1:c.3345G>A	8.37:g.8176540C>T		32.0	0.0	0		46.0	26.0	0.565217	NM_001080826	Q8N3N5	Silent	SNP	ENST00000520004.1	37	CCDS43706.1																																																																																			C|0.970;T|0.030	0.030	strong		0.667	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
ZP1	22917	hgsc.bcm.edu	37	11	60642633	60642633	+	Silent	SNP	C	C	T	rs112864814	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:60642633C>T	ENST00000278853.5	+	11	1686	c.1686C>T	c.(1684-1686)gaC>gaT	p.D562D		NM_207341.2	NP_997224.2	P60852	ZP1_HUMAN	zona pellucida glycoprotein 1 (sperm receptor)	562					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)				breast(3)|endometrium(2)|large_intestine(8)|lung(8)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	26						ACCGTAATGACACTGCCAGGC	0.627													C|||	78	0.0155751	0.056	0.0029	5008	,	,		19463	0.0		0.002	False		,,,				2504	0.0				p.D562D		Atlas-SNP	.											.	ZP1	69	.	0			c.C1686T						PASS	.	C		240,4166	142.3+/-177.5	3,234,1966	69.0	73.0	72.0		1686	-4.2	0.0	11	dbSNP_132	72	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	ZP1	NM_207341.2		3,235,6264	TT,TC,CC		0.0116,5.4471,1.8533		562/639	60642633	241,12763	2203	4299	6502	SO:0001819	synonymous_variant	22917	exon11			TAATGACACTGCC	BC067899	CCDS31572.1	11q12.2	2013-01-17			ENSG00000149506	ENSG00000149506		"""Zona pellucida glycoproteins"""	13187	protein-coding gene	gene with protein product		195000				10542331	Standard	NM_207341		Approved		uc001nqd.3	P60852	OTTHUMG00000167797	ENST00000278853.5:c.1686C>T	11.37:g.60642633C>T		99.0	0.0	0		126.0	60.0	0.47619	NM_207341		Silent	SNP	ENST00000278853.5	37	CCDS31572.1																																																																																			C|0.980;T|0.020	0.020	strong		0.627	ZP1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396329.1	NM_207341	
FANCA	2175	hgsc.bcm.edu	37	16	89874756	89874756	+	Missense_Mutation	SNP	G	G	A	rs17232246	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89874756G>A	ENST00000389301.3	-	6	572	c.542C>T	c.(541-543)gCg>gTg	p.A181V	FANCA_ENST00000389302.3_Missense_Mutation_p.A181V|FANCA_ENST00000568369.1_Missense_Mutation_p.A181V|FANCA_ENST00000534992.1_Missense_Mutation_p.A181V|FANCA_ENST00000543736.1_Missense_Mutation_p.A149V|FANCA_ENST00000563673.1_Missense_Mutation_p.A181V	NM_000135.2	NP_000126.2	O15360	FANCA_HUMAN	Fanconi anemia, complementation group A	181			A -> V (in FA; dbSNP:rs17232246).		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)		ATGCCACACCGCTTCAAGCAA	0.398			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia				G|||	267	0.0533147	0.1959	0.0115	5008	,	,		18304	0.0		0.0	False		,,,				2504	0.0				p.A181V		Atlas-SNP	.	yes	Rec		Fanconi anaemia A	16	16q24.3	2175	"""Fanconi anemia, complementation group A"""		L	.	FANCA	99	.	0			c.C542T						PASS	.	G	VAL/ALA,VAL/ALA	738,3658	304.9+/-288.7	64,610,1524	137.0	129.0	131.0		542,542	2.8	0.3	16	dbSNP_123	131	4,8596	2.2+/-6.3	0,4,4296	yes	missense,missense	FANCA	NM_000135.2,NM_001018112.1	64,64	64,614,5820	AA,AG,GG		0.0465,16.788,5.7094	benign,benign	181/1456,181/298	89874756	742,12254	2198	4300	6498	SO:0001583	missense	2175	exon6	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CACACCGCTTCAA	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.542C>T	16.37:g.89874756G>A	ENSP00000373952:p.Ala181Val	172.0	0.0	0		194.0	87.0	0.448454	NM_000135	A5D923|B4DRI7|H3BSR5|O75266|Q6PL10|Q92497|Q96H18|Q9UEA5|Q9UEL8|Q9UEL9|Q9UPK3|Q9Y6M2	Missense_Mutation	SNP	ENST00000389301.3	37	CCDS32515.1	65	0.02976190476190476	61	0.12398373983739837	4	0.011049723756906077	0	0.0	0	0.0	G	7.667	0.686109	0.14973	0.16788	4.65E-4	ENSG00000187741	ENST00000389301;ENST00000389302;ENST00000534992;ENST00000543736	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	4.77	2.81	0.32909	.	0.147328	0.30879	N	0.008682	T	0.00109	0.0003	L	0.58669	1.825	0.32276	N	0.568249	P;B;B;B;B;P	0.48230	0.907;0.241;0.06;0.06;0.06;0.907	B;B;B;B;B;B	0.33295	0.161;0.064;0.012;0.019;0.012;0.161	T	0.04165	-1.0972	10	0.38643	T	0.18	-6.3506	9.5774	0.39465	0.1724:0.0:0.8276:0.0	rs17232246	181;149;181;181;181;181	B4DRI7;Q0VAP4;A0PJU8;F5H8D5;O15360-2;O15360	.;.;.;.;.;FANCA_HUMAN	V	181;181;181;149	ENSP00000373952:A181V;ENSP00000373953:A181V;ENSP00000443675:A181V;ENSP00000443409:A149V	ENSP00000373952:A181V	A	-	2	0	FANCA	88402257	0.730000	0.28100	0.335000	0.25508	0.047000	0.14425	0.788000	0.26872	0.517000	0.28361	-0.924000	0.02725	GCG	G|0.950;A|0.050	0.050	strong		0.398	FANCA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000421927.1		
ARHGEF10	9639	hgsc.bcm.edu	37	8	1905222	1905222	+	Silent	SNP	A	A	G	rs146227529	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:1905222A>G	ENST00000398564.1	+	29	3903	c.3903A>G	c.(3901-3903)tcA>tcG	p.S1301S	ARHGEF10_ENST00000518288.1_Silent_p.S1300S|ARHGEF10_ENST00000521927.1_3'UTR|ARHGEF10_ENST00000262112.6_Silent_p.S1272S|ARHGEF10_ENST00000520359.1_Silent_p.S1238S|ARHGEF10_ENST00000349830.3_Silent_p.S1276S			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	1301	Ser-rich.				centrosome duplication (GO:0051298)|myelination in peripheral nervous system (GO:0022011)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cytosol (GO:0005829)	kinesin binding (GO:0019894)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(3)|large_intestine(11)|lung(11)|prostate(3)|skin(3)|stomach(3)|urinary_tract(1)	35		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		AGCACAGATCAGAGGACAGCA	0.572													A|||	16	0.00319489	0.0106	0.0029	5008	,	,		17994	0.0		0.0	False		,,,				2504	0.0				p.S1276S		Atlas-SNP	.											.	ARHGEF10	255	.	0			c.A3828G						PASS	.	A		40,4366	44.6+/-78.6	1,38,2164	71.0	67.0	68.0		3828	-11.4	0.0	8	dbSNP_134	68	0,8600		0,0,4300	no	coding-synonymous	ARHGEF10	NM_014629.2		1,38,6464	GG,GA,AA		0.0,0.9079,0.3076		1276/1345	1905222	40,12966	2203	4300	6503	SO:0001819	synonymous_variant	9639	exon29			CAGATCAGAGGAC	AF009205	CCDS34794.1	8p23	2014-09-17			ENSG00000104728	ENSG00000104728		"""Rho guanine nucleotide exchange factors"""	14103	protein-coding gene	gene with protein product		608136				9205841, 16896804	Standard	XM_005266039		Approved	KIAA0294, Gef10	uc003wpr.3	O15013	OTTHUMG00000163626	ENST00000398564.1:c.3903A>G	8.37:g.1905222A>G		67.0	0.0	0		72.0	38.0	0.527778	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Silent	SNP	ENST00000398564.1	37																																																																																				A|0.996;G|0.004	0.004	strong		0.572	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding			
CHRNA1	1134	hgsc.bcm.edu	37	2	175613477	175613477	+	Missense_Mutation	SNP	T	T	A	rs6739001	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:175613477T>A	ENST00000261007.5	-	9	1214	c.1148A>T	c.(1147-1149)gAc>gTc	p.D383V	CHRNA1_ENST00000348749.5_Missense_Mutation_p.D358V|CHRNA1_ENST00000409542.1_Missense_Mutation_p.D276V|CHRNA1_ENST00000409219.1_Intron|AC018890.6_ENST00000442996.1_RNA	NM_001039523.2	NP_001034612.1	P02708	ACHA_HUMAN	cholinergic receptor, nicotinic, alpha 1 (muscle)	383			D -> V (in dbSNP:rs6739001).		cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|muscle cell cellular homeostasis (GO:0046716)|musculoskeletal movement (GO:0050881)|neuromuscular junction development (GO:0007528)|neuromuscular process (GO:0050905)|neuromuscular synaptic transmission (GO:0007274)|neuron cellular homeostasis (GO:0070050)|neuronal action potential (GO:0019228)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue growth (GO:0048630)|synaptic transmission (GO:0007268)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cell surface (GO:0009986)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ion channel activity (GO:0005216)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(3)|prostate(3)|skin(4)	37					Galantamine(DB00674)	AATCTTTTTGTCTTGCTTTTC	0.408											OREG0015079	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	94	0.01877	0.0703	0.0014	5008	,	,		19250	0.0		0.0	False		,,,				2504	0.0				p.D383V		Atlas-SNP	.											.	CHRNA1	92	.	0			c.A1148T						PASS	.	T	VAL/ASP,VAL/ASP	251,4155	144.6+/-179.5	5,241,1957	137.0	130.0	133.0		1073,1148	5.5	1.0	2	dbSNP_116	133	1,8599		0,1,4299	yes	missense,missense	CHRNA1	NM_000079.3,NM_001039523.2	152,152	5,242,6256	AA,AT,TT		0.0116,5.6968,1.9376	benign,benign	358/458,383/483	175613477	252,12754	2203	4300	6503	SO:0001583	missense	1134	exon9			TTTTTGTCTTGCT	Y00762	CCDS2261.1, CCDS33331.1	2q31.1	2012-02-11	2006-02-01		ENSG00000138435	ENSG00000138435		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1955	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 1 (muscle)"""	100690	"""cholinergic receptor, nicotinic, alpha polypeptide 1 (muscle)"""	CHRNA			Standard	NM_001039523		Approved		uc002uje.2	P02708	OTTHUMG00000132357	ENST00000261007.5:c.1148A>T	2.37:g.175613477T>A	ENSP00000261007:p.Asp383Val	175.0	0.0	0	1924	134.0	59.0	0.440298	NM_001039523	B4DRV6|D3DPE8	Missense_Mutation	SNP	ENST00000261007.5	37	CCDS33331.1	37	0.01694139194139194	37	0.07520325203252033	0	0.0	0	0.0	0	0.0	T	14.25	2.478393	0.44044	0.056968	1.16E-4	ENSG00000138435	ENST00000348749;ENST00000261007;ENST00000409542	D;D;D	0.85773	-2.03;-2.03;-2.03	5.51	5.51	0.81932	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.943943	0.09150	N	0.841683	T	0.19967	0.0480	L	0.27053	0.805	0.80722	D	1	B;B	0.23540	0.003;0.087	B;B	0.25759	0.007;0.063	T	0.48559	-0.9025	10	0.40728	T	0.16	.	11.8621	0.52471	0.0:0.0:0.1458:0.8542	rs6739001;rs52820919;rs6739001	358;383	Q53SH4;P02708	.;ACHA_HUMAN	V	358;383;276	ENSP00000261008:D358V;ENSP00000261007:D383V;ENSP00000387026:D276V	ENSP00000261007:D383V	D	-	2	0	CHRNA1	175321723	0.997000	0.39634	0.998000	0.56505	0.992000	0.81027	2.634000	0.46528	2.217000	0.71921	0.533000	0.62120	GAC	T|0.971;A|0.029	0.029	strong		0.408	CHRNA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000334116.1		
DISP1	84976	hgsc.bcm.edu	37	1	223178226	223178226	+	Missense_Mutation	SNP	A	A	G	rs61743732	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:223178226A>G	ENST00000284476.6	+	8	3651	c.3487A>G	c.(3487-3489)Agt>Ggt	p.S1163G		NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	1163					determination of left/right symmetry (GO:0007368)|diaphragm development (GO:0060539)|dorsal/ventral pattern formation (GO:0009953)|embryonic pattern specification (GO:0009880)|patched ligand maturation (GO:0007225)|peptide transport (GO:0015833)|protein homotrimerization (GO:0070207)|regulation of protein secretion (GO:0050708)|smoothened signaling pathway (GO:0007224)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)|peptide transporter activity (GO:0015197)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(20)|lung(25)|prostate(4)|skin(1)|stomach(1)|urinary_tract(5)	69				GBM - Glioblastoma multiforme(131;0.102)		TACAAGTCCCAGTGACAAGGG	0.453													A|||	129	0.0257588	0.093	0.0058	5008	,	,		23051	0.0		0.002	False		,,,				2504	0.0				p.S1163G		Atlas-SNP	.											.	DISP1	145	.	0			c.A3487G						PASS	.	A	GLY/SER	372,4034	188.8+/-215.1	12,348,1843	85.0	89.0	88.0		3487	1.6	0.0	1	dbSNP_129	88	3,8597	3.0+/-9.4	0,3,4297	yes	missense	DISP1	NM_032890.3	56	12,351,6140	GG,GA,AA		0.0349,8.443,2.8833	benign	1163/1525	223178226	375,12631	2203	4300	6503	SO:0001583	missense	84976	exon10			AGTCCCAGTGACA	AK056569	CCDS1536.1	1q42.12	2008-02-05			ENSG00000154309	ENSG00000154309			19711	protein-coding gene	gene with protein product		607502				10619433	Standard	NM_032890		Approved	DISPA, MGC13130, DKFZP434I0428, MGC16796	uc001hnu.2	Q96F81	OTTHUMG00000037893	ENST00000284476.6:c.3487A>G	1.37:g.223178226A>G	ENSP00000284476:p.Ser1163Gly	27.0	0.0	0		28.0	12.0	0.428571	NM_032890	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Missense_Mutation	SNP	ENST00000284476.6	37	CCDS1536.1	56	0.02564102564102564	53	0.10772357723577236	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	A	0.004	-2.279509	0.00254	0.08443	3.49E-4	ENSG00000154309	ENST00000284476	D	0.91351	-2.83	5.66	1.56	0.23342	.	0.630262	0.17522	N	0.171240	T	0.03477	0.0100	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30880	-0.9963	10	0.05436	T	0.98	-4.8804	7.9026	0.29744	0.1384:0.2477:0.6138:0.0	rs61743732	1163	Q96F81	DISP1_HUMAN	G	1163	ENSP00000284476:S1163G	ENSP00000284476:S1163G	S	+	1	0	DISP1	221244849	0.084000	0.21492	0.004000	0.12327	0.204000	0.24138	2.705000	0.47127	0.030000	0.15379	-0.415000	0.06103	AGT	A|0.971;G|0.029	0.029	strong		0.453	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890	
EPHX1	2052	hgsc.bcm.edu	37	1	226032896	226032896	+	Silent	SNP	T	T	C	rs2234700	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:226032896T>C	ENST00000366837.4	+	9	1412	c.1216T>C	c.(1216-1218)Ttg>Ctg	p.L406L	RP11-285F7.2_ENST00000424332.1_RNA|EPHX1_ENST00000272167.5_Silent_p.L406L	NM_000120.3	NP_000111.1	P07099	HYEP_HUMAN	epoxide hydrolase 1, microsomal (xenobiotic)	406				L -> F (in Ref. 3; CAA68486). {ECO:0000305}.	aromatic compound catabolic process (GO:0019439)|response to toxic substance (GO:0009636)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	cis-stilbene-oxide hydrolase activity (GO:0033961)|epoxide hydrolase activity (GO:0004301)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	28	Breast(184;0.197)					TTTTGAGCTATTGCACACGCC	0.572													t|||	106	0.0211661	0.0741	0.0043	5008	,	,		13351	0.001		0.0	False		,,,				2504	0.0041				p.L406L		Atlas-SNP	.											.	EPHX1	57	.	0			c.T1216C						PASS	.	C	,	208,4198	127.8+/-164.7	7,194,2002	102.0	93.0	96.0		1216,1216	-10.0	0.0	1	dbSNP_98	96	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	EPHX1	NM_000120.3,NM_001136018.2	,	7,194,6302	CC,CT,TT		0.0,4.7208,1.5993	,	406/456,406/456	226032896	208,12798	2203	4300	6503	SO:0001819	synonymous_variant	2052	exon9			GAGCTATTGCACA	J03518	CCDS1547.1	1q42.1	2009-07-10			ENSG00000143819	ENSG00000143819	3.3.2.9		3401	protein-coding gene	gene with protein product		132810		EPHX		9925921	Standard	NM_000120		Approved		uc001hpk.3	P07099	OTTHUMG00000037743	ENST00000366837.4:c.1216T>C	1.37:g.226032896T>C		143.0	0.0	0		147.0	78.0	0.530612	NM_001136018	B2R8N0|Q5VTJ6|Q9NP75|Q9NPE7|Q9NQU6|Q9NQU7|Q9NQU8|Q9NQU9|Q9NQV0|Q9NQV1|Q9NQV2	Silent	SNP	ENST00000366837.4	37	CCDS1547.1																																																																																			T|0.980;C|0.020	0.020	strong		0.572	EPHX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092064.1	NM_000120	
TBC1D9B	23061	hgsc.bcm.edu	37	5	179300131	179300131	+	Silent	SNP	T	T	C	rs269469	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:179300131T>C	ENST00000356834.3	-	13	2341	c.2304A>G	c.(2302-2304)aaA>aaG	p.K768K	TBC1D9B_ENST00000519746.1_5'Flank|TBC1D9B_ENST00000355235.3_Silent_p.K768K|TBC1D9B_ENST00000444477.2_5'Flank	NM_198868.2	NP_942568.2	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	768						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	28	all_cancers(89;0.000197)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0236)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CATAGGACACTTTCAGGAGCT	0.612													T|||	624	0.124601	0.4455	0.0432	5008	,	,		17765	0.0		0.005	False		,,,				2504	0.0				p.K768K		Atlas-SNP	.											.	TBC1D9B	157	.	0			c.A2304G						PASS	.	T	,	1538,2866	480.4+/-358.8	282,974,946	56.0	56.0	56.0		2304,2304	-0.1	1.0	5	dbSNP_79	56	15,8585	9.1+/-34.3	0,15,4285	no	coding-synonymous,coding-synonymous	TBC1D9B	NM_015043.3,NM_198868.2	,	282,989,5231	CC,CT,TT		0.1744,34.9228,11.9425	,	768/1234,768/1251	179300131	1553,11451	2202	4300	6502	SO:0001819	synonymous_variant	23061	exon13			GGACACTTTCAGG	AB014576	CCDS4450.1, CCDS43408.1	5q35.3	2013-01-10			ENSG00000197226	ENSG00000197226		"""EF-hand domain containing"""	29097	protein-coding gene	gene with protein product						9734811	Standard	NM_198868		Approved	KIAA0676	uc003mlh.3	Q66K14	OTTHUMG00000130911	ENST00000356834.3:c.2304A>G	5.37:g.179300131T>C		144.0	0.0	0		139.0	60.0	0.431655	NM_198868	D3DWQ5|D3DWQ6|O75163|Q53EY0|Q6MZI2|Q96H49	Silent	SNP	ENST00000356834.3	37	CCDS43408.1																																																																																			T|0.899;C|0.101	0.101	strong		0.612	TBC1D9B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253501.3	NM_015043	
EGFR	1956	hgsc.bcm.edu	37	7	55238087	55238087	+	Intron	SNP	C	C	T	rs10258429	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:55238087C>T	ENST00000275493.2	+	16	2057				EGFR_ENST00000454757.2_Intron|EGFR_ENST00000455089.1_Intron|EGFR_ENST00000344576.2_Silent_p.H656H|EGFR_ENST00000442591.1_Intron	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor						activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	GCGTGTCCCACCAGAGCGGGA	0.512		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			C|||	563	0.11242	0.2398	0.049	5008	,	,		20745	0.0496		0.0736	False		,,,				2504	0.09				p.H656H		Atlas-SNP	.	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"""epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"""		"""E, O"""	.	EGFR	20426	.	0			c.C1968T						PASS	.	C	,	922,3484	352.1+/-311.5	101,720,1382	108.0	89.0	95.0		,1968	2.4	0.0	7	dbSNP_119	95	606,7994	158.6+/-212.1	23,560,3717	no	intron,coding-synonymous	EGFR	NM_005228.3,NM_201284.1	,	124,1280,5099	TT,TC,CC		7.0465,20.926,11.7484	,	,656/706	55238087	1528,11478	2203	4300	6503	SO:0001627	intron_variant	1956	exon16	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	GTCCCACCAGAGC		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.1881-781C>T	7.37:g.55238087C>T		161.0	0.0	0		147.0	79.0	0.537415	NM_201284	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																			C|0.889;T|0.111	0.111	strong		0.512	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
PCDHB8	56128	hgsc.bcm.edu	37	5	140558384	140558384	+	Missense_Mutation	SNP	C	C	T	rs116452537	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140558384C>T	ENST00000239444.2	+	1	1014	c.769C>T	c.(769-771)Cca>Tca	p.P257S	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	257	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)			NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGAGGACAGTCCAATAAGCTT	0.458													C|||	27	0.00539137	0.0204	0.0	5008	,	,		15847	0.0		0.0	False		,,,				2504	0.0				p.P257S		Atlas-SNP	.											.	PCDHB8	199	.	0			c.C769T						PASS	.	C	SER/PRO	68,4338	61.7+/-98.7	1,66,2136	209.0	277.0	254.0		769	3.3	0.9	5	dbSNP_132	254	0,8600		0,0,4300	yes	missense	PCDHB8	NM_019120.3	74	1,66,6436	TT,TC,CC		0.0,1.5433,0.5228	benign	257/802	140558384	68,12938	2203	4300	6503	SO:0001583	missense	56128	exon1			GACAGTCCAATAA	AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"""Cadherins / Protocadherins : Clustered"""	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.769C>T	5.37:g.140558384C>T	ENSP00000239444:p.Pro257Ser	469.0	1.0	0.0021322		285.0	140.0	0.491228	NM_019120	B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	37	CCDS4250.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	c	13.53	2.263792	0.39995	0.015433	0.0	ENSG00000120322	ENST00000239444	T	0.54279	0.58	4.25	3.33	0.38152	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.41971	0.1182	M	0.79011	2.435	0.32980	D	0.523474	B	0.26935	0.164	B	0.33690	0.168	T	0.67604	-0.5628	9	0.62326	D	0.03	.	13.5777	0.61883	0.0:0.8433:0.1567:0.0	.	257	Q9UN66	PCDB8_HUMAN	S	257	ENSP00000239444:P257S	ENSP00000239444:P257S	P	+	1	0	PCDHB8	140538568	0.033000	0.19621	0.908000	0.35775	0.609000	0.37215	2.681000	0.46926	1.911000	0.55334	0.585000	0.79938	CCA	C|0.994;T|0.006	0.006	strong		0.458	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
PDGFRB	5159	hgsc.bcm.edu	37	5	149509508	149509508	+	Missense_Mutation	SNP	G	G	A	rs74943037	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149509508G>A	ENST00000261799.4	-	10	1860	c.1391C>T	c.(1390-1392)aCg>aTg	p.T464M		NM_002609.3	NP_002600.1	P09619	PGFRB_HUMAN	platelet-derived growth factor receptor, beta polypeptide	464	Ig-like C2-type 5.				adrenal gland development (GO:0030325)|aorta morphogenesis (GO:0035909)|cardiac myofibril assembly (GO:0055003)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|cell migration involved in coronary angiogenesis (GO:0060981)|cell migration involved in vasculogenesis (GO:0035441)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|glycosaminoglycan biosynthetic process (GO:0006024)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|metanephric comma-shaped body morphogenesis (GO:0072278)|metanephric glomerular capillary formation (GO:0072277)|metanephric glomerular mesangial cell proliferation involved in metanephros development (GO:0072262)|metanephric mesenchymal cell migration (GO:0035789)|metanephric mesenchyme development (GO:0072075)|metanephric S-shaped body morphogenesis (GO:0072284)|negative regulation of apoptotic process (GO:0043066)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|positive regulation of calcium ion import (GO:0090280)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of chemotaxis (GO:0050921)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway (GO:0035793)|positive regulation of mitosis (GO:0045840)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to estradiol (GO:0032355)|response to fluid shear stress (GO:0034405)|response to hydrogen peroxide (GO:0042542)|response to hyperoxia (GO:0055093)|response to retinoic acid (GO:0032526)|response to toxic substance (GO:0009636)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|skeletal system morphogenesis (GO:0048705)|smooth muscle cell chemotaxis (GO:0071670)|smooth muscle tissue development (GO:0048745)|tissue homeostasis (GO:0001894)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intrinsic component of plasma membrane (GO:0031226)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|platelet-derived growth factor-activated receptor activity (GO:0005017)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|vascular endothelial growth factor binding (GO:0038085)	p.T464M(1)		breast(3)|central_nervous_system(5)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(3)|prostate(3)|skin(3)|stomach(6)|urinary_tract(1)	75		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		Becaplermin(DB00102)|Dasatinib(DB01254)|Imatinib(DB00619)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CCCCAGCAGCGTGGGCGGCAG	0.612			T	"""ETV6, TRIP11, HIP1, RAB5EP, H4, NIN, HCMOGT-1, PDE4DIP"""	"""MPD, AML, CMML, CML"""						OREG0016927	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	138	0.0275559	0.0953	0.0115	5008	,	,		20674	0.001		0.003	False		,,,				2504	0.0				p.T464M		Atlas-SNP	.		Dom	yes		5	5q31-q32	5159	"""platelet-derived growth factor receptor, beta polypeptide"""		L	PDGFRB,NS,carcinoma,0,1	PDGFRB	142	1	1	Substitution - Missense(1)	stomach(1)	c.C1391T						scavenged	.	G	MET/THR	393,4013	195.3+/-220.0	26,341,1836	102.0	74.0	84.0		1391	3.8	0.8	5	dbSNP_131	84	3,8597	3.0+/-9.4	0,3,4297	yes	missense	PDGFRB	NM_002609.3	81	26,344,6133	AA,AG,GG		0.0349,8.9197,3.0447	probably-damaging	464/1107	149509508	396,12610	2203	4300	6503	SO:0001583	missense	5159	exon10			AGCAGCGTGGGCG	M21616	CCDS4303.1	5q33.1	2013-01-29			ENSG00000113721	ENSG00000113721		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	8804	protein-coding gene	gene with protein product		173410		PDGFR			Standard	XM_005268464		Approved	JTK12, CD140b, PDGFR1	uc003lro.3	P09619	OTTHUMG00000130053	ENST00000261799.4:c.1391C>T	5.37:g.149509508G>A	ENSP00000261799:p.Thr464Met	100.0	1.0	0.01	1725	133.0	58.0	0.43609	NM_002609	B5A957|Q8N5L4	Missense_Mutation	SNP	ENST00000261799.4	37	CCDS4303.1	56	0.02564102564102564	51	0.10365853658536585	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	6.709	0.499568	0.12762	0.089197	3.49E-4	ENSG00000113721	ENST00000261799;ENST00000544453	T	0.76316	-1.01	4.64	3.76	0.43208	.	0.276731	0.27821	N	0.017704	T	0.06462	0.0166	L	0.59436	1.845	0.27164	N	0.961099	P;B	0.45634	0.863;0.122	B;B	0.39531	0.302;0.022	T	0.04140	-1.0974	10	0.33940	T	0.23	.	12.9704	0.58510	0.0865:0.0:0.9135:0.0	.	464;464	A8KAM8;P09619	.;PGFRB_HUMAN	M	464;134	ENSP00000261799:T464M	ENSP00000261799:T464M	T	-	2	0	PDGFRB	149489701	0.297000	0.24408	0.838000	0.33150	0.007000	0.05969	0.467000	0.22035	0.583000	0.29574	-1.598000	0.00824	ACG	G|0.972;A|0.028	0.028	strong		0.612	PDGFRB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252332.1	NM_002609	
NEIL3	55247	hgsc.bcm.edu	37	4	178283474	178283474	+	Missense_Mutation	SNP	A	A	G	rs35418725	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:178283474A>G	ENST00000264596.3	+	10	1785	c.1667A>G	c.(1666-1668)cAt>cGt	p.H556R		NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	556			H -> R (in dbSNP:rs35418725). {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)			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)		TTCTGCAACCATGGCAAGCGT	0.383								Base excision repair (BER), DNA glycosylases					A|||	24	0.00479233	0.0174	0.0014	5008	,	,		19183	0.0		0.0	False		,,,				2504	0.0				p.H556R		Atlas-SNP	.											.	NEIL3	89	.	0			c.A1667G						PASS	.	A	ARG/HIS	74,4332	60.5+/-97.4	0,74,2129	93.0	94.0	94.0		1667	3.5	1.0	4	dbSNP_126	94	0,8600		0,0,4300	yes	missense	NEIL3	NM_018248.2	29	0,74,6429	GG,GA,AA		0.0,1.6795,0.569	possibly-damaging	556/606	178283474	74,12932	2203	4300	6503	SO:0001583	missense	55247	exon10			GCAACCATGGCAA	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.1667A>G	4.37:g.178283474A>G	ENSP00000264596:p.His556Arg	146.0	0.0	0		124.0	55.0	0.443548	NM_018248	Q2PPJ3|Q8NG51|Q9NV95	Missense_Mutation	SNP	ENST00000264596.3	37	CCDS3828.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	A	17.52	3.409952	0.62399	0.016795	0.0	ENSG00000109674	ENST00000264596	T	0.26223	1.75	4.63	3.45	0.39498	Zinc finger, GRF-type (1);	0.000000	0.85682	D	0.000000	T	0.42017	0.1184	H	0.94542	3.55	0.58432	D	0.999995	D	0.64830	0.994	D	0.70487	0.969	T	0.61936	-0.6960	10	0.87932	D	0	-19.9676	10.3252	0.43790	0.9223:0.0:0.0777:0.0	rs35418725	556	Q8TAT5	NEIL3_HUMAN	R	556	ENSP00000264596:H556R	ENSP00000264596:H556R	H	+	2	0	NEIL3	178520468	1.000000	0.71417	0.983000	0.44433	0.753000	0.42808	8.872000	0.92352	0.937000	0.37394	0.402000	0.26972	CAT	A|0.996;G|0.004	0.004	strong		0.383	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1	NM_018248	
GLT1D1	144423	hgsc.bcm.edu	37	12	129360518	129360518	+	Missense_Mutation	SNP	G	G	A	rs73438369	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:129360518G>A	ENST00000442111.2	+	2	216	c.128G>A	c.(127-129)aGc>aAc	p.S43N	GLT1D1_ENST00000281703.6_Missense_Mutation_p.S43N|GLT1D1_ENST00000537468.1_Missense_Mutation_p.S32N|GLT1D1_ENST00000542193.1_5'UTR			Q96MS3	GL1D1_HUMAN	glycosyltransferase 1 domain containing 1	43					biosynthetic process (GO:0009058)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(13)|prostate(1)|skin(1)|urinary_tract(1)	26	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.97e-06)|Epithelial(86;3.97e-05)|all cancers(50;0.00019)		GACTTTGAAAGCCGATCTGAG	0.488													G|||	82	0.0163738	0.059	0.0058	5008	,	,		16943	0.0		0.0	False		,,,				2504	0.0				p.S43N		Atlas-SNP	.											.	GLT1D1	48	.	0			c.G128A						PASS	.	G	ASN/SER	227,4179	135.3+/-171.4	3,221,1979	162.0	164.0	163.0		128	4.7	0.1	12	dbSNP_130	163	3,8597	3.7+/-12.6	0,3,4297	yes	missense	GLT1D1	NM_144669.1	46	3,224,6276	AA,AG,GG		0.0349,5.1521,1.7684	probably-damaging	43/267	129360518	230,12776	2203	4300	6503	SO:0001583	missense	144423	exon2			TTGAAAGCCGATC		CCDS9265.1	12q24.32	2013-02-22			ENSG00000151948	ENSG00000151948		"""Glycosyltransferase group 1 domain containing"""	26483	protein-coding gene	gene with protein product							Standard	NM_144669		Approved	FLJ31978	uc001uhx.1	Q96MS3	OTTHUMG00000168437	ENST00000442111.2:c.128G>A	12.37:g.129360518G>A	ENSP00000394692:p.Ser43Asn	140.0	0.0	0		151.0	72.0	0.476821	NM_144669	Q86XG8	Missense_Mutation	SNP	ENST00000442111.2	37		31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	G	13.77	2.334875	0.41297	0.051521	3.49E-4	ENSG00000151948	ENST00000442111;ENST00000281703;ENST00000537468	T;T;T	0.79247	-1.25;0.74;0.69	5.54	4.65	0.58169	.	0.144833	0.64402	N	0.000006	T	0.46678	0.1405	M	0.77616	2.38	0.32213	N	0.576306	D;B	0.89917	1.0;0.037	D;B	0.76071	0.987;0.039	T	0.74163	-0.3754	10	0.22706	T	0.39	-25.057	9.1417	0.36908	0.0789:0.1461:0.775:0.0	.	32;43	F5H088;Q96MS3-2	.;.	N	43;43;32	ENSP00000394692:S43N;ENSP00000281703:S43N;ENSP00000438158:S32N	ENSP00000281703:S43N	S	+	2	0	GLT1D1	127926471	0.963000	0.33076	0.145000	0.22337	0.327000	0.28475	1.719000	0.38011	1.320000	0.45209	0.655000	0.94253	AGC	G|0.981;A|0.019	0.019	strong		0.488	GLT1D1-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000399740.1	NM_144669	
MAATS1	89876	hgsc.bcm.edu	37	3	119445139	119445139	+	Silent	SNP	A	A	G	rs9835381	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119445139A>G	ENST00000273390.5	+	7	881	c.804A>G	c.(802-804)aaA>aaG	p.K268K		NM_033364.3	NP_203528	Q7Z4T9	MAAT1_HUMAN	MYCBP-associated, testis expressed 1	268						mitochondrion (GO:0005739)											AGAGGAGGAAAATGATGAATG	0.517													G|||	70	0.0139776	0.0514	0.0014	5008	,	,		19708	0.0		0.0	False		,,,				2504	0.001				p.K268K		Atlas-SNP	.											.	.	.	.	0			c.A804G						PASS	.	G		209,4197	807.1+/-415.9	3,203,1997	69.0	67.0	67.0		804	4.6	1.0	3	dbSNP_119	67	4,8596	819.0+/-406.8	1,2,4297	no	coding-synonymous	C3orf15	NM_033364.3		4,205,6294	GG,GA,AA		0.0465,4.7435,1.6377		268/768	119445139	213,12793	2203	4300	6503	SO:0001819	synonymous_variant	89876	exon7			GAGGAAAATGATG	AB063296	CCDS2994.1	3q12-q13.3	2014-07-31	2012-12-07	2012-09-26	ENSG00000183833	ENSG00000183833			24010	protein-coding gene	gene with protein product	"""AMY-1-associating protein expressed in testis 1"", ""MYCBP-binding protein"", ""spermatogenesis associated 26"""	609910	"""chromosome 3 open reading frame 15"", ""MYCBP/AMY-1-associated, testis expressed 1"""	C3orf15		12223483, 14551891, 17967944	Standard	NM_033364		Approved	AAT1, AAT1alpha, SPATA26, CaM-IP2	uc003ede.4	Q7Z4T9	OTTHUMG00000159422	ENST00000273390.5:c.804A>G	3.37:g.119445139A>G		153.0	0.0	0		131.0	62.0	0.473282	NM_033364	A0AVK2|A8K1J9|B3KP23|B4DG52|B4DZ14|C9JUG4|Q68DX2|Q8TD41|Q96A45|Q96JE8	Silent	SNP	ENST00000273390.5	37	CCDS2994.1																																																																																			A|0.983;G|0.017	0.017	strong		0.517	MAATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355222.1	NM_033364	
ACVRL1	94	hgsc.bcm.edu	37	12	52308344	52308344	+	Silent	SNP	G	G	A	rs1058563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52308344G>A	ENST00000388922.4	+	6	1030	c.747G>A	c.(745-747)gtG>gtA	p.V249V	ACVRL1_ENST00000550683.1_Silent_p.V263V|ACVRL1_ENST00000419526.2_Silent_p.V75V	NM_000020.2	NP_000011.2	P37023	ACVL1_HUMAN	activin A receptor type II-like 1	249	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activin receptor signaling pathway (GO:0032924)|angiogenesis (GO:0001525)|artery development (GO:0060840)|blood circulation (GO:0008015)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|blood vessel maturation (GO:0001955)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|cellular response to BMP stimulus (GO:0071773)|cellular response to transforming growth factor beta stimulus (GO:0071560)|endothelial tube morphogenesis (GO:0061154)|in utero embryonic development (GO:0001701)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of focal adhesion assembly (GO:0051895)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of blood pressure (GO:0008217)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of DNA replication (GO:0006275)|regulation of endothelial cell proliferation (GO:0001936)|regulation of transcription, DNA-templated (GO:0006355)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|venous blood vessel development (GO:0060841)|wound healing, spreading of epidermal cells (GO:0035313)	cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	activin binding (GO:0048185)|activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|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 I (GO:0005025)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|urinary_tract(1)	20				BRCA - Breast invasive adenocarcinoma(357;0.0991)	Adenosine triphosphate(DB00171)	ATAACACAGTGTTGCTCAGAC	0.592													G|||	231	0.0461262	0.1619	0.0159	5008	,	,		10490	0.0		0.006	False		,,,				2504	0.0				p.V249V		Atlas-SNP	.											.	ACVRL1	60	.	0			c.G747A						PASS	.	G	,	576,3830	254.3+/-259.9	37,502,1664	94.0	71.0	79.0		747,747	1.9	0.4	12	dbSNP_86	79	17,8583	11.2+/-40.8	0,17,4283	no	coding-synonymous,coding-synonymous	ACVRL1	NM_000020.2,NM_001077401.1	,	37,519,5947	AA,AG,GG		0.1977,13.0731,4.5594	,	249/504,249/504	52308344	593,12413	2203	4300	6503	SO:0001819	synonymous_variant	94	exon6			CACAGTGTTGCTC	L17075	CCDS31804.1	12q13.13	2014-09-17			ENSG00000139567	ENSG00000139567			175	protein-coding gene	gene with protein product		601284		ACVRLK1, ORW2		8397373, 8640225	Standard	NM_000020		Approved	HHT2, ALK1, HHT	uc001rzk.3	P37023	OTTHUMG00000169507	ENST00000388922.4:c.747G>A	12.37:g.52308344G>A		190.0	0.0	0		221.0	113.0	0.511312	NM_000020	A6NGA8	Silent	SNP	ENST00000388922.4	37	CCDS31804.1																																																																																			G|0.957;A|0.043	0.043	strong		0.592	ACVRL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404520.2		
DDX49	54555	hgsc.bcm.edu	37	19	19035080	19035080	+	Missense_Mutation	SNP	G	G	C	rs143159618		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:19035080G>C	ENST00000247003.4	+	7	882	c.815G>C	c.(814-816)aGc>aCc	p.S272T	AC002985.3_ENST00000596918.1_Intron|DDX49_ENST00000599156.1_3'UTR|DDX49_ENST00000438170.2_Missense_Mutation_p.S165T	NM_019070.4	NP_061943.2	Q9Y6V7	DDX49_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 49	272	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.						ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(6)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	18			Epithelial(12;0.0289)			CGCAAATTCAGCTTCCCCACC	0.617													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17489	0.0		0.0	False		,,,				2504	0.0				p.S272T		Atlas-SNP	.											.	DDX49	37	.	0			c.G815C						PASS	.	G	THR/SER	6,4400	11.4+/-27.6	0,6,2197	122.0	71.0	88.0		815	-2.3	0.8	19	dbSNP_134	88	0,8600		0,0,4300	no	missense	DDX49	NM_019070.4	58	0,6,6497	CC,CG,GG		0.0,0.1362,0.0461	benign	272/484	19035080	6,13000	2203	4300	6503	SO:0001583	missense	54555	exon7			AATTCAGCTTCCC		CCDS12390.1	19p12	2008-02-05				ENSG00000105671		"""DEAD-boxes"""	18684	protein-coding gene	gene with protein product							Standard	NM_019070		Approved	FLJ10432	uc002nkq.2	Q9Y6V7		ENST00000247003.4:c.815G>C	19.37:g.19035080G>C	ENSP00000247003:p.Ser272Thr	214.0	0.0	0		231.0	99.0	0.428571	NM_019070	E7ENA0|Q53FJ1|Q9BVQ8	Missense_Mutation	SNP	ENST00000247003.4	37	CCDS12390.1	.	.	.	.	.	.	.	.	.	.	G	13.72	2.320348	0.41096	0.001362	0.0	ENSG00000105671	ENST00000247003;ENST00000438170	T;T	0.04862	3.54;3.54	5.03	-2.29	0.06805	Helicase, C-terminal (3);	0.775582	0.12437	N	0.469041	T	0.05410	0.0143	N	0.19112	0.55	0.24060	N	0.996013	B;B	0.06786	0.001;0.001	B;B	0.19946	0.027;0.027	T	0.29119	-1.0022	10	0.72032	D	0.01	-7.7016	15.0157	0.71581	0.3142:0.0:0.6858:0.0	.	272;272	A8K7A1;Q9Y6V7	.;DDX49_HUMAN	T	272;165	ENSP00000247003:S272T;ENSP00000395377:S165T	ENSP00000247003:S272T	S	+	2	0	DDX49	18896080	0.161000	0.22892	0.824000	0.32777	0.934000	0.57294	0.102000	0.15272	-1.026000	0.03330	-0.339000	0.08088	AGC	G|1.000;C|0.000	0.000	weak		0.617	DDX49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464593.1	NM_019070	
OR1E1	8387	hgsc.bcm.edu	37	17	3301246	3301246	+	Silent	SNP	G	G	A	rs11078447	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3301246G>A	ENST00000322608.2	-	1	458	c.459C>T	c.(457-459)acC>acT	p.T153T		NM_003553.2	NP_003544.2	P30953	OR1E1_HUMAN	olfactory receptor, family 1, subfamily E, member 1	153					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)			endometrium(3)|large_intestine(2)|lung(5)	10						TGGCATGGAAGGTGGTCAGCA	0.542													G|||	110	0.0219649	0.0772	0.0115	5008	,	,		22193	0.0		0.0	False		,,,				2504	0.0				p.T153T		Atlas-SNP	.											.	OR1E1	37	.	0			c.C459T						PASS	.	G		240,4166	140.8+/-176.2	5,230,1968	77.0	61.0	66.0		459	-9.4	0.0	17	dbSNP_120	66	2,8598		0,2,4298	no	coding-synonymous	OR1E1	NM_003553.2		5,232,6266	AA,AG,GG		0.0233,5.4471,1.8607		153/315	3301246	242,12764	2203	4300	6503	SO:0001819	synonymous_variant	8387	exon1			ATGGAAGGTGGTC	U04642	CCDS11024.1	17p13.3	2012-08-09			ENSG00000180016	ENSG00000180016		"""GPCR / Class A : Olfactory receptors"""	8189	protein-coding gene	gene with protein product				OR1E9P, OR1E5, OR1E6		8004088, 1370859	Standard	NM_003553		Approved	OR17-2, HGM071, OR17-32, OR13-66	uc002fvj.1	P30953	OTTHUMG00000090643	ENST00000322608.2:c.459C>T	17.37:g.3301246G>A		200.0	0.0	0		243.0	121.0	0.497942	NM_003553	O43884|P47882|P47885|Q6IFA9|Q6IFM5|Q9UBJ1|Q9UM60	Silent	SNP	ENST00000322608.2	37	CCDS11024.1																																																																																			G|0.983;A|0.017	0.017	strong		0.542	OR1E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207303.1	NM_003553	
GADL1	339896	hgsc.bcm.edu	37	3	30842517	30842517	+	Missense_Mutation	SNP	C	C	A	rs61738477	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:30842517C>A	ENST00000282538.5	-	12	1264	c.1114G>T	c.(1114-1116)Gat>Tat	p.D372Y	GADL1_ENST00000454381.3_Missense_Mutation_p.D372Y	NM_207359.2	NP_997242.2	Q6ZQY3	GADL1_HUMAN	glutamate decarboxylase-like 1	372					carboxylic acid metabolic process (GO:0019752)		aspartate 1-decarboxylase activity (GO:0004068)|pyridoxal phosphate binding (GO:0030170)|sulfinoalanine decarboxylase activity (GO:0004782)			breast(2)|endometrium(3)|kidney(2)|lung(17)|upper_aerodigestive_tract(1)	25						TAGCTCACATCATAGAATTTA	0.418													C|||	22	0.00439297	0.0144	0.0043	5008	,	,		19418	0.0		0.0	False		,,,				2504	0.0				p.D372Y		Atlas-SNP	.											.	GADL1	91	.	0			c.G1114T						PASS	.	C	TYR/ASP	66,4340	60.5+/-97.4	1,64,2138	132.0	117.0	122.0		1114	5.5	1.0	3	dbSNP_129	122	1,8599	1.2+/-3.3	0,1,4299	yes	missense	GADL1	NM_207359.2	160	1,65,6437	AA,AC,CC		0.0116,1.498,0.5151	probably-damaging	372/522	30842517	67,12939	2203	4300	6503	SO:0001583	missense	339896	exon12			TCACATCATAGAA	AK128643	CCDS2649.2	3p23-p22	2009-01-14			ENSG00000144644	ENSG00000144644			27949	protein-coding gene	gene with protein product		615601					Standard	NM_207359		Approved		uc003cep.2	Q6ZQY3	OTTHUMG00000130621	ENST00000282538.5:c.1114G>T	3.37:g.30842517C>A	ENSP00000282538:p.Asp372Tyr	99.0	0.0	0		122.0	46.0	0.377049	NM_207359		Missense_Mutation	SNP	ENST00000282538.5	37	CCDS2649.2	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	C	26.6	4.752769	0.89753	0.01498	1.16E-4	ENSG00000144644	ENST00000282538;ENST00000454381	T;T	0.43688	0.94;0.94	5.47	5.47	0.80525	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.052957	0.64402	D	0.000001	T	0.68696	0.3029	M	0.93375	3.41	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.80311	-0.1436	10	0.87932	D	0	.	19.3171	0.94218	0.0:1.0:0.0:0.0	.	372	Q6ZQY3	GADL1_HUMAN	Y	372	ENSP00000282538:D372Y;ENSP00000427059:D372Y	ENSP00000282538:D372Y	D	-	1	0	GADL1	30817521	1.000000	0.71417	0.998000	0.56505	0.976000	0.68499	7.487000	0.81328	2.571000	0.86741	0.585000	0.79938	GAT	C|0.996;A|0.004	0.004	strong		0.418	GADL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253106.2	NM_207359	
CLUAP1	23059	hgsc.bcm.edu	37	16	3556398	3556398	+	Missense_Mutation	SNP	G	G	T	rs34115694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3556398G>T	ENST00000576634.1	+	3	346	c.202G>T	c.(202-204)Gca>Tca	p.A68S	CLUAP1_ENST00000571025.1_Missense_Mutation_p.A68S|CLUAP1_ENST00000341633.5_Missense_Mutation_p.A68S|CLUAP1_ENST00000417763.2_5'UTR|LA16c-306E5.3_ENST00000574423.2_RNA	NM_015041.2	NP_055856.1	Q96AJ1	CLUA1_HUMAN	clusterin associated protein 1	68			A -> S (in dbSNP:rs34115694).		cilium assembly (GO:0042384)	centrosome (GO:0005813)|cilium (GO:0005929)|intracellular membrane-bounded organelle (GO:0043231)|intraciliary transport particle B (GO:0030992)|nucleus (GO:0005634)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(2)	16						CTTCATTAAGGCAATTGCCCA	0.438													G|||	130	0.0259585	0.0968	0.0029	5008	,	,		18976	0.0		0.0	False		,,,				2504	0.0				p.A68S		Atlas-SNP	.											.	CLUAP1	32	.	0			c.G202T						PASS	.	G	SER/ALA	337,4057	178.7+/-207.4	8,321,1868	158.0	139.0	146.0		202	5.5	1.0	16	dbSNP_126	146	3,8597	3.0+/-9.4	0,3,4297	yes	missense	CLUAP1	NM_015041.1	99	8,324,6165	TT,TG,GG		0.0349,7.6695,2.6166	benign	68/414	3556398	340,12654	2197	4300	6497	SO:0001583	missense	23059	exon3			ATTAAGGCAATTG	BC017070	CCDS32381.1, CCDS45398.1	16p13.3	2014-07-18				ENSG00000103351		"""Intraflagellar transport homologs"""	19009	protein-coding gene	gene with protein product	"""flagellar associated protein 22, qilin-like protein, homolog (Chlamydomonas)"", ""cilia and flagella associated protein 22"""					15480429, 9734811, 19253336	Standard	NM_015041		Approved	FLJ13297, KIAA0643, FAP22, CFAP22	uc002cvk.2	Q96AJ1		ENST00000576634.1:c.202G>T	16.37:g.3556398G>T	ENSP00000460850:p.Ala68Ser	98.0	0.0	0		101.0	63.0	0.623762	NM_015041	O75138|Q65ZA3|Q9H8R4|Q9H8T1	Missense_Mutation	SNP	ENST00000576634.1	37	CCDS32381.1	60	0.027472527472527472	59	0.11991869918699187	1	0.0027624309392265192	0	0.0	0	0.0	G	16.19	3.053615	0.55218	0.076695	3.49E-4	ENSG00000103351	ENST00000341633	T	0.43688	0.94	5.49	5.49	0.81192	.	0.046661	0.85682	D	0.000000	T	0.00384	0.0012	N	0.11789	0.175	0.80722	D	1	P	0.39903	0.694	B	0.39339	0.297	T	0.03969	-1.0988	10	0.12766	T	0.61	-16.0476	17.213	0.86935	0.0:0.0:1.0:0.0	rs34115694	68	Q96AJ1	CLUA1_HUMAN	S	68	ENSP00000344392:A68S	ENSP00000344392:A68S	A	+	1	0	CLUAP1	3496399	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.503000	0.81632	2.745000	0.94114	0.557000	0.71058	GCA	G|0.974;T|0.026	0.026	strong		0.438	CLUAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437883.2	NM_024793	
ACSM2A	123876	hgsc.bcm.edu	37	16	20471487	20471487	+	Missense_Mutation	SNP	G	G	C	rs137947890	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:20471487G>C	ENST00000573854.1	+	2	165	c.51G>C	c.(49-51)caG>caC	p.Q17H	ACSM2A_ENST00000575690.1_Missense_Mutation_p.Q17H|ACSM2A_ENST00000396104.2_Missense_Mutation_p.Q17H|ACSM2A_ENST00000417235.2_Intron|ACSM2A_ENST00000424070.1_Missense_Mutation_p.Q17H|ACSM2A_ENST00000219054.6_Missense_Mutation_p.Q17H|ACSM2A_ENST00000536134.1_5'UTR|ACSM2A_ENST00000575558.1_Intron	NM_001010845.2	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member 2A	17					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						GGGGTACTCAGATGTCCAGCC	0.493													G|||	85	0.0169728	0.0635	0.0014	5008	,	,		18245	0.0		0.0	False		,,,				2504	0.0				p.Q17H		Atlas-SNP	.											.	ACSM2A	120	.	0			c.G51C						PASS	.	G	HIS/GLN	220,4186	133.7+/-170.0	8,204,1991	46.0	48.0	47.0		51	1.0	0.0	16	dbSNP_134	47	5,8589	4.3+/-15.6	0,5,4292	no	missense	ACSM2A	NM_001010845.2	24	8,209,6283	CC,CG,GG		0.0582,4.9932,1.7308	benign	17/578	20471487	225,12775	2203	4297	6500	SO:0001583	missense	123876	exon3			TACTCAGATGTCC	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.51G>C	16.37:g.20471487G>C	ENSP00000459451:p.Gln17His	124.0	0.0	0		120.0	68.0	0.566667	NM_001010845	B3KTT9|O75202	Missense_Mutation	SNP	ENST00000573854.1	37	CCDS32401.1	30	0.013736263736263736	29	0.05894308943089431	0	0.0	0	0.0	1	0.0013192612137203166	G	7.282	0.609329	0.14066	0.049932	5.82E-4	ENSG00000183747	ENST00000219054;ENST00000424070;ENST00000396104	T;T;T	0.43688	0.94;2.24;0.94	3.28	1.03	0.20045	.	0.746597	0.11304	N	0.577908	T	0.02380	0.0073	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.15407	-1.0438	10	0.14252	T	0.57	-4.0391	5.9796	0.19399	0.1217:0.1954:0.6829:0.0	.	17	Q08AH3	ACS2A_HUMAN	H	17	ENSP00000219054:Q17H;ENSP00000394904:Q17H;ENSP00000379411:Q17H	ENSP00000219054:Q17H	Q	+	3	2	ACSM2A	20378988	0.000000	0.05858	0.001000	0.08648	0.661000	0.39034	0.388000	0.20735	0.709000	0.31976	0.454000	0.30748	CAG	.	.	weak		0.493	ACSM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436764.1	NM_001010845	
FBXW9	84261	hgsc.bcm.edu	37	19	12805431	12805431	+	Missense_Mutation	SNP	T	T	C	rs10424623	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12805431T>C	ENST00000380339.3	-	3	691	c.655A>G	c.(655-657)Act>Gct	p.T219A	FBXW9_ENST00000544494.1_5'UTR|FBXW9_ENST00000393261.3_Missense_Mutation_p.T219A|FBXW9_ENST00000587955.1_Missense_Mutation_p.T209A			Q5XUX1	FBXW9_HUMAN	F-box and WD repeat domain containing 9	219			T -> A (in dbSNP:rs10424623).		SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)					cervix(1)|lung(4)|ovary(1)|prostate(1)	7						TTTCGCTTAGTGCCTAAGGTC	0.562													T|||	748	0.149361	0.534	0.0461	5008	,	,		19047	0.0		0.0099	False		,,,				2504	0.0				p.T219A		Atlas-SNP	.											.	FBXW9	30	.	0			c.A655G						PASS	.	T	ALA/THR	1743,2441		372,999,721	65.0	74.0	71.0		655	2.1	0.2	19	dbSNP_119	71	133,8305		1,131,4087	yes	missense	FBXW9	NM_032301.2	58	373,1130,4808	CC,CT,TT		1.5762,41.6587,14.8629	benign	219/459	12805431	1876,10746	2092	4219	6311	SO:0001583	missense	84261	exon3			GCTTAGTGCCTAA	BC004290	CCDS12278.2	19p13.2	2013-01-09	2007-02-08		ENSG00000132004	ENSG00000132004		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	28136	protein-coding gene	gene with protein product		609074	"""F-box and WD-40 domain protein 9"""			12477932	Standard	NM_032301		Approved	MGC10870, Fbw9	uc002mum.1	Q5XUX1	OTTHUMG00000150152	ENST00000380339.3:c.655A>G	19.37:g.12805431T>C	ENSP00000369696:p.Thr219Ala	81.0	0.0	0		108.0	48.0	0.444444	NM_032301	B3KVP7|Q9BT89	Missense_Mutation	SNP	ENST00000380339.3	37		244	0.11172161172161173	220	0.44715447154471544	17	0.04696132596685083	0	0.0	7	0.009234828496042216	T	5.162	0.215402	0.09810	0.416587	0.015762	ENSG00000132004	ENST00000393261;ENST00000380339	T;T	0.51325	1.74;0.71	4.29	2.11	0.27256	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.565790	0.18087	N	0.152109	T	0.00012	0.0000	N	0.24115	0.695	0.21386	P	0.999707688	B;B;B	0.17268	0.013;0.009;0.021	B;B;B	0.16289	0.014;0.015;0.009	T	0.46219	-0.9207	9	0.32370	T	0.25	-17.2872	5.0146	0.14330	0.162:0.0922:0.0:0.7458	rs10424623	209;219;219	Q5XUX1-2;Q5XUX1;Q5XUX1-3	.;FBXW9_HUMAN;.	A	219	ENSP00000376945:T219A;ENSP00000369696:T219A	ENSP00000369696:T219A	T	-	1	0	FBXW9	12666431	0.259000	0.24043	0.235000	0.24058	0.003000	0.03518	0.704000	0.25661	0.190000	0.20209	0.379000	0.24179	ACT	T|0.921;C|0.079	0.079	strong		0.562	FBXW9-201	KNOWN	basic	protein_coding	protein_coding		NM_032301	
SPTA1	6708	hgsc.bcm.edu	37	1	158632531	158632531	+	Missense_Mutation	SNP	T	T	C	rs7547313	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158632531T>C	ENST00000368147.4	-	17	2605	c.2425A>G	c.(2425-2427)Atc>Gtc	p.I809V		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	809			I -> V (in dbSNP:rs7547313).		actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					GTCTCTTGGATCCAGGCCTCC	0.502													T|||	516	0.103035	0.3707	0.0331	5008	,	,		16779	0.0		0.003	False		,,,				2504	0.0				p.I809V		Atlas-SNP	.											SPTA1,NS,carcinoma,+2,1	SPTA1	720	1	0			c.A2425G						PASS	.	T	VAL/ILE	1083,2813		165,753,1030	100.0	103.0	102.0		2425	4.3	1.0	1	dbSNP_116	102	19,8255		0,19,4118	yes	missense	SPTA1	NM_003126.2	29	165,772,5148	CC,CT,TT		0.2296,27.7977,9.0551	possibly-damaging	809/2420	158632531	1102,11068	1948	4137	6085	SO:0001583	missense	6708	exon17			CTTGGATCCAGGC	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.2425A>G	1.37:g.158632531T>C	ENSP00000357129:p.Ile809Val	179.0	0.0	0		205.0	104.0	0.507317	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	183	0.08379120879120878	172	0.34959349593495936	11	0.03038674033149171	0	0.0	0	0.0	T	21.0	4.080651	0.76528	0.277977	0.002296	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.39787	1.06;1.06	4.28	4.28	0.50868	.	0.000000	0.32852	N	0.005568	T	0.40196	0.1107	L	0.37466	1.105	0.22531	P	0.999012003	D	0.76494	0.999	D	0.91635	0.999	T	0.38824	-0.9643	9	0.44086	T	0.13	.	10.915	0.47131	0.0:0.0:0.0:1.0	rs7547313;rs7547313	809	P02549	SPTA1_HUMAN	V	809	ENSP00000357130:I809V;ENSP00000357129:I809V	ENSP00000357129:I809V	I	-	1	0	SPTA1	156899155	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.011000	0.76359	1.786000	0.52430	0.460000	0.39030	ATC	T|0.946;C|0.054	0.054	strong		0.502	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
CYP4F12	66002	hgsc.bcm.edu	37	19	15791066	15791066	+	Missense_Mutation	SNP	C	C	T	rs61731193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15791066C>T	ENST00000550308.1	+	4	736	c.356C>T	c.(355-357)cCc>cTc	p.P119L	CYP4F12_ENST00000324632.10_Missense_Mutation_p.P119L	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	119					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	GCCATTGCACCCAAGGATAAT	0.567													.|||	103	0.0205671	0.0734	0.0072	5008	,	,		20736	0.0		0.001	False		,,,				2504	0.0				p.P119L		Atlas-SNP	.											.	CYP4F12	89	.	0			c.C356T						PASS	.	T	LEU/PRO	247,4133		2,243,1945	143.0	146.0	145.0		356	-1.3	0.0	19	dbSNP_129	145	3,8579		0,3,4288	yes	missense	CYP4F12	NM_023944.3	98	2,246,6233	TT,TC,CC		0.035,5.6393,1.9287	possibly-damaging	119/525	15791066	250,12712	2190	4291	6481	SO:0001583	missense	66002	exon4			TTGCACCCAAGGA	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.356C>T	19.37:g.15791066C>T	ENSP00000448998:p.Pro119Leu	254.0	0.0	0		355.0	89.0	0.250704	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	40	0.018315018315018316	37	0.07520325203252033	3	0.008287292817679558	0	0.0	0	0.0	.	7.772	0.707735	0.15239	0.056393	3.5E-4	ENSG00000186204	ENST00000550308;ENST00000324632	T;T	0.69175	-0.38;-0.38	2.36	-1.32	0.09201	.	0.825497	0.10255	N	0.696720	T	0.07863	0.0197	L	0.59912	1.85	0.09310	N	1	B;B;B	0.26512	0.151;0.046;0.014	B;B;B	0.36766	0.232;0.168;0.098	T	0.46857	-0.9161	10	0.52906	T	0.07	.	5.4101	0.16344	0.0:0.5515:0.0:0.4485	rs61731193	119;119;119	B4E2R2;B4E270;Q9HCS2	.;.;CP4FC_HUMAN	L	119	ENSP00000448998:P119L;ENSP00000321821:P119L	ENSP00000321821:P119L	P	+	2	0	CYP4F12	15652066	0.000000	0.05858	0.003000	0.11579	0.000000	0.00434	-0.870000	0.04228	-0.186000	0.10533	-1.139000	0.01908	CCC	C|0.988;T|0.012	0.012	strong		0.567	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
GPR144	347088	hgsc.bcm.edu	37	9	127231763	127231763	+	Missense_Mutation	SNP	G	G	A	rs114565703|rs386738474	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:127231763G>A	ENST00000334810.1	+	16	2495	c.2495G>A	c.(2494-2496)cGc>cAc	p.R832H				Q7Z7M1	GP144_HUMAN	G protein-coupled receptor 144	832					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)			central_nervous_system(1)|endometrium(3)	4						TCCAGTGCCCGCCGCCGTGCC	0.642													G|||	95	0.0189696	0.0681	0.0058	5008	,	,		17367	0.001		0.0	False		,,,				2504	0.0				p.R832H		Atlas-SNP	.											.	GPR144	33	.	0			c.G2495A						PASS	.	G	HIS/ARG	113,1271		6,101,585	29.0	36.0	34.0		2495	1.2	1.0	9	dbSNP_132	34	1,3181		0,1,1590	yes	missense	GPR144	NM_001161808.1	29	6,102,2175	AA,AG,GG		0.0314,8.1647,2.4967	probably-damaging	832/964	127231763	114,4452	692	1591	2283	SO:0001583	missense	347088	exon16			GTGCCCGCCGCCG	AY278562		9q34.11	2014-08-08			ENSG00000180264	ENSG00000180264		"""-"", ""GPCR / Class B : Orphans"""	18651	protein-coding gene	gene with protein product							Standard	XM_006710216		Approved	PGR24	uc010mwn.3	Q7Z7M1	OTTHUMG00000020652	ENST00000334810.1:c.2495G>A	9.37:g.127231763G>A	ENSP00000335156:p.Arg832His	131.0	1.0	0.00763359		143.0	137.0	0.958042	NM_001161808	Q86SL4|Q8NH12	Missense_Mutation	SNP	ENST00000334810.1	37	CCDS48016.1	41	0.018772893772893772	39	0.07926829268292683	2	0.0055248618784530384	0	0.0	0	0.0	G	13.71	2.318318	0.40996	0.081647	3.14E-4	ENSG00000180264	ENST00000334810	T	0.44881	0.91	4.22	1.21	0.21127	GPCR, family 2-like (1);	.	.	.	.	T	0.02342	0.0072	M	0.66506	2.035	0.35385	D	0.790234	P	0.36535	0.557	B	0.34093	0.175	T	0.09640	-1.0665	9	0.62326	D	0.03	.	8.9349	0.35693	0.2619:0.0:0.7381:0.0	.	832	Q7Z7M1	GP144_HUMAN	H	832	ENSP00000335156:R832H	ENSP00000335156:R832H	R	+	2	0	GPR144	126271584	0.917000	0.31117	0.993000	0.49108	0.883000	0.51084	0.680000	0.25306	-0.057000	0.13199	0.462000	0.41574	CGC	G|0.975;A|0.025	0.025	strong		0.642	GPR144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054026.2	NM_182611	
FBN3	84467	hgsc.bcm.edu	37	19	8150393	8150393	+	Missense_Mutation	SNP	C	C	T	rs17160151	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8150393C>T	ENST00000600128.1	-	56	7355	c.6941G>A	c.(6940-6942)aGc>aAc	p.S2314N	FBN3_ENST00000601739.1_Missense_Mutation_p.S2314N|FBN3_ENST00000270509.2_Missense_Mutation_p.S2314N			Q75N90	FBN3_HUMAN	fibrillin 3	2314	TB 9.		S -> N (in dbSNP:rs17160151).			proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						CTCACTGCTGCTGGACAGAGA	0.672													C|||	349	0.0696885	0.2549	0.0159	5008	,	,		15574	0.0		0.001	False		,,,				2504	0.0				p.S2314N		Atlas-SNP	.											.	FBN3	300	.	0			c.G6941A						PASS	.	C	ASN/SER	998,3396		110,778,1309	12.0	13.0	12.0		6941	2.3	0.0	19	dbSNP_123	12	19,8551		1,17,4267	yes	missense	FBN3	NM_032447.3	46	111,795,5576	TT,TC,CC		0.2217,22.7128,7.8448	probably-damaging	2314/2810	8150393	1017,11947	2197	4285	6482	SO:0001583	missense	84467	exon55			CTGCTGCTGGACA		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.6941G>A	19.37:g.8150393C>T	ENSP00000470498:p.Ser2314Asn	34.0	0.0	0		49.0	26.0	0.530612	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	139	0.06364468864468864	134	0.27235772357723576	4	0.011049723756906077	1	0.0017482517482517483	0	0.0	C	16.20	3.056882	0.55325	0.227128	0.002217	ENSG00000142449	ENST00000270509;ENST00000341066	D	0.90844	-2.74	4.72	2.31	0.28768	Matrix fibril-associated (2);TGF-beta binding (1);	0.056067	0.64402	U	0.000001	T	0.00144	0.0004	M	0.73962	2.25	0.37731	P	0.07474400000000003	D;P	0.71674	0.998;0.896	D;P	0.83275	0.996;0.596	T	0.00000	-1.2854	9	0.31617	T	0.26	.	13.4093	0.60933	0.0:0.5983:0.4017:0.0	rs17160151;rs17160151	2314;420	Q75N90;Q6ZNB8	FBN3_HUMAN;.	N	2314;420	ENSP00000270509:S2314N	ENSP00000270509:S2314N	S	-	2	0	FBN3	8056393	1.000000	0.71417	0.041000	0.18516	0.142000	0.21351	1.586000	0.36611	2.170000	0.68504	0.491000	0.48974	AGC	C|0.903;T|0.097	0.097	strong		0.672	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
NR5A1	2516	hgsc.bcm.edu	37	9	127245070	127245070	+	Silent	SNP	C	C	T	rs79833327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:127245070C>T	ENST00000373588.4	-	7	1549	c.1353G>A	c.(1351-1353)ctG>ctA	p.L451L		NM_004959.4	NP_004950.2	Q13285	STF1_HUMAN	nuclear receptor subfamily 5, group A, member 1	451	Important for dimerization.				adrenal gland development (GO:0030325)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|hormone metabolic process (GO:0042445)|intracellular receptor signaling pathway (GO:0030522)|luteinization (GO:0001553)|maintenance of protein location in nucleus (GO:0051457)|male gonad development (GO:0008584)|multicellular organismal aging (GO:0010259)|negative regulation of female gonad development (GO:2000195)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|primary sex determination (GO:0007538)|regulation of steroid biosynthetic process (GO:0050810)|tissue development (GO:0009888)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|phospholipid binding (GO:0005543)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			lung(1)|upper_aerodigestive_tract(1)	2						TTTCGATGAGCAGGTTGTTGC	0.697													C|||	45	0.00898562	0.0333	0.0014	5008	,	,		11167	0.0		0.0	False		,,,				2504	0.0				p.L451L		Atlas-SNP	.											.	NR5A1	32	.	0			c.G1353A						PASS	.	C		214,4188	122.1+/-159.5	5,204,1992	64.0	45.0	51.0		1353	3.9	1.0	9	dbSNP_131	51	2,8594		0,2,4296	no	coding-synonymous	NR5A1	NM_004959.4		5,206,6288	TT,TC,CC		0.0233,4.8614,1.6618		451/462	127245070	216,12782	2201	4298	6499	SO:0001819	synonymous_variant	2516	exon7			GATGAGCAGGTTG	D88155	CCDS6856.1	9q33	2013-01-16			ENSG00000136931	ENSG00000136931		"""Nuclear hormone receptors"""	7983	protein-coding gene	gene with protein product		184757		FTZF1		7789992	Standard	NM_004959		Approved	FTZ1, SF-1, ELP, AD4BP	uc004boo.1	Q13285	OTTHUMG00000020655	ENST00000373588.4:c.1353G>A	9.37:g.127245070C>T		113.0	0.0	0		115.0	42.0	0.365217	NM_004959	O15196|Q5T6F5	Silent	SNP	ENST00000373588.4	37	CCDS6856.1																																																																																			C|0.983;T|0.017	0.017	strong		0.697	NR5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054029.1	NM_004959	
DENND5A	23258	hgsc.bcm.edu	37	11	9286515	9286515	+	Silent	SNP	C	C	T	rs75717840	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:9286515C>T	ENST00000328194.3	-	1	422	c.102G>A	c.(100-102)gaG>gaA	p.E34E	DENND5A_ENST00000530044.1_Silent_p.E34E	NM_001243254.1|NM_015213.3	NP_001230183.1|NP_056028.2	Q6IQ26	DEN5A_HUMAN	DENN/MADD domain containing 5A	34					positive regulation of Rab GTPase activity (GO:0032851)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(7)|kidney(2)|large_intestine(8)|liver(1)|lung(16)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39						CACCCGACAGCTCGTCCGGCT	0.711													C|||	104	0.0207668	0.0772	0.0029	5008	,	,		8908	0.0		0.0	False		,,,				2504	0.0				p.E34E		Atlas-SNP	.											.	DENND5A	84	.	0			c.G102A						PASS	.	C		216,3890		5,206,1842	6.0	7.0	6.0		102	1.3	0.2	11	dbSNP_132	6	4,8126		0,4,4061	no	coding-synonymous	DENND5A	NM_015213.3		5,210,5903	TT,TC,CC		0.0492,5.2606,1.798		34/1288	9286515	220,12016	2053	4065	6118	SO:0001819	synonymous_variant	23258	exon1			CGACAGCTCGTCC	AB029014	CCDS31423.1, CCDS58119.1	11p15.3	2012-10-03	2008-08-14	2008-08-14	ENSG00000184014	ENSG00000184014		"""DENN/MADD domain containing"""	19344	protein-coding gene	gene with protein product			"""RAB6 interacting protein 1"""	RAB6IP1		10470851	Standard	NM_015213		Approved	KIAA1091, FLJ22354, FLJ33829, FLJ43455	uc001mhl.3	Q6IQ26	OTTHUMG00000165716	ENST00000328194.3:c.102G>A	11.37:g.9286515C>T		15.0	0.0	0		42.0	25.0	0.595238	NM_015213	B4DJ15|E9PS91|Q96GN3|Q9H6U7|Q9UFV0|Q9UPR1	Silent	SNP	ENST00000328194.3	37	CCDS31423.1																																																																																			C|0.980;T|0.020	0.020	strong		0.711	DENND5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385910.2	NM_015213	
AMOTL1	154810	hgsc.bcm.edu	37	11	94602457	94602457	+	Silent	SNP	G	G	A	rs181764487	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:94602457G>A	ENST00000433060.2	+	12	2724	c.2583G>A	c.(2581-2583)acG>acA	p.T861T	AMOTL1_ENST00000317837.9_Silent_p.T448T|AMOTL1_ENST00000317829.8_Silent_p.T811T	NM_130847.2	NP_570899.1	Q8IY63	AMOL1_HUMAN	angiomotin like 1	861					establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|hippo signaling (GO:0035329)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|Wnt signaling pathway (GO:0016055)	apical plasma membrane (GO:0016324)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|tight junction (GO:0005923)	identical protein binding (GO:0042802)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(14)|lung(8)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(2)	36		Acute lymphoblastic leukemia(157;2.38e-05)|all_hematologic(158;0.00824)				CCTCCACTACGGCAGCCAGCA	0.632													G|||	20	0.00399361	0.0106	0.0072	5008	,	,		14338	0.0		0.0	False		,,,				2504	0.001				p.T861T		Atlas-SNP	.											AMOTL1,NS,carcinoma,+1,2	AMOTL1	95	2	0			c.G2583A						PASS	.	G		24,4298		0,24,2137	25.0	34.0	31.0		2583	-10.3	0.0	11		31	2,8548		0,2,4273	no	coding-synonymous	AMOTL1	NM_130847.2		0,26,6410	AA,AG,GG		0.0234,0.5553,0.202		861/957	94602457	26,12846	2161	4275	6436	SO:0001819	synonymous_variant	154810	exon12			CACTACGGCAGCC	AF453742	CCDS44712.1, CCDS73368.1	11q21	2008-07-18				ENSG00000166025			17811	protein-coding gene	gene with protein product	"""junction-enriched and associated protein"""	614657				11733531	Standard	XM_005273798		Approved	JEAP	uc001pfb.3	Q8IY63		ENST00000433060.2:c.2583G>A	11.37:g.94602457G>A		120.0	0.0	0		139.0	69.0	0.496403	NM_130847	Q63HK7|Q8NDN0|Q8TEN8|Q8WXD1|Q96CM5	Silent	SNP	ENST00000433060.2	37	CCDS44712.1																																																																																			G|0.995;A|0.005	0.005	strong		0.632	AMOTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396474.3	NM_130847	
TTC28	23331	hgsc.bcm.edu	37	22	28378450	28378450	+	Missense_Mutation	SNP	T	T	C	rs61744744	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:28378450T>C	ENST00000397906.2	-	23	7346	c.7205A>G	c.(7204-7206)aAt>aGt	p.N2402S	TTC28-AS1_ENST00000435348.1_RNA|TTC28-AS1_ENST00000452612.1_RNA|TTC28-AS1_ENST00000425112.1_RNA|TTC28-AS1_ENST00000417497.1_RNA|TTC28-AS1_ENST00000454996.1_RNA|TTC28-AS1_ENST00000453632.1_RNA|TTC28-AS1_ENST00000419253.1_RNA|TTC28-AS1_ENST00000454741.1_RNA|TTC28-AS1_ENST00000430525.1_RNA|TTC28-AS1_ENST00000430853.1_RNA|TTC28-AS1_ENST00000434221.1_RNA|TTC28-AS1_ENST00000424161.1_RNA	NM_001145418.1	NP_001138890.1	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28	2402					mitotic nuclear division (GO:0007067)|regulation of mitotic cell cycle (GO:0007346)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)				endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)	12						CTCCTTCTTATTGTGCCGTGG	0.562													T|||	54	0.0107827	0.0393	0.0029	5008	,	,		16058	0.0		0.0	False		,,,				2504	0.0				p.N2402S		Atlas-SNP	.											.	TTC28	84	.	0			c.A7205G						PASS	.	T	SER/ASN	51,1333		1,49,642	48.0	49.0	49.0		7205	1.0	1.0	22	dbSNP_129	49	0,3182		0,0,1591	yes	missense	TTC28	NM_001145418.1	46	1,49,2233	CC,CT,TT		0.0,3.685,1.117	benign	2402/2482	28378450	51,4515	692	1591	2283	SO:0001583	missense	23331	exon23			TTCTTATTGTGCC	AB028966	CCDS46678.1	22q12.1	2013-01-10			ENSG00000100154	ENSG00000100154		"""Tetratricopeptide (TTC) repeat domain containing"""	29179	protein-coding gene	gene with protein product		615098				10470851	Standard	NM_001145418		Approved	KIAA1043	uc003adp.4	Q96AY4	OTTHUMG00000151006	ENST00000397906.2:c.7205A>G	22.37:g.28378450T>C	ENSP00000381003:p.Asn2402Ser	97.0	0.0	0		105.0	44.0	0.419048	NM_001145418	K7ZRV2|O95928|O95929|Q5W189|Q9NTE4|Q9UG31|Q9UGG5|Q9UPV8|Q9Y3S5	Missense_Mutation	SNP	ENST00000397906.2	37	CCDS46678.1	32	0.014652014652014652	30	0.06097560975609756	2	0.0055248618784530384	0	0.0	0	0.0	T	7.189	0.591145	0.13812	0.03685	0.0	ENSG00000100154	ENST00000397906	D	0.87029	-2.2	4.85	0.981	0.19756	.	0.332930	0.31188	N	0.008081	T	0.14830	0.0358	N	0.01576	-0.805	0.21256	N	0.999749	B	0.02656	0.0	B	0.01281	0.0	T	0.37731	-0.9693	10	0.07644	T	0.81	-8.3766	6.7827	0.23654	0.0:0.5722:0.0:0.4278	.	2402	Q96AY4	TTC28_HUMAN	S	2402	ENSP00000381003:N2402S	ENSP00000381003:N2402S	N	-	2	0	TTC28	26708450	0.994000	0.37717	0.998000	0.56505	0.993000	0.82548	0.376000	0.20535	0.289000	0.22422	0.533000	0.62120	AAT	T|0.988;C|0.012	0.012	strong		0.562	TTC28-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000320930.2	XM_929318	
ZNF804B	219578	hgsc.bcm.edu	37	7	88965992	88965992	+	Missense_Mutation	SNP	T	T	G	rs115968745	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:88965992T>G	ENST00000333190.4	+	4	4305	c.3696T>G	c.(3694-3696)atT>atG	p.I1232M		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	1232							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			ACCTCCCTATTGCTCATCTAC	0.468										HNSCC(36;0.09)			T|||	32	0.00638978	0.0212	0.0058	5008	,	,		20365	0.0		0.0	False		,,,				2504	0.0				p.I1232M		Atlas-SNP	.											.	ZNF804B	322	.	0			c.T3696G						PASS	.	T	MET/ILE	63,4343	59.3+/-96.0	0,63,2140	209.0	180.0	190.0		3696	-9.7	0.4	7	dbSNP_132	190	0,8600		0,0,4300	yes	missense	ZNF804B	NM_181646.2	10	0,63,6440	GG,GT,TT		0.0,1.4299,0.4844	possibly-damaging	1232/1350	88965992	63,12943	2203	4300	6503	SO:0001583	missense	219578	exon4			CCCTATTGCTCAT	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"""zinc finger 804B"""				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.3696T>G	7.37:g.88965992T>G	ENSP00000329638:p.Ile1232Met	169.0	0.0	0		193.0	93.0	0.481865	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	37	CCDS5613.1	9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	T	8.308	0.821452	0.16678	0.014299	0.0	ENSG00000182348	ENST00000333190	T	0.05319	3.46	4.84	-9.68	0.00528	.	0.284991	0.30611	N	0.009243	T	0.02342	0.0072	L	0.51422	1.61	0.09310	N	1	D	0.56035	0.974	P	0.48030	0.564	T	0.00807	-1.1558	10	0.56958	D	0.05	-13.7335	4.6179	0.12435	0.0977:0.4312:0.0933:0.3778	.	1232	A4D1E1	Z804B_HUMAN	M	1232	ENSP00000329638:I1232M	ENSP00000329638:I1232M	I	+	3	3	ZNF804B	88803928	0.240000	0.23847	0.392000	0.26245	0.014000	0.08584	-0.152000	0.10159	-1.527000	0.01758	-0.899000	0.02877	ATT	T|0.996;G|0.004	0.004	strong		0.468	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646	
TTBK1	84630	hgsc.bcm.edu	37	6	43251608	43251608	+	Missense_Mutation	SNP	C	C	T	rs146633224	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43251608C>T	ENST00000259750.4	+	14	3213	c.3130C>T	c.(3130-3132)Cgc>Tgc	p.R1044C		NM_032538.1	NP_115927.1	Q5TCY1	TTBK1_HUMAN	tau tubulin kinase 1	1044					substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(10)|liver(1)|lung(21)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0125)|OV - Ovarian serous cystadenocarcinoma(102;0.0399)			CTCCCCCAGACGCCATGCTAT	0.662													C|||	16	0.00319489	0.0098	0.0043	5008	,	,		14735	0.0		0.0	False		,,,				2504	0.0				p.R1044C		Atlas-SNP	.											.	TTBK1	124	.	0			c.C3130T						PASS	.	C	CYS/ARG	39,4331		0,39,2146	31.0	29.0	30.0		3130	4.0	0.6	6	dbSNP_134	30	8,8470		0,8,4231	yes	missense	TTBK1	NM_032538.1	180	0,47,6377	TT,TC,CC		0.0944,0.8924,0.3658	possibly-damaging	1044/1322	43251608	47,12801	2185	4239	6424	SO:0001583	missense	84630	exon14			CCCAGACGCCATG	AB058758	CCDS34455.1	6p21.1	2008-02-05			ENSG00000146216	ENSG00000146216			19140	protein-coding gene	gene with protein product						11347906	Standard	XM_006715229		Approved	KIAA1855	uc003ouq.1	Q5TCY1	OTTHUMG00000014725	ENST00000259750.4:c.3130C>T	6.37:g.43251608C>T	ENSP00000259750:p.Arg1044Cys	99.0	0.0	0		99.0	44.0	0.444444	NM_032538	A2A2U5|Q2L6C6|Q6ZNH0|Q8N444|Q96JH2	Missense_Mutation	SNP	ENST00000259750.4	37	CCDS34455.1	6	0.0027472527472527475	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	9.159	1.018106	0.19355	0.008924	9.44E-4	ENSG00000146216	ENST00000259750	T	0.54279	0.58	4.84	3.96	0.45880	.	1.368680	0.04907	N	0.452377	T	0.29914	0.0748	L	0.52573	1.65	0.21740	N	0.99957	B	0.06786	0.001	B	0.04013	0.001	T	0.37407	-0.9707	10	0.87932	D	0	.	8.0444	0.30540	0.0:0.7512:0.1604:0.0883	.	1044	Q5TCY1	TTBK1_HUMAN	C	1044	ENSP00000259750:R1044C	ENSP00000259750:R1044C	R	+	1	0	TTBK1	43359586	0.000000	0.05858	0.580000	0.28601	0.346000	0.29079	0.210000	0.17455	1.155000	0.42497	0.462000	0.41574	CGC	C|0.997;T|0.003	0.003	strong		0.662	TTBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040584.3		
RECQL	5965	hgsc.bcm.edu	37	12	21643223	21643223	+	Missense_Mutation	SNP	C	C	T	rs1065751	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:21643223C>T	ENST00000444129.2	-	4	772	c.304G>A	c.(304-306)Gta>Ata	p.V102I	RECQL_ENST00000421138.2_Missense_Mutation_p.V102I	NM_002907.3|NM_032941.2	NP_002898.2|NP_116559.1	P46063	RECQ1_HUMAN	RecQ helicase-like	102	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.		V -> I (in dbSNP:rs1065751).		DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand renaturation (GO:0000733)	membrane (GO:0016020)|nucleus (GO:0005634)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)			endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	17						GCCATTGTTACGTTAATAGTT	0.368								Other identified genes with known or suspected DNA repair function					C|||	225	0.0449281	0.1634	0.013	5008	,	,		15171	0.0		0.0	False		,,,				2504	0.0				p.V102I		Atlas-SNP	.											.	RECQL	45	.	0			c.G304A						PASS	.	C	ILE/VAL,ILE/VAL	617,3789	266.5+/-267.3	44,529,1630	122.0	123.0	123.0		304,304	5.3	0.1	12	dbSNP_86	123	4,8596	2.2+/-6.3	0,4,4296	yes	missense,missense	RECQL	NM_002907.3,NM_032941.2	29,29	44,533,5926	TT,TC,CC		0.0465,14.0036,4.7747	benign,benign	102/650,102/650	21643223	621,12385	2203	4300	6503	SO:0001583	missense	5965	exon5			TTGTTACGTTAAT	D37984	CCDS31756.1	12p12.1	2014-03-07	2014-03-07	2014-03-07	ENSG00000004700	ENSG00000004700			9948	protein-coding gene	gene with protein product	"""DNA helicase Q1-like"""	600537	"""RecQ protein-like (DNA helicase Q1-like)"""			7527136, 7961977	Standard	NM_002907		Approved	RecQ1, RecQL1	uc001rex.3	P46063	OTTHUMG00000169131	ENST00000444129.2:c.304G>A	12.37:g.21643223C>T	ENSP00000416739:p.Val102Ile	128.0	0.0	0		115.0	60.0	0.521739	NM_032941	A8K6G2	Missense_Mutation	SNP	ENST00000444129.2	37	CCDS31756.1	85	0.03891941391941392	80	0.16260162601626016	5	0.013812154696132596	0	0.0	0	0.0	C	15.74	2.923245	0.52653	0.140036	4.65E-4	ENSG00000004700	ENST00000444129;ENST00000421138;ENST00000396093;ENST00000314748;ENST00000542432;ENST00000536240	T;T;T;T;T;T	0.75477	-0.94;-0.94;2.49;2.49;2.49;0.93	5.29	5.29	0.74685	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.529047	0.19411	N	0.114924	T	0.00552	0.0018	L	0.36672	1.1	0.31263	P	0.6926570000000001	B	0.16166	0.016	B	0.14023	0.01	T	0.23332	-1.0191	9	0.66056	D	0.02	-2.6848	19.2899	0.94095	0.0:1.0:0.0:0.0	rs1065751;rs1065751	102	P46063	RECQ1_HUMAN	I	102	ENSP00000416739:V102I;ENSP00000395449:V102I;ENSP00000379400:V102I;ENSP00000318727:V102I;ENSP00000445555:V102I;ENSP00000439069:V102I	ENSP00000318727:V102I	V	-	1	0	RECQL	21534490	0.985000	0.35326	0.113000	0.21522	0.868000	0.49771	4.862000	0.62976	2.615000	0.88500	0.650000	0.86243	GTA	T|0.045;G|0.039	0.045	strong		0.368	RECQL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402371.1	NM_002907	
CCDC65	85478	hgsc.bcm.edu	37	12	49310831	49310831	+	Missense_Mutation	SNP	A	A	G	rs140228766	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:49310831A>G	ENST00000320516.4	+	4	737	c.549A>G	c.(547-549)atA>atG	p.I183M	RP11-302B13.5_ENST00000398092.4_Intron|CCDC65_ENST00000266984.5_Missense_Mutation_p.I183M	NM_033124.4	NP_149115.2	Q8IXS2	CCD65_HUMAN	coiled-coil domain containing 65	183										breast(1)|large_intestine(4)|lung(7)|ovary(1)|skin(2)	15						AGAACTATATAGATTCTGAGT	0.433													A|||	8	0.00159744	0.0053	0.0014	5008	,	,		21739	0.0		0.0	False		,,,				2504	0.0				p.I183M		Atlas-SNP	.											.	CCDC65	41	.	0			c.A549G						PASS	.	A	MET/ILE	15,4391	22.3+/-47.3	0,15,2188	107.0	95.0	99.0		549	-3.4	0.0	12	dbSNP_134	99	1,8599		0,1,4299	yes	missense	CCDC65	NM_033124.4	10	0,16,6487	GG,GA,AA		0.0116,0.3404,0.123	benign	183/485	49310831	16,12990	2203	4300	6503	SO:0001583	missense	85478	exon4			CTATATAGATTCT		CCDS8772.1	12q13.12	2014-07-18			ENSG00000139537	ENSG00000139537			29937	protein-coding gene	gene with protein product		611088				17089017, 21700706	Standard	NM_033124		Approved	NYD-SP28, FLJ35732, FAP250, CILD27	uc001rso.3	Q8IXS2		ENST00000320516.4:c.549A>G	12.37:g.49310831A>G	ENSP00000312706:p.Ile183Met	143.0	0.0	0		175.0	68.0	0.388571	NM_033124	A6NJG5|B2RBE2|Q8N7G4|Q8NA91|Q96JA0	Missense_Mutation	SNP	ENST00000320516.4	37	CCDS8772.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	A	11.22	1.573482	0.28092	0.003404	1.16E-4	ENSG00000139537	ENST00000266984;ENST00000320516	T;T	0.02472	4.28;4.28	5.32	-3.4	0.04853	.	0.540717	0.18922	N	0.127459	T	0.01454	0.0047	L	0.44542	1.39	0.21220	N	0.999755	B	0.02656	0.0	B	0.06405	0.002	T	0.40059	-0.9583	10	0.46703	T	0.11	-3.8361	1.8254	0.03119	0.4013:0.2222:0.2683:0.1081	.	183	Q8IXS2	CCD65_HUMAN	M	183	ENSP00000266984:I183M;ENSP00000312706:I183M	ENSP00000266984:I183M	I	+	3	3	CCDC65	47597098	0.000000	0.05858	0.049000	0.19019	0.979000	0.70002	-0.846000	0.04336	-0.658000	0.05366	-0.274000	0.10170	ATA	A|0.999;G|0.001	0.001	strong		0.433	CCDC65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408922.1	NM_033124	
ESRRG	2104	hgsc.bcm.edu	37	1	216692741	216692741	+	Silent	SNP	C	C	T	rs10863247	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:216692741C>T	ENST00000408911.3	-	6	1038	c.885G>A	c.(883-885)gcG>gcA	p.A295A	ESRRG_ENST00000366937.1_Silent_p.A307A|ESRRG_ENST00000366940.2_Silent_p.A272A|ESRRG_ENST00000391890.3_Silent_p.A279A|ESRRG_ENST00000361395.2_Silent_p.A272A|ESRRG_ENST00000359162.2_Silent_p.A272A|ESRRG_ENST00000493748.1_Silent_p.A272A|ESRRG_ENST00000487276.1_Silent_p.A272A|ESRRG_ENST00000493603.1_Silent_p.A272A|ESRRG_ENST00000361525.3_Silent_p.A272A|ESRRG_ENST00000463665.1_Silent_p.A233A|ESRRG_ENST00000360012.3_Silent_p.A272A|ESRRG_ENST00000366938.2_Silent_p.A272A	NM_001438.3	NP_001429.2	P62508	ERR3_HUMAN	estrogen-related receptor gamma	295					gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)	AF-2 domain binding (GO:0050682)|retinoic acid receptor activity (GO:0003708)|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)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(1)|large_intestine(8)|liver(1)|lung(29)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	49				OV - Ovarian serous cystadenocarcinoma(81;0.0358)|all cancers(67;0.0693)|GBM - Glioblastoma multiforme(131;0.0713)	Diethylstilbestrol(DB00255)	TCATCTGGTCCGCCAGGGACA	0.453													C|||	467	0.0932508	0.3351	0.0288	5008	,	,		17022	0.0		0.004	False		,,,				2504	0.0				p.A307A		Atlas-SNP	.											.	ESRRG	111	.	0			c.G921A						PASS	.	C	,,,	1256,3150	429.1+/-342.1	193,870,1140	56.0	55.0	56.0		816,885,816,816	-3.2	1.0	1	dbSNP_120	56	18,8582	13.3+/-46.6	0,18,4282	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ESRRG	NM_001134285.2,NM_001438.3,NM_206594.2,NM_206595.2	,,,	193,888,5422	TT,TC,CC		0.2093,28.5066,9.7955	,,,	272/436,295/459,272/436,272/436	216692741	1274,11732	2203	4300	6503	SO:0001819	synonymous_variant	2104	exon7			CTGGTCCGCCAGG	AF058291	CCDS1517.1, CCDS41468.1, CCDS58060.1, CCDS58061.1	1q41	2014-02-18			ENSG00000196482	ENSG00000196482		"""Nuclear hormone receptors"""	3474	protein-coding gene	gene with protein product		602969				9676434, 10072763	Standard	NM_001243505		Approved	NR3B3	uc001hkw.2	P62508	OTTHUMG00000037025	ENST00000408911.3:c.885G>A	1.37:g.216692741C>T		37.0	0.0	0		34.0	10.0	0.294118	NM_001243518	A8K4I0|A8K6I2|B3KY84|E9PGB7|F8W8J3|O75454|O96021|Q68DA0|Q6P274|Q6PK28|Q6TS38|Q9R1F3|Q9UNJ4	Silent	SNP	ENST00000408911.3	37	CCDS41468.1																																																																																			C|0.910;T|0.090	0.090	strong		0.453	ESRRG-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089882.2	NM_206595	
POMT1	10585	hgsc.bcm.edu	37	9	134393834	134393834	+	Silent	SNP	A	A	G	rs62620174	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:134393834A>G	ENST00000372228.3	+	14	1520	c.1341A>G	c.(1339-1341)gaA>gaG	p.E447E	RP11-334J6.6_ENST00000415423.1_RNA|POMT1_ENST00000419118.2_Silent_p.E273E|POMT1_ENST00000423007.1_Silent_p.E425E|POMT1_ENST00000354713.4_Silent_p.E395E|POMT1_ENST00000541219.1_Silent_p.E203E|POMT1_ENST00000485278.1_3'UTR|POMT1_ENST00000341012.7_Silent_p.E371E|POMT1_ENST00000402686.3_Silent_p.E425E|POMT1_ENST00000404875.2_Silent_p.E308E	NM_007171.3	NP_009102	Q9Y6A1	POMT1_HUMAN	protein-O-mannosyltransferase 1	447	MIR 2. {ECO:0000255|PROSITE- ProRule:PRU00131}.				carbohydrate metabolic process (GO:0005975)|extracellular matrix organization (GO:0030198)|mannosylation (GO:0097502)|multicellular organismal development (GO:0007275)|protein O-linked glycosylation (GO:0006493)	acrosomal vesicle (GO:0001669)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|sarcoplasmic reticulum (GO:0016529)	dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)|mannosyltransferase activity (GO:0000030)|metal ion binding (GO:0046872)			NS(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	31		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.65e-05)|Epithelial(140;0.000259)		TTTTGCAGGAAATTGTGAACA	0.418													A|||	111	0.0221645	0.0794	0.0086	5008	,	,		22316	0.0		0.0	False		,,,				2504	0.0				p.E447E		Atlas-SNP	.											.	POMT1	59	.	0			c.A1341G						PASS	.	A	,,,,	283,4123	154.4+/-187.8	8,267,1928	192.0	202.0	198.0		1275,1113,1275,924,1341	0.8	1.0	9	dbSNP_129	198	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	POMT1	NM_001077365.1,NM_001077366.1,NM_001136113.1,NM_001136114.1,NM_007171.3	,,,,	8,267,6228	GG,GA,AA		0.0,6.4231,2.1759	,,,,	425/726,371/672,425/726,308/609,447/748	134393834	283,12723	2203	4300	6503	SO:0001819	synonymous_variant	10585	exon14			GCAGGAAATTGTG	AF095136	CCDS6943.1, CCDS43894.1, CCDS43895.1, CCDS48045.1	9q34.1	2014-09-17			ENSG00000130714	ENSG00000130714	2.4.1.109	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	9202	protein-coding gene	gene with protein product	"""dolichyl-phosphate-mannose-protein mannosyltransferase"""	607423				10366449	Standard	NM_001077366		Approved	LGMD2K	uc004cav.3	Q9Y6A1	OTTHUMG00000020826	ENST00000372228.3:c.1341A>G	9.37:g.134393834A>G		110.0	0.0	0		115.0	68.0	0.591304	NM_007171	B3KQG0|B4DIF0|Q5JT01|Q5JT06|Q5JT08|Q8NC91|Q8TCA9|Q9NX32|Q9NX82|Q9UNT2	Silent	SNP	ENST00000372228.3	37	CCDS6943.1																																																																																			A|0.976;G|0.024	0.024	strong		0.418	POMT1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054737.1	NM_007171	
ZBTB7C	201501	hgsc.bcm.edu	37	18	45566903	45566903	+	Silent	SNP	T	T	C	rs114461217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:45566903T>C	ENST00000588982.1	-	3	1077	c.576A>G	c.(574-576)acA>acG	p.T192T	ZBTB7C_ENST00000332053.2_Silent_p.T192T|ZBTB7C_ENST00000535628.2_Silent_p.T192T|ZBTB7C_ENST00000586438.1_Silent_p.T192T|ZBTB7C_ENST00000590800.1_Silent_p.T192T			A1YPR0	ZBT7C_HUMAN	zinc finger and BTB domain containing 7C	192							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(8)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23						TGAGATGGTCTGTCTTGGAAG	0.567													C|||	43	0.00858626	0.0295	0.0043	5008	,	,		18424	0.0		0.001	False		,,,				2504	0.0				p.T192T		Atlas-SNP	.											.	ZBTB7C	73	.	0			c.A576G						PASS	.	C		134,4272	814.1+/-416.2	2,130,2071	110.0	107.0	108.0		576	-2.0	1.0	18	dbSNP_132	108	2,8598	819.2+/-406.8	0,2,4298	no	coding-synonymous	ZBTB7C	NM_001039360.2		2,132,6369	CC,CT,TT		0.0233,3.0413,1.0457		192/620	45566903	136,12870	2203	4300	6503	SO:0001819	synonymous_variant	201501	exon2			ATGGTCTGTCTTG	Y14591	CCDS32830.1	18q21.1	2013-01-08		2005-04-07	ENSG00000184828	ENSG00000184828		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	31700	protein-coding gene	gene with protein product			"""zinc finger and BTB domain containing 36"""	ZBTB36			Standard	NM_001039360		Approved	ZNF857C	uc002ldb.3	A1YPR0		ENST00000588982.1:c.576A>G	18.37:g.45566903T>C		365.0	1.0	0.00273973		376.0	168.0	0.446809	NM_001039360	O73453	Silent	SNP	ENST00000588982.1	37	CCDS32830.1																																																																																			T|0.990;C|0.010	0.010	strong		0.567	ZBTB7C-025	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450731.1	NM_001039360	
KRT31	3881	hgsc.bcm.edu	37	17	39553676	39553676	+	Missense_Mutation	SNP	G	G	C	rs6503628	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39553676G>C	ENST00000251645.2	-	1	168	c.116C>G	c.(115-117)gCc>gGc	p.A39G		NM_002277.2	NP_002268.2	Q15323	K1H1_HUMAN	keratin 31	39	Head.		A -> G (in dbSNP:rs6503628).		epidermis development (GO:0008544)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	31		Breast(137;0.000496)				GCTCACATTGGCGGGGATGTT	0.657													G|||	15	0.00299521	0.0113	0.0	5008	,	,		15172	0.0		0.0	False		,,,				2504	0.0				p.A39G		Atlas-SNP	.											.	KRT31	158	.	0			c.C116G						PASS	.	G	GLY/ALA	45,4361	43.1+/-76.7	0,45,2158	59.0	61.0	60.0		116	4.9	1.0	17	dbSNP_116	60	0,8600		0,0,4300	no	missense	KRT31	NM_002277.2	60	0,45,6458	CC,CG,GG		0.0,1.0213,0.346	benign	39/417	39553676	45,12961	2203	4300	6503	SO:0001583	missense	3881	exon1			ACATTGGCGGGGA	X86570	CCDS11391.1	17q21.2	2014-05-20	2006-07-17	2006-07-17	ENSG00000094796	ENSG00000094796		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6448	protein-coding gene	gene with protein product	"""hard keratin type I 1"""	601077	"""keratin, hair, acidic, 1"""	KRTHA1		7578244, 16831889	Standard	NM_002277		Approved	Ha-1	uc002hwn.3	Q15323	OTTHUMG00000133423	ENST00000251645.2:c.116C>G	17.37:g.39553676G>C	ENSP00000251645:p.Ala39Gly	215.0	0.0	0		205.0	90.0	0.439024	NM_002277	Q9UE12	Missense_Mutation	SNP	ENST00000251645.2	37	CCDS11391.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	g	6.953	0.545683	0.13312	0.010213	0.0	ENSG00000094796	ENST00000251645	D	0.82167	-1.58	5.87	4.9	0.64082	.	0.000000	0.64402	D	0.000004	T	0.61476	0.2350	L	0.28400	0.85	0.32486	N	0.54088	B	0.12013	0.005	B	0.10450	0.005	T	0.60209	-0.7308	10	0.06365	T	0.9	.	8.4419	0.32820	0.2275:0.0:0.7725:0.0	rs6503628;rs6503628	39	Q15323	K1H1_HUMAN	G	39	ENSP00000251645:A39G	ENSP00000251645:A39G	A	-	2	0	KRT31	36807202	0.992000	0.36948	1.000000	0.80357	0.902000	0.53008	2.205000	0.42770	1.500000	0.48636	0.650000	0.86243	GCC	G|0.997;C|0.003	0.003	strong		0.657	KRT31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257286.1	NM_002277	
C9orf84	158401	hgsc.bcm.edu	37	9	114454735	114454735	+	Silent	SNP	T	T	C	rs73656294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:114454735T>C	ENST00000318737.4	-	25	3458	c.3330A>G	c.(3328-3330)tcA>tcG	p.S1110S	C9orf84_ENST00000394779.3_Silent_p.S1071S|C9orf84_ENST00000374287.3_Silent_p.S1110S|C9orf84_ENST00000394777.4_Silent_p.S1036S	NM_173521.3	NP_775792.3	Q5VXU9	CI084_HUMAN	chromosome 9 open reading frame 84	1110										breast(1)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(10)|liver(1)|lung(7)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						AAATTTGCGGTGATTTTGTTA	0.323													T|||	67	0.0133786	0.0477	0.0058	5008	,	,		18851	0.0		0.0	False		,,,				2504	0.0				p.S1110S		Atlas-SNP	.											.	C9orf84	207	.	0			c.A3330G						PASS	.	T	,	151,4255		2,147,2054	53.0	58.0	57.0		3213,3330	3.0	1.0	9	dbSNP_130	57	1,8589		0,1,4294	no	coding-synonymous,coding-synonymous	C9orf84	NM_001080551.1,NM_173521.3	,	2,148,6348	CC,CT,TT		0.0116,3.4271,1.1696	,	1071/1406,1110/1445	114454735	152,12844	2203	4295	6498	SO:0001819	synonymous_variant	158401	exon25			TTGCGGTGATTTT	AL833535	CCDS6781.3, CCDS43863.1	9q32	2012-03-16			ENSG00000165181	ENSG00000165181			26535	protein-coding gene	gene with protein product							Standard	XM_005251738		Approved	FLJ32779	uc004bfr.3	Q5VXU9	OTTHUMG00000020495	ENST00000318737.4:c.3330A>G	9.37:g.114454735T>C		57.0	0.0	0		40.0	9.0	0.225	NM_173521	A2A2V3|Q2M1H8|Q96M73	Silent	SNP	ENST00000318737.4	37	CCDS6781.3																																																																																			T|0.988;C|0.012	0.012	strong		0.323	C9orf84-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053656.2	NM_173521	
LYST	1130	hgsc.bcm.edu	37	1	235971802	235971802	+	Silent	SNP	G	G	A	rs16832868	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:235971802G>A	ENST00000389794.3	-	5	2490	c.2316C>T	c.(2314-2316)gaC>gaT	p.D772D	LYST_ENST00000536965.1_Silent_p.D772D|LYST_ENST00000389793.2_Silent_p.D772D			Q99698	LYST_HUMAN	lysosomal trafficking regulator	772					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			TCTGAAGCACGTCCTGAGGCA	0.468													G|||	309	0.0617013	0.2201	0.0245	5008	,	,		17331	0.0		0.001	False		,,,				2504	0.0				p.D772D		Atlas-SNP	.											.	LYST	370	.	0			c.C2316T						PASS	.	G		827,3579	328.3+/-300.5	75,677,1451	88.0	86.0	87.0		2316	3.5	1.0	1	dbSNP_123	87	10,8590	6.4+/-24.3	0,10,4290	no	coding-synonymous	LYST	NM_000081.2		75,687,5741	AA,AG,GG		0.1163,18.7699,6.4355		772/3802	235971802	837,12169	2203	4300	6503	SO:0001819	synonymous_variant	1130	exon5			AAGCACGTCCTGA	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"""WD repeat domain containing"""	1968	protein-coding gene	gene with protein product		606897	"""Chediak-Higashi syndrome 1"""	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.2316C>T	1.37:g.235971802G>A		189.0	0.0	0		173.0	90.0	0.520231	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Silent	SNP	ENST00000389794.3	37	CCDS31062.1																																																																																			G|0.934;A|0.066	0.066	strong		0.468	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5		
KIF16B	55614	hgsc.bcm.edu	37	20	16492163	16492163	+	Silent	SNP	T	T	C	rs16997775	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:16492163T>C	ENST00000354981.2	-	6	613	c.456A>G	c.(454-456)gaA>gaG	p.E152E	KIF16B_ENST00000378003.2_5'UTR|KIF16B_ENST00000355755.3_Silent_p.E152E|KIF16B_ENST00000408042.1_Silent_p.E152E	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B	152	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						CGTTATAAATTTCTAAGTAGC	0.353													T|||	114	0.0227636	0.084	0.0029	5008	,	,		17037	0.0		0.001	False		,,,				2504	0.0				p.E152E		Atlas-SNP	.											.	KIF16B	305	.	0			c.A456G						PASS	.	T	,,	254,4152	141.9+/-177.2	7,240,1956	43.0	43.0	43.0		456,456,456	3.2	1.0	20	dbSNP_123	43	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	KIF16B	NM_001199865.1,NM_001199866.1,NM_024704.4	,,	7,241,6255	CC,CT,TT		0.0116,5.7649,1.9606	,,	152/1267,152/1393,152/1318	16492163	255,12751	2203	4300	6503	SO:0001819	synonymous_variant	55614	exon6			ATAAATTTCTAAG	AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"""Kinesins"""	15869	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 23"""	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.456A>G	20.37:g.16492163T>C		40.0	0.0	0		50.0	21.0	0.42	NM_001199865	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Silent	SNP	ENST00000354981.2	37	CCDS13122.1																																																																																			T|0.978;C|0.022	0.022	strong		0.353	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683	
GNB2L1	10399	hgsc.bcm.edu	37	5	180665123	180665123	+	Silent	SNP	G	G	A	rs11540200	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:180665123G>A	ENST00000512805.1	-	6	1161	c.753C>T	c.(751-753)gcC>gcT	p.A251A	GNB2L1_ENST00000511566.1_Intron|GNB2L1_ENST00000376817.4_Silent_p.A207A|GNB2L1_ENST00000505461.1_5'Flank|GNB2L1_ENST00000504726.1_Intron|GNB2L1_ENST00000511900.1_Silent_p.A203A|GNB2L1_ENST00000514455.1_Silent_p.A35A	NM_006098.4	NP_006089.1	P63244	GBLP_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 2-like 1	251					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cell cycle (GO:0007049)|gastrulation (GO:0007369)|negative regulation of cell growth (GO:0030308)|negative regulation of gene expression (GO:0010629)|negative regulation of hydrogen peroxide-induced neuron death (GO:1903208)|negative regulation of phagocytosis (GO:0050765)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein tyrosine kinase activity (GO:0061099)|negative regulation of translation (GO:0017148)|negative regulation of Wnt signaling pathway (GO:0030178)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP catabolic process (GO:0030822)|positive regulation of cell migration (GO:0030335)|positive regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051343)|positive regulation of gastrulation (GO:2000543)|positive regulation of GTPase activity (GO:0043547)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein homooligomerization (GO:0032464)|positive regulation of protein phosphorylation (GO:0001934)|regulation of cell cycle (GO:0051726)|regulation of cell division (GO:0051302)|regulation of establishment of cell polarity (GO:2000114)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of protein localization (GO:0032880)|rhythmic process (GO:0048511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|midbody (GO:0030496)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|phagocytic cup (GO:0001891)|small ribosomal subunit (GO:0015935)	cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|ion channel inhibitor activity (GO:0008200)|poly(A) RNA binding (GO:0044822)|protein complex scaffold (GO:0032947)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase inhibitor activity (GO:0030292)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|SH2 domain binding (GO:0042169)			lung(3)|skin(2)	5	all_cancers(89;8.79e-06)|all_epithelial(37;1.13e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0654)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.101)|all cancers(165;0.11)		TGGGGCCTGTGGCAGCACACA	0.522													G|||	104	0.0207668	0.0772	0.0029	5008	,	,		19698	0.0		0.0	False		,,,				2504	0.0				p.A251A		Atlas-SNP	.											.	GNB2L1	22	.	0			c.C753T						PASS	.	G		300,4106	161.4+/-193.6	13,274,1916	140.0	125.0	130.0		753	2.2	1.0	5	dbSNP_120	130	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	GNB2L1	NM_006098.4		13,277,6213	AA,AG,GG		0.0349,6.8089,2.3297		251/318	180665123	303,12703	2203	4300	6503	SO:0001819	synonymous_variant	10399	exon6			GCCTGTGGCAGCA	M24194	CCDS34324.1	5q35.3	2013-01-10				ENSG00000204628		"""WD repeat domain containing"""	4399	protein-coding gene	gene with protein product	"""Receptor for Activated C Kinase 1"""	176981				8302854, 2499885	Standard	NM_006098		Approved	Gnb2-rs1, RACK1, H12.3	uc003mni.1	P63244		ENST00000512805.1:c.753C>T	5.37:g.180665123G>A		158.0	0.0	0		168.0	75.0	0.446429	NM_006098	B3KTJ0|D3DWS0|P25388|P99049|Q53HU2|Q5J8M6|Q5VLR4|Q6FH47	Silent	SNP	ENST00000512805.1	37	CCDS34324.1	38|38	0.0173992673992674|0.0173992673992674	38|38	0.07723577235772358|0.07723577235772358	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	9.424|9.424	1.083839|1.083839	0.20309|0.20309	0.068089|0.068089	3.49E-4|3.49E-4	ENSG00000204628|ENSG00000204628	ENST00000509148;ENST00000502905;ENST00000504128|ENST00000507756;ENST00000509535	.|.	.|.	.|.	5.91|5.91	2.24|2.24	0.28232|0.28232	.|.	.|.	.|.	.|.	.|.	T|T	0.04770|0.04770	0.0129|0.0129	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.01630|0.01630	-1.1308|-1.1308	4|4	.|.	.|.	.|.	-15.4052|-15.4052	4.7881|4.7881	0.13234|0.13234	0.2979:0.0:0.5646:0.1376|0.2979:0.0:0.5646:0.1376	rs11540200;rs17851237|rs11540200;rs17851237	.|.	.|.	.|.	Y|L	25;132;158|182;109	.|.	.|.	H|P	-|-	1|2	0|0	GNB2L1|GNB2L1	180597729|180597729	0.998000|0.998000	0.40836|0.40836	0.973000|0.973000	0.42090|0.42090	0.780000|0.780000	0.44128|0.44128	0.478000|0.478000	0.22212|0.22212	0.142000|0.142000	0.18901|0.18901	-0.812000|-0.812000	0.03155|0.03155	CAC|CCA	G|0.977;A|0.023	0.023	strong		0.522	GNB2L1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372943.2	NM_006098	
ADAM32	203102	hgsc.bcm.edu	37	8	39091546	39091546	+	Missense_Mutation	SNP	G	G	A	rs114068623	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:39091546G>A	ENST00000379907.4	+	16	1890	c.1763G>A	c.(1762-1764)cGa>cAa	p.R588Q	ADAM32_ENST00000519315.1_Missense_Mutation_p.R482Q|ADAM32_ENST00000437682.2_Missense_Mutation_p.R489Q	NM_145004.5	NP_659441	Q8TC27	ADA32_HUMAN	ADAM metallopeptidase domain 32	588						integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	31		all_cancers(7;3e-05)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00771)|Breast(189;0.0503)	LUSC - Lung squamous cell carcinoma(45;6.2e-07)|Colorectal(1;0.00699)|READ - Rectum adenocarcinoma(1;0.146)			AAATTGCCTCGAACAGTTCCA	0.353													G|||	42	0.00838658	0.0318	0.0	5008	,	,		13545	0.0		0.0	False		,,,				2504	0.0				p.R588Q		Atlas-SNP	.											.	ADAM32	70	.	0			c.G1763A						PASS	.	G	GLN/ARG	96,3584		1,94,1745	63.0	55.0	58.0		1763	-9.3	0.0	8	dbSNP_132	58	0,8154		0,0,4077	yes	missense	ADAM32	NM_145004.5	43	1,94,5822	AA,AG,GG		0.0,2.6087,0.8112	possibly-damaging	588/788	39091546	96,11738	1840	4077	5917	SO:0001583	missense	203102	exon16			TGCCTCGAACAGT	BC026085	CCDS47846.1	8p11.22	2005-08-18	2005-08-18		ENSG00000197140	ENSG00000197140		"""ADAM metallopeptidase domain containing"""	15479	protein-coding gene	gene with protein product			"""a disintegrin and metalloproteinase domain 32"""			12568724	Standard	NM_145004		Approved		uc003xmt.4	Q8TC27	OTTHUMG00000164071	ENST00000379907.4:c.1763G>A	8.37:g.39091546G>A	ENSP00000369238:p.Arg588Gln	90.0	0.0	0		82.0	46.0	0.560976	NM_145004	Q8TC42	Missense_Mutation	SNP	ENST00000379907.4	37	CCDS47846.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	G	5.640	0.302788	0.10678	0.026087	0.0	ENSG00000197140	ENST00000437682;ENST00000519315;ENST00000379907	T;T;T	0.21361	2.01;2.01;2.01	4.66	-9.32	0.00643	ADAM, cysteine-rich (2);	10.959300	0.00735	U	0.000979	T	0.01905	0.0060	N	0.05383	-0.06	0.09310	N	1	P;P;P	0.51351	0.559;0.944;0.694	B;B;B	0.38755	0.148;0.281;0.067	T	0.41034	-0.9531	10	0.11182	T	0.66	.	2.6264	0.04930	0.1635:0.1349:0.4716:0.23	.	489;482;588	E7EPX8;E7ER82;Q8TC27	.;.;ADA32_HUMAN	Q	489;482;588	ENSP00000405978:R489Q;ENSP00000429422:R482Q;ENSP00000369238:R588Q	ENSP00000369238:R588Q	R	+	2	0	ADAM32	39210703	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.001000	0.00652	-2.751000	0.00374	-0.781000	0.03364	CGA	G|0.990;A|0.010	0.010	strong		0.353	ADAM32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377089.1	NM_145004	
IPO7	10527	hgsc.bcm.edu	37	11	9456506	9456506	+	Silent	SNP	T	T	C	rs148344816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:9456506T>C	ENST00000379719.3	+	19	2242	c.2100T>C	c.(2098-2100)taT>taC	p.Y700Y	CTD-2371O3.2_ENST00000531111.1_RNA	NM_006391.2	NP_006382.1	O95373	IPO7_HUMAN	importin 7	700					innate immune response (GO:0045087)|protein import into nucleus (GO:0006606)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)|small GTPase regulator activity (GO:0005083)|transporter activity (GO:0005215)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(12)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				all cancers(16;8.29e-09)|Epithelial(150;4.76e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0217)		TTCATAATTATGTAACAGTTG	0.308													T|||	6	0.00119808	0.0045	0.0	5008	,	,		19628	0.0		0.0	False		,,,				2504	0.0				p.Y700Y		Atlas-SNP	.											.	IPO7	72	.	0			c.T2100C						PASS	.	T		23,4379	29.9+/-59.1	0,23,2178	119.0	115.0	116.0		2100	3.3	1.0	11	dbSNP_134	116	0,8588		0,0,4294	no	coding-synonymous	IPO7	NM_006391.2		0,23,6472	CC,CT,TT		0.0,0.5225,0.1771		700/1039	9456506	23,12967	2201	4294	6495	SO:0001819	synonymous_variant	10527	exon19			TAATTATGTAACA	AF098799	CCDS31425.1	11p15.3	2010-12-02	2003-03-11	2003-03-14	ENSG00000205339	ENSG00000205339		"""Importins"""	9852	protein-coding gene	gene with protein product		605586	"""RAN binding protein 7"""	RANBP7		9214382	Standard	NM_006391		Approved	Imp7	uc001mho.3	O95373	OTTHUMG00000165753	ENST00000379719.3:c.2100T>C	11.37:g.9456506T>C		102.0	0.0	0		89.0	55.0	0.617977	NM_006391	A6NNM5|B2R786|Q1RMF7|Q9H177|Q9NTE3	Silent	SNP	ENST00000379719.3	37	CCDS31425.1																																																																																			T|0.998;C|0.002	0.002	strong		0.308	IPO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386022.1	NM_006391	
DDX31	64794	hgsc.bcm.edu	37	9	135493792	135493792	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:135493792G>A	ENST00000372159.3	-	18	2216	c.2065C>T	c.(2065-2067)Cga>Tga	p.R689*	DDX31_ENST00000438527.3_Nonsense_Mutation_p.R560*|DDX31_ENST00000372153.1_Intron	NM_022779.7	NP_073616.6	Q9H8H2	DDX31_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 31	689						nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(1)	27				OV - Ovarian serous cystadenocarcinoma(145;2.67e-06)|Epithelial(140;7.61e-05)		ACTGTGGCTCGCTCTCGGATT	0.507																																					p.R689X		Atlas-SNP	.											.	DDX31	76	.	0			c.C2065T						PASS	.						105.0	93.0	97.0					9																	135493792		2203	4300	6503	SO:0001587	stop_gained	64794	exon18			TGGCTCGCTCTCG	AF427339	CCDS6951.1, CCDS6952.1	9q34.2	2012-04-17	2003-06-13		ENSG00000125485	ENSG00000125485		"""DEAD-boxes"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	16715	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 25"""		"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 31"""				Standard	NM_022779		Approved	FLJ13633, FLJ23349, FLJ14578, PPP1R25	uc004cbq.1	Q9H8H2	OTTHUMG00000020843	ENST00000372159.3:c.2065C>T	9.37:g.135493792G>A	ENSP00000361232:p.Arg689*	129.0	0.0	0		120.0	48.0	0.4	NM_022779	Q5K6N2|Q5K6N3|Q5K6N4|Q5VZJ4|Q5VZJ9|Q96E91|Q96NY2|Q96SX5|Q9H5K6	Nonsense_Mutation	SNP	ENST00000372159.3	37	CCDS6951.1	.	.	.	.	.	.	.	.	.	.	G	40	8.126157	0.98667	.	.	ENSG00000125485	ENST00000372159;ENST00000372155;ENST00000438527	.	.	.	5.7	5.7	0.88788	.	0.264197	0.35320	N	0.003292	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	-6.5596	13.6113	0.62080	0.0:0.0:0.8456:0.1544	.	.	.	.	X	689;689;560	.	ENSP00000361228:R689X	R	-	1	2	DDX31	134483613	1.000000	0.71417	0.965000	0.40720	0.956000	0.61745	3.757000	0.55212	2.686000	0.91538	0.591000	0.81541	CGA	.	.	none		0.507	DDX31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054794.1	NM_138620	
SERPINB4	6318	hgsc.bcm.edu	37	18	61310738	61310738	+	Missense_Mutation	SNP	T	T	C	rs55883719	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61310738T>C	ENST00000341074.5	-	2	189	c.74A>G	c.(73-75)aAc>aGc	p.N25S	SERPINB4_ENST00000356424.6_Missense_Mutation_p.N25S	NM_002974.2	NP_002965.1	P48594	SPB4_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 4	25					negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	enzyme binding (GO:0019899)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(22)|ovary(3)|skin(4)|upper_aerodigestive_tract(1)	42						GAAGATGTTGTTCTCTTTTGA	0.428													T|||	278	0.0555112	0.1989	0.0144	5008	,	,		19831	0.0		0.004	False		,,,				2504	0.001				p.N25S		Atlas-SNP	.											.	SERPINB4	89	.	0			c.A74G						PASS	.	T	SER/ASN	663,3743	282.2+/-276.4	47,569,1587	277.0	244.0	255.0		74	1.3	0.0	18	dbSNP_129	255	13,8587	9.8+/-36.6	0,13,4287	no	missense	SERPINB4	NM_002974.2	46	47,582,5874	CC,CT,TT		0.1512,15.0477,5.1976		25/391	61310738	676,12330	2203	4300	6503	SO:0001583	missense	6318	exon2			ATGTTGTTCTCTT	X89015	CCDS11986.1	18q21.33	2014-02-18	2005-08-18		ENSG00000206073	ENSG00000206073		"""Serine (or cysteine) peptidase inhibitors"""	10570	protein-coding gene	gene with protein product	"""squamous cell carcinoma antigen 2"""	600518	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 4"""	SCCA2		7724531, 14630915, 24172014	Standard	NM_175041		Approved	PI11, LEUPIN, SCCA-2, SCCA1		P48594	OTTHUMG00000060405	ENST00000341074.5:c.74A>G	18.37:g.61310738T>C	ENSP00000343445:p.Asn25Ser	550.0	0.0	0		547.0	254.0	0.464351	NM_002974	A8K847	Missense_Mutation	SNP	ENST00000341074.5	37	CCDS11986.1	97|97	0.044413919413919416|0.044413919413919416	89|89	0.18089430894308944|0.18089430894308944	6|6	0.016574585635359115|0.016574585635359115	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	T|T	4.847|4.847	0.157400|0.157400	0.09236|0.09236	0.150477|0.150477	0.001512|0.001512	ENSG00000206073|ENSG00000206073	ENST00000341074;ENST00000356424;ENST00000436264|ENST00000413673	D;D;D|.	0.83837|.	-1.77;-1.77;-1.77|.	3.83|3.83	1.31|1.31	0.21738|0.21738	Serpin domain (3);|.	1.227650|.	0.06602|.	N|.	0.754050|.	T|T	0.00039|0.00039	0.0001|0.0001	N|N	0.20445|0.20445	0.575|0.575	0.80722|0.80722	P|P	0.0|0.0	B;P|.	0.36183|.	0.102;0.542|.	B;B|.	0.34991|.	0.108;0.193|.	T|T	0.22836|0.22836	-1.0205|-1.0205	9|4	0.66056|.	D|.	0.02|.	.|.	4.2735|4.2735	0.10797|0.10797	0.0:0.277:0.1709:0.5521|0.0:0.277:0.1709:0.5521	rs55883719|rs55883719	25;25|.	P48594;Q9BYF7|.	SPB4_HUMAN;.|.	S|A	25|27	ENSP00000343445:N25S;ENSP00000348795:N25S;ENSP00000399796:N25S|.	ENSP00000343445:N25S|.	N|T	-|-	2|1	0|0	SERPINB4|SERPINB4	59461718|59461718	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.034000|0.034000	0.12701|0.12701	-0.758000|-0.758000	0.04766|0.04766	0.168000|0.168000	0.19655|0.19655	0.416000|0.416000	0.27883|0.27883	AAC|ACA	.	.	weak		0.428	SERPINB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133794.2	NM_175041	
C17orf74	201243	hgsc.bcm.edu	37	17	7330437	7330437	+	Missense_Mutation	SNP	A	A	G	rs3892554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7330437A>G	ENST00000333870.3	+	3	1201	c.1127A>G	c.(1126-1128)cAg>cGg	p.Q376R	RP11-104H15.7_ENST00000575310.1_RNA|C17orf74_ENST00000574034.1_3'UTR	NM_175734.4	NP_783861.3	Q0P670	CQ074_HUMAN	chromosome 17 open reading frame 74	376			Q -> R (in dbSNP:rs3892554).			integral component of membrane (GO:0016021)				cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	22		Prostate(122;0.157)				TACAGCTCCCAGGACCCCCGT	0.677													G|||	275	0.0549121	0.1997	0.0144	5008	,	,		15995	0.0		0.001	False		,,,				2504	0.0				p.Q376R		Atlas-SNP	.											.	C17orf74	56	.	0			c.A1127G						PASS	.	G	ARG/GLN	610,3590		52,506,1542	26.0	33.0	31.0		1127	3.8	0.9	17	dbSNP_108	31	6,8406		0,6,4200	yes	missense	C17orf74	NM_175734.4	43	52,512,5742	GG,GA,AA		0.0713,14.5238,4.8842	benign	376/502	7330437	616,11996	2100	4206	6306	SO:0001583	missense	201243	exon3			GCTCCCAGGACCC	BC044816	CCDS42255.1	17p13.1	2012-05-30			ENSG00000184560	ENSG00000184560			27315	protein-coding gene	gene with protein product						12477932	Standard	NM_175734		Approved		uc002ggw.3	Q0P670	OTTHUMG00000178190	ENST00000333870.3:c.1127A>G	17.37:g.7330437A>G	ENSP00000328061:p.Gln376Arg	68.0	0.0	0		67.0	30.0	0.447761	NM_175734		Missense_Mutation	SNP	ENST00000333870.3	37	CCDS42255.1	94	0.04304029304029304	89	0.18089430894308944	5	0.013812154696132596	0	0.0	0	0.0	G	0.011	-1.711549	0.00712	0.145238	7.13E-4	ENSG00000184560	ENST00000333870	T	0.21734	1.99	4.81	3.84	0.44239	.	0.000000	0.40144	N	0.001179	T	0.00012	0.0000	N	0.02247	-0.625	0.09310	P	0.9999999828706	B	0.02656	0.0	B	0.01281	0.0	T	0.37776	-0.9691	9	0.02654	T	1	-11.9907	8.1233	0.30984	0.1913:0.0:0.8087:0.0	rs3892554;rs4069866;rs3892554	376	Q0P670	CQ074_HUMAN	R	376	ENSP00000328061:Q376R	ENSP00000328061:Q376R	Q	+	2	0	C17orf74	7271161	0.809000	0.29036	0.909000	0.35828	0.004000	0.04260	0.841000	0.27613	0.574000	0.29417	-1.383000	0.01170	CAG	A|0.955;G|0.045	0.045	strong		0.677	C17orf74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440933.2	NM_175734	
CACNA1A	773	hgsc.bcm.edu	37	19	13563767	13563767	+	Silent	SNP	G	G	A	rs1800039	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:13563767G>A	ENST00000360228.5	-	3	461	c.462C>T	c.(460-462)gcC>gcT	p.A154A	CACNA1A_ENST00000573710.2_Silent_p.A154A	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	154					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	CAAACCCAAGGGCAATGATTT	0.493													G|||	48	0.00958466	0.0356	0.0014	5008	,	,		21794	0.0		0.0	False		,,,				2504	0.0				p.A154A		Atlas-SNP	.											.	CACNA1A	715	.	0			c.C462T						PASS	.	G	,,,,	82,3876		1,80,1898	154.0	150.0	151.0		462,462,462,462,462	2.4	1.0	19	dbSNP_89	151	5,8333		0,5,4164	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1A	NM_000068.3,NM_001127221.1,NM_001127222.1,NM_001174080.1,NM_023035.2	,,,,	1,85,6062	AA,AG,GG		0.06,2.0718,0.7075	,,,,	154/2267,154/2262,154/2507,154/2264,154/2513	13563767	87,12209	1979	4169	6148	SO:0001819	synonymous_variant	773	exon3			CCCAAGGGCAATG	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.462C>T	19.37:g.13563767G>A		198.0	0.0	0		216.0	98.0	0.453704	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Silent	SNP	ENST00000360228.5	37	CCDS45998.1																																																																																			G|0.992;A|0.008	0.008	strong		0.493	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
CFAP46	54777	hgsc.bcm.edu	37	10	134626383	134626383	+	Silent	SNP	C	C	T	rs7090011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:134626383C>T	ENST00000368586.5	-	55	7507	c.7407G>A	c.(7405-7407)caG>caA	p.Q2469Q	TTC40_ENST00000263170.5_Silent_p.Q630Q	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						TGCCCAGGGCCTGCTCCCACT	0.562													C|||	171	0.0341454	0.1188	0.0173	5008	,	,		13691	0.0		0.002	False		,,,				2504	0.0				p.Q2469Q		Atlas-SNP	.											.	TTC40	100	.	0			c.G7407A						PASS	.	C		456,3950	215.5+/-234.4	29,398,1776	52.0	54.0	53.0		2343	3.9	0.9	10	dbSNP_116	53	9,8591	5.7+/-21.5	0,9,4291	no	coding-synonymous	C10orf92	NM_001200049.1		29,407,6067	TT,TC,CC		0.1047,10.3495,3.5753		781/1028	134626383	465,12541	2203	4300	6503	SO:0001819	synonymous_variant	54777	exon55			CAGGGCCTGCTCC																												ENST00000368586.5:c.7407G>A	10.37:g.134626383C>T		17.0	0.0	0		21.0	8.0	0.380952	NM_001200049		Silent	SNP	ENST00000368586.5	37	CCDS58101.1																																																																																			C|0.966;T|0.034	0.034	strong		0.562	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
MUC6	4588	hgsc.bcm.edu	37	11	1017522	1017522	+	Missense_Mutation	SNP	T	T	G	rs199592093		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1017522T>G	ENST00000421673.2	-	31	5329	c.5279A>C	c.(5278-5280)gAa>gCa	p.E1760A		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1760	Approximate repeats.|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)		TGAGGTGACTTCAGGATGGTG	0.567																																					p.E1760A		Atlas-SNP	.											.	MUC6	408	.	0			c.A5279C						PASS	.						751.0	715.0	727.0					11																	1017522		2200	4294	6494	SO:0001583	missense	4588	exon31			GTGACTTCAGGAT	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.5279A>C	11.37:g.1017522T>G	ENSP00000406861:p.Glu1760Ala	957.0	0.0	0		1236.0	124.0	0.100324	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	-	0.655	-0.808100	0.02819	.	.	ENSG00000184956	ENST00000421673	T	0.20332	2.08	0.235	0.235	0.15431	.	.	.	.	.	T	0.25195	0.0612	L	0.38175	1.15	0.09310	N	1	D	0.67145	0.996	D	0.70227	0.968	T	0.11966	-1.0566	8	0.05833	T	0.94	.	.	.	.	.	1760	Q6W4X9	MUC6_HUMAN	A	1760	ENSP00000406861:E1760A	ENSP00000406861:E1760A	E	-	2	0	MUC6	1007522	0.000000	0.05858	0.002000	0.10522	0.045000	0.14185	-3.356000	0.00499	0.263000	0.21812	0.260000	0.18958	GAA	.	.	weak		0.567	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
SLC35G6	643664	hgsc.bcm.edu	37	17	7385774	7385774	+	Silent	SNP	C	C	T	rs201649944	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7385774C>T	ENST00000412468.2	+	2	586	c.471C>T	c.(469-471)taC>taT	p.Y157Y	ZBTB4_ENST00000311403.4_Intron|ZBTB4_ENST00000380599.4_5'Flank|POLR2A_ENST00000322644.6_5'Flank|POLR2A_ENST00000572844.1_5'Flank	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	157	EamA 1.					integral component of membrane (GO:0016021)											TCAGTGGCTACGACTGGTGTG	0.602													c|||	3	0.000599042	0.0023	0.0	5008	,	,		20504	0.0		0.0	False		,,,				2504	0.0				p.Y157Y		Atlas-SNP	.											.	.	.	.	0			c.C471T						PASS	.	T	,	8,4398	14.3+/-33.2	0,8,2195	182.0	174.0	176.0		471,	-5.2	0.9	17		176	0,8600		0,0,4300	no	coding-synonymous,intron	ZBTB4,SLC35G6	NM_001102614.1,NM_020899.3	,	0,8,6495	TT,TC,CC		0.0,0.1816,0.0615	,	157/339,	7385774	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	643664	exon2			TGGCTACGACTGG		CCDS45603.1	17p13.1	2013-05-22	2011-08-03	2011-08-03		ENSG00000259224		"""Solute carriers"""	31351	protein-coding gene	gene with protein product			"""transmembrane protein 21B"", ""acyl-malonyl condensing enzyme 1-like 3"""	TMEM21B, AMAC1L3			Standard	NM_001102614		Approved		uc010cmj.1	P0C7Q6		ENST00000412468.2:c.471C>T	17.37:g.7385774C>T		235.0	1.0	0.00425532		235.0	120.0	0.510638	NM_001102614		Silent	SNP	ENST00000412468.2	37	CCDS45603.1																																																																																			C|0.999;T|0.001	0.001	weak		0.602	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614	
LIFR	3977	hgsc.bcm.edu	37	5	38523529	38523529	+	Missense_Mutation	SNP	C	C	T	rs140538535	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:38523529C>T	ENST00000263409.4	-	5	715	c.553G>A	c.(553-555)Gta>Ata	p.V185I	LIFR_ENST00000453190.2_Missense_Mutation_p.V185I|LIFR_ENST00000503088.1_5'UTR	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	185					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)			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)					ACTAATTTTACGAGCTCCATA	0.338			T	PLAG1	salivary adenoma								C|||	11	0.00219649	0.0076	0.0014	5008	,	,		16786	0.0		0.0	False		,,,				2504	0.0				p.V185I	Melanoma(13;4 730 6426 9861 34751)	Atlas-SNP	.		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	LIFR_ENST00000263409,NS,carcinoma,0,2	LIFR	348	2	0			c.G553A						PASS	.	C	ILE/VAL,ILE/VAL	11,4395	15.5+/-35.6	0,11,2192	79.0	86.0	84.0		553,553	1.8	0.0	5	dbSNP_134	84	0,8600		0,0,4300	yes	missense,missense	LIFR	NM_001127671.1,NM_002310.5	29,29	0,11,6492	TT,TC,CC		0.0,0.2497,0.0846	possibly-damaging,possibly-damaging	185/1098,185/1098	38523529	11,12995	2203	4300	6503	SO:0001583	missense	3977	exon5			ATTTTACGAGCTC	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.553G>A	5.37:g.38523529C>T	ENSP00000263409:p.Val185Ile	280.0	0.0	0		267.0	115.0	0.430712	NM_002310	Q6LCD9	Missense_Mutation	SNP	ENST00000263409.4	37	CCDS3927.1	.	.	.	.	.	.	.	.	.	.	C	8.760	0.923346	0.18056	0.002497	0.0	ENSG00000113594	ENST00000263409;ENST00000453190	T;T	0.65916	-0.18;-0.18	5.53	1.82	0.25136	Immunoglobulin-like fold (1);	0.720295	0.13949	N	0.351669	T	0.49355	0.1552	L	0.49513	1.565	0.09310	N	1	B	0.25809	0.135	B	0.10450	0.005	T	0.29088	-1.0023	10	0.23302	T	0.38	-9.8342	7.3065	0.26451	0.0:0.6505:0.0:0.3495	.	185	P42702	LIFR_HUMAN	I	185	ENSP00000263409:V185I;ENSP00000398368:V185I	ENSP00000263409:V185I	V	-	1	0	LIFR	38559286	0.000000	0.05858	0.023000	0.16930	0.988000	0.76386	-0.741000	0.04855	0.044000	0.15775	0.655000	0.94253	GTA	C|0.999;T|0.001	0.001	strong		0.338	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310	
MORN2	729967	hgsc.bcm.edu	37	2	39108693	39108693	+	Silent	SNP	G	G	A	rs6756998	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:39108693G>A	ENST00000410014.1	+	4	490	c.111G>A	c.(109-111)aaG>aaA	p.K37K	MORN2_ENST00000409665.1_Silent_p.K37K|MORN2_ENST00000340556.6_Silent_p.K37K|MORN2_ENST00000409077.2_Intron|MORN2_ENST00000409131.2_Silent_p.K15K			Q502X0	MORN2_HUMAN	MORN repeat containing 2	37										breast(1)	1						ATGGGGCAAAGTATACTGGAA	0.308													G|||	81	0.0161741	0.0582	0.0058	5008	,	,		14852	0.0		0.0	False		,,,				2504	0.0				p.K37K		Atlas-SNP	.											.	MORN2	3	.	0			c.G111A						PASS	.						83.0	71.0	75.0					2																	39108693		692	1590	2282	SO:0001819	synonymous_variant	729967	exon4			GGCAAAGTATACT	AY367766	CCDS46262.1	2p22.1	2010-06-04			ENSG00000188010	ENSG00000188010			30166	protein-coding gene	gene with protein product						12477932	Standard	NM_001145450		Approved	MOPT	uc010fak.3	Q502X0	OTTHUMG00000128589	ENST00000410014.1:c.111G>A	2.37:g.39108693G>A		100.0	0.0	0		115.0	60.0	0.521739	NM_001145450	Q6UL00	Silent	SNP	ENST00000410014.1	37	CCDS46262.1																																																																																			G|0.983;A|0.017	0.017	strong		0.308	MORN2-004	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331568.1	NM_194270	
ASXL1	171023	hgsc.bcm.edu	37	20	31024488	31024488	+	Missense_Mutation	SNP	C	C	T	rs6057581	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31024488C>T	ENST00000375687.4	+	13	4397	c.3973C>T	c.(3973-3975)Ctt>Ttt	p.L1325F	ASXL1_ENST00000306058.5_Missense_Mutation_p.L1320F	NM_015338.5	NP_056153	Q8IXJ9	ASXL1_HUMAN	additional sex combs like transcriptional regulator 1	1325			L -> F (in dbSNP:rs6057581).		bone development (GO:0060348)|monoubiquitinated histone H2A deubiquitination (GO:0035522)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035359)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to retinoic acid (GO:0032526)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|PR-DUB complex (GO:0035517)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)|retinoic acid receptor binding (GO:0042974)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(655)|kidney(5)|large_intestine(18)|liver(1)|lung(27)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	722						CCCGATGCCTCTTCCTGCTGA	0.572			"""F, N, Mis"""		"""MDS, CMML"""								C|||	145	0.0289537	0.1044	0.0058	5008	,	,		17355	0.0		0.003	False		,,,				2504	0.0				p.L1325F		Atlas-SNP	.		Rec	yes		20	20q11.1	171023	additional sex combs like 1		L	.	ASXL1	1114	.	0			c.C3973T						PASS	.	C	PHE/LEU	386,4020	187.4+/-214.1	13,360,1830	41.0	44.0	43.0		3973	1.3	0.0	20	dbSNP_114	43	4,8596	3.7+/-12.6	0,4,4296	yes	missense	ASXL1	NM_015338.5	22	13,364,6126	TT,TC,CC		0.0465,8.7608,2.9986	probably-damaging	1325/1542	31024488	390,12616	2203	4300	6503	SO:0001583	missense	171023	exon12			ATGCCTCTTCCTG	AJ438952	CCDS13201.1	20q11	2014-09-17	2014-06-17		ENSG00000171456	ENSG00000171456			18318	protein-coding gene	gene with protein product		612990	"""additional sex combs like 1 (Drosophila)"""			12657473	Standard	NM_015338		Approved	KIAA0978	uc002wxs.3	Q8IXJ9	OTTHUMG00000032218	ENST00000375687.4:c.3973C>T	20.37:g.31024488C>T	ENSP00000364839:p.Leu1325Phe	79.0	0.0	0		69.0	31.0	0.449275	NM_015338	B2RP59|Q5JWS9|Q8IYY7|Q9H466|Q9NQF8|Q9UFJ0|Q9UFP8|Q9Y2I4	Missense_Mutation	SNP	ENST00000375687.4	37	CCDS13201.1	47	0.02152014652014652	42	0.08536585365853659	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	C	9.497	1.102092	0.20632	0.087608	4.65E-4	ENSG00000171456	ENST00000358956;ENST00000375687;ENST00000421155;ENST00000412498;ENST00000306058	T;T	0.16597	2.33;2.33	4.56	1.29	0.21616	.	0.227351	0.28011	N	0.016945	T	0.00580	0.0019	L	0.36672	1.1	0.09310	N	1	D;D	0.64830	0.994;0.994	P;P	0.59221	0.854;0.854	T	0.09164	-1.0687	10	0.16896	T	0.51	-9.4128	1.2537	0.01987	0.1414:0.4193:0.1563:0.2829	rs6057581;rs6057581	1320;1325	A6NIZ6;Q8IXJ9	.;ASXL1_HUMAN	F	1325;1325;1325;1246;1320	ENSP00000364839:L1325F;ENSP00000305119:L1320F	ENSP00000305119:L1320F	L	+	1	0	ASXL1	30488149	0.000000	0.05858	0.010000	0.14722	0.276000	0.26787	-0.141000	0.10327	0.336000	0.23639	0.561000	0.74099	CTT	C|0.971;T|0.029	0.029	strong		0.572	ASXL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078624.2	NM_015338	
CDC14A	8556	hgsc.bcm.edu	37	1	100856380	100856380	+	Splice_Site	SNP	A	A	C	rs28361212	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:100856380A>C	ENST00000336454.3	+	4	664	c.309A>C	c.(307-309)gcA>gcC	p.A103A	CDC14A_ENST00000370124.3_Splice_Site_p.A103A|CDC14A_ENST00000542213.1_Splice_Site_p.A45A|CDC14A_ENST00000361544.6_Splice_Site_p.A103A|CDC14A_ENST00000370125.2_Splice_Site_p.A103A|CDC14A_ENST00000544534.1_Splice_Site_p.A103A	NM_003672.3	NP_003663.2	Q9UNH5	CC14A_HUMAN	cell division cycle 14A	103	A.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(5)|kidney(6)|large_intestine(6)|lung(10)|skin(2)|urinary_tract(1)	31		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)		GTGCCTATGCAGTAAGTACCT	0.378													G|||	482	0.096246	0.3533	0.0202	5008	,	,		19271	0.0		0.001	False		,,,				2504	0.0				p.A103A		Atlas-SNP	.											.	CDC14A	65	.	0			c.A309C						PASS	.	G	,,	1374,3032		208,958,1037	99.0	97.0	98.0		309,309,309	-11.2	0.1	1	dbSNP_125	98	3,8597		0,3,4297	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	CDC14A	NM_003672.3,NM_033312.2,NM_033313.2	,,	208,961,5334	CC,CA,AA		0.0349,31.1847,10.5874	,,	103/595,103/624,103/384	100856380	1377,11629	2203	4300	6503	SO:0001630	splice_region_variant	8556	exon4			CTATGCAGTAAGT	AF000367	CCDS769.1, CCDS770.1, CCDS771.1	1p21	2013-01-17	2013-01-17		ENSG00000079335	ENSG00000079335		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"""	1718	protein-coding gene	gene with protein product		603504	"""CDC10 (cell division cycle 10, S. cerevisiae, homolog)"", ""CDC14 cell division cycle 14 homolog A (S. cerevisiae)"""			9367992, 10409437	Standard	NM_033312		Approved	Cdc14A1, Cdc14A2, cdc14	uc001dtf.2	Q9UNH5	OTTHUMG00000010987	ENST00000336454.3:c.309+1A>C	1.37:g.100856380A>C		59.0	0.0	0		68.0	32.0	0.470588	NM_033313	A6MA65|B1AQ14|B1AQ15|O43171|O60727|O60728|Q52LH9|Q8IXX0	Silent	SNP	ENST00000336454.3	37	CCDS769.1																																																																																			A|0.885;C|0.115	0.115	strong		0.378	CDC14A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000030220.1	NM_033312	Silent
TDRD5	163589	hgsc.bcm.edu	37	1	179621253	179621253	+	Missense_Mutation	SNP	G	G	T	rs147309264	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:179621253G>T	ENST00000367614.1	+	13	2440	c.2081G>T	c.(2080-2082)gGt>gTt	p.G694V	TDRD5_ENST00000294848.8_Missense_Mutation_p.G694V|TDRD5_ENST00000444136.1_Missense_Mutation_p.G694V	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	694					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						ACAGAACTGGGTTATCCTTCC	0.403													G|||	16	0.00319489	0.0121	0.0	5008	,	,		16263	0.0		0.0	False		,,,				2504	0.0				p.G694V		Atlas-SNP	.											.	TDRD5	149	.	0			c.G2081T						PASS	.	G	VAL/GLY,VAL/GLY,VAL/GLY,VAL/GLY,VAL/GLY	39,4367	44.6+/-78.6	0,39,2164	103.0	97.0	99.0		2081,2081,2081,746,2081	2.4	0.0	1	dbSNP_134	99	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense	TDRD5	NM_001199085.1,NM_001199089.1,NM_001199091.1,NM_001199092.1,NM_173533.3	109,109,109,109,109	0,39,6464	TT,TG,GG		0.0,0.8852,0.2999	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	694/1036,694/1036,694/982,249/537,694/982	179621253	39,12967	2203	4300	6503	SO:0001583	missense	163589	exon13			AACTGGGTTATCC	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.2081G>T	1.37:g.179621253G>T	ENSP00000356586:p.Gly694Val	164.0	0.0	0		215.0	107.0	0.497674	NM_173533	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	37	CCDS1332.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	10.14	1.269759	0.23221	0.008852	0.0	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136;ENST00000417329	T;T;T;T	0.34859	2.61;2.61;2.85;1.34	5.28	2.41	0.29592	.	1.593960	0.03140	N	0.166439	T	0.28433	0.0703	L	0.44542	1.39	0.19775	N	0.999957	P;B	0.35872	0.525;0.265	B;B	0.39971	0.315;0.167	T	0.19257	-1.0311	10	0.26408	T	0.33	-22.1301	7.4534	0.27252	0.3467:0.0:0.6533:0.0	.	694;694	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	V	694;694;694;150	ENSP00000356586:G694V;ENSP00000294848:G694V;ENSP00000406052:G694V;ENSP00000410744:G150V	ENSP00000294848:G694V	G	+	2	0	TDRD5	177887876	0.005000	0.15991	0.016000	0.15963	0.936000	0.57629	0.997000	0.29731	0.244000	0.21351	-0.259000	0.10710	GGT	G|0.997;T|0.003	0.003	strong		0.403	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533	
IFT140	9742	hgsc.bcm.edu	37	16	1637998	1637998	+	Missense_Mutation	SNP	G	G	A	rs8058674	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1637998G>A	ENST00000426508.2	-	8	1201	c.838C>T	c.(838-840)Cgg>Tgg	p.R280W	IFT140_ENST00000439987.2_5'UTR|LA16c-395F10.2_ENST00000563162.1_RNA	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	280			R -> Q (in dbSNP:rs35404373).		cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				ATGTCTGCCCGGCGGCCGGTT	0.622													G|||	98	0.0195687	0.0734	0.0014	5008	,	,		16114	0.0		0.0	False		,,,				2504	0.0				p.R280W		Atlas-SNP	.											.	IFT140	128	.	0			c.C838T						PASS	.	G	TRP/ARG	276,4122	153.7+/-187.2	7,262,1930	43.0	37.0	39.0		838	3.2	0.0	16	dbSNP_116	39	1,8599	1.2+/-3.3	0,1,4299	no	missense	IFT140	NM_014714.3	101	7,263,6229	AA,AG,GG		0.0116,6.2756,2.1311	probably-damaging	280/1463	1637998	277,12721	2199	4300	6499	SO:0001583	missense	9742	exon8			CTGCCCGGCGGCC	AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	29077	protein-coding gene	gene with protein product		614620	"""WD and tetratricopeptide repeats 2"", ""intraflagellar transport 140 homolog (Chlamydomonas)"""	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.838C>T	16.37:g.1637998G>A	ENSP00000406012:p.Arg280Trp	103.0	0.0	0		94.0	50.0	0.531915	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Missense_Mutation	SNP	ENST00000426508.2	37	CCDS10439.1	37	0.01694139194139194	36	0.07317073170731707	1	0.0027624309392265192	0	0.0	0	0.0	G	11.60	1.686901	0.29962	0.062756	1.16E-4	ENSG00000187535	ENST00000397417;ENST00000426508;ENST00000439987	T	0.30448	1.53	5.32	3.15	0.36227	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.748429	0.13091	N	0.414548	T	0.01976	0.0062	L	0.60455	1.87	0.09310	N	1	D	0.60160	0.987	B	0.42653	0.394	T	0.15809	-1.0424	10	0.54805	T	0.06	.	2.9009	0.05705	0.3065:0.2411:0.4525:0.0	rs8058674	280	Q96RY7	IF140_HUMAN	W	280	ENSP00000406012:R280W	ENSP00000380562:R280W	R	-	1	2	IFT140	1577999	0.021000	0.18746	0.008000	0.14137	0.002000	0.02628	1.743000	0.38258	1.241000	0.43820	-0.136000	0.14681	CGG	G|0.978;A|0.022	0.022	strong		0.622	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714	
KLK14	43847	hgsc.bcm.edu	37	19	51582090	51582090	+	Silent	SNP	G	G	A	rs79507858	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51582090G>A	ENST00000156499.2	-	6	851	c.633C>T	c.(631-633)ggC>ggT	p.G211G	KLK14_ENST00000391802.1_Silent_p.G211G			Q9P0G3	KLK14_HUMAN	kallikrein-related peptidase 14	211	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				epidermis morphogenesis (GO:0048730)|fertilization (GO:0009566)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|proteolysis (GO:0006508)|seminal clot liquefaction (GO:0070684)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)			kidney(4)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(1)	11		all_neural(266;0.0199)		OV - Ovarian serous cystadenocarcinoma(262;0.00328)|GBM - Glioblastoma multiforme(134;0.00422)		AGTCCTTCCCGCCCTGGGGAA	0.542													g|||	153	0.0305511	0.1089	0.0115	5008	,	,		18957	0.0		0.001	False		,,,				2504	0.0				p.G211G	GBM(117;2161 2172 2448 22911)	Atlas-SNP	.											.	KLK14	49	.	0			c.C633T						PASS	.			376,3538		15,346,1596	234.0	237.0	236.0		633	-9.0	0.2	19	dbSNP_131	236	7,8311		0,7,4152	no	coding-synonymous	KLK14	NM_022046.4		15,353,5748	AA,AG,GG		0.0842,9.6065,3.1311		211/268	51582090	383,11849	1957	4159	6116	SO:0001819	synonymous_variant	43847	exon6			CTTCCCGCCCTGG	AF283670	CCDS12823.2	19q13.3-q13.4	2008-02-05	2006-10-27		ENSG00000129437	ENSG00000129437		"""Kallikreins"""	6362	protein-coding gene	gene with protein product		606135	"""kallikrein 14"""			16800724, 16800723	Standard	XM_006723224		Approved	KLK-L6	uc002pvs.1	Q9P0G3	OTTHUMG00000143721	ENST00000156499.2:c.633C>T	19.37:g.51582090G>A		61.0	0.0	0		93.0	93.0	1	NM_022046	A7UNK5|Q1RMZ2|Q6B089	Silent	SNP	ENST00000156499.2	37	CCDS12823.2																																																																																			G|0.981;A|0.019	0.019	strong		0.542	KLK14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289774.2	NM_022046	
ASMTL	8623	hgsc.bcm.edu	37	X	1522325	1522325	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:1522325C>T	ENST00000381317.3	-	13	1735	c.1703G>A	c.(1702-1704)cGc>cAc	p.R568H	ASMTL_ENST00000534940.1_Missense_Mutation_p.R510H|ASMTL_ENST00000381333.4_Missense_Mutation_p.R552H|ASMTL-AS1_ENST00000420411.2_RNA|ASMTL-AS1_ENST00000602357.1_RNA|ASMTL_ENST00000416733.2_Missense_Mutation_p.R492H|ASMTL-AS1_ENST00000419737.2_RNA|ASMTL-AS1_ENST00000443929.1_RNA|ASMTL-AS1_ENST00000425740.2_RNA	NM_004192.3	NP_004183.2	O95671	ASML_HUMAN	acetylserotonin O-methyltransferase-like	568	ASMT-like.					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)				CATCAGGGCGCGCTGCGCCAC	0.652													c|||	99	0.0197684	0.0726	0.0043	5008	,	,		19958	0.0		0.0	False		,,,				2504	0.0				p.R568H		Atlas-SNP	.											.	ASMTL	56	.	0			c.G1703A						PASS	.		HIS/ARG,HIS/ARG,HIS/ARG	309,3951		11,287,1832	78.0	86.0	84.0		1529,1655,1703	1.3	0.0	X	dbSNP_134	84	4,8470		0,4,4233	no	missense,missense,missense	ASMTL	NM_001173473.1,NM_001173474.1,NM_004192.3	29,29,29	11,291,6065	TT,TC,CC		0.0472,7.2535,2.458	possibly-damaging,possibly-damaging,possibly-damaging	510/564,552/606,568/622	1522325	313,12421	2130	4237	6367	SO:0001583	missense	8623	exon13			AGGGCGCGCTGCG	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.1703G>A	X.37:g.1522325C>T	ENSP00000370718:p.Arg568His	151.0	0.0	0		192.0	100.0	0.520833	NM_004192	B4DX75|F5GXH4|J3JS33|Q5JQ53|Q8NBH5|Q96G02|Q9BUL6	Missense_Mutation	SNP	ENST00000381317.3	37	CCDS43917.1	50	0.022893772893772892	50	0.1016260162601626	0	0.0	0	0.0	0	0.0	c	4.831	0.154519	0.09236	0.072535	4.72E-4	ENSG00000169093	ENST00000416733;ENST00000534940;ENST00000381333;ENST00000381317	T;T;T;T	0.22743	1.94;1.94;1.94;1.94	1.31	1.31	0.21738	O-methyltransferase, family 2 (1);	0.432093	0.20024	U	0.100843	T	0.00724	0.0024	L	0.50333	1.59	0.25285	N	0.989409	D;D;D	0.76494	0.998;0.999;0.999	D;D;P	0.64506	0.926;0.909;0.908	T	0.04481	-1.0948	10	0.13108	T	0.6	.	5.3914	0.16245	0.0:0.6424:0.3576:0.0	.	492;552;568	E7ER97;O95671-2;O95671	.;.;ASML_HUMAN	H	492;510;552;568	ENSP00000410578:R492H;ENSP00000446410:R510H;ENSP00000370734:R552H;ENSP00000370718:R568H	ENSP00000370718:R568H	R	-	2	0	ASMTL	1482325	0.000000	0.05858	0.001000	0.08648	0.046000	0.14306	-2.266000	0.01171	0.693000	0.31634	0.115000	0.15696	CGC	C|0.977;T|0.023	0.023	strong		0.652	ASMTL-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055595.1	NM_004192	
NDFIP2	54602	hgsc.bcm.edu	37	13	80094993	80094993	+	Missense_Mutation	SNP	C	C	T	rs55887763	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:80094993C>T	ENST00000218652.7	+	2	422	c.370C>T	c.(370-372)Cct>Tct	p.P124S	NDFIP2_ENST00000494647.1_3'UTR	NM_001161407.1|NM_019080.2	NP_001154879.1|NP_061953.2	Q9NV92	NFIP2_HUMAN	Nedd4 family interacting protein 2	124			P -> S (in dbSNP:rs55887763).		negative regulation of gene expression (GO:0010629)|negative regulation of protein transport (GO:0051224)|negative regulation of transporter activity (GO:0032410)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of protein ubiquitination (GO:0031398)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|perinuclear region of cytoplasm (GO:0048471)	signal transducer activity (GO:0004871)|WW domain binding (GO:0050699)			NS(1)|breast(1)|endometrium(2)|kidney(3)|lung(3)|ovary(2)|prostate(1)|skin(1)	14		Acute lymphoblastic leukemia(28;0.205)		GBM - Glioblastoma multiforme(99;0.0196)		AGAGCAGCCACCTACTTCAAA	0.403													T|||	254	0.0507188	0.1838	0.0101	5008	,	,		15571	0.0		0.004	False		,,,				2504	0.0				p.P124S		Atlas-SNP	.											.	NDFIP2	23	.	0			c.C370T						PASS	.	T	SER/PRO,SER/PRO	641,3765	767.1+/-413.5	43,555,1605	89.0	82.0	84.0		370,370	5.8	0.3	13	dbSNP_129	84	2,8598	819.2+/-406.8	0,2,4298	yes	missense,missense	NDFIP2	NM_001161407.1,NM_019080.2	74,74	43,557,5903	TT,TC,CC		0.0233,14.5483,4.9439	benign,benign	124/317,124/337	80094993	643,12363	2203	4300	6503	SO:0001583	missense	54602	exon2			CAGCCACCTACTT	AB032991	CCDS31998.1	13q22.1	2011-05-18			ENSG00000102471	ENSG00000102471			18537	protein-coding gene	gene with protein product		610041				10574461, 12050153	Standard	NM_019080		Approved	KIAA1165, N4wbp5a	uc001vlf.3	Q9NV92	OTTHUMG00000017136	ENST00000218652.7:c.370C>T	13.37:g.80094993C>T	ENSP00000218652:p.Pro124Ser	110.0	0.0	0		117.0	57.0	0.487179	NM_019080	Q7Z2H3|Q7Z428|Q8TAR3|Q9ULQ5	Missense_Mutation	SNP	ENST00000218652.7	37	CCDS31998.1	102	0.046703296703296704	99	0.20121951219512196	3	0.008287292817679558	0	0.0	0	0.0	T	1.479	-0.557610	0.03967	0.145483	2.33E-4	ENSG00000102471	ENST00000218652;ENST00000487865	T;T	0.25912	1.78;1.77	5.75	5.75	0.90469	.	0.192068	0.47455	N	0.000229	T	0.00012	0.0000	N	0.00210	-1.845	0.49213	P	2.3799999999996047E-4	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29274	-1.0017	9	0.02654	T	1	-11.3844	11.0315	0.47776	0.0:0.0739:0.0:0.9261	rs55887763;rs58237612	30;124	B4DGY6;Q9NV92	.;NFIP2_HUMAN	S	124;41	ENSP00000218652:P124S;ENSP00000419200:P41S	ENSP00000218652:P124S	P	+	1	0	NDFIP2	78992994	0.995000	0.38212	0.331000	0.25455	0.299000	0.27559	3.411000	0.52672	1.003000	0.39130	-0.254000	0.11334	CCT	C|0.952;T|0.048	0.048	strong		0.403	NDFIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045380.2		
ZNF189	7743	hgsc.bcm.edu	37	9	104170580	104170580	+	Missense_Mutation	SNP	A	A	G	rs148414030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:104170580A>G	ENST00000339664.2	+	3	659	c.530A>G	c.(529-531)cAg>cGg	p.Q177R	ZNF189_ENST00000259395.4_Missense_Mutation_p.Q135R|ZNF189_ENST00000374861.3_Missense_Mutation_p.Q163R	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	177					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				AAACCTTTTCAGTGCAATGAA	0.408													A|||	6	0.00119808	0.0045	0.0	5008	,	,		21632	0.0		0.0	False		,,,				2504	0.0				p.Q177R		Atlas-SNP	.											.	ZNF189	79	.	0			c.A530G						PASS	.	A	ARG/GLN,ARG/GLN	19,4387	25.3+/-52.1	0,19,2184	82.0	82.0	82.0		530,404	4.6	1.0	9	dbSNP_134	82	0,8600		0,0,4300	yes	missense,missense	ZNF189	NM_003452.2,NM_197977.1	43,43	0,19,6484	GG,GA,AA		0.0,0.4312,0.1461	benign,benign	177/627,135/585	104170580	19,12987	2203	4300	6503	SO:0001583	missense	7743	exon3			CTTTTCAGTGCAA	AF025770	CCDS6754.1, CCDS6755.1, CCDS65096.1, CCDS75867.1	9q22-q31	2013-01-08			ENSG00000136870	ENSG00000136870		"""Zinc fingers, C2H2-type"", ""-"""	12980	protein-coding gene	gene with protein product		603132				9653648	Standard	NM_003452		Approved		uc004bbh.2	O75820	OTTHUMG00000020383	ENST00000339664.2:c.530A>G	9.37:g.104170580A>G	ENSP00000342019:p.Gln177Arg	157.0	0.0	0		158.0	102.0	0.64557	NM_003452	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Missense_Mutation	SNP	ENST00000339664.2	37	CCDS6754.1	.	.	.	.	.	.	.	.	.	.	A	9.515	1.106655	0.20714	0.004312	0.0	ENSG00000136870	ENST00000374861;ENST00000339664;ENST00000259395	T;T;T	0.19105	2.17;2.17;2.17	4.55	4.55	0.56014	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.46442	D	0.000288	T	0.18841	0.0452	N	0.13235	0.315	0.27578	N	0.949673	B;B;B	0.34372	0.056;0.451;0.262	B;P;B	0.47102	0.115;0.537;0.115	T	0.10359	-1.0633	10	0.54805	T	0.06	.	7.7508	0.28896	0.8138:0.0:0.0:0.1862	.	162;163;177	B7ZLK9;Q5T7D8;O75820	.;.;ZN189_HUMAN	R	163;177;135	ENSP00000363995:Q163R;ENSP00000342019:Q177R;ENSP00000259395:Q135R	ENSP00000259395:Q135R	Q	+	2	0	ZNF189	103210401	0.000000	0.05858	0.995000	0.50966	0.991000	0.79684	0.093000	0.15086	2.272000	0.75746	0.460000	0.39030	CAG	A|0.998;G|0.002	0.002	strong		0.408	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452	
CCNH	902	hgsc.bcm.edu	37	5	86695228	86695228	+	Silent	SNP	A	A	T	rs150856919	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:86695228A>T	ENST00000256897.4	-	7	1079	c.855T>A	c.(853-855)ctT>ctA	p.L285L	CCNH_ENST00000508855.1_Silent_p.L211L|CCNH_ENST00000504878.1_Silent_p.L211L	NM_001239.3	NP_001230.1	P51946	CCNH_HUMAN	cyclin H	285					7-methylguanosine mRNA capping (GO:0006370)|ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|protein phosphorylation (GO:0006468)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	cyclin-dependent protein kinase activating kinase holoenzyme complex (GO:0019907)|holo TFIIH complex (GO:0005675)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|TFIIK complex (GO:0070985)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)|kinase activity (GO:0016301)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|liver(1)|lung(2)|ovary(2)	15		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;9.01e-39)|Epithelial(54;5.08e-33)|all cancers(79;4.28e-28)		CGTTAAGTGCAAGCTCAGCAG	0.388								Direct reversal of damage;Direct reversal of damage;Nucleotide excision repair (NER)																													p.L285L		Atlas-SNP	.											.	CCNH	40	.	0			c.T855A						PASS	.	A	,	4,4402	8.1+/-20.4	0,4,2199	221.0	187.0	198.0		696,855	4.5	1.0	5	dbSNP_134	198	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	CCNH	NM_001199189.1,NM_001239.3	,	0,4,6499	TT,TA,AA		0.0,0.0908,0.0308	,	232/271,285/324	86695228	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	902	exon7			AAGTGCAAGCTCA	U12685	CCDS4064.1	5q13.3-q14	2014-03-28			ENSG00000134480	ENSG00000134480		"""General transcription factor IIH complex subunits"""	1594	protein-coding gene	gene with protein product	"""CDK-activating kinase complex subunit"", ""cyclin-dependent kinase-activating kinase complex subunit"", ""MO15-associated protein"", ""CAK complex subunit"""	601953				9465303	Standard	NM_001239		Approved	p34, p37, CycH	uc003kjb.3	P51946	OTTHUMG00000119077	ENST00000256897.4:c.855T>A	5.37:g.86695228A>T		86.0	0.0	0		75.0	33.0	0.44	NM_001239	Q53X72|Q8TBL9	Silent	SNP	ENST00000256897.4	37	CCDS4064.1																																																																																			A|1.000;T|0.000	0.000	strong		0.388	CCNH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239291.3	NM_001239	
MUC4	4585	hgsc.bcm.edu	37	3	195481111	195481111	+	Missense_Mutation	SNP	G	G	T	rs73079395	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195481111G>T	ENST00000346145.4	-	18	2632	c.2593C>A	c.(2593-2595)Ctg>Atg	p.L865M	MUC4_ENST00000463781.3_Missense_Mutation_p.L5101M|MUC4_ENST00000349607.4_Missense_Mutation_p.L814M|MUC4_ENST00000475231.1_Missense_Mutation_p.L5049M	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	1858	Ser-rich.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TCCCCAGTCAGGTTTGGAGGG	0.662													.|||	325	0.0648962	0.2322	0.0245	5008	,	,		15840	0.0		0.001	False		,,,				2504	0.0				p.L5101M		Atlas-SNP	.											.	MUC4	1505	.	0			c.C15301A						PASS	.	G	MET/LEU,MET/LEU,MET/LEU	900,3506		99,702,1402	63.0	67.0	65.0		2593,15301,2440	1.3	0.6	3	dbSNP_130	65	6,8594		0,6,4294	yes	missense,missense,missense	MUC4	NM_004532.5,NM_018406.6,NM_138297.4	15,15,15	99,708,5696	TT,TG,GG		0.0698,20.4267,6.966	possibly-damaging,possibly-damaging,possibly-damaging	865/1177,5101/5413,814/1126	195481111	906,12100	2203	4300	6503	SO:0001583	missense	4585	exon19			CAGTCAGGTTTGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000346145.4:c.2593C>A	3.37:g.195481111G>T	ENSP00000304207:p.Leu865Met	232.0	0.0	0		307.0	155.0	0.504886	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	ENST00000346145.4	37	CCDS3310.1	113	0.051739926739926737	106	0.21544715447154472	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	.	8.877	0.950622	0.18431	0.204267	6.98E-4	ENSG00000145113	ENST00000349607;ENST00000346145;ENST00000463781;ENST00000475231;ENST00000392409	T;T;T;T	0.46451	0.87;1.23;1.21;1.16	4.96	1.32	0.21799	.	0.408184	0.20459	N	0.091933	T	0.00039	0.0001	L	0.43757	1.38	0.80722	P	0.0	P;B;P;B;B;P	0.39352	0.554;0.254;0.494;0.057;0.057;0.669	B;B;B;B;B;B	0.42112	0.078;0.118;0.19;0.015;0.015;0.376	T	0.15292	-1.0442	9	0.32370	T	0.25	-1.7434	12.0729	0.53626	0.0:0.0:0.611:0.389	.	4973;814;865;5101;5049;1806	E7ESK3;Q99102-12;Q99102-13;E9PDY6;E7ENC5;Q99102-10	.;.;.;.;.;.	M	814;865;5101;5049;1601	ENSP00000338109:L814M;ENSP00000304207:L865M;ENSP00000417498:L5101M;ENSP00000420243:L5049M	ENSP00000304207:L865M	L	-	1	2	MUC4	196966782	0.986000	0.35501	0.621000	0.29145	0.157000	0.22087	0.811000	0.27198	0.329000	0.23460	0.436000	0.28706	CTG	G|0.924;T|0.076	0.076	strong		0.662	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406	
PKD1L1	168507	hgsc.bcm.edu	37	7	47925485	47925485	+	Missense_Mutation	SNP	T	T	G	rs113527998	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:47925485T>G	ENST00000289672.2	-	18	3054	c.3004A>C	c.(3004-3006)Act>Cct	p.T1002P		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1002	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						GGAGCTGAAGTGGCAGGTTGG	0.607													G|||	199	0.0397364	0.1407	0.0101	5008	,	,		16333	0.0		0.005	False		,,,				2504	0.001				p.T1002P		Atlas-SNP	.											.	PKD1L1	328	.	0			c.A3004C						PASS	.	G	PRO/THR	657,3749	765.5+/-413.4	51,555,1597	86.0	87.0	86.0		3004	0.5	0.0	7	dbSNP_132	86	85,8515	815.6+/-407.0	1,83,4216	yes	missense	PKD1L1	NM_138295.3	38	52,638,5813	GG,GT,TT		0.9884,14.9115,5.7051	benign	1002/2850	47925485	742,12264	2203	4300	6503	SO:0001583	missense	168507	exon18			CTGAAGTGGCAGG	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.3004A>C	7.37:g.47925485T>G	ENSP00000289672:p.Thr1002Pro	185.0	0.0	0		198.0	81.0	0.409091	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	88	0.040293040293040296	81	0.16463414634146342	4	0.011049723756906077	0	0.0	3	0.00395778364116095	G	8.197	0.797394	0.16327	0.149115	0.009884	ENSG00000158683	ENST00000289672	T	0.20332	2.08	4.97	0.5	0.16919	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	2744.040000	0.00166	N	0.000000	T	0.00039	0.0001	N	0.00707	-1.245	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.25779	-1.0122	9	0.29301	T	0.29	0.945	0.5519	0.00664	0.2174:0.1517:0.32:0.3108	.	1002	Q8TDX9	PK1L1_HUMAN	P	1002	ENSP00000289672:T1002P	ENSP00000289672:T1002P	T	-	1	0	PKD1L1	47892010	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.139000	0.16036	-0.344000	0.08338	-0.132000	0.14878	ACT	T|0.950;G|0.050	0.050	strong		0.607	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
DDX25	29118	hgsc.bcm.edu	37	11	125778305	125778305	+	Silent	SNP	C	C	T	rs34007659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:125778305C>T	ENST00000263576.6	+	6	569	c.414C>T	c.(412-414)aaC>aaT	p.N138N	RP11-680F20.9_ENST00000533033.2_RNA|DDX25_ENST00000525943.1_3'UTR	NM_013264.4	NP_037396.3	Q9UHL0	DDX25_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 25	138	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|ovary(2)|upper_aerodigestive_tract(1)	10	all_hematologic(175;0.177)	Breast(109;0.0021)|all_lung(97;0.0203)|Lung NSC(97;0.0203)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.14e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.046)		GACCCCAGAACCTCATAGCAC	0.428													C|||	85	0.0169728	0.0613	0.0043	5008	,	,		20960	0.0		0.001	False		,,,				2504	0.0				p.N138N		Atlas-SNP	.											.	DDX25	65	.	0			c.C414T						PASS	.	C		201,3635		5,191,1722	170.0	163.0	165.0		414	2.3	1.0	11	dbSNP_126	165	5,8241		0,5,4118	no	coding-synonymous	DDX25	NM_013264.3		5,196,5840	TT,TC,CC		0.0606,5.2398,1.705		138/484	125778305	206,11876	1918	4123	6041	SO:0001819	synonymous_variant	29118	exon6			CCAGAACCTCATA	AF155140	CCDS44766.1	11q24	2012-02-23	2012-02-23		ENSG00000109832	ENSG00000109832		"""DEAD-boxes"""	18698	protein-coding gene	gene with protein product	"""gonadotropin-regulated testicular RNA helicase"""	607663	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 25"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 25"""			10608860, 15096601	Standard	NM_013264		Approved	GRTH	uc001qcz.5	Q9UHL0	OTTHUMG00000165859	ENST00000263576.6:c.414C>T	11.37:g.125778305C>T		153.0	0.0	0		146.0	83.0	0.568493	NM_013264	B2R6Z0|Q5XVN2|Q86W81|Q8IYP1	Silent	SNP	ENST00000263576.6	37	CCDS44766.1	31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	C	8.677	0.904182	0.17760	0.052398	6.06E-4	ENSG00000109832	ENST00000530129	.	.	.	5.18	2.26	0.28386	.	.	.	.	.	T	0.10165	0.0249	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.03773	-1.1005	4	.	.	.	-6.705	4.4905	0.11812	0.0:0.4806:0.1565:0.3629	rs34007659	.	.	.	S	150	.	.	P	+	1	0	DDX25	125283515	0.994000	0.37717	1.000000	0.80357	0.995000	0.86356	0.292000	0.19011	0.269000	0.21961	0.591000	0.81541	CCT	C|0.985;T|0.015	0.015	strong		0.428	DDX25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386736.3	NM_013264	
SUPV3L1	6832	hgsc.bcm.edu	37	10	70940066	70940066	+	Silent	SNP	C	C	T	rs12251842	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:70940066C>T	ENST00000359655.4	+	1	79	c.19C>T	c.(19-21)Cta>Tta	p.L7L	SUPV3L1_ENST00000483572.1_3'UTR	NM_003171.3	NP_003162.2	Q8IYB8	SUV3_HUMAN	suppressor of var1, 3-like 1 (S. cerevisiae)	7					ATP catabolic process (GO:0006200)|chromatin maintenance (GO:0070827)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA surveillance (GO:0035946)|mitochondrial ncRNA surveillance (GO:0035945)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA surveillance (GO:2000827)|mitochondrion morphogenesis (GO:0070584)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|RNA catabolic process (GO:0006401)	mitochondrial degradosome (GO:0045025)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3'-5' RNA helicase activity (GO:0034458)|ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CTCCCGTGCCCTATTGTGGGC	0.706													C|||	232	0.0463259	0.1672	0.0144	5008	,	,		16416	0.0		0.001	False		,,,				2504	0.0				p.L7L		Atlas-SNP	.											.	SUPV3L1	61	.	0			c.C19T						PASS	.	C		575,3829	214.1+/-233.5	41,493,1668	25.0	29.0	28.0		19	0.8	0.6	10	dbSNP_120	28	4,8594	2.2+/-6.3	0,4,4295	no	coding-synonymous	SUPV3L1	NM_003171.3		41,497,5963	TT,TC,CC		0.0465,13.0563,4.4532		7/787	70940066	579,12423	2202	4299	6501	SO:0001819	synonymous_variant	6832	exon1			CGTGCCCTATTGT	AF042169	CCDS7287.1	10q22.1	2008-08-01	2001-11-28		ENSG00000156502	ENSG00000156502			11471	protein-coding gene	gene with protein product		605122	"""suppressor of var1 (S.cerevisiae) 3-like 1"""			9925937, 16176273	Standard	XM_005270068		Approved	SUV3	uc001jpe.1	Q8IYB8	OTTHUMG00000018375	ENST00000359655.4:c.19C>T	10.37:g.70940066C>T		59.0	0.0	0		62.0	27.0	0.435484	NM_003171	A8K301|O43630	Silent	SNP	ENST00000359655.4	37	CCDS7287.1																																																																																			C|0.962;T|0.038	0.038	strong		0.706	SUPV3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048396.2	NM_003171	
HIPK4	147746	hgsc.bcm.edu	37	19	40895493	40895493	+	Missense_Mutation	SNP	G	G	A	rs79236726	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40895493G>A	ENST00000291823.2	-	1	601	c.317C>T	c.(316-318)gCg>gTg	p.A106V		NM_144685.3	NP_653286.2	Q8NE63	HIPK4_HUMAN	homeodomain interacting protein kinase 4	106	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		A -> T (in dbSNP:rs34434715). {ECO:0000269|PubMed:17344846}.		histone phosphorylation (GO:0016572)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of signal transduction by p53 class mediator (GO:1901796)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	20			Lung(22;4.95e-05)|LUSC - Lung squamous cell carcinoma(20;0.000292)			GGGGAGGGGCGCGAAGTTGTT	0.577													G|||	32	0.00638978	0.0242	0.0	5008	,	,		9839	0.0		0.0	False		,,,				2504	0.0				p.A106V		Atlas-SNP	.											HIPK4_ENST00000291823,colon,carcinoma,+1,2	HIPK4	100	2	0			c.C317T						scavenged	.	G	VAL/ALA	104,4302	82.4+/-120.9	2,100,2101	58.0	62.0	61.0		317	2.9	0.7	19	dbSNP_131	61	0,8600		0,0,4300	yes	missense	HIPK4	NM_144685.3	64	2,100,6401	AA,AG,GG		0.0,2.3604,0.7996	possibly-damaging	106/617	40895493	104,12902	2203	4300	6503	SO:0001583	missense	147746	exon1			AGGGGCGCGAAGT	BC034501	CCDS12555.1	19q13.2	2008-02-05				ENSG00000160396			19007	protein-coding gene	gene with protein product		611712					Standard	NM_144685		Approved	FLJ32818	uc002onp.3	Q8NE63		ENST00000291823.2:c.317C>T	19.37:g.40895493G>A	ENSP00000291823:p.Ala106Val	96.0	1.0	0.0104167		104.0	53.0	0.509615	NM_144685	A8K863|Q96M54	Missense_Mutation	SNP	ENST00000291823.2	37	CCDS12555.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	G	14.62	2.590686	0.46214	0.023604	0.0	ENSG00000160396	ENST00000291823;ENST00000452139	T	0.63255	-0.03	5.08	2.91	0.33838	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.51477	D	0.000083	T	0.27241	0.0668	N	0.04787	-0.16	0.34206	D	0.67376	P	0.50528	0.936	P	0.46419	0.516	T	0.54357	-0.8306	10	0.52906	T	0.07	.	9.804	0.40781	0.0:0.2864:0.5655:0.1481	.	106	Q8NE63	HIPK4_HUMAN	V	106;71	ENSP00000291823:A106V	ENSP00000291823:A106V	A	-	2	0	HIPK4	45587333	0.003000	0.15002	0.726000	0.30738	0.995000	0.86356	1.122000	0.31295	0.708000	0.31955	0.462000	0.41574	GCG	G|0.992;A|0.008	0.008	strong		0.577	HIPK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462593.1	NM_144685	
GIMAP5	55340	hgsc.bcm.edu	37	7	150439554	150439554	+	Silent	SNP	G	G	A	rs61751040	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150439554G>A	ENST00000358647.3	+	3	694	c.327G>A	c.(325-327)ccG>ccA	p.P109P	GIMAP5_ENST00000479556.1_3'UTR	NM_018384.4	NP_060854.2	Q96F15	GIMA5_HUMAN	GTPase, IMAP family member 5	109	AIG1-type G.				myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of lipid catabolic process (GO:0050995)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of T cell activation (GO:0050868)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0032831)|positive regulation of gamma-delta T cell differentiation (GO:0045588)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of membrane potential (GO:0045838)|positive regulation of natural killer cell cytokine production (GO:0002729)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|regulation of mitochondrial membrane permeability (GO:0046902)|T cell differentiation (GO:0030217)|T cell homeostasis (GO:0043029)|temperature homeostasis (GO:0001659)	integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrial outer membrane (GO:0005741)	GTP binding (GO:0005525)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|urinary_tract(2)	19			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TCTCTGCCCCGGGGCCCCACG	0.592													G|||	297	0.0593051	0.1785	0.0173	5008	,	,		18120	0.0159		0.0	False		,,,				2504	0.0337				p.P313P		Atlas-SNP	.											GIMAP5,NS,carcinoma,+1,1	.	.	1	0			c.G939A						scavenged	.	G	,	661,3745	280.5+/-275.4	42,577,1584	75.0	76.0	76.0		939,327	-8.3	0.0	7	dbSNP_129	76	12,8588	8.4+/-32.0	0,12,4288	no	coding-synonymous,coding-synonymous	GIMAP5,GIMAP1-GIMAP5	NM_001199577.1,NM_018384.4	,	42,589,5872	AA,AG,GG		0.1395,15.0023,5.1745	,	313/512,109/308	150439554	673,12333	2203	4300	6503	SO:0001819	synonymous_variant	0	exon6			TGCCCCGGGGCCC	AK002158	CCDS5907.1	7q36.1	2014-04-04	2004-10-29	2004-10-30	ENSG00000196329	ENSG00000196329		"""GTPases, IMAP"""	18005	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 5"""	608086	"""immune associated nucleotide 4 like 1 (mouse)"""	IAN4L1			Standard	NM_018384		Approved	HIMAP3, IAN5		Q96F15	OTTHUMG00000157542	ENST00000358647.3:c.327G>A	7.37:g.150439554G>A		95.0	1.0	0.0105263		109.0	52.0	0.477064	NM_001199577	D3DWZ5|Q6IA75|Q96NE4|Q9NUK9	Silent	SNP	ENST00000358647.3	37	CCDS5907.1																																																																																			G|0.953;A|0.047	0.047	strong		0.592	GIMAP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349108.2	NM_018384	
OR10G7	390265	hgsc.bcm.edu	37	11	123909524	123909524	+	Missense_Mutation	SNP	G	G	A	rs201246927		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123909524G>A	ENST00000330487.5	-	1	193	c.185C>T	c.(184-186)aCc>aTc	p.T62I		NM_001004463.1	NP_001004463.1	Q8NGN6	O10G7_HUMAN	olfactory receptor, family 10, subfamily G, member 7	62						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(4)|kidney(7)|large_intestine(6)|lung(20)|ovary(2)|prostate(2)|stomach(3)|urinary_tract(1)	47		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		GGACAGGTTGGTGAGGAAGTA	0.547																																					p.T62I		Atlas-SNP	.											OR10G7,NS,carcinoma,+1,1	OR10G7	103	1	0			c.C185T						scavenged	.						21.0	21.0	21.0					11																	123909524		2195	4272	6467	SO:0001583	missense	390265	exon1			AGGTTGGTGAGGA	AB065754	CCDS31705.1	11q24.1	2012-08-09			ENSG00000182634	ENSG00000182634		"""GPCR / Class A : Olfactory receptors"""	14842	protein-coding gene	gene with protein product							Standard	NM_001004463		Approved		uc001pzq.1	Q8NGN6	OTTHUMG00000165969	ENST00000330487.5:c.185C>T	11.37:g.123909524G>A	ENSP00000329689:p.Thr62Ile	624.0	0.0	0		468.0	56.0	0.119658	NM_001004463	Q6IFE8	Missense_Mutation	SNP	ENST00000330487.5	37	CCDS31705.1	58	0.026556776556776556	21	0.042682926829268296	17	0.04696132596685083	17	0.02972027972027972	3	0.00395778364116095	G	9.581	1.123605	0.20959	.	.	ENSG00000182634	ENST00000330487	T	0.01092	5.35	3.53	1.5	0.22942	GPCR, rhodopsin-like superfamily (1);	0.649434	0.13528	N	0.381190	T	0.00241	0.0007	L	0.28694	0.88	0.22213	N	0.999283	B	0.06786	0.001	B	0.15052	0.012	T	0.48875	-0.8996	10	0.66056	D	0.02	.	5.9703	0.19349	0.1371:0.3547:0.5082:0.0	.	62	Q8NGN6	O10G7_HUMAN	I	62	ENSP00000329689:T62I	ENSP00000329689:T62I	T	-	2	0	OR10G7	123414734	0.000000	0.05858	0.928000	0.36995	0.900000	0.52787	-0.620000	0.05565	0.261000	0.21753	0.557000	0.71058	ACC	A|1.000;|0.000	1.000	weak		0.547	OR10G7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387271.1	NM_001004463	
ARL5C	390790	hgsc.bcm.edu	37	17	37317566	37317566	+	Silent	SNP	C	C	A	rs11653423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:37317566C>A	ENST00000269586.7	-	4	293	c.294G>T	c.(292-294)cgG>cgT	p.R98R	ARL5C_ENST00000444555.1_Silent_p.R98R|ARL5C_ENST00000583123.1_5'Flank	NM_001143968.1	NP_001137440.1	A6NH57	ARL5C_HUMAN	ADP-ribosylation factor-like 5C	98					small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)										TGGTCAGCAGCCGATCCCGGT	0.567													C|||	436	0.0870607	0.3124	0.0317	5008	,	,		17838	0.0		0.001	False		,,,				2504	0.0				p.R98R		Atlas-SNP	.											.	ARL5C	3	.	0			c.G294T						PASS	.	C		378,1006		50,278,364	45.0	37.0	39.0		294	-2.4	0.0	17	dbSNP_120	39	13,3169		0,13,1578	no	coding-synonymous	ARL5C	NM_001143968.1		50,291,1942	AA,AC,CC		0.4085,27.3121,8.5633		98/180	37317566	391,4175	692	1591	2283	SO:0001819	synonymous_variant	390790	exon4			CAGCAGCCGATCC		CCDS45664.1	17q12	2014-05-09	2005-11-08	2005-11-08	ENSG00000141748	ENSG00000141748		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	31111	protein-coding gene	gene with protein product			"""ADP-ribosylation factor-like 12"""	ARL12			Standard	NM_001143968		Approved		uc010wea.2	A6NH57		ENST00000269586.7:c.294G>T	17.37:g.37317566C>A		63.0	0.0	0		60.0	35.0	0.583333	NM_001143968		Silent	SNP	ENST00000269586.7	37	CCDS45664.1																																																																																			C|0.933;A|0.067	0.067	strong		0.567	ARL5C-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444566.1	NM_001143968	
FBN3	84467	hgsc.bcm.edu	37	19	8196645	8196645	+	Missense_Mutation	SNP	G	G	A	rs61729592	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8196645G>A	ENST00000600128.1	-	15	2197	c.1783C>T	c.(1783-1785)Cgc>Tgc	p.R595C	FBN3_ENST00000601739.1_Missense_Mutation_p.R595C|FBN3_ENST00000270509.2_Missense_Mutation_p.R595C			Q75N90	FBN3_HUMAN	fibrillin 3	595	EGF-like 7; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						CACTGGCAGCGGAAGGAGCCC	0.672													G|||	11	0.00219649	0.0083	0.0	5008	,	,		15081	0.0		0.0	False		,,,				2504	0.0				p.R595C		Atlas-SNP	.											.	FBN3	300	.	0			c.C1783T						PASS	.	G	CYS/ARG	23,4383		0,23,2180	22.0	23.0	22.0		1783	3.0	0.9	19	dbSNP_129	22	1,8595		0,1,4297	yes	missense	FBN3	NM_032447.3	180	0,24,6477	AA,AG,GG		0.0116,0.522,0.1846	probably-damaging	595/2810	8196645	24,12978	2203	4298	6501	SO:0001583	missense	84467	exon14			GGCAGCGGAAGGA		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.1783C>T	19.37:g.8196645G>A	ENSP00000470498:p.Arg595Cys	156.0	0.0	0		181.0	96.0	0.530387	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Missense_Mutation	SNP	ENST00000600128.1	37	CCDS12196.1	.	.	.	.	.	.	.	.	.	.	g	13.30	2.197312	0.38806	0.00522	1.16E-4	ENSG00000142449	ENST00000270509	D	0.92545	-3.06	3.02	3.02	0.34903	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.063744	0.64402	U	0.000009	D	0.93419	0.7901	M	0.85041	2.73	0.52501	D	0.999955	D	0.65815	0.995	P	0.58077	0.832	D	0.93900	0.7187	10	0.87932	D	0	.	13.9673	0.64216	0.0:0.0:1.0:0.0	.	595	Q75N90	FBN3_HUMAN	C	595	ENSP00000270509:R595C	ENSP00000270509:R595C	R	-	1	0	FBN3	8102645	0.999000	0.42202	0.856000	0.33681	0.121000	0.20230	2.263000	0.43293	1.227000	0.43598	0.185000	0.17295	CGC	G|0.996;A|0.004	0.004	strong		0.672	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
PEX6	5190	hgsc.bcm.edu	37	6	42932080	42932080	+	Missense_Mutation	SNP	G	G	A	rs115180949	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42932080G>A	ENST00000304611.8	-	17	3005	c.2936C>T	c.(2935-2937)gCc>gTc	p.A979V	PEX6_ENST00000244546.4_3'UTR	NM_000287.3	NP_000278.3	Q13608	PEX6_HUMAN	peroxisomal biogenesis factor 6	979					ATP catabolic process (GO:0006200)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix, translocation (GO:0016561)|protein stabilization (GO:0050821)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(3)	15			all cancers(41;0.00235)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0562)			CTCCTAGCAGGCAGCAAACTT	0.637													G|||	47	0.00938498	0.034	0.0029	5008	,	,		17507	0.0		0.0	False		,,,				2504	0.0				p.A979V		Atlas-SNP	.											.	PEX6	44	.	0			c.C2936T						PASS	.	G	VAL/ALA	85,4321		0,85,2118	36.0	38.0	37.0		2936	5.0	1.0	6	dbSNP_132	37	3,8595		0,3,4296	yes	missense	PEX6	NM_000287.3	64	0,88,6414	AA,AG,GG		0.0349,1.9292,0.6767	possibly-damaging	979/981	42932080	88,12916	2203	4299	6502	SO:0001583	missense	5190	exon17			TAGCAGGCAGCAA	U56602	CCDS4877.1	6p22-p11	2010-04-21			ENSG00000124587	ENSG00000124587		"""ATPases / AAA-type"""	8859	protein-coding gene	gene with protein product		601498				8670792	Standard	NM_000287		Approved	PXAAA1, PAF-2	uc003otf.3	Q13608	OTTHUMG00000014713	ENST00000304611.8:c.2936C>T	6.37:g.42932080G>A	ENSP00000303511:p.Ala979Val	107.0	0.0	0		98.0	45.0	0.459184	NM_000287	Q5T8W1|Q8WYQ0|Q8WYQ1|Q8WYQ2|Q99476	Missense_Mutation	SNP	ENST00000304611.8	37	CCDS4877.1	16	0.007326007326007326	15	0.03048780487804878	1	0.0027624309392265192	0	0.0	0	0.0	G	36	5.602210	0.96614	0.019292	3.49E-4	ENSG00000124587	ENST00000304611	D	0.95377	-3.69	5.9	5.03	0.67393	.	0.307721	0.39985	N	0.001217	D	0.93119	0.7809	L	0.33485	1.01	0.80722	D	1	D	0.57257	0.979	P	0.52554	0.702	D	0.93230	0.6616	10	0.52906	T	0.07	-12.279	15.0391	0.71774	0.0698:0.0:0.9302:0.0	.	979	Q13608	PEX6_HUMAN	V	979	ENSP00000303511:A979V	ENSP00000303511:A979V	A	-	2	0	PEX6	43040058	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	5.035000	0.64158	2.803000	0.96430	0.609000	0.83330	GCC	G|0.993;A|0.007	0.007	strong		0.637	PEX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040569.1	NM_000287	
GLDC	2731	hgsc.bcm.edu	37	9	6587176	6587176	+	Silent	SNP	G	G	A	rs74461075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:6587176G>A	ENST00000321612.6	-	15	1965	c.1815C>T	c.(1813-1815)ctC>ctT	p.L605L		NM_000170.2	NP_000161.2	P23378	GCSP_HUMAN	glycine dehydrogenase (decarboxylating)	605					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|glycine dehydrogenase (decarboxylating) activity (GO:0004375)|lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|large_intestine(5)|lung(23)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		Acute lymphoblastic leukemia(23;0.161)		GBM - Glioblastoma multiforme(50;0.0421)|Lung(218;0.134)	Glycine(DB00145)	CATAACCTGTGAGTTCACACA	0.418													G|||	71	0.0141773	0.0514	0.0043	5008	,	,		19260	0.0		0.0	False		,,,				2504	0.0				p.L605L		Atlas-SNP	.											.	GLDC	118	.	0			c.C1815T						PASS	.	G		173,4233	112.9+/-151.0	3,167,2033	117.0	112.0	114.0		1815	3.5	1.0	9	dbSNP_131	114	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	GLDC	NM_000170.2		3,169,6331	AA,AG,GG		0.0233,3.9265,1.3455		605/1021	6587176	175,12831	2203	4300	6503	SO:0001819	synonymous_variant	2731	exon15			ACCTGTGAGTTCA	D90239	CCDS34987.1	9p22	2014-09-17	2006-05-22		ENSG00000178445	ENSG00000178445	1.4.4.2		4313	protein-coding gene	gene with protein product	"""glycine cleavage system protein P"", ""glycine decarboxylase"""	238300	"""glycine dehydrogenase (decarboxylating; glycine decarboxylase, glycine cleavage system protein P)"""			1993704, 1996985	Standard	NM_000170		Approved	GCSP, NKH	uc003zkc.3	P23378	OTTHUMG00000019524	ENST00000321612.6:c.1815C>T	9.37:g.6587176G>A		125.0	0.0	0		135.0	64.0	0.474074	NM_000170	Q2M2F8	Silent	SNP	ENST00000321612.6	37	CCDS34987.1																																																																																			G|0.987;A|0.013	0.013	strong		0.418	GLDC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051674.2	NM_000170	
LCE1C	353133	hgsc.bcm.edu	37	1	152777874	152777874	+	Silent	SNP	T	T	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152777874T>A	ENST00000607093.1	-	1	80	c.81A>T	c.(79-81)ccA>ccT	p.P27P	LCE1C_ENST00000368768.1_Silent_p.P27P			Q5T751	LCE1C_HUMAN	late cornified envelope 1C	27	Pro-rich.				keratinization (GO:0031424)					NS(1)|lung(4)|prostate(1)|skin(2)|urinary_tract(1)	9	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			ggggacactttggggTGgggc	0.647																																					p.P27P		Atlas-SNP	.											.	LCE1C	40	.	0			c.A81T						PASS	.						46.0	47.0	46.0					1																	152777874		2203	4300	6503	SO:0001819	synonymous_variant	353133	exon2			ACACTTTGGGGTG		CCDS1026.1	1q21.3	2008-02-05			ENSG00000197084	ENSG00000197084		"""Late cornified envelopes"""	29464	protein-coding gene	gene with protein product		612605				11698679	Standard	NM_001276331		Approved	LEP3	uc001fap.1	Q5T751	OTTHUMG00000012445	ENST00000607093.1:c.81A>T	1.37:g.152777874T>A		282.0	0.0	0		403.0	21.0	0.0521092	NM_178351		Silent	SNP	ENST00000607093.1	37	CCDS1026.1																																																																																			.	.	none		0.647	LCE1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034658.2	NM_178351	
LILRB3	11025	hgsc.bcm.edu	37	19	54721337	54721337	+	Missense_Mutation	SNP	G	G	A	rs75437884	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54721337G>A	ENST00000391750.1	-	13	1736	c.1600C>T	c.(1600-1602)Cac>Tac	p.H534Y	LILRA6_ENST00000440558.2_Missense_Mutation_p.H534Y|LILRB3_ENST00000346401.6_Missense_Mutation_p.H546Y|LILRB3_ENST00000245620.9_Missense_Mutation_p.H535Y|LILRA6_ENST00000391735.3_3'UTR|LILRA6_ENST00000419410.2_Missense_Mutation_p.H535Y|LILRB3_ENST00000469273.1_5'UTR|LILRB3_ENST00000407860.2_Missense_Mutation_p.H551Y|LILRA6_ENST00000270464.5_Missense_Mutation_p.H535Y|LILRB3_ENST00000424807.1_Missense_Mutation_p.H534Y			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	534					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)		TCTTCATCGTGTGGGCTCTGC	0.577																																					p.H535Y		Atlas-SNP	.											LILRB3,NS,lymphoid_neoplasm,+2,1	LILRB3	67	1	0			c.C1603T						PASS	.	G	TYR/HIS,TYR/HIS	47,4355	43.1+/-76.7	0,47,2154	76.0	81.0	80.0		1603,1600	-1.2	0.0	19	dbSNP_131	80	1,8597		0,1,4298	no	missense,missense	LILRB3	NM_001081450.1,NM_006864.2	83,83	0,48,6452	AA,AG,GG		0.0116,1.0677,0.3692	possibly-damaging,possibly-damaging	535/633,534/632	54721337	48,12952	2201	4299	6500	SO:0001583	missense	11025	exon12			CATCGTGTGGGCT	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.1600C>T	19.37:g.54721337G>A	ENSP00000375630:p.His534Tyr	534.0	0.0	0		384.0	90.0	0.234375	NM_001081450	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	8	0.003663003663003663	6	0.012195121951219513	2	0.0055248618784530384	0	0.0	0	0.0	G	10.80	1.452361	0.26074	0.010677	1.16E-4	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410	T;T;T;T;T;T;T;T	0.00487	7.1;7.1;7.07;7.07;7.05;7.1;7.07;7.09	2.47	-1.25	0.09405	.	.	.	.	.	T	0.00384	0.0012	L	0.54323	1.7	0.09310	N	1	D;B;D;P;B;P;P	0.56968	0.969;0.009;0.978;0.832;0.411;0.536;0.593	P;B;P;B;B;B;B	0.51615	0.65;0.004;0.675;0.249;0.059;0.031;0.32	T	0.51164	-0.8740	9	0.33141	T	0.24	.	5.0801	0.14651	0.1499:0.4983:0.3518:0.0	.	551;534;535;546;551;534;535	B5MCX0;F8WCY4;D3YTC4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;.;LIRB3_HUMAN;.	Y	534;534;546;535;551;534;535;535	ENSP00000375630:H534Y;ENSP00000412771:H534Y;ENSP00000345184:H546Y;ENSP00000245620:H535Y;ENSP00000384274:H551Y;ENSP00000390120:H534Y;ENSP00000270464:H535Y;ENSP00000411227:H535Y	ENSP00000270464:H535Y	H	-	1	0	LILRB3;LILRA6	59413149	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.974000	0.03794	-0.122000	0.11766	-0.506000	0.04501	CAC	G|0.996;A|0.004	0.004	strong		0.577	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
MGAT1	4245	hgsc.bcm.edu	37	5	180219842	180219842	+	Missense_Mutation	SNP	C	C	T	rs34344788	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:180219842C>T	ENST00000446023.2	-	3	880	c.130G>A	c.(130-132)Gat>Aat	p.D44N	MGAT1_ENST00000307826.4_Missense_Mutation_p.D44N|MGAT1_ENST00000333055.3_Missense_Mutation_p.D44N|MGAT1_ENST00000427865.2_Missense_Mutation_p.D44N|MGAT1_ENST00000393340.3_Missense_Mutation_p.D44N	NM_001114617.1|NM_001114618.1	NP_001108089.1|NP_001108090.1	P26572	MGAT1_HUMAN	mannosyl (alpha-1,3-)-glycoprotein beta-1,2-N-acetylglucosaminyltransferase	44					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-N-acetylglucosamine catabolic process (GO:0006049)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|vesicle (GO:0031982)	acetylglucosaminyltransferase activity (GO:0008375)|alpha-1,3-mannosylglycoprotein 2-beta-N-acetylglucosaminyltransferase activity (GO:0003827)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	13	all_cancers(89;1.11e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.0027)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00356)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GGGTCGCCATCGAGAGCGCTG	0.677													C|||	46	0.0091853	0.0333	0.0029	5008	,	,		14178	0.0		0.0	False		,,,				2504	0.0				p.D44N		Atlas-SNP	.											.	MGAT1	48	.	0			c.G130A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	81,4255		0,81,2087	10.0	11.0	10.0		130,130,130,130,130	3.0	0.0	5	dbSNP_126	10	1,8491		0,1,4245	yes	missense,missense,missense,missense,missense	MGAT1	NM_001114617.1,NM_001114618.1,NM_001114619.1,NM_001114620.1,NM_002406.3	23,23,23,23,23	0,82,6332	TT,TC,CC		0.0118,1.8681,0.6392	benign,benign,benign,benign,benign	44/446,44/446,44/446,44/446,44/446	180219842	82,12746	2168	4246	6414	SO:0001583	missense	4245	exon3			CGCCATCGAGAGC	M61829	CCDS4458.1	5q35.3	2013-02-25			ENSG00000131446	ENSG00000131446	2.4.1.101	"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	7044	protein-coding gene	gene with protein product		160995		MGAT, GLYT1		1827260	Standard	NM_002406		Approved	GNT-1, GLCNAC-TI	uc003mmg.4	P26572	OTTHUMG00000130937	ENST00000446023.2:c.130G>A	5.37:g.180219842C>T	ENSP00000404718:p.Asp44Asn	76.0	0.0	0		87.0	36.0	0.413793	NM_001114617	A8K404|B3KRU8|D3DWR1|Q6IBE3	Missense_Mutation	SNP	ENST00000446023.2	37	CCDS4458.1	15	0.006868131868131868	14	0.028455284552845527	1	0.0027624309392265192	0	0.0	0	0.0	C	0.065	-1.214664	0.01555	0.018681	1.18E-4	ENSG00000131446	ENST00000333055;ENST00000307826;ENST00000446023;ENST00000393340;ENST00000452920;ENST00000427865;ENST00000504671;ENST00000506889;ENST00000514283;ENST00000512695;ENST00000506269;ENST00000514438;ENST00000502678;ENST00000513431	T;T;T;T;T;T;T;T;T;T;T;T;T	0.81330	-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48;-1.48	4.75	2.97	0.34412	.	0.746358	0.12755	N	0.441841	T	0.39682	0.1087	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.26224	-1.0109	10	0.15952	T	0.53	-3.9185	10.5598	0.45140	0.0:0.8532:0.0:0.1468	rs34344788	44	P26572	MGAT1_HUMAN	N	44	ENSP00000332073:D44N;ENSP00000311888:D44N;ENSP00000404718:D44N;ENSP00000377010:D44N;ENSP00000402838:D44N;ENSP00000424891:D44N;ENSP00000425988:D44N;ENSP00000424382:D44N;ENSP00000427116:D44N;ENSP00000422906:D44N;ENSP00000421738:D44N;ENSP00000422588:D44N;ENSP00000423401:D44N	ENSP00000311888:D44N	D	-	1	0	MGAT1	180152448	0.001000	0.12720	0.001000	0.08648	0.003000	0.03518	0.842000	0.27627	0.691000	0.31592	-1.523000	0.00931	GAT	C|0.993;T|0.007	0.007	strong		0.677	MGAT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368189.1	NM_001114618	
USP6	9098	hgsc.bcm.edu	37	17	5039138	5039138	+	Silent	SNP	C	C	T	rs3213878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5039138C>T	ENST00000574788.1	+	17	2809	c.579C>T	c.(577-579)acC>acT	p.T193T	USP6_ENST00000304328.5_5'UTR|USP6_ENST00000250066.6_Silent_p.T193T|USP6_ENST00000332776.4_Silent_p.T193T			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	193	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						GCCACATCACCGCCTTGTTCC	0.607			T	"""COL1A1, CDH11, ZNF9, OMD"""	aneurysmal bone cysts								C|||	490	0.0978435	0.1853	0.0375	5008	,	,		20475	0.0774		0.1143	False		,,,				2504	0.0266				p.T193T		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	.	USP6	213	.	0			c.C579T						PASS	.	C		682,3724	287.2+/-279.2	60,562,1581	126.0	110.0	115.0		579	-1.7	0.2	17	dbSNP_106	115	949,7651	208.0+/-249.6	52,845,3403	no	coding-synonymous	USP6	NM_004505.2		112,1407,4984	TT,TC,CC		11.0349,15.4789,12.5404		193/1407	5039138	1631,11375	2203	4300	6503	SO:0001819	synonymous_variant	9098	exon9			CATCACCGCCTTG	X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"""Ubiquitin-specific peptidases"""	12629	protein-coding gene	gene with protein product	"""ubiquitin carboxyl-terminal hydrolase 6"", ""TBC1D3 and USP32 fusion"", ""Tre-2 oncogene"""	604334	"""ubiquitin specific protease 6 (Tre-2 oncogene)"", ""TRE oncogene, Smith Magenis syndrome chromosome region"", ""ubiquitin specific peptidase 6 (Tre-2 oncogene)"""	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.579C>T	17.37:g.5039138C>T		14.0	0.0	0		21.0	10.0	0.47619	NM_004505	Q15634|Q86WP6|Q8IWT4	Silent	SNP	ENST00000574788.1	37	CCDS11069.2																																																																																			C|0.883;T|0.117	0.117	strong		0.607	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505	
C4A	720	hgsc.bcm.edu	37	6	31963860	31963860	+	Missense_Mutation	SNP	C	C	G	rs79299066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31963860C>G	ENST00000428956.2	+	26	3443	c.3359C>G	c.(3358-3360)cCc>cGc	p.P1120R	C4A_ENST00000498271.1_Missense_Mutation_p.P1120R	NM_007293.2	NP_009224.2	P0C0L4	CO4A_HUMAN	complement component 4A (Rodgers blood group)	1120					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)	TTCCAGGACCCCTGTCCAGTG	0.617													c|||	18	0.00359425	0.0129	0.0014	5008	,	,		18899	0.0		0.0	False		,,,				2504	0.0				p.L1120R		Atlas-SNP	.											.	C4A	15	.	0			c.T3359G						PASS	.	T	ARG/PRO	18,3112		0,18,1547	76.0	76.0	76.0		3359	1.5	0.2	6	dbSNP_134	76	0,7074		0,0,3537	no	missense	C4A	NM_007293.2	103	0,18,5084	GG,GC,CC		0.0,0.5751,0.1764	probably-damaging	1120/1745	31963860	18,10186	1565	3537	5102	SO:0001583	missense	720	exon26			AGGACCCCTGTCC	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.3359C>G	6.37:g.31963860C>G	ENSP00000396688:p.Pro1120Arg	750.0	0.0	0		527.0	256.0	0.485768	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	Missense_Mutation	SNP	ENST00000428956.2	37	CCDS47404.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	c	5.827	0.336826	0.11013	0.005751	0.0	ENSG00000244731	ENST00000428956;ENST00000498271	T;T	0.32515	1.45;1.45	3.35	1.45	0.22620	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);A-macroglobulin complement component (1);	.	.	.	.	T	0.10723	0.0262	N	0.04260	-0.245	0.50813	D	0.999896	D;D	0.63046	0.992;0.992	D;D	0.66847	0.947;0.947	T	0.07424	-1.0773	9	0.12766	T	0.61	.	6.0472	0.19766	0.1829:0.699:0.0:0.1182	.	1120;1120	A6H8M8;P0C0L4	.;CO4A_HUMAN	R	1120	ENSP00000396688:P1120R;ENSP00000420212:P1120R	ENSP00000396688:P1120R	P	+	2	0	C4A	.	0.021000	0.18746	0.151000	0.22473	0.084000	0.17831	-0.000000	0.12993	-0.041000	0.13558	-2.139000	0.00339	CCC	.	.	alt		0.617	C4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076364.3	NM_007293	
MUC4	4585	hgsc.bcm.edu	37	3	195512219	195512219	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195512219C>T	ENST00000463781.3	-	2	6691	c.6232G>A	c.(6232-6234)Gcc>Acc	p.A2078T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A2078T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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)		AGAGGGGTGGCGTGACCTGTG	0.567																																					p.A2078T		Atlas-SNP	.											.	MUC4	1505	.	0			c.G6232A						PASS	.						19.0	20.0	20.0					3																	195512219		687	1571	2258	SO:0001583	missense	4585	exon2			GGGTGGCGTGACC	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.6232G>A	3.37:g.195512219C>T	ENSP00000417498:p.Ala2078Thr	439.0	1.0	0.0022779		220.0	75.0	0.340909	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	10.32	1.317466	0.23908	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32753	1.44;1.45	.	.	.	.	.	.	.	.	T	0.19446	0.0467	N	0.19112	0.55	0.53005	P	3.100000000000325E-5	D	0.53312	0.959	P	0.45971	0.499	T	0.23226	-1.0194	6	.	.	.	.	5.844	0.18652	0.0:0.9991:0.0:9.0E-4	.	2078	E7ESK3	.	T	2078	ENSP00000417498:A2078T;ENSP00000420243:A2078T	.	A	-	1	0	MUC4	196996614	0.000000	0.05858	0.046000	0.18839	0.072000	0.16883	-1.788000	0.01763	0.064000	0.16427	0.064000	0.15345	GCC	.	.	none		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
BIRC8	112401	hgsc.bcm.edu	37	19	53793162	53793162	+	Missense_Mutation	SNP	C	C	T	rs35880972	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53793162C>T	ENST00000426466.1	-	1	1713	c.466G>A	c.(466-468)Gct>Act	p.A156T		NM_033341.4	NP_203127.3	Q96P09	BIRC8_HUMAN	baculoviral IAP repeat containing 8	156			A -> T (in dbSNP:rs35880972).		apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(10)|urinary_tract(1)	19				GBM - Glioblastoma multiforme(134;0.00304)		TCTTTCTGAGCGCTCACTAGA	0.413													c|||	346	0.0690895	0.2466	0.0274	5008	,	,		18539	0.0		0.001	False		,,,				2504	0.0				p.A156T		Atlas-SNP	.											.	BIRC8	54	.	0			c.G466A						PASS	.	C	THR/ALA	885,3521	343.3+/-307.6	86,713,1404	102.0	102.0	102.0		466	-0.8	0.0	19	dbSNP_126	102	8,8592	5.0+/-18.6	0,8,4292	yes	missense	BIRC8	NM_033341.4	58	86,721,5696	TT,TC,CC		0.093,20.0862,6.8661	probably-damaging	156/237	53793162	893,12113	2203	4300	6503	SO:0001583	missense	112401	exon1			TCTGAGCGCTCAC	AF164682	CCDS12863.1	19q13.3-q13.4	2011-01-25	2011-01-25			ENSG00000163098		"""Baculoviral IAP repeat containing"""	14878	protein-coding gene	gene with protein product	"""IAP-like protein 2"", ""inhibitor of apoptosis-like protein 2"""		"""baculoviral IAP repeat-containing 8"""			11390657	Standard	NM_033341		Approved	ILP-2, hILP2	uc002qbk.3	Q96P09		ENST00000426466.1:c.466G>A	19.37:g.53793162C>T	ENSP00000412957:p.Ala156Thr	199.0	0.0	0		221.0	101.0	0.457014	NM_033341	Q6IPY1|Q96RW5	Missense_Mutation	SNP	ENST00000426466.1	37	CCDS12863.1	120	0.054945054945054944	111	0.22560975609756098	9	0.024861878453038673	0	0.0	0	0.0	C	8.392	0.840001	0.16891	0.200862	9.3E-4	ENSG00000163098	ENST00000426466	T	0.37915	1.17	0.628	-0.793	0.10922	.	.	.	.	.	T	0.00012	0.0000	M	0.79475	2.455	0.80722	P	0.0	P	0.37500	0.597	B	0.23852	0.049	T	0.06862	-1.0803	8	0.42905	T	0.14	-4.5555	5.2502	0.15517	0.0:0.7589:0.0:0.2411	rs35880972	156	Q96P09	BIRC8_HUMAN	T	156	ENSP00000412957:A156T	ENSP00000412957:A156T	A	-	1	0	BIRC8	58484974	0.119000	0.22226	0.005000	0.12908	0.004000	0.04260	0.493000	0.22451	-0.150000	0.11195	-0.356000	0.07607	GCT	C|0.937;T|0.063	0.063	strong		0.413	BIRC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464357.1	NM_033341	
UBA7	7318	hgsc.bcm.edu	37	3	49845526	49845526	+	Missense_Mutation	SNP	T	T	C	rs2230149	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:49845526T>C	ENST00000333486.3	-	20	2608	c.2450A>G	c.(2449-2451)cAt>cGt	p.H817R	MIR5193_ENST00000584510.1_RNA	NM_003335.2	NP_003326.2	P41226	UBA7_HUMAN	ubiquitin-like modifier activating enzyme 7	817			H -> R (in dbSNP:rs2230149).		cellular protein modification process (GO:0006464)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|ISG15-protein conjugation (GO:0032020)|modification-dependent protein catabolic process (GO:0019941)|negative regulation of type I interferon production (GO:0032480)|protein ubiquitination (GO:0016567)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ISG15 activating enzyme activity (GO:0019782)|ubiquitin activating enzyme activity (GO:0004839)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(15)|large_intestine(4)|lung(7)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	33				BRCA - Breast invasive adenocarcinoma(193;3.58e-06)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00607)		AAAGTCCACATGGAAGTTGCT	0.567													T|||	138	0.0275559	0.0983	0.0072	5008	,	,		22642	0.0		0.003	False		,,,				2504	0.0				p.H817R		Atlas-SNP	.											.	UBA7	64	.	0			c.A2450G						PASS	.	T	ARG/HIS	325,4081	171.6+/-201.8	20,285,1898	94.0	87.0	89.0		2450	5.3	0.9	3	dbSNP_98	89	1,8599	1.2+/-3.3	0,1,4299	yes	missense	UBA7	NM_003335.2	29	20,286,6197	CC,CT,TT		0.0116,7.3763,2.5065	probably-damaging	817/1013	49845526	326,12680	2203	4300	6503	SO:0001583	missense	7318	exon20			TCCACATGGAAGT	BC006378	CCDS2805.1	3p21	2007-11-30	2007-11-30	2007-11-30	ENSG00000182179	ENSG00000182179		"""Ubiquitin-like modifier activating enzymes"""	12471	protein-coding gene	gene with protein product	"""UBA1, ubiquitin-activating enzyme E1 homolog B (yeast)"", ""UBA7, ubiquitin-activating enzyme E1"""	191325	"""ubiquitin-activating enzyme E1-like"""	UBE1L		8327486	Standard	NM_003335		Approved	D8, UBE2, UBA1B	uc003cxr.3	P41226	OTTHUMG00000158267	ENST00000333486.3:c.2450A>G	3.37:g.49845526T>C	ENSP00000333266:p.His817Arg	90.0	0.0	0		84.0	38.0	0.452381	NM_003335	Q9BRB2	Missense_Mutation	SNP	ENST00000333486.3	37	CCDS2805.1	46	0.021062271062271064	41	0.08333333333333333	3	0.008287292817679558	0	0.0	2	0.002638522427440633	T	22.6	4.310618	0.81358	0.073763	1.16E-4	ENSG00000182179	ENST00000333486	T	0.47177	0.85	5.34	5.34	0.76211	Molybdenum cofactor biosynthesis, MoeB (1);Ubiquitin-like 1 activating enzyme, catalytic cysteine domain (1);	0.177580	0.53938	D	0.000047	T	0.19446	0.0467	H	0.96398	3.815	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.70263	-0.4920	10	0.87932	D	0	-17.9904	15.6299	0.76899	0.0:0.0:0.0:1.0	rs2230149;rs2234387;rs2230149	817	P41226	UBA7_HUMAN	R	817	ENSP00000333266:H817R	ENSP00000333266:H817R	H	-	2	0	UBA7	49820530	1.000000	0.71417	0.902000	0.35471	0.771000	0.43674	5.762000	0.68809	2.169000	0.68431	0.459000	0.35465	CAT	T|0.973;C|0.027	0.027	strong		0.567	UBA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350503.1	NM_003335	
SACS	26278	hgsc.bcm.edu	37	13	23905481	23905481	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:23905481C>T	ENST00000382292.3	-	9	12807	c.12534G>A	c.(12532-12534)ccG>ccA	p.P4178P	SACS_ENST00000382298.3_Silent_p.P4178P|SACS_ENST00000402364.1_Silent_p.P3428P			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	4178					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		CATATTCTCCCGGGTAAAAAA	0.413																																					p.P4178P		Atlas-SNP	.											.	SACS	871	.	0			c.G12534A						PASS	.						108.0	113.0	111.0					13																	23905481		2203	4300	6503	SO:0001819	synonymous_variant	26278	exon10			TTCTCCCGGGTAA	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.12534G>A	13.37:g.23905481C>T		103.0	0.0	0		105.0	59.0	0.561905	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	37	CCDS9300.2																																																																																			.	.	none		0.413	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
REV3L	5980	hgsc.bcm.edu	37	6	111695304	111695304	+	Silent	SNP	A	A	G	rs3218589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:111695304A>G	ENST00000358835.3	-	14	4708	c.4254T>C	c.(4252-4254)aaT>aaC	p.N1418N	REV3L_ENST00000368805.1_Silent_p.N1418N|REV3L_ENST00000435970.1_Silent_p.N1340N|REV3L_ENST00000368802.3_Silent_p.N1418N			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	1418					DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		AATGCAAAAAATTAGGGGTAT	0.388								DNA polymerases (catalytic subunits)					A|||	6	0.00119808	0.0045	0.0	5008	,	,		19794	0.0		0.0	False		,,,				2504	0.0				p.N1418N		Atlas-SNP	.											.	REV3L	386	.	0			c.T4254C						PASS	.	A		18,4388	25.3+/-52.1	0,18,2185	149.0	133.0	138.0		4254	3.7	1.0	6	dbSNP_106	138	0,8600		0,0,4300	no	coding-synonymous	REV3L	NM_002912.3		0,18,6485	GG,GA,AA		0.0,0.4085,0.1384		1418/3131	111695304	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	5980	exon13			CAAAAAATTAGGG	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"""DNA polymerases"""	9968	protein-coding gene	gene with protein product	"""polymerase, DNA, zeta"""	602776	"""REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta"", ""REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"""			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.4254T>C	6.37:g.111695304A>G		122.0	0.0	0		147.0	76.0	0.517007	NM_002912	O43214|Q5TC33	Silent	SNP	ENST00000358835.3	37	CCDS5091.2																																																																																			A|0.999;G|0.001	0.001	strong		0.388	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912	
OBSCN	84033	hgsc.bcm.edu	37	1	228565325	228565325	+	Silent	SNP	C	C	T	rs61743077	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228565325C>T	ENST00000422127.1	+	102	23459	c.23415C>T	c.(23413-23415)ctC>ctT	p.L7805L	OBSCN_ENST00000366707.4_Silent_p.L5439L|OBSCN_ENST00000570156.2_Silent_p.L8762L	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	7805	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				ACAACCTGCTCAAGGTCGTGG	0.562													C|||	54	0.0107827	0.0386	0.0029	5008	,	,		21756	0.0		0.001	False		,,,				2504	0.0				p.L8762L		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C26286T						PASS	.	C		187,4189		1,185,2002	95.0	97.0	96.0		23415	-2.4	0.9	1	dbSNP_129	96	0,8542		0,0,4271	no	coding-synonymous	OBSCN	NM_001098623.1		1,185,6273	TT,TC,CC		0.0,4.2733,1.4476		7805/7969	228565325	187,12731	2188	4271	6459	SO:0001819	synonymous_variant	84033	exon113			CCTGCTCAAGGTC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.23415C>T	1.37:g.228565325C>T		142.0	0.0	0		170.0	94.0	0.552941	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1	17	0.007783882783882784	15	0.03048780487804878	2	0.0055248618784530384	0	0.0	0	0.0	C	15.09	2.729743	0.48833	0.042733	0.0	ENSG00000154358	ENST00000441106	.	.	.	5.14	-2.38	0.06622	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.2	0.31419	0.0:0.1855:0.4897:0.3248	rs61743077	.	.	.	X	2422	.	.	Q	+	1	0	OBSCN	226631948	0.995000	0.38212	0.873000	0.34254	0.884000	0.51177	0.219000	0.17641	-0.368000	0.08040	0.313000	0.20887	CAA	C|0.992;T|0.008	0.008	strong		0.562	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
RANBP3L	202151	hgsc.bcm.edu	37	5	36257134	36257134	+	Missense_Mutation	SNP	G	G	A	rs16902872	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:36257134G>A	ENST00000296604.3	-	10	1297	c.812C>T	c.(811-813)gCt>gTt	p.A271V	RANBP3L_ENST00000515759.1_Missense_Mutation_p.A271V|RANBP3L_ENST00000502994.1_Missense_Mutation_p.A296V	NM_145000.3	NP_659437.3	Q86VV4	RNB3L_HUMAN	RAN binding protein 3-like	271			A -> V (in dbSNP:rs16902872).		intracellular transport (GO:0046907)					endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)|urinary_tract(1)	16	all_lung(31;4.52e-05)		Epithelial(62;0.0543)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.149)|Colorectal(62;0.202)			GAATGCAGCAGCTGATTCAAT	0.363													G|||	434	0.0866613	0.3132	0.0245	5008	,	,		15384	0.0		0.003	False		,,,				2504	0.0				p.A296V		Atlas-SNP	.											.	RANBP3L	41	.	0			c.C887T						PASS	.	G	VAL/ALA,VAL/ALA	1170,3236	408.6+/-334.7	146,878,1179	107.0	99.0	102.0		887,812	5.4	1.0	5	dbSNP_123	102	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	RANBP3L	NM_001161429.1,NM_145000.3	64,64	146,882,5475	AA,AG,GG		0.0465,26.5547,9.0266	probably-damaging,probably-damaging	296/491,271/466	36257134	1174,11832	2203	4300	6503	SO:0001583	missense	202151	exon11			GCAGCAGCTGATT	BC047660	CCDS3918.1, CCDS54843.1	5p13.2	2008-02-05			ENSG00000164188	ENSG00000164188			26353	protein-coding gene	gene with protein product						12477932	Standard	NM_145000		Approved	FLJ25422	uc011cow.2	Q86VV4	OTTHUMG00000131110	ENST00000296604.3:c.812C>T	5.37:g.36257134G>A	ENSP00000296604:p.Ala271Val	172.0	0.0	0		136.0	75.0	0.551471	NM_001161429	B7Z866|E9PGP9|Q96LK2	Missense_Mutation	SNP	ENST00000296604.3	37	CCDS3918.1	167	0.07646520146520147	158	0.32113821138211385	7	0.019337016574585635	0	0.0	2	0.002638522427440633	G	29.6	5.023090	0.93462	0.265547	4.65E-4	ENSG00000164188	ENST00000296604;ENST00000502994;ENST00000515759	T;T;T	0.59364	1.43;1.4;0.27	5.41	5.41	0.78517	.	0.000000	0.64402	D	0.000002	T	0.00012	0.0000	M	0.68952	2.095	0.18873	P	0.9999869983	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.00621	-1.1640	9	0.87932	D	0	-18.1197	18.337	0.90291	0.0:0.0:1.0:0.0	rs16902872;rs52805488;rs16902872	296;271	E9PGP9;Q86VV4	.;RNB3L_HUMAN	V	271;296;271	ENSP00000296604:A271V;ENSP00000421853:A296V;ENSP00000421149:A271V	ENSP00000296604:A271V	A	-	2	0	RANBP3L	36292891	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	7.191000	0.77763	2.697000	0.92050	0.591000	0.81541	GCT	G|0.906;A|0.094	0.094	strong		0.363	RANBP3L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253773.2	NM_145000	
LAMA5	3911	hgsc.bcm.edu	37	20	60884473	60884473	+	Silent	SNP	C	C	T	rs115306720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:60884473C>T	ENST00000252999.3	-	80	11073	c.11007G>A	c.(11005-11007)gcG>gcA	p.A3669A	LAMA5_ENST00000492698.1_5'Flank	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	3669	Laminin G-like 5. {ECO:0000255|PROSITE- ProRule:PRU00122}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			ACCGGTTCACCGCCAGCCTCC	0.706													C|||	143	0.0285543	0.1044	0.0058	5008	,	,		7633	0.0		0.001	False		,,,				2504	0.0				p.A3669A		Atlas-SNP	.											.	LAMA5	268	.	0			c.G11007A						PASS	.			311,3885		5,301,1792	7.0	9.0	9.0		11007	1.9	0.0	20	dbSNP_132	9	2,8320		0,2,4159	no	coding-synonymous	LAMA5	NM_005560.3		5,303,5951	TT,TC,CC		0.024,7.4118,2.5004		3669/3696	60884473	313,12205	2098	4161	6259	SO:0001819	synonymous_variant	3911	exon80			GTTCACCGCCAGC	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.11007G>A	20.37:g.60884473C>T		28.0	0.0	0		32.0	21.0	0.65625	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			C|0.976;T|0.024	0.024	strong		0.706	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
CFHR2	3080	hgsc.bcm.edu	37	1	196887411	196887411	+	Intron	SNP	T	T	C	rs200907976		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:196887411T>C	ENST00000367421.3	+	2	135				CFHR4_ENST00000251424.4_Missense_Mutation_p.Y291H|CFHR4_ENST00000367418.2_Missense_Mutation_p.Y291H|CFHR4_ENST00000608469.1_Missense_Mutation_p.Y161H|CFHR4_ENST00000367416.2_Missense_Mutation_p.Y537H			P36980	FHR2_HUMAN	complement factor H-related 2							extracellular region (GO:0005576)				large_intestine(2)|ovary(1)|skin(3)	6						TGACATAAAATATTATGCAAA	0.294													T|||	1	0.000199681	0.0	0.0014	5008	,	,		15761	0.0		0.0	False		,,,				2504	0.0				p.Y538H		Atlas-SNP	.											.	CFHR4	141	.	0			c.T1612C						PASS	.	T	HIS/TYR,HIS/TYR,HIS/TYR	6,4396	11.4+/-27.6	1,4,2196	112.0	122.0	119.0		1612,1609,871	-6.5	0.0	1		119	0,8598		0,0,4299	yes	missense,missense,missense	CFHR4	NM_001201550.2,NM_001201551.1,NM_006684.4	83,83,83	1,4,6495	CC,CT,TT		0.0,0.1363,0.0462	benign,benign,benign	538/579,537/578,291/332	196887411	6,12994	2201	4299	6500	SO:0001627	intron_variant	10877	exon10			ATAAAATATTATG	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.59-31174T>C	1.37:g.196887411T>C		354.0	1.0	0.00282486		393.0	216.0	0.549618	NM_001201550	Q14310|Q5T9T1	Missense_Mutation	SNP	ENST00000367421.3	37		.	.	.	.	.	.	.	.	.	.	T	10.95	1.496577	0.26861	0.001363	0.0	ENSG00000134365	ENST00000367416;ENST00000367418;ENST00000251424;ENST00000538553	D;D;D	0.82984	-1.67;-1.67;-1.67	3.24	-6.48	0.01896	Complement control module (1);	.	.	.	.	T	0.60130	0.2245	N	0.08118	0	0.09310	N	1	B;D;P	0.58970	0.069;0.984;0.826	B;P;B	0.46796	0.032;0.527;0.188	T	0.58901	-0.7554	9	0.23302	T	0.38	.	0.0302	0.00005	0.2859:0.209:0.2273:0.2777	.	537;538;291	C9J7J7;Q5DVJ7;Q92496	.;.;FHR4_HUMAN	H	537;291;291;291	ENSP00000356386:Y537H;ENSP00000356388:Y291H;ENSP00000251424:Y291H	ENSP00000251424:Y291H	Y	+	1	0	CFHR4	195154034	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-3.116000	0.00597	-2.574000	0.00466	-0.483000	0.04790	TAT	.	.	weak		0.294	CFHR2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_005666	
ALDH8A1	64577	hgsc.bcm.edu	37	6	135254034	135254034	+	Silent	SNP	G	G	A	rs114000920	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:135254034G>A	ENST00000265605.2	-	5	797	c.729C>T	c.(727-729)agC>agT	p.S243S	ALDH8A1_ENST00000367845.2_Silent_p.S243S|ALDH8A1_ENST00000367847.2_Silent_p.S193S	NM_022568.3	NP_072090.1	Q9H2A2	AL8A1_HUMAN	aldehyde dehydrogenase 8 family, member A1	243					9-cis-retinoic acid biosynthetic process (GO:0042904)|retinal metabolic process (GO:0042574)|retinoic acid metabolic process (GO:0042573)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)	retinal dehydrogenase activity (GO:0001758)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	36	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00401)|GBM - Glioblastoma multiforme(68;0.0058)		AGTGGGGAGCGCTCAGCTGGG	0.647													G|||	58	0.0115815	0.0416	0.0043	5008	,	,		17286	0.0		0.0	False		,,,				2504	0.0				p.S243S		Atlas-SNP	.											.	ALDH8A1	68	.	0			c.C729T						PASS	.	G	,,	126,4280	91.6+/-130.3	2,122,2079	68.0	70.0	69.0		579,729,729	-2.7	1.0	6	dbSNP_132	69	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	ALDH8A1	NM_001193480.1,NM_022568.3,NM_170771.2	,,	2,124,6377	AA,AG,GG		0.0233,2.8597,0.9842	,,	193/438,243/488,243/434	135254034	128,12878	2203	4300	6503	SO:0001819	synonymous_variant	64577	exon5			GGGAGCGCTCAGC	AL021939	CCDS5171.1, CCDS5172.1, CCDS55057.1	6q24.1-q25.1	2008-07-03			ENSG00000118514	ENSG00000118514		"""Aldehyde dehydrogenases"""	15471	protein-coding gene	gene with protein product		606467				11007799	Standard	NM_001193480		Approved	ALDH12	uc003qew.3	Q9H2A2	OTTHUMG00000015623	ENST00000265605.2:c.729C>T	6.37:g.135254034G>A		92.0	0.0	0		79.0	43.0	0.544304	NM_022568	B7Z521|O60793|Q24JS9|Q53GT3|Q5TI80	Silent	SNP	ENST00000265605.2	37	CCDS5171.1																																																																																			G|0.987;A|0.013	0.013	strong		0.647	ALDH8A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042334.2		
BPIFB3	359710	hgsc.bcm.edu	37	20	31644436	31644436	+	Silent	SNP	A	A	C	rs35539872	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31644436A>C	ENST00000375494.3	+	2	213	c.213A>C	c.(211-213)ggA>ggC	p.G71G	AL121756.1_ENST00000579962.1_RNA	NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	71	Leu-rich.				innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										TGGGCTCAGGAGGGCTGCTTG	0.617													A|||	232	0.0463259	0.1679	0.0144	5008	,	,		17539	0.0		0.0	False		,,,				2504	0.0				p.G71G		Atlas-SNP	.											.	.	.	.	0			c.A213C						PASS	.	A		604,3802	265.9+/-266.9	52,500,1651	89.0	90.0	90.0		213	0.8	0.6	20	dbSNP_126	90	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous	BPIFB3	NM_182658.1		52,505,5946	CC,CA,AA		0.0581,13.7086,4.6825		71/477	31644436	609,12397	2203	4300	6503	SO:0001819	synonymous_variant	359710	exon2			CTCAGGAGGGCTG	AF549189	CCDS13212.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186190	ENSG00000186190		"""BPI fold containing"""	16178	protein-coding gene	gene with protein product		615717	"""chromosome 20 open reading frame 185"""	C20orf185		11971875, 21787333	Standard	NM_182658		Approved	dJ726C3.4, LPLUNC3, RYA3	uc002wym.1	P59826	OTTHUMG00000032234	ENST00000375494.3:c.213A>C	20.37:g.31644436A>C		97.0	0.0	0		129.0	64.0	0.496124	NM_182658	Q5TDX7	Silent	SNP	ENST00000375494.3	37	CCDS13212.1																																																																																			A|0.957;C|0.043	0.043	strong		0.617	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658	
MRGPRX3	117195	hgsc.bcm.edu	37	11	18159406	18159406	+	Silent	SNP	C	C	G	rs28628238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:18159406C>G	ENST00000396275.2	+	3	1018	c.657C>G	c.(655-657)ctC>ctG	p.L219L		NM_054031.3	NP_473372.3	Q96LB0	MRGX3_HUMAN	MAS-related GPR, member X3	219						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						TGACCATCCTCCTCACAGTGC	0.542													.|||	273	0.0545128	0.1952	0.0216	5008	,	,		20315	0.0		0.0	False		,,,				2504	0.0				p.L219L		Atlas-SNP	.											.	MRGPRX3	59	.	0			c.C657G						PASS	.	G		816,3584	748.0+/-411.9	83,650,1467	113.0	107.0	109.0		657	1.3	0.3	11	dbSNP_125	109	5,8581	818.5+/-406.9	0,5,4288	no	coding-synonymous	MRGPRX3	NM_054031.3		83,655,5755	GG,GC,CC		0.0582,18.5455,6.3222		219/323	18159406	821,12165	2200	4293	6493	SO:0001819	synonymous_variant	117195	exon3			CATCCTCCTCACA		CCDS7830.1	11p15.1	2013-10-10			ENSG00000179826	ENSG00000179826		"""GPCR / Class A : Orphans"""	17980	protein-coding gene	gene with protein product		607229				11551509	Standard	NM_054031		Approved	MRGX3	uc001mnu.3	Q96LB0	OTTHUMG00000166435	ENST00000396275.2:c.657C>G	11.37:g.18159406C>G		123.0	0.0	0		138.0	137.0	0.992754	NM_054031	B0M0L1|Q8TDE0|Q8TDE1	Silent	SNP	ENST00000396275.2	37	CCDS7830.1																																																																																			C|0.948;G|0.052	0.052	strong		0.542	MRGPRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389767.1	NM_054031	
B4GALT3	8703	hgsc.bcm.edu	37	1	161141862	161141862	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:161141862C>T	ENST00000319769.5	-	8	1148	c.926G>A	c.(925-927)cGt>cAt	p.R309H	PPOX_ENST00000495483.1_Intron|PPOX_ENST00000432542.2_Intron|PPOX_ENST00000535223.1_Intron|B4GALT3_ENST00000367998.1_Missense_Mutation_p.R309H|B4GALT3_ENST00000470882.1_5'UTR	NM_001199873.1|NM_003779.3	NP_001186802.1|NP_003770.1	O60512	B4GT3_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 3	309					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)|N-acetyllactosamine synthase activity (GO:0003945)			cervix(1)|endometrium(5)|large_intestine(6)|lung(6)	18	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		N-Acetyl-D-glucosamine(DB00141)	ATTCTGGGTACGGACCAGGAG	0.502																																					p.R309H		Atlas-SNP	.											.	B4GALT3	39	.	0			c.G926A						PASS	.						73.0	77.0	76.0					1																	161141862		2203	4300	6503	SO:0001583	missense	8703	exon8			TGGGTACGGACCA	BC006099	CCDS1222.1	1q21-q23	2013-02-19			ENSG00000158850	ENSG00000158850		"""Beta 4-glycosyltransferases"""	926	protein-coding gene	gene with protein product		604014				9405390, 9597550	Standard	NM_001199873		Approved	beta4Gal-T3	uc001fys.2	O60512	OTTHUMG00000034348	ENST00000319769.5:c.926G>A	1.37:g.161141862C>T	ENSP00000320965:p.Arg309His	73.0	0.0	0		89.0	43.0	0.483146	NM_003779	D3DVG3|O60910|Q9BPZ4|Q9H8T2	Missense_Mutation	SNP	ENST00000319769.5	37	CCDS1222.1	.	.	.	.	.	.	.	.	.	.	C	12.45	1.940163	0.34283	.	.	ENSG00000158850	ENST00000319769;ENST00000407555;ENST00000367998;ENST00000367997	T;T	0.35421	1.31;1.31	5.28	4.35	0.52113	.	0.213738	0.49305	D	0.000153	T	0.09730	0.0239	N	0.13235	0.315	0.45307	D	0.998302	P	0.38167	0.621	B	0.34722	0.188	T	0.08146	-1.0736	10	0.13470	T	0.59	.	13.4642	0.61243	0.0:0.9213:0.0:0.0787	.	309	O60512	B4GT3_HUMAN	H	309;286;309;309	ENSP00000320965:R309H;ENSP00000356977:R309H	ENSP00000320965:R309H	R	-	2	0	B4GALT3	159408486	0.954000	0.32549	0.999000	0.59377	0.999000	0.98932	2.130000	0.42064	2.746000	0.94184	0.655000	0.94253	CGT	.	.	none		0.502	B4GALT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083054.1	NM_003779	
MYH11	4629	hgsc.bcm.edu	37	16	15841534	15841534	+	Silent	SNP	G	G	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:15841534G>T	ENST00000300036.5	-	19	2413	c.2304C>A	c.(2302-2304)atC>atA	p.I768I	MYH11_ENST00000452625.2_Silent_p.I775I|MYH11_ENST00000396324.3_Silent_p.I775I|MYH11_ENST00000576790.2_Silent_p.I768I	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	768	Actin-binding. {ECO:0000250}.|Myosin motor.				axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						TTCGGAAGAAGATTTTGCTCT	0.512			T	CBFB	AML																																p.I775I		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	MYH11	520	.	0			c.C2325A						PASS	.						97.0	93.0	94.0					16																	15841534		2197	4300	6497	SO:0001819	synonymous_variant	4629	exon20			GAAGAAGATTTTG	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.2304C>A	16.37:g.15841534G>T		110.0	0.0	0		96.0	55.0	0.572917	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Silent	SNP	ENST00000300036.5	37	CCDS10565.1																																																																																			.	.	none		0.512	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
ZNF689	115509	hgsc.bcm.edu	37	16	30616317	30616317	+	Silent	SNP	A	A	G	rs34007971	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:30616317A>G	ENST00000287461.3	-	3	1108	c.771T>C	c.(769-771)ggT>ggC	p.G257G	ZNF689_ENST00000566673.1_5'UTR|RP11-146F11.5_ENST00000563540.1_RNA	NM_138447.1	NP_612456.1	Q96CS4	ZN689_HUMAN	zinc finger protein 689	257					regulation of transcription, DNA-templated (GO:0006355)|skeletal muscle cell differentiation (GO:0035914)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|prostate(1)|urinary_tract(1)	14			Colorectal(24;0.198)			GGGGTTTTTCACCTGTGTGTG	0.602													G|||	360	0.071885	0.2595	0.0187	5008	,	,		16142	0.0		0.003	False		,,,				2504	0.001				p.G257G		Atlas-SNP	.											.	ZNF689	48	.	0			c.T771C						PASS	.	G		1032,3362	725.7+/-409.6	123,786,1288	86.0	80.0	82.0		771	-8.2	0.1	16	dbSNP_126	82	33,8567	817.8+/-406.9	1,31,4268	no	coding-synonymous	ZNF689	NM_138447.1		124,817,5556	GG,GA,AA		0.3837,23.4866,8.1961		257/501	30616317	1065,11929	2197	4300	6497	SO:0001819	synonymous_variant	115509	exon3			TTTTTCACCTGTG	BC014000	CCDS10686.1	16p11.2	2013-01-08			ENSG00000156853	ENSG00000156853		"""Zinc fingers, C2H2-type"", ""-"""	25173	protein-coding gene	gene with protein product							Standard	NM_138447		Approved	FLJ90415	uc031qvq.1	Q96CS4	OTTHUMG00000132415	ENST00000287461.3:c.771T>C	16.37:g.30616317A>G		62.0	0.0	0		90.0	47.0	0.522222	NM_138447	Q658J5	Silent	SNP	ENST00000287461.3	37	CCDS10686.1																																																																																			A|0.917;G|0.083	0.083	strong		0.602	ZNF689-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255552.1	NM_138447	
KIAA1211L	343990	hgsc.bcm.edu	37	2	99412654	99412654	+	Missense_Mutation	SNP	C	C	T	rs73962467	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:99412654C>T	ENST00000397899.2	-	9	3009	c.2678G>A	c.(2677-2679)cGg>cAg	p.R893Q		NM_207362.2	NP_997245.2	Q6NV74	K121L_HUMAN	KIAA1211-like	893																	CCCCTGCTTCCGGTCCACAGC	0.507													C|||	33	0.00658946	0.0219	0.0058	5008	,	,		19267	0.0		0.0	False		,,,				2504	0.0				p.R893Q		Atlas-SNP	.											.	.	.	.	0			c.G2678A						PASS	.	C	GLN/ARG	69,3687		3,63,1812	145.0	141.0	143.0		2678	0.3	0.2	2	dbSNP_130	143	1,8221		0,1,4110	yes	missense	C2orf55	NM_207362.2	43	3,64,5922	TT,TC,CC		0.0122,1.8371,0.5844	benign	893/963	99412654	70,11908	1878	4111	5989	SO:0001583	missense	343990	exon9			TGCTTCCGGTCCA	BC068277	CCDS42720.1	2q11.2	2012-08-03	2012-08-03	2012-08-03	ENSG00000196872	ENSG00000196872			33454	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 55"""	C2orf55			Standard	NM_207362		Approved	MGC42367	uc002szf.1	Q6NV74	OTTHUMG00000153171	ENST00000397899.2:c.2678G>A	2.37:g.99412654C>T	ENSP00000380996:p.Arg893Gln	119.0	0.0	0		112.0	54.0	0.482143	NM_207362		Missense_Mutation	SNP	ENST00000397899.2	37	CCDS42720.1	19	0.0086996336996337	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	C	5.887	0.347744	0.11126	0.018371	1.22E-4	ENSG00000196872	ENST00000397899	T	0.39592	1.07	5.17	0.328	0.15918	.	1.201180	0.05934	N	0.635672	T	0.06188	0.0160	N	0.11427	0.14	0.09310	N	1	B	0.19706	0.038	B	0.15870	0.014	T	0.14755	-1.0461	10	0.02654	T	1	-0.9202	3.636	0.08148	0.0:0.3473:0.1965:0.4562	.	893	Q6NV74	CB055_HUMAN	Q	893	ENSP00000380996:R893Q	ENSP00000380996:R893Q	R	-	2	0	C2orf55	98779086	0.996000	0.38824	0.172000	0.22920	0.097000	0.18754	0.215000	0.17562	0.182000	0.20032	0.563000	0.77884	CGG	C|0.991;T|0.009	0.009	strong		0.507	KIAA1211L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329933.1	NM_207362	
PIK3AP1	118788	hgsc.bcm.edu	37	10	98469734	98469734	+	Missense_Mutation	SNP	G	G	A	rs73334383	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:98469734G>A	ENST00000339364.5	-	2	139	c.20C>T	c.(19-21)cCc>cTc	p.P7L		NM_152309.2	NP_689522.2	Q6ZUJ8	BCAP_HUMAN	phosphoinositide-3-kinase adaptor protein 1	7					negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of inflammatory response (GO:0050727)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(27)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	52		Colorectal(252;0.0442)		Epithelial(162;6.29e-08)|all cancers(201;3.18e-06)		GCATCCTCTGGGCACCCCTGG	0.597													G|||	61	0.0121805	0.0416	0.0086	5008	,	,		17446	0.0		0.0	False		,,,				2504	0.0				p.P7L		Atlas-SNP	.											.	PIK3AP1	111	.	0			c.C20T						PASS	.	G	LEU/PRO	128,4168		2,124,2022	52.0	43.0	46.0		20	-9.5	0.0	10	dbSNP_130	46	2,8428		0,2,4213	yes	missense	PIK3AP1	NM_152309.2	98	2,126,6235	AA,AG,GG		0.0237,2.9795,1.0215	benign	7/806	98469734	130,12596	2148	4215	6363	SO:0001583	missense	118788	exon2			CCTCTGGGCACCC	AK092883	CCDS31259.1	10q24.2	2008-10-23			ENSG00000155629	ENSG00000155629			30034	protein-coding gene	gene with protein product		607942				1251844, 11163197	Standard	NM_152309		Approved	BCAP, FLJ35564	uc001kmq.3	Q6ZUJ8	OTTHUMG00000018838	ENST00000339364.5:c.20C>T	10.37:g.98469734G>A	ENSP00000339826:p.Pro7Leu	94.0	0.0	0		91.0	40.0	0.43956	NM_152309	Q5TB56|Q5VXJ9|Q8N6J6|Q8NAC8	Missense_Mutation	SNP	ENST00000339364.5	37	CCDS31259.1	26	0.011904761904761904	21	0.042682926829268296	5	0.013812154696132596	0	0.0	0	0.0	G	2.065	-0.414443	0.04766	0.029795	2.37E-4	ENSG00000155629	ENST00000339364	T	0.09255	3.0	4.73	-9.46	0.00597	.	2.649450	0.01208	N	0.007761	T	0.00906	0.0030	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.26467	-1.0102	10	0.22109	T	0.4	4.4446	5.2642	0.15589	0.1057:0.174:0.5472:0.173	.	7	Q6ZUJ8	BCAP_HUMAN	L	7	ENSP00000339826:P7L	ENSP00000339826:P7L	P	-	2	0	PIK3AP1	98459724	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.446000	0.06837	-2.205000	0.00742	-0.345000	0.07892	CCC	G|0.987;A|0.013	0.013	strong		0.597	PIK3AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049619.2	NM_152309	
AIFM3	150209	hgsc.bcm.edu	37	22	21333605	21333605	+	Missense_Mutation	SNP	G	G	C	rs61356271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:21333605G>C	ENST00000399167.2	+	17	1763	c.1523G>C	c.(1522-1524)aGc>aCc	p.S508T	AIFM3_ENST00000440238.2_Missense_Mutation_p.S508T|AIFM3_ENST00000465606.1_3'UTR|LZTR1_ENST00000215739.8_5'Flank|XXbac-B135H6.18_ENST00000610278.1_lincRNA|AIFM3_ENST00000399163.2_Missense_Mutation_p.S508T|AIFM3_ENST00000335375.5_Missense_Mutation_p.S496T|AIFM3_ENST00000333607.6_Missense_Mutation_p.S508T|AIFM3_ENST00000405089.1_Missense_Mutation_p.S514T	NM_144704.2	NP_653305.1	Q96NN9	AIFM3_HUMAN	apoptosis-inducing factor, mitochondrion-associated, 3	508			S -> T (in dbSNP:rs61356271).		cell redox homeostasis (GO:0045454)|execution phase of apoptosis (GO:0097194)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	21	all_cancers(11;3.71e-26)|all_epithelial(7;1.59e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0367)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)			GCGGAGATGAGCACTGTGCCC	0.672													g|||	270	0.0539137	0.1936	0.0202	5008	,	,		12709	0.0		0.0	False		,,,				2504	0.0				p.S514T		Atlas-SNP	.											.	AIFM3	49	.	0			c.G1541C						PASS	.	C	THR/SER,THR/SER,THR/SER	570,3784		38,494,1645	32.0	25.0	27.0		1523,1541,1523	0.2	0.8	22	dbSNP_129	27	8,8502		0,8,4247	yes	missense,missense,missense	AIFM3	NM_001018060.2,NM_001146288.1,NM_144704.2	58,58,58	38,502,5892	CC,CG,GG		0.094,13.0914,4.4932	,,	508/599,514/605,508/606	21333605	578,12286	2177	4255	6432	SO:0001583	missense	150209	exon17			AGATGAGCACTGT	AK094844	CCDS13786.1, CCDS33605.1, CCDS54503.1	22q11.21	2007-05-03			ENSG00000183773	ENSG00000183773			26398	protein-coding gene	gene with protein product						15764604	Standard	NM_144704		Approved	AIFL, FLJ30473		Q96NN9	OTTHUMG00000150804	ENST00000399167.2:c.1523G>C	22.37:g.21333605G>C	ENSP00000382120:p.Ser508Thr	133.0	0.0	0		183.0	98.0	0.535519	NM_001146288	B7WP37|D3DX37|D3DX38|Q6ZT44|Q8N1V3|Q8N5E0	Missense_Mutation	SNP	ENST00000399167.2	37	CCDS13786.1	83	0.038003663003663	75	0.1524390243902439	8	0.022099447513812154	0	0.0	0	0.0	g	5.235	0.228779	0.09916	0.130914	9.4E-4	ENSG00000183773	ENST00000399167;ENST00000399163;ENST00000405089;ENST00000335375;ENST00000440238;ENST00000333607	T;T;T;T;T;T	0.42513	0.97;0.97;0.97;0.97;0.97;0.97	4.65	0.178	0.15058	FAD/NAD-linked reductase, dimerisation (1);	0.334108	0.35772	N	0.003000	T	0.00109	0.0003	N	0.16266	0.395	0.54753	P	1.2000000000012001E-5	B;B;B;B	0.22983	0.078;0.05;0.05;0.029	B;B;B;B	0.18561	0.022;0.022;0.022;0.01	T	0.24333	-1.0163	9	0.10636	T	0.68	-15.7117	5.9493	0.19237	0.3378:0.1331:0.5291:0.0	rs61356271	496;514;508;508	B7Z9S7;Q96NN9-2;Q96NN9-3;Q96NN9	.;.;.;AIFM3_HUMAN	T	508;508;514;496;508;508	ENSP00000382120:S508T;ENSP00000382116:S508T;ENSP00000385800:S514T;ENSP00000335369:S496T;ENSP00000390798:S508T;ENSP00000327671:S508T	ENSP00000327671:S508T	S	+	2	0	AIFM3	19663605	0.785000	0.28726	0.846000	0.33378	0.236000	0.25371	0.863000	0.27913	-0.250000	0.09555	-2.308000	0.00257	AGC	G|0.946;C|0.054	0.054	strong		0.672	AIFM3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320150.1	NM_144704	
AHNAK2	113146	hgsc.bcm.edu	37	14	105414559	105414559	+	Missense_Mutation	SNP	T	T	C	rs11845746	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105414559T>C	ENST00000333244.5	-	7	7348	c.7229A>G	c.(7228-7230)aAg>aGg	p.K2410R	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2410			K -> R (in dbSNP:rs11845746).			costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TTTGGGCATCTTGAAACTGGG	0.627													.|||	283	0.0565096	0.2073	0.0115	5008	,	,		17440	0.0		0.001	False		,,,				2504	0.0				p.K2410R		Atlas-SNP	.											.	AHNAK2	719	.	0			c.A7229G						PASS	.	T	ARG/LYS	591,3093		71,449,1322	130.0	145.0	140.0		7229	2.9	0.5	14	dbSNP_120	140	5,8187		0,5,4091	no	missense	AHNAK2	NM_138420.2	26	71,454,5413	CC,CT,TT		0.061,16.0423,5.0185	probably-damaging	2410/5796	105414559	596,11280	1842	4096	5938	SO:0001583	missense	113146	exon7			GGCATCTTGAAAC	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.7229A>G	14.37:g.105414559T>C	ENSP00000353114:p.Lys2410Arg	208.0	0.0	0		240.0	236.0	0.983333	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	86	0.039377289377289376	82	0.16666666666666666	4	0.011049723756906077	0	0.0	0	0.0	-	12.77	2.037786	0.35989	0.160423	6.1E-4	ENSG00000185567	ENST00000333244	T	0.01265	5.08	4.08	2.93	0.34026	.	.	.	.	.	T	0.00039	0.0001	M	0.90759	3.145	0.49915	P	1.6599999999999948E-4	D	0.69078	0.997	D	0.77004	0.989	T	0.11767	-1.0574	8	0.39692	T	0.17	.	7.5349	0.27704	0.0:0.181:0.0:0.819	rs11845746;rs34729166;rs52811002;rs11845746	2410	Q8IVF2	AHNK2_HUMAN	R	2410	ENSP00000353114:K2410R	ENSP00000353114:K2410R	K	-	2	0	AHNAK2	104485604	0.002000	0.14202	0.526000	0.27913	0.064000	0.16182	0.833000	0.27504	0.468000	0.27243	0.397000	0.26171	AAG	T|0.967;C|0.033	0.033	strong		0.627	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
DMRT2	10655	hgsc.bcm.edu	37	9	1056517	1056517	+	Silent	SNP	C	C	G	rs16928356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:1056517C>G	ENST00000358146.2	+	3	930	c.930C>G	c.(928-930)acC>acG	p.T310T	DMRT2_ENST00000382255.3_3'UTR|DMRT2_ENST00000302441.6_Silent_p.T310T|DMRT2_ENST00000259622.6_3'UTR|DMRT2_ENST00000382251.3_Silent_p.T310T			Q9Y5R5	DMRT2_HUMAN	doublesex and mab-3 related transcription factor 2	310					embryonic skeletal system development (GO:0048706)|positive regulation of myotome development (GO:2000287)|regulation of somitogenesis (GO:0014807)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|lung(1)|prostate(2)	4		all_lung(10;1.49e-09)|Lung NSC(10;1.86e-09)		Lung(218;0.0195)|GBM - Glioblastoma multiforme(50;0.0388)		TTGATTTAACCATGCAGTATT	0.438													C|||	263	0.052516	0.1876	0.0173	5008	,	,		20652	0.0		0.003	False		,,,				2504	0.0				p.T310T		Atlas-SNP	.											.	DMRT2	70	.	0			c.C930G						PASS	.	C	,,	699,3707	291.5+/-281.6	55,589,1559	85.0	88.0	87.0		,,930	3.7	1.0	9	dbSNP_123	87	3,8597	1.2+/-3.3	0,3,4297	no	utr-3,utr-3,coding-synonymous	DMRT2	NM_001130865.2,NM_006557.6,NM_181872.4	,,	55,592,5856	GG,GC,CC		0.0349,15.8647,5.3975	,,	,,310/562	1056517	702,12304	2203	4300	6503	SO:0001819	synonymous_variant	10655	exon4			TTTAACCATGCAG	AF130729	CCDS6444.1, CCDS6445.1	9p24.3	2008-07-21			ENSG00000173253	ENSG00000173253			2935	protein-coding gene	gene with protein product	"""terra-like protein"""	604935				10332030	Standard	NM_181872		Approved		uc003zha.3	Q9Y5R5	OTTHUMG00000019437	ENST00000358146.2:c.930C>G	9.37:g.1056517C>G		160.0	0.0	0		138.0	137.0	0.992754	NM_181872	B1ANC0|B9EGJ1|Q9NPG6|Q9NQR6	Silent	SNP	ENST00000358146.2	37	CCDS6444.1																																																																																			C|0.951;G|0.049	0.049	strong		0.438	DMRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051492.1	NM_006557	
ZNF782	158431	hgsc.bcm.edu	37	9	99581440	99581440	+	Missense_Mutation	SNP	T	T	C	rs35403084	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:99581440T>C	ENST00000481138.1	-	6	1526	c.865A>G	c.(865-867)Aca>Gca	p.T289A	ZNF782_ENST00000535338.1_Missense_Mutation_p.T157A|ZNF782_ENST00000466833.1_5'Flank	NM_001001662.1	NP_001001662.1	Q6ZMW2	ZN782_HUMAN	zinc finger protein 782	289			T -> A (in dbSNP:rs35403084).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(2)|kidney(2)|large_intestine(12)|lung(8)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)	33		Acute lymphoblastic leukemia(62;0.0527)				TTCCCTCCTGTGAGAGTTTTG	0.363													T|||	174	0.0347444	0.1278	0.0072	5008	,	,		19195	0.0		0.0	False		,,,				2504	0.0				p.T289A		Atlas-SNP	.											.	ZNF782	64	.	0			c.A865G						PASS	.	T	ALA/THR	440,3966	207.8+/-229.1	21,398,1784	84.0	88.0	86.0		865	0.7	0.0	9	dbSNP_126	86	2,8598	2.2+/-6.3	0,2,4298	yes	missense	ZNF782	NM_001001662.1	58	21,400,6082	CC,CT,TT		0.0233,9.9864,3.3984	benign	289/700	99581440	442,12564	2203	4300	6503	SO:0001583	missense	158431	exon6			CTCCTGTGAGAGT	AK131468	CCDS35075.1	9q22.33	2013-01-08			ENSG00000196597	ENSG00000196597		"""Zinc fingers, C2H2-type"", ""-"""	33110	protein-coding gene	gene with protein product							Standard	NM_001001662		Approved	FLJ16636	uc004awp.1	Q6ZMW2	OTTHUMG00000020310	ENST00000481138.1:c.865A>G	9.37:g.99581440T>C	ENSP00000419397:p.Thr289Ala	81.0	0.0	0		92.0	57.0	0.619565	NM_001001662	B2RNR0	Missense_Mutation	SNP	ENST00000481138.1	37	CCDS35075.1	55|55	0.025183150183150184|0.025183150183150184	52|52	0.10569105691056911|0.10569105691056911	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	T|T	11.19|11.19	1.564629|1.564629	0.27915|0.27915	0.099864|0.099864	2.33E-4|2.33E-4	ENSG00000196597|ENSG00000196597	ENST00000289032|ENST00000481138;ENST00000535338	.|T;T	.|0.05996	.|3.5;3.36	3.29|3.29	0.74|0.74	0.18330|0.18330	.|Zinc finger, C2H2 (1);	.|1.047330	.|0.07644	.|N	.|0.930840	T|T	0.00144|0.00144	0.0004|0.0004	L|L	0.45051|0.45051	1.395|1.395	0.20821|0.20821	N|N	0.999841|0.999841	.|P	.|0.37525	.|0.598	.|B	.|0.32211	.|0.142	T|T	0.44757|0.44757	-0.9307|-0.9307	5|10	.|0.42905	.|T	.|0.14	.|.	8.5445|8.5445	0.33413|0.33413	0.0:0.0:0.3768:0.6232|0.0:0.0:0.3768:0.6232	rs35403084|rs35403084	.|289	.|Q6ZMW2	.|ZN782_HUMAN	R|A	277|289;157	.|ENSP00000419397:T289A;ENSP00000440624:T157A	.|ENSP00000419397:T289A	H|T	-|-	2|1	0|0	ZNF782|ZNF782	98621261|98621261	0.044000|0.044000	0.20184|0.20184	0.000000|0.000000	0.03702|0.03702	0.137000|0.137000	0.21094|0.21094	1.139000|1.139000	0.31504|0.31504	0.142000|0.142000	0.18901|0.18901	0.524000|0.524000	0.50904|0.50904	CAC|ACA	T|0.971;C|0.029	0.029	strong		0.363	ZNF782-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356810.1	NM_001001662	
DNAH5	1767	hgsc.bcm.edu	37	5	13701422	13701422	+	Missense_Mutation	SNP	G	G	T	rs113425437	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:13701422G>T	ENST00000265104.4	-	77	13566	c.13462C>A	c.(13462-13464)Ccc>Acc	p.P4488T		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4488					cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					AATCCCTGGGGGTTAAAAAAA	0.418									Kartagener syndrome				G|||	207	0.0413339	0.149	0.0144	5008	,	,		14515	0.0		0.0	False		,,,				2504	0.0				p.P4488T		Atlas-SNP	.											.	DNAH5	868	.	0			c.C13462A						PASS	.	G	THR/PRO	586,3820	256.1+/-261.0	32,522,1649	77.0	84.0	82.0		13462	4.9	1.0	5	dbSNP_132	82	1,8599	1.2+/-3.3	0,1,4299	yes	missense	DNAH5	NM_001369.2	38	32,523,5948	TT,TG,GG		0.0116,13.3,4.5133	probably-damaging	4488/4625	13701422	587,12419	2203	4300	6503	SO:0001583	missense	1767	exon77	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	CCTGGGGGTTAAA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.13462C>A	5.37:g.13701422G>T	ENSP00000265104:p.Pro4488Thr	80.0	0.0	0		73.0	41.0	0.561644	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	58	0.026556776556776556	53	0.10772357723577236	5	0.013812154696132596	0	0.0	0	0.0	G	24.4	4.523833	0.85600	0.133	1.16E-4	ENSG00000039139	ENST00000265104	T	0.16196	2.36	5.78	4.91	0.64330	Dynein heavy chain (1);	0.000000	0.85682	D	0.000000	T	0.00440	0.0014	M	0.67953	2.075	0.80722	D	1	D	0.55385	0.971	D	0.73708	0.981	T	0.00011	-1.2433	10	0.87932	D	0	.	14.6237	0.68605	0.0697:0.0:0.9303:0.0	.	4488	Q8TE73	DYH5_HUMAN	T	4488	ENSP00000265104:P4488T	ENSP00000265104:P4488T	P	-	1	0	DNAH5	13754422	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	7.987000	0.88182	1.454000	0.47793	0.591000	0.81541	CCC	G|0.961;T|0.039	0.039	strong		0.418	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
OR8K1	390157	hgsc.bcm.edu	37	11	56113923	56113923	+	Silent	SNP	C	C	T	rs61745885	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:56113923C>T	ENST00000279783.2	+	1	503	c.409C>T	c.(409-411)Ctg>Ttg	p.L137L		NM_001002907.1	NP_001002907.1	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K, member 1	137						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.L137M(1)		large_intestine(8)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Esophageal squamous(21;0.00448)					TAAACCTCTTCTGTACGTGAT	0.403										HNSCC(65;0.19)			C|||	35	0.00698882	0.0242	0.0029	5008	,	,		21543	0.0		0.001	False		,,,				2504	0.0				p.L137L		Atlas-SNP	.											OR8K1,shoulder,malignant_melanoma,0,1	OR8K1	93	1	1	Substitution - Missense(1)	skin(1)	c.C409T						PASS	.	C		108,4294	83.4+/-121.9	2,104,2095	213.0	211.0	211.0		409	3.1	0.9	11	dbSNP_129	211	3,8589	2.2+/-6.3	0,3,4293	no	coding-synonymous	OR8K1	NM_001002907.1		2,107,6388	TT,TC,CC		0.0349,2.4534,0.8542		137/320	56113923	111,12883	2201	4296	6497	SO:0001819	synonymous_variant	390157	exon1			CCTCTTCTGTACG	AB065835	CCDS31528.1	11q11	2012-08-09			ENSG00000150261	ENSG00000150261		"""GPCR / Class A : Olfactory receptors"""	14831	protein-coding gene	gene with protein product							Standard	NM_001002907		Approved		uc010rjg.2	Q8NGG5	OTTHUMG00000166858	ENST00000279783.2:c.409C>T	11.37:g.56113923C>T		152.0	0.0	0		148.0	71.0	0.47973	NM_001002907	B9EJB1|Q6IFC3|Q96RC1	Silent	SNP	ENST00000279783.2	37	CCDS31528.1																																																																																			C|0.993;T|0.007	0.007	strong		0.403	OR8K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391605.1	NM_001002907	
MCM2	4171	hgsc.bcm.edu	37	3	127340583	127340583	+	Silent	SNP	C	C	T	rs6794323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:127340583C>T	ENST00000265056.7	+	16	2926	c.2682C>T	c.(2680-2682)gaC>gaT	p.D894D	MCM2_ENST00000468414.1_3'UTR	NM_004526.2	NP_004517.2	P49736	MCM2_HUMAN	minichromosome maintenance complex component 2	894					cell cycle (GO:0007049)|cellular response to interleukin-4 (GO:0071353)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA unwinding involved in DNA replication (GO:0006268)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|nucleosome assembly (GO:0006334)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|MCM complex (GO:0042555)|microtubule cytoskeleton (GO:0015630)|nuclear origin of replication recognition complex (GO:0005664)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA replication origin binding (GO:0003688)|metal ion binding (GO:0046872)			ovary(3)|skin(2)|stomach(1)	6						TCAGCCACGACCTGAAAAGGA	0.498													C|||	319	0.0636981	0.2269	0.0231	5008	,	,		22127	0.0		0.003	False		,,,				2504	0.0				p.D894D		Atlas-SNP	.											.	MCM2	79	.	0			c.C2682T						PASS	.	C		764,3642	311.1+/-291.9	56,652,1495	99.0	93.0	95.0		2682	4.5	1.0	3	dbSNP_116	95	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	MCM2	NM_004526.2		56,660,5787	TT,TC,CC		0.093,17.34,5.9357		894/905	127340583	772,12234	2203	4300	6503	SO:0001819	synonymous_variant	4171	exon16			CCACGACCTGAAA	X67334	CCDS3043.1	3q21	2007-04-04	2007-04-04		ENSG00000073111	ENSG00000073111			6944	protein-coding gene	gene with protein product	"""mitotin"""	116945	"""minichromosome maintenance deficient (S. cerevisiae) 2 (mitotin)"", ""MCM2 minichromosome maintenance deficient 2, mitotin (S. cerevisiae)"""	CCNL1, CDCL1		1710453, 8258304	Standard	NM_004526		Approved	D3S3194, KIAA0030, BM28, cdc19	uc003ejp.4	P49736	OTTHUMG00000159637	ENST00000265056.7:c.2682C>T	3.37:g.127340583C>T		81.0	0.0	0		90.0	41.0	0.455556	NM_004526	Q14577|Q15023|Q8N2V1|Q969W7|Q96AE1|Q9BRM7	Silent	SNP	ENST00000265056.7	37	CCDS3043.1	133	0.060897435897435896	124	0.25203252032520324	9	0.024861878453038673	0	0.0	0	0.0	C	2.284	-0.364112	0.05103	0.1734	9.3E-4	ENSG00000073111	ENST00000491422	.	.	.	5.38	4.5	0.54988	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.23013	-1.0200	3	.	.	.	-47.6264	6.5614	0.22489	0.0:0.6888:0.0:0.3112	rs6794323;rs17538760;rs56589702;rs6794323	.	.	.	I	826	.	.	T	+	2	0	MCM2	128823273	1.000000	0.71417	0.993000	0.49108	0.308000	0.27856	1.539000	0.36104	1.263000	0.44181	0.313000	0.20887	ACC	C|0.930;T|0.070	0.070	strong		0.498	MCM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356612.1		
ADAMDEC1	27299	hgsc.bcm.edu	37	8	24250809	24250809	+	Missense_Mutation	SNP	T	T	C	rs77012108	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24250809T>C	ENST00000256412.4	+	3	462	c.242T>C	c.(241-243)aTc>aCc	p.I81T	RP11-624C23.1_ENST00000519689.1_RNA|ADAMDEC1_ENST00000522298.1_Missense_Mutation_p.I2T|RP11-624C23.1_ENST00000523578.1_RNA|ADAMDEC1_ENST00000538205.1_Missense_Mutation_p.I2T	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	81					immune response (GO:0006955)|negative regulation of cell adhesion (GO:0007162)	extracellular region (GO:0005576)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|large_intestine(4)|skin(2)|stomach(1)	9		Prostate(55;0.0181)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)		TATCAGATGATCTTAAATGGA	0.303													t|||	120	0.0239617	0.087	0.0072	5008	,	,		16054	0.0		0.0	False		,,,				2504	0.0				p.I81T	Ovarian(147;687 1849 3699 25981 31337)	Atlas-SNP	.											ADAMDEC1,arm,malignant_melanoma,-1,1	ADAMDEC1	69	1	0			c.T242C						PASS	.	C	THR/ILE,THR/ILE,THR/ILE	356,4050	176.6+/-205.7	19,318,1866	64.0	68.0	66.0		5,5,242	-10.9	0.0	8	dbSNP_131	66	2,8594	2.2+/-6.3	0,2,4296	yes	missense,missense,missense	ADAMDEC1	NM_001145271.1,NM_001145272.1,NM_014479.3	89,89,89	19,320,6162	CC,CT,TT		0.0233,8.0799,2.7534	benign,benign,benign	2/392,2/392,81/471	24250809	358,12644	2203	4298	6501	SO:0001583	missense	27299	exon3			AGATGATCTTAAA	Y13323	CCDS6044.1, CCDS55212.1	8p12	2008-08-07			ENSG00000134028	ENSG00000134028			16299	protein-coding gene	gene with protein product		606393				9271581, 12037602	Standard	NM_001145271		Approved	M12.219	uc003xdz.2	O15204	OTTHUMG00000097858	ENST00000256412.4:c.242T>C	8.37:g.24250809T>C	ENSP00000256412:p.Ile81Thr	124.0	0.0	0		127.0	68.0	0.535433	NM_014479	B7ZAK5	Missense_Mutation	SNP	ENST00000256412.4	37	CCDS6044.1	44	0.020146520146520148	41	0.08333333333333333	3	0.008287292817679558	0	0.0	0	0.0	t	0.013	-1.643647	0.00792	0.080799	2.33E-4	ENSG00000134028	ENST00000256412;ENST00000538205;ENST00000522298	T;T;T	0.04758	3.56;4.16;4.16	5.47	-10.9	0.00192	Peptidase M12B, propeptide (1);	1.393200	0.04190	N	0.328203	T	0.00144	0.0004	N	0.10837	0.055	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.41088	-0.9528	10	0.09843	T	0.71	0.1711	6.3932	0.21599	0.0997:0.5309:0.2221:0.1472	.	81	O15204	ADEC1_HUMAN	T	81;2;2	ENSP00000256412:I81T;ENSP00000442592:I2T;ENSP00000428993:I2T	ENSP00000256412:I81T	I	+	2	0	ADAMDEC1	24306754	0.000000	0.05858	0.001000	0.08648	0.254000	0.26022	-2.948000	0.00679	-1.756000	0.01318	-0.359000	0.07587	ATC	T|0.973;C|0.027	0.027	strong		0.303	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479	
VWF	7450	hgsc.bcm.edu	37	12	6103281	6103281	+	Silent	SNP	A	A	T	rs11537642	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:6103281A>T	ENST00000261405.5	-	37	6599	c.6345T>A	c.(6343-6345)acT>acA	p.T2115T		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	2115	VWFD 4. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	GCCGCTGCACAGTCCATTCCT	0.557													A|||	277	0.0553115	0.1982	0.0202	5008	,	,		20224	0.0		0.001	False		,,,				2504	0.0				p.T2115T		Atlas-SNP	.											.	VWF	338	.	0			c.T6345A						PASS	.	A		660,3746	280.2+/-275.2	55,550,1598	94.0	79.0	84.0		6345	-10.3	0.0	12	dbSNP_120	84	4,8596	2.2+/-6.3	0,4,4296	no	coding-synonymous	VWF	NM_000552.3		55,554,5894	TT,TA,AA		0.0465,14.9796,5.1053		2115/2814	6103281	664,12342	2203	4300	6503	SO:0001819	synonymous_variant	7450	exon37			CTGCACAGTCCAT		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.6345T>A	12.37:g.6103281A>T		71.0	0.0	0		88.0	36.0	0.409091	NM_000552	Q8TCE8|Q99806	Silent	SNP	ENST00000261405.5	37	CCDS8539.1																																																																																			A|0.955;T|0.045	0.045	strong		0.557	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
EEF2	1938	hgsc.bcm.edu	37	19	3980852	3980852	+	Silent	SNP	G	G	A	rs140573073	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3980852G>A	ENST00000309311.6	-	8	1225	c.1137C>T	c.(1135-1137)gaC>gaT	p.D379D	SNORD37_ENST00000384048.1_RNA|EEF2_ENST00000600720.1_5'Flank	NM_001961.3	NP_001952.1	P13639	EF2_HUMAN	eukaryotic translation elongation factor 2	379					cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|hematopoietic progenitor cell differentiation (GO:0002244)|positive regulation of gene expression (GO:0010628)|positive regulation of translation (GO:0045727)|translation (GO:0006412)|translational elongation (GO:0006414)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation activator activity (GO:0008494)|translation elongation factor activity (GO:0003746)			endometrium(4)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|GBM - Glioblastoma multiforme(1328;0.0223)|STAD - Stomach adenocarcinoma(1328;0.18)		TGGCAGCCTCGTCGTCCGGGG	0.652													G|||	14	0.00279553	0.0106	0.0	5008	,	,		15721	0.0		0.0	False		,,,				2504	0.0				p.D379D	Colon(165;1804 1908 4071 6587 18799)	Atlas-SNP	.											.	EEF2	57	.	0			c.C1137T						PASS	.	G		39,4347		0,39,2154	13.0	11.0	12.0		1137	-7.7	0.6	19	dbSNP_134	12	0,8556		0,0,4278	no	coding-synonymous	EEF2	NM_001961.3		0,39,6432	AA,AG,GG		0.0,0.8892,0.3013		379/859	3980852	39,12903	2193	4278	6471	SO:0001819	synonymous_variant	1938	exon8			AGCCTCGTCGTCC	Z11692	CCDS12117.1	19p13.3	2012-09-20			ENSG00000167658	ENSG00000167658			3214	protein-coding gene	gene with protein product	"""polypeptidyl-tRNA translocase"""	130610		EF2		2610926, 6427766	Standard	NM_001961		Approved	EEF-2	uc002lze.3	P13639		ENST00000309311.6:c.1137C>T	19.37:g.3980852G>A		32.0	0.0	0		53.0	27.0	0.509434	NM_001961	B2RMP5|D6W618|Q58J86	Silent	SNP	ENST00000309311.6	37	CCDS12117.1																																																																																			G|0.997;A|0.003	0.003	strong		0.652	EEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457615.2	NM_001961	
CCDC130	81576	hgsc.bcm.edu	37	19	13875453	13875453	+	IGR	SNP	C	C	T	rs141796284	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:13875453C>T	ENST00000586600.1	+	0	1922				MRI1_ENST00000040663.6_Silent_p.D17D|MRI1_ENST00000319545.8_Silent_p.D17D			P13994	CC130_HUMAN	coiled-coil domain containing 130						response to virus (GO:0009615)					endometrium(2)|kidney(1)|large_intestine(3)|ovary(1)|skin(2)|urinary_tract(1)	10			OV - Ovarian serous cystadenocarcinoma(19;6.02e-23)|Epithelial(5;2.58e-18)			AGATCCTAGACCAGCTGCTGC	0.706													C|||	22	0.00439297	0.0159	0.0014	5008	,	,		6970	0.0		0.0	False		,,,				2504	0.0				p.D17D		Atlas-SNP	.											.	MRI1	35	.	0			c.C51T						PASS	.	C	,	91,4295		0,91,2102	24.0	27.0	26.0		51,51	4.1	1.0	19	dbSNP_134	26	1,8565		0,1,4282	no	coding-synonymous,coding-synonymous	MRI1	NM_001031727.2,NM_032285.2	,	0,92,6384	TT,TC,CC		0.0117,2.0748,0.7103	,	17/370,17/323	13875453	92,12860	2193	4283	6476	SO:0001628	intergenic_variant	84245	exon1			CCTAGACCAGCTG	AF250306	CCDS12296.1	19p13.13	2008-02-05				ENSG00000104957			28118	protein-coding gene	gene with protein product						3203696	Standard	NM_030818		Approved	MGC10471	uc002mxc.1	P13994			19.37:g.13875453C>T		107.0	0.0	0		123.0	48.0	0.390244	NM_001031727	Q9BQ72	Silent	SNP	ENST00000586600.1	37	CCDS12296.1																																																																																			C|0.993;T|0.007	0.007	strong		0.706	CCDC130-001	KNOWN	alternative_5_UTR|upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453216.2	NM_030818	
DDX27	55661	hgsc.bcm.edu	37	20	47849904	47849904	+	Missense_Mutation	SNP	C	C	T	rs145681733		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:47849904C>T	ENST00000371764.4	+	10	1195	c.1186C>T	c.(1186-1188)Cgc>Tgc	p.R396C	DDX27_ENST00000484427.1_3'UTR	NM_017895.7	NP_060365.7	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	396	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.					nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	45			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			TTCCCACCACCGCCAGACCAT	0.582																																					p.R396C		Atlas-SNP	.											.	DDX27	74	.	0			c.C1186T						PASS	.	C	CYS/ARG	0,4406		0,0,2203	87.0	69.0	75.0		1186	6.0	1.0	20	dbSNP_134	75	1,8599	1.2+/-3.3	0,1,4299	no	missense	DDX27	NM_017895.7	180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	396/797	47849904	1,13005	2203	4300	6503	SO:0001583	missense	55661	exon10			CACCACCGCCAGA	AL049766	CCDS13416.1	20q13.13	2010-07-06	2003-06-13		ENSG00000124228	ENSG00000124228		"""DEAD-boxes"""	15837	protein-coding gene	gene with protein product			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 27"""				Standard	NM_017895		Approved	dJ686N3.1, DRS1	uc002xuh.3	Q96GQ7	OTTHUMG00000033072	ENST00000371764.4:c.1186C>T	20.37:g.47849904C>T	ENSP00000360828:p.Arg396Cys	85.0	0.0	0		83.0	34.0	0.409639	NM_017895	A0AVB6|B7ZLY1|Q5VXM7|Q8WYG4|Q969N7|Q96F57|Q96L97|Q9BWY9|Q9BXF0|Q9H990|Q9NWU3|Q9P0C2|Q9UGD6	Missense_Mutation	SNP	ENST00000371764.4	37	CCDS13416.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.700821	0.88924	0.0	1.16E-4	ENSG00000124228	ENST00000371764	T	0.49432	0.78	5.97	5.97	0.96955	DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.71929	0.3398	M	0.81614	2.55	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74234	-0.3731	10	0.87932	D	0	-14.1308	17.9218	0.88969	0.0:1.0:0.0:0.0	.	396	Q96GQ7	DDX27_HUMAN	C	396	ENSP00000360828:R396C	ENSP00000360828:R396C	R	+	1	0	DDX27	47283311	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.548000	0.53670	2.837000	0.97791	0.655000	0.94253	CGC	C|1.000;T|0.000	0.000	weak		0.582	DDX27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080485.1		
C7orf71	285941	hgsc.bcm.edu	37	7	26678881	26678881	+	Missense_Mutation	SNP	G	G	A	rs78525926	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:26678881G>A	ENST00000409974.3	+	2	834	c.118G>A	c.(118-120)Ggc>Agc	p.G40S		NM_001145531.1	NP_001139003.1	A4D174	CG071_HUMAN	chromosome 7 open reading frame 71	40																	gagacaaggcggctacctgca	0.537													G|||	197	0.0393371	0.1377	0.013	5008	,	,		16554	0.004		0.002	False		,,,				2504	0.0				p.G40S		Atlas-SNP	.											.	C7orf71	6	.	0			c.G118A						PASS	.	G	SER/GLY	155,1229		13,129,550	62.0	81.0	75.0		118	-0.7	0.0	7	dbSNP_132	75	3,3179		0,3,1588	yes	missense	C7orf71	NM_001145531.1	56	13,132,2138	AA,AG,GG		0.0943,11.1994,3.4604	possibly-damaging	40/170	26678881	158,4408	692	1591	2283	SO:0001583	missense	285941	exon2			CAAGGCGGCTACC		CCDS47565.1	7p15.2	2009-09-11			ENSG00000222004	ENSG00000222004			22364	protein-coding gene	gene with protein product							Standard	NM_001145531		Approved		uc003syb.3	A4D174	OTTHUMG00000152860	ENST00000409974.3:c.118G>A	7.37:g.26678881G>A	ENSP00000386749:p.Gly40Ser	36.0	0.0	0		28.0	28.0	1	NM_001145531		Missense_Mutation	SNP	ENST00000409974.3	37	CCDS47565.1	65	0.02976190476190476	59	0.11991869918699187	4	0.011049723756906077	2	0.0034965034965034965	0	0.0	g	6.292	0.421888	0.11928	0.111994	9.43E-4	ENSG00000222004	ENST00000409974	.	.	.	0.374	-0.714	0.11219	.	.	.	.	.	T	0.00109	0.0003	N	0.08118	0	0.09310	N	1	P	0.39404	0.672	B	0.18871	0.023	T	0.29274	-1.0017	7	0.28530	T	0.3	.	.	.	.	.	40	A4D174	CG071_HUMAN	S	40	.	ENSP00000386749:G40S	G	+	1	0	C7orf71	26645406	0.022000	0.18835	0.013000	0.15412	0.012000	0.07955	-0.172000	0.09868	-0.482000	0.06782	-0.478000	0.04885	GGC	G|0.964;A|0.036	0.036	strong		0.537	C7orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328272.1	NM_001145531	
ATP6AP2	10159	hgsc.bcm.edu	37	X	40464822	40464822	+	Missense_Mutation	SNP	G	G	C	rs35798522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:40464822G>C	ENST00000378438.4	+	9	1026	c.868G>C	c.(868-870)Gca>Cca	p.A290P	ATP6AP2_ENST00000535539.1_Missense_Mutation_p.A258P|ATP6AP2_ENST00000535777.1_Missense_Mutation_p.A212P|ATP6AP2_ENST00000544975.1_Missense_Mutation_p.A214P	NM_005765.2	NP_005756.2	O75787	RENR_HUMAN	ATPase, H+ transporting, lysosomal accessory protein 2	290			A -> P (in dbSNP:rs35798522).		angiotensin maturation (GO:0002003)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|eye pigmentation (GO:0048069)|head morphogenesis (GO:0060323)|positive regulation of transforming growth factor beta1 production (GO:0032914)|positive regulation of Wnt signaling pathway (GO:0030177)|proteolysis (GO:0006508)|regulation of MAPK cascade (GO:0043408)|rostrocaudal neural tube patterning (GO:0021903)	cell body (GO:0044297)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|receptor activity (GO:0004872)			endometrium(1)|large_intestine(1)|lung(2)	4						GAAGAACCCAGCAAGTCCCTA	0.343													G|||	83	0.0219868	0.0613	0.0029	3775	,	,		13663	0.0		0.0	False		,,,				2504	0.0				p.A290P		Atlas-SNP	.											.	ATP6AP2	45	.	0			c.G868C						PASS	.	G	PRO/ALA	239,3596		5,190,39,1437,532	61.0	57.0	58.0		868	-8.4	0.0	X	dbSNP_126	58	0,6726		0,0,0,2427,1872	yes	missense	ATP6AP2	NM_005765.2	27	5,190,39,3864,2404	CC,CG,C,GG,G		0.0,6.2321,2.263	benign	290/351	40464822	239,10322	2203	4299	6502	SO:0001583	missense	10159	exon9			AACCCAGCAAGTC	AF248966	CCDS14252.1	Xp11.4	2014-06-17	2003-08-28	2003-08-29	ENSG00000182220	ENSG00000182220			18305	protein-coding gene	gene with protein product	"""prorenin receptor"", ""renin receptor"""	300556	"""ATPase, H+ transporting, lysosomal interacting protein 2"""	ATP6IP2		9556572, 11590366	Standard	NM_005765		Approved	M8-9, APT6M8-9, ATP6M8-9, PRR, RENR	uc004det.3	O75787	OTTHUMG00000024103	ENST00000378438.4:c.868G>C	X.37:g.40464822G>C	ENSP00000367697:p.Ala290Pro	25.0	0.0	0		34.0	19.0	0.558824	NM_005765	B7Z9I3|Q5QTQ7|Q6T7F5|Q8NBP3|Q8NG15|Q96FV6|Q96LB5|Q9H2P8|Q9UG89	Missense_Mutation	SNP	ENST00000378438.4	37	CCDS14252.1	29|29	0.017480409885473176|0.017480409885473176	19|19	0.04025423728813559|0.04025423728813559	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	14.15|14.15	2.450072|2.450072	0.43531|0.43531	0.062321|0.062321	0.0|0.0	ENSG00000182220|ENSG00000182220	ENST00000535539;ENST00000378438;ENST00000544975;ENST00000535777|ENST00000423649	T;T;T;T|.	0.45276|.	0.9;0.9;0.9;0.9|.	5.65|5.65	-8.41|-8.41	0.00961|0.00961	.|.	1.054090|.	0.07412|.	N|.	0.892481|.	T|T	0.00845|0.00845	0.0028|0.0028	N|N	0.03608|0.03608	-0.345|-0.345	0.80722|0.80722	P|P	0.0|0.0	B;B;B;B|.	0.29531|.	0.0;0.0;0.0;0.247|.	B;B;B;B|.	0.32289|.	0.0;0.002;0.0;0.143|.	T|T	0.15263|0.15263	-1.0443|-1.0443	9|4	0.28530|.	T|.	0.3|.	-34.4303|-34.4303	1.913|1.913	0.03291|0.03291	0.1093:0.2223:0.4974:0.171|0.1093:0.2223:0.4974:0.171	rs35798522|rs35798522	212;258;214;290|.	B7Z1I9;B7Z9I3;B7Z413;O75787|.	.;.;.;RENR_HUMAN|.	P|T	258;290;214;212|230	ENSP00000438415:A258P;ENSP00000367697:A290P;ENSP00000440459:A214P;ENSP00000441536:A212P|.	ENSP00000367697:A290P|.	A|S	+|+	1|2	0|0	ATP6AP2|ATP6AP2	40349766|40349766	0.019000|0.019000	0.18553|0.18553	0.000000|0.000000	0.03702|0.03702	0.689000|0.689000	0.40095|0.40095	1.088000|1.088000	0.30877|0.30877	-3.069000|-3.069000	0.00254|0.00254	0.600000|0.600000	0.82982|0.82982	GCA|AGC	G|0.977;C|0.023	0.023	strong		0.343	ATP6AP2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060679.1	NM_005765	
ORM2	5005	hgsc.bcm.edu	37	9	117094200	117094200	+	Silent	SNP	C	C	T	rs1826232	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117094200C>T	ENST00000431067.2	+	5	567	c.531C>T	c.(529-531)gaC>gaT	p.D177D	ORM2_ENST00000412657.1_3'UTR	NM_000608.2	NP_000599.1	P19652	A1AG2_HUMAN	orosomucoid 2	177					acute-phase response (GO:0006953)|regulation of immune system process (GO:0002682)|transport (GO:0006810)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(1)	7		Myeloproliferative disorder(63;0.163)			Chlorpromazine(DB00477)|Oxycodone(DB00497)|Thalidomide(DB01041)	TGTACACCGACTGGAAAAAGG	0.567													T|||	747	0.149161	0.4894	0.0403	5008	,	,		18828	0.0605		0.002	False		,,,				2504	0.0092				p.D177D	NSCLC(65;867 1308 1814 2391 12508)	Atlas-SNP	.											ORM2,face,carcinoma,-2,1	ORM2	13	1	0			c.C531T						PASS	.	T		1790,2616	641.6+/-397.5	383,1024,796	92.0	92.0	92.0		531	-4.5	0.0	9	dbSNP_92	92	20,8580	818.0+/-406.9	0,20,4280	no	coding-synonymous	ORM2	NM_000608.2		383,1044,5076	TT,TC,CC		0.2326,40.6264,13.9167		177/202	117094200	1810,11196	2203	4300	6503	SO:0001819	synonymous_variant	5005	exon5			CACCGACTGGAAA		CCDS6804.1	9q32	2013-09-19			ENSG00000228278	ENSG00000228278		"""Lipocalins"""	8499	protein-coding gene	gene with protein product	"""alpha-1-acid glycoprotein, type 2"""	138610				4711474, 2970990	Standard	NM_000608		Approved	AGP-B, AGP-B', AGP2		P19652	OTTHUMG00000021014	ENST00000431067.2:c.531C>T	9.37:g.117094200C>T		136.0	0.0	0		160.0	49.0	0.30625	NM_000608	B2R5L2|Q16571|Q5T538|Q6IB74	Silent	SNP	ENST00000431067.2	37	CCDS6804.1																																																																																			C|0.873;T|0.127	0.127	strong		0.567	ORM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055432.1	NM_000608	
COG2	22796	hgsc.bcm.edu	37	1	230796533	230796533	+	Silent	SNP	T	T	G	rs16852160	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:230796533T>G	ENST00000366669.4	+	3	379	c.264T>G	c.(262-264)ctT>ctG	p.L88L	COG2_ENST00000535166.1_5'UTR|COG2_ENST00000534989.1_Silent_p.L29L|COG2_ENST00000366668.3_Silent_p.L88L	NM_001145036.1|NM_007357.2	NP_001138508.1|NP_031383.1	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2	88					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	cytosol (GO:0005829)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|Golgi transport complex (GO:0017119)	protein transporter activity (GO:0008565)			NS(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|urinary_tract(3)	27	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				TCAACCAGCTTTCTGTGCCTT	0.423													T|||	161	0.0321486	0.1127	0.0115	5008	,	,		16141	0.001		0.001	False		,,,				2504	0.002				p.L88L		Atlas-SNP	.											.	COG2	61	.	0			c.T264G						PASS	.	T	,	436,3970	208.8+/-229.8	20,396,1787	221.0	178.0	193.0		264,264	-0.9	1.0	1	dbSNP_123	193	13,8587	9.1+/-34.3	0,13,4287	no	coding-synonymous,coding-synonymous	COG2	NM_001145036.1,NM_007357.2	,	20,409,6074	GG,GT,TT		0.1512,9.8956,3.4523	,	88/738,88/739	230796533	449,12557	2203	4300	6503	SO:0001819	synonymous_variant	22796	exon3			CCAGCTTTCTGTG	Z34975	CCDS1584.1, CCDS44329.1	1q42.2	2008-02-05	2002-05-28	2002-05-31	ENSG00000135775	ENSG00000135775		"""Components of oligomeric golgi complex"""	6546	protein-coding gene	gene with protein product		606974	"""low density lipoprotein receptor defect C complementing"""	LDLC		7962052	Standard	NM_007357		Approved		uc001htw.3	Q14746	OTTHUMG00000037753	ENST00000366669.4:c.264T>G	1.37:g.230796533T>G		232.0	0.0	0		245.0	105.0	0.428571	NM_007357	Q86U99	Silent	SNP	ENST00000366669.4	37	CCDS1584.1																																																																																			T|0.962;G|0.038	0.038	strong		0.423	COG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092087.1	NM_007357	
INHA	3623	hgsc.bcm.edu	37	2	220439826	220439826	+	Missense_Mutation	SNP	G	G	A	rs12720061	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220439826G>A	ENST00000243786.2	+	2	859	c.679G>A	c.(679-681)Ggg>Agg	p.G227R		NM_002191.3	NP_002182.1	P05111	INHA_HUMAN	inhibin, alpha	227			G -> R (in dbSNP:rs12720061).		cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|erythrocyte differentiation (GO:0030218)|hemoglobin biosynthetic process (GO:0042541)|male gonad development (GO:0008584)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell cycle (GO:0045786)|negative regulation of follicle-stimulating hormone secretion (GO:0046882)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of phosphorylation (GO:0042326)|nervous system development (GO:0007399)|ovarian follicle development (GO:0001541)|positive regulation of follicle-stimulating hormone secretion (GO:0046881)|regulation of cell cycle (GO:0051726)|regulation of cell proliferation (GO:0042127)|response to external stimulus (GO:0009605)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|inhibin A complex (GO:0043512)|inhibin-betaglycan-ActRII complex (GO:0034673)|neuronal cell body (GO:0043025)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|hormone activity (GO:0005179)|receptor binding (GO:0005102)			large_intestine(2)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	10		Renal(207;0.0183)		Epithelial(149;4.58e-07)|all cancers(144;4.31e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		ACCCAGTGGAGGGGAGAGAGC	0.687													G|||	165	0.0329473	0.1225	0.0043	5008	,	,		18962	0.0		0.0	False		,,,				2504	0.0				p.G227R		Atlas-SNP	.											.	INHA	30	.	0			c.G679A	GRCh37	CM041026	INHA	M	rs12720061	PASS	.	G	ARG/GLY	400,4006	195.7+/-220.2	17,366,1820	38.0	41.0	40.0		679	5.5	0.9	2	dbSNP_121	40	4,8596	3.7+/-12.6	0,4,4296	yes	missense	INHA	NM_002191.3	125	17,370,6116	AA,AG,GG		0.0465,9.0785,3.1063	benign	227/367	220439826	404,12602	2203	4300	6503	SO:0001583	missense	3623	exon2			AGTGGAGGGGAGA		CCDS2444.1	2q35	2013-09-19			ENSG00000123999	ENSG00000123999			6065	protein-coding gene	gene with protein product		147380				3345731	Standard	NM_002191		Approved		uc002vmk.2	P05111	OTTHUMG00000059237	ENST00000243786.2:c.679G>A	2.37:g.220439826G>A	ENSP00000243786:p.Gly227Arg	121.0	0.0	0		139.0	75.0	0.539568	NM_002191	A8K8H5	Missense_Mutation	SNP	ENST00000243786.2	37	CCDS2444.1	52	0.023809523809523808	50	0.1016260162601626	2	0.0055248618784530384	0	0.0	0	0.0	G	13.05	2.120959	0.37436	0.090785	4.65E-4	ENSG00000123999	ENST00000243786	D	0.84944	-1.92	5.48	5.48	0.80851	.	0.394385	0.24085	N	0.041686	T	0.08935	0.0221	L	0.41079	1.255	0.25639	N	0.986228	B	0.21905	0.062	B	0.17722	0.019	T	0.16424	-1.0403	9	.	.	.	-13.0624	9.3942	0.38392	0.0778:0.145:0.7772:0.0	rs12720061;rs57625669	227	P05111	INHA_HUMAN	R	227	ENSP00000243786:G227R	.	G	+	1	0	INHA	220148070	0.002000	0.14202	0.937000	0.37676	0.995000	0.86356	1.128000	0.31369	2.564000	0.86499	0.561000	0.74099	GGG	G|0.973;A|0.027	0.027	strong		0.687	INHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131425.1		
KCNN1	3780	hgsc.bcm.edu	37	19	18084724	18084724	+	Silent	SNP	C	C	T	rs77030907	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18084724C>T	ENST00000222249.9	+	3	346	c.27C>T	c.(25-27)agC>agT	p.S9S	RNA5SP468_ENST00000516782.1_RNA	NM_002248.3	NP_002239.2	Q92952	KCNN1_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1	9					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			endometrium(1)|kidney(1)|lung(5)|urinary_tract(1)	8					Miconazole(DB01110)|Procaine(DB00721)	ACAATGGCAGCGTGGGGCGGC	0.756													C|||	48	0.00958466	0.0356	0.0014	5008	,	,		12575	0.0		0.0	False		,,,				2504	0.0				p.S9S		Atlas-SNP	.											.	KCNN1	74	.	0			c.C27T						PASS	.						3.0	3.0	3.0					19																	18084724		1475	3351	4826	SO:0001819	synonymous_variant	3780	exon3			TGGCAGCGTGGGG	U69883	CCDS67611.1	19p13.1	2012-07-05				ENSG00000105642		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6290	protein-coding gene	gene with protein product		602982				8781233, 10516439, 16382103	Standard	NM_002248		Approved	KCa2.1, hSK1	uc002nht.3	Q92952		ENST00000222249.9:c.27C>T	19.37:g.18084724C>T		2.0	0.0	0		12.0	7.0	0.583333	NM_002248	Q5KR10|Q6DJU4	Silent	SNP	ENST00000222249.9	37																																																																																				C|0.990;T|0.010	0.010	strong		0.756	KCNN1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471896.2	NM_002248	
CEACAM1	634	hgsc.bcm.edu	37	19	43031369	43031369	+	Missense_Mutation	SNP	G	G	A	rs8110904	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43031369G>A	ENST00000161559.6	-	2	382	c.248C>T	c.(247-249)gCa>gTa	p.A83V	CEACAM1_ENST00000358394.3_Missense_Mutation_p.A83V|LIPE-AS1_ENST00000457234.2_RNA|CEACAM1_ENST00000403461.1_Missense_Mutation_p.A83V|LIPE-AS1_ENST00000594624.2_RNA|CEACAM1_ENST00000308072.4_Missense_Mutation_p.A43V|CEACAM1_ENST00000599389.1_Missense_Mutation_p.A83V|CEACAM1_ENST00000352591.5_Missense_Mutation_p.A83V|CEACAM1_ENST00000403444.3_Missense_Mutation_p.A83V|LIPE-AS1_ENST00000594688.1_RNA|CEACAM1_ENST00000351134.3_Missense_Mutation_p.A83V	NM_001712.4	NP_001703.2	P13688	CEAM1_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 1 (biliary glycoprotein)	83	Ig-like V-type.		A -> V (in dbSNP:rs8110904). {ECO:0000269|Ref.9}.		angiogenesis (GO:0001525)|cell migration (GO:0016477)|homophilic cell adhesion (GO:0007156)|integrin-mediated signaling pathway (GO:0007229)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	17		Prostate(69;0.00682)		GBM - Glioblastoma multiforme(486;0.00148)	Arcitumomab(DB00113)	AGTTCCTATTGCATATCCTAC	0.507													a|||	526	0.105032	0.3707	0.0447	5008	,	,		20268	0.0		0.005	False		,,,				2504	0.0				p.A83V		Atlas-SNP	.											.	CEACAM1	43	.	0			c.C248T						PASS	.	A	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	1359,3047		96,1167,940	318.0	255.0	276.0		248,248,248,248,248,248	-6.2	0.0	19	dbSNP_116	276	22,8578		0,22,4278	yes	missense,missense,missense,missense,missense,missense	CEACAM1	NM_001024912.2,NM_001184813.1,NM_001184815.1,NM_001184816.1,NM_001205344.1,NM_001712.4	64,64,64,64,64,64	96,1189,5218	AA,AG,GG		0.2558,30.8443,10.6182	benign,benign,benign,benign,benign,benign	83/465,83/431,83/462,83/369,83/469,83/527	43031369	1381,11625	2203	4300	6503	SO:0001583	missense	634	exon2			CCTATTGCATATC	M72238	CCDS12609.1, CCDS46089.1, CCDS54272.1, CCDS54273.1, CCDS54274.1	19q13.2	2014-05-16			ENSG00000079385	ENSG00000079385		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1814	protein-coding gene	gene with protein product		109770		BGP		2457922, 2025273	Standard	NM_001712		Approved	BGP1, CD66a	uc002otv.3	P13688	OTTHUMG00000151078	ENST00000161559.6:c.248C>T	19.37:g.43031369G>A	ENSP00000161559:p.Ala83Val	449.0	1.0	0.00222717		456.0	238.0	0.52193	NM_001184816	A6NE38|A8MY49|O60430|Q069I7|Q13854|Q13857|Q13858|Q13859|Q13860|Q15600|Q15601|Q16170|Q5UB49|Q7KYP5|Q96CA7|Q9UQV9	Missense_Mutation	SNP	ENST00000161559.6	37	CCDS12609.1	199	0.09111721611721611	176	0.35772357723577236	18	0.049723756906077346	0	0.0	5	0.006596306068601583	a	0.459	-0.889785	0.02511	0.308443	0.002558	ENSG00000079385	ENST00000161559;ENST00000358394;ENST00000351134;ENST00000446434;ENST00000378065;ENST00000352591;ENST00000403444;ENST00000403461;ENST00000308072;ENST00000377806;ENST00000344391;ENST00000403136	T;T;T;T;T;T;T	0.62639	0.01;0.01;0.01;0.01;0.01;0.01;0.01	3.76	-6.23	0.02052	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.00053	-2.39	0.80722	P	0.0	B;B;B;B;B;B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.0;0.001;0.001;0.0;0.0;0.0	B;B;B;B;B;B;B;B;B;B	0.08055	0.002;0.001;0.0;0.001;0.001;0.003;0.002;0.001;0.001;0.001	T	0.04140	-1.0974	8	0.02654	T	1	.	2.5662	0.04784	0.2081:0.1227:0.4308:0.2384	rs8110904;rs10408262;rs12979523;rs60053543;rs8110904	83;83;83;83;83;83;83;83;83;83	P13688-7;P13688-10;P13688-3;P13688-4;P13688-2;P13688-11;P13688-6;P13688-5;P13688-8;P13688	.;.;.;.;.;.;.;.;.;CEAM1_HUMAN	V	83;83;83;110;43;83;83;83;43;83;83;83	ENSP00000161559:A83V;ENSP00000351165:A83V;ENSP00000325946:A83V;ENSP00000244291:A83V;ENSP00000384709:A83V;ENSP00000384083:A83V;ENSP00000312184:A43V	ENSP00000161559:A83V	A	-	2	0	CEACAM1	47723209	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.328000	0.00510	-2.234000	0.00715	-0.361000	0.07541	GCA	G|0.900;A|0.100	0.100	strong		0.507	CEACAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321190.2	NM_001712	
CCDC155	147872	hgsc.bcm.edu	37	19	49920719	49920719	+	Silent	SNP	C	C	T	rs79452032	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49920719C>T	ENST00000447857.3	+	20	1846	c.1641C>T	c.(1639-1641)ccC>ccT	p.P547P		NM_144688.4	NP_653289.3	Q8N6L0	KASH5_HUMAN	coiled-coil domain containing 155	547						chromosome, telomeric region (GO:0000781)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(10)|ovary(1)|stomach(1)	22						CCCCACCTCCCACCTGGCCCC	0.632													c|||	104	0.0207668	0.0673	0.013	5008	,	,		14619	0.0		0.006	False		,,,				2504	0.0				p.P547P		Atlas-SNP	.											.	CCDC155	46	.	0			c.C1641T						PASS	.			159,4033		5,149,1942	47.0	49.0	48.0		1641	-1.5	0.9	19	dbSNP_132	48	33,8283		1,31,4126	no	coding-synonymous	CCDC155	NM_144688.4		6,180,6068	TT,TC,CC		0.3968,3.7929,1.535		547/563	49920719	192,12316	2096	4158	6254	SO:0001819	synonymous_variant	147872	exon20			ACCTCCCACCTGG		CCDS46140.1	19q13.33	2014-01-21			ENSG00000161609	ENSG00000161609			26520	protein-coding gene	gene with protein product							Standard	NM_144688		Approved	FLJ32658, KASH5	uc002pnm.2	Q8N6L0	OTTHUMG00000183170	ENST00000447857.3:c.1641C>T	19.37:g.49920719C>T		62.0	0.0	0		83.0	41.0	0.493976	NM_144688	Q96MC3	Silent	SNP	ENST00000447857.3	37	CCDS46140.1																																																																																			C|0.987;T|0.013	0.013	strong		0.632	CCDC155-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465436.2	NM_144688	
NPR2	4882	hgsc.bcm.edu	37	9	35811215	35811215	+	IGR	SNP	C	C	T	rs73444820	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35811215C>T	ENST00000342694.2	+	0	3686				AL133410.1_ENST00000582432.1_RNA|HINT2_ENST00000474908.1_5'Flank|SPAG8_ENST00000484764.1_Silent_p.P274P|SPAG8_ENST00000396638.2_Silent_p.P276P|SPAG8_ENST00000340291.2_Silent_p.P276P|SPAG8_ENST00000479751.1_5'UTR	NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2						bone development (GO:0060348)|cell surface receptor signaling pathway (GO:0007166)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cGMP biosynthetic process (GO:0006182)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of oocyte maturation (GO:1900194)|ossification (GO:0001503)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|signal transduction (GO:0007165)|single organism reproductive process (GO:0044702)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(2)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)	ACTGGCCCCGCGGCAAAGTTT	0.507													c|||	99	0.0197684	0.0734	0.0029	5008	,	,		17255	0.0		0.0	False		,,,				2504	0.0				p.P276P		Atlas-SNP	.											SPAG8_ENST00000396638,caecum,carcinoma,0,2	SPAG8	67	2	0			c.G828A						scavenged	.	C	,	276,4130	148.0+/-182.4	7,262,1934	95.0	109.0	104.0		828,828	0.7	1.0	9	dbSNP_130	104	3,8597	3.0+/-9.4	0,3,4297	yes	coding-synonymous,coding-synonymous	SPAG8	NM_001039592.1,NM_172312.1	,	7,265,6231	TT,TC,CC		0.0349,6.2642,2.1452	,	276/486,276/502	35811215	279,12727	2203	4300	6503	SO:0001628	intergenic_variant	26206	exon2			GCCCCGCGGCAAA	AJ005282	CCDS6590.1	9p21-p12	2014-03-03	2014-03-03		ENSG00000159899	ENSG00000159899			7944	protein-coding gene	gene with protein product	"""guanylate cyclase B"""	108961	"""acromesomelic dysplasia, Maroteaux type"", ""atrionatriuretic peptide receptor B"", ""natriuretic peptide receptor B"""	ANPRB, NPRB, AMDM		9634515, 15146390	Standard	XM_005251478		Approved	GUCY2B, ANPb	uc003zyd.3	P20594	OTTHUMG00000019871		9.37:g.35811215C>T		89.0	1.0	0.011236		100.0	71.0	0.71	NM_001039592	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Silent	SNP	ENST00000342694.2	37	CCDS6590.1	26	0.011904761904761904	26	0.052845528455284556	0	0.0	0	0.0	0	0.0	c	6.691	0.496043	0.12762	0.062642	3.49E-4	ENSG00000137098	ENST00000497810	.	.	.	5.65	0.724	0.18236	.	.	.	.	.	T	0.11410	0.0278	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.05500	-1.0881	4	.	.	.	-7.0172	7.2861	0.26340	0.0:0.4303:0.0:0.5697	.	.	.	.	H	274	.	.	R	-	2	0	SPAG8	35801215	0.477000	0.25909	0.964000	0.40570	0.648000	0.38561	-1.146000	0.03191	0.200000	0.20447	-0.285000	0.09966	CGC	C|0.978;T|0.022	0.022	strong		0.507	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1		
AKNA	80709	hgsc.bcm.edu	37	9	117099574	117099574	+	Silent	SNP	A	A	G	rs148856699	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117099574A>G	ENST00000307564.4	-	22	4241	c.4080T>C	c.(4078-4080)ccT>ccC	p.P1360P	AKNA_ENST00000374075.5_Silent_p.P1279P|AKNA_ENST00000374088.3_Silent_p.P1360P|AKNA_ENST00000492875.1_5'UTR|AKNA_ENST00000374079.4_Silent_p.P305P|AKNA_ENST00000223791.3_Silent_p.P820P	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	1360					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						TAGGTCCTGCAGGCGCATAGT	0.652													G|||	29	0.00579073	0.0197	0.0029	5008	,	,		10995	0.0		0.001	False		,,,				2504	0.0				p.P1360P		Atlas-SNP	.											.	AKNA	119	.	0			c.T4080C						PASS	.	G		77,4329	810.3+/-416.0	1,75,2127	41.0	44.0	43.0		4080	-5.6	0.0	9	dbSNP_134	43	0,8598		0,0,4299	no	coding-synonymous	AKNA	NM_030767.4		1,75,6426	GG,GA,AA		0.0,1.7476,0.5921		1360/1440	117099574	77,12927	2203	4299	6502	SO:0001819	synonymous_variant	80709	exon22			TCCTGCAGGCGCA	AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.4080T>C	9.37:g.117099574A>G		136.0	0.0	0		147.0	99.0	0.673469	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Silent	SNP	ENST00000307564.4	37	CCDS6805.1	10	0.004578754578754579	8	0.016260162601626018	2	0.0055248618784530384	0	0.0	0	0.0	G	8.193	0.796449	0.16327	0.017476	0.0	ENSG00000106948	ENST00000320310	.	.	.	5.0	-5.55	0.02536	.	.	.	.	.	T	0.09202	0.0227	.	.	.	0.21822	N	0.999529	.	.	.	.	.	.	T	0.24476	-1.0159	4	.	.	.	-1.4841	3.3389	0.07111	0.561:0.1076:0.2123:0.119	.	.	.	.	P	371	.	.	L	-	2	0	AKNA	116139395	0.000000	0.05858	0.014000	0.15608	0.849000	0.48306	-0.506000	0.06359	-1.037000	0.03283	-0.349000	0.07799	CTG	A|0.995;G|0.005	0.005	strong		0.652	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767	
SERPINE3	647174	hgsc.bcm.edu	37	13	51936079	51936079	+	Silent	SNP	T	T	C	rs74084815	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:51936079T>C	ENST00000521255.1	+	7	1281	c.1221T>C	c.(1219-1221)tcT>tcC	p.S407S	RP11-24B19.3_ENST00000602636.1_RNA|SERPINE3_ENST00000524365.1_Intron|SERPINE3_ENST00000400389.4_Intron|RP11-24B19.4_ENST00000602881.1_RNA	NM_001101320.1	NP_001094790.1	A8MV23	SERP3_HUMAN	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 3	407					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			ovary(2)	2						AGTGTCTCTCTAGCAACAAGG	0.378													T|||	41	0.0081869	0.031	0.0	5008	,	,		16300	0.0		0.0	False		,,,				2504	0.0				p.S407S		Atlas-SNP	.											.	SERPINE3	37	.	0			c.T1221C						PASS	.	T	,,	102,3578		2,98,1740	133.0	120.0	124.0		,1221,	3.2	0.9	13	dbSNP_130	124	0,8172		0,0,4086	no	utr-3,coding-synonymous,utr-3	INTS6,SERPINE3	NM_001039937.1,NM_001101320.1,NM_012141.2	,,	2,98,5826	CC,CT,TT		0.0,2.7717,0.8606	,,	,407/425,	51936079	102,11750	1840	4086	5926	SO:0001819	synonymous_variant	647174	exon7			TCTCTCTAGCAAC	AX772926	CCDS53870.1	13q14.3	2014-02-18			ENSG00000253309	ENSG00000253309		"""Serine (or cysteine) peptidase inhibitors"""	24774	protein-coding gene	gene with protein product						24172014	Standard	NM_001101320		Approved		uc001vfh.2	A8MV23	OTTHUMG00000016943	ENST00000521255.1:c.1221T>C	13.37:g.51936079T>C		222.0	1.0	0.0045045		202.0	95.0	0.470297	NM_001101320	B1V8P3	Silent	SNP	ENST00000521255.1	37	CCDS53870.1																																																																																			T|0.992;C|0.008	0.008	strong		0.378	SERPINE3-001	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045021.2	NM_001101320	
ROBO4	54538	hgsc.bcm.edu	37	11	124765511	124765511	+	Missense_Mutation	SNP	T	T	G	rs60888551	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124765511T>G	ENST00000306534.3	-	6	1363	c.878A>C	c.(877-879)cAg>cCg	p.Q293P	ROBO4_ENST00000526899.1_5'Flank|ROBO4_ENST00000533054.1_Missense_Mutation_p.Q148P	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	293	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		CGGAGCTCCCTGGCCTCCCGG	0.657													T|||	366	0.0730831	0.2557	0.0202	5008	,	,		15539	0.0		0.0129	False		,,,				2504	0.001				p.Q293P		Atlas-SNP	.											.	ROBO4	130	.	0			c.A878C						PASS	.	T	PRO/GLN	667,3699		42,583,1558	34.0	43.0	40.0		878	0.9	0.6	11	dbSNP_129	40	44,8504		1,42,4231	yes	missense	ROBO4	NM_019055.5	76	43,625,5789	GG,GT,TT		0.5147,15.2771,5.5057	benign	293/1008	124765511	711,12203	2183	4274	6457	SO:0001583	missense	54538	exon6			GCTCCCTGGCCTC	AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17985	protein-coding gene	gene with protein product	"""magic roundabout"""	607528	"""roundabout homolog 4 (Drosophila)"""			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.878A>C	11.37:g.124765511T>G	ENSP00000304945:p.Gln293Pro	93.0	0.0	0		93.0	31.0	0.333333	NM_019055	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Missense_Mutation	SNP	ENST00000306534.3	37	CCDS8455.1	127	0.05815018315018315	108	0.21951219512195122	10	0.027624309392265192	0	0.0	9	0.011873350923482849	T	7.456	0.643746	0.14451	0.152771	0.005147	ENSG00000154133	ENST00000306534;ENST00000374963;ENST00000533054	T;T	0.64438	-0.1;0.26	4.72	0.925	0.19424	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.438357	0.17070	N	0.188195	T	0.00039	0.0001	L	0.29908	0.895	0.48341	P	3.670000000000062E-4	B;B	0.10296	0.002;0.003	B;B	0.08055	0.003;0.002	T	0.06303	-1.0834	9	0.30078	T	0.28	.	5.9357	0.19165	0.0:0.0891:0.3409:0.57	rs60888551	183;293	Q8WZ75-3;Q8WZ75	.;ROBO4_HUMAN	P	293;183;148	ENSP00000304945:Q293P;ENSP00000437129:Q148P	ENSP00000304945:Q293P	Q	-	2	0	ROBO4	124270721	0.108000	0.22018	0.642000	0.29436	0.276000	0.26787	0.391000	0.20784	0.293000	0.22520	0.459000	0.35465	CAG	T|0.952;G|0.048	0.048	strong		0.657	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387111.1	NM_019055	
NLRP11	204801	hgsc.bcm.edu	37	19	56303806	56303806	+	Missense_Mutation	SNP	A	A	C	rs80143194	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56303806A>C	ENST00000589093.1	-	7	2467	c.2374T>G	c.(2374-2376)Tgc>Ggc	p.C792G	NLRP11_ENST00000592953.1_Missense_Mutation_p.C693G|NLRP11_ENST00000589824.2_Missense_Mutation_p.C738G|NLRP11_ENST00000443188.1_Missense_Mutation_p.C792G|NLRP11_ENST00000360133.3_Missense_Mutation_p.C738G			P59045	NAL11_HUMAN	NLR family, pyrin domain containing 11	792							ATP binding (GO:0005524)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced ascorbate as one donor, and incorporation of one atom of oxygen (GO:0016715)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(14)|lung(22)|ovary(3)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	66		Colorectal(82;0.0002)		GBM - Glioblastoma multiforme(193;0.0325)		AGGGCGCTGCAGCAATTTTCA	0.498													A|||	151	0.0301518	0.1097	0.0086	5008	,	,		19216	0.0		0.0	False		,,,				2504	0.0				p.C792G		Atlas-SNP	.											.	NLRP11	139	.	0			c.T2374G						PASS	.	A	GLY/CYS	357,4049	184.0+/-211.4	11,335,1857	110.0	102.0	105.0		2374	-0.1	0.0	19	dbSNP_131	105	7,8593	4.3+/-15.6	0,7,4293	yes	missense	NLRP11	NM_145007.3	159	11,342,6150	CC,CA,AA		0.0814,8.1026,2.7987	probably-damaging	792/1034	56303806	364,12642	2203	4300	6503	SO:0001583	missense	204801	exon9			CGCTGCAGCAATT	AY095145	CCDS12935.1, CCDS74458.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179873		"""Nucleotide-binding domain and leucine rich repeat containing"""	22945	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 11"""	609664	"""NACHT, leucine rich repeat and PYD containing 11"""	NALP11		12563287, 12019269	Standard	NM_145007		Approved	PYPAF6, NOD17, PAN10, CLR19.6	uc010ygf.2	P59045		ENST00000589093.1:c.2374T>G	19.37:g.56303806A>C	ENSP00000466285:p.Cys792Gly	122.0	0.0	0		124.0	62.0	0.5	NM_145007	C9JSF5|Q2TV85|Q2TV86|Q53ZZ0|Q8NBF5	Missense_Mutation	SNP	ENST00000589093.1	37	CCDS12935.1	41	0.018772893772893772	40	0.08130081300813008	1	0.0027624309392265192	0	0.0	0	0.0	A	10.23	1.292437	0.23564	0.081026	8.14E-4	ENSG00000179873	ENST00000443188;ENST00000360133	T;T	0.53423	0.62;0.62	2.18	-0.114	0.13564	.	.	.	.	.	T	0.10637	0.0260	M	0.93062	3.375	0.09310	N	1	D;D	0.76494	0.999;0.999	D;D	0.71656	0.942;0.974	T	0.24368	-1.0162	9	0.87932	D	0	.	2.8277	0.05490	0.5109:0.3169:0.1722:0.0	.	792;738	P59045;P59045-2	NAL11_HUMAN;.	G	792;738	ENSP00000409898:C792G;ENSP00000353251:C738G	ENSP00000353251:C738G	C	-	1	0	NLRP11	60995618	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.262000	0.18460	-0.089000	0.12484	-0.340000	0.08031	TGC	A|0.976;C|0.024	0.024	strong		0.498	NLRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453657.1	NM_145007	
TACC2	10579	hgsc.bcm.edu	37	10	123843946	123843946	+	Missense_Mutation	SNP	C	C	T	rs60531929	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:123843946C>T	ENST00000369005.1	+	4	2271	c.1931C>T	c.(1930-1932)aCg>aTg	p.T644M	TACC2_ENST00000453444.2_Missense_Mutation_p.T644M|TACC2_ENST00000358010.1_Intron|TACC2_ENST00000515603.1_Missense_Mutation_p.T644M|TACC2_ENST00000515273.1_Missense_Mutation_p.T644M|TACC2_ENST00000513429.1_Intron|TACC2_ENST00000334433.3_Missense_Mutation_p.T644M	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	644					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				GCTGGGCACACGGACGGGCCC	0.612													C|||	150	0.0299521	0.1036	0.0173	5008	,	,		18351	0.0		0.001	False		,,,				2504	0.0				p.T644M		Atlas-SNP	.											.	TACC2	271	.	0			c.C1931T						PASS	.	C	,MET/THR	445,3961	208.8+/-229.8	26,393,1784	37.0	35.0	35.0		,1931	-10.0	0.0	10	dbSNP_129	35	9,8591	5.0+/-18.6	0,9,4291	yes	intron,missense	TACC2	NM_206861.1,NM_206862.2	,81	26,402,6075	TT,TC,CC		0.1047,10.0999,3.4907	,possibly-damaging	,644/2949	123843946	454,12552	2203	4300	6503	SO:0001583	missense	10579	exon4			GGCACACGGACGG	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.1931C>T	10.37:g.123843946C>T	ENSP00000358001:p.Thr644Met	32.0	0.0	0		31.0	16.0	0.516129	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	47	0.02152014652014652	41	0.08333333333333333	6	0.016574585635359115	0	0.0	0	0.0	C	6.831	0.522532	0.13066	0.100999	0.001047	ENSG00000138162	ENST00000369005;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000453444;ENST00000340076	T;T;T;T;T	0.03413	3.96;3.94;3.94;3.96;3.94	5.02	-10.0	0.00425	.	3.389020	0.01191	N	0.007326	T	0.00073	0.0002	N	0.14661	0.345	0.09310	N	1	P;P;P	0.42757	0.789;0.789;0.789	B;B;B	0.29785	0.107;0.107;0.107	T	0.45659	-0.9246	10	0.45353	T	0.12	11.5241	1.2386	0.01958	0.331:0.1646:0.0943:0.41	rs60531929	644;644;644	E9PBC6;E7EMZ9;O95359	.;.;TACC2_HUMAN	M	644;644;644;644;644;634	ENSP00000358001:T644M;ENSP00000424467:T644M;ENSP00000427618:T644M;ENSP00000334280:T644M;ENSP00000395048:T644M	ENSP00000334280:T644M	T	+	2	0	TACC2	123833936	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.942000	0.00167	-1.779000	0.01280	0.561000	0.74099	ACG	C|0.965;T|0.035	0.035	strong		0.612	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
LCN8	138307	hgsc.bcm.edu	37	9	139649701	139649701	+	Missense_Mutation	SNP	C	C	T	rs144857499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139649701C>T	ENST00000371688.3	-	5	711	c.416G>A	c.(415-417)cGg>cAg	p.R139Q	LCN8_ENST00000482893.1_5'UTR	NM_178469.3	NP_848564.2	Q6JVE9	LCN8_HUMAN	lipocalin 8	162					response to hormone (GO:0009725)|transport (GO:0006810)	extracellular region (GO:0005576)				endometrium(1)|large_intestine(1)|lung(6)|pancreas(1)|prostate(1)	10	all_cancers(76;0.0882)|all_epithelial(76;0.228)	Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;5.56e-06)|Epithelial(140;8.32e-05)		CTCACCAGGCCGGGCCGCCAG	0.682													C|||	7	0.00139776	0.0045	0.0014	5008	,	,		14888	0.0		0.0	False		,,,				2504	0.0				p.R139Q		Atlas-SNP	.											.	LCN8	14	.	0			c.G416A						PASS	.	C	GLN/ARG	25,4379	30.8+/-60.4	0,25,2177	39.0	48.0	45.0		416	1.9	0.2	9	dbSNP_134	45	1,8599		0,1,4299	yes	missense	LCN8	NM_178469.3	43	0,26,6476	TT,TC,CC		0.0116,0.5677,0.1999	probably-damaging	139/153	139649701	26,12978	2202	4300	6502	SO:0001583	missense	138307	exon5			CCAGGCCGGGCCG	AK124003	CCDS35183.1	9q34.3	2011-10-24	2005-01-11		ENSG00000204001	ENSG00000204001		"""Lipocalins"""	27038	protein-coding gene	gene with protein product		612902	"""chromosome 9 open reading frame 137"", ""lipocalin 5"""	LCN5			Standard	XM_005266058		Approved		uc004cjb.1	Q6JVE9	OTTHUMG00000020942	ENST00000371688.3:c.416G>A	9.37:g.139649701C>T	ENSP00000360753:p.Arg139Gln	78.0	0.0	0		80.0	55.0	0.6875	NM_178469	A1L4A8|A6NMN9|Q5T5R4	Missense_Mutation	SNP	ENST00000371688.3	37	CCDS35183.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	9.456	1.091903	0.20471	0.005677	1.16E-4	ENSG00000204001	ENST00000371688	T	0.34667	1.35	2.76	1.85	0.25348	.	.	.	.	.	T	0.14700	0.0355	N	0.24115	0.695	0.09310	N	1	B	0.23490	0.086	B	0.15870	0.014	T	0.15723	-1.0427	9	0.28530	T	0.3	.	5.487	0.16755	0.0:0.8418:0.0:0.1582	.	139	Q6JVE9-2	.	Q	139	ENSP00000360753:R139Q	ENSP00000360753:R139Q	R	-	2	0	LCN8	138769522	0.058000	0.20735	0.229000	0.23960	0.549000	0.35272	0.257000	0.18369	0.731000	0.32448	0.491000	0.48974	CGG	C|0.997;T|0.003	0.003	strong		0.682	LCN8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055109.1	NM_178469	
MUC5B	727897	hgsc.bcm.edu	37	11	1271582	1271582	+	Missense_Mutation	SNP	C	C	T	rs200110193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1271582C>T	ENST00000529681.1	+	31	13530	c.13472C>T	c.(13471-13473)aCc>aTc	p.T4491I	RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000447027.1_Missense_Mutation_p.T4494I	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	4491	23 X approximate tandem repeats, Ser/Thr- rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CCCACAGTCACCAGCTCCAAA	0.642													C|||	68	0.0135783	0.0469	0.0086	5008	,	,		18910	0.0		0.0	False		,,,				2504	0.0				p.T4491I		Atlas-SNP	.											.	MUC5B	473	.	0			c.C13472T						PASS	.	C	ILE/THR	95,4235		2,91,2072	114.0	152.0	139.0		13472	0.4	0.0	11		139	0,8520		0,0,4260	no	missense	MUC5B	NM_002458.2	89	2,91,6332	TT,TC,CC		0.0,2.194,0.7393	probably-damaging	4491/5763	1271582	95,12755	2165	4260	6425	SO:0001583	missense	727897	exon31			CAGTCACCAGCTC	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.13472C>T	11.37:g.1271582C>T	ENSP00000436812:p.Thr4491Ile	827.0	2.0	0.00241838		596.0	279.0	0.468121	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	-	1.101	-0.661133	0.03454	0.02194	0.0	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844;ENST00000535652	T;T	0.25749	1.78;1.97	0.399	0.399	0.16325	.	.	.	.	.	T	0.22475	0.0542	L	0.60455	1.87	0.09310	N	1	D;D	0.58970	0.984;0.984	P;P	0.59595	0.86;0.86	T	0.08351	-1.0726	8	0.87932	D	0	.	.	.	.	.	4964;4494	A7Y9J9;E9PBJ0	.;.	I	4491;4494;4435;4341;270	ENSP00000436812:T4491I;ENSP00000415793:T4494I	ENSP00000343037:T4435I	T	+	2	0	MUC5B	1228158	0.000000	0.05858	0.019000	0.16419	0.023000	0.10783	-0.180000	0.09754	0.440000	0.26502	0.162000	0.16502	ACC	.	.	weak		0.642	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
SMC1B	27127	hgsc.bcm.edu	37	22	45741416	45741416	+	Missense_Mutation	SNP	T	T	A	rs61737925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:45741416T>A	ENST00000357450.4	-	24	3529	c.3530A>T	c.(3529-3531)cAg>cTg	p.Q1177L	SMC1B_ENST00000404354.3_Missense_Mutation_p.Q1103L	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	1177					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)			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)		CATCTGAAACTGGTCTTGAGT	0.448													T|||	55	0.0109824	0.0408	0.0014	5008	,	,		18744	0.0		0.0	False		,,,				2504	0.0				p.Q1177L		Atlas-SNP	.											.	SMC1B	215	.	0			c.A3530T						PASS	.	T	LEU/GLN	155,3629		4,147,1741	133.0	127.0	129.0		3530	5.6	1.0	22	dbSNP_129	129	0,8236		0,0,4118	yes	missense	SMC1B	NM_148674.3	113	4,147,5859	AA,AT,TT		0.0,4.0962,1.2895	probably-damaging	1177/1236	45741416	155,11865	1892	4118	6010	SO:0001583	missense	27127	exon24			TGAAACTGGTCTT	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.3530A>T	22.37:g.45741416T>A	ENSP00000350036:p.Gln1177Leu	125.0	0.0	0		148.0	78.0	0.527027	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Missense_Mutation	SNP	ENST00000357450.4	37	CCDS43027.1	18	0.008241758241758242	18	0.036585365853658534	0	0.0	0	0.0	0	0.0	T	18.42	3.620931	0.66787	0.040962	0.0	ENSG00000077935	ENST00000357450;ENST00000404354	T;T	0.77358	2.94;-1.09	5.61	5.61	0.85477	.	0.105145	0.42682	D	0.000676	T	0.46580	0.1400	L	0.43152	1.355	0.28411	N	0.91821	P;P	0.41848	0.763;0.573	P;B	0.44897	0.463;0.236	T	0.62779	-0.6782	10	0.40728	T	0.16	.	15.8023	0.78463	0.0:0.0:0.0:1.0	rs61737925	1103;1177	Q8NDV3-2;Q8NDV3-3	.;.	L	1177;1103	ENSP00000350036:Q1177L;ENSP00000385902:Q1103L	ENSP00000350036:Q1177L	Q	-	2	0	SMC1B	44120080	1.000000	0.71417	0.991000	0.47740	0.981000	0.71138	3.975000	0.56859	2.142000	0.66516	0.397000	0.26171	CAG	T|0.960;A|0.040	0.040	strong		0.448	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674	
WBSCR27	155368	hgsc.bcm.edu	37	7	73249092	73249092	+	Missense_Mutation	SNP	C	C	T	rs73369956	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:73249092C>T	ENST00000297873.4	-	6	768	c.719G>A	c.(718-720)cGa>cAa	p.R240Q		NM_152559.2	NP_689772.2	Q8N6F8	WBS27_HUMAN	Williams Beuren syndrome chromosome region 27	240										NS(1)|central_nervous_system(1)|lung(2)|prostate(1)	5		Lung NSC(55;0.159)				CAACCTGGGTCGCCTTCCACT	0.632													C|||	173	0.0345447	0.1263	0.0072	5008	,	,		17029	0.0		0.001	False		,,,				2504	0.0				p.R240Q		Atlas-SNP	.											.	WBSCR27	21	.	0			c.G719A						PASS	.	C	GLN/ARG	448,3958	210.2+/-230.7	22,404,1777	47.0	43.0	44.0		719	-4.9	0.0	7	dbSNP_130	44	2,8598	2.2+/-6.3	0,2,4298	yes	missense	WBSCR27	NM_152559.2	43	22,406,6075	TT,TC,CC		0.0233,10.168,3.4599	benign	240/246	73249092	450,12556	2203	4300	6503	SO:0001583	missense	155368	exon6			CTGGGTCGCCTTC	AF534110	CCDS5561.1	7q11.23	2004-07-05			ENSG00000165171	ENSG00000165171			19068	protein-coding gene	gene with protein product		612546					Standard	NM_152559		Approved		uc003tzj.2	Q8N6F8	OTTHUMG00000130033	ENST00000297873.4:c.719G>A	7.37:g.73249092C>T	ENSP00000297873:p.Arg240Gln	111.0	0.0	0		103.0	103.0	1	NM_152559		Missense_Mutation	SNP	ENST00000297873.4	37	CCDS5561.1	61	0.027930402930402932	58	0.11788617886178862	3	0.008287292817679558	0	0.0	0	0.0	C	9.306	1.054385	0.19907	0.10168	2.33E-4	ENSG00000165171	ENST00000297873	T	0.36520	1.25	4.67	-4.88	0.03113	.	0.739448	0.13097	N	0.414080	T	0.00144	0.0004	N	0.02011	-0.69	0.09310	N	1	B	0.10296	0.003	B	0.01281	0.0	T	0.25398	-1.0133	10	0.19147	T	0.46	-0.2142	2.1565	0.03814	0.1345:0.2371:0.1332:0.4952	.	240	Q8N6F8	WBS27_HUMAN	Q	240	ENSP00000297873:R240Q	ENSP00000297873:R240Q	R	-	2	0	WBSCR27	72887028	0.000000	0.05858	0.000000	0.03702	0.104000	0.19210	-3.365000	0.00496	-0.582000	0.05929	0.549000	0.68633	CGA	C|0.962;T|0.038	0.038	strong		0.632	WBSCR27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252312.1	NM_152559	
AMER1	139285	hgsc.bcm.edu	37	X	63410110	63410110	+	Silent	SNP	T	T	C	rs61730681	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:63410110T>C	ENST00000330258.3	-	2	3329	c.3057A>G	c.(3055-3057)caA>caG	p.Q1019Q	AMER1_ENST00000403336.1_Intron|AMER1_ENST00000374869.3_Intron	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	1019	Pro-rich.				adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)									GACGAGCTAGTTGAGGCCCAG	0.567													C|||	1022	0.270728	0.7012	0.0937	3775	,	,		13676	0.003		0.0119	False		,,,				2504	0.0153				p.Q1019Q		Atlas-SNP	.											.	.	.	.	67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.A3057G						PASS	.	C		2803,865		883,571,466,95,104	54.0	61.0	58.0		3057	1.9	0.7	X	dbSNP_129	58	101,6502		0,78,23,2314,1796	no	coding-synonymous	FAM123B	NM_152424.3		883,649,489,2409,1900	CC,CT,C,TT,T		1.5296,23.5823,28.2738		1019/1136	63410110	2904,7367	2119	4211	6330	SO:0001819	synonymous_variant	139285	exon2			AGCTAGTTGAGGC	AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"""-"""	26837	protein-coding gene	gene with protein product	"""Wilms Tumor on the X"", ""adenomatous polyposis coli membrane recruitment 1"""	300647	"""family with sequence similarity 123B"""	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.3057A>G	X.37:g.63410110T>C		149.0	0.0	0		157.0	157.0	1	NM_152424	A2IB86|Q8N885	Silent	SNP	ENST00000330258.3	37	CCDS14377.2																																																																																			T|0.758;C|0.242	0.242	strong		0.567	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424	
KRTAP5-9	3846	hgsc.bcm.edu	37	11	71259709	71259709	+	Silent	SNP	C	C	T	rs180808688	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71259709C>T	ENST00000528743.2	+	1	244	c.6C>T	c.(4-6)ggC>ggT	p.G2G		NM_005553.3	NP_005544.4	P26371	KRA59_HUMAN	keratin associated protein 5-9	2					epidermis development (GO:0008544)	keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(6)|prostate(3)	11						GAACCATGGGCTGCTGTGGCT	0.642													c|||	10	0.00199681	0.0068	0.0014	5008	,	,		17898	0.0		0.0	False		,,,				2504	0.0				p.G2G		Atlas-SNP	.											.	KRTAP5-9	19	.	0			c.C6T						PASS	.	C		32,4366		0,32,2167	84.0	95.0	91.0		6	1.6	1.0	11		91	0,8588		0,0,4294	no	coding-synonymous	KRTAP5-9	NM_005553.3		0,32,6461	TT,TC,CC		0.0,0.7276,0.2464		2/170	71259709	32,12954	2199	4294	6493	SO:0001819	synonymous_variant	3846	exon1			CATGGGCTGCTGT	AB126078	CCDS53677.1	11q13.4	2008-02-05				ENSG00000254997		"""Keratin associated proteins"""	23604	protein-coding gene	gene with protein product		148021		KRN1		15144888	Standard	NM_005553		Approved	KRTAP5.9, KRTAP5-1	uc001oqs.1	P26371		ENST00000528743.2:c.6C>T	11.37:g.71259709C>T		453.0	1.0	0.00220751		521.0	234.0	0.449136	NM_005553	Q14564|Q3MIP8	Silent	SNP	ENST00000528743.2	37	CCDS53677.1																																																																																			C|0.999;T|0.001	0.001	strong		0.642	KRTAP5-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393901.2		
CRTAC1	55118	hgsc.bcm.edu	37	10	99696031	99696031	+	Missense_Mutation	SNP	G	G	A	rs80014629	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:99696031G>A	ENST00000370597.3	-	3	672	c.317C>T	c.(316-318)gCg>gTg	p.A106V	CRTAC1_ENST00000370591.2_Missense_Mutation_p.A106V|CRTAC1_ENST00000298819.4_Missense_Mutation_p.A106V	NM_018058.6	NP_060528.3	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1	106						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.A106V(1)		autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(6)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	35		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)		GTCCCGCAGCGCGTAGTAGGG	0.617													G|||	7	0.00139776	0.0053	0.0	5008	,	,		18551	0.0		0.0	False		,,,				2504	0.0				p.A106V		Atlas-SNP	.											CRTAC1,NS,carcinoma,0,2	CRTAC1	86	2	1	Substitution - Missense(1)	endometrium(1)	c.C317T						PASS	.	G	VAL/ALA,VAL/ALA	18,4388	24.3+/-50.5	0,18,2185	66.0	54.0	58.0		317,317	4.8	1.0	10	dbSNP_131	58	0,8600		0,0,4300	yes	missense,missense	CRTAC1	NM_001206528.2,NM_018058.6	64,64	0,18,6485	AA,AG,GG		0.0,0.4085,0.1384	benign,benign	106/646,106/662	99696031	18,12988	2203	4300	6503	SO:0001583	missense	55118	exon3			CGCAGCGCGTAGT	AJ276171	CCDS31266.1, CCDS55723.1	10q22	2007-12-03			ENSG00000095713	ENSG00000095713			14882	protein-coding gene	gene with protein product		606276				11139377	Standard	NM_018058		Approved	FLJ10320, CEP-68, ASPIC1	uc001kou.2	Q9NQ79	OTTHUMG00000018871	ENST00000370597.3:c.317C>T	10.37:g.99696031G>A	ENSP00000359629:p.Ala106Val	132.0	0.0	0		112.0	52.0	0.464286	NM_001206528	B1ALN4|Q5T4F8|Q8N4H6|Q8TE52|Q9NQ78|Q9NQ80|Q9NW46	Missense_Mutation	SNP	ENST00000370597.3	37	CCDS31266.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	14.45	2.537920	0.45176	0.004085	0.0	ENSG00000095713	ENST00000413387;ENST00000370597;ENST00000298819;ENST00000309155;ENST00000370591	T;T;T;T;T	0.75050	1.37;-0.9;1.27;-0.05;-0.06	4.76	4.76	0.60689	.	0.000000	0.85682	D	0.000000	T	0.65091	0.2658	L	0.57536	1.79	0.80722	D	1	P;P	0.50710	0.68;0.938	B;B	0.43386	0.089;0.418	T	0.68239	-0.5461	10	0.15066	T	0.55	-16.5833	17.7665	0.88480	0.0:0.0:1.0:0.0	.	106;106	Q9NQ79-2;Q9NQ79	.;CRAC1_HUMAN	V	2;106;106;98;106	ENSP00000408445:A2V;ENSP00000359629:A106V;ENSP00000298819:A106V;ENSP00000310810:A98V;ENSP00000359623:A106V	ENSP00000298819:A106V	A	-	2	0	CRTAC1	99686021	1.000000	0.71417	0.958000	0.39756	0.350000	0.29205	7.675000	0.84002	2.204000	0.70986	0.313000	0.20887	GCG	G|0.999;A|0.001	0.001	strong		0.617	CRTAC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049754.1	NM_018058	
PDE5A	8654	hgsc.bcm.edu	37	4	120440278	120440278	+	Missense_Mutation	SNP	A	A	G	rs116396619	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:120440278A>G	ENST00000354960.3	-	14	2241	c.1922T>C	c.(1921-1923)cTg>cCg	p.L641P	PDE5A_ENST00000512739.1_5'Flank|PDE5A_ENST00000394439.1_Missense_Mutation_p.L589P|RP11-33B1.1_ENST00000498873.1_RNA|PDE5A_ENST00000264805.5_Missense_Mutation_p.L599P	NM_001083.3	NP_001074.2	O76074	PDE5A_HUMAN	phosphodiesterase 5A, cGMP-specific	641	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|cGMP catabolic process (GO:0046069)|negative regulation of cardiac muscle contraction (GO:0055118)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of oocyte development (GO:0060282)|relaxation of cardiac muscle (GO:0055119)|signal transduction (GO:0007165)	cytosol (GO:0005829)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cGMP binding (GO:0030553)|metal ion binding (GO:0046872)			breast(4)|endometrium(2)|kidney(3)|large_intestine(8)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	27					Avanafil(DB06237)|Caffeine(DB00201)|Dipyridamole(DB00975)|Pentoxifylline(DB00806)|Sildenafil(DB00203)|Tadalafil(DB00820)|Theophylline(DB00277)|Udenafil(DB06267)|Vardenafil(DB00862)	AAGTATCTCCAGGTCAGTCAG	0.408													A|||	26	0.00519169	0.0174	0.0029	5008	,	,		18416	0.0		0.001	False		,,,				2504	0.0				p.L641P		Atlas-SNP	.											.	PDE5A	83	.	0			c.T1922C						PASS	.	A	PRO/LEU,PRO/LEU,PRO/LEU	58,4348	56.8+/-93.2	0,58,2145	125.0	104.0	111.0		1922,1796,1766	5.5	1.0	4	dbSNP_132	111	0,8600		0,0,4300	yes	missense,missense,missense	PDE5A	NM_001083.3,NM_033430.2,NM_033437.3	98,98,98	0,58,6445	GG,GA,AA		0.0,1.3164,0.4459	probably-damaging,probably-damaging,probably-damaging	641/876,599/834,589/824	120440278	58,12948	2203	4300	6503	SO:0001583	missense	8654	exon14			ATCTCCAGGTCAG	D89094	CCDS3713.1, CCDS34055.1	4q27	2008-05-15			ENSG00000138735	ENSG00000138735	3.1.4.17	"""Phosphodiesterases"""	8784	protein-coding gene	gene with protein product		603310				9714779, 9642111	Standard	NM_033437		Approved		uc003idh.3	O76074	OTTHUMG00000132971	ENST00000354960.3:c.1922T>C	4.37:g.120440278A>G	ENSP00000347046:p.Leu641Pro	241.0	1.0	0.00414938		261.0	129.0	0.494253	NM_001083	A0AV69|A8K2C4|O75026|O75887|Q86UI0|Q86V66|Q9Y6Z6	Missense_Mutation	SNP	ENST00000354960.3	37	CCDS3713.1	7	0.003205128205128205	6	0.012195121951219513	0	0.0	0	0.0	1	0.0013192612137203166	A	20.9	4.064397	0.76187	0.013164	0.0	ENSG00000138735	ENST00000354960;ENST00000394439;ENST00000264805	D;D;D	0.85702	-2.02;-2.02;-2.02	5.46	5.46	0.80206	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.000000	0.85682	D	0.000000	D	0.91520	0.7322	H	0.94964	3.605	0.80722	D	1	D;D	0.63046	0.992;0.989	D;D	0.72982	0.979;0.916	D	0.92792	0.6249	10	0.87932	D	0	.	9.4099	0.38485	0.9202:0.0:0.0798:0.0	.	641;599	O76074;O76074-2	PDE5A_HUMAN;.	P	641;589;599	ENSP00000347046:L641P;ENSP00000377957:L589P;ENSP00000264805:L599P	ENSP00000264805:L599P	L	-	2	0	PDE5A	120659726	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	7.113000	0.77095	2.081000	0.62600	0.533000	0.62120	CTG	A|0.996;G|0.004	0.004	strong		0.408	PDE5A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256529.1	NM_001083	
KIAA0922	23240	hgsc.bcm.edu	37	4	154525446	154525446	+	Silent	SNP	A	A	C	rs17030219	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:154525446A>C	ENST00000409663.3	+	25	3331	c.3279A>C	c.(3277-3279)tcA>tcC	p.S1093S	KIAA0922_ENST00000440693.1_Silent_p.S1010S|KIAA0922_ENST00000409959.3_Silent_p.S1094S	NM_015196.3	NP_056011.3	A2VDJ0	T131L_HUMAN	KIAA0922	1093						integral component of membrane (GO:0016021)				breast(2)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(16)|lung(20)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	63	all_hematologic(180;0.093)	Renal(120;0.118)				TTAAAACTTCAGAGAACACAG	0.408													A|||	52	0.0103834	0.0378	0.0014	5008	,	,		19441	0.0		0.001	False		,,,				2504	0.0				p.S1094S		Atlas-SNP	.											.	KIAA0922	214	.	0			c.A3282C						PASS	.	A	,	171,4235	111.6+/-149.8	2,167,2034	51.0	52.0	52.0		3282,3279	1.9	0.5	4	dbSNP_123	52	1,8599		0,1,4299	yes	coding-synonymous,coding-synonymous	KIAA0922	NM_001131007.1,NM_015196.3	,	2,168,6333	CC,CA,AA		0.0116,3.8811,1.3225	,	1094/1611,1093/1610	154525446	172,12834	2203	4300	6503	SO:0001819	synonymous_variant	23240	exon25			AACTTCAGAGAAC	AK096538	CCDS3783.2, CCDS47148.1	4q31.3	2008-02-05			ENSG00000121210	ENSG00000121210			29146	protein-coding gene	gene with protein product						10231032, 11230166	Standard	NM_015196		Approved	DKFZp586H1322, TMEM131L	uc010ipp.3	A2VDJ0	OTTHUMG00000153244	ENST00000409663.3:c.3279A>C	4.37:g.154525446A>C		135.0	0.0	0		134.0	75.0	0.559702	NM_001131007	B3KRV3|Q7LGA7|Q86Y92|Q8WU56|Q9H065|Q9Y2D7	Silent	SNP	ENST00000409663.3	37	CCDS3783.2																																																																																			A|0.987;C|0.013	0.013	strong		0.408	KIAA0922-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330370.1	NM_015196	
MATN2	4147	hgsc.bcm.edu	37	8	99028811	99028811	+	Silent	SNP	G	G	A	rs79255841	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:99028811G>A	ENST00000520016.1	+	10	1741	c.1617G>A	c.(1615-1617)tcG>tcA	p.S539S	MATN2_ENST00000521689.1_Silent_p.S539S|MATN2_ENST00000522025.2_Silent_p.S255S|MATN2_ENST00000524308.1_Silent_p.S498S|MATN2_ENST00000254898.5_Silent_p.S539S			O00339	MATN2_HUMAN	matrilin 2	539	EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			GTGAACATTCGTGTGTAAGCA	0.418													G|||	139	0.0277556	0.0953	0.0187	5008	,	,		19696	0.0		0.0	False		,,,				2504	0.0				p.S539S		Atlas-SNP	.											MATN2_ENST00000520016,NS,carcinoma,+1,2	MATN2	165	2	0			c.G1617A						PASS	.	G	,	355,3435		11,333,1551	108.0	102.0	104.0		1617,1617	-11.3	0.0	8	dbSNP_132	104	4,8248		0,4,4122	no	coding-synonymous,coding-synonymous	MATN2	NM_002380.3,NM_030583.2	,	11,337,5673	AA,AG,GG		0.0485,9.3668,2.9812	,	539/957,539/938	99028811	359,11683	1895	4126	6021	SO:0001819	synonymous_variant	4147	exon11			ACATTCGTGTGTA	U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15							6908	protein-coding gene	gene with protein product		602108				9083061, 11852232	Standard	XM_005250920		Approved		uc003yic.3	O00339		ENST00000520016.1:c.1617G>A	8.37:g.99028811G>A		208.0	0.0	0		204.0	104.0	0.509804	NM_002380	A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Silent	SNP	ENST00000520016.1	37	CCDS55264.1	41	0.018772893772893772	35	0.07113821138211382	6	0.016574585635359115	0	0.0	0	0.0	G	0.127	-1.118394	0.01785	0.093668	4.85E-4	ENSG00000132561	ENST00000518154;ENST00000517321	.	.	.	5.67	-11.3	0.00108	.	.	.	.	.	T	0.01156	0.0038	.	.	.	0.52099	D	0.999946	.	.	.	.	.	.	T	0.30851	-0.9964	4	.	.	.	-0.062	1.117	0.01716	0.232:0.3145:0.2304:0.2231	.	.	.	.	M	322;14	.	.	V	+	1	0	MATN2	99097987	0.000000	0.05858	0.012000	0.15200	0.010000	0.07245	-6.461000	0.00065	-2.310000	0.00650	-1.185000	0.01705	GTG	G|0.976;A|0.024	0.024	strong		0.418	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1		
IPO4	79711	hgsc.bcm.edu	37	14	24652350	24652350	+	Silent	SNP	G	G	A	rs377303706		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24652350G>A	ENST00000354464.6	-	23	2429	c.2253C>T	c.(2251-2253)gtC>gtT	p.V751V	RP11-468E2.2_ENST00000561419.1_3'UTR	NM_024658.3	NP_078934.3	Q8TEX9	IPO4_HUMAN	importin 4	751					DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(10)|ovary(1)|stomach(2)|urinary_tract(1)	33				GBM - Glioblastoma multiforme(265;0.0087)		AGGATGGCACGACTCGGGCCA	0.667																																					p.V751V		Atlas-SNP	.											.	IPO4	74	.	0			c.C2253T						PASS	.	C		6,4192		0,6,2093	42.0	48.0	46.0		2253	4.0	1.0	14		46	0,8460		0,0,4230	no	coding-synonymous	IPO4	NM_024658.3		0,6,6323	AA,AG,GG		0.0,0.1429,0.0474		751/1082	24652350	6,12652	2099	4230	6329	SO:0001819	synonymous_variant	79711	exon23			TGGCACGACTCGG	AF411122	CCDS9616.1	14q11.2	2003-03-10			ENSG00000196497	ENSG00000196497		"""Importins"""	19426	protein-coding gene	gene with protein product						11823430	Standard	NR_051979		Approved	Imp4, FLJ23338	uc001wmv.1	Q8TEX9	OTTHUMG00000028801	ENST00000354464.6:c.2253C>T	14.37:g.24652350G>A		138.0	0.0	0		136.0	72.0	0.529412	NM_024658	B2RN95|Q2NL96|Q86TZ9|Q8NCG8|Q96SJ3|Q9BTI4|Q9H5L0	Silent	SNP	ENST00000354464.6	37	CCDS9616.1																																																																																			.	.	weak		0.667	IPO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071931.4	NM_024658	
THNSL2	55258	hgsc.bcm.edu	37	2	88478341	88478341	+	Missense_Mutation	SNP	C	C	A	rs34136143	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:88478341C>A	ENST00000324166.5	+	4	2302	c.611C>A	c.(610-612)aCt>aAt	p.T204N	THNSL2_ENST00000496844.1_3'UTR|THNSL2_ENST00000377254.3_Missense_Mutation_p.T204N|THNSL2_ENST00000402102.1_Missense_Mutation_p.T204N|THNSL2_ENST00000358591.2_Missense_Mutation_p.T204N|THNSL2_ENST00000343544.4_Missense_Mutation_p.T204N|THNSL2_ENST00000449349.1_Missense_Mutation_p.T172N	NM_018271.4	NP_060741.3	Q86YJ6	THNS2_HUMAN	threonine synthase-like 2 (S. cerevisiae)	204			T -> N (in dbSNP:rs34136143).		2-oxobutyrate biosynthetic process (GO:0046360)|dephosphorylation (GO:0016311)|serine family amino acid catabolic process (GO:0009071)	extracellular space (GO:0005615)	lyase activity (GO:0016829)|pyridoxal phosphate binding (GO:0030170)|serine binding (GO:0070905)			breast(4)|lung(17)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)	27						CCGATCAAGACTGTGTTTGCC	0.552													C|||	221	0.0441294	0.0779	0.0144	5008	,	,		18531	0.005		0.0109	False		,,,				2504	0.0941				p.T204N		Atlas-SNP	.											.	THNSL2	66	.	0			c.C611A						PASS	.	C	ASN/THR	309,4097	166.2+/-197.5	9,291,1903	194.0	174.0	180.0		611	4.1	1.0	2	dbSNP_126	180	82,8518	48.9+/-108.6	0,82,4218	yes	missense	THNSL2	NM_018271.4	65	9,373,6121	AA,AC,CC		0.9535,7.0132,3.0063	benign	204/485	88478341	391,12615	2203	4300	6503	SO:0001583	missense	55258	exon4			TCAAGACTGTGTT		CCDS2002.2, CCDS58718.1, CCDS74539.1	2p11.2	2007-06-20			ENSG00000144115	ENSG00000144115			25602	protein-coding gene	gene with protein product		611261				17034760	Standard	NM_018271		Approved	FLJ10916	uc021vkr.1	Q86YJ6	OTTHUMG00000130314	ENST00000324166.5:c.611C>A	2.37:g.88478341C>A	ENSP00000327323:p.Thr204Asn	188.0	0.0	0		204.0	204.0	1	NM_018271	B3KTB1|B5MDX8|B7WPF8|D9ZZB8|Q6P2M7|Q6PI27|Q9NV54	Missense_Mutation	SNP	ENST00000324166.5	37	CCDS2002.2	54	0.024725274725274724	38	0.07723577235772358	7	0.019337016574585635	0	0.0	9	0.011873350923482849	C	9.986	1.229403	0.22542	0.070132	0.009535	ENSG00000144115	ENST00000358591;ENST00000377254;ENST00000402102;ENST00000449349;ENST00000544063;ENST00000343544;ENST00000324166	T;T;T;T;T;T	0.10860	2.83;2.83;2.83;2.83;2.83;2.83	5.08	4.07	0.47477	Threonine synthase (1);Pyridoxal phosphate-dependent enzyme, beta subunit (2);	0.601847	0.16677	N	0.204129	T	0.00300	0.0009	N	0.03016	-0.435	0.22880	N	0.998614	B;B;B;B	0.11235	0.001;0.0;0.004;0.001	B;B;B;B	0.09377	0.003;0.001;0.001;0.004	T	0.32161	-0.9917	10	0.59425	D	0.04	.	10.4043	0.44248	0.3747:0.6253:0.0:0.0	rs34136143	46;204;172;204	A8K0C1;Q86YJ6;C9JU10;Q86YJ6-2	.;THNS2_HUMAN;.;.	N	204;204;204;172;46;204;204	ENSP00000351402:T204N;ENSP00000366464:T204N;ENSP00000384475:T204N;ENSP00000407553:T172N;ENSP00000339563:T204N;ENSP00000327323:T204N	ENSP00000327323:T204N	T	+	2	0	THNSL2	88259456	0.998000	0.40836	0.951000	0.38953	0.214000	0.24535	4.088000	0.57678	2.553000	0.86117	0.561000	0.74099	ACT	C|0.974;A|0.026	0.026	strong		0.552	THNSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252662.1	NM_018271	
TRIM16	10626	hgsc.bcm.edu	37	17	15532430	15532430	+	Silent	SNP	G	G	A	rs7225221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:15532430G>A	ENST00000578237.1	-	11	2049	c.1194C>T	c.(1192-1194)acC>acT	p.T398T	RP11-385D13.1_ENST00000455584.2_Silent_p.T398T|TRIM16_ENST00000416464.2_Silent_p.T268T|TRIM16_ENST00000579219.1_Missense_Mutation_p.P95L|TRIM16_ENST00000577886.1_Silent_p.T182T|TRIM16_ENST00000336708.7_Silent_p.T398T			O95361	TRI16_HUMAN	tripartite motif containing 16	398	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of retinoic acid receptor signaling pathway (GO:0048386)|positive regulation of transcription, DNA-templated (GO:0045893)|response to growth hormone (GO:0060416)|response to organophosphorus (GO:0046683)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)|PML body (GO:0016605)	DNA binding (GO:0003677)|interleukin-1 binding (GO:0019966)|NACHT domain binding (GO:0032089)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)	19				UCEC - Uterine corpus endometrioid carcinoma (92;0.0839)|Epithelial(1;8.4e-29)|all cancers(1;3.06e-28)|Colorectal(1;1.57e-19)|OV - Ovarian serous cystadenocarcinoma(1;6.1e-17)|COAD - Colon adenocarcinoma(1;3.38e-12)|READ - Rectum adenocarcinoma(2;1.46e-05)|BRCA - Breast invasive adenocarcinoma(8;0.0559)		CCCAGGGCGTGGTGTTGGTGA	0.587													G|||	309	0.0617013	0.2269	0.0115	5008	,	,		19836	0.0		0.001	False		,,,				2504	0.0				p.T398T		Atlas-SNP	.											.	TRIM16	45	.	0			c.C1194T						PASS	.	G		746,3660		67,612,1524	44.0	42.0	43.0		1194	-1.7	0.8	17	dbSNP_116	43	5,8587		0,5,4291	no	coding-synonymous	TRIM16	NM_006470.3		67,617,5815	AA,AG,GG		0.0582,16.9315,5.7778		398/565	15532430	751,12247	2203	4296	6499	SO:0001819	synonymous_variant	10626	exon9			GGGCGTGGTGTTG	AF096870	CCDS11171.1	17p11.2	2011-04-20	2011-01-25		ENSG00000221926	ENSG00000221926		"""Tripartite motif containing / Tripartite motif containing"""	17241	protein-coding gene	gene with protein product	"""estrogen-responsive B box protein"""	609505	"""tripartite motif-containing 16"""			11331580	Standard	NM_006470		Approved	EBBP	uc002gor.1	O95361	OTTHUMG00000059067	ENST00000578237.1:c.1194C>T	17.37:g.15532430G>A		269.0	0.0	0		324.0	142.0	0.438272	NM_006470	Q6IAL8|Q7Z6I2|Q96BE8|Q96J43	Silent	SNP	ENST00000578237.1	37	CCDS11171.1	87	0.03983516483516483	83	0.16869918699186992	4	0.011049723756906077	0	0.0	0	0.0	.	12.03	1.816778	0.32145	0.169315	5.82E-4	ENSG00000251537	ENST00000455584	.	.	.	4.53	-1.68	0.08212	.	.	.	.	.	T	0.00073	0.0002	.	.	.	0.09310	P	0.9999999999999986	.	.	.	.	.	.	T	0.23726	-1.0180	3	.	.	.	.	5.0704	0.14604	0.0891:0.4085:0.378:0.1244	rs7225221	.	.	.	L	413	.	.	P	-	2	0	RP11-385D13.1	15473155	0.983000	0.35010	0.789000	0.31954	0.992000	0.81027	0.170000	0.16663	0.096000	0.17463	0.650000	0.86243	CCA	G|0.953;A|0.047	0.047	strong		0.587	TRIM16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130700.2	NM_006470	
NEFH	4744	hgsc.bcm.edu	37	22	29886341	29886341	+	Silent	SNP	C	C	T	rs61744118	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:29886341C>T	ENST00000310624.6	+	4	2745	c.2712C>T	c.(2710-2712)ccC>ccT	p.P904P		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	910	Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						AAAAAGTCCCCACCCCAGAGA	0.502													C|||	49	0.00978435	0.0363	0.0014	5008	,	,		18928	0.0		0.0	False		,,,				2504	0.0				p.P904P		Atlas-SNP	.											.	NEFH	178	.	0			c.C2712T						PASS	.	C		129,4277	88.7+/-127.4	2,125,2076	55.0	60.0	59.0		2712	-6.6	0.0	22	dbSNP_129	59	0,8600		0,0,4300	no	coding-synonymous	NEFH	NM_021076.3		2,125,6376	TT,TC,CC		0.0,2.9278,0.9918		904/1021	29886341	129,12877	2203	4300	6503	SO:0001819	synonymous_variant	4744	exon4			AGTCCCCACCCCA		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.2712C>T	22.37:g.29886341C>T		140.0	1.0	0.00714286		136.0	135.0	0.992647	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Silent	SNP	ENST00000310624.6	37	CCDS13858.1																																																																																			C|0.990;T|0.010	0.010	strong		0.502	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
SPTA1	6708	hgsc.bcm.edu	37	1	158618320	158618320	+	Silent	SNP	G	G	A	rs34773716	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158618320G>A	ENST00000368147.4	-	26	3873	c.3693C>T	c.(3691-3693)gaC>gaT	p.D1231D		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1231					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					GGGGTACGAGGTCCCTTTCAA	0.498													G|||	134	0.0267572	0.0938	0.013	5008	,	,		14013	0.0		0.001	False		,,,				2504	0.0				p.D1231D		Atlas-SNP	.											SPTA1,NS,carcinoma,-2,1	SPTA1	720	1	0			c.C3693T						PASS	.	G		250,3612		10,230,1691	115.0	116.0	115.0		3693	-0.7	0.4	1	dbSNP_126	115	5,8249		0,5,4122	yes	coding-synonymous	SPTA1	NM_003126.2		10,235,5813	AA,AG,GG		0.0606,6.4733,2.1047		1231/2420	158618320	255,11861	1931	4127	6058	SO:0001819	synonymous_variant	6708	exon26			TACGAGGTCCCTT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.3693C>T	1.37:g.158618320G>A		82.0	0.0	0		80.0	53.0	0.6625	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Silent	SNP	ENST00000368147.4	37	CCDS41423.1																																																																																			G|0.988;A|0.012	0.012	strong		0.498	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
RNF216	54476	hgsc.bcm.edu	37	7	5765034	5765034	+	Silent	SNP	C	C	T	rs77500990	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:5765034C>T	ENST00000425013.2	-	8	1478	c.1254G>A	c.(1252-1254)ctG>ctA	p.L418L	RNF216_ENST00000389902.3_Silent_p.L475L	NM_207111.3|NM_207116.2	NP_996994.1|NP_996999.1	Q9NWF9	RN216_HUMAN	ring finger protein 216	418					apoptotic process (GO:0006915)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|regulation of defense response to virus by host (GO:0050691)|regulation of interferon-beta production (GO:0032648)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)		FBXL18/RNF216(2)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)|skin(1)|urinary_tract(4)	33		Ovarian(82;0.07)		UCEC - Uterine corpus endometrioid carcinoma (126;0.135)|OV - Ovarian serous cystadenocarcinoma(56;2.69e-13)		TTTCTGGTGACAGCTCCTGCC	0.368													c|||	17	0.00339457	0.0129	0.0	5008	,	,		20317	0.0		0.0	False		,,,				2504	0.0				p.L475L		Atlas-SNP	.											.	RNF216	71	.	0			c.G1425A						PASS	.	C	,	52,4354	51.6+/-87.1	0,52,2151	143.0	123.0	130.0		1425,1254	-3.0	1.0	7	dbSNP_131	130	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous,coding-synonymous	RNF216	NM_207111.3,NM_207116.2	,	0,58,6445	TT,TC,CC		0.0698,1.1802,0.4459	,	475/924,418/867	5765034	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	54476	exon8			TGGTGACAGCTCC	AY062174	CCDS34594.1, CCDS34595.1	7p22.1	2014-02-12	2007-08-20		ENSG00000011275	ENSG00000011275		"""RING-type (C3HC4) zinc fingers"""	21698	protein-coding gene	gene with protein product		609948					Standard	NM_207111		Approved	TRIAD3, UBCE7IP1, ZIN	uc003sox.2	Q9NWF9	OTTHUMG00000155500	ENST00000425013.2:c.1254G>A	7.37:g.5765034C>T		144.0	0.0	0		150.0	79.0	0.526667	NM_207111	Q6Y691|Q75ML7|Q7Z2H7|Q7Z7C1|Q8NHW7|Q9NYT1	Silent	SNP	ENST00000425013.2	37	CCDS34595.1																																																																																			C|0.996;T|0.004	0.004	strong		0.368	RNF216-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000340374.1	NM_207111	
OR51F1	256892	hgsc.bcm.edu	37	11	4790868	4790868	+	Missense_Mutation	SNP	T	T	C	rs75972277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:4790868T>C	ENST00000380383.1	-	1	300	c.301A>G	c.(301-303)Atc>Gtc	p.I101V	MMP26_ENST00000477339.1_Intron|OR51F1_ENST00000343430.3_Missense_Mutation_p.I94V|MMP26_ENST00000380390.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	101						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	22		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.0778)		Epithelial(150;5.87e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0045)|LUSC - Lung squamous cell carcinoma(625;0.192)		TATAGACTGATTTCACGTGCC	0.428													T|||	230	0.0459265	0.1649	0.0159	5008	,	,		22485	0.0		0.001	False		,,,				2504	0.0				p.I94V		Atlas-SNP	.											.	OR51F1	60	.	0			c.A280G						PASS	.	T	VAL/ILE	655,3747	277.2+/-273.6	49,557,1595	78.0	75.0	76.0		280	1.3	0.2	11	dbSNP_132	76	12,8584	7.7+/-29.5	0,12,4286	yes	missense	OR51F1	NM_001004752.1	29	49,569,5881	CC,CT,TT		0.1396,14.8796,5.1316	probably-damaging	94/313	4790868	667,12331	2201	4298	6499	SO:0001583	missense	256892	exon1			GACTGATTTCACG	BK004771	CCDS31359.1	11p15.4	2012-08-09		2004-03-10	ENSG00000188069	ENSG00000188069		"""GPCR / Class A : Olfactory receptors"""	15196	protein-coding gene	gene with protein product				OR51F1P			Standard	NM_001004752		Approved		uc010qyl.2	A6NGY5	OTTHUMG00000066503	ENST00000380383.1:c.301A>G	11.37:g.4790868T>C	ENSP00000369744:p.Ile101Val	83.0	0.0	0		83.0	33.0	0.39759	NM_001004752		Missense_Mutation	SNP	ENST00000380383.1	37		96	0.04395604395604396	91	0.18495934959349594	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	t	14.41	2.525656	0.44969	0.148796	0.001396	ENSG00000188069	ENST00000343430;ENST00000380383	T;T	0.00590	6.36;6.36	4.91	1.3	0.21679	GPCR, rhodopsin-like superfamily (1);	0.114787	0.38381	N	0.001718	T	0.00012	0.0000	M	0.87097	2.86	0.24681	N	0.993366	D	0.67145	0.996	D	0.80764	0.994	T	0.45527	-0.9255	10	0.46703	T	0.11	.	8.2938	0.31973	0.0:0.2382:0.0:0.7618	.	101	A6NGY5	O51F1_HUMAN	V	94;101	ENSP00000345163:I94V;ENSP00000369744:I101V	ENSP00000345163:I94V	I	-	1	0	OR51F1	4747444	0.937000	0.31787	0.237000	0.24090	0.676000	0.39594	1.729000	0.38115	0.058000	0.16222	0.473000	0.43528	ATC	T|0.955;C|0.045	0.045	strong		0.428	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
TMPRSS15	5651	hgsc.bcm.edu	37	21	19704422	19704422	+	Missense_Mutation	SNP	T	T	A	rs8134187	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:19704422T>A	ENST00000284885.3	-	14	1666	c.1633A>T	c.(1633-1635)Agc>Tgc	p.S545C		NM_002772.2	NP_002763	P98073	ENTK_HUMAN	transmembrane protease, serine 15	545	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.		S -> C (in dbSNP:rs8134187).			brush border (GO:0005903)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(7)|large_intestine(19)|lung(36)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	85						TTAGGGTAGCTGTTTGGAAAG	0.428													T|||	277	0.0553115	0.202	0.0115	5008	,	,		17236	0.0		0.002	False		,,,				2504	0.0				p.S545C		Atlas-SNP	.											.	TMPRSS15	189	.	0			c.A1633T						PASS	.	T	CYS/SER	707,3699	295.9+/-283.9	60,587,1556	148.0	149.0	149.0		1633	1.7	0.7	21	dbSNP_116	149	2,8598	2.2+/-6.3	0,2,4298	yes	missense	TMPRSS15	NM_002772.2	112	60,589,5854	AA,AT,TT		0.0233,16.0463,5.4513	probably-damaging	545/1020	19704422	709,12297	2203	4300	6503	SO:0001583	missense	5651	exon14			GGTAGCTGTTTGG		CCDS13571.1	21q21	2010-12-09	2010-04-21	2010-04-21	ENSG00000154646	ENSG00000154646		"""Serine peptidases / Transmembrane"""	9490	protein-coding gene	gene with protein product	"""proenterokinase"", ""enteropeptidase"""	606635	"""protease, serine, 7 (enterokinase)"""	PRSS7		8052624	Standard	NM_002772		Approved	ENTK, MGC133046	uc002ykw.3	P98073	OTTHUMG00000074518	ENST00000284885.3:c.1633A>T	21.37:g.19704422T>A	ENSP00000284885:p.Ser545Cys	65.0	0.0	0		79.0	37.0	0.468354	NM_002772	Q2NKL7	Missense_Mutation	SNP	ENST00000284885.3	37	CCDS13571.1	80	0.03663003663003663	73	0.1483739837398374	6	0.016574585635359115	0	0.0	1	0.0013192612137203166	T	17.24	3.338863	0.60963	0.160463	2.33E-4	ENSG00000154646	ENST00000284885	T	0.19669	2.13	5.43	1.7	0.24286	CUB (5);	0.918548	0.09459	N	0.799265	T	0.00210	0.0006	M	0.86502	2.82	0.47094	P	6.829999999999892E-4	D	0.63046	0.992	P	0.57101	0.813	T	0.04373	-1.0956	8	.	.	.	.	8.8856	0.35400	0.0:0.2218:0.0:0.7782	rs8134187;rs52812192;rs8134187	545	P98073	ENTK_HUMAN	C	545	ENSP00000284885:S545C	.	S	-	1	0	TMPRSS15	18626293	0.208000	0.23494	0.691000	0.30163	0.977000	0.68977	0.449000	0.21744	0.107000	0.17824	-0.263000	0.10527	AGC	T|0.954;A|0.046	0.046	strong		0.428	TMPRSS15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158231.2	NM_002772	
ENGASE	64772	hgsc.bcm.edu	37	17	77079854	77079854	+	Silent	SNP	A	A	G	rs61729127	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:77079854A>G	ENST00000579016.1	+	10	1263	c.1263A>G	c.(1261-1263)gtA>gtG	p.V421V	ENGASE_ENST00000584568.1_3'UTR	NM_001042573.2	NP_001036038.1	Q8NFI3	ENASE_HUMAN	endo-beta-N-acetylglucosaminidase	421						cytoplasm (GO:0005737)	mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase activity (GO:0033925)			breast(2)|endometrium(4)|large_intestine(1)|lung(15)|prostate(2)|skin(1)	25						AAGAGGCGGTAGGGCCCTGGT	0.652													G|||	405	0.0808706	0.2912	0.0231	5008	,	,		17851	0.0		0.003	False		,,,				2504	0.001				p.V421V		Atlas-SNP	.											.	ENGASE	55	.	0			c.A1263G						PASS	.	G		847,3141		93,661,1240	50.0	59.0	56.0		1263	4.9	0.9	17	dbSNP_129	56	31,8303		0,31,4136	no	coding-synonymous	ENGASE	NM_001042573.1		93,692,5376	GG,GA,AA		0.372,21.2387,7.1255		421/744	77079854	878,11444	1994	4167	6161	SO:0001819	synonymous_variant	64772	exon10			GGCGGTAGGGCCC	AF512564	CCDS42394.1	17q25.3	2009-03-03			ENSG00000167280	ENSG00000167280	3.2.1.96		24622	protein-coding gene	gene with protein product	"""Mannosyl-glycoprotein endo-beta-N-acetylglucosaminidase"", ""Di-N-acetylchitobiosyl beta-N-acetylglucosaminidase"""	611898				12114544, 18586680	Standard	NM_001042573		Approved	FLJ21865	uc002jwv.4	Q8NFI3	OTTHUMG00000167714	ENST00000579016.1:c.1263A>G	17.37:g.77079854A>G		63.0	0.0	0		85.0	46.0	0.541176	NM_001042573	Q659F0|Q8TB86|Q9H6U4	Silent	SNP	ENST00000579016.1	37	CCDS42394.1																																																																																			A|0.956;G|0.044	0.044	strong		0.652	ENGASE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395807.1	NM_022759	
HAGH	3029	hgsc.bcm.edu	37	16	1869907	1869907	+	Silent	SNP	G	G	A	rs17849371	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1869907G>A	ENST00000397356.3	-	4	829	c.423C>T	c.(421-423)tcC>tcT	p.S141S	HAGH_ENST00000566709.1_Silent_p.S93S|HAGH_ENST00000455446.2_Silent_p.S141S|HAGH_ENST00000397353.2_Silent_p.S93S	NM_005326.4	NP_005317.2	Q16775	GLO2_HUMAN	hydroxyacylglutathione hydrolase	141					glutathione biosynthetic process (GO:0006750)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxyacylglutathione hydrolase activity (GO:0004416)|zinc ion binding (GO:0008270)			kidney(2)|lung(1)|ovary(1)|skin(1)	5		Hepatocellular(780;0.00335)			Glutathione(DB00143)	CCTGCAGTGTGGACAGGTGAG	0.627													G|||	218	0.0435304	0.1528	0.0173	5008	,	,		16762	0.0		0.004	False		,,,				2504	0.0				p.S141S	Pancreas(55;1048 1176 25227 40124 41333)	Atlas-SNP	.											.	HAGH	20	.	0			c.C423T						PASS	.	G	,	574,3824	251.5+/-258.2	41,492,1666	104.0	82.0	90.0		279,423	-1.1	0.5	16	dbSNP_123	90	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous,coding-synonymous	HAGH	NM_001040427.1,NM_005326.4	,	41,499,5959	AA,AG,GG		0.0814,13.0514,4.4699	,	93/261,141/309	1869907	581,12417	2199	4300	6499	SO:0001819	synonymous_variant	3029	exon4			CAGTGTGGACAGG	X90999	CCDS32366.1, CCDS10447.2, CCDS66900.1	16p13.3	2012-10-02	2003-11-04		ENSG00000063854	ENSG00000063854	3.1.2.6		4805	protein-coding gene	gene with protein product		138760	"""hydroxyacyl glutathione hydrolase"""			3025077, 7327557	Standard	NM_001286249		Approved	GLO2, GLXII, HAGH1	uc002cna.3	Q16775	OTTHUMG00000128662	ENST00000397356.3:c.423C>T	16.37:g.1869907G>A		84.0	0.0	0		78.0	28.0	0.358974	NM_005326	A8K290|B4DP33|B4DRA7|E7EN93	Silent	SNP	ENST00000397356.3	37	CCDS10447.2																																																																																			G|0.958;A|0.042	0.042	strong		0.627	HAGH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250548.2	NM_005326	
C14orf80	283643	hgsc.bcm.edu	37	14	105957446	105957446	+	5'Flank	SNP	G	G	A	rs76864584	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105957446G>A	ENST00000392523.4	+	0	0				C14orf80_ENST00000329886.7_Missense_Mutation_p.G3S|C14orf80_ENST00000551054.1_3'UTR|C14orf80_ENST00000392527.1_Missense_Mutation_p.G3S|CRIP1_ENST00000551180.1_3'UTR|C14orf80_ENST00000334656.7_Missense_Mutation_p.G3S|C14orf80_ENST00000392522.3_5'Flank|C14orf80_ENST00000354560.6_5'Flank|C14orf80_ENST00000450383.1_5'Flank			Q86SX3	CN080_HUMAN	chromosome 14 open reading frame 80											central_nervous_system(1)	1		Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0188)	Epithelial(152;0.239)		ATGCATGTCCGGCCAGCGCGG	0.627													G|||	273	0.0545128	0.202	0.0086	5008	,	,		12847	0.0		0.0	False		,,,				2504	0.0				p.G3S		Atlas-SNP	.											.	C14orf80	19	.	0			c.G7A						PASS	.						115.0	102.0	106.0					14																	105957446		692	1591	2283	SO:0001631	upstream_gene_variant	283643	exon2			ATGTCCGGCCAGC		CCDS45180.1, CCDS45181.1, CCDS45182.1, CCDS55955.1	14q32.33	2012-09-25			ENSG00000185347	ENSG00000185347			20127	protein-coding gene	gene with protein product							Standard	NM_001134875		Approved		uc001yrn.3	Q86SX3	OTTHUMG00000170426		14.37:g.105957446G>A	Exception_encountered	117.0	0.0	0		168.0	91.0	0.541667	NM_001134877	B5MDG3|E9PAQ4|Q86TT3|Q86TT4|Q86TT5|Q96B41|Q9H7H4	Missense_Mutation	SNP	ENST00000392523.4	37		96	0.04395604395604396	91	0.18495934959349594	5	0.013812154696132596	0	0.0	0	0.0	G	12.89	2.073301	0.36566	.	.	ENSG00000185347	ENST00000329886;ENST00000427614;ENST00000455454;ENST00000432805;ENST00000392527;ENST00000443229;ENST00000334656	.	.	.	1.43	0.424	0.16468	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	D;D	0.62365	0.991;0.991	P;P	0.45610	0.487;0.487	T	0.17471	-1.0368	7	0.87932	D	0	.	6.8588	0.24056	0.0:0.0:0.7222:0.2778	.	3;3	B5MDG3;Q86SX3-3	.;.	S	3	.	ENSP00000333010:G3S	G	+	1	0	C14orf80	105028491	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.549000	0.02182	-0.096000	0.12329	-0.708000	0.03648	GGC	G|0.956;A|0.044	0.044	strong		0.627	C14orf80-017	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409090.1	NM_001134875	
OR2T4	127074	hgsc.bcm.edu	37	1	248524974	248524974	+	Missense_Mutation	SNP	A	A	G	rs57795102	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248524974A>G	ENST00000366475.1	+	1	92	c.92A>G	c.(91-93)aAt>aGt	p.N31S		NM_001004696.1	NP_001004696.1	Q8NH00	OR2T4_HUMAN	olfactory receptor, family 2, subfamily T, member 4	31			N -> S (in dbSNP:rs57795102).			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)|kidney(2)|large_intestine(3)|liver(2)|lung(47)	56	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CCAATGGCCAATATCACCTGG	0.478													a|||	348	0.0694888	0.2337	0.0331	5008	,	,		15454	0.002		0.0109	False		,,,				2504	0.0031				p.N31S		Atlas-SNP	.											OR2T4,NS,adenocarcinoma,-1,1	OR2T4	126	1	0			c.A92G						PASS	.	A	SER/ASN	939,3461		137,665,1398	112.0	96.0	102.0		92	0.2	0.1	1	dbSNP_129	102	98,8342		12,74,4134	yes	missense	OR2T4	NM_001004696.1	46	149,739,5532	GG,GA,AA		1.1611,21.3409,8.0763	benign	31/349	248524974	1037,11803	2200	4220	6420	SO:0001583	missense	127074	exon1			TGGCCAATATCAC	BK004464	CCDS31113.1	1q44	2012-08-09			ENSG00000196944	ENSG00000196944		"""GPCR / Class A : Olfactory receptors"""	15016	protein-coding gene	gene with protein product							Standard	NM_001004696		Approved	OR2T4Q	uc001ieh.1	Q8NH00	OTTHUMG00000040453	ENST00000366475.1:c.92A>G	1.37:g.248524974A>G	ENSP00000355431:p.Asn31Ser	775.0	1.0	0.00129032		800.0	387.0	0.48375	NM_001004696	Q6IEZ8	Missense_Mutation	SNP	ENST00000366475.1	37	CCDS31113.1	149	0.06822344322344322	130	0.26422764227642276	10	0.027624309392265192	0	0.0	9	0.011873350923482849	A	3.277	-0.147841	0.06627	0.213409	0.011611	ENSG00000196944	ENST00000366475	T	0.36340	1.26	0.189	0.189	0.15119	.	1.272670	0.05590	N	0.574537	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.11235	0.004	B	0.09377	0.004	T	0.34428	-0.9829	8	0.25751	T	0.34	.	.	.	.	rs57795102	31	Q8NH00	OR2T4_HUMAN	S	31	ENSP00000355431:N31S	ENSP00000355431:N31S	N	+	2	0	OR2T4	246591597	0.000000	0.05858	0.062000	0.19696	0.036000	0.12997	-0.514000	0.06298	0.250000	0.21479	0.248000	0.18094	AAT	A|0.925;G|0.075	0.075	strong		0.478	OR2T4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097349.2	NM_001004696	
CEP162	22832	hgsc.bcm.edu	37	6	84856409	84856409	+	Silent	SNP	T	T	C	rs9449804	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:84856409T>C	ENST00000403245.3	-	25	3981	c.3867A>G	c.(3865-3867)aaA>aaG	p.K1289K	KIAA1009_ENST00000461137.1_5'UTR|KIAA1009_ENST00000257766.4_Silent_p.K1213K	NM_014895.2	NP_055710.2														breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(17)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	43		all_cancers(76;1.5e-06)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00258)		BRCA - Breast invasive adenocarcinoma(397;0.089)		TTCTTACCTCTTTCTGTAGAA	0.308													T|||	454	0.090655	0.2973	0.036	5008	,	,		16911	0.006		0.0169	False		,,,				2504	0.0133				p.K1289K		Atlas-SNP	.											.	KIAA1009	119	.	0			c.A3867G						PASS	.	T		1113,3285		164,785,1250	32.0	32.0	32.0		3867	-4.6	0.9	6	dbSNP_119	32	131,8451		6,119,4166	no	coding-synonymous	KIAA1009	NM_014895.2		170,904,5416	CC,CT,TT		1.5265,25.307,9.584		1289/1404	84856409	1244,11736	2199	4291	6490	SO:0001819	synonymous_variant	22832	exon25			TACCTCTTTCTGT																												ENST00000403245.3:c.3867A>G	6.37:g.84856409T>C		65.0	0.0	0		54.0	25.0	0.462963	NM_014895		Silent	SNP	ENST00000403245.3	37	CCDS34494.2																																																																																			T|0.900;C|0.100	0.100	strong		0.308	KIAA1009-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317315.1		
NEB	4703	hgsc.bcm.edu	37	2	152547268	152547268	+	Silent	SNP	G	G	A	rs373946448	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:152547268G>A	ENST00000172853.10	-	24	2430	c.2283C>T	c.(2281-2283)gcC>gcT	p.A761A	NEB_ENST00000427231.2_Silent_p.A761A|NEB_ENST00000397345.3_Silent_p.A761A|NEB_ENST00000604864.1_Silent_p.A761A|NEB_ENST00000603639.1_Silent_p.A761A|NEB_ENST00000409198.1_Silent_p.A761A			P20929	NEBU_HUMAN	nebulin	761					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)		TGTTGAGCTGGGCTTGCAACA	0.398													G|||	3	0.000599042	0.0023	0.0	5008	,	,		18181	0.0		0.0	False		,,,				2504	0.0				p.A761A		Atlas-SNP	.											.	NEB	1697	.	0			c.C2283T						PASS	.	G	,,	11,3913		0,11,1951	112.0	112.0	112.0		2283,2283,2283	0.6	1.0	2		112	0,8302		0,0,4151	no	coding-synonymous,coding-synonymous,coding-synonymous	NEB	NM_001164507.1,NM_001164508.1,NM_004543.4	,,	0,11,6102	AA,AG,GG		0.0,0.2803,0.09	,,	761/8526,761/8526,761/6670	152547268	11,12215	1962	4151	6113	SO:0001819	synonymous_variant	4703	exon24			GAGCTGGGCTTGC	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.2283C>T	2.37:g.152547268G>A		164.0	0.0	0		170.0	91.0	0.535294	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Silent	SNP	ENST00000172853.10	37																																																																																				.	.	weak		0.398	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
VWF	7450	hgsc.bcm.edu	37	12	6094249	6094249	+	Missense_Mutation	SNP	C	C	T	rs62641242	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:6094249C>T	ENST00000261405.5	-	40	7192	c.6938G>A	c.(6937-6939)cGc>cAc	p.R2313H		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	2313	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	TGCATTCTGGCGGAGGCGGGC	0.597													C|||	5	0.000998403	0.0015	0.0014	5008	,	,		17767	0.0		0.002	False		,,,				2504	0.0				p.R2313H		Atlas-SNP	.											.	VWF	338	.	0			c.G6938A	GRCh37	CM070320	VWF	M	rs62641242	PASS	.	C	HIS/ARG	3,4403	6.2+/-15.9	0,3,2200	92.0	88.0	89.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	6938	-2.6	0.1	12	dbSNP_129	89	1,8599	1.2+/-3.3	0,1,4299	yes	missense	VWF	NM_000552.3	29	0,4,6499	TT,TC,CC		0.0116,0.0681,0.0308	possibly-damaging	2313/2814	6094249	4,13002	2203	4300	6503	SO:0001583	missense	7450	exon40			TTCTGGCGGAGGC		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.6938G>A	12.37:g.6094249C>T	ENSP00000261405:p.Arg2313His	128.0	0.0	0		154.0	82.0	0.532468	NM_000552	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	3	0.0013736263736263737	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	6.785	0.513843	0.12944	6.81E-4	1.16E-4	ENSG00000110799	ENST00000261405	T	0.36699	1.24	5.33	-2.61	0.06171	von Willebrand factor, type C (3);	1.093970	0.07212	N	0.859422	T	0.22003	0.0530	N	0.14661	0.345	0.26288	N	0.978165	B	0.17268	0.021	B	0.12837	0.008	T	0.27739	-1.0065	10	0.38643	T	0.18	.	11.7285	0.51722	0.0:0.3397:0.0:0.6603	rs62641242	2313	P04275	VWF_HUMAN	H	2313	ENSP00000261405:R2313H	ENSP00000261405:R2313H	R	-	2	0	VWF	5964510	0.001000	0.12720	0.067000	0.19924	0.135000	0.20990	-0.426000	0.07008	-0.496000	0.06650	0.561000	0.74099	CGC	C|0.999;T|0.001	0.001	strong		0.597	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
IL21R	50615	hgsc.bcm.edu	37	16	27460437	27460437	+	Missense_Mutation	SNP	G	G	A	rs3093386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27460437G>A	ENST00000337929.3	+	9	1923	c.1450G>A	c.(1450-1452)Ggc>Agc	p.G484S	IL21R-AS1_ENST00000563191.1_RNA|IL21R_ENST00000564089.1_Missense_Mutation_p.G484S|IL21R_ENST00000395754.4_Missense_Mutation_p.G484S|IL21R_ENST00000395755.1_Missense_Mutation_p.G484S	NM_181078.2	NP_851564.1	Q9HBE5	IL21R_HUMAN	interleukin 21 receptor	484			G -> S (in dbSNP:rs3093386). {ECO:0000269|Ref.4}.		interleukin-21-mediated signaling pathway (GO:0038114)|natural killer cell activation (GO:0030101)	integral component of membrane (GO:0016021)	interleukin-21 receptor activity (GO:0001532)			breast(2)|large_intestine(3)|lung(1)|ovary(2)	8						ACCCCTGGCCGGCCTGGATAT	0.677			T	BCL6	NHL								G|||	180	0.0359425	0.1324	0.0058	5008	,	,		18816	0.0		0.001	False		,,,				2504	0.0				p.G506S		Atlas-SNP	.		Dom	yes		16	16p11	50615	interleukin 21 receptor		L	.	IL21R	95	.	0			c.G1516A						PASS	.	G	SER/GLY,SER/GLY,SER/GLY	415,3979		26,363,1808	42.0	39.0	40.0		1450,1450,1516	2.6	0.9	16	dbSNP_103	40	3,8597		0,3,4297	yes	missense,missense,missense	IL21R	NM_021798.3,NM_181078.2,NM_181079.4	56,56,56	26,366,6105	AA,AG,GG		0.0349,9.4447,3.2169	benign,benign,benign	484/539,484/539,506/561	27460437	418,12576	2197	4300	6497	SO:0001583	missense	50615	exon10			CTGGCCGGCCTGG	AF254067	CCDS10630.1	16p11	2014-09-17			ENSG00000103522	ENSG00000103522		"""Interleukins and interleukin receptors"", ""CD molecules"""	6006	protein-coding gene	gene with protein product		605383				11081504	Standard	NM_181078		Approved	CD360	uc002dos.2	Q9HBE5	OTTHUMG00000131675	ENST00000337929.3:c.1450G>A	16.37:g.27460437G>A	ENSP00000338010:p.Gly484Ser	103.0	0.0	0		112.0	58.0	0.517857	NM_181079	A8K9E8|D3DWF7|Q96HZ1|Q9HB91	Missense_Mutation	SNP	ENST00000337929.3	37	CCDS10630.1	64	0.029304029304029304	59	0.11991869918699187	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	14.35	2.509511	0.44660	0.094447	3.49E-4	ENSG00000103522	ENST00000337929;ENST00000395755;ENST00000395754	T;T;T	0.15952	2.38;2.38;2.38	4.9	2.64	0.31445	.	0.231408	0.37437	N	0.002082	T	0.00144	0.0004	L	0.50919	1.6	0.29586	N	0.848826	P	0.42357	0.777	B	0.30179	0.112	T	0.16512	-1.0400	10	0.15952	T	0.53	-30.5288	4.0671	0.09866	0.124:0.0:0.6404:0.2356	rs3093386;rs61328560;rs3093386	484	Q9HBE5	IL21R_HUMAN	S	484	ENSP00000338010:G484S;ENSP00000379104:G484S;ENSP00000379103:G484S	ENSP00000338010:G484S	G	+	1	0	IL21R	27367938	0.055000	0.20627	0.916000	0.36221	0.741000	0.42261	0.087000	0.14958	2.271000	0.75665	0.561000	0.74099	GGC	G|0.962;A|0.038	0.038	strong		0.677	IL21R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254578.2	NM_181078	
ALDH3A2	224	hgsc.bcm.edu	37	17	19559770	19559770	+	Missense_Mutation	SNP	C	C	T	rs115977487	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:19559770C>T	ENST00000176643.6	+	4	1009	c.563C>T	c.(562-564)gCg>gTg	p.A188V	ALDH3A2_ENST00000339618.4_Missense_Mutation_p.A188V|ALDH3A2_ENST00000395575.2_Missense_Mutation_p.A188V|ALDH3A2_ENST00000581518.1_Missense_Mutation_p.A188V|ALDH3A2_ENST00000579855.1_Missense_Mutation_p.A188V			P51648	AL3A2_HUMAN	aldehyde dehydrogenase 3 family, member A2	188					cellular aldehyde metabolic process (GO:0006081)|central nervous system development (GO:0007417)|epidermis development (GO:0008544)|oxidation-reduction process (GO:0055114)|peripheral nervous system development (GO:0007422)|phytol metabolic process (GO:0033306)|sesquiterpenoid metabolic process (GO:0006714)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)|peroxisome (GO:0005777)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|long-chain-alcohol oxidase activity (GO:0046577)|long-chain-aldehyde dehydrogenase activity (GO:0050061)|medium-chain-aldehyde dehydrogenase activity (GO:0052814)			endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(2)|ovary(2)|prostate(1)	13	all_cancers(12;1.39e-05)|all_epithelial(12;0.00158)|Breast(13;0.245)					GGAAACACTGCGGTTGGCAAA	0.438													C|||	67	0.0133786	0.0499	0.0014	5008	,	,		21110	0.0		0.0	False		,,,				2504	0.0				p.A188V		Atlas-SNP	.											.	ALDH3A2	41	.	0			c.C563T						PASS	.	C	VAL/ALA,VAL/ALA	141,4265	101.2+/-139.8	3,135,2065	115.0	108.0	111.0		563,563	1.2	0.0	17	dbSNP_132	111	0,8600		0,0,4300	yes	missense,missense	ALDH3A2	NM_000382.2,NM_001031806.1	64,64	3,135,6365	TT,TC,CC		0.0,3.2002,1.0841	benign,benign	188/486,188/509	19559770	141,12865	2203	4300	6503	SO:0001583	missense	224	exon4			ACACTGCGGTTGG	L47162	CCDS11210.1, CCDS32589.1	17p11.2	2010-05-07			ENSG00000072210	ENSG00000072210	1.2.1.3	"""Aldehyde dehydrogenases"""	403	protein-coding gene	gene with protein product	"""fatty aldehyde dehydrogenase"""	609523		SLS, ALDH10		7894487	Standard	NM_000382		Approved	FALDH	uc002gwa.1	P51648	OTTHUMG00000059471	ENST00000176643.6:c.563C>T	17.37:g.19559770C>T	ENSP00000176643:p.Ala188Val	219.0	1.0	0.00456621		265.0	135.0	0.509434	NM_001031806	Q6I9T3|Q93011|Q96J37	Missense_Mutation	SNP	ENST00000176643.6	37	CCDS11210.1	24	0.01098901098901099	24	0.04878048780487805	0	0.0	0	0.0	0	0.0	C	5.442	0.266672	0.10294	0.032002	0.0	ENSG00000072210	ENST00000176643;ENST00000395575;ENST00000339618	D;D;D	0.85484	-1.99;-1.99;-1.99	5.71	1.24	0.21308	Aldehyde dehydrogenase domain (1);Aldehyde dehydrogenase, N-terminal (1);Aldehyde/histidinol dehydrogenase (1);	0.860604	0.10663	N	0.648524	T	0.40791	0.1131	M	0.68317	2.08	0.09310	N	1	P;P	0.44044	0.825;0.79	B;B	0.34873	0.191;0.12	T	0.53878	-0.8376	10	0.31617	T	0.26	-0.0192	4.0327	0.09716	0.1051:0.5293:0.2073:0.1584	.	188;188	P51648;P51648-2	AL3A2_HUMAN;.	V	188	ENSP00000176643:A188V;ENSP00000378942:A188V;ENSP00000345774:A188V	ENSP00000176643:A188V	A	+	2	0	ALDH3A2	19500362	0.000000	0.05858	0.000000	0.03702	0.106000	0.19336	0.212000	0.17497	0.336000	0.23639	0.467000	0.42956	GCG	C|0.990;T|0.010	0.010	strong		0.438	ALDH3A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132268.1		
DDX51	317781	hgsc.bcm.edu	37	12	132628285	132628285	+	Silent	SNP	G	G	A	rs191101265	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132628285G>A	ENST00000397333.3	-	2	512	c.474C>T	c.(472-474)gtC>gtT	p.V158V	NOC4L_ENST00000330579.1_5'Flank	NM_175066.3	NP_778236.2	Q8N8A6	DDX51_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 51	158					rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(1)|lung(5)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.59e-08)|Epithelial(86;3.62e-07)|all cancers(50;2.13e-05)		CCAGGCCGGGGACCAGGGGTC	0.761													g|||	215	0.0429313	0.0492	0.0043	5008	,	,		10654	0.0476		0.0219	False		,,,				2504	0.0787				p.V158V		Atlas-SNP	.											.	DDX51	33	.	0			c.C474T						PASS	.			71,2853		0,71,1391	3.0	4.0	3.0		474	-1.3	0.0	12		3	17,6853		0,17,3418	no	coding-synonymous	DDX51	NM_175066.3		0,88,4809	AA,AG,GG		0.2475,2.4282,0.8985		158/667	132628285	88,9706	1462	3435	4897	SO:0001819	synonymous_variant	317781	exon2			GCCGGGGACCAGG	BC040185	CCDS41865.1	12q24.33	2005-10-12				ENSG00000185163		"""DEAD-boxes"""	20082	protein-coding gene	gene with protein product							Standard	NM_175066		Approved		uc001ujy.4	Q8N8A6		ENST00000397333.3:c.474C>T	12.37:g.132628285G>A		8.0	0.0	0		16.0	6.0	0.375	NM_175066	A8MPT9|Q5CZ71|Q8IXK5|Q96ED1	Silent	SNP	ENST00000397333.3	37	CCDS41865.1																																																																																			G|0.968;A|0.032	0.032	strong		0.761	DDX51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398978.1	NM_175066	
TTPAL	79183	hgsc.bcm.edu	37	20	43117986	43117986	+	Missense_Mutation	SNP	C	C	G	rs59069332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43117986C>G	ENST00000372904.3	+	6	976	c.833C>G	c.(832-834)gCt>gGt	p.A278G	TTPAL_ENST00000372906.2_3'UTR|TTPAL_ENST00000262605.4_Missense_Mutation_p.A278G	NM_024331.4	NP_077307.2	Q9BTX7	TTPAL_HUMAN	tocopherol (alpha) transfer protein-like	278	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.		A -> G (in dbSNP:rs59069332).			intracellular (GO:0005622)|membrane (GO:0016020)	transporter activity (GO:0005215)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|ovary(2)|skin(5)	18						GGGGGCACGGCTGGGGAGCTG	0.527													C|||	125	0.0249601	0.0923	0.0043	5008	,	,		20272	0.0		0.0	False		,,,				2504	0.0				p.A278G		Atlas-SNP	.											.	TTPAL	31	.	0			c.C833G						PASS	.	C	GLY/ALA,GLY/ALA	308,4098	166.2+/-197.5	16,276,1911	67.0	64.0	65.0		833,833	6.2	0.3	20	dbSNP_129	65	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	TTPAL	NM_001039199.1,NM_024331.3	60,60	16,278,6209	GG,GC,CC		0.0233,6.9905,2.3835	benign,benign	278/343,278/343	43117986	310,12696	2203	4300	6503	SO:0001583	missense	79183	exon5			GCACGGCTGGGGA	BC003071	CCDS13332.2	20q13.12	2008-06-23	2008-06-23	2008-06-23	ENSG00000124120	ENSG00000124120			16114	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 121"""	C20orf121			Standard	NM_024331		Approved	dJ179M20.3	uc002xmd.2	Q9BTX7	OTTHUMG00000032536	ENST00000372904.3:c.833C>G	20.37:g.43117986C>G	ENSP00000361995:p.Ala278Gly	125.0	0.0	0		144.0	83.0	0.576389	NM_001039199	E1P5X3|Q5QPC1|Q9H1G2|Q9NQG8	Missense_Mutation	SNP	ENST00000372904.3	37	CCDS13332.2	43	0.019688644688644688	41	0.08333333333333333	2	0.0055248618784530384	0	0.0	0	0.0	C	13.21	2.168458	0.38315	0.069905	2.33E-4	ENSG00000124120	ENST00000262605;ENST00000372904;ENST00000456317	D;D;D	0.84516	-1.86;-1.86;-1.86	6.17	6.17	0.99709	Cellular retinaldehyde-binding/triple function, C-terminal (4);	0.045191	0.85682	D	0.000000	T	0.24236	0.0587	N	0.03016	-0.435	0.80722	D	1	D;D	0.71674	0.998;0.982	P;P	0.62089	0.898;0.505	T	0.70174	-0.4944	10	0.21540	T	0.41	-16.9013	20.8794	0.99867	0.0:1.0:0.0:0.0	rs59069332	215;278	B2RA57;Q9BTX7	.;TTPAL_HUMAN	G	278;278;244	ENSP00000262605:A278G;ENSP00000361995:A278G;ENSP00000412720:A244G	ENSP00000262605:A278G	A	+	2	0	TTPAL	42551400	1.000000	0.71417	0.336000	0.25522	0.456000	0.32438	5.874000	0.69652	2.941000	0.99782	0.655000	0.94253	GCT	C|0.976;G|0.024	0.024	strong		0.527	TTPAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106886.2	NM_024331	
CSMD1	64478	hgsc.bcm.edu	37	8	3432586	3432586	+	Silent	SNP	T	T	G	rs146006696	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:3432586T>G	ENST00000520002.1	-	11	1783	c.1228A>C	c.(1228-1230)Aga>Cga	p.R410R	CSMD1_ENST00000537824.1_Silent_p.R409R|CSMD1_ENST00000539096.1_Silent_p.R409R|CSMD1_ENST00000400186.3_Silent_p.R410R|CSMD1_ENST00000602557.1_Silent_p.R410R|CSMD1_ENST00000602723.1_Silent_p.R410R|CSMD1_ENST00000542608.1_Silent_p.R409R			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	410						integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CCACATGTTCTCGCTGGAAAC	0.413													T|||	54	0.0107827	0.0393	0.0029	5008	,	,		20627	0.0		0.0	False		,,,				2504	0.0				p.R409R		Atlas-SNP	.											.	CSMD1	1469	.	0			c.A1225C						PASS	.	T		97,3963		2,93,1935	60.0	68.0	65.0		1225	2.6	0.8	8	dbSNP_134	65	0,8358		0,0,4179	no	coding-synonymous	CSMD1	NM_033225.5		2,93,6114	GG,GT,TT		0.0,2.3892,0.7811		409/3565	3432586	97,12321	2030	4179	6209	SO:0001819	synonymous_variant	64478	exon10			ATGTTCTCGCTGG			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.1228A>C	8.37:g.3432586T>G		60.0	0.0	0		75.0	31.0	0.413333	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Silent	SNP	ENST00000520002.1	37																																																																																				T|0.988;G|0.012	0.012	strong		0.413	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
SCN4A	6329	hgsc.bcm.edu	37	17	62029006	62029006	+	Silent	SNP	A	A	G	rs79893125	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:62029006A>G	ENST00000435607.1	-	14	2707	c.2631T>C	c.(2629-2631)gaT>gaC	p.D877D	SCN4A_ENST00000578147.1_Silent_p.D877D	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	877					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CCTTCTTCTCATCCTCGGGGG	0.657													G|||	485	0.096845	0.3026	0.0303	5008	,	,		13158	0.0169		0.0199	False		,,,				2504	0.0276				p.D877D		Atlas-SNP	.											.	SCN4A	205	.	0			c.T2631C						PASS	.	G		974,2962		135,704,1129	55.0	64.0	61.0		2631	-7.0	0.1	17	dbSNP_131	61	153,8095		6,141,3977	no	coding-synonymous	SCN4A	NM_000334.4		141,845,5106	GG,GA,AA		1.855,24.7459,9.2498		877/1837	62029006	1127,11057	1968	4124	6092	SO:0001819	synonymous_variant	6329	exon14			CTTCTCATCCTCG	U24693		17q23.3	2012-02-26	2007-01-23					"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.2631T>C	17.37:g.62029006A>G		305.0	1.0	0.00327869		332.0	155.0	0.466867	NM_000334	Q15478|Q16447|Q7Z6B1	Silent	SNP	ENST00000435607.1	37	CCDS45761.1																																																																																			A|0.936;G|0.064	0.064	strong		0.657	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334	
ZNF358	140467	hgsc.bcm.edu	37	19	7585762	7585762	+	Missense_Mutation	SNP	G	G	C	rs116797831	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7585762G>C	ENST00000597229.1	+	2	1804	c.1634G>C	c.(1633-1635)aGc>aCc	p.S545T	ZNF358_ENST00000394341.2_Missense_Mutation_p.S545T|MCOLN1_ENST00000264079.6_5'Flank|CTD-2207O23.11_ENST00000602083.1_RNA	NM_018083.4	NP_060553.4	Q9NW07	ZN358_HUMAN	zinc finger protein 358	545					embryonic forelimb morphogenesis (GO:0035115)|neural tube development (GO:0021915)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|lung(1)|skin(2)	8						GGCACTGTCAGCCCAGCCCTC	0.662													G|||	130	0.0259585	0.0938	0.0072	5008	,	,		16199	0.0		0.001	False		,,,				2504	0.0				p.S545T		Atlas-SNP	.											.	ZNF358	41	.	0			c.G1634C						PASS	.	G	THR/SER	369,4037	182.9+/-210.6	14,341,1848	88.0	70.0	76.0		1634	4.0	1.0	19	dbSNP_132	76	3,8597	3.0+/-9.4	0,3,4297	yes	missense	ZNF358	NM_018083.4	58	14,344,6145	CC,CG,GG		0.0349,8.3749,2.8602	possibly-damaging	545/569	7585762	372,12634	2203	4300	6503	SO:0001583	missense	140467	exon2			CTGTCAGCCCAGC	AK001252	CCDS32890.2	19p13.2	2013-01-08			ENSG00000198816	ENSG00000198816		"""Zinc fingers, C2H2-type"""	16838	protein-coding gene	gene with protein product							Standard	NM_018083		Approved	FLJ10390, ZFEND	uc002mgn.2	Q9NW07		ENST00000597229.1:c.1634G>C	19.37:g.7585762G>C	ENSP00000472305:p.Ser545Thr	183.0	0.0	0		207.0	117.0	0.565217	NM_018083	Q9BTM7	Missense_Mutation	SNP	ENST00000597229.1	37	CCDS32890.2	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	G	14.68	2.606694	0.46527	0.083749	3.49E-4	ENSG00000198816	ENST00000361576;ENST00000394341	T	0.07021	3.23	4.04	4.04	0.47022	.	.	.	.	.	T	0.00412	0.0013	N	0.24115	0.695	0.24806	N	0.992677	B	0.22851	0.076	B	0.18263	0.021	T	0.20672	-1.0268	9	0.72032	D	0.01	.	14.4919	0.67657	0.0:0.0:1.0:0.0	.	545	Q9NW07	ZN358_HUMAN	T	545	ENSP00000377873:S545T	ENSP00000354703:S545T	S	+	2	0	ZNF358	7491762	0.463000	0.25799	0.996000	0.52242	0.375000	0.29983	2.534000	0.45676	2.547000	0.85894	0.655000	0.94253	AGC	G|0.977;C|0.023	0.023	strong		0.662	ZNF358-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316747.1		
SLC26A6	65010	hgsc.bcm.edu	37	3	48664473	48664473	+	Missense_Mutation	SNP	C	C	T	rs59643945	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:48664473C>T	ENST00000395550.2	-	18	1956	c.1909G>A	c.(1909-1911)Gat>Aat	p.D637N	SLC26A6_ENST00000383733.3_Missense_Mutation_p.D618N|SLC26A6_ENST00000358747.6_Missense_Mutation_p.D616N|SLC26A6_ENST00000337000.8_Missense_Mutation_p.D529N|SLC26A6_ENST00000420764.2_Missense_Mutation_p.D636N|SLC26A6_ENST00000455886.2_Missense_Mutation_p.D601N			Q9BXS9	S26A6_HUMAN	solute carrier family 26 (anion exchanger), member 6	637	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.				angiotensin-activated signaling pathway (GO:0038166)|anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|cellular response to cAMP (GO:0071320)|cellular response to fructose stimulus (GO:0071332)|cellular response to interferon-gamma (GO:0071346)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|epithelial fluid transport (GO:0042045)|formate transport (GO:0015724)|intestinal absorption (GO:0050892)|intracellular pH elevation (GO:0051454)|ion transport (GO:0006811)|mannitol transport (GO:0015797)|oxalate transport (GO:0019532)|oxalic acid secretion (GO:0046724)|positive regulation of dipeptide transmembrane transport (GO:2001150)|protein kinase C signaling (GO:0070528)|regulation of intracellular pH (GO:0051453)|sperm capacitation (GO:0048240)|sulfate transmembrane transport (GO:1902358)|sulfate transport (GO:0008272)|transepithelial chloride transport (GO:0030321)|transepithelial transport (GO:0070633)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|chloride channel complex (GO:0034707)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane-bounded vesicle (GO:0031988)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)|vesicle membrane (GO:0012506)	anion:anion antiporter activity (GO:0015301)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride channel activity (GO:0005254)|chloride transmembrane transporter activity (GO:0015108)|efflux transmembrane transporter activity (GO:0015562)|formate efflux transmembrane transporter activity (GO:0015660)|formate transmembrane transporter activity (GO:0015499)|formate uptake transmembrane transporter activity (GO:0015659)|oxalate transmembrane transporter activity (GO:0019531)|PDZ domain binding (GO:0030165)|secondary active sulfate transmembrane transporter activity (GO:0008271)|sulfate transmembrane transporter activity (GO:0015116)		SLC26A6/PRKAR2A(2)	NS(1)|breast(1)|cervix(1)|endometrium(3)|large_intestine(1)|lung(11)|ovary(1)	19				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00609)		TCCATCTTATCTCCTGAGCTC	0.597													C|||	329	0.0656949	0.2231	0.0346	5008	,	,		18821	0.0		0.008	False		,,,				2504	0.002				p.D637N	NSCLC(13;369 479 28271 30152 44026)	Atlas-SNP	.											.	SLC26A6	45	.	0			c.G1909A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP,ASN/ASP	695,3405		68,559,1423	92.0	98.0	96.0		1846,1909,1906,1852	-0.5	0.0	3	dbSNP_129	96	49,8343		0,49,4147	yes	missense,missense,missense,missense	SLC26A6	NM_001040454.1,NM_022911.2,NM_134263.2,NM_134426.2	23,23,23,23	68,608,5570	TT,TC,CC		0.5839,16.9512,5.9558	benign,benign,benign,benign	616/739,637/760,636/759,618/741	48664473	744,11748	2050	4196	6246	SO:0001583	missense	65010	exon18			TCTTATCTCCTGA	AF279265	CCDS43087.1, CCDS46824.1, CCDS46825.1, CCDS46826.1, CCDS63627.1, CCDS63628.1	3p21.31	2013-08-05	2013-07-18		ENSG00000225697	ENSG00000225697		"""Solute carriers"""	14472	protein-coding gene	gene with protein product	"""pendrin-like protein 1"", ""pendrin L1"", ""sulfate anion transporter"", ""anion transporter 1"""	610068	"""solute carrier family 26, member 6"""			11087667, 11247665	Standard	NM_022911		Approved	DKFZp586E1422		Q9BXS9	OTTHUMG00000186381	ENST00000395550.2:c.1909G>A	3.37:g.48664473C>T	ENSP00000378920:p.Asp637Asn	208.0	1.0	0.00480769		175.0	96.0	0.548571	NM_022911	B4DMZ1|Q548A7|Q96Q90|Q9NQU1	Missense_Mutation	SNP	ENST00000395550.2	37	CCDS43087.1	116	0.05311355311355311	101	0.20528455284552846	11	0.03038674033149171	0	0.0	4	0.005277044854881266	C	9.598	1.128019	0.20959	0.169512	0.005839	ENSG00000225697	ENST00000420764;ENST00000395550;ENST00000383733;ENST00000337000;ENST00000447978;ENST00000358747;ENST00000455886	D;D;D;D;D;D	0.92545	-2.95;-2.93;-3.05;-2.96;-2.93;-3.06	3.63	-0.494	0.12034	Sulphate transporter/antisigma-factor antagonist STAS (3);	.	.	.	.	T	0.00241	0.0007	N	0.10972	0.075	0.80722	P	0.0	B;B;B;B;B;B;B	0.21905	0.004;0.0;0.005;0.0;0.001;0.0;0.062	B;B;B;B;B;B;B	0.28638	0.013;0.001;0.009;0.002;0.006;0.003;0.092	T	0.24548	-1.0157	8	0.51188	T	0.08	.	3.7251	0.08472	0.0:0.4123:0.1909:0.3969	rs59643945	601;631;529;618;636;637;4023	B4DMZ1;Q86YZ4;G3XAC1;Q9BXS9-2;Q548A7;Q9BXS9;Q5Y190	.;.;.;.;.;S26A6_HUMAN;.	N	636;637;618;529;631;616;601	ENSP00000404684:D636N;ENSP00000378920:D637N;ENSP00000373239:D618N;ENSP00000337648:D529N;ENSP00000351597:D616N;ENSP00000401066:D601N	ENSP00000337648:D529N	D	-	1	0	SLC26A6	48639477	0.001000	0.12720	0.000000	0.03702	0.151000	0.21798	0.206000	0.17375	-0.112000	0.11979	-0.339000	0.08088	GAT	C|0.962;T|0.038	0.038	strong		0.597	SLC26A6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000345040.1	NM_022911	
RP1L1	94137	hgsc.bcm.edu	37	8	10470764	10470764	+	Missense_Mutation	SNP	T	T	G	rs75814156	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10470764T>G	ENST00000382483.3	-	4	1067	c.844A>C	c.(844-846)Aac>Cac	p.N282H		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	282					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		ACCGGGGGGTTGCTAGGACCA	0.672													T|||	113	0.0225639	0.084	0.0029	5008	,	,		15048	0.0		0.0	False		,,,				2504	0.0				p.N282H		Atlas-SNP	.											RP1L1,NS,carcinoma,+2,1	RP1L1	453	1	0			c.A844C						PASS	.	T	HIS/ASN	236,3690		8,220,1735	55.0	62.0	60.0		844	0.6	0.0	8	dbSNP_131	60	2,8288		0,2,4143	yes	missense	RP1L1	NM_178857.5	68	8,222,5878	GG,GT,TT		0.0241,6.0112,1.9483	probably-damaging	282/2401	10470764	238,11978	1963	4145	6108	SO:0001583	missense	94137	exon4			GGGGGTTGCTAGG	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.844A>C	8.37:g.10470764T>G	ENSP00000371923:p.Asn282His	48.0	0.0	0		40.0	13.0	0.325	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	49	0.022435897435897436	49	0.09959349593495935	0	0.0	0	0.0	0	0.0	T	13.74	2.326457	0.41197	0.060112	2.41E-4	ENSG00000183638	ENST00000382483	T	0.04360	3.64	4.67	0.552	0.17230	.	0.788418	0.10319	N	0.688987	T	0.00144	0.0004	N	0.14661	0.345	0.09310	N	1	D	0.58970	0.984	P	0.46796	0.527	T	0.49960	-0.8883	10	0.59425	D	0.04	-5.163	5.688	0.17813	0.0:0.5952:0.1546:0.2502	.	282	A6NKC6	.	H	282	ENSP00000371923:N282H	ENSP00000371923:N282H	N	-	1	0	RP1L1	10508174	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.263000	0.18478	-0.050000	0.13356	-0.643000	0.03959	AAC	T|0.984;G|0.016	0.016	strong		0.672	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
ZKSCAN3	80317	hgsc.bcm.edu	37	6	28331573	28331573	+	Missense_Mutation	SNP	T	T	A	rs213227	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:28331573T>A	ENST00000377255.3	+	6	1035	c.738T>A	c.(736-738)caT>caA	p.H246Q	ZKSCAN3_ENST00000341464.5_Missense_Mutation_p.H98Q|ZKSCAN3_ENST00000252211.2_Missense_Mutation_p.H246Q	NM_001242894.1	NP_001229823.1	Q9BRR0	ZKSC3_HUMAN	zinc finger with KRAB and SCAN domains 3	246	KRAB.		H -> Q (in dbSNP:rs213227).		autophagy (GO:0006914)|lysosome organization (GO:0007040)|negative regulation of autophagy (GO:0010507)|negative regulation of cellular senescence (GO:2000773)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(4)|large_intestine(3)|lung(8)|pancreas(1)|skin(2)|stomach(2)|urinary_tract(1)	21						AGGAGAACCATGGCAGCCTGG	0.463													T|||	244	0.048722	0.1278	0.0346	5008	,	,		18669	0.0119		0.0189	False		,,,				2504	0.0204				p.H246Q		Atlas-SNP	.											.	ZKSCAN3	50	.	0			c.T738A						PASS	.	T	GLN/HIS,GLN/HIS,GLN/HIS	459,3947		25,409,1769	81.0	74.0	76.0		738,294,738	0.5	0.0	6	dbSNP_79	76	135,8465		1,133,4166	yes	missense,missense,missense	ZKSCAN3	NM_001242894.1,NM_001242895.1,NM_024493.3	24,24,24	26,542,5935	AA,AT,TT		1.5698,10.4176,4.5671	benign,benign,benign	246/539,98/391,246/539	28331573	594,12412	2203	4300	6503	SO:0001583	missense	80317	exon5			GAACCATGGCAGC	U71601	CCDS4650.1, CCDS56408.1	6p22.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000189298		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13853	protein-coding gene	gene with protein product		612791	"""zinc finger protein 306"", ""zinc finger protein 309"""	ZNF306, ZNF309		10520746, 22531714	Standard	NM_024493		Approved	Zfp47, ZF47, ZSCAN35	uc003nle.4	Q9BRR0	OTTHUMG00000014521	ENST00000377255.3:c.738T>A	6.37:g.28331573T>A	ENSP00000366465:p.His246Gln	91.0	0.0	0		100.0	47.0	0.47	NM_024493	B2R8W2|B3KVC0|H7BXX1|Q5VXH3|Q92972|Q9H4T3	Missense_Mutation	SNP	ENST00000377255.3	37	CCDS4650.1	90	0.04120879120879121	53	0.10772357723577236	14	0.03867403314917127	11	0.019230769230769232	12	0.0158311345646438	.	12.65	2.001597	0.35320	0.104176	0.015698	ENSG00000189298	ENST00000252211;ENST00000341464;ENST00000377255	T;T;T	0.01725	4.67;4.67;4.67	2.98	0.46	0.16684	Krueppel-associated box (3);	.	.	.	.	T	0.00468	0.0015	L	0.29908	0.895	0.80722	P	0.0	P	0.35821	0.523	B	0.33392	0.163	T	0.47983	-0.9074	8	0.25751	T	0.34	.	3.8184	0.08825	0.0:0.2424:0.4061:0.3515	rs213227;rs61181430;rs213227	246	Q9BRR0	ZKSC3_HUMAN	Q	246;98;246	ENSP00000252211:H246Q;ENSP00000341883:H98Q;ENSP00000366465:H246Q	ENSP00000252211:H246Q	H	+	3	2	ZKSCAN3	28439552	0.000000	0.05858	0.002000	0.10522	0.920000	0.55202	-0.612000	0.05616	0.086000	0.17137	0.460000	0.39030	CAT	T|0.958;A|0.042	0.042	strong		0.463	ZKSCAN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040189.3	NM_024493	
TRPM2	7226	hgsc.bcm.edu	37	21	45825818	45825818	+	Silent	SNP	C	C	T	rs17004645	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45825818C>T	ENST00000397928.1	+	18	3133	c.2688C>T	c.(2686-2688)cgC>cgT	p.R896R	TRPM2_ENST00000300482.5_Silent_p.R896R|TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000397932.2_Silent_p.R896R|TRPM2_ENST00000300481.9_Silent_p.R876R	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	896					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)			breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						ACCCCGGGCGCGTCATCCTCT	0.612													t|||	18	0.00359425	0.0136	0.0	5008	,	,		17476	0.0		0.0	False		,,,				2504	0.0				p.R896R		Atlas-SNP	.											TRPM2,NS,carcinoma,+1,1	TRPM2	196	1	0			c.C2688T						PASS	.	T		64,4342	814.1+/-416.2	3,58,2142	87.0	90.0	89.0		2688	1.1	0.8	21	dbSNP_123	89	0,8598		0,0,4299	no	coding-synonymous	TRPM2	NM_003307.3		3,58,6441	TT,TC,CC		0.0,1.4526,0.4922		896/1504	45825818	64,12940	2203	4299	6502	SO:0001819	synonymous_variant	7226	exon18			CGGGCGCGTCATC	AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Nudix motif containing"""	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.2688C>T	21.37:g.45825818C>T		55.0	0.0	0		46.0	21.0	0.456522	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Silent	SNP	ENST00000397928.1	37	CCDS13710.1																																																																																			C|0.993;T|0.007	0.007	strong		0.612	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307	
TDP1	55775	hgsc.bcm.edu	37	14	90451500	90451500	+	Silent	SNP	A	A	G	rs17126522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:90451500A>G	ENST00000335725.4	+	10	1327	c.1077A>G	c.(1075-1077)ccA>ccG	p.P359P	TDP1_ENST00000357382.3_Silent_p.P120P|TDP1_ENST00000555880.1_Silent_p.P359P|TDP1_ENST00000393454.2_Silent_p.P359P|TDP1_ENST00000393452.3_Silent_p.P359P	NM_018319.3	NP_060789.2	Q9NUW8	TYDP1_HUMAN	tyrosyl-DNA phosphodiesterase 1	359					cell death (GO:0008219)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	3'-tyrosyl-DNA phosphodiesterase activity (GO:0017005)|double-stranded DNA binding (GO:0003690)|exonuclease activity (GO:0004527)|single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|urinary_tract(1)	25		all_cancers(154;0.185)		COAD - Colon adenocarcinoma(157;0.23)		GTTCAACCCCAGGACGCTTTC	0.284								Repair of DNA-protein crosslinks					A|||	301	0.0601038	0.171	0.0288	5008	,	,		15009	0.0079		0.0179	False		,,,				2504	0.0297				p.P359P		Atlas-SNP	.											.	TDP1	47	.	0			c.A1077G						PASS	.	A	,	597,3809	246.5+/-255.1	44,509,1650	60.0	58.0	58.0		1077,1077	-11.2	0.7	14	dbSNP_123	58	171,8421	79.2+/-141.9	2,167,4127	no	coding-synonymous,coding-synonymous	TDP1	NM_001008744.1,NM_018319.3	,	46,676,5777	GG,GA,AA		1.9902,13.5497,5.9086	,	359/609,359/609	90451500	768,12230	2203	4296	6499	SO:0001819	synonymous_variant	55775	exon10			AACCCCAGGACGC	AF182002	CCDS9888.1	14q32.11	2008-08-11				ENSG00000042088			18884	protein-coding gene	gene with protein product		607198				11839309, 12244316	Standard	XM_005267847		Approved	FLJ11090, SCAN1	uc001xxz.3	Q9NUW8		ENST00000335725.4:c.1077A>G	14.37:g.90451500A>G		153.0	0.0	0		162.0	80.0	0.493827	NM_018319	Q2HXX4|Q86TV8|Q96BK7|Q9NZM7|Q9NZM8	Silent	SNP	ENST00000335725.4	37	CCDS9888.1																																																																																			A|0.938;G|0.062	0.062	strong		0.284	TDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411239.1	NM_018319	
BPIFC	254240	hgsc.bcm.edu	37	22	32843312	32843312	+	Silent	SNP	G	G	A	rs28733723	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:32843312G>A	ENST00000397452.1	-	4	371	c.261C>T	c.(259-261)gcC>gcT	p.A87A	BPIFC_ENST00000432451.2_5'UTR|BPIFC_ENST00000300399.3_Silent_p.A87A|BPIFC_ENST00000534972.1_5'UTR			Q8NFQ6	BPIFC_HUMAN	BPI fold containing family C	87						extracellular region (GO:0005576)	lipopolysaccharide binding (GO:0001530)|phospholipid binding (GO:0005543)										GAAATGAAAAGGCACTGATTT	0.463													G|||	147	0.029353	0.1074	0.0072	5008	,	,		18029	0.0		0.0	False		,,,				2504	0.0				p.A87A		Atlas-SNP	.											.	.	.	.	0			c.C261T						PASS	.	G		387,4019	189.2+/-215.4	14,359,1830	98.0	90.0	93.0		261	1.2	1.0	22	dbSNP_125	93	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	BPIFC	NM_174932.2		14,362,6127	AA,AG,GG		0.0349,8.7835,2.9986		87/508	32843312	390,12616	2203	4300	6503	SO:0001819	synonymous_variant	254240	exon3			TGAAAAGGCACTG	AF465766	CCDS13906.1	22q12.3	2011-08-04	2011-08-01	2011-08-01	ENSG00000184459	ENSG00000184459		"""BPI fold containing"""	16503	protein-coding gene	gene with protein product		614109	"""bactericidal/permeability-increasing protein-like 2"""	BPIL2			Standard	NM_174932		Approved	dJ149A16.7	uc003amn.2	Q8NFQ6	OTTHUMG00000058273	ENST00000397452.1:c.261C>T	22.37:g.32843312G>A		102.0	0.0	0		78.0	43.0	0.551282	NM_174932	A2RRF1	Silent	SNP	ENST00000397452.1	37	CCDS13906.1																																																																																			G|0.968;A|0.032	0.032	strong		0.463	BPIFC-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129029.2	NM_174932	
NOXO1	124056	hgsc.bcm.edu	37	16	2030029	2030029	+	Silent	SNP	C	C	T	rs34358073	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2030029C>T	ENST00000397280.4	-	5	573	c.570G>A	c.(568-570)gaG>gaA	p.E190E	NOXO1_ENST00000566005.1_Silent_p.E189E|NOXO1_ENST00000356120.4_Silent_p.E185E|AC005606.1_ENST00000598236.1_5'Flank|NOXO1_ENST00000354249.4_Silent_p.E184E|TBL3_ENST00000568546.1_3'UTR			Q8NFA2	NOXO1_HUMAN	NADPH oxidase organizer 1	190	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.				extracellular matrix disassembly (GO:0022617)|regulation of hydrogen peroxide metabolic process (GO:0010310)|regulation of respiratory burst (GO:0060263)|superoxide metabolic process (GO:0006801)	NADPH oxidase complex (GO:0043020)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)|phospholipid binding (GO:0005543)|superoxide-generating NADPH oxidase activator activity (GO:0016176)			lung(2)	2					Ecabet(DB05265)	CGTCCAGGCTCTCCTGGGCCT	0.652													C|||	194	0.038738	0.1415	0.0086	5008	,	,		16170	0.0		0.001	False		,,,				2504	0.0				p.E190E	Pancreas(104;2811 2841 4129)|Esophageal Squamous(25;910 1225 43728)	Atlas-SNP	.											.	NOXO1	13	.	0			c.G570A						PASS	.	C	,,	442,3932		20,402,1765	15.0	20.0	18.0		552,555,570	-0.2	0.0	16	dbSNP_126	18	3,8593		0,3,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	NOXO1	NM_144603.2,NM_172167.1,NM_172168.1	,,	20,405,6060	TT,TC,CC		0.0349,10.1052,3.431	,,	184/371,185/372,190/377	2030029	445,12525	2187	4298	6485	SO:0001819	synonymous_variant	124056	exon5			CAGGCTCTCCTGG	AF532985	CCDS10454.1, CCDS10455.1, CCDS42101.1, CCDS58406.1	16p13.3	2008-02-05			ENSG00000196408	ENSG00000196408			19404	protein-coding gene	gene with protein product		611256					Standard	NM_144603		Approved	P41NOXA, P41NOXB, P41NOXC, SH3PXD5, SNX28	uc002cnx.4	Q8NFA2	OTTHUMG00000128707	ENST00000397280.4:c.570G>A	16.37:g.2030029C>T		74.0	0.0	0		82.0	46.0	0.560976	NM_172168	Q86YM1|Q8NFA3|Q96B73	Silent	SNP	ENST00000397280.4	37	CCDS42101.1																																																																																			C|0.966;T|0.034	0.034	strong		0.652	NOXO1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250612.1		
JRK	8629	hgsc.bcm.edu	37	8	143746107	143746107	+	RNA	SNP	C	C	T	rs61747165	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:143746107C>T	ENST00000507178.2	-	0	1703							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				cctctgctggcgacgtggcag	0.682													C|||	63	0.0125799	0.0469	0.0014	5008	,	,		16019	0.0		0.0	False		,,,				2504	0.0				p.S457S		Atlas-SNP	.											.	.	.	.	0			c.G1371A						PASS	.	C	,	147,3827		0,147,1840	17.0	19.0	18.0		1371,1371	-6.5	0.0	8	dbSNP_129	18	1,8225		0,1,4112	no	coding-synonymous,coding-synonymous	JRK	NM_001077527.1,NM_003724.2	,	0,148,5952	TT,TC,CC		0.0122,3.699,1.2131	,	457/557,457/569	143746107	148,12052	1987	4113	6100			8629	exon2			TGCTGGCGACGTG	AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"""jerky (mouse) homolog"", ""jerky homolog (mouse)"""			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			8.37:g.143746107C>T		25.0	0.0	0		52.0	38.0	0.730769	NM_003724	O75565	Silent	SNP	ENST00000507178.2	37																																																																																				C|0.992;T|0.008	0.008	strong		0.682	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724	
ARHGAP17	55114	hgsc.bcm.edu	37	16	24942272	24942272	+	Missense_Mutation	SNP	T	T	A	rs111463480	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:24942272T>A	ENST00000289968.6	-	19	2417	c.2348A>T	c.(2347-2349)aAc>aTc	p.N783I	ARHGAP17_ENST00000441763.2_3'UTR|ARHGAP17_ENST00000303665.5_Missense_Mutation_p.N705I	NM_001006634.1	NP_001006635.1	Q68EM7	RHG17_HUMAN	Rho GTPase activating protein 17	783	Pro-rich.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	GTPase activator activity (GO:0005096)			breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|urinary_tract(2)	30				GBM - Glioblastoma multiforme(48;0.0407)		AGTTTCAGGGTTACCCCCTGC	0.632													T|||	3	0.000599042	0.0023	0.0	5008	,	,		14279	0.0		0.0	False		,,,				2504	0.0				p.N783I		Atlas-SNP	.											.	ARHGAP17	138	.	0			c.A2348T						PASS	.	T	ILE/ASN,ILE/ASN	1,4393	2.1+/-5.4	0,1,2196	71.0	80.0	77.0		2348,2114	5.1	0.6	16	dbSNP_132	77	0,8600		0,0,4300	no	missense,missense	ARHGAP17	NM_001006634.1,NM_018054.4	149,149	0,1,6496	AA,AT,TT		0.0,0.0228,0.0077	possibly-damaging,possibly-damaging	783/882,705/804	24942272	1,12993	2197	4300	6497	SO:0001583	missense	55114	exon19			TCAGGGTTACCCC	AJ306731	CCDS32408.1, CCDS32409.1	16p12.2-p12.1	2011-06-29				ENSG00000140750		"""Rho GTPase activating proteins"""	18239	protein-coding gene	gene with protein product		608293				10967100, 11431473	Standard	XM_005255413		Approved	RICH1, FLJ10308, NADRIN, FLJ13219, WBP15	uc002dnb.3	Q68EM7		ENST00000289968.6:c.2348A>T	16.37:g.24942272T>A	ENSP00000289968:p.Asn783Ile	161.0	0.0	0		179.0	76.0	0.424581	NM_001006634	A8K6M6|Q6ZUS4|Q7Z2F2|Q8NDG2|Q96KS2|Q96KS3|Q96SS8|Q9BVF6|Q9H8U5|Q9NW54	Missense_Mutation	SNP	ENST00000289968.6	37	CCDS32409.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	T	12.57	1.977941	0.34942	2.28E-4	0.0	ENSG00000140750	ENST00000289968;ENST00000303665;ENST00000455311	T;T	0.21361	2.01;2.06	5.13	5.13	0.70059	.	0.588411	0.14194	N	0.335149	T	0.34658	0.0905	L	0.44542	1.39	0.80722	D	1	B;B;D;P;P	0.64830	0.343;0.232;0.994;0.736;0.729	B;B;P;B;B	0.59703	0.134;0.063;0.862;0.205;0.372	T	0.02294	-1.1181	10	0.52906	T	0.07	.	12.8937	0.58087	0.0:0.0:0.0:1.0	.	705;783;316;616;344	Q68EM7-2;Q68EM7;Q68EM7-7;B4DWE9;B4DVF3	.;RHG17_HUMAN;.;.;.	I	783;705;783	ENSP00000289968:N783I;ENSP00000303130:N705I	ENSP00000289968:N783I	N	-	2	0	ARHGAP17	24849773	0.994000	0.37717	0.604000	0.28916	0.012000	0.07955	1.696000	0.37773	1.923000	0.55706	0.528000	0.53228	AAC	T|0.999;A|0.001	0.001	strong		0.632	ARHGAP17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436548.3	NM_018054	
KIRREL2	84063	hgsc.bcm.edu	37	19	36350474	36350474	+	Missense_Mutation	SNP	G	G	A	rs34494265	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36350474G>A	ENST00000360202.5	+	5	812	c.614G>A	c.(613-615)cGg>cAg	p.R205Q	KIRREL2_ENST00000592409.1_Missense_Mutation_p.R205Q|KIRREL2_ENST00000262625.7_Missense_Mutation_p.R205Q|NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000347900.6_Missense_Mutation_p.R155Q	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	205	Ig-like C2-type 2.				cell adhesion (GO:0007155)|negative regulation of protein phosphorylation (GO:0001933)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)		p.R205L(2)		breast(2)|central_nervous_system(1)|endometrium(6)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	48	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			TTTGTCTGCCGGGCCCGGAGC	0.627													G|||	91	0.0181709	0.0673	0.0029	5008	,	,		17806	0.0		0.0	False		,,,				2504	0.0				p.R205Q		Atlas-SNP	.											.	KIRREL2	170	.	2	Substitution - Missense(2)	lung(2)	c.G614A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	235,4171	139.2+/-174.8	4,227,1972	64.0	63.0	63.0		614,464,614	3.7	1.0	19	dbSNP_126	63	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	KIRREL2	NM_032123.5,NM_199179.2,NM_199180.2	43,43,43	4,228,6271	AA,AG,GG		0.0116,5.3336,1.8145	possibly-damaging,possibly-damaging,possibly-damaging	205/634,155/584,205/709	36350474	236,12770	2203	4300	6503	SO:0001583	missense	84063	exon5			TCTGCCGGGCCCG	AL136654	CCDS12479.1, CCDS12480.1, CCDS12481.1	19q13.13	2013-01-29				ENSG00000126259		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18816	protein-coding gene	gene with protein product		607762				12837264, 12504092	Standard	NM_199180		Approved	NLG1, NEPH3, FILTRIN, DKFZp564A1164, MGC15718	uc002ocb.4	Q6UWL6		ENST00000360202.5:c.614G>A	19.37:g.36350474G>A	ENSP00000353331:p.Arg205Gln	53.0	0.0	0		68.0	38.0	0.558824	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Missense_Mutation	SNP	ENST00000360202.5	37	CCDS12481.1	22	0.010073260073260074	20	0.04065040650406504	2	0.0055248618784530384	0	0.0	0	0.0	G	13.26	2.183768	0.38609	0.053336	1.16E-4	ENSG00000126259	ENST00000262625;ENST00000347900;ENST00000360202	T;T;T	0.74632	-0.86;-0.86;-0.86	4.72	3.68	0.42216	Immunoglobulin subtype (1);CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.203139	0.24398	N	0.038876	T	0.19366	0.0465	L	0.47078	1.49	0.25543	N	0.987161	B;P;P;P	0.38863	0.438;0.65;0.597;0.597	B;B;B;B	0.30716	0.119;0.119;0.072;0.072	T	0.22208	-1.0223	10	0.20519	T	0.43	-18.1018	8.1639	0.31215	0.106:0.0:0.894:0.0	rs34494265;rs34494265	205;205;155;205	F1T0I2;Q6UWL6;Q6UWL6-3;Q6UWL6-2	.;KIRR2_HUMAN;.;.	Q	205;155;205	ENSP00000262625:R205Q;ENSP00000345067:R155Q;ENSP00000353331:R205Q	ENSP00000262625:R205Q	R	+	2	0	KIRREL2	41042314	1.000000	0.71417	0.994000	0.49952	0.292000	0.27327	3.165000	0.50778	2.623000	0.88846	0.549000	0.68633	CGG	G|0.982;A|0.018	0.018	strong		0.627	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123	
GOLGA3	2802	hgsc.bcm.edu	37	12	133358984	133358984	+	Silent	SNP	A	A	G	rs76963006	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:133358984A>G	ENST00000450791.2	-	16	3546	c.3363T>C	c.(3361-3363)ctT>ctC	p.L1121L	GOLGA3_ENST00000204726.3_Silent_p.L1121L|GOLGA3_ENST00000456883.2_Silent_p.L1121L			Q08378	GOGA3_HUMAN	golgin A3	1121					intra-Golgi vesicle-mediated transport (GO:0006891)	cytosol (GO:0005829)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extrinsic component of Golgi membrane (GO:0090498)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	transporter activity (GO:0005215)			breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0176)|Lung NSC(355;0.204)		OV - Ovarian serous cystadenocarcinoma(86;2.27e-08)|Epithelial(86;3.34e-07)|all cancers(50;9.4e-06)		CGAGGCCCGTAAGCTTCCCTT	0.498													A|||	41	0.0081869	0.0303	0.0014	5008	,	,		19000	0.0		0.0	False		,,,				2504	0.0				p.L1121L		Atlas-SNP	.											.	GOLGA3	234	.	0			c.T3363C						PASS	.	A		117,4289	88.7+/-127.4	1,115,2087	216.0	201.0	207.0		3363	-8.6	0.0	12	dbSNP_132	207	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GOLGA3	NM_005895.3		1,116,6386	GG,GA,AA		0.0116,2.6555,0.9073		1121/1499	133358984	118,12888	2203	4300	6503	SO:0001819	synonymous_variant	2802	exon17			GCCCGTAAGCTTC	AF485338	CCDS9281.1, CCDS53846.1	12q24.33	2010-02-12	2010-02-12		ENSG00000090615	ENSG00000090615			4426	protein-coding gene	gene with protein product	"""SY2/SY10 protein"", ""Golgi complex-associated protein of 170 kD"""	602581	"""golgi autoantigen, golgin subfamily a, 3"""			8315394, 15829563	Standard	NM_001172557		Approved	golgin-160, GCP170, MEA-2	uc001ukz.1	Q08378	OTTHUMG00000168023	ENST00000450791.2:c.3363T>C	12.37:g.133358984A>G		234.0	0.0	0		201.0	107.0	0.532338	NM_005895	A5PKX6|O43241|Q6P9C7|Q86XW3|Q8TDA9|Q8WZA3	Silent	SNP	ENST00000450791.2	37	CCDS9281.1																																																																																			A|0.990;G|0.010	0.010	strong		0.498	GOLGA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397569.2	NM_005895	
RGS3	5998	hgsc.bcm.edu	37	9	116356549	116356549	+	Intron	SNP	C	C	G	rs113405588	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116356549C>G	ENST00000374140.2	+	23	3289				RGS3_ENST00000343817.5_Intron|RGS3_ENST00000374134.3_Intron|RGS3_ENST00000462143.1_Intron|RGS3_ENST00000394646.3_Intron|RGS3_ENST00000462403.1_Missense_Mutation_p.P117R|RGS3_ENST00000350696.5_Intron|RGS3_ENST00000342620.5_Intron	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3						inactivation of MAPK activity (GO:0000188)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						GTGGGGGGCCCTACAGAGATG	0.662													C|||	68	0.0135783	0.0492	0.0043	5008	,	,		13726	0.0		0.0	False		,,,				2504	0.0				p.P117R		Atlas-SNP	.											.	RGS3	251	.	0			c.C350G						PASS	.	C	,,,,ARG/PRO	206,4196		8,190,2003	37.0	45.0	42.0		,,,,350	5.2	0.8	9	dbSNP_132	42	1,8595		0,1,4297	yes	intron,intron,intron,intron,missense	RGS3	NM_021106.3,NM_130795.2,NM_134427.1,NM_144488.4,NM_144489.2	,,,,103	8,191,6300	GG,GC,CC		0.0116,4.6797,1.5926	,,,,	,,,,117/312	116356549	207,12791	2201	4298	6499	SO:0001627	intron_variant	5998	exon1			GGGGCCCTACAGA	AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"""Regulators of G-protein signaling"""	9999	protein-coding gene	gene with protein product		602189	"""regulator of G-protein signalling 3"""			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.3081-161C>G	9.37:g.116356549C>G		75.0	0.0	0		72.0	42.0	0.583333	NM_144489	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	37	CCDS43869.1	23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	C	14.66	2.600389	0.46423	0.046797	1.16E-4	ENSG00000138835	ENST00000462403	T	0.65364	-0.15	5.23	5.23	0.72850	.	.	.	.	.	T	0.09949	0.0244	N	0.14661	0.345	0.47819	D	0.99952	P	0.41313	0.745	B	0.36418	0.224	T	0.14200	-1.0481	9	0.49607	T	0.09	.	11.4969	0.50413	0.1792:0.8208:0.0:0.0	.	117	Q5VZ06	.	R	117	ENSP00000436168:P117R	ENSP00000436168:P117R	P	+	2	0	RGS3	115396370	0.373000	0.25073	0.808000	0.32385	0.977000	0.68977	2.249000	0.43169	2.442000	0.82660	0.558000	0.71614	CCT	C|0.988;G|0.012	0.012	strong		0.662	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790	
RP1L1	94137	hgsc.bcm.edu	37	8	10467130	10467130	+	Missense_Mutation	SNP	G	G	A	rs138261433	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10467130G>A	ENST00000382483.3	-	4	4701	c.4478C>T	c.(4477-4479)gCc>gTc	p.A1493V		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	1573					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		GGTGGGTTGGGCCTGCGTGTG	0.647													G|||	22	0.00439297	0.0159	0.0014	5008	,	,		16042	0.0		0.0	False		,,,				2504	0.0				p.A1493V		Atlas-SNP	.											.	RP1L1	453	.	0			c.C4478T						PASS	.	G	VAL/ALA	69,3877		0,69,1904	33.0	38.0	37.0		4478	-5.1	0.0	8	dbSNP_134	37	2,8318		0,2,4158	yes	missense	RP1L1	NM_178857.5	64	0,71,6062	AA,AG,GG		0.024,1.7486,0.5788	benign	1493/2401	10467130	71,12195	1973	4160	6133	SO:0001583	missense	94137	exon4			GGTTGGGCCTGCG	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.4478C>T	8.37:g.10467130G>A	ENSP00000371923:p.Ala1493Val	36.0	0.0	0		48.0	24.0	0.5	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	3.081	-0.189007	0.06299	0.017486	2.4E-4	ENSG00000183638	ENST00000382483	T	0.03860	3.78	4.78	-5.14	0.02875	.	1.690280	0.03804	N	0.264929	T	0.01092	0.0036	N	0.14661	0.345	0.09310	N	1	B	0.26483	0.15	B	0.19946	0.027	T	0.41680	-0.9495	10	0.09338	T	0.73	-0.4613	4.2452	0.10669	0.4089:0.0:0.2703:0.3208	.	1493	A6NKC6	.	V	1493	ENSP00000371923:A1493V	ENSP00000371923:A1493V	A	-	2	0	RP1L1	10504540	0.017000	0.18338	0.000000	0.03702	0.013000	0.08279	0.131000	0.15870	-1.100000	0.03030	0.561000	0.74099	GCC	G|0.998;A|0.002	0.002	strong		0.647	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
OR5J2	282775	hgsc.bcm.edu	37	11	55944501	55944501	+	Missense_Mutation	SNP	G	G	C	rs12279899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55944501G>C	ENST00000312298.1	+	1	408	c.408G>C	c.(406-408)atG>atC	p.M136I		NM_001005492.1	NP_001005492.1	Q8NH18	OR5J2_HUMAN	olfactory receptor, family 5, subfamily J, member 2	136			M -> I (in dbSNP:rs12279899).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	44	Esophageal squamous(21;0.00693)					CTGTAGCCATGTCTGATAGAA	0.453													.|||	111	0.0221645	0.0779	0.0115	5008	,	,		23867	0.0		0.0	False		,,,				2504	0.0				p.M136I		Atlas-SNP	.											.	OR5J2	98	.	0			c.G408C						PASS	.	G	ILE/MET	280,4122	156.6+/-189.7	9,262,1930	164.0	150.0	155.0		408	4.7	0.4	11	dbSNP_120	155	6,8586	4.3+/-15.6	0,6,4290	yes	missense	OR5J2	NM_001005492.1	10	9,268,6220	CC,CG,GG		0.0698,6.3607,2.201	probably-damaging	136/313	55944501	286,12708	2201	4296	6497	SO:0001583	missense	282775	exon1			AGCCATGTCTGAT	AB065595	CCDS31522.1	11q11	2012-08-09			ENSG00000174957	ENSG00000174957		"""GPCR / Class A : Olfactory receptors"""	19612	protein-coding gene	gene with protein product							Standard	NM_001005492		Approved		uc010rjb.2	Q8NH18	OTTHUMG00000166835	ENST00000312298.1:c.408G>C	11.37:g.55944501G>C	ENSP00000310788:p.Met136Ile	316.0	0.0	0		426.0	193.0	0.453052	NM_001005492	Q6IEU5	Missense_Mutation	SNP	ENST00000312298.1	37	CCDS31522.1	44	0.020146520146520148	39	0.07926829268292683	5	0.013812154696132596	0	0.0	0	0.0	G	16.43	3.120975	0.56613	0.063607	6.98E-4	ENSG00000174957	ENST00000312298	T	0.00551	6.65	4.67	4.67	0.58626	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000002	T	0.00073	0.0002	M	0.70595	2.14	0.51482	D	0.999923	P	0.41313	0.745	B	0.36719	0.231	T	0.75425	-0.3322	10	0.66056	D	0.02	.	17.6944	0.88277	0.0:0.0:1.0:0.0	rs12279899;rs52802580;rs12279899	136	Q8NH18	OR5J2_HUMAN	I	136	ENSP00000310788:M136I	ENSP00000310788:M136I	M	+	3	0	OR5J2	55701077	1.000000	0.71417	0.364000	0.25888	0.028000	0.11728	6.151000	0.71806	2.350000	0.79820	0.584000	0.79450	ATG	G|0.979;C|0.021	0.021	strong		0.453	OR5J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391544.1	NM_001005492	
ARHGEF17	9828	hgsc.bcm.edu	37	11	73078685	73078685	+	Missense_Mutation	SNP	G	G	A	rs143114785	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:73078685G>A	ENST00000263674.3	+	21	6402	c.6052G>A	c.(6052-6054)Gcc>Acc	p.A2018T		NM_014786.3	NP_055601.2	Q96PE2	ARHGH_HUMAN	Rho guanine nucleotide exchange factor (GEF) 17	2018					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(15)|ovary(2)|skin(2)	32						CCGAGGCCCCGCCCCTGCCAG	0.647													G|||	42	0.00838658	0.031	0.0014	5008	,	,		16959	0.0		0.0	False		,,,				2504	0.0				p.A2018T		Atlas-SNP	.											.	ARHGEF17	117	.	0			c.G6052A						PASS	.	G	THR/ALA	112,4288	86.8+/-125.4	0,112,2088	69.0	71.0	70.0		6052	-2.7	0.0	11	dbSNP_134	70	0,8586		0,0,4293	yes	missense	ARHGEF17	NM_014786.3	58	0,112,6381	AA,AG,GG		0.0,2.5455,0.8625	benign	2018/2064	73078685	112,12874	2200	4293	6493	SO:0001583	missense	9828	exon21			GGCCCCGCCCCTG	AF378754	CCDS8221.1	11q13.3	2011-11-16			ENSG00000110237	ENSG00000110237		"""Rho guanine nucleotide exchange factors"""	21726	protein-coding gene	gene with protein product	"""Rho-specific guanine-nucleotide exchange factor 164 kDa"", ""tumor endothelial marker 4"""					11559528, 12071859	Standard	NM_014786		Approved	TEM4, KIAA0337, p164-RhoGEF	uc001otu.3	Q96PE2	OTTHUMG00000167971	ENST00000263674.3:c.6052G>A	11.37:g.73078685G>A	ENSP00000263674:p.Ala2018Thr	72.0	0.0	0		70.0	37.0	0.528571	NM_014786	B2RP20|Q86XU2|Q8N2S0|Q9Y4G3	Missense_Mutation	SNP	ENST00000263674.3	37	CCDS8221.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	G	4.409	0.075520	0.08485	0.025455	0.0	ENSG00000110237	ENST00000263674	T	0.57436	0.4	5.42	-2.69	0.06022	.	0.281147	0.33753	N	0.004585	T	0.07728	0.0194	N	0.02830	-0.485	0.18873	N	0.999987	B	0.06786	0.001	B	0.06405	0.002	T	0.13124	-1.0521	10	0.15499	T	0.54	-2.6535	11.6716	0.51406	0.5979:0.0:0.4021:0.0	.	2018	Q96PE2	ARHGH_HUMAN	T	2018	ENSP00000263674:A2018T	ENSP00000263674:A2018T	A	+	1	0	ARHGEF17	72756333	0.001000	0.12720	0.004000	0.12327	0.145000	0.21501	-0.227000	0.09126	-0.943000	0.03691	-0.459000	0.05422	GCC	G|0.991;A|0.009	0.009	strong		0.647	ARHGEF17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397365.1	NM_014786	
FZD3	7976	hgsc.bcm.edu	37	8	28413375	28413375	+	Silent	SNP	C	C	T	rs62001924	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:28413375C>T	ENST00000240093.3	+	7	2152	c.1674C>T	c.(1672-1674)acC>acT	p.T558T	FZD3_ENST00000537916.1_Silent_p.T558T	NM_017412.3	NP_059108.1	Q9NPG1	FZD3_HUMAN	frizzled class receptor 3	558					canonical Wnt signaling pathway (GO:0060070)|cell proliferation in midbrain (GO:0033278)|commissural neuron axon guidance (GO:0071679)|establishment of planar polarity (GO:0001736)|facial nucleus development (GO:0021754)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|gonad development (GO:0008406)|hair follicle development (GO:0001942)|inner ear morphogenesis (GO:0042472)|neural tube closure (GO:0001843)|neuron differentiation (GO:0030182)|neuron migration (GO:0001764)|post-anal tail morphogenesis (GO:0036342)|vasculature development (GO:0001944)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|neuron projection membrane (GO:0032589)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(15)|ovary(1)|prostate(1)|skin(1)	41		Ovarian(32;2.06e-05)		KIRC - Kidney renal clear cell carcinoma(542;0.109)|Kidney(114;0.13)|Colorectal(74;0.23)		GAACATCCACCCATGCTTCTT	0.488													C|||	76	0.0151757	0.0575	0.0	5008	,	,		19431	0.0		0.0	False		,,,				2504	0.0				p.T558T		Atlas-SNP	.											.	FZD3	65	.	0			c.C1674T						PASS	.	C	,	204,4202	124.9+/-162.1	3,198,2002	95.0	77.0	83.0		1674,1674	0.3	1.0	8	dbSNP_129	83	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	FZD3	NM_017412.3,NM_145866.1	,	3,198,6302	TT,TC,CC		0.0,4.63,1.5685	,	558/667,558/667	28413375	204,12802	2203	4300	6503	SO:0001819	synonymous_variant	7976	exon7			ATCCACCCATGCT	AJ272427	CCDS6069.1	8p21	2014-06-27	2014-01-29		ENSG00000104290	ENSG00000104290		"""GPCR / Class F : Frizzled receptors"""	4041	protein-coding gene	gene with protein product		606143	"""frizzled (Drosophila) homolog 3"", ""frizzled homolog 3 (Drosophila)"", ""frizzled 3, seven transmembrane spanning receptor"", ""frizzled family receptor 3"""			10777673, 10873558	Standard	NM_145866		Approved		uc010lvb.3	Q9NPG1	OTTHUMG00000102145	ENST00000240093.3:c.1674C>T	8.37:g.28413375C>T		124.0	0.0	0		100.0	58.0	0.58	NM_017412	A8K615	Silent	SNP	ENST00000240093.3	37	CCDS6069.1																																																																																			C|0.984;T|0.016	0.016	strong		0.488	FZD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219986.2	NM_145866	
TTN	7273	hgsc.bcm.edu	37	2	179586779	179586779	+	Silent	SNP	A	A	G	rs16866469	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179586779A>G	ENST00000591111.1	-	76	21884	c.21660T>C	c.(21658-21660)caT>caC	p.H7220H	TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Silent_p.H6293H|RP11-171I2.1_ENST00000590024.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Silent_p.H7537H			Q8WZ42	TITIN_HUMAN	titin	12789	Ig-like 54.				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)			CACCAGTAACATGACACTCAA	0.428													A|||	101	0.0201677	0.0749	0.0029	5008	,	,		21079	0.0		0.0	False		,,,				2504	0.0				p.H7537H		Atlas-SNP	.											.	TTN	18412	.	0			c.T22611C						PASS	.	A	,,,	195,3703		6,183,1760	229.0	217.0	221.0		,18879,,	-2.7	1.0	2	dbSNP_123	221	6,8288		0,6,4141	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	6,189,5901	GG,GA,AA		0.0723,5.0026,1.6486	,,,	,6293/33424,,	179586779	201,11991	1949	4147	6096	SO:0001819	synonymous_variant	7273	exon78			AGTAACATGACAC	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.21660T>C	2.37:g.179586779A>G		123.0	0.0	0		120.0	58.0	0.483333	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|0.982;G|0.018	0.018	strong		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
TH	7054	hgsc.bcm.edu	37	11	2191006	2191006	+	Silent	SNP	C	C	T	rs34510659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:2191006C>T	ENST00000381178.1	-	3	297	c.279G>A	c.(277-279)tcG>tcA	p.S93S	TH_ENST00000333684.5_Silent_p.S66S|TH_ENST00000381175.1_Silent_p.S89S|TH_ENST00000352909.3_Silent_p.S62S	NM_199292.2	NP_954986.2	P07101	TY3H_HUMAN	tyrosine hydroxylase	93					anatomical structure morphogenesis (GO:0009653)|catecholamine biosynthetic process (GO:0042423)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|cellular response to growth factor stimulus (GO:0071363)|cellular response to manganese ion (GO:0071287)|cellular response to nicotine (GO:0071316)|cerebral cortex development (GO:0021987)|circadian sleep/wake cycle (GO:0042745)|dopamine biosynthetic process (GO:0042416)|dopamine biosynthetic process from tyrosine (GO:0006585)|eating behavior (GO:0042755)|embryonic camera-type eye morphogenesis (GO:0048596)|epinephrine biosynthetic process (GO:0042418)|eye photoreceptor cell development (GO:0042462)|fatty acid metabolic process (GO:0006631)|glycoside metabolic process (GO:0016137)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|isoquinoline alkaloid metabolic process (GO:0033076)|learning (GO:0007612)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|memory (GO:0007613)|multicellular organismal aging (GO:0010259)|neurotransmitter biosynthetic process (GO:0042136)|norepinephrine biosynthetic process (GO:0042421)|organ morphogenesis (GO:0009887)|phthalate metabolic process (GO:0018963)|phytoalexin metabolic process (GO:0052314)|pigmentation (GO:0043473)|regulation of heart contraction (GO:0008016)|response to activity (GO:0014823)|response to amphetamine (GO:0001975)|response to corticosterone (GO:0051412)|response to electrical stimulus (GO:0051602)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to ether (GO:0045472)|response to herbicide (GO:0009635)|response to hypoxia (GO:0001666)|response to light stimulus (GO:0009416)|response to lipopolysaccharide (GO:0032496)|response to nutrient levels (GO:0031667)|response to peptide hormone (GO:0043434)|response to pyrethroid (GO:0046684)|response to salt stress (GO:0009651)|response to water deprivation (GO:0009414)|response to zinc ion (GO:0010043)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|sphingolipid metabolic process (GO:0006665)|synaptic transmission, dopaminergic (GO:0001963)|synaptic vesicle amine transport (GO:0015842)|terpene metabolic process (GO:0042214)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|dendrite (GO:0030425)|melanosome membrane (GO:0033162)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perikaryon (GO:0043204)|smooth endoplasmic reticulum (GO:0005790)|synaptic vesicle (GO:0008021)|terminal bouton (GO:0043195)	amino acid binding (GO:0016597)|dopamine binding (GO:0035240)|enzyme binding (GO:0019899)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)|oxygen binding (GO:0019825)|tetrahydrobiopterin binding (GO:0034617)|tyrosine 3-monooxygenase activity (GO:0004511)			NS(1)|endometrium(1)|large_intestine(1)|lung(7)|skin(1)	11		all_epithelial(84;1.46e-23)|Lung NSC(207;4.44e-11)|all_lung(207;1.11e-09)|Ovarian(85;1.78e-06)|Breast(177;1.78e-05)|Medulloblastoma(188;0.0208)|all_neural(188;0.0416)	Colorectal(5;0.00245)|COAD - Colon adenocarcinoma(6;0.0239)	BRCA - Breast invasive adenocarcinoma(625;8.45e-09)|Lung(200;0.000152)|LUSC - Lung squamous cell carcinoma(625;0.00154)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)|Metyrosine(DB00765)|Tetrahydrobiopterin(DB00360)	CCCCGGGCTCCGAGGGGACTG	0.711													C|||	122	0.024361	0.0893	0.0058	5008	,	,		13970	0.0		0.0	False		,,,				2504	0.0				p.S93S		Atlas-SNP	.											.	TH	43	.	0			c.G279A						PASS	.	C	,,	343,4043		10,323,1860	17.0	20.0	19.0		186,279,267	-1.0	0.0	11	dbSNP_126	19	6,8586		0,6,4290	no	coding-synonymous,coding-synonymous,coding-synonymous	TH	NM_000360.3,NM_199292.2,NM_199293.2	,,	10,329,6150	TT,TC,CC		0.0698,7.8203,2.6892	,,	62/498,93/529,89/525	2191006	349,12629	2193	4296	6489	SO:0001819	synonymous_variant	7054	exon3			GGGCTCCGAGGGG	X05290	CCDS7730.1, CCDS7731.1, CCDS31338.1	11p15.5	2013-06-03			ENSG00000180176	ENSG00000180176	1.14.16.2		11782	protein-coding gene	gene with protein product	"""tyrosine 3-monooxygenase"""	191290					Standard	NM_199292		Approved	DYT5b	uc001lvq.3	P07101	OTTHUMG00000009559	ENST00000381178.1:c.279G>A	11.37:g.2191006C>T		74.0	0.0	0		68.0	40.0	0.588235	NM_199292	B7ZL70|B7ZL73|Q0PWM2|Q0PWM3|Q15585|Q15588|Q15589|Q2M3B4	Silent	SNP	ENST00000381178.1	37	CCDS7731.1																																																																																			C|0.971;T|0.029	0.029	strong		0.711	TH-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026597.1	NM_000360	
NCOR2	9612	hgsc.bcm.edu	37	12	124846788	124846788	+	Missense_Mutation	SNP	G	G	C	rs11057592	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124846788G>C	ENST00000405201.1	-	22	2984	c.2984C>G	c.(2983-2985)gCt>gGt	p.A995G	NCOR2_ENST00000397355.1_Missense_Mutation_p.A978G|NCOR2_ENST00000404621.1_Missense_Mutation_p.A977G|NCOR2_ENST00000429285.2_Missense_Mutation_p.A977G|NCOR2_ENST00000356219.3_Missense_Mutation_p.A994G|NCOR2_ENST00000404121.2_Missense_Mutation_p.A548G			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	995	Poly-Pro.				cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|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)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		GGCTGGGGGAGCTGGCTTGGT	0.682													G|||	117	0.0233626	0.0877	0.0014	5008	,	,		12732	0.0		0.0	False		,,,				2504	0.0				p.A995G		Atlas-SNP	.											.	NCOR2	475	.	0			c.C2984G						PASS	.	G	GLY/ALA,GLY/ALA,GLY/ALA	304,3804		12,280,1762	9.0	13.0	12.0		2930,2930,2984	3.0	0.0	12	dbSNP_120	12	4,8366		0,4,4181	yes	missense,missense,missense	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	60,60,60	12,284,5943	CC,CG,GG		0.0478,7.4002,2.4683	possibly-damaging,possibly-damaging,possibly-damaging	977/2459,977/2505,995/2515	124846788	308,12170	2054	4185	6239	SO:0001583	missense	9612	exon24			GGGGGAGCTGGCT	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"""nuclear receptor co-repressor 2"""			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.2984C>G	12.37:g.124846788G>C	ENSP00000384018:p.Ala995Gly	41.0	0.0	0		42.0	16.0	0.380952	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	37	CCDS41858.2	47	0.02152014652014652	46	0.09349593495934959	1	0.0027624309392265192	0	0.0	0	0.0	G	8.697	0.908871	0.17833	0.074002	4.78E-4	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285;ENST00000458234	T;T;T;T;T;T;T	0.31510	2.18;2.49;2.22;2.49;2.22;2.48;1.49	4.91	3.02	0.34903	.	0.502628	0.16789	U	0.199466	T	0.00998	0.0033	L	0.44542	1.39	0.09310	N	1	P;P;P	0.51933	0.824;0.824;0.949	B;B;P	0.45881	0.3;0.3;0.496	T	0.02179	-1.1200	10	0.27082	T	0.32	-2.9071	8.1686	0.31241	0.0881:0.1576:0.7543:0.0	rs11057592	977;978;995	C9J0Q5;C9J239;C9JFD3	.;.;.	G	995;977;994;978;994;548;977;995	ENSP00000384018:A995G;ENSP00000384202:A977G;ENSP00000348551:A994G;ENSP00000380513:A978G;ENSP00000385618:A548G;ENSP00000400281:A977G;ENSP00000402808:A995G	ENSP00000348551:A994G	A	-	2	0	NCOR2	123412741	0.024000	0.19004	0.009000	0.14445	0.009000	0.06853	0.963000	0.29293	0.454000	0.26884	0.462000	0.41574	GCT	G|0.973;C|0.027	0.027	strong		0.682	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
QRFP	347148	hgsc.bcm.edu	37	9	133768921	133768921	+	Missense_Mutation	SNP	G	G	A	rs140393161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:133768921G>A	ENST00000343079.1	-	1	304	c.305C>T	c.(304-306)cCt>cTt	p.P102L		NM_198180.1	NP_937823.1			pyroglutamylated RFamide peptide											cervix(1)|endometrium(3)|lung(1)|skin(2)	7	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;6.17e-05)|Epithelial(140;0.000267)		CCCCGCAGCAGGGAGGAAGCC	0.642													G|||	5	0.000998403	0.0038	0.0	5008	,	,		18404	0.0		0.0	False		,,,				2504	0.0				p.P102L		Atlas-SNP	.											.	QRFP	14	.	0			c.C305T						PASS	.	G	LEU/PRO	4,4400	6.2+/-15.9	0,4,2198	57.0	63.0	61.0		305	0.9	0.0	9	dbSNP_134	61	0,8600		0,0,4300	yes	missense	QRFP	NM_198180.1	98	0,4,6498	AA,AG,GG		0.0,0.0908,0.0308	benign	102/137	133768921	4,13000	2202	4300	6502	SO:0001583	missense	347148	exon1			GCAGCAGGGAGGA	AB109625	CCDS6936.1	9q34.12	2013-02-28			ENSG00000188710	ENSG00000188710		"""Endogenous ligands"""	29982	protein-coding gene	gene with protein product	"""prepro-QRFP"""	609795				12714592, 15808908	Standard	NM_198180		Approved	26RFa, P518	uc011mcb.2	P83859	OTTHUMG00000131663	ENST00000343079.1:c.305C>T	9.37:g.133768921G>A	ENSP00000345487:p.Pro102Leu	98.0	0.0	0		105.0	38.0	0.361905	NM_198180		Missense_Mutation	SNP	ENST00000343079.1	37	CCDS6936.1	5	0.0022893772893772895	3	0.006097560975609756	2	0.0055248618784530384	0	0.0	0	0.0	G	7.215	0.596183	0.13875	9.08E-4	0.0	ENSG00000188710	ENST00000343079	T	0.41065	1.01	4.12	0.912	0.19349	.	0.654924	0.13732	N	0.366612	T	0.19087	0.0458	L	0.37507	1.11	0.09310	N	1	B	0.14438	0.01	B	0.16289	0.015	T	0.18461	-1.0336	10	0.22109	T	0.4	-0.0237	3.2515	0.06816	0.1026:0.1401:0.4738:0.2835	.	102	P83859	OX26_HUMAN	L	102	ENSP00000345487:P102L	ENSP00000345487:P102L	P	-	2	0	QRFP	132758742	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.074000	0.11450	-0.057000	0.13199	0.313000	0.20887	CCT	G|0.999;A|0.001	0.001	strong		0.642	QRFP-001	KNOWN	mRNA_start_NF|mRNA_end_NF|cds_end_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254566.1	NM_198180	
POLR2A	5430	hgsc.bcm.edu	37	17	7412349	7412349	+	Silent	SNP	G	G	A	rs2228134	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7412349G>A	ENST00000322644.6	+	21	3951	c.3552G>A	c.(3550-3552)acG>acA	p.T1184T		NM_000937.4	NP_000928	P24928	RPB1_HUMAN	polymerase (RNA) II (DNA directed) polypeptide A, 220kDa	1184					7-methylguanosine mRNA capping (GO:0006370)|DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription-coupled nucleotide-excision repair (GO:0006283)|viral process (GO:0016032)	DNA-directed RNA polymerase II, core complex (GO:0005665)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA-directed RNA polymerase activity (GO:0003968)|ubiquitin protein ligase binding (GO:0031625)			breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(17)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	50		Prostate(122;0.173)				CCCAGAGCACGGTGGTGGCAG	0.547													G|||	380	0.0758786	0.2655	0.0288	5008	,	,		17738	0.0		0.001	False		,,,				2504	0.0082				p.T1184T		Atlas-SNP	.											POLR2A,colon,carcinoma,+1,1	POLR2A	157	1	0			c.G3552A						PASS	.	G		993,3413	370.3+/-319.5	115,763,1325	141.0	108.0	119.0		3552	-11.0	0.0	17	dbSNP_98	119	13,8587	9.1+/-34.3	0,13,4287	no	coding-synonymous	POLR2A	NM_000937.4		115,776,5612	AA,AG,GG		0.1512,22.5374,7.7349		1184/1971	7412349	1006,12000	2203	4300	6503	SO:0001819	synonymous_variant	5430	exon21			GAGCACGGTGGTG			17p13.1	2013-01-21	2002-08-29		ENSG00000181222	ENSG00000181222	2.7.7.6	"""RNA polymerase subunits"""	9187	protein-coding gene	gene with protein product	"""DNA-directed RNA polymerase II largest subunit, RNA polymerase II 220 kd subunit"", ""RNA polymerase II subunit B1"""	180660	"""polymerase (RNA) II (DNA directed) polypeptide A (220kD)"""	POLR2			Standard	NM_000937		Approved	POLRA, RPB1	uc002ghf.4	P24928	OTTHUMG00000177594	ENST00000322644.6:c.3552G>A	17.37:g.7412349G>A		262.0	1.0	0.00381679		251.0	135.0	0.537849	NM_000937	A6NN93|B9EH88|Q6NX41	Silent	SNP	ENST00000322644.6	37	CCDS32548.1																																																																																			G|0.935;A|0.065	0.065	strong		0.547	POLR2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437967.1	NM_000937	
RICTOR	253260	hgsc.bcm.edu	37	5	38960006	38960006	+	Silent	SNP	G	G	A	rs73751814	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:38960006G>A	ENST00000357387.3	-	21	1956	c.1926C>T	c.(1924-1926)ccC>ccT	p.P642P	RICTOR_ENST00000503698.1_5'Flank|RICTOR_ENST00000296782.5_Silent_p.P642P	NM_152756.3	NP_689969.2			RPTOR independent companion of MTOR, complex 2											NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|prostate(3)|skin(5)	75	all_lung(31;0.000396)					GACTTCTTTCGGGTTTCATTC	0.363													A|||	36	0.0071885	0.025	0.0043	5008	,	,		18686	0.0		0.0	False		,,,				2504	0.0				p.P642P		Atlas-SNP	.											.	RICTOR	182	.	0			c.C1926T						PASS	.	A		92,4314	817.2+/-416.3	1,90,2112	133.0	135.0	134.0		1926	-3.2	1.0	5	dbSNP_130	134	0,8600		0,0,4300	no	coding-synonymous	RICTOR	NM_152756.3		1,90,6412	AA,AG,GG		0.0,2.0881,0.7074		642/1709	38960006	92,12914	2203	4300	6503	SO:0001819	synonymous_variant	253260	exon21			TCTTTCGGGTTTC		CCDS34148.1, CCDS68861.1	5p13.1	2009-07-09			ENSG00000164327	ENSG00000164327			28611	protein-coding gene	gene with protein product	"""rapamycin-insensitive companion of mTOR"", ""pianissimo"""	609022				12477932	Standard	XM_005248278		Approved	MGC39830, AVO3, PIA, KIAA1999	uc003jlp.2	Q6R327	OTTHUMG00000162037	ENST00000357387.3:c.1926C>T	5.37:g.38960006G>A		136.0	0.0	0		158.0	82.0	0.518987	NM_152756		Silent	SNP	ENST00000357387.3	37	CCDS34148.1																																																																																			G|0.993;A|0.007	0.007	strong		0.363	RICTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366985.1	NM_152756	
B3GNT4	79369	hgsc.bcm.edu	37	12	122691058	122691058	+	Missense_Mutation	SNP	T	T	C	rs35203505	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:122691058T>C	ENST00000324189.4	+	3	616	c.260T>C	c.(259-261)cTg>cCg	p.L87P	B3GNT4_ENST00000535274.1_Missense_Mutation_p.L62P|B3GNT4_ENST00000546192.1_Missense_Mutation_p.L62P|B3GNT4_ENST00000545141.1_Intron	NM_030765.2	NP_110392.1	Q9C0J1	B3GN4_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 4	87			L -> P (in dbSNP:rs35203505).		carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	13	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000297)|Epithelial(86;0.000497)|BRCA - Breast invasive adenocarcinoma(302;0.222)		AGCGCCTCTCTGTCCCTGCCT	0.592													T|||	277	0.0553115	0.1982	0.0202	5008	,	,		16804	0.0		0.001	False		,,,				2504	0.0				p.L87P		Atlas-SNP	.											.	B3GNT4	35	.	0			c.T260C						PASS	.	T	PRO/LEU	794,3612	319.1+/-295.9	77,640,1486	236.0	227.0	230.0		260	-0.7	0.9	12	dbSNP_126	230	7,8593	5.7+/-21.5	0,7,4293	yes	missense	B3GNT4	NM_030765.2	98	77,647,5779	CC,CT,TT		0.0814,18.0209,6.1587	benign	87/379	122691058	801,12205	2203	4300	6503	SO:0001583	missense	79369	exon3			CCTCTCTGTCCCT	AB049586	CCDS9227.1	12q24	2013-02-19						"""Beta 3-glycosyltransferases"""	15683	protein-coding gene	gene with protein product		605864				11042166	Standard	NM_030765		Approved	B3GN-T4, beta3Gn-T4	uc001ubx.3	Q9C0J1		ENST00000324189.4:c.260T>C	12.37:g.122691058T>C	ENSP00000319636:p.Leu87Pro	194.0	0.0	0		187.0	82.0	0.438503	NM_030765	Q8N5W4|Q8N934|Q8ND21|Q8WWR5|Q8WY02|Q96QH5	Missense_Mutation	SNP	ENST00000324189.4	37	CCDS9227.1	118	0.05402930402930403	112	0.22764227642276422	6	0.016574585635359115	0	0.0	0	0.0	T	7.052	0.564562	0.13498	0.180209	8.14E-4	ENSG00000176383	ENST00000324189;ENST00000546192;ENST00000535274	T;T;T	0.36878	1.36;1.23;1.23	4.7	-0.663	0.11410	.	0.519308	0.14506	N	0.315425	T	0.00012	0.0000	L	0.40543	1.245	0.51233	P	9.00000000000345E-5	P	0.45283	0.855	B	0.41571	0.36	T	0.15263	-1.0443	9	0.30078	T	0.28	.	1.7591	0.02988	0.1302:0.2171:0.1337:0.519	rs35203505	87	Q9C0J1	B3GN4_HUMAN	P	87;62;62	ENSP00000319636:L87P;ENSP00000438840:L62P;ENSP00000444534:L62P	ENSP00000319636:L87P	L	+	2	0	B3GNT4	121257011	0.000000	0.05858	0.850000	0.33497	0.397000	0.30659	0.008000	0.13197	0.247000	0.21414	0.533000	0.62120	CTG	T|0.944;C|0.056	0.056	strong		0.592	B3GNT4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000401595.1	NM_030765	
SCTR	6344	hgsc.bcm.edu	37	2	120194673	120194673	+	IGR	SNP	G	G	A	rs114197773	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:120194673G>A	ENST00000019103.5	-	0	1865				TMEM37_ENST00000465296.1_3'UTR|TMEM37_ENST00000409826.1_Missense_Mutation_p.G89D|TMEM37_ENST00000306406.4_Missense_Mutation_p.G77D	NM_002980.2	NP_002971.2	P47872	SCTR_HUMAN	secretin receptor						digestion (GO:0007586)|excretion (GO:0007588)|G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic microtubule (GO:0005881)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	secretin receptor activity (GO:0015055)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)	19					Secretin(DB00021)	AGAGACCTGGGCCAGGCCCAT	0.652													G|||	140	0.0279553	0.0976	0.0101	5008	,	,		14451	0.0		0.004	False		,,,				2504	0.0				p.G77D		Atlas-SNP	.											.	TMEM37	40	.	0			c.G230A						PASS	.	G	ASP/GLY	327,4077	168.3+/-199.2	12,303,1887	51.0	54.0	53.0		230	2.8	0.8	2	dbSNP_132	53	8,8590	6.4+/-24.3	0,8,4291	yes	missense	TMEM37	NM_183240.2	94	12,311,6178	AA,AG,GG		0.093,7.4251,2.5765	benign	77/191	120194673	335,12667	2202	4299	6501	SO:0001628	intergenic_variant	140738	exon2			ACCTGGGCCAGGC		CCDS2127.1	2q14.1	2012-08-10			ENSG00000080293	ENSG00000080293		"""GPCR / Class B : Glucagon receptors"""	10608	protein-coding gene	gene with protein product		182098				1646711	Standard	NM_002980		Approved		uc002tma.3	P47872	OTTHUMG00000131407		2.37:g.120194673G>A		38.0	0.0	0		54.0	25.0	0.462963	NM_183240	Q12961|Q13213|Q53T00	Missense_Mutation	SNP	ENST00000019103.5	37	CCDS2127.1	47	0.02152014652014652	41	0.08333333333333333	3	0.008287292817679558	0	0.0	3	0.00395778364116095	G	5.612	0.297674	0.10622	0.074251	9.3E-4	ENSG00000171227	ENST00000409826;ENST00000306406	.	.	.	4.74	2.78	0.32641	.	0.572504	0.18041	N	0.153613	T	0.01387	0.0045	L	0.29908	0.895	0.09310	N	0.99999	B	0.21606	0.058	B	0.22601	0.04	T	0.06698	-1.0812	9	0.15499	T	0.54	-3.9992	8.7558	0.34645	0.2022:0.0:0.7978:0.0	.	77	Q8WXS4	CCGL_HUMAN	D	89;77	.	ENSP00000303148:G77D	G	+	2	0	TMEM37	119911143	0.094000	0.21725	0.818000	0.32626	0.630000	0.37929	0.340000	0.19892	1.234000	0.43709	0.561000	0.74099	GGC	G|0.973;A|0.027	0.027	strong		0.652	SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254198.2		
SORBS2	8470	hgsc.bcm.edu	37	4	186573817	186573817	+	Splice_Site	SNP	C	C	T	rs61732192	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:186573817C>T	ENST00000284776.7	-	7	842	c.333G>A	c.(331-333)ccG>ccA	p.P111P	SORBS2_ENST00000498125.1_5'UTR|SORBS2_ENST00000431808.1_Splice_Site_p.P111P|SORBS2_ENST00000319471.9_Splice_Site_p.P197P|SORBS2_ENST00000437304.2_Splice_Site_p.P290P|SORBS2_ENST00000393528.3_Splice_Site_p.P157P|SORBS2_ENST00000449407.2_Splice_Site_p.P197P|SORBS2_ENST00000448662.2_Splice_Site_p.P180P|SORBS2_ENST00000418609.1_Splice_Site_p.P30P|SORBS2_ENST00000355634.5_Splice_Site_p.P211P	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	111	SoHo. {ECO:0000255|PROSITE- ProRule:PRU00195}.				actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		CAGACATACCCGGCTTGTGCA	0.483													C|||	82	0.0163738	0.0598	0.0043	5008	,	,		22370	0.0		0.0	False		,,,				2504	0.0				p.P290P	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-SNP	.											SORBS2_ENST00000448662,NS,carcinoma,-1,4	SORBS2	300	4	0			c.G870A						scavenged	.	C	,,,,,,,	224,4182	132.9+/-169.3	5,214,1984	247.0	195.0	213.0		591,591,540,870,90,90,471,333	-10.3	0.0	4	dbSNP_129	213	0,8600		0,0,4300	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	SORBS2	NM_001145670.1,NM_001145671.1,NM_001145672.1,NM_001145673.1,NM_001145674.1,NM_001145675.1,NM_003603.5,NM_021069.4	,,,,,,,	5,214,6284	TT,TC,CC		0.0,5.084,1.7223	,,,,,,,	197/645,197/732,180/662,290/825,30/1005,30/493,157/667,111/1101	186573817	224,12782	2203	4300	6503	SO:0001630	splice_region_variant	8470	exon8			CATACCCGGCTTG		CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"""Arg/Abl interacting protein"""					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.334+1G>A	4.37:g.186573817C>T		174.0	1.0	0.00574713		149.0	75.0	0.503356	NM_001145673	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Silent	SNP	ENST00000284776.7	37	CCDS3845.1	33|33	0.01510989010989011|0.01510989010989011	31|31	0.06300813008130081|0.06300813008130081	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	C|C	4.660|4.660	0.122652|0.122652	0.08931|0.08931	0.05084|0.05084	0.0|0.0	ENSG00000154556|ENSG00000154556	ENST00000438278|ENST00000445625	.|.	.|.	.|.	5.16|5.16	-10.3|-10.3	0.00346|0.00346	.|.	.|.	.|.	.|.	.|.	T|T	0.06050|0.06050	0.0157|0.0157	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.43491|0.43491	-0.9388|-0.9388	4|4	.|.	.|.	.|.	-26.7084|-26.7084	3.9267|3.9267	0.09267|0.09267	0.206:0.1058:0.1231:0.5652|0.206:0.1058:0.1231:0.5652	.|.	.|.	.|.	.|.	R|Q	55|9	.|.	.|.	G|R	-|-	1|2	0|0	SORBS2|SORBS2	186810811|186810811	0.003000|0.003000	0.15002|0.15002	0.047000|0.047000	0.18901|0.18901	0.189000|0.189000	0.23516|0.23516	-1.527000|-1.527000	0.02227|0.02227	-3.174000|-3.174000	0.00224|0.00224	-0.819000|-0.819000	0.03115|0.03115	GGA|CGG	C|0.984;T|0.016	0.016	strong		0.483	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603	Silent
TCEAL3	85012	hgsc.bcm.edu	37	X	102864251	102864251	+	Missense_Mutation	SNP	C	C	G	rs12009847	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102864251C>G	ENST00000372628.1	+	3	617	c.259C>G	c.(259-261)Cag>Gag	p.Q87E	TCEAL3_ENST00000372627.5_Missense_Mutation_p.Q87E|TCEAL3_ENST00000477014.1_Intron|TCEAL3_ENST00000243286.3_Missense_Mutation_p.Q87E			Q969E4	TCAL3_HUMAN	transcription elongation factor A (SII)-like 3	87			Q -> E (in dbSNP:rs12009847).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)	16						GCCAGCCTCCCAGGCAAAGCC	0.617													C|||	235	0.0622517	0.1679	0.0173	3775	,	,		11795	0.0		0.001	False		,,,				2504	0.0				p.Q87E		Atlas-SNP	.											.	TCEAL3	24	.	0			c.C259G						PASS	.	C	GLU/GLN,GLU/GLN	702,3133		56,485,105,1091,466	97.0	92.0	94.0		259,259	2.3	0.2	X	dbSNP_120	94	6,6722		0,5,1,2423,1871	no	missense,missense	TCEAL3	NM_001006933.1,NM_032926.2	29,29	56,490,106,3514,2337	GG,GC,G,CC,C		0.0892,18.3051,6.7026	benign,benign	87/201,87/201	102864251	708,9855	2203	4300	6503	SO:0001583	missense	85012	exon3			GCCTCCCAGGCAA	BC008703	CCDS14511.1	Xq22.2	2014-03-21			ENSG00000196507	ENSG00000196507			28247	protein-coding gene	gene with protein product						16221301	Standard	NM_032926		Approved	MGC15737, WEX8	uc004ekr.3	Q969E4	OTTHUMG00000022106	ENST00000372628.1:c.259C>G	X.37:g.102864251C>G	ENSP00000361711:p.Gln87Glu	379.0	1.0	0.00263852		389.0	379.0	0.974293	NM_001006933	D3DXA4	Missense_Mutation	SNP	ENST00000372628.1	37	CCDS14511.1	84	0.05063291139240506	50	0.11682242990654206	2	0.0055248618784530384	0	0.0	0	0.0	C	0.004	-2.241804	0.00274	0.183051	8.92E-4	ENSG00000196507	ENST00000372628;ENST00000372627;ENST00000243286	T;T;T	0.21361	2.01;2.01;2.01	4.18	2.34	0.29019	.	0.536654	0.14096	N	0.341716	T	0.00039	0.0001	N	0.16602	0.42	0.80722	P	0.0	B	0.15141	0.012	B	0.12156	0.007	T	0.33085	-0.9882	9	0.02654	T	1	.	10.3974	0.44209	0.0:0.7424:0.2576:0.0	rs12009847;rs12009847	87	Q969E4	TCAL3_HUMAN	E	87	ENSP00000361711:Q87E;ENSP00000361710:Q87E;ENSP00000243286:Q87E	ENSP00000243286:Q87E	Q	+	1	0	TCEAL3	102750907	0.890000	0.30428	0.249000	0.24280	0.183000	0.23260	1.387000	0.34430	0.496000	0.27904	0.538000	0.68166	CAG	C|0.936;G|0.064	0.064	strong		0.617	TCEAL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057737.1	NM_032926	
AJUBA	84962	hgsc.bcm.edu	37	14	23444247	23444247	+	Silent	SNP	G	G	A	rs10130692	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:23444247G>A	ENST00000262713.2	-	5	1681	c.1306C>T	c.(1306-1308)Ctg>Ttg	p.L436L	AJUBA_ENST00000397388.3_Silent_p.L19L|AJUBA_ENST00000361265.4_Silent_p.L436L|RP11-298I3.5_ENST00000555074.1_Intron	NM_032876.4	NP_116265.1	Q96IF1	AJUBA_HUMAN	ajuba LIM protein	436	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				calcium-dependent cell-cell adhesion (GO:0016339)|cellular protein localization (GO:0034613)|focal adhesion assembly (GO:0048041)|G2/M transition of mitotic cell cycle (GO:0000086)|gene silencing by miRNA (GO:0035195)|glycerophospholipid biosynthetic process (GO:0046474)|lamellipodium assembly (GO:0030032)|mitotic cell cycle (GO:0000278)|negative regulation of hippo signaling (GO:0035331)|negative regulation of kinase activity (GO:0033673)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cellular biosynthetic process (GO:0031328)|positive regulation of gene silencing by miRNA (GO:2000637)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein complex assembly (GO:0031334)|regulation of cell migration (GO:0030334)|regulation of cellular response to hypoxia (GO:1900037)|regulation of GTPase activity (GO:0043087)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)|wound healing, spreading of epidermal cells (GO:0035313)	cell-cell junction (GO:0005911)|cytoplasmic mRNA processing body (GO:0000932)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transcription factor complex (GO:0005667)	alpha-catenin binding (GO:0045294)|chromatin binding (GO:0003682)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)										ATGCCATCCAGGCACTTGTTG	0.522													G|||	201	0.0401358	0.1452	0.0101	5008	,	,		22256	0.0		0.002	False		,,,				2504	0.0				p.L436L		Atlas-SNP	.											.	.	.	.	0			c.C1306T						PASS	.	G	,	552,3854	248.7+/-256.4	46,460,1697	150.0	138.0	142.0		1306,55	4.1	1.0	14	dbSNP_119	142	13,8587	9.1+/-34.3	0,13,4287	no	coding-synonymous,coding-synonymous	JUB	NM_032876.4,NM_198086.1	,	46,473,5984	AA,AG,GG		0.1512,12.5284,4.3441	,	436/539,19/122	23444247	565,12441	2203	4300	6503	SO:0001819	synonymous_variant	84962	exon5			CATCCAGGCACTT	AK025567	CCDS9581.1, CCDS9582.1	14q11.2	2011-11-10	2011-11-10	2011-11-10	ENSG00000129474	ENSG00000129474			20250	protein-coding gene	gene with protein product		609066	"""jub, ajuba homolog (Xenopus laevis)"""	JUB		10330178	Standard	NM_032876		Approved	MGC15563	uc001whz.3	Q96IF1	OTTHUMG00000028711	ENST00000262713.2:c.1306C>T	14.37:g.23444247G>A		60.0	0.0	0		81.0	49.0	0.604938	NM_032876	A8MX18|D3DS37	Silent	SNP	ENST00000262713.2	37	CCDS9581.1																																																																																			G|0.955;A|0.045	0.045	strong		0.522	AJUBA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071685.2		
HLTF	6596	hgsc.bcm.edu	37	3	148768130	148768130	+	Silent	SNP	T	T	C	rs16861365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:148768130T>C	ENST00000310053.5	-	15	1699	c.1506A>G	c.(1504-1506)gtA>gtG	p.V502V	HLTF_ENST00000392912.2_Silent_p.V502V|HLTF_ENST00000494055.1_Silent_p.V502V|HLTF_ENST00000465259.1_Silent_p.V501V	NM_003071.3|NM_139048.2	NP_003062.2|NP_620636.1	Q14527	HLTF_HUMAN	helicase-like transcription factor	502	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				chromatin modification (GO:0016568)|protein ubiquitination (GO:0016567)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			AATTCAAGTGTACATCTGATT	0.289													T|||	149	0.0297524	0.1097	0.0043	5008	,	,		15001	0.0		0.001	False		,,,				2504	0.0				p.V502V		Atlas-SNP	.											.	HLTF	87	.	0			c.A1506G						PASS	.	T	,	443,3959	207.5+/-228.8	25,393,1783	64.0	66.0	65.0		1506,1506	1.6	1.0	3	dbSNP_123	65	6,8578	4.3+/-15.6	0,6,4286	no	coding-synonymous,coding-synonymous	HLTF	NM_003071.3,NM_139048.2	,	25,399,6069	CC,CT,TT		0.0699,10.0636,3.4576	,	502/1010,502/1010	148768130	449,12537	2201	4292	6493	SO:0001819	synonymous_variant	6596	exon15			CAAGTGTACATCT	L34673	CCDS33875.1	3q25.1-q26.1	2006-11-09	2006-11-09	2006-11-09	ENSG00000071794	ENSG00000071794		"""RING-type (C3HC4) zinc fingers"""	11099	protein-coding gene	gene with protein product		603257	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 3"""	SNF2L3, SMARCA3		7558014	Standard	NM_139048		Approved	HIP116A, HLTF1, RNF80	uc003ewr.1	Q14527	OTTHUMG00000159534	ENST00000310053.5:c.1506A>G	3.37:g.148768130T>C		157.0	0.0	0		161.0	84.0	0.521739	NM_139048	D3DNH3|Q14536|Q16051|Q7KYJ6|Q86YA5|Q92652|Q96KM9	Silent	SNP	ENST00000310053.5	37	CCDS33875.1																																																																																			T|0.956;C|0.044	0.044	strong		0.289	HLTF-003	KNOWN	alternative_3_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356064.1		
TRIM36	55521	hgsc.bcm.edu	37	5	114482847	114482847	+	Silent	SNP	T	T	C	rs12109197	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:114482847T>C	ENST00000282369.3	-	3	664	c.543A>G	c.(541-543)gaA>gaG	p.E181E	TRIM36_ENST00000515104.1_5'UTR|TRIM36_ENST00000513154.1_Silent_p.E169E|TRIM36-IT1_ENST00000503723.1_RNA|TRIM36_ENST00000514154.1_Silent_p.E26E	NM_018700.3	NP_061170.2	Q9NQ86	TRI36_HUMAN	tripartite motif containing 36	181					acrosome reaction (GO:0007340)|regulation of cell cycle (GO:0051726)	acrosomal vesicle (GO:0001669)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(2)|large_intestine(4)|lung(15)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	37		all_cancers(142;0.00133)|all_epithelial(76;2.41e-05)|Prostate(80;0.00955)|Ovarian(225;0.0443)|Breast(839;0.195)		OV - Ovarian serous cystadenocarcinoma(64;3.62e-08)|Epithelial(69;7.69e-08)|all cancers(49;9.33e-06)		TTTTGAAGCATTCATTGCAGT	0.418													T|||	13	0.00259585	0.0098	0.0	5008	,	,		20229	0.0		0.0	False		,,,				2504	0.0				p.E181E		Atlas-SNP	.											.	TRIM36	126	.	0			c.A543G						PASS	.	T		20,4384	27.2+/-55.0	0,20,2182	144.0	141.0	142.0		543	-5.5	0.5	5	dbSNP_120	142	0,8600		0,0,4300	no	coding-synonymous	TRIM36	NM_018700.3		0,20,6482	CC,CT,TT		0.0,0.4541,0.1538		181/729	114482847	20,12984	2202	4300	6502	SO:0001819	synonymous_variant	55521	exon3			GAAGCATTCATTG	AJ272269	CCDS4115.1, CCDS34211.1, CCDS34212.1, CCDS75287.1	5q22	2013-02-11	2011-01-25		ENSG00000152503	ENSG00000152503		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"", ""Fibronectin type III domain containing"""	16280	protein-coding gene	gene with protein product	"""zinc-binding protein Rbcc728"", ""tripartite motif protein 36"", ""RING finger protein 98"""	609317	"""tripartite motif-containing 36"""			11331580	Standard	XM_005272031		Approved	RBCC728, RNF98, HAPRIN	uc003kqs.3	Q9NQ86	OTTHUMG00000128892	ENST00000282369.3:c.543A>G	5.37:g.114482847T>C		466.0	1.0	0.00214592		459.0	209.0	0.455338	NM_018700	A1L3Z1|A6NDD0|B7Z3V4|B7ZAV7|E9PFI8|Q0P5Z9	Silent	SNP	ENST00000282369.3	37	CCDS4115.1																																																																																			T|0.998;C|0.002	0.002	strong		0.418	TRIM36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250854.2	NM_018700	
DLAT	1737	hgsc.bcm.edu	37	11	111908137	111908137	+	Missense_Mutation	SNP	G	G	A	rs116125936	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:111908137G>A	ENST00000280346.6	+	6	1587	c.928G>A	c.(928-930)Gaa>Aaa	p.E310K	DLAT_ENST00000537636.1_Missense_Mutation_p.E81K|DLAT_ENST00000393051.1_Intron	NM_001931.4	NP_001922.2	P10515	ODP2_HUMAN	dihydrolipoamide S-acetyltransferase	310					cellular metabolic process (GO:0044237)|glucose metabolic process (GO:0006006)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrial pyruvate dehydrogenase complex (GO:0005967)|mitochondrion (GO:0005739)	dihydrolipoyllysine-residue acetyltransferase activity (GO:0004742)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(10)|ovary(1)|skin(1)	22		all_cancers(61;4.53e-11)|all_epithelial(67;2.76e-06)|Melanoma(852;9.42e-06)|all_hematologic(158;0.000885)|Acute lymphoblastic leukemia(157;0.000966)|Breast(348;0.0512)|Medulloblastoma(222;0.0523)|all_neural(223;0.0663)		Epithelial(105;4.87e-07)|BRCA - Breast invasive adenocarcinoma(274;6.83e-07)|all cancers(92;9.63e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0557)		TAGGCCAACCGAAGTAACAGA	0.448													G|||	24	0.00479233	0.0166	0.0029	5008	,	,		19194	0.0		0.0	False		,,,				2504	0.0				p.E310K		Atlas-SNP	.											.	DLAT	39	.	0			c.G928A						PASS	.	G	LYS/GLU	97,4305	78.3+/-116.7	0,97,2104	75.0	75.0	75.0		928	6.1	1.0	11	dbSNP_132	75	0,8594		0,0,4297	yes	missense	DLAT	NM_001931.4	56	0,97,6401	AA,AG,GG		0.0,2.2035,0.7464	benign	310/648	111908137	97,12899	2201	4297	6498	SO:0001583	missense	1737	exon6			CCAACCGAAGTAA	Y00978	CCDS8354.1	11q23.1	2008-02-05	2008-02-04		ENSG00000150768	ENSG00000150768	2.3.1.12		2896	protein-coding gene	gene with protein product	"""E2 component of pyruvate dehydrogenase complex"""	608770		DLTA		8102256	Standard	NM_001931		Approved	PDC-E2	uc001pmo.3	P10515	OTTHUMG00000133751	ENST00000280346.6:c.928G>A	11.37:g.111908137G>A	ENSP00000280346:p.Glu310Lys	97.0	0.0	0		64.0	21.0	0.328125	NM_001931	Q16783|Q53EP3	Missense_Mutation	SNP	ENST00000280346.6	37	CCDS8354.1	9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	G	15.75	2.925111	0.52759	0.022035	0.0	ENSG00000150768	ENST00000280346;ENST00000531306;ENST00000537636	T;T;T	0.21932	1.98;1.98;1.98	6.07	6.07	0.98685	Single hybrid motif (1);	0.512867	0.20290	N	0.095276	T	0.08179	0.0204	N	0.19112	0.55	0.40612	D	0.981685	B;B	0.21520	0.057;0.057	B;B	0.19148	0.024;0.024	T	0.16335	-1.0406	10	0.12103	T	0.63	-12.1494	20.6525	0.99598	0.0:0.0:1.0:0.0	.	310;310	Q86YI5;P10515	.;ODP2_HUMAN	K	310;142;81	ENSP00000280346:E310K;ENSP00000433432:E142K;ENSP00000442427:E81K	ENSP00000280346:E310K	E	+	1	0	DLAT	111413347	1.000000	0.71417	0.990000	0.47175	0.975000	0.68041	9.458000	0.97634	2.890000	0.99128	0.585000	0.79938	GAA	G|0.992;A|0.008	0.008	strong		0.448	DLAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258167.1	NM_001931	
DTNBP1	84062	hgsc.bcm.edu	37	6	15533469	15533469	+	Splice_Site	SNP	G	G	A	rs61739410	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:15533469G>A	ENST00000344537.5	-	8	840		c.e8+1		DTNBP1_ENST00000462989.2_Splice_Site|DTNBP1_ENST00000355917.3_Splice_Site|DTNBP1_ENST00000338950.5_Splice_Site	NM_032122.4	NP_115498.2	Q96EV8	DTBP1_HUMAN	dystrobrevin binding protein 1						actin cytoskeleton reorganization (GO:0031532)|anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|blood coagulation (GO:0007596)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|neuron projection development (GO:0031175)|neuron projection morphogenesis (GO:0048812)|platelet dense granule organization (GO:0060155)|positive regulation of gene expression (GO:0010628)|positive regulation of neurotransmitter secretion (GO:0001956)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of dopamine receptor signaling pathway (GO:0060159)|regulation of dopamine secretion (GO:0014059)	axon (GO:0030424)|BLOC-1 complex (GO:0031083)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|endoplasmic reticulum membrane (GO:0005789)|endosome (GO:0005768)|growth cone (GO:0030426)|neuron projection (GO:0043005)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasm (GO:0016528)|synaptic vesicle membrane (GO:0030672)				cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(5)|ovary(1)|skin(2)	14	Breast(50;0.0289)|Ovarian(93;0.103)	all_hematologic(90;0.0895)	Epithelial(50;0.211)			GCCCCCACTCGCCTCGCCGCT	0.627									Hermansky-Pudlak syndrome				G|||	140	0.0279553	0.0991	0.0086	5008	,	,		13972	0.0		0.002	False		,,,				2504	0.001				.		Atlas-SNP	.											.	DTNBP1	56	.	0			c.667+2C>T						PASS	.	G	,	389,4017	194.0+/-219.0	16,357,1830	70.0	61.0	64.0		,	1.8	0.5	6	dbSNP_129	64	6,8594	5.0+/-18.6	0,6,4294	yes	splice-5,splice-5	DTNBP1	NM_032122.4,NM_183040.2	,	16,363,6124	AA,AG,GG		0.0698,8.8289,3.0371	,	,	15533469	395,12611	2203	4300	6503	SO:0001630	splice_region_variant	84062	exon9	Familial Cancer Database	HPS, HPS1-8	CCACTCGCCTCGC	AF394226	CCDS4534.1, CCDS4535.1, CCDS75404.1, CCDS75405.1	6p22.3	2013-09-27			ENSG00000047579	ENSG00000047579		"""Biogenesis of lysosomal organelles complex-1 subunits"""	17328	protein-coding gene	gene with protein product	"""dysbindin-1"", ""biogenesis of lysosomal organelles complex-1, subunit 8"""	607145				11316798	Standard	NM_032122		Approved	Dysbindin, My031, HPS7, DBND, BLOC1S8	uc003nbm.3	Q96EV8	OTTHUMG00000014295	ENST00000344537.5:c.667+1C>T	6.37:g.15533469G>A		79.0	0.0	0		100.0	45.0	0.45	NM_032122	A8K3V3|Q5THY3|Q5THY4|Q96NV2|Q9H0U2|Q9H3J5	Splice_Site	SNP	ENST00000344537.5	37	CCDS4534.1	35	0.016025641025641024	30	0.06097560975609756	5	0.013812154696132596	0	0.0	0	0.0	G	4.160	0.028237	0.08054	0.088289	6.98E-4	ENSG00000047579	ENST00000344537;ENST00000462989;ENST00000355917;ENST00000397306;ENST00000509674;ENST00000511762;ENST00000338950;ENST00000543749	.	.	.	5.49	1.75	0.24633	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.453	0.32882	0.4003:0.0:0.5997:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	DTNBP1	15641448	1.000000	0.71417	0.499000	0.27577	0.023000	0.10783	2.892000	0.48625	0.001000	0.14605	-0.218000	0.12543	.	G|0.969;A|0.031	0.031	strong		0.627	DTNBP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000039933.2	NM_032122	Intron
ERICH3	127254	hgsc.bcm.edu	37	1	75038963	75038963	+	Missense_Mutation	SNP	C	C	A	rs75061423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:75038963C>A	ENST00000326665.5	-	14	2649	c.2431G>T	c.(2431-2433)Gcg>Tcg	p.A811S	C1orf173_ENST00000433746.2_5'UTR	NM_001002912.4	NP_001002912.4	Q5RHP9	ERIC3_HUMAN		811	Glu-rich.									NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(23)|lung(123)|ovary(3)|prostate(10)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)	184						GGCTTCCACGCCCTCAAGGGA	0.557													c|||	122	0.024361	0.0908	0.0029	5008	,	,		17211	0.0		0.0	False		,,,				2504	0.0				p.A811S		Atlas-SNP	.											.	C1orf173	380	.	0			c.G2431T						PASS	.	C	SER/ALA	345,4061	181.2+/-209.3	12,321,1870	91.0	88.0	89.0		2431	2.6	0.0	1	dbSNP_131	89	1,8599	1.2+/-3.3	0,1,4299	yes	missense	C1orf173	NM_001002912.4	99	12,322,6169	AA,AC,CC		0.0116,7.8302,2.6603	benign	811/1531	75038963	346,12660	2203	4300	6503	SO:0001583	missense	127254	exon14			TCCACGCCCTCAA																												ENST00000326665.5:c.2431G>T	1.37:g.75038963C>A	ENSP00000322609:p.Ala811Ser	121.0	0.0	0		126.0	60.0	0.47619	NM_001002912	Q68DL8|Q6GMR8|Q6ZSF9|Q8ND41	Missense_Mutation	SNP	ENST00000326665.5	37	CCDS30755.1	38	0.0173992673992674	37	0.07520325203252033	1	0.0027624309392265192	0	0.0	0	0.0	C	12.22	1.873823	0.33069	0.078302	1.16E-4	ENSG00000178965	ENST00000326665	T	0.11604	2.76	5.54	2.6	0.31112	.	.	.	.	.	T	0.01870	0.0059	N	0.22421	0.69	0.09310	N	1	B	0.15719	0.014	B	0.15870	0.014	T	0.47686	-0.9098	9	0.15952	T	0.53	-1.3011	7.1998	0.25874	0.0:0.5789:0.2768:0.1442	.	811	Q5RHP9	CA173_HUMAN	S	811	ENSP00000322609:A811S	ENSP00000322609:A811S	A	-	1	0	C1orf173	74811551	0.000000	0.05858	0.005000	0.12908	0.008000	0.06430	-0.211000	0.09332	0.701000	0.31803	0.561000	0.74099	GCG	A|0.022;C|0.978	0.022	strong		0.557	C1orf173-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026516.1		
ITGAV	3685	hgsc.bcm.edu	37	2	187490232	187490232	+	Silent	SNP	G	G	A	rs114767222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:187490232G>A	ENST00000261023.3	+	4	715	c.441G>A	c.(439-441)gaG>gaA	p.E147E	ITGAV_ENST00000374907.3_Silent_p.E147E|ITGAV_ENST00000433736.2_Silent_p.E101E	NM_002210.3	NP_002201	P06756	ITAV_HUMAN	integrin, alpha V	147					angiogenesis (GO:0001525)|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)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|apoptotic cell clearance (GO:0043277)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|endodermal cell differentiation (GO:0035987)|entry of symbiont into host cell by promotion of host phagocytosis (GO:0052066)|ERK1 and ERK2 cascade (GO:0070371)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|negative chemotaxis (GO:0050919)|negative regulation of entry of bacterium into host cell (GO:2000536)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of lipid storage (GO:0010888)|negative regulation of lipid transport (GO:0032369)|negative regulation of lipoprotein metabolic process (GO:0050748)|negative regulation of low-density lipoprotein particle receptor biosynthetic process (GO:0045715)|negative regulation of macrophage derived foam cell differentiation (GO:0010745)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast proliferation (GO:0033690)|regulation of apoptotic cell clearance (GO:2000425)|regulation of phagocytosis (GO:0050764)|substrate adhesion-dependent cell spreading (GO:0034446)|viral entry into host cell (GO:0046718)	alphav-beta3 integrin-IGF-1-IGF1R complex (GO:0035867)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin alphav-beta3 complex (GO:0034683)|integrin alphav-beta5 complex (GO:0034684)|integrin alphav-beta8 complex (GO:0034686)|integrin complex (GO:0008305)|lamellipodium membrane (GO:0031258)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	extracellular matrix binding (GO:0050840)|extracellular matrix protein binding (GO:1990430)|fibronectin binding (GO:0001968)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|transforming growth factor beta binding (GO:0050431)|virus receptor activity (GO:0001618)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	47			OV - Ovarian serous cystadenocarcinoma(117;0.0185)|Epithelial(96;0.072)|all cancers(119;0.189)	STAD - Stomach adenocarcinoma(3;0.106)|COAD - Colon adenocarcinoma(31;0.108)	Antithymocyte globulin(DB00098)	GGAGAACTGAGATGAAACAGG	0.403													G|||	50	0.00998403	0.034	0.0072	5008	,	,		17909	0.0		0.0	False		,,,				2504	0.0				p.E147E	Melanoma(58;108 1995 6081)	Atlas-SNP	.											.	ITGAV	124	.	0			c.G441A						PASS	.	G	,,	118,4288	88.7+/-127.4	2,114,2087	126.0	115.0	118.0		303,441,441	0.5	0.3	2	dbSNP_132	118	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	ITGAV	NM_001144999.1,NM_001145000.1,NM_002210.3	,,	2,114,6387	AA,AG,GG		0.0,2.6782,0.9073	,,	101/1003,147/1013,147/1049	187490232	118,12888	2203	4300	6503	SO:0001819	synonymous_variant	3685	exon4			AACTGAGATGAAA		CCDS2292.1, CCDS46470.1, CCDS46471.1	2q31-q32	2012-04-20	2012-04-20		ENSG00000138448	ENSG00000138448		"""CD molecules"", ""Integrins"""	6150	protein-coding gene	gene with protein product		193210	"""antigen identified by monoclonal antibody L230"", ""vitronectin receptor"", ""integrin, alpha V (vitronectin receptor, alpha polypeptide, antigen CD51)"""	VNRA, MSK8, VTNR		2454952	Standard	NM_001144999		Approved	CD51	uc002upq.4	P06756	OTTHUMG00000132635	ENST00000261023.3:c.441G>A	2.37:g.187490232G>A		95.0	0.0	0		85.0	33.0	0.388235	NM_001145000	A0AV67|B0LPF4|B7Z883|B7ZLX0|D3DPG8|E7EWZ6|Q53SK4|Q59EB7|Q6LD15	Silent	SNP	ENST00000261023.3	37	CCDS2292.1																																																																																			G|0.992;A|0.008	0.008	strong		0.403	ITGAV-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255882.2	NM_002210	
RBCK1	10616	hgsc.bcm.edu	37	20	398175	398175	+	Missense_Mutation	SNP	G	G	C	rs143804674	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:398175G>C	ENST00000356286.5	+	3	878	c.173G>C	c.(172-174)tGg>tCg	p.W58S	RBCK1_ENST00000353660.3_Missense_Mutation_p.W16S|RBCK1_ENST00000382181.2_5'UTR	NM_031229.2	NP_112506.2	Q9BYM8	HOIL1_HUMAN	RanBP-type and C3HC4-type zinc finger containing 1	58	Interaction with IRF3.|Interaction with TAB2.|Ubiquitin-like. {ECO:0000255|PROSITE- ProRule:PRU00214}.				negative regulation of necroptotic process (GO:0060546)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of apoptotic process (GO:0043065)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein linear polyubiquitination (GO:0097039)|protein polyubiquitination (GO:0000209)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	LUBAC complex (GO:0071797)	ligase activity (GO:0016874)|ubiquitin binding (GO:0043130)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			kidney(1)|lung(4)	5		all_epithelial(17;0.172)|Lung NSC(37;0.191)|Breast(17;0.231)				TGCAGGCTGTGGGTGAGCGTG	0.587																																					p.W58S		Atlas-SNP	.											.	RBCK1	38	.	0			c.G173C						PASS	.	G	SER/TRP,SER/TRP	5,4401	9.9+/-24.2	0,5,2198	66.0	55.0	58.0		47,173	4.2	1.0	20	dbSNP_134	58	0,8600		0,0,4300	yes	missense,missense	RBCK1	NM_006462.4,NM_031229.2	177,177	0,5,6498	CC,CG,GG		0.0,0.1135,0.0384	benign,benign	16/469,58/511	398175	5,13001	2203	4300	6503	SO:0001583	missense	10616	exon3			GGCTGTGGGTGAG	U67322	CCDS12998.1, CCDS13000.2	20p13	2014-09-17	2006-06-28	2006-06-28	ENSG00000125826	ENSG00000125826		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, RAN-binding domain containing"""	15864	protein-coding gene	gene with protein product	"""heme-oxidized IRP2 ubiquitin ligase 1"""	610924	"""chromosome 20 open reading frame 18"""	C20orf18			Standard	NM_031229		Approved	RBCK2, XAP4, RNF54, ZRANB4, UBCE7IP3, HOIL1	uc002wdp.4	Q9BYM8	OTTHUMG00000031634	ENST00000356286.5:c.173G>C	20.37:g.398175G>C	ENSP00000348632:p.Trp58Ser	85.0	0.0	0		94.0	54.0	0.574468	NM_031229	O95623|Q86SL2|Q96BS3|Q9BYM9	Missense_Mutation	SNP	ENST00000356286.5	37	CCDS13000.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.67|14.67	2.605738|2.605738	0.46527|0.46527	0.001135|0.001135	0.0|0.0	ENSG00000125826|ENSG00000125826	ENST00000414880|ENST00000411647;ENST00000356286;ENST00000441733;ENST00000353660;ENST00000400244;ENST00000400243	.|T;T;T;T	.|0.10477	.|2.87;2.87;2.87;2.87	5.12|5.12	4.17|4.17	0.49024|0.49024	.|Ubiquitin supergroup (1);	.|0.578121	.|0.16613	.|N	.|0.206802	T|T	0.09905|0.09905	0.0243|0.0243	L|L	0.47716|0.47716	1.5|1.5	0.80722|0.80722	D|D	1|1	.|B;B;B	.|0.19817	.|0.002;0.034;0.039	.|B;B;B	.|0.21708	.|0.002;0.036;0.01	T|T	0.08391|0.08391	-1.0724|-1.0724	5|10	.|0.12430	.|T	.|0.62	-21.4854|-21.4854	9.3395|9.3395	0.38071|0.38071	0.0967:0.0:0.9033:0.0|0.0967:0.0:0.9033:0.0	.|.	.|48;16;58	.|B4E0F5;Q9BYM8-3;Q9BYM8	.|.;.;HOIL1_HUMAN	R|S	91|58;58;57;16;58;99	.|ENSP00000415080:W58S;ENSP00000348632:W58S;ENSP00000387799:W57S;ENSP00000254960:W16S	.|ENSP00000254960:W16S	G|W	+|+	1|2	0|0	RBCK1|RBCK1	346175|346175	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.780000|0.780000	0.44128|0.44128	1.134000|1.134000	0.31442|0.31442	1.374000|1.374000	0.46228|0.46228	0.557000|0.557000	0.71058|0.71058	GGG|TGG	G|1.000;C|0.000	0.000	strong		0.587	RBCK1-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077461.3	NM_031229	
NPFFR2	10886	hgsc.bcm.edu	37	4	73012709	73012709	+	Missense_Mutation	SNP	T	T	C	rs61733659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:73012709T>C	ENST00000308744.6	+	4	847	c.749T>C	c.(748-750)gTc>gCc	p.V250A	NPFFR2_ENST00000395999.1_Missense_Mutation_p.V151A|NPFFR2_ENST00000506359.1_3'UTR|NPFFR2_ENST00000344413.5_3'UTR|NPFFR2_ENST00000358749.3_Missense_Mutation_p.V148A	NM_004885.2	NP_004876.2	Q9Y5X5	NPFF2_HUMAN	neuropeptide FF receptor 2	250					detection of abiotic stimulus (GO:0009582)|G-protein coupled receptor signaling pathway (GO:0007186)|regulation of adenylate cyclase activity (GO:0045761)|regulation of cAMP-dependent protein kinase activity (GO:2000479)|regulation of MAPK cascade (GO:0043408)	actin cytoskeleton (GO:0015629)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide receptor activity (GO:0008188)			NS(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(24)|ovary(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43			Lung(101;0.0935)|LUSC - Lung squamous cell carcinoma(112;0.138)			CAGTGTGTGGTCTACCCTTTT	0.393													T|||	47	0.00938498	0.0348	0.0014	5008	,	,		18136	0.0		0.0	False		,,,				2504	0.0				p.V250A		Atlas-SNP	.											.	NPFFR2	98	.	0			c.T749C						PASS	.	T	ALA/VAL,ALA/VAL,ALA/VAL	122,4284	91.6+/-130.3	5,112,2086	189.0	190.0	190.0		452,749,443	5.8	1.0	4	dbSNP_129	190	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense	NPFFR2	NM_001144756.1,NM_004885.2,NM_053036.2	64,64,64	5,114,6384	CC,CT,TT		0.0233,2.769,0.9534	possibly-damaging,possibly-damaging,possibly-damaging	151/424,250/523,148/421	73012709	124,12882	2203	4300	6503	SO:0001583	missense	10886	exon4			GTGTGGTCTACCC	AF236083	CCDS3551.1, CCDS3552.1, CCDS47072.1	4q21	2012-08-10	2006-02-15	2006-02-15	ENSG00000056291	ENSG00000056291		"""GPCR / Class A :  Neuropeptide receptors : FF/AF"", ""GPCR / Class A : RF amide peptide receptors"""	4525	protein-coding gene	gene with protein product	"""neuropeptide FF 2"""	607449	"""G protein-coupled receptor 74"""	GPR74		10079187, 10851242	Standard	NM_001144756		Approved	NPFF2, NPGPR	uc003hgg.2	Q9Y5X5	OTTHUMG00000129918	ENST00000308744.6:c.749T>C	4.37:g.73012709T>C	ENSP00000307822:p.Val250Ala	84.0	0.0	0		86.0	42.0	0.488372	NM_004885	Q96RV1|Q9NR49	Missense_Mutation	SNP	ENST00000308744.6	37	CCDS3551.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	T	17.37	3.371957	0.61624	0.02769	2.33E-4	ENSG00000056291	ENST00000308744;ENST00000395999;ENST00000358749	T;T;T	0.38887	1.11;1.11;1.11	5.81	5.81	0.92471	GPCR, rhodopsin-like superfamily (1);	0.256399	0.27725	N	0.018102	T	0.32133	0.0819	M	0.85299	2.745	0.80722	D	1	P;D	0.55385	0.772;0.971	P;P	0.57057	0.628;0.812	T	0.60662	-0.7219	10	0.87932	D	0	.	15.8328	0.78769	0.0:0.0:0.0:1.0	rs61733659	151;250	Q9Y5X5-3;Q9Y5X5	.;NPFF2_HUMAN	A	250;151;148	ENSP00000307822:V250A;ENSP00000379321:V151A;ENSP00000351599:V148A	ENSP00000307822:V250A	V	+	2	0	NPFFR2	73231573	1.000000	0.71417	0.974000	0.42286	0.178000	0.23041	7.911000	0.87458	2.221000	0.72209	0.528000	0.53228	GTC	T|0.990;C|0.010	0.010	strong		0.393	NPFFR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252170.2	NM_004885	
SOWAHA	134548	hgsc.bcm.edu	37	5	132150804	132150804	+	Silent	SNP	G	G	A	rs7719416	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:132150804G>A	ENST00000378693.2	+	1	1772	c.1491G>A	c.(1489-1491)aaG>aaA	p.K497K	AC004775.5_ENST00000607389.1_lincRNA	NM_175873.4	NP_787069.3	Q2M3V2	SWAHA_HUMAN	sosondowah ankyrin repeat domain family member A	497																	GAGGCTTGAAGAAGTCGAGCT	0.587													G|||	151	0.0301518	0.1097	0.0086	5008	,	,		18235	0.0		0.0	False		,,,				2504	0.0				p.K497K		Atlas-SNP	.											.	.	.	.	0			c.G1491A						PASS	.	G		458,3948	214.5+/-233.7	27,404,1772	47.0	50.0	49.0		1491	4.2	1.0	5	dbSNP_116	49	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous	ANKRD43	NM_175873.4		27,413,6063	AA,AG,GG		0.1047,10.3949,3.5907		497/550	132150804	467,12539	2203	4300	6503	SO:0001819	synonymous_variant	134548	exon1			CTTGAAGAAGTCG	AK090823	CCDS43361.1	5q23.3	2013-01-10	2012-01-12	2012-01-12	ENSG00000198944	ENSG00000198944		"""Ankyrin repeat domain containing"""	27033	protein-coding gene	gene with protein product			"""ankyrin repeat domain 43"""	ANKRD43		22234889	Standard	NM_175873		Approved		uc003kxw.3	Q2M3V2	OTTHUMG00000059844	ENST00000378693.2:c.1491G>A	5.37:g.132150804G>A		78.0	0.0	0		103.0	50.0	0.485437	NM_175873	Q8NAE7	Silent	SNP	ENST00000378693.2	37	CCDS43361.1																																																																																			G|0.965;A|0.035	0.035	strong		0.587	SOWAHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133062.1	NM_175873	
GNAI1	2770	hgsc.bcm.edu	37	7	79828573	79828573	+	Silent	SNP	A	A	G	rs6970347	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:79828573A>G	ENST00000351004.3	+	4	709	c.336A>G	c.(334-336)ggA>ggG	p.G112G	GNAI1_ENST00000457358.2_Silent_p.G60G	NM_002069.5	NP_002060.4	P63096	GNAI1_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 1	112					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|G-protein coupled receptor signaling pathway (GO:0007186)|platelet activation (GO:0030168)|response to peptide hormone (GO:0043434)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled serotonin receptor binding (GO:0031821)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	19						TGCTAGCTGGAGCTGCTGAAG	0.413													A|||	92	0.0183706	0.0673	0.0043	5008	,	,		18019	0.0		0.0	False		,,,				2504	0.0				p.G112G		Atlas-SNP	.											.	GNAI1	44	.	0			c.A336G						PASS	.	A		284,4122	157.8+/-190.6	14,256,1933	116.0	110.0	112.0		336	-3.0	1.0	7	dbSNP_116	112	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	GNAI1	NM_002069.5		14,258,6231	GG,GA,AA		0.0233,6.4458,2.199		112/355	79828573	286,12720	2203	4300	6503	SO:0001819	synonymous_variant	2770	exon4			AGCTGGAGCTGCT	AL049933	CCDS5595.1, CCDS59061.1	7q21-q22	2008-07-18			ENSG00000127955	ENSG00000127955			4384	protein-coding gene	gene with protein product	"""Gi1 protein alpha subunit"""	139310				3110783	Standard	NM_002069		Approved		uc003uhb.1	P63096	OTTHUMG00000023523	ENST00000351004.3:c.336A>G	7.37:g.79828573A>G		122.0	0.0	0		78.0	40.0	0.512821	NM_002069	A8KA88|B4E2V1|C9J3A4|P04898|P11015|P31871|Q5U074|Q8TAN5|Q9UGA4	Silent	SNP	ENST00000351004.3	37	CCDS5595.1																																																																																			A|0.982;G|0.018	0.018	strong		0.413	GNAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253254.1	NM_002069	
ZC3HAV1L	92092	hgsc.bcm.edu	37	7	138713674	138713674	+	Silent	SNP	C	C	G	rs7800990	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:138713674C>G	ENST00000275766.1	-	3	545	c.534G>C	c.(532-534)ctG>ctC	p.L178L		NM_080660.3	NP_542391.2	Q96H79	ZCCHL_HUMAN	zinc finger CCCH-type, antiviral 1-like	178										NS(2)|endometrium(2)|large_intestine(1)|lung(4)|skin(1)	10						AGTAGCCATACAGGGCTTCCC	0.433													G|||	185	0.0369409	0.1354	0.0072	5008	,	,		23164	0.0		0.001	False		,,,				2504	0.0				p.L178L		Atlas-SNP	.											.	ZC3HAV1L	15	.	0			c.G534C						PASS	.	G		554,3852	774.6+/-414.0	28,498,1677	71.0	69.0	70.0		534	-5.1	0.0	7	dbSNP_116	70	4,8596	819.0+/-406.8	0,4,4296	no	coding-synonymous	ZC3HAV1L	NM_080660.3		28,502,5973	GG,GC,CC		0.0465,12.5738,4.2903		178/301	138713674	558,12448	2203	4300	6503	SO:0001819	synonymous_variant	92092	exon3			GCCATACAGGGCT	BC008842	CCDS5850.1	7q34	2006-07-03	2006-07-03	2006-07-03	ENSG00000146858	ENSG00000146858			22423	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 39"""	C7orf39			Standard	NM_080660		Approved	MGC14289	uc003vum.1	Q96H79	OTTHUMG00000157229	ENST00000275766.1:c.534G>C	7.37:g.138713674C>G		93.0	0.0	0		78.0	43.0	0.551282	NM_080660	Q8WUD9	Silent	SNP	ENST00000275766.1	37	CCDS5850.1																																																																																			C|0.961;G|0.039	0.039	strong		0.433	ZC3HAV1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348090.1	NM_080660	
TLR6	10333	hgsc.bcm.edu	37	4	38829702	38829702	+	Missense_Mutation	SNP	C	C	T	rs5743816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:38829702C>T	ENST00000381950.1	-	1	1458	c.1393G>A	c.(1393-1395)Gtt>Att	p.V465I	TLR6_ENST00000436693.2_Missense_Mutation_p.V465I			Q9Y2C9	TLR6_HUMAN	toll-like receptor 6	465			V -> I (in dbSNP:rs5743816). {ECO:0000269|PubMed:21618349}.		activation of NF-kappaB-inducing kinase activity (GO:0007250)|cellular response to diacyl bacterial lipopeptide (GO:0071726)|defense response to bacterium (GO:0042742)|detection of diacyl bacterial lipopeptide (GO:0042496)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|nitric oxide metabolic process (GO:0046209)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 6 signaling pathway (GO:0034150)|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)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Toll-like receptor 2-Toll-like receptor 6 protein complex (GO:0035355)	diacyl lipopeptide binding (GO:0042498)|lipopeptide binding (GO:0071723)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						TGTTTAGGAACGCTCTTTATT	0.388													c|||	159	0.0317492	0.1006	0.0029	5008	,	,		20792	0.0069		0.001	False		,,,				2504	0.0164				p.V465I		Atlas-SNP	.											.	TLR6	67	.	0			c.G1393A						PASS	.						133.0	145.0	141.0					4																	38829702		2203	4300	6503	SO:0001583	missense	10333	exon2			TAGGAACGCTCTT		CCDS3446.1	4p16.1	2009-11-23			ENSG00000174130	ENSG00000174130		"""CD molecules"""	16711	protein-coding gene	gene with protein product		605403				10231569	Standard	NM_006068		Approved	CD286	uc010ifg.2	Q9Y2C9	OTTHUMG00000128579	ENST00000381950.1:c.1393G>A	4.37:g.38829702C>T	ENSP00000371376:p.Val465Ile	207.0	0.0	0		211.0	80.0	0.379147	NM_006068	B3Y640|B6CH35|B6RFS4|B6RFS5|Q2NKL3	Missense_Mutation	SNP	ENST00000381950.1	37	CCDS3446.1	49	0.022435897435897436	45	0.09146341463414634	3	0.008287292817679558	1	0.0017482517482517483	0	0.0	c	0	-2.849326	0.00066	.	.	ENSG00000174130	ENST00000436693;ENST00000381950	T;T	0.48522	0.81;0.81	5.14	2.63	0.31362	.	0.182497	0.38326	N	0.001737	T	0.00875	0.0029	N	0.16201	0.385	0.45554	P	0.0014960000000000528	B	0.02656	0.0	B	0.10450	0.005	T	0.11567	-1.0582	9	0.07325	T	0.83	.	9.4019	0.38437	0.0:0.2162:0.0:0.7838	rs5743816	465	Q9Y2C9	TLR6_HUMAN	I	465	ENSP00000389600:V465I;ENSP00000371376:V465I	ENSP00000371376:V465I	V	-	1	0	TLR6	38506097	0.066000	0.20996	0.500000	0.27589	0.056000	0.15407	0.404000	0.20999	0.787000	0.33731	-0.578000	0.04140	GTT	C|0.931;T|0.069	0.069	strong		0.388	TLR6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250431.1		
AFAP1L2	84632	hgsc.bcm.edu	37	10	116064528	116064528	+	Missense_Mutation	SNP	G	G	A	rs73365341	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:116064528G>A	ENST00000304129.4	-	11	1263	c.1234C>T	c.(1234-1236)Ctc>Ttc	p.L412F	AFAP1L2_ENST00000491814.1_5'Flank|AFAP1L2_ENST00000369271.3_Missense_Mutation_p.L412F|AFAP1L2_ENST00000545353.1_Missense_Mutation_p.L465F			Q8N4X5	AF1L2_HUMAN	actin filament associated protein 1-like 2	412	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				inflammatory response (GO:0006954)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of interleukin-6 production (GO:0032675)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)	protein tyrosine kinase activator activity (GO:0030296)|SH2 domain binding (GO:0042169)|SH3 domain binding (GO:0017124)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|prostate(2)	21		Colorectal(252;0.175)|Breast(234;0.231)		Epithelial(162;0.0219)|all cancers(201;0.0561)		AAGGAGTAGAGGTGGTCGGGG	0.682													G|||	531	0.10603	0.354	0.0375	5008	,	,		12908	0.0		0.0199	False		,,,				2504	0.0174				p.L412F		Atlas-SNP	.											.	AFAP1L2	90	.	0			c.C1234T						PASS	.	G	PHE/LEU,PHE/LEU	1464,2940	461.5+/-352.9	257,950,995	39.0	38.0	38.0		1234,1234	5.3	1.0	10	dbSNP_130	38	165,8435	76.3+/-139.0	3,159,4138	yes	missense,missense	AFAP1L2	NM_001001936.1,NM_032550.2	22,22	260,1109,5133	AA,AG,GG		1.9186,33.2425,12.5269	probably-damaging,probably-damaging	412/819,412/815	116064528	1629,11375	2202	4300	6502	SO:0001583	missense	84632	exon11			AGTAGAGGTGGTC	BC024314	CCDS31286.1, CCDS31287.1	10q26.11	2013-01-10	2007-02-07	2007-02-07	ENSG00000169129	ENSG00000169129		"""Pleckstrin homology (PH) domain containing"""	25901	protein-coding gene	gene with protein product		612420	"""KIAA1914"""	KIAA1914		11572484, 17412687	Standard	XM_005270239		Approved	FLJ14564, Em:AC005383.4, XB130	uc001lbn.3	Q8N4X5	OTTHUMG00000019086	ENST00000304129.4:c.1234C>T	10.37:g.116064528G>A	ENSP00000303042:p.Leu412Phe	40.0	0.0	0		49.0	49.0	1	NM_032550	A8K6P7|B3KVQ8|Q2UZW3|Q8TB54|Q96PX4|Q96SY5	Missense_Mutation	SNP	ENST00000304129.4	37	CCDS31286.1	224	0.10256410256410256	195	0.39634146341463417	15	0.04143646408839779	0	0.0	14	0.018469656992084433	G	26.3	4.722438	0.89298	0.332425	0.019186	ENSG00000169129	ENST00000369271;ENST00000304129;ENST00000392974;ENST00000545353	T;T;T	0.75589	-0.95;-0.95;-0.95	5.3	5.3	0.74995	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.62723	1.935	0.09310	P	0.999999814385	D;D;D;D;D	0.89917	1.0;1.0;0.997;1.0;1.0	D;D;D;D;D	0.97110	0.998;0.999;0.984;0.998;1.0	T	0.02104	-1.1213	9	0.45353	T	0.12	-16.927	18.9486	0.92632	0.0:0.0:1.0:0.0	.	465;466;440;412;412	F5GZE1;B7Z2Q0;Q8N4X5-4;Q8N4X5-2;Q8N4X5	.;.;.;.;AF1L2_HUMAN	F	412;412;439;465	ENSP00000358276:L412F;ENSP00000303042:L412F;ENSP00000444511:L465F	ENSP00000303042:L412F	L	-	1	0	AFAP1L2	116054518	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	7.973000	0.88032	2.470000	0.83445	0.563000	0.77884	CTC	G|0.884;A|0.116	0.116	strong		0.682	AFAP1L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050462.1	NM_032550	
GBP5	115362	hgsc.bcm.edu	37	1	89735229	89735229	+	Missense_Mutation	SNP	C	C	G	rs17130763	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:89735229C>G	ENST00000370459.3	-	2	137	c.10G>C	c.(10-12)Gag>Cag	p.E4Q	GBP5_ENST00000343435.5_Missense_Mutation_p.E4Q|RP4-620F22.2_ENST00000437128.1_RNA			Q96PP8	GBP5_HUMAN	guanylate binding protein 5	4	GTPase domain (Globular). {ECO:0000250}.		E -> Q (in dbSNP:rs17130763).			cytoplasm (GO:0005737)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(1)|endometrium(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)	24				all cancers(265;0.00784)|Epithelial(280;0.0286)		ATGTGGATCTCTAAAGCCATG	0.443													C|||	76	0.0151757	0.053	0.0086	5008	,	,		12783	0.0		0.0	False		,,,				2504	0.0				p.E4Q		Atlas-SNP	.											.	GBP5	65	.	0			c.G10C						PASS	.	C	GLN/GLU,GLN/GLU	202,4204	125.3+/-162.5	4,194,2005	169.0	164.0	166.0		10,10	1.5	0.0	1	dbSNP_123	166	0,8600		0,0,4300	yes	missense,missense	GBP5	NM_001134486.2,NM_052942.3	29,29	4,194,6305	GG,GC,CC		0.0,4.5847,1.5531	benign,benign	4/587,4/587	89735229	202,12804	2203	4300	6503	SO:0001583	missense	115362	exon3			GGATCTCTAAAGC	AF430642	CCDS722.1	1p22.2	2008-02-05			ENSG00000154451	ENSG00000154451			19895	protein-coding gene	gene with protein product		611467					Standard	NM_052942		Approved		uc001dnd.3	Q96PP8	OTTHUMG00000010006	ENST00000370459.3:c.10G>C	1.37:g.89735229C>G	ENSP00000359488:p.Glu4Gln	142.0	0.0	0		137.0	72.0	0.525547	NM_052942	B2RCE1|Q86TM5	Missense_Mutation	SNP	ENST00000370459.3	37	CCDS722.1	25	0.011446886446886446	21	0.042682926829268296	4	0.011049723756906077	0	0.0	0	0.0	C	11.40	1.626401	0.28978	0.045847	0.0	ENSG00000154451	ENST00000343435;ENST00000370459;ENST00000443807	T;T;T	0.66099	0.36;0.36;-0.19	5.0	1.48	0.22813	.	0.954043	0.08802	N	0.891614	T	0.35008	0.0917	M	0.62154	1.92	0.09310	N	1	B	0.20052	0.041	B	0.22152	0.038	T	0.32693	-0.9897	10	0.33141	T	0.24	-0.4944	5.2406	0.15469	0.1544:0.6219:0.0:0.2237	rs17130763;rs17130763	4	Q96PP8	GBP5_HUMAN	Q	4	ENSP00000340396:E4Q;ENSP00000359488:E4Q;ENSP00000403010:E4Q	ENSP00000340396:E4Q	E	-	1	0	GBP5	89507817	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	0.226000	0.17776	0.521000	0.28445	0.655000	0.94253	GAG	C|0.976;G|0.024	0.024	strong		0.443	GBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027700.1	NM_052942	
ABCA1	19	hgsc.bcm.edu	37	9	107547872	107547872	+	Silent	SNP	C	C	T	rs61741359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107547872C>T	ENST00000374736.3	-	49	6844	c.6450G>A	c.(6448-6450)ccG>ccA	p.P2150P		NM_005502.3	NP_005493.2	O95477	ABCA1_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 1	2150			P -> L (in HDLD2). {ECO:0000269|PubMed:11086027}.		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)			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)	GCTTCAGGTCCGGGTTGGACC	0.418													C|||	57	0.0113818	0.0386	0.0072	5008	,	,		17972	0.0		0.001	False		,,,				2504	0.0				p.P2150P		Atlas-SNP	.											.	ABCA1	244	.	0			c.G6450A						PASS	.	C		172,4234	112.5+/-150.6	0,172,2031	85.0	87.0	87.0		6450	2.2	1.0	9	dbSNP_129	87	0,8600		0,0,4300	yes	coding-synonymous	ABCA1	NM_005502.3		0,172,6331	TT,TC,CC		0.0,3.9038,1.3225		2150/2262	107547872	172,12834	2203	4300	6503	SO:0001819	synonymous_variant	19	exon49			CAGGTCCGGGTTG	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.6450G>A	9.37:g.107547872C>T		70.0	0.0	0		71.0	54.0	0.760563	NM_005502	Q5VX33|Q96S56|Q96T85|Q9NQV4|Q9UN06|Q9UN07|Q9UN08|Q9UN09	Silent	SNP	ENST00000374736.3	37	CCDS6762.1																																																																																			C|0.985;T|0.015	0.015	strong		0.418	ABCA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053491.1	NM_005502	
PKD1L1	168507	hgsc.bcm.edu	37	7	47925609	47925609	+	Silent	SNP	G	G	A	rs78480673	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:47925609G>A	ENST00000289672.2	-	18	2930	c.2880C>T	c.(2878-2880)ctC>ctT	p.L960L		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	960	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						AAATGGCACCGAGTCCCAGCG	0.488													g|||	194	0.038738	0.1377	0.0101	5008	,	,		17976	0.0		0.004	False		,,,				2504	0.001				p.L960L		Atlas-SNP	.											PKD1L1,NS,carcinoma,0,2	PKD1L1	328	2	0			c.C2880T						PASS	.	A		638,3768	272.8+/-271.0	47,544,1612	60.0	56.0	58.0		2880	-9.9	0.0	7	dbSNP_132	58	85,8515	48.1+/-107.5	1,83,4216	no	coding-synonymous	PKD1L1	NM_138295.3		48,627,5828	AA,AG,GG		0.9884,14.4803,5.559		960/2850	47925609	723,12283	2203	4300	6503	SO:0001819	synonymous_variant	168507	exon18			GGCACCGAGTCCC	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.2880C>T	7.37:g.47925609G>A		115.0	0.0	0		128.0	65.0	0.507812	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	37	CCDS34633.1																																																																																			G|0.951;A|0.049	0.049	strong		0.488	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
KIAA1683	80726	hgsc.bcm.edu	37	19	18376780	18376780	+	Missense_Mutation	SNP	T	T	C	rs12462974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18376780T>C	ENST00000600328.3	-	3	1763	c.1570A>G	c.(1570-1572)Aca>Gca	p.T524A	KIAA1683_ENST00000600359.3_Missense_Mutation_p.T478A|KIAA1683_ENST00000392413.4_Missense_Mutation_p.T524A			Q9H0B3	K1683_HUMAN	KIAA1683	524			T -> A (in dbSNP:rs12462974).			mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						TTTGCCACTGTTGGAGAGGCC	0.617													T|||	738	0.147364	0.4297	0.1282	5008	,	,		17239	0.0129		0.0288	False		,,,				2504	0.0399				p.T524A		Atlas-SNP	.											.	KIAA1683	190	.	0			c.A1570G						PASS	.	T	ALA/THR,ALA/THR,ALA/THR	1674,2732	510.1+/-367.4	321,1032,850	74.0	68.0	70.0		1570,1432,1570	-7.2	0.0	19	dbSNP_120	70	231,8369	95.6+/-157.4	4,223,4073	yes	missense,missense,missense	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	58,58,58	325,1255,4923	CC,CT,TT		2.686,37.9936,14.6471	benign,benign,benign	524/1368,478/1135,524/1181	18376780	1905,11101	2203	4300	6503	SO:0001583	missense	80726	exon3			CCACTGTTGGAGA	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.1570A>G	19.37:g.18376780T>C	ENSP00000470780:p.Thr524Ala	127.0	0.0	0		153.0	83.0	0.542484	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	37	CCDS32958.1	278	0.12728937728937728	213	0.4329268292682927	48	0.13259668508287292	1	0.0017482517482517483	16	0.021108179419525065	T	0.160	-1.082165	0.01888	0.379936	0.02686	ENSG00000130518	ENST00000392413;ENST00000359737;ENST00000427634	T;T;T	0.03242	4.07;4.08;4.0	3.97	-7.21	0.01490	.	1.083510	0.07343	N	0.881096	T	0.00012	0.0000	N	0.02539	-0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47686	-0.9098	9	0.02654	T	1	-2.4415	0.3148	0.00294	0.2788:0.2233:0.1381:0.3598	rs12462974;rs12462974	524;524	E9PDE0;Q9H0B3	.;K1683_HUMAN	A	524;524;478	ENSP00000376213:T524A;ENSP00000352774:T524A;ENSP00000404501:T478A	ENSP00000352774:T524A	T	-	1	0	KIAA1683	18237780	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.232000	0.09055	-1.289000	0.02375	-0.337000	0.08149	ACA	T|0.861;C|0.139	0.139	strong		0.617	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
CRNKL1	51340	hgsc.bcm.edu	37	20	20033194	20033194	+	Silent	SNP	G	G	T	rs145198573	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:20033194G>T	ENST00000377340.2	-	2	307	c.276C>A	c.(274-276)cgC>cgA	p.R92R	CRNKL1_ENST00000377327.4_Silent_p.R80R|CRNKL1_ENST00000536226.1_5'Flank|C20orf26_ENST00000377309.2_5'UTR|C20orf26_ENST00000377306.1_5'Flank|C20orf26_ENST00000245957.5_5'Flank|C20orf26_ENST00000389656.3_5'UTR	NM_001278628.1|NM_016652.4	NP_001265557.1|NP_057736.4	Q9BZJ0	CRNL1_HUMAN	crooked neck pre-mRNA splicing factor 1	92					mRNA splicing, via spliceosome (GO:0000398)|spliceosomal complex assembly (GO:0000245)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(2)|cervix(2)|endometrium(7)|large_intestine(11)|lung(12)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(6)	45						CGTCCTCCTTGCGGCAGCGCG	0.662													G|||	20	0.00399361	0.0151	0.0	5008	,	,		18175	0.0		0.0	False		,,,				2504	0.0				p.R92R		Atlas-SNP	.											.	CRNKL1	101	.	0			c.C276A						PASS	.	G	,	67,4339	60.5+/-97.4	0,67,2136	51.0	47.0	48.0		,276	-2.9	0.0	20	dbSNP_134	48	2,8598	1.2+/-3.3	0,2,4298	no	utr-5,coding-synonymous	C20orf26,CRNKL1	NM_015585.3,NM_016652.4	,	0,69,6434	TT,TG,GG		0.0233,1.5207,0.5305	,	,92/849	20033194	69,12937	2203	4300	6503	SO:0001819	synonymous_variant	51340	exon2			CTCCTTGCGGCAG	AF255443	CCDS33446.1, CCDS63238.1, CCDS63239.1	20p11.2	2013-10-03	2013-10-03		ENSG00000101343	ENSG00000101343			15762	protein-coding gene	gene with protein product	"""SYF3 pre-mRNA-splicing factor"""	610952	"""crooked neck (Drosophila Crn homolog)-like 1"", ""Crn, crooked neck-like 1 (Drosophila)"", ""crooked neck pre-mRNA splicing factor-like 1 (Drosophila)"""				Standard	NM_016652		Approved	CRN, CLF, SYF3, Clf1	uc002wrs.3	Q9BZJ0	OTTHUMG00000032000	ENST00000377340.2:c.276C>A	20.37:g.20033194G>T		68.0	0.0	0		76.0	37.0	0.486842	NM_016652	A8K9T4|Q5JY64|Q8WYI5|Q9BZI9|Q9BZJ1|Q9BZJ2|Q9GZW7|Q9H8F8|Q9NQH5|Q9NYD8	Silent	SNP	ENST00000377340.2	37	CCDS33446.1																																																																																			G|0.996;T|0.004	0.004	strong		0.662	CRNKL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000127787.1		
ANKRD34B	340120	hgsc.bcm.edu	37	5	79854667	79854667	+	Missense_Mutation	SNP	A	A	G	rs147745221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:79854667A>G	ENST00000338682.3	-	5	1844	c.1172T>C	c.(1171-1173)aTa>aCa	p.I391T		NM_001004441.2	NP_001004441.2	A5PLL1	AN34B_HUMAN	ankyrin repeat domain 34B	391						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(13)|pancreas(1)|prostate(1)|urinary_tract(1)	28		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;2.17e-46)|Epithelial(54;5.64e-41)|all cancers(79;3.24e-36)		TTTCTTTCCTATAAGTGCTTT	0.463													a|||	2	0.000399361	0.0015	0.0	5008	,	,		14523	0.0		0.0	False		,,,				2504	0.0				p.I391T		Atlas-SNP	.											.	ANKRD34B	61	.	0			c.T1172C						PASS	.	G	THR/ILE	12,4394	19.1+/-41.9	0,12,2191	57.0	62.0	60.0		1172	-5.4	0.0	5	dbSNP_134	60	0,8600		0,0,4300	yes	missense	ANKRD34B	NM_001004441.2	89	0,12,6491	GG,GA,AA		0.0,0.2724,0.0923	benign	391/515	79854667	12,12994	2203	4300	6503	SO:0001583	missense	340120	exon5			TTTCCTATAAGTG		CCDS34194.1	5q14.1	2014-08-12			ENSG00000189127	ENSG00000189127		"""Ankyrin repeat domain containing"""	33736	protein-coding gene	gene with protein product							Standard	NM_001004441		Approved	DP58	uc003kgw.3	A5PLL1	OTTHUMG00000162541	ENST00000338682.3:c.1172T>C	5.37:g.79854667A>G	ENSP00000339802:p.Ile391Thr	46.0	0.0	0		57.0	34.0	0.596491	NM_001004441	B2RPH1|Q68D79	Missense_Mutation	SNP	ENST00000338682.3	37	CCDS34194.1	.	.	.	.	.	.	.	.	.	.	a	4.439	0.081337	0.08533	0.002724	0.0	ENSG00000189127	ENST00000338682	T	0.20738	2.05	5.8	-5.38	0.02673	.	17.413900	0.01263	N	0.009220	T	0.17450	0.0419	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25293	-1.0136	10	0.40728	T	0.16	3.3058	10.1179	0.42603	0.5602:0.0:0.3519:0.0879	.	391	A5PLL1	AN34B_HUMAN	T	391	ENSP00000339802:I391T	ENSP00000339802:I391T	I	-	2	0	ANKRD34B	79890423	0.000000	0.05858	0.000000	0.03702	0.673000	0.39480	-0.530000	0.06179	-1.261000	0.02462	-0.976000	0.02587	ATA	A|0.999;G|0.001	0.001	strong		0.463	ANKRD34B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369475.1	NM_001004441	
XKR3	150165	hgsc.bcm.edu	37	22	17288849	17288849	+	Missense_Mutation	SNP	A	A	G	rs150400922	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:17288849A>G	ENST00000331428.5	-	2	217	c.115T>C	c.(115-117)Ttc>Ctc	p.F39L		NM_175878.3	NP_787074.2	Q5GH77	XKR3_HUMAN	XK, Kell blood group complex subunit-related family, member 3	39						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(6)|ovary(1)|pancreas(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				ACAGTTGAGAAGATAATGCTA	0.388													.|||	22	0.00439297	0.0159	0.0014	5008	,	,		19510	0.0		0.0	False		,,,				2504	0.0				p.F39L		Atlas-SNP	.											.	XKR3	51	.	0			c.T115C						PASS	.	A	LEU/PHE	71,3691		0,71,1810	115.0	110.0	112.0		115	0.5	0.0	22	dbSNP_134	112	0,8218		0,0,4109	yes	missense	XKR3	NM_175878.3	22	0,71,5919	GG,GA,AA		0.0,1.8873,0.5927	benign	39/460	17288849	71,11909	1881	4109	5990	SO:0001583	missense	150165	exon2			TTGAGAAGATAAT	AY989815	CCDS42975.1	22q11.1	2007-01-16	2006-01-12		ENSG00000172967	ENSG00000172967			28778	protein-coding gene	gene with protein product		611674	"""X Kell blood group precursor-related family, member 3"""			16431037	Standard	NM_175878		Approved	MGC57211, XTES	uc002zlv.3	Q5GH77	OTTHUMG00000143726	ENST00000331428.5:c.115T>C	22.37:g.17288849A>G	ENSP00000331704:p.Phe39Leu	185.0	0.0	0		209.0	94.0	0.449761	NM_175878	B2RPN1|Q52PG8|Q8N7E1	Missense_Mutation	SNP	ENST00000331428.5	37	CCDS42975.1	8	0.003663003663003663	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	.	4.134	0.023117	0.08006	0.018873	0.0	ENSG00000172967	ENST00000331428	T	0.61859	0.07	0.539	0.539	0.17156	.	0.396682	0.23023	U	0.052823	T	0.17577	0.0422	N	0.22421	0.69	0.19775	N	0.999951	B	0.02656	0.0	B	0.01281	0.0	T	0.04090	-1.0978	10	0.13853	T	0.58	.	2.6787	0.05087	0.5696:1.0E-4:0.0:0.4304	.	39	Q5GH77	XKR3_HUMAN	L	39	ENSP00000331704:F39L	ENSP00000331704:F39L	F	-	1	0	XKR3	15668849	0.930000	0.31532	0.021000	0.16686	0.010000	0.07245	0.129000	0.15830	0.485000	0.27652	0.246000	0.17985	TTC	A|0.996;G|0.004	0.004	strong		0.388	XKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289789.1	NM_175878	
C7orf55-LUC7L2	100996928	hgsc.bcm.edu	37	7	139090515	139090515	+	Silent	SNP	A	A	G	rs74758604	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:139090515A>G	ENST00000354926.4	+	5	846	c.492A>G	c.(490-492)gcA>gcG	p.A164A	C7orf55-LUC7L2_ENST00000263545.6_Silent_p.A163A|C7orf55-LUC7L2_ENST00000541170.3_Silent_p.A161A|LUC7L2_ENST00000541515.3_Silent_p.A230A	NM_001270643.1|NM_016019.4	NP_001257572.1|NP_057103.2			C7orf55-LUC7L2 readthrough																		AAGCACGGGCAAAGAAAAGAG	0.368													A|||	80	0.0159744	0.0582	0.0029	5008	,	,		17933	0.0		0.001	False		,,,				2504	0.0				p.A230A		Atlas-SNP	.											LUC7L2,NS,carcinoma,+2,1	.	.	1	0			c.A690G						PASS	.	A		171,3519		5,161,1679	100.0	103.0	102.0		492	1.4	1.0	7	dbSNP_132	102	1,8165		0,1,4082	no	coding-synonymous	LUC7L2	NM_016019.3		5,162,5761	GG,GA,AA		0.0122,4.6341,1.4507		164/393	139090515	172,11684	1845	4083	5928	SO:0001819	synonymous_variant	100996928	exon6			ACGGGCAAAGAAA		CCDS59084.1	7q34	2013-02-14			ENSG00000146963	ENSG00000146963			44671	other	readthrough							Standard	NM_001244584		Approved		uc011kqt.3		OTTHUMG00000151717	ENST00000354926.4:c.492A>G	7.37:g.139090515A>G		139.0	0.0	0		133.0	62.0	0.466165	NM_001244584		Silent	SNP	ENST00000354926.4	37	CCDS43656.1																																																																																			A|0.981;G|0.019	0.019	strong		0.368	C7orf55-LUC7L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323618.2		
BRAF	673	hgsc.bcm.edu	37	7	140449150	140449150	+	Silent	SNP	T	T	C	rs9648696	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140449150T>C	ENST00000288602.6	-	16	1989	c.1929A>G	c.(1927-1929)ggA>ggG	p.G643G		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	643	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	ACAGAACAATTCCAAATGCAT	0.348		61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome				C|||	1758	0.351038	0.7451	0.1585	5008	,	,		17576	0.1825		0.1531	False		,,,				2504	0.3323				p.G643G	Colon(40;35 892 2973 5743 27438)	Atlas-SNP	.		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	.	BRAF	36346	.	0			c.A1929G						PASS	.	C		2904,1502	476.8+/-357.7	963,978,262	105.0	108.0	107.0		1929	2.1	1.0	7	dbSNP_119	107	1258,7342	758.6+/-407.5	114,1030,3156	no	coding-synonymous	BRAF	NM_004333.4		1077,2008,3418	CC,CT,TT		14.6279,34.0899,32.0006		643/767	140449150	4162,8844	2203	4300	6503	SO:0001819	synonymous_variant	673	exon16	Familial Cancer Database	CFC, CFCS	AACAATTCCAAAT	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1929A>G	7.37:g.140449150T>C		141.0	0.0	0		148.0	148.0	1	NM_004333	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Silent	SNP	ENST00000288602.6	37	CCDS5863.1	611	0.27976190476190477	355	0.7215447154471545	58	0.16022099447513813	91	0.1590909090909091	107	0.14116094986807387	C	9.723	1.160251	0.21454	0.659101	0.146279	ENSG00000157764	ENST00000496384	.	.	.	5.02	2.11	0.27256	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.33317	-0.9873	3	.	.	.	.	5.8585	0.18732	0.0:0.5864:0.1264:0.2872	rs9648696;rs10238189;rs60896634	.	.	.	G	251	.	.	E	-	2	0	BRAF	140095619	1.000000	0.71417	0.998000	0.56505	0.947000	0.59692	1.503000	0.35715	-0.010000	0.14271	-0.355000	0.07637	GAA	T|0.696;C|0.304	0.304	strong		0.348	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333	
C1orf127	148345	hgsc.bcm.edu	37	1	11008102	11008102	+	Missense_Mutation	SNP	G	G	A	rs1281018	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11008102G>A	ENST00000377008.4	-	11	2035	c.1589C>T	c.(1588-1590)gCg>gTg	p.A530V	C1orf127_ENST00000377004.4_Missense_Mutation_p.A697V			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	530			A -> V (in dbSNP:rs1281018).							NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		TGCCAGGGGCGCTGCCAGCCT	0.622													G|||	442	0.0882588	0.2542	0.0245	5008	,	,		18073	0.0069		0.0447	False		,,,				2504	0.0378				p.A697V		Atlas-SNP	.											.	C1orf127	134	.	0			c.C2090T						PASS	.	G	VAL/ALA	809,3597	299.6+/-285.9	81,647,1475	36.0	38.0	37.0		2090	-2.0	0.0	1	dbSNP_87	37	346,8254	112.3+/-172.5	4,338,3958	yes	missense	C1orf127	NM_001170754.1	64	85,985,5433	AA,AG,GG		4.0233,18.3613,8.8805	possibly-damaging	697/824	11008102	1155,11851	2203	4300	6503	SO:0001583	missense	148345	exon12			AGGGGCGCTGCCA	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.1589C>T	1.37:g.11008102G>A	ENSP00000366207:p.Ala530Val	93.0	0.0	0		114.0	52.0	0.45614	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Missense_Mutation	SNP	ENST00000377008.4	37		165|165	0.07554945054945054|0.07554945054945054	115|115	0.23373983739837398|0.23373983739837398	8|8	0.022099447513812154|0.022099447513812154	2|2	0.0034965034965034965|0.0034965034965034965	40|40	0.052770448548812667|0.052770448548812667	G|G	7.224|7.224	0.597877|0.597877	0.13939|0.13939	0.183613|0.183613	0.040233|0.040233	ENSG00000175262|ENSG00000175262	ENST00000377004;ENST00000377008|ENST00000418570;ENST00000520253	T;T|.	0.33865|.	1.39;1.39|.	3.9|3.9	-2.05|-2.05	0.07321|0.07321	.|.	0.523531|.	0.14669|.	N|.	0.305451|.	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.14661|0.14661	0.345|0.345	0.80722|0.80722	P|P	0.0|0.0	P;P;P|.	0.42961|.	0.795;0.795;0.795|.	B;B;B|.	0.31390|.	0.129;0.129;0.081|.	T|T	0.35051|0.35051	-0.9804|-0.9804	9|4	0.18276|.	T|.	0.48|.	-0.422|-0.422	0.9467|0.9467	0.01367|0.01367	0.2137:0.3268:0.2711:0.1885|0.2137:0.3268:0.2711:0.1885	rs1281018;rs1281018|rs1281018;rs1281018	548;522;530|.	B7ZLG7;Q8N9H9-2;Q8N9H9|.	.;.;CA127_HUMAN|.	V|C	697;530|532;649	ENSP00000366203:A697V;ENSP00000366207:A530V|.	ENSP00000366203:A697V|.	A|R	-|-	2|1	0|0	C1orf127|C1orf127	10930689|10930689	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.030000|0.030000	0.12068|0.12068	-2.362000|-2.362000	0.01082|0.01082	-0.266000|-0.266000	0.09339|0.09339	-0.474000|-0.474000	0.04947|0.04947	GCG|CGC	G|0.914;A|0.086	0.086	strong		0.622	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	
MKRN1	23608	hgsc.bcm.edu	37	7	140158960	140158960	+	Silent	SNP	G	G	A	rs61736379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140158960G>A	ENST00000255977.2	-	4	842	c.618C>T	c.(616-618)gcC>gcT	p.A206A	MKRN1_ENST00000481705.1_5'Flank|MKRN1_ENST00000480552.1_Intron|MKRN1_ENST00000443720.2_Silent_p.A206A|MKRN1_ENST00000437223.2_Intron|MKRN1_ENST00000474576.1_Silent_p.A142A	NM_013446.3	NP_038474.2	Q9UHC7	MKRN1_HUMAN	makorin ring finger protein 1	206					protein polyubiquitination (GO:0000209)		chromatin binding (GO:0003682)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	16	Melanoma(164;0.00956)					TTGTCTCCACGGCGGTTTGCT	0.537													g|||	32	0.00638978	0.0227	0.0029	5008	,	,		17416	0.0		0.0	False		,,,				2504	0.0				p.A206A		Atlas-SNP	.											.	MKRN1	35	.	0			c.C618T						PASS	.	G	,	83,4323	70.9+/-108.8	1,81,2121	133.0	130.0	131.0		618,618	-9.8	0.0	7	dbSNP_129	131	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	MKRN1	NM_001145125.1,NM_013446.3	,	1,81,6421	AA,AG,GG		0.0,1.8838,0.6382	,	206/330,206/483	140158960	83,12923	2203	4300	6503	SO:0001819	synonymous_variant	23608	exon4			CTCCACGGCGGTT	AF192784	CCDS5860.1, CCDS47725.1	7q34	2013-01-09	2008-08-13		ENSG00000133606	ENSG00000133606		"""RING-type (C3HC4) zinc fingers"""	7112	protein-coding gene	gene with protein product		607754				10843807	Standard	NM_013446		Approved	RNF61	uc003vvt.2	Q9UHC7	OTTHUMG00000157412	ENST00000255977.2:c.618C>T	7.37:g.140158960G>A		198.0	0.0	0		260.0	125.0	0.480769	NM_013446	A4D1T7|B3KXB4|Q256Y7|Q59G11|Q6GSF1|Q9H0G0|Q9UEZ7|Q9UHW2	Silent	SNP	ENST00000255977.2	37	CCDS5860.1																																																																																			G|0.993;A|0.007	0.007	strong		0.537	MKRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348752.1	NM_013446	
SPAG7	9552	hgsc.bcm.edu	37	17	4863574	4863574	+	Silent	SNP	G	G	A	rs73343383	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4863574G>A	ENST00000206020.3	-	4	349	c.282C>T	c.(280-282)tcC>tcT	p.S94S	SPAG7_ENST00000575142.1_Silent_p.S83S|SPAG7_ENST00000573366.1_Silent_p.S43S	NM_004890.2	NP_004881.2	O75391	SPAG7_HUMAN	sperm associated antigen 7	94	R3H. {ECO:0000255|PROSITE- ProRule:PRU00382}.					nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			central_nervous_system(1)|endometrium(1)|kidney(2)|lung(3)|ovary(2)|urinary_tract(1)	10						CTTCCCCAAAGGAGAAGGATG	0.537													G|||	149	0.0297524	0.1089	0.0058	5008	,	,		18290	0.0		0.001	False		,,,				2504	0.0				p.S94S		Atlas-SNP	.											.	SPAG7	22	.	0			c.C282T						PASS	.	G		347,3719		20,307,1706	63.0	66.0	65.0		282	2.2	1.0	17	dbSNP_130	65	4,8392		0,4,4194	no	coding-synonymous	SPAG7	NM_004890.2		20,311,5900	AA,AG,GG		0.0476,8.5342,2.8166		94/228	4863574	351,12111	2033	4198	6231	SO:0001819	synonymous_variant	9552	exon4			CCCAAAGGAGAAG	AF047437	CCDS42240.1	17p13.2	2008-07-18				ENSG00000091640			11216	protein-coding gene	gene with protein product		610056				9653160	Standard	NM_004890		Approved	FSA-1, ACRP, MGC20134	uc002gae.3	O75391		ENST00000206020.3:c.282C>T	17.37:g.4863574G>A		163.0	0.0	0		127.0	67.0	0.527559	NM_004890	Q96EU5	Silent	SNP	ENST00000206020.3	37	CCDS42240.1																																																																																			G|0.978;A|0.022	0.022	strong		0.537	SPAG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438747.1	NM_004890	
UGGT2	55757	hgsc.bcm.edu	37	13	96508566	96508566	+	Missense_Mutation	SNP	T	T	A	rs35123499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:96508566T>A	ENST00000376747.3	-	34	3924	c.3854A>T	c.(3853-3855)tAt>tTt	p.Y1285F		NM_020121.3	NP_064506.3	Q9NYU1	UGGG2_HUMAN	UDP-glucose glycoprotein glucosyltransferase 2	1285	Glucosyltransferase.		Y -> F (in dbSNP:rs35123499).		cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|UDP-glucosylation (GO:0097359)	endoplasmic reticulum lumen (GO:0005788)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(17)|lung(20)|ovary(3)|pancreas(1)|prostate(4)|urinary_tract(2)	60						TCGGAATCCATACTCTTTAGC	0.348													T|||	91	0.0181709	0.0666	0.0029	5008	,	,		15927	0.0		0.001	False		,,,				2504	0.0				p.Y1285F		Atlas-SNP	.											.	UGGT2	127	.	0			c.A3854T						PASS	.	T	PHE/TYR	247,4159	142.7+/-177.9	6,235,1962	112.0	119.0	116.0		3854	5.2	1.0	13	dbSNP_126	116	0,8600		0,0,4300	yes	missense	UGGT2	NM_020121.3	22	6,235,6262	AA,AT,TT		0.0,5.606,1.8991	probably-damaging	1285/1517	96508566	247,12759	2203	4300	6503	SO:0001583	missense	55757	exon34			AATCCATACTCTT	AF227906	CCDS9480.1	13q32.1	2009-07-23	2009-07-23	2009-07-23	ENSG00000102595	ENSG00000102595			15664	protein-coding gene	gene with protein product	"""UDP-glucose:glycoprotein glucosyltransferase 2"""	605898	"""UDP-glucose ceramide glucosyltransferase-like 2"""	UGCGL2		10694380	Standard	NM_020121		Approved	FLJ11485, HUGT2, FLJ10873, MGC150689, MGC87276, MGC117360	uc001vmt.3	Q9NYU1	OTTHUMG00000017230	ENST00000376747.3:c.3854A>T	13.37:g.96508566T>A	ENSP00000365938:p.Tyr1285Phe	133.0	0.0	0		177.0	88.0	0.497175	NM_020121	A6NKL4|Q08AD0|Q5JQR8|Q8N5K0|Q9UFC4	Missense_Mutation	SNP	ENST00000376747.3	37	CCDS9480.1	31	0.014194139194139194	30	0.06097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	T	25.9	4.680767	0.88542	0.05606	0.0	ENSG00000102595	ENST00000376747	T	0.40756	1.02	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.14614	0.0353	L	0.53671	1.685	0.80722	D	1	D	0.71674	0.998	D	0.80764	0.994	T	0.41106	-0.9527	10	0.87932	D	0	-16.5421	15.0092	0.71536	0.0:0.0:0.0:1.0	rs35123499	1285	Q9NYU1	UGGG2_HUMAN	F	1285	ENSP00000365938:Y1285F	ENSP00000365938:Y1285F	Y	-	2	0	UGGT2	95306567	1.000000	0.71417	0.998000	0.56505	0.950000	0.60333	7.698000	0.84413	1.936000	0.56123	0.533000	0.62120	TAT	T|0.980;A|0.020	0.020	strong		0.348	UGGT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045507.1	NM_020121	
KNTC1	9735	hgsc.bcm.edu	37	12	123089955	123089955	+	Missense_Mutation	SNP	C	C	T	rs7310898	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:123089955C>T	ENST00000333479.7	+	51	5666	c.5489C>T	c.(5488-5490)cCt>cTt	p.P1830L	KNTC1_ENST00000436959.3_5'UTR|KNTC1_ENST00000537348.1_Missense_Mutation_p.P255L|KNTC1_ENST00000450485.2_Intron	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	1830			P -> L (in dbSNP:rs7310898).		mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		TCAACAAAACCTGGTGAAGTA	0.393													C|||	196	0.0391374	0.143	0.0101	5008	,	,		16684	0.0		0.0	False		,,,				2504	0.0				p.P1830L		Atlas-SNP	.											KNTC1,caecum,carcinoma,0,1	KNTC1	182	1	0			c.C5489T						PASS	.	C	LEU/PRO	433,3323		20,393,1465	57.0	56.0	56.0		5489	3.8	0.1	12	dbSNP_116	56	4,8242		0,4,4119	yes	missense	KNTC1	NM_014708.4	98	20,397,5584	TT,TC,CC		0.0485,11.5282,3.6411	possibly-damaging	1830/2210	123089955	437,11565	1878	4123	6001	SO:0001583	missense	9735	exon51			CAAAACCTGGTGA		CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"""rough deal homolog (Drosophila)"""	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.5489C>T	12.37:g.123089955C>T	ENSP00000328236:p.Pro1830Leu	172.0	0.0	0		172.0	71.0	0.412791	NM_014708	A7E2C4|B3KSG2	Missense_Mutation	SNP	ENST00000333479.7	37	CCDS45002.1	69	0.03159340659340659	64	0.13008130081300814	5	0.013812154696132596	0	0.0	0	0.0	C	25.8	4.677569	0.88445	0.115282	4.85E-4	ENSG00000184445	ENST00000333479;ENST00000537348;ENST00000546125	T;T;T	0.30182	1.54;1.54;1.54	5.64	3.79	0.43588	RZZ complex, subunit KNTC1/ROD, C-terminal (1);	0.330869	0.36932	N	0.002322	T	0.00328	0.0010	L	0.44542	1.39	0.50813	P	1.0299999999996423E-4	P	0.40534	0.72	P	0.44673	0.457	T	0.09975	-1.0650	9	0.72032	D	0.01	-12.0893	11.1536	0.48473	0.1268:0.806:0.0:0.0672	rs7310898;rs52809397;rs57876510;rs7310898	1830	P50748	KNTC1_HUMAN	L	1830;255;17	ENSP00000328236:P1830L;ENSP00000443622:P255L;ENSP00000439119:P17L	ENSP00000328236:P1830L	P	+	2	0	KNTC1	121655908	0.836000	0.29430	0.093000	0.20910	0.968000	0.65278	3.480000	0.53172	1.372000	0.46190	0.650000	0.86243	CCT	C|0.962;T|0.038	0.038	strong		0.393	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2		
LIPN	643418	hgsc.bcm.edu	37	10	90530683	90530683	+	Missense_Mutation	SNP	C	C	T	rs114737713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:90530683C>T	ENST00000404459.1	+	6	754	c.754C>T	c.(754-756)Ctc>Ttc	p.L252F		NM_001102469.1	NP_001095939.1	Q5VXI9	LIPN_HUMAN	lipase, family member N	252					lipid catabolic process (GO:0016042)	extracellular region (GO:0005576)	hydrolase activity, acting on ester bonds (GO:0016788)			endometrium(1)|kidney(1)|large_intestine(5)|lung(1)|skin(1)	9		Colorectal(252;0.0161)		Colorectal(12;4.83e-05)|COAD - Colon adenocarcinoma(12;6.5e-05)		CAATAAGATACTCTGGTTGAT	0.323													C|||	76	0.0151757	0.0545	0.0043	5008	,	,		17038	0.0		0.001	False		,,,				2504	0.0				p.L252F		Atlas-SNP	.											.	LIPN	28	.	0			c.C754T						PASS	.	C	PHE/LEU	117,3509		2,113,1698	67.0	64.0	65.0		754	1.9	0.4	10	dbSNP_132	65	3,8125		0,3,4061	yes	missense	LIPN	NM_001102469.1	22	2,116,5759	TT,TC,CC		0.0369,3.2267,1.0209	benign	252/399	90530683	120,11634	1813	4064	5877	SO:0001583	missense	643418	exon6			AAGATACTCTGGT		CCDS44456.1	10q23.31	2013-09-20	2007-02-27	2007-02-27	ENSG00000204020	ENSG00000204020			23452	protein-coding gene	gene with protein product		613924	"""lipase-like, ab-hydrolase domain containing 4"""	LIPL4			Standard	NM_001102469		Approved	bA186O14.3	uc010qmw.2	Q5VXI9	OTTHUMG00000018694	ENST00000404459.1:c.754C>T	10.37:g.90530683C>T	ENSP00000383923:p.Leu252Phe	136.0	0.0	0		150.0	76.0	0.506667	NM_001102469	A7KIH9	Missense_Mutation	SNP	ENST00000404459.1	37	CCDS44456.1	35	0.016025641025641024	32	0.06504065040650407	3	0.008287292817679558	0	0.0	0	0.0	C	6.188	0.402853	0.11696	0.032267	3.69E-4	ENSG00000204020	ENST00000404459	T	0.62232	0.04	4.86	1.85	0.25348	Alpha/beta hydrolase fold-1 (1);	0.760258	0.11368	N	0.571199	T	0.03783	0.0107	N	0.20845	0.615	0.09310	N	1	B	0.26975	0.165	B	0.25506	0.061	T	0.04635	-1.0937	10	0.10377	T	0.69	-8.2711	5.458	0.16602	0.0:0.4967:0.0:0.5032	.	252	Q5VXI9	LIPN_HUMAN	F	252	ENSP00000383923:L252F	ENSP00000383923:L252F	L	+	1	0	LIPN	90520663	0.003000	0.15002	0.412000	0.26496	0.894000	0.52154	-0.146000	0.10250	0.668000	0.31126	0.650000	0.86243	CTC	C|0.983;T|0.017	0.017	strong		0.323	LIPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049254.2	XM_926751	
TBXAS1	6916	hgsc.bcm.edu	37	7	139661964	139661964	+	Missense_Mutation	SNP	C	C	G	rs4529	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:139661964C>G	ENST00000336425.5	+	13	1455	c.1066C>G	c.(1066-1068)Cta>Gta	p.L356V	TBXAS1_ENST00000448866.1_Missense_Mutation_p.L356V|TBXAS1_ENST00000411653.1_Missense_Mutation_p.L356V|TBXAS1_ENST00000414508.2_Missense_Mutation_p.L357V|TBXAS1_ENST00000458722.1_Missense_Mutation_p.L402V|TBXAS1_ENST00000462275.1_3'UTR|TBXAS1_ENST00000436047.2_Missense_Mutation_p.L357V|TBXAS1_ENST00000263552.6_Missense_Mutation_p.L357V|TBXAS1_ENST00000425687.1_Missense_Mutation_p.L289V|TBXAS1_ENST00000416849.2_Missense_Mutation_p.L403V			P24557	THAS_HUMAN	thromboxane A synthase 1 (platelet)	356			L -> V (in allele CYP5A1*5; dbSNP:rs4529). {ECO:0000269|PubMed:10391209, ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:11465543}.		arachidonic acid metabolic process (GO:0019369)|cellular chloride ion homeostasis (GO:0030644)|cyclooxygenase pathway (GO:0019371)|icosanoid metabolic process (GO:0006690)|positive regulation of vasoconstriction (GO:0045907)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)|thromboxane-A synthase activity (GO:0004796)			breast(3)|endometrium(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	28	Melanoma(164;0.0142)				Ridogrel(DB01207)|Sulfasalazine(DB00795)	TGCCACCTACCTACTGGCCAC	0.502													C|||	209	0.0417332	0.1543	0.0058	5008	,	,		18923	0.0		0.001	False		,,,				2504	0.0				p.L403V		Atlas-SNP	.											.	TBXAS1	121	.	0			c.C1207G						PASS	.	C	VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU	512,3894	236.1+/-248.4	24,464,1715	111.0	98.0	102.0		1069,1069,1207,865,1069	4.2	1.0	7	dbSNP_52	102	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense,missense,missense	TBXAS1	NM_001061.4,NM_001130966.2,NM_001166253.1,NM_001166254.1,NM_030984.3	32,32,32,32,32	24,467,6012	GG,GC,CC		0.0349,11.6205,3.9597	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	357/535,357/535,403/581,289/467,357/461	139661964	515,12491	2203	4300	6503	SO:0001583	missense	6916	exon10			ACCTACCTACTGG	L36085	CCDS5855.1, CCDS5856.1, CCDS55174.1, CCDS55175.1	7q34-q35	2014-09-17	2008-07-31		ENSG00000059377	ENSG00000059377	5.3.99.5	"""Cytochrome P450s"""	11609	protein-coding gene	gene with protein product	"""cytochrome P450, family 5, subfamily A, polypeptide 1"""	274180	"""thromboxane A synthase 1 (platelet, cytochrome P450, subfamily V)"""			1714723, 8964509	Standard	NM_001061		Approved	CYP5, CYP5A1, THAS, TXS, TXAS, TS	uc011kqv.2	P24557	OTTHUMG00000157302	ENST00000336425.5:c.1066C>G	7.37:g.139661964C>G	ENSP00000338087:p.Leu356Val	136.0	0.0	0		114.0	55.0	0.482456	NM_001166253	B4DJG6|E7EMU9|E7EP08|E7ESB5|O14987|Q16843|Q16844|Q8IUN1|Q96CN2|Q9GZW4|Q9HD77|Q9HD78|Q9HD79|Q9HD80|Q9HD81|Q9HD82|Q9HD83|Q9HD84	Missense_Mutation	SNP	ENST00000336425.5	37		66	0.03021978021978022	62	0.12601626016260162	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	C	16.28	3.079361	0.55753	0.116205	3.49E-4	ENSG00000059377	ENST00000425687;ENST00000263552;ENST00000336425;ENST00000416849;ENST00000436047;ENST00000414508;ENST00000448866;ENST00000458722;ENST00000411653	T;T;T;T;T;T;T;T;T	0.70399	-0.48;-0.48;-0.48;-0.48;-0.48;-0.48;-0.48;-0.48;-0.48	5.98	4.15	0.48705	.	0.000000	0.85682	D	0.000000	T	0.02533	0.0077	M	0.71920	2.185	0.80722	D	1	P;D;P;D;P;P;P	0.63880	0.937;0.993;0.85;0.992;0.878;0.923;0.923	P;D;P;P;P;P;P	0.65573	0.896;0.936;0.775;0.811;0.722;0.696;0.696	T	0.46076	-0.9217	10	0.18276	T	0.48	.	5.3733	0.16152	0.2612:0.5412:0.1263:0.0712	rs4529;rs52804680;rs57867324;rs4529	337;403;308;289;357;357;356	B4DVP1;E7EP08;B4E0M5;E7ESB5;E7EMU9;Q53F23;P24557	.;.;.;.;.;.;THAS_HUMAN	V	289;357;356;403;357;357;356;402;356	ENSP00000388736:L289V;ENSP00000263552:L357V;ENSP00000338087:L356V;ENSP00000389414:L403V;ENSP00000392361:L357V;ENSP00000392702:L357V;ENSP00000402536:L356V;ENSP00000411274:L402V;ENSP00000411326:L356V	ENSP00000263552:L357V	L	+	1	2	TBXAS1	139308433	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	2.191000	0.42640	0.826000	0.34661	0.655000	0.94253	CTA	C|0.953;G|0.047	0.047	strong		0.502	TBXAS1-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000348373.1		
COL18A1	80781	hgsc.bcm.edu	37	21	46900670	46900670	+	Silent	SNP	C	C	T	rs112723616	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46900670C>T	ENST00000359759.4	+	12	2775	c.2754C>T	c.(2752-2754)ggC>ggT	p.G918G	COL18A1_ENST00000400337.2_Silent_p.G503G|COL18A1_ENST00000355480.5_Silent_p.G683G			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	918	Triple-helical region 3 (COL3).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		GCCTGCCCGGCGAGCCAGGCC	0.716													C|||	68	0.0135783	0.0454	0.0115	5008	,	,		11100	0.0		0.0	False		,,,				2504	0.0				p.G683G		Atlas-SNP	.											.	COL18A1	129	.	0			c.C2049T						PASS	.	C	,	141,3665		4,133,1766	21.0	26.0	24.0		2049,1509	-8.1	0.9	21	dbSNP_132	24	1,8213		0,1,4106	no	coding-synonymous,coding-synonymous	COL18A1	NM_030582.3,NM_130445.2	,	4,134,5872	TT,TC,CC		0.0122,3.7047,1.1814	,	683/1520,503/1340	46900670	142,11878	1903	4107	6010	SO:0001819	synonymous_variant	80781	exon12			GCCCGGCGAGCCA		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.2754C>T	21.37:g.46900670C>T		31.0	0.0	0		57.0	36.0	0.631579	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Silent	SNP	ENST00000359759.4	37																																																																																				C|0.990;T|0.010	0.010	strong		0.716	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
C1orf109	54955	hgsc.bcm.edu	37	1	38155319	38155319	+	Silent	SNP	C	C	T	rs61731880	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:38155319C>T	ENST00000358011.4	-	2	423	c.234G>A	c.(232-234)ctG>ctA	p.L78L	CDCA8_ENST00000373055.1_5'Flank|C1orf109_ENST00000464085.1_Silent_p.L78L|CDCA8_ENST00000327331.2_5'Flank	NM_017850.1	NP_060320.1	Q9NX04	CA109_HUMAN	chromosome 1 open reading frame 109	78										lung(2)|prostate(2)	4		Myeloproliferative disorder(586;0.0393)				CACCAGCCACCAGCTGCTTAC	0.547													C|||	196	0.0391374	0.1369	0.0202	5008	,	,		18248	0.0		0.001	False		,,,				2504	0.0				p.L78L		Atlas-SNP	.											.	C1orf109	13	.	0			c.G234A						PASS	.	C		501,3905	225.2+/-241.2	27,447,1729	93.0	99.0	97.0		234	2.7	0.5	1	dbSNP_129	97	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	C1orf109	NM_017850.1		27,450,6026	TT,TC,CC		0.0349,11.3709,3.8751		78/204	38155319	504,12502	2203	4300	6503	SO:0001819	synonymous_variant	54955	exon2			AGCCACCAGCTGC	AK000515	CCDS423.1	1p34.3	2012-06-21			ENSG00000116922	ENSG00000116922			26039	protein-coding gene	gene with protein product		614799				22548824	Standard	XM_005270979		Approved	FLJ20508	uc001cbp.3	Q9NX04	OTTHUMG00000004323	ENST00000358011.4:c.234G>A	1.37:g.38155319C>T		187.0	0.0	0		214.0	103.0	0.481308	NM_017850	D3DPT1|Q8WVD1	Silent	SNP	ENST00000358011.4	37	CCDS423.1																																																																																			C|0.966;T|0.034	0.034	strong		0.547	C1orf109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012486.1	NM_017850	
DPY19L3	147991	hgsc.bcm.edu	37	19	32930808	32930808	+	Missense_Mutation	SNP	G	G	A	rs139732410	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:32930808G>A	ENST00000342179.5	+	8	1062	c.847G>A	c.(847-849)Gca>Aca	p.A283T	DPY19L3_ENST00000586987.1_Missense_Mutation_p.A283T|DPY19L3_ENST00000392250.2_Missense_Mutation_p.A283T	NM_207325.2	NP_997208.2	Q6ZPD9	D19L3_HUMAN	dpy-19-like 3 (C. elegans)	283						integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(17)|ovary(4)|pancreas(1)	32	Esophageal squamous(110;0.162)					CATGCTGCCAGCAGTGAAGGT	0.373													G|||	12	0.00239617	0.0091	0.0	5008	,	,		17998	0.0		0.0	False		,,,				2504	0.0				p.A283T		Atlas-SNP	.											.	DPY19L3	70	.	0			c.G847A						PASS	.	G	THR/ALA,THR/ALA	31,4375	37.6+/-69.7	0,31,2172	153.0	142.0	146.0		847,847	3.5	0.1	19	dbSNP_134	146	0,8600		0,0,4300	yes	missense,missense	DPY19L3	NM_001172774.1,NM_207325.2	58,58	0,31,6472	AA,AG,GG		0.0,0.7036,0.2384	benign,benign	283/717,283/717	32930808	31,12975	2203	4300	6503	SO:0001583	missense	147991	exon8			CTGCCAGCAGTGA		CCDS12422.1	19q13.11	2008-02-05				ENSG00000178904			27120	protein-coding gene	gene with protein product		613894					Standard	NM_207325		Approved		uc002ntg.3	Q6ZPD9		ENST00000342179.5:c.847G>A	19.37:g.32930808G>A	ENSP00000344937:p.Ala283Thr	100.0	0.0	0		110.0	51.0	0.463636	NM_001172774	Q68DC7|Q6ZTB7|Q6ZTS2	Missense_Mutation	SNP	ENST00000342179.5	37	CCDS12422.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	5.569	0.289764	0.10567	0.007036	0.0	ENSG00000178904	ENST00000392250;ENST00000319326;ENST00000342179	T;T	0.54479	0.57;0.57	5.82	3.55	0.40652	.	0.164682	0.52532	D	0.000078	T	0.13927	0.0337	N	0.03084	-0.415	0.28833	N	0.897055	B	0.09022	0.002	B	0.08055	0.003	T	0.24154	-1.0168	10	0.05525	T	0.97	-8.0566	3.27	0.06878	0.1826:0.2943:0.523:0.0	.	283	Q6ZPD9	D19L3_HUMAN	T	283	ENSP00000376081:A283T;ENSP00000344937:A283T	ENSP00000315672:A283T	A	+	1	0	DPY19L3	37622648	0.997000	0.39634	0.084000	0.20598	0.988000	0.76386	3.927000	0.56499	1.448000	0.47680	0.557000	0.71058	GCA	G|0.998;A|0.002	0.002	strong		0.373	DPY19L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450311.1	NM_207325	
TNFRSF11A	8792	hgsc.bcm.edu	37	18	60036547	60036547	+	Missense_Mutation	SNP	G	G	A	rs35993683	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:60036547G>A	ENST00000586569.1	+	9	1435	c.1397G>A	c.(1396-1398)cGt>cAt	p.R466H	TNFRSF11A_ENST00000269485.7_Intron	NM_001270949.1|NM_003839.3	NP_001257878.1|NP_003830.1	Q9Y6Q6	TNR11_HUMAN	tumor necrosis factor receptor superfamily, member 11a, NFKB activator	466					adaptive immune response (GO:0002250)|cell-cell signaling (GO:0007267)|circadian temperature homeostasis (GO:0060086)|lymph node development (GO:0048535)|mammary gland alveolus development (GO:0060749)|monocyte chemotaxis (GO:0002548)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade via TNFSF11-mediated signaling (GO:0071848)|positive regulation of fever generation by positive regulation of prostaglandin secretion (GO:0071812)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|response to cytokine (GO:0034097)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to radiation (GO:0009314)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|TNFSF11-mediated signaling pathway (GO:0071847)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|tumor necrosis factor-activated receptor activity (GO:0005031)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(13)|skin(3)|upper_aerodigestive_tract(1)	29		Colorectal(73;0.188)				TCCCCAAAACGTGGACCCTTG	0.662													G|||	61	0.0121805	0.0439	0.0043	5008	,	,		18183	0.0		0.0	False		,,,				2504	0.0				p.R466H		Atlas-SNP	.											.	TNFRSF11A	51	.	0			c.G1397A						PASS	.	G	HIS/ARG	142,4260		0,142,2059	37.0	38.0	38.0		1397	-0.8	0.1	18	dbSNP_126	38	1,8587		0,1,4293	yes	missense	TNFRSF11A	NM_003839.2	29	0,143,6352	AA,AG,GG		0.0116,3.2258,1.1008	benign	466/617	60036547	143,12847	2201	4294	6495	SO:0001583	missense	8792	exon9			CAAAACGTGGACC	AF018253	CCDS11980.1, CCDS59324.1, CCDS74227.1, CCDS74228.1	18q22.1	2014-09-17			ENSG00000141655	ENSG00000141655		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11908	protein-coding gene	gene with protein product		603499	"""tumor necrosis factor receptor superfamily, member 11a, activator of NFKB"", ""Paget disease of bone 2"", ""loss of heterozygosity, 18, chromosomal region 1"""	PDB2, LOH18CR1		9367155, 10615125	Standard	NM_001270951		Approved	RANK, CD265, FEO	uc002lin.4	Q9Y6Q6	OTTHUMG00000132779	ENST00000586569.1:c.1397G>A	18.37:g.60036547G>A	ENSP00000465500:p.Arg466His	27.0	0.0	0		27.0	12.0	0.444444	NM_003839	I4EC36|I4EC38|I4EC39|I7JE63|N0GVH0|Q59EP9	Missense_Mutation	SNP	ENST00000586569.1	37	CCDS11980.1	18	0.008241758241758242	16	0.032520325203252036	2	0.0055248618784530384	0	0.0	0	0.0	G	12.75	2.032926	0.35893	0.032258	1.16E-4	ENSG00000141655	ENST00000269485	.	.	.	5.03	-0.8	0.10897	.	3.161140	0.01102	N	0.005394	T	0.06735	0.0172	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.11155	-1.0599	8	.	.	.	0.0539	6.8356	0.23935	0.4461:0.1218:0.4321:0.0	rs35993683;rs61751991	466	Q9Y6Q6	TNR11_HUMAN	H	466	.	.	R	+	2	0	TNFRSF11A	58187527	0.037000	0.19845	0.081000	0.20488	0.362000	0.29581	-0.004000	0.12878	-0.089000	0.12484	-0.244000	0.11960	CGT	G|0.989;A|0.011	0.011	strong		0.662	TNFRSF11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256186.2		
SI	6476	hgsc.bcm.edu	37	3	164750325	164750325	+	Silent	SNP	A	A	G	rs140829463	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:164750325A>G	ENST00000264382.3	-	24	2783	c.2721T>C	c.(2719-2721)taT>taC	p.Y907Y		NM_001041.3	NP_001032.2	P14410	SUIS_HUMAN	sucrase-isomaltase (alpha-glucosidase)	907	Isomaltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	brush border (GO:0005903)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|oligo-1,6-glucosidase activity (GO:0004574)|sucrose alpha-glucosidase activity (GO:0004575)			NS(4)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(6)|kidney(10)|large_intestine(18)|lung(124)|ovary(9)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(16)|urinary_tract(1)	218		Prostate(884;0.00314)|Melanoma(1037;0.0153)|all_neural(597;0.0199)			Acarbose(DB00284)|Scopolamine(DB00747)	TAGAAGCATCATAAGTGAAAT	0.313										HNSCC(35;0.089)			A|||	2	0.000399361	0.0015	0.0	5008	,	,		14779	0.0		0.0	False		,,,				2504	0.0				p.Y907Y		Atlas-SNP	.											.	SI	500	.	0			c.T2721C						PASS	.	A		10,4394	16.8+/-37.8	0,10,2192	133.0	128.0	130.0		2721	1.2	0.3	3	dbSNP_134	130	0,8600		0,0,4300	no	coding-synonymous	SI	NM_001041.3		0,10,6492	GG,GA,AA		0.0,0.2271,0.0769		907/1828	164750325	10,12994	2202	4300	6502	SO:0001819	synonymous_variant	6476	exon24			AGCATCATAAGTG	X63597	CCDS3196.1	3q25.2-q26.2	2004-04-06	2004-04-06		ENSG00000090402	ENSG00000090402	3.2.1.10		10856	protein-coding gene	gene with protein product	"""Oligosaccharide alpha-1,6-glucosidase"""	609845	"""sucrase-isomaltase"""			2962903, 1353958	Standard	NM_001041		Approved		uc003fei.3	P14410	OTTHUMG00000158065	ENST00000264382.3:c.2721T>C	3.37:g.164750325A>G		65.0	0.0	0		57.0	24.0	0.421053	NM_001041	A2RUC3|Q1JQ80|Q1RMC2	Silent	SNP	ENST00000264382.3	37	CCDS3196.1																																																																																			A|0.999;G|0.001	0.001	strong		0.313	SI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350116.1	NM_001041	
PLA2G4F	255189	hgsc.bcm.edu	37	15	42434905	42434905	+	Missense_Mutation	SNP	T	T	C	rs144100358	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42434905T>C	ENST00000382396.4	-	19	2236	c.2150A>G	c.(2149-2151)aAg>aGg	p.K717R	PLA2G4F_ENST00000397272.3_Missense_Mutation_p.K719R			Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	717	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)		CTCTGTCATCTTCAAGACCTG	0.607													T|||	38	0.00758786	0.028	0.0014	5008	,	,		15524	0.0		0.0	False		,,,				2504	0.0				p.K717R		Atlas-SNP	.											.	PLA2G4F	75	.	0			c.A2150G						PASS	.	T	ARG/LYS	97,4309	78.3+/-116.7	5,87,2111	70.0	58.0	62.0		2150	3.5	1.0	15	dbSNP_134	62	1,8597	1.2+/-3.3	0,1,4298	yes	missense	PLA2G4F	NM_213600.3	26	5,88,6409	CC,CT,TT		0.0116,2.2015,0.7536	benign	717/850	42434905	98,12906	2203	4299	6502	SO:0001583	missense	255189	exon19			GTCATCTTCAAGA		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.2150A>G	15.37:g.42434905T>C	ENSP00000371833:p.Lys717Arg	97.0	0.0	0		114.0	67.0	0.587719	NM_213600	Q6ZMC8	Missense_Mutation	SNP	ENST00000382396.4	37	CCDS32204.1	15	0.006868131868131868	14	0.028455284552845527	1	0.0027624309392265192	0	0.0	0	0.0	T	11.00	1.510289	0.27036	0.022015	1.16E-4	ENSG00000168907	ENST00000290497;ENST00000397272;ENST00000382396;ENST00000443825	T;T	0.11821	2.74;2.74	4.69	3.53	0.40419	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (2);	0.502059	0.18373	N	0.143181	T	0.02304	0.0071	N	0.12887	0.27	0.23611	N	0.997295	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.08055	0.001;0.003;0.001	T	0.32052	-0.9921	10	0.30854	T	0.27	-12.5606	10.4046	0.44249	0.0:0.0796:0.0:0.9204	.	504;719;717	A2RRC4;C9J281;Q68DD2	.;.;PA24F_HUMAN	R	713;719;717;717	ENSP00000380442:K719R;ENSP00000371833:K717R	ENSP00000290497:K713R	K	-	2	0	PLA2G4F	40222197	0.787000	0.28750	0.998000	0.56505	0.446000	0.32137	3.246000	0.51414	0.908000	0.36671	0.482000	0.46254	AAG	T|0.992;C|0.008	0.008	strong		0.607	PLA2G4F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000420463.1	NM_213600	
FBXW12	285231	hgsc.bcm.edu	37	3	48420987	48420987	+	Missense_Mutation	SNP	A	A	G	rs77256337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:48420987A>G	ENST00000296438.5	+	7	899	c.713A>G	c.(712-714)cAc>cGc	p.H238R	RN7SL321P_ENST00000581742.1_RNA|FBXW12_ENST00000436231.1_Missense_Mutation_p.H81R|FBXW12_ENST00000445170.1_Missense_Mutation_p.H219R|FBXW12_ENST00000415155.1_Missense_Mutation_p.H168R	NM_207102.2	NP_996985.2	Q6X9E4	FBW12_HUMAN	F-box and WD repeat domain containing 12	238										breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				BRCA - Breast invasive adenocarcinoma(193;0.000293)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		GTACTTCTACACTGCTCTCCT	0.428													A|||	33	0.00658946	0.0234	0.0029	5008	,	,		24553	0.0		0.0	False		,,,				2504	0.0				p.H238R		Atlas-SNP	.											.	FBXW12	44	.	0			c.A713G						PASS	.	A	ARG/HIS,ARG/HIS,ARG/HIS	77,4329	67.6+/-105.2	1,75,2127	301.0	269.0	280.0		503,656,713	-7.2	0.0	3	dbSNP_131	280	0,8600		0,0,4300	yes	missense,missense,missense	FBXW12	NM_001159927.1,NM_001159929.1,NM_207102.2	29,29,29	1,75,6427	GG,GA,AA		0.0,1.7476,0.592	benign,benign,benign	168/395,219/446,238/465	48420987	77,12929	2203	4300	6503	SO:0001583	missense	285231	exon7			TTCTACACTGCTC	AK097594, AY247969	CCDS2764.1, CCDS54577.1, CCDS54578.1	3p21.31	2011-07-01	2007-02-08	2004-07-21	ENSG00000164049	ENSG00000164049		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	20729	protein-coding gene	gene with protein product		609075	"""F-box only protein 35"", ""F-box and WD-40 domain protein 12"""	FBXO35		15040455	Standard	NM_207102		Approved	Fbw12	uc010hjv.3	Q6X9E4	OTTHUMG00000133530	ENST00000296438.5:c.713A>G	3.37:g.48420987A>G	ENSP00000296438:p.His238Arg	214.0	1.0	0.0046729		220.0	119.0	0.540909	NM_207102	E9PG36|Q494Y9|Q494Z0	Missense_Mutation	SNP	ENST00000296438.5	37	CCDS2764.1	8	0.003663003663003663	6	0.012195121951219513	2	0.0055248618784530384	0	0.0	0	0.0	A	1.575	-0.533025	0.04112	0.017476	0.0	ENSG00000164049	ENST00000458736;ENST00000296438;ENST00000436231;ENST00000445170;ENST00000415155	T;T;T;T	0.62232	1.62;0.04;1.62;3.52	4.03	-7.21	0.01490	WD40/YVTN repeat-like-containing domain (1);Quinoprotein amine dehydrogenase, beta chain-like (1);	1.379180	0.04600	N	0.398402	T	0.20414	0.0491	N	0.19112	0.55	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.0	T	0.10870	-1.0611	10	0.16420	T	0.52	-12.9603	1.3588	0.02187	0.1804:0.1139:0.2788:0.4269	.	137;219;168;238	E9PCA2;E9PG36;Q494Z0;Q6X9E4	.;.;.;FBW12_HUMAN	R	137;238;81;219;168	ENSP00000296438:H238R;ENSP00000413866:H81R;ENSP00000406139:H219R;ENSP00000414683:H168R	ENSP00000296438:H238R	H	+	2	0	FBXW12	48395991	0.005000	0.15991	0.000000	0.03702	0.020000	0.10135	-0.149000	0.10204	-1.503000	0.01812	-1.253000	0.01494	CAC	A|0.994;G|0.006	0.006	strong		0.428	FBXW12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257505.1	NM_207102	
CRTAC1	55118	hgsc.bcm.edu	37	10	99667840	99667840	+	Silent	SNP	A	A	G	rs35333633	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:99667840A>G	ENST00000370597.3	-	6	1135	c.780T>C	c.(778-780)aaT>aaC	p.N260N	CRTAC1_ENST00000370591.2_Silent_p.N260N|CRTAC1_ENST00000298819.4_Silent_p.N260N	NM_018058.6	NP_060528.3	Q9NQ79	CRAC1_HUMAN	cartilage acidic protein 1	260						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(6)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	35		Colorectal(252;0.24)		Epithelial(162;2.18e-10)|all cancers(201;3.27e-09)		GCCCATTCTCATTGTCGCAGA	0.607													G|||	285	0.0569089	0.2005	0.0231	5008	,	,		20899	0.0		0.004	False		,,,				2504	0.0				p.N260N		Atlas-SNP	.											.	CRTAC1	86	.	0			c.T780C						PASS	.	G	,	725,3681	757.9+/-412.8	68,589,1546	89.0	68.0	75.0		780,780	-2.7	1.0	10	dbSNP_126	75	7,8593	819.0+/-406.8	0,7,4293	no	coding-synonymous,coding-synonymous	CRTAC1	NM_001206528.2,NM_018058.6	,	68,596,5839	GG,GA,AA		0.0814,16.4548,5.6282	,	260/646,260/662	99667840	732,12274	2203	4300	6503	SO:0001819	synonymous_variant	55118	exon6			ATTCTCATTGTCG	AJ276171	CCDS31266.1, CCDS55723.1	10q22	2007-12-03			ENSG00000095713	ENSG00000095713			14882	protein-coding gene	gene with protein product		606276				11139377	Standard	NM_018058		Approved	FLJ10320, CEP-68, ASPIC1	uc001kou.2	Q9NQ79	OTTHUMG00000018871	ENST00000370597.3:c.780T>C	10.37:g.99667840A>G		115.0	0.0	0		153.0	75.0	0.490196	NM_001206528	B1ALN4|Q5T4F8|Q8N4H6|Q8TE52|Q9NQ78|Q9NQ80|Q9NW46	Silent	SNP	ENST00000370597.3	37	CCDS31266.1																																																																																			A|0.946;G|0.054	0.054	strong		0.607	CRTAC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000049754.1	NM_018058	
TTF2	8458	hgsc.bcm.edu	37	1	117637966	117637966	+	Silent	SNP	A	A	G	rs34079217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:117637966A>G	ENST00000369466.4	+	19	3056	c.3012A>G	c.(3010-3012)caA>caG	p.Q1004Q	MIR942_ENST00000401111.1_RNA	NM_003594.3	NP_003585.3	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase II	1004	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(24)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	50	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)		AGGCAATTCAAAGAAATTCAG	0.358													A|||	171	0.0341454	0.1263	0.0058	5008	,	,		22139	0.0		0.0	False		,,,				2504	0.0				p.Q1004Q		Atlas-SNP	.											.	TTF2	92	.	0			c.A3012G						PASS	.	A		535,3871	240.9+/-251.5	30,475,1698	133.0	136.0	135.0		3012	2.4	0.5	1	dbSNP_126	135	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	TTF2	NM_003594.3		30,481,5992	GG,GA,AA		0.0698,12.1425,4.1596		1004/1163	117637966	541,12465	2203	4300	6503	SO:0001819	synonymous_variant	8458	exon19			AATTCAAAGAAAT	AF073771	CCDS892.1	1p13.1	2014-02-18			ENSG00000116830	ENSG00000116830			12398	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 6"""	604718				9748214	Standard	NM_003594		Approved	HuF2, ZGRF6	uc001egy.3	Q9UNY4	OTTHUMG00000012030	ENST00000369466.4:c.3012A>G	1.37:g.117637966A>G		96.0	0.0	0		107.0	43.0	0.401869	NM_003594	A8K4Q2|O75921|Q5T2K7|Q5VVU8|Q8N6I8	Silent	SNP	ENST00000369466.4	37	CCDS892.1																																																																																			A|0.964;G|0.036	0.036	strong		0.358	TTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033277.3		
NF1	4763	hgsc.bcm.edu	37	17	29652884	29652884	+	Silent	SNP	T	T	C	rs10512435	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:29652884T>C	ENST00000358273.4	+	37	5265	c.4882T>C	c.(4882-4884)Tta>Cta	p.L1628L	NF1_ENST00000581113.2_3'UTR|NF1_ENST00000356175.3_Silent_p.L1607L	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1628	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.|Lipid binding.				actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(3)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		ATACCATGTCTTACTGACTTT	0.338			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)			T|||	107	0.0213658	0.0802	0.0014	5008	,	,		19715	0.0		0.0	False		,,,				2504	0.0				p.L1628L		Atlas-SNP	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1	1586	.	11	Whole gene deletion(8)|Unknown(3)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	c.T4882C						PASS	.	T	,	309,4097	164.7+/-196.3	6,297,1900	116.0	112.0	113.0		4819,4882	4.6	1.0	17	dbSNP_119	113	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	NF1	NM_000267.3,NM_001042492.2	,	6,298,6199	CC,CT,TT		0.0116,7.0132,2.3835	,	1607/2819,1628/2840	29652884	310,12696	2203	4300	6503	SO:0001819	synonymous_variant	4763	exon37	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	CATGTCTTACTGA		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.4882T>C	17.37:g.29652884T>C		93.0	0.0	0		76.0	42.0	0.552632	NM_001042492	O00662|Q14284|Q14930|Q14931|Q9UMK3	Silent	SNP	ENST00000358273.4	37	CCDS42292.1																																																																																			T|0.979;C|0.021	0.021	strong		0.338	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	
MSL1	339287	hgsc.bcm.edu	37	17	38285681	38285681	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38285681T>C	ENST00000398532.4	+	3	1491	c.1176T>C	c.(1174-1176)tcT>tcC	p.S392S	MSL1_ENST00000578648.1_Silent_p.S392S|MSL1_ENST00000579565.1_Silent_p.S129S|MSL1_ENST00000577454.1_Silent_p.S392S	NM_001012241.1	NP_001012241.1	Q68DK7	MSL1_HUMAN	male-specific lethal 1 homolog (Drosophila)	392					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)	MSL complex (GO:0072487)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|large_intestine(2)|lung(2)	7						AGCCCCGGTCTTCAGTGGACA	0.498																																					p.S129S		Atlas-SNP	.											.	MSL1	21	.	0			c.T387C						PASS	.						52.0	54.0	54.0					17																	38285681		1834	4093	5927	SO:0001819	synonymous_variant	339287	exon4			CCGGTCTTCAGTG		CCDS45670.1	17q21.1	2011-03-21			ENSG00000188895	ENSG00000188895			27905	protein-coding gene	gene with protein product		614801				16227571, 16543150	Standard	NM_001012241		Approved	hMSL1, MSL-1, DKFZp686P24239	uc002hua.4	Q68DK7		ENST00000398532.4:c.1176T>C	17.37:g.38285681T>C		80.0	0.0	0		95.0	5.0	0.0526316	NM_001012241	Q0VF46|Q69Z03	Silent	SNP	ENST00000398532.4	37																																																																																				.	.	none		0.498	MSL1-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000447409.2	NM_001012241	
TRIO	7204	hgsc.bcm.edu	37	5	14291259	14291259	+	Silent	SNP	G	G	A	rs61737132	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:14291259G>A	ENST00000344204.4	+	5	999	c.975G>A	c.(973-975)ctG>ctA	p.L325L	TRIO_ENST00000509967.2_Silent_p.L276L|TRIO_ENST00000537187.1_Silent_p.L325L	NM_007118.2	NP_009049.2	O75962	TRIO_HUMAN	trio Rho guanine nucleotide exchange factor	325					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytosol (GO:0005829)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(21)|lung(34)|ovary(4)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	118	Lung NSC(4;0.000742)					GGCAGCATCTGCACCAGATGT	0.562													G|||	213	0.0425319	0.152	0.0173	5008	,	,		19393	0.0		0.0	False		,,,				2504	0.0				p.L325L		Atlas-SNP	.											.	TRIO	305	.	0			c.G975A						PASS	.	G		550,3856	236.8+/-248.8	36,478,1689	54.0	52.0	53.0		975	4.2	1.0	5	dbSNP_129	53	4,8596	2.2+/-6.3	0,4,4296	no	coding-synonymous	TRIO	NM_007118.2		36,482,5985	AA,AG,GG		0.0465,12.483,4.2596		325/3098	14291259	554,12452	2203	4300	6503	SO:0001819	synonymous_variant	7204	exon5			GCATCTGCACCAG	AF091395	CCDS3883.1	5p14-p15.1	2013-01-11	2012-07-12		ENSG00000038382	ENSG00000038382		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"""	12303	protein-coding gene	gene with protein product		601893	"""triple functional domain (PTPRF interacting)"""			8643598	Standard	NM_007118		Approved	ARHGEF23	uc003jff.3	O75962	OTTHUMG00000131057	ENST00000344204.4:c.975G>A	5.37:g.14291259G>A		142.0	0.0	0		143.0	63.0	0.440559	NM_007118	D3DTD1|Q13458|Q59EQ7|Q6PJC9|Q6ZN05|Q8IWK8	Silent	SNP	ENST00000344204.4	37	CCDS3883.1																																																																																			G|0.963;A|0.037	0.037	strong		0.562	TRIO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253711.2	NM_007118	
WDR53	348793	hgsc.bcm.edu	37	3	196281263	196281263	+	Missense_Mutation	SNP	C	C	T	rs61730533	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:196281263C>T	ENST00000332629.5	-	4	1463	c.896G>A	c.(895-897)gGt>gAt	p.G299D	WDR53_ENST00000433160.1_Missense_Mutation_p.G140D|WDR53_ENST00000429115.1_Missense_Mutation_p.G138D	NM_182627.1	NP_872433.1	Q7Z5U6	WDR53_HUMAN	WD repeat domain 53	299										breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(7)|ovary(1)|skin(1)	13	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.6e-23)|all cancers(36;1.54e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.29e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00326)		AGTATTTCCACCCTGCTTGGT	0.418													C|||	283	0.0565096	0.1997	0.0245	5008	,	,		18151	0.0		0.002	False		,,,				2504	0.0				p.G299D		Atlas-SNP	.											.	WDR53	26	.	0			c.G896A						PASS	.	C	ASP/GLY	759,3647	310.0+/-291.3	63,633,1507	290.0	249.0	263.0		896	-3.3	0.0	3	dbSNP_129	263	11,8589	8.4+/-32.0	0,11,4289	yes	missense	WDR53	NM_182627.1	94	63,644,5796	TT,TC,CC		0.1279,17.2265,5.9203	benign	299/359	196281263	770,12236	2203	4300	6503	SO:0001583	missense	348793	exon4			TTTCCACCCTGCT	BC054030	CCDS3318.1	3q29	2013-01-09			ENSG00000185798	ENSG00000185798		"""WD repeat domain containing"""	28786	protein-coding gene	gene with protein product		615110				12477932	Standard	NM_182627		Approved	MGC64882, MGC12928	uc003fwt.3	Q7Z5U6	OTTHUMG00000155572	ENST00000332629.5:c.896G>A	3.37:g.196281263C>T	ENSP00000328079:p.Gly299Asp	523.0	1.0	0.00191205		549.0	259.0	0.471767	NM_182627	A0MNP1	Missense_Mutation	SNP	ENST00000332629.5	37	CCDS3318.1	113	0.051739926739926737	104	0.21138211382113822	8	0.022099447513812154	0	0.0	1	0.0013192612137203166	C	0.015	-1.543285	0.00934	0.172265	0.001279	ENSG00000185798	ENST00000332629;ENST00000429115;ENST00000433160	T;T;T	0.72282	-0.64;1.94;1.94	5.67	-3.35	0.04928	.	1.642950	0.02577	N	0.098418	T	0.00039	0.0001	N	0.12182	0.205	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.11966	-1.0566	9	0.02654	T	1	-15.4206	0.1558	0.00098	0.3118:0.235:0.2066:0.2466	.	299	Q7Z5U6	WDR53_HUMAN	D	299;138;140	ENSP00000328079:G299D;ENSP00000396668:G138D;ENSP00000410677:G140D	ENSP00000328079:G299D	G	-	2	0	WDR53	197765660	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-0.565000	0.05929	-0.487000	0.06735	-1.036000	0.02392	GGT	C|0.942;T|0.058	0.058	strong		0.418	WDR53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340689.1	NM_182627	
STOX1	219736	hgsc.bcm.edu	37	10	70646139	70646139	+	Missense_Mutation	SNP	G	G	A	rs7904300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:70646139G>A	ENST00000298596.6	+	3	2670	c.2587G>A	c.(2587-2589)Gcc>Acc	p.A863T	STOX1_ENST00000399165.4_Intron|STOX1_ENST00000399169.4_Missense_Mutation_p.A863T|STOX1_ENST00000421961.2_Missense_Mutation_p.A753T|STOX1_ENST00000399162.2_Intron	NM_152709.4	NP_689922.3	Q6ZVD7	STOX1_HUMAN	storkhead box 1	863			A -> T (in dbSNP:rs7904300).			cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(2)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|prostate(1)|skin(3)	28						CGCAAGAAAAGCCAGTTTTGA	0.423													G|||	145	0.0289537	0.1014	0.0144	5008	,	,		20639	0.0		0.001	False		,,,				2504	0.0				p.A863T		Atlas-SNP	.											.	STOX1	75	.	0			c.G2587A						PASS	.	G	,,THR/ALA,THR/ALA,THR/ALA	385,3671		22,341,1665	81.0	81.0	81.0		,,2587,2257,2587	-1.5	0.0	10	dbSNP_116	81	4,8436		0,4,4216	yes	intron,intron,missense,missense,missense	STOX1	NM_001130159.2,NM_001130160.2,NM_001130161.2,NM_001130162.2,NM_152709.4	,,58,58,58	22,345,5881	AA,AG,GG		0.0474,9.4921,3.113	,,benign,benign,benign	,,863/990,753/880,863/990	70646139	389,12107	2028	4220	6248	SO:0001583	missense	219736	exon3			AGAAAAGCCAGTT	AK057891	CCDS41535.1, CCDS44416.1, CCDS44417.1	10q22.1	2005-11-29	2005-04-04	2005-04-04	ENSG00000165730	ENSG00000165730			23508	protein-coding gene	gene with protein product		609397	"""chromosome 10 open reading frame 24"""	C10orf24			Standard	NM_152709		Approved	FLJ25162	uc001joq.3	Q6ZVD7	OTTHUMG00000018367	ENST00000298596.6:c.2587G>A	10.37:g.70646139G>A	ENSP00000298596:p.Ala863Thr	88.0	0.0	0		105.0	42.0	0.4	NM_152709	A2A3Q9|A5D6Y7|B0QZA4|B0QZA5|B0QZA6|Q4F8Q6|Q5I946|Q5I947|Q5I948|Q5VX38|Q5VX39|Q6ZRY3|Q96LR3|Q96LS0	Missense_Mutation	SNP	ENST00000298596.6	37	CCDS41535.1	56	0.02564102564102564	52	0.10569105691056911	4	0.011049723756906077	0	0.0	0	0.0	G	7.158	0.585121	0.13749	0.094921	4.74E-4	ENSG00000165730	ENST00000399169;ENST00000298596;ENST00000421961	T;T;T	0.66815	-0.23;-0.23;-0.23	6.17	-1.51	0.08664	.	0.471664	0.25324	N	0.031488	T	0.01695	0.0054	L	0.56769	1.78	0.80722	P	0.0	B	0.19445	0.036	B	0.17098	0.017	T	0.09618	-1.0666	9	0.46703	T	0.11	.	7.4728	0.27359	0.2424:0.2162:0.5415:0.0	rs7904300;rs52803686;rs7904300	863	Q6ZVD7	STOX1_HUMAN	T	863;863;753	ENSP00000382121:A863T;ENSP00000298596:A863T;ENSP00000394509:A753T	ENSP00000298596:A863T	A	+	1	0	STOX1	70316145	0.119000	0.22226	0.000000	0.03702	0.006000	0.05464	0.598000	0.24074	-0.561000	0.06094	0.655000	0.94253	GCC	G|0.968;A|0.032	0.032	strong		0.423	STOX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276849.3	NM_152709	
SENP7	57337	hgsc.bcm.edu	37	3	101090925	101090925	+	Missense_Mutation	SNP	C	C	A	rs115061809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:101090925C>A	ENST00000394095.2	-	7	776	c.723G>T	c.(721-723)caG>caT	p.Q241H	SENP7_ENST00000394091.1_Missense_Mutation_p.Q77H|SENP7_ENST00000314261.7_Missense_Mutation_p.Q175H|SENP7_ENST00000348610.3_Missense_Mutation_p.Q208H|SENP7_ENST00000394094.2_Missense_Mutation_p.Q176H|SENP7_ENST00000358203.3_Missense_Mutation_p.Q77H	NM_001282802.1|NM_020654.3	NP_001269731.1|NP_065705.3	Q9BQF6	SENP7_HUMAN	SUMO1/sentrin specific peptidase 7	241						intracellular (GO:0005622)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)			breast(2)|endometrium(1)|kidney(1)|large_intestine(16)|lung(15)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						TGTGCGCAGTCTGCTTTGCAG	0.368													C|||	50	0.00998403	0.0371	0.0014	5008	,	,		13309	0.0		0.0	False		,,,				2504	0.0				p.Q241H		Atlas-SNP	.											.	SENP7	170	.	0			c.G723T						PASS	.	C	HIS/GLN,HIS/GLN	156,4250	103.8+/-142.4	4,148,2051	135.0	127.0	129.0		528,723	1.7	0.2	3	dbSNP_132	129	0,8600		0,0,4300	yes	missense,missense	SENP7	NM_001077203.1,NM_020654.3	24,24	4,148,6351	AA,AC,CC		0.0,3.5406,1.1994	possibly-damaging,possibly-damaging	176/986,241/1051	101090925	156,12850	2203	4300	6503	SO:0001583	missense	57337	exon7			CGCAGTCTGCTTT		CCDS2941.2, CCDS43121.1, CCDS63704.1, CCDS63705.1, CCDS63706.1	3q12	2008-02-05	2005-08-17		ENSG00000138468	ENSG00000138468			30402	protein-coding gene	gene with protein product		612846	"""SUMO1/sentrin specific protease 7"""			11214970, 11230166	Standard	NM_001282802		Approved		uc003dut.3	Q9BQF6	OTTHUMG00000149927	ENST00000394095.2:c.723G>T	3.37:g.101090925C>A	ENSP00000377655:p.Gln241His	145.0	0.0	0		156.0	72.0	0.461538	NM_020654	A1L3A5|A8MW39|B7WNW8|Q7Z3F4|Q96PS5|Q9C0F6|Q9HBT5	Missense_Mutation	SNP	ENST00000394095.2	37	CCDS2941.2	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	10.27	1.303827	0.23736	0.035406	0.0	ENSG00000138468	ENST00000394095;ENST00000394094;ENST00000314261;ENST00000394091;ENST00000358203;ENST00000348610	T;T;T;T;T;T	0.20069	2.12;2.1;2.15;2.11;2.11;2.13	5.1	1.66	0.24008	.	0.601428	0.14885	N	0.292719	T	0.05273	0.0140	L	0.54323	1.7	0.09310	N	1	P;P;P;P	0.48503	0.911;0.846;0.797;0.694	P;P;P;B	0.47470	0.465;0.465;0.548;0.346	T	0.08743	-1.0707	10	0.87932	D	0	-0.6991	2.926	0.05784	0.2106:0.529:0.0:0.2604	.	77;175;208;241	Q9BQF6-4;Q9BQF6-5;Q9BQF6-2;Q9BQF6	.;.;.;SENP7_HUMAN	H	241;176;175;77;77;208	ENSP00000377655:Q241H;ENSP00000377654:Q176H;ENSP00000313624:Q175H;ENSP00000377651:Q77H;ENSP00000350936:Q77H;ENSP00000342159:Q208H	ENSP00000313624:Q175H	Q	-	3	2	SENP7	102573615	0.220000	0.23631	0.175000	0.22980	0.007000	0.05969	0.278000	0.18753	0.606000	0.29965	0.585000	0.79938	CAG	C|0.988;A|0.012	0.012	strong		0.368	SENP7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313957.2	NM_020654	
CATSPERG	57828	hgsc.bcm.edu	37	19	38834974	38834974	+	Missense_Mutation	SNP	G	G	A	rs61732182	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38834974G>A	ENST00000409235.3	+	6	750	c.635G>A	c.(634-636)cGg>cAg	p.R212Q	CATSPERG_ENST00000410018.1_Missense_Mutation_p.R212Q|CATSPERG_ENST00000215069.4_Missense_Mutation_p.R197Q	NM_021185.4	NP_067008.3	Q6ZRH7	CTSRG_HUMAN	catsper channel auxiliary subunit gamma	212					cell differentiation (GO:0030154)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|plasma membrane (GO:0005886)|sperm principal piece (GO:0097228)				breast(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(13)|ovary(1)|pancreas(2)|prostate(6)|skin(3)|stomach(1)|urinary_tract(2)	40						AAGAGAGACCGGGACAATAAC	0.537													G|||	14	0.00279553	0.0106	0.0	5008	,	,		19650	0.0		0.0	False		,,,				2504	0.0				p.R212Q		Atlas-SNP	.											.	CATSPERG	121	.	0			c.G635A						PASS	.	G	GLN/ARG	24,1360		0,24,668	133.0	116.0	121.0		635	-6.7	0.0	19	dbSNP_129	121	0,3182		0,0,1591	no	missense	CATSPERG	NM_021185.4	43	0,24,2259	AA,AG,GG		0.0,1.7341,0.5256	benign	212/1160	38834974	24,4542	692	1591	2283	SO:0001583	missense	57828	exon6			GAGACCGGGACAA	AK128220	CCDS12514.2	19q13.1	2014-05-13	2012-02-22	2009-07-17	ENSG00000099338	ENSG00000099338			25243	protein-coding gene	gene with protein product		613452	"""chromosome 19 open reading frame 15"", ""cation channel, sperm-associated, gamma"""	C19orf15		19516020	Standard	NM_021185		Approved	DKFZp434A1022, FLJ46353	uc002oih.4	Q6ZRH7	OTTHUMG00000153223	ENST00000409235.3:c.635G>A	19.37:g.38834974G>A	ENSP00000386962:p.Arg212Gln	117.0	0.0	0		127.0	69.0	0.543307	NM_021185	A6NEG6|Q659E1	Missense_Mutation	SNP	ENST00000409235.3	37	CCDS12514.2	4	0.0018315018315018315	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	G	2.197	-0.383886	0.04966	0.017341	0.0	ENSG00000099338	ENST00000410018;ENST00000409235;ENST00000409410;ENST00000215069	T;T;T;T	0.30981	1.51;1.51;1.51;1.51	4.61	-6.69	0.01772	.	2.425480	0.01465	N	0.016055	T	0.06096	0.0158	N	0.03177	-0.4	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.15350	-1.0440	10	0.27785	T	0.31	5.2025	7.9175	0.29827	0.255:0.2965:0.4485:0.0	rs61732182	212;212	Q6ZRH7;B8ZZI7	CTSRG_HUMAN;.	Q	212;212;212;197	ENSP00000387057:R212Q;ENSP00000386962:R212Q;ENSP00000386950:R212Q;ENSP00000215069:R197Q	ENSP00000215069:R197Q	R	+	2	0	CATSPERG	43526814	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.727000	0.00807	-1.348000	0.02205	-1.068000	0.02270	CGG	G|0.997;A|0.003	0.003	strong		0.537	CATSPERG-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330204.1	NM_021185	
CYP1A2	1544	hgsc.bcm.edu	37	15	75043592	75043592	+	Missense_Mutation	SNP	C	C	A	rs17861157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:75043592C>A	ENST00000343932.4	+	3	957	c.894C>A	c.(892-894)agC>agA	p.S298R		NM_000761.3	NP_000752.2	P05177	CP1A2_HUMAN	cytochrome P450, family 1, subfamily A, polypeptide 2	298			S -> R (in dbSNP:rs17861157). {ECO:0000269|PubMed:15469410}.		alkaloid metabolic process (GO:0009820)|arachidonic acid metabolic process (GO:0019369)|cellular respiration (GO:0045333)|cellular response to cadmium ion (GO:0071276)|dibenzo-p-dioxin metabolic process (GO:0018894)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|hydrogen peroxide biosynthetic process (GO:0050665)|lung development (GO:0030324)|methylation (GO:0032259)|monocarboxylic acid metabolic process (GO:0032787)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|oxidative deethylation (GO:0071615)|oxidative demethylation (GO:0070989)|porphyrin-containing compound metabolic process (GO:0006778)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|small molecule metabolic process (GO:0044281)|steroid catabolic process (GO:0006706)|toxin biosynthetic process (GO:0009403)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|demethylase activity (GO:0032451)|electron carrier activity (GO:0009055)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	33					"""""""Insulin(DB00071)|Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Agomelatine(DB06594)|Albendazole(DB00518)|Alitretinoin(DB00523)|Almotriptan(DB00918)|Alosetron(DB00969)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Aminophylline(DB01223)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Anagrelide(DB00261)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Asenapine(DB06216)|Atropine(DB00572)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzyl alcohol(DB06770)|Betaxolol(DB00195)|Bortezomib(DB00188)|Bromazepam(DB01558)|Bromocriptine(DB01200)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Caffeine(DB00201)|Carbamazepine(DB00564)|Carmustine(DB00262)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clenbuterol(DB01407)|Clevidipine(DB04920)|Clobetasol propionate(DB01013)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Conjugated Estrogens(DB00286)|Cyclobenzaprine(DB00924)|Dacarbazine(DB00851)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Diazepam(DB00829)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Domperidone(DB01184)|Dopamine(DB00988)|Doxepin(DB01142)|Duloxetine(DB00476)|Edetic Acid(DB00974)|Efavirenz(DB00625)|Eltrombopag(DB06210)|Enoxacin(DB00467)|Epinephrine(DB00668)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Estropipate(DB04574)|Ethanol(DB00898)|Etoposide(DB00773)|Etoricoxib(DB01628)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Frovatriptan(DB00998)|Gemfibrozil(DB01241)|Griseofulvin(DB00400)|Guanabenz(DB00629)|Haloperidol(DB00502)|Hesperetin(DB01094)|Hexobarbital(DB01355)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Imiquimod(DB00724)|inhaled insulin(DB05278)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Levobupivacaine(DB01002)|Levofloxacin(DB01137)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Lopinavir(DB01601)|Lorcaserin(DB04871)|Losartan(DB00678)|Lumiracoxib(DB01283)|Malathion(DB00772)|Maprotiline(DB00934)|Meclizine(DB00737)|Melatonin(DB01065)|Menadione(DB00170)|Methadone(DB00333)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Modafinil(DB00745)|Nabumetone(DB00461)|Nafcillin(DB00607)|Naproxen(DB00788)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niclosamide(DB06803)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitric Oxide(DB00435)|Nitroprusside(DB00325)|Norepinephrine(DB00368)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ofloxacin(DB01165)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxaliplatin(DB00526)|Oxtriphylline(DB01303)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pefloxacin(DB00487)|Pentamidine(DB00738)|Pentoxifylline(DB00806)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phentermine(DB00191)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Pimozide(DB01100)|Pipotiazine(DB01621)|Pomalidomide(DB08910)|Praziquantel(DB01058)|Primaquine(DB01087)|Primidone(DB00794)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Pyrazinamide(DB00339)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ramelteon(DB00980)|Ranitidine(DB00863)|Rasagiline(DB01367)|Rifabutin(DB00615)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Roxithromycin(DB00778)|Secobarbital(DB00418)|Selegiline(DB01037)|Sertraline(DB01104)|SIMEPREVIR(DB06290)|Sorafenib(DB00398)|Streptozocin(DB00428)|Sulindac(DB00605)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Tenofovir(DB00300)|Terbinafine(DB00857)|Thalidomide(DB01041)|Theobromine(DB01412)|Theophylline(DB00277)|Thiabendazole(DB00730)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tizanidine(DB00697)|Tocainide(DB01056)|Toremifene(DB00539)|Tranylcypromine(DB00752)|Triamterene(DB00384)|Trifluoperazine(DB00831)|Valproic Acid(DB00313)|Vemurafenib(DB08881)|Verapamil(DB00661)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)|Zolpidem(DB00425)"""	CTAGAGCCAGCGGCAACCTCA	0.562													C|||	120	0.0239617	0.0893	0.0029	5008	,	,		21893	0.0		0.0	False		,,,				2504	0.0				p.S298R		Atlas-SNP	.											.	CYP1A2	70	.	0			c.C894A						PASS	.	C	ARG/SER	308,4086	164.7+/-196.3	7,294,1896	138.0	110.0	120.0		894	-9.7	0.0	15	dbSNP_123	120	2,8590	2.2+/-6.3	0,2,4294	yes	missense	CYP1A2	NM_000761.3	110	7,296,6190	AA,AC,CC		0.0233,7.0096,2.3872	benign	298/517	75043592	310,12676	2197	4296	6493	SO:0001583	missense	1544	exon3			AGCCAGCGGCAAC	AF182274	CCDS32293.1	15q24.1	2013-11-11	2003-01-14		ENSG00000140505	ENSG00000140505	1.14.14.1	"""Cytochrome P450s"""	2596	protein-coding gene	gene with protein product		124060	"""cytochrome P450, subfamily I (aromatic compound-inducible), polypeptide 2"""			15128046	Standard	NM_000761		Approved	P3-450, CP12	uc002ayr.1	P05177	OTTHUMG00000172901	ENST00000343932.4:c.894C>A	15.37:g.75043592C>A	ENSP00000342007:p.Ser298Arg	111.0	1.0	0.00900901		119.0	119.0	1	NM_000761	Q16754|Q6NWU5|Q9BXX7|Q9UK49	Missense_Mutation	SNP	ENST00000343932.4	37	CCDS32293.1	41	0.018772893772893772	41	0.08333333333333333	0	0.0	0	0.0	0	0.0	C	12.56	1.975261	0.34848	0.070096	2.33E-4	ENSG00000140505	ENST00000343932	T	0.79653	-1.29	4.85	-9.7	0.00521	.	0.549195	0.21605	N	0.071895	T	0.06962	0.0177	L	0.27053	0.805	0.09310	N	1	B	0.31174	0.311	B	0.28784	0.094	T	0.38112	-0.9676	10	0.59425	D	0.04	.	8.7855	0.34818	0.0:0.2777:0.1818:0.5405	rs17861157;rs56991650	298	P05177-2	.	R	298	ENSP00000342007:S298R	ENSP00000342007:S298R	S	+	3	2	CYP1A2	72830645	0.000000	0.05858	0.000000	0.03702	0.023000	0.10783	-4.224000	0.00271	-3.301000	0.00192	-0.369000	0.07265	AGC	C|0.973;A|0.027	0.027	strong		0.562	CYP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421263.2	NM_000761	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254074	39254074	+	Missense_Mutation	SNP	G	G	T	rs78662167		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39254074G>T	ENST00000333822.4	-	1	319	c.263C>A	c.(262-264)aCc>aAc	p.T88N		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	88	25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						GTGGCAGCAGGTGGGCTGGCA	0.662																																					p.T88N		Atlas-SNP	.											.	KRTAP4-8	57	.	0			c.C263A						PASS	.						7.0	11.0	10.0					17																	39254074		684	1571	2255	SO:0001583	missense	728224	exon1			CAGCAGGTGGGCT	AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"""Keratin associated proteins"""	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.263C>A	17.37:g.39254074G>T	ENSP00000328444:p.Thr88Asn	139.0	0.0	0		133.0	19.0	0.142857	NM_031960	A8MSH3	Missense_Mutation	SNP	ENST00000333822.4	37	CCDS45674.1	.	.	.	.	.	.	.	.	.	.	.	12.61	1.990330	0.35131	.	.	ENSG00000204880	ENST00000333822;ENST00000332991	T	0.01464	4.86	3.31	-6.61	0.01818	.	.	.	.	.	T	0.02848	0.0085	M	0.87547	2.89	0.09310	N	0.999995	B	0.09022	0.002	B	0.08055	0.003	T	0.35674	-0.9779	9	0.52906	T	0.07	.	2.3202	0.04208	0.2779:0.4366:0.1148:0.1707	.	88	Q9BYQ9	KRA48_HUMAN	N	88;73	ENSP00000328444:T88N	ENSP00000414561:T73N	T	-	2	0	KRTAP4-8	36507600	0.000000	0.05858	0.000000	0.03702	0.921000	0.55340	-5.373000	0.00127	-4.086000	0.00075	0.449000	0.29647	ACC	G|0.500;T|0.500	0.500	weak		0.662	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
C9orf173	441476	hgsc.bcm.edu	37	9	140146526	140146526	+	Silent	SNP	G	G	A	rs74822962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140146526G>A	ENST00000412566.1	+	3	351	c.342G>A	c.(340-342)ccG>ccA	p.P114P	C9orf173_ENST00000388931.3_Silent_p.P114P			Q8N7X2	CI173_HUMAN	chromosome 9 open reading frame 173	114								p.P114P(1)		kidney(1)|large_intestine(1)|lung(5)|pancreas(1)	8						TGCCGAGCCCGTCCGTACGAG	0.672													G|||	36	0.0071885	0.0257	0.0029	5008	,	,		16156	0.0		0.0	False		,,,				2504	0.0				p.P114P		Atlas-SNP	.											C9orf173,colon,carcinoma,0,1	C9orf173	19	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G342A						PASS	.	G		64,4044		0,64,1990	40.0	50.0	47.0		342	-7.8	0.0	9	dbSNP_132	47	1,8369		0,1,4184	no	coding-synonymous	C9orf173	NM_001004353.2		0,65,6174	AA,AG,GG		0.0119,1.5579,0.5209		114/309	140146526	65,12413	2054	4185	6239	SO:0001819	synonymous_variant	441476	exon3			GAGCCCGTCCGTA		CCDS48065.1, CCDS59156.1, CCDS75940.1, CCDS75941.1	9q34.3	2009-10-02			ENSG00000197768	ENSG00000197768			37285	protein-coding gene	gene with protein product							Standard	NM_001256699		Approved	FLJ40246	uc004cmk.2	Q8N7X2		ENST00000412566.1:c.342G>A	9.37:g.140146526G>A		58.0	0.0	0		71.0	52.0	0.732394	NM_001256701	A2RU24|B7ZM72|B7ZM76|Q8NEA3	Silent	SNP	ENST00000412566.1	37	CCDS48065.1																																																																																			G|0.991;A|0.009	0.009	strong		0.672	C9orf173-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001004353	
ZFC3H1	196441	hgsc.bcm.edu	37	12	72020103	72020103	+	Silent	SNP	G	G	A	rs56384440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:72020103G>A	ENST00000378743.3	-	22	4612	c.4254C>T	c.(4252-4254)gaC>gaT	p.D1418D		NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	1418					RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						CCTGCACCTCGTCCTTGGTTC	0.413													G|||	121	0.0241613	0.0862	0.0086	5008	,	,		17082	0.0		0.001	False		,,,				2504	0.0				p.D1418D		Atlas-SNP	.											.	ZFC3H1	172	.	0			c.C4254T						PASS	.	G		253,3587		9,235,1676	185.0	176.0	179.0		4254	-7.2	0.5	12	dbSNP_129	179	3,8243		0,3,4120	no	coding-synonymous	ZFC3H1	NM_144982.4		9,238,5796	AA,AG,GG		0.0364,6.5885,2.1182		1418/1990	72020103	256,11830	1920	4123	6043	SO:0001819	synonymous_variant	196441	exon22			CACCTCGTCCTTG	AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"""Zinc finger, C3H1-type containing"""	28328	protein-coding gene	gene with protein product			"""proline/serine-rich coiled-coil 2"", ""coiled-coil domain containing 131"""	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.4254C>T	12.37:g.72020103G>A		173.0	0.0	0		147.0	70.0	0.47619	NM_144982	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Silent	SNP	ENST00000378743.3	37	CCDS41813.1																																																																																			A|0.013;G|0.987	0.013	strong		0.413	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982	
NUDT9	53343	hgsc.bcm.edu	37	4	88344063	88344063	+	Silent	SNP	G	G	C	rs11937770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88344063G>C	ENST00000302174.4	+	1	330	c.6G>C	c.(4-6)gcG>gcC	p.A2A	NUDT9_ENST00000473942.1_Intron	NM_024047.4	NP_076952.1	Q9BW91	NUDT9_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 9	2					ADP catabolic process (GO:0046032)|IDP catabolic process (GO:0046709)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|mitochondrial matrix (GO:0005759)	adenosine-diphosphatase activity (GO:0043262)|ADP-ribose diphosphatase activity (GO:0047631)|ADP-sugar diphosphatase activity (GO:0019144)			endometrium(1)|large_intestine(4)|lung(6)	11		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000937)		CGCTCATGGCGGGACGCCTCC	0.667													C|||	539	0.107628	0.3865	0.0187	5008	,	,		15327	0.001		0.003	False		,,,				2504	0.0112				p.A2A		Atlas-SNP	.											.	NUDT9	21	.	0			c.G6C						PASS	.	C	,	1471,2935	670.9+/-402.4	263,945,995	59.0	65.0	63.0		6,	1.3	0.7	4	dbSNP_120	63	20,8580	809.7+/-407.1	0,20,4280	no	coding-synonymous,intron	NUDT9	NM_024047.3,NM_198038.1	,	263,965,5275	CC,CG,GG		0.2326,33.3863,11.4639	,	2/351,	88344063	1491,11515	2203	4300	6503	SO:0001819	synonymous_variant	53343	exon1			CATGGCGGGACGC	AY026252	CCDS3620.1, CCDS3621.1	4q22.1	2008-08-29			ENSG00000170502	ENSG00000170502		"""Nudix motif containing"""	8056	protein-coding gene	gene with protein product		606022				11385575, 12427752	Standard	NM_024047		Approved	MGC3037	uc003hqq.3	Q9BW91	OTTHUMG00000130591	ENST00000302174.4:c.6G>C	4.37:g.88344063G>C		37.0	0.0	0		21.0	20.0	0.952381	NM_001248011	Q8NBN1|Q8NCB9|Q8NG25	Silent	SNP	ENST00000302174.4	37	CCDS3620.1																																																																																			G|0.895;C|0.105	0.105	strong		0.667	NUDT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253035.2		
GJB4	127534	hgsc.bcm.edu	37	1	35227041	35227041	+	Silent	SNP	C	C	T	rs76188300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:35227041C>T	ENST00000339480.1	+	2	556	c.186C>T	c.(184-186)aaC>aaT	p.N62N	RP1-34M23.5_ENST00000542839.1_RNA	NM_153212.2	NP_694944.1	Q9NTQ9	CXB4_HUMAN	gap junction protein, beta 4, 30.3kDa	62					cell communication (GO:0007154)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|skin(1)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				GCTGCCCCAACGTCTGCTATG	0.612													C|||	181	0.0361422	0.1293	0.013	5008	,	,		21540	0.0		0.001	False		,,,				2504	0.0				p.N62N		Atlas-SNP	.											.	GJB4	51	.	0			c.C186T						PASS	.	C		513,3893	236.5+/-248.6	25,463,1715	177.0	125.0	143.0		186	-6.0	0.8	1	dbSNP_131	143	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	GJB4	NM_153212.2		25,468,6010	TT,TC,CC		0.0581,11.6432,3.9828		62/267	35227041	518,12488	2203	4300	6503	SO:0001819	synonymous_variant	127534	exon2			CCCCAACGTCTGC		CCDS383.1	1p35-p34	2008-05-14	2007-11-06		ENSG00000189433	ENSG00000189433		"""Ion channels / Gap junction proteins (connexins)"""	4286	protein-coding gene	gene with protein product	"""connexin 30.3"""	605425	"""gap junction protein, beta 4 (connexin 30.3)"", ""gap junction protein, beta 4"""				Standard	NM_153212		Approved	CX30.3	uc001bxv.1	Q9NTQ9	OTTHUMG00000004052	ENST00000339480.1:c.186C>T	1.37:g.35227041C>T		148.0	0.0	0		166.0	77.0	0.463855	NM_153212	B3KQ82	Silent	SNP	ENST00000339480.1	37	CCDS383.1																																																																																			C|0.964;T|0.036	0.036	strong		0.612	GJB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011560.1	NM_153212	
ABCB11	8647	hgsc.bcm.edu	37	2	169853220	169853220	+	Silent	SNP	G	G	A	rs11568377	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:169853220G>A	ENST00000263817.6	-	6	526	c.402C>T	c.(400-402)atC>atT	p.I134I		NM_003742.2	NP_003733.2	O95342	ABCBB_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 11	134	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|canalicular bile acid transport (GO:0015722)|small molecule metabolic process (GO:0044281)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|bile acid-exporting ATPase activity (GO:0015432)|canalicular bile acid transmembrane transporter activity (GO:0015126)|sodium-exporting ATPase activity, phosphorylative mechanism (GO:0008554)|transporter activity (GO:0005215)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(16)|lung(26)|ovary(3)|stomach(1)	57					Adenosine triphosphate(DB00171)|Bosentan(DB00559)|Chlorpromazine(DB00477)|Cimetidine(DB00501)|Clofazimine(DB00845)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Digoxin(DB00390)|Doxorubicin(DB00997)|Ethinyl Estradiol(DB00977)|Fluorescein(DB00693)|Fusidic Acid(DB02703)|Glyburide(DB01016)|Ketoconazole(DB01026)|Novobiocin(DB01051)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Ponatinib(DB08901)|Pravastatin(DB00175)|Progesterone(DB00396)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Rosuvastatin(DB01098)|Tamoxifen(DB00675)|Ursodeoxycholic acid(DB01586)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	TTTCGCTCTCGATGTTCAGCA	0.378													A|||	331	0.0660942	0.2179	0.0202	5008	,	,		13403	0.001		0.001	False		,,,				2504	0.0276				p.I134I		Atlas-SNP	.											.	ABCB11	136	.	0			c.C402T						PASS	.	A		590,3158		41,508,1325	60.0	57.0	58.0		402	2.8	0.9	2	dbSNP_121	58	3,8211		0,3,4104	no	coding-synonymous	ABCB11	NM_003742.2		41,511,5429	AA,AG,GG		0.0365,15.7417,4.9574		134/1322	169853220	593,11369	1874	4107	5981	SO:0001819	synonymous_variant	8647	exon6			GCTCTCGATGTTC	AF091582	CCDS46444.1	2q24	2012-03-14			ENSG00000073734	ENSG00000073734		"""ATP binding cassette transporters / subfamily B"""	42	protein-coding gene	gene with protein product	"""ABC member 16, MDR/TAP subfamily"""	603201	"""progressive familial intrahepatic cholestasis 2"", ""bile salt export pump"""	BSEP, PFIC2		9806540	Standard	NM_003742		Approved	ABC16, SPGP, PFIC-2, PGY4	uc002ueo.1	O95342	OTTHUMG00000154039	ENST00000263817.6:c.402C>T	2.37:g.169853220G>A		84.0	0.0	0		59.0	59.0	1	NM_003742	Q53TL2|Q9UNB2	Silent	SNP	ENST00000263817.6	37	CCDS46444.1																																																																																			G|0.935;A|0.065	0.065	strong		0.378	ABCB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333616.2	NM_003742	
SPATA5L1	79029	hgsc.bcm.edu	37	15	45695612	45695612	+	Silent	SNP	C	C	T	rs1346265	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:45695612C>T	ENST00000305560.6	+	1	1084	c.985C>T	c.(985-987)Ctg>Ttg	p.L329L	SPATA5L1_ENST00000559860.1_Silent_p.L329L|GATM_ENST00000458245.5_5'Flank	NM_024063.2	NP_076968.2	Q9BVQ7	SPA5L_HUMAN	spermatogenesis associated 5-like 1	329						cytoplasm (GO:0005737)	ATP binding (GO:0005524)			kidney(2)|large_intestine(3)|lung(1)|ovary(3)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	14		Lung NSC(122;8.3e-05)|all_lung(180;0.000547)|Melanoma(134;0.0417)		all cancers(107;7.31e-17)|GBM - Glioblastoma multiforme(94;6.28e-07)		GTTGACGCTGCTGGACGGCGC	0.687													C|||	803	0.160343	0.528	0.0476	5008	,	,		14072	0.0079		0.002	False		,,,				2504	0.0634				p.L329L		Atlas-SNP	.											.	SPATA5L1	40	.	0			c.C985T						PASS	.	C		1987,2399		467,1053,673	21.0	26.0	24.0		985	1.4	1.0	15	dbSNP_88	24	12,8564		0,12,4276	no	coding-synonymous	SPATA5L1	NM_024063.2		467,1065,4949	TT,TC,CC		0.1399,45.3032,15.422		329/754	45695612	1999,10963	2193	4288	6481	SO:0001819	synonymous_variant	79029	exon1			ACGCTGCTGGACG	AK023232	CCDS10123.1	15q15.1	2010-04-21			ENSG00000171763	ENSG00000171763		"""ATPases / AAA-type"""	28762	protein-coding gene	gene with protein product						12477932	Standard	NM_024063		Approved	MGC5347, FLJ12286	uc001zve.3	Q9BVQ7	OTTHUMG00000131425	ENST00000305560.6:c.985C>T	15.37:g.45695612C>T		62.0	0.0	0		79.0	35.0	0.443038	NM_024063	C9JHR5|Q9H8W7|Q9HA41	Silent	SNP	ENST00000305560.6	37	CCDS10123.1																																																																																			C|0.860;T|0.140	0.140	strong		0.687	SPATA5L1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000254218.1	NM_024063	
PVRL2	5819	hgsc.bcm.edu	37	19	45368805	45368805	+	Silent	SNP	C	C	T	rs34929997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45368805C>T	ENST00000252483.5	+	2	366	c.366C>T	c.(364-366)gaC>gaT	p.D122D	PVRL2_ENST00000252485.4_Silent_p.D122D	NM_001042724.1	NP_001036189.1	Q92692	PVRL2_HUMAN	poliovirus receptor-related 2 (herpesvirus entry mediator B)	122	Ig-like V-type.				acrosome assembly (GO:0001675)|adherens junction organization (GO:0034332)|adhesion of symbiont to host (GO:0044406)|cell junction assembly (GO:0034329)|cell part morphogenesis (GO:0032990)|cell-cell junction organization (GO:0045216)|cilium organization (GO:0044782)|coreceptor-mediated virion attachment to host cell (GO:0046814)|cytoskeleton organization (GO:0007010)|establishment of mitochondrion localization (GO:0051654)|fertilization (GO:0009566)|fusion of virus membrane with host plasma membrane (GO:0019064)|homophilic cell adhesion (GO:0007156)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of mast cell activation (GO:0033005)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|sperm mitochondrion organization (GO:0030382)|spermatid development (GO:0007286)|spermatid nucleus differentiation (GO:0007289)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|large_intestine(6)|lung(5)	13	Lung NSC(12;0.00195)|all_lung(12;0.00522)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0143)		AGCTCCAGGACGCCACGCTGG	0.662													T|||	87	0.0173722	0.0651	0.0	5008	,	,		19055	0.0		0.001	False		,,,				2504	0.0				p.D122D		Atlas-SNP	.											.	PVRL2	58	.	0			c.C366T						PASS	.	T	,	215,4179		4,207,1986	22.0	20.0	20.0		366,366	-6.6	0.3	19	dbSNP_126	20	4,8566		0,4,4281	no	coding-synonymous,coding-synonymous	PVRL2	NM_001042724.1,NM_002856.2	,	4,211,6267	TT,TC,CC		0.0467,4.893,1.6893	,	122/539,122/480	45368805	219,12745	2197	4285	6482	SO:0001819	synonymous_variant	5819	exon2			CCAGGACGCCACG	X80038	CCDS12645.1, CCDS42576.1	19q13.32	2013-01-29			ENSG00000130202	ENSG00000130202		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9707	protein-coding gene	gene with protein product		600798		HVEB		7622062, 10196354	Standard	NM_001042724		Approved	PVRR2, PRR2, CD112	uc002ozw.1	Q92692	OTTHUMG00000180839	ENST00000252483.5:c.366C>T	19.37:g.45368805C>T		47.0	0.0	0		33.0	11.0	0.333333	NM_002856	A8K5L5|O75455|Q6IBI6|Q96J29	Silent	SNP	ENST00000252483.5	37	CCDS42576.1																																																																																			C|0.980;T|0.020	0.020	strong		0.662	PVRL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453231.1	NM_002856	
TTYH2	94015	hgsc.bcm.edu	37	17	72227040	72227040	+	Missense_Mutation	SNP	G	G	A	rs150215307	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:72227040G>A	ENST00000269346.4	+	3	390	c.316G>A	c.(316-318)Gtt>Att	p.V106I	TTYH2_ENST00000529107.1_Missense_Mutation_p.V85I	NM_032646.5	NP_116035.5	Q9BSA4	TTYH2_HUMAN	tweety family member 2	106						chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			breast(2)|endometrium(1)|kidney(3)|large_intestine(8)|lung(14)|ovary(3)|pancreas(1)|stomach(3)|upper_aerodigestive_tract(1)	36						TGCGGTGGGCGTTGGTTTCTA	0.483													g|||	23	0.00459265	0.0159	0.0014	5008	,	,		20070	0.0		0.0	False		,,,				2504	0.001				p.V106I		Atlas-SNP	.											.	TTYH2	63	.	0			c.G316A						PASS	.	A	ILE/VAL	58,4348	56.2+/-92.4	0,58,2145	174.0	137.0	150.0		316	3.4	0.9	17	dbSNP_134	150	2,8598	1.2+/-3.3	0,2,4298	yes	missense	TTYH2	NM_032646.5	29	0,60,6443	AA,AG,GG		0.0233,1.3164,0.4613	benign	106/535	72227040	60,12946	2203	4300	6503	SO:0001583	missense	94015	exon3			GTGGGCGTTGGTT		CCDS32717.1, CCDS45770.1	17q25.1	2013-09-02	2013-09-02		ENSG00000141540	ENSG00000141540			13877	protein-coding gene	gene with protein product		608855	"""tweety (Drosophila) homolog 2"", ""tweety homolog 2 (Drosophila)"""			11597145	Standard	XM_005257824		Approved	C17orf29	uc002jkc.3	Q9BSA4	OTTHUMG00000166018	ENST00000269346.4:c.316G>A	17.37:g.72227040G>A	ENSP00000269346:p.Val106Ile	183.0	0.0	0		162.0	59.0	0.364198	NM_032646	B3KX97|Q3B7H8|Q3B7R9|Q6AWB4|Q8NBB7|Q96PK1	Missense_Mutation	SNP	ENST00000269346.4	37	CCDS32717.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	g	8.083	0.772809	0.16051	0.013164	2.33E-4	ENSG00000141540	ENST00000269346;ENST00000529107	T;T	0.12984	2.63;2.63	5.35	3.38	0.38709	.	0.185685	0.46758	N	0.000263	T	0.06234	0.0161	L	0.41961	1.31	0.80722	D	1	B;B	0.33857	0.429;0.092	B;B	0.28305	0.088;0.037	T	0.24870	-1.0148	10	0.13470	T	0.59	-8.4172	7.2697	0.26250	0.3324:0.0:0.6676:0.0	.	85;106	B4DKD1;Q9BSA4	.;TTYH2_HUMAN	I	106;85	ENSP00000269346:V106I;ENSP00000433089:V85I	ENSP00000269346:V106I	V	+	1	0	TTYH2	69738635	0.567000	0.26626	0.943000	0.38184	0.688000	0.40055	1.396000	0.34531	0.658000	0.30925	-0.119000	0.15052	GTT	G|0.995;A|0.005	0.005	strong		0.483	TTYH2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387459.1		
KDM3A	55818	hgsc.bcm.edu	37	2	86709704	86709704	+	Silent	SNP	C	C	T	rs34673273	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:86709704C>T	ENST00000409556.1	+	19	3174	c.2809C>T	c.(2809-2811)Ctg>Ttg	p.L937L	KDM3A_ENST00000409064.1_Silent_p.L937L|KDM3A_ENST00000542128.1_Silent_p.L885L|KDM3A_ENST00000312912.5_Silent_p.L937L			Q9Y4C1	KDM3A_HUMAN	lysine (K)-specific demethylase 3A	937					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)			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						gcccagcattctgggctttga	0.443													C|||	122	0.024361	0.09	0.0043	5008	,	,		19735	0.0		0.0	False		,,,				2504	0.0				p.L937L	NSCLC(96;1150 1523 6936 46253 49736)	Atlas-SNP	.											.	KDM3A	179	.	0			c.C2809T						PASS	.	C	,	377,4029	193.3+/-218.5	18,341,1844	126.0	119.0	121.0		2809,2809	3.7	1.0	2	dbSNP_126	121	1,8599	3.0+/-9.4	0,1,4299	no	coding-synonymous,coding-synonymous	KDM3A	NM_001146688.1,NM_018433.5	,	18,342,6143	TT,TC,CC		0.0116,8.5565,2.9064	,	937/1322,937/1322	86709704	378,12628	2203	4300	6503	SO:0001819	synonymous_variant	55818	exon18			AGCATTCTGGGCT	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.2809C>T	2.37:g.86709704C>T		144.0	0.0	0		185.0	96.0	0.518919	NM_001146688	D6W5M3|Q53S72|Q68D47|Q68UT9|Q6N050|Q8IY08	Silent	SNP	ENST00000409556.1	37	CCDS1990.1																																																																																			C|0.969;T|0.031	0.031	strong		0.443	KDM3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252522.2	NM_018433	
MAGED2	10916	hgsc.bcm.edu	37	X	54837277	54837277	+	Missense_Mutation	SNP	G	G	C	rs12014977	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:54837277G>C	ENST00000375068.1	+	4	794	c.561G>C	c.(559-561)gaG>gaC	p.E187D	MAGED2_ENST00000347546.4_Missense_Mutation_p.E169D|MAGED2_ENST00000375060.1_Missense_Mutation_p.E149D|MAGED2_ENST00000375053.2_Missense_Mutation_p.E187D|MAGED2_ENST00000218439.4_Missense_Mutation_p.E187D|MAGED2_ENST00000396224.1_Missense_Mutation_p.E187D|MAGED2_ENST00000375058.1_Missense_Mutation_p.E187D|MAGED2_ENST00000375062.4_Missense_Mutation_p.E149D|MAGED2_ENST00000497484.1_3'UTR			Q9UNF1	MAGD2_HUMAN	melanoma antigen family D, 2	187			E -> D (in dbSNP:rs12014977).			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						ATGGGGAAGAGGATGGCAGCA	0.552													G|||	91	0.024106	0.0666	0.0043	3775	,	,		4773	0.0		0.0	False		,,,				2504	0.0				p.E187D		Atlas-SNP	.											.	MAGED2	74	.	0			c.G561C						PASS	.	G	ASP/GLU,ASP/GLU,ASP/GLU	275,3560		8,225,34,1399,537	59.0	57.0	58.0		561,561,561	2.1	1.0	X	dbSNP_120	58	4,6724		0,4,0,2424,1872	yes	missense,missense,missense	MAGED2	NM_014599.4,NM_177433.1,NM_201222.1	45,45,45	8,229,34,3823,2409	CC,CG,C,GG,G		0.0595,7.1708,2.6413	probably-damaging,probably-damaging,probably-damaging	187/607,187/607,187/607	54837277	279,10284	2203	4300	6503	SO:0001583	missense	10916	exon4			GGAAGAGGATGGC	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.561G>C	X.37:g.54837277G>C	ENSP00000364209:p.Glu187Asp	150.0	0.0	0		196.0	105.0	0.535714	NM_201222	A6NMX0|O76058|Q5BJF3|Q8NAL6|Q9H218|Q9P0U9|Q9UM52	Missense_Mutation	SNP	ENST00000375068.1	37	CCDS14362.1	35	0.02109704641350211	20	0.0425531914893617	1	0.0028089887640449437	0	0.0	0	0.0	G	16.72	3.200742	0.58126	0.071708	5.95E-4	ENSG00000102316	ENST00000375068;ENST00000375053;ENST00000347546;ENST00000343474;ENST00000375062;ENST00000218439;ENST00000375058;ENST00000375060;ENST00000396224	T;T;T;T;T;T;T;T;T	0.71698	1.26;1.26;3.95;-0.59;0.91;1.26;1.26;0.91;1.26	3.85	2.06	0.26882	.	0.000000	0.44097	D	0.000493	T	0.15998	0.0385	L	0.27053	0.805	0.38540	P	0.05080499999999999	D;P;D	0.61697	0.99;0.956;0.982	D;D;D	0.72982	0.979;0.931;0.952	T	0.56866	-0.7908	9	0.29301	T	0.29	.	7.4321	0.27134	0.2294:0.0:0.7706:0.0	rs12014977;rs52798808;rs12014977	169;149;187	Q9UNF1-2;Q5H907;Q9UNF1	.;.;MAGD2_HUMAN	D	187;187;131;169;149;187;187;149;187	ENSP00000364209:E187D;ENSP00000364193:E187D;ENSP00000336962:E131D;ENSP00000340290:E169D;ENSP00000364202:E149D;ENSP00000218439:E187D;ENSP00000364198:E187D;ENSP00000364200:E149D;ENSP00000379526:E187D	ENSP00000218439:E187D	E	+	3	2	MAGED2	54854002	0.885000	0.30320	1.000000	0.80357	0.993000	0.82548	-0.682000	0.05185	0.430000	0.26230	-0.192000	0.12808	GAG	G|0.973;C|0.027	0.027	strong		0.552	MAGED2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056821.2	NM_014599	
GPR110	266977	hgsc.bcm.edu	37	6	46977783	46977783	+	Missense_Mutation	SNP	C	C	T	rs45598235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:46977783C>T	ENST00000371253.2	-	11	1603	c.1388G>A	c.(1387-1389)cGt>cAt	p.R463H	GPR110_ENST00000449332.2_5'UTR|GPR110_ENST00000283297.5_Missense_Mutation_p.R266H	NM_153840.2	NP_722582.2	Q5T601	GP110_HUMAN	G protein-coupled receptor 110	463					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)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	29						AATTAACACACGGCCTCTGAT	0.438													C|||	186	0.0371406	0.0787	0.0389	5008	,	,		20334	0.0		0.0447	False		,,,				2504	0.0102				p.R463H		Atlas-SNP	.											GPR110,NS,carcinoma,0,1	GPR110	102	1	0			c.G1388A						PASS	.	C	HIS/ARG	378,4028	190.9+/-216.7	14,350,1839	97.0	92.0	94.0		1388	-3.6	0.0	6	dbSNP_127	94	328,8272	115.3+/-175.2	7,314,3979	yes	missense	GPR110	NM_153840.2	29	21,664,5818	TT,TC,CC		3.814,8.5792,5.4283	benign	463/911	46977783	706,12300	2203	4300	6503	SO:0001583	missense	266977	exon11			AACACACGGCCTC	AB083618	CCDS4920.1, CCDS34471.1	6p21.1	2014-08-08			ENSG00000153292	ENSG00000153292		"""-"", ""GPCR / Class B : Orphans"""	18990	protein-coding gene	gene with protein product						12435584, 14623098	Standard	XM_005249006		Approved	hGPCR36, PGR19	uc003oyt.3	Q5T601	OTTHUMG00000014795	ENST00000371253.2:c.1388G>A	6.37:g.46977783C>T	ENSP00000360299:p.Arg463His	134.0	0.0	0		176.0	85.0	0.482955	NM_153840	Q5KU15|Q5T5Z9|Q5T600|Q86SM1|Q8IXE3|Q8IZF8|Q96DQ1|Q9H615	Missense_Mutation	SNP	ENST00000371253.2	37	CCDS34471.1	83	0.038003663003663	43	0.08739837398373984	13	0.03591160220994475	0	0.0	27	0.03562005277044855	C	8.205	0.798930	0.16397	0.085792	0.03814	ENSG00000153292	ENST00000371252;ENST00000371253;ENST00000283297	T;T	0.34472	1.37;1.36	5.2	-3.63	0.04529	.	1.386990	0.04430	N	0.369085	T	0.04588	0.0125	N	0.02202	-0.64	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.28996	-1.0026	10	0.35671	T	0.21	-0.5469	6.9695	0.24640	0.0:0.2802:0.2071:0.5127	rs45598235	463	Q5T601	GP110_HUMAN	H	463;463;266	ENSP00000360299:R463H;ENSP00000283297:R266H	ENSP00000283297:R266H	R	-	2	0	GPR110	47085742	0.000000	0.05858	0.022000	0.16811	0.063000	0.16089	-0.885000	0.04161	-0.181000	0.10619	-1.467000	0.01014	CGT	C|0.952;T|0.048	0.048	strong		0.438	GPR110-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040810.2	NM_153840	
CHI3L1	1116	hgsc.bcm.edu	37	1	203152851	203152851	+	Missense_Mutation	SNP	C	C	T	rs147131854	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:203152851C>T	ENST00000255409.3	-	5	508	c.383G>A	c.(382-384)cGc>cAc	p.R128H		NM_001276.2	NP_001267.2	P36222	CH3L1_HUMAN	chitinase 3-like 1 (cartilage glycoprotein-39)	128					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cellular response to tumor necrosis factor (GO:0071356)|chitin catabolic process (GO:0006032)|inflammatory response (GO:0006954)|interleukin-8 secretion (GO:0072606)|lung development (GO:0030324)|positive regulation of angiogenesis (GO:0045766)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase B signaling (GO:0051897)|response to interleukin-1 (GO:0070555)|response to interleukin-6 (GO:0070741)|response to mechanical stimulus (GO:0009612)|response to tumor necrosis factor (GO:0034612)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|extracellular matrix structural constituent (GO:0005201)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)	p.R128H(1)		breast(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|skin(1)	18						GCCATGGGTGCGCAGAAATGG	0.532													C|||	2	0.000399361	0.0	0.0	5008	,	,		22573	0.0		0.0	False		,,,				2504	0.002				p.R128H		Atlas-SNP	.											CHI3L1,colon,carcinoma,0,1	CHI3L1	51	1	1	Substitution - Missense(1)	large_intestine(1)	c.G383A						PASS	.	C	HIS/ARG	5,4401	9.9+/-24.2	0,5,2198	136.0	109.0	118.0		383	5.7	0.9	1	dbSNP_134	118	5,8595	4.3+/-15.6	0,5,4295	yes	missense	CHI3L1	NM_001276.2	29	0,10,6493	TT,TC,CC		0.0581,0.1135,0.0769	probably-damaging	128/384	203152851	10,12996	2203	4300	6503	SO:0001583	missense	1116	exon5			TGGGTGCGCAGAA	BC008568	CCDS1435.1	1q32.1	2008-02-05			ENSG00000133048	ENSG00000133048			1932	protein-coding gene	gene with protein product		601525				8245017, 9244440	Standard	NM_001276		Approved	GP39, YKL40	uc001gzi.2	P36222	OTTHUMG00000042122	ENST00000255409.3:c.383G>A	1.37:g.203152851C>T	ENSP00000255409:p.Arg128His	101.0	0.0	0		103.0	50.0	0.485437	NM_001276	B2R7B0|P30923|Q8IVA4|Q96HI7	Missense_Mutation	SNP	ENST00000255409.3	37	CCDS1435.1	.	.	.	.	.	.	.	.	.	.	C	19.23	3.787628	0.70337	0.001135	5.81E-4	ENSG00000133048	ENST00000255409	T	0.07114	3.22	5.69	5.69	0.88448	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.50627	D	0.000104	T	0.35799	0.0944	M	0.87456	2.885	0.54753	D	0.999988	D	0.89917	1.0	D	0.97110	1.0	T	0.15407	-1.0438	10	0.62326	D	0.03	-35.3845	17.3057	0.87194	0.0:1.0:0.0:0.0	.	128	P36222	CH3L1_HUMAN	H	128	ENSP00000255409:R128H	ENSP00000255409:R128H	R	-	2	0	CHI3L1	201419474	1.000000	0.71417	0.910000	0.35882	0.095000	0.18619	7.061000	0.76699	2.664000	0.90586	0.655000	0.94253	CGC	C|0.999;T|0.001	0.001	strong		0.532	CHI3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100265.1	NM_001276	
MT-CO1	4512	hgsc.bcm.edu	37	M	6150	6150	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:6150G>A	ENST00000361624.2	+	1	247	c.247G>A	c.(247-249)Gtt>Att	p.V83I	MT-TL1_ENST00000386347.1_RNA|MT-ATP6_ENST00000361899.2_5'Flank|MT-TD_ENST00000387419.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-TY_ENST00000387409.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ATP8_ENST00000361851.1_5'Flank|MT-TN_ENST00000387400.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-TI_ENST00000387365.1_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-CO2_ENST00000361739.1_5'Flank			P00395	COX1_HUMAN	mitochondrially encoded cytochrome c oxidase I	83					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex IV (GO:0005751)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(4)|endometrium(25)|kidney(19)|lung(3)|prostate(3)	54						GCAACTGACTAGTTCCCCTAA	0.463																																					p.V83I		Atlas-SNP	.											.	.	.	.	0			c.G247A						PASS	.																																			SO:0001583	missense	5742	exon1			TGACTAGTTCCCC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198804	ENSG00000198804		"""Mitochondrial respiratory chain complex / Complex IV"""	7419	protein-coding gene	gene with protein product		516030	"""cytochrome c oxidase I"""	MTCO1		7219534	Standard			Approved	COX1, COI		P00395		ENST00000361624.2:c.247G>A	M.37:g.6150G>A	ENSP00000354499:p.Val83Ile	8.0	0.0	0		9.0	9.0	1	ENST00000361624	Q34770	Missense_Mutation	SNP	ENST00000361624.2	37																																																																																				.	.	none		0.463	MT-CO1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024028	
ZNF43	7594	hgsc.bcm.edu	37	19	21991663	21991663	+	Silent	SNP	A	A	G	rs61733114	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:21991663A>G	ENST00000354959.4	-	4	1345	c.1176T>C	c.(1174-1176)caT>caC	p.H392H	ZNF43_ENST00000595461.1_Silent_p.H386H|ZNF43_ENST00000598381.1_Silent_p.H386H|ZNF43_ENST00000594012.1_Silent_p.H386H	NM_003423.3	NP_003414.2	P17038	ZNF43_HUMAN	zinc finger protein 43	392					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)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|liver(1)|lung(16)|ovary(2)|prostate(3)|stomach(3)|upper_aerodigestive_tract(2)	51		Renal(1328;0.000219)|Hepatocellular(1079;0.121)		GBM - Glioblastoma multiforme(1328;5.97e-05)|STAD - Stomach adenocarcinoma(1328;0.0127)		TCTTTTCAGTATGAATTTTCT	0.363													a|||	195	0.0389377	0.1392	0.0159	5008	,	,		20000	0.0		0.0	False		,,,				2504	0.0				p.H401H		Atlas-SNP	.											.	ZNF43	152	.	0			c.T1203C						PASS	.	A		469,3937	213.8+/-233.3	27,415,1761	55.0	59.0	58.0		1176	-2.5	0.0	19	dbSNP_129	58	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	ZNF43	NM_003423.2		27,423,6053	GG,GA,AA		0.093,10.6446,3.6675		392/810	21991663	477,12529	2203	4300	6503	SO:0001819	synonymous_variant	7594	exon4			TTCAGTATGAATT	X59244	CCDS12413.2, CCDS59367.1, CCDS74321.1	19p13.1-p12	2013-01-08	2006-05-11		ENSG00000198521	ENSG00000198521		"""Zinc fingers, C2H2-type"", ""-"""	13109	protein-coding gene	gene with protein product		603972	"""zinc finger protein 39-like 1 (KOX 27)"", ""zinc finger protein 43 (HTF6)"""	ZNF39L1		1711675	Standard	NM_001256649		Approved	HTF6, KOX27	uc031rka.1	P17038	OTTHUMG00000128543	ENST00000354959.4:c.1176T>C	19.37:g.21991663A>G		52.0	0.0	0		49.0	28.0	0.571429	NM_001256653	A8K5N8|P28160|Q53XQ2|Q5H9T3|Q96DG1	Silent	SNP	ENST00000354959.4	37	CCDS12413.2																																																																																			A|0.968;G|0.032	0.032	strong		0.363	ZNF43-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250380.2	NM_003423	
WDR31	114987	hgsc.bcm.edu	37	9	116085148	116085148	+	Silent	SNP	A	A	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116085148A>C	ENST00000374193.4	-	7	759	c.513T>G	c.(511-513)ctT>ctG	p.L171L	WDR31_ENST00000374195.3_Silent_p.L46L|WDR31_ENST00000341761.4_Silent_p.L170L|WDR31_ENST00000461942.1_5'UTR	NM_001012361.2|NM_145241.3	NP_001012361.1|NP_660284.1	Q8NA23	WDR31_HUMAN	WD repeat domain 31	171										NS(1)|large_intestine(1)|lung(2)|prostate(2)	6						CATCCCACAGAAGCAGGGTGT	0.527																																					p.L171L		Atlas-SNP	.											.	WDR31	23	.	0			c.T513G						PASS	.						124.0	104.0	111.0					9																	116085148		2203	4300	6503	SO:0001819	synonymous_variant	114987	exon7			CCACAGAAGCAGG	BC012352	CCDS6792.1, CCDS35110.1	9q33.1	2013-01-09			ENSG00000148225	ENSG00000148225		"""WD repeat domain containing"""	21421	protein-coding gene	gene with protein product	"""similar to spermatid WD-repeat protein"""						Standard	NM_145241		Approved	FLJ35921	uc004bhb.3	Q8NA23	OTTHUMG00000020525	ENST00000374193.4:c.513T>G	9.37:g.116085148A>C		176.0	0.0	0		195.0	68.0	0.348718	NM_001012361	Q5W0T9|Q96EG8	Silent	SNP	ENST00000374193.4	37	CCDS35110.1																																																																																			.	.	none		0.527	WDR31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053734.2	NM_145241	
FAM166A	401565	hgsc.bcm.edu	37	9	140140188	140140188	+	Silent	SNP	G	G	A	rs112239130	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140140188G>A	ENST00000344774.4	-	2	228	c.174C>T	c.(172-174)ccC>ccT	p.P58P	FAM166A_ENST00000388932.2_Silent_p.P58P	NM_001001710.1	NP_001001710.1	Q6J272	F166A_HUMAN	family with sequence similarity 166, member A	58						nucleus (GO:0005634)				kidney(3)|lung(7)|ovary(2)|prostate(1)|urinary_tract(2)	15						GTTTGGACATGGGGGACAGCA	0.622													G|||	33	0.00658946	0.0234	0.0029	5008	,	,		18282	0.0		0.0	False		,,,				2504	0.0				p.P58P		Atlas-SNP	.											.	FAM166A	44	.	0			c.C174T						PASS	.	G		69,4337	63.5+/-100.7	0,69,2134	55.0	58.0	57.0		174	-2.9	0.3	9	dbSNP_132	57	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	FAM166A	NM_001001710.1		0,70,6432	AA,AG,GG		0.0116,1.566,0.5383		58/318	140140188	70,12934	2203	4299	6502	SO:0001819	synonymous_variant	401565	exon2			GGACATGGGGGAC	BC132916	CCDS35186.1	9q34.3	2008-08-08			ENSG00000188163	ENSG00000188163			33818	protein-coding gene	gene with protein product							Standard	XR_245332		Approved		uc004cmi.1	Q6J272	OTTHUMG00000159545	ENST00000344774.4:c.174C>T	9.37:g.140140188G>A		135.0	0.0	0		116.0	76.0	0.655172	NM_001001710	A6NND9|Q8N830	Silent	SNP	ENST00000344774.4	37	CCDS35186.1																																																																																			G|0.992;A|0.008	0.008	strong		0.622	FAM166A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356125.1	NM_001001710	
KLF16	83855	hgsc.bcm.edu	37	19	1854701	1854701	+	Silent	SNP	G	G	A	rs76157530	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1854701G>A	ENST00000250916.4	-	2	586	c.516C>T	c.(514-516)gaC>gaT	p.D172D	KLF16_ENST00000592313.1_5'UTR|CTB-31O20.6_ENST00000592884.1_RNA	NM_031918.3	NP_114124.1	Q9BXK1	KLF16_HUMAN	Kruppel-like factor 16	172					dopamine receptor signaling pathway (GO:0007212)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|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)			lung(1)	1		Ovarian(11;1.78e-06)|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)		GGGCCAGCTCGTCGGAGCGGG	0.672													G|||	55	0.0109824	0.0401	0.0029	5008	,	,		10702	0.0		0.0	False		,,,				2504	0.0				p.D172D		Atlas-SNP	.											.	KLF16	9	.	0			c.C516T						PASS	.	G		133,4271	90.6+/-129.3	3,127,2072	35.0	39.0	37.0		516	-1.2	1.0	19	dbSNP_131	37	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KLF16	NM_031918.3		3,128,6371	AA,AG,GG		0.0116,3.02,1.0305		172/253	1854701	134,12870	2202	4300	6502	SO:0001819	synonymous_variant	83855	exon2			CAGCTCGTCGGAG	AF327440	CCDS12075.1	19p13.3	2013-10-15			ENSG00000129911	ENSG00000129911		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	16857	protein-coding gene	gene with protein product		606139				11438660	Standard	NM_031918		Approved	NSLP2, BTEB4, DRRF	uc002luc.3	Q9BXK1	OTTHUMG00000179994	ENST00000250916.4:c.516C>T	19.37:g.1854701G>A		30.0	0.0	0		43.0	25.0	0.581395	NM_031918		Silent	SNP	ENST00000250916.4	37	CCDS12075.1																																																																																			G|0.989;A|0.011	0.011	strong		0.672	KLF16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449214.1		
ABCC11	85320	hgsc.bcm.edu	37	16	48234214	48234214	+	Silent	SNP	C	C	T	rs61745566	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:48234214C>T	ENST00000394747.1	-	14	2404	c.2055G>A	c.(2053-2055)acG>acA	p.T685T	ABCC11_ENST00000394748.1_Silent_p.T685T|ABCC11_ENST00000356608.2_Silent_p.T685T|ABCC11_ENST00000353782.5_Silent_p.T685T|ABCC11_ENST00000537808.1_Silent_p.T685T	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	685	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	CCAGGACGACCGTCTTCCCCC	0.552													C|||	108	0.0215655	0.0787	0.0043	5008	,	,		17717	0.0		0.0	False		,,,				2504	0.001				p.T685T		Atlas-SNP	.											.	ABCC11	177	.	0			c.G2055A						PASS	.	C	,,	233,4169	140.0+/-175.5	7,219,1975	114.0	98.0	104.0		2055,2055,2055	-11.4	0.0	16	dbSNP_129	104	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	ABCC11	NM_032583.3,NM_033151.3,NM_145186.2	,,	7,224,6270	TT,TC,CC		0.0581,5.293,1.8305	,,	685/1383,685/1383,685/1345	48234214	238,12764	2201	4300	6501	SO:0001819	synonymous_variant	85320	exon14			GACGACCGTCTTC	AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"""ATP binding cassette transporters / subfamily C"""	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.2055G>A	16.37:g.48234214C>T		62.0	0.0	0		61.0	27.0	0.442623	NM_033151	Q8TDJ0|Q96JA6|Q9BX80	Silent	SNP	ENST00000394747.1	37	CCDS10732.1																																																																																			C|0.980;T|0.020	0.020	strong		0.552	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583	
WDR19	57728	hgsc.bcm.edu	37	4	39267749	39267749	+	Missense_Mutation	SNP	G	G	A	rs16995209	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:39267749G>A	ENST00000399820.3	+	29	3404	c.3250G>A	c.(3250-3252)Ggc>Agc	p.G1084S	WDR19_ENST00000288634.7_Missense_Mutation_p.G924S	NM_025132.3	NP_079408.3	Q8NEZ3	WDR19_HUMAN	WD repeat domain 19	1084			G -> S (in dbSNP:rs16995209).		ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium assembly (GO:0042384)|digestive system development (GO:0055123)|ear morphogenesis (GO:0042471)|embryonic camera-type eye development (GO:0031076)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic limb morphogenesis (GO:0030326)|in utero embryonic development (GO:0001701)|intraciliary retrograde transport (GO:0035721)|myotome development (GO:0061055)|neurological system process (GO:0050877)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|motile cilium (GO:0031514)|nonmotile primary cilium (GO:0031513)|photoreceptor connecting cilium (GO:0032391)				large_intestine(1)	1						GGAGAACGATGGCATGCCTAA	0.453													G|||	185	0.0369409	0.1301	0.0173	5008	,	,		15274	0.0		0.001	False		,,,				2504	0.0				p.G1084S		Atlas-SNP	.											.	WDR19	96	.	0			c.G3250A						PASS	.	G	SER/GLY	417,3589		21,375,1607	68.0	72.0	71.0		3250	5.4	1.0	4	dbSNP_123	71	3,8325		0,3,4161	yes	missense	WDR19	NM_025132.3	56	21,378,5768	AA,AG,GG		0.036,10.4094,3.4052	probably-damaging	1084/1343	39267749	420,11914	2003	4164	6167	SO:0001583	missense	57728	exon29			AACGATGGCATGC	AB046858, AY029257	CCDS47042.1	4p14	2014-02-21			ENSG00000157796	ENSG00000157796		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	18340	protein-coding gene	gene with protein product	"""intraflagellar transport 144 homolog (Chlamydomonas)"""	608151				12906858, 22019273	Standard	XM_005262658		Approved	Pwdmp, KIAA1638, FLJ23127, ORF26, DYF-2, Oseg6, IFT144, NPHP13	uc003gtv.3	Q8NEZ3	OTTHUMG00000160466	ENST00000399820.3:c.3250G>A	4.37:g.39267749G>A	ENSP00000382717:p.Gly1084Ser	141.0	0.0	0		161.0	66.0	0.409938	NM_025132	B5MEF2|Q8N5B4|Q9H5S0|Q9HCD4	Missense_Mutation	SNP	ENST00000399820.3	37	CCDS47042.1	54	0.024725274725274724	49	0.09959349593495935	5	0.013812154696132596	0	0.0	0	0.0	G	18.81	3.703584	0.68501	0.104094	3.6E-4	ENSG00000157796	ENST00000399820;ENST00000288634	T;T	0.68624	-0.34;-0.34	5.44	5.44	0.79542	.	0.000000	0.85682	D	0.000000	T	0.11324	0.0276	M	0.91090	3.175	0.80722	D	1	P	0.41947	0.766	P	0.47162	0.54	T	0.60662	-0.7219	10	0.52906	T	0.07	-18.5327	19.2559	0.93945	0.0:0.0:1.0:0.0	rs16995209;rs52802549;rs16995209	1084	Q8NEZ3	WDR19_HUMAN	S	1084;924	ENSP00000382717:G1084S;ENSP00000288634:G924S	ENSP00000288634:G924S	G	+	1	0	WDR19	38944144	1.000000	0.71417	0.983000	0.44433	0.048000	0.14542	9.108000	0.94275	2.539000	0.85634	0.455000	0.32223	GGC	G|0.962;A|0.038	0.038	strong		0.453	WDR19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360689.1		
PTPN1	5770	hgsc.bcm.edu	37	20	49197955	49197955	+	Silent	SNP	C	C	T	rs74607837	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:49197955C>T	ENST00000371621.3	+	9	1416	c.1242C>T	c.(1240-1242)tgC>tgT	p.C414C	PTPN1_ENST00000541713.1_Silent_p.C341C	NM_001278618.1|NM_002827.2	NP_001265547.1|NP_002818.1	P18031	PTN1_HUMAN	protein tyrosine phosphatase, non-receptor type 1	414					actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|endoplasmic reticulum unfolded protein response (GO:0030968)|insulin receptor signaling pathway (GO:0008286)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|peptidyl-tyrosine dephosphorylation (GO:0035335)|peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity (GO:1990264)|platelet activation (GO:0030168)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|regulation of endocytosis (GO:0030100)|regulation of hepatocyte growth factor receptor signaling pathway (GO:1902202)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of signal transduction (GO:0009966)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|sorting endosome (GO:0097443)	enzyme binding (GO:0019899)|ephrin receptor binding (GO:0046875)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|skin(2)	16		Lung NSC(126;0.163)			Tiludronate(DB01133)	TCAACATGTGCGTGGCTACGG	0.627													C|||	81	0.0161741	0.059	0.0043	5008	,	,		18745	0.0		0.0	False		,,,				2504	0.0				p.C414C		Atlas-SNP	.											.	PTPN1	36	.	0			c.C1242T						PASS	.	C		223,4183	133.7+/-170.0	6,211,1986	110.0	74.0	86.0		1242	0.4	0.8	20	dbSNP_132	86	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	PTPN1	NM_002827.2		6,215,6282	TT,TC,CC		0.0465,5.0613,1.7453		414/436	49197955	227,12779	2203	4300	6503	SO:0001819	synonymous_variant	5770	exon9			CATGTGCGTGGCT		CCDS13430.1, CCDS63309.1	20q13.1-q13.2	2011-06-09			ENSG00000196396	ENSG00000196396		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9642	protein-coding gene	gene with protein product		176885		PTP1B		2164224	Standard	NM_002827		Approved		uc002xvl.3	P18031	OTTHUMG00000032729	ENST00000371621.3:c.1242C>T	20.37:g.49197955C>T		138.0	0.0	0		162.0	81.0	0.5	NM_002827	Q5TGD8|Q9BQV9|Q9NQQ4	Silent	SNP	ENST00000371621.3	37	CCDS13430.1																																																																																			C|0.980;T|0.020	0.020	strong		0.627	PTPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079694.2		
KRTAP3-2	83897	hgsc.bcm.edu	37	17	39156085	39156085	+	Silent	SNP	G	G	T	rs386797022|rs548322379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39156085G>T	ENST00000391587.1	-	1	53	c.21C>A	c.(19-21)cgC>cgA	p.R7R		NM_031959.2	NP_114165.1	Q9BYR7	KRA32_HUMAN	keratin associated protein 3-2	7	3 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)	structural molecule activity (GO:0005198)	p.R7R(1)		endometrium(1)|large_intestine(1)|lung(1)	3		Breast(137;0.00043)				CACTGCAGCTGCGAGAGGCAC	0.552													.|||	307	0.0613019	0.2216	0.0173	5008	,	,		18167	0.0		0.002	False		,,,				2504	0.0				p.R7R		Atlas-SNP	.											KRTAP3-2,rectum,carcinoma,0,1	KRTAP3-2	11	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C21A						PASS	.						65.0	75.0	72.0					17																	39156085		2203	4296	6499	SO:0001819	synonymous_variant	83897	exon1			GCAGCTGCGAGAG	AJ406932	CCDS32644.1	17q21.2	2013-06-25			ENSG00000212900	ENSG00000212900		"""Keratin associated proteins"""	16779	protein-coding gene	gene with protein product						11279113	Standard	NM_031959		Approved	KAP3.2	uc002hvs.3	Q9BYR7	OTTHUMG00000133581	ENST00000391587.1:c.21C>A	17.37:g.39156085G>T		172.0	0.0	0		174.0	58.0	0.333333	NM_031959		Silent	SNP	ENST00000391587.1	37	CCDS32644.1																																																																																			.	.	none		0.552	KRTAP3-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257685.1		
TAGLN	6876	hgsc.bcm.edu	37	11	117075014	117075014	+	Missense_Mutation	SNP	A	A	G	rs12284316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117075014A>G	ENST00000532870.1	+	4	1686	c.545A>G	c.(544-546)aAc>aGc	p.N182S	TAGLN_ENST00000530649.1_Missense_Mutation_p.N182S|TAGLN_ENST00000392951.4_Missense_Mutation_p.N182S|PCSK7_ENST00000529458.1_5'Flank			Q01995	TAGL_HUMAN	transgelin	182			N -> S (in dbSNP:rs12284316).		epithelial cell differentiation (GO:0030855)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)				central_nervous_system(1)|large_intestine(4)|lung(1)|urinary_tract(1)	7	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.63e-06)|Epithelial(105;5.49e-05)|all cancers(92;0.000435)		ATGGGCAGCAACAGAGGGGCC	0.612													A|||	15	0.00299521	0.0113	0.0	5008	,	,		18601	0.0		0.0	False		,,,				2504	0.0				p.N182S		Atlas-SNP	.											.	TAGLN	17	.	0			c.A545G						PASS	.	A	SER/ASN,SER/ASN	46,4356	48.2+/-83.0	0,46,2155	80.0	83.0	82.0		545,545	4.6	1.0	11	dbSNP_120	82	0,8592		0,0,4296	yes	missense,missense	TAGLN	NM_001001522.1,NM_003186.3	46,46	0,46,6451	GG,GA,AA		0.0,1.045,0.354	probably-damaging,probably-damaging	182/202,182/202	117075014	46,12948	2201	4296	6497	SO:0001583	missense	6876	exon5			GCAGCAACAGAGG	M95787	CCDS8381.1	11q23.2	2008-07-21				ENSG00000149591			11553	protein-coding gene	gene with protein product	"""SM22-alpha"", ""transgelin variant 2"""	600818				8117285, 1520290	Standard	NM_003186		Approved	SM22, WS3-10, TAGLN1, SMCC, DKFZp686P11128	uc001pqm.3	Q01995		ENST00000532870.1:c.545A>G	11.37:g.117075014A>G	ENSP00000432282:p.Asn182Ser	312.0	1.0	0.00320513		255.0	146.0	0.572549	NM_001001522	O15542	Missense_Mutation	SNP	ENST00000532870.1	37	CCDS8381.1	6|6	0.0027472527472527475|0.0027472527472527475	6|6	0.012195121951219513|0.012195121951219513	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	A|A	22.5|22.5	4.294103|4.294103	0.81025|0.81025	0.01045|0.01045	0.0|0.0	ENSG00000149591|ENSG00000149591	ENST00000392951;ENST00000525531;ENST00000278968;ENST00000530649;ENST00000532870|ENST00000529622	T;T;T;T;T|.	0.68331|.	-0.32;-0.32;-0.32;-0.32;-0.32|.	4.63|4.63	4.63|4.63	0.57726|0.57726	Calponin homology domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.82231|0.82231	0.4992|0.4992	H|H	0.95745|0.95745	3.715|3.715	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	D|.	0.71414|.	0.973|.	D|D	0.88266|0.88266	0.2926|0.2926	10|5	0.87932|.	D|.	0|.	.|.	13.0278|13.0278	0.58825|0.58825	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	rs12284316|rs12284316	182|.	Q01995|.	TAGL_HUMAN|.	S|A	182|132	ENSP00000376678:N182S;ENSP00000432054:N182S;ENSP00000278968:N182S;ENSP00000431941:N182S;ENSP00000432282:N182S|.	ENSP00000278968:N182S|.	N|T	+|+	2|1	0|0	TAGLN|TAGLN	116580224|116580224	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.966000|0.966000	0.64601|0.64601	8.709000|8.709000	0.91379|0.91379	1.954000|1.954000	0.56735|0.56735	0.402000|0.402000	0.26972|0.26972	AAC|ACA	A|0.996;G|0.004	0.004	strong		0.612	TAGLN-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392864.1	NM_001001522	
AKNA	80709	hgsc.bcm.edu	37	9	117110112	117110112	+	Missense_Mutation	SNP	T	T	C	rs1265891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117110112T>C	ENST00000307564.4	-	16	3451	c.3290A>G	c.(3289-3291)cAg>cGg	p.Q1097R	AKNA_ENST00000374075.5_Missense_Mutation_p.Q1016R|AKNA_ENST00000374088.3_Missense_Mutation_p.Q1097R|AKNA_ENST00000492875.1_5'Flank|AKNA_ENST00000374079.4_Missense_Mutation_p.Q42R|AKNA_ENST00000223791.3_Missense_Mutation_p.Q557R	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	1097			Q -> R (in dbSNP:rs1265891).		positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						CTGGAGTGGCTGGTGCAGGCT	0.667													C|||	1051	0.209864	0.6891	0.0605	5008	,	,		14024	0.0526		0.003	False		,,,				2504	0.0429				p.Q1097R		Atlas-SNP	.											.	AKNA	119	.	0			c.A3290G						PASS	.	C	ARG/GLN	2091,2139		503,1085,527	15.0	15.0	15.0		3290	-3.5	0.0	9	dbSNP_87	15	21,8365		0,21,4172	no	missense	AKNA	NM_030767.4	43	503,1106,4699	CC,CT,TT		0.2504,49.4326,16.7406	benign	1097/1440	117110112	2112,10504	2115	4193	6308	SO:0001583	missense	80709	exon16			AGTGGCTGGTGCA	AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.3290A>G	9.37:g.117110112T>C	ENSP00000303769:p.Gln1097Arg	138.0	1.0	0.00724638		101.0	101.0	1	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	SNP	ENST00000307564.4	37	CCDS6805.1	398	0.18223443223443223	337	0.6849593495934959	27	0.07458563535911603	32	0.055944055944055944	2	0.002638522427440633	C	6.830	0.522364	0.13066	0.494326	0.002504	ENSG00000106948	ENST00000307564;ENST00000374079;ENST00000320310;ENST00000374088;ENST00000223791;ENST00000374075	T;T;T;T;T	0.17370	2.74;2.28;2.74;2.51;2.74	5.44	-3.52	0.04682	.	1.042290	0.07587	N	0.921372	T	0.00012	0.0000	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	0.40459	-0.9562	9	0.02654	T	1	-2.0827	6.3932	0.21599	0.0:0.2694:0.3256:0.405	rs1265891;rs52814197;rs1265891	1097;1016	Q7Z591;Q7Z591-2	AKNA_HUMAN;.	R	1097;42;109;1097;557;1016	ENSP00000303769:Q1097R;ENSP00000363192:Q42R;ENSP00000363201:Q1097R;ENSP00000223791:Q557R;ENSP00000363188:Q1016R	ENSP00000223791:Q557R	Q	-	2	0	AKNA	116149933	0.001000	0.12720	0.019000	0.16419	0.639000	0.38242	-0.315000	0.08081	-0.930000	0.03752	-0.726000	0.03593	CAG	T|0.754;C|0.246	0.246	strong		0.667	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767	
TEKT3	64518	hgsc.bcm.edu	37	17	15217535	15217535	+	Silent	SNP	C	C	T	rs144456077	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:15217535C>T	ENST00000395930.1	-	6	933	c.747G>A	c.(745-747)gcG>gcA	p.A249A	TEKT3_ENST00000338696.2_Silent_p.A249A|RNU6-799P_ENST00000363567.1_RNA	NM_031898.2	NP_114104.1	Q9BXF9	TEKT3_HUMAN	tektin 3	249					cilium morphogenesis (GO:0060271)|regulation of fertilization (GO:0080154)|sperm motility (GO:0030317)	acrosomal membrane (GO:0002080)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				endometrium(1)|kidney(3)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	23				UCEC - Uterine corpus endometrioid carcinoma (92;0.0877)		CATGCTGGGACGCTCTGTTGG	0.547													C|||	20	0.00399361	0.0151	0.0	5008	,	,		21690	0.0		0.0	False		,,,				2504	0.0				p.A249A		Atlas-SNP	.											TEKT3,NS,adenocarcinoma,0,1	TEKT3	64	1	0			c.G747A						PASS	.	C		47,4359	49.6+/-84.7	0,47,2156	174.0	111.0	132.0		747	-10.9	0.0	17	dbSNP_134	132	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	TEKT3	NM_031898.2		0,51,6452	TT,TC,CC		0.0465,1.0667,0.3921		249/491	15217535	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	64518	exon6			CTGGGACGCTCTG	AF334676	CCDS11169.1	17p12	2011-05-23			ENSG00000125409	ENSG00000125409			14293	protein-coding gene	gene with protein product		612683				11381029, 14735490	Standard	NM_031898		Approved	FLJ32828	uc002gon.3	Q9BXF9	OTTHUMG00000058965	ENST00000395930.1:c.747G>A	17.37:g.15217535C>T		286.0	0.0	0		312.0	159.0	0.509615	NM_031898	B2RAS7|D3DTT0|Q8N5R5|Q96M48	Silent	SNP	ENST00000395930.1	37	CCDS11169.1																																																																																			C|0.996;T|0.004	0.004	strong		0.547	TEKT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130385.2	NM_031898	
GPR107	57720	hgsc.bcm.edu	37	9	132854643	132854643	+	Silent	SNP	T	T	C	rs34227818	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:132854643T>C	ENST00000372406.1	+	9	1353	c.846T>C	c.(844-846)caT>caC	p.H282H	GPR107_ENST00000347136.6_Silent_p.H282H|GPR107_ENST00000372410.3_Silent_p.H282H	NM_001136557.1	NP_001130029.1	Q5VW38	GP107_HUMAN	G protein-coupled receptor 107	282						integral component of membrane (GO:0016021)				endometrium(2)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	11		Ovarian(14;0.000531)				TCTGGATTCATATCCTTCGAA	0.423													T|||	120	0.0239617	0.0825	0.0144	5008	,	,		15888	0.0		0.001	False		,,,				2504	0.0				p.H282H		Atlas-SNP	.											.	GPR107	30	.	0			c.T846C						PASS	.	T	,,	325,4081	173.0+/-202.9	5,315,1883	147.0	144.0	145.0		846,846,846	2.2	1.0	9	dbSNP_126	145	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous,coding-synonymous,coding-synonymous	GPR107	NM_001136557.1,NM_001136558.1,NM_020960.4	,,	5,322,6176	CC,CT,TT		0.0814,7.3763,2.5527	,,	282/601,282/572,282/553	132854643	332,12674	2203	4300	6503	SO:0001819	synonymous_variant	57720	exon9			GATTCATATCCTT	AF376725	CCDS35162.1, CCDS48041.1, CCDS48042.1	9q34.2	2014-01-30			ENSG00000148358	ENSG00000148358		"""GPCR / Unclassified : 7TM orphan receptors"""	17830	protein-coding gene	gene with protein product							Standard	NM_020960		Approved	KIAA1624, RP11-88G17, FLJ20998, LUSTR1	uc004bzd.2	Q5VW38	OTTHUMG00000020804	ENST00000372406.1:c.846T>C	9.37:g.132854643T>C		163.0	0.0	0		203.0	126.0	0.62069	NM_001136557	A6NJ53|Q2TB81|Q5JPA3|Q5VW39|Q96T26|Q9H658|Q9HCE8	Silent	SNP	ENST00000372406.1	37	CCDS48041.1																																																																																			T|0.980;C|0.020	0.020	strong		0.423	GPR107-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054643.2		
TICRR	90381	hgsc.bcm.edu	37	15	90164769	90164769	+	Silent	SNP	T	T	C	rs75934760	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90164769T>C	ENST00000268138.7	+	19	3405	c.3300T>C	c.(3298-3300)ccT>ccC	p.P1100P	TICRR_ENST00000560985.1_Silent_p.P1099P|KIF7_ENST00000558928.1_Intron			Q7Z2Z1	TICRR_HUMAN	TOPBP1-interacting checkpoint and replication regulator	1100					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|formation of translation preinitiation complex (GO:0001731)|mitotic DNA replication checkpoint (GO:0033314)|regulation of DNA-dependent DNA replication initiation (GO:0030174)|response to ionizing radiation (GO:0010212)	nucleus (GO:0005634)	chromatin binding (GO:0003682)										CGGAGGTACCTGCAGCTTACC	0.428													T|||	221	0.0441294	0.1558	0.0216	5008	,	,		19124	0.0		0.0	False		,,,				2504	0.0				p.P1100P		Atlas-SNP	.											.	.	.	.	0			c.T3300C						PASS	.	T		445,3261		33,379,1441	55.0	54.0	54.0		3300	1.5	0.0	15	dbSNP_132	54	6,8188		0,6,4091	no	coding-synonymous	C15orf42	NM_152259.3		33,385,5532	CC,CT,TT		0.0732,12.0076,3.7899		1100/1911	90164769	451,11449	1853	4097	5950	SO:0001819	synonymous_variant	90381	exon19			GGTACCTGCAGCT	AK123612	CCDS10352.2	15q26.1	2012-07-11	2012-07-11	2012-07-11	ENSG00000140534	ENSG00000140534			28704	protein-coding gene	gene with protein product	"""TOPBP1-interacting replication-stimulating protein"", ""SLD3 homolog (S. cerevisiae)"""	613298	"""chromosome 15 open reading frame 42"""	C15orf42		20116089, 20080954	Standard	NM_152259		Approved	MGC45866, FLJ41618, Treslin, SLD3	uc002boe.3	Q7Z2Z1	OTTHUMG00000149648	ENST00000268138.7:c.3300T>C	15.37:g.90164769T>C		70.0	0.0	0		55.0	26.0	0.472727	NM_152259	B2RE07|B3KVV9|D3IUT4|Q8N4X8|Q8NCH6|Q9BU55	Silent	SNP	ENST00000268138.7	37	CCDS10352.2																																																																																			T|0.973;C|0.027	0.027	strong		0.428	TICRR-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000312856.1	NM_152259	
MOGS	7841	hgsc.bcm.edu	37	2	74688884	74688884	+	Missense_Mutation	SNP	G	G	A	rs13405869	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74688884G>A	ENST00000233616.4	-	4	2194	c.2032C>T	c.(2032-2034)Cgg>Tgg	p.R678W	MOGS_ENST00000452063.2_Missense_Mutation_p.R572W|MOGS_ENST00000462443.1_5'Flank|MOGS_ENST00000409065.1_3'UTR	NM_006302.2	NP_006293.2	Q13724	MOGS_HUMAN	mannosyl-oligosaccharide glucosidase	678					cellular protein metabolic process (GO:0044267)|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 membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucosidase activity (GO:0015926)|mannosyl-oligosaccharide glucosidase activity (GO:0004573)			cervix(1)|endometrium(6)|large_intestine(3)|lung(10)|prostate(1)|urinary_tract(2)	23						GGTTGGGGCCGACCCACCACC	0.597													G|||	133	0.0265575	0.0961	0.0086	5008	,	,		18324	0.0		0.0	False		,,,				2504	0.0				p.R678W		Atlas-SNP	.											.	MOGS	58	.	0			c.C2032T						PASS	.	G	TRP/ARG,TRP/ARG	309,3659		17,275,1692	64.0	76.0	72.0		1714,2032	-0.3	0.9	2	dbSNP_121	72	3,8293		0,3,4145	yes	missense,missense	MOGS	NM_001146158.1,NM_006302.2	101,101	17,278,5837	AA,AG,GG		0.0362,7.7873,2.544	probably-damaging,probably-damaging	572/732,678/838	74688884	312,11952	1984	4148	6132	SO:0001583	missense	7841	exon4			GGGGCCGACCCAC	X87237	CCDS42700.1, CCDS54370.1	2p13.1	2012-01-31			ENSG00000115275	ENSG00000115275	3.2.1.106		24862	protein-coding gene	gene with protein product	"""glucosidase I"", ""processing A-glucosidase I"""	601336				7635146, 8786151	Standard	NM_006302		Approved	GCS1, CWH41, DER7	uc010ffj.3	Q13724	OTTHUMG00000152886	ENST00000233616.4:c.2032C>T	2.37:g.74688884G>A	ENSP00000233616:p.Arg678Trp	126.0	0.0	0		118.0	47.0	0.398305	NM_006302	A8K938|F5H6D0|Q17RN9|Q8TCT5	Missense_Mutation	SNP	ENST00000233616.4	37	CCDS42700.1	63	0.028846153846153848	59	0.11991869918699187	4	0.011049723756906077	0	0.0	0	0.0	G	8.207	0.799569	0.16397	0.077873	3.62E-4	ENSG00000115275	ENST00000233616;ENST00000452063	T;T	0.39406	1.08;1.08	5.01	-0.259	0.12971	Six-hairpin glycosidase-like (1);	0.118143	0.52532	N	0.000072	T	0.01124	0.0037	M	0.61703	1.905	0.09310	P	0.999999999995561	D	0.89917	1.0	D	0.81914	0.995	T	0.21621	-1.0240	9	0.52906	T	0.07	-11.998	8.8519	0.35206	0.0776:0.0:0.271:0.6514	rs13405869	678	Q13724	MOGS_HUMAN	W	678;572	ENSP00000233616:R678W;ENSP00000388201:R572W	ENSP00000233616:R678W	R	-	1	2	MOGS	74542392	0.955000	0.32602	0.865000	0.33974	0.148000	0.21650	0.271000	0.18626	-0.231000	0.09825	-2.140000	0.00339	CGG	G|0.980;A|0.020	0.020	strong		0.597	MOGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328382.1	NM_006302	
PCLO	27445	hgsc.bcm.edu	37	7	82764924	82764924	+	Missense_Mutation	SNP	C	C	T	rs138200846	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:82764924C>T	ENST00000333891.9	-	3	2279	c.1942G>A	c.(1942-1944)Ggg>Agg	p.G648R	PCLO_ENST00000423517.2_Missense_Mutation_p.G648R	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						GCCAGATCCCCGCCTAGAGCT	0.453													C|||	35	0.00698882	0.0242	0.0043	5008	,	,		14124	0.0		0.0	False		,,,				2504	0.0				p.G648R		Atlas-SNP	.											.	PCLO	1506	.	0			c.G1942A						PASS	.	C	ARG/GLY,ARG/GLY	88,3802		0,88,1857	57.0	57.0	57.0		1942,1942	5.3	1.0	7	dbSNP_134	57	1,8259		0,1,4129	yes	missense,missense	PCLO	NM_014510.2,NM_033026.5	125,125	0,89,5986	TT,TC,CC		0.0121,2.2622,0.7325	probably-damaging,probably-damaging	648/4936,648/5143	82764924	89,12061	1945	4130	6075	SO:0001583	missense	27445	exon3			GATCCCCGCCTAG	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.1942G>A	7.37:g.82764924C>T	ENSP00000334319:p.Gly648Arg	159.0	0.0	0		155.0	83.0	0.535484	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	10	0.004578754578754579	8	0.016260162601626018	2	0.0055248618784530384	0	0.0	0	0.0	C	7.181	0.589683	0.13812	0.022622	1.21E-4	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.17528	2.27;2.27	5.31	5.31	0.75309	.	.	.	.	.	T	0.11153	0.0272	L	0.34521	1.04	0.25271	N	0.989512	D;D	0.69078	0.997;0.997	P;P	0.50970	0.655;0.655	T	0.04481	-1.0948	9	0.87932	D	0	.	12.3476	0.55130	0.0:0.9226:0.0:0.0774	.	648;648	Q9Y6V0-5;Q9Y6V0-6	.;.	R	594;648;648	ENSP00000334319:G648R;ENSP00000388393:G648R	ENSP00000334319:G648R	G	-	1	0	PCLO	82602860	0.380000	0.25131	0.990000	0.47175	0.708000	0.40852	2.840000	0.48215	2.485000	0.83878	0.591000	0.81541	GGG	C|0.995;T|0.005	0.005	strong		0.453	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
UCK1	83549	hgsc.bcm.edu	37	9	134404337	134404337	+	Silent	SNP	G	G	A	rs11557925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:134404337G>A	ENST00000372215.4	-	5	690	c.597C>T	c.(595-597)tgC>tgT	p.C199C	UCK1_ENST00000372211.3_Silent_p.C204C|UCK1_ENST00000372210.3_Silent_p.C190C|UCK1_ENST00000459858.1_5'UTR|UCK1_ENST00000372208.3_Intron	NM_001261450.1|NM_001261451.1|NM_031432.2	NP_001248379.1|NP_001248380.1|NP_113620.1	Q9HA47	UCK1_HUMAN	uridine-cytidine kinase 1	199					CTP salvage (GO:0044211)|nucleobase-containing small molecule metabolic process (GO:0055086)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)	cytosol (GO:0005829)	ATP binding (GO:0005524)|nucleoside kinase activity (GO:0019206)|uridine kinase activity (GO:0004849)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|skin(1)|upper_aerodigestive_tract(1)	6				OV - Ovarian serous cystadenocarcinoma(145;2.34e-05)|Epithelial(140;0.000219)		GTACCGGCAGGCAGAACTCCT	0.602													G|||	111	0.0221645	0.0794	0.0086	5008	,	,		17080	0.0		0.0	False		,,,				2504	0.0				p.C204C	Melanoma(42;523 1129 28385 43975 48113)	Atlas-SNP	.											.	UCK1	29	.	0			c.C612T						PASS	.	G	,	281,4125	153.7+/-187.2	8,265,1930	74.0	57.0	63.0		,597	3.7	1.0	9	dbSNP_120	63	0,8600		0,0,4300	no	intron,coding-synonymous	UCK1	NM_001135954.1,NM_031432.2	,	8,265,6230	AA,AG,GG		0.0,6.3777,2.1605	,	,199/278	134404337	281,12725	2203	4300	6503	SO:0001819	synonymous_variant	83549	exon5			CGGCAGGCAGAAC	AF237290	CCDS6944.1, CCDS48046.1, CCDS59151.1, CCDS59152.1	9q34.1	2008-02-05			ENSG00000130717	ENSG00000130717	2.7.1.48		14859	protein-coding gene	gene with protein product		609328				11306702	Standard	NM_031432		Approved	URK1, FLJ12255	uc031tfj.1	Q9HA47	OTTHUMG00000020823	ENST00000372215.4:c.597C>T	9.37:g.134404337G>A		34.0	0.0	0		35.0	20.0	0.571429	NM_001261451	Q5JT09|Q5JT10|Q5JT12|Q5JT13|Q6IA74|Q96BJ0	Silent	SNP	ENST00000372215.4	37	CCDS6944.1																																																																																			G|0.976;A|0.024	0.024	strong		0.602	UCK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054726.1	NM_031432	
CCDC138	165055	hgsc.bcm.edu	37	2	109429277	109429277	+	Splice_Site	SNP	G	G	C	rs58170568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:109429277G>C	ENST00000295124.4	+	9	995	c.935G>C	c.(934-936)aGg>aCg	p.R312T	CCDC138_ENST00000412964.2_Splice_Site_p.R312T	NM_144978.1	NP_659415.1	Q96M89	CC138_HUMAN	coiled-coil domain containing 138	312										endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	14						CTGTTGCAGAGGAAGTACGAG	0.318													G|||	31	0.0061901	0.0212	0.0043	5008	,	,		19524	0.0		0.0	False		,,,				2504	0.0				p.R312T		Atlas-SNP	.											.	CCDC138	49	.	0			c.G935C						PASS	.	G	THR/ARG	77,4329	68.1+/-105.8	1,75,2127	88.0	90.0	89.0		935	5.5	1.0	2	dbSNP_129	89	0,8598		0,0,4299	yes	missense-near-splice	CCDC138	NM_144978.1	71	1,75,6426	CC,CG,GG		0.0,1.7476,0.5921	benign	312/666	109429277	77,12927	2203	4299	6502	SO:0001630	splice_region_variant	165055	exon9			TGCAGAGGAAGTA	AK057307	CCDS2080.1	2q13	2008-02-05			ENSG00000163006	ENSG00000163006			26531	protein-coding gene	gene with protein product						12477932	Standard	NM_144978		Approved	FLJ32745	uc002ten.1	Q96M89	OTTHUMG00000130980	ENST00000295124.4:c.934-1G>C	2.37:g.109429277G>C		165.0	0.0	0		163.0	76.0	0.466258	NM_144978	Q05DF1|Q4ZG07|Q53TE1|Q6ZUY5|Q86VL7	Missense_Mutation	SNP	ENST00000295124.4	37	CCDS2080.1	14|14	0.00641025641025641|0.00641025641025641	11|11	0.022357723577235773|0.022357723577235773	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	G|G	13.96|13.96	2.393929|2.393929	0.42410|0.42410	0.017476|0.017476	0.0|0.0	ENSG00000163006|ENSG00000163006	ENST00000456512|ENST00000412964;ENST00000295124	.|D;D	.|0.89681	.|-2.55;-2.55	5.49|5.49	5.49|5.49	0.81192|0.81192	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.89670|0.89670	0.6782|0.6782	M|M	0.72894|0.72894	2.215|2.215	0.44798|0.44798	D|D	0.997805|0.997805	.|D;B	.|0.76494	.|0.999;0.441	.|D;B	.|0.83275	.|0.996;0.2	D|D	0.89997|0.89997	0.4112|0.4112	5|10	.|0.45353	.|T	.|0.12	.|.	18.1478|18.1478	0.89663|0.89663	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs58170568|rs58170568	.|312;312	.|Q96M89-2;Q96M89	.|.;CC138_HUMAN	R|T	209|312	.|ENSP00000411800:R312T;ENSP00000295124:R312T	.|ENSP00000295124:R312T	G|R	+|+	1|2	0|0	CCDC138|CCDC138	108795709|108795709	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.398000|0.398000	0.30690|0.30690	5.570000|5.570000	0.67398|0.67398	2.572000|2.572000	0.86782|0.86782	0.655000|0.655000	0.94253|0.94253	GGA|AGG	G|0.993;C|0.007	0.007	strong		0.318	CCDC138-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253593.1	NM_144978	Missense_Mutation
CXorf57	55086	hgsc.bcm.edu	37	X	105883826	105883826	+	Missense_Mutation	SNP	T	T	G	rs5962707	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:105883826T>G	ENST00000372548.4	+	10	1888	c.1779T>G	c.(1777-1779)atT>atG	p.I593M	CXorf57_ENST00000372544.2_Missense_Mutation_p.I496M|CXorf57_ENST00000497124.1_3'UTR|MIR548AN_ENST00000408286.2_RNA	NM_018015.5	NP_060485.4	Q6NSI4	CX057_HUMAN	chromosome X open reading frame 57	593			I -> M (in dbSNP:rs5962707). {ECO:0000269|PubMed:15489334}.				poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(5)|large_intestine(6)|lung(11)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	31						GAGTAGAAATTCAAGAAAGAA	0.333													T|||	445	0.117881	0.3185	0.0346	3775	,	,		11888	0.0		0.0	False		,,,				2504	0.0				p.I593M		Atlas-SNP	.											.	CXorf57	107	.	0			c.T1779G						PASS	.	T	MET/ILE,MET/ILE	1450,2385		216,789,229,627,342	118.0	111.0	113.0		1488,1779	1.0	0.0	X	dbSNP_114	113	8,6720		0,7,1,2421,1871	yes	missense,missense	CXorf57	NM_001184782.1,NM_018015.5	10,10	216,796,230,3048,2213	GG,GT,G,TT,T		0.1189,37.8096,13.8029	benign,benign	496/759,593/856	105883826	1458,9105	2203	4300	6503	SO:0001583	missense	55086	exon10			AGAAATTCAAGAA	AK024253	CCDS14519.1, CCDS55470.1	Xq22.3	2008-02-05			ENSG00000147231	ENSG00000147231			25486	protein-coding gene	gene with protein product							Standard	NM_018015		Approved	FLJ14191, FLJ10178	uc004emi.4	Q6NSI4	OTTHUMG00000022150	ENST00000372548.4:c.1779T>G	X.37:g.105883826T>G	ENSP00000361628:p.Ile593Met	406.0	0.0	0		419.0	145.0	0.346062	NM_018015	H7BY89|Q4G0L7|Q5JQS1|Q5JRF9|Q6PHY5|Q6PII9|Q6PJU8|Q9H7W5|Q9NWA6	Missense_Mutation	SNP	ENST00000372548.4	37	CCDS14519.1	168	0.10126582278481013	105	0.2734375	6	0.01694915254237288	0	0.0	0	0.0	T	6.656	0.489589	0.12641	0.378096	0.001189	ENSG00000147231	ENST00000372544;ENST00000372548;ENST00000421550	T;T;T	0.64618	0.88;-0.11;0.88	3.51	0.993	0.19825	.	1.046520	0.07422	N	0.894082	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B	0.12630	0.006;0.006	B;B	0.06405	0.002;0.002	T	0.28808	-1.0032	9	0.56958	D	0.05	0.7933	3.0646	0.06210	0.0:0.141:0.2513:0.6078	rs5962707;rs52800882;rs5962707	593;593	A8K6R5;Q6NSI4	.;CX057_HUMAN	M	496;593;304	ENSP00000361623:I496M;ENSP00000361628:I593M;ENSP00000405866:I304M	ENSP00000361623:I496M	I	+	3	3	CXorf57	105770482	0.005000	0.15991	0.001000	0.08648	0.152000	0.21847	0.853000	0.27777	0.098000	0.17522	0.339000	0.21740	ATT	0|0.014;G|0.148	0.148	strong		0.333	CXorf57-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057800.2	NM_018015	
NPSR1	387129	hgsc.bcm.edu	37	7	34917759	34917759	+	Missense_Mutation	SNP	C	C	T	rs13230135	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:34917759C>T	ENST00000359791.1	+	9	1225	c.1097C>T	c.(1096-1098)aCt>aTt	p.T366I	NPSR1_ENST00000531252.1_Missense_Mutation_p.T355I	NM_207173.1	NP_997056.1	Q6W5P4	NPSR1_HUMAN	neuropeptide S receptor 1	0						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|vasopressin receptor activity (GO:0005000)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(7)	31					Halothane(DB01159)	TGGAAGGGTACTTGGCCAGGT	0.572													C|||	45	0.00898562	0.031	0.0043	5008	,	,		17115	0.0		0.0	False		,,,				2504	0.001				p.T366I		Atlas-SNP	.											.	NPSR1	134	.	0			c.C1097T						PASS	.	C	ILE/THR	157,4249	99.8+/-138.5	2,153,2048	76.0	60.0	65.0		1097	-1.2	0.0	7	dbSNP_121	65	3,8597	3.0+/-9.4	0,3,4297	no	missense	NPSR1	NM_207173.1	89	2,156,6345	TT,TC,CC		0.0349,3.5633,1.2302		366/378	34917759	160,12846	2203	4300	6503	SO:0001583	missense	387129	exon9			AGGGTACTTGGCC	AY255536	CCDS5443.1, CCDS5444.1, CCDS75579.1, CCDS75580.1, CCDS75581.1	7p14.3	2012-08-08	2006-05-10	2006-05-10	ENSG00000187258	ENSG00000187258		"""GPCR / Class A : Neuropeptide receptors : S"""	23631	protein-coding gene	gene with protein product		608595	"""G protein-coupled receptor 154"""	GPR154		12679517, 15073379	Standard	NM_207173		Approved	PGR14, GPRA	uc003tei.1	Q6W5P4	OTTHUMG00000099383	ENST00000359791.1:c.1097C>T	7.37:g.34917759C>T	ENSP00000352839:p.Thr366Ile	224.0	0.0	0		288.0	146.0	0.506944	NM_207173	A2RTZ4|Q2XP58|Q56H76|Q56H77|Q56H78|Q6JSL4|Q6JSL5|Q6JSL6|Q6JSL7|Q6JSL8|Q6W5P3|Q6ZMB8	Missense_Mutation	SNP	ENST00000359791.1	37	CCDS5443.1	17	0.007783882783882784	14	0.028455284552845527	3	0.008287292817679558	0	0.0	0	0.0	C	8.876	0.950372	0.18431	0.035633	3.49E-4	ENSG00000187258	ENST00000359791;ENST00000531252	T;T	0.72167	-0.63;-0.25	2.64	-1.25	0.09405	.	.	.	.	.	T	0.13798	0.0334	N	0.08118	0	0.09310	N	1	B;B;B	0.26975	0.165;0.003;0.003	B;B;B	0.18561	0.022;0.006;0.006	T	0.07578	-1.0765	9	0.46703	T	0.11	.	3.1688	0.06545	0.0:0.3835:0.2193:0.3971	rs13230135	300;355;366	B7ZMA2;Q6W5P4-5;Q6W5P4-4	.;.;.	I	366;355	ENSP00000352839:T366I;ENSP00000433258:T355I	ENSP00000352839:T366I	T	+	2	0	NPSR1	34884284	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.050000	0.11904	-0.336000	0.08438	-0.324000	0.08512	ACT	C|0.987;T|0.013	0.013	strong		0.572	NPSR1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000216838.1	NM_207173	
SULT1A1	6817	hgsc.bcm.edu	37	16	28617413	28617413	+	Missense_Mutation	SNP	A	A	G	rs28374453		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:28617413A>G	ENST00000395607.1	-	7	1012	c.739T>C	c.(739-741)Ttc>Ctc	p.F247L	SULT1A1_ENST00000350842.4_Missense_Mutation_p.F169L|SULT1A1_ENST00000314752.7_Missense_Mutation_p.F247L|SULT1A1_ENST00000569554.1_Missense_Mutation_p.F247L|SULT1A1_ENST00000395609.1_Missense_Mutation_p.F247L	NM_177530.2|NM_177534.2	NP_803566.1|NP_803878.1	P50225	ST1A1_HUMAN	sulfotransferase family, cytosolic, 1A, phenol-preferring, member 1	247					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|amine metabolic process (GO:0009308)|catecholamine metabolic process (GO:0006584)|estrogen metabolic process (GO:0008210)|flavonoid metabolic process (GO:0009812)|small molecule metabolic process (GO:0044281)|sulfation (GO:0051923)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	aryl sulfotransferase activity (GO:0004062)|flavonol 3-sulfotransferase activity (GO:0047894)|steroid sulfotransferase activity (GO:0050294)|sulfotransferase activity (GO:0008146)	p.F247L(5)|p.F169L(5)		endometrium(2)|kidney(7)|large_intestine(2)|lung(2)|ovary(1)|stomach(2)	16					Acetaminophen(DB00316)|Tamoxifen(DB00675)	TGGTCCATGAACTCCTGGGGG	0.607																																					p.F247L		Atlas-SNP	.											SULT1A1_ENST00000350842,NS,carcinoma,0,10	SULT1A1	53	10	10	Substitution - Missense(10)	kidney(10)	c.T739C						scavenged	.						264.0	206.0	226.0					16																	28617413		2197	4300	6497	SO:0001583	missense	6817	exon6			CCATGAACTCCTG	U52852	CCDS10637.1, CCDS32420.1	16p12.1	2008-02-05			ENSG00000196502	ENSG00000196502	2.8.2.1	"""Sulfotransferases, cytosolic"""	11453	protein-coding gene	gene with protein product		171150		STP, STP1		8288252, 8912648	Standard	NM_177534		Approved	P-PST	uc002dqj.3	P50225	OTTHUMG00000131765	ENST00000395607.1:c.739T>C	16.37:g.28617413A>G	ENSP00000378971:p.Phe247Leu	516.0	0.0	0		271.0	83.0	0.306273	NM_177534	Q2NL71|Q86U58|Q92818|Q9BVU6|Q9UGG7	Missense_Mutation	SNP	ENST00000395607.1	37	CCDS32420.1	56	0.02564102564102564	29	0.05894308943089431	5	0.013812154696132596	1	0.0017482517482517483	21	0.027704485488126648	a	7.042	0.562645	0.13498	.	.	ENSG00000196502	ENST00000314752;ENST00000350842;ENST00000395609;ENST00000395607	T;T;T;T	0.01548	4.78;4.78;4.78;4.78	2.17	-4.34	0.03666	Sulfotransferase domain (1);	0.865026	0.10074	N	0.719350	T	0.00144	0.0004	N	0.12920	0.275	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	0.46414	-0.9193	10	0.22109	T	0.4	.	1.793	0.03056	0.1608:0.4101:0.2253:0.2039	rs28374453	199;169;247	Q59GG0;P50225-2;P50225	.;.;ST1A1_HUMAN	L	247;169;247;247	ENSP00000321988:F247L;ENSP00000329399:F169L;ENSP00000378972:F247L;ENSP00000378971:F247L	ENSP00000321988:F247L	F	-	1	0	SULT1A1	28524914	0.000000	0.05858	0.001000	0.08648	0.047000	0.14425	-3.681000	0.00394	-1.249000	0.02500	0.248000	0.18094	TTC	A|0.974;G|0.026	0.026	strong		0.607	SULT1A1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254694.2	NM_001055	
SARDH	1757	hgsc.bcm.edu	37	9	136535746	136535746	+	Missense_Mutation	SNP	C	C	T	rs61685718	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136535746C>T	ENST00000371872.4	-	19	2712	c.2455G>A	c.(2455-2457)Gca>Aca	p.A819T	SARDH_ENST00000439388.1_Missense_Mutation_p.A819T|SARDH_ENST00000422262.2_Missense_Mutation_p.A651T|SARDH_ENST00000371868.1_Missense_Mutation_p.A247T	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	819					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		CGGAGGCCTGCGGCCCGCTGC	0.697													C|||	75	0.014976	0.0545	0.0043	5008	,	,		13059	0.0		0.0	False		,,,				2504	0.0				p.A819T		Atlas-SNP	.											SARDH,colon,carcinoma,0,1	SARDH	112	1	0			c.G2455A						PASS	.	C	THR/ALA,THR/ALA	197,4115		3,191,1962	11.0	11.0	11.0		2455,2455	-10.0	0.0	9	dbSNP_129	11	6,8490		0,6,4242	yes	missense,missense	SARDH	NM_001134707.1,NM_007101.3	58,58	3,197,6204	TT,TC,CC		0.0706,4.5686,1.5849	benign,benign	819/919,819/919	136535746	203,12605	2156	4248	6404	SO:0001583	missense	1757	exon19			GGCCTGCGGCCCG		CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.2455G>A	9.37:g.136535746C>T	ENSP00000360938:p.Ala819Thr	107.0	0.0	0		119.0	41.0	0.344538	NM_007101	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Missense_Mutation	SNP	ENST00000371872.4	37	CCDS6978.1	27	0.012362637362637362	24	0.04878048780487805	3	0.008287292817679558	0	0.0	0	0.0	C	5.568	0.289698	0.10567	0.045686	7.06E-4	ENSG00000123453	ENST00000371872;ENST00000371868;ENST00000439388;ENST00000422262	T;T;T;T	0.76839	-1.05;-1.05;-1.05;-1.05	5.01	-10.0	0.00425	Glycine cleavage T-protein, C-terminal barrel (1);	1.295140	0.05116	N	0.489711	T	0.12774	0.0310	N	0.11131	0.1	0.09310	N	0.999999	B;B	0.09022	0.001;0.002	B;B	0.13407	0.005;0.009	T	0.26224	-1.0109	10	0.30854	T	0.27	5.8048	0.49	0.00562	0.358:0.2261:0.1855:0.2303	rs61685718;rs61745311	819;247	Q9UL12;Q5SYV2	SARDH_HUMAN;.	T	819;247;819;651	ENSP00000360938:A819T;ENSP00000360934:A247T;ENSP00000403084:A819T;ENSP00000415537:A651T	ENSP00000360934:A247T	A	-	1	0	SARDH	135525567	0.000000	0.05858	0.000000	0.03702	0.480000	0.33159	-0.744000	0.04839	-2.619000	0.00441	-0.485000	0.04761	GCA	C|0.987;T|0.013	0.013	strong		0.697	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1		
SMURF2	64750	hgsc.bcm.edu	37	17	62567987	62567987	+	Silent	SNP	G	G	A	rs34788315	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:62567987G>A	ENST00000262435.9	-	10	1132	c.945C>T	c.(943-945)ttC>ttT	p.F315F	SMURF2_ENST00000578200.1_Intron	NM_022739.3	NP_073576.1	Q9HAU4	SMUF2_HUMAN	SMAD specific E3 ubiquitin protein ligase 2	315	WW 3. {ECO:0000255|PROSITE- ProRule:PRU00224}.				BMP signaling pathway (GO:0030509)|gene expression (GO:0010467)|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)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|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 protein catabolic process (GO:0006511)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|SMAD binding (GO:0046332)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)|skin(4)	22	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;9.88e-12)			TATGGTCAACGAAATAAACTC	0.383													G|||	160	0.0319489	0.115	0.0115	5008	,	,		17923	0.0		0.0	False		,,,				2504	0.0				p.F315F		Atlas-SNP	.											.	SMURF2	63	.	0			c.C945T						PASS	.	G		414,3992	204.1+/-226.4	13,388,1802	118.0	106.0	110.0		945	0.8	1.0	17	dbSNP_126	110	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SMURF2	NM_022739.3		13,390,6100	AA,AG,GG		0.0233,9.3963,3.1985		315/749	62567987	416,12590	2203	4300	6503	SO:0001819	synonymous_variant	64750	exon10			GTCAACGAAATAA	AF301463	CCDS32707.1	17q22-q23	2012-10-05			ENSG00000108854	ENSG00000108854			16809	protein-coding gene	gene with protein product		605532				11016919	Standard	XM_005257585		Approved		uc002jep.1	Q9HAU4	OTTHUMG00000179189	ENST00000262435.9:c.945C>T	17.37:g.62567987G>A		205.0	0.0	0		182.0	92.0	0.505495	NM_022739	Q52LL1|Q9H260	Silent	SNP	ENST00000262435.9	37	CCDS32707.1																																																																																			G|0.964;A|0.036	0.036	strong		0.383	SMURF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445227.1	NM_022739	
OAF	220323	hgsc.bcm.edu	37	11	120097551	120097551	+	Silent	SNP	G	G	A	rs873058	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:120097551G>A	ENST00000328965.4	+	3	906	c.393G>A	c.(391-393)gcG>gcA	p.A131A	OAF_ENST00000531220.1_Silent_p.A15A	NM_178507.2	NP_848602.1	Q86UD1	OAF_HUMAN	OAF homolog (Drosophila)	131						extracellular vesicular exosome (GO:0070062)				kidney(1)|lung(5)	6		Breast(109;0.00663)|Medulloblastoma(222;0.0523)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;5.1e-06)		TGCGGCAGGCGGAGGAGGTTC	0.612													G|||	71	0.0141773	0.0507	0.0058	5008	,	,		16367	0.0		0.0	False		,,,				2504	0.0				p.A131A		Atlas-SNP	.											.	OAF	12	.	0			c.G393A						PASS	.	G		213,4193	129.0+/-165.8	5,203,1995	64.0	59.0	61.0		393	-10.4	0.6	11	dbSNP_86	61	2,8598		0,2,4298	no	coding-synonymous	OAF	NM_178507.2		5,205,6293	AA,AG,GG		0.0233,4.8343,1.6531		131/274	120097551	215,12791	2203	4300	6503	SO:0001819	synonymous_variant	220323	exon3			GCAGGCGGAGGAG	BC047726	CCDS8430.1	11q23.3	2010-11-23			ENSG00000184232	ENSG00000184232			28752	protein-coding gene	gene with protein product						12477932	Standard	NM_178507		Approved	MGC52117	uc001pxb.3	Q86UD1	OTTHUMG00000166139	ENST00000328965.4:c.393G>A	11.37:g.120097551G>A		85.0	0.0	0		70.0	45.0	0.642857	NM_178507		Silent	SNP	ENST00000328965.4	37	CCDS8430.1																																																																																			G|0.982;A|0.018	0.018	strong		0.612	OAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388036.2	NM_178507	
SOWAHA	134548	hgsc.bcm.edu	37	5	132149593	132149593	+	Missense_Mutation	SNP	G	G	A	rs114865630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:132149593G>A	ENST00000378693.2	+	1	561	c.280G>A	c.(280-282)Ggc>Agc	p.G94S		NM_175873.4	NP_787069.3	Q2M3V2	SWAHA_HUMAN	sosondowah ankyrin repeat domain family member A	94	Pro-rich.																CGCACCCTTCGGCCCCCCGGG	0.726													G|||	151	0.0301518	0.1097	0.0086	5008	,	,		9361	0.0		0.0	False		,,,				2504	0.0				p.G94S		Atlas-SNP	.											.	.	.	.	0			c.G280A						PASS	.	G	SER/GLY	228,2496		11,206,1145	9.0	13.0	12.0		280	-6.5	0.0	5	dbSNP_132	12	4,6042		0,4,3019	no	missense	ANKRD43	NM_175873.4	56	11,210,4164	AA,AG,GG		0.0662,8.37,2.6454	benign	94/550	132149593	232,8538	1362	3023	4385	SO:0001583	missense	134548	exon1			CCCTTCGGCCCCC	AK090823	CCDS43361.1	5q23.3	2013-01-10	2012-01-12	2012-01-12	ENSG00000198944	ENSG00000198944		"""Ankyrin repeat domain containing"""	27033	protein-coding gene	gene with protein product			"""ankyrin repeat domain 43"""	ANKRD43		22234889	Standard	NM_175873		Approved		uc003kxw.3	Q2M3V2	OTTHUMG00000059844	ENST00000378693.2:c.280G>A	5.37:g.132149593G>A	ENSP00000367965:p.Gly94Ser	4.0	0.0	0		16.0	12.0	0.75	NM_175873	Q8NAE7	Missense_Mutation	SNP	ENST00000378693.2	37	CCDS43361.1	68	0.031135531135531136	57	0.11585365853658537	11	0.03038674033149171	0	0.0	0	0.0	g	7.170	0.587390	0.13812	0.0837	6.62E-4	ENSG00000198944	ENST00000378693	T	0.35421	1.31	3.95	-6.54	0.01860	.	.	.	.	.	T	0.00210	0.0006	N	0.14661	0.345	0.80722	P	0.0	B	0.18610	0.029	B	0.08055	0.003	T	0.37753	-0.9692	8	0.06236	T	0.91	7.4965	10.6849	0.45837	0.0:0.0953:0.7015:0.2032	.	94	Q2M3V2	ANR43_HUMAN	S	94	ENSP00000367965:G94S	ENSP00000367965:G94S	G	+	1	0	ANKRD43	132177492	0.000000	0.05858	0.002000	0.10522	0.064000	0.16182	-3.229000	0.00549	-0.876000	0.04017	0.290000	0.19541	GGC	G|0.964;A|0.036	0.036	strong		0.726	SOWAHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133062.1	NM_175873	
GEMIN4	50628	hgsc.bcm.edu	37	17	648916	648916	+	Silent	SNP	T	T	C	rs12942598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:648916T>C	ENST00000319004.5	-	2	2485	c.2367A>G	c.(2365-2367)acA>acG	p.T789T	GEMIN4_ENST00000576778.1_Silent_p.T778T	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	789					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		TCTCAAAAAGTGTGGCTGGCA	0.587													T|||	74	0.0147764	0.0008	0.0331	5008	,	,		19967	0.0		0.0398	False		,,,				2504	0.0102				p.T789T		Atlas-SNP	.											.	GEMIN4	116	.	0			c.A2367G						PASS	.	T		28,3812		0,28,1892	16.0	17.0	17.0		2367	-5.6	1.0	17	dbSNP_121	17	360,7860		8,344,3758	no	coding-synonymous	GEMIN4	NM_015721.2		8,372,5650	CC,CT,TT		4.3796,0.7292,3.2172		789/1059	648916	388,11672	1920	4110	6030	SO:0001819	synonymous_variant	50628	exon2			AAAAAGTGTGGCT	AF177341	CCDS45559.1	17p13.3	2008-07-18				ENSG00000179409			15717	protein-coding gene	gene with protein product	"""HCC-associated protein 1"", ""component of gems 4"""	606969				10725331	Standard	NM_015721		Approved	HHRF-1, DKFZP434B131, p97, DKFZP434D174, HC56, HCAP1	uc002frs.1	P57678		ENST00000319004.5:c.2367A>G	17.37:g.648916T>C		80.0	0.0	0		98.0	38.0	0.387755	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Silent	SNP	ENST00000319004.5	37	CCDS45559.1																																																																																			T|0.974;C|0.026	0.026	strong		0.587	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721	
MBOAT1	154141	hgsc.bcm.edu	37	6	20109842	20109842	+	Missense_Mutation	SNP	T	T	C	rs2065649	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:20109842T>C	ENST00000324607.7	-	12	1512	c.1348A>G	c.(1348-1350)Atc>Gtc	p.I450V	MBOAT1_ENST00000541730.1_Missense_Mutation_p.I301V	NM_001080480.1	NP_001073949.1	Q6ZNC8	MBOA1_HUMAN	membrane bound O-acyltransferase domain containing 1	450			I -> V (in dbSNP:rs2065649).		glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	transferase activity, transferring acyl groups other than amino-acyl groups (GO:0016747)			breast(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(5)	20	all_cancers(95;0.244)|Breast(50;0.0379)|Ovarian(93;0.0473)|all_epithelial(95;0.109)		OV - Ovarian serous cystadenocarcinoma(7;0.00392)|all cancers(50;0.0117)|Epithelial(50;0.0454)			TATAAGCTGATGGTCGGTTCA	0.468													T|||	239	0.0477236	0.1641	0.0259	5008	,	,		18796	0.0		0.004	False		,,,				2504	0.0				p.I450V		Atlas-SNP	.											.	MBOAT1	48	.	0			c.A1348G						PASS	.	T	VAL/ILE	691,3715	289.5+/-280.5	54,583,1566	149.0	133.0	139.0		1348	3.0	1.0	6	dbSNP_94	139	13,8587	9.8+/-36.6	0,13,4287	yes	missense	MBOAT1	NM_001080480.1	29	54,596,5853	CC,CT,TT		0.1512,15.6832,5.4129	benign	450/496	20109842	704,12302	2203	4300	6503	SO:0001583	missense	154141	exon12			AGCTGATGGTCGG	AK093994	CCDS34346.1	6p22.3	2013-10-11	2006-06-29	2006-06-29	ENSG00000172197	ENSG00000172197			21579	protein-coding gene	gene with protein product	"""lysophosphatidylethanolamine acyltransferase 1"""	611732	"""O-acyltransferase (membrane bound) domain containing 1"""	OACT1		18287005	Standard	NM_001080480		Approved	MGC44669, dJ434O11.1, LPEAT1	uc003ncx.2	Q6ZNC8	OTTHUMG00000014334	ENST00000324607.7:c.1348A>G	6.37:g.20109842T>C	ENSP00000324944:p.Ile450Val	113.0	0.0	0		102.0	47.0	0.460784	NM_001080480	A9EDQ5|B4DL59|B4E3J4|Q86XC2|Q8N9R5	Missense_Mutation	SNP	ENST00000324607.7	37	CCDS34346.1	75	0.034340659340659344	66	0.13414634146341464	9	0.024861878453038673	0	0.0	0	0.0	T	12.51	1.960413	0.34565	0.156832	0.001512	ENSG00000172197	ENST00000541730;ENST00000324607	T;T	0.18502	2.21;2.68	5.38	2.96	0.34315	.	0.312699	0.38548	N	0.001653	T	0.06142	0.0159	L	0.61036	1.89	0.09310	P	0.9999999999999988	B;B	0.18741	0.03;0.006	B;B	0.20577	0.03;0.003	T	0.17198	-1.0377	9	0.39692	T	0.17	-7.5096	4.338	0.11095	0.0:0.238:0.164:0.598	rs2065649;rs2065649	301;450	Q6ZNC8-2;Q6ZNC8	.;MBOA1_HUMAN	V	301;450	ENSP00000441568:I301V;ENSP00000324944:I450V	ENSP00000324944:I450V	I	-	1	0	MBOAT1	20217821	0.259000	0.24043	0.995000	0.50966	0.991000	0.79684	-0.065000	0.11617	0.409000	0.25649	0.533000	0.62120	ATC	T|0.949;C|0.051	0.051	strong		0.468	MBOAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039980.1		
FAAH	2166	hgsc.bcm.edu	37	1	46876488	46876488	+	Silent	SNP	G	G	C	rs74783386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:46876488G>C	ENST00000243167.8	+	11	1362	c.1278G>C	c.(1276-1278)ctG>ctC	p.L426L		NM_001441.2	NP_001432.2	O00519	FAAH1_HUMAN	fatty acid amide hydrolase	426					fatty acid catabolic process (GO:0009062)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)	acylglycerol lipase activity (GO:0047372)|carbon-nitrogen ligase activity, with glutamine as amido-N-donor (GO:0016884)|fatty acid amide hydrolase activity (GO:0017064)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	22	Acute lymphoblastic leukemia(166;0.155)				Propofol(DB00818)|Thiopental(DB00599)	CTGTGCAGCTGCCAAGGCTGT	0.617													C|||	42	0.00838658	0.0076	0.0	5008	,	,		18450	0.0159		0.0	False		,,,				2504	0.0164				p.L426L		Atlas-SNP	.											.	FAAH	36	.	0			c.G1278C						PASS	.	C		8,4398	825.1+/-416.5	0,8,2195	93.0	80.0	84.0		1278	1.2	1.0	1	dbSNP_131	84	4,8596	819.0+/-406.8	0,4,4296	no	coding-synonymous	FAAH	NM_001441.2		0,12,6491	CC,CG,GG		0.0465,0.1816,0.0923		426/580	46876488	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	2166	exon11			GCAGCTGCCAAGG	U82535	CCDS535.1	1p35-p34	2008-02-05			ENSG00000117480	ENSG00000117480			3553	protein-coding gene	gene with protein product		602935				9122178	Standard	NM_001441		Approved	FAAH-1	uc001cpu.2	O00519	OTTHUMG00000007811	ENST00000243167.8:c.1278G>C	1.37:g.46876488G>C		168.0	0.0	0		176.0	80.0	0.454545	NM_001441	D3DQ19|Q52M86|Q5TDF8	Silent	SNP	ENST00000243167.8	37	CCDS535.1																																																																																			G|0.998;C|0.002	0.002	strong		0.617	FAAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021443.1	NM_001441	
CEACAM8	1088	hgsc.bcm.edu	37	19	43098931	43098931	+	Missense_Mutation	SNP	C	C	A	rs28367882	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43098931C>A	ENST00000244336.5	-	1	151	c.50G>T	c.(49-51)gGg>gTg	p.G17V	LIPE-AS1_ENST00000594624.2_RNA|CEACAM8_ENST00000599005.1_Missense_Mutation_p.G17V|LIPE-AS1_ENST00000594688.1_RNA	NM_001816.3	NP_001807.2	P31997	CEAM8_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 8	17			G -> V (in dbSNP:rs28367882).		immune response (GO:0006955)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	16		Prostate(69;0.00899)				GAGCAGGAGCCCCTGCCAGGG	0.632													.|||	355	0.0708866	0.2542	0.0231	5008	,	,		18261	0.0		0.003	False		,,,				2504	0.0				p.G17V		Atlas-SNP	.											.	CEACAM8	44	.	0			c.G50T						PASS	.	C	VAL/GLY	873,3533	340.5+/-306.2	92,689,1422	102.0	95.0	97.0		50	-0.8	0.0	19	dbSNP_125	97	18,8582	10.5+/-38.8	0,18,4282	no	missense	CEACAM8	NM_001816.3	109	92,707,5704	AA,AC,CC		0.2093,19.8139,6.8507	possibly-damaging	17/350	43098931	891,12115	2203	4300	6503	SO:0001583	missense	1088	exon1			AGGAGCCCCTGCC	D90064	CCDS12610.1	19q13.2	2013-01-29			ENSG00000124469	ENSG00000124469		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1820	protein-coding gene	gene with protein product		615747		CGM6		2208113, 2306228	Standard	NM_001816		Approved	CD66b	uc002oud.2	P31997	OTTHUMG00000151124	ENST00000244336.5:c.50G>T	19.37:g.43098931C>A	ENSP00000244336:p.Gly17Val	85.0	0.0	0		64.0	33.0	0.515625	NM_001816	O60399|Q16574	Missense_Mutation	SNP	ENST00000244336.5	37	CCDS12610.1	124	0.056776556776556776	110	0.22357723577235772	11	0.03038674033149171	0	0.0	3	0.00395778364116095	c	6.456	0.452336	0.12283	0.198139	0.002093	ENSG00000124469	ENST00000244336	T	0.21031	2.03	1.48	-0.838	0.10762	.	.	.	.	.	T	0.00012	0.0000	M	0.88704	2.975	0.80722	P	0.0	P	0.40000	0.698	P	0.46758	0.526	T	0.05716	-1.0868	8	0.72032	D	0.01	.	4.0532	0.09804	0.0:0.5677:0.0:0.4323	rs28367882;rs59229803	17	P31997	CEAM8_HUMAN	V	17	ENSP00000244336:G17V	ENSP00000244336:G17V	G	-	2	0	CEACAM8	47790771	0.000000	0.05858	0.010000	0.14722	0.009000	0.06853	0.062000	0.14389	-0.173000	0.10761	-0.671000	0.03813	GGG	C|0.939;A|0.061	0.061	strong		0.632	CEACAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321430.1		
MED22	6837	hgsc.bcm.edu	37	9	136208405	136208405	+	Missense_Mutation	SNP	C	C	T	rs145653063	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136208405C>T	ENST00000491289.1	-	5	1134	c.553G>A	c.(553-555)Gcc>Acc	p.A185T	MED22_ENST00000471524.1_5'Flank|MED22_ENST00000344469.5_3'UTR|MED22_ENST00000476080.1_3'UTR|MED22_ENST00000343730.5_Missense_Mutation_p.A185T			Q15528	MED22_HUMAN	mediator complex subunit 22	185						cytoplasm (GO:0005737)|mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			endometrium(1)|large_intestine(1)|ovary(1)|urinary_tract(1)	4				OV - Ovarian serous cystadenocarcinoma(145;1.14e-06)|Epithelial(140;8.2e-06)|all cancers(34;6.94e-05)		TGGGCAGGGGCTGCCACCTGT	0.677													C|||	52	0.0103834	0.0378	0.0029	5008	,	,		15147	0.0		0.0	False		,,,				2504	0.0				p.A185T		Atlas-SNP	.											.	MED22	13	.	0			c.G553A						PASS	.	C	THR/ALA,	116,4286	85.3+/-124.0	2,112,2087	22.0	26.0	25.0		553,	1.2	0.0	9	dbSNP_134	25	5,8589	3.7+/-12.6	0,5,4292	no	missense,utr-3	MED22	NM_133640.3,NM_181491.1	58,	2,117,6379	TT,TC,CC		0.0582,2.6352,0.9311	benign,	185/201,	136208405	121,12875	2201	4297	6498	SO:0001583	missense	6837	exon5			CAGGGGCTGCCAC		CCDS6963.1, CCDS6964.1	9q34.1	2008-02-05	2007-07-30	2007-07-30	ENSG00000148297	ENSG00000148297			11477	protein-coding gene	gene with protein product		185641	"""surfeit 5"""	SURF5		8499913, 15175163	Standard	NM_133640		Approved	Med24	uc004cdc.3	Q15528	OTTHUMG00000020869	ENST00000491289.1:c.553G>A	9.37:g.136208405C>T	ENSP00000420393:p.Ala185Thr	106.0	0.0	0		115.0	39.0	0.33913	NM_133640	B3KW83|B3KWX4|O76072|Q5T8U0	Missense_Mutation	SNP	ENST00000491289.1	37	CCDS6963.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	C	0.576	-0.838931	0.02692	0.026352	5.82E-4	ENSG00000148297	ENST00000491289;ENST00000343730	.	.	.	4.15	1.23	0.21249	.	0.579278	0.18389	N	0.142701	T	0.02418	0.0074	N	0.04880	-0.145	0.18873	N	0.999985	B	0.02656	0.0	B	0.01281	0.0	T	0.23154	-1.0196	9	0.05620	T	0.96	-4.6055	2.9823	0.05957	0.1951:0.4783:0.0:0.3266	.	185	Q15528	MED22_HUMAN	T	185	.	ENSP00000342343:A185T	A	-	1	0	MED22	135198226	0.879000	0.30193	0.041000	0.18516	0.049000	0.14656	1.605000	0.36815	0.146000	0.19002	0.563000	0.77884	GCC	C|0.989;T|0.011	0.011	strong		0.677	MED22-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054898.2	NM_133640	
LLGL2	3993	hgsc.bcm.edu	37	17	73566094	73566094	+	Missense_Mutation	SNP	G	G	C	rs115026154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73566094G>C	ENST00000392550.3	+	15	1749	c.1632G>C	c.(1630-1632)caG>caC	p.Q544H	LLGL2_ENST00000167462.5_Missense_Mutation_p.Q544H|LLGL2_ENST00000577200.1_Missense_Mutation_p.Q544H	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	544					cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			CTGTGGAGCAGGTGGAGGCCG	0.672													G|||	70	0.0139776	0.0514	0.0029	5008	,	,		15575	0.0		0.0	False		,,,				2504	0.0				p.Q544H		Atlas-SNP	.											.	LLGL2	155	.	0			c.G1632C						PASS	.	G	HIS/GLN,HIS/GLN	256,4148	140.0+/-175.5	7,242,1953	34.0	33.0	34.0		1632,1632	0.4	1.0	17	dbSNP_132	34	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	LLGL2	NM_001031803.1,NM_004524.2	24,24	7,243,6252	CC,CG,GG		0.0116,5.8129,1.9763	benign,benign	544/1021,544/1016	73566094	257,12747	2202	4300	6502	SO:0001583	missense	3993	exon15			GGAGCAGGTGGAG	X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"""WD repeat domain containing"""	6629	protein-coding gene	gene with protein product			"""lethal giant larvae (Drosophila) homolog 2"""				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.1632G>C	17.37:g.73566094G>C	ENSP00000376333:p.Gln544His	87.0	0.0	0		100.0	62.0	0.62	NM_004524	Q14521|Q9BR62	Missense_Mutation	SNP	ENST00000392550.3	37	CCDS32733.1	33	0.01510989010989011	32	0.06504065040650407	1	0.0027624309392265192	0	0.0	0	0.0	G	10.86	1.471205	0.26423	0.058129	1.16E-4	ENSG00000073350	ENST00000167462;ENST00000392550;ENST00000545227	T;T	0.44083	0.93;0.93	5.2	0.448	0.16614	WD40/YVTN repeat-like-containing domain (1);	0.309685	0.35013	N	0.003504	T	0.01254	0.0041	N	0.16478	0.41	0.27032	N	0.964225	B;B;B;B;B	0.06786	0.001;0.0;0.001;0.0;0.0	B;B;B;B;B	0.10450	0.005;0.002;0.004;0.003;0.001	T	0.05484	-1.0882	10	0.17832	T	0.49	-0.9242	1.9897	0.03444	0.1345:0.225:0.353:0.2875	.	171;533;533;544;544	B4DVR9;B3KX47;G3V1I9;Q6P1M3-2;Q6P1M3	.;.;.;.;L2GL2_HUMAN	H	544;544;533	ENSP00000167462:Q544H;ENSP00000376333:Q544H	ENSP00000167462:Q544H	Q	+	3	2	LLGL2	71077689	0.829000	0.29322	1.000000	0.80357	0.904000	0.53231	0.044000	0.13992	0.541000	0.28827	0.549000	0.68633	CAG	G|0.977;C|0.023	0.023	strong		0.672	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524	
CYP4F12	66002	hgsc.bcm.edu	37	19	15794423	15794423	+	Silent	SNP	C	C	T	rs114945576|rs386807235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15794423C>T	ENST00000550308.1	+	7	1148	c.768C>T	c.(766-768)ttC>ttT	p.F256F	CYP4F12_ENST00000324632.10_Silent_p.F256F	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	256					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	GGCGGCGCTTCCACAGGGCCT	0.557													.|||	73	0.0145767	0.0522	0.0043	5008	,	,		20890	0.0		0.001	False		,,,				2504	0.0				p.F256F		Atlas-SNP	.											.	CYP4F12	89	.	0			c.C768T						PASS	.						79.0	81.0	80.0					19																	15794423		2199	4295	6494	SO:0001819	synonymous_variant	66002	exon7			GCGCTTCCACAGG	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.768C>T	19.37:g.15794423C>T		124.0	0.0	0		189.0	52.0	0.275132	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Silent	SNP	ENST00000550308.1	37	CCDS42517.1																																																																																			C|0.990;T|0.010	0.010	strong		0.557	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
GGT7	2686	hgsc.bcm.edu	37	20	33447314	33447314	+	Missense_Mutation	SNP	C	C	T	rs61319953	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33447314C>T	ENST00000336431.5	-	7	990	c.946G>A	c.(946-948)Gta>Ata	p.V316I		NM_178026.2	NP_821158.2	Q9UJ14	GGT7_HUMAN	gamma-glutamyltransferase 7	316					glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|integral component of membrane (GO:0016021)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			NS(2)|breast(1)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|skin(2)	20						GTGCCAAGTACATCCAGCACC	0.657													C|||	177	0.0353435	0.1256	0.0159	5008	,	,		13069	0.0		0.0	False		,,,				2504	0.0				p.V316I		Atlas-SNP	.											.	GGT7	41	.	0			c.G946A						PASS	.	C	ILE/VAL	418,3988	196.0+/-220.5	16,386,1801	36.0	31.0	33.0		946	-3.3	0.0	20	dbSNP_129	33	4,8594	2.2+/-6.3	0,4,4295	yes	missense	GGT7	NM_178026.2	29	16,390,6096	TT,TC,CC		0.0465,9.4871,3.2452	benign	316/663	33447314	422,12582	2203	4299	6502	SO:0001583	missense	2686	exon7			CAAGTACATCCAG	AL049709	CCDS13242.2	20q11.22	2008-11-24	2008-03-10	2008-03-10	ENSG00000131067	ENSG00000131067		"""Gamma-glutamyltransferases"""	4259	protein-coding gene	gene with protein product		612342	"""gamma-glutamyltransferase-like 3"""	GGTL5, GGTL3		8104871, 18357469	Standard	NM_178026		Approved	D20S101, dJ18C9.2	uc002xay.3	Q9UJ14	OTTHUMG00000032314	ENST00000336431.5:c.946G>A	20.37:g.33447314C>T	ENSP00000338964:p.Val316Ile	76.0	0.0	0		70.0	34.0	0.485714	NM_178026	Q8N899|Q8NF66|Q9BYP5|Q9BYP6	Missense_Mutation	SNP	ENST00000336431.5	37	CCDS13242.2	57	0.0260989010989011	50	0.1016260162601626	7	0.019337016574585635	0	0.0	0	0.0	C	10.57	1.386090	0.25031	0.094871	4.65E-4	ENSG00000131067	ENST00000336431	T	0.06218	3.33	5.84	-3.3	0.05003	.	1.463100	0.03616	N	0.235604	T	0.00073	0.0002	N	0.02011	-0.69	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.42949	-0.9421	10	0.17369	T	0.5	-16.9643	1.2329	0.01947	0.249:0.302:0.0955:0.3535	rs61319953	316;316	A4FU32;Q9UJ14	.;GGT7_HUMAN	I	316	ENSP00000338964:V316I	ENSP00000338964:V316I	V	-	1	0	GGT7	32910975	0.000000	0.05858	0.004000	0.12327	0.858000	0.48976	-0.023000	0.12456	-0.350000	0.08262	-0.254000	0.11334	GTA	C|0.971;T|0.029	0.029	strong		0.657	GGT7-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078816.2	NM_178026	
LRP2	4036	hgsc.bcm.edu	37	2	169993977	169993977	+	Silent	SNP	C	C	T	rs34029982	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:169993977C>T	ENST00000263816.3	-	76	13830	c.13545G>A	c.(13543-13545)ggG>ggA	p.G4515G		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	4515					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	TGGGCTGCTTCCCCATTTCCA	0.438													C|||	26	0.00519169	0.0197	0.0	5008	,	,		18764	0.0		0.0	False		,,,				2504	0.0				p.G4515G		Atlas-SNP	.											.	LRP2	751	.	0			c.G13545A						PASS	.	C		95,4311	69.2+/-107.0	0,95,2108	151.0	144.0	146.0		13545	3.6	1.0	2	dbSNP_126	146	0,8600		0,0,4300	no	coding-synonymous	LRP2	NM_004525.2		0,95,6408	TT,TC,CC		0.0,2.1562,0.7304		4515/4656	169993977	95,12911	2203	4300	6503	SO:0001819	synonymous_variant	4036	exon76			CTGCTTCCCCATT		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.13545G>A	2.37:g.169993977C>T		113.0	0.0	0		96.0	46.0	0.479167	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																			C|0.992;T|0.008	0.008	strong		0.438	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
ZNF467	168544	hgsc.bcm.edu	37	7	149462055	149462055	+	Silent	SNP	G	G	A	rs863021	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149462055G>A	ENST00000302017.3	-	5	1949	c.1536C>T	c.(1534-1536)agC>agT	p.S512S	ZNF467_ENST00000484747.1_Intron	NM_207336.1	NP_997219.1	Q7Z7K2	ZN467_HUMAN	zinc finger protein 467	512					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(2)|liver(1)|lung(7)|urinary_tract(1)	13	Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CGTGGGGGCGGCTGCCAGTGT	0.726													G|||	330	0.0658946	0.239	0.0173	5008	,	,		8834	0.0		0.002	False		,,,				2504	0.0				p.S512S		Atlas-SNP	.											.	ZNF467	50	.	0			c.C1536T						PASS	.	G		861,3477		106,649,1414	16.0	21.0	19.0		1536	-4.4	1.0	7	dbSNP_86	19	20,8504		1,18,4243	no	coding-synonymous	ZNF467	NM_207336.1		107,667,5657	AA,AG,GG		0.2346,19.8479,6.8496		512/596	149462055	881,11981	2169	4262	6431	SO:0001819	synonymous_variant	168544	exon5			GGGGCGGCTGCCA	BC029296	CCDS5899.1	7q36.1	2013-01-08			ENSG00000181444	ENSG00000181444		"""Zinc fingers, C2H2-type"""	23154	protein-coding gene	gene with protein product		614040				12426389	Standard	NM_207336		Approved	EZI, Zfp467	uc003wgd.2	Q7Z7K2	OTTHUMG00000157883	ENST00000302017.3:c.1536C>T	7.37:g.149462055G>A		4.0	0.0	0		17.0	8.0	0.470588	NM_207336		Silent	SNP	ENST00000302017.3	37	CCDS5899.1																																																																																			G|0.947;A|0.053	0.053	strong		0.726	ZNF467-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349833.1	NM_207336	
NUFIP2	57532	hgsc.bcm.edu	37	17	27620934	27620934	+	Silent	SNP	G	G	A	rs1054145	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:27620934G>A	ENST00000225388.4	-	1	202	c.144C>T	c.(142-144)caC>caT	p.H48H	NUFIP2_ENST00000579665.1_Silent_p.H48H	NM_020772.2	NP_065823.1	Q7Z417	NUFP2_HUMAN	nuclear fragile X mental retardation protein interacting protein 2	48	His-rich.					cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|polysomal ribosome (GO:0042788)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|prostate(2)|skin(4)|urinary_tract(1)	24			BRCA - Breast invasive adenocarcinoma(11;0.000457)|Colorectal(6;0.0178)|COAD - Colon adenocarcinoma(6;0.0551)			ggtgatgatggtggtggtggt	0.592													G|||	77	0.0153754	0.0522	0.0072	5008	,	,		10946	0.0		0.003	False		,,,				2504	0.0				p.H48H		Atlas-SNP	.											NUFIP2,NS,carcinoma,-2,1	NUFIP2	60	1	0			c.C144T						PASS	.	G		227,4179	135.3+/-171.4	7,213,1983	144.0	141.0	142.0		144	3.2	1.0	17	dbSNP_86	142	2,8598	3.0+/-9.4	0,2,4298	no	coding-synonymous	NUFIP2	NM_020772.2		7,215,6281	AA,AG,GG		0.0233,5.1521,1.7607		48/696	27620934	229,12777	2203	4300	6503	SO:0001819	synonymous_variant	57532	exon1			ATGATGGTGGTGG	AB037742	CCDS32600.1	17q11.1	2006-03-01				ENSG00000108256			17634	protein-coding gene	gene with protein product		609356				12837692, 16407062	Standard	NM_020772		Approved	KIAA1321, MGC117262, PIG1, 182-FIP, FIP-82, 82-FIP	uc002hdy.4	Q7Z417		ENST00000225388.4:c.144C>T	17.37:g.27620934G>A		476.0	0.0	0		525.0	275.0	0.52381	NM_020772	A1L3A6|Q9P2M5	Silent	SNP	ENST00000225388.4	37	CCDS32600.1																																																																																			G|0.981;A|0.019	0.019	strong		0.592	NUFIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447015.2	NM_020772	
MTTP	4547	hgsc.bcm.edu	37	4	100512919	100512919	+	Missense_Mutation	SNP	C	C	G	rs17599091	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:100512919C>G	ENST00000265517.5	+	6	933	c.730C>G	c.(730-732)Caa>Gaa	p.Q244E	MTTP_ENST00000511045.1_Missense_Mutation_p.Q271E|MTTP_ENST00000457717.1_Missense_Mutation_p.Q244E			P55157	MTP_HUMAN	microsomal triglyceride transfer protein	244	Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.		Q -> E (in dbSNP:rs17599091). {ECO:0000269|PubMed:11792722}.		cholesterol homeostasis (GO:0042632)|lipid metabolic process (GO:0006629)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|protein lipidation (GO:0006497)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|microvillus membrane (GO:0031528)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(14)|lung(19)|ovary(4)|prostate(5)|skin(1)|urinary_tract(1)	57				OV - Ovarian serous cystadenocarcinoma(123;6.04e-09)	Hesperetin(DB01094)|Lomitapide(DB08827)	GAATTTCCTACAAACCATTAA	0.303													C|||	103	0.0205671	0.0477	0.0086	5008	,	,		18429	0.0		0.0239	False		,,,				2504	0.0102				p.Q244E		Atlas-SNP	.											.	MTTP	127	.	0			c.C730G						PASS	.	C	GLU/GLN	240,4166	137.7+/-173.5	7,226,1970	65.0	64.0	64.0		730	3.5	0.6	4	dbSNP_123	64	289,8311	107.0+/-167.8	4,281,4015	yes	missense	MTTP	NM_000253.2	29	11,507,5985	GG,GC,CC		3.3605,5.4471,4.0674	benign	244/895	100512919	529,12477	2203	4300	6503	SO:0001583	missense	4547	exon7			TTCCTACAAACCA		CCDS3651.1, CCDS75169.1	4q24	2008-02-05	2005-11-04	2005-11-04	ENSG00000138823	ENSG00000138823			7467	protein-coding gene	gene with protein product		157147	"""microsomal triglyceride transfer protein (large polypeptide, 88kD)"", ""microsomal triglyceride transfer protein (large polypeptide, 88kDa)"""	MTP		8111381	Standard	XM_005263025		Approved	ABL	uc003hvc.4	P55157	OTTHUMG00000131023	ENST00000265517.5:c.730C>G	4.37:g.100512919C>G	ENSP00000265517:p.Gln244Glu	117.0	0.0	0		150.0	60.0	0.4	NM_000253	A8K428|Q08AM4|Q6P5T3	Missense_Mutation	SNP	ENST00000265517.5	37	CCDS3651.1	49	0.022435897435897436	25	0.0508130081300813	3	0.008287292817679558	0	0.0	21	0.027704485488126648	C	0.588	-0.834158	0.02713	0.054471	0.033605	ENSG00000138823	ENST00000511045;ENST00000457717;ENST00000265517;ENST00000538053	T;T;T	0.40225	1.04;1.04;1.04	5.53	3.47	0.39725	Lipid transport protein, beta-sheet shell (1);Lipid transport protein, N-terminal (3);Vitellinogen, beta-sheet N-terminal (1);	0.964707	0.08632	N	0.916909	T	0.05135	0.0137	L	0.38531	1.155	0.09310	N	1	B;B	0.14805	0.003;0.011	B;B	0.19148	0.008;0.024	T	0.25502	-1.0130	10	0.02654	T	1	-25.7225	7.9279	0.29885	0.3471:0.5753:0.0:0.0775	rs17599091;rs52789259	271;244	E9PBP6;P55157	.;MTP_HUMAN	E	271;244;244;244	ENSP00000427679:Q271E;ENSP00000400821:Q244E;ENSP00000265517:Q244E	ENSP00000265517:Q244E	Q	+	1	0	MTTP	100731942	0.044000	0.20184	0.609000	0.28983	0.195000	0.23768	0.419000	0.21247	1.429000	0.47314	0.650000	0.86243	CAA	C|0.964;G|0.036	0.036	strong		0.303	MTTP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253662.3		
DDX51	317781	hgsc.bcm.edu	37	12	132628281	132628281	+	Missense_Mutation	SNP	C	C	T	rs78871841	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132628281C>T	ENST00000397333.3	-	2	516	c.478G>A	c.(478-480)Ggc>Agc	p.G160S	NOC4L_ENST00000330579.1_5'Flank	NM_175066.3	NP_778236.2	Q8N8A6	DDX51_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 51	160					rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(1)|lung(5)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	10	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.59e-08)|Epithelial(86;3.62e-07)|all cancers(50;2.13e-05)		AGCACCAGGCCGGGGACCAGG	0.751													c|||	254	0.0507188	0.0802	0.0043	5008	,	,		10953	0.0476		0.0219	False		,,,				2504	0.0767				p.G160S		Atlas-SNP	.											.	DDX51	33	.	0			c.G478A						PASS	.		SER/GLY	138,2788		1,136,1326	3.0	4.0	3.0		478	1.6	0.0	12	dbSNP_131	3	24,6890		0,24,3433	yes	missense	DDX51	NM_175066.3	56	1,160,4759	TT,TC,CC		0.3471,4.7163,1.6463	benign	160/667	132628281	162,9678	1463	3457	4920	SO:0001583	missense	317781	exon2			CCAGGCCGGGGAC	BC040185	CCDS41865.1	12q24.33	2005-10-12				ENSG00000185163		"""DEAD-boxes"""	20082	protein-coding gene	gene with protein product							Standard	NM_175066		Approved		uc001ujy.4	Q8N8A6		ENST00000397333.3:c.478G>A	12.37:g.132628281C>T	ENSP00000380495:p.Gly160Ser	8.0	0.0	0		16.0	6.0	0.375	NM_175066	A8MPT9|Q5CZ71|Q8IXK5|Q96ED1	Missense_Mutation	SNP	ENST00000397333.3	37	CCDS41865.1	82	0.037545787545787544	30	0.06097560975609756	6	0.016574585635359115	26	0.045454545454545456	20	0.026385224274406333	c	0.472	-0.883980	0.02530	0.047163	0.003471	ENSG00000185163	ENST00000397333	T	0.01725	4.67	2.49	1.59	0.23543	.	0.789795	0.11401	U	0.567852	T	0.00178	0.0005	L	0.27053	0.805	0.09310	N	1	B	0.22211	0.066	B	0.09377	0.004	T	0.49504	-0.8933	10	0.13853	T	0.58	-1.4426	5.097	0.14739	0.0:0.8312:0.0:0.1688	.	160	Q8N8A6	DDX51_HUMAN	S	160	ENSP00000380495:G160S	ENSP00000380495:G160S	G	-	1	0	DDX51	131194234	0.000000	0.05858	0.012000	0.15200	0.059000	0.15707	0.104000	0.15313	0.624000	0.30286	0.479000	0.44913	GGC	C|0.962;T|0.038	0.038	strong		0.751	DDX51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398978.1	NM_175066	
CD36	948	hgsc.bcm.edu	37	7	80300449	80300449	+	Nonsense_Mutation	SNP	T	T	G	rs3211938	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:80300449T>G	ENST00000435819.1	+	13	1659	c.975T>G	c.(973-975)taT>taG	p.Y325*	CD36_ENST00000534394.1_Nonsense_Mutation_p.Y249*|CD36_ENST00000544133.1_Intron|CD36_ENST00000309881.7_Nonsense_Mutation_p.Y325*|CD36_ENST00000538969.1_Nonsense_Mutation_p.Y265*|CD36_ENST00000394788.3_Nonsense_Mutation_p.Y325*|CD36_ENST00000433696.2_Nonsense_Mutation_p.Y286*|CD36_ENST00000447544.2_Nonsense_Mutation_p.Y325*|CD36_ENST00000432207.1_Nonsense_Mutation_p.Y325*			P16671	CD36_HUMAN	CD36 molecule (thrombospondin receptor)	325					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 cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|cellular lipid metabolic process (GO:0044255)|cellular response to bacterial lipopeptide (GO:0071221)|cellular response to hydroperoxide (GO:0071447)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|cGMP-mediated signaling (GO:0019934)|cholesterol transport (GO:0030301)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response (GO:0045087)|lipid metabolic process (GO:0006629)|lipid storage (GO:0019915)|lipoprotein transport (GO:0042953)|long-chain fatty acid import (GO:0044539)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle mediated signaling (GO:0055096)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription factor import into nucleus (GO:0042992)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nitric oxide mediated signal transduction (GO:0007263)|phagocytosis, recognition (GO:0006910)|plasma lipoprotein particle clearance (GO:0034381)|plasma membrane long-chain fatty acid transport (GO:0015911)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of blood coagulation (GO:0030194)|positive regulation of blood microparticle formation (GO:2000334)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis, engulfment (GO:0060100)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of removal of superoxide radicals (GO:2000121)|response to stilbenoid (GO:0035634)|small molecule metabolic process (GO:0044281)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|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)	cell surface (GO:0009986)|endocytic vesicle membrane (GO:0030666)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)	high-density lipoprotein particle binding (GO:0008035)|lipid binding (GO:0008289)|lipoprotein particle binding (GO:0071813)|lipoteichoic acid receptor activity (GO:0070892)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|thrombospondin receptor activity (GO:0070053)|transforming growth factor beta binding (GO:0050431)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(10)|large_intestine(1)|lung(6)|ovary(1)	21						GTACATCATATGGTGTGCTAG	0.363													T|||	155	0.0309505	0.1157	0.0029	5008	,	,		16040	0.0		0.0	False		,,,				2504	0.0				p.Y325X		Atlas-SNP	.											.	CD36	185	.	0			c.T975G	GRCh37	CM001647	CD36	M	rs3211938	PASS	.	T	stop/TYR,stop/TYR,stop/TYR,stop/TYR,stop/TYR	361,4045	182.6+/-210.3	16,329,1858	76.0	75.0	75.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	975,975,975,975,975	-0.8	0.5	7	dbSNP_105	75	2,8598	1.2+/-3.3	0,2,4298	yes	stop-gained,stop-gained,stop-gained,stop-gained,stop-gained	CD36	NM_000072.3,NM_001001547.2,NM_001001548.2,NM_001127443.1,NM_001127444.1	,,,,	16,331,6156	GG,GT,TT		0.0233,8.1934,2.791	,,,,	325/473,325/473,325/473,325/473,325/473	80300449	363,12643	2203	4300	6503	SO:0001587	stop_gained	948	exon8			ATCATATGGTGTG	Z32770	CCDS34673.1	7q11.2	2010-02-26	2006-03-28		ENSG00000135218	ENSG00000135218		"""CD molecules"""	1663	protein-coding gene	gene with protein product		173510	"""CD36 antigen (collagen type I receptor, thrombospondin receptor)"""			7503937	Standard	NM_001001548		Approved	SCARB3, GPIV, FAT, GP4, GP3B	uc003uhg.4	P16671	OTTHUMG00000155383	ENST00000435819.1:c.975T>G	7.37:g.80300449T>G	ENSP00000399421:p.Tyr325*	49.0	0.0	0		47.0	47.0	1	NM_001127444	D9IX66|D9IX67|D9IX68|D9IX69|Q13966|Q16093|Q8TCV7|Q9BPZ8|Q9BQC2|Q9BZM8|Q9BZN3|Q9BZN4|Q9BZN5	Nonsense_Mutation	SNP	ENST00000435819.1	37	CCDS34673.1	72	0.03296703296703297	72	0.14634146341463414	0	0.0	0	0.0	0	0.0	T	35	5.563074	0.96527	0.081934	2.33E-4	ENSG00000135218	ENST00000435819;ENST00000309881;ENST00000534394;ENST00000394788;ENST00000447544;ENST00000432207;ENST00000419819;ENST00000538969;ENST00000433696	.	.	.	5.57	-0.823	0.10815	.	0.163457	0.53938	D	0.000054	.	.	.	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	.	.	.	.	.	.	.	-13.6549	9.8443	0.41017	0.0:0.3443:0.0:0.6557	rs3211938;rs10372565;rs17154273;rs3211938	.	.	.	X	325;325;249;325;325;325;325;265;286	.	.	Y	+	3	2	CD36	80138385	0.999000	0.42202	0.528000	0.27938	0.976000	0.68499	0.485000	0.22324	-0.378000	0.07918	0.397000	0.26171	TAT	T|0.967;G|0.033	0.033	strong		0.363	CD36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339767.6	NM_001001547	
LRRC8B	23507	hgsc.bcm.edu	37	1	90049088	90049088	+	Silent	SNP	G	G	A	rs35903285	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:90049088G>A	ENST00000330947.2	+	5	1239	c.879G>A	c.(877-879)gtG>gtA	p.V293V	RP5-1007M22.2_ENST00000443562.1_RNA|LRRC8B_ENST00000358200.4_Silent_p.V293V|LRRC8B_ENST00000439853.1_Silent_p.V293V	NM_001134476.1	NP_001127948.1	Q6P9F7	LRC8B_HUMAN	leucine rich repeat containing 8 family, member B	293					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(2)|lung(5)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	26		all_lung(203;0.17)		all cancers(265;0.00515)|Epithelial(280;0.0241)		CAGTTGATGTGCAGGCTTTTA	0.353													G|||	110	0.0219649	0.0787	0.0086	5008	,	,		22049	0.0		0.0	False		,,,				2504	0.0				p.V293V		Atlas-SNP	.											.	LRRC8B	49	.	0			c.G879A						PASS	.	G	,	315,4091	167.3+/-198.3	12,291,1900	154.0	153.0	153.0		879,879	-0.2	0.9	1	dbSNP_126	153	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous,coding-synonymous	LRRC8B	NM_001134476.1,NM_015350.2	,	12,295,6196	AA,AG,GG		0.0465,7.1493,2.4527	,	293/804,293/804	90049088	319,12687	2203	4300	6503	SO:0001819	synonymous_variant	23507	exon5			TGATGTGCAGGCT	AF385436	CCDS724.1	1p22.2	2008-02-05			ENSG00000197147	ENSG00000197147			30692	protein-coding gene	gene with protein product	"""T cell activation leucine repeat rich protein"""	612888				9039502	Standard	NM_015350		Approved	TA-LRRP, KIAA0231	uc001dni.3	Q6P9F7	OTTHUMG00000010129	ENST00000330947.2:c.879G>A	1.37:g.90049088G>A		67.0	0.0	0		94.0	43.0	0.457447	NM_015350	D3DT28|Q6UY21|Q8N106|Q92627	Silent	SNP	ENST00000330947.2	37	CCDS724.1																																																																																			G|0.976;A|0.024	0.024	strong		0.353	LRRC8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028008.1	NM_015350	
HOMEZ	57594	hgsc.bcm.edu	37	14	23745723	23745723	+	Silent	SNP	G	G	A	rs11844797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:23745723G>A	ENST00000357460.5	-	2	878	c.714C>T	c.(712-714)aaC>aaT	p.N238N	HOMEZ_ENST00000431326.2_Silent_p.N240N|HOMEZ_ENST00000561013.1_Silent_p.N240N	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	238					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|lung(7)	12	all_cancers(95;5.54e-06)			GBM - Glioblastoma multiforme(265;0.00643)		CATGTGACTGGTTGGGACCCC	0.532													G|||	250	0.0499201	0.1853	0.0072	5008	,	,		18809	0.0		0.0	False		,,,				2504	0.0				p.N238N		Atlas-SNP	.											.	HOMEZ	80	.	0			c.C714T						PASS	.	G		638,3510		52,534,1488	76.0	79.0	78.0		714	2.2	0.0	14	dbSNP_120	78	12,8408		1,10,4199	no	coding-synonymous	HOMEZ	NM_020834.2		53,544,5687	AA,AG,GG		0.1425,15.3809,5.1719		238/551	23745723	650,11918	2074	4210	6284	SO:0001819	synonymous_variant	57594	exon2			TGACTGGTTGGGA	AB037864	CCDS45085.1	14q11.2	2011-06-20	2007-02-15	2007-02-15		ENSG00000215271		"""Homeoboxes / ZF class"""	20164	protein-coding gene	gene with protein product		608119	"""KIAA1443"""	KIAA1443		12925734	Standard	NM_020834		Approved		uc001wja.2	Q8IX15		ENST00000357460.5:c.714C>T	14.37:g.23745723G>A		155.0	0.0	0		134.0	67.0	0.5	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	Silent	SNP	ENST00000357460.5	37	CCDS45085.1																																																																																			G|0.948;A|0.052	0.052	strong		0.532	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834	
COL20A1	57642	hgsc.bcm.edu	37	20	61960961	61960961	+	Missense_Mutation	SNP	T	T	C	rs6011740	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61960961T>C	ENST00000358894.6	+	35	3906	c.3806T>C	c.(3805-3807)aTg>aCg	p.M1269T	COL20A1_ENST00000422202.1_Missense_Mutation_p.M1282T|COL20A1_ENST00000496810.1_3'UTR|COL20A1_ENST00000435874.1_Missense_Mutation_p.M1282T|COL20A1_ENST00000326996.6_Missense_Mutation_p.M1301T	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	1269					extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)				NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					GTTGGTCAGATGGGCAGCCCT	0.652													C|||	244	0.048722	0.1611	0.0072	5008	,	,		18080	0.0		0.0	False		,,,				2504	0.0266				p.M1269T		Atlas-SNP	.											.	COL20A1	137	.	0			c.T3806C						PASS	.	C	THR/MET	497,3519		37,423,1548	28.0	33.0	32.0		3806	-4.9	0.0	20	dbSNP_114	32	5,8331		0,5,4163	yes	missense	COL20A1	NM_020882.2	81	37,428,5711	CC,CT,TT		0.06,12.3755,4.0641	benign	1269/1285	61960961	502,11850	2008	4168	6176	SO:0001583	missense	57642	exon35			GTCAGATGGGCAG	BC043183	CCDS46628.1	20q13.33	2014-02-12			ENSG00000101203	ENSG00000101203		"""Collagens"", ""Fibronectin type III domain containing"""	14670	protein-coding gene	gene with protein product						10819331	Standard	NM_020882		Approved	KIAA1510	uc011aau.2	Q9P218	OTTHUMG00000032964	ENST00000358894.6:c.3806T>C	20.37:g.61960961T>C	ENSP00000351767:p.Met1269Thr	39.0	0.0	0		31.0	14.0	0.451613	NM_020882	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Missense_Mutation	SNP	ENST00000358894.6	37	CCDS46628.1	72	0.03296703296703297	70	0.14227642276422764	2	0.0055248618784530384	0	0.0	0	0.0	C	0.007	-1.963878	0.00461	0.123755	6.0E-4	ENSG00000101203	ENST00000358894;ENST00000326996;ENST00000435874;ENST00000422202	D;D;D;D	0.85955	-2.02;-2.05;-2.02;-2.02	3.15	-4.86	0.03132	.	3.567220	0.01372	N	0.012620	T	0.00695	0.0023	N	0.01874	-0.695	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27502	-1.0072	9	0.19147	T	0.46	.	1.7705	0.03010	0.1455:0.2136:0.1439:0.497	rs6011740;rs6011740	1282;1269	Q9P218-2;Q9P218	.;COKA1_HUMAN	T	1269;1301;1282;1282	ENSP00000351767:M1269T;ENSP00000323077:M1301T;ENSP00000408690:M1282T;ENSP00000414753:M1282T	ENSP00000323077:M1301T	M	+	2	0	COL20A1	61431405	0.000000	0.05858	0.000000	0.03702	0.124000	0.20399	-3.643000	0.00405	-1.192000	0.02691	-0.642000	0.03964	ATG	T|0.949;C|0.051	0.051	strong		0.652	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882	
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011571	46011571	+	Silent	SNP	G	G	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46011571G>T	ENST00000400368.1	-	1	815	c.795C>A	c.(793-795)ccC>ccA	p.P265P	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	265	29 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(6)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23						CGTGCTGGCAGGGGGAGGAGG	0.642																																					p.P265P		Atlas-SNP	.											.	KRTAP10-6	57	.	0			c.C795A						PASS	.						118.0	120.0	119.0					21																	46011571		2203	4300	6503	SO:0001819	synonymous_variant	386674	exon1			CTGGCAGGGGGAG	AB076353	CCDS42959.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000188155	ENSG00000188155		"""Keratin associated proteins"""	20523	protein-coding gene	gene with protein product			"""keratin associated protein 18-6"""	KRTAP18-6			Standard	NM_198688		Approved	KRTAP18.6, KAP18.6, KAP10.6	uc002zfm.3	P60371	OTTHUMG00000057634	ENST00000400368.1:c.795C>A	21.37:g.46011571G>T		280.0	0.0	0		341.0	21.0	0.0615836	NM_198688		Silent	SNP	ENST00000400368.1	37	CCDS42959.1																																																																																			.	.	none		0.642	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688	
MYH8	4626	hgsc.bcm.edu	37	17	10312792	10312792	+	Silent	SNP	C	C	T	rs73275411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:10312792C>T	ENST00000403437.2	-	16	1795	c.1701G>A	c.(1699-1701)caG>caA	p.Q567Q	RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_002472.2	NP_002463.2	P13535	MYH8_HUMAN	myosin, heavy chain 8, skeletal muscle, perinatal	567	Myosin motor.				ATP catabolic process (GO:0006200)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|skeletal muscle contraction (GO:0003009)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|myosin light chain binding (GO:0032027)|structural constituent of muscle (GO:0008307)			NS(3)|breast(8)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(61)|ovary(3)|prostate(3)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	134						CCTTGGGCTTCTGGAAGTTGG	0.517									Trismus-Pseudocamptodactyly Syndrome with Cardiac Myxoma and Freckling				C|||	88	0.0175719	0.0666	0.0	5008	,	,		18938	0.0		0.0	False		,,,				2504	0.0				p.Q567Q		Atlas-SNP	.											.	MYH8	346	.	0			c.G1701A						PASS	.	C		288,4118	158.5+/-191.2	12,264,1927	119.0	118.0	118.0		1701	3.3	1.0	17	dbSNP_131	118	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MYH8	NM_002472.2		12,265,6226	TT,TC,CC		0.0116,6.5365,2.2221		567/1938	10312792	289,12717	2203	4300	6503	SO:0001819	synonymous_variant	4626	exon16	Familial Cancer Database	Carney Complex Variant	GGGCTTCTGGAAG		CCDS11153.1	17p13.1	2013-09-19	2006-09-29		ENSG00000133020	ENSG00000133020		"""Myosins / Myosin superfamily : Class II"""	7578	protein-coding gene	gene with protein product		160741	"""myosin, heavy polypeptide 8, skeletal muscle, perinatal"""			2373371	Standard	NM_002472		Approved	MyHC-peri, MyHC-pn	uc002gmm.2	P13535	OTTHUMG00000130361	ENST00000403437.2:c.1701G>A	17.37:g.10312792C>T		316.0	0.0	0		251.0	134.0	0.533865	NM_002472	Q14910	Silent	SNP	ENST00000403437.2	37	CCDS11153.1																																																																																			C|0.976;T|0.024	0.024	strong		0.517	MYH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252724.2	NM_002472	
KRTAP26-1	388818	hgsc.bcm.edu	37	21	31692173	31692173	+	Missense_Mutation	SNP	C	C	T	rs78165499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31692173C>T	ENST00000360542.3	-	1	434	c.181G>A	c.(181-183)Ggt>Agt	p.G61S		NM_203405.1	NP_981950.1	Q6PEX3	KR261_HUMAN	keratin associated protein 26-1	61						intermediate filament (GO:0005882)				endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16						GTTGGTTCACCGCAGGTCTCT	0.572													C|||	49	0.00978435	0.0325	0.0029	5008	,	,		19017	0.003		0.0	False		,,,				2504	0.001				p.G61S		Atlas-SNP	.											.	KRTAP26-1	58	.	0			c.G181A						PASS	.	C	SER/GLY	143,4263	101.2+/-139.8	1,141,2061	115.0	113.0	113.0		181	-0.3	0.0	21	dbSNP_131	113	0,8600		0,0,4300	yes	missense	KRTAP26-1	NM_203405.1	56	1,141,6361	TT,TC,CC		0.0,3.2456,1.0995	benign	61/211	31692173	143,12863	2203	4300	6503	SO:0001583	missense	388818	exon1			GTTCACCGCAGGT	AB096936	CCDS13588.1	21q22.11	2007-11-23			ENSG00000197683	ENSG00000197683		"""Keratin associated proteins"""	33760	protein-coding gene	gene with protein product							Standard	NM_203405		Approved		uc002ynw.3	Q6PEX3	OTTHUMG00000057766	ENST00000360542.3:c.181G>A	21.37:g.31692173C>T	ENSP00000353742:p.Gly61Ser	231.0	0.0	0		196.0	114.0	0.581633	NM_203405	B0RZD3	Missense_Mutation	SNP	ENST00000360542.3	37	CCDS13588.1	21	0.009615384615384616	16	0.032520325203252036	2	0.0055248618784530384	3	0.005244755244755245	0	0.0	C	5.629	0.300713	0.10678	0.032456	0.0	ENSG00000197683	ENST00000360542	T	0.03242	4.0	5.01	-0.306	0.12780	.	1.404840	0.04481	N	0.377750	T	0.00936	0.0031	N	0.19112	0.55	0.09310	N	1	B	0.21753	0.06	B	0.22753	0.041	T	0.45469	-0.9259	10	0.42905	T	0.14	2.1832	3.3195	0.07045	0.1879:0.4114:0.0:0.4007	.	61	Q6PEX3	KR261_HUMAN	S	61	ENSP00000353742:G61S	ENSP00000353742:G61S	G	-	1	0	KRTAP26-1	30614044	0.000000	0.05858	0.000000	0.03702	0.960000	0.62799	-0.293000	0.08320	0.113000	0.18004	0.655000	0.94253	GGT	C|0.988;T|0.012	0.012	strong		0.572	KRTAP26-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128218.1	NM_203405	
E2F4	1874	hgsc.bcm.edu	37	16	67229827	67229827	+	Silent	SNP	C	C	T	rs3730404	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67229827C>T	ENST00000379378.3	+	7	1010	c.951C>T	c.(949-951)agC>agT	p.S317S		NM_001950.3	NP_001941.2	Q16254	E2F4_HUMAN	E2F transcription factor 4, p107/p130-binding	317	Poly-Ser.				blood circulation (GO:0008015)|cell volume homeostasis (GO:0006884)|cilium assembly (GO:0042384)|epithelial cell development (GO:0002064)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of cell size (GO:0008361)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|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)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			breast(4)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)	11		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000697)|Epithelial(162;0.00303)|all cancers(182;0.0325)		gcagcagcagcagcagcaaca	0.612													C|||	311	0.0621006	0.1762	0.0086	5008	,	,		18005	0.003		0.003	False		,,,				2504	0.0675				p.S317S		Atlas-SNP	.											.	E2F4	25	.	0			c.C951T						PASS	.	-		587,3809	256.1+/-261.0	39,509,1650	47.0	50.0	49.0		951	0.5	1.0	16	dbSNP_107	49	7,8591	3.7+/-12.6	0,7,4292	no	coding-synonymous	E2F4	NM_001950.3		39,516,5942	TT,TC,CC		0.0814,13.353,4.5713		317/414	67229827	594,12400	2198	4299	6497	SO:0001819	synonymous_variant	1874	exon7			CAGCAGCAGCAGC	BC021050	CCDS32464.1	16q22.1	2014-05-06			ENSG00000205250	ENSG00000205250			3118	protein-coding gene	gene with protein product		600659				7958924, 7892279	Standard	NM_001950		Approved	E2F-4	uc002erz.3	Q16254	OTTHUMG00000172975	ENST00000379378.3:c.951C>T	16.37:g.67229827C>T		118.0	0.0	0		115.0	63.0	0.547826	NM_001950	A6NGR8|B5BU56|Q12991|Q15328	Silent	SNP	ENST00000379378.3	37	CCDS32464.1																																																																																			C|0.949;T|0.051	0.051	strong		0.612	E2F4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421565.1	NM_001950	
PCDHB14	56122	hgsc.bcm.edu	37	5	140604694	140604694	+	Silent	SNP	G	G	A	rs76971158	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140604694G>A	ENST00000239449.4	+	1	1617	c.1617G>A	c.(1615-1617)ccG>ccA	p.P539P	PCDHB14_ENST00000515856.2_Silent_p.P386P	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	539	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCGGGTCCCCGGCGTTGAGCA	0.672													g|||	132	0.0263578	0.0946	0.0086	5008	,	,		16525	0.0		0.001	False		,,,				2504	0.0				p.P539P	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											PCDHB14,caecum,carcinoma,0,1	PCDHB14	132	1	0			c.G1617A						PASS	.	G		301,4105		7,287,1909	51.0	57.0	55.0		1617	-4.4	0.6	5	dbSNP_131	55	4,8592		0,4,4294	no	coding-synonymous	PCDHB14	NM_018934.2		7,291,6203	AA,AG,GG		0.0465,6.8316,2.3458		539/799	140604694	305,12697	2203	4298	6501	SO:0001819	synonymous_variant	56122	exon1			GTCCCCGGCGTTG	AF152493	CCDS4256.1	5q31	2010-01-26			ENSG00000120327	ENSG00000120327		"""Cadherins / Protocadherins : Clustered"""	8685	other	protocadherin		606340				10380929	Standard	NM_018934		Approved	PCDH-BETA14	uc003ljb.3	Q9Y5E9	OTTHUMG00000129619	ENST00000239449.4:c.1617G>A	5.37:g.140604694G>A		194.0	0.0	0		247.0	119.0	0.481781	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Silent	SNP	ENST00000239449.4	37	CCDS4256.1																																																																																			G|0.978;A|0.022	0.022	strong		0.672	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934	
TTF2	8458	hgsc.bcm.edu	37	1	117618024	117618024	+	Missense_Mutation	SNP	G	G	C	rs17036832	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:117618024G>C	ENST00000369466.4	+	5	862	c.818G>C	c.(817-819)aGc>aCc	p.S273T		NM_003594.3	NP_003585.3	Q9UNY4	TTF2_HUMAN	transcription termination factor, RNA polymerase II	273					ATP catabolic process (GO:0006200)|DNA-templated transcription, termination (GO:0006353)|mRNA processing (GO:0006397)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)	cytoplasm (GO:0005737)|spliceosomal complex (GO:0005681)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|liver(1)|lung(24)|ovary(1)|prostate(2)|skin(2)|urinary_tract(2)	50	Lung SC(450;0.225)	all_cancers(81;4.23e-06)|all_epithelial(167;3.65e-07)|all_lung(203;2.81e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0553)|Colorectal(144;0.179)|LUSC - Lung squamous cell carcinoma(189;0.19)		AACTCAATAAGCAAGCCCCAG	0.473													G|||	125	0.0249601	0.09	0.0072	5008	,	,		19352	0.0		0.001	False		,,,				2504	0.0				p.S273T		Atlas-SNP	.											.	TTF2	92	.	0			c.G818C						PASS	.	G	THR/SER	262,4144	143.8+/-178.8	17,228,1958	98.0	109.0	105.0		818	-1.2	0.0	1	dbSNP_123	105	5,8595	4.3+/-15.6	0,5,4295	yes	missense	TTF2	NM_003594.3	58	17,233,6253	CC,CG,GG		0.0581,5.9464,2.0529	benign	273/1163	117618024	267,12739	2203	4300	6503	SO:0001583	missense	8458	exon5			CAATAAGCAAGCC	AF073771	CCDS892.1	1p13.1	2014-02-18			ENSG00000116830	ENSG00000116830			12398	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 6"""	604718				9748214	Standard	NM_003594		Approved	HuF2, ZGRF6	uc001egy.3	Q9UNY4	OTTHUMG00000012030	ENST00000369466.4:c.818G>C	1.37:g.117618024G>C	ENSP00000358478:p.Ser273Thr	120.0	0.0	0		118.0	58.0	0.491525	NM_003594	A8K4Q2|O75921|Q5T2K7|Q5VVU8|Q8N6I8	Missense_Mutation	SNP	ENST00000369466.4	37	CCDS892.1	49	0.022435897435897436	45	0.09146341463414634	4	0.011049723756906077	0	0.0	0	0.0	G	10.55	1.380822	0.24944	0.059464	5.81E-4	ENSG00000116830	ENST00000369466	D	0.86956	-2.19	5.13	-1.21	0.09524	.	0.471757	0.18081	N	0.152313	T	0.61974	0.2390	L	0.56769	1.78	0.09310	N	1	B;B	0.20052	0.002;0.041	B;B	0.14578	0.003;0.011	T	0.48502	-0.9030	10	0.24483	T	0.36	-0.004	1.0168	0.01509	0.3182:0.2659:0.2795:0.1364	rs17036832;rs52826473;rs17036832	273;273	Q9UNY4;Q9UNY4-2	TTF2_HUMAN;.	T	273	ENSP00000358478:S273T	ENSP00000358478:S273T	S	+	2	0	TTF2	117419547	0.000000	0.05858	0.005000	0.12908	0.093000	0.18481	-0.924000	0.03996	-0.081000	0.12662	0.655000	0.94253	AGC	A|0.000;C|0.019;G|0.980	0.019	strong		0.473	TTF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033277.3		
ADAMTS8	11095	hgsc.bcm.edu	37	11	130284495	130284495	+	Silent	SNP	C	C	T	rs142963990	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:130284495C>T	ENST00000257359.6	-	5	2203	c.1497G>A	c.(1495-1497)acG>acA	p.T499T		NM_007037.4	NP_008968.4	Q9UP79	ATS8_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 8	499	Disintegrin.				negative regulation of cell proliferation (GO:0008285)|phosphate ion transmembrane transport (GO:0035435)	proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)|low-affinity phosphate transmembrane transporter activity (GO:0009673)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	10	all_hematologic(175;0.0429)	Lung NSC(97;0.000601)|Breast(109;0.000962)|all_lung(97;0.00125)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.039)|Lung(977;0.213)		GCCCGCACGGCGTGCCGTCAG	0.662													C|||	20	0.00399361	0.0151	0.0	5008	,	,		17513	0.0		0.0	False		,,,				2504	0.0				p.T499T		Atlas-SNP	.											.	ADAMTS8	172	.	0			c.G1497A						PASS	.	C		53,3979		0,53,1963	48.0	54.0	52.0		1497	-11.2	0.2	11	dbSNP_134	52	0,8342		0,0,4171	no	coding-synonymous	ADAMTS8	NM_007037.4		0,53,6134	TT,TC,CC		0.0,1.3145,0.4283		499/890	130284495	53,12321	2016	4171	6187	SO:0001819	synonymous_variant	11095	exon5			GCACGGCGTGCCG	AF060153	CCDS41732.1	11q25	2008-07-18	2005-08-19		ENSG00000134917	ENSG00000134917		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	224	protein-coding gene	gene with protein product		605175	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 8"""			10438512	Standard	NM_007037		Approved	METH2, FLJ41712, ADAM-TS8	uc001qgg.4	Q9UP79	OTTHUMG00000165656	ENST00000257359.6:c.1497G>A	11.37:g.130284495C>T		258.0	1.0	0.00387597		271.0	127.0	0.468635	NM_007037	Q9NZS0	Silent	SNP	ENST00000257359.6	37	CCDS41732.1																																																																																			C|0.996;T|0.004	0.004	strong		0.662	ADAMTS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385636.1	NM_007037	
TF	7018	hgsc.bcm.edu	37	3	133486988	133486988	+	Silent	SNP	C	C	T	rs7845	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:133486988C>T	ENST00000402696.3	+	13	2087	c.1602C>T	c.(1600-1602)taC>taT	p.Y534Y	TF_ENST00000264998.3_Silent_p.Y407Y	NM_001063.3	NP_001054	P02787	TRFE_HUMAN	transferrin	534	Transferrin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00741}.				blood coagulation (GO:0007596)|cellular iron ion homeostasis (GO:0006879)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|retina homeostasis (GO:0001895)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|basal plasma membrane (GO:0009925)|blood microparticle (GO:0072562)|cell surface (GO:0009986)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|early endosome (GO:0005769)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|secretory granule lumen (GO:0034774)|vesicle (GO:0031982)	ferric iron binding (GO:0008199)			NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(7)|large_intestine(13)|liver(2)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49					Aluminium(DB01370)|Bismuth Subsalicylate(DB01294)|Gallium nitrate(DB05260)|Iron Dextran(DB00893)	AGGGATACTACGGCTACACAG	0.448													C|||	71	0.0141773	0.0522	0.0029	5008	,	,		19620	0.0		0.0	False		,,,				2504	0.0				p.Y534Y		Atlas-SNP	.											.	TF	116	.	0			c.C1602T						PASS	.	C		174,4232	113.3+/-151.4	5,164,2034	81.0	83.0	82.0		1602	-2.4	1.0	3	dbSNP_52	82	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TF	NM_001063.3		5,166,6332	TT,TC,CC		0.0233,3.9492,1.3532		534/699	133486988	176,12830	2203	4300	6503	SO:0001819	synonymous_variant	7018	exon13			ATACTACGGCTAC		CCDS3080.1	3q21	2012-10-02			ENSG00000091513	ENSG00000091513			11740	protein-coding gene	gene with protein product		190000				6585826	Standard	NM_001063		Approved	PRO1557, PRO2086	uc003epv.2	P02787	OTTHUMG00000150356	ENST00000402696.3:c.1602C>T	3.37:g.133486988C>T		78.0	0.0	0		81.0	36.0	0.444444	NM_001063	O43890|Q1HBA5|Q9NQB8|Q9UHV0	Silent	SNP	ENST00000402696.3	37	CCDS3080.1																																																																																			C|0.985;G|0.000;T|0.015	0.015	strong		0.448	TF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317775.1	NM_001063	
CYP4F12	66002	hgsc.bcm.edu	37	19	15795939	15795939	+	Silent	SNP	A	A	G	rs61729075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15795939A>G	ENST00000550308.1	+	9	1427	c.1047A>G	c.(1045-1047)gaA>gaG	p.E349E	CYP4F12_ENST00000324632.10_Silent_p.E349E	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	349					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	GGCACCCAGAATACCAGGAGC	0.582													.|||	99	0.0197684	0.0711	0.0058	5008	,	,		18068	0.0		0.001	False		,,,				2504	0.0				p.E349E		Atlas-SNP	.											.	CYP4F12	89	.	0			c.A1047G						PASS	.	G		383,4023		7,369,1827	66.0	62.0	63.0		1047	-0.9	1.0	19	dbSNP_129	63	3,8597		0,3,4297	no	coding-synonymous	CYP4F12	NM_023944.3		7,372,6124	GG,GA,AA		0.0349,8.6927,2.9679		349/525	15795939	386,12620	2203	4300	6503	SO:0001819	synonymous_variant	66002	exon9			CCCAGAATACCAG	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.1047A>G	19.37:g.15795939A>G		157.0	0.0	0		258.0	71.0	0.275194	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Silent	SNP	ENST00000550308.1	37	CCDS42517.1																																																																																			A|0.981;G|0.019	0.019	strong		0.582	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
ZDHHC1	29800	hgsc.bcm.edu	37	16	67440289	67440289	+	Silent	SNP	C	C	T	rs8058306	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67440289C>T	ENST00000348579.2	-	3	407	c.66G>A	c.(64-66)acG>acA	p.T22T		NM_013304.2	NP_037436.1	Q8WTX9	ZDHC1_HUMAN	zinc finger, DHHC-type containing 1	22					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|urinary_tract(1)	10		Ovarian(137;0.223)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0178)|all cancers(182;5.71e-53)|Epithelial(162;4.73e-52)|OV - Ovarian serous cystadenocarcinoma(108;1.53e-29)|Kidney(780;4.37e-05)|BRCA - Breast invasive adenocarcinoma(181;5.8e-05)|GBM - Glioblastoma multiforme(240;0.0022)		GTGCCGGTGCCGTCCACACAC	0.622													C|||	361	0.0720847	0.205	0.013	5008	,	,		17815	0.003		0.003	False		,,,				2504	0.0767				p.T22T		Atlas-SNP	.											.	ZDHHC1	28	.	0			c.G66A						PASS	.	C		710,3678		52,606,1536	26.0	23.0	24.0		66	-9.3	0.1	16	dbSNP_116	24	11,8577		0,11,4283	no	coding-synonymous	ZDHHC1	NM_013304.2		52,617,5819	TT,TC,CC		0.1281,16.1805,5.5564		22/486	67440289	721,12255	2194	4294	6488	SO:0001819	synonymous_variant	29800	exon3			CGGTGCCGTCCAC	U90653	CCDS10836.1	16q22.1	2010-03-25	2003-01-27		ENSG00000159714	ENSG00000159714		"""Zinc fingers, DHHC-type"""	17916	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 1"""	C16orf1		10395086	Standard	NM_013304		Approved	HSU90653, ZNF377	uc010vjm.2	Q8WTX9	OTTHUMG00000137522	ENST00000348579.2:c.66G>A	16.37:g.67440289C>T		138.0	0.0	0		161.0	71.0	0.440994	NM_013304	O15461	Silent	SNP	ENST00000348579.2	37	CCDS10836.1																																																																																			C|0.924;T|0.076	0.076	strong		0.622	ZDHHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268845.1	NM_013304	
MUC4	4585	hgsc.bcm.edu	37	3	195515030	195515030	+	Missense_Mutation	SNP	C	C	A	rs538504516	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195515030C>A	ENST00000463781.3	-	2	3880	c.3421G>T	c.(3421-3423)Gac>Tac	p.D1141Y	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D1141Y	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	608					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGAAGTGTCGGTGACAGGA	0.572													.|||	4	0.000798722	0.0015	0.0	5008	,	,		15001	0.0		0.001	False		,,,				2504	0.001				p.D1141Y		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	0			c.G3421T						scavenged	.						8.0	6.0	7.0					3																	195515030		651	1358	2009	SO:0001583	missense	4585	exon2			AAGTGTCGGTGAC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3421G>T	3.37:g.195515030C>A	ENSP00000417498:p.Asp1141Tyr	143.0	0.0	0		436.0	23.0	0.0527523	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	.	.	.	.	.	.	.	.	.	.	-	1.771	-0.484381	0.04383	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34859	1.34;1.34	0.663	-1.33	0.09172	.	.	.	.	.	T	0.32882	0.0844	N	0.14661	0.345	0.09310	N	1	D	0.69078	0.997	D	0.72982	0.979	T	0.19192	-1.0313	8	.	.	.	.	3.7507	0.08565	0.214:0.2493:0.5366:0.0	.	1141	E7ESK3	.	Y	1141	ENSP00000417498:D1141Y;ENSP00000420243:D1141Y	.	D	-	1	0	MUC4	196999425	0.000000	0.05858	0.000000	0.03702	0.066000	0.16364	-2.687000	0.00833	-1.284000	0.02390	0.064000	0.15345	GAC	.	.	none		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CFC1	55997	hgsc.bcm.edu	37	2	131356322	131356322	+	Missense_Mutation	SNP	C	C	T	rs201431919	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:131356322C>T	ENST00000259216.4	-	3	402	c.140G>A	c.(139-141)cGa>cAa	p.R47Q		NM_032545.3	NP_115934.1	P0CG37	CFC1_HUMAN	cripto, FRL-1, cryptic family 1	47					determination of left/right symmetry (GO:0007368)|gastrulation (GO:0007369)|nodal signaling pathway (GO:0038092)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)	nodal binding (GO:0038100)			endometrium(1)|lung(4)	5	Colorectal(110;0.1)					CGGTGACTGTCGGTGCTTCTG	0.537													c|||	372	0.0742812	0.2663	0.0259	5008	,	,		16561	0.0		0.002	False		,,,				2504	0.0				p.R47Q		Atlas-SNP	.											CFC1,fourth_ventricle,glioma,0,1	.	.	1	0			c.G140A	GRCh37	CM023185	CFC1	M		PASS	.						15.0	23.0	21.0					2																	131356322		2174	4254	6428	SO:0001583	missense	653275	exon3			GACTGTCGGTGCT	AF312769	CCDS2162.1, CCDS74573.1, CCDS74574.1	2q21.2	2014-02-04			ENSG00000136698	ENSG00000136698			18292	protein-coding gene	gene with protein product		605194	"""heterotaxy 2 (autosomal dominant)"""	HTX2		11062482, 10858660	Standard	NM_032545		Approved	CRYPTIC, HTX2	uc002tro.2	P0CG37	OTTHUMG00000131628	ENST00000259216.4:c.140G>A	2.37:g.131356322C>T	ENSP00000259216:p.Arg47Gln	1076.0	0.0	0		797.0	540.0	0.677541	NM_001079530	B2RCY0|B9EJD3|Q53T05|Q9GZR3	Missense_Mutation	SNP	ENST00000259216.4	37	CCDS2162.1	101	0.04624542124542125	92	0.18699186991869918	9	0.024861878453038673	0	0.0	0	0.0	.	0.054	-1.241061	0.01493	.	.	ENSG00000136698	ENST00000259216	D	0.88818	-2.43	1.91	0.598	0.17512	.	0.638739	0.14771	N	0.299398	T	0.00109	0.0003	N	0.00197	-1.87	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22836	-1.0205	10	0.07030	T	0.85	-32.4582	1.7088	0.02888	0.2856:0.1859:0.0:0.5285	.	47	P0CG37	CFC1_HUMAN	Q	47	ENSP00000259216:R47Q	ENSP00000259216:R47Q	R	-	2	0	CFC1	131072792	0.006000	0.16342	0.003000	0.11579	0.092000	0.18411	0.487000	0.22356	-0.207000	0.10187	-0.665000	0.03846	CGA	C|0.969;T|0.031	0.031	strong		0.537	CFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333367.1	NM_032545	
MSLN	10232	hgsc.bcm.edu	37	16	815593	815593	+	Missense_Mutation	SNP	G	G	C	rs115279916	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:815593G>C	ENST00000382862.3	+	9	866	c.771G>C	c.(769-771)caG>caC	p.Q257H	MSLN_ENST00000566549.1_Missense_Mutation_p.Q257H|MSLN_ENST00000563941.1_Missense_Mutation_p.Q257H|MSLN_ENST00000545450.2_Missense_Mutation_p.Q257H	NM_013404.4	NP_037536.2	Q13421	MSLN_HUMAN	mesothelin	257					cell adhesion (GO:0007155)|pancreas development (GO:0031016)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(2)|kidney(2)|lung(11)|pancreas(1)|prostate(1)|skin(3)	20		Hepatocellular(780;0.00335)				TGCTGGGCCAGCCCATCATCC	0.706													G|||	81	0.0161741	0.059	0.0043	5008	,	,		14281	0.0		0.0	False		,,,				2504	0.0				p.Q257H		Atlas-SNP	.											.	MSLN	109	.	0			c.G771C						PASS	.	G	HIS/GLN,HIS/GLN,HIS/GLN	207,4145	119.2+/-156.9	5,197,1974	31.0	32.0	32.0		771,771,771	1.0	0.0	16	dbSNP_132	32	1,8569	1.2+/-3.3	0,1,4284	yes	missense,missense,missense	MSLN	NM_001177355.1,NM_005823.5,NM_013404.4	24,24,24	5,198,6258	CC,CG,GG		0.0117,4.7564,1.6097	benign,benign,benign	257/623,257/623,257/631	815593	208,12714	2176	4285	6461	SO:0001583	missense	10232	exon10			GGGCCAGCCCATC	U40434	CCDS32356.1, CCDS45370.1	16p13.3	2008-04-16			ENSG00000102854	ENSG00000102854			7371	protein-coding gene	gene with protein product		601051				7665620, 8552591	Standard	NM_005823		Approved	CAK1, MPF	uc002cjw.2	Q13421	OTTHUMG00000047992	ENST00000382862.3:c.771G>C	16.37:g.815593G>C	ENSP00000372313:p.Gln257His	60.0	0.0	0		117.0	65.0	0.555556	NM_005823	D3DU65|Q14859|Q4VQD5|Q96GR6|Q96KJ5|Q9BR17|Q9BTR2|Q9UCB2|Q9UK57	Missense_Mutation	SNP	ENST00000382862.3	37	CCDS32356.1	24	0.01098901098901099	22	0.044715447154471545	2	0.0055248618784530384	0	0.0	0	0.0	G	2.785	-0.252545	0.05829	0.047564	1.17E-4	ENSG00000102854	ENST00000446427;ENST00000445361;ENST00000545450;ENST00000382862	T;T	0.12569	2.67;2.67	3.03	1.03	0.20045	.	1.781050	0.03402	N	0.203448	T	0.01489	0.0048	N	0.25647	0.755	0.09310	N	1	B;B;B;B	0.15141	0.007;0.008;0.012;0.007	B;B;B;B	0.12156	0.004;0.007;0.007;0.004	T	0.30119	-0.9989	10	0.39692	T	0.17	-0.1169	4.9829	0.14175	0.2994:0.0:0.7006:0.0	.	256;257;257;257	Q13421-4;Q13421;Q13421-2;Q13421-3	.;MSLN_HUMAN;.;.	H	257	ENSP00000442965:Q257H;ENSP00000372313:Q257H	ENSP00000372313:Q257H	Q	+	3	2	MSLN	755594	0.001000	0.12720	0.000000	0.03702	0.003000	0.03518	0.687000	0.25407	0.060000	0.16281	-0.271000	0.10264	CAG	G|0.985;C|0.015	0.015	strong		0.706	MSLN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109253.2		
MUC17	140453	hgsc.bcm.edu	37	7	100678693	100678693	+	Silent	SNP	T	T	C	rs78176991	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100678693T>C	ENST00000306151.4	+	3	4060	c.3996T>C	c.(3994-3996)taT>taC	p.Y1332Y		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1332	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					CCTCAACTTATAGTGAAGGAA	0.448																																					p.Y1332Y		Atlas-SNP	.											.	MUC17	804	.	0			c.T3996C						PASS	.						241.0	232.0	235.0					7																	100678693		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			AACTTATAGTGAA	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.3996T>C	7.37:g.100678693T>C		148.0	0.0	0		144.0	16.0	0.111111	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			T|0.994;C|0.006	0.006	strong		0.448	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
CCAR2	57805	hgsc.bcm.edu	37	8	22473646	22473646	+	Missense_Mutation	SNP	A	A	C	rs143150726	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22473646A>C	ENST00000308511.4	+	14	1979	c.1730A>C	c.(1729-1731)gAg>gCg	p.E577A	RP11-582J16.5_ENST00000521025.1_RNA|CCAR2_ENST00000389279.3_Missense_Mutation_p.E577A|CCAR2_ENST00000520861.1_Missense_Mutation_p.E252A			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	577					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mRNA processing (GO:0006397)|negative regulation of catalytic activity (GO:0043086)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage checkpoint (GO:2000003)|regulation of circadian rhythm (GO:0042752)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of protein stability (GO:0031647)|response to UV (GO:0009411)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|DBIRD complex (GO:0044609)|mitochondrial matrix (GO:0005759)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)										GAGAAGGAGGAGGCGGCCAAG	0.532													A|||	11	0.00219649	0.0045	0.0	5008	,	,		17062	0.003		0.0	False		,,,				2504	0.002				p.E577A		Atlas-SNP	.											.	KIAA1967	72	.	0			c.A1730C						PASS	.	A	ALA/GLU	14,4392	22.3+/-47.3	0,14,2189	91.0	87.0	88.0		1730	4.2	1.0	8	dbSNP_134	88	1,8599	1.2+/-3.3	0,1,4299	yes	missense	KIAA1967	NM_021174.5	107	0,15,6488	CC,CA,AA		0.0116,0.3177,0.1153	probably-damaging	577/924	22473646	15,12991	2203	4300	6503	SO:0001583	missense	57805	exon14			AGGAGGAGGCGGC	AL834351	CCDS34863.1	8p22	2013-08-22	2013-08-22	2013-08-22		ENSG00000158941			23360	protein-coding gene	gene with protein product	"""deleted in breast cancer"""	607359	"""KIAA1967"""	KIAA1967		12370419	Standard	NM_021174		Approved	DBC-1, DBC1, NET35	uc003xci.3	Q8N163		ENST00000308511.4:c.1730A>C	8.37:g.22473646A>C	ENSP00000310670:p.Glu577Ala	113.0	0.0	0		116.0	44.0	0.37931	NM_021174	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Missense_Mutation	SNP	ENST00000308511.4	37	CCDS34863.1	5	0.0022893772893772895	2	0.0040650406504065045	0	0.0	3	0.005244755244755245	0	0.0	A	15.25	2.777147	0.49786	0.003177	1.16E-4	ENSG00000158941	ENST00000308511;ENST00000389279;ENST00000520861	T;T;T	0.34667	1.37;1.37;1.35	5.41	4.24	0.50183	.	0.332894	0.27991	N	0.017029	T	0.16557	0.0398	N	0.19112	0.55	0.37034	D	0.896847	B;B	0.14805	0.011;0.007	B;B	0.16722	0.016;0.004	T	0.09840	-1.0656	10	0.23302	T	0.38	-22.2627	10.6868	0.45848	0.8393:0.1607:0.0:0.0	.	252;577	G3V119;Q8N163	.;K1967_HUMAN	A	577;577;252	ENSP00000310670:E577A;ENSP00000373930:E577A;ENSP00000429773:E252A	ENSP00000310670:E577A	E	+	2	0	KIAA1967	22529591	1.000000	0.71417	0.972000	0.41901	0.846000	0.48090	4.106000	0.57804	1.041000	0.40125	0.460000	0.39030	GAG	A|0.998;C|0.002	0.002	strong		0.532	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174	
GBE1	2632	hgsc.bcm.edu	37	3	81586149	81586149	+	Silent	SNP	G	G	A	rs2229520	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:81586149G>A	ENST00000429644.2	-	13	2359	c.1716C>T	c.(1714-1716)gaC>gaT	p.D572D	GBE1_ENST00000489715.1_Silent_p.D531D	NM_000158.3	NP_000149	Q04446	GLGB_HUMAN	glucan (1,4-alpha-), branching enzyme 1	572					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	1,4-alpha-glucan branching enzyme activity (GO:0003844)|cation binding (GO:0043169)|hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)			breast(1)|endometrium(5)|large_intestine(2)|lung(4)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18		Lung NSC(201;0.0117)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0654)|Epithelial(33;0.00305)|LUSC - Lung squamous cell carcinoma(29;0.00646)|BRCA - Breast invasive adenocarcinoma(55;0.00813)|Lung(72;0.0129)|KIRC - Kidney renal clear cell carcinoma(39;0.212)|Kidney(39;0.247)		GAAGAAGGTCGTCGTCAGTTA	0.413									Glycogen Storage Disease, type IV				A|||	77	0.0153754	0.0552	0.0058	5008	,	,		16494	0.0		0.0	False		,,,				2504	0.0				p.D572D		Atlas-SNP	.											.	GBE1	111	.	0			c.C1716T						PASS	.	A		195,3489		3,189,1650	114.0	110.0	111.0		1716	0.1	1.0	3	dbSNP_98	111	2,8168		0,2,4083	no	coding-synonymous	GBE1	NM_000158.3		3,191,5733	AA,AG,GG		0.0245,5.2932,1.6619		572/703	81586149	197,11657	1842	4085	5927	SO:0001819	synonymous_variant	2632	exon13	Familial Cancer Database	Andersen Disease, Brancher deficiency	AAGGTCGTCGTCA		CCDS54612.1	3p12.2	2013-09-20	2008-08-01		ENSG00000114480	ENSG00000114480	2.4.1.18		4180	protein-coding gene	gene with protein product	"""glycogen branching enzyme"", ""Andersen disease"", ""glycogen storage disease type IV"""	607839				8463281	Standard	NM_000158		Approved		uc021xav.1	Q04446	OTTHUMG00000158978	ENST00000429644.2:c.1716C>T	3.37:g.81586149G>A		107.0	0.0	0		127.0	49.0	0.385827	NM_000158	B3KWV3|Q96EN0	Silent	SNP	ENST00000429644.2	37	CCDS54612.1																																																																																			G|0.987;A|0.013	0.013	strong		0.413	GBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352760.2		
IFT140	9742	hgsc.bcm.edu	37	16	1634225	1634225	+	Missense_Mutation	SNP	G	G	A	rs8060532	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1634225G>A	ENST00000426508.2	-	11	1715	c.1352C>T	c.(1351-1353)gCc>gTc	p.A451V	IFT140_ENST00000439987.2_5'UTR|LA16c-395F10.2_ENST00000563162.1_RNA	NM_014714.3	NP_055529.2	Q96RY7	IF140_HUMAN	intraflagellar transport 140	451			A -> V (in dbSNP:rs8060532).		cilium assembly (GO:0042384)|intraciliary retrograde transport (GO:0035721)|protein localization to cilium (GO:0061512)|regulation of cilium assembly (GO:1902017)|renal system development (GO:0072001)|retina development in camera-type eye (GO:0060041)|skeletal system morphogenesis (GO:0048705)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|intraciliary transport particle A (GO:0030991)|photoreceptor connecting cilium (GO:0032391)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(12)|lung(10)|ovary(5)|pancreas(1)|prostate(4)|skin(4)|stomach(2)|urinary_tract(1)	53		Hepatocellular(780;0.219)				CACCTTGGTGGCAAACACTCC	0.632													G|||	129	0.0257588	0.0961	0.0029	5008	,	,		17110	0.0		0.0	False		,,,				2504	0.0				p.A451V		Atlas-SNP	.											.	IFT140	128	.	0			c.C1352T						PASS	.	G	VAL/ALA	393,4005	194.0+/-219.0	19,355,1825	41.0	34.0	36.0		1352	1.4	0.6	16	dbSNP_116	36	2,8598	1.2+/-3.3	0,2,4298	yes	missense	IFT140	NM_014714.3	64	19,357,6123	AA,AG,GG		0.0233,8.9359,3.0389	benign	451/1463	1634225	395,12603	2199	4300	6499	SO:0001583	missense	9742	exon11			TTGGTGGCAAACA	AB011162	CCDS10439.1	16p13.3	2014-07-03	2014-07-03	2005-11-02	ENSG00000187535	ENSG00000187535		"""Intraflagellar transport homologs"", ""WD repeat domain containing"""	29077	protein-coding gene	gene with protein product		614620	"""WD and tetratricopeptide repeats 2"", ""intraflagellar transport 140 homolog (Chlamydomonas)"""	WDTC2		9628581	Standard	NM_014714		Approved	gs114, KIAA0590	uc002cmb.3	Q96RY7	OTTHUMG00000128585	ENST00000426508.2:c.1352C>T	16.37:g.1634225G>A	ENSP00000406012:p.Ala451Val	41.0	0.0	0		43.0	24.0	0.55814	NM_014714	A2A2A8|D3DU75|O60332|Q9UG52	Missense_Mutation	SNP	ENST00000426508.2	37	CCDS10439.1	55	0.025183150183150184	54	0.10975609756097561	1	0.0027624309392265192	0	0.0	0	0.0	G	0.024	-1.389209	0.01185	0.089359	2.33E-4	ENSG00000187535	ENST00000397417;ENST00000426508;ENST00000439987	T	0.58210	0.35	5.51	1.37	0.22104	.	0.719273	0.14508	N	0.315333	T	0.00754	0.0025	L	0.43923	1.385	0.26845	N	0.968287	B;B	0.18461	0.009;0.028	B;B	0.21360	0.007;0.034	T	0.08973	-1.0696	10	0.02654	T	1	.	8.7453	0.34583	0.3607:0.0:0.6392:0.0	rs8060532;rs8060532	451;176	Q96RY7;B4DR58	IF140_HUMAN;.	V	451	ENSP00000406012:A451V	ENSP00000380562:A451V	A	-	2	0	IFT140	1574226	1.000000	0.71417	0.621000	0.29145	0.082000	0.17680	4.038000	0.57318	0.105000	0.17753	-0.150000	0.13652	GCC	G|0.969;A|0.031	0.031	strong		0.632	IFT140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250438.2	NM_014714	
PRPH2	5961	hgsc.bcm.edu	37	6	42689940	42689940	+	Missense_Mutation	SNP	G	G	A	rs61755770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42689940G>A	ENST00000230381.5	-	1	372	c.133C>T	c.(133-135)Ctc>Ttc	p.L45F		NM_000322.4	NP_000313.2	P23942	PRPH2_HUMAN	peripherin 2 (retinal degeneration, slow)	45			L -> F (in RP7; in combination with a null mutation of ROM1; dbSNP:rs61755770).		cell adhesion (GO:0007155)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	18	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.00178)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0904)			CTCTTTCGGAGTTCAATCTTC	0.512													G|||	30	0.00599042	0.0212	0.0029	5008	,	,		20575	0.0		0.0	False		,,,				2504	0.0				p.L45F		Atlas-SNP	.											.	PRPH2	47	.	0			c.C133T	GRCh37	CM951114	PRPH2	M	rs61755770	PASS	.	G	PHE/LEU	68,4338	61.7+/-98.7	0,68,2135	109.0	93.0	98.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	133	4.7	1.0	6	dbSNP_129	98	0,8600		0,0,4300	yes	missense	PRPH2	NM_000322.4	22	0,68,6435	AA,AG,GG		0.0,1.5433,0.5228	probably-damaging	45/347	42689940	68,12938	2203	4300	6503	SO:0001583	missense	5961	exon1			TTCGGAGTTCAAT		CCDS4871.1	6p21.1	2013-09-20	2006-11-23	2006-11-23	ENSG00000112619	ENSG00000112619		"""Tetraspanins"""	9942	protein-coding gene	gene with protein product	retinal peripherin	179605	"""retinal degeneration, slow (retinitis pigmentosa 7)"", ""retinal degeneration, slow"""	RP7, RDS		1749427	Standard	NM_000322		Approved	TSPAN22, rd2, CACD2	uc003osk.3	P23942	OTTHUMG00000014701	ENST00000230381.5:c.133C>T	6.37:g.42689940G>A	ENSP00000230381:p.Leu45Phe	94.0	0.0	0		121.0	68.0	0.561983	NM_000322	Q5TFH5|Q6DK65	Missense_Mutation	SNP	ENST00000230381.5	37	CCDS4871.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	G	20.2	3.948475	0.73787	0.015433	0.0	ENSG00000112619	ENST00000230381	T	0.80393	-1.37	5.61	4.71	0.59529	.	0.000000	0.85682	D	0.000000	D	0.87845	0.6280	M	0.85859	2.78	0.58432	D	0.999991	D	0.60160	0.987	D	0.66497	0.944	D	0.87105	0.2181	10	0.40728	T	0.16	.	15.9296	0.79648	0.0:0.0:0.8645:0.1355	rs61755770	45	P23942	PRPH2_HUMAN	F	45	ENSP00000230381:L45F	ENSP00000230381:L45F	L	-	1	0	PRPH2	42797918	1.000000	0.71417	0.951000	0.38953	0.943000	0.58893	6.097000	0.71452	2.631000	0.89168	0.655000	0.94253	CTC	G|0.994;A|0.006	0.006	strong		0.512	PRPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040556.1	NM_000322	
DCTN1	1639	hgsc.bcm.edu	37	2	74597937	74597937	+	Missense_Mutation	SNP	G	G	T	rs13420401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74597937G>T	ENST00000361874.3	-	10	1176	c.859C>A	c.(859-861)Ctg>Atg	p.L287M	DCTN1_ENST00000409240.1_Missense_Mutation_p.L250M|DCTN1_ENST00000407639.2_Missense_Mutation_p.L153M|DCTN1_ENST00000409567.3_Missense_Mutation_p.L267M|DCTN1_ENST00000409438.1_Missense_Mutation_p.L153M|DCTN1_ENST00000495643.1_5'Flank|DCTN1_ENST00000409868.1_Missense_Mutation_p.L270M|DCTN1_ENST00000394003.3_Missense_Mutation_p.L280M	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	287			L -> M (in dbSNP:rs13420401).		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|G2/M transition of mitotic cell cycle (GO:0000086)|melanosome transport (GO:0032402)|microtubule-based transport (GO:0010970)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nervous system development (GO:0007399)	cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|dynein complex (GO:0030286)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(1)|skin(3)	45						TTTGCCTCCAGCGCCTCCTTG	0.567													G|||	229	0.0457268	0.1649	0.0159	5008	,	,		21252	0.0		0.0	False		,,,				2504	0.0				p.L287M		Atlas-SNP	.											.	DCTN1	110	.	0			c.C859A						PASS	.	G	MET/LEU,MET/LEU,MET/LEU,MET/LEU,MET/LEU,MET/LEU	604,3802	264.1+/-265.8	38,528,1637	99.0	96.0	97.0		799,457,748,838,859,457	3.5	0.7	2	dbSNP_121	97	6,8594	3.7+/-12.6	0,6,4294	yes	missense,missense,missense,missense,missense,missense	DCTN1	NM_001135040.2,NM_001135041.2,NM_001190836.1,NM_001190837.1,NM_004082.4,NM_023019.3	15,15,15,15,15,15	38,534,5931	TT,TG,GG		0.0698,13.7086,4.6901	benign,benign,benign,benign,benign,benign	267/1254,153/1140,250/1237,280/1272,287/1279,153/1145	74597937	610,12396	2203	4300	6503	SO:0001583	missense	1639	exon10			CCTCCAGCGCCTC		CCDS1939.1, CCDS46341.1, CCDS46342.1, CCDS54368.1, CCDS54369.1	2p13	2014-09-17	2010-06-24		ENSG00000204843	ENSG00000204843			2711	protein-coding gene	gene with protein product	"""p150 glued homolog (Drosophila)"""	601143	"""dynactin 1 (p150, Glued (Drosophila) homolog)"""			1828535	Standard	NM_001190836		Approved		uc002skx.3	Q14203	OTTHUMG00000129963	ENST00000361874.3:c.859C>A	2.37:g.74597937G>T	ENSP00000354791:p.Leu287Met	113.0	0.0	0		138.0	73.0	0.528986	NM_004082	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Missense_Mutation	SNP	ENST00000361874.3	37	CCDS1939.1	85	0.03891941391941392	79	0.16056910569105692	6	0.016574585635359115	0	0.0	0	0.0	G	10.70	1.423353	0.25639	0.137086	6.98E-4	ENSG00000204843	ENST00000361874;ENST00000394003;ENST00000393999;ENST00000407639;ENST00000409438;ENST00000409240;ENST00000409868;ENST00000409567	T;T;T;T;T;T;T	0.79845	-0.86;-1.08;-0.79;-0.79;-1.31;-1.04;-1.09	5.66	3.48	0.39840	.	0.000000	0.33792	N	0.004541	T	0.00784	0.0026	M	0.75264	2.295	0.30403	P	0.7798160000000001	B;B;B;B;P;B	0.35575	0.204;0.245;0.034;0.129;0.51;0.057	B;B;B;B;B;B	0.32624	0.049;0.049;0.007;0.043;0.149;0.015	T	0.37798	-0.9690	9	0.33940	T	0.23	-5.9903	8.5044	0.33179	0.0832:0.0:0.6425:0.2743	rs13420401;rs58339203	267;250;287;280;153;153	E9PGE1;E9PFS5;Q14203;A8MY36;Q14203-2;G5E9H4	.;.;DCTN1_HUMAN;.;.;.	M	287;280;270;153;153;250;270;267	ENSP00000354791:L287M;ENSP00000377571:L280M;ENSP00000384844:L153M;ENSP00000387270:L153M;ENSP00000386406:L250M;ENSP00000387327:L270M;ENSP00000386843:L267M	ENSP00000354791:L287M	L	-	1	2	DCTN1	74451445	0.680000	0.27605	0.708000	0.30435	0.947000	0.59692	0.896000	0.28377	1.345000	0.45676	0.655000	0.94253	CTG	G|0.954;T|0.046	0.046	strong		0.567	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082	
PPP1R26	9858	hgsc.bcm.edu	37	9	138378308	138378308	+	Missense_Mutation	SNP	G	G	A	rs35142799	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:138378308G>A	ENST00000356818.2	+	4	2501	c.1952G>A	c.(1951-1953)gGc>gAc	p.G651D	PPP1R26_ENST00000604351.1_Missense_Mutation_p.G651D|PPP1R26_ENST00000602993.1_Intron|PPP1R26_ENST00000605660.1_Missense_Mutation_p.G651D|PPP1R26_ENST00000401470.3_Missense_Mutation_p.G651D|PPP1R26_ENST00000605286.1_Missense_Mutation_p.G651D	NM_014811.3	NP_055626.3	Q5T8A7	PPR26_HUMAN	protein phosphatase 1, regulatory subunit 26	651					negative regulation of phosphatase activity (GO:0010923)	nucleus (GO:0005634)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										GGAGGGGAGGGCACCGCCAGG	0.652													G|||	36	0.0071885	0.0272	0.0	5008	,	,		17736	0.0		0.0	False		,,,				2504	0.0				p.G651D		Atlas-SNP	.											.	.	.	.	0			c.G1952A						PASS	.	G	ASP/GLY	100,4300	73.1+/-111.1	1,98,2101	29.0	33.0	31.0		1952	0.7	0.0	9	dbSNP_126	31	0,8600		0,0,4300	no	missense	KIAA0649	NM_014811.3	94	1,98,6401	AA,AG,GG		0.0,2.2727,0.7692	benign	651/1210	138378308	100,12900	2200	4300	6500	SO:0001583	missense	9858	exon4			GGGAGGGCACCGC	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.1952G>A	9.37:g.138378308G>A	ENSP00000349274:p.Gly651Asp	120.0	0.0	0		147.0	107.0	0.727891	NM_014811	Q86WU0|Q8WVV0|Q9Y4D3	Missense_Mutation	SNP	ENST00000356818.2	37	CCDS6988.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	3.546	-0.092690	0.07053	0.022727	0.0	ENSG00000196422	ENST00000356818	T	0.20738	2.05	4.34	0.693	0.18056	.	0.864323	0.09973	N	0.732016	T	0.07143	0.0181	L	0.29908	0.895	0.09310	N	1	B	0.16396	0.017	B	0.12156	0.007	T	0.26189	-1.0110	10	0.52906	T	0.07	-15.8819	6.8421	0.23969	0.1852:0.6278:0.187:0.0	rs35142799	651	Q5T8A7	PPR26_HUMAN	D	651	ENSP00000349274:G651D	ENSP00000349274:G651D	G	+	2	0	KIAA0649	137518129	0.060000	0.20803	0.001000	0.08648	0.006000	0.05464	1.152000	0.31663	0.249000	0.21456	0.561000	0.74099	GGC	G|0.994;A|0.006	0.006	strong		0.652	PPP1R26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054987.1	NM_014811	
DNAJC13	23317	hgsc.bcm.edu	37	3	132218075	132218075	+	Missense_Mutation	SNP	C	C	T	rs61748102	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:132218075C>T	ENST00000260818.6	+	37	4510	c.4262C>T	c.(4261-4263)gCg>gTg	p.A1421V		NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	1421					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						TTGTTGCCTGCGGCTACAGAG	0.438													C|||	64	0.0127796	0.0242	0.0101	5008	,	,		18844	0.0		0.0209	False		,,,				2504	0.0041				p.A1421V		Atlas-SNP	.											.	DNAJC13	253	.	0			c.C4262T						PASS	.	C	VAL/ALA	112,4294	88.7+/-127.4	0,112,2091	93.0	93.0	93.0		4262	5.4	1.0	3	dbSNP_129	93	162,8438	76.0+/-138.7	1,160,4139	yes	missense	DNAJC13	NM_015268.3	64	1,272,6230	TT,TC,CC		1.8837,2.542,2.1067	probably-damaging	1421/2244	132218075	274,12732	2203	4300	6503	SO:0001583	missense	23317	exon37			TGCCTGCGGCTAC	AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"""Heat shock proteins / DNAJ (HSP40)"""	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.4262C>T	3.37:g.132218075C>T	ENSP00000260818:p.Ala1421Val	142.0	0.0	0		148.0	66.0	0.445946	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	37	CCDS33857.1	36	0.016483516483516484	13	0.026422764227642278	6	0.016574585635359115	0	0.0	17	0.022427440633245383	C	34	5.360586	0.95877	0.02542	0.018837	ENSG00000138246	ENST00000260818;ENST00000538066	T	0.52754	0.65	5.42	5.42	0.78866	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.44030	0.1274	M	0.81802	2.56	0.80722	D	1	D	0.71674	0.998	P	0.56648	0.803	T	0.64698	-0.6346	10	0.72032	D	0.01	.	19.5793	0.95459	0.0:1.0:0.0:0.0	rs61748102	1421	O75165	DJC13_HUMAN	V	1421;68	ENSP00000260818:A1421V	ENSP00000260818:A1421V	A	+	2	0	DNAJC13	133700765	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	7.535000	0.82014	2.706000	0.92434	0.555000	0.69702	GCG	C|0.981;T|0.019	0.019	strong		0.438	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268	
PHIP	55023	hgsc.bcm.edu	37	6	79700648	79700648	+	Silent	SNP	C	C	T	rs149171291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:79700648C>T	ENST00000275034.4	-	20	2423	c.2256G>A	c.(2254-2256)agG>agA	p.R752R		NM_017934.5	NP_060404	Q8WWQ0	PHIP_HUMAN	pleckstrin homology domain interacting protein	752					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(10)|kidney(4)|large_intestine(20)|lung(20)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	68		all_cancers(76;0.00125)|Acute lymphoblastic leukemia(125;1.1e-05)|all_hematologic(105;0.00117)|all_epithelial(107;0.219)		BRCA - Breast invasive adenocarcinoma(397;0.231)		TCTCTTCTGACCTGTAAGTCT	0.313													C|||	10	0.00199681	0.0068	0.0014	5008	,	,		17543	0.0		0.0	False		,,,				2504	0.0				p.R752R		Atlas-SNP	.											.	PHIP	177	.	0			c.G2256A						PASS	.	C		29,4377	35.2+/-66.4	0,29,2174	110.0	110.0	110.0		2256	-0.4	1.0	6	dbSNP_134	110	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	PHIP	NM_017934.5		0,30,6472	TT,TC,CC		0.0116,0.6582,0.2307		752/1822	79700648	30,12974	2203	4299	6502	SO:0001819	synonymous_variant	55023	exon20			TTCTGACCTGTAA	AF310250	CCDS4987.1	6q14	2013-01-09			ENSG00000146247	ENSG00000146247		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	15673	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 14"""	612870		WDR11		11018022	Standard	NM_017934		Approved	ndrp, FLJ20705, DCAF14, BRWD2	uc003pir.3	Q8WWQ0	OTTHUMG00000015071	ENST00000275034.4:c.2256G>A	6.37:g.79700648C>T		243.0	1.0	0.00411523		220.0	101.0	0.459091	NM_017934	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Silent	SNP	ENST00000275034.4	37	CCDS4987.1																																																																																			C|0.997;T|0.003	0.003	strong		0.313	PHIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041297.2		
NLRC3	197358	hgsc.bcm.edu	37	16	3613239	3613239	+	RNA	SNP	C	C	T	rs8057436	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3613239C>T	ENST00000301749.7	-	0	2104				NLRC3_ENST00000324659.8_RNA|NLRC3_ENST00000603507.1_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000448023.2_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						CAGTGCAACACGTTGATGGCC	0.706													C|||	189	0.0377396	0.1331	0.0144	5008	,	,		16561	0.0		0.001	False		,,,				2504	0.002				p.V567M		Atlas-SNP	.											.	NLRC3	103	.	0			c.G1699A						PASS	.	C	MET/VAL	433,3803		13,407,1698	12.0	15.0	14.0		1699	-7.5	0.0	16	dbSNP_116	14	27,8409		0,27,4191	yes	missense	NLRC3	NM_178844.2	21	13,434,5889	TT,TC,CC		0.3201,10.2219,3.6301	benign	567/1066	3613239	460,12212	2118	4218	6336			197358	exon5			GCAACACGTTGAT	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"""Nucleotide-binding domain and leucine rich repeat containing"""	29889	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3"", ""NOD-like receptor C3"""	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3613239C>T		24.0	0.0	0		32.0	20.0	0.625	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Missense_Mutation	SNP	ENST00000301749.7	37		69	0.03159340659340659	61	0.12398373983739837	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	C	2.395	-0.338967	0.05243	0.102219	0.003201	ENSG00000167984	ENST00000419350;ENST00000301749;ENST00000359128;ENST00000448023;ENST00000324659	D;D;D;D	0.85556	-2.0;-2.0;-2.0;-2.0	5.1	-7.47	0.01365	.	0.710025	0.13675	N	0.370619	T	0.03011	0.0089	.	.	.	0.09310	N	1	B	0.23650	0.089	B	0.20577	0.03	T	0.23691	-1.0181	9	0.46703	T	0.11	.	11.4138	0.49941	0.0:0.2375:0.0978:0.6647	rs8057436;rs8057436	614	C9JLH9	.	M	567;567;567;614;549	ENSP00000301749:V567M;ENSP00000352039:V567M;ENSP00000414415:V614M;ENSP00000323897:V549M	ENSP00000301749:V567M	V	-	1	0	NLRC3	3553240	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.154000	0.00580	-1.430000	0.01985	-0.812000	0.03155	GTG	C|0.969;T|0.031	0.031	strong		0.706	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844	
OR1F1	4992	hgsc.bcm.edu	37	16	3254622	3254622	+	Missense_Mutation	SNP	G	G	A	rs8045183	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3254622G>A	ENST00000304646.2	+	1	376	c.376G>A	c.(376-378)Gtg>Atg	p.V126M	AJ003147.9_ENST00000576468.1_RNA	NM_012360.1	NP_036492.1	O43749	OR1F1_HUMAN	olfactory receptor, family 1, subfamily F, member 1	126			V -> M (in dbSNP:rs8045183).		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)			breast(1)|endometrium(1)|large_intestine(2)|lung(7)	11						CTTTGTCGCCGTGTGCCACCC	0.502													g|||	159	0.0317492	0.115	0.0086	5008	,	,		24960	0.0		0.001	False		,,,				2504	0.0				p.V126M		Atlas-SNP	.											.	OR1F1	36	.	0			c.G376A						PASS	.	A	MET/VAL	402,3992	199.4+/-223.0	11,380,1806	220.0	175.0	190.0		376	-6.7	0.0	16	dbSNP_116	190	7,8593	5.7+/-21.5	0,7,4293	no	missense	OR1F1	NM_012360.1	21	11,387,6099	AA,AG,GG		0.0814,9.1488,3.1476	possibly-damaging	126/313	3254622	409,12585	2197	4300	6497	SO:0001583	missense	4992	exon1			GTCGCCGTGTGCC	Y14442	CCDS10496.1	16p13.3	2012-08-09			ENSG00000168124	ENSG00000168124		"""GPCR / Class A : Olfactory receptors"""	8194	protein-coding gene	gene with protein product		603232		OR1F4, OR1F6, OR1F7, OR1F8, OR1F9, OR1F5, OR1F10, OR1F13P		9288094, 9500546	Standard	NM_012360		Approved	Olfmf, OR16-36, OR16-37, OR16-88, OR16-89, OR16-90, OLFMF, OR3-145	uc010uwu.2	O43749	OTTHUMG00000133153	ENST00000304646.2:c.376G>A	16.37:g.3254622G>A	ENSP00000305424:p.Val126Met	243.0	1.0	0.00411523		250.0	126.0	0.504	NM_012360	O15246|Q6IFL5	Missense_Mutation	SNP	ENST00000304646.2	37	CCDS10496.1	68	0.031135531135531136	65	0.13211382113821138	3	0.008287292817679558	0	0.0	0	0.0	G	13.94	2.388405	0.42308	0.091488	8.14E-4	ENSG00000168124	ENST00000304646	T	0.49432	0.78	5.27	-6.68	0.01778	GPCR, rhodopsin-like superfamily (1);	0.893841	0.09289	N	0.822529	T	0.00695	0.0023	M	0.72118	2.19	0.80722	P	0.0	D	0.55800	0.973	P	0.51135	0.66	T	0.48714	-0.9011	9	0.87932	D	0	.	10.8187	0.46591	0.7188:0.1085:0.1727:0.0	rs8045183;rs52799876;rs8045183	126	O43749	OR1F1_HUMAN	M	126	ENSP00000305424:V126M	ENSP00000305424:V126M	V	+	1	0	OR1F1	3194623	0.418000	0.25440	0.000000	0.03702	0.630000	0.37929	0.957000	0.29215	-1.050000	0.03230	0.393000	0.25936	GTG	G|0.966;A|0.034	0.034	strong		0.502	OR1F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206985.1		
PKD1L2	114780	hgsc.bcm.edu	37	16	81232426	81232426	+	RNA	SNP	A	A	C	rs9934856	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:81232426A>C	ENST00000525539.1	-	0	1383				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						CCAAGCTCCAAATGGTCAGAA	0.557													A|||	101	0.0201677	0.0734	0.0058	5008	,	,		20314	0.0		0.0	False		,,,				2504	0.0				p.L462V		Atlas-SNP	.											.	PKD1L2	361	.	0			c.T1384G						PASS	.	A	VAL/LEU,VAL/LEU	224,3784		6,212,1786	128.0	131.0	130.0		1384,1384	-7.3	0.0	16	dbSNP_119	130	0,8340		0,0,4170	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	32,32	6,212,5956	CC,CA,AA		0.0,5.5888,1.8141	benign,benign	462/992,462/2460	81232426	224,12124	2004	4170	6174			114780	exon7			GCTCCAAATGGTC	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81232426A>C		245.0	0.0	0		203.0	111.0	0.546798	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	A	2.456	-0.325238	0.05350	0.055888	0.0	ENSG00000166473	ENST00000337114	T	0.01304	5.03	4.77	-7.3	0.01446	Egg jelly receptor, REJ-like (1);	0.379301	0.24776	N	0.035687	T	0.00144	0.0004	.	.	.	0.09310	N	1	B;B	0.15473	0.013;0.001	B;B	0.19666	0.026;0.002	T	0.44498	-0.9324	9	0.23302	T	0.38	-1.4298	11.0124	0.47669	0.1809:0.5054:0.3137:0.0	rs9934856;rs52821211;rs56414767;rs9934856	462;462	Q7Z442-3;Q7Z442	.;PK1L2_HUMAN	V	462	ENSP00000337397:L462V	ENSP00000337397:L462V	L	-	1	2	PKD1L2	79789927	0.000000	0.05858	0.001000	0.08648	0.041000	0.13682	-0.318000	0.08050	-1.278000	0.02408	-1.249000	0.01516	TTG	A|0.984;C|0.016;G|0.000	0.016	strong		0.557	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
GAB4	128954	hgsc.bcm.edu	37	22	17447237	17447237	+	Silent	SNP	C	C	G	rs115898475	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:17447237C>G	ENST00000400588.1	-	6	1148	c.1041G>C	c.(1039-1041)gtG>gtC	p.V347V	GAB4_ENST00000523144.1_5'Flank	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	347										breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(24)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44		all_epithelial(15;0.112)|Lung NSC(13;0.248)				CTGACAGGCCCACAAGCGTTC	0.527													C|||	31	0.0061901	0.0227	0.0014	5008	,	,		21894	0.0		0.0	False		,,,				2504	0.0				p.V347V		Atlas-SNP	.											.	GAB4	95	.	0			c.G1041C						PASS	.	C		72,3902		0,72,1915	26.0	28.0	28.0		1041	1.7	0.2	22	dbSNP_132	28	0,8384		0,0,4192	no	coding-synonymous	GAB4	NM_001037814.1		0,72,6107	GG,GC,CC		0.0,1.8118,0.5826		347/575	17447237	72,12286	1987	4192	6179	SO:0001819	synonymous_variant	128954	exon6			CAGGCCCACAAGC	AK057252	CCDS42976.1	22q11.2	2013-01-10			ENSG00000215568	ENSG00000215568		"""Pleckstrin homology (PH) domain containing"""	18325	protein-coding gene	gene with protein product							Standard	NM_001037814		Approved		uc002zlw.3	Q2WGN9	OTTHUMG00000149992	ENST00000400588.1:c.1041G>C	22.37:g.17447237C>G		64.0	0.0	0		55.0	33.0	0.6	NM_001037814		Silent	SNP	ENST00000400588.1	37	CCDS42976.1																																																																																			C|0.994;G|0.006	0.006	strong		0.527	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882	
TICAM2	353376	hgsc.bcm.edu	37	5	114916763	114916763	+	Missense_Mutation	SNP	C	C	T	rs113049216	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:114916763C>T	ENST00000427199.2	-	2	632	c.191G>A	c.(190-192)aGc>aAc	p.S64N	TMED7-TICAM2_ENST00000282382.4_Missense_Mutation_p.S233N|TMED7-TICAM2_ENST00000333314.3_3'UTR|TICAM2_ENST00000408996.4_Missense_Mutation_p.S233N|TICAM2_ENST00000513729.1_5'Flank	NM_021649.6	NP_067681.1	Q86XR7	TCAM2_HUMAN	toll-like receptor adaptor molecule 2	64					cellular response to lipopolysaccharide (GO:0071222)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of chemokine (C-C motif) ligand 5 production (GO:0071650)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|positive regulation of chemokine (C-C motif) ligand 5 production (GO:0071651)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-18-mediated signaling pathway (GO:2000494)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|response to interleukin-12 (GO:0070671)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRAM-dependent toll-like receptor 4 signaling pathway (GO:0035669)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)|signal transducer activity (GO:0004871)			cervix(1)|kidney(1)|lung(2)|soft_tissue(1)	5		all_cancers(142;0.0223)|all_epithelial(76;0.000869)|Prostate(80;0.0115)|Ovarian(225;0.156)		OV - Ovarian serous cystadenocarcinoma(64;4.38e-07)|Epithelial(69;1.62e-06)|all cancers(49;6.93e-05)		CTCTTCCACGCTCTGAGCTCC	0.463													C|||	56	0.0111821	0.0408	0.0014	5008	,	,		18559	0.0		0.001	False		,,,				2504	0.0				p.S233N		Atlas-SNP	.											.	.	.	.	0			c.G698A						PASS	.	C	ASN/SER,,ASN/SER	167,4237	111.6+/-149.8	2,163,2037	289.0	294.0	293.0		698,,191	-0.3	0.0	5	dbSNP_132	293	0,8600		0,0,4300	yes	missense,utr-3,missense	TICAM2,TMED7-TICAM2	NM_001164468.2,NM_001164469.2,NM_021649.6	46,,46	2,163,6337	TT,TC,CC		0.0,3.792,1.2842	,,	233/405,,64/236	114916763	167,12837	2202	4300	6502	SO:0001583	missense	100302736	exon4			TCCACGCTCTGAG	AY232653	CCDS4119.1	5q22.3	2012-11-21			ENSG00000243414	ENSG00000243414			21354	protein-coding gene	gene with protein product		608321					Standard	NM_021649		Approved	TRAM, TICAM-2, TIRP		Q86XR7	OTTHUMG00000162905	ENST00000427199.2:c.191G>A	5.37:g.114916763C>T	ENSP00000415139:p.Ser64Asn	122.0	0.0	0		148.0	68.0	0.459459	NM_001164468	B3Y698|Q6JUT2	Missense_Mutation	SNP	ENST00000427199.2	37	CCDS4119.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	C	11.76	1.736040	0.30774	0.03792	0.0	ENSG00000243414;ENSG00000243414;ENSG00000251201	ENST00000408996;ENST00000427199;ENST00000282382	T;T	0.23348	1.91;1.91	5.14	-0.31	0.12765	.	1.924210	0.03117	N	0.163224	T	0.03739	0.0106	N	0.14661	0.345	0.09310	N	1	B;B	0.14012	0.009;0.009	B;B	0.14023	0.006;0.01	T	0.22277	-1.0221	10	0.21540	T	0.41	.	10.3083	0.43693	0.2337:0.2165:0.5498:0.0	.	233;64	Q6JUT2;Q86XR7	.;TCAM2_HUMAN	N	233;64;233	ENSP00000386341:S233N;ENSP00000282382:S233N	ENSP00000415139:S64N	S	-	2	0	TICAM2;TMED7-TICAM2	114944662	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.694000	0.01915	-0.079000	0.12707	0.585000	0.79938	AGC	C|0.989;T|0.011	0.011	strong		0.463	TICAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338755.1	NM_021649	
PPAN	56342	hgsc.bcm.edu	37	19	10221804	10221804	+	Missense_Mutation	SNP	G	G	T	rs200927331	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:10221804G>T	ENST00000253107.7	+	12	1491	c.1385G>T	c.(1384-1386)gGc>gTc	p.G462V	PPAN_ENST00000393793.1_Missense_Mutation_p.G409V|SNORD105B_ENST00000458770.1_RNA|PPAN-P2RY11_ENST00000393796.4_Intron|P2RY11_ENST00000321826.4_5'Flank|PPAN_ENST00000556468.1_Intron|PPAN-P2RY11_ENST00000428358.1_Intron	NM_020230.5	NP_064615.3	Q9NQ55	SSF1_HUMAN	peter pan homolog (Drosophila)	462					RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(3)|liver(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	15			OV - Ovarian serous cystadenocarcinoma(20;2.19e-08)|Epithelial(33;1.76e-05)|all cancers(31;3.54e-05)			GGTGGGCGAGGCCGGGGCCGG	0.701													G|||	6	0.00119808	0.0045	0.0	5008	,	,		11572	0.0		0.0	False		,,,				2504	0.0				p.G462V		Atlas-SNP	.											.	PPAN	43	.	0			c.G1385T						PASS	.	G	,,VAL/GLY	13,4349		0,13,2168	8.0	10.0	9.0		,,1385	2.9	0.0	19		9	0,8536		0,0,4268	no	intron,intron,missense	PPAN,PPAN-P2RY11	NM_001040664.2,NM_001198690.1,NM_020230.5	,,109	0,13,6436	TT,TG,GG		0.0,0.298,0.1008	,,	,,462/474	10221804	13,12885	2181	4268	6449	SO:0001583	missense	56342	exon12			GGCGAGGCCGGGG	BC033202	CCDS12225.1	19p13.2	2008-02-05	2001-11-28		ENSG00000130810	ENSG00000130810			9227	protein-coding gene	gene with protein product		607793	"""peter pan (Drosophila) homolog"""			10873382	Standard	NM_020230		Approved	SSF1, SSF2, SSF, BXDC3		Q9NQ55	OTTHUMG00000156826	ENST00000253107.7:c.1385G>T	19.37:g.10221804G>T	ENSP00000253107:p.Gly462Val	8.0	0.0	0		14.0	7.0	0.5	NM_020230	C9J3F9|Q9BW97|Q9H170	Missense_Mutation	SNP	ENST00000253107.7	37	CCDS12225.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.74|10.74	1.436723|1.436723	0.25900|0.25900	0.00298|0.00298	0.0|0.0	ENSG00000130810|ENSG00000130810	ENST00000444703|ENST00000253107;ENST00000342696;ENST00000393793	.|T;T	.|0.28454	.|1.61;1.61	3.98|3.98	2.93|2.93	0.34026|0.34026	.|.	.|.	.|.	.|.	.|.	T|T	0.24431|0.24431	0.0592|0.0592	L|L	0.29908|0.29908	0.895|0.895	0.40426|0.40426	D|D	0.979893|0.979893	.|P	.|0.52316	.|0.952	.|P	.|0.46585	.|0.521	T|T	0.02450|0.02450	-1.1157|-1.1157	5|9	.|0.36615	.|T	.|0.2	.|.	8.2265|8.2265	0.31572|0.31572	0.1174:0.0:0.8826:0.0|0.1174:0.0:0.8826:0.0	.|.	.|462	.|Q9NQ55	.|SSF1_HUMAN	S|V	197|462;449;409	.|ENSP00000253107:G462V;ENSP00000377382:G409V	.|ENSP00000253107:G462V	A|G	+|+	1|2	0|0	PPAN|PPAN	10082804|10082804	0.477000|0.477000	0.25909|0.25909	0.002000|0.002000	0.10522|0.10522	0.002000|0.002000	0.02628|0.02628	1.932000|1.932000	0.40143|0.40143	0.975000|0.975000	0.38392|0.38392	-0.258000|-0.258000	0.10820|0.10820	GCC|GGC	.	.	weak		0.701	PPAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316658.1	NM_020230	
SIRPB1	10326	hgsc.bcm.edu	37	20	1546906	1546906	+	Silent	SNP	C	C	T	rs11907593	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1546906C>T	ENST00000381605.4	-	5	1156	c.1092G>A	c.(1090-1092)gcG>gcA	p.A364A	SIRPB1_ENST00000381603.3_Silent_p.A147A|RP4-576H24.4_ENST00000564763.1_Intron|SIRPB1_ENST00000262929.5_Silent_p.A146A	NM_006065.3	NP_006056.2	O00241	SIRB1_HUMAN	signal-regulatory protein beta 1	364					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						TAGGAGCCAGCGCTGCTTCTG	0.607													.|||	92	0.0183706	0.0666	0.0058	5008	,	,		16446	0.0		0.0	False		,,,				2504	0.0				p.A364A		Atlas-SNP	.											.	SIRPB1	83	.	0			c.G1092A						PASS	.	C	,	172,4234		4,164,2035	42.0	35.0	38.0		441,1092	-6.0	0.0	20	dbSNP_120	38	4,8592		0,4,4294	no	coding-synonymous,coding-synonymous	SIRPB1	NM_001083910.2,NM_006065.3	,	4,168,6329	TT,TC,CC		0.0465,3.9038,1.3536	,	147/182,364/399	1546906	176,12826	2203	4298	6501	SO:0001819	synonymous_variant	10326	exon5			AGCCAGCGCTGCT	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.1092G>A	20.37:g.1546906C>T		71.0	0.0	0		73.0	51.0	0.69863	NM_006065	A6NLM2|B2R8V0|Q5TFQ9|Q5TFR0|Q8TB12|Q9H1U5|Q9Y4V0	Silent	SNP	ENST00000381605.4	37	CCDS13019.1																																																																																			C|0.984;T|0.016	0.016	strong		0.607	SIRPB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077555.2	NM_006065	
DGKZ	8525	hgsc.bcm.edu	37	11	46388024	46388024	+	Missense_Mutation	SNP	G	G	A	rs11827702	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:46388024G>A	ENST00000454345.1	+	2	343	c.218G>A	c.(217-219)cGg>cAg	p.R73Q	DGKZ_ENST00000343674.6_Intron|DGKZ_ENST00000525434.1_3'UTR|DGKZ_ENST00000543978.1_Intron|DGKZ_ENST00000532868.2_Intron|DGKZ_ENST00000421244.2_Intron|DGKZ_ENST00000456247.2_Intron|DGKZ_ENST00000527911.1_Intron|DGKZ_ENST00000395574.3_Intron|DGKZ_ENST00000528615.1_Intron|DGKZ_ENST00000318201.8_Intron	NM_001105540.1	NP_001099010.1	Q13574	DGKZ_HUMAN	diacylglycerol kinase, zeta	73					blood coagulation (GO:0007596)|cell migration (GO:0016477)|intracellular signal transduction (GO:0035556)|lipid phosphorylation (GO:0046834)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of Ras protein signal transduction (GO:0046580)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|enzyme inhibitor activity (GO:0004857)|lipid kinase activity (GO:0001727)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)|protein C-terminus binding (GO:0008022)			central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(12)|pancreas(1)|prostate(1)|skin(1)	25				GBM - Glioblastoma multiforme(35;0.0259)|Lung(87;0.141)		TCCAGCCGCCGGCGCTCCAGC	0.701													G|||	204	0.0407348	0.1475	0.0101	5008	,	,		12532	0.0		0.001	False		,,,				2504	0.001				p.R73Q		Atlas-SNP	.											.	DGKZ	199	.	0			c.G218A						PASS	.	G	GLN/ARG,,,,,,	346,3634		8,330,1652	13.0	15.0	15.0		218,,,,,,	3.2	1.0	11	dbSNP_120	15	4,8270		0,4,4133	yes	missense,intron,intron,intron,intron,intron,intron	DGKZ	NM_001105540.1,NM_001199266.1,NM_001199267.1,NM_001199268.1,NM_003646.3,NM_201532.2,NM_201533.3	43,,,,,,	8,334,5785	AA,AG,GG		0.0483,8.6935,2.8562	possibly-damaging,,,,,,	73/1118,,,,,,	46388024	350,11904	1990	4137	6127	SO:0001583	missense	8525	exon2			GCCGCCGGCGCTC	U51477	CCDS7918.1, CCDS41640.1, CCDS44579.1, CCDS44580.1, CCDS55757.1, CCDS55758.1, CCDS55759.1, CCDS44579.2	11p11.2	2010-11-24	2010-11-24		ENSG00000149091	ENSG00000149091	2.7.1.107		2857	protein-coding gene	gene with protein product		601441	"""diacylglycerol kinase, zeta 104kDa"""			8626588	Standard	NM_003646		Approved	DAGK5, hDGKzeta, DGK-ZETA, DAGK6	uc001ncn.1	Q13574	OTTHUMG00000166437	ENST00000454345.1:c.218G>A	11.37:g.46388024G>A	ENSP00000412178:p.Arg73Gln	23.0	0.0	0		44.0	26.0	0.590909	NM_001105540	B7Z2M9|B7Z6M3|E9PPW4|F6UCU9|G3V0F6|J3KNJ6|O00542|Q6ZVG7|Q8IVW9	Missense_Mutation	SNP	ENST00000454345.1	37	CCDS41640.1	68	0.031135531135531136	63	0.12804878048780488	5	0.013812154696132596	0	0.0	0	0.0	G	23.1	4.371425	0.82573	0.086935	4.83E-4	ENSG00000149091	ENST00000454345	T	0.74002	-0.8	4.15	3.15	0.36227	.	2.389100	0.02186	N	0.060943	T	0.03520	0.0101	L	0.34521	1.04	0.80722	D	1	D	0.76494	0.999	P	0.61275	0.886	T	0.57745	-0.7758	10	0.72032	D	0.01	.	12.8442	0.57821	0.0:0.0:0.8362:0.1637	rs11827702	73	Q13574	DGKZ_HUMAN	Q	73	ENSP00000412178:R73Q	ENSP00000412178:R73Q	R	+	2	0	DGKZ	46344600	1.000000	0.71417	1.000000	0.80357	0.539000	0.34962	6.808000	0.75206	2.033000	0.60031	0.462000	0.41574	CGG	G|0.968;A|0.032	0.032	strong		0.701	DGKZ-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389772.1	NM_001105540	
GPR144	347088	hgsc.bcm.edu	37	9	127231765	127231765	+	Missense_Mutation	SNP	C	C	T	rs76434769|rs386738474	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:127231765C>T	ENST00000334810.1	+	16	2497	c.2497C>T	c.(2497-2499)Cgc>Tgc	p.R833C				Q7Z7M1	GP144_HUMAN	G protein-coupled receptor 144	833					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)			central_nervous_system(1)|endometrium(3)	4						CAGTGCCCGCCGCCGTGCCCG	0.642													C|||	88	0.0175719	0.0635	0.0058	5008	,	,		17409	0.0		0.0	False		,,,				2504	0.0				p.R833C		Atlas-SNP	.											.	GPR144	33	.	0			c.C2497T						PASS	.	C	CYS/ARG	110,1274		6,98,588	29.0	35.0	33.0		2497	4.2	1.0	9	dbSNP_131	33	1,3181		0,1,1590	yes	missense	GPR144	NM_001161808.1	180	6,99,2178	TT,TC,CC		0.0314,7.948,2.431	benign	833/964	127231765	111,4455	692	1591	2283	SO:0001583	missense	347088	exon16			GCCCGCCGCCGTG	AY278562		9q34.11	2014-08-08			ENSG00000180264	ENSG00000180264		"""-"", ""GPCR / Class B : Orphans"""	18651	protein-coding gene	gene with protein product							Standard	XM_006710216		Approved	PGR24	uc010mwn.3	Q7Z7M1	OTTHUMG00000020652	ENST00000334810.1:c.2497C>T	9.37:g.127231765C>T	ENSP00000335156:p.Arg833Cys	134.0	1.0	0.00746269		143.0	140.0	0.979021	NM_001161808	Q86SL4|Q8NH12	Missense_Mutation	SNP	ENST00000334810.1	37	CCDS48016.1	37	0.01694139194139194	35	0.07113821138211382	2	0.0055248618784530384	0	0.0	0	0.0	C	14.13	2.444880	0.43429	0.07948	3.14E-4	ENSG00000180264	ENST00000334810	T	0.40476	1.03	4.22	4.22	0.49857	GPCR, family 2-like (1);	.	.	.	.	T	0.03305	0.0096	M	0.80183	2.485	0.51767	D	0.999936	P	0.39847	0.691	B	0.38880	0.284	T	0.03017	-1.1082	9	0.52906	T	0.07	.	9.7035	0.40200	0.331:0.669:0.0:0.0	.	833	Q7Z7M1	GP144_HUMAN	C	833	ENSP00000335156:R833C	ENSP00000335156:R833C	R	+	1	0	GPR144	126271586	0.841000	0.29509	0.998000	0.56505	0.895000	0.52256	1.068000	0.30629	1.890000	0.54733	0.462000	0.41574	CGC	C|0.977;T|0.023	0.023	strong		0.642	GPR144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054026.2	NM_182611	
TMEM176A	55365	hgsc.bcm.edu	37	7	150500832	150500832	+	Missense_Mutation	SNP	C	C	T	rs76937000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150500832C>T	ENST00000484928.1	+	5	1048	c.467C>T	c.(466-468)tCg>tTg	p.S156L	TMEM176A_ENST00000461345.1_Missense_Mutation_p.S97L|TMEM176A_ENST00000004103.3_Missense_Mutation_p.S156L|TMEM176B_ENST00000447204.2_5'Flank			Q96HP8	T176A_HUMAN	transmembrane protein 176A	156					negative regulation of dendritic cell differentiation (GO:2001199)	integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|lung(7)|ovary(2)|stomach(1)	12			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		ATCTCCAGCTCGAGTGACTGG	0.517													C|||	100	0.0199681	0.0741	0.0029	5008	,	,		18259	0.0		0.0	False		,,,				2504	0.0				p.S156L		Atlas-SNP	.											.	TMEM176A	35	.	0			c.C467T						PASS	.	C	LEU/SER	286,4120	159.6+/-192.1	11,264,1928	64.0	66.0	65.0		467	1.5	0.0	7	dbSNP_131	65	3,8597	2.2+/-6.3	0,3,4297	yes	missense	TMEM176A	NM_018487.2	145	11,267,6225	TT,TC,CC		0.0349,6.4911,2.2221	possibly-damaging	156/236	150500832	289,12717	2203	4300	6503	SO:0001583	missense	55365	exon5			CCAGCTCGAGTGA	AF258340	CCDS5909.1	7q36.1	2006-09-04			ENSG00000002933	ENSG00000002933			24930	protein-coding gene	gene with protein product		610334				12097419, 8889548	Standard	NM_018487		Approved	HCA112	uc003whx.1	Q96HP8	OTTHUMG00000158114	ENST00000484928.1:c.467C>T	7.37:g.150500832C>T	ENSP00000417626:p.Ser156Leu	50.0	0.0	0		75.0	38.0	0.506667	NM_018487	D3DX00|Q9NYC7	Missense_Mutation	SNP	ENST00000484928.1	37	CCDS5909.1	38	0.0173992673992674	36	0.07317073170731707	2	0.0055248618784530384	0	0.0	0	0.0	C	9.342	1.063261	0.20067	0.064911	3.49E-4	ENSG00000002933	ENST00000484928;ENST00000004103;ENST00000461345;ENST00000475536;ENST00000468689	T;T;T;T;T	0.12774	3.16;3.16;2.65;2.85;4.31	2.47	1.51	0.23008	.	5.604390	0.00166	N	0.000010	T	0.00936	0.0031	M	0.64997	1.995	0.09310	N	1	P	0.44627	0.839	B	0.29663	0.105	T	0.34403	-0.9830	10	0.62326	D	0.03	-1.4451	6.1594	0.20356	0.301:0.699:0.0:0.0	.	156	Q96HP8	T176A_HUMAN	L	156;156;97;108;97	ENSP00000417626:S156L;ENSP00000004103:S156L;ENSP00000420818:S97L;ENSP00000417834:S108L;ENSP00000420081:S97L	ENSP00000004103:S156L	S	+	2	0	TMEM176A	150131765	0.000000	0.05858	0.006000	0.13384	0.003000	0.03518	-0.768000	0.04715	0.569000	0.29329	0.555000	0.69702	TCG	C|0.977;T|0.023	0.023	strong		0.517	TMEM176A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350222.1	NM_018487	
OR4A5	81318	hgsc.bcm.edu	37	11	51412370	51412370	+	Missense_Mutation	SNP	T	T	A	rs149177099	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:51412370T>A	ENST00000319760.6	-	1	78	c.26A>T	c.(25-27)gAa>gTa	p.E9V		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	9						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)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(28)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	49		all_lung(304;0.236)				GAGGACAAATTCTGTAATATT	0.423													.|||	42	0.00838658	0.0272	0.0086	5008	,	,		18603	0.0		0.0	False		,,,				2504	0.0				p.E9V		Atlas-SNP	.											OR4A5,NS,carcinoma,-1,1	OR4A5	116	1	0			c.A26T						PASS	.	T	VAL/GLU	130,4266		1,128,2069	28.0	27.0	27.0		26	2.0	0.3	11	dbSNP_134	27	6,8576		0,6,4285	no	missense	OR4A5	NM_001005272.3	121	1,134,6354	AA,AT,TT		0.0699,2.9572,1.0479	probably-damaging	9/316	51412370	136,12842	2198	4291	6489	SO:0001583	missense	81318	exon1			ACAAATTCTGTAA	AB065506	CCDS73289.1	11p11.12	2012-08-09			ENSG00000221840	ENSG00000221840		"""GPCR / Class A : Olfactory receptors"""	15162	protein-coding gene	gene with protein product							Standard	NM_001005272		Approved		uc001nhi.2	Q8NH83	OTTHUMG00000166764	ENST00000319760.6:c.26A>T	11.37:g.51412370T>A	ENSP00000367664:p.Glu9Val	94.0	0.0	0		88.0	38.0	0.431818	NM_001005272	Q6IF84	Missense_Mutation	SNP	ENST00000319760.6	37	CCDS31497.1	13	0.005952380952380952	10	0.02032520325203252	3	0.008287292817679558	0	0.0	0	0.0	.	4.648	0.120435	0.08881	0.029572	6.99E-4	ENSG00000221840	ENST00000319760	T	0.01139	5.28	2.01	2.01	0.26516	.	0.000000	0.48286	D	0.000188	T	0.00845	0.0028	M	0.84511	2.7	0.09310	N	0.999991	P	0.35714	0.517	B	0.37833	0.259	T	0.24512	-1.0158	10	0.72032	D	0.01	.	7.9849	0.30205	0.0:0.0:0.0:1.0	.	9	Q8NH83	OR4A5_HUMAN	V	9	ENSP00000367664:E9V	ENSP00000367664:E9V	E	-	2	0	OR4A5	51268946	0.027000	0.19231	0.318000	0.25279	0.086000	0.17979	1.684000	0.37649	1.181000	0.42912	0.136000	0.15936	GAA	T|0.990;A|0.010	0.010	strong		0.423	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272	
OR5L1	219437	hgsc.bcm.edu	37	11	55579078	55579078	+	Missense_Mutation	SNP	A	A	T	rs2869020	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55579078A>T	ENST00000333973.2	+	1	225	c.136A>T	c.(136-138)Att>Ttt	p.I46F		NM_001004738.1	NP_001004738.1	Q8NGL2	OR5L1_HUMAN	olfactory receptor, family 5, subfamily L, member 1	46			I -> F (in dbSNP:rs2869020).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(4)|liver(4)|lung(36)|ovary(2)|pancreas(1)|prostate(5)|skin(9)|stomach(4)|upper_aerodigestive_tract(3)	78		all_epithelial(135;0.208)				CCTGGGCATGATTGCACTGAT	0.493													N|||	121	0.0241613	0.0862	0.0101	5008	,	,		19133	0.0		0.0	False		,,,				2504	0.0				p.I46F		Atlas-SNP	.											.	OR5L1	145	.	0			c.A136T						PASS	.	A	PHE/ILE	307,4093	167.3+/-198.3	16,275,1909	330.0	288.0	302.0		136	0.6	0.1	11	dbSNP_101	302	6,8586	5.7+/-21.5	0,6,4290	yes	missense	OR5L1	NM_001004738.1	21	16,281,6199	TT,TA,AA		0.0698,6.9773,2.4092	benign	46/312	55579078	313,12679	2200	4296	6496	SO:0001583	missense	219437	exon1			GGCATGATTGCAC	AB065780	CCDS31509.1	11q11	2012-08-09			ENSG00000186117	ENSG00000186117		"""GPCR / Class A : Olfactory receptors"""	8350	protein-coding gene	gene with protein product							Standard	NM_001004738		Approved	OST262	uc001nhw.1	Q8NGL2	OTTHUMG00000166810	ENST00000333973.2:c.136A>T	11.37:g.55579078A>T	ENSP00000335529:p.Ile46Phe	238.0	1.0	0.00420168		238.0	107.0	0.44958	NM_001004738	B2RNK6|Q6IFD0	Missense_Mutation	SNP	ENST00000333973.2	37	CCDS31509.1	43	0.019688644688644688	39	0.07926829268292683	4	0.011049723756906077	0	0.0	0	0.0	a	12.72	2.022276	0.35701	0.069773	6.98E-4	ENSG00000186117	ENST00000333973	T	0.00638	6.04	4.32	0.548	0.17208	GPCR, rhodopsin-like superfamily (1);	0.454491	0.18670	N	0.134475	T	0.00109	0.0003	M	0.84219	2.685	0.09310	N	1	B	0.29612	0.251	B	0.35039	0.194	T	0.39603	-0.9606	10	0.87932	D	0	-7.0075	8.3108	0.32071	0.6568:0.0:0.3432:0.0	rs2869020;rs52812745;rs2869020	46	Q8NGL2	OR5L1_HUMAN	F	46	ENSP00000335529:I46F	ENSP00000335529:I46F	I	+	1	0	OR5L1	55335654	0.000000	0.05858	0.057000	0.19452	0.019000	0.09904	-0.143000	0.10296	-0.167000	0.10871	0.358000	0.22013	ATT	A|0.976;T|0.024	0.024	strong		0.493	OR5L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391514.1	NM_001004738	
CRAT	1384	hgsc.bcm.edu	37	9	131860421	131860421	+	Silent	SNP	G	G	A	rs16930895	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131860421G>A	ENST00000318080.2	-	11	1629	c.1335C>T	c.(1333-1335)taC>taT	p.Y445Y	RP11-247A12.1_ENST00000434250.1_RNA	NM_000755.3|NM_001257363.1	NP_000746|NP_001244292.1	P43155	CACP_HUMAN	carnitine O-acetyltransferase	445					carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carnitine O-acetyltransferase activity (GO:0004092)|receptor binding (GO:0005102)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|skin(1)|urinary_tract(2)	13				UCEC - Uterine corpus endometrioid carcinoma (4;0.0178)	L-Carnitine(DB00583)	ATGCCTGTCCGTAGATCCTGG	0.642													G|||	198	0.0395367	0.1445	0.0086	5008	,	,		20455	0.0		0.001	False		,,,				2504	0.0				p.Y445Y		Atlas-SNP	.											.	CRAT	43	.	0			c.C1335T						PASS	.	G		605,3801	264.1+/-265.8	34,537,1632	113.0	114.0	114.0		1335	1.2	0.6	9	dbSNP_123	114	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	CRAT	NM_000755.3		34,540,5929	AA,AG,GG		0.0349,13.7313,4.6748		445/627	131860421	608,12398	2203	4300	6503	SO:0001819	synonymous_variant	1384	exon11			CTGTCCGTAGATC	X78706	CCDS6919.1	9q34.1	2010-04-27	2010-04-27		ENSG00000095321	ENSG00000095321	2.3.1.7		2342	protein-coding gene	gene with protein product		600184	"""carnitine acetyltransferase"""			7829107	Standard	NM_000755		Approved	CAT1	uc004bxh.3	P43155	OTTHUMG00000147343	ENST00000318080.2:c.1335C>T	9.37:g.131860421G>A		53.0	0.0	0		37.0	17.0	0.459459	NM_000755	Q5T952|Q9BW16	Silent	SNP	ENST00000318080.2	37	CCDS6919.1	82	0.037545787545787544	77	0.1565040650406504	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	5.678	0.309678	0.10733	0.137313	3.49E-4	ENSG00000095321	ENST00000455396	.	.	.	5.65	1.21	0.21127	.	.	.	.	.	T	0.00241	0.0007	.	.	.	0.09310	P	0.999999999693856	.	.	.	.	.	.	T	0.10706	-1.0618	3	.	.	.	-22.048	9.4792	0.38891	0.4152:0.0:0.5848:0.0	rs16930895;rs17486087;rs16930895	.	.	.	W	44	.	.	R	-	1	2	CRAT	130900242	0.002000	0.14202	0.565000	0.28409	0.678000	0.39670	-0.028000	0.12350	0.332000	0.23536	0.561000	0.74099	CGG	G|0.943;A|0.057	0.057	strong		0.642	CRAT-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253700.1		
RBM11	54033	hgsc.bcm.edu	37	21	15599354	15599354	+	Missense_Mutation	SNP	G	G	A	rs139439630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:15599354G>A	ENST00000400577.3	+	5	595	c.586G>A	c.(586-588)Gac>Aac	p.D196N	RBM11_ENST00000468643.1_3'UTR	NM_144770.3	NP_658983.3	P57052	RBM11_HUMAN	RNA binding motif protein 11	196					cell differentiation (GO:0030154)|cellular response to oxidative stress (GO:0034599)|mRNA processing (GO:0006397)|multicellular organismal development (GO:0007275)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(U) RNA binding (GO:0008266)|protein homodimerization activity (GO:0042803)			endometrium(3)|kidney(3)|lung(7)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16				Epithelial(23;0.000314)|COAD - Colon adenocarcinoma(22;0.00242)|Colorectal(24;0.0129)|Lung(58;0.141)		ACAACCAAGTGACTCTGACCT	0.468													.|||	17	0.00339457	0.0008	0.0072	5008	,	,		21404	0.0		0.0099	False		,,,				2504	0.001				p.D196N		Atlas-SNP	.											.	RBM11	41	.	0			c.G586A						PASS	.	G	ASN/ASP	9,3953		0,9,1972	326.0	307.0	313.0		586	1.9	0.1	21	dbSNP_134	313	140,8188		2,136,4026	yes	missense	RBM11	NM_144770.3	23	2,145,5998	AA,AG,GG		1.6811,0.2272,1.2124	probably-damaging	196/282	15599354	149,12141	1981	4164	6145	SO:0001583	missense	54033	exon5			CCAAGTGACTCTG	AF130358	CCDS46635.1	21q11	2013-02-12			ENSG00000185272	ENSG00000185272		"""RNA binding motif (RRM) containing"""	9897	protein-coding gene	gene with protein product						12036298	Standard	NM_144770		Approved		uc002yjo.4	P57052	OTTHUMG00000074263	ENST00000400577.3:c.586G>A	21.37:g.15599354G>A	ENSP00000383421:p.Asp196Asn	342.0	0.0	0		361.0	160.0	0.443213	NM_144770	Q6YNC2|Q8NBA1|Q8NFF6	Missense_Mutation	SNP	ENST00000400577.3	37	CCDS46635.1	13	0.005952380952380952	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	9	0.011873350923482849	G	9.181	1.023488	0.19433	0.002272	0.016811	ENSG00000185272	ENST00000400577	T	0.08720	3.06	1.87	1.87	0.25490	.	0.067005	0.64402	D	0.000010	T	0.03827	0.0108	N	0.08118	0	0.22926	N	0.998552	D	0.57571	0.98	P	0.61658	0.892	T	0.38308	-0.9667	10	0.17832	T	0.49	.	11.1988	0.48728	0.0:0.0:1.0:0.0	.	196	P57052	RBM11_HUMAN	N	196	ENSP00000383421:D196N	ENSP00000383421:D196N	D	+	1	0	RBM11	14521225	0.107000	0.21998	0.112000	0.21494	0.343000	0.28985	1.259000	0.32956	1.330000	0.45394	0.195000	0.17529	GAC	G|0.988;A|0.012	0.012	strong		0.468	RBM11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157818.1	NM_144770	
EPPK1	83481	hgsc.bcm.edu	37	8	144940462	144940462	+	Silent	SNP	G	G	A	rs56146920		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144940462G>A	ENST00000525985.1	-	2	7031	c.6960C>T	c.(6958-6960)tcC>tcT	p.S2320S				P58107	EPIPL_HUMAN	epiplakin 1	2320						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			CCTGGAAGAGGGAGATCTGCT	0.701																																					p.S2320S		Atlas-SNP	.											.	EPPK1	199	.	0			c.C6960T						PASS	.	G		13,4351		0,13,2169	199.0	190.0	193.0		6960	-0.8	1.0	8	dbSNP_129	193	1,8519		0,1,4259	no	coding-synonymous	EPPK1	NM_031308.1		0,14,6428	AA,AG,GG		0.0117,0.2979,0.1087		2320/2420	144940462	14,12870	2182	4260	6442	SO:0001819	synonymous_variant	83481	exon1			GAAGAGGGAGATC	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.6960C>T	8.37:g.144940462G>A		174.0	0.0	0		198.0	11.0	0.0555556	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																				G|0.500;A|0.500	0.500	weak		0.701	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
OR52L1	338751	hgsc.bcm.edu	37	11	6007679	6007679	+	Missense_Mutation	SNP	C	C	T	rs61742092|rs386750238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6007679C>T	ENST00000332249.4	-	1	536	c.482G>A	c.(481-483)tGc>tAc	p.C161Y		NM_001005173.2	NP_001005173.2	Q8NGH7	O52L1_HUMAN	olfactory receptor, family 52, subfamily L, member 1	161			C -> R (in dbSNP:rs4436524). {ECO:0000269|PubMed:14983052, ECO:0000269|PubMed:15489334, 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)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|pancreas(1)|skin(3)|soft_tissue(1)	30		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.98e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CATTCCGATGCACCCTATGAC	0.512													.|||	122	0.024361	0.0855	0.013	5008	,	,		23519	0.0		0.0	False		,,,				2504	0.0				p.C161Y	Melanoma(121;653 1666 10547 22796 51255)	Atlas-SNP	.											OR52L1_ENST00000332249,NS,carcinoma,-1,2	OR52L1	100	2	0			c.G482A						PASS	.	C	TYR/CYS	26,4038		3,20,2009	76.0	73.0	74.0		482	0.5	0.0	11	dbSNP_129	74	2,8378		0,2,4188	no	missense	OR52L1	NM_001005173.2	194	3,22,6197	TT,TC,CC		0.0239,0.6398,0.225	benign	161/330	6007679	28,12416	2032	4190	6222	SO:0001583	missense	338751	exon1			CCGATGCACCCTA	AB065819	CCDS44529.1	11p15.4	2012-08-09			ENSG00000183313	ENSG00000183313		"""GPCR / Class A : Olfactory receptors"""	14785	protein-coding gene	gene with protein product							Standard	NM_001005173		Approved		uc001mcd.2	Q8NGH7	OTTHUMG00000165374	ENST00000332249.4:c.482G>A	11.37:g.6007679C>T	ENSP00000330338:p.Cys161Tyr	164.0	0.0	0		160.0	70.0	0.4375	NM_001005173	B2RPA6|Q6IFK9	Missense_Mutation	SNP	ENST00000332249.4	37	CCDS44529.1	32	0.014652014652014652	29	0.05894308943089431	3	0.008287292817679558	0	0.0	0	0.0	C	0.004	-2.262469	0.00262	0.006398	2.39E-4	ENSG00000183313	ENST00000332249	T	0.36520	1.25	3.85	0.545	0.17190	GPCR, rhodopsin-like superfamily (1);	0.486110	0.17495	N	0.172195	T	0.01558	0.0050	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.15867	-1.0422	10	0.18276	T	0.48	.	4.1238	0.10118	0.0:0.4045:0.2702:0.3253	.	161	Q8NGH7	O52L1_HUMAN	Y	161	ENSP00000330338:C161Y	ENSP00000330338:C161Y	C	-	2	0	OR52L1	5964255	0.000000	0.05858	0.027000	0.17364	0.006000	0.05464	-3.285000	0.00526	0.235000	0.21160	0.313000	0.20887	TGC	A|0.000;C|0.988;T|0.012	0.012	strong		0.512	OR52L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383754.1	NM_001005173	
ERCC5	2073	hgsc.bcm.edu	37	13	103514939	103514939	+	Silent	SNP	C	C	T	rs4150316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:103514939C>T	ENST00000355739.4	+	8	2863	c.1440C>T	c.(1438-1440)caC>caT	p.H480H	BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.R906C|ERCC5_ENST00000375954.1_5'Flank	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	480					DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|response to UV (GO:0009411)|response to UV-C (GO:0010225)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	51	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					CACTTGTTCACGTGGGGACTG	0.493			"""Mis, N, F"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				C|||	180	0.0359425	0.1331	0.0043	5008	,	,		20640	0.0		0.001	False		,,,				2504	0.0				p.H934H		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (G)	13	13q33	2073	"""excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))"""		E	.	.	.	.	0			c.C2802T						PASS	.	C	,	495,3911	228.8+/-243.5	32,431,1740	71.0	60.0	64.0		1440,2802	-10.5	0.0	13	dbSNP_110	64	13,8587	9.8+/-36.6	0,13,4287	no	coding-synonymous,coding-synonymous	ERCC5,BIVM-ERCC5	NM_000123.3,NM_001204425.1	,	32,444,6027	TT,TC,CC		0.1512,11.2347,3.9059	,	480/1187,934/1641	103514939	508,12498	2203	4300	6503	SO:0001819	synonymous_variant	0	exon16	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	TGTTCACGTGGGG	X71342	CCDS32004.1	13q22-q34	2014-09-17	2014-03-07		ENSG00000134899	ENSG00000134899			3437	protein-coding gene	gene with protein product	"""Cockayne syndrome"""	133530	"""xeroderma pigmentosum, complementation group G"", ""excision repair cross-complementing rodent repair deficiency, complementation group 5"""	ERCM2, XPGC		8088806	Standard	NM_000123		Approved			P28715	OTTHUMG00000017310	ENST00000355739.4:c.1440C>T	13.37:g.103514939C>T		111.0	0.0	0		120.0	69.0	0.575	NM_001204425	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Silent	SNP	ENST00000355739.4	37	CCDS32004.1																																																																																			C|0.959;T|0.041	0.041	strong		0.493	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1		
CYP3A7	1551	hgsc.bcm.edu	37	7	99317993	99317993	+	Silent	SNP	G	G	A	rs45466796	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99317993G>A	ENST00000336374.2	-	4	263	c.261C>T	c.(259-261)ccC>ccT	p.P87P		NM_000765.3	NP_000756.2	P24462	CP3A7_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 7	87					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxygen binding (GO:0019825)			autonomic_ganglia(1)|breast(3)|endometrium(2)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	32	Lung NSC(181;0.0144)|Esophageal squamous(72;0.0166)|all_lung(186;0.0228)				Alfentanil(DB00802)|Alprazolam(DB00404)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amlodipine(DB00381)|Aprepitant(DB00673)|Aripiprazole(DB01238)|Astemizole(DB00637)|Atorvastatin(DB01076)|Buprenorphine(DB00921)|Buspirone(DB00490)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clotrimazole(DB00257)|Cocaine(DB00907)|Codeine(DB00318)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diltiazem(DB00343)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Eplerenone(DB00700)|Erythromycin(DB00199)|Estradiol(DB00783)|Ethosuximide(DB00593)|Ethylmorphine(DB01466)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluticasone Propionate(DB00588)|Fluvoxamine(DB00176)|Gestodene(DB06730)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nifedipine(DB01115)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinidine(DB00908)|Quinine(DB00468)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Salmeterol(DB00938)|Saquinavir(DB01232)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Testosterone(DB00624)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	TGATCATGTCGGGATCTGTGA	0.388													G|||	111	0.0221645	0.0802	0.0072	5008	,	,		18474	0.0		0.0	False		,,,				2504	0.0				p.P87P		Atlas-SNP	.											.	CYP3A7	59	.	0			c.C261T						PASS	.	G		281,4125	156.3+/-189.4	8,265,1930	129.0	117.0	121.0		261	-2.8	0.0	7	dbSNP_127	121	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	CYP3A7	NM_000765.3		8,267,6228	AA,AG,GG		0.0233,6.3777,2.1759		87/504	99317993	283,12723	2203	4300	6503	SO:0001819	synonymous_variant	1551	exon4			CATGTCGGGATCT	AF315325	CCDS5673.1	7q21-q22.1	2007-12-14	2003-01-14		ENSG00000160870	ENSG00000160870		"""Cytochrome P450s"""	2640	protein-coding gene	gene with protein product		605340	"""cytochrome P450, subfamily IIIA, polypeptide 7"""			2722762	Standard	NM_000765		Approved	CP37, P450-HFLA		P24462	OTTHUMG00000156726	ENST00000336374.2:c.261C>T	7.37:g.99317993G>A		251.0	0.0	0		299.0	142.0	0.474916	NM_000765	A4D288|Q9H241	Silent	SNP	ENST00000336374.2	37	CCDS5673.1																																																																																			G|0.983;A|0.017	0.017	strong		0.388	CYP3A7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345484.1		
ABI3	51225	hgsc.bcm.edu	37	17	47295165	47295165	+	Missense_Mutation	SNP	G	G	A	rs137924898	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:47295165G>A	ENST00000225941.1	+	3	848	c.350G>A	c.(349-351)cGg>cAg	p.R117Q	ABI3_ENST00000419580.2_Missense_Mutation_p.R111Q	NM_001135186.1|NM_016428.2	NP_001128658.1|NP_057512	Q9P2A4	ABI3_HUMAN	ABI family, member 3	117					cellular component movement (GO:0006928)|regulation of cell migration (GO:0030334)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|membrane (GO:0016020)				breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	12			Epithelial(5;6.37e-06)|all cancers(6;6.36e-05)			ACTGTCCAGCGGCTGCCCCCC	0.612										HNSCC(55;0.14)			G|||	11	0.00219649	0.0083	0.0	5008	,	,		13980	0.0		0.0	False		,,,				2504	0.0				p.R117Q		Atlas-SNP	.											.	ABI3	35	.	0			c.G350A						PASS	.	G	GLN/ARG,GLN/ARG	46,4360	47.5+/-82.1	0,46,2157	95.0	94.0	94.0		332,350	2.8	1.0	17	dbSNP_134	94	1,8599		0,1,4299	yes	missense,missense	ABI3	NM_001135186.1,NM_016428.2	43,43	0,47,6456	AA,AG,GG		0.0116,1.044,0.3614	possibly-damaging,possibly-damaging	111/361,117/367	47295165	47,12959	2203	4300	6503	SO:0001583	missense	51225	exon3			TCCAGCGGCTGCC	AB037886	CCDS11546.1, CCDS45725.1	17q21.3	2011-03-04	2008-09-12		ENSG00000108798	ENSG00000108798			29859	protein-coding gene	gene with protein product		606363				10978530, 11956071	Standard	NM_001135186		Approved	NESH, SSH3BP3	uc002iop.1	Q9P2A4	OTTHUMG00000161306	ENST00000225941.1:c.350G>A	17.37:g.47295165G>A	ENSP00000225941:p.Arg117Gln	64.0	0.0	0		59.0	28.0	0.474576	NM_016428	C9IZN8|Q9H0P6	Missense_Mutation	SNP	ENST00000225941.1	37	CCDS11546.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	G	12.92	2.082944	0.36758	0.01044	1.16E-4	ENSG00000108798	ENST00000225941;ENST00000419580	T;T	0.09911	2.93;2.97	4.92	2.85	0.33270	Abl-interactor, homeo-domain homologous domain (1);	0.258373	0.28219	N	0.016153	T	0.06325	0.0163	L	0.45581	1.43	0.43390	D	0.995501	B;B	0.11235	0.003;0.004	B;B	0.12837	0.005;0.008	T	0.16276	-1.0408	10	0.39692	T	0.17	-17.6666	5.5446	0.17057	0.1921:0.1608:0.6471:0.0	.	111;117	Q9P2A4-2;Q9P2A4	.;ABI3_HUMAN	Q	117;111	ENSP00000225941:R117Q;ENSP00000406651:R111Q	ENSP00000225941:R117Q	R	+	2	0	ABI3	44650164	1.000000	0.71417	1.000000	0.80357	0.716000	0.41182	1.567000	0.36407	0.604000	0.29930	0.555000	0.69702	CGG	G|0.997;A|0.003	0.003	strong		0.612	ABI3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364475.1	NM_016428	
EBNA1BP2	10969	hgsc.bcm.edu	37	1	43630156	43630156	+	Silent	SNP	A	A	C	rs11559311	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:43630156A>C	ENST00000236051.2	-	9	1020	c.879T>G	c.(877-879)ccT>ccG	p.P293P	EBNA1BP2_ENST00000431635.2_Silent_p.P348P	NM_006824.2	NP_006815.2	Q99848	EBP2_HUMAN	EBNA1 binding protein 2	293					ribosome biogenesis (GO:0042254)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(4)|lung(9)	16	Ovarian(52;0.00579)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				TTCGTTTTCCAGGTCTCTTCT	0.443													A|||	410	0.081869	0.2405	0.0605	5008	,	,		19601	0.001		0.0368	False		,,,				2504	0.0123				p.P348P		Atlas-SNP	.											.	EBNA1BP2	37	.	0			c.T1044G						PASS	.	A	,	913,3493	351.1+/-311.1	102,709,1392	176.0	155.0	162.0		1044,879	-0.3	1.0	1	dbSNP_120	162	356,8244	119.7+/-179.0	6,344,3950	no	coding-synonymous,coding-synonymous	EBNA1BP2	NM_001159936.1,NM_006824.2	,	108,1053,5342	CC,CA,AA		4.1395,20.7217,9.757	,	348/362,293/307	43630156	1269,11737	2203	4300	6503	SO:0001819	synonymous_variant	10969	exon10			TTTTCCAGGTCTC	U86602	CCDS478.1, CCDS53308.1	1p35-p33	2011-02-10	2001-11-28		ENSG00000117395	ENSG00000117395			15531	protein-coding gene	gene with protein product		614443	"""EBNA1-binding protein 2"""			10074103, 11438656	Standard	NM_001159936		Approved	NOBP, EBP2, P40	uc010ojx.2	Q99848	OTTHUMG00000007284	ENST00000236051.2:c.879T>G	1.37:g.43630156A>C		140.0	0.0	0		158.0	80.0	0.506329	NM_001159936	Q96A66	Silent	SNP	ENST00000236051.2	37	CCDS478.1																																																																																			A|0.912;C|0.088	0.088	strong		0.443	EBNA1BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019015.1		
PCDHB14	56122	hgsc.bcm.edu	37	5	140605092	140605092	+	Missense_Mutation	SNP	C	C	G	rs76671799	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140605092C>G	ENST00000239449.4	+	1	2015	c.2015C>G	c.(2014-2016)cCg>cGg	p.P672R	PCDHB14_ENST00000515856.2_Missense_Mutation_p.P519R	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	672					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCCTACCTGCCGCTCCCTGAG	0.692													c|||	132	0.0263578	0.0946	0.0086	5008	,	,		14125	0.0		0.001	False		,,,				2504	0.0				p.P672R	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.C2015G						PASS	.	C	ARG/PRO	234,4046		6,222,1912	46.0	53.0	51.0		2015	0.6	0.5	5	dbSNP_131	51	3,8453		0,3,4225	no	missense	PCDHB14	NM_018934.2	103	6,225,6137	GG,GC,CC		0.0355,5.4673,1.8609	benign	672/799	140605092	237,12499	2140	4228	6368	SO:0001583	missense	56122	exon1			ACCTGCCGCTCCC	AF152493	CCDS4256.1	5q31	2010-01-26			ENSG00000120327	ENSG00000120327		"""Cadherins / Protocadherins : Clustered"""	8685	other	protocadherin		606340				10380929	Standard	NM_018934		Approved	PCDH-BETA14	uc003ljb.3	Q9Y5E9	OTTHUMG00000129619	ENST00000239449.4:c.2015C>G	5.37:g.140605092C>G	ENSP00000239449:p.Pro672Arg	40.0	0.0	0		66.0	29.0	0.439394	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Missense_Mutation	SNP	ENST00000239449.4	37	CCDS4256.1	45	0.020604395604395604	42	0.08536585365853659	3	0.008287292817679558	0	0.0	0	0.0	-	12.23	1.876740	0.33162	0.054673	3.55E-4	ENSG00000120327	ENST00000515856;ENST00000239449	T;T	0.51817	0.7;0.69	3.83	0.644	0.17776	.	.	.	.	.	T	0.02533	0.0077	M	0.82923	2.615	0.19945	N	0.999944	B	0.28378	0.209	B	0.30029	0.11	T	0.10177	-1.0641	9	0.39692	T	0.17	.	6.8594	0.24058	0.5742:0.2934:0.1324:0.0	.	672	Q9Y5E9	PCDBE_HUMAN	R	519;672	ENSP00000444518:P519R;ENSP00000239449:P672R	ENSP00000239449:P672R	P	+	2	0	PCDHB14	140585276	0.000000	0.05858	0.479000	0.27329	0.090000	0.18270	0.062000	0.14389	0.695000	0.31675	-0.251000	0.11542	CCG	C|0.978;G|0.022	0.022	strong		0.692	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934	
EPHA1	2041	hgsc.bcm.edu	37	7	143088592	143088592	+	Silent	SNP	G	G	A	rs56307701	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:143088592G>A	ENST00000275815.3	-	18	2975	c.2889C>T	c.(2887-2889)caC>caT	p.H963H	EPHA1_ENST00000458129.1_5'Flank	NM_005232.4	NP_005223.4	P21709	EPHA1_HUMAN	EPH receptor A1	963	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.				activation of Rho GTPase activity (GO:0032862)|angiogenesis (GO:0001525)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of cell migration (GO:0030336)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of stress fiber assembly (GO:0051496)|protein autophosphorylation (GO:0046777)|regulation of Rac GTPase activity (GO:0032314)|substrate adhesion-dependent cell spreading (GO:0034446)	integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(11)|lung(21)|ovary(4)|skin(1)|stomach(1)|urinary_tract(3)	51	Melanoma(164;0.205)	Myeloproliferative disorder(862;0.0255)				TGCGCTTCTGGTGCCCGGGCA	0.632													G|||	60	0.0119808	0.0446	0.0014	5008	,	,		16965	0.0		0.0	False		,,,				2504	0.0				p.H963H		Atlas-SNP	.											.	EPHA1	193	.	0			c.C2889T						PASS	.	G		187,4219	118.4+/-156.1	3,181,2019	89.0	59.0	69.0		2889	3.4	1.0	7	dbSNP_129	69	4,8596	2.2+/-6.3	0,4,4296	no	coding-synonymous	EPHA1	NM_005232.4		3,185,6315	AA,AG,GG		0.0465,4.2442,1.4686		963/977	143088592	191,12815	2203	4300	6503	SO:0001819	synonymous_variant	2041	exon18			CTTCTGGTGCCCG	M18391	CCDS5884.1	7q32-q36	2013-02-11	2004-10-28		ENSG00000146904	ENSG00000146904	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3385	protein-coding gene	gene with protein product		179610	"""EphA1"""	EPHT, EPHT1		9267020	Standard	NM_005232		Approved	EPH	uc003wcz.3	P21709	OTTHUMG00000155894	ENST00000275815.3:c.2889C>T	7.37:g.143088592G>A		134.0	0.0	0		175.0	84.0	0.48	NM_005232	A1L3V3|B5A966|B5A967|Q15405	Silent	SNP	ENST00000275815.3	37	CCDS5884.1																																																																																			G|0.988;A|0.013	0.013	strong		0.632	EPHA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342154.1		
COL27A1	85301	hgsc.bcm.edu	37	9	117068826	117068826	+	Silent	SNP	G	G	A	rs1249762	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117068826G>A	ENST00000356083.3	+	58	5356	c.4965G>A	c.(4963-4965)gtG>gtA	p.V1655V		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	1655					extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						ACCGGCTGGTGCTGGACCAGG	0.587											OREG0019417	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	112	0.0223642	0.0847	0.0	5008	,	,		14302	0.0		0.0	False		,,,				2504	0.0				p.V1655V		Atlas-SNP	.											.	COL27A1	200	.	0			c.G4965A						PASS	.	G		298,4108	162.9+/-194.8	12,274,1917	61.0	64.0	63.0		4965	4.4	1.0	9	dbSNP_87	63	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	COL27A1	NM_032888.2		12,275,6216	AA,AG,GG		0.0116,6.7635,2.2989		1655/1861	117068826	299,12707	2203	4300	6503	SO:0001819	synonymous_variant	85301	exon58			GCTGGTGCTGGAC	AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"""Collagens"""	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.4965G>A	9.37:g.117068826G>A		62.0	0.0	0	1478	73.0	31.0	0.424658	NM_032888	Q66K43|Q96JF7	Silent	SNP	ENST00000356083.3	37	CCDS6802.1																																																																																			G|0.974;A|0.026	0.026	strong		0.587	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
DNAH5	1767	hgsc.bcm.edu	37	5	13753517	13753517	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:13753517A>T	ENST00000265104.4	-	63	10801	c.10697T>A	c.(10696-10698)aTg>aAg	p.M3566K		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	3566					cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					ATCAATCAACATCTCACTGAG	0.403									Kartagener syndrome																												p.M3566K		Atlas-SNP	.											DNAH5,NS,carcinoma,+1,1	DNAH5	868	1	0			c.T10697A						PASS	.						136.0	131.0	133.0					5																	13753517		2203	4300	6503	SO:0001583	missense	1767	exon63	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	ATCAACATCTCAC	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.10697T>A	5.37:g.13753517A>T	ENSP00000265104:p.Met3566Lys	218.0	0.0	0		216.0	24.0	0.111111	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	A	21.4	4.141563	0.77775	.	.	ENSG00000039139	ENST00000265104	T	0.25250	1.81	5.77	5.77	0.91146	.	0.087828	0.85682	D	0.000000	T	0.48314	0.1493	M	0.89478	3.035	0.80722	D	1	B	0.34290	0.447	B	0.44044	0.439	T	0.54139	-0.8338	10	0.66056	D	0.02	.	16.3948	0.83586	1.0:0.0:0.0:0.0	.	3566	Q8TE73	DYH5_HUMAN	K	3566	ENSP00000265104:M3566K	ENSP00000265104:M3566K	M	-	2	0	DNAH5	13806517	1.000000	0.71417	1.000000	0.80357	0.797000	0.45037	8.851000	0.92205	2.326000	0.78906	0.533000	0.62120	ATG	.	.	none		0.403	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
LAMA1	284217	hgsc.bcm.edu	37	18	7043335	7043335	+	Missense_Mutation	SNP	A	A	G	rs9950267	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:7043335A>G	ENST00000389658.3	-	8	1139	c.1046T>C	c.(1045-1047)tTg>tCg	p.L349S		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	349	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.		L -> S (in dbSNP:rs9950267).		axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				AGCAGTATTCAAACTTTTCTT	0.358													A|||	305	0.0609026	0.2179	0.0245	5008	,	,		18061	0.0		0.0	False		,,,				2504	0.0				p.L349S		Atlas-SNP	.											.	LAMA1	458	.	0			c.T1046C						PASS	.	A	SER/LEU	821,3585	325.6+/-299.2	69,683,1451	195.0	169.0	178.0		1046	5.8	0.1	18	dbSNP_119	178	11,8589	8.4+/-32.0	0,11,4289	yes	missense	LAMA1	NM_005559.3	145	69,694,5740	GG,GA,AA		0.1279,18.6337,6.397	probably-damaging	349/3076	7043335	832,12174	2203	4300	6503	SO:0001583	missense	284217	exon8			GTATTCAAACTTT	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.1046T>C	18.37:g.7043335A>G	ENSP00000374309:p.Leu349Ser	160.0	0.0	0		137.0	135.0	0.985401	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	96	0.04395604395604396	87	0.17682926829268292	9	0.024861878453038673	0	0.0	0	0.0	A	13.81	2.349439	0.41599	0.186337	0.001279	ENSG00000101680	ENST00000389658	T	0.20200	2.09	5.76	5.76	0.90799	EGF-like, laminin (3);	0.273866	0.29212	N	0.012820	T	0.00109	0.0003	M	0.84511	2.7	0.25975	P	0.9824494	D	0.76494	0.999	D	0.67900	0.954	T	0.00282	-1.1850	9	0.56958	D	0.05	.	16.3668	0.83335	1.0:0.0:0.0:0.0	rs9950267;rs9950267	349	P25391	LAMA1_HUMAN	S	349	ENSP00000374309:L349S	ENSP00000374309:L349S	L	-	2	0	LAMA1	7033335	0.998000	0.40836	0.125000	0.21846	0.015000	0.08874	6.262000	0.72514	2.322000	0.78497	0.528000	0.53228	TTG	A|0.939;G|0.061	0.061	strong		0.358	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
ZNF678	339500	hgsc.bcm.edu	37	1	227842405	227842405	+	Missense_Mutation	SNP	C	C	A	rs61283390	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:227842405C>A	ENST00000343776.5	+	4	799	c.454C>A	c.(454-456)Ccc>Acc	p.P152T	ZNF678_ENST00000608949.1_Intron|ZNF678_ENST00000397097.3_Missense_Mutation_p.P207T	NM_178549.3	NP_848644.2	Q5SXM1	ZN678_HUMAN	zinc finger protein 678	152			P -> T (in dbSNP:rs61283390).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|pancreas(1)|prostate(1)	24		Prostate(94;0.0885)				TGGAGAGAAACCCTACAAATG	0.353													C|||	51	0.0101837	0.0371	0.0029	5008	,	,		20735	0.0		0.0	False		,,,				2504	0.0				p.P207T		Atlas-SNP	.											.	ZNF678	137	.	0			c.C619A						PASS	.	C	THR/PRO	173,4229	104.7+/-143.2	5,163,2033	56.0	65.0	62.0		619	-3.1	0.0	1	dbSNP_129	62	0,8598		0,0,4299	no	missense	ZNF678	NM_178549.3	38	5,163,6332	AA,AC,CC		0.0,3.93,1.3308	possibly-damaging	207/581	227842405	173,12827	2201	4299	6500	SO:0001583	missense	339500	exon4			GAGAAACCCTACA	BC042500		1q42.13	2013-01-08			ENSG00000181450	ENSG00000181450		"""Zinc fingers, C2H2-type"", ""-"""	28652	protein-coding gene	gene with protein product	"""hypothetical protein MGC42493"""					12477932	Standard	NM_178549		Approved	MGC42493	uc021pjy.1	Q5SXM1	OTTHUMG00000037700	ENST00000343776.5:c.454C>A	1.37:g.227842405C>A	ENSP00000344828:p.Pro152Thr	62.0	0.0	0		90.0	52.0	0.577778	NM_178549	Q8IVQ9	Missense_Mutation	SNP	ENST00000343776.5	37		23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	C	10.34	1.322066	0.23994	0.0393	0.0	ENSG00000181450	ENST00000343776;ENST00000397097;ENST00000440339	T;T;T	0.28895	2.31;2.31;1.59	1.55	-3.11	0.05299	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.16642	0.0400	M	0.78637	2.42	0.24660	N	0.993474	D	0.54964	0.969	P	0.61275	0.886	T	0.25433	-1.0132	9	0.66056	D	0.02	.	7.8273	0.29322	0.0:0.7281:0.0:0.2719	rs61283390;rs61739464	152	Q5SXM1	ZN678_HUMAN	T	152;207;207	ENSP00000344828:P152T;ENSP00000440403:P207T;ENSP00000394651:P207T	ENSP00000344828:P152T	P	+	1	0	ZNF678	225909028	0.030000	0.19436	0.000000	0.03702	0.000000	0.00434	0.807000	0.27140	-0.880000	0.03997	-0.924000	0.02725	CCC	C|0.987;A|0.013	0.013	strong		0.353	ZNF678-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000091976.2	NM_178549	
DDX27	55661	hgsc.bcm.edu	37	20	47838020	47838020	+	Missense_Mutation	SNP	C	C	T	rs114928867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:47838020C>T	ENST00000371764.4	+	2	227	c.218C>T	c.(217-219)gCt>gTt	p.A73V	DDX27_ENST00000484427.1_3'UTR	NM_017895.7	NP_060365.7	Q96GQ7	DDX27_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 27	73	Asp/Glu/Lys-rich.					nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	45			BRCA - Breast invasive adenocarcinoma(12;0.000899)|COAD - Colon adenocarcinoma(4;0.14)|Colorectal(8;0.166)			CGACAAAAAGCTTTGGGGAAG	0.522													C|||	14	0.00279553	0.0106	0.0	5008	,	,		18783	0.0		0.0	False		,,,				2504	0.0				p.A73V		Atlas-SNP	.											.	DDX27	74	.	0			c.C218T						PASS	.	C	VAL/ALA	47,4359	50.2+/-85.5	0,47,2156	83.0	72.0	76.0		218	5.2	1.0	20	dbSNP_132	76	0,8600		0,0,4300	yes	missense	DDX27	NM_017895.7	64	0,47,6456	TT,TC,CC		0.0,1.0667,0.3614	benign	73/797	47838020	47,12959	2203	4300	6503	SO:0001583	missense	55661	exon2			AAAAAGCTTTGGG	AL049766	CCDS13416.1	20q13.13	2010-07-06	2003-06-13		ENSG00000124228	ENSG00000124228		"""DEAD-boxes"""	15837	protein-coding gene	gene with protein product			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 27"""				Standard	NM_017895		Approved	dJ686N3.1, DRS1	uc002xuh.3	Q96GQ7	OTTHUMG00000033072	ENST00000371764.4:c.218C>T	20.37:g.47838020C>T	ENSP00000360828:p.Ala73Val	115.0	0.0	0		126.0	59.0	0.468254	NM_017895	A0AVB6|B7ZLY1|Q5VXM7|Q8WYG4|Q969N7|Q96F57|Q96L97|Q9BWY9|Q9BXF0|Q9H990|Q9NWU3|Q9P0C2|Q9UGD6	Missense_Mutation	SNP	ENST00000371764.4	37	CCDS13416.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	13.11	2.138594	0.37728	0.010667	0.0	ENSG00000124228	ENST00000535160;ENST00000371764	T	0.01474	4.85	5.16	5.16	0.70880	.	0.553075	0.18353	N	0.143813	T	0.01156	0.0038	N	0.22421	0.69	0.37063	D	0.89816	B	0.24823	0.112	B	0.19148	0.024	T	0.60459	-0.7259	10	0.30078	T	0.28	-17.0082	11.1111	0.48232	0.1841:0.8159:0.0:0.0	.	73	Q96GQ7	DDX27_HUMAN	V	73	ENSP00000360828:A73V	ENSP00000360828:A73V	A	+	2	0	DDX27	47271427	0.984000	0.35163	1.000000	0.80357	0.550000	0.35303	1.360000	0.34125	2.698000	0.92095	0.561000	0.74099	GCT	C|0.997;T|0.003	0.003	strong		0.522	DDX27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080485.1		
TJP3	27134	hgsc.bcm.edu	37	19	3747910	3747910	+	Missense_Mutation	SNP	G	G	A	rs10408494	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3747910G>A	ENST00000541714.2	+	19	2903	c.2441G>A	c.(2440-2442)gGc>gAc	p.G814D	TJP3_ENST00000589378.1_Missense_Mutation_p.G823D|TJP3_ENST00000262968.9_Missense_Mutation_p.G847D|TJP3_ENST00000539908.2_Missense_Mutation_p.G778D|TJP3_ENST00000587686.1_Missense_Mutation_p.G833D|TJP3_ENST00000382008.3_Missense_Mutation_p.G828D	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	814					regulation of G1/S transition of mitotic cell cycle (GO:2000045)	apical plasma membrane (GO:0016324)|nucleus (GO:0005634)|tight junction (GO:0005923)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0118)|STAD - Stomach adenocarcinoma(1328;0.18)		GGCGAGGGCGGCGCGTACACG	0.692													G|||	244	0.048722	0.1747	0.0187	5008	,	,		15847	0.0		0.0	False		,,,				2504	0.0				p.G823D		Atlas-SNP	.											.	TJP3	79	.	0			c.G2468A						PASS	.	G	ASP/GLY	642,3762	260.7+/-263.8	41,560,1601	36.0	32.0	33.0		2540	2.8	0.9	19	dbSNP_119	33	4,8594	3.0+/-9.4	0,4,4295	yes	missense	TJP3	NM_014428.1	94	41,564,5896	AA,AG,GG		0.0465,14.5777,4.9685	benign	847/953	3747910	646,12356	2202	4299	6501	SO:0001583	missense	27134	exon19			AGGGCGGCGCGTA	AC005954	CCDS32873.1, CCDS32873.2, CCDS59332.1	19p13.3	2012-07-12	2012-07-12			ENSG00000105289			11829	protein-coding gene	gene with protein product	"""zona occludens 3"""	612689					Standard	NM_001267560		Approved	ZO-3	uc010xhu.3	O95049		ENST00000541714.2:c.2441G>A	19.37:g.3747910G>A	ENSP00000439278:p.Gly814Asp	100.0	0.0	0		140.0	80.0	0.571429	NM_001267561	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Missense_Mutation	SNP	ENST00000541714.2	37	CCDS32873.2	85	0.03891941391941392	81	0.16463414634146342	4	0.011049723756906077	0	0.0	0	0.0	G	9.121	1.008881	0.19199	0.145777	4.65E-4	ENSG00000105289	ENST00000541714;ENST00000539908;ENST00000382008;ENST00000262968	T;T;T;T	0.11821	2.74;2.92;2.78;2.85	2.81	2.81	0.32909	.	0.137458	0.47455	U	0.000231	T	0.00073	0.0002	M	0.62723	1.935	0.31716	P	0.638979	P;P;P;P	0.47762	0.835;0.9;0.745;0.835	B;B;B;B	0.41813	0.367;0.367;0.202;0.367	T	0.18903	-1.0322	9	0.87932	D	0	.	12.4552	0.55700	0.0:0.0:1.0:0.0	rs10408494	833;847;828;814	O95049-3;O95049-2;O95049;F5H2X0	.;.;ZO3_HUMAN;.	D	814;778;828;847	ENSP00000439278:G814D;ENSP00000439991:G778D;ENSP00000371438:G828D;ENSP00000262968:G847D	ENSP00000262968:G847D	G	+	2	0	TJP3	3698910	1.000000	0.71417	0.950000	0.38849	0.016000	0.09150	4.057000	0.57455	1.069000	0.40788	0.511000	0.50034	GGC	G|0.950;A|0.050	0.050	strong		0.692	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1		
TRIM15	89870	hgsc.bcm.edu	37	6	30139971	30139971	+	Missense_Mutation	SNP	G	G	C	rs115649931	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30139971G>C	ENST00000376694.4	+	7	1712	c.1243G>C	c.(1243-1245)Gtg>Ctg	p.V415L	TRIM15_ENST00000376688.1_Intron	NM_033229.2	NP_150232.2	Q9C019	TRI15_HUMAN	tripartite motif containing 15	415	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				innate immune response (GO:0045087)|mesodermal cell fate determination (GO:0007500)|negative regulation of intracellular transport of viral material (GO:1901253)|negative regulation of viral release from host cell (GO:1902187)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of RIG-I signaling pathway (GO:1900246)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of type I interferon production (GO:0032481)	intracellular (GO:0005622)	zinc ion binding (GO:0008270)			large_intestine(2)|lung(8)|prostate(2)|skin(1)|urinary_tract(1)	14						CCCGCGCGGCGTGAGAGTCGC	0.682													G|||	26	0.00519169	0.0182	0.0029	5008	,	,		12909	0.0		0.0	False		,,,				2504	0.0				p.V415L		Atlas-SNP	.											.	TRIM15	34	.	0			c.G1243C						PASS	.	G	LEU/VAL	53,2929		0,53,1438	16.0	13.0	14.0		1243	3.7	0.0	6	dbSNP_133	14	0,5354		0,0,2677	yes	missense	TRIM15	NM_033229.2	32	0,53,4115	CC,CG,GG		0.0,1.7773,0.6358	probably-damaging	415/466	30139971	53,8283	1491	2677	4168	SO:0001583	missense	89870	exon7			CGCGGCGTGAGAG	AF220132, U34249	CCDS4677.1	6p21.33	2013-01-09	2011-01-25		ENSG00000204610	ENSG00000204610		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16284	protein-coding gene	gene with protein product			"""zinc finger protein 178"", ""tripartite motif-containing 15"""	ZNF178		11331580, 8304341, 8812418	Standard	NM_033229		Approved	ZNFB7, RNF93	uc010jrx.3	Q9C019	OTTHUMG00000031031	ENST00000376694.4:c.1243G>C	6.37:g.30139971G>C	ENSP00000365884:p.Val415Leu	41.0	0.0	0		57.0	32.0	0.561404	NM_033229	A2BEC9|O95604|Q8IUX9|Q9C018	Missense_Mutation	SNP	ENST00000376694.4	37	CCDS4677.1	.	.	.	.	.	.	.	.	.	.	G	12.18	1.859376	0.32884	0.017773	0.0	ENSG00000204610	ENST00000376695;ENST00000376694	T	0.74002	-0.8	4.54	3.67	0.42095	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.39759	U	0.001266	T	0.51126	0.1656	L	0.58669	1.825	0.48087	D	0.999587	B	0.33448	0.412	B	0.32393	0.145	T	0.54702	-0.8254	10	0.45353	T	0.12	.	5.7541	0.18162	0.1022:0.0:0.7065:0.1913	.	415	Q9C019	TRI15_HUMAN	L	346;415	ENSP00000365884:V415L	ENSP00000365884:V415L	V	+	1	0	TRIM15	30247950	0.042000	0.20092	0.011000	0.14972	0.017000	0.09413	0.313000	0.19415	0.886000	0.36113	0.478000	0.44815	GTG	G|0.990;C|0.010	0.010	strong		0.682	TRIM15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076026.2	NM_033229	
ABCA7	10347	hgsc.bcm.edu	37	19	1052086	1052086	+	Silent	SNP	G	G	A	rs61576791	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1052086G>A	ENST00000263094.6	+	22	3339	c.3108G>A	c.(3106-3108)acG>acA	p.T1036T	ABCA7_ENST00000433129.1_Silent_p.T1036T|ABCA7_ENST00000435683.2_Silent_p.T898T	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1036	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|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)		ACTACCTGACGCTGGTGAAGG	0.672													G|||	323	0.0644968	0.2383	0.0101	5008	,	,		10142	0.0		0.001	False		,,,				2504	0.0				p.T1036T		Atlas-SNP	.											.	ABCA7	174	.	0			c.G3108A						PASS	.			761,3593		76,609,1492	29.0	25.0	26.0		3108	-8.9	0.0	19	dbSNP_129	26	7,8557		0,7,4275	no	coding-synonymous	ABCA7	NM_019112.3		76,616,5767	AA,AG,GG		0.0817,17.4782,5.9452		1036/2147	1052086	768,12150	2177	4282	6459	SO:0001819	synonymous_variant	10347	exon22			CCTGACGCTGGTG	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.3108G>A	19.37:g.1052086G>A		91.0	0.0	0		102.0	44.0	0.431373	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Silent	SNP	ENST00000263094.6	37	CCDS12055.1																																																																																			G|0.938;A|0.062	0.062	strong		0.672	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
PXDN	7837	hgsc.bcm.edu	37	2	1642700	1642700	+	Missense_Mutation	SNP	G	G	A	rs61747875	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:1642700G>A	ENST00000252804.4	-	21	4174	c.4124C>T	c.(4123-4125)aCa>aTa	p.T1375I		NM_012293.1	NP_036425.1	Q92626	PXDN_HUMAN	peroxidasin homolog (Drosophila)	1375					extracellular matrix organization (GO:0030198)|hydrogen peroxide catabolic process (GO:0042744)|immune response (GO:0006955)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|oxidation-reduction process (GO:0055114)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|heme binding (GO:0020037)|interleukin-1 receptor antagonist activity (GO:0005152)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			breast(1)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(24)|lung(48)|ovary(3)|pancreas(8)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	112	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.0845)|Lung NSC(108;0.00641)|all_epithelial(98;0.00716)		all cancers(51;0.0492)|OV - Ovarian serous cystadenocarcinoma(76;0.0973)|Epithelial(75;0.17)|GBM - Glioblastoma multiforme(21;0.228)		ATCTGAGCGTGTGCTGAAGGC	0.537													G|||	52	0.0103834	0.0363	0.0043	5008	,	,		20910	0.0		0.001	False		,,,				2504	0.0				p.T1375I		Atlas-SNP	.											.	PXDN	255	.	0			c.C4124T						PASS	.	G	ILE/THR	103,4175		1,101,2037	127.0	133.0	131.0		4124	3.0	0.1	2	dbSNP_129	131	5,8483		0,5,4239	yes	missense	PXDN	NM_012293.1	89	1,106,6276	AA,AG,GG		0.0589,2.4077,0.846	benign	1375/1480	1642700	108,12658	2139	4244	6383	SO:0001583	missense	7837	exon21			GAGCGTGTGCTGA	AF200348	CCDS46221.1	2p25.3	2013-01-11			ENSG00000130508	ENSG00000130508		"""Immunoglobulin superfamily / I-set domain containing"""	14966	protein-coding gene	gene with protein product		605158				10441517, 9039502	Standard	XM_005264707		Approved	KIAA0230, PRG2, MG50, D2S448, D2S448E, PXN	uc002qxa.3	Q92626	OTTHUMG00000059697	ENST00000252804.4:c.4124C>T	2.37:g.1642700G>A	ENSP00000252804:p.Thr1375Ile	130.0	0.0	0		131.0	53.0	0.40458	NM_012293	A8QM65|D6W4Y0|Q4KMG2	Missense_Mutation	SNP	ENST00000252804.4	37	CCDS46221.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	G	10.13	1.265304	0.23136	0.024077	5.89E-4	ENSG00000130508	ENST00000252804	T	0.61040	0.14	5.43	3.05	0.35203	.	0.558829	0.19914	N	0.103226	T	0.08268	0.0206	N	0.03608	-0.345	0.20074	N	0.999932	B	0.16603	0.018	B	0.15484	0.013	T	0.07693	-1.0759	10	0.41790	T	0.15	-30.0156	7.522	0.27633	0.1358:0.0:0.1542:0.71	.	1375	Q92626	PXDN_HUMAN	I	1375	ENSP00000252804:T1375I	ENSP00000252804:T1375I	T	-	2	0	PXDN	1621707	0.735000	0.28153	0.080000	0.20451	0.000000	0.00434	3.286000	0.51724	0.446000	0.26666	-1.114000	0.02060	ACA	G|0.990;A|0.010	0.010	strong		0.537	PXDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322505.1	XM_056455	
STRADA	92335	hgsc.bcm.edu	37	17	61787892	61787892	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:61787892C>T	ENST00000336174.6	-	8	652	c.540G>A	c.(538-540)ctG>ctA	p.L180L	STRADA_ENST00000392950.4_Silent_p.L143L|STRADA_ENST00000447001.3_Silent_p.L136L|STRADA_ENST00000375840.4_Silent_p.L122L|RP11-51F16.8_ENST00000580553.1_Intron|STRADA_ENST00000245865.5_Silent_p.L122L|STRADA_ENST00000579340.1_Silent_p.L122L|STRADA_ENST00000580039.1_5'UTR|STRADA_ENST00000582137.1_Silent_p.L151L	NM_001003787.2	NP_001003787.1	Q7RTN6	STRAA_HUMAN	STE20-related kinase adaptor alpha	180	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of protein kinase activity (GO:0032147)|cell cycle arrest (GO:0007050)|insulin receptor signaling pathway (GO:0008286)|protein export from nucleus (GO:0006611)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase binding (GO:0019900)|protein kinase activator activity (GO:0030295)|transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|liver(1)|lung(2)|ovary(1)|prostate(2)	13						CGAGGGCCTTCAGCACCCCCT	0.512																																					p.L180L		Atlas-SNP	.											.	STRADA	27	.	0			c.G540A						PASS	.						109.0	90.0	97.0					17																	61787892		2203	4300	6503	SO:0001819	synonymous_variant	92335	exon8			GGCCTTCAGCACC	AF308302	CCDS11642.1, CCDS32703.1, CCDS42367.1, CCDS54156.1, CCDS58585.1	17q23.3	2014-09-04			ENSG00000266173	ENSG00000266173			30172	protein-coding gene	gene with protein product	"""STE20-like pseudokinase"""	608626				12805220, 17921699	Standard	NM_153335		Approved	NY-BR-96, LYK5, Stlk, STRAD	uc002jbm.3	Q7RTN6	OTTHUMG00000178908	ENST00000336174.6:c.540G>A	17.37:g.61787892C>T		121.0	0.0	0		143.0	69.0	0.482517	NM_001003787	B4DDE3|B4DW17|J3KTC9|Q5JPI2|Q7Z4K9|Q8NC31|Q8NCF1|Q9H272	Silent	SNP	ENST00000336174.6	37	CCDS32703.1																																																																																			.	.	none		0.512	STRADA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443894.1		
TBC1D32	221322	hgsc.bcm.edu	37	6	121576518	121576518	+	Missense_Mutation	SNP	C	C	G	rs201833154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:121576518C>G	ENST00000398212.2	-	17	2023	c.1974G>C	c.(1972-1974)gaG>gaC	p.E658D	TBC1D32_ENST00000275159.6_Missense_Mutation_p.E658D	NM_152730.4	NP_689943.4	Q96NH3	BROMI_HUMAN	TBC1 domain family, member 32	658					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)										AATCAGAACCCTCTACTGGAG	0.289													C|||	7	0.00139776	0.0053	0.0	5008	,	,		8412	0.0		0.0	False		,,,				2504	0.0				p.E658D		Atlas-SNP	.											C6orf170,colon,carcinoma,-2,1	C6orf170	146	1	0			c.G1974C						PASS	.	C	ASP/GLU	21,3563		0,21,1771	55.0	55.0	55.0		1974	-6.1	0.0	6		55	0,8094		0,0,4047	yes	missense	C6orf170	NM_152730.4	45	0,21,5818	GG,GC,CC		0.0,0.5859,0.1798	benign	658/1258	121576518	21,11657	1792	4047	5839	SO:0001583	missense	221322	exon17			AGAACCCTCTACT	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.1974G>C	6.37:g.121576518C>G	ENSP00000381270:p.Glu658Asp	136.0	0.0	0		141.0	73.0	0.51773	NM_152730	Q5SZD6|Q5SZM6|Q6ZMY4|Q6ZUR7|Q8NB47	Missense_Mutation	SNP	ENST00000398212.2	37	CCDS43501.1	.	.	.	.	.	.	.	.	.	.	C	6.113	0.389161	0.11581	0.005859	0.0	ENSG00000146350	ENST00000275159;ENST00000398212	T;T	0.17370	2.28;2.28	5.81	-6.14	0.02111	.	0.553654	0.18121	N	0.151042	T	0.02571	0.0078	L	0.38175	1.15	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.40701	-0.9549	10	0.22109	T	0.4	.	6.2469	0.20823	0.1049:0.2255:0.0805:0.5892	.	658;658	Q96NH3-4;Q96NH3	.;BROMI_HUMAN	D	658	ENSP00000275159:E658D;ENSP00000381270:E658D	ENSP00000275159:E658D	E	-	3	2	C6orf170	121618217	0.000000	0.05858	0.006000	0.13384	0.982000	0.71751	-1.136000	0.03222	-1.369000	0.02147	-0.150000	0.13652	GAG	.	.	weak		0.289	TBC1D32-005	PUTATIVE	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380937.2	NM_152730	
RP1L1	94137	hgsc.bcm.edu	37	8	10470130	10470130	+	Missense_Mutation	SNP	C	C	T	rs79401306	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10470130C>T	ENST00000382483.3	-	4	1701	c.1478G>A	c.(1477-1479)cGg>cAg	p.R493Q		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	493					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		TCCAGCTTTCCGCTCAGCCCC	0.721													C|||	103	0.0205671	0.0764	0.0029	5008	,	,		15146	0.0		0.0	False		,,,				2504	0.0				p.R493Q		Atlas-SNP	.											.	RP1L1	453	.	0			c.G1478A						PASS	.	C	GLN/ARG	205,3593		6,193,1700	26.0	30.0	29.0		1478	-2.6	0.0	8	dbSNP_131	29	3,8241		0,3,4119	yes	missense	RP1L1	NM_178857.5	43	6,196,5819	TT,TC,CC		0.0364,5.3976,1.7273	possibly-damaging	493/2401	10470130	208,11834	1899	4122	6021	SO:0001583	missense	94137	exon4			GCTTTCCGCTCAG	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.1478G>A	8.37:g.10470130C>T	ENSP00000371923:p.Arg493Gln	24.0	0.0	0		33.0	11.0	0.333333	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	44	0.020146520146520148	44	0.08943089430894309	0	0.0	0	0.0	0	0.0	C	7.544	0.661253	0.14645	0.053976	3.64E-4	ENSG00000183638	ENST00000382483	T	0.04083	3.71	4.06	-2.57	0.06248	.	.	.	.	.	T	0.00109	0.0003	N	0.08118	0	0.09310	N	1	B	0.16396	0.017	B	0.04013	0.001	T	0.45190	-0.9278	9	0.41790	T	0.15	14.544	4.0305	0.09706	0.1672:0.3134:0.0:0.5194	.	493	A6NKC6	.	Q	493	ENSP00000371923:R493Q	ENSP00000371923:R493Q	R	-	2	0	RP1L1	10507540	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.619000	0.05572	-0.838000	0.04218	0.561000	0.74099	CGG	C|0.987;T|0.013	0.013	strong		0.721	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
PDP1	54704	hgsc.bcm.edu	37	8	94935623	94935623	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:94935623A>G	ENST00000297598.4	+	2	1605	c.1336A>G	c.(1336-1338)Ata>Gta	p.I446V	PDP1_ENST00000520728.1_Missense_Mutation_p.I446V|PDP1_ENST00000517764.1_Missense_Mutation_p.I446V|PDP1_ENST00000396200.3_Missense_Mutation_p.I471V	NM_001161781.1|NM_018444.3	NP_001155253.1|NP_060914.2	Q9P0J1	PDP1_HUMAN	pyruvate dehyrogenase phosphatase catalytic subunit 1	446					cellular metabolic process (GO:0044237)|peptidyl-threonine dephosphorylation (GO:0035970)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	[pyruvate dehydrogenase (lipoamide)] phosphatase activity (GO:0004741)|metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|liver(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)	18						CCAACAGCCAATAGCTGTTGG	0.493																																					p.I471V		Atlas-SNP	.											PDP1,caecum,carcinoma,-2,1	PDP1	97	1	0			c.A1411G						PASS	.						80.0	80.0	80.0					8																	94935623		2203	4300	6503	SO:0001583	missense	54704	exon3			CAGCCAATAGCTG	AF155661	CCDS6259.1, CCDS55262.1	8q22.1	2012-04-17	2009-06-12	2009-06-12	ENSG00000164951	ENSG00000164951	3.1.3.43	"""Serine/threonine phosphatases / Protein phosphatases, Mg2+/Mn2+ dependent"""	9279	protein-coding gene	gene with protein product		605993	"""protein phosphatase 2C, magnesium-dependent, catalytic subunit"""	PPM2C		8396421	Standard	NM_001161779		Approved	PDP, PDH	uc003ygf.3	Q9P0J1		ENST00000297598.4:c.1336A>G	8.37:g.94935623A>G	ENSP00000297598:p.Ile446Val	159.0	0.0	0		221.0	117.0	0.529412	NM_001161780	B3KX71|J3KPU0|Q5U5K1	Missense_Mutation	SNP	ENST00000297598.4	37	CCDS6259.1	.	.	.	.	.	.	.	.	.	.	A	5.314	0.243239	0.10077	.	.	ENSG00000164951	ENST00000297598;ENST00000520728;ENST00000396200;ENST00000517764	T;T;T;T	0.41065	1.03;1.03;1.01;1.03	6.03	6.03	0.97812	Protein phosphatase 2C-like (3);	0.127835	0.64402	D	0.000016	T	0.16896	0.0406	N	0.02247	-0.625	0.42964	D	0.994412	B;B	0.12013	0.005;0.001	B;B	0.10450	0.005;0.005	T	0.18871	-1.0323	10	0.02654	T	1	-7.6316	12.4101	0.55461	0.86:0.14:0.0:0.0	.	497;446	B4DYX8;Q9P0J1	.;PDP1_HUMAN	V	446;446;471;446	ENSP00000297598:I446V;ENSP00000428317:I446V;ENSP00000379503:I471V;ENSP00000430380:I446V	ENSP00000297598:I446V	I	+	1	0	PDP1	95004799	1.000000	0.71417	0.994000	0.49952	0.997000	0.91878	4.348000	0.59379	2.308000	0.77769	0.533000	0.62120	ATA	.	.	none		0.493	PDP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000378415.2	NM_018444	
TSPAN18	90139	hgsc.bcm.edu	37	11	44948263	44948263	+	Silent	SNP	C	C	T	rs34695714	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:44948263C>T	ENST00000520358.2	+	9	1069	c.654C>T	c.(652-654)taC>taT	p.Y218Y	TSPAN18_ENST00000340160.3_Silent_p.Y218Y			Q96SJ8	TSN18_HUMAN	tetraspanin 18	218						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(6)|lung(3)	10						TCGAGACCTACGTCTACTTGG	0.602											OREG0020922	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	129	0.0257588	0.0953	0.0043	5008	,	,		17858	0.0		0.0	False		,,,				2504	0.0				p.Y218Y		Atlas-SNP	.											TSPAN18,colon,carcinoma,+1,1	TSPAN18	38	1	0			c.C654T						PASS	.	C		320,4086	169.8+/-200.3	6,308,1889	217.0	187.0	197.0		654	-1.0	1.0	11	dbSNP_126	197	2,8596	2.2+/-6.3	0,2,4297	no	coding-synonymous	TSPAN18	NM_130783.4		6,310,6186	TT,TC,CC		0.0233,7.2628,2.4762		218/249	44948263	322,12682	2203	4299	6502	SO:0001819	synonymous_variant	90139	exon8			GACCTACGTCTAC	AY358087	CCDS7910.1	11p11.2	2013-02-14				ENSG00000157570		"""Tetraspanins"""	20660	protein-coding gene	gene with protein product						11756464	Standard	NM_130783		Approved	TSPAN	uc001mye.4	Q96SJ8		ENST00000520358.2:c.654C>T	11.37:g.44948263C>T		107.0	0.0	0	927	124.0	65.0	0.524194	NM_130783	Q6UY44|Q8NBI9	Silent	SNP	ENST00000520358.2	37	CCDS7910.1	58	0.026556776556776556	57	0.11585365853658537	1	0.0027624309392265192	0	0.0	0	0.0	C	3.000	-0.206236	0.06180	0.072628	2.33E-4	ENSG00000157570	ENST00000518429	.	.	.	4.54	-1.0	0.10196	.	.	.	.	.	T	0.00666	0.0022	.	.	.	0.09310	P	0.9999999999999879	.	.	.	.	.	.	T	0.23511	-1.0186	3	.	.	.	.	9.8138	0.40840	0.0:0.4987:0.0:0.5013	rs34695714	.	.	.	C	222	.	.	R	+	1	0	TSPAN18	44904839	0.935000	0.31712	0.991000	0.47740	0.329000	0.28539	0.060000	0.14342	-0.186000	0.10533	0.479000	0.44913	CGT	C|0.972;T|0.028	0.028	strong		0.602	TSPAN18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376197.3	NM_130783	
ZNF180	7733	hgsc.bcm.edu	37	19	45001398	45001398	+	Silent	SNP	G	G	A	rs10423647	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45001398G>A	ENST00000221327.4	-	2	351	c.70C>T	c.(70-72)Ctg>Ttg	p.L24L	ZNF180_ENST00000586637.1_5'UTR|ZNF180_ENST00000587047.1_Silent_p.A25A|ZNF180_ENST00000592529.1_5'UTR|ZNF180_ENST00000391956.4_Silent_p.L24L|ZNF180_ENST00000585514.1_5'UTR	NM_013256.3	NP_037388.2	Q9UJW8	ZN180_HUMAN	zinc finger protein 180	24					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(14)|lung(6)|ovary(2)|urinary_tract(1)	33		Prostate(69;0.0435)				CTCTCCTCCAGGCACAGCAGG	0.622													G|||	453	0.0904553	0.3275	0.0173	5008	,	,		16153	0.0		0.004	False		,,,				2504	0.0041				p.L24L	Esophageal Squamous(180;1353 2003 32862 46574 49854)	Atlas-SNP	.											.	ZNF180	103	.	0			c.C70T						PASS	.	G		1089,3317	389.3+/-327.3	128,833,1242	42.0	39.0	40.0		70	2.5	0.2	19	dbSNP_119	40	10,8590	5.7+/-21.5	0,10,4290	no	coding-synonymous	ZNF180	NM_013256.3		128,843,5532	AA,AG,GG		0.1163,24.7163,8.4499		24/693	45001398	1099,11907	2203	4300	6503	SO:0001819	synonymous_variant	7733	exon2			CCTCCAGGCACAG	AF192913	CCDS12639.1, CCDS62707.1, CCDS62708.1	19q13.2	2013-01-08	2006-08-22			ENSG00000167384		"""Zinc fingers, C2H2-type"", ""-"""	12970	protein-coding gene	gene with protein product		606740	"""zinc finger protein 180 (HHZ168)"""				Standard	NM_001288762		Approved	HHZ168	uc002ozf.4	Q9UJW8		ENST00000221327.4:c.70C>T	19.37:g.45001398G>A		32.0	0.0	0		44.0	20.0	0.454545	NM_013256	B2RCN6|B3KV56|K7EQX9|Q58F03|Q9P1U2	Silent	SNP	ENST00000221327.4	37	CCDS12639.1																																																																																			G|0.906;A|0.094	0.094	strong		0.622	ZNF180-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451601.1	NM_013256	
TRAPPC9	83696	hgsc.bcm.edu	37	8	140743460	140743460	+	Silent	SNP	G	G	A	rs148857575	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:140743460G>A	ENST00000438773.2	-	23	3424	c.3291C>T	c.(3289-3291)tcC>tcT	p.S1097S	TRAPPC9_ENST00000389328.4_Silent_p.S1195S|TRAPPC9_ENST00000522504.1_5'UTR|TRAPPC9_ENST00000389327.3_Silent_p.S1088S	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	1097					cell differentiation (GO:0030154)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						CCGACTGGCCGGACGGCTGCA	0.622													G|||	12	0.00239617	0.0083	0.0014	5008	,	,		14736	0.0		0.0	False		,,,				2504	0.0				p.S1195S		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.C3585T						PASS	.	G	,	30,4376	36.8+/-68.6	0,30,2173	38.0	38.0	38.0		3291,3585	-9.9	0.0	8	dbSNP_134	38	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	TRAPPC9	NM_001160372.1,NM_031466.5	,	0,30,6473	AA,AG,GG		0.0,0.6809,0.2307	,	1097/1149,1195/1247	140743460	30,12976	2203	4300	6503	SO:0001819	synonymous_variant	83696	exon23			CTGGCCGGACGGC	BC006206	CCDS34946.1, CCDS55278.1	8q24.3	2010-10-22			ENSG00000167632	ENSG00000167632		"""Trafficking protein particle complex"""	30832	protein-coding gene	gene with protein product	"""TRAPP 120 kDa subunit"", ""tularik gene 1"""	611966				11572484	Standard	NM_031466		Approved	IKBKBBP, NIBP, KIAA1882, T1, TRS120, MRT13	uc003yvh.2	Q96Q05	OTTHUMG00000164187	ENST00000438773.2:c.3291C>T	8.37:g.140743460G>A		76.0	0.0	0		85.0	43.0	0.505882	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Silent	SNP	ENST00000438773.2	37	CCDS55278.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	0.021	-1.421690	0.01126	0.006809	0.0	ENSG00000167632	ENST00000520857	.	.	.	4.93	-9.86	0.00473	.	.	.	.	.	T	0.35624	0.0938	.	.	.	0.38039	D	0.935405	.	.	.	.	.	.	T	0.56792	-0.7920	4	.	.	.	.	6.719	0.23321	0.0688:0.4132:0.3666:0.1514	.	.	.	.	W	941	.	.	R	-	1	2	TRAPPC9	140812642	0.000000	0.05858	0.000000	0.03702	0.044000	0.14063	-3.021000	0.00642	-4.055000	0.00078	-3.274000	0.00048	CGG	G|0.998;A|0.002	0.002	strong		0.622	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466	
BRCA1	672	hgsc.bcm.edu	37	17	41245643	41245643	+	Silent	SNP	A	A	G	rs369373293		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:41245643A>G	ENST00000357654.3	-	10	2023	c.1905T>C	c.(1903-1905)aaT>aaC	p.N635N	BRCA1_ENST00000309486.4_Silent_p.N339N|BRCA1_ENST00000471181.2_Silent_p.N635N|BRCA1_ENST00000591849.1_Intron|BRCA1_ENST00000493795.1_Silent_p.N588N|BRCA1_ENST00000354071.3_Silent_p.N635N|BRCA1_ENST00000351666.3_Intron|BRCA1_ENST00000352993.3_Intron|BRCA1_ENST00000491747.2_Intron|BRCA1_ENST00000346315.3_Silent_p.N635N|BRCA1_ENST00000586385.1_Intron|BRCA1_ENST00000468300.1_Intron|BRCA1_ENST00000591534.1_Intron	NM_007294.3	NP_009225.1	P38398	BRCA1_HUMAN	breast cancer 1, early onset	635					androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to indole-3-methanol (GO:0071681)|cellular response to tumor necrosis factor (GO:0071356)|chromosome segregation (GO:0007059)|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)|fatty acid biosynthetic process (GO:0006633)|G2 DNA damage checkpoint (GO:0031572)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of centriole replication (GO:0046600)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of DNA repair (GO:0045739)|positive regulation of gene expression (GO:0010628)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 acetylation (GO:2000617)|positive regulation of histone H4-K16 acetylation (GO:2000620)|positive regulation of histone H4-K20 methylation (GO:0070512)|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 vascular endothelial growth factor production (GO:0010575)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K6-linked ubiquitination (GO:0085020)|protein ubiquitination (GO:0016567)|regulation of apoptotic process (GO:0042981)|regulation of cell proliferation (GO:0042127)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to estrogen (GO:0043627)|response to ionizing radiation (GO:0010212)	BRCA1-A complex (GO:0070531)|BRCA1-BARD1 complex (GO:0031436)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|gamma-tubulin ring complex (GO:0008274)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	androgen receptor binding (GO:0050681)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(30)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(7)|lung(28)|ovary(36)|skin(2)|stomach(4)|urinary_tract(2)	120		Breast(137;0.000717)		BRCA - Breast invasive adenocarcinoma(366;0.126)		ATTCAGTACAATTAGGTGGGC	0.388			"""D, Mis, N, F, S"""		ovarian	"""breast, ovarian"""		Homologous recombination	Hereditary Breast-Ovarian Cancer, BRCA1 type	TCGA Ovarian(2;0.000030)																											p.N635N		Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	17	17q21	672	familial breast/ovarian cancer gene 1		E	.	BRCA1	304	.	0			c.T1905C						PASS	.	A	,,,,	2,4404	4.2+/-10.8	0,2,2201	94.0	92.0	93.0		1905,1764,,,1905	1.6	0.0	17		93	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,intron,intron,coding-synonymous	BRCA1	NM_007294.3,NM_007297.3,NM_007298.3,NM_007299.3,NM_007300.3	,,,,	0,2,6501	GG,GA,AA		0.0,0.0454,0.0154	,,,,	635/1864,588/1817,,,635/1885	41245643	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	672	exon10	Familial Cancer Database		AGTACAATTAGGT	U14680	CCDS11453.1, CCDS11454.1, CCDS11455.1, CCDS11456.1, CCDS11459.1, CCDS11455.2, CCDS11456.2, CCDS11459.2, CCDS11454.2	17q21.31	2014-09-17			ENSG00000012048	ENSG00000012048		"""RING-type (C3HC4) zinc fingers"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1100	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 1"", ""protein phosphatase 1, regulatory subunit 53"""	113705				1676470	Standard	NM_007300		Approved	RNF53, BRCC1, PPP1R53	uc002ict.3	P38398	OTTHUMG00000157426	ENST00000357654.3:c.1905T>C	17.37:g.41245643A>G		122.0	0.0	0		136.0	61.0	0.448529	NM_007300	O15129|Q1RMC1|Q3LRJ0|Q3LRJ6|Q6IN79|Q7KYU9	Silent	SNP	ENST00000357654.3	37	CCDS11453.1																																																																																			.	.	weak		0.388	BRCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348798.2	NM_007294	
TMBIM6	7009	hgsc.bcm.edu	37	12	50153060	50153060	+	Silent	SNP	A	A	G	rs12310796	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:50153060A>G	ENST00000267115.5	+	8	655	c.570A>G	c.(568-570)caA>caG	p.Q190Q	TMBIM6_ENST00000423828.1_Silent_p.Q248Q|TMBIM6_ENST00000549385.1_Silent_p.Q190Q|TMBIM6_ENST00000547798.1_Silent_p.Q153Q|TMBIM6_ENST00000395006.4_Silent_p.Q190Q|TMBIM6_ENST00000552699.1_Silent_p.Q248Q	NM_003217.2	NP_003208.2	P55061	BI1_HUMAN	transmembrane BAX inhibitor motif containing 6	190					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleus (GO:0005634)				lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	6						TTGATACTCAACTCATTATTG	0.418													A|||	27	0.00539137	0.0204	0.0	5008	,	,		20350	0.0		0.0	False		,,,				2504	0.0				p.Q248Q		Atlas-SNP	.											.	TMBIM6	26	.	0			c.A744G						PASS	.	A	,	81,4325	69.2+/-107.0	0,81,2122	212.0	192.0	199.0		744,570	3.0	1.0	12	dbSNP_120	199	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	TMBIM6	NM_001098576.1,NM_003217.2	,	0,81,6422	GG,GA,AA		0.0,1.8384,0.6228	,	248/296,190/238	50153060	81,12925	2203	4300	6503	SO:0001819	synonymous_variant	7009	exon8			TACTCAACTCATT	X75861	CCDS31797.1, CCDS44875.1	12q13.12	2013-10-08	2008-09-17	2008-09-17	ENSG00000139644	ENSG00000139644			11723	protein-coding gene	gene with protein product	"""BAX inhibitor 1"""	600748	"""testis enhanced gene transcript"""	TEGT		8530040, 9660918	Standard	NM_001098576		Approved	BI-1, BAXI1	uc001ruy.2	P55061	OTTHUMG00000169652	ENST00000267115.5:c.570A>G	12.37:g.50153060A>G		142.0	0.0	0		128.0	58.0	0.453125	NM_001098576	B2R5M4|F8W034|O14938|Q643A7|Q96J50	Silent	SNP	ENST00000267115.5	37	CCDS31797.1																																																																																			A|0.993;G|0.007	0.007	strong		0.418	TMBIM6-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405289.1	NM_003217	
FLT3LG	2323	hgsc.bcm.edu	37	19	49977929	49977929	+	Splice_Site	SNP	A	A	G	rs75750998	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49977929A>G	ENST00000594009.1	+	1	112	c.33A>G	c.(31-33)acA>acG	p.T11T	FLT3LG_ENST00000597551.1_Splice_Site_p.T11T|FLT3LG_ENST00000204637.2_5'UTR|CTD-3148I10.15_ENST00000595815.1_RNA|FLT3LG_ENST00000600429.1_Splice_Site_p.T11T|CTD-3148I10.9_ENST00000599536.1_3'UTR|FLT3LG_ENST00000344019.3_Splice_Site_p.T11T|FLT3LG_ENST00000595510.1_5'UTR|FLT3LG_ENST00000596435.1_Splice_Site_p.T11T	NM_001204503.1	NP_001191432.1	P49771	FLT3L_HUMAN	fms-related tyrosine kinase 3 ligand	11					embryonic hemopoiesis (GO:0035162)|lymphocyte differentiation (GO:0030098)|positive regulation of cell proliferation (GO:0008284)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of protein phosphorylation (GO:0001934)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|intrinsic component of external side of plasma membrane (GO:0031233)|membrane (GO:0016020)	receptor binding (GO:0005102)			large_intestine(2)|lung(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	10		all_lung(116;1.62e-07)|Lung NSC(112;8.47e-07)|all_neural(266;0.0381)|Ovarian(192;0.0392)		OV - Ovarian serous cystadenocarcinoma(262;0.00154)|GBM - Glioblastoma multiforme(486;0.0246)		GGAGCCCAACAGTGCGTAAAC	0.612													a|||	162	0.0323482	0.1036	0.0259	5008	,	,		12436	0.0		0.007	False		,,,				2504	0.0				p.T11T		Atlas-SNP	.											.	FLT3LG	22	.	0			c.A33G						PASS	.	A	,,	347,4059	173.0+/-202.9	13,321,1869	40.0	38.0	38.0		33,33,33	-4.8	0.9	19	dbSNP_131	38	13,8585	9.8+/-36.6	0,13,4286	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	FLT3LG	NM_001204502.1,NM_001204503.1,NM_001459.3	,,	13,334,6155	GG,GA,AA		0.1512,7.8756,2.7684	,,	11/236,11/236,11/236	49977929	360,12644	2203	4299	6502	SO:0001630	splice_region_variant	2323	exon1			CCCAACAGTGCGT	U04806	CCDS12767.1, CCDS62753.1	19q13.3	2014-01-30				ENSG00000090554		"""Endogenous ligands"""	3766	protein-coding gene	gene with protein product		600007				8145851, 7824267	Standard	NM_001204502		Approved		uc010yau.2	P49771		ENST00000594009.1:c.33+1A>G	19.37:g.49977929A>G		285.0	0.0	0		357.0	183.0	0.512605	NM_001204503	A0AVC2|B9EGH2|Q05C96	Silent	SNP	ENST00000594009.1	37	CCDS12767.1																																																																																			A|0.974;G|0.026	0.026	strong		0.612	FLT3LG-007	KNOWN	alternative_3_UTR|alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465305.1		Silent
GLI3	2737	hgsc.bcm.edu	37	7	42004897	42004897	+	Silent	SNP	G	G	C	rs35448119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:42004897G>C	ENST00000395925.3	-	15	3858	c.3774C>G	c.(3772-3774)ctC>ctG	p.L1258L	GLI3_ENST00000479210.1_5'UTR	NM_000168.5	NP_000159.3	P10071	GLI3_HUMAN	GLI family zinc finger 3	1258					anterior semicircular canal development (GO:0060873)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|camera-type eye morphogenesis (GO:0048593)|cell differentiation involved in kidney development (GO:0061005)|cerebral cortex radial glia guided migration (GO:0021801)|developmental growth (GO:0048589)|embryonic digestive tract development (GO:0048566)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic digit morphogenesis (GO:0042733)|embryonic skeletal system morphogenesis (GO:0048704)|forebrain dorsal/ventral pattern formation (GO:0021798)|forebrain radial glial cell differentiation (GO:0021861)|frontal suture morphogenesis (GO:0060364)|heart development (GO:0007507)|hindgut morphogenesis (GO:0007442)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|lambdoid suture morphogenesis (GO:0060366)|lateral ganglionic eminence cell proliferation (GO:0022018)|lateral semicircular canal development (GO:0060875)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|mammary gland specification (GO:0060594)|melanocyte differentiation (GO:0030318)|metanephros development (GO:0001656)|negative regulation of alpha-beta T cell differentiation (GO:0046639)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative thymic T cell selection (GO:0045060)|nose morphogenesis (GO:0043585)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte differentiation (GO:0048709)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein processing (GO:0016485)|proximal/distal pattern formation (GO:0009954)|response to estrogen (GO:0043627)|sagittal suture morphogenesis (GO:0060367)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|smoothened signaling pathway involved in spinal cord motor neuron cell fate specification (GO:0021776)|smoothened signaling pathway involved in ventral spinal cord interneuron specification (GO:0021775)|T cell differentiation in thymus (GO:0033077)|thymocyte apoptotic process (GO:0070242)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|wound healing (GO:0042060)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|primary cilium (GO:0072372)|transcriptional repressor complex (GO:0017053)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|histone acetyltransferase binding (GO:0035035)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|biliary_tract(1)|breast(4)|central_nervous_system(2)|endometrium(12)|kidney(7)|large_intestine(25)|lung(49)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	112						GCTGCCTGTTGAGACAGTTCC	0.627									Pallister-Hall syndrome;Greig Cephalopolysyndactyly				G|||	69	0.013778	0.0484	0.0072	5008	,	,		16948	0.0		0.0	False		,,,				2504	0.0				p.L1258L		Atlas-SNP	.											.	GLI3	312	.	0			c.C3774G						PASS	.	G		195,4211	123.3+/-160.7	7,181,2015	62.0	65.0	64.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3774	-9.7	0.0	7	dbSNP_126	64	0,8600		0,0,4300	no	coding-synonymous	GLI3	NM_000168.5		7,181,6315	CC,CG,GG		0.0,4.4258,1.4993		1258/1581	42004897	195,12811	2203	4300	6503	SO:0001819	synonymous_variant	2737	exon15	Familial Cancer Database	;	CCTGTTGAGACAG		CCDS5465.1	7p13	2013-01-25	2009-03-05		ENSG00000106571	ENSG00000106571		"""Zinc fingers, C2H2-type"""	4319	protein-coding gene	gene with protein product	"""zinc finger protein GLI3"", ""oncogene GLI3"", ""DNA-binding protein"""	165240	"""Greig cephalopolysyndactyly syndrome"", ""GLI-Kruppel family member GLI3"", ""glioma-associated oncogene family zinc finger 3"""	GCPS, PHS		2118997	Standard	NM_000168		Approved	PAP-A, PAPA, PAPA1, PAPB, ACLS, PPDIV	uc011kbh.2	P10071	OTTHUMG00000023630	ENST00000395925.3:c.3774C>G	7.37:g.42004897G>C		100.0	0.0	0		88.0	41.0	0.465909	NM_000168	A4D1W1|O75219|Q17RW4|Q75MT0|Q75MU9|Q9UDT5|Q9UJ39	Silent	SNP	ENST00000395925.3	37	CCDS5465.1																																																																																			G|0.984;C|0.016	0.016	strong		0.627	GLI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250806.3	NM_000168	
KCNK12	56660	hgsc.bcm.edu	37	2	47748487	47748487	+	Silent	SNP	G	G	A	rs77883212	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:47748487G>A	ENST00000327876.4	-	2	1459	c.852C>T	c.(850-852)atC>atT	p.I284I	MSH2_ENST00000461394.1_Intron	NM_022055.1	NP_071338.1	Q9HB15	KCNKC_HUMAN	potassium channel, subfamily K, member 12	284						integral component of membrane (GO:0016021)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.0?(2)|p.?(2)		NS(1)|endometrium(1)|lung(3)|ovary(1)	6		all_hematologic(82;0.0495)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			CGCCGAGCAGGATGAAGAGGA	0.607													G|||	48	0.00958466	0.0333	0.0058	5008	,	,		13662	0.0		0.0	False		,,,				2504	0.0				p.I284I		Atlas-SNP	.											.	KCNK12	11	.	4	Whole gene deletion(2)|Unknown(2)	haematopoietic_and_lymphoid_tissue(3)|prostate(1)	c.C852T						PASS	.	G		151,4255	103.0+/-141.5	2,147,2054	57.0	54.0	55.0		852	1.5	1.0	2	dbSNP_132	55	4,8594	3.0+/-9.4	0,4,4295	no	coding-synonymous	KCNK12	NM_022055.1		2,151,6349	AA,AG,GG		0.0465,3.4271,1.1919		284/431	47748487	155,12849	2203	4299	6502	SO:0001819	synonymous_variant	56660	exon2			GAGCAGGATGAAG	AF287302	CCDS1835.1	2p16.3	2012-03-07			ENSG00000184261	ENSG00000184261		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6274	protein-coding gene	gene with protein product		607366				11060316	Standard	NM_022055		Approved	THIK-2, THIK2, K2p12.1	uc002rwb.3	Q9HB15	OTTHUMG00000129131	ENST00000327876.4:c.852C>T	2.37:g.47748487G>A		86.0	0.0	0		81.0	35.0	0.432099	NM_022055		Silent	SNP	ENST00000327876.4	37	CCDS1835.1																																																																																			G|0.986;A|0.014	0.014	strong		0.607	KCNK12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251182.2	NM_022055	
ERN1	2081	hgsc.bcm.edu	37	17	62137893	62137893	+	Missense_Mutation	SNP	T	T	C	rs79107850	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:62137893T>C	ENST00000433197.3	-	11	1237	c.1142A>G	c.(1141-1143)aAc>aGc	p.N381S		NM_001433.3	NP_001424.3			endoplasmic reticulum to nucleus signaling 1											central_nervous_system(4)|kidney(1)|lung(2)|ovary(1)|stomach(1)	9						GGGTAGATTGTTGGGAAATCT	0.473													T|||	33	0.00658946	0.0234	0.0029	5008	,	,		21401	0.0		0.0	False		,,,				2504	0.0				p.N381S		Atlas-SNP	.											.	ERN1	102	.	0			c.A1142G						PASS	.	T	SER/ASN	60,3790		1,58,1866	164.0	158.0	160.0		1142	5.3	1.0	17	dbSNP_131	160	0,8276		0,0,4138	yes	missense	ERN1	NM_001433.3	46	1,58,6004	CC,CT,TT		0.0,1.5584,0.4948	benign	381/978	62137893	60,12066	1925	4138	6063	SO:0001583	missense	2081	exon11			AGATTGTTGGGAA	AF059198	CCDS45762.1	17q23	2011-08-12	2007-08-14			ENSG00000178607			3449	protein-coding gene	gene with protein product	"""inositol-requiring enzyme 1"""	604033	"""ER to nucleus signalling 1"""			9637683	Standard	NM_001433		Approved	IRE1, IRE1P	uc002jdz.2	O75460		ENST00000433197.3:c.1142A>G	17.37:g.62137893T>C	ENSP00000401445:p.Asn381Ser	135.0	0.0	0		150.0	64.0	0.426667	NM_001433		Missense_Mutation	SNP	ENST00000433197.3	37	CCDS45762.1	17	0.007783882783882784	15	0.03048780487804878	2	0.0055248618784530384	0	0.0	0	0.0	T	8.605	0.887770	0.17540	0.015584	0.0	ENSG00000178607	ENST00000433197	T	0.58060	0.36	5.33	5.33	0.75918	.	0.150729	0.64402	D	0.000013	T	0.11110	0.0271	N	0.14661	0.345	0.30788	N	0.741199	B	0.06786	0.001	B	0.01281	0.0	T	0.16158	-1.0412	10	0.07175	T	0.84	-44.0147	8.0501	0.30572	0.0:0.1225:0.0:0.8775	.	381	O75460	ERN1_HUMAN	S	381	ENSP00000401445:N381S	ENSP00000401445:N381S	N	-	2	0	ERN1	59491625	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	4.120000	0.57897	2.008000	0.58898	0.379000	0.24179	AAC	T|0.990;C|0.010	0.010	strong		0.473	ERN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443734.2	NM_001433	
OC90	729330	hgsc.bcm.edu	37	8	133036743	133036743	+	Silent	SNP	A	A	G	rs11991659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133036743A>G	ENST00000443356.2	-	15	1553	c.1467T>C	c.(1465-1467)ccT>ccC	p.P489P	OC90_ENST00000603859.1_Silent_p.P473P|OC90_ENST00000254627.3_Silent_p.P473P|OC90_ENST00000262283.5_Silent_p.P685P			Q02509	OC90_HUMAN	otoconin 90	489					lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(23)|ovary(2)|prostate(1)|skin(1)	37	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)			TTCCATGAAGAGGCCCGATCC	0.577													G|||	252	0.0503195	0.174	0.013	5008	,	,		19645	0.002		0.008	False		,,,				2504	0.0031				p.P473P		Atlas-SNP	.											OC90_ENST00000262283,brain,primitive_neuroectodermal_tumour-medulloblastoma,-1,2	OC90	163	2	0			c.T1419C						PASS	.	G		470,3414		23,424,1495	23.0	26.0	25.0		1419	0.9	0.0	8	dbSNP_120	25	67,8215		1,65,4075	no	coding-synonymous	OC90	NM_001080399.2		24,489,5570	GG,GA,AA		0.809,12.1009,4.4139		473/478	133036743	537,11629	1942	4141	6083	SO:0001819	synonymous_variant	729330	exon14			ATGAAGAGGCCCG	Z14310	CCDS47919.1	8q24.22	2011-03-01			ENSG00000253117	ENSG00000253117			8100	protein-coding gene	gene with protein product		601658		PLA2L		10329003, 9860971	Standard	NM_001080399		Approved		uc011lix.1	Q02509	OTTHUMG00000164672	ENST00000443356.2:c.1467T>C	8.37:g.133036743A>G		52.0	0.0	0		34.0	20.0	0.588235	NM_001080399	B4DNG8	Silent	SNP	ENST00000443356.2	37																																																																																				A|0.952;G|0.048	0.048	strong		0.577	OC90-201	KNOWN	basic	protein_coding	protein_coding		NM_001080399	
TTN	7273	hgsc.bcm.edu	37	2	179610695	179610695	+	Intron	SNP	C	C	T	rs72648915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179610695C>T	ENST00000591111.1	-	46	10585				TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Intron|TTN_ENST00000360870.5_Missense_Mutation_p.V5478M|TTN-AS1_ENST00000578746.1_RNA|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Intron			Q8WZ42	TITIN_HUMAN	titin						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)			TTTGCTATCACAGCAAATATT	0.403													T|||	192	0.0383387	0.1399	0.0101	5008	,	,		20502	0.0		0.0	False		,,,				2504	0.0				p.V5478M		Atlas-SNP	.											.	TTN	18412	.	0			c.G16432A						PASS	.	T	,,MET/VAL,,	529,3877	774.4+/-414.0	33,463,1707	108.0	105.0	106.0		,,16432,,	-6.2	0.0	2	dbSNP_130	106	7,8593	817.5+/-406.9	0,7,4293	no	intron,intron,missense,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,21,,	33,470,6000	TT,TC,CC		0.0814,12.0064,4.1212	,,,,	,,5478/5605,,	179610695	536,12470	2203	4300	6503	SO:0001627	intron_variant	7273	exon46			CTATCACAGCAAA	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.10361-4047G>A	2.37:g.179610695C>T		97.0	0.0	0		100.0	47.0	0.47	NM_133379	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		68	0.031135531135531136	63	0.12804878048780488	5	0.013812154696132596	0	0.0	0	0.0	T	0.009	-1.801722	0.00611	0.120064	8.14E-4	ENSG00000155657	ENST00000360870;ENST00000306136	T	0.59083	0.29	6.07	-6.15	0.02105	.	.	.	.	.	T	0.00300	0.0009	N	0.12182	0.205	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.05550	-1.0878	8	0.25106	T	0.35	.	5.6092	0.17396	0.098:0.3526:0.417:0.1325	.	5478	Q8WZ42-6	.	M	5478;759	ENSP00000354117:V5478M	ENSP00000304714:V759M	V	-	1	0	TTN	179318940	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-0.290000	0.08354	-1.567000	0.01671	-1.170000	0.01741	GTG	C|0.961;T|0.039	0.039	strong		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
IKBKE	9641	hgsc.bcm.edu	37	1	206658404	206658404	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:206658404C>T	ENST00000367120.3	+	14	1871	c.1498C>T	c.(1498-1500)Cgg>Tgg	p.R500W	IKBKE_ENST00000537984.1_Missense_Mutation_p.R415W	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	500	Interaction with DDX3X.				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)					GTCCAGGCTGCGGACTGTGAG	0.617																																					p.R500W		Atlas-SNP	.											.	IKBKE	77	.	0			c.C1498T						PASS	.						47.0	42.0	44.0					1																	206658404		2203	4300	6503	SO:0001583	missense	9641	exon14			AGGCTGCGGACTG	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.1498C>T	1.37:g.206658404C>T	ENSP00000356087:p.Arg500Trp	162.0	0.0	0		122.0	56.0	0.459016	NM_001193322	D3DT78|Q3B754|Q3KR43|Q5JTS6	Missense_Mutation	SNP	ENST00000367120.3	37	CCDS30996.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.070122	0.76301	.	.	ENSG00000143466	ENST00000367120;ENST00000537984	T;T	0.64085	-0.08;0.08	5.24	4.32	0.51571	.	0.527792	0.20321	N	0.094636	T	0.60274	0.2256	L	0.36672	1.1	0.22961	N	0.998503	D;D	0.69078	0.991;0.997	P;P	0.50192	0.549;0.634	T	0.55611	-0.8114	10	0.66056	D	0.02	2.2858	12.7736	0.57436	0.1634:0.8366:0.0:0.0	.	415;500	Q3B754;Q14164	.;IKKE_HUMAN	W	500;415	ENSP00000356087:R500W;ENSP00000444529:R415W	ENSP00000356087:R500W	R	+	1	2	IKBKE	204725027	0.993000	0.37304	1.000000	0.80357	0.994000	0.84299	1.450000	0.35134	1.204000	0.43247	0.563000	0.77884	CGG	.	.	none		0.617	IKBKE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088484.1		
GTPBP3	84705	hgsc.bcm.edu	37	19	17450038	17450038	+	Silent	SNP	C	C	T	rs11880362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17450038C>T	ENST00000324894.8	+	6	839	c.771C>T	c.(769-771)ccC>ccT	p.P257P	GTPBP3_ENST00000598038.1_3'UTR|GTPBP3_ENST00000358792.7_Silent_p.P289P|GTPBP3_ENST00000361619.5_Silent_p.P279P|GTPBP3_ENST00000600625.1_Silent_p.P257P	NM_032620.3|NM_133644.3	NP_116009.2|NP_598399.2	Q969Y2	GTPB3_HUMAN	GTP binding protein 3 (mitochondrial)	257	TrmE-type G.				tRNA modification (GO:0006400)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|skin(2)|upper_aerodigestive_tract(1)	18						TCACTGGACCCCCCAATGCGG	0.667													c|||	103	0.0205671	0.0726	0.0101	5008	,	,		12031	0.0		0.0	False		,,,				2504	0.0				p.P289P		Atlas-SNP	.											.	GTPBP3	40	.	0			c.C867T						PASS	.	C	,,,	288,4118		9,270,1924	20.0	22.0	21.0		771,837,771,867	-6.3	0.9	19	dbSNP_120	21	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GTPBP3	NM_001128855.2,NM_001195422.1,NM_032620.3,NM_133644.3	,,,	9,271,6223	TT,TC,CC		0.0116,6.5365,2.2221	,,,	257/472,279/515,257/493,289/525	17450038	289,12717	2203	4300	6503	SO:0001819	synonymous_variant	84705	exon5			TGGACCCCCCAAT	AF360742	CCDS32950.1, CCDS32951.1, CCDS56088.1, CCDS59364.1	19p13.2	2008-02-05				ENSG00000130299			14880	protein-coding gene	gene with protein product		608536				1290633	Standard	NM_001128855		Approved	MSS1, THDF1, GTPBG3, MTGP1, FLJ14700	uc010xpo.2	Q969Y2		ENST00000324894.8:c.771C>T	19.37:g.17450038C>T		43.0	0.0	0		47.0	23.0	0.489362	NM_133644	A6NFH1|A6NIG5|A6NKR4|A8K7B4|B7Z4V8|Q8TCY6|Q8WUW9|Q969G4|Q9BX61	Silent	SNP	ENST00000324894.8	37	CCDS32951.1																																																																																			C|0.972;T|0.028	0.028	strong		0.667	GTPBP3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463624.1	NM_032620	
MRPS24	64951	hgsc.bcm.edu	37	7	43906544	43906544	+	Silent	SNP	C	C	T	rs9154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:43906544C>T	ENST00000317534.5	-	4	319	c.258G>A	c.(256-258)acG>acA	p.T86T	URGCP-MRPS24_ENST00000603700.1_3'UTR|MRPS24_ENST00000467084.1_5'UTR	NM_032014.2	NP_114403.1	Q96EL2	RT24_HUMAN	mitochondrial ribosomal protein S24	86					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrial small ribosomal subunit (GO:0005763)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)	p.T86T(1)		large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	5						CATCCTCCACCGTTCGCTCTG	0.557													C|||	248	0.0495208	0.1831	0.0058	5008	,	,		17550	0.0		0.002	False		,,,				2504	0.0				p.T86T		Atlas-SNP	.											MRPS24,colon,carcinoma,-1,2	MRPS24	9	2	1	Substitution - coding silent(1)	lung(1)	c.G258A						PASS	.	C	,	694,3712	291.0+/-281.2	51,592,1560	68.0	64.0	65.0		,258	-10.5	0.1	7	dbSNP_52	65	5,8595	4.3+/-15.6	0,5,4295	no	utr-3,coding-synonymous	MRPS24,URGCP-MRPS24	NM_001204871.1,NM_032014.2	,	51,597,5855	TT,TC,CC		0.0581,15.7512,5.3744	,	,86/168	43906544	699,12307	2203	4300	6503	SO:0001819	synonymous_variant	64951	exon4			CTCCACCGTTCGC	AB061207	CCDS5473.1	7p14	2012-09-13			ENSG00000062582	ENSG00000062582		"""Mitochondrial ribosomal proteins / small subunits"""	14510	protein-coding gene	gene with protein product		611986				8127713, 11279123	Standard	NM_032014		Approved	MRP-S24, HSPC335	uc003tit.1	Q96EL2	OTTHUMG00000023175	ENST00000317534.5:c.258G>A	7.37:g.43906544C>T		55.0	0.0	0		68.0	28.0	0.411765	NM_032014	A4D1U9|P82668|Q96Q23|Q9P047	Silent	SNP	ENST00000317534.5	37	CCDS5473.1																																																																																			C|0.953;T|0.047	0.047	strong		0.557	MRPS24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250949.1	NM_032014	
CYP4F12	66002	hgsc.bcm.edu	37	19	15795690	15795690	+	Missense_Mutation	SNP	G	G	C	rs61729079	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15795690G>C	ENST00000550308.1	+	8	1363	c.983G>C	c.(982-984)gGa>gCa	p.G328A	CYP4F12_ENST00000324632.10_Missense_Mutation_p.G328A	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	328					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	TTCATGTTTGGAGGTGAGGGT	0.532													.|||	99	0.0197684	0.0711	0.0058	5008	,	,		18415	0.0		0.001	False		,,,				2504	0.0				p.G328A		Atlas-SNP	.											.	CYP4F12	89	.	0			c.G983C						PASS	.	G	ALA/GLY	380,4022		6,368,1827	89.0	84.0	85.0		983	-5.2	0.0	19	dbSNP_129	85	3,8597		0,3,4297	yes	missense	CYP4F12	NM_023944.3	60	6,371,6124	CC,CG,GG		0.0349,8.6324,2.9457	benign	328/525	15795690	383,12619	2201	4300	6501	SO:0001583	missense	66002	exon8			TGTTTGGAGGTGA	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.983G>C	19.37:g.15795690G>C	ENSP00000448998:p.Gly328Ala	96.0	0.0	0		151.0	48.0	0.317881	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	39	0.017857142857142856	37	0.07520325203252033	2	0.0055248618784530384	0	0.0	0	0.0	.	0.001	-3.085659	0.00035	0.086324	3.49E-4	ENSG00000186204	ENST00000550308;ENST00000324632	T;T	0.64085	-0.08;-0.08	2.58	-5.16	0.02857	.	0.269718	0.28176	N	0.016308	T	0.01029	0.0034	N	0.02368	-0.58	0.09310	N	0.999999	B	0.02656	0.0	B	0.08055	0.003	T	0.17107	-1.0380	10	0.25106	T	0.35	.	8.4642	0.32947	0.2353:0.4491:0.3156:0.0	rs61729079	328	Q9HCS2	CP4FC_HUMAN	A	328	ENSP00000448998:G328A;ENSP00000321821:G328A	ENSP00000321821:G328A	G	+	2	0	CYP4F12	15656690	0.000000	0.05858	0.041000	0.18516	0.005000	0.04900	-1.520000	0.02241	-5.413000	0.00015	-4.134000	0.00010	GGA	G|0.981;C|0.019	0.019	strong		0.532	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
RPGR	6103	hgsc.bcm.edu	37	X	38145841	38145841	+	Intron	SNP	C	C	T	rs147388235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:38145841C>T	ENST00000339363.3	-	14	2688				RPGR_ENST00000378505.2_Missense_Mutation_p.R804K|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000309513.3_Intron|RPGR_ENST00000318842.7_Intron|RPGR_ENST00000342811.3_Intron|RPGR_ENST00000338898.3_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						ttcctcccctctcccctctgt	0.572													C|||	38	0.0100662	0.0265	0.0043	3775	,	,		7854	0.0		0.0	False		,,,				2504	0.0				p.R804K		Atlas-SNP	.											.	RPGR	175	.	0			c.G2411A						PASS	.		,LYS/ARG	114,3133		2,98,12,1355,325	209.0	149.0	170.0		,2411	-0.9	0.0	X	dbSNP_134	170	3,5559		0,0,3,2116,1327	yes	intron,missense	RPGR	NM_000328.2,NM_001034853.1	,26	2,98,15,3471,1652	TT,TC,T,CC,C		0.0539,3.5109,1.3282	,benign	,804/1153	38145841	117,8692	1792	3446	5238	SO:0001627	intron_variant	6103	exon15			TCCCCTCTCCCCT	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+505G>A	X.37:g.38145841C>T		469.0	1.0	0.0021322		522.0	236.0	0.452107	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Missense_Mutation	SNP	ENST00000339363.3	37		13	0.007836045810729355	9	0.018367346938775512	3	0.008287292817679558	0	0.0	0	0.0	c	5.090	0.202211	0.09652	0.035109	5.39E-4	ENSG00000156313	ENST00000378505	T	0.02301	4.35	2.0	-0.924	0.10462	.	0.274603	0.23272	U	0.050002	T	0.00300	0.0009	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46400	-0.9194	10	0.31617	T	0.26	.	4.6346	0.12518	0.0:0.4094:0.1765:0.4141	.	804	E9PE28	.	K	804	ENSP00000367766:R804K	ENSP00000367766:R804K	R	-	2	0	RPGR	38030785	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	0.188000	0.17018	-0.612000	0.05701	-0.921000	0.02739	AGA	C|0.985;T|0.015	0.015	strong		0.572	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
POLRMT	5442	hgsc.bcm.edu	37	19	617804	617804	+	Silent	SNP	G	G	A	rs144281668	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:617804G>A	ENST00000588649.2	-	18	3552	c.3468C>T	c.(3466-3468)caC>caT	p.H1156H	AC005559.2_ENST00000591847.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	1156	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)			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)		CATCAGCTGCGTGAGTCCAGT	0.642													g|||	3	0.000599042	0.0023	0.0	5008	,	,		11388	0.0		0.0	False		,,,				2504	0.0				p.H1156H		Atlas-SNP	.											.	POLRMT	91	.	0			c.C3468T						PASS	.	G		13,4391		0,13,2189	83.0	65.0	71.0		3468	-7.8	0.0	19	dbSNP_134	71	1,8597		0,1,4298	no	coding-synonymous	POLRMT	NM_005035.3		0,14,6487	AA,AG,GG		0.0116,0.2952,0.1077		1156/1231	617804	14,12988	2202	4299	6501	SO:0001819	synonymous_variant	5442	exon18			AGCTGCGTGAGTC		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.3468C>T	19.37:g.617804G>A		128.0	0.0	0		139.0	58.0	0.417266	NM_005035	O60370	Silent	SNP	ENST00000588649.2	37	CCDS12036.1																																																																																			G|0.999;A|0.001	0.001	strong		0.642	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035	
SPTAN1	6709	hgsc.bcm.edu	37	9	131362361	131362361	+	Silent	SNP	T	T	C	rs945831	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131362361T>C	ENST00000372731.4	+	27	3656	c.3546T>C	c.(3544-3546)gaT>gaC	p.D1182D	SPTAN1_ENST00000358161.5_Silent_p.D1182D|SPTAN1_ENST00000372739.3_Silent_p.D1182D	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1182					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						TTGAATAGGATGAAACTGATT	0.433													T|||	175	0.0349441	0.1263	0.0115	5008	,	,		18973	0.0		0.0	False		,,,				2504	0.0				p.D1182D	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.T3546C						PASS	.	T	,,	478,3928	223.3+/-239.8	28,422,1753	124.0	113.0	117.0		3546,3486,3546	6.1	1.0	9	dbSNP_86	117	8,8592	5.0+/-18.6	0,8,4292	no	coding-synonymous,coding-synonymous,coding-synonymous	SPTAN1	NM_001130438.2,NM_001195532.1,NM_003127.3	,,	28,430,6045	CC,CT,TT		0.093,10.8488,3.7367	,,	1182/2478,1162/2453,1182/2473	131362361	486,12520	2203	4300	6503	SO:0001819	synonymous_variant	6709	exon27			ATAGGATGAAACT	M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"""EF-hand domain containing"""	11273	protein-coding gene	gene with protein product	"""alpha-fodrin"""	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.3546T>C	9.37:g.131362361T>C		202.0	0.0	0		229.0	93.0	0.406114	NM_003127	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Silent	SNP	ENST00000372731.4	37	CCDS6905.1																																																																																			T|0.963;C|0.037	0.037	strong		0.433	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127	
RIF1	55183	hgsc.bcm.edu	37	2	152320501	152320501	+	Silent	SNP	T	T	C	rs7566841	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:152320501T>C	ENST00000243326.5	+	29	4950	c.4467T>C	c.(4465-4467)acT>acC	p.T1489T	RIF1_ENST00000430328.2_Silent_p.T1489T|RIF1_ENST00000453091.2_Silent_p.T1489T|RIF1_ENST00000428287.2_Silent_p.T1489T|RIF1_ENST00000444746.2_Silent_p.T1489T			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		ATGAGAAGACTCTTGGGGAAA	0.368													T|||	101	0.0201677	0.0734	0.0043	5008	,	,		19435	0.0		0.001	False		,,,				2504	0.0				p.T1489T		Atlas-SNP	.											.	RIF1	244	.	0			c.T4467C						PASS	.	T	,,,	213,4191		4,205,1993	57.0	65.0	62.0		4467,4467,4467,4467	1.7	0.1	2	dbSNP_116	62	1,8589		0,1,4294	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RIF1	NM_001177663.1,NM_001177664.1,NM_001177665.1,NM_018151.4	,,,	4,206,6287	CC,CT,TT		0.0116,4.8365,1.6469	,,,	1489/2447,1489/2447,1489/2447,1489/2473	152320501	214,12780	2202	4295	6497	SO:0001819	synonymous_variant	55183	exon30			GAAGACTCTTGGG	AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"""RAP1 interacting factor homolog (yeast)"""			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.4467T>C	2.37:g.152320501T>C		113.0	0.0	0		80.0	50.0	0.625	NM_018151	A0AVS0|Q9NS16	Silent	SNP	ENST00000243326.5	37	CCDS2194.1																																																																																			T|0.981;C|0.019	0.019	strong		0.368	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3		
CNNM1	26507	hgsc.bcm.edu	37	10	101120671	101120671	+	Silent	SNP	G	G	A	rs61735150	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:101120671G>A	ENST00000356713.4	+	3	2086	c.1797G>A	c.(1795-1797)acG>acA	p.T599T	CNNM1_ENST00000446890.1_Silent_p.T528T|CNNM1_ENST00000370534.4_Silent_p.T234T|CNNM1_ENST00000370528.3_Silent_p.T528T	NM_020348.2	NP_065081.2	Q9NRU3	CNNM1_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 1	599					ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(5)|ovary(1)|prostate(1)|skin(1)	25		Colorectal(252;0.234)		Epithelial(162;6.82e-10)|all cancers(201;5.62e-08)		TTTCGGACACGGAGATGCGGG	0.542													G|||	20	0.00399361	0.0144	0.0014	5008	,	,		20089	0.0		0.0	False		,,,				2504	0.0				p.T599T		Atlas-SNP	.											CNNM1_ENST00000356713,NS,carcinoma,0,2	CNNM1	101	2	0			c.G1797A						PASS	.	G		86,4320	72.5+/-110.5	0,86,2117	117.0	111.0	113.0		1797	-11.5	0.0	10	dbSNP_129	113	0,8600		0,0,4300	no	coding-synonymous	CNNM1	NM_020348.2		0,86,6417	AA,AG,GG		0.0,1.9519,0.6612		599/952	101120671	86,12920	2203	4300	6503	SO:0001819	synonymous_variant	26507	exon3			GGACACGGAGATG	AF169226	CCDS7478.2	10q24.2	2014-08-08	2014-08-07		ENSG00000119946	ENSG00000119946			102	protein-coding gene	gene with protein product		607802	"""cyclin M1"""	ACDP1		21393841	Standard	NM_020348		Approved		uc001kpp.4	Q9NRU3	OTTHUMG00000018881	ENST00000356713.4:c.1797G>A	10.37:g.101120671G>A		75.0	0.0	0		93.0	46.0	0.494624	NM_020348	Q4QQG7|Q4QQH8|Q4QQP9|Q9NT45	Silent	SNP	ENST00000356713.4	37	CCDS7478.2																																																																																			G|0.992;A|0.008	0.008	strong		0.542	CNNM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049792.2	NM_020348	
MESP2	145873	hgsc.bcm.edu	37	15	90320000	90320000	+	Missense_Mutation	SNP	G	G	A	rs28462216	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90320000G>A	ENST00000341735.3	+	1	412	c.412G>A	c.(412-414)Gtg>Atg	p.V138M	MESP2_ENST00000560219.1_Intron|MESP2_ENST00000558723.1_Intron	NM_001039958.1	NP_001035047.1	Q0VG99	MESP2_HUMAN	mesoderm posterior basic helix-loop-helix transcription factor 2	138			V -> M (in dbSNP:rs28462216).		mesodermal cell migration (GO:0008078)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction involved in regulation of gene expression (GO:0023019)|somite rostral/caudal axis specification (GO:0032525)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6	Lung NSC(78;0.0221)|all_lung(78;0.0448)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)			CCTATCGGCCGTGCTGGGTCT	0.736													G|||	393	0.0784744	0.2572	0.0216	5008	,	,		13798	0.0		0.002	False		,,,				2504	0.0368				p.V138M		Atlas-SNP	.											.	MESP2	20	.	0			c.G412A						PASS	.	G	MET/VAL	771,3403		58,655,1374	7.0	9.0	8.0		412	1.8	1.0	15	dbSNP_125	8	5,8363		0,5,4179	no	missense	MESP2	NM_001039958.1	21	58,660,5553	AA,AG,GG		0.0598,18.4715,6.1872	benign	138/398	90320000	776,11766	2087	4184	6271	SO:0001583	missense	145873	exon1			TCGGCCGTGCTGG		CCDS42078.1	15q26.1	2014-06-30	2014-06-30			ENSG00000188095		"""Basic helix-loop-helix proteins"""	29659	protein-coding gene	gene with protein product		605195	"""mesoderm posterior 2 homolog (mouse)"""			11578861	Standard	NM_001039958		Approved	SCDO2, bHLHc6	uc002bon.3	Q0VG99		ENST00000341735.3:c.412G>A	15.37:g.90320000G>A	ENSP00000342392:p.Val138Met	36.0	0.0	0		42.0	42.0	1	NM_001039958	Q7RTU2	Missense_Mutation	SNP	ENST00000341735.3	37	CCDS42078.1	130	0.05952380952380952	121	0.2459349593495935	8	0.022099447513812154	0	0.0	1	0.0013192612137203166	G	13.92	2.380200	0.42207	0.184715	5.98E-4	ENSG00000188095	ENST00000341735	D	0.88509	-2.39	3.89	1.76	0.24704	Helix-loop-helix DNA-binding (3);	.	.	.	.	T	0.00109	0.0003	L	0.55481	1.735	0.47905	P	4.5799999999995844E-4	D	0.63880	0.993	P	0.49528	0.614	T	0.00146	-1.1991	8	0.51188	T	0.08	-6.0463	11.5389	0.50655	0.0:0.6191:0.3809:0.0	rs28462216;rs60624982	138	Q0VG99	MESP2_HUMAN	M	138	ENSP00000342392:V138M	ENSP00000342392:V138M	V	+	1	0	MESP2	88121004	0.564000	0.26602	1.000000	0.80357	0.565000	0.35776	0.973000	0.29422	0.785000	0.33685	0.313000	0.20887	GTG	G|0.940;A|0.060	0.060	strong		0.736	MESP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416421.1	XM_085261	
ICE1	23379	hgsc.bcm.edu	37	5	5464237	5464237	+	Missense_Mutation	SNP	A	A	C	rs10065646	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:5464237A>C	ENST00000296564.7	+	13	5012	c.4790A>C	c.(4789-4791)cAa>cCa	p.Q1597P		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		1597			Q -> P (in dbSNP:rs10065646).		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						ACAAAAACTCAAAGAAGCCAA	0.418													A|||	242	0.0483227	0.1725	0.0187	5008	,	,		20166	0.0		0.001	False		,,,				2504	0.0				p.Q1597P		Atlas-SNP	.											.	KIAA0947	301	.	0			c.A4790C						PASS	.	A	PRO/GLN	500,3252		44,412,1420	47.0	47.0	47.0		4790	-0.5	0.0	5	dbSNP_119	47	9,8207		0,9,4099	yes	missense	KIAA0947	NM_015325.1	76	44,421,5519	CC,CA,AA		0.1095,13.3262,4.253	benign	1597/2267	5464237	509,11459	1876	4108	5984	SO:0001583	missense	23379	exon13			AAACTCAAAGAAG																												ENST00000296564.7:c.4790A>C	5.37:g.5464237A>C	ENSP00000296564:p.Gln1597Pro	43.0	0.0	0		43.0	23.0	0.534884	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Missense_Mutation	SNP	ENST00000296564.7	37	CCDS47187.1	100	0.045787545787545784	88	0.17886178861788618	12	0.03314917127071823	0	0.0	0	0.0	A	9.076	0.998101	0.19043	0.133262	0.001095	ENSG00000164151	ENST00000296564	T	0.10763	2.84	5.27	-0.478	0.12093	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B	0.15930	0.015	B	0.16722	0.016	T	0.46289	-0.9202	8	0.29301	T	0.29	0.0	7.2058	0.25907	0.3909:0.4671:0.0:0.1421	rs10065646;rs52803291;rs10065646	1597	Q9Y2F5	K0947_HUMAN	P	1597	ENSP00000296564:Q1597P	ENSP00000296564:Q1597P	Q	+	2	0	KIAA0947	5517237	0.000000	0.05858	0.000000	0.03702	0.560000	0.35617	-0.688000	0.05150	-0.319000	0.08652	0.377000	0.23210	CAA	A|0.932;C|0.068	0.068	strong		0.418	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1		
SIPA1L3	23094	hgsc.bcm.edu	37	19	38610394	38610394	+	Missense_Mutation	SNP	G	G	A	rs140119542	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38610394G>A	ENST00000222345.6	+	9	3249	c.2740G>A	c.(2740-2742)Ggg>Agg	p.G914R		NM_015073.1	NP_055888.1	O60292	SI1L3_HUMAN	signal-induced proliferation-associated 1 like 3	914					hematopoietic progenitor cell differentiation (GO:0002244)|regulation of small GTPase mediated signal transduction (GO:0051056)	extracellular space (GO:0005615)	GTPase activator activity (GO:0005096)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(22)|ovary(2)|prostate(4)|skin(3)	59			Lung(45;0.000246)|LUSC - Lung squamous cell carcinoma(53;0.000292)			CTGCTACTGCGGGGATGTCAT	0.532													G|||	3	0.000599042	0.0008	0.0	5008	,	,		20769	0.0		0.0	False		,,,				2504	0.002				p.G914R		Atlas-SNP	.											SIPA1L3,caecum,carcinoma,0,1	SIPA1L3	150	1	0			c.G2740A						PASS	.	G	ARG/GLY	1,4403	2.1+/-5.4	0,1,2201	98.0	108.0	105.0		2740	5.8	1.0	19	dbSNP_134	105	1,8599	1.2+/-3.3	0,1,4299	no	missense	SIPA1L3	NM_015073.1	125	0,2,6500	AA,AG,GG		0.0116,0.0227,0.0154	benign	914/1782	38610394	2,13002	2202	4300	6502	SO:0001583	missense	23094	exon9			TACTGCGGGGATG	AB011117	CCDS33007.1	19q13.13	2008-02-05			ENSG00000105738	ENSG00000105738			23801	protein-coding gene	gene with protein product							Standard	XM_005258671		Approved	KIAA0545	uc002ohk.3	O60292	OTTHUMG00000073727	ENST00000222345.6:c.2740G>A	19.37:g.38610394G>A	ENSP00000222345:p.Gly914Arg	61.0	0.0	0		66.0	33.0	0.5	NM_015073	Q2TV87	Missense_Mutation	SNP	ENST00000222345.6	37	CCDS33007.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	8.917	0.960050	0.18507	2.27E-4	1.16E-4	ENSG00000105738	ENST00000222345	T	0.73152	-0.72	5.75	5.75	0.90469	.	0.183723	0.47852	D	0.000205	T	0.44871	0.1314	N	0.02345	-0.59	0.38997	D	0.959275	B	0.17852	0.024	B	0.14578	0.011	T	0.51725	-0.8669	10	0.02654	T	1	-42.3387	18.7237	0.91705	0.0:0.0:1.0:0.0	.	914	O60292	SI1L3_HUMAN	R	914	ENSP00000222345:G914R	ENSP00000222345:G914R	G	+	1	0	SIPA1L3	43302234	0.002000	0.14202	0.997000	0.53966	0.994000	0.84299	0.479000	0.22228	2.725000	0.93324	0.655000	0.94253	GGG	G|1.000;A|0.000	0.000	strong		0.532	SIPA1L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156294.2	XM_032278	
ACER2	340485	hgsc.bcm.edu	37	9	19450598	19450598	+	Silent	SNP	G	G	C	rs7855739	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:19450598G>C	ENST00000340967.2	+	6	818	c.792G>C	c.(790-792)ctG>ctC	p.L264L	RP11-363E7.4_ENST00000563205.1_RNA	NM_001010887.2	NP_001010887.2	Q5QJU3	ACER2_HUMAN	alkaline ceramidase 2	264					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to drug (GO:0035690)|ceramide metabolic process (GO:0006672)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of protein glycosylation in Golgi (GO:0090285)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|response to retinoic acid (GO:0032526)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	ceramidase activity (GO:0017040)|dihydroceramidase activity (GO:0071633)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)	13						TGTCCCTCCTGTGTGCCAACA	0.517													G|||	375	0.0748802	0.2579	0.0216	5008	,	,		19358	0.003		0.0	False		,,,				2504	0.0164				p.L264L		Atlas-SNP	.											.	ACER2	24	.	0			c.G792C						PASS	.	G		1024,3382	378.7+/-323.0	131,762,1310	145.0	131.0	136.0		792	-0.3	0.9	9	dbSNP_116	136	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	ACER2	NM_001010887.2		131,770,5602	CC,CG,GG		0.093,23.241,7.9348		264/276	19450598	1032,11974	2203	4300	6503	SO:0001819	synonymous_variant	340485	exon6			CCTCCTGTGTGCC	AK123581	CCDS34992.1	9p21.3	2013-01-25	2008-12-19	2008-12-19	ENSG00000177076	ENSG00000177076	3.5.1.23	"""Alkaline ceramidase"""	23675	protein-coding gene	gene with protein product		613492	"""N-acylsphingosine amidohydrolase 3-like"""	ASAH3L		18945876	Standard	XM_005251447		Approved	FLJ41587	uc003zny.1	Q5QJU3	OTTHUMG00000019644	ENST00000340967.2:c.792G>C	9.37:g.19450598G>C		282.0	1.0	0.0035461		330.0	328.0	0.993939	NM_001010887	A2A3R8|Q569G5|Q5VZR7|Q71RD2	Silent	SNP	ENST00000340967.2	37	CCDS34992.1																																																																																			G|0.933;C|0.067	0.067	strong		0.517	ACER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051864.1	XM_294540	
PDIA4	9601	hgsc.bcm.edu	37	7	148701245	148701245	+	Missense_Mutation	SNP	C	C	T	rs61739277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:148701245C>T	ENST00000286091.4	-	10	1811	c.1579G>A	c.(1579-1581)Gtc>Atc	p.V527I		NM_004911.4	NP_004902.1	P13667	PDIA4_HUMAN	protein disulfide isomerase family A, member 4	527	Thioredoxin 3. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein secretion (GO:0009306)|response to endoplasmic reticulum stress (GO:0034976)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)	poly(A) RNA binding (GO:0044822)|protein disulfide isomerase activity (GO:0003756)			large_intestine(6)|lung(15)|ovary(2)|prostate(1)	24	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00385)			ACGACCTTGACGGGTCCCTTG	0.567													C|||	47	0.00938498	0.034	0.0029	5008	,	,		12360	0.0		0.0	False		,,,				2504	0.0				p.V527I		Atlas-SNP	.											.	PDIA4	57	.	0			c.G1579A						PASS	.	C	ILE/VAL	104,4302	83.4+/-121.9	1,102,2100	167.0	152.0	157.0		1579	4.9	0.8	7	dbSNP_129	157	0,8600		0,0,4300	yes	missense	PDIA4	NM_004911.4	29	1,102,6400	TT,TC,CC		0.0,2.3604,0.7996	benign	527/646	148701245	104,12902	2203	4300	6503	SO:0001583	missense	9601	exon10			CCTTGACGGGTCC	BC001928	CCDS5893.1	7q35	2009-11-20	2005-06-29		ENSG00000155660	ENSG00000155660	5.3.4.1	"""Protein disulfide isomerases"""	30167	protein-coding gene	gene with protein product			"""protein disulfide isomerase-associated 4"""			2549034, 2002068	Standard	NM_004911		Approved	ERP70, ERP72	uc003wff.2	P13667	OTTHUMG00000150248	ENST00000286091.4:c.1579G>A	7.37:g.148701245C>T	ENSP00000286091:p.Val527Ile	208.0	0.0	0		175.0	78.0	0.445714	NM_004911	A8K4K6|Q549T6	Missense_Mutation	SNP	ENST00000286091.4	37	CCDS5893.1	13	0.005952380952380952	11	0.022357723577235773	2	0.0055248618784530384	0	0.0	0	0.0	C	15.92	2.975631	0.53720	0.023604	0.0	ENSG00000155660	ENST00000286091	T	0.26810	1.71	5.81	4.92	0.64577	Thioredoxin domain (1);Thioredoxin-like fold (3);	0.056360	0.64402	D	0.000001	T	0.25306	0.0615	M	0.77406	2.37	0.80722	D	1	B	0.28419	0.211	B	0.40410	0.328	T	0.30268	-0.9984	10	0.72032	D	0.01	.	15.1664	0.72828	0.0:0.9316:0.0:0.0684	.	527	P13667	PDIA4_HUMAN	I	527	ENSP00000286091:V527I	ENSP00000286091:V527I	V	-	1	0	PDIA4	148332178	1.000000	0.71417	0.785000	0.31869	0.119000	0.20118	5.851000	0.69481	2.751000	0.94390	0.555000	0.69702	GTC	C|0.992;T|0.008	0.008	strong		0.567	PDIA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317077.1	NM_004911	
KRT72	140807	hgsc.bcm.edu	37	12	52995127	52995127	+	Missense_Mutation	SNP	C	C	T	rs61747194	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52995127C>T	ENST00000537672.2	-	1	120	c.110G>A	c.(109-111)cGg>cAg	p.R37Q	KRT72_ENST00000398066.3_5'UTR|KRT72_ENST00000354310.4_Missense_Mutation_p.R37Q|KRT72_ENST00000293745.2_Missense_Mutation_p.R37Q|RP11-641A6.2_ENST00000551089.1_RNA	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	37	Gly-rich.|Head.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(357;0.195)		GCCCTTGACCCGGGCCCGGAA	0.726													C|||	67	0.0133786	0.0484	0.0029	5008	,	,		12331	0.0		0.001	False		,,,				2504	0.0				p.R37Q		Atlas-SNP	.											.	KRT72	70	.	0			c.G110A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	143,3439		0,143,1648	3.0	4.0	3.0		110,110,110	4.0	0.1	12	dbSNP_129	3	3,7115		0,3,3556	yes	missense,missense,missense	KRT72	NM_001146225.1,NM_001146226.1,NM_080747.2	43,43,43	0,146,5204	TT,TC,CC		0.0421,3.9922,1.3645	benign,benign,benign	37/512,37/470,37/512	52995127	146,10554	1791	3559	5350	SO:0001583	missense	140807	exon1			TTGACCCGGGCCC	AY033495	CCDS8833.1, CCDS53795.1	12q13.13	2013-06-25			ENSG00000170486	ENSG00000170486		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28932	protein-coding gene	gene with protein product		608246				12648212, 11703281, 16831889	Standard	NM_080747		Approved	K6IRS2, KRT6IRS2, KRT6, K6irs	uc001saq.2	Q14CN4	OTTHUMG00000169744	ENST00000537672.2:c.110G>A	12.37:g.52995127C>T	ENSP00000441160:p.Arg37Gln	45.0	0.0	0		46.0	21.0	0.456522	NM_001146225	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Missense_Mutation	SNP	ENST00000537672.2	37	CCDS8833.1	29|29	0.013278388278388278|0.013278388278388278	27|27	0.054878048780487805|0.054878048780487805	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	C|C	14.43|14.43	2.532485|2.532485	0.45073|0.45073	0.039922|0.039922	4.21E-4|4.21E-4	ENSG00000170486|ENSG00000170486	ENST00000549979|ENST00000537672;ENST00000293745;ENST00000354310	.|T;T;T	.|0.75260	.|-0.92;-0.92;-0.92	4.04|4.04	4.04|4.04	0.47022|0.47022	.|.	.|0.000000	.|0.53938	.|D	.|0.000058	T|T	0.20740|0.20740	0.0499|0.0499	L|L	0.27053|0.27053	0.805|0.805	0.19575|0.19575	N|N	0.999962|0.999962	.|B;B	.|0.18610	.|0.016;0.029	.|B;B	.|0.21708	.|0.001;0.036	T|T	0.34229|0.34229	-0.9837|-0.9837	5|10	.|0.52906	.|T	.|0.07	.|.	9.2743|9.2743	0.37690|0.37690	0.1593:0.6857:0.155:0.0|0.1593:0.6857:0.155:0.0	.|.	.|37;37	.|B4DEI8;Q14CN4	.|.;K2C72_HUMAN	R|Q	23|37	.|ENSP00000441160:R37Q;ENSP00000293745:R37Q;ENSP00000346269:R37Q	.|ENSP00000293745:R37Q	G|R	-|-	1|2	0|0	KRT72|KRT72	51281394|51281394	.|.	.|.	0.107000|0.107000	0.21349|0.21349	0.130000|0.130000	0.20726|0.20726	.|.	.|.	2.543000|2.543000	0.85770|0.85770	0.561000|0.561000	0.74099|0.74099	GGG|CGG	C|0.987;T|0.013	0.013	strong		0.726	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405693.1	NM_080747	
USP19	10869	hgsc.bcm.edu	37	3	49149020	49149020	+	Missense_Mutation	SNP	T	T	C	rs13321689	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:49149020T>C	ENST00000398888.2	-	20	3139	c.2821A>G	c.(2821-2823)Acc>Gcc	p.T941A	USP19_ENST00000453664.1_Missense_Mutation_p.T1032A|USP19_ENST00000398896.1_Missense_Mutation_p.T749A|USP19_ENST00000398892.3_Missense_Mutation_p.T981A|USP19_ENST00000417901.1_Missense_Mutation_p.T1044A|USP19_ENST00000434032.2_Missense_Mutation_p.T1042A|USP19_ENST00000398898.2_Missense_Mutation_p.T981A	NM_006677.2	NP_006668.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	941	USP.				ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of skeletal muscle tissue development (GO:0048642)|positive regulation of cell cycle process (GO:0090068)|protein deubiquitination (GO:0016579)|regulation of cellular response to hypoxia (GO:1900037)|regulation of protein stability (GO:0031647)|response to endoplasmic reticulum stress (GO:0034976)|skeletal muscle atrophy (GO:0014732)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|ubiquitin-specific protease activity (GO:0004843)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(10)|lung(5)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		ATTCCACTGGTGCTGGGCACA	0.637													T|||	96	0.0191693	0.0688	0.0072	5008	,	,		17360	0.0		0.0	False		,,,				2504	0.0				p.T1044A		Atlas-SNP	.											.	USP19	158	.	0			c.A3130G						PASS	.	T	ALA/THR,ALA/THR,ALA/THR,ALA/THR	283,3485		9,265,1610	27.0	29.0	29.0		3124,3130,3094,2821	4.9	1.0	3	dbSNP_121	29	6,8216		0,6,4105	yes	missense,missense,missense,missense	USP19	NM_001199160.1,NM_001199161.1,NM_001199162.1,NM_006677.2	58,58,58,58	9,271,5715	CC,CT,TT		0.073,7.5106,2.4103	benign,benign,benign,benign	1042/1420,1044/1385,1032/1373,941/1319	49149020	289,11701	1884	4111	5995	SO:0001583	missense	10869	exon21			CACTGGTGCTGGG	AB020698	CCDS43090.1, CCDS56254.1, CCDS56255.1, CCDS56256.1	3p21.31	2005-10-13	2005-08-08		ENSG00000172046	ENSG00000172046		"""Zinc fingers, MYND-type"", ""Ubiquitin-specific peptidases"""	12617	protein-coding gene	gene with protein product		614471	"""ubiquitin specific protease 19"""			12838346	Standard	NM_001199160		Approved	KIAA0891, ZMYND9	uc011bch.2	O94966	OTTHUMG00000133611	ENST00000398888.2:c.2821A>G	3.37:g.49149020T>C	ENSP00000381863:p.Thr941Ala	65.0	0.0	0		64.0	39.0	0.609375	NM_001199161	A5PKX8|A6H8U2|B4DGT3|B4DTZ0|E7EN22|E7ETS0|E9PEG8|Q3KQW4|Q641Q9|Q6NZY8|Q86XV9	Missense_Mutation	SNP	ENST00000398888.2	37	CCDS43090.1	42	0.019230769230769232	37	0.07520325203252033	5	0.013812154696132596	0	0.0	0	0.0	T	2.392	-0.339698	0.05243	0.075106	7.3E-4	ENSG00000172046	ENST00000398896;ENST00000398898;ENST00000417901;ENST00000453664;ENST00000398892;ENST00000398888;ENST00000434032	T;T;T;T;T;T;T	0.18657	2.2;2.21;2.3;2.3;2.2;2.3;2.29	6.04	4.93	0.64822	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.787862	0.12324	N	0.478992	T	0.00384	0.0012	N	0.02213	-0.635	0.09310	N	1	B;B;B;B;B	0.10296	0.003;0.003;0.001;0.0;0.001	B;B;B;B;B	0.14578	0.011;0.011;0.005;0.005;0.005	T	0.38001	-0.9681	10	0.14252	T	0.57	-11.953	5.3341	0.15947	0.0:0.0978:0.2401:0.6621	rs13321689	1042;1032;941;981;749	E9PEG8;E7EN22;O94966;B5MEG5;E7ESU0	.;.;UBP19_HUMAN;.;.	A	749;981;1044;1032;981;941;1042	ENSP00000381870:T749A;ENSP00000381872:T981A;ENSP00000395260:T1044A;ENSP00000400090:T1032A;ENSP00000381867:T981A;ENSP00000381863:T941A;ENSP00000401197:T1042A	ENSP00000381863:T941A	T	-	1	0	USP19	49124024	0.999000	0.42202	1.000000	0.80357	0.996000	0.88848	0.989000	0.29629	2.330000	0.79161	0.529000	0.55759	ACC	T|0.972;C|0.028	0.028	strong		0.637	USP19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257721.1	NM_006677	
ZBTB37	84614	hgsc.bcm.edu	37	1	173839435	173839435	+	Silent	SNP	G	G	A	rs9425761	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:173839435G>A	ENST00000367701.5	+	2	263	c.72G>A	c.(70-72)caG>caA	p.Q24Q	ZBTB37_ENST00000367704.1_Silent_p.Q24Q|ZBTB37_ENST00000427304.1_Silent_p.Q24Q|GAS5_ENST00000364084.1_RNA|ZBTB37_ENST00000432989.1_Silent_p.Q24Q|ZBTB37_ENST00000367702.1_Silent_p.Q24Q			Q5TC79	ZBT37_HUMAN	zinc finger and BTB domain containing 37	24					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(4)	13						ATCTAAACCAGTTGCGCATGC	0.527													G|||	560	0.111821	0.4009	0.0346	5008	,	,		17279	0.0		0.006	False		,,,				2504	0.0				p.Q24Q		Atlas-SNP	.											.	ZBTB37	38	.	0			c.G72A						PASS	.	G	,	1333,3073	446.1+/-347.9	199,935,1069	79.0	73.0	75.0		72,72	3.8	1.0	1	dbSNP_119	75	31,8569	20.4+/-63.3	0,31,4269	no	coding-synonymous,coding-synonymous	ZBTB37	NM_001122770.1,NM_032522.3	,	199,966,5338	AA,AG,GG		0.3605,30.2542,10.4875	,	24/504,24/362	173839435	1364,11642	2203	4300	6503	SO:0001819	synonymous_variant	84614	exon3			AAACCAGTTGCGC	AK057310	CCDS1312.1, CCDS44278.1	1q24.2	2013-01-08			ENSG00000185278	ENSG00000185278		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	28365	protein-coding gene	gene with protein product						12477932	Standard	NM_032522		Approved	MGC2629, ZNF908	uc009wwp.1	Q5TC79	OTTHUMG00000037274	ENST00000367701.5:c.72G>A	1.37:g.173839435G>A		170.0	0.0	0		192.0	89.0	0.463542	NM_032522	Q5TC80|Q96M87|Q9BQ88	Silent	SNP	ENST00000367701.5	37	CCDS44278.1																																																																																			G|0.875;A|0.125	0.125	strong		0.527	ZBTB37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090729.2	NM_032522	
SPAG17	200162	hgsc.bcm.edu	37	1	118512719	118512719	+	Missense_Mutation	SNP	G	G	T	rs140504036	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:118512719G>T	ENST00000336338.5	-	46	6412	c.6347C>A	c.(6346-6348)cCa>cAa	p.P2116Q	SPAG17_ENST00000492438.1_5'Flank	NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	2116						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		TGTGCTGGGTGGGGGCTGCTT	0.393													G|||	3	0.000599042	0.0023	0.0	5008	,	,		18332	0.0		0.0	False		,,,				2504	0.0				p.P2116Q		Atlas-SNP	.											.	SPAG17	263	.	0			c.C6347A						PASS	.	G	GLN/PRO	8,4398	14.3+/-33.2	0,8,2195	141.0	139.0	140.0		6347	5.3	1.0	1	dbSNP_134	140	0,8600		0,0,4300	yes	missense	SPAG17	NM_206996.2	76	0,8,6495	TT,TG,GG		0.0,0.1816,0.0615	probably-damaging	2116/2224	118512719	8,12998	2203	4300	6503	SO:0001583	missense	200162	exon46			CTGGGTGGGGGCT		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.6347C>A	1.37:g.118512719G>T	ENSP00000337804:p.Pro2116Gln	59.0	0.0	0		49.0	49.0	1	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.974497	0.74246	0.001816	0.0	ENSG00000155761	ENST00000336338;ENST00000437255	T	0.21031	2.03	5.3	5.3	0.74995	.	0.067501	0.64402	D	0.000011	T	0.37732	0.1014	M	0.78049	2.395	0.32515	N	0.536992	D	0.67145	0.996	D	0.65573	0.936	T	0.30909	-0.9962	10	0.87932	D	0	.	15.9899	0.80197	0.0:0.0:1.0:0.0	.	2116	Q6Q759	SPG17_HUMAN	Q	2116;596	ENSP00000337804:P2116Q	ENSP00000337804:P2116Q	P	-	2	0	SPAG17	118314242	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.801000	0.69115	2.775000	0.95449	0.650000	0.86243	CCA	G|0.999;T|0.001	0.001	strong		0.393	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
SRGAP2	23380	hgsc.bcm.edu	37	1	206574931	206574931	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:206574931G>A	ENST00000414007.1	+	4	563	c.563G>A	c.(562-564)cGc>cAc	p.R188H	SRGAP2_ENST00000419187.2_5'UTR			O75044	SRGP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2	328	F-BAR domain.				actin filament severing (GO:0051014)|axon guidance (GO:0007411)|dendritic spine development (GO:0060996)|extension of a leading process involved in cell motility in cerebral cortex radial glia guided migration (GO:0021816)|filopodium assembly (GO:0046847)|lamellipodium assembly involved in ameboidal cell migration (GO:0003363)|negative regulation of neuron migration (GO:2001223)|neuron projection morphogenesis (GO:0048812)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|substrate adhesion-dependent cell spreading (GO:0034446)	cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic spine head (GO:0044327)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	protein homodimerization activity (GO:0042803)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)			NS(1)|breast(1)|kidney(1)|lung(1)	4	Breast(84;0.137)					GACAAGCAGCGCCTCATGGAG	0.527																																					p.R174H		Atlas-SNP	.											SRGAP2_ENST00000414007,NS,carcinoma,0,3	.	.	3	0			c.G521A						scavenged	.						16.0	14.0	14.0					1																	206574931		1795	4026	5821	SO:0001583	missense	100996712	exon4			AGCAGCGCCTCAT	AB007925	CCDS73017.1	1q32.1	2014-08-13	2004-11-12	2004-11-12	ENSG00000163486	ENSG00000266028		"""Rho GTPase activating proteins"""	19751	protein-coding gene	gene with protein product		606524	"""formin binding protein 2"""	FNBP2		15046868, 11672528	Standard	XM_005277510		Approved	KIAA0456, ARHGAP34, SRGAP2A	uc001hdy.3	O75044	OTTHUMG00000184381	ENST00000414007.1:c.563G>A	1.37:g.206574931G>A	ENSP00000390898:p.Arg188His	1644.0	1.0	0.000608273		1642.0	188.0	0.114495	NM_001271887		Missense_Mutation	SNP	ENST00000414007.1	37		.	.	.	.	.	.	.	.	.	.	G	28.8	4.949468	0.92660	.	.	ENSG00000163486	ENST00000414359;ENST00000414007	T	0.13778	2.56	6.02	6.02	0.97574	.	0.054744	0.64402	D	0.000001	T	0.21881	0.0527	.	.	.	0.80722	D	1.000000	D;P;B	0.60160	0.987;0.602;0.174	P;B;B	0.45474	0.482;0.107;0.02	T	0.00601	-1.1650	8	0.49607	T	0.09	.	20.5373	0.99239	0.0:0.0:1.0:0.0	.	175;328;327	B4DDU0;O75044;B7Z3G4	.;FNBP2_HUMAN;.	H	241;188	ENSP00000390898:R188H	ENSP00000390898:R188H	R	+	2	0	SRGAP2	204641554	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.558000	0.73942	2.857000	0.98124	0.650000	0.86243	CGC	.	.	none		0.527	SRGAP2-201	KNOWN	basic	protein_coding	protein_coding		NM_015326	
NAT10	55226	hgsc.bcm.edu	37	11	34133767	34133767	+	Silent	SNP	G	G	A	rs36003235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:34133767G>A	ENST00000257829.3	+	4	575	c.369G>A	c.(367-369)ctG>ctA	p.L123L	NAT10_ENST00000527971.1_Silent_p.L123L|NAT10_ENST00000531159.2_Silent_p.L51L	NM_024662.2	NP_078938	Q9H0A0	NAT10_HUMAN	N-acetyltransferase 10 (GCN5-related)	123						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|N-acetyltransferase activity (GO:0008080)|poly(A) RNA binding (GO:0044822)			endometrium(4)|large_intestine(8)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	23		Acute lymphoblastic leukemia(5;0.0119)|all_hematologic(20;0.0231)				TGTGTGTGCTGCAGGTGGGTG	0.517													G|||	32	0.00638978	0.0219	0.0043	5008	,	,		20244	0.0		0.0	False		,,,				2504	0.0				p.L123L		Atlas-SNP	.											.	NAT10	78	.	0			c.G369A						PASS	.	G	,	49,4355	50.9+/-86.3	0,49,2153	115.0	82.0	93.0		153,369	-2.1	1.0	11	dbSNP_126	93	1,8595		0,1,4297	no	coding-synonymous,coding-synonymous	NAT10	NM_001144030.1,NM_024662.2	,	0,50,6450	AA,AG,GG		0.0116,1.1126,0.3846	,	51/954,123/1026	34133767	50,12950	2202	4298	6500	SO:0001819	synonymous_variant	55226	exon4			TGTGCTGCAGGTG	AF489535	CCDS7889.1, CCDS44568.1	11p13	2011-11-16	2008-09-24		ENSG00000135372	ENSG00000135372	2.3.1.-		29830	protein-coding gene	gene with protein product		609221	"""N-acetyltransferase 10"""			14592445, 21177859	Standard	NM_024662		Approved	hALP, FLJ10774, FLJ12179, NET43, KIAA1709	uc001mvk.3	Q9H0A0	OTTHUMG00000166249	ENST00000257829.3:c.369G>A	11.37:g.34133767G>A		168.0	0.0	0		163.0	77.0	0.472393	NM_024662	B4DFD5|E7ESU4|E9PMN9|Q86WK5|Q9C0F4|Q9HA61|Q9NVF2	Silent	SNP	ENST00000257829.3	37	CCDS7889.1																																																																																			G|0.996;A|0.004	0.004	strong		0.517	NAT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388693.1	NM_024662	
TMEM102	284114	hgsc.bcm.edu	37	17	7339903	7339903	+	Missense_Mutation	SNP	C	C	G	rs76805816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7339903C>G	ENST00000323206.1	+	3	878	c.605C>G	c.(604-606)gCg>gGg	p.A202G	FGF11_ENST00000293829.4_5'Flank|FGF11_ENST00000575235.1_5'Flank|RP11-104H15.9_ENST00000570444.1_RNA|RP11-104H15.8_ENST00000576615.1_RNA|RP11-104H15.7_ENST00000575310.1_RNA|RP11-104H15.10_ENST00000575331.1_RNA|TMEM102_ENST00000396568.1_Missense_Mutation_p.A202G	NM_178518.2	NP_848613.1	Q8N9M5	TM102_HUMAN	transmembrane protein 102	202					apoptotic process (GO:0006915)|positive regulation of cell adhesion (GO:0045785)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of T cell migration (GO:2000406)|regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901028)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to cytokine (GO:0034097)|signal transduction (GO:0007165)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|protein complex (GO:0043234)				kidney(1)|lung(3)|skin(1)	5		Prostate(122;0.173)				GAGCACGAGGCGCCGGTGTCT	0.557													C|||	179	0.0357428	0.1286	0.0115	5008	,	,		18254	0.0		0.001	False		,,,				2504	0.0				p.A202G		Atlas-SNP	.											.	TMEM102	11	.	0			c.C605G						PASS	.	C	GLY/ALA	481,3925	224.3+/-240.5	32,417,1754	90.0	92.0	91.0		605	3.2	0.0	17	dbSNP_132	91	2,8598	2.2+/-6.3	0,2,4298	yes	missense	TMEM102	NM_178518.2	60	32,419,6052	GG,GC,CC		0.0233,10.9169,3.7137	possibly-damaging	202/509	7339903	483,12523	2203	4300	6503	SO:0001583	missense	284114	exon3			ACGAGGCGCCGGT	AK094197	CCDS11104.1	17p13.1	2008-04-21			ENSG00000181284	ENSG00000181284			26722	protein-coding gene	gene with protein product		613936				12477932	Standard	NM_178518		Approved	FLJ36878	uc002ggx.1	Q8N9M5	OTTHUMG00000132901	ENST00000323206.1:c.605C>G	17.37:g.7339903C>G	ENSP00000315387:p.Ala202Gly	89.0	0.0	0		131.0	62.0	0.473282	NM_178518	D3DTP8	Missense_Mutation	SNP	ENST00000323206.1	37	CCDS11104.1	64	0.029304029304029304	59	0.11991869918699187	5	0.013812154696132596	0	0.0	0	0.0	C	9.073	0.997424	0.19043	0.109169	2.33E-4	ENSG00000181284	ENST00000323206;ENST00000396568	T;T	0.44482	0.92;0.92	5.36	3.25	0.37280	.	1.011090	0.07935	N	0.978275	T	0.00384	0.0012	N	0.14661	0.345	0.09310	N	1	B	0.20887	0.049	B	0.20384	0.029	T	0.05162	-1.0902	10	0.49607	T	0.09	-0.6557	6.9622	0.24603	0.0:0.7316:0.1752:0.0931	.	202	Q8N9M5	TM102_HUMAN	G	202	ENSP00000315387:A202G;ENSP00000379815:A202G	ENSP00000315387:A202G	A	+	2	0	TMEM102	7280627	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	-0.442000	0.06871	1.399000	0.46721	0.655000	0.94253	GCG	C|0.967;G|0.033	0.033	strong		0.557	TMEM102-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256405.1	NM_178518	
MAP3K19	80122	hgsc.bcm.edu	37	2	135745648	135745648	+	Missense_Mutation	SNP	G	G	A	rs113683052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:135745648G>A	ENST00000375845.3	-	7	824	c.794C>T	c.(793-795)cCg>cTg	p.P265L	MAP3K19_ENST00000392918.3_Intron|MAP3K19_ENST00000375844.3_Intron|MAP3K19_ENST00000392915.1_Missense_Mutation_p.P282L|MAP3K19_ENST00000315513.3_5'UTR|MAP3K19_ENST00000392917.3_Intron|MAP3K19_ENST00000358371.4_Missense_Mutation_p.P152L	NM_001018044.2|NM_025052.3	NP_001018054.1|NP_079328.3	Q56UN5	M3K19_HUMAN	mitogen-activated protein kinase kinase kinase 19	265							ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)										TAGGGCTCCCGGAGGCTCGTT	0.448													G|||	44	0.00878594	0.031	0.0043	5008	,	,		19304	0.0		0.0	False		,,,				2504	0.0				p.P265L		Atlas-SNP	.											.	.	.	.	0			c.C794T						PASS	.	G	,LEU/PRO	119,4287	89.7+/-128.4	0,119,2084	78.0	83.0	81.0		,794	1.0	0.0	2	dbSNP_132	81	2,8598	2.2+/-6.3	0,2,4298	yes	intron,missense	YSK4	NM_001018046.1,NM_025052.3	,98	0,121,6382	AA,AG,GG		0.0233,2.7009,0.9303	,benign	,265/1329	135745648	121,12885	2203	4300	6503	SO:0001583	missense	80122	exon7			GCTCCCGGAGGCT	AK026727	CCDS2176.2, CCDS33293.1, CCDS63021.1, CCDS63020.1, CCDS63022.1	2q21.3	2012-10-16	2012-10-16	2012-10-16	ENSG00000176601	ENSG00000176601		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	26249	protein-coding gene	gene with protein product			"""Yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)"", ""yeast Sps1/Ste20-related kinase 4 (S. cerevisiae)"", ""YSK4 Sps1/Ste20-related kinase homolog (S. cerevisiae)"""	YSK4		12477932	Standard	NM_001282883		Approved	FLJ23074	uc002tue.1	Q56UN5	OTTHUMG00000074083	ENST00000375845.3:c.794C>T	2.37:g.135745648G>A	ENSP00000365005:p.Pro265Leu	119.0	0.0	0		106.0	45.0	0.424528	NM_025052	B2RP57|B7ZMH9|E2QRE3|Q56UN1|Q56UN2|Q56UN3|Q56UN4|Q8N4E9|Q9H5T2	Missense_Mutation	SNP	ENST00000375845.3	37	CCDS2176.2	9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	G	2.128	-0.399907	0.04865	0.027009	2.33E-4	ENSG00000176601	ENST00000375845;ENST00000358371;ENST00000392915	T;T;T	0.69306	-0.39;-0.39;1.98	4.72	1.02	0.19986	.	0.637582	0.12907	N	0.429241	T	0.22205	0.0535	N	0.22421	0.69	0.09310	N	0.999997	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.19386	-1.0307	10	0.52906	T	0.07	.	2.7976	0.05405	0.1402:0.0796:0.1588:0.6214	.	152;282;265	Q56UN5-3;A8MWG7;Q56UN5	.;.;YSK4_HUMAN	L	265;152;282	ENSP00000365005:P265L;ENSP00000351140:P152L;ENSP00000376647:P282L	ENSP00000351140:P152L	P	-	2	0	YSK4	135462118	0.000000	0.05858	0.004000	0.12327	0.000000	0.00434	-0.057000	0.11768	0.020000	0.15106	-0.271000	0.10264	CCG	G|0.989;A|0.011	0.011	strong		0.448	MAP3K19-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000158244.1	NM_025052	
CLDND2	125875	hgsc.bcm.edu	37	19	51870771	51870771	+	Missense_Mutation	SNP	C	C	A	rs61737052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51870771C>A	ENST00000291715.1	-	3	795	c.370G>T	c.(370-372)Gtc>Ttc	p.V124F	CTD-2616J11.10_ENST00000595500.1_RNA|ETFB_ENST00000309244.4_5'Flank|CTD-2616J11.11_ENST00000600067.1_Intron|CLDND2_ENST00000601435.1_Missense_Mutation_p.V124F	NM_152353.2	NP_689566.1	Q8NHS1	CLDN2_HUMAN	claudin domain containing 2	124						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(2)	4		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000211)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		GAGAAGAAGACGTTGTTCTTC	0.582													C|||	269	0.0537141	0.1906	0.0245	5008	,	,		14710	0.0		0.0	False		,,,				2504	0.0				p.V124F		Atlas-SNP	.											.	CLDND2	11	.	0			c.G370T						PASS	.	C	PHE/VAL	698,3708	280.2+/-275.2	57,584,1562	72.0	73.0	73.0		370	1.1	0.3	19	dbSNP_129	73	11,8589	7.1+/-27.0	0,11,4289	yes	missense	CLDND2	NM_152353.2	50	57,595,5851	AA,AC,CC		0.1279,15.842,5.4513	possibly-damaging	124/168	51870771	709,12297	2203	4300	6503	SO:0001583	missense	125875	exon3			AGAAGACGTTGTT	BC029518	CCDS12829.1	19q13.41	2008-02-05				ENSG00000160318			28511	protein-coding gene	gene with protein product						12477932	Standard	NM_152353		Approved	MGC33839	uc002pwi.1	Q8NHS1		ENST00000291715.1:c.370G>T	19.37:g.51870771C>A	ENSP00000291715:p.Val124Phe	179.0	0.0	0		192.0	101.0	0.526042	NM_152353		Missense_Mutation	SNP	ENST00000291715.1	37	CCDS12829.1	86	0.039377289377289376	74	0.15040650406504066	12	0.03314917127071823	0	0.0	0	0.0	C	17.60	3.430878	0.62844	0.15842	0.001279	ENSG00000160318	ENST00000291715	D	0.88586	-2.4	4.63	1.11	0.20524	.	0.377447	0.18697	N	0.133682	T	0.01835	0.0058	M	0.67953	2.075	0.80722	P	0.0	P	0.50272	0.933	P	0.48982	0.597	T	0.58081	-0.7699	9	0.10636	T	0.68	-10.6815	5.0991	0.14749	0.0:0.6298:0.17:0.2002	.	124	Q8NHS1	CLDN2_HUMAN	F	124	ENSP00000291715:V124F	ENSP00000291715:V124F	V	-	1	0	CLDND2	56562583	0.348000	0.24861	0.346000	0.25655	0.864000	0.49448	0.320000	0.19540	0.362000	0.24319	0.491000	0.48974	GTC	C|0.949;A|0.051	0.051	strong		0.582	CLDND2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464268.1	NM_152353	
OR51L1	119682	hgsc.bcm.edu	37	11	5020542	5020542	+	Silent	SNP	A	A	T	rs368384016		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5020542A>T	ENST00000321543.1	+	1	330	c.330A>T	c.(328-330)acA>acT	p.T110T		NM_001004755.1	NP_001004755.1	Q8NGJ5	O51L1_HUMAN	olfactory receptor, family 51, subfamily L, member 1	110						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)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(19)|skin(2)|stomach(1)	31		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.75e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		ACACATTCACATTCCTGGAGT	0.502																																					p.T110T		Atlas-SNP	.											.	OR51L1	60	.	0			c.A330T						PASS	.	A		6,4396	11.4+/-27.6	0,6,2195	296.0	222.0	247.0		330	-0.0	1.0	11		247	0,8596		0,0,4298	no	coding-synonymous	OR51L1	NM_001004755.1		0,6,6493	TT,TA,AA		0.0,0.1363,0.0462		110/316	5020542	6,12992	2201	4298	6499	SO:0001819	synonymous_variant	119682	exon1			ATTCACATTCCTG	AB065799	CCDS31369.1	11p15.4	2012-08-09			ENSG00000176798	ENSG00000176798		"""GPCR / Class A : Olfactory receptors"""	14759	protein-coding gene	gene with protein product							Standard	NM_001004755		Approved		uc010qyu.2	Q8NGJ5	OTTHUMG00000066605	ENST00000321543.1:c.330A>T	11.37:g.5020542A>T		374.0	0.0	0		423.0	203.0	0.479905	NM_001004755	Q6IFE5	Silent	SNP	ENST00000321543.1	37	CCDS31369.1																																																																																			.	.	weak		0.502	OR51L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142812.1	NM_001004755	
MS4A6A	64231	hgsc.bcm.edu	37	11	59943082	59943082	+	Silent	SNP	C	C	T	rs138028890	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:59943082C>T	ENST00000530839.1	-	6	834	c.342G>A	c.(340-342)gtG>gtA	p.V114V	MS4A6A_ENST00000420732.2_Silent_p.V114V|MS4A6A_ENST00000323961.3_Silent_p.V114V|MS4A6A_ENST00000412309.2_Silent_p.V142V|MS4A6A_ENST00000528851.1_Silent_p.V114V|MS4A6A_ENST00000529054.1_Silent_p.V142V|MS4A6A_ENST00000426738.2_Silent_p.V69V|MS4A6A_ENST00000529906.1_5'Flank|MS4A6A_ENST00000533023.1_Silent_p.V50V	NM_152852.2	NP_690591.1	Q9H2W1	M4A6A_HUMAN	membrane-spanning 4-domains, subfamily A, member 6A	114						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GGCTGCTATGCACCTGAAAGA	0.448													C|||	9	0.00179712	0.0068	0.0	5008	,	,		21254	0.0		0.0	False		,,,				2504	0.0				p.V142V		Atlas-SNP	.											.	MS4A6A	85	.	0			c.G426A						PASS	.	C	,,	26,4376	31.7+/-61.6	0,26,2175	95.0	84.0	88.0		342,342,342	-5.1	0.0	11	dbSNP_134	88	0,8590		0,0,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	MS4A6A	NM_022349.2,NM_152851.1,NM_152852.1	,,	0,26,6470	TT,TC,CC		0.0,0.5906,0.2001	,,	114/226,114/179,114/249	59943082	26,12966	2201	4295	6496	SO:0001819	synonymous_variant	64231	exon6			GCTATGCACCTGA	AB013104	CCDS7981.1, CCDS44615.1, CCDS44616.1, CCDS58134.1	11q12.1	2008-03-25			ENSG00000110077	ENSG00000110077			13375	protein-coding gene	gene with protein product		606548		MS4A6		11245982, 11401424	Standard	NM_152852		Approved	CD20L3	uc010rla.2	Q9H2W1	OTTHUMG00000167241	ENST00000530839.1:c.342G>A	11.37:g.59943082C>T		94.0	0.0	0		110.0	64.0	0.581818	NM_001247999	A8K755|F8W9K1|Q7Z4E8|Q8TBV7|Q8TEZ4|Q8TEZ5|Q96PG6|Q9H2L1|Q9H2N3|Q9H3V1|Q9HC76	Silent	SNP	ENST00000530839.1	37	CCDS7981.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	1.565	-0.535705	0.04082	0.005906	0.0	ENSG00000110077	ENST00000533989	.	.	.	4.99	-5.13	0.02884	.	.	.	.	.	T	0.11196	0.0273	.	.	.	0.18873	N	0.999984	.	.	.	.	.	.	T	0.25187	-1.0139	4	.	.	.	.	0.3632	0.00367	0.2373:0.2707:0.2458:0.2462	.	.	.	.	Y	49	.	.	C	-	2	0	MS4A6A	59699658	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.770000	0.01791	-0.810000	0.04375	-0.976000	0.02587	TGC	C|0.997;T|0.003	0.003	strong		0.448	MS4A6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393848.1		
INCENP	3619	hgsc.bcm.edu	37	11	61897542	61897542	+	Silent	SNP	G	G	A	rs145875137	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61897542G>A	ENST00000394818.3	+	4	745	c.543G>A	c.(541-543)caG>caA	p.Q181Q	INCENP_ENST00000278849.4_Silent_p.Q181Q	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	181					chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	central element (GO:0000801)|chromocenter (GO:0010369)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lateral element (GO:0000800)|microtubule (GO:0005874)|midbody (GO:0030496)|pericentric heterochromatin (GO:0005721)|protein complex (GO:0043234)|spindle (GO:0005819)				breast(1)|endometrium(1)|kidney(6)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						ATGCTGAGCAGCATGTCACCC	0.617													G|||	13	0.00259585	0.0098	0.0	5008	,	,		16459	0.0		0.0	False		,,,				2504	0.0				p.Q181Q		Atlas-SNP	.											.	INCENP	122	.	0			c.G543A						PASS	.	G	,	50,4354	50.9+/-86.3	0,50,2152	65.0	56.0	59.0		543,543	1.8	0.0	11	dbSNP_134	59	1,8597		0,1,4298	no	coding-synonymous,coding-synonymous	INCENP	NM_001040694.1,NM_020238.2	,	0,51,6450	AA,AG,GG		0.0116,1.1353,0.3922	,	181/919,181/915	61897542	51,12951	2202	4299	6501	SO:0001819	synonymous_variant	3619	exon4			TGAGCAGCATGTC	AF282265	CCDS31582.1, CCDS44624.1	11q12.3	2013-01-17	2002-08-29		ENSG00000149503	ENSG00000149503			6058	protein-coding gene	gene with protein product		604411	"""inner centromere protein antigens (135kD, 155kD)"""			1860899, 11453556	Standard	NM_001040694		Approved	FLJ31633	uc001nsw.1	Q9NQS7	OTTHUMG00000167470	ENST00000394818.3:c.543G>A	11.37:g.61897542G>A		42.0	0.0	0		40.0	20.0	0.5	NM_001040694	A8MQD2|Q5Y192	Silent	SNP	ENST00000394818.3	37	CCDS44624.1																																																																																			G|0.996;A|0.004	0.004	strong		0.617	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2	NM_020238	
TAAR1	134864	hgsc.bcm.edu	37	6	132967032	132967032	+	Silent	SNP	T	T	G	rs73775159	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:132967032T>G	ENST00000275216.1	-	1	110	c.111A>C	c.(109-111)acA>acC	p.T37T		NM_138327.1	NP_612200.1	Q96RJ0	TAAR1_HUMAN	trace amine associated receptor 1	37					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|trace-amine receptor activity (GO:0001594)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)	18	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00616)|GBM - Glioblastoma multiforme(226;0.0154)	Amphetamine(DB00182)|Dextroamphetamine(DB01576)|Methamphetamine(DB01577)|Propylhexedrine(DB06714)	TGCCAACGAGTGTGGTCAGAA	0.383													T|||	59	0.0117812	0.0431	0.0029	5008	,	,		20615	0.0		0.0	False		,,,				2504	0.0				p.T37T		Atlas-SNP	.											.	TAAR1	41	.	0			c.A111C						PASS	.	T		160,4246	108.2+/-146.6	1,158,2044	168.0	165.0	166.0		111	-3.0	0.0	6	dbSNP_130	166	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	TAAR1	NM_138327.1		1,160,6342	GG,GT,TT		0.0233,3.6314,1.2456		37/340	132967032	162,12844	2203	4300	6503	SO:0001819	synonymous_variant	134864	exon1			AACGAGTGTGGTC	AY180374	CCDS5158.1	6q23.1	2012-08-08	2005-02-23	2005-02-24	ENSG00000146399	ENSG00000146399		"""GPCR / Class A : Trace amine associated receptors"""	17734	protein-coding gene	gene with protein product		609333	"""trace amine receptor 1"""	TRAR1		11459929, 15718104	Standard	NM_138327		Approved	TAR1, TA1	uc003qdm.1	Q96RJ0	OTTHUMG00000015583	ENST00000275216.1:c.111A>C	6.37:g.132967032T>G		221.0	0.0	0		272.0	144.0	0.529412	NM_138327	Q2M1W5|Q3MIH8|Q5VUQ1	Silent	SNP	ENST00000275216.1	37	CCDS5158.1																																																																																			T|0.989;G|0.011	0.011	strong		0.383	TAAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042259.1	NM_138327	
LINC00283	100874057	hgsc.bcm.edu	37	13	103398300	103398300	+	RNA	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:103398300G>A	ENST00000430111.1	+	0	3894									long intergenic non-protein coding RNA 283																		GATTTGACAAGCTCATTATCC	0.398																																					p.L1583F		Atlas-SNP	.											.	.	.	.	0			c.C4747T						PASS	.						298.0	234.0	254.0					13																	103398300		692	1590	2282			643677	exon4			TGACAAGCTCATT			13q33.1	2012-10-12	2011-08-10	2011-08-10	ENSG00000231633	ENSG00000231633		"""Long non-coding RNAs"""	38809	non-coding RNA	RNA, long non-coding			"""non-protein coding RNA 283"""	NCRNA00283			Standard			Approved				OTTHUMG00000017311		13.37:g.103398300G>A		207.0	0.0	0		227.0	27.0	0.118943	NM_001146197		Missense_Mutation	SNP	ENST00000430111.1	37																																																																																				.	.	none		0.398	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
MYCBPAP	84073	hgsc.bcm.edu	37	17	48594973	48594973	+	Missense_Mutation	SNP	G	G	A	rs75706684	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48594973G>A	ENST00000323776.5	+	4	673	c.511G>A	c.(511-513)Gat>Aat	p.D171N	MYCBPAP_ENST00000436259.2_Missense_Mutation_p.D134N	NM_032133.4	NP_115509.4			MYCBP associated protein									p.D134N(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(8)|ovary(4)|pancreas(1)|skin(2)|urinary_tract(2)	31	Breast(11;1.23e-18)		BRCA - Breast invasive adenocarcinoma(22;1.23e-09)			TGACAGCTTCGATGGCAGTGA	0.512													G|||	135	0.0269569	0.0961	0.0086	5008	,	,		6764	0.0		0.002	False		,,,				2504	0.0				p.D171N		Atlas-SNP	.											MYCBPAP,NS,NS,0,1	MYCBPAP	135	1	1	Substitution - Missense(1)	pancreas(1)	c.G511A						PASS	.	G	ASN/ASP	371,4035	188.1+/-214.6	26,319,1858	68.0	68.0	68.0		511	-5.3	0.0	17	dbSNP_131	68	5,8595	3.7+/-12.6	0,5,4295	yes	missense	MYCBPAP	NM_032133.4	23	26,324,6153	AA,AG,GG		0.0581,8.4203,2.891	benign	171/985	48594973	376,12630	2203	4300	6503	SO:0001583	missense	84073	exon4			AGCTTCGATGGCA	BC028393	CCDS32680.2	17q21.33	2004-02-19			ENSG00000136449	ENSG00000136449			19677	protein-coding gene	gene with protein product		609835				12151104	Standard	NM_032133		Approved	AMAP-1, DKFZp434N1415	uc010wmr.2	Q8TBZ2	OTTHUMG00000157184	ENST00000323776.5:c.511G>A	17.37:g.48594973G>A	ENSP00000323184:p.Asp171Asn	169.0	0.0	0		196.0	100.0	0.510204	NM_032133		Missense_Mutation	SNP	ENST00000323776.5	37	CCDS32680.2	47	0.02152014652014652	41	0.08333333333333333	4	0.011049723756906077	0	0.0	2	0.002638522427440633	G	16.50	3.139471	0.56936	0.084203	5.81E-4	ENSG00000136449	ENST00000323776;ENST00000452039;ENST00000436259	T;T	0.26957	1.72;1.7	5.6	-5.28	0.02755	.	1.777540	0.02671	N	0.108617	T	0.00724	0.0024	L	0.27053	0.805	0.09310	N	1	D;D	0.63880	0.993;0.993	P;P	0.46543	0.52;0.52	T	0.23868	-1.0176	10	0.11794	T	0.64	3.2954	0.1959	0.00139	0.2453:0.2206:0.2006:0.3335	.	134;171	Q8TBZ2;B4DZQ1	MYBPP_HUMAN;.	N	171;186;134	ENSP00000323184:D171N;ENSP00000397209:D134N	ENSP00000323184:D171N	D	+	1	0	MYCBPAP	45949972	0.000000	0.05858	0.000000	0.03702	0.636000	0.38137	0.053000	0.14184	-0.811000	0.04369	-0.219000	0.12488	GAT	G|0.970;A|0.030	0.030	strong		0.512	MYCBPAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347814.1	NM_032133	
PPIG	9360	hgsc.bcm.edu	37	2	170493784	170493784	+	Silent	SNP	T	T	C	rs114584157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170493784T>C	ENST00000260970.3	+	14	2236	c.2016T>C	c.(2014-2016)aaT>aaC	p.N672N	PPIG_ENST00000448752.2_Silent_p.N672N|PPIG_ENST00000409714.3_Silent_p.N657N	NM_004792.2	NP_004783.2	Q13427	PPIG_HUMAN	peptidylprolyl isomerase G (cyclophilin G)	672					protein folding (GO:0006457)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(17)|ovary(2)|stomach(1)|urinary_tract(1)	43					L-Proline(DB00172)	GTGATCATAATAGCTCAAATA	0.353													T|||	8	0.00159744	0.0061	0.0	5008	,	,		19790	0.0		0.0	False		,,,				2504	0.0				p.N672N		Atlas-SNP	.											.	PPIG	100	.	0			c.T2016C						PASS	.	T		42,4364	43.1+/-76.7	1,40,2162	70.0	74.0	73.0		2016	2.2	1.0	2	dbSNP_132	73	0,8600		0,0,4300	no	coding-synonymous	PPIG	NM_004792.2		1,40,6462	CC,CT,TT		0.0,0.9532,0.3229		672/755	170493784	42,12964	2203	4300	6503	SO:0001819	synonymous_variant	9360	exon14			TCATAATAGCTCA	X99717	CCDS2235.1	2q31.1	2010-07-23	2006-01-12		ENSG00000138398	ENSG00000138398	6.1.1.16		14650	protein-coding gene	gene with protein product	"""SR-related CTD-associated factor 10"""	606093	"""peptidyl-prolyl isomerase G (cyclophilin G)"""			8973360, 9153302	Standard	NM_004792		Approved	CARS-Cyp, SRCyp, SCAF10	uc002uez.3	Q13427	OTTHUMG00000132206	ENST00000260970.3:c.2016T>C	2.37:g.170493784T>C		137.0	0.0	0		123.0	44.0	0.357724	NM_004792	D3DPC5|D3DPC6|O00706|Q53R40|Q53SN4|Q96DG9	Silent	SNP	ENST00000260970.3	37	CCDS2235.1																																																																																			T|0.997;C|0.003	0.003	strong		0.353	PPIG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255264.2		
CHRD	8646	hgsc.bcm.edu	37	3	184099050	184099050	+	Missense_Mutation	SNP	C	C	T	rs34095724	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184099050C>T	ENST00000204604.1	+	3	526	c.280C>T	c.(280-282)Cct>Tct	p.P94S	CHRD_ENST00000348986.3_Missense_Mutation_p.P94S|CHRD_ENST00000482805.1_3'UTR|CHRD_ENST00000545352.1_5'Flank|EIF2B5_ENST00000444495.1_Intron|CHRD_ENST00000450923.1_Missense_Mutation_p.P94S	NM_003741.2	NP_003732.2	Q9H2X0	CHRD_HUMAN	chordin	94	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.		P -> S (in dbSNP:rs34095724).		BMP signaling pathway involved in spinal cord dorsal/ventral patterning (GO:0021919)|floor plate development (GO:0033504)|forebrain development (GO:0030900)|gastrulation with mouth forming second (GO:0001702)|mesoderm formation (GO:0001707)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell migration (GO:0030336)|negative regulation of osteoblast differentiation (GO:0045668)|osteoblast differentiation (GO:0001649)|positive regulation of cell adhesion (GO:0045785)|positive regulation of mesenchymal cell proliferation (GO:0002053)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)	cytokine binding (GO:0019955)|heparin binding (GO:0008201)			NS(1)|biliary_tract(1)|breast(2)|endometrium(2)|kidney(3)|large_intestine(5)|lung(23)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	48	all_cancers(143;6.33e-11)|Ovarian(172;0.0339)		Epithelial(37;4.96e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TACCAGGGGCCCTGGCAGGGT	0.657													C|||	195	0.0389377	0.093	0.0173	5008	,	,		14626	0.002		0.0378	False		,,,				2504	0.0204				p.P94S		Atlas-SNP	.											.	CHRD	149	.	0			c.C280T						PASS	.	C	SER/PRO	410,3994		18,374,1810	21.0	26.0	24.0		280	4.3	1.0	3	dbSNP_126	24	292,8302		2,288,4007	yes	missense	CHRD	NM_003741.2	74	20,662,5817	TT,TC,CC		3.3977,9.3097,5.4008	benign	94/956	184099050	702,12296	2202	4297	6499	SO:0001583	missense	8646	exon3			AGGGGCCCTGGCA	AF076612	CCDS3266.1	3q27	2008-07-18			ENSG00000090539	ENSG00000090539			1949	protein-coding gene	gene with protein product		603475				9782094, 11472837	Standard	NM_003741		Approved		uc003fov.3	Q9H2X0	OTTHUMG00000141267	ENST00000204604.1:c.280C>T	3.37:g.184099050C>T	ENSP00000204604:p.Pro94Ser	232.0	0.0	0		259.0	135.0	0.521236	NM_003741	O95254|Q2M1I8|Q6UW83|Q9H2D3|Q9H2W8|Q9H2W9|Q9P0Z2|Q9P0Z3|Q9P0Z4|Q9P0Z5	Missense_Mutation	SNP	ENST00000204604.1	37	CCDS3266.1	92	0.04212454212454213	53	0.10772357723577236	9	0.024861878453038673	1	0.0017482517482517483	29	0.03825857519788918	C	3.315	-0.140029	0.06669	0.093097	0.033977	ENSG00000090539	ENST00000204604;ENST00000450923;ENST00000348986	T;T;T	0.13307	2.83;2.6;2.61	5.18	4.3	0.51218	von Willebrand factor, type C (3);	0.242099	0.43110	D	0.000610	T	0.00144	0.0004	N	0.12182	0.205	0.80722	D	1	B;B	0.11235	0.0;0.004	B;B	0.15870	0.007;0.014	T	0.49960	-0.8883	10	0.20519	T	0.43	-8.4545	7.7367	0.28819	0.0:0.5773:0.3366:0.0861	rs34095724	94;94	E7ESX1;Q9H2X0	.;CHRD_HUMAN	S	94	ENSP00000204604:P94S;ENSP00000408972:P94S;ENSP00000334036:P94S	ENSP00000204604:P94S	P	+	1	0	CHRD	185581744	0.001000	0.12720	1.000000	0.80357	0.678000	0.39670	0.462000	0.21956	1.169000	0.42739	0.561000	0.74099	CCT	C|0.949;T|0.051	0.051	strong		0.657	CHRD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000280432.1	NM_003741	
KRTAP22-2	100288287	hgsc.bcm.edu	37	21	31962649	31962649	+	Silent	SNP	G	G	A	rs78392137	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31962649G>A	ENST00000382830.2	-	1	67	c.45C>T	c.(43-45)tgC>tgT	p.C15C	KRTAP6-3_ENST00000391624.1_5'Flank	NM_001164434.1	NP_001157906.1	Q3LI68	KR222_HUMAN	keratin associated protein 22-2	15						intermediate filament (GO:0005882)											AGCCATAGCTGCAACCATAGT	0.423													G|||	55	0.0109824	0.0401	0.0029	5008	,	,		18361	0.0		0.0	False		,,,				2504	0.0				p.C15C		Atlas-SNP	.											.	KRTAP22-2	6	.	0			c.C45T						PASS	.						133.0	118.0	122.0					21																	31962649		692	1591	2283	SO:0001819	synonymous_variant	100288287	exon1			ATAGCTGCAACCA	AB096950	CCDS46641.1	21q22.11	2009-11-23			ENSG00000206106	ENSG00000206106		"""Keratin associated proteins"""	37091	protein-coding gene	gene with protein product							Standard	NM_001164434		Approved	KAP22.2	uc021wih.1	Q3LI68	OTTHUMG00000065630	ENST00000382830.2:c.45C>T	21.37:g.31962649G>A		123.0	0.0	0		149.0	79.0	0.530201	NM_001164434		Silent	SNP	ENST00000382830.2	37	CCDS46641.1																																																																																			G|0.990;A|0.010	0.010	strong		0.423	KRTAP22-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140633.2	XM_002343740	
GGT1	2678	hgsc.bcm.edu	37	22	24984261	24984261	+	Intron	SNP	G	G	A	rs201281973	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:24984261G>A	ENST00000248923.4	+	1	59				FAM211B_ENST00000318753.8_Nonsense_Mutation_p.R115*|FAM211B_ENST00000495297.1_5'Flank	NM_013430.2	NP_038347.2	P19440	GGT1_HUMAN	gamma-glutamyltransferase 1						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)	ATGAGCTGTCGGCAGATCTTG	0.617													G|||	2	0.000399361	0.0015	0.0	5008	,	,		19843	0.0		0.0	False		,,,				2504	0.0				p.R115X		Atlas-SNP	.											C22orf36,colon,carcinoma,0,1	.	.	1	0			c.C343T						PASS	.	G	,stop/ARG	4,4270		0,4,2133	116.0	128.0	124.0		,343	-0.4	0.0	22		124	0,8470		0,0,4235	yes	intron,stop-gained	GGT1,C22orf36	NM_013430.2,NM_207644.2	,	0,4,6368	AA,AG,GG		0.0,0.0936,0.0314	,	,115/316	24984261	4,12740	2137	4235	6372	SO:0001627	intron_variant	388886	exon3			GCTGTCGGCAGAT	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	ENST00000248923.4:c.-429+4485G>A	22.37:g.24984261G>A		195.0	0.0	0		201.0	106.0	0.527363	NM_207644	Q08247|Q14404|Q8TBS1|Q9UMK1	Nonsense_Mutation	SNP	ENST00000248923.4	37	CCDS42992.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	15.90	2.969710	0.53614	9.36E-4	0.0	ENSG00000178026	ENST00000318753	.	.	.	3.5	-0.358	0.12575	.	0.000000	0.64402	U	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	3.9843	0.09509	0.3955:0.0:0.4411:0.1634	.	.	.	.	X	115	.	ENSP00000320520:R115X	R	-	1	2	C22orf36	23314261	0.993000	0.37304	0.045000	0.18777	0.635000	0.38103	0.761000	0.26489	-0.007000	0.14345	0.462000	0.41574	CGA	G|1.000;A|0.000	0.000	strong		0.617	GGT1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319110.1	NM_013430	
DEF8	54849	hgsc.bcm.edu	37	16	90032296	90032296	+	Silent	SNP	T	T	G	rs11861894	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:90032296T>G	ENST00000268676.7	+	13	1553	c.1464T>G	c.(1462-1464)acT>acG	p.T488T	DEF8_ENST00000567874.1_Silent_p.T367T|DEF8_ENST00000569453.1_Silent_p.T427T|DEF8_ENST00000563594.1_Silent_p.T427T|DEF8_ENST00000570182.1_Silent_p.T417T|DEF8_ENST00000563795.1_Silent_p.T410T	NM_207514.2	NP_997397.1	Q6ZN54	DEFI8_HUMAN	differentially expressed in FDCP 8 homolog (mouse)	488					intracellular signal transduction (GO:0035556)		zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(8)|upper_aerodigestive_tract(1)	12		all_cancers(9;7.59e-13)|Lung NSC(15;1.56e-06)|all_lung(18;2.18e-06)|all_neural(9;0.0019)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0274)		ACTCCACCACTTGTCCCAAGT	0.627													G|||	806	0.160942	0.4599	0.0591	5008	,	,		17453	0.0089		0.0258	False		,,,				2504	0.1247				p.T488T		Atlas-SNP	.											.	DEF8	28	.	0			c.T1464G						PASS	.	G	,,,,,	1762,2634	642.8+/-397.7	346,1070,782	51.0	43.0	46.0		1251,1101,1281,1230,1281,1464	-6.2	0.6	16	dbSNP_120	46	253,8347	806.5+/-407.2	4,245,4051	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DEF8	NM_001242816.1,NM_001242817.1,NM_001242818.1,NM_001242819.1,NM_001242820.1,NM_207514.2	,,,,,	350,1315,4833	GG,GT,TT		2.9419,40.0819,15.5048	,,,,,	417/442,367/392,427/452,410/435,427/452,488/513	90032296	2015,10981	2198	4300	6498	SO:0001819	synonymous_variant	54849	exon13			CACCACTTGTCCC	AK131370	CCDS10989.1, CCDS45555.1, CCDS58493.1, CCDS58494.1, CCDS58495.1, CCDS58496.1	16q24.3	2011-01-31			ENSG00000140995	ENSG00000140995			25969	protein-coding gene	gene with protein product						12477932	Standard	NM_207514		Approved	FLJ20186	uc002fpn.2	Q6ZN54	OTTHUMG00000138989	ENST00000268676.7:c.1464T>G	16.37:g.90032296T>G		122.0	0.0	0		109.0	63.0	0.577982	NM_207514	B3KT65|B4DK62|B4E0S9|B7Z3H6|H3BUG7|Q8N8N3|Q9NXL0	Silent	SNP	ENST00000268676.7	37	CCDS10989.1																																																																																			T|0.861;G|0.139	0.139	strong		0.627	DEF8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000272878.1	NM_207514	
IFNA14	3448	hgsc.bcm.edu	37	9	21239578	21239578	+	Silent	SNP	C	C	T	rs141933410		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21239578C>T	ENST00000380222.2	-	1	400	c.357G>A	c.(355-357)ctG>ctA	p.L119L		NM_002172.2	NP_002163.2	P01570	IFN14_HUMAN	interferon, alpha 14	119					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)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(7)	11				Lung(24;2.12e-22)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)		CACAGGCTTCCAGGTCATTCA	0.448																																					p.L119L		Atlas-SNP	.											.	IFNA14	29	.	0			c.G357A						PASS	.						150.0	156.0	154.0					9																	21239578		2203	4300	6503	SO:0001819	synonymous_variant	3448	exon1			GGCTTCCAGGTCA		CCDS6501.1	9p22	2010-08-24			ENSG00000228083	ENSG00000228083		"""Interferons"""	5420	protein-coding gene	gene with protein product		147579				1385305	Standard	NM_002172		Approved	LEIF2H, IFN-alphaH	uc010mis.3	P01570	OTTHUMG00000019665	ENST00000380222.2:c.357G>A	9.37:g.21239578C>T		360.0	0.0	0		429.0	43.0	0.100233	NM_002172	Q5VZ56|Q7M4S1	Silent	SNP	ENST00000380222.2	37	CCDS6501.1																																																																																			C|0.999;G|0.000;T|0.001	0.001	strong		0.448	IFNA14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051894.1	NM_002172	
ERCC5	2073	hgsc.bcm.edu	37	13	103518036	103518036	+	Silent	SNP	A	A	G	rs55686372	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:103518036A>G	ENST00000355739.4	+	9	3397	c.1974A>G	c.(1972-1974)caA>caG	p.Q658Q	BIVM-ERCC5_ENST00000602836.1_Missense_Mutation_p.K1084E|ERCC5_ENST00000375954.1_5'UTR	NM_000123.3	NP_000114	P28715	ERCC5_HUMAN	excision repair cross-complementation group 5	658					DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|negative regulation of apoptotic process (GO:0043066)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|response to UV (GO:0009411)|response to UV-C (GO:0010225)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	intermediate filament cytoskeleton (GO:0045111)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|double-stranded DNA binding (GO:0003690)|endodeoxyribonuclease activity (GO:0004520)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)|single-stranded DNA binding (GO:0003697)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(8)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	51	all_neural(89;0.0438)|Medulloblastoma(90;0.163)|Lung SC(71;0.211)					TTGAAGTGCAAAGTGTGATTA	0.413			"""Mis, N, F"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				A|||	27	0.00539137	0.0197	0.0014	5008	,	,		18928	0.0		0.0	False		,,,				2504	0.0				p.Q1112Q		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (G)	13	13q33	2073	"""excision repair cross-complementing rodent repair deficiency, complementation group 5 (xeroderma pigmentosum, complementation group G (Cockayne syndrome))"""		E	.	.	.	.	0			c.A3336G						PASS	.	A	,	74,4332	64.1+/-101.4	2,70,2131	33.0	32.0	32.0		1974,3336	-1.4	0.5	13	dbSNP_129	32	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ERCC5,BIVM-ERCC5	NM_000123.3,NM_001204425.1	,	2,70,6431	GG,GA,AA		0.0,1.6795,0.569	,	658/1187,1112/1641	103518036	74,12932	2203	4300	6503	SO:0001819	synonymous_variant	0	exon17	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	AGTGCAAAGTGTG	X71342	CCDS32004.1	13q22-q34	2014-09-17	2014-03-07		ENSG00000134899	ENSG00000134899			3437	protein-coding gene	gene with protein product	"""Cockayne syndrome"""	133530	"""xeroderma pigmentosum, complementation group G"", ""excision repair cross-complementing rodent repair deficiency, complementation group 5"""	ERCM2, XPGC		8088806	Standard	NM_000123		Approved			P28715	OTTHUMG00000017310	ENST00000355739.4:c.1974A>G	13.37:g.103518036A>G		61.0	0.0	0		63.0	29.0	0.460317	NM_001204425	A6NGT4|Q5JUS4|Q5JUS5|Q7Z2V3|Q8IZL6|Q8N1B7|Q9HD59|Q9HD60	Silent	SNP	ENST00000355739.4	37	CCDS32004.1																																																																																			A|0.995;G|0.005	0.005	strong		0.413	ERCC5-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045708.1		
MAN2B2	23324	hgsc.bcm.edu	37	4	6621677	6621677	+	Silent	SNP	C	C	G	rs147252633	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:6621677C>G	ENST00000285599.3	+	18	2874	c.2838C>G	c.(2836-2838)tcC>tcG	p.S946S	MAN2B2_ENST00000504248.1_Silent_p.S895S	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	946					mannose metabolic process (GO:0006013)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	30						CGCTGGGGTCCGTGGTGGCAG	0.652													C|||	15	0.00299521	0.0106	0.0014	5008	,	,		17764	0.0		0.0	False		,,,				2504	0.0				p.S946S		Atlas-SNP	.											.	MAN2B2	80	.	0			c.C2838G						PASS	.	C		58,4348	53.6+/-89.4	0,58,2145	50.0	55.0	53.0		2838	-0.9	0.0	4	dbSNP_134	53	0,8600		0,0,4300	no	coding-synonymous	MAN2B2	NM_015274.1		0,58,6445	GG,GC,CC		0.0,1.3164,0.4459		946/1010	6621677	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	23324	exon18			GGGGTCCGTGGTG	BC033307	CCDS33951.1	4p16.2	2005-11-09			ENSG00000013288	ENSG00000013288			29623	protein-coding gene	gene with protein product	"""core-specific lysosomal alpha-1,6-Mannosidase"""					10231032, 16115860	Standard	XR_241647		Approved	KIAA0935	uc003gjf.1	Q9Y2E5	OTTHUMG00000160073	ENST00000285599.3:c.2838C>G	4.37:g.6621677C>G		204.0	0.0	0		181.0	88.0	0.486188	NM_015274	Q66MP2|Q86T67	Silent	SNP	ENST00000285599.3	37	CCDS33951.1																																																																																			C|0.994;G|0.006	0.006	strong		0.652	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274	
ZNF469	84627	hgsc.bcm.edu	37	16	88500822	88500822	+	Missense_Mutation	SNP	C	C	G	rs77490207	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88500822C>G	ENST00000437464.1	+	2	6860	c.6860C>G	c.(6859-6861)cCc>cGc	p.P2287R	ZNF469_ENST00000565624.1_Missense_Mutation_p.P2315R	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	2287					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						GGAGCCCCGCCCCACACCAAC	0.682													C|||	86	0.0171725	0.0613	0.0072	5008	,	,		14649	0.0		0.0	False		,,,				2504	0.0				p.P2287R		Atlas-SNP	.											.	ZNF469	121	.	0			c.C6860G						PASS	.						6.0	11.0	10.0					16																	88500822		677	1564	2241	SO:0001583	missense	84627	exon2			CCCCGCCCCACAC	AB058761	CCDS45544.1	16q24	2010-08-04				ENSG00000225614		"""Zinc fingers, C2H2-type"""	23216	protein-coding gene	gene with protein product		612078				11347906	Standard	NM_001127464		Approved	KIAA1858	uc002fku.2	Q96JG9		ENST00000437464.1:c.6860C>G	16.37:g.88500822C>G	ENSP00000402343:p.Pro2287Arg	62.0	0.0	0		60.0	31.0	0.516667	NM_001127464		Missense_Mutation	SNP	ENST00000437464.1	37	CCDS45544.1	25	0.011446886446886446	23	0.046747967479674794	2	0.0055248618784530384	0	0.0	0	0.0	C	7.590	0.670481	0.14776	.	.	ENSG00000225614	ENST00000437464	T	0.46063	0.88	4.4	2.43	0.29744	.	.	.	.	.	T	0.04182	0.0116	N	0.14661	0.345	0.09310	N	1	P	0.40476	0.718	B	0.39258	0.295	T	0.03684	-1.1013	9	0.72032	D	0.01	.	6.5162	0.22248	0.0:0.7728:0.0:0.2272	.	2287	Q96JG9	ZN469_HUMAN	R	2287	ENSP00000402343:P2287R	ENSP00000402343:P2287R	P	+	2	0	ZNF469	87028323	0.001000	0.12720	0.000000	0.03702	0.011000	0.07611	1.264000	0.33015	0.325000	0.23359	0.462000	0.41574	CCC	C|0.988;G|0.012	0.012	strong		0.682	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
LIFR	3977	hgsc.bcm.edu	37	5	38510768	38510768	+	Silent	SNP	T	T	C	rs141925289	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:38510768T>C	ENST00000263409.4	-	7	951	c.789A>G	c.(787-789)gtA>gtG	p.V263V	LIFR_ENST00000453190.2_Silent_p.V263V|LIFR_ENST00000503088.1_5'UTR	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	263					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)			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)					TGTCTGAGCCTACAAGTATCA	0.348			T	PLAG1	salivary adenoma								T|||	21	0.00419329	0.0159	0.0	5008	,	,		17591	0.0		0.0	False		,,,				2504	0.0				p.V263V	Melanoma(13;4 730 6426 9861 34751)	Atlas-SNP	.		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	.	LIFR	348	.	0			c.A789G						PASS	.	T	,	38,4368	40.0+/-72.8	0,38,2165	80.0	73.0	76.0		789,789	-0.2	1.0	5	dbSNP_134	76	0,8600		0,0,4300	yes	coding-synonymous,coding-synonymous	LIFR	NM_001127671.1,NM_002310.5	,	0,38,6465	CC,CT,TT		0.0,0.8625,0.2922	,	263/1098,263/1098	38510768	38,12968	2203	4300	6503	SO:0001819	synonymous_variant	3977	exon7			TGAGCCTACAAGT	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.789A>G	5.37:g.38510768T>C		118.0	0.0	0		123.0	54.0	0.439024	NM_002310	Q6LCD9	Silent	SNP	ENST00000263409.4	37	CCDS3927.1																																																																																			T|0.997;C|0.003	0.003	strong		0.348	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310	
RAB11FIP1	80223	hgsc.bcm.edu	37	8	37730017	37730017	+	Missense_Mutation	SNP	G	G	A	rs16887092	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:37730017G>A	ENST00000330843.4	-	4	2315	c.2303C>T	c.(2302-2304)gCt>gTt	p.A768V	RAB11FIP1_ENST00000524118.1_Intron|RAB11FIP1_ENST00000522727.1_Intron|RAB11FIP1_ENST00000287263.4_Intron|RAB11FIP1_ENST00000523182.1_5'UTR	NM_001002814.2	NP_001002814.2	Q6WKZ4	RFIP1_HUMAN	RAB11 family interacting protein 1 (class I)	768			A -> V (in dbSNP:rs16887092).		protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)				NS(1)|breast(1)|central_nervous_system(4)|endometrium(3)|large_intestine(6)|lung(20)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	49		Lung NSC(58;0.118)|all_lung(54;0.195)	LUSC - Lung squamous cell carcinoma(8;3.62e-11)			CACTTCTTCAGCTGCATCCCT	0.577													A|||	540	0.107827	0.3722	0.0418	5008	,	,		18823	0.0079		0.005	False		,,,				2504	0.0061				p.A768V		Atlas-SNP	.											.	RAB11FIP1	105	.	0			c.C2303T						PASS	.	A	VAL/ALA,	1370,3036	690.5+/-405.3	218,934,1051	87.0	89.0	88.0		2303,	-4.6	0.0	8	dbSNP_123	88	13,8587	818.7+/-406.8	0,13,4287	yes	missense,intron	RAB11FIP1	NM_001002814.2,NM_025151.4	64,	218,947,5338	AA,AG,GG		0.1512,31.094,10.6336	benign,	768/1284,	37730017	1383,11623	2203	4300	6503	SO:0001583	missense	80223	exon4			TCTTCAGCTGCAT	AK092296	CCDS34881.1, CCDS34882.1	8p11.22	2005-10-04			ENSG00000156675	ENSG00000156675			30265	protein-coding gene	gene with protein product		608737				11786538, 11495908	Standard	NM_001002814		Approved	RCP, FLJ22622, FLJ22524, Rab11-FIP1	uc003xkm.2	Q6WKZ4	OTTHUMG00000164026	ENST00000330843.4:c.2303C>T	8.37:g.37730017G>A	ENSP00000331342:p.Ala768Val	114.0	0.0	0		113.0	113.0	1	NM_001002814	J3KNP0|Q307T1|Q6AZK4|Q6WKZ2|Q6WKZ6|Q86YV4|Q8TDL1|Q9H642	Missense_Mutation	SNP	ENST00000330843.4	37	CCDS34882.1	196	0.08974358974358974	178	0.3617886178861789	16	0.04419889502762431	0	0.0	2	0.002638522427440633	A	7.240	0.600997	0.13939	0.31094	0.001512	ENSG00000156675	ENST00000330843	T	0.09817	2.94	4.11	-4.62	0.03370	.	3.975120	0.00866	N	0.001966	T	0.00012	0.0000	N	0.12182	0.205	0.58432	P	1.0000000000287557E-6	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46512	-0.9186	9	0.20046	T	0.44	3.6141	6.7903	0.23695	0.2589:0.0:0.5516:0.1895	rs16887092;rs52799569;rs16887092	97;768	Q67C35;Q6WKZ4	.;RFIP1_HUMAN	V	768	ENSP00000331342:A768V	ENSP00000331342:A768V	A	-	2	0	RAB11FIP1	37849175	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.799000	0.01746	-1.042000	0.03262	-0.982000	0.02568	GCT	G|0.890;A|0.110	0.110	strong		0.577	RAB11FIP1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376816.1	NM_025151	
TRAF3IP1	26146	hgsc.bcm.edu	37	2	239237783	239237783	+	Missense_Mutation	SNP	C	C	T	rs34723381	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:239237783C>T	ENST00000373327.4	+	5	937	c.715C>T	c.(715-717)Cgg>Tgg	p.R239W	TRAF3IP1_ENST00000391994.2_Missense_Mutation_p.R239W|TRAF3IP1_ENST00000391993.3_Missense_Mutation_p.R239W	NM_015650.3	NP_056465.2	Q8TDR0	MIPT3_HUMAN	TNF receptor-associated factor 3 interacting protein 1	239	Abolishes microtubules-binding when missing.|Arg-rich.|DISC1-interaction domain.		R -> W (in dbSNP:rs34723381).		cilium assembly (GO:0042384)|embryonic camera-type eye development (GO:0031076)|embryonic digit morphogenesis (GO:0042733)|embryonic heart tube development (GO:0035050)|intraciliary transport (GO:0042073)|negative regulation of defense response to virus (GO:0050687)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube patterning (GO:0021532)|post-anal tail morphogenesis (GO:0036342)	axoneme (GO:0005930)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|skin(2)	23		all_epithelial(40;3.22e-10)|Breast(86;0.000523)|Renal(207;0.00571)|Ovarian(221;0.156)|all_hematologic(139;0.182)		Epithelial(121;9.92e-24)|OV - Ovarian serous cystadenocarcinoma(60;7.85e-12)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.01e-07)|BRCA - Breast invasive adenocarcinoma(100;7.72e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0184)		caacagggagcgggacagaga	0.597													C|||	228	0.0455272	0.1611	0.0216	5008	,	,		16990	0.0		0.0	False		,,,				2504	0.0				p.R239W		Atlas-SNP	.											.	TRAF3IP1	58	.	0			c.C715T						PASS	.	C	TRP/ARG,TRP/ARG	516,3828		27,462,1683	71.0	72.0	72.0		715,715	3.2	0.1	2	dbSNP_126	72	8,8478		0,8,4235	yes	missense,missense	TRAF3IP1	NM_001139490.1,NM_015650.3	101,101	27,470,5918	TT,TC,CC		0.0943,11.8785,4.0842	probably-damaging,probably-damaging	239/626,239/692	239237783	524,12306	2172	4243	6415	SO:0001583	missense	26146	exon5			AGGGAGCGGGACA	AF230877	CCDS33415.1, CCDS46557.1	2q37.3	2014-02-21			ENSG00000204104	ENSG00000204104		"""Intraflagellar transport homologs"""	17861	protein-coding gene	gene with protein product	"""microtubule interacting protein that associates with TRAF3"""	607380				10791955, 12935900	Standard	NM_015650		Approved	MIP-T3, DKFZP434F124, MIPT3, IFT54	uc002vye.3	Q8TDR0	OTTHUMG00000152872	ENST00000373327.4:c.715C>T	2.37:g.239237783C>T	ENSP00000362424:p.Arg239Trp	142.0	0.0	0		132.0	55.0	0.416667	NM_015650	Q6PCT1|Q7L8N9|Q9NRD6|Q9Y4Q1	Missense_Mutation	SNP	ENST00000373327.4	37	CCDS33415.1	101	0.04624542124542125	91	0.18495934959349594	10	0.027624309392265192	0	0.0	0	0.0	C	15.99	2.996440	0.54147	0.118785	9.43E-4	ENSG00000204104	ENST00000391993;ENST00000373327;ENST00000391994;ENST00000440998	T;T;T	0.15372	2.43;2.43;2.43	4.12	3.17	0.36434	.	0.811391	0.10616	N	0.653948	T	0.00073	0.0002	M	0.61703	1.905	0.46096	P	0.0011360000000000259	D;D	0.69078	0.997;0.997	P;P	0.55055	0.656;0.767	T	0.10847	-1.0612	9	0.72032	D	0.01	-4.3779	12.5493	0.56218	0.0:0.7311:0.2689:0.0	rs34723381	239;239	Q8TDR0-2;Q8TDR0	.;MIPT3_HUMAN	W	239	ENSP00000375851:R239W;ENSP00000362424:R239W;ENSP00000375852:R239W	ENSP00000362424:R239W	R	+	1	2	TRAF3IP1	238902522	0.112000	0.22096	0.055000	0.19348	0.014000	0.08584	0.585000	0.23879	2.023000	0.59567	0.467000	0.42956	CGG	C|0.950;T|0.050	0.050	strong		0.597	TRAF3IP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328312.1	NM_015650	
THBD	7056	hgsc.bcm.edu	37	20	23029971	23029971	+	Silent	SNP	G	G	T	rs201268201	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:23029971G>T	ENST00000377103.2	-	1	407	c.171C>A	c.(169-171)ggC>ggA	p.G57G		NM_000361.2	NP_000352.1	P07204	TRBM_HUMAN	thrombomodulin	57	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				blood coagulation (GO:0007596)|female pregnancy (GO:0007565)|leukocyte migration (GO:0050900)|negative regulation of blood coagulation (GO:0030195)|negative regulation of fibrinolysis (GO:0051918)|negative regulation of platelet activation (GO:0010544)|response to cAMP (GO:0051591)|response to lipopolysaccharide (GO:0032496)|response to X-ray (GO:0010165)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			endometrium(2)|large_intestine(3)|ovary(1)|skin(1)	7	Colorectal(13;0.0518)|Lung NSC(19;0.0542)|all_lung(19;0.118)				Drotrecogin alfa(DB00055)|Ibuprofen(DB01050)	TCATTAGGTGGCCCCGCAGTC	0.677													G|||	2	0.000399361	0.0015	0.0	5008	,	,		11359	0.0		0.0	False		,,,				2504	0.0				p.G57G		Atlas-SNP	.											.	THBD	26	.	0			c.C171A						PASS	.	G		3,4261		0,3,2129	8.0	9.0	9.0		171	1.3	1.0	20		9	0,8380		0,0,4190	no	coding-synonymous	THBD	NM_000361.2		0,3,6319	TT,TG,GG		0.0,0.0704,0.0237		57/576	23029971	3,12641	2132	4190	6322	SO:0001819	synonymous_variant	7056	exon1			TAGGTGGCCCCGC		CCDS13148.1	20p11.21	2014-09-17			ENSG00000178726	ENSG00000178726		"""CD molecules"""	11784	protein-coding gene	gene with protein product		188040					Standard	NM_000361		Approved	CD141	uc002wss.3	P07204	OTTHUMG00000032053	ENST00000377103.2:c.171C>A	20.37:g.23029971G>T		32.0	0.0	0		40.0	30.0	0.75	NM_000361	Q8IV29|Q9UC32	Silent	SNP	ENST00000377103.2	37	CCDS13148.1																																																																																			G|0.999;T|0.001	0.001	strong		0.677	THBD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078307.2		
RABGAP1L	9910	hgsc.bcm.edu	37	1	174219724	174219724	+	Missense_Mutation	SNP	A	A	G	rs7339904	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:174219724A>G	ENST00000251507.4	+	6	1003	c.829A>G	c.(829-831)Agt>Ggt	p.S277G	RABGAP1L_ENST00000367689.3_5'UTR|RABGAP1L_ENST00000357444.6_Missense_Mutation_p.S240G	NM_014857.4	NP_055672.3	B7ZAP0	RBG10_HUMAN	RAB GTPase activating protein 1-like	0										NS(1)|breast(2)|endometrium(4)|kidney(5)|large_intestine(7)|lung(21)|ovary(2)|prostate(1)|skin(2)	45						GTTTACCTTCAGTGTCTCCTT	0.388													A|||	328	0.0654952	0.2405	0.0144	5008	,	,		16084	0.0		0.0	False		,,,				2504	0.0				p.S277G		Atlas-SNP	.											.	RABGAP1L	103	.	0			c.A829G						PASS	.	A	GLY/SER	917,3489	353.1+/-312.0	107,703,1393	141.0	138.0	139.0		829	4.7	1.0	1	dbSNP_116	139	6,8594	5.0+/-18.6	0,6,4294	yes	missense	RABGAP1L	NM_014857.4	56	107,709,5687	GG,GA,AA		0.0698,20.8125,7.0967	benign	277/816	174219724	923,12083	2203	4300	6503	SO:0001583	missense	9910	exon6			ACCTTCAGTGTCT	AF279778	CCDS1314.1, CCDS41437.1, CCDS55662.1, CCDS58046.1	1q24	2011-11-21			ENSG00000152061	ENSG00000152061			24663	protein-coding gene	gene with protein product		609238				10585558	Standard	NM_014857		Approved	HHL, TBC1D18, KIAA0471, FLJ38519	uc001gjx.3	B7ZAP0	OTTHUMG00000034899	ENST00000251507.4:c.829A>G	1.37:g.174219724A>G	ENSP00000251507:p.Ser277Gly	97.0	0.0	0		104.0	56.0	0.538462	NM_014857	B7ZAA4	Missense_Mutation	SNP	ENST00000251507.4	37	CCDS1314.1	137	0.06272893772893773	132	0.2682926829268293	5	0.013812154696132596	0	0.0	0	0.0	A	15.94	2.982019	0.53827	0.208125	6.98E-4	ENSG00000152061	ENST00000357444;ENST00000251507;ENST00000457696;ENST00000367692	T;T;T	0.47528	0.87;3.46;0.84	5.8	4.68	0.58851	.	0.235735	0.48767	N	0.000180	T	0.00012	0.0000	L	0.38531	1.155	0.09310	P	1.0	P;B;B	0.35328	0.495;0.017;0.372	B;B;B	0.30401	0.115;0.066;0.083	T	0.27571	-1.0070	9	0.23891	T	0.37	.	11.7008	0.51569	0.9314:0.0:0.0686:0.0	rs7339904;rs52822913;rs7339904	277;277;240	B7WPG6;Q5R372;Q5R372-2	.;RBG1L_HUMAN;.	G	240;277;277;277	ENSP00000350027:S240G;ENSP00000251507:S277G;ENSP00000403136:S277G	ENSP00000251507:S277G	S	+	1	0	RABGAP1L	172486347	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	5.023000	0.64084	1.044000	0.40200	0.459000	0.35465	AGT	A|0.914;G|0.086	0.086	strong		0.388	RABGAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084497.1	NM_001243765	
RASA1	5921	hgsc.bcm.edu	37	5	86681125	86681125	+	Silent	SNP	A	A	T	rs137898246		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:86681125A>T	ENST00000274376.6	+	22	3330	c.2766A>T	c.(2764-2766)ccA>ccT	p.P922P	RASA1_ENST00000456692.2_Silent_p.P745P|RASA1_ENST00000506290.1_Silent_p.P756P|RASA1_ENST00000512763.1_Silent_p.P755P	NM_002890.2	NP_002881.1	P20936	RASA1_HUMAN	RAS p21 protein activator (GTPase activating protein) 1	922	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				blood vessel morphogenesis (GO:0048514)|embryo development (GO:0009790)|intracellular signal transduction (GO:0035556)|mitotic cytokinesis (GO:0000281)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of actin filament polymerization (GO:0030833)|regulation of cell shape (GO:0008360)|regulation of RNA metabolic process (GO:0051252)|signal transduction (GO:0007165)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|ruffle (GO:0001726)	glycoprotein binding (GO:0001948)|GTPase binding (GO:0051020)|potassium channel inhibitor activity (GO:0019870)|Ras GTPase activator activity (GO:0005099)|receptor binding (GO:0005102)			NS(1)|cervix(1)|endometrium(7)|kidney(4)|large_intestine(12)|lung(13)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	48		all_cancers(142;8.25e-07)|Lung NSC(167;0.000185)|all_lung(232;0.000222)|Colorectal(57;0.00542)|Ovarian(174;0.0423)		OV - Ovarian serous cystadenocarcinoma(54;4.72e-41)|Epithelial(54;1.51e-36)|all cancers(79;3.76e-31)		CAGATTCTCCATCTCCTATTG	0.363																																					p.P922P		Atlas-SNP	.											.	RASA1	213	.	0			c.A2766T						PASS	.	A	,	5,4401	8.1+/-20.4	0,5,2198	124.0	111.0	116.0		2766,2235	-1.5	1.0	5	dbSNP_134	116	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	RASA1	NM_002890.2,NM_022650.2	,	0,5,6498	TT,TA,AA		0.0,0.1135,0.0384	,	922/1048,745/871	86681125	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	5921	exon22			TTCTCCATCTCCT		CCDS34200.1, CCDS47243.1	5q13	2013-02-14			ENSG00000145715	ENSG00000145715		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	9871	protein-coding gene	gene with protein product	"""capillary malformation-arteriovenous malformation"""	139150		RASA		15917201	Standard	NM_022650		Approved	GAP, CM-AVM, p120GAP, p120RASGAP	uc003kiw.3	P20936	OTTHUMG00000162605	ENST00000274376.6:c.2766A>T	5.37:g.86681125A>T		115.0	0.0	0		122.0	68.0	0.557377	NM_002890	B2R6W3|Q9UDI1	Silent	SNP	ENST00000274376.6	37	CCDS34200.1																																																																																			A|1.000;G|0.000;T|0.000	0.000	strong		0.363	RASA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369729.1	NM_002890	
PRPH2	5961	hgsc.bcm.edu	37	6	42666244	42666244	+	Splice_Site	SNP	A	A	C	rs140406696		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42666244A>C	ENST00000230381.5	-	3	1069	c.830T>G	c.(829-831)gTg>gGg	p.V277G		NM_000322.4	NP_000313.2	P23942	PRPH2_HUMAN	peripherin 2 (retinal degeneration, slow)	277					cell adhesion (GO:0007155)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	18	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.00178)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0904)			TGTAATGGTCACCTGGTGGTG	0.572													A|||	1	0.000199681	0.0008	0.0	5008	,	,		19706	0.0		0.0	False		,,,				2504	0.0				p.V277G		Atlas-SNP	.											.	PRPH2	47	.	0			c.T830G						PASS	.	A	GLY/VAL	5,4401	9.9+/-24.2	0,5,2198	74.0	73.0	73.0		830	5.0	0.9	6	dbSNP_134	73	0,8600		0,0,4300	yes	missense-near-splice	PRPH2	NM_000322.4	109	0,5,6498	CC,CA,AA		0.0,0.1135,0.0384	benign	277/347	42666244	5,13001	2203	4300	6503	SO:0001630	splice_region_variant	5961	exon3			ATGGTCACCTGGT		CCDS4871.1	6p21.1	2013-09-20	2006-11-23	2006-11-23	ENSG00000112619	ENSG00000112619		"""Tetraspanins"""	9942	protein-coding gene	gene with protein product	retinal peripherin	179605	"""retinal degeneration, slow (retinitis pigmentosa 7)"", ""retinal degeneration, slow"""	RP7, RDS		1749427	Standard	NM_000322		Approved	TSPAN22, rd2, CACD2	uc003osk.3	P23942	OTTHUMG00000014701	ENST00000230381.5:c.829-1T>G	6.37:g.42666244A>C		76.0	0.0	0		82.0	40.0	0.487805	NM_000322	Q5TFH5|Q6DK65	Missense_Mutation	SNP	ENST00000230381.5	37	CCDS4871.1	.	.	.	.	.	.	.	.	.	.	A	15.09	2.730591	0.48939	0.001135	0.0	ENSG00000112619	ENST00000230381	D	0.81739	-1.53	5.0	5.0	0.66597	.	0.243684	0.40818	N	0.001012	T	0.74261	0.3693	L	0.46157	1.445	0.58432	D	0.999993	P	0.41673	0.759	P	0.46585	0.521	T	0.79167	-0.1915	10	0.66056	D	0.02	.	14.6991	0.69145	1.0:0.0:0.0:0.0	.	277	P23942	PRPH2_HUMAN	G	277	ENSP00000230381:V277G	ENSP00000230381:V277G	V	-	2	0	PRPH2	42774222	0.998000	0.40836	0.926000	0.36857	0.031000	0.12232	4.115000	0.57865	1.858000	0.53909	0.533000	0.62120	GTG	A|1.000;C|0.000	0.000	weak		0.572	PRPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040556.1	NM_000322	Missense_Mutation
KIAA1683	80726	hgsc.bcm.edu	37	19	18376509	18376509	+	Missense_Mutation	SNP	G	G	A	rs16982285	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18376509G>A	ENST00000600328.3	-	3	2034	c.1841C>T	c.(1840-1842)gCg>gTg	p.A614V	KIAA1683_ENST00000600359.3_Missense_Mutation_p.A568V|KIAA1683_ENST00000392413.4_Missense_Mutation_p.A614V			Q9H0B3	K1683_HUMAN	KIAA1683	614			A -> V (in dbSNP:rs16982285).			mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						GTCTGTTTTCGCCTGTTTCTG	0.562													A|||	738	0.147364	0.4297	0.1282	5008	,	,		20460	0.0129		0.0288	False		,,,				2504	0.0399				p.A614V		Atlas-SNP	.											KIAA1683_ENST00000392413,colon,carcinoma,0,2	KIAA1683	190	2	0			c.C1841T						PASS	.	A	VAL/ALA,VAL/ALA,VAL/ALA	1675,2731	654.3+/-399.7	321,1033,849	59.0	64.0	62.0		1841,1703,1841	-7.1	0.0	19	dbSNP_123	62	231,8369	808.4+/-407.2	4,223,4073	yes	missense,missense,missense	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	64,64,64	325,1256,4922	AA,AG,GG		2.686,38.0163,14.6548	benign,benign,benign	614/1368,568/1135,614/1181	18376509	1906,11100	2203	4300	6503	SO:0001583	missense	80726	exon3			GTTTTCGCCTGTT	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.1841C>T	19.37:g.18376509G>A	ENSP00000470780:p.Ala614Val	152.0	0.0	0		149.0	66.0	0.442953	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	37	CCDS32958.1	278	0.12728937728937728	213	0.4329268292682927	48	0.13259668508287292	1	0.0017482517482517483	16	0.021108179419525065	A	1.743	-0.491261	0.04322	0.380163	0.02686	ENSG00000130518	ENST00000392413;ENST00000359737;ENST00000427634	T;T;T	0.03717	3.9;3.9;3.83	3.81	-7.09	0.01553	.	3.072470	0.01420	N	0.014343	T	0.00012	0.0000	N	0.00583	-1.355	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48502	-0.9030	9	0.20046	T	0.44	-0.0309	4.2064	0.10490	0.1471:0.3414:0.3989:0.1126	rs16982285;rs16982285	614;614	E9PDE0;Q9H0B3	.;K1683_HUMAN	V	614;614;568	ENSP00000376213:A614V;ENSP00000352774:A614V;ENSP00000404501:A568V	ENSP00000352774:A614V	A	-	2	0	KIAA1683	18237509	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.555000	0.05999	-2.263000	0.00689	-2.747000	0.00125	GCG	G|0.854;A|0.146	0.146	strong		0.562	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
ZBTB9	221504	hgsc.bcm.edu	37	6	33423698	33423698	+	Missense_Mutation	SNP	C	C	G	rs9469425	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33423698C>G	ENST00000395064.2	+	2	1089	c.821C>G	c.(820-822)gCc>gGc	p.A274G		NM_152735.3	NP_689948.1	Q96C00	ZBTB9_HUMAN	zinc finger and BTB domain containing 9	274	Pro-rich.		A -> G (in dbSNP:rs9469425).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|skin(1)|upper_aerodigestive_tract(2)	11						GAGCTTCCTGCCCCTCCTGCA	0.567													C|||	344	0.0686901	0.2534	0.013	5008	,	,		19073	0.0		0.0	False		,,,				2504	0.0				p.A274G		Atlas-SNP	.											.	ZBTB9	23	.	0			c.C821G						PASS	.	C	GLY/ALA	876,3530	338.6+/-305.4	75,726,1402	58.0	61.0	60.0		821	4.4	0.1	6	dbSNP_119	60	8,8592	6.4+/-24.3	0,8,4292	yes	missense	ZBTB9	NM_152735.3	60	75,734,5694	GG,GC,CC		0.093,19.882,6.7969	possibly-damaging	274/474	33423698	884,12122	2203	4300	6503	SO:0001583	missense	221504	exon2			TTCCTGCCCCTCC	AK122644	CCDS4780.1	6p21.31	2013-01-09			ENSG00000213588	ENSG00000213588		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	28323	protein-coding gene	gene with protein product						12477932	Standard	NM_152735		Approved	MGC23166, ZNF919	uc003oeq.3	Q96C00	OTTHUMG00000140180	ENST00000395064.2:c.821C>G	6.37:g.33423698C>G	ENSP00000378503:p.Ala274Gly	82.0	0.0	0		58.0	35.0	0.603448	NM_152735	A2AB19	Missense_Mutation	SNP	ENST00000395064.2	37	CCDS4780.1	139	0.06364468864468864	136	0.2764227642276423	3	0.008287292817679558	0	0.0	0	0.0	C	6.353	0.433225	0.12045	0.19882	9.3E-4	ENSG00000213588	ENST00000395064	T	0.07114	3.22	5.28	4.39	0.52855	.	3.470690	0.02755	U	0.117890	T	0.03095	0.0091	L	0.29908	0.895	0.54753	P	1.6000000000016E-5	B	0.24186	0.099	B	0.22601	0.04	T	0.30937	-0.9961	9	0.33940	T	0.23	.	11.5797	0.50883	0.0:0.8205:0.1795:0.0	rs9469425	274	Q96C00	ZBTB9_HUMAN	G	274	ENSP00000378503:A274G	ENSP00000378503:A274G	A	+	2	0	ZBTB9	33531676	0.051000	0.20477	0.114000	0.21550	0.988000	0.76386	1.337000	0.33862	1.419000	0.47118	0.655000	0.94253	GCC	C|0.921;G|0.079	0.079	strong		0.567	ZBTB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276533.1	NM_152735	
SPP1	6696	hgsc.bcm.edu	37	4	88903774	88903774	+	Missense_Mutation	SNP	G	G	A	rs7435825	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:88903774G>A	ENST00000395080.3	+	7	798	c.671G>A	c.(670-672)aGt>aAt	p.S224N	SPP1_ENST00000360804.4_Missense_Mutation_p.S197N|SPP1_ENST00000509659.1_3'UTR|SPP1_ENST00000237623.7_Missense_Mutation_p.S210N	NM_001040058.1|NM_001251830.1	NP_001035147.1|NP_001238759.1	P10451	OSTP_HUMAN	secreted phosphoprotein 1	224			S -> N (in dbSNP:rs7435825).		biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|negative regulation of collateral sprouting of intact axon in response to injury (GO:0048685)|neutrophil chemotaxis (GO:0030593)|osteoblast differentiation (GO:0001649)|positive regulation of bone resorption (GO:0045780)|positive regulation of cell-substrate adhesion (GO:0010811)|response to steroid hormone (GO:0048545)|response to vitamin D (GO:0033280)	apical part of cell (GO:0045177)|cell projection (GO:0042995)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix binding (GO:0050840)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(3)|skin(1)	13		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-05)		GGGAAGGACAGTTATGAAACG	0.517													G|||	253	0.0505192	0.1861	0.0101	5008	,	,		19566	0.0		0.0	False		,,,				2504	0.0				p.S237N		Atlas-SNP	.											.	SPP1	35	.	0			c.G710A						PASS	.	G	ASN/SER,ASN/SER,ASN/SER	628,3778	269.2+/-268.9	47,534,1622	158.0	145.0	149.0		629,671,590	4.0	0.6	4	dbSNP_116	149	4,8596	3.0+/-9.4	0,4,4296	yes	missense,missense,missense	SPP1	NM_000582.2,NM_001040058.1,NM_001040060.1	46,46,46	47,538,5918	AA,AG,GG		0.0465,14.2533,4.8593	probably-damaging,probably-damaging,probably-damaging	210/301,224/315,197/288	88903774	632,12374	2203	4300	6503	SO:0001583	missense	6696	exon8			AGGACAGTTATGA		CCDS3626.1, CCDS34027.1, CCDS43250.1	4q22.1	2014-01-30	2008-07-31		ENSG00000118785	ENSG00000118785		"""Endogenous ligands"""	11255	protein-coding gene	gene with protein product	"""early T-lymphocyte activation 1"""	166490	"""osteopontin"", ""bone sialoprotein I"""	BNSP, OPN		1575754	Standard	NM_001251829		Approved	BSPI, ETA-1	uc003hra.3	P10451	OTTHUMG00000130599	ENST00000395080.3:c.671G>A	4.37:g.88903774G>A	ENSP00000378517:p.Ser224Asn	186.0	0.0	0		182.0	85.0	0.467033	NM_001251830	B2RDA1|Q15681|Q15682|Q15683|Q4W597|Q567T5|Q8NBK2|Q96IZ1	Missense_Mutation	SNP	ENST00000395080.3	37	CCDS43250.1	94	0.04304029304029304	92	0.18699186991869918	2	0.0055248618784530384	0	0.0	0	0.0	G	15.46	2.840614	0.51057	0.142533	4.65E-4	ENSG00000118785	ENST00000359072;ENST00000535912;ENST00000237623;ENST00000395080;ENST00000360804;ENST00000508233	T;T;T;T	0.47869	0.83;0.83;0.83;0.83	4.84	3.99	0.46301	.	0.332965	0.27563	N	0.018811	T	0.00073	0.0002	L	0.61218	1.895	0.33157	P	0.453592	P;B;P;B;P	0.41366	0.747;0.003;0.594;0.006;0.594	B;B;B;B;B	0.42771	0.397;0.011;0.261;0.028;0.261	T	0.08066	-1.0740	9	0.72032	D	0.01	.	9.3187	0.37950	0.1012:0.0:0.8988:0.0	rs7435825;rs52832944;rs7435825	237;183;210;197;224	B7Z351;Q3LGB0;B2RDA1;Q567T5;P10451	.;.;.;.;OSTP_HUMAN	N	202;183;210;224;197;183	ENSP00000237623:S210N;ENSP00000378517:S224N;ENSP00000354042:S197N;ENSP00000422973:S183N	ENSP00000237623:S210N	S	+	2	0	SPP1	89122798	0.999000	0.42202	0.648000	0.29521	0.342000	0.28953	1.862000	0.39448	1.159000	0.42565	0.453000	0.30009	AGT	G|0.958;A|0.042	0.042	strong		0.517	SPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253048.3		
LLGL2	3993	hgsc.bcm.edu	37	17	73566469	73566469	+	Missense_Mutation	SNP	C	C	T	rs150412778	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73566469C>T	ENST00000392550.3	+	16	2032	c.1915C>T	c.(1915-1917)Cca>Tca	p.P639S	LLGL2_ENST00000167462.5_Missense_Mutation_p.P639S|LLGL2_ENST00000577200.1_Missense_Mutation_p.P639S	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	639					cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			CTTGGAGGGCCCACTCTCCCG	0.682													C|||	35	0.00698882	0.0265	0.0	5008	,	,		16144	0.0		0.0	False		,,,				2504	0.0				p.P639S		Atlas-SNP	.											.	LLGL2	155	.	0			c.C1915T						PASS	.	C	SER/PRO,SER/PRO	109,4289	78.3+/-116.7	1,107,2091	34.0	29.0	31.0		1915,1915	4.9	1.0	17	dbSNP_134	31	1,8591		0,1,4295	yes	missense,missense	LLGL2	NM_001031803.1,NM_004524.2	74,74	1,108,6386	TT,TC,CC		0.0116,2.4784,0.8468	probably-damaging,probably-damaging	639/1021,639/1016	73566469	110,12880	2199	4296	6495	SO:0001583	missense	3993	exon16			GAGGGCCCACTCT	X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"""WD repeat domain containing"""	6629	protein-coding gene	gene with protein product			"""lethal giant larvae (Drosophila) homolog 2"""				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.1915C>T	17.37:g.73566469C>T	ENSP00000376333:p.Pro639Ser	102.0	0.0	0		104.0	58.0	0.557692	NM_004524	Q14521|Q9BR62	Missense_Mutation	SNP	ENST00000392550.3	37	CCDS32733.1	17	0.007783882783882784	17	0.034552845528455285	0	0.0	0	0.0	0	0.0	C	15.72	2.916820	0.52546	0.024784	1.16E-4	ENSG00000073350	ENST00000167462;ENST00000392550;ENST00000545227	T;T	0.56611	0.45;0.45	4.95	4.95	0.65309	.	0.000000	0.85682	D	0.000000	T	0.52075	0.1712	M	0.77103	2.36	0.80722	D	1	P;D;D;D;P	0.89917	0.729;1.0;1.0;0.959;0.931	P;D;D;P;P	0.91635	0.544;0.997;0.999;0.835;0.688	T	0.70296	-0.4911	10	0.56958	D	0.05	4.4938	18.2389	0.89960	0.0:1.0:0.0:0.0	.	266;628;628;639;639	B4DVR9;B3KX47;G3V1I9;Q6P1M3-2;Q6P1M3	.;.;.;.;L2GL2_HUMAN	S	639;639;628	ENSP00000167462:P639S;ENSP00000376333:P639S	ENSP00000167462:P639S	P	+	1	0	LLGL2	71078064	1.000000	0.71417	0.996000	0.52242	0.660000	0.38997	7.766000	0.85320	2.314000	0.78098	0.549000	0.68633	CCA	C|0.989;T|0.011	0.011	strong		0.682	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524	
MICA	100507436	hgsc.bcm.edu	37	6	31379802	31379802	+	Missense_Mutation	SNP	A	A	G	rs41546915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31379802A>G	ENST00000449934.2	+	4	746	c.692A>G	c.(691-693)tAt>tGt	p.Y231C	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				TCCAGCTTCTATCCCCGGAAT	0.587													a|||	3	0.000599042	0.0023	0.0	5008	,	,		19291	0.0		0.0	False		,,,				2504	0.0				p.Y231C		Atlas-SNP	.											.	MICA	21	.	0			c.A692G						PASS	.						18.0	22.0	21.0					6																	31379802		692	1591	2283	SO:0001583	missense	100507436	exon4			GCTTCTATCCCCG	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.692A>G	6.37:g.31379802A>G	ENSP00000413079:p.Tyr231Cys	129.0	0.0	0		79.0	39.0	0.493671	NM_001177519		Missense_Mutation	SNP	ENST00000449934.2	37	CCDS56412.1	.	.	.	.	.	.	.	.	.	.	a	12.79	2.044981	0.36085	.	.	ENSG00000204520	ENST00000376222;ENST00000364810;ENST00000399172;ENST00000449934;ENST00000421350	T;T	0.04317	3.65;3.65	2.38	-2.63	0.06133	.	1.496520	0.04824	N	0.437454	T	0.13586	0.0329	H	0.95294	3.65	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.06807	-1.0806	10	0.87932	D	0	.	3.1987	0.06643	0.4334:0.1971:0.0:0.3695	rs41546915	93;231	Q5SS58;Q96QC4	.;.	C	93;231;188;231;122	ENSP00000413079:Y231C;ENSP00000402410:Y122C	ENSP00000365394:Y231C	Y	+	2	0	MICA	31487781	0.626000	0.27120	0.004000	0.12327	0.037000	0.13140	-0.027000	0.12371	-0.196000	0.10366	0.365000	0.22127	TAT	.	.	weak		0.587	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
TUBGCP6	85378	hgsc.bcm.edu	37	22	50667859	50667859	+	Silent	SNP	A	A	G	rs6010211	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50667859A>G	ENST00000248846.5	-	4	1368	c.1264T>C	c.(1264-1266)Ttg>Ctg	p.L422L	TUBGCP6_ENST00000439308.2_Silent_p.L422L			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	422					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		TTGCTGTACAAAGAGTCCAGG	0.567													A|||	297	0.0593051	0.2171	0.0144	5008	,	,		20076	0.0		0.0	False		,,,				2504	0.0				p.L422L		Atlas-SNP	.											.	TUBGCP6	132	.	0			c.T1264C						PASS	.	A		817,3585	317.4+/-295.1	79,659,1463	78.0	57.0	64.0		1264	-2.6	0.0	22	dbSNP_114	64	0,8600		0,0,4300	no	coding-synonymous	TUBGCP6	NM_020461.3		79,659,5763	GG,GA,AA		0.0,18.5597,6.2836		422/1820	50667859	817,12185	2201	4300	6501	SO:0001819	synonymous_variant	85378	exon4			TGTACAAAGAGTC	AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"""gamma-tubulin complex component 6"""	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.1264T>C	22.37:g.50667859A>G		158.0	0.0	0		208.0	86.0	0.413462	NM_020461	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Silent	SNP	ENST00000248846.5	37	CCDS14087.1																																																																																			A|0.936;G|0.064	0.064	strong		0.567	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461	
PI16	221476	hgsc.bcm.edu	37	6	36930795	36930795	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36930795A>T	ENST00000373674.3	+	5	1005	c.677A>T	c.(676-678)gAc>gTc	p.D226V	PI16_ENST00000491324.1_3'UTR	NM_001199159.1|NM_153370.2	NP_001186088.1|NP_699201.2	Q6UXB8	PI16_HUMAN	peptidase inhibitor 16	226					negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	peptidase inhibitor activity (GO:0030414)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(13)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GAAGCATCAGACTCTAGGAAA	0.547																																					p.D226V		Atlas-SNP	.											.	PI16	50	.	0			c.A677T						PASS	.						87.0	81.0	83.0					6																	36930795		2203	4300	6503	SO:0001583	missense	221476	exon6			CATCAGACTCTAG		CCDS34440.1	6p21.31	2014-01-28	2005-08-17		ENSG00000164530	ENSG00000164530			21245	protein-coding gene	gene with protein product	"""microseminoprotein, beta-binding protein"""		"""protease inhibitor 16"""				Standard	NM_001199159		Approved	MGC45378, dJ90K10.5, MSMBBP	uc003ona.3	Q6UXB8	OTTHUMG00000014611	ENST00000373674.3:c.677A>T	6.37:g.36930795A>T	ENSP00000362778:p.Asp226Val	93.0	0.0	0		130.0	54.0	0.415385	NM_001199159	Q6ZVG9|Q8IYL8|Q8NBK0|Q8TCB8	Missense_Mutation	SNP	ENST00000373674.3	37	CCDS34440.1	.	.	.	.	.	.	.	.	.	.	A	4.768	0.142776	0.09083	.	.	ENSG00000164530	ENST00000536757;ENST00000373674;ENST00000539035	T	0.06849	3.25	4.56	-5.47	0.02600	.	1.282230	0.05284	N	0.519917	T	0.00936	0.0031	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.06405	0.001;0.002	T	0.46176	-0.9210	10	0.35671	T	0.21	.	2.847	0.05546	0.4899:0.2078:0.1969:0.1054	.	226;226	Q6UXB8;Q6UXB8-2	PI16_HUMAN;.	V	226;226;78	ENSP00000362778:D226V	ENSP00000362778:D226V	D	+	2	0	PI16	37038773	0.000000	0.05858	0.000000	0.03702	0.103000	0.19146	-1.147000	0.03188	-1.317000	0.02292	-1.155000	0.01812	GAC	.	.	none		0.547	PI16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040380.1	NM_153370	
SIGLEC12	89858	hgsc.bcm.edu	37	19	52000616	52000616	+	Missense_Mutation	SNP	T	T	C	rs28572419	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52000616T>C	ENST00000291707.3	-	6	1544	c.1489A>G	c.(1489-1491)Atc>Gtc	p.I497V	SIGLEC12_ENST00000598614.1_Missense_Mutation_p.I379V	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	497					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|biliary_tract(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(1)|lung(23)|ovary(4)|prostate(2)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)	61		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		ACGAAGATGATGCAGAAGTAC	0.567													N|||	165	0.0329473	0.1203	0.0086	5008	,	,		17500	0.0		0.0	False		,,,				2504	0.0				p.I497V		Atlas-SNP	.											.	SIGLEC12	243	.	0			c.A1489G						PASS	.	C	VAL/ILE,VAL/ILE	455,3951		24,407,1772	157.0	138.0	144.0		1135,1489	-3.4	0.0	19	dbSNP_125	144	5,8595		0,5,4295	yes	missense,missense	SIGLEC12	NM_033329.1,NM_053003.2	29,29	24,412,6067	CC,CT,TT		0.0581,10.3268,3.5368	benign,benign	379/478,497/596	52000616	460,12546	2203	4300	6503	SO:0001583	missense	89858	exon6			AGATGATGCAGAA	AF282256	CCDS12833.1, CCDS59416.1	19q13.41	2013-01-29	2011-06-29	2004-10-20	ENSG00000254521	ENSG00000254521		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15482	protein-coding gene	gene with protein product		606094	"""SIGLEC-like 1"", ""sialic acid binding Ig-like lectin 12"""	SIGLECL1		11409877, 11328818, 21555517	Standard	NM_053003		Approved	SLG, S2V, Siglec-XII, Siglec-12, Siglec-L1	uc002pwx.1	Q96PQ1	OTTHUMG00000165524	ENST00000291707.3:c.1489A>G	19.37:g.52000616T>C	ENSP00000291707:p.Ile497Val	184.0	1.0	0.00543478		212.0	120.0	0.566038	NM_053003	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	37	CCDS12833.1	61	0.027930402930402932	57	0.11585365853658537	4	0.011049723756906077	0	0.0	0	0.0	.	0.004	-2.281268	0.00251	0.103268	5.81E-4	ENSG00000254521	ENST00000291707	T	0.35236	1.32	1.69	-3.38	0.04883	.	.	.	.	.	T	0.00178	0.0005	N	0.05124	-0.11	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.0;0.003	T	0.16041	-1.0416	9	0.29301	T	0.29	.	0.7952	0.01065	0.1706:0.202:0.3393:0.2881	rs28572419	497;379	Q96PQ1;Q96PQ1-2	SIG12_HUMAN;.	V	497	ENSP00000291707:I497V	ENSP00000291707:I497V	I	-	1	0	SIGLEC12	56692428	0.000000	0.05858	0.000000	0.03702	0.060000	0.15804	-2.840000	0.00738	-1.881000	0.01123	-0.751000	0.03497	ATC	T|0.968;C|0.032	0.032	strong		0.567	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003	
UTP20	27340	hgsc.bcm.edu	37	12	101679569	101679569	+	Missense_Mutation	SNP	A	A	G	rs140064475	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:101679569A>G	ENST00000261637.4	+	4	410	c.236A>G	c.(235-237)aAt>aGt	p.N79S		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	79					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						CAATCATTCAATCAGTTGGTG	0.368													A|||	11	0.00219649	0.0083	0.0	5008	,	,		18123	0.0		0.0	False		,,,				2504	0.0				p.N79S		Atlas-SNP	.											.	UTP20	222	.	0			c.A236G						PASS	.	A	SER/ASN	23,4383	30.8+/-60.4	0,23,2180	99.0	99.0	99.0		236	5.6	1.0	12	dbSNP_134	99	1,8599	1.2+/-3.3	0,1,4299	yes	missense	UTP20	NM_014503.2	46	0,24,6479	GG,GA,AA		0.0116,0.522,0.1845	probably-damaging	79/2786	101679569	24,12982	2203	4300	6503	SO:0001583	missense	27340	exon4			CATTCAATCAGTT	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"""down regulated in metastasis"""	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.236A>G	12.37:g.101679569A>G	ENSP00000261637:p.Asn79Ser	69.0	0.0	0		44.0	25.0	0.568182	NM_014503	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	37	CCDS9081.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	15.61	2.883689	0.51908	0.00522	1.16E-4	ENSG00000120800	ENST00000261637	T	0.40476	1.03	5.56	5.56	0.83823	.	0.104115	0.64402	D	0.000005	T	0.48132	0.1483	L	0.57536	1.79	0.48040	D	0.999572	D	0.62365	0.991	P	0.58013	0.831	T	0.53215	-0.8470	10	0.46703	T	0.11	-26.0442	15.7176	0.77681	1.0:0.0:0.0:0.0	.	79	O75691	UTP20_HUMAN	S	79	ENSP00000261637:N79S	ENSP00000261637:N79S	N	+	2	0	UTP20	100203700	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.098000	0.76974	2.104000	0.64026	0.528000	0.53228	AAT	A|0.998;G|0.002	0.002	strong		0.368	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	
KEL	3792	hgsc.bcm.edu	37	7	142640004	142640004	+	Silent	SNP	T	T	C	rs8176039	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:142640004T>C	ENST00000355265.2	-	17	2373	c.1899A>G	c.(1897-1899)ttA>ttG	p.L633L		NM_000420.2	NP_000411.1	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	633					vasoconstriction (GO:0042310)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(34)|ovary(3)|prostate(2)|skin(1)	60	Melanoma(164;0.059)					CAGCATTCTCTAAGAATGTGA	0.517													C|||	353	0.0704872	0.2519	0.0274	5008	,	,		21440	0.0		0.001	False		,,,				2504	0.0				p.L633L		Atlas-SNP	.											.	KEL	128	.	0			c.A1899G						PASS	.	C		957,3449	735.8+/-410.7	105,747,1351	103.0	94.0	97.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1899	1.8	0.2	7	dbSNP_117	97	10,8590	818.3+/-406.9	0,10,4290	no	coding-synonymous	KEL	NM_000420.2		105,757,5641	CC,CT,TT		0.1163,21.7204,7.435		633/733	142640004	967,12039	2203	4300	6503	SO:0001819	synonymous_variant	3792	exon17			ATTCTCTAAGAAT	BC003135	CCDS34766.1	7q33	2014-07-19	2006-10-10		ENSG00000197993	ENSG00000197993		"""CD molecules"", ""Blood group antigens"""	6308	protein-coding gene	gene with protein product		613883	"""Kell blood group"", ""Kell blood group, metalloendopeptidase"""			1712490, 7683930	Standard	NM_000420		Approved	ECE3, CD238	uc003wcb.3	P23276	OTTHUMG00000157159	ENST00000355265.2:c.1899A>G	7.37:g.142640004T>C		113.0	0.0	0		129.0	64.0	0.496124	NM_000420	B2RBV4|Q96RS8|Q99885	Silent	SNP	ENST00000355265.2	37	CCDS34766.1																																																																																			A|0.102;C|0.060	0.060	strong		0.517	KEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347671.2	NM_000420	
WDR62	284403	hgsc.bcm.edu	37	19	36583692	36583692	+	Missense_Mutation	SNP	A	A	G	rs61747277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36583692A>G	ENST00000270301.7	+	19	2312	c.2312A>G	c.(2311-2313)aAg>aGg	p.K771R	WDR62_ENST00000401500.2_Missense_Mutation_p.K771R			O43379	WDR62_HUMAN	WD repeat domain 62	771					cerebral cortex development (GO:0021987)|neurogenesis (GO:0022008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle pole (GO:0000922)				cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(15)|prostate(4)|stomach(2)|urinary_tract(3)	43	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			ACAAATGACAAGAAGCGGAGT	0.622													A|||	92	0.0183706	0.0673	0.0029	5008	,	,		16554	0.0		0.001	False		,,,				2504	0.0				p.K771R		Atlas-SNP	.											.	WDR62	102	.	0			c.A2312G						PASS	.	A	ARG/LYS,ARG/LYS	268,4138	149.9+/-184.0	11,246,1946	72.0	75.0	74.0		2312,2312	-4.4	0.0	19	dbSNP_129	74	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense	WDR62	NM_001083961.1,NM_173636.4	26,26	11,252,6240	GG,GA,AA		0.0698,6.0826,2.1067	benign,benign	771/1524,771/1519	36583692	274,12732	2203	4300	6503	SO:0001583	missense	284403	exon19			ATGACAAGAAGCG	BX647726	CCDS33001.1, CCDS46059.1	19q13.12	2013-01-09	2005-05-09	2005-05-09	ENSG00000075702	ENSG00000075702		"""WD repeat domain containing"""	24502	protein-coding gene	gene with protein product		613583	"""chromosome 19 open reading frame 14"", ""microcephaly, primary autosomal recessive 2"""	C19orf14, MCPH2		19910486, 20729831, 20890278, 21496009	Standard	NM_001083961		Approved	DKFZP434J046, FLJ33298	uc002odd.2	O43379	OTTHUMG00000048139	ENST00000270301.7:c.2312A>G	19.37:g.36583692A>G	ENSP00000270301:p.Lys771Arg	151.0	0.0	0		170.0	76.0	0.447059	NM_173636	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Missense_Mutation	SNP	ENST00000270301.7	37	CCDS33001.1	34	0.015567765567765568	32	0.06504065040650407	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	A	5.908	0.351581	0.11182	0.060826	6.98E-4	ENSG00000075702	ENST00000401500;ENST00000270301	T;T	0.43294	0.95;0.95	5.01	-4.44	0.03557	.	0.201397	0.41938	D	0.000797	T	0.00906	0.0030	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.18935	-1.0321	10	0.15952	T	0.53	0.0189	7.3192	0.26517	0.5771:0.1282:0.2946:0.0	rs61747277	771;771	O43379-4;O43379	.;WDR62_HUMAN	R	771	ENSP00000384792:K771R;ENSP00000270301:K771R	ENSP00000270301:K771R	K	+	2	0	WDR62	41275532	.	.	0.000000	0.03702	0.001000	0.01503	.	.	-0.452000	0.07087	-0.132000	0.14878	AAG	A|0.982;G|0.018	0.018	strong		0.622	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671	
FLG	2312	hgsc.bcm.edu	37	1	152282899	152282899	+	Missense_Mutation	SNP	G	G	T	rs3120648	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152282899G>T	ENST00000368799.1	-	3	4498	c.4463C>A	c.(4462-4464)aCc>aAc	p.T1488N	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	1488	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCCACGAATGGTGTCCTGACC	0.582									Ichthyosis				G|||	402	0.0802716	0.2905	0.0245	5008	,	,		21397	0.0		0.001	False		,,,				2504	0.0				p.T1488N		Atlas-SNP	.											.	FLG	900	.	0			c.C4463A						PASS	.	G	ASN/THR	1035,3371	381.1+/-324.0	111,813,1279	386.0	372.0	377.0		4463	-2.2	0.0	1	dbSNP_103	377	10,8590	7.7+/-29.5	0,10,4290	no	missense	FLG	NM_002016.1	65	111,823,5569	TT,TG,GG		0.1163,23.4907,8.0348	benign	1488/4062	152282899	1045,11961	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CGAATGGTGTCCT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.4463C>A	1.37:g.152282899G>T	ENSP00000357789:p.Thr1488Asn	461.0	0.0	0		424.0	423.0	0.997642	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	141	0.06456043956043957	132	0.2682926829268293	9	0.024861878453038673	0	0.0	0	0.0	G	9.042	0.989984	0.18966	0.234907	0.001163	ENSG00000143631	ENST00000368799	T	0.01725	4.67	3.12	-2.23	0.06930	.	.	.	.	.	T	0.00666	0.0022	M	0.78223	2.4	0.80722	P	0.0	B	0.20052	0.041	B	0.13407	0.009	T	0.46679	-0.9174	8	0.13470	T	0.59	.	2.2485	0.04037	0.1236:0.3919:0.3103:0.1742	rs3120648;rs58109062	1488	P20930	FILA_HUMAN	N	1488	ENSP00000357789:T1488N	ENSP00000357789:T1488N	T	-	2	0	FLG	150549523	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.592000	0.05747	-0.155000	0.11098	-0.321000	0.08615	ACC	G|0.915;T|0.085	0.085	strong		0.582	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
CCDC157	550631	hgsc.bcm.edu	37	22	30772567	30772567	+	Missense_Mutation	SNP	T	T	C	rs202178544	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30772567T>C	ENST00000405659.1	+	12	2801	c.2092T>C	c.(2092-2094)Tct>Cct	p.S698P	RP1-130H16.16_ENST00000332468.4_RNA|CCDC157_ENST00000338306.3_Missense_Mutation_p.S698P			Q569K6	CC157_HUMAN	coiled-coil domain containing 157	698										central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(1)	15						CACATCCCCATCTCGGCAGCC	0.667													T|||	6	0.00119808	0.0038	0.0014	5008	,	,		15299	0.0		0.0	False		,,,				2504	0.0				p.S698P		Atlas-SNP	.											CCDC157_ENST00000405659,bladder,carcinoma,0,4	CCDC157	86	4	0			c.T2092C						PASS	.						71.0	79.0	76.0					22																	30772567		2203	4300	6503	SO:0001583	missense	550631	exon12			TCCCCATCTCGGC	BC018040	CCDS33632.2	22q12.2	2009-03-05			ENSG00000187860	ENSG00000187860			33854	protein-coding gene	gene with protein product							Standard	NM_001017437		Approved		uc011aku.2	Q569K6	OTTHUMG00000151007	ENST00000405659.1:c.2092T>C	22.37:g.30772567T>C	ENSP00000385357:p.Ser698Pro	109.0	0.0	0		125.0	15.0	0.12	NM_001017437	Q0VD76|Q9BYA4	Missense_Mutation	SNP	ENST00000405659.1	37	CCDS33632.2	.	.	.	.	.	.	.	.	.	.	T	7.336	0.619980	0.14193	.	.	ENSG00000187860	ENST00000405659;ENST00000338306	T;T	0.39229	1.09;1.09	3.04	-2.83	0.05769	.	1.188910	0.06203	N	0.683596	T	0.20373	0.0490	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19549	-1.0302	10	0.25106	T	0.35	-1.9381	7.0241	0.24930	0.0:0.3799:0.0:0.6201	.	698	Q569K6	CC157_HUMAN	P	698	ENSP00000385357:S698P;ENSP00000343087:S698P	ENSP00000343087:S698P	S	+	1	0	CCDC157	29102567	0.000000	0.05858	0.008000	0.14137	0.026000	0.11368	-0.341000	0.07811	-0.707000	0.05022	-0.415000	0.06103	TCT	.	.	weak		0.667	CCDC157-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320936.1	NM_001017437	
OBSCN	84033	hgsc.bcm.edu	37	1	228399628	228399628	+	Silent	SNP	G	G	A	rs114375717	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228399628G>A	ENST00000422127.1	+	2	188	c.144G>A	c.(142-144)caG>caA	p.Q48Q	C1orf145_ENST00000295012.5_Intron|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000570156.2_Silent_p.Q48Q|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000284548.11_Silent_p.Q48Q	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	48	Ig-like 1.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AGGACCAGCAGCCGGTGGCGG	0.682													G|||	39	0.00778754	0.0287	0.0014	5008	,	,		11232	0.0		0.0	False		,,,				2504	0.0				p.Q48Q		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G144A						PASS	.	G	,	120,3834		0,120,1857	8.0	10.0	10.0		144,144	1.5	0.9	1	dbSNP_132	10	0,8146		0,0,4073	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	0,120,5930	AA,AG,GG		0.0,3.0349,0.9917	,	48/7969,48/6621	228399628	120,11980	1977	4073	6050	SO:0001819	synonymous_variant	84033	exon2			CCAGCAGCCGGTG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.144G>A	1.37:g.228399628G>A		62.0	0.0	0		71.0	42.0	0.591549	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			G|0.992;A|0.008	0.008	strong		0.682	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
URB1	9875	hgsc.bcm.edu	37	21	33755787	33755787	+	Missense_Mutation	SNP	G	G	A	rs148857803	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:33755787G>A	ENST00000382751.3	-	4	626	c.511C>T	c.(511-513)Cat>Tat	p.H171Y		NM_014825.2	NP_055640.2	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog (S. cerevisiae)	171						nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(3)|skin(1)|stomach(1)	19						AAATCAAAATGGCTGCAGACG	0.572													G|||	10	0.00199681	0.0068	0.0014	5008	,	,		17128	0.0		0.0	False		,,,				2504	0.0				p.H171Y		Atlas-SNP	.											.	URB1	176	.	0			c.C511T						PASS	.	G	TYR/HIS	4,1380		0,4,688	75.0	77.0	76.0		511	3.5	1.0	21	dbSNP_134	76	5,3177		0,5,1586	yes	missense	URB1	NM_014825.2	83	0,9,2274	AA,AG,GG		0.1571,0.289,0.1971	possibly-damaging	171/2272	33755787	9,4557	692	1591	2283	SO:0001583	missense	9875	exon4			CAAAATGGCTGCA	AB011111	CCDS46645.1	21q22.11	2006-11-28	2006-11-28	2006-11-28	ENSG00000142207	ENSG00000142207			17344	protein-coding gene	gene with protein product	nucleolar preribosomal-associated protein 1	608865	"""chromosome 21 open reading frame 108"""	C21orf108		9628581	Standard	NM_014825		Approved	KIAA0539, NPA1	uc002ypn.2	O60287	OTTHUMG00000064919	ENST00000382751.3:c.511C>T	21.37:g.33755787G>A	ENSP00000372199:p.His171Tyr	70.0	0.0	0		68.0	27.0	0.397059	NM_014825	D3DSE5|Q96NX1|Q9NYQ1	Missense_Mutation	SNP	ENST00000382751.3	37	CCDS46645.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	G	17.51	3.407946	0.62399	0.00289	0.001571	ENSG00000142207	ENST00000382751	T	0.32515	1.45	5.34	3.46	0.39613	.	0.670476	0.15407	N	0.263997	T	0.25717	0.0626	L	0.50333	1.59	0.30481	N	0.772369	P	0.42203	0.773	P	0.48598	0.583	T	0.12785	-1.0534	10	0.19147	T	0.46	-1.1195	8.4059	0.32614	0.0838:0.0:0.7613:0.1549	.	171	O60287	NPA1P_HUMAN	Y	171	ENSP00000372199:H171Y	ENSP00000372199:H171Y	H	-	1	0	URB1	32677658	1.000000	0.71417	0.961000	0.40146	0.971000	0.66376	2.136000	0.42121	0.579000	0.29504	0.563000	0.77884	CAT	G|0.998;A|0.002	0.002	strong		0.572	URB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139400.2		
MCM8	84515	hgsc.bcm.edu	37	20	5974265	5974265	+	Missense_Mutation	SNP	A	A	G	rs16991638	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:5974265A>G	ENST00000378896.3	+	18	2731	c.2354A>G	c.(2353-2355)aAc>aGc	p.N785S	MCM8_ENST00000378886.2_Missense_Mutation_p.N825S|MCM8_ENST00000265187.4_Missense_Mutation_p.N769S|MCM8_ENST00000378883.1_Missense_Mutation_p.N738S	NM_001281520.1|NM_032485.4|NM_182802.1	NP_001268449.1|NP_115874.3|NP_877954.1	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	785			N -> S (in dbSNP:rs16991638).		cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)|G1/S transition of mitotic cell cycle (GO:0000082)|male gamete generation (GO:0048232)|mitotic cell cycle (GO:0000278)	MCM8-MCM9 complex (GO:0097362)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	23						GCTCTCAACAACGTTGCTGAA	0.358													A|||	378	0.0754792	0.1853	0.1009	5008	,	,		18096	0.001		0.0199	False		,,,				2504	0.0429				p.N785S		Atlas-SNP	.											.	MCM8	125	.	0			c.A2354G						PASS	.	A	SER/ASN,SER/ASN	703,3703	283.4+/-277.1	58,587,1558	57.0	62.0	61.0		2354,2306	0.4	1.0	20	dbSNP_123	61	181,8419	82.3+/-144.9	2,177,4121	yes	missense,missense	MCM8	NM_032485.4,NM_182802.1	46,46	60,764,5679	GG,GA,AA		2.1047,15.9555,6.7969	benign,benign	785/841,769/825	5974265	884,12122	2203	4300	6503	SO:0001583	missense	84515	exon18			TCAACAACGTTGC	AJ439063	CCDS13094.1, CCDS13095.1, CCDS63226.1, CCDS63227.1	20p12.3	2007-04-04	2007-04-04	2003-07-09	ENSG00000125885	ENSG00000125885			16147	protein-coding gene	gene with protein product	"""REC homolog (Drosophila)"""	608187	"""chromosome 20 open reading frame 154"""	C20orf154		12527764	Standard	NM_032485		Approved	MGC4816, MGC12866, MGC119522, MGC119523, dJ967N21.5, REC	uc002wmi.3	Q9UJA3	OTTHUMG00000031822	ENST00000378896.3:c.2354A>G	20.37:g.5974265A>G	ENSP00000368174:p.Asn785Ser	46.0	0.0	0		48.0	17.0	0.354167	NM_032485	B2RBG7|D3DW08|E7EQU7|Q495R4|Q495R6|Q495R7|Q86US4|Q969I5	Missense_Mutation	SNP	ENST00000378896.3	37	CCDS13094.1	128	0.05860805860805861	86	0.17479674796747968	26	0.0718232044198895	1	0.0017482517482517483	15	0.01978891820580475	A	9.100	1.003892	0.19199	0.159555	0.021047	ENSG00000125885	ENST00000378896;ENST00000378883;ENST00000378886;ENST00000265187	T;T;T;T	0.02812	4.25;4.15;4.23;4.25	5.82	0.411	0.16392	.	0.769958	0.13000	N	0.421768	T	0.00012	0.0000	N	0.01576	-0.805	0.54753	P	1.3000000000040757E-5	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.0	T	0.45056	-0.9287	9	0.17832	T	0.49	-3.3433	6.6121	0.22757	0.2319:0.3374:0.4307:0.0	rs16991638;rs56419414;rs16991638	738;825;769;785	Q9UJA3-2;E7EQU7;Q9UJA3-3;Q9UJA3	.;.;.;MCM8_HUMAN	S	785;738;825;769	ENSP00000368174:N785S;ENSP00000368161:N738S;ENSP00000368164:N825S;ENSP00000265187:N769S	ENSP00000265187:N769S	N	+	2	0	MCM8	5922265	0.001000	0.12720	0.997000	0.53966	0.995000	0.86356	-0.073000	0.11468	0.055000	0.16094	0.533000	0.62120	AAC	A|0.934;G|0.066	0.066	strong		0.358	MCM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077900.1	NM_032485	
POLR1A	25885	hgsc.bcm.edu	37	2	86305404	86305404	+	Missense_Mutation	SNP	T	T	C	rs35239368	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:86305404T>C	ENST00000263857.6	-	10	1468	c.1090A>G	c.(1090-1092)Aaa>Gaa	p.K364E	POLR1A_ENST00000409681.1_Missense_Mutation_p.K364E			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	364			K -> E (in dbSNP:rs35239368).		gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						AAAGAGTCTTTTTCCTGGAAG	0.408													T|||	658	0.13139	0.447	0.036	5008	,	,		19186	0.0		0.003	False		,,,				2504	0.0399				p.K364E		Atlas-SNP	.											.	POLR1A	137	.	0			c.A1090G						PASS	.	T	GLU/LYS	1319,2381		256,807,787	94.0	84.0	87.0		1090	1.3	1.0	2	dbSNP_126	87	12,8170		0,12,4079	yes	missense	POLR1A	NM_015425.3	56	256,819,4866	CC,CT,TT		0.1467,35.6486,11.2018	benign	364/1721	86305404	1331,10551	1850	4091	5941	SO:0001583	missense	25885	exon10			AGTCTTTTTCCTG	AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"""RNA polymerase subunits"""	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.1090A>G	2.37:g.86305404T>C	ENSP00000263857:p.Lys364Glu	111.0	0.0	0		128.0	64.0	0.5	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Missense_Mutation	SNP	ENST00000263857.6	37	CCDS42706.1	212	0.09706959706959707	200	0.4065040650406504	10	0.027624309392265192	0	0.0	2	0.002638522427440633	T	6.764	0.509783	0.12883	0.356486	0.001467	ENSG00000068654	ENST00000263857;ENST00000409681	T;T	0.66280	-0.2;-0.2	5.22	1.33	0.21861	RNA polymerase, N-terminal (1);	1.947470	0.02022	N	0.047881	T	0.00012	0.0000	N	0.02011	-0.69	0.52501	P	4.700000000001925E-5	B;B	0.11235	0.0;0.004	B;B	0.08055	0.001;0.003	T	0.32719	-0.9896	9	0.02654	T	1	-9.8026	6.3055	0.21137	0.1469:0.0:0.4215:0.4317	rs35239368	364;364	B9ZVN9;O95602	.;RPA1_HUMAN	E	364	ENSP00000263857:K364E;ENSP00000386300:K364E	ENSP00000263857:K364E	K	-	1	0	POLR1A	86158915	0.098000	0.21812	0.985000	0.45067	0.766000	0.43426	0.898000	0.28404	0.901000	0.36495	0.459000	0.35465	AAA	T|0.930;C|0.070	0.070	strong		0.408	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425	
RBM10	8241	hgsc.bcm.edu	37	X	47041414	47041414	+	Silent	SNP	C	C	T	rs112102343	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:47041414C>T	ENST00000377604.3	+	16	2500	c.1758C>T	c.(1756-1758)acC>acT	p.T586T	RBM10_ENST00000345781.6_Silent_p.T509T|RBM10_ENST00000329236.7_Silent_p.T508T	NM_001204467.1|NM_001204468.1|NM_005676.4	NP_001191396.1|NP_001191397.1|NP_005667.2	P98175	RBM10_HUMAN	RNA binding motif protein 10	586	Tyr-rich.				3'-UTR-mediated mRNA stabilization (GO:0070935)|mRNA processing (GO:0006397)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of smooth muscle cell apoptotic process (GO:0034393)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(8)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	48						ACCCCCAGACCGGCCTCTACT	0.602													C|||	41	0.0108609	0.028	0.0043	3775	,	,		13729	0.001		0.0	False		,,,				2504	0.0				p.T651T	Melanoma(171;120 2705 19495 39241)	Atlas-SNP	.											.	RBM10	117	.	0			c.C1953T						PASS	.		,,,,	149,3686		3,118,25,1511,546	84.0	75.0	78.0		1527,1755,1953,1758,1524	-8.1	0.9	X	dbSNP_132	78	2,6726		0,2,0,2426,1872	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RBM10	NM_001204466.1,NM_001204467.1,NM_001204468.1,NM_005676.4,NM_152856.2	,,,,	3,120,25,3937,2418	TT,TC,T,CC,C		0.0297,3.8853,1.4295	,,,,	509/854,585/930,651/996,586/931,508/853	47041414	151,10412	2203	4300	6503	SO:0001819	synonymous_variant	8241	exon16			CCAGACCGGCCTC	U35373	CCDS14274.1, CCDS56600.1, CCDS75969.1	Xp11.3	2014-06-09			ENSG00000182872	ENSG00000182872		"""Zinc fingers, RAN-binding domain containing"", ""G patch domain containing"", ""RNA binding motif (RRM) containing"""	9896	protein-coding gene	gene with protein product		300080				8590280, 8808293	Standard	NM_005676		Approved	DXS8237E, KIAA0122, GPATC9, ZRANB5, GPATCH9	uc004dhi.3	P98175	OTTHUMG00000021432	ENST00000377604.3:c.1758C>T	X.37:g.47041414C>T		111.0	0.0	0		144.0	73.0	0.506944	NM_001204468	C4AM81|Q14136|Q5JRR2|Q9BTE4|Q9BTX0|Q9NTB1	Silent	SNP	ENST00000377604.3	37	CCDS14274.1																																																																																			C|0.986;T|0.014	0.014	strong		0.602	RBM10-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056381.1	NM_005676	
HS3ST3B1	9953	hgsc.bcm.edu	37	17	14248345	14248345	+	Splice_Site	SNP	G	G	A	rs77608217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:14248345G>A	ENST00000360954.2	+	2	991	c.555G>A	c.(553-555)cgG>cgA	p.R185R		NM_006041.1	NP_006032.1	Q9Y662	HS3SB_HUMAN	heparan sulfate (glucosamine) 3-O-sulfotransferase 3B1	185					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)	[heparan sulfate]-glucosamine 3-sulfotransferase 1 activity (GO:0008467)|[heparan sulfate]-glucosamine 3-sulfotransferase 3 activity (GO:0033872)			large_intestine(3)|lung(3)|skin(1)	7				UCEC - Uterine corpus endometrioid carcinoma (92;0.0887)		CGTTTCTCAGGGACCTGATGC	0.577													G|||	17	0.00339457	0.0129	0.0	5008	,	,		17223	0.0		0.0	False		,,,				2504	0.0				p.R185R		Atlas-SNP	.											.	HS3ST3B1	19	.	0			c.G555A						PASS	.	G		70,4336	62.9+/-100.1	1,68,2134	61.0	63.0	63.0		555	2.6	1.0	17	dbSNP_131	63	0,8600		0,0,4300	yes	coding-synonymous-near-splice	HS3ST3B1	NM_006041.1		1,68,6434	AA,AG,GG		0.0,1.5887,0.5382		185/391	14248345	70,12936	2203	4300	6503	SO:0001630	splice_region_variant	9953	exon2			TCTCAGGGACCTG	AF105377	CCDS11167.1	17p12	2007-04-02			ENSG00000125430	ENSG00000125430	2.8.2.23	"""Sulfotransferases, membrane-bound"""	5198	protein-coding gene	gene with protein product		604058				9988767	Standard	NM_006041		Approved	3OST3B1, 30ST3B1	uc002goh.1	Q9Y662	OTTHUMG00000058810	ENST00000360954.2:c.555-1G>A	17.37:g.14248345G>A		241.0	0.0	0		290.0	148.0	0.510345	NM_006041	B3KN58|D3DTS6	Silent	SNP	ENST00000360954.2	37	CCDS11167.1																																																																																			G|0.995;A|0.005	0.005	strong		0.577	HS3ST3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000129998.1	NM_006041	Silent
C2orf54	79919	hgsc.bcm.edu	37	2	241835110	241835110	+	Missense_Mutation	SNP	G	G	A	rs146162100	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:241835110G>A	ENST00000388934.4	-	1	463	c.305C>T	c.(304-306)cCg>cTg	p.P102L		NM_001085437.1	NP_001078906	Q08AI8	CB054_HUMAN	chromosome 2 open reading frame 54	102										haematopoietic_and_lymphoid_tissue(1)|lung(4)|prostate(1)	6		all_epithelial(40;3.99e-16)|Breast(86;2.35e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0294)|Lung NSC(271;0.094)|Esophageal squamous(248;0.129)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;8.14e-32)|all cancers(36;4.77e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;4.88e-06)|Lung(119;0.000452)|LUSC - Lung squamous cell carcinoma(224;0.00415)|Colorectal(34;0.021)|COAD - Colon adenocarcinoma(134;0.15)		GCCATCCTCCGGCTGGGTGGC	0.637													G|||	47	0.00938498	0.0348	0.0	5008	,	,		21036	0.0		0.0	False		,,,				2504	0.001				p.P102L		Atlas-SNP	.											.	C2orf54	14	.	0			c.C305T						PASS	.	G	LEU/PRO	108,3930		1,106,1912	39.0	43.0	42.0		305	2.0	0.0	2	dbSNP_134	42	0,8320		0,0,4160	yes	missense	C2orf54	NM_001085437.1	98	1,106,6072	AA,AG,GG		0.0,2.6746,0.8739	benign	102/448	241835110	108,12250	2019	4160	6179	SO:0001583	missense	79919	exon1			TCCTCCGGCTGGG	AK026324, AK056601	CCDS42839.1, CCDS42840.1, CCDS63187.1	2q37.3	2011-02-23			ENSG00000172478	ENSG00000172478			26216	protein-coding gene	gene with protein product							Standard	NM_001282921		Approved	FLJ22671	uc002wae.4	Q08AI8	OTTHUMG00000151906	ENST00000388934.4:c.305C>T	2.37:g.241835110G>A	ENSP00000373586:p.Pro102Leu	143.0	0.0	0		142.0	68.0	0.478873	NM_001085437	B3KPP9|H7BXM3|Q08AI9|Q53QU5|Q9H622	Missense_Mutation	SNP	ENST00000388934.4	37	CCDS42839.1	21	0.009615384615384616	21	0.042682926829268296	0	0.0	0	0.0	0	0.0	G	4.191	0.034120	0.08101	0.026746	0.0	ENSG00000172478	ENST00000388934;ENST00000414499;ENST00000454476	T;T;T	0.11495	2.77;2.77;2.77	4.87	2.03	0.26663	.	0.889113	0.09556	N	0.786255	T	0.01730	0.0055	L	0.40543	1.245	0.09310	N	1	B	0.18461	0.028	B	0.13407	0.009	T	0.40021	-0.9585	10	0.27082	T	0.32	4.8878	4.8735	0.13644	0.2407:0.0:0.558:0.2014	.	102	Q08AI8	CB054_HUMAN	L	102;102;92	ENSP00000373586:P102L;ENSP00000390935:P102L;ENSP00000394874:P92L	ENSP00000373586:P102L	P	-	2	0	C2orf54	241483783	0.000000	0.05858	0.001000	0.08648	0.047000	0.14425	-0.397000	0.07269	0.474000	0.27392	0.561000	0.74099	CCG	G|0.990;A|0.010	0.010	strong		0.637	C2orf54-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000324353.1	NM_024861, NM_001085437	
HBS1L	10767	hgsc.bcm.edu	37	6	135358398	135358398	+	Intron	SNP	G	G	A	rs116294454	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:135358398G>A	ENST00000367837.5	-	4	637				HBS1L_ENST00000445176.2_Intron|HBS1L_ENST00000367824.4_Intron|HBS1L_ENST00000367820.2_Intron|HBS1L_ENST00000367826.2_Intron|HBS1L_ENST00000415177.2_Intron|HBS1L_ENST00000367822.5_Silent_p.N399N|HBS1L_ENST00000314674.3_Intron	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase						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)		CAGATGACTGGTTACAAAGGT	0.408													G|||	88	0.0175719	0.0628	0.0072	5008	,	,		19700	0.0		0.0	False		,,,				2504	0.0				p.N399N		Atlas-SNP	.											.	HBS1L	75	.	0			c.C1197T						PASS	.	G	,,	48,1336		1,46,645	138.0	114.0	122.0		,1197,	3.8	0.5	6	dbSNP_132	122	2,3180		0,2,1589	no	intron,coding-synonymous,intron	HBS1L	NM_001145158.1,NM_001145207.1,NM_006620.3	,,	1,48,2234	AA,AG,GG		0.0629,3.4682,1.0951	,,	,399/633,	135358398	50,4516	692	1591	2283	SO:0001627	intron_variant	10767	exon5			TGACTGGTTACAA	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.430+2312C>T	6.37:g.135358398G>A		77.0	0.0	0		98.0	48.0	0.489796	NM_001145207	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Silent	SNP	ENST00000367837.5	37	CCDS5173.1																																																																																			G|0.978;A|0.022	0.022	strong		0.408	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2		
ZNF319	57567	hgsc.bcm.edu	37	16	58031996	58031996	+	Silent	SNP	G	G	A	rs115738968	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:58031996G>A	ENST00000299237.2	-	2	796	c.174C>T	c.(172-174)ccC>ccT	p.P58P	USB1_ENST00000561743.1_5'Flank	NM_020807.1	NP_065858.1	Q9P2F9	ZN319_HUMAN	zinc finger protein 319	58	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			large_intestine(2)|lung(4)|ovary(1)|urinary_tract(1)	8						GCTGCAGGCCGGGGTCTGGCT	0.701													G|||	42	0.00838658	0.0272	0.0058	5008	,	,		16696	0.0		0.002	False		,,,				2504	0.0				p.P58P		Atlas-SNP	.											.	ZNF319	42	.	0			c.C174T						PASS	.	G		102,4294	79.3+/-117.8	4,94,2100	33.0	36.0	35.0		174	-10.4	0.0	16	dbSNP_132	35	19,8577	13.3+/-46.6	0,19,4279	no	coding-synonymous	ZNF319	NM_020807.1		4,113,6379	AA,AG,GG		0.221,2.3203,0.9313		58/583	58031996	121,12871	2198	4298	6496	SO:0001819	synonymous_variant	57567	exon2			CAGGCCGGGGTCT	AB037809	CCDS32462.1	16q21	2013-01-08				ENSG00000166188		"""Zinc fingers, C2H2-type"""	13644	protein-coding gene	gene with protein product						10718198, 11161788	Standard	XM_005256069		Approved	KIAA1388, Zfp319	uc002emx.1	Q9P2F9		ENST00000299237.2:c.174C>T	16.37:g.58031996G>A		49.0	0.0	0		34.0	18.0	0.529412	NM_020807	Q52LH8	Silent	SNP	ENST00000299237.2	37	CCDS32462.1																																																																																			G|0.992;A|0.008	0.008	strong		0.701	ZNF319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430317.1		
LZTS2	84445	hgsc.bcm.edu	37	10	102762439	102762439	+	Silent	SNP	C	C	T	rs142122181|rs35061268	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:102762439C>T	ENST00000370220.1	+	1	3207	c.144C>T	c.(142-144)caC>caT	p.H48H	LZTS2_ENST00000370223.3_Silent_p.H48H					leucine zipper, putative tumor suppressor 2											breast(1)|large_intestine(6)|lung(7)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22				Epithelial(162;7.3e-09)|all cancers(201;3.72e-07)		CCCGCCACCACGGCCCTCCTG	0.682													C|||	6	0.00119808	0.003	0.0014	5008	,	,		16468	0.0		0.001	False		,,,				2504	0.0				p.H48H	Esophageal Squamous(8;38 437 13604 19902 37640)	Atlas-SNP	.											.	LZTS2	57	.	0			c.C144T						PASS	.	C		22,4384		0,22,2181	36.0	43.0	41.0		144	-9.3	0.0	10	dbSNP_134	41	2,8596		0,2,4297	no	coding-synonymous	LZTS2	NM_032429.2		0,24,6478	TT,TC,CC		0.0233,0.4993,0.1846		48/670	102762439	24,12980	2203	4299	6502	SO:0001819	synonymous_variant	84445	exon2			CCACCACGGCCCT	AB058716	CCDS7507.1	10q24	2004-03-18			ENSG00000107816	ENSG00000107816			29381	protein-coding gene	gene with protein product		610454				11347906, 11709705	Standard	NM_032429		Approved	KIAA1813, LAPSER1	uc001ksj.3	Q9BRK4	OTTHUMG00000018914	ENST00000370220.1:c.144C>T	10.37:g.102762439C>T		108.0	0.0	0		122.0	70.0	0.57377	NM_032429		Silent	SNP	ENST00000370220.1	37	CCDS7507.1																																																																																			C|0.998;T|0.002	0.002	strong		0.682	LZTS2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049872.1	XM_046743	
C1orf127	148345	hgsc.bcm.edu	37	1	11009679	11009679	+	Splice_Site	SNP	G	G	A	rs1281013	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11009679G>A	ENST00000377008.4	-	10	1236		c.e10+1		C1orf127_ENST00000377004.4_Splice_Site			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127											NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		CCATAGACGTGCTTTGGCCAG	0.612													G|||	346	0.0690895	0.2035	0.0144	5008	,	,		17717	0.004		0.0427	False		,,,				2504	0.0204				.		Atlas-SNP	.											.	C1orf127	134	.	0			c.1290+2C>T						PASS	.	G		719,3679		64,591,1544	34.0	29.0	31.0			-0.6	0.0	1	dbSNP_87	31	331,8269		4,323,3973	yes	splice-5	C1orf127	NM_001170754.1		68,914,5517	AA,AG,GG		3.8488,16.3483,8.0782			11009679	1050,11948	2199	4300	6499	SO:0001630	splice_region_variant	148345	exon12			AGACGTGCTTTGG	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.789+1C>T	1.37:g.11009679G>A		103.0	0.0	0		100.0	51.0	0.51	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Splice_Site	SNP	ENST00000377008.4	37		166	0.076007326007326	122	0.24796747967479674	4	0.011049723756906077	1	0.0017482517482517483	39	0.051451187335092345	G	2.596	-0.293985	0.05568	0.163483	0.038488	ENSG00000175262	ENST00000418570;ENST00000377004;ENST00000377008	.	.	.	3.68	-0.578	0.11724	.	.	.	.	.	.	.	.	.	.	.	0.51012	P	9.899999999996023E-5	.	.	.	.	.	.	.	.	.	.	.	.	.	.	1.2328	0.01946	0.2149:0.1807:0.4347:0.1697	rs1281013;rs1281013	.	.	.	.	-1	.	.	.	-	.	.	C1orf127	10932266	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.106000	0.15354	-0.247000	0.09597	-0.354000	0.07668	.	G|0.907;A|0.093	0.093	strong		0.612	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	Intron
OR6P1	128366	hgsc.bcm.edu	37	1	158532908	158532908	+	Missense_Mutation	SNP	T	T	C	rs114056876	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158532908T>C	ENST00000334632.1	-	1	486	c.487A>G	c.(487-489)Att>Gtt	p.I163V		NM_001160325.1	NP_001153797.1	Q8NGX9	OR6P1_HUMAN	olfactory receptor, family 6, subfamily P, member 1	163						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(4)|lung(1)	6						AATTGGGAAATAAAAAGAAGC	0.493													T|||	79	0.0157748	0.0582	0.0029	5008	,	,		21050	0.0		0.0	False		,,,				2504	0.0				p.I163V		Atlas-SNP	.											.	OR6P1	47	.	0			c.A487G						PASS	.	T	VAL/ILE	76,1308		3,70,619	63.0	61.0	61.0		487	4.0	1.0	1	dbSNP_132	61	1,3181		0,1,1590	yes	missense	OR6P1	NM_001160325.1	29	3,71,2209	CC,CT,TT		0.0314,5.4913,1.6864	probably-damaging	163/318	158532908	77,4489	692	1591	2283	SO:0001583	missense	128366	exon1			GGGAAATAAAAAG	BK004193	CCDS53391.1	1q23.1	2012-08-09			ENSG00000186440	ENSG00000186440		"""GPCR / Class A : Olfactory receptors"""	15036	protein-coding gene	gene with protein product							Standard	NM_001160325		Approved		uc010pim.2	Q8NGX9	OTTHUMG00000019633	ENST00000334632.1:c.487A>G	1.37:g.158532908T>C	ENSP00000334721:p.Ile163Val	92.0	0.0	0		90.0	49.0	0.544444	NM_001160325	Q6IFR9	Missense_Mutation	SNP	ENST00000334632.1	37	CCDS53391.1	26	0.011904761904761904	26	0.052845528455284556	0	0.0	0	0.0	0	0.0	T	10.53	1.375197	0.24857	0.054913	3.14E-4	ENSG00000186440	ENST00000334632	T	0.00069	8.77	5.11	3.95	0.45737	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47093	D	0.000248	T	0.00109	0.0003	L	0.35414	1.06	0.09310	N	1	D	0.71674	0.998	D	0.80764	0.994	T	0.41645	-0.9497	10	0.32370	T	0.25	.	6.8131	0.23814	0.0:0.0827:0.1524:0.7648	.	163	Q8NGX9	OR6P1_HUMAN	V	163	ENSP00000334721:I163V	ENSP00000334721:I163V	I	-	1	0	OR6P1	156799532	0.003000	0.15002	0.998000	0.56505	0.033000	0.12548	0.919000	0.28692	2.147000	0.66899	0.482000	0.46254	ATT	T|0.988;C|0.012	0.012	strong		0.493	OR6P1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051848.1		
PCDHA5	56143	hgsc.bcm.edu	37	5	140201418	140201418	+	Missense_Mutation	SNP	C	C	T	rs386692889|rs56285019	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140201418C>T	ENST00000529859.1	+	1	58	c.58C>T	c.(58-60)Ctt>Ttt	p.L20F	PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA5_ENST00000378126.3_Missense_Mutation_p.L20F|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Missense_Mutation_p.L20F	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	20					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(3)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTGGCTTCTCCTTGCCTACTG	0.567													.|||	264	0.0527157	0.1952	0.0058	5008	,	,		14691	0.001		0.001	False		,,,				2504	0.0				p.L20F		Atlas-SNP	.											.	PCDHA5	361	.	0			c.C58T						PASS	.	C	,,,,PHE/LEU,,PHE/LEU	13,4393		4,5,2194	61.0	68.0	66.0		,,,,58,,58	2.0	0.0	5	dbSNP_129	66	0,8600		0,0,4300	yes	intron,intron,intron,intron,missense,intron,missense	PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_031411.1,NM_031501.1	,,,,22,,22	4,5,6494	TT,TC,CC		0.0,0.2951,0.1	,,,,,,	,,,,20/937,,20/817	140201418	13,12993	2203	4300	6503	SO:0001583	missense	56143	exon1			CTTCTCCTTGCCT	AF152483	CCDS54917.1	5q31	2010-11-26				ENSG00000204965		"""Cadherins / Protocadherins : Clustered"""	8671	other	complex locus constituent	"""ortholog of mouse CNR6"", ""KIAA0345-like 9"""	606311		CNRS6		10380929, 10662547	Standard	NM_018908		Approved	CNR6, CRNR6, CNRN6, PCDH-ALPHA5		Q9Y5H7		ENST00000529859.1:c.58C>T	5.37:g.140201418C>T	ENSP00000436557:p.Leu20Phe	95.0	0.0	0		92.0	50.0	0.543478	NM_018908	O75284|Q8N4R3	Missense_Mutation	SNP	ENST00000529859.1	37	CCDS54917.1	76	0.0347985347985348	73	0.1483739837398374	3	0.008287292817679558	0	0.0	0	0.0	C	2.978	-0.211037	0.06140	0.002951	0.0	ENSG00000204965	ENST00000529619;ENST00000529859;ENST00000378126	T;T;T	0.54479	0.6;0.57;0.6	3.81	2.0	0.26442	.	.	.	.	.	T	0.00271	0.0008	L	0.52823	1.66	0.80722	P	0.0	B;B;B	0.09022	0.001;0.001;0.002	B;B;B	0.08055	0.001;0.002;0.003	T	0.12889	-1.0530	8	0.11794	T	0.64	.	7.5552	0.27820	0.0:0.7302:0.0:0.2698	rs56285019;rs61730628	20;20;20	Q9Y5H7;Q9Y5H7-3;Q9Y5H7-2	PCDA5_HUMAN;.;.	F	20	ENSP00000433416:L20F;ENSP00000436557:L20F;ENSP00000367366:L20F	ENSP00000367366:L20F	L	+	1	0	PCDHA5	140181602	0.000000	0.05858	0.012000	0.15200	0.358000	0.29455	-0.212000	0.09319	0.224000	0.20940	0.543000	0.68304	CTT	C|0.952;T|0.048	0.048	strong		0.567	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908	
ARMC5	79798	hgsc.bcm.edu	37	16	31477795	31477795	+	Missense_Mutation	SNP	G	G	C	rs115611533	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31477795G>C	ENST00000563544.1	+	7	2939	c.2393G>C	c.(2392-2394)gGt>gCt	p.G798A	ARMC5_ENST00000412665.2_Missense_Mutation_p.G442A|ARMC5_ENST00000457010.2_3'UTR|ARMC5_ENST00000268314.4_Missense_Mutation_p.G798A|ARMC5_ENST00000538189.1_Missense_Mutation_p.G830A|ARMC5_ENST00000408912.3_Missense_Mutation_p.G893A			Q96C12	ARMC5_HUMAN	armadillo repeat containing 5	798	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.									central_nervous_system(1)|endometrium(4)|large_intestine(3)|liver(2)|lung(12)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						CTGTCGCCTGGTGCAGCCTGG	0.687													g|||	41	0.0081869	0.0287	0.0043	5008	,	,		16435	0.0		0.0	False		,,,				2504	0.0				p.G798A		Atlas-SNP	.											.	ARMC5	94	.	0			c.G2393C						PASS	.		ALA/GLY,	94,3996		2,90,1953	29.0	35.0	33.0		2393,	4.7	0.3	16	dbSNP_132	33	1,8347		0,1,4173	yes	missense,utr-3	ARMC5	NM_001105247.1,NM_024742.2	60,	2,91,6126	CC,CG,GG		0.012,2.2983,0.7638	benign,	798/936,	31477795	95,12343	2045	4174	6219	SO:0001583	missense	79798	exon6			CGCCTGGTGCAGC	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.2393G>C	16.37:g.31477795G>C	ENSP00000456877:p.Gly798Ala	35.0	0.0	0		50.0	26.0	0.52	NM_001105247	Q86WM9|Q9H7P8|Q9H925	Missense_Mutation	SNP	ENST00000563544.1	37	CCDS45472.1	17	0.007783882783882784	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	0	0.0	g	0.136	-1.108013	0.01813	0.022983	1.2E-4	ENSG00000140691	ENST00000408912;ENST00000538189;ENST00000268314;ENST00000412665	T;T;T;T	0.70045	-0.45;-0.45;-0.45;-0.45	5.64	4.69	0.59074	BTB/POZ-like (1);BTB/POZ fold (1);	0.393509	0.28549	N	0.014953	T	0.22244	0.0536	N	0.13235	0.315	0.09310	N	1	B;B;B;B	0.22800	0.031;0.031;0.075;0.015	B;B;B;B	0.20184	0.028;0.028;0.017;0.012	T	0.07214	-1.0784	10	0.10377	T	0.69	-26.6313	12.3369	0.55073	0.0816:0.0:0.9184:0.0	.	830;830;893;798	B4DH27;F5H156;B4DIU9;Q96C12	.;.;.;ARMC5_HUMAN	A	893;830;798;442	ENSP00000386125:G893A;ENSP00000443995:G830A;ENSP00000268314:G798A;ENSP00000400183:G442A	ENSP00000268314:G798A	G	+	2	0	ARMC5	31385296	0.704000	0.27836	0.271000	0.24616	0.056000	0.15407	4.288000	0.59007	1.389000	0.46526	0.546000	0.68486	GGT	G|0.992;C|0.008	0.008	strong		0.687	ARMC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432847.1	NM_024742	
TMPRSS9	360200	hgsc.bcm.edu	37	19	2389793	2389793	+	Missense_Mutation	SNP	A	A	G	rs8100709	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2389793A>G	ENST00000332578.3	+	1	10	c.10A>G	c.(10-12)Act>Gct	p.T4A		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	4			T -> A (in dbSNP:rs8100709).		plasminogen activation (GO:0031639)	integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				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)		CATGGAGCCCACTGTGGCTGA	0.617													A|||	250	0.0499201	0.1815	0.0101	5008	,	,		19564	0.0		0.003	False		,,,				2504	0.0				p.T4A		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.A10G						PASS	.	A	ALA/THR	754,3652	303.2+/-287.8	55,644,1504	63.0	45.0	51.0		10	-4.2	0.0	19	dbSNP_116	51	20,8580	13.3+/-46.6	0,20,4280	yes	missense	TMPRSS9	NM_182973.1	58	55,664,5784	GG,GA,AA		0.2326,17.113,5.9511	benign	4/1060	2389793	774,12232	2203	4300	6503	SO:0001583	missense	360200	exon1			GAGCCCACTGTGG	AJ488946	CCDS12088.1	19p13.3	2010-04-13						"""Serine peptidases / Transmembrane"""	30079	protein-coding gene	gene with protein product	"""polyserase 1"""	610477				12886014	Standard	NM_182973		Approved		uc010xgx.2	Q7Z410		ENST00000332578.3:c.10A>G	19.37:g.2389793A>G	ENSP00000330264:p.Thr4Ala	61.0	0.0	0		76.0	41.0	0.539474	NM_182973	Q6ZND6|Q7Z411	Missense_Mutation	SNP	ENST00000332578.3	37	CCDS12088.1	84	0.038461538461538464	81	0.16463414634146342	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	A	2.015	-0.426184	0.04701	0.17113	0.002326	ENSG00000178297	ENST00000395264;ENST00000332578	D	0.87256	-2.23	4.16	-4.2	0.03823	.	1.292730	0.05536	N	0.564908	T	0.00524	0.0017	N	0.11560	0.145	0.80722	P	0.0	B;B	0.09022	0.0;0.002	B;B	0.04013	0.001;0.001	T	0.07558	-1.0766	9	0.29301	T	0.29	.	12.5441	0.56188	0.2898:0.0:0.7102:0.0	rs8100709;rs52805984;rs8100709	4;4	Q7Z410;E7EMP4	TMPS9_HUMAN;.	A	4	ENSP00000330264:T4A	ENSP00000330264:T4A	T	+	1	0	TMPRSS9	2340793	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.994000	0.03716	-0.882000	0.03987	-0.432000	0.05891	ACT	A|0.948;G|0.052	0.052	strong		0.617	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973	
LLGL2	3993	hgsc.bcm.edu	37	17	73559453	73559453	+	Silent	SNP	C	C	T	rs139362844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:73559453C>T	ENST00000392550.3	+	8	852	c.735C>T	c.(733-735)ctC>ctT	p.L245L	LLGL2_ENST00000167462.5_Silent_p.L245L|LLGL2_ENST00000578363.1_Silent_p.L245L|LLGL2_ENST00000577200.1_Silent_p.L245L|LLGL2_ENST00000375227.4_Silent_p.L245L	NM_001031803.1	NP_001026973.1	Q6P1M3	L2GL2_HUMAN	lethal giant larvae homolog 2 (Drosophila)	245					cell cycle (GO:0007049)|cell division (GO:0051301)|exocytosis (GO:0006887)|regulation of establishment or maintenance of cell polarity (GO:0032878)	cytoplasm (GO:0005737)	PDZ domain binding (GO:0030165)			NS(1)|breast(3)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(13;3.15e-09)|all_epithelial(9;5.78e-10)|Breast(9;5.8e-10)|all_lung(278;0.246)		all cancers(21;1.8e-07)|Epithelial(20;1.38e-06)|Lung(188;0.0696)|LUSC - Lung squamous cell carcinoma(166;0.112)			GCCGCCTGCTCGTCAGCTGTC	0.647													C|||	16	0.00319489	0.0121	0.0	5008	,	,		17901	0.0		0.0	False		,,,				2504	0.0				p.L245L		Atlas-SNP	.											.	LLGL2	155	.	0			c.C735T						PASS	.	C	,,	27,4375	30.8+/-60.4	1,25,2175	34.0	33.0	33.0		735,735,735	-7.7	0.6	17	dbSNP_134	33	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	LLGL2	NM_001015002.1,NM_001031803.1,NM_004524.2	,,	1,25,6475	TT,TC,CC		0.0,0.6134,0.2077	,,	245/357,245/1021,245/1016	73559453	27,12975	2201	4300	6501	SO:0001819	synonymous_variant	3993	exon8			CCTGCTCGTCAGC	X87342	CCDS11725.1, CCDS32733.1, CCDS45776.1	17q25.1	2013-01-10	2001-11-28			ENSG00000073350		"""WD repeat domain containing"""	6629	protein-coding gene	gene with protein product			"""lethal giant larvae (Drosophila) homolog 2"""				Standard	XR_243659		Approved	HGL	uc002joh.3	Q6P1M3		ENST00000392550.3:c.735C>T	17.37:g.73559453C>T		77.0	0.0	0		93.0	49.0	0.526882	NM_001015002	Q14521|Q9BR62	Silent	SNP	ENST00000392550.3	37	CCDS32733.1																																																																																			C|0.996;T|0.004	0.004	strong		0.647	LLGL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447633.1	NM_004524	
NSUN5	55695	hgsc.bcm.edu	37	7	72717686	72717686	+	Silent	SNP	C	C	T	rs145622470	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:72717686C>T	ENST00000252594.6	-	9	1212	c.1197G>A	c.(1195-1197)ccG>ccA	p.P399P	NSUN5_ENST00000310326.8_Silent_p.P399P|NSUN5_ENST00000438747.2_Silent_p.P399P|NSUN5_ENST00000428206.1_Silent_p.P361P			Q96P11	NSUN5_HUMAN	NOP2/Sun domain family, member 5	399					rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|large_intestine(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	8		Lung NSC(55;0.163)				GCTCGGCACCCGGGAACGTGC	0.642													.|||	35	0.00698882	0.025	0.0029	5008	,	,		16592	0.0		0.0	False		,,,				2504	0.0				p.P399P		Atlas-SNP	.											.	NSUN5	47	.	0			c.G1197A						PASS	.	C	,,,	92,4314		0,92,2111	49.0	48.0	48.0		1197,1083,1197,1197	-4.7	0.0	7	dbSNP_134	48	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NSUN5	NM_001168347.1,NM_001168348.1,NM_018044.3,NM_148956.2	,,,	0,92,6411	TT,TC,CC		0.0,2.0881,0.7074	,,,	399/471,361/392,399/430,399/467	72717686	92,12914	2203	4300	6503	SO:0001819	synonymous_variant	55695	exon9			GGCACCCGGGAAC	AF420249	CCDS5546.1, CCDS5547.1, CCDS55118.1, CCDS55119.1	7q11.23	2010-04-08	2009-11-23	2005-01-14	ENSG00000130305	ENSG00000130305		"""NOP2/Sun domain containing"""	16385	protein-coding gene	gene with protein product	"""NOP2/Sun domain family, member 5A"""	615732	"""Williams Beuren syndrome chromosome region 20A"", ""NOL1/NOP2/Sun domain family, member 5"""	WBSCR20, WBSCR20A		11978965, 12073013	Standard	NM_148956		Approved	NOL1R, p120, (NOL1), FLJ10267, NSUN5A, Ynl022cL	uc011kev.2	Q96P11	OTTHUMG00000129869	ENST00000252594.6:c.1197G>A	7.37:g.72717686C>T		111.0	0.0	0		131.0	70.0	0.534351	NM_148956	B3KX04|B4DP79|G3V0G9|Q6ZUI8|Q96HT9|Q9NW70	Silent	SNP	ENST00000252594.6	37	CCDS5547.1																																																																																			C|0.993;T|0.007	0.007	strong		0.642	NSUN5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252113.1	NM_148956	
PUS10	150962	hgsc.bcm.edu	37	2	61188643	61188643	+	Missense_Mutation	SNP	C	C	T	rs113622721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:61188643C>T	ENST00000316752.6	-	10	1090	c.829G>A	c.(829-831)Gct>Act	p.A277T	PUS10_ENST00000407787.1_Missense_Mutation_p.A277T	NM_144709.2	NP_653310.2	Q3MIT2	PUS10_HUMAN	pseudouridylate synthase 10	277					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)	22			LUSC - Lung squamous cell carcinoma(5;1.56e-06)|Lung(5;2.48e-05)|Epithelial(17;0.113)			TCAAGAACAGCGCATACAGCC	0.348													C|||	87	0.0173722	0.0658	0.0	5008	,	,		19044	0.0		0.0	False		,,,				2504	0.0				p.A277T		Atlas-SNP	.											.	PUS10	49	.	0			c.G829A						PASS	.	C	THR/ALA	177,4229	114.6+/-152.6	4,169,2030	222.0	236.0	232.0		829	-2.4	1.0	2	dbSNP_132	232	4,8596	3.0+/-9.4	0,4,4296	yes	missense	PUS10	NM_144709.2	58	4,173,6326	TT,TC,CC		0.0465,4.0172,1.3917	benign	277/530	61188643	181,12825	2203	4300	6503	SO:0001583	missense	150962	exon10			GAACAGCGCATAC	AK056874	CCDS1865.1	2p16.1	2008-02-05	2008-01-09	2008-01-09	ENSG00000162927	ENSG00000162927			26505	protein-coding gene	gene with protein product		612787	"""coiled-coil domain containing 139"""	CCDC139		17900615	Standard	NM_144709		Approved	FLJ32312	uc002sao.3	Q3MIT2	OTTHUMG00000129423	ENST00000316752.6:c.829G>A	2.37:g.61188643C>T	ENSP00000326003:p.Ala277Thr	211.0	0.0	0		235.0	112.0	0.476596	NM_144709	Q5JPJ5|Q96MI8	Missense_Mutation	SNP	ENST00000316752.6	37	CCDS1865.1	47	0.02152014652014652	47	0.09552845528455285	0	0.0	0	0.0	0	0.0	C	4.727	0.135097	0.09032	0.040172	4.65E-4	ENSG00000162927	ENST00000316752;ENST00000407787	T;T	0.38722	1.12;1.12	5.91	-2.41	0.06562	.	0.476386	0.23506	N	0.047441	T	0.00241	0.0007	N	0.00583	-1.355	0.31617	N	0.650811	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.27806	-1.0063	10	0.10902	T	0.67	-7.5462	4.7823	0.13208	0.4331:0.1848:0.0:0.3822	.	277;277	A8K6R4;Q3MIT2	.;PUS10_HUMAN	T	277	ENSP00000326003:A277T;ENSP00000386074:A277T	ENSP00000326003:A277T	A	-	1	0	PUS10	61042147	0.997000	0.39634	0.991000	0.47740	0.993000	0.82548	0.379000	0.20585	-0.138000	0.11434	-0.247000	0.11927	GCT	C|0.985;T|0.015	0.015	strong		0.348	PUS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251582.2	NM_144709	
CRNN	49860	hgsc.bcm.edu	37	1	152382436	152382436	+	Missense_Mutation	SNP	C	C	G	rs6695830	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152382436C>G	ENST00000271835.3	-	3	1184	c.1122G>C	c.(1120-1122)caG>caC	p.Q374H	RP1-91G5.3_ENST00000411804.1_RNA	NM_016190.2	NP_057274.1	Q9UBG3	CRNN_HUMAN	cornulin	374	Gln-rich.		Q -> H (in dbSNP:rs6695830).		response to heat (GO:0009408)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			GGGTCTGTCCCTGTTCTCTAG	0.592													C|||	366	0.0730831	0.261	0.0231	5008	,	,		25184	0.0		0.005	False		,,,				2504	0.0				p.Q374H		Atlas-SNP	.											CRNN,NS,carcinoma,-2,1	CRNN	78	1	0			c.G1122C						PASS	.	C	HIS/GLN	855,3551	336.0+/-304.2	78,699,1426	171.0	145.0	154.0		1122	1.0	0.0	1	dbSNP_116	154	23,8577	16.6+/-54.9	0,23,4277	yes	missense	CRNN	NM_016190.2	24	78,722,5703	GG,GC,CC		0.2674,19.4054,6.7507	possibly-damaging	374/496	152382436	878,12128	2203	4300	6503	SO:0001583	missense	49860	exon3			CTGTCCCTGTTCT	AF077831	CCDS1010.1	1q21	2014-01-28	2005-06-13	2005-06-13	ENSG00000143536	ENSG00000143536		"""EF-hand domain containing"""	1230	protein-coding gene	gene with protein product		611312	"""chromosome 1 open reading frame 10"""	C1orf10		11056050, 15854041	Standard	NM_016190		Approved	SEP53	uc001ezx.2	Q9UBG3	OTTHUMG00000012383	ENST00000271835.3:c.1122G>C	1.37:g.152382436C>G	ENSP00000271835:p.Gln374His	361.0	0.0	0		341.0	340.0	0.997067	NM_016190	B2RE60|Q8N613	Missense_Mutation	SNP	ENST00000271835.3	37	CCDS1010.1	120	0.054945054945054944	114	0.23170731707317074	4	0.011049723756906077	0	0.0	2	0.002638522427440633	C	14.19	2.462134	0.43736	0.194054	0.002674	ENSG00000143536	ENST00000271835	T	0.05139	3.49	4.86	0.955	0.19602	.	0.889113	0.09605	N	0.779761	T	0.04182	0.0116	L	0.54323	1.7	0.80722	P	0.0	D	0.56035	0.974	P	0.49012	0.598	T	0.36286	-0.9754	9	0.62326	D	0.03	.	6.7488	0.23475	0.0:0.6177:0.0:0.3823	rs6695830;rs6695830	374	Q9UBG3	CRNN_HUMAN	H	374	ENSP00000271835:Q374H	ENSP00000271835:Q374H	Q	-	3	2	CRNN	150649060	0.361000	0.24972	0.006000	0.13384	0.150000	0.21749	0.677000	0.25262	0.018000	0.15052	-0.225000	0.12378	CAG	C|0.939;G|0.061	0.061	strong		0.592	CRNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034503.1	NM_016190	
RPP38	10557	hgsc.bcm.edu	37	10	15145917	15145917	+	Missense_Mutation	SNP	A	A	C	rs12249258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:15145917A>C	ENST00000378197.4	+	3	1118	c.604A>C	c.(604-606)Agt>Cgt	p.S202R	RPP38_ENST00000451677.1_Intron|RPP38_ENST00000378202.5_Missense_Mutation_p.S202R|NMT2_ENST00000466201.1_Intron	NM_183005.4	NP_892117.1	P78345	RPP38_HUMAN	ribonuclease P/MRP 38kDa subunit	202			S -> R (in dbSNP:rs12249258).		RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA processing (GO:0008033)	nucleolar ribonuclease P complex (GO:0005655)|nucleus (GO:0005634)	ribonuclease P activity (GO:0004526)			breast(1)|endometrium(3)|large_intestine(1)|lung(2)|ovary(1)	8						CAGAGTCCCCAGTTTAAGTGT	0.463													A|||	241	0.048123	0.1725	0.013	5008	,	,		20068	0.0		0.004	False		,,,				2504	0.0				p.S202R	GBM(118;1591 1611 9649 34378 50720)	Atlas-SNP	.											.	RPP38	26	.	0			c.A604C						PASS	.	A	ARG/SER,ARG/SER,ARG/SER	543,3863	244.7+/-253.9	41,461,1701	68.0	69.0	69.0		604,604,604	-3.0	0.0	10	dbSNP_120	69	5,8595	3.7+/-12.6	0,5,4295	yes	missense,missense,missense	RPP38	NM_001097590.1,NM_006414.3,NM_183005.3	110,110,110	41,466,5996	CC,CA,AA		0.0581,12.3241,4.2134	benign,benign,benign	202/284,202/284,202/284	15145917	548,12458	2203	4300	6503	SO:0001583	missense	10557	exon2			GTCCCCAGTTTAA	U77664	CCDS7108.1	10p13	2012-05-21			ENSG00000152464	ENSG00000152464			30329	protein-coding gene	gene with protein product		606116				9037013, 9630247	Standard	NM_183005		Approved		uc001inx.5	P78345	OTTHUMG00000017728	ENST00000378197.4:c.604A>C	10.37:g.15145917A>C	ENSP00000367439:p.Ser202Arg	92.0	0.0	0		87.0	44.0	0.505747	NM_001265601	B3KPY0|D3DRT8|Q53F71|Q8NHS8	Missense_Mutation	SNP	ENST00000378197.4	37	CCDS7108.1	96	0.04395604395604396	86	0.17479674796747968	7	0.019337016574585635	0	0.0	3	0.00395778364116095	A	5.707	0.315044	0.10789	0.123241	5.81E-4	ENSG00000152464	ENST00000378203;ENST00000378202;ENST00000378197	T;T;T	0.10192	2.9;2.9;2.9	5.88	-2.97	0.05530	.	1.421770	0.04406	N	0.365158	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.43360	-0.9396	9	0.15952	T	0.53	-0.0859	5.4796	0.16717	0.2215:0.5329:0.1457:0.0999	rs12249258;rs52829912;rs57326558;rs12249258	202	P78345	RPP38_HUMAN	R	202	ENSP00000367445:S202R;ENSP00000367444:S202R;ENSP00000367439:S202R	ENSP00000367439:S202R	S	+	1	0	RPP38	15185923	0.000000	0.05858	0.006000	0.13384	0.561000	0.35649	-0.048000	0.11944	-0.396000	0.07703	0.482000	0.46254	AGT	A|0.946;C|0.054	0.054	strong		0.463	RPP38-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046976.1	NM_006414	
BPTF	2186	hgsc.bcm.edu	37	17	65919092	65919092	+	Silent	SNP	G	G	A	rs59088743	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:65919092G>A	ENST00000321892.4	+	16	6133	c.6072G>A	c.(6070-6072)agG>agA	p.R2024R	BPTF_ENST00000424123.3_Silent_p.R1885R|BPTF_ENST00000335221.5_Silent_p.R2024R|BPTF_ENST00000306378.6_Silent_p.R1898R			Q12830	BPTF_HUMAN	bromodomain PHD finger transcription factor	2024					anterior/posterior pattern specification (GO:0009952)|ATP catabolic process (GO:0006200)|brain development (GO:0007420)|chromatin remodeling (GO:0006338)|embryonic placenta development (GO:0001892)|endoderm development (GO:0007492)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NURF complex (GO:0016589)	sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(16)|lung(23)|ovary(3)|pancreas(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	78	all_cancers(12;6e-11)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0984)|LUSC - Lung squamous cell carcinoma(166;0.24)			GGGAGATCAGGGCATTTGCTG	0.398													G|||	95	0.0189696	0.0666	0.0086	5008	,	,		18950	0.0		0.001	False		,,,				2504	0.0				p.R2024R		Atlas-SNP	.											.	BPTF	415	.	0			c.G6072A						PASS	.	G	,	247,4159	143.1+/-178.2	7,233,1963	144.0	139.0	141.0		6072,5694	3.8	1.0	17	dbSNP_129	141	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous,coding-synonymous	BPTF	NM_004459.6,NM_182641.3	,	7,241,6255	AA,AG,GG		0.093,5.606,1.9606	,	2024/2904,1898/2921	65919092	255,12751	2203	4300	6503	SO:0001819	synonymous_variant	2186	exon16			GATCAGGGCATTT	AY282495	CCDS11673.1	17q24	2013-01-28	2006-12-01	2006-12-01	ENSG00000171634	ENSG00000171634		"""Zinc fingers, PHD-type"""	3581	protein-coding gene	gene with protein product		601819	"""fetal Alzheimer antigen"""	FALZ		8975731, 10662542, 16728976	Standard	NM_182641		Approved	FAC1, NURF301	uc002jgf.3	Q12830	OTTHUMG00000132254	ENST00000321892.4:c.6072G>A	17.37:g.65919092G>A		107.0	0.0	0		138.0	59.0	0.427536	NM_004459	Q6NX67|Q7Z7D6|Q9UIG2	Silent	SNP	ENST00000321892.4	37																																																																																				G|0.981;A|0.019	0.019	strong		0.398	BPTF-201	KNOWN	basic	protein_coding	protein_coding		NM_182641, NM_004459	
GRM5	2915	hgsc.bcm.edu	37	11	88337922	88337922	+	Missense_Mutation	SNP	G	G	A	rs61741175	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:88337922G>A	ENST00000305447.4	-	4	1507	c.1358C>T	c.(1357-1359)aCg>aTg	p.T453M	GRM5_ENST00000393297.1_Missense_Mutation_p.T453M|GRM5_ENST00000418177.2_Missense_Mutation_p.T453M|GRM5_ENST00000455756.2_Missense_Mutation_p.T453M|GRM5_ENST00000305432.5_Missense_Mutation_p.T453M	NM_001143831.2	NP_001137303.1	P41594	GRM5_HUMAN	glutamate receptor, metabotropic 5	453					activation of MAPKKK activity (GO:0000185)|cognition (GO:0050890)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|learning (GO:0007612)|locomotory behavior (GO:0007626)|negative regulation of locomotion (GO:0040013)|phospholipase C-activating G-protein coupled glutamate receptor signaling pathway (GO:0007206)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein phosphorylation (GO:0006468)|regulation of synaptic transmission, glutamatergic (GO:0051966)|regulation of transcription, DNA-templated (GO:0006355)|synaptic transmission (GO:0007268)	astrocyte projection (GO:0097449)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)			NS(1)|breast(5)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(18)|lung(40)|ovary(3)|pancreas(1)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	90		Acute lymphoblastic leukemia(157;2.54e-05)|all_hematologic(158;0.00834)			Acamprosate(DB00659)|Rufinamide(DB06201)	GAATAGGATCGTATCTCCAGA	0.448													G|||	136	0.0271565	0.0946	0.0144	5008	,	,		20219	0.0		0.001	False		,,,				2504	0.0				p.T453M		Atlas-SNP	.											GRM5_ENST00000418177,right_upper_lobe,carcinoma,+1,2	GRM5	414	2	0			c.C1358T						PASS	.	G	MET/THR,MET/THR	352,4050	181.9+/-209.8	14,324,1863	58.0	60.0	59.0		1358,1358	2.1	1.0	11	dbSNP_129	59	2,8596	2.2+/-6.3	0,2,4297	yes	missense,missense	GRM5	NM_000842.3,NM_001143831.2	81,81	14,326,6160	AA,AG,GG		0.0233,7.9964,2.7231	benign,benign	453/1181,453/1213	88337922	354,12646	2201	4299	6500	SO:0001583	missense	2915	exon5			AGGATCGTATCTC	D28538	CCDS8283.1, CCDS44694.1	11q14.3	2014-06-12			ENSG00000168959	ENSG00000168959		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4597	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 86"""	604102				7908515	Standard	NM_001143831		Approved	MGLUR5, GPRC1E, mGlu5, PPP1R86	uc001pcq.3	P41594	OTTHUMG00000134306	ENST00000305447.4:c.1358C>T	11.37:g.88337922G>A	ENSP00000306138:p.Thr453Met	49.0	0.0	0		54.0	28.0	0.518519	NM_000842	Q6J164	Missense_Mutation	SNP	ENST00000305447.4	37	CCDS44694.1	47	0.02152014652014652	43	0.08739837398373984	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	G	9.419	1.082463	0.20309	0.079964	2.33E-4	ENSG00000168959	ENST00000418177;ENST00000455756;ENST00000305432;ENST00000305447;ENST00000393297	D;D;D;D;D	0.82433	-1.61;-1.61;-1.61;-1.61;-1.61	5.77	2.13	0.27403	Extracellular ligand-binding receptor (1);	0.320592	0.41294	N	0.000913	T	0.10121	0.0248	L	0.45137	1.4	0.22479	N	0.999063	B;B	0.19935	0.04;0.002	B;B	0.15484	0.013;0.002	T	0.12041	-1.0563	9	.	.	.	.	9.7316	0.40363	0.7425:0.0:0.2575:0.0	.	453;453	P41594-2;P41594	.;GRM5_HUMAN	M	453	ENSP00000402912:T453M;ENSP00000405690:T453M;ENSP00000305905:T453M;ENSP00000306138:T453M;ENSP00000376975:T453M	.	T	-	2	0	GRM5	87977570	0.706000	0.27856	1.000000	0.80357	0.863000	0.49368	0.371000	0.20450	0.461000	0.27071	-1.721000	0.00707	ACG	G|0.972;A|0.028	0.028	strong		0.448	GRM5-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000259226.1	NM_000842	
DNAH10	196385	hgsc.bcm.edu	37	12	124354954	124354954	+	Missense_Mutation	SNP	C	C	T	rs7977449	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124354954C>T	ENST00000409039.3	+	43	7232	c.7207C>T	c.(7207-7209)Cgg>Tgg	p.R2403W		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2403			R -> W (in dbSNP:rs7977449).		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)		TGATAACAAACGGAATCAATG	0.393													C|||	118	0.0235623	0.0295	0.0086	5008	,	,		21920	0.0526		0.007	False		,,,				2504	0.0133				p.R2403W		Atlas-SNP	.											.	DNAH10	888	.	0			c.C7207T						PASS	.	C	TRP/ARG	109,3641		3,103,1769	91.0	88.0	89.0		7207	2.2	0.0	12	dbSNP_116	89	59,8163		0,59,4052	yes	missense	DNAH10	NM_207437.3	101	3,162,5821	TT,TC,CC		0.7176,2.9067,1.4033	probably-damaging	2403/4472	124354954	168,11804	1875	4111	5986	SO:0001583	missense	196385	exon43			AACAAACGGAATC	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.7207C>T	12.37:g.124354954C>T	ENSP00000386770:p.Arg2403Trp	99.0	0.0	0		79.0	34.0	0.43038	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	63	0.028846153846153848	19	0.03861788617886179	3	0.008287292817679558	37	0.06468531468531469	4	0.005277044854881266	C	15.02	2.709681	0.48517	0.029067	0.007176	ENSG00000197653	ENST00000409039	T	0.22945	1.93	5.21	2.23	0.28157	.	1.696560	0.05959	U	0.640214	T	0.03434	0.0099	L	0.49778	1.585	0.09310	N	1	P	0.52316	0.952	P	0.44860	0.462	T	0.13255	-1.0516	10	0.66056	D	0.02	.	8.4827	0.33052	0.5085:0.4206:0.0:0.0709	rs7977449;rs7977449	2403	Q8IVF4	DYH10_HUMAN	W	2403	ENSP00000386770:R2403W	ENSP00000386770:R2403W	R	+	1	2	DNAH10	122920907	0.005000	0.15991	0.000000	0.03702	0.001000	0.01503	0.510000	0.22723	0.571000	0.29365	0.655000	0.94253	CGG	C|0.971;T|0.029	0.029	strong		0.393	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
OR4A16	81327	hgsc.bcm.edu	37	11	55110989	55110989	+	Missense_Mutation	SNP	C	C	G	rs116541488	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55110989C>G	ENST00000314721.2	+	1	363	c.313C>G	c.(313-315)Ctt>Gtt	p.L105V		NM_001005274.1	NP_001005274.1	Q8NH70	O4A16_HUMAN	olfactory receptor, family 4, subfamily A, member 16	105						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(28)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	51						AGAACACTTACTTGGTGGTGC	0.448													.|||	50	0.00998403	0.0333	0.0086	5008	,	,		22391	0.0		0.0	False		,,,				2504	0.0				p.L105V		Atlas-SNP	.											.	OR4A16	120	.	0			c.C313G						PASS	.	C	VAL/LEU	142,4260	100.3+/-138.9	1,140,2060	201.0	188.0	192.0		313	1.4	0.2	11	dbSNP_132	192	5,8587	5.0+/-18.6	0,5,4291	yes	missense	OR4A16	NM_001005274.1	32	1,145,6351	GG,GC,CC		0.0582,3.2258,1.1313	benign	105/329	55110989	147,12847	2201	4296	6497	SO:0001583	missense	81327	exon1			CACTTACTTGGTG	AB065519	CCDS31499.1	11q11	2012-08-09			ENSG00000181961	ENSG00000181961		"""GPCR / Class A : Olfactory receptors"""	15153	protein-coding gene	gene with protein product							Standard	NM_001005274		Approved	OR4A16Q	uc010rie.2	Q8NH70	OTTHUMG00000166710	ENST00000314721.2:c.313C>G	11.37:g.55110989C>G	ENSP00000325128:p.Leu105Val	307.0	0.0	0		289.0	128.0	0.442907	NM_001005274	Q6IFL3	Missense_Mutation	SNP	ENST00000314721.2	37	CCDS31499.1	16	0.007326007326007326	13	0.026422764227642278	3	0.008287292817679558	0	0.0	0	0.0	c	0.720	-0.783973	0.02907	0.032258	5.82E-4	ENSG00000181961	ENST00000314721	T	0.00700	5.82	2.57	1.37	0.22104	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00356	0.0011	L	0.41079	1.255	0.09310	N	1	B	0.25007	0.116	B	0.29353	0.101	T	0.48658	-0.9016	9	0.87932	D	0	.	4.5335	0.12017	0.0:0.3127:0.0:0.6873	.	105	Q8NH70	O4A16_HUMAN	V	105	ENSP00000325128:L105V	ENSP00000325128:L105V	L	+	1	0	OR4A16	54867565	0.036000	0.19791	0.157000	0.22605	0.029000	0.11900	0.995000	0.29706	0.240000	0.21263	-0.664000	0.03847	CTT	C|0.988;G|0.012	0.012	strong		0.448	OR4A16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391160.1	NM_001005274	
DND1	373863	hgsc.bcm.edu	37	5	140051009	140051009	+	Silent	SNP	G	G	A	rs146252353	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140051009G>A	ENST00000542735.1	-	4	974	c.931C>T	c.(931-933)Cta>Tta	p.L311L	WDR55_ENST00000520764.1_3'UTR|WDR55_ENST00000358337.5_3'UTR	NM_194249.2	NP_919225.1	Q8IYX4	DND1_HUMAN	DND microRNA-mediated repression inhibitor 1	311					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)			CGGCCATCTAGGGTCAGCACA	0.622													G|||	28	0.00559105	0.0212	0.0	5008	,	,		20864	0.0		0.0	False		,,,				2504	0.0				p.L311L		Atlas-SNP	.											.	DND1	15	.	0			c.C931T						PASS	.	G		78,4010		0,78,1966	22.0	23.0	23.0		931	-1.9	0.0	5	dbSNP_134	23	0,8094		0,0,4047	no	coding-synonymous	DND1	NM_194249.2		0,78,6013	AA,AG,GG		0.0,1.908,0.6403		311/354	140051009	78,12104	2044	4047	6091	SO:0001819	synonymous_variant	373863	exon4			CATCTAGGGTCAG	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.931C>T	5.37:g.140051009G>A		407.0	0.0	0		406.0	202.0	0.497537	NM_194249		Silent	SNP	ENST00000542735.1	37	CCDS4236.1																																																																																			G|0.994;A|0.006	0.006	strong		0.622	DND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251669.2	NM_194249	
BBS5	129880	hgsc.bcm.edu	37	2	170336102	170336102	+	Silent	SNP	C	C	G	rs10188609	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170336102C>G	ENST00000295240.3	+	1	415	c.39C>G	c.(37-39)gtC>gtG	p.V13V	BBS5_ENST00000392663.2_Silent_p.V13V|RP11-724O16.1_ENST00000513963.1_Silent_p.V13V|BBS5_ENST00000554017.1_Silent_p.V13V	NM_152384.2	NP_689597.1	Q8N3I7	BBS5_HUMAN	Bardet-Biedl syndrome 5	13					cilium assembly (GO:0042384)|heart looping (GO:0001947)|melanosome transport (GO:0032402)|motile cilium assembly (GO:0044458)|protein transport (GO:0015031)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	BBSome (GO:0034464)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphatidylinositol-3-phosphate binding (GO:0032266)|RNA polymerase II repressing transcription factor binding (GO:0001103)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						ATCGGGATGTCCGTTTCGACC	0.637									Bardet-Biedl syndrome				C|||	233	0.0465256	0.1702	0.0115	5008	,	,		17042	0.0		0.0	False		,,,				2504	0.0				p.V13V		Atlas-SNP	.											.	BBS5	27	.	0			c.C39G						PASS	.	C		613,3793	265.3+/-266.6	56,501,1646	134.0	121.0	125.0		39	5.1	1.0	2	dbSNP_119	125	0,8600		0,0,4300	no	coding-synonymous	BBS5	NM_152384.2		56,501,5946	GG,GC,CC		0.0,13.9128,4.7132		13/342	170336102	613,12393	2203	4300	6503	SO:0001819	synonymous_variant	129880	exon1	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	GGATGTCCGTTTC	AY604003	CCDS2233.1	2q31	2011-08-02			ENSG00000163093	ENSG00000163093			970	protein-coding gene	gene with protein product		603650				9888993, 10053027	Standard	NM_152384		Approved	DKFZp762I194		Q8N3I7	OTTHUMG00000132207	ENST00000295240.3:c.39C>G	2.37:g.170336102C>G		104.0	0.0	0		81.0	33.0	0.407407	NM_152384	D3DPC3|Q6PKN0	Silent	SNP	ENST00000295240.3	37	CCDS2233.1																																																																																			C|0.954;G|0.046	0.046	strong		0.637	BBS5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255265.2	NM_152384	
ZNF668	79759	hgsc.bcm.edu	37	16	31073244	31073244	+	Silent	SNP	C	C	A	rs34831291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31073244C>A	ENST00000538906.1	-	3	1789	c.1005G>T	c.(1003-1005)ccG>ccT	p.P335P	ZNF668_ENST00000417110.2_Missense_Mutation_p.N144K|ZNF668_ENST00000539836.3_Silent_p.P358P|ZNF668_ENST00000564456.1_5'Flank|ZNF668_ENST00000535577.1_Silent_p.P335P|ZNF668_ENST00000426488.2_Silent_p.P358P|ZNF668_ENST00000300849.4_Silent_p.P335P|ZNF668_ENST00000394983.2_Silent_p.P335P	NM_001172668.1	NP_001166139	Q96K58	ZN668_HUMAN	zinc finger protein 668	335					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	27						GGCACTTGAACGGCCGGTCGC	0.652													C|||	36	0.0071885	0.0242	0.0058	5008	,	,		15280	0.0		0.0	False		,,,				2504	0.0				p.P358P	Colon(181;1111 1980 5060 10512 25785)	Atlas-SNP	.											.	ZNF668	121	.	0			c.G1074T						PASS	.	C	,,,	133,4259		3,127,2066	35.0	37.0	36.0		1005,1074,1005,1005	-11.3	0.5	16	dbSNP_126	36	1,8591		0,1,4295	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF668	NM_001172668.1,NM_001172669.1,NM_001172670.1,NM_024706.4	,,,	3,128,6361	AA,AC,CC		0.0116,3.0282,1.032	,,,	335/620,358/643,335/620,335/620	31073244	134,12850	2196	4296	6492	SO:0001819	synonymous_variant	79759	exon4			CTTGAACGGCCGG		CCDS10701.1, CCDS54003.1	16p11.2	2013-01-08			ENSG00000167394	ENSG00000167394		"""Zinc fingers, C2H2-type"""	25821	protein-coding gene	gene with protein product						12477932	Standard	NM_024706		Approved	FLJ13479	uc021tgt.1	Q96K58	OTTHUMG00000047357	ENST00000538906.1:c.1005G>T	16.37:g.31073244C>A		53.0	0.0	0		53.0	25.0	0.471698	NM_001172669	C9JHH8|F5H7E7|Q59EV1|Q8N669|Q9H8L4	Silent	SNP	ENST00000538906.1	37	CCDS10701.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	C	3.701	-0.061523	0.07317	0.030282	1.16E-4	ENSG00000232748	ENST00000417110	.	.	.	5.63	-11.3	0.00108	.	.	.	.	.	T	0.27594	0.0678	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.66356	-0.5944	5	0.87932	D	0	-27.0566	5.6564	0.17644	0.17:0.1581:0.4906:0.1812	rs34831291	.	.	.	K	144	.	ENSP00000391989:N144K	N	+	3	2	AC135050.1	30980745	0.000000	0.05858	0.522000	0.27862	0.356000	0.29392	-5.729000	0.00102	-1.861000	0.01153	-1.119000	0.02030	AAC	C|0.990;A|0.010	0.010	strong		0.652	ZNF668-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108516.2	NM_024706	
SERPINA1	5265	hgsc.bcm.edu	37	14	94844975	94844975	+	Silent	SNP	G	G	A	rs9630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:94844975G>A	ENST00000448921.1	-	7	1640	c.1068C>T	c.(1066-1068)gcC>gcT	p.A356A	SERPINA1_ENST00000355814.4_Silent_p.A356A|SERPINA1_ENST00000393087.4_Silent_p.A356A|SERPINA1_ENST00000449399.3_Silent_p.A356A|SERPINA1_ENST00000393088.4_Silent_p.A356A|SERPINA1_ENST00000437397.1_Silent_p.A356A|SERPINA1_ENST00000440909.1_Silent_p.A356A|SERPINA1_ENST00000404814.4_Silent_p.A356A	NM_001002236.2|NM_001127701.1|NM_001127703.1|NM_001127704.1|NM_001127705.1	NP_001002236.1|NP_001121173.1|NP_001121175.1|NP_001121176.1|NP_001121177.1	P01009	A1AT_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1	356					acute-phase response (GO:0006953)|blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of proteolysis (GO:0030162)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)	glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(5)|skin(6)|stomach(1)	24		all_cancers(154;0.0649)|all_epithelial(191;0.223)		Epithelial(152;0.135)|COAD - Colon adenocarcinoma(157;0.207)|all cancers(159;0.221)		CCTTATGCACGGCCTGGAGGG	0.592													G|||	50	0.00998403	0.0356	0.0043	5008	,	,		19798	0.0		0.0	False		,,,				2504	0.0				p.A356A		Atlas-SNP	.											.	SERPINA1	51	.	0			c.C1068T						PASS	.	G	,,,,,,,,,,	122,4284	90.2+/-128.9	1,120,2082	80.0	59.0	66.0		1068,1068,1068,1068,1068,1068,1068,1068,1068,1068,1068	-9.6	0.0	14	dbSNP_52	66	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SERPINA1	NM_000295.4,NM_001002235.2,NM_001002236.2,NM_001127700.1,NM_001127701.1,NM_001127702.1,NM_001127703.1,NM_001127704.1,NM_001127705.1,NM_001127706.1,NM_001127707.1	,,,,,,,,,,	1,121,6381	AA,AG,GG		0.0116,2.769,0.9457	,,,,,,,,,,	356/419,356/419,356/419,356/419,356/419,356/419,356/419,356/419,356/419,356/419,356/419	94844975	123,12883	2203	4300	6503	SO:0001819	synonymous_variant	5265	exon7			ATGCACGGCCTGG	X01683	CCDS9925.1	14q32.1	2014-02-18	2005-08-18		ENSG00000197249	ENSG00000197249		"""Serine (or cysteine) peptidase inhibitors"""	8941	protein-coding gene	gene with protein product	"""protease inhibitor 1 (anti-elastase), alpha-1-antitrypsin"""	107400	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1"""	PI		24172014	Standard	NM_000295		Approved	AAT, A1A, PI1, alpha-1-antitrypsin, A1AT, alpha1AT	uc010aux.3	P01009	OTTHUMG00000150355	ENST00000448921.1:c.1068C>T	14.37:g.94844975G>A		154.0	0.0	0		168.0	82.0	0.488095	NM_001127701	A6PX14|B2RDQ8|Q0PVP5|Q13672|Q53XB8|Q5U0M1|Q7M4R2|Q86U18|Q86U19|Q96BF9|Q96ES1|Q9P1P0|Q9UCE6|Q9UCM3	Silent	SNP	ENST00000448921.1	37	CCDS9925.1																																																																																			G|0.989;A|0.011	0.011	strong		0.592	SERPINA1-203	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317768.2	NM_001002235	
PNMAL1	55228	hgsc.bcm.edu	37	19	46973693	46973693	+	Silent	SNP	C	C	T	rs73552938	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:46973693C>T	ENST00000313683.10	-	2	905	c.600G>A	c.(598-600)ccG>ccA	p.P200P	PNMAL1_ENST00000602246.1_Intron|PNMAL1_ENST00000438932.2_Silent_p.P200P	NM_001103149.1|NM_018215.3	NP_001096619.1|NP_060685.2	Q86V59	PNML1_HUMAN	paraneoplastic Ma antigen family-like 1	200										cervix(1)|endometrium(2)|large_intestine(8)|lung(8)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000166)|all cancers(93;0.0014)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)		CTGCAAGCCCCGGTTCTTTCT	0.592													C|||	99	0.0197684	0.0696	0.0101	5008	,	,		18070	0.0		0.0	False		,,,				2504	0.0				p.P200P		Atlas-SNP	.											PNMAL1_ENST00000438932,lower_third,carcinoma,-1,2	PNMAL1	87	2	0			c.G600A						scavenged	.	C	,	250,4156	143.5+/-178.5	4,242,1957	58.0	60.0	59.0		600,600	-7.7	0.0	19	dbSNP_130	59	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	PNMAL1	NM_001103149.1,NM_018215.3	,	4,244,6255	TT,TC,CC		0.0233,5.6741,1.9376	,	200/379,200/440	46973693	252,12754	2203	4300	6503	SO:0001819	synonymous_variant	55228	exon2			AAGCCCCGGTTCT	BC026026	CCDS33059.1, CCDS46124.1	19q13.32	2014-02-12	2012-02-09			ENSG00000182013		"""Paraneoplastic Ma antigens"""	25578	protein-coding gene	gene with protein product			"""PNMA-like 1"""			12477932	Standard	NM_018215		Approved	KIAA1183L, FLJ10781	uc002peq.4	Q86V59		ENST00000313683.10:c.600G>A	19.37:g.46973693C>T		61.0	1.0	0.0163934		65.0	64.0	0.984615	NM_018215	A8K2F3|Q5U638|Q8N3H4|Q9NVE8	Silent	SNP	ENST00000313683.10	37	CCDS33059.1	41	0.018772893772893772	38	0.07723577235772358	3	0.008287292817679558	0	0.0	0	0.0	C	4.609	0.113215	0.08831	0.056741	2.33E-4	ENSG00000182013	ENST00000417103	.	.	.	3.84	-7.67	0.01272	.	.	.	.	.	T	0.01558	0.0050	.	.	.	0.21386	N	0.99971	.	.	.	.	.	.	T	0.13845	-1.0494	5	0.46703	T	0.11	-21.5671	4.3527	0.11163	0.0894:0.1015:0.3706:0.4386	.	.	.	.	R	180	.	ENSP00000389114:G180R	G	-	1	0	PNMAL1	51665533	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-5.361000	0.00128	-3.560000	0.00141	-0.345000	0.07892	GGG	C|0.977;T|0.023	0.023	strong		0.592	PNMAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403929.1	NM_018215	
PCDHA10	56139	hgsc.bcm.edu	37	5	140237826	140237826	+	Silent	SNP	G	G	C	rs180990865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140237826G>C	ENST00000307360.5	+	1	2193	c.2193G>C	c.(2191-2193)ggG>ggC	p.G731G	PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	731					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGCATGTGGGCCGGTGAAGC	0.672													.|||	66	0.0131789	0.0492	0.0014	5008	,	,		13681	0.0		0.0	False		,,,				2504	0.0				p.G731G		Atlas-SNP	.											.	PCDHA10	358	.	0			c.G2193C						PASS	.	G	,,,,,,,,,,,,,	90,2554		6,78,1238	32.0	32.0	32.0		,2193,,,,,,,,,,,2193,	-2.2	0.0	5		32	0,4582		0,0,2291	no	intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,intron	PCDHA9,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031859.1,NM_031860.1	,,,,,,,,,,,,,	6,78,3529	CC,CG,GG		0.0,3.4039,1.2455	,,,,,,,,,,,,,	,731/949,,,,,,,,,,,731/845,	140237826	90,7136	1322	2291	3613	SO:0001819	synonymous_variant	56139	exon1			ATGTGGGCCGGTG	AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"""Cadherins / Protocadherins : Clustered"""	8664	other	complex locus constituent	"""KIAA0345-like 4"", ""ortholog to mouse CNR8"""	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.2193G>C	5.37:g.140237826G>C		235.0	0.0	0		234.0	108.0	0.461538	NM_031859	A1L493|O75280|Q9NRU2	Silent	SNP	ENST00000307360.5	37	CCDS54921.1																																																																																			G|0.989;C|0.011	0.011	strong		0.672	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901	
PODN	127435	hgsc.bcm.edu	37	1	53544271	53544271	+	Silent	SNP	G	G	C	rs62000444	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:53544271G>C	ENST00000312553.5	+	8	1240	c.1233G>C	c.(1231-1233)acG>acC	p.T411T	PODN_ENST00000371500.3_Silent_p.T392T|PODN_ENST00000395871.2_Silent_p.T269T|RP11-334A14.5_ENST00000447867.1_RNA	NM_001199081.1|NM_153703.4	NP_001186010.1|NP_714914.2	Q7Z5L7	PODN_HUMAN	podocan	363					negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	collagen binding (GO:0005518)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(11)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						GGTTGCACACGGTGCACCTGT	0.662													G|||	54	0.0107827	0.034	0.0115	5008	,	,		19751	0.0		0.001	False		,,,				2504	0.0				p.T411T		Atlas-SNP	.											.	PODN	86	.	0			c.G1233C						PASS	.	G	,,,	95,4311	76.2+/-114.5	1,93,2109	66.0	61.0	63.0		1176,1176,807,1233	-1.9	1.0	1	dbSNP_129	63	9,8591	6.4+/-24.3	0,9,4291	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PODN	NM_001199080.1,NM_001199081.1,NM_001199082.1,NM_153703.4	,,,	1,102,6400	CC,CG,GG		0.1047,2.1562,0.7996	,,,	392/643,392/643,269/520,411/662	53544271	104,12902	2203	4300	6503	SO:0001819	synonymous_variant	127435	exon8			GCACACGGTGCAC	AY313607	CCDS573.1, CCDS55601.1, CCDS55602.1	1p32.3	2008-02-05			ENSG00000174348	ENSG00000174348		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	23174	protein-coding gene	gene with protein product	"""podocan proteoglycan"""	608661					Standard	NM_153703		Approved	PCAN, PODOCAN, MGC24995, SLRR5A	uc010onr.2	Q7Z5L7	OTTHUMG00000008934	ENST00000312553.5:c.1233G>C	1.37:g.53544271G>C		97.0	0.0	0		120.0	61.0	0.508333	NM_153703	B4DKN5|B4E373|Q5VVZ2|Q5VVZ3|Q6PIR3|Q6UXL8|Q8N641	Silent	SNP	ENST00000312553.5	37	CCDS573.1																																																																																			G|0.992;C|0.008	0.008	strong		0.662	PODN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000024735.1	NM_153703	
SULT6B1	391365	hgsc.bcm.edu	37	2	37406645	37406645	+	Missense_Mutation	SNP	T	T	C	rs61737618	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:37406645T>C	ENST00000535679.1	-	4	484	c.485A>G	c.(484-486)tAt>tGt	p.Y162C	SULT6B1_ENST00000260637.3_Missense_Mutation_p.Y124C|SULT6B1_ENST00000407963.1_Missense_Mutation_p.Y124C|SULT6B1_ENST00000379149.2_Intron			Q6IMI4	ST6B1_HUMAN	sulfotransferase family, cytosolic, 6B, member 1	162						cytoplasm (GO:0005737)	sulfotransferase activity (GO:0008146)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(3)|lung(5)|ovary(1)	12		all_hematologic(82;0.248)				CCAAGAGCCATAGCTTGGAAT	0.378													T|||	9	0.00179712	0.0068	0.0	5008	,	,		19591	0.0		0.0	False		,,,				2504	0.0				p.Y124C		Atlas-SNP	.											.	SULT6B1	46	.	0			c.A371G						PASS	.	T	CYS/TYR	33,4373	38.4+/-70.7	0,33,2170	161.0	151.0	154.0		371	3.0	1.0	2	dbSNP_129	154	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SULT6B1	NM_001032377.1	194	0,34,6469	CC,CT,TT		0.0116,0.749,0.2614	probably-damaging	124/266	37406645	34,12972	2203	4300	6503	SO:0001583	missense	391365	exon4			GAGCCATAGCTTG	AY289770, AY289774	CCDS33182.1	2p22.2	2007-07-26			ENSG00000138068	ENSG00000138068		"""Sulfotransferases, cytosolic"""	33433	protein-coding gene	gene with protein product						14676822	Standard	XM_005264307		Approved		uc002rpu.3	Q6IMI4	OTTHUMG00000152160	ENST00000535679.1:c.485A>G	2.37:g.37406645T>C	ENSP00000444081:p.Tyr162Cys	60.0	0.0	0		60.0	33.0	0.55	NM_001032377	B2RTS7	Missense_Mutation	SNP	ENST00000535679.1	37		3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	T	15.08	2.726804	0.48833	0.00749	1.16E-4	ENSG00000138068	ENST00000535679;ENST00000260637;ENST00000407963	D;D;D	0.82167	-1.58;-1.58;-1.58	4.27	3.02	0.34903	Sulfotransferase domain (1);	1.254540	0.05257	N	0.515113	D	0.86522	0.5953	M	0.73372	2.23	0.40291	D	0.9785	D	0.71674	0.998	D	0.65443	0.935	T	0.81870	-0.0734	10	0.40728	T	0.16	.	9.6717	0.40017	0.1561:0.0:0.0:0.8439	.	162	Q6IMI4	ST6B1_HUMAN	C	162;124;124	ENSP00000444081:Y162C;ENSP00000260637:Y124C;ENSP00000384950:Y124C	ENSP00000260637:Y124C	Y	-	2	0	SULT6B1	37260149	0.715000	0.27946	0.981000	0.43875	0.855000	0.48748	0.833000	0.27504	1.928000	0.55862	0.459000	0.35465	TAT	T|0.997;C|0.003	0.003	strong		0.378	SULT6B1-203	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001032377	
NAF1	92345	hgsc.bcm.edu	37	4	164087753	164087753	+	Missense_Mutation	SNP	G	G	A	rs12331663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:164087753G>A	ENST00000274054.2	-	1	320	c.127C>T	c.(127-129)Ccg>Tcg	p.P43S	NAF1_ENST00000422287.2_Missense_Mutation_p.P43S	NM_138386.2	NP_612395.2	Q96HR8	NAF1_HUMAN	nuclear assembly factor 1 ribonucleoprotein	43			P -> S (in dbSNP:rs12331663).		pseudouridine synthesis (GO:0001522)|ribosome biogenesis (GO:0042254)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(3)|large_intestine(1)|lung(10)|ovary(2)	21	all_hematologic(180;0.166)	Prostate(90;0.109)				GACTGTAGCGGCGGCTGTGTC	0.657													G|||	148	0.0295527	0.1104	0.0029	5008	,	,		11685	0.0		0.0	False		,,,				2504	0.0				p.P43S		Atlas-SNP	.											.	NAF1	69	.	0			c.C127T						PASS	.	G	SER/PRO,SER/PRO	409,3655		27,355,1650	8.0	12.0	11.0		127,127	0.6	0.0	4	dbSNP_120	11	7,8217		0,7,4105	yes	missense,missense	NAF1	NM_001128931.1,NM_138386.2	74,74	27,362,5755	AA,AG,GG		0.0851,10.064,3.3854	benign,benign	43/390,43/495	164087753	416,11872	2032	4112	6144	SO:0001583	missense	92345	exon1			GTAGCGGCGGCTG		CCDS3803.1, CCDS47159.1	4q32.2	2013-03-05	2013-03-05			ENSG00000145414			25126	protein-coding gene	gene with protein product			"""nuclear assembly factor 1 homolog (S. cerevisiae)"""			16618814, 16601202	Standard	NM_138386		Approved		uc003iqj.3	Q96HR8		ENST00000274054.2:c.127C>T	4.37:g.164087753G>A	ENSP00000274054:p.Pro43Ser	94.0	0.0	0		90.0	49.0	0.544444	NM_138386	D3DP28|E9PAZ2	Missense_Mutation	SNP	ENST00000274054.2	37	CCDS3803.1	58	0.026556776556776556	56	0.11382113821138211	2	0.0055248618784530384	0	0.0	0	0.0	G	9.310	1.055342	0.19907	0.10064	8.51E-4	ENSG00000145414	ENST00000422287;ENST00000274054	T;T	0.31510	1.49;1.51	2.42	0.648	0.17801	.	0.570177	0.14188	N	0.335578	T	0.00210	0.0006	N	0.08118	0	0.09310	N	1	B;B	0.31655	0.0;0.334	B;B	0.18561	0.0;0.022	T	0.21484	-1.0244	10	0.07644	T	0.81	-0.4303	4.7772	0.13185	0.3241:0.0:0.6759:0.0	rs12331663;rs52833318;rs12331663	43;43	E9PAZ2;Q96HR8	.;NAF1_HUMAN	S	43	ENSP00000408963:P43S;ENSP00000274054:P43S	ENSP00000274054:P43S	P	-	1	0	NAF1	164307203	0.000000	0.05858	0.010000	0.14722	0.377000	0.30045	-0.380000	0.07427	0.135000	0.18707	-0.680000	0.03767	CCG	G|0.963;A|0.037	0.037	strong		0.657	NAF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364684.2	NM_138386	
PNMAL1	55228	hgsc.bcm.edu	37	19	46973315	46973315	+	Silent	SNP	G	G	A	rs61628326	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:46973315G>A	ENST00000313683.10	-	2	1283	c.978C>T	c.(976-978)gcC>gcT	p.A326A	PNMAL1_ENST00000602246.1_Intron|PNMAL1_ENST00000438932.2_Silent_p.A326A	NM_001103149.1|NM_018215.3	NP_001096619.1|NP_060685.2	Q86V59	PNML1_HUMAN	paraneoplastic Ma antigen family-like 1	326										cervix(1)|endometrium(2)|large_intestine(8)|lung(8)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000166)|all cancers(93;0.0014)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)		CTGGGCTCTCGGCTTCTGCCC	0.602													G|||	75	0.014976	0.0545	0.0043	5008	,	,		17043	0.0		0.0	False		,,,				2504	0.0				p.A326A		Atlas-SNP	.											.	PNMAL1	87	.	0			c.C978T						PASS	.	G	,	195,4211	118.0+/-155.7	8,179,2016	110.0	122.0	118.0		978,978	-7.3	0.0	19	dbSNP_129	118	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous	PNMAL1	NM_001103149.1,NM_018215.3	,	8,183,6312	AA,AG,GG		0.0465,4.4258,1.5301	,	326/379,326/440	46973315	199,12807	2203	4300	6503	SO:0001819	synonymous_variant	55228	exon2			GCTCTCGGCTTCT	BC026026	CCDS33059.1, CCDS46124.1	19q13.32	2014-02-12	2012-02-09			ENSG00000182013		"""Paraneoplastic Ma antigens"""	25578	protein-coding gene	gene with protein product			"""PNMA-like 1"""			12477932	Standard	NM_018215		Approved	KIAA1183L, FLJ10781	uc002peq.4	Q86V59		ENST00000313683.10:c.978C>T	19.37:g.46973315G>A		94.0	0.0	0		97.0	54.0	0.556701	NM_018215	A8K2F3|Q5U638|Q8N3H4|Q9NVE8	Silent	SNP	ENST00000313683.10	37	CCDS33059.1																																																																																			G|0.982;A|0.018	0.018	strong		0.602	PNMAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403929.1	NM_018215	
LPA	4018	hgsc.bcm.edu	37	6	161026103	161026103	+	Missense_Mutation	SNP	G	G	A	rs189364869	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:161026103G>A	ENST00000316300.5	-	18	2964	c.2920C>T	c.(2920-2922)Cgg>Tgg	p.R974W	LPA_ENST00000447678.1_Missense_Mutation_p.R974W			P08519	APOA_HUMAN	lipoprotein, Lp(a)	3482	Kringle 9. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	GCTGGGGTCCGACTATGCGAG	0.443													G|||	4	0.000798722	0.003	0.0	5008	,	,		21608	0.0		0.0	False		,,,				2504	0.0				p.R974W		Atlas-SNP	.											.	LPA	237	.	0			c.C2920T						PASS	.	G	TRP/ARG	12,4376	17.9+/-39.9	0,12,2182	367.0	381.0	376.0		2920	0.9	0.0	6		376	0,8596		0,0,4298	no	missense	LPA	NM_005577.2	101	0,12,6480	AA,AG,GG		0.0,0.2735,0.0924	probably-damaging	974/2041	161026103	12,12972	2194	4298	6492	SO:0001583	missense	4018	exon19			GGGTCCGACTATG	X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.2920C>T	6.37:g.161026103G>A	ENSP00000321334:p.Arg974Trp	49.0	0.0	0		73.0	30.0	0.410959	NM_005577	Q5VTD7|Q9UD88	Missense_Mutation	SNP	ENST00000316300.5	37	CCDS43523.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	g	7.632	0.679154	0.14907	0.002735	0.0	ENSG00000198670	ENST00000316300;ENST00000447678	T;T	0.62941	-0.01;-0.01	2.16	0.902	0.19290	Kringle (4);Kringle-like fold (1);	.	.	.	.	T	0.61022	0.2314	M	0.78456	2.415	0.09310	N	1	D	0.89917	1.0	D	0.77557	0.99	T	0.47911	-0.9080	9	0.36615	T	0.2	.	5.0035	0.14277	0.0:0.0:0.3278:0.6722	.	3482	P08519	APOA_HUMAN	W	974	ENSP00000321334:R974W;ENSP00000395608:R974W	ENSP00000321334:R974W	R	-	1	2	LPA	160946093	0.049000	0.20398	0.002000	0.10522	0.135000	0.20990	0.804000	0.27098	0.095000	0.17434	0.184000	0.17185	CGG	G|0.999;A|0.001	0.001	strong		0.443	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577	
PHF10	55274	hgsc.bcm.edu	37	6	170105725	170105725	+	Silent	SNP	T	T	C	rs4286788	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:170105725T>C	ENST00000339209.4	-	10	1332	c.1209A>G	c.(1207-1209)caA>caG	p.Q403Q	C6orf120_ENST00000332290.2_3'UTR|PHF10_ENST00000366780.4_Silent_p.Q401Q	NM_018288.3|NM_133325.2	NP_060758.2|NP_579866.2	Q8WUB8	PHF10_HUMAN	PHD finger protein 10	403					nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	npBAF complex (GO:0071564)	zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|liver(3)|lung(4)|prostate(2)|urinary_tract(1)	14		Breast(66;5.08e-05)|Ovarian(120;0.208)		OV - Ovarian serous cystadenocarcinoma(33;1.4e-21)|BRCA - Breast invasive adenocarcinoma(81;1.4e-07)|GBM - Glioblastoma multiforme(31;0.00176)		TATTCTCACATTGGGAGCAGT	0.353													T|||	21	0.00419329	0.0151	0.0014	5008	,	,		19342	0.0		0.0	False		,,,				2504	0.0				p.Q403Q		Atlas-SNP	.											.	PHF10	76	.	0			c.A1209G						PASS	.	T	,,	63,4343	59.3+/-96.0	0,63,2140	114.0	110.0	111.0		,1209,1203	-0.5	1.0	6	dbSNP_111	111	0,8600		0,0,4300	no	utr-3,coding-synonymous,coding-synonymous	PHF10,C6orf120	NM_001029863.1,NM_018288.3,NM_133325.2	,,	0,63,6440	CC,CT,TT		0.0,1.4299,0.4844	,,	,403/499,401/497	170105725	63,12943	2203	4300	6503	SO:0001819	synonymous_variant	55274	exon10			CTCACATTGGGAG	AF338735	CCDS5308.2, CCDS5309.2	6q27	2014-05-13			ENSG00000130024	ENSG00000130024		"""Zinc fingers, PHD-type"""	18250	protein-coding gene	gene with protein product		613069				11827455	Standard	NM_018288		Approved	FLJ10975, XAP135, BAF45a	uc011egy.2	Q8WUB8	OTTHUMG00000016058	ENST00000339209.4:c.1209A>G	6.37:g.170105725T>C		166.0	0.0	0		140.0	63.0	0.45	NM_018288	Q2YDA3|Q53HG8|Q9BXD2|Q9NV26	Silent	SNP	ENST00000339209.4	37	CCDS5308.2																																																																																			T|0.995;C|0.005	0.005	strong		0.353	PHF10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346732.1	NM_018288	
MED12L	116931	hgsc.bcm.edu	37	3	150874033	150874033	+	Silent	SNP	T	T	C	rs61734152	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:150874033T>C	ENST00000474524.1	+	5	680	c.642T>C	c.(640-642)gaT>gaC	p.D214D	MED12L_ENST00000273432.4_Silent_p.D214D|MED12L_ENST00000422248.2_Silent_p.D214D|MED12L_ENST00000309237.4_Silent_p.D214D	NM_053002.4	NP_443728.3	Q86YW9	MD12L_HUMAN	mediator complex subunit 12-like	214						mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(27)|lung(50)|ovary(6)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	128			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			GCACGGGCGATGGCCCTGTCC	0.473													T|||	81	0.0161741	0.059	0.0029	5008	,	,		19291	0.0		0.001	False		,,,				2504	0.0				p.D214D		Atlas-SNP	.											MED12L,NS,carcinoma,+2,1	MED12L	271	1	0			c.T642C						PASS	.	T		264,4142	150.3+/-184.3	8,248,1947	113.0	106.0	109.0		642	-8.9	0.0	3	dbSNP_129	109	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	MED12L	NM_053002.4		8,252,6243	CC,CT,TT		0.0465,5.9918,2.0606		214/2146	150874033	268,12738	2203	4300	6503	SO:0001819	synonymous_variant	116931	exon5			GGGCGATGGCCCT	AB046855, AF388364	CCDS33876.1	3q25.1	2007-07-30	2007-07-30		ENSG00000144893	ENSG00000144893			16050	protein-coding gene	gene with protein product		611318	"""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)-like"""			11524702	Standard	XM_006713487		Approved	KIAA1635, TNRC11L, TRALPUSH, TRALP	uc003eyp.3	Q86YW9	OTTHUMG00000159844	ENST00000474524.1:c.642T>C	3.37:g.150874033T>C		66.0	0.0	0		75.0	27.0	0.36	NM_053002	Q96PC7|Q96PC8|Q9H9M5|Q9HCD7|Q9UI69	Silent	SNP	ENST00000474524.1	37	CCDS33876.1																																																																																			T|0.983;C|0.017	0.017	strong		0.473	MED12L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357707.2	NM_053002	
KCNT2	343450	hgsc.bcm.edu	37	1	196303117	196303117	+	Silent	SNP	C	C	T	rs116401401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:196303117C>T	ENST00000294725.9	-	17	2772	c.1857G>A	c.(1855-1857)gaG>gaA	p.E619E	KCNT2_ENST00000498426.1_5'UTR|KCNT2_ENST00000367431.4_Silent_p.E569E|KCNT2_ENST00000609185.1_Silent_p.E569E|KCNT2_ENST00000451324.2_Silent_p.E230E|KCNT2_ENST00000367433.5_Silent_p.E619E			Q6UVM3	KCNT2_HUMAN	potassium channel, subfamily T, member 2	619					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(16)|lung(43)|ovary(5)|pancreas(1)|prostate(1)|skin(11)|stomach(2)|upper_aerodigestive_tract(1)	97						CTTTGCTTCCCTCTGTAGGAA	0.393													C|||	25	0.00499201	0.0166	0.0043	5008	,	,		16218	0.0		0.0	False		,,,				2504	0.0				p.E619E		Atlas-SNP	.											.	KCNT2	243	.	0			c.G1857A						PASS	.	C		52,4354	52.3+/-87.9	0,52,2151	126.0	115.0	118.0		1857	0.6	1.0	1	dbSNP_132	118	0,8600		0,0,4300	no	coding-synonymous	KCNT2	NM_198503.2		0,52,6451	TT,TC,CC		0.0,1.1802,0.3998		619/1136	196303117	52,12954	2203	4300	6503	SO:0001819	synonymous_variant	343450	exon17			GCTTCCCTCTGTA	BX647852, AY359444, AK127807	CCDS1384.1, CCDS72994.1, CCDS72995.1	1q31.3	2012-07-05			ENSG00000162687	ENSG00000162687		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18866	protein-coding gene	gene with protein product	"""sodium and chloride activated ATP sensitive potassium channel"""	610044				16382103	Standard	NM_198503		Approved	KCa4.2, SLICK, SLO2.1	uc001gtd.1	Q6UVM3	OTTHUMG00000035611	ENST00000294725.9:c.1857G>A	1.37:g.196303117C>T		122.0	0.0	0		147.0	72.0	0.489796	NM_198503	Q3SY59|Q5VTN1|Q6ZMT3	Silent	SNP	ENST00000294725.9	37	CCDS1384.1																																																																																			C|0.995;T|0.005	0.005	strong		0.393	KCNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086418.2	NM_198503	
CABYR	26256	hgsc.bcm.edu	37	18	21736486	21736486	+	Nonsense_Mutation	SNP	C	C	T	rs35554127	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:21736486C>T	ENST00000399481.2	+	2	879	c.727C>T	c.(727-729)Cga>Tga	p.R243*	CABYR_ENST00000399499.1_Intron|CABYR_ENST00000581397.1_Intron|RP11-799B12.4_ENST00000583267.1_lincRNA|CABYR_ENST00000327201.6_Intron|CABYR_ENST00000415309.2_Intron|CABYR_ENST00000399496.3_Intron			O75952	CABYR_HUMAN	calcium binding tyrosine-(Y)-phosphorylation regulated	341					epithelial cilium movement (GO:0003351)|sperm capacitation (GO:0048240)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|motile cilium (GO:0031514)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|protein heterodimerization activity (GO:0046982)|SH3 domain binding (GO:0017124)			breast(1)|endometrium(2)|large_intestine(4)|lung(4)	11	all_cancers(21;9.13e-05)|all_epithelial(16;5.49e-07)|Lung NSC(20;0.00171)|all_lung(20;0.0055)|Colorectal(14;0.0305)|Ovarian(20;0.17)					GCAGTCACCACGAGTTAGTCC	0.378													C|||	71	0.0141773	0.0537	0.0	5008	,	,		21641	0.0		0.0	False		,,,				2504	0.0				p.R341X		Atlas-SNP	.											.	CABYR	51	.	0			c.C1021T						PASS	.	C	stop/ARG,,,stop/ARG,,	194,4212	118.8+/-156.5	3,188,2012	60.0	63.0	62.0		1021,,,967,,	3.4	1.0	18	dbSNP_126	62	0,8600		0,0,4300	yes	stop-gained,intron,intron,stop-gained,intron,intron	CABYR	NM_012189.2,NM_138643.1,NM_138644.1,NM_153768.1,NM_153769.1,NM_153770.1	,,,,,	3,188,6312	TT,TC,CC		0.0,4.4031,1.4916	,,,,,	341/494,,,323/476,,	21736486	194,12812	2203	4300	6503	SO:0001587	stop_gained	26256	exon4			TCACCACGAGTTA	AF088868	CCDS11881.1, CCDS11882.1, CCDS11883.1, CCDS42420.1, CCDS45840.1	18q11.2	2009-08-06	2007-11-22		ENSG00000154040	ENSG00000154040			15569	protein-coding gene	gene with protein product	"""fibrousheathin 2"", ""cancer/testis antigen 88"""	612135				11820818, 17317841, 16139264	Standard	NM_012189		Approved	FSP-2, CBP86, CT88	uc002kux.3	O75952	OTTHUMG00000037365	ENST00000399481.2:c.727C>T	18.37:g.21736486C>T	ENSP00000382404:p.Arg243*	62.0	0.0	0		70.0	35.0	0.5	NM_012189	B2R857|Q8WXW5|Q9HAY3|Q9HAY4|Q9HAY5|Q9HCY9	Nonsense_Mutation	SNP	ENST00000399481.2	37		26	0.011904761904761904	26	0.052845528455284556	0	0.0	0	0.0	0	0.0	C	23.4	4.416434	0.83449	0.044031	0.0	ENSG00000154040	ENST00000399481	.	.	.	5.31	3.39	0.38822	.	0.460245	0.20298	N	0.095093	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-4.8475	6.5485	0.22420	0.0:0.784:0.0:0.216	rs35554127	.	.	.	X	243	.	.	R	+	1	2	CABYR	19990484	0.415000	0.25416	0.972000	0.41901	0.862000	0.49288	0.095000	0.15127	1.466000	0.48025	0.655000	0.94253	CGA	C|0.986;T|0.014	0.014	strong		0.378	CABYR-201	KNOWN	basic	protein_coding	protein_coding		NM_153770	
MOB3A	126308	hgsc.bcm.edu	37	19	2078290	2078290	+	Silent	SNP	G	G	A	rs34483500	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2078290G>A	ENST00000357066.3	-	3	649	c.270C>T	c.(268-270)gtC>gtT	p.V90V	MOB3A_ENST00000592143.1_Intron|MOB3A_ENST00000592280.1_Silent_p.V90V	NM_130807.2	NP_570719.1	Q96BX8	MOB3A_HUMAN	MOB kinase activator 3A	90						intracellular (GO:0005622)	metal ion binding (GO:0046872)										CCCCCGACATGACGGGGCAGG	0.612													G|||	24	0.00479233	0.0174	0.0014	5008	,	,		16424	0.0		0.0	False		,,,				2504	0.0				p.V90V		Atlas-SNP	.											MOBKL2A,colon,carcinoma,-2,1	.	.	1	0			c.C270T						PASS	.	G		60,4346	57.4+/-93.9	1,58,2144	68.0	54.0	59.0		270	1.0	1.0	19	dbSNP_126	59	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MOB3A	NM_130807.2		1,59,6443	AA,AG,GG		0.0116,1.3618,0.469		90/218	2078290	61,12945	2203	4300	6503	SO:0001819	synonymous_variant	126308	exon3			CGACATGACGGGG	AK095471	CCDS12081.1	19p13.3	2011-09-28	2011-09-28	2011-09-28	ENSG00000172081	ENSG00000172081		"""MOB kinase activators"""	29802	protein-coding gene	gene with protein product	"""MOB LAK"""		"""MOB1, Mps One Binder kinase activator-like 2A (yeast)"""	MOBKL2A		12477932	Standard	NM_130807		Approved	MOB1C, MOB-LAK, moblak	uc002luv.3	Q96BX8		ENST00000357066.3:c.270C>T	19.37:g.2078290G>A		152.0	0.0	0		165.0	86.0	0.521212	NM_130807	B3KTF1|O75249|Q8TF69	Silent	SNP	ENST00000357066.3	37	CCDS12081.1																																																																																			G|0.994;A|0.006	0.006	strong		0.612	MOB3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450893.1	NM_130807	
MYRIP	25924	hgsc.bcm.edu	37	3	40223771	40223771	+	Missense_Mutation	SNP	G	G	A	rs59923220	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:40223771G>A	ENST00000302541.6	+	9	1276	c.934G>A	c.(934-936)Gct>Act	p.A312T	MYRIP_ENST00000539167.1_Missense_Mutation_p.A125T|MYRIP_ENST00000444716.1_Missense_Mutation_p.A312T|MYRIP_ENST00000459828.1_3'UTR|MYRIP_ENST00000396217.3_Missense_Mutation_p.A223T|MYRIP_ENST00000425621.1_Missense_Mutation_p.A312T	NM_001284423.1|NM_001284426.1|NM_015460.2	NP_001271352.1|NP_001271355.1|NP_056275.2	Q8NFW9	MYRIP_HUMAN	myosin VIIA and Rab interacting protein	312	Myosin-binding.		A -> T (in dbSNP:rs59923220). {ECO:0000269|PubMed:15489334}.		intracellular protein transport (GO:0006886)|positive regulation of insulin secretion (GO:0032024)	actin cytoskeleton (GO:0015629)|dense core granule (GO:0031045)|exocyst (GO:0000145)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|synapse (GO:0045202)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(2)|lung(10)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				KIRC - Kidney renal clear cell carcinoma(284;0.174)|Kidney(284;0.206)		TCCAGTGGAGGCTCCATCGAG	0.567													G|||	391	0.0780751	0.2746	0.0346	5008	,	,		17481	0.0		0.004	False		,,,				2504	0.0				p.A312T		Atlas-SNP	.											.	MYRIP	98	.	0			c.G934A						PASS	.	G	THR/ALA	1037,3369	382.8+/-324.6	108,821,1274	76.0	77.0	77.0		934	0.8	0.1	3	dbSNP_129	77	13,8587	9.8+/-36.6	0,13,4287	yes	missense	MYRIP	NM_015460.2	58	108,834,5561	AA,AG,GG		0.1512,23.5361,8.0732	benign	312/860	40223771	1050,11956	2203	4300	6503	SO:0001583	missense	25924	exon9			GTGGAGGCTCCAT	AF396687	CCDS2689.1, CCDS68390.1, CCDS68391.1, CCDS68392.1	3p21.33	2010-08-20			ENSG00000170011	ENSG00000170011		"""A-kinase anchor proteins"""	19156	protein-coding gene	gene with protein product	"""synaptotagmin-like protein homologue lacking C2 domains-c"", ""rab effector MYRIP"", ""Slp homologue lacking C2 domains"""	611790				11964381, 12221080	Standard	NM_001284425		Approved	DKFZp586F1018, exophilin-8, MyRIP, SLAC2-C, SLAC2C	uc003cka.3	Q8NFW9	OTTHUMG00000131392	ENST00000302541.6:c.934G>A	3.37:g.40223771G>A	ENSP00000301972:p.Ala312Thr	124.0	0.0	0		140.0	62.0	0.442857	NM_015460	B3KWM3|B3KWW4|B7Z2H1|B7Z9V3|G3XAI8|Q32M41|Q32M42|Q569F7|Q8IUF5|Q9Y3V4	Missense_Mutation	SNP	ENST00000302541.6	37	CCDS2689.1	161	0.07371794871794872	150	0.3048780487804878	10	0.027624309392265192	0	0.0	1	0.0013192612137203166	G	9.859	1.195685	0.22037	0.235361	0.001512	ENSG00000170011	ENST00000444716;ENST00000302541;ENST00000425621;ENST00000396217;ENST00000539167	T;T;T;T;T	0.25250	1.81;1.81;1.81;1.81;1.81	5.27	0.792	0.18625	Myelin-associated oligodendrocytic basic protein (MOBP) (1);	0.590955	0.16727	N	0.202020	T	0.00012	0.0000	L	0.40543	1.245	0.54753	P	1.799999999996249E-5	B;B;B	0.22080	0.064;0.001;0.003	B;B;B	0.22152	0.038;0.006;0.009	T	0.43032	-0.9416	8	.	.	.	.	6.3243	0.21234	0.2573:0.0:0.6071:0.1356	rs59923220	223;312;312	Q32M42;G3XAI8;Q8NFW9	.;.;MYRIP_HUMAN	T	312;312;312;223;125	ENSP00000398665:A312T;ENSP00000301972:A312T;ENSP00000389323:A312T;ENSP00000379519:A223T;ENSP00000438297:A125T	.	A	+	1	0	MYRIP	40198775	0.997000	0.39634	0.096000	0.21009	0.003000	0.03518	0.665000	0.25083	0.211000	0.20683	-0.136000	0.14681	GCT	G|0.927;A|0.073	0.073	strong		0.567	MYRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254181.2	NM_015460	
FMO2	2327	hgsc.bcm.edu	37	1	171176879	171176879	+	Silent	SNP	G	G	A	rs6671692	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:171176879G>A	ENST00000209929.7	+	8	1364	c.1206G>A	c.(1204-1206)gaG>gaA	p.E402E	RP1-127D3.4_ENST00000422841.1_RNA|RP1-127D3.4_ENST00000445290.1_RNA|RP1-127D3.4_ENST00000445909.1_RNA|FMO2_ENST00000529935.1_3'UTR|FMO2_ENST00000441535.1_Silent_p.E402E			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	401					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	22	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TGCCCTCAGAGAGAACTATGA	0.313													G|||	232	0.0463259	0.1573	0.0115	5008	,	,		19971	0.0		0.001	False		,,,				2504	0.0153				p.E402E		Atlas-SNP	.											.	FMO2	66	.	0			c.G1206A						PASS	.	G		502,3904	229.4+/-244.0	26,450,1727	100.0	106.0	104.0		1206	5.8	0.5	1	dbSNP_116	104	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	FMO2	NM_001460.2		26,456,6021	AA,AG,GG		0.0698,11.3936,3.9059		402/472	171176879	508,12498	2203	4300	6503	SO:0001819	synonymous_variant	2327	exon8			CTCAGAGAGAACT	BC005894	CCDS1293.1	1q24.3	2011-08-04	2006-07-17		ENSG00000094963	ENSG00000094963			3770	protein-coding gene	gene with protein product		603955	"""flavin containing monooxygenase 2"""			1417778, 9804831	Standard	XR_426768		Approved		uc001ghk.1	Q99518	OTTHUMG00000035504	ENST00000209929.7:c.1206G>A	1.37:g.171176879G>A		206.0	0.0	0		196.0	86.0	0.438776	NM_001460	Q53XR0	Silent	SNP	ENST00000209929.7	37	CCDS1293.1																																																																																			G|0.953;A|0.047	0.047	strong		0.313	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460	
SDK1	221935	hgsc.bcm.edu	37	7	3991479	3991479	+	Silent	SNP	A	A	G	rs6961589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:3991479A>G	ENST00000404826.2	+	7	1216	c.1077A>G	c.(1075-1077)ccA>ccG	p.P359P	SDK1_ENST00000389531.3_Silent_p.P359P	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	359	Ig-like C2-type 3.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		ACACCGGGCCATACGTCTGCG	0.602													G|||	341	0.0680911	0.2398	0.0303	5008	,	,		16870	0.0		0.002	False		,,,				2504	0.001				p.P359P		Atlas-SNP	.											.	SDK1	361	.	0			c.A1077G						PASS	.	G		958,3448	731.8+/-410.3	104,750,1349	52.0	52.0	52.0		1077	0.9	0.0	7	dbSNP_116	52	9,8591	817.5+/-406.9	0,9,4291	no	coding-synonymous	SDK1	NM_152744.3		104,759,5640	GG,GA,AA		0.1047,21.7431,7.435		359/2214	3991479	967,12039	2203	4300	6503	SO:0001819	synonymous_variant	221935	exon7			CGGGCCATACGTC	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19307	protein-coding gene	gene with protein product		607216	"""sidekick homolog 1 (chicken)"", ""sidekick homolog 1, cell adhesion molecule (chicken)"""			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.1077A>G	7.37:g.3991479A>G		25.0	0.0	0		38.0	15.0	0.394737	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Silent	SNP	ENST00000404826.2	37	CCDS34590.1	110	0.05036630036630037	102	0.2073170731707317	6	0.016574585635359115	0	0.0	2	0.002638522427440633	G	0.457	-0.890886	0.02491	0.217431	0.001047	ENSG00000146555	ENST00000426596	.	.	.	4.87	0.937	0.19494	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.22253	P	0.999251882	.	.	.	.	.	.	T	0.24190	-1.0167	3	.	.	.	.	3.246	0.06797	0.1411:0.2537:0.474:0.1313	rs6961589;rs17134087;rs6961589	.	.	.	R	78	.	.	H	+	2	0	SDK1	3958005	0.838000	0.29461	0.001000	0.08648	0.000000	0.00434	1.014000	0.29950	-0.265000	0.09352	-2.011000	0.00436	CAT	A|0.926;G|0.074	0.074	strong		0.602	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
POMZP3	22932	hgsc.bcm.edu	37	7	76240877	76240877	+	Missense_Mutation	SNP	A	A	T	rs73365247	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:76240877A>T	ENST00000310842.4	-	6	1153	c.469T>A	c.(469-471)Tgt>Agt	p.C157S	UPK3B_ENST00000443097.2_Intron|POMZP3_ENST00000275569.4_Intron|UPK3B_ENST00000419923.2_Intron|AC004980.7_ENST00000418663.1_RNA	NM_012230.3	NP_036362.3	Q6PJE2	POZP3_HUMAN	POM121 and ZP3 fusion	157										kidney(3)|lung(2)	5		Myeloproliferative disorder(862;0.204)				CAGCATTGACAGATGTCAGCC	0.517													a|||	295	0.0589058	0.2148	0.0144	5008	,	,		18707	0.001		0.0	False		,,,				2504	0.0				p.C157S		Atlas-SNP	.											.	POMZP3	19	.	0			c.T469A						PASS	.	A	SER/CYS,	887,3517		137,613,1452	74.0	76.0	75.0		469,	0.8	0.8	7	dbSNP_130	75	16,8566		1,14,4276	no	missense,intron	POMZP3	NM_012230.3,NM_152992.2	112,	138,627,5728	TT,TA,AA		0.1864,20.1408,6.9536	probably-damaging,	157/188,	76240877	903,12083	2202	4291	6493	SO:0001583	missense	22932	exon6			ATTGACAGATGTC	U10099	CCDS5590.1, CCDS43606.1	7q11.2	2010-06-24	2010-06-24		ENSG00000146707	ENSG00000146707			9203	protein-coding gene	gene with protein product	"""POM-ZP3 fusion protein"", ""POM121/ZP3 fusion protein"""	600587	"""POM (POM121 rat homolog) and ZP3 fusion"", ""POM (POM121 homolog, rat) and ZP3 fusion"""			7789967	Standard	NM_012230		Approved	POM-ZP3, POM121	uc003uft.3	Q6PJE2	OTTHUMG00000023514	ENST00000310842.4:c.469T>A	7.37:g.76240877A>T	ENSP00000309233:p.Cys157Ser	226.0	0.0	0		284.0	110.0	0.387324	NM_012230	F6STJ3|Q12903|Q9BWB4	Missense_Mutation	SNP	ENST00000310842.4	37	CCDS43606.1	143|143	0.06547619047619048|0.06547619047619048	138|138	0.2804878048780488|0.2804878048780488	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	0|0	0.0|0.0	N|N	17.67|17.67	3.447194|3.447194	0.63178|0.63178	0.201408|0.201408	0.001864|0.001864	ENSG00000146707|ENSG00000146707	ENST00000310842|ENST00000441393	T|.	0.65732|.	-0.17|.	0.786|0.786	0.786|0.786	0.18590|0.18590	.|.	0.000000|.	0.85682|.	U|.	0.000000|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.88310|0.88310	2.945|2.945	0.09310|0.09310	P|P	0.9999947731|0.9999947731	D|.	0.89917|.	1.0|.	D|.	0.91635|.	0.999|.	T|T	0.04650|0.04650	-1.0936|-1.0936	9|4	0.87932|.	D|.	0|.	.|.	3.9669|3.9669	0.09436|0.09436	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	157|.	Q6PJE2|.	POZP3_HUMAN|.	S|Q	157|93	ENSP00000309233:C157S|.	ENSP00000309233:C157S|.	C|L	-|-	1|2	0|0	POMZP3|POMZP3	76078813|76078813	1.000000|1.000000	0.71417|0.71417	0.795000|0.795000	0.32087|0.32087	0.753000|0.753000	0.42808|0.42808	2.176000|2.176000	0.42500|0.42500	0.612000|0.612000	0.30071|0.30071	0.305000|0.305000	0.20034|0.20034	TGT|CTG	A|0.957;T|0.043	0.043	strong		0.517	POMZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341775.1	NM_012230	
SBSN	374897	hgsc.bcm.edu	37	19	36018435	36018435	+	Missense_Mutation	SNP	G	G	A	rs147913080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36018435G>A	ENST00000452271.2	-	1	777	c.749C>T	c.(748-750)gCg>gTg	p.A250V	SBSN_ENST00000518157.1_Intron	NM_001166034.1	NP_001159506.1	Q6UWP8	SBSN_HUMAN	suprabasin	250	Ala/Gly/His-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				large_intestine(5)|lung(6)|ovary(1)|prostate(2)	14	all_lung(56;1.62e-08)|Lung NSC(56;2.47e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			GGCCTGCCCCGCAGCATGGTG	0.627													G|||	143	0.0285543	0.1044	0.0072	5008	,	,		20537	0.0		0.0	False		,,,				2504	0.0				p.A250V		Atlas-SNP	.											.	SBSN	58	.	0			c.C749T						PASS	.	G	VAL/ALA,,	148,1236		8,132,552	29.0	36.0	34.0		749,,	-5.1	0.0	19	dbSNP_134	34	0,3182		0,0,1591	no	missense,intron,intron	SBSN	NM_001166034.1,NM_001166035.1,NM_198538.3	64,,	8,132,2143	AA,AG,GG		0.0,10.6936,3.2413	benign,,	250/591,,	36018435	148,4418	692	1591	2283	SO:0001583	missense	374897	exon1			TGCCCCGCAGCAT	AY358701	CCDS12464.1, CCDS54253.1	19q13.13	2008-02-05							24950	protein-coding gene	gene with protein product		609969				12228223	Standard	NM_198538		Approved	UNQ698, HLAR698	uc002oad.2	Q6UWP8		ENST00000452271.2:c.749C>T	19.37:g.36018435G>A	ENSP00000430242:p.Ala250Val	6.0	0.0	0		5.0	5.0	1	NM_001166034	A8K5J0|E9PBV3	Missense_Mutation	SNP	ENST00000452271.2	37	CCDS54253.1	50	0.022893772893772892	40	0.08130081300813008	3	0.008287292817679558	7	0.012237762237762238	0	0.0	G	10.51	1.369069	0.24771	0.106936	0.0	ENSG00000189001	ENST00000452271	T	0.48201	0.82	4.63	-5.14	0.02875	.	.	.	.	.	T	0.00580	0.0019	L	0.40543	1.245	0.09310	N	1	B	0.11235	0.004	B	0.10450	0.005	T	0.16424	-1.0403	9	0.17369	T	0.5	.	7.6648	0.28423	0.3905:0.1283:0.4812:0.0	.	250	E9PBV3	.	V	250	ENSP00000430242:A250V	ENSP00000430242:A250V	A	-	2	0	SBSN	40710275	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.794000	0.01753	-0.578000	0.05959	-1.069000	0.02264	GCG	G|0.977;A|0.023	0.023	strong		0.627	SBSN-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109463.3	NM_198538	
COL20A1	57642	hgsc.bcm.edu	37	20	61959758	61959758	+	Missense_Mutation	SNP	C	C	T	rs115749294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61959758C>T	ENST00000358894.6	+	34	3789	c.3689C>T	c.(3688-3690)cCg>cTg	p.P1230L	COL20A1_ENST00000422202.1_Missense_Mutation_p.P1243L|COL20A1_ENST00000435874.1_Missense_Mutation_p.P1243L|COL20A1_ENST00000326996.6_Missense_Mutation_p.P1262L	NM_020882.2	NP_065933.2	Q9P218	COKA1_HUMAN	collagen, type XX, alpha 1	1230				P -> Q (in Ref. 2; AAH43183). {ECO:0000305}.	extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)				NS(3)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(21)|ovary(1)|prostate(3)|urinary_tract(2)	36	all_cancers(38;1.39e-10)					AAGCTGGAGCCGGGCACTGAG	0.662													C|||	37	0.00738818	0.028	0.0	5008	,	,		15679	0.0		0.0	False		,,,				2504	0.0				p.P1230L		Atlas-SNP	.											.	COL20A1	137	.	0			c.C3689T						PASS	.	C	LEU/PRO	92,3808		1,90,1859	26.0	31.0	29.0		3689	1.2	0.0	20	dbSNP_132	29	4,8234		0,4,4115	yes	missense	COL20A1	NM_020882.2	98	1,94,5974	TT,TC,CC		0.0486,2.359,0.7909	benign	1230/1285	61959758	96,12042	1950	4119	6069	SO:0001583	missense	57642	exon34			TGGAGCCGGGCAC	BC043183	CCDS46628.1	20q13.33	2014-02-12			ENSG00000101203	ENSG00000101203		"""Collagens"", ""Fibronectin type III domain containing"""	14670	protein-coding gene	gene with protein product						10819331	Standard	NM_020882		Approved	KIAA1510	uc011aau.2	Q9P218	OTTHUMG00000032964	ENST00000358894.6:c.3689C>T	20.37:g.61959758C>T	ENSP00000351767:p.Pro1230Leu	88.0	0.0	0		131.0	75.0	0.572519	NM_020882	Q4VXQ4|Q6PI59|Q8WUT2|Q96CY9|Q9BQU6|Q9BQU7	Missense_Mutation	SNP	ENST00000358894.6	37	CCDS46628.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	C	4.851	0.158169	0.09236	0.02359	4.86E-4	ENSG00000101203	ENST00000358894;ENST00000326996;ENST00000435874;ENST00000422202;ENST00000415763;ENST00000455906	D;D;D;D;D;D	0.90900	-2.22;-2.18;-2.14;-2.14;-2.75;-2.59	3.37	1.25	0.21368	.	0.343274	0.25598	N	0.029561	T	0.56848	0.2013	N	0.12746	0.255	0.09310	N	1	B;B	0.12013	0.003;0.005	B;B	0.08055	0.001;0.003	T	0.58983	-0.7539	10	0.35671	T	0.21	.	5.6298	0.17504	0.0:0.6946:0.0:0.3054	.	1243;1230	Q9P218-2;Q9P218	.;COKA1_HUMAN	L	1230;1262;1243;1243;371;226	ENSP00000351767:P1230L;ENSP00000323077:P1262L;ENSP00000408690:P1243L;ENSP00000414753:P1243L;ENSP00000410799:P371L;ENSP00000406345:P226L	ENSP00000323077:P1262L	P	+	2	0	COL20A1	61430202	0.006000	0.16342	0.001000	0.08648	0.097000	0.18754	0.478000	0.22212	0.356000	0.24157	0.313000	0.20887	CCG	C|0.995;T|0.005	0.005	strong		0.662	COL20A1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000144595.2	NM_020882	
DSG1	1828	hgsc.bcm.edu	37	18	28923906	28923906	+	Missense_Mutation	SNP	A	A	G	rs116081362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:28923906A>G	ENST00000257192.4	+	13	2051	c.1839A>G	c.(1837-1839)atA>atG	p.I613M	RP11-534N16.1_ENST00000581856.1_RNA|RP11-534N16.1_ENST00000578119.1_RNA|DSG1_ENST00000462981.2_5'UTR|RNU6-167P_ENST00000384292.1_RNA	NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	613					apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell-cell junction assembly (GO:0007043)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|protein stabilization (GO:0050821)|response to progesterone (GO:0032570)|single organismal cell-cell adhesion (GO:0016337)	apical plasma membrane (GO:0016324)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)|toxic substance binding (GO:0015643)			NS(2)|central_nervous_system(2)|endometrium(5)|kidney(7)|large_intestine(11)|lung(36)|ovary(3)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	76			OV - Ovarian serous cystadenocarcinoma(10;0.00559)			CCACTGTCATACCACAAATAC	0.318													A|||	142	0.0283546	0.1021	0.0086	5008	,	,		15765	0.0		0.001	False		,,,				2504	0.0				p.I613M		Atlas-SNP	.											.	DSG1	176	.	0			c.A1839G						PASS	.	A	MET/ILE	385,4021	192.6+/-218.0	16,353,1834	124.0	114.0	118.0		1839	0.9	0.0	18	dbSNP_132	118	3,8593	3.0+/-9.4	0,3,4295	yes	missense	DSG1	NM_001942.2	10	16,356,6129	GG,GA,AA		0.0349,8.7381,2.9842	benign	613/1050	28923906	388,12614	2203	4298	6501	SO:0001583	missense	1828	exon13			TGTCATACCACAA	X56654	CCDS11896.1	18q12.1	2014-05-13			ENSG00000134760	ENSG00000134760		"""Cadherins / Major cadherins"""	3048	protein-coding gene	gene with protein product		125670		DSG		1889810	Standard	NM_001942		Approved	CDHF4	uc002kwp.3	Q02413	OTTHUMG00000131983	ENST00000257192.4:c.1839A>G	18.37:g.28923906A>G	ENSP00000257192:p.Ile613Met	145.0	0.0	0		161.0	73.0	0.453416	NM_001942	B7Z845	Missense_Mutation	SNP	ENST00000257192.4	37	CCDS11896.1	53	0.024267399267399268	49	0.09959349593495935	4	0.011049723756906077	0	0.0	0	0.0	A	7.734	0.699824	0.15106	0.087381	3.49E-4	ENSG00000134760	ENST00000257192	T	0.42513	0.97	4.98	0.91	0.19337	.	0.499779	0.18540	N	0.138233	T	0.00637	0.0021	N	0.14661	0.345	0.09310	N	0.999997	P	0.40266	0.71	P	0.45167	0.472	T	0.02533	-1.1145	10	0.37606	T	0.19	.	3.6502	0.08201	0.3746:0.2209:0.4045:0.0	.	613	Q02413	DSG1_HUMAN	M	613	ENSP00000257192:I613M	ENSP00000257192:I613M	I	+	3	3	DSG1	27177904	0.212000	0.23540	0.009000	0.14445	0.000000	0.00434	0.194000	0.17135	0.046000	0.15833	-0.291000	0.09656	ATA	A|0.967;G|0.033	0.033	strong		0.318	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
UNC13B	10497	hgsc.bcm.edu	37	9	35398900	35398900	+	Missense_Mutation	SNP	G	G	T	rs12339582	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35398900G>T	ENST00000378495.3	+	32	3918	c.3696G>T	c.(3694-3696)gaG>gaT	p.E1232D	UNC13B_ENST00000378496.4_Missense_Mutation_p.E1232D|UNC13B_ENST00000396787.1_Missense_Mutation_p.E1244D|UNC13B_ENST00000481299.1_3'UTR	NM_006377.3	NP_006368.3	O14795	UN13B_HUMAN	unc-13 homolog B (C. elegans)	1232			E -> D (in dbSNP:rs12339582).		apoptotic process (GO:0006915)|excretion (GO:0007588)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synaptic vesicle priming (GO:0010808)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle priming (GO:0016082)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|neuromuscular junction (GO:0031594)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|terminal bouton (GO:0043195)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(16)|liver(2)|lung(17)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	63	all_epithelial(49;0.212)		LUSC - Lung squamous cell carcinoma(32;0.00343)|Lung(28;0.00778)|STAD - Stomach adenocarcinoma(86;0.194)			GGATTGATGAGTGTGTTCGAC	0.582													G|||	153	0.0305511	0.1067	0.0043	5008	,	,		21512	0.0079		0.001	False		,,,				2504	0.0				p.E1232D		Atlas-SNP	.											.	UNC13B	153	.	0			c.G3696T						PASS	.	G	ASP/GLU	379,4027	191.9+/-217.4	16,347,1840	126.0	129.0	128.0		3696	4.1	1.0	9	dbSNP_120	128	4,8596	3.7+/-12.6	0,4,4296	yes	missense	UNC13B	NM_006377.3	45	16,351,6136	TT,TG,GG		0.0465,8.6019,2.9448	benign	1232/1592	35398900	383,12623	2203	4300	6503	SO:0001583	missense	10497	exon32			TGATGAGTGTGTT	AF020202	CCDS6579.1	9p13.3	2008-05-15	2003-10-17	2003-10-17	ENSG00000198722	ENSG00000198722			12566	protein-coding gene	gene with protein product		605836	"""unc-13-like (C. elegans)"""	UNC13		9607201	Standard	NM_006377		Approved	hmunc13, Unc13h2	uc003zwq.3	O14795	OTTHUMG00000019856	ENST00000378495.3:c.3696G>T	9.37:g.35398900G>T	ENSP00000367756:p.Glu1232Asp	186.0	0.0	0		200.0	88.0	0.44	NM_006377	Q5VYM8	Missense_Mutation	SNP	ENST00000378495.3	37	CCDS6579.1	69	0.03159340659340659	62	0.12601626016260162	2	0.0055248618784530384	4	0.006993006993006993	1	0.0013192612137203166	G	13.61	2.288018	0.40494	0.086019	4.65E-4	ENSG00000198722	ENST00000396787;ENST00000378495;ENST00000378496;ENST00000535471	T;T;T	0.10099	2.91;2.91;2.91	5.94	4.07	0.47477	.	0.102509	0.64402	D	0.000003	T	0.00073	0.0002	N	0.25332	0.735	0.50171	D	0.999858	B;B	0.15473	0.013;0.011	B;B	0.14023	0.009;0.01	T	0.52223	-0.8604	10	0.24483	T	0.36	-27.2563	7.8494	0.29446	0.1495:0.1355:0.715:0.0	rs12339582;rs17849224;rs12339582	1232;1232	F8W8M9;O14795	.;UN13B_HUMAN	D	1244;1232;1232;819	ENSP00000380006:E1244D;ENSP00000367756:E1232D;ENSP00000367757:E1232D	ENSP00000367756:E1232D	E	+	3	2	UNC13B	35388900	0.992000	0.36948	1.000000	0.80357	0.998000	0.95712	0.238000	0.18004	1.493000	0.48517	0.557000	0.71058	GAG	G|0.960;T|0.040	0.040	strong		0.582	UNC13B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052296.1	NM_006377	
LRP1B	53353	hgsc.bcm.edu	37	2	141274456	141274456	+	Splice_Site	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:141274456A>G	ENST00000389484.3	-	50	9121		c.e50+1			NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B						protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		ACAATGTCTCACCACAGTGGA	0.328										TSP Lung(27;0.18)																											.	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											.	LRP1B	1315	.	0			c.8149+2T>C						PASS	.						146.0	134.0	138.0					2																	141274456		2203	4300	6503	SO:0001630	splice_region_variant	53353	exon51			TGTCTCACCACAG	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.8149+1T>C	2.37:g.141274456A>G		80.0	0.0	0		66.0	12.0	0.181818	NM_018557	Q8WY29|Q8WY30|Q8WY31	Splice_Site	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	A	18.09	3.546269	0.65198	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	.	.	.	4.92	4.92	0.64577	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5612	0.68136	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	LRP1B	140990926	1.000000	0.71417	0.994000	0.49952	0.576000	0.36127	9.278000	0.95766	1.815000	0.52974	0.460000	0.39030	.	.	.	none		0.328	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	Intron
MUC2	4583	hgsc.bcm.edu	37	11	1093362	1093362	+	Silent	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1093362C>G	ENST00000441003.2	+	30	5208	c.5181C>G	c.(5179-5181)acC>acG	p.T1727T	MUC2_ENST00000333592.6_Silent_p.T15T|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Silent_p.T1694T	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)	tctccaccaccactacggtga	0.647																																					p.T1727T		Atlas-SNP	.											.	MUC2	614	.	0			c.C5181G						PASS	.						187.0	230.0	215.0					11																	1093362		1968	3798	5766	SO:0001819	synonymous_variant	4583	exon30			CACCACCACTACG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5181C>G	11.37:g.1093362C>G		117.0	0.0	0		132.0	8.0	0.0606061	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.	.	none		0.647	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
C14orf80	283643	hgsc.bcm.edu	37	14	105958010	105958010	+	Missense_Mutation	SNP	G	G	T	rs587675709	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105958010G>T	ENST00000392523.4	+	2	320	c.199G>T	c.(199-201)Ggc>Tgc	p.G67C	C14orf80_ENST00000329886.7_Missense_Mutation_p.G28C|C14orf80_ENST00000551054.1_3'UTR|C14orf80_ENST00000392527.1_Missense_Mutation_p.G26C|C14orf80_ENST00000334656.7_Missense_Mutation_p.G26C|C14orf80_ENST00000392522.3_Missense_Mutation_p.G67C|C14orf80_ENST00000354560.6_Missense_Mutation_p.G67C|C14orf80_ENST00000450383.1_5'UTR			Q86SX3	CN080_HUMAN	chromosome 14 open reading frame 80	67										central_nervous_system(1)	1		Melanoma(154;0.226)	OV - Ovarian serous cystadenocarcinoma(23;0.00596)|Epithelial(46;0.0188)	Epithelial(152;0.239)		ACTCCCTGCGGGCAACGCCTT	0.692													G|||	4	0.000798722	0.003	0.0	5008	,	,		10467	0.0		0.0	False		,,,				2504	0.0				p.G67C		Atlas-SNP	.											.	C14orf80	19	.	0			c.G199T						PASS	.						12.0	13.0	13.0					14																	105958010		692	1587	2279	SO:0001583	missense	283643	exon2			CCTGCGGGCAACG		CCDS45180.1, CCDS45181.1, CCDS45182.1, CCDS55955.1	14q32.33	2012-09-25			ENSG00000185347	ENSG00000185347			20127	protein-coding gene	gene with protein product							Standard	NM_001134875		Approved		uc001yrn.3	Q86SX3	OTTHUMG00000170426	ENST00000392523.4:c.199G>T	14.37:g.105958010G>T	ENSP00000376308:p.Gly67Cys	147.0	0.0	0		154.0	77.0	0.5	NM_001134876	B5MDG3|E9PAQ4|Q86TT3|Q86TT4|Q86TT5|Q96B41|Q9H7H4	Missense_Mutation	SNP	ENST00000392523.4	37		.	.	.	.	.	.	.	.	.	.	G	17.21	3.331819	0.60853	.	.	ENSG00000185347	ENST00000329886;ENST00000427614;ENST00000455454;ENST00000432805;ENST00000392527;ENST00000443229;ENST00000334656;ENST00000392522;ENST00000392523;ENST00000354560;ENST00000548920	.	.	.	5.35	-5.54	0.02544	.	2.792540	0.01787	N	0.032086	T	0.22820	0.0551	L	0.40543	1.245	0.09310	N	1	B;P;B;P;B	0.50272	0.002;0.933;0.007;0.932;0.015	B;B;B;B;B	0.43445	0.002;0.394;0.002;0.42;0.009	T	0.37407	-0.9707	9	0.48119	T	0.1	-2.1135	2.1586	0.03819	0.2184:0.4083:0.1687:0.2046	.	67;67;67;26;28	Q86SX3-2;E9PAQ4;Q86SX3;B5MDG3;Q86SX3-3	.;.;CN080_HUMAN;.;.	C	28;26;26;26;26;26;26;67;67;67;67	.	ENSP00000333010:G28C	G	+	1	0	C14orf80	105029055	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.058000	0.11750	-0.676000	0.05238	0.561000	0.74099	GGC	.	.	none		0.692	C14orf80-017	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000409090.1	NM_001134875	
HIST1H3B	8358	hgsc.bcm.edu	37	6	26031962	26031962	+	Silent	SNP	G	G	A	rs34966100	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:26031962G>A	ENST00000244661.2	-	1	326	c.327C>T	c.(325-327)aaC>aaT	p.N109N		NM_003537.3	NP_003528.1	P68431	H31_HUMAN	histone cluster 1, H3b	109					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)			breast(3)|central_nervous_system(10)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|skin(1)	25						TGGCGCAAAGGTTTGTGTCCT	0.527													G|||	176	0.0351438	0.1203	0.013	5008	,	,		18951	0.0		0.004	False		,,,				2504	0.0041				p.N109N		Atlas-SNP	.											.	HIST1H3B	59	.	0			c.C327T						PASS	.	G		396,4010	198.4+/-222.2	12,372,1819	78.0	79.0	79.0		327	4.2	1.0	6	dbSNP_126	79	55,8545	34.3+/-88.2	0,55,4245	no	coding-synonymous	HIST1H3B	NM_003537.3		12,427,6064	AA,AG,GG		0.6395,8.9877,3.4676		109/137	26031962	451,12555	2203	4300	6503	SO:0001819	synonymous_variant	8358	exon1			GCAAAGGTTTGTG	X00090	CCDS4573.1	6p22.1	2011-01-27	2006-10-11	2003-03-14	ENSG00000124693	ENSG00000274267		"""Histones / Replication-dependent"""	4776	protein-coding gene	gene with protein product		602819	"""H3 histone family, member L"", ""histone 1, H3b"""	H3FL		6647026, 9119399, 12408966	Standard	NM_003537		Approved	H3/l	uc003nfs.1	P68431	OTTHUMG00000014415	ENST00000244661.2:c.327C>T	6.37:g.26031962G>A		113.0	0.0	0		141.0	59.0	0.41844	NM_003537	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000244661.2	37	CCDS4573.1																																																																																			G|0.966;A|0.034	0.034	strong		0.527	HIST1H3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040077.1	NM_003537	
YTHDF1	54915	hgsc.bcm.edu	37	20	61834169	61834169	+	Missense_Mutation	SNP	G	G	A	rs34379989	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61834169G>A	ENST00000370339.3	-	4	1464	c.1123C>T	c.(1123-1125)Cac>Tac	p.H375Y	YTHDF1_ENST00000370334.4_Intron|YTHDF1_ENST00000370333.4_Missense_Mutation_p.H325Y	NM_017798.3	NP_060268.2	Q9BYJ9	YTHD1_HUMAN	YTH domain family, member 1	375							N6-methyladenosine-containing RNA binding (GO:1990247)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(5)|lung(7)|ovary(2)	24						TTGTAGCTGTGAGCAGCCTTC	0.537													G|||	66	0.0131789	0.0477	0.0043	5008	,	,		18939	0.0		0.0	False		,,,				2504	0.0				p.H375Y		Atlas-SNP	.											.	YTHDF1	66	.	0			c.C1123T						PASS	.	G	TYR/HIS	145,4261	98.9+/-137.6	2,141,2060	87.0	89.0	88.0		1123	4.7	1.0	20	dbSNP_126	88	0,8600		0,0,4300	yes	missense	YTHDF1	NM_017798.3	83	2,141,6360	AA,AG,GG		0.0,3.291,1.1149	possibly-damaging	375/560	61834169	145,12861	2203	4300	6503	SO:0001583	missense	54915	exon4			AGCTGTGAGCAGC	AK000398	CCDS13511.1	20q13.33	2010-03-15	2004-11-16	2004-06-04	ENSG00000149658	ENSG00000149658			15867	protein-coding gene	gene with protein product			"""YTH domain family 1"""	C20orf21			Standard	NM_017798		Approved	FLJ20391	uc002yeh.3	Q9BYJ9	OTTHUMG00000032955	ENST00000370339.3:c.1123C>T	20.37:g.61834169G>A	ENSP00000359364:p.His375Tyr	140.0	0.0	0		148.0	66.0	0.445946	NM_017798	Q8N3G5|Q8TBT1|Q96AN4|Q96S57|Q9BTI7|Q9NX79	Missense_Mutation	SNP	ENST00000370339.3	37	CCDS13511.1	21	0.009615384615384616	20	0.04065040650406504	1	0.0027624309392265192	0	0.0	0	0.0	G	14.56	2.572951	0.45798	0.03291	0.0	ENSG00000149658	ENST00000370339;ENST00000370333;ENST00000342761	T;T	0.23147	1.92;1.92	4.72	4.72	0.59763	.	0.000000	0.85682	D	0.000000	T	0.09512	0.0234	M	0.63428	1.95	0.58432	D	0.999999	P	0.39696	0.683	B	0.40565	0.333	T	0.06499	-1.0823	10	0.87932	D	0	-43.1736	18.0486	0.89341	0.0:0.0:1.0:0.0	rs34379989	375	Q9BYJ9	YTHD1_HUMAN	Y	375;325;191	ENSP00000359364:H375Y;ENSP00000359358:H325Y	ENSP00000339489:H191Y	H	-	1	0	YTHDF1	61304614	1.000000	0.71417	1.000000	0.80357	0.712000	0.41017	7.661000	0.83786	2.339000	0.79563	0.591000	0.81541	CAC	G|0.991;A|0.009	0.009	strong		0.537	YTHDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080110.2	NM_017798	
CDC14A	8556	hgsc.bcm.edu	37	1	100933576	100933576	+	Silent	SNP	T	T	C	rs17122597	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:100933576T>C	ENST00000336454.3	+	10	1258	c.903T>C	c.(901-903)caT>caC	p.H301H	CDC14A_ENST00000370124.3_Silent_p.H301H|RP5-837M10.4_ENST00000432210.1_RNA|CDC14A_ENST00000542213.1_Silent_p.H243H|CDC14A_ENST00000361544.6_Silent_p.H301H|CDC14A_ENST00000370125.2_3'UTR|CDC14A_ENST00000544534.1_Silent_p.H301H	NM_003672.3	NP_003663.2	Q9UNH5	CC14A_HUMAN	cell division cycle 14A	301	B.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(5)|kidney(6)|large_intestine(6)|lung(10)|skin(2)|urinary_tract(1)	31		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)		GGTTTACACATGCTGAAATAA	0.398													C|||	302	0.0603035	0.2216	0.0086	5008	,	,		20803	0.0		0.003	False		,,,				2504	0.0				p.H301H		Atlas-SNP	.											.	CDC14A	65	.	0			c.T903C						PASS	.	C	,,	894,3512	741.8+/-411.3	94,706,1403	159.0	159.0	159.0		903,903,903	-7.4	0.3	1	dbSNP_123	159	5,8595	819.1+/-406.8	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	CDC14A	NM_003672.3,NM_033312.2,NM_033313.2	,,	94,711,5698	CC,CT,TT		0.0581,20.2905,6.9122	,,	301/595,301/624,301/384	100933576	899,12107	2203	4300	6503	SO:0001819	synonymous_variant	8556	exon10			TACACATGCTGAA	AF000367	CCDS769.1, CCDS770.1, CCDS771.1	1p21	2013-01-17	2013-01-17		ENSG00000079335	ENSG00000079335		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"""	1718	protein-coding gene	gene with protein product		603504	"""CDC10 (cell division cycle 10, S. cerevisiae, homolog)"", ""CDC14 cell division cycle 14 homolog A (S. cerevisiae)"""			9367992, 10409437	Standard	NM_033312		Approved	Cdc14A1, Cdc14A2, cdc14	uc001dtf.2	Q9UNH5	OTTHUMG00000010987	ENST00000336454.3:c.903T>C	1.37:g.100933576T>C		109.0	0.0	0		129.0	67.0	0.51938	NM_033313	A6MA65|B1AQ14|B1AQ15|O43171|O60727|O60728|Q52LH9|Q8IXX0	Silent	SNP	ENST00000336454.3	37	CCDS769.1																																																																																			T|0.931;C|0.069	0.069	strong		0.398	CDC14A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000030220.1	NM_033312	
CCDC168	643677	hgsc.bcm.edu	37	13	103385309	103385309	+	Missense_Mutation	SNP	A	A	G	rs80279368	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:103385309A>G	ENST00000322527.2	-	1	3850	c.3851T>C	c.(3850-3852)gTt>gCt	p.V1284A		NM_001146197.1	NP_001139669.1	Q8NDH2	CC168_HUMAN	coiled-coil domain containing 168	1284																	AAATTCCAGAACACCTTCCTC	0.443													A|||	182	0.0363419	0.1339	0.0058	5008	,	,		20458	0.0		0.001	False		,,,				2504	0.0				p.V5913A		Atlas-SNP	.											.	.	.	.	0			c.T17738C						PASS	.	A	ALA/VAL	184,1200		18,148,526	178.0	136.0	149.0		17738	-1.5	0.0	13	dbSNP_132	149	6,3176		0,6,1585	yes	missense	CCDC168	NM_001146197.1	64	18,154,2111	GG,GA,AA		0.1886,13.2948,4.1612	benign	5913/7082	103385309	190,4376	692	1591	2283	SO:0001583	missense	643677	exon4			TCCAGAACACCTT		CCDS73596.1	13q33.1	2014-06-17	2011-08-09	2011-08-09	ENSG00000175820	ENSG00000175820			26851	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 40"""	C13orf40			Standard	NM_001146197		Approved	FLJ40176	uc001vpm.3	Q8NDH2	OTTHUMG00000187287	ENST00000322527.2:c.3851T>C	13.37:g.103385309A>G	ENSP00000320232:p.Val1284Ala	208.0	0.0	0		261.0	141.0	0.54023	NM_001146197	Q8N800	Missense_Mutation	SNP	ENST00000322527.2	37		65	0.02976190476190476	64	0.13008130081300814	1	0.0027624309392265192	0	0.0	0	0.0	A	0.487	-0.877060	0.02550	0.132948	0.001886	ENSG00000175820	ENST00000322527	T	0.03635	3.86	2.89	-1.46	0.08800	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.80722	P	0.0	B	0.28713	0.22	B	0.20184	0.028	T	0.47142	-0.9140	8	0.23302	T	0.38	.	0.4721	0.00533	0.4296:0.2212:0.1341:0.2151	.	1284	Q8NDH2	CC168_HUMAN	A	1284	ENSP00000320232:V1284A	ENSP00000320232:V1284A	V	-	2	0	CCDC168	102183310	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.200000	0.09478	-0.254000	0.09500	-0.467000	0.05162	GTT	A|0.965;G|0.035	0.035	strong		0.443	CCDC168-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001146197	
WDR72	256764	hgsc.bcm.edu	37	15	53997415	53997415	+	Missense_Mutation	SNP	G	G	T	rs142505794		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:53997415G>T	ENST00000396328.1	-	11	1357	c.1118C>A	c.(1117-1119)gCc>gAc	p.A373D	WDR72_ENST00000559418.1_Missense_Mutation_p.A383D|WDR72_ENST00000557913.1_Missense_Mutation_p.A370D|WDR72_ENST00000360509.5_Missense_Mutation_p.A373D	NM_001277176.1|NM_182758.2	NP_001264105.1|NP_877435.3	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	373										NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(18)|lung(29)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	71				all cancers(107;0.0511)		AGTCCAGGTGGCAGTTACTGG	0.358																																					p.A373D		Atlas-SNP	.											.	WDR72	177	.	0			c.C1118A						PASS	.	G	ASP/ALA	1,4387	2.1+/-5.4	0,1,2193	61.0	62.0	61.0		1118	4.8	1.0	15	dbSNP_134	61	0,8586		0,0,4293	no	missense	WDR72	NM_182758.2	126	0,1,6486	TT,TG,GG		0.0,0.0228,0.0077	benign	373/1103	53997415	1,12973	2194	4293	6487	SO:0001583	missense	256764	exon11			CAGGTGGCAGTTA	BX537884	CCDS10151.1, CCDS73730.1	15q21.3	2013-01-09			ENSG00000166415	ENSG00000166415		"""WD repeat domain containing"""	26790	protein-coding gene	gene with protein product		613214					Standard	NM_182758		Approved	FLJ38736	uc002acj.2	Q3MJ13	OTTHUMG00000131939	ENST00000396328.1:c.1118C>A	15.37:g.53997415G>T	ENSP00000379619:p.Ala373Asp	34.0	0.0	0		38.0	23.0	0.605263	NM_182758	Q7Z3I3|Q8N8X2	Missense_Mutation	SNP	ENST00000396328.1	37	CCDS10151.1	.	.	.	.	.	.	.	.	.	.	G	13.53	2.265633	0.40095	2.28E-4	0.0	ENSG00000166415	ENST00000396328;ENST00000360509	T;T	0.52295	0.67;0.67	5.75	4.84	0.62591	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.281989	0.35262	N	0.003332	T	0.33876	0.0878	N	0.14661	0.345	0.24960	N	0.991737	B	0.21606	0.058	B	0.18561	0.022	T	0.31641	-0.9936	10	0.59425	D	0.04	.	15.9329	0.79679	0.0:0.1353:0.8647:0.0	.	373	Q3MJ13	WDR72_HUMAN	D	373	ENSP00000379619:A373D;ENSP00000353699:A373D	ENSP00000353699:A373D	A	-	2	0	WDR72	51784707	0.988000	0.35896	0.997000	0.53966	0.830000	0.47004	3.442000	0.52900	1.434000	0.47414	0.460000	0.39030	GCC	G|1.000;T|0.000	0.000	weak		0.358	WDR72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254893.2	NM_182758	
LAMA4	3910	hgsc.bcm.edu	37	6	112513025	112513025	+	Silent	SNP	G	G	A	rs61742228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:112513025G>A	ENST00000230538.7	-	6	928	c.531C>T	c.(529-531)ccC>ccT	p.P177P	LAMA4_ENST00000389463.4_Silent_p.P177P|LAMA4_ENST00000522006.1_Silent_p.P177P|LAMA4_ENST00000524032.1_5'UTR|LAMA4_ENST00000424408.2_Silent_p.P177P	NM_001105206.2	NP_001098676.2	Q16363	LAMA4_HUMAN	laminin, alpha 4	177	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.				blood vessel development (GO:0001568)|brown fat cell differentiation (GO:0050873)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(42)|ovary(4)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(8)	100		all_cancers(87;0.000196)|all_hematologic(75;0.000114)|all_epithelial(87;0.00542)|Colorectal(196;0.0209)		all cancers(137;0.0335)|OV - Ovarian serous cystadenocarcinoma(136;0.0578)|Epithelial(106;0.0748)|BRCA - Breast invasive adenocarcinoma(108;0.242)		CAATGAGTAAGGGGTTTCCAT	0.393													G|||	60	0.0119808	0.0446	0.0014	5008	,	,		21553	0.0		0.0	False		,,,				2504	0.0				p.P177P		Atlas-SNP	.											.	LAMA4	227	.	0			c.C531T						PASS	.	G	,,	188,4218	109.5+/-147.8	8,172,2023	68.0	63.0	64.0		531,531,531	4.0	1.0	6	dbSNP_129	64	2,8598		0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	LAMA4	NM_001105206.1,NM_001105207.1,NM_002290.3	,,	8,174,6321	AA,AG,GG		0.0233,4.2669,1.4609	,,	177/1824,177/1817,177/1817	112513025	190,12816	2203	4300	6503	SO:0001819	synonymous_variant	3910	exon6			GAGTAAGGGGTTT		CCDS34514.1, CCDS43491.1, CCDS43492.1	6q21	2014-09-17			ENSG00000112769	ENSG00000112769		"""Laminins"""	6484	protein-coding gene	gene with protein product		600133				7959779	Standard	NM_001105206		Approved	LAMA3	uc003pvu.3	Q16363	OTTHUMG00000015386	ENST00000230538.7:c.531C>T	6.37:g.112513025G>A		97.0	0.0	0		100.0	51.0	0.51	NM_001105206	Q14731|Q14735|Q15335|Q4LE44|Q5SZG8|Q9BTB8|Q9UE18|Q9UJN9	Silent	SNP	ENST00000230538.7	37	CCDS43491.1																																																																																			G|0.985;A|0.015	0.015	strong		0.393	LAMA4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041876.2	NM_001105206	
LCE2B	26239	hgsc.bcm.edu	37	1	152659392	152659392	+	Missense_Mutation	SNP	C	C	T	rs61730791	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152659392C>T	ENST00000368780.3	+	2	127	c.73C>T	c.(73-75)Cca>Tca	p.P25S	LCE2B_ENST00000417924.2_Missense_Mutation_p.P25S	NM_014357.4	NP_055172.1	O14633	LCE2B_HUMAN	late cornified envelope 2B	25	Cys-rich.|Pro-rich.				epidermis development (GO:0008544)|keratinization (GO:0031424)					endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	11	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCCAAAATGTCCACCTAAGTG	0.572													C|||	65	0.0129792	0.0461	0.0043	5008	,	,		15748	0.0		0.001	False		,,,				2504	0.0				p.P25S		Atlas-SNP	.											.	LCE2B	40	.	0			c.C73T						PASS	.	C	SER/PRO	146,4260	102.5+/-141.1	4,138,2061	123.0	122.0	123.0		73	1.5	0.0	1	dbSNP_129	123	1,8599		0,1,4299	yes	missense	LCE2B	NM_014357.4	74	4,139,6360	TT,TC,CC		0.0116,3.3137,1.1302	benign	25/111	152659392	147,12859	2203	4300	6503	SO:0001583	missense	26239	exon2			AAATGTCCACCTA	BI670514	CCDS1020.1	1q21	2008-02-05	2004-10-11	2004-10-15	ENSG00000159455	ENSG00000159455		"""Late cornified envelopes"""	16610	protein-coding gene	gene with protein product		612610	"""small proline rich-like (epidermal differentiation complex) 1B"""	SPRL1B		11698679, 9344646	Standard	NM_014357		Approved	LEP10, XP5	uc001fai.3	O14633	OTTHUMG00000012404	ENST00000368780.3:c.73C>T	1.37:g.152659392C>T	ENSP00000357769:p.Pro25Ser	237.0	0.0	0		240.0	124.0	0.516667	NM_014357	Q5TA80	Missense_Mutation	SNP	ENST00000368780.3	37	CCDS1020.1	24	0.01098901098901099	21	0.042682926829268296	3	0.008287292817679558	0	0.0	0	0.0	C	1.661	-0.511564	0.04200	0.033137	1.16E-4	ENSG00000159455	ENST00000417924;ENST00000368780	T;T	0.03607	3.87;3.87	2.46	1.45	0.22620	.	.	.	.	.	T	0.01940	0.0061	M	0.77820	2.39	0.09310	N	1	B	0.14012	0.009	B	0.17722	0.019	T	0.40213	-0.9575	9	0.87932	D	0	.	4.1955	0.10441	0.0:0.7428:0.0:0.2572	rs61730791	25	O14633	LCE2B_HUMAN	S	25	ENSP00000414043:P25S;ENSP00000357769:P25S	ENSP00000357769:P25S	P	+	1	0	LCE2B	150926016	0.000000	0.05858	0.001000	0.08648	0.514000	0.34195	-0.555000	0.05999	0.257000	0.21650	0.313000	0.20887	CCA	C|0.986;T|0.014	0.014	strong		0.572	LCE2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034524.1	NM_014357	
PROP1	5626	hgsc.bcm.edu	37	5	177421275	177421275	+	Silent	SNP	C	C	T	rs2233784	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:177421275C>T	ENST00000308304.2	-	2	482	c.174G>A	c.(172-174)ccG>ccA	p.P58P		NM_006261.4	NP_006252	O75360	PROP1_HUMAN	PROP paired-like homeobox 1	58					blood vessel development (GO:0001568)|canonical Wnt signaling pathway (GO:0060070)|cell migration (GO:0016477)|central nervous system development (GO:0007417)|dorsal/ventral pattern formation (GO:0009953)|hypophysis morphogenesis (GO:0048850)|hypothalamus cell differentiation (GO:0021979)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|somatotropin secreting cell differentiation (GO:0060126)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)			endometrium(1)|large_intestine(2)|lung(9)|stomach(1)	13	all_cancers(89;0.00176)|Renal(175;0.000269)|Lung NSC(126;0.00858)|all_lung(126;0.0139)	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)			GTCCTCCTTGCGGGGAGAACC	0.662													c|||	125	0.0249601	0.0908	0.0072	5008	,	,		15546	0.0		0.0	False		,,,				2504	0.0				p.P58P		Atlas-SNP	.											PROP1,NS,carcinoma,-2,1	PROP1	28	1	0			c.G174A						PASS	.	T		357,4043		13,331,1856	25.0	26.0	26.0		174	-6.3	0.0	5	dbSNP_98	26	3,8597		0,3,4297	no	coding-synonymous	PROP1	NM_006261.4		13,334,6153	TT,TC,CC		0.0349,8.1136,2.7692		58/227	177421275	360,12640	2200	4300	6500	SO:0001819	synonymous_variant	5626	exon2			TCCTTGCGGGGAG	AF076215	CCDS4430.1	5q35.3	2011-06-20	2007-07-12		ENSG00000175325	ENSG00000175325		"""Homeoboxes / PRD class"""	9455	protein-coding gene	gene with protein product		601538	"""prophet of Pit1, paired-like homeodomain transcription factor"""			9462743	Standard	NM_006261		Approved		uc003mif.1	O75360	OTTHUMG00000130887	ENST00000308304.2:c.174G>A	5.37:g.177421275C>T		107.0	0.0	0		131.0	68.0	0.519084	NM_006261		Silent	SNP	ENST00000308304.2	37	CCDS4430.1																																																																																			C|0.969;T|0.031	0.031	strong		0.662	PROP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253472.1	NM_006261	
FBXW9	84261	hgsc.bcm.edu	37	19	12807066	12807066	+	Silent	SNP	G	G	C	rs6511832	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12807066G>C	ENST00000380339.3	-	1	366	c.330C>G	c.(328-330)ctC>ctG	p.L110L	FBXW9_ENST00000544494.1_5'UTR|FBXW9_ENST00000393261.3_Silent_p.L110L|FBXW9_ENST00000587955.1_Silent_p.L110L			Q5XUX1	FBXW9_HUMAN	F-box and WD repeat domain containing 9	110	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)					cervix(1)|lung(4)|ovary(1)|prostate(1)	7						CGAGGTCGCGGAGCGCGTGGC	0.721													C|||	748	0.149361	0.534	0.0461	5008	,	,		12393	0.0		0.0099	False		,,,				2504	0.0				p.L110L		Atlas-SNP	.											.	FBXW9	30	.	0			c.C330G						PASS	.	C		1528,2426		306,916,755	10.0	14.0	13.0		330	2.8	1.0	19	dbSNP_116	13	117,8057		1,115,3971	no	coding-synonymous	FBXW9	NM_032301.2		307,1031,4726	CC,CG,GG		1.4314,38.6444,13.5637		110/459	12807066	1645,10483	1977	4087	6064	SO:0001819	synonymous_variant	84261	exon1			GTCGCGGAGCGCG	BC004290	CCDS12278.2	19p13.2	2013-01-09	2007-02-08		ENSG00000132004	ENSG00000132004		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	28136	protein-coding gene	gene with protein product		609074	"""F-box and WD-40 domain protein 9"""			12477932	Standard	NM_032301		Approved	MGC10870, Fbw9	uc002mum.1	Q5XUX1	OTTHUMG00000150152	ENST00000380339.3:c.330C>G	19.37:g.12807066G>C		38.0	0.0	0		50.0	21.0	0.42	NM_032301	B3KVP7|Q9BT89	Silent	SNP	ENST00000380339.3	37																																																																																				G|0.902;C|0.098	0.098	strong		0.721	FBXW9-201	KNOWN	basic	protein_coding	protein_coding		NM_032301	
PPFIA1	8500	hgsc.bcm.edu	37	11	70200516	70200516	+	Missense_Mutation	SNP	C	C	T	rs139448605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:70200516C>T	ENST00000253925.7	+	17	2488	c.2273C>T	c.(2272-2274)gCg>gTg	p.A758V	PPFIA1_ENST00000389547.3_Missense_Mutation_p.A758V|AP000487.6_ENST00000528607.1_RNA	NM_003626.3	NP_003617.1	Q13136	LIPA1_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	758					cell-matrix adhesion (GO:0007160)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of stress fiber assembly (GO:0051497)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|presynaptic active zone (GO:0048786)	signal transducer activity (GO:0004871)			breast(3)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	65			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			CACAAAGGGGCGCTGCACACC	0.567													C|||	50	0.00998403	0.0378	0.0	5008	,	,		15864	0.0		0.0	False		,,,				2504	0.0				p.A758V		Atlas-SNP	.											.	PPFIA1	114	.	0			c.C2273T						PASS	.	C	VAL/ALA,VAL/ALA	116,4284	88.2+/-126.9	0,116,2084	51.0	44.0	46.0		2273,2273	4.4	0.0	11	dbSNP_134	46	2,8586	1.2+/-3.3	0,2,4292	yes	missense,missense	PPFIA1	NM_003626.2,NM_177423.1	64,64	0,118,6376	TT,TC,CC		0.0233,2.6364,0.9085	benign,benign	758/1203,758/1186	70200516	118,12870	2200	4294	6494	SO:0001583	missense	8500	exon17			AAGGGGCGCTGCA	U22816	CCDS31627.1, CCDS31628.1	11q13.3	2013-01-10			ENSG00000131626	ENSG00000131626		"""Sterile alpha motif (SAM) domain containing"""	9245	protein-coding gene	gene with protein product	"""Liprin-alpha1"""	611054				7796809, 9624153	Standard	NM_003626		Approved	LIP.1, LIPRIN	uc001opo.3	Q13136	OTTHUMG00000167266	ENST00000253925.7:c.2273C>T	11.37:g.70200516C>T	ENSP00000253925:p.Ala758Val	51.0	0.0	0		63.0	26.0	0.412698	NM_177423	A6NLE3|Q13135|Q14567|Q8N4I2	Missense_Mutation	SNP	ENST00000253925.7	37	CCDS31627.1	14|14	0.00641025641025641|0.00641025641025641	14|14	0.028455284552845527|0.028455284552845527	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	14.81|14.81	2.646317|2.646317	0.47258|0.47258	0.026364|0.026364	2.33E-4|2.33E-4	ENSG00000131626|ENSG00000131626	ENST00000253925;ENST00000389547;ENST00000544950|ENST00000528750	T;T|.	0.28255|.	1.62;1.62|.	5.36|5.36	4.45|4.45	0.53987|0.53987	.|.	0.314716|.	0.29508|.	N|.	0.011941|.	T|T	0.36580|0.36580	0.0972|0.0972	M|M	0.62723|0.62723	1.935|1.935	0.31697|0.31697	N|N	0.64121|0.64121	B;B|.	0.23377|.	0.012;0.084|.	B;B|.	0.15870|.	0.004;0.014|.	T|T	0.59920|0.59920	-0.7363|-0.7363	10|5	0.29301|.	T|.	0.29|.	.|.	14.198|14.198	0.65684|0.65684	0.0:0.9277:0.0:0.0723|0.0:0.9277:0.0:0.0723	.|.	758;758|.	Q13136;Q13136-2|.	LIPA1_HUMAN;.|.	V|C	758;758;255|201	ENSP00000253925:A758V;ENSP00000374198:A758V|.	ENSP00000253925:A758V|.	A|R	+|+	2|1	0|0	PPFIA1|PPFIA1	69878164|69878164	0.926000|0.926000	0.31397|0.31397	0.009000|0.009000	0.14445|0.14445	0.490000|0.490000	0.33462|0.33462	2.135000|2.135000	0.42112|0.42112	1.272000|1.272000	0.44329|0.44329	0.561000|0.561000	0.74099|0.74099	GCG|CGC	C|0.992;T|0.008	0.008	strong		0.567	PPFIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393905.1	NM_003626	
PSKH2	85481	hgsc.bcm.edu	37	8	87076651	87076651	+	Missense_Mutation	SNP	T	T	C	rs16879427	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:87076651T>C	ENST00000276616.2	-	2	469	c.395A>G	c.(394-396)cAa>cGa	p.Q132R	PSKH2_ENST00000517981.1_5'UTR	NM_033126.1	NP_149117.1	Q96QS6	KPSH2_HUMAN	protein serine kinase H2	132	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		Q -> R (in dbSNP:rs16879427). {ECO:0000269|PubMed:17344846}.				ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|kidney(11)|large_intestine(2)|lung(26)|ovary(1)|prostate(1)|stomach(3)|urinary_tract(1)	47			STAD - Stomach adenocarcinoma(118;0.129)			CATGTAAACTTGATCCTCAGT	0.542													C|||	503	0.100439	0.3533	0.036	5008	,	,		15987	0.0		0.005	False		,,,				2504	0.0061				p.Q132R		Atlas-SNP	.											PSKH2,right_upper_lobe,carcinoma,-1,1	PSKH2	79	1	0			c.A395G						PASS	.	C	ARG/GLN	1304,3102	697.8+/-406.3	192,920,1091	86.0	82.0	83.0		395	2.5	0.0	8	dbSNP_123	83	19,8581	818.4+/-406.9	0,19,4281	yes	missense	PSKH2	NM_033126.1	43	192,939,5372	CC,CT,TT		0.2209,29.596,10.1722	benign	132/386	87076651	1323,11683	2203	4300	6503	SO:0001583	missense	85481	exon2			TAAACTTGATCCT	AY037806	CCDS6240.1	8q21.13	2004-06-03				ENSG00000147613			18997	protein-coding gene	gene with protein product							Standard	NM_033126		Approved		uc011lfy.2	Q96QS6		ENST00000276616.2:c.395A>G	8.37:g.87076651T>C	ENSP00000276616:p.Gln132Arg	110.0	0.0	0		142.0	70.0	0.492958	NM_033126	A0AV22	Missense_Mutation	SNP	ENST00000276616.2	37	CCDS6240.1	186	0.08516483516483517	172	0.34959349593495936	12	0.03314917127071823	0	0.0	2	0.002638522427440633	C	0.021	-1.427937	0.01117	0.29596	0.002209	ENSG00000147613	ENST00000276616	T	0.64803	-0.12	5.22	2.46	0.29980	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.	.	.	.	T	0.00012	0.0000	N	0.10874	0.06	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.28586	-1.0039	8	0.07175	T	0.84	.	9.205	0.37285	0.0:0.6926:0.0:0.3074	rs16879427;rs52809304;rs16879427	132	Q96QS6	KPSH2_HUMAN	R	132	ENSP00000276616:Q132R	ENSP00000276616:Q132R	Q	-	2	0	PSKH2	87145767	0.895000	0.30542	0.003000	0.11579	0.206000	0.24218	1.883000	0.39658	-0.015000	0.14150	-0.702000	0.03669	CAA	T|0.874;C|0.126	0.126	strong		0.542	PSKH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374628.1	NM_033126	
WDR88	126248	hgsc.bcm.edu	37	19	33666345	33666345	+	Missense_Mutation	SNP	C	C	A	rs77589178	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33666345C>A	ENST00000355868.3	+	11	1362	c.1286C>A	c.(1285-1287)aCc>aAc	p.T429N	AC008738.2_ENST00000577275.1_RNA|CTD-2540B15.10_ENST00000590117.1_RNA|WDR88_ENST00000361680.2_3'UTR	NM_173479.3	NP_775750.3	Q6ZMY6	WDR88_HUMAN	WD repeat domain 88	429										breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25	Esophageal squamous(110;0.137)					AAGAGTGACACCTCTTCTGAA	0.478													C|||	111	0.0221645	0.0832	0.0014	5008	,	,		20731	0.0		0.0	False		,,,				2504	0.0				p.T429N		Atlas-SNP	.											.	WDR88	50	.	0			c.C1286A						PASS	.	C	ASN/THR	263,4143	150.3+/-184.3	11,241,1951	179.0	171.0	174.0		1286	-5.6	0.0	19	dbSNP_131	174	0,8600		0,0,4300	yes	missense	WDR88	NM_173479.3	65	11,241,6251	AA,AC,CC		0.0,5.9691,2.0221	benign	429/473	33666345	263,12743	2203	4300	6503	SO:0001583	missense	126248	exon11			GTGACACCTCTTC	BC031227	CCDS12429.1	19q13.11	2013-01-09	2007-04-04	2007-04-04		ENSG00000166359		"""WD repeat domain containing"""	26999	protein-coding gene	gene with protein product			"""PQQ repeat and WD repeat domain containing"""	PQWD		12477932	Standard	NM_173479		Approved		uc002nui.3	Q6ZMY6		ENST00000355868.3:c.1286C>A	19.37:g.33666345C>A	ENSP00000348129:p.Thr429Asn	257.0	1.0	0.00389105		224.0	103.0	0.459821	NM_173479	Q8NEF8	Missense_Mutation	SNP	ENST00000355868.3	37	CCDS12429.1	46	0.021062271062271064	45	0.09146341463414634	1	0.0027624309392265192	0	0.0	0	0.0	C	4.208	0.037382	0.08148	0.059691	0.0	ENSG00000166359	ENST00000355868	T	0.56941	0.43	4.92	-5.61	0.02489	.	3.589250	0.00520	N	0.000190	T	0.01189	0.0039	N	0.22421	0.69	0.09310	N	1	B	0.13594	0.008	B	0.09377	0.004	T	0.04140	-1.0974	10	0.40728	T	0.16	.	0.5128	0.00598	0.4107:0.1392:0.196:0.2542	.	429	Q6ZMY6	WDR88_HUMAN	N	429	ENSP00000348129:T429N	ENSP00000348129:T429N	T	+	2	0	WDR88	38358185	0.000000	0.05858	0.000000	0.03702	0.069000	0.16628	-1.093000	0.03362	-0.598000	0.05806	-0.314000	0.08810	ACC	C|0.975;A|0.025	0.025	strong		0.478	WDR88-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450840.1	NM_173479	
AHNAK2	113146	hgsc.bcm.edu	37	14	105418276	105418276	+	Missense_Mutation	SNP	G	G	A	rs35374867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105418276G>A	ENST00000333244.5	-	7	3631	c.3512C>T	c.(3511-3513)cCa>cTa	p.P1171L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1171						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CCCGAACGATGGCATCTTGAA	0.617													.|||	175	0.0349441	0.1286	0.0058	5008	,	,		18260	0.0		0.001	False		,,,				2504	0.0				p.P1171L		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C3512T						PASS	.	G	LEU/PRO	399,3475		46,307,1584	189.0	192.0	191.0		3512	4.4	1.0	14	dbSNP_126	191	5,8237		0,5,4116	no	missense	AHNAK2	NM_138420.2	98	46,312,5700	AA,AG,GG		0.0607,10.2994,3.3344	benign	1171/5796	105418276	404,11712	1937	4121	6058	SO:0001583	missense	113146	exon7			AACGATGGCATCT	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.3512C>T	14.37:g.105418276G>A	ENSP00000353114:p.Pro1171Leu	285.0	0.0	0		303.0	140.0	0.462046	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	60	0.027472527472527472	57	0.11585365853658537	3	0.008287292817679558	0	0.0	0	0.0	g	19.11	3.763478	0.69763	0.102994	6.07E-4	ENSG00000185567	ENST00000333244	T	0.05717	3.4	4.4	4.4	0.53042	.	.	.	.	.	T	0.00552	0.0018	H	0.95712	3.71	0.49483	D	0.999799	D	0.89917	1.0	D	0.91635	0.999	T	0.06826	-1.0805	9	0.72032	D	0.01	-13.4451	16.6046	0.84825	0.0:0.0:1.0:0.0	.	1171	Q8IVF2	AHNK2_HUMAN	L	1171	ENSP00000353114:P1171L	ENSP00000353114:P1171L	P	-	2	0	AHNAK2	104489321	1.000000	0.71417	0.967000	0.41034	0.114000	0.19823	5.979000	0.70508	1.998000	0.58463	0.491000	0.48974	CCA	G|0.978;A|0.022	0.022	strong		0.617	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
MLXIPL	51085	hgsc.bcm.edu	37	7	73020328	73020328	+	Missense_Mutation	SNP	G	G	T	rs34922362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:73020328G>T	ENST00000313375.3	-	6	779	c.732C>A	c.(730-732)gaC>gaA	p.D244E	MLXIPL_ENST00000434326.1_Intron|MLXIPL_ENST00000354613.1_Missense_Mutation_p.D244E|MLXIPL_ENST00000395189.1_Intron|MLXIPL_ENST00000429400.2_Missense_Mutation_p.D244E|MLXIPL_ENST00000414749.2_Missense_Mutation_p.D244E	NM_032951.2|NM_032953.2	NP_116569.1|NP_116571.1	Q9NP71	MLXPL_HUMAN	MLX interacting protein-like	244			D -> E (in dbSNP:rs34922362).		anatomical structure morphogenesis (GO:0009653)|energy reserve metabolic process (GO:0006112)|fatty acid homeostasis (GO:0055089)|glucose homeostasis (GO:0042593)|glucose mediated signaling pathway (GO:0010255)|intracellular signal transduction (GO:0035556)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of oxidative phosphorylation (GO:0090324)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular metabolic process (GO:0031325)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of glycolytic process (GO:0045821)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of energy homeostasis (GO:2000505)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride homeostasis (GO:0070328)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	carbohydrate response element binding (GO:0035538)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			cervix(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	13		Lung NSC(55;0.0659)|all_lung(88;0.152)				AGCAATTGAGGTCCAGGAGCT	0.637													G|||	110	0.0219649	0.0825	0.0014	5008	,	,		17810	0.0		0.0	False		,,,				2504	0.0				p.D244E		Atlas-SNP	.											.	MLXIPL	54	.	0			c.C732A						PASS	.	G	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	239,4165		6,227,1969	33.0	32.0	32.0		732,732,732,732	1.8	1.0	7	dbSNP_126	32	0,8594		0,0,4297	yes	missense,missense,missense,missense	MLXIPL	NM_032951.2,NM_032952.2,NM_032953.2,NM_032954.2	45,45,45,45	6,227,6266	TT,TG,GG		0.0,5.4269,1.8387	benign,benign,benign,benign	244/853,244/834,244/851,244/832	73020328	239,12759	2202	4297	6499	SO:0001583	missense	51085	exon6			ATTGAGGTCCAGG	AK055029	CCDS5553.1, CCDS5554.1, CCDS47605.1, CCDS47606.1	7q11.23	2013-05-21	2005-10-31	2005-10-31	ENSG00000009950	ENSG00000009950			12744	protein-coding gene	gene with protein product	"""carbohydrate response element binding protein"""	605678	"""Williams Beuren syndrome chromosome region 14"""	WBSCR14		9860302	Standard	XM_005250399		Approved	WS-bHLH, MIO, CHREBP, MONDOB, bHLHd14	uc003tyn.1	Q9NP71	OTTHUMG00000129995	ENST00000313375.3:c.732C>A	7.37:g.73020328G>T	ENSP00000320886:p.Asp244Glu	73.0	0.0	0		76.0	33.0	0.434211	NM_032954	C5HU02|C5HU03|C5HU04|Q96E48|Q9BY03|Q9BY04|Q9BY05|Q9BY06|Q9Y2P3	Missense_Mutation	SNP	ENST00000313375.3	37	CCDS5553.1	47	0.02152014652014652	46	0.09349593495934959	1	0.0027624309392265192	0	0.0	0	0.0	G	13.57	2.277764	0.40294	0.054269	0.0	ENSG00000009950	ENST00000414749;ENST00000429400;ENST00000313375;ENST00000354613;ENST00000456640	T;T;T;T;T	0.59364	1.81;1.85;1.82;1.83;0.27	3.68	1.79	0.24919	.	0.068000	0.56097	D	0.000024	T	0.03305	0.0096	L	0.59436	1.845	0.80722	D	1	P;D;D;D	0.54207	0.941;0.965;0.965;0.965	B;P;P;P	0.47015	0.333;0.534;0.534;0.534	T	0.01432	-1.1356	10	0.87932	D	0	-11.5469	5.3046	0.15797	0.2859:0.0:0.7141:0.0	rs34922362	244;244;244;244	Q9NP71;Q9NP71-2;Q9NP71-3;Q9NP71-4	MLXPL_HUMAN;.;.;.	E	244;244;244;244;206	ENSP00000412330:D244E;ENSP00000406296:D244E;ENSP00000320886:D244E;ENSP00000346629:D244E;ENSP00000402615:D206E	ENSP00000320886:D244E	D	-	3	2	MLXIPL	72658264	1.000000	0.71417	0.986000	0.45419	0.877000	0.50540	2.652000	0.46682	0.221000	0.20879	0.313000	0.20887	GAC	G|0.978;T|0.022	0.022	strong		0.637	MLXIPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252262.1	NM_032951	
CTRC	11330	hgsc.bcm.edu	37	1	15767036	15767036	+	Silent	SNP	C	C	A	rs497078	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:15767036C>A	ENST00000375949.4	+	3	206	c.180C>A	c.(178-180)ggC>ggA	p.G60G	CTRC_ENST00000483406.1_3'UTR|CTRC_ENST00000375943.2_Intron	NM_007272.2	NP_009203.2	Q99895	CTRC_HUMAN	chymotrypsin C (caldecrin)	60	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				proteolysis (GO:0006508)		peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)	13		Breast(348;0.000207)|all_lung(284;0.00021)|Colorectal(325;0.000257)|Lung NSC(340;0.000269)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)|Hepatocellular(190;0.0634)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.56e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		ATACGTGTGGCGGGACTTTGA	0.627													C|||	90	0.0179712	0.0651	0.0058	5008	,	,		14713	0.0		0.0	False		,,,				2504	0.0				p.G60G		Atlas-SNP	.											.	CTRC	28	.	0			c.C180A						PASS	.						144.0	95.0	111.0					1																	15767036		2203	4300	6503	SO:0001819	synonymous_variant	11330	exon3			GTGTGGCGGGACT	BC015118	CCDS156.1	1p36.21	2009-02-18			ENSG00000162438	ENSG00000162438	3.4.21.2		2523	protein-coding gene	gene with protein product	"""elastase 4"""	601405				8635596	Standard	NM_007272		Approved	CLCR, ELA4	uc001awi.1	Q99895	OTTHUMG00000002255	ENST00000375949.4:c.180C>A	1.37:g.15767036C>A		105.0	0.0	0		108.0	40.0	0.37037	NM_007272	A8K082|O00765|Q9NUH5	Silent	SNP	ENST00000375949.4	37	CCDS156.1																																																																																			A|0.000;C|0.887;T|0.113	0.000	strong		0.627	CTRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006435.1	NM_007272	
SNX7	51375	hgsc.bcm.edu	37	1	99150590	99150590	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:99150590A>G	ENST00000306121.3	+	2	339	c.330A>G	c.(328-330)atA>atG	p.I110M	SNX7_ENST00000529992.1_Missense_Mutation_p.I110M|SNX7_ENST00000370189.5_Missense_Mutation_p.I46M	NM_015976.4	NP_057060.2	Q9UNH6	SNX7_HUMAN	sorting nexin 7	46	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				apoptotic process (GO:0006915)|intracellular protein transport (GO:0006886)	cytoplasmic vesicle (GO:0031410)|endosome (GO:0005768)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)	13		all_epithelial(167;7.64e-07)|all_lung(203;0.0006)|Lung NSC(277;0.00137)		Epithelial(280;0.0521)|all cancers(265;0.0687)|COAD - Colon adenocarcinoma(174;0.15)|Lung(183;0.207)|Colorectal(170;0.234)		TTACTACAATAGAAACTTTCA	0.318																																					p.I110M		Atlas-SNP	.											.	SNX7	76	.	0			c.A330G						PASS	.						80.0	73.0	75.0					1																	99150590		2203	4300	6503	SO:0001583	missense	51375	exon2			TACAATAGAAACT	AF121857	CCDS755.2, CCDS756.1, CCDS756.2	1p21	2008-05-22			ENSG00000162627	ENSG00000162627		"""Sorting nexins"""	14971	protein-coding gene	gene with protein product		614904					Standard	NM_015976		Approved		uc010ouc.2	Q9UNH6	OTTHUMG00000010723	ENST00000306121.3:c.330A>G	1.37:g.99150590A>G	ENSP00000304429:p.Ile110Met	223.0	0.0	0		184.0	95.0	0.516304	NM_015976	A8KAF3|D3DT50|Q53FQ3|Q5VT09|Q5VT10|Q86U82|Q8WVD4|Q96FW9|Q9Y3Z7	Missense_Mutation	SNP	ENST00000306121.3	37	CCDS755.2	.	.	.	.	.	.	.	.	.	.	A	5.637	0.302207	0.10678	.	.	ENSG00000162627	ENST00000370189;ENST00000529992;ENST00000306121;ENST00000454199	T;T;T;T	0.39997	1.05;1.05;1.05;1.05	5.39	0.163	0.14986	.	0.106693	0.64402	D	0.000006	T	0.09335	0.0230	N	0.02213	-0.635	0.48135	D	0.999592	P;B;B	0.44260	0.83;0.0;0.001	P;B;B	0.58210	0.835;0.007;0.019	T	0.19712	-1.0297	10	0.02654	T	1	-24.3064	4.5265	0.11983	0.2744:0.137:0.0:0.5886	.	110;110;46	E9PNL2;Q9UNH6-3;Q9UNH6-2	.;.;.	M	46;110;110;46	ENSP00000359208:I46M;ENSP00000434731:I110M;ENSP00000304429:I110M;ENSP00000388266:I46M	ENSP00000304429:I110M	I	+	3	3	SNX7	98923178	0.994000	0.37717	0.996000	0.52242	0.469000	0.32828	0.198000	0.17217	-0.237000	0.09739	-0.451000	0.05528	ATA	.	.	none		0.318	SNX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029609.2		
TAS1R2	80834	hgsc.bcm.edu	37	1	19166100	19166100	+	Missense_Mutation	SNP	C	C	T	rs9988418	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19166100C>T	ENST00000375371.3	-	6	2534	c.2513G>A	c.(2512-2514)aGg>aAg	p.R838K		NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	838			R -> K (in dbSNP:rs9988418).		detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	GCACTAGTCCCTCCTCATGGT	0.612													c|||	288	0.057508	0.1944	0.0303	5008	,	,		15986	0.001		0.003	False		,,,				2504	0.0061				p.R838K		Atlas-SNP	.											.	TAS1R2	134	.	0			c.G2513A						PASS	.		LYS/ARG	613,3793	264.1+/-265.8	43,527,1633	64.0	51.0	55.0		2513	-5.4	0.0	1	dbSNP_119	55	60,8540	35.9+/-90.5	1,58,4241	yes	missense	TAS1R2	NM_152232.2	26	44,585,5874	TT,TC,CC		0.6977,13.9128,5.1745	benign	838/840	19166100	673,12333	2203	4300	6503	SO:0001583	missense	80834	exon6			TAGTCCCTCCTCA		CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	14905	protein-coding gene	gene with protein product		606226	"""G protein-coupled receptor 71"""	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.2513G>A	1.37:g.19166100C>T	ENSP00000364520:p.Arg838Lys	134.0	0.0	0		186.0	83.0	0.446237	NM_152232	Q5TZ19	Missense_Mutation	SNP	ENST00000375371.3	37	CCDS187.1	91	0.041666666666666664	71	0.1443089430894309	16	0.04419889502762431	1	0.0017482517482517483	3	0.00395778364116095	C	0.013	-1.638637	0.00799	0.139128	0.006977	ENSG00000179002	ENST00000375371	D	0.87650	-2.28	5.19	-5.36	0.02689	.	0.573210	0.15415	N	0.263527	T	0.00608	0.0020	N	0.01576	-0.805	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.34279	-0.9835	9	0.02654	T	1	.	6.9586	0.24585	0.135:0.5063:0.0:0.3587	rs9988418;rs52814741;rs9988418	838	Q8TE23	TS1R2_HUMAN	K	838	ENSP00000364520:R838K	ENSP00000364520:R838K	R	-	2	0	TAS1R2	19038687	0.002000	0.14202	0.003000	0.11579	0.095000	0.18619	-0.049000	0.11924	-1.382000	0.02109	-0.364000	0.07487	AGG	C|0.950;T|0.050	0.050	strong		0.612	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1		
FH	2271	hgsc.bcm.edu	37	1	241663825	241663825	+	Silent	SNP	G	G	A	rs2070080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:241663825G>A	ENST00000366560.3	-	9	1340	c.1302C>T	c.(1300-1302)tgC>tgT	p.C434C		NM_000143.3	NP_000134.2	P07954	FUMH_HUMAN	fumarate hydratase	434					cellular metabolic process (GO:0044237)|fumarate metabolic process (GO:0006106)|homeostasis of number of cells within a tissue (GO:0048873)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|tricarboxylic acid cycle enzyme complex (GO:0045239)	fumarate hydratase activity (GO:0004333)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|skin(2)	26	Ovarian(103;0.103)	all_cancers(173;2.37e-314)|all_epithelial(177;5.17e-286)|Breast(1374;1.06e-10)|Acute lymphoblastic leukemia(190;4.93e-10)|all_neural(198;0.00118)	OV - Ovarian serous cystadenocarcinoma(106;0.0214)	Colorectal(1306;2.33e-53)|COAD - Colon adenocarcinoma(196;1.05e-44)|KIRC - Kidney renal clear cell carcinoma(1967;0.000109)		TTCCCACCACGCAGTTTTCTG	0.438			"""Mis, N, F"""			"""lieomyomatosis, renal"""			Hereditary Leiomyomatosis and Renal Cell Cancer				G|||	183	0.0365415	0.1346	0.0072	5008	,	,		15620	0.0		0.0	False		,,,				2504	0.0				p.C434C	Melanoma(148;1573 2486 7381 46575)	Atlas-SNP	.	yes	Rec		hereditary leiomyomatosis and renal cell cancer	1	1q42.1	2271	fumarate hydratase		"""E, M"""	FH,NS,carcinoma,0,1	FH	64	1	0			c.C1302T						PASS	.	G		428,3978	207.2+/-228.6	19,390,1794	135.0	129.0	131.0		1302	-10.7	0.7	1	dbSNP_96	131	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous	FH	NM_000143.3		19,395,6089	AA,AG,GG		0.0581,9.714,3.3292		434/511	241663825	433,12573	2203	4300	6503	SO:0001819	synonymous_variant	2271	exon9	Familial Cancer Database	HLRCC, Reed syndrome, Hereditary Multiple Leiomyomata of Skin and Uterus	CACCACGCAGTTT	BC003108	CCDS1617.1	1q42.1	2014-09-17			ENSG00000091483	ENSG00000091483	4.2.1.2		3700	protein-coding gene	gene with protein product		136850					Standard	NM_000143		Approved	fumarase	uc001hyx.3	P07954	OTTHUMG00000039597	ENST00000366560.3:c.1302C>T	1.37:g.241663825G>A		149.0	0.0	0		142.0	68.0	0.478873	NM_000143	B1ANK7	Silent	SNP	ENST00000366560.3	37	CCDS1617.1																																																																																			G|0.972;A|0.028	0.028	strong		0.438	FH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095490.1	NM_000143	
RFX8	731220	hgsc.bcm.edu	37	2	102031324	102031324	+	Missense_Mutation	SNP	T	T	G	rs6753088	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:102031324T>G	ENST00000376826.2	-	10	891	c.892A>C	c.(892-894)Atg>Ctg	p.M298L	RFX8_ENST00000428343.1_Missense_Mutation_p.M185L			Q6ZV50	RFX8_HUMAN	RFX family member 8, lacking RFX DNA binding domain	298					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|kidney(1)|stomach(1)	3						ACCTTAGCCATGTTGGAAAGG	0.413													t|||	64	0.0127796	0.0454	0.0043	5008	,	,		21079	0.0		0.001	False		,,,				2504	0.0				p.M185L		Atlas-SNP	.											.	RFX8	16	.	0			c.A553C						PASS	.	T	LEU/MET	61,1323		2,57,633	211.0	163.0	178.0		553	5.1	1.0	2	dbSNP_116	178	3,3179		0,3,1588	yes	missense	RFX8	NM_001145664.1	15	2,60,2221	GG,GT,TT		0.0943,4.4075,1.4017	benign	185/474	102031324	64,4502	692	1591	2283	SO:0001583	missense	731220	exon7			TAGCCATGTTGGA	AK124976	CCDS46376.1	2q11.2	2012-11-15	2012-11-15		ENSG00000196460	ENSG00000196460			37253	protein-coding gene	gene with protein product			"""regulatory factor X, 8"", ""RFX gene family member 8, lacking RFX DNA binding domain"""				Standard	NM_001145664		Approved	FLJ42986	uc010yvx.1	Q6ZV50	OTTHUMG00000130693	ENST00000376826.2:c.892A>C	2.37:g.102031324T>G	ENSP00000366022:p.Met298Leu	83.0	0.0	0		94.0	41.0	0.43617	NM_001145664	B4DQ32	Missense_Mutation	SNP	ENST00000376826.2	37		23	0.010531135531135532	21	0.042682926829268296	2	0.0055248618784530384	0	0.0	0	0.0	T	10.11	1.261043	0.23051	0.044075	9.43E-4	ENSG00000196460	ENST00000376826;ENST00000428343	T;T	0.68765	-0.35;1.71	5.08	5.08	0.68730	.	.	.	.	.	T	0.32376	0.0827	N	0.24115	0.695	0.28290	N	0.923599	P	0.51147	0.942	D	0.67231	0.95	T	0.46652	-0.9176	9	0.02654	T	1	.	11.2069	0.48775	0.0:0.0:0.0:1.0	rs6753088;rs6753088	185	Q6ZV50-3	.	L	298;185	ENSP00000366022:M298L;ENSP00000401536:M185L	ENSP00000366022:M298L	M	-	1	0	RFX8	101397756	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.845000	0.55880	2.153000	0.67306	0.454000	0.30748	ATG	T|0.991;G|0.009	0.009	strong		0.413	RFX8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001145664	
COG5	10466	hgsc.bcm.edu	37	7	106938740	106938740	+	Missense_Mutation	SNP	C	C	T	rs35258567	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:106938740C>T	ENST00000347053.3	-	12	1303	c.1253G>A	c.(1252-1254)cGt>cAt	p.R418H	COG5_ENST00000393603.2_Missense_Mutation_p.R418H|COG5_ENST00000297135.3_Missense_Mutation_p.R418H	NM_181733.2	NP_859422.2	Q9UP83	COG5_HUMAN	component of oligomeric golgi complex 5	418					intra-Golgi vesicle-mediated transport (GO:0006891)|protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(17)|ovary(2)|skin(4)|stomach(1)	40						ATTATAAAGACGTAATAATTT	0.343													C|||	7	0.00139776	0.0053	0.0	5008	,	,		12763	0.0		0.0	False		,,,				2504	0.0				p.R418H		Atlas-SNP	.											COG5,colon,carcinoma,-1,1	COG5	78	1	0			c.G1253A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG	15,4391	22.3+/-47.3	0,15,2188	89.0	84.0	86.0		1253,1253,1253	4.8	1.0	7	dbSNP_126	86	0,8600		0,0,4300	yes	missense,missense,missense	COG5	NM_001161520.1,NM_006348.3,NM_181733.2	29,29,29	0,15,6488	TT,TC,CC		0.0,0.3404,0.1153	probably-damaging,probably-damaging,probably-damaging	418/824,418/861,418/840	106938740	15,12991	2203	4300	6503	SO:0001583	missense	10466	exon12			TAAAGACGTAATA	AF058718	CCDS5742.1, CCDS5743.1, CCDS55152.1	7q31	2010-06-24	2001-12-07	2002-05-10	ENSG00000164597	ENSG00000164597		"""Components of oligomeric golgi complex"""	14857	protein-coding gene	gene with protein product		606821	"""golgi transport complex 1 (90 kDa subunit)"""	GOLTC1		9792665, 11980916	Standard	NM_006348		Approved	GTC90	uc003vec.2	Q9UP83	OTTHUMG00000023895	ENST00000347053.3:c.1253G>A	7.37:g.106938740C>T	ENSP00000334703:p.Arg418His	104.0	0.0	0		125.0	58.0	0.464	NM_006348	A4D0R6|A4D0R7|O14555|O95008|Q6NUL5	Missense_Mutation	SNP	ENST00000347053.3	37	CCDS5743.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	14.56	2.571964	0.45798	0.003404	0.0	ENSG00000164597	ENST00000347053;ENST00000297135;ENST00000393603	T;T;T	0.71934	-0.61;-0.61;-0.61	5.68	4.8	0.61643	.	0.055380	0.64402	D	0.000001	T	0.67173	0.2865	M	0.76170	2.325	0.49687	D	0.999819	B;P	0.41366	0.203;0.747	B;B	0.31495	0.026;0.131	T	0.72191	-0.4365	10	0.56958	D	0.05	-11.5895	14.608	0.68495	0.0:0.9302:0.0:0.0698	rs35258567	418;418	Q9UP83;Q9UP83-2	COG5_HUMAN;.	H	418	ENSP00000334703:R418H;ENSP00000297135:R418H;ENSP00000377228:R418H	ENSP00000297135:R418H	R	-	2	0	COG5	106725976	1.000000	0.71417	1.000000	0.80357	0.471000	0.32888	4.194000	0.58393	1.417000	0.47077	-0.142000	0.14014	CGT	C|0.999;T|0.001	0.001	strong		0.343	COG5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000060216.4		
POT1	25913	hgsc.bcm.edu	37	7	124464037	124464037	+	Silent	SNP	T	T	G	rs17147565	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:124464037T>G	ENST00000357628.3	-	19	2482	c.1884A>C	c.(1882-1884)acA>acC	p.T628T	POT1_ENST00000393329.1_Silent_p.T497T	NM_015450.2	NP_056265.2	Q9NUX5	POTE1_HUMAN	protection of telomeres 1	628					DNA duplex unwinding (GO:0032508)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of DNA strand elongation (GO:0060383)|positive regulation of helicase activity (GO:0051096)|positive regulation of telomerase activity (GO:0051973)|positive regulation of telomere maintenance via telomerase (GO:0032212)|telomere capping (GO:0016233)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DEAD/H-box RNA helicase binding (GO:0017151)|single-stranded telomeric DNA binding (GO:0043047)|telomerase inhibitor activity (GO:0010521)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(4)|liver(1)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47						CTTCTGCAACTGTGGTGTCAA	0.363													T|||	144	0.028754	0.1044	0.0086	5008	,	,		18834	0.0		0.0	False		,,,				2504	0.0				p.T628T	Esophageal Squamous(149;1032 1141 16047 36610 40540 42429 44687 51642)	Atlas-SNP	.											POT1_ENST00000357628,NS,carcinoma,-2,2	POT1	186	2	0			c.A1884C						PASS	.	T	,	448,3956	212.5+/-232.4	28,392,1782	192.0	166.0	175.0		1491,1884	-0.8	0.9	7	dbSNP_123	175	2,8592	2.2+/-6.3	0,2,4295	no	coding-synonymous,coding-synonymous	POT1	NM_001042594.1,NM_015450.2	,	28,394,6077	GG,GT,TT		0.0233,10.1726,3.4621	,	497/504,628/635	124464037	450,12548	2202	4297	6499	SO:0001819	synonymous_variant	25913	exon19			TGCAACTGTGGTG	AK022580	CCDS5793.1	7q31.33	2013-01-21	2013-01-21		ENSG00000128513	ENSG00000128513			17284	protein-coding gene	gene with protein product		606478	"""protection of telomeres 1 homolog (S. pombe)"""			11349150, 12391173	Standard	NR_003102		Approved	hPot1, DKFZp586D211	uc003vlm.3	Q9NUX5	OTTHUMG00000157194	ENST00000357628.3:c.1884A>C	7.37:g.124464037T>G		200.0	0.0	0		194.0	102.0	0.525773	NM_015450	O95018|Q5MJ36|Q9H662|Q9NW19|Q9UG95	Silent	SNP	ENST00000357628.3	37	CCDS5793.1	52	0.023809523809523808	49	0.09959349593495935	3	0.008287292817679558	0	0.0	0	0.0	T	9.568	1.120153	0.20877	0.101726	2.33E-4	ENSG00000128513	ENST00000436534	.	.	.	5.95	-0.844	0.10741	.	.	.	.	.	T	0.01940	0.0061	.	.	.	0.58432	D	0.999991	.	.	.	.	.	.	T	0.02917	-1.1094	4	.	.	.	0.0241	5.3043	0.15795	0.1235:0.3184:0.0:0.5581	rs17147565;rs17147565	.	.	.	R	127	.	.	S	-	1	0	POT1	124251273	0.779000	0.28652	0.918000	0.36340	0.990000	0.78478	0.164000	0.16542	-0.092000	0.12417	0.533000	0.62120	AGT	T|0.970;G|0.030	0.030	strong		0.363	POT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347861.1		
TGM3	7053	hgsc.bcm.edu	37	20	2291722	2291722	+	Missense_Mutation	SNP	A	A	C	rs6048066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:2291722A>C	ENST00000381458.5	+	4	550	c.487A>C	c.(487-489)Atc>Ctc	p.I163L		NM_003245.3	NP_003236.3	Q08188	TGM3_HUMAN	transglutaminase 3	163			I -> L (in dbSNP:rs6048066). {ECO:0000269|Ref.3}.		cell envelope organization (GO:0043163)|cellular protein modification process (GO:0006464)|hair follicle morphogenesis (GO:0031069)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein tetramerization (GO:0051262)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	calcium ion binding (GO:0005509)|catalytic activity (GO:0003824)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)|transferase activity, transferring acyl groups (GO:0016746)			breast(3)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(11)|lung(10)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	39					L-Glutamine(DB00130)	TGCCGGCATCATCTTTGTGGG	0.458													A|||	605	0.120807	0.4304	0.0519	5008	,	,		21488	0.0		0.0	False		,,,				2504	0.0				p.I163L		Atlas-SNP	.											.	TGM3	105	.	0			c.A487C						PASS	.	A	LEU/ILE	1503,2903	479.4+/-358.5	255,993,955	158.0	148.0	151.0		487	5.7	0.5	20	dbSNP_114	151	11,8589	7.1+/-27.0	0,11,4289	yes	missense	TGM3	NM_003245.3	5	255,1004,5244	CC,CA,AA		0.1279,34.1126,11.6408	possibly-damaging	163/694	2291722	1514,11492	2203	4300	6503	SO:0001583	missense	7053	exon4			GGCATCATCTTTG	L10386	CCDS33435.1	20q11.2	2013-05-02	2013-05-02		ENSG00000125780	ENSG00000125780	2.3.2.13	"""Transglutaminases"""	11779	protein-coding gene	gene with protein product	"""E polypeptide, protein-glutamine-gamma-glutamyltransferase"""	600238	"""transglutaminase 3 (E polypeptide, protein-glutamine-gamma-glutamyltransferase)"""			7851911, 9452468	Standard	NM_003245		Approved	TGE	uc002wfx.4	Q08188	OTTHUMG00000031690	ENST00000381458.5:c.487A>C	20.37:g.2291722A>C	ENSP00000370867:p.Ile163Leu	169.0	0.0	0		169.0	93.0	0.550296	NM_003245	A8K5N6|B2RCR6|D3DVX1|O95933|Q32ML9|Q32MM0	Missense_Mutation	SNP	ENST00000381458.5	37	CCDS33435.1	224	0.10256410256410256	203	0.41260162601626016	19	0.052486187845303865	0	0.0	2	0.002638522427440633	A	18.58	3.653803	0.67472	0.341126	0.001279	ENSG00000125780	ENST00000381458;ENST00000420960	D	0.85171	-1.95	5.71	5.71	0.89125	.	0.243134	0.42821	D	0.000652	T	0.00012	0.0000	M	0.81179	2.53	0.20403	P	0.9999028236	P	0.48407	0.91	D	0.80764	0.994	T	0.00000	-1.2810	9	0.72032	D	0.01	.	13.9352	0.64021	1.0:0.0:0.0:0.0	rs6048066;rs7272340;rs52800893;rs6048066	163	Q08188	TGM3_HUMAN	L	163	ENSP00000370867:I163L	ENSP00000370867:I163L	I	+	1	0	TGM3	2239722	0.997000	0.39634	0.532000	0.27989	0.430000	0.31655	3.089000	0.50183	2.184000	0.69523	0.454000	0.30748	ATC	A|0.871;C|0.129	0.129	strong		0.458	TGM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077579.2	NM_003245	
C3orf22	152065	hgsc.bcm.edu	37	3	126270923	126270923	+	Silent	SNP	G	G	C	rs34760151	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:126270923G>C	ENST00000318225.2	-	3	510	c.132C>G	c.(130-132)ccC>ccG	p.P44P		NM_152533.1	NP_689746.1	Q8N5N4	CC022_HUMAN	chromosome 3 open reading frame 22	44										large_intestine(1)|lung(3)|ovary(2)|prostate(1)	7				GBM - Glioblastoma multiforme(114;0.147)		TGACCTCCCAGGGCTGCAGGG	0.602													G|||	481	0.0960463	0.2685	0.0403	5008	,	,		18751	0.002		0.0288	False		,,,				2504	0.0685				p.P44P		Atlas-SNP	.											.	C3orf22	17	.	0			c.C132G						PASS	.	G		894,3512	348.0+/-309.7	98,698,1407	83.0	77.0	79.0		132	-0.0	0.0	3	dbSNP_126	79	294,8306	108.0+/-168.7	6,282,4012	no	coding-synonymous	C3orf22	NM_152533.1		104,980,5419	CC,CG,GG		3.4186,20.2905,9.1342		44/142	126270923	1188,11818	2203	4300	6503	SO:0001819	synonymous_variant	152065	exon3			CTCCCAGGGCTGC		CCDS3040.1	3q21.3	2011-09-30			ENSG00000180697	ENSG00000180697			28534	protein-coding gene	gene with protein product						12477932	Standard	NM_152533		Approved	MGC34728	uc003ejb.3	Q8N5N4	OTTHUMG00000162731	ENST00000318225.2:c.132C>G	3.37:g.126270923G>C		83.0	0.0	0		106.0	50.0	0.471698	NM_152533	B3KUS9	Silent	SNP	ENST00000318225.2	37	CCDS3040.1																																																																																			G|0.912;C|0.088	0.088	strong		0.602	C3orf22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370231.2	NM_152533	
PSG6	5675	hgsc.bcm.edu	37	19	43420290	43420290	+	Silent	SNP	A	A	G	rs76022539	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43420290A>G	ENST00000292125.2	-	2	458	c.414T>C	c.(412-414)acT>acC	p.T138T	PSG6_ENST00000601833.1_Silent_p.T67T|PSG6_ENST00000187910.2_Silent_p.T138T|PSG6_ENST00000402603.4_Silent_p.T138T	NM_002782.4	NP_002773.1	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6	138	Ig-like V-type.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(19)|ovary(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	44		Prostate(69;0.00899)				ATAAGGTGACAGTGAAATATC	0.512													.|||	179	0.0357428	0.1225	0.0101	5008	,	,		19988	0.0089		0.0	False		,,,				2504	0.001				p.T138T		Atlas-SNP	.											.	PSG6	89	.	0			c.T414C						PASS	.	G	,	501,3901		35,431,1735	253.0	220.0	231.0		414,414	0.1	0.0	19	dbSNP_131	231	4,8594		0,4,4295	no	coding-synonymous,coding-synonymous	PSG6	NM_001031850.2,NM_002782.3	,	35,435,6030	GG,GA,AA		0.0465,11.3812,3.8846	,	138/425,138/436	43420290	505,12495	2201	4299	6500	SO:0001819	synonymous_variant	5675	exon2			GGTGACAGTGAAA		CCDS12613.1, CCDS33038.1	19q13.2	2013-01-29			ENSG00000170848	ENSG00000170848		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9523	protein-coding gene	gene with protein product		176395				1690992	Standard	NM_002782		Approved			Q00889	OTTHUMG00000151127	ENST00000292125.2:c.414T>C	19.37:g.43420290A>G		207.0	0.0	0		176.0	89.0	0.505682	NM_001031850	O75244|Q15224|Q15235|Q549K1	Silent	SNP	ENST00000292125.2	37	CCDS12613.1																																																																																			A|0.961;G|0.039	0.039	strong		0.512	PSG6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321436.1	NM_002782	
KCTD7	154881	hgsc.bcm.edu	37	7	66094184	66094184	+	Silent	SNP	C	C	T	rs587780370		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:66094184C>T	ENST00000275532.3	+	1	317	c.133C>T	c.(133-135)Ctg>Ttg	p.L45L	KCTD7_ENST00000443322.1_Silent_p.L45L	NM_001167961.2|NM_153033.4	NP_001161433.1|NP_694578.1	Q96MP8	KCTD7_HUMAN	potassium channel tetramerization domain containing 7	45					cell death (GO:0008219)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|urinary_tract(1)	16						GCTGCCCCTGCTGCCACAGGA	0.776																																					p.L45L		Atlas-SNP	.											KCTD7,brain,glioma,-2,1	KCTD7	26	1	0			c.C133T						scavenged	.																																			SO:0001819	synonymous_variant	154881	exon1			CCCCTGCTGCCAC	AK056631	CCDS5534.1, CCDS55117.1	7q11.21	2014-09-17	2013-06-20		ENSG00000243335	ENSG00000243335			21957	protein-coding gene	gene with protein product		611725	"""potassium channel tetramerisation domain containing 7"""			12477932	Standard	NM_001167961		Approved	FLJ32069, EPM3, CLN14	uc003tve.3	Q96MP8	OTTHUMG00000129543	ENST00000275532.3:c.133C>T	7.37:g.66094184C>T		2.0	0.0	0		8.0	5.0	0.625	NM_001167961	A4D2M4|Q8IVR0	Silent	SNP	ENST00000275532.3	37	CCDS5534.1																																																																																			.	.	none		0.776	KCTD7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251733.2	NM_153033	
SLCO2A1	6578	hgsc.bcm.edu	37	3	133653566	133653566	+	Silent	SNP	G	G	A	rs72978391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:133653566G>A	ENST00000310926.4	-	14	2196	c.1923C>T	c.(1921-1923)ggC>ggT	p.G641G	SLCO2A1_ENST00000493729.1_Silent_p.G565G	NM_005630.2	NP_005621.2	Q92959	SO2A1_HUMAN	solute carrier organic anion transporter family, member 2A1	641					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)	GTCAGATGAGGCCTGCCGCCT	0.557													G|||	160	0.0319489	0.112	0.0144	5008	,	,		18588	0.0		0.002	False		,,,				2504	0.0				p.G641G		Atlas-SNP	.											.	SLCO2A1	72	.	0			c.C1923T						PASS	.	G		407,3999	201.8+/-224.7	15,377,1811	121.0	103.0	109.0		1923	2.6	0.7	3	dbSNP_130	109	7,8593	4.3+/-15.6	0,7,4293	no	coding-synonymous	SLCO2A1	NM_005630.2		15,384,6104	AA,AG,GG		0.0814,9.2374,3.1831		641/644	133653566	414,12592	2203	4300	6503	SO:0001819	synonymous_variant	6578	exon14			GATGAGGCCTGCC		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.1923C>T	3.37:g.133653566G>A		49.0	0.0	0		74.0	32.0	0.432432	NM_005630	Q86V98|Q8IUN2	Silent	SNP	ENST00000310926.4	37	CCDS3084.1																																																																																			G|0.970;A|0.030	0.030	strong		0.557	SLCO2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357131.1	NM_005630	
TAT	6898	hgsc.bcm.edu	37	16	71602665	71602665	+	Silent	SNP	C	C	T	rs16973331	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:71602665C>T	ENST00000355962.4	-	11	1306	c.1173G>A	c.(1171-1173)gaG>gaA	p.E391E	RP11-432I5.1_ENST00000561529.1_RNA	NM_000353.2	NP_000344.1	P17735	ATTY_HUMAN	tyrosine aminotransferase	391					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate metabolic process (GO:0006536)|L-phenylalanine catabolic process (GO:0006559)|response to glucocorticoid (GO:0051384)|response to mercury ion (GO:0046689)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	amino acid binding (GO:0016597)|L-phenylalanine:2-oxoglutarate aminotransferase activity (GO:0080130)|L-tyrosine:2-oxoglutarate aminotransferase activity (GO:0004838)|pyridoxal phosphate binding (GO:0030170)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(3)	29		Ovarian(137;0.125)		Kidney(780;0.0157)	L-Phenylalanine(DB00120)|L-Tyrosine(DB00135)	GCTCCGTGAACTCCACATCGT	0.522													C|||	189	0.0377396	0.1377	0.0101	5008	,	,		16730	0.0		0.0	False		,,,				2504	0.0				p.E391E	Melanoma(198;542 2142 10292 21661 50033)|Esophageal Squamous(48;487 1013 5572 44395 52594)	Atlas-SNP	.											.	TAT	80	.	0			c.G1173A						PASS	.	C		561,3835	250.9+/-257.8	44,473,1681	84.0	70.0	75.0		1173	-0.3	1.0	16	dbSNP_123	75	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous	TAT	NM_000353.2		44,478,5976	TT,TC,CC		0.0581,12.7616,4.3552		391/455	71602665	566,12430	2198	4300	6498	SO:0001819	synonymous_variant	6898	exon11			CGTGAACTCCACA		CCDS10903.1	16q22.1	2012-10-02			ENSG00000198650	ENSG00000198650	2.6.1.5		11573	protein-coding gene	gene with protein product		613018					Standard	NM_000353		Approved		uc002fap.2	P17735	OTTHUMG00000137590	ENST00000355962.4:c.1173G>A	16.37:g.71602665C>T		118.0	0.0	0		134.0	63.0	0.470149	NM_000353	B2R8I1|D3DWS2	Silent	SNP	ENST00000355962.4	37	CCDS10903.1																																																																																			C|0.958;T|0.042	0.042	strong		0.522	TAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268989.1		
SERPINB7	8710	hgsc.bcm.edu	37	18	61471593	61471593	+	Silent	SNP	A	A	G	rs11873045	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61471593A>G	ENST00000398019.2	+	8	1192	c.867A>G	c.(865-867)caA>caG	p.Q289Q	SERPINB7_ENST00000540675.1_Silent_p.Q272Q|SERPINB7_ENST00000336429.2_Silent_p.Q289Q|SERPINB7_ENST00000546027.1_Silent_p.Q289Q	NM_003784.3	NP_003775.1	O75635	SPB7_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 7	289					negative regulation of endopeptidase activity (GO:0010951)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of glomerular mesangial cell proliferation (GO:0072126)|positive regulation of platelet-derived growth factor production (GO:0090362)|positive regulation of transforming growth factor beta1 production (GO:0032914)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	serine-type endopeptidase inhibitor activity (GO:0004867)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(3)|lung(14)|prostate(1)|skin(3)	27		Esophageal squamous(42;0.129)				AAATGAAACAATATTTGAGAG	0.398													A|||	252	0.0503195	0.18	0.0173	5008	,	,		18557	0.0		0.002	False		,,,				2504	0.0				p.Q289Q		Atlas-SNP	.											.	SERPINB7	66	.	0			c.A867G						PASS	.	A	,	699,3707	288.4+/-279.8	52,595,1556	49.0	51.0	50.0		867,867	-1.4	0.0	18	dbSNP_120	50	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous,coding-synonymous	SERPINB7	NM_001040147.1,NM_003784.2	,	52,601,5850	GG,GA,AA		0.0698,15.8647,5.4206	,	289/381,289/381	61471593	705,12301	2203	4300	6503	SO:0001819	synonymous_variant	8710	exon8			GAAACAATATTTG	AF027866	CCDS11988.1, CCDS58633.1	18q21.33	2014-02-18	2005-08-18		ENSG00000166396	ENSG00000166396		"""Serine (or cysteine) peptidase inhibitors"""	13902	protein-coding gene	gene with protein product		603357	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 7"""			24172014	Standard	NM_003784		Approved	MEGSIN	uc002ljl.4	O75635	OTTHUMG00000060591	ENST00000398019.2:c.867A>G	18.37:g.61471593A>G		44.0	0.0	0		60.0	35.0	0.583333	NM_001261830	B4DUW8|F5GZC0|Q1ED45|Q3KPG4	Silent	SNP	ENST00000398019.2	37	CCDS11988.1																																																																																			A|0.943;G|0.057	0.057	strong		0.398	SERPINB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134007.1	NM_003784	
OR2J3	442186	hgsc.bcm.edu	37	6	29080386	29080386	+	Missense_Mutation	SNP	T	T	C	rs79293918	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29080386T>C	ENST00000377169.1	+	1	719	c.719T>C	c.(718-720)gTg>gCg	p.V240A		NM_001005216.2	NP_001005216.2	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J, member 3	240						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(5)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24						CTTCAGAAAGTGTTTGGAACA	0.448													T|||	116	0.0231629	0.0651	0.0101	5008	,	,		22544	0.0079		0.0119	False		,,,				2504	0.0031				p.V240A		Atlas-SNP	.											.	OR2J3	53	.	0			c.T719C						PASS	.	T	ALA/VAL	185,2355		4,177,1089	118.0	123.0	121.0		719	1.6	0.9	6	dbSNP_131	121	26,5120		0,26,2547	yes	missense	OR2J3	NM_001005216.2	64	4,203,3636	CC,CT,TT		0.5052,7.2835,2.7453	possibly-damaging	240/312	29080386	211,7475	1270	2573	3843	SO:0001583	missense	442186	exon1			AGAAAGTGTTTGG		CCDS43433.1	6p22.2-p21.31	2012-08-09			ENSG00000204701	ENSG00000204701		"""GPCR / Class A : Olfactory receptors"""	8261	protein-coding gene	gene with protein product		615016					Standard	NM_001005216		Approved	OR6-6	uc011dll.2	O76001	OTTHUMG00000031092	ENST00000377169.1:c.719T>C	6.37:g.29080386T>C	ENSP00000366374:p.Val240Ala	386.0	0.0	0		370.0	177.0	0.478378	NM_001005216	B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Missense_Mutation	SNP	ENST00000377169.1	37	CCDS43433.1	54	0.024725274725274724	32	0.06504065040650407	6	0.016574585635359115	6	0.01048951048951049	10	0.013192612137203167	T	0.005	-2.139654	0.00335	0.072835	0.005052	ENSG00000204701	ENST00000377169	T	0.00009	9.47	2.78	1.63	0.23807	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.00123	-2.06	0.40080	D	0.976121	B	0.09022	0.002	B	0.13407	0.009	T	0.00849	-1.1541	9	0.02654	T	1	.	3.5019	0.07676	0.0:0.4818:0.0:0.5182	.	240	O76001	OR2J3_HUMAN	A	240	ENSP00000366374:V240A	ENSP00000366374:V240A	V	+	2	0	OR2J3	29188365	0.981000	0.34729	0.937000	0.37676	0.020000	0.10135	1.790000	0.38734	1.268000	0.44264	0.358000	0.22013	GTG	T|0.981;C|0.019	0.019	strong		0.448	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2		
KREMEN2	79412	hgsc.bcm.edu	37	16	3016716	3016716	+	Missense_Mutation	SNP	C	C	G	rs111311295	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3016716C>G	ENST00000303746.5	+	5	1137	c.560C>G	c.(559-561)cCc>cGc	p.P187R	PAQR4_ENST00000572687.1_5'Flank|PKMYT1_ENST00000571102.1_5'Flank|KREMEN2_ENST00000575769.1_Missense_Mutation_p.P187R|PAQR4_ENST00000576565.1_5'Flank|KREMEN2_ENST00000571007.1_Intron|PAQR4_ENST00000293978.8_5'Flank|KREMEN2_ENST00000572045.1_Missense_Mutation_p.P187R|KREMEN2_ENST00000575885.1_Intron|KREMEN2_ENST00000319500.6_Missense_Mutation_p.P187R|PAQR4_ENST00000318782.8_5'Flank			Q8NCW0	KREM2_HUMAN	kringle containing transmembrane protein 2	187	WSC. {ECO:0000255|PROSITE- ProRule:PRU00558, ECO:0000305}.			Missing (in Ref. 2; BAC11365). {ECO:0000305}.	Wnt signaling pathway (GO:0016055)	integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(1)|large_intestine(1)	4						CGCCTGGCCCCCGCCACCGAC	0.692																																					p.P187R		Atlas-SNP	.											.	KREMEN2	13	.	0			c.C560G						PASS	.	C	ARG/PRO,ARG/PRO	14,4368		0,14,2177	19.0	24.0	22.0		560,560	2.9	0.0	16	dbSNP_132	22	0,8584		0,0,4292	yes	missense,missense	KREMEN2	NM_024507.2,NM_172229.1	103,103	0,14,6469	GG,GC,CC		0.0,0.3195,0.108	probably-damaging,probably-damaging	187/421,187/463	3016716	14,12952	2191	4292	6483	SO:0001583	missense	79412	exon5			TGGCCCCCGCCAC	BC003533	CCDS10483.1, CCDS10484.1, CCDS58412.1, CCDS58413.1	16p13.11	2008-08-04			ENSG00000131650	ENSG00000131650			18797	protein-coding gene	gene with protein product		609899				12050670	Standard	NM_172229		Approved	MGC10791, KRM2	uc002csg.3	Q8NCW0	OTTHUMG00000128976	ENST00000303746.5:c.560C>G	16.37:g.3016716C>G	ENSP00000304422:p.Pro187Arg	120.0	0.0	0		124.0	60.0	0.483871	NM_024507	B4DXF6|I3L2S2|Q8N2J4|Q8NCW1|Q96GL8|Q9BTP9	Missense_Mutation	SNP	ENST00000303746.5	37	CCDS10483.1	.	.	.	.	.	.	.	.	.	.	C	14.59	2.579580	0.46006	0.003195	0.0	ENSG00000131650	ENST00000303746;ENST00000319500	T;T	0.54071	0.59;0.59	4.91	2.92	0.33932	Carbohydrate-binding WSC (2);	0.151142	0.30732	N	0.008999	T	0.57242	0.2040	M	0.78285	2.405	0.30519	N	0.768604	P;P;P;P	0.37101	0.527;0.527;0.527;0.582	B;B;B;P	0.46299	0.377;0.377;0.377;0.511	T	0.60151	-0.7319	10	0.49607	T	0.09	.	5.5586	0.17131	0.0:0.6523:0.1625:0.1852	.	187;187;187;187	Q8NCW0-2;Q8NCW0-4;Q8NCW0-3;Q8NCW0	.;.;.;KREM2_HUMAN	R	187	ENSP00000304422:P187R;ENSP00000322079:P187R	ENSP00000304422:P187R	P	+	2	0	KREMEN2	2956717	0.083000	0.21467	0.035000	0.18076	0.983000	0.72400	1.656000	0.37355	1.066000	0.40716	0.456000	0.33151	CCC	C|0.999;G|0.001	0.001	strong		0.692	KREMEN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250964.2	NM_145347	
APBA3	9546	hgsc.bcm.edu	37	19	3760056	3760056	+	Silent	SNP	G	G	A	rs61729800	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3760056G>A	ENST00000316757.3	-	2	407	c.207C>T	c.(205-207)ggC>ggT	p.G69G	MRPL54_ENST00000330133.4_5'Flank	NM_004886.3	NP_004877.1	O96018	APBA3_HUMAN	amyloid beta (A4) precursor protein-binding, family A, member 3	69					in utero embryonic development (GO:0001701)|negative regulation of catalytic activity (GO:0043086)|protein transport (GO:0015031)|regulation of gene expression (GO:0010468)|synaptic transmission (GO:0007268)	perinuclear region of cytoplasm (GO:0048471)	beta-amyloid binding (GO:0001540)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)			endometrium(1)|large_intestine(1)|skin(1)	3		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00467)|STAD - Stomach adenocarcinoma(1328;0.18)		CCACCAGATCGCCTGGCAGAG	0.637													G|||	145	0.0289537	0.1067	0.0058	5008	,	,		16441	0.0		0.0	False		,,,				2504	0.0				p.G69G		Atlas-SNP	.											APBA3,colon,carcinoma,0,1	APBA3	28	1	0			c.C207T						PASS	.	G		388,4014	187.4+/-214.1	19,350,1832	46.0	47.0	47.0		207	-8.0	0.0	19	dbSNP_129	47	5,8595	2.2+/-6.3	0,5,4295	no	coding-synonymous	APBA3	NM_004886.3		19,355,6127	AA,AG,GG		0.0581,8.8142,3.0226		69/576	3760056	393,12609	2201	4300	6501	SO:0001819	synonymous_variant	9546	exon2			CAGATCGCCTGGC	AB021638	CCDS12110.1	19p13.3	2008-07-18	2008-07-18			ENSG00000011132			580	protein-coding gene	gene with protein product	"""X11-like 2"""	604262				10049767	Standard	NM_004886		Approved	X11L2, mint3	uc002lyp.1	O96018		ENST00000316757.3:c.207C>T	19.37:g.3760056G>A		115.0	0.0	0		100.0	42.0	0.42	NM_004886	O60483|Q9UPZ2	Silent	SNP	ENST00000316757.3	37	CCDS12110.1																																																																																			G|0.973;A|0.027	0.027	strong		0.637	APBA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453634.2		
CEP192	55125	hgsc.bcm.edu	37	18	13040858	13040858	+	Silent	SNP	A	A	G	rs145309087	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:13040858A>G	ENST00000325971.8	+	12	1644	c.51A>G	c.(49-51)ccA>ccG	p.P17P	CEP192_ENST00000430049.2_Silent_p.P138P|CEP192_ENST00000506447.1_Silent_p.P613P			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	17					centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						TTAGATCACCAGAGAAGAGAG	0.299													A|||	62	0.0123802	0.0439	0.0058	5008	,	,		17505	0.0		0.0	False		,,,				2504	0.0				p.P613P		Atlas-SNP	.											.	CEP192	340	.	0			c.A1839G						PASS	.	A		158,4248	105.2+/-143.6	1,156,2046	67.0	70.0	69.0		1839	0.3	1.0	18	dbSNP_134	69	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous	CEP192	NM_032142.3		1,157,6342	GG,GA,AA		0.0116,3.586,1.2231		613/2538	13040858	159,12841	2203	4297	6500	SO:0001819	synonymous_variant	55125	exon14			ATCACCAGAGAAG	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.51A>G	18.37:g.13040858A>G		169.0	0.0	0		171.0	90.0	0.526316	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Silent	SNP	ENST00000325971.8	37																																																																																				A|0.987;G|0.013	0.013	strong		0.299	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
RNF17	56163	hgsc.bcm.edu	37	13	25374636	25374636	+	Silent	SNP	A	A	G	rs35957316	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:25374636A>G	ENST00000255324.5	+	13	1774	c.1722A>G	c.(1720-1722)caA>caG	p.Q574Q	RNF17_ENST00000381921.1_Silent_p.Q574Q|RNF17_ENST00000255325.6_Silent_p.Q574Q	NM_001184993.1|NM_031277.2	NP_001171922.1|NP_112567.2	Q9BXT8	RNF17_HUMAN	ring finger protein 17	574					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on ester bonds (GO:0016788)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(15)|ovary(1)|prostate(3)|skin(6)	36		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0114)|OV - Ovarian serous cystadenocarcinoma(117;0.0311)|Epithelial(112;0.0524)		CATTAGCACAACCATGCTCAT	0.358													A|||	244	0.048722	0.1755	0.0159	5008	,	,		18152	0.0		0.001	False		,,,				2504	0.0				p.Q574Q		Atlas-SNP	.											.	RNF17	259	.	0			c.A1722G						PASS	.	A	,	649,3757	277.8+/-273.9	46,557,1600	125.0	121.0	123.0		1722,1722	0.6	0.9	13	dbSNP_126	123	12,8588	8.4+/-32.0	0,12,4288	no	coding-synonymous,coding-synonymous	RNF17	NM_001184993.1,NM_031277.2	,	46,569,5888	GG,GA,AA		0.1395,14.7299,5.0823	,	574/1620,574/1624	25374636	661,12345	2203	4300	6503	SO:0001819	synonymous_variant	56163	exon13			AGCACAACCATGC	AF285602, AK001907	CCDS9308.2	13q12.13	2013-01-23			ENSG00000132972	ENSG00000132972		"""RING-type (C3HC4) zinc fingers"", ""Tudor domain containing"""	10060	protein-coding gene	gene with protein product	"""spermatogenesis associated 23"""	605793	"""tudor domain containing 4"""	TDRD4		11279525	Standard	NM_001184993		Approved	Mmip-2, SPATA23, FLJ11045	uc001upr.3	Q9BXT8	OTTHUMG00000016589	ENST00000255324.5:c.1722A>G	13.37:g.25374636A>G		80.0	0.0	0		87.0	46.0	0.528736	NM_001184993	Q5T2J9|Q6P1W3|Q9BXT7|Q9NUY9	Silent	SNP	ENST00000255324.5	37	CCDS9308.2																																																																																			A|0.952;G|0.048	0.048	strong		0.358	RNF17-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044217.1	NM_031994	
FBL	2091	hgsc.bcm.edu	37	19	40329747	40329747	+	Silent	SNP	C	C	T	rs150137200	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40329747C>T	ENST00000221801.3	-	5	590	c.477G>A	c.(475-477)ccG>ccA	p.P159P	FBL_ENST00000593503.1_5'Flank	NM_001436.3	NP_001427.2	P22087	FBRL_HUMAN	fibrillarin	159					histone glutamine methylation (GO:1990258)|osteoblast differentiation (GO:0001649)|rRNA processing (GO:0006364)|snoRNA metabolic process (GO:0016074)|tRNA processing (GO:0008033)	box C/D snoRNP complex (GO:0031428)|Cajal body (GO:0015030)|extracellular vesicular exosome (GO:0070062)|granular component (GO:0001652)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone-glutamine methyltransferase activity (GO:1990259)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)	9	all_cancers(60;5.79e-06)|all_lung(34;5.2e-08)|Lung NSC(34;6.14e-08)|Ovarian(47;0.06)	Renal(1328;0.000518)|Hepatocellular(1079;0.0893)	Epithelial(26;5.74e-25)|OV - Ovarian serous cystadenocarcinoma(5;3.13e-24)|all cancers(26;8.59e-23)	GBM - Glioblastoma multiforme(1328;0.000826)|STAD - Stomach adenocarcinoma(1328;0.138)		CCTTAGCCCCCGGTTTGATGT	0.577													C|||	12	0.00239617	0.0076	0.0	5008	,	,		20414	0.0		0.0	False		,,,				2504	0.002				p.P159P		Atlas-SNP	.											.	FBL	37	.	0			c.G477A						PASS	.	C		35,4371	40.0+/-72.8	0,35,2168	143.0	128.0	133.0		477	-9.6	0.9	19	dbSNP_134	133	0,8600		0,0,4300	no	coding-synonymous	FBL	NM_001436.3		0,35,6468	TT,TC,CC		0.0,0.7944,0.2691		159/322	40329747	35,12971	2203	4300	6503	SO:0001819	synonymous_variant	2091	exon5			AGCCCCCGGTTTG	AC005393	CCDS12545.1	19q13.1	2010-02-17			ENSG00000105202	ENSG00000105202			3599	protein-coding gene	gene with protein product		134795				1846968, 2026646	Standard	NM_001436		Approved	RNU3IP1, FLRN, FIB	uc002omn.3	P22087		ENST00000221801.3:c.477G>A	19.37:g.40329747C>T		180.0	0.0	0		183.0	81.0	0.442623	NM_001436	B5BUE8|O75259|Q6IAT5|Q9UPI6	Silent	SNP	ENST00000221801.3	37	CCDS12545.1																																																																																			C|0.996;T|0.004	0.004	strong		0.577	FBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462509.4	NM_001436	
CDX1	1044	hgsc.bcm.edu	37	5	149562398	149562398	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149562398G>T	ENST00000231656.8	+	2	595	c.513G>T	c.(511-513)aaG>aaT	p.K171N		NM_001804.2	NP_001795.2	P47902	CDX1_HUMAN	caudal type homeobox 1	171					anterior/posterior pattern specification (GO:0009952)|bone morphogenesis (GO:0060349)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleus (GO:0005634)	RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)			central_nervous_system(1)|kidney(2)|lung(1)|ovary(1)	5		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			AGCTGGAGAAGGAGTTTCATT	0.552																																					p.K171N		Atlas-SNP	.											.	CDX1	11	.	0			c.G513T						PASS	.						139.0	140.0	140.0					5																	149562398		2203	4300	6503	SO:0001583	missense	1044	exon2			GGAGAAGGAGTTT	U51095	CCDS4304.1	5q32	2012-03-09	2007-07-09		ENSG00000113722	ENSG00000113722		"""Homeoboxes / ANTP class : HOXL subclass"""	1805	protein-coding gene	gene with protein product		600746	"""caudal type homeo box transcription factor 1"""			8530027	Standard	NM_001804		Approved		uc003lrq.3	P47902	OTTHUMG00000169772	ENST00000231656.8:c.513G>T	5.37:g.149562398G>T	ENSP00000231656:p.Lys171Asn	124.0	0.0	0		160.0	71.0	0.44375	NM_001804	Q4VAU4|Q9NYK8	Missense_Mutation	SNP	ENST00000231656.8	37	CCDS4304.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.156375	0.78114	.	.	ENSG00000113722	ENST00000231656;ENST00000377812	D	0.96491	-4.03	5.87	3.03	0.35002	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.110690	0.64402	D	0.000012	D	0.97170	0.9075	M	0.65677	2.01	0.80722	D	1	D	0.56287	0.975	D	0.67900	0.954	D	0.96399	0.9295	10	0.87932	D	0	-13.0587	11.532	0.50616	0.1832:0.0:0.8168:0.0	.	171	P47902	CDX1_HUMAN	N	171;60	ENSP00000231656:K171N	ENSP00000231656:K171N	K	+	3	2	CDX1	149542591	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.447000	0.52936	0.342000	0.23796	-0.345000	0.07892	AAG	.	.	none		0.552	CDX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252328.7	NM_001804	
DIAPH2	1730	hgsc.bcm.edu	37	X	96354707	96354707	+	Silent	SNP	T	T	C	rs20387	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:96354707T>C	ENST00000324765.8	+	20	2609	c.2262T>C	c.(2260-2262)caT>caC	p.H754H	DIAPH2_ENST00000373061.3_Silent_p.H754H|DIAPH2_ENST00000373054.4_Silent_p.H750H|DIAPH2_ENST00000373049.4_Silent_p.H754H|DIAPH2_ENST00000355827.4_Silent_p.H754H			O60879	DIAP2_HUMAN	diaphanous-related formin 2	754	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				actin filament polymerization (GO:0030041)|cytokinesis (GO:0000910)|female gamete generation (GO:0007292)|multicellular organismal development (GO:0007275)|oogenesis (GO:0048477)	endosome (GO:0005768)	receptor binding (GO:0005102)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	51						TTGTGAAACATCTTCCTGAGC	0.308													T|||	17	0.00450331	0.0121	0.0014	3775	,	,		10804	0.0		0.0	False		,,,				2504	0.0				p.H754H		Atlas-SNP	.											.	DIAPH2	148	.	0			c.T2262C						PASS	.	T	,	74,3761		0,62,12,1570,559	84.0	69.0	74.0		2262,2262	0.1	0.9	X	dbSNP_67	74	1,6727		0,0,1,2428,1871	no	coding-synonymous,coding-synonymous	DIAPH2	NM_006729.4,NM_007309.3	,	0,62,13,3998,2430	CC,CT,C,TT,T		0.0149,1.9296,0.71	,	754/1102,754/1097	96354707	75,10488	2203	4300	6503	SO:0001819	synonymous_variant	1730	exon20			GAAACATCTTCCT	Y15909	CCDS14467.1, CCDS14468.1	Xq22	2013-05-24	2013-05-24		ENSG00000147202	ENSG00000147202			2877	protein-coding gene	gene with protein product		300108	"""diaphanous (Drosophila, homolog) 2"", ""diaphanous homolog 2 (Drosophila)"""			9360932	Standard	NM_006729		Approved	POF, DIA, POF2, DIA2	uc004efu.4	O60879	OTTHUMG00000022689	ENST00000324765.8:c.2262T>C	X.37:g.96354707T>C		124.0	0.0	0		142.0	75.0	0.528169	NM_007309	A6NG19|O60878|Q8WX06|Q8WX48|Q9UJL2	Silent	SNP	ENST00000324765.8	37	CCDS14467.1																																																																																			T|0.993;C|0.007	0.007	strong		0.308	DIAPH2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058871.2	NM_006729, NM_007309	
C1orf177	163747	hgsc.bcm.edu	37	1	55277553	55277553	+	Silent	SNP	C	C	T	rs61691036	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55277553C>T	ENST00000371273.3	+	5	582	c.567C>T	c.(565-567)tcC>tcT	p.S189S	C1orf177_ENST00000358193.3_Silent_p.S189S	NM_001110533.1	NP_001104003	Q3ZCV2	CA177_HUMAN	chromosome 1 open reading frame 177	189										breast(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(6)|prostate(2)	17						GGTCTCATTCCGAGGGCCTCA	0.617													C|||	73	0.0145767	0.0522	0.0029	5008	,	,		17175	0.0		0.0	False		,,,				2504	0.002				p.S189S		Atlas-SNP	.											.	C1orf177	36	.	0			c.C567T						PASS	.	C	,	248,4158	145.0+/-179.8	10,228,1965	75.0	70.0	71.0		567,567	-0.4	0.9	1	dbSNP_129	71	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	C1orf177	NM_001110533.1,NM_152607.2	,	10,230,6263	TT,TC,CC		0.0233,5.6287,1.9222	,	189/419,189/415	55277553	250,12756	2203	4300	6503	SO:0001819	synonymous_variant	163747	exon5			TCATTCCGAGGGC	AK097520	CCDS599.1, CCDS44153.1	1p32.3	2012-07-25			ENSG00000162398	ENSG00000162398			26854	protein-coding gene	gene with protein product							Standard	NM_152607		Approved	FLJ40201	uc001cyb.4	Q3ZCV2	OTTHUMG00000009986	ENST00000371273.3:c.567C>T	1.37:g.55277553C>T		142.0	0.0	0		214.0	112.0	0.523364	NM_001110533	B7WPL2|Q8N7Y9	Silent	SNP	ENST00000371273.3	37	CCDS44153.1																																																																																			C|0.979;T|0.021	0.021	strong		0.617	C1orf177-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000027674.1	NM_152607	
RYR2	6262	hgsc.bcm.edu	37	1	237620034	237620034	+	Splice_Site	SNP	G	G	A	rs78281932	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:237620034G>A	ENST00000366574.2	+	16	1928	c.1611G>A	c.(1609-1611)ctG>ctA	p.L537L	RYR2_ENST00000360064.6_Splice_Site_p.L535L|RYR2_ENST00000542537.1_Splice_Site_p.L521L	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	537					BMP signaling pathway (GO:0030509)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|calcium-mediated signaling (GO:0019722)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle contraction (GO:0060048)|cardiac muscle hypertrophy (GO:0003300)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular calcium ion homeostasis (GO:0006874)|cellular response to caffeine (GO:0071313)|cellular response to epinephrine stimulus (GO:0071872)|cytosolic calcium ion homeostasis (GO:0051480)|detection of calcium ion (GO:0005513)|embryonic heart tube morphogenesis (GO:0003143)|establishment of protein localization to endoplasmic reticulum (GO:0072599)|ion transmembrane transport (GO:0034220)|left ventricular cardiac muscle tissue morphogenesis (GO:0003220)|positive regulation of calcium-transporting ATPase activity (GO:1901896)|positive regulation of heart rate (GO:0010460)|positive regulation of ryanodine-sensitive calcium-release channel activity by adrenergic receptor signaling pathway involved in positive regulation of cardiac muscle contraction (GO:0086094)|positive regulation of sequestering of calcium ion (GO:0051284)|Purkinje myocyte to ventricular cardiac muscle cell signaling (GO:0086029)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|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)|response to redox state (GO:0051775)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|type B pancreatic cell apoptotic process (GO:0097050)|ventricular cardiac muscle cell action potential (GO:0086005)	calcium channel complex (GO:0034704)|extracellular vesicular exosome (GO:0070062)|junctional sarcoplasmic reticulum membrane (GO:0014701)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|Z disc (GO:0030018)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|intracellular ligand-gated calcium channel activity (GO:0005218)|ion channel binding (GO:0044325)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|suramin binding (GO:0043924)			NS(4)|breast(8)|central_nervous_system(11)|cervix(2)|endometrium(39)|haematopoietic_and_lymphoid_tissue(5)|kidney(17)|large_intestine(83)|liver(4)|lung(353)|ovary(18)|pancreas(5)|prostate(12)|skin(8)|stomach(1)|upper_aerodigestive_tract(12)|urinary_tract(4)	586	Ovarian(103;0.103)	all_cancers(173;0.000368)|Melanoma(53;0.0179)|all_epithelial(177;0.0225)	OV - Ovarian serous cystadenocarcinoma(106;0.00606)			ATGAGTTGCTGGGTAAGAAGC	0.433													G|||	300	0.0599042	0.2148	0.0202	5008	,	,		18734	0.0		0.001	False		,,,				2504	0.001				p.L537L		Atlas-SNP	.											.	RYR2	1273	.	0			c.G1611A						PASS	.	G		683,3123		48,587,1268	158.0	154.0	155.0		1611	-3.0	1.0	1	dbSNP_131	155	10,8242		0,10,4116	yes	coding-synonymous-near-splice	RYR2	NM_001035.2		48,597,5384	AA,AG,GG		0.1212,17.9453,5.7472		537/4968	237620034	693,11365	1903	4126	6029	SO:0001630	splice_region_variant	6262	exon16			GTTGCTGGGTAAG	X91869	CCDS55691.1	1q43	2014-09-17			ENSG00000198626	ENSG00000198626		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10484	protein-coding gene	gene with protein product		180902	"""arrhythmogenic right ventricular dysplasia 2"""	ARVD2		2380170, 8406504, 11159936	Standard	NM_001035		Approved	ARVC2, VTSIP	uc001hyl.1	Q92736	OTTHUMG00000039543	ENST00000366574.2:c.1612+1G>A	1.37:g.237620034G>A		105.0	0.0	0		107.0	54.0	0.504673	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	37	CCDS55691.1																																																																																			G|0.960;A|0.040	0.040	strong		0.433	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	Silent
SARS2	54938	hgsc.bcm.edu	37	19	39410465	39410465	+	Silent	SNP	G	G	A	rs35389151	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39410465G>A	ENST00000221431.6	-	7	855	c.696C>T	c.(694-696)cgC>cgT	p.R232R	SARS2_ENST00000600042.1_Silent_p.R234R|SARS2_ENST00000448145.2_Silent_p.R232R|SARS2_ENST00000430193.3_Silent_p.R232R|SARS2_ENST00000594171.1_Silent_p.R42R|SARS2_ENST00000598831.1_5'Flank|CTC-360G5.8_ENST00000599996.1_Missense_Mutation_p.R302W	NM_017827.3	NP_060297.1	Q9NP81	SYSM_HUMAN	seryl-tRNA synthetase 2, mitochondrial	232					gene expression (GO:0010467)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)|seryl-tRNA aminoacylation (GO:0006434)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|serine-tRNA ligase activity (GO:0004828)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	15	all_cancers(60;2.74e-06)|all_epithelial(25;4.36e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			CTCCAGCCCCGCGCAGGTAAT	0.652													g|||	4	0.000798722	0.0015	0.0	5008	,	,		15718	0.001		0.0	False		,,,				2504	0.001				p.R234R		Atlas-SNP	.											.	SARS2	33	.	0			c.C702T						PASS	.	G	,	23,4383	28.1+/-56.4	0,23,2180	36.0	37.0	37.0		702,696	-9.3	0.2	19	dbSNP_126	37	5,8595	5.0+/-18.6	0,5,4295	no	coding-synonymous,coding-synonymous	SARS2	NM_001145901.1,NM_017827.3	,	0,28,6475	AA,AG,GG		0.0581,0.522,0.2153	,	234/521,232/519	39410465	28,12978	2203	4300	6503	SO:0001819	synonymous_variant	54938	exon8			AGCCCCGCGCAGG	AB029948	CCDS33017.1, CCDS54265.1	19q13.2	2014-05-06	2007-02-23			ENSG00000104835	6.1.1.11	"""Aminoacyl tRNA synthetases / Class II"""	17697	protein-coding gene	gene with protein product	"""serine tRNA ligase 2, mitochondrial"""	612804	"""serine-tRNA ligase, mitochondrial"", ""seryl-tRNA synthetase 2"""	SARSM		10764807	Standard	NM_001145901		Approved	FLJ20450, mtSerRS, SerRSmt, SARS, SERS, SYS	uc010xup.1	Q9NP81	OTTHUMG00000182691	ENST00000221431.6:c.696C>T	19.37:g.39410465G>A		124.0	0.0	0		153.0	80.0	0.522876	NM_001145901	A6NHW7|B4DE10|Q9BVP3	Silent	SNP	ENST00000221431.6	37	CCDS33017.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	0	0.0	g	4.214	0.038427	0.08148	0.00522	5.81E-4	ENSG00000104835	ENST00000455102	T	0.30182	1.54	4.63	-9.26	0.00662	.	.	.	.	.	T	0.11410	0.0278	.	.	.	.	.	.	.	.	.	.	.	.	T	0.17319	-1.0373	5	0.18710	T	0.47	.	9.0126	0.36150	0.6017:0.0:0.1514:0.2469	rs35389151	.	.	.	V	211	ENSP00000414954:A211V	ENSP00000414954:A211V	A	-	2	0	FBXO17	44102305	0.000000	0.05858	0.195000	0.23364	0.321000	0.28281	-4.751000	0.00190	-2.795000	0.00354	-4.032000	0.00013	GCG	G|0.997;A|0.003	0.003	strong		0.652	SARS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463139.1	NM_017827	
SGSM1	129049	hgsc.bcm.edu	37	22	25294155	25294155	+	Missense_Mutation	SNP	A	A	C	rs6004350	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:25294155A>C	ENST00000400359.4	+	20	2411	c.2404A>C	c.(2404-2406)Acg>Ccg	p.T802P	SGSM1_ENST00000400358.4_Missense_Mutation_p.T747P|SNORD56_ENST00000362913.1_RNA	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	802	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.		T -> P (in dbSNP:rs6004350).			Golgi apparatus (GO:0005794)	Rab GTPase activator activity (GO:0005097)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(14)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	41						GAACACCCCCACGGTGCTGCG	0.627													C|||	496	0.0990415	0.3578	0.0317	5008	,	,		20487	0.0		0.001	False		,,,				2504	0.0				p.T802P		Atlas-SNP	.											SGSM1_ENST00000400359,NS,carcinoma,-1,2	SGSM1	150	2	0			c.A2404C						PASS	.	C	PRO/THR,PRO/THR,PRO/THR,PRO/THR	1165,3097		173,819,1139	52.0	64.0	60.0		2404,2239,2056,2221	0.4	0.0	22	dbSNP_114	60	10,8508		0,10,4249	yes	missense,missense,missense,missense	SGSM1	NM_001039948.2,NM_001098497.1,NM_001098498.1,NM_133454.2	38,38,38,38	173,829,5388	CC,CA,AA		0.1174,27.3346,9.1941	benign,benign,benign,benign	802/1149,747/1094,686/1033,741/1088	25294155	1175,11605	2131	4259	6390	SO:0001583	missense	129049	exon20			ACCCCCACGGTGC	AB075821	CCDS46674.1, CCDS46675.1, CCDS74834.1	22q11.23	2013-07-09	2007-08-14	2007-08-14	ENSG00000167037	ENSG00000167037		"""Small G protein signaling modulators"""	29410	protein-coding gene	gene with protein product		611417	"""RUN and TBC1 domain containing 2"""	RUTBC2		11853319, 17509819, 22637480	Standard	NM_133454		Approved	KIAA1941	uc003abg.2	Q2NKQ1	OTTHUMG00000150837	ENST00000400359.4:c.2404A>C	22.37:g.25294155A>C	ENSP00000383212:p.Thr802Pro	104.0	0.0	0		118.0	66.0	0.559322	NM_001039948	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	Missense_Mutation	SNP	ENST00000400359.4	37	CCDS46674.1	169	0.07738095238095238	159	0.3231707317073171	10	0.027624309392265192	0	0.0	0	0.0	C	2.963	-0.214065	0.06101	0.273346	0.001174	ENSG00000167037	ENST00000403206;ENST00000400358;ENST00000400359	T;T	0.07021	3.23;3.24	5.24	0.383	0.16239	Rab-GAP/TBC domain (2);	0.597033	0.15795	N	0.244222	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.0;0.001;0.0	T	0.48875	-0.8996	9	0.28530	T	0.3	-11.8193	5.2429	0.15481	0.2279:0.4713:0.2332:0.0676	rs6004350;rs52792982;rs6004350	747;802;819;802	Q2NKQ1-4;C9J7S8;Q2NKQ1-3;Q2NKQ1	.;.;.;SGSM1_HUMAN	P	802;747;802	ENSP00000383211:T747P;ENSP00000383212:T802P	ENSP00000383211:T747P	T	+	1	0	SGSM1	23624155	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.080000	0.14802	0.007000	0.14760	-0.187000	0.12897	ACG	A|0.872;C|0.128	0.128	strong		0.627	SGSM1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320282.1	XM_059318	
USP35	57558	hgsc.bcm.edu	37	11	77921013	77921013	+	Silent	SNP	A	A	G	rs78142936	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:77921013A>G	ENST00000529308.1	+	10	2373	c.2112A>G	c.(2110-2112)ggA>ggG	p.G704G	USP35_ENST00000441408.2_Silent_p.G290G|USP35_ENST00000526425.1_Silent_p.G435G|USP35_ENST00000530267.1_Silent_p.G272G|USP35_ENST00000530535.1_3'UTR	NM_020798.2	NP_065849.1	Q9P2H5	UBP35_HUMAN	ubiquitin specific peptidase 35	704	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(3)|urinary_tract(1)	23	all_cancers(14;3.77e-18)|all_epithelial(13;6.16e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.04e-25)			gaggggaaggagagagggaga	0.547													A|||	394	0.0786741	0.2814	0.0231	5008	,	,		18681	0.0		0.005	False		,,,				2504	0.001				p.G704G		Atlas-SNP	.											.	USP35	179	.	0			c.A2112G						PASS	.	A		976,3208		101,774,1217	46.0	61.0	56.0		2112	0.8	0.0	11	dbSNP_131	56	25,8435		1,23,4206	no	coding-synonymous	USP35	NM_020798.2		102,797,5423	GG,GA,AA		0.2955,23.327,7.9168		704/1019	77921013	1001,11643	2092	4230	6322	SO:0001819	synonymous_variant	57558	exon10			GGAAGGAGAGAGG	AB037793	CCDS41693.1	11q13.4	2008-02-05	2005-08-08			ENSG00000118369		"""Ubiquitin-specific peptidases"""	20061	protein-coding gene	gene with protein product			"""ubiquitin specific protease 35"""			12838346	Standard	NM_020798		Approved	KIAA1372	uc021qny.1	Q9P2H5		ENST00000529308.1:c.2112A>G	11.37:g.77921013A>G		50.0	0.0	0		77.0	41.0	0.532468	NM_020798		Silent	SNP	ENST00000529308.1	37	CCDS41693.1																																																																																			A|0.935;G|0.065	0.065	strong		0.547	USP35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390026.1	XM_290527	
ADAM18	8749	hgsc.bcm.edu	37	8	39581395	39581395	+	Missense_Mutation	SNP	T	T	A	rs79109719	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:39581395T>A	ENST00000265707.5	+	19	2191	c.2146T>A	c.(2146-2148)Tca>Aca	p.S716T	ADAM18_ENST00000523755.1_3'UTR|ADAM18_ENST00000379866.1_Missense_Mutation_p.S692T|ADAM18_ENST00000541111.1_Missense_Mutation_p.S130T	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	716					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(31)|ovary(1)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)	71		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)			AATAAGTAAATCATGTAACAG	0.308													T|||	141	0.028155	0.0998	0.0101	5008	,	,		14093	0.0		0.002	False		,,,				2504	0.0				p.S716T		Atlas-SNP	.											.	ADAM18	169	.	0			c.T2146A						PASS	.		THR/SER	403,4001	192.3+/-217.7	22,359,1821	99.0	104.0	102.0		2146	2.3	0.0	8	dbSNP_131	102	3,8591	2.2+/-6.3	0,3,4294	yes	missense	ADAM18	NM_014237.2	58	22,362,6115	AA,AT,TT		0.0349,9.1508,3.1236	benign	716/740	39581395	406,12592	2202	4297	6499	SO:0001583	missense	8749	exon19			AGTAAATCATGTA	AJ133004	CCDS6113.1, CCDS55225.1	8p11.22	2008-08-07	2005-08-18		ENSG00000168619	ENSG00000168619		"""ADAM metallopeptidase domain containing"""	196	protein-coding gene	gene with protein product			"""a disintegrin and metalloproteinase domain 18"""			12200459	Standard	NM_014237		Approved	tMDCIII, ADAM27	uc003xni.3	Q9Y3Q7	OTTHUMG00000164040	ENST00000265707.5:c.2146T>A	8.37:g.39581395T>A	ENSP00000265707:p.Ser716Thr	79.0	0.0	0		70.0	70.0	1	NM_014237	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Missense_Mutation	SNP	ENST00000265707.5	37	CCDS6113.1	57	0.0260989010989011	51	0.10365853658536585	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	T	4.809	0.150384	0.09185	0.091508	3.49E-4	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000541111	D;D;D	0.93366	-3.21;-3.21;-3.21	4.77	2.32	0.28847	.	2.401010	0.01912	N	0.039915	T	0.34135	0.0887	L	0.56769	1.78	0.09310	N	1	B;B	0.22604	0.072;0.043	B;B	0.33960	0.173;0.084	T	0.61778	-0.6993	10	0.22706	T	0.39	.	5.2918	0.15731	0.0:0.0953:0.1793:0.7254	.	692;716	Q9Y3Q7-2;Q9Y3Q7	.;ADA18_HUMAN	T	716;692;130	ENSP00000265707:S716T;ENSP00000369195:S692T;ENSP00000444729:S130T	ENSP00000265707:S716T	S	+	1	0	ADAM18	39700552	0.004000	0.15560	0.003000	0.11579	0.007000	0.05969	0.525000	0.22956	0.376000	0.24707	0.451000	0.29950	TCA	T|0.968;A|0.032	0.032	strong		0.308	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237	
DEGS2	123099	hgsc.bcm.edu	37	14	100615707	100615707	+	Silent	SNP	G	G	A	rs113575369	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:100615707G>A	ENST00000305631.5	-	2	998	c.423C>T	c.(421-423)gaC>gaT	p.D141D	DEGS2_ENST00000557117.1_5'UTR|DEGS2_ENST00000553834.1_Intron	NM_206918.2	NP_996801.2			delta(4)-desaturase, sphingolipid 2											breast(1)|lung(6)|skin(1)	8		Melanoma(154;0.212)				GCACGTCCACGTCCAGCCCGT	0.672													G|||	60	0.0119808	0.0431	0.0043	5008	,	,		16559	0.0		0.0	False		,,,				2504	0.0				p.D141D		Atlas-SNP	.											.	DEGS2	25	.	0			c.C423T						PASS	.	G		130,4272	88.7+/-127.4	1,128,2072	29.0	28.0	29.0		423	-1.0	1.0	14	dbSNP_132	29	1,8595		0,1,4297	no	coding-synonymous	DEGS2	NM_206918.2		1,129,6369	AA,AG,GG		0.0116,2.9532,1.0078		141/324	100615707	131,12867	2201	4298	6499	SO:0001819	synonymous_variant	123099	exon2			GTCCACGTCCAGC		CCDS9956.1	14q32.2	2013-09-02	2011-12-09	2004-12-14	ENSG00000168350	ENSG00000168350		"""Fatty acid desaturases"""	20113	protein-coding gene	gene with protein product	"""sphingolipid delta(4)-desaturase 2"", ""dihydroceramide desaturase 2"""	610862	"""chromosome 14 open reading frame 66"", ""degenerative spermatocyte homolog 2, lipid desaturase (Drosophila)"""	C14orf66			Standard	NM_206918		Approved	DES2, FADS8	uc001ygx.2	Q6QHC5	OTTHUMG00000171537	ENST00000305631.5:c.423C>T	14.37:g.100615707G>A		73.0	0.0	0		119.0	67.0	0.563025	NM_206918		Silent	SNP	ENST00000305631.5	37	CCDS9956.1																																																																																			G|0.991;A|0.009	0.009	strong		0.672	DEGS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414003.1	NM_206918	
RIPPLY3	53820	hgsc.bcm.edu	37	21	38390419	38390419	+	Missense_Mutation	SNP	G	G	A	rs61735126	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:38390419G>A	ENST00000329553.2	+	4	695	c.485G>A	c.(484-486)cGa>cAa	p.R162Q	RIPPLY3_ENST00000485272.1_3'UTR	NM_018962.2	NP_061835.1	P57055	DSCR6_HUMAN	ripply transcriptional repressor 3	162					heart development (GO:0007507)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|pharyngeal system development (GO:0060037)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)											CAAGGGCAGCGATCCTCAGGA	0.627													G|||	67	0.0133786	0.0469	0.0058	5008	,	,		16442	0.0		0.001	False		,,,				2504	0.0				p.R162Q		Atlas-SNP	.											.	DSCR6	16	.	0			c.G485A						PASS	.	G	GLN/ARG	146,4260	99.4+/-138.0	4,138,2061	47.0	46.0	46.0		485	0.1	0.0	21	dbSNP_129	46	1,8599	1.2+/-3.3	0,1,4299	yes	missense	DSCR6	NM_018962.2	43	4,139,6360	AA,AG,GG		0.0116,3.3137,1.1302	probably-damaging	162/191	38390419	147,12859	2203	4300	6503	SO:0001583	missense	53820	exon4			GGCAGCGATCCTC	AB037158	CCDS13648.1	21q22.2	2013-07-23	2013-07-23	2013-06-04	ENSG00000183145	ENSG00000183145			3047	protein-coding gene	gene with protein product		609892	"""Down syndrome critical region gene 6"", ""ripply3 homolog (zebrafish)"""	DSCR6		10814524, 22354841	Standard	NM_018962		Approved			P57055	OTTHUMG00000086639	ENST00000329553.2:c.485G>A	21.37:g.38390419G>A	ENSP00000331734:p.Arg162Gln	35.0	0.0	0		55.0	26.0	0.472727	NM_018962		Missense_Mutation	SNP	ENST00000329553.2	37	CCDS13648.1	25	0.011446886446886446	22	0.044715447154471545	3	0.008287292817679558	0	0.0	0	0.0	G	10.33	1.319066	0.23994	0.033137	1.16E-4	ENSG00000183145	ENST00000329553	.	.	.	3.52	0.127	0.14727	.	1.934300	0.03067	N	0.156638	T	0.06188	0.0160	N	0.19112	0.55	0.09310	N	1	D	0.63880	0.993	P	0.46543	0.52	T	0.12967	-1.0527	9	0.45353	T	0.12	2.0523	6.2061	0.20604	0.0:0.4264:0.3815:0.1922	rs61735126	162	P57055	DSCR6_HUMAN	Q	162	.	ENSP00000331734:R162Q	R	+	2	0	DSCR6	37312289	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.614000	0.05604	0.232000	0.21100	-0.311000	0.09066	CGA	G|0.989;A|0.011	0.011	strong		0.627	RIPPLY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194703.1		
PARP15	165631	hgsc.bcm.edu	37	3	122351055	122351055	+	Missense_Mutation	SNP	G	G	A	rs34383355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122351055G>A	ENST00000464300.2	+	10	1627	c.1561G>A	c.(1561-1563)Gca>Aca	p.A521T	PARP15_ENST00000483793.1_Missense_Mutation_p.A326T|PARP15_ENST00000493645.1_Missense_Mutation_p.A218T|PARP15_ENST00000465304.1_3'UTR|PARP15_ENST00000310366.4_Missense_Mutation_p.A287T	NM_001113523.1	NP_001106995.1	Q460N3	PAR15_HUMAN	poly (ADP-ribose) polymerase family, member 15	521	PARP catalytic. {ECO:0000255|PROSITE- ProRule:PRU00397}.		A -> T (in dbSNP:rs34383355).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(114;0.0531)		TTCTTCCTACGCAATAGAGAA	0.358													G|||	100	0.0199681	0.0734	0.0029	5008	,	,		22011	0.0		0.001	False		,,,				2504	0.0				p.A521T		Atlas-SNP	.											PARP15_ENST00000464300,NS,carcinoma,0,2	PARP15	115	2	0			c.G1561A						PASS	.	G	THR/ALA,THR/ALA	252,4154	145.7+/-180.5	6,240,1957	64.0	63.0	63.0		859,1561	-7.6	0.0	3	dbSNP_126	63	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense	PARP15	NM_152615.1,NM_001113523.1	58,58	6,243,6254	AA,AG,GG		0.0349,5.7195,1.9606	benign,benign	287/445,521/679	122351055	255,12751	2203	4300	6503	SO:0001583	missense	165631	exon10			TCCTACGCAATAG	AK097916	CCDS3016.1, CCDS46893.1	3q21	2010-02-16			ENSG00000173200	ENSG00000173200		"""Poly (ADP-ribose) polymerases"""	26876	protein-coding gene	gene with protein product		612066				15273990	Standard	NM_001113523		Approved	FLJ40597, pART7	uc003efm.2	Q460N3	OTTHUMG00000159523	ENST00000464300.2:c.1561G>A	3.37:g.122351055G>A	ENSP00000417214:p.Ala521Thr	47.0	0.0	0		23.0	15.0	0.652174	NM_001113523	J3KR47|Q8N1K3	Missense_Mutation	SNP	ENST00000464300.2	37	CCDS46893.1	32	0.014652014652014652	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	1.319	-0.600018	0.03744	0.057195	3.49E-4	ENSG00000173200	ENST00000464300;ENST00000483793;ENST00000542823;ENST00000310366;ENST00000493645	T;T;T;T	0.12984	2.63;2.63;2.63;2.63	3.77	-7.55	0.01327	Poly(ADP-ribose) polymerase, catalytic domain (2);	.	.	.	.	T	0.00384	0.0012	N	0.01576	-0.805	0.09310	N	1	B;B;B;B;B	0.17465	0.0;0.0;0.0;0.022;0.0	B;B;B;B;B	0.10450	0.002;0.0;0.0;0.005;0.002	T	0.43376	-0.9395	9	0.13470	T	0.59	.	6.614	0.22766	0.2724:0.3821:0.3455:0.0	rs34383355;rs56885169	218;287;268;326;499	B7ZL48;Q460N3-2;F5H8I1;C9J7L3;Q460N3	.;.;.;.;PAR15_HUMAN	T	521;326;268;287;218	ENSP00000417214:A521T;ENSP00000417785:A326T;ENSP00000308436:A287T;ENSP00000419488:A218T	ENSP00000308436:A287T	A	+	1	0	PARP15	123833745	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	0.060000	0.14342	-1.640000	0.01525	-1.085000	0.02201	GCA	G|0.981;A|0.019	0.019	strong		0.358	PARP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355964.2	NM_152615	
KIF21A	55605	hgsc.bcm.edu	37	12	39734066	39734066	+	Silent	SNP	T	T	G	rs150241656	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:39734066T>G	ENST00000361418.5	-	16	2226	c.2211A>C	c.(2209-2211)gcA>gcC	p.A737A	KIF21A_ENST00000361961.3_Silent_p.A724A|KIF21A_ENST00000541463.2_Silent_p.A724A|KIF21A_ENST00000544797.2_Silent_p.A724A|KIF21A_ENST00000395670.3_Silent_p.A737A			Q7Z4S6	KI21A_HUMAN	kinesin family member 21A	737					ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(41)|ovary(5)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(2)	86		Lung NSC(34;0.179)|all_lung(34;0.213)				CTTTTTGAGCTGCTTGAAGTC	0.363													T|||	6	0.00119808	0.0045	0.0	5008	,	,		18446	0.0		0.0	False		,,,				2504	0.0				p.A737A		Atlas-SNP	.											.	KIF21A	238	.	0			c.A2211C						PASS	.	T	,,,	31,4375	36.8+/-68.6	0,31,2172	125.0	109.0	114.0		2172,2211,2172,2172	-4.0	0.8	12	dbSNP_134	114	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KIF21A	NM_001173463.1,NM_001173464.1,NM_001173465.1,NM_017641.3	,,,	0,31,6470	GG,GT,TT		0.0,0.7036,0.2384	,,,	724/1638,737/1675,724/1622,724/1662	39734066	31,12971	2203	4298	6501	SO:0001819	synonymous_variant	55605	exon16			TTGAGCTGCTTGA	AK000059	CCDS31773.1, CCDS53774.1, CCDS53775.1, CCDS53776.1	12q12	2013-01-10						"""Kinesins"", ""WD repeat domain containing"""	19349	protein-coding gene	gene with protein product		608283	"""fibrosis of the extraocular muscles, congenital, 1"""	FEOM1		10225949	Standard	NM_017641		Approved	FLJ20052	uc001rly.3	Q7Z4S6	OTTHUMG00000169335	ENST00000361418.5:c.2211A>C	12.37:g.39734066T>G		270.0	0.0	0		269.0	136.0	0.505576	NM_001173464	A8MX28|B0I1R9|B9EGE4|F5H0C3|F5H219|Q2UVF1|Q6UKL9|Q7Z668|Q86WZ5|Q8IVZ8|Q9C0F5|Q9NXU4|Q9Y590	Silent	SNP	ENST00000361418.5	37	CCDS53776.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	10.31	1.314750	0.23908	0.007036	0.0	ENSG00000139116	ENST00000552961	.	.	.	5.22	-4.01	0.04045	.	.	.	.	.	T	0.38665	0.1049	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40327	-0.9569	4	.	.	.	.	5.0229	0.14370	0.5061:0.2038:0.0:0.2901	.	.	.	.	P	85	.	.	Q	-	2	0	KIF21A	38020333	0.026000	0.19158	0.768000	0.31515	0.987000	0.75469	-1.450000	0.02390	-0.615000	0.05679	0.533000	0.62120	CAG	T|0.998;G|0.002	0.002	strong		0.363	KIF21A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403581.1	NM_017641	
CCT8	10694	hgsc.bcm.edu	37	21	30433876	30433876	+	Missense_Mutation	SNP	C	C	T	rs8129954	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:30433876C>T	ENST00000286788.4	-	12	1431	c.1225G>A	c.(1225-1227)Gta>Ata	p.V409I	AF129075.5_ENST00000457162.2_RNA|CCT8_ENST00000540844.1_Missense_Mutation_p.V336I|CCT8_ENST00000542732.1_Missense_Mutation_p.V390I|CCT8_ENST00000470450.1_5'UTR	NM_006585.2	NP_006576.2	P50990	TCPQ_HUMAN	chaperonin containing TCP1, subunit 8 (theta)	409			V -> I (in dbSNP:rs8129954).		'de novo' posttranslational protein folding (GO:0051084)|ATP catabolic process (GO:0006200)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	aggresome (GO:0016235)|cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|microtubule (GO:0005874)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(1)|prostate(3)	14						CCTCCGGGTACAAGACGTTTA	0.363													C|||	115	0.0229633	0.0809	0.0043	5008	,	,		17710	0.003		0.002	False		,,,				2504	0.0				p.V409I		Atlas-SNP	.											.	CCT8	38	.	0			c.G1225A						PASS	.	C	ILE/VAL	346,4060	179.0+/-207.6	14,318,1871	87.0	83.0	84.0		1225	4.3	1.0	21	dbSNP_116	84	3,8597	2.2+/-6.3	0,3,4297	yes	missense	CCT8	NM_006585.2	29	14,321,6168	TT,TC,CC		0.0349,7.8529,2.6834	benign	409/549	30433876	349,12657	2203	4300	6503	SO:0001583	missense	10694	exon12			CGGGTACAAGACG	Z37163	CCDS33528.1, CCDS68180.1	21q21.3	2011-09-02			ENSG00000156261	ENSG00000156261		"""Heat Shock Proteins / Chaperonins"""	1623	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 112"""	C21orf112		7890169	Standard	NM_006585		Approved	Cctq, PRED71	uc002ynb.3	P50990	OTTHUMG00000044595	ENST00000286788.4:c.1225G>A	21.37:g.30433876C>T	ENSP00000286788:p.Val409Ile	67.0	0.0	0		76.0	35.0	0.460526	NM_006585	A6NN54|B4DEM7|B4DQH4|Q4VBP8	Missense_Mutation	SNP	ENST00000286788.4	37	CCDS33528.1	30	0.013736263736263736	28	0.056910569105691054	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	15.31	2.797070	0.50208	0.078529	3.49E-4	ENSG00000156261	ENST00000389159;ENST00000286788;ENST00000542732;ENST00000540844	D;D;D	0.82526	-1.62;-1.62;-1.62	5.19	4.3	0.51218	.	0.194901	0.43110	D	0.000602	T	0.28067	0.0692	M	0.64260	1.97	0.44454	D	0.997383	B;B;B;B;B	0.22746	0.074;0.057;0.071;0.058;0.01	B;B;B;B;B	0.35770	0.151;0.151;0.21;0.133;0.019	T	0.66638	-0.5873	10	0.51188	T	0.08	-15.0082	15.657	0.77144	0.1381:0.8619:0.0:0.0	rs8129954;rs8129954	336;390;409;408;409	B4DQH4;B4DEM7;Q53HU0;G5E9B2;P50990	.;.;.;.;TCPQ_HUMAN	I	408;409;390;336	ENSP00000286788:V409I;ENSP00000444984:V390I;ENSP00000442730:V336I	ENSP00000286788:V409I	V	-	1	0	CCT8	29355747	1.000000	0.71417	0.994000	0.49952	0.915000	0.54546	2.928000	0.48908	1.542000	0.49330	0.650000	0.86243	GTA	C|0.973;T|0.027	0.027	strong		0.363	CCT8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171822.1		
FBXL4	26235	hgsc.bcm.edu	37	6	99374436	99374436	+	Silent	SNP	T	T	C	rs17058965	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:99374436T>C	ENST00000369244.2	-	4	857	c.429A>G	c.(427-429)ctA>ctG	p.L143L	FBXL4_ENST00000229971.1_Silent_p.L143L	NM_001278716.1	NP_001265645.1	Q9UKA2	FBXL4_HUMAN	F-box and leucine-rich repeat protein 4	143					ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(4)|prostate(3)|skin(2)	18		all_cancers(76;1.56e-06)|Acute lymphoblastic leukemia(125;4.93e-10)|all_hematologic(75;3.55e-07)|all_epithelial(107;0.00893)|Colorectal(196;0.069)|Lung NSC(302;0.197)		BRCA - Breast invasive adenocarcinoma(108;0.0413)		GATAGGTTTCTAGAACATGTA	0.418													T|||	21	0.00419329	0.0151	0.0014	5008	,	,		19281	0.0		0.0	False		,,,				2504	0.0				p.L143L		Atlas-SNP	.											.	FBXL4	54	.	0			c.A429G						PASS	.	T		59,4347	57.4+/-93.9	0,59,2144	93.0	82.0	86.0		429	1.5	1.0	6	dbSNP_123	86	0,8600		0,0,4300	no	coding-synonymous	FBXL4	NM_012160.3		0,59,6444	CC,CT,TT		0.0,1.3391,0.4536		143/622	99374436	59,12947	2203	4300	6503	SO:0001819	synonymous_variant	26235	exon3			GGTTTCTAGAACA	AF176699	CCDS5041.1	6q16.1-q16.3	2011-06-09			ENSG00000112234	ENSG00000112234		"""F-boxes / Leucine-rich repeats"""	13601	protein-coding gene	gene with protein product		605654				10531035	Standard	NM_012160		Approved	FBL4, FBL5	uc003ppf.1	Q9UKA2	OTTHUMG00000015259	ENST00000369244.2:c.429A>G	6.37:g.99374436T>C		152.0	0.0	0		157.0	78.0	0.496815	NM_012160	B2R7Q5|E1P530|O95919|Q5BJH0|Q9UJU0	Silent	SNP	ENST00000369244.2	37	CCDS5041.1																																																																																			T|0.996;C|0.004	0.004	strong		0.418	FBXL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041587.2		
LCE3C	353144	hgsc.bcm.edu	37	1	152573464	152573464	+	Missense_Mutation	SNP	G	G	A	rs148755167	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152573464G>A	ENST00000333881.3	+	1	327	c.257G>A	c.(256-258)cGt>cAt	p.R86H		NM_178434.2	NP_848521.1	Q5T5A8	LCE3C_HUMAN	late cornified envelope 3C	86					keratinization (GO:0031424)					lung(1)	1	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)	UCEC - Uterine corpus endometrioid carcinoma (5;0.153)|KIRC - Kidney renal clear cell carcinoma(4;0.0313)|Kidney(5;0.0367)		GGCTCCTGCCGTGGCCATGGC	0.597													G|||	62	0.0123802	0.0469	0.0	5008	,	,		6910	0.0		0.0	False		,,,				2504	0.0				p.R86H		Atlas-SNP	.											.	LCE3C	3	.	0			c.G257A						PASS	.	G	HIS/ARG	128,3478		23,82,1698	32.0	32.0	32.0		257	3.1	0.5	1	dbSNP_134	32	2,5326		0,2,2662	no	missense	LCE3C	NM_178434.2	29	23,84,4360	AA,AG,GG		0.0375,3.5496,1.4551	benign	86/95	152573464	130,8804	1803	2664	4467	SO:0001583	missense	353144	exon1			CCTGCCGTGGCCA	BI670516	CCDS1015.1	1q21.3	2008-02-05		2004-10-15	ENSG00000244057	ENSG00000244057		"""Late cornified envelopes"""	16612	protein-coding gene	gene with protein product		612615	"""small proline rich-like (epidermal differentiation complex) 3A"""	SPRL3A		11698679	Standard	NM_178434		Approved	LEP15	uc001fac.2	Q5T5A8	OTTHUMG00000014403	ENST00000333881.3:c.257G>A	1.37:g.152573464G>A	ENSP00000334644:p.Arg86His	62.0	0.0	0		161.0	79.0	0.490683	NM_178434	A1L420	Missense_Mutation	SNP	ENST00000333881.3	37	CCDS1015.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	G	3.891	-0.024030	0.07634	0.035496	3.75E-4	ENSG00000244057	ENST00000333881	T	0.03524	3.9	4.01	3.08	0.35506	.	.	.	.	.	T	0.00967	0.0032	.	.	.	0.09310	N	1	B	0.18741	0.03	B	0.06405	0.002	T	0.47156	-0.9139	8	0.29301	T	0.29	.	9.3733	0.38268	0.0:0.2192:0.7808:0.0	.	86	Q5T5A8	LCE3C_HUMAN	H	86	ENSP00000334644:R86H	ENSP00000334644:R86H	R	+	2	0	LCE3C	150840088	0.520000	0.26250	0.478000	0.27316	0.166000	0.22503	1.037000	0.30241	0.858000	0.35431	0.313000	0.20887	CGT	G|0.988;A|0.012	0.012	strong		0.597	LCE3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040061.2	NM_178434	
OR4X1	390113	hgsc.bcm.edu	37	11	48285424	48285424	+	Silent	SNP	A	A	G	rs713323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:48285424A>G	ENST00000320048.1	+	1	12	c.12A>G	c.(10-12)acA>acG	p.T4T		NM_001004726.1	NP_001004726.1	Q8NH49	OR4X1_HUMAN	olfactory receptor, family 4, subfamily X, member 1 (gene/pseudogene)	4						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)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(1)	28						TGGTTGCTACAAACAATGTGA	0.428													A|||	80	0.0159744	0.0575	0.0058	5008	,	,		20768	0.0		0.0	False		,,,				2504	0.0				p.T4T		Atlas-SNP	.											.	OR4X1	75	.	0			c.A12G						PASS	.	A		203,4199	125.7+/-162.9	5,193,2003	94.0	90.0	91.0		12	-1.7	0.0	11	dbSNP_86	91	0,8596		0,0,4298	no	coding-synonymous	OR4X1	NM_001004726.1		5,193,6301	GG,GA,AA		0.0,4.6115,1.5618		4/306	48285424	203,12795	2201	4298	6499	SO:0001819	synonymous_variant	390113	exon1			TGCTACAAACAAT	AB065544	CCDS31487.1	11p11.2	2013-10-10	2013-10-10		ENSG00000176567	ENSG00000176567		"""GPCR / Class A : Olfactory receptors"""	14854	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily X, member 1"""				Standard	NM_001004726		Approved		uc010rht.2	Q8NH49	OTTHUMG00000165301	ENST00000320048.1:c.12A>G	11.37:g.48285424A>G		160.0	0.0	0		167.0	82.0	0.491018	NM_001004726	Q6IF74	Silent	SNP	ENST00000320048.1	37	CCDS31487.1																																																																																			A|0.982;G|0.018	0.018	strong		0.428	OR4X1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383373.1	NM_001004726	
MST1L	11223	hgsc.bcm.edu	37	1	17083839	17083839	+	RNA	SNP	A	A	T	rs549455414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17083839A>T	ENST00000455405.2	-	0	749							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										AATTCCTTTCAGGACCCAGCA	0.577													.|||	182	0.0363419	0.1293	0.0159	5008	,	,		38722	0.0		0.0	False		,,,				2504	0.0				p.L653Q		Atlas-SNP	.											Q13209_HUMAN,NS,carcinoma,+1,1	.	.	1	0			c.T1958A						PASS	.																																					11223	exon15			CCTTTCAGGACCC	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.17083839A>T		420.0	0.0	0		500.0	151.0	0.302	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	13.19	2.163948	0.38217	.	.	ENSG00000186715	ENST00000334998;ENST00000442552	.	.	.	.	.	.	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.32753	N	0.005696	T	0.64057	0.2564	.	.	.	.	.	.	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.67914	-0.5547	6	0.52906	T	0.07	.	5.2253	0.15391	0.9998:0.0:2.0E-4:0.0	.	653;679	Q2TV78-2;Q2TV78	.;MSTP9_HUMAN	Q	653;679	.	ENSP00000439273:L653Q	L	-	2	0	MST1P9	16956426	1.000000	0.71417	0.950000	0.38849	0.000000	0.00434	5.601000	0.67606	0.419000	0.25927	0.000000	0.15137	CTG	.	.	none		0.577	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
INADL	10207	hgsc.bcm.edu	37	1	62455982	62455982	+	Silent	SNP	G	G	A	rs6681983	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:62455982G>A	ENST00000371158.2	+	28	3927	c.3813G>A	c.(3811-3813)ccG>ccA	p.P1271P	INADL_ENST00000316485.6_Silent_p.P1271P|INADL_ENST00000543708.1_Silent_p.P55P|INADL_ENST00000545929.1_5'UTR	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1271	PDZ 7. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						GAATTAACCCGGAAGGACCTG	0.433													G|||	99	0.0197684	0.0711	0.0072	5008	,	,		15469	0.0		0.0	False		,,,				2504	0.0				p.P1271P		Atlas-SNP	.											.	INADL	179	.	0			c.G3813A						PASS	.	G		187,4219	119.6+/-157.3	4,179,2020	94.0	89.0	90.0		3813	-11.7	0.0	1	dbSNP_116	90	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	INADL	NM_176877.2		4,182,6317	AA,AG,GG		0.0349,4.2442,1.4609		1271/1802	62455982	190,12816	2203	4300	6503	SO:0001819	synonymous_variant	10207	exon28			TAACCCGGAAGGA	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.3813G>A	1.37:g.62455982G>A		94.0	0.0	0		73.0	34.0	0.465753	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Silent	SNP	ENST00000371158.2	37	CCDS617.2																																																																																			G|0.985;A|0.015	0.015	strong		0.433	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
STRIP2	57464	hgsc.bcm.edu	37	7	129098602	129098602	+	Missense_Mutation	SNP	G	G	A	rs571423095		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:129098602G>A	ENST00000249344.2	+	11	1364	c.1324G>A	c.(1324-1326)Gga>Aga	p.G442R	STRIP2_ENST00000435494.2_Missense_Mutation_p.G442R	NM_020704.2	NP_065755.1	Q9ULQ0	STRP2_HUMAN	striatin interacting protein 2	442					cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)		p.G442R(1)									CAAGTTCATCGGATTCACCCT	0.517													G|||	1	0.000199681	0.0	0.0014	5008	,	,		17567	0.0		0.0	False		,,,				2504	0.0				p.G442R		Atlas-SNP	.											FAM40B,lymph_node,lymphoid_neoplasm,0,1	.	.	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G1324A						PASS	.						110.0	95.0	100.0					7																	129098602		2203	4300	6503	SO:0001583	missense	57464	exon11			TTCATCGGATTCA	AB032996	CCDS34752.1, CCDS47709.1	7q32.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000128578	ENSG00000128578			22209	protein-coding gene	gene with protein product	"""FAR11 factor arrest 11 homolog B (yeast)"""		"""family with sequence similarity 40, member B"""	FAM40B		22782902, 22298706, 18782753	Standard	NM_020704		Approved	KIAA1170, FAR11B	uc011koy.2	Q9ULQ0	OTTHUMG00000157695	ENST00000249344.2:c.1324G>A	7.37:g.129098602G>A	ENSP00000249344:p.Gly442Arg	141.0	0.0	0		112.0	45.0	0.401786	NM_020704	Q8WUZ4	Missense_Mutation	SNP	ENST00000249344.2	37	CCDS34752.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.608630	0.87258	.	.	ENSG00000128578	ENST00000249344;ENST00000435494;ENST00000450266	T;T	0.48836	0.8;0.8	5.34	5.34	0.76211	.	0.102042	0.64402	D	0.000002	T	0.73087	0.3542	M	0.85099	2.735	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	T	0.76016	-0.3113	10	0.54805	T	0.06	-3.4152	18.3766	0.90437	0.0:0.0:1.0:0.0	.	442;442	Q9ULQ0;Q9ULQ0-2	FA40B_HUMAN;.	R	442;442;113	ENSP00000249344:G442R;ENSP00000392393:G442R	ENSP00000249344:G442R	G	+	1	0	FAM40B	128885838	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.747000	0.98863	2.655000	0.90218	0.561000	0.74099	GGA	.	.	none		0.517	STRIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349418.1	NM_001134336	
ANKRD53	79998	hgsc.bcm.edu	37	2	71212380	71212380	+	Silent	SNP	C	C	A	rs61732288	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71212380C>A	ENST00000360589.3	+	6	1577	c.1543C>A	c.(1543-1545)Cga>Aga	p.R515R	ANKRD53_ENST00000272421.6_3'UTR|ANKRD53_ENST00000441349.1_3'UTR|AC007040.11_ENST00000606025.1_Intron|ANKRD53_ENST00000457410.1_Silent_p.R481R	NM_001115116.1	NP_001108588.1	Q8N9V6	ANR53_HUMAN	ankyrin repeat domain 53	515										endometrium(2)|large_intestine(3)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	11						GGCAGCTGTGCGATCTCATCA	0.572											OREG0014687	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	184	0.0367412	0.1331	0.0101	5008	,	,		13411	0.0		0.001	False		,,,				2504	0.0				p.R515R		Atlas-SNP	.											.	ANKRD53	55	.	0			c.C1543A						PASS	.	C	,	182,1202		12,158,522	31.0	32.0	31.0		1543,	-0.8	0.1	2	dbSNP_129	31	2,3180		0,2,1589	no	coding-synonymous,utr-3	ANKRD53	NM_001115116.1,NM_024933.3	,	12,160,2111	AA,AC,CC		0.0629,13.1503,4.0298	,	515/531,	71212380	184,4382	692	1591	2283	SO:0001819	synonymous_variant	79998	exon6			GCTGTGCGATCTC	BC035234	CCDS1913.1, CCDS46321.1	2p13.3	2013-01-10			ENSG00000144031	ENSG00000144031		"""Ankyrin repeat domain containing"""	25691	protein-coding gene	gene with protein product							Standard	NM_024933		Approved	FLJ12056, FLJ36160	uc002shl.4	Q8N9V6	OTTHUMG00000129712	ENST00000360589.3:c.1543C>A	2.37:g.71212380C>A		134.0	0.0	0	1128	135.0	56.0	0.414815	NM_001115116	Q8IYP8	Silent	SNP	ENST00000360589.3	37	CCDS46321.1																																																																																			C|0.968;A|0.032	0.032	strong		0.572	ANKRD53-004	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330275.2	NM_024933	
TCF12	6938	hgsc.bcm.edu	37	15	57384061	57384061	+	Silent	SNP	A	A	G	rs34560099	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:57384061A>G	ENST00000267811.5	+	5	601	c.297A>G	c.(295-297)ccA>ccG	p.P99P	TCF12_ENST00000557843.1_Silent_p.P99P|TCF12_ENST00000333725.5_Silent_p.P99P|TCF12_ENST00000452095.2_Silent_p.P95P|TCF12_ENST00000438423.2_Silent_p.P99P	NM_003205.3|NM_207038.1	NP_003196.1|NP_996921.1	Q99081	HTF4_HUMAN	transcription factor 12	99					immune response (GO:0006955)|muscle organ development (GO:0007517)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SMAD binding (GO:0046332)|transcription factor binding (GO:0008134)		TCF12/NR4A3(2)	breast(2)|central_nervous_system(5)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	36		Colorectal(260;0.0907)		all cancers(107;0.000313)|GBM - Glioblastoma multiforme(80;0.00878)|STAD - Stomach adenocarcinoma(283;0.239)		GCTTGTCCCCAACACCTTTCA	0.423			T	TEC	extraskeletal myxoid chondrosarcoma								A|||	237	0.0473243	0.1626	0.0216	5008	,	,		18239	0.0		0.007	False		,,,				2504	0.0				p.P99P		Atlas-SNP	.		Dom	yes		15	15q21	6938	"""transcription factor 12 (HTF4, helix-loop-helix transcription factors 4)"""		M	.	TCF12	242	.	0			c.A297G						PASS	.	A	,,,	551,3833	247.8+/-255.9	35,481,1676	109.0	107.0	108.0		297,297,297,297	4.6	1.0	15	dbSNP_126	108	37,8547	25.1+/-72.6	1,35,4256	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TCF12	NM_003205.3,NM_207036.1,NM_207037.1,NM_207038.1	,,,	36,516,5932	GG,GA,AA		0.431,12.5684,4.5342	,,,	99/683,99/707,99/707,99/683	57384061	588,12380	2192	4292	6484	SO:0001819	synonymous_variant	6938	exon5			GTCCCCAACACCT	BC050556	CCDS10159.1, CCDS10160.1, CCDS42042.1	15q21	2013-05-21	2008-07-31		ENSG00000140262	ENSG00000140262		"""Basic helix-loop-helix proteins"""	11623	protein-coding gene	gene with protein product	"""helix-loop-helix transcription factor 4"""	600480				1886779	Standard	NM_003205		Approved	HEB, HTF4, HsT17266, bHLHb20	uc002aeb.3	Q99081	OTTHUMG00000132047	ENST00000267811.5:c.297A>G	15.37:g.57384061A>G		90.0	0.0	0		91.0	33.0	0.362637	NM_207036	Q7Z3D9|Q86TC1|Q86VM2	Silent	SNP	ENST00000267811.5	37	CCDS10159.1																																																																																			A|0.959;G|0.041	0.041	strong		0.423	TCF12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255069.3	NM_003205	
PEX1	5189	hgsc.bcm.edu	37	7	92118654	92118654	+	Silent	SNP	G	G	A	rs34825053	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:92118654G>A	ENST00000248633.4	-	23	3815	c.3720C>T	c.(3718-3720)caC>caT	p.H1240H	AC007566.10_ENST00000427458.1_RNA|PEX1_ENST00000438045.1_Silent_p.H918H|PEX1_ENST00000428214.1_Silent_p.H1183H|AC007566.10_ENST00000441539.1_RNA	NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	peroxisomal biogenesis factor 1	1240					ATP catabolic process (GO:0006200)|microtubule-based peroxisome localization (GO:0060152)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			ATGGTCTTGTGTGACCAAGTG	0.388													G|||	21	0.00419329	0.0151	0.0014	5008	,	,		15394	0.0		0.0	False		,,,				2504	0.0				p.H1240H		Atlas-SNP	.											.	PEX1	102	.	0			c.C3720T						PASS	.	G		71,4335	64.1+/-101.4	1,69,2133	144.0	115.0	125.0		3720	2.3	0.9	7	dbSNP_126	125	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PEX1	NM_000466.2		1,70,6432	AA,AG,GG		0.0116,1.6114,0.5536		1240/1284	92118654	72,12934	2203	4300	6503	SO:0001819	synonymous_variant	5189	exon23			TCTTGTGTGACCA	AF026086	CCDS5627.1, CCDS64710.1	7q21.2	2010-04-21	2008-08-26		ENSG00000127980	ENSG00000127980		"""ATPases / AAA-type"""	8850	protein-coding gene	gene with protein product		602136	"""peroxisome biogenesis factor 1"", ""Zellweger syndrome 1"", ""Zellweger syndrome"""	ZWS1, ZWS		9398848	Standard	NM_001282677		Approved		uc003uly.3	O43933	OTTHUMG00000023926	ENST00000248633.4:c.3720C>T	7.37:g.92118654G>A		122.0	0.0	0		140.0	61.0	0.435714	NM_000466	A4D1G3|A8KA90|B4DIM7|E9PE75|Q96S71|Q96S72|Q96S73|Q99994	Silent	SNP	ENST00000248633.4	37	CCDS5627.1																																																																																			G|0.992;A|0.008	0.008	strong		0.388	PEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254066.3	NM_000466	
CBLC	23624	hgsc.bcm.edu	37	19	45284495	45284495	+	Missense_Mutation	SNP	C	C	T	rs114569424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45284495C>T	ENST00000270279.3	+	3	595	c.532C>T	c.(532-534)Ctc>Ttc	p.L178F	CBLC_ENST00000341505.4_Missense_Mutation_p.L178F	NM_012116.3	NP_036248.3	Q9ULV8	CBLC_HUMAN	Cbl proto-oncogene C, E3 ubiquitin protein ligase	178	Cbl-PTB. {ECO:0000255|PROSITE- ProRule:PRU00839}.|EF-hand-like.				cell surface receptor signaling pathway (GO:0007166)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of MAP kinase activity (GO:0043407)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|ligase activity (GO:0016874)|phosphotyrosine binding (GO:0001784)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|lung(6)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Lung NSC(12;0.00136)|all_lung(12;0.00371)	Ovarian(192;0.231)				GTTTGAGTCCCTCCTGGGCAC	0.652			M		AML								c|||	39	0.00778754	0.0242	0.0058	5008	,	,		16049	0.0		0.0	False		,,,				2504	0.0031				p.L178F		Atlas-SNP	.		Rec	yes		19	19q13.2	23624	Cas-Br-M (murine) ecotropic retroviral transforming sequence c		L	.	CBLC	41	.	0			c.C532T						PASS	.		PHE/LEU,PHE/LEU	59,4347		0,59,2144	68.0	57.0	61.0		532,532	1.7	0.0	19	dbSNP_132	61	0,8600		0,0,4300	yes	missense,missense	CBLC	NM_001130852.1,NM_012116.3	22,22	0,59,6444	TT,TC,CC		0.0,1.3391,0.4536	probably-damaging,probably-damaging	178/429,178/475	45284495	59,12947	2203	4300	6503	SO:0001583	missense	23624	exon3			GAGTCCCTCCTGG	AB028645	CCDS12643.1, CCDS46109.1	19q13.2	2013-07-09	2013-07-09		ENSG00000142273	ENSG00000142273		"""RING-type (C3HC4) zinc fingers"""	15961	protein-coding gene	gene with protein product		608453	"""Cas-Br-M (murine) ectropic retroviral transforming sequence c"", ""Cas-Br-M (murine) ecotropic retroviral transforming sequence c"""			10362357, 10571044	Standard	NM_012116		Approved	CBL-3, CBL-SL, RNF57	uc002ozs.3	Q9ULV8	OTTHUMG00000150715	ENST00000270279.3:c.532C>T	19.37:g.45284495C>T	ENSP00000270279:p.Leu178Phe	91.0	0.0	0		97.0	48.0	0.494845	NM_001130852	Q8N1E5|Q9Y5Z2|Q9Y5Z3	Missense_Mutation	SNP	ENST00000270279.3	37	CCDS12643.1	21	0.009615384615384616	17	0.034552845528455285	4	0.011049723756906077	0	0.0	0	0.0	.	12.98	2.099594	0.37048	0.013391	0.0	ENSG00000142273	ENST00000270279;ENST00000341505	D;D	0.87256	-2.23;-2.23	3.95	1.72	0.24424	Adaptor protein Cbl, PTB domain (1);EF-hand-like domain (1);Adaptor protein Cbl, EF hand-like (1);	0.976806	0.08347	N	0.959896	T	0.74238	0.3690	L	0.57536	1.79	0.09310	N	1	D;D	0.61697	0.958;0.99	P;P	0.53549	0.682;0.729	T	0.68142	-0.5487	10	0.23891	T	0.37	-15.6691	7.2319	0.26046	0.1838:0.4585:0.3578:0.0	.	178;178	Q9ULV8-2;Q9ULV8	.;CBLC_HUMAN	F	178	ENSP00000270279:L178F;ENSP00000340250:L178F	ENSP00000270279:L178F	L	+	1	0	CBLC	49976335	0.003000	0.15002	0.005000	0.12908	0.756000	0.42949	1.111000	0.31159	0.318000	0.23185	0.306000	0.20318	CTC	C|0.994;T|0.006	0.006	strong		0.652	CBLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319732.2	NM_012116	
PCDHB14	56122	hgsc.bcm.edu	37	5	140604419	140604419	+	Missense_Mutation	SNP	G	G	A	rs61731253	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140604419G>A	ENST00000239449.4	+	1	1342	c.1342G>A	c.(1342-1344)Gcc>Acc	p.A448T	PCDHB14_ENST00000515856.2_Missense_Mutation_p.A295T	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	448	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CAATGACAACGCCCCCACCTT	0.582													g|||	103	0.0205671	0.0734	0.0072	5008	,	,		17391	0.0		0.001	False		,,,				2504	0.0				p.A448T	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.G1342A						PASS	.	G	THR/ALA	278,4128		6,266,1931	145.0	140.0	142.0		1342	3.5	1.0	5	dbSNP_129	142	0,8600		0,0,4300	no	missense	PCDHB14	NM_018934.2	58	6,266,6231	AA,AG,GG		0.0,6.3096,2.1375	benign	448/799	140604419	278,12728	2203	4300	6503	SO:0001583	missense	56122	exon1			GACAACGCCCCCA	AF152493	CCDS4256.1	5q31	2010-01-26			ENSG00000120327	ENSG00000120327		"""Cadherins / Protocadherins : Clustered"""	8685	other	protocadherin		606340				10380929	Standard	NM_018934		Approved	PCDH-BETA14	uc003ljb.3	Q9Y5E9	OTTHUMG00000129619	ENST00000239449.4:c.1342G>A	5.37:g.140604419G>A	ENSP00000239449:p.Ala448Thr	161.0	0.0	0		200.0	108.0	0.54	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Missense_Mutation	SNP	ENST00000239449.4	37	CCDS4256.1	39	0.017857142857142856	37	0.07520325203252033	2	0.0055248618784530384	0	0.0	0	0.0	-	8.743	0.919419	0.17982	0.063096	0.0	ENSG00000120327	ENST00000515856;ENST00000239449	T;T	0.03181	4.02;4.02	4.5	3.55	0.40652	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.00300	0.0009	M	0.75777	2.31	0.30169	N	0.801422	P	0.49559	0.925	B	0.34652	0.187	T	0.21827	-1.0234	9	0.56958	D	0.05	.	9.2019	0.37263	0.0:0.2719:0.6013:0.1268	rs61731253	448	Q9Y5E9	PCDBE_HUMAN	T	295;448	ENSP00000444518:A295T;ENSP00000239449:A448T	ENSP00000239449:A448T	A	+	1	0	PCDHB14	140584603	0.003000	0.15002	1.000000	0.80357	0.089000	0.18198	-0.272000	0.08560	2.235000	0.73313	0.556000	0.70494	GCC	G|0.979;A|0.021	0.021	strong		0.582	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934	
ALG11	440138	hgsc.bcm.edu	37	13	52598668	52598668	+	Missense_Mutation	SNP	C	C	A	rs148434423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:52598668C>A	ENST00000521508.1	+	3	807	c.802C>A	c.(802-804)Cta>Ata	p.L268I	UTP14C_ENST00000521776.2_5'Flank|ALG11_ENST00000523764.1_Intron|ALG11_ENST00000519151.1_3'UTR	NM_001004127.2	NP_001004127.2	Q2TAA5	ALG11_HUMAN	ALG11, alpha-1,2-mannosyltransferase	268					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)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GDP-Man:Man3GlcNAc2-PP-Dol alpha-1,2-mannosyltransferase activity (GO:0004377)			endometrium(1)|large_intestine(6)|lung(4)|ovary(2)	13		Breast(56;0.00173)|Lung NSC(96;0.0108)|Prostate(109;0.0412)|Hepatocellular(98;0.152)|Glioma(44;0.236)		GBM - Glioblastoma multiforme(99;2.44e-08)		TATTCTCTCACTATGGAAAGT	0.378													C|||	2	0.000399361	0.0015	0.0	5008	,	,		22470	0.0		0.0	False		,,,				2504	0.0				p.L268I		Atlas-SNP	.											.	ALG11	39	.	0			c.C802A						PASS	.	C	ILE/LEU	8,4398	15.5+/-35.6	0,8,2195	120.0	111.0	114.0		802	5.2	1.0	13	dbSNP_134	114	0,8600		0,0,4300	yes	missense	ALG11	NM_001004127.2	5	0,8,6495	AA,AC,CC		0.0,0.1816,0.0615	possibly-damaging	268/493	52598668	8,12998	2203	4300	6503	SO:0001583	missense	440138	exon3			CTCTCACTATGGA	AK025456	CCDS31977.1	13q14.3	2013-02-22	2013-02-22		ENSG00000253710	ENSG00000253710	2.4.1.131	"""Glycosyltransferase group 1 domain containing"""	32456	protein-coding gene	gene with protein product	"""GDP-Man:Man(3)GlcNAc(2)-PP-dolichol alpha-1,2-mannosyltransferase"""	613666	"""asparagine-linked glycosylation 11 homolog (S. cerevisiae, alpha-1,2-mannosyltransferase)"", ""asparagine-linked glycosylation 11, alpha-1,2-mannosyltransferase homolog (yeast)"""			20080937	Standard	NM_001004127		Approved	KIAA0266		Q2TAA5	OTTHUMG00000016959	ENST00000521508.1:c.802C>A	13.37:g.52598668C>A	ENSP00000430236:p.Leu268Ile	223.0	0.0	0		216.0	100.0	0.462963	NM_001004127	A5PLP3|B4DKW9|Q5TAN9|Q6DKI6|Q96FI7	Missense_Mutation	SNP	ENST00000521508.1	37	CCDS31977.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	12.85	2.062733	0.36373	0.001816	0.0	ENSG00000253710	ENST00000521508	T	0.80304	-1.36	6.03	5.19	0.71726	.	0.000000	0.64402	U	0.000002	T	0.81517	0.4839	L	0.50993	1.605	0.80722	D	1	D	0.57571	0.98	P	0.52309	0.695	T	0.78563	-0.2156	10	0.20519	T	0.43	.	15.3059	0.73992	0.0:0.9333:0.0:0.0667	.	268	Q2TAA5	ALG11_HUMAN	I	268	ENSP00000430236:L268I	ENSP00000430236:L268I	L	+	1	2	ALG11	51496669	0.993000	0.37304	0.970000	0.41538	0.930000	0.56654	3.054000	0.49908	1.569000	0.49696	0.557000	0.71058	CTA	C|0.999;A|0.001	0.001	strong		0.378	ALG11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045050.1	NM_001004127	
DDX3X	1654	hgsc.bcm.edu	37	X	41204446	41204446	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:41204446G>C	ENST00000399959.2	+	11	1894	c.1039G>C	c.(1039-1041)Gat>Cat	p.D347H	RN7SL15P_ENST00000582825.1_RNA|DDX3X_ENST00000542215.1_3'UTR|DDX3X_ENST00000478993.1_3'UTR|DDX3X_ENST00000457138.2_Missense_Mutation_p.D331H|DDX3X_ENST00000441189.2_Intron	NM_001193416.1|NM_001193417.1|NM_001356.3	NP_001180345.1|NP_001180346.1|NP_001347.3	O00571	DDX3X_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 3, X-linked	347	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.|Interaction with GSK3B.|Necessary for interaction with XPO1.				ATP catabolic process (GO:0006200)|cellular response to arsenic-containing substance (GO:0071243)|cellular response to osmotic stress (GO:0071470)|chromosome segregation (GO:0007059)|DNA duplex unwinding (GO:0032508)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway (GO:0097193)|mature ribosome assembly (GO:0042256)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of protein complex assembly (GO:0031333)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell growth (GO:0030307)|positive regulation of chemokine (C-C motif) ligand 5 production (GO:0071651)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of translation (GO:0045727)|positive regulation of translational initiation (GO:0045948)|response to virus (GO:0009615)|RNA secondary structure unwinding (GO:0010501)|stress granule assembly (GO:0034063)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|extracellular vesicular exosome (GO:0070062)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|ATPase activity (GO:0016887)|DNA binding (GO:0003677)|eukaryotic initiation factor 4E binding (GO:0008190)|mRNA 5'-UTR binding (GO:0048027)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|RNA binding (GO:0003723)|RNA stem-loop binding (GO:0035613)|transcription factor binding (GO:0008134)|translation initiation factor binding (GO:0031369)			NS(3)|breast(8)|central_nervous_system(36)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(1)	84						CTTGGTGTTAGATGAAGCTGA	0.393										HNSCC(61;0.18)																											p.D347H		Atlas-SNP	.											.	DDX3X	138	.	0			c.G1039C						PASS	.						145.0	134.0	137.0					X																	41204446		2102	4246	6348	SO:0001583	missense	1654	exon11			GTGTTAGATGAAG	U50553	CCDS43931.1, CCDS55404.1	Xp11.3-p11.23	2013-07-16	2013-07-16	2003-06-20	ENSG00000215301	ENSG00000215301		"""DEAD-boxes"""	2745	protein-coding gene	gene with protein product		300160	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked"""	DDX3		9381176, 9730595	Standard	NM_001193416		Approved	DBX, HLP2, DDX14	uc004dfe.3	O00571	OTTHUMG00000021369	ENST00000399959.2:c.1039G>C	X.37:g.41204446G>C	ENSP00000382840:p.Asp347His	129.0	0.0	0		131.0	25.0	0.19084	NM_001193416	A8K538|B4E3E8|O15536	Missense_Mutation	SNP	ENST00000399959.2	37	CCDS43931.1	.	.	.	.	.	.	.	.	.	.	g	25.1	4.598675	0.87055	.	.	ENSG00000215301	ENST00000399959;ENST00000457138	T;T	0.55588	0.51;0.51	5.5	5.5	0.81552	RNA helicase, ATP-dependent, DEAD-box, conserved site (1);DEAD-like helicase (2);DNA/RNA helicase, DEAD/DEAH box type, N-terminal (1);	0.099615	0.64402	D	0.000001	D	0.85106	0.5621	H	0.99299	4.505	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.999;0.997;0.997	D	0.91820	0.5466	10	0.87932	D	0	-16.0361	18.5127	0.90923	0.0:0.0:1.0:0.0	.	347;331;359;347	B4DLU5;B4E3E8;Q59GX6;O00571	.;.;.;DDX3X_HUMAN	H	347;331	ENSP00000382840:D347H;ENSP00000392494:D331H	ENSP00000382840:D347H	D	+	1	0	DDX3X	41089390	1.000000	0.71417	0.998000	0.56505	0.869000	0.49853	9.807000	0.99171	2.313000	0.78055	0.597000	0.82753	GAT	.	.	none		0.393	DDX3X-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056253.1	NM_024005	
ITLN1	55600	hgsc.bcm.edu	37	1	160853312	160853312	+	Silent	SNP	C	C	T	rs79969862	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:160853312C>T	ENST00000326245.3	-	3	178	c.63G>A	c.(61-63)gaG>gaA	p.E21E	ITLN1_ENST00000487531.1_5'Flank	NM_017625.2	NP_060095.2	Q8WWA0	ITLN1_HUMAN	intelectin 1 (galactofuranose binding)	21					positive regulation of glucose import (GO:0046326)|positive regulation of protein phosphorylation (GO:0001934)|response to nematode (GO:0009624)	anchored component of membrane (GO:0031225)|brush border membrane (GO:0031526)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	21	all_cancers(52;2.99e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00737)			AAGTATTAGCCTCATCTAGGG	0.463													C|||	89	0.0177716	0.0461	0.0043	5008	,	,		18185	0.0		0.0	False		,,,				2504	0.0256				p.E21E		Atlas-SNP	.											.	ITLN1	45	.	0			c.G63A						PASS	.	C		182,4224	117.1+/-155.0	5,172,2026	159.0	145.0	150.0		63	-3.0	0.0	1	dbSNP_132	150	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ITLN1	NM_017625.2		5,173,6325	TT,TC,CC		0.0116,4.1307,1.407		21/314	160853312	183,12823	2203	4300	6503	SO:0001819	synonymous_variant	55600	exon3			ATTAGCCTCATCT	AB036706	CCDS1211.1	1q21.3	2008-02-05			ENSG00000179914	ENSG00000179914			18259	protein-coding gene	gene with protein product		609873				11313366, 11181563	Standard	NM_017625		Approved	ITLN, FLJ20022, LFR, HL-1, hIntL	uc001fxc.3	Q8WWA0	OTTHUMG00000028604	ENST00000326245.3:c.63G>A	1.37:g.160853312C>T		154.0	0.0	0		149.0	61.0	0.409396	NM_017625	Q5IWS4|Q5VYI4|Q6YDJ3|Q9NP67	Silent	SNP	ENST00000326245.3	37	CCDS1211.1																																																																																			C|0.984;T|0.016	0.016	strong		0.463	ITLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071462.1	NM_017625	
F10	2159	hgsc.bcm.edu	37	13	113798236	113798236	+	Missense_Mutation	SNP	G	G	A	rs3211783	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:113798236G>A	ENST00000375559.3	+	6	612	c.574G>A	c.(574-576)Ggg>Agg	p.G192R	F10_ENST00000409306.1_Missense_Mutation_p.G192R|F10_ENST00000375551.3_Missense_Mutation_p.G192R	NM_000504.3	NP_000495.1	P00742	FA10_HUMAN	coagulation factor X	192	O-glycosylated at one site.		G -> R (in dbSNP:rs3211783). {ECO:0000269|Ref.3}.		blood coagulation (GO:0007596)|blood coagulation, extrinsic pathway (GO:0007598)|blood coagulation, intrinsic pathway (GO:0007597)|cellular protein metabolic process (GO:0044267)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of cell migration (GO:0030335)|positive regulation of protein kinase B signaling (GO:0051897)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|intrinsic component of external side of plasma membrane (GO:0031233)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phospholipid binding (GO:0005543)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(4)|lung(10)|pancreas(1)|stomach(1)	18	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.113)|all_lung(25;0.0364)|all_epithelial(44;0.0373)|Lung NSC(25;0.128)|Breast(118;0.188)	all cancers(43;0.0805)|Epithelial(84;0.231)		Antihemophilic Factor(DB00025)|Apixaban(DB06605)|Coagulation Factor IX(DB00100)|Coagulation factor VIIa(DB00036)|Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)|Menadione(DB00170)|Rivaroxaban(DB06228)	CAGCAGCAGCGGGGAGGCCCC	0.632													G|||	148	0.0295527	0.1089	0.0058	5008	,	,		16770	0.0		0.0	False		,,,				2504	0.0				p.G192R		Atlas-SNP	.											.	F10	53	.	0			c.G574A						PASS	.	G	ARG/GLY	378,4028	188.8+/-215.1	17,344,1842	71.0	61.0	64.0		574	0.6	0.0	13	dbSNP_105	64	4,8596	3.7+/-12.6	0,4,4296	yes	missense	F10	NM_000504.3	125	17,348,6138	AA,AG,GG		0.0465,8.5792,2.9371	benign	192/489	113798236	382,12624	2203	4300	6503	SO:0001583	missense	2159	exon6			AGCAGCGGGGAGG		CCDS9530.1	13q34	2012-10-02			ENSG00000126218	ENSG00000126218	3.4.21.6		3528	protein-coding gene	gene with protein product		613872					Standard	XM_005268298		Approved		uc001vsx.3	P00742	OTTHUMG00000017374	ENST00000375559.3:c.574G>A	13.37:g.113798236G>A	ENSP00000364709:p.Gly192Arg	47.0	0.0	0		59.0	29.0	0.491525	NM_000504	Q14340	Missense_Mutation	SNP	ENST00000375559.3	37	CCDS9530.1	46	0.021062271062271064	45	0.09146341463414634	1	0.0027624309392265192	0	0.0	0	0.0	G	6.631	0.484887	0.12641	0.085792	4.65E-4	ENSG00000126218	ENST00000409306;ENST00000375551;ENST00000375559	D;D;D	0.95588	-3.73;-3.75;-2.9	4.72	0.594	0.17485	.	2.606730	0.01382	N	0.012940	T	0.31482	0.0798	L	0.29908	0.895	0.09310	N	1	P;P;P	0.49961	0.93;0.93;0.682	B;B;B	0.34931	0.136;0.192;0.053	T	0.74542	-0.3631	10	0.18276	T	0.48	.	4.0037	0.09592	0.4003:0.1745:0.4252:0.0	rs3211783	192;192;192	B7ZBK1;Q5JVE8;P00742	.;.;FA10_HUMAN	R	192	ENSP00000387092:G192R;ENSP00000364701:G192R;ENSP00000364709:G192R	ENSP00000364701:G192R	G	+	1	0	F10	112846237	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.422000	0.07043	0.081000	0.16988	-0.333000	0.08304	GGG	G|0.973;A|0.027	0.027	strong		0.632	F10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045841.3		
PBK	55872	hgsc.bcm.edu	37	8	27668587	27668587	+	Missense_Mutation	SNP	C	C	G	rs17057901	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:27668587C>G	ENST00000301905.4	-	7	1123	c.660G>C	c.(658-660)gaG>gaC	p.E220D	ESCO2_ENST00000397418.2_Intron|PBK_ENST00000522944.1_Missense_Mutation_p.E231D	NM_018492.2	NP_060962.2	Q96KB5	TOPK_HUMAN	PDZ binding kinase	220	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		E -> D (in dbSNP:rs17057901).		mitotic nuclear division (GO:0007067)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			endometrium(1)|large_intestine(2)|lung(1)	4		Ovarian(32;0.000953)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0213)|KIRC - Kidney renal clear cell carcinoma(542;0.101)|Kidney(114;0.121)|Colorectal(74;0.141)		TAACACCATTCTCCTCCACAG	0.428													C|||	105	0.0209665	0.0741	0.0101	5008	,	,		19638	0.0		0.0	False		,,,				2504	0.0				p.E220D		Atlas-SNP	.											.	PBK	29	.	0			c.G660C						PASS	.	C	ASP/GLU	299,4107	163.6+/-195.4	12,275,1916	134.0	114.0	121.0		660	-1.1	0.8	8	dbSNP_123	121	4,8596	3.7+/-12.6	0,4,4296	yes	missense	PBK	NM_018492.2	45	12,279,6212	GG,GC,CC		0.0465,6.7862,2.3297	benign	220/323	27668587	303,12703	2203	4300	6503	SO:0001583	missense	55872	exon7			ACCATTCTCCTCC	AB027249	CCDS6063.1, CCDS64858.1	8p21.2	2009-08-06			ENSG00000168078	ENSG00000168078			18282	protein-coding gene	gene with protein product	"""T-LAK cell-originated protein kinase"", ""cancer/testis antigen 84"""	611210				10781613, 10779557	Standard	NM_018492		Approved	TOPK, FLJ14385, Nori-3, SPK, CT84	uc003xgi.3	Q96KB5	OTTHUMG00000102113	ENST00000301905.4:c.660G>C	8.37:g.27668587C>G	ENSP00000301905:p.Glu220Asp	176.0	0.0	0		139.0	67.0	0.482014	NM_018492	B4DX68|D3DST2|Q9NPD9|Q9NYL7|Q9NZK6	Missense_Mutation	SNP	ENST00000301905.4	37	CCDS6063.1	31	0.014194139194139194	28	0.056910569105691054	3	0.008287292817679558	0	0.0	0	0.0	C	13.60	2.284682	0.40394	0.067862	4.65E-4	ENSG00000168078	ENST00000301905;ENST00000522944	T;T	0.33654	1.4;1.4	5.49	-1.13	0.09775	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.043945	0.85682	D	0.000000	T	0.01661	0.0053	N	0.21448	0.665	0.44843	D	0.997853	B;B	0.24675	0.109;0.04	B;B	0.35312	0.2;0.075	T	0.06770	-1.0808	10	0.15066	T	0.55	-24.1822	10.3658	0.44024	0.0:0.4018:0.0:0.5982	rs17057901;rs17057901	231;220	B4DX68;Q96KB5	.;TOPK_HUMAN	D	220;231	ENSP00000301905:E220D;ENSP00000428489:E231D	ENSP00000301905:E220D	E	-	3	2	PBK	27724506	0.005000	0.15991	0.807000	0.32361	0.928000	0.56348	-0.940000	0.03929	-0.140000	0.11394	0.655000	0.94253	GAG	C|0.978;G|0.022	0.022	strong		0.428	PBK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219952.2	NM_018492	
NTSR2	23620	hgsc.bcm.edu	37	2	11800180	11800180	+	Silent	SNP	G	G	A	rs35653499	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:11800180G>A	ENST00000306928.5	-	3	1012	c.978C>T	c.(976-978)gaC>gaT	p.D326D		NM_012344.3	NP_036476	O95665	NTR2_HUMAN	neurotensin receptor 2	326					cell surface receptor signaling pathway (GO:0007166)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|regulation of membrane potential (GO:0042391)|sensory perception (GO:0007600)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled neurotensin receptor activity (GO:0016492)|G-protein coupled receptor activity (GO:0004930)			breast(1)|large_intestine(7)|lung(7)|prostate(1)|urinary_tract(1)	17	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.129)|OV - Ovarian serous cystadenocarcinoma(76;0.24)	Levocabastine(DB01106)	CAGTCCACGCGTCATCAGGTA	0.602													G|||	81	0.0161741	0.0446	0.0086	5008	,	,		21158	0.0159		0.0	False		,,,				2504	0.0				p.D326D		Atlas-SNP	.											.	NTSR2	36	.	0			c.C978T						PASS	.	G		196,4210	122.1+/-159.5	7,182,2014	105.0	89.0	95.0		978	-1.8	0.0	2	dbSNP_126	95	0,8600		0,0,4300	no	coding-synonymous	NTSR2	NM_012344.3		7,182,6314	AA,AG,GG		0.0,4.4485,1.507		326/411	11800180	196,12810	2203	4300	6503	SO:0001819	synonymous_variant	23620	exon3			CCACGCGTCATCA	Y10148	CCDS1681.1	2p25.1	2012-08-08			ENSG00000169006	ENSG00000169006		"""GPCR / Class A : Neurotensin receptors"""	8040	protein-coding gene	gene with protein product		605538				8647296, 9851594	Standard	NM_012344		Approved	NTR2	uc002rbq.4	O95665	OTTHUMG00000119083	ENST00000306928.5:c.978C>T	2.37:g.11800180G>A		93.0	0.0	0		105.0	55.0	0.52381	NM_012344	Q53QQ5|Q57Z87|Q8IY58|Q8TBH6	Silent	SNP	ENST00000306928.5	37	CCDS1681.1																																																																																			G|0.982;A|0.018	0.018	strong		0.602	NTSR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239297.1		
PER3	8863	hgsc.bcm.edu	37	1	7887499	7887499	+	Missense_Mutation	SNP	T	T	G	rs35899625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:7887499T>G	ENST00000361923.2	+	17	2661	c.2486T>G	c.(2485-2487)tTg>tGg	p.L829W	PER3_ENST00000377532.3_Missense_Mutation_p.L837W|RP3-467L1.4_ENST00000451646.1_RNA	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	829	Pro-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)			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)		GGGCTGCCCTTGTCCGAGGGC	0.592													T|||	12	0.00239617	0.0083	0.0014	5008	,	,		17848	0.0		0.0	False		,,,				2504	0.0				p.L829W		Atlas-SNP	.											.	PER3	95	.	0			c.T2486G						PASS	.	T	TRP/LEU	46,4360	48.2+/-83.0	1,44,2158	104.0	104.0	104.0		2486	-1.6	0.0	1	dbSNP_126	104	0,8600		0,0,4300	yes	missense	PER3	NM_016831.1	61	1,44,6458	GG,GT,TT		0.0,1.044,0.3537	possibly-damaging	829/1202	7887499	46,12960	2203	4300	6503	SO:0001583	missense	8863	exon17			TGCCCTTGTCCGA	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.2486T>G	1.37:g.7887499T>G	ENSP00000355031:p.Leu829Trp	144.0	0.0	0		207.0	116.0	0.560386	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	T	14.56	2.570910	0.45798	0.01044	0.0	ENSG00000049246	ENST00000377532;ENST00000361923;ENST00000539773	T;T	0.11063	2.81;2.81	3.82	-1.61	0.08399	.	2.355770	0.02257	N	0.067230	T	0.10981	0.0268	N	0.14661	0.345	0.09310	N	1	D;D;D;D	0.60575	0.979;0.983;0.988;0.979	P;P;P;P	0.62089	0.793;0.842;0.898;0.793	T	0.32666	-0.9898	10	0.38643	T	0.18	.	9.3251	0.37988	0.0:0.4119:0.0:0.5881	rs35899625	829;837;837;829	A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;PER3_HUMAN	W	837;829;40	ENSP00000366755:L837W;ENSP00000355031:L829W	ENSP00000355031:L829W	L	+	2	0	PER3	7810086	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.331000	0.07914	-0.204000	0.10235	-0.337000	0.08149	TTG	T|0.995;G|0.005	0.005	strong		0.592	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
DSP	1832	hgsc.bcm.edu	37	6	7576569	7576569	+	Silent	SNP	T	T	C	rs146407262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:7576569T>C	ENST00000379802.3	+	19	3014	c.2673T>C	c.(2671-2673)taT>taC	p.Y891Y	DSP_ENST00000418664.2_Silent_p.Y891Y	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	891	Globular 1.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		TGAGGAATTATCGTGATAACT	0.383													T|||	35	0.00698882	0.0257	0.0014	5008	,	,		18556	0.0		0.0	False		,,,				2504	0.0				p.Y891Y		Atlas-SNP	.											.	DSP	306	.	0			c.T2673C						PASS	.	T	,	100,4306	79.9+/-118.3	1,98,2104	107.0	110.0	109.0		2673,2673	-6.6	0.9	6	dbSNP_134	109	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	DSP	NM_001008844.1,NM_004415.2	,	1,98,6404	CC,CT,TT		0.0,2.2696,0.7689	,	891/2273,891/2872	7576569	100,12906	2203	4300	6503	SO:0001819	synonymous_variant	1832	exon19			GAATTATCGTGAT	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"""desmoplakin (DPI, DPII)"""			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.2673T>C	6.37:g.7576569T>C		89.0	0.0	0		85.0	38.0	0.447059	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Silent	SNP	ENST00000379802.3	37	CCDS4501.1																																																																																			T|0.991;C|0.009	0.009	strong		0.383	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
DHTKD1	55526	hgsc.bcm.edu	37	10	12160868	12160868	+	Silent	SNP	C	C	T	rs12769375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:12160868C>T	ENST00000263035.4	+	15	2585	c.2523C>T	c.(2521-2523)ttC>ttT	p.F841F	U6_ENST00000606801.1_RNA	NM_018706.5	NP_061176	Q96HY7	DHTK1_HUMAN	dehydrogenase E1 and transketolase domain containing 1	841					cell death (GO:0008219)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hematopoietic progenitor cell differentiation (GO:0002244)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(1)	44		Renal(717;0.228)	BRCA - Breast invasive adenocarcinoma(52;0.188)			TCTGCCCCTTCCCGTTGGATT	0.448													C|||	48	0.00958466	0.0356	0.0014	5008	,	,		17605	0.0		0.0	False		,,,				2504	0.0				p.F841F		Atlas-SNP	.											.	DHTKD1	104	.	0			c.C2523T						PASS	.	C		153,4253	104.7+/-143.2	4,145,2054	146.0	143.0	144.0		2523	3.2	1.0	10	dbSNP_121	144	0,8600		0,0,4300	no	coding-synonymous	DHTKD1	NM_018706.5		4,145,6354	TT,TC,CC		0.0,3.4725,1.1764		841/920	12160868	153,12853	2203	4300	6503	SO:0001819	synonymous_variant	55526	exon15			CCCCTTCCCGTTG	BC002477	CCDS7087.1	10p14	2003-11-24			ENSG00000181192	ENSG00000181192			23537	protein-coding gene	gene with protein product		614984				10997877	Standard	NM_018706		Approved	KIAA1630, MGC3090, DKFZP762M115	uc001ild.5	Q96HY7	OTTHUMG00000017677	ENST00000263035.4:c.2523C>T	10.37:g.12160868C>T		83.0	0.0	0		78.0	35.0	0.448718	NM_018706	Q68CU5|Q9BUM8|Q9HCE2	Silent	SNP	ENST00000263035.4	37	CCDS7087.1																																																																																			C|0.985;T|0.015	0.015	strong		0.448	DHTKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046777.1	NM_018706	
ZP4	57829	hgsc.bcm.edu	37	1	238053226	238053226	+	Missense_Mutation	SNP	G	G	A	rs34370253	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:238053226G>A	ENST00000366570.4	-	3	499	c.341C>T	c.(340-342)gCg>gTg	p.A114V	RP11-193H5.1_ENST00000450451.1_RNA	NM_021186.3	NP_067009.1	Q12836	ZP4_HUMAN	zona pellucida glycoprotein 4	114			A -> V (in dbSNP:rs34370253).		acrosomal vesicle exocytosis (GO:0060478)|binding of sperm to zona pellucida (GO:0007339)|intracellular signal transduction (GO:0035556)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of humoral immune response (GO:0002922)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of T cell proliferation (GO:0042102)|protein kinase A signaling (GO:0010737)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	acrosin binding (GO:0032190)|signal transducer activity (GO:0004871)			breast(6)|cervix(2)|endometrium(5)|kidney(2)|large_intestine(8)|lung(42)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	73	Ovarian(103;0.103)	all_cancers(173;0.00175)|all_epithelial(177;0.162)|all_neural(198;0.164)|Melanoma(53;0.211)|Prostate(94;0.214)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)			GTGTTCAGCCGCGCCTGCTCC	0.567													G|||	154	0.0307508	0.1089	0.013	5008	,	,		19719	0.0		0.001	False		,,,				2504	0.0				p.A114V	NSCLC(166;160 2029 11600 18754 19936)	Atlas-SNP	.											ZP4,caecum,carcinoma,0,1	ZP4	161	1	0			c.C341T						PASS	.	G	VAL/ALA	386,4020	194.0+/-219.0	14,358,1831	199.0	206.0	203.0		341	-6.6	0.0	1	dbSNP_126	203	6,8594	4.3+/-15.6	0,6,4294	yes	missense	ZP4	NM_021186.3	64	14,364,6125	AA,AG,GG		0.0698,8.7608,3.014	benign	114/541	238053226	392,12614	2203	4300	6503	SO:0001583	missense	57829	exon3			TCAGCCGCGCCTG	U05781	CCDS1615.1	1q43	2013-01-17			ENSG00000116996	ENSG00000116996		"""Zona pellucida glycoproteins"""	15770	protein-coding gene	gene with protein product		613514				7841460	Standard	NM_021186		Approved	ZPB	uc001hym.3	Q12836	OTTHUMG00000039586	ENST00000366570.4:c.341C>T	1.37:g.238053226G>A	ENSP00000355529:p.Ala114Val	210.0	1.0	0.0047619		172.0	84.0	0.488372	NM_021186	B2RAE1	Missense_Mutation	SNP	ENST00000366570.4	37	CCDS1615.1	56	0.02564102564102564	52	0.10569105691056911	4	0.011049723756906077	0	0.0	0	0.0	G	0.052	-1.248697	0.01469	0.087608	6.98E-4	ENSG00000116996	ENST00000366570	T	0.74632	-0.86	4.37	-6.58	0.01836	.	0.845246	0.10705	N	0.643569	T	0.00875	0.0029	N	0.11201	0.11	0.09310	N	1	B	0.17667	0.023	B	0.10450	0.005	T	0.13522	-1.0506	10	0.02654	T	1	0.4495	3.7495	0.08561	0.5715:0.1196:0.1878:0.1212	rs34370253	114	Q12836	ZP4_HUMAN	V	114	ENSP00000355529:A114V	ENSP00000355529:A114V	A	-	2	0	ZP4	236119849	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.059000	0.11731	-2.021000	0.00939	-2.828000	0.00107	GCG	G|0.972;A|0.028	0.028	strong		0.567	ZP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095476.1		
PSG8	440533	hgsc.bcm.edu	37	19	43268242	43268242	+	Missense_Mutation	SNP	C	C	T	rs76352186	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43268242C>T	ENST00000306511.4	-	2	353	c.256G>A	c.(256-258)Ggt>Agt	p.G86S	PSG8_ENST00000406636.3_Intron|PSG8_ENST00000404209.4_Missense_Mutation_p.G86S|PSG8_ENST00000401467.2_Missense_Mutation_p.G86S	NM_182707.2	NP_874366.1	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8	86	Ig-like V-type.					extracellular region (GO:0005576)				breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(19)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	40		Prostate(69;0.00899)				ATTATTTGACCGTCTACTACA	0.433													.|||	285	0.0569089	0.1952	0.0202	5008	,	,		22232	0.0		0.006	False		,,,				2504	0.0072				p.G86S		Atlas-SNP	.											.	PSG8	101	.	0			c.G256A						PASS	.	T	SER/GLY,,SER/GLY	772,3634	311.9+/-292.3	84,604,1515	248.0	265.0	259.0		256,,256	-2.7	0.0	19	dbSNP_131	259	131,8467	67.3+/-129.8	1,129,4169	no	missense,intron,missense	PSG8	NM_001130167.1,NM_001130168.1,NM_182707.2	56,,56	85,733,5684	TT,TC,CC		1.5236,17.5216,6.944	benign,,benign	86/420,,86/427	43268242	903,12101	2203	4299	6502	SO:0001583	missense	440533	exon2			TTTGACCGTCTAC	M74106	CCDS33037.1, CCDS46090.1, CCDS46091.1	19q13.2	2013-01-29			ENSG00000124467	ENSG00000124467		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9525	protein-coding gene	gene with protein product		176397				1672663, 1572651	Standard	NM_182707		Approved		uc002ouo.2	Q9UQ74	OTTHUMG00000151118	ENST00000306511.4:c.256G>A	19.37:g.43268242C>T	ENSP00000305005:p.Gly86Ser	247.0	1.0	0.00404858		233.0	98.0	0.420601	NM_001130167	A5PKV3|B2RPL4|B4DTI6|O60410|Q68CR6	Missense_Mutation	SNP	ENST00000306511.4	37	CCDS33037.1	126	0.057692307692307696	112	0.22764227642276422	8	0.022099447513812154	0	0.0	6	0.0079155672823219	c	0.005	-2.167646	0.00315	0.175216	0.015236	ENSG00000124467	ENST00000404209;ENST00000401467;ENST00000407488;ENST00000306511	T;T;T	0.63913	-0.07;-0.07;-0.07	1.35	-2.7	0.06004	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	N	0.15975	0.35	0.80722	P	0.0	B;B;B;B;B	0.20780	0.002;0.003;0.048;0.001;0.001	B;B;B;B;B	0.23018	0.004;0.011;0.043;0.005;0.009	T	0.06303	-1.0834	8	0.08599	T	0.76	.	5.2757	0.15649	0.0:0.4599:0.1655:0.3746	.	86;86;86;86;86	B5MCQ0;Q9UQ74;E7ENH0;Q9UQ74-3;A5PKV3	.;PSG8_HUMAN;.;.;.	S	86	ENSP00000385869:G86S;ENSP00000386090:G86S;ENSP00000305005:G86S	ENSP00000305005:G86S	G	-	1	0	PSG8	47960082	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.991000	0.01478	-3.700000	0.00119	-2.741000	0.00127	GGT	C|0.936;T|0.064	0.064	strong		0.433	PSG8-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464526.1		
WDR11	55717	hgsc.bcm.edu	37	10	122649481	122649481	+	Missense_Mutation	SNP	C	C	T	rs150399543	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:122649481C>T	ENST00000263461.6	+	18	2549	c.2303C>T	c.(2302-2304)gCa>gTa	p.A768V	WDR11_ENST00000604509.1_3'UTR	NM_018117.11	NP_060587.8	Q8WWQ0	PHIP_HUMAN	WD repeat domain 11	0					cytoskeleton organization (GO:0007010)|insulin receptor signaling pathway (GO:0008286)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell morphogenesis (GO:0022604)|regulation of growth (GO:0040008)|regulation of protein phosphorylation (GO:0001932)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	insulin receptor binding (GO:0005158)|lysine-acetylated histone binding (GO:0070577)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(9)|prostate(2)|skin(2)|stomach(5)	38						AAATTAATAGCAATGTACAAT	0.393													C|||	12	0.00239617	0.0091	0.0	5008	,	,		15112	0.0		0.0	False		,,,				2504	0.0				p.A768V		Atlas-SNP	.											WDR11,NS,carcinoma,-1,1	WDR11	95	1	0			c.C2303T						PASS	.	C	VAL/ALA	30,4376	23.3+/-48.9	0,30,2173	114.0	108.0	110.0		2303	5.5	1.0	10	dbSNP_134	110	0,8600		0,0,4300	yes	missense	WDR11	NM_018117.11	64	0,30,6473	TT,TC,CC		0.0,0.6809,0.2307	benign	768/1225	122649481	30,12976	2203	4300	6503	SO:0001583	missense	55717	exon18			TAATAGCAATGTA	AF320223	CCDS7619.1	10q26	2013-01-21	2010-01-06	2010-01-06	ENSG00000120008	ENSG00000120008		"""WD repeat domain containing"""	13831	protein-coding gene	gene with protein product		606417	"""bromodomain and WD repeat domain containing 2"""	BRWD2		10718198, 11536051	Standard	NM_018117		Approved	KIAA1351, FLJ10506, WDR15, HH14, DR11	uc021pzt.1	Q9BZH6	OTTHUMG00000019171	ENST00000263461.6:c.2303C>T	10.37:g.122649481C>T	ENSP00000263461:p.Ala768Val	65.0	0.0	0		58.0	26.0	0.448276	NM_018117	A7J992|B2RPK4|Q05CQ9|Q5VVH4|Q66I29|Q69YV1|Q8NBZ5|Q96H52|Q96ME2|Q9H261	Missense_Mutation	SNP	ENST00000263461.6	37	CCDS7619.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	c	9.054	0.992836	0.18966	0.006809	0.0	ENSG00000120008	ENST00000263461	T	0.50001	0.76	5.49	5.49	0.81192	WD40/YVTN repeat-like-containing domain (1);	0.184844	0.49916	D	0.000125	T	0.11024	0.0269	N	0.00648	-1.295	0.44477	D	0.99741	B;B;B;B	0.06786	0.001;0.0;0.001;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.30357	-0.9981	10	0.02654	T	1	-9.4036	13.0155	0.58754	0.0:0.9262:0.0:0.0738	.	768;768;59;297	Q9BZH6;B2RCJ6;Q9NWV7;Q659C9	WDR11_HUMAN;.;.;.	V	768	ENSP00000263461:A768V	ENSP00000263461:A768V	A	+	2	0	WDR11	122639471	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.417000	0.66423	2.733000	0.93635	0.655000	0.94253	GCA	C|0.997;T|0.003	0.003	strong		0.393	WDR11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050707.2		
BAZ2B	29994	hgsc.bcm.edu	37	2	160287443	160287443	+	Missense_Mutation	SNP	A	A	C	rs200904019	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160287443A>C	ENST00000392783.2	-	10	2620	c.2125T>G	c.(2125-2127)Tgt>Ggt	p.C709G	BAZ2B_ENST00000355831.2_Missense_Mutation_p.C709G|BAZ2B_ENST00000343439.5_Intron|BAZ2B_ENST00000392782.1_Missense_Mutation_p.C707G	NM_013450.2	NP_038478.2	Q9UIF8	BAZ2B_HUMAN	bromodomain adjacent to zinc finger domain, 2B	709					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(7)|liver(2)|lung(41)|ovary(3)|prostate(1)|skin(2)|soft_tissue(1)|urinary_tract(1)	82						GATTCAGAACATAAGGCAGCA	0.453													A|||	6	0.00119808	0.0045	0.0	5008	,	,		18357	0.0		0.0	False		,,,				2504	0.0				p.C709G		Atlas-SNP	.											.	BAZ2B	196	.	0			c.T2125G						PASS	.	A	GLY/CYS	20,3846		0,20,1913	145.0	144.0	144.0		2125	5.7	1.0	2		144	0,8272		0,0,4136	yes	missense	BAZ2B	NM_013450.2	159	0,20,6049	CC,CA,AA		0.0,0.5173,0.1648	probably-damaging	709/2169	160287443	20,12118	1933	4136	6069	SO:0001583	missense	29994	exon10			CAGAACATAAGGC	AB032255	CCDS2209.2, CCDS74594.1	2q24.2	2013-01-28			ENSG00000123636	ENSG00000123636		"""Zinc fingers, PHD-type"""	963	protein-coding gene	gene with protein product		605683				10662543	Standard	XM_005246488		Approved	WALp4	uc002uao.3	Q9UIF8	OTTHUMG00000132027	ENST00000392783.2:c.2125T>G	2.37:g.160287443A>C	ENSP00000376534:p.Cys709Gly	172.0	0.0	0		162.0	70.0	0.432099	NM_013450	D3DPA8|Q96EA1|Q96SQ8|Q9P252|Q9Y4N8	Missense_Mutation	SNP	ENST00000392783.2	37	CCDS2209.2	4	0.0018315018315018315	1	0.0020325203252032522	0	0.0	3	0.005244755244755245	0	0.0	A	14.89	2.670797	0.47781	0.005173	0.0	ENSG00000123636	ENST00000392782;ENST00000392783;ENST00000355831	T;T;T	0.21191	2.02;2.02;2.02	5.71	5.71	0.89125	.	0.000000	0.40222	U	0.001146	T	0.27063	0.0663	L	0.32530	0.975	0.80722	D	1	D;D;D	0.71674	0.996;0.978;0.998	P;D;D	0.75484	0.889;0.922;0.986	T	0.02398	-1.1165	10	0.25751	T	0.34	-8.1218	15.968	0.79987	1.0:0.0:0.0:0.0	.	513;707;709	Q9UIF8-4;Q9UIF8-5;Q9UIF8	.;.;BAZ2B_HUMAN	G	707;709;709	ENSP00000376533:C707G;ENSP00000376534:C709G;ENSP00000348087:C709G	ENSP00000348087:C709G	C	-	1	0	BAZ2B	159995689	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.327000	0.52045	2.175000	0.68902	0.523000	0.50628	TGT	A|0.998;C|0.002	0.002	strong		0.453	BAZ2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255037.2		
ADAMTS7	11173	hgsc.bcm.edu	37	15	79065509	79065509	+	Missense_Mutation	SNP	T	T	C	rs146076001	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:79065509T>C	ENST00000388820.4	-	14	2257	c.2047A>G	c.(2047-2049)Atg>Gtg	p.M683V	ADAMTS7_ENST00000566303.1_Intron	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	683	Cys-rich.				cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						CGGTCCTCCATAGCACCGGAG	0.677													T|||	3	0.000599042	0.0023	0.0	5008	,	,		9782	0.0		0.0	False		,,,				2504	0.0				p.M683V		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.A2047G						PASS	.	T	VAL/MET	3,4287		0,3,2142	15.0	14.0	15.0		2047	-4.2	0.1	15	dbSNP_134	15	0,8154		0,0,4077	no	missense	ADAMTS7	NM_014272.3	21	0,3,6219	CC,CT,TT		0.0,0.0699,0.0241	benign	683/1687	79065509	3,12441	2145	4077	6222	SO:0001583	missense	11173	exon14			CCTCCATAGCACC	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	223	protein-coding gene	gene with protein product	"""COMPase"", ""a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"""	605009	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"""			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.2047A>G	15.37:g.79065509T>C	ENSP00000373472:p.Met683Val	461.0	1.0	0.0021692		783.0	340.0	0.434227	NM_014272	Q14F51|Q6P7J9	Missense_Mutation	SNP	ENST00000388820.4	37	CCDS32303.1	.	.	.	.	.	.	.	.	.	.	T	0.018	-1.480661	0.01027	6.99E-4	0.0	ENSG00000136378	ENST00000388820	T	0.68025	-0.3	3.75	-4.16	0.03869	.	0.686315	0.12999	N	0.421839	T	0.22282	0.0537	N	0.00347	-1.61	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.43621	-0.9380	10	0.02654	T	1	.	10.8048	0.46512	0.0:0.4278:0.0:0.5722	.	683;683	A8MQ00;Q9UKP4	.;ATS7_HUMAN	V	683	ENSP00000373472:M683V	ENSP00000373472:M683V	M	-	1	0	ADAMTS7	76852564	0.000000	0.05858	0.065000	0.19835	0.592000	0.36648	0.103000	0.15292	-0.746000	0.04766	0.386000	0.25728	ATG	T|1.000;C|0.000	0.000	weak		0.677	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
ACSS1	84532	hgsc.bcm.edu	37	20	25038484	25038484	+	Silent	SNP	G	G	A	rs66817095	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:25038484G>A	ENST00000323482.4	-	1	334	c.255C>T	c.(253-255)acC>acT	p.T85T	ACSS1_ENST00000376726.3_Silent_p.T85T|ACSS1_ENST00000432802.2_Silent_p.T85T	NM_001252675.1|NM_032501.3	NP_001239604.1|NP_115890.2	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	85					acetate biosynthetic process (GO:0019413)|acetyl-CoA biosynthetic process (GO:0006085)|acetyl-CoA biosynthetic process from acetate (GO:0019427)|ethanol oxidation (GO:0006069)|propionate biosynthetic process (GO:0019542)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	mitochondrial matrix (GO:0005759)	acetate-CoA ligase activity (GO:0003987)|AMP binding (GO:0016208)|ATP binding (GO:0005524)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	TGTGGTAGGGGGTGTCCCACA	0.662																																					p.T85T		Atlas-SNP	.											.	ACSS1	46	.	0			c.C255T						PASS	.						42.0	47.0	45.0					20																	25038484		2203	4300	6503	SO:0001819	synonymous_variant	84532	exon1			GTAGGGGGTGTCC		CCDS13167.1, CCDS58764.1, CCDS58765.1	20p11.23-p11.21	2012-07-13	2005-09-08	2005-09-08	ENSG00000154930	ENSG00000154930	6.2.1.1	"""Acyl-CoA synthetase family"""	16091	protein-coding gene	gene with protein product		614355	"""acetyl-Coenzyme A synthetase 2 (AMP forming)-like"""	ACAS2L			Standard	NM_032501		Approved	dJ568C11.3, AceCS2L, MGC33843	uc002wub.3	Q9NUB1	OTTHUMG00000032112	ENST00000323482.4:c.255C>T	20.37:g.25038484G>A		141.0	0.0	0		135.0	66.0	0.488889	NM_001252677	B3KXL2|B4DJZ3|D3DW48|F5H6F4|F8W7Y1|Q5TF42|Q8IV99|Q8N234|Q96JI1|Q96JX6|Q9NU28	Silent	SNP	ENST00000323482.4	37	CCDS13167.1																																																																																			G|0.845;T|0.155	.	alt		0.662	ACSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078386.2	NM_032501	
ADCY2	108	hgsc.bcm.edu	37	5	7690872	7690872	+	Silent	SNP	G	G	A	rs10079813	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:7690872G>A	ENST00000338316.4	+	5	878	c.789G>A	c.(787-789)agG>agA	p.R263R	ADCY2_ENST00000513693.1_3'UTR|ADCY2_ENST00000537121.1_Silent_p.R83R	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	263					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						TCATCCAGAGGCTGCAGGGCC	0.567													G|||	98	0.0195687	0.0741	0.0	5008	,	,		15611	0.0		0.0	False		,,,				2504	0.0				p.R263R		Atlas-SNP	.											.	ADCY2	337	.	0			c.G789A						PASS	.	G		292,4114	159.6+/-192.1	7,278,1918	70.0	66.0	67.0		789	1.9	1.0	5	dbSNP_119	67	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	ADCY2	NM_020546.2		7,281,6215	AA,AG,GG		0.0349,6.6273,2.2682		263/1092	7690872	295,12711	2203	4300	6503	SO:0001819	synonymous_variant	108	exon5			CCAGAGGCTGCAG	AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"""Adenylate cyclases"""	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.789G>A	5.37:g.7690872G>A		107.0	0.0	0		119.0	53.0	0.445378	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Silent	SNP	ENST00000338316.4	37	CCDS3872.2																																																																																			G|0.976;A|0.024	0.024	strong		0.567	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546	
RIMS2	9699	hgsc.bcm.edu	37	8	104897606	104897606	+	Missense_Mutation	SNP	C	C	G	rs146399863	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:104897606C>G	ENST00000436393.2	+	2	354	c.113C>G	c.(112-114)gCt>gGt	p.A38G	RIMS2_ENST00000507740.1_Missense_Mutation_p.A68G|RIMS2_ENST00000522174.1_3'UTR|RIMS2_ENST00000406091.3_Missense_Mutation_p.A260G|RIMS2_ENST00000262231.10_Missense_Mutation_p.A68G			Q9UQ26	RIMS2_HUMAN	regulating synaptic membrane exocytosis 2	291	RabBD. {ECO:0000255|PROSITE- ProRule:PRU00234}.				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)			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)			TCACAGTATGCTACTTCGGAT	0.398										HNSCC(12;0.0054)			C|||	2	0.000399361	0.0015	0.0	5008	,	,		21790	0.0		0.0	False		,,,				2504	0.0				p.A260G		Atlas-SNP	.											.	RIMS2	1357	.	0			c.C779G						PASS	.	C	GLY/ALA,GLY/ALA	6,3780		0,6,1887	92.0	83.0	86.0		779,203	4.4	1.0	8	dbSNP_134	86	0,8240		0,0,4120	yes	missense,missense	RIMS2	NM_001100117.2,NM_014677.4	60,60	0,6,6007	GG,GC,CC		0.0,0.1585,0.0499	benign,benign	260/1350,68/1164	104897606	6,12020	1893	4120	6013	SO:0001583	missense	9699	exon4			AGTATGCTACTTC	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		ENST00000436393.2:c.113C>G	8.37:g.104897606C>G	ENSP00000390665:p.Ala38Gly	75.0	0.0	0		84.0	45.0	0.535714	NM_001100117	B3KX91|F8WD47|O43413|Q86XL9|Q8IWV9|Q8IWW1	Missense_Mutation	SNP	ENST00000436393.2	37		2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	14.15	2.450412	0.43531	0.001585	0.0	ENSG00000176406	ENST00000504942;ENST00000329869;ENST00000406091;ENST00000402998;ENST00000515551;ENST00000262231;ENST00000507740;ENST00000408894;ENST00000436393	T;T;T;T;T;T;T	0.37584	1.19;1.19;2.19;2.26;2.25;2.18;2.62	5.31	4.42	0.53409	.	.	.	.	.	T	0.41419	0.1158	L	0.51422	1.61	0.80722	D	1	B;P;P;P;P	0.45902	0.278;0.676;0.868;0.694;0.559	B;B;P;B;B	0.48141	0.248;0.273;0.568;0.332;0.361	T	0.31138	-0.9954	9	0.54805	T	0.06	.	12.9673	0.58492	0.0:0.9206:0.0:0.0794	.	291;38;68;68;260	Q9UQ26;D6RA03;Q9UQ26-1;Q9UQ26-3;F8WD47	RIMS2_HUMAN;.;.;.;.	G	260;291;260;291;68;68;68;68;38	ENSP00000427018:A260G;ENSP00000384892:A260G;ENSP00000425205:A68G;ENSP00000262231:A68G;ENSP00000423559:A68G;ENSP00000386228:A68G;ENSP00000390665:A38G	ENSP00000262231:A68G	A	+	2	0	RIMS2	104966782	1.000000	0.71417	0.973000	0.42090	0.970000	0.65996	4.441000	0.59981	1.204000	0.43247	0.460000	0.39030	GCT	C|0.999;G|0.001	0.001	strong		0.398	RIMS2-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000367217.1	NM_001100117	
TANK	10010	hgsc.bcm.edu	37	2	162088034	162088034	+	Missense_Mutation	SNP	C	C	T	rs2229759	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:162088034C>T	ENST00000392749.2	+	7	1312	c.1073C>T	c.(1072-1074)cCg>cTg	p.P358L	TANK_ENST00000259075.2_Missense_Mutation_p.P358L|AC009299.2_ENST00000421122.2_RNA|TANK_ENST00000405852.1_Missense_Mutation_p.P358L|TANK_ENST00000406287.1_Intron|TANK_ENST00000402568.1_Intron|AC009299.2_ENST00000445372.1_RNA	NM_001199135.1	NP_001186064.1	Q92844	TANK_HUMAN	TRAF family member-associated NFKB activator	358			P -> L (in dbSNP:rs2229759).		I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(7)|ovary(1)|prostate(1)	21						CTCGATTCCCCGGGAAAAGCA	0.433													C|||	128	0.0255591	0.0938	0.0058	5008	,	,		19086	0.0		0.0	False		,,,				2504	0.0				p.P358L		Atlas-SNP	.											TANK,NS,carcinoma,-1,1	TANK	35	1	0			c.C1073T						PASS	.	C	LEU/PRO,LEU/PRO	230,4176	129.8+/-166.5	4,222,1977	45.0	45.0	45.0		1073,1073	5.6	1.0	2	dbSNP_98	45	3,8595	3.0+/-9.4	0,3,4296	yes	missense,missense	TANK	NM_001199135.1,NM_004180.2	98,98	4,225,6273	TT,TC,CC		0.0349,5.2202,1.7918	probably-damaging,probably-damaging	358/426,358/426	162088034	233,12771	2203	4299	6502	SO:0001583	missense	10010	exon7			ATTCCCCGGGAAA	U59863	CCDS2215.1, CCDS46436.1	2q24-q31	2008-02-05			ENSG00000136560	ENSG00000136560			11562	protein-coding gene	gene with protein product		603893		TRAF2		8710854, 8855313	Standard	NM_004180		Approved	I-TRAF	uc002ubr.2	Q92844	OTTHUMG00000132037	ENST00000392749.2:c.1073C>T	2.37:g.162088034C>T	ENSP00000376505:p.Pro358Leu	39.0	0.0	0		24.0	12.0	0.5	NM_004180	D3DPB5|Q7Z4J6|Q92885	Missense_Mutation	SNP	ENST00000392749.2	37	CCDS2215.1	49	0.022435897435897436	47	0.09552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	C	16.38	3.106713	0.56291	0.052202	3.49E-4	ENSG00000136560	ENST00000259075;ENST00000392749;ENST00000405852;ENST00000437623;ENST00000439442	T;T;T;T;T	0.35973	1.68;1.68;1.29;1.28;1.61	5.57	5.57	0.84162	.	0.280521	0.34460	N	0.003944	T	0.01489	0.0048	L	0.59436	1.845	0.80722	D	1	D	0.63046	0.992	P	0.48454	0.578	T	0.00126	-1.2021	10	0.87932	D	0	-5.8187	15.5156	0.75822	0.1389:0.8611:0.0:0.0	rs2229759;rs35125118	358	Q92844	TANK_HUMAN	L	358;358;358;249;113	ENSP00000259075:P358L;ENSP00000376505:P358L;ENSP00000385487:P358L;ENSP00000412556:P249L;ENSP00000387439:P113L	ENSP00000259075:P358L	P	+	2	0	TANK	161796280	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	3.944000	0.56629	2.784000	0.95788	0.585000	0.79938	CCG	C|0.977;T|0.023	0.023	strong		0.433	TANK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324232.1	NM_133484	
XAB2	56949	hgsc.bcm.edu	37	19	7684502	7684502	+	Silent	SNP	G	G	A	rs4134869	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7684502G>A	ENST00000358368.4	-	19	2575	c.2538C>T	c.(2536-2538)gcC>gcT	p.A846A	XAB2_ENST00000534844.1_Silent_p.A843A	NM_020196.2	NP_064581.2	Q9HCS7	SYF1_HUMAN	XPA binding protein 2	846					blastocyst development (GO:0001824)|DNA repair (GO:0006281)|mRNA splicing, via spliceosome (GO:0000398)|nucleotide-excision repair (GO:0006289)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	26						CAAACACTGCGGCTGGCACGC	0.647								Direct reversal of damage;Nucleotide excision repair (NER)					g|||	196	0.0391374	0.1415	0.0115	5008	,	,		8459	0.001		0.0	False		,,,				2504	0.0				p.A846A		Atlas-SNP	.											.	XAB2	69	.	0			c.C2538T						PASS	.			613,3789		55,503,1643	26.0	24.0	25.0		2538	-7.2	0.1	19	dbSNP_108	25	4,8592		0,4,4294	no	coding-synonymous	XAB2	NM_020196.2		55,507,5937	AA,AG,GG		0.0465,13.9255,4.7469		846/856	7684502	617,12381	2201	4298	6499	SO:0001819	synonymous_variant	56949	exon19			CACTGCGGCTGGC	AB026111	CCDS32892.1	19p13.3	2013-08-21				ENSG00000076924			14089	protein-coding gene	gene with protein product	"""SYF1 homolog, RNA splicing factor (S. cerevisiae)"", ""SYF1 pre-mRNA-splicing factor"""	610850				10944529	Standard	NM_020196		Approved	HCNP, HCRN, SYF1, NTC90	uc002mgx.3	Q9HCS7		ENST00000358368.4:c.2538C>T	19.37:g.7684502G>A		142.0	0.0	0		161.0	78.0	0.484472	NM_020196	Q8TET6|Q96HB0|Q96IW0|Q9NRG6|Q9ULP3	Silent	SNP	ENST00000358368.4	37	CCDS32892.1																																																																																			G|0.944;A|0.056	0.056	strong		0.647	XAB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461021.1	NM_020196	
BMPER	168667	hgsc.bcm.edu	37	7	33946464	33946464	+	Silent	SNP	C	C	T	rs112068976	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:33946464C>T	ENST00000297161.2	+	3	542	c.168C>T	c.(166-168)gtC>gtT	p.V56V	BMPER_ENST00000426693.1_Silent_p.V56V	NM_133468.4	NP_597725.1	Q8N8U9	BMPER_HUMAN	BMP binding endothelial regulator	56	VWFC 1. {ECO:0000255|PROSITE- ProRule:PRU00220}.				blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|endothelial cell activation (GO:0042118)|inner ear development (GO:0048839)|negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of endothelial cell migration (GO:0010594)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|ureteric bud development (GO:0001657)	extracellular space (GO:0005615)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(24)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						AAGGTGAAGTCCTCCAGATTC	0.378													C|||	4	0.000798722	0.003	0.0	5008	,	,		18193	0.0		0.0	False		,,,				2504	0.0				p.V56V		Atlas-SNP	.											BMPER,NS,carcinoma,+1,1	BMPER	131	1	0			c.C168T						PASS	.	C		15,4391	22.3+/-47.3	0,15,2188	142.0	130.0	134.0		168	-6.9	0.3	7	dbSNP_132	134	0,8600		0,0,4300	no	coding-synonymous	BMPER	NM_133468.3		0,15,6488	TT,TC,CC		0.0,0.3404,0.1153		56/686	33946464	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	168667	exon3			TGAAGTCCTCCAG		CCDS5442.1	7p14.3	2009-02-18			ENSG00000164619	ENSG00000164619			24154	protein-coding gene	gene with protein product	"""crossveinless-2"""	608699				12897139, 14766204	Standard	NM_133468		Approved	Cv2, CRIM3	uc011kap.2	Q8N8U9	OTTHUMG00000128675	ENST00000297161.2:c.168C>T	7.37:g.33946464C>T		107.0	0.0	0		95.0	51.0	0.536842	NM_133468	A8K1P8|Q8TF36	Silent	SNP	ENST00000297161.2	37	CCDS5442.1																																																																																			C|0.999;T|0.001	0.001	strong		0.378	BMPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250570.2	NM_133468	
FCGBP	8857	hgsc.bcm.edu	37	19	40364397	40364397	+	Missense_Mutation	SNP	C	C	T	rs148917660		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40364397C>T	ENST00000221347.6	-	31	14252	c.14245G>A	c.(14245-14247)Ggt>Agt	p.G4749S		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	4749	TIL 11.					extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			CAGGAGTCACCGCAGAGCTCA	0.647													C|||	1	0.000199681	0.0008	0.0	5008	,	,		14509	0.0		0.0	False		,,,				2504	0.0				p.G4749S		Atlas-SNP	.											.	FCGBP	416	.	0			c.G14245A						PASS	.	C	SER/GLY	28,4376		0,28,2174	36.0	35.0	35.0		14245	4.1	0.0	19	dbSNP_134	35	0,8600		0,0,4300	no	missense	FCGBP	NM_003890.2	56	0,28,6474	TT,TC,CC		0.0,0.6358,0.2153	probably-damaging	4749/5406	40364397	28,12976	2202	4300	6502	SO:0001583	missense	8857	exon31			AGTCACCGCAGAG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.14245G>A	19.37:g.40364397C>T	ENSP00000221347:p.Gly4749Ser	60.0	0.0	0		77.0	41.0	0.532468	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	11.23	1.577576	0.28180	0.006358	0.0	ENSG00000090920	ENST00000221347	T	0.77750	-1.12	5.14	4.1	0.47936	Protease inhibitor I8, cysteine-rich trypsin inhibitor-like (2);	0.072904	0.53938	U	0.000047	T	0.59932	0.2230	M	0.66439	2.03	0.09310	N	1	P	0.40731	0.728	B	0.30495	0.116	T	0.58645	-0.7600	10	0.06891	T	0.86	.	12.6598	0.56808	0.0:0.9183:0.0:0.0817	.	4749	Q9Y6R7	FCGBP_HUMAN	S	4749	ENSP00000221347:G4749S	ENSP00000221347:G4749S	G	-	1	0	FCGBP	45056237	0.096000	0.21769	0.026000	0.17262	0.357000	0.29423	2.708000	0.47152	1.312000	0.45043	0.313000	0.20887	GGT	C|0.997;T|0.003	0.003	strong		0.647	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
PTPRN2	5799	hgsc.bcm.edu	37	7	157959794	157959794	+	Missense_Mutation	SNP	T	T	C	rs73745196	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:157959794T>C	ENST00000389418.4	-	6	748	c.739A>G	c.(739-741)Agt>Ggt	p.S247G	PTPRN2_ENST00000409483.1_Missense_Mutation_p.S209G|PTPRN2_ENST00000389416.4_Missense_Mutation_p.S230G|PTPRN2_ENST00000404321.2_Missense_Mutation_p.S270G|PTPRN2_ENST00000389413.3_Missense_Mutation_p.S247G	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	247				S -> G (in Ref. 2; CAA69880). {ECO:0000305}.	negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		GCATAGGCACTGAGGGCCGCC	0.662													C|||	100	0.0199681	0.0688	0.0086	5008	,	,		16162	0.0		0.003	False		,,,				2504	0.0				p.S247G		Atlas-SNP	.											.	PTPRN2	243	.	0			c.A739G						PASS	.		GLY/SER,GLY/SER,GLY/SER	297,4109	770.2+/-413.7	12,273,1918	27.0	23.0	25.0		739,688,739	-0.8	0.0	7	dbSNP_130	25	0,8600		0,0,4300	yes	missense,missense,missense	PTPRN2	NM_002847.3,NM_130842.2,NM_130843.2	56,56,56	12,273,6218	CC,CT,TT		0.0,6.7408,2.2836	benign,benign,benign	247/1016,230/999,247/987	157959794	297,12709	2203	4300	6503	SO:0001583	missense	5799	exon6			AGGCACTGAGGGC	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.739A>G	7.37:g.157959794T>C	ENSP00000374069:p.Ser247Gly	87.0	0.0	0		64.0	35.0	0.546875	NM_130843	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	37	CCDS5947.1	49	0.022435897435897436	42	0.08536585365853659	4	0.011049723756906077	0	0.0	3	0.00395778364116095	C	0.036	-1.306812	0.01353	0.067408	0.0	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	T;T;T;T;T	0.02916	4.12;4.13;4.12;4.12;4.11	4.59	-0.828	0.10799	.	0.484707	0.13807	N	0.361341	T	0.00073	0.0002	N	0.04203	-0.255	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.48080	-0.9066	10	0.19147	T	0.46	.	10.525	0.44943	0.0:0.1914:0.0:0.8086	.	270;209;247;230;247	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	G	209;247;230;247;270	ENSP00000387114:S209G;ENSP00000374064:S247G;ENSP00000374067:S230G;ENSP00000374069:S247G;ENSP00000385464:S270G	ENSP00000374064:S247G	S	-	1	0	PTPRN2	157652555	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.189000	0.09629	-0.624000	0.05611	-1.071000	0.02255	AGT	T|0.974;C|0.026	0.026	strong		0.662	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
TCHH	7062	hgsc.bcm.edu	37	1	152082320	152082320	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152082320T>C	ENST00000368804.1	-	2	3372	c.3373A>G	c.(3373-3375)Aga>Gga	p.R1125G		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1125	10 X 30 AA tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			cgttcctctctcagcagctgc	0.612																																					p.R1125G		Atlas-SNP	.											TCHH,NS,carcinoma,0,5	TCHH	275	5	0			c.A3373G						scavenged	.						93.0	94.0	94.0					1																	152082320		1979	4139	6118	SO:0001583	missense	7062	exon3			CCTCTCTCAGCAG	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.3373A>G	1.37:g.152082320T>C	ENSP00000357794:p.Arg1125Gly	219.0	1.0	0.00456621		292.0	12.0	0.0410959	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	T	5.521	0.281051	0.10458	.	.	ENSG00000159450	ENST00000368804	T	0.06849	3.25	2.38	1.02	0.19986	.	.	.	.	.	T	0.04407	0.0121	L	0.29908	0.895	0.09310	N	1	D	0.58268	0.982	P	0.59171	0.853	T	0.40590	-0.9555	9	0.28530	T	0.3	.	5.1512	0.15011	0.0:0.0:0.3026:0.6974	.	1125	Q07283	TRHY_HUMAN	G	1125	ENSP00000357794:R1125G	ENSP00000357794:R1125G	R	-	1	2	TCHH	150348944	0.001000	0.12720	0.006000	0.13384	0.018000	0.09664	1.171000	0.31896	0.940000	0.37473	0.379000	0.24179	AGA	.	.	none		0.612	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
TNFRSF13B	23495	hgsc.bcm.edu	37	17	16843708	16843708	+	Missense_Mutation	SNP	T	T	A	rs74811083|rs376630110	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:16843708T>A	ENST00000261652.2	-	4	575	c.563A>T	c.(562-564)aAg>aTg	p.K188M	TNFRSF13B_ENST00000437538.2_Missense_Mutation_p.K142M|TNFRSF13B_ENST00000583789.1_Missense_Mutation_p.K142M|TNFRSF13B_ENST00000581616.2_5'Flank|TNFRSF13B_ENST00000579315.1_Intron	NM_012452.2	NP_036584.1	O14836	TR13B_HUMAN	tumor necrosis factor receptor superfamily, member 13B	188					B cell homeostasis (GO:0001782)|cell surface receptor signaling pathway (GO:0007166)|hematopoietic progenitor cell differentiation (GO:0002244)|negative regulation of B cell proliferation (GO:0030889)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	receptor activity (GO:0004872)			endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(7)|skin(1)	16						ATCCCCCCTCTTCTTGAGGAA	0.647									IgA Deficiency, Selective				.|||	74	0.0147764	0.053	0.0058	5008	,	,		15377	0.0		0.0	False		,,,				2504	0.0				p.K188M		Atlas-SNP	.											.	TNFRSF13B	34	.	0			c.A563T						PASS	.	T	MET/LYS	217,4189	132.1+/-168.6	3,211,1989	73.0	74.0	74.0		563	2.4	0.8	17	dbSNP_131	74	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TNFRSF13B	NM_012452.2	95	3,212,6288	AA,AT,TT		0.0116,4.9251,1.6761	benign	188/294	16843708	218,12788	2203	4300	6503	SO:0001583	missense	23495	exon4	Familial Cancer Database	IGAD1, IGAD2	CCCCTCTTCTTGA	AF023614	CCDS11181.1	17p11.2	2014-09-17			ENSG00000240505	ENSG00000240505		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	18153	protein-coding gene	gene with protein product		604907				9311921	Standard	NM_012452		Approved	TACI, CD267	uc002gqs.1	O14836	OTTHUMG00000059262	ENST00000261652.2:c.563A>T	17.37:g.16843708T>A	ENSP00000261652:p.Lys188Met	74.0	0.0	0		94.0	58.0	0.617021	NM_012452	B2R8B0|B7Z6V8|Q32LX4|Q7Z6F5	Missense_Mutation	SNP	ENST00000261652.2	37	CCDS11181.1	25	0.011446886446886446	22	0.044715447154471545	3	0.008287292817679558	0	0.0	0	0.0	t	3.080	-0.189246	0.06299	0.049251	1.16E-4	ENSG00000240505	ENST00000437538;ENST00000261652	D;D	0.94417	-3.42;-3.38	3.43	2.43	0.29744	.	0.227067	0.28778	N	0.014167	T	0.70527	0.3234	L	0.39898	1.24	0.28171	N	0.928553	P;P	0.49447	0.924;0.875	P;B	0.47981	0.563;0.36	T	0.77109	-0.2709	10	0.87932	D	0	-20.7502	6.3592	0.21419	0.0:0.8441:0.0:0.1559	.	142;188	O14836-2;O14836	.;TR13B_HUMAN	M	142;188	ENSP00000413453:K142M;ENSP00000261652:K188M	ENSP00000261652:K188M	K	-	2	0	TNFRSF13B	16784433	0.992000	0.36948	0.846000	0.33378	0.143000	0.21401	0.653000	0.24902	0.520000	0.28426	-0.477000	0.04895	AAG	T|0.985;A|0.015	0.015	strong		0.647	TNFRSF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131474.2		
BPIFA3	128861	hgsc.bcm.edu	37	20	31812206	31812206	+	Missense_Mutation	SNP	A	A	G	rs112731808	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31812206A>G	ENST00000375454.3	+	3	534	c.324A>G	c.(322-324)atA>atG	p.I108M	BPIFA3_ENST00000490499.1_3'UTR|BPIFA3_ENST00000375452.3_Intron	NM_178466.3	NP_848561.2	Q9BQP9	BPIA3_HUMAN	BPI fold containing family A, member 3	108						extracellular region (GO:0005576)	lipid binding (GO:0008289)										GGATCCAGATATCATTCCATA	0.483													G|||	99	0.0197684	0.0446	0.0072	5008	,	,		20967	0.0308		0.004	False		,,,				2504	0.0				p.I108M		Atlas-SNP	.											.	.	.	.	0			c.A324G						PASS	.	G	,MET/ILE	187,4219	809.5+/-416.0	5,177,2021	173.0	153.0	160.0		,324	3.4	0.6	20	dbSNP_132	160	13,8587	818.7+/-406.8	0,13,4287	yes	intron,missense	BPIFA3	NM_001042439.1,NM_178466.3	,10	5,190,6308	GG,GA,AA		0.1512,4.2442,1.5378	,benign	,108/255	31812206	200,12806	2203	4300	6503	SO:0001583	missense	128861	exon3			CCAGATATCATTC		CCDS13216.2, CCDS42865.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131059	ENSG00000131059		"""BPI fold containing"""	16204	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 71"""	C20orf71		11971875, 21787333	Standard	XR_244132		Approved	bA49G10.4, SPLUNC3	uc002wyr.3	Q9BQP9	OTTHUMG00000032245	ENST00000375454.3:c.324A>G	20.37:g.31812206A>G	ENSP00000364603:p.Ile108Met	168.0	0.0	0		190.0	94.0	0.494737	NM_178466	Q5JWG8|Q6NZ38	Missense_Mutation	SNP	ENST00000375454.3	37	CCDS13216.2	55	0.025183150183150184	28	0.056910569105691054	3	0.008287292817679558	20	0.03496503496503497	4	0.005277044854881266	G	0.006	-2.099179	0.00360	0.042442	0.001512	ENSG00000131059	ENST00000375454	T	0.04970	3.52	4.35	3.41	0.39046	.	0.313773	0.27986	N	0.017055	T	0.00300	0.0009	N	0.01168	-0.975	0.43841	D	0.996421	B	0.02656	0.0	B	0.04013	0.001	T	0.55016	-0.8206	10	0.30854	T	0.27	-4.1596	7.0156	0.24887	0.2026:0.0:0.7974:0.0	.	108	Q9BQP9	BPIA3_HUMAN	M	108	ENSP00000364603:I108M	ENSP00000364603:I108M	I	+	3	3	BPIFA3	31275867	0.997000	0.39634	0.603000	0.28903	0.084000	0.17831	1.446000	0.35090	0.804000	0.34136	-0.213000	0.12676	ATA	A|0.983;G|0.017	0.017	strong		0.483	BPIFA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078672.1	NM_178466	
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39306004	39306004	+	Missense_Mutation	SNP	A	A	G	rs238829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39306004A>G	ENST00000343246.4	-	1	50	c.16T>C	c.(16-18)Tgt>Cgt	p.C6R		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	6	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].		C -> R (in dbSNP:rs238829).		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			ACAGAGCCACAACAGGAGCTG	0.592													A|||	189	0.0377396	0.1377	0.0101	5008	,	,		18094	0.0		0.0	False		,,,				2504	0.0				p.C6R		Atlas-SNP	.											.	KRTAP4-5	34	.	0			c.T16C						PASS	.	A	ARG/CYS	502,3898		31,440,1729	34.0	36.0	35.0		16	4.2	1.0	17	dbSNP_79	35	1,8595		0,1,4297	yes	missense	KRTAP4-5	NM_033188.3	180	31,441,6026	GG,GA,AA		0.0116,11.4091,3.8704	probably-damaging	6/182	39306004	503,12493	2200	4298	6498	SO:0001583	missense	85289	exon1			AGCCACAACAGGA	AJ406937	CCDS32650.1	17q21.2	2013-06-25			ENSG00000198271	ENSG00000198271		"""Keratin associated proteins"""	18899	protein-coding gene	gene with protein product						11279113	Standard	NM_033188		Approved	KAP4.5	uc002hwb.3	Q9BYR2	OTTHUMG00000133638	ENST00000343246.4:c.16T>C	17.37:g.39306004A>G	ENSP00000340546:p.Cys6Arg	307.0	0.0	0		346.0	153.0	0.442197	NM_033188		Missense_Mutation	SNP	ENST00000343246.4	37	CCDS32650.1	76	0.0347985347985348	70	0.14227642276422764	6	0.016574585635359115	0	0.0	0	0.0	.	8.628	0.892905	0.17613	0.114091	1.16E-4	ENSG00000198271	ENST00000343246	T	0.03065	4.06	4.25	4.25	0.50352	.	0.000000	0.40385	U	0.001109	T	0.00178	0.0005	H	0.94698	3.57	0.21325	P	0.999724217	D	0.59767	0.986	P	0.61800	0.894	T	0.04178	-1.0971	9	0.87932	D	0	.	11.6139	0.51078	1.0:0.0:0.0:0.0	rs238829;rs52814152;rs238829	6	Q9BYR2	KRA45_HUMAN	R	6	ENSP00000340546:C6R	ENSP00000340546:C6R	C	-	1	0	KRTAP4-5	36559530	0.995000	0.38212	1.000000	0.80357	0.017000	0.09413	1.548000	0.36201	1.900000	0.55004	0.533000	0.62120	TGT	A|0.962;G|0.038	0.038	strong		0.592	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1		
OR1L1	26737	hgsc.bcm.edu	37	9	125424277	125424277	+	Missense_Mutation	SNP	A	A	G	rs70157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:125424277A>G	ENST00000373686.1	+	1	433	c.433A>G	c.(433-435)Agt>Ggt	p.S145G	OR1L1_ENST00000309623.1_Missense_Mutation_p.S95G			Q8NH94	OR1L1_HUMAN	olfactory receptor, family 1, subfamily L, member 1	145			S -> G (in dbSNP:rs70157). {ECO:0000269|PubMed:14983052, 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)			breast(1)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)|skin(5)|upper_aerodigestive_tract(1)	17						CATCTCTTACAGTGAGTGTCT	0.428													.|||	649	0.129593	0.4713	0.036	5008	,	,		24856	0.0		0.001	False		,,,				2504	0.0				p.S95G		Atlas-SNP	.											.	OR1L1	54	.	0			c.A283G						PASS	.	G	GLY/SER	1689,2717	654.4+/-399.7	329,1031,843	202.0	199.0	200.0		283	1.1	0.0	9	dbSNP_79	200	10,8590	818.9+/-406.8	0,10,4290	yes	missense	OR1L1	NM_001005236.3	56	329,1041,5133	GG,GA,AA		0.1163,38.3341,13.0632	benign	95/311	125424277	1699,11307	2203	4300	6503	SO:0001583	missense	26737	exon1			TCTTACAGTGAGT		CCDS35127.1, CCDS35127.2	9q33.2	2013-09-20			ENSG00000173679	ENSG00000173679		"""GPCR / Class A : Olfactory receptors"""	8213	protein-coding gene	gene with protein product				OR1L2			Standard	NM_001005236		Approved	OR9-C	uc022bmz.1	Q8NH94	OTTHUMG00000020618	ENST00000373686.1:c.433A>G	9.37:g.125424277A>G	ENSP00000362790:p.Ser145Gly	169.0	0.0	0		180.0	114.0	0.633333	NM_001005236	Q5T7Z3|Q6IFN2	Missense_Mutation	SNP	ENST00000373686.1	37		228	0.1043956043956044	217	0.4410569105691057	11	0.03038674033149171	0	0.0	0	0.0	G	2.229	-0.376473	0.05000	0.383341	0.001163	ENSG00000173679	ENST00000373686;ENST00000309623	T;T	0.00402	7.56;7.56	3.11	1.14	0.20703	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.11756	0.17	0.80722	P	0.0	B	0.02656	0.0	B	0.06405	0.002	T	0.22941	-1.0202	8	0.46703	T	0.11	.	1.3175	0.02110	0.2108:0.169:0.4474:0.1728	rs70157;rs700052;rs56487442;rs70157	145	Q8NH94	OR1L1_HUMAN	G	145;95	ENSP00000362790:S145G;ENSP00000310773:S95G	ENSP00000310773:S95G	S	+	1	0	OR1L1	124464098	0.000000	0.05858	0.002000	0.10522	0.015000	0.08874	-3.542000	0.00436	-0.119000	0.11830	-0.642000	0.03964	AGT	A|0.860;G|0.140	0.140	strong		0.428	OR1L1-201	KNOWN	basic	protein_coding	protein_coding			
LHX3	8022	hgsc.bcm.edu	37	9	139096782	139096782	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139096782C>T	ENST00000371748.5	-	1	173	c.77G>A	c.(76-78)cGg>cAg	p.R26Q	LHX3_ENST00000371746.3_5'Flank	NM_178138.4	NP_835258.1	Q9UBR4	LHX3_HUMAN	LIM homeobox 3	26					inner ear development (GO:0048839)|lung development (GO:0030324)|medial motor column neuron differentiation (GO:0021526)|motor neuron axon guidance (GO:0008045)|negative regulation of apoptotic process (GO:0043066)|organ morphogenesis (GO:0009887)|pituitary gland development (GO:0021983)|placenta development (GO:0001890)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|spinal cord association neuron differentiation (GO:0021527)|spinal cord motor neuron cell fate specification (GO:0021520)|ventral spinal cord interneuron specification (GO:0021521)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		Myeloproliferative disorder(178;0.0511)		Epithelial(140;8.43e-08)|OV - Ovarian serous cystadenocarcinoma(145;1.26e-07)		GGGCTTACCCCGAGTCCCGCC	0.721																																					p.R26Q		Atlas-SNP	.											.	LHX3	23	.	0			c.G77A						PASS	.						15.0	16.0	15.0					9																	139096782		2173	4271	6444	SO:0001583	missense	8022	exon1			TTACCCCGAGTCC	AF096169	CCDS6994.1, CCDS6995.1	9q34.3	2011-06-20			ENSG00000107187	ENSG00000107187		"""Homeoboxes / LIM class"""	6595	protein-coding gene	gene with protein product		600577				10598593, 10717474	Standard	NM_178138		Approved		uc004cgz.3	Q9UBR4	OTTHUMG00000020924	ENST00000371748.5:c.77G>A	9.37:g.139096782C>T	ENSP00000360813:p.Arg26Gln	39.0	0.0	0		36.0	12.0	0.333333	NM_178138	Q5TB39|Q5TB40|Q9NZB5|Q9P0I8|Q9P0I9	Missense_Mutation	SNP	ENST00000371748.5	37	CCDS6994.1	.	.	.	.	.	.	.	.	.	.	C	0.014	-1.571243	0.00895	.	.	ENSG00000107187	ENST00000371748	D	0.87729	-2.29	2.48	-3.37	0.04898	.	.	.	.	.	T	0.68805	0.3041	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.55503	-0.8131	9	0.08599	T	0.76	.	5.7854	0.18331	0.0:0.2132:0.172:0.6149	.	26	Q9UBR4	LHX3_HUMAN	Q	26	ENSP00000360813:R26Q	ENSP00000360813:R26Q	R	-	2	0	LHX3	138236603	0.000000	0.05858	0.000000	0.03702	0.239000	0.25481	-1.334000	0.02665	-0.951000	0.03654	-0.350000	0.07774	CGG	.	.	none		0.721	LHX3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055048.3		
POM121L2	94026	hgsc.bcm.edu	37	6	27277716	27277716	+	Missense_Mutation	SNP	A	A	T	rs61736082	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:27277716A>T	ENST00000444565.1	-	1	2233	c.2234T>A	c.(2233-2235)aTc>aAc	p.I745N	POM121L2_ENST00000377451.2_Missense_Mutation_p.I681N	NM_033482.3	NP_258443.2	Q96KW2	P12L2_HUMAN	POM121 transmembrane nucleoporin-like 2	745										breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|skin(1)	7						CAGGTTGGAGATGCTGGGGGT	0.547													A|||	151	0.0301518	0.0983	0.0159	5008	,	,		20168	0.001		0.005	False		,,,				2504	0.0041				p.I745N		Atlas-SNP	.											.	POM121L2	61	.	0			c.T2234A						PASS	.	A	ASN/ILE	119,1265		4,111,577	60.0	58.0	58.0		2234	-7.9	0.0	6	dbSNP_129	58	38,3144		0,38,1553	yes	missense	POM121L2	NM_033482.3	149	4,149,2130	TT,TA,AA		1.1942,8.5983,3.4385	benign	745/1036	27277716	157,4409	692	1591	2283	SO:0001583	missense	94026	exon1			TTGGAGATGCTGG	AL021808	CCDS59497.1	6p21.3	2012-03-13	2012-03-13		ENSG00000158553	ENSG00000158553			13973	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 2 (rat)"", ""POM121 membrane glycoprotein-like 2"""				Standard	NM_033482		Approved	POM121-L	uc011dku.1	Q96KW2	OTTHUMG00000014475	ENST00000444565.1:c.2234T>A	6.37:g.27277716A>T	ENSP00000392726:p.Ile745Asn	173.0	0.0	0		161.0	79.0	0.490683	NM_033482	C9J1I7	Missense_Mutation	SNP	ENST00000444565.1	37	CCDS59497.1	58	0.026556776556776556	46	0.09349593495934959	6	0.016574585635359115	1	0.0017482517482517483	5	0.006596306068601583	A	6.160	0.397724	0.11696	0.085983	0.011942	ENSG00000158553	ENST00000377451;ENST00000444565	T;T	0.14893	2.47;2.47	3.95	-7.89	0.01174	.	2.196470	0.02896	N	0.134806	T	0.02083	0.0065	L	0.29908	0.895	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.35549	-0.9784	10	0.17369	T	0.5	.	0.5556	0.00670	0.1881:0.2896:0.1786:0.3437	rs61736082	745	C9J1I7	.	N	681;745	ENSP00000366671:I681N;ENSP00000392726:I745N	ENSP00000366671:I681N	I	-	2	0	POM121L2	27385695	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.893000	0.04127	-1.522000	0.01769	0.254000	0.18369	ATC	A|0.952;T|0.048	0.048	strong		0.547	POM121L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040143.2	NM_033482	
ARSG	22901	hgsc.bcm.edu	37	17	66397521	66397521	+	Silent	SNP	C	C	T	rs62638719	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:66397521C>T	ENST00000448504.2	+	11	2029	c.1233C>T	c.(1231-1233)agC>agT	p.S411S	ARSG_ENST00000452479.2_Silent_p.S247S|ARSG_ENST00000582154.1_3'UTR	NM_014960.4	NP_055775.2	Q96EG1	ARSG_HUMAN	arylsulfatase G	411					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sulfur compound metabolic process (GO:0006790)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular space (GO:0005615)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			NS(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	26			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			ACCCCAACAGCGGGGCAGCTG	0.557													C|||	11	0.00219649	0.0083	0.0	5008	,	,		19346	0.0		0.0	False		,,,				2504	0.0				p.S411S		Atlas-SNP	.											ARSG,NS,carcinoma,+1,1	ARSG	55	1	0			c.C1233T						PASS	.	C		65,4341	60.5+/-97.4	0,65,2138	90.0	90.0	90.0		1233	-10.0	0.1	17	dbSNP_129	90	0,8600		0,0,4300	no	coding-synonymous	ARSG	NM_014960.3		0,65,6438	TT,TC,CC		0.0,1.4753,0.4998		411/526	66397521	65,12941	2203	4300	6503	SO:0001819	synonymous_variant	22901	exon11			CAACAGCGGGGCA	AB023218	CCDS11676.1	17q24.2	2013-07-15	2006-02-15		ENSG00000141337	ENSG00000141337		"""Arylsulfatase family"""	24102	protein-coding gene	gene with protein product		610008				12461688, 16174644	Standard	NM_014960		Approved	KIAA1001	uc002jhc.2	Q96EG1	OTTHUMG00000179810	ENST00000448504.2:c.1233C>T	17.37:g.66397521C>T		124.0	0.0	0		173.0	105.0	0.606936	NM_001267727	Q6UXF2|Q9Y2K4	Silent	SNP	ENST00000448504.2	37	CCDS11676.1																																																																																			C|0.996;T|0.004	0.004	strong		0.557	ARSG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448369.1	NM_014960	
NR5A1	2516	hgsc.bcm.edu	37	9	127262864	127262864	+	Silent	SNP	C	C	T	rs1110062	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:127262864C>T	ENST00000373588.4	-	4	571	c.375G>A	c.(373-375)ccG>ccA	p.P125P		NM_004959.4	NP_004950.2	Q13285	STF1_HUMAN	nuclear receptor subfamily 5, group A, member 1	125					adrenal gland development (GO:0030325)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|hormone metabolic process (GO:0042445)|intracellular receptor signaling pathway (GO:0030522)|luteinization (GO:0001553)|maintenance of protein location in nucleus (GO:0051457)|male gonad development (GO:0008584)|multicellular organismal aging (GO:0010259)|negative regulation of female gonad development (GO:2000195)|positive regulation of male gonad development (GO:2000020)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|primary sex determination (GO:0007538)|regulation of steroid biosynthetic process (GO:0050810)|tissue development (GO:0009888)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|phospholipid binding (GO:0005543)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			lung(1)|upper_aerodigestive_tract(1)	2						GCACCCCCATCGGGGGCCCTG	0.682													C|||	436	0.0870607	0.3154	0.0245	5008	,	,		12705	0.002		0.0	False		,,,				2504	0.0				p.P125P		Atlas-SNP	.											.	NR5A1	32	.	0			c.G375A						PASS	.	C		1188,3052		158,872,1090	19.0	22.0	21.0		375	-9.1	0.0	9	dbSNP_86	21	9,8255		0,9,4123	no	coding-synonymous	NR5A1	NM_004959.4		158,881,5213	TT,TC,CC		0.1089,28.0189,9.5729		125/462	127262864	1197,11307	2120	4132	6252	SO:0001819	synonymous_variant	2516	exon4			CCCCATCGGGGGC	D88155	CCDS6856.1	9q33	2013-01-16			ENSG00000136931	ENSG00000136931		"""Nuclear hormone receptors"""	7983	protein-coding gene	gene with protein product		184757		FTZF1		7789992	Standard	NM_004959		Approved	FTZ1, SF-1, ELP, AD4BP	uc004boo.1	Q13285	OTTHUMG00000020655	ENST00000373588.4:c.375G>A	9.37:g.127262864C>T		36.0	0.0	0		53.0	53.0	1	NM_004959	O15196|Q5T6F5	Silent	SNP	ENST00000373588.4	37	CCDS6856.1																																																																																			C|0.948;T|0.052	0.052	strong		0.682	NR5A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054029.1	NM_004959	
SFXN2	118980	hgsc.bcm.edu	37	10	104486489	104486489	+	Silent	SNP	C	C	T	rs35153373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:104486489C>T	ENST00000369893.5	+	2	263	c.96C>T	c.(94-96)gaC>gaT	p.D32D	SFXN2_ENST00000602785.1_3'UTR	NM_178858.4	NP_849189.1	Q96NB2	SFXN2_HUMAN	sideroflexin 2	32					iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|prostate(1)	13		Colorectal(252;0.207)		Epithelial(162;4.53e-09)|all cancers(201;1.2e-07)|BRCA - Breast invasive adenocarcinoma(275;0.218)		ACATCACGGACCCCCGCACTG	0.597													C|||	98	0.0195687	0.0719	0.0043	5008	,	,		19104	0.0		0.0	False		,,,				2504	0.0				p.D32D		Atlas-SNP	.											.	SFXN2	40	.	0			c.C96T						PASS	.	C		273,4133	153.3+/-186.9	5,263,1935	91.0	90.0	90.0		96	1.1	1.0	10	dbSNP_126	90	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SFXN2	NM_178858.4		5,264,6234	TT,TC,CC		0.0116,6.1961,2.1067		32/323	104486489	274,12732	2203	4300	6503	SO:0001819	synonymous_variant	118980	exon2			CACGGACCCCCGC	AF462052	CCDS7539.1	10q24.32	2006-03-13			ENSG00000156398	ENSG00000156398		"""Sideroflexins"""	16086	protein-coding gene	gene with protein product		615570					Standard	NM_178858		Approved		uc001kwb.2	Q96NB2	OTTHUMG00000018967	ENST00000369893.5:c.96C>T	10.37:g.104486489C>T		139.0	0.0	0		156.0	77.0	0.49359	NM_178858	Q5JSM6	Silent	SNP	ENST00000369893.5	37	CCDS7539.1																																																																																			C|0.980;T|0.020	0.020	strong		0.597	SFXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050096.2	XM_058359	
IMMT	10989	hgsc.bcm.edu	37	2	86385812	86385812	+	Silent	SNP	T	T	C	rs2228352	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:86385812T>C	ENST00000410111.3	-	10	1452	c.1065A>G	c.(1063-1065)gtA>gtG	p.V355V	Y_RNA_ENST00000363371.1_RNA|IMMT_ENST00000490238.1_5'UTR|IMMT_ENST00000409051.2_Silent_p.V308V|IMMT_ENST00000449247.2_Silent_p.V344V|IMMT_ENST00000254636.5_Silent_p.V256V|IMMT_ENST00000442664.2_Silent_p.V354V	NM_001100169.1|NM_001100170.1|NM_006839.2	NP_001093639.1|NP_001093640.1|NP_006830.2	Q16891	MIC60_HUMAN	inner membrane protein, mitochondrial	355					mitochondrial calcium ion homeostasis (GO:0051560)|response to cold (GO:0009409)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	30						GATACTGAGATACAACCTTAG	0.433													T|||	224	0.0447284	0.1331	0.0115	5008	,	,		20269	0.0		0.001	False		,,,				2504	0.0399				p.V355V		Atlas-SNP	.											.	IMMT	65	.	0			c.A1065G						PASS	.	T	,,	366,3392		15,336,1528	60.0	55.0	56.0		1062,1032,1065	-7.7	0.7	2	dbSNP_98	56	3,8249		0,3,4123	no	coding-synonymous,coding-synonymous,coding-synonymous	IMMT	NM_001100169.1,NM_001100170.1,NM_006839.2	,,	15,339,5651	CC,CT,TT		0.0364,9.7392,3.0724	,,	354/758,344/748,355/759	86385812	369,11641	1879	4126	6005	SO:0001819	synonymous_variant	10989	exon10			CTGAGATACAACC	D21094	CCDS46355.1, CCDS46356.1, CCDS46357.1	2p11.2	2011-10-04	2010-04-29		ENSG00000132305	ENSG00000132305			6047	protein-coding gene	gene with protein product	"""mitofilin"", ""mitochondrial inner membrane organizing system 2"""	600378	"""inner membrane protein, mitochondrial (mitofilin)"""			9168817, 8039717	Standard	NM_001100169		Approved	P87, P89, HMP, MINOS2	uc002sqz.4	Q16891	OTTHUMG00000153170	ENST00000410111.3:c.1065A>G	2.37:g.86385812T>C		109.0	0.0	0		117.0	50.0	0.42735	NM_006839	B1H0U5|B2R5N6|Q14539|Q15092|Q68D41|Q69HW5|Q6IBL0|Q7Z3X1|Q8TAJ5|Q9P0V2	Silent	SNP	ENST00000410111.3	37	CCDS46355.1	56	0.02564102564102564	51	0.10365853658536585	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	T	9.781	1.175415	0.21704	0.097392	3.64E-4	ENSG00000132305	ENST00000419070	.	.	.	5.76	-7.73	0.01245	.	.	.	.	.	T	0.01940	0.0061	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49011	-0.8983	4	.	.	.	-18.6743	10.0221	0.42048	0.0:0.2774:0.1707:0.5519	rs2228352;rs2228352	.	.	.	V	210	.	.	I	-	1	0	IMMT	86239323	0.003000	0.15002	0.651000	0.29564	0.993000	0.82548	-1.546000	0.02188	-1.085000	0.03088	-0.256000	0.11100	ATC	T|0.968;C|0.032	0.032	strong		0.433	IMMT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000329909.2	NM_006839	
MST1L	11223	hgsc.bcm.edu	37	1	17086976	17086976	+	RNA	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17086976G>A	ENST00000455405.2	-	0	0							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										TCCGGAGCGTGGGCATGTACC	0.607																																					p.P116P		Atlas-SNP	.											Q13209_HUMAN,NS,carcinoma,-2,2	.	.	2	0			c.C348T						PASS	.																																					11223	exon4			GAGCGTGGGCATG	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.17086976G>A		396.0	0.0	0		491.0	53.0	0.107943	NM_001271733	B7WPB1|Q13209	Silent	SNP	ENST00000455405.2	37																																																																																				.	.	none		0.607	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
PADI4	23569	hgsc.bcm.edu	37	1	17668508	17668508	+	Silent	SNP	C	C	T	rs16825565	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17668508C>T	ENST00000375448.4	+	7	749	c.723C>T	c.(721-723)ccC>ccT	p.P241P	AC004824.2_ENST00000602074.1_Intron	NM_012387.2	NP_036519.2	Q9UM07	PADI4_HUMAN	peptidyl arginine deiminase, type IV	241					cellular protein modification process (GO:0006464)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|histone citrullination (GO:0036414)|histone H3-R26 citrullination (GO:0036413)|innate immune response (GO:0045087)|nucleosome assembly (GO:0006334)|protein citrullination (GO:0018101)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	arginine deiminase activity (GO:0016990)|calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(13)|ovary(2)|skin(2)|urinary_tract(3)	26		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000338)|Lung NSC(340;0.00042)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00537)|BRCA - Breast invasive adenocarcinoma(304;8.54e-06)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(64;0.000223)|KIRC - Kidney renal clear cell carcinoma(64;0.00313)|STAD - Stomach adenocarcinoma(196;0.00707)|READ - Rectum adenocarcinoma(331;0.0689)|Lung(427;0.199)	L-Citrulline(DB00155)	TGATGGTCCCCGGTGGAAAGC	0.602													C|||	74	0.0147764	0.0537	0.0043	5008	,	,		17108	0.0		0.0	False		,,,				2504	0.0				p.P241P		Atlas-SNP	.											.	PADI4	70	.	0			c.C723T						PASS	.	C		190,4216	119.6+/-157.3	6,178,2019	85.0	78.0	81.0		723	-9.9	0.0	1	dbSNP_123	81	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	PADI4	NM_012387.2		6,180,6317	TT,TC,CC		0.0233,4.3123,1.4762		241/664	17668508	192,12814	2203	4300	6503	SO:0001819	synonymous_variant	23569	exon7			GGTCCCCGGTGGA	AB017919	CCDS180.1	1p36.13	2014-06-06	2003-02-12		ENSG00000159339	ENSG00000159339	3.5.3.15	"""Peptidyl arginine deiminases"""	18368	protein-coding gene	gene with protein product		605347	"""peptidyl arginine deiminase, type V"""	PADI5		10488123	Standard	NM_012387		Approved	PAD, PDI5, PDI4	uc001baj.2	Q9UM07	OTTHUMG00000002371	ENST00000375448.4:c.723C>T	1.37:g.17668508C>T		143.0	0.0	0		122.0	54.0	0.442623	NM_012387	A8K392|B2RBW0|Q5VTZ8|Q70SX4	Silent	SNP	ENST00000375448.4	37	CCDS180.1																																																																																			C|0.984;T|0.016	0.016	strong		0.602	PADI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006799.1	NM_012387	
LAMC2	3918	hgsc.bcm.edu	37	1	183184650	183184650	+	Missense_Mutation	SNP	G	G	C	rs12065473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:183184650G>C	ENST00000264144.4	+	3	396	c.331G>C	c.(331-333)Gcc>Ccc	p.A111P	LAMC2_ENST00000493293.1_Missense_Mutation_p.A111P	NM_005562.2	NP_005553.2	Q13753	LAMC2_HUMAN	laminin, gamma 2	111	Laminin EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00460}.		A -> P (in dbSNP:rs12065473).		cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	cell cortex (GO:0005938)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-2 complex (GO:0005607)|laminin-5 complex (GO:0005610)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	heparin binding (GO:0008201)			breast(2)|endometrium(6)|kidney(8)|large_intestine(11)|lung(18)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55						TGTGACAGGAGCCAGATGCGA	0.547													G|||	160	0.0319489	0.1135	0.013	5008	,	,		19074	0.0		0.001	False		,,,				2504	0.0				p.A111P		Atlas-SNP	.											.	LAMC2	113	.	0			c.G331C						PASS	.	G	PRO/ALA,PRO/ALA	484,3922	226.9+/-242.2	23,438,1742	124.0	110.0	115.0		331,331	2.0	0.7	1	dbSNP_120	115	7,8593	5.0+/-18.6	0,7,4293	yes	missense,missense	LAMC2	NM_005562.2,NM_018891.2	27,27	23,445,6035	CC,CG,GG		0.0814,10.985,3.7752	benign,benign	111/1194,111/1112	183184650	491,12515	2203	4300	6503	SO:0001583	missense	3918	exon3			ACAGGAGCCAGAT	Z15008	CCDS1352.1, CCDS44285.1	1q25-q31	2013-03-01	2002-08-29		ENSG00000058085	ENSG00000058085		"""Laminins"""	6493	protein-coding gene	gene with protein product		150292	"""laminin, gamma 2 (nicein (100kD), kalinin (105kD), BM600 (100kD), Herlitz junctional epidermolysis bullosa))"""	EBR2, LAMB2T, LAMNB2, EBR2A		1383240	Standard	NM_005562		Approved	nicein-100kDa, kalinin-105kDa, BM600-100kDa	uc001gqa.2	Q13753	OTTHUMG00000035520	ENST00000264144.4:c.331G>C	1.37:g.183184650G>C	ENSP00000264144:p.Ala111Pro	150.0	0.0	0		173.0	77.0	0.445087	NM_005562	Q02536|Q02537|Q13752|Q14941|Q14DF7|Q2M1N2|Q5VYE8	Missense_Mutation	SNP	ENST00000264144.4	37	CCDS1352.1	51	0.023351648351648352	46	0.09349593495934959	5	0.013812154696132596	0	0.0	0	0.0	G	16.35	3.099112	0.56183	0.10985	8.14E-4	ENSG00000058085	ENST00000493293;ENST00000537180;ENST00000264144	T;T	0.61392	0.11;0.11	4.97	2.0	0.26442	EGF-like, laminin (4);Growth factor, receptor (1);	0.621389	0.16329	N	0.219195	T	0.00637	0.0021	N	0.05230	-0.09	0.27001	N	0.964914	B;B	0.26041	0.14;0.034	B;B	0.31495	0.131;0.039	T	0.04678	-1.0934	10	0.30854	T	0.27	.	5.6168	0.17436	0.2342:0.148:0.6178:0.0	rs12065473;rs52806764;rs12065473	111;111	Q13753;Q13753-2	LAMC2_HUMAN;.	P	111	ENSP00000432063:A111P;ENSP00000264144:A111P	ENSP00000264144:A111P	A	+	1	0	LAMC2	181451273	0.946000	0.32159	0.668000	0.29813	0.953000	0.61014	1.823000	0.39062	0.139000	0.18822	-0.137000	0.14449	GCC	G|0.963;C|0.037	0.037	strong		0.547	LAMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086258.1	NM_005562	
ADH1B	125	hgsc.bcm.edu	37	4	100237169	100237169	+	Silent	SNP	C	C	T	rs139645116	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:100237169C>T	ENST00000305046.8	-	5	520	c.453G>A	c.(451-453)acG>acA	p.T151T	ADH1B_ENST00000394887.3_Silent_p.T111T|ADH1B_ENST00000504498.1_5'Flank			P00325	ADH1B_HUMAN	alcohol dehydrogenase 1B (class I), beta polypeptide	151					ethanol oxidation (GO:0006069)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	alcohol dehydrogenase activity, zinc-dependent (GO:0004024)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	33				OV - Ovarian serous cystadenocarcinoma(123;1.02e-07)	Ethanol(DB00898)|Fomepizole(DB01213)	CATCCACCACCGTGTACTGGG	0.582													.|||	13	0.00259585	0.0098	0.0	5008	,	,		18733	0.0		0.0	False		,,,				2504	0.0				p.T151T		Atlas-SNP	.											.	ADH1B	68	.	0			c.G453A						PASS	.	C		31,4375	36.0+/-67.5	0,31,2172	131.0	118.0	122.0		453	-7.9	0.1	4	dbSNP_134	122	0,8600		0,0,4300	no	coding-synonymous	ADH1B	NM_000668.4		0,31,6472	TT,TC,CC		0.0,0.7036,0.2384		151/376	100237169	31,12975	2203	4300	6503	SO:0001819	synonymous_variant	125	exon5			CACCACCGTGTAC	AF153821	CCDS34033.1, CCDS68761.1	4q23	2008-02-05	2007-11-06		ENSG00000196616	ENSG00000196616	1.1.1.1	"""Alcohol dehydrogenases"""	250	protein-coding gene	gene with protein product		103720		ADH2		3006456	Standard	NM_000668		Approved		uc003hus.4	P00325	OTTHUMG00000161413	ENST00000305046.8:c.453G>A	4.37:g.100237169C>T		317.0	1.0	0.00315457		286.0	137.0	0.479021	NM_000668	A8MYN5|B4DRS9|B4DVC3|Q13711|Q4ZGI9|Q96KI7	Silent	SNP	ENST00000305046.8	37	CCDS34033.1																																																																																			C|0.998;T|0.002	0.002	strong		0.582	ADH1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364853.1	NM_000668	
TRAPPC3L	100128327	hgsc.bcm.edu	37	6	116818225	116818225	+	Silent	SNP	C	C	T	rs114678052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:116818225C>T	ENST00000368602.3	-	5	533	c.438G>A	c.(436-438)gcG>gcA	p.A146A	TRAPPC3L_ENST00000356128.4_Silent_p.A62A|RP11-259P20.1_ENST00000420595.2_RNA	NM_001139444.2	NP_001132916.1	Q5T215	TPC3L_HUMAN	trafficking protein particle complex 3-like	146					vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)											TAACATCAGCCGCCAAATGAA	0.333													A|||	240	0.0479233	0.171	0.0101	5008	,	,		17317	0.0		0.007	False		,,,				2504	0.0				p.A146A		Atlas-SNP	.											.	BET3L	18	.	0			c.G438A						PASS	.						110.0	85.0	93.0					6																	116818225		692	1591	2283	SO:0001819	synonymous_variant	100128327	exon5			ATCAGCCGCCAAA	AK002042	CCDS47468.1	6q22.31	2013-05-01	2013-05-01	2013-05-01	ENSG00000173626	ENSG00000173626			21090	protein-coding gene	gene with protein product		614137	"""BET3 like (S. cerevisiae)"""	BET3L		21525244	Standard	NM_001139444		Approved	bA259P20.2, FLJ11180		Q5T215	OTTHUMG00000015440	ENST00000368602.3:c.438G>A	6.37:g.116818225C>T		87.0	0.0	0		79.0	79.0	1	NM_001139444	Q5T213|Q5T214	Silent	SNP	ENST00000368602.3	37	CCDS47468.1																																																																																			C|0.968;T|0.032	0.032	strong		0.333	TRAPPC3L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000101701.1	XM_166322	
LRP11	84918	hgsc.bcm.edu	37	6	150158486	150158486	+	Missense_Mutation	SNP	A	A	G	rs375299752		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:150158486A>G	ENST00000239367.2	-	4	1032	c.1027T>C	c.(1027-1029)Ttc>Ctc	p.F343L	LRP11_ENST00000463728.1_5'Flank|LRP11_ENST00000546019.1_Missense_Mutation_p.F88L	NM_032832.5	NP_116221.3	Q86VZ4	LRP11_HUMAN	low density lipoprotein receptor-related protein 11	343	LDL-receptor class A. {ECO:0000255|PROSITE-ProRule:PRU00124}.					integral component of membrane (GO:0016021)				cervix(1)|kidney(5)|large_intestine(1)|lung(1)	8		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;4.56e-12)|GBM - Glioblastoma multiforme(68;0.225)		TTCTGGCAGAAGTCTTCATCA	0.517																																					p.F343L		Atlas-SNP	.											.	LRP11	27	.	0			c.T1027C						PASS	.	A	LEU/PHE	2,4404	4.2+/-10.8	0,2,2201	122.0	101.0	108.0		1027	5.3	0.9	6		108	0,8600		0,0,4300	no	missense	LRP11	NM_032832.5	22	0,2,6501	GG,GA,AA		0.0,0.0454,0.0154	probably-damaging	343/501	150158486	2,13004	2203	4300	6503	SO:0001583	missense	84918	exon4			GGCAGAAGTCTTC	AK027641	CCDS5220.1	6q24.3	2013-02-27			ENSG00000120256	ENSG00000120256		"""Low density lipoprotein receptors"""	16936	protein-coding gene	gene with protein product							Standard	NM_032832		Approved	bA350J20.3, MANSC3	uc003qng.2	Q86VZ4	OTTHUMG00000015801	ENST00000239367.2:c.1027T>C	6.37:g.150158486A>G	ENSP00000239367:p.Phe343Leu	120.0	0.0	0		107.0	41.0	0.383178	NM_032832	Q5VYC0|Q96SN6	Missense_Mutation	SNP	ENST00000239367.2	37	CCDS5220.1	.	.	.	.	.	.	.	.	.	.	A	28.9	4.958758	0.92726	4.54E-4	0.0	ENSG00000120256	ENST00000239367;ENST00000546019	D;D	0.95272	-3.66;-3.66	5.32	5.32	0.75619	Low-density lipoprotein (LDL) receptor class A, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.93416	0.7900	N	0.24115	0.695	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94587	0.7784	10	0.51188	T	0.08	-22.8051	14.5589	0.68120	1.0:0.0:0.0:0.0	.	343	Q86VZ4	LRP11_HUMAN	L	343;88	ENSP00000239367:F343L;ENSP00000440196:F88L	ENSP00000239367:F343L	F	-	1	0	LRP11	150200179	1.000000	0.71417	0.923000	0.36655	0.767000	0.43475	8.118000	0.89577	2.134000	0.65973	0.455000	0.32223	TTC	.	.	weak		0.517	LRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042664.1	NM_032832	
WDR59	79726	hgsc.bcm.edu	37	16	74943471	74943471	+	Missense_Mutation	SNP	T	T	C	rs61734551	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:74943471T>C	ENST00000262144.6	-	16	1700	c.1570A>G	c.(1570-1572)Acg>Gcg	p.T524A		NM_030581.3	NP_085058.3	Q6PJI9	WDR59_HUMAN	WD repeat domain 59	524										breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)	27						CCGTAAGCCGTGGTCACCCGC	0.547													T|||	66	0.0131789	0.0484	0.0029	5008	,	,		16262	0.0		0.0	False		,,,				2504	0.0				p.T524A		Atlas-SNP	.											.	WDR59	66	.	0			c.A1570G						PASS	.	T	ALA/THR	124,4272	92.5+/-131.2	0,124,2074	89.0	95.0	93.0		1570	4.8	1.0	16	dbSNP_129	93	2,8598	2.2+/-6.3	0,2,4298	yes	missense	WDR59	NM_030581.3	58	0,126,6372	CC,CT,TT		0.0233,2.8207,0.9695	benign	524/975	74943471	126,12870	2198	4300	6498	SO:0001583	missense	79726	exon16			AAGCCGTGGTCAC	AB067510	CCDS32488.1	16q22.3	2013-01-09				ENSG00000103091		"""WD repeat domain containing"""	25706	protein-coding gene	gene with protein product						11572484	Standard	XM_005256146		Approved	FLJ12270	uc002fdh.1	Q6PJI9		ENST00000262144.6:c.1570A>G	16.37:g.74943471T>C	ENSP00000262144:p.Thr524Ala	43.0	0.0	0		44.0	21.0	0.477273	NM_030581	B3KRC3|Q71RE7|Q96PW5|Q9BSW6|Q9HA43	Missense_Mutation	SNP	ENST00000262144.6	37	CCDS32488.1	20	0.009157509157509158	19	0.03861788617886179	1	0.0027624309392265192	0	0.0	0	0.0	T	10.57	1.388491	0.25118	0.028207	2.33E-4	ENSG00000103091	ENST00000262144	T	0.67698	-0.28	5.86	4.76	0.60689	.	0.137136	0.64402	D	0.000005	T	0.14313	0.0346	N	0.08118	0	0.34596	D	0.715995	B	0.12013	0.005	B	0.14023	0.01	T	0.30794	-0.9966	10	0.08381	T	0.77	-12.4732	13.1941	0.59728	0.0:0.0:0.1332:0.8668	.	524	Q6PJI9	WDR59_HUMAN	A	524	ENSP00000262144:T524A	ENSP00000262144:T524A	T	-	1	0	WDR59	73500972	1.000000	0.71417	0.997000	0.53966	0.015000	0.08874	5.542000	0.67218	1.129000	0.42072	-0.323000	0.08544	ACG	T|0.988;C|0.012	0.012	strong		0.547	WDR59-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410601.3	NM_030581	
OR6P1	128366	hgsc.bcm.edu	37	1	158532605	158532605	+	Missense_Mutation	SNP	C	C	A	rs115786820	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158532605C>A	ENST00000334632.1	-	1	789	c.790G>T	c.(790-792)Gcc>Tcc	p.A264S		NM_001160325.1	NP_001153797.1	Q8NGX9	OR6P1_HUMAN	olfactory receptor, family 6, subfamily P, member 1	264						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(4)|lung(1)	6						GTGTACATGGCCCGGGGCCGT	0.512													C|||	79	0.0157748	0.0582	0.0029	5008	,	,		20887	0.0		0.0	False		,,,				2504	0.0				p.A264S		Atlas-SNP	.											.	OR6P1	47	.	0			c.G790T						PASS	.	C	SER/ALA	76,1308		3,70,619	157.0	127.0	136.0		790	4.0	1.0	1	dbSNP_132	136	1,3181		0,1,1590	yes	missense	OR6P1	NM_001160325.1	99	3,71,2209	AA,AC,CC		0.0314,5.4913,1.6864	probably-damaging	264/318	158532605	77,4489	692	1591	2283	SO:0001583	missense	128366	exon1			ACATGGCCCGGGG	BK004193	CCDS53391.1	1q23.1	2012-08-09			ENSG00000186440	ENSG00000186440		"""GPCR / Class A : Olfactory receptors"""	15036	protein-coding gene	gene with protein product							Standard	NM_001160325		Approved		uc010pim.2	Q8NGX9	OTTHUMG00000019633	ENST00000334632.1:c.790G>T	1.37:g.158532605C>A	ENSP00000334721:p.Ala264Ser	140.0	0.0	0		175.0	87.0	0.497143	NM_001160325	Q6IFR9	Missense_Mutation	SNP	ENST00000334632.1	37	CCDS53391.1	26	0.011904761904761904	26	0.052845528455284556	0	0.0	0	0.0	0	0.0	C	10.32	1.317865	0.23994	0.054913	3.14E-4	ENSG00000186440	ENST00000334632	T	0.00019	9.06	4.91	3.95	0.45737	GPCR, rhodopsin-like superfamily (1);	0.168012	0.28006	N	0.016962	T	0.00039	0.0001	N	0.03253	-0.375	0.09310	N	1	D	0.57571	0.98	P	0.54346	0.749	T	0.38134	-0.9675	10	0.02654	T	1	.	7.4127	0.27025	0.1677:0.7458:0.0:0.0864	.	264	Q8NGX9	OR6P1_HUMAN	S	264	ENSP00000334721:A264S	ENSP00000334721:A264S	A	-	1	0	OR6P1	156799229	0.000000	0.05858	0.966000	0.40874	0.008000	0.06430	-0.210000	0.09345	2.551000	0.86045	0.591000	0.81541	GCC	C|0.987;A|0.013	0.013	strong		0.512	OR6P1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051848.1		
CYP4F12	66002	hgsc.bcm.edu	37	19	15794425	15794425	+	Missense_Mutation	SNP	A	A	G	rs116788636|rs386807235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15794425A>G	ENST00000550308.1	+	7	1150	c.770A>G	c.(769-771)cAc>cGc	p.H257R	CYP4F12_ENST00000324632.10_Missense_Mutation_p.H257R	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	257					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	CGGCGCTTCCACAGGGCCTGC	0.547													.|||	73	0.0145767	0.0522	0.0043	5008	,	,		20966	0.0		0.001	False		,,,				2504	0.0				p.H257R		Atlas-SNP	.											.	CYP4F12	89	.	0			c.A770G						PASS	.	A	ARG/HIS	173,4223		0,173,2025	79.0	81.0	80.0		770	-4.9	0.1	19	dbSNP_132	80	1,8589		0,1,4294	no	missense	CYP4F12	NM_023944.3	29	0,174,6319	GG,GA,AA		0.0116,3.9354,1.3399	benign	257/525	15794425	174,12812	2198	4295	6493	SO:0001583	missense	66002	exon7			GCTTCCACAGGGC	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.770A>G	19.37:g.15794425A>G	ENSP00000448998:p.His257Arg	124.0	0.0	0		184.0	49.0	0.266304	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	20	0.009157509157509158	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	.	0.001	-3.865349	0.00003	0.039354	1.16E-4	ENSG00000186204	ENST00000550308;ENST00000324632	T;T	0.67865	-0.29;-0.29	2.47	-4.94	0.03057	.	1.089430	0.07278	N	0.870346	T	0.05090	0.0136	N	0.00368	-1.59	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.11542	-1.0583	10	0.02654	T	1	.	5.3926	0.16251	0.2262:0.0:0.5255:0.2483	.	257	Q9HCS2	CP4FC_HUMAN	R	257	ENSP00000448998:H257R;ENSP00000321821:H257R	ENSP00000321821:H257R	H	+	2	0	CYP4F12	15655425	0.000000	0.05858	0.056000	0.19401	0.005000	0.04900	-0.089000	0.11180	-1.586000	0.01632	-4.406000	0.00006	CAC	A|0.990;G|0.010	0.010	strong		0.547	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
FAM129C	199786	hgsc.bcm.edu	37	19	17638141	17638141	+	Missense_Mutation	SNP	G	G	A	rs73504235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17638141G>A	ENST00000335393.4	+	2	223	c.85G>A	c.(85-87)Gac>Aac	p.D29N	FAM129C_ENST00000300971.2_Missense_Mutation_p.D29N|FAM129C_ENST00000352727.3_Missense_Mutation_p.D29N|FAM129C_ENST00000599164.1_5'UTR|FAM129C_ENST00000449408.2_5'UTR|FAM129C_ENST00000601861.1_5'UTR|FAM129C_ENST00000332386.5_Missense_Mutation_p.D29N|FAM129C_ENST00000597887.1_3'UTR|FAM129C_ENST00000600871.1_5'UTR|FAM129C_ENST00000595684.1_Missense_Mutation_p.D29N|FAM129C_ENST00000599124.1_5'UTR	NM_173544.4	NP_775815	Q86XR2	NIBL2_HUMAN	family with sequence similarity 129, member C	29										autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(2)|lung(14)|ovary(1)|skin(3)|stomach(1)	33						CCCGGGAGACGACAGCAGCAT	0.687													G|||	46	0.0091853	0.0348	0.0	5008	,	,		11779	0.0		0.0	False		,,,				2504	0.0				p.D29N		Atlas-SNP	.											.	FAM129C	110	.	0			c.G85A						PASS	.	G	ASN/ASP,ASN/ASP	96,3940		1,94,1923	26.0	21.0	23.0		85,85	-6.0	0.0	19	dbSNP_130	23	3,7943		0,3,3970	yes	missense,missense	FAM129C	NM_001098524.1,NM_173544.4	23,23	1,97,5893	AA,AG,GG		0.0378,2.3786,0.8262	benign,benign	29/652,29/698	17638141	99,11883	2018	3973	5991	SO:0001583	missense	199786	exon2			GGAGACGACAGCA	AY254198	CCDS12362.1, CCDS42521.1	19p13.11	2008-02-05				ENSG00000167483			24130	protein-coding gene	gene with protein product	B cell novel protein 1	609967				12886250	Standard	NM_173544		Approved	FLJ39802, BCNP1	uc021uqj.1	Q86XR2		ENST00000335393.4:c.85G>A	19.37:g.17638141G>A	ENSP00000335040:p.Asp29Asn	238.0	0.0	0		221.0	221.0	1	NM_001098524	B4DNU3|B4DVN7|Q7Z6H6|Q86XR3|Q86XR4|Q8TEQ3	Missense_Mutation	SNP	ENST00000335393.4	37	CCDS12362.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	G	7.241	0.601307	0.13939	0.023786	3.78E-4	ENSG00000167483	ENST00000335393;ENST00000332386;ENST00000352727;ENST00000300971	T;T;T;T	0.26518	1.92;2.05;1.73;1.75	3.01	-6.03	0.02185	.	1.713730	0.03912	N	0.282032	T	0.04318	0.0119	N	0.08118	0	0.18873	N	0.999985	B;B	0.10296	0.003;0.003	B;B	0.01281	0.0;0.0	T	0.16100	-1.0414	10	0.14656	T	0.56	.	1.1511	0.01786	0.4056:0.0975:0.15:0.3469	.	29;29	Q86XR2;Q86XR2-3	NIBL2_HUMAN;.	N	29	ENSP00000335040:D29N;ENSP00000333447:D29N;ENSP00000341067:D29N;ENSP00000300971:D29N	ENSP00000300971:D29N	D	+	1	0	FAM129C	17499141	0.000000	0.05858	0.000000	0.03702	0.031000	0.12232	-4.173000	0.00280	-3.604000	0.00133	-0.339000	0.08088	GAC	G|0.990;A|0.010	0.010	strong		0.687	FAM129C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464206.1	NM_173544	
FOXC1	2296	hgsc.bcm.edu	37	6	1611085	1611085	+	Silent	SNP	C	C	T	rs2230096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:1611085C>T	ENST00000380874.2	+	1	405	c.405C>T	c.(403-405)tgC>tgT	p.C135C		NM_001453.2	NP_001444.2	Q12948	FOXC1_HUMAN	forkhead box C1	135					artery morphogenesis (GO:0048844)|blood vessel remodeling (GO:0001974)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|cardiac muscle cell proliferation (GO:0060038)|collagen fibril organization (GO:0030199)|embryonic heart tube development (GO:0035050)|eye development (GO:0001654)|germ cell migration (GO:0008354)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|in utero embryonic development (GO:0001701)|lacrimal gland development (GO:0032808)|lymph vessel development (GO:0001945)|negative regulation of apoptotic process involved in outflow tract morphogenesis (GO:1902257)|negative regulation of mitotic cell cycle (GO:0045930)|neural crest cell development (GO:0014032)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|ovarian follicle development (GO:0001541)|paraxial mesoderm formation (GO:0048341)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood vessel size (GO:0050880)|regulation of organ growth (GO:0046620)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|somitogenesis (GO:0001756)|ureteric bud development (GO:0001657)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cytoplasm (GO:0005737)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA binding, bending (GO:0008301)|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 regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	8	Ovarian(93;0.0733)	all_cancers(2;4.45e-07)|all_epithelial(2;4.33e-05)|all_lung(73;0.0713)|all_hematologic(90;0.0895)		Epithelial(2;0.0904)|OV - Ovarian serous cystadenocarcinoma(45;0.095)|all cancers(2;0.168)		TCAACGAGTGCTTCGTCAAGG	0.602													c|||	160	0.0319489	0.115	0.0101	5008	,	,		11123	0.0		0.001	False		,,,				2504	0.0				p.C135C	Pancreas(133;719 1821 3197 26645 35015)	Atlas-SNP	.											.	FOXC1	19	.	0			c.C405T						PASS	.	C		454,3952	215.1+/-234.2	26,402,1775	85.0	94.0	91.0		405	3.7	1.0	6	dbSNP_98	91	4,8596	2.2+/-6.3	0,4,4296	no	coding-synonymous	FOXC1	NM_001453.2		26,406,6071	TT,TC,CC		0.0465,10.3041,3.5215		135/554	1611085	458,12548	2203	4300	6503	SO:0001819	synonymous_variant	2296	exon1			CGAGTGCTTCGTC	AF048693	CCDS4473.1	6p25	2008-04-10			ENSG00000054598	ENSG00000054598		"""Forkhead boxes"""	3800	protein-coding gene	gene with protein product		601090		FKHL7, IRID1		7957066, 9620769	Standard	NM_001453		Approved	FREAC3, ARA, IGDA, IHG1	uc003mtp.3	Q12948	OTTHUMG00000016182	ENST00000380874.2:c.405C>T	6.37:g.1611085C>T		270.0	0.0	0		295.0	130.0	0.440678	NM_001453	Q86UP7|Q9BYM1|Q9NUE5|Q9UDD0|Q9UP06	Silent	SNP	ENST00000380874.2	37	CCDS4473.1																																																																																			C|0.970;T|0.030	0.030	strong		0.602	FOXC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043450.1		
ZNF107	51427	hgsc.bcm.edu	37	7	64168641	64168641	+	Silent	SNP	A	A	G	rs73363327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:64168641A>G	ENST00000395391.1	+	4	3334	c.1959A>G	c.(1957-1959)agA>agG	p.R653R	ZNF107_ENST00000423627.1_Silent_p.R653R|ZNF107_ENST00000344930.3_Silent_p.R653R			Q9UII5	ZN107_HUMAN	zinc finger protein 107	653					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)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(18)|ovary(1)|stomach(1)	37		Lung NSC(55;0.00948)|all_lung(88;0.0249)				CCCTTAATAGACATAAGATAA	0.363													a|||	131	0.0261581	0.0983	0.0014	5008	,	,		18481	0.0		0.0	False		,,,				2504	0.0				p.R653R		Atlas-SNP	.											.	ZNF107	107	.	0			c.A1959G						PASS	.	A	,	297,4075		9,279,1898	30.0	34.0	33.0		1959,1959	-0.3	0.1	7	dbSNP_131	33	3,8583		0,3,4290	no	coding-synonymous,coding-synonymous	ZNF107	NM_001013746.1,NM_016220.3	,	9,282,6188	GG,GA,AA		0.0349,6.7932,2.3152	,	653/784,653/784	64168641	300,12658	2186	4293	6479	SO:0001819	synonymous_variant	51427	exon7			TAATAGACATAAG	AB027251	CCDS5527.1, CCDS75605.1, CCDS75606.1	7q11.2	2013-01-08	2007-06-26			ENSG00000196247		"""Zinc fingers, C2H2-type"""	12887	protein-coding gene	gene with protein product		603989	"""zinc finger protein 588"", ""zinc finger protein 107 (Y8)"""	ZNF588		8467795	Standard	NM_016220		Approved	ZFD25, smap-7	uc003tte.3	Q9UII5		ENST00000395391.1:c.1959A>G	7.37:g.64168641A>G		44.0	0.0	0		25.0	9.0	0.36	NM_016220		Silent	SNP	ENST00000395391.1	37	CCDS5527.1																																																																																			A|0.985;G|0.015	0.015	strong		0.363	ZNF107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251593.1	NM_016220	
PPFIBP2	8495	hgsc.bcm.edu	37	11	7673029	7673029	+	Missense_Mutation	SNP	T	T	C	rs77873429	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:7673029T>C	ENST00000299492.4	+	23	2778	c.2390T>C	c.(2389-2391)aTg>aCg	p.M797T	PPFIBP2_ENST00000530582.1_3'UTR|PPFIBP2_ENST00000533792.1_Missense_Mutation_p.M639T|PPFIBP2_ENST00000530181.1_Missense_Mutation_p.M654T|PPFIBP2_ENST00000528883.1_Missense_Mutation_p.M685T	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	797					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)	DNA binding (GO:0003677)|integrase activity (GO:0008907)			breast(8)|cervix(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		CGAGAGAAAATGGCCTCACCA	0.597													T|||	471	0.0940495	0.2708	0.0476	5008	,	,		19476	0.0149		0.004	False		,,,				2504	0.0624				p.M797T		Atlas-SNP	.											.	PPFIBP2	87	.	0			c.T2390C						PASS	.	T	THR/MET	1144,3258	408.0+/-334.4	146,852,1203	134.0	129.0	130.0		2390	5.8	1.0	11	dbSNP_131	130	40,8552	27.4+/-76.7	0,40,4256	yes	missense	PPFIBP2	NM_003621.2	81	146,892,5459	CC,CT,TT		0.4655,25.9882,9.1119	benign	797/877	7673029	1184,11810	2201	4296	6497	SO:0001583	missense	8495	exon23			AGAAAATGGCCTC	AF034803	CCDS31419.1, CCDS58116.1, CCDS58117.1	11p15.4	2013-01-10			ENSG00000166387	ENSG00000166387		"""Sterile alpha motif (SAM) domain containing"""	9250	protein-coding gene	gene with protein product		603142				9624153	Standard	NM_003621		Approved	Cclp1	uc001mfj.5	Q8ND30	OTTHUMG00000165617	ENST00000299492.4:c.2390T>C	11.37:g.7673029T>C	ENSP00000299492:p.Met797Thr	67.0	0.0	0		59.0	17.0	0.288136	NM_003621	B7Z433|E9PK77|O75337|Q8WW26	Missense_Mutation	SNP	ENST00000299492.4	37	CCDS31419.1	160	0.07326007326007326	129	0.2621951219512195	15	0.04143646408839779	13	0.022727272727272728	3	0.00395778364116095	T	7.418	0.636121	0.14386	0.259882	0.004655	ENSG00000166387	ENST00000299492;ENST00000537211;ENST00000533792;ENST00000541115;ENST00000528883;ENST00000530181	T;T;T;T	0.29655	1.98;1.57;1.98;1.56	5.77	5.77	0.91146	.	0.127954	0.53938	D	0.000047	T	0.00012	0.0000	L	0.38531	1.155	0.25772	P	0.984823	B;B;B;B;B;B	0.06786	0.0;0.0;0.0;0.001;0.0;0.0	B;B;B;B;B;B	0.06405	0.001;0.001;0.002;0.001;0.002;0.001	T	0.31861	-0.9928	9	0.18276	T	0.48	-17.2519	14.3292	0.66541	0.0:0.0:0.0:1.0	.	685;685;720;639;654;797	E9PK77;B7Z433;F5GWB0;E9PP16;E9PMU1;Q8ND30	.;.;.;.;.;LIPB2_HUMAN	T	797;138;639;720;685;654	ENSP00000299492:M797T;ENSP00000436498:M639T;ENSP00000435469:M685T;ENSP00000437321:M654T	ENSP00000299492:M797T	M	+	2	0	PPFIBP2	7629605	1.000000	0.71417	0.994000	0.49952	0.142000	0.21351	2.644000	0.46613	2.326000	0.78906	0.533000	0.62120	ATG	T|0.914;C|0.086	0.086	strong		0.597	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621	
VWA5A	4013	hgsc.bcm.edu	37	11	123989383	123989383	+	Missense_Mutation	SNP	G	G	A	rs35215239	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123989383G>A	ENST00000456829.2	+	6	864	c.613G>A	c.(613-615)Gag>Aag	p.E205K	VWA5A_ENST00000392748.1_Missense_Mutation_p.E205K|VWA5A_ENST00000449321.1_Missense_Mutation_p.E205K|VWA5A_ENST00000361352.5_Missense_Mutation_p.E205K|VWA5A_ENST00000392744.4_Missense_Mutation_p.E221K|VWA5A_ENST00000360334.4_Missense_Mutation_p.E205K	NM_001130142.1	NP_001123614.1	O00534	VMA5A_HUMAN	von Willebrand factor A domain containing 5A	205			E -> K (in dbSNP:rs35215239).					p.E205*(1)		autonomic_ganglia(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(11)|lung(17)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	47						GAGTCCTACCGAGTACCTAGG	0.517													G|||	109	0.0217652	0.0809	0.0029	5008	,	,		20475	0.0		0.0	False		,,,				2504	0.0				p.E205K		Atlas-SNP	.											VWA5A,larynx,carcinoma,0,1	VWA5A	102	1	1	Substitution - Nonsense(1)	upper_aerodigestive_tract(1)	c.G613A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU	253,4149	145.7+/-180.5	8,237,1956	90.0	82.0	85.0		613,613,613	-2.8	0.0	11	dbSNP_126	85	3,8595	3.0+/-9.4	0,3,4296	yes	missense,missense,missense	VWA5A	NM_001130142.1,NM_014622.4,NM_198315.2	56,56,56	8,240,6252	AA,AG,GG		0.0349,5.7474,1.9692	benign,benign,benign	205/787,205/787,205/416	123989383	256,12744	2201	4299	6500	SO:0001583	missense	4013	exon5			CCTACCGAGTACC	AF002672	CCDS8444.1, CCDS8445.1	11q24.1	2008-07-25	2008-07-25	2008-07-25	ENSG00000110002	ENSG00000110002			6658	protein-coding gene	gene with protein product		602929	"""loss of heterozygosity, 11, chromosomal region 2, gene A"""	LOH11CR2A		9417908, 14504409	Standard	NM_001130142		Approved	BCSC-1	uc001pzt.3	O00534	OTTHUMG00000165971	ENST00000456829.2:c.613G>A	11.37:g.123989383G>A	ENSP00000407726:p.Glu205Lys	91.0	0.0	0		78.0	28.0	0.358974	NM_014622	Q6UN19|Q6UN20|Q9BVF8	Missense_Mutation	SNP	ENST00000456829.2	37	CCDS8444.1	40	0.018315018315018316	39	0.07926829268292683	1	0.0027624309392265192	0	0.0	0	0.0	G	7.535	0.659528	0.14645	0.057474	3.49E-4	ENSG00000110002	ENST00000456829;ENST00000360334;ENST00000392748;ENST00000524524;ENST00000530025;ENST00000361352;ENST00000449321;ENST00000392744	T;T;T;T;T;T	0.22743	3.78;1.94;3.78;2.28;2.28;2.27	5.6	-2.84	0.05751	.	0.832622	0.11287	N	0.579757	T	0.00608	0.0020	L	0.52364	1.645	0.09310	N	1	B;B	0.31859	0.091;0.343	B;B	0.24269	0.023;0.052	T	0.30736	-0.9968	10	0.08599	T	0.76	-11.1706	6.7445	0.23454	0.2766:0.318:0.4054:0.0	rs35215239	221;205	B4DHS6;O00534	.;VMA5A_HUMAN	K	205;205;205;205;205;205;205;221	ENSP00000407726:E205K;ENSP00000353485:E205K;ENSP00000376504:E205K;ENSP00000355070:E205K;ENSP00000404683:E205K;ENSP00000376501:E221K	ENSP00000353485:E205K	E	+	1	0	VWA5A	123494593	0.001000	0.12720	0.003000	0.11579	0.055000	0.15305	-0.395000	0.07287	-0.184000	0.10567	-0.315000	0.08773	GAG	G|0.978;A|0.022	0.022	strong		0.517	VWA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387273.1	NM_014622	
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011526	46011526	+	Silent	SNP	T	T	A	rs371768583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46011526T>A	ENST00000400368.1	-	1	860	c.840A>T	c.(838-840)acA>acT	p.T280T	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	280	29 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)		p.T280T(1)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(6)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23						GGCAGCATGATGTGGAAGCCC	0.652													.|||	5	0.000998403	0.0008	0.0	5008	,	,		22429	0.001		0.0	False		,,,				2504	0.0031				p.T280T		Atlas-SNP	.											KRTAP10-6,NS,carcinoma,0,2	KRTAP10-6	57	2	1	Substitution - coding silent(1)	kidney(1)	c.A840T						scavenged	.						106.0	110.0	109.0					21																	46011526		2203	4300	6503	SO:0001819	synonymous_variant	386674	exon1			GCATGATGTGGAA	AB076353	CCDS42959.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000188155	ENSG00000188155		"""Keratin associated proteins"""	20523	protein-coding gene	gene with protein product			"""keratin associated protein 18-6"""	KRTAP18-6			Standard	NM_198688		Approved	KRTAP18.6, KAP18.6, KAP10.6	uc002zfm.3	P60371	OTTHUMG00000057634	ENST00000400368.1:c.840A>T	21.37:g.46011526T>A		245.0	2.0	0.00816326		300.0	34.0	0.113333	NM_198688		Silent	SNP	ENST00000400368.1	37	CCDS42959.1																																																																																			.	.	weak		0.652	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688	
GLCE	26035	hgsc.bcm.edu	37	15	69561181	69561181	+	Silent	SNP	T	T	C	rs56045514	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:69561181T>C	ENST00000261858.2	+	5	1680	c.1452T>C	c.(1450-1452)caT>caC	p.H484H	GLCE_ENST00000559420.2_Silent_p.H420H	NM_015554.1	NP_056369.1	O94923	GLCE_HUMAN	glucuronic acid epimerase	484					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparin biosynthetic process (GO:0030210)|small molecule metabolic process (GO:0044281)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	heparosan-N-sulfate-glucuronate 5-epimerase activity (GO:0047464)|racemase and epimerase activity, acting on carbohydrates and derivatives (GO:0016857)|UDP-glucuronate 5'-epimerase activity (GO:0050379)			NS(1)|breast(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	18						CTGAGCAGCATGGAGTTAAAG	0.353													T|||	323	0.0644968	0.2383	0.0086	5008	,	,		21803	0.0		0.002	False		,,,				2504	0.0				p.H484H		Atlas-SNP	.											.	GLCE	48	.	0			c.T1452C						PASS	.	T		685,3715	279.6+/-274.9	68,549,1583	58.0	65.0	62.0		1452	-6.6	0.8	15	dbSNP_129	62	5,8591	3.7+/-12.6	0,5,4293	no	coding-synonymous	GLCE	NM_015554.1		68,554,5876	CC,CT,TT		0.0582,15.5682,5.3093		484/618	69561181	690,12306	2200	4298	6498	SO:0001819	synonymous_variant	26035	exon5			GCAGCATGGAGTT	AB020643	CCDS32277.1	15q23	2007-01-30	2007-01-30			ENSG00000138604	5.1.3.12		17855	protein-coding gene	gene with protein product	"""heparan sulfate epimerase"""	612134	"""D-glucuronyl C5-epimerase"", ""UDP-glucuronic acid epimerase"""			15853773	Standard	NM_015554		Approved	KIAA0836, HSEPI	uc002ary.1	O94923		ENST00000261858.2:c.1452T>C	15.37:g.69561181T>C		60.0	0.0	0		62.0	35.0	0.564516	NM_015554	Q6GUQ2	Silent	SNP	ENST00000261858.2	37	CCDS32277.1																																																																																			T|0.951;C|0.049	0.049	strong		0.353	GLCE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_015554	
RELN	5649	hgsc.bcm.edu	37	7	103124265	103124265	+	Missense_Mutation	SNP	A	A	G	rs150638029	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:103124265A>G	ENST00000428762.1	-	62	10175	c.10016T>C	c.(10015-10017)aTg>aCg	p.M3339T	RELN_ENST00000343529.5_Missense_Mutation_p.M3339T|CTB-107G13.1_ENST00000422488.1_RNA|RELN_ENST00000424685.2_Missense_Mutation_p.M3339T|RELN_ENST00000473945.1_5'UTR|RN7SKP86_ENST00000410454.1_RNA	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	3339					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)		CGTCTGCGACATGCTCCCAAT	0.453																																					p.M3339T	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.T10016C						PASS	.	A	THR/MET,THR/MET	2,4404	4.2+/-10.8	0,2,2201	106.0	99.0	101.0		10016,10016	2.9	0.0	7	dbSNP_134	101	0,8600		0,0,4300	no	missense,missense	RELN	NM_005045.3,NM_173054.2	81,81	0,2,6501	GG,GA,AA		0.0,0.0454,0.0154	benign,benign	3339/3461,3339/3459	103124265	2,13004	2203	4300	6503	SO:0001583	missense	5649	exon62			TGCGACATGCTCC		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.10016T>C	7.37:g.103124265A>G	ENSP00000392423:p.Met3339Thr	91.0	0.0	0		92.0	50.0	0.543478	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	A	3.338	-0.135242	0.06711	4.54E-4	0.0	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000424828;ENST00000448171	T;T;T	0.20463	2.07;2.07;2.07	5.64	2.87	0.33458	.	0.695276	0.14403	N	0.321778	T	0.08403	0.0209	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39354	-0.9618	10	0.17832	T	0.49	.	8.0051	0.30321	0.4314:0.0:0.5686:0.0	.	3339;3339	P78509-2;P78509	.;RELN_HUMAN	T	3339;3339;3339;856;3339	ENSP00000392423:M3339T;ENSP00000345694:M3339T;ENSP00000388446:M3339T	ENSP00000345694:M3339T	M	-	2	0	RELN	102911501	0.017000	0.18338	0.013000	0.15412	0.558000	0.35554	1.440000	0.35024	0.327000	0.23409	-1.055000	0.02315	ATG	A|1.000;G|0.000	0.000	strong		0.453	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
SLC28A1	9154	hgsc.bcm.edu	37	15	85448796	85448796	+	Silent	SNP	A	A	T	rs8187755	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:85448796A>T	ENST00000286749.3	+	7	720	c.630A>T	c.(628-630)ggA>ggT	p.G210G	SLC28A1_ENST00000537703.1_Silent_p.G132G|SLC28A1_ENST00000394573.1_Silent_p.G210G|SLC28A1_ENST00000537624.1_Silent_p.G210G|SLC28A1_ENST00000537216.1_Silent_p.G210G|SLC28A1_ENST00000538177.1_Silent_p.G210G			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	210					nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	TGTCTTGGGGACTTGGACTGC	0.587													A|||	156	0.0311502	0.1142	0.0072	5008	,	,		19535	0.0		0.0	False		,,,				2504	0.0				p.G210G		Atlas-SNP	.											SLC28A1_ENST00000537624,NS,carcinoma,+1,2	SLC28A1	118	2	0			c.A630T						scavenged	.	A		404,4002	200.8+/-224.0	20,364,1819	215.0	172.0	186.0		630	1.1	1.0	15	dbSNP_123	186	3,8595	2.2+/-6.3	0,3,4296	no	coding-synonymous	SLC28A1	NM_004213.3		20,367,6115	TT,TA,AA		0.0349,9.1693,3.1298		210/650	85448796	407,12597	2203	4299	6502	SO:0001819	synonymous_variant	9154	exon8			TTGGGGACTTGGA	U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"""Solute carriers"""	11001	protein-coding gene	gene with protein product		606207	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"""			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.630A>T	15.37:g.85448796A>T		182.0	1.0	0.00549451		198.0	74.0	0.373737	NM_004213	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Silent	SNP	ENST00000286749.3	37	CCDS10334.1																																																																																			A|0.973;T|0.027	0.027	strong		0.587	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2		
SLC28A1	9154	hgsc.bcm.edu	37	15	85478573	85478573	+	Silent	SNP	C	C	A	rs8187779	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:85478573C>A	ENST00000286749.3	+	14	1495	c.1405C>A	c.(1405-1407)Cgg>Agg	p.R469R	SLC28A1_ENST00000394573.1_Silent_p.R469R|SLC28A1_ENST00000537624.1_Silent_p.R469R|SLC28A1_ENST00000537216.1_Silent_p.R469R|SLC28A1_ENST00000538177.1_Intron			O00337	S28A1_HUMAN	solute carrier family 28 (concentrative nucleoside transporter), member 1	469					nucleobase-containing compound metabolic process (GO:0006139)|nucleoside transmembrane transport (GO:1901642)|nucleoside transport (GO:0015858)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	nucleoside binding (GO:0001882)|nucleoside transmembrane transporter activity (GO:0005337)|nucleoside:sodium symporter activity (GO:0005415)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	41			BRCA - Breast invasive adenocarcinoma(143;0.0587)		Gemcitabine(DB00441)|Stavudine(DB00649)|Zidovudine(DB00495)	CTACATCCTGCGGCCTGTAGC	0.607													C|||	34	0.00678914	0.0227	0.0043	5008	,	,		20483	0.0		0.001	False		,,,				2504	0.0				p.R469R		Atlas-SNP	.											SLC28A1,colon,carcinoma,-1,1	SLC28A1	118	1	0			c.C1405A						scavenged	.	C		79,4327	68.7+/-106.4	2,75,2126	110.0	88.0	95.0		1405	2.2	1.0	15	dbSNP_123	95	4,8594	3.7+/-12.6	0,4,4295	no	coding-synonymous	SLC28A1	NM_004213.3		2,79,6421	AA,AC,CC		0.0465,1.793,0.6383		469/650	85478573	83,12921	2203	4299	6502	SO:0001819	synonymous_variant	9154	exon15			ATCCTGCGGCCTG	U62967	CCDS10334.1, CCDS10335.1, CCDS73777.1	15q25.3	2013-07-17	2013-07-17		ENSG00000156222	ENSG00000156222		"""Solute carriers"""	11001	protein-coding gene	gene with protein product		606207	"""solute carrier family 28 (sodium-coupled nucleoside transporter), member 1"""			9124315	Standard	NM_004213		Approved	CNT1	uc002blg.3	O00337	OTTHUMG00000148668	ENST00000286749.3:c.1405C>A	15.37:g.85478573C>A		174.0	1.0	0.00574713		142.0	77.0	0.542253	NM_004213	A0AV42|A8K7I2|O00335|O00336|Q5U5S6|Q5U648|Q9UEZ9	Silent	SNP	ENST00000286749.3	37	CCDS10334.1																																																																																			C|0.995;A|0.005	0.005	strong		0.607	SLC28A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308998.2		
SCO1	6341	hgsc.bcm.edu	37	17	10600653	10600653	+	Missense_Mutation	SNP	G	G	A	rs1802083	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:10600653G>A	ENST00000255390.5	-	1	232	c.172C>T	c.(172-174)Cct>Tct	p.P58S	SCO1_ENST00000577427.1_Missense_Mutation_p.P58S|ADPRM_ENST00000379774.4_5'Flank|SCO1_ENST00000582053.1_Intron	NM_004589.2	NP_004580.1	O75880	SCO1_HUMAN	SCO1 cytochrome c oxidase assembly protein	58			P -> S (in dbSNP:rs1802083).		cellular copper ion homeostasis (GO:0006878)|copper ion transport (GO:0006825)|generation of precursor metabolites and energy (GO:0006091)|respiratory chain complex IV assembly (GO:0008535)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|myofibril (GO:0030016)	copper ion binding (GO:0005507)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|urinary_tract(1)	10						CAATAGCCAGGGCGCCCCGAG	0.726													G|||	309	0.0617013	0.2216	0.0159	5008	,	,		10465	0.0		0.005	False		,,,				2504	0.0				p.P58S	Melanoma(128;591 1731 19711 31891 44645)	Atlas-SNP	.											.	SCO1	24	.	0			c.C172T						PASS	.	G	SER/PRO	629,3663		35,559,1552	6.0	7.0	7.0		172	1.7	0.0	17	dbSNP_89	7	11,8423		0,11,4206	no	missense	SCO1	NM_004589.2	74	35,570,5758	AA,AG,GG		0.1304,14.6552,5.0291	benign	58/302	10600653	640,12086	2146	4217	6363	SO:0001583	missense	6341	exon1			AGCCAGGGCGCCC	AF026852	CCDS11158.1	17p13.1	2012-10-15	2012-10-15		ENSG00000133028	ENSG00000133028		"""Mitochondrial respiratory chain complex assembly factors"""	10603	protein-coding gene	gene with protein product		603644	"""SCO (cytochrome oxidase deficient, yeast) homolog 1"", ""SCO cytochrome oxidase deficient homolog 1 (yeast)"""	SCOD1		9878253	Standard	NM_004589		Approved		uc002gmr.4	O75880	OTTHUMG00000130364	ENST00000255390.5:c.172C>T	17.37:g.10600653G>A	ENSP00000255390:p.Pro58Ser	29.0	0.0	0		43.0	21.0	0.488372	NM_004589	B2RDM0	Missense_Mutation	SNP	ENST00000255390.5	37	CCDS11158.1	110	0.05036630036630037	99	0.20121951219512196	9	0.024861878453038673	0	0.0	2	0.002638522427440633	G	10.34	1.324239	0.24080	0.146552	0.001304	ENSG00000133028	ENST00000255390;ENST00000396047	D	0.84873	-1.91	3.87	1.72	0.24424	.	0.533478	0.16696	N	0.203334	T	0.00178	0.0005	N	0.14661	0.345	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.03184	-1.1063	9	0.12430	T	0.62	-1.1139	10.6528	0.45657	0.0:0.4881:0.5119:0.0	rs1802083	58;58	A8MY34;O75880	.;SCO1_HUMAN	S	58	ENSP00000255390:P58S	ENSP00000255390:P58S	P	-	1	0	SCO1	10541378	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.044000	0.03532	0.504000	0.28082	-0.171000	0.13296	CCT	G|0.948;A|0.052	0.052	strong		0.726	SCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252729.2	NM_004589	
LCE1C	353133	hgsc.bcm.edu	37	1	152777877	152777877	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152777877G>A	ENST00000607093.1	-	1	77	c.78C>T	c.(76-78)acC>acT	p.T26T	LCE1C_ENST00000368768.1_Silent_p.T26T			Q5T751	LCE1C_HUMAN	late cornified envelope 1C	26	Pro-rich.				keratinization (GO:0031424)					NS(1)|lung(4)|prostate(1)|skin(2)|urinary_tract(1)	9	Lung NSC(65;9.06e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			gacactttggggTGgggcact	0.647																																					p.T26T		Atlas-SNP	.											.	LCE1C	40	.	0			c.C78T						PASS	.						45.0	46.0	46.0					1																	152777877		2203	4300	6503	SO:0001819	synonymous_variant	353133	exon2			CTTTGGGGTGGGG		CCDS1026.1	1q21.3	2008-02-05			ENSG00000197084	ENSG00000197084		"""Late cornified envelopes"""	29464	protein-coding gene	gene with protein product		612605				11698679	Standard	NM_001276331		Approved	LEP3	uc001fap.1	Q5T751	OTTHUMG00000012445	ENST00000607093.1:c.78C>T	1.37:g.152777877G>A		279.0	0.0	0		409.0	29.0	0.0709046	NM_178351		Silent	SNP	ENST00000607093.1	37	CCDS1026.1																																																																																			.	.	none		0.647	LCE1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034658.2	NM_178351	
NLRC3	197358	hgsc.bcm.edu	37	16	3613690	3613690	+	RNA	SNP	G	G	A	rs144685315	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3613690G>A	ENST00000301749.7	-	0	1653				NLRC3_ENST00000324659.8_RNA|NLRC3_ENST00000603507.1_RNA|NLRC3_ENST00000359128.5_RNA|NLRC3_ENST00000419350.2_RNA|NLRC3_ENST00000448023.2_RNA	NM_178844.2	NP_849172.2	Q7RTR2	NLRC3_HUMAN	NLR family, CARD domain containing 3						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|regulation of protein ubiquitination (GO:0031396)|response to lipopolysaccharide (GO:0032496)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(16)|ovary(2)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						TGTCTTGCTCGTAAAACACGT	0.602													G|||	11	0.00219649	0.0083	0.0	5008	,	,		20370	0.0		0.0	False		,,,				2504	0.0				p.Y416Y		Atlas-SNP	.											.	NLRC3	103	.	0			c.C1248T						PASS	.	G		28,4006		0,28,1989	62.0	62.0	62.0		1248	-6.6	0.9	16	dbSNP_134	62	0,8352		0,0,4176	no	coding-synonymous	NLRC3	NM_178844.2		0,28,6165	AA,AG,GG		0.0,0.6941,0.2261		416/1066	3613690	28,12358	2017	4176	6193			197358	exon5			TTGCTCGTAAAAC	BK001112	CCDS73817.1	16p13.3	2014-03-25			ENSG00000167984	ENSG00000167984		"""Nucleotide-binding domain and leucine rich repeat containing"""	29889	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 3"", ""NOD-like receptor C3"""	615648				15705585, 12766759	Standard	NM_178844		Approved	CLR16.2, FLJ00348, NOD3	uc010btn.3	Q7RTR2	OTTHUMG00000177561		16.37:g.3613690G>A		91.0	0.0	0		93.0	46.0	0.494624	NM_178844	Q5EY36|Q8NF48|Q8NI01|Q8NI02|Q8TEL3	Silent	SNP	ENST00000301749.7	37																																																																																				G|0.999;A|0.001	0.001	strong		0.602	NLRC3-201	KNOWN	basic|appris_principal	protein_coding	polymorphic_pseudogene		NM_178844	
PLA2G4C	8605	hgsc.bcm.edu	37	19	48602933	48602933	+	Missense_Mutation	SNP	T	T	C	rs2307282	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:48602933T>C	ENST00000599921.1	-	5	799	c.442A>G	c.(442-444)Aga>Gga	p.R148G	PLA2G4C_ENST00000599111.1_Missense_Mutation_p.R158G|PLA2G4C_ENST00000413144.2_Missense_Mutation_p.R148G|PLA2G4C_ENST00000354276.3_Missense_Mutation_p.R148G			Q9UP65	PA24C_HUMAN	phospholipase A2, group IVC (cytosolic, calcium-independent)	148	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.		R -> G (in dbSNP:rs2307282). {ECO:0000269|Ref.3}.		arachidonic acid metabolic process (GO:0019369)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|parturition (GO:0007567)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cell cortex (GO:0005938)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)	calcium-independent phospholipase A2 activity (GO:0047499)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(12)|lung(13)|ovary(2)|prostate(1)|skin(3)	38		all_cancers(25;2.84e-05)|all_lung(116;4.62e-05)|Lung NSC(112;7.61e-05)|all_epithelial(76;0.000192)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;8.09e-05)|all cancers(93;0.000517)|Epithelial(262;0.0135)|GBM - Glioblastoma multiforme(486;0.0717)		CTTACTTCTCTGGTTTGCTTA	0.527													T|||	221	0.0441294	0.1566	0.013	5008	,	,		17533	0.0		0.0	False		,,,				2504	0.0051				p.R158G		Atlas-SNP	.											PLA2G4C,middle_lobe,carcinoma,+1,1	PLA2G4C	76	1	0			c.A472G						PASS	.	T	GLY/ARG,GLY/ARG,GLY/ARG	504,3902	234.6+/-247.4	33,438,1732	102.0	98.0	99.0		472,442,442	0.8	0.4	19	dbSNP_100	99	13,8587	8.4+/-32.0	0,13,4287	yes	missense,missense,missense	PLA2G4C	NM_001159322.1,NM_001159323.1,NM_003706.2	125,125,125	33,451,6019	CC,CT,TT		0.1512,11.4389,3.9751	probably-damaging,probably-damaging,probably-damaging	158/552,148/528,148/542	48602933	517,12489	2203	4300	6503	SO:0001583	missense	8605	exon5			CTTCTCTGGTTTG	AF065214	CCDS12710.1, CCDS54286.1, CCDS59403.1	19q13.3	2008-09-19					3.1.1.4		9037	protein-coding gene	gene with protein product		603602				9705332	Standard	NM_003706		Approved	cPLA2-gamma	uc002phx.3	Q9UP65		ENST00000599921.1:c.442A>G	19.37:g.48602933T>C	ENSP00000469473:p.Arg148Gly	113.0	0.0	0		84.0	38.0	0.452381	NM_001159322	B2RB71|B4DI40|O75457|Q6IBI8|Q9UG68	Missense_Mutation	SNP	ENST00000599921.1	37	CCDS12710.1	73	0.033424908424908424	67	0.13617886178861788	6	0.016574585635359115	0	0.0	0	0.0	T	16.81	3.226912	0.58668	0.114389	0.001512	ENSG00000105499	ENST00000354276;ENST00000413144	T;T	0.03920	3.76;3.76	3.17	0.779	0.18550	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.158082	0.39985	U	0.001218	T	0.00039	0.0001	N	0.05487	-0.04	0.26973	N	0.965549	D;D;D	0.63046	0.992;0.992;0.992	D;D;D	0.63192	0.912;0.912;0.912	T	0.44143	-0.9347	10	0.15499	T	0.54	-15.3518	7.5148	0.27593	0.0:0.0:0.4963:0.5037	rs2307282;rs52815563;rs56435935;rs2307282	158;148;148	B4DI40;Q8WWC5;Q9UP65	.;.;PA24C_HUMAN	G	148	ENSP00000346228:R148G;ENSP00000400036:R148G	ENSP00000346228:R148G	R	-	1	2	PLA2G4C	53294745	0.937000	0.31787	0.417000	0.26559	0.668000	0.39293	0.459000	0.21908	-0.144000	0.11314	0.338000	0.21704	AGA	T|0.956;C|0.044	0.044	strong		0.527	PLA2G4C-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465551.1		
BIRC6	57448	hgsc.bcm.edu	37	2	32673884	32673884	+	Silent	SNP	A	A	G	rs150651833	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:32673884A>G	ENST00000421745.2	+	22	4640	c.4506A>G	c.(4504-4506)ccA>ccG	p.P1502P		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	1502					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					ATAGCTCACCATTTGATCCAG	0.318													A|||	9	0.00179712	0.0061	0.0014	5008	,	,		14704	0.0		0.0	False		,,,				2504	0.0				p.P1502P	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											.	BIRC6	838	.	0			c.A4506G						PASS	.	A		24,4382	30.8+/-60.4	0,24,2179	120.0	123.0	122.0		4506	-3.2	1.0	2	dbSNP_134	122	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	BIRC6	NM_016252.3		0,28,6475	GG,GA,AA		0.0465,0.5447,0.2153		1502/4858	32673884	28,12978	2203	4300	6503	SO:0001819	synonymous_variant	57448	exon22			CTCACCATTTGAT	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.4506A>G	2.37:g.32673884A>G		155.0	0.0	0		136.0	57.0	0.419118	NM_016252	Q9ULD1	Silent	SNP	ENST00000421745.2	37	CCDS33175.2																																																																																			A|0.998;G|0.002	0.002	strong		0.318	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
PTGES	9536	hgsc.bcm.edu	37	9	132510960	132510960	+	Silent	SNP	G	G	A	rs3205181	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:132510960G>A	ENST00000340607.4	-	2	217	c.183C>T	c.(181-183)agC>agT	p.S61S	PTGES_ENST00000481476.1_5'UTR	NM_004878.4	NP_004869.1	O14684	PTGES_HUMAN	prostaglandin E synthase	61					acute inflammatory response (GO:0002526)|arachidonic acid metabolic process (GO:0019369)|chronic inflammatory response (GO:0002544)|cyclooxygenase pathway (GO:0019371)|negative regulation of cell proliferation (GO:0008285)|prostaglandin biosynthetic process (GO:0001516)|prostaglandin metabolic process (GO:0006693)|response to calcium ion (GO:0051592)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|response to organic cyclic compound (GO:0014070)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)	glutathione binding (GO:0043295)|prostaglandin-E synthase activity (GO:0050220)			lung(1)|skin(1)	2		Ovarian(14;0.00556)				CGTCGGGGTCGCTCCTGCAAT	0.607													G|||	132	0.0263578	0.093	0.0115	5008	,	,		16751	0.0		0.001	False		,,,				2504	0.0				p.S61S		Atlas-SNP	.											.	PTGES	7	.	0			c.C183T						PASS	.	G		367,4039	185.7+/-212.7	14,339,1850	49.0	42.0	44.0		183	-12.2	0.0	9	dbSNP_105	44	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	PTGES	NM_004878.4		14,345,6144	AA,AG,GG		0.0698,8.3296,2.8679		61/153	132510960	373,12633	2203	4300	6503	SO:0001819	synonymous_variant	9536	exon2			GGGGTCGCTCCTG	AF010316	CCDS6927.1	9q34.3	2008-07-21			ENSG00000148344	ENSG00000148344			9599	protein-coding gene	gene with protein product	"""microsomal glutathione S-transferase 1-like 1"", ""tumor protein p53 inducible protein 12"", ""p53-induced gene 12"", ""microsomal prostaglandin E synthase-1"", ""glutathione S-transferase 1-like 1"", ""MGST1-like 1"""	605172		MGST1L1		9305847, 10091672	Standard	NM_004878		Approved	MGST-IV, PIG12, MGST1-L1, TP53I12	uc004byi.3	O14684	OTTHUMG00000020791	ENST00000340607.4:c.183C>T	9.37:g.132510960G>A		49.0	0.0	0		71.0	48.0	0.676056	NM_004878	O14900|Q5SZC0	Silent	SNP	ENST00000340607.4	37	CCDS6927.1																																																																																			G|0.969;A|0.031	0.031	strong		0.607	PTGES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054599.2	NM_004878	
TOM1	10043	hgsc.bcm.edu	37	22	35713931	35713931	+	Silent	SNP	C	C	T	rs57755951	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:35713931C>T	ENST00000449058.2	+	2	239	c.114C>T	c.(112-114)gaC>gaT	p.D38D	TOM1_ENST00000436462.2_Missense_Mutation_p.T17I|TOM1_ENST00000382034.5_5'UTR|TOM1_ENST00000411850.1_Silent_p.D38D|TOM1_ENST00000447733.1_Silent_p.D5D|TOM1_ENST00000425375.1_Silent_p.D38D	NM_005488.2	NP_005479.1	O60784	TOM1_HUMAN	target of myb1 (chicken)	38	VHS. {ECO:0000255|PROSITE- ProRule:PRU00218}.				endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	clathrin binding (GO:0030276)			NS(1)|breast(2)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(2)	19						AGATCTGCGACATCATCAACG	0.597													C|||	80	0.0159744	0.0582	0.0043	5008	,	,		20039	0.0		0.0	False		,,,				2504	0.0				p.D38D		Atlas-SNP	.											.	TOM1	43	.	0			c.C114T						PASS	.	C	,,,	211,4195	130.2+/-166.9	8,195,2000	107.0	106.0	106.0		15,114,114,114	5.4	1.0	22	dbSNP_129	106	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TOM1	NM_001135729.1,NM_001135730.1,NM_001135732.1,NM_005488.2	,,,	8,197,6298	TT,TC,CC		0.0233,4.7889,1.6377	,,,	5/461,38/448,38/494,38/493	35713931	213,12793	2203	4300	6503	SO:0001819	synonymous_variant	10043	exon2			CTGCGACATCATC	AJ006973	CCDS13913.1, CCDS46696.1, CCDS46697.1, CCDS46698.1	22q13.1	2011-01-31	2001-11-28		ENSG00000100284	ENSG00000100284			11982	protein-coding gene	gene with protein product		604700	"""target of myb1 (chicken) homolog"""			10329004, 15047686	Standard	NM_005488		Approved		uc003anp.3	O60784	OTTHUMG00000150958	ENST00000449058.2:c.114C>T	22.37:g.35713931C>T		181.0	0.0	0		197.0	94.0	0.477157	NM_001135732	B4DEL9|B4DNA1|Q5TIJ6|Q86X74	Silent	SNP	ENST00000449058.2	37	CCDS13913.1	23	0.010531135531135532	23	0.046747967479674794	0	0.0	0	0.0	0	0.0	C	13.28	2.189681	0.38707	0.047889	2.33E-4	ENSG00000100284	ENST00000436462	T	0.21361	2.01	5.36	5.36	0.76844	.	.	.	.	.	T	0.01695	0.0054	.	.	.	0.80722	D	1	D	0.53312	0.959	B	0.43623	0.425	T	0.08351	-1.0726	8	0.02654	T	1	-30.6633	12.4314	0.55575	0.0:0.9231:0.0:0.0769	rs57755951	17	E7EPD0	.	I	17	ENSP00000402556:T17I	ENSP00000402556:T17I	T	+	2	0	TOM1	34043931	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	4.017000	0.57167	2.502000	0.84385	0.561000	0.74099	ACA	C|0.982;T|0.018	0.018	strong		0.597	TOM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320641.1	NM_005488	
PDGFRL	5157	hgsc.bcm.edu	37	8	17434813	17434813	+	Missense_Mutation	SNP	G	G	A	rs114432448	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:17434813G>A	ENST00000541323.1	+	2	497	c.52G>A	c.(52-54)Gat>Aat	p.D18N	PDGFRL_ENST00000398074.3_Missense_Mutation_p.D18N|PDGFRL_ENST00000251630.6_Missense_Mutation_p.D18N	NM_006207.2	NP_006198.1	Q15198	PGFRL_HUMAN	platelet-derived growth factor receptor-like	18					G-protein coupled receptor signaling pathway (GO:0007186)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)	extracellular region (GO:0005576)	platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)	9				Colorectal(111;0.0752)		AGCGCTGGAGGATGGTGAGTG	0.677											OREG0018579	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	61	0.0121805	0.0431	0.0058	5008	,	,		10540	0.0		0.0	False		,,,				2504	0.0				p.D18N		Atlas-SNP	.											.	PDGFRL	27	.	0			c.G52A						PASS	.	G	ASN/ASP	171,4235	109.5+/-147.8	4,163,2036	54.0	51.0	52.0		52	0.6	0.7	8	dbSNP_132	52	0,8600		0,0,4300	yes	missense	PDGFRL	NM_006207.2	23	4,163,6336	AA,AG,GG		0.0,3.8811,1.3148	benign	18/376	17434813	171,12835	2203	4300	6503	SO:0001583	missense	5157	exon2			CTGGAGGATGGTG	D37965	CCDS6003.1	8p22-p21.3	2013-01-29			ENSG00000104213	ENSG00000104213		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	8805	protein-coding gene	gene with protein product		604584					Standard	NM_006207		Approved	PRLTS	uc003wxr.3	Q15198	OTTHUMG00000130818	ENST00000541323.1:c.52G>A	8.37:g.17434813G>A	ENSP00000444211:p.Asp18Asn	152.0	0.0	0	718	140.0	68.0	0.485714	NM_006207	A8K085|Q6FH04	Missense_Mutation	SNP	ENST00000541323.1	37	CCDS6003.1	15	0.006868131868131868	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	0	0.0	G	3.726	-0.056629	0.07362	0.038811	0.0	ENSG00000104213	ENST00000251630;ENST00000541323;ENST00000398074	T;T;T	0.32023	1.47;1.47;1.47	3.59	0.567	0.17325	.	0.436898	0.23854	N	0.043902	T	0.02848	0.0085	N	0.22421	0.69	0.27009	N	0.964738	B	0.02656	0.0	B	0.01281	0.0	T	0.20538	-1.0272	10	0.09843	T	0.71	-12.0401	3.4884	0.07629	0.388:0.1982:0.4137:0.0	.	18	Q15198	PGFRL_HUMAN	N	18	ENSP00000251630:D18N;ENSP00000444211:D18N;ENSP00000381149:D18N	ENSP00000251630:D18N	D	+	1	0	PDGFRL	17479098	0.860000	0.29831	0.667000	0.29798	0.381000	0.30169	0.234000	0.17930	0.097000	0.17492	0.462000	0.41574	GAT	G|0.987;A|0.013	0.013	strong		0.677	PDGFRL-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253366.3	NM_006207	
HKDC1	80201	hgsc.bcm.edu	37	10	70980243	70980243	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:70980243C>A	ENST00000354624.5	+	1	185	c.52C>A	c.(52-54)Cag>Aag	p.Q18K	RP11-227H15.4_ENST00000450995.1_RNA|HKDC1_ENST00000395086.2_Missense_Mutation_p.Q18K	NM_025130.3	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	18	Hexokinase type-1 1.				carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)	cytosol (GO:0005829)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|mannokinase activity (GO:0019158)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						GAAGGAGGACCAGATCAAGAA	0.468																																					p.Q18K		Atlas-SNP	.											.	HKDC1	98	.	0			c.C52A						PASS	.						81.0	76.0	78.0					10																	70980243		2203	4300	6503	SO:0001583	missense	80201	exon1			GAGGACCAGATCA		CCDS7288.1	10q22.1	2006-10-24			ENSG00000156510	ENSG00000156510			23302	protein-coding gene	gene with protein product						12477932	Standard	NM_025130		Approved	FLJ37767, FLJ22761	uc001jpf.4	Q2TB90	OTTHUMG00000018371	ENST00000354624.5:c.52C>A	10.37:g.70980243C>A	ENSP00000346643:p.Gln18Lys	54.0	0.0	0		70.0	37.0	0.528571	NM_025130	B5MDN9|Q2TB91|Q5VTC7|Q7Z373|Q8WU37|Q96EH2|Q9H5Y9	Missense_Mutation	SNP	ENST00000354624.5	37	CCDS7288.1	.	.	.	.	.	.	.	.	.	.	C	16.98	3.270551	0.59540	.	.	ENSG00000156510	ENST00000354624;ENST00000395087;ENST00000395086	D;D	0.98968	-5.28;-5.28	5.44	5.44	0.79542	Hexokinase, N-terminal (1);	0.149729	0.47093	D	0.000250	D	0.98232	0.9415	M	0.86740	2.835	0.54753	D	0.99998	B	0.14438	0.01	B	0.20184	0.028	D	0.98393	1.0564	10	0.25106	T	0.35	-10.1756	19.279	0.94044	0.0:1.0:0.0:0.0	.	18	Q2TB90	HKDC1_HUMAN	K	18	ENSP00000346643:Q18K;ENSP00000378521:Q18K	ENSP00000346643:Q18K	Q	+	1	0	HKDC1	70650249	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	7.339000	0.79282	2.554000	0.86153	0.655000	0.94253	CAG	.	.	none		0.468	HKDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048389.1	NM_025130	
PODNL1	79883	hgsc.bcm.edu	37	19	14043843	14043843	+	Missense_Mutation	SNP	C	C	T	rs80103045	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14043843C>T	ENST00000339560.5	-	8	1487	c.1214G>A	c.(1213-1215)cGc>cAc	p.R405H	PODNL1_ENST00000538517.2_Missense_Mutation_p.R314H|PODNL1_ENST00000254320.3_Missense_Mutation_p.R323H|PODNL1_ENST00000538371.2_Missense_Mutation_p.R403H	NM_024825.3	NP_079101.3	Q6PEZ8	PONL1_HUMAN	podocan-like 1	405	Leu-rich.					proteinaceous extracellular matrix (GO:0005578)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|skin(1)	8			OV - Ovarian serous cystadenocarcinoma(19;5.26e-23)			ACGCAACCGGCGGAAGGCCCG	0.711													C|||	153	0.0305511	0.1074	0.0029	5008	,	,		15309	0.0		0.001	False		,,,				2504	0.0082				p.R405H		Atlas-SNP	.											.	PODNL1	27	.	0			c.G1214A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG	318,3856		6,306,1775	6.0	7.0	7.0		1208,941,1214	3.8	0.9	19	dbSNP_131	7	17,8171		0,17,4077	yes	missense,missense,missense	PODNL1	NM_001146254.1,NM_001146255.1,NM_024825.3	29,29,29	6,323,5852	TT,TC,CC		0.2076,7.6186,2.7099	probably-damaging,probably-damaging,probably-damaging	403/511,314/422,405/513	14043843	335,12027	2087	4094	6181	SO:0001583	missense	79883	exon8			AACCGGCGGAAGG	AK027100	CCDS12300.1, CCDS54225.1, CCDS54226.1	19p13.12	2008-02-05							26275	protein-coding gene	gene with protein product						12477932	Standard	NM_024825		Approved	FLJ23447, SLRR5B	uc010xnj.2	Q6PEZ8		ENST00000339560.5:c.1214G>A	19.37:g.14043843C>T	ENSP00000345175:p.Arg405His	4.0	0.0	0		4.0	4.0	1	NM_024825	B7Z564|Q9H5G9	Missense_Mutation	SNP	ENST00000339560.5	37	CCDS12300.1	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	C	13.68	2.309090	0.40895	0.076186	0.002076	ENSG00000132000	ENST00000538371;ENST00000538517;ENST00000339560;ENST00000545071;ENST00000254320	T;T;T;T	0.57436	0.4;0.4;0.4;0.4	4.79	3.76	0.43208	.	0.451987	0.18547	N	0.138005	T	0.02267	0.0070	N	0.16066	0.365	0.26971	N	0.965586	B;B;B;B	0.29037	0.046;0.231;0.113;0.224	B;B;B;B	0.33690	0.046;0.115;0.052;0.168	T	0.04400	-1.0954	10	0.51188	T	0.08	.	10.0503	0.42212	0.0:0.9024:0.0:0.0976	.	403;323;314;405	F5H7F9;B7Z3M0;G3V1J6;Q6PEZ8	.;.;.;PONL1_HUMAN	H	403;314;405;255;323	ENSP00000442553:R403H;ENSP00000440080:R314H;ENSP00000345175:R405H;ENSP00000254320:R323H	ENSP00000254320:R323H	R	-	2	0	PODNL1	13904843	0.997000	0.39634	0.903000	0.35520	0.313000	0.28021	2.510000	0.45468	1.015000	0.39444	0.453000	0.30009	CGC	C|0.980;T|0.020	0.020	strong		0.711	PODNL1-003	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457967.1	NM_024825	
SLC5A5	6528	hgsc.bcm.edu	37	19	17988794	17988794	+	Silent	SNP	C	C	T	rs35209536	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17988794C>T	ENST00000222248.3	+	7	1208	c.861C>T	c.(859-861)gtC>gtT	p.V287V		NM_000453.2	NP_000444.1	Q92911	SC5A5_HUMAN	solute carrier family 5 (sodium/iodide cotransporter), member 5	287					cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to gonadotropin stimulus (GO:0071371)|iodide transport (GO:0015705)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	iodide transmembrane transporter activity (GO:0015111)|sodium:iodide symporter activity (GO:0008507)			NS(2)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|skin(3)	31						TCAACCAGGTCGGCCTGTTCC	0.632													C|||	97	0.019369	0.0703	0.0058	5008	,	,		18147	0.0		0.0	False		,,,				2504	0.0				p.V287V	Melanoma(65;1008 1708 7910 46650)	Atlas-SNP	.											.	SLC5A5	67	.	0			c.C861T						PASS	.	C		255,4151	148.4+/-182.8	10,235,1958	104.0	75.0	85.0		861	0.3	1.0	19	dbSNP_126	85	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SLC5A5	NM_000453.2		10,236,6257	TT,TC,CC		0.0116,5.7876,1.9683		287/644	17988794	256,12750	2203	4300	6503	SO:0001819	synonymous_variant	6528	exon7			CCAGGTCGGCCTG		CCDS12368.1	19p13.11	2013-07-19	2013-07-19		ENSG00000105641	ENSG00000105641		"""Solute carriers"""	11040	protein-coding gene	gene with protein product		601843	"""solute carrier family 5 (sodium iodide symporter), member 5"""			9231811	Standard	NM_000453		Approved	NIS	uc002nhr.4	Q92911		ENST00000222248.3:c.861C>T	19.37:g.17988794C>T		65.0	0.0	0		84.0	41.0	0.488095	NM_000453	O43702|Q2M335|Q9NYB6	Silent	SNP	ENST00000222248.3	37	CCDS12368.1																																																																																			C|0.982;T|0.018	0.018	strong		0.632	SLC5A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466690.1		
SMG6	23293	hgsc.bcm.edu	37	17	2203462	2203462	+	Silent	SNP	T	T	C	rs140746531	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:2203462T>C	ENST00000263073.6	-	2	635	c.585A>G	c.(583-585)ccA>ccG	p.P195P	SMG6_ENST00000544865.1_Silent_p.P164P	NM_017575.4	NP_060045.4	Q86US8	EST1A_HUMAN	SMG6 nonsense mediated mRNA decay factor	195	Interaction with telomeric DNA.				gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of dephosphorylation (GO:0035303)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|telomere maintenance (GO:0000723)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|telomerase holoenzyme complex (GO:0005697)	endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|telomeric DNA binding (GO:0042162)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(7)|lung(10)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45						CAGCCCTGTCTGGTTTATTCG	0.512													T|||	3	0.000599042	0.0023	0.0	5008	,	,		17852	0.0		0.0	False		,,,				2504	0.0				p.P195P	Melanoma(59;28 1088 11621 25887 46638 50814)	Atlas-SNP	.											.	SMG6	97	.	0			c.A585G						PASS	.	T	,	6,4400	12.9+/-30.5	0,6,2197	249.0	270.0	263.0		492,585	0.1	0.3	17	dbSNP_134	263	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SMG6	NM_001170957.1,NM_017575.4	,	0,6,6497	CC,CT,TT		0.0,0.1362,0.0461	,	164/1389,195/1420	2203462	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	23293	exon2			CCTGTCTGGTTTA	AB018275	CCDS11016.1, CCDS58498.1	17p13.3	2013-07-02	2013-07-02	2006-02-16	ENSG00000070366	ENSG00000070366			17809	protein-coding gene	gene with protein product	"""EST1 telomerase component homolog A (S. cerevisiae)"""	610963	"""chromosome 17 open reading frame 31"", ""smg-6 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	C17orf31		12676087, 12699629	Standard	NM_017575		Approved	KIAA0732, SMG-6, EST1A	uc002fub.1	Q86US8	OTTHUMG00000177578	ENST00000263073.6:c.585A>G	17.37:g.2203462T>C		73.0	0.0	0		97.0	49.0	0.505155	NM_017575	B7Z874|O94837|Q86VH6|Q9UF60	Silent	SNP	ENST00000263073.6	37	CCDS11016.1																																																																																			T|1.000;C|0.000	0.000	strong		0.512	SMG6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437826.3		
POU5F1B	5462	hgsc.bcm.edu	37	8	128428592	128428592	+	Missense_Mutation	SNP	G	G	A	rs140000439	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:128428592G>A	ENST00000465342.2	+	2	1638	c.481G>A	c.(481-483)Gga>Aga	p.G161R	CASC8_ENST00000501396.1_RNA|CASC8_ENST00000502082.1_RNA|POU5F1B_ENST00000391675.1_Missense_Mutation_p.G161R|CASC8_ENST00000523825.1_RNA			Q06416	P5F1B_HUMAN	POU class 5 homeobox 1B	161	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(1)|prostate(1)|urinary_tract(1)	3						GATCACCCTGGGATATACACA	0.522													g|||	78	0.0155751	0.053	0.0115	5008	,	,		17902	0.0		0.0	False		,,,				2504	0.0				p.G161R		Atlas-SNP	.											.	POU5F1B	32	.	0			c.G481A						PASS	.	G	ARG/GLY	73,1311		2,69,621	47.0	54.0	52.0		481	1.1	0.8	8	dbSNP_134	52	0,3182		0,0,1591	no	missense	POU5F1B	NM_001159542.1	125	2,69,2212	AA,AG,GG		0.0,5.2746,1.5988	probably-damaging	161/360	128428592	73,4493	692	1591	2283	SO:0001583	missense	5462	exon1			ACCCTGGGATATA	AF268615	CCDS55274.1	8q24.21	2011-06-20	2009-04-15	2009-04-15	ENSG00000212993	ENSG00000212993		"""Homeoboxes / POU class"""	9223	protein-coding gene	gene with protein product		615739	"""POU domain class 5, transcription factor 1 pseudogene 1"", ""POU class 5 homeobox 1 pseudogene 1"""	OTF3P1, POU5F1P1		1408763	Standard	NM_001159542		Approved	OTF3C	uc003ysf.3	Q06416	OTTHUMG00000157807	ENST00000465342.2:c.481G>A	8.37:g.128428592G>A	ENSP00000419298:p.Gly161Arg	155.0	0.0	0		161.0	81.0	0.503106	NM_001159542	D5K9S4|D5K9S9|D5K9T0|D5K9T1|D5K9T3|D5K9U3|D5K9U6|D5K9V4|D5K9V6|D5K9W0|D5K9W2|D5K9W7|D5K9X2|D5K9X3|D5K9X5|D5K9X8|D5K9X9|E9LRB1|E9LRB2|E9LRH5|E9LRH6|E9LRH7|E9LRK4|E9LRK5|E9LRK7|E9LRK8|E9LRM7|E9LRM9|E9LRN2|E9LRN4|E9LRN5|E9LRP8|E9LRQ0|E9LRQ2|E9LRQ3|E9LRQ4|E9LRQ5|E9LRS3|Q2VIK6|Q9BZV7|Q9BZV9	Missense_Mutation	SNP	ENST00000465342.2	37	CCDS55274.1	32	0.014652014652014652	28	0.056910569105691054	4	0.011049723756906077	0	0.0	0	0.0	G	23.4	4.412629	0.83340	0.052746	0.0	ENSG00000212993	ENST00000465342;ENST00000391675	T;T	0.77877	-1.13;-1.13	1.14	1.14	0.20703	POU-specific (4);Lambda repressor-like, DNA-binding (2);POU (1);	0.000000	0.40144	N	0.001164	T	0.50137	0.1598	M	0.87682	2.9	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.74328	-0.3701	10	0.87932	D	0	.	8.3083	0.32055	0.0:0.0:1.0:0.0	.	161	Q06416	P5F1B_HUMAN	R	161	ENSP00000419298:G161R;ENSP00000375557:G161R	ENSP00000375557:G161R	G	+	1	0	POU5F1B	128497774	1.000000	0.71417	0.759000	0.31340	0.727000	0.41649	6.555000	0.73928	0.968000	0.38212	0.134000	0.15878	GGA	G|0.985;A|0.015	0.015	strong		0.522	POU5F1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349649.2	NM_001159542	
SYCP2	10388	hgsc.bcm.edu	37	20	58441612	58441612	+	Silent	SNP	C	C	T	rs58905758	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:58441612C>T	ENST00000357552.3	-	40	4383	c.4158G>A	c.(4156-4158)acG>acA	p.T1386T	SYCP2_ENST00000371001.2_Silent_p.T1386T			Q9BX26	SYCP2_HUMAN	synaptonemal complex protein 2	1386					female meiotic division (GO:0007143)|fertilization (GO:0009566)|male genitalia morphogenesis (GO:0048808)|male meiosis (GO:0007140)|negative regulation of apoptotic process (GO:0043066)|synaptonemal complex assembly (GO:0007130)	lateral element (GO:0000800)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	DNA binding (GO:0003677)			NS(4)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(14)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	53	all_lung(29;0.00344)		BRCA - Breast invasive adenocarcinoma(7;1.19e-09)			TCCAAGACTGCGTAGTAAAAT	0.318													C|||	87	0.0173722	0.0635	0.0029	5008	,	,		15377	0.0		0.001	False		,,,				2504	0.0				p.T1386T		Atlas-SNP	.											.	SYCP2	204	.	0			c.G4158A						PASS	.	C		199,4207	122.5+/-159.9	4,191,2008	85.0	87.0	86.0		4158	-2.6	0.1	20	dbSNP_129	86	2,8594	2.2+/-6.3	0,2,4296	no	coding-synonymous	SYCP2	NM_014258.2		4,193,6304	TT,TC,CC		0.0233,4.5166,1.5459		1386/1531	58441612	201,12801	2203	4298	6501	SO:0001819	synonymous_variant	10388	exon39			AGACTGCGTAGTA	Y08982	CCDS13482.1	20q13.33	2007-07-02			ENSG00000196074	ENSG00000196074			11490	protein-coding gene	gene with protein product		604105				10341103, 9592139	Standard	NM_014258		Approved	SCP2	uc002yaz.3	Q9BX26	OTTHUMG00000032872	ENST00000357552.3:c.4158G>A	20.37:g.58441612C>T		63.0	0.0	0		47.0	29.0	0.617021	NM_014258	A2RUE5|O75763|Q5JX11|Q9NTX8|Q9UG27	Silent	SNP	ENST00000357552.3	37	CCDS13482.1																																																																																			C|0.983;T|0.017	0.017	strong		0.318	SYCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079930.3	NM_014258	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057952	46057952	+	Silent	SNP	C	C	A	rs74701761	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46057952C>A	ENST00000380095.1	+	1	680	c.618C>A	c.(616-618)gtC>gtA	p.V206V	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	206	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						GCGTGCCCGTCCCCTCCTGCG	0.706													C|||	103	0.0205671	0.0756	0.0043	5008	,	,		19027	0.0		0.0	False		,,,				2504	0.0				p.V206V		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.C618A						PASS	.						91.0	95.0	94.0					21																	46057952		2203	4300	6503	SO:0001819	synonymous_variant	353333	exon1			GCCCGTCCCCTCC	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.618C>A	21.37:g.46057952C>A		294.0	0.0	0		473.0	113.0	0.238901	NM_181688		Silent	SNP	ENST00000380095.1	37	CCDS33585.1																																																																																			C|0.982;A|0.018	0.018	strong		0.706	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
NKX2-5	1482	hgsc.bcm.edu	37	5	172662014	172662014	+	Missense_Mutation	SNP	G	G	A	rs28936670	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:172662014G>A	ENST00000329198.4	-	1	346	c.73C>T	c.(73-75)Cgc>Tgc	p.R25C	NKX2-5_ENST00000521848.1_Missense_Mutation_p.R25C|NKX2-5_ENST00000424406.2_Missense_Mutation_p.R25C	NM_001166175.1|NM_001166176.1|NM_004387.3	NP_001159647.1|NP_001159648.1|NP_004378.1	P52952	NKX25_HUMAN	NK2 homeobox 5	25			R -> C (in ASD7, TOF, CHNG5 and HLHS2; exhibits significant functional impairment with reduction of transactivation properties and dominant- negative effect; the mutant protein activity on the DIO2, TG and TPO promoters is significantly impaired; dbSNP:rs28936670). {ECO:0000269|PubMed:10587520, ECO:0000269|PubMed:11714651, ECO:0000269|PubMed:14607454, ECO:0000269|PubMed:15342699, ECO:0000269|PubMed:15810002, ECO:0000269|PubMed:16418214}.		adult heart development (GO:0007512)|apoptotic process involved in heart morphogenesis (GO:0003278)|atrial cardiac muscle cell development (GO:0055014)|atrial septum morphogenesis (GO:0060413)|atrioventricular node cell development (GO:0060928)|atrioventricular node cell fate commitment (GO:0060929)|BMP signaling pathway (GO:0030509)|bundle of His development (GO:0003166)|canonical Wnt signaling pathway (GO:0060070)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle contraction (GO:0060048)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac ventricle formation (GO:0003211)|cell differentiation (GO:0030154)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|heart trabecula formation (GO:0060347)|hemopoiesis (GO:0030097)|negative regulation of apoptotic process (GO:0043066)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract septum morphogenesis (GO:0003148)|pharyngeal system development (GO:0060037)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart contraction (GO:0045823)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription via serum response element binding (GO:0010735)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of voltage-gated calcium channel activity (GO:1901387)|proepicardium development (GO:0003342)|pulmonary myocardium development (GO:0003350)|Purkinje myocyte differentiation (GO:0003168)|regulation of cardiac muscle cell proliferation (GO:0060043)|regulation of cardiac muscle contraction (GO:0055117)|right ventricular cardiac muscle tissue morphogenesis (GO:0003221)|sarcomere organization (GO:0045214)|septum secundum development (GO:0003285)|spleen development (GO:0048536)|thyroid gland development (GO:0030878)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular cardiac myofibril assembly (GO:0055005)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|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 transcription cofactor activity (GO:0001104)|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)|serum response element binding (GO:0010736)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|large_intestine(2)|lung(7)|prostate(1)	12	Renal(175;0.000159)|Lung NSC(126;0.00229)|all_lung(126;0.004)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			GCCAGGCTGCGCTGCTGCTGT	0.672													G|||	51	0.0101837	0.0363	0.0029	5008	,	,		12104	0.0		0.001	False		,,,				2504	0.0				p.R25C	Esophageal Squamous(72;810 1219 2387 13420 44943)	Atlas-SNP	.											.	NKX2-5	42	.	0			c.C73T	GRCh37	CM993125	NKX2-5	M	rs28936670	PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG	115,4231		0,115,2058	20.0	25.0	23.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	73,73,73	3.9	1.0	5	dbSNP_125	23	8,8528		0,8,4260	yes	missense,missense,missense	NKX2-5	NM_001166175.1,NM_001166176.1,NM_004387.3	180,180,180	0,123,6318	AA,AG,GG		0.0937,2.6461,0.9548	probably-damaging,probably-damaging,probably-damaging	25/113,25/152,25/325	172662014	123,12759	2173	4268	6441	SO:0001583	missense	1482	exon1			GGCTGCGCTGCTG	AB021133	CCDS4387.1, CCDS54949.1, CCDS54950.1	5q34	2014-09-17	2011-06-01	2002-10-04	ENSG00000183072	ENSG00000183072		"""Homeoboxes / ANTP class : NKL subclass"""	2488	protein-coding gene	gene with protein product	"""tinman paralog (Drosophila)"""	600584	"""cardiac-specific homeo box"", ""NK2 transcription factor related, locus 5 (Drosophila)"""	CSX, NKX2E		7665173, 8900537	Standard	NM_004387		Approved	CSX1, NKX2.5, NKX4-1	uc003mcm.2	P52952	OTTHUMG00000130522	ENST00000329198.4:c.73C>T	5.37:g.172662014G>A	ENSP00000327758:p.Arg25Cys	181.0	0.0	0		157.0	77.0	0.490446	NM_004387	A8K3K0|B4DNB6|E9PBU6	Missense_Mutation	SNP	ENST00000329198.4	37	CCDS4387.1	10	0.004578754578754579	7	0.014227642276422764	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	17.06	3.293107	0.60086	0.026461	9.37E-4	ENSG00000183072	ENST00000329198;ENST00000424406;ENST00000521848;ENST00000517440	D;D;D;D	0.90385	-2.66;-2.53;-2.6;-2.55	4.76	3.89	0.44902	.	0.491101	0.15624	N	0.252757	T	0.66157	0.2761	L	0.40543	1.245	0.38768	A	0.954489	B;B;B	0.29646	0.253;0.089;0.002	B;B;B	0.21546	0.035;0.008;0.001	T	0.76594	-0.2902	9	0.56958	D	0.05	.	3.5512	0.07847	0.0824:0.2014:0.467:0.2492	rs28936670	25;25;25	B4DNB6;E5RH49;P52952	.;.;NKX25_HUMAN	C	25	ENSP00000327758:R25C;ENSP00000395378:R25C;ENSP00000427906:R25C;ENSP00000429905:R25C	ENSP00000327758:R25C	R	-	1	0	NKX2-5	172594620	0.992000	0.36948	0.993000	0.49108	0.842000	0.47809	1.185000	0.32065	1.118000	0.41863	0.462000	0.41574	CGC	G|0.993;A|0.007	0.007	strong		0.672	NKX2-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252942.2		
ATAD3A	55210	hgsc.bcm.edu	37	1	1458915	1458915	+	Missense_Mutation	SNP	C	C	T	rs113107431	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1458915C>T	ENST00000378755.5	+	9	1169	c.1075C>T	c.(1075-1077)Ccc>Tcc	p.P359S	ATAD3A_ENST00000536055.1_Missense_Mutation_p.P232S|ATAD3A_ENST00000378756.3_Missense_Mutation_p.P311S	NM_018188.3	NP_060658.3	Q9NVI7	ATD3A_HUMAN	ATPase family, AAA domain containing 3A	359					cell growth (GO:0016049)|negative regulation of apoptotic process (GO:0043066)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(4)|kidney(6)|large_intestine(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.12e-36)|OV - Ovarian serous cystadenocarcinoma(86;2.18e-22)|Colorectal(212;0.000164)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00233)|BRCA - Breast invasive adenocarcinoma(365;0.00469)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0347)|Lung(427;0.147)		CCTCAGTCGACCCCAGGACGC	0.706													c|||	108	0.0215655	0.0756	0.0115	5008	,	,		12132	0.0		0.0	False		,,,				2504	0.0				p.P359S		Atlas-SNP	.											.	ATAD3A	35	.	0			c.C1075T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO	341,4065	171.6+/-201.8	11,319,1873	48.0	47.0	47.0		931,694,1075	4.8	0.8	1	dbSNP_132	47	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense,missense	ATAD3A	NM_001170535.1,NM_001170536.1,NM_018188.3	74,74,74	11,321,6171	TT,TC,CC		0.0233,7.7394,2.6372	benign,benign,benign	311/587,232/508,359/635	1458915	343,12663	2203	4300	6503	SO:0001583	missense	55210	exon9			AGTCGACCCCAGG	AK025865	CCDS31.1, CCDS53259.1, CCDS53260.1	1p36.33	2010-04-21		2007-02-08	ENSG00000197785	ENSG00000197785		"""ATPases / AAA-type"""	25567	protein-coding gene	gene with protein product		612316				12477932	Standard	NM_018188		Approved	FLJ10709	uc001afz.2	Q9NVI7	OTTHUMG00000000575	ENST00000378755.5:c.1075C>T	1.37:g.1458915C>T	ENSP00000368030:p.Pro359Ser	131.0	0.0	0		181.0	102.0	0.563536	NM_018188	B3KPB3|D2K8Q1|G3V1I6|Q5SV23|Q8N275|Q96A50	Missense_Mutation	SNP	ENST00000378755.5	37	CCDS31.1	55|55	0.025183150183150184|0.025183150183150184	49|49	0.09959349593495935|0.09959349593495935	6|6	0.016574585635359115|0.016574585635359115	0|0	0.0|0.0	0|0	0.0|0.0	c|c	9.414|9.414	1.081264|1.081264	0.20309|0.20309	0.077394|0.077394	2.33E-4|2.33E-4	ENSG00000197785|ENSG00000197785	ENST00000378756;ENST00000378755;ENST00000536055|ENST00000339113	D;D;D|.	0.94723|.	-3.25;-3.12;-3.5|.	4.8|4.8	4.8|4.8	0.61643|0.61643	.|.	0.325455|.	0.33895|.	N|.	0.004457|.	T|T	0.01835|0.01835	0.0058|0.0058	L|L	0.41906|0.41906	1.305|1.305	0.34198|0.34198	D|D	0.672866|0.672866	B;B|.	0.28439|.	0.047;0.212|.	B;B|.	0.22601|.	0.027;0.04|.	T|T	0.30416|0.30416	-0.9979|-0.9979	10|5	0.33940|.	T|.	0.23|.	.|.	8.613|8.613	0.33815|0.33815	0.1587:0.665:0.1764:0.0|0.1587:0.665:0.1764:0.0	.|.	311;359|.	D2K8Q1;Q9NVI7|.	.;ATD3A_HUMAN|.	S|I	311;359;232|296	ENSP00000368031:P311S;ENSP00000368030:P359S;ENSP00000439290:P232S|.	ENSP00000368030:P359S|.	P|T	+|+	1|2	0|0	ATAD3A|ATAD3A	1448778|1448778	1.000000|1.000000	0.71417|0.71417	0.842000|0.842000	0.33263|0.33263	0.047000|0.047000	0.14425|0.14425	3.205000|3.205000	0.51090|0.51090	2.220000|2.220000	0.72140|0.72140	0.556000|0.556000	0.70494|0.70494	CCC|ACC	C|0.972;T|0.028	0.028	strong		0.706	ATAD3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000001365.1	NM_018188	
MUC4	4585	hgsc.bcm.edu	37	3	195509113	195509113	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195509113G>A	ENST00000463781.3	-	2	9797	c.9338C>T	c.(9337-9339)gCa>gTa	p.A3113V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A3113V	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACCTGTGGATGCTGAGGAAGG	0.587																																					p.A3113V		Atlas-SNP	.											.	MUC4	1505	.	0			c.C9338T						PASS	.																																			SO:0001583	missense	4585	exon2			GTGGATGCTGAGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.9338C>T	3.37:g.195509113G>A	ENSP00000417498:p.Ala3113Val	177.0	0.0	0		313.0	60.0	0.191693	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	1.513	-0.549035	0.04024	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31510	1.49;1.5	.	.	.	.	.	.	.	.	T	0.12220	0.0297	N	0.19112	0.55	0.09310	N	1	P	0.42584	0.784	B	0.31686	0.134	T	0.15549	-1.0433	7	.	.	.	.	3.8973	0.09144	0.0:0.0:0.5926:0.4074	.	2985	E7ESK3	.	V	3113	ENSP00000417498:A3113V;ENSP00000420243:A3113V	.	A	-	2	0	MUC4	196993892	0.000000	0.05858	0.006000	0.13384	0.000000	0.00434	-1.817000	0.01719	-0.889000	0.03950	0.000000	0.15137	GCA	.	.	none		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PRDM16	63976	hgsc.bcm.edu	37	1	3322139	3322139	+	Silent	SNP	C	C	T	rs61745281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:3322139C>T	ENST00000270722.5	+	8	1162	c.1113C>T	c.(1111-1113)tgC>tgT	p.C371C	PRDM16_ENST00000378398.3_Silent_p.C372C|PRDM16_ENST00000514189.1_Silent_p.C372C|PRDM16_ENST00000441472.2_Silent_p.C371C|PRDM16_ENST00000442529.2_Silent_p.C371C|PRDM16_ENST00000511072.1_Silent_p.C372C|PRDM16_ENST00000378391.2_Silent_p.C371C|PRDM16_ENST00000512462.1_3'UTR			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	371					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)		GCCCCGACTGCGGGAAGACCT	0.657			T	EVI1	"""MDS, AML"""								c|||	139	0.0277556	0.0998	0.0101	5008	,	,		14941	0.0		0.0	False		,,,				2504	0.0				p.C371C		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16	147	.	0			c.C1113T						PASS	.	C	,	363,4035		14,335,1850	41.0	48.0	46.0		1113,1113	-4.0	1.0	1	dbSNP_129	46	6,8576		0,6,4285	no	coding-synonymous,coding-synonymous	PRDM16	NM_022114.3,NM_199454.2	,	14,341,6135	TT,TC,CC		0.0699,8.2538,2.8428	,	371/1277,371/1258	3322139	369,12611	2199	4291	6490	SO:0001819	synonymous_variant	63976	exon8			CGACTGCGGGAAG	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.1113C>T	1.37:g.3322139C>T		56.0	0.0	0		66.0	36.0	0.545455	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Silent	SNP	ENST00000270722.5	37	CCDS41236.2																																																																																			C|0.984;T|0.016	0.016	strong		0.657	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114	
SPATA9	83890	hgsc.bcm.edu	37	5	95011166	95011166	+	Missense_Mutation	SNP	G	G	A	rs140676515	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:95011166G>A	ENST00000274432.8	-	3	469	c.328C>T	c.(328-330)Cgt>Tgt	p.R110C	RFESD_ENST00000508206.1_Intron|SPATA9_ENST00000395899.3_Missense_Mutation_p.R110C|SPATA9_ENST00000477047.2_5'UTR	NM_031952.3	NP_114158.2	Q9BWV2	SPAT9_HUMAN	spermatogenesis associated 9	110					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)				large_intestine(3)|lung(4)	7		all_cancers(142;1.28e-06)|all_epithelial(76;1.55e-09)|all_lung(232;0.00307)|Lung NSC(167;0.00452)|Ovarian(225;0.00473)|Colorectal(57;0.0846)|Breast(839;0.198)		all cancers(79;8.91e-16)		CTCAGCAGACGACCAGATATG	0.433													G|||	5	0.000998403	0.0038	0.0	5008	,	,		18649	0.0		0.0	False		,,,				2504	0.0				p.R110C		Atlas-SNP	.											SPATA9,NS,carcinoma,+1,1	SPATA9	17	1	0			c.C328T						scavenged	.	G	CYS/ARG	29,4377	35.2+/-66.4	0,29,2174	133.0	113.0	120.0		328	3.9	0.0	5	dbSNP_134	120	0,8600		0,0,4300	yes	missense	SPATA9	NM_031952.3	180	0,29,6474	AA,AG,GG		0.0,0.6582,0.223	probably-damaging	110/255	95011166	29,12977	2203	4300	6503	SO:0001583	missense	83890	exon3			GCAGACGACCAGA	AK093225	CCDS4076.1	5q15	2008-02-05			ENSG00000145757	ENSG00000145757			22988	protein-coding gene	gene with protein product		608039				12493713	Standard	NM_031952		Approved	NYD-SP16, FLJ35906	uc003klj.1	Q9BWV2	OTTHUMG00000121169	ENST00000274432.8:c.328C>T	5.37:g.95011166G>A	ENSP00000274432:p.Arg110Cys	120.0	1.0	0.00833333		137.0	63.0	0.459854	NM_031952	A8K8H3|Q4G122|Q86X33|Q8NA28	Missense_Mutation	SNP	ENST00000274432.8	37	CCDS4076.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	12.73	2.024694	0.35701	0.006582	0.0	ENSG00000145757	ENST00000274432;ENST00000395899	T	0.31510	1.49	4.76	3.88	0.44766	.	0.000000	0.51477	D	0.000082	T	0.26448	0.0646	L	0.27053	0.805	0.19300	N	0.999974	D	0.67145	0.996	P	0.57371	0.819	T	0.05818	-1.0862	10	0.87932	D	0	-8.0846	10.6281	0.45519	0.0:0.0:0.8093:0.1907	.	110	Q9BWV2	SPAT9_HUMAN	C	110	ENSP00000274432:R110C	ENSP00000274432:R110C	R	-	1	0	SPATA9	95036922	0.074000	0.21230	0.029000	0.17559	0.011000	0.07611	1.948000	0.40303	1.329000	0.45376	0.655000	0.94253	CGT	G|0.998;A|0.002	0.002	strong		0.433	SPATA9-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304036.1	NM_031952	
OR8K5	219453	hgsc.bcm.edu	37	11	55927591	55927591	+	Missense_Mutation	SNP	A	A	G	rs2512938	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55927591A>G	ENST00000313447.1	-	1	202	c.203T>C	c.(202-204)tTt>tCt	p.F68S		NM_001004058.2	NP_001004058.2	Q8NH50	OR8K5_HUMAN	olfactory receptor, family 8, subfamily K, member 5	68			F -> S (in dbSNP:rs2512938).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(3)|lung(24)|ovary(2)|pancreas(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	34	Esophageal squamous(21;0.00693)	Lung NSC(402;0.197)|all_epithelial(135;0.236)				AAGATCAACAAAAGCCAAATG	0.398													.|||	111	0.0221645	0.0779	0.0115	5008	,	,		21695	0.0		0.0	False		,,,				2504	0.0				p.F68S		Atlas-SNP	.											.	OR8K5	82	.	0			c.T203C						PASS	.	A	SER/PHE	280,4122	155.9+/-189.0	9,262,1930	110.0	109.0	109.0		203	2.7	0.9	11	dbSNP_100	109	6,8586	4.3+/-15.6	0,6,4290	yes	missense	OR8K5	NM_001004058.2	155	9,268,6220	GG,GA,AA		0.0698,6.3607,2.201	possibly-damaging	68/308	55927591	286,12708	2201	4296	6497	SO:0001583	missense	219453	exon1			TCAACAAAAGCCA	BK004347	CCDS31521.1	11q11	2012-08-09			ENSG00000181752	ENSG00000181752		"""GPCR / Class A : Olfactory receptors"""	15315	protein-coding gene	gene with protein product							Standard	NM_001004058		Approved		uc010rja.2	Q8NH50	OTTHUMG00000166820	ENST00000313447.1:c.203T>C	11.37:g.55927591A>G	ENSP00000323853:p.Phe68Ser	126.0	0.0	0		138.0	68.0	0.492754	NM_001004058	Q6IFB5	Missense_Mutation	SNP	ENST00000313447.1	37	CCDS31521.1	44	0.020146520146520148	39	0.07926829268292683	5	0.013812154696132596	0	0.0	0	0.0	A	11.51	1.659357	0.29515	0.063607	6.98E-4	ENSG00000181752	ENST00000313447	T	0.01005	5.45	3.87	2.69	0.31865	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00178	0.0005	M	0.79475	2.455	0.23834	N	0.996718	D	0.56746	0.977	P	0.47744	0.556	T	0.48559	-0.9025	9	0.72032	D	0.01	.	8.9967	0.36057	0.8337:0.0:0.0:0.1663	rs2512938;rs56484064;rs2512938	68	Q8NH50	OR8K5_HUMAN	S	68	ENSP00000323853:F68S	ENSP00000323853:F68S	F	-	2	0	OR8K5	55684167	0.082000	0.21442	0.937000	0.37676	0.050000	0.14768	3.809000	0.55606	0.621000	0.30232	-0.555000	0.04198	TTT	A|0.974;G|0.026	0.026	strong		0.398	OR8K5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391543.1	NM_001004058	
GSTO2	119391	hgsc.bcm.edu	37	10	106058940	106058940	+	Silent	SNP	C	C	T	rs157078	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:106058940C>T	ENST00000338595.2	+	7	950	c.630C>T	c.(628-630)gaC>gaT	p.D210D	GSTO2_ENST00000450629.2_Silent_p.D176D|GSTO2_ENST00000429569.2_Missense_Mutation_p.P113S|GSTO2_ENST00000369707.2_Silent_p.D182D	NM_183239.1	NP_899062.1	Q9H4Y5	GSTO2_HUMAN	glutathione S-transferase omega 2	210	GST C-terminal.				cellular response to arsenic-containing substance (GO:0071243)|glutathione derivative biosynthetic process (GO:1901687)|L-ascorbic acid metabolic process (GO:0019852)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione dehydrogenase (ascorbate) activity (GO:0045174)|glutathione transferase activity (GO:0004364)|methylarsonate reductase activity (GO:0050610)|oxidoreductase activity (GO:0016491)			NS(1)|breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	11		Colorectal(252;0.178)		Epithelial(162;1.14e-09)|all cancers(201;3.89e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0155)	Glutathione(DB00143)	TGAAGTGGGACCCCACAGTCT	0.522													C|||	247	0.0493211	0.1823	0.0086	5008	,	,		16782	0.0		0.0	False		,,,				2504	0.0				p.D210D		Atlas-SNP	.											.	GSTO2	23	.	0			c.C630T						PASS	.	C	,,,	643,3763	276.0+/-272.9	61,521,1621	104.0	100.0	101.0		528,546,444,630	4.1	1.0	10	dbSNP_79	101	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GSTO2	NM_001191013.1,NM_001191014.1,NM_001191015.1,NM_183239.1	,,,	61,523,5919	TT,TC,CC		0.0233,14.5937,4.9592	,,,	176/210,182/216,148/182,210/244	106058940	645,12361	2203	4300	6503	SO:0001819	synonymous_variant	119391	exon7			GTGGGACCCCACA	AY191318	CCDS7556.1, CCDS53574.1, CCDS53575.1	10q25.1	2012-06-21			ENSG00000065621	ENSG00000065621	2.5.1.18, 1.8.5.1, 1.20.4.2	"""Glutathione S-transferases / Soluble"""	23064	protein-coding gene	gene with protein product		612314				12618591	Standard	NM_001191013		Approved		uc001kyb.3	Q9H4Y5	OTTHUMG00000019006	ENST00000338595.2:c.630C>T	10.37:g.106058940C>T		126.0	0.0	0		130.0	61.0	0.469231	NM_183239	A8K771|B4DJW6|E7ESD6|Q49TW5|Q5GM70|Q5JU15|Q86WP3	Silent	SNP	ENST00000338595.2	37	CCDS7556.1	76	0.0347985347985348	71	0.1443089430894309	5	0.013812154696132596	0	0.0	0	0.0	C	13.14	2.149018	0.37923	0.145937	2.33E-4	ENSG00000065621	ENST00000429569	T	0.13901	2.55	5.9	4.06	0.47325	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.24759	N	0.992935	B	0.12630	0.006	B	0.11329	0.006	T	0.36553	-0.9743	8	0.33141	T	0.24	-34.5724	8.1478	0.31121	0.0:0.8242:0.0:0.1758	rs157078;rs545826;rs157078	113	B4DML4	.	S	113	ENSP00000407381:P113S	ENSP00000407381:P113S	P	+	1	0	GSTO2	106048930	1.000000	0.71417	1.000000	0.80357	0.528000	0.34623	0.617000	0.24359	1.501000	0.48654	0.563000	0.77884	CCC	C|0.952;T|0.048	0.048	strong		0.522	GSTO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050210.2	NM_183239	
PRR21	643905	hgsc.bcm.edu	37	2	240982200	240982200	+	Missense_Mutation	SNP	C	C	T	rs114958540	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:240982200C>T	ENST00000408934.1	-	1	199	c.200G>A	c.(199-201)tGt>tAt	p.C67Y		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	67	Pro-rich.									NS(1)|breast(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(5)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	29						GGTGAAGGGACATGGGTGAAG	0.607													N|||	410	0.081869	0.0651	0.0605	5008	,	,		14426	0.1677		0.0666	False		,,,				2504	0.047				p.C67Y		Atlas-SNP	.											PRR21,NS,carcinoma,+1,2	PRR21	53	2	0			c.G200A						scavenged	.						136.0	123.0	127.0					2																	240982200		2202	4300	6502	SO:0001583	missense	643905	exon1			AAGGGACATGGGT	AF453950	CCDS33417.1	2q37.3	2009-04-20			ENSG00000221961	ENSG00000221961			33866	protein-coding gene	gene with protein product							Standard	NM_001080835		Approved		uc010zod.2	Q8WXC7	OTTHUMG00000159174	ENST00000408934.1:c.200G>A	2.37:g.240982200C>T	ENSP00000386166:p.Cys67Tyr	147.0	2.0	0.0136054		170.0	10.0	0.0588235	NM_001080835		Missense_Mutation	SNP	ENST00000408934.1	37	CCDS33417.1	.	.	.	.	.	.	.	.	.	.	N	2.358	-0.347289	0.05208	.	.	ENSG00000221961	ENST00000408934;ENST00000486799	T;T	0.13420	2.59;2.59	1.46	-2.3	0.06785	.	.	.	.	.	T	0.05731	0.0150	N	0.08118	0	0.09310	N	1	B	0.21071	0.051	B	0.15870	0.014	T	0.43637	-0.9379	9	0.19590	T	0.45	.	8.228	0.31582	0.0:0.7349:0.0:0.2651	.	67	Q8WXC7	PRR21_HUMAN	Y	67	ENSP00000386166:C67Y;ENSP00000418240:C67Y	ENSP00000386166:C67Y	C	-	2	0	PRR21	240630873	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.852000	0.04308	-0.717000	0.04955	-1.756000	0.00673	TGT	C|0.980;T|0.019	0.019	strong		0.607	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
CYP4F12	66002	hgsc.bcm.edu	37	19	15794470	15794470	+	Missense_Mutation	SNP	G	G	A	rs150943202	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15794470G>A	ENST00000550308.1	+	7	1195	c.815G>A	c.(814-816)cGg>cAg	p.R272Q	CYP4F12_ENST00000324632.10_Missense_Mutation_p.R272Q	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	272					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	GCTGTCATCCGGGAGCGGCGT	0.542													.|||	73	0.0145767	0.0522	0.0043	5008	,	,		20675	0.0		0.001	False		,,,				2504	0.0				p.R272Q		Atlas-SNP	.											CYP4F12,NS,haematopoietic_neoplasm,+1,1	CYP4F12	89	1	0			c.G815A						PASS	.	G	GLN/ARG	240,4156		0,240,1958	93.0	94.0	94.0		815	0.3	1.0	19	dbSNP_134	94	2,8594		0,2,4296	yes	missense	CYP4F12	NM_023944.3	43	0,242,6254	AA,AG,GG		0.0233,5.4595,1.8627	benign	272/525	15794470	242,12750	2198	4298	6496	SO:0001583	missense	66002	exon7			TCATCCGGGAGCG	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.815G>A	19.37:g.15794470G>A	ENSP00000448998:p.Arg272Gln	101.0	0.0	0		155.0	36.0	0.232258	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	25	0.011446886446886446	24	0.04878048780487805	1	0.0027624309392265192	0	0.0	0	0.0	.	0.017	-1.504706	0.00992	0.054595	2.33E-4	ENSG00000186204	ENST00000550308;ENST00000324632	T;T	0.67523	-0.27;-0.27	2.46	0.278	0.15673	.	0.278314	0.28877	N	0.013843	T	0.05456	0.0144	N	0.02751	-0.505	0.24533	N	0.994106	B	0.02656	0.0	B	0.04013	0.001	T	0.14531	-1.0469	10	0.02654	T	1	.	5.8094	0.18457	0.7285:0.0:0.2715:0.0	.	272	Q9HCS2	CP4FC_HUMAN	Q	272	ENSP00000448998:R272Q;ENSP00000321821:R272Q	ENSP00000321821:R272Q	R	+	2	0	CYP4F12	15655470	1.000000	0.71417	0.993000	0.49108	0.356000	0.29392	1.185000	0.32065	-0.008000	0.14320	-0.475000	0.04921	CGG	G|0.989;A|0.011	0.011	strong		0.542	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
ENTPD5	957	hgsc.bcm.edu	37	14	74454675	74454675	+	Missense_Mutation	SNP	C	C	G	rs60372237	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:74454675C>G	ENST00000334696.6	-	4	450	c.131G>C	c.(130-132)aGc>aCc	p.S44T	ENTPD5_ENST00000556242.1_Missense_Mutation_p.S44T|ENTPD5_ENST00000557325.1_Missense_Mutation_p.S44T|ENTPD5_ENST00000554664.1_5'Flank	NM_001249.2	NP_001240.1	O75356	ENTP5_HUMAN	ectonucleoside triphosphate diphosphohydrolase 5	44					'de novo' posttranslational protein folding (GO:0051084)|ATP metabolic process (GO:0046034)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|positive regulation of glycolytic process (GO:0045821)|protein N-linked glycosylation (GO:0006487)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	guanosine-diphosphatase activity (GO:0004382)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	10				BRCA - Breast invasive adenocarcinoma(234;0.00394)		GGTGCTGGCGCTGACATTGAT	0.493													C|||	17	0.00339457	0.0129	0.0	5008	,	,		18640	0.0		0.0	False		,,,				2504	0.0				p.S44T		Atlas-SNP	.											.	ENTPD5	26	.	0			c.G131C						PASS	.	C	THR/SER	21,4385	28.1+/-56.4	0,21,2182	115.0	100.0	105.0		131	5.2	1.0	14	dbSNP_129	105	0,8600		0,0,4300	yes	missense	ENTPD5	NM_001249.2	58	0,21,6482	GG,GC,CC		0.0,0.4766,0.1615	benign	44/429	74454675	21,12985	2203	4300	6503	SO:0001583	missense	957	exon4			CTGGCGCTGACAT	AF039918	CCDS9825.1	14q24	2003-10-03	2003-10-03			ENSG00000187097			3367	protein-coding gene	gene with protein product		603162	"""proto-oncogene CPH"""	CD39L4, PCPH		9271669, 9676430	Standard	NM_001249		Approved	NTPDase-5	uc010tuo.2	O75356		ENST00000334696.6:c.131G>C	14.37:g.74454675C>G	ENSP00000335246:p.Ser44Thr	104.0	0.0	0		95.0	47.0	0.494737	NM_001249	A1L4C5|Q96RX0	Missense_Mutation	SNP	ENST00000334696.6	37	CCDS9825.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	13.72	2.320324	0.41096	0.004766	0.0	ENSG00000187097	ENST00000557325;ENST00000334696;ENST00000553284;ENST00000556242	T;T;T	0.30714	2.26;2.52;1.52	5.2	5.2	0.72013	.	0.672949	0.15537	N	0.257193	T	0.09291	0.0229	N	0.19112	0.55	0.24994	N	0.991512	B;B	0.22146	0.065;0.053	B;B	0.18561	0.022;0.013	T	0.11446	-1.0587	10	0.13470	T	0.59	-12.6302	10.8164	0.46578	0.0:0.9069:0.0:0.0931	rs60372237	44;44	O75356;G3V4I0	ENTP5_HUMAN;.	T	44	ENSP00000451810:S44T;ENSP00000335246:S44T;ENSP00000451591:S44T	ENSP00000335246:S44T	S	-	2	0	ENTPD5	73524428	0.858000	0.29795	1.000000	0.80357	0.972000	0.66771	1.528000	0.35985	2.708000	0.92522	0.551000	0.68910	AGC	C|0.997;G|0.003	0.003	strong		0.493	ENTPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412637.1	NM_001249	
DLG1	1739	hgsc.bcm.edu	37	3	196842831	196842831	+	Silent	SNP	A	A	G	rs79212676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:196842831A>G	ENST00000419354.1	-	14	1795	c.1509T>C	c.(1507-1509)agT>agC	p.S503S	DLG1_ENST00000357674.4_Silent_p.S470S|DLG1_ENST00000443183.1_Silent_p.S387S|DLG1_ENST00000346964.2_Silent_p.S503S|DLG1_ENST00000452595.1_Silent_p.S387S|DLG1_ENST00000314062.3_Silent_p.S452S|DLG1_ENST00000450955.1_Silent_p.S470S|DLG1_ENST00000392382.2_Silent_p.S470S|DLG1_ENST00000422288.1_Silent_p.S452S|DLG1_ENST00000448528.2_Silent_p.S503S			Q12959	DLG1_HUMAN	discs, large homolog 1 (Drosophila)	503	PDZ 3. {ECO:0000255|PROSITE- ProRule:PRU00143}.				actin filament organization (GO:0007015)|activation of protein kinase activity (GO:0032147)|amyloid precursor protein metabolic process (GO:0042982)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|cortical actin cytoskeleton organization (GO:0030866)|dephosphorylation (GO:0016311)|embryonic skeletal system morphogenesis (GO:0048704)|endothelial cell proliferation (GO:0001935)|establishment or maintenance of cell polarity (GO:0007163)|hard palate development (GO:0060022)|immunological synapse formation (GO:0001771)|lens development in camera-type eye (GO:0002088)|membrane raft organization (GO:0031579)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell proliferation (GO:0042130)|nucleotide phosphorylation (GO:0046939)|peristalsis (GO:0030432)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell proliferation (GO:0008284)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of potassium ion transport (GO:0043268)|protein localization to plasma membrane (GO:0072659)|regulation of membrane potential (GO:0042391)|regulation of myelination (GO:0031641)|regulation of sodium ion transmembrane transport (GO:1902305)|reproductive structure development (GO:0048608)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle tissue development (GO:0048745)|synaptic transmission (GO:0007268)|T cell activation (GO:0042110)|T cell cytokine production (GO:0002369)|tight junction assembly (GO:0070830)|viral process (GO:0016032)	basal lamina (GO:0005605)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell projection membrane (GO:0031253)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|immunological synapse (GO:0001772)|intercalated disc (GO:0014704)|lateral loop (GO:0043219)|lateral plasma membrane (GO:0016328)|membrane raft (GO:0045121)|microtubule (GO:0005874)|MPP7-DLG1-LIN7 complex (GO:0097025)|myelin sheath abaxonal region (GO:0035748)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|tight junction (GO:0005923)	cytoskeletal protein binding (GO:0008092)|guanylate kinase activity (GO:0004385)|ion channel binding (GO:0044325)|L27 domain binding (GO:0097016)|mitogen-activated protein kinase kinase binding (GO:0031434)|phosphatase binding (GO:0019902)|phosphoprotein phosphatase activity (GO:0004721)|potassium channel regulator activity (GO:0015459)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|liver(1)|lung(9)|ovary(3)|prostate(1)|skin(1)|urinary_tract(1)	26	all_cancers(143;6.22e-10)|Ovarian(172;0.0418)|Breast(254;0.0589)	Lung NSC(153;0.133)	Epithelial(36;3.23e-24)|all cancers(36;2.15e-22)|OV - Ovarian serous cystadenocarcinoma(49;3.88e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.0148)		TGAGCTCTCCACTTAGATCAG	0.408													A|||	40	0.00798722	0.0265	0.0072	5008	,	,		16788	0.0		0.0	False		,,,				2504	0.0				p.S503S		Atlas-SNP	.											.	DLG1	120	.	0			c.T1509C						PASS	.	A	,,,,	118,4288	88.7+/-127.4	1,116,2086	119.0	114.0	116.0		1509,1410,1161,1161,1509	3.2	1.0	3	dbSNP_131	116	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DLG1	NM_001098424.1,NM_001204386.1,NM_001204387.1,NM_001204388.1,NM_004087.2	,,,,	1,116,6386	GG,GA,AA		0.0,2.6782,0.9073	,,,,	503/905,470/893,387/801,387/789,503/927	196842831	118,12888	2203	4300	6503	SO:0001819	synonymous_variant	1739	exon14			CTCTCCACTTAGA	U13897	CCDS3327.1, CCDS43194.1, CCDS56300.1, CCDS56301.1, CCDS75072.1	3q29	2008-12-15	2001-11-28		ENSG00000075711	ENSG00000075711			2900	protein-coding gene	gene with protein product	"""discs large homolog 1"", ""presynaptic protein SAP97"", ""synapse-associated protein 97"""	601014	"""discs, large (Drosophila) homolog 1"""			7937897, 8825652	Standard	NM_004087		Approved	SAP97, SAP-97, hdlg, DLGH1, dJ1061C18.1.1	uc003fxn.4	Q12959	OTTHUMG00000047972	ENST00000419354.1:c.1509T>C	3.37:g.196842831A>G		170.0	0.0	0		195.0	88.0	0.451282	NM_001098424	A5YKK7|B4DGU1|B4DGZ8|B7ZMM0|B9EIQ5|D3DXB8|D3DXB9|E7EWL7|E9PG21|Q12958	Silent	SNP	ENST00000419354.1	37	CCDS43194.1																																																																																			A|0.990;G|0.010	0.010	strong		0.408	DLG1-008	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000258170.2	NM_004087	
C1orf95	375057	hgsc.bcm.edu	37	1	226785102	226785102	+	Intron	SNP	A	A	G	rs73098850	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:226785102A>G	ENST00000366788.3	+	2	487				C1orf95_ENST00000366789.4_Intron	NM_001003665.3	NP_001003665.1	Q69YW2	STUM_HUMAN	chromosome 1 open reading frame 95							integral component of membrane (GO:0016021)				large_intestine(1)|lung(4)|ovary(3)	8	Breast(184;0.133)	Prostate(94;0.0885)		GBM - Glioblastoma multiforme(131;0.113)		CGTTCCCTGTATTTTCCCACG	0.468													A|||	272	0.0543131	0.1914	0.0245	5008	,	,		21325	0.0		0.001	False		,,,				2504	0.001				.		Atlas-SNP	.											.	C1orf95	16	.	0			c.383-2A>G						PASS	.	A		248,1136		22,204,466	354.0	286.0	306.0			-2.8	0.0	1	dbSNP_130	306	0,3182		0,0,1591	yes	intron	C1orf95	NM_001003665.3		22,204,2057	GG,GA,AA		0.0,17.9191,5.4314			226785102	248,4318	692	1591	2283	SO:0001627	intron_variant	375057	exon3			CCCTGTATTTTCC	AF035308	CCDS31044.1	1q42.12	2012-06-26			ENSG00000203685	ENSG00000203685			30491	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_001003665		Approved	DKFZp761P211	uc021pjw.1	Q69YW2	OTTHUMG00000037583	ENST00000366788.3:c.382+420A>G	1.37:g.226785102A>G		171.0	0.0	0		205.0	101.0	0.492683	NM_001003665	A6NGL2	Splice_Site	SNP	ENST00000366788.3	37	CCDS31044.1																																																																																			A|0.961;G|0.039	0.039	strong		0.468	C1orf95-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091634.1	NM_001003665	
AGPAT1	10554	hgsc.bcm.edu	37	6	32139186	32139186	+	Missense_Mutation	SNP	G	G	A	rs11964847	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32139186G>A	ENST00000395499.1	-	2	667	c.88C>T	c.(88-90)Ccc>Tcc	p.P30S	AGPAT1_ENST00000490711.1_5'UTR|AGPAT1_ENST00000336984.6_Missense_Mutation_p.P30S|AGPAT1_ENST00000375107.3_Missense_Mutation_p.P30S|AGPAT1_ENST00000395496.1_Missense_Mutation_p.P30S|PPT2-EGFL8_ENST00000422437.1_3'UTR|AGPAT1_ENST00000375104.2_Missense_Mutation_p.P30S|AGPAT1_ENST00000412465.2_5'UTR|AGPAT1_ENST00000395497.1_Missense_Mutation_p.P30S			Q99943	PLCA_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 1	30			P -> S (in dbSNP:rs11964847).		CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of cellular metabolic process (GO:0031325)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			central_nervous_system(1)|large_intestine(3)|lung(6)|ovary(2)	12						TTGGCACTGGGGCTGCAGAAC	0.597													G|||	14	0.00279553	0.0098	0.0014	5008	,	,		19885	0.0		0.0	False		,,,				2504	0.0				p.P30S		Atlas-SNP	.											AGPAT1,NS,carcinoma,+1,1	AGPAT1	22	1	0			c.C88T						PASS	.	G	SER/PRO,SER/PRO	15,3007		0,15,1496	90.0	69.0	76.0		88,88	2.0	1.0	6	dbSNP_120	76	0,5418		0,0,2709	yes	missense,missense	AGPAT1	NM_006411.3,NM_032741.4	74,74	0,15,4205	AA,AG,GG		0.0,0.4964,0.1777	benign,benign	30/284,30/284	32139186	15,8425	1511	2709	4220	SO:0001583	missense	10554	exon2			CACTGGGGCTGCA	U56417	CCDS4744.1	6p21.3	2013-02-05	2013-02-05		ENSG00000204310	ENSG00000204310	2.3.1.51	"""1-acylglycerol-3-phosphate O-acyltransferases"""	324	protein-coding gene	gene with protein product	"""lysophosphatidic acid acyltransferase, alpha"""	603099	"""1-acylglycerol-3-phosphate O-acyltransferase 1 (lysophosphatidic acid acyltransferase, alpha)"""			9461603, 9291118	Standard	NM_032741		Approved	LPAAT-alpha	uc003oae.3	Q99943	OTTHUMG00000031210	ENST00000395499.1:c.88C>T	6.37:g.32139186G>A	ENSP00000378877:p.Pro30Ser	136.0	0.0	0		133.0	65.0	0.488722	NM_006411	A2BFI5|Q5BL03	Missense_Mutation	SNP	ENST00000395499.1	37	CCDS4744.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	4.129	0.022157	0.08006	0.004964	0.0	ENSG00000204310	ENST00000395496;ENST00000375107;ENST00000395499;ENST00000375104;ENST00000395497;ENST00000336984	T;T;T;T;T;T	0.44482	0.92;0.92;0.92;0.92;0.92;0.92	5.11	1.98	0.26296	.	0.468866	0.25546	N	0.029922	T	0.04092	0.0114	N	0.01705	-0.755	0.80722	D	1	B	0.02656	0.0	B	0.04013	0.001	T	0.30001	-0.9993	10	0.09590	T	0.72	-13.782	2.9511	0.05862	0.1065:0.3516:0.3918:0.1502	rs11964847;rs11964847	30	Q99943	PLCA_HUMAN	S	30	ENSP00000378874:P30S;ENSP00000364248:P30S;ENSP00000378877:P30S;ENSP00000364245:P30S;ENSP00000378875:P30S;ENSP00000337463:P30S	ENSP00000337463:P30S	P	-	1	0	AGPAT1	32247164	0.970000	0.33590	1.000000	0.80357	0.998000	0.95712	0.297000	0.19101	1.132000	0.42129	0.561000	0.74099	CCC	G|0.995;A|0.005	0.005	strong		0.597	AGPAT1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268941.1	NM_006411	
VPS13A	23230	hgsc.bcm.edu	37	9	79929004	79929004	+	Missense_Mutation	SNP	C	C	T	rs140993797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:79929004C>T	ENST00000360280.3	+	36	4471	c.4211C>T	c.(4210-4212)aCc>aTc	p.T1404I	VPS13A_ENST00000376636.3_Missense_Mutation_p.T1365I|VPS13A_ENST00000376634.4_Missense_Mutation_p.T1404I|VPS13A_ENST00000357409.5_Missense_Mutation_p.T1404I|VPS13A_ENST00000423463.2_3'UTR	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	1404					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						GATGATCTCACCATGGTGCTG	0.388																																					p.T1404I		Atlas-SNP	.											.	VPS13A	735	.	0			c.C4211T						PASS	.	C	ILE/THR,ILE/THR,ILE/THR,ILE/THR	3,4403	6.2+/-15.9	0,3,2200	115.0	86.0	96.0		4094,4211,4211,4211	4.5	1.0	9	dbSNP_134	96	0,8600		0,0,4300	yes	missense,missense,missense,missense	VPS13A	NM_001018037.1,NM_001018038.2,NM_015186.3,NM_033305.2	89,89,89,89	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	benign,benign,benign,benign	1365/3136,1404/3070,1404/3096,1404/3175	79929004	3,13003	2203	4300	6503	SO:0001583	missense	23230	exon36			ATCTCACCATGGT	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"""chorein"""	605978	"""chorea acanthocytosis"", ""vacuolar protein sorting 13A (yeast)"""	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.4211C>T	9.37:g.79929004C>T	ENSP00000353422:p.Thr1404Ile	77.0	0.0	0		94.0	62.0	0.659574	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	37	CCDS6655.1	.	.	.	.	.	.	.	.	.	.	C	15.27	2.782618	0.49891	6.81E-4	0.0	ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409	T;T;T;T	0.47528	1.02;0.84;0.93;1.02	5.44	4.53	0.55603	.	0.285219	0.33290	N	0.005074	T	0.38799	0.1054	L	0.29908	0.895	0.80722	D	1	B;B;B;B	0.22414	0.002;0.019;0.069;0.033	B;B;B;B	0.27715	0.008;0.027;0.082;0.06	T	0.17930	-1.0353	10	0.37606	T	0.19	.	14.5567	0.68106	0.0:0.9276:0.0:0.0724	.	1365;1404;1404;1404	Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4	.;VP13A_HUMAN;.;.	I	1404;1365;1404;1404	ENSP00000365821:T1404I;ENSP00000365823:T1365I;ENSP00000353422:T1404I;ENSP00000349985:T1404I	ENSP00000349985:T1404I	T	+	2	0	VPS13A	79118824	0.999000	0.42202	1.000000	0.80357	0.995000	0.86356	2.410000	0.44592	1.399000	0.46721	0.650000	0.86243	ACC	C|1.000;T|0.000	0.000	strong		0.388	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	
XDH	7498	hgsc.bcm.edu	37	2	31598339	31598339	+	Silent	SNP	G	G	C	rs45612839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:31598339G>C	ENST00000379416.3	-	15	1557	c.1509C>G	c.(1507-1509)ggC>ggG	p.G503G		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	503					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	AGTCCACCATGCCACCAGGGG	0.602													G|||	314	0.0626997	0.2277	0.0159	5008	,	,		17654	0.0		0.002	False		,,,				2504	0.0				p.G503G	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											.	XDH	191	.	0			c.C1509G						PASS	.	G		857,3549	338.1+/-305.1	72,713,1418	86.0	80.0	82.0		1509	2.4	1.0	2	dbSNP_127	82	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	XDH	NM_000379.3		72,720,5711	CC,CG,GG		0.0814,19.4507,6.6431		503/1334	31598339	864,12142	2203	4300	6503	SO:0001819	synonymous_variant	7498	exon15			CACCATGCCACCA	D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"""xanthene dehydrogenase"""			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.1509C>G	2.37:g.31598339G>C		130.0	0.0	0		118.0	55.0	0.466102	NM_000379	Q16681|Q16712|Q4PJ16	Silent	SNP	ENST00000379416.3	37	CCDS1775.1																																																																																			G|0.936;C|0.064	0.064	strong		0.602	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379	
PTGFRN	5738	hgsc.bcm.edu	37	1	117527444	117527444	+	Silent	SNP	C	C	T	rs17036676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:117527444C>T	ENST00000393203.2	+	8	2457	c.2310C>T	c.(2308-2310)cgC>cgT	p.R770R		NM_020440.2	NP_065173.2	Q9P2B2	FPRP_HUMAN	prostaglandin F2 receptor inhibitor	770	Ig-like C2-type 6.				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)		GCCTGGAGCGCGTGAGTGTGC	0.587													C|||	23	0.00459265	0.0166	0.0014	5008	,	,		21854	0.0		0.0	False		,,,				2504	0.0				p.R770R		Atlas-SNP	.											PTGFRN,NS,chondrosarcoma,+1,1	PTGFRN	91	1	0			c.C2310T						PASS	.	C		60,4346	56.2+/-92.4	1,58,2144	219.0	170.0	187.0		2310	-11.2	0.0	1	dbSNP_123	187	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	PTGFRN	NM_020440.2		1,60,6442	TT,TC,CC		0.0233,1.3618,0.4767		770/880	117527444	62,12944	2203	4300	6503	SO:0001819	synonymous_variant	5738	exon8			GGAGCGCGTGAGT	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.2310C>T	1.37:g.117527444C>T		149.0	0.0	0		193.0	94.0	0.487047	NM_020440	Q5VVU9|Q8N2K6	Silent	SNP	ENST00000393203.2	37	CCDS890.1																																																																																			C|0.994;T|0.006	0.006	strong		0.587	PTGFRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033271.1	NM_020440	
TCOF1	6949	hgsc.bcm.edu	37	5	149755845	149755845	+	Silent	SNP	A	A	G	rs34796297	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149755845A>G	ENST00000504761.2	+	13	2094	c.2094A>G	c.(2092-2094)gaA>gaG	p.E698E	TCOF1_ENST00000323668.7_Silent_p.E621E|TCOF1_ENST00000439160.2_Silent_p.E698E|TCOF1_ENST00000513346.1_Silent_p.E698E|TCOF1_ENST00000445265.2_Silent_p.E621E|TCOF1_ENST00000451292.1_Silent_p.E698E|TCOF1_ENST00000377797.3_Silent_p.E698E|TCOF1_ENST00000394269.3_Silent_p.E698E			Q13428	TCOF_HUMAN	Treacher Collins-Franceschetti syndrome 1	698					skeletal system development (GO:0001501)|transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:0042790)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|transporter activity (GO:0005215)			NS(1)|breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	35		all_hematologic(541;0.224)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GCAGTGAGGAATCAGATAGTG	0.602													A|||	111	0.0221645	0.0787	0.0086	5008	,	,		18022	0.0		0.001	False		,,,				2504	0.0				p.E698E		Atlas-SNP	.											.	TCOF1	154	.	0			c.A2094G						PASS	.	A	,,,,,	268,4128		13,242,1943	119.0	142.0	134.0		1863,2094,2094,2094,1863,2094	1.1	0.3	5	dbSNP_126	134	0,8590		0,0,4295	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TCOF1	NM_000356.3,NM_001008657.2,NM_001135243.1,NM_001135244.1,NM_001135245.1,NM_001195141.1	,,,,,	13,242,6238	GG,GA,AA		0.0,6.0965,2.0638	,,,,,	621/1412,698/959,698/1489,698/1452,621/1413,698/1451	149755845	268,12718	2198	4295	6493	SO:0001819	synonymous_variant	6949	exon13			TGAGGAATCAGAT		CCDS4306.1, CCDS47305.1, CCDS47306.1, CCDS47307.1, CCDS54936.1	5q32	2014-06-18			ENSG00000070814	ENSG00000070814			11654	protein-coding gene	gene with protein product		606847				1765376	Standard	NM_001008657		Approved	treacle, TCS	uc003lry.3	Q13428	OTTHUMG00000130081	ENST00000504761.2:c.2094A>G	5.37:g.149755845A>G		42.0	0.0	0		54.0	23.0	0.425926	NM_001135243	A0JLU0|B4E111|Q6SC72|Q7Z5W9|Q96A52|Q99408|Q99860	Silent	SNP	ENST00000504761.2	37	CCDS54936.1																																																																																			A|0.984;G|0.016	0.016	strong		0.602	TCOF1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380552.1	NM_001008656	
LCE3D	84648	hgsc.bcm.edu	37	1	152552311	152552311	+	Silent	SNP	G	G	A	rs149516289	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152552311G>A	ENST00000368787.3	-	2	158	c.102C>T	c.(100-102)tcC>tcT	p.S34S		NM_032563.1	NP_115952.1	Q9BYE3	LCE3D_HUMAN	late cornified envelope 3D	34					keratinization (GO:0031424)					breast(1)|endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)|stomach(2)	15	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)	UCEC - Uterine corpus endometrioid carcinoma (5;0.153)|KIRC - Kidney renal clear cell carcinoma(4;0.0323)|Kidney(5;0.0378)		CACAGCCAGAGGAAGCTGGAG	0.662													G|||	43	0.00858626	0.0325	0.0	5008	,	,		16707	0.0		0.0	False		,,,				2504	0.0				p.S34S		Atlas-SNP	.											.	LCE3D	28	.	0			c.C102T						PASS	.	G		102,4304	81.4+/-119.9	2,98,2103	75.0	83.0	81.0		102	-1.4	0.1	1	dbSNP_134	81	0,8600		0,0,4300	no	coding-synonymous	LCE3D	NM_032563.1		2,98,6403	AA,AG,GG		0.0,2.315,0.7843		34/93	152552311	102,12904	2203	4300	6503	SO:0001819	synonymous_variant	84648	exon2			GCCAGAGGAAGCT	BI670519	CCDS1014.1	1q21	2008-02-05	2004-05-21	2004-10-15	ENSG00000163202	ENSG00000163202		"""Late cornified envelopes"""	16615	protein-coding gene	gene with protein product		612616	"""small proline rich-like (epidermal differentiation complex) 6B"""	SPRL6B, SPRL6A		11698679	Standard	NM_032563		Approved	LEP16	uc001fab.3	Q9BYE3	OTTHUMG00000012384	ENST00000368787.3:c.102C>T	1.37:g.152552311G>A		271.0	0.0	0		263.0	137.0	0.520913	NM_032563	Q3MIL1	Silent	SNP	ENST00000368787.3	37	CCDS1014.1																																																																																			G|0.992;A|0.008	0.008	strong		0.662	LCE3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034504.1	NM_032563	
MSMP	692094	hgsc.bcm.edu	37	9	35754052	35754052	+	Missense_Mutation	SNP	C	C	T	rs189235807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35754052C>T	ENST00000436428.2	-	1	214	c.75G>A	c.(73-75)atG>atA	p.M25I	RP11-112J3.15_ENST00000425499.2_RNA|MSMP_ENST00000414286.1_Intron|RGP1_ENST00000378078.4_3'UTR	NM_001044264.2	NP_001037729.1	Q1L6U9	MSMP_HUMAN	microseminoprotein, prostate associated	25						cytoplasm (GO:0005737)|extracellular space (GO:0005615)				endometrium(2)|kidney(1)|lung(3)|prostate(3)	9						GGAGTAGAGACATCACCAAGC	0.577													C|||	11	0.00219649	0.0076	0.0	5008	,	,		19648	0.0		0.0	False		,,,				2504	0.001				p.M25I		Atlas-SNP	.											.	MSMP	15	.	0			c.G75A						PASS	.	C	ILE/MET	14,4138		0,14,2062	158.0	168.0	165.0		75	-7.9	0.5	9		165	0,8454		0,0,4227	yes	missense	MSMP	NM_001044264.2	10	0,14,6289	TT,TC,CC		0.0,0.3372,0.1111	benign	25/140	35754052	14,12592	2076	4227	6303	SO:0001583	missense	692094	exon1			TAGAGACATCACC	DQ012170	CCDS43797.1	9p13.3	2012-10-02			ENSG00000215183	ENSG00000215183			29663	protein-coding gene	gene with protein product		612191				17338636	Standard	NM_001044264		Approved	PC-3, PSMP	uc003zyb.2	Q1L6U9	OTTHUMG00000019882	ENST00000436428.2:c.75G>A	9.37:g.35754052C>T	ENSP00000419194:p.Met25Ile	161.0	0.0	0		139.0	63.0	0.453237	NM_001044264		Missense_Mutation	SNP	ENST00000436428.2	37	CCDS43797.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	8.661	0.900498	0.17686	0.003372	0.0	ENSG00000215183	ENST00000436428	T	0.40476	1.03	5.92	-7.93	0.01156	.	1.391910	0.05859	N	0.622637	T	0.12050	0.0293	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20907	-1.0261	10	0.08599	T;T	0.76;0.76	.	4.3929	0.11350	0.1292:0.1236:0.4683:0.2788	.	25	Q1L6U9	MSMP_HUMAN	I	25	ENSP00000419194:M25I	ENSP00000419194:M25I;ENSP00000419194:M25I	M	-	3	0	MSMP	35744052	0.000000	0.05858	0.494000	0.27515	0.988000	0.76386	-3.267000	0.00533	-0.951000	0.03654	-0.140000	0.14226	ATG	C|1.000;T|0.000	0.000	strong		0.577	MSMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052384.2	NM_001044264	
KCNAB1	7881	hgsc.bcm.edu	37	3	155838488	155838488	+	Missense_Mutation	SNP	G	G	C	rs67167156	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:155838488G>C	ENST00000490337.1	+	1	152	c.88G>C	c.(88-90)Ggg>Cgg	p.G30R	KCNAB1_ENST00000389636.5_Missense_Mutation_p.G30R	NM_172160.2	NP_751892.1	Q14722	KCAB1_HUMAN	potassium voltage-gated channel, shaker-related subfamily, beta member 1	30					learning or memory (GO:0007611)|potassium ion transport (GO:0006813)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel regulator activity (GO:0015459)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	28			LUSC - Lung squamous cell carcinoma(72;0.0461)|Lung(72;0.0465)			TTCTGTAGCAGGGAAAGACAA	0.547													G|||	90	0.0179712	0.0666	0.0029	5008	,	,		19474	0.0		0.0	False		,,,				2504	0.0				p.G30R		Atlas-SNP	.											.	KCNAB1	176	.	0			c.G88C						PASS	.	G	ARG/GLY	235,4171	139.6+/-175.2	6,223,1974	86.0	94.0	92.0		88	-2.0	0.0	3	dbSNP_130	92	2,8598	1.2+/-3.3	0,2,4298	yes	missense	KCNAB1	NM_172160.2	125	6,225,6272	CC,CG,GG		0.0233,5.3336,1.8222	benign	30/420	155838488	237,12769	2203	4300	6503	SO:0001583	missense	7881	exon1			GTAGCAGGGAAAG	U33428	CCDS3174.1, CCDS3175.1, CCDS33882.1	3q26.1	2006-11-29			ENSG00000169282	ENSG00000169282		"""Potassium channels"", ""Aldo-keto reductases"""	6228	protein-coding gene	gene with protein product		601141				8838324, 7499366	Standard	NM_172160		Approved	AKR6A3, KCNA1B, hKvBeta3, Kvb1.3, hKvb3	uc003far.2	Q14722	OTTHUMG00000158552	ENST00000490337.1:c.88G>C	3.37:g.155838488G>C	ENSP00000419952:p.Gly30Arg	110.0	0.0	0		99.0	61.0	0.616162	NM_172160	A8K9H8|A8KAD4|B3KPZ4|Q13031|Q13302|Q16547|Q6PI60|Q99869	Missense_Mutation	SNP	ENST00000490337.1	37	CCDS3174.1	32	0.014652014652014652	31	0.06300813008130081	1	0.0027624309392265192	0	0.0	0	0.0	G	11.35	1.613207	0.28712	0.053336	2.33E-4	ENSG00000169282	ENST00000490337;ENST00000389636	T;T	0.10960	3.21;2.82	5.47	-1.96	0.07525	.	.	.	.	.	T	0.00608	0.0020	N	0.08118	0	0.09310	N	0.999998	B;B	0.19583	0.037;0.01	B;B	0.15870	0.014;0.014	T	0.37731	-0.9693	9	0.59425	D	0.04	-10.322	11.9133	0.52751	0.8314:0.0:0.1686:0.0	.	30;30	B7Z8E5;Q14722	.;KCAB1_HUMAN	R	30	ENSP00000419952:G30R;ENSP00000374287:G30R	ENSP00000374287:G30R	G	+	1	0	KCNAB1	157321182	0.884000	0.30299	0.000000	0.03702	0.802000	0.45316	0.538000	0.23160	-0.249000	0.09569	0.557000	0.71058	GGG	G|0.981;C|0.019	0.019	strong		0.547	KCNAB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351411.1	NM_003471	
NOTCH1	4851	hgsc.bcm.edu	37	9	139391636	139391636	+	Silent	SNP	G	G	A	rs2229974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139391636G>A	ENST00000277541.6	-	34	6630	c.6555C>T	c.(6553-6555)gaC>gaT	p.D2185D		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	2185					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K2182fs*61(1)|p.S2163_T2283del(1)		breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		AGCCCTTGCCGTCCTGGGACT	0.662			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)			G|||	3481	0.695088	0.6278	0.6542	5008	,	,		16337	0.9494		0.5775	False		,,,				2504	0.6738				p.D2185D		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	.	NOTCH1	1980	.	2	Deletion - Frameshift(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(2)	c.C6555T						PASS	.	G		2777,1589		891,995,297	47.0	54.0	52.0		6555	-0.8	1.0	9	dbSNP_98	52	4726,3816		1319,2088,864	no	coding-synonymous	NOTCH1	NM_017617.3		2210,3083,1161	AA,AG,GG		44.6734,36.3949,41.8733		2185/2556	139391636	7503,5405	2183	4271	6454	SO:0001819	synonymous_variant	4851	exon34			CTTGCCGTCCTGG	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.6555C>T	9.37:g.139391636G>A		121.0	0.0	0		133.0	77.0	0.578947	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			G|0.341;A|0.659	0.659	strong		0.662	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
HECW2	57520	hgsc.bcm.edu	37	2	197087061	197087061	+	Silent	SNP	T	T	C	rs16847486	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:197087061T>C	ENST00000260983.3	-	24	4202	c.4020A>G	c.(4018-4020)ctA>ctG	p.L1340L	HECW2_ENST00000409111.1_Silent_p.L984L	NM_020760.1	NP_065811.1	Q9P2P5	HECW2_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 2	1340	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			biliary_tract(1)|breast(3)|central_nervous_system(4)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(24)|lung(45)|ovary(5)|pancreas(2)|prostate(2)|skin(10)|upper_aerodigestive_tract(2)|urinary_tract(2)	113						TCAGGTCACATAGACTAAGAT	0.388													T|||	140	0.0279553	0.0976	0.0159	5008	,	,		21341	0.0		0.0	False		,,,				2504	0.0				p.L1340L		Atlas-SNP	.											.	HECW2	239	.	0			c.A4020G						PASS	.	T		443,3963	214.8+/-234.0	23,397,1783	120.0	104.0	110.0		4020	-1.3	0.8	2	dbSNP_123	110	10,8590	7.1+/-27.0	0,10,4290	no	coding-synonymous	HECW2	NM_020760.1		23,407,6073	CC,CT,TT		0.1163,10.0545,3.483		1340/1573	197087061	453,12553	2203	4300	6503	SO:0001819	synonymous_variant	57520	exon24			GTCACATAGACTA	AL390186	CCDS33354.1	2q32.3	2004-12-13			ENSG00000138411	ENSG00000138411			29853	protein-coding gene	gene with protein product						10718198, 12890487	Standard	NM_020760		Approved	KIAA1301, NEDL2	uc002utm.1	Q9P2P5	OTTHUMG00000154435	ENST00000260983.3:c.4020A>G	2.37:g.197087061T>C		79.0	0.0	0		93.0	55.0	0.591398	NM_020760	B8ZZB4|Q17RT5|Q68DF8|Q9NPS9	Silent	SNP	ENST00000260983.3	37	CCDS33354.1																																																																																			T|0.965;C|0.035	0.035	strong		0.388	HECW2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335199.3	NM_020760	
RYR1	6261	hgsc.bcm.edu	37	19	38964275	38964275	+	Missense_Mutation	SNP	A	A	G	rs34694816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38964275A>G	ENST00000359596.3	+	28	4024	c.4024A>G	c.(4024-4026)Agc>Ggc	p.S1342G	RYR1_ENST00000355481.4_Missense_Mutation_p.S1342G|RYR1_ENST00000360985.3_Missense_Mutation_p.S1342G			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	1342	6 X approximate repeats.		S -> G (in dbSNP:rs34694816). {ECO:0000269|PubMed:19191329}.		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)			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)	TGGGGGCTGGAGCGAGGCAGA	0.741													G|||	271	0.0541134	0.1936	0.0187	5008	,	,		12448	0.0		0.002	False		,,,				2504	0.0				p.S1342G		Atlas-SNP	.											.	RYR1	708	.	0			c.A4024G						PASS	.	G	GLY/SER,GLY/SER	450,3742		20,410,1666	6.0	8.0	7.0		4024,4024	4.0	1.0	19	dbSNP_126	7	5,8089		0,5,4042	yes	missense,missense	RYR1	NM_000540.2,NM_001042723.1	56,56	20,415,5708	GG,GA,AA		0.0618,10.7347,3.7034	benign,benign	1342/5039,1342/5034	38964275	455,11831	2096	4047	6143	SO:0001583	missense	6261	exon28			GGCTGGAGCGAGG	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.4024A>G	19.37:g.38964275A>G	ENSP00000352608:p.Ser1342Gly	11.0	0.0	0		24.0	10.0	0.416667	NM_001042723	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	37	CCDS33011.1	114	0.0521978021978022	104	0.21138211382113822	9	0.024861878453038673	0	0.0	1	0.0013192612137203166	G	9.860	1.196031	0.22037	0.107347	6.18E-4	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985	D;D;D	0.96745	-4.11;-4.11;-4.11	5.07	4.03	0.46877	.	0.085426	0.46758	N	0.000270	T	0.00440	0.0014	N	0.08118	0	0.51012	P	9.199999999998099E-5	B;B	0.09022	0.0;0.002	B;B	0.04013	0.0;0.001	T	0.47355	-0.9124	9	0.20519	T	0.43	.	8.5434	0.33406	0.1826:0.0:0.8174:0.0	rs34694816	1342;1342	P21817-2;P21817	.;RYR1_HUMAN	G	1342	ENSP00000352608:S1342G;ENSP00000347667:S1342G;ENSP00000354254:S1342G	ENSP00000347667:S1342G	S	+	1	0	RYR1	43656115	1.000000	0.71417	0.983000	0.44433	0.196000	0.23810	4.468000	0.60162	1.142000	0.42291	-0.355000	0.07637	AGC	A|0.949;G|0.051	0.051	strong		0.741	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
MYO18B	84700	hgsc.bcm.edu	37	22	26422993	26422993	+	Silent	SNP	C	C	T	rs7290069	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:26422993C>T	ENST00000407587.2	+	43	7225	c.7056C>T	c.(7054-7056)tgC>tgT	p.C2352C	MYO18B_ENST00000536101.1_Silent_p.C2351C|MYO18B_ENST00000335473.7_Silent_p.C2351C			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2351						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						TCAGTTCCTGCGAGTCCCTCT	0.567													C|||	172	0.034345	0.1256	0.0072	5008	,	,		19058	0.001		0.0	False		,,,				2504	0.0				p.C2351C		Atlas-SNP	.											MYO18B,NS,carcinoma,+2,1	MYO18B	322	1	0			c.C7053T						PASS	.	C		437,3431		26,385,1523	79.0	88.0	85.0		7053	-0.2	1.0	22	dbSNP_116	85	3,8269		0,3,4133	no	coding-synonymous	MYO18B	NM_032608.5		26,388,5656	TT,TC,CC		0.0363,11.2978,3.6244		2351/2568	26422993	440,11700	1934	4136	6070	SO:0001819	synonymous_variant	84700	exon43			TTCCTGCGAGTCC	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.7056C>T	22.37:g.26422993C>T		45.0	0.0	0		41.0	19.0	0.463415	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37		65	0.02976190476190476	63	0.12804878048780488	1	0.0027624309392265192	1	0.0017482517482517483	0	0.0	C	8.758	0.922959	0.18056	0.112978	3.63E-4	ENSG00000133454	ENST00000543971	.	.	.	4.89	-0.211	0.13172	.	.	.	.	.	T	0.00496	0.0016	.	.	.	0.09310	P	0.9999999999999841	.	.	.	.	.	.	T	0.17961	-1.0352	3	.	.	.	.	9.1903	0.37195	0.0:0.5439:0.0:0.4561	rs7290069	.	.	.	V	301	.	.	A	+	2	0	MYO18B	24752993	0.125000	0.22332	0.988000	0.46212	0.824000	0.46624	-1.147000	0.03188	0.125000	0.18397	0.462000	0.41574	GCG	C|0.968;T|0.032	0.032	strong		0.567	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
S100A2	6273	hgsc.bcm.edu	37	1	153534027	153534027	+	Missense_Mutation	SNP	C	C	T	rs1047325	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:153534027C>T	ENST00000368708.3	-	3	554	c.182G>A	c.(181-183)aGc>aAc	p.S61N	S100A2_ENST00000368707.4_3'UTR|S100A2_ENST00000368710.1_Missense_Mutation_p.S61N|S100A2_ENST00000497140.1_Missense_Mutation_p.S28N|S100A2_ENST00000368709.1_Missense_Mutation_p.S61N|S100A2_ENST00000487430.2_Missense_Mutation_p.S61N	NM_005978.3	NP_005969.1	P29034	S10A2_HUMAN	S100 calcium binding protein A2	62	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				endothelial cell migration (GO:0043542)		calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)			endometrium(1)|large_intestine(2)|lung(1)|ovary(1)	5	all_lung(78;5.98e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)		Olopatadine(DB00768)	CTCATCCAGGCTGCCCATCAG	0.537													T|||	757	0.151158	0.4463	0.0821	5008	,	,		21128	0.0109		0.0527	False		,,,				2504	0.047				p.S61N		Atlas-SNP	.											.	S100A2	14	.	0			c.G182A						PASS	.	T	ASN/SER	1775,2631	643.4+/-397.8	363,1049,791	235.0	219.0	224.0		182	-4.6	0.0	1	dbSNP_86	224	441,8159	799.7+/-407.4	15,411,3874	yes	missense	S100A2	NM_005978.3	46	378,1460,4665	TT,TC,CC		5.1279,40.286,17.0383	benign	61/98	153534027	2216,10790	2203	4300	6503	SO:0001583	missense	6273	exon3			TCCAGGCTGCCCA	BC002829	CCDS1044.1	1q21	2013-01-10	2001-11-28		ENSG00000196754	ENSG00000196754		"""S100 calcium binding proteins"", ""EF-hand domain containing"""	10492	protein-coding gene	gene with protein product		176993	"""S100 calcium-binding protein A2"""	S100L		8341667	Standard	NM_005978		Approved	CAN19	uc001fcb.3	P29034	OTTHUMG00000035031	ENST00000368708.3:c.182G>A	1.37:g.153534027C>T	ENSP00000357697:p.Ser61Asn	253.0	0.0	0		250.0	248.0	0.992	NM_005978	O00266|Q3KRB9|Q5RHS8|Q9BU83	Missense_Mutation	SNP	ENST00000368708.3	37	CCDS1044.1	274	0.12545787545787546	208	0.42276422764227645	30	0.08287292817679558	4	0.006993006993006993	32	0.04221635883905013	T	5.767	0.325859	0.10900	0.40286	0.051279	ENSG00000196754	ENST00000368708;ENST00000368710;ENST00000368709;ENST00000368707	T;T;T	0.14266	2.52;2.52;2.52	4.77	-4.58	0.03410	S100/Calbindin-D9k, conserved site (1);EF-hand-like domain (1);	0.948424	0.08683	N	0.909215	T	0.01940	0.0061	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.43940	-0.9360	8	0.44086	T	0.13	.	1.7661	0.03002	0.1195:0.308:0.2454:0.3271	rs1047325;rs3174843;rs52793522;rs56586255;rs60177723;rs1047325	62	P29034	S10A2_HUMAN	N	61;61;61;102	ENSP00000357697:S61N;ENSP00000357699:S61N;ENSP00000357698:S61N	ENSP00000357696:S102N	S	-	2	0	S100A2	151800651	0.019000	0.18553	0.000000	0.03702	0.286000	0.27126	0.583000	0.23849	-1.416000	0.02019	-0.254000	0.11334	AGC	C|0.841;T|0.159	0.159	strong		0.537	S100A2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084789.1	NM_005978	
PLXNB2	23654	hgsc.bcm.edu	37	22	50716068	50716068	+	Silent	SNP	C	C	T	rs11547732	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50716068C>T	ENST00000449103.1	-	33	5288	c.5148G>A	c.(5146-5148)gcG>gcA	p.A1716A	PLXNB2_ENST00000359337.4_Silent_p.A1716A			O15031	PLXB2_HUMAN	plexin B2	1716					brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		TGAAGGTCTGCGCGATGACTG	0.632													C|||	471	0.0940495	0.3374	0.0303	5008	,	,		16203	0.0		0.004	False		,,,				2504	0.0				p.A1716A		Atlas-SNP	.											.	PLXNB2	172	.	0			c.G5148A						PASS	.	C		1148,3132		141,866,1133	60.0	66.0	64.0		5148	-7.9	0.0	22	dbSNP_120	64	10,8510		0,10,4250	no	coding-synonymous	PLXNB2	NM_012401.3		141,876,5383	TT,TC,CC		0.1174,26.8224,9.0469		1716/1839	50716068	1158,11642	2140	4260	6400	SO:0001819	synonymous_variant	23654	exon33			GGTCTGCGCGATG		CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"""Plexins"""	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.5148G>A	22.37:g.50716068C>T		153.0	0.0	0		188.0	95.0	0.505319	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Silent	SNP	ENST00000449103.1	37	CCDS43035.1	161	0.07371794871794872	147	0.29878048780487804	13	0.03591160220994475	0	0.0	1	0.0013192612137203166	C	0.034	-1.315528	0.01331	0.268224	0.001174	ENSG00000196576	ENST00000399964	.	.	.	3.94	-7.87	0.01183	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.9999999999955255	.	.	.	.	.	.	T	0.48937	-0.8990	4	0.87932	D	0	.	3.99	0.09533	0.1301:0.3253:0.341:0.2036	rs11547732	.	.	.	H	346	.	ENSP00000382845:R346H	R	-	2	0	PLXNB2	49058195	0.000000	0.05858	0.009000	0.14445	0.067000	0.16453	-3.257000	0.00537	-6.532000	0.00003	-2.734000	0.00129	CGC	T|0.048;G|0.000;C|0.952;A|0.000	0.048	strong		0.632	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401	
EPPIN	57119	hgsc.bcm.edu	37	20	44174306	44174306	+	Silent	SNP	G	G	A	rs374858005		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:44174306G>A	ENST00000354280.4	-	2	261	c.195C>T	c.(193-195)tgC>tgT	p.C65C	EPPIN_ENST00000555685.1_Silent_p.C65C|EPPIN_ENST00000409554.1_Silent_p.C65C|EPPIN-WFDC6_ENST00000504988.1_Silent_p.C65C|EPPIN_ENST00000336443.3_Silent_p.C49C	NM_020398.3	NP_065131.1	O95925	EPPI_HUMAN	epididymal peptidase inhibitor	65	WAP. {ECO:0000255|PROSITE- ProRule:PRU00722}.				defense response to bacterium (GO:0042742)|negative regulation of peptidase activity (GO:0010466)	extracellular region (GO:0005576)	serine-type endopeptidase inhibitor activity (GO:0004867)										ATTTTTTTCCGCAGCTGAAGA	0.453													G|||	1	0.000199681	0.0	0.0	5008	,	,		20884	0.0		0.0	False		,,,				2504	0.001				p.C65C		Atlas-SNP	.											.	.	.	.	0			c.C195T						PASS	.	G	,	1,4405	2.1+/-5.4	0,1,2202	320.0	284.0	296.0		195,195	-3.6	0.9	20		296	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	SPINLW1,SPINLW1-WFDC6	NM_001198986.1,NM_020398.3	,	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	,	65/180,65/134	44174306	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	100526773	exon2			TTTTCCGCAGCTG	AF286370	CCDS13359.1	20q13.12	2014-01-21	2012-08-22	2012-08-22	ENSG00000101448	ENSG00000101448		"""WAP four-disulfide core domain containing"""	15932	protein-coding gene	gene with protein product	"""epididymal protease inhibitor"", ""cancer/testis antigen 72"""	609031	"""serine protease inhibitor-like, with Kunitz and WAP domains 1 (eppin)"", ""serine peptidase inhibitor-like, with Kunitz and WAP domains 1 (eppin)"""	SPINLW1		11404006, 12206714	Standard	NM_020398		Approved	EPPIN1, EPPIN2, EPPIN3, dJ461P17.2, WAP7, WFDC7, CT71		O95925	OTTHUMG00000032588	ENST00000354280.4:c.195C>T	20.37:g.44174306G>A		256.0	1.0	0.00390625		278.0	132.0	0.47482	NM_001198986	A6PVD6|Q86TP9|Q96SD7|Q9HD30	Silent	SNP	ENST00000354280.4	37	CCDS13359.1																																																																																			.	.	weak		0.453	EPPIN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079467.4		
AP3D1	8943	hgsc.bcm.edu	37	19	2116616	2116616	+	Silent	SNP	T	T	C	rs73512353	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2116616T>C	ENST00000345016.5	-	17	2220	c.1989A>G	c.(1987-1989)gaA>gaG	p.E663E	AP3D1_ENST00000356926.4_Silent_p.E572E|AP3D1_ENST00000350812.6_Silent_p.E494E|AP3D1_ENST00000355272.6_Silent_p.E663E	NM_003938.6	NP_003929.4	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1 subunit	663					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|endosome to melanosome transport (GO:0035646)|eye pigment biosynthetic process (GO:0006726)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein localization to membrane (GO:0072657)|protein localization to organelle (GO:0033365)|regulation of sequestering of zinc ion (GO:0061088)|synaptic vesicle membrane organization (GO:0048499)	endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane coat (GO:0030117)|terminal bouton (GO:0043195)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(23)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		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)		GAGCCAGCTCTTCCTCGTCCG	0.692													T|||	38	0.00758786	0.0265	0.0043	5008	,	,		15549	0.0		0.0	False		,,,				2504	0.0				p.E663E		Atlas-SNP	.											.	AP3D1	81	.	0			c.A1989G						PASS	.	T	,	64,4056		1,62,1997	15.0	17.0	16.0		1716,1989	2.8	1.0	19	dbSNP_130	16	0,8376		0,0,4188	no	coding-synonymous,coding-synonymous	AP3D1	NM_001077523.1,NM_003938.5	,	1,62,6185	CC,CT,TT		0.0,1.5534,0.5122	,	572/1113,663/1154	2116616	64,12432	2060	4188	6248	SO:0001819	synonymous_variant	8943	exon17			CAGCTCTTCCTCG	U91930	CCDS42459.1, CCDS58638.1	19p13.3	2014-09-04			ENSG00000065000	ENSG00000065000			568	protein-coding gene	gene with protein product		607246				9151686, 9303295	Standard	NM_003938		Approved	ADTD	uc002lva.4	O14617	OTTHUMG00000180354	ENST00000345016.5:c.1989A>G	19.37:g.2116616T>C		67.0	0.0	0		59.0	27.0	0.457627	NM_001261826	O00202|O75262|Q59HF5|Q96G11|Q9H3C6	Silent	SNP	ENST00000345016.5	37	CCDS42459.1																																																																																			T|0.992;C|0.008	0.008	strong		0.692	AP3D1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450912.1		
EEF1D	1936	hgsc.bcm.edu	37	8	144671489	144671489	+	Intron	SNP	G	G	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144671489G>C	ENST00000529272.1	-	2	397				EEF1D_ENST00000395119.3_Intron|EEF1D_ENST00000526838.1_Intron|EEF1D_ENST00000528610.1_Intron|EEF1D_ENST00000524624.1_Intron|EEF1D_ENST00000532400.1_Intron|EEF1D_ENST00000419152.2_Intron|EEF1D_ENST00000532741.1_Missense_Mutation_p.P305A|EEF1D_ENST00000531621.1_Intron|EEF1D_ENST00000423316.2_Missense_Mutation_p.P255A|EEF1D_ENST00000442189.2_Missense_Mutation_p.P255A|EEF1D_ENST00000317198.6_Intron			P29692	EF1D_HUMAN	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)						cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|translation elongation factor activity (GO:0003746)|translation factor activity, nucleic acid binding (GO:0008135)			breast(2)|cervix(1)|endometrium(1)|kidney(4)|lung(2)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Colorectal(110;0.134)|BRCA - Breast invasive adenocarcinoma(115;0.239)			TTCCCTGGGGGATGGCCGTCA	0.697																																					p.P255A		Atlas-SNP	.											.	EEF1D	48	.	0			c.C763G						PASS	.						5.0	7.0	6.0					8																	144671489		2037	4109	6146	SO:0001627	intron_variant	1936	exon3			CTGGGGGATGGCC	AK024550	CCDS6404.1, CCDS6405.1, CCDS47930.1, CCDS56559.1	8q24	2011-09-15			ENSG00000104529	ENSG00000104529			3211	protein-coding gene	gene with protein product		130592				8334168	Standard	NM_001960		Approved	EF-1D, FLJ20897	uc003yyt.3	P29692	OTTHUMG00000165191	ENST00000529272.1:c.4-2470C>G	8.37:g.144671489G>C		59.0	0.0	0		64.0	25.0	0.390625	NM_001130053	B4DDU4|D3DWK3|E9PBQ9|Q4VBZ6|Q969J1|Q96I38	Missense_Mutation	SNP	ENST00000529272.1	37	CCDS6405.1	.	.	.	.	.	.	.	.	.	.	G	14.22	2.470797	0.43942	.	.	ENSG00000104529	ENST00000532741;ENST00000442189;ENST00000423316;ENST00000356793;ENST00000337369;ENST00000526710;ENST00000531281	.	.	.	4.4	4.4	0.53042	.	0.309039	0.29940	N	0.010803	T	0.51312	0.1667	L	0.44542	1.39	0.80722	D	1	P;P;P	0.50528	0.894;0.894;0.936	B;B;P	0.50405	0.437;0.437;0.64	T	0.50381	-0.8835	9	0.45353	T	0.12	.	9.8627	0.41125	0.0939:0.0:0.9061:0.0	.	255;305;255	D3DWK1;E9PRY8;P29692-2	.;.;.	A	305;255;255;207;255;255;255	.	ENSP00000338323:P255A	P	-	1	0	EEF1D	144742632	1.000000	0.71417	0.988000	0.46212	0.875000	0.50365	3.368000	0.52357	2.277000	0.76020	0.561000	0.74099	CCC	.	.	none		0.697	EEF1D-006	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382592.2	NM_032378	
CDC27	996	hgsc.bcm.edu	37	17	45214661	45214661	+	Silent	SNP	G	G	A	rs111322439		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:45214661G>A	ENST00000066544.3	-	14	1863	c.1770C>T	c.(1768-1770)ttC>ttT	p.F590F	CDC27_ENST00000531206.1_Silent_p.F596F|CDC27_ENST00000446365.2_Silent_p.F529F|CDC27_ENST00000527547.1_Silent_p.F589F	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	590					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)			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						TAGCTCTCTGGAAGAATTTAA	0.383																																					p.F596F		Atlas-SNP	.											CDC27_ENST00000531206,rectum,carcinoma,0,4	CDC27	337	4	0			c.C1788T						scavenged	.						58.0	61.0	60.0					17																	45214661		2203	4300	6503	SO:0001819	synonymous_variant	996	exon14			TCTCTGGAAGAAT	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.1770C>T	17.37:g.45214661G>A		27.0	0.0	0		23.0	5.0	0.217391	NM_001114091	G3V1C4|Q16349|Q96F35	Silent	SNP	ENST00000066544.3	37	CCDS11509.1																																																																																			G|0.500;A|0.500	0.500	weak		0.383	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
COL6A3	1293	hgsc.bcm.edu	37	2	238289842	238289842	+	Missense_Mutation	SNP	G	G	A	rs34741387	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:238289842G>A	ENST00000295550.4	-	5	2065	c.1613C>T	c.(1612-1614)aCg>aTg	p.T538M	COL6A3_ENST00000346358.4_Missense_Mutation_p.T538M|COL6A3_ENST00000353578.4_Missense_Mutation_p.T332M|COL6A3_ENST00000347401.3_Missense_Mutation_p.T337M|COL6A3_ENST00000392004.3_Missense_Mutation_p.T332M|COL6A3_ENST00000392003.2_Missense_Mutation_p.T131M|COL6A3_ENST00000472056.1_Missense_Mutation_p.T131M|COL6A3_ENST00000409809.1_Missense_Mutation_p.T332M	NM_004369.3	NP_004360.2	P12111	CO6A3_HUMAN	collagen, type VI, alpha 3	538	Nonhelical region.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.		T -> M (in dbSNP:rs34741387).		axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|response to glucose (GO:0009749)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.T538K(1)|p.T332K(1)		breast(6)|central_nervous_system(7)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(64)|lung(62)|ovary(14)|pancreas(2)|prostate(11)|skin(14)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	217		Breast(86;0.000301)|Renal(207;0.000966)|all_hematologic(139;0.067)|Ovarian(221;0.0694)|all_lung(227;0.0943)|Melanoma(123;0.203)		Epithelial(121;1.23e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.34e-10)|Kidney(56;5.71e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.51e-07)|BRCA - Breast invasive adenocarcinoma(100;0.00025)|Lung(119;0.0142)|LUSC - Lung squamous cell carcinoma(224;0.034)		GGCTGAACTCGTGAATAGGTT	0.552													G|||	44	0.00878594	0.031	0.0043	5008	,	,		18735	0.0		0.0	False		,,,				2504	0.0				p.T538M		Atlas-SNP	.											.	COL6A3	608	.	2	Substitution - Missense(2)	lung(2)	c.C1613T						PASS	.	G	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	115,4291	85.3+/-124.0	1,113,2089	69.0	80.0	76.0		1613,392,995,392,995	3.6	0.5	2	dbSNP_126	76	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense,missense,missense	COL6A3	NM_004369.3,NM_057164.4,NM_057165.4,NM_057166.4,NM_057167.3	81,81,81,81,81	1,114,6388	AA,AG,GG		0.0116,2.6101,0.8919	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	538/3178,131/1037,332/1238,131/2571,332/2972	238289842	116,12890	2203	4300	6503	SO:0001583	missense	1293	exon5			GAACTCGTGAATA	X52022	CCDS33409.1, CCDS33410.1, CCDS33411.1, CCDS33412.1, CCDS33410.2, CCDS33411.2, CCDS54439.1	2q37	2014-09-17			ENSG00000163359	ENSG00000163359		"""Collagens"""	2213	protein-coding gene	gene with protein product		120250				1339440, 11992252	Standard	NM_004369		Approved		uc002vwl.2	P12111	OTTHUMG00000150020	ENST00000295550.4:c.1613C>T	2.37:g.238289842G>A	ENSP00000295550:p.Thr538Met	50.0	0.0	0		58.0	33.0	0.568965	NM_004369	A8MT30|B4E3U5|B7ZMJ7|E9PFQ6|E9PGQ9|Q16501|Q53QF4|Q53QF6	Missense_Mutation	SNP	ENST00000295550.4	37	CCDS33412.1	9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	G	11.65	1.702027	0.30232	0.026101	1.16E-4	ENSG00000163359	ENST00000295550;ENST00000347401;ENST00000353578;ENST00000472056;ENST00000409809;ENST00000346358;ENST00000392004;ENST00000392003;ENST00000433762	D;D;D;D;D;D;D;D;D	0.84070	-1.8;-1.8;-1.8;-1.8;-1.8;-1.8;-1.8;-1.8;-1.8	5.6	3.62	0.41486	von Willebrand factor, type A (3);	0.360229	0.23277	N	0.049959	T	0.80964	0.4725	M	0.87547	2.89	0.24906	N	0.992072	D;D;D;D;D;D	0.89917	0.999;1.0;0.984;0.998;1.0;0.994	D;D;P;D;D;P	0.79784	0.916;0.993;0.87;0.964;0.99;0.88	T	0.77525	-0.2555	10	0.51188	T	0.08	.	12.068	0.53598	0.0695:0.0:0.8014:0.129	rs34741387	538;131;131;332;332;538	E9PCV6;E9PFQ6;A8MT30;E9PGQ9;P12111-2;P12111	.;.;.;.;.;CO6A3_HUMAN	M	538;337;332;131;332;538;332;131;538	ENSP00000295550:T538M;ENSP00000315609:T337M;ENSP00000315873:T332M;ENSP00000418285:T131M;ENSP00000386844:T332M;ENSP00000295546:T538M;ENSP00000375861:T332M;ENSP00000375860:T131M;ENSP00000389539:T538M	ENSP00000295550:T538M	T	-	2	0	COL6A3	237954581	0.193000	0.23313	0.484000	0.27391	0.010000	0.07245	0.549000	0.23329	1.366000	0.46076	0.655000	0.94253	ACG	G|0.991;A|0.009	0.009	strong		0.552	COL6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315790.2	NM_004369	
DHRS11	79154	hgsc.bcm.edu	37	17	34958531	34958531	+	IGR	SNP	C	C	T	rs60978234	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34958531C>T	ENST00000251312.5	+	0	1598				MRM1_ENST00000250156.7_Missense_Mutation_p.P98S|MRM1_ENST00000585770.1_5'UTR	NM_024308.3	NP_077284.2	Q6UWP2	DHR11_HUMAN	dehydrogenase/reductase (SDR family) member 11							extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			endometrium(1)|lung(4)	5						GCGGGACATTCCAGTTCTGCG	0.701													C|||	23	0.00459265	0.0166	0.0	5008	,	,		15249	0.0		0.001	False		,,,				2504	0.0				p.P98S		Atlas-SNP	.											MRM1,NS,haematopoietic_neoplasm,-2,1	MRM1	19	1	0			c.C292T						PASS	.	C	SER/PRO	68,4320		1,66,2127	22.0	26.0	24.0		292	4.9	1.0	17	dbSNP_129	24	0,8576		0,0,4288	yes	missense	MRM1	NM_024864.3	74	1,66,6415	TT,TC,CC		0.0,1.5497,0.5245	probably-damaging	98/354	34958531	68,12896	2194	4288	6482	SO:0001628	intergenic_variant	79922	exon1			GACATTCCAGTTC		CCDS11315.2	17q12	2014-05-06			ENSG00000108272	ENSG00000278535		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	28639	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 24C, member 1"""					12975309, 19027726	Standard	NM_024308		Approved	MGC4172, SDR24C1	uc002hnd.3	Q6UWP2	OTTHUMG00000188442		17.37:g.34958531C>T		21.0	0.0	0		21.0	8.0	0.380952	NM_024864	B2RDZ3|Q9BUC7|Q9H674	Missense_Mutation	SNP	ENST00000251312.5	37	CCDS11315.2	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	14.72	2.620552	0.46736	0.015497	0.0	ENSG00000129282	ENST00000250156	T	0.28666	1.6	4.9	4.9	0.64082	RNA 2-O ribose methyltransferase, substrate binding (2);	0.065831	0.64402	D	0.000006	T	0.21509	0.0518	M	0.69463	2.115	0.80722	D	1	B	0.32968	0.392	B	0.42062	0.374	T	0.07139	-1.0788	10	0.07175	T	0.84	-13.0363	15.1676	0.72840	0.0:1.0:0.0:0.0	rs60978234	98	Q6IN84	MRM1_HUMAN	S	98	ENSP00000250156:P98S	ENSP00000250156:P98S	P	+	1	0	MRM1	32032644	0.845000	0.29573	0.969000	0.41365	0.561000	0.35649	3.772000	0.55325	2.423000	0.82170	0.555000	0.69702	CCA	C|0.993;T|0.007	0.007	strong		0.701	DHRS11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256681.2	NM_024308	
ZSCAN18	65982	hgsc.bcm.edu	37	19	58597611	58597611	+	Missense_Mutation	SNP	G	G	C	rs147947490	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58597611G>C	ENST00000240727.6	-	6	1167	c.768C>G	c.(766-768)gaC>gaG	p.D256E	ZSCAN18_ENST00000600404.1_Missense_Mutation_p.D312E|ZSCAN18_ENST00000601144.1_Missense_Mutation_p.D256E|ZSCAN18_ENST00000421612.2_Missense_Mutation_p.D121E	NM_023926.4	NP_076415.3	Q8TBC5	ZSC18_HUMAN	zinc finger and SCAN domain containing 18	256					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|skin(3)	19		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.114)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		TGGAGGCAGCGTCAGGCTGGG	0.542													G|||	25	0.00499201	0.0174	0.0014	5008	,	,		17998	0.0		0.001	False		,,,				2504	0.0				p.D312E		Atlas-SNP	.											.	ZSCAN18	104	.	0			c.C936G						PASS	.	G	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	74,4332	65.3+/-102.7	1,72,2130	74.0	64.0	67.0		936,768,363,768	-1.3	0.0	19	dbSNP_134	67	2,8598	2.2+/-6.3	0,2,4298	no	missense,missense,missense,missense	ZSCAN18	NM_001145542.1,NM_001145543.1,NM_001145544.1,NM_023926.4	45,45,45,45	1,74,6428	CC,CG,GG		0.0233,1.6795,0.5843	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	312/567,256/511,121/375,256/511	58597611	76,12930	2203	4300	6503	SO:0001583	missense	65982	exon6			GGCAGCGTCAGGC	AY280799, AY279352	CCDS12971.1, CCDS46214.1, CCDS46215.1	19q13.43	2013-01-09	2007-02-20	2007-02-20		ENSG00000121413		"""-"", ""Zinc fingers, C2H2-type"""	21037	protein-coding gene	gene with protein product			"""zinc finger protein 447"""	ZNF447			Standard	NM_001145542		Approved	FLJ12895	uc010yht.1	Q8TBC5		ENST00000240727.6:c.768C>G	19.37:g.58597611G>C	ENSP00000240727:p.Asp256Glu	90.0	0.0	0		106.0	48.0	0.45283	NM_001145542	B4DG23|E9PBI0|Q9BRK7|Q9H9A0	Missense_Mutation	SNP	ENST00000240727.6	37	CCDS12971.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	12.06	1.825940	0.32237	0.016795	2.33E-4	ENSG00000121413	ENST00000433686;ENST00000240727;ENST00000421612	T;T	0.02197	4.64;4.4	3.3	-1.28	0.09318	.	0.195954	0.25233	N	0.032148	T	0.00845	0.0028	N	0.14661	0.345	0.09310	N	1	D;D;D;P	0.56521	0.976;0.976;0.972;0.953	P;P;P;B	0.48270	0.506;0.506;0.572;0.369	T	0.52990	-0.8501	10	0.28530	T	0.3	-5.2194	7.362	0.26752	0.4923:0.0:0.5077:0.0	.	312;121;256;256	B4DG23;E9PBI0;Q8TBC5-2;Q8TBC5	.;.;.;ZSC18_HUMAN	E	312;256;121	ENSP00000240727:D256E;ENSP00000392653:D121E	ENSP00000240727:D256E	D	-	3	2	ZSCAN18	63289423	0.065000	0.20965	0.014000	0.15608	0.577000	0.36160	0.093000	0.15086	-0.370000	0.08016	-0.291000	0.09656	GAC	G|0.993;C|0.007	0.007	strong		0.542	ZSCAN18-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466706.1	NM_023926	
GEN1	348654	hgsc.bcm.edu	37	2	17962117	17962117	+	Silent	SNP	T	T	A	rs61762986	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:17962117T>A	ENST00000381254.2	+	14	1852	c.1638T>A	c.(1636-1638)tcT>tcA	p.S546S	GEN1_ENST00000317402.7_Silent_p.S546S|SMC6_ENST00000402989.1_Intron	NM_001130009.1	NP_001123481.1	Q17RS7	GEN_HUMAN	GEN1 Holliday junction 5' flap endonuclease	546					DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|regulation of centrosome duplication (GO:0010824)|resolution of mitotic recombination intermediates (GO:0071140)|resolution of recombination intermediates (GO:0071139)	centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	crossover junction endodeoxyribonuclease activity (GO:0008821)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					AGTTCATGTCTTCTCTAAGAC	0.363								Homologous recombination					T|||	50	0.00998403	0.0121	0.0216	5008	,	,		18882	0.0		0.0189	False		,,,				2504	0.0				p.S546S		Atlas-SNP	.											.	GEN1	79	.	0			c.T1638A						PASS	.	T	,	64,4342	61.1+/-98.1	1,62,2140	82.0	77.0	79.0		1638,1638	0.0	0.7	2	dbSNP_129	79	126,8474	64.2+/-126.4	4,118,4178	no	coding-synonymous,coding-synonymous	GEN1	NM_001130009.1,NM_182625.3	,	5,180,6318	AA,AT,TT		1.4651,1.4526,1.4609	,	546/909,546/909	17962117	190,12816	2203	4300	6503	SO:0001819	synonymous_variant	348654	exon14			CATGTCTTCTCTA	AK098188	CCDS1691.1	2p24.2	2013-06-04	2013-06-04		ENSG00000178295	ENSG00000178295			26881	protein-coding gene	gene with protein product	"""Holliday junction resolvase"""	612449	"""Gen endonuclease homolog 1 (Drosophila)"""			15576351	Standard	NM_182625		Approved	FLJ40869, Gen	uc002rct.2	Q17RS7	OTTHUMG00000121173	ENST00000381254.2:c.1638T>A	2.37:g.17962117T>A		109.0	0.0	0		116.0	57.0	0.491379	NM_182625	Q17RS9|Q6ZN37	Silent	SNP	ENST00000381254.2	37	CCDS1691.1																																																																																			T|0.987;A|0.013	0.013	strong		0.363	GEN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241661.2	NM_182625	
MUC4	4585	hgsc.bcm.edu	37	3	195506462	195506462	+	Missense_Mutation	SNP	G	G	C	rs547195540	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195506462G>C	ENST00000463781.3	-	2	12448	c.11989C>G	c.(11989-11991)Cac>Gac	p.H3997D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H3997D	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)		GGGGTGGCGTGACCTGTGGAT	0.602													.|||	35	0.00698882	0.0227	0.0	5008	,	,		9048	0.003		0.002	False		,,,				2504	0.0				p.H3997D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,+2,2	MUC4	1505	2	0			c.C11989G						PASS	.						12.0	9.0	10.0					3																	195506462		664	1461	2125	SO:0001583	missense	4585	exon2			TGGCGTGACCTGT	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.11989C>G	3.37:g.195506462G>C	ENSP00000417498:p.His3997Asp	113.0	0.0	0		85.0	39.0	0.458824	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	2.909	-0.225781	0.06022	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33438	1.41;1.5	0.764	-0.498	0.12019	.	0.000000	0.25267	N	0.031920	T	0.15003	0.0362	N	0.19112	0.55	0.09310	N	1	B	0.14805	0.011	B	0.21546	0.035	T	0.21827	-1.0234	9	.	.	.	.	5.621	0.17457	0.0:0.0:0.6825:0.3174	.	3869	E7ESK3	.	D	3997	ENSP00000417498:H3997D;ENSP00000420243:H3997D	.	H	-	1	0	MUC4	196991241	0.000000	0.05858	0.001000	0.08648	0.189000	0.23516	-0.901000	0.04093	-0.142000	0.11354	0.064000	0.15345	CAC	.	.	none		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SDK1	221935	hgsc.bcm.edu	37	7	4116697	4116697	+	Silent	SNP	G	G	A	rs61735695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:4116697G>A	ENST00000404826.2	+	21	3217	c.3078G>A	c.(3076-3078)acG>acA	p.T1026T	SDK1_ENST00000389531.3_Silent_p.T1026T	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1026	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		TGAACAGCACGACGCACGAGT	0.567													G|||	56	0.0111821	0.0408	0.0029	5008	,	,		21381	0.0		0.0	False		,,,				2504	0.0				p.T1026T		Atlas-SNP	.											SDK1,NS,carcinoma,+1,2	SDK1	361	2	0			c.G3078A						PASS	.	G		134,4272	96.7+/-135.4	2,130,2071	171.0	132.0	145.0		3078	-6.5	0.0	7	dbSNP_129	145	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SDK1	NM_152744.3		2,131,6370	AA,AG,GG		0.0116,3.0413,1.038		1026/2214	4116697	135,12871	2203	4300	6503	SO:0001819	synonymous_variant	221935	exon21			CAGCACGACGCAC	AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19307	protein-coding gene	gene with protein product		607216	"""sidekick homolog 1 (chicken)"", ""sidekick homolog 1, cell adhesion molecule (chicken)"""			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.3078G>A	7.37:g.4116697G>A		134.0	0.0	0		129.0	56.0	0.434109	NM_152744	Q8TEN9|Q8TEP5|Q96N44	Silent	SNP	ENST00000404826.2	37	CCDS34590.1																																																																																			G|0.990;A|0.010	0.010	strong		0.567	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1	NM_152744	
DAAM1	23002	hgsc.bcm.edu	37	14	59821936	59821936	+	Silent	SNP	C	C	T	rs61755340	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:59821936C>T	ENST00000395125.1	+	20	2463	c.2440C>T	c.(2440-2442)Ctg>Ttg	p.L814L	DAAM1_ENST00000360909.3_Silent_p.L804L|DAAM1_ENST00000553966.1_Intron|DAAM1_ENST00000351081.1_Silent_p.L814L	NM_014992.2	NP_055807.1	Q9Y4D1	DAAM1_HUMAN	dishevelled associated activator of morphogenesis 1	814	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.				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)		CAAGCAGTTGCTGGAGGTGGT	0.383													C|||	61	0.0121805	0.0446	0.0029	5008	,	,		23182	0.0		0.0	False		,,,				2504	0.0				p.L814L		Atlas-SNP	.											.	DAAM1	95	.	0			c.C2440T						PASS	.	C		90,4316	73.6+/-111.7	1,88,2114	188.0	176.0	180.0		2440	0.6	0.8	14	dbSNP_129	180	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	DAAM1	NM_014992.1		1,92,6410	TT,TC,CC		0.0465,2.0427,0.7227		814/1079	59821936	94,12912	2203	4300	6503	SO:0001819	synonymous_variant	23002	exon20			CAGTTGCTGGAGG	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.2440C>T	14.37:g.59821936C>T		275.0	0.0	0		280.0	126.0	0.45	NM_014992	Q86U34|Q8N1Z8|Q8TB39	Silent	SNP	ENST00000395125.1	37	CCDS9737.1																																																																																			C|0.993;T|0.007	0.007	strong		0.383	DAAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276942.2	NM_014992	
FLT4	2324	hgsc.bcm.edu	37	5	180043439	180043439	+	Silent	SNP	G	G	A	rs56127961	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:180043439G>A	ENST00000261937.6	-	23	3225	c.3147C>T	c.(3145-3147)gaC>gaT	p.D1049D	FLT4_ENST00000502649.1_Silent_p.D1049D|FLT4_ENST00000393347.3_Silent_p.D1049D	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	1049	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		D -> N (in dbSNP:rs56310180). {ECO:0000269|PubMed:17344846}.		blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TCTTCACCACGTCGCTTTCCG	0.622													G|||	72	0.014377	0.053	0.0014	5008	,	,		19924	0.001		0.0	False		,,,				2504	0.0				p.D1049D	Colon(97;1075 1466 27033 27547 35871)	Atlas-SNP	.											.	FLT4	356	.	0			c.C3147T						PASS	.	G	,	183,4223	116.7+/-154.6	5,173,2025	126.0	115.0	118.0		3147,3147	-5.8	0.4	5	dbSNP_129	118	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	FLT4	NM_002020.4,NM_182925.4	,	5,173,6325	AA,AG,GG		0.0,4.1534,1.407	,	1049/1299,1049/1364	180043439	183,12823	2203	4300	6503	SO:0001819	synonymous_variant	2324	exon23			CACCACGTCGCTT	X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.3147C>T	5.37:g.180043439G>A		154.0	0.0	0		193.0	94.0	0.487047	NM_182925	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Silent	SNP	ENST00000261937.6	37	CCDS4457.1																																																																																			G|0.982;A|0.018	0.018	strong		0.622	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4		
ADAM12	8038	hgsc.bcm.edu	37	10	127824167	127824167	+	Silent	SNP	C	C	T	rs12098586	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:127824167C>T	ENST00000368679.4	-	5	720	c.411G>A	c.(409-411)acG>acA	p.T137T	ADAM12_ENST00000368676.4_Silent_p.T137T	NM_003474.4	NP_003465.3	O43184	ADA12_HUMAN	ADAM metallopeptidase domain 12	137					cell adhesion (GO:0007155)|epidermal growth factor receptor signaling pathway (GO:0007173)|myoblast fusion (GO:0007520)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			biliary_tract(1)|breast(7)|central_nervous_system(4)|endometrium(5)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69		all_epithelial(44;7.06e-05)|all_lung(145;0.00563)|Lung NSC(174;0.00834)|Colorectal(57;0.102)|all_neural(114;0.107)|Breast(234;0.22)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.216)		GACCAGAACACGTGCTGAGAC	0.498													c|||	207	0.0413339	0.1415	0.0259	5008	,	,		19767	0.0		0.002	False		,,,				2504	0.0				p.T137T		Atlas-SNP	.											.	ADAM12	388	.	0			c.G411A						PASS	.	C	,	514,3892	237.4+/-249.2	33,448,1722	161.0	120.0	134.0		411,411	-6.5	0.9	10	dbSNP_120	134	24,8576	17.9+/-57.8	0,24,4276	no	coding-synonymous,coding-synonymous	ADAM12	NM_003474.4,NM_021641.3	,	33,472,5998	TT,TC,CC		0.2791,11.6659,4.1366	,	137/910,137/739	127824167	538,12468	2203	4300	6503	SO:0001819	synonymous_variant	8038	exon5			AGAACACGTGCTG	AF023476	CCDS7653.1, CCDS7654.1	10q26	2008-07-29	2008-07-29		ENSG00000148848	ENSG00000148848		"""ADAM metallopeptidase domain containing"""	190	protein-coding gene	gene with protein product	"""meltrin alpha"""	602714	"""a disintegrin and metalloproteinase domain 12 (meltrin alpha)"""			9417060, 18342566	Standard	NM_003474		Approved	MCMPMltna, MLTN	uc001ljk.2	O43184	OTTHUMG00000019243	ENST00000368679.4:c.411G>A	10.37:g.127824167C>T		143.0	0.0	0		125.0	61.0	0.488	NM_021641	O60470|Q5JRP0|Q5JRP1|Q6P9E3|Q6UWB0	Silent	SNP	ENST00000368679.4	37	CCDS7653.1																																																																																			C|0.960;T|0.040	0.040	strong		0.498	ADAM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050961.1		
SIK2	23235	hgsc.bcm.edu	37	11	111594520	111594520	+	Silent	SNP	G	G	A	rs75997369	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:111594520G>A	ENST00000304987.3	+	15	2621	c.2448G>A	c.(2446-2448)acG>acA	p.T816T		NM_015191.1	NP_056006.1	Q9H0K1	SIK2_HUMAN	salt-inducible kinase 2	816					insulin receptor signaling pathway (GO:0008286)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of insulin receptor signaling pathway (GO:0046626)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(2)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	30						CTCTGCCCACGCAGCTACAGC	0.637													G|||	9	0.00179712	0.0068	0.0	5008	,	,		10597	0.0		0.0	False		,,,				2504	0.0				p.T816T		Atlas-SNP	.											.	SIK2	89	.	0			c.G2448A						PASS	.	G		48,4354	49.6+/-84.7	0,48,2153	64.0	72.0	69.0		2448	-8.7	0.0	11	dbSNP_131	69	0,8594		0,0,4297	no	coding-synonymous	SIK2	NM_015191.1		0,48,6450	AA,AG,GG		0.0,1.0904,0.3693		816/927	111594520	48,12948	2201	4297	6498	SO:0001819	synonymous_variant	23235	exon15			GCCCACGCAGCTA	AB018324	CCDS8347.1	11q23.1	2008-12-23	2008-12-23	2008-12-23	ENSG00000170145	ENSG00000170145			21680	protein-coding gene	gene with protein product		608973	"""SNF1-like kinase 2"""	SNF1LK2		15067358	Standard	NM_015191		Approved	KIAA0781, QIK, DKFZp434K1115, LOH11CR1I	uc001plt.3	Q9H0K1	OTTHUMG00000150644	ENST00000304987.3:c.2448G>A	11.37:g.111594520G>A		82.0	0.0	0		57.0	36.0	0.631579	NM_015191	A8K5B8|B0YJ94|O94878|Q17RV0|Q6AZE2|Q76N03|Q8NCV7|Q96CZ8	Silent	SNP	ENST00000304987.3	37	CCDS8347.1																																																																																			G|0.997;A|0.003	0.003	strong		0.637	SIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319352.3	NM_015191	
DYSF	8291	hgsc.bcm.edu	37	2	71838661	71838661	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71838661G>A	ENST00000258104.3	+	38	4349	c.4072G>A	c.(4072-4074)Gtg>Atg	p.V1358M	DYSF_ENST00000409651.1_Missense_Mutation_p.V1390M|DYSF_ENST00000410020.3_Missense_Mutation_p.V1376M|DYSF_ENST00000429174.2_Missense_Mutation_p.V1358M|DYSF_ENST00000410041.1_Missense_Mutation_p.V1376M|DYSF_ENST00000409744.1_Missense_Mutation_p.V1345M|DYSF_ENST00000409366.1_Missense_Mutation_p.V1359M|DYSF_ENST00000479049.2_3'UTR|DYSF_ENST00000394120.2_Missense_Mutation_p.V1359M|DYSF_ENST00000409582.3_Missense_Mutation_p.V1375M|DYSF_ENST00000413539.2_Missense_Mutation_p.V1389M|DYSF_ENST00000409762.1_Missense_Mutation_p.V1375M	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1358	C2 5. {ECO:0000255|PROSITE- ProRule:PRU00041}.				plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						CCCCAGCCTCGTGGTAGAGTG	0.567																																					p.V1390M		Atlas-SNP	.											DYSF_ENST00000410020,NS,carcinoma,0,2	DYSF	536	2	0			c.G4168A						PASS	.						58.0	57.0	57.0					2																	71838661		2203	4300	6503	SO:0001583	missense	8291	exon39			AGCCTCGTGGTAG	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.4072G>A	2.37:g.71838661G>A	ENSP00000258104:p.Val1358Met	79.0	0.0	0		66.0	31.0	0.469697	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Missense_Mutation	SNP	ENST00000258104.3	37	CCDS1918.1	.	.	.	.	.	.	.	.	.	.	G	16.19	3.054472	0.55218	.	.	ENSG00000135636	ENST00000413539;ENST00000409762;ENST00000409582;ENST00000429174;ENST00000258104;ENST00000409651;ENST00000394120;ENST00000409744;ENST00000409366;ENST00000410020;ENST00000410041	D;D;D;D;D;D;D;D;D;D;D	0.82711	-1.64;-1.64;-1.64;-1.64;-1.64;-1.64;-1.64;-1.64;-1.64;-1.64;-1.64	5.54	4.65	0.58169	C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.213647	0.42548	D	0.000687	D	0.86053	0.5841	L	0.54323	1.7	0.32057	N	0.596244	D;D;D;D;D;D;P;P;B;P;B;P;P;D;P	0.71674	0.984;0.998;0.998;0.995;0.995;0.995;0.851;0.773;0.415;0.769;0.077;0.46;0.769;0.995;0.807	P;P;P;P;P;D;P;P;B;B;B;B;B;P;P	0.66497	0.843;0.855;0.9;0.9;0.9;0.944;0.554;0.684;0.433;0.433;0.087;0.238;0.433;0.855;0.569	D	0.85452	0.1161	10	0.40728	T	0.16	-21.6668	8.921	0.35612	0.1689:0.0:0.8311:0.0	.	101;1390;1376;1359;1345;1376;1345;1375;1344;1389;1375;1358;1344;1359;1358	B7Z8G4;O75923-8;O75923-13;O75923-10;O75923-9;O75923-11;O75923-12;O75923-5;O75923-6;O75923-2;O75923-7;O75923-4;O75923-3;O75923-14;O75923	.;.;.;.;.;.;.;.;.;.;.;.;.;.;DYSF_HUMAN	M	1389;1375;1375;1358;1358;1390;1359;1345;1359;1376;1376	ENSP00000407046:V1389M;ENSP00000387137:V1375M;ENSP00000386547:V1375M;ENSP00000398305:V1358M;ENSP00000258104:V1358M;ENSP00000386683:V1390M;ENSP00000377678:V1359M;ENSP00000386285:V1345M;ENSP00000386512:V1359M;ENSP00000386881:V1376M;ENSP00000386617:V1376M	ENSP00000258104:V1358M	V	+	1	0	DYSF	71692169	0.054000	0.20591	0.944000	0.38274	0.395000	0.30598	0.451000	0.21779	2.623000	0.88846	0.561000	0.74099	GTG	.	.	none		0.567	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
TNRC6A	27327	hgsc.bcm.edu	37	16	24802204	24802204	+	Silent	SNP	C	C	T	rs113288384		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:24802204C>T	ENST00000395799.3	+	6	2370	c.2241C>T	c.(2239-2241)gaC>gaT	p.D747D	TNRC6A_ENST00000315183.7_Silent_p.D747D	NM_014494.2	NP_055309.2	Q8NDV7	TNR6A_HUMAN	trinucleotide repeat containing 6A	747	Interaction with argonaute family proteins.|Sufficient for interaction with AGO1 and AGO4.|Sufficient for interaction with AGO2.				cellular response to starvation (GO:0009267)|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)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(13)|kidney(5)|large_intestine(13)|liver(1)|lung(20)|ovary(3)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64				GBM - Glioblastoma multiforme(48;0.0394)		GAAAGACTGACAATGGGACAG	0.473													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20045	0.0		0.0	False		,,,				2504	0.0				p.D747D		Atlas-SNP	.											.	TNRC6A	171	.	0			c.C2241T						PASS	.	C		2,4392	4.2+/-10.8	0,2,2195	53.0	55.0	55.0		2241	3.9	1.0	16	dbSNP_132	55	0,8600		0,0,4300	no	coding-synonymous	TNRC6A	NM_014494.2		0,2,6495	TT,TC,CC		0.0,0.0455,0.0154		747/1963	24802204	2,12992	2197	4300	6497	SO:0001819	synonymous_variant	27327	exon6			GACTGACAATGGG	U80739	CCDS10624.2	16p11.2	2009-09-22	2004-12-17	2004-12-17	ENSG00000090905	ENSG00000090905		"""Trinucleotide (CAG) repeat containing"""	11969	protein-coding gene	gene with protein product		610739	"""trinucleotide repeat containing 6"""	TNRC6		9225980	Standard	NM_014494		Approved	CAGH26, KIAA1460, GW182	uc002dmm.3	Q8NDV7	OTTHUMG00000096999	ENST00000395799.3:c.2241C>T	16.37:g.24802204C>T		49.0	0.0	0		52.0	26.0	0.5	NM_014494	C9JAR8|O15408|Q658L5|Q6NVB5|Q8NEZ0|Q8TBT8|Q8TCR0|Q9NV59|Q9P268	Silent	SNP	ENST00000395799.3	37	CCDS10624.2																																																																																			C|0.999;T|0.001	0.001	strong		0.473	TNRC6A-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214081.1	NM_020847	
ZNF474	133923	hgsc.bcm.edu	37	5	121487954	121487954	+	Missense_Mutation	SNP	G	G	A	rs116158782	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:121487954G>A	ENST00000296600.4	+	2	652	c.269G>A	c.(268-270)cGc>cAc	p.R90H	CTC-441N14.2_ENST00000504829.1_RNA|CTC-441N14.1_ENST00000505209.1_RNA|ZNF474_ENST00000514925.1_Intron	NM_207317.1	NP_997200.1	Q6S9Z5	ZN474_HUMAN	zinc finger protein 474	90							metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|stomach(1)	21		all_cancers(142;0.229)|Prostate(80;0.0387)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000197)|Epithelial(69;0.00029)|all cancers(49;0.00415)		ATCCCGGCCCGCAGGCCTGGA	0.493													G|||	47	0.00938498	0.0348	0.0014	5008	,	,		17011	0.0		0.0	False		,,,				2504	0.0				p.R90H		Atlas-SNP	.											.	ZNF474	43	.	0			c.G269A						PASS	.	G	HIS/ARG	146,4260	102.1+/-140.7	3,140,2060	76.0	86.0	82.0		269	4.7	1.0	5	dbSNP_132	82	5,8593	4.3+/-15.6	0,5,4294	yes	missense	ZNF474	NM_207317.1	29	3,145,6354	AA,AG,GG		0.0582,3.3137,1.1612	probably-damaging	90/365	121487954	151,12853	2203	4299	6502	SO:0001583	missense	133923	exon2			CGGCCCGCAGGCC	AK057483	CCDS4130.1	5q23.2	2008-02-05			ENSG00000164185	ENSG00000164185		"""Zinc fingers, C2H2-type"""	23245	protein-coding gene	gene with protein product							Standard	NM_207317		Approved	4933409D10Rik, FLJ32921	uc003ksv.3	Q6S9Z5	OTTHUMG00000128911	ENST00000296600.4:c.269G>A	5.37:g.121487954G>A	ENSP00000296600:p.Arg90His	131.0	0.0	0		128.0	56.0	0.4375	NM_207317	A8K4M0|Q96M07	Missense_Mutation	SNP	ENST00000296600.4	37	CCDS4130.1	25	0.011446886446886446	24	0.04878048780487805	1	0.0027624309392265192	0	0.0	0	0.0	G	15.38	2.817454	0.50633	0.033137	5.82E-4	ENSG00000164185	ENST00000296600	T	0.50001	0.76	5.58	4.66	0.58398	.	0.157757	0.33980	N	0.004370	T	0.19525	0.0469	L	0.36672	1.1	0.36400	D	0.863073	D	0.89917	1.0	D	0.73708	0.981	T	0.55010	-0.8207	10	0.62326	D	0.03	-6.5368	15.9342	0.79688	0.0:0.135:0.865:0.0	.	90	Q6S9Z5	ZN474_HUMAN	H	90	ENSP00000296600:R90H	ENSP00000296600:R90H	R	+	2	0	ZNF474	121515853	0.999000	0.42202	1.000000	0.80357	0.102000	0.19082	1.797000	0.38804	2.624000	0.88883	0.655000	0.94253	CGC	G|0.988;A|0.012	0.012	strong		0.493	ZNF474-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250883.2	NM_207317	
LILRB3	11025	hgsc.bcm.edu	37	19	54721272	54721272	+	Missense_Mutation	SNP	C	C	T	rs114189491	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54721272C>T	ENST00000391750.1	-	13	1801	c.1665G>A	c.(1663-1665)atG>atA	p.M555I	LILRA6_ENST00000440558.2_Missense_Mutation_p.M555I|LILRB3_ENST00000346401.6_Missense_Mutation_p.M567I|LILRB3_ENST00000245620.9_Missense_Mutation_p.M556I|LILRA6_ENST00000391735.3_3'UTR|LILRA6_ENST00000419410.2_Missense_Mutation_p.M556I|LILRB3_ENST00000469273.1_5'UTR|LILRB3_ENST00000407860.2_Missense_Mutation_p.M572I|LILRA6_ENST00000270464.5_Missense_Mutation_p.M556I|LILRB3_ENST00000424807.1_Missense_Mutation_p.M555I			O75022	LIRB3_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 3	555					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)		GAGGAGAGGCCATTTCTCTCC	0.577													.|||	174	0.0347444	0.1293	0.0043	5008	,	,		17886	0.0		0.0	False		,,,				2504	0.0				p.M556I		Atlas-SNP	.											.	LILRB3	67	.	0			c.G1668A						PASS	.	C	ILE/MET,ILE/MET	451,3953	216.4+/-235.1	26,399,1777	130.0	130.0	130.0		1668,1665	-0.9	0.0	19	dbSNP_132	130	3,8597	3.0+/-9.4	0,3,4297	no	missense,missense	LILRB3	NM_001081450.1,NM_006864.2	10,10	26,402,6074	TT,TC,CC		0.0349,10.2407,3.4912	benign,benign	556/633,555/632	54721272	454,12550	2202	4300	6502	SO:0001583	missense	11025	exon12			AGAGGCCATTTCT	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.1665G>A	19.37:g.54721272C>T	ENSP00000375630:p.Met555Ile	602.0	0.0	0		418.0	208.0	0.497608	NM_001081450	C9J1P3|C9JIP1|O15471|Q86U49	Missense_Mutation	SNP	ENST00000391750.1	37	CCDS33105.1	63	0.028846153846153848	62	0.12601626016260162	1	0.0027624309392265192	0	0.0	0	0.0	C	12.21	1.870077	0.33069	0.102407	3.49E-4	ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000204577;ENSG00000244482;ENSG00000244482;ENSG00000244482	ENST00000391750;ENST00000424807;ENST00000346401;ENST00000245620;ENST00000407860;ENST00000440558;ENST00000270464;ENST00000419410	T;T;T;T;T;T;T;T	0.00477	7.16;7.16;7.14;7.17;7.14;7.16;7.16;7.18	2.45	-0.895	0.10560	.	.	.	.	.	T	0.00012	0.0000	L	0.50919	1.6	0.09310	N	1	D;B;B;B;B;B;P	0.56287	0.975;0.39;0.197;0.121;0.014;0.006;0.78	D;B;B;B;B;B;P	0.65684	0.937;0.026;0.109;0.015;0.002;0.001;0.458	T	0.55179	-0.8181	9	0.54805	T	0.06	.	2.7524	0.05284	0.0:0.4373:0.2613:0.3014	.	572;555;556;567;572;555;556	B5MCX0;F8WCY4;D3YTC4;F8W6G6;O75022-2;O75022;O75022-3	.;.;.;.;.;LIRB3_HUMAN;.	I	555;555;567;556;572;555;556;556	ENSP00000375630:M555I;ENSP00000412771:M555I;ENSP00000345184:M567I;ENSP00000245620:M556I;ENSP00000384274:M572I;ENSP00000390120:M555I;ENSP00000270464:M556I;ENSP00000411227:M556I	ENSP00000270464:M556I	M	-	3	0	LILRB3;LILRA6	59413084	0.000000	0.05858	0.000000	0.03702	0.042000	0.13812	-0.049000	0.11924	-0.089000	0.12484	0.121000	0.15741	ATG	C|0.961;T|0.039	0.039	strong		0.577	LILRB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142844.5	NM_006864	
ASPSCR1	79058	hgsc.bcm.edu	37	17	79943475	79943475	+	Silent	SNP	A	A	G	rs4796860	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:79943475A>G	ENST00000306739.4	+	4	463	c.366A>G	c.(364-366)ccA>ccG	p.P122P	ASPSCR1_ENST00000580534.1_Silent_p.P45P|ASPSCR1_ENST00000306729.7_Silent_p.P122P|ASPSCR1_ENST00000581647.1_Silent_p.P122P	NM_024083.3	NP_076988.1	Q9BZE9	ASPC1_HUMAN	alveolar soft part sarcoma chromosome region, candidate 1	122					glucose homeostasis (GO:0042593)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|regulation of glucose import (GO:0046324)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)			ASPSCR1/TFE3(167)	breast(2)|large_intestine(2)	4	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			GCCATTTTCCACAGATCAGGT	0.582			T	TFE3	alveolar soft part sarcoma								A|||	55	0.0109824	0.0401	0.0029	5008	,	,		19456	0.0		0.0	False		,,,				2504	0.0				p.P122P		Atlas-SNP	.		Dom	yes		17	17q25	79058	"""alveolar soft part sarcoma chromosome region, candidate 1"""		M	.	ASPSCR1	27	.	0			c.A366G						PASS	.	A		235,4171	136.9+/-172.8	5,225,1973	77.0	68.0	71.0		366	1.8	1.0	17	dbSNP_111	71	0,8600		0,0,4300	yes	coding-synonymous	ASPSCR1	NM_024083.2		5,225,6273	GG,GA,AA		0.0,5.3336,1.8069		122/554	79943475	235,12771	2203	4300	6503	SO:0001819	synonymous_variant	79058	exon4			TTTTCCACAGATC	AF324219	CCDS11796.1, CCDS58611.1	17q25	2011-06-28				ENSG00000169696		"""UBX domain containing"""	13825	protein-coding gene	gene with protein product	"""UBX domain protein 9"""	606236				11244503, 10506710	Standard	NM_024083		Approved	ASPS, ASPL, UBXD9, UBXN9	uc002kcy.3	Q9BZE9		ENST00000306739.4:c.366A>G	17.37:g.79943475A>G		177.0	0.0	0		178.0	82.0	0.460674	NM_001251888	A8K3K9|Q7Z6N7|Q8WV59|Q96LS5|Q96M40	Silent	SNP	ENST00000306739.4	37	CCDS11796.1																																																																																			A|0.983;G|0.017	0.017	strong		0.582	ASPSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441972.1	NM_024083	
CELSR1	9620	hgsc.bcm.edu	37	22	46760037	46760037	+	Missense_Mutation	SNP	G	G	A	rs375307146|rs6008777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46760037G>A	ENST00000262738.3	-	34	8890	c.8891C>T	c.(8890-8892)tCg>tTg	p.S2964L		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2964			S -> L (in NTD; shows reduced protein localization to the cell membrane; dbSNP:rs6008777). {ECO:0000269|PubMed:22095531}.		anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		AGACGTGCGCGAGGATGTGGG	0.682													G|||	116	0.0231629	0.0832	0.0086	5008	,	,		14793	0.0		0.0	False		,,,				2504	0.0				p.S2964L		Atlas-SNP	.											CELSR1,colon,carcinoma,+1,1	CELSR1	242	1	0			c.C8891T						PASS	.	G	LEU/SER	399,4005	190.2+/-216.2	29,341,1832	40.0	46.0	44.0		8891	4.8	0.1	22	dbSNP_114	44	4,8594	3.0+/-9.4	0,4,4295	yes	missense	CELSR1	NM_014246.1	145	29,345,6127	AA,AG,GG		0.0465,9.0599,3.0995	probably-damaging	2964/3015	46760037	403,12599	2202	4299	6501	SO:0001583	missense	9620	exon34			GTGCGCGAGGATG	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	1850	protein-coding gene	gene with protein product	"""flamingo homolog 2 (Drosophila)"""	604523	"""cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"""			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.8891C>T	22.37:g.46760037G>A	ENSP00000262738:p.Ser2964Leu	122.0	0.0	0		159.0	85.0	0.534591	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Missense_Mutation	SNP	ENST00000262738.3	37	CCDS14076.1	37	0.01694139194139194	35	0.07113821138211382	2	0.0055248618784530384	0	0.0	0	0.0	G	14.11	2.438063	0.43326	0.090599	4.65E-4	ENSG00000075275	ENST00000262738	T	0.71579	-0.58	4.85	4.85	0.62838	.	0.000000	0.36374	U	0.002632	T	0.11367	0.0277	M	0.74258	2.255	0.37738	D	0.925504	D	0.67145	0.996	P	0.47786	0.557	T	0.57046	-0.7878	10	0.33141	T	0.24	.	17.569	0.87930	0.0:0.0:1.0:0.0	rs6008777	2964	Q9NYQ6	CELR1_HUMAN	L	2964	ENSP00000262738:S2964L	ENSP00000262738:S2964L	S	-	2	0	CELSR1	45138701	0.994000	0.37717	0.060000	0.19600	0.011000	0.07611	3.602000	0.54066	2.211000	0.71520	0.563000	0.77884	TCG	G|0.971;A|0.029	0.029	strong		0.682	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
CLCA4	22802	hgsc.bcm.edu	37	1	87012929	87012929	+	Missense_Mutation	SNP	C	C	T	rs2231580	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:87012929C>T	ENST00000370563.3	+	1	169	c.127C>T	c.(127-129)Cca>Tca	p.P43S	CLCA4_ENST00000263723.5_5'UTR	NM_012128.3	NP_036260.2	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	43			P -> S (in dbSNP:rs2231580).		chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44		Lung NSC(277;0.238)		all cancers(265;0.0202)|Epithelial(280;0.0404)		TCCTAGTGTGCCAGAAGATGA	0.289													C|||	197	0.0393371	0.143	0.0115	5008	,	,		17655	0.0		0.0	False		,,,				2504	0.0				p.P43S		Atlas-SNP	.											.	CLCA4	131	.	0			c.C127T						PASS	.	C	SER/PRO	430,3208		15,400,1404	112.0	103.0	106.0		127	2.5	0.9	1	dbSNP_98	106	1,8149		0,1,4074	yes	missense	CLCA4	NM_012128.3	74	15,401,5478	TT,TC,CC		0.0123,11.8197,3.6563	benign	43/920	87012929	431,11357	1819	4075	5894	SO:0001583	missense	22802	exon1			AGTGTGCCAGAAG	AF127035	CCDS41355.1	1p31-p22	2012-02-26	2009-01-29		ENSG00000016602	ENSG00000016602			2018	protein-coding gene	gene with protein product			"""chloride channel, calcium activated, family member 4"", ""chloride channel regulator 4"""			10437792	Standard	NM_012128		Approved	CaCC2	uc009wcs.3	Q14CN2	OTTHUMG00000010260	ENST00000370563.3:c.127C>T	1.37:g.87012929C>T	ENSP00000359594:p.Pro43Ser	95.0	0.0	0		94.0	50.0	0.531915	NM_012128	A8MQC9|B7Z1Q5|Q6UX81|Q9UNF7	Missense_Mutation	SNP	ENST00000370563.3	37	CCDS41355.1	71	0.03250915750915751	67	0.13617886178861788	4	0.011049723756906077	0	0.0	0	0.0	C	13.02	2.111801	0.37242	0.118197	1.23E-4	ENSG00000016602	ENST00000370563	T	0.15487	2.42	5.51	2.51	0.30379	Chloride channel calcium-activated (1);	0.460669	0.22684	N	0.056907	T	0.11324	0.0276	L	0.50993	1.605	0.80722	D	1	P	0.40534	0.72	P	0.53102	0.718	T	0.17961	-1.0352	10	0.34782	T	0.22	-0.5846	2.8316	0.05502	0.1469:0.5502:0.1426:0.1603	rs2231580;rs52821083;rs60157342;rs2231580	43	Q14CN2	CLCA4_HUMAN	S	43	ENSP00000359594:P43S	ENSP00000359594:P43S	P	+	1	0	CLCA4	86785517	0.986000	0.35501	0.942000	0.38095	0.500000	0.33767	0.870000	0.28010	0.336000	0.23639	0.655000	0.94253	CCA	C|0.971;T|0.029	0.029	strong		0.289	CLCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028292.1	NM_012128	
DNAH10	196385	hgsc.bcm.edu	37	12	124409630	124409630	+	Missense_Mutation	SNP	G	G	T	rs74845458	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124409630G>T	ENST00000409039.3	+	67	11471	c.11446G>T	c.(11446-11448)Gtc>Ttc	p.V3816F	RP11-380L11.4_ENST00000602952.1_RNA|CCDC92_ENST00000544798.1_Intron	NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3816					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)		GCAGTTTCCCGTCCCCTTGGG	0.473													T|||	327	0.0652955	0.2322	0.0231	5008	,	,		20433	0.0		0.003	False		,,,				2504	0.001				p.V3816F		Atlas-SNP	.											DNAH10_same_name,NS,carcinoma,0,2	DNAH10	888	2	0			c.G11446T						PASS	.	T	PHE/VAL	709,3179		59,591,1294	174.0	167.0	170.0		11446	1.5	0.3	12	dbSNP_131	170	39,8265		1,37,4114	yes	missense	DNAH10	NM_207437.3	50	60,628,5408	TT,TG,GG		0.4697,18.2356,6.1352	benign	3816/4472	124409630	748,11444	1944	4152	6096	SO:0001583	missense	196385	exon67			TTTCCCGTCCCCT	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.11446G>T	12.37:g.124409630G>T	ENSP00000386770:p.Val3816Phe	258.0	0.0	0		282.0	136.0	0.482269	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	113	0.051739926739926737	100	0.2032520325203252	11	0.03038674033149171	0	0.0	2	0.002638522427440633	T	0.013	-1.642308	0.00799	0.182356	0.004697	ENSG00000197653	ENST00000409039	T	0.09538	2.97	5.45	1.5	0.22942	Dynein heavy chain (1);	0.344630	0.30085	N	0.010460	T	0.00012	0.0000	N	0.00277	-1.72	0.19945	P	0.9999460444	B	0.02656	0.0	B	0.01281	0.0	T	0.40308	-0.9570	9	0.12430	T	0.62	.	2.5158	0.04667	0.11:0.1927:0.1142:0.5831	.	3816	Q8IVF4	DYH10_HUMAN	F	3816	ENSP00000386770:V3816F	ENSP00000386770:V3816F	V	+	1	0	DNAH10	122975583	0.935000	0.31712	0.251000	0.24312	0.009000	0.06853	1.289000	0.33307	0.040000	0.15660	-1.401000	0.01141	GTC	G|0.958;T|0.042	0.042	strong		0.473	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
SACS	26278	hgsc.bcm.edu	37	13	23929189	23929189	+	Missense_Mutation	SNP	C	C	G	rs190617851		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:23929189C>G	ENST00000382292.3	-	7	1835	c.1562G>C	c.(1561-1563)aGc>aCc	p.S521T	SACS_ENST00000476776.1_5'Flank|SACS_ENST00000382298.3_Missense_Mutation_p.S521T|SACS_ENST00000402364.1_5'UTR			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	521					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		GAAATCAGAGCTCTTTTCCAT	0.458													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20393	0.0		0.0	False		,,,				2504	0.0				p.S521T		Atlas-SNP	.											.	SACS	871	.	0			c.G1562C						PASS	.	C	THR/SER	1,4405	2.1+/-5.4	0,1,2202	77.0	85.0	82.0		1562	2.3	0.0	13		82	0,8600		0,0,4300	no	missense	SACS	NM_014363.4	58	0,1,6502	GG,GC,CC		0.0,0.0227,0.0077	benign	521/4580	23929189	1,13005	2203	4300	6503	SO:0001583	missense	26278	exon8			TCAGAGCTCTTTT	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.1562G>C	13.37:g.23929189C>G	ENSP00000371729:p.Ser521Thr	86.0	0.0	0		93.0	44.0	0.473118	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Missense_Mutation	SNP	ENST00000382292.3	37	CCDS9300.2	1|1	4.578754578754579E-4|4.578754578754579E-4	1|1	0.0020325203252032522|0.0020325203252032522	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	12.48|12.48	1.950654|1.950654	0.34377|0.34377	2.27E-4|2.27E-4	0.0|0.0	ENSG00000151835|ENSG00000151835	ENST00000455470|ENST00000382292;ENST00000382298;ENST00000423156	.|T;T;T	.|0.21191	.|2.02;2.02;2.02	5.48|5.48	2.34|2.34	0.29019|0.29019	.|.	.|0.444341	.|0.27384	.|N	.|0.019604	T|T	0.11495|0.11495	0.0280|0.0280	L|L	0.34521|0.34521	1.04|1.04	0.26264|0.26264	N|N	0.978528|0.978528	.|B;B;B	.|0.31625	.|0.332;0.332;0.0	.|B;B;B	.|0.30572	.|0.075;0.117;0.002	T|T	0.24190|0.24190	-1.0167|-1.0167	5|10	.|0.14656	.|T	.|0.56	.|.	3.6068|3.6068	0.08045|0.08045	0.0:0.2101:0.4786:0.3113|0.0:0.2101:0.4786:0.3113	.|.	.|420;308;521	.|B2REB1;E9PAL4;Q9NZJ4	.|.;.;SACS_HUMAN	D|T	420|521;521;145	.|ENSP00000371729:S521T;ENSP00000371735:S521T;ENSP00000390925:S145T	.|ENSP00000371729:S521T	E|S	-|-	3|2	2|0	SACS|SACS	22827189|22827189	0.968000|0.968000	0.33430|0.33430	0.001000|0.001000	0.08648|0.08648	0.923000|0.923000	0.55619|0.55619	1.379000|1.379000	0.34340|0.34340	0.259000|0.259000	0.21709|0.21709	0.561000|0.561000	0.74099|0.74099	GAG|AGC	C|1.000;G|0.000	0.000	strong		0.458	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
CCDC88C	440193	hgsc.bcm.edu	37	14	91744348	91744348	+	Missense_Mutation	SNP	C	C	T	rs114849211	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:91744348C>T	ENST00000389857.6	-	29	5062	c.4976G>A	c.(4975-4977)cGg>cAg	p.R1659Q	CCDC88C_ENST00000331194.7_Missense_Mutation_p.R183Q	NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	1659					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)	p.R1659Q(2)|p.R183Q(1)		central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				CGAGCAGGGCCGCACTCCGAC	0.677													C|||	52	0.0103834	0.0386	0.0014	5008	,	,		17086	0.0		0.0	False		,,,				2504	0.0				p.R1659Q		Atlas-SNP	.											KIAA1509,caecum,carcinoma,-1,6	CCDC88C	192	6	3	Substitution - Missense(3)	urinary_tract(3)	c.G4976A						PASS	.	C	GLN/ARG	103,3867		0,103,1882	12.0	15.0	14.0		4976	4.5	0.2	14	dbSNP_132	14	1,8315		0,1,4157	yes	missense	CCDC88C	NM_001080414.3	43	0,104,6039	TT,TC,CC		0.012,2.5945,0.8465	probably-damaging	1659/2029	91744348	104,12182	1985	4158	6143	SO:0001583	missense	440193	exon29			CAGGGCCGCACTC		CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"""Dvl-associating protein with a high frequency of leucine residues"", ""spinocerebellar ataxia 40"""	611204	"""KIAA1509"""	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.4976G>A	14.37:g.91744348C>T	ENSP00000374507:p.Arg1659Gln	77.0	0.0	0		103.0	57.0	0.553398	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Missense_Mutation	SNP	ENST00000389857.6	37	CCDS45151.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	C	16.75	3.209248	0.58343	0.025945	1.2E-4	ENSG00000015133	ENST00000389857;ENST00000427583;ENST00000331194	T;T	0.55930	2.19;0.49	5.55	4.47	0.54385	.	0.000000	0.47455	U	0.000221	T	0.40423	0.1116	L	0.54323	1.7	0.09310	N	0.999999	D;P;P	0.89917	1.0;0.812;0.812	D;B;B	0.80764	0.994;0.141;0.141	T	0.44757	-0.9307	10	0.72032	D	0.01	-41.3463	9.9503	0.41634	0.0:0.8456:0.0:0.1544	.	1659;183;109	Q9P219;Q9P219-2;Q9P219-3	DAPLE_HUMAN;.;.	Q	1659;183;183	ENSP00000374507:R1659Q;ENSP00000330332:R183Q	ENSP00000330332:R183Q	R	-	2	0	CCDC88C	90814101	0.903000	0.30736	0.169000	0.22859	0.580000	0.36256	2.140000	0.42159	2.608000	0.88229	0.462000	0.41574	CGG	C|0.994;T|0.006	0.006	strong		0.677	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353	
WNT4	54361	hgsc.bcm.edu	37	1	22446768	22446768	+	Silent	SNP	G	G	A	rs34228276	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:22446768G>A	ENST00000290167.6	-	5	874	c.831C>T	c.(829-831)ccC>ccT	p.P277P	WNT4_ENST00000542383.1_Silent_p.P222P	NM_030761.4	NP_110388.2	P56705	WNT4_HUMAN	wingless-type MMTV integration site family, member 4	277			P -> L (in dbSNP:rs34228276).		adrenal gland development (GO:0030325)|androgen biosynthetic process (GO:0006702)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cellular response to starvation (GO:0009267)|cellular response to transforming growth factor beta stimulus (GO:0071560)|embryonic epithelial tube formation (GO:0001838)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization to plasma membrane (GO:0090002)|female gonad development (GO:0008585)|female sex determination (GO:0030237)|immature T cell proliferation in thymus (GO:0033080)|kidney development (GO:0001822)|liver development (GO:0001889)|male gonad development (GO:0008584)|mammary gland epithelium development (GO:0061180)|mesenchymal to epithelial transition (GO:0060231)|metanephric mesenchymal cell differentiation (GO:0072162)|metanephric nephron morphogenesis (GO:0072273)|metanephric tubule formation (GO:0072174)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell migration (GO:0030336)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of gene expression (GO:0010629)|negative regulation of male gonad development (GO:2000019)|negative regulation of steroid biosynthetic process (GO:0010894)|negative regulation of testicular blood vessel morphogenesis (GO:0061369)|negative regulation of testosterone biosynthetic process (GO:2000225)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of wound healing (GO:0061045)|neuron differentiation (GO:0030182)|non-canonical Wnt signaling pathway via MAPK cascade (GO:0038030)|oocyte development (GO:0048599)|paramesonephric duct development (GO:0061205)|positive regulation of aldosterone biosynthetic process (GO:0032349)|positive regulation of bone mineralization (GO:0030501)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of cortisol biosynthetic process (GO:2000066)|positive regulation of dermatome development (GO:0061184)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of meiosis (GO:0045836)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription, DNA-templated (GO:0045893)|protein palmitoylation (GO:0018345)|regulation of cell-cell adhesion (GO:0022407)|renal vesicle formation (GO:0072033)|renal vesicle induction (GO:0072034)|smooth muscle cell differentiation (GO:0051145)|somatotropin secreting cell differentiation (GO:0060126)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|thyroid-stimulating hormone-secreting cell differentiation (GO:0060129)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)	8		Colorectal(325;3.46e-05)|all_lung(284;5.94e-05)|Lung NSC(340;6.55e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;9.02e-26)|Colorectal(126;1.71e-07)|COAD - Colon adenocarcinoma(152;1.17e-05)|GBM - Glioblastoma multiforme(114;2.01e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000568)|KIRC - Kidney renal clear cell carcinoma(1967;0.00277)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.138)		CACAGAAGTCGGGGCTAGGCT	0.647													G|||	117	0.0233626	0.0582	0.0173	5008	,	,		19089	0.003		0.0229	False		,,,				2504	0.002				p.P277P		Atlas-SNP	.											.	WNT4	33	.	0			c.C831T						PASS	.	G		288,4118	158.9+/-191.5	8,272,1923	121.0	102.0	108.0		831	-6.9	0.9	1	dbSNP_126	108	180,8420	82.0+/-144.6	0,180,4120	no	coding-synonymous	WNT4	NM_030761.4		8,452,6043	AA,AG,GG		2.093,6.5365,3.5983		277/352	22446768	468,12538	2203	4300	6503	SO:0001819	synonymous_variant	54361	exon5			GAAGTCGGGGCTA	AL031281	CCDS223.1	1p36.23-p35.1	2013-02-28			ENSG00000162552	ENSG00000162552		"""Wingless-type MMTV integration sites"", ""Endogenous ligands"""	12783	protein-coding gene	gene with protein product		603490				8168088	Standard	NM_030761		Approved	WNT-4	uc001bfs.4	P56705	OTTHUMG00000002894	ENST00000290167.6:c.831C>T	1.37:g.22446768G>A		179.0	0.0	0		204.0	103.0	0.504902	NM_030761	B4DJF9|Q5TZQ0|Q96T81|Q9BXF5|Q9H1J8|Q9UJM2	Silent	SNP	ENST00000290167.6	37	CCDS223.1																																																																																			G|0.968;A|0.032	0.032	strong		0.647	WNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008088.2		
ZNF469	84627	hgsc.bcm.edu	37	16	88504483	88504483	+	Silent	SNP	C	C	G	rs375672779	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88504483C>G	ENST00000437464.1	+	2	10521	c.10521C>G	c.(10519-10521)acC>acG	p.T3507T	ZNF469_ENST00000565624.1_Silent_p.T3535T	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	3507					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						ACCCCGTGACCCACCCGATCA	0.647													C|||	5	0.000998403	0.0038	0.0	5008	,	,		14786	0.0		0.0	False		,,,				2504	0.0				p.T3507T		Atlas-SNP	.											.	ZNF469	121	.	0			c.C10521G						PASS	.	C		6,1378		0,6,686	53.0	61.0	59.0		10521	1.2	0.0	16		59	0,3182		0,0,1591	no	coding-synonymous	ZNF469	NM_001127464.1		0,6,2277	GG,GC,CC		0.0,0.4335,0.1314		3507/3926	88504483	6,4560	692	1591	2283	SO:0001819	synonymous_variant	84627	exon2			CGTGACCCACCCG	AB058761	CCDS45544.1	16q24	2010-08-04				ENSG00000225614		"""Zinc fingers, C2H2-type"""	23216	protein-coding gene	gene with protein product		612078				11347906	Standard	NM_001127464		Approved	KIAA1858	uc002fku.2	Q96JG9		ENST00000437464.1:c.10521C>G	16.37:g.88504483C>G		77.0	0.0	0		81.0	50.0	0.617284	NM_001127464		Silent	SNP	ENST00000437464.1	37	CCDS45544.1																																																																																			.	.	weak		0.647	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
RP1L1	94137	hgsc.bcm.edu	37	8	10464465	10464465	+	Silent	SNP	G	G	A	rs112520779	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10464465G>A	ENST00000382483.3	-	4	7366	c.7143C>T	c.(7141-7143)ctC>ctT	p.L2381L		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	2461					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		CAGTGGGGGCGAGACTTCCGA	0.547													G|||	14	0.00279553	0.0106	0.0	5008	,	,		17836	0.0		0.0	False		,,,				2504	0.0				p.L2381L		Atlas-SNP	.											RP1L1,NS,carcinoma,-2,1	RP1L1	453	1	0			c.C7143T						PASS	.	G		26,3806		0,26,1890	109.0	115.0	113.0		7143	-6.4	0.0	8	dbSNP_132	113	0,8232		0,0,4116	no	coding-synonymous	RP1L1	NM_178857.5		0,26,6006	AA,AG,GG		0.0,0.6785,0.2155		2381/2401	10464465	26,12038	1916	4116	6032	SO:0001819	synonymous_variant	94137	exon4			GGGGGCGAGACTT	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.7143C>T	8.37:g.10464465G>A		52.0	0.0	0		65.0	43.0	0.661538	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	37	CCDS43708.1																																																																																			A|0.002;G|0.998;T|0.000	0.002	strong		0.547	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
MT-ND4	4538	hgsc.bcm.edu	37	M	11959	11959	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:11959A>G	ENST00000361381.2	+	1	1200	c.1200A>G	c.(1198-1200)atA>atG	p.I400M	MT-TR_ENST00000387439.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	400					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						GGACTCAACATACTAGTCACA	0.453																																					p.M400M		Atlas-SNP	.											.	.	.	.	0			c.A1200G						PASS	.																																			SO:0001583	missense	0	exon1			CAACATACTAGTC			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.1200A>G	M.37:g.11959A>G	ENSP00000354961:p.Ile400Met	8.0	0.0	0		9.0	8.0	0.888889	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Silent	SNP	ENST00000361381.2	37																																																																																				.	.	none		0.453	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
ROBO1	6091	hgsc.bcm.edu	37	3	79174619	79174619	+	Silent	SNP	C	C	T	rs139237706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:79174619C>T	ENST00000464233.1	-	3	272	c.159G>A	c.(157-159)tcG>tcA	p.S53S		NM_002941.3	NP_002932.1	Q9Y6N7	ROBO1_HUMAN	roundabout, axon guidance receptor, homolog 1 (Drosophila)	53					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|axon midline choice point recognition (GO:0016199)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|homophilic cell adhesion (GO:0007156)|mammary duct terminal end bud growth (GO:0060763)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|negative regulation of negative chemotaxis (GO:0050925)|nervous system development (GO:0007399)|positive regulation of axonogenesis (GO:0050772)|Roundabout signaling pathway (GO:0035385)	axolemma (GO:0030673)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|identical protein binding (GO:0042802)|LRR domain binding (GO:0030275)			breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(2)|lung(25)|urinary_tract(1)	44		Lung SC(41;0.0257)|Lung NSC(201;0.0439)		LUSC - Lung squamous cell carcinoma(21;0.008)|Epithelial(33;0.00999)|Lung(72;0.0177)|BRCA - Breast invasive adenocarcinoma(55;0.0274)		TATAGCCCAGCGAATTGTCAT	0.488													C|||	6	0.00119808	0.003	0.0014	5008	,	,		17914	0.0		0.0	False		,,,				2504	0.001				p.S53S		Atlas-SNP	.											.	ROBO1	833	.	0			c.G159A						PASS	.	C		11,3935		0,11,1962	139.0	134.0	135.0		159	5.4	1.0	3	dbSNP_134	135	0,8292		0,0,4146	no	coding-synonymous	ROBO1	NM_002941.3		0,11,6108	TT,TC,CC		0.0,0.2788,0.0899		53/1652	79174619	11,12227	1973	4146	6119	SO:0001819	synonymous_variant	6091	exon3			GCCCAGCGAATTG	AF040990	CCDS46872.1, CCDS46872.2, CCDS54610.1, CCDS54611.1	3p12.3	2013-02-11	2001-11-28		ENSG00000169855	ENSG00000169855		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	10249	protein-coding gene	gene with protein product		602430	"""roundabout (axon guidance receptor, Drosophila) homolog 1"""			9458045, 9608531	Standard	NM_002941		Approved	DUTT1, FLJ21882, SAX3	uc003dqe.2	Q9Y6N7	OTTHUMG00000158843	ENST00000464233.1:c.159G>A	3.37:g.79174619C>T		192.0	0.0	0		195.0	94.0	0.482051	NM_002941	B2RXI1|D3DU36|E9PD49|Q1RMC7|Q7Z300|Q9BUS7	Silent	SNP	ENST00000464233.1	37	CCDS54611.1																																																																																			C|0.998;T|0.002	0.002	strong		0.488	ROBO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352610.1	NM_002941	
TGM6	343641	hgsc.bcm.edu	37	20	2411118	2411118	+	Missense_Mutation	SNP	T	T	A	rs142406714	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:2411118T>A	ENST00000202625.2	+	11	1766	c.1705T>A	c.(1705-1707)Tac>Aac	p.Y569N	TGM6_ENST00000381423.1_Missense_Mutation_p.Y569N	NM_198994.2	NP_945345.2	O95932	TGM3L_HUMAN	transglutaminase 6	569					cell death (GO:0008219)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|endometrium(6)|kidney(2)|large_intestine(2)|lung(32)|ovary(4)|prostate(1)|skin(4)	52					L-Glutamine(DB00130)	TACAATATCTTACTCTAAGTA	0.458													T|||	3	0.000599042	0.0023	0.0	5008	,	,		19164	0.0		0.0	False		,,,				2504	0.0				p.Y569N		Atlas-SNP	.											.	TGM6	126	.	0			c.T1705A						PASS	.	T	ASN/TYR	5,4401	9.9+/-24.2	0,5,2198	92.0	87.0	88.0		1705	5.9	1.0	20	dbSNP_134	88	0,8600		0,0,4300	yes	missense	TGM6	NM_198994.2	143	0,5,6498	AA,AT,TT		0.0,0.1135,0.0384	probably-damaging	569/707	2411118	5,13001	2203	4300	6503	SO:0001583	missense	343641	exon11			ATATCTTACTCTA	AF540970	CCDS13025.1, CCDS58761.1	20p13	2010-12-19	2004-07-05	2004-07-07	ENSG00000166948	ENSG00000166948		"""Transglutaminases"""	16255	protein-coding gene	gene with protein product	"""spinocerebellar ataxia 35"""	613900	"""transglutaminase 3-like"""	TGM3L		11390390, 21106500	Standard	NM_198994		Approved	dJ734P14.3, TGY, SCA35	uc002wfy.1	O95932	OTTHUMG00000031692	ENST00000202625.2:c.1705T>A	20.37:g.2411118T>A	ENSP00000202625:p.Tyr569Asn	57.0	0.0	0		70.0	41.0	0.585714	NM_198994	Q5JXU4|Q5JXU5|Q719M2|Q719M3|Q9Y4U8	Missense_Mutation	SNP	ENST00000202625.2	37	CCDS13025.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.069978	0.76301	0.001135	0.0	ENSG00000166948	ENST00000202625;ENST00000381423	T;T	0.71341	-0.56;-0.56	5.88	5.88	0.94601	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.203565	0.43919	D	0.000512	D	0.84428	0.5470	M	0.83384	2.64	0.43846	D	0.996433	D;D	0.89917	1.0;1.0	D;D	0.83275	0.994;0.996	D	0.86612	0.1873	10	0.87932	D	0	-31.5353	12.6797	0.56914	0.0:0.0:0.0:1.0	.	569;569	O95932-2;O95932	.;TGM3L_HUMAN	N	569	ENSP00000202625:Y569N;ENSP00000370831:Y569N	ENSP00000202625:Y569N	Y	+	1	0	TGM6	2359118	1.000000	0.71417	0.998000	0.56505	0.961000	0.63080	4.493000	0.60341	2.242000	0.73789	0.533000	0.62120	TAC	T|1.000;A|0.000	0.000	weak		0.458	TGM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077581.2	NM_198994	
UBR4	23352	hgsc.bcm.edu	37	1	19500830	19500830	+	Missense_Mutation	SNP	T	T	G	rs143098074	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19500830T>G	ENST00000375254.3	-	22	2992	c.2965A>C	c.(2965-2967)Aag>Cag	p.K989Q	UBR4_ENST00000375217.2_Missense_Mutation_p.K989Q|UBR4_ENST00000375226.2_Missense_Mutation_p.K989Q|UBR4_ENST00000375267.2_Missense_Mutation_p.K989Q	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	989					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)		GTTACATTCTTGTTTTCCTTT	0.423													T|||	9	0.00179712	0.0068	0.0	5008	,	,		19353	0.0		0.0	False		,,,				2504	0.0				p.K989Q		Atlas-SNP	.											.	UBR4	415	.	0			c.A2965C						PASS	.	T	GLN/LYS	7,4399	12.9+/-30.5	0,7,2196	155.0	131.0	139.0		2965	5.8	1.0	1	dbSNP_134	139	0,8600		0,0,4300	yes	missense	UBR4	NM_020765.2	53	0,7,6496	GG,GT,TT		0.0,0.1589,0.0538	benign	989/5184	19500830	7,12999	2203	4300	6503	SO:0001583	missense	23352	exon22			CATTCTTGTTTTC	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.2965A>C	1.37:g.19500830T>G	ENSP00000364403:p.Lys989Gln	49.0	0.0	0		68.0	34.0	0.5	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	.	.	.	.	.	.	.	.	.	.	T	16.68	3.189502	0.57909	0.001589	0.0	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000419533	T;T;T;T	0.25912	1.78;1.78;1.78;1.77	5.76	5.76	0.90799	.	0.104877	0.64402	D	0.000006	T	0.21921	0.0528	L	0.36672	1.1	0.80722	D	1	P	0.34522	0.455	B	0.31869	0.137	T	0.02885	-1.1098	10	0.29301	T	0.29	.	15.7251	0.77751	0.0:0.0:0.0:1.0	.	989	Q5T4S7	UBR4_HUMAN	Q	989;989;989;989;205	ENSP00000364403:K989Q;ENSP00000364416:K989Q;ENSP00000364365:K989Q;ENSP00000364374:K989Q	ENSP00000364365:K989Q	K	-	1	0	UBR4	19373417	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.368000	0.79567	2.197000	0.70478	0.533000	0.62120	AAG	T|0.999;G|0.001	0.001	strong		0.423	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
EIF2AK2	5610	hgsc.bcm.edu	37	2	37353464	37353464	+	Silent	SNP	A	A	G	rs2307478	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:37353464A>G	ENST00000233057.4	-	11	1198	c.876T>C	c.(874-876)acT>acC	p.T292T	EIF2AK2_ENST00000395127.2_Silent_p.T292T|EIF2AK2_ENST00000405334.1_Intron	NM_001135651.2	NP_001129123.1	P19525	E2AK2_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 2	292	Interaction with TRAF5.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|defense response to virus (GO:0051607)|endoplasmic reticulum unfolded protein response (GO:0030968)|evasion or tolerance by virus of host immune response (GO:0030683)|innate immune response (GO:0045087)|modulation by virus of host morphology or physiology (GO:0019048)|modulation by virus of host process (GO:0019054)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of translation (GO:0017148)|negative regulation of viral genome replication (GO:0045071)|positive regulation of chemokine production (GO:0032722)|positive regulation of cytokine production (GO:0001819)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of NIK/NF-kappaB signaling (GO:1901224)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of hematopoietic progenitor cell differentiation (GO:1901532)|regulation of hematopoietic stem cell differentiation (GO:1902036)|regulation of hematopoietic stem cell proliferation (GO:1902033)|regulation of NLRP3 inflammasome complex assembly (GO:1900225)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|viral life cycle (GO:0019058)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|eukaryotic translation initiation factor 2alpha kinase activity (GO:0004694)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(7)|ovary(2)|pancreas(1)	22		all_hematologic(82;0.248)				TAATAACGTAAGTCTTTCCGT	0.313													A|||	82	0.0163738	0.0613	0.0014	5008	,	,		17810	0.0		0.0	False		,,,				2504	0.0				p.T292T		Atlas-SNP	.											.	EIF2AK2	54	.	0			c.T876C						PASS	.	A	,,	237,4169	141.1+/-176.5	6,225,1972	95.0	93.0	93.0		876,,876	-2.7	0.0	2	dbSNP_100	93	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous,intron,coding-synonymous	EIF2AK2	NM_001135651.1,NM_001135652.1,NM_002759.2	,,	6,226,6270	GG,GA,AA		0.0116,5.379,1.8302	,,	292/552,,292/552	37353464	238,12766	2203	4299	6502	SO:0001819	synonymous_variant	5610	exon11			AACGTAAGTCTTT	BC057805	CCDS1786.1, CCDS46259.1	2p22-p21	2014-06-12	2005-01-19	2005-01-19	ENSG00000055332	ENSG00000055332			9437	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 83"""	176871	"""protein kinase, interferon-inducible double stranded RNA dependent"""	PRKR		1351683	Standard	NM_001135651		Approved	PKR, EIF2AK1, PPP1R83	uc010fac.3	P19525	OTTHUMG00000100962	ENST00000233057.4:c.876T>C	2.37:g.37353464A>G		196.0	0.0	0		152.0	79.0	0.519737	NM_001135651	A8K3P0|D6W584|E9PC80|Q52M43|Q7Z6F6|Q9UIR4	Silent	SNP	ENST00000233057.4	37	CCDS1786.1																																																																																			A|0.985;G|0.015	0.015	strong		0.313	EIF2AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218571.2	NM_002759	
CMTR1	23070	hgsc.bcm.edu	37	6	37426429	37426429	+	Silent	SNP	T	T	C	rs35608753	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:37426429T>C	ENST00000373451.4	+	9	983	c.819T>C	c.(817-819)ttT>ttC	p.F273F		NM_015050.2	NP_055865.1	Q8N1G2	CMTR1_HUMAN	cap methyltransferase 1	273	RrmJ-type SAM-dependent 2'-O-MTase. {ECO:0000255|PROSITE-ProRule:PRU00945}.				7-methylguanosine mRNA capping (GO:0006370)|cap1 mRNA methylation (GO:0097309)|mRNA methylation (GO:0080009)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	mRNA (nucleoside-2'-O-)-methyltransferase activity (GO:0004483)|nucleic acid binding (GO:0003676)										TTCTGTACTTTGCTGATGTCT	0.527													T|||	46	0.0091853	0.031	0.0072	5008	,	,		19737	0.0		0.0	False		,,,				2504	0.0				p.F273F		Atlas-SNP	.											.	FTSJD2	64	.	0			c.T819C						PASS	.	T		196,4210	122.5+/-159.9	3,190,2010	87.0	77.0	80.0		819	3.5	1.0	6	dbSNP_126	80	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FTSJD2	NM_015050.2		3,191,6309	CC,CT,TT		0.0116,4.4485,1.5147		273/836	37426429	197,12809	2203	4300	6503	SO:0001819	synonymous_variant	23070	exon9			GTACTTTGCTGAT	BC031890	CCDS4835.1	6p21.2	2013-07-23	2013-07-23	2013-07-23	ENSG00000137200	ENSG00000137200	2.1.1.57	"""G patch domain containing"""	21077	protein-coding gene	gene with protein product			"""KIAA0082"", ""FtsJ methyltransferase domain containing 2"""	KIAA0082, FTSJD2		20713356	Standard	NM_015050		Approved	MTr1, ISG95	uc003ons.3	Q8N1G2	OTTHUMG00000014624	ENST00000373451.4:c.819T>C	6.37:g.37426429T>C		99.0	0.0	0		156.0	67.0	0.429487	NM_015050	A8K949|Q14670|Q96FJ9	Silent	SNP	ENST00000373451.4	37	CCDS4835.1																																																																																			T|0.986;C|0.014	0.014	strong		0.527	CMTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040408.1	NM_015050	
ANKRD40	91369	hgsc.bcm.edu	37	17	48774319	48774319	+	Silent	SNP	G	G	A	rs3815378	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48774319G>A	ENST00000285243.6	-	4	1211	c.942C>T	c.(940-942)ccC>ccT	p.P314P	Y_RNA_ENST00000364470.1_RNA|RP11-294J22.6_ENST00000574246.1_RNA	NM_052855.3	NP_443087.1	Q6AI12	ANR40_HUMAN	ankyrin repeat domain 40	314										breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|skin(1)|urinary_tract(1)	11			BRCA - Breast invasive adenocarcinoma(22;2.03e-09)			ACAGAGTATTGGGTAACTTTC	0.438													G|||	215	0.0429313	0.0908	0.0807	5008	,	,		19551	0.0327		0.002	False		,,,				2504	0.0041				p.P314P		Atlas-SNP	.											.	ANKRD40	35	.	0			c.C942T						PASS	.	G		367,4039	187.8+/-214.3	12,343,1848	133.0	128.0	130.0		942	3.4	1.0	17	dbSNP_107	130	13,8587	9.8+/-36.6	0,13,4287	no	coding-synonymous	ANKRD40	NM_052855.3		12,356,6135	AA,AG,GG		0.1512,8.3296,2.9217		314/369	48774319	380,12626	2203	4300	6503	SO:0001819	synonymous_variant	91369	exon4			AGTATTGGGTAAC	BC012978	CCDS11572.1	17q21.33	2013-01-10			ENSG00000154945	ENSG00000154945		"""Ankyrin repeat domain containing"""	28233	protein-coding gene	gene with protein product						12477932	Standard	NM_052855		Approved	MGC15396	uc002iso.3	Q6AI12	OTTHUMG00000162255	ENST00000285243.6:c.942C>T	17.37:g.48774319G>A		123.0	0.0	0		115.0	44.0	0.382609	NM_052855	Q96E32	Silent	SNP	ENST00000285243.6	37	CCDS11572.1																																																																																			G|0.963;A|0.037	0.037	strong		0.438	ANKRD40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368201.2	NM_052855	
FUCA1	2517	hgsc.bcm.edu	37	1	24189740	24189740	+	Silent	SNP	G	G	A	rs541724746		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:24189740G>A	ENST00000374479.3	-	3	553	c.546C>T	c.(544-546)taC>taT	p.Y182Y		NM_000147.4	NP_000138.2	P04066	FUCO_HUMAN	fucosidase, alpha-L- 1, tissue	182					fucose metabolic process (GO:0006004)|glycosaminoglycan catabolic process (GO:0006027)|glycoside catabolic process (GO:0016139)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-L-fucosidase activity (GO:0004560)|fucose binding (GO:0042806)			breast(1)|endometrium(1)|large_intestine(3)|lung(3)	8		Colorectal(325;3.46e-05)|Renal(390;0.000219)|Lung NSC(340;0.000233)|all_lung(284;0.000321)|Ovarian(437;0.00348)|Breast(348;0.00957)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.11e-24)|Colorectal(126;5.69e-08)|COAD - Colon adenocarcinoma(152;3.15e-06)|GBM - Glioblastoma multiforme(114;9.04e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000986)|KIRC - Kidney renal clear cell carcinoma(1967;0.00342)|STAD - Stomach adenocarcinoma(196;0.0128)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.144)		AGAGTGAGTGGTATAGTCCAT	0.358													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17635	0.0		0.0	False		,,,				2504	0.0				p.Y182Y		Atlas-SNP	.											.	FUCA1	24	.	0			c.C546T						PASS	.						94.0	88.0	90.0					1																	24189740		2203	4300	6503	SO:0001819	synonymous_variant	2517	exon3			TGAGTGGTATAGT	BC017338	CCDS244.2	1p34	2012-10-02			ENSG00000179163	ENSG00000179163	3.2.1.51		4006	protein-coding gene	gene with protein product		612280				2803312	Standard	NM_000147		Approved		uc001bie.3	P04066	OTTHUMG00000002965	ENST00000374479.3:c.546C>T	1.37:g.24189740G>A		63.0	0.0	0		74.0	36.0	0.486486	NM_000147	B2RBG3|Q14334|Q14335|Q3LID0|Q8NAC2	Silent	SNP	ENST00000374479.3	37	CCDS244.2																																																																																			.	.	none		0.358	FUCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008259.2	NM_000147	
PCDHB11	56125	hgsc.bcm.edu	37	5	140580958	140580958	+	Silent	SNP	C	C	A	rs74949746	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140580958C>A	ENST00000354757.3	+	1	1611	c.1611C>A	c.(1609-1611)ggC>ggA	p.G537G	PCDHB11_ENST00000536699.1_Silent_p.G172G	NM_018931.2	NP_061754.1	Q9Y5F2	PCDBB_HUMAN	protocadherin beta 11	537	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CAGACCGCGGCTCCCCGGCTT	0.672													C|||	58	0.0115815	0.0431	0.0014	5008	,	,		16231	0.0		0.0	False		,,,				2504	0.0				p.G537G		Atlas-SNP	.											PCDHB11,right_upper_lobe,carcinoma,+2,2	PCDHB11	162	2	0			c.C1611A						PASS	.	C		154,4250	103.4+/-141.9	4,146,2052	38.0	51.0	47.0		1611	-2.2	0.0	5	dbSNP_131	47	0,8598		0,0,4299	no	coding-synonymous	PCDHB11	NM_018931.2		4,146,6351	AA,AC,CC		0.0,3.4968,1.1844		537/798	140580958	154,12848	2202	4299	6501	SO:0001819	synonymous_variant	56125	exon1			CCGCGGCTCCCCG	AF152490	CCDS4253.1	5q31	2010-01-26			ENSG00000197479	ENSG00000197479		"""Cadherins / Protocadherins : Clustered"""	8682	other	protocadherin	"""cadherin ME2"""	606337				10380929	Standard	NM_018931		Approved	PCDH-BETA11, ME2	uc003liy.3	Q9Y5F2	OTTHUMG00000129618	ENST00000354757.3:c.1611C>A	5.37:g.140580958C>A		284.0	0.0	0		433.0	213.0	0.491917	NM_018931	B4DSF7|Q2M223	Silent	SNP	ENST00000354757.3	37	CCDS4253.1																																																																																			C|0.991;A|0.009	0.009	strong		0.672	PCDHB11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251813.1	NM_018931	
RREB1	6239	hgsc.bcm.edu	37	6	7231280	7231280	+	Missense_Mutation	SNP	T	T	C	rs115093903	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:7231280T>C	ENST00000349384.6	+	10	3262	c.2948T>C	c.(2947-2949)tTg>tCg	p.L983S	RREB1_ENST00000379933.3_Missense_Mutation_p.L983S|RREB1_ENST00000379938.2_Missense_Mutation_p.L983S|RREB1_ENST00000334984.6_Missense_Mutation_p.L983S	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	983	Pro-rich.				multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				CCTGTAACTTTGGGGCCCAGC	0.692													T|||	74	0.0147764	0.0545	0.0029	5008	,	,		12856	0.0		0.0	False		,,,				2504	0.0				p.L983S		Atlas-SNP	.											.	RREB1	242	.	0			c.T2948C						PASS	.	T	SER/LEU,SER/LEU,SER/LEU,SER/LEU	180,4222		4,172,2025	18.0	21.0	20.0		2948,2948,2948,2948	3.3	0.0	6	dbSNP_132	20	0,8600		0,0,4300	no	missense,missense,missense,missense	RREB1	NM_001003698.3,NM_001003699.3,NM_001003700.1,NM_001168344.1	145,145,145,145	4,172,6325	CC,CT,TT		0.0,4.0891,1.3844	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	983/1688,983/1743,983/1477,983/1688	7231280	180,12822	2201	4300	6501	SO:0001583	missense	6239	exon10			TAACTTTGGGGCC	U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"""Zinc fingers, C2H2-type"""	10449	protein-coding gene	gene with protein product	"""hindsight homolog (drosophila)"""	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.2948T>C	6.37:g.7231280T>C	ENSP00000305560:p.Leu983Ser	85.0	0.0	0		74.0	36.0	0.486486	NM_001003700	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	37	CCDS34336.1	18	0.008241758241758242	18	0.036585365853658534	0	0.0	0	0.0	0	0.0	T	12.76	2.034987	0.35893	0.040891	0.0	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384;ENST00000334984	T;T;T;T	0.11495	2.89;2.85;2.89;2.77	5.74	3.35	0.38373	.	0.784404	0.10919	N	0.619695	T	0.03095	0.0091	L	0.43152	1.355	0.09310	N	1	B;B;B	0.32245	0.277;0.361;0.038	B;B;B	0.32289	0.143;0.107;0.037	T	0.46105	-0.9215	10	0.22109	T	0.4	-0.1912	8.4336	0.32773	0.0:0.1663:0.0:0.8337	.	983;983;983	Q92766-3;Q92766;Q92766-2	.;RREB1_HUMAN;.	S	983	ENSP00000369265:L983S;ENSP00000369270:L983S;ENSP00000305560:L983S;ENSP00000335574:L983S	ENSP00000335574:L983S	L	+	2	0	RREB1	7176279	0.264000	0.24093	0.003000	0.11579	0.012000	0.07955	1.900000	0.39828	0.442000	0.26555	0.533000	0.62120	TTG	T|0.989;C|0.011	0.011	strong		0.692	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1		
ARMC12	221481	hgsc.bcm.edu	37	6	35705059	35705059	+	Intron	SNP	G	G	A	rs56183341	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:35705059G>A	ENST00000373866.3	+	1	185				ARMC12_ENST00000373869.3_Intron|RP3-510O8.4_ENST00000452048.1_RNA|ARMC12_ENST00000288065.2_Silent_p.P58P			Q5T9G4	ARM12_HUMAN	armadillo repeat containing 12							nucleus (GO:0005634)											GTGAGTGTCCGGGCCCTGGGG	0.612											OREG0017379	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	43	0.00858626	0.0295	0.0014	5008	,	,		19230	0.0		0.0	False		,,,				2504	0.0031				p.P58P		Atlas-SNP	.											.	.	.	.	0			c.G174A						PASS	.	G		106,4300	81.9+/-120.4	1,104,2098	68.0	64.0	65.0		174	-0.4	0.0	6	dbSNP_129	65	0,8600		0,0,4300	no	coding-synonymous	C6orf81	NM_145028.3		1,104,6398	AA,AG,GG		0.0,2.4058,0.815		58/368	35705059	106,12900	2203	4300	6503	SO:0001627	intron_variant	221481	exon1			GTGTCCGGGCCCT	AK058119	CCDS4809.1, CCDS69093.1, CCDS69094.1	6p21.31	2013-02-14	2011-12-14	2011-12-14	ENSG00000157343	ENSG00000157343		"""Armadillo repeat containing"""	21099	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 81"""	C6orf81			Standard	XM_005248920		Approved	FLJ25390	uc003ola.3	Q5T9G4	OTTHUMG00000014577	ENST00000373866.3:c.163+11G>A	6.37:g.35705059G>A		116.0	0.0	0	857	116.0	56.0	0.482759	NM_145028	Q8NEB2|Q96LL8	Silent	SNP	ENST00000373866.3	37																																																																																				G|0.992;A|0.008	0.008	strong		0.612	ARMC12-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000040311.2	NM_145028	
GRIN3B	116444	hgsc.bcm.edu	37	19	1008704	1008704	+	Missense_Mutation	SNP	G	G	A	rs61744375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1008704G>A	ENST00000234389.3	+	7	2573	c.2554G>A	c.(2554-2556)Gag>Aag	p.E852K		NM_138690.1	NP_619635.1	O60391	NMD3B_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3B	852					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|protein insertion into membrane (GO:0051205)|regulation of calcium ion transport (GO:0051924)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|neurotransmitter receptor activity (GO:0030594)			breast(1)|kidney(1)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	11		Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;0.000226)|all_lung(49;0.000353)|Breast(49;0.00066)		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)	Acamprosate(DB00659)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Glycine(DB00145)|Halothane(DB01159)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CTCGCTGGGCGAGCACGCCTT	0.697													g|||	151	0.0301518	0.1059	0.0144	5008	,	,		11084	0.0		0.001	False		,,,				2504	0.0				p.E852K		Atlas-SNP	.											.	GRIN3B	46	.	0			c.G2554A						PASS	.	G	LYS/GLU	422,3978	195.3+/-220.0	23,376,1801	35.0	30.0	31.0		2554	3.8	1.0	19	dbSNP_129	31	0,8596		0,0,4298	yes	missense	GRIN3B	NM_138690.1	56	23,376,6099	AA,AG,GG		0.0,9.5909,3.2472	probably-damaging	852/1044	1008704	422,12574	2200	4298	6498	SO:0001583	missense	116444	exon7			CTGGGCGAGCACG		CCDS32861.1	19p13.3	2014-05-06			ENSG00000116032	ENSG00000116032		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16768	protein-coding gene	gene with protein product		606651					Standard	XM_003403700		Approved	GluN3B	uc002lqo.1	O60391	OTTHUMG00000181904	ENST00000234389.3:c.2554G>A	19.37:g.1008704G>A	ENSP00000234389:p.Glu852Lys	21.0	0.0	0		38.0	26.0	0.684211	NM_138690	Q5EAK7|Q7RTW9	Missense_Mutation	SNP	ENST00000234389.3	37	CCDS32861.1	58	0.026556776556776556	52	0.10569105691056911	6	0.016574585635359115	0	0.0	0	0.0	G	31	5.090219	0.94149	0.095909	0.0	ENSG00000116032	ENST00000234389	T	0.24350	1.86	3.78	3.78	0.43462	.	0.000000	0.85682	U	0.000000	T	0.01222	0.0040	M	0.68317	2.08	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.00609	-1.1646	10	0.87932	D	0	.	14.2074	0.65744	0.0:0.0:1.0:0.0	rs61744375	852	O60391	NMD3B_HUMAN	K	852	ENSP00000234389:E852K	ENSP00000234389:E852K	E	+	1	0	GRIN3B	959704	1.000000	0.71417	0.982000	0.44146	0.976000	0.68499	9.163000	0.94750	1.661000	0.50771	0.462000	0.41574	GAG	G|0.965;A|0.035	0.035	strong		0.697	GRIN3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103923.2		
RBM15	64783	hgsc.bcm.edu	37	1	110884493	110884493	+	Silent	SNP	T	T	C	rs61745292	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:110884493T>C	ENST00000369784.3	+	1	3366	c.2466T>C	c.(2464-2466)acT>acC	p.T822T	RBM15_ENST00000487146.2_Silent_p.T822T|RBM15_ENST00000602849.1_Silent_p.T822T|RP5-1074L1.1_ENST00000449169.1_RNA	NM_022768.4	NP_073605.4	Q96T37	RBM15_HUMAN	RNA binding motif protein 15	822	SPOC. {ECO:0000255|PROSITE- ProRule:PRU00249}.				negative regulation of myeloid cell differentiation (GO:0045638)|patterning of blood vessels (GO:0001569)|placenta blood vessel development (GO:0060674)|positive regulation of transcription of Notch receptor target (GO:0007221)|spleen development (GO:0048536)|ventricular septum morphogenesis (GO:0060412)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			ovary(3)	3		all_cancers(81;2.89e-06)|all_epithelial(167;2.96e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)|Breast(1374;0.0634)		BRCA - Breast invasive adenocarcinoma(282;0.000224)|Epithelial(280;0.000476)|Kidney(133;0.000539)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|all cancers(265;0.00144)|Lung(183;0.0238)|Colorectal(144;0.103)|LUSC - Lung squamous cell carcinoma(189;0.135)		AGGGTTCAACTGGAGGCAAAG	0.517			T	MKL1	acute megakaryocytic leukemia								T|||	146	0.0291534	0.1051	0.0086	5008	,	,		19970	0.0		0.001	False		,,,				2504	0.0				p.T822T		Atlas-SNP	.		Dom	yes		1	1p13	64783	RNA binding motif protein 15		L	.	RBM15	93	.	0			c.T2466C						PASS	.	T	,	324,4082	171.2+/-201.5	12,300,1891	79.0	77.0	78.0		2466,2466	-0.2	1.0	1	dbSNP_129	78	9,8591	5.7+/-21.5	0,9,4291	no	coding-synonymous,coding-synonymous	RBM15	NM_001201545.1,NM_022768.4	,	12,309,6182	CC,CT,TT		0.1047,7.3536,2.5604	,	822/970,822/978	110884493	333,12673	2203	4300	6503	SO:0001819	synonymous_variant	64783	exon1			TTCAACTGGAGGC	AF368063	CCDS822.1, CCDS59198.1	1p13	2013-02-12			ENSG00000162775	ENSG00000162775		"""RNA binding motif (RRM) containing"""	14959	protein-coding gene	gene with protein product	"""one twenty-two"""	606077				11431691, 11344311	Standard	NM_001201545		Approved	OTT, OTT1	uc001dzl.1	Q96T37	OTTHUMG00000011284	ENST00000369784.3:c.2466T>C	1.37:g.110884493T>C		120.0	0.0	0		140.0	60.0	0.428571	NM_022768	A1A693|Q3ZB86|Q4V760|Q5D058|Q5T613|Q86VW9|Q96PE4|Q96SC5|Q96SC6|Q96SC9|Q96SD0|Q96T38|Q9BRA5|Q9H6R8|Q9H9Y0	Silent	SNP	ENST00000369784.3	37	CCDS822.1																																																																																			T|0.974;C|0.026	0.026	strong		0.517	RBM15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000031114.2	NM_022768	
C2CD4D	100191040	hgsc.bcm.edu	37	1	151810486	151810486	+	Missense_Mutation	SNP	G	G	A	rs188475396	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:151810486G>A	ENST00000454109.1	-	2	1565	c.980C>T	c.(979-981)aCg>aTg	p.T327M		NM_001136003.1	NP_001129475.1	B7Z1M9	C2D4D_HUMAN	C2 calcium-dependent domain containing 4D	327										skin(1)	1						AATGAGGGGCGTCTCGCACTC	0.721													G|||	47	0.00938498	0.0348	0.0014	5008	,	,		11347	0.0		0.0	False		,,,				2504	0.0				p.T327M		Atlas-SNP	.											.	C2CD4D	3	.	0			c.C980T						PASS	.	G	MET/THR	38,1346		0,38,654	27.0	35.0	33.0		980	1.5	1.0	1		33	0,3182		0,0,1591	yes	missense	C2CD4D	NM_001136003.1	81	0,38,2245	AA,AG,GG		0.0,2.7457,0.8322	probably-damaging	327/354	151810486	38,4528	692	1591	2283	SO:0001583	missense	100191040	exon2			AGGGGCGTCTCGC	BC171843	CCDS44224.1	1q21.3	2012-07-02			ENSG00000225556	ENSG00000225556			37210	protein-coding gene	gene with protein product	"""family with sequence similarity 148, member D"""						Standard	NM_001136003		Approved	FAM148D	uc010pdq.1	B7Z1M9	OTTHUMG00000167218	ENST00000454109.1:c.980C>T	1.37:g.151810486G>A	ENSP00000389554:p.Thr327Met	97.0	0.0	0		114.0	53.0	0.464912	NM_001136003	B2RXG8	Missense_Mutation	SNP	ENST00000454109.1	37	CCDS44224.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	G	14.96	2.692350	0.48202	0.027457	0.0	ENSG00000225556	ENST00000454109	T	0.39592	1.07	3.44	1.53	0.23141	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	.	.	.	.	T	0.07098	0.0180	N	0.08118	0	0.25420	N	0.988275	B	0.22211	0.066	B	0.09377	0.004	T	0.32561	-0.9902	9	0.38643	T	0.18	.	5.4754	0.16692	0.377:0.0:0.623:0.0	.	327	B7Z1M9	C2D4D_HUMAN	M	327	ENSP00000389554:T327M	ENSP00000389554:T327M	T	-	2	0	C2CD4D	150077110	0.981000	0.34729	0.986000	0.45419	0.885000	0.51271	2.379000	0.44318	0.179000	0.19938	0.462000	0.41574	ACG	G|0.994;A|0.006	0.006	strong		0.721	C2CD4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393778.1	NM_001136003	
CFAP61	26074	hgsc.bcm.edu	37	20	20340872	20340872	+	Missense_Mutation	SNP	A	A	G	rs75487354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:20340872A>G	ENST00000245957.5	+	27	3608	c.3532A>G	c.(3532-3534)Ata>Gta	p.I1178V	C20orf26_ENST00000377309.2_3'UTR	NM_015585.3	NP_056400.3	Q8NHU2	CT026_HUMAN		1178										NS(2)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(42)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	77				READ - Rectum adenocarcinoma(2;0.171)		TCTTCCTTCCATAGAGCAGTT	0.418											OREG0025807	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	a|||	68	0.0135783	0.0507	0.0014	5008	,	,		18359	0.0		0.0	False		,,,				2504	0.0				p.I1178V		Atlas-SNP	.											.	C20orf26	188	.	0			c.A3532G						PASS	.		VAL/ILE	217,4189	131.4+/-167.9	6,205,1992	144.0	155.0	151.0		3532	0.1	0.7	20	dbSNP_131	151	5,8595	3.7+/-12.6	0,5,4295	yes	missense	C20orf26	NM_015585.3	29	6,210,6287	GG,GA,AA		0.0581,4.9251,1.7069	benign	1178/1238	20340872	222,12784	2203	4300	6503	SO:0001583	missense	26074	exon27			CCTTCCATAGAGC																												ENST00000245957.5:c.3532A>G	20.37:g.20340872A>G	ENSP00000245957:p.Ile1178Val	63.0	0.0	0	740	62.0	29.0	0.467742	NM_015585	A6NHA1|Q5JXV4|Q5TE18|Q8N5R9|Q96M59|Q9BQL2|Q9H127|Q9H128|Q9NQH4|Q9UFV8|Q9Y4V7	Missense_Mutation	SNP	ENST00000245957.5	37	CCDS33447.1	17	0.007783882783882784	17	0.034552845528455285	0	0.0	0	0.0	0	0.0	a	7.203	0.593934	0.13875	0.049251	5.81E-4	ENSG00000089101	ENST00000343997;ENST00000389655;ENST00000245957	T	0.09255	3.0	5.09	0.0811	0.14423	.	0.335985	0.22190	N	0.063396	T	0.00695	0.0023	N	0.19112	0.55	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.48043	-0.9069	10	0.17369	T	0.5	.	2.2354	0.04007	0.5253:0.1361:0.0764:0.2623	.	1178	Q8NHU2	CT026_HUMAN	V	1118;1144;1178	ENSP00000245957:I1178V	ENSP00000245957:I1178V	I	+	1	0	C20orf26	20288872	0.027000	0.19231	0.727000	0.30756	0.085000	0.17905	-0.093000	0.11111	0.028000	0.15324	0.441000	0.28932	ATA	A|0.984;G|0.016	0.016	strong		0.418	C20orf26-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078228.3		
ABCC5	10057	hgsc.bcm.edu	37	3	183696387	183696387	+	Silent	SNP	G	G	A	rs1053386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:183696387G>A	ENST00000334444.6	-	9	1440	c.1200C>T	c.(1198-1200)agC>agT	p.S400S	ABCC5_ENST00000265586.6_Silent_p.S400S|ABCC5_ENST00000492216.1_5'UTR	NM_005688.2	NP_005679.2	O15440	MRP5_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 5	400	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.			S -> G (in Ref. 1; AAD04169). {ECO:0000305}.	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)			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)	CCACAGTGATGCTCTGGAAGT	0.488													G|||	455	0.0908546	0.3321	0.0216	5008	,	,		19202	0.0		0.001	False		,,,				2504	0.0				p.S400S		Atlas-SNP	.											.	ABCC5	142	.	0			c.C1200T						PASS	.	G		1053,3073		142,769,1152	91.0	108.0	103.0		1200	2.9	1.0	3	dbSNP_86	103	6,8404		0,6,4199	no	coding-synonymous	ABCC5	NM_005688.2		142,775,5351	AA,AG,GG		0.0713,25.5211,8.4477		400/1438	183696387	1059,11477	2063	4205	6268	SO:0001819	synonymous_variant	10057	exon9			AGTGATGCTCTGG	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.1200C>T	3.37:g.183696387G>A		46.0	0.0	0		49.0	49.0	1	NM_005688	B9EIQ2|O14517|Q29ZA9|Q29ZB1|Q86UX3|Q86W30|Q9UN85|Q9UNP5|Q9UQC3	Silent	SNP	ENST00000334444.6	37	CCDS43176.1																																																																																			G|0.913;A|0.087	0.087	strong		0.488	ABCC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346350.1	NM_005688	
FCGBP	8857	hgsc.bcm.edu	37	19	40399508	40399508	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40399508C>T	ENST00000221347.6	-	13	6194	c.6187G>A	c.(6187-6189)Ggc>Agc	p.G2063S		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	2063						extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GGCTGGCAGCCGTGCTGGCCG	0.657																																					p.G2063S		Atlas-SNP	.											FCGBP,NS,carcinoma,0,1	FCGBP	416	1	0			c.G6187A						scavenged	.						1.0	1.0	1.0					19																	40399508		183	426	609	SO:0001583	missense	8857	exon13			GGCAGCCGTGCTG	D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.6187G>A	19.37:g.40399508C>T	ENSP00000221347:p.Gly2063Ser	141.0	0.0	0		138.0	28.0	0.202899	NM_003890	O95784	Missense_Mutation	SNP	ENST00000221347.6	37	CCDS12546.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.485186	0.44147	.	.	ENSG00000090920	ENST00000221347	T	0.05025	3.51	3.01	3.01	0.34805	von Willebrand factor, type D domain (1);	.	.	.	.	T	0.20170	0.0485	M	0.77103	2.36	0.31064	N	0.713759	D	0.76494	0.999	D	0.66196	0.942	T	0.07868	-1.0750	9	0.14656	T	0.56	.	12.9123	0.58187	0.0:1.0:0.0:0.0	.	2063	Q9Y6R7	FCGBP_HUMAN	S	2063	ENSP00000221347:G2063S	ENSP00000221347:G2063S	G	-	1	0	FCGBP	45091348	0.935000	0.31712	0.871000	0.34182	0.831000	0.47069	-0.229000	0.09098	1.536000	0.49237	0.298000	0.19748	GGC	.	.	weak		0.657	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462507.1	NM_003890	
PTGFRN	5738	hgsc.bcm.edu	37	1	117484581	117484581	+	Silent	SNP	C	C	T	rs77895792	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:117484581C>T	ENST00000393203.2	+	2	441	c.294C>T	c.(292-294)gcC>gcT	p.A98A		NM_020440.2	NP_065173.2	Q9P2B2	FPRP_HUMAN	prostaglandin F2 receptor inhibitor	98	Ig-like C2-type 1.				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)		GGCGGACTGCCAACGACGCCG	0.592													C|||	23	0.00459265	0.0166	0.0014	5008	,	,		17326	0.0		0.0	False		,,,				2504	0.0				p.A98A		Atlas-SNP	.											.	PTGFRN	91	.	0			c.C294T						PASS	.	C		46,4360	46.7+/-81.2	0,46,2157	85.0	79.0	81.0		294	4.2	1.0	1	dbSNP_131	81	0,8600		0,0,4300	no	coding-synonymous	PTGFRN	NM_020440.2		0,46,6457	TT,TC,CC		0.0,1.044,0.3537		98/880	117484581	46,12960	2203	4300	6503	SO:0001819	synonymous_variant	5738	exon2			GACTGCCAACGAC	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.294C>T	1.37:g.117484581C>T		205.0	0.0	0		199.0	100.0	0.502513	NM_020440	Q5VVU9|Q8N2K6	Silent	SNP	ENST00000393203.2	37	CCDS890.1																																																																																			C|0.995;T|0.005	0.005	strong		0.592	PTGFRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033271.1	NM_020440	
SLC12A9	56996	hgsc.bcm.edu	37	7	100456506	100456506	+	Silent	SNP	C	C	T	rs78261122	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100456506C>T	ENST00000354161.3	+	6	932	c.807C>T	c.(805-807)agC>agT	p.S269S	SLC12A9_ENST00000540482.1_Silent_p.S269S|SLC12A9_ENST00000428758.1_Silent_p.S269S|SLC12A9_ENST00000275729.3_Silent_p.S180S|SLC12A9_ENST00000415287.1_Silent_p.S180S	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9	269				S -> N (in Ref. 1; AAF88060). {ECO:0000305}.	chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation:chloride symporter activity (GO:0015377)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(20)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	41	Lung NSC(181;0.041)|all_lung(186;0.0581)					ATTTTGCCAGCGTCTTTGCTG	0.587													C|||	32	0.00638978	0.0242	0.0	5008	,	,		19182	0.0		0.0	False		,,,				2504	0.0				p.S269S		Atlas-SNP	.											.	SLC12A9	81	.	0			c.C807T						PASS	.	C		102,4304	80.9+/-119.3	3,96,2104	99.0	77.0	84.0		807	-2.4	1.0	7	dbSNP_132	84	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	SLC12A9	NM_020246.2		3,99,6401	TT,TC,CC		0.0349,2.315,0.8073		269/915	100456506	105,12901	2203	4300	6503	SO:0001819	synonymous_variant	56996	exon6			TGCCAGCGTCTTT	AF284422	CCDS5707.1, CCDS59068.1, CCDS59069.1	7q22	2013-07-18	2013-07-18		ENSG00000146828	ENSG00000146828		"""Solute carriers"""	17435	protein-coding gene	gene with protein product	"""cation-chloride cotransporter-interacting protein"""					10871601, 11239002	Standard	NM_020246		Approved	CIP1	uc003uwp.4	Q9BXP2	OTTHUMG00000156045	ENST00000354161.3:c.807C>T	7.37:g.100456506C>T		148.0	0.0	0		196.0	90.0	0.459184	NM_001267812	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Silent	SNP	ENST00000354161.3	37	CCDS5707.1																																																																																			C|0.994;T|0.006	0.006	strong		0.587	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246	
ECE2	9718	hgsc.bcm.edu	37	3	184005719	184005719	+	Missense_Mutation	SNP	G	G	A	rs35875049	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184005719G>A	ENST00000402825.3	+	11	1712	c.1712G>A	c.(1711-1713)cGg>cAg	p.R571Q	ECE2_ENST00000404464.3_Missense_Mutation_p.R453Q|ECE2_ENST00000357474.5_Missense_Mutation_p.R499Q|EIF2B5_ENST00000444495.1_Intron|ECE2_ENST00000359140.4_Missense_Mutation_p.R424Q	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2	571	Endothelin-converting enzyme 2 region.		R -> Q (in dbSNP:rs35875049).		brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|cell-cell signaling (GO:0007267)|heart development (GO:0007507)|peptide hormone processing (GO:0016486)	cytoplasmic vesicle membrane (GO:0030659)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|methyltransferase activity (GO:0008168)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(13)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(4)	49	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			ACGTTTGACCGGCAAAGCAAA	0.483													G|||	185	0.0369409	0.1346	0.0101	5008	,	,		19271	0.0		0.0	False		,,,				2504	0.0				p.R571Q		Atlas-SNP	.											ECE2_ENST00000402825,colon,carcinoma,0,3	ECE2	303	3	0			c.G1712A						scavenged	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	421,3985	206.5+/-228.1	19,383,1801	78.0	70.0	73.0		1271,1496,1358,1712	4.1	1.0	3	dbSNP_126	73	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense,missense	ECE2	NM_001037324.2,NM_001100120.1,NM_001100121.1,NM_014693.3	43,43,43,43	19,386,6098	AA,AG,GG		0.0349,9.5552,3.26	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	424/737,499/812,453/766,571/884	184005719	424,12582	2203	4300	6503	SO:0001583	missense	9718	exon11			TTGACCGGCAAAG	AF428263	CCDS3255.1, CCDS33899.1, CCDS3256.2, CCDS43179.1, CCDS46969.1	3q27.1	2007-07-26			ENSG00000145194	ENSG00000145194			13275	protein-coding gene	gene with protein product		610145				11718899	Standard	NM_032331		Approved	KIAA0604, MGC2408	uc003fni.4	O60344	OTTHUMG00000150551	ENST00000402825.3:c.1712G>A	3.37:g.184005719G>A	ENSP00000384223:p.Arg571Gln	65.0	1.0	0.0153846		64.0	30.0	0.46875	NM_014693	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Missense_Mutation	SNP	ENST00000402825.3	37	CCDS3256.2	76	0.0347985347985348	73	0.1483739837398374	3	0.008287292817679558	0	0.0	0	0.0	G	10.80	1.452917	0.26161	0.095552	3.49E-4	ENSG00000145194	ENST00000402825;ENST00000359140;ENST00000404464;ENST00000357474;ENST00000430587	T;T;T;T;T	0.73897	-0.79;-0.79;-0.79;-0.79;-0.79	4.95	4.07	0.47477	Peptidase M13 (1);Metallopeptidase, catalytic domain (1);	0.167177	0.42682	N	0.000677	T	0.00300	0.0009	N	0.04203	-0.255	0.31828	P	0.62512	B;B;B;B;B;B;B	0.32829	0.028;0.134;0.386;0.009;0.334;0.11;0.307	B;B;B;B;B;B;B	0.26416	0.028;0.041;0.064;0.003;0.038;0.024;0.069	T	0.08330	-1.0727	9	0.18276	T	0.48	-16.4724	8.5975	0.33725	0.1774:0.0:0.8226:0.0	rs35875049	173;424;442;453;499;424;571	B4DHU4;B4DKF3;B4DF19;O60344-2;O60344-5;O60344-3;O60344	.;.;.;.;.;.;ECE2_HUMAN	Q	571;424;453;499;445	ENSP00000384223:R571Q;ENSP00000352052:R424Q;ENSP00000385846:R453Q;ENSP00000350066:R499Q;ENSP00000398444:R445Q	ENSP00000350066:R499Q	R	+	2	0	ECE2	185488413	0.996000	0.38824	1.000000	0.80357	0.786000	0.44442	2.550000	0.45811	1.078000	0.41014	-0.140000	0.14226	CGG	G|0.967;A|0.033	0.033	strong		0.483	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3	NM_014693	
ANKRD13B	124930	hgsc.bcm.edu	37	17	27939427	27939427	+	Silent	SNP	G	G	C	rs147156385	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:27939427G>C	ENST00000394859.3	+	12	1420	c.1266G>C	c.(1264-1266)ccG>ccC	p.P422P	RP11-68I3.2_ENST00000581474.1_RNA	NM_152345.4	NP_689558.4	Q86YJ7	AN13B_HUMAN	ankyrin repeat domain 13B	422						endosome (GO:0005768)|plasma membrane (GO:0005886)				cervix(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(1)|skin(2)	16						CAGAAATCCCGATCTTCCACA	0.637													G|||	9	0.00179712	0.0068	0.0	5008	,	,		12004	0.0		0.0	False		,,,				2504	0.0				p.P422P		Atlas-SNP	.											ANKRD13B,NS,carcinoma,0,1	ANKRD13B	39	1	0			c.G1266C						PASS	.	G		31,4373		0,31,2171	45.0	45.0	45.0		1266	-0.6	1.0	17	dbSNP_134	45	2,8596		0,2,4297	no	coding-synonymous	ANKRD13B	NM_152345.4		0,33,6468	CC,CG,GG		0.0233,0.7039,0.2538		422/627	27939427	33,12969	2202	4299	6501	SO:0001819	synonymous_variant	124930	exon12			AATCCCGATCTTC	AK092673	CCDS11251.1	17q11.2	2013-01-10			ENSG00000198720	ENSG00000198720		"""Ankyrin repeat domain containing"""	26363	protein-coding gene	gene with protein product		615124					Standard	NM_152345		Approved	FLJ25555	uc002hei.3	Q86YJ7	OTTHUMG00000132731	ENST00000394859.3:c.1266G>C	17.37:g.27939427G>C		249.0	1.0	0.00401606		213.0	104.0	0.488263	NM_152345	Q8N7S9	Silent	SNP	ENST00000394859.3	37	CCDS11251.1																																																																																			G|0.998;C|0.002	0.002	strong		0.637	ANKRD13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256077.1	NM_152345	
MT-ND4	4538	hgsc.bcm.edu	37	M	11887	11887	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:11887G>A	ENST00000361381.2	+	1	1128	c.1128G>A	c.(1126-1128)ctG>ctA	p.L376L	MT-TR_ENST00000387439.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	376					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						ATTAACCTACTGGGAGAACTC	0.458																																					p.L376L		Atlas-SNP	.											.	.	.	.	0			c.G1128A						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			CCTACTGGGAGAA			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.1128G>A	M.37:g.11887G>A		6.0	0.0	0		12.0	12.0	1	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Silent	SNP	ENST00000361381.2	37																																																																																				.	.	none		0.458	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
PCDHA7	56141	hgsc.bcm.edu	37	5	140216125	140216125	+	Silent	SNP	G	G	A	rs61730621	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140216125G>A	ENST00000525929.1	+	1	2157	c.2157G>A	c.(2155-2157)acG>acA	p.T719T	PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA7_ENST00000378125.3_Silent_p.T719T|PCDHA6_ENST00000527624.1_Intron	NM_018910.2	NP_061733.1	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7	719					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|biliary_tract(1)|breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCTGTACACGGCGTTGCGGT	0.612													.|||	74	0.0147764	0.0552	0.0014	5008	,	,		18171	0.0		0.0	False		,,,				2504	0.0				p.T719T	NSCLC(160;258 2013 5070 22440 28951)	Atlas-SNP	.											.	PCDHA7	367	.	0			c.G2157A						PASS	.	G	,,,,,,,,,	237,4169	140.8+/-176.2	15,207,1981	103.0	87.0	92.0		,,,,,,2157,,,2157	-3.3	0.4	5	dbSNP_129	92	1,8599	1.2+/-3.3	0,1,4299	no	intron,intron,intron,intron,intron,intron,coding-synonymous,intron,intron,coding-synonymous	PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_031411.1,NM_031849.1,NM_031852.1	,,,,,,,,,	15,208,6280	AA,AG,GG		0.0116,5.379,1.8299	,,,,,,,,,	,,,,,,719/938,,,719/790	140216125	238,12768	2203	4300	6503	SO:0001819	synonymous_variant	56141	exon1			GTACACGGCGTTG	AF152485	CCDS54918.1	5q31	2010-11-26				ENSG00000204963		"""Cadherins / Protocadherins : Clustered"""	8673	other	complex locus constituent	"""KIAA0345-like 7"", ""ortholog to mouse CNR4"""	606313		CNRS4		10380929, 10662547	Standard	NM_018910		Approved	CNR4, CRNR4		Q9UN72		ENST00000525929.1:c.2157G>A	5.37:g.140216125G>A		302.0	1.0	0.00331126		338.0	183.0	0.54142	NM_031852	O75282	Silent	SNP	ENST00000525929.1	37	CCDS54918.1																																																																																			G|0.982;A|0.018	0.018	strong		0.612	PCDHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372887.2	NM_018910	
NOD2	64127	hgsc.bcm.edu	37	16	50746191	50746191	+	Missense_Mutation	SNP	G	G	A	rs5743279	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:50746191G>A	ENST00000300589.2	+	4	2474	c.2369G>A	c.(2368-2370)cGg>cAg	p.R790Q	RP11-327F22.6_ENST00000602304.1_RNA	NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	790			R -> Q (in dbSNP:rs5743279).		activation of MAPK activity (GO:0000187)|activation of MAPK activity involved in innate immune response (GO:0035419)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|cytokine production involved in immune response (GO:0002367)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|detection of muramyl dipeptide (GO:0032498)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|macrophage inflammatory protein-1 alpha production (GO:0071608)|maintenance of gastrointestinal epithelium (GO:0030277)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-18 production (GO:0032701)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell mediated immunity (GO:0002710)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of tumor necrosis factor production (GO:0032720)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of B cell activation (GO:0050871)|positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria (GO:0006965)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell cytokine production (GO:0002732)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gamma-delta T cell activation (GO:0046645)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of prostaglandin-E synthase activity (GO:2000363)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type 2 immune response (GO:0002830)|protein oligomerization (GO:0051259)|regulation of inflammatory response (GO:0050727)|regulation of neutrophil chemotaxis (GO:0090022)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to muramyl dipeptide (GO:0032495)|response to nutrient (GO:0007584)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|enzyme binding (GO:0019899)|muramyl dipeptide binding (GO:0032500)|peptidoglycan binding (GO:0042834)|protein kinase binding (GO:0019901)	p.R790L(1)		cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52		all_cancers(37;0.0156)				CAGCACCTCCGGCGGCCCGTG	0.607													G|||	51	0.0101837	0.0371	0.0029	5008	,	,		21469	0.0		0.0	False		,,,				2504	0.0				p.R790Q		Atlas-SNP	.											NOD2,colon,carcinoma,+1,2	NOD2	118	2	1	Substitution - Missense(1)	lung(1)	c.G2369A						PASS	.	G	GLN/ARG	149,4247	101.2+/-139.8	2,145,2051	95.0	88.0	90.0		2369	-0.2	1.0	16	dbSNP_114	90	1,8599	1.2+/-3.3	0,1,4299	yes	missense	NOD2	NM_022162.1	43	2,146,6350	AA,AG,GG		0.0116,3.3894,1.1542	benign	790/1041	50746191	150,12846	2198	4300	6498	SO:0001583	missense	64127	exon4			ACCTCCGGCGGCC	AF178930	CCDS10746.1	16q12	2014-09-17	2006-12-08	2006-12-08	ENSG00000167207	ENSG00000167207		"""Nucleotide-binding domain and leucine rich repeat containing"""	5331	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 2"", ""NOD-like receptor C2"", ""NLR family, CARD domain containing 2"""	605956	"""caspase recruitment domain family, member 15"""	IBD1, CARD15		7809109, 8587604	Standard	XM_005256084		Approved	BLAU, CD, PSORAS1, CLR16.3, NLRC2	uc002egm.1	Q9HC29	OTTHUMG00000133171	ENST00000300589.2:c.2369G>A	16.37:g.50746191G>A	ENSP00000300589:p.Arg790Gln	102.0	0.0	0		125.0	67.0	0.536	NM_022162	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Missense_Mutation	SNP	ENST00000300589.2	37	CCDS10746.1	14	0.00641025641025641	13	0.026422764227642278	1	0.0027624309392265192	0	0.0	0	0.0	G	0.038	-1.298744	0.01364	0.033894	1.16E-4	ENSG00000167207	ENST00000526417;ENST00000300589	T	0.51817	0.69	5.3	-0.17	0.13335	.	0.234851	0.28983	N	0.013509	T	0.09774	0.0240	N	0.21194	0.64	0.09310	N	1	B;B;B	0.27166	0.002;0.17;0.039	B;B;B	0.19391	0.001;0.025;0.003	T	0.10042	-1.0647	10	0.20519	T	0.43	.	8.9611	0.35847	0.5027:0.0:0.4973:0.0	rs5743279;rs5743279	574;763;790	D6CHF9;Q9HC29-2;Q9HC29	.;.;NOD2_HUMAN	Q	763;790	ENSP00000300589:R790Q	ENSP00000300589:R790Q	R	+	2	0	NOD2	49303692	0.000000	0.05858	0.988000	0.46212	0.065000	0.16274	0.196000	0.17176	0.076000	0.16826	-0.254000	0.11334	CGG	G|0.989;A|0.011	0.011	strong		0.607	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162	
SLC37A3	84255	hgsc.bcm.edu	37	7	140048445	140048445	+	Silent	SNP	G	G	A	rs73472776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140048445G>A	ENST00000326232.9	-	10	1208	c.1005C>T	c.(1003-1005)taC>taT	p.Y335Y	SLC37A3_ENST00000447932.2_Silent_p.Y335Y|SLC37A3_ENST00000429996.2_3'UTR|SLC37A3_ENST00000340308.3_Silent_p.Y335Y	NM_207113.1	NP_996996.1	Q8NCC5	SPX3_HUMAN	solute carrier family 37, member 3	335					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|stomach(3)	24	Melanoma(164;0.0142)					CTCCAACGTCGTACCAAATGG	0.443													G|||	156	0.0311502	0.1104	0.0144	5008	,	,		17310	0.0		0.0	False		,,,				2504	0.0				p.Y335Y	Esophageal Squamous(133;211 1716 4665 11387 37873)	Atlas-SNP	.											.	SLC37A3	80	.	0			c.C1005T						PASS	.	G	,	461,3945	220.4+/-237.8	24,413,1766	129.0	119.0	123.0		1005,1005	2.0	1.0	7	dbSNP_130	123	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	SLC37A3	NM_032295.2,NM_207113.1	,	24,416,6063	AA,AG,GG		0.0349,10.463,3.5676	,	335/444,335/495	140048445	464,12542	2203	4300	6503	SO:0001819	synonymous_variant	84255	exon10			AACGTCGTACCAA	AK074823	CCDS5858.1, CCDS5859.1, CCDS75669.1	7q34	2013-07-17	2013-07-17		ENSG00000157800	ENSG00000157800		"""Solute carriers"""	20651	protein-coding gene	gene with protein product							Standard	NM_001287498		Approved	DKFZp761N0624	uc003vvo.3	Q8NCC5	OTTHUMG00000157343	ENST00000326232.9:c.1005C>T	7.37:g.140048445G>A		57.0	0.0	0		56.0	29.0	0.517857	NM_207113	Q6PIU7|Q86SS4|Q9BQG7	Silent	SNP	ENST00000326232.9	37	CCDS5859.1	61	0.027930402930402932	57	0.11585365853658537	4	0.011049723756906077	0	0.0	0	0.0	G	8.221	0.802514	0.16397	0.10463	3.49E-4	ENSG00000157800	ENST00000485734;ENST00000485861	.	.	.	5.26	2.05	0.26809	.	.	.	.	.	T	0.01124	0.0037	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.00386	-1.1772	4	.	.	.	-14.7147	6.5083	0.22208	0.4561:0.0:0.5439:0.0	.	.	.	.	M	114;172	.	.	T	-	2	0	SLC37A3	139694914	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	0.648000	0.24828	0.613000	0.30089	0.462000	0.41574	ACG	G|0.961;A|0.039	0.039	strong		0.443	SLC37A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348492.1	NM_032295	
TBC1D24	57465	hgsc.bcm.edu	37	16	2546356	2546356	+	Silent	SNP	T	T	C	rs13339237	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2546356T>C	ENST00000293970.5	+	2	340	c.207T>C	c.(205-207)ccT>ccC	p.P69P	TBC1D24_ENST00000567020.1_Silent_p.P69P|TBC1D24_ENST00000434757.2_Silent_p.P69P|RP11-20I23.1_ENST00000564543.1_Silent_p.P69P	NM_001199107.1	NP_001186036.1	Q9ULP9	TBC24_HUMAN	TBC1 domain family, member 24	69	Rab-GAP TBC.				neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|terminal bouton (GO:0043195)	Rab GTPase activator activity (GO:0005097)			endometrium(2)|kidney(4)|large_intestine(3)|lung(4)	13						CGGTCACGCCTGACGCCAGCG	0.672													C|||	326	0.0650958	0.2322	0.0231	5008	,	,		18489	0.0		0.003	False		,,,				2504	0.0				p.P69P		Atlas-SNP	.											.	TBC1D24	35	.	0			c.T207C						PASS	.	C	,	748,3566		62,624,1471	45.0	55.0	52.0		207,207	-11.2	0.0	16	dbSNP_121	52	18,8500		0,18,4241	no	coding-synonymous,coding-synonymous	TBC1D24	NM_001199107.1,NM_020705.2	,	62,642,5712	CC,CT,TT		0.2113,17.3389,5.9695	,	69/560,69/554	2546356	766,12066	2157	4259	6416	SO:0001819	synonymous_variant	57465	exon2			CACGCCTGACGCC	AB032997	CCDS42107.1, CCDS55980.1	16p13.3	2014-05-07				ENSG00000162065			29203	protein-coding gene	gene with protein product	"""TBC/LysM-associated domain containing 6"""	613577	"""deafness, autosomal recessive 86"""	DFNB86		10574461, 24387994, 24729539	Standard	NM_001199107		Approved	KIAA1171, TLDC6, DFNA65	uc002cql.3	Q9ULP9		ENST00000293970.5:c.207T>C	16.37:g.2546356T>C		116.0	1.0	0.00862069		105.0	105.0	1	NM_001199107	A0JNW3|B9A6M6|Q2KJ08	Silent	SNP	ENST00000293970.5	37	CCDS55980.1																																																																																			T|0.941;C|0.059	0.059	strong		0.672	TBC1D24-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000435637.1	NM_020705	
CCDC107	203260	hgsc.bcm.edu	37	9	35661088	35661088	+	Silent	SNP	G	G	A	rs10441686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35661088G>A	ENST00000426546.2	+	5	822	c.756G>A	c.(754-756)agG>agA	p.R252R	CCDC107_ENST00000378407.3_3'UTR|CCDC107_ENST00000378409.3_Silent_p.R225R|ARHGEF39_ENST00000343259.3_3'UTR|ARHGEF39_ENST00000378395.2_3'UTR|CCDC107_ENST00000378406.1_3'UTR|ARHGEF39_ENST00000490970.1_5'Flank|ARHGEF39_ENST00000378387.3_3'UTR|CCDC107_ENST00000421582.2_3'UTR|CCDC107_ENST00000327351.2_3'UTR	NM_001195200.1|NM_001195201.1|NM_001195217.1|NM_174923.2	NP_001182129.1|NP_001182130.1|NP_001182146.1|NP_777583.2	Q8WV48	CC107_HUMAN	coiled-coil domain containing 107	252						integral component of membrane (GO:0016021)				endometrium(1)|lung(3)|skin(1)	5	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			TACGGAGAAGGTGCAGCCAGG	0.572													G|||	357	0.0712859	0.1982	0.0216	5008	,	,		19466	0.0139		0.0328	False		,,,				2504	0.0337				p.R252R		Atlas-SNP	.											.	CCDC107	12	.	0			c.G756A						PASS	.	G	,,,,	694,3712	290.7+/-281.1	47,600,1556	63.0	64.0	64.0		675,,,,756	0.4	1.0	9	dbSNP_119	64	229,8371	93.8+/-155.7	2,225,4073	no	coding-synonymous,utr-3,utr-3,utr-3,coding-synonymous	C9orf100,CCDC107	NM_001195200.1,NM_001195201.1,NM_001195217.1,NM_032818.2,NM_174923.2	,,,,	49,825,5629	AA,AG,GG		2.6628,15.7512,7.0967	,,,,	225/257,,,,252/284	35661088	923,12083	2203	4300	6503	SO:0001819	synonymous_variant	203260	exon5			GAGAAGGTGCAGC	AK075523	CCDS6583.1, CCDS56573.1, CCDS56574.1, CCDS56575.1	9q13.3	2008-02-05			ENSG00000159884	ENSG00000159884			28465	protein-coding gene	gene with protein product						12477932	Standard	NM_174923		Approved	MGC31967	uc011lox.2	Q8WV48	OTTHUMG00000019868	ENST00000426546.2:c.756G>A	9.37:g.35661088G>A		133.0	0.0	0		134.0	64.0	0.477612	NM_174923	A6XND6|Q5T4R5|Q5T4R8|Q5T4R9|Q86VB6|Q8N2E4	Silent	SNP	ENST00000426546.2	37	CCDS6583.1																																																																																			G|0.925;A|0.075	0.075	strong		0.572	CCDC107-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052325.1	NM_174923	
ABL1	25	hgsc.bcm.edu	37	9	133759546	133759546	+	Silent	SNP	G	G	A	rs34717358	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:133759546G>A	ENST00000318560.5	+	11	2250	c.1869G>A	c.(1867-1869)gaG>gaA	p.E623E		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	623					actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	CCTTCCGGGAGATGGACGGCC	0.602			"""T, Mis"""	"""BCR, ETV6, NUP214"""	"""CML, ALL, T-ALL"""								G|||	116	0.0231629	0.0613	0.0245	5008	,	,		16665	0.0		0.0179	False		,,,				2504	0.0				p.E642E		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.G1926A						PASS	.	G	,	232,4174		6,220,1977	46.0	56.0	52.0		1869,1926	4.7	1.0	9	dbSNP_126	52	145,8455		0,145,4155	no	coding-synonymous,coding-synonymous	ABL1	NM_005157.4,NM_007313.2	,	6,365,6132	AA,AG,GG		1.686,5.2655,2.8987	,	623/1131,642/1150	133759546	377,12629	2203	4300	6503	SO:0001819	synonymous_variant	25	exon11			CCGGGAGATGGAC	M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"""SH2 domain containing"""	76	protein-coding gene	gene with protein product		189980	"""v-abl Abelson murine leukemia viral oncogene homolog 1"", ""c-abl oncogene 1, receptor tyrosine kinase"", ""c-abl oncogene 1, non-receptor tyrosine kinase"""	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.1869G>A	9.37:g.133759546G>A		52.0	0.0	0		80.0	63.0	0.7875	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	37	CCDS35166.1																																																																																			G|0.971;A|0.029	0.029	strong		0.602	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313	
GPR179	440435	hgsc.bcm.edu	37	17	36487060	36487060	+	Missense_Mutation	SNP	C	C	T	rs78470373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:36487060C>T	ENST00000342292.4	-	11	2412	c.2392G>A	c.(2392-2394)Gcc>Acc	p.A798T	GPR179_ENST00000584976.1_5'Flank	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	798					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				GTTCGAGAGGCCTTCTTGGCC	0.652													C|||	53	0.0105831	0.0386	0.0029	5008	,	,		15168	0.0		0.0	False		,,,				2504	0.0				p.A798T		Atlas-SNP	.											.	GPR179	170	.	0			c.G2392A						PASS	.	C	THR/ALA	133,3827		3,127,1850	10.0	12.0	11.0		2392	4.3	0.8	17	dbSNP_131	11	1,8293		0,1,4146	no	missense	GPR179	NM_001004334.2	58	3,128,5996	TT,TC,CC		0.0121,3.3586,1.0935	benign	798/2368	36487060	134,12120	1980	4147	6127	SO:0001583	missense	440435	exon11			GAGAGGCCTTCTT		CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"""GPCR / Class C : Orphans"""	31371	protein-coding gene	gene with protein product		614515	"""GPR158-like 1"", ""GPR179"""	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.2392G>A	17.37:g.36487060C>T	ENSP00000345060:p.Ala798Thr	47.0	0.0	0		46.0	26.0	0.565217	NM_001004334		Missense_Mutation	SNP	ENST00000342292.4	37	CCDS42308.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	C	11.74	1.727989	0.30593	0.033586	1.21E-4	ENSG00000188888	ENST00000342292	T	0.54071	0.59	5.3	4.34	0.51931	.	1.005240	0.08006	N	0.989502	T	0.22859	0.0552	L	0.44542	1.39	0.31348	N	0.682852	B	0.26195	0.144	B	0.18263	0.021	T	0.31558	-0.9939	10	0.27785	T	0.31	-0.0366	12.8987	0.58113	0.0:0.9207:0.0:0.0793	.	798	Q6PRD1	GP179_HUMAN	T	798	ENSP00000345060:A798T	ENSP00000345060:A798T	A	-	1	0	GPR179	33740586	0.007000	0.16637	0.813000	0.32504	0.033000	0.12548	1.245000	0.32790	1.469000	0.48083	0.655000	0.94253	GCC	C|0.995;T|0.005	0.005	strong		0.652	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2		
CLDND2	125875	hgsc.bcm.edu	37	19	51871157	51871157	+	Missense_Mutation	SNP	G	G	A	rs74538792	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51871157G>A	ENST00000291715.1	-	2	718	c.293C>T	c.(292-294)gCc>gTc	p.A98V	CTD-2616J11.10_ENST00000595500.1_RNA|ETFB_ENST00000309244.4_5'Flank|CTD-2616J11.11_ENST00000600067.1_Missense_Mutation_p.A33V|CLDND2_ENST00000601435.1_Missense_Mutation_p.A98V	NM_152353.2	NP_689566.1	Q8NHS1	CLDN2_HUMAN	claudin domain containing 2	98						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(2)	4		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000211)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		GAAGAGGAAGGCGCTCGTGGT	0.721													G|||	174	0.0347444	0.1195	0.0202	5008	,	,		12598	0.001		0.001	False		,,,				2504	0.0				p.A98V		Atlas-SNP	.											.	CLDND2	11	.	0			c.C293T						PASS	.	G	VAL/ALA	394,3980		20,354,1813	18.0	21.0	20.0		293	-2.1	0.0	19	dbSNP_131	20	6,8554		0,6,4274	yes	missense	CLDND2	NM_152353.2	64	20,360,6087	AA,AG,GG		0.0701,9.0078,3.0926	benign	98/168	51871157	400,12534	2187	4280	6467	SO:0001583	missense	125875	exon2			AGGAAGGCGCTCG	BC029518	CCDS12829.1	19q13.41	2008-02-05				ENSG00000160318			28511	protein-coding gene	gene with protein product						12477932	Standard	NM_152353		Approved	MGC33839	uc002pwi.1	Q8NHS1		ENST00000291715.1:c.293C>T	19.37:g.51871157G>A	ENSP00000291715:p.Ala98Val	61.0	0.0	0		80.0	41.0	0.5125	NM_152353		Missense_Mutation	SNP	ENST00000291715.1	37	CCDS12829.1	59	0.027014652014652016	49	0.09959349593495935	10	0.027624309392265192	0	0.0	0	0.0	G	13.11	2.139648	0.37728	0.090078	7.01E-4	ENSG00000160318	ENST00000291715	D	0.88046	-2.33	4.69	-2.13	0.07144	.	2.567250	0.01253	N	0.008934	T	0.08758	0.0217	L	0.31664	0.95	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.49844	-0.8896	10	0.09590	T	0.72	-3.6824	5.168	0.15096	0.4412:0.164:0.3948:0.0	.	98	Q8NHS1	CLDN2_HUMAN	V	98	ENSP00000291715:A98V	ENSP00000291715:A98V	A	-	2	0	CLDND2	56562969	0.000000	0.05858	0.000000	0.03702	0.107000	0.19398	-0.512000	0.06313	-0.169000	0.10834	0.561000	0.74099	GCC	G|0.968;A|0.032	0.032	strong		0.721	CLDND2-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464268.1	NM_152353	
SPRTN	83932	hgsc.bcm.edu	37	1	231487133	231487133	+	Silent	SNP	G	G	A	rs73116379	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:231487133G>A	ENST00000295050.7	+	4	870	c.534G>A	c.(532-534)ccG>ccA	p.P178P	SPRTN_ENST00000391858.4_Silent_p.P178P|SPRTN_ENST00000008440.9_Silent_p.P135P|SPRTN_ENST00000469904.1_3'UTR	NM_001010984.2|NM_032018.5	NP_001010984.1|NP_114407.3	Q9H040	SPRTN_HUMAN	SprT-like N-terminal domain	178	SprT-like.				cellular response to DNA damage stimulus (GO:0006974)|positive regulation of protein ubiquitination (GO:0031398)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA binding (GO:0003677)|K63-linked polyubiquitin binding (GO:0070530)|metal ion binding (GO:0046872)|ubiquitin binding (GO:0043130)										ACAGGCCACCGTATTACGGCT	0.512													G|||	76	0.0151757	0.053	0.0072	5008	,	,		14878	0.0		0.001	False		,,,				2504	0.0				p.P178P		Atlas-SNP	.											.	.	.	.	0			c.G534A						PASS	.	G	,	218,4188	131.4+/-167.9	7,204,1992	68.0	67.0	68.0		534,534	-11.5	0.0	1	dbSNP_130	68	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	C1orf124	NM_001010984.1,NM_032018.4	,	7,207,6289	AA,AG,GG		0.0349,4.9478,1.6992	,	178/251,178/490	231487133	221,12785	2203	4300	6503	SO:0001819	synonymous_variant	83932	exon4			GCCACCGTATTAC	AL512744	CCDS1594.1, CCDS31054.1, CCDS58066.1	1q42.12-q43	2013-01-30	2012-06-18	2012-06-18	ENSG00000010072	ENSG00000010072			25356	protein-coding gene	gene with protein product	"""SprT-like domain at the N terminus"", ""DNA damage-targeting VCP (p97) adaptor"""		"""chromosome 1 open reading frame 124"""	C1orf124		22681887	Standard	NM_032018		Approved	DKFZP547N043, Spartan, DVC1	uc001hur.4	Q9H040	OTTHUMG00000038022	ENST00000295050.7:c.534G>A	1.37:g.231487133G>A		95.0	0.0	0		104.0	48.0	0.461538	NM_032018	B1AKT0|B5MEF7|Q5TE78|Q6UWW6|Q96BC5|Q96KA0	Silent	SNP	ENST00000295050.7	37	CCDS1594.1																																																																																			G|0.983;A|0.017	0.017	strong		0.512	SPRTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092858.1	NM_032018	
DICER1	23405	hgsc.bcm.edu	37	14	95572111	95572111	+	Silent	SNP	A	A	C	rs12018992	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:95572111A>C	ENST00000526495.1	-	21	3288	c.2997T>G	c.(2995-2997)ctT>ctG	p.L999L	DICER1_ENST00000393063.1_Silent_p.L999L|DICER1_ENST00000556045.1_5'UTR|DICER1_ENST00000343455.3_Silent_p.L999L|DICER1_ENST00000527414.1_Silent_p.L999L|DICER1_ENST00000541352.1_Silent_p.L999L			Q9UPY3	DICER_HUMAN	dicer 1, ribonuclease type III	999	PAZ. {ECO:0000255|PROSITE- ProRule:PRU00142}.				angiogenesis (GO:0001525)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac muscle cell development (GO:0055013)|cerebral cortex development (GO:0021987)|defense response to virus (GO:0051607)|embryonic hindlimb morphogenesis (GO:0035116)|gene expression (GO:0010467)|hair follicle cell proliferation (GO:0071335)|hair follicle morphogenesis (GO:0031069)|inner ear receptor cell development (GO:0060119)|intestinal epithelial cell development (GO:0060576)|lung development (GO:0030324)|mRNA stabilization (GO:0048255)|multicellular organism growth (GO:0035264)|negative regulation of Schwann cell proliferation (GO:0010626)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nerve development (GO:0021675)|neuron projection morphogenesis (GO:0048812)|olfactory bulb interneuron differentiation (GO:0021889)|peripheral nervous system myelin formation (GO:0032290)|positive regulation of gene expression (GO:0010628)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of myelination (GO:0031643)|positive regulation of Schwann cell differentiation (GO:0014040)|post-embryonic development (GO:0009791)|pre-miRNA processing (GO:0031054)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|production of siRNA involved in RNA interference (GO:0030422)|regulation of cell cycle (GO:0051726)|regulation of enamel mineralization (GO:0070173)|regulation of neuron differentiation (GO:0045664)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of viral genome replication (GO:0045069)|reproductive structure development (GO:0048608)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|spinal cord motor neuron differentiation (GO:0021522)|spindle assembly (GO:0051225)|spleen development (GO:0048536)|stem cell maintenance (GO:0019827)|targeting of mRNA for destruction involved in RNA interference (GO:0030423)|zygote asymmetric cell division (GO:0010070)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|growth cone (GO:0030426)|RISC complex (GO:0016442)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|miRNA binding (GO:0035198)|ribonuclease III activity (GO:0004525)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(13)|kidney(3)|large_intestine(10)|lung(33)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)	75		all_cancers(154;0.0621)|all_epithelial(191;0.223)		Epithelial(152;0.211)|COAD - Colon adenocarcinoma(157;0.215)		GAGGTGTCAAAAGATTAAGTC	0.383			"""Mis F, N"""		"""sex cord-stromal tumour, TGCT, embryonal rhadomyosarcoma"""	pleuropulmonary blastoma			Familial Multinodular Goiter ;DICER 1 syndrome				A|||	99	0.0197684	0.0711	0.0072	5008	,	,		19488	0.0		0.0	False		,,,				2504	0.0				p.L999L		Atlas-SNP	.	yes	Rec	yes	Familial Pleuropulmonary Blastoma	14	14q32.13	23405	"""dicer 1, ribonuclease type III """		"""E, M, O"""	.	DICER1	181	.	0			c.T2997G						PASS	.	A	,,	252,4154	141.9+/-177.2	11,230,1962	62.0	62.0	62.0		2997,2997,2997	4.2	1.0	14	dbSNP_120	62	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	DICER1	NM_001195573.1,NM_030621.3,NM_177438.2	,,	11,231,6261	CC,CA,AA		0.0116,5.7195,1.9453	,,	999/1830,999/1923,999/1923	95572111	253,12753	2203	4300	6503	SO:0001819	synonymous_variant	23405	exon20	Familial Cancer Database	Adolescent Multinodular Goiter, incl. Multinodular Euthyroid Goiter & Non-Medullary Thyroid Cancer;incl. Pleuropulmonary Blastoma, Familial ; Cystic Nephroma, Familial	TGTCAAAAGATTA	AB028449	CCDS9931.1, CCDS55941.1	14q32.13	2014-09-17	2008-02-20		ENSG00000100697	ENSG00000100697			17098	protein-coding gene	gene with protein product	"""dicer 1, double-stranded RNA-specific endoribonuclease"""	606241	"""Dicer1, Dcr-1 homolog (Drosophila)"", ""multinodular goitre 1"""	MNG1		10051563, 10786632, 21205968	Standard	NM_177438		Approved	Dicer, KIAA0928, K12H4.8-LIKE, HERNA	uc001ydw.2	Q9UPY3	OTTHUMG00000166134	ENST00000526495.1:c.2997T>G	14.37:g.95572111A>C		127.0	0.0	0		115.0	47.0	0.408696	NM_030621	A7E2D3|B3KRG4|E0AD28|O95943|Q9UQ02	Silent	SNP	ENST00000526495.1	37	CCDS9931.1																																																																																			A|0.977;C|0.023	0.023	strong		0.383	DICER1-004	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387997.1		
C1orf106	55765	hgsc.bcm.edu	37	1	200860731	200860731	+	Silent	SNP	G	G	A	rs141245080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:200860731G>A	ENST00000367342.4	+	1	263	c.63G>A	c.(61-63)cgG>cgA	p.R21R		NM_018265.3	NP_060735.3	Q3KP66	CA106_HUMAN	chromosome 1 open reading frame 106	21										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|ovary(1)|prostate(2)|skin(3)|stomach(1)|urinary_tract(2)	21						GGGAGGCTCGGGGGGAGGGAA	0.622													G|||	43	0.00858626	0.0303	0.0029	5008	,	,		15948	0.0		0.001	False		,,,				2504	0.0				p.R35R		Atlas-SNP	.											.	C1orf106	59	.	0			c.G105A						PASS	.	G		142,4264	94.8+/-133.5	3,136,2064	25.0	29.0	27.0		63	1.5	0.0	1	dbSNP_134	27	1,8599		0,1,4299	no	coding-synonymous	C1orf106	NM_018265.3		3,137,6363	AA,AG,GG		0.0116,3.2229,1.0995		21/664	200860731	143,12863	2203	4300	6503	SO:0001819	synonymous_variant	55765	exon1			GGCTCGGGGGGAG	AK001763	CCDS44292.1	1q32.1	2011-02-15			ENSG00000163362	ENSG00000163362			25599	protein-coding gene	gene with protein product						14702039	Standard	NM_018265		Approved	FLJ10901	uc001gvo.4	Q3KP66	OTTHUMG00000035789	ENST00000367342.4:c.63G>A	1.37:g.200860731G>A		182.0	0.0	0		188.0	106.0	0.56383	NM_018265	B4E1K9|E9PFY0|Q9NV65|Q9NVI0	Silent	SNP	ENST00000367342.4	37																																																																																				A|0.008;C|0.001;G|0.991	0.008	strong		0.622	C1orf106-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000087057.2	NM_018265	
PCDHGA2	56113	hgsc.bcm.edu	37	5	140719294	140719294	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140719294G>A	ENST00000394576.2	+	1	756	c.756G>A	c.(754-756)ccG>ccA	p.P252P	PCDHGA1_ENST00000517417.1_Intron	NM_018915.2	NP_061738.1	Q9Y5H1	PCDG2_HUMAN	protocadherin gamma subfamily A, 2	252	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(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(32)|ovary(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	77			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TAAGCATTCCGGAGAATACGC	0.552																																					p.P252P		Atlas-SNP	.											.	PCDHGA2	205	.	0			c.G756A						PASS	.						74.0	77.0	76.0					5																	140719294		2203	4300	6503	SO:0001819	synonymous_variant	56113	exon1			CATTCCGGAGAAT	AF152508	CCDS47289.1	5q31	2011-03-28			ENSG00000081853	ENSG00000081853		"""Cadherins / Protocadherins : Clustered"""	8700	other	protocadherin		606289				10380929	Standard	NM_018915		Approved	PCDH-GAMMA-A2		Q9Y5H1	OTTHUMG00000163679	ENST00000394576.2:c.756G>A	5.37:g.140719294G>A		64.0	0.0	0		48.0	26.0	0.541667	NM_018915	Q52LL6|Q9Y5D5	Silent	SNP	ENST00000394576.2	37	CCDS47289.1																																																																																			.	.	none		0.552	PCDHGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374738.1	NM_018915	
PREPL	9581	hgsc.bcm.edu	37	2	44550528	44550528	+	Missense_Mutation	SNP	T	T	C	rs75128515	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:44550528T>C	ENST00000409936.1	-	12	2206	c.1769A>G	c.(1768-1770)aAc>aGc	p.N590S	PREPL_ENST00000260648.6_Missense_Mutation_p.N590S|PREPL_ENST00000409957.1_Missense_Mutation_p.N501S|PREPL_ENST00000409411.1_Missense_Mutation_p.N501S|PREPL_ENST00000378520.3_Missense_Mutation_p.N524S|PREPL_ENST00000378511.3_Missense_Mutation_p.N528S|PREPL_ENST00000541738.1_Missense_Mutation_p.N501S|PREPL_ENST00000409272.1_Missense_Mutation_p.N590S|PREPL_ENST00000410081.1_Missense_Mutation_p.N590S	NM_001171606.1	NP_001165077.1	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like	590						cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(19)|ovary(1)|prostate(1)|skin(2)	33		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				CATCATGGTGTTGAGAACATC	0.348													T|||	50	0.00998403	0.0363	0.0029	5008	,	,		17612	0.0		0.0	False		,,,				2504	0.0				p.N590S		Atlas-SNP	.											.	PREPL	69	.	0			c.A1769G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN,SER/ASN	146,4260	103.0+/-141.5	2,142,2059	115.0	103.0	107.0		1583,1571,1769,1769,1502,1502,1769	4.2	1.0	2	dbSNP_131	107	2,8598	1.2+/-3.3	0,2,4298	yes	missense,missense,missense,missense,missense,missense,missense	PREPL	NM_001042385.2,NM_001042386.2,NM_001171603.1,NM_001171606.1,NM_001171613.1,NM_001171617.1,NM_006036.4	46,46,46,46,46,46,46	2,144,6357	CC,CT,TT		0.0233,3.3137,1.1379	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	528/666,524/662,590/728,590/728,501/639,501/639,590/728	44550528	148,12858	2203	4300	6503	SO:0001583	missense	9581	exon12			ATGGTGTTGAGAA	AB007896	CCDS33190.1, CCDS42675.1, CCDS42676.1, CCDS54353.1	2p22.1	2008-02-05			ENSG00000138078	ENSG00000138078			30228	protein-coding gene	gene with protein product		609557				11524703	Standard	NM_006036		Approved	KIAA0436	uc002ruk.2	Q4J6C6	OTTHUMG00000152791	ENST00000409936.1:c.1769A>G	2.37:g.44550528T>C	ENSP00000386543:p.Asn590Ser	89.0	0.0	0		136.0	68.0	0.5	NM_001171603	A7E2X6|D6W5A3|O43163|Q4J6C3|Q4J6C4|Q4ZG39|Q6ZMW7|Q96DW7	Missense_Mutation	SNP	ENST00000409936.1	37	CCDS33190.1	22	0.010073260073260074	22	0.044715447154471545	0	0.0	0	0.0	0	0.0	T	17.70	3.454601	0.63290	0.033137	2.33E-4	ENSG00000138078	ENST00000541738;ENST00000409411;ENST00000409957;ENST00000409936;ENST00000260648;ENST00000409272;ENST00000410081;ENST00000378520;ENST00000378511	T;T;T;T;T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6;1.6;1.6;1.6;1.6	5.3	4.15	0.48705	Peptidase S9, prolyl oligopeptidase, catalytic domain (1);	0.105776	0.64402	D	0.000005	T	0.16342	0.0393	L	0.49778	1.585	0.40476	D	0.980399	D;B;B	0.61697	0.99;0.302;0.374	D;B;B	0.72982	0.979;0.162;0.383	T	0.05699	-1.0869	10	0.52906	T	0.07	-17.8051	10.6101	0.45417	0.0:0.0754:0.0:0.9246	.	528;524;590	Q4J6C6-3;Q4J6C6-2;Q4J6C6	.;.;PPCEL_HUMAN	S	501;501;501;590;590;590;590;524;528	ENSP00000439626:N501S;ENSP00000387095:N501S;ENSP00000387241:N501S;ENSP00000386543:N590S;ENSP00000260648:N590S;ENSP00000386909:N590S;ENSP00000386509:N590S;ENSP00000367781:N524S;ENSP00000367772:N528S	ENSP00000260648:N590S	N	-	2	0	PREPL	44404032	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.187000	0.58344	0.864000	0.35578	0.533000	0.62120	AAC	T|0.987;C|0.013	0.013	strong		0.348	PREPL-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327900.1	NM_006036	
CYP4B1	1580	hgsc.bcm.edu	37	1	47283814	47283814	+	Silent	SNP	T	T	C	rs74072926	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:47283814T>C	ENST00000271153.4	+	11	1317	c.1281T>C	c.(1279-1281)tcT>tcC	p.S427S	CYP4B1_ENST00000371923.4_Silent_p.S428S|CYP4B1_ENST00000452782.2_Silent_p.S265S|CYP4B1_ENST00000371919.4_Silent_p.S413S			P13584	CP4B1_HUMAN	cytochrome P450, family 4, subfamily B, polypeptide 1	427					biphenyl metabolic process (GO:0018879)|exogenous drug catabolic process (GO:0042738)|fluorene metabolic process (GO:0018917)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|drug binding (GO:0008144)|fluorene oxygenase activity (GO:0018585)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(12)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	36	Acute lymphoblastic leukemia(166;0.155)				Midazolam(DB00683)|Phenobarbital(DB01174)|Thiamine(DB00152)	TCTTTGACTCTCTGCGCTTTT	0.577													T|||	24	0.00479233	0.0166	0.0029	5008	,	,		20927	0.0		0.0	False		,,,				2504	0.0				p.S428S		Atlas-SNP	.											CYP4B1,bladder,carcinoma,+1,2	CYP4B1	81	2	0			c.T1284C						PASS	.	T	,	36,4370	42.3+/-75.8	0,36,2167	147.0	136.0	140.0		1281,1284	-4.7	0.8	1	dbSNP_130	140	2,8598	3.0+/-9.4	0,2,4298	no	coding-synonymous,coding-synonymous	CYP4B1	NM_000779.3,NM_001099772.1	,	0,38,6465	CC,CT,TT		0.0233,0.8171,0.2922	,	427/512,428/513	47283814	38,12968	2203	4300	6503	SO:0001819	synonymous_variant	1580	exon11			TGACTCTCTGCGC	BC017758	CCDS542.1, CCDS41328.1	1p33	2013-11-11	2003-01-14		ENSG00000142973	ENSG00000142973		"""Cytochrome P450s"""	2644	protein-coding gene	gene with protein product		124075	"""cytochrome P450, subfamily IVB, polypeptide 1"""				Standard	NM_000779		Approved		uc001cqn.4	P13584	OTTHUMG00000007984	ENST00000271153.4:c.1281T>C	1.37:g.47283814T>C		202.0	0.0	0		187.0	95.0	0.508021	NM_001099772	Q1HBI2|Q8TD85|Q8WWF2|Q8WWU9|Q8WWV0	Silent	SNP	ENST00000271153.4	37	CCDS542.1																																																																																			T|0.995;C|0.005	0.005	strong		0.577	CYP4B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000021911.1	NM_000779	
RTL1	388015	hgsc.bcm.edu	37	14	101347090	101347090	+	Missense_Mutation	SNP	C	C	T	rs73349352	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:101347090C>T	ENST00000534062.1	-	1	4094	c.4036G>A	c.(4036-4038)Gaa>Aaa	p.E1346K	MIR433_ENST00000384837.1_RNA|MIR431_ENST00000385266.1_RNA|MIR127_ENST00000384876.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	1346					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						GGCAGCTCTTCTAGCCTTGCC	0.627													C|||	213	0.0425319	0.1536	0.0144	5008	,	,		14165	0.0		0.0	False		,,,				2504	0.0				p.E1346K		Atlas-SNP	.											.	RTL1	120	.	0			c.G4036A						PASS	.						32.0	32.0	32.0					14																	101347090		692	1591	2283	SO:0001583	missense	388015	exon1			GCTCTTCTAGCCT		CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.4036G>A	14.37:g.101347090C>T	ENSP00000435342:p.Glu1346Lys	153.0	0.0	0		173.0	86.0	0.49711	NM_001134888	E9PKS8	Missense_Mutation	SNP	ENST00000534062.1	37	CCDS53910.1	73	0.033424908424908424	70	0.14227642276422764	3	0.008287292817679558	0	0.0	0	0.0	C	12.39	1.924506	0.34002	.	.	ENSG00000254656	ENST00000534062	T	0.28255	1.62	3.29	0.236	0.15471	.	.	.	.	.	T	0.00144	0.0004	N	0.24115	0.695	0.80722	P	0.0	B	0.34103	0.437	B	0.24541	0.054	T	0.09552	-1.0669	8	0.87932	D	0	.	10.9898	0.47543	0.0:0.4239:0.5761:0.0	.	1346	E9PKS8	.	K	1346	ENSP00000435342:E1346K	ENSP00000435342:E1346K	E	-	1	0	RTL1	100416843	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	-0.458000	0.06737	0.044000	0.15775	-0.222000	0.12452	GAA	C|0.966;T|0.034	0.034	strong		0.627	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888	
PCDH11X	27328	hgsc.bcm.edu	37	X	91090533	91090533	+	Silent	SNP	C	C	T	rs56704613	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:91090533C>T	ENST00000373094.1	+	1	875	c.30C>T	c.(28-30)ttC>ttT	p.F10F	PCDH11X_ENST00000395337.2_Silent_p.F10F|PCDH11X_ENST00000504220.2_Silent_p.F10F|PCDH11X_ENST00000298274.8_Silent_p.F10F|PCDH11X_ENST00000361724.1_Silent_p.F10F|PCDH11X_ENST00000373088.1_Silent_p.F10F|PCDH11X_ENST00000361655.2_Silent_p.F10F|PCDH11X_ENST00000373097.1_Silent_p.F10F|PCDH11X_ENST00000406881.1_Silent_p.F10F	NM_032968.3	NP_116750.1	Q9BZA7	PC11X_HUMAN	protocadherin 11 X-linked	10					homophilic cell adhesion (GO:0007156)|negative regulation of phosphatase activity (GO:0010923)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(30)|liver(4)|lung(92)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	159						CGTACATTTTCGCGGTCCTGC	0.488													C|||	266	0.0704636	0.1868	0.0245	3775	,	,		12350	0.0		0.002	False		,,,				2504	0.0				p.F10F	NSCLC(38;925 1092 2571 38200 45895)	Atlas-SNP	.											.	PCDH11X	714	.	0			c.C30T						PASS	.	C	,,,,,,,	788,3047		66,529,127,1037,444	131.0	105.0	114.0		30,30,30,30,30,30,30,30	1.0	1.0	X	dbSNP_129	114	5,6723		0,4,1,2424,1871	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PCDH11X	NM_001168360.1,NM_001168361.1,NM_001168362.1,NM_001168363.1,NM_014522.1,NM_032967.2,NM_032968.3,NM_032969.3	,,,,,,,	66,533,128,3461,2315	TT,TC,T,CC,C		0.0743,20.5476,7.5073	,,,,,,,	10/1340,10/1066,10/1311,10/1330,10/1022,10/1026,10/1348,10/1338	91090533	793,9770	2203	4300	6503	SO:0001819	synonymous_variant	27328	exon1			CATTTTCGCGGTC	AB026187	CCDS14461.1, CCDS14462.1, CCDS55458.1, CCDS55459.1, CCDS55460.1, CCDS55461.1	Xq21.3	2014-06-13	2002-05-22	2002-05-24	ENSG00000102290	ENSG00000102290		"""Cadherins / Protocadherins : Non-clustered"""	8656	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 119"""	300246	"""protocadherin 11"""	PCDH11		10644456	Standard	NM_001168360		Approved	PCDH-X, PCDHX, PPP1R119	uc004efm.2	Q9BZA7	OTTHUMG00000021965	ENST00000373094.1:c.30C>T	X.37:g.91090533C>T		517.0	0.0	0		479.0	477.0	0.995825	NM_001168363	A6NIQ4|Q2TJH0|Q2TJH1|Q2TJH3|Q5JVZ0|Q70LR8|Q70LS7|Q70LS8|Q70LS9|Q70LT7|Q70LT8|Q70LT9|Q70LU0|Q70LU1|Q96RV4|Q96RW0|Q9BZA6|Q9H4E0|Q9P2M0|Q9P2X5	Silent	SNP	ENST00000373094.1	37	CCDS14461.1																																																																																			C|0.922;T|0.078	0.078	strong		0.488	PCDH11X-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057436.1	NM_032969	
CD1E	913	hgsc.bcm.edu	37	1	158326645	158326645	+	Missense_Mutation	SNP	G	G	A	rs61734680	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158326645G>A	ENST00000368167.3	+	6	1365	c.1126G>A	c.(1126-1128)Gta>Ata	p.V376I	CD1E_ENST00000368160.3_Missense_Mutation_p.V364I|CD1E_ENST00000368157.1_Missense_Mutation_p.V120I|CD1E_ENST00000452291.2_Missense_Mutation_p.V187I|CD1E_ENST00000368165.3_Missense_Mutation_p.V286I|CD1E_ENST00000368164.3_3'UTR|CD1E_ENST00000368163.3_Missense_Mutation_p.V309I|CD1E_ENST00000368156.1_Missense_Mutation_p.V274I|CD1E_ENST00000368166.3_Missense_Mutation_p.V175I|CD1E_ENST00000368155.3_Missense_Mutation_p.V219I|CD1E_ENST00000368154.1_Missense_Mutation_p.V132I|CD1E_ENST00000444681.2_Missense_Mutation_p.V277I|CD1E_ENST00000368161.3_3'UTR	NM_030893.3	NP_112155.2	P15812	CD1E_HUMAN	CD1e molecule	376					antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(27)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|urinary_tract(1)	49	all_hematologic(112;0.0378)					CAAAAACAGAGTATTGAAGAA	0.438													G|||	198	0.0395367	0.1483	0.0029	5008	,	,		17554	0.0		0.0	False		,,,				2504	0.0				p.V376I		Atlas-SNP	.											.	CD1E	129	.	0			c.G1126A						PASS	.	G	ILE/VAL,,ILE/VAL,ILE/VAL,,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	507,3337		39,429,1454	111.0	108.0	109.0		1090,,925,523,,856,655,358,559,394,829,820,1126	-7.8	0.0	1	dbSNP_129	109	6,8242		0,6,4118	yes	missense,utr-3,missense,missense,utr-3,missense,missense,missense,missense,missense,missense,missense,missense	CD1E	NM_001042583.2,NM_001042584.2,NM_001042585.2,NM_001042586.2,NM_001042587.2,NM_001185107.1,NM_001185108.1,NM_001185110.1,NM_001185112.1,NM_001185113.1,NM_001185114.1,NM_001185115.1,NM_030893.3	29,,29,29,,29,29,29,29,29,29,29,29	39,435,5572	AA,AG,GG		0.0727,13.1894,4.2425	benign,,benign,benign,,benign,benign,benign,benign,benign,benign,benign,benign	364/377,,309/322,175/188,,286/299,219/232,120/133,187/200,132/145,277/290,274/287,376/389	158326645	513,11579	1922	4124	6046	SO:0001583	missense	913	exon6			AACAGAGTATTGA	AJ289111	CCDS41417.1, CCDS41418.1, CCDS41419.1, CCDS41420.1, CCDS41421.1, CCDS41422.1, CCDS53387.1, CCDS53388.1, CCDS53389.1, CCDS53390.1, CCDS53384.1, CCDS53385.1, CCDS53386.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158488	ENSG00000158488		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1638	protein-coding gene	gene with protein product		188411	"""CD1E antigen, e polypeptide"", ""CD1e antigen"""			10948205	Standard	NM_001042585		Approved		uc001fse.3	P15812	OTTHUMG00000017515	ENST00000368167.3:c.1126G>A	1.37:g.158326645G>A	ENSP00000357149:p.Val376Ile	97.0	0.0	0		99.0	48.0	0.484848	NM_030893	B4DZV3|E7EP01|Q5TDJ9|Q5TDK3|Q5TDK4|Q5TDK5|Q5TDK6|Q5TDK8|Q5TDL1|Q712E4|Q712E5|Q712E6|Q712E7|Q712E8|Q712E9|Q712F0|Q712F1|Q712F2|Q712F3|Q712F4|Q712F5|Q96TD0|Q96TD1|Q9UMM1|Q9Y5M3	Missense_Mutation	SNP	ENST00000368167.3	37	CCDS41417.1	66	0.03021978021978022	65	0.13211382113821138	1	0.0027624309392265192	0	0.0	0	0.0	G	7.949	0.744370	0.15710	0.131894	7.27E-4	ENSG00000158488	ENST00000444681;ENST00000368167;ENST00000452291;ENST00000368165;ENST00000368166;ENST00000368163;ENST00000368157;ENST00000368160;ENST00000368156;ENST00000368155;ENST00000368154	T;T;T;T;T;T;T;T;T;T;T	0.48522	5.17;4.63;3.37;3.4;3.55;3.38;0.81;4.72;3.58;3.47;0.81	3.9	-7.8	0.01214	.	1.447200	0.04683	N	0.412624	T	0.05686	0.0149	N	0.03608	-0.345	0.09310	N	1	B;B;B;B;B;B;B;P;B;B	0.42078	0.002;0.009;0.0;0.001;0.001;0.001;0.003;0.77;0.003;0.0	B;B;B;B;B;B;B;B;B;B	0.38712	0.0;0.004;0.0;0.001;0.001;0.0;0.001;0.28;0.002;0.0	T	0.14476	-1.0471	10	0.30078	T	0.28	-0.168	2.001	0.03467	0.2855:0.3958:0.1205:0.1982	rs61734680	277;286;219;175;364;376;187;132;274;309	E7EP01;P15812-5;P15812-7;P15812-9;P15812-2;P15812;P15812-8;P15812-11;P15812-6;P15812-4	.;.;.;.;.;CD1E_HUMAN;.;.;.;.	I	277;376;187;286;175;309;120;364;274;219;132	ENSP00000402906:V277I;ENSP00000357149:V376I;ENSP00000416228:V187I;ENSP00000357147:V286I;ENSP00000357148:V175I;ENSP00000357145:V309I;ENSP00000357139:V120I;ENSP00000357142:V364I;ENSP00000357138:V274I;ENSP00000357137:V219I;ENSP00000357136:V132I	ENSP00000357136:V132I	V	+	1	0	CD1E	156593269	0.002000	0.14202	0.000000	0.03702	0.000000	0.00434	-0.133000	0.10451	-1.713000	0.01392	-2.501000	0.00191	GTA	G|0.978;A|0.022	0.022	strong		0.438	CD1E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046353.3	NM_030893	
NPY2R	4887	hgsc.bcm.edu	37	4	156135250	156135250	+	Silent	SNP	C	C	T	rs2342674	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:156135250C>T	ENST00000329476.3	+	2	648	c.159C>T	c.(157-159)ctC>ctT	p.L53L	NPY2R_ENST00000506608.1_Silent_p.L53L	NM_000910.2	NP_000901.1	P49146	NPY2R_HUMAN	neuropeptide Y receptor Y2	53					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|behavioral fear response (GO:0001662)|cardiac left ventricle morphogenesis (GO:0003214)|locomotory behavior (GO:0007626)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of feeding behavior (GO:2000252)|negative regulation of neurological system process (GO:0031645)|negative regulation of secretion (GO:0051048)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuropeptide signaling pathway (GO:0007218)|nitric oxide mediated signal transduction (GO:0007263)|outflow tract morphogenesis (GO:0003151)|positive regulation of cell adhesion (GO:0045785)|positive regulation of circadian sleep/wake cycle, non-REM sleep (GO:0046010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of peptide secretion (GO:0002793)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of sensory perception of pain (GO:0051930)|secretion (GO:0046903)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel regulator activity (GO:0005246)|neuropeptide Y receptor activity (GO:0004983)|peptide YY receptor activity (GO:0001601)|receptor activity (GO:0004872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(17)|prostate(1)|skin(5)|urinary_tract(1)	36	all_hematologic(180;0.24)	Renal(120;0.0854)			Cysteamine(DB00847)	AAGTTGTTCTCATATTGGCCT	0.468													C|||	144	0.028754	0.1067	0.0043	5008	,	,		21334	0.0		0.0	False		,,,				2504	0.0				p.L53L		Atlas-SNP	.											.	NPY2R	87	.	0			c.C159T						PASS	.	C		400,4006	199.1+/-222.7	17,366,1820	213.0	198.0	203.0		159	1.6	0.9	4	dbSNP_100	203	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	NPY2R	NM_000910.2		17,368,6118	TT,TC,CC		0.0233,9.0785,3.0909		53/382	156135250	402,12604	2203	4300	6503	SO:0001819	synonymous_variant	4887	exon2			TGTTCTCATATTG	U42766	CCDS3791.1	4q31	2012-08-08				ENSG00000185149		"""GPCR / Class A : Neuropeptide receptors : Y"""	7957	protein-coding gene	gene with protein product		162642				7559383	Standard	NM_000910		Approved		uc003ioq.3	P49146		ENST00000329476.3:c.159C>T	4.37:g.156135250C>T		262.0	0.0	0		272.0	133.0	0.488971	NM_000910	Q13281|Q13457|Q4W5G7|Q6AZZ6|Q9UE67	Silent	SNP	ENST00000329476.3	37	CCDS3791.1																																																																																			C|0.967;T|0.033	0.033	strong		0.468	NPY2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365128.1	NM_000910	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32548534	32548534	+	Missense_Mutation	SNP	C	C	T	rs71547382		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32548534C>T	ENST00000360004.5	-	4	857	c.752G>A	c.(751-753)aGg>aAg	p.R251K		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	251					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|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)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						TTTCTGATTCCTGAAGTAGAT	0.537										Multiple Myeloma(14;0.17)																											p.R251K		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.G752A						PASS	.																																			SO:0001583	missense	3123	exon4			TGATTCCTGAAGT	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.752G>A	6.37:g.32548534C>T	ENSP00000353099:p.Arg251Lys	191.0	0.0	0		439.0	28.0	0.0637813	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	12.57	1.976489	0.34848	.	.	ENSG00000196126	ENST00000360004	T	0.00635	6.06	3.98	1.66	0.24008	.	0.334220	0.32578	N	0.005907	T	0.00241	0.0007	L	0.33710	1.025	0.28819	N	0.897785	B;B;B	0.18166	0.026;0.026;0.0	B;B;B	0.17979	0.02;0.02;0.001	T	0.44757	-0.9307	10	0.38643	T	0.18	.	6.6584	0.23000	0.0:0.6946:0.0:0.3054	.	251;251;251	P04229;Q29974;P01911	2B11_HUMAN;2B1G_HUMAN;2B1F_HUMAN	K	251	ENSP00000353099:R251K	ENSP00000353099:R251K	R	-	2	0	HLA-DRB1	32656512	0.000000	0.05858	0.929000	0.37066	0.845000	0.48019	-0.186000	0.09670	0.802000	0.34089	0.453000	0.30009	AGG	C|1.000;|0.000	.	weak		0.537	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
SLC35G3	146861	hgsc.bcm.edu	37	17	33520904	33520904	+	Silent	SNP	G	G	A	rs61753879	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:33520904G>A	ENST00000297307.5	-	1	508	c.423C>T	c.(421-423)tgC>tgT	p.C141C	RP11-799D4.2_ENST00000590144.1_RNA	NM_152462.2	NP_689675.1	Q8N808	S35G3_HUMAN	solute carrier family 35, member G3	141	EamA 1.					integral component of membrane (GO:0016021)											GGACGGCGGAGCAGACGGTGG	0.582													G|||	87	0.0173722	0.0635	0.0043	5008	,	,		19375	0.0		0.0	False		,,,				2504	0.0				p.C141C		Atlas-SNP	.											.	.	.	.	0			c.C423T						PASS	.	G		259,4147	148.4+/-182.8	5,249,1949	163.0	154.0	157.0		423		0.3	17	dbSNP_129	157	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SLC35G3	NM_152462.2		5,250,6248	AA,AG,GG		0.0116,5.8783,1.9991		141/339	33520904	260,12746	2203	4300	6503	SO:0001819	synonymous_variant	146861	exon1			GGCGGAGCAGACG	AK097473	CCDS11293.1	17q21.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000164729	ENSG00000164729		"""Solute carriers"""	26848	protein-coding gene	gene with protein product			"""transmembrane protein 21A"", ""acyl-malonyl condensing enzyme 1"""	TMEM21A, AMAC1			Standard	NM_152462		Approved	FLJ40154	uc002hjd.2	Q8N808	OTTHUMG00000132929	ENST00000297307.5:c.423C>T	17.37:g.33520904G>A		195.0	0.0	0		211.0	104.0	0.492891	NM_152462	B9EGE9	Silent	SNP	ENST00000297307.5	37	CCDS11293.1																																																																																			G|0.977;A|0.023	0.023	strong		0.582	SLC35G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256445.2	NM_152462	
OR4F6	390648	hgsc.bcm.edu	37	15	102346030	102346030	+	Silent	SNP	G	G	A	rs401632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:102346030G>A	ENST00000328882.4	+	1	129	c.108G>A	c.(106-108)gtG>gtA	p.V36V		NM_001005326.1	NP_001005326.1	Q8NGB9	OR4F6_HUMAN	olfactory receptor, family 4, subfamily F, member 6	36						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|large_intestine(1)|lung(16)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	22	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.00039)|Lung(145;0.17)|LUSC - Lung squamous cell carcinoma(107;0.187)			TGTTCTATGTGTCAAGCCTGA	0.498													g|||	235	0.0469249	0.1732	0.0086	5008	,	,		20248	0.0		0.0	False		,,,				2504	0.0				p.V36V		Atlas-SNP	.											.	OR4F6	45	.	0			c.G108A						PASS	.	G		769,3637		68,633,1502	254.0	233.0	240.0		108	0.4	0.1	15	dbSNP_80	240	23,8577		0,23,4277	no	coding-synonymous	OR4F6	NM_001005326.1		68,656,5779	AA,AG,GG		0.2674,17.4535,6.0895		36/313	102346030	792,12214	2203	4300	6503	SO:0001819	synonymous_variant	390648	exon1			CTATGTGTCAAGC	AC025234	CCDS32341.1	15q26.3	2014-02-19	2002-02-28		ENSG00000184140	ENSG00000184140		"""GPCR / Class A : Olfactory receptors"""	15372	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily F, member 12"""	OR4F12			Standard	NM_001005326		Approved		uc010utr.2	Q8NGB9	OTTHUMG00000172267	ENST00000328882.4:c.108G>A	15.37:g.102346030G>A		267.0	1.0	0.00374532		279.0	135.0	0.483871	NM_001005326	B9EH28|Q6IF95	Silent	SNP	ENST00000328882.4	37	CCDS32341.1																																																																																			G|0.944;A|0.056	0.056	strong		0.498	OR4F6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417593.1		
SPDYA	245711	hgsc.bcm.edu	37	2	29063342	29063342	+	3'UTR	SNP	T	T	C	rs6747208	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:29063342T>C	ENST00000462832.1	+	0	1756				SPDYA_ENST00000379579.4_Intron|SPDYA_ENST00000334056.5_Intron					speedy/RINGO cell cycle regulator family member A											cervix(1)|endometrium(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	9	Acute lymphoblastic leukemia(172;0.155)					GAAGGTATGATTTAGTAATAT	0.373													T|||	36	0.0071885	0.0272	0.0	5008	,	,		19472	0.0		0.0	False		,,,				2504	0.0				p.I286T		Atlas-SNP	.											.	SPDYA	41	.	0			c.T857C						PASS	.	T	THR/ILE,,	85,4321	68.7+/-106.4	0,85,2118	69.0	68.0	69.0		857,,	1.7	0.9	2	dbSNP_116	69	1,8599	1.2+/-3.3	0,1,4299	yes	missense,intron,intron	SPDYA	NM_001008779.1,NM_001142634.1,NM_182756.3	89,,	0,86,6417	CC,CT,TT		0.0116,1.9292,0.6612	,,	286/287,,	29063342	86,12920	2203	4300	6503	SO:0001624	3_prime_UTR_variant	245711	exon5			GTATGATTTAGTA	AA424209	CCDS1767.2	2p23	2013-05-08	2013-05-08	2006-03-31	ENSG00000163806	ENSG00000163806		"""Speedy homologs"""	30613	protein-coding gene	gene with protein product		614029	"""speedy homolog 1 (Drosophila)"", ""speedy homolog A (Xenopus laevis)"""	SPDY1		11980914, 12839962, 15611625	Standard	NM_182756		Approved	SPY1, Ringo3	uc002rmk.3	Q5MJ70	OTTHUMG00000074041	ENST00000462832.1:c.*1753T>C	2.37:g.29063342T>C		110.0	0.0	0		109.0	56.0	0.513761	NM_001008779		Missense_Mutation	SNP	ENST00000462832.1	37																																																																																				T|0.993;C|0.007	0.007	strong		0.373	SPDYA-003	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000157172.2	NM_182756	
GPRC6A	222545	hgsc.bcm.edu	37	6	117130561	117130561	+	Silent	SNP	T	T	G	rs76688215	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:117130561T>G	ENST00000310357.3	-	2	435	c.414A>C	c.(412-414)ccA>ccC	p.P138P	GPRC6A_ENST00000368549.3_Silent_p.P138P|GPRC6A_ENST00000530250.1_Silent_p.P138P	NM_148963.2	NP_683766.2	Q5T6X5	GPC6A_HUMAN	G protein-coupled receptor, class C, group 6, member A	138					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)		CCTTAACTCTTGGCATGTAGC	0.443													T|||	76	0.0151757	0.0545	0.0029	5008	,	,		19458	0.0		0.002	False		,,,				2504	0.0				p.P138P		Atlas-SNP	.											.	GPRC6A	152	.	0			c.A414C						PASS	.	T		161,4245	109.9+/-148.2	3,155,2045	96.0	91.0	93.0		414	0.9	1.0	6	dbSNP_132	93	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	GPRC6A	NM_148963.2		3,159,6341	GG,GT,TT		0.0465,3.6541,1.2686		138/927	117130561	165,12841	2203	4300	6503	SO:0001819	synonymous_variant	222545	exon2			AACTCTTGGCATG	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.414A>C	6.37:g.117130561T>G		113.0	0.0	0		135.0	63.0	0.466667	NM_148963	Q6JK43|Q6JK44|Q8NGU8|Q8NHZ9|Q8TDT6	Silent	SNP	ENST00000310357.3	37	CCDS5112.1																																																																																			T|0.984;G|0.016	0.016	strong		0.443	GPRC6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041966.2		
MYO10	4651	hgsc.bcm.edu	37	5	16673800	16673800	+	Silent	SNP	G	G	A	rs3188408	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:16673800G>A	ENST00000513610.1	-	36	5617	c.5163C>T	c.(5161-5163)acC>acT	p.T1721T	MYO10_ENST00000515803.1_Silent_p.T1060T|MYO10_ENST00000427430.2_Silent_p.T1078T|MYO10_ENST00000505695.1_Silent_p.T1060T|MYO10_ENST00000274203.9_Silent_p.T1078T	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	1721	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						CCTCCCCAGCGGTGGTGTGGG	0.537													G|||	151	0.0301518	0.1074	0.0058	5008	,	,		16446	0.0		0.001	False		,,,				2504	0.0041				p.T1721T		Atlas-SNP	.											.	MYO10	198	.	0			c.C5163T						PASS	.	G		383,3691		24,335,1678	50.0	52.0	51.0		5163	-10.6	0.2	5	dbSNP_105	51	3,8375		0,3,4186	no	coding-synonymous	MYO10	NM_012334.2		24,338,5864	AA,AG,GG		0.0358,9.4011,3.0999		1721/2059	16673800	386,12066	2037	4189	6226	SO:0001819	synonymous_variant	4651	exon36			CCCAGCGGTGGTG	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"""Myosins / Myosin superfamily : Class X"", ""Pleckstrin homology (PH) domain containing"""	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.5163C>T	5.37:g.16673800G>A		125.0	0.0	0		135.0	65.0	0.481481	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	37	CCDS54834.1																																																																																			G|0.980;A|0.020	0.020	strong		0.537	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
FAM9A	171482	hgsc.bcm.edu	37	X	8764370	8764370	+	Missense_Mutation	SNP	C	C	T	rs148031370	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:8764370C>T	ENST00000543214.1	-	6	562	c.427G>A	c.(427-429)Gca>Aca	p.A143T	FAM9A_ENST00000381003.3_Missense_Mutation_p.A143T	NM_001171186.1	NP_001164657.1	Q8IZU1	FAM9A_HUMAN	family with sequence similarity 9, member A	143						nucleus (GO:0005634)				endometrium(11)|kidney(2)|large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	18		Hepatocellular(5;0.219)				CTGTAAGCTGCTTTATCTATT	0.294													c|||	11	0.00291391	0.0	0.0	3775	,	,		13462	0.0		0.0099	False		,,,				2504	0.001				p.A143T		Atlas-SNP	.											.	FAM9A	57	.	0			c.G427A						PASS	.	T	THR/ALA,THR/ALA	2,3833		0,2,0,1630,571	163.0	125.0	138.0		427,427	-0.3	0.0	X	dbSNP_134	138	35,6691		0,24,11,2404,1859	yes	missense,missense	FAM9A	NM_001171186.1,NM_174951.3	58,58	0,26,11,4034,2430	TT,TC,T,CC,C		0.5204,0.0522,0.3503	possibly-damaging,possibly-damaging	143/333,143/333	8764370	37,10524	2203	4298	6501	SO:0001583	missense	171482	exon6			AAGCTGCTTTATC		CCDS14131.1	Xp22.32	2012-11-29			ENSG00000183304	ENSG00000183304			18403	protein-coding gene	gene with protein product	"""testis expressed 39A"""	300477					Standard	NM_174951		Approved	TEX39A	uc004csg.3	Q8IZU1	OTTHUMG00000021110	ENST00000543214.1:c.427G>A	X.37:g.8764370C>T	ENSP00000440163:p.Ala143Thr	148.0	0.0	0		140.0	65.0	0.464286	NM_174951	B7ZLH5|Q2M2D1	Missense_Mutation	SNP	ENST00000543214.1	37	CCDS14131.1	8	0.004822182037371911	0	0.0	0	0.0	0	0.0	6	0.007957559681697613	c	5.235	0.228805	0.09916	5.22E-4	0.005204	ENSG00000183304	ENST00000381003;ENST00000543214	.	.	.	0.678	-0.327	0.12694	.	.	.	.	.	T	0.21307	0.0513	N	0.22421	0.69	0.09310	N	1	D	0.58620	0.983	P	0.53861	0.736	T	0.17379	-1.0371	7	0.14656	T	0.56	.	.	.	.	.	143	Q8IZU1	FAM9A_HUMAN	T	143	.	ENSP00000370391:A143T	A	-	1	0	FAM9A	8724370	0.971000	0.33674	0.000000	0.03702	0.005000	0.04900	0.178000	0.16820	-0.205000	0.10219	0.458000	0.33432	GCA	C|0.996;T|0.004	0.004	strong		0.294	FAM9A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055697.1	NM_174951	
ANK3	288	hgsc.bcm.edu	37	10	61830256	61830256	+	Silent	SNP	T	T	C	rs61732400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:61830256T>C	ENST00000280772.2	-	37	10574	c.10383A>G	c.(10381-10383)caA>caG	p.Q3461Q	ANK3_ENST00000373827.2_Intron|ANK3_ENST00000503366.1_Intron|ANK3_ENST00000355288.2_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	3461					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						CAAGTTTACTTTGGCTAAAAG	0.438													T|||	159	0.0317492	0.1135	0.0115	5008	,	,		21138	0.001		0.0	False		,,,				2504	0.0				p.Q3461Q		Atlas-SNP	.											.	ANK3	703	.	0			c.A10383G						PASS	.	T	,,,	449,3957	215.1+/-234.2	19,411,1773	83.0	80.0	81.0		,,,10383	-2.4	1.0	10	dbSNP_129	81	6,8594	4.3+/-15.6	0,6,4294	no	intron,intron,intron,coding-synonymous	ANK3	NM_001149.3,NM_001204403.1,NM_001204404.1,NM_020987.3	,,,	19,417,6067	CC,CT,TT		0.0698,10.1906,3.4984	,,,	,,,3461/4378	61830256	455,12551	2203	4300	6503	SO:0001819	synonymous_variant	288	exon37			TTTACTTTGGCTA	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"""Ankyrin repeat domain containing"""	494	protein-coding gene	gene with protein product	"""ankyrin-3, node of Ranvier"", ""ankyrin-G"""	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.10383A>G	10.37:g.61830256T>C		114.0	0.0	0		120.0	62.0	0.516667	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	37	CCDS7258.1																																																																																			T|0.970;C|0.030	0.030	strong		0.438	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987	
TOX3	27324	hgsc.bcm.edu	37	16	52484317	52484317	+	Missense_Mutation	SNP	C	C	T	rs114182621	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:52484317C>T	ENST00000219746.9	-	4	834	c.550G>A	c.(550-552)Gcc>Acc	p.A184T	TOX3_ENST00000407228.3_Missense_Mutation_p.A179T	NM_001080430.2	NP_001073899.2	O15405	TOX3_HUMAN	TOX high mobility group box family member 3	184					apoptotic process (GO:0006915)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|estrogen response element binding (GO:0034056)|phosphoprotein binding (GO:0051219)|protein homodimerization activity (GO:0042803)			NS(2)|endometrium(6)|kidney(1)|lung(8)|prostate(3)|stomach(3)|upper_aerodigestive_tract(1)	24						CCCAACTGGGCGCTGAGCTGA	0.582													C|||	28	0.00559105	0.0189	0.0029	5008	,	,		17831	0.001		0.0	False		,,,				2504	0.0				p.A184T		Atlas-SNP	.											.	TOX3	121	.	0			c.G550A						PASS	.	C	THR/ALA,THR/ALA	74,4182		2,70,2056	150.0	158.0	155.0		550,535	3.8	1.0	16	dbSNP_132	155	0,8480		0,0,4240	yes	missense,missense	TOX3	NM_001080430.2,NM_001146188.1	58,58	2,70,6296	TT,TC,CC		0.0,1.7387,0.581	probably-damaging,probably-damaging	184/577,179/572	52484317	74,12662	2128	4240	6368	SO:0001583	missense	27324	exon4			ACTGGGCGCTGAG	U80736	CCDS54008.1, CCDS54009.1	16q12.1	2008-02-05	2007-03-20	2007-03-20		ENSG00000103460		"""Trinucleotide (CAG) repeat containing"""	11972	protein-coding gene	gene with protein product		611416	"""trinucleotide repeat containing 9"""	TNRC9		9225980	Standard	NM_001080430		Approved	CAGF9	uc002egw.2	O15405		ENST00000219746.9:c.550G>A	16.37:g.52484317C>T	ENSP00000219746:p.Ala184Thr	118.0	0.0	0		140.0	70.0	0.5	NM_001080430	B4DRD0|B5MCW4	Missense_Mutation	SNP	ENST00000219746.9	37	CCDS54009.1	15	0.006868131868131868	13	0.026422764227642278	1	0.0027624309392265192	1	0.0017482517482517483	0	0.0	C	13.54	2.267516	0.40095	0.017387	0.0	ENSG00000103460	ENST00000219746;ENST00000407228	T;T	0.11495	2.77;2.77	5.71	3.77	0.43336	.	0.129794	0.49916	D	0.000134	T	0.04588	0.0125	M	0.68593	2.085	0.45025	D	0.998041	B;B	0.17268	0.008;0.021	B;B	0.06405	0.002;0.002	T	0.02411	-1.1163	10	0.72032	D	0.01	.	11.9513	0.52956	0.0:0.8601:0.0:0.1399	.	179;184	B4DRD0;O15405	.;TOX3_HUMAN	T	184;179	ENSP00000219746:A184T;ENSP00000385705:A179T	ENSP00000219746:A184T	A	-	1	0	TOX3	51041818	1.000000	0.71417	0.992000	0.48379	0.014000	0.08584	3.357000	0.52277	0.763000	0.33175	0.563000	0.77884	GCC	C|0.992;T|0.008	0.008	strong		0.582	TOX3-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000422534.1	XM_049037	
ZNF800	168850	hgsc.bcm.edu	37	7	127026184	127026184	+	Silent	SNP	A	A	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:127026184A>C	ENST00000393313.1	-	3	678	c.87T>G	c.(85-87)ccT>ccG	p.P29P	ZNF800_ENST00000265827.3_Silent_p.P29P|ZNF800_ENST00000393312.1_Silent_p.P29P			Q2TB10	ZN800_HUMAN	zinc finger protein 800	29					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(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(8)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	32						GTAACAAAGGAGGATCTCCAG	0.343																																					p.P29P		Atlas-SNP	.											.	ZNF800	78	.	0			c.T87G						PASS	.						110.0	104.0	106.0					7																	127026184		2203	4300	6503	SO:0001819	synonymous_variant	168850	exon3			CAAAGGAGGATCT	AF218032	CCDS5795.1	7q31.33	2008-05-02			ENSG00000048405	ENSG00000048405		"""Zinc fingers, C2H2-type"""	27267	protein-coding gene	gene with protein product						12477932	Standard	NM_176814		Approved		uc003vly.1	Q2TB10	OTTHUMG00000023456	ENST00000393313.1:c.87T>G	7.37:g.127026184A>C		72.0	0.0	0		83.0	42.0	0.506024	NM_176814	Q9HBN0	Silent	SNP	ENST00000393313.1	37	CCDS5795.1																																																																																			.	.	none		0.343	ZNF800-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141823.1	NM_176814	
PLIN4	729359	hgsc.bcm.edu	37	19	4512534	4512534	+	Missense_Mutation	SNP	C	C	T	rs61730732	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4512534C>T	ENST00000301286.3	-	3	1395	c.1396G>A	c.(1396-1398)Gcc>Acc	p.A466T		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	466	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						GCCCCTTTGGCCACATTCGCA	0.597													C|||	45	0.00898562	0.0333	0.0014	5008	,	,		22756	0.0		0.0	False		,,,				2504	0.0				p.A466T		Atlas-SNP	.											.	PLIN4	191	.	0			c.G1396A						PASS	.	C	THR/ALA	146,3788		3,140,1824	114.0	122.0	119.0		1396	5.0	1.0	19	dbSNP_129	119	0,8308		0,0,4154	yes	missense	PLIN4	NM_001080400.1	58	3,140,5978	TT,TC,CC		0.0,3.7112,1.1926	possibly-damaging	466/1358	4512534	146,12096	1967	4154	6121	SO:0001583	missense	729359	exon3			CTTTGGCCACATT	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"""Perilipins"""	29393	protein-coding gene	gene with protein product		613247	"""KIAA1881"""	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.1396G>A	19.37:g.4512534C>T	ENSP00000301286:p.Ala466Thr	182.0	0.0	0		227.0	100.0	0.440529	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	22	0.010073260073260074	22	0.044715447154471545	0	0.0	0	0.0	0	0.0	C	17.51	3.406822	0.62399	0.037112	0.0	ENSG00000167676	ENST00000301286	T	0.09350	2.99	4.99	4.99	0.66335	.	0.000000	0.52532	D	0.000078	T	0.08670	0.0215	M	0.86573	2.825	0.34738	D	0.730428	D	0.61080	0.989	P	0.56474	0.799	T	0.37619	-0.9698	10	0.30854	T	0.27	-55.3504	15.8081	0.78531	0.0:1.0:0.0:0.0	.	466	Q96Q06	PLIN4_HUMAN	T	466	ENSP00000301286:A466T	ENSP00000301286:A466T	A	-	1	0	PLIN4	4463534	0.165000	0.22948	0.996000	0.52242	0.008000	0.06430	1.816000	0.38992	2.342000	0.79632	0.549000	0.68633	GCC	C|0.991;T|0.009	0.009	strong		0.597	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
KRTAP5-9	3846	hgsc.bcm.edu	37	11	71259818	71259818	+	Missense_Mutation	SNP	G	G	A	rs146869772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71259818G>A	ENST00000528743.2	+	1	353	c.115G>A	c.(115-117)Gtc>Atc	p.V39I		NM_005553.3	NP_005544.4	P26371	KRA59_HUMAN	keratin associated protein 5-9	39	8 X 4 AA repeats of C-C-X-P.				epidermis development (GO:0008544)	keratin filament (GO:0045095)		p.V39I(1)		kidney(1)|large_intestine(1)|lung(6)|prostate(3)	11						CTGTGCACCCGTCTACTGCTG	0.667													g|||	10	0.00199681	0.0068	0.0014	5008	,	,		17781	0.0		0.0	False		,,,				2504	0.0				p.V39I		Atlas-SNP	.											KRTAP5-9,caecum,carcinoma,0,1	KRTAP5-9	19	1	1	Substitution - Missense(1)	large_intestine(1)	c.G115A						PASS	.	G	ILE/VAL	37,4363		0,37,2163	80.0	91.0	87.0		115	1.6	0.0	11	dbSNP_134	87	0,8588		0,0,4294	no	missense	KRTAP5-9	NM_005553.3	29	0,37,6457	AA,AG,GG		0.0,0.8409,0.2849	possibly-damaging	39/170	71259818	37,12951	2200	4294	6494	SO:0001583	missense	3846	exon1			GCACCCGTCTACT	AB126078	CCDS53677.1	11q13.4	2008-02-05				ENSG00000254997		"""Keratin associated proteins"""	23604	protein-coding gene	gene with protein product		148021		KRN1		15144888	Standard	NM_005553		Approved	KRTAP5.9, KRTAP5-1	uc001oqs.1	P26371		ENST00000528743.2:c.115G>A	11.37:g.71259818G>A	ENSP00000431443:p.Val39Ile	293.0	0.0	0		324.0	145.0	0.447531	NM_005553	Q14564|Q3MIP8	Missense_Mutation	SNP	ENST00000528743.2	37	CCDS53677.1	3	0.0013736263736263737	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	0	0.0	N	4.044	0.005754	0.07866	0.008409	0.0	ENSG00000254997	ENST00000528743	T	0.03745	3.82	1.57	1.57	0.23409	.	.	.	.	.	T	0.04003	0.0112	L	0.42487	1.325	0.09310	N	1	P	0.51537	0.946	P	0.50270	0.636	T	0.38067	-0.9678	9	0.49607	T	0.09	.	6.6099	0.22745	0.0:0.0:1.0:0.0	.	39	P26371	KRA59_HUMAN	I	39	ENSP00000431443:V39I	ENSP00000431443:V39I	V	+	1	0	KRTAP5-9	70937466	0.000000	0.05858	0.015000	0.15790	0.167000	0.22549	-0.373000	0.07494	1.189000	0.43028	0.442000	0.29010	GTC	G|0.999;A|0.001	0.001	strong		0.667	KRTAP5-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393901.2		
FAM149A	25854	hgsc.bcm.edu	37	4	187088170	187088170	+	Missense_Mutation	SNP	G	G	A	rs141044925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:187088170G>A	ENST00000356371.5	+	12	2086	c.2086G>A	c.(2086-2088)Ggt>Agt	p.G696S	FAM149A_ENST00000502970.1_Missense_Mutation_p.G405S|FAM149A_ENST00000503432.1_Missense_Mutation_p.G405S|FAM149A_ENST00000514153.1_Missense_Mutation_p.G405S|FAM149A_ENST00000227065.4_Missense_Mutation_p.G405S|FAM149A_ENST00000389354.5_Missense_Mutation_p.G405S			A5PLN7	F149A_HUMAN	family with sequence similarity 149, member A	696										breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(2)	25		all_cancers(14;4.27e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.0066)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.19e-10)|BRCA - Breast invasive adenocarcinoma(30;1.22e-05)|GBM - Glioblastoma multiforme(59;0.000122)|STAD - Stomach adenocarcinoma(60;0.000288)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.166)		CATGCCTGACGGTACAGAACG	0.468													G|||	30	0.00599042	0.0212	0.0029	5008	,	,		17105	0.0		0.0	False		,,,				2504	0.0				p.G405S		Atlas-SNP	.											.	FAM149A	52	.	0			c.G1213A						PASS	.	G	SER/GLY,SER/GLY	64,4342	59.3+/-96.0	0,64,2139	91.0	85.0	87.0		1213,1213	-3.5	0.0	4	dbSNP_134	87	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	FAM149A	NM_001006655.2,NM_015398.2	56,56	0,66,6437	AA,AG,GG		0.0233,1.4526,0.5075	benign,benign	405/483,405/483	187088170	66,12940	2203	4300	6503	SO:0001583	missense	25854	exon11			CCTGACGGTACAG	AK057166	CCDS34117.1	4q35.1	2012-04-19			ENSG00000109794	ENSG00000109794			24527	protein-coding gene	gene with protein product							Standard	NM_015398		Approved	DKFZP564J102, MST119, MSTP119	uc010isl.3	A5PLN7	OTTHUMG00000160565	ENST00000356371.5:c.2086G>A	4.37:g.187088170G>A	ENSP00000348732:p.Gly696Ser	119.0	0.0	0		129.0	51.0	0.395349	NM_001006655	B5MDB8|Q2TAN6|Q7Z2S5|Q9Y4T9	Missense_Mutation	SNP	ENST00000356371.5	37		9|9	0.004120879120879121|0.004120879120879121	8|8	0.016260162601626018|0.016260162601626018	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	G|G	2.916|2.916	-0.224222|-0.224222	0.06061|0.06061	0.014526|0.014526	2.33E-4|2.33E-4	ENSG00000109794|ENSG00000109794	ENST00000503432;ENST00000356371;ENST00000227065;ENST00000502970;ENST00000514153;ENST00000389354|ENST00000512271	T;T;T;T;T;T|.	0.10005|.	2.92;2.94;2.92;2.92;2.92;2.92|.	5.72|5.72	-3.45|-3.45	0.04781|0.04781	.|.	0.347222|.	0.34268|.	N|.	0.004119|.	T|T	0.02047|0.02047	0.0064|0.0064	N|N	0.00500|0.00500	-1.43|-1.43	0.09310|0.09310	N|N	1|1	B;B|.	0.28880|.	0.226;0.085|.	B;B|.	0.16722|.	0.016;0.007|.	T|T	0.35895|0.35895	-0.9770|-0.9770	10|5	0.05620|.	T|.	0.96|.	-2.9758|-2.9758	1.239|1.239	0.01959|0.01959	0.3995:0.2553:0.2218:0.1234|0.3995:0.2553:0.2218:0.1234	.|.	696;696|.	A5PLN7-3;A5PLN7|.	.;F149A_HUMAN|.	S|Q	405;696;405;405;405;405|82	ENSP00000426835:G405S;ENSP00000348732:G696S;ENSP00000227065:G405S;ENSP00000427155:G405S;ENSP00000424380:G405S;ENSP00000374005:G405S|.	ENSP00000227065:G405S|.	G|R	+|+	1|2	0|0	FAM149A|FAM149A	187325164|187325164	0.000000|0.000000	0.05858|0.05858	0.023000|0.023000	0.16930|0.16930	0.003000|0.003000	0.03518|0.03518	0.194000|0.194000	0.17135|0.17135	-0.400000|-0.400000	0.07656|0.07656	-0.469000|-0.469000	0.05056|0.05056	GGT|CGG	G|0.995;A|0.005	0.005	strong		0.468	FAM149A-201	KNOWN	basic	protein_coding	protein_coding		NM_001006655	
TEKT2	27285	hgsc.bcm.edu	37	1	36551495	36551495	+	Missense_Mutation	SNP	T	T	C	rs419653	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:36551495T>C	ENST00000207457.3	+	4	468	c.341T>C	c.(340-342)aTt>aCt	p.I114T	ADPRHL2_ENST00000373178.4_5'Flank	NM_014466.2	NP_055281.2	Q9UIF3	TEKT2_HUMAN	tektin 2 (testicular)	114			I -> T (in dbSNP:rs419653).		cell projection organization (GO:0030030)|inner dynein arm assembly (GO:0036159)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)				breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|pancreas(1)|skin(2)	13		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GATGTGGCCATTGAGTGCCTG	0.587													T|||	65	0.0129792	0.0484	0.0014	5008	,	,		19232	0.0		0.0	False		,,,				2504	0.0				p.I114T		Atlas-SNP	.											.	TEKT2	32	.	0			c.T341C						PASS	.	T	THR/ILE	134,4272	95.7+/-134.4	5,124,2074	58.0	53.0	55.0		341	5.8	0.7	1	dbSNP_80	55	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TEKT2	NM_014466.2	89	5,125,6373	CC,CT,TT		0.0116,3.0413,1.038	benign	114/431	36551495	135,12871	2203	4300	6503	SO:0001583	missense	27285	exon4			TGGCCATTGAGTG	AB033823	CCDS401.1	1p34.3	2008-02-05			ENSG00000092850	ENSG00000092850			11725	protein-coding gene	gene with protein product		608953				12029069, 11751288	Standard	NM_014466		Approved	TEKTB1	uc001bzr.3	Q9UIF3	OTTHUMG00000007629	ENST00000207457.3:c.341T>C	1.37:g.36551495T>C	ENSP00000207457:p.Ile114Thr	143.0	0.0	0		160.0	65.0	0.40625	NM_014466	A6NIS6|O60638	Missense_Mutation	SNP	ENST00000207457.3	37	CCDS401.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	T	11.29	1.595161	0.28445	0.030413	1.16E-4	ENSG00000092850	ENST00000207457	T	0.02177	4.41	5.79	5.79	0.91817	.	0.454845	0.25833	N	0.028007	T	0.00468	0.0015	N	0.12182	0.205	0.33226	D	0.55525	B	0.23990	0.095	B	0.23574	0.047	T	0.49969	-0.8882	10	0.14252	T	0.57	.	16.1354	0.81481	0.0:0.0:0.0:1.0	rs419653;rs419653	114	Q9UIF3	TEKT2_HUMAN	T	114	ENSP00000207457:I114T	ENSP00000207457:I114T	I	+	2	0	TEKT2	36324082	0.589000	0.26807	0.652000	0.29579	0.988000	0.76386	1.835000	0.39181	2.207000	0.71202	0.533000	0.62120	ATT	T|0.990;C|0.010	0.010	strong		0.587	TEKT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000020200.1	NM_014466	
GATA4	2626	hgsc.bcm.edu	37	8	11614559	11614559	+	Silent	SNP	A	A	G	rs112435835	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11614559A>G	ENST00000335135.4	+	6	1671	c.1113A>G	c.(1111-1113)tcA>tcG	p.S371S	GATA4_ENST00000528712.1_Silent_p.S165S|GATA4_ENST00000532059.1_Silent_p.S372S	NM_002052.3	NP_002043.2	P43694	GATA4_HUMAN	GATA binding protein 4	371					atrial septum morphogenesis (GO:0060413)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|atrioventricular valve morphogenesis (GO:0003181)|blood coagulation (GO:0007596)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac right ventricle morphogenesis (GO:0003215)|cardiac ventricle morphogenesis (GO:0003208)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell-cell signaling (GO:0007267)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to glucose stimulus (GO:0071333)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic foregut morphogenesis (GO:0048617)|embryonic heart tube anterior/posterior pattern specification (GO:0035054)|endocardial cushion development (GO:0003197)|endoderm development (GO:0007492)|endoderm formation (GO:0001706)|epithelial cell fate commitment (GO:0072148)|gastrulation with mouth forming second (GO:0001702)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|intestinal epithelial cell differentiation (GO:0060575)|lung lobe formation (GO:0060464)|male gonad development (GO:0008584)|negative regulation of autophagy (GO:0010507)|positive regulation of angiogenesis (GO:0045766)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to mechanical stimulus (GO:0009612)|seminiferous tubule development (GO:0072520)|Sertoli cell differentiation (GO:0060008)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular cardiac muscle tissue development (GO:0003229)|ventricular septum development (GO:0003281)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	activating transcription factor binding (GO:0033613)|chromatin binding (GO:0003682)|co-SMAD binding (GO:0070410)|DNA binding (GO:0003677)|enhancer sequence-specific DNA binding (GO:0001158)|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 factor binding transcription factor activity (GO:0001076)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(10)	13	all_epithelial(15;0.0839)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.199)		CTGGCCTGTCATCTCACTACG	0.662													A|||	51	0.0101837	0.0371	0.0029	5008	,	,		20298	0.0		0.0	False		,,,				2504	0.0				p.S371S		Atlas-SNP	.											.	GATA4	29	.	0			c.A1113G						PASS	.	A		94,4312	76.8+/-115.0	2,90,2111	90.0	70.0	76.0		1113	-11.7	0.0	8	dbSNP_132	76	0,8600		0,0,4300	no	coding-synonymous	GATA4	NM_002052.3		2,90,6411	GG,GA,AA		0.0,2.1335,0.7227		371/443	11614559	94,12912	2203	4300	6503	SO:0001819	synonymous_variant	2626	exon6			CCTGTCATCTCAC	AK097060	CCDS5983.1	8p23.1-p22	2013-01-25	2001-11-28		ENSG00000136574	ENSG00000136574		"""GATA zinc finger domain containing"""	4173	protein-coding gene	gene with protein product		600576	"""GATA-binding protein 4"""			7665171	Standard	NM_002052		Approved		uc003wuc.2	P43694	OTTHUMG00000090800	ENST00000335135.4:c.1113A>G	8.37:g.11614559A>G		301.0	0.0	0		259.0	132.0	0.509652	NM_002052	B7ZKX0|B7ZKZ4|Q3MJ45|Q5IFM8	Silent	SNP	ENST00000335135.4	37	CCDS5983.1																																																																																			A|0.993;G|0.007	0.007	strong		0.662	GATA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207587.2	NM_002052	
DLC1	10395	hgsc.bcm.edu	37	8	13357331	13357331	+	Missense_Mutation	SNP	C	C	T	rs35173269	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:13357331C>T	ENST00000276297.4	-	2	659	c.250G>A	c.(250-252)Gat>Aat	p.D84N	DLC1_ENST00000511869.1_Missense_Mutation_p.D84N|DLC1_ENST00000316609.5_Missense_Mutation_p.D84N	NM_182643.2	NP_872584.2	Q96QB1	RHG07_HUMAN	DLC1 Rho GTPase activating protein	84					actin cytoskeleton organization (GO:0030036)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|focal adhesion assembly (GO:0048041)|forebrain development (GO:0030900)|heart morphogenesis (GO:0003007)|hindbrain morphogenesis (GO:0021575)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neural tube closure (GO:0001843)|positive regulation of execution phase of apoptosis (GO:1900119)|positive regulation of protein dephosphorylation (GO:0035307)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	lipid binding (GO:0008289)|Rho GTPase activator activity (GO:0005100)|SH2 domain binding (GO:0042169)			NS(2)|breast(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(39)|lung(32)|ovary(4)|pancreas(2)|prostate(4)|skin(2)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	110						TCGTCCACATCCTTTGAAAGA	0.453													C|||	62	0.0123802	0.0454	0.0014	5008	,	,		20510	0.0		0.001	False		,,,				2504	0.0				p.D84N		Atlas-SNP	.											.	DLC1	411	.	0			c.G250A						PASS	.	C	ASN/ASP,ASN/ASP	215,4191	132.1+/-168.6	8,199,1996	224.0	226.0	226.0		250,250	4.7	0.1	8	dbSNP_126	226	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	DLC1	NM_024767.3,NM_182643.2	23,23	8,202,6293	TT,TC,CC		0.0349,4.8797,1.6761	benign,benign	84/464,84/1529	13357331	218,12788	2203	4300	6503	SO:0001583	missense	10395	exon2			CCACATCCTTTGA	AF035119	CCDS5989.1, CCDS5990.1, CCDS5991.1, CCDS5991.2, CCDS55201.1	8p22	2014-06-20	2014-06-20		ENSG00000164741	ENSG00000164741		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	2897	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 12"""	604258	"""deleted in liver cancer 1"""			9605766, 11214970	Standard	NM_182643		Approved	HP, ARHGAP7, STARD12, DLC-1, p122-RhoGAP	uc003wwm.2	Q96QB1	OTTHUMG00000090825	ENST00000276297.4:c.250G>A	8.37:g.13357331C>T	ENSP00000276297:p.Asp84Asn	63.0	0.0	0		65.0	34.0	0.523077	NM_182643	B4DR10|B8PTI0|E9PDZ8|E9PF76|E9PGY9|O14868|O43199|Q7Z5R8|Q86UC6|Q9C0E0|Q9H7A2	Missense_Mutation	SNP	ENST00000276297.4	37	CCDS5989.1	20	0.009157509157509158	19	0.03861788617886179	0	0.0	0	0.0	1	0.0013192612137203166	C	11.29	1.596099	0.28445	0.048797	3.49E-4	ENSG00000164741	ENST00000276297;ENST00000316609;ENST00000511869	T;T;T	0.32753	1.44;1.44;1.44	5.55	4.68	0.58851	.	0.542075	0.15368	N	0.266008	T	0.03136	0.0092	N	0.14661	0.345	0.21147	N	0.99977	B;B;B	0.22211	0.039;0.066;0.039	B;B;B	0.24006	0.032;0.05;0.023	T	0.10291	-1.0636	10	0.72032	D	0.01	.	10.6747	0.45778	0.0:0.8543:0.0:0.1457	rs35173269;rs61757613	84;84;84	E9PF76;Q96QB1-3;Q96QB1	.;.;RHG07_HUMAN	N	84	ENSP00000276297:D84N;ENSP00000321034:D84N;ENSP00000425878:D84N	ENSP00000276297:D84N	D	-	1	0	DLC1	13401702	1.000000	0.71417	0.145000	0.22337	0.066000	0.16364	3.124000	0.50461	1.500000	0.48636	0.655000	0.94253	GAT	C|0.981;T|0.019	0.019	strong		0.453	DLC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207632.2	NM_182643, NM_006094	
IFNA6	3443	hgsc.bcm.edu	37	9	21350487	21350487	+	Silent	SNP	G	G	A	rs61736258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:21350487G>A	ENST00000380210.1	-	1	890	c.400C>T	c.(400-402)Ctg>Ttg	p.L134L		NM_021002.2	NP_066282.1	P05013	IFNA6_HUMAN	interferon, alpha 6	134					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)|type I interferon receptor binding (GO:0005132)			large_intestine(3)|lung(7)|skin(1)	11				Lung(24;7.66e-27)|LUSC - Lung squamous cell carcinoma(38;1.4e-13)|OV - Ovarian serous cystadenocarcinoma(39;0.116)		TCATTCATCAGGGGAGTCCCT	0.498													G|||	124	0.0247604	0.09	0.0072	5008	,	,		20965	0.0		0.0	False		,,,				2504	0.0				p.L134L		Atlas-SNP	.											.	IFNA6	27	.	0			c.C400T						PASS	.	G		351,4055	181.2+/-209.3	15,321,1867	200.0	202.0	202.0		400	0.6	0.0	9	dbSNP_129	202	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	IFNA6	NM_021002.2		15,323,6165	AA,AG,GG		0.0233,7.9664,2.7141		134/190	21350487	353,12653	2203	4300	6503	SO:0001819	synonymous_variant	3443	exon1			TCATCAGGGGAGT		CCDS6504.1	9p22	2010-12-10			ENSG00000120235	ENSG00000120235		"""Interferons"""	5427	protein-coding gene	gene with protein product		147566				1385305	Standard	NM_021002		Approved	IFN-alphaK	uc011lni.2	P05013	OTTHUMG00000019676	ENST00000380210.1:c.400C>T	9.37:g.21350487G>A		371.0	0.0	0		361.0	179.0	0.495845	NM_021002	Q5VYQ1	Silent	SNP	ENST00000380210.1	37	CCDS6504.1																																																																																			G|0.971;A|0.029	0.029	strong		0.498	IFNA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051905.1	NM_021002	
MIA2	117153	hgsc.bcm.edu	37	14	39717002	39717002	+	Silent	SNP	A	A	G	rs17109049	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:39717002A>G	ENST00000280082.3	+	4	1423	c.1224A>G	c.(1222-1224)gcA>gcG	p.A408A	MIA2_ENST00000556784.1_Silent_p.A407A|RP11-407N17.3_ENST00000553728.1_Silent_p.A408A	NM_054024.3	NP_473365.3	Q96PC5	MIA2_HUMAN	melanoma inhibitory activity 2	408					cholesterol homeostasis (GO:0042632)|triglyceride homeostasis (GO:0070328)	endoplasmic reticulum exit site (GO:0070971)|extracellular region (GO:0005576)				NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	31	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0216)		ATGGTGGGGCAGATGAACATG	0.333													A|||	380	0.0758786	0.2769	0.0202	5008	,	,		18395	0.0		0.0	False		,,,				2504	0.0				p.A408A		Atlas-SNP	.											.	MIA2	82	.	0			c.A1224G						PASS	.	A		1093,3313	385.1+/-325.6	116,861,1226	74.0	79.0	77.0		1224	3.1	0.0	14	dbSNP_123	77	11,8589	7.7+/-29.5	0,11,4289	no	coding-synonymous	MIA2	NM_054024.3		116,872,5515	GG,GA,AA		0.1279,24.8071,8.4884		408/655	39717002	1104,11902	2203	4300	6503	SO:0001819	synonymous_variant	117153	exon4			TGGGGCAGATGAA	BC035981	CCDS9672.1	14q13.2	2007-05-01			ENSG00000150526	ENSG00000150526			18432	protein-coding gene	gene with protein product		608001				12586826	Standard	NM_054024		Approved	FLJ22404	uc001wux.3	Q96PC5	OTTHUMG00000028831	ENST00000280082.3:c.1224A>G	14.37:g.39717002A>G		41.0	0.0	0		46.0	46.0	1	NM_054024	A1L4H0|Q9H6C1	Silent	SNP	ENST00000280082.3	37	CCDS9672.1																																																																																			A|0.921;G|0.079	0.079	strong		0.333	MIA2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276768.3	NM_054024	
EHHADH	1962	hgsc.bcm.edu	37	3	184922267	184922267	+	Missense_Mutation	SNP	T	T	C	rs115754857	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184922267T>C	ENST00000231887.3	-	6	922	c.847A>G	c.(847-849)Act>Gct	p.T283A	EHHADH_ENST00000456310.1_Missense_Mutation_p.T187A	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	283	3-hydroxyacyl-CoA dehydrogenase.				fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			CCGGAGGGAGTTGACCACTTA	0.488													T|||	82	0.0163738	0.0605	0.0029	5008	,	,		21681	0.0		0.0	False		,,,				2504	0.0				p.T283A		Atlas-SNP	.											.	EHHADH	73	.	0			c.A847G						PASS	.	T	ALA/THR,ALA/THR	170,4236	112.1+/-150.2	3,164,2036	121.0	118.0	119.0		559,847	1.6	0.4	3	dbSNP_132	119	0,8600		0,0,4300	yes	missense,missense	EHHADH	NM_001166415.1,NM_001966.3	58,58	3,164,6336	CC,CT,TT		0.0,3.8584,1.3071	benign,benign	187/628,283/724	184922267	170,12836	2203	4300	6503	SO:0001583	missense	1962	exon6			AGGGAGTTGACCA	L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"""enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"""	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.847A>G	3.37:g.184922267T>C	ENSP00000231887:p.Thr283Ala	61.0	0.0	0		56.0	21.0	0.375	NM_001966	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Missense_Mutation	SNP	ENST00000231887.3	37	CCDS33901.1	18	0.008241758241758242	17	0.034552845528455285	1	0.0027624309392265192	0	0.0	0	0.0	T	7.470	0.646535	0.14451	0.038584	0.0	ENSG00000113790	ENST00000537544;ENST00000231887;ENST00000456310	T;T	0.74526	-0.44;-0.85	5.53	1.61	0.23674	.	0.442567	0.26761	N	0.022621	T	0.21674	0.0522	L	0.27053	0.805	0.09310	N	1	B	0.09022	0.002	B	0.11329	0.006	T	0.15492	-1.0435	10	0.35671	T	0.21	-3.3999	1.5805	0.02633	0.1344:0.1596:0.1395:0.5665	.	283	Q08426	ECHP_HUMAN	A	283;283;187	ENSP00000231887:T283A;ENSP00000387746:T187A	ENSP00000231887:T283A	T	-	1	0	EHHADH	186404961	0.100000	0.21855	0.382000	0.26119	0.937000	0.57800	1.287000	0.33284	0.035000	0.15519	-0.309000	0.09137	ACT	T|0.986;C|0.014	0.014	strong		0.488	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1		
MRPS24	64951	hgsc.bcm.edu	37	7	43908661	43908661	+	Silent	SNP	G	G	T	rs17854882	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:43908661G>T	ENST00000317534.5	-	3	182	c.121C>A	c.(121-123)Cga>Aga	p.R41R	URGCP-MRPS24_ENST00000603700.1_Missense_Mutation_p.P86Q|MRPS24_ENST00000467084.1_5'UTR	NM_032014.2	NP_114403.1	Q96EL2	RT24_HUMAN	mitochondrial ribosomal protein S24	41					translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrial small ribosomal subunit (GO:0005763)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	5						ACGCGTACTCGGGCCGCCCGG	0.647													G|||	150	0.0299521	0.112	0.0014	5008	,	,		10791	0.0		0.001	False		,,,				2504	0.0				p.P86Q		Atlas-SNP	.											.	.	.	.	0			c.C257A						PASS	.	G	GLN/PRO,	422,3984	205.8+/-227.6	21,380,1802	58.0	53.0	55.0		257,121	2.7	0.9	7	dbSNP_123	55	3,8597	3.0+/-9.4	0,3,4297	yes	missense,coding-synonymous	MRPS24,URGCP-MRPS24	NM_001204871.1,NM_032014.2	76,	21,383,6099	TT,TG,GG		0.0349,9.5778,3.2677	,	86/111,41/168	43908661	425,12581	2203	4300	6503	SO:0001819	synonymous_variant	0	exon6			GTACTCGGGCCGC	AB061207	CCDS5473.1	7p14	2012-09-13			ENSG00000062582	ENSG00000062582		"""Mitochondrial ribosomal proteins / small subunits"""	14510	protein-coding gene	gene with protein product		611986				8127713, 11279123	Standard	NM_032014		Approved	MRP-S24, HSPC335	uc003tit.1	Q96EL2	OTTHUMG00000023175	ENST00000317534.5:c.121C>A	7.37:g.43908661G>T		83.0	0.0	0		151.0	73.0	0.483444	NM_001204871	A4D1U9|P82668|Q96Q23|Q9P047	Missense_Mutation	SNP	ENST00000317534.5	37	CCDS5473.1																																																																																			G|0.971;T|0.029	0.029	strong		0.647	MRPS24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250949.1	NM_032014	
CCDC102B	79839	hgsc.bcm.edu	37	18	66678182	66678182	+	Missense_Mutation	SNP	C	C	A	rs17080065	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:66678182C>A	ENST00000360242.5	+	7	1392	c.1275C>A	c.(1273-1275)aaC>aaA	p.N425K	CCDC102B_ENST00000584156.1_Missense_Mutation_p.N425K|CCDC102B_ENST00000319445.6_Missense_Mutation_p.N425K	NM_024781.2	NP_079057	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B	425			N -> K (in dbSNP:rs17080065).							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)				AATTACTGAACCTTCAACATG	0.323													C|||	129	0.0257588	0.093	0.0086	5008	,	,		17732	0.0		0.0	False		,,,				2504	0.0				p.N425K		Atlas-SNP	.											.	CCDC102B	92	.	0			c.C1275A						PASS	.	C	LYS/ASN,LYS/ASN	354,4052	155.5+/-188.7	19,316,1868	62.0	60.0	60.0		1275,1275	-3.1	0.0	18	dbSNP_123	60	3,8597	1.2+/-3.3	0,3,4297	yes	missense,missense	CCDC102B	NM_001093729.1,NM_024781.2	94,94	19,319,6165	AA,AC,CC		0.0349,8.0345,2.7449	benign,benign	425/514,425/514	66678182	357,12649	2203	4300	6503	SO:0001583	missense	79839	exon9			ACTGAACCTTCAA	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.1275C>A	18.37:g.66678182C>A	ENSP00000353377:p.Asn425Lys	97.0	0.0	0		88.0	50.0	0.568182	NM_001093729	Q7Z467|Q8NDK7|Q9H5C1	Missense_Mutation	SNP	ENST00000360242.5	37	CCDS11996.2	47	0.02152014652014652	44	0.08943089430894309	3	0.008287292817679558	0	0.0	0	0.0	C	5.485	0.274466	0.10403	0.080345	3.49E-4	ENSG00000150636	ENST00000319445;ENST00000360242	T;T	0.11169	2.8;2.8	5.4	-3.11	0.05299	.	1.868220	0.02591	N	0.099920	T	0.00241	0.0007	N	0.22421	0.69	0.34315	D	0.685947	B	0.26400	0.148	B	0.24394	0.053	T	0.37572	-0.9700	10	0.10902	T	0.67	1.3033	1.8352	0.03138	0.4717:0.2442:0.0991:0.185	rs17080065;rs58253666;rs17080065	425	Q68D86	C102B_HUMAN	K	425	ENSP00000316237:N425K;ENSP00000353377:N425K	ENSP00000316237:N425K	N	+	3	2	CCDC102B	64829162	0.005000	0.15991	0.007000	0.13788	0.610000	0.37248	-1.893000	0.01609	-0.763000	0.04658	-0.355000	0.07637	AAC	C|0.972;A|0.028	0.028	strong		0.323	CCDC102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256225.2	NM_024781	
GPR148	344561	hgsc.bcm.edu	37	2	131487691	131487691	+	Missense_Mutation	SNP	C	C	T	rs143265147	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:131487691C>T	ENST00000309926.4	+	1	1049	c.967C>T	c.(967-969)Cgc>Tgc	p.R323C		NM_207364.2	NP_997247.2	Q8TDV2	GP148_HUMAN	G protein-coupled receptor 148	323						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(15)|skin(3)|upper_aerodigestive_tract(1)	27	Colorectal(110;0.1)					GTACCTGCTCCGCTACCGGCA	0.577													.|||	23	0.00459265	0.0144	0.0043	5008	,	,		20324	0.0		0.001	False		,,,				2504	0.0				p.R323C		Atlas-SNP	.											GPR148,NS,carcinoma,0,1	GPR148	54	1	0			c.C967T						PASS	.	C	CYS/ARG	56,4350		1,54,2148	60.0	51.0	54.0		967	-4.1	0.0	2	dbSNP_134	54	1,8599		0,1,4299	yes	missense	GPR148	NM_207364.2	180	1,55,6447	TT,TC,CC		0.0116,1.271,0.4383	benign	323/348	131487691	57,12949	2203	4300	6503	SO:0001583	missense	344561	exon1			CTGCTCCGCTACC	AY255532	CCDS2163.1	2q21.2	2012-08-21			ENSG00000173302	ENSG00000173302		"""GPCR / Class A : Orphans"""	23623	protein-coding gene	gene with protein product						12679517	Standard	NM_207364		Approved	PGR6	uc002trv.2	Q8TDV2	OTTHUMG00000131655	ENST00000309926.4:c.967C>T	2.37:g.131487691C>T	ENSP00000308908:p.Arg323Cys	78.0	0.0	0		114.0	58.0	0.508772	NM_207364	Q2M369|Q86SP7|Q86U87	Missense_Mutation	SNP	ENST00000309926.4	37	CCDS2163.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	.	8.765	0.924629	0.18056	0.01271	1.16E-4	ENSG00000173302	ENST00000309926	T	0.40476	1.03	3.49	-4.14	0.03892	GPCR, rhodopsin-like superfamily (1);	0.000000	0.46442	U	0.000284	T	0.13586	0.0329	L	0.27053	0.805	0.32198	N	0.578142	B	0.18741	0.03	B	0.13407	0.009	T	0.01810	-1.1269	10	0.52906	T	0.07	-10.4178	0.3322	0.00320	0.2767:0.2483:0.1305:0.3444	.	323	Q8TDV2	GP148_HUMAN	C	323	ENSP00000308908:R323C	ENSP00000308908:R323C	R	+	1	0	GPR148	131204161	0.959000	0.32827	0.000000	0.03702	0.359000	0.29487	-0.164000	0.09983	-0.512000	0.06505	-0.261000	0.10672	CGC	C|0.996;T|0.004	0.004	strong		0.577	GPR148-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254552.3	XM_293092	
ACKR3	57007	hgsc.bcm.edu	37	2	237489796	237489796	+	Missense_Mutation	SNP	G	G	A	rs35095494	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:237489796G>A	ENST00000272928.3	+	2	998	c.688G>A	c.(688-690)Gtc>Atc	p.V230I		NM_020311.2	NP_064707.1	P25106	ACKR3_HUMAN	atypical chemokine receptor 3	230					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|chemokine-mediated signaling pathway (GO:0070098)|chemotaxis (GO:0006935)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|receptor internalization (GO:0031623)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell surface (GO:0009986)|coated pit (GO:0005905)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C-X-C chemokine binding (GO:0019958)|C-X-C chemokine receptor activity (GO:0016494)|coreceptor activity (GO:0015026)|scavenger receptor activity (GO:0005044)										CATTATCGCTGTCTTCTACTT	0.572													G|||	59	0.0117812	0.0431	0.0029	5008	,	,		21400	0.0		0.0	False		,,,				2504	0.0				p.V230I		Atlas-SNP	.											.	CXCR7	72	.	0			c.G688A						PASS	.	G	ILE/VAL	212,4194	128.6+/-165.4	5,202,1996	103.0	88.0	93.0		688	0.6	0.3	2	dbSNP_126	93	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CXCR7	NM_020311.2	29	5,204,6294	AA,AG,GG		0.0233,4.8116,1.6454	benign	230/363	237489796	214,12792	2203	4300	6503	SO:0001583	missense	57007	exon2			ATCGCTGTCTTCT	BC008459	CCDS2516.1	2q37.3	2013-07-17	2013-07-16	2013-07-16	ENSG00000144476	ENSG00000144476		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : Atypical"""	23692	protein-coding gene	gene with protein product		610376	"""chemokine orphan receptor 1"", ""chemokine (C-X-C motif) receptor 7"""	CMKOR1, CXCR7		16107333, 16148	Standard	NM_020311		Approved	RDC1, GPR159	uc002vwd.3	P25106	OTTHUMG00000133295	ENST00000272928.3:c.688G>A	2.37:g.237489796G>A	ENSP00000272928:p.Val230Ile	136.0	0.0	0		172.0	90.0	0.523256	NM_020311	A8K6J4|Q53RV4|Q8NE10|Q92938|Q92986	Missense_Mutation	SNP	ENST00000272928.3	37	CCDS2516.1	21	0.009615384615384616	20	0.04065040650406504	1	0.0027624309392265192	0	0.0	0	0.0	G	6.438	0.448991	0.12223	0.048116	2.33E-4	ENSG00000144476	ENST00000272928	T	0.37235	1.21	5.7	0.629	0.17687	GPCR, rhodopsin-like superfamily (1);	0.285365	0.33346	N	0.005017	T	0.02807	0.0084	N	0.25245	0.725	0.26027	N	0.981791	B	0.09022	0.002	B	0.14023	0.01	T	0.12142	-1.0559	9	.	.	.	.	5.5847	0.17267	0.3325:0.2292:0.4382:0.0	rs35095494	230	P25106	CXCR7_HUMAN	I	230	ENSP00000272928:V230I	.	V	+	1	0	CXCR7	237154535	0.001000	0.12720	0.276000	0.24689	0.421000	0.31385	-0.112000	0.10791	0.052000	0.16007	-0.140000	0.14226	GTC	G|0.984;A|0.016	0.016	strong		0.572	ACKR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257079.2	NM_020311	
ADAMDEC1	27299	hgsc.bcm.edu	37	8	24251659	24251659	+	Splice_Site	SNP	T	T	C	rs7007084	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24251659T>C	ENST00000256412.4	+	4	582	c.362T>C	c.(361-363)aTg>aCg	p.M121T	RP11-624C23.1_ENST00000519689.1_RNA|ADAMDEC1_ENST00000522298.1_Splice_Site_p.M42T|RP11-624C23.1_ENST00000523578.1_RNA|ADAMDEC1_ENST00000538205.1_Splice_Site_p.M42T	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	121			M -> T (in dbSNP:rs7007084).		immune response (GO:0006955)|negative regulation of cell adhesion (GO:0007162)	extracellular region (GO:0005576)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|large_intestine(4)|skin(2)|stomach(1)	9		Prostate(55;0.0181)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)		CCTGAGAACATGGTAGGGTCC	0.423													T|||	133	0.0265575	0.0968	0.0072	5008	,	,		18292	0.0		0.0	False		,,,				2504	0.0				p.M121T	Ovarian(147;687 1849 3699 25981 31337)	Atlas-SNP	.											.	ADAMDEC1	69	.	0			c.T362C						PASS	.	T	THR/MET,THR/MET,THR/MET	391,4015	191.6+/-217.2	21,349,1833	72.0	68.0	69.0		125,125,362	-0.3	0.2	8	dbSNP_116	69	3,8597	3.0+/-9.4	0,3,4297	yes	missense-near-splice,missense-near-splice,missense-near-splice	ADAMDEC1	NM_001145271.1,NM_001145272.1,NM_014479.3	81,81,81	21,352,6130	CC,CT,TT		0.0349,8.8743,3.0294	benign,benign,benign	42/392,42/392,121/471	24251659	394,12612	2203	4300	6503	SO:0001630	splice_region_variant	27299	exon4			AGAACATGGTAGG	Y13323	CCDS6044.1, CCDS55212.1	8p12	2008-08-07			ENSG00000134028	ENSG00000134028			16299	protein-coding gene	gene with protein product		606393				9271581, 12037602	Standard	NM_001145271		Approved	M12.219	uc003xdz.2	O15204	OTTHUMG00000097858	ENST00000256412.4:c.363+1T>C	8.37:g.24251659T>C		76.0	0.0	0		65.0	32.0	0.492308	NM_014479	B7ZAK5	Missense_Mutation	SNP	ENST00000256412.4	37	CCDS6044.1	49	0.022435897435897436	46	0.09349593495934959	3	0.008287292817679558	0	0.0	0	0.0	T	0.640	-0.813614	0.02798	0.088743	3.49E-4	ENSG00000134028	ENST00000256412;ENST00000538205;ENST00000522298	T;T;T	0.05139	3.49;3.49;3.49	5.46	-0.309	0.12769	Peptidase M12B, propeptide (1);	0.592394	0.17862	N	0.159489	T	0.00144	0.0004	N	0.17872	0.535	0.09310	N	0.999996	B	0.11235	0.004	B	0.08055	0.003	T	0.43718	-0.9374	10	0.37606	T	0.19	-3.7358	1.3321	0.02137	0.3046:0.0864:0.1576:0.4513	rs7007084;rs52800945;rs7007084	121	O15204	ADEC1_HUMAN	T	121;42;42	ENSP00000256412:M121T;ENSP00000442592:M42T;ENSP00000428993:M42T	ENSP00000256412:M121T	M	+	2	0	ADAMDEC1	24307604	0.195000	0.23338	0.163000	0.22734	0.026000	0.11368	0.147000	0.16202	0.072000	0.16694	-0.371000	0.07208	ATG	T|0.967;C|0.033	0.033	strong		0.423	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479	Missense_Mutation
CCT8L2	150160	hgsc.bcm.edu	37	22	17072347	17072347	+	Nonsense_Mutation	SNP	C	C	T	rs139948519	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:17072347C>T	ENST00000359963.3	-	1	1353	c.1094G>A	c.(1093-1095)tGg>tAg	p.W365*		NM_014406.4	NP_055221.1	Q96SF2	TCPQM_HUMAN	chaperonin containing TCP1, subunit 8 (theta)-like 2	365					anion transport (GO:0006820)|cellular protein metabolic process (GO:0044267)|potassium ion transmembrane transport (GO:0071805)|transport (GO:0006810)	cytoplasm (GO:0005737)	anion channel activity (GO:0005253)|ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)			breast(3)|endometrium(7)|kidney(1)|large_intestine(8)|liver(2)|lung(37)|ovary(3)|prostate(3)|skin(2)|stomach(1)	67	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				TGTACATTCCCATTCAAATAC	0.612													c|||	113	0.0225639	0.0598	0.0029	5008	,	,		18689	0.0		0.002	False		,,,				2504	0.0307				p.W365X		Atlas-SNP	.											.	CCT8L2	150	.	0			c.G1094A						PASS	.	C	stop/TRP	301,4105	164.7+/-196.3	7,287,1909	88.0	83.0	85.0		1094	2.0	0.2	22	dbSNP_134	85	28,8572	19.2+/-60.6	0,28,4272	no	stop-gained	CCT8L2	NM_014406.4		7,315,6181	TT,TC,CC		0.3256,6.8316,2.5296		365/558	17072347	329,12677	2203	4300	6503	SO:0001587	stop_gained	150160	exon1			CATTCCCATTCAA	AP003553	CCDS13738.1	22q11.1	2011-09-01			ENSG00000198445	ENSG00000198445			15553	protein-coding gene	gene with protein product							Standard	NM_014406		Approved	CESK1	uc002zlp.1	Q96SF2	OTTHUMG00000141302	ENST00000359963.3:c.1094G>A	22.37:g.17072347C>T	ENSP00000353048:p.Trp365*	69.0	0.0	0		53.0	29.0	0.54717	NM_014406	A4QPH3|Q9UJS3	Nonsense_Mutation	SNP	ENST00000359963.3	37	CCDS13738.1	29	0.013278388278388278	26	0.052845528455284556	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	c	18.96	3.734449	0.69189	0.068316	0.003256	ENSG00000198445	ENST00000359963	.	.	.	1.98	1.98	0.26296	.	0.261754	0.21132	U	0.079635	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	-8.0904	7.4423	0.27190	0.0:1.0:0.0:0.0	.	.	.	.	X	365	.	ENSP00000353048:W365X	W	-	2	0	CCT8L2	15452347	0.722000	0.28017	0.224000	0.23877	0.129000	0.20672	1.546000	0.36179	1.115000	0.41800	0.379000	0.24179	TGG	C|0.982;T|0.018	0.018	strong		0.612	CCT8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280580.1		
TTC24	164118	hgsc.bcm.edu	37	1	156555577	156555577	+	Missense_Mutation	SNP	C	C	T	rs147693801	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156555577C>T	ENST00000368237.3	+	8	1529	c.1529C>T	c.(1528-1530)aCg>aTg	p.T510M	TTC24_ENST00000368236.3_Missense_Mutation_p.T510M|TTC24_ENST00000478081.1_3'UTR|AL365181.1_ENST00000581084.1_RNA			A2A3L6	TTC24_HUMAN	tetratricopeptide repeat domain 24	510										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(10)|pancreas(1)|prostate(1)	20	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					ACCAAGCACACGCCCTGCAGA	0.517													C|||	55	0.0109824	0.0393	0.0029	5008	,	,		20692	0.0		0.001	False		,,,				2504	0.0				p.T510M		Atlas-SNP	.											TTC24,right_upper_lobe,carcinoma,-1,1	TTC24	46	1	0			c.C1529T						PASS	.	C	MET/THR	122,4138		3,116,2011	117.0	119.0	118.0		1529	-0.6	0.0	1	dbSNP_134	118	0,8462		0,0,4231	yes	missense	TTC24	NM_001105669.2	81	3,116,6242	TT,TC,CC		0.0,2.8638,0.959	benign	510/583	156555577	122,12600	2130	4231	6361	SO:0001583	missense	164118	exon9			AGCACACGCCCTG		CCDS53379.1	1q22	2013-01-10			ENSG00000187862	ENSG00000187862		"""Tetratricopeptide (TTC) repeat domain containing"""	32348	protein-coding gene	gene with protein product							Standard	NM_001105669		Approved		uc021pbf.1	A2A3L6	OTTHUMG00000033202	ENST00000368237.3:c.1529C>T	1.37:g.156555577C>T	ENSP00000357220:p.Thr510Met	123.0	0.0	0		155.0	65.0	0.419355	NM_001105669	Q5T3H7	Missense_Mutation	SNP	ENST00000368237.3	37	CCDS53379.1	13|13	0.005952380952380952|0.005952380952380952	12|12	0.024390243902439025|0.024390243902439025	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	C|C	4.199|4.199	0.035700|0.035700	0.08148|0.08148	0.028638|0.028638	0.0|0.0	ENSG00000187862|ENSG00000187862	ENST00000340086|ENST00000368236;ENST00000368237	.|T;T	.|0.26223	.|1.75;1.75	3.22|3.22	-0.612|-0.612	0.11597|0.11597	.|.	.|17.220800	.|0.00397	.|N	.|0.000056	T|T	0.03915|0.03915	0.0110|0.0110	N|N	0.08118|0.08118	0|0	0.09310|0.09310	N|N	1|1	.|B	.|0.06786	.|0.001	.|B	.|0.01281	.|0.0	T|T	0.29971|0.29971	-0.9994|-0.9994	5|10	.|0.48119	.|T	.|0.1	.|.	3.0131|3.0131	0.06051|0.06051	0.0:0.2819:0.2328:0.4852|0.0:0.2819:0.2328:0.4852	.|.	.|510	.|A2A3L6	.|TTC24_HUMAN	C|M	283|510	.|ENSP00000357219:T510M;ENSP00000357220:T510M	.|ENSP00000357219:T510M	R|T	+|+	1|2	0|0	TTC24|TTC24	154822201|154822201	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.015000|0.015000	0.08874|0.08874	0.040000|0.040000	0.13905|0.13905	-0.118000|-0.118000	0.11851|0.11851	-0.379000|-0.379000	0.06801|0.06801	CGC|ACG	C|0.994;T|0.006	0.006	strong		0.517	TTC24-006	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000158547.1	XM_089384	
U2SURP	23350	hgsc.bcm.edu	37	3	142747230	142747230	+	Silent	SNP	G	G	A	rs80238215	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:142747230G>A	ENST00000473835.2	+	15	1518	c.1428G>A	c.(1426-1428)aaG>aaA	p.K476K	U2SURP_ENST00000397933.2_Silent_p.K67K|U2SURP_ENST00000493598.2_Silent_p.K475K	NM_001080415.1	NP_001073884.1	O15042	SR140_HUMAN	U2 snRNP-associated SURP domain containing	476					RNA processing (GO:0006396)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(1)|skin(1)	31						ATAGGTGGAAGCTTTATTCTA	0.313													G|||	35	0.00698882	0.0234	0.0058	5008	,	,		15948	0.0		0.0	False		,,,				2504	0.0				p.K476K		Atlas-SNP	.											.	U2SURP	66	.	0			c.G1428A						PASS	.	G		61,3529		1,59,1735	74.0	70.0	71.0		1428	2.0	1.0	3	dbSNP_132	71	0,8136		0,0,4068	no	coding-synonymous	U2SURP	NM_001080415.1		1,59,5803	AA,AG,GG		0.0,1.6992,0.5202		476/1030	142747230	61,11665	1795	4068	5863	SO:0001819	synonymous_variant	23350	exon15			GTGGAAGCTTTAT	BK000564	CCDS46928.1	3q23	2013-02-12			ENSG00000163714	ENSG00000163714		"""RNA binding motif (RRM) containing"""	30855	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein a"", ""Ser/Arg-rich domain protein, 140 kDa"", ""U2 associated SR140 protein"""					9205841, 12234937	Standard	NM_001080415		Approved	fSAPa, SR140	uc003evh.1	O15042	OTTHUMG00000159323	ENST00000473835.2:c.1428G>A	3.37:g.142747230G>A		232.0	0.0	0		184.0	85.0	0.461957	NM_001080415	A0PJ60|Q0D2M1|Q2NKQ7|Q9BR70	Silent	SNP	ENST00000473835.2	37	CCDS46928.1																																																																																			G|0.991;A|0.009	0.009	strong		0.313	U2SURP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354603.2	NM_001080415	
HTR3E	285242	hgsc.bcm.edu	37	3	183824398	183824398	+	Missense_Mutation	SNP	G	G	A	rs13324468	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:183824398G>A	ENST00000415389.2	+	9	1754	c.1288G>A	c.(1288-1290)Gcg>Acg	p.A430T	HTR3E_ENST00000440596.2_Missense_Mutation_p.A456T|HTR3E_ENST00000335304.2_Missense_Mutation_p.A445T|HTR3E_ENST00000436361.2_Missense_Mutation_p.A430T|HTR3E-AS1_ENST00000431427.1_RNA|HTR3E_ENST00000425359.2_Missense_Mutation_p.A415T	NM_001256613.1|NM_198313.2	NP_001243542.1|NP_938055.1	A5X5Y0	5HT3E_HUMAN	5-hydroxytryptamine (serotonin) receptor 3E, ionotropic	430			A -> T (in dbSNP:rs13324468).		ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	40	all_cancers(143;1.46e-10)|Ovarian(172;0.0303)		Epithelial(37;7.06e-36)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)		Ergoloid mesylate(DB01049)	GTTCAGCCACGCGATGGACGC	0.607													G|||	210	0.0419329	0.1543	0.0086	5008	,	,		18903	0.0		0.0	False		,,,				2504	0.0				p.A456T	Melanoma(7;227 727 6634 44770)	Atlas-SNP	.											.	HTR3E	65	.	0			c.G1366A						PASS	.	G	THR/ALA	520,3886	239.0+/-250.2	27,466,1710	171.0	152.0	158.0		1333	-5.5	0.0	3	dbSNP_121	158	5,8595	4.3+/-15.6	0,5,4295	no	missense	HTR3E	NM_182589.2	58	27,471,6005	AA,AG,GG		0.0581,11.8021,4.0366	benign	445/472	183824398	525,12481	2203	4300	6503	SO:0001583	missense	285242	exon7			AGCCACGCGATGG	AY159813	CCDS3251.1, CCDS58868.1, CCDS58869.1, CCDS58870.1, CCDS58871.1	3q27	2012-05-22	2012-02-03		ENSG00000186038	ENSG00000186038		"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	24005	protein-coding gene	gene with protein product		610123	"""5-hydroxytryptamine (serotonin) receptor 3, family member E"""			12801637, 15157181	Standard	NM_001256613		Approved		uc010hxr.3	A5X5Y0	OTTHUMG00000156857	ENST00000415389.2:c.1288G>A	3.37:g.183824398G>A	ENSP00000401444:p.Ala430Thr	328.0	0.0	0		283.0	146.0	0.515901	NM_001256614	A8IKD7|E9PGF1|Q495G1|Q495G3|Q6V706|Q6V707|Q7Z6B2	Missense_Mutation	SNP	ENST00000415389.2	37	CCDS58868.1	109	0.04990842490842491	104	0.21138211382113822	5	0.013812154696132596	0	0.0	0	0.0	g	4.180	0.031992	0.08101	0.118021	5.81E-4	ENSG00000186038	ENST00000415389;ENST00000425359;ENST00000335304;ENST00000436361;ENST00000440596	D;D;D;D;D	0.81908	-1.55;-1.55;-1.55;-1.55;-1.55	4.07	-5.5	0.02576	Neurotransmitter-gated ion-channel transmembrane domain (1);	2.871980	0.03018	N	0.150396	T	0.00109	0.0003	N	0.04043	-0.29	0.80722	P	0.0	B;B;B;B;B	0.12013	0.001;0.0;0.005;0.001;0.001	B;B;B;B;B	0.11329	0.005;0.004;0.006;0.002;0.002	T	0.10019	-1.0648	9	0.49607	T	0.09	.	7.9969	0.30273	0.2122:0.3113:0.4765:0.0	rs13324468;rs56491361;rs13324468	456;430;430;445;415	E9PGF1;A5X5Y0;A5X5Y0-4;A5X5Y0-3;A5X5Y0-2	.;5HT3E_HUMAN;.;.;.	T	430;415;445;430;456	ENSP00000401444:A430T;ENSP00000401900:A415T;ENSP00000335511:A445T;ENSP00000395833:A430T;ENSP00000406050:A456T	ENSP00000335511:A445T	A	+	1	0	HTR3E	185307092	0.000000	0.05858	0.038000	0.18304	0.020000	0.10135	0.081000	0.14823	-1.048000	0.03238	-2.223000	0.00295	GCG	G|0.941;A|0.059	0.059	strong		0.607	HTR3E-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346284.1	NM_182589	
CBL	867	hgsc.bcm.edu	37	11	119170480	119170480	+	Missense_Mutation	SNP	G	G	A	rs17122769	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:119170480G>A	ENST00000264033.4	+	16	3086	c.2710G>A	c.(2710-2712)Gta>Ata	p.V904I		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	904	Interaction with CD2AP.		V -> I (in dbSNP:rs17122769).		cell surface receptor signaling pathway (GO:0007166)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|flotillin complex (GO:0016600)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ephrin receptor binding (GO:0046875)|ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(194)|kidney(3)|large_intestine(9)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	251		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		TCCTGCCCATGTAGCTACCTA	0.493			"""T, Mis S, O"""	MLL	"""AML, JMML, MDS"""				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies				G|||	30	0.00599042	0.0219	0.0014	5008	,	,		21109	0.0		0.0	False		,,,				2504	0.0				p.V904I		Atlas-SNP	.		"""Dom, Rec"""	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	.	CBL	408	.	0			c.G2710A						PASS	.	G	ILE/VAL	65,4333	61.1+/-98.1	0,65,2134	239.0	244.0	242.0		2710	4.9	0.1	11	dbSNP_123	242	2,8588	2.2+/-6.3	0,2,4293	yes	missense	CBL	NM_005188.2	29	0,67,6427	AA,AG,GG		0.0233,1.4779,0.5159	benign	904/907	119170480	67,12921	2199	4295	6494	SO:0001583	missense	867	exon16	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CBL-associated JMML	GCCCATGTAGCTA	X57110	CCDS8418.1	11q23.3	2014-09-17	2012-02-23		ENSG00000110395	ENSG00000110395		"""RING-type (C3HC4) zinc fingers"""	1541	protein-coding gene	gene with protein product	"""oncogene CBL2"""	165360	"""Cas-Br-M (murine) ecotropic retroviral transforming sequence"""	CBL2		2013228	Standard	NM_005188		Approved	RNF55, c-Cbl	uc001pwe.4	P22681	OTTHUMG00000166170	ENST00000264033.4:c.2710G>A	11.37:g.119170480G>A	ENSP00000264033:p.Val904Ile	72.0	0.0	0		69.0	30.0	0.434783	NM_005188	A3KMP8	Missense_Mutation	SNP	ENST00000264033.4	37	CCDS8418.1	8	0.003663003663003663	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	G	11.37	1.617349	0.28801	0.014779	2.33E-4	ENSG00000110395	ENST00000264033	T	0.78816	-1.21	5.8	4.89	0.63831	.	0.120265	0.56097	D	0.000027	T	0.49372	0.1553	N	0.03115	-0.41	0.44677	D	0.997661	B	0.12013	0.005	B	0.14023	0.01	T	0.50499	-0.8821	10	0.30854	T	0.27	-23.714	14.7175	0.69280	0.0692:0.0:0.9308:0.0	rs17122769;rs52793379;rs17122769	904	P22681	CBL_HUMAN	I	904	ENSP00000264033:V904I	ENSP00000264033:V904I	V	+	1	0	CBL	118675690	0.997000	0.39634	0.064000	0.19789	0.936000	0.57629	2.667000	0.46808	1.461000	0.47929	0.655000	0.94253	GTA	G|0.993;A|0.007	0.007	strong		0.493	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4	NM_005188	
ZYG11A	440590	hgsc.bcm.edu	37	1	53326421	53326421	+	Missense_Mutation	SNP	A	A	G	rs61744306	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:53326421A>G	ENST00000371528.1	+	4	1175	c.1027A>G	c.(1027-1029)Atg>Gtg	p.M343V	ZYG11A_ENST00000371532.1_Start_Codon_SNP_p.M1V	NM_001004339.2	NP_001004339.2	Q6WRX3	ZY11A_HUMAN	zyg-11 family member A, cell cycle regulator	343										breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|skin(1)	10						AGGAGCCAGTATGAGTCAGAT	0.423													A|||	69	0.013778	0.0303	0.0231	5008	,	,		17868	0.0		0.0109	False		,,,				2504	0.002				p.M343V		Atlas-SNP	.											.	ZYG11A	46	.	0			c.A1027G						PASS	.	A	VAL/MET	32,1352		0,32,660	114.0	96.0	102.0		1027	-0.3	0.9	1	dbSNP_129	102	18,3164		0,18,1573	yes	missense	ZYG11A	NM_001004339.2	21	0,50,2233	GG,GA,AA		0.5657,2.3121,1.0951	benign	343/760	53326421	50,4516	692	1591	2283	SO:0001583	missense	440590	exon4			GCCAGTATGAGTC		CCDS44148.1	1p32.3	2013-01-17	2012-12-10		ENSG00000203995	ENSG00000203995		"""ZYG11 cell cycle regulator family"""	32058	protein-coding gene	gene with protein product			"""zyg-11 homolog A (C. elegans)"""				Standard	NM_001004339		Approved	ZYG11	uc001cuk.2	Q6WRX3	OTTHUMG00000008923	ENST00000371528.1:c.1027A>G	1.37:g.53326421A>G	ENSP00000360583:p.Met343Val	255.0	0.0	0		246.0	103.0	0.418699	NM_001004339	A6NCK5	Missense_Mutation	SNP	ENST00000371528.1	37	CCDS44148.1	31	0.014194139194139194	13	0.026422764227642278	12	0.03314917127071823	0	0.0	6	0.0079155672823219	A	9.069	0.996332	0.19043	0.023121	0.005657	ENSG00000203995	ENST00000371532;ENST00000371528	T;T	0.05025	3.51;3.51	4.89	-0.281	0.12882	.	0.423208	0.27787	N	0.017844	T	0.00967	0.0032	N	0.22421	0.69	0.25986	N	0.982306	B	0.02656	0.0	B	0.04013	0.001	T	0.43814	-0.9368	10	0.14656	T	0.56	-1.518	3.1939	0.06626	0.2766:0.0:0.3675:0.3559	rs61744306	343	Q6WRX3	ZY11A_HUMAN	V	1;343	ENSP00000360587:M1V;ENSP00000360583:M343V	ENSP00000360583:M343V	M	+	1	0	ZYG11A	53099009	1.000000	0.71417	0.936000	0.37596	0.987000	0.75469	1.184000	0.32053	0.032000	0.15435	0.459000	0.35465	ATG	A|0.983;G|0.017	0.017	strong		0.423	ZYG11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024856.3	NM_001004339	
EIF3K	27335	hgsc.bcm.edu	37	19	39125677	39125677	+	Missense_Mutation	SNP	G	G	A	rs138580388	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39125677G>A	ENST00000538434.1	+	6	518	c.283G>A	c.(283-285)Gac>Aac	p.D95N	EIF3K_ENST00000545173.2_Missense_Mutation_p.D182N|EIF3K_ENST00000588934.1_Intron|EIF3K_ENST00000248342.4_Missense_Mutation_p.D182N|EIF3K_ENST00000593149.1_Missense_Mutation_p.D95N|EIF3K_ENST00000592558.1_Missense_Mutation_p.D156N					eukaryotic translation initiation factor 3, subunit K										EIF3K/CYP39A1(2)	central_nervous_system(1)|endometrium(1)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	8	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)			CTGGAGTGCCGACGAGTCGGG	0.542											OREG0025450	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	12	0.00239617	0.0091	0.0	5008	,	,		18892	0.0		0.0	False		,,,				2504	0.0				p.D182N		Atlas-SNP	.											.	EIF3K	22	.	0			c.G544A						PASS	.	G	ASN/ASP	25,4381	31.7+/-61.6	0,25,2178	89.0	80.0	83.0		544	3.2	0.1	19	dbSNP_134	83	0,8600		0,0,4300	yes	missense	EIF3K	NM_013234.2	23	0,25,6478	AA,AG,GG		0.0,0.5674,0.1922	benign	182/219	39125677	25,12981	2203	4300	6503	SO:0001583	missense	27335	exon7			AGTGCCGACGAGT	AB019392	CCDS12517.1, CCDS74360.1	19q13.2	2012-05-28	2007-07-27	2007-07-27	ENSG00000178982	ENSG00000178982			24656	protein-coding gene	gene with protein product		609596	"""eukaryotic translation initiation factor 3, subunit 12"""	EIF3S12		11042152, 14519125	Standard	XM_006723147		Approved	eIF3k, PRO1474, HSPC029, PTD001, PLAC-24, M9, ARG134	uc002oiz.1	Q9UBQ5		ENST00000538434.1:c.283G>A	19.37:g.39125677G>A	ENSP00000440999:p.Asp95Asn	70.0	0.0	0	883	106.0	46.0	0.433962	NM_013234		Missense_Mutation	SNP	ENST00000538434.1	37		3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	5.726	0.318348	0.10845	0.005674	0.0	ENSG00000178982	ENST00000248342;ENST00000538434;ENST00000545173	.	.	.	5.36	3.2	0.36748	Winged helix-turn-helix transcription repressor DNA-binding (1);	0.062209	0.64402	D	0.000005	T	0.18676	0.0448	N	0.25201	0.72	0.09310	N	0.999998	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.14504	-1.0470	9	0.87932	D	0	-16.4366	5.4949	0.16797	0.1755:0.0:0.661:0.1635	.	95;182;182	B4DQ48;B7ZAM9;Q9UBQ5	.;.;EIF3K_HUMAN	N	182;95;182	.	ENSP00000248342:D182N	D	+	1	0	EIF3K	43817517	0.010000	0.17322	0.080000	0.20451	0.512000	0.34134	0.612000	0.24283	1.397000	0.46682	0.549000	0.68633	GAC	G|0.998;A|0.002	0.002	strong		0.542	EIF3K-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000453409.1	NM_013234	
LRWD1	222229	hgsc.bcm.edu	37	7	102106459	102106459	+	Silent	SNP	G	G	A	rs146433593	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:102106459G>A	ENST00000292616.5	+	2	428	c.276G>A	c.(274-276)aaG>aaA	p.K92K	MIR5090_ENST00000582533.1_RNA|ALKBH4_ENST00000292566.3_5'Flank	NM_152892.1	NP_690852.1	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain containing 1	92					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|DNA replication initiation (GO:0006270)|establishment of protein localization to chromatin (GO:0071169)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|telomeric heterochromatin (GO:0031933)	chromatin binding (GO:0003682)|methyl-CpG binding (GO:0008327)|methylated histone binding (GO:0035064)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|skin(1)|stomach(2)	20						AGTTCCCCAAGCTCGAGGAAC	0.637													G|||	18	0.00359425	0.0136	0.0	5008	,	,		19209	0.0		0.0	False		,,,				2504	0.0				p.K92K		Atlas-SNP	.											.	LRWD1	41	.	0			c.G276A						PASS	.	G		59,4347	57.4+/-93.9	0,59,2144	46.0	45.0	45.0		276	-5.5	0.0	7	dbSNP_134	45	0,8600		0,0,4300	no	coding-synonymous	LRWD1	NM_152892.1		0,59,6444	AA,AG,GG		0.0,1.3391,0.4536		92/648	102106459	59,12947	2203	4300	6503	SO:0001819	synonymous_variant	222229	exon2			CCCCAAGCTCGAG	AL133057	CCDS34715.1	7q22.1	2013-01-10			ENSG00000161036	ENSG00000161036		"""WD repeat domain containing"""	21769	protein-coding gene	gene with protein product	"""origin recognition complex associated"", ""centromere protein 33"""	615167				20932478, 20850016, 20180869	Standard	NM_152892		Approved	DKFZp434K1815, ORCA, CENP-33	uc003uzn.3	Q9UFC0	OTTHUMG00000157718	ENST00000292616.5:c.276G>A	7.37:g.102106459G>A		96.0	0.0	0		108.0	56.0	0.518519	NM_152892	A8K4K2|B2R9G2|Q8N0T9|Q8WV43|Q96GJ2	Silent	SNP	ENST00000292616.5	37	CCDS34715.1																																																																																			G|0.995;A|0.005	0.005	strong		0.637	LRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349493.1	NM_152892	
ZNF611	81856	hgsc.bcm.edu	37	19	53219140	53219140	+	Missense_Mutation	SNP	C	C	T	rs146379839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53219140C>T	ENST00000319783.1	-	5	324	c.8G>A	c.(7-9)cGt>cAt	p.R3H	ZNF611_ENST00000595798.1_De_novo_Start_OutOfFrame|ZNF611_ENST00000602162.1_Intron|ZNF611_ENST00000543227.1_Missense_Mutation_p.R3H|ZNF611_ENST00000596702.1_Missense_Mutation_p.R3H|ZNF611_ENST00000453741.2_De_novo_Start_OutOfFrame|ZNF611_ENST00000540744.1_Missense_Mutation_p.R3H|ZNF611_ENST00000600943.1_Missense_Mutation_p.R3H	NM_030972.3	NP_112234.3	Q8N823	ZN611_HUMAN	zinc finger protein 611	3					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(262;0.0233)|GBM - Glioblastoma multiforme(134;0.04)		TGCTTCCTCACGTAACATGAG	0.428													-|||	5	0.000998403	0.003	0.0	5008	,	,		22412	0.001		0.0	False		,,,				2504	0.0				p.R3H		Atlas-SNP	.											.	ZNF611	72	.	0			c.G8A						PASS	.	C	HIS/ARG,HIS/ARG,,HIS/ARG	4,3018		0,4,1507	186.0	202.0	196.0		8,8,,8	-2.1	0.0	19	dbSNP_134	196	1,5417		0,1,2708	no	missense,missense,utr-5,missense	ZNF611	NM_001161499.1,NM_001161500.1,NM_001161501.1,NM_030972.3	29,29,,29	0,5,4215	TT,TC,CC		0.0185,0.1324,0.0592	benign,benign,,benign	3/706,3/706,,3/706	53219140	5,8435	1511	2709	4220	SO:0001583	missense	81856	exon5			TCCTCACGTAACA	AK091389	CCDS12855.1, CCDS54312.1	19q13.42	2013-01-08			ENSG00000213020	ENSG00000213020		"""Zinc fingers, C2H2-type"", ""-"""	28766	protein-coding gene	gene with protein product						12477932	Standard	NM_030972		Approved	MGC5384	uc010ydq.2	Q8N823	OTTHUMG00000154908	ENST00000319783.1:c.8G>A	19.37:g.53219140C>T	ENSP00000322427:p.Arg3His	54.0	0.0	0		37.0	13.0	0.351351	NM_030972	B3KRD5|Q69YG9	Missense_Mutation	SNP	ENST00000319783.1	37	CCDS12855.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	0	0.0	.	7.679	0.688533	0.14973	0.001324	1.85E-4	ENSG00000213020	ENST00000543227;ENST00000540744;ENST00000319783	T;T;T	0.08282	3.11;3.11;3.11	1.87	-2.06	0.07298	.	.	.	.	.	T	0.05044	0.0135	L	0.29908	0.895	0.18873	N	0.999986	B	0.02656	0.0	B	0.01281	0.0	T	0.41520	-0.9504	9	0.33141	T	0.24	.	2.9174	0.05757	0.361:0.2646:0.3743:0.0	.	3	Q8N823	ZN611_HUMAN	H	3	ENSP00000437616:R3H;ENSP00000439211:R3H;ENSP00000322427:R3H	ENSP00000322427:R3H	R	-	2	0	ZNF611	57910952	0.000000	0.05858	0.000000	0.03702	0.491000	0.33493	-0.868000	0.04236	-0.407000	0.07576	0.298000	0.19748	CGT	C|0.999;T|0.001	0.001	strong		0.428	ZNF611-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337612.1	NM_030972	
CHTF18	63922	hgsc.bcm.edu	37	16	842972	842972	+	Missense_Mutation	SNP	C	C	G	rs534605273		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:842972C>G	ENST00000262315.9	+	13	1642	c.1579C>G	c.(1579-1581)Ctg>Gtg	p.L527V	CHTF18_ENST00000455171.2_Missense_Mutation_p.L555V|CHTF18_ENST00000317063.6_Intron	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	527					cell cycle (GO:0007049)|DNA replication (GO:0006260)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(1)|kidney(3)|liver(2)|lung(4)|prostate(1)	11		Hepatocellular(780;0.00335)				CCAGGTCTCCCTGCGGCAGGG	0.657													c|||	1	0.000199681	0.0008	0.0	5008	,	,		14564	0.0		0.0	False		,,,				2504	0.0				p.L527V		Atlas-SNP	.											.	CHTF18	52	.	0			c.C1579G						PASS	.						9.0	12.0	11.0					16																	842972		1892	4037	5929	SO:0001583	missense	63922	exon13			GTCTCCCTGCGGC	BC018184	CCDS45371.1	16p13.3	2010-04-21	2003-12-09		ENSG00000127586	ENSG00000127586		"""ATPases / AAA-type"""	18435	protein-coding gene	gene with protein product		613201	"""chromosome 16 open reading frame 41"""	C16orf41		12171929	Standard	NM_022092		Approved	CHL12, C321D2.4, Ctf18	uc002cke.4	Q8WVB6	OTTHUMG00000047838	ENST00000262315.9:c.1579C>G	16.37:g.842972C>G	ENSP00000262315:p.Leu527Val	63.0	0.0	0		102.0	50.0	0.490196	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Missense_Mutation	SNP	ENST00000262315.9	37	CCDS45371.1	.	.	.	.	.	.	.	.	.	.	c	2.016	-0.425888	0.04701	.	.	ENSG00000127586	ENST00000455171;ENST00000262315	T;T	0.17370	2.28;2.28	4.9	0.103	0.14526	.	.	.	.	.	T	0.09949	0.0244	L	0.38838	1.175	0.25065	N	0.991037	B;B	0.29909	0.261;0.172	B;B	0.26202	0.067;0.03	T	0.31251	-0.9950	9	0.31617	T	0.26	.	1.2554	0.01990	0.1656:0.3096:0.3219:0.2029	.	555;527	Q8WVB6-2;Q8WVB6	.;CTF18_HUMAN	V	555;527	ENSP00000406252:L555V;ENSP00000262315:L527V	ENSP00000262315:L527V	L	+	1	2	CHTF18	782973	0.000000	0.05858	0.502000	0.27614	0.443000	0.32047	-0.035000	0.12205	0.474000	0.27392	0.556000	0.70494	CTG	.	.	none		0.657	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092	
ZC3H18	124245	hgsc.bcm.edu	37	16	88643806	88643806	+	Missense_Mutation	SNP	C	C	G	rs114866066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88643806C>G	ENST00000301011.5	+	2	475	c.275C>G	c.(274-276)cCg>cGg	p.P92R	ZC3H18_ENST00000452588.2_Missense_Mutation_p.P92R	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	92						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(9)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	42				BRCA - Breast invasive adenocarcinoma(80;0.0542)		AGCCGGGGCCCGACCAGCTCC	0.622													C|||	5	0.000998403	0.0038	0.0	5008	,	,		18131	0.0		0.0	False		,,,				2504	0.0				p.P92R	Ovarian(121;375 2276 20373 38669)	Atlas-SNP	.											.	ZC3H18	90	.	0			c.C275G						PASS	.	C	ARG/PRO	22,4372	27.2+/-55.0	0,22,2175	29.0	33.0	32.0		275	3.4	0.8	16	dbSNP_132	32	0,8600		0,0,4300	yes	missense	ZC3H18	NM_144604.3	103	0,22,6475	GG,GC,CC		0.0,0.5007,0.1693	benign	92/954	88643806	22,12972	2197	4300	6497	SO:0001583	missense	124245	exon2			GGGGCCCGACCAG	BC001584	CCDS10967.1, CCDS73924.1	16q24.2-q24.3	2012-07-05			ENSG00000158545	ENSG00000158545		"""Zinc fingers, CCCH-type domain containing"""	25091	protein-coding gene	gene with protein product						17579712	Standard	NM_144604		Approved	NHN1	uc002fky.3	Q86VM9	OTTHUMG00000137679	ENST00000301011.5:c.275C>G	16.37:g.88643806C>G	ENSP00000301011:p.Pro92Arg	43.0	0.0	0		31.0	18.0	0.580645	NM_144604	Q96DG4|Q96MP7	Missense_Mutation	SNP	ENST00000301011.5	37	CCDS10967.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	6.042	0.376025	0.11466	0.005007	0.0	ENSG00000158545	ENST00000301011;ENST00000289509;ENST00000452588	T;T	0.30448	1.53;1.56	5.57	3.36	0.38483	.	0.366727	0.28908	N	0.013743	T	0.13243	0.0321	L	0.36672	1.1	0.09310	N	1	B;B	0.27416	0.178;0.178	B;B	0.28916	0.096;0.096	T	0.11179	-1.0598	10	0.18276	T	0.48	-21.7543	2.9583	0.05884	0.5017:0.3387:0.0:0.1595	.	92;92	E7ERS3;Q86VM9	.;ZCH18_HUMAN	R	92	ENSP00000301011:P92R;ENSP00000416951:P92R	ENSP00000289509:P92R	P	+	2	0	ZC3H18	87171307	0.247000	0.23920	0.778000	0.31720	0.046000	0.14306	0.728000	0.26013	1.310000	0.45006	0.561000	0.74099	CCG	C|0.999;G|0.001	0.001	strong		0.622	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269168.1	NM_144604	
ETV7	51513	hgsc.bcm.edu	37	6	36339176	36339176	+	Missense_Mutation	SNP	C	C	T	rs34306145	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:36339176C>T	ENST00000340181.4	-	5	836	c.595G>A	c.(595-597)Ggc>Agc	p.G199S	ETV7_ENST00000373737.4_Intron|ETV7_ENST00000538992.1_Missense_Mutation_p.G48S|ETV7_ENST00000373738.1_Missense_Mutation_p.G144S|ETV7_ENST00000339796.5_Missense_Mutation_p.G199S	NM_001207037.1|NM_001207040.1|NM_016135.3	NP_001193966.1|NP_001193969.1|NP_057219.1	Q9Y603	ETV7_HUMAN	ets variant 7	199			G -> S (in dbSNP:rs34306145).		cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ morphogenesis (GO:0009887)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	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)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)|ovary(1)|skin(4)	10						GTCCTGCAGCCGAGCTCTGCA	0.637													C|||	60	0.0119808	0.0446	0.0	5008	,	,		18231	0.0		0.0	False		,,,				2504	0.001				p.G199S		Atlas-SNP	.											.	ETV7	31	.	0			c.G595A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY,,SER/GLY,SER/GLY,SER/GLY,SER/GLY	155,4251	98.5+/-137.1	4,147,2052	48.0	42.0	44.0		595,430,418,,430,352,142,595	-4.3	0.0	6	dbSNP_126	44	0,8600		0,0,4300	yes	missense,missense,missense,intron,missense,missense,missense,missense	ETV7	NM_001207035.1,NM_001207036.1,NM_001207037.1,NM_001207038.1,NM_001207039.1,NM_001207040.1,NM_001207041.1,NM_016135.3	56,56,56,,56,56,56,56	4,147,6352	TT,TC,CC		0.0,3.5179,1.1918	benign,benign,benign,,benign,benign,benign,benign	199/318,144/287,140/283,,144/263,118/261,48/191,199/342	36339176	155,12851	2203	4300	6503	SO:0001583	missense	51513	exon5			TGCAGCCGAGCTC	AF116508	CCDS4819.1, CCDS56422.1, CCDS56423.1, CCDS56424.1, CCDS56425.1, CCDS75440.1, CCDS75441.1	6p21	2008-09-12	2008-09-12		ENSG00000010030	ENSG00000010030			18160	protein-coding gene	gene with protein product	"""TEL2 oncogene"""	605255	"""ets variant gene 7 (TEL2 oncogene)"""			10828014, 11108721	Standard	NM_016135		Approved	TEL2, TEL-2	uc003omb.3	Q9Y603	OTTHUMG00000014594	ENST00000340181.4:c.595G>A	6.37:g.36339176C>T	ENSP00000341843:p.Gly199Ser	58.0	0.0	0		49.0	20.0	0.408163	NM_001207035	B3KVC2|B4DVB6|B4E1G4|Q5R3L3|Q5R3L4|Q9NZ65|Q9NZ66|Q9NZ68|Q9NZR8|Q9UNJ7|Q9Y5K4|Q9Y604	Missense_Mutation	SNP	ENST00000340181.4	37	CCDS4819.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	C	6.332	0.429441	0.11987	0.035179	0.0	ENSG00000010030	ENST00000339796;ENST00000340181;ENST00000373738;ENST00000538992	T;T;T;T	0.13307	2.6;2.6;2.6;2.6	3.49	-4.27	0.03744	.	1.429630	0.04667	N	0.409962	T	0.03739	0.0106	N	0.17082	0.46	0.09310	N	1	B;D;B;P;B	0.69078	0.101;0.997;0.012;0.708;0.229	B;P;B;B;B	0.52481	0.056;0.7;0.017;0.087;0.014	T	0.25152	-1.0140	10	0.09084	T	0.74	.	11.3935	0.49827	0.0:0.3082:0.0:0.6918	rs34306145	140;144;199;144;199	Q9Y603-2;Q9Y603-4;Q9Y603;Q9Y603-6;Q9Y603-5	.;.;ETV7_HUMAN;.;.	S	199;199;144;48	ENSP00000342260:G199S;ENSP00000341843:G199S;ENSP00000362843:G144S;ENSP00000440592:G48S	ENSP00000342260:G199S	G	-	1	0	ETV7	36447154	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.280000	0.08468	-1.429000	0.01987	-2.010000	0.00438	GGC	C|0.987;T|0.013	0.013	strong		0.637	ETV7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040341.1	NM_016135	
ZNF658	26149	hgsc.bcm.edu	37	9	40774091	40774091	+	Missense_Mutation	SNP	C	C	T	rs79262629	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:40774091C>T	ENST00000602553.1	-	5	1478	c.1184G>A	c.(1183-1185)cGg>cAg	p.R395Q	ZNF658_ENST00000441795.1_Missense_Mutation_p.R393Q|ZNF658_ENST00000377626.3_Missense_Mutation_p.R395Q			Q5TYW1	ZN658_HUMAN	zinc finger protein 658	395					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(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)		GTGTGCTTTCCGGTAAAAGGA	0.393													C|||	70	0.0139776	0.0522	0.0	5008	,	,		20923	0.001		0.0	False		,,,				2504	0.0				p.R395Q		Atlas-SNP	.											ZNF658,lower_third,carcinoma,-1,1	ZNF658	100	1	0			c.G1184A						scavenged	.	C	GLN/ARG	152,4254	103.4+/-141.9	2,148,2053	218.0	217.0	218.0		1184	-0.9	0.0	9	dbSNP_131	218	2,8598	2.2+/-6.3	0,2,4298	yes	missense	ZNF658	NM_033160.5	43	2,150,6351	TT,TC,CC		0.0233,3.4498,1.1841	benign	395/1060	40774091	154,12852	2203	4300	6503	SO:0001583	missense	26149	exon5			GCTTTCCGGTAAA	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.1184G>A	9.37:g.40774091C>T	ENSP00000473484:p.Arg395Gln	532.0	2.0	0.0037594		543.0	183.0	0.337017	NM_033160	Q6PIP3|Q96M55|Q9H9S6|Q9UG02	Missense_Mutation	SNP	ENST00000602553.1	37	CCDS35023.1	18	0.008241758241758242	18	0.036585365853658534	0	0.0	0	0.0	0	0.0	c	0.018	-1.473237	0.01044	0.034498	2.33E-4	ENSG00000196409	ENST00000441795;ENST00000377626	T;T	0.14893	2.47;2.47	1.8	-0.939	0.10408	Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00936	0.0031	N	0.01473	-0.845	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.41805	-0.9488	9	0.07990	T	0.79	.	5.7522	0.18152	0.0:0.5247:0.0:0.4753	.	395;395	Q5TYW1-2;Q5TYW1	.;ZN658_HUMAN	Q	393;395	ENSP00000408462:R393Q;ENSP00000366853:R395Q	ENSP00000366853:R395Q	R	-	2	0	ZNF658	40764091	0.000000	0.05858	0.000000	0.03702	0.211000	0.24417	-0.970000	0.03810	-0.174000	0.10743	-0.820000	0.03113	CGG	C|0.990;T|0.010	0.010	strong		0.393	ZNF658-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467800.1	NM_033160	
TRIP11	9321	hgsc.bcm.edu	37	14	92474136	92474136	+	Missense_Mutation	SNP	C	C	T	rs372171033		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:92474136C>T	ENST00000267622.4	-	10	1748	c.1375G>A	c.(1375-1377)Gct>Act	p.A459T		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	459					protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		TCTCTTGTAGCTGTACTTTTA	0.303			T	PDGFRB	AML								c|||	1	0.000199681	0.0008	0.0	5008	,	,		19781	0.0		0.0	False		,,,				2504	0.0				p.A459T	Ovarian(84;609 1888 9852 42686)	Atlas-SNP	.		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	.	TRIP11	184	.	0			c.G1375A						PASS	.	C	THR/ALA	5,4399	9.9+/-24.2	0,5,2197	105.0	97.0	100.0		1375	-3.3	0.0	14		100	0,8598		0,0,4299	no	missense	TRIP11	NM_004239.3	58	0,5,6496	TT,TC,CC		0.0,0.1135,0.0385	benign	459/1980	92474136	5,12997	2202	4299	6501	SO:0001583	missense	9321	exon10			TTGTAGCTGTACT	L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.1375G>A	14.37:g.92474136C>T	ENSP00000267622:p.Ala459Thr	127.0	0.0	0		83.0	35.0	0.421687	NM_004239	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	37	CCDS9899.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	4.257|4.257	0.046773|0.046773	0.08243|0.08243	0.001135|0.001135	0.0|0.0	ENSG00000100815|ENSG00000100815	ENST00000267622;ENST00000542257|ENST00000554357	T|.	0.64438|.	-0.1|.	5.85|5.85	-3.26|-3.26	0.05064|0.05064	.|.	1.114810|.	0.06492|.	N|.	0.734730|.	T|T	0.19846|0.19846	0.0477|0.0477	N|N	0.16656|0.16656	0.425|0.425	0.09310|0.09310	N|N	1|1	B;B|.	0.13594|.	0.003;0.008|.	B;B|.	0.13407|.	0.004;0.009|.	T|T	0.33007|0.33007	-0.9885|-0.9885	10|5	0.14252|.	T|.	0.57|.	.|.	7.9021|7.9021	0.29740|0.29740	0.1338:0.334:0.0:0.5322|0.1338:0.334:0.0:0.5322	.|.	195;459|.	F5H1Z0;Q15643|.	.;TRIPB_HUMAN|.	T|N	459;195|174	ENSP00000267622:A459T|.	ENSP00000267622:A459T|.	A|S	-|-	1|2	0|0	TRIP11|TRIP11	91543889|91543889	0.000000|0.000000	0.05858|0.05858	0.002000|0.002000	0.10522|0.10522	0.220000|0.220000	0.24768|0.24768	-0.819000|-0.819000	0.04462|0.04462	-0.445000|-0.445000	0.07159|0.07159	0.561000|0.561000	0.74099|0.74099	GCT|AGC	.	.	weak		0.303	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1		
MTA1	9112	hgsc.bcm.edu	37	14	105931109	105931109	+	Silent	SNP	C	C	T	rs36015555	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105931109C>T	ENST00000331320.7	+	15	1657	c.1443C>T	c.(1441-1443)atC>atT	p.I481I	MTA1_ENST00000406191.1_Silent_p.I481I|MTA1_ENST00000405646.1_Silent_p.I464I|MTA1_ENST00000435036.2_Silent_p.I17I	NM_001203258.1|NM_004689.3	NP_001190187.1|NP_004680.2	Q13330	MTA1_HUMAN	metastasis associated 1	481					circadian regulation of gene expression (GO:0032922)|double-strand break repair (GO:0006302)|entrainment of circadian clock by photoperiod (GO:0043153)|locomotor rhythm (GO:0045475)|positive regulation of protein autoubiquitination (GO:1902499)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|regulation of gene expression, epigenetic (GO:0040029)|regulation of inflammatory response (GO:0050727)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|secretory granule organization (GO:0033363)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|microtubule (GO:0005874)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|stomach(1)	14		all_cancers(154;0.0293)|all_epithelial(191;0.128)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00897)|Epithelial(46;0.026)	Epithelial(152;0.19)		TGACGCGGATCGCCCGGCGCC	0.672													C|||	257	0.0513179	0.1884	0.0115	5008	,	,		16374	0.0		0.0	False		,,,				2504	0.0				p.I481I		Atlas-SNP	.											.	MTA1	61	.	0			c.C1443T						PASS	.	C	,	712,3684		67,578,1553	32.0	28.0	29.0		,1443	-1.1	0.9	14	dbSNP_126	29	7,8587		0,7,4290	no	utr-3,coding-synonymous	MTA1	NM_001203258.1,NM_004689.3	,	67,585,5843	TT,TC,CC		0.0815,16.1965,5.535	,	,481/716	105931109	719,12271	2198	4297	6495	SO:0001819	synonymous_variant	9112	exon15			GCGGATCGCCCGG	U35113	CCDS32169.1, CCDS55954.1	14q32.33	2013-01-25			ENSG00000182979	ENSG00000182979		"""GATA zinc finger domain containing"""	7410	protein-coding gene	gene with protein product		603526				8083195, 7607577	Standard	NM_004689		Approved		uc001yqx.3	Q13330	OTTHUMG00000150362	ENST00000331320.7:c.1443C>T	14.37:g.105931109C>T		42.0	0.0	0		60.0	39.0	0.65	NM_004689	A5PLK4|Q86SW2|Q8NFI8|Q96GI8	Silent	SNP	ENST00000331320.7	37	CCDS32169.1																																																																																			C|0.947;T|0.053	0.053	strong		0.672	MTA1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317849.15		
FLG	2312	hgsc.bcm.edu	37	1	152284457	152284457	+	Missense_Mutation	SNP	T	T	A	rs376429887|rs3120652	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152284457T>A	ENST00000368799.1	-	3	2940	c.2905A>T	c.(2905-2907)Aac>Tac	p.N969Y	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	969	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCACGATGGTTTCTGGAAGCA	0.582									Ichthyosis				T|||	297	0.0593051	0.2141	0.0187	5008	,	,		21442	0.0		0.001	False		,,,				2504	0.0				p.N969Y		Atlas-SNP	.											.	FLG	900	.	0			c.A2905T						PASS	.	T	TYR/ASN	721,3685	260.4+/-263.7	46,629,1528	236.0	238.0	237.0		2905	-6.0	0.0	1	dbSNP_103	237	9,8591	7.1+/-27.0	0,9,4291	no	missense	FLG	NM_002016.1	143	46,638,5819	AA,AT,TT		0.1047,16.364,5.6128	possibly-damaging	969/4062	152284457	730,12276	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	GATGGTTTCTGGA	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.2905A>T	1.37:g.152284457T>A	ENSP00000357789:p.Asn969Tyr	446.0	0.0	0		538.0	214.0	0.39777	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	83	0.038003663003663	78	0.15853658536585366	5	0.013812154696132596	0	0.0	0	0.0	t	2.680	-0.275489	0.05679	0.16364	0.001047	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.01647	4.71	3.01	-6.01	0.02199	.	.	.	.	.	T	0.00724	0.0024	M	0.68317	2.08	0.80722	P	0.0	P	0.39831	0.69	B	0.34093	0.175	T	0.03433	-1.1037	8	0.59425	D	0.04	.	8.703	0.34338	0.0:0.0998:0.6558:0.2444	.	969	P20930	FILA_HUMAN	Y	969;176	ENSP00000357789:N969Y	ENSP00000357789:N969Y	N	-	1	0	FLG	150551081	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-1.749000	0.01824	-1.940000	0.01043	-0.641000	0.03968	AAC	T|0.942;A|0.058	0.058	strong		0.582	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
SPG7	6687	hgsc.bcm.edu	37	16	89623301	89623301	+	Missense_Mutation	SNP	A	A	G	rs35749032	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89623301A>G	ENST00000268704.2	+	17	2203	c.2188A>G	c.(2188-2190)Aac>Gac	p.N730D	SPG7_ENST00000565891.1_3'UTR	NM_003119.2	NP_003110.1	Q9UQ90	SPG7_HUMAN	spastic paraplegia 7 (pure and complicated autosomal recessive)	730			N -> D (in dbSNP:rs35749032). {ECO:0000269|PubMed:16534102}.		anterograde axon cargo transport (GO:0008089)|cell death (GO:0008219)|mitochondrion organization (GO:0007005)|nervous system development (GO:0007399)|proteolysis (GO:0006508)	integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|metalloendopeptidase activity (GO:0004222)|peptidase activity (GO:0008233)|unfolded protein binding (GO:0051082)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|ovary(2)|urinary_tract(1)	20		all_hematologic(23;0.00824)|Colorectal(91;0.102)		all cancers(4;1.39e-07)|OV - Ovarian serous cystadenocarcinoma(4;5.64e-06)|BRCA - Breast invasive adenocarcinoma(80;0.015)		CTAGCTGGCAAACGCCCTTCT	0.562													A|||	85	0.0169728	0.062	0.0043	5008	,	,		19441	0.0		0.0	False		,,,				2504	0.0				p.N730D		Atlas-SNP	.											.	SPG7	75	.	0			c.A2188G						PASS	.	A	ASP/ASN	203,4193	123.3+/-160.7	7,189,2002	111.0	110.0	110.0		2188	4.5	0.0	16	dbSNP_126	110	1,8595		0,1,4297	yes	missense	SPG7	NM_003119.2	23	7,190,6299	GG,GA,AA		0.0116,4.6178,1.5702	benign	730/796	89623301	204,12788	2198	4298	6496	SO:0001583	missense	6687	exon17			CTGGCAAACGCCC	Y16610	CCDS10977.1, CCDS10978.1	16q24.3	2010-04-21	2007-04-23		ENSG00000197912	ENSG00000197912		"""ATPases / AAA-type"""	11237	protein-coding gene	gene with protein product	"""paraplegin"""	602783	"""cell matrix adhesion regulator"""	CMAR		9635427, 9634528	Standard	XM_006721264		Approved	CAR, SPG5C	uc002fnj.3	Q9UQ90	OTTHUMG00000138046	ENST00000268704.2:c.2188A>G	16.37:g.89623301A>G	ENSP00000268704:p.Asn730Asp	91.0	0.0	0		93.0	45.0	0.483871	NM_003119	O75756|Q2TB70|Q58F00|Q96IB0	Missense_Mutation	SNP	ENST00000268704.2	37	CCDS10977.1	30	0.013736263736263736	29	0.05894308943089431	1	0.0027624309392265192	0	0.0	0	0.0	A	7.955	0.745801	0.15710	0.046178	1.16E-4	ENSG00000197912	ENST00000268704	D	0.84370	-1.84	5.59	4.49	0.54785	Peptidase M41 (1);Peptidase M41, FtsH (2);	0.304067	0.39687	N	0.001298	T	0.25121	0.0610	N	0.12746	0.255	0.36713	D	0.880754	B	0.06786	0.001	B	0.09377	0.004	T	0.55250	-0.8170	10	0.36615	T	0.2	-6.0E-4	10.7824	0.46386	0.9228:0.0:0.0772:0.0	rs35749032	730	Q9UQ90	SPG7_HUMAN	D	730	ENSP00000268704:N730D	ENSP00000268704:N730D	N	+	1	0	SPG7	88150802	0.057000	0.20700	0.002000	0.10522	0.321000	0.28281	1.649000	0.37281	0.925000	0.37094	0.460000	0.39030	AAC	A|0.982;G|0.018	0.018	strong		0.562	SPG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269921.2	NM_003119	
RPAP1	26015	hgsc.bcm.edu	37	15	41815063	41815063	+	Missense_Mutation	SNP	C	C	T	rs61748721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:41815063C>T	ENST00000304330.4	-	19	2758	c.2642G>A	c.(2641-2643)cGt>cAt	p.R881H	RPAP1_ENST00000561603.1_Missense_Mutation_p.R881H	NM_015540.2	NP_056355.2	Q9BWH6	RPAP1_HUMAN	RNA polymerase II associated protein 1	881	Leu-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(6)|lung(16)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	45		all_cancers(109;6.59e-20)|all_epithelial(112;7.67e-17)|Lung NSC(122;5.34e-11)|all_lung(180;4.17e-10)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		OV - Ovarian serous cystadenocarcinoma(18;2.84e-17)|GBM - Glioblastoma multiforme(113;1.68e-06)|Colorectal(105;0.0163)|BRCA - Breast invasive adenocarcinoma(123;0.117)		CAGACTGAGACGGGGGCAGCC	0.632													C|||	177	0.0353435	0.1324	0.0029	5008	,	,		16841	0.0		0.0	False		,,,				2504	0.0				p.R881H		Atlas-SNP	.											.	RPAP1	111	.	0			c.G2642A						PASS	.	C	HIS/ARG	531,3875	241.5+/-251.9	29,473,1701	56.0	50.0	52.0		2642	-1.3	0.0	15	dbSNP_129	52	3,8597	2.2+/-6.3	0,3,4297	yes	missense	RPAP1	NM_015540.2	29	29,476,5998	TT,TC,CC		0.0349,12.0517,4.1058	benign	881/1394	41815063	534,12472	2203	4300	6503	SO:0001583	missense	26015	exon19			CTGAGACGGGGGC	BC000246	CCDS10079.1	15q14	2004-03-16			ENSG00000103932	ENSG00000103932			24567	protein-coding gene	gene with protein product		611475				10718198	Standard	XM_005254297		Approved	DKFZP727M111, KIAA1403, MGC858, FLJ12732	uc001zod.3	Q9BWH6	OTTHUMG00000130342	ENST00000304330.4:c.2642G>A	15.37:g.41815063C>T	ENSP00000306123:p.Arg881His	44.0	0.0	0		51.0	29.0	0.568627	NM_015540	Q9H9I2|Q9NSQ5|Q9P2E4|Q9UFS7	Missense_Mutation	SNP	ENST00000304330.4	37	CCDS10079.1	60	0.027472527472527472	59	0.11991869918699187	1	0.0027624309392265192	0	0.0	0	0.0	C	10.52	1.373816	0.24857	0.120517	3.49E-4	ENSG00000103932	ENST00000304330	T	0.11930	2.73	5.27	-1.3	0.09259	.	0.689147	0.15432	N	0.262677	T	0.00109	0.0003	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.36986	-0.9725	10	0.41790	T	0.15	-23.5071	5.7717	0.18257	0.0626:0.3333:0.3812:0.2229	.	881	Q9BWH6	RPAP1_HUMAN	H	881	ENSP00000306123:R881H	ENSP00000306123:R881H	R	-	2	0	RPAP1	39602355	0.005000	0.15991	0.000000	0.03702	0.660000	0.38997	0.344000	0.19962	-0.381000	0.07882	-1.067000	0.02272	CGT	C|0.958;T|0.042	0.042	strong		0.632	RPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252694.2	NM_015540	
PKD1L2	114780	hgsc.bcm.edu	37	16	81208473	81208473	+	RNA	SNP	G	G	T	rs115666278	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:81208473G>T	ENST00000527937.1	-	0	511				PKD1L2_ENST00000533478.1_RNA|PKD1L2_ENST00000337114.4_RNA|PKD1L2_ENST00000525539.1_RNA|PKD1L2_ENST00000531391.1_RNA			Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						CTCTGACACGGCAGCCTGGAA	0.557													G|||	302	0.0603035	0.2186	0.0187	5008	,	,		19807	0.0		0.0	False		,,,				2504	0.0				p.A877D		Atlas-SNP	.											.	PKD1L2	361	.	0			c.C2630A						PASS	.	G	ASP/ALA,ASP/ALA	829,3309		91,647,1331	66.0	64.0	65.0		2630,2630	-1.8	0.0	16	dbSNP_132	65	8,8426		0,8,4209	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	126,126	91,655,5540	TT,TG,GG		0.0949,20.0338,6.6577	possibly-damaging,possibly-damaging	877/992,877/2460	81208473	837,11735	2069	4217	6286			114780	exon16			GACACGGCAGCCT	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81208473G>T		84.0	0.0	0		90.0	43.0	0.477778	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000527937.1	37		126|126	0.057692307692307696|0.057692307692307696	121|121	0.2459349593495935|0.2459349593495935	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	0|0	0.0|0.0	G|G	13.39|13.39	2.221594|2.221594	0.39300|0.39300	0.200338|0.200338	9.49E-4|9.49E-4	ENSG00000166473|ENSG00000166473	ENST00000531391;ENST00000337114;ENST00000527937|ENST00000526632	T;T;T|.	0.57107|.	0.42;0.42;0.42|.	4.55|4.55	-1.81|-1.81	0.07882|0.07882	Egg jelly receptor, REJ-like (1);|.	1.422600|.	0.04339|.	N|.	0.353783|.	T|.	0.00012|.	0.0000|.	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	P;P;B|.	0.37636|.	0.513;0.603;0.009|.	B;B;B|.	0.40009|.	0.299;0.316;0.009|.	T|.	0.29458|.	-1.0011|.	8|.	0.66056|.	D|.	0.02|.	-0.6932|-0.6932	8.1615|8.1615	0.31201|0.31201	0.6442:0.0:0.3558:0.0|0.6442:0.0:0.3558:0.0	.|.	133;877;877|.	Q7Z442-6;Q7Z442-3;Q7Z442|.	.;.;PK1L2_HUMAN|.	D|X	192;877;133|404	ENSP00000436309:A192D;ENSP00000337397:A877D;ENSP00000432818:A133D|.	ENSP00000337397:A877D|.	A|C	-|-	2|3	0|2	PKD1L2|PKD1L2	79765974|79765974	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.081000|0.081000	0.17604|0.17604	0.031000|0.031000	0.13710|0.13710	-0.115000|-0.115000	0.11915|0.11915	0.555000|0.555000	0.69702|0.69702	GCC|TGC	G|0.963;T|0.037	0.037	strong		0.557	PKD1L2-007	KNOWN	basic|exp_conf	protein_coding	polymorphic_pseudogene	OTTHUMT00000387978.1		
NLRP6	171389	hgsc.bcm.edu	37	11	284299	284299	+	Silent	SNP	A	A	G	rs7108261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:284299A>G	ENST00000312165.5	+	6	2271	c.2271A>G	c.(2269-2271)gcA>gcG	p.A757A	NLRP6_ENST00000534750.1_Silent_p.A756A	NM_138329.1	NP_612202.2	P59044	NALP6_HUMAN	NLR family, pyrin domain containing 6	757					G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of immune response (GO:0050777)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|regulation of inflammatory response (GO:0050727)|response to bacterium (GO:0009617)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|vasopressin receptor activity (GO:0005000)			breast(1)|skin(1)|upper_aerodigestive_tract(2)	4		all_cancers(49;1.12e-06)|all_epithelial(84;0.000375)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.28e-28)|Epithelial(43;2.47e-27)|OV - Ovarian serous cystadenocarcinoma(40;4.66e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.0485)|LUSC - Lung squamous cell carcinoma(625;0.122)		CAGCCCCCGCACTGACGGAGC	0.637													G|||	862	0.172125	0.6165	0.062	5008	,	,		17322	0.0		0.004	False		,,,				2504	0.0				p.A757A		Atlas-SNP	.											NALP6,NS,carcinoma,+1,1	NLRP6	4	1	0			c.A2271G						scavenged	.	G		2265,2141	587.2+/-386.6	600,1065,538	41.0	43.0	42.0		2271	-0.8	0.0	11	dbSNP_116	42	25,8575	14.6+/-50.1	0,25,4275	yes	coding-synonymous	NLRP6	NM_138329.1		600,1090,4813	GG,GA,AA		0.2907,48.5928,17.6073		757/893	284299	2290,10716	2203	4300	6503	SO:0001819	synonymous_variant	171389	exon6			CCCCGCACTGACG	AF479748	CCDS7693.1, CCDS60680.1	11p15	2006-12-08	2006-12-08	2006-12-08	ENSG00000174885	ENSG00000174885		"""Nucleotide-binding domain and leucine rich repeat containing"""	22944	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 6"""	609650	"""NACHT, leucine rich repeat and PYD containing 6"""	NALP6		12563287, 12019269	Standard	NM_138329		Approved	PYPAF5, PAN3, CLR11.4	uc010qvs.3	P59044	OTTHUMG00000119070	ENST00000312165.5:c.2271A>G	11.37:g.284299A>G		67.0	1.0	0.0149254		94.0	42.0	0.446809	NM_138329	A8K9F3|E9PJZ8	Silent	SNP	ENST00000312165.5	37	CCDS7693.1																																																																																			A|0.837;G|0.163	0.163	strong		0.637	NLRP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239283.1	NM_138329	
COPG1	22820	hgsc.bcm.edu	37	3	128984409	128984409	+	Silent	SNP	G	G	A	rs78889622	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:128984409G>A	ENST00000314797.6	+	14	1346	c.1242G>A	c.(1240-1242)aaG>aaA	p.K414K		NM_016128.3	NP_057212.1	Q9Y678	COPG1_HUMAN	coatomer protein complex, subunit gamma 1	414					COPI coating of Golgi vesicle (GO:0048205)|establishment of Golgi localization (GO:0051683)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|organelle transport along microtubule (GO:0072384)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)	structural molecule activity (GO:0005198)										TTGAGTATAAGCGCGCTATCG	0.517													G|||	150	0.0299521	0.1036	0.0173	5008	,	,		21492	0.0		0.001	False		,,,				2504	0.0				p.K414K		Atlas-SNP	.											.	.	.	.	0			c.G1242A						PASS	.	G		378,4028	191.9+/-217.4	11,356,1836	175.0	158.0	164.0		1242	4.1	1.0	3	dbSNP_131	164	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	COPG	NM_016128.3		11,363,6129	AA,AG,GG		0.0814,8.5792,2.9602		414/875	128984409	385,12621	2203	4300	6503	SO:0001819	synonymous_variant	22820	exon14			GTATAAGCGCGCT	AB047846	CCDS33851.1	3q21.3	2012-02-23	2012-02-23	2012-02-23	ENSG00000181789	ENSG00000181789			2236	protein-coding gene	gene with protein product	"""coat protein gamma-cop"""	615525	"""coatomer protein complex, subunit gamma"""	COPG		11056392	Standard	NM_016128		Approved		uc003els.3	Q9Y678	OTTHUMG00000159451	ENST00000314797.6:c.1242G>A	3.37:g.128984409G>A		126.0	0.0	0		140.0	63.0	0.45	NM_016128	A8K6M8|B3KMF6|Q54AC4	Silent	SNP	ENST00000314797.6	37	CCDS33851.1																																																																																			G|0.973;A|0.027	0.027	strong		0.517	COPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355456.1	NM_016128	
MIS18BP1	55320	hgsc.bcm.edu	37	14	45693648	45693648	+	Silent	SNP	G	G	A	rs35223850	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:45693648G>A	ENST00000310806.4	-	11	2600	c.2142C>T	c.(2140-2142)tgC>tgT	p.C714C		NM_018353.4	NP_060823.3	Q6P0N0	M18BP_HUMAN	MIS18 binding protein 1	714					CENP-A containing nucleosome assembly (GO:0034080)|mitotic nuclear division (GO:0007067)|nucleosome assembly (GO:0006334)	chromosome, centromeric region (GO:0000775)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(10)|liver(1)|lung(13)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	39						CACGTTCATCGCAATCTTCCT	0.343													G|||	138	0.0275559	0.0325	0.0159	5008	,	,		19114	0.0		0.0686	False		,,,				2504	0.0153				p.C714C		Atlas-SNP	.											.	MIS18BP1	92	.	0			c.C2142T						PASS	.	G		154,4252	106.5+/-144.9	0,154,2049	69.0	70.0	69.0		2142	0.4	0.0	14	dbSNP_126	69	517,8083	144.5+/-200.4	17,483,3800	no	coding-synonymous	MIS18BP1	NM_018353.4		17,637,5849	AA,AG,GG		6.0116,3.4952,5.1592		714/1133	45693648	671,12335	2203	4300	6503	SO:0001819	synonymous_variant	55320	exon11			TTCATCGCAATCT	AB067490	CCDS9684.1	14q21.1	2011-06-03	2011-02-23	2011-02-23	ENSG00000129534	ENSG00000129534			20190	protein-coding gene	gene with protein product	"""kinetochore null 2 homolog (C. elegans)"""		"""chromosome 14 open reading frame 106"""	C14orf106		17339379, 17199038	Standard	NM_018353		Approved	M18BP1, FLJ11186, KIAA1903, KNL2	uc001wwf.3	Q6P0N0	OTTHUMG00000140266	ENST00000310806.4:c.2142C>T	14.37:g.45693648G>A		115.0	0.0	0		85.0	42.0	0.494118	NM_018353	D3DSA7|Q86V14|Q96PY4|Q9NUR5|Q9Y4X9	Silent	SNP	ENST00000310806.4	37	CCDS9684.1																																																																																			G|0.954;A|0.046	0.046	strong		0.343	MIS18BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276795.2		
KIAA1731	85459	hgsc.bcm.edu	37	11	93460264	93460264	+	Missense_Mutation	SNP	C	C	G	rs61740994	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:93460264C>G	ENST00000325212.6	+	24	6784	c.6622C>G	c.(6622-6624)Cag>Gag	p.Q2208E	KIAA1731_ENST00000531700.1_Missense_Mutation_p.Q388E|KIAA1731_ENST00000411936.1_Missense_Mutation_p.Q2208E|KIAA1731_ENST00000344196.4_Missense_Mutation_p.Q388E			Q9C0D2	K1731_HUMAN	KIAA1731	2208						centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)	11		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				CATGAAAAATCAGAACTATCC	0.368													C|||	38	0.00758786	0.0287	0.0	5008	,	,		19790	0.0		0.0	False		,,,				2504	0.0				p.Q2208E		Atlas-SNP	.											.	KIAA1731	173	.	0			c.C6622G						PASS	.	C	GLU/GLN	18,1366		0,18,674	56.0	46.0	49.0		6622	2.3	0.8	11	dbSNP_129	49	0,3182		0,0,1591	yes	missense	KIAA1731	NM_033395.1	29	0,18,2265	GG,GC,CC		0.0,1.3006,0.3942	benign	2208/2602	93460264	18,4548	692	1591	2283	SO:0001583	missense	85459	exon24			AAAAATCAGAACT	AB051518	CCDS44708.1	11q21	2014-03-11			ENSG00000166004	ENSG00000166004			29366	protein-coding gene	gene with protein product						20844083	Standard	NM_033395		Approved		uc009ywb.1	Q9C0D2	OTTHUMG00000167449	ENST00000325212.6:c.6622C>G	11.37:g.93460264C>G	ENSP00000316681:p.Gln2208Glu	185.0	0.0	0		160.0	83.0	0.51875	NM_033395	C9J5H9|C9JQY8|Q8N7L4|Q8N919|Q8N9B0|Q96LT8	Missense_Mutation	SNP	ENST00000325212.6	37	CCDS44708.1	23	0.010531135531135532	7	0.014227642276422764	3	0.008287292817679558	7	0.012237762237762238	6	0.0079155672823219	C	4.054	0.007826	0.07866	0.013006	0.0	ENSG00000166004	ENST00000325212;ENST00000411936;ENST00000344196;ENST00000531700;ENST00000531404;ENST00000529185	T;T	0.09163	3.02;3.01	5.61	2.34	0.29019	.	.	.	.	.	T	0.09423	0.0232	L	0.48642	1.525	0.09310	N	0.999992	B;B;B	0.15930	0.006;0.015;0.006	B;B;B	0.16722	0.011;0.016;0.011	T	0.23332	-1.0191	9	0.72032	D	0.01	.	15.8875	0.79261	0.0:0.6088:0.3912:0.0	rs61740994	2208;2208;388	Q9C0D2;Q9C0D2-3;Q9C0D2-2	K1731_HUMAN;.;.	E	2208;2208;388;388;220;74	ENSP00000316681:Q2208E;ENSP00000406505:Q2208E	ENSP00000316681:Q2208E	Q	+	1	0	KIAA1731	93099912	0.004000	0.15560	0.849000	0.33467	0.253000	0.25986	0.239000	0.18023	0.665000	0.31066	0.585000	0.79938	CAG	C|0.989;G|0.011	0.011	strong		0.368	KIAA1731-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000394640.1	NM_033395	
TP53BP2	7159	hgsc.bcm.edu	37	1	223984072	223984072	+	Silent	SNP	G	G	A	rs141654811	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:223984072G>A	ENST00000343537.7	-	13	2460	c.2169C>T	c.(2167-2169)gaC>gaT	p.D723D	TP53BP2_ENST00000391879.2_5'UTR|TP53BP2_ENST00000498843.1_5'UTR|TP53BP2_ENST00000391878.2_Silent_p.D594D	NM_001031685.2	NP_001026855.2	Q13625	ASPP2_HUMAN	tumor protein p53 binding protein 2	717					cell cycle (GO:0007049)|central nervous system development (GO:0007417)|embryo development ending in birth or egg hatching (GO:0009792)|heart development (GO:0007507)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell cycle (GO:0045786)|positive regulation of signal transduction (GO:0009967)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|NF-kappaB binding (GO:0051059)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(131;0.0958)		AGGCTTCTAGGTCAGCATCAC	0.438																																					p.D723D		Atlas-SNP	.											.	TP53BP2	144	.	0			c.C2169T						PASS	.	G	,	0,4406		0,0,2203	142.0	137.0	139.0		2169,1782	2.8	0.8	1	dbSNP_134	139	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	TP53BP2	NM_001031685.2,NM_005426.2	,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,	723/1135,594/1006	223984072	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	7159	exon13			TTCTAGGTCAGCA	U09582	CCDS1538.1, CCDS44319.1	1q41	2014-06-24	2014-06-24		ENSG00000143514	ENSG00000143514		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	12000	protein-coding gene	gene with protein product		602143	"""tumor protein p53-binding protein, 2"""			8668206, 8016121	Standard	NM_005426		Approved	PPP1R13A, ASPP2, 53BP2	uc010pvb.2	Q13625	OTTHUMG00000037379	ENST00000343537.7:c.2169C>T	1.37:g.223984072G>A		283.0	0.0	0		247.0	112.0	0.453441	NM_001031685	B4DG66|Q12892|Q86X75|Q96KQ3	Silent	SNP	ENST00000343537.7	37	CCDS44319.1																																																																																			G|1.000;A|0.000	0.000	strong		0.438	TP53BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090985.3	NM_001031685, NM_005426	
LRPPRC	10128	hgsc.bcm.edu	37	2	44175293	44175293	+	Silent	SNP	G	G	A	rs35881858	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:44175293G>A	ENST00000260665.7	-	18	1945	c.1888C>T	c.(1888-1890)Ctg>Ttg	p.L630L		NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	630					mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				TAGCTTTCCAGGAGATTACGA	0.358													G|||	126	0.0251597	0.0923	0.0043	5008	,	,		15884	0.0		0.001	False		,,,				2504	0.0				p.L630L		Atlas-SNP	.											.	LRPPRC	105	.	0			c.C1888T						PASS	.	G		269,4135	149.2+/-183.4	6,257,1939	94.0	99.0	97.0		1888	3.8	0.8	2	dbSNP_126	97	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	LRPPRC	NM_133259.3		6,260,6236	AA,AG,GG		0.0349,6.1081,2.0917		630/1395	44175293	272,12732	2202	4300	6502	SO:0001819	synonymous_variant	10128	exon18			TTTCCAGGAGATT	M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"""Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"""	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.1888C>T	2.37:g.44175293G>A		32.0	0.0	0		53.0	19.0	0.358491	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Silent	SNP	ENST00000260665.7	37	CCDS33189.1																																																																																			G|0.983;A|0.017	0.017	strong		0.358	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259	
TJP1	7082	hgsc.bcm.edu	37	15	30012209	30012209	+	Silent	SNP	A	A	C	rs376115263		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:30012209A>C	ENST00000346128.6	-	20	3249	c.2775T>G	c.(2773-2775)gcT>gcG	p.A925A	TJP1_ENST00000400011.2_Intron|TJP1_ENST00000356107.6_Silent_p.A925A|TJP1_ENST00000545208.2_Intron	NM_003257.3|NM_175610.2	NP_003248.3|NP_783297.2	Q07157	ZO1_HUMAN	tight junction protein 1	925					apoptotic process (GO:0006915)|blastocyst formation (GO:0001825)|cell-cell junction assembly (GO:0007043)|cell-cell signaling involved in cell-cell junction organization (GO:1901350)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to glucose stimulus (GO:0071333)|hippo signaling (GO:0035329)|membrane organization (GO:0061024)|negative regulation of vascular permeability (GO:0043116)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to magnetism (GO:0071000)|sensory perception of sound (GO:0007605)	apical junction complex (GO:0043296)|apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|gap junction (GO:0005921)|intercalated disc (GO:0014704)|intercellular canaliculus (GO:0046581)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)				breast(4)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|urinary_tract(1)	68		all_lung(180;7.48e-11)|Breast(32;0.000153)		all cancers(64;3.29e-10)|Epithelial(43;5.34e-09)|BRCA - Breast invasive adenocarcinoma(123;0.0034)|GBM - Glioblastoma multiforme(186;0.0139)|Lung(196;0.186)		CTGGAGATGAAGCTTCTGCTT	0.353																																					p.A925A	Melanoma(77;681 1843 6309 6570)	Atlas-SNP	.											.	TJP1	140	.	0			c.T2775G						PASS	.	A	,	3,3687		0,3,1842	125.0	115.0	118.0		2775,	4.2	1.0	15		118	0,8186		0,0,4093	no	coding-synonymous,intron	TJP1	NM_003257.3,NM_175610.2	,	0,3,5935	CC,CA,AA		0.0,0.0813,0.0253	,	925/1749,	30012209	3,11873	1845	4093	5938	SO:0001819	synonymous_variant	7082	exon20			AGATGAAGCTTCT		CCDS42007.1, CCDS45199.1, CCDS73702.1	15q13	2012-07-12	2012-07-12		ENSG00000104067	ENSG00000104067			11827	protein-coding gene	gene with protein product	"""zona occludens 1"", ""tight junction protein ZO-1"""	601009				8825647	Standard	XM_005254616		Approved	ZO-1, MGC133289, DKFZp686M05161	uc001zcr.3	Q07157	OTTHUMG00000137397	ENST00000346128.6:c.2775T>G	15.37:g.30012209A>C		80.0	0.0	0		86.0	41.0	0.476744	NM_003257	B4E3K1|Q2NKP3|Q4ZGJ6	Silent	SNP	ENST00000346128.6	37	CCDS42007.1																																																																																			.	.	weak		0.353	TJP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000268237.3	NM_003257	
FUT7	2529	hgsc.bcm.edu	37	9	139925459	139925459	+	Silent	SNP	G	G	A	rs11145973	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139925459G>A	ENST00000314412.6	-	2	1750	c.732C>T	c.(730-732)aaC>aaT	p.N244N	ABCA2_ENST00000371605.3_5'Flank|ABCA2_ENST00000265662.5_5'Flank|ABCA2_ENST00000492260.1_5'Flank|C9orf139_ENST00000314330.2_Intron|ABCA2_ENST00000341511.6_5'Flank	NM_004479.3	NP_004470.1	Q11130	FUT7_HUMAN	fucosyltransferase 7 (alpha (1,3) fucosyltransferase)	244					CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|fucosylation (GO:0036065)|L-fucose catabolic process (GO:0042355)|leukocyte migration involved in immune response (GO:0002522)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	alpha-(1->3)-fucosyltransferase activity (GO:0046920)|fucosyltransferase activity (GO:0008417)			NS(1)|endometrium(1)|lung(4)|ovary(1)|skin(1)	8	all_cancers(76;0.0893)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.96e-05)|Epithelial(140;0.000486)		CCACCAGTGCGTTGCGCCAGA	0.627													g|||	24	0.00479233	0.0166	0.0	5008	,	,		17645	0.0		0.001	False		,,,				2504	0.001				p.N244N		Atlas-SNP	.											.	FUT7	24	.	0			c.C732T						PASS	.		,	89,4317	67.0+/-104.6	2,85,2116	88.0	104.0	99.0		732,	-1.4	0.9	9	dbSNP_120	99	0,8598		0,0,4299	no	coding-synonymous,intron	FUT7,C9orf139	NM_004479.3,NM_207511.1	,	2,85,6415	AA,AG,GG		0.0,2.02,0.6844	,	244/343,	139925459	89,12915	2203	4299	6502	SO:0001819	synonymous_variant	2529	exon2			CAGTGCGTTGCGC	X78031, AB012668	CCDS7022.1	9q34.3	2013-02-26			ENSG00000180549	ENSG00000180549		"""Fucosyltransferases"""	4018	protein-coding gene	gene with protein product		602030				8207002, 8182079	Standard	NM_004479		Approved		uc004ckq.2	Q11130	OTTHUMG00000020964	ENST00000314412.6:c.732C>T	9.37:g.139925459G>A		76.0	0.0	0		98.0	71.0	0.72449	NM_004479	B2R7U7|Q6DK54	Silent	SNP	ENST00000314412.6	37	CCDS7022.1																																																																																			G|0.993;A|0.007	0.007	strong		0.627	FUT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055220.1	NM_004479	
CLEC2L	154790	hgsc.bcm.edu	37	7	139225215	139225215	+	Silent	SNP	T	T	C	rs112553913	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:139225215T>C	ENST00000422142.2	+	3	486	c.414T>C	c.(412-414)atT>atC	p.I138I		NM_001080511.2	NP_001073980.2	P0C7M8	CLC2L_HUMAN	C-type lectin domain family 2, member L	138	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.					integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(1)|endometrium(1)|kidney(2)|lung(1)	5	Melanoma(164;0.233)					TGGCTGTGATTCAGAGCCAGA	0.592													T|||	149	0.0297524	0.1097	0.0014	5008	,	,		17539	0.0		0.003	False		,,,				2504	0.0				p.I138I		Atlas-SNP	.											.	CLEC2L	14	.	0			c.T414C						PASS	.	T		311,3699		9,293,1703	13.0	17.0	16.0		414	-4.7	1.0	7	dbSNP_132	16	7,8351		0,7,4172	no	coding-synonymous	CLEC2L	NM_001080511.2		9,300,5875	CC,CT,TT		0.0838,7.7556,2.5712		138/215	139225215	318,12050	2005	4179	6184	SO:0001819	synonymous_variant	154790	exon3			TGTGATTCAGAGC	AK057548	CCDS47724.1	7q34	2011-05-18			ENSG00000236279	ENSG00000236279		"""C-type lectin domain containing"""	21969	protein-coding gene	gene with protein product							Standard	NM_001080511		Approved	FLJ32986	uc010lnd.3	P0C7M8	OTTHUMG00000164900	ENST00000422142.2:c.414T>C	7.37:g.139225215T>C		139.0	0.0	0		126.0	67.0	0.531746	NM_001080511		Silent	SNP	ENST00000422142.2	37	CCDS47724.1	60	0.027472527472527472	58	0.11788617886178862	0	0.0	0	0.0	2	0.002638522427440633	T	9.732	1.162489	0.21538	0.077556	8.38E-4	ENSG00000236279	ENST00000521281	.	.	.	4.81	-4.68	0.03309	.	.	.	.	.	T	0.01124	0.0037	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33599	-0.9862	4	.	.	.	-13.0213	11.495	0.50402	0.0:0.2389:0.0:0.7611	.	.	.	.	S	62	.	.	F	+	2	0	CLEC2L	138875755	0.368000	0.25031	0.986000	0.45419	0.949000	0.60115	-1.179000	0.03090	-0.764000	0.04651	-0.376000	0.06991	TTC	T|0.972;C|0.028	0.028	strong		0.592	CLEC2L-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380878.1	NM_001080511	
CYTH2	9266	hgsc.bcm.edu	37	19	48977189	48977189	+	Silent	SNP	C	C	T	rs28582663	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:48977189C>T	ENST00000452733.2	+	6	938	c.462C>T	c.(460-462)ccC>ccT	p.P154P	CYTH2_ENST00000427476.1_Silent_p.P154P			Q99418	CYH2_HUMAN	cytohesin 2	154	SEC7. {ECO:0000255|PROSITE- ProRule:PRU00189}.				actin cytoskeleton organization (GO:0030036)|endocytosis (GO:0006897)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)	cytoplasm (GO:0005737)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|inositol 1,4,5 trisphosphate binding (GO:0070679)|lipid binding (GO:0008289)			endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15						TTCGCCTACCCGGAGAGGCCC	0.607													C|||	61	0.0121805	0.0431	0.0043	5008	,	,		16544	0.0		0.0	False		,,,				2504	0.001				p.P154P		Atlas-SNP	.											.	CYTH2	33	.	0			c.C462T						PASS	.	C	,	193,4213	123.3+/-160.7	1,191,2011	48.0	47.0	47.0		462,462	-7.4	0.9	19	dbSNP_125	47	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	CYTH2	NM_004228.6,NM_017457.5	,	1,192,6310	TT,TC,CC		0.0116,4.3804,1.4916	,	154/400,154/401	48977189	194,12812	2203	4300	6503	SO:0001819	synonymous_variant	9266	exon6			CCTACCCGGAGAG	X99753	CCDS12722.1	19q13.32	2014-05-02	2008-08-14	2008-08-14	ENSG00000105443	ENSG00000105443		"""Pleckstrin homology (PH) domain containing"""	9502	protein-coding gene	gene with protein product		602488	"""pleckstrin homology, Sec7 and coiled/coil domains 2 (cytohesin-2)"", ""pleckstrin homology, Sec7 and coiled-coil domains 2"""	PSCD2L, PSCD2		8706128, 8945478, 20525696	Standard	NM_004228		Approved	CTS18.1, Sec7p-L, ARNO, Sec7p-like, cytohesin-2	uc002pjj.4	Q99418	OTTHUMG00000150245	ENST00000452733.2:c.462C>T	19.37:g.48977189C>T		89.0	0.0	0		74.0	74.0	1	NM_017457	A8K8P0|Q8IXY9|Q92958	Silent	SNP	ENST00000452733.2	37	CCDS12722.1																																																																																			C|0.982;T|0.018	0.018	strong		0.607	CYTH2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317060.1	NM_004228	
ADORA3	140	hgsc.bcm.edu	37	1	112045709	112045709	+	Missense_Mutation	SNP	G	G	C	rs77883500	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:112045709G>C	ENST00000241356.4	-	1	673	c.268C>G	c.(268-270)Ctg>Gtg	p.L90V	ADORA3_ENST00000369716.4_Missense_Mutation_p.L90V|ADORA3_ENST00000486342.1_5'UTR|ADORA3_ENST00000369717.4_Intron	NM_000677.3	NP_000668.1	P33765	AA3R_HUMAN	adenosine A3 receptor	90					activation of adenylate cyclase activity (GO:0007190)|histamine secretion by mast cell (GO:0002553)|inflammatory response (GO:0006954)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of inflammatory response (GO:0050729)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of mast cell degranulation (GO:0043306)|positive regulation of mucus secretion (GO:0070257)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|regulation of heart contraction (GO:0008016)|response to wounding (GO:0009611)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	G-protein coupled adenosine receptor activity (GO:0001609)			NS(1)|breast(2)|endometrium(1)|large_intestine(2)|lung(3)|ovary(2)|skin(1)	12		all_cancers(81;1.63e-06)|all_epithelial(167;5.01e-06)|all_lung(203;8.02e-05)|Lung NSC(277;0.000156)		all cancers(265;0.0185)|Colorectal(144;0.0186)|Lung(183;0.0238)|COAD - Colon adenocarcinoma(174;0.0644)|Epithelial(280;0.0872)|LUSC - Lung squamous cell carcinoma(189;0.134)	Adenosine(DB00640)|Aminophylline(DB01223)|Enprofylline(DB00824)	AAGATAAGCAGTAGGCAAGTC	0.552													G|||	86	0.0171725	0.0613	0.0058	5008	,	,		21547	0.0		0.001	False		,,,				2504	0.0				p.L90V		Atlas-SNP	.											.	ADORA3	104	.	0			c.C268G						PASS	.	G	VAL/LEU,,VAL/LEU	184,4222	117.5+/-155.4	2,180,2021	84.0	64.0	70.0		268,,268	1.1	0.7	1	dbSNP_131	70	1,8599		0,1,4299	yes	missense,intron,missense	ADORA3	NM_000677.3,NM_001081976.1,NM_020683.6	32,,32	2,181,6320	CC,CG,GG		0.0116,4.1761,1.4224	benign,,benign	90/319,,90/348	112045709	185,12821	2203	4300	6503	SO:0001583	missense	140	exon1			TAAGCAGTAGGCA	BC029831	CCDS838.1, CCDS839.1, CCDS41369.1	1p13.2	2014-09-17			ENSG00000121933	ENSG00000121933		"""GPCR / Class A : Adenosine receptors"", ""Immunoglobulin superfamily / V-set domain containing"""	268	protein-coding gene	gene with protein product		600445				7607699	Standard	NM_020683		Approved	AD026	uc001ebf.3	P33765	OTTHUMG00000011957	ENST00000241356.4:c.268C>G	1.37:g.112045709G>C	ENSP00000241356:p.Leu90Val	262.0	0.0	0		291.0	135.0	0.463918	NM_020683	A2A3P4|Q6UWU0|Q9BYZ1	Missense_Mutation	SNP	ENST00000241356.4	37	CCDS839.1	33	0.01510989010989011	32	0.06504065040650407	1	0.0027624309392265192	0	0.0	0	0.0	G	4.114	0.019297	0.08006	0.041761	1.16E-4	ENSG00000121933	ENST00000369716;ENST00000241356	T;T	0.37235	1.21;1.21	5.26	1.07	0.20283	GPCR, rhodopsin-like superfamily (1);	0.645763	0.12883	N	0.431230	T	0.05777	0.0151	N	0.05510	-0.035	0.22292	N	0.999222	B;B	0.21381	0.055;0.004	B;B	0.24394	0.053;0.012	T	0.45101	-0.9284	10	0.10377	T	0.69	-1.0214	11.5274	0.50588	0.0:0.1113:0.3199:0.5688	.	90;90	P33765;P33765-2	AA3R_HUMAN;.	V	90	ENSP00000358730:L90V;ENSP00000241356:L90V	ENSP00000241356:L90V	L	-	1	2	ADORA3	111847232	0.001000	0.12720	0.667000	0.29798	0.701000	0.40568	-0.483000	0.06536	0.013000	0.14918	0.561000	0.74099	CTG	G|0.985;C|0.015	0.015	strong		0.552	ADORA3-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033065.1	NM_000677, NM_020683	
MT-CYB	4519	hgsc.bcm.edu	37	M	15139	15139	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:15139T>C	ENST00000361789.2	+	1	393	c.393T>C	c.(391-393)taT>taC	p.Y131Y	MT-TT_ENST00000387460.2_RNA|MT-TE_ENST00000387459.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-ND6_ENST00000361681.2_5'Flank|MT-TH_ENST00000387441.1_RNA			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	131					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						TTCATAGGCTATGTCCTCCCG	0.458											OREG0007583	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.Y131Y		Atlas-SNP	.											.	.	.	.	0			c.T393C						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			AGGCTATGTCCTC			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156		ENST00000361789.2:c.393T>C	M.37:g.15139T>C		15.0	0.0	0	585	17.0	17.0	1	ENST00000361789	Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	Silent	SNP	ENST00000361789.2	37																																																																																				.	.	none		0.458	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024038	
CBLC	23624	hgsc.bcm.edu	37	19	45281375	45281375	+	Missense_Mutation	SNP	C	C	T	rs115775900	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45281375C>T	ENST00000270279.3	+	1	250	c.187C>T	c.(187-189)Cgg>Tgg	p.R63W	CBLC_ENST00000341505.4_Missense_Mutation_p.R63W	NM_012116.3	NP_036248.3	Q9ULV8	CBLC_HUMAN	Cbl proto-oncogene C, E3 ubiquitin protein ligase	63	4H.|Cbl-PTB. {ECO:0000255|PROSITE- ProRule:PRU00839}.				cell surface receptor signaling pathway (GO:0007166)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of MAP kinase activity (GO:0043407)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|ligase activity (GO:0016874)|phosphotyrosine binding (GO:0001784)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|lung(6)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Lung NSC(12;0.00136)|all_lung(12;0.00371)	Ovarian(192;0.231)				CCATTCTcggcgggcggccgg	0.711			M		AML								c|||	64	0.0127796	0.0454	0.0043	5008	,	,		8428	0.0		0.0	False		,,,				2504	0.001				p.R63W		Atlas-SNP	.		Rec	yes		19	19q13.2	23624	Cas-Br-M (murine) ecotropic retroviral transforming sequence c		L	.	CBLC	41	.	0			c.C187T						PASS	.		TRP/ARG,TRP/ARG	85,3747		1,83,1832	8.0	11.0	10.0		187,187	-2.5	0.0	19	dbSNP_132	10	1,7799		0,1,3899	yes	missense,missense	CBLC	NM_001130852.1,NM_012116.3	101,101	1,84,5731	TT,TC,CC		0.0128,2.2182,0.7393	probably-damaging,probably-damaging	63/429,63/475	45281375	86,11546	1916	3900	5816	SO:0001583	missense	23624	exon1			TCTCGGCGGGCGG	AB028645	CCDS12643.1, CCDS46109.1	19q13.2	2013-07-09	2013-07-09		ENSG00000142273	ENSG00000142273		"""RING-type (C3HC4) zinc fingers"""	15961	protein-coding gene	gene with protein product		608453	"""Cas-Br-M (murine) ectropic retroviral transforming sequence c"", ""Cas-Br-M (murine) ecotropic retroviral transforming sequence c"""			10362357, 10571044	Standard	NM_012116		Approved	CBL-3, CBL-SL, RNF57	uc002ozs.3	Q9ULV8	OTTHUMG00000150715	ENST00000270279.3:c.187C>T	19.37:g.45281375C>T	ENSP00000270279:p.Arg63Trp	6.0	0.0	0		10.0	8.0	0.8	NM_001130852	Q8N1E5|Q9Y5Z2|Q9Y5Z3	Missense_Mutation	SNP	ENST00000270279.3	37	CCDS12643.1	32	0.014652014652014652	29	0.05894308943089431	3	0.008287292817679558	0	0.0	0	0.0	.	16.25	3.071238	0.55646	0.022182	1.28E-4	ENSG00000142273	ENST00000270279;ENST00000341505	T;T	0.76968	-1.06;-1.06	3.35	-2.49	0.06403	Adaptor protein Cbl, N-terminal helical (3);Adaptor protein Cbl, PTB domain (1);	0.588184	0.13455	N	0.386611	T	0.40272	0.1110	M	0.65975	2.015	0.09310	N	1	D;D	0.71674	0.998;0.998	P;P	0.62491	0.903;0.756	T	0.63506	-0.6622	10	0.87932	D	0	-6.6255	10.0273	0.42079	0.6988:0.3012:0.0:0.0	.	63;63	Q9ULV8-2;Q9ULV8	.;CBLC_HUMAN	W	63	ENSP00000270279:R63W;ENSP00000340250:R63W	ENSP00000270279:R63W	R	+	1	2	CBLC	49973215	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.696000	0.05104	-0.081000	0.12662	0.556000	0.70494	CGG	C|0.983;T|0.017	0.017	strong		0.711	CBLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319732.2	NM_012116	
ETNK2	55224	hgsc.bcm.edu	37	1	204109238	204109238	+	Missense_Mutation	SNP	G	G	A	rs565275436		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:204109238G>A	ENST00000367202.4	-	5	943	c.793C>T	c.(793-795)Cgg>Tgg	p.R265W	ETNK2_ENST00000367198.2_Missense_Mutation_p.R87W|ETNK2_ENST00000477125.1_5'UTR|ETNK2_ENST00000367197.1_5'UTR|ETNK2_ENST00000367199.2_Missense_Mutation_p.R196W|ETNK2_ENST00000367201.3_Missense_Mutation_p.R265W|RP11-74C13.3_ENST00000433869.1_RNA	NM_018208.2	NP_060678.2	Q9NVF9	EKI2_HUMAN	ethanolamine kinase 2	265					glycerophospholipid biosynthetic process (GO:0046474)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|placenta development (GO:0001890)|post-embryonic development (GO:0009791)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|ethanolamine kinase activity (GO:0004305)			breast(1)|central_nervous_system(1)|large_intestine(4)|ovary(1)	7	all_cancers(21;0.032)|Breast(84;0.116)|all_epithelial(62;0.196)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.109)			TCAATGAACCGCACGTGACCT	0.488													G|||	1	0.000199681	0.0008	0.0	5008	,	,		22874	0.0		0.0	False		,,,				2504	0.0				p.R265W		Atlas-SNP	.											ETNK2_ENST00000367202,NS,carcinoma,0,2	ETNK2	48	2	0			c.C793T						PASS	.						152.0	134.0	140.0					1																	204109238		2203	4300	6503	SO:0001583	missense	55224	exon5			TGAACCGCACGTG	AK001623	CCDS1442.2, CCDS73006.1	1q32.1	2008-02-05			ENSG00000143845	ENSG00000143845			25575	protein-coding gene	gene with protein product		609859				12477932	Standard	XM_005245302		Approved	FLJ10761, EKI2	uc001hao.4	Q9NVF9	OTTHUMG00000036061	ENST00000367202.4:c.793C>T	1.37:g.204109238G>A	ENSP00000356170:p.Arg265Trp	100.0	0.0	0		111.0	53.0	0.477477	NM_018208	B7Z7K1|Q5SXX5|Q68CK3|Q96G05	Missense_Mutation	SNP	ENST00000367202.4	37	CCDS1442.2	.	.	.	.	.	.	.	.	.	.	G	15.70	2.910054	0.52439	.	.	ENSG00000143845	ENST00000367201;ENST00000367202;ENST00000367199;ENST00000455266;ENST00000367198;ENST00000422699;ENST00000452983;ENST00000444817	T;T;T;T;T;T;T	0.58652	0.32;0.32;0.32;0.32;0.32;0.32;0.32	5.4	1.99	0.26369	Protein kinase-like domain (1);Choline/ethanolamine kinase (1);	0.207171	0.44097	D	0.000494	T	0.71281	0.3321	M	0.82323	2.585	0.40505	D	0.98068	D;D;D	0.89917	0.995;0.996;1.0	P;P;P	0.62014	0.663;0.773;0.897	T	0.73398	-0.3995	10	0.62326	D	0.03	-8.4891	9.3644	0.38215	0.0756:0.0:0.6588:0.2656	.	224;265;265	Q9NVF9-3;Q9NVF9;Q9NVF9-2	.;EKI2_HUMAN;.	W	265;265;196;131;87;131;122;111	ENSP00000356169:R265W;ENSP00000356170:R265W;ENSP00000356167:R196W;ENSP00000356166:R87W;ENSP00000405497:R131W;ENSP00000398091:R122W;ENSP00000406241:R111W	ENSP00000356166:R87W	R	-	1	2	ETNK2	202375861	0.148000	0.22702	0.308000	0.25141	0.327000	0.28475	2.116000	0.41930	0.590000	0.29694	0.650000	0.86243	CGG	.	.	none		0.488	ETNK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087893.1	NM_018208	
COL1A2	1278	hgsc.bcm.edu	37	7	94028386	94028386	+	Missense_Mutation	SNP	G	G	A	rs139528613	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:94028386G>A	ENST00000297268.6	+	4	593	c.122G>A	c.(121-123)cGt>cAt	p.R41H		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	41					blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)	p.R41L(1)	COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	AGAGGACCACGTGGAGAAAGG	0.373										HNSCC(75;0.22)			G|||	15	0.00299521	0.0113	0.0	5008	,	,		15654	0.0		0.0	False		,,,				2504	0.0				p.R41H		Atlas-SNP	.											.	COL1A2	240	.	1	Substitution - Missense(1)	lung(1)	c.G122A						PASS	.	G	HIS/ARG	54,4352	54.2+/-90.2	0,54,2149	125.0	124.0	125.0		122	5.8	1.0	7	dbSNP_134	125	1,8599	1.2+/-3.3	0,1,4299	yes	missense	COL1A2	NM_000089.3	29	0,55,6448	AA,AG,GG		0.0116,1.2256,0.4229	probably-damaging	41/1367	94028386	55,12951	2203	4300	6503	SO:0001583	missense	1278	exon4			GACCACGTGGAGA	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"""Collagens"""	2198	protein-coding gene	gene with protein product	"""alpha 2(I)-collagen"", ""alpha-2 collagen type I"", ""type I procollagen"", ""collagen I, alpha-2 polypeptide"", ""collagen of skin, tendon and bone, alpha-2 chain"""	120160	"""osteogenesis imperfecta type IV"""	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.122G>A	7.37:g.94028386G>A	ENSP00000297268:p.Arg41His	81.0	0.0	0		76.0	44.0	0.578947	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Missense_Mutation	SNP	ENST00000297268.6	37	CCDS34682.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	19.99	3.928117	0.73327	0.012256	1.16E-4	ENSG00000164692	ENST00000297268	D	0.93712	-3.27	5.85	5.85	0.93711	.	.	.	.	.	D	0.93350	0.7880	L	0.55103	1.725	0.43430	D	0.995594	D;D	0.69078	0.997;0.994	D;P	0.63033	0.91;0.727	D	0.93121	0.6525	9	0.72032	D	0.01	.	14.6939	0.69107	0.071:0.0:0.929:0.0	.	41;41	B4DTF5;P08123	.;CO1A2_HUMAN	H	41	ENSP00000297268:R41H	ENSP00000297268:R41H	R	+	2	0	COL1A2	93866322	0.971000	0.33674	1.000000	0.80357	0.993000	0.82548	2.827000	0.48112	2.941000	0.99782	0.655000	0.94253	CGT	G|0.996;A|0.004	0.004	strong		0.373	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089	
RETSAT	54884	hgsc.bcm.edu	37	2	85570440	85570440	+	Silent	SNP	G	G	A	rs150706527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:85570440G>A	ENST00000295802.4	-	11	1870	c.1758C>T	c.(1756-1758)gcC>gcT	p.A586A	RETSAT_ENST00000457495.2_Silent_p.A525A|RETSAT_ENST00000263854.6_3'UTR|RETSAT_ENST00000475624.2_5'Flank	NM_017750.3	NP_060220.3	Q6NUM9	RETST_HUMAN	retinol saturase (all-trans-retinol 13,14-reductase)	586					oxidation-reduction process (GO:0055114)|retinol metabolic process (GO:0042572)	endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|nuclear outer membrane (GO:0005640)	all-trans-retinol 13,14-reductase activity (GO:0051786)|oxidoreductase activity (GO:0016491)			NS(2)|breast(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|skin(2)|urinary_tract(1)	30					Vitamin A(DB00162)	GCTTCAGGATGGCGCTGCTGC	0.552													G|||	17	0.00339457	0.0129	0.0	5008	,	,		32923	0.0		0.0	False		,,,				2504	0.0				p.A586A		Atlas-SNP	.											RETSAT,NS,carcinoma,-2,1	RETSAT	56	1	0			c.C1758T						PASS	.	G		51,4355	50.9+/-86.3	0,51,2152	81.0	84.0	83.0		1758	1.9	1.0	2	dbSNP_134	83	0,8600		0,0,4300	no	coding-synonymous	RETSAT	NM_017750.3		0,51,6452	AA,AG,GG		0.0,1.1575,0.3921		586/611	85570440	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	54884	exon11			CAGGATGGCGCTG	AK075261	CCDS1972.1	2p11.2	2008-02-05			ENSG00000042445	ENSG00000042445	1.3.99.23		25991	protein-coding gene	gene with protein product						12975309, 15358783	Standard	NM_017750		Approved	FLJ20296	uc002spd.3	Q6NUM9	OTTHUMG00000154611	ENST00000295802.4:c.1758C>T	2.37:g.85570440G>A		299.0	0.0	0		328.0	73.0	0.222561	NM_017750	A6NIK3|Q53R95|Q53SA9|Q6UX05|Q8N2H5|Q96FA4|Q9NXE5	Silent	SNP	ENST00000295802.4	37	CCDS1972.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	7.937	0.741884	0.15642	0.011575	0.0	ENSG00000042445	ENST00000449375	.	.	.	4.89	1.86	0.25419	.	.	.	.	.	T	0.38134	0.1029	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.21655	-1.0239	4	.	.	.	-15.1159	4.0777	0.09912	0.1989:0.0:0.6169:0.1842	.	.	.	.	L	375	.	.	P	-	2	0	RETSAT	85423951	0.882000	0.30256	0.993000	0.49108	0.657000	0.38888	0.224000	0.17738	0.579000	0.29504	0.462000	0.41574	CCA	G|0.996;A|0.004	0.004	strong		0.552	RETSAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252489.1	NM_017750	
DHX9	1660	hgsc.bcm.edu	37	1	182827297	182827297	+	Silent	SNP	G	G	A	rs73063095	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:182827297G>A	ENST00000367549.3	+	8	842	c.732G>A	c.(730-732)ctG>ctA	p.L244L		NM_001357.4	NP_001348.2	Q08211	DHX9_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 9	244	DRBM 2. {ECO:0000255|PROSITE- ProRule:PRU00266}.|Interaction with BRCA1.|Interaction with CREBBP.				ATP catabolic process (GO:0006200)|cellular response to heat (GO:0034605)|circadian rhythm (GO:0007623)|CRD-mediated mRNA stabilization (GO:0070934)|DNA duplex unwinding (GO:0032508)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|osteoblast differentiation (GO:0001649)|positive regulation of type I interferon production (GO:0032481)|RNA splicing (GO:0008380)	centrosome (GO:0005813)|CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)|RNA polymerase II transcription factor binding (GO:0001085)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(10)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	49						CCTGTGCCCTGTCACTTGTCA	0.408													G|||	104	0.0207668	0.0741	0.0072	5008	,	,		20027	0.001		0.0	False		,,,				2504	0.0				p.L244L	Colon(69;210 1162 3697 13559 39565)	Atlas-SNP	.											.	DHX9	114	.	0			c.G732A						PASS	.	G		243,3731		8,227,1752	100.0	95.0	97.0		732	1.1	1.0	1	dbSNP_130	97	0,8354		0,0,4177	no	coding-synonymous	DHX9	NM_001357.4		8,227,5929	AA,AG,GG		0.0,6.1147,1.9711		244/1271	182827297	243,12085	1987	4177	6164	SO:0001819	synonymous_variant	1660	exon8			TGCCCTGTCACTT	L13848	CCDS41444.1	1q25	2013-05-13	2013-05-13	2003-06-20	ENSG00000135829	ENSG00000135829		"""DEAH-boxes"""	2750	protein-coding gene	gene with protein product	"""NDH II"", ""RNA helicase A"""	603115	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9 (RNA helicase A, nuclear DNA helicase II; leukophysin)"", ""DEAH (Asp-Glu-Ala-His) box polypeptide 9"""	LKP, DDX9		8344961, 9111062	Standard	NM_001357		Approved	RHA	uc001gpr.3	Q08211	OTTHUMG00000035337	ENST00000367549.3:c.732G>A	1.37:g.182827297G>A		178.0	0.0	0		173.0	76.0	0.439306	NM_001357	B2RNV4|Q05CI5|Q12803|Q32Q22|Q5VY62|Q6PD69|Q99556	Silent	SNP	ENST00000367549.3	37	CCDS41444.1																																																																																			G|0.986;A|0.014	0.014	strong		0.408	DHX9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085522.2	NM_030588	
GALNT9	50614	hgsc.bcm.edu	37	12	132681664	132681664	+	Silent	SNP	G	G	A	rs111344752	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132681664G>A	ENST00000328957.8	-	11	1799	c.1800C>T	c.(1798-1800)caC>caT	p.H600H	GALNT9_ENST00000541995.1_Silent_p.H234H|GALNT9_ENST00000535228.1_Silent_p.H351H|GALNT9_ENST00000397325.2_Silent_p.H234H	NM_001122636.1	NP_001116108.1	Q9HCQ5	GALT9_HUMAN	polypeptide N-acetylgalactosaminyltransferase 9	600	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(1)|large_intestine(2)|lung(5)	9	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.241)		OV - Ovarian serous cystadenocarcinoma(86;7.49e-08)|Epithelial(86;3.55e-07)|all cancers(50;2.09e-05)		AGTGCCGTGCGTGTTTGATCC	0.642													g|||	68	0.0135783	0.0499	0.0014	5008	,	,		15532	0.0		0.0	False		,,,				2504	0.001				p.H600H	Colon(186;2147 2752 13553 41466)	Atlas-SNP	.											.	GALNT9	74	.	0			c.C1800T						PASS	.		,	176,3898		3,170,1864	85.0	100.0	95.0		723,702	-6.2	0.0	12	dbSNP_132	95	0,8376		0,0,4188	no	coding-synonymous,coding-synonymous	GALNT9	NM_001122636.1.dup,NM_021808.3	,	3,170,6052	AA,AG,GG		0.0,4.3201,1.4137	,	241/245,234/238	132681664	176,12274	2037	4188	6225	SO:0001819	synonymous_variant	50614	exon11			CCGTGCGTGTTTG	AB040672	CCDS41866.1	12q24.33	2014-03-13	2014-03-13		ENSG00000182870	ENSG00000182870	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4131	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 9"""	606251	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 9 (GalNAc-T9)"""			10978536, 12407114	Standard	NM_021808		Approved	GALNAC-T9	uc001ukc.4	Q9HCQ5	OTTHUMG00000168256	ENST00000328957.8:c.1800C>T	12.37:g.132681664G>A		134.0	0.0	0		129.0	64.0	0.496124	NM_001122636	Q52LR8|Q6NT54|Q8NFR1	Silent	SNP	ENST00000328957.8	37		20	0.009157509157509158	20	0.04065040650406504	0	0.0	0	0.0	0	0.0	g	0.018	-1.482667	0.01027	0.043201	0.0	ENSG00000182870	ENST00000411988	.	.	.	4.45	-6.24	0.02046	.	.	.	.	.	T	0.09905	0.0243	.	.	.	0.30680	N	0.752399	.	.	.	.	.	.	T	0.35375	-0.9791	4	.	.	.	.	8.9918	0.36028	0.5625:0.0:0.3379:0.0995	.	.	.	.	C	373	.	.	R	-	1	0	GALNT9	131247617	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-0.994000	0.03716	-1.273000	0.02424	-1.585000	0.00851	CGC	G|0.990;A|0.010	0.010	strong		0.642	GALNT9-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000402967.1	NM_001122636	
EPB41	2035	hgsc.bcm.edu	37	1	29391505	29391505	+	Silent	SNP	G	G	A	rs79677225	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:29391505G>A	ENST00000343067.4	+	16	2146	c.2019G>A	c.(2017-2019)aaG>aaA	p.K673K	EPB41_ENST00000349460.4_Silent_p.K450K|EPB41_ENST00000373797.1_Silent_p.K659K|EPB41_ENST00000373800.3_Silent_p.K431K|EPB41_ENST00000398863.2_Silent_p.K619K|EPB41_ENST00000356093.2_Silent_p.K640K|EPB41_ENST00000347529.3_Silent_p.K584K|EPB41_ENST00000373798.1_Silent_p.K673K	NM_001166005.1	NP_001159477.1	P11171	41_HUMAN	erythrocyte membrane protein band 4.1	673	Spectrin--actin-binding.				actin cytoskeleton organization (GO:0030036)|blood circulation (GO:0008015)|cortical actin cytoskeleton organization (GO:0030866)|positive regulation of protein binding (GO:0032092)	cortical cytoskeleton (GO:0030863)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	1-phosphatidylinositol binding (GO:0005545)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|urinary_tract(1)	14		Colorectal(325;3.46e-05)|Prostate(1639;0.000244)|Lung NSC(340;0.00328)|all_lung(284;0.00412)|Breast(348;0.00765)|all_neural(195;0.0199)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)|Medulloblastoma(700;0.123)		Colorectal(126;3.12e-07)|COAD - Colon adenocarcinoma(152;1.21e-05)|STAD - Stomach adenocarcinoma(196;0.00395)|KIRC - Kidney renal clear cell carcinoma(1967;0.0249)|BRCA - Breast invasive adenocarcinoma(304;0.0289)|READ - Rectum adenocarcinoma(331;0.0757)		ATTTAGACAAGAGTCAAGAGG	0.433													G|||	46	0.0091853	0.0325	0.0043	5008	,	,		19618	0.0		0.0	False		,,,				2504	0.0				p.K673K		Atlas-SNP	.											.	EPB41	118	.	0			c.G2019A						PASS	.	G	,,,,,	99,4307	79.3+/-117.8	2,95,2106	98.0	92.0	94.0		2019,1977,1230,1293,1350,1752	-0.5	1.0	1	dbSNP_132	94	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	EPB41	NM_001166005.1,NM_001166006.1,NM_001166007.1,NM_004437.3,NM_203342.2,NM_203343.2	,,,,,	2,95,6406	AA,AG,GG		0.0,2.2469,0.7612	,,,,,	673/865,659/721,410/602,431/589,450/642,584/776	29391505	99,12907	2203	4300	6503	SO:0001819	synonymous_variant	2035	exon16			AGACAAGAGTCAA	BC039079	CCDS330.1, CCDS331.1, CCDS332.1, CCDS53288.1, CCDS53289.1	1p33-p32	2014-05-09	2014-05-09		ENSG00000159023	ENSG00000159023			3377	protein-coding gene	gene with protein product		130500	"""elliptocytosis 1, RH-linked"""	EL1			Standard	NM_001166005		Approved	4.1R	uc001brm.2	P11171	OTTHUMG00000003644	ENST00000343067.4:c.2019G>A	1.37:g.29391505G>A		79.0	0.0	0		62.0	25.0	0.403226	NM_001166005	B1ALH8|B1ALH9|D3DPM9|D3DPN0|P11176|Q14245|Q5TB35|Q5VXN8|Q8IXV9|Q9Y578|Q9Y579	Silent	SNP	ENST00000343067.4	37	CCDS53288.1																																																																																			G|0.991;A|0.009	0.009	strong		0.433	EPB41-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000010312.1	NM_203342	
PPP6R3	55291	hgsc.bcm.edu	37	11	68341661	68341661	+	Silent	SNP	C	C	A	rs114505709	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:68341661C>A	ENST00000393800.2	+	13	1682	c.1428C>A	c.(1426-1428)ccC>ccA	p.P476P	PPP6R3_ENST00000265636.5_Silent_p.P425P|PPP6R3_ENST00000393801.3_Silent_p.P476P|PPP6R3_ENST00000265637.4_Silent_p.P476P|PPP6R3_ENST00000527403.2_Silent_p.P476P|PPP6R3_ENST00000524904.1_Silent_p.P476P|PPP6R3_ENST00000393799.2_Silent_p.P476P|PPP6R3_ENST00000534534.1_Silent_p.P244P|PPP6R3_ENST00000524845.1_Silent_p.P476P|PPP6R3_ENST00000529710.1_Silent_p.P425P	NM_001164161.1|NM_001164162.1|NM_001164163.1	NP_001157633.1|NP_001157634.1|NP_001157635.1	Q5H9R7	PP6R3_HUMAN	protein phosphatase 6, regulatory subunit 3	476					regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein phosphatase binding (GO:0019903)			breast(2)|endometrium(6)|kidney(3)|large_intestine(10)|liver(2)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37						ACAAGGGCCCCAACAGTGCAT	0.448													C|||	37	0.00738818	0.025	0.0029	5008	,	,		20069	0.0		0.002	False		,,,				2504	0.0				p.P476P		Atlas-SNP	.											.	PPP6R3	159	.	0			c.C1428A						PASS	.	C	,,,,,	105,4295	80.9+/-119.3	3,99,2098	143.0	122.0	129.0		1428,1428,1428,1428,1275,1275	0.1	1.0	11	dbSNP_132	129	0,8588		0,0,4294	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PPP6R3	NM_001164160.1,NM_001164161.1,NM_001164162.1,NM_001164163.1,NM_001164164.1,NM_018312.4	,,,,,	3,99,6392	AA,AC,CC		0.0,2.3864,0.8084	,,,,,	476/880,476/874,476/868,476/845,425/792,425/794	68341661	105,12883	2200	4294	6494	SO:0001819	synonymous_variant	55291	exon13			GGGCCCCAACAGT	AF264779	CCDS8182.1, CCDS53671.1, CCDS53672.1, CCDS53673.1, CCDS53674.1, CCDS53675.1	11q13	2012-04-17	2010-06-28	2010-06-28	ENSG00000110075	ENSG00000110075		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	1173	protein-coding gene	gene with protein product	"""sporulation-induced transcript 4-associated protein"""	610879	"""chromosome 11 open reading frame 23"", ""SAPS domain family, member 3"""	C11orf23, SAPS3		11401438, 16769727	Standard	NM_018312		Approved	SAPLa, DKFZp781E2374, DKFZp781O2362, DKFZp781E17107, SAP190, SAPL, PP6R3, FLJ11058, FLJ43065, KIAA1558, MGC125711, MGC125712	uc001onv.3	Q5H9R7		ENST00000393800.2:c.1428C>A	11.37:g.68341661C>A		54.0	0.0	0		68.0	23.0	0.338235	NM_001164162	Q3B7I1|Q3I4Y0|Q3KR35|Q68CR3|Q7L4R8|Q8N3B2|Q96MB2|Q9H2K5|Q9H2K6|Q9HCL4|Q9NUY3	Silent	SNP	ENST00000393800.2	37	CCDS53672.1																																																																																			C|0.991;A|0.009	0.009	strong		0.448	PPP6R3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395275.1	NM_018312	
FLG	2312	hgsc.bcm.edu	37	1	152284382	152284382	+	Missense_Mutation	SNP	C	C	T	rs149595328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152284382C>T	ENST00000368799.1	-	3	3015	c.2980G>A	c.(2980-2982)Ggt>Agt	p.G994S	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	994	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)	p.G994C(1)		autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGCCCGTGACCGGCTCTGTCT	0.577									Ichthyosis				T|||	23	0.00459265	0.0166	0.0014	5008	,	,		20620	0.0		0.0	False		,,,				2504	0.0				p.G994S		Atlas-SNP	.											FLG,NS,carcinoma,+1,2	FLG	900	2	1	Substitution - Missense(1)	lung(1)	c.G2980A						PASS	.	C	SER/GLY	62,4344	820.7+/-416.4	0,62,2141	242.0	245.0	244.0		2980	-0.6	0.0	1	dbSNP_134	244	0,8600		0,0,4300	no	missense	FLG	NM_002016.1	56	0,62,6441	TT,TC,CC		0.0,1.4072,0.4767	benign	994/4062	152284382	62,12944	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CGTGACCGGCTCT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.2980G>A	1.37:g.152284382C>T	ENSP00000357789:p.Gly994Ser	581.0	0.0	0		674.0	50.0	0.074184	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	t	7.940	0.742605	0.15642	0.014072	0.0	ENSG00000143631	ENST00000368799;ENST00000392689	T	0.00649	5.98	2.34	-0.615	0.11587	.	.	.	.	.	T	0.00144	0.0004	L	0.32530	0.975	0.09310	N	1	B	0.29232	0.238	B	0.12156	0.007	T	0.28713	-1.0035	9	0.06625	T	0.88	.	5.25	0.15517	0.0:0.5849:0.0:0.4151	.	994	P20930	FILA_HUMAN	S	994;201	ENSP00000357789:G994S	ENSP00000357789:G994S	G	-	1	0	FLG	150551006	0.000000	0.05858	0.001000	0.08648	0.126000	0.20510	-0.003000	0.12901	0.047000	0.15862	0.291000	0.19559	GGT	C|0.995;T|0.005	0.005	strong		0.577	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
SYNE2	23224	hgsc.bcm.edu	37	14	64604634	64604634	+	Silent	SNP	T	T	C	rs8007874	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:64604634T>C	ENST00000344113.4	+	79	14988	c.14776T>C	c.(14776-14778)Ttg>Ctg	p.L4926L	SYNE2_ENST00000394768.2_Silent_p.L1311L|SYNE2_ENST00000357395.3_Silent_p.L1311L|SYNE2_ENST00000554584.1_Silent_p.L4843L|ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Silent_p.L1560L|SYNE2_ENST00000358025.3_Silent_p.L4926L	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	4926					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AGAGCAGTGGTTGTCCCTGAA	0.512													T|||	228	0.0455272	0.1687	0.0072	5008	,	,		16544	0.0		0.0	False		,,,				2504	0.0				p.L4926L		Atlas-SNP	.											.	SYNE2	577	.	0			c.T14776C						PASS	.	T	,	577,3829	255.5+/-260.7	39,499,1665	83.0	73.0	76.0		14776,14776	-3.5	1.0	14	dbSNP_116	76	6,8594	3.0+/-9.4	0,6,4294	no	coding-synonymous,coding-synonymous	SYNE2	NM_015180.4,NM_182914.2	,	39,505,5959	CC,CT,TT		0.0698,13.0958,4.4825	,	4926/6886,4926/6908	64604634	583,12423	2203	4300	6503	SO:0001819	synonymous_variant	23224	exon79			CAGTGGTTGTCCC	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.14776T>C	14.37:g.64604634T>C		107.0	0.0	0		95.0	51.0	0.536842	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	37	CCDS41963.1																																																																																			T|0.941;C|0.059	0.059	strong		0.512	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
TMPRSS9	360200	hgsc.bcm.edu	37	19	2389813	2389813	+	Silent	SNP	C	C	T	rs8100380	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2389813C>T	ENST00000332578.3	+	1	30	c.30C>T	c.(28-30)ctC>ctT	p.L10L		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	10					plasminogen activation (GO:0031639)	integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				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)		ACGTACACCTCGTGCCCAGGA	0.632													C|||	247	0.0493211	0.1793	0.0101	5008	,	,		18167	0.0		0.003	False		,,,				2504	0.0				p.L10L		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.C30T						PASS	.	C		753,3653	306.3+/-289.4	56,641,1506	76.0	55.0	62.0		30	-4.5	0.0	19	dbSNP_116	62	20,8580	13.3+/-46.6	0,20,4280	no	coding-synonymous	TMPRSS9	NM_182973.1		56,661,5786	TT,TC,CC		0.2326,17.0903,5.9434		10/1060	2389813	773,12233	2203	4300	6503	SO:0001819	synonymous_variant	360200	exon1			ACACCTCGTGCCC	AJ488946	CCDS12088.1	19p13.3	2010-04-13						"""Serine peptidases / Transmembrane"""	30079	protein-coding gene	gene with protein product	"""polyserase 1"""	610477				12886014	Standard	NM_182973		Approved		uc010xgx.2	Q7Z410		ENST00000332578.3:c.30C>T	19.37:g.2389813C>T		81.0	0.0	0		86.0	45.0	0.523256	NM_182973	Q6ZND6|Q7Z411	Silent	SNP	ENST00000332578.3	37	CCDS12088.1																																																																																			C|0.948;T|0.052	0.052	strong		0.632	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973	
PCDH12	51294	hgsc.bcm.edu	37	5	141329059	141329059	+	Missense_Mutation	SNP	T	T	G	rs61737141	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:141329059T>G	ENST00000231484.3	-	3	4278	c.3068A>C	c.(3067-3069)gAg>gCg	p.E1023A	AC005740.6_ENST00000607378.1_RNA	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	1023					calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGAGAGGTCCTCTTCAGGATC	0.562													T|||	32	0.00638978	0.0242	0.0	5008	,	,		18789	0.0		0.0	False		,,,				2504	0.0				p.E1023A		Atlas-SNP	.											.	PCDH12	133	.	0			c.A3068C						PASS	.	T	ALA/GLU	125,4281	93.0+/-131.7	3,119,2081	159.0	152.0	154.0		3068	3.3	1.0	5	dbSNP_129	154	0,8600		0,0,4300	yes	missense	PCDH12	NM_016580.2	107	3,119,6381	GG,GT,TT		0.0,2.837,0.9611	possibly-damaging	1023/1185	141329059	125,12881	2203	4300	6503	SO:0001583	missense	51294	exon3			AGGTCCTCTTCAG	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"""Cadherins / Protocadherins : Non-clustered"""	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.3068A>C	5.37:g.141329059T>G	ENSP00000231484:p.Glu1023Ala	93.0	0.0	0		94.0	52.0	0.553191	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	37	CCDS4269.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	T	14.87	2.663251	0.47572	0.02837	0.0	ENSG00000113555	ENST00000231484	T	0.52754	0.65	5.8	3.34	0.38264	.	0.387701	0.27739	N	0.018060	T	0.15609	0.0376	L	0.57536	1.79	0.26311	N	0.977823	B	0.29716	0.255	B	0.26614	0.071	T	0.06716	-1.0811	10	0.33141	T	0.24	.	5.3998	0.16288	0.1828:0.0:0.1684:0.6488	.	1023	Q9NPG4	PCD12_HUMAN	A	1023	ENSP00000231484:E1023A	ENSP00000231484:E1023A	E	-	2	0	PCDH12	141309243	0.960000	0.32886	1.000000	0.80357	0.985000	0.73830	1.632000	0.37102	2.224000	0.72417	0.533000	0.62120	GAG	T|0.989;G|0.011	0.011	strong		0.562	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580	
ZNF257	113835	hgsc.bcm.edu	37	19	22256358	22256358	+	Missense_Mutation	SNP	A	A	G	rs73930397	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22256358A>G	ENST00000594947.1	+	3	362	c.218A>G	c.(217-219)aAa>aGa	p.K73R	ZNF257_ENST00000600162.1_Missense_Mutation_p.K73R	NM_033468.2	NP_258429.2	Q9Y2Q1	ZN257_HUMAN	zinc finger protein 257	73	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)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|lung(4)	6		all_lung(12;0.0961)|Lung NSC(12;0.103)				ATGGTAGCCAAACCCCCAGGT	0.443													A|||	224	0.0447284	0.1634	0.0115	5008	,	,		15865	0.0		0.0	False		,,,				2504	0.0				p.K73R		Atlas-SNP	.											.	ZNF257	156	.	0			c.A218G						PASS	.	A	ARG/LYS	735,3671	295.3+/-283.6	61,613,1529	125.0	136.0	132.0		218	-1.7	0.2	19	dbSNP_130	132	8,8592	6.4+/-24.3	0,8,4292	yes	missense	ZNF257	NM_033468.2	26	61,621,5821	GG,GA,AA		0.093,16.6818,5.7127	benign	73/564	22256358	743,12263	2203	4300	6503	SO:0001583	missense	113835	exon3			TAGCCAAACCCCC	AF070651	CCDS46030.1	19p12	2014-02-14			ENSG00000197134	ENSG00000197134		"""Zinc fingers, C2H2-type"", ""-"""	13498	protein-coding gene	gene with protein product		606957				10585455	Standard	NM_033468		Approved	BMZF-4	uc010ecx.3	Q9Y2Q1	OTTHUMG00000182927	ENST00000594947.1:c.218A>G	19.37:g.22256358A>G	ENSP00000470209:p.Lys73Arg	57.0	0.0	0		57.0	27.0	0.473684	NM_033468	B3KPS4|E9PG34|Q8NE34	Missense_Mutation	SNP	ENST00000594947.1	37	CCDS46030.1	87	0.03983516483516483	83	0.16869918699186992	4	0.011049723756906077	0	0.0	0	0.0	A	0.702	-0.790515	0.02884	0.166818	9.3E-4	ENSG00000197134	ENST00000435820;ENST00000397123	.	.	.	0.86	-1.72	0.08107	Krueppel-associated box (1);	.	.	.	.	T	0.00039	0.0001	N	0.04508	-0.205	0.80722	P	0.0	B	0.06786	0.001	B	0.10450	0.005	T	0.24297	-1.0164	7	0.30854	T	0.27	.	2.1458	0.03787	0.3751:0.3325:0.2924:0.0	.	73	Q9Y2Q1	ZN257_HUMAN	R	73	.	ENSP00000380312:K73R	K	+	2	0	ZNF257	22048198	0.000000	0.05858	0.249000	0.24280	0.256000	0.26092	-0.441000	0.06879	-1.510000	0.01796	-1.552000	0.00895	AAA	A|0.967;G|0.033	0.033	strong		0.443	ZNF257-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464382.1		
IMPA2	3613	hgsc.bcm.edu	37	18	12009913	12009913	+	Missense_Mutation	SNP	G	G	A	rs16976948	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:12009913G>A	ENST00000269159.3	+	3	504	c.262G>A	c.(262-264)Gcc>Acc	p.A88T	IMPA2_ENST00000588752.1_3'UTR|IMPA2_ENST00000589238.1_5'UTR|IMPA2_ENST00000588927.1_5'UTR	NM_014214.2	NP_055029.1	O14732	IMPA2_HUMAN	inositol(myo)-1(or 4)-monophosphatase 2	88			A -> T (in dbSNP:rs16976948).		inositol biosynthetic process (GO:0006021)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylinositol phosphorylation (GO:0046854)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	inositol monophosphate 1-phosphatase activity (GO:0008934)|inositol monophosphate 3-phosphatase activity (GO:0052832)|inositol monophosphate 4-phosphatase activity (GO:0052833)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|skin(2)|stomach(2)|urinary_tract(1)	12					Lithium(DB01356)	GGCTTCTGGGGCCAAGTGTGT	0.562													G|||	89	0.0177716	0.0605	0.0115	5008	,	,		16273	0.0		0.001	False		,,,				2504	0.0				p.A88T		Atlas-SNP	.											.	IMPA2	27	.	0			c.G262A						PASS	.	G	THR/ALA	260,4146	149.2+/-183.4	4,252,1947	123.0	122.0	122.0		262	3.5	1.0	18	dbSNP_123	122	1,8599	1.2+/-3.3	0,1,4299	yes	missense	IMPA2	NM_014214.2	58	4,253,6246	AA,AG,GG		0.0116,5.901,2.0068	benign	88/289	12009913	261,12745	2203	4300	6503	SO:0001583	missense	3613	exon3			TCTGGGGCCAAGT	AF014398	CCDS11855.1	18p11.2	2008-03-18			ENSG00000141401	ENSG00000141401	3.1.3.25		6051	protein-coding gene	gene with protein product		605922				9322233	Standard	NM_014214		Approved		uc002kqp.2	O14732	OTTHUMG00000131693	ENST00000269159.3:c.262G>A	18.37:g.12009913G>A	ENSP00000269159:p.Ala88Thr	98.0	0.0	0		111.0	55.0	0.495495	NM_014214	B0YJ29|Q9UJT3	Missense_Mutation	SNP	ENST00000269159.3	37	CCDS11855.1	39	0.017857142857142856	36	0.07317073170731707	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	12.73	2.024554	0.35701	0.05901	1.16E-4	ENSG00000141401	ENST00000269159	T	0.52057	0.68	5.48	3.53	0.40419	.	0.385345	0.27181	N	0.020543	T	0.01940	0.0061	N	0.05259	-0.085	0.80722	D	1	B	0.11235	0.004	B	0.12837	0.008	T	0.02115	-1.1211	10	0.34782	T	0.22	-15.8924	11.554	0.50737	0.0:0.0:0.4818:0.5182	rs16976948;rs16976948	88	O14732	IMPA2_HUMAN	T	88	ENSP00000269159:A88T	ENSP00000269159:A88T	A	+	1	0	IMPA2	11999913	1.000000	0.71417	0.997000	0.53966	0.929000	0.56500	4.218000	0.58554	1.274000	0.44362	0.491000	0.48974	GCC	G|0.979;A|0.021	0.021	strong		0.562	IMPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254601.1		
CCL4L2	388372	hgsc.bcm.edu	37	17	34641448	34641448	+	Splice_Site	SNP	A	A	G	rs184899362		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34641448A>G	ENST00000394465.2	+	3	508		c.e3-1		TBC1D3H_ENST00000400684.4_Intron|TBC1D3C_ENST00000308078.7_Intron|TBC1D3H_ENST00000535446.1_Intron|CCL4L2_ENST00000482104.1_3'UTR|CCL4L2_ENST00000339270.6_Splice_Site|TBC1D3C_ENST00000451448.2_Intron			Q8NHW4	CC4L_HUMAN	chemokine (C-C motif) ligand 4-like 2						cell chemotaxis (GO:0060326)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular space (GO:0005615)		p.?(1)		endometrium(1)	1		Breast(25;0.102)|Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CTTGTTCTACAGATTCCAAAC	0.522																																					.		Atlas-SNP	.											CCL4L2,NS,carcinoma,0,1	.	.	1	1	Unknown(1)	endometrium(1)	c.192-2A>G						scavenged	.						219.0	152.0	175.0					17																	34641448		2159	4154	6313	SO:0001630	splice_region_variant	9560	exon3			TTCTACAGATTCC			17q12	2005-08-09			ENSG00000197262			"""Chemokine ligands"""	24066	protein-coding gene	gene with protein product		603782				15028295	Standard	NM_001291468		Approved		uc010cuj.3	Q8NHW4	OTTHUMG00000133066	ENST00000394465.2:c.192-1A>G	17.37:g.34641448A>G		871.0	0.0	0		334.0	28.0	0.0838323	NM_001001435	B2RUZ3|B7ZMA8|Q50EM1|Q50EM2|Q50EM3|Q50EM4|Q50EM5|Q50EM6|Q50EM7|Q50EM8|Q569J2|Q6NSB0	Splice_Site	SNP	ENST00000394465.2	37	CCDS11311.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	N	11.83	1.756201	0.31137	.	.	ENSG00000197262	ENST00000394465;ENST00000339270	.	.	.	3.1	3.1	0.35709	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.8193	0.29278	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CCL4L2	31665561	1.000000	0.71417	0.994000	0.49952	0.682000	0.39822	4.719000	0.61937	1.074000	0.40909	0.344000	0.21773	.	G|1.000;|0.000	1.000	weak		0.522	CCL4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256699.1	NM_207007	Intron
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324410	39324410	+	Silent	SNP	G	G	A	rs73985507	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39324410G>A	ENST00000391356.2	-	1	14	c.15C>T	c.(13-15)tgC>tgT	p.C5C		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	5					aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			CAGAGCCACAGCAGGAGCTGA	0.592													A|||	519	0.103634	0.3759	0.0288	5008	,	,		16931	0.0		0.002	False		,,,				2504	0.0				p.C5C		Atlas-SNP	.											.	KRTAP4-3	40	.	0			c.C15T						PASS	.	A		1379,2993		223,933,1030	29.0	31.0	30.0		15	-1.4	0.9	17	dbSNP_130	30	5,8573		0,5,4284	no	coding-synonymous	KRTAP4-3	NM_033187.1		223,938,5314	AA,AG,GG		0.0583,31.5416,10.6873		5/196	39324410	1384,11566	2186	4289	6475	SO:0001819	synonymous_variant	85290	exon1			GCCACAGCAGGAG	AJ406935	CCDS42331.1	17q21.2	2013-06-25			ENSG00000196156	ENSG00000196156		"""Keratin associated proteins"""	18908	protein-coding gene	gene with protein product							Standard	NM_033187		Approved	KAP4.3	uc010cxl.3	Q9BYR4	OTTHUMG00000133639	ENST00000391356.2:c.15C>T	17.37:g.39324410G>A		148.0	0.0	0		211.0	211.0	1	NM_033187		Silent	SNP	ENST00000391356.2	37	CCDS42331.1																																																																																			G|0.944;A|0.056	0.056	strong		0.592	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1		
ALOX5AP	241	hgsc.bcm.edu	37	13	31309719	31309719	+	5'UTR	SNP	C	C	T	rs17245407	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:31309719C>T	ENST00000380490.3	+	0	75					NM_001204406.1|NM_001629.3	NP_001191335.1|NP_001620.2	P20292	AL5AP_HUMAN	arachidonate 5-lipoxygenase-activating protein						arachidonic acid metabolic process (GO:0019369)|cellular response to calcium ion (GO:0071277)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|leukotriene production involved in inflammatory response (GO:0002540)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|positive regulation of acute inflammatory response (GO:0002675)|protein homotrimerization (GO:0070207)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)	arachidonic acid binding (GO:0050544)|enzyme activator activity (GO:0008047)|protein N-terminus binding (GO:0047485)			endometrium(1)|large_intestine(1)|ovary(1)|prostate(1)	4		Lung SC(185;0.0257)|Breast(139;0.203)		all cancers(112;0.0187)|Epithelial(112;0.0803)|OV - Ovarian serous cystadenocarcinoma(117;0.0864)		CAGAGCAGTCCTCTCTGGGGA	0.517													C|||	146	0.0291534	0.1082	0.0043	5008	,	,		17333	0.0		0.0	False		,,,				2504	0.0				p.L50F		Atlas-SNP	.											.	ALOX5AP	12	.	0			c.C148T						PASS	.	C	PHE/LEU,	437,3969	211.2+/-231.4	20,397,1786	126.0	100.0	109.0		148,	1.0	0.0	13	dbSNP_123	109	1,8599	1.2+/-3.3	0,1,4299	yes	missense,utr-5	ALOX5AP	NM_001204406.1,NM_001629.3	22,	20,398,6085	TT,TC,CC		0.0116,9.9183,3.3677	,	50/219,	31309719	438,12568	2203	4300	6503	SO:0001623	5_prime_UTR_variant	241	exon2			GCAGTCCTCTCTG	AH001462	CCDS9337.1, CCDS73558.1	13q12	2008-07-18			ENSG00000132965	ENSG00000132965			436	protein-coding gene	gene with protein product	"""five-lipoxygenase activating protein"", ""MK-886-binding protein"""	603700				1673682, 10036194	Standard	NM_001629		Approved	FLAP	uc010tdr.2	P20292	OTTHUMG00000016677	ENST00000380490.3:c.-24C>T	13.37:g.31309719C>T		77.0	0.0	0		127.0	75.0	0.590551	NM_001204406	Q5VV04	Missense_Mutation	SNP	ENST00000380490.3	37	CCDS9337.1																																																																																			C|0.968;T|0.032	0.032	strong		0.517	ALOX5AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044372.1	NM_001629	
ACAD8	27034	hgsc.bcm.edu	37	11	134131033	134131033	+	Silent	SNP	C	C	T	rs36115758	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:134131033C>T	ENST00000281182.4	+	7	907	c.801C>T	c.(799-801)ctC>ctT	p.L267L	ACAD8_ENST00000524547.1_3'UTR|ACAD8_ENST00000537423.1_Silent_p.L190L|ACAD8_ENST00000543332.1_Silent_p.L169L|ACAD8_ENST00000374752.4_Silent_p.L140L	NM_014384.2	NP_055199.1	Q9UKU7	ACAD8_HUMAN	acyl-CoA dehydrogenase family, member 8	267					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|lipid metabolic process (GO:0006629)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|valine catabolic process (GO:0006574)	mitochondrial matrix (GO:0005759)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	14	all_hematologic(175;0.127)	all_cancers(12;8e-23)|all_epithelial(12;2.59e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|all_neural(223;0.0189)|Medulloblastoma(222;0.0245)|Esophageal squamous(93;0.0559)		Epithelial(10;1.92e-10)|all cancers(11;2.26e-09)|BRCA - Breast invasive adenocarcinoma(10;8.73e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00154)|Lung(977;0.21)	Flavin adenine dinucleotide(DB03147)	AGGGCTTCCTCATTGCCGTGA	0.597													C|||	41	0.0081869	0.0287	0.0043	5008	,	,		18819	0.0		0.0	False		,,,				2504	0.0				p.L267L	GBM(65;238 1125 33403 41853 48889)	Atlas-SNP	.											.	ACAD8	33	.	0			c.C801T						PASS	.	C		84,4318	71.4+/-109.4	1,82,2118	68.0	65.0	66.0		801	0.9	1.0	11	dbSNP_126	66	0,8594		0,0,4297	no	coding-synonymous	ACAD8	NM_014384.2		1,82,6415	TT,TC,CC		0.0,1.9082,0.6464		267/416	134131033	84,12912	2201	4297	6498	SO:0001819	synonymous_variant	27034	exon7			CTTCCTCATTGCC	AF126245	CCDS8498.1	11q25	2014-09-17	2010-04-30		ENSG00000151498	ENSG00000151498			87	protein-coding gene	gene with protein product		604773	"""acyl-Coenzyme A dehydrogenase family, member 8"""			10524212	Standard	NM_014384		Approved		uc001qhk.3	Q9UKU7	OTTHUMG00000167177	ENST00000281182.4:c.801C>T	11.37:g.134131033C>T		132.0	0.0	0		118.0	57.0	0.483051	NM_014384	B7Z5W4|Q6ZWP6|Q9BUS8	Silent	SNP	ENST00000281182.4	37	CCDS8498.1																																																																																			C|0.993;T|0.007	0.007	strong		0.597	ACAD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393607.1	NM_014384	
RTN4RL1	146760	hgsc.bcm.edu	37	17	1840079	1840079	+	Missense_Mutation	SNP	C	C	T	rs143202933	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:1840079C>T	ENST00000331238.6	-	2	1516	c.1037G>A	c.(1036-1038)cGg>cAg	p.R346Q		NM_178568.2	NP_848663.1			reticulon 4 receptor-like 1											breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|prostate(2)|skin(1)	11						GTGGCCGGGCCGGGGGCCGTG	0.687													C|||	14	0.00279553	0.0	0.0014	5008	,	,		13824	0.0		0.007	False		,,,				2504	0.0061				p.R346Q	GBM(68;949 1139 14865 32798 38342)	Atlas-SNP	.											.	RTN4RL1	21	.	0			c.G1037A						PASS	.	C	GLN/ARG	2,3884		0,2,1941	16.0	19.0	18.0		1037	4.2	0.9	17	dbSNP_134	18	25,8203		0,25,4089	yes	missense	RTN4RL1	NM_178568.2	43	0,27,6030	TT,TC,CC		0.3038,0.0515,0.2229	benign	346/442	1840079	27,12087	1943	4114	6057	SO:0001583	missense	146760	exon2			CCGGGCCGGGGGC	AF532859	CCDS45569.1	17p13.3	2008-02-05				ENSG00000185924			21329	protein-coding gene	gene with protein product	"""nogo-66 receptor homolog 2"""	610461					Standard	NM_178568		Approved	NGRH2, NgR3, DKFZp547J144	uc002ftp.3	Q86UN2		ENST00000331238.6:c.1037G>A	17.37:g.1840079C>T	ENSP00000330631:p.Arg346Gln	129.0	0.0	0		158.0	71.0	0.449367	NM_178568		Missense_Mutation	SNP	ENST00000331238.6	37	CCDS45569.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	6.698	0.497343	0.12762	5.15E-4	0.003038	ENSG00000185924	ENST00000331238	T	0.61980	0.06	4.17	4.17	0.49024	.	0.000000	0.33670	N	0.004666	T	0.57989	0.2091	L	0.54323	1.7	0.44042	D	0.996779	D	0.63880	0.993	P	0.53146	0.719	T	0.60601	-0.7231	10	0.12103	T	0.63	.	16.5187	0.84308	0.0:1.0:0.0:0.0	.	346	Q86UN2	R4RL1_HUMAN	Q	346	ENSP00000330631:R346Q	ENSP00000330631:R346Q	R	-	2	0	RTN4RL1	1786829	0.997000	0.39634	0.889000	0.34880	0.009000	0.06853	2.063000	0.41423	1.883000	0.54544	0.549000	0.68633	CGG	C|0.997;T|0.003	0.003	strong		0.687	RTN4RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450155.2	NM_178568	
SLC4A4	8671	hgsc.bcm.edu	37	4	72338467	72338467	+	Silent	SNP	C	C	T	rs35169468	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:72338467C>T	ENST00000264485.5	+	14	1800	c.1683C>T	c.(1681-1683)tcC>tcT	p.S561S	SLC4A4_ENST00000425175.1_Silent_p.S561S|SLC4A4_ENST00000351898.6_Silent_p.S561S|SLC4A4_ENST00000514331.1_3'UTR|SLC4A4_ENST00000512686.1_Silent_p.S517S|SLC4A4_ENST00000340595.3_Silent_p.S517S	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	561					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	58			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)		Sodium bicarbonate(DB01390)	GCCTGTGGTCCGCCTTCCTAT	0.433													C|||	81	0.0161741	0.0446	0.0072	5008	,	,		17363	0.0		0.0	False		,,,				2504	0.0174				p.S561S		Atlas-SNP	.											.	SLC4A4	269	.	0			c.C1683T						PASS	.	C	,,	161,4245	110.8+/-149.0	2,157,2044	175.0	173.0	174.0		1683,1683,1551	-3.7	1.0	4	dbSNP_126	174	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC4A4	NM_001098484.2,NM_001134742.1,NM_003759.3	,,	2,159,6342	TT,TC,CC		0.0233,3.6541,1.2533	,,	561/1080,561/1095,517/1036	72338467	163,12843	2203	4300	6503	SO:0001819	synonymous_variant	8671	exon14			GTGGTCCGCCTTC	AF007216	CCDS3549.1, CCDS43236.1, CCDS47071.1	4q13.3	2013-07-19	2013-07-19		ENSG00000080493	ENSG00000080493		"""Solute carriers"""	11030	protein-coding gene	gene with protein product		603345	"""solute carrier family 4, sodium bicarbonate cotransporter, member 4"""	SLC4A5		9235899, 9651366	Standard	NM_001098484		Approved	NBC1, HNBC1, NBC2, pNBC, hhNMC	uc010iic.3	Q9Y6R1	OTTHUMG00000129907	ENST00000264485.5:c.1683C>T	4.37:g.72338467C>T		117.0	0.0	0		124.0	52.0	0.419355	NM_001098484	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Silent	SNP	ENST00000264485.5	37	CCDS43236.1																																																																																			C|0.988;T|0.012	0.012	strong		0.433	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759	
LUZP1	7798	hgsc.bcm.edu	37	1	23419806	23419806	+	Missense_Mutation	SNP	A	A	C	rs12091554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:23419806A>C	ENST00000302291.4	-	4	1750	c.949T>G	c.(949-951)Tcc>Gcc	p.S317A	LUZP1_ENST00000314174.5_Missense_Mutation_p.S317A|LUZP1_ENST00000418342.1_Missense_Mutation_p.S317A|LUZP1_ENST00000374623.3_Missense_Mutation_p.S317A			Q86V48	LUZP1_HUMAN	leucine zipper protein 1	317			S -> A (in dbSNP:rs12091554).		artery development (GO:0060840)|neural fold bending (GO:0021503)|ventricular septum development (GO:0003281)	membrane (GO:0016020)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(2)	31		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Ovarian(437;0.00373)|Breast(348;0.00815)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;4.88e-27)|Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;4.31e-06)|GBM - Glioblastoma multiforme(114;8.64e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00176)|STAD - Stomach adenocarcinoma(196;0.0146)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0967)|LUSC - Lung squamous cell carcinoma(448;0.199)		TTATTTTTGGACTTCATTTTC	0.338													C|||	242	0.0483227	0.1702	0.0245	5008	,	,		21716	0.0		0.0	False		,,,				2504	0.0				p.S317A		Atlas-SNP	.											.	LUZP1	83	.	0			c.T949G						PASS	.	C	ALA/SER,ALA/SER	637,3769	765.9+/-413.4	65,507,1631	164.0	156.0	159.0		949,949	5.2	1.0	1	dbSNP_120	159	12,8588	818.3+/-406.9	0,12,4288	yes	missense,missense	LUZP1	NM_001142546.1,NM_033631.3	99,99	65,519,5919	CC,CA,AA		0.1395,14.4576,4.99	benign,benign	317/1077,317/1077	23419806	649,12357	2203	4300	6503	SO:0001583	missense	7798	exon4			TTTTGGACTTCAT	BC051733	CCDS30628.1	1p36	2008-02-05			ENSG00000169641	ENSG00000169641			14985	protein-coding gene	gene with protein product		601422				8812416	Standard	NM_033631		Approved	LUZP	uc010odv.1	Q86V48	OTTHUMG00000003227	ENST00000302291.4:c.949T>G	1.37:g.23419806A>C	ENSP00000303758:p.Ser317Ala	216.0	0.0	0		169.0	79.0	0.467456	NM_033631	Q5TH93|Q8N4X3|Q8TEH1	Missense_Mutation	SNP	ENST00000302291.4	37	CCDS30628.1	82	0.037545787545787544	73	0.1483739837398374	9	0.024861878453038673	0	0.0	0	0.0	C	1.368	-0.586747	0.03827	0.144576	0.001395	ENSG00000169641	ENST00000418342;ENST00000374623;ENST00000302291;ENST00000314174	T;T;T;T	0.12361	2.92;2.92;2.92;2.69	6.08	5.16	0.70880	.	0.000000	0.48286	N	0.000191	T	0.00039	0.0001	N	0.00729	-1.24	0.47065	P	6.960000000000299E-4	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.34453	-0.9828	9	0.11485	T	0.65	.	10.4106	0.44291	0.1361:0.7953:0.0:0.0686	rs12091554;rs52806883;rs12091554	317;317	Q86V48-2;Q86V48	.;LUZP1_HUMAN	A	317	ENSP00000393460:S317A;ENSP00000363752:S317A;ENSP00000303758:S317A;ENSP00000313705:S317A	ENSP00000303758:S317A	S	-	1	0	LUZP1	23292393	1.000000	0.71417	1.000000	0.80357	0.771000	0.43674	3.887000	0.56197	1.603000	0.50134	-0.121000	0.15023	TCC	A|0.952;C|0.048	0.048	strong		0.338	LUZP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008900.3	NM_033631	
DYX1C1	161582	hgsc.bcm.edu	37	15	55790414	55790414	+	Missense_Mutation	SNP	G	G	T	rs16976354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:55790414G>T	ENST00000321149.3	-	2	481	c.114C>A	c.(112-114)aaC>aaA	p.N38K	DYX1C1_ENST00000348518.3_Missense_Mutation_p.N38K|DYX1C1_ENST00000457155.2_Missense_Mutation_p.N38K|DYX1C1-CCPG1_ENST00000565113.1_RNA|DYX1C1_ENST00000380679.1_Missense_Mutation_p.N38K|DYX1C1_ENST00000448430.2_Missense_Mutation_p.N38K	NM_130810.3	NP_570722.2	Q8WXU2	DYXC1_HUMAN	dyslexia susceptibility 1 candidate 1	38	CS. {ECO:0000255|PROSITE- ProRule:PRU00547}.|Mediates interaction with ESR1 and STUB1.		N -> K (in dbSNP:rs16976354).		cilium movement (GO:0003341)|determination of left/right symmetry (GO:0007368)|inner dynein arm assembly (GO:0036159)|neuron migration (GO:0001764)|outer dynein arm assembly (GO:0036158)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of proteasomal protein catabolic process (GO:0061136)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	estrogen receptor binding (GO:0030331)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18				all cancers(107;0.0118)|GBM - Glioblastoma multiforme(80;0.171)		CCTTCAGATAGTTTTCCGTGC	0.562													G|||	311	0.0621006	0.2262	0.0159	5008	,	,		16045	0.0		0.001	False		,,,				2504	0.0				p.N38K		Atlas-SNP	.											.	DYX1C1	54	.	0			c.C114A						PASS	.	G	LYS/ASN,LYS/ASN,LYS/ASN	849,3537	325.3+/-299.0	72,705,1416	45.0	42.0	43.0		114,114,114	-1.6	0.1	15	dbSNP_123	43	0,8582		0,0,4291	yes	missense,missense,missense	DYX1C1	NM_001033559.2,NM_001033560.1,NM_130810.3	94,94,94	72,705,5707	TT,TG,GG		0.0,19.357,6.5469	benign,benign,benign	38/377,38/382,38/421	55790414	849,12119	2193	4291	6484	SO:0001583	missense	161582	exon2			CAGATAGTTTTCC		CCDS10154.1, CCDS32243.1, CCDS32244.1	15q21.3	2014-09-11			ENSG00000256061	ENSG00000256061		"""Tetratricopeptide (TTC) repeat domain containing"""	21493	protein-coding gene	gene with protein product		608706				12954984	Standard	NM_130810		Approved	EKN1, FLJ37882, CILD25	uc002adc.3	Q8WXU2	OTTHUMG00000132008	ENST00000321149.3:c.114C>A	15.37:g.55790414G>T	ENSP00000323275:p.Asn38Lys	110.0	0.0	0		132.0	53.0	0.401515	NM_001033560	Q6P5Y9|Q8N1S6	Missense_Mutation	SNP	ENST00000321149.3	37	CCDS10154.1	103	0.04716117216117216	97	0.19715447154471544	6	0.016574585635359115	0	0.0	0	0.0	G	12.94	2.089312	0.36855	0.19357	0.0	ENSG00000256061	ENST00000420792;ENST00000448430;ENST00000380679;ENST00000457155;ENST00000321149;ENST00000348518	T;T;T;T;T	0.12984	2.63;2.63;2.63;2.63;2.63	4.82	-1.59	0.08453	CS-like domain (1);CS domain (1);HSP20-like chaperone (1);	1.338300	0.05207	U	0.506081	T	0.00012	0.0000	L	0.41573	1.285	0.58432	P	9.000000000036756E-6	B;B;P	0.44044	0.307;0.109;0.825	B;B;B	0.39217	0.117;0.122;0.294	T	0.26224	-1.0109	9	0.07813	T	0.8	.	5.7047	0.17901	0.459:0.2611:0.2799:0.0	rs16976354;rs52829594;rs58871707;rs16976354	38;38;38	Q8WXU2-3;Q8WXU2;Q8WXU2-2	.;DYXC1_HUMAN;.	K	38	ENSP00000403412:N38K;ENSP00000370054:N38K;ENSP00000402640:N38K;ENSP00000323275:N38K;ENSP00000299561:N38K	ENSP00000323275:N38K	N	-	3	2	DYX1C1	53577706	0.085000	0.21516	0.131000	0.22000	0.920000	0.55202	0.021000	0.13489	0.043000	0.15746	0.655000	0.94253	AAC	G|0.928;T|0.072	0.072	strong		0.562	DYX1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254976.1	NM_130810	
NPR3	4883	hgsc.bcm.edu	37	5	32712119	32712119	+	Silent	SNP	T	T	C	rs6859964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:32712119T>C	ENST00000265074.8	+	1	580	c.237T>C	c.(235-237)gcT>gcC	p.A79A	NPR3_ENST00000415685.2_Intron|NPR3_ENST00000434067.2_Intron|NPR3_ENST00000415167.2_Silent_p.A79A	NM_000908.3|NM_001204375.1	NP_000899.1|NP_001191304.1	P17342	ANPRC_HUMAN	natriuretic peptide receptor 3	79					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)	TCGAGTATGCTCTGCGCAGCG	0.642													T|||	226	0.0451278	0.1679	0.0043	5008	,	,		14376	0.0		0.001	False		,,,				2504	0.0				p.A79A		Atlas-SNP	.											.	NPR3	65	.	0			c.T237C						PASS	.	T	,,	522,3402		36,450,1476	25.0	30.0	28.0		237,237,	1.2	1.0	5	dbSNP_116	28	2,8314		0,2,4156	no	coding-synonymous,coding-synonymous,intron	NPR3	NM_000908.3,NM_001204375.1,NM_001204376.1	,,	36,452,5632	CC,CT,TT		0.0241,13.3028,4.281	,,	79/541,79/542,	32712119	524,11716	1962	4158	6120	SO:0001819	synonymous_variant	4883	exon1			GTATGCTCTGCGC		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.237T>C	5.37:g.32712119T>C		99.0	0.0	0		124.0	61.0	0.491935	NM_000908	A2RRD1|B4DT84|E7EPG9	Silent	SNP	ENST00000265074.8	37	CCDS56357.1																																																																																			T|0.956;C|0.044	0.044	strong		0.642	NPR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317550.3	NM_000908	
CFAP43	80217	hgsc.bcm.edu	37	10	105906077	105906077	+	Missense_Mutation	SNP	T	T	C	rs369682196		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:105906077T>C	ENST00000357060.3	-	30	3914	c.3799A>G	c.(3799-3801)Aga>Gga	p.R1267G	WDR96_ENST00000428666.1_Intron	NM_025145.5	NP_079421.5														NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(14)|lung(21)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						AGGTCTTCTCTAGATTTCCGA	0.418																																					p.R1267G		Atlas-SNP	.											WDR96,NS,carcinoma,+1,1	WDR96	183	1	0			c.A3799G						PASS	.	T	GLY/ARG	1,4405	2.1+/-5.4	0,1,2202	139.0	125.0	130.0		3799	3.5	0.0	10		130	0,8600		0,0,4300	no	missense	WDR96	NM_025145.5	125	0,1,6502	CC,CT,TT		0.0,0.0227,0.0077	benign	1267/1666	105906077	1,13005	2203	4300	6503	SO:0001583	missense	80217	exon30			CTTCTCTAGATTT																												ENST00000357060.3:c.3799A>G	10.37:g.105906077T>C	ENSP00000349568:p.Arg1267Gly	127.0	0.0	0		167.0	85.0	0.508982	NM_025145		Missense_Mutation	SNP	ENST00000357060.3	37	CCDS31281.1	.	.	.	.	.	.	.	.	.	.	T	7.040	0.562289	0.13498	2.27E-4	0.0	ENSG00000197748	ENST00000357060	T	0.14640	2.49	6.07	3.55	0.40652	.	0.466125	0.21837	N	0.068397	T	0.15132	0.0365	M	0.63428	1.95	0.09310	N	1	P	0.43094	0.799	B	0.36092	0.217	T	0.08973	-1.0696	10	0.51188	T	0.08	.	13.497	0.61432	0.0:0.0:0.2551:0.7449	.	1267	Q8NDM7	WDR96_HUMAN	G	1267	ENSP00000349568:R1267G	ENSP00000349568:R1267G	R	-	1	2	WDR96	105896067	0.005000	0.15991	0.036000	0.18154	0.021000	0.10359	1.590000	0.36654	1.078000	0.41014	0.533000	0.62120	AGA	.	.	none		0.418	WDR96-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
CCNI	10983	hgsc.bcm.edu	37	4	77976374	77976374	+	Missense_Mutation	SNP	C	C	T	rs4252903	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:77976374C>T	ENST00000237654.4	-	6	1195	c.619G>A	c.(619-621)Gtt>Att	p.V207I	CCNI_ENST00000537948.1_Missense_Mutation_p.V193I|CCNI_ENST00000504697.1_5'Flank	NM_006835.2	NP_006826.1	Q14094	CCNI_HUMAN	cyclin I	207			V -> I (in dbSNP:rs4252903). {ECO:0000269|Ref.4}.		regulation of cell cycle (GO:0051726)|spermatogenesis (GO:0007283)					NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)	9						TCCAGACTAACCATGGCCAGA	0.438													C|||	38	0.00758786	0.0287	0.0	5008	,	,		16139	0.0		0.0	False		,,,				2504	0.0				p.V207I		Atlas-SNP	.											.	CCNI	22	.	0			c.G619A						PASS	.	C	ILE/VAL	99,4307	79.3+/-117.8	2,95,2106	113.0	101.0	105.0		619	2.2	1.0	4	dbSNP_111	105	1,8599		0,1,4299	yes	missense	CCNI	NM_006835.2	29	2,96,6405	TT,TC,CC		0.0116,2.2469,0.7689	benign	207/378	77976374	100,12906	2203	4300	6503	SO:0001583	missense	10983	exon6			GACTAACCATGGC	D50310	CCDS3580.1	4q21.1	2014-07-03			ENSG00000118816	ENSG00000118816			1595	protein-coding gene	gene with protein product						7493655	Standard	NM_006835		Approved	CCNI1	uc003hkm.3	Q14094	OTTHUMG00000130106	ENST00000237654.4:c.619G>A	4.37:g.77976374C>T	ENSP00000237654:p.Val207Ile	171.0	0.0	0		220.0	102.0	0.463636	NM_006835	B2R6M0|B7Z6X4	Missense_Mutation	SNP	ENST00000237654.4	37	CCDS3580.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	5.722	0.317763	0.10845	0.022469	1.16E-4	ENSG00000118816	ENST00000237654;ENST00000537948	T;T	0.13657	2.57;2.57	5.87	2.22	0.28083	Cyclin-like (1);	0.328648	0.36268	N	0.002681	T	0.02083	0.0065	N	0.04959	-0.14	0.37675	D	0.92327	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.36335	-0.9752	10	0.07030	T	0.85	-3.5062	6.2538	0.20861	0.0:0.6096:0.1228:0.2676	rs4252903;rs52822018;rs4252903	193;207	B7Z6X4;Q14094	.;CCNI_HUMAN	I	207;193	ENSP00000237654:V207I;ENSP00000441001:V193I	ENSP00000237654:V207I	V	-	1	0	CCNI	78195398	0.993000	0.37304	1.000000	0.80357	0.993000	0.82548	0.319000	0.19522	0.484000	0.27630	0.655000	0.94253	GTT	C|0.992;T|0.008	0.008	strong		0.438	CCNI-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252412.2	NM_006835	
TTN	7273	hgsc.bcm.edu	37	2	179416659	179416659	+	Missense_Mutation	SNP	C	C	T	rs11887722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179416659C>T	ENST00000591111.1	-	285	86269	c.86045G>A	c.(86044-86046)aGg>aAg	p.R28682K	TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R21450K|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592630.1_RNA|RP11-65L3.2_ENST00000603415.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.R27755K|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R21383K|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R21258K|TTN_ENST00000589042.1_Missense_Mutation_p.R30323K			Q8WZ42	TITIN_HUMAN	titin	28682					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)			ACCAGGAATCCTGAACTGGTG	0.448													C|||	180	0.0359425	0.1271	0.0159	5008	,	,		22703	0.0		0.001	False		,,,				2504	0.0				p.R30323K		Atlas-SNP	.											.	TTN	18412	.	0			c.G90968A						PASS	.	C	LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG	418,3824		24,370,1727	132.0	141.0	138.0		64349,64148,83264,63773	5.8	1.0	2	dbSNP_120	138	8,8456		0,8,4224	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	26,26,26,26	24,378,5951	TT,TC,CC		0.0945,9.8538,3.3527	benign,benign,benign,benign	21450/27119,21383/27052,27755/33424,21258/26927	179416659	426,12280	2121	4232	6353	SO:0001583	missense	7273	exon335			GGAATCCTGAACT	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.86045G>A	2.37:g.179416659C>T	ENSP00000465570:p.Arg28682Lys	84.0	0.0	0		109.0	56.0	0.513761	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		86	0.039377289377289376	78	0.15853658536585366	8	0.022099447513812154	0	0.0	0	0.0	C	13.17	2.157290	0.38119	0.098538	9.45E-4	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.62105	0.05;0.29;0.27;0.26	5.76	5.76	0.90799	Fibronectin, type III (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00178	0.0005	N	0.03608	-0.345	0.21933	P	0.999463905	B;B;B;B	0.06786	0.001;0.001;0.001;0.001	B;B;B;B	0.06405	0.002;0.002;0.002;0.002	T	0.03184	-1.1063	8	0.87932	D	0	.	12.6943	0.56994	0.0:0.8821:0.0:0.1179	rs11887722;rs52822649;rs11887722	21258;21383;21450;28682	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	K	27755;21258;21450;21383;21255	ENSP00000343764:R27755K;ENSP00000434586:R21258K;ENSP00000340554:R21450K;ENSP00000352154:R21383K	ENSP00000340554:R21450K	R	-	2	0	TTN	179124905	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	1.947000	0.40293	2.719000	0.93026	0.655000	0.94253	AGG	C|0.949;T|0.051	0.051	strong		0.448	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
MST1L	11223	hgsc.bcm.edu	37	1	17083797	17083797	+	RNA	SNP	C	C	T	rs564582425	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17083797C>T	ENST00000455405.2	-	0	791							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										GGCTGGCCAGCGCGACCTTGT	0.567													.|||	219	0.04373	0.1543	0.0216	5008	,	,		29509	0.0		0.0	False		,,,				2504	0.0				p.R667H		Atlas-SNP	.											.	.	.	.	0			c.G2000A						PASS	.																																					11223	exon15			GGCCAGCGCGACC	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.17083797C>T		221.0	0.0	0		339.0	162.0	0.477876	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	6.905	0.536454	0.13188	.	.	ENSG00000186715	ENST00000334998;ENST00000442552	.	.	.	.	.	.	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.563499	0.14822	N	0.296388	T	0.26376	0.0644	.	.	.	.	.	.	B;B	0.19935	0.04;0.003	B;B	0.11329	0.006;0.003	T	0.18840	-1.0324	6	0.51188	T	0.08	.	2.9647	0.05903	0.0:0.6115:0.0:0.3885	.	667;693	Q2TV78-2;Q2TV78	.;MSTP9_HUMAN	H	667;693	.	ENSP00000439273:R667H	R	-	2	0	MST1P9	16956384	0.999000	0.42202	0.921000	0.36526	0.000000	0.00434	2.097000	0.41748	0.502000	0.28037	0.000000	0.15137	CGC	.	.	none		0.567	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
TENM1	10178	hgsc.bcm.edu	37	X	123838882	123838882	+	Silent	SNP	C	C	T	rs138596900	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:123838882C>T	ENST00000371130.3	-	5	1059	c.996G>A	c.(994-996)ttG>ttA	p.L332L	TENM1_ENST00000422452.2_Silent_p.L332L	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	332					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										AGGCTAGTAACAAGGCCAAAG	0.453													C|||	71	0.0188079	0.0514	0.0043	3775	,	,		14198	0.0		0.0	False		,,,				2504	0.0				p.L332L		Atlas-SNP	.											.	.	.	.	0			c.G996A						PASS	.	C	,,	212,3623		5,173,29,1454,542	163.0	146.0	152.0		996,996,996	5.7	1.0	X	dbSNP_134	152	0,6728		0,0,0,2428,1872	no	coding-synonymous,coding-synonymous,coding-synonymous	ODZ1	NM_001163278.1,NM_001163279.1,NM_014253.3	,,	5,173,29,3882,2414	TT,TC,T,CC,C		0.0,5.528,2.007	,,	332/2733,332/2732,332/2726	123838882	212,10351	2203	4300	6503	SO:0001819	synonymous_variant	10178	exon5			TAGTAACAAGGCC	AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"""tenascin M"", ""odz, odd Oz/ten-m homolog 1 (Drosophila)"""	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.996G>A	X.37:g.123838882C>T		131.0	0.0	0		128.0	40.0	0.3125	NM_001163278	B2RTR5|Q5JZ17	Silent	SNP	ENST00000371130.3	37	CCDS14609.1																																																																																			C|0.979;T|0.021	0.021	strong		0.453	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253	
PGAM2	5224	hgsc.bcm.edu	37	7	44104913	44104913	+	Silent	SNP	G	G	A	rs111656877	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:44104913G>A	ENST00000297283.3	-	1	273	c.216C>T	c.(214-216)gaC>gaT	p.D72D	AC017116.11_ENST00000445938.1_RNA	NM_000290.3	NP_000281.2	P15259	PGAM2_HUMAN	phosphoglycerate mutase 2 (muscle)	72					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|response to mercury ion (GO:0046689)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|striated muscle contraction (GO:0006941)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity (GO:0046538)|bisphosphoglycerate 2-phosphatase activity (GO:0004083)|bisphosphoglycerate mutase activity (GO:0004082)|cofactor binding (GO:0048037)|phosphoglycerate mutase activity (GO:0004619)			large_intestine(2)|lung(4)|ovary(1)|stomach(1)	8						GGTCCGTGCCGTCCAGGATGG	0.627													G|||	52	0.0103834	0.0371	0.0029	5008	,	,		17290	0.0		0.0	False		,,,				2504	0.001				p.D72D		Atlas-SNP	.											.	PGAM2	20	.	0			c.C216T						PASS	.	G		218,4188	131.4+/-167.9	7,204,1992	93.0	78.0	83.0		216	-11.9	0.0	7	dbSNP_132	83	0,8600		0,0,4300	no	coding-synonymous	PGAM2	NM_000290.3		7,204,6292	AA,AG,GG		0.0,4.9478,1.6761		72/254	44104913	218,12788	2203	4300	6503	SO:0001819	synonymous_variant	5224	exon1			CGTGCCGTCCAGG		CCDS34624.1	7p13-p12	2008-11-17			ENSG00000164708	ENSG00000164708	5.4.2.1, 3.1.3.13, 5.4.2.4		8889	protein-coding gene	gene with protein product		612931					Standard	NM_000290		Approved	PGAM-M	uc003tjs.3	P15259	OTTHUMG00000155355	ENST00000297283.3:c.216C>T	7.37:g.44104913G>A		109.0	0.0	0		121.0	57.0	0.471074	NM_000290		Silent	SNP	ENST00000297283.3	37	CCDS34624.1																																																																																			G|0.984;A|0.016	0.016	strong		0.627	PGAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339614.1		
RAP1GAP2	23108	hgsc.bcm.edu	37	17	2911352	2911352	+	Silent	SNP	C	C	T	rs36016465	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:2911352C>T	ENST00000254695.8	+	17	1497	c.1407C>T	c.(1405-1407)caC>caT	p.H469H	RAP1GAP2_ENST00000542807.1_Silent_p.H469H|RAP1GAP2_ENST00000366401.4_Silent_p.H454H|RAP1GAP2_ENST00000540393.2_Silent_p.H450H	NM_015085.4	NP_055900.4	Q684P5	RPGP2_HUMAN	RAP1 GTPase activating protein 2	469					negative regulation of neuron projection development (GO:0010977)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)|nuclear membrane (GO:0031965)	Rap GTPase activator activity (GO:0046582)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	11						ATGAGCTCCACGCCCACACAC	0.597													C|||	77	0.0153754	0.056	0.0029	5008	,	,		18125	0.0		0.001	False		,,,				2504	0.0				p.H469H		Atlas-SNP	.											.	RAP1GAP2	90	.	0			c.C1407T						PASS	.	C	,	139,3993		2,135,1929	63.0	69.0	67.0		1362,1407	-9.6	0.0	17	dbSNP_126	67	2,8384		0,2,4191	no	coding-synonymous,coding-synonymous	RAP1GAP2	NM_001100398.1,NM_015085.4	,	2,137,6120	TT,TC,CC		0.0238,3.364,1.1264	,	454/716,469/731	2911352	141,12377	2066	4193	6259	SO:0001819	synonymous_variant	23108	exon17			GCTCCACGCCCAC	AB028962	CCDS45573.1, CCDS45574.1	17p13.3	2009-09-14	2009-09-14	2009-09-14		ENSG00000132359			29176	protein-coding gene	gene with protein product			"""GTPase activating RANGAP domain-like 4"", ""GTPase activating Rap/RanGAP domain-like 4"""	GARNL4		15632203	Standard	NM_015085		Approved	KIAA1039	uc010ckd.3	Q684P5		ENST00000254695.8:c.1407C>T	17.37:g.2911352C>T		74.0	0.0	0		128.0	72.0	0.5625	NM_015085	B2RTY5|Q684P4|Q6AI00|Q6ZVF0|Q9UPW2	Silent	SNP	ENST00000254695.8	37	CCDS45573.1																																																																																			C|0.988;T|0.012	0.012	strong		0.597	RAP1GAP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438208.2		
CUL9	23113	hgsc.bcm.edu	37	6	43152366	43152366	+	Silent	SNP	C	C	A	rs41274928	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43152366C>A	ENST00000252050.4	+	2	402	c.318C>A	c.(316-318)ggC>ggA	p.G106G	CUL9_ENST00000372647.2_Silent_p.G106G|CUL9_ENST00000354495.3_Silent_p.G106G	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	106					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						ATCCAGGAGGCCTGGATGAAG	0.607													C|||	248	0.0495208	0.1112	0.0288	5008	,	,		20915	0.003		0.0288	False		,,,				2504	0.0501				p.G106G		Atlas-SNP	.											.	CUL9	248	.	0			c.C318A						PASS	.	C		459,3947	217.1+/-235.6	32,395,1776	89.0	96.0	94.0		318	0.7	1.0	6	dbSNP_127	94	267,8333	101.9+/-163.1	2,263,4035	no	coding-synonymous	CUL9	NM_015089.2		34,658,5811	AA,AC,CC		3.1047,10.4176,5.582		106/2518	43152366	726,12280	2203	4300	6503	SO:0001819	synonymous_variant	23113	exon2			AGGAGGCCTGGAT	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"""parkin-like cytoplasmic p53 binding protein"", ""p53-associated parkin-like cytoplasmic protein"""	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.318C>A	6.37:g.43152366C>A		156.0	0.0	0		184.0	95.0	0.516304	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	37	CCDS4890.1																																																																																			C|0.948;A|0.052	0.052	strong		0.607	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	
HMGXB3	22993	hgsc.bcm.edu	37	5	149404213	149404213	+	Missense_Mutation	SNP	G	G	T	rs115942845	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149404213G>T	ENST00000502717.1	+	7	1894	c.1430G>T	c.(1429-1431)aGt>aTt	p.S477I	HMGXB3_ENST00000503427.1_Missense_Mutation_p.S445I	NM_014983.2	NP_055798	Q12766	HMGX3_HUMAN	HMG box domain containing 3	723					phosphorylation (GO:0016310)	nucleus (GO:0005634)	DNA binding (GO:0003677)|kinase activity (GO:0016301)			central_nervous_system(1)|endometrium(3)|kidney(3)|skin(2)	9						AGTACCTCCAGTCCACTCCCT	0.483													G|||	21	0.00419329	0.0159	0.0	5008	,	,		19720	0.0		0.0	False		,,,				2504	0.0				p.S477I		Atlas-SNP	.											.	HMGXB3	31	.	0			c.G1430T						PASS	.	G	ILE/SER	15,1369		0,15,677	51.0	51.0	51.0		1430	-0.2	0.1	5	dbSNP_132	51	2,3180		0,2,1589	yes	missense	HMGXB3	NM_014983.2	142	0,17,2266	TT,TG,GG		0.0629,1.0838,0.3723	possibly-damaging	477/1293	149404213	17,4549	692	1591	2283	SO:0001583	missense	22993	exon7			CCTCCAGTCCACT	D83778	CCDS54935.1	5q33.1	2011-07-01		2009-01-05	ENSG00000113716	ENSG00000113716		"""High mobility group / Non-canonical"""	28982	protein-coding gene	gene with protein product				HMGX3		8724849	Standard	NM_014983		Approved	SMF, KIAA0194	uc003lrk.4	Q12766	OTTHUMG00000163493	ENST00000502717.1:c.1430G>T	5.37:g.149404213G>T	ENSP00000421917:p.Ser477Ile	57.0	0.0	0		60.0	34.0	0.566667	NM_014983	G5E9Y4|Q86UG3|Q9UMF4	Missense_Mutation	SNP	ENST00000502717.1	37	CCDS54935.1	13	0.005952380952380952	12	0.024390243902439025	1	0.0027624309392265192	0	0.0	0	0.0	G	9.220	1.033161	0.19590	0.010838	6.29E-4	ENSG00000113716	ENST00000503427;ENST00000502717	.	.	.	5.94	-0.254	0.12992	.	0.898615	0.10134	N	0.711723	T	0.16428	0.0395	L	0.47716	1.5	0.09310	N	1	B	0.24823	0.112	B	0.22386	0.039	T	0.33445	-0.9868	9	0.87932	D	0	-0.0037	1.2728	0.02025	0.1957:0.217:0.3649:0.2223	.	723	Q12766	HMGX3_HUMAN	I	445;477	.	ENSP00000421917:S477I	S	+	2	0	HMGXB3	149384406	0.040000	0.19996	0.095000	0.20976	0.343000	0.28985	0.365000	0.20348	-0.110000	0.12022	-0.188000	0.12872	AGT	G|0.995;T|0.005	0.005	strong		0.483	HMGXB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373771.1	XM_001717202	
NLRP7	199713	hgsc.bcm.edu	37	19	55451083	55451083	+	Silent	SNP	A	A	G	rs1654636	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55451083A>G	ENST00000590030.1	-	3	1144	c.1104T>C	c.(1102-1104)atT>atC	p.I368I	NLRP7_ENST00000340844.2_Silent_p.I368I|NLRP7_ENST00000328092.5_Silent_p.I368I|NLRP7_ENST00000448121.2_Silent_p.I368I|NLRP7_ENST00000588756.1_Silent_p.I368I|NLRP7_ENST00000446217.1_Silent_p.I396I|NLRP7_ENST00000592784.1_Silent_p.I368I			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	368	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.						ATP binding (GO:0005524)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		TCGTGCACACAATCCAGCACA	0.642													.|||	123	0.0245607	0.0666	0.0202	5008	,	,		16521	0.002		0.0189	False		,,,				2504	0.0				p.I368I		Atlas-SNP	.											NLRP7_ENST00000328092,NS,carcinoma,-2,2	NLRP7	411	2	0			c.T1104C						scavenged	.						37.0	40.0	39.0					19																	55451083		2201	4299	6500	SO:0001819	synonymous_variant	199713	exon4			GCACACAATCCAG	AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"""Nucleotide-binding domain and leucine rich repeat containing"""	22947	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"""	609661	"""NACHT, leucine rich repeat and PYD containing 7"""	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.1104T>C	19.37:g.55451083A>G		199.0	0.0	0		94.0	18.0	0.191489	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Silent	SNP	ENST00000590030.1	37	CCDS33109.1																																																																																			A|0.949;G|0.051	0.051	strong		0.642	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176	
KRTAP13-2	337959	hgsc.bcm.edu	37	21	31744456	31744456	+	Missense_Mutation	SNP	G	G	A	rs16986753	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31744456G>A	ENST00000399889.2	-	1	101	c.76C>T	c.(76-78)Cgt>Tgt	p.R26C		NM_181621.3	NP_853652.1	Q52LG2	KR132_HUMAN	keratin associated protein 13-2	26			R -> C (in dbSNP:rs16986753).			intermediate filament (GO:0005882)				endometrium(1)|kidney(1)|lung(14)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	21						GAAAAGCCACGTGAGGATGCT	0.562													A|||	26	0.00519169	0.0189	0.0014	5008	,	,		19332	0.0		0.0	False		,,,				2504	0.0				p.R26C		Atlas-SNP	.											.	KRTAP13-2	29	.	0			c.C76T						PASS	.	A	CYS/ARG	99,4307	816.6+/-416.3	1,97,2105	134.0	119.0	124.0		76	2.0	0.1	21	dbSNP_123	124	1,8599	819.2+/-406.8	0,1,4299	no	missense	KRTAP13-2	NM_181621.3	180	1,98,6404	AA,AG,GG		0.0116,2.2469,0.7689	benign	26/176	31744456	100,12906	2203	4300	6503	SO:0001583	missense	337959	exon1			AGCCACGTGAGGA	AP001708	CCDS13589.1	21q22.1	2011-02-10			ENSG00000182816	ENSG00000182816		"""Keratin associated proteins"""	18923	protein-coding gene	gene with protein product						12359730	Standard	NM_181621		Approved	KAP13-2	uc002ynz.4	Q52LG2	OTTHUMG00000057793	ENST00000399889.2:c.76C>T	21.37:g.31744456G>A	ENSP00000382777:p.Arg26Cys	273.0	0.0	0		247.0	116.0	0.469636	NM_181621		Missense_Mutation	SNP	ENST00000399889.2	37	CCDS13589.1	16	0.007326007326007326	16	0.032520325203252036	0	0.0	0	0.0	0	0.0	A	0.003	-2.531073	0.00145	0.022469	1.16E-4	ENSG00000182816	ENST00000399889	T	0.02974	4.09	4.64	2.01	0.26516	.	0.321942	0.22259	N	0.062423	T	0.00241	0.0007	N	0.00337	-1.62	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.43877	-0.9364	10	0.02654	T	1	.	1.3696	0.02208	0.5367:0.1853:0.0995:0.1786	rs16986753;rs52808457;rs16986753	26	Q52LG2	KR132_HUMAN	C	26	ENSP00000382777:R26C	ENSP00000382777:R26C	R	-	1	0	KRTAP13-2	30666327	0.992000	0.36948	0.144000	0.22314	0.017000	0.09413	1.031000	0.30165	0.330000	0.23485	-1.228000	0.01579	CGT	G|0.989;A|0.011	0.011	strong		0.562	KRTAP13-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128245.1		
TAF2	6873	hgsc.bcm.edu	37	8	120793332	120793332	+	Silent	SNP	T	T	C	rs28619538	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:120793332T>C	ENST00000378164.2	-	17	2512	c.2214A>G	c.(2212-2214)acA>acG	p.T738T		NM_003184.3	NP_003175	Q6P1X5	TAF2_HUMAN	TAF2 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 150kDa	738					G2/M transition of mitotic cell cycle (GO:0000086)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to organic cyclic compound (GO:0014070)|transcription initiation from RNA polymerase II promoter (GO:0006367)	transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	metallopeptidase activity (GO:0008237)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(2)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(21)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	49	Lung NSC(37;9.35e-07)|Ovarian(258;0.011)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			TAAAGTTGTTTGTTTTCACAA	0.348													T|||	117	0.0233626	0.0825	0.0086	5008	,	,		16206	0.0		0.002	False		,,,				2504	0.0				p.T738T		Atlas-SNP	.											.	TAF2	204	.	0			c.A2214G						PASS	.	T		271,4135	152.9+/-186.6	5,261,1937	79.0	84.0	82.0		2214	2.8	1.0	8	dbSNP_125	82	35,8565	24.0+/-70.4	0,35,4265	no	coding-synonymous	TAF2	NM_003184.3		5,296,6202	CC,CT,TT		0.407,6.1507,2.3528		738/1200	120793332	306,12700	2203	4300	6503	SO:0001819	synonymous_variant	6873	exon17			GTTGTTTGTTTTC	AF040701	CCDS34937.1	8q24	2012-07-18	2002-08-29	2001-12-07	ENSG00000064313	ENSG00000064313			11536	protein-coding gene	gene with protein product		604912	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, B, 150kD"""	TAF2B		9774672, 9418870	Standard	NM_003184		Approved	TAFII150, CIF150	uc003you.3	Q6P1X5	OTTHUMG00000165009	ENST00000378164.2:c.2214A>G	8.37:g.120793332T>C		75.0	0.0	0		62.0	36.0	0.580645	NM_003184	B2RE82|O43487|O43604|O60668|Q86WW7|Q8IWK4	Silent	SNP	ENST00000378164.2	37	CCDS34937.1																																																																																			T|0.977;C|0.023	0.023	strong		0.348	TAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381436.1	NM_003184	
OC90	729330	hgsc.bcm.edu	37	8	133053909	133053909	+	Silent	SNP	G	G	C	rs115883855	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133053909G>C	ENST00000443356.2	-	5	293	c.207C>G	c.(205-207)gtC>gtG	p.V69V	OC90_ENST00000603859.1_Silent_p.V69V|OC90_ENST00000254627.3_Silent_p.V69V|OC90_ENST00000262283.5_Silent_p.V265V			Q02509	OC90_HUMAN	otoconin 90	69					lipid catabolic process (GO:0016042)|phospholipid metabolic process (GO:0006644)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(23)|ovary(2)|prostate(1)|skin(1)	37	Esophageal squamous(12;0.00693)|Ovarian(258;0.00769)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000805)			AATTGGTGAAGACAGCCTGCA	0.577													G|||	53	0.0105831	0.0386	0.0029	5008	,	,		17110	0.0		0.0	False		,,,				2504	0.0				p.V69V		Atlas-SNP	.											OC90_ENST00000262283,caecum,carcinoma,0,2	OC90	163	2	0			c.C207G						PASS	.	G		121,3849		1,119,1865	33.0	33.0	33.0		207	2.8	1.0	8	dbSNP_132	33	0,8330		0,0,4165	no	coding-synonymous	OC90	NM_001080399.2		1,119,6030	CC,CG,GG		0.0,3.0479,0.9837		69/478	133053909	121,12179	1985	4165	6150	SO:0001819	synonymous_variant	729330	exon5			GGTGAAGACAGCC	Z14310	CCDS47919.1	8q24.22	2011-03-01			ENSG00000253117	ENSG00000253117			8100	protein-coding gene	gene with protein product		601658		PLA2L		10329003, 9860971	Standard	NM_001080399		Approved		uc011lix.1	Q02509	OTTHUMG00000164672	ENST00000443356.2:c.207C>G	8.37:g.133053909G>C		121.0	0.0	0		139.0	70.0	0.503597	NM_001080399	B4DNG8	Silent	SNP	ENST00000443356.2	37																																																																																				G|0.989;C|0.011	0.011	strong		0.577	OC90-201	KNOWN	basic	protein_coding	protein_coding		NM_001080399	
PDZD2	23037	hgsc.bcm.edu	37	5	32093079	32093079	+	Silent	SNP	A	A	G	rs16889443	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:32093079A>G	ENST00000438447.1	+	21	8182	c.7794A>G	c.(7792-7794)ggA>ggG	p.G2598G	PDZD2_ENST00000282493.3_Silent_p.G2598G			O15018	PDZD2_HUMAN	PDZ domain containing 2	2598					cell adhesion (GO:0007155)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)				NS(2)|breast(4)|central_nervous_system(5)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(31)|lung(58)|ovary(6)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	148						CGTCAGTGGGATCGAAATCTA	0.408													G|||	425	0.0848642	0.3064	0.0259	5008	,	,		18742	0.0		0.002	False		,,,				2504	0.0				p.G2598G		Atlas-SNP	.											.	PDZD2	306	.	0			c.A7794G						PASS	.	G		925,3481	737.3+/-410.9	104,717,1382	83.0	84.0	84.0		7794	1.9	0.1	5	dbSNP_123	84	6,8594	818.6+/-406.8	0,6,4294	no	coding-synonymous	PDZD2	NM_178140.2		104,723,5676	GG,GA,AA		0.0698,20.9941,7.1582		2598/2840	32093079	931,12075	2203	4300	6503	SO:0001819	synonymous_variant	23037	exon20			AGTGGGATCGAAA	AB002298	CCDS34137.1	5p14.1	2008-02-05	2006-01-24	2006-01-24		ENSG00000133401			18486	protein-coding gene	gene with protein product		610697	"""PDZ domain containing 3"""	PDZK3		9205841	Standard	XM_005248271		Approved	KIAA0300	uc003jhm.3	O15018		ENST00000438447.1:c.7794A>G	5.37:g.32093079A>G		144.0	0.0	0		194.0	100.0	0.515464	NM_178140	Q9BXD4	Silent	SNP	ENST00000438447.1	37	CCDS34137.1																																																																																			A|0.932;G|0.068	0.068	strong		0.408	PDZD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366608.1		
JRK	8629	hgsc.bcm.edu	37	8	143746722	143746722	+	RNA	SNP	G	G	A	rs60195180	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:143746722G>A	ENST00000507178.2	-	0	1088							O75564	JERKY_HUMAN	Jrk homolog (mouse)							nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;2.31e-05)				ccttataggcgacgggcaggt	0.577													G|||	63	0.0125799	0.0469	0.0014	5008	,	,		18089	0.0		0.0	False		,,,				2504	0.0				p.V252V		Atlas-SNP	.											.	.	.	.	0			c.C756T						PASS	.	G	,	90,2688		0,90,1299	13.0	15.0	14.0		756,756	-7.2	0.0	8	dbSNP_129	14	3,5557		0,3,2777	no	coding-synonymous,coding-synonymous	JRK	NM_001077527.1,NM_003724.2	,	0,93,4076	AA,AG,GG		0.054,3.2397,1.1154	,	252/557,252/569	143746722	93,8245	1389	2780	4169			8629	exon2			ATAGGCGACGGGC	AF072467	CCDS75796.1, CCDS75797.1	8q24.3	2014-03-28	2014-03-28			ENSG00000234616			6199	protein-coding gene	gene with protein product		603210	"""jerky (mouse) homolog"", ""jerky homolog (mouse)"""			9675132	Standard	NM_003724		Approved	JH8, jerky	uc003ywo.3	O75564			8.37:g.143746722G>A		99.0	0.0	0		107.0	43.0	0.401869	NM_003724	O75565	Silent	SNP	ENST00000507178.2	37																																																																																				G|0.992;A|0.008	0.008	strong		0.577	JRK-003	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000362914.1	NM_003724	
ADRBK1	156	hgsc.bcm.edu	37	11	67052322	67052322	+	Silent	SNP	C	C	T	rs115867067	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:67052322C>T	ENST00000308595.5	+	19	1949	c.1659C>T	c.(1657-1659)taC>taT	p.Y553Y	ADRBK1_ENST00000527176.1_3'UTR|ADRBK1_ENST00000526285.1_Intron	NM_001619.3	NP_001610.2	P25098	ARBK1_HUMAN	adrenergic, beta, receptor kinase 1	553					activation of phospholipase C activity (GO:0007202)|cardiac muscle contraction (GO:0060048)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|heart development (GO:0007507)|innate immune response (GO:0045087)|negative regulation of striated muscle contraction (GO:0045988)|negative regulation of the force of heart contraction by chemical signal (GO:0003108)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of catecholamine secretion (GO:0033605)|receptor internalization (GO:0031623)|signal transduction (GO:0007165)|tachykinin receptor signaling pathway (GO:0007217)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|ATP binding (GO:0005524)|beta-adrenergic receptor kinase activity (GO:0047696)|Edg-2 lysophosphatidic acid receptor binding (GO:0031755)|G-protein coupled receptor kinase activity (GO:0004703)|protein kinase activity (GO:0004672)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(2)|liver(2)|lung(8)|prostate(2)	22			BRCA - Breast invasive adenocarcinoma(15;2.26e-06)		Adenosine triphosphate(DB00171)	CCTCAGACTACGCCCTGGGCA	0.587													C|||	66	0.0131789	0.0484	0.0029	5008	,	,		15108	0.0		0.0	False		,,,				2504	0.0				p.Y553Y		Atlas-SNP	.											.	ADRBK1	51	.	0			c.C1659T						PASS	.	C		168,4230	108.2+/-146.6	4,160,2035	77.0	56.0	63.0		1659	1.0	1.0	11	dbSNP_132	63	1,8589		0,1,4294	no	coding-synonymous	ADRBK1	NM_001619.3		4,161,6329	TT,TC,CC		0.0116,3.8199,1.3012		553/690	67052322	169,12819	2199	4295	6494	SO:0001819	synonymous_variant	156	exon19			AGACTACGCCCTG	X61157	CCDS8156.1	11q13	2013-01-10			ENSG00000173020	ENSG00000173020		"""Pleckstrin homology (PH) domain containing"""	289	protein-coding gene	gene with protein product		109635				2037065	Standard	NM_001619		Approved	GRK2, BARK1	uc009yrn.1	P25098	OTTHUMG00000167104	ENST00000308595.5:c.1659C>T	11.37:g.67052322C>T		52.0	0.0	0		76.0	25.0	0.328947	NM_001619	B0ZBE1|Q13837|Q6GTT3	Silent	SNP	ENST00000308595.5	37	CCDS8156.1																																																																																			C|0.987;T|0.013	0.013	strong		0.587	ADRBK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393153.1	NM_001619	
JARID2	3720	hgsc.bcm.edu	37	6	15517415	15517415	+	Silent	SNP	C	C	T	rs11970076	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:15517415C>T	ENST00000341776.2	+	17	3718	c.3474C>T	c.(3472-3474)gtC>gtT	p.V1158V	JARID2_ENST00000397311.3_Silent_p.V986V	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	1158					central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				ACGAAAACGTCGTGTTCTGTC	0.597													C|||	80	0.0159744	0.0575	0.0043	5008	,	,		17419	0.0		0.001	False		,,,				2504	0.0				p.V1158V		Atlas-SNP	.											.	JARID2	135	.	0			c.C3474T						PASS	.	C		229,4177	134.1+/-170.4	6,217,1980	179.0	140.0	153.0		3474	-3.5	1.0	6	dbSNP_120	153	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	JARID2	NM_004973.2		6,220,6277	TT,TC,CC		0.0349,5.1975,1.7838		1158/1247	15517415	232,12774	2203	4300	6503	SO:0001819	synonymous_variant	3720	exon17			AAACGTCGTGTTC	U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"""jumonji (mouse) homolog"", ""Jumonji, AT rich interactive domain 2"""	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.3474C>T	6.37:g.15517415C>T		78.0	0.0	0		136.0	74.0	0.544118	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Silent	SNP	ENST00000341776.2	37	CCDS4533.1																																																																																			C|0.983;T|0.017	0.017	strong		0.597	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973	
ZNF582	147948	hgsc.bcm.edu	37	19	56901457	56901457	+	Missense_Mutation	SNP	C	C	T	rs61743722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56901457C>T	ENST00000301310.4	-	4	303	c.145G>A	c.(145-147)Gtt>Att	p.V49I	ZNF582_ENST00000586929.1_Missense_Mutation_p.V49I|AC006116.12_ENST00000589671.1_RNA	NM_144690.1	NP_653291.1	Q96NG8	ZN582_HUMAN	zinc finger protein 582	49	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)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0547)		GGTTTGGAAACGGCAAGACCT	0.542													C|||	133	0.0265575	0.093	0.0144	5008	,	,		17157	0.0		0.0	False		,,,				2504	0.0				p.V49I	Ovarian(183;1887 2032 4349 30507 51343)	Atlas-SNP	.											.	ZNF582	56	.	0			c.G145A						PASS	.	C	ILE/VAL	389,4017	196.7+/-221.0	18,353,1832	91.0	86.0	88.0		145	-9.4	0.0	19	dbSNP_129	88	2,8598		0,2,4298	yes	missense	ZNF582	NM_144690.1	29	18,355,6130	TT,TC,CC		0.0233,8.8289,3.0063	benign	49/518	56901457	391,12615	2203	4300	6503	SO:0001583	missense	147948	exon4			TGGAAACGGCAAG	AK055489	CCDS33121.1	19q13.43	2013-07-15			ENSG00000018869	ENSG00000018869		"""Zinc fingers, C2H2-type"", ""-"""	26421	protein-coding gene	gene with protein product		615600				12477932	Standard	NM_144690		Approved	FLJ30927	uc002qmz.1	Q96NG8	OTTHUMG00000181939	ENST00000301310.4:c.145G>A	19.37:g.56901457C>T	ENSP00000301310:p.Val49Ile	83.0	0.0	0		93.0	44.0	0.473118	NM_144690	B4DQZ9|B7Z9R3|Q6PJT6	Missense_Mutation	SNP	ENST00000301310.4	37	CCDS33121.1	52	0.023809523809523808	46	0.09349593495934959	6	0.016574585635359115	0	0.0	0	0.0	C	6.754	0.507989	0.12883	0.088289	2.33E-4	ENSG00000018869	ENST00000301310	T	0.00808	5.67	4.82	-9.39	0.00619	Krueppel-associated box (3);	.	.	.	.	T	0.00039	0.0001	N	0.05012	-0.13	0.28889	N	0.893944	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47459	-0.9116	9	0.06757	T	0.87	.	15.7899	0.78345	0.1051:0.7097:0.0:0.1853	.	49;80	Q96NG8;B4DQZ9	ZN582_HUMAN;.	I	49	ENSP00000301310:V49I	ENSP00000301310:V49I	V	-	1	0	ZNF582	61593269	0.000000	0.05858	0.000000	0.03702	0.945000	0.59286	-3.092000	0.00608	-2.299000	0.00659	-0.238000	0.12139	GTT	C|0.972;T|0.028	0.028	strong		0.542	ZNF582-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458387.2	NM_144690	
TTC8	123016	hgsc.bcm.edu	37	14	89343670	89343670	+	Silent	SNP	G	G	C	rs142073418	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:89343670G>C	ENST00000345383.5	+	14	1518	c.1434G>C	c.(1432-1434)gcG>gcC	p.A478A	TTC8_ENST00000338104.6_Silent_p.A504A|TTC8_ENST00000536576.1_Silent_p.A249A|TTC8_ENST00000354441.6_Silent_p.A223A|TTC8_ENST00000358622.5_Silent_p.A290A|TTC8_ENST00000380656.2_Silent_p.A488A|TTC8_ENST00000346301.4_Silent_p.A448A	NM_198309.2	NP_938051.1	Q8TAM2	TTC8_HUMAN	tetratricopeptide repeat domain 8	514					axon guidance (GO:0007411)|camera-type eye photoreceptor cell differentiation (GO:0060219)|cilium assembly (GO:0042384)|establishment of anatomical structure orientation (GO:0048560)|fat cell differentiation (GO:0045444)|multicellular organism growth (GO:0035264)|nonmotile primary cilium assembly (GO:0035058)|olfactory bulb development (GO:0021772)|protein transport (GO:0015031)|regulation of protein localization (GO:0032880)|renal tubule development (GO:0061326)|sensory perception of smell (GO:0007608)|sensory processing (GO:0050893)	BBSome (GO:0034464)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|prostate(1)	15						ATGTTGCTGCGCAGAAGTCTG	0.378													G|||	7	0.00139776	0.0008	0.0014	5008	,	,		15836	0.0		0.002	False		,,,				2504	0.0031				p.A488A		Atlas-SNP	.											TTC8,NS,carcinoma,+2,1	TTC8	42	1	0			c.G1464C						PASS	.	G	,,	6,4400	11.4+/-27.6	0,6,2197	81.0	71.0	74.0		1464,1434,1344	-0.1	1.0	14	dbSNP_134	74	45,8555	27.4+/-76.7	0,45,4255	no	coding-synonymous,coding-synonymous,coding-synonymous	TTC8	NM_144596.2,NM_198309.2,NM_198310.2	,,	0,51,6452	CC,CG,GG		0.5233,0.1362,0.3921	,,	488/516,478/506,448/476	89343670	51,12955	2203	4300	6503	SO:0001819	synonymous_variant	123016	exon15			TGCTGCGCAGAAG	AK093891	CCDS9885.1, CCDS9886.1, CCDS32137.1, CCDS73674.1, CCDS73675.1	14q31.3	2013-02-14				ENSG00000165533		"""Tetratricopeptide (TTC) repeat domain containing"""	20087	protein-coding gene	gene with protein product		608132				14520415, 20451172	Standard	NM_144596		Approved	BBS8, RP51	uc001xxi.3	Q8TAM2		ENST00000345383.5:c.1434G>C	14.37:g.89343670G>C		119.0	0.0	0		120.0	54.0	0.45	NM_144596	A6NFG2|B3KWA5|Q67B97|Q86SY0|Q86TV9|Q86U26|Q8NDH9|Q96DG8	Silent	SNP	ENST00000345383.5	37	CCDS9885.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	8.459	0.854948	0.17106	0.001362	0.005233	ENSG00000165533	ENST00000554686	.	.	.	5.4	-0.12	0.13539	.	.	.	.	.	T	0.34687	0.0906	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.19031	-1.0318	4	.	.	.	-15.2774	2.8711	0.05617	0.4346:0.0675:0.1193:0.3786	.	.	.	.	P	410	.	.	R	+	2	0	TTC8	88413423	0.828000	0.29307	0.998000	0.56505	0.891000	0.51852	-0.119000	0.10676	0.094000	0.17404	-0.384000	0.06662	CGC	G|0.997;C|0.003	0.003	strong		0.378	TTC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410861.1	NM_144596	
POLM	27434	hgsc.bcm.edu	37	7	44116207	44116207	+	Missense_Mutation	SNP	C	C	A	rs28382653	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:44116207C>A	ENST00000242248.5	-	6	837	c.736G>T	c.(736-738)Gtc>Ttc	p.V246F	POLM_ENST00000395831.3_Intron|POLM_ENST00000335195.6_Missense_Mutation_p.V246F|POLM_ENST00000492971.1_5'UTR	NM_013284.2	NP_037416.1	Q9NP87	DPOLM_HUMAN	polymerase (DNA directed), mu	246			V -> F (in dbSNP:rs28382653). {ECO:0000269|Ref.3}.		DNA recombination (GO:0006310)|DNA repair (GO:0006281)	nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(1)|lung(6)|ovary(3)|skin(2)	22						TTCACACCGACCCCGAAGATC	0.607								DNA polymerases (catalytic subunits)					C|||	52	0.0103834	0.0378	0.0029	5008	,	,		19742	0.0		0.0	False		,,,				2504	0.0				p.V246F		Atlas-SNP	.											.	POLM	50	.	0			c.G736T						PASS	.	C	PHE/VAL	220,4186	132.5+/-169.0	7,206,1990	97.0	92.0	94.0		736	5.7	1.0	7	dbSNP_125	94	0,8600		0,0,4300	yes	missense	POLM	NM_013284.2	50	7,206,6290	AA,AC,CC		0.0,4.9932,1.6915	probably-damaging	246/495	44116207	220,12786	2203	4300	6503	SO:0001583	missense	27434	exon6			CACCGACCCCGAA	AF176097	CCDS34625.1, CCDS64635.1, CCDS64636.1	7p13	2012-05-18			ENSG00000122678	ENSG00000122678		"""DNA polymerases"""	9185	protein-coding gene	gene with protein product	"""Pol iota"""	606344				10982892	Standard	XM_005249708		Approved	Tdt-N	uc003tjt.3	Q9NP87	OTTHUMG00000155353	ENST00000242248.5:c.736G>T	7.37:g.44116207C>A	ENSP00000242248:p.Val246Phe	69.0	0.0	0		93.0	42.0	0.451613	NM_013284	D3DVK4|Q6P5X8|Q86WQ9	Missense_Mutation	SNP	ENST00000242248.5	37	CCDS34625.1	21	0.009615384615384616	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	0	0.0	C	18.48	3.633258	0.67015	0.049932	0.0	ENSG00000122678	ENST00000335195;ENST00000242248	T;T	0.59502	0.26;0.26	5.68	5.68	0.88126	DNA-directed DNA polymerase X (1);DNA polymerase lambda, fingers domain (2);	.	.	.	.	T	0.40272	0.1110	M	0.82056	2.57	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.994;1.0	T	0.68066	-0.5507	9	0.87932	D	0	.	15.2786	0.73764	0.0:1.0:0.0:0.0	rs28382653	246;246	Q6P5X8;Q9NP87	.;DPOLM_HUMAN	F	246	ENSP00000335141:V246F;ENSP00000242248:V246F	ENSP00000242248:V246F	V	-	1	0	POLM	44082732	0.998000	0.40836	0.995000	0.50966	0.809000	0.45718	4.994000	0.63901	2.672000	0.90937	0.650000	0.86243	GTC	C|0.983;A|0.017	0.017	strong		0.607	POLM-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339594.1	NM_013284	
FYCO1	79443	hgsc.bcm.edu	37	3	46009620	46009620	+	Silent	SNP	C	C	T	rs34147726	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:46009620C>T	ENST00000296137.2	-	8	1411	c.1206G>A	c.(1204-1206)gaG>gaA	p.E402E	FYCO1_ENST00000535325.1_Silent_p.E402E	NM_024513.3	NP_078789.2	Q9BQS8	FYCO1_HUMAN	FYVE and coiled-coil domain containing 1	402					plus-end-directed vesicle transport along microtubule (GO:0072383)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)	metal ion binding (GO:0046872)			NS(4)|breast(3)|central_nervous_system(1)|endometrium(11)|kidney(2)|large_intestine(9)|lung(17)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	54				BRCA - Breast invasive adenocarcinoma(193;0.00147)|KIRC - Kidney renal clear cell carcinoma(197;0.0272)|Kidney(197;0.0323)		TCTCCCCTAGCTCCTGCATCT	0.572													C|||	489	0.0976438	0.354	0.0303	5008	,	,		19633	0.0		0.0	False		,,,				2504	0.0				p.E402E		Atlas-SNP	.											.	FYCO1	115	.	0			c.G1206A						PASS	.	C		1328,3078	445.1+/-347.6	201,926,1076	195.0	195.0	195.0		1206	2.8	0.9	3	dbSNP_126	195	13,8587	9.1+/-34.3	0,13,4287	no	coding-synonymous	FYCO1	NM_024513.2		201,939,5363	TT,TC,CC		0.1512,30.1407,10.3106		402/1479	46009620	1341,11665	2203	4300	6503	SO:0001819	synonymous_variant	79443	exon8			CCCTAGCTCCTGC	AJ292348	CCDS2734.1	3p21.3	2008-02-05			ENSG00000163820	ENSG00000163820		"""Zinc fingers, FYVE domain containing"""	14673	protein-coding gene	gene with protein product		607182				11896456	Standard	NM_024513		Approved	FLJ13335, ZFYVE7	uc003cpb.5	Q9BQS8	OTTHUMG00000133447	ENST00000296137.2:c.1206G>A	3.37:g.46009620C>T		149.0	0.0	0		139.0	59.0	0.42446	NM_024513	B7ZKT7|Q3MJE6|Q86T41|Q86TB1|Q8TEF9|Q96IV5|Q9H8P9	Silent	SNP	ENST00000296137.2	37	CCDS2734.1																																																																																			C|0.907;T|0.093	0.093	strong		0.572	FYCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257320.2	NM_024513	
KIAA1804	84451	hgsc.bcm.edu	37	1	233489682	233489682	+	Silent	SNP	G	G	A	rs56268427	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:233489682G>A	ENST00000366624.3	+	3	1377	c.1116G>A	c.(1114-1116)ccG>ccA	p.P372P	MLK4_ENST00000366623.3_Silent_p.P372P	NM_032435.2	NP_115811.2																					GCCCTGAGCCGTTTGCCAAGC	0.468													G|||	255	0.0509185	0.1823	0.0173	5008	,	,		18556	0.0		0.002	False		,,,				2504	0.0				p.P372P		Atlas-SNP	.											.	KIAA1804	129	.	0			c.G1116A						PASS	.	G		698,3708	291.0+/-281.2	53,592,1558	126.0	110.0	116.0		1116	-9.8	0.1	1	dbSNP_129	116	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	KIAA1804	NM_032435.2		53,599,5851	AA,AG,GG		0.0814,15.842,5.4206		372/1037	233489682	705,12301	2203	4300	6503	SO:0001819	synonymous_variant	0	exon3			TGAGCCGTTTGCC																												ENST00000366624.3:c.1116G>A	1.37:g.233489682G>A		200.0	0.0	0		212.0	107.0	0.504717	NM_032435		Silent	SNP	ENST00000366624.3	37	CCDS1598.1																																																																																			G|0.951;A|0.049	0.049	strong		0.468	MLK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092495.1		
ZSWIM1	90204	hgsc.bcm.edu	37	20	44512013	44512013	+	Missense_Mutation	SNP	C	C	G	rs115926000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:44512013C>G	ENST00000372523.1	+	2	877	c.782C>G	c.(781-783)aCc>aGc	p.T261S	ZSWIM1_ENST00000372520.1_Missense_Mutation_p.T261S	NM_080603.4	NP_542170.3	Q9BR11	ZSWM1_HUMAN	zinc finger, SWIM-type containing 1	261						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|large_intestine(4)|lung(3)|ovary(1)|skin(1)	13		Myeloproliferative disorder(115;0.028)				CTCGAGGTCACCACCCACATC	0.562													C|||	11	0.00219649	0.0068	0.0	5008	,	,		20333	0.0		0.002	False		,,,				2504	0.0				p.T261S		Atlas-SNP	.											.	ZSWIM1	35	.	0			c.C782G						PASS	.	C	SER/THR	31,4375	37.6+/-69.7	0,31,2172	110.0	94.0	99.0		782	3.1	1.0	20	dbSNP_132	99	4,8596	3.7+/-12.6	0,4,4296	yes	missense	ZSWIM1	NM_080603.4	58	0,35,6468	GG,GC,CC		0.0465,0.7036,0.2691	benign	261/486	44512013	35,12971	2203	4300	6503	SO:0001583	missense	90204	exon2			AGGTCACCACCCA	AL008726	CCDS13382.2	20q13.12	2013-09-20	2003-12-17	2003-12-19	ENSG00000168612	ENSG00000168612		"""Zinc fingers, SWIM-type"""	16155	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 162"""	C20orf162			Standard	NM_080603		Approved	dJ337O18.5	uc010ghi.3	Q9BR11	OTTHUMG00000074023	ENST00000372523.1:c.782C>G	20.37:g.44512013C>G	ENSP00000361601:p.Thr261Ser	172.0	0.0	0		203.0	106.0	0.522168	NM_080603	Q5JZH2|Q9BR12|Q9BV30	Missense_Mutation	SNP	ENST00000372523.1	37	CCDS13382.2	4	0.0018315018315018315	3	0.006097560975609756	0	0.0	0	0.0	1	0.0013192612137203166	C	12.19	1.864270	0.32977	0.007036	4.65E-4	ENSG00000168612	ENST00000372523;ENST00000372520	T;T	0.24151	1.87;1.87	5.13	3.11	0.35812	.	0.437391	0.18795	U	0.130955	T	0.09905	0.0243	N	0.24115	0.695	0.19300	N	0.999977	B	0.30482	0.281	B	0.30029	0.11	T	0.26744	-1.0094	10	0.10902	T	0.67	-20.7697	8.035	0.30486	0.0:0.6753:0.0:0.3247	.	261	Q9BR11	ZSWM1_HUMAN	S	261	ENSP00000361601:T261S;ENSP00000361598:T261S	ENSP00000361598:T261S	T	+	2	0	ZSWIM1	43945420	0.268000	0.24133	0.996000	0.52242	0.990000	0.78478	0.495000	0.22483	0.669000	0.31146	0.555000	0.69702	ACC	C|0.998;G|0.002	0.002	strong		0.562	ZSWIM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157064.2	NM_080603	
NEIL2	252969	hgsc.bcm.edu	37	8	11643731	11643731	+	Silent	SNP	G	G	A	rs113110839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11643731G>A	ENST00000284503.6	+	5	1547	c.948G>A	c.(946-948)ccG>ccA	p.P316P	NEIL2_ENST00000528323.1_Silent_p.P200P|NEIL2_ENST00000455213.2_Silent_p.P316P|NEIL2_ENST00000436750.3_Silent_p.P316P|NEIL2_ENST00000403422.3_Silent_p.P255P	NM_145043.2	NP_659480.1	Q969S2	NEIL2_HUMAN	nei endonuclease VIII-like 2 (E. coli)	316					base-excision repair (GO:0006284)|nucleotide-excision repair (GO:0006289)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	damaged DNA binding (GO:0003684)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10	all_epithelial(15;0.103)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.166)		GGTGGTGCCCGCAGTGCCAGC	0.612								Base excision repair (BER), DNA glycosylases					G|||	23	0.00459265	0.0166	0.0014	5008	,	,		17965	0.0		0.0	False		,,,				2504	0.0				p.P316P		Atlas-SNP	.											.	NEIL2	14	.	0			c.G948A						PASS	.	G	,,,	42,4362		0,42,2160	23.0	21.0	22.0		948,765,600,948	-10.7	0.2	8	dbSNP_132	22	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NEIL2	NM_001135746.1,NM_001135747.1,NM_001135748.1,NM_145043.2	,,,	0,42,6459	AA,AG,GG		0.0,0.9537,0.323	,,,	316/333,255/272,200/217,316/333	11643731	42,12960	2202	4299	6501	SO:0001819	synonymous_variant	252969	exon5			GTGCCCGCAGTGC	AK056206	CCDS5984.1, CCDS47802.1, CCDS47803.1	8p23.1	2010-04-27	2010-04-27		ENSG00000154328	ENSG00000154328			18956	protein-coding gene	gene with protein product		608933	"""nei like 2 (E. coli)"""			12097317, 17686777	Standard	NM_145043		Approved	NEH2, FLJ31644, MGC2832, MGC4505	uc003wue.2	Q969S2	OTTHUMG00000090753	ENST00000284503.6:c.948G>A	8.37:g.11643731G>A		199.0	0.0	0		235.0	126.0	0.53617	NM_001135746	B4DFR7|Q7Z3Q7|Q8N842|Q8NG52	Silent	SNP	ENST00000284503.6	37	CCDS5984.1																																																																																			G|0.996;A|0.004	0.004	strong		0.612	NEIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207583.3	NM_145043	
OR10Z1	128368	hgsc.bcm.edu	37	1	158576394	158576394	+	Missense_Mutation	SNP	C	C	A	rs116792162	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158576394C>A	ENST00000361284.1	+	1	166	c.166C>A	c.(166-168)Cac>Aac	p.H56N		NM_001004478.1	NP_001004478.1	Q8NGY1	O10Z1_HUMAN	olfactory receptor, family 10, subfamily Z, member 1	56						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(6)|lung(21)|pancreas(1)|prostate(3)|skin(4)	37	all_hematologic(112;0.0378)					TAGCCATCTGCACACCCCCAT	0.512													C|||	36	0.0071885	0.0265	0.0014	5008	,	,		20596	0.0		0.0	False		,,,				2504	0.0				p.H56N		Atlas-SNP	.											OR10Z1,right_upper_lobe,carcinoma,-1,1	OR10Z1	99	1	0			c.C166A						PASS	.	C	ASN/HIS	101,4305	79.9+/-118.3	1,99,2103	257.0	247.0	251.0		166	5.4	0.9	1	dbSNP_132	251	1,8599	1.2+/-3.3	0,1,4299	yes	missense	OR10Z1	NM_001004478.1	68	1,100,6402	AA,AC,CC		0.0116,2.2923,0.7843	probably-damaging	56/314	158576394	102,12904	2203	4300	6503	SO:0001583	missense	128368	exon1			CATCTGCACACCC	AB065635	CCDS30901.1	1q23.1	2012-08-23			ENSG00000198967	ENSG00000198967		"""GPCR / Class A : Olfactory receptors"""	14996	protein-coding gene	gene with protein product							Standard	NM_001004478		Approved		uc010pio.2	Q8NGY1	OTTHUMG00000019637	ENST00000361284.1:c.166C>A	1.37:g.158576394C>A	ENSP00000354707:p.His56Asn	316.0	0.0	0		368.0	182.0	0.494565	NM_001004478	Q5VYL0|Q6IFR7	Missense_Mutation	SNP	ENST00000361284.1	37	CCDS30901.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	16.63	3.176489	0.57692	0.022923	1.16E-4	ENSG00000198967	ENST00000361284	T	0.15952	2.38	5.36	5.36	0.76844	GPCR, rhodopsin-like superfamily (1);	0.000000	0.43579	D	0.000544	T	0.42449	0.1203	M	0.92268	3.29	0.34002	D	0.650477	D	0.76494	0.999	D	0.79108	0.992	T	0.56312	-0.8000	10	0.66056	D	0.02	.	13.5532	0.61745	0.1563:0.8437:0.0:0.0	.	56	Q8NGY1	O10Z1_HUMAN	N	56	ENSP00000354707:H56N	ENSP00000354707:H56N	H	+	1	0	OR10Z1	156843018	0.443000	0.25641	0.927000	0.36925	0.716000	0.41182	1.115000	0.31209	2.783000	0.95769	0.655000	0.94253	CAC	C|0.992;A|0.008	0.008	strong		0.512	OR10Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051853.1	NM_001004478	
NCKAP5	344148	hgsc.bcm.edu	37	2	133887676	133887676	+	Missense_Mutation	SNP	T	T	C	rs35356262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:133887676T>C	ENST00000409261.1	-	6	588	c.215A>G	c.(214-216)aAg>aGg	p.K72R	NCKAP5_ENST00000405974.3_Missense_Mutation_p.K72R|NCKAP5_ENST00000409213.1_Missense_Mutation_p.K72R|NCKAP5_ENST00000317721.6_Missense_Mutation_p.K72R	NM_207363.2	NP_997246.2	O14513	NCKP5_HUMAN	NCK-associated protein 5	72										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						ATGTATCAGCTTCTCATGCTA	0.403													T|||	6	0.00119808	0.0045	0.0	5008	,	,		20515	0.0		0.0	False		,,,				2504	0.0				p.K72R		Atlas-SNP	.											.	NCKAP5	322	.	0			c.A215G						PASS	.	T	ARG/LYS,ARG/LYS	25,3761		0,25,1868	69.0	65.0	66.0		215,215	3.8	1.0	2	dbSNP_126	66	0,8236		0,0,4118	yes	missense,missense	NCKAP5	NM_207363.2,NM_207481.3	26,26	0,25,5986	CC,CT,TT		0.0,0.6603,0.208	probably-damaging,probably-damaging	72/1910,72/591	133887676	25,11997	1893	4118	6011	SO:0001583	missense	344148	exon6			ATCAGCTTCTCAT	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.215A>G	2.37:g.133887676T>C	ENSP00000387128:p.Lys72Arg	99.0	0.0	0		81.0	37.0	0.45679	NM_207481	B8ZZL0|Q29SS9|Q29ST0|Q2NL90|Q6ZVE2|Q8NAS3	Missense_Mutation	SNP	ENST00000409261.1	37	CCDS46418.1	2|2	9.157509157509158E-4|9.157509157509158E-4	2|2	0.0040650406504065045|0.0040650406504065045	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	T|T	22.4|22.4	4.279946|4.279946	0.80692|0.80692	0.006603|0.006603	0.0|0.0	ENSG00000176771|ENSG00000176771	ENST00000409261;ENST00000409213;ENST00000317721;ENST00000405974;ENST00000537661;ENST00000542834|ENST00000427594	T;T;T;T|.	0.51817|.	2.68;0.69;2.68;0.69|.	6.17|6.17	3.85|3.85	0.44370|0.44370	.|.	.|.	.|.	.|.	.|.	T|T	0.19765|0.19765	0.0475|0.0475	L|L	0.27053|0.27053	0.805|0.805	0.24242|0.24242	N|N	0.995352|0.995352	B;B;B;D|.	0.58620|.	0.006;0.063;0.126;0.983|.	B;B;B;P|.	0.56865|.	0.005;0.033;0.074;0.808|.	T|T	0.14952|0.14952	-1.0454|-1.0454	9|5	0.66056|.	D|.	0.02|.	.|.	7.094|7.094	0.25299|0.25299	0.0:0.1686:0.0:0.8314|0.0:0.1686:0.0:0.8314	rs35356262|rs35356262	72;47;72;72|.	F5GYX5;O14513-3;O14513-2;O14513|.	.;.;.;NCKP5_HUMAN|.	R|G	72;72;72;72;72;47|68	ENSP00000387128:K72R;ENSP00000386952:K72R;ENSP00000380603:K72R;ENSP00000385692:K72R|.	ENSP00000380603:K72R|.	K|S	-|-	2|1	0|0	NCKAP5|NCKAP5	133604146|133604146	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	3.758000|3.758000	0.55220|0.55220	1.163000|1.163000	0.42636|0.42636	0.533000|0.533000	0.62120|0.62120	AAG|AGC	T|0.999;C|0.001	0.001	strong		0.403	NCKAP5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331663.1	NM_207481	
MAGEA8	4107	hgsc.bcm.edu	37	X	149013963	149013963	+	Missense_Mutation	SNP	C	C	T	rs12010332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:149013963C>T	ENST00000542674.1	+	3	1438	c.917C>T	c.(916-918)tCc>tTc	p.S306F	MAGEA8_ENST00000286482.1_Missense_Mutation_p.S306F|MAGEA8_ENST00000535454.1_Missense_Mutation_p.S306F	NM_001166401.1	NP_001159873.1	P43361	MAGA8_HUMAN	melanoma antigen family A, 8	306	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.		S -> F (in dbSNP:rs12010332).							NS(1)|breast(2)|endometrium(2)|large_intestine(2)|lung(12)|upper_aerodigestive_tract(1)	20	Acute lymphoblastic leukemia(192;6.56e-05)					TCCTACCCATCCCTGCATGAA	0.572													c|||	182	0.0482119	0.1248	0.0144	3775	,	,		15794	0.004		0.002	False		,,,				2504	0.001				p.S306F		Atlas-SNP	.											.	MAGEA8	40	.	0			c.C917T						PASS	.	C	PHE/SER,PHE/SER,PHE/SER	568,3267		39,405,85,1188,486	92.0	88.0	89.0		917,917,917	0.7	0.0	X	dbSNP_120	89	8,6718		0,6,2,2422,1868	yes	missense,missense,missense	MAGEA8	NM_001166400.1,NM_001166401.1,NM_005364.4	155,155,155	39,411,87,3610,2354	TT,TC,T,CC,C		0.1189,14.811,5.454	probably-damaging,probably-damaging,probably-damaging	306/319,306/319,306/319	149013963	576,9985	2203	4298	6501	SO:0001583	missense	4107	exon3			ACCCATCCCTGCA		CCDS14692.1	Xq28	2009-03-13			ENSG00000156009	ENSG00000156009			6806	protein-coding gene	gene with protein product	"""MAGE-8 antigen"", ""cancer/testis antigen family 1, member 8"""	300341		MAGE8		8575766	Standard	NM_005364		Approved	MGC2182, CT1.8	uc004fdw.2	P43361	OTTHUMG00000022635	ENST00000542674.1:c.917C>T	X.37:g.149013963C>T	ENSP00000443776:p.Ser306Phe	284.0	0.0	0		293.0	293.0	1	NM_005364	Q9BUN9	Missense_Mutation	SNP	ENST00000542674.1	37	CCDS14692.1	72	0.0433996383363472	47	0.10262008733624454	3	0.008426966292134831	1	0.0017482517482517483	1	0.0013192612137203166	.	3.559	-0.090020	0.07053	0.14811	0.001189	ENSG00000156009	ENST00000535454;ENST00000542674;ENST00000286482	T;T;T	0.01871	4.59;4.59;4.59	0.68	0.68	0.17980	.	5.208330	0.00397	N	0.000056	T	0.00039	0.0001	L	0.59967	1.855	0.80722	P	0.0	D	0.71674	0.998	P	0.57679	0.825	T	0.48210	-0.9055	8	0.08837	T	0.75	.	.	.	.	rs12010332;rs52806623;rs12010332	306	P43361	MAGA8_HUMAN	F	306	ENSP00000438293:S306F;ENSP00000443776:S306F;ENSP00000286482:S306F	ENSP00000286482:S306F	S	+	2	0	MAGEA8	148774621	0.000000	0.05858	0.001000	0.08648	0.501000	0.33797	-0.990000	0.03732	0.588000	0.29660	0.190000	0.17370	TCC	C|0.947;T|0.053	0.053	strong		0.572	MAGEA8-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058728.1	NM_005364	
ZNF500	26048	hgsc.bcm.edu	37	16	4810583	4810583	+	Missense_Mutation	SNP	C	C	T	rs151148153	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4810583C>T	ENST00000219478.6	-	5	969	c.670G>A	c.(670-672)Gtg>Atg	p.V224M	ZNF500_ENST00000545009.1_Missense_Mutation_p.V224M			O60304	ZN500_HUMAN	zinc finger protein 500	224	KRAB.				transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	21						TCCAAGTTCACGGGCACCTGC	0.632													C|||	11	0.00219649	0.0076	0.0014	5008	,	,		20443	0.0		0.0	False		,,,				2504	0.0				p.V224M		Atlas-SNP	.											.	ZNF500	45	.	0			c.G670A						PASS	.	C	MET/VAL	65,4329	61.1+/-98.1	0,65,2132	96.0	79.0	85.0		670	3.2	0.1	16	dbSNP_134	85	6,8594	5.0+/-18.6	0,6,4294	yes	missense	ZNF500	NM_021646.1	21	0,71,6426	TT,TC,CC		0.0698,1.4793,0.5464	possibly-damaging	224/481	4810583	71,12923	2197	4300	6497	SO:0001583	missense	26048	exon5			AGTTCACGGGCAC	AB011129	CCDS32383.1	16p13.3	2013-01-09				ENSG00000103199		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	23716	protein-coding gene	gene with protein product						9628581	Standard	XM_005255243		Approved	ZKSCAN18, KIAA0557, ZSCAN50	uc002cxp.1	O60304		ENST00000219478.6:c.670G>A	16.37:g.4810583C>T	ENSP00000219478:p.Val224Met	103.0	0.0	0		108.0	45.0	0.416667	NM_021646	A8K6X7|B4DNN9|Q0VAL2|Q96CQ8|Q9BTG0	Missense_Mutation	SNP	ENST00000219478.6	37	CCDS32383.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	C	14.40	2.524884	0.44969	0.014793	6.98E-4	ENSG00000103199	ENST00000545009;ENST00000219478	T;T	0.05925	3.37;3.37	3.16	3.16	0.36331	Krueppel-associated box (3);	.	.	.	.	T	0.11495	0.0280	L	0.51853	1.615	0.21445	N	0.99968	D;D	0.76494	0.995;0.999	P;P	0.61874	0.82;0.895	T	0.04165	-1.0972	9	0.48119	T	0.1	.	12.1628	0.54113	0.0:1.0:0.0:0.0	.	224;224	B4DNN9;O60304	.;ZN500_HUMAN	M	224	ENSP00000445714:V224M;ENSP00000219478:V224M	ENSP00000219478:V224M	V	-	1	0	ZNF500	4750584	0.000000	0.05858	0.066000	0.19879	0.003000	0.03518	0.802000	0.27069	1.785000	0.52413	0.655000	0.94253	GTG	C|0.995;T|0.005	0.005	strong		0.632	ZNF500-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432461.1	XM_085507	
ZNF594	84622	hgsc.bcm.edu	37	17	5085758	5085758	+	Silent	SNP	G	G	A	rs144567321		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5085758G>A	ENST00000399604.4	-	1	1934	c.1794C>T	c.(1792-1794)tgC>tgT	p.C598C	ZNF594_ENST00000575779.1_Silent_p.C598C			Q96JF6	ZN594_HUMAN	zinc finger protein 594	598					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.C598C(1)		NS(1)|breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						CACATTCTTTGCATTCATATG	0.413																																					p.C598C		Atlas-SNP	.											ZNF594,colon,carcinoma,-2,3	ZNF594	89	3	1	Substitution - coding silent(1)	ovary(1)	c.C1794T						PASS	.						163.0	165.0	165.0					17																	5085758		2036	4211	6247	SO:0001819	synonymous_variant	84622	exon2			TTCTTTGCATTCA	AB058774	CCDS42241.1	17p13	2013-01-08			ENSG00000180626	ENSG00000180626		"""Zinc fingers, C2H2-type"""	29392	protein-coding gene	gene with protein product						11347906	Standard	NM_032530		Approved	KIAA1871	uc010cla.1	Q96JF6	OTTHUMG00000132059	ENST00000399604.4:c.1794C>T	17.37:g.5085758G>A		138.0	0.0	0		92.0	16.0	0.173913	NM_032530	Q6RFS0	Silent	SNP	ENST00000399604.4	37	CCDS42241.1																																																																																			G|0.994;A|0.006	0.006	strong		0.413	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737	
COMMD8	54951	hgsc.bcm.edu	37	4	47462210	47462210	+	Missense_Mutation	SNP	A	A	C	rs114141818	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:47462210A>C	ENST00000381571.4	-	2	240	c.173T>G	c.(172-174)aTt>aGt	p.I58S		NM_017845.3	NP_060315.1	Q9NX08	COMD8_HUMAN	COMM domain containing 8	58										large_intestine(2)|lung(5)|prostate(1)	8						AAATTTGGCAATATCTTCTAA	0.353													a|||	64	0.0127796	0.0469	0.0029	5008	,	,		16655	0.0		0.0	False		,,,				2504	0.0				p.I58S		Atlas-SNP	.											.	COMMD8	15	.	0			c.T173G						PASS	.	G	SER/ILE	201,4205	126.1+/-163.2	3,195,2005	104.0	106.0	106.0		173	1.7	0.0	4	dbSNP_132	106	2,8598		0,2,4298	yes	missense	COMMD8	NM_017845.3	142	3,197,6303	CC,CA,AA		0.0233,4.562,1.5608	benign	58/184	47462210	203,12803	2203	4300	6503	SO:0001583	missense	54951	exon2			TTGGCAATATCTT	AY542163	CCDS3475.1	4p12	2008-02-05			ENSG00000169019	ENSG00000169019			26036	protein-coding gene	gene with protein product						15799966	Standard	NM_017845		Approved	FLJ20502	uc003gxi.3	Q9NX08	OTTHUMG00000099435	ENST00000381571.4:c.173T>G	4.37:g.47462210A>C	ENSP00000370984:p.Ile58Ser	119.0	0.0	0		108.0	108.0	1	NM_017845	Q8WUR4|Q9HC15	Missense_Mutation	SNP	ENST00000381571.4	37	CCDS3475.1	20	0.009157509157509158	20	0.04065040650406504	0	0.0	0	0.0	0	0.0	a	1.694	-0.503300	0.04261	0.04562	2.33E-4	ENSG00000169019	ENST00000381571	T	0.11277	2.79	5.57	1.71	0.24356	.	0.431904	0.26832	N	0.022272	T	0.01189	0.0039	L	0.35723	1.085	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.28933	-1.0028	10	0.44086	T	0.13	-30.318	8.7378	0.34539	0.6292:0.0:0.3708:0.0	.	58	Q9NX08	COMD8_HUMAN	S	58	ENSP00000370984:I58S	ENSP00000370984:I58S	I	-	2	0	COMMD8	47156967	0.102000	0.21896	0.018000	0.16275	0.009000	0.06853	1.363000	0.34159	0.090000	0.17273	-0.253000	0.11424	ATT	A|0.985;C|0.015	0.015	strong		0.353	COMMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216898.2	NM_017845	
FJX1	24147	hgsc.bcm.edu	37	11	35641428	35641428	+	Missense_Mutation	SNP	G	G	A	rs12286850	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:35641428G>A	ENST00000317811.4	+	1	1694	c.1244G>A	c.(1243-1245)cGc>cAc	p.R415H	FJX1_ENST00000532914.1_3'UTR	NM_014344.3	NP_055159.2	Q86VR8	FJX1_HUMAN	four jointed box 1 (Drosophila)	415			R -> H (in dbSNP:rs12286850).		retina layer formation (GO:0010842)	extracellular space (GO:0005615)				lung(1)|urinary_tract(1)	2	all_cancers(35;0.177)|all_lung(20;0.0238)|Lung NSC(22;0.0494)|all_epithelial(35;0.0739)	all_hematologic(20;0.107)				CTGCTACAGCGCCGCCTCGAC	0.667													G|||	358	0.0714856	0.2617	0.0159	5008	,	,		13330	0.0		0.001	False		,,,				2504	0.0				p.R415H	Melanoma(161;10 2587 27165 47356)	Atlas-SNP	.											.	FJX1	32	.	0			c.G1244A						PASS	.	G	HIS/ARG	717,3093		68,581,1256	6.0	7.0	7.0		1244	4.3	1.0	11	dbSNP_120	7	9,8147		0,9,4069	yes	missense	FJX1	NM_014344.3	29	68,590,5325	AA,AG,GG		0.1103,18.8189,6.0672	probably-damaging	415/438	35641428	726,11240	1905	4078	5983	SO:0001583	missense	24147	exon1			TACAGCGCCGCCT	AJ245599	CCDS44570.1	11p13	2012-05-18				ENSG00000179431			17166	protein-coding gene	gene with protein product	"""putative secreted ligand homologous to fjx1"""	612206				7647465, 10072791	Standard	NM_014344		Approved	FLJ22416, FLJ25593	uc001mwh.3	Q86VR8		ENST00000317811.4:c.1244G>A	11.37:g.35641428G>A	ENSP00000400223:p.Arg415His	57.0	0.0	0		47.0	27.0	0.574468	NM_014344	B2RCA9|Q9UGK6	Missense_Mutation	SNP	ENST00000317811.4	37	CCDS44570.1	124	0.056776556776556776	118	0.23983739837398374	6	0.016574585635359115	0	0.0	0	0.0	G	13.12	2.141657	0.37825	0.188189	0.001103	ENSG00000179431	ENST00000317811	T	0.80480	-1.38	5.21	4.29	0.51040	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.35833	P	0.174551	B	0.11235	0.004	B	0.08055	0.003	T	0.03354	-1.1045	8	0.51188	T	0.08	-3.1322	7.4212	0.27073	0.1565:0.1395:0.7039:0.0	rs12286850	415	Q86VR8	FJX1_HUMAN	H	415	ENSP00000400223:R415H	ENSP00000400223:R415H	R	+	2	0	FJX1	35598004	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.527000	0.45615	1.184000	0.42957	0.555000	0.69702	CGC	G|0.908;A|0.092	0.092	strong		0.667	FJX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389078.1	NM_014344	
SP110	3431	hgsc.bcm.edu	37	2	231065630	231065630	+	Missense_Mutation	SNP	G	G	A	rs59573011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:231065630G>A	ENST00000358662.4	-	10	1178	c.1100C>T	c.(1099-1101)aCg>aTg	p.T367M	SP110_ENST00000540870.1_Missense_Mutation_p.T373M|SP110_ENST00000258381.6_Missense_Mutation_p.T367M|SP110_ENST00000486146.2_5'Flank|SP110_ENST00000392048.3_Missense_Mutation_p.T365M|SP110_ENST00000338556.3_Missense_Mutation_p.T69M|SP110_ENST00000258382.5_Missense_Mutation_p.T367M	NM_004509.3	NP_004500	Q9HB58	SP110_HUMAN	SP110 nuclear body protein	367			T -> M (in dbSNP:rs59573011). {ECO:0000269|PubMed:16816019}.		regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			breast(4)|endometrium(3)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Renal(207;0.0112)|all_lung(227;0.0223)|Lung NSC(271;0.0983)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.169)		Epithelial(121;2.61e-12)|all cancers(144;6.39e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.0097)		TGTACTAGGCGTCTTCTGGGA	0.443													G|||	83	0.0165735	0.0598	0.0058	5008	,	,		18713	0.0		0.0	False		,,,				2504	0.0				p.T373M		Atlas-SNP	.											.	SP110	105	.	0			c.C1118T						PASS	.	G	MET/THR,MET/THR,MET/THR,MET/THR	231,4175	137.7+/-173.5	9,213,1981	228.0	200.0	210.0		1118,1100,1100,1100	-0.6	0.0	2	dbSNP_129	210	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense,missense	SP110	NM_001185015.1,NM_004509.3,NM_004510.3,NM_080424.2	81,81,81,81	9,215,6279	AA,AG,GG		0.0233,5.2429,1.7915	probably-damaging,probably-damaging,probably-damaging,probably-damaging	373/556,367/690,367/550,367/714	231065630	233,12773	2203	4300	6503	SO:0001583	missense	3431	exon11			CTAGGCGTCTTCT	L22343	CCDS2474.1, CCDS2475.1, CCDS2476.1, CCDS54435.1	2q37.1	2014-09-17	2001-12-19	2001-12-20	ENSG00000135899	ENSG00000135899			5401	protein-coding gene	gene with protein product		604457	"""interferon-induced protein 41, 30kD"""	IFI41, IFI75		7693701, 10388521	Standard	NM_080424		Approved		uc002vqg.3	Q9HB58	OTTHUMG00000133204	ENST00000358662.4:c.1100C>T	2.37:g.231065630G>A	ENSP00000351488:p.Thr367Met	167.0	0.0	0		196.0	86.0	0.438776	NM_001185015	B4DVI4|F5H1M1|Q14976|Q14977|Q53TG2|Q8WUZ6|Q9HCT8	Missense_Mutation	SNP	ENST00000358662.4	37	CCDS2474.1	29	0.013278388278388278	26	0.052845528455284556	3	0.008287292817679558	0	0.0	0	0.0	G	12.50	1.957341	0.34565	0.052429	2.33E-4	ENSG00000135899	ENST00000258381;ENST00000358662;ENST00000392048;ENST00000258382;ENST00000540870;ENST00000338556	T;T;T;T;T;T	0.65364	1.07;0.92;-0.15;-0.15;-0.15;2.46	2.49	-0.633	0.11519	.	.	.	.	.	T	0.11580	0.0282	N	0.22421	0.69	0.09310	N	1	D;D;D;D;P	0.67145	0.985;0.996;0.985;0.994;0.512	P;P;P;B;B	0.48030	0.541;0.564;0.541;0.389;0.047	T	0.10730	-1.0617	9	0.51188	T	0.08	.	2.8987	0.05699	0.3085:0.2426:0.4489:0.0	rs59573011	365;69;373;367;367	G5E9C0;E7ER70;F5H1M1;Q9HB58;Q9HB58-6	.;.;.;SP110_HUMAN;.	M	367;367;365;367;373;69	ENSP00000258381:T367M;ENSP00000351488:T367M;ENSP00000375902:T365M;ENSP00000258382:T367M;ENSP00000439558:T373M;ENSP00000344049:T69M	ENSP00000258381:T367M	T	-	2	0	SP110	230773874	0.014000	0.17966	0.025000	0.17156	0.009000	0.06853	-0.059000	0.11731	-0.148000	0.11234	0.557000	0.71058	ACG	G|0.980;A|0.020	0.020	strong		0.443	SP110-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000332414.1	NM_080424	
LHFP	10186	hgsc.bcm.edu	37	13	40175311	40175311	+	Silent	SNP	G	G	A	rs34616166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:40175311G>A	ENST00000379589.3	-	2	505	c.43C>T	c.(43-45)Ctg>Ttg	p.L15L	LHFP_ENST00000495922.1_5'Flank	NM_005780.2	NP_005771.1	Q9Y693	LHFP_HUMAN	lipoma HMGIC fusion partner	15						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)		HMGA2/LHFP(2)	breast(1)|endometrium(2)|large_intestine(1)|liver(1)|lung(6)|prostate(2)	13		Lung NSC(96;3.55e-06)|Breast(139;0.00408)|Ovarian(182;0.0107)|Prostate(109;0.0118)|Lung SC(185;0.0719)|Hepatocellular(188;0.114)		OV - Ovarian serous cystadenocarcinoma(117;6.48e-46)|Epithelial(112;8.43e-42)|all cancers(112;1.42e-36)|GBM - Glioblastoma multiforme(144;0.00187)|BRCA - Breast invasive adenocarcinoma(63;0.00886)|KIRC - Kidney renal clear cell carcinoma(186;0.048)|Kidney(163;0.0601)|LUSC - Lung squamous cell carcinoma(192;0.105)		AGAAAAGACAGCAAAGCCCAG	0.537			T	HMGA2	lipoma								G|||	341	0.0680911	0.2466	0.0159	5008	,	,		20157	0.0		0.004	False		,,,				2504	0.0				p.L15L		Atlas-SNP	.		Dom	yes		13	13q12	10186	lipoma HMGIC fusion partner		M	.	LHFP	31	.	0			c.C43T						PASS	.	G		827,3579	318.0+/-295.4	77,673,1453	66.0	59.0	61.0		43	5.4	1.0	13	dbSNP_126	61	10,8590	7.1+/-27.0	0,10,4290	no	coding-synonymous	LHFP	NM_005780.2		77,683,5743	AA,AG,GG		0.1163,18.7699,6.4355		15/201	40175311	837,12169	2203	4300	6503	SO:0001819	synonymous_variant	10186	exon2			AAGACAGCAAAGC	AF098807	CCDS9369.1	13q12	2008-07-18			ENSG00000183722	ENSG00000183722			6586	protein-coding gene	gene with protein product		606710				10329012	Standard	NM_005780		Approved	MGC22429	uc001uxf.3	Q9Y693	OTTHUMG00000016767	ENST00000379589.3:c.43C>T	13.37:g.40175311G>A		89.0	0.0	0		123.0	70.0	0.569106	NM_005780	B2R7M2|Q53FC0|Q96SH5	Silent	SNP	ENST00000379589.3	37	CCDS9369.1																																																																																			G|0.941;A|0.059	0.059	strong		0.537	LHFP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044619.1	NM_005780	
URB2	9816	hgsc.bcm.edu	37	1	229787055	229787055	+	Missense_Mutation	SNP	G	G	A	rs41310553	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229787055G>A	ENST00000258243.2	+	8	4359	c.4223G>A	c.(4222-4224)cGg>cAg	p.R1408Q		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	1408						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						CGGGAAGGGCGGCAGAAGGAC	0.388													G|||	41	0.0081869	0.0083	0.0159	5008	,	,		17462	0.0		0.0139	False		,,,				2504	0.0051				p.R1408Q		Atlas-SNP	.											.	URB2	152	.	0			c.G4223A						PASS	.	G	GLN/ARG	58,4348	56.8+/-93.2	0,58,2145	87.0	84.0	85.0		4223	4.9	1.0	1	dbSNP_127	85	149,8451	72.9+/-135.5	1,147,4152	yes	missense	URB2	NM_014777.2	43	1,205,6297	AA,AG,GG		1.7326,1.3164,1.5916	probably-damaging	1408/1525	229787055	207,12799	2203	4300	6503	SO:0001583	missense	9816	exon8			AAGGGCGGCAGAA	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.4223G>A	1.37:g.229787055G>A	ENSP00000258243:p.Arg1408Gln	121.0	0.0	0		115.0	63.0	0.547826	NM_014777	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	37	CCDS31052.1	20	0.009157509157509158	3	0.006097560975609756	7	0.019337016574585635	0	0.0	10	0.013192612137203167	G	25.7	4.661699	0.88154	0.013164	0.017326	ENSG00000135763	ENST00000258243;ENST00000434387	T;T	0.45668	0.89;0.89	5.78	4.86	0.63082	Nucleolar 27S pre-rRNA processing, Urb2/Npa2, C-terminal (1);	0.116848	0.53938	D	0.000042	T	0.46210	0.1381	M	0.69823	2.125	0.40363	D	0.97926	D	0.89917	1.0	D	0.69824	0.966	T	0.59968	-0.7354	9	.	.	.	-18.2991	14.7398	0.69445	0.0695:0.0:0.9305:0.0	rs41310553	1408	Q14146	URB2_HUMAN	Q	1408;24	ENSP00000258243:R1408Q;ENSP00000395107:R24Q	.	R	+	2	0	URB2	227853678	0.967000	0.33354	0.971000	0.41717	0.989000	0.77384	5.262000	0.65501	1.435000	0.47434	0.655000	0.94253	CGG	G|0.986;A|0.014	0.014	strong		0.388	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777	
PCDHA13	56136	hgsc.bcm.edu	37	5	140264091	140264091	+	Silent	SNP	G	G	C	rs10076265	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140264091G>C	ENST00000289272.2	+	1	2238	c.2238G>C	c.(2236-2238)ggG>ggC	p.G746G	PCDHA11_ENST00000398640.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA13_ENST00000409494.1_Silent_p.G746G|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA3_ENST00000522353.2_Intron	NM_018904.2|NM_031865.1	NP_061727.1|NP_114071.1	Q9Y5I0	PCDAD_HUMAN	protocadherin alpha 13	746	6 X 4 AA repeats of P-X-X-P.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|biliary_tract(2)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(18)|liver(3)|lung(23)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(2)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGCGGCAGGGAGTTGGTCGT	0.677													g|||	74	0.0147764	0.053	0.0058	5008	,	,		14743	0.0		0.0	False		,,,				2504	0.0				p.G746G	Melanoma(147;1739 1852 5500 27947 37288)	Atlas-SNP	.											PCDHA13,colon,carcinoma,+2,1	PCDHA13	213	1	0			c.G2238C						PASS	.	G	,,,,,,,,,,,,,,,,	248,4158	136.5+/-172.5	6,236,1961	48.0	53.0	52.0		,,,,2238,,,,,,,,,,,,2238	2.8	1.0	5	dbSNP_119	52	1,8599	1.2+/-3.3	0,1,4299	no	intron,intron,intron,intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018904.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031865.1	,,,,,,,,,,,,,,,,	6,237,6260	CC,CG,GG		0.0116,5.6287,1.9145	,,,,,,,,,,,,,,,,	,,,,746/951,,,,,,,,,,,,746/808	140264091	249,12757	2203	4300	6503	SO:0001819	synonymous_variant	56136	exon1			GGCAGGGAGTTGG	AF152478	CCDS4240.1	5q31	2010-11-26			ENSG00000239389	ENSG00000239389		"""Cadherins / Protocadherins : Clustered"""	8667	other	complex locus constituent	"""KIAA0345-like 1"", ""ortholog of mouse CNR5"""	606319		CNRS5		10380929, 10662547	Standard	NM_018904		Approved	CNR5, CRNR5, CNRN5, PCDH-ALPHA13		Q9Y5I0	OTTHUMG00000129614	ENST00000289272.2:c.2238G>C	5.37:g.140264091G>C		153.0	0.0	0		159.0	83.0	0.522013	NM_031865	O75277	Silent	SNP	ENST00000289272.2	37	CCDS4240.1																																																																																			G|0.982;C|0.018	0.018	strong		0.677	PCDHA13-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335000.1	NM_018904	
ZNF578	147660	hgsc.bcm.edu	37	19	53014492	53014492	+	Silent	SNP	T	T	A	rs145508251	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53014492T>A	ENST00000421239.2	+	6	1102	c.858T>A	c.(856-858)ccT>ccA	p.P286P	CTD-3099C6.5_ENST00000599143.1_RNA	NM_001099694.1	NP_001093164.1	Q96N58	ZN578_HUMAN	zinc finger protein 578	286					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)								GBM - Glioblastoma multiforme(134;0.00819)|OV - Ovarian serous cystadenocarcinoma(262;0.01)		GTGAGAAACCTTACAAGTGTA	0.378													T|||	51	0.0101837	0.0363	0.0029	5008	,	,		24259	0.0		0.001	False		,,,				2504	0.0				p.P286P		Atlas-SNP	.											.	.	.	.	0			c.T858A						PASS	.	T		92,4314		0,92,2111	111.0	115.0	114.0		858	-0.1	0.3	19	dbSNP_134	114	8,8590		0,8,4291	no	coding-synonymous	ZNF578	NM_001099694.1		0,100,6402	AA,AT,TT		0.093,2.0881,0.769		286/591	53014492	100,12904	2203	4299	6502	SO:0001819	synonymous_variant	147660	exon6			GAAACCTTACAAG	AK095562	CCDS54310.1	19q13.41	2013-09-20			ENSG00000258405	ENSG00000258405		"""Zinc fingers, C2H2-type"", ""-"""	26449	protein-coding gene	gene with protein product							Standard	NM_001099694		Approved	FLJ31384	uc002pzp.4	Q96N58	OTTHUMG00000156468	ENST00000421239.2:c.858T>A	19.37:g.53014492T>A		106.0	0.0	0		153.0	68.0	0.444444	NM_001099694	B4DR51|I3L1Y6	Silent	SNP	ENST00000421239.2	37	CCDS54310.1																																																																																			T|0.993;A|0.007	0.007	strong		0.378	ZNF578-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344298.3	NM_152472	
PCDHGA4	56111	hgsc.bcm.edu	37	5	140736328	140736328	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140736328G>A	ENST00000571252.1	+	1	1561	c.1561G>A	c.(1561-1563)Gac>Aac	p.D521N	PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018917.2	NP_061740	Q9Y5G9	PCDG4_HUMAN	protocadherin gamma subfamily A, 4	521	Cadherin 5. {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)			TTGCTCCTTCGACTATGAGCA	0.527																																					p.D521N		Atlas-SNP	.											.	PCDHGA4	150	.	0			c.G1561A						PASS	.						131.0	140.0	137.0					5																	140736328		2131	4270	6401	SO:0001583	missense	56111	exon1			TCCTTCGACTATG	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.1561G>A	5.37:g.140736328G>A	ENSP00000458570:p.Asp521Asn	129.0	0.0	0		142.0	73.0	0.514085	NM_018917	Q9Y5D3	Missense_Mutation	SNP	ENST00000571252.1	37	CCDS58979.1																																																																																			.	.	none		0.527	PCDHGA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437959.1	NM_018917	
SAMD4B	55095	hgsc.bcm.edu	37	19	39873877	39873877	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39873877A>G	ENST00000314471.6	+	15	3037	c.2002A>G	c.(2002-2004)Atc>Gtc	p.I668V	SAMD4B_ENST00000596368.1_Intron|SAMD4B_ENST00000598913.1_Missense_Mutation_p.I668V	NM_018028.2	NP_060498.2	Q5PRF9	SMAG2_HUMAN	sterile alpha motif domain containing 4B	668					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(1)|endometrium(5)|large_intestine(1)|lung(4)|skin(1)|urinary_tract(2)	15	all_cancers(60;2.5e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;9.6e-28)|all cancers(26;9.14e-25)|Lung(45;0.000168)|LUSC - Lung squamous cell carcinoma(53;0.000199)			TGACCTGGAGATCAATCCCAC	0.577																																					p.I668V		Atlas-SNP	.											SAMD4B,NS,carcinoma,0,2	SAMD4B	48	2	0			c.A2002G						PASS	.						169.0	131.0	144.0					19																	39873877		2203	4300	6503	SO:0001583	missense	55095	exon15			CTGGAGATCAATC		CCDS33020.1	19q13.2	2013-01-10				ENSG00000179134		"""Sterile alpha motif (SAM) domain containing"""	25492	protein-coding gene	gene with protein product	"""smaug homolog B (Drosophila)"""					16221671	Standard	XM_005259029		Approved	FLJ10211, MGC99832, SMGB, hSmaug2	uc002olb.3	Q5PRF9		ENST00000314471.6:c.2002A>G	19.37:g.39873877A>G	ENSP00000317224:p.Ile668Val	169.0	0.0	0		160.0	76.0	0.475	NM_018028	A5Z0M6|Q6P194	Missense_Mutation	SNP	ENST00000314471.6	37	CCDS33020.1	.	.	.	.	.	.	.	.	.	.	A	21.7	4.187852	0.78789	.	.	ENSG00000179134	ENST00000314471	.	.	.	4.2	4.2	0.49525	.	0.000000	0.64402	D	0.000001	T	0.63379	0.2506	L	0.43152	1.355	0.43846	D	0.996437	P;P	0.43314	0.803;0.803	P;P	0.55824	0.785;0.785	T	0.66559	-0.5893	9	0.87932	D	0	.	11.256	0.49054	1.0:0.0:0.0:0.0	.	668;668	Q5PRF9;A5Z0M6	SMAG2_HUMAN;.	V	668	.	ENSP00000317224:I668V	I	+	1	0	SAMD4B	44565717	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	8.422000	0.90262	1.774000	0.52232	0.240000	0.17902	ATC	.	.	none		0.577	SAMD4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464467.1	NM_018028	
MT-ND5	4540	hgsc.bcm.edu	37	M	13650	13650	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:13650C>T	ENST00000361567.2	+	1	1314	c.1314C>T	c.(1312-1314)ccC>ccT	p.P438P	MT-TT_ENST00000387460.2_RNA|MT-TE_ENST00000387459.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	438					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						CCTCGCTTCCCCACCCTTACT	0.478																																					p.P438P		Atlas-SNP	.											.	.	.	.	0			c.C1314T						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			CTTCCCCACCCTT			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1314C>T	M.37:g.13650C>T		8.0	0.0	0		9.0	9.0	1	ENST00000361567	Q34773|Q8WCY3	Silent	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.478	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
GAD1	2571	hgsc.bcm.edu	37	2	171713564	171713564	+	Silent	SNP	C	C	T	rs769392	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:171713564C>T	ENST00000358196.3	+	15	2000	c.1450C>T	c.(1450-1452)Ctg>Ttg	p.L484L		NM_000817.2	NP_000808.2	Q99259	DCE1_HUMAN	glutamate decarboxylase 1 (brain, 67kDa)	484					gamma-aminobutyric acid biosynthetic process (GO:0009449)|glutamate catabolic process (GO:0006538)|glutamate decarboxylation to succinate (GO:0006540)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|protein-pyridoxal-5-phosphate linkage (GO:0018352)|response to drug (GO:0042493)|synaptic transmission (GO:0007268)	clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	glutamate binding (GO:0016595)|glutamate decarboxylase activity (GO:0004351)|pyridoxal phosphate binding (GO:0030170)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(15)|ovary(1)|urinary_tract(2)	35						CAACAAATGCCTGGAACTGGC	0.418													C|||	213	0.0425319	0.1505	0.0202	5008	,	,		19163	0.0		0.0	False		,,,				2504	0.0				p.L484L		Atlas-SNP	.											.	GAD1	79	.	0			c.C1450T						PASS	.	C		566,3840	254.3+/-259.9	31,504,1668	162.0	175.0	171.0		1450	1.6	1.0	2	dbSNP_98	171	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	GAD1	NM_000817.2		31,507,5965	TT,TC,CC		0.0349,12.8461,4.3749		484/595	171713564	569,12437	2203	4300	6503	SO:0001819	synonymous_variant	2571	exon15			AAATGCCTGGAAC		CCDS2239.1, CCDS2240.1	2q31	2008-02-05	2002-08-29		ENSG00000128683	ENSG00000128683	4.1.1.15		4092	protein-coding gene	gene with protein product		605363	"""glutamate decarboxylase 1 (brain, 67kD)"""	GAD		1549570	Standard	XM_005246443		Approved		uc002ugi.3	Q99259	OTTHUMG00000044175	ENST00000358196.3:c.1450C>T	2.37:g.171713564C>T		65.0	0.0	0		73.0	27.0	0.369863	NM_000817	Q49AK1|Q53TQ7|Q9BU91|Q9UHH4	Silent	SNP	ENST00000358196.3	37	CCDS2239.1																																																																																			C|0.959;T|0.041	0.041	strong		0.418	GAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102664.2		
ERO1LB	56605	hgsc.bcm.edu	37	1	236381833	236381833	+	Silent	SNP	A	A	G	rs11811758	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:236381833A>G	ENST00000354619.5	-	16	1588	c.1387T>C	c.(1387-1389)Tta>Cta	p.L463L	GPR137B_ENST00000477559.1_Intron	NM_019891.3	NP_063944.3	Q86YB8	ERO1B_HUMAN	ERO1-like beta (S. cerevisiae)	463					4-hydroxyproline metabolic process (GO:0019471)|cell redox homeostasis (GO:0045454)|extracellular matrix organization (GO:0030198)|glucose homeostasis (GO:0042593)|insulin processing (GO:0030070)|protein folding (GO:0006457)|protein maturation by protein folding (GO:0022417)	endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor (GO:0016671)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|unfolded protein binding (GO:0051082)			NS(1)|endometrium(3)|large_intestine(8)|lung(8)|skin(2)|urinary_tract(1)	23	Ovarian(103;0.0634)|Breast(184;0.247)	all_cancers(173;0.123)|Acute lymphoblastic leukemia(190;0.205)|Prostate(94;0.219)	OV - Ovarian serous cystadenocarcinoma(106;0.00162)		Flavin adenine dinucleotide(DB03147)	CTGTGTTGTAATAAGACTTTA	0.318													A|||	231	0.0461262	0.1626	0.0216	5008	,	,		15266	0.0		0.001	False		,,,				2504	0.0				p.L463L		Atlas-SNP	.											.	ERO1LB	48	.	0			c.T1387C						PASS	.	A		620,3778	261.0+/-264.0	45,530,1624	57.0	63.0	61.0		1387	-4.8	0.8	1	dbSNP_120	61	8,8554	6.4+/-24.3	0,8,4273	no	coding-synonymous	ERO1LB	NM_019891.3		45,538,5897	GG,GA,AA		0.0934,14.0973,4.8457		463/468	236381833	628,12332	2199	4281	6480	SO:0001819	synonymous_variant	56605	exon16			GTTGTAATAAGAC	AF252538	CCDS31064.1	1q42.2-q43	2008-02-05			ENSG00000086619	ENSG00000086619			14355	protein-coding gene	gene with protein product		615437				10818100	Standard	NM_019891		Approved	ERO1-L(beta)	uc001hxt.3	Q86YB8	OTTHUMG00000039955	ENST00000354619.5:c.1387T>C	1.37:g.236381833A>G		244.0	0.0	0		216.0	121.0	0.560185	NM_019891	B4DF57|Q5T1H4|Q8IZ11|Q9NR62	Silent	SNP	ENST00000354619.5	37	CCDS31064.1																																																																																			A|0.961;G|0.039	0.039	strong		0.318	ERO1LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096371.1	NM_019891	
GXYLT2	727936	hgsc.bcm.edu	37	3	72971414	72971414	+	Silent	SNP	A	A	G	rs61741329	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:72971414A>G	ENST00000389617.4	+	3	689	c.528A>G	c.(526-528)acA>acG	p.T176T		NM_001080393.1	NP_001073862.1	A0PJZ3	GXLT2_HUMAN	glucoside xylosyltransferase 2	176					O-glycan processing (GO:0016266)	integral component of membrane (GO:0016021)	UDP-xylosyltransferase activity (GO:0035252)			NS(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	18						ACCCCATCACATTTTCTGTTG	0.448													A|||	177	0.0353435	0.1256	0.0159	5008	,	,		18993	0.0		0.0	False		,,,				2504	0.0				p.T176T		Atlas-SNP	.											.	GXYLT2	43	.	0			c.A528G						PASS	.	A		362,3352		19,324,1514	210.0	215.0	213.0		528	-2.9	1.0	3	dbSNP_129	213	4,8206		0,4,4101	no	coding-synonymous	GXYLT2	NM_001080393.1		19,328,5615	GG,GA,AA		0.0487,9.7469,3.0694		176/444	72971414	366,11558	1857	4105	5962	SO:0001819	synonymous_variant	727936	exon3			CATCACATTTTCT	AC098481	CCDS46870.1	3p13	2013-02-22	2009-11-17	2009-11-17	ENSG00000172986	ENSG00000172986		"""Glycosyltransferase family 8 domain containing"""	33383	protein-coding gene	gene with protein product		613322	"""glycosyltransferase 8 domain containing 4"""	GLT8D4		19940119	Standard	NM_001080393		Approved		uc003dpg.3	A0PJZ3	OTTHUMG00000158815	ENST00000389617.4:c.528A>G	3.37:g.72971414A>G		148.0	0.0	0		131.0	60.0	0.458015	NM_001080393		Silent	SNP	ENST00000389617.4	37	CCDS46870.1																																																																																			A|0.976;G|0.024	0.024	strong		0.448	GXYLT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352318.1	NM_001080393	
TTC39B	158219	hgsc.bcm.edu	37	9	15191209	15191209	+	Silent	SNP	A	A	G	rs74818741	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:15191209A>G	ENST00000512701.2	-	10	1011	c.975T>C	c.(973-975)ttT>ttC	p.F325F	TTC39B_ENST00000541445.1_3'UTR|TTC39B_ENST00000355694.2_Silent_p.F259F|TTC39B_ENST00000297615.5_Silent_p.F256F|TTC39B_ENST00000380850.4_Silent_p.F325F|TTC39B_ENST00000507993.1_Silent_p.F160F|TTC39B_ENST00000507285.1_Silent_p.F160F			Q5VTQ0	TT39B_HUMAN	tetratricopeptide repeat domain 39B	325										NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)	21						AAAATCCAATAAATTCTAGTA	0.323													A|||	137	0.0273562	0.1014	0.0043	5008	,	,		17741	0.0		0.0	False		,,,				2504	0.0				p.F325F		Atlas-SNP	.											.	TTC39B	83	.	0			c.T975C						PASS	.	A	,,,,	346,4060	176.9+/-206.0	13,320,1870	69.0	73.0	72.0		969,975,768,480,975	1.3	1.0	9	dbSNP_132	72	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTC39B	NM_001168339.1,NM_001168340.1,NM_001168341.1,NM_001168342.1,NM_152574.2	,,,,	13,321,6168	GG,GA,AA		0.0116,7.8529,2.6684	,,,,	323/681,325/670,256/614,160/518,325/683	15191209	347,12657	2203	4299	6502	SO:0001819	synonymous_variant	158219	exon10			TCCAATAAATTCT	AK091187	CCDS6477.1, CCDS6477.2, CCDS55294.1, CCDS55295.1, CCDS55296.1	9p22.2	2013-01-11	2008-06-23	2008-06-23	ENSG00000155158	ENSG00000155158		"""Tetratricopeptide (TTC) repeat domain containing"""	23704	protein-coding gene	gene with protein product		613574	"""chromosome 9 open reading frame 52"""	C9orf52			Standard	NM_001168339		Approved	FLJ33868	uc003zlr.2	Q5VTQ0	OTTHUMG00000019581	ENST00000512701.2:c.975T>C	9.37:g.15191209A>G		110.0	0.0	0		98.0	49.0	0.5	NM_001168340	A5PLN1|B4DQ10|B4DQX4|B4DW93|Q8IVR7|Q8IXZ6|Q8N267	Silent	SNP	ENST00000512701.2	37	CCDS6477.2																																																																																			A|0.969;G|0.031	0.031	strong		0.323	TTC39B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051758.3	NM_152574	
FAM208A	23272	hgsc.bcm.edu	37	3	56667213	56667213	+	Silent	SNP	T	T	C	rs34828128	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:56667213T>C	ENST00000493960.2	-	18	3616	c.3606A>G	c.(3604-3606)caA>caG	p.Q1202Q	FAM208A_ENST00000431842.2_Silent_p.Q765Q|FAM208A_ENST00000355628.5_Silent_p.Q1141Q	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	1202							poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(11)|prostate(3)|skin(1)	32						AAAGAGCTGGTTGAGCAGAAA	0.353													T|||	31	0.0061901	0.0	0.0101	5008	,	,		18670	0.0		0.0149	False		,,,				2504	0.0092				p.Q1202Q		Atlas-SNP	.											.	FAM208A	113	.	0			c.A3606G						PASS	.	T	,	17,4389	24.3+/-50.5	0,17,2186	114.0	116.0	115.0		3606,2295	-1.5	1.0	3	dbSNP_126	115	154,8446	73.8+/-136.5	3,148,4149	no	coding-synonymous,coding-synonymous	FAM208A	NM_001112736.1,NM_015224.3	,	3,165,6335	CC,CT,TT		1.7907,0.3858,1.3148	,	1202/1513,765/1234	56667213	171,12835	2203	4300	6503	SO:0001819	synonymous_variant	23272	exon18			AGCTGGTTGAGCA	AF180425	CCDS2877.1, CCDS46853.1	3p14.3	2011-09-14	2011-09-14	2011-09-14	ENSG00000163946	ENSG00000163946			30314	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 63"""	C3orf63		10470851, 11149944	Standard	NM_015224		Approved	se89-1, RAP140, KIAA1105	uc003die.4	Q9UK61	OTTHUMG00000158827	ENST00000493960.2:c.3606A>G	3.37:g.56667213T>C		179.0	0.0	0		156.0	68.0	0.435897	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Silent	SNP	ENST00000493960.2	37	CCDS46853.1																																																																																			T|0.987;C|0.013	0.013	strong		0.353	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224	
CACNA1S	779	hgsc.bcm.edu	37	1	201058428	201058428	+	Silent	SNP	G	G	A	rs61734621	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:201058428G>A	ENST00000362061.3	-	6	1084	c.858C>T	c.(856-858)taC>taT	p.Y286Y	CACNA1S_ENST00000367338.3_Silent_p.Y286Y	NM_000069.2	NP_000060.2	Q13698	CAC1S_HUMAN	calcium channel, voltage-dependent, L type, alpha 1S subunit	286					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport (GO:0006816)|endoplasmic reticulum organization (GO:0007029)|extraocular skeletal muscle development (GO:0002074)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|myoblast fusion (GO:0007520)|neuromuscular junction development (GO:0007528)|skeletal muscle adaptation (GO:0043501)|skeletal muscle fiber development (GO:0048741)|skeletal system development (GO:0001501)|striated muscle contraction (GO:0006941)	cytoplasm (GO:0005737)|I band (GO:0031674)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(19)|lung(37)|ovary(6)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	102					Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TAATGCACTGGTACACGGTGA	0.607													G|||	79	0.0157748	0.056	0.0058	5008	,	,		19962	0.0		0.0	False		,,,				2504	0.001				p.Y286Y		Atlas-SNP	.											.	CACNA1S	249	.	0			c.C858T						PASS	.	G		217,4189	134.9+/-171.1	6,205,1992	104.0	83.0	90.0		858	3.9	1.0	1	dbSNP_129	90	15,8585	11.2+/-40.8	0,15,4285	no	coding-synonymous	CACNA1S	NM_000069.2		6,220,6277	AA,AG,GG		0.1744,4.9251,1.7838		286/1874	201058428	232,12774	2203	4300	6503	SO:0001819	synonymous_variant	779	exon6			GCACTGGTACACG	L33798	CCDS1407.1	1q32	2012-03-07			ENSG00000081248	ENSG00000081248		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1397	protein-coding gene	gene with protein product		114208		HOKPP, MHS5, CACNL1A3		7916735, 16382099	Standard	NM_000069		Approved	Cav1.1, hypoPP	uc001gvv.3	Q13698	OTTHUMG00000035784	ENST00000362061.3:c.858C>T	1.37:g.201058428G>A		220.0	1.0	0.00454545		261.0	125.0	0.478927	NM_000069	A4IF51|B1ALM2|Q12896|Q13934	Silent	SNP	ENST00000362061.3	37	CCDS1407.1																																																																																			G|0.984;A|0.016	0.016	strong		0.607	CACNA1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087049.1	NM_000069	
SNAPC2	6618	hgsc.bcm.edu	37	19	7987428	7987428	+	Missense_Mutation	SNP	C	C	T	rs116635738	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7987428C>T	ENST00000221573.6	+	5	835	c.784C>T	c.(784-786)Cgc>Tgc	p.R262C	SNAPC2_ENST00000597584.1_Missense_Mutation_p.R25C	NM_003083.3	NP_003074.1	Q13487	SNPC2_HUMAN	small nuclear RNA activating complex, polypeptide 2, 45kDa	262					gene expression (GO:0010467)|snRNA transcription (GO:0009301)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|urinary_tract(1)	6						GACGTACCTACGCCTGACAGC	0.657													C|||	54	0.0107827	0.0356	0.0072	5008	,	,		16883	0.0		0.0	False		,,,				2504	0.002				p.R262C		Atlas-SNP	.											SNAPC2,colon,carcinoma,0,1	SNAPC2	20	1	0			c.C784T						PASS	.	C	CYS/ARG	140,4266	100.3+/-138.9	1,138,2064	71.0	70.0	70.0		784	2.2	0.0	19	dbSNP_132	70	4,8596	3.0+/-9.4	0,4,4296	yes	missense	SNAPC2	NM_003083.3	180	1,142,6360	TT,TC,CC		0.0465,3.1775,1.1072	possibly-damaging	262/335	7987428	144,12862	2203	4300	6503	SO:0001583	missense	6618	exon5			TACCTACGCCTGA	U44898	CCDS12190.1	19p13	2008-07-22	2002-08-29			ENSG00000104976			11135	protein-coding gene	gene with protein product		605076	"""small nuclear RNA activating complex, polypeptide 2, 45kD"""			8633057	Standard	NM_003083		Approved	SNAP45, PTFdelta	uc002miw.2	Q13487		ENST00000221573.6:c.784C>T	19.37:g.7987428C>T	ENSP00000221573:p.Arg262Cys	55.0	0.0	0		68.0	34.0	0.5	NM_003083	B2RBZ6|D6W663|Q13486	Missense_Mutation	SNP	ENST00000221573.6	37	CCDS12190.1	19	0.0086996336996337	16	0.032520325203252036	3	0.008287292817679558	0	0.0	0	0.0	c	14.33	2.503755	0.44558	0.031775	4.65E-4	ENSG00000104976	ENST00000221573	T	0.48836	0.8	4.44	2.15	0.27550	.	1.239960	0.05573	N	0.571328	T	0.19287	0.0463	N	0.22421	0.69	0.09310	N	1	D	0.67145	0.996	P	0.48227	0.571	T	0.30966	-0.9960	10	0.72032	D	0.01	-0.7906	8.8971	0.35472	0.4346:0.5654:0.0:0.0	.	262	Q13487	SNPC2_HUMAN	C	262	ENSP00000221573:R262C	ENSP00000221573:R262C	R	+	1	0	SNAPC2	7893428	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	0.478000	0.22212	1.074000	0.40909	-0.509000	0.04479	CGC	C|0.991;T|0.009	0.009	strong		0.657	SNAPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461358.1	NM_003083	
TMPRSS11F	389208	hgsc.bcm.edu	37	4	68938185	68938185	+	Missense_Mutation	SNP	C	C	T	rs1438391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:68938185C>T	ENST00000356291.2	-	5	429	c.370G>A	c.(370-372)Gat>Aat	p.D124N	UBA6-AS1_ENST00000500538.2_RNA|UBA6-AS1_ENST00000511571.1_RNA|UBA6-AS1_ENST00000499180.2_RNA	NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	124	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.		D -> N (in dbSNP:rs1438391).			extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(4)	39						ATAAGAATATCCACACCTTGT	0.303													C|||	190	0.0379393	0.1301	0.0216	5008	,	,		12334	0.0		0.003	False		,,,				2504	0.0				p.D124N		Atlas-SNP	.											.	TMPRSS11F	79	.	0			c.G370A						PASS	.	C	ASN/ASP	471,3935	220.0+/-237.6	24,423,1756	89.0	89.0	89.0		370	3.6	0.0	4	dbSNP_88	89	35,8565	22.8+/-68.1	0,35,4265	yes	missense	TMPRSS11F	NM_207407.2	23	24,458,6021	TT,TC,CC		0.407,10.69,3.8905	benign	124/439	68938185	506,12500	2203	4300	6503	SO:0001583	missense	389208	exon5			GAATATCCACACC	AK122625	CCDS3520.1	4q13.2	2010-04-13			ENSG00000198092	ENSG00000198092		"""Serine peptidases / Transmembrane"""	29994	protein-coding gene	gene with protein product							Standard	NM_207407		Approved	FLJ16046	uc003hdt.1	Q6ZWK6	OTTHUMG00000129307	ENST00000356291.2:c.370G>A	4.37:g.68938185C>T	ENSP00000348639:p.Asp124Asn	54.0	0.0	0		58.0	28.0	0.482759	NM_207407	A8MXX2	Missense_Mutation	SNP	ENST00000356291.2	37	CCDS3520.1	70	0.03205128205128205	61	0.12398373983739837	9	0.024861878453038673	0	0.0	0	0.0	C	1.216	-0.628370	0.03610	0.1069	0.00407	ENSG00000198092	ENST00000356291	T	0.37235	1.21	6.07	3.63	0.41609	SEA (3);	0.702903	0.13299	N	0.398399	T	0.00144	0.0004	N	0.01048	-1.04	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.26292	-1.0107	9	0.12103	T	0.63	.	5.8211	0.18528	0.0:0.0872:0.1681:0.7447	rs1438391;rs1438391	124	Q6ZWK6	TM11F_HUMAN	N	124	ENSP00000348639:D124N	ENSP00000348639:D124N	D	-	1	0	TMPRSS11F	68620780	0.556000	0.26538	0.016000	0.15963	0.005000	0.04900	1.049000	0.30392	0.514000	0.28300	-0.302000	0.09304	GAT	C|0.960;T|0.040	0.040	strong		0.303	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407	
CFI	3426	hgsc.bcm.edu	37	4	110681527	110681527	+	Missense_Mutation	SNP	C	C	T	rs112534524	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:110681527C>T	ENST00000394634.2	-	6	989	c.782G>A	c.(781-783)gGc>gAc	p.G261D	CFI_ENST00000512148.1_Missense_Mutation_p.G261D|CFI_ENST00000394635.3_Missense_Mutation_p.G261D	NM_000204.3	NP_000195	P05156	CFAI_HUMAN	complement factor I	261	LDL-receptor class A 2. {ECO:0000255|PROSITE-ProRule:PRU00124}.				complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|skin(2)|stomach(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000331)		GAAGCCTTTGCCTTGGCATGC	0.413													C|||	2	0.000399361	0.0	0.0	5008	,	,		19374	0.0		0.002	False		,,,				2504	0.0				p.G261D		Atlas-SNP	.											.	CFI	59	.	0			c.G782A	GRCh37	CM071595	CFI	M	rs112534524	PASS	.	C	ASP/GLY	5,4401	9.9+/-24.2	0,5,2198	127.0	113.0	117.0		782	2.2	0.0	4	dbSNP_132	117	17,8583	12.6+/-44.7	0,17,4283	yes	missense	CFI	NM_000204.3	94	0,22,6481	TT,TC,CC		0.1977,0.1135,0.1692	possibly-damaging	261/584	110681527	22,12984	2203	4300	6503	SO:0001583	missense	3426	exon6			CCTTTGCCTTGGC	J02770	CCDS34049.1	4q25	2014-09-17	2006-02-10	2006-02-10		ENSG00000205403	3.4.21.45	"""Complement system"""	5394	protein-coding gene	gene with protein product	"""Konglutinogen-activating factor"", ""C3b-inactivator"""	217030	"""I factor (complement)"""	IF		2956252	Standard	NM_000204		Approved	FI, C3b-INA, KAF	uc003hzr.4	P05156		ENST00000394634.2:c.782G>A	4.37:g.110681527C>T	ENSP00000378130:p.Gly261Asp	157.0	0.0	0		134.0	49.0	0.365672	NM_000204	O60442	Missense_Mutation	SNP	ENST00000394634.2	37	CCDS34049.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	10.82	1.457707	0.26161	0.001135	0.001977	ENSG00000205403	ENST00000394635;ENST00000394634;ENST00000540104;ENST00000512148;ENST00000536228	D;D;D	0.95272	-3.66;-3.66;-3.66	5.92	2.15	0.27550	.	0.579484	0.20634	N	0.088529	D	0.86251	0.5888	N	0.12471	0.22	0.09310	N	1	B;B;B	0.22800	0.074;0.036;0.075	B;B;B	0.28465	0.09;0.029;0.081	T	0.76713	-0.2858	10	0.44086	T	0.13	-6.4257	5.5586	0.17131	0.0:0.5559:0.1361:0.3081	.	261;261;261	E7ETH0;G3XAM2;P05156	.;.;CFAI_HUMAN	D	261;261;261;261;243	ENSP00000378131:G261D;ENSP00000378130:G261D;ENSP00000427438:G261D	ENSP00000378130:G261D	G	-	2	0	CFI	110900976	0.000000	0.05858	0.002000	0.10522	0.008000	0.06430	-0.052000	0.11865	0.424000	0.26061	0.655000	0.94253	GGC	C|0.998;G|0.000;T|0.002	0.002	strong		0.413	CFI-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_000204	
RASA3	22821	hgsc.bcm.edu	37	13	114773022	114773022	+	Missense_Mutation	SNP	C	C	T	rs74116414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:114773022C>T	ENST00000334062.7	-	18	1850	c.1729G>A	c.(1729-1731)Gtg>Atg	p.V577M	RASA3_ENST00000389544.4_Missense_Mutation_p.V545M	NM_007368.2	NP_031394.2	Q14644	RASA3_HUMAN	RAS p21 protein activator 3	577	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				calcium ion transmembrane transport (GO:0070588)|intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	calcium-release channel activity (GO:0015278)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47	Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188)	BRCA - Breast invasive adenocarcinoma(86;0.128)			TCTTTAAGCACGATGGGCTGC	0.562													N|||	129	0.0257588	0.0923	0.0101	5008	,	,		20382	0.0		0.0	False		,,,				2504	0.0				p.V577M		Atlas-SNP	.											.	RASA3	83	.	0			c.G1729A						PASS	.	C	MET/VAL	302,4100	162.5+/-194.5	14,274,1913	141.0	102.0	115.0		1729	0.1	1.0	13	dbSNP_130	115	5,8593	3.7+/-12.6	0,5,4294	yes	missense	RASA3	NM_007368.2	21	14,279,6207	TT,TC,CC		0.0582,6.8605,2.3615	benign	577/835	114773022	307,12693	2201	4299	6500	SO:0001583	missense	22821	exon18			TAAGCACGATGGG		CCDS32016.1	13q34	2013-01-10			ENSG00000185989	ENSG00000185989		"""Pleckstrin homology (PH) domain containing"""	20331	protein-coding gene	gene with protein product		605182				7637787, 9382842	Standard	NM_007368		Approved	GAP1IP4BP, GAPIII	uc001vui.3	Q14644	OTTHUMG00000017399	ENST00000334062.7:c.1729G>A	13.37:g.114773022C>T	ENSP00000335029:p.Val577Met	47.0	0.0	0		48.0	20.0	0.416667	NM_007368	A6NL15|F8W6X8|Q8IUY2	Missense_Mutation	SNP	ENST00000334062.7	37	CCDS32016.1	37	0.01694139194139194	35	0.07113821138211382	2	0.0055248618784530384	0	0.0	0	0.0	C	13.21	2.168248	0.38315	0.068605	5.82E-4	ENSG00000185989	ENST00000334062;ENST00000389544	D;D	0.94650	-3.48;-3.48	4.43	0.0618	0.14342	Rho GTPase activation protein (1);Pleckstrin homology-type (1);Pleckstrin homology domain (2);Ras GTPase-activating protein (1);	0.117907	0.56097	D	0.000028	T	0.59293	0.2183	M	0.76170	2.325	0.80722	D	1	B	0.14012	0.009	B	0.35688	0.208	T	0.72232	-0.4353	9	.	.	.	.	3.085	0.06275	0.2028:0.1354:0.5245:0.1373	.	577	Q14644	RASA3_HUMAN	M	577;545	ENSP00000335029:V577M;ENSP00000374195:V545M	.	V	-	1	0	RASA3	113791124	1.000000	0.71417	0.999000	0.59377	0.169000	0.22640	0.524000	0.22940	0.107000	0.17824	-0.928000	0.02712	GTG	C|0.976;T|0.024	0.024	strong		0.562	RASA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045957.2	NM_007368	
DSP	1832	hgsc.bcm.edu	37	6	7585795	7585795	+	Missense_Mutation	SNP	C	C	A	rs34884895	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:7585795C>A	ENST00000379802.3	+	24	8641	c.8300C>A	c.(8299-8301)aCc>aAc	p.T2767N	DSP_ENST00000418664.2_Missense_Mutation_p.T2168N	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	2767	4.5 X 38 AA tandem repeats (Domain C).|Globular 2.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		CTGCAAGACACCAGCAGCTAT	0.512													C|||	35	0.00698882	0.0257	0.0014	5008	,	,		807	0.0		0.0	False		,,,				2504	0.0				p.T2767N		Atlas-SNP	.											.	DSP	306	.	0			c.C8300A						PASS	.	C	ASN/THR,ASN/THR	100,4306	79.3+/-117.8	1,98,2104	70.0	80.0	77.0		6503,8300	2.2	1.0	6	dbSNP_126	77	0,8600		0,0,4300	yes	missense,missense	DSP	NM_001008844.1,NM_004415.2	65,65	1,98,6404	AA,AC,CC		0.0,2.2696,0.7689	possibly-damaging,possibly-damaging	2168/2273,2767/2872	7585795	100,12906	2203	4300	6503	SO:0001583	missense	1832	exon24			AAGACACCAGCAG	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"""desmoplakin (DPI, DPII)"""			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.8300C>A	6.37:g.7585795C>A	ENSP00000369129:p.Thr2767Asn	90.0	0.0	0		90.0	49.0	0.544444	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	37	CCDS4501.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	C	15.09	2.730333	0.48939	0.022696	0.0	ENSG00000096696	ENST00000379802;ENST00000418664	T;T	0.73258	-0.73;-0.73	5.49	2.23	0.28157	.	0.171164	0.41396	D	0.000892	T	0.64283	0.2584	L	0.60455	1.87	0.22292	N	0.999227	D;P	0.67145	0.996;0.899	D;P	0.68483	0.958;0.689	T	0.57562	-0.7790	10	0.26408	T	0.33	.	8.2741	0.31862	0.0:0.6483:0.0:0.3517	rs34884895	2215;2767	Q4LE79;P15924	.;DESP_HUMAN	N	2767;2168	ENSP00000369129:T2767N;ENSP00000396591:T2168N	ENSP00000369129:T2767N	T	+	2	0	DSP	7530794	0.206000	0.23470	1.000000	0.80357	0.997000	0.91878	0.743000	0.26231	0.204000	0.20548	0.561000	0.74099	ACC	C|0.991;A|0.009	0.009	strong		0.512	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
AKT1	207	hgsc.bcm.edu	37	14	105238783	105238783	+	Silent	SNP	G	G	A	rs11555434	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105238783G>A	ENST00000554581.1	-	11	2659	c.1179C>T	c.(1177-1179)ggC>ggT	p.G393G	AKT1_ENST00000402615.2_Silent_p.G393G|AKT1_ENST00000554848.1_Silent_p.G393G|AKT1_ENST00000407796.2_Silent_p.G393G|AKT1_ENST00000544168.1_Silent_p.G331G|AKT1_ENST00000555458.1_Silent_p.G88G|AKT1_ENST00000555528.1_Silent_p.G393G|AKT1_ENST00000349310.3_Silent_p.G393G|AKT1_ENST00000554192.1_Silent_p.G80G|RP11-982M15.2_ENST00000557223.1_RNA|AKT1_ENST00000554585.1_5'UTR			P31749	AKT1_HUMAN	v-akt murine thymoma viral oncogene homolog 1	393	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation-induced cell death of T cells (GO:0006924)|aging (GO:0007568)|anagen (GO:0042640)|apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell projection organization (GO:0030030)|cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to mechanical stimulus (GO:0071260)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|execution phase of apoptosis (GO:0097194)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|gene expression (GO:0010467)|germ cell development (GO:0007281)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|glycogen cell differentiation involved in embryonic placenta development (GO:0060709)|hyaluronan metabolic process (GO:0030212)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway (GO:0097193)|labyrinthine layer blood vessel development (GO:0060716)|mammary gland epithelial cell differentiation (GO:0060644)|maternal placenta development (GO:0001893)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of JNK cascade (GO:0046329)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of proteolysis (GO:0045861)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide metabolic process (GO:0046209)|osteoblast differentiation (GO:0001649)|peptidyl-serine phosphorylation (GO:0018105)|peripheral nervous system myelin maintenance (GO:0032287)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell growth (GO:0030307)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell cycle checkpoint (GO:1901976)|regulation of cell migration (GO:0030334)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of neuron projection development (GO:0010975)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of translation (GO:0006417)|response to fluid shear stress (GO:0034405)|response to food (GO:0032094)|response to heat (GO:0009408)|response to UV-A (GO:0070141)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|striated muscle cell differentiation (GO:0051146)|T cell costimulation (GO:0031295)|translation (GO:0006412)	cell-cell junction (GO:0005911)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|kinase activity (GO:0016301)|nitric-oxide synthase regulator activity (GO:0030235)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			NS(3)|breast(97)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(7)|lung(10)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|thyroid(10)|urinary_tract(15)	176		all_cancers(154;3.77e-06)|all_lung(585;3.24e-07)|all_epithelial(191;3.45e-05)|all_neural(303;0.0459)|Melanoma(154;0.155)	all cancers(16;0.000486)|OV - Ovarian serous cystadenocarcinoma(23;0.00647)|Epithelial(46;0.0153)|GBM - Glioblastoma multiforme(11;0.116)	all cancers(159;0.0107)|OV - Ovarian serous cystadenocarcinoma(161;0.0132)|Epithelial(152;0.243)	Adenosine triphosphate(DB00171)|Arsenic trioxide(DB01169)	CGGAGCCCCCGCCAAGCCTGC	0.642		1	Mis		"""breast, colorectal, ovarian, NSCLC"""								g|||	44	0.00878594	0.0325	0.0014	5008	,	,		18738	0.0		0.0	False		,,,				2504	0.0				p.G393G		Atlas-SNP	.		Dom	yes		14	14q32.32	207	v-akt murine thymoma viral oncogene homolog 1		E	.	AKT1	379	.	0			c.C1179T						PASS	.		,,	113,4291	81.4+/-119.9	5,103,2094	65.0	48.0	54.0		1179,1179,1179	-6.1	0.5	14	dbSNP_120	54	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	AKT1	NM_001014431.1,NM_001014432.1,NM_005163.2	,,	5,107,6390	AA,AG,GG		0.0465,2.5658,0.8997	,,	393/481,393/481,393/481	105238783	117,12887	2202	4300	6502	SO:0001819	synonymous_variant	207	exon12			GCCCCCGCCAAGC	M63167	CCDS9994.1	14q32.33	2014-09-17			ENSG00000142208	ENSG00000142208	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	391	protein-coding gene	gene with protein product		164730					Standard	XM_005267401		Approved	RAC, PKB, PRKBA, AKT	uc001ypn.3	P31749	OTTHUMG00000170795	ENST00000554581.1:c.1179C>T	14.37:g.105238783G>A		103.0	0.0	0		130.0	60.0	0.461538	NM_005163	B2RAM5|B7Z5R1|Q9BWB6	Silent	SNP	ENST00000554581.1	37	CCDS9994.1																																																																																			G|0.992;A|0.008	0.008	strong		0.642	AKT1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410418.1	NM_005163	
PDCD2	5134	hgsc.bcm.edu	37	6	170892759	170892759	+	Silent	SNP	T	T	A	rs73258640	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:170892759T>A	ENST00000541970.1	-	2	438	c.360A>T	c.(358-360)acA>acT	p.T120T	PDCD2_ENST00000443345.2_Silent_p.T87T|PDCD2_ENST00000542896.1_Silent_p.T120T|PDCD2_ENST00000392090.2_Silent_p.T87T|PDCD2_ENST00000537445.1_Silent_p.T87T|PDCD2_ENST00000453163.2_Silent_p.T120T	NM_001199462.1|NM_002598.3	NP_001186391.1|NP_002589.2	Q16342	PDCD2_HUMAN	programmed cell death 2	120					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(1)|lung(5)	9		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;6.91e-23)|BRCA - Breast invasive adenocarcinoma(81;4.82e-06)|GBM - Glioblastoma multiforme(31;0.142)		CTGATTCTCCTGTTTCTGGGG	0.433													.|||	61	0.0121805	0.0439	0.0029	5008	,	,		17113	0.0		0.001	False		,,,				2504	0.0				p.T120T	Colon(60;1476 1726 39478)	Atlas-SNP	.											.	PDCD2	13	.	0			c.A360T						PASS	.	T	,,,,,	162,4244		5,152,2046	63.0	62.0	62.0		360,261,261,261,360,360	-2.4	0.0	6	dbSNP_130	62	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDCD2	NM_001199461.1,NM_001199462.1,NM_001199463.1,NM_001199464.1,NM_002598.3,NM_144781.2	,,,,,	5,152,6346	AA,AT,TT		0.0,3.6768,1.2456	,,,,,	120/222,87/312,87/196,87/189,120/345,120/229	170892759	162,12844	2203	4300	6503	SO:0001819	synonymous_variant	5134	exon2			TTCTCCTGTTTCT	AJ420535	CCDS5316.1, CCDS47521.1, CCDS56460.1, CCDS56461.1, CCDS56462.1, CCDS75557.1	6q27	2008-02-05			ENSG00000071994	ENSG00000071994		"""Zinc fingers, MYND-type"""	8762	protein-coding gene	gene with protein product		600866				7606924	Standard	NM_002598		Approved	ZMYND7, RP8	uc003qxw.3	Q16342	OTTHUMG00000016083	ENST00000541970.1:c.360A>T	6.37:g.170892759T>A		90.0	0.0	0		95.0	43.0	0.452632	NM_002598	E9PCU7|F5GYS7|Q58HM9|Q58HN0|Q9UH12	Silent	SNP	ENST00000541970.1	37	CCDS5316.1																																																																																			T|0.985;A|0.015	0.015	strong		0.433	PDCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043269.2	NM_002598	
CAMSAP3	57662	hgsc.bcm.edu	37	19	7682862	7682862	+	Silent	SNP	C	C	G	rs4134883	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7682862C>G	ENST00000160298.4	+	17	3770	c.3669C>G	c.(3667-3669)gtC>gtG	p.V1223V	CAMSAP3_ENST00000446248.2_Silent_p.V1250V	NM_020902.1	NP_065953.1	Q9P1Y5	CAMP3_HUMAN	calmodulin regulated spectrin-associated protein family, member 3	1223	CKK. {ECO:0000255|PROSITE- ProRule:PRU00841}.				epithelial cell-cell adhesion (GO:0090136)|microtubule anchoring (GO:0034453)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of phosphatase activity (GO:0010923)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of organelle organization (GO:0033043)|zonula adherens maintenance (GO:0045218)	cytoplasm (GO:0005737)|microtubule minus-end (GO:0036449)|zonula adherens (GO:0005915)	microtubule minus-end binding (GO:0051011)			cervix(1)|endometrium(7)|kidney(3)|lung(6)|urinary_tract(2)	19						CCATGAGCGTCGATGCCTTCA	0.642													C|||	194	0.038738	0.1407	0.0115	5008	,	,		15396	0.0		0.0	False		,,,				2504	0.0				p.V1250V		Atlas-SNP	.											.	CAMSAP3	131	.	0			c.C3750G						PASS	.	C	,	540,3516		43,454,1531	52.0	59.0	57.0		3750,3669	0.3	1.0	19	dbSNP_108	57	2,8342		0,2,4170	no	coding-synonymous,coding-synonymous	CAMSAP3	NM_001080429.2,NM_020902.1	,	43,456,5701	GG,GC,CC		0.024,13.3136,4.371	,	1250/1277,1223/1250	7682862	542,11858	2028	4172	6200	SO:0001819	synonymous_variant	57662	exon19			GAGCGTCGATGCC	AB040976	CCDS42489.1, CCDS45947.1	19p13.3-p13.2	2014-06-12	2011-08-18	2011-08-18		ENSG00000076826			29307	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 80"""	612685	"""KIAA1543"""	KIAA1543		11318610, 10819331, 19041755, 19508979	Standard	NM_001080429		Approved	Nezha, PPP1R80	uc002mgu.4	Q9P1Y5		ENST00000160298.4:c.3669C>G	19.37:g.7682862C>G		126.0	0.0	0		96.0	42.0	0.4375	NM_001080429	Q8NDF1	Silent	SNP	ENST00000160298.4	37	CCDS42489.1																																																																																			C|0.969;G|0.031	0.031	strong		0.642	CAMSAP3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459300.1	XM_048362	
MMP11	4320	hgsc.bcm.edu	37	22	24124471	24124471	+	Silent	SNP	C	C	A	rs28382569	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:24124471C>A	ENST00000215743.3	+	7	1186	c.1134C>A	c.(1132-1134)acC>acA	p.T378T	AP000349.1_ENST00000598975.1_Missense_Mutation_p.R248L	NM_005940.3	NP_005931.2	P24347	MMP11_HUMAN	matrix metallopeptidase 11 (stromelysin 3)	378					basement membrane organization (GO:0071711)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|negative regulation of fat cell differentiation (GO:0045599)|proteolysis (GO:0006508)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(2)|lung(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)	27		Medulloblastoma(6;9.86e-08)|all_neural(6;0.000318)			Marimastat(DB00786)	cacccctcaccgagctGGGCC	0.632													C|||	54	0.0107827	0.0371	0.0029	5008	,	,		18519	0.0		0.003	False		,,,				2504	0.0				p.T378T		Atlas-SNP	.											.	MMP11	53	.	0			c.C1134A						PASS	.	C		168,4238	112.1+/-150.2	5,158,2040	59.0	57.0	58.0		1134	-2.9	0.6	22	dbSNP_125	58	0,8600		0,0,4300	no	coding-synonymous	MMP11	NM_005940.3		5,158,6340	AA,AC,CC		0.0,3.813,1.2917		378/489	24124471	168,12838	2203	4300	6503	SO:0001819	synonymous_variant	4320	exon7			CCTCACCGAGCTG		CCDS13816.1	22q11.23	2008-06-11	2005-08-08		ENSG00000099953	ENSG00000099953			7157	protein-coding gene	gene with protein product		185261	"""matrix metalloproteinase 11 (stromelysin 3)"""	STMY3		1639418, 7657606, 12006591	Standard	NM_005940		Approved		uc002zxx.3	P24347	OTTHUMG00000150742	ENST00000215743.3:c.1134C>A	22.37:g.24124471C>A		87.0	0.0	0		84.0	46.0	0.547619	NM_005940	Q5FX24|Q6PEZ6|Q9UC26	Silent	SNP	ENST00000215743.3	37	CCDS13816.1																																																																																			A|0.014;C|0.986	0.014	strong		0.632	MMP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319891.2	NM_005940	
SRP68	6730	hgsc.bcm.edu	37	17	74036544	74036544	+	Missense_Mutation	SNP	C	C	T	rs75353721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74036544C>T	ENST00000307877.2	-	15	1773	c.1612G>A	c.(1612-1614)Gct>Act	p.A538T	SRP68_ENST00000355113.5_Missense_Mutation_p.A437T|SRP68_ENST00000539137.1_Missense_Mutation_p.A500T|SRP68_ENST00000542536.2_5'UTR|SRP68_ENST00000602720.1_Missense_Mutation_p.A199T	NM_014230.3	NP_055045.2	Q9UHB9	SRP68_HUMAN	signal recognition particle 68kDa	538					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)|ribosome (GO:0005840)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|endoplasmic reticulum signal peptide binding (GO:0030942)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			NS(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|lung(4)|ovary(2)|prostate(3)	23						GTTTGATGAGCGTCGTTTGCA	0.438													C|||	43	0.00858626	0.0295	0.0043	5008	,	,		21078	0.001		0.0	False		,,,				2504	0.0				p.A538T		Atlas-SNP	.											SRP68,colon,carcinoma,+2,1	SRP68	61	1	0			c.G1612A						scavenged	.	C	THR/ALA	73,4333	66.4+/-103.9	2,69,2132	150.0	125.0	134.0		1612	-4.7	0.0	17	dbSNP_131	134	0,8600		0,0,4300	yes	missense	SRP68	NM_014230.2	58	2,69,6432	TT,TC,CC		0.0,1.6568,0.5613	benign	538/628	74036544	73,12933	2203	4300	6503	SO:0001583	missense	6730	exon15			GATGAGCGTCGTT	AF195951	CCDS11738.1, CCDS58600.1, CCDS58601.1	17q25.1	2010-04-30	2002-08-29		ENSG00000167881	ENSG00000167881			11302	protein-coding gene	gene with protein product		604858	"""signal recognition particle 68kD"""			10618370	Standard	NM_014230		Approved		uc002jqk.2	Q9UHB9		ENST00000307877.2:c.1612G>A	17.37:g.74036544C>T	ENSP00000312066:p.Ala538Thr	225.0	2.0	0.00888889		246.0	127.0	0.51626	NM_014230	B3KUU5|B3KWY7|G3V1U4|Q8NCJ4|Q8WUK2	Missense_Mutation	SNP	ENST00000307877.2	37	CCDS11738.1	14	0.00641025641025641	12	0.024390243902439025	1	0.0027624309392265192	1	0.0017482517482517483	0	0.0	C	2.222	-0.378212	0.05000	0.016568	0.0	ENSG00000167881	ENST00000411758;ENST00000539137;ENST00000542536;ENST00000307877;ENST00000304220;ENST00000355113	.	.	.	6.07	-4.7	0.03288	.	1.163030	0.05794	N	0.610958	T	0.07143	0.0181	N	0.14661	0.345	0.09310	N	1	B;B	0.12013	0.005;0.003	B;B	0.04013	0.001;0.001	T	0.17440	-1.0369	9	0.14656	T	0.56	-0.5259	0.5188	0.00608	0.2244:0.2613:0.1636:0.3507	.	500;538	G3V1U4;Q9UHB9	.;SRP68_HUMAN	T	278;500;199;538;507;437	.	ENSP00000307756:A507T	A	-	1	0	SRP68	71548139	0.023000	0.18921	0.001000	0.08648	0.069000	0.16628	-0.142000	0.10311	-0.743000	0.04784	-0.266000	0.10368	GCT	C|0.993;T|0.007	0.007	strong		0.438	SRP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449487.1	NM_014230	
VWF	7450	hgsc.bcm.edu	37	12	6138575	6138575	+	Missense_Mutation	SNP	C	C	T	rs141087261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:6138575C>T	ENST00000261405.5	-	22	3154	c.2900G>A	c.(2899-2901)gGc>gAc	p.G967D		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	967	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	GAGGGCTTTGCCCAGCAGCAG	0.547													C|||	47	0.00938498	0.0325	0.0058	5008	,	,		20111	0.0		0.0	False		,,,				2504	0.0				p.G967D		Atlas-SNP	.											.	VWF	338	.	0			c.G2900A						PASS	.	C	ASP/GLY	109,4297	84.8+/-123.5	2,105,2096	140.0	125.0	130.0		2900	3.7	0.9	12	dbSNP_134	130	0,8600		0,0,4300	yes	missense	VWF	NM_000552.3	94	2,105,6396	TT,TC,CC		0.0,2.4739,0.8381	benign	967/2814	6138575	109,12897	2203	4300	6503	SO:0001583	missense	7450	exon22			GCTTTGCCCAGCA		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.2900G>A	12.37:g.6138575C>T	ENSP00000261405:p.Gly967Asp	90.0	0.0	0		131.0	74.0	0.564885	NM_000552	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	18	0.008241758241758242	16	0.032520325203252036	2	0.0055248618784530384	0	0.0	0	0.0	C	18.66	3.671977	0.67928	0.024739	0.0	ENSG00000110799	ENST00000261405	T	0.61040	0.14	4.58	3.69	0.42338	von Willebrand factor, type D domain (3);	0.382429	0.19030	N	0.124571	T	0.38081	0.1027	L	0.36672	1.1	0.80722	D	1	D	0.52996	0.957	P	0.61800	0.894	T	0.50759	-0.8790	10	0.42905	T	0.14	.	11.8305	0.52293	0.0:0.9149:0.0:0.0851	.	967	P04275	VWF_HUMAN	D	967	ENSP00000261405:G967D	ENSP00000261405:G967D	G	-	2	0	VWF	6008836	1.000000	0.71417	0.913000	0.36048	0.642000	0.38348	5.586000	0.67503	1.152000	0.42452	0.484000	0.47621	GGC	C|0.992;T|0.008	0.008	strong		0.547	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
HSD17B4	3295	hgsc.bcm.edu	37	5	118877660	118877660	+	Missense_Mutation	SNP	A	A	G	rs28943594	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:118877660A>G	ENST00000256216.6	+	24	2315	c.2182A>G	c.(2182-2184)Atg>Gtg	p.M728V	HSD17B4_ENST00000509514.1_Missense_Mutation_p.M466V|HSD17B4_ENST00000414835.2_Missense_Mutation_p.M588V|HSD17B4_ENST00000504811.1_Missense_Mutation_p.M753V|HSD17B4_ENST00000510025.1_Missense_Mutation_p.M704V|HSD17B4_ENST00000515320.1_Missense_Mutation_p.M710V|HSD17B4_ENST00000513628.1_Missense_Mutation_p.M591V|HSD17B4_ENST00000522415.1_3'UTR	NM_000414.3	NP_000405.1	P51659	DHB4_HUMAN	hydroxysteroid (17-beta) dehydrogenase 4	728	SCP2.		M -> V (in dbSNP:rs28943594).		alpha-linolenic acid metabolic process (GO:0036109)|androgen metabolic process (GO:0008209)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|estrogen metabolic process (GO:0008210)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|metabolic process (GO:0008152)|osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|Sertoli cell development (GO:0060009)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)|very long-chain fatty-acyl-CoA metabolic process (GO:0036111)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	17-beta-hydroxysteroid dehydrogenase (NAD+) activity (GO:0044594)|3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity (GO:0033989)|isomerase activity (GO:0016853)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(2)	25		all_cancers(142;0.0206)|Prostate(80;0.0322)		OV - Ovarian serous cystadenocarcinoma(64;0.000247)|Epithelial(69;0.000849)|all cancers(49;0.0122)		GAAACTTCAGATGATTCTTAA	0.423													A|||	167	0.0333466	0.1218	0.0043	5008	,	,		15072	0.0		0.001	False		,,,				2504	0.002				p.M753V	Colon(35;490 801 34689 41394 43344)	Atlas-SNP	.											.	HSD17B4	63	.	0			c.A2257G						PASS	.	A	VAL/MET,VAL/MET,VAL/MET	405,3999	198.4+/-222.2	21,363,1818	65.0	64.0	64.0		2182,2257,2128	3.5	1.0	5	dbSNP_125	64	14,8586	10.5+/-38.8	0,14,4286	yes	missense,missense,missense	HSD17B4	NM_000414.3,NM_001199291.1,NM_001199292.1	21,21,21	21,377,6104	GG,GA,AA		0.1628,9.1962,3.2221	benign,benign,benign	728/737,753/762,710/719	118877660	419,12585	2202	4300	6502	SO:0001583	missense	3295	exon25			CTTCAGATGATTC		CCDS4126.1, CCDS56378.1, CCDS56379.1	5q2	2011-09-20			ENSG00000133835	ENSG00000133835	4.2.1.107, 1.1.1.35	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	5213	protein-coding gene	gene with protein product	"""17beta-estradiol dehydrogenase type IV"", ""peroxisomal multifunctional protein 2"", ""17-beta-HSD IV"", ""17-beta-hydroxysteroid dehydrogenase 4"", ""D-bifunctional protein, peroxisomal"", ""D-3-hydroxyacyl-CoA dehydratase"", ""3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholest-24-enoyl-CoA hydratase"", ""beta-keto-reductase"", ""beta-hydroxyacyl dehydrogenase"", ""short chain dehydrogenase/reductase family 8C, member 1"""	601860				8938456, 19027726	Standard	NM_000414		Approved	MFE-2, DBP, SDR8C1	uc003ksj.3	P51659	OTTHUMG00000128899	ENST00000256216.6:c.2182A>G	5.37:g.118877660A>G	ENSP00000256216:p.Met728Val	222.0	0.0	0		172.0	87.0	0.505814	NM_001199291	B4DNV1|B4DVS5|E9PB82|F5HE57	Missense_Mutation	SNP	ENST00000256216.6	37	CCDS4126.1	67	0.030677655677655676	64	0.13008130081300814	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	A	11.01	1.512125	0.27036	0.091962	0.001628	ENSG00000133835	ENST00000256216;ENST00000515320;ENST00000510025;ENST00000504811;ENST00000414835;ENST00000513628;ENST00000509514	T;T;T;T;T;T;T	0.21361	2.01;2.01;2.01;2.01;2.01;2.01;2.01	5.94	3.46	0.39613	SCP2 sterol-binding domain (2);	0.276882	0.46145	D	0.000301	T	0.00144	0.0004	N	0.21282	0.65	0.31931	P	0.612166	B;B;B;B;B	0.11235	0.004;0.0;0.0;0.001;0.0	B;B;B;B;B	0.10450	0.003;0.003;0.005;0.001;0.003	T	0.29671	-1.0004	8	.	.	.	-10.0531	8.5921	0.33693	0.7361:0.1351:0.0:0.1288	rs28943594	753;710;704;466;728	F5HE57;E9PB82;E7EWE5;E7EPL9;P51659	.;.;.;.;DHB4_HUMAN	V	728;710;704;753;588;591;466	ENSP00000256216:M728V;ENSP00000424613:M710V;ENSP00000424940:M704V;ENSP00000420914:M753V;ENSP00000411960:M588V;ENSP00000425993:M591V;ENSP00000426272:M466V	.	M	+	1	0	HSD17B4	118905559	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	4.250000	0.58772	0.446000	0.26666	0.455000	0.32223	ATG	A|0.967;G|0.033	0.033	strong		0.423	HSD17B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250863.3	NM_000414	
NUGGC	389643	hgsc.bcm.edu	37	8	27925220	27925220	+	Silent	SNP	A	A	G	rs114951850	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:27925220A>G	ENST00000413272.2	-	6	664	c.522T>C	c.(520-522)caT>caC	p.H174H	NUGGC_ENST00000341513.6_Silent_p.H174H	NM_001010906.1	NP_001010906.1	Q68CJ6	SLIP_HUMAN	nuclear GTPase, germinal center associated	174					cellular response to DNA damage stimulus (GO:0006974)|somatic hypermutation of immunoglobulin genes (GO:0016446)	nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)										CCTCCGTCCTATGCAGGAGTT	0.547													A|||	104	0.0207668	0.0756	0.0058	5008	,	,		18753	0.0		0.0	False		,,,				2504	0.0				p.H174H		Atlas-SNP	.											.	.	.	.	0			c.T522C						PASS	.	A		193,3875		6,181,1847	68.0	69.0	69.0		522	-2.4	0.0	8	dbSNP_132	69	5,8431		0,5,4213	no	coding-synonymous	C8orf80	NM_001010906.1		6,186,6060	GG,GA,AA		0.0593,4.7443,1.5835		174/797	27925220	198,12306	2034	4218	6252	SO:0001819	synonymous_variant	389643	exon6			CGTCCTATGCAGG	AB075870	CCDS47833.1	8p21.1	2012-06-07	2012-06-07	2012-06-07	ENSG00000189233	ENSG00000189233			33550	protein-coding gene	gene with protein product	"""speckled-like pattern in the germinal center"""		"""chromosome 8 open reading frame 80"""	C8orf80		19734146	Standard	NM_001010906		Approved	HMFN0672, SLIP-GC	uc003xgm.4	Q68CJ6	OTTHUMG00000155970	ENST00000413272.2:c.522T>C	8.37:g.27925220A>G		212.0	0.0	0		247.0	130.0	0.526316	NM_001010906	Q6ZP73	Silent	SNP	ENST00000413272.2	37	CCDS47833.1																																																																																			A|0.985;G|0.015	0.015	strong		0.547	NUGGC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000342494.1	NM_001010906	
SYNE3	161176	hgsc.bcm.edu	37	14	95923644	95923644	+	Missense_Mutation	SNP	C	C	T	rs74082143	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:95923644C>T	ENST00000334258.5	-	4	673	c.659G>A	c.(658-660)cGg>cAg	p.R220Q	SYNE3_ENST00000557275.1_Missense_Mutation_p.R220Q|SYNE3_ENST00000553340.1_Missense_Mutation_p.R220Q|SYNE3_ENST00000554873.1_5'Flank	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	220					cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)			breast(1)|endometrium(2)|lung(25)	28						CTCATGCTCCCGGGCCACCTG	0.622													C|||	57	0.0113818	0.0416	0.0029	5008	,	,		15755	0.0		0.0	False		,,,				2504	0.0				p.R220Q		Atlas-SNP	.											.	SYNE3	130	.	0			c.G659A						PASS	.	C	GLN/ARG	164,4242	110.8+/-149.0	4,156,2043	172.0	146.0	155.0		659	-9.7	0.2	14	dbSNP_130	155	1,8599	1.2+/-3.3	0,1,4299	yes	missense	C14orf49	NM_152592.3	43	4,157,6342	TT,TC,CC		0.0116,3.7222,1.2686	benign	220/976	95923644	165,12841	2203	4300	6503	SO:0001583	missense	161176	exon4			TGCTCCCGGGCCA	AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"""chromosome 14 open reading frame 49"""	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.659G>A	14.37:g.95923644C>T	ENSP00000334308:p.Arg220Gln	77.0	0.0	0		86.0	38.0	0.44186	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	37	CCDS9935.1	24	0.01098901098901099	22	0.044715447154471545	2	0.0055248618784530384	0	0.0	0	0.0	C	8.880	0.951469	0.18431	0.037222	1.16E-4	ENSG00000176438	ENST00000334258;ENST00000557275;ENST00000553340	T;T;T	0.08634	3.67;3.67;3.07	5.59	-9.72	0.00515	.	1.176260	0.06544	N	0.743757	T	0.00784	0.0026	N	0.12471	0.22	0.09310	N	1	B;B;B	0.09022	0.001;0.002;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.46428	-0.9192	10	0.16420	T	0.52	-9.6805	10.7358	0.46124	0.0756:0.1571:0.0:0.7673	.	220;220;220	Q6ZMZ3-2;Q6ZMZ3-3;Q6ZMZ3	.;.;SYNE3_HUMAN	Q	220	ENSP00000334308:R220Q;ENSP00000450562:R220Q;ENSP00000450774:R220Q	ENSP00000334308:R220Q	R	-	2	0	C14orf49	94993397	0.009000	0.17119	0.165000	0.22776	0.027000	0.11550	0.063000	0.14410	-1.210000	0.02627	-0.263000	0.10527	CGG	C|0.989;T|0.011	0.011	strong		0.622	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592	
PIP4K2A	5305	hgsc.bcm.edu	37	10	22830842	22830842	+	Silent	SNP	C	C	T	rs61731109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:22830842C>T	ENST00000376573.4	-	8	1155	c.927G>A	c.(925-927)ccG>ccA	p.P309P	PIP4K2A_ENST00000323883.7_Silent_p.P169P|PIP4K2A_ENST00000545335.1_Silent_p.P250P	NM_005028.4	NP_005019.2	P48426	PI42A_HUMAN	phosphatidylinositol-5-phosphate 4-kinase, type II, alpha	309	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				megakaryocyte development (GO:0035855)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|1-phosphatidylinositol-5-phosphate 4-kinase activity (GO:0016309)|ATP binding (GO:0005524)			endometrium(4)|kidney(13)|large_intestine(4)|lung(6)|ovary(1)|skin(1)	29						GGGTTCCCACCGGGTGGGTGC	0.592													C|||	98	0.0195687	0.0522	0.0101	5008	,	,		18503	0.0		0.0149	False		,,,				2504	0.0072				p.P309P		Atlas-SNP	.											.	PIP4K2A	59	.	0			c.G927A						PASS	.	C		217,4189	133.7+/-170.0	6,205,1992	79.0	73.0	75.0		927	-12.1	0.0	10	dbSNP_129	75	110,8490	58.3+/-119.8	1,108,4191	no	coding-synonymous	PIP4K2A	NM_005028.4		7,313,6183	TT,TC,CC		1.2791,4.9251,2.5142		309/407	22830842	327,12679	2203	4300	6503	SO:0001819	synonymous_variant	5305	exon8			TCCCACCGGGTGG	S78798	CCDS7141.1	10p12.2	2007-08-21	2007-08-14	2007-08-14	ENSG00000150867	ENSG00000150867			8997	protein-coding gene	gene with protein product		603140	"""phosphatidylinositol-4-phosphate 5-kinase, type II, alpha"""	PIP5K2A		7852364, 9367159	Standard	NM_005028		Approved	PIP5KIIA, PIP5KIIalpha	uc001irl.4	P48426	OTTHUMG00000017810	ENST00000376573.4:c.927G>A	10.37:g.22830842C>T		109.0	0.0	0		98.0	41.0	0.418367	NM_005028	B0YJ66|B4DGX2|D3DRV1|P53807|Q5VUX3	Silent	SNP	ENST00000376573.4	37	CCDS7141.1																																																																																			C|0.976;T|0.024	0.024	strong		0.592	PIP4K2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047193.1	NM_005028	
MDC1	9656	hgsc.bcm.edu	37	6	30668374	30668374	+	Silent	SNP	G	G	A	rs9468812	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30668374G>A	ENST00000376406.3	-	15	6785	c.6138C>T	c.(6136-6138)ttC>ttT	p.F2046F	MDC1_ENST00000376405.2_Silent_p.F1782F|MDC1-AS1_ENST00000442150.1_RNA	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	2046	BRCT 2. {ECO:0000255|PROSITE- ProRule:PRU00033}.|Required for nuclear localization (NLS2).				DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						AGCAATGAGGGAAGTCCTGAG	0.542								Other conserved DNA damage response genes					G|||	234	0.0467252	0.1278	0.0432	5008	,	,		16633	0.0208		0.0129	False		,,,				2504	0.001				p.F2046F		Atlas-SNP	.											.	MDC1	218	.	0			c.C6138T						PASS	.	G		320,2702		21,278,1212	114.0	107.0	109.0		6138	-4.1	0.0	6	dbSNP_119	109	63,5355		0,63,2646	no	coding-synonymous	MDC1	NM_014641.2		21,341,3858	AA,AG,GG		1.1628,10.589,4.5379		2046/2090	30668374	383,8057	1511	2709	4220	SO:0001819	synonymous_variant	9656	exon15			ATGAGGGAAGTCC	D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.6138C>T	6.37:g.30668374G>A		107.0	0.0	0		102.0	50.0	0.490196	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Silent	SNP	ENST00000376406.3	37	CCDS34384.1																																																																																			G|0.958;A|0.042	0.042	strong		0.542	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641	
SMPDL3B	27293	hgsc.bcm.edu	37	1	28285123	28285123	+	Missense_Mutation	SNP	G	G	A	rs34560878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:28285123G>A	ENST00000373894.3	+	8	1333	c.1142G>A	c.(1141-1143)cGc>cAc	p.R381H	XKR8_ENST00000373884.5_5'Flank|RP11-460I13.2_ENST00000448015.1_RNA|SMPDL3B_ENST00000549094.1_Missense_Mutation_p.R333H	NM_014474.2	NP_055289.2	Q92485	ASM3B_HUMAN	sphingomyelin phosphodiesterase, acid-like 3B	381			R -> H (in dbSNP:rs34560878).		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)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	16		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000431)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;5.68e-24)|Colorectal(126;1.65e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00587)|READ - Rectum adenocarcinoma(331;0.055)		GTGCTGGACCGCATCGCTGGC	0.642													G|||	73	0.0145767	0.0507	0.0086	5008	,	,		19689	0.0		0.0	False		,,,				2504	0.0				p.R381H		Atlas-SNP	.											.	SMPDL3B	54	.	0			c.G1142A						PASS	.	G	HIS/ARG	188,4218	120.0+/-157.7	4,180,2019	69.0	64.0	65.0		1142	-1.2	0.0	1	dbSNP_126	65	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SMPDL3B	NM_014474.2	29	4,181,6318	AA,AG,GG		0.0116,4.2669,1.4532	benign	381/456	28285123	189,12817	2203	4300	6503	SO:0001583	missense	27293	exon8			TGGACCGCATCGC	Y08134	CCDS30655.1, CCDS30656.1	1p35.3	2008-02-05			ENSG00000130768	ENSG00000130768			21416	protein-coding gene	gene with protein product							Standard	NM_014474		Approved	ASML3B	uc001bpg.3	Q92485	OTTHUMG00000003910	ENST00000373894.3:c.1142G>A	1.37:g.28285123G>A	ENSP00000363001:p.Arg381His	146.0	0.0	0		173.0	86.0	0.49711	NM_014474	B7ZB35|Q5T0Z0|Q96CB7	Missense_Mutation	SNP	ENST00000373894.3	37	CCDS30655.1	19	0.0086996336996337	15	0.03048780487804878	4	0.011049723756906077	0	0.0	0	0.0	G	11.15	1.553282	0.27739	0.042669	1.16E-4	ENSG00000130768	ENST00000373894;ENST00000549094	D;D	0.90732	-2.72;-2.72	5.09	-1.23	0.09465	.	0.392324	0.27043	N	0.021217	T	0.65491	0.2696	M	0.73962	2.25	0.20074	N	0.999932	B;B	0.20887	0.049;0.029	B;B	0.17098	0.017;0.007	T	0.71331	-0.4625	10	0.52906	T	0.07	-4.737	5.5703	0.17192	0.488:0.0:0.3824:0.1296	rs34560878	333;381	F8VWW8;Q92485	.;ASM3B_HUMAN	H	381;333	ENSP00000363001:R381H;ENSP00000449450:R333H	ENSP00000363001:R381H	R	+	2	0	SMPDL3B	28157710	0.916000	0.31088	0.009000	0.14445	0.001000	0.01503	0.985000	0.29578	-0.071000	0.12886	-1.288000	0.01363	CGC	G|0.986;A|0.014	0.014	strong		0.642	SMPDL3B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011170.1	NM_014474	
BPIFB1	92747	hgsc.bcm.edu	37	20	31877770	31877770	+	Missense_Mutation	SNP	C	C	T	rs114635109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31877770C>T	ENST00000253354.1	+	4	498	c.337C>T	c.(337-339)Ccc>Tcc	p.P113S		NM_033197.2	NP_149974.2	Q8TDL5	BPIB1_HUMAN	BPI fold containing family B, member 1	113					innate immune response in mucosa (GO:0002227)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipid binding (GO:0008289)										AGTCAAGATCCCCCTGGACAT	0.582													C|||	45	0.00898562	0.0318	0.0029	5008	,	,		19004	0.0		0.001	False		,,,				2504	0.0				p.P113S		Atlas-SNP	.											.	.	.	.	0			c.C337T						PASS	.	C	SER/PRO	170,4236	111.6+/-149.8	4,162,2037	124.0	95.0	105.0		337	5.4	1.0	20	dbSNP_132	105	1,8599	1.2+/-3.3	0,1,4299	yes	missense	BPIFB1	NM_033197.2	74	4,163,6336	TT,TC,CC		0.0116,3.8584,1.3148	probably-damaging	113/485	31877770	171,12835	2203	4300	6503	SO:0001583	missense	92747	exon4			AAGATCCCCCTGG	BC008429	CCDS13218.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000125999	ENSG00000125999		"""BPI fold containing"""	16108	protein-coding gene	gene with protein product	"""von Ebner minor salivary gland protein"""		"""chromosome 20 open reading frame 114"""	C20orf114		11971875, 21787333	Standard	NM_033197		Approved	dJ1187J4.1, MGC14597, bA49G10.6, LPLUNC1, VEMSGP	uc002wyw.1	Q8TDL5	OTTHUMG00000032252	ENST00000253354.1:c.337C>T	20.37:g.31877770C>T	ENSP00000253354:p.Pro113Ser	115.0	0.0	0		112.0	63.0	0.5625	NM_033197	A8K2H8|Q5QP43|Q6UWY1|Q6ZRU7|Q96HK6|Q9BQP8|Q9BWZ6|Q9H4V6	Missense_Mutation	SNP	ENST00000253354.1	37	CCDS13218.1	14	0.00641025641025641	12	0.024390243902439025	2	0.0055248618784530384	0	0.0	0	0.0	C	19.64	3.865475	0.71949	0.038584	1.16E-4	ENSG00000125999	ENST00000423645;ENST00000253354	T;T	0.06142	3.34;3.7	5.4	5.4	0.78164	.	0.000000	0.64402	D	0.000008	T	0.06645	0.0170	M	0.80847	2.515	0.39655	D	0.970525	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.00099	-1.2067	10	0.38643	T	0.18	-35.2487	15.0609	0.71951	0.0:1.0:0.0:0.0	.	113;113	B2R7Z6;Q8TDL5	.;BPIB1_HUMAN	S	113	ENSP00000390471:P113S;ENSP00000253354:P113S	ENSP00000253354:P113S	P	+	1	0	BPIFB1	31341431	0.958000	0.32768	0.987000	0.45799	0.713000	0.41058	3.494000	0.53273	2.722000	0.93159	0.655000	0.94253	CCC	C|0.988;T|0.012	0.012	strong		0.582	BPIFB1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106499.2	NM_033197	
NOS2	4843	hgsc.bcm.edu	37	17	26107840	26107840	+	Silent	SNP	G	G	A	rs34719207	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:26107840G>A	ENST00000313735.6	-	9	1190	c.957C>T	c.(955-957)ttC>ttT	p.F319F		NM_000625.4	NP_000616.3	P35228	NOS2_HUMAN	nitric oxide synthase 2, inducible	319					arginine catabolic process (GO:0006527)|blood coagulation (GO:0007596)|cellular response to interferon-gamma (GO:0071346)|cellular response to lipopolysaccharide (GO:0071222)|circadian rhythm (GO:0007623)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|inflammatory response (GO:0006954)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|negative regulation of protein catabolic process (GO:0042177)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide mediated signal transduction (GO:0007263)|peptidyl-cysteine S-nitrosylation (GO:0018119)|phagosome maturation (GO:0090382)|positive regulation of guanylate cyclase activity (GO:0031284)|positive regulation of killing of cells of other organism (GO:0051712)|positive regulation of leukocyte mediated cytotoxicity (GO:0001912)|positive regulation of vasodilation (GO:0045909)|regulation of cell proliferation (GO:0042127)|regulation of cellular respiration (GO:0043457)|regulation of insulin secretion (GO:0050796)|response to bacterium (GO:0009617)|response to hypoxia (GO:0001666)|superoxide metabolic process (GO:0006801)	cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	arginine binding (GO:0034618)|flavin adenine dinucleotide binding (GO:0050660)|FMN binding (GO:0010181)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|NADP binding (GO:0050661)|NADPH-hemoprotein reductase activity (GO:0003958)|nitric-oxide synthase activity (GO:0004517)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|tetrahydrobiopterin binding (GO:0034617)			autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(28)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	56					Dexamethasone(DB01234)|Doxorubicin(DB00997)|L-Arginine(DB00125)|L-Citrulline(DB00155)|Miconazole(DB01110)|Triflusal(DB08814)	GTGGGATTTCGAAGAGCTCAG	0.607													G|||	22	0.00439297	0.0151	0.0014	5008	,	,		19507	0.0		0.001	False		,,,				2504	0.0				p.F319F		Atlas-SNP	.											.	NOS2	113	.	0			c.C957T						PASS	.	G		50,4356	50.9+/-86.3	0,50,2153	80.0	70.0	73.0		957	-11.0	0.1	17	dbSNP_126	73	0,8600		0,0,4300	no	coding-synonymous	NOS2	NM_000625.4		0,50,6453	AA,AG,GG		0.0,1.1348,0.3844		319/1154	26107840	50,12956	2203	4300	6503	SO:0001819	synonymous_variant	4843	exon9			GATTTCGAAGAGC	U20141	CCDS11223.1	17q11.2	2014-06-12	2008-09-16	2008-09-16	ENSG00000007171	ENSG00000007171	1.14.13.39		7873	protein-coding gene	gene with protein product		163730	"""nitric oxide synthase 2A (inducible, hepatocytes)"""	NOS2A		7682706	Standard	NM_000625		Approved	iNOS, NOS, HEP-NOS	uc002gzu.3	P35228	OTTHUMG00000132445	ENST00000313735.6:c.957C>T	17.37:g.26107840G>A		123.0	0.0	0		128.0	70.0	0.546875	NM_000625	A1L3U5|B7ZLY2|O60757|O94994|Q16263|Q16692|Q4TTS5|Q9UD42	Silent	SNP	ENST00000313735.6	37	CCDS11223.1																																																																																			G|0.996;A|0.004	0.004	strong		0.607	NOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255597.1	NM_000625	
DCDC2B	149069	hgsc.bcm.edu	37	1	32677370	32677370	+	Silent	SNP	C	C	T	rs182464428	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:32677370C>T	ENST00000409358.1	+	3	327	c.327C>T	c.(325-327)ccC>ccT	p.P109P		NM_001099434.1	NP_001092904.1	A2VCK2	DCD2B_HUMAN	doublecortin domain containing 2B	109					intracellular signal transduction (GO:0035556)					breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)	11		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				AGGGTCCTCCCGTGACTCGCC	0.617													C|||	5	0.000998403	0.0038	0.0	5008	,	,		15943	0.0		0.0	False		,,,				2504	0.0				p.P109P		Atlas-SNP	.											.	DCDC2B	24	.	0			c.C327T						PASS	.	C		18,4196		0,18,2089	36.0	38.0	38.0		327	-6.6	0.0	1		38	0,8482		0,0,4241	no	coding-synonymous	DCDC2B	NM_001099434.1		0,18,6330	TT,TC,CC		0.0,0.4271,0.1418		109/350	32677370	18,12678	2107	4241	6348	SO:0001819	synonymous_variant	149069	exon3			TCCTCCCGTGACT	BC128073	CCDS44100.1	1p35.1	2008-05-13			ENSG00000222046	ENSG00000222046			32576	protein-coding gene	gene with protein product							Standard	NM_001099434		Approved		uc001bun.2	A2VCK2	OTTHUMG00000005741	ENST00000409358.1:c.327C>T	1.37:g.32677370C>T		85.0	0.0	0		76.0	36.0	0.473684	NM_001099434	B7ZBC6	Silent	SNP	ENST00000409358.1	37	CCDS44100.1																																																																																			C|0.998;T|0.002	0.002	strong		0.617	DCDC2B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328293.1	XM_940631	
CBL	867	hgsc.bcm.edu	37	11	119170362	119170362	+	Silent	SNP	C	C	T	rs1893177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:119170362C>T	ENST00000264033.4	+	16	2968	c.2592C>T	c.(2590-2592)ctC>ctT	p.L864L		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	864	Interaction with CD2AP.|UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				cell surface receptor signaling pathway (GO:0007166)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|flotillin complex (GO:0016600)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ephrin receptor binding (GO:0046875)|ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(194)|kidney(3)|large_intestine(9)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	251		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		TCGAGAACCTCATGAGTCAGG	0.537			"""T, Mis S, O"""	MLL	"""AML, JMML, MDS"""				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies				C|||	172	0.034345	0.1203	0.0187	5008	,	,		19424	0.0		0.0	False		,,,				2504	0.0				p.L864L		Atlas-SNP	.		"""Dom, Rec"""	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	.	CBL	408	.	0			c.C2592T						PASS	.	C		478,3920	224.9+/-240.9	22,434,1743	217.0	217.0	217.0		2592	4.7	1.0	11	dbSNP_92	217	1,8589	1.2+/-3.3	0,1,4294	no	coding-synonymous	CBL	NM_005188.2		22,435,6037	TT,TC,CC		0.0116,10.8686,3.688		864/907	119170362	479,12509	2199	4295	6494	SO:0001819	synonymous_variant	867	exon16	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CBL-associated JMML	GAACCTCATGAGT	X57110	CCDS8418.1	11q23.3	2014-09-17	2012-02-23		ENSG00000110395	ENSG00000110395		"""RING-type (C3HC4) zinc fingers"""	1541	protein-coding gene	gene with protein product	"""oncogene CBL2"""	165360	"""Cas-Br-M (murine) ecotropic retroviral transforming sequence"""	CBL2		2013228	Standard	NM_005188		Approved	RNF55, c-Cbl	uc001pwe.4	P22681	OTTHUMG00000166170	ENST00000264033.4:c.2592C>T	11.37:g.119170362C>T		113.0	0.0	0		79.0	47.0	0.594937	NM_005188	A3KMP8	Silent	SNP	ENST00000264033.4	37	CCDS8418.1																																																																																			C|0.948;T|0.052	0.052	strong		0.537	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4	NM_005188	
GGT5	2687	hgsc.bcm.edu	37	22	24622124	24622124	+	Silent	SNP	G	G	A	rs73879043	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:24622124G>A	ENST00000327365.4	-	8	1565	c.1149C>T	c.(1147-1149)ggC>ggT	p.G383G	GGT5_ENST00000263112.7_Silent_p.G351G|GGT5_ENST00000418439.2_Silent_p.G306G|GGT5_ENST00000398292.3_Silent_p.G383G	NM_001099781.1|NM_004121.2	NP_001093251.1|NP_004112.2	P36269	GGT5_HUMAN	gamma-glutamyltransferase 5	383					arachidonic acid metabolic process (GO:0019369)|cellular amino acid metabolic process (GO:0006520)|glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|inflammatory response (GO:0006954)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|small molecule metabolic process (GO:0044281)	anchored component of external side of plasma membrane (GO:0031362)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(2)|prostate(3)|skin(3)	28						CTGTCCCGTGGCCCCAGGCCT	0.687													G|||	101	0.0201677	0.0711	0.0101	5008	,	,		14159	0.0		0.0	False		,,,				2504	0.0				p.G383G		Atlas-SNP	.											.	GGT5	61	.	0			c.C1149T						PASS	.	G	,,	236,4170	131.8+/-168.3	6,224,1973	30.0	32.0	31.0		1149,1053,1149	1.6	0.1	22	dbSNP_130	31	0,8596		0,0,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	GGT5	NM_001099781.1,NM_001099782.1,NM_004121.2	,,	6,224,6271	AA,AG,GG		0.0,5.3563,1.8151	,,	383/588,351/555,383/587	24622124	236,12766	2203	4298	6501	SO:0001819	synonymous_variant	2687	exon8			CCCGTGGCCCCAG	M64099	CCDS13825.1, CCDS42989.1, CCDS42990.1	22q11.23	2008-03-25	2008-03-10	2008-03-10	ENSG00000099998	ENSG00000099998		"""Gamma-glutamyltransferases"""	4260	protein-coding gene	gene with protein product		137168	"""gamma-glutamyltransferase-like activity 1"""	GGTLA1		1676842, 8095916, 18357469	Standard	NM_004121		Approved	GGT-REL	uc002zzp.4	P36269	OTTHUMG00000150796	ENST00000327365.4:c.1149C>T	22.37:g.24622124G>A		122.0	0.0	0		101.0	54.0	0.534653	NM_001099781	Q53XM9|Q6GMP0|Q96FC1|Q9UFM5	Silent	SNP	ENST00000327365.4	37	CCDS13825.1																																																																																			G|0.981;A|0.019	0.019	strong		0.687	GGT5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000320119.1	NM_004121	
ESPL1	9700	hgsc.bcm.edu	37	12	53680135	53680135	+	Silent	SNP	C	C	T	rs61741367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:53680135C>T	ENST00000257934.4	+	18	3706	c.3615C>T	c.(3613-3615)tcC>tcT	p.S1205S	ESPL1_ENST00000552462.1_Silent_p.S1205S	NM_012291.4	NP_036423.4	Q14674	ESPL1_HUMAN	extra spindle pole bodies homolog 1 (S. cerevisiae)	1205					apoptotic process (GO:0006915)|cytokinesis (GO:0000910)|establishment of mitotic spindle localization (GO:0040001)|homologous chromosome segregation (GO:0045143)|meiotic spindle organization (GO:0000212)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of sister chromatid cohesion (GO:0045875)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)	centrosome (GO:0005813)|cytosol (GO:0005829)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(10)|large_intestine(12)|lung(21)|ovary(2)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(8)	70						TCCAAGCTTCCCTGAATCATA	0.582													C|||	180	0.0359425	0.1316	0.0086	5008	,	,		17444	0.0		0.0	False		,,,				2504	0.0				p.S1205S	Colon(53;1069 1201 2587 5382)	Atlas-SNP	.											.	ESPL1	158	.	0			c.C3615T						PASS	.	C		503,3903	233.3+/-246.5	36,431,1736	79.0	87.0	84.0		3615	0.4	0.3	12	dbSNP_129	84	7,8593	4.3+/-15.6	0,7,4293	no	coding-synonymous	ESPL1	NM_012291.4		36,438,6029	TT,TC,CC		0.0814,11.4163,3.9213		1205/2121	53680135	510,12496	2203	4300	6503	SO:0001819	synonymous_variant	9700	exon18			AGCTTCCCTGAAT	D79987	CCDS8852.1	12q13.13	2014-08-04	2013-05-03		ENSG00000135476	ENSG00000135476	3.4.22.49		16856	protein-coding gene	gene with protein product	"""separin"", ""separase"", ""separin, cysteine protease"""	604143	"""extra spindle poles like 1 (S. cerevisiae)"""			8724849, 16258266	Standard	NM_012291		Approved	KIAA0165, ESP1, SEPA	uc001sck.2	Q14674	OTTHUMG00000169674	ENST00000257934.4:c.3615C>T	12.37:g.53680135C>T		48.0	0.0	0		73.0	32.0	0.438356	NM_012291		Silent	SNP	ENST00000257934.4	37	CCDS8852.1																																																																																			C|0.957;T|0.043	0.043	strong		0.582	ESPL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406899.2	NM_012291	
VTI1B	10490	hgsc.bcm.edu	37	14	68141105	68141105	+	Silent	SNP	C	C	T	rs2234510	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:68141105C>T	ENST00000554659.1	-	1	443	c.102G>A	c.(100-102)ggG>ggA	p.G34G	RP11-1012A1.4_ENST00000554493.1_Intron|RP11-1012A1.4_ENST00000553306.1_Intron	NM_006370.2	NP_006361.1	Q9UEU0	VTI1B_HUMAN	vesicle transport through interaction with t-SNAREs 1B	34					cell proliferation (GO:0008283)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|SNARE complex (GO:0031201)|synaptic vesicle (GO:0008021)	SNARE binding (GO:0000149)			endometrium(1)|large_intestine(2)|stomach(1)|upper_aerodigestive_tract(1)	5				all cancers(60;0.000344)|OV - Ovarian serous cystadenocarcinoma(108;0.00212)|BRCA - Breast invasive adenocarcinoma(234;0.00941)		TCCCCGCCGTCCCCAGCAGCC	0.697													C|||	150	0.0299521	0.1097	0.0072	5008	,	,		8683	0.0		0.0	False		,,,				2504	0.0				p.G34G		Atlas-SNP	.											.	VTI1B	15	.	0			c.G102A						PASS	.	C		347,3945		9,329,1808	8.0	9.0	9.0		102	0.4	0.4	14	dbSNP_98	9	1,8419		0,1,4209	no	coding-synonymous	VTI1B	NM_006370.2		9,330,6017	TT,TC,CC		0.0119,8.0848,2.7376		34/233	68141105	348,12364	2146	4210	6356	SO:0001819	synonymous_variant	10490	exon1			CGCCGTCCCCAGC	AF060902	CCDS9786.1	14q23.3	2012-12-10	2012-12-10		ENSG00000100568	ENSG00000100568			17793	protein-coding gene	gene with protein product		603207	"""vesicle transport through interaction with t-SNAREs homolog 1B (yeast)"""			9636656, 9446565	Standard	NM_006370		Approved	VTI2	uc001xjt.3	Q9UEU0	OTTHUMG00000171251	ENST00000554659.1:c.102G>A	14.37:g.68141105C>T		24.0	0.0	0		63.0	32.0	0.507937	NM_006370	O43547|Q96J28	Silent	SNP	ENST00000554659.1	37	CCDS9786.1																																																																																			C|0.973;T|0.027	0.027	strong		0.697	VTI1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412558.2		
ZBED4	9889	hgsc.bcm.edu	37	22	50278588	50278588	+	Silent	SNP	C	C	T	rs61731526	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50278588C>T	ENST00000216268.5	+	2	1755	c.1278C>T	c.(1276-1278)tcC>tcT	p.S426S		NM_014838.2	NP_055653.2	O75132	ZBED4_HUMAN	zinc finger, BED-type containing 4	426						cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(3)|kidney(2)|large_intestine(11)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	44		all_cancers(38;8.58e-10)|all_epithelial(38;1.15e-08)|all_lung(38;0.000109)|Lung NSC(38;0.0018)|Breast(42;0.00191)|Ovarian(80;0.0164)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)|BRCA - Breast invasive adenocarcinoma(115;0.2)|LUAD - Lung adenocarcinoma(64;0.247)		CCTCGGCGTCCTCTCCTGAGA	0.532													C|||	23	0.00459265	0.0159	0.0029	5008	,	,		19928	0.0		0.0	False		,,,				2504	0.0				p.S426S		Atlas-SNP	.											.	ZBED4	102	.	0			c.C1278T						PASS	.	C		44,4362	40.8+/-73.8	0,44,2159	59.0	63.0	62.0		1278	-0.5	0.3	22	dbSNP_129	62	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ZBED4	NM_014838.2		0,46,6457	TT,TC,CC		0.0233,0.9986,0.3537		426/1172	50278588	46,12960	2203	4300	6503	SO:0001819	synonymous_variant	9889	exon2			GGCGTCCTCTCCT	AB014537	CCDS33677.1	22q13.33	2013-05-03			ENSG00000100426	ENSG00000100426		"""Zinc fingers, BED-type"""	20721	protein-coding gene	gene with protein product		612552				23533661	Standard	NM_014838		Approved	KIAA0637	uc003bix.2	O75132	OTTHUMG00000150291	ENST00000216268.5:c.1278C>T	22.37:g.50278588C>T		42.0	0.0	0		55.0	19.0	0.345455	NM_014838	B2RZH1|Q1ECU0|Q9UGG8	Silent	SNP	ENST00000216268.5	37	CCDS33677.1																																																																																			C|0.996;T|0.004	0.004	strong		0.532	ZBED4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317408.2	NM_014838	
PIAS4	51588	hgsc.bcm.edu	37	19	4012971	4012971	+	Silent	SNP	C	C	T	rs61729790	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4012971C>T	ENST00000262971.2	+	2	193	c.78C>T	c.(76-78)ttC>ttT	p.F26F		NM_015897.2	NP_056981.2	Q8N2W9	PIAS4_HUMAN	protein inhibitor of activated STAT, 4	26	SAP. {ECO:0000255|PROSITE- ProRule:PRU00186, ECO:0000305}.				negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|positive regulation of keratinocyte apoptotic process (GO:1902174)|positive regulation of protein sumoylation (GO:0033235)|protein sumoylation (GO:0016925)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	DNA binding (GO:0003677)|SUMO ligase activity (GO:0019789)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(1)|lung(3)|pancreas(1)|skin(3)	17				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		TCCTGGGTTTCGTGGGCCGGA	0.562													c|||	507	0.101238	0.3699	0.0245	5008	,	,		15489	0.0		0.001	False		,,,				2504	0.0				p.F26F		Atlas-SNP	.											.	PIAS4	40	.	0			c.C78T						PASS	.	T		1226,3180	424.2+/-340.4	166,894,1143	115.0	110.0	112.0		78	-8.9	0.1	19	dbSNP_129	112	11,8589	7.1+/-27.0	0,11,4289	no	coding-synonymous	PIAS4	NM_015897.2		166,905,5432	TT,TC,CC		0.1279,27.8257,9.511		26/511	4012971	1237,11769	2203	4300	6503	SO:0001819	synonymous_variant	51588	exon2			GGGTTTCGTGGGC	AF077952	CCDS12118.1	19p13.3	2011-10-11						"""Zinc fingers, MIZ-type"""	17002	protein-coding gene	gene with protein product	"""zinc finger, MIZ-type containing 6"""	605989				9724754	Standard	NM_015897		Approved	Piasg, PIASY, FLJ12419, ZMIZ6	uc002lzg.3	Q8N2W9		ENST00000262971.2:c.78C>T	19.37:g.4012971C>T		198.0	0.0	0		163.0	163.0	1	NM_015897	O75926|Q96G19|Q9UN16	Silent	SNP	ENST00000262971.2	37	CCDS12118.1																																																																																			C|0.910;T|0.090	0.090	strong		0.562	PIAS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457496.1	NM_015897	
ZNF264	9422	hgsc.bcm.edu	37	19	57723182	57723182	+	Silent	SNP	C	C	T	rs61730346	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:57723182C>T	ENST00000263095.6	+	4	1131	c.717C>T	c.(715-717)acC>acT	p.T239T	ZNF264_ENST00000536056.1_Silent_p.T239T	NM_003417.4	NP_003408.1	O43296	ZN264_HUMAN	zinc finger protein 264	239					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(8)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	27		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0135)		GTGGGAAAACCTTTATTAAGA	0.448													.|||	48	0.00958466	0.0356	0.0	5008	,	,		21386	0.0		0.001	False		,,,				2504	0.0				p.T239T		Atlas-SNP	.											.	ZNF264	65	.	0			c.C717T						PASS	.	C		120,4286	89.2+/-127.9	2,116,2085	97.0	96.0	96.0		717	-2.4	0.0	19	dbSNP_129	96	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ZNF264	NM_003417.4		2,118,6383	TT,TC,CC		0.0233,2.7236,0.938		239/628	57723182	122,12884	2203	4300	6503	SO:0001819	synonymous_variant	9422	exon4			GAAAACCTTTATT	AB007872	CCDS33127.1	19q13.4	2013-01-08				ENSG00000083844		"""Zinc fingers, C2H2-type"", ""-"""	13057	protein-coding gene	gene with protein product		604668				9455477	Standard	NM_003417		Approved	KIAA0412	uc002qob.3	O43296		ENST00000263095.6:c.717C>T	19.37:g.57723182C>T		65.0	0.0	0		81.0	47.0	0.580247	NM_003417	A8K8Y9|Q9P1V0	Silent	SNP	ENST00000263095.6	37	CCDS33127.1																																																																																			C|0.990;T|0.010	0.010	strong		0.448	ZNF264-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465080.1		
CDHR2	54825	hgsc.bcm.edu	37	5	176011968	176011968	+	Missense_Mutation	SNP	G	G	A	rs114527399	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:176011968G>A	ENST00000510636.1	+	19	2960	c.2686G>A	c.(2686-2688)Gcc>Acc	p.A896T	CDHR2_ENST00000261944.5_Missense_Mutation_p.A896T|CDHR2_ENST00000506348.1_Missense_Mutation_p.A896T	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	896	Cadherin 8. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|liver(1)|lung(23)|ovary(3)|prostate(5)|skin(4)|urinary_tract(1)	56						GGTTGTGCGGGCCTGTGACCT	0.627													G|||	9	0.00179712	0.0068	0.0	5008	,	,		19273	0.0		0.0	False		,,,				2504	0.0				p.A896T		Atlas-SNP	.											.	CDHR2	152	.	0			c.G2686A						PASS	.	G	THR/ALA,THR/ALA	29,4319		0,29,2145	29.0	25.0	26.0		2686,2686	5.4	1.0	5	dbSNP_132	26	0,8520		0,0,4260	yes	missense,missense	CDHR2	NM_001171976.1,NM_017675.4	58,58	0,29,6405	AA,AG,GG		0.0,0.667,0.2254	probably-damaging,probably-damaging	896/1311,896/1311	176011968	29,12839	2174	4260	6434	SO:0001583	missense	54825	exon19			GTGCGGGCCTGTG	AB047004	CCDS34297.1	5q35.2	2011-07-01	2010-01-25	2010-01-25		ENSG00000074276		"""Cadherins / Cadherin-related"""	18231	protein-coding gene	gene with protein product	"""protocadherin LKC"""		"""protocadherin 24"""	PCDH24		11082270, 12117771	Standard	NM_001171976		Approved	PC-LKC, FLJ20124, FLJ20383, PCLKC	uc003mem.2	Q9BYE9		ENST00000510636.1:c.2686G>A	5.37:g.176011968G>A	ENSP00000424565:p.Ala896Thr	80.0	0.0	0		79.0	37.0	0.468354	NM_017675	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	37	CCDS34297.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	21.9	4.219121	0.79464	0.00667	0.0	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.75589	-0.95;-0.95;-0.95	5.42	5.42	0.78866	Cadherin (4);Cadherin-like (1);	.	.	.	.	D	0.86493	0.5946	H	0.95611	3.695	0.42064	D	0.991178	D	0.62365	0.991	P	0.59595	0.86	D	0.90838	0.4721	9	0.62326	D	0.03	-45.3354	19.2279	0.93824	0.0:0.0:1.0:0.0	.	896	Q9BYE9	CDHR2_HUMAN	T	896	ENSP00000424565:A896T;ENSP00000261944:A896T;ENSP00000421078:A896T	ENSP00000261944:A896T	A	+	1	0	CDHR2	175944574	1.000000	0.71417	0.999000	0.59377	0.304000	0.27724	7.214000	0.77958	2.547000	0.85894	0.549000	0.68633	GCC	G|0.996;A|0.004	0.004	strong		0.627	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675	
MXD3	83463	hgsc.bcm.edu	37	5	176734945	176734945	+	Missense_Mutation	SNP	C	C	A	rs35691394	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:176734945C>A	ENST00000439742.2	-	5	820	c.342G>T	c.(340-342)caG>caT	p.Q114H	MXD3_ENST00000427908.2_Missense_Mutation_p.Q114H|MXD3_ENST00000423571.2_Missense_Mutation_p.Q114H|MXD3_ENST00000513063.1_Missense_Mutation_p.Q114H	NM_031300.3	NP_112590.1	Q9BW11	MAD3_HUMAN	MAX dimerization protein 3	114			Q -> H (in dbSNP:rs35691394).		negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)					all_cancers(89;2.49e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	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)			GTCGGGCCCGCTGCTCCTGAT	0.711													C|||	7	0.00139776	0.0053	0.0	5008	,	,		15589	0.0		0.0	False		,,,				2504	0.0				p.Q114H		Atlas-SNP	.											.	MXD3	13	.	0			c.G342T						PASS	.	C	HIS/GLN,HIS/GLN	29,4071		0,29,2021	5.0	6.0	5.0		342,342	4.1	1.0	5	dbSNP_126	5	1,8135		0,1,4067	no	missense,missense	MXD3	NM_001142935.1,NM_031300.3	24,24	0,30,6088	AA,AC,CC		0.0123,0.7073,0.2452	possibly-damaging,possibly-damaging	114/194,114/207	176734945	30,12206	2050	4068	6118	SO:0001583	missense	83463	exon5			GGCCCGCTGCTCC	BC000745	CCDS4416.1, CCDS47347.1	5q35.3	2013-03-20			ENSG00000213347	ENSG00000213347		"""MAX dimerization proteins"", ""Basic helix-loop-helix proteins"""	14008	protein-coding gene	gene with protein product		609450					Standard	NM_031300		Approved	MAD3, bHLHc13	uc003mgb.2	Q9BW11	OTTHUMG00000130854	ENST00000439742.2:c.342G>T	5.37:g.176734945C>A	ENSP00000401867:p.Gln114His	23.0	0.0	0		39.0	22.0	0.564103	NM_001142935	B4E0J1|Q53HK1|Q7Z4Y0|Q8NDJ7|Q96ME3	Missense_Mutation	SNP	ENST00000439742.2	37	CCDS4416.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	19.48	3.835342	0.71373	0.007073	1.23E-4	ENSG00000213347	ENST00000427908;ENST00000423571;ENST00000439742;ENST00000303165;ENST00000513063;ENST00000513169;ENST00000502529	D;D;D;D;T;T	0.88975	-2.45;-2.45;-2.45;-2.45;0.88;0.9	5.0	4.13	0.48395	Helix-loop-helix DNA-binding (3);	0.422928	0.25416	N	0.030831	D	0.87249	0.6130	L	0.44542	1.39	0.33730	D	0.618086	D;D;D;D	0.71674	0.998;0.989;0.981;0.99	P;P;P;P	0.62560	0.904;0.769;0.687;0.825	D	0.90640	0.4574	10	0.59425	D	0.04	-0.452	10.1788	0.42955	0.0:0.8454:0.0:0.1546	rs35691394	114;105;114;114	Q9BW11-3;F8W9D2;Q9BW11;B4E0J1	.;.;MAD3_HUMAN;.	H	114;114;114;105;114;31;104	ENSP00000416921:Q114H;ENSP00000389716:Q114H;ENSP00000401867:Q114H;ENSP00000421463:Q114H;ENSP00000427104:Q31H;ENSP00000425029:Q104H	ENSP00000307720:Q105H	Q	-	3	2	MXD3	176667551	0.001000	0.12720	0.979000	0.43373	0.681000	0.39784	1.288000	0.33296	1.226000	0.43582	0.561000	0.74099	CAG	C|0.997;A|0.003	0.003	strong		0.711	MXD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253427.1		
EXOC4	60412	hgsc.bcm.edu	37	7	133682285	133682285	+	Silent	SNP	C	C	T	rs34608222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:133682285C>T	ENST00000253861.4	+	15	2276	c.2247C>T	c.(2245-2247)ctC>ctT	p.L749L	EXOC4_ENST00000545148.1_Silent_p.L359L|EXOC4_ENST00000539845.1_Silent_p.L648L|EXOC4_ENST00000541309.1_Silent_p.L37L	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	749					cellular protein metabolic process (GO:0044267)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)	protein N-terminus binding (GO:0047485)			NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(16)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	50		Esophageal squamous(399;0.129)				ACACGGATCTCCCCCCAGTGT	0.458													C|||	62	0.0123802	0.0439	0.0043	5008	,	,		19403	0.0		0.001	False		,,,				2504	0.0				p.L749L		Atlas-SNP	.											.	EXOC4	118	.	0			c.C2247T						PASS	.	C		209,4197	126.6+/-163.6	9,191,2003	141.0	114.0	123.0		2247	-2.3	0.6	7	dbSNP_126	123	0,8600		0,0,4300	no	coding-synonymous	EXOC4	NM_021807.3		9,191,6303	TT,TC,CC		0.0,4.7435,1.607		749/975	133682285	209,12797	2203	4300	6503	SO:0001819	synonymous_variant	60412	exon15			GGATCTCCCCCCA	AL831989	CCDS5829.1, CCDS43648.1	7q31	2013-01-22	2005-11-01	2005-11-01	ENSG00000131558	ENSG00000131558			30389	protein-coding gene	gene with protein product		608185	"""SEC8-like 1 (S. cerevisiae)"""	SEC8L1		11214970, 12687004	Standard	XM_005250523		Approved	KIAA1699, MGC27170, SEC8, Sec8p	uc003vrk.3	Q96A65	OTTHUMG00000155259	ENST00000253861.4:c.2247C>T	7.37:g.133682285C>T		106.0	0.0	0		117.0	56.0	0.478632	NM_021807	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Silent	SNP	ENST00000253861.4	37	CCDS5829.1																																																																																			C|0.986;T|0.014	0.014	strong		0.458	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807	
SPAG7	9552	hgsc.bcm.edu	37	17	4863540	4863540	+	Missense_Mutation	SNP	T	T	C	rs73343382	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4863540T>C	ENST00000206020.3	-	4	383	c.316A>G	c.(316-318)Atc>Gtc	p.I106V	SPAG7_ENST00000575142.1_Missense_Mutation_p.I95V|SPAG7_ENST00000573366.1_Missense_Mutation_p.I55V	NM_004890.2	NP_004881.2	O75391	SPAG7_HUMAN	sperm associated antigen 7	106	R3H. {ECO:0000255|PROSITE- ProRule:PRU00382}.					nucleus (GO:0005634)	nucleic acid binding (GO:0003676)			central_nervous_system(1)|endometrium(1)|kidney(2)|lung(3)|ovary(2)|urinary_tract(1)	10						TTTTTGAAGATCATGACATAG	0.488													T|||	154	0.0307508	0.1127	0.0058	5008	,	,		19237	0.0		0.001	False		,,,				2504	0.0				p.I106V		Atlas-SNP	.											.	SPAG7	22	.	0			c.A316G						PASS	.	T	VAL/ILE	363,3671		20,323,1674	75.0	79.0	78.0		316	5.3	1.0	17	dbSNP_130	78	4,8376		0,4,4186	yes	missense	SPAG7	NM_004890.2	29	20,327,5860	CC,CT,TT		0.0477,8.9985,2.9563	benign	106/228	4863540	367,12047	2017	4190	6207	SO:0001583	missense	9552	exon4			TGAAGATCATGAC	AF047437	CCDS42240.1	17p13.2	2008-07-18				ENSG00000091640			11216	protein-coding gene	gene with protein product		610056				9653160	Standard	NM_004890		Approved	FSA-1, ACRP, MGC20134	uc002gae.3	O75391		ENST00000206020.3:c.316A>G	17.37:g.4863540T>C	ENSP00000206020:p.Ile106Val	197.0	0.0	0		183.0	95.0	0.519126	NM_004890	Q96EU5	Missense_Mutation	SNP	ENST00000206020.3	37	CCDS42240.1	46	0.021062271062271064	44	0.08943089430894309	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	0.871	-0.732127	0.03135	0.089985	4.77E-4	ENSG00000091640	ENST00000206020	T	0.43688	0.94	5.3	5.3	0.74995	Single-stranded nucleic acid binding R3H (3);	0.117351	0.56097	D	0.000028	T	0.00967	0.0032	N	0.25789	0.76	0.41244	D	0.986669	B	0.10296	0.003	B	0.12837	0.008	T	0.02610	-1.1134	10	0.02654	T	1	-4.764	13.2379	0.59979	0.0:0.0:0.0:1.0	.	106	O75391	SPAG7_HUMAN	V	106	ENSP00000206020:I106V	ENSP00000206020:I106V	I	-	1	0	SPAG7	4804263	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.809000	0.38922	2.225000	0.72522	0.533000	0.62120	ATC	T|0.978;C|0.022	0.022	strong		0.488	SPAG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438747.1	NM_004890	
PKD1L1	168507	hgsc.bcm.edu	37	7	47924233	47924233	+	Silent	SNP	G	G	A	rs79566365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:47924233G>A	ENST00000289672.2	-	19	3278	c.3228C>T	c.(3226-3228)gaC>gaT	p.D1076D		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	1076	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						CTTCTTGAATGTCACTGTAAT	0.448													A|||	194	0.038738	0.1377	0.0101	5008	,	,		20921	0.0		0.004	False		,,,				2504	0.001				p.D1076D		Atlas-SNP	.											.	PKD1L1	328	.	0			c.C3228T						PASS	.	A		641,3765	767.0+/-413.5	47,547,1609	147.0	131.0	136.0		3228	-4.3	0.0	7	dbSNP_132	136	85,8515	815.6+/-407.0	1,83,4216	no	coding-synonymous	PKD1L1	NM_138295.3		48,630,5825	AA,AG,GG		0.9884,14.5483,5.582		1076/2850	47924233	726,12280	2203	4300	6503	SO:0001819	synonymous_variant	168507	exon19			TTGAATGTCACTG	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.3228C>T	7.37:g.47924233G>A		87.0	0.0	0		92.0	36.0	0.391304	NM_138295	Q6UWK1	Silent	SNP	ENST00000289672.2	37	CCDS34633.1																																																																																			G|0.951;A|0.049	0.049	strong		0.448	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
ASB16	92591	hgsc.bcm.edu	37	17	42248205	42248205	+	Silent	SNP	C	C	T	rs56265171	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:42248205C>T	ENST00000293414.1	+	1	132	c.48C>T	c.(46-48)ctC>ctT	p.L16L		NM_080863.4	NP_543139.4	Q96NS5	ASB16_HUMAN	ankyrin repeat and SOCS box containing 16	16					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|liver(2)|lung(2)|prostate(1)	14		Breast(137;0.00765)|Prostate(33;0.0313)		BRCA - Breast invasive adenocarcinoma(366;0.114)		TGCGCTCTCTCCGCCTGCAGC	0.697													C|||	168	0.0335463	0.1203	0.0115	5008	,	,		15859	0.0		0.001	False		,,,				2504	0.0				p.L16L		Atlas-SNP	.											.	ASB16	34	.	0			c.C48T						PASS	.	C		417,3989	196.4+/-220.7	17,383,1803	36.0	34.0	35.0		48	1.8	1.0	17	dbSNP_129	35	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous	ASB16	NM_080863.4		17,388,6098	TT,TC,CC		0.0581,9.4644,3.2447		16/454	42248205	422,12584	2203	4300	6503	SO:0001819	synonymous_variant	92591	exon1			CTCTCTCCGCCTG	AK054727	CCDS11478.1	17q21.31	2013-01-10	2011-01-25		ENSG00000161664	ENSG00000161664		"""Ankyrin repeat domain containing"""	19768	protein-coding gene	gene with protein product		615056	"""ankyrin repeat and SOCS box-containing 16"""			12076535	Standard	NM_080863		Approved	FLJ30165	uc002ifl.1	Q96NS5	OTTHUMG00000181809	ENST00000293414.1:c.48C>T	17.37:g.42248205C>T		180.0	0.0	0		190.0	103.0	0.542105	NM_080863	B2RBC0|Q8WXK0	Silent	SNP	ENST00000293414.1	37	CCDS11478.1																																																																																			C|0.967;T|0.033	0.033	strong		0.697	ASB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457703.1		
FREM1	158326	hgsc.bcm.edu	37	9	14824088	14824088	+	Missense_Mutation	SNP	T	T	C	rs7864984	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:14824088T>C	ENST00000380880.3	-	12	2887	c.2104A>G	c.(2104-2106)Atg>Gtg	p.M702V	FREM1_ENST00000380881.4_Missense_Mutation_p.M703V|FREM1_ENST00000422223.2_Missense_Mutation_p.M702V			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	702					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)		CTGTCCACCATAAATAATTTC	0.393													T|||	185	0.0369409	0.1309	0.0086	5008	,	,		20998	0.0		0.004	False		,,,				2504	0.002				p.M702V		Atlas-SNP	.											.	FREM1	261	.	0			c.A2104G						PASS	.	T	VAL/MET	360,3416		13,334,1541	63.0	60.0	61.0		2104	0.8	0.8	9	dbSNP_116	61	16,8218		0,16,4101	yes	missense	FREM1	NM_144966.5	21	13,350,5642	CC,CT,TT		0.1943,9.5339,3.1307	benign	702/2180	14824088	376,11634	1888	4117	6005	SO:0001583	missense	158326	exon13			CCACCATAAATAA	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.2104A>G	9.37:g.14824088T>C	ENSP00000370262:p.Met702Val	91.0	0.0	0		92.0	44.0	0.478261	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	55	0.025183150183150184	51	0.10365853658536585	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	T	7.670	0.686751	0.14973	0.095339	0.001943	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.25414	1.8;1.8;1.8	5.83	0.775	0.18527	.	0.246267	0.48767	D	0.000171	T	0.00580	0.0019	M	0.71581	2.175	0.28563	N	0.911019	B	0.22211	0.066	B	0.17098	0.017	T	0.20538	-1.0272	10	0.17832	T	0.49	-9.8199	8.6558	0.34062	0.1862:0.0:0.3315:0.4823	rs7864984;rs57027040;rs7864984	702	Q5H8C1	FREM1_HUMAN	V	703;702;702	ENSP00000370263:M703V;ENSP00000412940:M702V;ENSP00000370262:M702V	ENSP00000370257:M705V	M	-	1	0	FREM1	14814088	0.995000	0.38212	0.842000	0.33263	0.462000	0.32619	0.335000	0.19806	-0.394000	0.07727	-3.035000	0.00072	ATG	T|0.978;C|0.022	0.022	strong		0.393	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
NLN	57486	hgsc.bcm.edu	37	5	65054587	65054587	+	Missense_Mutation	SNP	G	G	A	rs34339013	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:65054587G>A	ENST00000380985.5	+	2	413	c.235G>A	c.(235-237)Ggt>Agt	p.G79S	NLN_ENST00000502464.1_Intron	NM_020726.4	NP_065777.1	Q9BYT8	NEUL_HUMAN	neurolysin (metallopeptidase M3 family)	79			G -> S (in dbSNP:rs34339013).			mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	26		Lung NSC(167;7.21e-05)|Prostate(74;0.0174)|Ovarian(174;0.186)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0743)|Lung(70;0.00616)		TGGAATGCTCGGTATTGAGGA	0.423													G|||	132	0.0263578	0.093	0.0115	5008	,	,		16846	0.0		0.001	False		,,,				2504	0.0				p.G79S		Atlas-SNP	.											.	NLN	51	.	0			c.G235A						PASS	.	G	SER/GLY	321,4085	171.9+/-202.1	14,293,1896	138.0	122.0	128.0		235	-1.6	0.0	5	dbSNP_126	128	0,8600		0,0,4300	yes	missense	NLN	NM_020726.4	56	14,293,6196	AA,AG,GG		0.0,7.2855,2.4681	benign	79/705	65054587	321,12685	2203	4300	6503	SO:0001583	missense	57486	exon2			ATGCTCGGTATTG	AJ300837	CCDS3989.1	5q12.3	2008-02-05	2005-03-31		ENSG00000123213	ENSG00000123213	3.4.24.16		16058	protein-coding gene	gene with protein product		611530	"""angiotensin binding protein"""	AGTBP		10574462	Standard	NM_020726		Approved	KIAA1226	uc003juf.3	Q9BYT8	OTTHUMG00000097803	ENST00000380985.5:c.235G>A	5.37:g.65054587G>A	ENSP00000370372:p.Gly79Ser	127.0	0.0	0		129.0	70.0	0.542636	NM_020726	Q9ULJ4	Missense_Mutation	SNP	ENST00000380985.5	37	CCDS3989.1	32	0.014652014652014652	27	0.054878048780487805	5	0.013812154696132596	0	0.0	0	0.0	G	8.053	0.766380	0.15983	0.072855	0.0	ENSG00000123213	ENST00000380985;ENST00000340159	T	0.06933	3.24	5.5	-1.6	0.08426	Neurolysin/Thimet oligopeptidase, N-terminal (1);	0.775582	0.12614	N	0.453646	T	0.00241	0.0007	N	0.01352	-0.895	0.09310	N	0.999999	B;B	0.27679	0.001;0.185	B;B	0.14578	0.001;0.011	T	0.44862	-0.9300	10	0.20519	T	0.43	-0.0913	12.5135	0.56019	0.3907:0.0:0.6093:0.0	rs34339013	79;79	Q9BYT8;Q9BQD0	NEUL_HUMAN;.	S	79	ENSP00000370372:G79S	ENSP00000339283:G79S	G	+	1	0	NLN	65090343	0.024000	0.19004	0.001000	0.08648	0.784000	0.44337	0.931000	0.28871	-0.729000	0.04875	-0.880000	0.02959	GGT	G|0.973;A|0.027	0.027	strong		0.423	NLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215060.1		
UACA	55075	hgsc.bcm.edu	37	15	70957106	70957106	+	Silent	SNP	A	A	G	rs78551559	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:70957106A>G	ENST00000322954.6	-	17	4193	c.4008T>C	c.(4006-4008)aaT>aaC	p.N1336N	UACA_ENST00000379983.2_Silent_p.N1323N|UACA_ENST00000560441.1_Silent_p.N1321N|UACA_ENST00000539319.1_Silent_p.N1227N	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	1336					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						GGGAAAGGCCATTGAGTGCCT	0.413													A|||	83	0.0165735	0.0605	0.0043	5008	,	,		17428	0.0		0.0	False		,,,				2504	0.0				p.N1336N		Atlas-SNP	.											.	UACA	235	.	0			c.T4008C						PASS	.	A	,	203,4195	126.6+/-163.6	3,197,1999	150.0	127.0	135.0		3969,4008	-4.9	0.0	15	dbSNP_132	135	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous,coding-synonymous	UACA	NM_001008224.1,NM_018003.2	,	3,198,6296	GG,GA,AA		0.0116,4.6157,1.57	,	1323/1404,1336/1417	70957106	204,12790	2199	4298	6497	SO:0001819	synonymous_variant	55075	exon17			AAGGCCATTGAGT	AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"""Ankyrin repeat domain containing"""	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.4008T>C	15.37:g.70957106A>G		203.0	0.0	0		203.0	101.0	0.497537	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Silent	SNP	ENST00000322954.6	37	CCDS10235.1																																																																																			A|0.983;G|0.017	0.017	strong		0.413	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2		
MISP	126353	hgsc.bcm.edu	37	19	757483	757483	+	Silent	SNP	G	G	A	rs35484463	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:757483G>A	ENST00000215582.6	+	2	640	c.537G>A	c.(535-537)acG>acA	p.T179T		NM_173481.2	NP_775752.1	Q8IVT2	MISP_HUMAN	mitotic spindle positioning	179					mitotic nuclear division (GO:0007067)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											CTCGGTCCACGCCCCTGGAGG	0.652													G|||	94	0.01877	0.0681	0.0058	5008	,	,		16831	0.0		0.0	False		,,,				2504	0.0				p.T179T		Atlas-SNP	.											.	C19orf21	56	.	0			c.G537A						PASS	.	G		220,4166		7,206,1980	19.0	23.0	22.0		537	-5.4	0.0	19	dbSNP_126	22	1,8587		0,1,4293	no	coding-synonymous	C19orf21	NM_173481.2		7,207,6273	AA,AG,GG		0.0116,5.016,1.7034		179/680	757483	221,12753	2193	4294	6487	SO:0001819	synonymous_variant	126353	exon2			GTCCACGCCCCTG	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.537G>A	19.37:g.757483G>A		95.0	0.0	0		95.0	42.0	0.442105	NM_173481		Silent	SNP	ENST00000215582.6	37	CCDS12042.1																																																																																			G|0.982;A|0.018	0.018	strong		0.652	MISP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457600.2	NM_173481	
SIGLEC9	27180	hgsc.bcm.edu	37	19	51630485	51630485	+	Missense_Mutation	SNP	C	C	A	rs273688	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51630485C>A	ENST00000250360.3	+	4	1014	c.947C>A	c.(946-948)gCt>gAt	p.A316D	SIGLEC9_ENST00000440804.3_Missense_Mutation_p.A316D	NM_014441.2	NP_055256.1	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9	316	Ig-like C2-type 2.		A -> D (in dbSNP:rs273688).		cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(3)|lung(25)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	45		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)		AGGGATGCAGCTGAATTCACC	0.637													.|||	529	0.105631	0.3805	0.0331	5008	,	,		20814	0.0		0.0	False		,,,				2504	0.0031				p.A316D		Atlas-SNP	.											SIGLEC9,NS,carcinoma,+1,1	SIGLEC9	85	1	0			c.C947A						PASS	.	A	ASP/ALA,ASP/ALA	1473,2933		252,969,982	41.0	40.0	40.0		947,947	-0.0	0.0	19	dbSNP_79	40	11,8589		0,11,4289	no	missense,missense	SIGLEC9	NM_001198558.1,NM_014441.2	126,126	252,980,5271	AA,AC,CC		0.1279,33.4317,11.4101	benign,benign	316/480,316/464	51630485	1484,11522	2203	4300	6503	SO:0001583	missense	27180	exon4			ATGCAGCTGAATT	AF135027	CCDS12825.1, CCDS56100.1	19q13.3-q13.4	2013-01-29			ENSG00000129450	ENSG00000129450		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10878	protein-coding gene	gene with protein product		605640				10903842	Standard	NM_014441		Approved	CD329	uc002pvu.3	Q9Y336		ENST00000250360.3:c.947C>A	19.37:g.51630485C>A	ENSP00000250360:p.Ala316Asp	121.0	0.0	0		105.0	58.0	0.552381	NM_001198558	Q6GTU4|Q9BYI9	Missense_Mutation	SNP	ENST00000250360.3	37	CCDS12825.1	196	0.08974358974358974	183	0.3719512195121951	13	0.03591160220994475	0	0.0	0	0.0	.	6.207	0.406368	0.11754	0.334317	0.001279	ENSG00000129450	ENST00000440804;ENST00000250360	T;T	0.12255	2.7;2.7	2.3	-0.0215	0.13951	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.635768	0.12920	N	0.428257	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B	0.16166	0.016	B	0.12156	0.007	T	0.46665	-0.9175	9	0.72032	D	0.01	.	5.4292	0.16444	0.1485:0.2067:0.6448:0.0	rs273688;rs60086561;rs273688	316	Q9Y336	SIGL9_HUMAN	D	316	ENSP00000413861:A316D;ENSP00000250360:A316D	ENSP00000250360:A316D	A	+	2	0	SIGLEC9	56322297	0.018000	0.18449	0.000000	0.03702	0.001000	0.01503	0.516000	0.22817	-0.622000	0.05626	-3.343000	0.00043	GCT	C|0.895;A|0.105	0.105	strong		0.637	SIGLEC9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464224.1	NM_014441	
C2orf16	84226	hgsc.bcm.edu	37	2	27801739	27801739	+	Missense_Mutation	SNP	T	T	C	rs13416968	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27801739T>C	ENST00000408964.2	+	1	2351	c.2300T>C	c.(2299-2301)aTa>aCa	p.I767T		NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	767			I -> T (in dbSNP:rs13416968).			extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					GCTTTGGATATAAAAAACCCT	0.408													T|||	55	0.0109824	0.0378	0.0043	5008	,	,		19518	0.0		0.002	False		,,,				2504	0.0				p.I767T		Atlas-SNP	.											.	C2orf16	357	.	0			c.T2300C						PASS	.	T	THR/ILE	113,3507		3,107,1700	138.0	136.0	137.0		2300	2.4	0.6	2	dbSNP_121	137	2,8150		0,2,4074	yes	missense	C2orf16	NM_032266.3	89	3,109,5774	CC,CT,TT		0.0245,3.1215,0.9769	probably-damaging	767/1985	27801739	115,11657	1810	4076	5886	SO:0001583	missense	84226	exon1			TGGATATAAAAAA	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.2300T>C	2.37:g.27801739T>C	ENSP00000386190:p.Ile767Thr	156.0	0.0	0		219.0	104.0	0.474886	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	21	0.009615384615384616	19	0.03861788617886179	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	3.675	-0.066708	0.07273	0.031215	2.45E-4	ENSG00000221843	ENST00000408964	T	0.09723	2.95	4.83	2.41	0.29592	.	.	.	.	.	T	0.01353	0.0044	N	0.24115	0.695	0.09310	N	1	B	0.24368	0.102	B	0.18561	0.022	T	0.38802	-0.9644	9	0.37606	T	0.19	.	4.9147	0.13840	0.0:0.0967:0.1882:0.7151	rs13416968;rs13416968	767	Q68DN1	CB016_HUMAN	T	767	ENSP00000386190:I767T	ENSP00000386190:I767T	I	+	2	0	C2orf16	27655243	0.169000	0.23002	0.607000	0.28956	0.030000	0.12068	0.133000	0.15912	0.420000	0.25954	-0.488000	0.04728	ATA	T|0.986;C|0.014	0.014	strong		0.408	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
EVL	51466	hgsc.bcm.edu	37	14	100563868	100563868	+	Silent	SNP	G	G	A	rs35006525	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:100563868G>A	ENST00000402714.2	+	3	829	c.225G>A	c.(223-225)acG>acA	p.T75T	EVL_ENST00000555048.1_3'UTR|EVL_ENST00000392920.3_Silent_p.T77T|EVL_ENST00000544450.2_Silent_p.T81T			Q9UI08	EVL_HUMAN	Enah/Vasp-like	75	WH1. {ECO:0000255|PROSITE- ProRule:PRU00410}.				actin filament organization (GO:0007015)|actin polymerization or depolymerization (GO:0008154)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of ruffle assembly (GO:1900028)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of stress fiber assembly (GO:0051496)|protein homotetramerization (GO:0051289)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|membrane (GO:0016020)	profilin binding (GO:0005522)|SH3 domain binding (GO:0017124)			cervix(1)|large_intestine(5)|lung(3)|ovary(3)|urinary_tract(2)	14		Melanoma(154;0.152)				ATCAGGCCACGCCAACCTTCC	0.458													G|||	74	0.0147764	0.0545	0.0029	5008	,	,		21124	0.0		0.0	False		,,,				2504	0.0				p.T77T		Atlas-SNP	.											.	EVL	42	.	0			c.G231A						PASS	.	G		217,4189	131.0+/-167.6	6,205,1992	89.0	81.0	84.0		231	-9.0	0.8	14	dbSNP_126	84	0,8600		0,0,4300	no	coding-synonymous	EVL	NM_016337.2		6,205,6292	AA,AG,GG		0.0,4.9251,1.6685		77/419	100563868	217,12789	2203	4300	6503	SO:0001819	synonymous_variant	51466	exon3			GGCCACGCCAACC	AF112209	CCDS9955.1	14q32.2	2014-08-13			ENSG00000196405	ENSG00000196405			20234	protein-coding gene	gene with protein product						10945997, 10993894	Standard	NM_016337		Approved	RNB6	uc001ygu.3	Q9UI08	OTTHUMG00000171530	ENST00000402714.2:c.225G>A	14.37:g.100563868G>A		77.0	0.0	0		93.0	51.0	0.548387	NM_016337	A8K105|O95884|Q7Z522|Q8TBV1|Q9UF25|Q9UIC2	Silent	SNP	ENST00000402714.2	37																																																																																				G|0.986;A|0.014	0.014	strong		0.458	EVL-006	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000413958.1		
CAMK2N2	94032	hgsc.bcm.edu	37	3	183978936	183978936	+	Silent	SNP	G	G	A	rs75699255	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:183978936G>A	ENST00000296238.3	-	1	315	c.138C>T	c.(136-138)ccC>ccT	p.P46P	ECE2_ENST00000402825.3_Intron|EIF2B5_ENST00000444495.1_Intron	NM_033259.2	NP_150284.1	Q96S95	CK2N2_HUMAN	calcium/calmodulin-dependent protein kinase II inhibitor 2	46	Inhibitory domain. {ECO:0000250}.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium-dependent protein kinase inhibitor activity (GO:0008427)					all_cancers(143;1.09e-10)|Ovarian(172;0.0339)		Epithelial(37;2.51e-33)|OV - Ovarian serous cystadenocarcinoma(80;5.69e-22)			GGCCCAGCTTGGGGGGTCGCT	0.736													G|||	200	0.0399361	0.146	0.0101	5008	,	,		8663	0.0		0.0	False		,,,				2504	0.0				p.P46P		Atlas-SNP	.											.	CAMK2N2	2	.	0			c.C138T						PASS	.	G	,	416,3990		19,378,1806	18.0	21.0	20.0		,138	-0.8	1.0	3	dbSNP_132	20	3,8597		0,3,4297	no	intron,coding-synonymous	ECE2,CAMK2N2	NM_014693.3,NM_033259.2	,	19,381,6103	AA,AG,GG		0.0349,9.4417,3.2216	,	,46/80	183978936	419,12587	2203	4300	6503	SO:0001819	synonymous_variant	94032	exon1			CAGCTTGGGGGGT	AY037149	CCDS3257.1	3q27.1	2006-03-27			ENSG00000163888	ENSG00000163888			24197	protein-coding gene	gene with protein product		608721				11444830, 9724800	Standard	NM_033259		Approved	CaM-KIIN	uc003fnj.1	Q96S95	OTTHUMG00000156821	ENST00000296238.3:c.138C>T	3.37:g.183978936G>A		42.0	0.0	0		50.0	31.0	0.62	NM_033259		Silent	SNP	ENST00000296238.3	37	CCDS3257.1																																																																																			G|0.962;A|0.038	0.038	strong		0.736	CAMK2N2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346010.1	NM_033259	
MT-ND4	4538	hgsc.bcm.edu	37	M	10793	10793	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:10793C>T	ENST00000361381.2	+	1	34	c.34C>T	c.(34-36)Cta>Tta	p.L12L	MT-TR_ENST00000387439.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-TK_ENST00000387421.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	12					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						CAATTATATTACTACCACTGA	0.378																																					p.L12L		Atlas-SNP	.											.	.	.	.	0			c.C34T						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			ATATTACTACCAC			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.34C>T	M.37:g.10793C>T		6.0	0.0	0		9.0	9.0	1	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Silent	SNP	ENST00000361381.2	37																																																																																				.	.	none		0.378	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
BCR	613	hgsc.bcm.edu	37	22	23651650	23651650	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:23651650A>G	ENST00000305877.8	+	17	3803	c.3052A>G	c.(3052-3054)Acc>Gcc	p.T1018A	BCR_ENST00000359540.3_Missense_Mutation_p.T974A	NM_004327.3	NP_004318.3	P11274	BCR_HUMAN	breakpoint cluster region	1018					actin cytoskeleton organization (GO:0030036)|brain development (GO:0007420)|inner ear morphogenesis (GO:0042472)|negative regulation of cell migration (GO:0030336)|negative regulation of inflammatory response (GO:0050728)|negative regulation of neutrophil degranulation (GO:0043314)|neuromuscular process controlling balance (GO:0050885)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of phagocytosis (GO:0050766)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|kinase activity (GO:0016301)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)|Rac GTPase activator activity (GO:0030675)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)		BCR/JAK2(6)	central_nervous_system(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	35					Bosutinib(DB06616)|Ponatinib(DB08901)	CTGGCAGCGCACCGTCATCGC	0.607			T	"""ABL1,  FGFR1, JAK2 """	"""CML, ALL, AML"""																																p.T1018A		Atlas-SNP	.		Dom	yes		22	22q11.21	613	breakpoint cluster region		L	BCR,NS,carcinoma,0,1	BCR	74	1	0			c.A3052G						scavenged	.						33.0	25.0	28.0					22																	23651650		2201	4300	6501	SO:0001583	missense	613	exon17			CAGCGCACCGTCA		CCDS13806.1, CCDS13807.1	22q11	2013-01-10			ENSG00000186716	ENSG00000186716		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	1014	protein-coding gene	gene with protein product		151410		D22S11, BCR1		1657398, 18070886	Standard	NM_004327		Approved	D22S662, CML, PHL, ALL	uc002zww.3	P11274	OTTHUMG00000150655	ENST00000305877.8:c.3052A>G	22.37:g.23651650A>G	ENSP00000303507:p.Thr1018Ala	330.0	0.0	0		294.0	108.0	0.367347	NM_004327	P78501|Q12842|Q4LE80|Q6NZI3	Missense_Mutation	SNP	ENST00000305877.8	37	CCDS13806.1	.	.	.	.	.	.	.	.	.	.	A	7.060	0.566244	0.13560	.	.	ENSG00000186716	ENST00000305877;ENST00000359540;ENST00000334149	T;T	0.39787	1.06;1.8	4.7	2.52	0.30459	C2 calcium/lipid-binding domain, CaLB (1);	0.051625	0.85682	D	0.000000	T	0.28067	0.0692	L	0.44542	1.39	0.80722	D	1	B;B;B	0.22909	0.077;0.059;0.077	B;B;B	0.26614	0.071;0.039;0.044	T	0.04203	-1.0969	10	0.12430	T	0.62	.	4.6914	0.12783	0.6936:0.0:0.1642:0.1422	.	607;974;1018	B4E065;P11274-2;P11274	.;.;BCR_HUMAN	A	1018;974;683	ENSP00000303507:T1018A;ENSP00000352535:T974A	ENSP00000303507:T1018A	T	+	1	0	BCR	21981650	1.000000	0.71417	0.512000	0.27736	0.011000	0.07611	4.359000	0.59449	0.765000	0.33221	-0.991000	0.02546	ACC	A|0.500;G|0.500	0.500	weak		0.607	BCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075819.1	NM_004327	
ARAP1	116985	hgsc.bcm.edu	37	11	72403832	72403832	+	Splice_Site	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:72403832T>C	ENST00000393609.3	-	30	4157		c.e30-2		ARAP1_ENST00000393605.3_Splice_Site|ARAP1_ENST00000429686.1_Intron|ARAP1_ENST00000455638.2_Intron|ARAP1_ENST00000334211.8_Splice_Site|ARAP1_ENST00000426523.1_Intron|ARAP1_ENST00000359373.5_Intron|ARAP1_ENST00000495878.1_Intron|ARAP1-AS1_ENST00000542022.1_RNA	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1						actin filament reorganization involved in cell cycle (GO:0030037)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of receptor recycling (GO:0001921)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of cellular component movement (GO:0051270)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|large_intestine(10)|lung(8)|ovary(1)|skin(3)|urinary_tract(1)	27						CCTCTGGCTCTGTTTGATAGA	0.587																																					.	Ovarian(102;1198 1520 13195 17913 37529)	Atlas-SNP	.											.	ARAP1	168	.	0			c.3220-2A>G						PASS	.						46.0	46.0	46.0					11																	72403832		2200	4293	6493	SO:0001630	splice_region_variant	116985	exon29			TGGCTCTGTTTGA	AF411983	CCDS8217.2, CCDS41687.1, CCDS44671.1	11q13.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000186635	ENSG00000186635		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16925	protein-coding gene	gene with protein product		606646	"""centaurin, delta 2"""	CENTD2			Standard	NM_001040118		Approved		uc001osu.3	Q96P48	OTTHUMG00000157102	ENST00000393609.3:c.3955-2A>G	11.37:g.72403832T>C		48.0	0.0	0		64.0	29.0	0.453125	NM_015242	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Splice_Site	SNP	ENST00000393609.3	37	CCDS41687.1	.	.	.	.	.	.	.	.	.	.	T	17.85	3.491402	0.64074	.	.	ENSG00000186635	ENST00000393605;ENST00000334211;ENST00000393609	.	.	.	5.73	4.54	0.55810	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.4138	0.32659	0.1738:0.0:0.0:0.8262	.	.	.	.	.	-1	.	.	.	-	.	.	ARAP1	72081480	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.927000	0.40094	2.184000	0.69523	0.448000	0.29417	.	.	.	none		0.587	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118	Intron
GOLGA8B	440270	hgsc.bcm.edu	37	15	34825091	34825091	+	Missense_Mutation	SNP	T	T	A	rs200439797		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:34825091T>A	ENST00000342314.5	-	3	338	c.241A>T	c.(241-243)Agg>Tgg	p.R81W	GOLGA8B_ENST00000267731.7_Missense_Mutation_p.R81W|GOLGA8A_ENST00000543376.1_Intron|GOLGA8B_ENST00000438958.2_Missense_Mutation_p.R111W	NM_001023567.4	NP_001018861.3	A8MQT2	GOG8B_HUMAN	golgin A8 family, member B	81						Golgi apparatus (GO:0005794)|membrane (GO:0016020)				endometrium(1)	1		all_lung(180;2.78e-08)		all cancers(64;8.27e-19)|GBM - Glioblastoma multiforme(113;6.98e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0156)		TTTATGGACCTCGAGTTCAGG	0.552																																					p.R81W		Atlas-SNP	.											GOLGA8B_ENST00000267731,right_upper_lobe,carcinoma,+1,2	GOLGA8B	7	2	0			c.A241T						scavenged	.						34.0	19.0	24.0					15																	34825091		686	1359	2045	SO:0001583	missense	440270	exon3			TGGACCTCGAGTT	AF164622	CCDS45211.1	15q14	2011-10-25	2010-02-12		ENSG00000215252	ENSG00000215252			31973	protein-coding gene	gene with protein product		609619	"""golgi autoantigen, golgin subfamily a, 8B"""				Standard	NM_001023567		Approved		uc001ziq.3	A8MQT2	OTTHUMG00000129549	ENST00000342314.5:c.241A>T	15.37:g.34825091T>A	ENSP00000343064:p.Arg81Trp	1385.0	0.0	0		1873.0	467.0	0.249333	NM_001023567	A6NLZ2|O94937|Q2M3S9|Q9NZG8|Q9NZW0|Q9NZW3	Missense_Mutation	SNP	ENST00000342314.5	37	CCDS45211.1	.	.	.	.	.	.	.	.	.	.	t	13.59	2.284070	0.40394	.	.	ENSG00000215252	ENST00000342314;ENST00000267731;ENST00000438958	T;T;T	0.22743	1.94;1.94;2.5	1.55	0.322	0.15888	.	.	.	.	.	T	0.34745	0.0908	M	0.66939	2.045	0.21355	N	0.999712	D	0.67145	0.996	D	0.64687	0.928	T	0.13575	-1.0504	9	0.66056	D	0.02	.	3.6826	0.08316	0.3389:0.0:0.0:0.6611	.	81	A8MQT2	GOG8B_HUMAN	W	81;81;111	ENSP00000343064:R81W;ENSP00000267731:R81W;ENSP00000400063:R111W	ENSP00000267731:R81W	R	-	1	2	GOLGA8B	32612383	1.000000	0.71417	0.371000	0.25978	0.004000	0.04260	4.296000	0.59055	0.067000	0.16545	-1.078000	0.02229	AGG	T|0.998;A|0.002	0.002	weak		0.552	GOLGA8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251739.2	NM_001023567	
LRRK1	79705	hgsc.bcm.edu	37	15	101606084	101606084	+	Silent	SNP	G	G	A	rs116529941	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:101606084G>A	ENST00000388948.3	+	32	5801	c.5442G>A	c.(5440-5442)gcG>gcA	p.A1814A	RP11-505E24.2_ENST00000559857.1_RNA|LRRK1_ENST00000284395.5_Silent_p.A1811A|LRRK1_ENST00000532145.1_3'UTR	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			ACTCCATCGCGGACGTGAGCA	0.622													G|||	6	0.00119808	0.0045	0.0	5008	,	,		17606	0.0		0.0	False		,,,				2504	0.0				p.A1814A		Atlas-SNP	.											.	LRRK1	310	.	0			c.G5442A						PASS	.	G		10,4162		0,10,2076	61.0	69.0	66.0		5442	-11.0	0.0	15	dbSNP_132	66	0,8430		0,0,4215	no	coding-synonymous	LRRK1	NM_024652.3		0,10,6291	AA,AG,GG		0.0,0.2397,0.0794		1814/2016	101606084	10,12592	2086	4215	6301	SO:0001819	synonymous_variant	79705	exon32			CATCGCGGACGTG	AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.5442G>A	15.37:g.101606084G>A		111.0	0.0	0		136.0	75.0	0.551471	NM_024652		Silent	SNP	ENST00000388948.3	37	CCDS42086.1																																																																																			G|0.997;A|0.003	0.003	strong		0.622	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652	
ACSS2	55902	hgsc.bcm.edu	37	20	33513983	33513983	+	Missense_Mutation	SNP	G	G	C	rs45486997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33513983G>C	ENST00000360596.2	+	16	2013	c.1802G>C	c.(1801-1803)gGc>gCc	p.G601A	ACSS2_ENST00000336325.4_Missense_Mutation_p.G551A|ACSS2_ENST00000253382.5_Missense_Mutation_p.G614A|ACSS2_ENST00000476922.1_Intron	NM_018677.3	NP_061147.1	Q9NR19	ACSA_HUMAN	acyl-CoA synthetase short-chain family member 2	601					acetate biosynthetic process (GO:0019413)|acetyl-CoA biosynthetic process from acetate (GO:0019427)|ethanol oxidation (GO:0006069)|lipid biosynthetic process (GO:0008610)|propionate biosynthetic process (GO:0019542)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	acetate-CoA ligase activity (GO:0003987)|AMP binding (GO:0016208)|ATP binding (GO:0005524)			cervix(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(9)	21					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	GCTGTGGTGGGCCACCCTCAT	0.557													G|||	190	0.0379393	0.1316	0.0231	5008	,	,		19053	0.0		0.0	False		,,,				2504	0.0				p.G614A		Atlas-SNP	.											.	ACSS2	75	.	0			c.G1841C						PASS	.	G	ALA/GLY,ALA/GLY,ALA/GLY	487,3919	224.3+/-240.5	27,433,1743	138.0	105.0	116.0		1841,1517,1802	4.3	0.9	20	dbSNP_127	116	17,8583	11.9+/-42.8	0,17,4283	yes	missense,missense,missense	ACSS2	NM_001076552.2,NM_001242393.1,NM_018677.3	60,60,60	27,450,6026	CC,CG,GG		0.1977,11.0531,3.8751	benign,benign,benign	614/715,506/607,601/702	33513983	504,12502	2203	4300	6503	SO:0001583	missense	55902	exon17			TGGTGGGCCACCC	AF263614	CCDS13243.1, CCDS42868.1, CCDS42868.2	20q11.22	2012-07-13	2005-09-08	2005-09-08	ENSG00000131069	ENSG00000131069	6.2.1.1	"""Acyl-CoA synthetase family"""	15814	protein-coding gene	gene with protein product		605832	"""acetyl-Coenzyme A synthetase 2 (ADP forming)"""	ACAS2		10843999	Standard	NM_018677		Approved	ACS, ACSA, AceCS, dJ1161H23.1	uc010gey.2	Q9NR19	OTTHUMG00000032317	ENST00000360596.2:c.1802G>C	20.37:g.33513983G>C	ENSP00000353804:p.Gly601Ala	185.0	0.0	0		182.0	95.0	0.521978	NM_001076552	A6NE90|Q5QPH2|Q5QPH3|Q8N238|Q96EL0|Q9NQP7|Q9UJ15	Missense_Mutation	SNP	ENST00000360596.2	37	CCDS13243.1	57	0.0260989010989011	50	0.1016260162601626	7	0.019337016574585635	0	0.0	0	0.0	G	15.09	2.729599	0.48833	0.110531	0.001977	ENSG00000131069	ENST00000336325;ENST00000360596;ENST00000374693;ENST00000542204;ENST00000253382	T;T;T	0.62941	-0.01;-0.01;-0.01	5.25	4.29	0.51040	.	0.241356	0.49305	N	0.000155	T	0.02083	0.0065	L	0.53780	1.695	0.51012	D	0.9999	B;B	0.10296	0.001;0.003	B;B	0.12156	0.007;0.007	T	0.15983	-1.0418	10	0.87932	D	0	-12.1309	15.8996	0.79362	0.0:0.1355:0.8645:0.0	rs45486997;rs60500786	614;601	Q5QPH3;Q9NR19	.;ACSA_HUMAN	A	551;601;599;309;614	ENSP00000337190:G551A;ENSP00000353804:G601A;ENSP00000253382:G614A	ENSP00000253382:G614A	G	+	2	0	ACSS2	32977644	1.000000	0.71417	0.898000	0.35279	0.962000	0.63368	7.711000	0.84669	1.417000	0.47077	0.563000	0.77884	GGC	G|0.968;C|0.032	0.032	strong		0.557	ACSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078823.3	NM_018677	
FAT1	2195	hgsc.bcm.edu	37	4	187557863	187557863	+	Missense_Mutation	SNP	G	G	A	rs60068521	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:187557863G>A	ENST00000441802.2	-	5	4057	c.3848C>T	c.(3847-3849)cCc>cTc	p.P1283L		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1283	Cadherin 11. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						TTCTGCATTGGGGCCCTCATC	0.502										HNSCC(5;0.00058)			G|||	6	0.00119808	0.0045	0.0	5008	,	,		15954	0.0		0.0	False		,,,				2504	0.0				p.P1283L	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.C3848T						PASS	.	G	LEU/PRO	4,3800		0,4,1898	224.0	226.0	225.0		3848	5.0	1.0	4	dbSNP_129	225	0,8238		0,0,4119	yes	missense	FAT1	NM_005245.3	98	0,4,6017	AA,AG,GG		0.0,0.1052,0.0332	benign	1283/4589	187557863	4,12038	1902	4119	6021	SO:0001583	missense	2195	exon5			GCATTGGGGCCCT	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.3848C>T	4.37:g.187557863G>A	ENSP00000406229:p.Pro1283Leu	306.0	0.0	0		300.0	155.0	0.516667	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	15.34	2.804208	0.50315	0.001052	0.0	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.54071	0.59	4.99	4.99	0.66335	Cadherin (4);Cadherin-like (1);	0.172618	0.52532	D	0.000077	T	0.61999	0.2392	L	0.41415	1.275	0.80722	D	1	D	0.67145	0.996	D	0.63957	0.92	T	0.54906	-0.8223	10	0.22109	T	0.4	.	18.4667	0.90758	0.0:0.0:1.0:0.0	rs60068521	1283	Q14517	FAT1_HUMAN	L	1283	ENSP00000406229:P1283L	ENSP00000260147:P1283L	P	-	2	0	FAT1	187794857	1.000000	0.71417	1.000000	0.80357	0.584000	0.36387	9.657000	0.98554	2.599000	0.87857	0.561000	0.74099	CCC	G|0.999;A|0.001	0.001	strong		0.502	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
ADAM7	8756	hgsc.bcm.edu	37	8	24349482	24349482	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24349482G>A	ENST00000175238.6	+	14	1506	c.1423G>A	c.(1423-1425)Ggc>Agc	p.G475S	ADAM7_ENST00000520720.1_Missense_Mutation_p.G247S|RP11-624C23.1_ENST00000519689.1_RNA|ADAM7_ENST00000380789.1_Missense_Mutation_p.G475S|RP11-561E1.1_ENST00000519364.1_RNA|RP11-624C23.1_ENST00000523578.1_RNA	NM_003817.3	NP_003808.2	Q9H2U9	ADAM7_HUMAN	ADAM metallopeptidase domain 7	475	Disintegrin. {ECO:0000255|PROSITE- ProRule:PRU00068}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|endometrium(5)|kidney(1)|large_intestine(17)|lung(24)|ovary(1)|skin(15)	64		Prostate(55;0.0181)		Colorectal(74;0.0199)|COAD - Colon adenocarcinoma(73;0.0754)|BRCA - Breast invasive adenocarcinoma(99;0.182)		GATGTGCACTGGCCACTCGCC	0.463																																					p.G475S		Atlas-SNP	.											ADAM7,colon,carcinoma,-2,1	ADAM7	165	1	0			c.G1423A						PASS	.																																			SO:0001583	missense	8756	exon14			TGCACTGGCCACT	AF090327	CCDS6045.1	8p21.2	2005-08-18	2005-08-18		ENSG00000069206	ENSG00000069206		"""ADAM metallopeptidase domain containing"""	214	protein-coding gene	gene with protein product		607310	"""a disintegrin and metalloproteinase domain 7"""				Standard	NM_003817		Approved	GP-83, EAPI	uc003xeb.3	Q9H2U9	OTTHUMG00000097859	ENST00000175238.6:c.1423G>A	8.37:g.24349482G>A	ENSP00000175238:p.Gly475Ser	130.0	0.0	0		97.0	57.0	0.587629	NM_003817	A8K8X7|O75959|Q6PEJ6	Missense_Mutation	SNP	ENST00000175238.6	37	CCDS6045.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.891293	0.91889	.	.	ENSG00000069206	ENST00000175238;ENST00000380789;ENST00000520720;ENST00000335595	T;T;T	0.57107	0.42;0.42;0.42	5.78	5.78	0.91487	Blood coagulation inhibitor, Disintegrin (6);	0.000000	0.56097	D	0.000026	D	0.83889	0.5352	H	0.98487	4.245	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.89755	0.3943	10	0.87932	D	0	.	17.5062	0.87746	0.0:0.0:1.0:0.0	.	247;475	E5RK87;Q9H2U9	.;ADAM7_HUMAN	S	475;475;247;290	ENSP00000175238:G475S;ENSP00000370166:G475S;ENSP00000430400:G247S	ENSP00000175238:G475S	G	+	1	0	ADAM7	24405372	1.000000	0.71417	0.997000	0.53966	0.784000	0.44337	7.643000	0.83403	2.749000	0.94314	0.655000	0.94253	GGC	.	.	none		0.463	ADAM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215150.1	NM_003817	
MUT	4594	hgsc.bcm.edu	37	6	49409599	49409599	+	Missense_Mutation	SNP	G	G	A	rs140727018	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:49409599G>A	ENST00000274813.3	-	10	1889	c.1762C>T	c.(1762-1764)Cgc>Tgc	p.R588C		NM_000255.3	NP_000246.2	P22033	MUTA_HUMAN	methylmalonyl CoA mutase	588					cellular lipid metabolic process (GO:0044255)|cobalamin metabolic process (GO:0009235)|fatty acid beta-oxidation (GO:0006635)|homocysteine metabolic process (GO:0050667)|post-embryonic development (GO:0009791)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	cobalamin binding (GO:0031419)|metal ion binding (GO:0046872)|methylmalonyl-CoA mutase activity (GO:0004494)|modified amino acid binding (GO:0072341)			endometrium(2)|kidney(1)|large_intestine(4)|lung(17)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	30	Lung NSC(77;0.0376)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	AATTCCTGGCGATATGCTCCA	0.388													G|||	2	0.000399361	0.0015	0.0	5008	,	,		10715	0.0		0.0	False		,,,				2504	0.0				p.R588C		Atlas-SNP	.											.	MUT	70	.	0			c.C1762T						PASS	.	G	CYS/ARG	16,4390	23.3+/-48.9	0,16,2187	231.0	210.0	217.0		1762	4.7	1.0	6	dbSNP_134	217	0,8600		0,0,4300	yes	missense	MUT	NM_000255.3	180	0,16,6487	AA,AG,GG		0.0,0.3631,0.123	probably-damaging	588/751	49409599	16,12990	2203	4300	6503	SO:0001583	missense	4594	exon10			CCTGGCGATATGC		CCDS4924.1	6p21	2012-10-02	2010-04-30		ENSG00000146085	ENSG00000146085	5.4.99.2		7526	protein-coding gene	gene with protein product		609058	"""methylmalonyl Coenzyme A mutase"""			2907507, 9503014	Standard	NM_000255		Approved		uc003ozg.4	P22033	OTTHUMG00000014814	ENST00000274813.3:c.1762C>T	6.37:g.49409599G>A	ENSP00000274813:p.Arg588Cys	237.0	0.0	0		256.0	134.0	0.523438	NM_000255	A8K953|Q5SYZ3|Q96B11|Q9UD64	Missense_Mutation	SNP	ENST00000274813.3	37	CCDS4924.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	22.7	4.329566	0.81690	0.003631	0.0	ENSG00000146085	ENST00000274813;ENST00000540138	D	0.95069	-3.6	5.59	4.72	0.59763	Cobalamin (vitamin B12)-binding (2);	0.000000	0.85682	D	0.000000	D	0.96156	0.8747	M	0.76170	2.325	0.80722	D	1	D	0.89917	1.0	D	0.73708	0.981	D	0.96378	0.9279	10	0.59425	D	0.04	-20.2086	15.0369	0.71754	0.0:0.0:0.8569:0.1431	.	588	P22033	MUTA_HUMAN	C	588;35	ENSP00000274813:R588C	ENSP00000274813:R588C	R	-	1	0	MUT	49517558	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.507000	0.81676	1.345000	0.45676	0.585000	0.79938	CGC	G|0.999;A|0.001	0.001	strong		0.388	MUT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040854.1		
FAM151A	338094	hgsc.bcm.edu	37	1	55075334	55075334	+	Silent	SNP	G	G	A	rs201640566	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55075334G>A	ENST00000302250.2	-	8	1525	c.1365C>T	c.(1363-1365)ccC>ccT	p.P455P	FAM151A_ENST00000371304.2_Intron|ACOT11_ENST00000371316.3_Intron|ACOT11_ENST00000343744.2_3'UTR|ACOT11_ENST00000481208.1_3'UTR	NM_176782.2	NP_788954.2	Q8WW52	F151A_HUMAN	family with sequence similarity 151, member A	455						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	12						CCACATGGCCGGGGACCGAAA	0.642													g|||	2	0.000399361	0.0008	0.0014	5008	,	,		18259	0.0		0.0	False		,,,				2504	0.0				p.P455P		Atlas-SNP	.											.	FAM151A	58	.	0			c.C1365T						PASS	.						32.0	35.0	34.0					1																	55075334		2202	4300	6502	SO:0001819	synonymous_variant	338094	exon8			ATGGCCGGGGACC	AK091901	CCDS594.1	1p32.3	2008-02-05	2007-12-18	2007-12-18	ENSG00000162391	ENSG00000162391			25032	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 179"""	C1orf179		17273976	Standard	NM_176782		Approved	MGC27169	uc001cxn.3	Q8WW52	OTTHUMG00000009888	ENST00000302250.2:c.1365C>T	1.37:g.55075334G>A		66.0	0.0	0		58.0	29.0	0.5	NM_176782	Q5VUG5|Q6DKH5|Q6UWV0|Q8NAX9|Q96KY5	Silent	SNP	ENST00000302250.2	37	CCDS594.1																																																																																			G|1.000;A|0.000	0.000	strong		0.642	FAM151A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027342.1	NM_176782	
OR2T12	127064	hgsc.bcm.edu	37	1	248458718	248458718	+	Missense_Mutation	SNP	T	T	C	rs79635253	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248458718T>C	ENST00000317996.1	-	1	162	c.163A>G	c.(163-165)Agg>Ggg	p.R55G		NM_001004692.1	NP_001004692.1	Q8NG77	O2T12_HUMAN	olfactory receptor, family 2, subfamily T, member 12	55						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|kidney(3)|large_intestine(3)|lung(25)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0201)			TACATGGGCCTGTGGAGCCGG	0.527													-|||	151	0.0301518	0.0915	0.0144	5008	,	,		12875	0.001		0.0169	False		,,,				2504	0.002				p.R55G		Atlas-SNP	.											.	OR2T12	113	.	0			c.A163G						PASS	.	T	GLY/ARG	443,3963	195.7+/-220.2	54,335,1814	81.0	65.0	70.0		163	1.5	0.2	1	dbSNP_131	70	170,8426	69.0+/-131.5	10,150,4138	no	missense	OR2T12	NM_001004692.1	125	64,485,5952	CC,CT,TT		1.9777,10.0545,4.7147	benign	55/321	248458718	613,12389	2203	4298	6501	SO:0001583	missense	127064	exon1			TGGGCCTGTGGAG	BK004485	CCDS31110.1	1q44	2012-08-09			ENSG00000177201	ENSG00000177201		"""GPCR / Class A : Olfactory receptors"""	19592	protein-coding gene	gene with protein product							Standard	NM_001004692		Approved		uc010pzj.2	Q8NG77	OTTHUMG00000040457	ENST00000317996.1:c.163A>G	1.37:g.248458718T>C	ENSP00000324583:p.Arg55Gly	491.0	1.0	0.00203666		530.0	345.0	0.650943	NM_001004692		Missense_Mutation	SNP	ENST00000317996.1	37	CCDS31110.1	82	0.037545787545787544	51	0.10365853658536585	8	0.022099447513812154	0	0.0	23	0.030343007915567283	t	9.783	1.175918	0.21704	0.100545	0.019777	ENSG00000177201	ENST00000317996	T	0.00384	7.6	1.55	1.55	0.23275	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36303	U	0.002679	T	0.00012	0.0000	L	0.52011	1.625	0.09310	N	0.999998	B	0.12013	0.005	B	0.14023	0.01	T	0.51371	-0.8714	10	0.87932	D	0	.	4.983	0.14176	0.2683:0.0:0.0:0.7317	.	55	Q8NG77	O2T12_HUMAN	G	55	ENSP00000324583:R55G	ENSP00000324583:R55G	R	-	1	2	OR2T12	246525341	0.001000	0.12720	0.159000	0.22649	0.174000	0.22865	-0.039000	0.12124	0.540000	0.28808	0.147000	0.16070	AGG	T|0.961;C|0.039	0.039	strong		0.527	OR2T12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097353.1	NM_001004692	
OR2T27	403239	hgsc.bcm.edu	37	1	248813421	248813421	+	Silent	SNP	G	G	A	rs200410497	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248813421G>A	ENST00000344889.3	-	1	764	c.765C>T	c.(763-765)gcC>gcT	p.A255A		NM_001001824.1	NP_001001824.1	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T, member 27	255						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(2)|large_intestine(4)|lung(20)|skin(3)|stomach(1)	32	all_cancers(71;1.15e-05)|all_epithelial(71;5.29e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.089)|Lung NSC(105;0.0969)|Melanoma(84;0.199)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ATGTGTACATGGCAGCCCCAT	0.527													G|||	320	0.0638978	0.2292	0.0231	5008	,	,		17935	0.0		0.001	False		,,,				2504	0.0				p.A255A		Atlas-SNP	.											.	OR2T27	52	.	0			c.C765T						PASS	.	G		669,3711		76,517,1597	39.0	30.0	33.0		765	0.1	0.0	1	dbSNP_134	33	6,8522		0,6,4258	no	coding-synonymous	OR2T27	NM_001001824.1		76,523,5855	AA,AG,GG		0.0704,15.274,5.2293		255/318	248813421	675,12233	2190	4264	6454	SO:0001819	synonymous_variant	403239	exon1			GTACATGGCAGCC		CCDS31124.1	1q44	2012-08-09			ENSG00000187701	ENSG00000187701		"""GPCR / Class A : Olfactory receptors"""	31252	protein-coding gene	gene with protein product							Standard	NM_001001824		Approved		uc010pzo.2	Q8NH04	OTTHUMG00000040376	ENST00000344889.3:c.765C>T	1.37:g.248813421G>A		163.0	0.0	0		154.0	69.0	0.448052	NM_001001824		Silent	SNP	ENST00000344889.3	37	CCDS31124.1																																																																																			G|0.969;A|0.031	0.031	strong		0.527	OR2T27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097124.1	NM_001001824	
SYNGAP1	8831	hgsc.bcm.edu	37	6	33393583	33393583	+	Silent	SNP	C	C	T	rs73402305	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:33393583C>T	ENST00000418600.2	+	3	299	c.198C>T	c.(196-198)ccC>ccT	p.P66P	SYNGAP1_ENST00000496374.1_3'UTR|SYNGAP1_ENST00000293748.5_Silent_p.P66P	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	66					dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						AGATACACCCCCTACTGATCC	0.697													c|||	259	0.0517173	0.1921	0.0058	5008	,	,		9030	0.0		0.001	False		,,,				2504	0.0				p.P66P		Atlas-SNP	.											SYNGAP1_ENST00000293748,NS,carcinoma,+2,2	SYNGAP1	202	2	0			c.C198T						PASS	.	C		653,3753	259.8+/-263.3	41,571,1591	47.0	40.0	43.0		198	0.8	1.0	6	dbSNP_131	43	8,8592	5.0+/-18.6	0,8,4292	no	coding-synonymous	SYNGAP1	NM_006772.2		41,579,5883	TT,TC,CC		0.093,14.8207,5.0823		66/1344	33393583	661,12345	2203	4300	6503	SO:0001819	synonymous_variant	8831	exon3			ACACCCCCTACTG	AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"""synaptic Ras GTPase activating protein 1 homolog (rat)"""			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.198C>T	6.37:g.33393583C>T		183.0	0.0	0		168.0	77.0	0.458333	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Silent	SNP	ENST00000418600.2	37	CCDS34434.2																																																																																			C|0.937;T|0.063	0.063	strong		0.697	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407	
NBAS	51594	hgsc.bcm.edu	37	2	15358939	15358939	+	Missense_Mutation	SNP	A	A	C	rs114448506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:15358939A>C	ENST00000281513.5	-	48	6415	c.6390T>G	c.(6388-6390)ttT>ttG	p.F2130L	NBAS_ENST00000441750.1_Missense_Mutation_p.F2010L	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	2130					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						CTTCAGTTCTAAAGAACACGA	0.517													A|||	12	0.00239617	0.0091	0.0	5008	,	,		19280	0.0		0.0	False		,,,				2504	0.0				p.F2130L		Atlas-SNP	.											.	NBAS	246	.	0			c.T6390G						PASS	.	A	LEU/PHE	37,4369	42.3+/-75.8	0,37,2166	68.0	73.0	71.0		6390	-4.2	0.0	2	dbSNP_132	71	1,8599	1.2+/-3.3	0,1,4299	yes	missense	NBAS	NM_015909.2	22	0,38,6465	CC,CA,AA		0.0116,0.8398,0.2922	possibly-damaging	2130/2372	15358939	38,12968	2203	4300	6503	SO:0001583	missense	51594	exon48			AGTTCTAAAGAAC	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.6390T>G	2.37:g.15358939A>C	ENSP00000281513:p.Phe2130Leu	221.0	0.0	0		238.0	127.0	0.533613	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Missense_Mutation	SNP	ENST00000281513.5	37	CCDS1685.1	5|5	0.0022893772893772895|0.0022893772893772895	5|5	0.01016260162601626|0.01016260162601626	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	A|A	14.99|14.99	2.699080|2.699080	0.48307|0.48307	0.008398|0.008398	1.16E-4|1.16E-4	ENSG00000151779|ENSG00000151779	ENST00000441750;ENST00000281513|ENST00000442506	T;T|.	0.09255|.	3.0;3.17|.	5.63|5.63	-4.15|-4.15	0.03881|0.03881	.|.	0.248251|.	0.47455|.	D|.	0.000222|.	T|.	0.55752|.	0.1940|.	M|M	0.65498|0.65498	2.005|2.005	0.32809|0.32809	D|D	0.501197|0.501197	P;B|.	0.43231|.	0.801;0.397|.	P;B|.	0.44811|.	0.461;0.176|.	T|.	0.65405|.	-0.6176|.	10|.	0.87932|.	D|.	0|.	.|.	16.982|16.982	0.86331|0.86331	0.1405:0.0:0.8595:0.0|0.1405:0.0:0.8595:0.0	.|.	2010;2130|.	A2RRP1-2;A2RRP1|.	.;NBAS_HUMAN|.	L|X	2010;2130|1178	ENSP00000413201:F2010L;ENSP00000281513:F2130L|.	ENSP00000281513:F2130L|.	F|L	-|-	3|2	2|0	NBAS|NBAS	15276390|15276390	0.998000|0.998000	0.40836|0.40836	0.001000|0.001000	0.08648|0.08648	0.824000|0.824000	0.46624|0.46624	1.102000|1.102000	0.31050|0.31050	-1.413000|-1.413000	0.02027|0.02027	-0.326000|-0.326000	0.08463|0.08463	TTT|TTA	A|0.997;C|0.003	0.003	strong		0.517	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909	
IFNAR1	3454	hgsc.bcm.edu	37	21	34713317	34713317	+	Silent	SNP	T	T	C	rs9981753	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:34713317T>C	ENST00000270139.3	+	3	365	c.213T>C	c.(211-213)gaT>gaC	p.D71D	IFNAR1_ENST00000416947.2_Silent_p.D2D|IFNAR1_ENST00000442357.2_Silent_p.D71D	NM_000629.2	NP_000620.2	P17181	INAR1_HUMAN	interferon (alpha, beta and omega) receptor 1	71	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to virus (GO:0009615)|T cell activation (GO:0042110)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	type I interferon receptor activity (GO:0004905)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|skin(2)	14					"""""""Interferon Alfa-2a(DB00034)|""""Interferon Alfa-2b(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1a(DB00060)|Interferon beta-1b(DB00068)|Natural alpha interferon(DB05258)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)"""	CTGGGATGGATAATTGGATAA	0.284													T|||	95	0.0189696	0.0658	0.0072	5008	,	,		17150	0.0		0.003	False		,,,				2504	0.0				p.D71D	Esophageal Squamous(73;817 1211 32990 35667 42746)	Atlas-SNP	.											.	IFNAR1	44	.	0			c.T213C						PASS	.	T		244,4162	132.1+/-168.6	6,232,1965	55.0	59.0	58.0		213	3.1	0.0	21	dbSNP_119	58	14,8582	9.8+/-36.6	0,14,4284	no	coding-synonymous	IFNAR1	NM_000629.2		6,246,6249	CC,CT,TT		0.1629,5.5379,1.9843		71/558	34713317	258,12744	2203	4298	6501	SO:0001819	synonymous_variant	3454	exon3			GATGGATAATTGG		CCDS13624.1	21q22.1	2008-05-02			ENSG00000142166	ENSG00000142166		"""Interferons"""	5432	protein-coding gene	gene with protein product		107450		IFNAR		8181059	Standard	NM_000629		Approved	IFRC	uc002yrn.3	P17181	OTTHUMG00000065126	ENST00000270139.3:c.213T>C	21.37:g.34713317T>C		140.0	0.0	0		100.0	42.0	0.42	NM_000629	B2R6L9|B4DNT3|D3DSF0|Q53GW9|Q53H11|Q6PKD7|Q7M4L2|Q8WTZ2	Silent	SNP	ENST00000270139.3	37	CCDS13624.1																																																																																			T|0.986;C|0.014	0.014	strong		0.284	IFNAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139823.4		
TRPM1	4308	hgsc.bcm.edu	37	15	31294773	31294773	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:31294773C>T	ENST00000256552.6	-	28	4277	c.4130G>A	c.(4129-4131)gGt>gAt	p.G1377D	RP11-348B17.1_ENST00000561299.1_RNA|TRPM1_ENST00000542188.1_Missense_Mutation_p.G1394D|TRPM1_ENST00000397795.2_Missense_Mutation_p.G1355D	NM_001252024.1	NP_001238953.1			transient receptor potential cation channel, subfamily M, member 1											NS(2)|breast(3)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(15)|lung(48)|ovary(2)|pancreas(1)|prostate(3)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(3)	99		all_lung(180;1.92e-11)		all cancers(64;3.52e-16)|Epithelial(43;1.65e-11)|GBM - Glioblastoma multiforme(186;3.57e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00533)|COAD - Colon adenocarcinoma(236;0.0609)|Lung(196;0.199)		AATATCTGGACCTAATTTTGA	0.393																																					p.G1394D		Atlas-SNP	.											.	TRPM1	183	.	0			c.G4181A						PASS	.						160.0	153.0	155.0					15																	31294773		1917	4138	6055	SO:0001583	missense	4308	exon27			TCTGGACCTAATT	AF071787	CCDS10024.2, CCDS58345.1, CCDS58346.1, CCDS58347.1	15q13.3	2014-01-28		2002-01-18	ENSG00000134160	ENSG00000134160		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	7146	protein-coding gene	gene with protein product		603576	"""melastatin 1"""	MLSN1		9806836, 9537257, 16382100	Standard	NM_001252020		Approved	LTRPC1, CSNB1C	uc021sia.1	Q7Z4N2	OTTHUMG00000129267	ENST00000256552.6:c.4130G>A	15.37:g.31294773C>T	ENSP00000256552:p.Gly1377Asp	74.0	0.0	0		88.0	38.0	0.431818	NM_001252020		Missense_Mutation	SNP	ENST00000256552.6	37	CCDS58346.1	.	.	.	.	.	.	.	.	.	.	C	4.656	0.121910	0.08931	.	.	ENSG00000134160	ENST00000397795;ENST00000542188;ENST00000256552;ENST00000397793	T;T;T	0.52526	0.67;0.66;0.68	4.81	2.63	0.31362	.	0.300372	0.27851	N	0.017600	T	0.26919	0.0659	N	0.17082	0.46	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.002;0.003	T	0.10132	-1.0643	10	0.52906	T	0.07	-6.7074	5.797	0.18392	0.1392:0.6449:0.1355:0.0804	.	1349;1355	Q7Z4N2-3;Q7Z4N2	.;TRPM1_HUMAN	D	1355;1394;1377;1355	ENSP00000380897:G1355D;ENSP00000437849:G1394D;ENSP00000256552:G1377D	ENSP00000256552:G1377D	G	-	2	0	TRPM1	29082065	0.035000	0.19736	0.093000	0.20910	0.043000	0.13939	0.395000	0.20850	2.201000	0.70794	0.650000	0.86243	GGT	.	.	none		0.393	TRPM1-004	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417166.2	NM_002420	
MCMBP	79892	hgsc.bcm.edu	37	10	121602830	121602830	+	Silent	SNP	G	G	A	rs34297798	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:121602830G>A	ENST00000360003.3	-	9	1105	c.936C>T	c.(934-936)gcC>gcT	p.A312A	MCMBP_ENST00000369077.3_Silent_p.A312A|MCMBP_ENST00000466047.1_5'UTR	NM_001256378.1|NM_001256379.1|NM_024834.3	NP_001243307.1|NP_001243308.1|NP_079110.1	Q9BTE3	MCMBP_HUMAN	minichromosome maintenance complex binding protein	312					DNA-dependent DNA replication (GO:0006261)|mitotic nuclear division (GO:0007067)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(2)|skin(2)	21						GCAACTTCTGGGCTAAGATCA	0.483													G|||	44	0.00878594	0.0303	0.0058	5008	,	,		20195	0.0		0.0	False		,,,				2504	0.0				p.A312A		Atlas-SNP	.											.	MCMBP	49	.	0			c.C936T						PASS	.	G		113,4293	86.8+/-125.4	0,113,2090	289.0	228.0	249.0		936	-1.7	1.0	10	dbSNP_126	249	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	MCMBP	NM_024834.2		0,117,6386	AA,AG,GG		0.0465,2.5647,0.8996		312/643	121602830	117,12889	2203	4300	6503	SO:0001819	synonymous_variant	79892	exon9			CTTCTGGGCTAAG	BC007219	CCDS7617.1, CCDS58099.1	10q26.13	2013-10-11	2011-01-05	2011-01-05	ENSG00000197771	ENSG00000197771			25782	protein-coding gene	gene with protein product		610909	"""chromosome 10 open reading frame 119"""	C10orf119		17296731	Standard	NM_024834		Approved	FLJ13081, MCM-BP	uc001ler.3	Q9BTE3	OTTHUMG00000019159	ENST00000360003.3:c.936C>T	10.37:g.121602830G>A		190.0	0.0	0		214.0	111.0	0.518692	NM_024834	B3KSP7|Q6IA56|Q9BVT9|Q9H916	Silent	SNP	ENST00000360003.3	37	CCDS7617.1																																																																																			G|0.990;A|0.010	0.010	strong		0.483	MCMBP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050684.1	NM_024834	
SHPRH	257218	hgsc.bcm.edu	37	6	146276280	146276280	+	Missense_Mutation	SNP	C	C	T	rs182151362	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:146276280C>T	ENST00000367505.2	-	2	443	c.179G>A	c.(178-180)aGt>aAt	p.S60N	SHPRH_ENST00000367503.3_Missense_Mutation_p.S60N|SHPRH_ENST00000438092.2_Missense_Mutation_p.S60N|SHPRH_ENST00000275233.7_Missense_Mutation_p.S60N			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	60					DNA repair (GO:0006281)|nucleosome assembly (GO:0006334)|protein polyubiquitination (GO:0000209)	nucleosome (GO:0000786)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(33)|ovary(3)|pancreas(2)|prostate(7)|skin(1)|urinary_tract(1)	79		Ovarian(120;0.0365)		OV - Ovarian serous cystadenocarcinoma(155;1.47e-07)|GBM - Glioblastoma multiforme(68;0.0124)		TTCCTTTAGACTATCACTTAG	0.408													C|||	22	0.00439297	0.0144	0.0014	5008	,	,		18451	0.0		0.002	False		,,,				2504	0.0				p.S60N		Atlas-SNP	.											.	SHPRH	169	.	0			c.G179A						PASS	.	C	ASN/SER,ASN/SER	53,3687		0,53,1817	106.0	97.0	100.0		179,179	1.9	0.0	6		100	4,8210		0,4,4103	yes	missense,missense	SHPRH	NM_001042683.2,NM_173082.3	46,46	0,57,5920	TT,TC,CC		0.0487,1.4171,0.4768	benign,benign	60/1684,60/1660	146276280	57,11897	1870	4107	5977	SO:0001583	missense	257218	exon2			TTTAGACTATCAC	AB095943	CCDS43513.1, CCDS47496.1, CCDS43513.2	6q24.2	2012-02-23	2012-02-23		ENSG00000146414	ENSG00000146414		"""RING-type (C3HC4) zinc fingers"""	19336	protein-coding gene	gene with protein product		608048	"""SNF2 histone linker PHD RING helicase"""			12837266	Standard	NM_001042683		Approved	FLJ90837, KIAA2023, bA545I5.2	uc003qlf.3	Q149N8	OTTHUMG00000015750	ENST00000367505.2:c.179G>A	6.37:g.146276280C>T	ENSP00000356475:p.Ser60Asn	86.0	0.0	0		115.0	52.0	0.452174	NM_173082	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Missense_Mutation	SNP	ENST00000367505.2	37	CCDS43513.2	4	0.0018315018315018315	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	C	4.394	0.072688	0.08436	0.014171	4.87E-4	ENSG00000146414	ENST00000367505;ENST00000367503;ENST00000438092;ENST00000275233	T;T;T;T	0.64260	-0.09;-0.09;-0.09;-0.09	5.66	1.9	0.25705	.	0.291823	0.32068	N	0.006636	T	0.34250	0.0891	L	0.50333	1.59	0.09310	N	1	B;B	0.31548	0.22;0.328	B;B	0.32864	0.073;0.154	T	0.21690	-1.0238	10	0.49607	T	0.09	0.0517	8.8158	0.34996	0.0:0.6472:0.0:0.3528	.	60;60	Q149N8;Q149N8-4	SHPRH_HUMAN;.	N	60	ENSP00000356475:S60N;ENSP00000356473:S60N;ENSP00000412797:S60N;ENSP00000275233:S60N	ENSP00000275233:S60N	S	-	2	0	SHPRH	146317973	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	0.321000	0.19558	0.332000	0.23536	-0.136000	0.14681	AGT	C|0.998;T|0.002	0.002	strong		0.408	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082	
CCDC88C	440193	hgsc.bcm.edu	37	14	91739873	91739873	+	Missense_Mutation	SNP	A	A	G	rs7145583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:91739873A>G	ENST00000389857.6	-	30	5269	c.5183T>C	c.(5182-5184)tTt>tCt	p.F1728S	CCDC88C_ENST00000331194.7_Missense_Mutation_p.F252S	NM_001080414.3	NP_001073883.2	Q9P219	DAPLE_HUMAN	coiled-coil domain containing 88C	1728					protein destabilization (GO:0031648)|protein homooligomerization (GO:0051260)|regulation of protein phosphorylation (GO:0001932)|Wnt signaling pathway (GO:0016055)		PDZ domain binding (GO:0030165)|protein self-association (GO:0043621)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|ovary(6)|pancreas(1)|urinary_tract(1)	24		all_cancers(154;0.0468)				GGGGGCCACAAAGTTGGTGGG	0.622													A|||	28	0.00559105	0.0189	0.0043	5008	,	,		16431	0.0		0.0	False		,,,				2504	0.0				p.F1728S		Atlas-SNP	.											.	CCDC88C	192	.	0			c.T5183C						PASS	.	A	SER/PHE	63,3873		1,61,1906	29.0	33.0	32.0		5183	3.5	0.8	14	dbSNP_116	32	1,8255		0,1,4127	yes	missense	CCDC88C	NM_001080414.3	155	1,62,6033	GG,GA,AA		0.0121,1.6006,0.5249	benign	1728/2029	91739873	64,12128	1968	4128	6096	SO:0001583	missense	440193	exon30			GCCACAAAGTTGG		CCDS45151.1	14q32.12	2014-07-30	2007-05-31	2007-05-31		ENSG00000015133			19967	protein-coding gene	gene with protein product	"""Dvl-associating protein with a high frequency of leucine residues"", ""spinocerebellar ataxia 40"""	611204	"""KIAA1509"""	KIAA1509		17185515, 25062847	Standard	NM_001080414		Approved	DAPLE, HkRP2, SCA40	uc010aty.3	Q9P219		ENST00000389857.6:c.5183T>C	14.37:g.91739873A>G	ENSP00000374507:p.Phe1728Ser	183.0	0.0	0		150.0	72.0	0.48	NM_001080414	Q69YK1|Q7L1M2|Q86SX7|Q8IYG8	Missense_Mutation	SNP	ENST00000389857.6	37	CCDS45151.1	7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	A	7.279	0.608712	0.14066	0.016006	1.21E-4	ENSG00000015133	ENST00000389857;ENST00000427583;ENST00000331194	T;T	0.47528	2.39;0.84	4.7	3.52	0.40303	.	0.410931	0.18701	U	0.133580	T	0.25644	0.0624	M	0.64997	1.995	0.27192	N	0.960401	B;B;B	0.32160	0.242;0.231;0.358	B;B;B	0.33042	0.154;0.157;0.157	T	0.17410	-1.0370	10	0.30078	T	0.28	0.4499	6.9029	0.24293	0.6516:0.1293:0.0:0.2191	rs7145583	1728;252;178	Q9P219;Q9P219-2;Q9P219-3	DAPLE_HUMAN;.;.	S	1728;252;252	ENSP00000374507:F1728S;ENSP00000330332:F252S	ENSP00000330332:F252S	F	-	2	0	CCDC88C	90809626	0.999000	0.42202	0.816000	0.32577	0.093000	0.18481	2.620000	0.46410	0.630000	0.30394	0.377000	0.23210	TTT	A|0.997;G|0.003	0.003	strong		0.622	CCDC88C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411650.1	XM_029353	
NPHP4	261734	hgsc.bcm.edu	37	1	5965824	5965824	+	Missense_Mutation	SNP	G	G	C	rs12093500	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:5965824G>C	ENST00000378156.4	-	14	1896	c.1631C>G	c.(1630-1632)gCc>gGc	p.A544G	NPHP4_ENST00000478423.2_5'UTR	NM_015102.3	NP_055917.1	O75161	NPHP4_HUMAN	nephronophthisis 4	544			A -> G (in dbSNP:rs12093500). {ECO:0000269|PubMed:15776426}.		actin cytoskeleton organization (GO:0030036)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|visual behavior (GO:0007632)	cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|cervix(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(15)|ovary(2)|pancreas(1)|prostate(4)	47	Ovarian(185;0.0634)	all_cancers(23;7.53e-41)|all_epithelial(116;3.96e-23)|all_lung(118;5.12e-09)|all_hematologic(16;5.45e-07)|Lung NSC(185;5.49e-07)|all_neural(13;3.21e-06)|Acute lymphoblastic leukemia(12;3.44e-05)|Breast(487;0.000601)|Renal(390;0.0007)|Colorectal(325;0.00113)|Hepatocellular(190;0.00213)|Glioma(11;0.00223)|Myeloproliferative disorder(586;0.0256)|Ovarian(437;0.04)|Lung SC(97;0.128)|Medulloblastoma(700;0.213)		Epithelial(90;1.69e-36)|GBM - Glioblastoma multiforme(13;5.07e-29)|OV - Ovarian serous cystadenocarcinoma(86;1.05e-19)|Colorectal(212;4.54e-07)|COAD - Colon adenocarcinoma(227;3.14e-05)|Kidney(185;0.00012)|BRCA - Breast invasive adenocarcinoma(365;0.00102)|KIRC - Kidney renal clear cell carcinoma(229;0.00179)|STAD - Stomach adenocarcinoma(132;0.00472)|READ - Rectum adenocarcinoma(331;0.0649)		GGAGATACCGGCCTCCAACGG	0.572													C|||	127	0.0253594	0.0877	0.0115	5008	,	,		18214	0.0		0.003	False		,,,				2504	0.0				p.A544G		Atlas-SNP	.											.	NPHP4	119	.	0			c.C1631G						PASS	.	C	GLY/ALA	306,3584		10,286,1649	28.0	31.0	30.0		1631	4.5	0.3	1	dbSNP_120	30	14,8254		0,14,4120	yes	missense	NPHP4	NM_015102.3	60	10,300,5769	CC,CG,GG		0.1693,7.8663,2.632	benign	544/1427	5965824	320,11838	1945	4134	6079	SO:0001583	missense	261734	exon14			ATACCGGCCTCCA	AB014573	CCDS44052.1	1p36	2010-03-26			ENSG00000131697	ENSG00000131697			19104	protein-coding gene	gene with protein product	"""nephroretinin"", ""nephrocystin-4"", ""POC10 centriolar protein homolog (Chlamydomonas)"""	607215				11920287, 12205563	Standard	XR_244787		Approved	SLSN4, KIAA0673, POC10	uc001alq.2	O75161	OTTHUMG00000000701	ENST00000378156.4:c.1631C>G	1.37:g.5965824G>C	ENSP00000367398:p.Ala544Gly	101.0	0.0	0		132.0	64.0	0.484848	NM_015102	Q8IWC0	Missense_Mutation	SNP	ENST00000378156.4	37	CCDS44052.1	39	0.017857142857142856	30	0.06097560975609756	6	0.016574585635359115	0	0.0	3	0.00395778364116095	C	0.007	-1.936935	0.00484	0.078663	0.001693	ENSG00000131697	ENST00000378156	D	0.87334	-2.24	5.42	4.5	0.54988	.	0.527792	0.18448	N	0.140932	T	0.08626	0.0214	N	0.00436	-1.5	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.06643	-1.0815	10	0.10377	T	0.69	.	16.1591	0.81686	0.0:0.6272:0.3728:0.0	rs12093500;rs61332996;rs12093500	544	O75161	NPHP4_HUMAN	G	544	ENSP00000367398:A544G	ENSP00000367398:A544G	A	-	2	0	NPHP4	5888411	.	.	0.285000	0.24819	0.013000	0.08279	.	.	0.644000	0.30656	-0.216000	0.12614	GCC	G|0.980;C|0.020	0.020	strong		0.572	NPHP4-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001715.2		
OR5I1	10798	hgsc.bcm.edu	37	11	55703523	55703523	+	Silent	SNP	G	G	A	rs11231594	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55703523G>A	ENST00000301532.3	-	1	353	c.354C>T	c.(352-354)gcC>gcT	p.A118A		NM_006637.1	NP_006628.1	Q13606	OR5I1_HUMAN	olfactory receptor, family 5, subfamily I, member 1	118					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)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(34)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	52						AGGCCATGGCGGCCAGGATGA	0.433													G|||	121	0.0241613	0.0862	0.0101	5008	,	,		19053	0.0		0.0	False		,,,				2504	0.0				p.A118A		Atlas-SNP	.											.	OR5I1	110	.	0			c.C354T						PASS	.	G		304,4098	162.9+/-194.8	16,272,1913	52.0	55.0	54.0		354	-2.7	0.3	11	dbSNP_120	54	6,8578	5.7+/-21.5	0,6,4286	no	coding-synonymous	OR5I1	NM_006637.1		16,278,6199	AA,AG,GG		0.0699,6.906,2.3872		118/315	55703523	310,12676	2201	4292	6493	SO:0001819	synonymous_variant	10798	exon1			CATGGCGGCCAGG	BC069093	CCDS7949.1	11q11	2012-08-09			ENSG00000167825	ENSG00000167825		"""GPCR / Class A : Olfactory receptors"""	8347	protein-coding gene	gene with protein product		608496				9017400, 9787077	Standard	NM_006637		Approved	HSOlf1, OLF1	uc010ris.2	Q13606	OTTHUMG00000166821	ENST00000301532.3:c.354C>T	11.37:g.55703523G>A		86.0	0.0	0		96.0	44.0	0.458333	NM_006637	Q6IEU4	Silent	SNP	ENST00000301532.3	37	CCDS7949.1																																																																																			G|0.974;A|0.026	0.026	strong		0.433	OR5I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391528.1	NM_006637	
SCO1	6341	hgsc.bcm.edu	37	17	10595250	10595250	+	Silent	SNP	T	T	C	rs2271228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:10595250T>C	ENST00000255390.5	-	4	654	c.594A>G	c.(592-594)ccA>ccG	p.P198P	SCO1_ENST00000577427.1_Silent_p.P167P|SCO1_ENST00000582053.1_5'Flank	NM_004589.2	NP_004580.1	O75880	SCO1_HUMAN	SCO1 cytochrome c oxidase assembly protein	198					cellular copper ion homeostasis (GO:0006878)|copper ion transport (GO:0006825)|generation of precursor metabolites and energy (GO:0006091)|respiratory chain complex IV assembly (GO:0008535)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|myofibril (GO:0030016)	copper ion binding (GO:0005507)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|urinary_tract(1)	10						TGATGAAAAGTGGAGTTAGAT	0.358													T|||	249	0.0497204	0.1679	0.0072	5008	,	,		21532	0.0169		0.003	False		,,,				2504	0.002				p.P198P	Melanoma(128;591 1731 19711 31891 44645)	Atlas-SNP	.											SCO1,NS,carcinoma,-1,1	SCO1	24	1	0			c.A594G						scavenged	.	T		567,3839	253.4+/-259.3	36,495,1672	112.0	109.0	110.0		594	-2.1	1.0	17	dbSNP_100	110	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	SCO1	NM_004589.2		36,500,5967	CC,CT,TT		0.0581,12.8688,4.398		198/302	10595250	572,12434	2203	4300	6503	SO:0001819	synonymous_variant	6341	exon4			GAAAAGTGGAGTT	AF026852	CCDS11158.1	17p13.1	2012-10-15	2012-10-15		ENSG00000133028	ENSG00000133028		"""Mitochondrial respiratory chain complex assembly factors"""	10603	protein-coding gene	gene with protein product		603644	"""SCO (cytochrome oxidase deficient, yeast) homolog 1"", ""SCO cytochrome oxidase deficient homolog 1 (yeast)"""	SCOD1		9878253	Standard	NM_004589		Approved		uc002gmr.4	O75880	OTTHUMG00000130364	ENST00000255390.5:c.594A>G	17.37:g.10595250T>C		124.0	1.0	0.00806452		143.0	59.0	0.412587	NM_004589	B2RDM0	Silent	SNP	ENST00000255390.5	37	CCDS11158.1																																																																																			T|0.961;C|0.039	0.039	strong		0.358	SCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252729.2	NM_004589	
CCNB1	891	hgsc.bcm.edu	37	5	68471232	68471232	+	Silent	SNP	C	C	T	rs2069439	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:68471232C>T	ENST00000256442.5	+	7	1204	c.951C>T	c.(949-951)gtC>gtT	p.V317V	snoU13_ENST00000459230.1_RNA	NM_031966.3	NP_114172.1	P14635	CCNB1_HUMAN	cyclin B1	317					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cellular response to fatty acid (GO:0071398)|cellular response to hypoxia (GO:0071456)|cellular response to iron(III) ion (GO:0071283)|cellular response to organic cyclic compound (GO:0071407)|digestive tract development (GO:0048565)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|mitotic metaphase plate congression (GO:0007080)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle checkpoint (GO:0071174)|mitotic spindle stabilization (GO:0043148)|negative regulation of gene expression (GO:0010629)|negative regulation of protein phosphorylation (GO:0001933)|oocyte maturation (GO:0001556)|positive regulation of attachment of spindle microtubules to kinetochore (GO:0051987)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of mRNA 3'-end processing (GO:0031442)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein complex assembly (GO:0006461)|protein phosphorylation (GO:0006468)|regulation of cell cycle (GO:0051726)|regulation of chromosome condensation (GO:0060623)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to DDT (GO:0046680)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|spermatogenesis (GO:0007283)|tissue regeneration (GO:0042246)|ventricular cardiac muscle cell development (GO:0055015)	centrosome (GO:0005813)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	kinase activity (GO:0016301)|patched binding (GO:0005113)|protein kinase binding (GO:0019901)			large_intestine(2)|lung(5)|skin(1)	8		Lung NSC(167;5.51e-05)|Prostate(74;0.00634)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;1.24e-56)|Epithelial(20;1.12e-52)|all cancers(19;2.63e-48)|Lung(70;0.0177)		AGGTTGATGTCGAGCAACATA	0.393													C|||	4	0.000798722	0.003	0.0	5008	,	,		20276	0.0		0.0	False		,,,				2504	0.0				p.V317V		Atlas-SNP	.											CCNB1,NS,carcinoma,+1,1	CCNB1	36	1	0			c.C951T						PASS	.	C		26,4380	33.5+/-64.1	0,26,2177	156.0	145.0	149.0		951	-7.2	0.9	5	dbSNP_96	149	0,8600		0,0,4300	no	coding-synonymous	CCNB1	NM_031966.2		0,26,6477	TT,TC,CC		0.0,0.5901,0.1999		317/434	68471232	26,12980	2203	4300	6503	SO:0001819	synonymous_variant	891	exon7			TGATGTCGAGCAA	U22364	CCDS3997.1	5q12	2008-07-18			ENSG00000134057	ENSG00000134057			1579	protein-coding gene	gene with protein product	"""G2/mitotic-specific cyclin B1"""	123836		CCNB		1386342	Standard	NM_031966		Approved		uc003jvm.3	P14635	OTTHUMG00000097817	ENST00000256442.5:c.951C>T	5.37:g.68471232C>T		137.0	0.0	0		125.0	47.0	0.376	NM_031966	A8K066|Q5TZP9	Silent	SNP	ENST00000256442.5	37	CCDS3997.1																																																																																			C|0.998;T|0.002	0.002	strong		0.393	CCNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215084.1	NM_031966	
OR2H1	26716	hgsc.bcm.edu	37	6	29429733	29429733	+	Missense_Mutation	SNP	G	G	A	rs61732185	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29429733G>A	ENST00000377136.1	+	4	652	c.187G>A	c.(187-189)Gac>Aac	p.D63N	OR2H1_ENST00000396792.2_Missense_Mutation_p.D63N|OR2H1_ENST00000442615.1_Missense_Mutation_p.D63N|OR2H1_ENST00000377132.1_Missense_Mutation_p.D63N|OR2H1_ENST00000377133.1_Missense_Mutation_p.D63N|OR2H1_ENST00000473369.1_Intron			Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H, member 1	63			D -> N (in allele 6M1-16*02; dbSNP:rs61732185). {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)			large_intestine(5)|lung(12)	17						TTTCCTCTCTGACCTCTCCTT	0.532													G|||	174	0.0347444	0.1044	0.013	5008	,	,		20350	0.0119		0.0119	False		,,,				2504	0.0031				p.D63N		Atlas-SNP	.											.	OR2H1	38	.	0			c.G187A						PASS	.	G	ASN/ASP	301,2721		17,267,1227	137.0	134.0	135.0		187	0.4	1.0	6	dbSNP_129	135	33,5385		0,33,2676	yes	missense	OR2H1	NM_030883.3	23	17,300,3903	AA,AG,GG		0.6091,9.9603,3.9573	benign	63/317	29429733	334,8106	1511	2709	4220	SO:0001583	missense	26716	exon3			CTCTCTGACCTCT	AF044491	CCDS4660.1	6p22.1	2014-02-19	2002-02-28		ENSG00000204688	ENSG00000204688		"""GPCR / Class A : Olfactory receptors"""	8252	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily H, member 8"""	OR2H6, OR2H8			Standard	NM_030883		Approved	OR6-2	uc003nmi.3	Q9GZK4	OTTHUMG00000031050	ENST00000377136.1:c.187G>A	6.37:g.29429733G>A	ENSP00000366340:p.Asp63Asn	257.0	0.0	0		303.0	143.0	0.471947	NM_030883	B0S7T4|O43629|O43661|O43662|Q5SUN6|Q9GZK9	Missense_Mutation	SNP	ENST00000377136.1	37	CCDS4660.1	88	0.040293040293040296	60	0.12195121951219512	8	0.022099447513812154	10	0.017482517482517484	10	0.013192612137203167	G	1.564	-0.535865	0.04082	0.099603	0.006091	ENSG00000204688	ENST00000377136;ENST00000377133;ENST00000442615;ENST00000377132;ENST00000396792	T;T;T;T;T	0.00940	5.52;5.52;5.52;5.52;5.52	2.88	0.407	0.16371	GPCR, rhodopsin-like superfamily (1);	0.156786	0.30126	N	0.010354	T	0.00039	0.0001	N	0.00003	-3.425	0.24176	N	0.995605	B	0.02656	0.0	B	0.01281	0.0	T	0.12604	-1.0541	10	0.02654	T	1	.	4.2744	0.10802	0.6269:0.1713:0.2018:0.0	rs61732185	63	Q9GZK4	OR2H1_HUMAN	N	63	ENSP00000366340:D63N;ENSP00000366337:D63N;ENSP00000393254:D63N;ENSP00000366336:D63N;ENSP00000380010:D63N	ENSP00000366336:D63N	D	+	1	0	OR2H1	29537712	0.036000	0.19791	0.986000	0.45419	0.919000	0.55068	1.592000	0.36676	0.072000	0.16694	-0.354000	0.07668	GAC	G|0.964;A|0.036	0.036	strong		0.532	OR2H1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194014.3		
DUSP13	51207	hgsc.bcm.edu	37	10	76854463	76854463	+	Missense_Mutation	SNP	G	G	C	rs16931996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:76854463G>C	ENST00000472493.2	-	4	646	c.568C>G	c.(568-570)Cga>Gga	p.R190G	DUSP13_ENST00000372702.3_3'UTR|DUSP13_ENST00000478873.2_Missense_Mutation_p.R326G|DUSP13_ENST00000607131.1_Missense_Mutation_p.R283G|DUSP13_ENST00000491677.2_Missense_Mutation_p.R319G|DUSP13_ENST00000464872.1_Missense_Mutation_p.R139G|DUSP13_ENST00000605915.1_Missense_Mutation_p.R212G|DUSP13_ENST00000372700.3_Missense_Mutation_p.R240G	NM_016364.3	NP_057448.3	Q9UII6	DS13B_HUMAN	dual specificity phosphatase 13	190			R -> G (in dbSNP:rs16931996).		meiotic nuclear division (GO:0007126)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)		protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			large_intestine(3)|lung(3)|prostate(1)|urinary_tract(1)	8	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)					CGCCCCAGTCGGTTGTCCAGA	0.642													G|||	149	0.0297524	0.1082	0.0072	5008	,	,		17269	0.0		0.001	False		,,,				2504	0.0				p.R283G	NSCLC(174;1655 2059 12324 40663 42963)	Atlas-SNP	.											.	DUSP13	82	.	0			c.C847G						PASS	.	G	,GLY/ARG,GLY/ARG,GLY/ARG	462,3944	213.8+/-233.3	24,414,1765	47.0	45.0	46.0		,718,847,568	3.6	1.0	10	dbSNP_123	46	3,8597	3.0+/-9.4	0,3,4297	yes	utr-3,missense,missense,missense	DUSP13	NM_001007271.1,NM_001007272.1,NM_001007273.1,NM_016364.3	,125,125,125	24,417,6062	CC,CG,GG		0.0349,10.4857,3.5753	,probably-damaging,probably-damaging,probably-damaging	,240/249,283/292,190/199	76854463	465,12541	2203	4300	6503	SO:0001583	missense	51207	exon6			CCAGTCGGTTGTC	AB027004	CCDS7346.1, CCDS31224.1, CCDS53542.1	10q23.1	2013-10-25			ENSG00000079393	ENSG00000079393		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	19681	protein-coding gene	gene with protein product		613191				10585869	Standard	XM_005269883		Approved	BEDP, TMDP, FLJ32450, DUSP13A, DUSP13B	uc001jwu.3	Q6B8I1	OTTHUMG00000018516	ENST00000472493.2:c.568C>G	10.37:g.76854463G>C	ENSP00000444580:p.Arg190Gly	81.0	0.0	0		56.0	35.0	0.625	NM_001007273	A8K776|A8K782|B3KPY1|B3KXT0|B4DUK0|Q5JSC6|Q6IAR0|Q96GC2	Missense_Mutation	SNP	ENST00000472493.2	37	CCDS7346.1	59	0.027014652014652016	55	0.11178861788617886	4	0.011049723756906077	0	0.0	0	0.0	G	19.55	3.847958	0.71603	0.104857	3.49E-4	ENSG00000079393	ENST00000308475;ENST00000472493;ENST00000491677;ENST00000372698;ENST00000464872;ENST00000372700	T;T;T;T;T	0.61627	0.09;0.09;0.09;0.09;0.09	5.52	3.61	0.41365	Dual specificity phosphatase, subgroup, catalytic domain (2);	0.557970	0.19913	N	0.103241	T	0.03564	0.0102	M	0.74647	2.275	0.34897	D	0.74614	P;D;B	0.54772	0.556;0.968;0.157	B;P;B	0.54706	0.248;0.759;0.146	T	0.53500	-0.8430	10	0.49607	T	0.09	-3.9628	14.5469	0.68038	0.0:0.0:0.61:0.39	rs16931996;rs52804188;rs16931996	240;319;190	Q9UII6-4;F2Z2C4;Q9UII6	.;.;DUS13_HUMAN	G	190;190;319;283;139;240	ENSP00000311051:R190G;ENSP00000444580:R190G;ENSP00000436312:R319G;ENSP00000434041:R139G;ENSP00000361785:R240G	ENSP00000311051:R190G	R	-	1	2	DUSP13	76524469	0.947000	0.32204	1.000000	0.80357	0.987000	0.75469	1.817000	0.39002	0.635000	0.30488	-0.169000	0.13324	CGA	G|0.956;C|0.044	0.044	strong		0.642	DUSP13-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048786.3		
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305774	39305774	+	Missense_Mutation	SNP	C	C	G	rs137947981		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39305774C>G	ENST00000343246.4	-	1	280	c.246G>C	c.(244-246)caG>caC	p.Q82H		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	82	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.Q82H(1)		central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			agcaggtggtctggcagcagc	0.652																																					p.Q82H		Atlas-SNP	.											KRTAP4-5,NS,carcinoma,0,1	KRTAP4-5	34	1	1	Substitution - Missense(1)	lung(1)	c.G246C						PASS	.						14.0	21.0	19.0					17																	39305774		2102	4215	6317	SO:0001583	missense	85289	exon1			GGTGGTCTGGCAG	AJ406937	CCDS32650.1	17q21.2	2013-06-25			ENSG00000198271	ENSG00000198271		"""Keratin associated proteins"""	18899	protein-coding gene	gene with protein product						11279113	Standard	NM_033188		Approved	KAP4.5	uc002hwb.3	Q9BYR2	OTTHUMG00000133638	ENST00000343246.4:c.246G>C	17.37:g.39305774C>G	ENSP00000340546:p.Gln82His	136.0	0.0	0		86.0	50.0	0.581395	NM_033188		Missense_Mutation	SNP	ENST00000343246.4	37	CCDS32650.1	.	.	.	.	.	.	.	.	.	.	.	6.243	0.412973	0.11812	.	.	ENSG00000198271	ENST00000343246	T	0.00594	6.33	2.03	-0.354	0.12591	.	.	.	.	.	T	0.01320	0.0043	M	0.79693	2.465	0.09310	N	1	B	0.21147	0.052	B	0.35182	0.197	T	0.25950	-1.0117	9	0.45353	T	0.12	.	12.081	0.53671	0.0:0.7361:0.2639:0.0	.	87	Q9BYR2	KRA45_HUMAN	H	82	ENSP00000340546:Q82H	ENSP00000340546:Q82H	Q	-	3	2	KRTAP4-5	36559300	0.000000	0.05858	0.005000	0.12908	0.001000	0.01503	-3.389000	0.00488	-0.371000	0.08004	-1.872000	0.00552	CAG	.	.	weak		0.652	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1		
WDFY4	57705	hgsc.bcm.edu	37	10	49984879	49984879	+	Missense_Mutation	SNP	C	C	T	rs76547526	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:49984879C>T	ENST00000325239.5	+	15	2975	c.2948C>T	c.(2947-2949)cCg>cTg	p.P983L	WDFY4_ENST00000413659.2_Missense_Mutation_p.P983L	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	983						integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						ACACAGGCCCCGCAGCCCTTG	0.642													C|||	79	0.0157748	0.0522	0.0115	5008	,	,		15744	0.0		0.001	False		,,,				2504	0.001				p.P983L		Atlas-SNP	.											.	WDFY4	205	.	0			c.C2948T						PASS	.	C	LEU/PRO	56,1328		1,54,637	20.0	19.0	20.0		2948	-8.1	0.0	10	dbSNP_132	20	5,3177		0,5,1586	yes	missense	WDFY4	NM_020945.1	98	1,59,2223	TT,TC,CC		0.1571,4.0462,1.336	benign	983/3185	49984879	61,4505	692	1591	2283	SO:0001583	missense	57705	exon16			AGGCCCCGCAGCC	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.2948C>T	10.37:g.49984879C>T	ENSP00000320563:p.Pro983Leu	62.0	0.0	0		62.0	31.0	0.5	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	37	CCDS44385.1	25	0.011446886446886446	23	0.046747967479674794	2	0.0055248618784530384	0	0.0	0	0.0	C	10.44	1.349541	0.24426	0.040462	0.001571	ENSG00000128815	ENST00000454161;ENST00000426033;ENST00000325239;ENST00000413659	T;T	0.55234	0.53;1.56	4.97	-8.11	0.01082	.	.	.	.	.	T	0.01765	0.0056	N	0.00583	-1.355	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.15206	-1.0445	8	.	.	.	.	3.6296	0.08126	0.1173:0.3616:0.3583:0.1628	.	983	Q6ZS81	WDFY4_HUMAN	L	992;983;983;983	ENSP00000320563:P983L;ENSP00000403789:P983L	.	P	+	2	0	WDFY4	49654885	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-2.111000	0.01333	-0.982000	0.03515	-0.238000	0.12139	CCG	C|0.988;T|0.012	0.012	strong		0.642	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
MYO18B	84700	hgsc.bcm.edu	37	22	26272270	26272270	+	Missense_Mutation	SNP	A	A	G	rs695633	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:26272270A>G	ENST00000407587.2	+	24	4367	c.4198A>G	c.(4198-4200)Att>Gtt	p.I1400V	MYO18B_ENST00000536101.1_Missense_Mutation_p.I1399V|MYO18B_ENST00000335473.7_Missense_Mutation_p.I1399V			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	1399						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						TAGTGCCACCATTGGAACTGA	0.582													A|||	180	0.0359425	0.1316	0.0086	5008	,	,		16872	0.0		0.0	False		,,,				2504	0.0				p.I1399V		Atlas-SNP	.											.	MYO18B	322	.	0			c.A4195G						PASS	.	A	VAL/ILE	447,3717		25,397,1660	37.0	42.0	40.0		4195	-8.4	0.0	22	dbSNP_83	40	11,8423		0,11,4206	yes	missense	MYO18B	NM_032608.5	29	25,408,5866	GG,GA,AA		0.1304,10.7349,3.6355	benign	1399/2568	26272270	458,12140	2082	4217	6299	SO:0001583	missense	84700	exon24			GCCACCATTGGAA	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.4198A>G	22.37:g.26272270A>G	ENSP00000386096:p.Ile1400Val	99.0	0.0	0		103.0	102.0	0.990291	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		55	0.025183150183150184	51	0.10365853658536585	4	0.011049723756906077	0	0.0	0	0.0	A	5.587	0.293142	0.10567	0.107349	0.001304	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.86297	-2.08;-2.08;-2.1	4.83	-8.43	0.00953	.	0.552403	0.17941	N	0.156858	T	0.05364	0.0142	M	0.63428	1.95	0.80722	P	0.0	B;B;B;B	0.17268	0.007;0.007;0.021;0.013	B;B;B;B	0.14023	0.01;0.004;0.009;0.01	T	0.45906	-0.9229	9	0.37606	T	0.19	.	0.9513	0.01376	0.2422:0.331:0.22:0.2068	rs695633;rs695633	912;1399;1400;1399	Q8IUG5-2;Q8IUG5;F5GXR6;F5GYU7	.;MY18B_HUMAN;.;.	V	1399;1399;1400	ENSP00000441229:I1399V;ENSP00000334563:I1399V;ENSP00000386096:I1400V	ENSP00000334563:I1399V	I	+	1	0	MYO18B	24602270	0.000000	0.05858	0.000000	0.03702	0.935000	0.57460	-1.506000	0.02271	-1.625000	0.01554	0.528000	0.53228	ATT	A|0.967;G|0.033	0.033	strong		0.582	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
BBS12	166379	hgsc.bcm.edu	37	4	123664333	123664333	+	Missense_Mutation	SNP	G	G	C	rs7665271	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:123664333G>C	ENST00000314218.3	+	2	1479	c.1286G>C	c.(1285-1287)aGt>aCt	p.S429T	BBS12_ENST00000542236.1_Missense_Mutation_p.S429T	NM_152618.2	NP_689831.2	Q6ZW61	BBS12_HUMAN	Bardet-Biedl syndrome 12	429			S -> T (in dbSNP:rs7665271).		cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|eating behavior (GO:0042755)|intraciliary transport (GO:0042073)|negative regulation of fat cell differentiation (GO:0045599)|photoreceptor cell maintenance (GO:0045494)	cilium (GO:0005929)	ATP binding (GO:0005524)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|prostate(4)	21						TGTATAAACAGTAAGCGGTTG	0.453									Bardet-Biedl syndrome				G|||	186	0.0371406	0.1301	0.0173	5008	,	,		20575	0.0		0.002	False		,,,				2504	0.0				p.S429T		Atlas-SNP	.											.	BBS12	63	.	0			c.G1286C						PASS	.	G	THR/SER,THR/SER	451,3955	215.5+/-234.4	21,409,1773	75.0	79.0	78.0		1286,1286	-0.6	0.0	4	dbSNP_116	78	12,8588	9.1+/-34.3	0,12,4288	yes	missense,missense	BBS12	NM_001178007.1,NM_152618.2	58,58	21,421,6061	CC,CG,GG		0.1395,10.236,3.5599	possibly-damaging,possibly-damaging	429/711,429/711	123664333	463,12543	2203	4300	6503	SO:0001583	missense	166379	exon3	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	TAAACAGTAAGCG	AK123553	CCDS3728.1	4q27	2014-06-17	2006-12-13	2006-12-13	ENSG00000181004	ENSG00000181004		"""Heat Shock Proteins / Chaperonins"""	26648	protein-coding gene	gene with protein product		610683	"""chromosome 4 open reading frame 24"""	C4orf24		17160889	Standard	NM_001178007		Approved	FLJ35630, FLJ41559	uc003ieu.3	Q6ZW61	OTTHUMG00000133070	ENST00000314218.3:c.1286G>C	4.37:g.123664333G>C	ENSP00000319062:p.Ser429Thr	78.0	0.0	0		105.0	43.0	0.409524	NM_001178007	D3DNX5|Q7Z342|Q7Z482|Q8NAB8	Missense_Mutation	SNP	ENST00000314218.3	37	CCDS3728.1	75	0.034340659340659344	65	0.13211382113821138	9	0.024861878453038673	0	0.0	1	0.0013192612137203166	G	0.004	-2.356069	0.00217	0.10236	0.001395	ENSG00000181004	ENST00000314218;ENST00000542236	T;T	0.79033	-1.23;-1.23	5.58	-0.599	0.11645	.	0.533090	0.21899	N	0.067461	T	0.01627	0.0052	M	0.67953	2.075	0.80722	P	0.0	B	0.18461	0.028	B	0.15052	0.012	T	0.21177	-1.0253	9	0.38643	T	0.18	-14.2272	7.1191	0.25433	0.2915:0.3132:0.3953:0.0	rs7665271;rs7665271	429	Q6ZW61	BBS12_HUMAN	T	429	ENSP00000319062:S429T;ENSP00000438273:S429T	ENSP00000319062:S429T	S	+	2	0	BBS12	123883783	0.005000	0.15991	0.000000	0.03702	0.013000	0.08279	0.239000	0.18023	-0.537000	0.06290	-0.157000	0.13467	AGT	G|0.959;C|0.041	0.041	strong		0.453	BBS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256710.1	NM_152618	
DYRK2	8445	hgsc.bcm.edu	37	12	68052166	68052166	+	Silent	SNP	C	C	T	rs56178357	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:68052166C>T	ENST00000344096.3	+	3	1892	c.1479C>T	c.(1477-1479)agC>agT	p.S493S	RP11-335O4.3_ENST00000425371.2_RNA|DYRK2_ENST00000393555.3_Silent_p.S420S	NM_006482.2	NP_006473.2	Q92630	DYRK2_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	493	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of NFAT protein import into nucleus (GO:0051534)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of glycogen biosynthetic process (GO:0045725)|protein phosphorylation (GO:0006468)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	30			Lung(24;6.81e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(7;0.000573)		CACCGGAGAGCAGAGAGTGGG	0.572													C|||	538	0.107428	0.382	0.0447	5008	,	,		19022	0.0		0.002	False		,,,				2504	0.0				p.S493S		Atlas-SNP	.											.	DYRK2	63	.	0			c.C1479T						PASS	.	C	,	1334,3072	442.3+/-346.6	195,944,1064	59.0	62.0	61.0		1260,1479	5.2	1.0	12	dbSNP_129	61	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous,coding-synonymous	DYRK2	NM_003583.3,NM_006482.2	,	195,953,5355	TT,TC,CC		0.1047,30.2769,10.326	,	420/529,493/602	68052166	1343,11663	2203	4300	6503	SO:0001819	synonymous_variant	8445	exon3			GGAGAGCAGAGAG	Y09216	CCDS8978.1, CCDS8979.1	12q15	2008-07-03				ENSG00000127334			3093	protein-coding gene	gene with protein product		603496				9748265	Standard	NM_003583		Approved		uc001str.4	Q92630		ENST00000344096.3:c.1479C>T	12.37:g.68052166C>T		163.0	0.0	0		170.0	85.0	0.5	NM_006482	B2R9V9|Q9BRB5	Silent	SNP	ENST00000344096.3	37	CCDS8978.1																																																																																			C|0.909;T|0.091	0.091	strong		0.572	DYRK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402218.1		
OR1J2	26740	hgsc.bcm.edu	37	9	125274015	125274015	+	Missense_Mutation	SNP	C	C	T	rs150890302	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:125274015C>T	ENST00000335302.5	+	1	935	c.935C>T	c.(934-936)tCt>tTt	p.S312F		NM_054107.1	NP_473448.1	Q8NGS2	OR1J2_HUMAN	olfactory receptor, family 1, subfamily J, member 2	312						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|skin(7)|stomach(1)	26						ACATTTTTCTCTTGGTGACAT	0.378													C|||	11	0.00219649	0.0076	0.0014	5008	,	,		20140	0.0		0.0	False		,,,				2504	0.0				p.S312F		Atlas-SNP	.											.	OR1J2	64	.	0			c.C935T						PASS	.	C	PHE/SER	35,4371	29.0+/-57.7	0,35,2168	39.0	42.0	41.0		935	-0.7	0.0	9	dbSNP_134	41	0,8600		0,0,4300	yes	missense	OR1J2	NM_054107.1	155	0,35,6468	TT,TC,CC		0.0,0.7944,0.2691	benign	312/314	125274015	35,12971	2203	4300	6503	SO:0001583	missense	26740	exon1			TTTTCTCTTGGTG		CCDS35121.1	9q33.2	2013-09-20			ENSG00000197233	ENSG00000197233		"""GPCR / Class A : Olfactory receptors"""	8209	protein-coding gene	gene with protein product				OR1J3, OR1J5			Standard	XM_005251920		Approved	OST044	uc011lyv.2	Q8NGS2	OTTHUMG00000020604	ENST00000335302.5:c.935C>T	9.37:g.125274015C>T	ENSP00000335575:p.Ser312Phe	117.0	0.0	0		96.0	36.0	0.375	NM_054107	A3KFL9|Q6IF14|Q96R90|Q9NZP1	Missense_Mutation	SNP	ENST00000335302.5	37	CCDS35121.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	10.26	1.301654	0.23736	0.007944	0.0	ENSG00000197233	ENST00000335302	T	0.01505	4.82	4.67	-0.71	0.11234	.	2.214490	0.02811	U	0.124264	T	0.00845	0.0028	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.47114	-0.9142	10	0.52906	T	0.07	.	1.4467	0.02366	0.1417:0.3067:0.138:0.4137	.	312	Q8NGS2	OR1J2_HUMAN	F	312	ENSP00000335575:S312F	ENSP00000335575:S312F	S	+	2	0	OR1J2	124313836	0.000000	0.05858	0.000000	0.03702	0.120000	0.20174	-1.098000	0.03346	0.218000	0.20820	0.632000	0.83419	TCT	C|0.998;T|0.002	0.002	strong		0.378	OR1J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053932.1		
DOCK2	1794	hgsc.bcm.edu	37	5	169116304	169116304	+	Silent	SNP	T	T	A	rs189140579	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:169116304T>A	ENST00000256935.8	+	9	890	c.810T>A	c.(808-810)atT>atA	p.I270I		NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	270					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CTAAGGAGATTGAGATGCTCA	0.537																																					p.I270I		Atlas-SNP	.											DOCK2,caecum,carcinoma,+2,1	DOCK2	389	1	0			c.T810A						PASS	.						147.0	125.0	133.0					5																	169116304		2203	4300	6503	SO:0001819	synonymous_variant	1794	exon9			GGAGATTGAGATG	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"""dedicator of cyto-kinesis 2"""				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.810T>A	5.37:g.169116304T>A		132.0	0.0	0		155.0	70.0	0.451613	NM_004946	Q2M3I0|Q96AK7	Silent	SNP	ENST00000256935.8	37	CCDS4371.1																																																																																			T|1.000;C|0.000	.	alt		0.537	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	
USP49	25862	hgsc.bcm.edu	37	6	41774340	41774340	+	Missense_Mutation	SNP	G	G	T	rs111948785	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:41774340G>T	ENST00000394253.3	-	3	711	c.382C>A	c.(382-384)Ctg>Atg	p.L128M	USP49_ENST00000297229.2_Missense_Mutation_p.L128M|USP49_ENST00000373009.3_Missense_Mutation_p.L128M|USP49_ENST00000373006.1_Missense_Mutation_p.L128M|USP49_ENST00000373010.1_Missense_Mutation_p.L128M			Q70CQ1	UBP49_HUMAN	ubiquitin specific peptidase 49	128					histone H2B conserved C-terminal lysine deubiquitination (GO:0035616)|mRNA splicing, via spliceosome (GO:0000398)|protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|histone binding (GO:0042393)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(3)|prostate(2)|skin(2)	23	Ovarian(28;0.0919)|Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000309)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			CGCTGCGGCAGGACCACGTCC	0.687													G|||	81	0.0161741	0.0537	0.0072	5008	,	,		12628	0.0		0.001	False		,,,				2504	0.0041				p.L128M		Atlas-SNP	.											.	USP49	58	.	0			c.C382A						PASS	.	G	MET/LEU	222,4184		6,210,1987	23.0	24.0	23.0		382	4.6	0.1	6	dbSNP_132	23	14,8582		0,14,4284	yes	missense	USP49	NM_018561.3	15	6,224,6271	TT,TG,GG		0.1629,5.0386,1.8151	benign	128/641	41774340	236,12766	2203	4298	6501	SO:0001583	missense	25862	exon4			GCGGCAGGACCAC	AJ586139	CCDS4861.1, CCDS69111.1	6p12.1	2008-02-05	2005-08-08		ENSG00000164663	ENSG00000164663		"""Ubiquitin-specific peptidases"""	20078	protein-coding gene	gene with protein product			"""ubiquitin specific protease 49"""			14715245	Standard	NM_018561		Approved	MGC20741	uc003ori.3	Q70CQ1	OTTHUMG00000014688	ENST00000394253.3:c.382C>A	6.37:g.41774340G>T	ENSP00000377797:p.Leu128Met	33.0	0.0	0		37.0	37.0	1	NM_018561	Q5T3D9|Q5T3E0|Q96CK4	Missense_Mutation	SNP	ENST00000394253.3	37		.	.	.	.	.	.	.	.	.	.	G	9.151	1.016215	0.19355	0.050386	0.001629	ENSG00000164663	ENST00000394253;ENST00000373010;ENST00000373009;ENST00000373006;ENST00000297229	T;T;T;T;T	0.06933	3.72;3.24;3.72;3.5;3.5	4.6	4.6	0.57074	.	0.851504	0.10514	N	0.665818	T	0.01905	0.0060	N	0.12182	0.205	0.09310	N	1	B	0.13594	0.008	B	0.16722	0.016	T	0.44513	-0.9323	10	0.33940	T	0.23	-1.5488	10.2169	0.43173	0.0:0.0:0.7493:0.2507	.	128	Q70CQ1-2	.	M	128	ENSP00000377797:L128M;ENSP00000362101:L128M;ENSP00000362100:L128M;ENSP00000362097:L128M;ENSP00000297229:L128M	ENSP00000297229:L128M	L	-	1	2	USP49	41882318	0.566000	0.26618	0.076000	0.20297	0.974000	0.67602	2.655000	0.46707	2.376000	0.81061	0.655000	0.94253	CTG	A|0.000;G|0.986;T|0.014	0.014	strong		0.687	USP49-007	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000316513.3	NM_018561	
CPAMD8	27151	hgsc.bcm.edu	37	19	17113083	17113083	+	Missense_Mutation	SNP	G	G	A	rs10426545	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17113083G>A	ENST00000443236.1	-	9	923	c.892C>T	c.(892-894)Cgg>Tgg	p.R298W	CPAMD8_ENST00000388925.4_Missense_Mutation_p.R251W	NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	251						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						CACCTGGCCCGCACAGTGCCT	0.607													N|||	120	0.0239617	0.0885	0.0043	5008	,	,		16334	0.0		0.0	False		,,,				2504	0.0				p.R298W		Atlas-SNP	.											CPAMD8,brain,primitive_neuroectodermal_tumour-medulloblastoma,+1,1	CPAMD8	192	1	0			c.C892T						scavenged	.	G	TRP/ARG	332,3516		18,296,1610	21.0	22.0	22.0		892	1.5	0.0	19	dbSNP_119	22	13,8241		0,13,4114	no	missense	CPAMD8	NM_015692.2	101	18,309,5724	AA,AG,GG		0.1575,8.6279,2.8508	probably-damaging	298/1933	17113083	345,11757	1924	4127	6051	SO:0001583	missense	27151	exon9			TGGCCCGCACAGT	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.892C>T	19.37:g.17113083G>A	ENSP00000402505:p.Arg298Trp	148.0	1.0	0.00675676		128.0	52.0	0.40625	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	37	CCDS42519.1	28	0.01282051282051282	25	0.0508130081300813	3	0.008287292817679558	0	0.0	0	0.0	N	15.04	2.714927	0.48622	0.086279	0.001575	ENSG00000160111	ENST00000291440;ENST00000388925	T;T	0.12039	2.72;2.72	2.61	1.51	0.23008	.	1.430970	0.04807	U	0.434632	T	0.00496	0.0016	L	0.46157	1.445	0.31995	N	0.604078	D	0.59357	0.985	B	0.40534	0.332	T	0.29610	-1.0006	10	0.59425	D	0.04	.	8.4214	0.32703	0.0:0.0:0.5788:0.4212	rs10426545;rs10426545	251	Q8IZJ3	CPMD8_HUMAN	W	298;251	ENSP00000291440:R298W;ENSP00000373577:R251W	ENSP00000291440:R298W	R	-	1	2	CPAMD8	16974083	0.962000	0.33011	0.047000	0.18901	0.941000	0.58515	1.586000	0.36611	0.217000	0.20800	0.466000	0.42574	CGG	G|0.982;A|0.018	0.018	strong		0.607	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
RPL6	6128	hgsc.bcm.edu	37	12	112843105	112843105	+	Missense_Mutation	SNP	T	T	C	rs141161168	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:112843105T>C	ENST00000424576.2	-	7	975	c.790A>G	c.(790-792)Att>Gtt	p.I264V	RPL6_ENST00000202773.9_Missense_Mutation_p.I264V	NM_001024662.1	NP_001019833.1	Q02878	RL6_HUMAN	ribosomal protein L6	264				AVDSQILPKIKAIPQLQ -> LWTHKFYQKSKLFLSSS (in Ref. 1; CAA49188). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			cervix(1)|large_intestine(6)|lung(3)	10						AGCTGAGGAATAGCTTTGATT	0.363													T|||	3	0.000599042	0.0023	0.0	5008	,	,		18604	0.0		0.0	False		,,,				2504	0.0				p.I264V		Atlas-SNP	.											.	RPL6	20	.	0			c.A790G						PASS	.	T	VAL/ILE,VAL/ILE	12,4366		0,12,2177	20.0	22.0	22.0		790,790	-1.2	0.0	12	dbSNP_134	22	0,8470		0,0,4235	no	missense,missense	RPL6	NM_000970.3,NM_001024662.1	29,29	0,12,6412	CC,CT,TT		0.0,0.2741,0.0934	benign,benign	264/289,264/289	112843105	12,12836	2189	4235	6424	SO:0001583	missense	6128	exon7			GAGGAATAGCTTT	X69391	CCDS9162.1	12q24.13	2014-06-05				ENSG00000089009		"""L ribosomal proteins"""	10362	protein-coding gene	gene with protein product		603703		TXREB1		8479925, 8457378	Standard	XM_005253920		Approved	TAXREB107, L6	uc001ttv.3	Q02878		ENST00000424576.2:c.790A>G	12.37:g.112843105T>C	ENSP00000403172:p.Ile264Val	90.0	0.0	0		80.0	34.0	0.425	NM_001024662	Q2M3Q3|Q8WW97	Missense_Mutation	SNP	ENST00000424576.2	37	CCDS9162.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	4.047	0.006419	0.07866	0.002741	0.0	ENSG00000089009	ENST00000202773;ENST00000424576;ENST00000549923	T;T	0.28069	1.63;1.63	5.15	-1.17	0.09648	.	0.242260	0.41294	N	0.000912	T	0.09423	0.0232	N	0.01656	-0.775	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.34054	-0.9844	10	0.10902	T	0.67	.	12.53	0.56109	0.0:0.4627:0.0:0.5373	.	264	Q02878	RL6_HUMAN	V	264;264;204	ENSP00000202773:I264V;ENSP00000403172:I264V	ENSP00000202773:I264V	I	-	1	0	RPL6	111327488	0.025000	0.19082	0.010000	0.14722	0.906000	0.53458	0.202000	0.17295	-0.480000	0.06803	-1.431000	0.01090	ATT	T|1.000;C|0.000	0.000	strong		0.363	RPL6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405422.1		
MYBBP1A	10514	hgsc.bcm.edu	37	17	4448324	4448324	+	Silent	SNP	C	C	T	rs9910964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4448324C>T	ENST00000254718.4	-	17	2613	c.2307G>A	c.(2305-2307)gcG>gcA	p.A769A	MYBBP1A_ENST00000381556.2_Silent_p.A769A			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	769	Glu-rich.				cellular response to glucose starvation (GO:0042149)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|osteoblast differentiation (GO:0001649)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|NLS-dependent protein nuclear import complex (GO:0042564)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)	24						CACTCACCAGCGCCTTCCCAG	0.711													C|||	363	0.072484	0.2572	0.0231	5008	,	,		4471	0.0		0.007	False		,,,				2504	0.0				p.A769A		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.G2307A						PASS	.	C	,	821,3251		77,667,1292	88.0	62.0	71.0		2307,2307	-1.9	1.0	17	dbSNP_119	71	16,7960		0,16,3972	yes	coding-synonymous,coding-synonymous	MYBBP1A	NM_001105538.1,NM_014520.3	,	77,683,5264	TT,TC,CC		0.2006,20.1621,6.9472	,	769/1333,769/1329	4448324	837,11211	2036	3988	6024	SO:0001819	synonymous_variant	10514	exon17			CACCAGCGCCTTC	AF147709	CCDS11046.1, CCDS42238.1	17p13.3	2008-07-18			ENSG00000132382	ENSG00000132382			7546	protein-coding gene	gene with protein product	"""p53-activated protein-2"""	604885				10644447	Standard	NM_014520		Approved	P160, PAP2, FLJ37886	uc002fxz.4	Q9BQG0	OTTHUMG00000090747	ENST00000254718.4:c.2307G>A	17.37:g.4448324C>T		62.0	0.0	0		62.0	31.0	0.5	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Silent	SNP	ENST00000254718.4	37	CCDS11046.1																																																																																			C|0.916;T|0.084	0.084	strong		0.711	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520	
GLTSCR1	29998	hgsc.bcm.edu	37	19	48182859	48182859	+	Silent	SNP	G	G	A	rs60219834	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:48182859G>A	ENST00000396720.3	+	6	626	c.432G>A	c.(430-432)acG>acA	p.T144T	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	144										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|pancreas(3)|prostate(4)|skin(2)	20		all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355)		CAGGCCCGACGGGCGCTGGAG	0.741													G|||	283	0.0565096	0.1997	0.0245	5008	,	,		10296	0.0		0.002	False		,,,				2504	0.0				p.T144T		Atlas-SNP	.											.	GLTSCR1	79	.	0			c.G432A						PASS	.						8.0	10.0	9.0					19																	48182859		677	1571	2248	SO:0001819	synonymous_variant	29998	exon6			CCCGACGGGCGCT	AF182077	CCDS46134.1	19q13.3	2012-11-29			ENSG00000063169	ENSG00000063169			4332	protein-coding gene	gene with protein product		605690				10708517	Standard	NM_015711		Approved		uc002phh.4	Q9NZM4		ENST00000396720.3:c.432G>A	19.37:g.48182859G>A		4.0	0.0	0		12.0	8.0	0.666667	NM_015711	A8MW01	Silent	SNP	ENST00000396720.3	37	CCDS46134.1																																																																																			G|0.943;A|0.057	0.057	strong		0.741	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711	
ALMS1	7840	hgsc.bcm.edu	37	2	73676315	73676315	+	Silent	SNP	A	A	G	rs76266696	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:73676315A>G	ENST00000264448.6	+	8	2769	c.2658A>G	c.(2656-2658)gtA>gtG	p.V886V	ALMS1_ENST00000409009.1_Silent_p.V844V|ALMS1_ENST00000377715.1_Silent_p.V886V	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	886	34 X 47 AA approximate tandem repeat.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CTCTGAAAGTATCAATTGTTC	0.463													A|||	39	0.00778754	0.028	0.0029	5008	,	,		20537	0.0		0.0	False		,,,				2504	0.0				p.V886V		Atlas-SNP	.											.	ALMS1	384	.	0			c.A2658G						PASS	.	A		90,3660		1,88,1786	98.0	102.0	101.0		2658	-0.3	0.0	2	dbSNP_132	101	2,8196		0,2,4097	no	coding-synonymous	ALMS1	NM_015120.4		1,90,5883	GG,GA,AA		0.0244,2.4,0.77		886/4168	73676315	92,11856	1875	4099	5974	SO:0001819	synonymous_variant	7840	exon8			GAAAGTATCAATT	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.2658A>G	2.37:g.73676315A>G		260.0	0.0	0		264.0	128.0	0.484848	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	37	CCDS42697.1																																																																																			A|0.994;G|0.006	0.006	strong		0.463	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
ZNF536	9745	hgsc.bcm.edu	37	19	31039357	31039357	+	Missense_Mutation	SNP	C	C	A	rs61741995	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:31039357C>A	ENST00000355537.3	+	4	2978	c.2831C>A	c.(2830-2832)cCc>cAc	p.P944H		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	944					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					CTGGCTGACCCCCCTTCCATG	0.522													C|||	77	0.0153754	0.0545	0.0072	5008	,	,		17880	0.0		0.0	False		,,,				2504	0.0				p.P944H		Atlas-SNP	.											.	ZNF536	424	.	0			c.C2831A						PASS	.	C	HIS/PRO	239,4167	141.5+/-176.9	7,225,1971	132.0	143.0	139.0		2831	3.3	0.0	19	dbSNP_129	139	16,8584	11.2+/-40.8	0,16,4284	yes	missense	ZNF536	NM_014717.1	77	7,241,6255	AA,AC,CC		0.186,5.4244,1.9606	benign	944/1301	31039357	255,12751	2203	4300	6503	SO:0001583	missense	9745	exon4			CTGACCCCCCTTC		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"""Zinc fingers, C2H2-type"""	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.2831C>A	19.37:g.31039357C>A	ENSP00000347730:p.Pro944His	27.0	0.0	0		30.0	18.0	0.6	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	37	CCDS32984.1	22	0.010073260073260074	20	0.04065040650406504	2	0.0055248618784530384	0	0.0	0	0.0	C	3.103	-0.184365	0.06340	0.054244	0.00186	ENSG00000198597	ENST00000355537	T	0.08634	3.07	5.69	3.34	0.38264	.	0.451539	0.25613	N	0.029467	T	0.00784	0.0026	N	0.24115	0.695	0.09310	N	1	P;P	0.36495	0.556;0.556	B;B	0.34038	0.174;0.174	T	0.38824	-0.9643	10	0.46703	T	0.11	-2.4559	7.0172	0.24895	0.0:0.6863:0.1357:0.178	rs61741995	944;944	A7E228;O15090	.;ZN536_HUMAN	H	944	ENSP00000347730:P944H	ENSP00000347730:P944H	P	+	2	0	ZNF536	35731197	0.090000	0.21635	0.000000	0.03702	0.954000	0.61252	0.907000	0.28531	0.576000	0.29452	0.491000	0.48974	CCC	C|0.982;A|0.018	0.018	strong		0.522	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717	
CCAR2	57805	hgsc.bcm.edu	37	8	22476717	22476717	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22476717C>T	ENST00000308511.4	+	20	2825	c.2576C>T	c.(2575-2577)gCa>gTa	p.A859V	BIN3_ENST00000519335.1_5'Flank|RP11-582J16.5_ENST00000521025.1_RNA|CCAR2_ENST00000389279.3_Missense_Mutation_p.A859V|CCAR2_ENST00000520861.1_Missense_Mutation_p.A534V			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	859	Interaction with NR1D1. {ECO:0000269|PubMed:23398316}.				cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mRNA processing (GO:0006397)|negative regulation of catalytic activity (GO:0043086)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage checkpoint (GO:2000003)|regulation of circadian rhythm (GO:0042752)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of protein stability (GO:0031647)|response to UV (GO:0009411)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|DBIRD complex (GO:0044609)|mitochondrial matrix (GO:0005759)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)										ACGCTGGCGGCAGAGATGCAG	0.642																																					p.A859V		Atlas-SNP	.											.	KIAA1967	72	.	0			c.C2576T						PASS	.						16.0	16.0	16.0					8																	22476717		2197	4296	6493	SO:0001583	missense	57805	exon20			TGGCGGCAGAGAT	AL834351	CCDS34863.1	8p22	2013-08-22	2013-08-22	2013-08-22		ENSG00000158941			23360	protein-coding gene	gene with protein product	"""deleted in breast cancer"""	607359	"""KIAA1967"""	KIAA1967		12370419	Standard	NM_021174		Approved	DBC-1, DBC1, NET35	uc003xci.3	Q8N163		ENST00000308511.4:c.2576C>T	8.37:g.22476717C>T	ENSP00000310670:p.Ala859Val	92.0	0.0	0		107.0	51.0	0.476636	NM_021174	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Missense_Mutation	SNP	ENST00000308511.4	37	CCDS34863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.81|14.81	2.646522|2.646522	0.47258|0.47258	.|.	.|.	ENSG00000158941|ENSG00000158941	ENST00000308511;ENST00000389279;ENST00000520861|ENST00000520738	T;T;T|.	0.00453|.	7.33;7.33;7.33|.	5.44|5.44	4.57|4.57	0.56435|0.56435	.|.	0.147376|.	0.43260|.	D|.	0.000594|.	T|.	0.30916|.	0.0780|.	N|N	0.19112|0.19112	0.55|0.55	0.09310|0.09310	N|N	1|1	B;B|.	0.06786|.	0.001;0.0|.	B;B|.	0.09377|.	0.004;0.001|.	T|.	0.19160|.	-1.0314|.	10|.	0.36615|.	T|.	0.2|.	-8.609|-8.609	9.9844|9.9844	0.41832|0.41832	0.0:0.9094:0.0:0.0906|0.0:0.9094:0.0:0.0906	.|.	534;859|.	G3V119;Q8N163|.	.;K1967_HUMAN|.	V|X	859;859;534|551	ENSP00000310670:A859V;ENSP00000373930:A859V;ENSP00000429773:A534V|.	ENSP00000310670:A859V|.	A|Q	+|+	2|1	0|0	KIAA1967|KIAA1967	22532662|22532662	0.011000|0.011000	0.17503|0.17503	0.022000|0.022000	0.16811|0.16811	0.782000|0.782000	0.44232|0.44232	1.737000|1.737000	0.38197|0.38197	1.534000|1.534000	0.49203|0.49203	0.655000|0.655000	0.94253|0.94253	GCA|CAG	.	.	none		0.642	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174	
ALKBH7	84266	hgsc.bcm.edu	37	19	6374229	6374229	+	Silent	SNP	C	C	A	rs116186903	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6374229C>A	ENST00000245812.3	+	2	608	c.220C>A	c.(220-222)Cga>Aga	p.R74R	ALKBH7_ENST00000599849.1_Silent_p.R13R|ALKBH7_ENST00000596657.1_5'UTR	NM_032306.3	NP_115682.1	Q9BT30	ALKB7_HUMAN	alkB, alkylation repair homolog 7 (E. coli)	74					cellular response to DNA damage stimulus (GO:0006974)|fatty acid metabolic process (GO:0006631)|regulation of lipid storage (GO:0010883)|regulation of mitochondrial membrane permeability involved in programmed necrotic cell death (GO:1902445)	mitochondrial matrix (GO:0005759)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	6						CCACGGCTTCCGAGAGACAGA	0.657													C|||	33	0.00658946	0.0234	0.0029	5008	,	,		15595	0.0		0.0	False		,,,				2504	0.0				p.R74R		Atlas-SNP	.											.	ALKBH7	18	.	0			c.C220A						PASS	.	C		78,4322		1,76,2123	29.0	32.0	31.0		220	3.6	1.0	19	dbSNP_132	31	0,8590		0,0,4295	no	coding-synonymous	ALKBH7	NM_032306.3		1,76,6418	AA,AC,CC		0.0,1.7727,0.6005		74/222	6374229	78,12912	2200	4295	6495	SO:0001819	synonymous_variant	84266	exon2			GGCTTCCGAGAGA	AY427650	CCDS12163.1	19p13.3	2008-02-05	2006-02-09	2006-02-09		ENSG00000125652		"""Alkylation repair homologs"""	21306	protein-coding gene	gene with protein product		613305	"""spermatogenesis associated 11"""	SPATA11		12477932	Standard	NM_032306		Approved	MGC10974	uc002meo.2	Q9BT30		ENST00000245812.3:c.220C>A	19.37:g.6374229C>A		57.0	0.0	0		67.0	43.0	0.641791	NM_032306	B2R4U9|Q53FF3	Silent	SNP	ENST00000245812.3	37	CCDS12163.1																																																																																			C|0.994;A|0.006	0.006	strong		0.657	ALKBH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453036.1	NM_032306	
MAATS1	89876	hgsc.bcm.edu	37	3	119449165	119449165	+	Missense_Mutation	SNP	C	C	G	rs9819218	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:119449165C>G	ENST00000273390.5	+	8	1036	c.959C>G	c.(958-960)tCt>tGt	p.S320C		NM_033364.3	NP_203528	Q7Z4T9	MAAT1_HUMAN	MYCBP-associated, testis expressed 1	320			S -> C (in dbSNP:rs9819218).			mitochondrion (GO:0005739)											GCCCGGTGGTCTAAACTGCAG	0.443													C|||	68	0.0135783	0.0507	0.0014	5008	,	,		19022	0.0		0.0	False		,,,				2504	0.0				p.S320C		Atlas-SNP	.											.	.	.	.	0			c.C959G						PASS	.	C	CYS/SER	201,4205	126.1+/-163.2	3,195,2005	197.0	200.0	199.0		959	0.0	0.7	3	dbSNP_119	199	4,8596	1.2+/-3.3	1,2,4297	yes	missense	C3orf15	NM_033364.3	112	4,197,6302	GG,GC,CC		0.0465,4.562,1.5762	benign	320/768	119449165	205,12801	2203	4300	6503	SO:0001583	missense	89876	exon8			GGTGGTCTAAACT	AB063296	CCDS2994.1	3q12-q13.3	2014-07-31	2012-12-07	2012-09-26	ENSG00000183833	ENSG00000183833			24010	protein-coding gene	gene with protein product	"""AMY-1-associating protein expressed in testis 1"", ""MYCBP-binding protein"", ""spermatogenesis associated 26"""	609910	"""chromosome 3 open reading frame 15"", ""MYCBP/AMY-1-associated, testis expressed 1"""	C3orf15		12223483, 14551891, 17967944	Standard	NM_033364		Approved	AAT1, AAT1alpha, SPATA26, CaM-IP2	uc003ede.4	Q7Z4T9	OTTHUMG00000159422	ENST00000273390.5:c.959C>G	3.37:g.119449165C>G	ENSP00000273390:p.Ser320Cys	108.0	0.0	0		127.0	63.0	0.496063	NM_033364	A0AVK2|A8K1J9|B3KP23|B4DG52|B4DZ14|C9JUG4|Q68DX2|Q8TD41|Q96A45|Q96JE8	Missense_Mutation	SNP	ENST00000273390.5	37	CCDS2994.1	20	0.009157509157509158	20	0.04065040650406504	0	0.0	0	0.0	0	0.0	C	10.39	1.336987	0.24253	0.04562	4.65E-4	ENSG00000183833	ENST00000273390	T	0.24723	1.84	5.2	0.0316	0.14171	.	0.702681	0.14937	N	0.289762	T	0.02649	0.0080	L	0.43152	1.355	0.09310	N	1	B;B;B;B;B	0.20887	0.049;0.016;0.02;0.006;0.005	B;B;B;B;B	0.28232	0.087;0.032;0.036;0.009;0.004	T	0.21552	-1.0242	10	0.45353	T	0.12	-11.3776	1.5557	0.02584	0.26:0.3334:0.2513:0.1553	rs9819218;rs56635541;rs9819218	320;81;258;320;320	Q7Z4T9;Q9UFB4;Q7Z4T9-3;Q4G0Y0;Q7Z4T9-7	AAT1_HUMAN;.;.;.;.	C	320	ENSP00000273390:S320C	ENSP00000273390:S320C	S	+	2	0	C3orf15	120931855	0.002000	0.14202	0.668000	0.29813	0.882000	0.50991	0.021000	0.13489	0.001000	0.14605	-0.259000	0.10710	TCT	C|0.982;G|0.018	0.018	strong		0.443	MAATS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355222.1	NM_033364	
NBPF7	343505	hgsc.bcm.edu	37	1	120378657	120378657	+	IGR	SNP	G	G	A	rs6684816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:120378657G>A								REG4 (24374 upstream) : ADAM30 (57498 downstream)																							CTTTGGAATTGGAGTGTTCGC	0.443													g|||	111	0.0221645	0.0756	0.0086	5008	,	,		21408	0.0		0.004	False		,,,				2504	0.001				p.S363S		Atlas-SNP	.											.	NBPF7	46	.	0			c.C1089T						PASS	.	G		224,3620		5,214,1703	107.0	105.0	105.0		1089	-1.0	0.0	1	dbSNP_116	105	45,8253		1,43,4105	no	coding-synonymous	NBPF7	NM_001047980.1		6,257,5808	AA,AG,GG		0.5423,5.8273,2.2155		363/422	120378657	269,11873	1922	4149	6071	SO:0001628	intergenic_variant	343505	exon7			GGAATTGGAGTGT																													1.37:g.120378657G>A		164.0	0.0	0		202.0	96.0	0.475248	NM_001047980		Silent	SNP		37																																																																																				A|0.016;G|0.984	0.016	strong	0	0.443								
OR1E2	8388	hgsc.bcm.edu	37	17	3336697	3336697	+	Missense_Mutation	SNP	G	G	A	rs77501388	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:3336697G>A	ENST00000248384.1	-	1	438	c.439C>T	c.(439-441)Ccc>Tcc	p.P147S		NM_003554.1	NP_003545.1	P47887	OR1E2_HUMAN	olfactory receptor, family 1, subfamily E, member 2	147					sensory perception of chemical stimulus (GO:0007606)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)|receptor activity (GO:0004872)			endometrium(3)|large_intestine(3)|lung(3)	9						CAGAGCATGGGGCTCATGATG	0.567													G|||	120	0.0239617	0.0885	0.0043	5008	,	,		19503	0.0		0.0	False		,,,				2504	0.0				p.P147S		Atlas-SNP	.											OR1E2,right_upper_lobe,carcinoma,+1,1	OR1E2	25	1	0			c.C439T						PASS	.																																			SO:0001583	missense	8388	exon1			GCATGGGGCTCAT	U04686	CCDS11026.1	17p13.3	2012-08-09			ENSG00000127780	ENSG00000127780		"""GPCR / Class A : Olfactory receptors"""	8190	protein-coding gene	gene with protein product				OR1E4		8004088, 9500546	Standard	NM_003554		Approved	OR17-93, OR17-135	uc010vre.2	P47887	OTTHUMG00000090651	ENST00000248384.1:c.439C>T	17.37:g.3336697G>A	ENSP00000248384:p.Pro147Ser	221.0	0.0	0		230.0	98.0	0.426087	NM_003554	O43877|O95632|Q0VAD5|Q0VAD6|Q9UL13	Missense_Mutation	SNP	ENST00000248384.1	37	CCDS11026.1	45	0.020604395604395604	45	0.09146341463414634	0	0.0	0	0.0	0	0.0	G	9.675	1.147752	0.21288	.	.	ENSG00000127780	ENST00000248384;ENST00000454364	T	0.05649	3.41	5.47	4.51	0.55191	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000009	T	0.00144	0.0004	N	0.08118	0	0.09310	N	0.999998	B	0.31077	0.307	B	0.27608	0.081	T	0.45862	-0.9232	10	0.62326	D	0.03	.	6.8412	0.23963	0.0829:0.0:0.6588:0.2582	.	147	P47887	OR1E2_HUMAN	S	147;137	ENSP00000248384:P147S	ENSP00000248384:P147S	P	-	1	0	OR1E2	3283447	0.000000	0.05858	0.943000	0.38184	0.313000	0.28021	-0.200000	0.09478	1.550000	0.49438	0.650000	0.86243	CCC	G|0.987;A|0.013	0.013	strong		0.567	OR1E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207311.1		
SALL1	6299	hgsc.bcm.edu	37	16	51173823	51173823	+	Silent	SNP	G	G	A	rs61740811	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:51173823G>A	ENST00000251020.4	-	2	2343	c.2310C>T	c.(2308-2310)atC>atT	p.I770I	SALL1_ENST00000566102.1_Intron|SALL1_ENST00000440970.1_Silent_p.I673I|SALL1_ENST00000541611.1_Intron	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	770					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			TCTTCTGGCAGATGGGGCAGG	0.567													G|||	201	0.0401358	0.1392	0.0231	5008	,	,		19398	0.0		0.001	False		,,,				2504	0.0				p.I770I	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.C2310T						PASS	.	G	,	539,3857	246.8+/-255.3	25,489,1684	86.0	90.0	89.0		2019,2310	4.2	1.0	16	dbSNP_129	89	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous,coding-synonymous	SALL1	NM_001127892.1,NM_002968.2	,	25,493,5980	AA,AG,GG		0.0465,12.2611,4.1782	,	673/1228,770/1325	51173823	543,12453	2198	4300	6498	SO:0001819	synonymous_variant	6299	exon2			CTGGCAGATGGGG	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"""Zinc fingers, C2H2-type"""	10524	protein-coding gene	gene with protein product		602218	"""sal (Drosophila)-like 1"", ""sal-like 1 (Drosophila)"""	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.2310C>T	16.37:g.51173823G>A		221.0	0.0	0		228.0	114.0	0.5	NM_002968	Q99881|Q9NSC3|Q9P1R0	Silent	SNP	ENST00000251020.4	37	CCDS10747.1																																																																																			G|0.957;A|0.043	0.043	strong		0.567	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968	
HCN4	10021	hgsc.bcm.edu	37	15	73617723	73617723	+	Silent	SNP	G	G	T	rs141966309	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:73617723G>T	ENST00000261917.3	-	5	2646	c.1653C>A	c.(1651-1653)atC>atA	p.I551I		NM_005477.2	NP_005468.1	Q9Y3Q4	HCN4_HUMAN	hyperpolarization activated cyclic nucleotide-gated potassium channel 4	551					blood circulation (GO:0008015)|cation transport (GO:0006812)|cellular response to cAMP (GO:0071320)|cellular response to cGMP (GO:0071321)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|sodium ion transmembrane transport (GO:0035725)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)|terminal bouton (GO:0043195)	cAMP binding (GO:0030552)|cation channel activity (GO:0005261)|identical protein binding (GO:0042802)|intracellular cAMP activated cation channel activity (GO:0005222)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated sodium channel activity (GO:0005248)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(13)|liver(1)|lung(18)|ovary(6)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	55				COAD - Colon adenocarcinoma(1;0.142)		AGTAGTCGTGGATGCGCTGCC	0.647													g|||	7	0.00139776	0.0053	0.0	5008	,	,		16066	0.0		0.0	False		,,,				2504	0.0				p.I551I		Atlas-SNP	.											.	HCN4	150	.	0			c.C1653A						PASS	.	G		23,4373	30.8+/-60.4	1,21,2176	107.0	111.0	110.0		1653	3.3	1.0	15	dbSNP_134	110	0,8594		0,0,4297	no	coding-synonymous	HCN4	NM_005477.2		1,21,6473	TT,TG,GG		0.0,0.5232,0.1771		551/1204	73617723	23,12967	2198	4297	6495	SO:0001819	synonymous_variant	10021	exon5			GTCGTGGATGCGC	AJ132429	CCDS10248.1	15q24.1	2011-07-05			ENSG00000138622	ENSG00000138622		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	16882	protein-coding gene	gene with protein product		605206				10228147, 10430953, 16382102	Standard	NM_005477		Approved		uc002avp.3	Q9Y3Q4	OTTHUMG00000137563	ENST00000261917.3:c.1653C>A	15.37:g.73617723G>T		217.0	0.0	0		196.0	94.0	0.479592	NM_005477	Q9UMQ7	Silent	SNP	ENST00000261917.3	37	CCDS10248.1																																																																																			G|0.998;T|0.002	0.002	strong		0.647	HCN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268900.2	NM_005477	
ABTB2	25841	hgsc.bcm.edu	37	11	34176262	34176262	+	Missense_Mutation	SNP	T	T	C	rs2473928	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:34176262T>C	ENST00000435224.2	-	15	3176	c.2752A>G	c.(2752-2754)Act>Gct	p.T918A	ABTB2_ENST00000298992.2_Missense_Mutation_p.T732A	NM_145804.2	NP_665803.2	Q8N961	ABTB2_HUMAN	ankyrin repeat and BTB (POZ) domain containing 2	918			T -> A (in dbSNP:rs2473928).		cellular response to toxic substance (GO:0097237)	nucleus (GO:0005634)				breast(2)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)				AGGATGTCAGTGGTGGGGATC	0.602													C|||	142	0.0283546	0.1044	0.0058	5008	,	,		20312	0.0		0.0	False		,,,				2504	0.0				p.T918A		Atlas-SNP	.											.	ABTB2	101	.	0			c.A2752G						PASS	.	C	ALA/THR	328,4076	796.1+/-415.3	14,300,1888	153.0	134.0	140.0		2752	-0.4	0.0	11	dbSNP_100	140	3,8593	819.0+/-406.8	0,3,4295	yes	missense	ABTB2	NM_145804.2	58	14,303,6183	CC,CT,TT		0.0349,7.4478,2.5462	benign	918/1026	34176262	331,12669	2202	4298	6500	SO:0001583	missense	25841	exon15			TGTCAGTGGTGGG	AK056863	CCDS7890.1, CCDS7890.2	11p13	2013-10-02			ENSG00000166016	ENSG00000166016		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	23842	protein-coding gene	gene with protein product							Standard	NM_145804		Approved	DKFZP586C1619, BTBD22, ABTB2A	uc001mvl.2	Q8N961	OTTHUMG00000044382	ENST00000435224.2:c.2752A>G	11.37:g.34176262T>C	ENSP00000410157:p.Thr918Ala	106.0	0.0	0		122.0	69.0	0.565574	NM_145804	A8K6S9|E9PRW7|Q52LD6|Q6MZW4|Q8NB44	Missense_Mutation	SNP	ENST00000435224.2	37	CCDS7890.2	41	0.018772893772893772	40	0.08130081300813008	1	0.0027624309392265192	0	0.0	0	0.0	C	0.013	-1.626374	0.00813	0.074478	3.49E-4	ENSG00000166016	ENST00000435224;ENST00000298992	T;T	0.65732	-0.17;-0.17	4.79	-0.445	0.12242	BTB/POZ-like (1);BTB/POZ (1);BTB/POZ fold (2);	0.385085	0.29178	N	0.012911	T	0.02012	0.0063	N	0.20807	0.61	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.07481	-1.0770	10	0.02654	T	1	-15.8719	6.5214	0.22277	0.1139:0.4201:0.0:0.466	rs2473928;rs16925228;rs52811333;rs2473928	732	Q8N961	ABTB2_HUMAN	A	918;732	ENSP00000410157:T918A;ENSP00000298992:T732A	ENSP00000298992:T732A	T	-	1	0	ABTB2	34132838	0.000000	0.05858	0.016000	0.15963	0.433000	0.31745	-0.763000	0.04740	-0.594000	0.05836	-2.820000	0.00109	ACT	T|0.973;C|0.027	0.027	strong		0.602	ABTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388703.3	NM_145804	
IL1RL1	9173	hgsc.bcm.edu	37	2	102957136	102957136	+	Missense_Mutation	SNP	C	C	T	rs114797672	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:102957136C>T	ENST00000233954.1	+	5	729	c.458C>T	c.(457-459)gCt>gTt	p.A153V	IL1RL1_ENST00000311734.2_Missense_Mutation_p.A153V|IL1RL1_ENST00000404917.2_Missense_Mutation_p.A36V|IL1RL1_ENST00000393393.3_Missense_Mutation_p.A153V|IL1RL1_ENST00000409584.1_Missense_Mutation_p.A153V	NM_016232.4	NP_057316.3	Q01638	ILRL1_HUMAN	interleukin 1 receptor-like 1	153	Ig-like C2-type 2.				immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of T-helper 1 type immune response (GO:0002826)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of macrophage activation (GO:0043032)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	cytokine receptor activity (GO:0004896)|interleukin-1 receptor activity (GO:0004908)|interleukin-33 receptor activity (GO:0002114)|receptor signaling protein activity (GO:0005057)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(3)|urinary_tract(1)	16						AATTGTCAGGCTCTTCAAGGA	0.373													c|||	20	0.00399361	0.0136	0.0029	5008	,	,		17359	0.0		0.0	False		,,,				2504	0.0				p.A153V		Atlas-SNP	.											.	IL1RL1	114	.	0			c.C458T						PASS	.	C	VAL/ALA,VAL/ALA	92,4314	75.7+/-113.9	1,90,2112	125.0	121.0	122.0		458,458	1.9	0.4	2	dbSNP_132	122	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	IL1RL1	NM_003856.2,NM_016232.4	64,64	1,91,6411	TT,TC,CC		0.0116,2.0881,0.7151	benign,benign	153/329,153/557	102957136	93,12913	2203	4300	6503	SO:0001583	missense	9173	exon5			GTCAGGCTCTTCA	D12764	CCDS2057.1, CCDS2058.1, CCDS74548.1	2q12	2013-01-29			ENSG00000115602	ENSG00000115602		"""Interleukins and interleukin receptors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5998	protein-coding gene	gene with protein product	"""homolog of mouse growth stimulation-expressed"""	601203				1482686, 10191101, 16286016	Standard	NM_016232		Approved	ST2, FIT-1, ST2L, ST2V, DER4, T1, IL33R	uc002tbu.1	Q01638	OTTHUMG00000130782	ENST00000233954.1:c.458C>T	2.37:g.102957136C>T	ENSP00000233954:p.Ala153Val	301.0	0.0	0		268.0	128.0	0.477612	NM_016232	A8K6B3|B4E0I3|Q53TU7|Q8NEJ3|Q9ULV7|Q9UQ44	Missense_Mutation	SNP	ENST00000233954.1	37	CCDS2057.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	C	10.58	1.390800	0.25118	0.020881	1.16E-4	ENSG00000115602	ENST00000233954;ENST00000393393;ENST00000404917;ENST00000311734;ENST00000409584	T;T;T;T;T	0.12774	2.65;2.65;2.65;2.65;2.65	5.07	1.88	0.25563	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.784816	0.11927	N	0.516068	T	0.03136	0.0092	N	0.11560	0.145	0.29045	N	0.884885	B;B;B	0.22480	0.07;0.056;0.034	B;B;B	0.27262	0.078;0.046;0.034	T	0.40117	-0.9580	10	0.28530	T	0.3	.	5.6013	0.17355	0.1466:0.6513:0.0:0.2021	.	36;153;153	B4E0I3;Q01638-2;Q01638	.;.;ILRL1_HUMAN	V	153;153;36;153;153	ENSP00000233954:A153V;ENSP00000377052:A153V;ENSP00000384822:A36V;ENSP00000310371:A153V;ENSP00000386618:A153V	ENSP00000233954:A153V	A	+	2	0	IL1RL1	102323568	0.043000	0.20138	0.398000	0.26321	0.905000	0.53344	0.083000	0.14871	0.044000	0.15775	0.563000	0.77884	GCT	C|0.992;T|0.008	0.008	strong		0.373	IL1RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253296.1	NM_016232	
STRN3	29966	hgsc.bcm.edu	37	14	31364948	31364948	+	Missense_Mutation	SNP	A	A	G	rs114922597	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:31364948A>G	ENST00000357479.5	-	17	2340	c.2144T>C	c.(2143-2145)aTg>aCg	p.M715T	STRN3_ENST00000355683.5_Missense_Mutation_p.M631T	NM_001083893.1	NP_001077362.1	Q13033	STRN3_HUMAN	striatin, calmodulin binding protein 3	715					negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to estradiol (GO:0032355)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	armadillo repeat domain binding (GO:0070016)|calmodulin binding (GO:0005516)|protein complex binding (GO:0032403)|protein phosphatase 2A binding (GO:0051721)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20	Hepatocellular(127;0.0877)|Breast(36;0.148)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.0119)|BRCA - Breast invasive adenocarcinoma(188;0.0805)	GBM - Glioblastoma multiforme(265;0.0124)		AGAATGGATCATTTTACCTAA	0.333													A|||	40	0.00798722	0.0287	0.0029	5008	,	,		19925	0.0		0.0	False		,,,				2504	0.0				p.M715T		Atlas-SNP	.											.	STRN3	117	.	0			c.T2144C						PASS	.	A	THR/MET,THR/MET	117,4289	89.7+/-128.4	2,113,2088	63.0	58.0	60.0		2144,1892	4.6	1.0	14	dbSNP_132	60	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	STRN3	NM_001083893.1,NM_014574.3	81,81	2,115,6386	GG,GA,AA		0.0233,2.6555,0.915	benign,benign	715/798,631/714	31364948	119,12887	2203	4300	6503	SO:0001583	missense	29966	exon17			TGGATCATTTTAC		CCDS9641.1, CCDS41938.1	14q13-q21	2013-01-10			ENSG00000196792	ENSG00000196792		"""WD repeat domain containing"""	15720	protein-coding gene	gene with protein product	"""cell cycle S/G2 nuclear autoantigen"""	614766				7864889, 10681496	Standard	NM_014574		Approved	SG2NA	uc001wqu.2	Q13033	OTTHUMG00000140201	ENST00000357479.5:c.2144T>C	14.37:g.31364948A>G	ENSP00000350071:p.Met715Thr	112.0	0.0	0		134.0	54.0	0.402985	NM_001083893	A2RTX7|A6NHZ7|Q9NRA5	Missense_Mutation	SNP	ENST00000357479.5	37	CCDS41938.1	19	0.0086996336996337	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	A	10.37	1.331773	0.24167	0.026555	2.33E-4	ENSG00000196792	ENST00000355683;ENST00000357479	T;T	0.59502	0.26;0.26	5.77	4.64	0.57946	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.332419	0.39985	N	0.001209	T	0.12518	0.0304	N	0.04090	-0.28	0.37999	D	0.934155	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.11275	-1.0594	10	0.46703	T	0.11	0.4649	7.2945	0.26385	0.7812:0.1462:0.0726:0.0	.	631;715	Q13033-2;Q13033	.;STRN3_HUMAN	T	631;715	ENSP00000347909:M631T;ENSP00000350071:M715T	ENSP00000347909:M631T	M	-	2	0	STRN3	30434699	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.949000	0.49074	2.204000	0.70986	0.383000	0.25322	ATG	A|0.990;G|0.010	0.010	strong		0.333	STRN3-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409713.1	NM_014574	
VNN1	8876	hgsc.bcm.edu	37	6	133004281	133004281	+	Nonstop_Mutation	SNP	A	A	G	rs61729583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:133004281A>G	ENST00000367928.4	-	7	1553	c.1540T>C	c.(1540-1542)Tag>Cag	p.*514Q		NM_004666.2	NP_004657.2	O95497	VNN1_HUMAN	vanin 1	0					acute inflammatory response (GO:0002526)|cellular component movement (GO:0006928)|chronic inflammatory response (GO:0002544)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|pantothenate metabolic process (GO:0015939)|positive regulation of T cell differentiation in thymus (GO:0033089)|response to oxidative stress (GO:0006979)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	GPI anchor binding (GO:0034235)|pantetheine hydrolase activity (GO:0017159)			NS(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)	31	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.0027)|GBM - Glioblastoma multiforme(226;0.0189)		TCAATATTCTACCAACTTAAT	0.333													A|||	148	0.0295527	0.1082	0.0058	5008	,	,		16408	0.0		0.001	False		,,,				2504	0.0				p.X514Q		Atlas-SNP	.											.	VNN1	69	.	0			c.T1540C						PASS	.	A	GLN/stop	395,4011	196.7+/-221.0	18,359,1826	94.0	89.0	90.0		1540	4.7	0.9	6	dbSNP_129	90	4,8596	3.0+/-9.4	0,4,4296	yes	stop-lost	VNN1	NM_004666.2		18,363,6122	GG,GA,AA		0.0465,8.965,3.0678		514/514	133004281	399,12607	2203	4300	6503	SO:0001578	stop_lost	8876	exon7			TATTCTACCAACT	AJ132099	CCDS5159.1	6q23-q24	2013-02-13			ENSG00000112299	ENSG00000112299	3.5.1.92	"""Vanins"""	12705	protein-coding gene	gene with protein product		603570				9790769	Standard	NM_004666		Approved	Tiff66	uc003qdo.3	O95497	OTTHUMG00000015587	ENST00000367928.4:c.1540T>C	6.37:g.133004281A>G	ENSP00000356905:p.*514Gluext*13	71.0	0.0	0		87.0	36.0	0.413793	NM_004666	A8K310|Q4JFW6|Q4VAS7|Q4VAS8|Q4VAS9|Q9UF16|Q9UJF4	Missense_Mutation	SNP	ENST00000367928.4	37	CCDS5159.1	47	0.02152014652014652	44	0.08943089430894309	3	0.008287292817679558	0	0.0	0	0.0	A	10.88	1.475064	0.26511	0.08965	4.65E-4	ENSG00000112299	ENST00000367928	.	.	.	5.86	4.71	0.59529	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.1002	0.36664	0.917:0.0:0.083:0.0	.	.	.	.	Q	514	.	.	X	-	1	0	VNN1	133045974	0.003000	0.15002	0.944000	0.38274	0.058000	0.15608	1.546000	0.36179	2.237000	0.73441	0.528000	0.53228	TAG	A|0.971;G|0.029	0.029	strong		0.333	VNN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042263.1		
NLRP4	147945	hgsc.bcm.edu	37	19	56369095	56369095	+	Silent	SNP	C	C	T	rs147356242	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56369095C>T	ENST00000301295.6	+	3	758	c.336C>T	c.(334-336)tcC>tcT	p.S112S	NLRP4_ENST00000587891.1_Silent_p.S37S|NLRP4_ENST00000346986.5_Silent_p.S112S	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	112					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		GCTTATGGTCCAGCAAGTCTG	0.473													C|||	26	0.00519169	0.0189	0.0014	5008	,	,		19927	0.0		0.0	False		,,,				2504	0.0				p.S112S		Atlas-SNP	.											.	NLRP4	331	.	0			c.C336T						PASS	.	C		58,4348	57.4+/-93.9	0,58,2145	114.0	106.0	109.0		336	2.4	0.0	19	dbSNP_134	109	0,8600		0,0,4300	no	coding-synonymous	NLRP4	NM_134444.4		0,58,6445	TT,TC,CC		0.0,1.3164,0.4459		112/995	56369095	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	147945	exon3			ATGGTCCAGCAAG	AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"""Nucleotide-binding domain and leucine rich repeat containing"""	22943	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4"", ""cancer/testis antigen 58"""	609645	"""NACHT, leucine rich repeat and PYD containing 4"""	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.336C>T	19.37:g.56369095C>T		41.0	0.0	0		55.0	29.0	0.527273	NM_134444	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	37	CCDS12936.1																																																																																			C|0.994;T|0.006	0.006	strong		0.473	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
GIMAP6	474344	hgsc.bcm.edu	37	7	150324976	150324976	+	Missense_Mutation	SNP	T	T	C	rs11977216	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150324976T>C	ENST00000328902.5	-	3	926	c.710A>G	c.(709-711)cAa>cGa	p.Q237R	GIMAP6_ENST00000493969.1_3'UTR	NM_001244072.1|NM_024711.5	NP_001231001.1|NP_078987.3	Q6P9H5	GIMA6_HUMAN	GTPase, IMAP family member 6	237	AIG1-type G.		Q -> R (in dbSNP:rs11977216).			cytosol (GO:0005829)	GTP binding (GO:0005525)			endometrium(4)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	29			OV - Ovarian serous cystadenocarcinoma(82;0.0145)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CTGGGTATATTGGTAAGCCTT	0.512													T|||	163	0.0325479	0.1203	0.0058	5008	,	,		23011	0.0		0.0	False		,,,				2504	0.0				p.Q307R		Atlas-SNP	.											.	GIMAP6	60	.	0			c.A920G						PASS	.	T	ARG/GLN	479,3927	224.9+/-240.9	27,425,1751	164.0	152.0	156.0		710	-0.0	0.0	7	dbSNP_120	156	4,8596	3.7+/-12.6	0,4,4296	yes	missense	GIMAP6	NM_024711.5	43	27,429,6047	CC,CT,TT		0.0465,10.8715,3.7137	benign	237/293	150324976	483,12523	2203	4300	6503	SO:0001583	missense	474344	exon3			GTATATTGGTAAG	AK026343	CCDS34778.1, CCDS59087.1, CCDS75676.1	7q36.1	2014-04-04			ENSG00000133561	ENSG00000133561		"""GTPases, IMAP"""	21918	protein-coding gene	gene with protein product	"""immune-associated nucleotide-binding protein 6"""					15474311	Standard	NM_001244072		Approved	FLJ22690, IAN6	uc022apv.1	Q6P9H5	OTTHUMG00000159137	ENST00000328902.5:c.710A>G	7.37:g.150324976T>C	ENSP00000330374:p.Gln237Arg	324.0	0.0	0		290.0	128.0	0.441379	NM_001244072	C9J7B6|D3DWZ4|Q5ZPR6|Q9H612	Missense_Mutation	SNP	ENST00000328902.5	37	CCDS34778.1	47	0.02152014652014652	44	0.08943089430894309	3	0.008287292817679558	0	0.0	0	0.0	T	2.860	-0.236349	0.05944	0.108715	4.65E-4	ENSG00000133561	ENST00000328902;ENST00000392862	T	0.05199	3.48	4.05	-0.00736	0.14009	AIG1 (1);	0.847263	0.10486	N	0.668996	T	0.00073	0.0002	N	0.04994	-0.135	0.09310	N	0.999999	B;B	0.18013	0.002;0.025	B;B	0.18263	0.021;0.018	T	0.47923	-0.9079	10	0.11794	T	0.64	.	3.0119	0.06047	0.3789:0.1102:0.0:0.5109	rs11977216;rs52790742;rs56467483;rs58007032;rs11977216	237;157	Q6P9H5;Q6P9H5-2	GIMA6_HUMAN;.	R	237;298	ENSP00000330374:Q237R	ENSP00000330374:Q237R	Q	-	2	0	GIMAP6	149955909	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.176000	0.09811	-0.160000	0.11002	-0.336000	0.08194	CAA	T|0.964;C|0.036	0.036	strong		0.512	GIMAP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353457.1	NM_024711	
MUC6	4588	hgsc.bcm.edu	37	11	1017945	1017945	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1017945A>G	ENST00000421673.2	-	31	4906	c.4856T>C	c.(4855-4857)tTc>tCc	p.F1619S		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1619	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)			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)		AGAGGTGGAGAAAGGTGGAAC	0.542																																					p.F1619S		Atlas-SNP	.											.	MUC6	408	.	0			c.T4856C						PASS	.																																			SO:0001583	missense	4588	exon31			GTGGAGAAAGGTG	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.4856T>C	11.37:g.1017945A>G	ENSP00000406861:p.Phe1619Ser	1032.0	0.0	0		1212.0	49.0	0.040429	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	A	0.026	-1.375208	0.01214	.	.	ENSG00000184956	ENST00000421673	T	0.19669	2.13	2.39	-1.65	0.08291	.	.	.	.	.	T	0.14227	0.0344	L	0.41710	1.295	0.09310	N	1	B	0.29341	0.242	B	0.35931	0.214	T	0.39860	-0.9593	9	0.06625	T	0.88	.	6.4604	0.21954	0.6729:0.0:0.3271:0.0	.	1619	Q6W4X9	MUC6_HUMAN	S	1619	ENSP00000406861:F1619S	ENSP00000406861:F1619S	F	-	2	0	MUC6	1007945	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.579000	0.05834	-0.502000	0.06596	-0.917000	0.02746	TTC	.	.	none		0.542	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
AHNAK2	113146	hgsc.bcm.edu	37	14	105417503	105417503	+	Missense_Mutation	SNP	G	G	T	rs146582718	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105417503G>T	ENST00000333244.5	-	7	4404	c.4285C>A	c.(4285-4287)Cct>Act	p.P1429T	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1429						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TCTATTTCAGGGCCCTTGAGG	0.612													.|||	321	0.0640974	0.2307	0.0159	5008	,	,		12778	0.0		0.005	False		,,,				2504	0.0				p.P1429T		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C4285A						PASS	.	G	THR/PRO	721,2755		187,347,1204	98.0	74.0	83.0		4285	3.9	0.1	14	dbSNP_134	83	22,5768		3,16,2876	no	missense	AHNAK2	NM_138420.2	38	190,363,4080	TT,TG,GG		0.38,20.7422,8.0186	probably-damaging	1429/5796	105417503	743,8523	1738	2895	4633	SO:0001583	missense	113146	exon7			TTTCAGGGCCCTT	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.4285C>A	14.37:g.105417503G>T	ENSP00000353114:p.Pro1429Thr	389.0	0.0	0		411.0	406.0	0.987835	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	102	0.046703296703296704	99	0.20121951219512196	3	0.008287292817679558	0	0.0	0	0.0	g	11.78	1.742050	0.30865	0.207422	0.0038	ENSG00000185567	ENST00000333244	T	0.02656	4.21	3.87	3.87	0.44632	.	.	.	.	.	T	0.00012	0.0000	M	0.93328	3.405	0.38700	P	0.047036999999999995	D	0.89917	1.0	D	0.77557	0.99	T	0.06607	-1.0817	8	0.40728	T	0.16	-26.1992	9.0134	0.36155	0.1094:0.0:0.8906:0.0	.	1429	Q8IVF2	AHNK2_HUMAN	T	1429	ENSP00000353114:P1429T	ENSP00000353114:P1429T	P	-	1	0	AHNAK2	104488548	0.998000	0.40836	0.081000	0.20488	0.012000	0.07955	2.751000	0.47508	1.727000	0.51537	0.306000	0.20318	CCT	G|0.962;T|0.038	0.038	strong		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
SLC7A9	11136	hgsc.bcm.edu	37	19	33333179	33333179	+	Silent	SNP	C	C	T	rs111630604	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33333179C>T	ENST00000023064.4	-	11	1310	c.1119G>A	c.(1117-1119)tcG>tcA	p.S373S	SLC7A9_ENST00000587772.1_Silent_p.S373S|SLC7A9_ENST00000590341.1_Silent_p.S373S	NM_001126335.1|NM_001243036.1|NM_014270.4	NP_001119807.1|NP_001229965.1|NP_055085.1	P82251	BAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, bo,+ system), member 9	373					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|L-cystine transport (GO:0015811)|leukocyte migration (GO:0050900)|neutral amino acid transport (GO:0015804)|protein complex assembly (GO:0006461)|transmembrane transport (GO:0055085)|transport (GO:0006810)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-cystine transmembrane transporter activity (GO:0015184)|neutral amino acid transmembrane transporter activity (GO:0015175)|peptide antigen binding (GO:0042605)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	32	Esophageal squamous(110;0.137)				L-Cystine(DB00138)	AATTGACTAACGAGTTTATGT	0.393													C|||	50	0.00998403	0.0325	0.0086	5008	,	,		19257	0.0		0.0	False		,,,				2504	0.001				p.S373S	GBM(181;1335 2108 9644 44178 46689)	Atlas-SNP	.											SLC7A9,NS,carcinoma,-1,3	SLC7A9	78	3	0			c.G1119A						PASS	.	C	,	144,4262	102.1+/-140.7	5,134,2064	114.0	108.0	110.0		1119,1119	-11.4	0.0	19	dbSNP_132	110	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	SLC7A9	NM_001126335.1,NM_014270.4	,	5,134,6364	TT,TC,CC		0.0,3.2683,1.1072	,	373/488,373/488	33333179	144,12862	2203	4300	6503	SO:0001819	synonymous_variant	11136	exon11			GACTAACGAGTTT	AF141289	CCDS12425.1	19q13.11	2013-07-19	2013-07-19		ENSG00000021488	ENSG00000021488		"""Solute carriers"""	11067	protein-coding gene	gene with protein product		604144		CSNU3		10471498	Standard	NM_014270		Approved		uc021usa.1	P82251	OTTHUMG00000180287	ENST00000023064.4:c.1119G>A	19.37:g.33333179C>T		72.0	0.0	0		76.0	35.0	0.460526	NM_001243036	B2R9A6	Silent	SNP	ENST00000023064.4	37	CCDS12425.1																																																																																			C|0.987;T|0.013	0.013	strong		0.393	SLC7A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450585.1		
TMEM223	79064	hgsc.bcm.edu	37	11	62559301	62559301	+	Missense_Mutation	SNP	C	C	T	rs2956139	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:62559301C>T	ENST00000307366.7	-	1	192	c.166G>A	c.(166-168)Ggc>Agc	p.G56S	NXF1_ENST00000533048.1_5'Flank|TMEM223_ENST00000525631.1_Missense_Mutation_p.G56S|TMEM223_ENST00000527073.1_5'Flank	NM_001080501.2	NP_001073970.1	A0PJW6	TM223_HUMAN	transmembrane protein 223	56						integral component of membrane (GO:0016021)											CAGAAGACGCCCTGGCCCGCG	0.672													C|||	121	0.0241613	0.0855	0.0086	5008	,	,		14072	0.0		0.002	False		,,,				2504	0.0				p.G56S		Atlas-SNP	.											.	TMEM223	22	.	0			c.G166A						PASS	.	C	SER/GLY	221,3653		5,211,1721	17.0	26.0	23.0		166	5.0	1.0	11	dbSNP_101	23	2,8218		0,2,4108	yes	missense	TMEM223	NM_001080501.2	56	5,213,5829	TT,TC,CC		0.0243,5.7047,1.8439	benign	56/203	62559301	223,11871	1937	4110	6047	SO:0001583	missense	79064	exon1			AGACGCCCTGGCC		CCDS44628.1	11q12.3	2008-12-08				ENSG00000168569			28464	protein-coding gene	gene with protein product							Standard	NM_001080501		Approved	MGC3196	uc001nve.2	A0PJW6		ENST00000307366.7:c.166G>A	11.37:g.62559301C>T	ENSP00000303987:p.Gly56Ser	125.0	0.0	0		128.0	58.0	0.453125	NM_001080501	Q504S0|Q86YD4|Q8WUC5|Q96HG0	Missense_Mutation	SNP	ENST00000307366.7	37	CCDS44628.1	57|57	0.0260989010989011|0.0260989010989011	53|53	0.10772357723577236|0.10772357723577236	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	C|C	21.4|21.4	4.141694|4.141694	0.77775|0.77775	0.057047|0.057047	2.43E-4|2.43E-4	ENSG00000168569|ENSG00000168569	ENST00000528367|ENST00000525631;ENST00000307366	.|T;T	.|0.41758	.|0.99;0.99	5.94|5.94	5.02|5.02	0.67125|0.67125	.|.	0.275955|0.275955	0.35407|0.35407	N|N	0.003221|0.003221	T|T	0.00608|0.00608	0.0020|0.0020	L|L	0.34521|0.34521	1.04|1.04	0.35563|0.35563	D|D	0.804871|0.804871	.|B	.|0.30281	.|0.275	.|B	.|0.28916	.|0.096	T|T	0.09952|0.09952	-1.0651|-1.0651	6|9	.|.	.|.	.|.	-15.5835|-15.5835	13.3061|13.3061	0.60352|0.60352	0.0:0.9227:0.0:0.0773|0.0:0.9227:0.0:0.0773	rs2956139|rs2956139	.|56	.|A0PJW6	.|TM223_HUMAN	E|S	55|56	.|ENSP00000436670:G56S;ENSP00000303987:G56S	.|.	G|G	-|-	2|1	0|0	TMEM223|TMEM223	62315877|62315877	0.994000|0.994000	0.37717|0.37717	1.000000|1.000000	0.80357|0.80357	0.887000|0.887000	0.51463|0.51463	1.735000|1.735000	0.38176|0.38176	1.499000|1.499000	0.48617|0.48617	0.561000|0.561000	0.74099|0.74099	GGG|GGC	C|0.973;T|0.027	0.027	strong		0.672	TMEM223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395674.1		
CR1	1378	hgsc.bcm.edu	37	1	207782889	207782889	+	Missense_Mutation	SNP	A	A	G	rs17047661	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:207782889A>G	ENST00000367049.4	+	37	6151	c.6151A>G	c.(6151-6153)Aga>Gga	p.R2051G	RP11-78B10.2_ENST00000596003.1_RNA|CR1_ENST00000367051.1_Missense_Mutation_p.R1601G|CR1_ENST00000400960.2_Missense_Mutation_p.R1601G|CR1_ENST00000367052.1_Missense_Mutation_p.R1601G|RP11-78B10.2_ENST00000597497.1_RNA|CR1_ENST00000367053.1_Missense_Mutation_p.R1601G	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1601					complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						AAATGCAATTAGAGTACCAGG	0.468													a|||	984	0.196486	0.7103	0.0519	5008	,	,		19576	0.0		0.0089	False		,,,				2504	0.0				p.R2051G		Atlas-SNP	.											.	CR1	354	.	0			c.A6151G	GRCh37	CM015242	CR1	M	rs17047661	PASS	.	C	GLY/ARG,GLY/ARG	2160,1626		630,900,363	59.0	58.0	58.0		4801,6151	-2.0	0.0	1	dbSNP_123	58	27,8203		0,27,4088	yes	missense,missense	CR1	NM_000573.3,NM_000651.4	125,125	630,927,4451	GG,GA,AA		0.3281,42.9477,18.2007	probably-damaging,probably-damaging	1601/2040,2051/2490	207782889	2187,9829	1893	4115	6008	SO:0001583	missense	1378	exon37			GCAATTAGAGTAC	Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"""CD molecules"", ""Blood group antigens"", ""Complement system"""	2334	protein-coding gene	gene with protein product		120620	"""complement component (3b/4b) receptor 1, including Knops blood group system"""			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.6151A>G	1.37:g.207782889A>G	ENSP00000356016:p.Arg2051Gly	131.0	0.0	0		152.0	77.0	0.506579	NM_000651	Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	37	CCDS44308.1	333	0.15247252747252749	314	0.6382113821138211	17	0.04696132596685083	0	0.0	2	0.002638522427440633	a	8.718	0.913598	0.17907	0.570523	0.003281	ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000534202;ENST00000367049	T;T;T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11;1.62;-0.11	2.54	-2.03	0.07365	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.00012	0.0000	M	0.80422	2.495	0.80722	P	0.0	B;D;D	0.59767	0.257;0.982;0.986	B;D;P	0.69479	0.069;0.964;0.79	T	0.47222	-0.9134	8	0.23891	T	0.37	.	4.646	0.12572	0.3825:0.4843:0.1331:0.0	rs17047661;rs52836690;rs17047661	1601;1601;2051	Q5SR44;P17927;E9PDY4	.;CR1_HUMAN;.	G	1601;1601;1601;1601;1151;2051	ENSP00000356019:R1601G;ENSP00000356018:R1601G;ENSP00000356020:R1601G;ENSP00000383744:R1601G;ENSP00000436139:R1151G;ENSP00000356016:R2051G	ENSP00000356016:R2051G	R	+	1	2	CR1	205849512	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.157000	0.10085	-0.445000	0.07159	-0.525000	0.04345	AGA	A|0.769;G|0.231	0.231	strong		0.468	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1	NM_000573	
CAPN3	825	hgsc.bcm.edu	37	15	42680058	42680058	+	Silent	SNP	T	T	C	rs17593	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42680058T>C	ENST00000397163.3	+	4	825	c.606T>C	c.(604-606)agT>agC	p.S202S	CAPN3_ENST00000349748.3_Silent_p.S202S|CAPN3_ENST00000356316.3_Silent_p.S115S|CAPN3_ENST00000357568.3_Silent_p.S202S|CAPN3_ENST00000318023.7_Silent_p.S202S|RP11-164J13.1_ENST00000495723.1_RNA	NM_000070.2	NP_000061.1	P20807	CAN3_HUMAN	calpain 3, (p94)	202	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.		Missing (in LGMD2A). {ECO:0000269|PubMed:9452114}.		apoptotic process (GO:0006915)|autolysis (GO:0001896)|cellular response to calcium ion (GO:0071277)|cellular response to salt stress (GO:0071472)|G1 to G0 transition involved in cell differentiation (GO:0070315)|muscle cell cellular homeostasis (GO:0046716)|muscle organ development (GO:0007517)|muscle structure development (GO:0061061)|myofibril assembly (GO:0030239)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of proteolysis (GO:0045862)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of satellite cell activation involved in skeletal muscle regeneration (GO:0014718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein localization to membrane (GO:0072657)|proteolysis (GO:0006508)|regulation of catalytic activity (GO:0050790)|regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043122)|regulation of myoblast differentiation (GO:0045661)|response to calcium ion (GO:0051592)|response to muscle activity (GO:0014850)|sarcomere organization (GO:0045214)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|myofibril (GO:0030016)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|T-tubule (GO:0030315)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|catalytic activity (GO:0003824)|cysteine-type peptidase activity (GO:0008234)|ligase regulator activity (GO:0055103)|peptidase activity (GO:0008233)|protein complex scaffold (GO:0032947)|signal transducer activity (GO:0004871)|sodium ion binding (GO:0031402)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(21)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	47		all_cancers(109;1.65e-16)|all_epithelial(112;8.34e-15)|Lung NSC(122;3.56e-09)|all_lung(180;1.68e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;7.36e-07)		AGTTCTGGAGTGCTCTGCTGG	0.498													C|||	321	0.0640974	0.2095	0.0159	5008	,	,		22401	0.0		0.0089	False		,,,				2504	0.0245				p.S202S		Atlas-SNP	.											.	CAPN3	172	.	0			c.T606C						PASS	.	C	,,	698,3708	761.2+/-413.0	49,600,1554	192.0	164.0	174.0		606,606,606	-4.9	0.8	15	dbSNP_63	174	38,8560	817.5+/-406.9	0,38,4261	no	coding-synonymous,coding-synonymous,coding-synonymous	CAPN3	NM_000070.2,NM_024344.1,NM_173087.1	,,	49,638,5815	CC,CT,TT		0.442,15.842,5.6598	,,	202/822,202/816,202/730	42680058	736,12268	2203	4299	6502	SO:0001819	synonymous_variant	825	exon4			CTGGAGTGCTCTG	X85030	CCDS10085.1, CCDS10086.1, CCDS32207.1, CCDS45245.1, CCDS45246.1	15q15.1	2014-09-17			ENSG00000092529	ENSG00000092529	3.4.22.52	"""EF-hand domain containing"""	1480	protein-coding gene	gene with protein product		114240		LGMD2, LGMD2A		2555341, 7720071	Standard	NM_024344		Approved	CANP3, p94, nCL-1	uc001zpn.1	P20807	OTTHUMG00000130619	ENST00000397163.3:c.606T>C	15.37:g.42680058T>C		159.0	1.0	0.00628931		163.0	163.0	1	NM_000070	A6H8K6|Q7L4R0|Q9BQC8|Q9BTU4|Q9Y5S6|Q9Y5S7	Silent	SNP	ENST00000397163.3	37	CCDS45245.1																																																																																			T|0.944;C|0.056	0.056	strong		0.498	CAPN3-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421075.1		
ZC4H2	55906	hgsc.bcm.edu	37	X	64139051	64139051	+	Silent	SNP	T	T	C	rs6524946	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:64139051T>C	ENST00000374839.3	-	4	538	c.432A>G	c.(430-432)acA>acG	p.T144T	ZC4H2_ENST00000337990.2_Silent_p.T121T|ZC4H2_ENST00000488608.1_5'UTR|ZC4H2_ENST00000447788.2_Intron|ZC4H2_ENST00000545618.1_Silent_p.T139T	NM_018684.3	NP_061154.1	Q9NQZ6	ZC4H2_HUMAN	zinc finger, C4H2 domain containing	144					nervous system development (GO:0007399)|neuromuscular junction development (GO:0007528)|spinal cord motor neuron differentiation (GO:0021522)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	metal ion binding (GO:0046872)			endometrium(2)|large_intestine(4)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	24						CCTGAGGTTCTGTCTGCCATT	0.547													C|||	354	0.0937748	0.2549	0.0245	3775	,	,		13414	0.0		0.0	False		,,,				2504	0.0				p.T144T		Atlas-SNP	.											.	ZC4H2	64	.	0			c.A432G						PASS	.	C	,,	1115,2720		134,678,169,820,402	60.0	51.0	54.0		363,,432	-4.2	0.3	X	dbSNP_116	54	4,6724		0,2,2,2426,1870	no	coding-synonymous,intron,coding-synonymous	ZC4H2	NM_001178032.2,NM_001178033.2,NM_018684.3	,,	134,680,171,3246,2272	CC,CT,C,TT,T		0.0595,29.0743,10.5936	,,	121/202,,144/225	64139051	1119,9444	2203	4300	6503	SO:0001819	synonymous_variant	55906	exon4			AGGTTCTGTCTGC	AF270491	CCDS14380.1, CCDS55431.1, CCDS55432.1	Xq11.1	2013-07-23	2008-10-01	2008-10-01	ENSG00000126970	ENSG00000126970		"""Zinc fingers"""	24931	protein-coding gene	gene with protein product		300897	"""KIAA1166"", ""Wieacker-Wolff syndrome"""	KIAA1166, WWS		10574461, 12097419, 23623388	Standard	NM_018684		Approved	HCA127	uc004dvu.3	Q9NQZ6	OTTHUMG00000021712	ENST00000374839.3:c.432A>G	X.37:g.64139051T>C		154.0	0.0	0		129.0	62.0	0.48062	NM_018684	B2RDC2|B3KVZ5|B4DED0|E7EM74|G3V1L3|Q53H73|Q5JTF9|Q9H9C3|Q9H9H7|Q9ULQ4	Silent	SNP	ENST00000374839.3	37	CCDS14380.1																																																																																			T|0.894;C|0.106	0.106	strong		0.547	ZC4H2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056958.1	NM_018684	
MYOM2	9172	hgsc.bcm.edu	37	8	2088697	2088697	+	Missense_Mutation	SNP	G	G	C	rs34735757	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:2088697G>C	ENST00000262113.4	+	33	3993	c.3852G>C	c.(3850-3852)gaG>gaC	p.E1284D	MYOM2_ENST00000523438.1_Missense_Mutation_p.E709D|MYOM2_ENST00000520298.1_3'UTR	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	1284			E -> D (in dbSNP:rs34735757).		muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		GGAGTGAAGAGATGGCTTGGC	0.458													G|||	55	0.0109824	0.0386	0.0043	5008	,	,		15452	0.001		0.0	False		,,,				2504	0.0				p.E1284D		Atlas-SNP	.											.	MYOM2	251	.	0			c.G3852C						PASS	.	G	ASP/GLU	155,4251	106.9+/-145.3	1,153,2049	121.0	116.0	118.0		3852	-1.4	0.7	8	dbSNP_126	118	1,8599		0,1,4299	yes	missense	MYOM2	NM_003970.2	45	1,154,6348	CC,CG,GG		0.0116,3.5179,1.1994	benign	1284/1466	2088697	156,12850	2203	4300	6503	SO:0001583	missense	9172	exon33			TGAAGAGATGGCT		CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7614	protein-coding gene	gene with protein product		603509	"""myomesin (M-protein) 2 (165kD)"", ""myomesin (M-protein) 2, 165kDa"""				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.3852G>C	8.37:g.2088697G>C	ENSP00000262113:p.Glu1284Asp	68.0	0.0	0		76.0	35.0	0.460526	NM_003970	Q7Z3Y2	Missense_Mutation	SNP	ENST00000262113.4	37	CCDS5957.1	23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	G	11.14	1.551354	0.27739	0.035179	1.16E-4	ENSG00000036448	ENST00000262113;ENST00000523438	T;T	0.34667	1.35;1.35	5.02	-1.4	0.08968	Immunoglobulin-like fold (1);	0.345909	0.29473	N	0.012055	T	0.03739	0.0106	L	0.28556	0.865	0.29986	N	0.817304	B	0.06786	0.001	B	0.06405	0.002	T	0.06285	-1.0835	10	0.24483	T	0.36	.	0.3472	0.00343	0.231:0.2232:0.1729:0.373	rs34735757	1284	P54296	MYOM2_HUMAN	D	1284;709	ENSP00000262113:E1284D;ENSP00000428396:E709D	ENSP00000262113:E1284D	E	+	3	2	MYOM2	2076104	0.995000	0.38212	0.652000	0.29579	0.922000	0.55478	0.369000	0.20416	-0.371000	0.08004	0.655000	0.94253	GAG	G|0.986;C|0.014	0.014	strong		0.458	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
MT-ND1	4535	hgsc.bcm.edu	37	M	3594	3594	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:3594C>T	ENST00000361390.2	+	1	288	c.288C>T	c.(286-288)gtC>gtT	p.V96V	MT-CO1_ENST00000361624.2_5'Flank|MT-RNR1_ENST00000389680.2_RNA|MT-TL1_ENST00000386347.1_RNA|MT-ND2_ENST00000361453.3_5'Flank|MT-TA_ENST00000387392.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-TF_ENST00000387314.1_RNA|MT-TV_ENST00000387342.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-TI_ENST00000387365.1_RNA|MT-RNR2_ENST00000387347.2_RNA			P03886	NU1M_HUMAN	mitochondrially encoded NADH dehydrogenase 1	96					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(13)|kidney(17)|lung(2)|prostate(1)	34					Desflurane(DB01189)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	AACCCCCTGGTCAACCTCAAC	0.542																																					p.V96V		Atlas-SNP	.											.	.	.	.	0			c.C288T						PASS	.																																			SO:0001819	synonymous_variant	10625	exon1			CCTGGTCAACCTC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198888	ENSG00000198888	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7455	protein-coding gene	gene with protein product	"""complex I ND1 subunit"", ""NADH-ubiquinone oxidoreductase chain 1"""	516000	"""NADH dehydrogenase 1"""	MTND1			Standard			Approved	ND1, NAD1		P03886		ENST00000361390.2:c.288C>T	M.37:g.3594C>T		5.0	0.0	0		9.0	9.0	1	ENST00000361390	C0JKH6|Q37523	Silent	SNP	ENST00000361390.2	37																																																																																				.	.	none		0.542	MT-ND1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024026	
SLC38A8	146167	hgsc.bcm.edu	37	16	84056442	84056442	+	Missense_Mutation	SNP	G	G	C	rs11861325	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84056442G>C	ENST00000299709.3	-	6	742	c.743C>G	c.(742-744)tCc>tGc	p.S248C		NM_001080442.1	NP_001073911.1	A6NNN8	S38A8_HUMAN	solute carrier family 38, member 8	248					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						GGCCCAGTGGGAGAGGCTCCG	0.617													G|||	179	0.0357428	0.1271	0.0115	5008	,	,		17454	0.0		0.001	False		,,,				2504	0.002				p.S248C		Atlas-SNP	.											.	SLC38A8	60	.	0			c.C743G						PASS	.	G	CYS/SER	463,3937	217.1+/-235.6	27,409,1764	84.0	67.0	73.0		743	1.0	0.0	16	dbSNP_120	73	4,8596	3.0+/-9.4	0,4,4296	yes	missense	SLC38A8	NM_001080442.1	112	27,413,6060	CC,CG,GG		0.0465,10.5227,3.5923	probably-damaging	248/436	84056442	467,12533	2200	4300	6500	SO:0001583	missense	146167	exon6			CAGTGGGAGAGGC		CCDS32495.1	16q23.3	2013-05-22				ENSG00000166558		"""Solute carriers"""	32434	protein-coding gene	gene with protein product		615585					Standard	XM_006721135		Approved		uc002fhg.1	A6NNN8		ENST00000299709.3:c.743C>G	16.37:g.84056442G>C	ENSP00000299709:p.Ser248Cys	71.0	0.0	0		79.0	37.0	0.468354	NM_001080442		Missense_Mutation	SNP	ENST00000299709.3	37	CCDS32495.1	71	0.03250915750915751	65	0.13211382113821138	6	0.016574585635359115	0	0.0	0	0.0	G	9.359	1.067547	0.20067	0.105227	4.65E-4	ENSG00000166558	ENST00000299709	T	0.02421	4.3	5.37	0.968	0.19680	.	0.403682	0.28322	N	0.015761	T	0.00109	0.0003	M	0.67953	2.075	0.43114	D	0.994829	D	0.65815	0.995	P	0.61800	0.894	T	0.12344	-1.0551	10	0.62326	D	0.03	.	10.254	0.43385	0.0736:0.4038:0.5226:0.0	rs11861325	248	A6NNN8	S38A8_HUMAN	C	248	ENSP00000299709:S248C	ENSP00000299709:S248C	S	-	2	0	SLC38A8	82613943	0.961000	0.32948	0.019000	0.16419	0.034000	0.12701	4.054000	0.57434	-0.033000	0.13736	0.549000	0.68633	TCC	G|0.961;C|0.039	0.039	strong		0.617	SLC38A8-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432623.1	NM_001080442	
ZFP42	132625	hgsc.bcm.edu	37	4	188924450	188924450	+	Silent	SNP	A	A	G	rs61731386	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:188924450A>G	ENST00000326866.4	+	4	897	c.489A>G	c.(487-489)tcA>tcG	p.S163S	ZFP42_ENST00000509524.1_Silent_p.S163S	NM_174900.3	NP_777560.2	Q96MM3	ZFP42_HUMAN	ZFP42 zinc finger protein	163					female gonad development (GO:0008585)|in utero embryonic development (GO:0001701)|male gonad development (GO:0008584)|meiotic nuclear division (GO:0007126)|regulation of genetic imprinting (GO:2000653)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(14;6.2e-52)|all_epithelial(14;7.36e-37)|all_lung(41;2.29e-15)|Lung NSC(41;6.7e-15)|Breast(6;1.53e-05)|Melanoma(20;3.01e-05)|Hepatocellular(41;0.00335)|all_hematologic(60;0.014)|Renal(120;0.0183)|Prostate(90;0.0421)|Colorectal(36;0.227)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;4.21e-06)|GBM - Glioblastoma multiforme(59;8.93e-05)|STAD - Stomach adenocarcinoma(60;0.000279)|LUSC - Lung squamous cell carcinoma(40;0.00902)|READ - Rectum adenocarcinoma(43;0.157)		TTGACCTATCAGATCCTAAAC	0.453													A|||	187	0.0373403	0.1362	0.0086	5008	,	,		17571	0.0		0.001	False		,,,				2504	0.0				p.S163S		Atlas-SNP	.											.	ZFP42	87	.	0			c.A489G						PASS	.	A		449,3957	202.5+/-225.2	25,399,1779	103.0	116.0	112.0		489	-1.9	0.0	4	dbSNP_129	112	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ZFP42	NM_174900.3		25,401,6077	GG,GA,AA		0.0233,10.1906,3.4676		163/311	188924450	451,12555	2203	4300	6503	SO:0001819	synonymous_variant	132625	exon4			CCTATCAGATCCT	AK056719	CCDS3849.1	4q35.2	2014-09-04	2012-11-27		ENSG00000179059	ENSG00000179059		"""Zinc fingers, C2H2-type"""	30949	protein-coding gene	gene with protein product		614572	"""zinc finger protein 42 homolog (mouse)"", ""zinc finger protein 42"""			12110702	Standard	NM_174900		Approved	REX1, ZNF754	uc003izh.1	Q96MM3	OTTHUMG00000160235	ENST00000326866.4:c.489A>G	4.37:g.188924450A>G		59.0	0.0	0		60.0	37.0	0.616667	NM_174900	D3DP65|Q8WXE2	Silent	SNP	ENST00000326866.4	37	CCDS3849.1																																																																																			A|0.972;G|0.028	0.028	strong		0.453	ZFP42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359794.1	NM_174900	
WNK4	65266	hgsc.bcm.edu	37	17	40946913	40946913	+	Missense_Mutation	SNP	C	C	T	rs56226218	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:40946913C>T	ENST00000246914.5	+	14	2495	c.2474C>T	c.(2473-2475)cCa>cTa	p.P825L		NM_032387.4	NP_115763.2	Q96J92	WNK4_HUMAN	WNK lysine deficient protein kinase 4	825					chloride transport (GO:0006821)|distal tubule morphogenesis (GO:0072156)|intracellular signal transduction (GO:0035556)|ion homeostasis (GO:0050801)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|protein localization (GO:0008104)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)|renal sodium ion absorption (GO:0070294)	cytoplasm (GO:0005737)|tight junction (GO:0005923)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|prostate(1)|skin(5)|stomach(1)	35		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.0749)		CCCATTTCCCCAGGTCCCATC	0.577													C|||	140	0.0279553	0.1021	0.0072	5008	,	,		15756	0.0		0.0	False		,,,				2504	0.0				p.P825L	Esophageal Squamous(6;201 374 4964 23855 42828)	Atlas-SNP	.											.	WNK4	182	.	0			c.C2474T						PASS	.	C	LEU/PRO	391,4015	196.4+/-220.7	17,357,1829	135.0	123.0	127.0		2474	4.6	0.9	17	dbSNP_129	127	1,8599	1.2+/-3.3	0,1,4299	yes	missense	WNK4	NM_032387.4	98	17,358,6128	TT,TC,CC		0.0116,8.8743,3.014	benign	825/1244	40946913	392,12614	2203	4300	6503	SO:0001583	missense	65266	exon14			TTTCCCCAGGTCC	AJ309861	CCDS11439.1	17q21-q22	2005-01-19	2005-01-19	2005-01-19		ENSG00000126562			14544	protein-coding gene	gene with protein product		601844	"""protein kinase, lysine deficient 4"""	PRKWNK4			Standard	NM_032387		Approved		uc002ibj.3	Q96J92		ENST00000246914.5:c.2474C>T	17.37:g.40946913C>T	ENSP00000246914:p.Pro825Leu	235.0	1.0	0.00425532		279.0	145.0	0.519713	NM_032387	B0LPI0|Q8N8X3|Q8N8Z2|Q96DT8|Q9BYS5	Missense_Mutation	SNP	ENST00000246914.5	37	CCDS11439.1	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	C	12.50	1.956295	0.34565	0.088743	1.16E-4	ENSG00000126562	ENST00000246914;ENST00000316085	T	0.73363	-0.74	5.58	4.59	0.56863	.	0.143817	0.32301	N	0.006288	T	0.04588	0.0125	L	0.29908	0.895	0.47659	D	0.999481	B;B;B	0.32653	0.379;0.261;0.006	B;B;B	0.28553	0.091;0.042;0.012	T	0.14587	-1.0467	10	0.51188	T	0.08	-4.1586	8.3488	0.32290	0.1564:0.7652:0.0:0.0784	rs56226218;rs61755625	825;825;825	Q96J92-3;B0LPI0;Q96J92	.;.;WNK4_HUMAN	L	825;597	ENSP00000246914:P825L	ENSP00000246914:P825L	P	+	2	0	WNK4	38200439	0.989000	0.36119	0.913000	0.36048	0.211000	0.24417	3.653000	0.54446	1.444000	0.47605	0.591000	0.81541	CCA	C|0.974;T|0.026	0.026	strong		0.577	WNK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452389.1		
HADHB	3032	hgsc.bcm.edu	37	2	26505745	26505745	+	Silent	SNP	G	G	A	rs7572240	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:26505745G>A	ENST00000317799.5	+	11	1070	c.966G>A	c.(964-966)gcG>gcA	p.A322A	HADHB_ENST00000494615.1_3'UTR|HADHB_ENST00000405867.3_Silent_p.A199A|HADHB_ENST00000537713.1_Silent_p.A307A|HADHB_ENST00000545822.1_Silent_p.A300A	NM_000183.2	NP_000174.1	P55084	ECHB_HUMAN	hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase (trifunctional protein), beta subunit	322					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|mitochondrial envelope (GO:0005740)|mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acyltransferase activity (GO:0003988)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|skin(1)	19	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TAATCATGGCGGAGGAAAAGG	0.388													g|||	101	0.0201677	0.0726	0.0043	5008	,	,		18252	0.0		0.002	False		,,,				2504	0.0				p.A322A		Atlas-SNP	.											.	HADHB	50	.	0			c.G966A						PASS	.	G		268,4138	151.0+/-185.0	6,256,1941	91.0	87.0	89.0		966	-8.4	0.7	2	dbSNP_116	89	4,8596	2.2+/-6.3	0,4,4296	no	coding-synonymous	HADHB	NM_000183.2		6,260,6237	AA,AG,GG		0.0465,6.0826,2.0913		322/475	26505745	272,12734	2203	4300	6503	SO:0001819	synonymous_variant	3032	exon11			CATGGCGGAGGAA		CCDS1722.1, CCDS62871.1, CCDS62872.1	2p23	2010-04-30	2010-04-30		ENSG00000138029	ENSG00000138029	2.3.1.16		4803	protein-coding gene	gene with protein product	"""mitochondrial trifunctional protein, beta subunit"""	143450	"""hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), beta subunit"""			9605857	Standard	NM_000183		Approved	MTPB	uc002rgz.3	P55084	OTTHUMG00000096978	ENST00000317799.5:c.966G>A	2.37:g.26505745G>A		71.0	0.0	0		53.0	26.0	0.490566	NM_000183	B2RB16|B4E2W0|O14969|Q53TA6|Q96C77|Q9H3F5|Q9T2V8	Silent	SNP	ENST00000317799.5	37	CCDS1722.1																																																																																			G|0.982;A|0.018	0.018	strong		0.388	HADHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214050.2	NM_000183	
GOLM1	51280	hgsc.bcm.edu	37	9	88650332	88650332	+	Missense_Mutation	SNP	C	C	G	rs61741197	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:88650332C>G	ENST00000388712.3	-	8	1134	c.966G>C	c.(964-966)caG>caC	p.Q322H	GOLM1_ENST00000388711.3_Missense_Mutation_p.Q322H|GOLM1_ENST00000257504.6_5'Flank	NM_016548.3	NP_057632.2	Q8NBJ4	GOLM1_HUMAN	golgi membrane protein 1	322					nucleus organization (GO:0006997)|regulation of lipid metabolic process (GO:0019216)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|liver(1)|lung(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)	17						GGATGACAAGCTGGTCTCGCT	0.652											OREG0019278	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	249	0.0497204	0.1823	0.0115	5008	,	,		15263	0.0		0.0	False		,,,				2504	0.0				p.Q322H		Atlas-SNP	.											.	GOLM1	36	.	0			c.G966C						PASS	.	C	HIS/GLN,HIS/GLN	673,3733	284.6+/-277.7	59,555,1589	76.0	84.0	81.0		966,966	2.7	1.0	9	dbSNP_129	81	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	GOLM1	NM_016548.3,NM_177937.2	24,24	59,556,5888	GG,GC,CC		0.0116,15.2746,5.1822	possibly-damaging,possibly-damaging	322/402,322/402	88650332	674,12332	2203	4300	6503	SO:0001583	missense	51280	exon8			GACAAGCTGGTCT	AF236056	CCDS35054.1	9q21.33	2012-12-13	2007-07-30	2007-07-30	ENSG00000135052	ENSG00000135052			15451	protein-coding gene	gene with protein product		606804	"""golgi phosphoprotein 2"", ""chromosome 9 open reading frame 155"""	GOLPH2, C9orf155		10831838, 18953438, 22542941	Standard	NM_016548		Approved	GP73, FLJ23608, bA379P1.3	uc004aol.3	Q8NBJ4	OTTHUMG00000020130	ENST00000388712.3:c.966G>C	9.37:g.88650332C>G	ENSP00000373364:p.Gln322His	93.0	0.0	0	1261	104.0	71.0	0.682692	NM_016548	Q6IAF4|Q9NRB9	Missense_Mutation	SNP	ENST00000388712.3	37	CCDS35054.1	90	0.04120879120879121	84	0.17073170731707318	6	0.016574585635359115	0	0.0	0	0.0	C	11.23	1.576207	0.28092	0.152746	1.16E-4	ENSG00000135052	ENST00000388712;ENST00000388711	T;T	0.47177	0.85;0.85	4.54	2.7	0.31948	.	0.524964	0.19303	N	0.117587	T	0.00241	0.0007	L	0.56769	1.78	0.33372	P	0.42634399999999995	D	0.64830	0.994	D	0.64321	0.924	T	0.06625	-1.0816	9	0.40728	T	0.16	-0.0466	6.3297	0.21262	0.0:0.7825:0.0:0.2175	rs61741197	322	Q8NBJ4	GOLM1_HUMAN	H	322	ENSP00000373364:Q322H;ENSP00000373363:Q322H	ENSP00000373363:Q322H	Q	-	3	2	GOLM1	87840152	1.000000	0.71417	0.997000	0.53966	0.445000	0.32107	1.172000	0.31908	1.282000	0.44496	0.462000	0.41574	CAG	C|0.947;G|0.053	0.053	strong		0.652	GOLM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052904.2	NM_177937	
HDAC4	9759	hgsc.bcm.edu	37	2	240003873	240003873	+	Silent	SNP	G	G	A	rs10168964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:240003873G>A	ENST00000345617.3	-	21	3353	c.2562C>T	c.(2560-2562)gaC>gaT	p.D854D	HDAC4_ENST00000543185.1_Silent_p.D438D	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	854	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|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)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		GGACGCTGGGGTCGCTGTAGA	0.587													G|||	381	0.0760783	0.2799	0.0159	5008	,	,		15695	0.0		0.0	False		,,,				2504	0.0				p.D854D		Atlas-SNP	.											.	HDAC4	127	.	0			c.C2562T						PASS	.	G		1088,3318	396.7+/-330.2	134,820,1249	172.0	156.0	161.0		2562	3.0	1.0	2	dbSNP_119	161	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	HDAC4	NM_006037.3		134,826,5543	AA,AG,GG		0.0698,24.6936,8.4115		854/1085	240003873	1094,11912	2203	4300	6503	SO:0001819	synonymous_variant	9759	exon21			GCTGGGGTCGCTG	AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"""brachydactyly-mental retardation syndrome"""	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.2562C>T	2.37:g.240003873G>A		243.0	0.0	0		326.0	324.0	0.993865	NM_006037	Q9UND6	Silent	SNP	ENST00000345617.3	37	CCDS2529.1																																																																																			G|0.924;A|0.076	0.076	strong		0.587	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037	
KRTAP1-4	728255	hgsc.bcm.edu	37	17	39186254	39186254	+	Missense_Mutation	SNP	T	T	G	rs575093773	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39186254T>G	ENST00000377747.4	-	1	102	c.77A>C	c.(76-78)cAg>cCg	p.Q26P	KRTAP1-5_ENST00000361883.5_5'Flank	NM_001257305.1	NP_001244234.1	P0C5Y4	KRA14_HUMAN	keratin associated protein 1-4	26						keratin filament (GO:0045095)				lung(1)	1						GCAGCTTGGCTGGCAGCAGCT	0.627													t|||	25	0.00499201	0.0189	0.0	5008	,	,		17746	0.0		0.0	False		,,,				2504	0.0				p.Q26P		Atlas-SNP	.											.	KRTAP1-4	4	.	0			c.A77C						PASS	.																																			SO:0001583	missense	728255	exon1			CTTGGCTGGCAGC	AC007455	CCDS58548.1	17q21.2	2010-06-22			ENSG00000204887	ENSG00000204887		"""Keratin associated proteins"""	18904	protein-coding gene	gene with protein product		608821					Standard	NM_001257305		Approved	KAP1.4	uc031raf.1	P0C5Y4	OTTHUMG00000133631	ENST00000377747.4:c.77A>C	17.37:g.39186254T>G	ENSP00000366976:p.Gln26Pro	135.0	0.0	0		137.0	68.0	0.49635	NM_001257305	A6NJ92	Missense_Mutation	SNP	ENST00000377747.4	37	CCDS58548.1	.	.	.	.	.	.	.	.	.	.	T	9.987	1.229625	0.22542	.	.	ENSG00000204887	ENST00000377747	T	0.35789	1.29	4.07	4.07	0.47477	.	0.000000	0.38778	N	0.001578	T	0.44891	0.1315	.	.	.	.	.	.	.	.	.	.	.	.	T	0.61043	-0.7142	6	0.66056	D	0.02	.	9.7179	0.40284	0.0:0.0:0.0:1.0	.	.	.	.	P	26	ENSP00000366976:Q26P	ENSP00000366976:Q26P	Q	-	2	0	KRTAP1-4	36439780	1.000000	0.71417	0.822000	0.32727	0.016000	0.09150	1.181000	0.32017	2.072000	0.62099	0.533000	0.62120	CAG	.	.	none		0.627	KRTAP1-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257776.3		
OR52H1	390067	hgsc.bcm.edu	37	11	5566460	5566460	+	Silent	SNP	G	G	A	rs115541630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5566460G>A	ENST00000322653.4	-	1	319	c.294C>T	c.(292-294)cgC>cgT	p.R98R	HBG2_ENST00000380259.2_Intron	NM_001005289.1	NP_001005289.1	Q8NGJ2	O52H1_HUMAN	olfactory receptor, family 52, subfamily H, member 1	98						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|ovary(1)|prostate(1)|skin(2)	20		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;5.33e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ATGTGATTTCGCGAGCCCCTA	0.468													G|||	61	0.0121805	0.0439	0.0043	5008	,	,		22055	0.0		0.0	False		,,,				2504	0.0				p.R98R		Atlas-SNP	.											OR52H1,NS,carcinoma,0,1	OR52H1	46	1	0			c.C294T						PASS	.	G		242,4160	142.7+/-177.9	6,230,1965	73.0	70.0	71.0		294	-9.5	0.0	11	dbSNP_132	71	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous	OR52H1	NM_001005289.1		6,231,6261	AA,AG,GG		0.0116,5.4975,1.8698		98/321	5566460	243,12753	2201	4297	6498	SO:0001819	synonymous_variant	390067	exon1			GATTTCGCGAGCC	AB065802	CCDS31386.1	11p15.4	2012-08-09			ENSG00000181616	ENSG00000181616		"""GPCR / Class A : Olfactory receptors"""	15218	protein-coding gene	gene with protein product							Standard	NM_001005289		Approved		uc010qzh.2	Q8NGJ2	OTTHUMG00000066909	ENST00000322653.4:c.294C>T	11.37:g.5566460G>A		104.0	0.0	0		117.0	58.0	0.495726	NM_001005289	B9EH26|Q6IF79	Silent	SNP	ENST00000322653.4	37	CCDS31386.1																																																																																			G|0.983;A|0.017	0.017	strong		0.468	OR52H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143400.1	NM_001005289	
PCDHB14	56122	hgsc.bcm.edu	37	5	140604641	140604641	+	Missense_Mutation	SNP	G	G	C	rs142548755	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140604641G>C	ENST00000239449.4	+	1	1564	c.1564G>C	c.(1564-1566)Gag>Cag	p.E522Q	PCDHB14_ENST00000515856.2_Missense_Mutation_p.E369Q	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	522	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GCTGGACTACGAGGCCCTACA	0.687													g|||	27	0.00539137	0.0204	0.0	5008	,	,		16691	0.0		0.0	False		,,,				2504	0.0				p.E522Q	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.G1564C						PASS	.	G	GLN/GLU	69,4337		0,69,2134	86.0	91.0	90.0		1564	4.2	1.0	5	dbSNP_134	90	0,8600		0,0,4300	no	missense	PCDHB14	NM_018934.2	29	0,69,6434	CC,CG,GG		0.0,1.566,0.5305	probably-damaging	522/799	140604641	69,12937	2203	4300	6503	SO:0001583	missense	56122	exon1			GACTACGAGGCCC	AF152493	CCDS4256.1	5q31	2010-01-26			ENSG00000120327	ENSG00000120327		"""Cadherins / Protocadherins : Clustered"""	8685	other	protocadherin		606340				10380929	Standard	NM_018934		Approved	PCDH-BETA14	uc003ljb.3	Q9Y5E9	OTTHUMG00000129619	ENST00000239449.4:c.1564G>C	5.37:g.140604641G>C	ENSP00000239449:p.Glu522Gln	246.0	0.0	0		281.0	137.0	0.487544	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Missense_Mutation	SNP	ENST00000239449.4	37	CCDS4256.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	-	20.7	4.042145	0.75732	0.01566	0.0	ENSG00000120327	ENST00000515856;ENST00000239449	T;T	0.72942	-0.7;-0.7	4.15	4.15	0.48705	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.81917	0.4924	H	0.96048	3.76	0.45634	D	0.998568	D	0.89917	1.0	D	0.97110	1.0	D	0.89840	0.4002	9	0.87932	D	0	.	16.4819	0.84160	0.0:0.0:1.0:0.0	.	522	Q9Y5E9	PCDBE_HUMAN	Q	369;522	ENSP00000444518:E369Q;ENSP00000239449:E522Q	ENSP00000239449:E522Q	E	+	1	0	PCDHB14	140584825	1.000000	0.71417	1.000000	0.80357	0.755000	0.42902	7.687000	0.84139	2.048000	0.60808	0.556000	0.70494	GAG	G|0.994;C|0.006	0.006	strong		0.687	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934	
PXYLP1	92370	hgsc.bcm.edu	37	3	141006162	141006162	+	Silent	SNP	G	G	A	rs34601454	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:141006162G>A	ENST00000286353.4	+	5	509	c.372G>A	c.(370-372)ccG>ccA	p.P124P	ACPL2_ENST00000393007.1_Silent_p.P108P|ACPL2_ENST00000393010.2_Silent_p.P124P|ACPL2_ENST00000502783.1_Silent_p.P86P|ACPL2_ENST00000508812.1_Silent_p.P115P|ACPL2_ENST00000504264.1_Silent_p.P107P|RP11-438D8.2_ENST00000507698.1_RNA	NM_001037172.1|NM_001282728.1	NP_001032249.1|NP_001269657.1	Q8TE99	PXYP1_HUMAN		124						extracellular region (GO:0005576)	acid phosphatase activity (GO:0003993)			endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|prostate(2)|skin(2)	23						CTAGGAAACCGTATCACCCAA	0.473													G|||	162	0.0323482	0.1157	0.013	5008	,	,		20337	0.0		0.0	False		,,,				2504	0.0				p.P124P		Atlas-SNP	.											.	ACPL2	50	.	0			c.G372A						PASS	.	G	,	377,4029	189.9+/-215.9	16,345,1842	151.0	158.0	155.0		372,372	-11.3	0.0	3	dbSNP_126	155	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	ACPL2	NM_001037172.1,NM_152282.3	,	16,348,6139	AA,AG,GG		0.0349,8.5565,2.9217	,	124/481,124/481	141006162	380,12626	2203	4300	6503	SO:0001819	synonymous_variant	92370	exon7			GAAACCGTATCAC																												ENST00000286353.4:c.372G>A	3.37:g.141006162G>A		115.0	0.0	0		97.0	41.0	0.42268	NM_152282	D3DNF5|Q49AJ2|W0TR04	Silent	SNP	ENST00000286353.4	37	CCDS3116.1																																																																																			G|0.969;A|0.031	0.031	strong		0.473	ACPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359533.2		
PARVB	29780	hgsc.bcm.edu	37	22	44495953	44495953	+	Missense_Mutation	SNP	A	A	G	rs56194750	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:44495953A>G	ENST00000338758.7	+	3	286	c.223A>G	c.(223-225)Atg>Gtg	p.M75V	PARVB_ENST00000477795.1_3'UTR|PARVB_ENST00000404989.1_Missense_Mutation_p.M38V|PARVB_ENST00000406477.3_Missense_Mutation_p.M108V	NM_013327.4	NP_037459.2	Q9HBI1	PARVB_HUMAN	parvin, beta	75					actin cytoskeleton reorganization (GO:0031532)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell projection assembly (GO:0030031)|establishment or maintenance of cell polarity regulating cell shape (GO:0071963)|lamellipodium assembly (GO:0030032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(3)|large_intestine(7)|lung(8)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Ovarian(80;0.0246)|all_neural(38;0.0423)				GGAGCGCACGATGATTGACCC	0.572													A|||	3	0.000599042	0.0	0.0014	5008	,	,		18925	0.0		0.002	False		,,,				2504	0.0				p.M108V		Atlas-SNP	.											.	PARVB	44	.	0			c.A322G						PASS	.	A	VAL/MET,VAL/MET	4,4402	8.1+/-20.4	0,4,2199	123.0	100.0	108.0		322,223	3.5	0.9	22	dbSNP_129	108	35,8565	23.4+/-69.3	0,35,4265	yes	missense,missense	PARVB	NM_001003828.2,NM_013327.4	21,21	0,39,6464	GG,GA,AA		0.407,0.0908,0.2999	benign,benign	108/398,75/365	44495953	39,12967	2203	4300	6503	SO:0001583	missense	29780	exon4			CGCACGATGATTG	AF151814	CCDS14056.1, CCDS46724.1, CCDS58808.1, CCDS74874.1	22q13.2-q13.33	2013-01-24			ENSG00000188677	ENSG00000188677		"""Parvins"""	14653	protein-coding gene	gene with protein product	"""affixin"""	608121				10810093, 11171322	Standard	NM_001003828		Approved	CGI-56	uc003ben.3	Q9HBI1	OTTHUMG00000150665	ENST00000338758.7:c.223A>G	22.37:g.44495953A>G	ENSP00000342492:p.Met75Val	78.0	0.0	0		97.0	48.0	0.494845	NM_001003828	B0QYM8|B0QYN1|B2R9X6|Q5TGJ5|Q86X93|Q96PN1|Q9NSP7|Q9UGT3|Q9Y368|Q9Y3L6|Q9Y3L7	Missense_Mutation	SNP	ENST00000338758.7	37	CCDS14056.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	A	12.33	1.905546	0.33628	9.08E-4	0.00407	ENSG00000188677	ENST00000406477;ENST00000338758;ENST00000402876;ENST00000444029;ENST00000404989	T;T;T;T;T	0.34275	1.37;1.37;1.37;1.37;1.37	4.5	3.45	0.39498	Calponin homology domain (1);	0.131379	0.64402	N	0.000001	T	0.31513	0.0799	L	0.52905	1.665	0.47511	D	0.999442	B;B;B;B	0.16166	0.005;0.001;0.003;0.016	B;B;B;B	0.23018	0.006;0.005;0.008;0.043	T	0.07908	-1.0748	10	0.40728	T	0.16	-2.8779	7.5657	0.27876	0.8909:0.0:0.1091:0.0	rs56194750	75;38;75;108	A6NG58;B0QYM8;Q9HBI1;Q9HBI1-2	.;.;PARVB_HUMAN;.	V	108;75;75;73;38	ENSP00000384515:M108V;ENSP00000342492:M75V;ENSP00000385331:M75V;ENSP00000393758:M73V;ENSP00000384353:M38V	ENSP00000342492:M75V	M	+	1	0	PARVB	42827286	1.000000	0.71417	0.919000	0.36401	0.989000	0.77384	4.938000	0.63519	0.585000	0.29608	0.460000	0.39030	ATG	A|0.997;G|0.003	0.003	strong		0.572	PARVB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319518.2	NM_001003828	
DNAH3	55567	hgsc.bcm.edu	37	16	21042391	21042391	+	Silent	SNP	G	G	A	rs114086288	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:21042391G>A	ENST00000261383.3	-	37	5414	c.5415C>T	c.(5413-5415)aaC>aaT	p.N1805N	DNAH3_ENST00000415178.1_Silent_p.N1805N	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	1805	AAA 2. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		CCAGAACAGTGTTCATATTTT	0.378													G|||	55	0.0109824	0.0401	0.0014	5008	,	,		20518	0.0		0.001	False		,,,				2504	0.0				p.N1805N		Atlas-SNP	.											.	DNAH3	1142	.	0			c.C5415T						PASS	.	G		133,4269	96.7+/-135.4	3,127,2071	103.0	96.0	98.0		5415	4.7	1.0	16	dbSNP_132	98	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DNAH3	NM_017539.1		3,128,6370	AA,AG,GG		0.0116,3.0214,1.0306		1805/4117	21042391	134,12868	2201	4300	6501	SO:0001819	synonymous_variant	55567	exon37			AACAGTGTTCATA	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.5415C>T	16.37:g.21042391G>A		114.0	0.0	0		103.0	55.0	0.533981	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Silent	SNP	ENST00000261383.3	37	CCDS10594.1																																																																																			G|0.989;A|0.011	0.011	strong		0.378	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
APOBEC3A	200315	hgsc.bcm.edu	37	22	39357634	39357634	+	Silent	SNP	A	A	G	rs2294363		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:39357634A>G	ENST00000402255.1	+	4	621	c.417A>G	c.(415-417)gcA>gcG	p.A139A	APOBEC3A_ENST00000249116.2_Silent_p.A139A			P31941	ABC3A_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3A	139					cellular response to xenobiotic stimulus (GO:0071466)|clearance of foreign intracellular DNA by conversion of DNA cytidine to uridine (GO:0044356)|cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|DNA demethylation (GO:0080111)|innate immune response (GO:0045087)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cytidine deaminase activity (GO:0004126)|deoxycytidine deaminase activity (GO:0047844)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(2)|ovary(1)|skin(1)	5	Melanoma(58;0.04)					ATAAGGAGGCACTGCAAATGC	0.577																																					p.A139A		Atlas-SNP	.											.	APOBEC3A	20	.	0			c.A417G						PASS	.						38.0	49.0	46.0					22																	39357634		1812	3940	5752	SO:0001819	synonymous_variant	200315	exon3			GGAGGCACTGCAA	U03891	CCDS13981.1	22q13.1-q13.2	2014-01-28			ENSG00000128383	ENSG00000128383		"""Apolipoprotein B mRNA editing enzymes"""	17343	protein-coding gene	gene with protein product	"""phorbolin I"""	607109				11863358, 10469298	Standard	NM_145699		Approved	ARP3, PHRBN		P31941	OTTHUMG00000151004	ENST00000402255.1:c.417A>G	22.37:g.39357634A>G		51.0	0.0	0		45.0	45.0	1	NM_145699	A0AVM1|Q12807|Q5JZ93|Q9UH18	Silent	SNP	ENST00000402255.1	37	CCDS13981.1																																																																																			A|0.167;G|0.833	0.833	weak		0.577	APOBEC3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320915.2	NM_145699	
PRR30	339779	hgsc.bcm.edu	37	2	27361049	27361049	+	Missense_Mutation	SNP	G	G	C	rs61739485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27361049G>C	ENST00000335524.3	-	3	674	c.149C>G	c.(148-150)cCg>cGg	p.P50R		NM_178553.3	NP_848648.2	Q53SZ7	PRR30_HUMAN		50	Pro-rich.									cervix(1)|endometrium(2)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	20	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGAAGAGAACGGTGGTTGAGA	0.592													G|||	118	0.0235623	0.0817	0.0115	5008	,	,		18470	0.0		0.002	False		,,,				2504	0.0				p.P50R		Atlas-SNP	.											.	C2orf53	45	.	0			c.C149G						PASS	.	G	ARG/PRO	269,4137	150.3+/-184.3	10,249,1944	99.0	90.0	93.0		149	0.8	0.0	2	dbSNP_129	93	3,8597	3.0+/-9.4	0,3,4297	yes	missense	C2orf53	NM_178553.3	103	10,252,6241	CC,CG,GG		0.0349,6.1053,2.0913	benign	50/413	27361049	272,12734	2203	4300	6503	SO:0001583	missense	339779	exon3			GAGAACGGTGGTT																												ENST00000335524.3:c.149C>G	2.37:g.27361049G>C	ENSP00000335017:p.Pro50Arg	144.0	0.0	0		144.0	50.0	0.347222	NM_178553	Q86UE2	Missense_Mutation	SNP	ENST00000335524.3	37	CCDS1739.1	29	0.013278388278388278	26	0.052845528455284556	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	8.058	0.767521	0.15983	0.061053	3.49E-4	ENSG00000186143	ENST00000335524	T	0.48522	0.81	3.88	0.835	0.18886	.	.	.	.	.	T	0.04227	0.0117	L	0.27053	0.805	0.09310	N	1	B	0.14438	0.01	B	0.12837	0.008	T	0.09015	-1.0694	9	0.56958	D	0.05	-0.0394	8.7685	0.34717	0.0:0.256:0.5932:0.1508	rs61739485	50	Q53SZ7	CB053_HUMAN	R	50	ENSP00000335017:P50R	ENSP00000335017:P50R	P	-	2	0	C2orf53	27214553	0.014000	0.17966	0.000000	0.03702	0.002000	0.02628	1.283000	0.33237	-0.082000	0.12640	0.561000	0.74099	CCG	G|0.972;C|0.028	0.028	strong		0.592	C2orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250188.1		
PIEZO1	9780	hgsc.bcm.edu	37	16	88793156	88793156	+	Silent	SNP	G	G	A	rs376432833	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88793156G>A	ENST00000301015.9	-	25	3912	c.3666C>T	c.(3664-3666)aaC>aaT	p.N1222N		NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	1222					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1)	10						TGACGGTGACGTTGTACAGAA	0.682													G|||	2	0.000399361	0.0015	0.0	5008	,	,		13543	0.0		0.0	False		,,,				2504	0.0				p.N1222N		Atlas-SNP	.											.	PIEZO1	79	.	0			c.C3666T						PASS	.						46.0	44.0	45.0					16																	88793156		692	1589	2281	SO:0001819	synonymous_variant	9780	exon25			GGTGACGTTGTAC	D87071	CCDS54058.1	16q24.3	2011-08-31	2011-08-31	2011-08-31	ENSG00000103335	ENSG00000103335			28993	protein-coding gene	gene with protein product		611184	"""family with sequence similarity 38, member A"""	FAM38A		20813920, 21056836, 21299953, 21696149	Standard	NM_001142864		Approved	KIAA0233	uc010vpb.2	Q92508	OTTHUMG00000156776	ENST00000301015.9:c.3666C>T	16.37:g.88793156G>A		51.0	0.0	0		56.0	22.0	0.392857	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Silent	SNP	ENST00000301015.9	37	CCDS54058.1	.	.	.	.	.	.	.	.	.	.	G	9.795	1.178913	0.21787	.	.	ENSG00000103335	ENST00000451779	.	.	.	4.51	-4.22	0.03800	.	.	.	.	.	T	0.49440	0.1557	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45026	-0.9289	4	.	.	.	-35.03	6.9812	0.24704	0.4239:0.1109:0.4652:0.0	.	.	.	.	C	1168	.	.	R	-	1	0	FAM38A	87320657	0.145000	0.22656	0.883000	0.34634	0.954000	0.61252	-0.542000	0.06091	-1.093000	0.03058	-0.424000	0.05967	CGT	.	.	weak		0.682	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
CFH	3075	hgsc.bcm.edu	37	1	196706659	196706659	+	Missense_Mutation	SNP	C	C	A	rs114743644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:196706659C>A	ENST00000367429.4	+	17	2891	c.2651C>A	c.(2650-2652)tCc>tAc	p.S884Y		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	884	Sushi 15. {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						ATTAATTCATCCAGGTCTTCA	0.338													C|||	4	0.000798722	0.0023	0.0014	5008	,	,		13290	0.0		0.0	False		,,,				2504	0.0				p.S884Y		Atlas-SNP	.											.	CFH	251	.	0			c.C2651A						PASS	.	C	TYR/SER	13,4393		0,13,2190	72.0	68.0	70.0		2651	3.6	0.0	1	dbSNP_133	70	0,8600		0,0,4300	yes	missense	CFH	NM_000186.3	144	0,13,6490	AA,AC,CC		0.0,0.2951,0.1	probably-damaging	884/1232	196706659	13,12993	2203	4300	6503	SO:0001583	missense	3075	exon17			ATTCATCCAGGTC	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.2651C>A	1.37:g.196706659C>A	ENSP00000356399:p.Ser884Tyr	103.0	0.0	0		92.0	46.0	0.5	NM_000186	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Missense_Mutation	SNP	ENST00000367429.4	37	CCDS1385.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	.	13.20	2.165002	0.38217	0.002951	0.0	ENSG00000000971	ENST00000367429	T	0.64438	-0.1	5.52	3.61	0.41365	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.50837	0.1639	M	0.67625	2.065	0.09310	N	0.999999	P	0.39250	0.665	B	0.35727	0.209	T	0.42032	-0.9475	9	0.07482	T	0.82	.	6.1966	0.20553	0.1744:0.6935:0.0:0.1321	.	884	P08603	CFAH_HUMAN	Y	884	ENSP00000356399:S884Y	ENSP00000356399:S884Y	S	+	2	0	CFH	194973282	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	0.262000	0.18460	1.455000	0.47813	0.650000	0.86243	TCC	C|0.999;A|0.001	0.001	strong		0.338	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2	NM_000186	
KCNH1	3756	hgsc.bcm.edu	37	1	210857145	210857145	+	Silent	SNP	C	C	T	rs112047226	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:210857145C>T	ENST00000271751.4	-	11	2475	c.2448G>A	c.(2446-2448)gcG>gcA	p.A816A	KCNH1_ENST00000367007.4_Silent_p.A789A			O95259	KCNH1_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 1	816					myoblast fusion (GO:0007520)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|phosphorelay sensor kinase activity (GO:0000155)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(13)|lung(35)|ovary(4)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	68				OV - Ovarian serous cystadenocarcinoma(81;0.0109)|all cancers(67;0.141)|Epithelial(68;0.185)		CGGACCCTGGCGCCTGTAGCT	0.662													C|||	50	0.00998403	0.034	0.0072	5008	,	,		16634	0.0		0.0	False		,,,				2504	0.0				p.A816A		Atlas-SNP	.											KCNH1,colon,carcinoma,-1,1	KCNH1	199	1	0			c.G2448A						PASS	.	C	,	127,4279	89.7+/-128.4	3,121,2079	44.0	50.0	48.0		2367,2448	-9.5	0.0	1	dbSNP_132	48	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	KCNH1	NM_002238.3,NM_172362.2	,	3,121,6379	TT,TC,CC		0.0,2.8824,0.9765	,	789/963,816/990	210857145	127,12879	2203	4300	6503	SO:0001819	synonymous_variant	3756	exon11			CCCTGGCGCCTGT	AJ001366	CCDS1496.1, CCDS31015.1	1q32.2	2012-07-05			ENSG00000143473	ENSG00000143473		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6250	protein-coding gene	gene with protein product		603305				9738473, 16382104	Standard	NM_172362		Approved	Kv10.1, eag, h-eag, eag1	uc001hib.2	O95259	OTTHUMG00000036309	ENST00000271751.4:c.2448G>A	1.37:g.210857145C>T		56.0	0.0	0		74.0	32.0	0.432432	NM_172362	B1AQ26|O76035|Q14CL3	Silent	SNP	ENST00000271751.4	37	CCDS1496.1																																																																																			C|0.987;T|0.013	0.013	strong		0.662	KCNH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088332.1	NM_002238	
ZNF80	7634	hgsc.bcm.edu	37	3	113955890	113955890	+	Missense_Mutation	SNP	C	C	T	rs112412956	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:113955890C>T	ENST00000482457.2	-	1	535	c.32G>A	c.(31-33)gGt>gAt	p.G11D	RP11-553L6.2_ENST00000481773.1_RNA|RP11-553L6.2_ENST00000493033.1_RNA	NM_007136.3	NP_009067.2	P51504	ZNF80_HUMAN	zinc finger protein 80	11					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)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|urinary_tract(2)	32		Lung NSC(201;0.0233)|all_neural(597;0.0837)				CAGACCATCACCTGTCCCCAA	0.522													c|||	73	0.0145767	0.053	0.0043	5008	,	,		21555	0.0		0.0	False		,,,				2504	0.0				p.G11D	GBM(23;986 1114 21716)	Atlas-SNP	.											.	ZNF80	75	.	0			c.G32A						PASS	.	T	ASP/GLY	188,4218	120.8+/-158.4	5,178,2020	111.0	111.0	111.0		32	-0.9	0.0	3	dbSNP_132	111	0,8600		0,0,4300	yes	missense	ZNF80	NM_007136.3	94	5,178,6320	TT,TC,CC		0.0,4.2669,1.4455	benign	11/274	113955890	188,12818	2203	4300	6503	SO:0001583	missense	7634	exon1			CCATCACCTGTCC	X65233	CCDS2979.1	3q13.31	2013-01-08	2006-05-12		ENSG00000174255	ENSG00000174255		"""Zinc fingers, C2H2-type"""	13155	protein-coding gene	gene with protein product		194553	"""zinc finger protein 80 (pT17)"""			8478004	Standard	NM_007136		Approved	pT17	uc010hqo.3	P51504	OTTHUMG00000159332	ENST00000482457.2:c.32G>A	3.37:g.113955890C>T	ENSP00000417192:p.Gly11Asp	131.0	0.0	0		153.0	78.0	0.509804	NM_007136	Q6NSW4|Q6NT14	Missense_Mutation	SNP	ENST00000482457.2	37	CCDS2979.1	28	0.01282051282051282	26	0.052845528455284556	2	0.0055248618784530384	0	0.0	0	0.0	c	0.052	-1.246531	0.01481	0.042669	0.0	ENSG00000174255	ENST00000482457	T	0.20463	2.07	2.88	-0.868	0.10652	.	.	.	.	.	T	0.01254	0.0041	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.29119	-1.0022	9	0.87932	D	0	.	3.3265	0.07068	0.1783:0.2377:0.0:0.5841	.	11	P51504	ZNF80_HUMAN	D	11	ENSP00000417192:G11D	ENSP00000309812:G11D	G	-	2	0	ZNF80	115438580	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.250000	0.02885	-0.172000	0.10779	-2.079000	0.00380	GGT	C|0.987;T|0.013	0.013	strong		0.522	ZNF80-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354696.2	NM_007136	
CSMD3	114788	hgsc.bcm.edu	37	8	113275878	113275878	+	Silent	SNP	C	C	T	rs16883323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:113275878C>T	ENST00000297405.5	-	61	10096	c.9852G>A	c.(9850-9852)ccG>ccA	p.P3284P	CSMD3_ENST00000455883.2_Silent_p.P3115P|CSMD3_ENST00000343508.3_Silent_p.P3244P|CSMD3_ENST00000352409.3_Silent_p.P3214P	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	3284	Sushi 25. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						GTAAGCACTGCGGTACTTCAC	0.398										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			C|||	180	0.0359425	0.1324	0.0072	5008	,	,		16096	0.0		0.0	False		,,,				2504	0.0				p.P3284P		Atlas-SNP	.											CSMD3_ENST00000343508,caecum,carcinoma,0,4	CSMD3	2325	4	0			c.G9852A						PASS	.	C	,,	438,3968	208.8+/-229.8	21,396,1786	86.0	72.0	77.0		9345,9852,9732	-2.2	1.0	8	dbSNP_123	77	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	,,	21,401,6081	TT,TC,CC		0.0581,9.941,3.4061	,,	3115/3539,3284/3708,3244/3668	113275878	443,12563	2203	4300	6503	SO:0001819	synonymous_variant	114788	exon61			GCACTGCGGTACT	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.9852G>A	8.37:g.113275878C>T		65.0	0.0	0		70.0	36.0	0.514286	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																			C|0.969;T|0.031	0.031	strong		0.398	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
KIF9	64147	hgsc.bcm.edu	37	3	47286320	47286320	+	Missense_Mutation	SNP	T	T	C	rs115610071	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:47286320T>C	ENST00000265529.3	-	16	2155	c.1475A>G	c.(1474-1476)aAg>aGg	p.K492R	KIF9_ENST00000452770.2_Missense_Mutation_p.K492R|KIF9_ENST00000335044.2_Missense_Mutation_p.K492R|KIF9-AS1_ENST00000429315.3_RNA|KIF9_ENST00000487440.1_5'UTR|KIF9_ENST00000352910.4_Missense_Mutation_p.K399R|KIF9_ENST00000444589.2_Missense_Mutation_p.K492R			Q9HAQ2	KIF9_HUMAN	kinesin family member 9	492					ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|extracellular matrix disassembly (GO:0022617)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|organelle disassembly (GO:1903008)|regulation of podosome assembly (GO:0071801)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|podosome (GO:0002102)|vesicle (GO:0031982)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|protein dimerization activity (GO:0046983)			central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(15)|skin(4)|stomach(2)|upper_aerodigestive_tract(2)	34		Acute lymphoblastic leukemia(5;0.164)		BRCA - Breast invasive adenocarcinoma(193;0.000284)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		CTTGGCTTTCTTCCCAGGTTT	0.567													T|||	19	0.00379393	0.0	0.0086	5008	,	,		19521	0.001		0.008	False		,,,				2504	0.0041				p.K492R	Colon(44;962 1147 15977 24541)	Atlas-SNP	.											.	KIF9	59	.	0			c.A1475G						PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS	7,4399	12.9+/-30.5	0,7,2196	177.0	149.0	158.0		1475,1475,1475	4.7	1.0	3	dbSNP_132	158	103,8497	56.4+/-117.6	2,99,4199	yes	missense,missense,missense	KIF9	NM_001134878.1,NM_022342.4,NM_182902.3	26,26,26	2,106,6395	CC,CT,TT		1.1977,0.1589,0.8458	benign,benign,benign	492/791,492/726,492/791	47286320	110,12896	2203	4300	6503	SO:0001583	missense	64147	exon15			GCTTTCTTCCCAG	AF311212	CCDS2751.1, CCDS2752.1	3p21.31	2008-03-03			ENSG00000088727	ENSG00000088727		"""Kinesins"""	16666	protein-coding gene	gene with protein product		607910				11483511	Standard	NM_022342		Approved	MGC104186	uc003cqx.3	Q9HAQ2	OTTHUMG00000133512	ENST00000265529.3:c.1475A>G	3.37:g.47286320T>C	ENSP00000265529:p.Lys492Arg	216.0	0.0	0		175.0	84.0	0.48	NM_182902	Q86Z28|Q9H8A4	Missense_Mutation	SNP	ENST00000265529.3	37	CCDS2752.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	T	8.708	0.911321	0.17833	0.001589	0.011977	ENSG00000088727	ENST00000335044;ENST00000265529;ENST00000444589;ENST00000452770;ENST00000352910	T;T;T;T;T	0.51574	0.7;0.7;0.7;0.7;0.7	4.65	4.65	0.58169	.	0.263417	0.32372	N	0.006192	T	0.19208	0.0461	N	0.16478	0.41	0.24963	N	0.991717	P;B	0.38020	0.615;0.373	B;B	0.34779	0.189;0.051	T	0.07849	-1.0751	10	0.23302	T	0.38	.	7.0449	0.25040	0.0:0.0998:0.0:0.9002	.	492;492	Q9HAQ2-2;Q9HAQ2	.;KIF9_HUMAN	R	492;492;492;492;399	ENSP00000333942:K492R;ENSP00000265529:K492R;ENSP00000414987:K492R;ENSP00000391100:K492R;ENSP00000292334:K399R	ENSP00000265529:K492R	K	-	2	0	KIF9	47261324	1.000000	0.71417	1.000000	0.80357	0.030000	0.12068	2.914000	0.48797	2.095000	0.63458	0.528000	0.53228	AAG	T|0.992;C|0.008	0.008	strong		0.567	KIF9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257475.2		
THAP4	51078	hgsc.bcm.edu	37	2	242572693	242572693	+	Silent	SNP	C	C	T	rs147500721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242572693C>T	ENST00000407315.1	-	2	1310	c.879G>A	c.(877-879)ccG>ccA	p.P293P		NM_015963.5	NP_057047.4	Q8WY91	THAP4_HUMAN	THAP domain containing 4	293							DNA binding (GO:0003677)|metal ion binding (GO:0046872)			kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)	9		all_cancers(19;2.09e-34)|all_epithelial(40;2.09e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Ovarian(221;0.069)|Lung NSC(271;0.0886)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.2)		Epithelial(32;2.3e-33)|all cancers(36;8.99e-31)|OV - Ovarian serous cystadenocarcinoma(60;3.68e-15)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;1.65e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00154)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0844)		AAGGCTTCTGCGGTGTCGCGG	0.657													C|||	46	0.0091853	0.0325	0.0029	5008	,	,		15917	0.0		0.001	False		,,,				2504	0.0				p.P293P		Atlas-SNP	.											.	THAP4	27	.	0			c.G879A						PASS	.	C		190,4216	121.7+/-159.2	5,180,2018	74.0	80.0	78.0		879	-11.0	0.2	2	dbSNP_134	78	0,8592		0,0,4296	no	coding-synonymous	THAP4	NM_015963.5		5,180,6314	TT,TC,CC		0.0,4.3123,1.4618		293/578	242572693	190,12808	2203	4296	6499	SO:0001819	synonymous_variant	51078	exon2			CTTCTGCGGTGTC	AF258556	CCDS2551.1, CCDS54440.1	2q37.3	2013-01-25			ENSG00000176946	ENSG00000176946		"""THAP (C2CH-type zinc finger) domain containing"""	23187	protein-coding gene	gene with protein product		612533				12575992, 10810093	Standard	NM_015963		Approved	CGI-36	uc002wbt.3	Q8WY91	OTTHUMG00000133410	ENST00000407315.1:c.879G>A	2.37:g.242572693C>T		69.0	0.0	0		76.0	44.0	0.578947	NM_015963	Q53NU7|Q6GRN0|Q6IPJ3|Q9NW26|Q9Y325	Silent	SNP	ENST00000407315.1	37	CCDS2551.1																																																																																			C|0.985;T|0.015	0.015	strong		0.657	THAP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257267.3	NM_015963	
SPPL2A	84888	hgsc.bcm.edu	37	15	51023216	51023216	+	Silent	SNP	G	G	C	rs76947817	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:51023216G>C	ENST00000261854.5	-	10	1309	c.1035C>G	c.(1033-1035)ggC>ggG	p.G345G		NM_032802.3	NP_116191.2	Q8TCT8	SPP2A_HUMAN	signal peptide peptidase like 2A	345					membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|regulation of immune response (GO:0050776)	extracellular vesicular exosome (GO:0070062)|Golgi-associated vesicle membrane (GO:0030660)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15				all cancers(107;0.000712)|GBM - Glioblastoma multiforme(94;0.00314)		GGAGGAGAAGGCCTAGAAGTA	0.313													G|||	86	0.0171725	0.0635	0.0029	5008	,	,		15019	0.0		0.0	False		,,,				2504	0.0				p.G345G	Melanoma(50;790 1209 4069 22965 33125)	Atlas-SNP	.											.	SPPL2A	26	.	0			c.C1035G						PASS	.	G		240,4152	134.5+/-170.7	6,228,1962	64.0	60.0	61.0		1035	1.6	1.0	15	dbSNP_131	61	1,8575	1.2+/-3.3	0,1,4287	no	coding-synonymous	SPPL2A	NM_032802.3		6,229,6249	CC,CG,GG		0.0117,5.4645,1.8584		345/521	51023216	241,12727	2196	4288	6484	SO:0001819	synonymous_variant	84888	exon10			GAGAAGGCCTAGA		CCDS10138.1	15q21.2	2012-02-21			ENSG00000138600	ENSG00000138600			30227	protein-coding gene	gene with protein product	"""intramembrane protease 3"", ""presenilin-like protein 2"""	608238				12077416, 12139484	Standard	NM_032802		Approved	IMP3, PSL2	uc001zyv.3	Q8TCT8	OTTHUMG00000131647	ENST00000261854.5:c.1035C>G	15.37:g.51023216G>C		220.0	0.0	0		214.0	104.0	0.485981	NM_032802	B2RDS0|Q8TAW1|Q96SZ8	Silent	SNP	ENST00000261854.5	37	CCDS10138.1																																																																																			G|0.977;C|0.023	0.023	strong		0.313	SPPL2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254543.3	NM_032802	
SENP6	26054	hgsc.bcm.edu	37	6	76373002	76373002	+	Silent	SNP	G	G	A	rs16886792	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:76373002G>A	ENST00000447266.2	+	9	1240	c.762G>A	c.(760-762)acG>acA	p.T254T	SENP6_ENST00000370014.3_Silent_p.T254T|SENP6_ENST00000327284.8_Silent_p.T247T|SENP6_ENST00000370010.2_Silent_p.T247T	NM_015571.2	NP_056386.2	Q9GZR1	SENP6_HUMAN	SUMO1/sentrin specific peptidase 6	254					protein desumoylation (GO:0016926)|protein modification by small protein removal (GO:0070646)|protein sumoylation (GO:0016925)|regulation of kinetochore assembly (GO:0090234)|regulation of spindle assembly (GO:0090169)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	SUMO-specific protease activity (GO:0016929)			breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(2)|lung(12)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_hematologic(105;0.189)				TATTAAGAACGTCAATTCATC	0.353													G|||	71	0.0141773	0.053	0.0014	5008	,	,		17025	0.0		0.0	False		,,,				2504	0.0				p.T254T		Atlas-SNP	.											.	SENP6	189	.	0			c.G762A						PASS	.	G	,	190,3488		6,178,1655	108.0	102.0	104.0		741,762	-6.3	1.0	6	dbSNP_123	104	2,8180		0,2,4089	no	coding-synonymous,coding-synonymous	SENP6	NM_001100409.1,NM_015571.2	,	6,180,5744	AA,AG,GG		0.0244,5.1659,1.6189	,	247/1106,254/1113	76373002	192,11668	1839	4091	5930	SO:0001819	synonymous_variant	26054	exon9			AAGAACGTCAATT		CCDS43483.1, CCDS47454.1	6q13-q14.3	2008-02-05	2005-08-17		ENSG00000112701	ENSG00000112701			20944	protein-coding gene	gene with protein product		605003	"""SUMO1/sentrin specific protease 6"""				Standard	NM_015571		Approved	SUSP1, KIAA0797	uc003pid.4	Q9GZR1	OTTHUMG00000015060	ENST00000447266.2:c.762G>A	6.37:g.76373002G>A		88.0	0.0	0		114.0	57.0	0.5	NM_015571	A6NNY9|O94891|Q5VUL3|Q5VUL4|Q8TBY4|Q9UJV5	Silent	SNP	ENST00000447266.2	37	CCDS47454.1																																																																																			G|0.985;A|0.015	0.015	strong		0.353	SENP6-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041272.2	NM_015571	
ABCB9	23457	hgsc.bcm.edu	37	12	123466304	123466304	+	5'Flank	SNP	A	A	G	rs74758272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:123466304A>G	ENST00000542678.1	-	0	0				RP11-197N18.2_ENST00000540866.2_RNA|ARL6IP4_ENST00000412505.2_Missense_Mutation_p.K97R|ARL6IP4_ENST00000315580.5_Missense_Mutation_p.K239R|ARL6IP4_ENST00000454885.2_Missense_Mutation_p.K105R|ARL6IP4_ENST00000357866.4_Missense_Mutation_p.K108R|ARL6IP4_ENST00000543566.1_Missense_Mutation_p.K220R|ARL6IP4_ENST00000439686.2_Missense_Mutation_p.K108R|ARL6IP4_ENST00000426960.2_Missense_Mutation_p.K97R|ARL6IP4_ENST00000453766.2_Missense_Mutation_p.K231R|ARL6IP4_ENST00000392435.2_Missense_Mutation_p.K220R			Q9NP78	ABCB9_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 9						peptide transport (GO:0015833)|protein transport (GO:0015031)|transmembrane transport (GO:0055085)	integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)	ATP binding (GO:0005524)|peptide-transporting ATPase activity (GO:0015440)|protein homodimerization activity (GO:0042803)|substrate-specific transmembrane transporter activity (GO:0022891)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(1)	18	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;6.84e-05)|Epithelial(86;0.000152)|BRCA - Breast invasive adenocarcinoma(302;0.111)		aagaagaagaagaagaggaag	0.577													A|||	546	0.109026	0.3941	0.0346	5008	,	,		19865	0.0		0.001	False		,,,				2504	0.0				p.K239R	Ovarian(49;786 1333 9175 38236)	Atlas-SNP	.											.	ARL6IP4	14	.	0			c.A716G						PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	1308,3046		202,904,1071	26.0	27.0	27.0		692,659,659,716	2.6	1.0	12	dbSNP_131	27	23,8529		0,23,4253	yes	missense,missense,missense,missense	ARL6IP4	NM_001002251.1,NM_001002252.1,NM_016638.2,NM_018694.2	26,26,26,26	202,927,5324	GG,GA,AA		0.2689,30.0413,10.313	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	231/353,220/339,220/342,239/361	123466304	1331,11575	2177	4276	6453	SO:0001631	upstream_gene_variant	51329	exon3			AGAAGAAGAAGAG	U66676	CCDS9241.1, CCDS58286.1, CCDS58287.1, CCDS58288.1	12q24	2012-03-14			ENSG00000150967	ENSG00000150967		"""ATP binding cassette transporters / subfamily B"""	50	protein-coding gene	gene with protein product		605453				8894702	Standard	NM_019625		Approved	EST122234	uc001udm.4	Q9NP78			12.37:g.123466304A>G	Exception_encountered	72.0	0.0	0		75.0	36.0	0.48	NM_018694	B4E2J0|Q5W9G7|Q769F3|Q769F4|Q96AB1|Q9P208	Missense_Mutation	SNP	ENST00000542678.1	37	CCDS9241.1	193	0.08836996336996338	184	0.37398373983739835	9	0.024861878453038673	0	0.0	0	0.0	A	12.68	2.010868	0.35511	0.300413	0.002689	ENSG00000182196	ENST00000544323;ENST00000543566;ENST00000315580;ENST00000542099;ENST00000392435;ENST00000413381;ENST00000426960;ENST00000453766;ENST00000454885;ENST00000412505;ENST00000439686;ENST00000456762;ENST00000357866	T;T;T;T;T;T;T;T;T;T;T;T;T	0.53857	1.22;0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.6;0.69;0.6;0.6;0.69	4.96	2.59	0.31030	.	0.666484	0.15025	N	0.284816	T	0.00012	0.0000	L	0.56769	1.78	0.28457	P	0.9160855999999999	B;B;P;P;P;P	0.39326	0.026;0.021;0.617;0.668;0.467;0.617	B;B;B;B;B;B	0.40444	0.027;0.016;0.221;0.329;0.167;0.221	T	0.34850	-0.9812	9	0.27785	T	0.31	.	4.0754	0.09901	0.6128:0.0:0.2434:0.1437	.	105;231;220;220;239;231	B3V0L1;Q66PJ3-5;Q66PJ3-4;B3V0L0;Q66PJ3;Q66PJ3-2	.;.;.;.;AR6P4_HUMAN;.	R	220;220;239;228;220;108;97;231;105;97;108;98;108	ENSP00000445309:K220R;ENSP00000442718:K220R;ENSP00000313422:K239R;ENSP00000442200:K228R;ENSP00000376230:K220R;ENSP00000441406:K108R;ENSP00000406036:K97R;ENSP00000414847:K231R;ENSP00000396723:K105R;ENSP00000413132:K97R;ENSP00000396365:K108R;ENSP00000391598:K98R;ENSP00000350532:K108R	ENSP00000313422:K239R	K	+	2	0	ARL6IP4	122032257	1.000000	0.71417	0.994000	0.49952	0.062000	0.15995	1.400000	0.34577	0.336000	0.23639	0.397000	0.26171	AAG	A|0.880;G|0.120	0.120	strong		0.577	ABCB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400956.1	NM_019624	
PREPL	9581	hgsc.bcm.edu	37	2	44571008	44571008	+	Silent	SNP	A	A	T	rs72875319	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:44571008A>T	ENST00000409936.1	-	5	929	c.492T>A	c.(490-492)gcT>gcA	p.A164A	PREPL_ENST00000260648.6_Silent_p.A164A|PREPL_ENST00000409957.1_Silent_p.A75A|PREPL_ENST00000409411.1_Silent_p.A75A|PREPL_ENST00000378520.3_Silent_p.A164A|PREPL_ENST00000378511.3_Silent_p.A164A|PREPL_ENST00000541738.1_Silent_p.A75A|PREPL_ENST00000409272.1_Silent_p.A164A|PREPL_ENST00000540817.1_5'UTR|PREPL_ENST00000410081.1_Silent_p.A164A	NM_001171606.1	NP_001165077.1	Q4J6C6	PPCEL_HUMAN	prolyl endopeptidase-like	164						cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)	serine-type endopeptidase activity (GO:0004252)|serine-type exopeptidase activity (GO:0070008)			breast(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(19)|ovary(1)|prostate(1)|skin(2)	33		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)				TTTCATCTGGAGCAACTCTGA	0.363													A|||	190	0.0379393	0.1309	0.0231	5008	,	,		16552	0.0		0.001	False		,,,				2504	0.0				p.A164A		Atlas-SNP	.											.	PREPL	69	.	0			c.T492A						PASS	.	A	,,,,,,	487,3919	228.8+/-243.5	28,431,1744	110.0	113.0	112.0		492,492,492,492,225,225,492	4.5	1.0	2	dbSNP_130	112	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PREPL	NM_001042385.2,NM_001042386.2,NM_001171603.1,NM_001171606.1,NM_001171613.1,NM_001171617.1,NM_006036.4	,,,,,,	28,433,6042	TT,TA,AA		0.0233,11.0531,3.7598	,,,,,,	164/666,164/662,164/728,164/728,75/639,75/639,164/728	44571008	489,12517	2203	4300	6503	SO:0001819	synonymous_variant	9581	exon5			ATCTGGAGCAACT	AB007896	CCDS33190.1, CCDS42675.1, CCDS42676.1, CCDS54353.1	2p22.1	2008-02-05			ENSG00000138078	ENSG00000138078			30228	protein-coding gene	gene with protein product		609557				11524703	Standard	NM_006036		Approved	KIAA0436	uc002ruk.2	Q4J6C6	OTTHUMG00000152791	ENST00000409936.1:c.492T>A	2.37:g.44571008A>T		116.0	0.0	0		114.0	50.0	0.438596	NM_001171603	A7E2X6|D6W5A3|O43163|Q4J6C3|Q4J6C4|Q4ZG39|Q6ZMW7|Q96DW7	Silent	SNP	ENST00000409936.1	37	CCDS33190.1																																																																																			A|0.966;T|0.034	0.034	strong		0.363	PREPL-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327900.1	NM_006036	
DTX2	113878	hgsc.bcm.edu	37	7	76132805	76132805	+	Silent	SNP	C	C	G	rs73703182	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:76132805C>G	ENST00000324432.5	+	10	1962	c.1452C>G	c.(1450-1452)ccC>ccG	p.P484P	DTX2_ENST00000446600.1_Silent_p.P393P|DTX2_ENST00000446820.2_Silent_p.P437P|DTX2_ENST00000430490.2_Silent_p.P484P|DTX2_ENST00000307569.8_Silent_p.P437P|DTX2_ENST00000413936.2_Silent_p.P484P	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	484					Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(1)|skin(1)|stomach(2)	27						GGACCCAGCCCCAGGGAAAGA	0.572													.|||	88	0.0175719	0.0651	0.0029	5008	,	,		18601	0.0		0.0	False		,,,				2504	0.0				p.P484P		Atlas-SNP	.											.	DTX2	64	.	0			c.C1452G						PASS	.	C	,,,	241,4159		11,219,1970	70.0	66.0	67.0		1452,1452,1311,1452	3.0	1.0	7	dbSNP_130	67	2,8592		0,2,4295	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DTX2	NM_001102594.1,NM_001102595.1,NM_001102596.1,NM_020892.2	,,,	11,221,6265	GG,GC,CC		0.0233,5.4773,1.8701	,,,	484/623,484/623,437/576,484/623	76132805	243,12751	2200	4297	6497	SO:0001819	synonymous_variant	113878	exon9			CCAGCCCCAGGGA		CCDS5587.1, CCDS43605.1	7q11.23	2014-01-28	2014-01-28		ENSG00000091073	ENSG00000091073		"""RING-type (C3HC4) zinc fingers"""	15973	protein-coding gene	gene with protein product		613141	"""deltex (Drosophila) homolog 2"", ""deltex homolog 2 (Drosophila)"""			12670957	Standard	NM_020892		Approved	RNF58, KIAA1528	uc003ufh.4	Q86UW9	OTTHUMG00000162594	ENST00000324432.5:c.1452C>G	7.37:g.76132805C>G		183.0	0.0	0		173.0	95.0	0.549133	NM_001102594	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Silent	SNP	ENST00000324432.5	37	CCDS5587.1																																																																																			C|0.977;G|0.023	0.023	strong		0.572	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2		
KANK2	25959	hgsc.bcm.edu	37	19	11289307	11289307	+	Missense_Mutation	SNP	C	C	T	rs149142528	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11289307C>T	ENST00000586659.1	-	5	1653	c.1339G>A	c.(1339-1341)Gtg>Atg	p.V447M	KANK2_ENST00000355150.5_Missense_Mutation_p.V447M|KANK2_ENST00000589894.1_Missense_Mutation_p.V447M|KANK2_ENST00000432929.2_Missense_Mutation_p.V447M|KANK2_ENST00000589359.1_Missense_Mutation_p.V447M			Q63ZY3	KANK2_HUMAN	KN motif and ankyrin repeat domains 2	447					apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				endometrium(2)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						TGGGTGGGCACTCGGCCTGTG	0.672													C|||	79	0.0157748	0.0575	0.0043	5008	,	,		12124	0.0		0.0	False		,,,				2504	0.0				p.V447M		Atlas-SNP	.											.	KANK2	47	.	0			c.G1339A						PASS	.	C	MET/VAL,MET/VAL	197,4209	123.7+/-161.0	4,189,2010	42.0	44.0	43.0		1339,1339	1.1	0.0	19	dbSNP_134	43	4,8596	3.0+/-9.4	0,4,4296	yes	missense,missense	KANK2	NM_001136191.2,NM_015493.6	21,21	4,193,6306	TT,TC,CC		0.0465,4.4712,1.5454	benign,benign	447/852,447/860	11289307	201,12805	2203	4300	6503	SO:0001583	missense	25959	exon3			TGGGCACTCGGCC	AK000011	CCDS12255.1, CCDS54219.1	19p13.2	2013-01-10	2008-01-29	2008-01-29		ENSG00000197256		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	29300	protein-coding gene	gene with protein product		614610	"""matrix-remodelling associated 3"", ""ankyrin repeat domain 25"""	MXRA3, ANKRD25		10819331, 17996375, 19554261	Standard	NM_015493		Approved	KIAA1518	uc002mqm.3	Q63ZY3		ENST00000586659.1:c.1339G>A	19.37:g.11289307C>T	ENSP00000465650:p.Val447Met	66.0	0.0	0		69.0	29.0	0.42029	NM_015493	B0I1P4|Q3KQZ3|Q6GUF5|Q9H8S4|Q9NUP0|Q9P210	Missense_Mutation	SNP	ENST00000586659.1	37	CCDS12255.1	30	0.013736263736263736	26	0.052845528455284556	4	0.011049723756906077	0	0.0	0	0.0	C	9.193	1.026620	0.19512	0.044712	4.65E-4	ENSG00000197256	ENST00000432929;ENST00000355150	T;T	0.37411	1.2;1.2	3.5	1.14	0.20703	.	2.220440	0.02225	N	0.064340	T	0.06050	0.0157	L	0.42245	1.32	0.09310	N	1	B;B	0.28512	0.214;0.001	B;B	0.22753	0.041;0.006	T	0.12142	-1.0559	10	0.46703	T	0.11	-28.0739	7.049	0.25063	0.1975:0.6112:0.1913:0.0	.	447;447	Q63ZY3;Q63ZY3-2	KANK2_HUMAN;.	M	447	ENSP00000395650:V447M;ENSP00000347276:V447M	ENSP00000347276:V447M	V	-	1	0	KANK2	11150307	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.164000	0.09983	0.241000	0.21283	0.467000	0.42956	GTG	C|0.987;T|0.013	0.013	strong		0.672	KANK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453066.2	NM_015493	
ZPBP2	124626	hgsc.bcm.edu	37	17	38027824	38027824	+	Missense_Mutation	SNP	G	G	A	rs35829084	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38027824G>A	ENST00000348931.4	+	4	543	c.352G>A	c.(352-354)Gca>Aca	p.A118T	ZPBP2_ENST00000377940.3_Missense_Mutation_p.A96T|ZPBP2_ENST00000584588.1_Missense_Mutation_p.A118T	NM_199321.2	NP_955353.1	Q6X784	ZPBP2_HUMAN	zona pellucida binding protein 2	118			A -> T (in dbSNP:rs35829084).		acrosome assembly (GO:0001675)|binding of sperm to zona pellucida (GO:0007339)	acrosomal vesicle (GO:0001669)|cell body (GO:0044297)|extracellular region (GO:0005576)|nucleus (GO:0005634)|zona pellucida receptor complex (GO:0002199)				kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	15	Colorectal(19;0.000442)		Lung(15;0.00849)|LUSC - Lung squamous cell carcinoma(15;0.171)			GACTGTTAAAGCAGAAACTCA	0.318													G|||	148	0.0295527	0.1089	0.0058	5008	,	,		16323	0.0		0.0	False		,,,				2504	0.0				p.A118T		Atlas-SNP	.											.	ZPBP2	33	.	0			c.G352A						PASS	.	G	THR/ALA,THR/ALA	382,4024	189.9+/-215.9	25,332,1846	77.0	80.0	79.0		286,352	4.4	1.0	17	dbSNP_126	79	3,8589	2.2+/-6.3	0,3,4293	yes	missense,missense	ZPBP2	NM_198844.2,NM_199321.2	58,58	25,335,6139	AA,AG,GG		0.0349,8.67,2.962	probably-damaging,probably-damaging	96/317,118/339	38027824	385,12613	2203	4296	6499	SO:0001583	missense	124626	exon4			GTTAAAGCAGAAA	BC043152	CCDS11352.1, CCDS11353.2	17q21.1	2013-01-11			ENSG00000186075	ENSG00000186075		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	20678	protein-coding gene	gene with protein product		608499					Standard	XM_005257031		Approved	ZPBPL, MGC41930	uc002hte.3	Q6X784	OTTHUMG00000133022	ENST00000348931.4:c.352G>A	17.37:g.38027824G>A	ENSP00000335384:p.Ala118Thr	186.0	0.0	0		154.0	85.0	0.551948	NM_199321	A8K8L8|Q6X783|Q86XL5	Missense_Mutation	SNP	ENST00000348931.4	37	CCDS11352.1	57	0.0260989010989011	55	0.11178861788617886	2	0.0055248618784530384	0	0.0	0	0.0	G	9.022	0.985096	0.18889	0.0867	3.49E-4	ENSG00000186075	ENST00000348931;ENST00000377940	T;T	0.55760	0.5;0.5	5.36	4.39	0.52855	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.455087	0.21308	N	0.076697	T	0.00784	0.0026	L	0.39898	1.24	0.22226	N	0.999272	B;B	0.26635	0.112;0.155	B;B	0.20955	0.029;0.032	T	0.00904	-1.1520	10	0.27785	T	0.31	-4.4881	6.3234	0.21231	0.2041:0.0:0.7959:0.0	rs35829084	96;118	Q6X784-2;Q6X784	.;ZPBP2_HUMAN	T	118;96	ENSP00000335384:A118T;ENSP00000367174:A96T	ENSP00000335384:A118T	A	+	1	0	ZPBP2	35281350	0.997000	0.39634	0.995000	0.50966	0.248000	0.25809	2.785000	0.47782	2.506000	0.84524	0.460000	0.39030	GCA	G|0.968;A|0.032	0.032	strong		0.318	ZPBP2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256609.2	NM_198844	
SLC27A5	10998	hgsc.bcm.edu	37	19	59023213	59023213	+	Missense_Mutation	SNP	A	A	C	rs146147877	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:59023213A>C	ENST00000263093.2	-	1	219	c.110T>G	c.(109-111)cTg>cGg	p.L37R	SLC27A5_ENST00000601355.1_Missense_Mutation_p.L37R	NM_012254.2	NP_036386.1	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid transporter), member 5	37					bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|ketone body biosynthetic process (GO:0046951)|plasma membrane long-chain fatty acid transport (GO:0015911)|small molecule metabolic process (GO:0044281)|triglyceride mobilization (GO:0006642)|very long-chain fatty acid metabolic process (GO:0000038)	basal plasma membrane (GO:0009925)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|protein complex (GO:0043234)	ATP binding (GO:0005524)|cholate-CoA ligase activity (GO:0047747)|fatty acid transporter activity (GO:0015245)|very long-chain fatty acid-CoA ligase activity (GO:0031957)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|ovary(1)|skin(1)|urinary_tract(1)	19		all_cancers(17;4.4e-22)|all_epithelial(17;2.15e-16)|Lung NSC(17;1.24e-06)|all_lung(17;5.41e-06)|Colorectal(82;3.46e-05)|Renal(17;0.00179)|all_neural(62;0.00607)|Ovarian(87;0.0443)|Breast(46;0.0928)|Medulloblastoma(540;0.184)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)|Lung(386;0.181)		GGGATCCCCCAGGAGCCAGCG	0.687													A|||	24	0.00479233	0.0182	0.0	5008	,	,		17742	0.0		0.0	False		,,,				2504	0.0				p.L37R		Atlas-SNP	.											.	SLC27A5	58	.	0			c.T110G						PASS	.	A	ARG/LEU	53,4285		0,53,2116	8.0	9.0	9.0		110	4.3	1.0	19	dbSNP_134	9	0,8524		0,0,4262	yes	missense	SLC27A5	NM_012254.2	102	0,53,6378	CC,CA,AA		0.0,1.2218,0.4121	probably-damaging	37/691	59023213	53,12809	2169	4262	6431	SO:0001583	missense	10998	exon1			TCCCCCAGGAGCC	AF064255	CCDS12983.1	19q13.43	2013-07-15			ENSG00000083807	ENSG00000083807		"""Acyl-CoA synthetase family"", ""Solute carriers"""	10999	protein-coding gene	gene with protein product	"""fatty-acid-Coenzyme A ligase, very long-chain 3"""	603314				10479480, 10749848	Standard	NM_012254		Approved	FATP5, VLACSR, VLCS-H2, VLCSH2, FACVL3, FLJ22987, ACSVL6, ACSB	uc002qtc.2	Q9Y2P5	OTTHUMG00000183543	ENST00000263093.2:c.110T>G	19.37:g.59023213A>C	ENSP00000263093:p.Leu37Arg	58.0	0.0	0		74.0	37.0	0.5	NM_012254	B3KVP6|B4DPQ1	Missense_Mutation	SNP	ENST00000263093.2	37	CCDS12983.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	a	14.75	2.628307	0.46944	0.012218	0.0	ENSG00000083807	ENST00000263093	T	0.59638	0.25	4.31	4.31	0.51392	.	0.334193	0.17602	N	0.168398	T	0.48241	0.1489	M	0.62723	1.935	0.37946	D	0.932495	D	0.58620	0.983	P	0.53401	0.725	T	0.66368	-0.5941	10	0.87932	D	0	-16.4075	10.4112	0.44294	1.0:0.0:0.0:0.0	.	37	Q9Y2P5	S27A5_HUMAN	R	37	ENSP00000263093:L37R	ENSP00000263093:L37R	L	-	2	0	SLC27A5	63715025	1.000000	0.71417	0.975000	0.42487	0.133000	0.20885	3.179000	0.50887	1.889000	0.54706	0.374000	0.22700	CTG	A|0.995;C|0.005	0.005	strong		0.687	SLC27A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467060.1	NM_012254	
C17orf64	124773	hgsc.bcm.edu	37	17	58506748	58506748	+	Missense_Mutation	SNP	C	C	T	rs57928695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:58506748C>T	ENST00000269127.4	+	5	539	c.455C>T	c.(454-456)cCg>cTg	p.P152L		NM_181707.2	NP_859058.2	Q86WR6	CQ064_HUMAN	chromosome 17 open reading frame 64	152										breast(2)|large_intestine(1)|lung(3)	6	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)		Epithelial(12;5.81e-13)|all cancers(12;2.17e-11)|Colorectal(3;0.01)			TCGGATGCGCCGGAGAGGTCC	0.607													C|||	710	0.141773	0.5068	0.0519	5008	,	,		18332	0.0		0.004	False		,,,				2504	0.0				p.P152L		Atlas-SNP	.											.	C17orf64	19	.	0			c.C455T						PASS	.	C	LEU/PRO	1696,2710	493.1+/-362.6	345,1006,852	34.0	36.0	35.0		455	1.6	0.0	17	dbSNP_129	35	14,8586	9.8+/-36.6	0,14,4286	yes	missense	C17orf64	NM_181707.2	98	345,1020,5138	TT,TC,CC		0.1628,38.493,13.1478	probably-damaging	152/237	58506748	1710,11296	2203	4300	6503	SO:0001583	missense	124773	exon5			ATGCGCCGGAGAG	BC048806	CCDS32698.2	17q23.2	2005-12-16			ENSG00000141371	ENSG00000141371			26990	protein-coding gene	gene with protein product						12477932	Standard	NM_181707		Approved		uc002iyq.3	Q86WR6	OTTHUMG00000157171	ENST00000269127.4:c.455C>T	17.37:g.58506748C>T	ENSP00000269127:p.Pro152Leu	108.0	0.0	0		147.0	75.0	0.510204	NM_181707	Q8IY87	Missense_Mutation	SNP	ENST00000269127.4	37	CCDS32698.2	255	0.11675824175824176	237	0.4817073170731707	15	0.04143646408839779	0	0.0	3	0.00395778364116095	C	9.889	1.203580	0.22121	0.38493	0.001628	ENSG00000141371	ENST00000269127	.	.	.	4.82	1.65	0.23941	.	0.420949	0.20436	N	0.092377	T	0.00012	0.0000	M	0.70595	2.14	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.35201	-0.9798	8	0.51188	T	0.08	-4.574	4.2009	0.10466	0.1819:0.6217:0.0:0.1964	rs57928695;rs61745732	152	Q86WR6	CQ064_HUMAN	L	152	.	ENSP00000269127:P152L	P	+	2	0	C17orf64	55861530	0.000000	0.05858	0.002000	0.10522	0.003000	0.03518	-0.833000	0.04396	0.094000	0.17404	0.561000	0.74099	CCG	C|0.882;T|0.118	0.118	strong		0.607	C17orf64-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000347743.1	NM_181707	
MT-ND5	4540	hgsc.bcm.edu	37	M	13260	13260	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:13260T>C	ENST00000361567.2	+	1	924	c.924T>C	c.(922-924)agT>agC	p.S308S	MT-TR_ENST00000387439.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-TE_ENST00000387459.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	308					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						TCCACTTCAAGTCAACTAGGA	0.443																																					p.S308S		Atlas-SNP	.											.	.	.	.	0			c.T924C						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			TTCAAGTCAACTA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.924T>C	M.37:g.13260T>C		12.0	0.0	0		11.0	11.0	1	ENST00000361567	Q34773|Q8WCY3	Silent	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.443	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
MAST2	23139	hgsc.bcm.edu	37	1	46496368	46496368	+	Silent	SNP	C	C	T	rs376559790		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:46496368C>T	ENST00000361297.2	+	22	2926	c.2643C>T	c.(2641-2643)gaC>gaT	p.D881D	MAST2_ENST00000372009.2_Silent_p.D811D	NM_015112.2	NP_055927.2			microtubule associated serine/threonine kinase 2											breast(1)|lung(3)|ovary(5)|stomach(2)	11	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.184)					AGAAGGAGGACCATTCAGATG	0.642																																					p.D881D		Atlas-SNP	.											.	MAST2	136	.	0			c.C2643T						PASS	.						21.0	24.0	23.0					1																	46496368		2045	4187	6232	SO:0001819	synonymous_variant	23139	exon22			GGAGGACCATTCA	AB047005	CCDS41326.1	1p34.1	2008-02-05			ENSG00000086015	ENSG00000086015			19035	protein-coding gene	gene with protein product		612257					Standard	NM_015112		Approved	MAST205, KIAA0807	uc001cov.3	Q6P0Q8	OTTHUMG00000008007	ENST00000361297.2:c.2643C>T	1.37:g.46496368C>T		117.0	0.0	0		119.0	5.0	0.0420168	NM_015112		Silent	SNP	ENST00000361297.2	37	CCDS41326.1																																																																																			.	.	none		0.642	MAST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021977.1	NM_015112	
TCHH	7062	hgsc.bcm.edu	37	1	152082304	152082304	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152082304T>G	ENST00000368804.1	-	2	3388	c.3389A>C	c.(3388-3390)aAg>aCg	p.K1130T		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1130	10 X 30 AA tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(20)|kidney(9)|large_intestine(16)|lung(33)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(4)	105	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			gcgccttctcttctcccgttc	0.612																																					p.K1130T		Atlas-SNP	.											TCHH,NS,malignant_melanoma,0,1	TCHH	275	1	0			c.A3389C						scavenged	.						92.0	93.0	92.0					1																	152082304		1979	4147	6126	SO:0001583	missense	7062	exon3			CTTCTCTTCTCCC	L09190	CCDS41396.1	1q21-q23	2013-01-10		2006-01-27	ENSG00000159450	ENSG00000159450		"""EF-hand domain containing"""	11791	protein-coding gene	gene with protein product		190370		THH		1431214	Standard	NM_007113		Approved		uc001ezp.3	Q07283	OTTHUMG00000013066	ENST00000368804.1:c.3389A>C	1.37:g.152082304T>G	ENSP00000357794:p.Lys1130Thr	215.0	2.0	0.00930233		289.0	13.0	0.0449827	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	.	.	.	.	.	.	.	.	.	.	T	6.052	0.377976	0.11466	.	.	ENSG00000159450	ENST00000368804	T	0.05925	3.37	2.57	-0.117	0.13551	.	.	.	.	.	T	0.00845	0.0028	L	0.27053	0.805	0.09310	N	1	P	0.43477	0.808	B	0.33799	0.17	T	0.41787	-0.9489	9	0.13108	T	0.6	.	2.8858	0.05661	0.0:0.3012:0.2466:0.4522	.	1130	Q07283	TRHY_HUMAN	T	1130	ENSP00000357794:K1130T	ENSP00000357794:K1130T	K	-	2	0	TCHH	150348928	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.337000	0.07852	-0.279000	0.09167	0.379000	0.24179	AAG	.	.	none		0.612	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
PLEKHG4B	153478	hgsc.bcm.edu	37	5	162929	162929	+	Silent	SNP	G	G	C	rs75342794	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:162929G>C	ENST00000283426.6	+	11	1724	c.1674G>C	c.(1672-1674)tcG>tcC	p.S558S		NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	558							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		AGGCTACCTCGGTGGCTGCAG	0.652													G|||	255	0.0509185	0.1838	0.0159	5008	,	,		15694	0.0		0.001	False		,,,				2504	0.0				p.S558S		Atlas-SNP	.											PLEKHG4B_ENST00000283426,NS,carcinoma,+2,1	PLEKHG4B	167	1	0			c.G1674C						PASS	.	G		691,3685		51,589,1548	25.0	27.0	26.0		1674	-1.1	0.0	5	dbSNP_131	26	13,8555		0,13,4271	no	coding-synonymous	PLEKHG4B	NM_052909.3		51,602,5819	CC,CG,GG		0.1517,15.7907,5.4388		558/1272	162929	704,12240	2188	4284	6472	SO:0001819	synonymous_variant	153478	exon11			TACCTCGGTGGCT	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"""Pleckstrin homology (PH) domain containing"""	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.1674G>C	5.37:g.162929G>C		166.0	0.0	0		187.0	99.0	0.529412	NM_052909		Silent	SNP	ENST00000283426.6	37	CCDS34124.1																																																																																			G|0.941;C|0.059	0.059	strong		0.652	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909	
KIF7	374654	hgsc.bcm.edu	37	15	90196113	90196113	+	Missense_Mutation	SNP	G	G	A	rs141865394	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90196113G>A	ENST00000394412.3	-	2	125	c.49C>T	c.(49-51)Cgg>Tgg	p.R17W		NM_198525.2	NP_940927.2	Q2M1P5	KIF7_HUMAN	kinesin family member 7	17	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of smoothened signaling pathway (GO:0045879)|positive regulation of smoothened signaling pathway (GO:0045880)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|kinesin complex (GO:0005871)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(5)|lung(11)|ovary(2)|stomach(1)|urinary_tract(1)	25	Lung NSC(78;0.0237)|all_lung(78;0.0478)		BRCA - Breast invasive adenocarcinoma(143;0.128)			AGGGCAACCCGCACTGGGGCC	0.687													G|||	26	0.00519169	0.0174	0.0029	5008	,	,		15541	0.001		0.0	False		,,,				2504	0.0				p.R17W		Atlas-SNP	.											.	KIF7	130	.	0			c.C49T						PASS	.						12.0	17.0	16.0					15																	90196113		688	1589	2277	SO:0001583	missense	374654	exon2			CAACCCGCACTGG	AY358384	CCDS32325.2	15q26.1	2011-06-02			ENSG00000166813	ENSG00000166813		"""Kinesins"""	30497	protein-coding gene	gene with protein product		611254				11416179, 15547730	Standard	NM_198525		Approved	JBTS12	uc002bof.2	Q2M1P5	OTTHUMG00000157177	ENST00000394412.3:c.49C>T	15.37:g.90196113G>A	ENSP00000377934:p.Arg17Trp	90.0	0.0	0		100.0	54.0	0.54	NM_198525	Q3SXY0|Q6UXE9|Q8IW72	Missense_Mutation	SNP	ENST00000394412.3	37	CCDS32325.2	13	0.005952380952380952	10	0.02032520325203252	2	0.0055248618784530384	1	0.0017482517482517483	0	0.0	G	12.35	1.912773	0.33721	.	.	ENSG00000166813	ENST00000394412	T	0.74526	-0.85	4.66	2.23	0.28157	Kinesin, motor domain (3);	.	.	.	.	T	0.80597	0.4653	H	0.96048	3.76	0.35264	D	0.779872	D	0.76494	0.999	P	0.59424	0.857	D	0.89286	0.3615	9	0.87932	D	0	.	12.8485	0.57844	0.0:0.0:0.5816:0.4184	.	17	Q2M1P5	KIF7_HUMAN	W	17	ENSP00000377934:R17W	ENSP00000377934:R17W	R	-	1	2	KIF7	87997117	0.008000	0.16893	0.921000	0.36526	0.005000	0.04900	0.750000	0.26334	0.144000	0.18951	-0.262000	0.10625	CGG	G|0.994;A|0.006	0.006	strong		0.687	KIF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347782.1	NM_198525	
CPN1	1369	hgsc.bcm.edu	37	10	101835764	101835764	+	Silent	SNP	C	C	G	rs61754515	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:101835764C>G	ENST00000370418.3	-	2	575	c.324G>C	c.(322-324)cgG>cgC	p.R108R		NM_001308.2	NP_001299.1	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1	108	Catalytic.				response to glucocorticoid (GO:0051384)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	33		Colorectal(252;0.234)		Epithelial(162;4.77e-10)|all cancers(201;3.82e-08)		GGTTCCTGTTCCGGAACTCCT	0.602													C|||	187	0.0373403	0.1324	0.0159	5008	,	,		18603	0.0		0.001	False		,,,				2504	0.0				p.R108R		Atlas-SNP	.											.	CPN1	62	.	0			c.G324C						PASS	.			560,3846	250.3+/-257.4	33,494,1676	143.0	118.0	126.0		324	-2.5	0.1	10	dbSNP_129	126	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	CPN1	NM_001308.2		33,499,5971	GG,GC,CC		0.0581,12.7099,4.3441		108/459	101835764	565,12441	2203	4300	6503	SO:0001819	synonymous_variant	1369	exon2			CCTGTTCCGGAAC	X14329	CCDS7486.1	10q24.2	2012-02-10	2007-02-23		ENSG00000120054	ENSG00000120054	3.4.17.3		2312	protein-coding gene	gene with protein product	"""anaphylatoxin inactivator"", ""arginine carboxypeptidase"", ""carboxypeptidase K"", ""kininase I"", ""lysine carboxypeptidase"""	603103	"""carboxypeptidase N, polypeptide 1, 50kD"""			9628828, 2912725	Standard	NM_001308		Approved		uc001kql.2	P15169	OTTHUMG00000018896	ENST00000370418.3:c.324G>C	10.37:g.101835764C>G		91.0	0.0	0		88.0	46.0	0.522727	NM_001308	B1AP59	Silent	SNP	ENST00000370418.3	37	CCDS7486.1																																																																																			C|0.959;G|0.041	0.041	strong		0.602	CPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049828.1	NM_001308	
USP35	57558	hgsc.bcm.edu	37	11	77911224	77911224	+	Missense_Mutation	SNP	T	T	C	rs115848453	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:77911224T>C	ENST00000529308.1	+	5	1243	c.982T>C	c.(982-984)Tct>Cct	p.S328P	USP35_ENST00000441408.2_5'UTR|USP35_ENST00000526425.1_Missense_Mutation_p.S59P|USP35_ENST00000530267.1_Intron|USP35_ENST00000530535.1_Intron	NM_020798.2	NP_065849.1	Q9P2H5	UBP35_HUMAN	ubiquitin specific peptidase 35	328					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(3)|urinary_tract(1)	23	all_cancers(14;3.77e-18)|all_epithelial(13;6.16e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.04e-25)			AGCTGCCTTGTCTGTGCTCAA	0.602													T|||	28	0.00559105	0.0212	0.0	5008	,	,		18945	0.0		0.0	False		,,,				2504	0.0				p.S328P		Atlas-SNP	.											.	USP35	179	.	0			c.T982C						PASS	.	T	PRO/SER	46,4006		1,44,1981	105.0	108.0	107.0		982	5.0	1.0	11	dbSNP_132	107	0,8330		0,0,4165	yes	missense	USP35	NM_020798.2	74	1,44,6146	CC,CT,TT		0.0,1.1352,0.3715	probably-damaging	328/1019	77911224	46,12336	2026	4165	6191	SO:0001583	missense	57558	exon5			GCCTTGTCTGTGC	AB037793	CCDS41693.1	11q13.4	2008-02-05	2005-08-08			ENSG00000118369		"""Ubiquitin-specific peptidases"""	20061	protein-coding gene	gene with protein product			"""ubiquitin specific protease 35"""			12838346	Standard	NM_020798		Approved	KIAA1372	uc021qny.1	Q9P2H5		ENST00000529308.1:c.982T>C	11.37:g.77911224T>C	ENSP00000431876:p.Ser328Pro	152.0	0.0	0		182.0	71.0	0.39011	NM_020798		Missense_Mutation	SNP	ENST00000529308.1	37	CCDS41693.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	T	9.269	1.045301	0.19748	0.011352	0.0	ENSG00000118369	ENST00000528910;ENST00000529308;ENST00000526425	T;T;T	0.68624	-0.34;-0.34;0.91	4.97	4.97	0.65823	Armadillo-like helical (1);	0.253449	0.28161	N	0.016373	T	0.40094	0.1103	N	0.13098	0.295	0.80722	D	1	D	0.53885	0.963	P	0.48425	0.577	T	0.50972	-0.8764	10	0.29301	T	0.29	-4.9719	14.8266	0.70117	0.0:0.0:0.0:1.0	.	328	Q9P2H5	UBP35_HUMAN	P	84;328;59	ENSP00000436001:S84P;ENSP00000431876:S328P;ENSP00000434942:S59P	ENSP00000434942:S59P	S	+	1	0	USP35	77588872	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.519000	0.45546	2.092000	0.63282	0.533000	0.62120	TCT	T|0.995;C|0.005	0.005	strong		0.602	USP35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390026.1	XM_290527	
ATP10A	57194	hgsc.bcm.edu	37	15	25963484	25963484	+	Missense_Mutation	SNP	C	C	T	rs116055743	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:25963484C>T	ENST00000356865.6	-	8	1537	c.1426G>A	c.(1426-1428)Ggc>Agc	p.G476S		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	476					ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|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)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		GACACCGAGCCCCCTCTGGGC	0.706													C|||	24	0.00479233	0.0182	0.0	5008	,	,		14866	0.0		0.0	False		,,,				2504	0.0				p.G476S		Atlas-SNP	.											.	ATP10A	270	.	0			c.G1426A						PASS	.	C	SER/GLY	84,4314		0,84,2115	29.0	25.0	26.0		1426	0.9	0.0	15	dbSNP_132	26	0,8594		0,0,4297	yes	missense	ATP10A	NM_024490.3	56	0,84,6412	TT,TC,CC		0.0,1.91,0.6466	benign	476/1500	25963484	84,12908	2199	4297	6496	SO:0001583	missense	57194	exon8			CCGAGCCCCCTCT	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.1426G>A	15.37:g.25963484C>T	ENSP00000349325:p.Gly476Ser	136.0	0.0	0		126.0	65.0	0.515873	NM_024490	Q4G0S9|Q969I4	Missense_Mutation	SNP	ENST00000356865.6	37	CCDS32178.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	9.534	1.111487	0.20714	0.0191	0.0	ENSG00000206190	ENST00000356865	T	0.64991	-0.13	5.14	0.881	0.19166	HAD-like domain (1);	0.228496	0.44688	N	0.000436	T	0.29684	0.0741	L	0.46741	1.465	0.19300	N	0.999978	B	0.10296	0.003	B	0.11329	0.006	T	0.24261	-1.0165	10	0.07030	T	0.85	-7.1028	8.7017	0.34329	0.0:0.6623:0.0:0.3377	.	476	O60312	AT10A_HUMAN	S	476	ENSP00000349325:G476S	ENSP00000349325:G476S	G	-	1	0	ATP10A	23514577	0.382000	0.25148	0.000000	0.03702	0.225000	0.24961	2.423000	0.44705	-0.104000	0.12154	0.655000	0.94253	GGC	C|0.994;T|0.006	0.006	strong		0.706	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	
DGKI	9162	hgsc.bcm.edu	37	7	137263067	137263067	+	Silent	SNP	T	T	A	rs61751966	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:137263067T>A	ENST00000288490.5	-	16	1647	c.1647A>T	c.(1645-1647)gcA>gcT	p.A549A	DGKI_ENST00000446122.1_Silent_p.A549A|DGKI_ENST00000424189.2_Silent_p.A549A|DGKI_ENST00000453654.2_Silent_p.A249A	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	549					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|positive regulation of Ras protein signal transduction (GO:0046579)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of Rap GTPase activity (GO:0032317)	cytoplasm (GO:0005737)|guanyl-nucleotide exchange factor complex (GO:0032045)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(46)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	84						TCTCTGGATTTGCTTCTGTGA	0.373													T|||	88	0.0175719	0.0325	0.0058	5008	,	,		19858	0.0		0.0089	False		,,,				2504	0.0327				p.A549A		Atlas-SNP	.											DGKI_ENST00000288490,NS,carcinoma,-2,2	DGKI	335	2	0			c.A1647T						PASS	.	T		99,4305	78.8+/-117.2	0,99,2103	67.0	68.0	68.0		1647	2.7	1.0	7	dbSNP_129	68	57,8541	35.9+/-90.5	1,55,4243	no	coding-synonymous	DGKI	NM_004717.2		1,154,6346	AA,AT,TT		0.6629,2.248,1.1998		549/1066	137263067	156,12846	2202	4299	6501	SO:0001819	synonymous_variant	9162	exon16			TGGATTTGCTTCT	AF061936	CCDS5845.1	7q32.3-q33	2013-01-10			ENSG00000157680	ENSG00000157680		"""Ankyrin repeat domain containing"""	2855	protein-coding gene	gene with protein product		604072				9830018	Standard	NM_004717		Approved	DGK-IOTA	uc003vtt.3	O75912	OTTHUMG00000155697	ENST00000288490.5:c.1647A>T	7.37:g.137263067T>A		98.0	0.0	0		123.0	63.0	0.512195	NM_004717	A4D1Q9|Q9NZ49	Silent	SNP	ENST00000288490.5	37	CCDS5845.1																																																																																			T|0.987;A|0.013	0.013	strong		0.373	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717	
TTN	7273	hgsc.bcm.edu	37	2	179613147	179613147	+	Intron	SNP	G	G	C	rs75785339	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179613147G>C	ENST00000591111.1	-	45	10585				TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Intron|TTN_ENST00000360870.5_Missense_Mutation_p.H4660Q|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Intron			Q8WZ42	TITIN_HUMAN	titin						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)			TAGAGATATTGTGTGTGTCAG	0.373													C|||	193	0.0385383	0.1407	0.0101	5008	,	,		18083	0.0		0.0	False		,,,				2504	0.0				p.H4660Q		Atlas-SNP	.											.	TTN	18412	.	0			c.C13980G						PASS	.	C	,,GLN/HIS,,	523,3883	761.1+/-413.0	31,461,1711	88.0	98.0	95.0		,,13980,,	0.5	0.0	2	dbSNP_131	95	8,8588	808.7+/-407.2	0,8,4290	yes	intron,intron,missense,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,24,,	31,469,6001	CC,CG,GG		0.0931,11.8702,4.084	,,,,	,,4660/5605,,	179613147	531,12471	2203	4298	6501	SO:0001627	intron_variant	7273	exon46			GATATTGTGTGTG	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.10360+4703C>G	2.37:g.179613147G>C		282.0	0.0	0		317.0	147.0	0.463722	NM_133379	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		68	0.031135531135531136	63	0.12804878048780488	5	0.013812154696132596	0	0.0	0	0.0	C	6.309	0.425027	0.11987	0.118702	9.31E-4	ENSG00000155657	ENST00000360870	T	0.54479	0.57	5.05	0.501	0.16925	.	.	.	.	.	T	0.00210	0.0006	N	0.02539	-0.55	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.14952	-1.0454	8	0.16896	T	0.51	.	0.9872	0.01449	0.2832:0.2095:0.3228:0.1845	.	4660	Q8WZ42-6	.	Q	4660	ENSP00000354117:H4660Q	ENSP00000354117:H4660Q	H	-	3	2	TTN	179321392	0.000000	0.05858	0.002000	0.10522	0.016000	0.09150	-1.023000	0.03607	0.113000	0.18004	-0.127000	0.14921	CAC	G|0.964;C|0.036	0.036	strong		0.373	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
CAGE1	285782	hgsc.bcm.edu	37	6	7379031	7379031	+	Missense_Mutation	SNP	G	G	A	rs10223538	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:7379031G>A	ENST00000512086.1	-	4	708	c.506C>T	c.(505-507)aCt>aTt	p.T169I	CAGE1_ENST00000502583.1_Missense_Mutation_p.T169I|CAGE1_ENST00000509324.1_Intron|CAGE1_ENST00000338150.4_Missense_Mutation_p.T169I|CAGE1_ENST00000379918.4_Missense_Mutation_p.T169I|CAGE1_ENST00000296742.7_Missense_Mutation_p.T33I			Q8TC20	CAGE1_HUMAN	cancer antigen 1	169			T -> I (in dbSNP:rs10223538).							breast(1)|cervix(1)|endometrium(3)|kidney(2)|lung(11)|urinary_tract(1)	19	Ovarian(93;0.0418)					AGAAACACTAGTTTCCATTGG	0.388													G|||	216	0.043131	0.1543	0.0159	5008	,	,		16170	0.0		0.0	False		,,,				2504	0.001				p.T169I		Atlas-SNP	.											.	CAGE1	165	.	0			c.C506T						PASS	.	G	ILE/THR,ILE/THR,ILE/THR	470,3226		30,410,1408	123.0	121.0	122.0		506,506,98	0.7	0.5	6	dbSNP_119	122	5,8187		0,5,4091	yes	missense,missense,missense	CAGE1	NM_001170692.1,NM_001170693.1,NM_205864.2	89,89,89	30,415,5499	AA,AG,GG		0.061,12.7165,3.9956	possibly-damaging,possibly-damaging,possibly-damaging	169/840,169/825,33/642	7379031	475,11413	1848	4096	5944	SO:0001583	missense	285782	exon4			ACACTAGTTTCCA	BC026194	CCDS47367.1, CCDS54964.1, CCDS54965.1	6p24.3	2009-08-06	2005-01-26	2005-01-27	ENSG00000164304	ENSG00000164304			21622	protein-coding gene	gene with protein product	"""cancer/testis antigen 95"""	608304	"""cancer/testis antigen 3"""	CTAG3		12531476	Standard	NM_205864		Approved	bA69L16.7, CT95	uc003mxl.2	Q8TC20	OTTHUMG00000014200	ENST00000512086.1:c.506C>T	6.37:g.7379031G>A	ENSP00000427583:p.Thr169Ile	169.0	0.0	0		149.0	72.0	0.483221	NM_001170693	D6RCT9|Q5TAM0|Q86TM4|Q8N7R5	Missense_Mutation	SNP	ENST00000512086.1	37		74	0.03388278388278388	69	0.1402439024390244	5	0.013812154696132596	0	0.0	0	0.0	G	13.88	2.367959	0.42003	0.127165	6.1E-4	ENSG00000164304	ENST00000541116;ENST00000379918;ENST00000502583;ENST00000296742;ENST00000512086;ENST00000338150;ENST00000542431;ENST00000512691	T;T;T;T;T;T	0.36878	1.23;1.23;1.23;1.23;1.23;1.23	5.23	0.698	0.18087	.	0.571069	0.16966	N	0.192296	T	0.12817	0.0311	L	0.56769	1.78	0.09310	N	1	B	0.20052	0.041	B	0.21917	0.037	T	0.26189	-1.0110	10	0.87932	D	0	-2.6713	2.1016	0.03681	0.1193:0.3601:0.3254:0.1953	rs10223538;rs52806665;rs10223538	169	Q8TC20	CAGE1_HUMAN	I	169;169;169;33;169;169;169;181	ENSP00000369250:T169I;ENSP00000425493:T169I;ENSP00000296742:T33I;ENSP00000427583:T169I;ENSP00000338107:T169I;ENSP00000423789:T181I	ENSP00000296742:T33I	T	-	2	0	CAGE1	7324030	0.274000	0.24191	0.457000	0.27056	0.637000	0.38172	0.554000	0.23407	0.271000	0.22005	0.655000	0.94253	ACT	G|0.944;A|0.056	0.056	strong		0.388	CAGE1-008	PUTATIVE	non_canonical_conserved|basic	protein_coding	protein_coding	OTTHUMT00000367136.1	NM_175745	
TP53INP1	94241	hgsc.bcm.edu	37	8	95942773	95942773	+	Silent	SNP	G	G	A	rs77630257	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:95942773G>A	ENST00000342697.4	-	4	1064	c.657C>T	c.(655-657)caC>caT	p.H219H	TP53INP1_ENST00000378776.4_Silent_p.H164H|TP53INP1_ENST00000448464.2_3'UTR|NDUFAF6_ENST00000396113.1_Intron	NM_033285.3	NP_150601.1	Q96A56	T53I1_HUMAN	tumor protein p53 inducible nuclear protein 1	219					apoptotic process (GO:0006915)|autophagic cell death (GO:0048102)|autophagy (GO:0006914)|cell cycle arrest (GO:0007050)|cellular response to ethanol (GO:0071361)|cellular response to hydroperoxide (GO:0071447)|cellular response to methyl methanesulfonate (GO:0072703)|cellular response to UV (GO:0034644)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of autophagy (GO:0010508)|positive regulation of transcription, DNA-templated (GO:0045893)|response to heat (GO:0009408)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	autophagic vacuole (GO:0005776)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|nucleus (GO:0005634)	antioxidant activity (GO:0016209)			kidney(2)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	9	Breast(36;8.75e-07)					CTTGCCGAGGGTGGCAATCCC	0.473													G|||	42	0.00838658	0.0303	0.0029	5008	,	,		19735	0.0		0.0	False		,,,				2504	0.0				p.H219H		Atlas-SNP	.											.	TP53INP1	22	.	0			c.C657T						PASS	.	G	,	125,4281	92.5+/-131.2	1,123,2079	205.0	211.0	209.0		,657	5.2	1.0	8	dbSNP_132	209	0,8600		0,0,4300	no	utr-3,coding-synonymous	TP53INP1	NM_001135733.1,NM_033285.3	,	1,123,6379	AA,AG,GG		0.0,2.837,0.9611	,	,219/241	95942773	125,12881	2203	4300	6503	SO:0001819	synonymous_variant	94241	exon4			CCGAGGGTGGCAA	AF409115	CCDS6265.1, CCDS47899.1	8q22	2004-03-11				ENSG00000164938			18022	protein-coding gene	gene with protein product		606185				11511362, 12438758	Standard	NM_033285		Approved	DKFZp434M1317, FLJ22139, P53DINP1, SIP, TP53INP1A, TP53INP1B, Teap	uc003yhg.3	Q96A56		ENST00000342697.4:c.657C>T	8.37:g.95942773G>A		195.0	0.0	0		201.0	82.0	0.40796	NM_033285	B2RCE5|Q969R9	Silent	SNP	ENST00000342697.4	37	CCDS6265.1																																																																																			A|0.010;G|0.990	0.010	strong		0.473	TP53INP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379818.1		
MUC4	4585	hgsc.bcm.edu	37	3	195509076	195509076	+	Missense_Mutation	SNP	G	G	T	rs35479616		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195509076G>T	ENST00000463781.3	-	2	9834	c.9375C>A	c.(9373-9375)gaC>gaA	p.D3125E	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D3125E	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)		CTGAGGAAGTGTCGGTGACAG	0.582																																					p.D3125E		Atlas-SNP	.											.	MUC4	1505	.	0			c.C9375A						PASS	.						12.0	7.0	9.0					3																	195509076		656	1515	2171	SO:0001583	missense	4585	exon2			GGAAGTGTCGGTG	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.9375C>A	3.37:g.195509076G>T	ENSP00000417498:p.Asp3125Glu	161.0	0.0	0		282.0	24.0	0.0851064	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	7.172	0.587888	0.13812	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29397	1.59;1.57	.	.	.	.	.	.	.	.	T	0.14787	0.0357	N	0.19112	0.55	0.19300	N	0.999979	B	0.19200	0.034	B	0.04013	0.001	T	0.27606	-1.0069	7	.	.	.	.	3.2503	0.06812	0.362:0.0:0.638:0.0	.	2997	E7ESK3	.	E	3125	ENSP00000417498:D3125E;ENSP00000420243:D3125E	.	D	-	3	2	MUC4	196993855	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-1.931000	0.01556	-0.000000	0.14550	0.000000	0.15137	GAC	.	.	none		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
DES	1674	hgsc.bcm.edu	37	2	220290674	220290674	+	Missense_Mutation	SNP	G	G	A	rs73991549	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:220290674G>A	ENST00000373960.3	+	9	1461	c.1375G>A	c.(1375-1377)Gtc>Atc	p.V459I	AC053503.6_ENST00000431827.1_RNA	NM_001927.3	NP_001918.3	P17661	DESM_HUMAN	desmin	459	Tail.				cytoskeleton organization (GO:0007010)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|regulation of heart contraction (GO:0008016)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intermediate filament (GO:0005882)|neuromuscular junction (GO:0031594)|sarcolemma (GO:0042383)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|identical protein binding (GO:0042802)|structural constituent of cytoskeleton (GO:0005200)	p.V459I(1)		breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(10)|skin(1)	18		Renal(207;0.0183)		Epithelial(149;5.25e-07)|all cancers(144;0.000103)|Lung(261;0.00533)|LUSC - Lung squamous cell carcinoma(224;0.008)		TCCCCAGGTCGTCAGTGAGGC	0.607													G|||	49	0.00978435	0.0325	0.0072	5008	,	,		19604	0.0		0.001	False		,,,				2504	0.0				p.V459I		Atlas-SNP	.											DES,brain,glioma,0,2	DES	53	2	1	Substitution - Missense(1)	central_nervous_system(1)	c.G1375A	GRCh37	CM070889	DES	M	rs73991549	PASS	.	G	ILE/VAL	157,4249	107.3+/-145.7	2,153,2048	173.0	151.0	158.0		1375	4.2	1.0	2	dbSNP_130	158	1,8599	1.2+/-3.3	0,1,4299	yes	missense	DES	NM_001927.3	29	2,154,6347	AA,AG,GG		0.0116,3.5633,1.2148	benign	459/471	220290674	158,12848	2203	4300	6503	SO:0001583	missense	1674	exon9			CAGGTCGTCAGTG	AF521879	CCDS33383.1	2q35	2014-09-17			ENSG00000175084	ENSG00000175084		"""Intermediate filaments type III"""	2770	protein-coding gene	gene with protein product	"""intermediate filament protein"""	125660				2673923, 9736733	Standard	NM_001927		Approved	CMD1I, CSM1, CSM2	uc002vll.3	P17661	OTTHUMG00000058924	ENST00000373960.3:c.1375G>A	2.37:g.220290674G>A	ENSP00000363071:p.Val459Ile	54.0	0.0	0		51.0	26.0	0.509804	NM_001927	Q15787|Q549R7|Q549R8|Q549R9|Q8IZR1|Q8IZR6|Q8NES2|Q8NEU6|Q8TAC4|Q8TCX2|Q8TD99|Q9UHN5|Q9UJ80	Missense_Mutation	SNP	ENST00000373960.3	37	CCDS33383.1	14	0.00641025641025641	12	0.024390243902439025	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	8.078	0.771762	0.16051	0.035633	1.16E-4	ENSG00000175084	ENST00000373960	D	0.96913	-4.17	5.17	4.23	0.50019	.	0.000000	0.35207	N	0.003373	T	0.77572	0.4150	L	0.41961	1.31	0.39176	D	0.962688	P	0.36587	0.559	B	0.31547	0.132	D	0.86120	0.1568	10	0.06891	T	0.86	.	13.8879	0.63719	0.0:0.1537:0.8463:0.0	.	459	P17661	DESM_HUMAN	I	459	ENSP00000363071:V459I	ENSP00000363071:V459I	V	+	1	0	DES	219998918	1.000000	0.71417	0.999000	0.59377	0.834000	0.47266	7.003000	0.76310	2.409000	0.81822	0.655000	0.94253	GTC	G|0.989;A|0.011	0.011	strong		0.607	DES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130240.1	NM_001927	
ABL1	25	hgsc.bcm.edu	37	9	133760592	133760592	+	Missense_Mutation	SNP	C	C	T	rs2229067	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:133760592C>T	ENST00000318560.5	+	11	3296	c.2915C>T	c.(2914-2916)tCg>tTg	p.S972L		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	972	F-actin-binding.|Pro-rich.		S -> L (in dbSNP:rs2229067). {ECO:0000269|PubMed:17344846, ECO:0000269|Ref.4}.		actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	GCCAAGCCGTCGGGGACCCCC	0.672			"""T, Mis"""	"""BCR, ETV6, NUP214"""	"""CML, ALL, T-ALL"""								C|||	93	0.0185703	0.0431	0.0245	5008	,	,		15811	0.0		0.0189	False		,,,				2504	0.0				p.S991L		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.C2972T						PASS	.	C	LEU/SER,LEU/SER	190,4214	111.6+/-149.8	4,182,2016	41.0	51.0	48.0		2915,2972	2.4	0.0	9	dbSNP_98	48	172,8420	75.7+/-138.4	0,172,4124	yes	missense,missense	ABL1	NM_005157.4,NM_007313.2	145,145	4,354,6140	TT,TC,CC		2.0019,4.3143,2.7855	benign,benign	972/1131,991/1150	133760592	362,12634	2202	4296	6498	SO:0001583	missense	25	exon11			AGCCGTCGGGGAC	M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"""SH2 domain containing"""	76	protein-coding gene	gene with protein product		189980	"""v-abl Abelson murine leukemia viral oncogene homolog 1"", ""c-abl oncogene 1, receptor tyrosine kinase"", ""c-abl oncogene 1, non-receptor tyrosine kinase"""	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.2915C>T	9.37:g.133760592C>T	ENSP00000323315:p.Ser972Leu	95.0	0.0	0		96.0	60.0	0.625	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Missense_Mutation	SNP	ENST00000318560.5	37	CCDS35166.1	39	0.017857142857142856	16	0.032520325203252036	9	0.024861878453038673	0	0.0	14	0.018469656992084433	C	9.404	1.078707	0.20227	0.043143	0.020019	ENSG00000097007	ENST00000444970;ENST00000372348;ENST00000318560	T;T	0.11495	2.77;2.77	5.27	2.43	0.29744	F-actin binding (1);	1.170500	0.05873	N	0.625078	T	0.01800	0.0057	N	0.22421	0.69	0.09310	N	1	B;B	0.11235	0.001;0.004	B;B	0.12156	0.004;0.007	T	0.35871	-0.9771	10	0.42905	T	0.14	.	7.9383	0.29944	0.0:0.6637:0.0:0.3363	rs2229067;rs2229067	972;1009	P00519;Q59FK4	ABL1_HUMAN;.	L	787;991;972	ENSP00000361423:S991L;ENSP00000323315:S972L	ENSP00000323315:S972L	S	+	2	0	ABL1	132750413	0.000000	0.05858	0.009000	0.14445	0.707000	0.40811	0.591000	0.23969	0.613000	0.30089	-0.258000	0.10820	TCG	C|0.971;T|0.029	0.029	strong		0.672	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313	
TPO	7173	hgsc.bcm.edu	37	2	1418188	1418188	+	Missense_Mutation	SNP	C	C	T	rs151268825	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:1418188C>T	ENST00000345913.4	+	2	99	c.8C>T	c.(7-9)gCg>gTg	p.A3V	TPO_ENST00000382198.1_Missense_Mutation_p.A3V|TPO_ENST00000539820.1_Missense_Mutation_p.A3V|TPO_ENST00000349624.3_Missense_Mutation_p.A3V|TPO_ENST00000497517.2_Intron|TPO_ENST00000382269.3_Missense_Mutation_p.A3V|TPO_ENST00000337415.3_Missense_Mutation_p.A3V|TPO_ENST00000346956.3_Missense_Mutation_p.A3V|TPO_ENST00000329066.4_Missense_Mutation_p.A3V|TPO_ENST00000382201.3_Missense_Mutation_p.A3V	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	3					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	AGAATGAGAGCGCTCGCTGTG	0.522													C|||	16	0.00319489	0.0106	0.0014	5008	,	,		16782	0.0		0.0	False		,,,				2504	0.001				p.A3V		Atlas-SNP	.											TPO,NS,carcinoma,-1,1	TPO	224	1	0			c.C8T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	16,4390	22.3+/-47.3	0,16,2187	71.0	69.0	70.0		8,8,8,8,8,8	-5.3	0.0	2	dbSNP_134	70	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense	TPO	NM_000547.5,NM_001206744.1,NM_001206745.1,NM_175719.3,NM_175721.3,NM_175722.3	64,64,64,64,64,64	0,16,6487	TT,TC,CC		0.0,0.3631,0.123	benign,benign,benign,benign,benign,benign	3/934,3/934,3/877,3/877,3/890,3/761	1418188	16,12990	2203	4300	6503	SO:0001583	missense	7173	exon2			TGAGAGCGCTCGC		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.8C>T	2.37:g.1418188C>T	ENSP00000318820:p.Ala3Val	144.0	0.0	0		128.0	65.0	0.507812	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	37	CCDS1643.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	10.67	1.414818	0.25465	0.003631	0.0	ENSG00000115705	ENST00000382269;ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000539820;ENST00000329066;ENST00000382201;ENST00000423320;ENST00000382198	T;T;T;T;T;T;T;T;T;T	0.65732	0.31;-0.17;-0.17;-0.11;0.15;0.31;-0.17;-0.06;0.34;0.15	5.39	-5.3	0.02738	.	1.351910	0.04684	N	0.412836	T	0.41903	0.1179	N	0.13043	0.29	0.09310	N	1	B;B;B;B;B	0.17852	0.003;0.012;0.024;0.014;0.004	B;B;B;B;B	0.10450	0.005;0.003;0.003;0.001;0.002	T	0.32161	-0.9917	10	0.41790	T	0.15	-1.8566	9.1002	0.36664	0.0:0.1854:0.127:0.6876	.	3;3;3;3;3	P07202-4;P07202-5;E9PFM6;P07202-2;P07202	.;.;.;.;PERT_HUMAN	V	3	ENSP00000371704:A3V;ENSP00000337263:A3V;ENSP00000318820:A3V;ENSP00000263886:A3V;ENSP00000332044:A3V;ENSP00000444840:A3V;ENSP00000329869:A3V;ENSP00000371636:A3V;ENSP00000390994:A3V;ENSP00000371633:A3V	ENSP00000329869:A3V	A	+	2	0	TPO	1397195	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.480000	0.00983	-0.936000	0.03723	-0.768000	0.03414	GCG	C|0.999;T|0.001	0.001	strong		0.522	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547	
OGG1	4968	hgsc.bcm.edu	37	3	9796508	9796508	+	Missense_Mutation	SNP	G	G	A	rs1805373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:9796508G>A	ENST00000344629.7	+	4	1029	c.686G>A	c.(685-687)cGa>cAa	p.R229Q	OGG1_ENST00000302008.8_Missense_Mutation_p.R229Q|OGG1_ENST00000339511.5_Missense_Mutation_p.R229Q|OGG1_ENST00000302003.7_Missense_Mutation_p.R229Q|OGG1_ENST00000449570.2_Missense_Mutation_p.R229Q|OGG1_ENST00000383826.5_Intron|OGG1_ENST00000302036.7_Missense_Mutation_p.R229Q|OGG1_ENST00000349503.5_Missense_Mutation_p.R229Q			O15527	OGG1_HUMAN	8-oxoguanine DNA glycosylase	229			R -> Q (in dbSNP:rs1805373). {ECO:0000269|Ref.13}.		acute inflammatory response (GO:0002526)|base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|cellular response to cadmium ion (GO:0071276)|depurination (GO:0045007)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleotide-excision repair (GO:0006289)|regulation of protein import into nucleus, translocation (GO:0033158)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|response to oxidative stress (GO:0006979)|response to radiation (GO:0009314)	mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	8-oxo-7,8-dihydroguanine DNA N-glycosylase activity (GO:0034039)|damaged DNA binding (GO:0003684)|endonuclease activity (GO:0004519)|oxidized purine nucleobase lesion DNA N-glycosylase activity (GO:0008534)			kidney(2)|large_intestine(2)|lung(2)|skin(1)|urinary_tract(1)	8	Medulloblastoma(99;0.227)					CAGCAGCTACGAGAGTCCTCA	0.642								Base excision repair (BER), DNA glycosylases					G|||	141	0.028155	0.1029	0.0072	5008	,	,		19186	0.0		0.0	False		,,,				2504	0.0				p.R229Q		Atlas-SNP	.											.	OGG1	57	.	0			c.G686A	GRCh37	CM074394	OGG1	M	rs1805373	PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,,GLN/ARG,GLN/ARG	384,4022	185.7+/-212.7	11,362,1830	33.0	28.0	30.0		686,686,686,686,686,,686,686	3.1	0.8	3	dbSNP_98	30	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense,missense,missense,missense,intron,missense,missense	OGG1	NM_002542.5,NM_016819.3,NM_016820.3,NM_016821.2,NM_016826.2,NM_016827.2,NM_016828.2,NM_016829.2	43,43,43,43,43,,43,43	11,365,6127	AA,AG,GG		0.0349,8.7154,2.9755	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,,possibly-damaging,possibly-damaging	229/346,229/325,229/411,229/425,229/358,,229/357,229/323	9796508	387,12619	2203	4300	6503	SO:0001583	missense	4968	exon4			AGCTACGAGAGTC	U96710	CCDS2576.1, CCDS2577.1, CCDS2578.1, CCDS2579.1, CCDS2580.1, CCDS2581.1, CCDS43046.1, CCDS46742.1	3p26	2010-11-23			ENSG00000114026	ENSG00000114026	3.2.2.-, 4.2.99.18		8125	protein-coding gene	gene with protein product	"""8-hydroxyguanine DNA glycosylase"", ""OGG1 type 1e"", ""OGG1 type 1d"", ""OGG1 type 1g"", ""OGG1 type 1h"""	601982				9207108, 10449904	Standard	NM_002542		Approved	HMMH, HOGG1, OGH1, MUTM	uc003bsj.3	O15527	OTTHUMG00000097091	ENST00000344629.7:c.686G>A	3.37:g.9796508G>A	ENSP00000342851:p.Arg229Gln	137.0	0.0	0		146.0	59.0	0.40411	NM_016819	A8K1E3|O00390|O00670|O00705|O14876|O95488|P78554|Q9BW42|Q9UIK0|Q9UIK1|Q9UIK2|Q9UL34|Q9Y2C0|Q9Y2C1|Q9Y6C3|Q9Y6C4	Missense_Mutation	SNP	ENST00000344629.7	37	CCDS2581.1	43|43	0.019688644688644688|0.019688644688644688	39|39	0.07926829268292683|0.07926829268292683	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	0|0	0.0|0.0	G|G	16.07|16.07	3.017581|3.017581	0.54576|0.54576	0.087154|0.087154	3.49E-4|3.49E-4	ENSG00000114026|ENSG00000114026	ENST00000441094|ENST00000302003;ENST00000344629;ENST00000302036;ENST00000349503;ENST00000339511;ENST00000449570;ENST00000302008;ENST00000339542	.|T;T;T;T;T;T;T	.|0.56275	.|0.47;0.47;0.47;0.47;0.47;0.47;0.47	5.78|5.78	3.07|3.07	0.35406|0.35406	.|HhH-GPD domain (2);DNA glycosylase (2);	.|0.261230	.|0.45361	.|N	.|0.000369	T|T	0.03520|0.03520	0.0101|0.0101	M|M	0.76938|0.76938	2.355|2.355	0.53005|0.53005	D|D	0.999968|0.999968	.|D;D;P;P;D;P;B;P	.|0.61697	.|0.982;0.99;0.954;0.907;0.977;0.954;0.312;0.933	.|B;B;B;B;B;B;B;B	.|0.43331	.|0.345;0.416;0.299;0.133;0.133;0.299;0.019;0.082	T|T	0.02320|0.02320	-1.1177|-1.1177	5|10	.|0.54805	.|T	.|0.06	-3.3716|-3.3716	11.2674|11.2674	0.49118|0.49118	0.1972:0.0:0.8028:0.0|0.1972:0.0:0.8028:0.0	rs1805373;rs2266693;rs52816862;rs56468739;rs1805373|rs1805373;rs2266693;rs52816862;rs56468739;rs1805373	.|72;229;229;229;229;229;229;229	.|F8WA07;E5KPM6;E5KPM5;E5KPM7;E5KPM9;E5KPN0;O15527;O15527-2	.|.;.;.;.;.;.;OGG1_HUMAN;.	K|Q	127|229;229;229;229;229;229;229;72	.|ENSP00000305584:R229Q;ENSP00000342851:R229Q;ENSP00000306561:R229Q;ENSP00000303132:R229Q;ENSP00000345520:R229Q;ENSP00000403598:R229Q;ENSP00000305527:R229Q	.|ENSP00000305584:R229Q	E|R	+|+	1|2	0|0	OGG1|OGG1	9771508|9771508	0.813000|0.813000	0.29090|0.29090	0.768000|0.768000	0.31515|0.31515	0.370000|0.370000	0.29829|0.29829	2.465000|2.465000	0.45075|0.45075	0.384000|0.384000	0.24942|0.24942	-0.203000|-0.203000	0.12734|0.12734	GAG|CGA	G|0.969;A|0.031	0.031	strong		0.642	OGG1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214223.2	NM_016821	
SFSWAP	6433	hgsc.bcm.edu	37	12	132237789	132237789	+	Silent	SNP	C	C	T	rs202066133		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:132237789C>T	ENST00000261674.4	+	8	1344	c.1203C>T	c.(1201-1203)acC>acT	p.T401T	SFSWAP_ENST00000541286.1_Silent_p.T401T	NM_004592.3	NP_004583.2	Q12872	SFSWA_HUMAN	splicing factor, suppressor of white-apricot family	401					mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	RNA binding (GO:0003723)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(8)|ovary(1)|skin(2)	25						CTGGCGTGACCGTGTCTAACT	0.637													C|||	1	0.000199681	0.0008	0.0	5008	,	,		16980	0.0		0.0	False		,,,				2504	0.0				p.T401T		Atlas-SNP	.											.	SFSWAP	69	.	0			c.C1203T						PASS	.	C		3,4403	6.2+/-15.9	0,3,2200	174.0	146.0	156.0		1203	-2.4	0.9	12		156	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	SFSWAP	NM_004592.2		0,4,6499	TT,TC,CC		0.0116,0.0681,0.0308		401/952	132237789	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	6433	exon8			CGTGACCGTGTCT	U08377	CCDS9273.1, CCDS58290.1	12q24.33	2014-04-14	2014-04-14	2010-09-15	ENSG00000061936	ENSG00000061936			10790	protein-coding gene	gene with protein product		601945	"""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot, Drosophila homolog)"", ""splicing factor, arginine/serine-rich 8 (suppressor-of-white-apricot homolog, Drosophila)"", ""splicing factor, suppressor of white-apricot homolog (Drosophila)"""	SFRS8		8940107	Standard	NM_004592		Approved	SWAP	uc010tbn.2	Q12872	OTTHUMG00000168319	ENST00000261674.4:c.1203C>T	12.37:g.132237789C>T		167.0	0.0	0		170.0	70.0	0.411765	NM_001261411	B2RN45|B7ZM97|F5H6B8|Q6PJF7	Silent	SNP	ENST00000261674.4	37	CCDS9273.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	7.548	0.662175	0.14645	6.81E-4	1.16E-4	ENSG00000061936	ENST00000537164	.	.	.	5.41	-2.37	0.06643	.	.	.	.	.	T	0.51517	0.1679	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45818	-0.9235	4	.	.	.	-14.7257	7.8087	0.29217	0.0:0.2462:0.2063:0.5475	.	.	.	.	L	41	.	.	P	+	2	0	SFSWAP	130803742	0.647000	0.27304	0.908000	0.35775	0.652000	0.38707	-0.321000	0.08018	-0.413000	0.07507	0.561000	0.74099	CCG	C|1.000;T|0.000	0.000	strong		0.637	SFSWAP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399276.1	NM_004592	
CEMIP	57214	hgsc.bcm.edu	37	15	81217024	81217024	+	Silent	SNP	G	G	A	rs28566789	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:81217024G>A	ENST00000394685.3	+	18	2684	c.2265G>A	c.(2263-2265)ccG>ccA	p.P755P	KIAA1199_ENST00000220244.3_Silent_p.P755P|RP11-351M8.2_ENST00000560873.1_RNA|KIAA1199_ENST00000356249.5_Silent_p.P755P			Q8WUJ3	CEMIP_HUMAN		755					hyaluronan catabolic process (GO:0030214)|positive regulation of cell migration (GO:0030335)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase C activity (GO:1900020)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|sensory perception of sound (GO:0007605)	clathrin-coated vesicle membrane (GO:0030665)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	clathrin heavy chain binding (GO:0032050)|ER retention sequence binding (GO:0046923)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						ACAAGCGGCCGTTCCTCTCAA	0.532													G|||	139	0.0277556	0.0998	0.0086	5008	,	,		19966	0.0		0.001	False		,,,				2504	0.0				p.P755P		Atlas-SNP	.											.	KIAA1199	118	.	0			c.G2265A						PASS	.	G		341,4065	178.3+/-207.1	17,307,1879	123.0	101.0	108.0		2265	-0.2	1.0	15	dbSNP_125	108	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	KIAA1199	NM_018689.1		17,309,6177	AA,AG,GG		0.0233,7.7394,2.6372		755/1362	81217024	343,12663	2203	4300	6503	SO:0001819	synonymous_variant	57214	exon17			GCGGCCGTTCCTC																												ENST00000394685.3:c.2265G>A	15.37:g.81217024G>A		184.0	0.0	0		196.0	92.0	0.469388	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Silent	SNP	ENST00000394685.3	37	CCDS10315.1																																																																																			G|0.973;A|0.027	0.027	strong		0.532	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1		
SORBS1	10580	hgsc.bcm.edu	37	10	97154762	97154762	+	Silent	SNP	G	G	A	rs17110703	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:97154762G>A	ENST00000361941.3	-	12	1319	c.1293C>T	c.(1291-1293)tcC>tcT	p.S431S	SORBS1_ENST00000371241.1_Intron|SORBS1_ENST00000371246.2_Silent_p.S431S|SORBS1_ENST00000371245.3_Intron|SORBS1_ENST00000371247.2_Silent_p.S431S|SORBS1_ENST00000354106.3_Silent_p.S422S|SORBS1_ENST00000474353.2_Intron|SORBS1_ENST00000353505.5_Intron|SORBS1_ENST00000306402.6_Intron|SORBS1_ENST00000371249.2_Intron|SORBS1_ENST00000347291.4_Silent_p.S299S|SORBS1_ENST00000371239.1_Intron|SORBS1_ENST00000371227.4_Intron|SORBS1_ENST00000607232.1_Intron|SORBS1_ENST00000277982.5_Silent_p.S431S|SORBS1_ENST00000393949.1_Silent_p.S422S	NM_001034954.1	NP_001030126			sorbin and SH3 domain containing 1											NS(1)|breast(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(19)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	42		Colorectal(252;0.0429)		Epithelial(162;1.7e-06)|all cancers(201;6.52e-05)		TGGTACCTTCGGAAGTTTGCT	0.393													G|||	188	0.0375399	0.1369	0.0086	5008	,	,		19554	0.0		0.001	False		,,,				2504	0.0				p.S431S		Atlas-SNP	.											.	SORBS1	185	.	0			c.C1293T						PASS	.	G	,,,,,,	505,3901	233.6+/-246.7	26,453,1724	237.0	281.0	266.0		1293,1293,,,,,	4.9	1.0	10	dbSNP_123	266	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous,coding-synonymous,intron,intron,intron,intron,intron	SORBS1	NM_001034954.1,NM_001034955.1,NM_001034956.1,NM_001034957.1,NM_006434.2,NM_015385.2,NM_024991.1	,,,,,,	26,462,6015	AA,AG,GG		0.1047,11.4616,3.952	,,,,,,	431/1293,431/1152,,,,,	97154762	514,12492	2203	4300	6503	SO:0001819	synonymous_variant	10580	exon12			ACCTTCGGAAGTT	AF136381	CCDS7442.1, CCDS31252.1, CCDS31253.1, CCDS31254.1, CCDS31255.1, CCDS31256.1, CCDS73169.1	10q23.33	2011-07-25	2002-05-08		ENSG00000095637	ENSG00000095637			14565	protein-coding gene	gene with protein product	"""c-Cbl-associated protein"""	605264	"""SH3-domain protein 5 (ponsin)"""	SH3D5		10085297, 11001060	Standard	XM_005269405		Approved	FLJ12406, CAP, sh3p12, ponsin, KIAA1296	uc001kkp.3	Q9BX66	OTTHUMG00000018812	ENST00000361941.3:c.1293C>T	10.37:g.97154762G>A		228.0	0.0	0		214.0	108.0	0.504673	NM_001034955		Silent	SNP	ENST00000361941.3	37	CCDS31255.1																																																																																			G|0.952;A|0.048	0.048	strong		0.393	SORBS1-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049517.1		
PIK3C2G	5288	hgsc.bcm.edu	37	12	18715673	18715673	+	Silent	SNP	A	A	G	rs11044184	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:18715673A>G	ENST00000266497.5	+	25	3542	c.3504A>G	c.(3502-3504)aaA>aaG	p.K1168K	PIK3C2G_ENST00000538779.1_Silent_p.K1209K|PIK3C2G_ENST00000433979.1_Silent_p.K1168K			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	1168	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				TCCCTGTTAAATTGAATAACT	0.383													A|||	273	0.0545128	0.1989	0.0144	5008	,	,		17230	0.0		0.0	False		,,,				2504	0.0				p.K1168K		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.A3504G						PASS	.	A		672,3034		63,546,1244	68.0	64.0	65.0		3504	-0.7	1.0	12	dbSNP_120	65	5,8185		0,5,4090	no	coding-synonymous	PIK3C2G	NM_004570.4		63,551,5334	GG,GA,AA		0.0611,18.1328,5.691		1168/1446	18715673	677,11219	1853	4095	5948	SO:0001819	synonymous_variant	5288	exon26			TGTTAAATTGAAT	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"""phosphoinositide-3-kinase, class 2, gamma polypeptide"""			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.3504A>G	12.37:g.18715673A>G		181.0	0.0	0		192.0	85.0	0.442708	NM_004570	A1L3U0	Silent	SNP	ENST00000266497.5	37	CCDS44839.1																																																																																			A|0.941;G|0.059	0.059	strong		0.383	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570	
CDC5L	988	hgsc.bcm.edu	37	6	44387305	44387305	+	Silent	SNP	T	T	C	rs11571982	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:44387305T>C	ENST00000371477.3	+	9	1511	c.1212T>C	c.(1210-1212)acT>acC	p.T404T		NM_001253.3	NP_001244.1	Q99459	CDC5L_HUMAN	cell division cycle 5-like	404	Interaction with PPP1R8.				cell cycle (GO:0007049)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)|Prp19 complex (GO:0000974)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|WD40-repeat domain binding (GO:0071987)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(1)|skin(4)	29	all_lung(25;0.00433)|Ovarian(13;0.0273)|all_hematologic(164;0.208)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TTGTACAGACTCCAAACACAG	0.398													T|||	58	0.0115815	0.0393	0.0086	5008	,	,		20954	0.0		0.0	False		,,,				2504	0.0				p.T404T		Atlas-SNP	.											.	CDC5L	86	.	0			c.T1212C						PASS	.	T		140,4266	100.3+/-138.9	1,138,2064	154.0	138.0	143.0		1212	0.3	1.0	6	dbSNP_120	143	0,8600		0,0,4300	no	coding-synonymous	CDC5L	NM_001253.2		1,138,6364	CC,CT,TT		0.0,3.1775,1.0764		404/803	44387305	140,12866	2203	4300	6503	SO:0001819	synonymous_variant	988	exon9			ACAGACTCCAAAC	D85423	CCDS4912.1	6p21.1	2013-01-17	2013-01-17		ENSG00000096401	ENSG00000096401			1743	protein-coding gene	gene with protein product		602868	"""CDC5 (cell division cycle 5, S. pombe, homolog)-like"", ""CDC5 cell division cycle 5-like (S. pombe)"""			9598309, 9038199	Standard	NM_001253		Approved	PCDC5RP, hCDC5, CEF1, CDC5	uc003oxl.3	Q99459	OTTHUMG00000014767	ENST00000371477.3:c.1212T>C	6.37:g.44387305T>C		144.0	0.0	0		126.0	61.0	0.484127	NM_001253	Q76N46|Q99974	Silent	SNP	ENST00000371477.3	37	CCDS4912.1																																																																																			T|0.989;C|0.011	0.011	strong		0.398	CDC5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040743.1		
CDC14A	8556	hgsc.bcm.edu	37	1	100928421	100928421	+	Silent	SNP	C	C	T	rs74667145	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:100928421C>T	ENST00000336454.3	+	9	1177	c.822C>T	c.(820-822)atC>atT	p.I274I	CDC14A_ENST00000370124.3_Silent_p.I274I|RP5-837M10.4_ENST00000432210.1_RNA|CDC14A_ENST00000542213.1_Silent_p.I216I|CDC14A_ENST00000361544.6_Silent_p.I274I|CDC14A_ENST00000370125.2_3'UTR|CDC14A_ENST00000544534.1_Silent_p.I274I	NM_003672.3	NP_003663.2	Q9UNH5	CC14A_HUMAN	cell division cycle 14A	274	B.				cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(5)|kidney(6)|large_intestine(6)|lung(10)|skin(2)|urinary_tract(1)	31		all_epithelial(167;3.71e-06)|all_lung(203;0.00097)|Lung NSC(277;0.001)		Epithelial(280;0.0676)|all cancers(265;0.127)|COAD - Colon adenocarcinoma(174;0.201)|Lung(183;0.227)|Colorectal(144;0.241)		AAGGGGCCATCGCCGTTCACT	0.527													C|||	9	0.00179712	0.0068	0.0	5008	,	,		18751	0.0		0.0	False		,,,				2504	0.0				p.I274I		Atlas-SNP	.											.	CDC14A	65	.	0			c.C822T						PASS	.	C	,,	20,4386	28.1+/-56.4	0,20,2183	60.0	51.0	54.0		822,822,822	-3.7	0.1	1	dbSNP_132	54	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	CDC14A	NM_003672.3,NM_033312.2,NM_033313.2	,,	0,20,6483	TT,TC,CC		0.0,0.4539,0.1538	,,	274/595,274/624,274/384	100928421	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	8556	exon9			GGCCATCGCCGTT	AF000367	CCDS769.1, CCDS770.1, CCDS771.1	1p21	2013-01-17	2013-01-17		ENSG00000079335	ENSG00000079335		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : CDC14s"""	1718	protein-coding gene	gene with protein product		603504	"""CDC10 (cell division cycle 10, S. cerevisiae, homolog)"", ""CDC14 cell division cycle 14 homolog A (S. cerevisiae)"""			9367992, 10409437	Standard	NM_033312		Approved	Cdc14A1, Cdc14A2, cdc14	uc001dtf.2	Q9UNH5	OTTHUMG00000010987	ENST00000336454.3:c.822C>T	1.37:g.100928421C>T		70.0	0.0	0		73.0	35.0	0.479452	NM_033313	A6MA65|B1AQ14|B1AQ15|O43171|O60727|O60728|Q52LH9|Q8IXX0	Silent	SNP	ENST00000336454.3	37	CCDS769.1																																																																																			C|0.999;T|0.001	0.001	strong		0.527	CDC14A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000030220.1	NM_033312	
PDE6A	5145	hgsc.bcm.edu	37	5	149324153	149324153	+	Silent	SNP	G	G	A	rs34230349	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:149324153G>A	ENST00000255266.5	-	1	203	c.84C>T	c.(82-84)taC>taT	p.Y28Y		NM_000440.2	NP_000431.2	P16499	PDE6A_HUMAN	phosphodiesterase 6A, cGMP-specific, rod, alpha	28					cytosolic calcium ion homeostasis (GO:0051480)|GMP metabolic process (GO:0046037)|phototransduction, visible light (GO:0007603)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	44			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Caffeine(DB00201)	GCTTGGCCCGGTAGTGGAGGT	0.572													G|||	84	0.0167732	0.0461	0.0058	5008	,	,		18582	0.0099		0.0	False		,,,				2504	0.0092				p.Y28Y		Atlas-SNP	.											.	PDE6A	98	.	0			c.C84T						PASS	.	G		199,4207	124.5+/-161.8	2,195,2006	48.0	43.0	45.0		84	2.0	1.0	5	dbSNP_126	45	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	PDE6A	NM_000440.2		2,196,6305	AA,AG,GG		0.0116,4.5166,1.5378		28/861	149324153	200,12806	2203	4300	6503	SO:0001819	synonymous_variant	5145	exon1			GGCCCGGTAGTGG		CCDS4299.1	5q31.2-q34	2013-02-14			ENSG00000132915	ENSG00000132915	3.1.4.17	"""Phosphodiesterases"""	8785	protein-coding gene	gene with protein product		180071		PDEA		2155175	Standard	NM_000440		Approved	RP43	uc003lrg.4	P16499	OTTHUMG00000130047	ENST00000255266.5:c.84C>T	5.37:g.149324153G>A		97.0	0.0	0		75.0	34.0	0.453333	NM_000440	Q0P638	Silent	SNP	ENST00000255266.5	37	CCDS4299.1																																																																																			G|0.984;A|0.016	0.016	strong		0.572	PDE6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252326.2		
ABCC1	4363	hgsc.bcm.edu	37	16	16230427	16230427	+	Silent	SNP	C	C	T	rs34526519	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:16230427C>T	ENST00000399410.3	+	29	4393	c.4218C>T	c.(4216-4218)gcC>gcT	p.A1406A	ABCC1_ENST00000399408.2_Silent_p.A1416A|ABCC1_ENST00000351154.5_Silent_p.A1347A|ABCC1_ENST00000345148.5_Silent_p.A1406A|ABCC1_ENST00000349029.5_Silent_p.A1291A|ABCC1_ENST00000346370.5_Silent_p.A1350A	NM_004996.3	NP_004987.2	P33527	MRP1_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 1	1406	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				arachidonic acid metabolic process (GO:0019369)|ATP catabolic process (GO:0006200)|cobalamin metabolic process (GO:0009235)|leukotriene metabolic process (GO:0006691)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			breast(3)|endometrium(9)|kidney(3)|large_intestine(12)|lung(20)|ovary(5)|prostate(1)|skin(3)	56					Abiraterone(DB05812)|Aminohippurate(DB00345)|Amprenavir(DB00701)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Diclofenac(DB00586)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Epirubicin(DB00445)|Erythromycin(DB00199)|Etoposide(DB00773)|Fluorescein(DB00693)|Glutathione(DB00143)|Glyburide(DB01016)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Methotrexate(DB00563)|Mifepristone(DB00834)|Mitoxantrone(DB01204)|Ofloxacin(DB01165)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Probenecid(DB01032)|Progesterone(DB00396)|Rifampicin(DB01045)|Ritonavir(DB00503)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sulfinpyrazone(DB01138)|Vandetanib(DB05294)|Vemurafenib(DB08881)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Zoledronate(DB00399)	TGGAGCTGGCCCACCTGAAGG	0.562													C|||	28	0.00559105	0.0166	0.0058	5008	,	,		18552	0.0		0.002	False		,,,				2504	0.0				p.A1406A		Atlas-SNP	.											.	ABCC1	156	.	0			c.C4218T						PASS	.	C	,,,,	64,3882		0,64,1909	51.0	52.0	52.0		4218,4041,4050,3873,4218	-12.1	0.2	16	dbSNP_126	52	6,8310		0,6,4152	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ABCC1	NM_004996.3,NM_019862.2,NM_019898.2,NM_019899.2,NM_019900.2	,,,,	0,70,6061	TT,TC,CC		0.0722,1.6219,0.5709	,,,,	1406/1532,1347/1473,1350/1476,1291/1417,1406/1467	16230427	70,12192	1973	4158	6131	SO:0001819	synonymous_variant	4363	exon29			GCTGGCCCACCTG	L05628	CCDS42122.1	16p13.1	2012-03-14			ENSG00000103222	ENSG00000103222		"""ATP binding cassette transporters / subfamily C"""	51	protein-coding gene	gene with protein product		158343	"""multidrug resistance associated protein 1"""	MRP, MRP1		8098549, 1360704	Standard	NM_004996		Approved	GS-X	uc010bvi.3	P33527	OTTHUMG00000048267	ENST00000399410.3:c.4218C>T	16.37:g.16230427C>T		88.0	0.0	0		118.0	54.0	0.457627	NM_004996	A3RJX2|C9JPJ4|O14819|O43333|P78419|Q59GI9|Q9UQ97|Q9UQ99|Q9UQA0	Silent	SNP	ENST00000399410.3	37	CCDS42122.1																																																																																			C|0.994;T|0.006	0.006	strong		0.562	ABCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109701.1	NM_004996	
SCARB1	949	hgsc.bcm.edu	37	12	125263039	125263039	+	3'UTR	SNP	C	C	T	rs701103	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:125263039C>T	ENST00000415380.2	-	0	1870				SCARB1_ENST00000339570.5_Missense_Mutation_p.G499R|SCARB1_ENST00000261693.6_3'UTR|SCARB1_ENST00000376788.1_3'UTR			Q8WTV0	SCRB1_HUMAN	scavenger receptor class B, member 1						adhesion of symbiont to host (GO:0044406)|androgen biosynthetic process (GO:0006702)|blood vessel endothelial cell migration (GO:0043534)|cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol import (GO:0070508)|detection of lipopolysaccharide (GO:0032497)|endothelial cell proliferation (GO:0001935)|high-density lipoprotein particle clearance (GO:0034384)|high-density lipoprotein particle remodeling (GO:0034375)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|lipoprotein metabolic process (GO:0042157)|low-density lipoprotein particle clearance (GO:0034383)|phospholipid transport (GO:0015914)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of triglyceride biosynthetic process (GO:0010867)|receptor-mediated endocytosis (GO:0006898)|recognition of apoptotic cell (GO:0043654)|regulation of phagocytosis (GO:0050764)|regulation of phosphatidylcholine catabolic process (GO:0010899)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|viral process (GO:0016032)|wound healing (GO:0042060)	caveola (GO:0005901)|cell surface (GO:0009986)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|microvillus membrane (GO:0031528)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|apolipoprotein A-I binding (GO:0034186)|apolipoprotein binding (GO:0034185)|high-density lipoprotein particle binding (GO:0008035)|high-density lipoprotein particle receptor activity (GO:0070506)|lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|low-density lipoprotein particle binding (GO:0030169)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|prostate(1)	17	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000116)|Epithelial(86;0.000415)|all cancers(50;0.00395)	Phosphatidylserine(DB00144)	GGGGGCTGTCCGCTGGGAGAG	0.692													C|||	305	0.0609026	0.2224	0.0144	5008	,	,		12888	0.0		0.001	False		,,,				2504	0.0				p.G499R		Atlas-SNP	.											.	SCARB1	40	.	0			c.G1495A						PASS	.	C	ARG/GLY,	644,3422		39,566,1428	7.0	11.0	10.0		1495,	1.5	0.0	12	dbSNP_86	10	16,8256		0,16,4120	yes	missense,utr-3	SCARB1	NM_001082959.1,NM_005505.4	125,	39,582,5548	TT,TC,CC		0.1934,15.8387,5.3493	,	499/507,	125263039	660,11678	2033	4136	6169	SO:0001624	3_prime_UTR_variant	949	exon12			GCTGTCCGCTGGG	Z22555	CCDS9259.1, CCDS45008.1	12q24.32	2008-08-05	2002-09-06	2002-09-06	ENSG00000073060	ENSG00000073060			1664	protein-coding gene	gene with protein product		601040	"""CD36 antigen (collagen type I receptor, thrombospondin receptor)-like 1"""	CD36L1		7689561	Standard	NM_001082959		Approved	SRB1, CLA-1, CLA1, SR-BI	uc001ugm.4	Q8WTV0	OTTHUMG00000168544	ENST00000415380.2:c.*86G>A	12.37:g.125263039C>T		28.0	0.0	0		51.0	29.0	0.568627	NM_001082959	F8W8N0|Q14016|Q52LZ5|Q6KFX4	Missense_Mutation	SNP	ENST00000415380.2	37		100	0.045787545787545784	92	0.18699186991869918	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	C	12.90	2.077750	0.36662	0.158387	0.001934	ENSG00000073060	ENST00000339570	T	0.61158	0.13	4.36	1.45	0.22620	.	.	.	.	.	T	0.00073	0.0002	L	0.36672	1.1	0.53688	P	2.4000000000024002E-5	B	0.33135	0.399	B	0.24006	0.05	T	0.03773	-1.1005	8	0.44086	T	0.13	.	4.3702	0.11244	0.0:0.5966:0.1882:0.2152	rs701103;rs747156;rs60594950	499	F8W8N0	.	R	499	ENSP00000343795:G499R	ENSP00000343795:G499R	G	-	1	0	SCARB1	123828992	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.608000	0.05641	-0.010000	0.14271	0.455000	0.32223	GGA	C|0.956;T|0.044	0.044	strong		0.692	SCARB1-006	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000400165.1	NM_005505	
KRT16	3868	hgsc.bcm.edu	37	17	39768756	39768756	+	Missense_Mutation	SNP	C	C	T	rs367990963	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39768756C>T	ENST00000301653.4	-	1	249	c.185G>A	c.(184-186)tGc>tAc	p.C62Y		NM_005557.3	NP_005548.2	P08779	K1C16_HUMAN	keratin 16	62	Head.				aging (GO:0007568)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|epidermis development (GO:0008544)|hair cycle (GO:0042633)|intermediate filament cytoskeleton organization (GO:0045104)|negative regulation of cell migration (GO:0030336)	cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		Breast(137;0.000307)				CCCCAGCCCGCAGGCTCCCCC	0.687													c|||	4	0.000798722	0.003	0.0	5008	,	,		14972	0.0		0.0	False		,,,				2504	0.0				p.C62Y		Atlas-SNP	.											.	KRT16	45	.	0			c.G185A						PASS	.	C	TYR/CYS	4,4352		0,4,2174	28.0	35.0	32.0		185	3.3	1.0	17		32	0,8536		0,0,4268	no	missense	KRT16	NM_005557.3	194	0,4,6442	TT,TC,CC		0.0,0.0918,0.031	benign	62/474	39768756	4,12888	2178	4268	6446	SO:0001583	missense	3868	exon1			AGCCCGCAGGCTC	S79867	CCDS11401.1	17q21.2	2013-01-16	2008-08-01		ENSG00000186832	ENSG00000186832		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6423	protein-coding gene	gene with protein product	"""focal non-epidermolytic palmoplantar keratoderma"""	148067				2451124, 16831889	Standard	NM_005557		Approved	NEPPK	uc002hxg.4	P08779	OTTHUMG00000133495	ENST00000301653.4:c.185G>A	17.37:g.39768756C>T	ENSP00000301653:p.Cys62Tyr	72.0	0.0	0		77.0	37.0	0.480519	NM_005557	A8K488|P30654|Q16402|Q9UBG8	Missense_Mutation	SNP	ENST00000301653.4	37	CCDS11401.1	.	.	.	.	.	.	.	.	.	.	C	14.27	2.484513	0.44147	9.18E-4	0.0	ENSG00000186832	ENST00000301653	T	0.75260	-0.92	4.33	3.33	0.38152	.	0.000000	0.53938	D	0.000045	T	0.55924	0.1951	N	0.19112	0.55	0.30188	N	0.799798	B	0.31256	0.316	B	0.28553	0.091	T	0.55717	-0.8097	10	0.35671	T	0.21	.	9.6049	0.39628	0.1605:0.6847:0.1548:0.0	.	62	P08779	K1C16_HUMAN	Y	62	ENSP00000301653:C62Y	ENSP00000301653:C62Y	C	-	2	0	KRT16	37022282	0.046000	0.20272	0.997000	0.53966	0.971000	0.66376	0.141000	0.16076	1.127000	0.42034	0.462000	0.41574	TGC	.	.	weak		0.687	KRT16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257408.1	NM_005557	
PARP14	54625	hgsc.bcm.edu	37	3	122419292	122419292	+	Missense_Mutation	SNP	A	A	G	rs7632072	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122419292A>G	ENST00000474629.2	+	6	2157	c.1891A>G	c.(1891-1893)Act>Gct	p.T631A		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	631					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		CTCCCCAAACACTGTAATCAT	0.348													A|||	278	0.0555112	0.1218	0.0576	5008	,	,		21423	0.001		0.0487	False		,,,				2504	0.0276				p.T631A		Atlas-SNP	.											.	PARP14	242	.	0			c.A1891G						PASS	.	A	ALA/THR	342,3342		18,306,1518	31.0	30.0	31.0		1891	2.1	0.0	3	dbSNP_116	31	361,7841		5,351,3745	yes	missense	PARP14	NM_017554.2	58	23,657,5263	GG,GA,AA		4.4014,9.2834,5.9145	probably-damaging	631/1802	122419292	703,11183	1842	4101	5943	SO:0001583	missense	54625	exon6			CCAAACACTGTAA	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"""Poly (ADP-ribose) polymerases"""	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.1891A>G	3.37:g.122419292A>G	ENSP00000418194:p.Thr631Ala	65.0	0.0	0		87.0	42.0	0.482759	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	37	CCDS46894.1	111	0.050824175824175824	49	0.09959349593495935	22	0.06077348066298342	1	0.0017482517482517483	39	0.051451187335092345	A	13.04	2.119612	0.37436	0.092834	0.044014	ENSG00000173193	ENST00000474629;ENST00000398162	T	0.10099	2.91	6.06	2.12	0.27331	.	0.174182	0.39759	N	0.001269	T	0.00271	0.0008	M	0.66939	2.045	0.09310	N	1	P;B	0.38827	0.649;0.376	B;B	0.33690	0.168;0.055	T	0.30268	-0.9984	10	0.36615	T	0.2	.	3.82	0.08832	0.663:0.1354:0.0717:0.1299	rs7632072;rs52827643;rs7632072	631;631	Q460N5-4;Q460N5	.;PAR14_HUMAN	A	631;550	ENSP00000418194:T631A	ENSP00000381228:T550A	T	+	1	0	PARP14	123901982	0.014000	0.17966	0.001000	0.08648	0.003000	0.03518	1.250000	0.32850	0.497000	0.27926	0.533000	0.62120	ACT	A|0.950;G|0.050	0.050	strong		0.348	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554	
C9orf50	375759	hgsc.bcm.edu	37	9	132377769	132377769	+	Missense_Mutation	SNP	G	G	A	rs117566704	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:132377769G>A	ENST00000372478.4	-	4	1075	c.874C>T	c.(874-876)Cgc>Tgc	p.R292C	NTMT1_ENST00000372486.1_Intron	NM_199350.3	NP_955382.3	Q5SZB4	CI050_HUMAN	chromosome 9 open reading frame 50	292										central_nervous_system(1)|endometrium(4)|large_intestine(2)|ovary(1)|skin(1)|urinary_tract(1)	10		Ovarian(14;0.00556)				TTACCTGAGCGTCTGCGCTCC	0.642													g|||	3	0.000599042	0.0015	0.0	5008	,	,		18538	0.0		0.0	False		,,,				2504	0.001				p.R292C		Atlas-SNP	.											.	C9orf50	25	.	0			c.C874T						PASS	.		CYS/ARG	11,4395	17.9+/-39.9	0,11,2192	53.0	45.0	48.0		874	0.8	0.0	9	dbSNP_132	48	0,8600		0,0,4300	yes	missense	C9orf50	NM_199350.3	180	0,11,6492	AA,AG,GG		0.0,0.2497,0.0846	benign	292/432	132377769	11,12995	2203	4300	6503	SO:0001583	missense	375759	exon4			CTGAGCGTCTGCG	AK093122	CCDS35159.1	9q34.2	2012-03-15			ENSG00000179058	ENSG00000179058			23677	protein-coding gene	gene with protein product							Standard	NM_199350		Approved	FLJ35803	uc004byc.4	Q5SZB4	OTTHUMG00000020786	ENST00000372478.4:c.874C>T	9.37:g.132377769G>A	ENSP00000361556:p.Arg292Cys	62.0	0.0	0		63.0	35.0	0.555556	NM_199350	Q2M1I2|Q8NA65	Missense_Mutation	SNP	ENST00000372478.4	37	CCDS35159.1	.	.	.	.	.	.	.	.	.	.	g	6.146	0.395061	0.11638	0.002497	0.0	ENSG00000179058	ENST00000372478	T	0.18657	2.2	3.17	0.799	0.18667	.	1.485060	0.04472	N	0.376207	T	0.11196	0.0273	N	0.05124	-0.11	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30238	-0.9985	10	0.46703	T	0.11	1.6017	5.7707	0.18251	0.5791:0.0:0.4209:0.0	.	292	Q5SZB4	CI050_HUMAN	C	292	ENSP00000361556:R292C	ENSP00000361556:R292C	R	-	1	0	C9orf50	131417590	0.001000	0.12720	0.000000	0.03702	0.005000	0.04900	0.457000	0.21875	-0.097000	0.12307	-1.479000	0.00991	CGC	A|0.001;C|0.002;G|0.998	0.001	strong		0.642	C9orf50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054593.1	NM_199350	
SSTR3	6753	hgsc.bcm.edu	37	22	37602611	37602611	+	Missense_Mutation	SNP	C	C	G	rs229568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:37602611C>G	ENST00000328544.3	-	2	1765	c.1232G>C	c.(1231-1233)aGc>aCc	p.S411T	SSTR3_ENST00000402501.1_Missense_Mutation_p.S411T	NM_001051.3	NP_001042.1	P32745	SSR3_HUMAN	somatostatin receptor 3	411			S -> T (in dbSNP:rs229568).		cell-cell signaling (GO:0007267)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucocorticoid stimulus (GO:0071385)|cerebellum development (GO:0021549)|forebrain development (GO:0030900)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|hormone-mediated apoptotic signaling pathway (GO:0008628)|negative regulation of cell proliferation (GO:0008285)|response to starvation (GO:0042594)|somatostatin signaling pathway (GO:0038170)|spermatogenesis (GO:0007283)	ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			NS(1)|breast(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)	14					Pasireotide(DB06663)	GCGCATCGTGCTGGACTTCTC	0.657													C|||	319	0.0636981	0.2284	0.0202	5008	,	,		16100	0.0		0.003	False		,,,				2504	0.0				p.S411T		Atlas-SNP	.											.	SSTR3	42	.	0			c.G1232C						PASS	.	C	THR/SER	912,3494	340.7+/-306.4	97,718,1388	55.0	59.0	58.0		1232	3.4	0.0	22	dbSNP_79	58	7,8593	5.7+/-21.5	0,7,4293	yes	missense	SSTR3	NM_001051.2	58	97,725,5681	GG,GC,CC		0.0814,20.699,7.066	benign	411/419	37602611	919,12087	2203	4300	6503	SO:0001583	missense	6753	exon2			ATCGTGCTGGACT		CCDS13944.1	22q13.1	2012-08-08			ENSG00000183473	ENSG00000278195		"""GPCR / Class A : Somatostatin receptors"""	11332	protein-coding gene	gene with protein product		182453				8449518	Standard	XM_006724311		Approved		uc003arb.3	P32745	OTTHUMG00000150537	ENST00000328544.3:c.1232G>C	22.37:g.37602611C>G	ENSP00000330138:p.Ser411Thr	64.0	0.0	0		72.0	34.0	0.472222	NM_001051	A8K550|Q53ZR7	Missense_Mutation	SNP	ENST00000328544.3	37	CCDS13944.1	117	0.05357142857142857	107	0.21747967479674796	8	0.022099447513812154	0	0.0	2	0.002638522427440633	C	8.330	0.826175	0.16749	0.20699	8.14E-4	ENSG00000183473	ENST00000328544;ENST00000402501	T;T	0.73047	-0.71;-0.71	5.51	3.4	0.38934	.	1.198980	0.05892	N	0.628461	T	0.00073	0.0002	L	0.43152	1.355	0.42474	P	0.00717000000000001	B	0.27559	0.181	B	0.19148	0.024	T	0.04255	-1.0965	9	0.56958	D	0.05	.	12.2253	0.54457	0.0:0.8595:0.0:0.1405	rs229568;rs16997931;rs229568	411	P32745	SSR3_HUMAN	T	411	ENSP00000330138:S411T;ENSP00000384904:S411T	ENSP00000330138:S411T	S	-	2	0	SSTR3	35932557	0.000000	0.05858	0.027000	0.17364	0.063000	0.16089	0.291000	0.18994	1.328000	0.45358	0.491000	0.48974	AGC	C|0.934;G|0.066	0.066	strong		0.657	SSTR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318802.1		
C10orf71	118461	hgsc.bcm.edu	37	10	50531520	50531520	+	Silent	SNP	C	C	A	rs73307889	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:50531520C>A	ENST00000374144.3	+	3	1218	c.930C>A	c.(928-930)acC>acA	p.T310T	C10orf71_ENST00000323868.4_Silent_p.T310T			Q711Q0	CJ071_HUMAN	chromosome 10 open reading frame 71	310										endometrium(1)	1						GGGACACGACCTTGCTAAGAG	0.567													C|||	98	0.0195687	0.0719	0.0043	5008	,	,		19049	0.0		0.0	False		,,,				2504	0.0				p.T310T		Atlas-SNP	.											C10orf71_ENST00000374144,NS,carcinoma,+1,2	C10orf71	179	2	0			c.C930A						scavenged	.	C	,	237,3885		7,223,1831	70.0	79.0	76.0		930,930	-1.9	0.0	10	dbSNP_130	76	3,8405		0,3,4201	no	coding-synonymous,coding-synonymous	C10orf71	NM_001135196.1,NM_199459.3	,	7,226,6032	AA,AC,CC		0.0357,5.7496,1.9154	,	310/1436,310/720	50531520	240,12290	2061	4204	6265	SO:0001819	synonymous_variant	118461	exon3			CACGACCTTGCTA	AL833265	CCDS44387.1	10q11.23	2012-05-31			ENSG00000177354	ENSG00000177354			26973	protein-coding gene	gene with protein product							Standard	NM_001135196		Approved	FLJ45913	uc021pqa.2	Q711Q0	OTTHUMG00000018190	ENST00000374144.3:c.930C>A	10.37:g.50531520C>A		78.0	1.0	0.0128205		72.0	34.0	0.472222	NM_001135196	A0AVL8	Silent	SNP	ENST00000374144.3	37	CCDS44387.1																																																																																			C|0.984;A|0.016	0.016	strong		0.567	C10orf71-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047984.2	NM_199459	
ACOT12	134526	hgsc.bcm.edu	37	5	80655766	80655766	+	Missense_Mutation	SNP	T	T	G	rs147339997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:80655766T>G	ENST00000307624.3	-	5	480	c.452A>C	c.(451-453)gAa>gCa	p.E151A	ACOT12_ENST00000513751.1_Missense_Mutation_p.E151A	NM_130767.2	NP_570123.1	Q8WYK0	ACO12_HUMAN	acyl-CoA thioesterase 12	151					acetyl-CoA metabolic process (GO:0006084)|acyl-CoA metabolic process (GO:0006637)|fatty acid metabolic process (GO:0006631)|pyruvate metabolic process (GO:0006090)	cytosol (GO:0005829)	acetyl-CoA hydrolase activity (GO:0003986)|ATP binding (GO:0005524)|carboxylic ester hydrolase activity (GO:0052689)|lipid binding (GO:0008289)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(2)	23		Lung NSC(167;0.0176)|all_lung(232;0.0205)|Ovarian(174;0.135)		OV - Ovarian serous cystadenocarcinoma(54;1.37e-45)|Epithelial(54;1.25e-39)|all cancers(79;5.01e-34)		AAAGGTATCTTCATGTTGTAA	0.333													T|||	11	0.00219649	0.0083	0.0	5008	,	,		17992	0.0		0.0	False		,,,				2504	0.0				p.E151A		Atlas-SNP	.											.	ACOT12	57	.	0			c.A452C						PASS	.	T	ALA/GLU	45,4361	47.5+/-82.1	0,45,2158	127.0	124.0	125.0		452	5.0	0.7	5	dbSNP_134	125	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ACOT12	NM_130767.2	107	0,46,6457	GG,GT,TT		0.0116,1.0213,0.3537	possibly-damaging	151/556	80655766	46,12960	2203	4300	6503	SO:0001583	missense	134526	exon5			GTATCTTCATGTT	AB078619	CCDS4055.1	5q14.1	2011-09-13			ENSG00000172497	ENSG00000172497		"""Acyl CoA thioesterases"", ""StAR-related lipid transfer (START) domain containing"""	24436	protein-coding gene	gene with protein product	"""StAR-related lipid transfer (START) domain containing 15"""	614315				16103133, 16940157	Standard	NM_130767		Approved	Cach, THEAL, STARD15	uc003khl.4	Q8WYK0	OTTHUMG00000131305	ENST00000307624.3:c.452A>C	5.37:g.80655766T>G	ENSP00000303246:p.Glu151Ala	165.0	0.0	0		152.0	79.0	0.519737	NM_130767	B3KVK9|Q5FWE9	Missense_Mutation	SNP	ENST00000307624.3	37	CCDS4055.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	T	0.472	-0.883839	0.02530	0.010213	1.16E-4	ENSG00000172497	ENST00000307624;ENST00000513751	T;T	0.30981	1.51;1.51	5.04	5.04	0.67666	.	0.058734	0.64402	D	0.000004	T	0.14570	0.0352	L	0.35249	1.045	0.47094	D	0.999312	B;B	0.13145	0.0;0.007	B;B	0.12156	0.001;0.007	T	0.06734	-1.0810	10	0.11794	T	0.64	-31.4031	9.2551	0.37579	0.0:0.0858:0.0:0.9142	.	151;151	Q5FWE9;Q8WYK0	.;ACO12_HUMAN	A	151	ENSP00000303246:E151A;ENSP00000421628:E151A	ENSP00000303246:E151A	E	-	2	0	ACOT12	80691522	0.996000	0.38824	0.705000	0.30386	0.094000	0.18550	1.765000	0.38481	2.030000	0.59900	0.533000	0.62120	GAA	T|0.996;G|0.004	0.004	strong		0.333	ACOT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254074.1	NM_130767	
ZNF577	84765	hgsc.bcm.edu	37	19	52375809	52375809	+	Silent	SNP	A	A	G	rs142094475	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:52375809A>G	ENST00000301399.5	-	7	1799	c.1434T>C	c.(1432-1434)taT>taC	p.Y478Y	ZNF577_ENST00000451628.2_Silent_p.Y419Y|ZNF577_ENST00000412216.1_Intron|ZNF577_ENST00000420592.1_Silent_p.Y419Y|ZNF577_ENST00000485702.1_Intron	NM_032679.2	NP_116068.2	Q9BSK1	ZN577_HUMAN	zinc finger protein 577	478					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	21		all_neural(266;0.0602)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		TATCTGTAAGATACAAGATAT	0.353													A|||	8	0.00159744	0.0023	0.0072	5008	,	,		19580	0.0		0.0	False		,,,				2504	0.0				p.Y478Y		Atlas-SNP	.											.	ZNF577	63	.	0			c.T1434C						PASS	.	A	,	19,4385		0,19,2183	40.0	40.0	40.0		1257,1434	1.9	0.0	19	dbSNP_134	40	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ZNF577	NM_001135590.1,NM_032679.2	,	0,19,6483	GG,GA,AA		0.0,0.4314,0.1461	,	419/427,478/486	52375809	19,12985	2202	4300	6502	SO:0001819	synonymous_variant	84765	exon7			TGTAAGATACAAG	AL832871	CCDS12842.2, CCDS46160.1	19q13.41	2013-09-20			ENSG00000161551	ENSG00000161551		"""Zinc fingers, C2H2-type"", ""-"""	28673	protein-coding gene	gene with protein product						12477932	Standard	NM_032679		Approved	MGC4400	uc010yde.2	Q9BSK1	OTTHUMG00000157045	ENST00000301399.5:c.1434T>C	19.37:g.52375809A>G		67.0	0.0	0		56.0	26.0	0.464286	NM_032679	A8K0B4|A8K6Z7|C9JFB9	Silent	SNP	ENST00000301399.5	37	CCDS12842.2																																																																																			A|0.998;G|0.002	0.002	strong		0.353	ZNF577-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347243.1	NM_032679	
CCDC184	387856	hgsc.bcm.edu	37	12	48577925	48577925	+	Missense_Mutation	SNP	A	A	G	rs140861476		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:48577925A>G	ENST00000316554.3	+	1	560	c.20A>G	c.(19-21)gAg>gGg	p.E7G		NM_001013635.3	NP_001013657.3	Q52MB2	CC184_HUMAN		7						cytoplasm (GO:0005737)				central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)	4						GGTCTGCTGGAGATCATGACC	0.706																																					p.E7G		Atlas-SNP	.											.	C12orf68	11	.	0			c.A20G						PASS	.	A	GLY/GLU	3,4403		0,3,2200	28.0	36.0	33.0		20	4.9	1.0	12	dbSNP_134	33	0,8598		0,0,4299	no	missense	C12orf68	NM_001013635.3	98	0,3,6499	GG,GA,AA		0.0,0.0681,0.0231	benign	7/195	48577925	3,13001	2203	4299	6502	SO:0001583	missense	387856	exon1			TGCTGGAGATCAT																												ENST00000316554.3:c.20A>G	12.37:g.48577925A>G	ENSP00000320849:p.Glu7Gly	49.0	0.0	0		47.0	22.0	0.468085	NM_001013635	Q96MK5|Q96N39	Missense_Mutation	SNP	ENST00000316554.3	37	CCDS31785.1	.	.	.	.	.	.	.	.	.	.	A	14.73	2.623833	0.46840	6.81E-4	0.0	ENSG00000177875	ENST00000316554	T	0.57273	0.41	4.9	4.9	0.64082	.	0.000000	0.52532	D	0.000075	T	0.50939	0.1645	N	0.08118	0	0.35002	D	0.756066	D	0.76494	0.999	D	0.78314	0.991	T	0.66304	-0.5957	10	0.87932	D	0	-21.6442	10.8402	0.46710	1.0:0.0:0.0:0.0	.	7	Q52MB2	CL068_HUMAN	G	7	ENSP00000320849:E7G	ENSP00000320849:E7G	E	+	2	0	C12orf68	46864192	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.151000	0.58105	2.049000	0.60858	0.491000	0.48974	GAG	A|1.000;G|0.000	0.000	weak		0.706	C12orf68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406514.1		
PRR14L	253143	hgsc.bcm.edu	37	22	32109305	32109305	+	Missense_Mutation	SNP	T	T	C	rs112331962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:32109305T>C	ENST00000327423.6	-	4	4709	c.4520A>G	c.(4519-4521)cAt>cGt	p.H1507R	PRR14L_ENST00000397493.2_Missense_Mutation_p.H1507R|PRR14L_ENST00000434485.1_Missense_Mutation_p.H1507R	NM_173566.2	NP_775837.2	Q5THK1	PR14L_HUMAN	proline rich 14-like	1507										endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(5)|skin(1)|urinary_tract(2)	14						AAAGGCACCATGTATTTGATC	0.473													T|||	191	0.038139	0.1377	0.013	5008	,	,		19854	0.0		0.0	False		,,,				2504	0.0				p.H1507R		Atlas-SNP	.											.	PRR14L	198	.	0			c.A4520G						PASS	.	T	ARG/HIS	138,1246		3,132,557	169.0	140.0	149.0		4520	-0.7	0.0	22	dbSNP_132	149	3,3179		0,3,1588	yes	missense	PRR14L	NM_173566.2	29	3,135,2145	CC,CT,TT		0.0943,9.9711,3.088	benign	1507/2152	32109305	141,4425	692	1591	2283	SO:0001583	missense	253143	exon4			GCACCATGTATTT	BC040859	CCDS13900.2	22q12.2	2011-01-25	2011-01-25	2011-01-25	ENSG00000183530	ENSG00000183530			28738	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 30"""	C22orf30		12477932	Standard	NM_173566		Approved	MGC50372	uc003alp.4	Q5THK1	OTTHUMG00000030139	ENST00000327423.6:c.4520A>G	22.37:g.32109305T>C	ENSP00000331845:p.His1507Arg	101.0	0.0	0		100.0	50.0	0.5	NM_173566	Q5THK4|Q6ZNN1|Q6ZWH0|Q8IW74|Q9H5T4	Missense_Mutation	SNP	ENST00000327423.6	37	CCDS13900.2	66	0.03021978021978022	63	0.12804878048780488	3	0.008287292817679558	0	0.0	0	0.0	T	3.362	-0.130293	0.06753	0.099711	9.43E-4	ENSG00000183530	ENST00000397493;ENST00000327423;ENST00000434485	T;T;T	0.05786	3.39;3.41;3.4	5.59	-0.745	0.11098	.	0.617385	0.14488	N	0.316502	T	0.00039	0.0001	L	0.44542	1.39	0.09310	N	1	B;B;B	0.12013	0.003;0.003;0.005	B;B;B	0.09377	0.004;0.003;0.004	T	0.44892	-0.9298	9	.	.	.	0.0323	1.9244	0.03314	0.1203:0.3338:0.2122:0.3338	.	1507;1507;1507	Q5THK1-2;Q5THK1;Q5THK1-4	.;PR14L_HUMAN;.	R	1507	ENSP00000380630:H1507R;ENSP00000331845:H1507R;ENSP00000388314:H1507R	.	H	-	2	0	PRR14L	30439305	0.000000	0.05858	0.024000	0.17045	0.610000	0.37248	-1.136000	0.03222	0.073000	0.16731	-1.151000	0.01829	CAT	T|0.975;C|0.025	0.025	strong		0.473	PRR14L-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074993.2	NM_173566	
FBXO10	26267	hgsc.bcm.edu	37	9	37537892	37537892	+	Missense_Mutation	SNP	G	G	T	rs7044561	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:37537892G>T	ENST00000432825.2	-	3	682	c.634C>A	c.(634-636)Cac>Aac	p.H212N	FBXO10_ENST00000543968.1_5'Flank|RP11-613M10.8_ENST00000544475.1_5'UTR|FBXO10_ENST00000541829.1_Intron	NM_012166.2	NP_036298.2	Q9UK96	FBX10_HUMAN	F-box protein 10	212			H -> N (found in a patient with lymphoma; dbSNP:rs7044561). {ECO:0000269|PubMed:23431138}.		apoptotic process (GO:0006915)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of apoptotic process (GO:0042981)	cytoplasm (GO:0005737)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(5)|large_intestine(11)|lung(15)|prostate(1)|upper_aerodigestive_tract(1)	34				GBM - Glioblastoma multiforme(29;0.0107)		ACCTGGATGTGCCCGTTCTCA	0.488													G|||	76	0.0151757	0.0575	0.0	5008	,	,		21854	0.0		0.0	False		,,,				2504	0.0				p.H212N		Atlas-SNP	.											.	FBXO10	75	.	0			c.C634A						PASS	.	G	ASN/HIS	171,3729		8,155,1787	85.0	85.0	85.0		634	5.3	1.0	9	dbSNP_116	85	5,8263		0,5,4129	yes	missense	FBXO10	NM_012166.2	68	8,160,5916	TT,TG,GG		0.0605,4.3846,1.4464	benign	212/957	37537892	176,11992	1950	4134	6084	SO:0001583	missense	26267	exon3			GGATGTGCCCGTT	AF174598	CCDS47966.1	9p13.1	2014-01-29	2004-06-15		ENSG00000147912	ENSG00000147912		"""F-boxes /  ""other"""""	13589	protein-coding gene	gene with protein product		609092	"""F-box only protein 10"""			10531035, 10531037, 19300908	Standard	NM_012166		Approved	FBX10	uc004aab.3	Q9UK96	OTTHUMG00000019926	ENST00000432825.2:c.634C>A	9.37:g.37537892G>T	ENSP00000403802:p.His212Asn	137.0	0.0	0		149.0	75.0	0.503356	NM_012166	Q08AL3|Q08AL4|Q5JRT8|Q9UKC3	Missense_Mutation	SNP	ENST00000432825.2	37	CCDS47966.1	22	0.010073260073260074	22	0.044715447154471545	0	0.0	0	0.0	0	0.0	G	16.84	3.233921	0.58886	0.043846	6.05E-4	ENSG00000147912	ENST00000432825	T	0.40756	1.02	5.3	5.3	0.74995	Pectin lyase fold/virulence factor (1);Pectin lyase fold (1);	0.054328	0.85682	D	0.000000	T	0.06462	0.0166	N	0.14661	0.345	0.80722	D	1	B	0.25105	0.118	B	0.23852	0.049	T	0.05484	-1.0882	10	0.02654	T	1	-29.9635	18.0885	0.89466	0.0:0.0:1.0:0.0	rs7044561;rs52804171;rs7044561	212	Q9UK96	FBX10_HUMAN	N	212	ENSP00000403802:H212N	ENSP00000276960:H212N	H	-	1	0	FBXO10	37527892	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	9.345000	0.97053	2.631000	0.89168	0.655000	0.94253	CAC	G|0.983;T|0.017	0.017	strong		0.488	FBXO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052472.3		
MBP	4155	hgsc.bcm.edu	37	18	74701936	74701936	+	Silent	SNP	G	G	A	rs76912958	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:74701936G>A	ENST00000397869.3	-	2	304	c.258C>T	c.(256-258)ccC>ccT	p.P86P	MBP_ENST00000397865.5_Silent_p.P86P|MBP_ENST00000528160.1_Intron|MBP_ENST00000527041.1_Intron|MBP_ENST00000359645.3_Silent_p.P112P|MBP_ENST00000526111.1_Silent_p.P64P|MBP_ENST00000580402.1_Silent_p.P219P|MBP_ENST00000397875.3_Silent_p.P86P|MBP_ENST00000382582.3_Silent_p.P112P|MBP_ENST00000579129.1_Silent_p.P219P|MBP_ENST00000355994.2_Silent_p.P219P|MBP_ENST00000354542.4_Intron|MBP_ENST00000578193.1_Silent_p.P86P|MBP_ENST00000397866.4_Silent_p.P86P			P13727	PRG2_HUMAN	myelin basic protein	0					defense response to bacterium (GO:0042742)|defense response to nematode (GO:0002215)|immune response (GO:0006955)|negative regulation of interleukin-10 production (GO:0032693)|positive regulation of interleukin-4 production (GO:0032753)	cytoplasmic vesicle (GO:0031410)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)|heparin binding (GO:0008201)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	19		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.79e-06)|BRCA - Breast invasive adenocarcinoma(31;0.113)|READ - Rectum adenocarcinoma(1;0.188)	Sargramostim(DB00020)	AGTGGACTACGGGGTTTTCAT	0.572													G|||	129	0.0257588	0.0923	0.0101	5008	,	,		17532	0.0		0.0	False		,,,				2504	0.0				p.P219P	NSCLC(17;72 1131 19392)	Atlas-SNP	.											.	MBP	45	.	0			c.C657T						PASS	.	G	,,,,	327,4079	172.3+/-202.3	8,311,1884	179.0	160.0	167.0		336,258,258,657,336	-6.3	1.0	18	dbSNP_131	167	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MBP	NM_001025081.1,NM_001025090.1,NM_001025092.1,NM_001025101.1,NM_002385.2	,,,,	8,315,6180	AA,AG,GG		0.0465,7.4217,2.545	,,,,	112/198,86/172,86/161,219/305,112/187	74701936	331,12675	2203	4300	6503	SO:0001819	synonymous_variant	4155	exon5			GACTACGGGGTTT		CCDS12011.1, CCDS32847.1, CCDS42448.1, CCDS42449.1, CCDS42450.1	18q23	2008-08-01			ENSG00000197971	ENSG00000197971			6925	protein-coding gene	gene with protein product		159430				2425357	Standard	XM_005266699		Approved		uc010xfd.2	P02686	OTTHUMG00000132874	ENST00000397869.3:c.258C>T	18.37:g.74701936G>A		153.0	0.0	0		148.0	72.0	0.486486	NM_001025101	A6XMW0|B2R5I1|P81448|Q14227|Q6ICT2	Silent	SNP	ENST00000397869.3	37																																																																																				G|0.977;A|0.023	0.023	strong		0.572	MBP-024	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000267964.1	NM_001025081	
PWWP2B	170394	hgsc.bcm.edu	37	10	134219291	134219291	+	Silent	SNP	C	C	T	rs139452616	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:134219291C>T	ENST00000305233.5	+	2	1346	c.1287C>T	c.(1285-1287)gaC>gaT	p.D429D	PWWP2B_ENST00000368609.4_Silent_p.D429D	NM_138499.3	NP_612508.3	Q6NUJ5	PWP2B_HUMAN	PWWP domain containing 2B	429										central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(5)|urinary_tract(1)	9		all_cancers(35;6.69e-12)|all_epithelial(44;1.55e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Breast(234;0.106)|Colorectal(31;0.109)|Melanoma(40;0.123)|Glioma(114;0.203)|all_hematologic(284;0.224)		OV - Ovarian serous cystadenocarcinoma(35;7.49e-05)|Epithelial(32;0.00016)|all cancers(32;0.000186)		ACAGCCTGGACGAGGCCAGAT	0.697													C|||	57	0.0113818	0.0393	0.0058	5008	,	,		15963	0.0		0.001	False		,,,				2504	0.0				p.D429D		Atlas-SNP	.											.	PWWP2B	33	.	0			c.C1287T						PASS	.	C	,	156,4234	103.4+/-141.9	3,150,2042	30.0	29.0	29.0		1287,1287	-7.2	0.1	10	dbSNP_134	29	2,8594	2.2+/-6.3	0,2,4296	no	coding-synonymous,coding-synonymous	PWWP2B	NM_001098637.1,NM_138499.3	,	3,152,6338	TT,TC,CC		0.0233,3.5535,1.2167	,	429/500,429/591	134219291	158,12828	2195	4298	6493	SO:0001819	synonymous_variant	170394	exon2			CCTGGACGAGGCC	AK128663	CCDS7667.2	10q26.3	2009-06-03	2007-10-22	2007-10-22	ENSG00000171813	ENSG00000171813			25150	protein-coding gene	gene with protein product			"""PWWP domain containing 2"""	PWWP2			Standard	NM_001098637		Approved	bA432J24.1, FLJ46823	uc001lll.4	Q6NUJ5	OTTHUMG00000019286	ENST00000305233.5:c.1287C>T	10.37:g.134219291C>T		19.0	0.0	0		17.0	12.0	0.705882	NM_001098637	A6NM90|B5MDQ1|H9KV61|Q5SZI0|Q6ZQX5|Q96F43	Silent	SNP	ENST00000305233.5	37	CCDS7667.2																																																																																			C|0.986;T|0.014	0.014	strong		0.697	PWWP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051075.3	NM_138499	
LTBP2	4053	hgsc.bcm.edu	37	14	74973926	74973926	+	Missense_Mutation	SNP	C	C	A	rs139481866	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:74973926C>A	ENST00000261978.4	-	26	4249	c.3863G>T	c.(3862-3864)gGc>gTc	p.G1288V	LTBP2_ENST00000556690.1_Intron	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	1288	Cys-rich.|EGF-like 14; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				protein secretion (GO:0009306)|protein targeting (GO:0006605)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|liver(1)|lung(29)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		AGGCTGGCAGCCCAGAACACA	0.567													C|||	9	0.00179712	0.0053	0.0029	5008	,	,		19539	0.0		0.0	False		,,,				2504	0.0				p.G1288V		Atlas-SNP	.											.	LTBP2	158	.	0			c.G3863T						PASS	.	C	VAL/GLY	20,4386	28.1+/-56.4	0,20,2183	85.0	80.0	82.0		3863	2.4	0.8	14	dbSNP_134	82	0,8600		0,0,4300	yes	missense	LTBP2	NM_000428.2	109	0,20,6483	AA,AC,CC		0.0,0.4539,0.1538	probably-damaging	1288/1822	74973926	20,12986	2203	4300	6503	SO:0001583	missense	4053	exon26			TGGCAGCCCAGAA		CCDS9831.1	14q24.3	2011-10-20	2001-12-04			ENSG00000119681		"""Latent transforming growth factor, beta binding proteins"""	6715	protein-coding gene	gene with protein product		602091	"""chromosome 14 open reading frame 141"""	LTBP3, C14orf141		7798248	Standard	NM_000428		Approved		uc001xqa.3	Q14767		ENST00000261978.4:c.3863G>T	14.37:g.74973926C>A	ENSP00000261978:p.Gly1288Val	310.0	0.0	0		339.0	178.0	0.525074	NM_000428	Q99907|Q9NS51	Missense_Mutation	SNP	ENST00000261978.4	37	CCDS9831.1	6	0.0027472527472527475	4	0.008130081300813009	2	0.0055248618784530384	0	0.0	0	0.0	C	14.80	2.643520	0.47258	0.004539	0.0	ENSG00000119681	ENST00000261978	D	0.86694	-2.16	5.22	2.36	0.29203	EGF-like calcium-binding (2);	0.521247	0.16060	N	0.231509	D	0.83147	0.5191	L	0.37630	1.12	0.80722	D	1	D	0.67145	0.996	D	0.66351	0.943	T	0.78610	-0.2137	10	0.30078	T	0.28	.	6.5858	0.22620	0.0:0.6598:0.1289:0.2113	.	1288	Q14767	LTBP2_HUMAN	V	1288	ENSP00000261978:G1288V	ENSP00000261978:G1288V	G	-	2	0	LTBP2	74043679	0.996000	0.38824	0.761000	0.31378	0.370000	0.29829	0.463000	0.21972	0.192000	0.20272	-0.224000	0.12420	GGC	C|0.998;A|0.002	0.002	strong		0.567	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428	
KIAA1551	55196	hgsc.bcm.edu	37	12	32134122	32134122	+	Missense_Mutation	SNP	T	T	C	rs75434030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:32134122T>C	ENST00000312561.4	+	4	647	c.233T>C	c.(232-234)aTg>aCg	p.M78T	KIAA1551_ENST00000535596.1_Intron	NM_018169.3	NP_060639	Q9HCM1	K1551_HUMAN	KIAA1551	78																	GTTTCTGATATGCATAATGGG	0.373													T|||	33	0.00658946	0.0242	0.0014	5008	,	,		22474	0.0		0.0	False		,,,				2504	0.0				p.M78T		Atlas-SNP	.											.	.	.	.	0			c.T233C						PASS	.	T	THR/MET	109,4297	84.8+/-123.5	1,107,2095	85.0	83.0	83.0		233	-1.3	0.0	12	dbSNP_131	83	1,8599	1.2+/-3.3	0,1,4299	yes	missense	C12orf35	NM_018169.3	81	1,108,6394	CC,CT,TT		0.0116,2.4739,0.8458	possibly-damaging	78/1748	32134122	110,12896	2203	4300	6503	SO:0001583	missense	55196	exon4			CTGATATGCATAA	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.233T>C	12.37:g.32134122T>C	ENSP00000310338:p.Met78Thr	124.0	0.0	0		168.0	91.0	0.541667	NM_018169	B2RTU5|Q4KN17|Q9NVL6|Q9NWP9	Missense_Mutation	SNP	ENST00000312561.4	37	CCDS8725.2	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	T	10.56	1.385451	0.25031	0.024739	1.16E-4	ENSG00000174718	ENST00000312561;ENST00000381054	T;T	0.09073	3.02;3.02	5.39	-1.28	0.09318	.	0.664905	0.14503	N	0.315631	T	0.01976	0.0062	L	0.29908	0.895	0.09310	N	1	B	0.13145	0.007	B	0.15484	0.013	T	0.40720	-0.9548	9	.	.	.	.	1.6516	0.02773	0.1117:0.2639:0.2202:0.4042	.	78	Q9HCM1	CL035_HUMAN	T	78	ENSP00000310338:M78T;ENSP00000370442:M78T	.	M	+	2	0	C12orf35	32025389	0.000000	0.05858	0.000000	0.03702	0.058000	0.15608	-0.467000	0.06664	-0.141000	0.11374	0.528000	0.53228	ATG	T|0.995;C|0.005	0.005	strong		0.373	KIAA1551-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250307.2	NM_018169	
RFX7	64864	hgsc.bcm.edu	37	15	56387581	56387581	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:56387581C>T	ENST00000559447.2	-	9	2325	c.2054G>A	c.(2053-2055)tGg>tAg	p.W685*	RFX7_ENST00000317318.6_Nonsense_Mutation_p.W782*|RFX7_ENST00000422057.1_Nonsense_Mutation_p.W685*|RFX7_ENST00000423270.1_Nonsense_Mutation_p.W782*			Q2KHR2	RFX7_HUMAN	regulatory factor X, 7	685					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.W685*(1)|p.W782*(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(3)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						GATTTGTTGCCATCCATTTGG	0.378																																					p.W782X		Atlas-SNP	.											RFX7_ENST00000423270,NS,lymphoid_neoplasm,0,2	RFX7	170	2	2	Substitution - Nonsense(2)	haematopoietic_and_lymphoid_tissue(2)	c.G2345A						PASS	.						124.0	116.0	118.0					15																	56387581		1850	4096	5946	SO:0001587	stop_gained	64864	exon9			TGTTGCCATCCAT			15q21.3	2008-08-04	2008-08-04	2008-08-04		ENSG00000181827			25777	protein-coding gene	gene with protein product		612660	"""regulatory factor X domain containing 2"""	RFXDC2			Standard	NM_022841		Approved	FLJ12994	uc010bfn.3	Q2KHR2		ENST00000559447.2:c.2054G>A	15.37:g.56387581C>T	ENSP00000453281:p.Trp685*	79.0	0.0	0		95.0	27.0	0.284211	NM_022841	Q6ZRR1|Q6ZTY6|Q8N3J0|Q9H7A9|Q9H956	Nonsense_Mutation	SNP	ENST00000559447.2	37		.	.	.	.	.	.	.	.	.	.	C	30	5.054224	0.93793	.	.	ENSG00000181827	ENST00000422057;ENST00000317318;ENST00000423270	.	.	.	5.44	4.32	0.51571	.	0.000000	0.64402	D	0.000007	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.19147	T	0.46	-4.9265	14.1694	0.65500	0.0:0.9149:0.0:0.0851	.	.	.	.	X	685;782;782	.	ENSP00000313299:W782X	W	-	2	0	RFX7	54174873	1.000000	0.71417	1.000000	0.80357	0.825000	0.46686	5.485000	0.66850	2.531000	0.85337	0.563000	0.77884	TGG	.	.	none		0.378	RFX7-001	KNOWN	non_canonical_U12|basic	protein_coding	protein_coding	OTTHUMT00000418841.3	NM_022841	
NUP35	129401	hgsc.bcm.edu	37	2	183993085	183993085	+	Silent	SNP	A	A	G	rs61743390	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:183993085A>G	ENST00000295119.4	+	2	214	c.111A>G	c.(109-111)ggA>ggG	p.G37G	NUP35_ENST00000497330.1_3'UTR|NUP35_ENST00000409798.1_Silent_p.G20G|NUP35_ENST00000541912.1_5'UTR	NM_138285.3	NP_612142.2	Q8NFH5	NUP53_HUMAN	nucleoporin 35kDa	37					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)	intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)	8						TCTTACCTGGATTTTTAATGG	0.438													A|||	44	0.00878594	0.0333	0.0	5008	,	,		14995	0.0		0.0	False		,,,				2504	0.0				p.G37G		Atlas-SNP	.											.	NUP35	28	.	0			c.A111G						PASS	.	A		148,4258	101.6+/-140.2	0,148,2055	80.0	78.0	79.0		111	2.7	1.0	2	dbSNP_129	79	2,8598		0,2,4298	no	coding-synonymous	NUP35	NM_138285.3		0,150,6353	GG,GA,AA		0.0233,3.3591,1.1533		37/327	183993085	150,12856	2203	4300	6503	SO:0001819	synonymous_variant	129401	exon2			ACCTGGATTTTTA	AF514993	CCDS2290.1, CCDS74614.1	2q32	2008-02-05			ENSG00000163002	ENSG00000163002			29797	protein-coding gene	gene with protein product		608140					Standard	XM_005246284		Approved	MP44	uc002upf.3	Q8NFH5	OTTHUMG00000132621	ENST00000295119.4:c.111A>G	2.37:g.183993085A>G		90.0	0.0	0		99.0	44.0	0.444444	NM_138285	B4DP57|B4DYB4|Q4ZFZ9|Q53S95|Q8TDJ1	Silent	SNP	ENST00000295119.4	37	CCDS2290.1																																																																																			A|0.989;G|0.011	0.011	strong		0.438	NUP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255865.1	NM_138285	
TICAM2	353376	hgsc.bcm.edu	37	5	114916351	114916351	+	Silent	SNP	T	T	G	rs7705473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:114916351T>G	ENST00000427199.2	-	2	1044	c.603A>C	c.(601-603)ggA>ggC	p.G201G	TMED7-TICAM2_ENST00000282382.4_Silent_p.G370G|TMED7-TICAM2_ENST00000333314.3_3'UTR|TICAM2_ENST00000408996.4_Silent_p.G370G|TICAM2_ENST00000513729.1_5'Flank	NM_021649.6	NP_067681.1	Q86XR7	TCAM2_HUMAN	toll-like receptor adaptor molecule 2	201	TIR. {ECO:0000255|PROSITE- ProRule:PRU00204}.				cellular response to lipopolysaccharide (GO:0071222)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of chemokine (C-C motif) ligand 5 production (GO:0071650)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|positive regulation of chemokine (C-C motif) ligand 5 production (GO:0071651)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-18-mediated signaling pathway (GO:2000494)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|response to interleukin-12 (GO:0070671)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|TRAM-dependent toll-like receptor 4 signaling pathway (GO:0035669)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|plasma membrane (GO:0005886)	phospholipid binding (GO:0005543)|signal transducer activity (GO:0004871)			cervix(1)|kidney(1)|lung(2)|soft_tissue(1)	5		all_cancers(142;0.0223)|all_epithelial(76;0.000869)|Prostate(80;0.0115)|Ovarian(225;0.156)		OV - Ovarian serous cystadenocarcinoma(64;4.38e-07)|Epithelial(69;1.62e-06)|all cancers(49;6.93e-05)		GTGTAGGAAATCCACGACTTT	0.418													G|||	60	0.0119808	0.0439	0.0014	5008	,	,		18528	0.0		0.001	False		,,,				2504	0.0				p.G370G		Atlas-SNP	.											.	.	.	.	0			c.A1110C						PASS	.	G	,,	169,4235	809.3+/-416.0	2,165,2035	76.0	80.0	79.0		1110,,603	5.9	1.0	5	dbSNP_116	79	0,8600		0,0,4300	no	coding-synonymous,utr-3,coding-synonymous	TICAM2,TMED7-TICAM2	NM_001164468.2,NM_001164469.2,NM_021649.6	,,	2,165,6335	GG,GT,TT		0.0,3.8374,1.2996	,,	370/405,,201/236	114916351	169,12835	2202	4300	6502	SO:0001819	synonymous_variant	100302736	exon4			AGGAAATCCACGA	AY232653	CCDS4119.1	5q22.3	2012-11-21			ENSG00000243414	ENSG00000243414			21354	protein-coding gene	gene with protein product		608321					Standard	NM_021649		Approved	TRAM, TICAM-2, TIRP		Q86XR7	OTTHUMG00000162905	ENST00000427199.2:c.603A>C	5.37:g.114916351T>G		179.0	0.0	0		172.0	97.0	0.563953	NM_001164468	B3Y698|Q6JUT2	Silent	SNP	ENST00000427199.2	37	CCDS4119.1																																																																																			T|0.989;G|0.011	0.011	strong		0.418	TICAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338755.1	NM_021649	
COL6A5	256076	hgsc.bcm.edu	37	3	130150704	130150704	+	Missense_Mutation	SNP	A	A	G	rs61750883	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:130150704A>G	ENST00000432398.2	+	33	6138	c.5644A>G	c.(5644-5646)Atc>Gtc	p.I1882V	COL6A5_ENST00000265379.6_Missense_Mutation_p.I1882V	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	1882	Nonhelical region.|VWFA 8. {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						TAGGTCATCCATCATCACGGC	0.473													A|||	60	0.0119808	0.0431	0.0043	5008	,	,		20100	0.0		0.0	False		,,,				2504	0.0				p.I1882V		Atlas-SNP	.											.	COL6A5	205	.	0			c.A5644G						PASS	.	A	VAL/ILE	68,1316		3,62,627	197.0	163.0	173.0		5644	-2.3	0.4	3	dbSNP_129	173	0,3182		0,0,1591	yes	missense	COL6A5	NM_153264.5	29	3,62,2218	GG,GA,AA		0.0,4.9133,1.4893	benign	1882/2527	130150704	68,4498	692	1591	2283	SO:0001583	missense	256076	exon33			TCATCCATCATCA	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.5644A>G	3.37:g.130150704A>G	ENSP00000390895:p.Ile1882Val	68.0	0.0	0		68.0	33.0	0.485294	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		14|14	0.00641025641025641|0.00641025641025641	14|14	0.028455284552845527|0.028455284552845527	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	A|A	1.127|1.127	-0.653563|-0.653563	0.03480|0.03480	0.049133|0.049133	0.0|0.0	ENSG00000172752|ENSG00000172752	ENST00000512836|ENST00000432398;ENST00000265379	.|T;T	.|0.13196	.|2.61;2.61	5.64|5.64	-2.28|-2.28	0.06826|0.06826	.|.	.|.	.|.	.|.	.|.	T|T	0.02193|0.02193	0.0068|0.0068	L|L	0.52266|0.52266	1.64|1.64	0.09310|0.09310	N|N	1|1	.|P	.|0.40083	.|0.702	.|P	.|0.45449	.|0.481	T|T	0.22730|0.22730	-1.0208|-1.0208	5|9	.|0.16420	.|T	.|0.52	.|.	11.0646|11.0646	0.47968|0.47968	0.5749:0.0:0.4251:0.0|0.5749:0.0:0.4251:0.0	rs61750883|rs61750883	.|1882	.|A8TX70-2	.|.	R|V	133|1882	.|ENSP00000390895:I1882V;ENSP00000265379:I1882V	.|ENSP00000265379:I1882V	H|I	+|+	2|1	0|0	COL6A5|COL6A5	131633394|131633394	0.004000|0.004000	0.15560|0.15560	0.400000|0.400000	0.26346|0.26346	0.036000|0.036000	0.12997|0.12997	0.173000|0.173000	0.16724|0.16724	-0.386000|-0.386000	0.07821|0.07821	-0.379000|-0.379000	0.06801|0.06801	CAT|ATC	A|0.993;G|0.007	0.007	strong		0.473	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
TTC3	7267	hgsc.bcm.edu	37	21	38538319	38538319	+	Missense_Mutation	SNP	A	A	G	rs61998236	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:38538319A>G	ENST00000399017.2	+	33	6550	c.3803A>G	c.(3802-3804)gAt>gGt	p.D1268G	TTC3_ENST00000355666.1_Missense_Mutation_p.D1268G|TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000354749.2_Missense_Mutation_p.D1268G	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1268					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				GTTTCTGAGGATGGGCAACCC	0.473													A|||	125	0.0249601	0.0908	0.0058	5008	,	,		18238	0.0		0.001	False		,,,				2504	0.0				p.D1268G	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.A3803G						PASS	.	A	GLY/ASP,GLY/ASP	324,4080	159.2+/-191.8	10,304,1888	60.0	67.0	65.0		3803,3803	1.4	0.0	21	dbSNP_129	65	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	TTC3	NM_001001894.1,NM_003316.3	94,94	10,306,6186	GG,GA,AA		0.0233,7.3569,2.5069	possibly-damaging,possibly-damaging	1268/2026,1268/2026	38538319	326,12678	2202	4300	6502	SO:0001583	missense	7267	exon33			CTGAGGATGGGCA	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.3803A>G	21.37:g.38538319A>G	ENSP00000381981:p.Asp1268Gly	194.0	0.0	0		184.0	88.0	0.478261	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	37	CCDS13651.1	58	0.026556776556776556	53	0.10772357723577236	5	0.013812154696132596	0	0.0	0	0.0	A	11.72	1.723822	0.30593	0.073569	2.33E-4	ENSG00000182670	ENST00000355666;ENST00000399017;ENST00000354749	T;T;T	0.13196	2.61;2.61;2.61	3.85	1.38	0.22167	.	0.913911	0.09206	N	0.834038	T	0.00241	0.0007	L	0.51422	1.61	0.09310	N	1	B;B	0.17268	0.021;0.001	B;B	0.15484	0.013;0.002	T	0.38308	-0.9667	9	.	.	.	-2.4084	3.1193	0.06386	0.6771:0.0:0.1149:0.208	rs61998236	326;1268	Q5GIT6;P53804	.;TTC3_HUMAN	G	1268	ENSP00000347889:D1268G;ENSP00000381981:D1268G;ENSP00000346791:D1268G	.	D	+	2	0	TTC3	37460189	0.001000	0.12720	0.000000	0.03702	0.406000	0.30931	0.854000	0.27791	0.292000	0.22492	0.533000	0.62120	GAT	A|0.974;G|0.026	0.026	strong		0.473	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		
SLC12A3	6559	hgsc.bcm.edu	37	16	56919216	56919216	+	Missense_Mutation	SNP	A	A	G	rs61746763	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:56919216A>G	ENST00000563236.1	+	15	1890	c.1865A>G	c.(1864-1866)aAc>aGc	p.N622S	SLC12A3_ENST00000566786.1_Missense_Mutation_p.N621S|SLC12A3_ENST00000438926.2_Missense_Mutation_p.N622S|SLC12A3_ENST00000262502.5_Missense_Mutation_p.N621S			P55017	S12A3_HUMAN	solute carrier family 12 (sodium/chloride transporter), member 3	622					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|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)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:chloride symporter activity (GO:0015378)|transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(28)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)	GGCTCCTACAACCTGGCCCTC	0.597													A|||	84	0.0167732	0.0598	0.0058	5008	,	,		19315	0.0		0.001	False		,,,				2504	0.0				p.N622S		Atlas-SNP	.											.	SLC12A3	99	.	0			c.A1865G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN	155,4165		1,153,2006	80.0	62.0	68.0		1865,1862,1865	5.4	1.0	16	dbSNP_129	68	15,8429		0,15,4207	yes	missense,missense,missense	SLC12A3	NM_000339.2,NM_001126107.1,NM_001126108.1	46,46,46	1,168,6213	GG,GA,AA		0.1776,3.588,1.3319	benign,benign,benign	622/1031,621/1030,622/1022	56919216	170,12594	2160	4222	6382	SO:0001583	missense	6559	exon15			CCTACAACCTGGC		CCDS10770.1, CCDS45491.1, CCDS58464.1	16q13	2013-07-18	2013-07-18		ENSG00000070915	ENSG00000070915		"""Solute carriers"""	10912	protein-coding gene	gene with protein product		600968				8812482	Standard	NM_000339		Approved	NCCT	uc002ekd.4	P55017	OTTHUMG00000133284	ENST00000563236.1:c.1865A>G	16.37:g.56919216A>G	ENSP00000456149:p.Asn622Ser	70.0	0.0	0		50.0	20.0	0.4	NM_001126108	A8MSJ2|C9JNN9	Missense_Mutation	SNP	ENST00000563236.1	37	CCDS58464.1	39	0.017857142857142856	37	0.07520325203252033	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	A	12.22	1.872882	0.33069	0.03588	0.001776	ENSG00000070915	ENST00000438926;ENST00000262502	.	.	.	5.4	5.4	0.78164	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	T	0.06826	0.0174	L	0.37561	1.115	0.80722	D	1	B;P;B	0.36110	0.048;0.537;0.343	B;P;B	0.50049	0.039;0.629;0.343	T	0.11446	-1.0587	9	0.11794	T	0.64	.	15.1083	0.72336	1.0:0.0:0.0:0.0	rs61746763	621;622;622	P55017-3;P55017;P55017-2	.;S12A3_HUMAN;.	S	621;622	.	ENSP00000262502:N622S	N	+	2	0	SLC12A3	55476717	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	7.253000	0.78320	2.048000	0.60808	0.533000	0.62120	AAC	A|0.981;G|0.019	0.019	strong		0.597	SLC12A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432337.1		
BMP1	649	hgsc.bcm.edu	37	8	22059413	22059413	+	Silent	SNP	C	C	G	rs28710878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22059413C>G	ENST00000306385.5	+	16	2875	c.2205C>G	c.(2203-2205)ctC>ctG	p.L735L	BMP1_ENST00000354870.5_3'UTR	NM_006129.4	NP_006120.1	P13497	BMP1_HUMAN	bone morphogenetic protein 1	735	EGF-like 2; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cartilage condensation (GO:0001502)|cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|lipoprotein metabolic process (GO:0042157)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|positive regulation of cartilage development (GO:0061036)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|membrane-bounded vesicle (GO:0031988)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(3)	30				Colorectal(74;0.00229)|COAD - Colon adenocarcinoma(73;0.0661)|READ - Rectum adenocarcinoma(644;0.11)		GCTTCGTCCTCCATGACAACA	0.587													C|||	171	0.0341454	0.1218	0.0144	5008	,	,		20500	0.0		0.0	False		,,,				2504	0.0				p.L735L		Atlas-SNP	.											.	BMP1	131	.	0			c.C2205G						PASS	.	C		457,3949	210.8+/-231.2	22,413,1768	97.0	69.0	78.0		2205	-2.0	0.9	8	dbSNP_125	78	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	BMP1	NM_006129.4		22,415,6066	GG,GC,CC		0.0233,10.3722,3.5291		735/987	22059413	459,12547	2203	4300	6503	SO:0001819	synonymous_variant	649	exon16			CGTCCTCCATGAC		CCDS6026.1, CCDS34856.1	8p21	2013-02-06	2004-08-09		ENSG00000168487	ENSG00000168487	3.4.24.19	"""Bone morphogenetic proteins"""	1067	protein-coding gene	gene with protein product	"""procollagen C-endopeptidase"""	112264	"""procollagen C-endopeptidase"""	PCOLC		2004778	Standard	NM_006129		Approved		uc003xbg.3	P13497	OTTHUMG00000097761	ENST00000306385.5:c.2205C>G	8.37:g.22059413C>G		64.0	0.0	0		88.0	39.0	0.443182	NM_006129	A8K6F5|B2RN46|D3DSR0|Q13292|Q13872|Q14874|Q99421|Q99422|Q99423|Q9UL38	Silent	SNP	ENST00000306385.5	37	CCDS6026.1																																																																																			C|0.970;G|0.030	0.030	strong		0.587	BMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214995.2	NM_006132	
LAMA1	284217	hgsc.bcm.edu	37	18	6966296	6966296	+	Splice_Site	SNP	G	G	A	rs73390557	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:6966296G>A	ENST00000389658.3	-	49	6993	c.6900C>T	c.(6898-6900)agC>agT	p.S2300S		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2300					axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				CATTCTGGGAGCTGCAAAGCA	0.458													G|||	223	0.0445288	0.1573	0.0187	5008	,	,		17231	0.001		0.001	False		,,,				2504	0.0				p.S2300S		Atlas-SNP	.											.	LAMA1	458	.	0			c.C6900T						PASS	.	G		631,3775	267.7+/-268.0	35,561,1607	40.0	39.0	39.0		6900	0.6	1.0	18	dbSNP_130	39	6,8594	3.7+/-12.6	0,6,4294	yes	coding-synonymous-near-splice	LAMA1	NM_005559.3		35,567,5901	AA,AG,GG		0.0698,14.3214,4.8977		2300/3076	6966296	637,12369	2203	4300	6503	SO:0001630	splice_region_variant	284217	exon49			CTGGGAGCTGCAA	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.6900-1C>T	18.37:g.6966296G>A		55.0	0.0	0		32.0	13.0	0.40625	NM_005559		Silent	SNP	ENST00000389658.3	37	CCDS32787.1																																																																																			G|0.950;A|0.050	0.050	strong		0.458	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	Silent
TRIM22	10346	hgsc.bcm.edu	37	11	5719649	5719649	+	Silent	SNP	T	T	C	rs78484876	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5719649T>C	ENST00000379965.3	+	4	901	c.624T>C	c.(622-624)ggT>ggC	p.G208G	TRIM5_ENST00000380027.1_Intron	NM_001199573.1|NM_006074.4	NP_001186502.1|NP_006065.2	Q8IYM9	TRI22_HUMAN	tripartite motif containing 22	208					defense response to virus (GO:0051607)|immune response (GO:0006955)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein trimerization (GO:0070206)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			kidney(3)|large_intestine(8)|lung(9)|prostate(1)|stomach(2)	23		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;7.54e-09)|BRCA - Breast invasive adenocarcinoma(625;0.14)		TGGAGGAAGGTGAGGTGAATG	0.512													T|||	135	0.0269569	0.0825	0.0072	5008	,	,		20336	0.0		0.004	False		,,,				2504	0.0174				p.G208G	GBM(104;491 2336 5222)	Atlas-SNP	.											.	TRIM22	66	.	0			c.T624C						PASS	.	T	,	248,3932		10,228,1852	70.0	78.0	76.0		612,624	-3.5	0.0	11	dbSNP_132	76	25,8435		0,25,4205	no	coding-synonymous,coding-synonymous	TRIM22	NM_001199573.1,NM_006074.4	,	10,253,6057	CC,CT,TT		0.2955,5.933,2.1598	,	204/495,208/499	5719649	273,12367	2090	4230	6320	SO:0001819	synonymous_variant	10346	exon4			GGAAGGTGAGGTG	X82200	CCDS41612.1	11p15	2013-01-09	2011-01-25		ENSG00000132274	ENSG00000132274		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16379	protein-coding gene	gene with protein product		606559	"""tripartite motif-containing 22"""			11331580, 11096452	Standard	NM_006074		Approved	STAF50, GPSTAF50, RNF94	uc001mbr.3	Q8IYM9	OTTHUMG00000066904	ENST00000379965.3:c.624T>C	11.37:g.5719649T>C		217.0	1.0	0.00460829		239.0	116.0	0.485356	NM_006074	Q05CQ0|Q15521	Silent	SNP	ENST00000379965.3	37	CCDS41612.1																																																																																			T|0.990;C|0.010	0.010	strong		0.512	TRIM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143387.2	NM_006074	
AMER1	139285	hgsc.bcm.edu	37	X	63412690	63412690	+	Missense_Mutation	SNP	A	A	C	rs34677493	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:63412690A>C	ENST00000330258.3	-	2	749	c.477T>G	c.(475-477)ttT>ttG	p.F159L	AMER1_ENST00000403336.1_Missense_Mutation_p.F159L|AMER1_ENST00000374869.3_Missense_Mutation_p.F159L	NM_152424.3	NP_689637.3	Q5JTC6	AMER1_HUMAN	APC membrane recruitment protein 1	159			F -> L (in dbSNP:rs34677493).		adipose tissue development (GO:0060612)|bone development (GO:0060348)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|regulation of canonical Wnt signaling pathway (GO:0060828)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.0?(67)									GCATAGAGGGAAACTTCTCAG	0.532													A|||	528	0.139868	0.3722	0.0288	3775	,	,		12073	0.0		0.004	False		,,,				2504	0.0123				p.F159L		Atlas-SNP	.											.	.	.	.	67	Whole gene deletion(67)	kidney(65)|ovary(1)|large_intestine(1)	c.T477G						PASS	.	A	LEU/PHE	1683,2152		332,780,239,520,332	42.0	43.0	43.0		477	0.9	0.0	X	dbSNP_126	43	42,6686		0,35,7,2393,1865	yes	missense	FAM123B	NM_152424.3	22	332,815,246,2913,2197	CC,CA,C,AA,A		0.6243,43.8853,16.3306	benign	159/1136	63412690	1725,8838	2203	4300	6503	SO:0001583	missense	139285	exon2			AGAGGGAAACTTC	AK097146	CCDS14377.2	Xq11.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184675	ENSG00000184675		"""-"""	26837	protein-coding gene	gene with protein product	"""Wilms Tumor on the X"", ""adenomatous polyposis coli membrane recruitment 1"""	300647	"""family with sequence similarity 123B"""	FAM123B		21304492, 21498506, 20843316	Standard	NM_152424		Approved	RP11-403E24.2, FLJ39827, WTX	uc004dvo.3	Q5JTC6	OTTHUMG00000021703	ENST00000330258.3:c.477T>G	X.37:g.63412690A>C	ENSP00000329117:p.Phe159Leu	63.0	0.0	0		70.0	35.0	0.5	NM_152424	A2IB86|Q8N885	Missense_Mutation	SNP	ENST00000330258.3	37	CCDS14377.2	193	0.11633514165159735	121	0.32180851063829785	7	0.019886363636363636	0	0.0	1	0.0013227513227513227	A	0.031	-1.334923	0.01287	0.438853	0.006243	ENSG00000184675	ENST00000374869;ENST00000330258;ENST00000403336	T;T;T	0.16457	2.34;2.34;2.34	4.93	0.952	0.19584	.	0.964567	0.08637	N	0.916136	T	0.00012	0.0000	N	0.22421	0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.08055	0.003	T	0.48410	-0.9038	9	0.27082	T	0.32	0.9455	0.4629	0.00519	0.2626:0.1486:0.1604:0.4284	rs34677493	159	Q5JTC6	F123B_HUMAN	L	159	ENSP00000364003:F159L;ENSP00000329117:F159L;ENSP00000384722:F159L	ENSP00000329117:F159L	F	-	3	2	FAM123B	63329415	0.000000	0.05858	0.000000	0.03702	0.092000	0.18411	-0.359000	0.07632	0.182000	0.20032	0.486000	0.48141	TTT	0|0.013;C|0.188	0.188	strong		0.532	AMER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316584.1	NM_152424	
CLEC16A	23274	hgsc.bcm.edu	37	16	11114174	11114174	+	Silent	SNP	A	A	G	rs61741309	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:11114174A>G	ENST00000409790.1	+	12	1658	c.1428A>G	c.(1426-1428)caA>caG	p.Q476Q	CLEC16A_ENST00000409552.3_Silent_p.Q458Q	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A									p.0?(1)		breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						AGAGCACGCAATGGAGCAGGT	0.632													A|||	245	0.0489217	0.18	0.0101	5008	,	,		21149	0.0		0.0	False		,,,				2504	0.0				p.Q476Q		Atlas-SNP	.											.	CLEC16A	101	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.A1428G						PASS	.	A		489,3493		31,427,1533	16.0	19.0	18.0		1428	4.4	1.0	16	dbSNP_129	18	4,8358		0,4,4177	no	coding-synonymous	CLEC16A	NM_015226.2		31,431,5710	GG,GA,AA		0.0478,12.2803,3.9938		476/1054	11114174	493,11851	1991	4181	6172	SO:0001819	synonymous_variant	23274	exon11			CACGCAATGGAGC	AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"""C-type lectin domain containing"""	29013	protein-coding gene	gene with protein product		611303	"""KIAA0350"""	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.1428A>G	16.37:g.11114174A>G		74.0	0.0	0		116.0	60.0	0.517241	NM_015226		Silent	SNP	ENST00000409790.1	37	CCDS45409.1																																																																																			A|0.962;G|0.038	0.038	strong		0.632	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226	
GEN1	348654	hgsc.bcm.edu	37	2	17961321	17961321	+	Silent	SNP	A	A	G	rs16983864	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:17961321A>G	ENST00000381254.2	+	13	1555	c.1341A>G	c.(1339-1341)gcA>gcG	p.A447A	GEN1_ENST00000317402.7_Silent_p.A447A|SMC6_ENST00000402989.1_Intron	NM_001130009.1	NP_001123481.1	Q17RS7	GEN_HUMAN	GEN1 Holliday junction 5' flap endonuclease	447					DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|regulation of centrosome duplication (GO:0010824)|resolution of mitotic recombination intermediates (GO:0071140)|resolution of recombination intermediates (GO:0071139)	centrosome (GO:0005813)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	crossover junction endodeoxyribonuclease activity (GO:0008821)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					TGTTTGAAGCAGCATATCCTG	0.308								Homologous recombination					A|||	236	0.0471246	0.1377	0.0072	5008	,	,		18870	0.0308		0.005	False		,,,				2504	0.0133				p.A447A		Atlas-SNP	.											.	GEN1	79	.	0			c.A1341G						PASS	.	A	,	466,3940	216.4+/-235.1	23,420,1760	62.0	64.0	64.0		1341,1341	-0.6	1.0	2	dbSNP_123	64	34,8566	22.8+/-68.1	0,34,4266	no	coding-synonymous,coding-synonymous	GEN1	NM_001130009.1,NM_182625.3	,	23,454,6026	GG,GA,AA		0.3953,10.5765,3.8444	,	447/909,447/909	17961321	500,12506	2203	4300	6503	SO:0001819	synonymous_variant	348654	exon13			TGAAGCAGCATAT	AK098188	CCDS1691.1	2p24.2	2013-06-04	2013-06-04		ENSG00000178295	ENSG00000178295			26881	protein-coding gene	gene with protein product	"""Holliday junction resolvase"""	612449	"""Gen endonuclease homolog 1 (Drosophila)"""			15576351	Standard	NM_182625		Approved	FLJ40869, Gen	uc002rct.2	Q17RS7	OTTHUMG00000121173	ENST00000381254.2:c.1341A>G	2.37:g.17961321A>G		52.0	0.0	0		53.0	26.0	0.490566	NM_182625	Q17RS9|Q6ZN37	Silent	SNP	ENST00000381254.2	37	CCDS1691.1																																																																																			A|0.963;G|0.037	0.037	strong		0.308	GEN1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241661.2	NM_182625	
LRRIQ3	127255	hgsc.bcm.edu	37	1	74649119	74649119	+	Splice_Site	SNP	C	C	T	rs143858191	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:74649119C>T	ENST00000395089.1	-	1	249		c.e1+1		LRRIQ3_ENST00000370911.3_Splice_Site|LRRIQ3_ENST00000370909.2_Splice_Site|LRRIQ3_ENST00000354431.4_Splice_Site			A6PVS8	LRIQ3_HUMAN	leucine-rich repeats and IQ motif containing 3											NS(2)|breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(13)|liver(1)|lung(27)|ovary(3)|prostate(1)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(5)	73						CTATTGCTTACCTGATTTCCA	0.299													C|||	12	0.00239617	0.0091	0.0	5008	,	,		16045	0.0		0.0	False		,,,				2504	0.0				.		Atlas-SNP	.											.	LRRIQ3	146	.	0			c.249+1G>A						PASS	.	C		32,4368	34.3+/-65.2	2,28,2170	61.0	67.0	65.0			5.3	1.0	1	dbSNP_134	65	0,8588		0,0,4294	yes	splice-5	LRRIQ3	NM_001105659.1		2,28,6464	TT,TC,CC		0.0,0.7273,0.2464			74649119	32,12956	2200	4294	6494	SO:0001630	splice_region_variant	127255	exon3			TGCTTACCTGATT	BX647210	CCDS41350.1	1p31.1	2008-06-12	2008-06-12	2008-06-12	ENSG00000162620	ENSG00000162620			28318	protein-coding gene	gene with protein product			"""leucine rich repeat containing 44"""	LRRC44		12477932	Standard	NM_001105659		Approved	MGC22773	uc001dfy.4	A6PVS8	OTTHUMG00000009508	ENST00000395089.1:c.249+1G>A	1.37:g.74649119C>T		131.0	0.0	0		119.0	55.0	0.462185	NM_001105659	A6PVS9|Q6P5P7|Q6ZMV4|Q8WUE0	Splice_Site	SNP	ENST00000395089.1	37	CCDS41350.1	5	0.0022893772893772895	4	0.008130081300813009	0	0.0	0	0.0	1	0.0013192612137203166	C	17.79	3.476396	0.63737	0.007273	0.0	ENSG00000162620	ENST00000395089;ENST00000354431;ENST00000370909;ENST00000388972;ENST00000444984;ENST00000370911	.	.	.	5.27	5.27	0.74061	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.0114	0.89225	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	LRRIQ3	74421707	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	5.083000	0.64456	2.601000	0.87937	0.655000	0.94253	.	C|0.998;T|0.002	0.002	strong		0.299	LRRIQ3-008	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316539.1	NM_145258	Intron
TTLL2	83887	hgsc.bcm.edu	37	6	167755063	167755063	+	Missense_Mutation	SNP	G	G	A	rs34931196	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:167755063G>A	ENST00000239587.5	+	3	1763	c.1675G>A	c.(1675-1677)Gtt>Att	p.V559I		NM_031949.4	NP_114155.4	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	559			V -> I (in dbSNP:rs34931196).		cellular protein modification process (GO:0006464)		ligase activity (GO:0016874)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(66;7.8e-06)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		CTTTGTTCTTGTTTTTCCTTT	0.468													G|||	140	0.0279553	0.1036	0.0043	5008	,	,		20361	0.0		0.0	False		,,,				2504	0.0				p.V559I		Atlas-SNP	.											.	TTLL2	82	.	0			c.G1675A						PASS	.	G	ILE/VAL	347,4059	179.7+/-208.2	15,317,1871	92.0	89.0	90.0		1675	1.7	0.9	6	dbSNP_126	90	4,8596	3.7+/-12.6	0,4,4296	yes	missense	TTLL2	NM_031949.4	29	15,321,6167	AA,AG,GG		0.0465,7.8756,2.6988	benign	559/593	167755063	351,12655	2203	4300	6503	SO:0001583	missense	83887	exon3			GTTCTTGTTTTTC	AK093039	CCDS5301.1	6q27	2013-02-14		2004-01-14	ENSG00000120440	ENSG00000120440		"""Tubulin tyrosine ligase-like family"""	21211	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 104"""	C6orf104		11054573	Standard	XM_006715572		Approved	NYD-TSPG, dJ366N23.3	uc003qvs.1	Q9BWV7	OTTHUMG00000016023	ENST00000239587.5:c.1675G>A	6.37:g.167755063G>A	ENSP00000239587:p.Val559Ile	177.0	0.0	0		166.0	67.0	0.403614	NM_031949	B2RB11|B3KS77|Q7Z6R8|Q86X22	Missense_Mutation	SNP	ENST00000239587.5	37	CCDS5301.1	52	0.023809523809523808	50	0.1016260162601626	2	0.0055248618784530384	0	0.0	0	0.0	G	0.039	-1.293630	0.01375	0.078756	4.65E-4	ENSG00000120440	ENST00000239587;ENST00000540954	T	0.02121	4.44	4.04	1.67	0.24075	.	0.415985	0.21849	N	0.068208	T	0.00300	0.0009	N	0.04203	-0.255	0.21627	N	0.99962	B	0.06786	0.001	B	0.04013	0.001	T	0.41734	-0.9492	10	0.02654	T	1	.	6.3218	0.21223	0.6774:0.0:0.3226:0.0	rs34931196	559	Q9BWV7	TTLL2_HUMAN	I	559;486	ENSP00000239587:V559I	ENSP00000239587:V559I	V	+	1	0	TTLL2	167675053	1.000000	0.71417	0.874000	0.34290	0.452000	0.32318	0.911000	0.28584	0.164000	0.19529	-0.339000	0.08088	GTT	G|0.970;A|0.030	0.030	strong		0.468	TTLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043127.3	NM_031949	
ZNF41	7592	hgsc.bcm.edu	37	X	47308509	47308509	+	Missense_Mutation	SNP	A	A	C	rs34301930	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:47308509A>C	ENST00000377065.4	-	5	1299	c.660T>G	c.(658-660)aaT>aaG	p.N220K	ZNF41_ENST00000397050.2_Missense_Mutation_p.N230K|ZNF41_ENST00000465311.1_5'Flank|ZNF41_ENST00000313116.7_Missense_Mutation_p.N220K	NM_153380.2	NP_700359.1	P51814	ZNF41_HUMAN	zinc finger protein 41	262					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|upper_aerodigestive_tract(2)	24		all_lung(315;0.000129)				AATTGTTACCATTTCCAAAAA	0.368													A|||	113	0.0299338	0.0832	0.0043	3775	,	,		14437	0.0		0.0	False		,,,				2504	0.0				p.N220K		Atlas-SNP	.											.	ZNF41	71	.	0			c.T660G						PASS	.	A	LYS/ASN,LYS/ASN	343,3492		8,285,42,1339,529	150.0	140.0	144.0		660,660	3.2	0.3	X	dbSNP_126	144	3,6725		0,3,0,2425,1872	yes	missense,missense	ZNF41	NM_007130.2,NM_153380.2	94,94	8,288,42,3764,2401	CC,CA,C,AA,A		0.0446,8.9439,3.2756	possibly-damaging,possibly-damaging	220/780,220/780	47308509	346,10217	2203	4300	6503	SO:0001583	missense	7592	exon5			GTTACCATTTCCA	X60155	CCDS14279.1	Xp11.23	2013-01-08			ENSG00000147124	ENSG00000147124		"""Zinc fingers, C2H2-type"", ""-"""	13107	protein-coding gene	gene with protein product		314995				2037297	Standard	NM_007130		Approved	MGC8941, MRX89	uc004dhy.4	P51814	OTTHUMG00000021448	ENST00000377065.4:c.660T>G	X.37:g.47308509A>C	ENSP00000366265:p.Asn220Lys	197.0	0.0	0		230.0	123.0	0.534783	NM_007130	A8K1V6|B4DH01|Q96LE8|Q9UMC4|Q9UMV5|Q9UMV6|Q9UMV7|Q9UMV8|Q9UMV9|Q9UMW0|Q9UMW1	Missense_Mutation	SNP	ENST00000377065.4	37	CCDS14279.1	36	0.0216998191681736	25	0.05296610169491525	0	0.0	0	0.0	0	0.0	A	4.551	0.102356	0.08731	0.089439	4.46E-4	ENSG00000147124	ENST00000313116;ENST00000377065;ENST00000397050	T;T;T	0.06068	3.35;3.35;3.35	3.2	3.2	0.36748	.	0.000000	0.37715	N	0.001972	T	0.00210	0.0006	N	0.08118	0	0.44254	P	0.0028960000000000097	P;P;B;P;P	0.50156	0.932;0.932;0.257;0.932;0.888	B;B;B;P;B	0.47981	0.424;0.424;0.074;0.563;0.36	T	0.37957	-0.9683	9	0.62326	D	0.03	.	9.1657	0.37050	1.0:0.0:0.0:0.0	rs34301930	220;222;230;254;262	P51814-6;P51814-2;P51814-3;P51814-5;P51814	.;.;.;.;ZNF41_HUMAN	K	220;220;230	ENSP00000315173:N220K;ENSP00000366265:N220K;ENSP00000380243:N230K	ENSP00000315173:N220K	N	-	3	2	ZNF41	47193453	0.000000	0.05858	0.255000	0.24374	0.075000	0.17131	0.061000	0.14366	1.514000	0.48869	0.412000	0.27726	AAT	A|0.966;C|0.034	0.034	strong		0.368	ZNF41-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056429.1	NM_153380	
MGAM	8972	hgsc.bcm.edu	37	7	141750613	141750613	+	Missense_Mutation	SNP	T	T	A	rs145430437	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:141750613T>A	ENST00000549489.2	+	24	2849	c.2754T>A	c.(2752-2754)aaT>aaA	p.N918K	MGAM_ENST00000475668.2_Missense_Mutation_p.N918K	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	918					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)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TGAAACACAATGGTGTCCCAA	0.373													t|||	53	0.0105831	0.0378	0.0043	5008	,	,		20002	0.0		0.0	False		,,,				2504	0.0				p.N918K		Atlas-SNP	.											.	MGAM	767	.	0			c.T2754A						PASS	.	T	LYS/ASN	121,3617		1,119,1749	105.0	95.0	98.0		2754	0.9	0.1	7	dbSNP_134	98	0,8200		0,0,4100	no	missense	MGAM	NM_004668.2	94	1,119,5849	AA,AT,TT		0.0,3.237,1.0136	possibly-damaging	918/1858	141750613	121,11817	1869	4100	5969	SO:0001583	missense	8972	exon24			ACACAATGGTGTC	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.2754T>A	7.37:g.141750613T>A	ENSP00000447378:p.Asn918Lys	261.0	0.0	0		259.0	112.0	0.432432	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	37	CCDS47727.1	27	0.012362637362637362	25	0.0508130081300813	2	0.0055248618784530384	0	0.0	0	0.0	T	16.84	3.233340	0.58886	0.03237	0.0	ENSG00000257335	ENST00000549489;ENST00000475668;ENST00000548812	D	0.89746	-2.56	5.81	0.868	0.19090	.	0.000000	0.53938	D	0.000059	T	0.57140	0.2033	M	0.86028	2.79	0.09310	N	1	P	0.45768	0.866	B	0.34590	0.186	T	0.69258	-0.5192	10	0.72032	D	0.01	.	9.1608	0.37021	0.0:0.3617:0.0:0.6383	.	918	O43451	MGA_HUMAN	K	918;918;795	ENSP00000447378:N918K	ENSP00000316431:N795K	N	+	3	2	MGAM	141397082	0.061000	0.20836	0.090000	0.20809	0.275000	0.26752	-0.197000	0.09518	-0.065000	0.13021	-0.479000	0.04858	AAT	T|0.988;A|0.012	0.012	strong		0.373	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
APOBEC3B	9582	hgsc.bcm.edu	37	22	39380131	39380131	+	Silent	SNP	C	C	T	rs113972364	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:39380131C>T	ENST00000333467.3	+	2	114	c.69C>T	c.(67-69)aaC>aaT	p.N23N	APOBEC3B_ENST00000407298.3_Silent_p.N23N|APOBEC3B_ENST00000402182.3_Silent_p.N23N	NM_001270411.1|NM_004900.4	NP_001257340.1|NP_004891	Q9UH17	ABC3B_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3B	23					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)					ACTTTGAAAACGAACCCATCC	0.522													C|||	118	0.0235623	0.087	0.0043	5008	,	,		17697	0.0		0.0	False		,,,				2504	0.0				p.N23N		Atlas-SNP	.											.	APOBEC3B	32	.	0			c.C69T						PASS	.	C		276,4118		27,222,1948	73.0	76.0	75.0		69	0.2	0.0	22	dbSNP_132	75	3,8517		0,3,4257	no	coding-synonymous	APOBEC3B	NM_004900.3		27,225,6205	TT,TC,CC		0.0352,6.2813,2.1604		23/383	39380131	279,12635	2197	4260	6457	SO:0001819	synonymous_variant	9582	exon2			TGAAAACGAACCC	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.69C>T	22.37:g.39380131C>T		243.0	0.0	0		244.0	96.0	0.393443	NM_004900	B0QYD2|O95618|Q20WL1|Q5IFJ4|Q7Z2N3|Q7Z6D6|Q9UE74	Silent	SNP	ENST00000333467.3	37	CCDS13982.1																																																																																			C|0.974;T|0.026	0.026	strong		0.522	APOBEC3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321233.1	NM_004900	
EXPH5	23086	hgsc.bcm.edu	37	11	108380740	108380740	+	Missense_Mutation	SNP	G	G	C	rs36005552	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:108380740G>C	ENST00000265843.4	-	6	5604	c.5494C>G	c.(5494-5496)Cga>Gga	p.R1832G	EXPH5_ENST00000428840.1_Missense_Mutation_p.R1756G|EXPH5_ENST00000525344.1_Missense_Mutation_p.R1825G|EXPH5_ENST00000443411.1_Missense_Mutation_p.R1644G	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1832					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		AGGGTCAGTCGACTCAGGGCA	0.443													G|||	30	0.00599042	0.0212	0.0029	5008	,	,		20136	0.0		0.0	False		,,,				2504	0.0				p.R1832G		Atlas-SNP	.											.	EXPH5	193	.	0			c.C5494G						PASS	.	G	GLY/ARG	134,4268	96.2+/-134.9	0,134,2067	63.0	63.0	63.0		5494	0.4	0.0	11	dbSNP_126	63	0,8596		0,0,4298	yes	missense	EXPH5	NM_015065.2	125	0,134,6365	CC,CG,GG		0.0,3.0441,1.0309	benign	1832/1990	108380740	134,12864	2201	4298	6499	SO:0001583	missense	23086	exon6			TCAGTCGACTCAG		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.5494C>G	11.37:g.108380740G>C	ENSP00000265843:p.Arg1832Gly	115.0	0.0	0		89.0	56.0	0.629214	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	11	0.005036630036630037	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	0	0.0	G	8.864	0.947649	0.18356	0.030441	0.0	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000439956	T;T;T;T	0.03181	4.24;4.17;4.02;4.24	6.17	0.414	0.16406	.	1.706240	0.03093	N	0.160006	T	0.01092	0.0036	L	0.27053	0.805	0.09310	N	1	B	0.14438	0.01	B	0.18263	0.021	T	0.43294	-0.9400	10	0.41790	T	0.15	7.6536	3.311	0.07016	0.1263:0.1752:0.4527:0.2458	rs36005552	1832	Q8NEV8	EXPH5_HUMAN	G	1832;1756;1644;1825;662	ENSP00000265843:R1832G;ENSP00000391966:R1756G;ENSP00000411390:R1644G;ENSP00000432546:R1825G	ENSP00000265843:R1832G	R	-	1	2	EXPH5	107885950	0.000000	0.05858	0.047000	0.18901	0.426000	0.31534	0.086000	0.14935	0.144000	0.18951	0.655000	0.94253	CGA	G|0.990;C|0.010	0.010	strong		0.443	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
CROT	54677	hgsc.bcm.edu	37	7	86986863	86986863	+	Intron	SNP	T	T	C	rs75642989	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:86986863T>C	ENST00000331536.3	+	4	300				CROT_ENST00000412227.2_Intron|CROT_ENST00000442291.1_Intron|CROT_ENST00000419147.2_Silent_p.D52D	NM_021151.3	NP_066974.2	Q9UKG9	OCTC_HUMAN	carnitine O-octanoyltransferase						carnitine metabolic process (GO:0009437)|cellular lipid metabolic process (GO:0044255)|coenzyme A metabolic process (GO:0015936)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|fatty acid metabolic process (GO:0006631)|fatty acid transport (GO:0015908)|generation of precursor metabolites and energy (GO:0006091)|medium-chain fatty acid metabolic process (GO:0051791)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carnitine O-octanoyltransferase activity (GO:0008458)|receptor binding (GO:0005102)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37	Esophageal squamous(14;0.0058)|all_lung(186;0.201)|Lung NSC(181;0.203)				L-Carnitine(DB00583)	ttgatccagatgctaagagag	0.483													C|||	89	0.0177716	0.0658	0.0029	5008	,	,		19249	0.0		0.0	False		,,,				2504	0.0				p.D52D		Atlas-SNP	.											.	CROT	81	.	0			c.T156C						PASS	.	C	,	61,1323		2,57,633	146.0	124.0	130.0		156,	0.2	0.0	7	dbSNP_132	130	1,3181		0,1,1590	no	coding-synonymous,intron	CROT	NM_001143935.1,NM_021151.3	,	2,58,2223	CC,CT,TT		0.0314,4.4075,1.3579	,	52/641,	86986863	62,4504	692	1591	2283	SO:0001627	intron_variant	54677	exon4			TCCAGATGCTAAG		CCDS5604.1, CCDS47634.1, CCDS59062.1	7q21.1	2010-02-26			ENSG00000005469	ENSG00000005469			2366	protein-coding gene	gene with protein product		606090				10486279	Standard	NM_021151		Approved	COT	uc003uit.3	Q9UKG9	OTTHUMG00000023653	ENST00000331536.3:c.116-1659T>C	7.37:g.86986863T>C		59.0	0.0	0		72.0	37.0	0.513889	NM_001143935	A4D1D6|E7EQF2|Q86V17|Q8IUW9|Q9Y6I2	Silent	SNP	ENST00000331536.3	37	CCDS5604.1																																																																																			T|0.986;C|0.014	0.014	strong		0.483	CROT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253485.1	NM_021151	
SFXN2	118980	hgsc.bcm.edu	37	10	104486822	104486822	+	Silent	SNP	C	C	T	rs35094483	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:104486822C>T	ENST00000369893.5	+	3	407	c.240C>T	c.(238-240)ccC>ccT	p.P80P	SFXN2_ENST00000602785.1_3'UTR	NM_178858.4	NP_849189.1	Q96NB2	SFXN2_HUMAN	sideroflexin 2	80					iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|prostate(1)	13		Colorectal(252;0.207)		Epithelial(162;4.53e-09)|all cancers(201;1.2e-07)|BRCA - Breast invasive adenocarcinoma(275;0.218)		CCTTCCACCCCGACACTGGGG	0.597													C|||	166	0.033147	0.121	0.0086	5008	,	,		18582	0.0		0.0	False		,,,				2504	0.0				p.P80P		Atlas-SNP	.											.	SFXN2	40	.	0			c.C240T						PASS	.	C		444,3962	212.2+/-232.1	13,418,1772	84.0	74.0	77.0		240	-5.3	1.0	10	dbSNP_126	77	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SFXN2	NM_178858.4		13,420,6070	TT,TC,CC		0.0233,10.0772,3.4292		80/323	104486822	446,12560	2203	4300	6503	SO:0001819	synonymous_variant	118980	exon3			CCACCCCGACACT	AF462052	CCDS7539.1	10q24.32	2006-03-13			ENSG00000156398	ENSG00000156398		"""Sideroflexins"""	16086	protein-coding gene	gene with protein product		615570					Standard	NM_178858		Approved		uc001kwb.2	Q96NB2	OTTHUMG00000018967	ENST00000369893.5:c.240C>T	10.37:g.104486822C>T		192.0	0.0	0		191.0	190.0	0.994764	NM_178858	Q5JSM6	Silent	SNP	ENST00000369893.5	37	CCDS7539.1																																																																																			C|0.969;T|0.031	0.031	strong		0.597	SFXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050096.2	XM_058359	
FAAH	2166	hgsc.bcm.edu	37	1	46874246	46874246	+	Missense_Mutation	SNP	C	C	T	rs77101686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:46874246C>T	ENST00000243167.8	+	8	1151	c.1067C>T	c.(1066-1068)gCg>gTg	p.A356V	FAAH_ENST00000493735.1_3'UTR	NM_001441.2	NP_001432.2	O00519	FAAH1_HUMAN	fatty acid amide hydrolase	356					fatty acid catabolic process (GO:0009062)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)	acylglycerol lipase activity (GO:0047372)|carbon-nitrogen ligase activity, with glutamine as amido-N-donor (GO:0016884)|fatty acid amide hydrolase activity (GO:0017064)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	22	Acute lymphoblastic leukemia(166;0.155)				Propofol(DB00818)|Thiopental(DB00599)	CTTGAGGCTGCGGGGCACACG	0.617													C|||	42	0.00838658	0.0076	0.0	5008	,	,		20191	0.0159		0.0	False		,,,				2504	0.0164				p.A356V		Atlas-SNP	.											FAAH,colon,carcinoma,-1,1	FAAH	36	1	0			c.C1067T						scavenged	.	C	VAL/ALA	8,4398	15.5+/-35.6	0,8,2195	152.0	156.0	155.0		1067	5.4	1.0	1	dbSNP_131	155	4,8596	3.7+/-12.6	0,4,4296	yes	missense	FAAH	NM_001441.2	64	0,12,6491	TT,TC,CC		0.0465,0.1816,0.0923	probably-damaging	356/580	46874246	12,12994	2203	4300	6503	SO:0001583	missense	2166	exon8			AGGCTGCGGGGCA	U82535	CCDS535.1	1p35-p34	2008-02-05			ENSG00000117480	ENSG00000117480			3553	protein-coding gene	gene with protein product		602935				9122178	Standard	NM_001441		Approved	FAAH-1	uc001cpu.2	O00519	OTTHUMG00000007811	ENST00000243167.8:c.1067C>T	1.37:g.46874246C>T	ENSP00000243167:p.Ala356Val	59.0	1.0	0.0169492		68.0	43.0	0.632353	NM_001441	D3DQ19|Q52M86|Q5TDF8	Missense_Mutation	SNP	ENST00000243167.8	37	CCDS535.1	12	0.005494505494505495	1	0.0020325203252032522	0	0.0	11	0.019230769230769232	0	0.0	C	31	5.097033	0.94197	0.001816	4.65E-4	ENSG00000117480	ENST00000243167;ENST00000396325	T	0.56776	0.44	5.4	5.4	0.78164	Amidase signature domain (2);	0.000000	0.85682	D	0.000000	T	0.65238	0.2672	M	0.90425	3.115	0.80722	D	1	D	0.89917	1.0	D	0.65573	0.936	T	0.79065	-0.1956	10	0.87932	D	0	0.6812	19.1897	0.93660	0.0:1.0:0.0:0.0	.	356	O00519	FAAH1_HUMAN	V	356;63	ENSP00000243167:A356V	ENSP00000243167:A356V	A	+	2	0	FAAH	46646833	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	5.585000	0.67497	2.548000	0.85928	0.655000	0.94253	GCG	C|0.998;T|0.002	0.002	strong		0.617	FAAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021443.1	NM_001441	
DCTN1	1639	hgsc.bcm.edu	37	2	74593482	74593482	+	Silent	SNP	G	G	A	rs140986485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74593482G>A	ENST00000361874.3	-	23	2966	c.2649C>T	c.(2647-2649)agC>agT	p.S883S	DCTN1_ENST00000409240.1_Silent_p.S846S|DCTN1_ENST00000407639.2_Silent_p.S749S|DCTN1_ENST00000409567.3_Silent_p.S863S|DCTN1_ENST00000409438.1_Silent_p.S749S|DCTN1_ENST00000495643.1_5'UTR|DCTN1_ENST00000409868.1_Silent_p.S866S|DCTN1_ENST00000394003.3_Silent_p.S876S|RP11-287D1.3_ENST00000451608.2_5'Flank	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	883					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|G2/M transition of mitotic cell cycle (GO:0000086)|melanosome transport (GO:0032402)|microtubule-based transport (GO:0010970)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nervous system development (GO:0007399)	cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|dynein complex (GO:0030286)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(1)|skin(3)	45						CATAGGGGCTGCTGGAGGGGG	0.582													G|||	13	0.00259585	0.0098	0.0	5008	,	,		18862	0.0		0.0	False		,,,				2504	0.0				p.S883S		Atlas-SNP	.											.	DCTN1	110	.	0			c.C2649T						PASS	.	G	,,,,,	26,4380	32.6+/-62.9	0,26,2177	50.0	54.0	53.0		2589,2247,2538,2628,2649,2247	5.4	1.0	2	dbSNP_134	53	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DCTN1	NM_001135040.2,NM_001135041.2,NM_001190836.1,NM_001190837.1,NM_004082.4,NM_023019.3	,,,,,	0,26,6477	AA,AG,GG		0.0,0.5901,0.1999	,,,,,	863/1254,749/1140,846/1237,876/1272,883/1279,749/1145	74593482	26,12980	2203	4300	6503	SO:0001819	synonymous_variant	1639	exon23			GGGGCTGCTGGAG		CCDS1939.1, CCDS46341.1, CCDS46342.1, CCDS54368.1, CCDS54369.1	2p13	2014-09-17	2010-06-24		ENSG00000204843	ENSG00000204843			2711	protein-coding gene	gene with protein product	"""p150 glued homolog (Drosophila)"""	601143	"""dynactin 1 (p150, Glued (Drosophila) homolog)"""			1828535	Standard	NM_001190836		Approved		uc002skx.3	Q14203	OTTHUMG00000129963	ENST00000361874.3:c.2649C>T	2.37:g.74593482G>A		140.0	0.0	0		138.0	64.0	0.463768	NM_004082	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Silent	SNP	ENST00000361874.3	37	CCDS1939.1																																																																																			G|0.997;A|0.003	0.003	strong		0.582	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082	
ZNF597	146434	hgsc.bcm.edu	37	16	3486736	3486736	+	Silent	SNP	G	G	A	rs34461484	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3486736G>A	ENST00000301744.4	-	4	1198	c.963C>T	c.(961-963)gaC>gaT	p.D321D		NM_152457.1	NP_689670.1	Q96LX8	ZN597_HUMAN	zinc finger protein 597	321					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|urinary_tract(1)	13						AGCGTTCAGAGTCCTCGTCGT	0.488													G|||	102	0.0203674	0.0726	0.0072	5008	,	,		20540	0.0		0.001	False		,,,				2504	0.0				p.D321D		Atlas-SNP	.											.	ZNF597	41	.	0			c.C963T						PASS	.	G		239,4155	141.9+/-177.2	4,231,1962	70.0	66.0	67.0		963	-7.5	0.0	16	dbSNP_126	67	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	ZNF597	NM_152457.1		4,236,6257	AA,AG,GG		0.0581,5.4392,1.8778		321/425	3486736	244,12750	2197	4300	6497	SO:0001819	synonymous_variant	146434	exon4			TTCAGAGTCCTCG	AK057633	CCDS10505.1	16p13.3	2013-01-08			ENSG00000167981	ENSG00000167981		"""Zinc fingers, C2H2-type"", ""-"""	26573	protein-coding gene	gene with protein product		614685				12477932	Standard	NM_152457		Approved	FLJ33071	uc002cvd.3	Q96LX8	OTTHUMG00000129359	ENST00000301744.4:c.963C>T	16.37:g.3486736G>A		43.0	0.0	0		50.0	24.0	0.48	NM_152457		Silent	SNP	ENST00000301744.4	37	CCDS10505.1																																																																																			G|0.985;A|0.015	0.015	strong		0.488	ZNF597-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251511.2	NM_152457	
OR2T27	403239	hgsc.bcm.edu	37	1	248813473	248813473	+	Missense_Mutation	SNP	A	A	C	rs78776291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248813473A>C	ENST00000344889.3	-	1	712	c.713T>G	c.(712-714)gTg>gGg	p.V238G		NM_001001824.1	NP_001001824.1	Q8NH04	O2T27_HUMAN	olfactory receptor, family 2, subfamily T, member 27	238						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(2)|large_intestine(4)|lung(20)|skin(3)|stomach(1)	32	all_cancers(71;1.15e-05)|all_epithelial(71;5.29e-06)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.089)|Lung NSC(105;0.0969)|Melanoma(84;0.199)	all_cancers(173;0.237)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			GCAGGTGGCCACAGCCTTTCC	0.527													A|||	333	0.0664936	0.2375	0.0245	5008	,	,		19295	0.0		0.002	False		,,,				2504	0.0				p.V238G		Atlas-SNP	.											.	OR2T27	52	.	0			c.T713G						PASS	.	A	GLY/VAL	869,3497		137,595,1451	49.0	32.0	38.0		713	2.3	0.6	1	dbSNP_131	38	8,8502		0,8,4247	no	missense	OR2T27	NM_001001824.1	109	137,603,5698	CC,CA,AA		0.094,19.9038,6.8111	possibly-damaging	238/318	248813473	877,11999	2183	4255	6438	SO:0001583	missense	403239	exon1			GTGGCCACAGCCT		CCDS31124.1	1q44	2012-08-09			ENSG00000187701	ENSG00000187701		"""GPCR / Class A : Olfactory receptors"""	31252	protein-coding gene	gene with protein product							Standard	NM_001001824		Approved		uc010pzo.2	Q8NH04	OTTHUMG00000040376	ENST00000344889.3:c.713T>G	1.37:g.248813473A>C	ENSP00000342008:p.Val238Gly	110.0	0.0	0		193.0	108.0	0.559586	NM_001001824		Missense_Mutation	SNP	ENST00000344889.3	37	CCDS31124.1	119	0.05448717948717949	116	0.23577235772357724	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	.	9.994	1.231495	0.22626	0.199038	9.4E-4	ENSG00000187701	ENST00000344889	T	0.00158	8.65	3.42	2.28	0.28536	GPCR, rhodopsin-like superfamily (1);	0.212577	0.23378	N	0.048838	T	0.00012	0.0000	L	0.33339	1.005	0.34364	P	0.308697	P	0.37038	0.579	B	0.43623	0.425	T	0.27400	-1.0075	9	0.87932	D	0	.	7.831	0.29342	0.8936:0.0:0.1064:0.0	.	238	Q8NH04	O2T27_HUMAN	G	238	ENSP00000342008:V238G	ENSP00000342008:V238G	V	-	2	0	OR2T27	246880096	0.031000	0.19500	0.564000	0.28396	0.057000	0.15508	3.181000	0.50903	0.513000	0.28278	-0.548000	0.04221	GTG	A|0.941;C|0.059	0.059	strong		0.527	OR2T27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097124.1	NM_001001824	
AARS2	57505	hgsc.bcm.edu	37	6	44279824	44279824	+	Silent	SNP	C	C	T	rs75506489	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:44279824C>T	ENST00000244571.4	-	2	422	c.420G>A	c.(418-420)ggG>ggA	p.G140G	RP11-444E17.6_ENST00000505802.1_Intron	NM_020745.3	NP_065796			alanyl-tRNA synthetase 2, mitochondrial											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(3)|skin(2)|stomach(1)	34	Hepatocellular(11;0.00908)|all_lung(25;0.0101)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			AATATTCACCCCCAAAGGCCC	0.483													C|||	108	0.0215655	0.0809	0.0014	5008	,	,		21967	0.0		0.0	False		,,,				2504	0.0				p.G140G		Atlas-SNP	.											.	AARS2	77	.	0			c.G420A						PASS	.	C		220,4186	132.5+/-169.0	3,214,1986	177.0	170.0	172.0		420	1.7	1.0	6	dbSNP_132	172	1,8599		0,1,4299	no	coding-synonymous	AARS2	NM_020745.2		3,215,6285	TT,TC,CC		0.0116,4.9932,1.6992		140/986	44279824	221,12785	2203	4300	6503	SO:0001819	synonymous_variant	57505	exon2			TTCACCCCCAAAG	AB033096	CCDS34464.1	6p21.1	2012-10-26	2012-10-26	2007-02-23	ENSG00000124608	ENSG00000124608	6.1.1.7	"""Aminoacyl tRNA synthetases / Class II"""	21022	protein-coding gene	gene with protein product	"""alanine tRNA ligase 2, mitochondrial"""	612035	"""alanyl-tRNA synthetase like"", ""alanyl-tRNA synthetase 2, mitochondrial (putative)"""	AARSL		15779907, 21549344	Standard	NM_020745		Approved	KIAA1270, bA444E17.1	uc010jza.1	Q5JTZ9	OTTHUMG00000014766	ENST00000244571.4:c.420G>A	6.37:g.44279824C>T		125.0	0.0	0		137.0	53.0	0.386861	NM_020745		Silent	SNP	ENST00000244571.4	37	CCDS34464.1																																																																																			C|0.980;T|0.020	0.020	strong		0.483	AARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040741.2	NM_020745	
DDX58	23586	hgsc.bcm.edu	37	9	32492529	32492529	+	Missense_Mutation	SNP	G	G	A	rs55789327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:32492529G>A	ENST00000379883.2	-	4	588	c.431C>T	c.(430-432)tCt>tTt	p.S144F	DDX58_ENST00000545044.1_Intron|DDX58_ENST00000379882.1_Missense_Mutation_p.S99F|DDX58_ENST00000542096.1_Missense_Mutation_p.S73F|DDX58_ENST00000379868.1_Intron	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	144	CARD 2.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell migration (GO:0030334)|regulation of type III interferon production (GO:0034344)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RIG-I signaling pathway (GO:0039529)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|identical protein binding (GO:0042802)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		CCCCTTAGTAGAGCAAATCTA	0.373													G|||	239	0.0477236	0.1104	0.0072	5008	,	,		21117	0.0407		0.0	False		,,,				2504	0.0481				p.S144F		Atlas-SNP	.											.	DDX58	82	.	0			c.C431T						PASS	.	G	PHE/SER	349,4057	179.4+/-207.9	15,319,1869	120.0	115.0	117.0		431	-2.0	0.0	9	dbSNP_129	117	6,8594	5.0+/-18.6	0,6,4294	yes	missense	DDX58	NM_014314.3	155	15,325,6163	AA,AG,GG		0.0698,7.921,2.7295	benign	144/926	32492529	355,12651	2203	4300	6503	SO:0001583	missense	23586	exon4			TTAGTAGAGCAAA	AF038963	CCDS6526.1	9p12	2011-08-05			ENSG00000107201	ENSG00000107201		"""DEAD-boxes"""	19102	protein-coding gene	gene with protein product	"""RNA helicase RIG-I"", ""retinoic acid inducible gene I"""	609631				21690088	Standard	NM_014314		Approved	RIG-I, FLJ13599, DKFZp434J1111	uc003zra.3	O95786	OTTHUMG00000019746	ENST00000379883.2:c.431C>T	9.37:g.32492529G>A	ENSP00000369213:p.Ser144Phe	208.0	0.0	0		203.0	108.0	0.53202	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Missense_Mutation	SNP	ENST00000379883.2	37	CCDS6526.1	82	0.037545787545787544	54	0.10975609756097561	4	0.011049723756906077	24	0.04195804195804196	0	0.0	G	8.541	0.873187	0.17322	0.07921	6.98E-4	ENSG00000107201	ENST00000379882;ENST00000379883;ENST00000542096;ENST00000542960	T;T;T	0.35789	1.29;1.29;1.29	5.22	-2.04	0.07343	.	1.364960	0.05002	N	0.469210	T	0.00384	0.0012	N	0.20685	0.6	0.09310	N	1	B;B;B	0.10296	0.003;0.002;0.002	B;B;B	0.09377	0.004;0.002;0.002	T	0.21109	-1.0255	10	0.56958	D	0.05	0.2274	1.0358	0.01548	0.407:0.1539:0.2819:0.1572	rs55789327	99;73;144	O95786-2;B3KWW1;O95786	.;.;DDX58_HUMAN	F	99;144;73;144	ENSP00000369212:S99F;ENSP00000369213:S144F;ENSP00000442160:S73F	ENSP00000369212:S99F	S	-	2	0	DDX58	32482529	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.367000	0.07553	-0.191000	0.10448	-0.157000	0.13467	TCT	G|0.972;A|0.028	0.028	strong		0.373	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314	
RFC1	5981	hgsc.bcm.edu	37	4	39306504	39306504	+	Silent	SNP	C	C	G	rs2066792	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:39306504C>G	ENST00000381897.1	-	15	2176	c.2043G>C	c.(2041-2043)cgG>cgC	p.R681R	RFC1_ENST00000349703.2_Silent_p.R680R	NM_001204747.1|NM_002913.4	NP_001191676.1|NP_002904.3	P35251	RFC1_HUMAN	replication factor C (activator 1) 1, 145kDa	681					DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA-dependent DNA replication (GO:0006261)|mitotic cell cycle (GO:0000278)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription, DNA-templated (GO:0045893)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|telomere maintenance via telomerase (GO:0007004)|transcription, DNA-templated (GO:0006351)|transcription-coupled nucleotide-excision repair (GO:0006283)	cell junction (GO:0030054)|DNA replication factor C complex (GO:0005663)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA clamp loader activity (GO:0003689)|double-stranded DNA binding (GO:0003690)|enzyme activator activity (GO:0008047)|sequence-specific DNA binding (GO:0043565)			haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	16						TGCTCTTACTCCGGGTGTCAC	0.433													C|||	397	0.0792732	0.2821	0.0346	5008	,	,		17846	0.0		0.0	False		,,,				2504	0.0				p.R681R	Colon(109;59 1555 12203 17579 39824)|Esophageal Squamous(18;360 542 16186 28570 51157)	Atlas-SNP	.											.	RFC1	114	.	0			c.G2043C						PASS	.	C	,	1058,3348	387.9+/-326.7	128,802,1273	261.0	268.0	266.0		2043,2040	1.7	1.0	4	dbSNP_94	266	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous,coding-synonymous	RFC1	NM_001204747.1,NM_002913.4	,	128,807,5568	GG,GC,CC		0.0581,24.0127,8.1732	,	681/1149,680/1148	39306504	1063,11943	2203	4300	6503	SO:0001819	synonymous_variant	5981	exon15			CTTACTCCGGGTG	L23320	CCDS3450.1, CCDS56329.1	4p14-p13	2010-04-21	2002-08-29		ENSG00000035928	ENSG00000035928		"""ATPases / AAA-type"""	9969	protein-coding gene	gene with protein product		102579	"""replication factor C (activator 1) 1 (145kD)"""			8114700	Standard	NM_002913		Approved	A1, PO-GA, RFC140, MHCBFB	uc003gty.2	P35251	OTTHUMG00000099363	ENST00000381897.1:c.2043G>C	4.37:g.39306504C>G		143.0	0.0	0		161.0	77.0	0.478261	NM_001204747	A8K6E7|Q5XKF5|Q6PKU0|Q86V41|Q86V46	Silent	SNP	ENST00000381897.1	37	CCDS56329.1																																																																																			C|0.922;G|0.078	0.078	strong		0.433	RFC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216808.1	NM_002913	
PCDHB14	56122	hgsc.bcm.edu	37	5	140603794	140603794	+	Silent	SNP	C	C	T	rs59600730	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140603794C>T	ENST00000239449.4	+	1	717	c.717C>T	c.(715-717)gcC>gcT	p.A239A	PCDHB14_ENST00000515856.2_Silent_p.A86A	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	239	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ATGATAATGCCCCTGAGTTTC	0.517													t|||	132	0.0263578	0.0946	0.0086	5008	,	,		16922	0.0		0.001	False		,,,				2504	0.0				p.A239A	Ovarian(141;50 1831 27899 33809 37648)	Atlas-SNP	.											.	PCDHB14	132	.	0			c.C717T						PASS	.	T		304,4102		8,288,1907	70.0	72.0	71.0		717	-1.6	1.0	5	dbSNP_129	71	3,8597		0,3,4297	no	coding-synonymous	PCDHB14	NM_018934.2		8,291,6204	TT,TC,CC		0.0349,6.8997,2.3604		239/799	140603794	307,12699	2203	4300	6503	SO:0001819	synonymous_variant	56122	exon1			TAATGCCCCTGAG	AF152493	CCDS4256.1	5q31	2010-01-26			ENSG00000120327	ENSG00000120327		"""Cadherins / Protocadherins : Clustered"""	8685	other	protocadherin		606340				10380929	Standard	NM_018934		Approved	PCDH-BETA14	uc003ljb.3	Q9Y5E9	OTTHUMG00000129619	ENST00000239449.4:c.717C>T	5.37:g.140603794C>T		98.0	0.0	0		74.0	25.0	0.337838	NM_018934	B4DPE2|Q4FZA4|Q4KN11	Silent	SNP	ENST00000239449.4	37	CCDS4256.1																																																																																			C|0.977;T|0.023	0.023	strong		0.517	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2	NM_018934	
PLOD2	5352	hgsc.bcm.edu	37	3	145794607	145794607	+	Missense_Mutation	SNP	A	A	G	rs115199093	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:145794607A>G	ENST00000360060.3	-	14	1753	c.1576T>C	c.(1576-1578)Tat>Cat	p.Y526H	PLOD2_ENST00000461497.1_Missense_Mutation_p.Y207H|PLOD2_ENST00000282903.5_Missense_Mutation_p.Y547H|PLOD2_ENST00000494950.1_Missense_Mutation_p.Y492H|RP11-274H2.2_ENST00000480247.1_RNA	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	526					cellular protein modification process (GO:0006464)|extracellular matrix organization (GO:0030198)|response to hypoxia (GO:0001666)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-lysine 5-dioxygenase activity (GO:0008475)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29					Vitamin C(DB00126)	TCATTGTTATAATGGGAAGTA	0.299													A|||	8	0.00159744	0.0053	0.0014	5008	,	,		15142	0.0		0.0	False		,,,				2504	0.0				p.Y547H		Atlas-SNP	.											.	PLOD2	81	.	0			c.T1639C						PASS	.	A	HIS/TYR,HIS/TYR	26,4380	32.6+/-62.9	0,26,2177	90.0	98.0	96.0		1576,1639	3.7	1.0	3	dbSNP_132	96	1,8573	1.2+/-3.3	0,1,4286	yes	missense,missense	PLOD2	NM_000935.2,NM_182943.2	83,83	0,27,6463	GG,GA,AA		0.0117,0.5901,0.208	benign,benign	526/738,547/759	145794607	27,12953	2203	4287	6490	SO:0001583	missense	5352	exon15			TGTTATAATGGGA	U84573	CCDS3131.1, CCDS3132.1	3q24	2011-08-24	2005-01-04		ENSG00000152952	ENSG00000152952			9082	protein-coding gene	gene with protein product	"""lysyl hydroxlase 2"""	601865	"""procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2"""			9054364	Standard	XM_005247535		Approved	LH2	uc003evr.1	O00469	OTTHUMG00000159417	ENST00000360060.3:c.1576T>C	3.37:g.145794607A>G	ENSP00000353170:p.Tyr526His	154.0	0.0	0		156.0	78.0	0.5	NM_182943	B3KWS3|Q59ED2|Q8N170	Missense_Mutation	SNP	ENST00000360060.3	37	CCDS3131.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	A	17.15	3.315084	0.60524	0.005901	1.17E-4	ENSG00000152952	ENST00000461497;ENST00000282903;ENST00000360060;ENST00000494950	D;D;D;D	0.85484	-1.99;-1.99;-1.99;-1.99	5.12	3.72	0.42706	.	0.178784	0.50627	D	0.000101	T	0.80834	0.4699	L	0.51422	1.61	0.45183	D	0.99819	P;P;P;P	0.47545	0.865;0.773;0.738;0.897	P;P;P;P	0.52109	0.628;0.492;0.69;0.497	T	0.79610	-0.1732	10	0.42905	T	0.14	-10.2013	8.8487	0.35186	0.8839:0.0:0.1161:0.0	.	492;526;547;207	E7ETU9;O00469;O00469-2;B3KWS3	.;PLOD2_HUMAN;.;.	H	207;547;526;492	ENSP00000419354:Y207H;ENSP00000282903:Y547H;ENSP00000353170:Y526H;ENSP00000420094:Y492H	ENSP00000282903:Y547H	Y	-	1	0	PLOD2	147277297	1.000000	0.71417	0.998000	0.56505	0.993000	0.82548	3.164000	0.50770	0.604000	0.29930	0.529000	0.55759	TAT	A|0.998;G|0.002	0.002	strong		0.299	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935	
MUC4	4585	hgsc.bcm.edu	37	3	195508385	195508385	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195508385C>G	ENST00000463781.3	-	2	10525	c.10066G>C	c.(10066-10068)Ggt>Cgt	p.G3356R	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.G3356R	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)		GTGGCGTGACCTGTGGATACT	0.597																																					p.G3356R		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.G10066C						PASS	.						39.0	30.0	33.0					3																	195508385		690	1584	2274	SO:0001583	missense	4585	exon2			CGTGACCTGTGGA	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.10066G>C	3.37:g.195508385C>G	ENSP00000417498:p.Gly3356Arg	413.0	0.0	0		352.0	26.0	0.0738636	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	5.357	0.251158	0.10130	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.49720	0.77;0.87	1.03	1.03	0.20045	.	.	.	.	.	T	0.22513	0.0543	N	0.19112	0.55	0.09310	N	1	P	0.50156	0.932	B	0.34824	0.19	T	0.10200	-1.0640	8	.	.	.	.	3.5123	0.07713	0.0:0.6981:0.0:0.3019	.	3228	E7ESK3	.	R	3356	ENSP00000417498:G3356R;ENSP00000420243:G3356R	.	G	-	1	0	MUC4	196993164	0.000000	0.05858	0.003000	0.11579	0.018000	0.09664	-1.956000	0.01522	0.494000	0.27859	0.089000	0.15464	GGT	.	.	none		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
FLG	2312	hgsc.bcm.edu	37	1	152285541	152285541	+	Silent	SNP	T	T	C	rs116417983	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152285541T>C	ENST00000368799.1	-	3	1856	c.1821A>G	c.(1819-1821)caA>caG	p.Q607Q	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	607	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			GCCCCGATGATTGTCCCTGGC	0.567									Ichthyosis				T|||	94	0.01877	0.0688	0.0043	5008	,	,		18467	0.0		0.0	False		,,,				2504	0.0				p.Q607Q		Atlas-SNP	.											.	FLG	900	.	0			c.A1821G						PASS	.	T		186,4220	120.0+/-157.7	5,176,2022	287.0	283.0	284.0		1821	-1.6	0.0	1	dbSNP_132	284	0,8600		0,0,4300	no	coding-synonymous	FLG	NM_002016.1		5,176,6322	CC,CT,TT		0.0,4.2215,1.4301		607/4062	152285541	186,12820	2203	4300	6503	SO:0001819	synonymous_variant	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CGATGATTGTCCC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.1821A>G	1.37:g.152285541T>C		535.0	0.0	0		542.0	253.0	0.46679	NM_002016	Q01720|Q5T583|Q9UC71	Silent	SNP	ENST00000368799.1	37	CCDS30860.1																																																																																			T|0.986;C|0.014	0.014	strong		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
CAPN6	827	hgsc.bcm.edu	37	X	110491865	110491865	+	Silent	SNP	G	G	A	rs17879776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:110491865G>A	ENST00000324068.1	-	10	1583	c.1416C>T	c.(1414-1416)acC>acT	p.T472T	CAPN6_ENST00000541758.1_Silent_p.T217T	NM_014289.3	NP_055104.2	Q9Y6Q1	CAN6_HUMAN	calpain 6	472	Domain III.				microtubule bundle formation (GO:0001578)|proteolysis (GO:0006508)|regulation of cytoskeleton organization (GO:0051493)	perinuclear region of cytoplasm (GO:0048471)|spindle microtubule (GO:0005876)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|microtubule binding (GO:0008017)			cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(25)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	47						GCTGGAACATGGTTGGGACAA	0.522													G|||	24	0.00635762	0.0174	0.0014	3775	,	,		13145	0.0		0.0	False		,,,				2504	0.0				p.T472T		Atlas-SNP	.											.	CAPN6	120	.	0			c.C1416T						PASS	.	G		91,3744		1,78,11,1553,560	105.0	87.0	93.0		1416	4.2	1.0	X	dbSNP_124	93	0,6728		0,0,0,2428,1872	no	coding-synonymous	CAPN6	NM_014289.3		1,78,11,3981,2432	AA,AG,A,GG,G		0.0,2.3729,0.8615		472/642	110491865	91,10472	2203	4300	6503	SO:0001819	synonymous_variant	827	exon10			GAACATGGTTGGG	AF029232	CCDS14555.1	Xq23	2008-07-29			ENSG00000077274	ENSG00000077274			1483	protein-coding gene	gene with protein product		300146				9503024, 9339374	Standard	NM_014289		Approved	CAPNX, CalpM, CANPX	uc004epc.2	Q9Y6Q1	OTTHUMG00000022203	ENST00000324068.1:c.1416C>T	X.37:g.110491865G>A		150.0	0.0	0		141.0	50.0	0.35461	NM_014289	D3DUY7|Q9UEQ1|Q9UJA8	Silent	SNP	ENST00000324068.1	37	CCDS14555.1																																																																																			G|0.991;A|0.009	0.009	strong		0.522	CAPN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057922.1		
EIF4G1	1981	hgsc.bcm.edu	37	3	184039304	184039304	+	Missense_Mutation	SNP	A	A	G	rs16858632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184039304A>G	ENST00000346169.2	+	10	1203	c.932A>G	c.(931-933)tAt>tGt	p.Y311C	EIF4G1_ENST00000382330.3_Missense_Mutation_p.Y318C|EIF4G1_ENST00000434061.2_Missense_Mutation_p.Y115C|EIF4G1_ENST00000342981.4_Missense_Mutation_p.Y311C|EIF4G1_ENST00000352767.3_Missense_Mutation_p.Y318C|EIF4G1_ENST00000441154.1_Missense_Mutation_p.Y147C|EIF4G1_ENST00000350481.5_Missense_Mutation_p.Y147C|EIF4G1_ENST00000427845.1_Missense_Mutation_p.Y224C|EIF4G1_ENST00000414031.1_Missense_Mutation_p.Y271C|EIF4G1_ENST00000424196.1_Missense_Mutation_p.Y318C|EIF4G1_ENST00000435046.2_Missense_Mutation_p.Y115C|EIF4G1_ENST00000392537.2_Missense_Mutation_p.Y224C|EIF4G1_ENST00000319274.6_Missense_Mutation_p.Y311C|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000411531.1_Missense_Mutation_p.Y271C	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	311			Y -> C (in dbSNP:rs16858632). {ECO:0000269|PubMed:21907011}.		cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			GGGGAGCCATATCGCCTCTCT	0.493													A|||	104	0.0207668	0.0749	0.0072	5008	,	,		19071	0.0		0.0	False		,,,				2504	0.0				p.Y318C		Atlas-SNP	.											.	EIF4G1	151	.	0			c.A953G						PASS	.	A	CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR	263,4143	151.0+/-185.0	8,247,1948	61.0	61.0	61.0		953,953,344,932,932,440,671	3.1	1.0	3	dbSNP_123	61	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense,missense,missense,missense,missense	EIF4G1	NM_001194946.1,NM_001194947.1,NM_004953.4,NM_182917.4,NM_198241.2,NM_198242.2,NM_198244.2	194,194,194,194,194,194,194	8,250,6245	GG,GA,AA		0.0349,5.9691,2.0452	benign,benign,benign,benign,benign,benign,benign	318/1607,318/1607,115/1405,311/1601,311/1600,147/1436,224/1513	184039304	266,12740	2203	4300	6503	SO:0001583	missense	1981	exon11			AGCCATATCGCCT	D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"""Parkinson disease"""	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.932A>G	3.37:g.184039304A>G	ENSP00000316879:p.Tyr311Cys	157.0	0.0	0		137.0	64.0	0.467153	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Missense_Mutation	SNP	ENST00000346169.2	37	CCDS3259.1	36	0.016483516483516484	34	0.06910569105691057	2	0.0055248618784530384	0	0.0	0	0.0	A	11.01	1.512111	0.27036	0.059691	3.49E-4	ENSG00000114867	ENST00000346169;ENST00000414031;ENST00000392537;ENST00000444134;ENST00000450424;ENST00000421110;ENST00000382330;ENST00000426123;ENST00000350481;ENST00000352767;ENST00000427845;ENST00000342981;ENST00000319274;ENST00000424196;ENST00000411531;ENST00000444861;ENST00000441154;ENST00000428387;ENST00000434061;ENST00000427607;ENST00000457456;ENST00000435046	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.52526	4.06;4.06;3.96;0.66;2.96;2.96;4.06;3.13;3.87;4.06;3.97;4.06;4.06;4.06;4.06;2.54;3.87;0.81;3.87;0.84;1.32;3.87	5.5	3.12	0.35913	.	0.732877	0.13056	N	0.417280	T	0.02418	0.0074	N	0.19112	0.55	0.29831	N	0.830056	B;B;B;B	0.26081	0.0;0.0;0.141;0.001	B;B;B;B	0.22753	0.001;0.001;0.041;0.001	T	0.05468	-1.0883	10	0.54805	T	0.06	-0.6548	6.9547	0.24563	0.755:0.1607:0.0843:0.0	rs16858632;rs16858632	318;311;311;318	E9PFM1;D3DNT2;Q04637;B2RU10	.;.;IF4G1_HUMAN;.	C	311;271;224;115;311;318;318;252;147;318;224;311;311;318;271;147;147;115;115;115;115;115	ENSP00000316879:Y311C;ENSP00000391935:Y271C;ENSP00000376320:Y224C;ENSP00000407244:Y115C;ENSP00000391412:Y311C;ENSP00000413159:Y318C;ENSP00000371767:Y318C;ENSP00000403269:Y252C;ENSP00000317600:Y147C;ENSP00000338020:Y318C;ENSP00000407682:Y224C;ENSP00000343450:Y311C;ENSP00000323737:Y311C;ENSP00000416255:Y318C;ENSP00000395974:Y271C;ENSP00000398145:Y147C;ENSP00000399858:Y147C;ENSP00000411707:Y115C;ENSP00000411826:Y115C;ENSP00000409545:Y115C;ENSP00000399969:Y115C;ENSP00000404754:Y115C	ENSP00000323737:Y311C	Y	+	2	0	EIF4G1	185521998	0.889000	0.30405	0.999000	0.59377	0.971000	0.66376	1.202000	0.32271	1.106000	0.41623	0.533000	0.62120	TAT	A|0.976;G|0.024	0.024	strong		0.493	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917	
CLEC4C	170482	hgsc.bcm.edu	37	12	7890040	7890040	+	Missense_Mutation	SNP	G	G	T	rs77889141	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:7890040G>T	ENST00000542353.1	-	5	856	c.366C>A	c.(364-366)aaC>aaA	p.N122K	CLEC4C_ENST00000354629.5_Missense_Mutation_p.N91K|CLEC4C_ENST00000360345.3_Missense_Mutation_p.N122K|CLEC4C_ENST00000540085.1_Missense_Mutation_p.N91K	NM_130441.2	NP_569708.1	Q8WTT0	CLC4C_HUMAN	C-type lectin domain family 4, member C	122	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				innate immune response (GO:0045087)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			autonomic_ganglia(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				Kidney(36;0.0915)		CTTCCCTGGTGTTGATCACCA	0.408													G|||	88	0.0175719	0.0635	0.0043	5008	,	,		-128	0.0		0.001	False		,,,				2504	0.0				p.N122K		Atlas-SNP	.											.	CLEC4C	44	.	0			c.C366A						PASS	.	G	LYS/ASN,LYS/ASN	235,4171	137.7+/-173.5	10,215,1978	129.0	126.0	127.0		366,273	2.6	0.2	12	dbSNP_131	127	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	CLEC4C	NM_130441.2,NM_203503.1	94,94	10,218,6275	TT,TG,GG		0.0349,5.3336,1.8299	possibly-damaging,possibly-damaging	122/214,91/183	7890040	238,12768	2203	4300	6503	SO:0001583	missense	170482	exon5			CCTGGTGTTGATC	AF325460	CCDS8583.1, CCDS8584.1	12p13.2-p12.3	2008-02-05	2004-02-13	2005-02-11	ENSG00000198178	ENSG00000198178		"""C-type lectin domain containing"", ""CD molecules"""	13258	protein-coding gene	gene with protein product		606677	"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 7"""	CLECSF11, CLECSF7		11031109, 11536172	Standard	NM_130441		Approved	HECL, DLEC, BDCA2, CD303	uc001qth.1	Q8WTT0	OTTHUMG00000168441	ENST00000542353.1:c.366C>A	12.37:g.7890040G>T	ENSP00000440428:p.Asn122Lys	67.0	0.0	0		54.0	27.0	0.5	NM_130441	D3DUU3|Q3T1C3|Q6UXS8|Q8WXX8	Missense_Mutation	SNP	ENST00000542353.1	37	CCDS8583.1	21	0.009615384615384616	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	0	0.0	G	10.90	1.482342	0.26598	0.053336	3.49E-4	ENSG00000198178	ENST00000542353;ENST00000354629;ENST00000540085;ENST00000360345;ENST00000537530;ENST00000543765	T;T;T;T;T;T	0.17528	2.27;2.27;2.27;2.27;2.27;2.27	2.62	2.62	0.31277	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	.	.	.	.	T	0.03390	0.0098	L	0.46614	1.455	0.09310	N	1	P;P	0.51057	0.557;0.941	B;P	0.51615	0.169;0.675	T	0.04885	-1.0920	9	0.27082	T	0.32	.	8.9424	0.35738	0.0:0.0:1.0:0.0	.	91;122	Q8WTT0-2;Q8WTT0	.;CLC4C_HUMAN	K	122;91;91;122;44;82	ENSP00000440428:N122K;ENSP00000346648:N91K;ENSP00000445338:N91K;ENSP00000353500:N122K;ENSP00000438649:N44K;ENSP00000442457:N82K	ENSP00000346648:N91K	N	-	3	2	CLEC4C	7781307	0.976000	0.34144	0.165000	0.22776	0.054000	0.15201	1.943000	0.40253	1.784000	0.52394	0.603000	0.83216	AAC	G|0.981;T|0.019	0.019	strong		0.408	CLEC4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399750.1	NM_203503	
TDRD5	163589	hgsc.bcm.edu	37	1	179564885	179564885	+	Missense_Mutation	SNP	A	A	G	rs147268063	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:179564885A>G	ENST00000367614.1	+	4	1122	c.763A>G	c.(763-765)Atg>Gtg	p.M255V	TDRD5_ENST00000294848.8_Missense_Mutation_p.M255V|TDRD5_ENST00000444136.1_Missense_Mutation_p.M255V	NM_001199091.1	NP_001186020.1	Q8NAT2	TDRD5_HUMAN	tudor domain containing 5	255					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						AATAATGAGCATGGAAAAGAC	0.383													A|||	16	0.00319489	0.0121	0.0	5008	,	,		17514	0.0		0.0	False		,,,				2504	0.0				p.M255V		Atlas-SNP	.											.	TDRD5	149	.	0			c.A763G						PASS	.	A	VAL/MET,VAL/MET,VAL/MET,VAL/MET	39,4367	44.6+/-78.6	0,39,2164	88.0	89.0	89.0		763,763,763,763	-11.4	0.0	1	dbSNP_134	89	0,8600		0,0,4300	yes	missense,missense,missense,missense	TDRD5	NM_001199085.1,NM_001199089.1,NM_001199091.1,NM_173533.3	21,21,21,21	0,39,6464	GG,GA,AA		0.0,0.8852,0.2999	benign,benign,benign,benign	255/1036,255/1036,255/982,255/982	179564885	39,12967	2203	4300	6503	SO:0001583	missense	163589	exon4			ATGAGCATGGAAA	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.763A>G	1.37:g.179564885A>G	ENSP00000356586:p.Met255Val	113.0	0.0	0		149.0	72.0	0.483221	NM_173533	A1L4G5|B7ZLV0|Q5EBN4|Q5VTV0|Q6ZSK2	Missense_Mutation	SNP	ENST00000367614.1	37	CCDS1332.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	3.552	-0.091465	0.07053	0.008852	0.0	ENSG00000162782	ENST00000367614;ENST00000294848;ENST00000444136	T;T;T	0.10960	2.82;2.82;3.01	5.69	-11.4	0.00090	.	1.295340	0.05464	N	0.551832	T	0.02455	0.0075	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29792	-1.0000	10	0.16896	T	0.51	-18.0062	3.1803	0.06582	0.3073:0.3169:0.2888:0.0871	.	255;255	Q8NAT2-1;Q8NAT2	.;TDRD5_HUMAN	V	255	ENSP00000356586:M255V;ENSP00000294848:M255V;ENSP00000406052:M255V	ENSP00000294848:M255V	M	+	1	0	TDRD5	177831508	0.000000	0.05858	0.000000	0.03702	0.648000	0.38561	-0.275000	0.08525	-1.928000	0.01059	0.477000	0.44152	ATG	A|0.997;G|0.003	0.003	strong		0.383	TDRD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000085295.1	NM_173533	
TXNDC11	51061	hgsc.bcm.edu	37	16	11773261	11773261	+	Silent	SNP	G	G	C	rs8191350	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:11773261G>C	ENST00000356957.3	-	13	2855	c.2748C>G	c.(2746-2748)acC>acG	p.T916T	TXNDC11_ENST00000283033.5_Silent_p.T889T|TXNDC11_ENST00000570917.1_5'UTR			Q6PKC3	TXD11_HUMAN	thioredoxin domain containing 11	916					cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)			endometrium(3)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	21						ACGTGTTCTCGGTAAGGAGGT	0.617													G|||	117	0.0233626	0.087	0.0029	5008	,	,		17720	0.0		0.0	False		,,,				2504	0.0				p.T889T		Atlas-SNP	.											.	TXNDC11	75	.	0			c.C2667G						PASS	.	G		362,4032	181.2+/-209.3	18,326,1853	61.0	60.0	61.0		2667	-11.3	0.0	16	dbSNP_117	61	4,8596	2.2+/-6.3	0,4,4296	no	coding-synonymous	TXNDC11	NM_015914.5		18,330,6149	CC,CG,GG		0.0465,8.2385,2.8167		889/959	11773261	366,12628	2197	4300	6497	SO:0001819	synonymous_variant	51061	exon12			GTTCTCGGTAAGG	BC013727	CCDS32387.1	16p13.13	2008-09-29				ENSG00000153066			28030	protein-coding gene	gene with protein product	"""EF-hand binding protein 1"""					8619474, 9110174	Standard	XM_005255346		Approved	EFP1	uc002dbg.1	Q6PKC3		ENST00000356957.3:c.2748C>G	16.37:g.11773261G>C		101.0	0.0	0		119.0	53.0	0.445378	NM_015914	O95887|Q6PJA6|Q8N2Q4|Q96K45|Q96K53	Silent	SNP	ENST00000356957.3	37																																																																																				G|0.970;C|0.030	0.030	strong		0.617	TXNDC11-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000437057.1	NM_015914	
DBN1	1627	hgsc.bcm.edu	37	5	176885145	176885145	+	Missense_Mutation	SNP	A	A	C	rs139935466	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:176885145A>C	ENST00000309007.5	-	12	1909	c.1690T>G	c.(1690-1692)Tca>Gca	p.S564A	DBN1_ENST00000292385.5_Missense_Mutation_p.S566A|DBN1_ENST00000393563.4_Missense_Mutation_p.S296A|DBN1_ENST00000393565.1_Missense_Mutation_p.S610A|DBN1_ENST00000512501.1_Missense_Mutation_p.S296A	NM_004395.3	NP_004386	Q16643	DREB_HUMAN	drebrin 1	564					actin filament organization (GO:0007015)|cell communication by chemical coupling (GO:0010643)|cell communication by electrical coupling (GO:0010644)|maintenance of protein location in cell (GO:0032507)|neural precursor cell proliferation (GO:0061351)|regulation of dendrite development (GO:0050773)|regulation of neuronal synaptic plasticity (GO:0048168)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|gap junction (GO:0005921)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|profilin binding (GO:0005522)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(12)|ovary(1)|skin(2)	25	all_cancers(89;2.17e-05)|Renal(175;0.000269)|Lung NSC(126;0.0014)|all_lung(126;0.0025)	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)			TCAAGGGCTGAGGGCAGAGTT	0.642													A|||	23	0.00459265	0.0151	0.0014	5008	,	,		15225	0.0		0.002	False		,,,				2504	0.0				p.S566A		Atlas-SNP	.											.	DBN1	122	.	0			c.T1696G						PASS	.	A	ALA/SER,ALA/SER	45,4361		1,43,2159	35.0	40.0	39.0		1690,1696	2.1	1.0	5	dbSNP_134	39	0,8592		0,0,4296	yes	missense,missense	DBN1	NM_004395.3,NM_080881.2	99,99	1,43,6455	CC,CA,AA		0.0,1.0213,0.3462	possibly-damaging,possibly-damaging	564/650,566/652	176885145	45,12953	2203	4296	6499	SO:0001583	missense	1627	exon13			GGGCTGAGGGCAG		CCDS4420.1, CCDS4421.1	5q35.3	2008-02-05			ENSG00000113758	ENSG00000113758			2695	protein-coding gene	gene with protein product		126660		D0S117E		8216329	Standard	NM_004395		Approved		uc003mgy.2	Q16643	OTTHUMG00000130856	ENST00000309007.5:c.1690T>G	5.37:g.176885145A>C	ENSP00000308532:p.Ser564Ala	117.0	0.0	0		107.0	43.0	0.401869	NM_080881	A8MV58|B2RBG0|Q9UFZ5	Missense_Mutation	SNP	ENST00000309007.5	37	CCDS4420.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	A	3.494	-0.103186	0.06967	0.010213	0.0	ENSG00000113758	ENST00000309007;ENST00000292385;ENST00000393565;ENST00000512501;ENST00000393563	T;T;T;T;T	0.32023	1.48;1.48;1.47;1.47;1.5	4.71	2.09	0.27110	.	1.730350	0.02752	N	0.117546	T	0.09686	0.0238	N	0.08118	0	0.18873	N	0.999983	P;B;B;B	0.35107	0.484;0.401;0.005;0.247	B;B;B;B	0.34038	0.174;0.115;0.004;0.107	T	0.24584	-1.0156	10	0.37606	T	0.19	-8.9664	9.4796	0.38893	0.7209:0.0:0.0:0.2791	.	514;610;564;566	B3KSQ7;A8MV58;Q16643;Q16643-2	.;.;DREB_HUMAN;.	A	564;566;610;296;296	ENSP00000308532:S564A;ENSP00000292385:S566A;ENSP00000377195:S610A;ENSP00000423208:S296A;ENSP00000377193:S296A	ENSP00000292385:S566A	S	-	1	0	DBN1	176817751	0.998000	0.40836	0.954000	0.39281	0.247000	0.25773	1.322000	0.33689	0.916000	0.36871	0.379000	0.24179	TCA	A|0.995;C|0.005	0.005	strong		0.642	DBN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253429.2	NM_080881	
DNAH14	127602	hgsc.bcm.edu	37	1	225373101	225373101	+	Missense_Mutation	SNP	G	G	T	rs6679852	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:225373101G>T	ENST00000445597.2	+	24	4363	c.4363G>T	c.(4363-4365)Gtt>Ttt	p.V1455F	DNAH14_ENST00000439375.2_Missense_Mutation_p.V1860F|DNAH14_ENST00000430092.1_Missense_Mutation_p.V1860F			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	1455					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						CTTCTTATCAGTTGCAGAAAG	0.328													G|||	28	0.00559105	0.0204	0.0014	5008	,	,		14919	0.0		0.0	False		,,,				2504	0.0				p.V1860F		Atlas-SNP	.											.	DNAH14	300	.	0			c.G5578T						PASS	.	G	PHE/VAL	41,1343		0,41,651	110.0	97.0	101.0		5578	-9.8	0.0	1	dbSNP_116	101	0,3182		0,0,1591	no	missense	DNAH14	NM_001373.1	50	0,41,2242	TT,TG,GG		0.0,2.9624,0.8979	benign	1860/4516	225373101	41,4525	692	1591	2283	SO:0001583	missense	127602	exon36			TTATCAGTTGCAG	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.4363G>T	1.37:g.225373101G>T	ENSP00000409472:p.Val1455Phe	128.0	0.0	0		119.0	55.0	0.462185	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	G	6.488	0.458267	0.12342	0.029624	0.0	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375;ENST00000328556	T;T;T;T	0.31247	3.21;1.5;1.5;1.7	4.91	-9.83	0.00482	.	.	.	.	.	T	0.03520	0.0101	N	0.14661	0.345	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.12477	-1.0546	9	0.17369	T	0.5	.	4.9175	0.13853	0.126:0.2314:0.4721:0.1704	rs6679852;rs52818506;rs6679852	1860	Q0VDD8-4	.	F	1455;1860;1860;954	ENSP00000409472:V1455F;ENSP00000414402:V1860F;ENSP00000392061:V1860F;ENSP00000332424:V954F	ENSP00000332424:V954F	V	+	1	0	DNAH14	223439724	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-2.758000	0.00787	-2.863000	0.00326	-0.467000	0.05162	GTT	G|0.994;T|0.006	0.006	strong		0.328	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
NMT1	4836	hgsc.bcm.edu	37	17	43181223	43181223	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:43181223C>T	ENST00000592782.1	+	11	1442	c.1311C>T	c.(1309-1311)gaC>gaT	p.D437D	NMT1_ENST00000258960.2_Silent_p.D437D			P30419	NMT1_HUMAN	N-myristoyltransferase 1	437					apoptotic process (GO:0006915)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|N-terminal protein myristoylation (GO:0006499)|phototransduction, visible light (GO:0007603)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|protein lipoylation (GO:0009249)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	catalytic activity (GO:0003824)|glycylpeptide N-tetradecanoyltransferase activity (GO:0004379)			breast(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)	8		Prostate(33;0.155)				TCATGAGCGACGCCCTTGTCC	0.567																																					p.D437D		Atlas-SNP	.											.	NMT1	31	.	0			c.C1311T						PASS	.						226.0	220.0	222.0					17																	43181223		2203	4300	6503	SO:0001819	synonymous_variant	4836	exon10			GAGCGACGCCCTT		CCDS11494.1	17q21.31	2012-10-02			ENSG00000136448	ENSG00000136448			7857	protein-coding gene	gene with protein product	"""alternative, short form NMT-S"", ""myristoyl-CoA:protein N-myristoyltransferase"", ""long form, NMT-L"""	160993				1570339	Standard	NM_021079		Approved	NMT	uc002ihz.3	P30419	OTTHUMG00000180003	ENST00000592782.1:c.1311C>T	17.37:g.43181223C>T		95.0	0.0	0		115.0	51.0	0.443478	NM_021079	A8K7C1|Q9UE09	Silent	SNP	ENST00000592782.1	37	CCDS11494.1																																																																																			.	.	none		0.567	NMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449239.1	NM_021079	
ZNF460	10794	hgsc.bcm.edu	37	19	57802782	57802782	+	Silent	SNP	C	C	T	rs80302225	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:57802782C>T	ENST00000360338.3	+	3	1195	c.873C>T	c.(871-873)taC>taT	p.Y291Y	ZNF460_ENST00000537645.1_Silent_p.Y250Y	NM_006635.3	NP_006626.3	Q14592	ZN460_HUMAN	zinc finger protein 460	291					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(3)|large_intestine(2)|lung(9)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0694)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CCTTTACCTACCGCTCCAATT	0.493													c|||	23	0.00459265	0.0166	0.0014	5008	,	,		22183	0.0		0.0	False		,,,				2504	0.0				p.Y291Y		Atlas-SNP	.											.	ZNF460	59	.	0			c.C873T						PASS	.	C		66,4340	62.9+/-100.1	2,62,2139	88.0	81.0	83.0		873	0.3	0.0	19	dbSNP_132	83	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ZNF460	NM_006635.3		2,63,6438	TT,TC,CC		0.0116,1.498,0.5151		291/563	57802782	67,12939	2203	4300	6503	SO:0001819	synonymous_variant	10794	exon3			TACCTACCGCTCC	X78931	CCDS12949.1	19q13.4	2013-01-08				ENSG00000197714		"""Zinc fingers, C2H2-type"", ""-"""	21628	protein-coding gene	gene with protein product		604755	"""zinc finger protein 272"""	ZNF272		15004467	Standard	NM_006635		Approved	HZF8	uc002qog.2	Q14592		ENST00000360338.3:c.873C>T	19.37:g.57802782C>T		76.0	0.0	0		63.0	27.0	0.428571	NM_006635	A4FU64|B4DNX9|Q2VPC7|Q6VSF8	Silent	SNP	ENST00000360338.3	37	CCDS12949.1																																																																																			C|0.994;T|0.006	0.006	strong		0.493	ZNF460-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465727.1	NM_006635	
PTPN13	5783	hgsc.bcm.edu	37	4	87653594	87653594	+	Silent	SNP	A	A	G	rs201078979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:87653594A>G	ENST00000411767.2	+	11	1713	c.1650A>G	c.(1648-1650)ccA>ccG	p.P550P	PTPN13_ENST00000436978.1_Silent_p.P550P|PTPN13_ENST00000511467.1_Silent_p.P550P|PTPN13_ENST00000316707.6_Silent_p.P550P|PTPN13_ENST00000427191.2_Silent_p.P550P			Q12923	PTN13_HUMAN	protein tyrosine phosphatase, non-receptor type 13 (APO-1/CD95 (Fas)-associated phosphatase)	550					peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	protein tyrosine phosphatase activity (GO:0004725)			NS(4)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(23)|lung(24)|ovary(4)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	93		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.00082)		CAATTGAACCATTTATATCTT	0.289													A|||	8	0.00159744	0.0061	0.0	5008	,	,		17350	0.0		0.0	False		,,,				2504	0.0				p.P550P		Atlas-SNP	.											.	PTPN13	203	.	0			c.A1650G						PASS	.	A	,,,	19,3581		0,19,1781	57.0	53.0	54.0		1650,1650,1650,1650	3.2	1.0	4		54	1,8119		0,1,4059	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PTPN13	NM_006264.2,NM_080683.2,NM_080684.2,NM_080685.2	,,,	0,20,5840	GG,GA,AA		0.0123,0.5278,0.1706	,,,	550/2467,550/2486,550/2295,550/2491	87653594	20,11700	1800	4060	5860	SO:0001819	synonymous_variant	5783	exon11			TGAACCATTTATA		CCDS47093.1, CCDS47094.1, CCDS47095.1, CCDS47096.1	4q21.3	2011-06-09			ENSG00000163629	ENSG00000163629		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9646	protein-coding gene	gene with protein product		600267				8287977	Standard	NM_006264		Approved	PTP1E, PTP-BAS, PTPL1, PTP-BL	uc003hpy.3	Q12923	OTTHUMG00000160968	ENST00000411767.2:c.1650A>G	4.37:g.87653594A>G		87.0	0.0	0		77.0	31.0	0.402597	NM_006264	B2RTR0|Q15159|Q15263|Q15264|Q15265|Q15674|Q16826|Q8IWH7|Q9NYN9|Q9UDA8	Silent	SNP	ENST00000411767.2	37	CCDS47094.1																																																																																			A|0.999;G|0.001	0.001	strong		0.289	PTPN13-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363191.1		
OR4D9	390199	hgsc.bcm.edu	37	11	59282838	59282838	+	Silent	SNP	G	G	A	rs75125922	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:59282838G>A	ENST00000329328.3	+	1	453	c.453G>A	c.(451-453)ggG>ggA	p.G151G		NM_001004711.1	NP_001004711.1	Q8NGE8	OR4D9_HUMAN	olfactory receptor, family 4, subfamily D, member 9	151				ASWVGGF -> GFLGGGL (in Ref. 2; AC019093). {ECO:0000305}.		integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(3)|lung(14)|prostate(5)|upper_aerodigestive_tract(1)	26						CCTGGGTGGGGGGCTTTGTCC	0.547													G|||	180	0.0359425	0.1331	0.0058	5008	,	,		18390	0.0		0.0	False		,,,				2504	0.0				p.G151G		Atlas-SNP	.											.	OR4D9	47	.	0			c.G453A						PASS	.	G		451,3951	215.8+/-234.7	18,415,1768	81.0	79.0	79.0		453	2.1	1.0	11	dbSNP_131	79	2,8588	1.2+/-3.3	0,2,4293	no	coding-synonymous	OR4D9	NM_001004711.1		18,417,6061	AA,AG,GG		0.0233,10.2453,3.4868		151/315	59282838	453,12539	2201	4295	6496	SO:0001819	synonymous_variant	390199	exon1			GGTGGGGGGCTTT	AB065861	CCDS31564.1	11q12.1	2012-08-09	2003-12-15		ENSG00000172742	ENSG00000172742		"""GPCR / Class A : Olfactory receptors"""	15178	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily D, member 9 pseudogene"""				Standard	NM_001004711		Approved		uc010rkv.2	Q8NGE8	OTTHUMG00000167343	ENST00000329328.3:c.453G>A	11.37:g.59282838G>A		102.0	0.0	0		144.0	72.0	0.5	NM_001004711	Q6IFF3	Silent	SNP	ENST00000329328.3	37	CCDS31564.1																																																																																			G|0.966;A|0.034	0.034	strong		0.547	OR4D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394237.1	NM_001004711	
HIST1H4C	8364	hgsc.bcm.edu	37	6	26104382	26104382	+	Silent	SNP	C	C	T	rs2229767	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:26104382C>T	ENST00000377803.2	+	1	279	c.207C>T	c.(205-207)gaC>gaT	p.D69D		NM_003542.3	NP_003533.1	P62805	H4_HUMAN	histone cluster 1, H4c	69					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|skin(1)	7						TTATTCGAGACGCCGTCACCT	0.542													c|||	175	0.0349441	0.1248	0.013	5008	,	,		17220	0.0		0.001	False		,,,				2504	0.0				p.D69D		Atlas-SNP	.											.	HIST1H4C	14	.	0			c.C207T						PASS	.	T		437,3969		27,383,1793	74.0	66.0	69.0		207	0.8	1.0	6	dbSNP_98	69	29,8571		0,29,4271	no	coding-synonymous	HIST1H4C	NM_003542.3		27,412,6064	TT,TC,CC		0.3372,9.9183,3.583		69/104	26104382	466,12540	2203	4300	6503	SO:0001819	synonymous_variant	8364	exon1			TCGAGACGCCGTC	X60486	CCDS4583.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000197061	ENSG00000197061		"""Histones / Replication-dependent"""	4787	protein-coding gene	gene with protein product		602827	"""H4 histone family, member G"", ""histone 1, H4c"""	H4FG		9119399, 12408966	Standard	NM_003542		Approved	H4/g, dJ221C16.1	uc003ngi.3	P62805	OTTHUMG00000014429	ENST00000377803.2:c.207C>T	6.37:g.26104382C>T		97.0	0.0	0		171.0	81.0	0.473684	NM_003542	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Silent	SNP	ENST00000377803.2	37	CCDS4583.1																																																																																			C|0.963;T|0.037	0.037	strong		0.542	HIST1H4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040092.2	NM_003542	
DNAH9	1770	hgsc.bcm.edu	37	17	11540079	11540079	+	Silent	SNP	C	C	T	rs8065057	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:11540079C>T	ENST00000262442.4	+	9	1832	c.1764C>T	c.(1762-1764)caC>caT	p.H588H	DNAH9_ENST00000454412.2_Silent_p.H588H	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	588	Stem. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		ACAGTCAGCACGTCCAGGAGG	0.438													T|||	54	0.0107827	0.0393	0.0029	5008	,	,		22057	0.0		0.0	False		,,,				2504	0.0				p.H588H		Atlas-SNP	.											.	DNAH9	695	.	0			c.C1764T						PASS	.	T		210,4196	807.3+/-415.9	3,204,1996	145.0	138.0	140.0		1764	-0.4	0.6	17	dbSNP_116	140	2,8598	819.2+/-406.8	0,2,4298	no	coding-synonymous	DNAH9	NM_001372.3		3,206,6294	TT,TC,CC		0.0233,4.7662,1.63		588/4487	11540079	212,12794	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon9			TCAGCACGTCCAG	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.1764C>T	17.37:g.11540079C>T		77.0	0.0	0		93.0	36.0	0.387097	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			C|0.984;T|0.016	0.016	strong		0.438	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
CCAR2	57805	hgsc.bcm.edu	37	8	22472473	22472473	+	Silent	SNP	G	G	A	rs112997942	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22472473G>A	ENST00000308511.4	+	11	1413	c.1164G>A	c.(1162-1164)gcG>gcA	p.A388A	RP11-582J16.5_ENST00000521025.1_RNA|CCAR2_ENST00000389279.3_Silent_p.A388A|CCAR2_ENST00000520861.1_Silent_p.A63A			Q8N163	CCAR2_HUMAN	cell cycle and apoptosis regulator 2	388					cell cycle (GO:0007049)|cellular response to DNA damage stimulus (GO:0006974)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|mRNA processing (GO:0006397)|negative regulation of catalytic activity (GO:0043086)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage checkpoint (GO:2000003)|regulation of circadian rhythm (GO:0042752)|regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of protein stability (GO:0031647)|response to UV (GO:0009411)|RNA splicing (GO:0008380)	cytoplasm (GO:0005737)|DBIRD complex (GO:0044609)|mitochondrial matrix (GO:0005759)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)										TCCGCTGTGCGCAGGCCCAGA	0.627													G|||	37	0.00738818	0.0265	0.0029	5008	,	,		20145	0.0		0.0	False		,,,				2504	0.0				p.A388A		Atlas-SNP	.											.	KIAA1967	72	.	0			c.G1164A						PASS	.	G		87,4317	67.0+/-104.6	0,87,2115	46.0	34.0	38.0		1164	-11.1	0.0	8	dbSNP_132	38	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KIAA1967	NM_021174.5		0,88,6414	AA,AG,GG		0.0116,1.9755,0.6767		388/924	22472473	88,12916	2202	4300	6502	SO:0001819	synonymous_variant	57805	exon11			CTGTGCGCAGGCC	AL834351	CCDS34863.1	8p22	2013-08-22	2013-08-22	2013-08-22		ENSG00000158941			23360	protein-coding gene	gene with protein product	"""deleted in breast cancer"""	607359	"""KIAA1967"""	KIAA1967		12370419	Standard	NM_021174		Approved	DBC-1, DBC1, NET35	uc003xci.3	Q8N163		ENST00000308511.4:c.1164G>A	8.37:g.22472473G>A		86.0	0.0	0		107.0	52.0	0.485981	NM_021174	A6NL03|B2RB79|D3DSR6|Q6P0Q9|Q8N3G7|Q8N8M1|Q8TF34|Q9H9Q9|Q9HD12|Q9NT55	Silent	SNP	ENST00000308511.4	37	CCDS34863.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	G	9.159	1.018179	0.19355	0.019755	1.16E-4	ENSG00000158941	ENST00000520738	.	.	.	5.53	-11.1	0.00147	.	.	.	.	.	T	0.25531	0.0621	.	.	.	0.40931	D	0.984397	.	.	.	.	.	.	T	0.49351	-0.8949	4	.	.	.	-11.8395	5.7525	0.18154	0.4761:0.2759:0.182:0.066	.	.	.	.	H	80	.	.	R	+	2	0	KIAA1967	22528418	0.000000	0.05858	0.010000	0.14722	0.924000	0.55760	-2.064000	0.01387	-2.862000	0.00326	-0.793000	0.03317	CGC	G|0.993;A|0.007	0.007	strong		0.627	CCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375865.1	NM_021174	
REPIN1	29803	hgsc.bcm.edu	37	7	150068981	150068981	+	Silent	SNP	G	G	A	rs149624173	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150068981G>A	ENST00000425389.2	+	1	729	c.651G>A	c.(649-651)agG>agA	p.R217R	REPIN1_ENST00000397281.2_Silent_p.R217R|REPIN1_ENST00000444957.1_Silent_p.R217R|REPIN1_ENST00000479668.1_3'UTR|REPIN1_ENST00000540729.1_Silent_p.R217R|REPIN1_ENST00000489432.2_Silent_p.R274R|REPIN1_ENST00000466559.1_3'UTR|RP4-584D14.5_ENST00000488310.1_RNA	NM_014374.3	NP_055189.2	Q9BWE0	REPI1_HUMAN	replication initiator 1	217					DNA replication (GO:0006260)|regulation of fatty acid transport (GO:2000191)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cytosolic ribosome (GO:0022626)|lipid particle (GO:0005811)|nuclear membrane (GO:0031965)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(2)|lung(7)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	14	Ovarian(565;0.183)|Melanoma(164;0.226)		OV - Ovarian serous cystadenocarcinoma(82;0.011)			cccggcccaggggccgccccg	0.716													G|||	21	0.00419329	0.0159	0.0	5008	,	,		9749	0.0		0.0	False		,,,				2504	0.0				p.R274R		Atlas-SNP	.											.	REPIN1	74	.	0			c.G822A						PASS	.	G	,,,	38,3468		0,38,1715	8.0	10.0	9.0		822,651,651,651	1.7	0.9	7	dbSNP_134	9	0,7798		0,0,3899	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	REPIN1	NM_001099695.1,NM_001099696.2,NM_013400.3,NM_014374.3	,,,	0,38,5614	AA,AG,GG		0.0,1.0839,0.3362	,,,	274/625,217/568,217/568,217/568	150068981	38,11266	1753	3899	5652	SO:0001819	synonymous_variant	29803	exon3			GCCCAGGGGCCGC	AF201303	CCDS43677.1, CCDS47745.1	7q36.1	2013-01-08	2003-08-07	2003-08-08				"""Zinc fingers, C2H2-type"""	17922	protein-coding gene	gene with protein product	"""replication initiation region protein (60kD)"", ""zinc finger protein AP4"", ""zinc finger protein 464 (RIP60)"""		"""zinc finger protein 464 (RIP60)"""	ZNF464		10606657	Standard	NM_013400		Approved	RIP60, AP4, H_DJ0584D14.12, Zfp464	uc010lpr.1	Q9BWE0		ENST00000425389.2:c.651G>A	7.37:g.150068981G>A		7.0	0.0	0		7.0	4.0	0.571429	NM_001099695	C9J3L7|D3DWZ1|Q7LE03|Q9BUZ6|Q9NZH2|Q9UMP5	Silent	SNP	ENST00000425389.2	37	CCDS43677.1																																																																																			G|0.994;A|0.006	0.006	strong		0.716	REPIN1-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376940.1	NM_014374	
SLFN13	146857	hgsc.bcm.edu	37	17	33769211	33769211	+	Missense_Mutation	SNP	C	C	T	rs77814846	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:33769211C>T	ENST00000285013.6	-	5	1568	c.1293G>A	c.(1291-1293)atG>atA	p.M431I	SLFN13_ENST00000526861.1_Missense_Mutation_p.M431I|SLFN13_ENST00000360502.2_Missense_Mutation_p.M113I|SLFN13_ENST00000533791.1_Missense_Mutation_p.M431I|SLFN13_ENST00000534689.1_Missense_Mutation_p.M113I|SLFN13_ENST00000542635.1_Missense_Mutation_p.M431I	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	431						intracellular (GO:0005622)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(1)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	31				UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		AGAAAGGTCGCATTTGCTTGT	0.488													C|||	74	0.0147764	0.053	0.0058	5008	,	,		18201	0.0		0.0	False		,,,				2504	0.0				p.M431I		Atlas-SNP	.											.	SLFN13	79	.	0			c.G1293A						PASS	.	C	ILE/MET	199,4207	124.9+/-162.1	3,193,2007	91.0	82.0	85.0		1293	-6.2	0.0	17	dbSNP_131	85	2,8598	2.2+/-6.3	0,2,4298	yes	missense	SLFN13	NM_144682.5	10	3,195,6305	TT,TC,CC		0.0233,4.5166,1.5454	benign	431/898	33769211	201,12805	2203	4300	6503	SO:0001583	missense	146857	exon5			AGGTCGCATTTGC	AL832726	CCDS32620.1	17q12	2006-04-05				ENSG00000154760			26481	protein-coding gene	gene with protein product		614957				9846487	Standard	NM_144682		Approved	FLJ31952	uc002hjl.2	Q68D06		ENST00000285013.6:c.1293G>A	17.37:g.33769211C>T	ENSP00000285013:p.Met431Ile	158.0	0.0	0		155.0	76.0	0.490323	NM_144682	E1P645|Q658M1|Q6ZS51|Q96A81	Missense_Mutation	SNP	ENST00000285013.6	37	CCDS32620.1	31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	c	0.430	-0.903761	0.02453	0.045166	2.33E-4	ENSG00000154760	ENST00000285013;ENST00000360502;ENST00000526861;ENST00000542635;ENST00000534689;ENST00000532210	T;T;T;T;T;T	0.16597	4.64;4.06;4.64;4.64;4.06;2.33	3.09	-6.17	0.02091	.	0.757041	0.12071	N	0.502241	T	0.00552	0.0018	N	0.17474	0.49	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.13407	0.009;0.0	T	0.36866	-0.9730	10	0.05525	T	0.97	.	1.256	0.01991	0.1521:0.2533:0.1508:0.4438	.	113;431	Q68D06-2;Q68D06	.;SLN13_HUMAN	I	431;113;431;431;113;100	ENSP00000285013:M431I;ENSP00000353692:M113I;ENSP00000434439:M431I;ENSP00000444016:M431I;ENSP00000435442:M113I;ENSP00000435328:M100I	ENSP00000285013:M431I	M	-	3	0	SLFN13	30793324	0.000000	0.05858	0.001000	0.08648	0.138000	0.21146	-0.875000	0.04205	-1.010000	0.03396	0.205000	0.17691	ATG	C|0.987;T|0.013	0.013	strong		0.488	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682	
GPR179	440435	hgsc.bcm.edu	37	17	36482372	36482372	+	Silent	SNP	A	A	C	rs58740367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:36482372A>C	ENST00000342292.4	-	11	7100	c.7080T>G	c.(7078-7080)acT>acG	p.T2360T	GPR179_ENST00000584976.1_Intron	NM_001004334.2	NP_001004334.2	Q6PRD1	GP179_HUMAN	G protein-coupled receptor 179	2360					visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(4)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(16)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Breast(7;2.97e-12)	Breast(25;0.0101)|Ovarian(249;0.15)				AAGGATAGACAGTGGGAGGGG	0.498													A|||	291	0.058107	0.2148	0.0101	5008	,	,		20612	0.0		0.0	False		,,,				2504	0.0				p.T2360T		Atlas-SNP	.											.	GPR179	170	.	0			c.T7080G						PASS	.	A		644,3154		58,528,1313	73.0	67.0	69.0		7080	1.3	0.1	17	dbSNP_129	69	3,8259		0,3,4128	no	coding-synonymous	GPR179	NM_001004334.2		58,531,5441	CC,CA,AA		0.0363,16.9563,5.3648		2360/2368	36482372	647,11413	1899	4131	6030	SO:0001819	synonymous_variant	440435	exon11			ATAGACAGTGGGA		CCDS42308.1	17q21.1	2014-05-06	2006-02-16	2006-02-16	ENSG00000188888	ENSG00000277399		"""GPCR / Class C : Orphans"""	31371	protein-coding gene	gene with protein product		614515	"""GPR158-like 1"", ""GPR179"""	GPR158L1			Standard	NM_001004334		Approved	CSNB1E	uc002hpz.3	Q6PRD1	OTTHUMG00000188545	ENST00000342292.4:c.7080T>G	17.37:g.36482372A>C		72.0	0.0	0		59.0	59.0	1	NM_001004334		Silent	SNP	ENST00000342292.4	37	CCDS42308.1																																																																																			A|0.955;C|0.045	0.045	strong		0.498	GPR179-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255329.2		
PCDHB15	56121	hgsc.bcm.edu	37	5	140627184	140627184	+	Missense_Mutation	SNP	C	C	G	rs79326925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140627184C>G	ENST00000231173.3	+	1	2038	c.2038C>G	c.(2038-2040)Caa>Gaa	p.Q680E		NM_018935.2	NP_061758.1	Q9Y5E8	PCDBF_HUMAN	protocadherin beta 15	680					cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.Q680K(1)		NS(1)|breast(3)|endometrium(8)|kidney(3)|large_intestine(14)|liver(1)|lung(18)|ovary(3)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	61			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGCCCCGGCCCAAGCCCAGGC	0.672													C|||	103	0.0205671	0.0734	0.0072	5008	,	,		16390	0.0		0.001	False		,,,				2504	0.0				p.Q680E		Atlas-SNP	.											.	PCDHB15	138	.	1	Substitution - Missense(1)	lung(1)	c.C2038G						PASS	.	C	GLU/GLN	247,4147		5,237,1955	62.0	68.0	66.0		2038	0.1	0.0	5	dbSNP_131	66	0,8572		0,0,4286	no	missense	PCDHB15	NM_018935.2	29	5,237,6241	GG,GC,CC		0.0,5.6213,1.905	benign	680/788	140627184	247,12719	2197	4286	6483	SO:0001583	missense	56121	exon1			CCGGCCCAAGCCC	AF152494	CCDS4257.1	5q31	2011-06-07			ENSG00000113248	ENSG00000113248		"""Cadherins / Protocadherins : Clustered"""	8686	other	protocadherin		606341				10380929	Standard	NM_018935		Approved	PCDH-BETA15	uc003lje.3	Q9Y5E8	OTTHUMG00000129609	ENST00000231173.3:c.2038C>G	5.37:g.140627184C>G	ENSP00000231173:p.Gln680Glu	117.0	0.0	0		109.0	63.0	0.577982	NM_018935	Q8IUX5	Missense_Mutation	SNP	ENST00000231173.3	37	CCDS4257.1	39	0.017857142857142856	37	0.07520325203252033	2	0.0055248618784530384	0	0.0	0	0.0	C	8.308	0.821498	0.16678	0.056213	0.0	ENSG00000113248	ENST00000231173	T	0.46063	0.88	4.25	0.0585	0.14328	.	.	.	.	.	T	0.01592	0.0051	L	0.31120	0.905	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.09185	-1.0686	9	0.10636	T	0.68	.	15.5586	0.76219	0.0:0.5083:0.4917:0.0	.	680	Q9Y5E8	PCDBF_HUMAN	E	680	ENSP00000231173:Q680E	ENSP00000231173:Q680E	Q	+	1	0	PCDHB15	140607368	0.000000	0.05858	0.000000	0.03702	0.360000	0.29518	-0.150000	0.10189	-0.255000	0.09486	0.549000	0.68633	CAA	C|0.979;G|0.021	0.021	strong		0.672	PCDHB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251804.2	NM_018935	
NCLN	56926	hgsc.bcm.edu	37	19	3207398	3207398	+	Silent	SNP	G	G	A	rs76473246	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3207398G>A	ENST00000246117.4	+	14	1994	c.1563G>A	c.(1561-1563)ccG>ccA	p.P521P	NCLN_ENST00000590671.1_Silent_p.P447P	NM_020170.3	NP_064555.2	Q969V3	NCLN_HUMAN	nicalin	521					regulation of signal transduction (GO:0009966)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				kidney(1)|lung(3)|skin(1)	5		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.83e-113)|Epithelial(107;1.65e-111)|all cancers(105;1.53e-103)|BRCA - Breast invasive adenocarcinoma(158;0.00139)|STAD - Stomach adenocarcinoma(1328;0.18)		GAGTCAAGCCGGCCGTCTTTG	0.652													A|||	149	0.0297524	0.1059	0.013	5008	,	,		16237	0.0		0.0	False		,,,				2504	0.0				p.P521P		Atlas-SNP	.											.	NCLN	27	.	0			c.G1563A						PASS	.	A		442,3964	778.2+/-414.3	15,412,1776	137.0	132.0	134.0		1563	-8.7	0.7	19	dbSNP_131	134	4,8596	812.7+/-407.1	0,4,4296	no	coding-synonymous	NCLN	NM_020170.3		15,416,6072	AA,AG,GG		0.0465,10.0318,3.4292		521/564	3207398	446,12560	2203	4300	6503	SO:0001819	synonymous_variant	56926	exon14			CAAGCCGGCCGTC	BC025926	CCDS32869.1	19p13.3	2010-08-13	2010-08-13			ENSG00000125912			26923	protein-coding gene	gene with protein product	"""nicastrin-like protein"""	609156	"""nicalin homolog (zebrafish)"""			11230166	Standard	NM_020170		Approved	NICALIN, NET59	uc002lxi.3	Q969V3		ENST00000246117.4:c.1563G>A	19.37:g.3207398G>A		117.0	0.0	0		94.0	46.0	0.489362	NM_020170	D6W613|O75252|Q6FI60|Q6ZMB7|Q8TAT7|Q96H48|Q96IS7|Q9BQH9|Q9BTX4|Q9NPP2	Silent	SNP	ENST00000246117.4	37	CCDS32869.1																																																																																			G|0.967;A|0.033	0.033	strong		0.652	NCLN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452545.1	NM_020170	
SMARCA2	6595	hgsc.bcm.edu	37	9	2039779	2039779	+	Silent	SNP	G	G	A	rs376509101|rs62639301	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:2039779G>A	ENST00000382203.1	+	4	878	c.669G>A	c.(667-669)caG>caA	p.Q223Q	SMARCA2_ENST00000349721.2_Silent_p.Q223Q|SMARCA2_ENST00000491574.1_3'UTR|SMARCA2_ENST00000357248.2_Silent_p.Q223Q|RP11-264I13.2_ENST00000426860.1_RNA|SMARCA2_ENST00000382194.1_Silent_p.Q223Q			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	223	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)		agcagcaacagcagcagcagc	0.642																																					p.Q223Q		Atlas-SNP	.											SMARCA2_ENST00000349721,NS,carcinoma,0,2	SMARCA2	313	2	0			c.G669A						scavenged	.						10.0	13.0	12.0					9																	2039779		2187	4260	6447	SO:0001819	synonymous_variant	6595	exon4			GCAACAGCAGCAG	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.669G>A	9.37:g.2039779G>A		66.0	1.0	0.0151515		98.0	51.0	0.520408	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Silent	SNP	ENST00000382203.1	37	CCDS34977.1																																																																																			G|0.889;A|0.111	0.111	strong		0.642	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070	
THOP1	7064	hgsc.bcm.edu	37	19	2790508	2790508	+	Missense_Mutation	SNP	C	C	T	rs76198851	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2790508C>T	ENST00000307741.6	+	2	309	c.106C>T	c.(106-108)Cgc>Tgc	p.R36C		NM_003249.3	NP_003240.1	P52888	THOP1_HUMAN	thimet oligopeptidase 1	36					intracellular signal transduction (GO:0035556)|peptide metabolic process (GO:0006518)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)			NS(1)|central_nervous_system(1)|endometrium(1)|lung(8)|ovary(2)|skin(1)	14				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)		GATAGAGGAGCGCACCAGGGA	0.612													C|||	13	0.00259585	0.0098	0.0	5008	,	,		20345	0.0		0.0	False		,,,				2504	0.0				p.R36C		Atlas-SNP	.											.	THOP1	49	.	0			c.C106T						PASS	.	C	CYS/ARG	28,4378	36.0+/-67.5	0,28,2175	115.0	95.0	102.0		106	3.9	0.0	19	dbSNP_131	102	0,8600		0,0,4300	yes	missense	THOP1	NM_003249.3	180	0,28,6475	TT,TC,CC		0.0,0.6355,0.2153	probably-damaging	36/690	2790508	28,12978	2203	4300	6503	SO:0001583	missense	7064	exon2			GAGGAGCGCACCA		CCDS12095.1	19p13.3	2008-02-05				ENSG00000172009	3.4.24.15		11793	protein-coding gene	gene with protein product		601117				9790774	Standard	NM_003249		Approved		uc002lwj.3	P52888		ENST00000307741.6:c.106C>T	19.37:g.2790508C>T	ENSP00000304467:p.Arg36Cys	50.0	0.0	0		46.0	27.0	0.586957	NM_003249	B3KSE2|Q9UCB3	Missense_Mutation	SNP	ENST00000307741.6	37	CCDS12095.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	16.20	3.056103	0.55325	0.006355	0.0	ENSG00000172009	ENST00000307741	T	0.08193	3.12	4.9	3.86	0.44501	Neurolysin/Thimet oligopeptidase, N-terminal (1);	0.130158	0.52532	D	0.000063	T	0.11879	0.0289	M	0.68952	2.095	0.50039	D	0.999846	D	0.67145	0.996	P	0.53450	0.726	T	0.00494	-1.1706	10	0.66056	D	0.02	-22.5297	8.1975	0.31405	0.1546:0.7598:0.0:0.0856	.	36	P52888	THOP1_HUMAN	C	36	ENSP00000304467:R36C	ENSP00000304467:R36C	R	+	1	0	THOP1	2741508	0.704000	0.27836	0.010000	0.14722	0.544000	0.35116	3.482000	0.53186	1.055000	0.40461	0.561000	0.74099	CGC	C|0.998;T|0.002	0.002	strong		0.612	THOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451587.2		
ZNF469	84627	hgsc.bcm.edu	37	16	88501999	88501999	+	Silent	SNP	G	G	A	rs116696830	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88501999G>A	ENST00000437464.1	+	2	8037	c.8037G>A	c.(8035-8037)gcG>gcA	p.A2679A	ZNF469_ENST00000565624.1_Silent_p.A2707A	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	2679					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						AGGGTGCAGCGGAGACTGACC	0.662													G|||	61	0.0121805	0.0416	0.0072	5008	,	,		15538	0.0		0.0	False		,,,				2504	0.001				p.A2679A		Atlas-SNP	.											.	ZNF469	121	.	0			c.G8037A						PASS	.	G		51,1333		1,49,642	26.0	31.0	30.0		8037	-9.1	0.0	16	dbSNP_132	30	0,3180		0,0,1590	yes	coding-synonymous	ZNF469	NM_001127464.1		1,49,2232	AA,AG,GG		0.0,3.685,1.1174		2679/3926	88501999	51,4513	692	1590	2282	SO:0001819	synonymous_variant	84627	exon2			TGCAGCGGAGACT	AB058761	CCDS45544.1	16q24	2010-08-04				ENSG00000225614		"""Zinc fingers, C2H2-type"""	23216	protein-coding gene	gene with protein product		612078				11347906	Standard	NM_001127464		Approved	KIAA1858	uc002fku.2	Q96JG9		ENST00000437464.1:c.8037G>A	16.37:g.88501999G>A		61.0	0.0	0		80.0	38.0	0.475	NM_001127464		Silent	SNP	ENST00000437464.1	37	CCDS45544.1																																																																																			G|0.992;A|0.008	0.008	strong		0.662	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
BHLHE41	79365	hgsc.bcm.edu	37	12	26275297	26275297	+	Missense_Mutation	SNP	G	G	T	rs121912617	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:26275297G>T	ENST00000242728.4	-	5	1498	c.1151C>A	c.(1150-1152)cCg>cAg	p.P384Q	RP11-283G6.3_ENST00000535914.1_RNA|RP11-283G6.3_ENST00000545819.1_RNA	NM_030762.2	NP_110389.1	Q9C0J9	BHE41_HUMAN	basic helix-loop-helix family, member e41	384	Ala/Gly-rich.		P -> R (associated with short sleep phenotype). {ECO:0000269|PubMed:19679812}.		cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|circadian regulation of gene expression (GO:0032922)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of transcription by competitive promoter binding (GO:0010944)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|organ morphogenesis (GO:0009887)	nucleus (GO:0005634)	bHLH transcription factor binding (GO:0043425)|E-box binding (GO:0070888)|histone deacetylase binding (GO:0042826)|MRF binding (GO:0043426)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|transcription corepressor activity (GO:0003714)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(1)	5						CAGCGGGAACGGGGCGGCAGC	0.741													G|||	36	0.0071885	0.0227	0.0086	5008	,	,		4052	0.0		0.0	False		,,,				2504	0.0				p.P384Q		Atlas-SNP	.											.	BHLHE41	20	.	0			c.C1151A						PASS	.						2.0	3.0	2.0					12																	26275297		1465	3164	4629	SO:0001583	missense	79365	exon5			GGGAACGGGGCGG	AB044088	CCDS8706.1	12p12.1	2011-12-05	2009-01-12	2009-01-12	ENSG00000123095	ENSG00000123095		"""Basic helix-loop-helix proteins"""	16617	protein-coding gene	gene with protein product	"""differentially expressed in chondrocytes 2"", ""Enhancer-of-split and hairy-related protein 1"""	606200	"""basic helix-loop-helix domain containing, class B, 3"""	BHLHB3		11162494, 18557763	Standard	NM_030762		Approved	DEC2, SHARP-1, SHARP1, bHLHe41	uc001rhb.3	Q9C0J9	OTTHUMG00000169174	ENST00000242728.4:c.1151C>A	12.37:g.26275297G>T	ENSP00000242728:p.Pro384Gln	4.0	0.0	0		5.0	4.0	0.8	NM_030762	A2I2N8	Missense_Mutation	SNP	ENST00000242728.4	37	CCDS8706.1	.	.	.	.	.	.	.	.	.	.	G	14.73	2.622122	0.46840	.	.	ENSG00000123095	ENST00000242728	T	0.79141	-1.24	3.09	3.09	0.35607	.	1.892810	0.04121	U	0.316359	T	0.75280	0.3828	L	0.38838	1.175	0.80722	D	1	D	0.53151	0.958	P	0.44860	0.462	T	0.68443	-0.5407	10	0.87932	D	0	.	11.9445	0.52920	0.0:0.0:1.0:0.0	.	384	Q9C0J9	BHE41_HUMAN	Q	384	ENSP00000242728:P384Q	ENSP00000242728:P384Q	P	-	2	0	BHLHE41	26166564	1.000000	0.71417	0.985000	0.45067	0.044000	0.14063	7.845000	0.86875	1.435000	0.47434	0.471000	0.43371	CCG	.	.	alt		0.741	BHLHE41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402714.1	NM_030762	
APC2	10297	hgsc.bcm.edu	37	19	1469030	1469030	+	Silent	SNP	A	A	G	rs265278	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1469030A>G	ENST00000535453.1	+	14	7443	c.5730A>G	c.(5728-5730)aaA>aaG	p.K1910K	APC2_ENST00000233607.2_Silent_p.K1910K|C19orf25_ENST00000588427.1_Intron|APC2_ENST00000238483.4_Silent_p.K1636K			P02655	APOC2_HUMAN	adenomatosis polyposis coli 2	0					cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|chylomicron remnant clearance (GO:0034382)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle clearance (GO:0034384)|lipid catabolic process (GO:0016042)|lipoprotein metabolic process (GO:0042157)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of lipid metabolic process (GO:0045833)|negative regulation of receptor-mediated endocytosis (GO:0048261)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipid catabolic process (GO:0060697)|positive regulation of triglyceride catabolic process (GO:0010898)|positive regulation of very-low-density lipoprotein particle remodeling (GO:0010902)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)|very-low-density lipoprotein particle remodeling (GO:0034372)	chylomicron (GO:0042627)|early endosome (GO:0005769)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate-density lipoprotein particle (GO:0034363)|low-density lipoprotein particle (GO:0034362)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	lipase inhibitor activity (GO:0055102)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|kidney(4)|large_intestine(2)|lung(5)|pancreas(1)|skin(2)	18		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|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)		CGGTGCCCAAAACGCCGGCGC	0.756													G|||	998	0.199281	0.6036	0.062	5008	,	,		7467	0.0248		0.0497	False		,,,				2504	0.0838				p.K1910K		Atlas-SNP	.											.	APC2	50	.	0			c.A5730G						PASS	.	G		912,2062		65,782,640	2.0	3.0	3.0		5730	4.1	0.0	19	dbSNP_79	3	244,6352		4,236,3058	no	coding-synonymous	APC2	NM_005883.2		69,1018,3698	GG,GA,AA		3.6992,30.6658,12.0794		1910/2304	1469030	1156,8414	1487	3298	4785	SO:0001819	synonymous_variant	10297	exon15			GCCCAAAACGCCG		CCDS12068.1	19p13.3	2013-02-14			ENSG00000115266	ENSG00000115266		"""Armadillo repeat containing"""	24036	protein-coding gene	gene with protein product	"""adenomatous polyposis coli like"""	612034				9823329, 10021369	Standard	XM_005259475		Approved	APCL	uc002lsr.1	O95996		ENST00000535453.1:c.5730A>G	19.37:g.1469030A>G		10.0	0.0	0		23.0	17.0	0.73913	NM_005883	C0JYY4|Q9BS39|Q9UDE3|Q9UNK3	Silent	SNP	ENST00000535453.1	37	CCDS12068.1																																																																																			A|0.833;G|0.167	0.167	strong		0.756	APC2-004	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449539.2	NM_005883	
FUK	197258	hgsc.bcm.edu	37	16	70508544	70508544	+	Missense_Mutation	SNP	C	C	T	rs17883716	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:70508544C>T	ENST00000288078.6	+	17	2334	c.2102C>T	c.(2101-2103)cCg>cTg	p.P701L	FUK_ENST00000571514.1_Missense_Mutation_p.P192L|FUK_ENST00000378912.2_Missense_Mutation_p.P733L	NM_145059.2	NP_659496.2	Q8N0W3	FUK_HUMAN	fucokinase	701			P -> L (in dbSNP:rs17883716). {ECO:0000269|Ref.3}.			cytoplasm (GO:0005737)	ATP binding (GO:0005524)|fucokinase activity (GO:0050201)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(11)|ovary(2)|prostate(2)	23		Ovarian(137;0.0694)				GTGGAACTGCCGGGACCTGGG	0.657													C|||	2	0.000399361	0.0	0.0	5008	,	,		17514	0.0		0.002	False		,,,				2504	0.0				p.P701L		Atlas-SNP	.											.	FUK	72	.	0			c.C2102T						PASS	.	C	LEU/PRO	3,4111		0,3,2054	34.0	43.0	40.0		2102	3.7	0.9	16	dbSNP_124	40	25,8379		0,25,4177	yes	missense	FUK	NM_145059.2	98	0,28,6231	TT,TC,CC		0.2975,0.0729,0.2237	possibly-damaging	701/1085	70508544	28,12490	2057	4202	6259	SO:0001583	missense	197258	exon17			AACTGCCGGGACC		CCDS10891.2	16q22.1	2008-02-05			ENSG00000157353	ENSG00000157353	2.7.1.52		29500	protein-coding gene	gene with protein product	"""L-fucose kinase"""	608675				12056818	Standard	XM_006721161		Approved	FLJ39408	uc002eyy.3	Q8N0W3	OTTHUMG00000074085	ENST00000288078.6:c.2102C>T	16.37:g.70508544C>T	ENSP00000288078:p.Pro701Leu	93.0	0.0	0		96.0	47.0	0.489583	NM_145059	Q5PSM3|Q5XKL6|Q6ZRA0|Q96MT9	Missense_Mutation	SNP	ENST00000288078.6	37	CCDS10891.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	16.20	3.054738	0.55325	7.29E-4	0.002975	ENSG00000157353	ENST00000288078;ENST00000378912;ENST00000538525	T;T	0.08634	3.12;3.07	5.77	3.72	0.42706	.	0.176184	0.50627	N	0.000110	T	0.09468	0.0233	M	0.66939	2.045	0.80722	D	1	P;P;P	0.52692	0.579;0.955;0.955	B;B;B	0.42087	0.072;0.375;0.267	T	0.27365	-1.0076	10	0.12766	T	0.61	-16.2145	9.0313	0.36260	0.146:0.7799:0.0:0.0741	rs17883716;rs17883716	733;607;701	Q8N0W3-2;B2RDL5;Q8N0W3	.;.;FUK_HUMAN	L	701;733;15	ENSP00000288078:P701L;ENSP00000368192:P733L	ENSP00000288078:P701L	P	+	2	0	FUK	69066045	0.990000	0.36364	0.878000	0.34440	0.674000	0.39518	2.878000	0.48515	1.463000	0.47967	-0.140000	0.14226	CCG	C|0.995;T|0.005	0.005	strong		0.657	FUK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157291.2	NM_145059	
MECOM	2122	hgsc.bcm.edu	37	3	168833976	168833976	+	Missense_Mutation	SNP	C	C	T	rs149928659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:168833976C>T	ENST00000464456.1	-	7	2320	c.1120G>A	c.(1120-1122)Gag>Aag	p.E374K	MECOM_ENST00000494292.1_Missense_Mutation_p.E562K|MECOM_ENST00000433243.2_Missense_Mutation_p.E375K|MECOM_ENST00000264674.3_Missense_Mutation_p.E439K|MECOM_ENST00000472280.1_Missense_Mutation_p.E375K|MECOM_ENST00000468789.1_Missense_Mutation_p.E374K|MECOM_ENST00000460814.1_Missense_Mutation_p.E374K|MECOM_ENST00000392736.3_Missense_Mutation_p.E374K	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						GAGGACCTCTCGGGCTGGAGC	0.493													C|||	2	0.000399361	0.0015	0.0	5008	,	,		17401	0.0		0.0	False		,,,				2504	0.0				p.E562K		Atlas-SNP	.											.	MECOM	216	.	0			c.G1684A						PASS	.						360.0	301.0	321.0					3																	168833976		2203	4300	6503	SO:0001583	missense	2122	exon8			ACCTCTCGGGCTG	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.1120G>A	3.37:g.168833976C>T	ENSP00000419770:p.Glu374Lys	240.0	0.0	0		187.0	90.0	0.481283	NM_004991	Q13466|Q6FH90	Missense_Mutation	SNP	ENST00000464456.1	37	CCDS54669.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	13.87	2.365132	0.41902	.	.	ENSG00000085276	ENST00000264674;ENST00000392736;ENST00000464456;ENST00000472280;ENST00000494292;ENST00000468789;ENST00000460814;ENST00000433243	T;T;T;T;T;T;T;T	0.07021	3.29;3.28;3.25;3.38;3.23;3.28;3.24;3.38	6.03	6.03	0.97812	.	0.000000	0.53938	D	0.000059	T	0.11495	0.0280	L	0.54323	1.7	0.51482	D	0.999928	P;P;P;P;P	0.45569	0.826;0.789;0.861;0.789;0.491	B;B;B;B;B	0.35510	0.204;0.128;0.101;0.182;0.06	T	0.01608	-1.1313	10	0.59425	D	0.04	-16.0383	20.5568	0.99304	0.0:1.0:0.0:0.0	.	562;375;562;439;374	Q03112-3;Q03112-6;E7EQ57;Q03112-4;Q03112	.;.;.;.;EVI1_HUMAN	K	439;374;374;375;562;374;374;375	ENSP00000264674:E439K;ENSP00000376493:E374K;ENSP00000419770:E374K;ENSP00000420048:E375K;ENSP00000417899:E562K;ENSP00000419995:E374K;ENSP00000420466:E374K;ENSP00000394302:E375K	ENSP00000264674:E439K	E	-	1	0	MECOM	170316670	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.830000	0.69324	2.861000	0.98227	0.655000	0.94253	GAG	C|0.999;T|0.001	0.001	strong		0.493	MECOM-020	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351519.1	NM_005241, NM_004991	
RBM44	375316	hgsc.bcm.edu	37	2	238725833	238725833	+	Missense_Mutation	SNP	A	A	G	rs73086770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:238725833A>G	ENST00000409864.1	+	3	528	c.274A>G	c.(274-276)Agt>Ggt	p.S92G	RBM44_ENST00000444524.2_Intron|RBM44_ENST00000316997.4_Missense_Mutation_p.S92G			Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	91						cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)	nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)			breast(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(7)|ovary(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)		TAACACAGAGAGTACTCAGTT	0.323													A|||	182	0.0363419	0.1286	0.0144	5008	,	,		19482	0.0		0.002	False		,,,				2504	0.0				p.S92G		Atlas-SNP	.											.	RBM44	167	.	0			c.A274G						PASS	.	A	GLY/SER	365,3309		23,319,1495	60.0	60.0	60.0		274	3.2	0.0	2	dbSNP_130	60	19,8129		0,19,4055	yes	missense	RBM44	NM_001080504.2	56	23,338,5550	GG,GA,AA		0.2332,9.9347,3.2482	possibly-damaging	92/1053	238725833	384,11438	1837	4074	5911	SO:0001583	missense	375316	exon3			ACAGAGAGTACTC	AK097730	CCDS46554.1	2q37.3	2013-02-12			ENSG00000177483	ENSG00000177483		"""RNA binding motif (RRM) containing"""	24756	protein-coding gene	gene with protein product							Standard	NM_001080504		Approved	FLJ40411	uc002vxi.4	Q6ZP01	OTTHUMG00000152937	ENST00000409864.1:c.274A>G	2.37:g.238725833A>G	ENSP00000386727:p.Ser92Gly	185.0	0.0	0		213.0	85.0	0.399061	NM_001080504	A0AUW3	Missense_Mutation	SNP	ENST00000409864.1	37	CCDS46554.1	88	0.040293040293040296	79	0.16056910569105692	8	0.022099447513812154	0	0.0	1	0.0013192612137203166	A	9.408	1.079719	0.20309	0.099347	0.002332	ENSG00000177483	ENST00000316997;ENST00000409864	T;T	0.33216	1.42;1.42	5.62	3.15	0.36227	.	0.588960	0.17242	N	0.181502	T	0.00073	0.0002	L	0.39898	1.24	0.80722	P	0.0	P	0.49090	0.919	B	0.39339	0.297	T	0.11941	-1.0567	9	0.32370	T	0.25	-3.005	9.875	0.41197	0.6671:0.3329:0.0:0.0	.	91	Q6ZP01	RBM44_HUMAN	G	92	ENSP00000321179:S92G;ENSP00000386727:S92G	ENSP00000321179:S92G	S	+	1	0	RBM44	238390572	0.000000	0.05858	0.000000	0.03702	0.785000	0.44390	0.011000	0.13264	0.374000	0.24650	0.460000	0.39030	AGT	A|0.967;G|0.033	0.033	strong		0.323	RBM44-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328733.2	NM_001080504	
TNFSF15	9966	hgsc.bcm.edu	37	9	117568219	117568219	+	Missense_Mutation	SNP	C	C	T	rs150191342	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117568219C>T	ENST00000374045.4	-	1	187	c.74G>A	c.(73-75)aGg>aAg	p.R25K		NM_001204344.1|NM_005118.3	NP_001191273.1|NP_005109.2	O95150	TNF15_HUMAN	tumor necrosis factor (ligand) superfamily, member 15	25					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|cytokine metabolic process (GO:0042107)|immune response (GO:0006955)|positive regulation of cytokine secretion (GO:0050715)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|skin(1)	11						GGCCTTGGGCCTGCAGCTGCC	0.627													C|||	20	0.00399361	0.0151	0.0	5008	,	,		17651	0.0		0.0	False		,,,				2504	0.0				p.R25K		Atlas-SNP	.											.	TNFSF15	23	.	0			c.G74A						PASS	.	C	LYS/ARG	54,4352	53.6+/-89.4	1,52,2150	64.0	58.0	60.0		74	3.2	0.5	9	dbSNP_134	60	0,8600		0,0,4300	yes	missense	TNFSF15	NM_005118.3	26	1,52,6450	TT,TC,CC		0.0,1.2256,0.4152	benign	25/252	117568219	54,12952	2203	4300	6503	SO:0001583	missense	9966	exon1			TTGGGCCTGCAGC	AF039390	CCDS6809.1	9q32	2008-07-21			ENSG00000181634	ENSG00000181634		"""Tumor necrosis factor (ligand) superfamily"""	11931	protein-coding gene	gene with protein product	"""vascular endothelial cell growth inhibitor"", ""TNF superfamily ligand TL1A"", ""TNF ligand-related molecule 1"", ""vascular endothelial growth inhibitor-192A"""	604052				9434163	Standard	NM_005118		Approved	TL1, VEGI, TL1A, VEGI192A, MGC129934, MGC129935	uc004bjh.3	O95150	OTTHUMG00000021011	ENST00000374045.4:c.74G>A	9.37:g.117568219C>T	ENSP00000363157:p.Arg25Lys	104.0	0.0	0		108.0	75.0	0.694444	NM_005118	Q3SX69|Q5VJK8|Q5VWH1|Q8NFE9	Missense_Mutation	SNP	ENST00000374045.4	37	CCDS6809.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	12.31	1.898972	0.33535	0.012256	0.0	ENSG00000181634	ENST00000374045	T	0.28069	1.63	5.11	3.23	0.37069	.	2.547720	0.01464	N	0.015995	T	0.14700	0.0355	N	0.24115	0.695	0.48696	D	0.999692	B	0.20261	0.043	B	0.19946	0.027	T	0.44862	-0.9300	10	0.02654	T	1	-17.7812	6.6172	0.22782	0.0:0.7011:0.1969:0.102	.	25	O95150	TNF15_HUMAN	K	25	ENSP00000363157:R25K	ENSP00000363157:R25K	R	-	2	0	TNFSF15	116608040	0.122000	0.22280	0.461000	0.27105	0.699000	0.40488	0.565000	0.23578	0.616000	0.30141	0.484000	0.47621	AGG	C|0.996;T|0.004	0.004	strong		0.627	TNFSF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055424.2	NM_005118	
TSHZ3	57616	hgsc.bcm.edu	37	19	31767717	31767717	+	Silent	SNP	G	G	A	rs61744745	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:31767717G>A	ENST00000240587.4	-	2	3309	c.2982C>T	c.(2980-2982)caC>caT	p.H994H		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	994					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					GTGACTCTAGGTGACTGATGT	0.473													G|||	174	0.0347444	0.1301	0.0029	5008	,	,		20088	0.0		0.0	False		,,,				2504	0.0				p.H994H		Atlas-SNP	.											.	TSHZ3	549	.	0			c.C2982T						PASS	.	G		440,3966	211.8+/-231.9	19,402,1782	120.0	105.0	110.0		2982	2.5	1.0	19	dbSNP_129	110	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	TSHZ3	NM_020856.2		19,406,6078	AA,AG,GG		0.0465,9.9864,3.4138		994/1082	31767717	444,12562	2203	4300	6503	SO:0001819	synonymous_variant	57616	exon2			CTCTAGGTGACTG	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	30700	protein-coding gene	gene with protein product	"""teashirt 3"""	614119	"""zinc finger protein 537"", ""teashirt family zinc finger 3"""	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.2982C>T	19.37:g.31767717G>A		155.0	0.0	0		167.0	86.0	0.51497	NM_020856	Q9H0G6|Q9P254	Silent	SNP	ENST00000240587.4	37	CCDS12421.2																																																																																			G|0.961;A|0.039	0.039	strong		0.473	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856	
SERPINA5	5104	hgsc.bcm.edu	37	14	95056407	95056407	+	Missense_Mutation	SNP	G	G	C	rs6114	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:95056407G>C	ENST00000554866.1	+	3	763	c.649G>C	c.(649-651)Ggc>Cgc	p.G217R	RP11-986E7.7_ENST00000553947.1_5'Flank|SERPINA5_ENST00000329597.7_Missense_Mutation_p.G217R|SERPINA5_ENST00000554276.1_Missense_Mutation_p.G217R|SERPINA5_ENST00000553780.1_Missense_Mutation_p.G217R			P05154	IPSP_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5	217			G -> R (in dbSNP:rs6114). {ECO:0000269|PubMed:10391209, ECO:0000269|Ref.6}.		fusion of sperm to egg plasma membrane (GO:0007342)|lipid transport (GO:0006869)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|spermatogenesis (GO:0007283)	acrosomal membrane (GO:0002080)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|platelet alpha granule (GO:0031091)|platelet dense tubular network (GO:0031094)|protein C inhibitor-coagulation factor V complex (GO:0097181)|protein C inhibitor-coagulation factor Xa complex (GO:0097182)|protein C inhibitor-coagulation factor XI complex (GO:0097183)|protein C inhibitor-KLK3 complex (GO:0036029)|protein C inhibitor-plasma kallikrein complex (GO:0036030)|protein C inhibitor-PLAT complex (GO:0036026)|protein C inhibitor-PLAU complex (GO:0036027)|protein C inhibitor-thrombin complex (GO:0036028)|protein C inhibitor-TMPRSS11E complex (GO:0036025)|protein C inhibitor-TMPRSS7 complex (GO:0036024)|protein complex (GO:0043234)	acrosin binding (GO:0032190)|glycosaminoglycan binding (GO:0005539)|heparin binding (GO:0008201)|phosphatidylcholine binding (GO:0031210)|protease binding (GO:0002020)|retinoic acid binding (GO:0001972)|serine-type endopeptidase inhibitor activity (GO:0004867)			endometrium(3)|large_intestine(5)|lung(18)|ovary(2)|skin(5)|upper_aerodigestive_tract(3)	36				COAD - Colon adenocarcinoma(157;0.21)	Drotrecogin alfa(DB00055)|Urokinase(DB00013)	CAACCACAAAGGCACCCAAGA	0.453													G|||	129	0.0257588	0.0923	0.0101	5008	,	,		19756	0.0		0.0	False		,,,				2504	0.0				p.G217R		Atlas-SNP	.											.	SERPINA5	69	.	0			c.G649C						PASS	.	G	ARG/GLY	374,4032	190.5+/-216.4	22,330,1851	71.0	65.0	67.0		649	-2.1	0.0	14	dbSNP_52	67	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SERPINA5	NM_000624.4	125	22,331,6150	CC,CG,GG		0.0116,8.4884,2.8833	benign	217/407	95056407	375,12631	2203	4300	6503	SO:0001583	missense	5104	exon4			CACAAAGGCACCC	M68516	CCDS9928.1	14q32.1	2014-02-18	2005-08-18		ENSG00000188488	ENSG00000188488		"""Serine (or cysteine) peptidase inhibitors"""	8723	protein-coding gene	gene with protein product		601841	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 5"""	PLANH3, PCI		1714450, 8381582, 24172014	Standard	NM_000624		Approved	PAI3, PROCI	uc001ydm.3	P05154	OTTHUMG00000170860	ENST00000554866.1:c.649G>C	14.37:g.95056407G>C	ENSP00000451126:p.Gly217Arg	141.0	0.0	0		121.0	50.0	0.413223	NM_000624	Q07616|Q9UG30	Missense_Mutation	SNP	ENST00000554866.1	37	CCDS9928.1	53	0.024267399267399268	48	0.0975609756097561	5	0.013812154696132596	0	0.0	0	0.0	G	1.396	-0.579550	0.03854	0.084884	1.16E-4	ENSG00000188488	ENST00000553780;ENST00000554760;ENST00000554866;ENST00000329597;ENST00000556775;ENST00000537685;ENST00000438291;ENST00000554276	D;D;D;D;D;D	0.83591	-1.74;-1.74;-1.74;-1.74;-1.74;-1.74	4.63	-2.09	0.07232	Serpin domain (3);	1.511820	0.03611	N	0.234832	T	0.03564	0.0102	N	0.02751	-0.505	0.09310	N	1	B;B	0.18461	0.024;0.028	B;B	0.26864	0.074;0.023	T	0.23226	-1.0194	10	0.33141	T	0.24	.	3.7717	0.08645	0.3912:0.0:0.3351:0.2737	rs6114;rs6114	217;217	G3V5Q9;P05154	.;IPSP_HUMAN	R	217;217;217;217;217;69;141;217	ENSP00000450837:G217R;ENSP00000452469:G217R;ENSP00000451126:G217R;ENSP00000333203:G217R;ENSP00000450745:G217R;ENSP00000451610:G217R	ENSP00000333203:G217R	G	+	1	0	SERPINA5	94126160	0.000000	0.05858	0.000000	0.03702	0.143000	0.21401	-1.700000	0.01905	-0.323000	0.08602	-0.378000	0.06908	GGC	G|0.974;C|0.026	0.026	strong		0.453	SERPINA5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410726.1	NM_000624	
ACOT11	26027	hgsc.bcm.edu	37	1	55073630	55073630	+	Silent	SNP	C	C	T	rs78753605	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:55073630C>T	ENST00000371316.3	+	15	1600	c.1518C>T	c.(1516-1518)atC>atT	p.I506I	ACOT11_ENST00000343744.2_Silent_p.I506I|ACOT11_ENST00000481208.1_3'UTR	NM_015547.3	NP_056362.1	Q8WXI4	ACO11_HUMAN	acyl-CoA thioesterase 11	506	START. {ECO:0000255|PROSITE- ProRule:PRU00197}.				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						CCTATGTCATCGCGCTGAGGT	0.642													C|||	83	0.0165735	0.0605	0.0029	5008	,	,		18552	0.001		0.0	False		,,,				2504	0.0				p.I506I	Ovarian(148;1440 1861 22015 32453 51933)	Atlas-SNP	.											.	ACOT11	105	.	0			c.C1518T						PASS	.	C	,	201,4205	126.6+/-163.6	4,193,2006	93.0	90.0	91.0		1518,1518	-6.9	0.9	1	dbSNP_132	91	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	ACOT11	NM_015547.3,NM_147161.3	,	4,194,6305	TT,TC,CC		0.0116,4.562,1.5531	,	506/608,506/595	55073630	202,12804	2203	4300	6503	SO:0001819	synonymous_variant	26027	exon15			TGTCATCGCGCTG	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.1518C>T	1.37:g.55073630C>T		165.0	0.0	0		157.0	87.0	0.55414	NM_147161	B1AQ22|D3DQ50|O75187|Q52LP1|Q53ER9|Q96DI1|Q9H883	Silent	SNP	ENST00000371316.3	37	CCDS592.1																																																																																			C|0.984;T|0.016	0.016	strong		0.642	ACOT11-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027356.1	NM_015547	
CSMD1	64478	hgsc.bcm.edu	37	8	3245054	3245054	+	Missense_Mutation	SNP	C	C	T	rs73657835	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:3245054C>T	ENST00000520002.1	-	19	3302	c.2747G>A	c.(2746-2748)aGg>aAg	p.R916K	CSMD1_ENST00000537824.1_Missense_Mutation_p.R915K|CSMD1_ENST00000539096.1_Missense_Mutation_p.R915K|CSMD1_ENST00000400186.3_Missense_Mutation_p.R916K|CSMD1_ENST00000602557.1_Missense_Mutation_p.R916K|CSMD1_ENST00000602723.1_Missense_Mutation_p.R916K|CSMD1_ENST00000542608.1_Missense_Mutation_p.R915K			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	916	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		CTGGTGGTTCCTCTCACAGAC	0.597													C|||	175	0.0349441	0.1225	0.0173	5008	,	,		18677	0.0		0.001	False		,,,				2504	0.0				p.R915K		Atlas-SNP	.											CSMD1_ENST00000537824,NS,carcinoma,+1,2	CSMD1	1469	2	0			c.G2744A						PASS	.	C	LYS/ARG	365,3837		16,333,1752	43.0	49.0	47.0		2744	1.2	0.1	8	dbSNP_130	47	0,8430		0,0,4215	yes	missense	CSMD1	NM_033225.5	26	16,333,5967	TT,TC,CC		0.0,8.6863,2.8895	benign	915/3565	3245054	365,12267	2101	4215	6316	SO:0001583	missense	64478	exon18			TGGTTCCTCTCAC			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.2747G>A	8.37:g.3245054C>T	ENSP00000430733:p.Arg916Lys	86.0	0.0	0		84.0	42.0	0.5	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	37		73	0.033424908424908424	67	0.13617886178861788	6	0.016574585635359115	0	0.0	0	0.0	C	0.079	-1.186530	0.01620	0.086863	0.0	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	T;T;T;T;T	0.62788	-0.0;-0.0;-0.0;-0.0;-0.0	5.11	1.25	0.21368	Complement control module (2);Sushi/SCR/CCP (3);	0.221554	0.38959	N	0.001512	T	0.00178	0.0005	N	0.01277	-0.915	0.09310	N	0.999999	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.001;0.003	T	0.08659	-1.0711	10	0.02654	T	1	.	8.3499	0.32297	0.0:0.6186:0.0:0.3814	.	916;916;916	E5RIG2;Q96PZ7;Q96PZ7-4	.;CSMD1_HUMAN;.	K	916;916;778;915;915;915	ENSP00000383047:R916K;ENSP00000430733:R916K;ENSP00000441462:R915K;ENSP00000446243:R915K;ENSP00000441675:R915K	ENSP00000320445:R778K	R	-	2	0	CSMD1	3232461	0.012000	0.17670	0.095000	0.20976	0.375000	0.29983	0.150000	0.16263	-0.053000	0.13289	-0.157000	0.13467	AGG	C|0.966;T|0.034	0.034	strong		0.597	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
FER1L6	654463	hgsc.bcm.edu	37	8	124987404	124987404	+	Missense_Mutation	SNP	A	A	G	rs77810887	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:124987404A>G	ENST00000522917.1	+	8	747	c.541A>G	c.(541-543)Aac>Gac	p.N181D	FER1L6_ENST00000399018.1_Missense_Mutation_p.N181D	NM_001039112.2	NP_001034201.2	Q2WGJ9	FR1L6_HUMAN	fer-1-like family member 6	181						integral component of membrane (GO:0016021)				NS(2)|breast(3)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(18)|liver(1)|lung(49)|ovary(5)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(1)	118	Lung NSC(37;4.1e-12)|Ovarian(258;0.00438)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00186)			TCAGTTCTGCAACAAGTGGGC	0.557													G|||	75	0.014976	0.056	0.0014	5008	,	,		19342	0.0		0.0	False		,,,				2504	0.0				p.N181D		Atlas-SNP	.											.	FER1L6	268	.	0			c.A541G						PASS	.	G	ASP/ASN	198,3804		4,190,1807	93.0	91.0	92.0		541	5.5	1.0	8	dbSNP_131	92	0,8352		0,0,4176	yes	missense	FER1L6	NM_001039112.2	23	4,190,5983	GG,GA,AA		0.0,4.9475,1.6027	benign	181/1858	124987404	198,12156	2001	4176	6177	SO:0001583	missense	654463	exon8			TTCTGCAACAAGT	AB196633	CCDS43767.1	8q24.13	2014-06-27	2014-06-27		ENSG00000214814	ENSG00000214814			28065	protein-coding gene	gene with protein product			"""fer-1-like 6 (C. elegans)"""				Standard	NM_001039112		Approved	C8ORFK23	uc003yqw.3	Q2WGJ9	OTTHUMG00000164998	ENST00000522917.1:c.541A>G	8.37:g.124987404A>G	ENSP00000428280:p.Asn181Asp	252.0	0.0	0		288.0	150.0	0.520833	NM_001039112		Missense_Mutation	SNP	ENST00000522917.1	37	CCDS43767.1	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	G	8.521	0.868834	0.17322	0.049475	0.0	ENSG00000214814	ENST00000522917;ENST00000399018	T;T	0.80480	-1.38;-1.38	5.5	5.5	0.81552	C2 calcium/lipid-binding domain, CaLB (1);FerIin domain (1);	0.220886	0.37012	N	0.002292	T	0.24812	0.0602	N	0.10760	0.04	0.22342	N	0.999181	B	0.02656	0.0	B	0.06405	0.002	T	0.24404	-1.0161	10	0.28530	T	0.3	.	14.8757	0.70493	0.069:0.0:0.931:0.0	.	181	Q2WGJ9	FR1L6_HUMAN	D	181	ENSP00000428280:N181D;ENSP00000381982:N181D	ENSP00000381982:N181D	N	+	1	0	FER1L6	125056585	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.931000	0.40134	1.487000	0.48415	-0.215000	0.12644	AAC	A|0.988;G|0.012	0.012	strong		0.557	FER1L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381400.1	NM_001039112	
TACC2	10579	hgsc.bcm.edu	37	10	123970173	123970173	+	Missense_Mutation	SNP	T	T	C	rs7083331	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:123970173T>C	ENST00000369005.1	+	9	6573	c.6233T>C	c.(6232-6234)aTc>aCc	p.I2078T	TACC2_ENST00000360561.3_Missense_Mutation_p.I156T|TACC2_ENST00000369004.3_Missense_Mutation_p.I156T|TACC2_ENST00000368999.1_Missense_Mutation_p.I156T|TACC2_ENST00000453444.2_Missense_Mutation_p.I2082T|TACC2_ENST00000369001.1_5'UTR|TACC2_ENST00000358010.1_Missense_Mutation_p.I224T|TACC2_ENST00000515603.1_Missense_Mutation_p.I2033T|TACC2_ENST00000515273.1_Missense_Mutation_p.I2082T|TACC2_ENST00000513429.1_Missense_Mutation_p.I224T|TACC2_ENST00000260733.3_Missense_Mutation_p.I156T|TACC2_ENST00000369000.1_5'UTR|TACC2_ENST00000334433.3_Missense_Mutation_p.I2078T	NM_206862.2	NP_996744.2	O95359	TACC2_HUMAN	transforming, acidic coiled-coil containing protein 2	2078			I -> T (in dbSNP:rs7083331).		astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)	nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(15)|lung(27)|ovary(6)|prostate(3)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	83		all_neural(114;0.0656)|Lung NSC(174;0.136)|all_lung(145;0.17)|Breast(234;0.197)				TCCGTCCCCATCTCTAAGTCT	0.567													T|||	522	0.104233	0.3737	0.0375	5008	,	,		16691	0.0		0.002	False		,,,				2504	0.0				p.I2078T		Atlas-SNP	.											.	TACC2	271	.	0			c.T6233C						PASS	.	T	THR/ILE,THR/ILE,THR/ILE,THR/ILE	1380,3026	456.5+/-351.3	234,912,1057	98.0	95.0	96.0		467,467,671,6233	2.1	0.1	10	dbSNP_116	96	21,8579	14.0+/-48.4	0,21,4279	yes	missense,missense,missense,missense	TACC2	NM_006997.2,NM_206860.1,NM_206861.1,NM_206862.2	89,89,89,89	234,933,5336	CC,CT,TT		0.2442,31.3209,10.772	benign,benign,benign,benign	156/1027,156/997,224/1095,2078/2949	123970173	1401,11605	2203	4300	6503	SO:0001583	missense	10579	exon9			TCCCCATCTCTAA	AF095791	CCDS7625.1, CCDS7626.1, CCDS7627.1, CCDS7628.1	10q26	2008-07-29			ENSG00000138162	ENSG00000138162			11523	protein-coding gene	gene with protein product		605302				14767476	Standard	XM_005269388		Approved	AZU-1	uc001lfv.3	O95359	OTTHUMG00000019181	ENST00000369005.1:c.6233T>C	10.37:g.123970173T>C	ENSP00000358001:p.Ile2078Thr	93.0	0.0	0		96.0	46.0	0.479167	NM_206862	Q4VXL0|Q4VXL3|Q4VXL6|Q4VXL7|Q5U5T7|Q86WG6|Q86WG7|Q8TCK9|Q9BVQ1|Q9NZ41|Q9NZR5	Missense_Mutation	SNP	ENST00000369005.1	37	CCDS7626.1	188	0.08608058608058608	177	0.3597560975609756	10	0.027624309392265192	0	0.0	1	0.0013192612137203166	T	2.370	-0.344560	0.05208	0.313209	0.002442	ENSG00000138162	ENST00000369005;ENST00000513429;ENST00000515273;ENST00000515603;ENST00000334433;ENST00000358010;ENST00000453444;ENST00000340076;ENST00000360561;ENST00000368999;ENST00000369004;ENST00000260733;ENST00000514539	T;T;T;T;T;T;T;T;T;T;T;T	0.08370	4.02;3.63;4.02;4.04;4.02;3.63;4.02;3.52;3.52;3.52;3.52;3.1	5.5	2.1	0.27182	.	1.500250	0.04801	N	0.433439	T	0.00012	0.0000	N	0.01352	-0.895	0.52099	P	5.8000000000002494E-5	B;B;B;B;B;B;B;B;B	0.13145	0.002;0.007;0.0;0.007;0.007;0.0;0.0;0.001;0.007	B;B;B;B;B;B;B;B;B	0.12156	0.004;0.007;0.001;0.007;0.007;0.002;0.002;0.004;0.007	T	0.47535	-0.9110	9	0.11794	T	0.64	0.8103	7.4447	0.27205	0.0:0.4578:0.0:0.5422	rs7083331;rs52830245;rs7083331	173;2082;156;2033;2082;156;156;224;2078	E9PGB3;E9PBC6;D6RAA5;E7EMZ9;B7ZMJ9;O95359-6;O95359-1;O95359-5;O95359	.;.;.;.;.;.;.;.;TACC2_HUMAN	T	2078;224;2082;2033;2078;224;2082;2068;156;156;156;156;173	ENSP00000358001:I2078T;ENSP00000425062:I224T;ENSP00000424467:I2082T;ENSP00000427618:I2033T;ENSP00000334280:I2078T;ENSP00000350701:I224T;ENSP00000395048:I2082T;ENSP00000353763:I156T;ENSP00000357995:I156T;ENSP00000422815:I156T;ENSP00000260733:I156T;ENSP00000420967:I173T	ENSP00000260733:I156T	I	+	2	0	TACC2	123960163	0.000000	0.05858	0.128000	0.21923	0.313000	0.28021	0.587000	0.23909	0.130000	0.18549	0.533000	0.62120	ATC	T|0.899;C|0.101	0.101	strong		0.567	TACC2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090004.1		
CYP4A22	284541	hgsc.bcm.edu	37	1	47603338	47603338	+	Missense_Mutation	SNP	G	G	A	rs112604161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:47603338G>A	ENST00000371891.3	+	1	212	c.181G>A	c.(181-183)Ggg>Agg	p.G61R	CYP4A22_ENST00000294337.3_Missense_Mutation_p.G61R|CYP4A22_ENST00000485117.1_3'UTR|CYP4A22_ENST00000371890.3_Missense_Mutation_p.G61R|CYP4A22-AS1_ENST00000444042.2_lincRNA	NM_001010969.2	NP_001010969.2	Q5TCH4	CP4AM_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 22	61						endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						CTGGCTCTTCGGGCACATCCA	0.602													G|||	54	0.0107827	0.0378	0.0014	5008	,	,		19903	0.0		0.003	False		,,,				2504	0.0				p.G61R	Pancreas(88;1240 1470 2099 14214 37557)	Atlas-SNP	.											.	CYP4A22	60	.	0			c.G181A						PASS	.	G	ARG/GLY	153,4253	102.5+/-141.1	4,145,2054	46.0	40.0	42.0		181	2.5	0.0	1	dbSNP_132	42	1,8599	1.2+/-3.3	0,1,4299	no	missense	CYP4A22	NM_001010969.2	125	4,146,6353	AA,AG,GG		0.0116,3.4725,1.1841	probably-damaging	61/520	47603338	154,12852	2203	4300	6503	SO:0001583	missense	284541	exon1			CTCTTCGGGCACA		CCDS30707.1	1p33	2007-12-14			ENSG00000162365	ENSG00000162365		"""Cytochrome P450s"""	20575	protein-coding gene	gene with protein product		615341					Standard	XM_005270768		Approved		uc001cqv.1	Q5TCH4	OTTHUMG00000007845	ENST00000371891.3:c.181G>A	1.37:g.47603338G>A	ENSP00000360958:p.Gly61Arg	110.0	0.0	0		171.0	82.0	0.479532	NM_001010969	Q5TCH3|Q6JXK7|Q6JXK8|Q9NRM4	Missense_Mutation	SNP	ENST00000371891.3	37	CCDS30707.1	21	0.009615384615384616	19	0.03861788617886179	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	g	17.36	3.368930	0.61624	0.034725	1.16E-4	ENSG00000162365	ENST00000371890;ENST00000371891;ENST00000294337	T;T;T	0.78481	-1.08;-1.18;-1.18	2.47	2.47	0.30058	.	0.000000	0.85682	D	0.000000	T	0.75474	0.3854	H	0.96460	3.825	0.53005	D	0.999967	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.86371	0.1723	10	0.87932	D	0	.	13.1509	0.59488	0.0:0.0:1.0:0.0	.	61;61	Q5TCH5;Q5TCH4	.;CP4AM_HUMAN	R	61	ENSP00000360957:G61R;ENSP00000360958:G61R;ENSP00000294337:G61R	ENSP00000294337:G61R	G	+	1	0	CYP4A22	47375925	1.000000	0.71417	0.009000	0.14445	0.114000	0.19823	4.707000	0.61852	1.071000	0.40834	0.205000	0.17691	GGG	G|0.987;A|0.013	0.013	strong		0.602	CYP4A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021635.1	XM_208213	
ELL	8178	hgsc.bcm.edu	37	19	18561473	18561473	+	Silent	SNP	G	G	A	rs34868531	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18561473G>A	ENST00000262809.4	-	8	1350	c.1279C>T	c.(1279-1281)Ctg>Ttg	p.L427L	ELL_ENST00000596124.3_Silent_p.L294L	NM_006532.3	NP_006523.1	P55199	ELL_HUMAN	elongation factor RNA polymerase II	427					gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of viral transcription (GO:0050434)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	phosphatase binding (GO:0019902)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(5)|prostate(1)	19				GBM - Glioblastoma multiforme(1328;7.81e-07)		AGCAGGGGCAGGCCGAGGCGC	0.677			T	MLL	AL								G|||	107	0.0213658	0.0681	0.0144	5008	,	,		12206	0.0		0.007	False		,,,				2504	0.0				p.L427L		Atlas-SNP	.		Dom	yes		19	19p13.1	8178	ELL gene (11-19 lysine-rich leukemia gene)		L	.	ELL	52	.	0			c.C1279T						PASS	.	G		212,4120		2,208,1956	19.0	11.0	14.0		1279	-0.1	0.0	19	dbSNP_126	14	45,8491		0,45,4223	no	coding-synonymous	ELL	NM_006532.3		2,253,6179	AA,AG,GG		0.5272,4.8938,1.9972		427/622	18561473	257,12611	2166	4268	6434	SO:0001819	synonymous_variant	8178	exon8			GGGGCAGGCCGAG	U16282	CCDS12380.1	19p13.1	2012-04-17	2005-05-23			ENSG00000105656		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23114	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 68"""	600284	"""chromosome 19 open reading frame 17"""	C19orf17		7991593, 8596958	Standard	NM_006532		Approved	Men, ELL1, PPP1R68	uc002njh.3	P55199		ENST00000262809.4:c.1279C>T	19.37:g.18561473G>A		50.0	0.0	0		106.0	58.0	0.54717	NM_006532		Silent	SNP	ENST00000262809.4	37	CCDS12380.1																																																																																			G|0.980;A|0.020	0.020	strong		0.677	ELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466362.1	NM_006532	
CNTNAP1	8506	hgsc.bcm.edu	37	17	40841001	40841001	+	Missense_Mutation	SNP	G	G	C	rs35437096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:40841001G>C	ENST00000264638.4	+	10	1781	c.1564G>C	c.(1564-1566)Gtg>Ctg	p.V522L	CTD-3193K9.3_ENST00000592440.1_RNA	NM_003632.2	NP_003623.1	P78357	CNTP1_HUMAN	contactin associated protein 1	522	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.		V -> L (in dbSNP:rs35437096).		axon cargo transport (GO:0008088)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytoskeleton organization (GO:0007010)|neuromuscular process controlling balance (GO:0050885)|neuromuscular process controlling posture (GO:0050884)|neuron projection morphogenesis (GO:0048812)|neuronal action potential propagation (GO:0019227)|paranodal junction assembly (GO:0030913)|positive regulation of signal transduction (GO:0009967)|protein localization to paranode region of axon (GO:0002175)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|paranode region of axon (GO:0033270)|voltage-gated potassium channel complex (GO:0008076)	receptor activity (GO:0004872)|SH3 domain binding (GO:0017124)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|lung(15)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.143)		CCTGACTCTGGTGGAGGGCCG	0.562													G|||	202	0.0403355	0.143	0.0173	5008	,	,		17992	0.0		0.001	False		,,,				2504	0.0				p.V522L		Atlas-SNP	.											CNTNAP1,uveal_tract,malignant_melanoma,-1,1	CNTNAP1	116	1	0			c.G1564C						scavenged	.	G	LEU/VAL	536,3870	243.1+/-252.9	38,460,1705	138.0	126.0	130.0		1564	3.7	1.0	17	dbSNP_126	130	4,8596	3.7+/-12.6	0,4,4296	yes	missense	CNTNAP1	NM_003632.2	32	38,464,6001	CC,CG,GG		0.0465,12.1652,4.1519	benign	522/1385	40841001	540,12466	2203	4300	6503	SO:0001583	missense	8506	exon10			ACTCTGGTGGAGG	U87223	CCDS11436.1	17q21	2008-07-18				ENSG00000108797			8011	protein-coding gene	gene with protein product	"""neurexin 4"""	602346		NRXN4		9118959	Standard	NM_003632		Approved	p190, Caspr, CNTNAP	uc002iay.3	P78357		ENST00000264638.4:c.1564G>C	17.37:g.40841001G>C	ENSP00000264638:p.Val522Leu	118.0	1.0	0.00847458		109.0	53.0	0.486239	NM_003632		Missense_Mutation	SNP	ENST00000264638.4	37	CCDS11436.1	58	0.026556776556776556	48	0.0975609756097561	9	0.024861878453038673	0	0.0	1	0.0013192612137203166	G	13.62	2.290608	0.40494	0.121652	4.65E-4	ENSG00000108797	ENST00000264638	T	0.76186	-1.0	4.73	3.72	0.42706	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.181748	0.37715	N	0.001970	T	0.01695	0.0054	L	0.45352	1.415	0.33613	D	0.60377	B	0.06786	0.001	B	0.06405	0.002	T	0.37478	-0.9704	10	0.39692	T	0.17	.	9.0628	0.36444	0.083:0.2588:0.6582:0.0	rs35437096	522	P78357	CNTP1_HUMAN	L	522	ENSP00000264638:V522L	ENSP00000264638:V522L	V	+	1	0	CNTNAP1	38094527	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	2.118000	0.41949	2.449000	0.82847	0.561000	0.74099	GTG	G|0.961;C|0.039	0.039	strong		0.562	CNTNAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452342.1	NM_003632	
ABLIM1	3983	hgsc.bcm.edu	37	10	116203801	116203801	+	Silent	SNP	A	A	C	rs74158004	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:116203801A>C	ENST00000277895.5	-	17	2017	c.1920T>G	c.(1918-1920)tcT>tcG	p.S640S	ABLIM1_ENST00000533213.2_Silent_p.S580S|ABLIM1_ENST00000369266.3_Silent_p.S317S|ABLIM1_ENST00000369252.4_Silent_p.S580S|ABLIM1_ENST00000392952.3_Silent_p.S317S|ABLIM1_ENST00000369253.2_Silent_p.S263S	NM_002313.5	NP_002304.3	O14639	ABLM1_HUMAN	actin binding LIM protein 1	640					axon guidance (GO:0007411)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|visual perception (GO:0007601)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	actin binding (GO:0003779)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	30		Colorectal(252;0.0373)|Breast(234;0.231)		Epithelial(162;0.0132)|all cancers(201;0.0383)		AGTTGATGGGAGAATCGTAGC	0.512													C|||	165	0.0329473	0.1233	0.0029	5008	,	,		16633	0.0		0.0	False		,,,				2504	0.0				p.S640S		Atlas-SNP	.											.	ABLIM1	131	.	0			c.T1920G						PASS	.	C	,,,	418,3988	788.2+/-414.9	31,356,1816	185.0	183.0	184.0		1740,1824,1920,951	-1.1	1.0	10	dbSNP_130	184	2,8598	819.2+/-406.8	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ABLIM1	NM_001003407.1,NM_001003408.1,NM_002313.5,NM_006720.3	,,,	31,358,6114	CC,CA,AA		0.0233,9.4871,3.2293	,,,	580/719,608/747,640/779,317/456	116203801	420,12586	2203	4300	6503	SO:0001819	synonymous_variant	3983	exon17			GATGGGAGAATCG	AF005654	CCDS7590.1, CCDS31289.1	10q25	2008-07-07		2002-09-13	ENSG00000099204	ENSG00000099204			78	protein-coding gene	gene with protein product		602330		LIMAB1, ABLIM		9245787	Standard	NM_002313		Approved	abLIM, limatin	uc021pyw.1	O14639	OTTHUMG00000019088	ENST00000277895.5:c.1920T>G	10.37:g.116203801A>C		112.0	0.0	0		124.0	57.0	0.459677	NM_002313	A6NI16|A6NJ06|A8MXA9|B3KVH2|Q15039|Q5JVV1|Q5JVV2|Q5T6N2|Q5T6N3|Q5T6N5|Q68CQ9|Q9BUP1	Silent	SNP	ENST00000277895.5	37	CCDS7590.1	57	0.0260989010989011	56	0.11382113821138211	1	0.0027624309392265192	0	0.0	0	0.0	C	7.510	0.654490	0.14580	0.094871	2.33E-4	ENSG00000099204	ENST00000392955	.	.	.	5.79	-1.12	0.09808	.	.	.	.	.	T	0.00967	0.0032	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.04268	-1.0964	4	.	.	.	.	3.7237	0.08466	0.5347:0.1057:0.0608:0.2988	.	.	.	.	R	514	.	.	L	-	2	0	ABLIM1	116193791	0.990000	0.36364	0.988000	0.46212	0.621000	0.37620	0.259000	0.18405	-0.380000	0.07894	-2.704000	0.00135	CTC	A|0.963;C|0.037	0.037	strong		0.512	ABLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050469.3		
CTC1	80169	hgsc.bcm.edu	37	17	8135446	8135446	+	Silent	SNP	G	G	A	rs3027235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:8135446G>A	ENST00000315684.8	-	13	2167	c.2160C>T	c.(2158-2160)acC>acT	p.T720T		NM_025099.5	NP_079375.3	Q2NKJ3	CTC1_HUMAN	CTS telomere maintenance complex component 1	720					bone marrow development (GO:0048539)|cellular response to DNA damage stimulus (GO:0006974)|hematopoietic stem cell proliferation (GO:0071425)|multicellular organism growth (GO:0035264)|positive regulation of DNA replication (GO:0045740)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|replicative senescence (GO:0090399)|spleen development (GO:0048536)|telomere maintenance (GO:0000723)|telomere maintenance via telomere lengthening (GO:0010833)|thymus development (GO:0048538)	nuclear chromosome, telomeric region (GO:0000784)|nucleus (GO:0005634)|Stn1-Ten1 complex (GO:0070188)	single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(8)|ovary(1)|skin(4)	29						CCTCTGGGCCGGTGGGATCTG	0.577													G|||	217	0.0433307	0.087	0.1009	5008	,	,		17092	0.0099		0.0139	False		,,,				2504	0.0082				p.T720T		Atlas-SNP	.											.	CTC1	75	.	0			c.C2160T						PASS	.	G		260,3684		9,242,1721	21.0	22.0	22.0		2160	2.3	0.0	17	dbSNP_102	22	124,8160		3,118,4021	no	coding-synonymous	CTC1	NM_025099.5		12,360,5742	AA,AG,GG		1.4969,6.5923,3.1403		720/1218	8135446	384,11844	1972	4142	6114	SO:0001819	synonymous_variant	80169	exon13			TGGGCCGGTGGGA	AL831955	CCDS42259.1	17p13.1	2011-02-21	2011-02-21	2011-02-21	ENSG00000178971	ENSG00000178971			26169	protein-coding gene	gene with protein product	"""conserved telomere maintenance component 1"", ""alpha accessory factor 132"", ""conserved telomere capping protein 1"""	613129	"""tmp494178"", ""chromosome 17 open reading frame 68"""	C17orf68		19854130, 19854131	Standard	NM_025099		Approved	FLJ22170, AAF132	uc002gkq.4	Q2NKJ3		ENST00000315684.8:c.2160C>T	17.37:g.8135446G>A		53.0	0.0	0		92.0	41.0	0.445652	NM_025099	B3KR66|C9JEX5|Q1PCD1|Q2TBE3|Q8N3S6|Q9H6L0	Silent	SNP	ENST00000315684.8	37	CCDS42259.1																																																																																			G|0.964;A|0.036	0.036	strong		0.577	CTC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442012.1	NM_025099	
CNPY4	245812	hgsc.bcm.edu	37	7	99722173	99722173	+	Missense_Mutation	SNP	G	G	A	rs60551236	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99722173G>A	ENST00000262932.3	+	5	634	c.502G>A	c.(502-504)Gga>Aga	p.G168R	CNPY4_ENST00000480692.1_3'UTR|RP11-506M12.1_ENST00000494221.1_RNA|MBLAC1_ENST00000398075.2_5'Flank	NM_152755.1	NP_689968.1	Q8N129	CNPY4_HUMAN	canopy FGF signaling regulator 4	168	Glu-rich.		G -> R (in dbSNP:rs60551236).			extracellular region (GO:0005576)				breast(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					AGACATTGTGGGAGACTGGTA	0.507													G|||	109	0.0217652	0.0794	0.0058	5008	,	,		20245	0.0		0.0	False		,,,				2504	0.0				p.G168R		Atlas-SNP	.											.	CNPY4	18	.	0			c.G502A						PASS	.	G	ARG/GLY	343,4063	179.7+/-208.2	14,315,1874	105.0	105.0	105.0		502	5.9	1.0	7	dbSNP_129	105	2,8598	1.2+/-3.3	0,2,4298	yes	missense	CNPY4	NM_152755.1	125	14,317,6172	AA,AG,GG		0.0233,7.7848,2.6526	possibly-damaging	168/249	99722173	345,12661	2203	4300	6503	SO:0001583	missense	245812	exon5			ATTGTGGGAGACT	AK075537	CCDS34701.1	7q22.1	2013-07-23	2013-07-23		ENSG00000166997	ENSG00000166997			28631	protein-coding gene	gene with protein product	"""protein associated with TLR4"""	610047	"""canopy 4 homolog (zebrafish)"""			12975309	Standard	NM_152755		Approved	MGC40499, PRAT4B	uc003uto.3	Q8N129	OTTHUMG00000154817	ENST00000262932.3:c.502G>A	7.37:g.99722173G>A	ENSP00000262932:p.Gly168Arg	100.0	0.0	0		96.0	46.0	0.479167	NM_152755	Q8WUN9	Missense_Mutation	SNP	ENST00000262932.3	37	CCDS34701.1	27	0.012362637362637362	26	0.052845528455284556	1	0.0027624309392265192	0	0.0	0	0.0	G	29.2	4.986631	0.93106	0.077848	2.33E-4	ENSG00000166997	ENST00000262932	T	0.34859	1.34	5.94	5.94	0.96194	.	0.106425	0.64402	D	0.000007	T	0.02304	0.0071	N	0.08118	0	0.43489	D	0.995729	D	0.64830	0.994	D	0.66497	0.944	T	0.04400	-1.0954	10	0.23302	T	0.38	-10.3151	15.8634	0.79043	0.0:0.0:1.0:0.0	rs60551236	168	Q8N129	CNPY4_HUMAN	R	168	ENSP00000262932:G168R	ENSP00000262932:G168R	G	+	1	0	CNPY4	99560109	1.000000	0.71417	0.998000	0.56505	0.975000	0.68041	7.907000	0.87430	2.826000	0.97356	0.561000	0.74099	GGA	G|0.979;A|0.021	0.021	strong		0.507	CNPY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337224.4	NM_152755	
CTAGE5	4253	hgsc.bcm.edu	37	14	39736693	39736693	+	Silent	SNP	G	G	T	rs34909359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:39736693G>T	ENST00000280083.3	+	1	344	c.30G>T	c.(28-30)ccG>ccT	p.P10P	CTAGE5_ENST00000396158.2_Silent_p.P10P|CTAGE5_ENST00000396165.4_Intron|CTAGE5_ENST00000348007.3_Silent_p.P10P|CTAGE5_ENST00000556148.1_5'UTR|RP11-407N17.5_ENST00000605298.1_RNA|RP11-407N17.3_ENST00000553728.1_Intron|RP11-407N17.3_ENST00000603904.1_Intron|CTAGE5_ENST00000341502.5_Silent_p.P10P|CTAGE5_ENST00000341749.3_Intron|RP11-407N17.5_ENST00000553520.1_RNA|CTAGE5_ENST00000557038.1_Intron			O15320	CTGE5_HUMAN	CTAGE family, member 5	10					positive regulation of catalytic activity (GO:0043085)	membrane (GO:0016020)	enzyme activator activity (GO:0008047)		CTAGE5/SIP1(2)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.000565)|Lung(238;0.000711)	GBM - Glioblastoma multiforme(112;0.0475)		CCCCTCAACCGTATTTGGGGC	0.662													G|||	100	0.0199681	0.0711	0.0086	5008	,	,		16634	0.0		0.0	False		,,,				2504	0.0				p.P10P		Atlas-SNP	.											.	CTAGE5	75	.	0			c.G30T						PASS	.	G	,,,	285,4121	149.2+/-183.4	6,273,1924	31.0	33.0	32.0		30,,30,	2.4	0.0	14	dbSNP_126	32	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,intron,coding-synonymous,intron	CTAGE5	NM_005930.3,NM_203354.2,NM_203355.2,NM_203356.2	,,,	6,275,6222	TT,TG,GG		0.0233,6.4685,2.2067	,,,	10/805,,10/762,	39736693	287,12719	2203	4300	6503	SO:0001819	synonymous_variant	4253	exon1			TCAACCGTATTTG	U94780	CCDS9673.1, CCDS9674.1, CCDS9675.1, CCDS9676.1, CCDS58316.1, CCDS58317.1	14q21.1	2009-09-11	2004-08-24	2004-08-26	ENSG00000150527	ENSG00000150527			7057	protein-coding gene	gene with protein product		602132	"""meningioma expressed antigen 6 (coiled-coil proline-rich)"""	MGEA, MGEA6		9356211, 11149944	Standard	NM_203355		Approved	MEA6, cTAGE-5A, cTAGE-5B, cTAGE-5C, cTAGE-5D, MGEA11	uc001wvi.4	O15320	OTTHUMG00000140258	ENST00000280083.3:c.30G>T	14.37:g.39736693G>T		74.0	0.0	0		73.0	33.0	0.452055	NM_001247989	B3KRA6|B4DQS6|D3DSA6|G3XAC5|O00169|Q6MZN2|Q6P2R8|Q86TF6|Q8IX92|Q8IX93	Silent	SNP	ENST00000280083.3	37	CCDS9674.1																																																																																			G|0.979;T|0.021	0.021	strong		0.662	CTAGE5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000276771.2	NM_005930	
CLU	1191	hgsc.bcm.edu	37	8	27457512	27457512	+	Missense_Mutation	SNP	T	T	G	rs9331936	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:27457512T>G	ENST00000316403.10	-	7	1354	c.949A>C	c.(949-951)Aac>Cac	p.N317H	CLU_ENST00000405140.3_Missense_Mutation_p.N317H|CLU_ENST00000523500.1_Missense_Mutation_p.N317H|CLU_ENST00000546343.1_Missense_Mutation_p.N328H|CLU_ENST00000560366.1_Missense_Mutation_p.N369H			P10909	CLUS_HUMAN	clusterin	317			N -> H (in dbSNP:rs9331936). {ECO:0000269|Ref.6}.		blood coagulation (GO:0007596)|cell morphogenesis (GO:0000902)|central nervous system myelin maintenance (GO:0032286)|chaperone-mediated protein complex assembly (GO:0051131)|chaperone-mediated protein folding (GO:0061077)|complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|lipid metabolic process (GO:0006629)|microglial cell activation (GO:0001774)|microglial cell proliferation (GO:0061518)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902230)|negative regulation of protein homooligomerization (GO:0032463)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of apoptotic process (GO:0043065)|positive regulation of beta-amyloid formation (GO:1902004)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of neurofibrillary tangle assembly (GO:1902998)|positive regulation of neuron death (GO:1901216)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of tau-protein kinase activity (GO:1902949)|positive regulation of tumor necrosis factor production (GO:0032760)|protein import (GO:0017038)|protein stabilization (GO:0050821)|regulation of beta-amyloid clearance (GO:1900221)|regulation of neuron death (GO:1901214)|regulation of neuronal signal transduction (GO:1902847)|release of cytochrome c from mitochondria (GO:0001836)|response to misfolded protein (GO:0051788)|response to virus (GO:0009615)|reverse cholesterol transport (GO:0043691)	apical dendrite (GO:0097440)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|spherical high-density lipoprotein particle (GO:0034366)	misfolded protein binding (GO:0051787)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)	21		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0204)|Colorectal(74;0.132)		TGGGAGGGGTTGTTGGTGGAA	0.527													T|||	327	0.0652955	0.2398	0.013	5008	,	,		20819	0.0		0.001	False		,,,				2504	0.0				p.N317H		Atlas-SNP	.											.	CLU	54	.	0			c.A949C						PASS	.	T	HIS/ASN	869,3537	336.3+/-304.3	81,707,1415	57.0	53.0	54.0		949	-1.3	0.0	8	dbSNP_119	54	10,8590	7.1+/-27.0	0,10,4290	yes	missense	CLU	NM_203339.2	68	81,717,5705	GG,GT,TT		0.1163,19.7231,6.7584	probably-damaging	317/450	27457512	879,12127	2203	4300	6503	SO:0001583	missense	1191	exon7			AGGGGTTGTTGGT	M64722	CCDS47832.1	8p21-p12	2012-11-30	2006-02-10		ENSG00000120885	ENSG00000120885			2095	protein-coding gene	gene with protein product	"""complement lysis inhibitor"", ""sulfated glycoprotein 2"", ""testosterone-repressed prostate message 2"", ""apolipoprotein J"""	185430	"""clusterin (complement lysis inhibitor, SP-40,40, sulfated glycoprotein 2, testosterone-repressed prostate message 2, apolipoprotein J)"""	CLI, APOJ		1585460	Standard	NR_038335		Approved	SGP-2, SP-40, TRPM-2, KUB1, CLU1, CLU2	uc003xfz.2	P10909	OTTHUMG00000102114	ENST00000316403.10:c.949A>C	8.37:g.27457512T>G	ENSP00000315130:p.Asn317His	78.0	0.0	0		81.0	45.0	0.555556	NM_001831	B2R9Q1|B3KSE6|P11380|P11381|Q2TU75|Q5HYC1|Q7Z5B9	Missense_Mutation	SNP	ENST00000316403.10	37	CCDS47832.1	135|135	0.061813186813186816|0.061813186813186816	131|131	0.266260162601626|0.266260162601626	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	0|0	0.0|0.0	T|T	15.93|15.93	2.978011|2.978011	0.53720|0.53720	0.197231|0.197231	0.001163|0.001163	ENSG00000120885|ENSG00000120885	ENST00000316403;ENST00000546343;ENST00000405140;ENST00000523500;ENST00000380446;ENST00000520012|ENST00000522098	T;T;T|.	0.24350|.	1.86;1.86;1.86|.	5.62|5.62	-1.32|-1.32	0.09201|0.09201	Clusterin, C-terminal (1);|.	0.361968|.	0.34603|.	N|.	0.003825|.	T|T	0.00012|0.00012	0.0000|0.0000	M|M	0.76838|0.76838	2.35|2.35	0.80722|0.80722	P|P	0.0|0.0	D;D;D;D|.	0.76494|.	0.998;0.999;0.999;0.999|.	D;D;D;D|.	0.72338|.	0.972;0.974;0.974;0.977|.	T|T	0.11591|0.11591	-1.0581|-1.0581	9|4	0.62326|.	D|.	0.03|.	-24.2564|-24.2564	5.937|5.937	0.19171|0.19171	0.0:0.4821:0.1723:0.3456|0.0:0.4821:0.1723:0.3456	rs9331936;rs11555230|rs9331936;rs11555230	182;369;328;317|.	E7ETA7;P10909-2;P10909-5;P10909|.	.;.;.;CLUS_HUMAN|.	H|P	369;328;317;317;142;182|179	ENSP00000446413:N328H;ENSP00000385419:N317H;ENSP00000429620:N317H|.	ENSP00000315130:N369H|.	N|Q	-|-	1|2	0|0	CLU|CLU	27513429|27513429	1.000000|1.000000	0.71417|0.71417	0.002000|0.002000	0.10522|0.10522	0.004000|0.004000	0.04260|0.04260	2.424000|2.424000	0.44714|0.44714	-0.154000|-0.154000	0.11118|0.11118	-0.250000|-0.250000	0.11733|0.11733	AAC|CAA	T|0.922;G|0.078	0.078	strong		0.527	CLU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219953.3	NM_001831	
DCHS2	54798	hgsc.bcm.edu	37	4	155219318	155219318	+	Missense_Mutation	SNP	C	C	G	rs28561984	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:155219318C>G	ENST00000357232.4	-	18	4782	c.4783G>C	c.(4783-4785)Gag>Cag	p.E1595Q		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1595	Cadherin 14. {ECO:0000255|PROSITE- ProRule:PRU00043}.		E -> Q (in dbSNP:rs28561984).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		GTAGGCGACTCGGGGGAAAGA	0.428													G|||	406	0.0810703	0.261	0.0418	5008	,	,		19868	0.0109		0.0179	False		,,,				2504	0.0031				p.E1595Q		Atlas-SNP	.											.	DCHS2	594	.	0			c.G4783C						PASS	.						89.0	90.0	89.0					4																	155219318		2203	4300	6503	SO:0001583	missense	54798	exon18			GCGACTCGGGGGA	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.4783G>C	4.37:g.155219318C>G	ENSP00000349768:p.Glu1595Gln	212.0	0.0	0		206.0	94.0	0.456311	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	173	0.07921245421245421	142	0.2886178861788618	11	0.03038674033149171	6	0.01048951048951049	14	0.018469656992084433	G	0.003	-2.426918	0.00186	.	.	ENSG00000197410	ENST00000357232	T	0.61627	0.09	5.66	0.139	0.14798	Cadherin (2);Cadherin-like (1);	0.917277	0.09327	N	0.817476	T	0.00012	0.0000	N	0.02916	-0.46	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.25916	-1.0118	9	0.10377	T	0.69	.	3.0954	0.06308	0.1424:0.376:0.2865:0.1951	rs28561984	1595	Q6V1P9	PCD23_HUMAN	Q	1595	ENSP00000349768:E1595Q	ENSP00000349768:E1595Q	E	-	1	0	DCHS2	155438768	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	0.438000	0.21559	-0.142000	0.11354	-0.127000	0.14921	GAG	C|0.867;G|0.027;T|0.106	0.027	strong		0.428	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
HLA-C	3107	hgsc.bcm.edu	37	6	31237275	31237275	+	Missense_Mutation	SNP	G	G	A	rs41559915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31237275G>A	ENST00000376228.5	-	6	1057	c.1043C>T	c.(1042-1044)gCt>gTt	p.A348V	HLA-C_ENST00000383329.3_Missense_Mutation_p.A354V	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	354					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						CTTACACGCAGCCTGAGAGCA	0.557													G|||	167	0.0333466	0.0605	0.013	5008	,	,		18640	0.0069		0.006	False		,,,				2504	0.0665				p.A348V		Atlas-SNP	.											HLA-C_ENST00000383329,NS,carcinoma,-1,2	HLA-C	92	2	0			c.C1043T						PASS	.	G	VAL/ALA	216,4190		7,202,1994	64.0	68.0	67.0		1043	1.8	0.0	6	dbSNP_127	67	39,8561		0,39,4261	yes	missense	HLA-C	NM_002117.5	64	7,241,6255	AA,AG,GG		0.4535,4.9024,1.9606	benign	348/367	31237275	255,12751	2203	4300	6503	SO:0001583	missense	3107	exon6			CACGCAGCCTGAG	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.1043C>T	6.37:g.31237275G>A	ENSP00000365402:p.Ala348Val	157.0	0.0	0		155.0	81.0	0.522581	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	33	0.01510989010989011	22	0.044715447154471545	5	0.013812154696132596	1	0.0017482517482517483	5	0.006596306068601583	.	11.21	1.572853	0.28092	0.049024	0.004535	ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000539307	T;T	0.04317	3.65;3.65	2.67	1.75	0.24633	MHC class I, alpha chain, C-terminal (1);	.	.	.	.	T	0.13243	0.0321	M	0.93106	3.38	0.09310	N	1	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.85130	0.997;0.997;0.997	T	0.03898	-1.0994	9	0.72032	D	0.01	.	6.7409	0.23435	0.0:0.0:0.7201:0.2799	rs41559915	348;354;348	A6H578;A2AEA2;P10321	.;.;1C07_HUMAN	V	348;354;385	ENSP00000365402:A348V;ENSP00000372819:A354V	ENSP00000365402:A348V	A	-	2	0	HLA-C	31345254	0.040000	0.19996	0.002000	0.10522	0.176000	0.22953	1.465000	0.35299	0.670000	0.31165	0.298000	0.19748	GCT	G|0.981;A|0.019	0.019	strong		0.557	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
SLC26A10	65012	hgsc.bcm.edu	37	12	58017665	58017665	+	Nonsense_Mutation	SNP	G	G	A	rs115563091	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:58017665G>A	ENST00000320442.4	+	8	1411	c.1100G>A	c.(1099-1101)tGg>tAg	p.W367*	SLC26A10_ENST00000379218.2_Nonsense_Mutation_p.W367*	NM_133489.2	NP_597996.2	Q8NG04	S2610_HUMAN	solute carrier family 26, member 10	367						integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|sulfate transmembrane transporter activity (GO:0015116)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)	19	Melanoma(17;0.122)					GTGCTGCTGTGGCTGGGGCCC	0.562													G|||	6	0.00119808	0.0045	0.0	5008	,	,		18555	0.0		0.0	False		,,,				2504	0.0				p.W367X		Atlas-SNP	.											.	SLC26A10	89	.	0			c.G1100A						PASS	.	G	stop/TRP	21,4385		0,21,2182	98.0	100.0	100.0		1100	3.9	1.0	12	dbSNP_132	100	0,8600		0,0,4300	yes	stop-gained	SLC26A10	NM_133489.2		0,21,6482	AA,AG,GG		0.0,0.4766,0.1615		367/564	58017665	21,12985	2203	4300	6503	SO:0001587	stop_gained	65012	exon8			TGCTGTGGCTGGG		CCDS8949.2	12q13	2013-07-18			ENSG00000135502	ENSG00000135502		"""Solute carriers"""	14470	protein-coding gene	gene with protein product							Standard	NM_133489		Approved		uc001spe.3	Q8NG04	OTTHUMG00000128505	ENST00000320442.4:c.1100G>A	12.37:g.58017665G>A	ENSP00000320217:p.Trp367*	70.0	0.0	0		71.0	40.0	0.56338	NM_133489	A6NMJ2|B6ZDQ3|Q6ZWI7	Nonsense_Mutation	SNP	ENST00000320442.4	37	CCDS8949.2	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	.	37	6.630732	0.97718	0.004766	0.0	ENSG00000135502	ENST00000320442;ENST00000379218	.	.	.	3.92	3.92	0.45320	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.16896	T	0.51	.	14.2309	0.65892	0.0:0.0:1.0:0.0	.	.	.	.	X	367	.	ENSP00000320217:W367X	W	+	2	0	SLC26A10	56303932	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	4.320000	0.59203	2.471000	0.83476	0.561000	0.74099	TGG	G|0.999;A|0.001	0.001	strong		0.562	SLC26A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250311.2		
KLHL36	79786	hgsc.bcm.edu	37	16	84691256	84691256	+	Silent	SNP	C	C	T	rs12102528	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84691256C>T	ENST00000564996.1	+	3	984	c.843C>T	c.(841-843)ccC>ccT	p.P281P	KLHL36_ENST00000258157.5_Silent_p.P281P	NM_024731.2	NP_079007.2	Q8N4N3	KLH36_HUMAN	kelch-like family member 36	281					protein ubiquitination (GO:0016567)					endometrium(3)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13						CGGCCCAGCCCGTCATGCAGA	0.677													C|||	79	0.0157748	0.0567	0.0058	5008	,	,		17332	0.0		0.0	False		,,,				2504	0.0				p.P281P		Atlas-SNP	.											.	KLHL36	51	.	0			c.C843T						PASS	.	C		208,4182		6,196,1993	29.0	28.0	28.0		843	-3.6	1.0	16	dbSNP_120	28	1,8595		0,1,4297	no	coding-synonymous	KLHL36	NM_024731.2		6,197,6290	TT,TC,CC		0.0116,4.738,1.6094		281/617	84691256	209,12777	2195	4298	6493	SO:0001819	synonymous_variant	79786	exon3			CCAGCCCGTCATG	AK022605	CCDS10948.1	16q24.1	2013-02-22	2013-02-22	2008-07-07	ENSG00000135686	ENSG00000135686		"""Kelch-like"", ""BTB/POZ domain containing"""	17844	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 44"", ""kelch-like 36 (Drosophila)"""	C16orf44			Standard	NM_024731		Approved	FLJ12543	uc002fig.3	Q8N4N3	OTTHUMG00000137642	ENST00000564996.1:c.843C>T	16.37:g.84691256C>T		45.0	0.0	0		59.0	23.0	0.38983	NM_024731	Q8N5G6|Q9H9U6	Silent	SNP	ENST00000564996.1	37	CCDS10948.1																																																																																			C|0.984;T|0.016	0.016	strong		0.677	KLHL36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269084.2		
TMEM8B	51754	hgsc.bcm.edu	37	9	35842480	35842480	+	Silent	SNP	A	A	G	rs7037450	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35842480A>G	ENST00000377991.4	+	7	1060	c.45A>G	c.(43-45)gaA>gaG	p.E15E	TMEM8B_ENST00000377996.1_Silent_p.E15E|TMEM8B_ENST00000473947.1_Intron|TMEM8B_ENST00000377988.2_Silent_p.E15E|TMEM8B_ENST00000439587.2_Silent_p.E15E	NM_001042589.2	NP_001036054.1	A6NDV4	TMM8B_HUMAN	transmembrane protein 8B	15					cell-matrix adhesion (GO:0007160)|regulation of growth (GO:0040008)|regulation of mitotic cell cycle (GO:0007346)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|large_intestine(2)|lung(1)|ovary(1)	7						TGCCCCCAGAACCGCCATCCC	0.701													G|||	154	0.0307508	0.1089	0.0101	5008	,	,		17224	0.0		0.003	False		,,,				2504	0.0				p.E15E		Atlas-SNP	.											.	TMEM8B	53	.	0			c.A45G						PASS	.	G	,,	474,3932	759.4+/-412.9	36,402,1765	32.0	33.0	32.0		45,45,45	4.8	1.0	9	dbSNP_116	32	21,8577	804.0+/-407.3	0,21,4278	no	coding-synonymous,coding-synonymous,coding-synonymous	TMEM8B	NM_001042589.1,NM_001042590.1,NM_016446.3	,,	36,423,6043	GG,GA,AA		0.2442,10.7581,3.8065	,,	15/473,15/473,15/339	35842480	495,12509	2203	4299	6502	SO:0001819	synonymous_variant	51754	exon6			CCCAGAACCGCCA	BC043384	CCDS6595.1, CCDS43800.1	9p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000137103	ENSG00000137103			21427	protein-coding gene	gene with protein product	"""nasopharyngeal carcinoma expressed 6"""		"""chromosome 9 open reading frame 127"""	C9orf127		12918109, 8619474	Standard	NM_016446		Approved	NAG-5, NGX6	uc003zym.4	A6NDV4	OTTHUMG00000019885	ENST00000377991.4:c.45A>G	9.37:g.35842480A>G		115.0	0.0	0		105.0	52.0	0.495238	NM_001042590	B3KQF3|O75539|Q49AB1|Q4KMX5|Q5TCW5|Q9HBY2|Q9P0U7	Silent	SNP	ENST00000377991.4	37	CCDS43800.1																																																																																			A|0.962;G|0.038	0.038	strong		0.701	TMEM8B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052388.2	NM_016446	
CEP85L	387119	hgsc.bcm.edu	37	6	118887215	118887215	+	Missense_Mutation	SNP	T	T	A	rs9489444	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:118887215T>A	ENST00000368491.3	-	3	1118	c.497A>T	c.(496-498)gAt>gTt	p.D166V	CEP85L_ENST00000368488.5_Missense_Mutation_p.D169V|CEP85L_ENST00000392500.3_Missense_Mutation_p.D169V|CEP85L_ENST00000419517.2_Missense_Mutation_p.D166V|CEP85L_ENST00000360290.3_Missense_Mutation_p.D64V|CEP85L_ENST00000472713.1_5'UTR	NM_001042475.2	NP_001035940.1	Q5SZL2	CE85L_HUMAN	centrosomal protein 85kDa-like	166			D -> V (in dbSNP:rs9489444).			centrosome (GO:0005813)|cytoplasm (GO:0005737)											GCCACAGTTATCCGGGGCAGT	0.498													T|||	191	0.038139	0.121	0.0144	5008	,	,		20125	0.0099		0.004	False		,,,				2504	0.0072				p.D169V		Atlas-SNP	.											.	CEP85L	26	.	0			c.A506T						PASS	.	T	VAL/ASP,VAL/ASP,VAL/ASP	363,4043	186.0+/-213.0	18,327,1858	134.0	122.0	126.0		497,506,497	2.1	0.0	6	dbSNP_119	126	36,8564	24.6+/-71.5	0,36,4264	yes	missense,missense,missense	C6orf204	NM_001042475.2,NM_001178035.1,NM_206921.2	152,152,152	18,363,6122	AA,AT,TT		0.4186,8.2388,3.0678	benign,benign,benign	166/806,169/809,166/497	118887215	399,12607	2203	4300	6503	SO:0001583	missense	387119	exon4			CAGTTATCCGGGG	AF308284	CCDS5119.2, CCDS43498.1, CCDS55052.1	6q22.31	2011-11-25	2011-11-25	2011-11-25	ENSG00000111860	ENSG00000111860			21638	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 204"""	C6orf204			Standard	NM_206921		Approved	NY-BR-15, bA57K17.2	uc003pya.2	Q5SZL2	OTTHUMG00000015465	ENST00000368491.3:c.497A>T	6.37:g.118887215T>A	ENSP00000357477:p.Asp166Val	175.0	0.0	0		202.0	114.0	0.564356	NM_001178035	A1A4E1|A2A3P2|A2IDE5|F8W6J2|G3V0H3|Q2TAM2|Q5T323|Q7Z5K7|Q9H289	Missense_Mutation	SNP	ENST00000368491.3	37	CCDS43498.1	72	0.03296703296703297	60	0.12195121951219512	6	0.016574585635359115	3	0.005244755244755245	3	0.00395778364116095	T	4.848	0.157562	0.09236	0.082388	0.004186	ENSG00000111860	ENST00000368491;ENST00000368488;ENST00000434604;ENST00000392500;ENST00000360290;ENST00000419517	T;T;T;T;T;T	0.25912	2.94;2.93;2.35;2.11;1.77;2.12	5.86	2.12	0.27331	.	0.629920	0.16930	N	0.193714	T	0.04998	0.0134	N	0.24115	0.695	0.47308	P	6.110000000000282E-4	B;B;B;B;B	0.18610	0.029;0.023;0.013;0.005;0.005	B;B;B;B;B	0.15052	0.011;0.012;0.012;0.007;0.004	T	0.32322	-0.9911	9	0.38643	T	0.18	-0.0495	4.4874	0.11797	0.1127:0.0771:0.117:0.6932	rs9489444;rs52812528;rs9489444	64;169;166;169;166	B4DYT2;Q5SZL2-2;G3V0H3;F8W6J2;Q5SZL2	.;.;.;.;CF204_HUMAN	V	166;169;169;169;64;166	ENSP00000357477:D166V;ENSP00000357474:D169V;ENSP00000392131:D169V;ENSP00000376288:D169V;ENSP00000353434:D64V;ENSP00000393317:D166V	ENSP00000353434:D64V	D	-	2	0	C6orf204	118993908	0.760000	0.28428	0.001000	0.08648	0.018000	0.09664	1.002000	0.29796	0.130000	0.18549	0.533000	0.62120	GAT	T|0.964;A|0.036	0.036	strong		0.498	CEP85L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041996.2	NM_001042475	
MORC1	27136	hgsc.bcm.edu	37	3	108780895	108780895	+	Silent	SNP	T	T	A	rs79817474	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:108780895T>A	ENST00000483760.1	-	11	949	c.906A>T	c.(904-906)atA>atT	p.I302I	MORC1_ENST00000232603.5_Silent_p.I302I					MORC family CW-type zinc finger 1											breast(7)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(47)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	105						CTTCTTTCAATATGGATTCAG	0.343													T|||	38	0.00758786	0.0265	0.0043	5008	,	,		19655	0.0		0.0	False		,,,				2504	0.0				p.I302I		Atlas-SNP	.											.	MORC1	211	.	0			c.A906T						PASS	.	T		125,4281	92.0+/-130.7	2,121,2080	191.0	175.0	181.0		906	-8.9	0.0	3	dbSNP_132	181	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	MORC1	NM_014429.3		2,123,6378	AA,AT,TT		0.0233,2.837,0.9765		302/985	108780895	127,12879	2203	4300	6503	SO:0001819	synonymous_variant	27136	exon11			TTTCAATATGGAT	AF084946	CCDS2955.1	3q13	2011-10-26	2005-06-15	2005-06-15	ENSG00000114487	ENSG00000114487			7198	protein-coding gene	gene with protein product	"""cancer/testis antigen 33"""	603205	"""microrchidia (mouse) homolog"", ""microrchidia homolog (mouse)"""	MORC		10369865	Standard	NM_014429		Approved	ZCW6, CT33	uc003dxl.3	Q86VD1	OTTHUMG00000159209	ENST00000483760.1:c.906A>T	3.37:g.108780895T>A		128.0	0.0	0		121.0	68.0	0.561983	NM_014429		Silent	SNP	ENST00000483760.1	37																																																																																				T|0.989;A|0.011	0.011	strong		0.343	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1		
MT-ND5	4540	hgsc.bcm.edu	37	M	14000	14000	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:14000T>A	ENST00000361567.2	+	1	1664	c.1664T>A	c.(1663-1665)cTa>cAa	p.L555Q	MT-TT_ENST00000387460.2_RNA|MT-TE_ENST00000387459.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	555					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						CCTCCTAGACCTAACCTGACT	0.438																																					p.L555Q		Atlas-SNP	.											.	.	.	.	0			c.T1664A						PASS	.																																			SO:0001583	missense	0	exon1			TAGACCTAACCTG			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1664T>A	M.37:g.14000T>A	ENSP00000354813:p.Leu555Gln	8.0	0.0	0		8.0	8.0	1	ENST00000361567	Q34773|Q8WCY3	Missense_Mutation	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.438	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
SLC26A8	116369	hgsc.bcm.edu	37	6	35987425	35987425	+	Silent	SNP	T	T	C	rs61743377	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:35987425T>C	ENST00000490799.1	-	2	413	c.60A>G	c.(58-60)tcA>tcG	p.S20S	SLC26A8_ENST00000394602.2_Silent_p.S20S|SLC26A8_ENST00000355574.2_Silent_p.S20S	NM_052961.3	NP_443193.1			solute carrier family 26 (anion exchanger), member 8											breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(16)|ovary(3)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	46						CATATGCGAATGAGTTTCGCC	0.448													T|||	74	0.0147764	0.0552	0.0014	5008	,	,		18599	0.0		0.0	False		,,,				2504	0.0				p.S20S		Atlas-SNP	.											.	SLC26A8	95	.	0			c.A60G						PASS	.	T	,,	234,4172	136.9+/-172.8	5,224,1974	182.0	140.0	154.0		60,60,60	-2.6	0.0	6	dbSNP_129	154	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC26A8	NM_001193476.1,NM_052961.3,NM_138718.2	,,	5,225,6273	CC,CT,TT		0.0116,5.3109,1.8069	,,	20/971,20/971,20/866	35987425	235,12771	2203	4300	6503	SO:0001819	synonymous_variant	116369	exon2			TGCGAATGAGTTT	AF331522	CCDS4813.1, CCDS4814.1	6p21	2013-07-18	2013-07-18		ENSG00000112053	ENSG00000112053		"""Solute carriers"""	14468	protein-coding gene	gene with protein product		608480	"""solute carrier family 26, member 8"""			11834742, 11829495	Standard	NM_001193476		Approved		uc003olm.3	Q96RN1	OTTHUMG00000014586	ENST00000490799.1:c.60A>G	6.37:g.35987425T>C		227.0	0.0	0		205.0	89.0	0.434146	NM_052961		Silent	SNP	ENST00000490799.1	37	CCDS4813.1																																																																																			T|0.986;C|0.014	0.014	strong		0.448	SLC26A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040325.2		
OR13F1	138805	hgsc.bcm.edu	37	9	107266813	107266813	+	Silent	SNP	C	C	T	rs61754949	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107266813C>T	ENST00000334726.2	+	1	359	c.270C>T	c.(268-270)aaC>aaT	p.N90N		NM_001004485.1	NP_001004485.1	Q8NGS4	O13F1_HUMAN	olfactory receptor, family 13, subfamily F, member 1	90						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						CAGGGAGAAACACTATTTCAT	0.517													C|||	55	0.0109824	0.0401	0.0029	5008	,	,		20598	0.0		0.0	False		,,,				2504	0.0				p.N90N		Atlas-SNP	.											.	OR13F1	75	.	0			c.C270T						PASS	.	C		161,4245	108.2+/-146.6	3,155,2045	132.0	117.0	122.0		270	2.2	0.9	9	dbSNP_129	122	0,8600		0,0,4300	no	coding-synonymous	OR13F1	NM_001004485.1		3,155,6345	TT,TC,CC		0.0,3.6541,1.2379		90/320	107266813	161,12845	2203	4300	6503	SO:0001819	synonymous_variant	138805	exon1			GAGAAACACTATT		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.270C>T	9.37:g.107266813C>T		196.0	0.0	0		168.0	47.0	0.279762	NM_001004485	Q6IF50	Silent	SNP	ENST00000334726.2	37	CCDS35087.1																																																																																			C|0.987;T|0.013	0.013	strong		0.517	OR13F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053475.1		
ZNF844	284391	hgsc.bcm.edu	37	19	12186372	12186372	+	Missense_Mutation	SNP	G	G	A	rs10422576	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12186372G>A	ENST00000439326.3	+	4	612	c.437G>A	c.(436-438)cGt>cAt	p.R146H	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	146			R -> H (in dbSNP:rs10422576).		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						TGTCAACAACGTAAGAAAGCC	0.423													.|||	104	0.0207668	0.0772	0.0029	5008	,	,		18101	0.0		0.0	False		,,,				2504	0.0				p.R146H		Atlas-SNP	.											.	ZNF844	69	.	0			c.G437A						PASS	.	A	HIS/ARG	76,1308		2,72,618	88.0	76.0	79.0		437	-2.1	0.0	19	dbSNP_119	79	0,3182		0,0,1591	yes	missense	ZNF844	NM_001136501.1	29	2,72,2209	AA,AG,GG		0.0,5.4913,1.6645	probably-damaging	146/667	12186372	76,4490	692	1591	2283	SO:0001583	missense	284391	exon4			AACAACGTAAGAA	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.437G>A	19.37:g.12186372G>A	ENSP00000392024:p.Arg146His	86.0	0.0	0		110.0	57.0	0.518182	NM_001136501	Q5JPI8	Missense_Mutation	SNP	ENST00000439326.3	37	CCDS45985.1	38	0.0173992673992674	36	0.07317073170731707	2	0.0055248618784530384	0	0.0	0	0.0	A	6.262	0.416387	0.11870	0.054913	0.0	ENSG00000223547	ENST00000439326;ENST00000541708	T	0.27720	1.65	2.12	-2.12	0.07165	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00815	0.0027	N	0.02916	-0.46	0.18873	N	0.999986	B	0.02656	0.0	B	0.01281	0.0	T	0.21211	-1.0252	9	0.72032	D	0.01	.	6.0456	0.19758	0.4102:0.0:0.5898:0.0	rs56481038	146	Q08AG5	ZN844_HUMAN	H	146	ENSP00000392024:R146H	ENSP00000392024:R146H	R	+	2	0	ZNF844	12047372	0.809000	0.29036	0.000000	0.03702	0.005000	0.04900	1.933000	0.40153	-0.554000	0.06150	-1.906000	0.00525	CGT	.	.	weak		0.423	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2		
PSG8	440533	hgsc.bcm.edu	37	19	43269686	43269686	+	Silent	SNP	C	C	T	rs61393109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43269686C>T	ENST00000306511.4	-	1	145	c.48G>A	c.(46-48)aaG>aaA	p.K16K	PSG8_ENST00000406636.3_Silent_p.K16K|PSG8_ENST00000404209.4_Silent_p.K16K|PSG8_ENST00000401467.2_Intron	NM_182707.2	NP_874366.1	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8	16						extracellular region (GO:0005576)				breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(19)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	40		Prostate(69;0.00899)				GCAGGAGCCCCTTCCAGGTGA	0.577													.|||	54	0.0107827	0.0386	0.0043	5008	,	,		18083	0.0		0.0	False		,,,				2504	0.0				p.K16K		Atlas-SNP	.											.	PSG8	101	.	0			c.G48A						PASS	.	C	,,	106,2916		3,100,1408	111.0	113.0	112.0		48,48,48	-2.0	0.0	19	dbSNP_129	112	1,5417		0,1,2708	no	coding-synonymous,coding-synonymous,coding-synonymous	PSG8	NM_001130167.1,NM_001130168.1,NM_182707.2	,,	3,101,4116	TT,TC,CC		0.0185,3.5076,1.2678	,,	16/420,16/298,16/427	43269686	107,8333	1511	2709	4220	SO:0001819	synonymous_variant	440533	exon1			GAGCCCCTTCCAG	M74106	CCDS33037.1, CCDS46090.1, CCDS46091.1	19q13.2	2013-01-29			ENSG00000124467	ENSG00000124467		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9525	protein-coding gene	gene with protein product		176397				1672663, 1572651	Standard	NM_182707		Approved		uc002ouo.2	Q9UQ74	OTTHUMG00000151118	ENST00000306511.4:c.48G>A	19.37:g.43269686C>T		31.0	0.0	0		43.0	20.0	0.465116	NM_001130168	A5PKV3|B2RPL4|B4DTI6|O60410|Q68CR6	Silent	SNP	ENST00000306511.4	37	CCDS33037.1																																																																																			C|0.988;T|0.012	0.012	strong		0.577	PSG8-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464526.1		
CDC42EP2	10435	hgsc.bcm.edu	37	11	65088498	65088498	+	Silent	SNP	T	T	C	rs4149835	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:65088498T>C	ENST00000544348.1	+	2	735	c.129T>C	c.(127-129)atT>atC	p.I43I	CDC42EP2_ENST00000533419.1_Silent_p.I43I|CDC42EP2_ENST00000279249.2_Silent_p.I43I			O14613	BORG1_HUMAN	CDC42 effector protein (Rho GTPase binding) 2	43	CRIB. {ECO:0000255|PROSITE- ProRule:PRU00057}.				actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|plasma membrane (GO:0005886)	GTP-Rho binding (GO:0017049)|Rho GTPase activator activity (GO:0005100)			lung(1)	1						CCATTCATATTGGCAGTGGCG	0.612													C|||	393	0.0784744	0.2791	0.0303	5008	,	,		19020	0.0		0.003	False		,,,				2504	0.0				p.I43I		Atlas-SNP	.											.	CDC42EP2	13	.	0			c.T129C						PASS	.	C		1061,3341	705.0+/-407.2	120,821,1260	59.0	59.0	59.0		129	-9.5	0.1	11	dbSNP_110	59	9,8585	804.3+/-407.3	0,9,4288	no	coding-synonymous	CDC42EP2	NM_006779.3		120,830,5548	CC,CT,TT		0.1047,24.1027,8.2333		43/211	65088498	1070,11926	2201	4297	6498	SO:0001819	synonymous_variant	10435	exon2			TCATATTGGCAGT	AF098290	CCDS8099.1	11q13	2008-07-18				ENSG00000149798			16263	protein-coding gene	gene with protein product	"""CRIB-containing BOGR1 protein"""	606132				10490598, 11035016	Standard	NM_006779		Approved	CEP2, BORG1	uc001odl.3	O14613		ENST00000544348.1:c.129T>C	11.37:g.65088498T>C		133.0	0.0	0		128.0	57.0	0.445312	NM_006779	B2RD85|Q9UNS0	Silent	SNP	ENST00000544348.1	37	CCDS8099.1																																																																																			T|0.914;C|0.086	0.086	strong		0.612	CDC42EP2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387258.1	NM_006779	
CEACAM4	1089	hgsc.bcm.edu	37	19	42125710	42125710	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42125710A>G	ENST00000221954.2	-	7	838	c.728T>C	c.(727-729)gTc>gCc	p.V243A		NM_001817.2	NP_001808.2	O75871	CEAM4_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 4	243						integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				NS(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|skin(3)|urinary_tract(1)	16						AACCTAAGAGACCACATCTGC	0.532																																					p.V243A		Atlas-SNP	.											CEACAM4,NS,neuroblastoma,+1,1	CEACAM4	42	1	0			c.T728C						PASS	.						114.0	109.0	111.0					19																	42125710		2203	4300	6503	SO:0001583	missense	1089	exon7			TAAGAGACCACAT	D90276	CCDS33033.1	19q13.2	2013-01-11			ENSG00000105352	ENSG00000105352		"""Immunoglobulin superfamily / V-set domain containing"""	1816	protein-coding gene	gene with protein product				CGM7		2050678	Standard	XM_005258434		Approved		uc002orh.1	O75871	OTTHUMG00000151065	ENST00000221954.2:c.728T>C	19.37:g.42125710A>G	ENSP00000221954:p.Val243Ala	103.0	0.0	0		116.0	55.0	0.474138	NM_001817	Q03715|Q7LDZ7	Missense_Mutation	SNP	ENST00000221954.2	37	CCDS33033.1	.	.	.	.	.	.	.	.	.	.	A	0.008	-1.908731	0.00508	.	.	ENSG00000105352	ENST00000221954	T	0.01139	5.28	2.4	-3.74	0.04385	.	.	.	.	.	T	0.00440	0.0014	N	0.02142	-0.665	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.43956	-0.9359	9	0.06365	T	0.9	.	3.7364	0.08512	0.3171:0.4027:0.2802:0.0	.	243	O75871	CEAM4_HUMAN	A	243	ENSP00000221954:V243A	ENSP00000221954:V243A	V	-	2	0	CEACAM4	46817550	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.439000	0.02414	-0.683000	0.05190	-0.427000	0.05922	GTC	.	.	none		0.532	CEACAM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321148.1	NM_001817	
FAH	2184	hgsc.bcm.edu	37	15	80460421	80460421	+	Silent	SNP	C	C	T	rs116272698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:80460421C>T	ENST00000407106.1	+	7	638	c.483C>T	c.(481-483)ggC>ggT	p.G161G	FAH_ENST00000558627.1_3'UTR|FAH_ENST00000539156.1_Silent_p.G91G|FAH_ENST00000561421.1_Silent_p.G161G|RP11-2E17.2_ENST00000568836.1_lincRNA|FAH_ENST00000261755.5_Silent_p.G161G			P16930	FAAA_HUMAN	fumarylacetoacetate hydrolase (fumarylacetoacetase)	161					arginine catabolic process (GO:0006527)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	fumarylacetoacetase activity (GO:0004334)|metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						GCTACCATGGCCGTGCCTCCT	0.522									Tyrosinemia, type 1				C|||	45	0.00898562	0.0318	0.0043	5008	,	,		19054	0.0		0.0	False		,,,				2504	0.0				p.G161G		Atlas-SNP	.											.	FAH	36	.	0			c.C483T						PASS	.	C		124,4282	91.1+/-129.8	0,124,2079	116.0	93.0	101.0		483	-0.1	1.0	15	dbSNP_132	101	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FAH	NM_000137.2		0,125,6378	TT,TC,CC		0.0116,2.8143,0.9611		161/420	80460421	125,12881	2203	4300	6503	SO:0001819	synonymous_variant	2184	exon6	Familial Cancer Database	Fumarylacetoacetase Deficiency, Hepatorenal Tyrosinemia, Hereditary Tyrosinemia 1, HT1	CCATGGCCGTGCC	M55150	CCDS10314.1	15q25.1	2012-08-30			ENSG00000103876	ENSG00000103876	3.7.1.2		3579	protein-coding gene	gene with protein product		613871				1998338, 2336361	Standard	NM_000137		Approved		uc002bfm.2	P16930	OTTHUMG00000144187	ENST00000407106.1:c.483C>T	15.37:g.80460421C>T		215.0	0.0	0		220.0	105.0	0.477273	NM_000137	B2R9X1|D3DW95|Q53XA7	Silent	SNP	ENST00000407106.1	37	CCDS10314.1																																																																																			C|0.990;T|0.010	0.010	strong		0.522	FAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291392.2		
FAAH	2166	hgsc.bcm.edu	37	1	46877885	46877885	+	Missense_Mutation	SNP	C	C	G	rs75429705	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:46877885C>G	ENST00000243167.8	+	13	1511	c.1427C>G	c.(1426-1428)gCc>gGc	p.A476G		NM_001441.2	NP_001432.2	O00519	FAAH1_HUMAN	fatty acid amide hydrolase	476					fatty acid catabolic process (GO:0009062)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)	acylglycerol lipase activity (GO:0047372)|carbon-nitrogen ligase activity, with glutamine as amido-N-donor (GO:0016884)|fatty acid amide hydrolase activity (GO:0017064)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	22	Acute lymphoblastic leukemia(166;0.155)				Propofol(DB00818)|Thiopental(DB00599)	CCCATGCTGGCCCCTGCTCTG	0.637													G|||	43	0.00858626	0.0076	0.0	5008	,	,		17547	0.0169		0.0	False		,,,				2504	0.0164				p.A476G		Atlas-SNP	.											.	FAAH	36	.	0			c.C1427G						PASS	.	G	GLY/ALA	6,4354		0,6,2174	73.0	72.0	72.0		1427	4.7	1.0	1	dbSNP_131	72	4,8536		0,4,4266	no	missense	FAAH	NM_001441.2	60	0,10,6440	GG,GC,CC		0.0468,0.1376,0.0775	benign	476/580	46877885	10,12890	2180	4270	6450	SO:0001583	missense	2166	exon13			TGCTGGCCCCTGC	U82535	CCDS535.1	1p35-p34	2008-02-05			ENSG00000117480	ENSG00000117480			3553	protein-coding gene	gene with protein product		602935				9122178	Standard	NM_001441		Approved	FAAH-1	uc001cpu.2	O00519	OTTHUMG00000007811	ENST00000243167.8:c.1427C>G	1.37:g.46877885C>G	ENSP00000243167:p.Ala476Gly	207.0	1.0	0.00483092		196.0	107.0	0.545918	NM_001441	D3DQ19|Q52M86|Q5TDF8	Missense_Mutation	SNP	ENST00000243167.8	37	CCDS535.1	12	0.005494505494505495	1	0.0020325203252032522	0	0.0	11	0.019230769230769232	0	0.0	G	6.661	0.490412	0.12702	0.001376	4.68E-4	ENSG00000117480	ENST00000243167	T	0.64991	-0.13	4.66	4.66	0.58398	Amidase signature domain (2);	0.120287	0.56097	N	0.000022	T	0.22085	0.0532	N	0.04297	-0.235	0.21105	N	0.999789	B	0.02656	0.0	B	0.01281	0.0	T	0.04537	-1.0944	10	0.08599	T	0.76	-24.7092	15.0542	0.71901	0.0:0.1428:0.8572:0.0	.	476	O00519	FAAH1_HUMAN	G	476	ENSP00000243167:A476G	ENSP00000243167:A476G	A	+	2	0	FAAH	46650472	1.000000	0.71417	1.000000	0.80357	0.361000	0.29550	6.705000	0.74644	1.203000	0.43233	-0.120000	0.15030	GCC	C|0.997;G|0.003	0.003	strong		0.637	FAAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021443.1	NM_001441	
BCAN	63827	hgsc.bcm.edu	37	1	156621252	156621252	+	Silent	SNP	G	G	A	rs146863260	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156621252G>A	ENST00000329117.5	+	7	1404	c.1068G>A	c.(1066-1068)tcG>tcA	p.S356S	BCAN_ENST00000361588.5_Silent_p.S356S|RP11-284F21.7_ENST00000448869.1_RNA	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	356			S -> L (in dbSNP:rs12065791).		carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hippocampus development (GO:0021766)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					CCACAGACTCGGCCCAGCCTT	0.562													G|||	19	0.00379393	0.0144	0.0	5008	,	,		18343	0.0		0.0	False		,,,				2504	0.0				p.S356S		Atlas-SNP	.											.	BCAN	174	.	0			c.G1068A						PASS	.	G	,	62,4344	58.7+/-95.3	0,62,2141	47.0	44.0	45.0		1068,1068	1.5	0.9	1	dbSNP_134	45	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	BCAN	NM_021948.4,NM_198427.1	,	0,62,6441	AA,AG,GG		0.0,1.4072,0.4767	,	356/912,356/672	156621252	62,12944	2203	4300	6503	SO:0001819	synonymous_variant	63827	exon7			AGACTCGGCCCAG	BC027971	CCDS1149.1, CCDS1150.1	1q31	2013-05-07			ENSG00000132692	ENSG00000132692		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	23059	protein-coding gene	gene with protein product	"""chondroitin sulfate proteoglycan 7"", ""brevican proteoglycan"""	600347				11054543, 11873941	Standard	NM_021948		Approved	BEHAB, MGC13038, CSPG7	uc001fpp.3	Q96GW7	OTTHUMG00000033322	ENST00000329117.5:c.1068G>A	1.37:g.156621252G>A		35.0	0.0	0		51.0	24.0	0.470588	NM_198427	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Silent	SNP	ENST00000329117.5	37	CCDS1149.1																																																																																			G|0.994;A|0.006	0.006	strong		0.562	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948	
CYP8B1	1582	hgsc.bcm.edu	37	3	42916596	42916596	+	Missense_Mutation	SNP	T	T	C	rs35764459	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:42916596T>C	ENST00000316161.4	-	1	1037	c.713A>G	c.(712-714)aAg>aGg	p.K238R	KRBOX1_ENST00000426937.1_Intron|RP11-141M3.5_ENST00000471537.1_RNA|CYP8B1_ENST00000437102.1_Missense_Mutation_p.K238R	NM_004391.2	NP_004382.2	Q9UNU6	CP8B1_HUMAN	cytochrome P450, family 8, subfamily B, polypeptide 1	238			K -> R (in dbSNP:rs35764459).		bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|lipid metabolic process (GO:0006629)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	7alpha-hydroxycholest-4-en-3-one 12alpha-hydroxylase activity (GO:0033778)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|sterol 12-alpha-hydroxylase activity (GO:0008397)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(2)|prostate(2)|skin(5)	23				KIRC - Kidney renal clear cell carcinoma(284;0.213)|Kidney(284;0.249)		GGAGAGCATCTTGTGAAAGAG	0.572													T|||	108	0.0215655	0.0779	0.0072	5008	,	,		18049	0.0		0.0	False		,,,				2504	0.0				p.K238R		Atlas-SNP	.											.	CYP8B1	59	.	0			c.A713G						PASS	.	T	ARG/LYS	305,4099		8,289,1905	25.0	27.0	26.0		713	4.2	0.0	3	dbSNP_126	26	7,8589		0,7,4291	yes	missense	CYP8B1	NM_004391.2	26	8,296,6196	CC,CT,TT		0.0814,6.9255,2.4	benign	238/502	42916596	312,12688	2202	4298	6500	SO:0001583	missense	1582	exon1			AGCATCTTGTGAA	AF090318	CCDS2707.1	3p22.1	2004-02-27	2003-01-14		ENSG00000180432	ENSG00000180432		"""Cytochrome P450s"""	2653	protein-coding gene	gene with protein product		602172	"""cytochrome P450, subfamily VIIIB (sterol 12-alpha-hydroxylase), polypeptide 1"""			10051404	Standard	NM_004391		Approved	CYP12	uc003cmh.3	Q9UNU6	OTTHUMG00000133047	ENST00000316161.4:c.713A>G	3.37:g.42916596T>C	ENSP00000318867:p.Lys238Arg	98.0	0.0	0		98.0	46.0	0.469388	NM_004391	B2RCY3|O75958|Q6NWT2|Q6NWT3	Missense_Mutation	SNP	ENST00000316161.4	37	CCDS2707.1	40	0.018315018315018316	38	0.07723577235772358	2	0.0055248618784530384	0	0.0	0	0.0	T	10.40	1.340138	0.24339	0.069255	8.14E-4	ENSG00000180432	ENST00000437102;ENST00000316161	T;T	0.69685	-0.42;-0.42	5.34	4.18	0.49190	.	0.469912	0.21438	N	0.074528	T	0.05410	0.0143	L	0.38838	1.175	0.09310	N	1	B;B	0.28258	0.205;0.205	B;B	0.29077	0.098;0.098	T	0.05566	-1.0877	10	0.42905	T	0.14	-8.3878	8.1412	0.31084	0.0:0.1655:0.0:0.8345	rs35764459;rs56678767	238;238	C9JFR9;Q9UNU6	.;CP8B1_HUMAN	R	238	ENSP00000404499:K238R;ENSP00000318867:K238R	ENSP00000318867:K238R	K	-	2	0	CYP8B1	42891600	0.004000	0.15560	0.011000	0.14972	0.684000	0.39900	1.063000	0.30567	0.885000	0.36088	0.449000	0.29647	AAG	T|0.977;C|0.023	0.023	strong		0.572	CYP8B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256653.1	NM_004391	
JAK2	3717	hgsc.bcm.edu	37	9	5050706	5050706	+	Silent	SNP	C	C	T	rs2230722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:5050706C>T	ENST00000381652.3	+	6	983	c.489C>T	c.(487-489)caC>caT	p.H163H	JAK2_ENST00000539801.1_Silent_p.H163H|JAK2_ENST00000544510.1_Silent_p.H14H	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	163	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.|Interaction with cytokine/interferon/growth hormone receptors. {ECO:0000250}.				actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)		BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	ATTTTGTGCACGGATGGATAA	0.343		1	"""T, Mis, O"""	"""ETV6, PCM1, BCR"""	"""ALL, AML, MPD,  CML"""				Polycythemia Vera, Familial				T|||	1794	0.358227	0.4887	0.3905	5008	,	,		15245	0.2708		0.3002	False		,,,				2504	0.3088				p.H163H		Atlas-SNP	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2	35466	.	0			c.C489T						PASS	.	T		2047,2359	609.9+/-391.4	488,1071,644	110.0	123.0	118.0		489	-0.9	0.9	9	dbSNP_119	118	2589,6011	689.4+/-404.4	366,1857,2077	no	coding-synonymous	JAK2	NM_004972.3		854,2928,2721	TT,TC,CC		30.1047,46.4594,35.6451		163/1133	5050706	4636,8370	2203	4300	6503	SO:0001819	synonymous_variant	3717	exon6	Familial Cancer Database		TGTGCACGGATGG		CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"""SH2 domain containing"""	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.489C>T	9.37:g.5050706C>T		86.0	0.0	0		74.0	32.0	0.432432	NM_004972	O14636|O75297	Silent	SNP	ENST00000381652.3	37	CCDS6457.1																																																																																			C|0.647;T|0.353	0.353	strong		0.343	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1		
SYCP1	6847	hgsc.bcm.edu	37	1	115537343	115537343	+	Silent	SNP	T	T	C	rs17033011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:115537343T>C	ENST00000369522.3	+	31	2968	c.2728T>C	c.(2728-2730)Ttg>Ctg	p.L910L	SYCP1_ENST00000477590.1_3'UTR|SYCP1_ENST00000369518.1_Silent_p.L910L	NM_001282541.1|NM_003176.2	NP_001269470.1|NP_003167.2	Q15431	SYCP1_HUMAN	synaptonemal complex protein 1	910					chiasma assembly (GO:0051026)|lateral element assembly (GO:0051878)|meiotic DNA repair synthesis (GO:0000711)|reciprocal meiotic recombination (GO:0007131)|regulation of protein localization (GO:0032880)|sperm chromatin condensation (GO:0035092)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|male germ cell nucleus (GO:0001673)|transverse filament (GO:0000802)	DNA binding (GO:0003677)		RGS22/SYCP1(2)	NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(17)|lung(20)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	48	Lung SC(450;0.211)	all_cancers(81;8.65e-08)|all_epithelial(167;3.32e-07)|all_lung(203;6.55e-06)|Lung NSC(69;1.11e-05)|Acute lymphoblastic leukemia(138;0.221)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		AGAAGAGACATTGAAAACACT	0.274													T|||	185	0.0369409	0.1354	0.0086	5008	,	,		12816	0.0		0.0	False		,,,				2504	0.0				p.L910L		Atlas-SNP	.											.	SYCP1	149	.	0			c.T2728C						PASS	.			470,3920	196.0+/-220.5	22,426,1747	32.0	35.0	34.0		2728	-1.8	0.0	1	dbSNP_123	34	6,8570	4.3+/-15.6	0,6,4282	no	coding-synonymous	SYCP1	NM_003176.2		22,432,6029	CC,CT,TT		0.07,10.7062,3.6711		910/977	115537343	476,12490	2195	4288	6483	SO:0001819	synonymous_variant	6847	exon31			GAGACATTGAAAA	D67035	CCDS879.1, CCDS72840.1	1p13-p12	2009-03-12			ENSG00000198765	ENSG00000198765			11487	protein-coding gene	gene with protein product	"""cancer/testis antigen 8"""	602162				9560255	Standard	XM_005271154		Approved	HOM-TES-14, SCP1, CT8	uc001efr.3	Q15431	OTTHUMG00000012057	ENST00000369522.3:c.2728T>C	1.37:g.115537343T>C		93.0	0.0	0		108.0	53.0	0.490741	NM_003176	O14963|Q5VXJ6	Silent	SNP	ENST00000369522.3	37	CCDS879.1																																																																																			T|0.954;C|0.046	0.046	strong		0.274	SYCP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033386.1	NM_003176	
FAM110A	83541	hgsc.bcm.edu	37	20	825579	825579	+	Silent	SNP	G	G	A	rs8124809	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:825579G>A	ENST00000304189.2	+	3	513	c.132G>A	c.(130-132)gaG>gaA	p.E44E	FAM110A_ENST00000541082.1_Silent_p.E44E|FAM110A_ENST00000381941.3_Silent_p.E44E|FAM110A_ENST00000381939.1_Silent_p.E44E|FAM110A_ENST00000246100.3_Silent_p.E44E			Q9BQ89	F110A_HUMAN	family with sequence similarity 110, member A	44						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|lung(2)	3						GCGCTGTGGAGCGCCTGGAGG	0.687													G|||	73	0.0145767	0.053	0.0043	5008	,	,		11046	0.0		0.0	False		,,,				2504	0.0				p.E44E		Atlas-SNP	.											.	FAM110A	18	.	0			c.G132A						PASS	.	G	,,	204,4158		1,202,1978	12.0	12.0	12.0		132,132,132	4.0	1.0	20	dbSNP_116	12	3,8543		0,3,4270	no	coding-synonymous,coding-synonymous,coding-synonymous	FAM110A	NM_001042353.1,NM_031424.4,NM_207121.3	,,	1,205,6248	AA,AG,GG		0.0351,4.6768,1.6037	,,	44/296,44/296,44/296	825579	207,12701	2181	4273	6454	SO:0001819	synonymous_variant	83541	exon2			TGTGGAGCGCCTG	BC012800	CCDS13008.1	20p13	2007-06-21	2007-03-21	2007-03-21	ENSG00000125898	ENSG00000125898			16188	protein-coding gene	gene with protein product		611393	"""chromosome 20 open reading frame 55"""	C20orf55		17499476	Standard	NM_001042353		Approved	bA371L19.3	uc002wef.1	Q9BQ89	OTTHUMG00000031649	ENST00000304189.2:c.132G>A	20.37:g.825579G>A		87.0	0.0	0		157.0	86.0	0.547771	NM_207121	D3DVW2|Q5R1M7	Silent	SNP	ENST00000304189.2	37	CCDS13008.1																																																																																			A|0.020;C|0.000;G|0.979	0.020	strong		0.687	FAM110A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077489.1	NM_031424	
ABCC12	94160	hgsc.bcm.edu	37	16	48174766	48174766	+	Silent	SNP	A	A	G	rs16945872	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:48174766A>G	ENST00000311303.3	-	4	834	c.489T>C	c.(487-489)atT>atC	p.I163I	ABCC12_ENST00000416054.1_Silent_p.I163I|ABCC12_ENST00000448542.1_Silent_p.I163I	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	163	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.					integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|liver(1)|lung(43)|ovary(2)|prostate(3)|skin(7)|urinary_tract(1)	90		all_cancers(37;0.0474)|all_lung(18;0.047)				TGCACAGTCCAATGCCAACCC	0.537													a|||	189	0.0377396	0.1399	0.0058	5008	,	,		19380	0.0		0.0	False		,,,				2504	0.0				p.I163I		Atlas-SNP	.											.	ABCC12	190	.	0			c.T489C						PASS	.	A		477,3925	225.9+/-241.6	24,429,1748	98.0	96.0	97.0		489	-2.6	0.0	16	dbSNP_123	97	7,8593	4.3+/-15.6	0,7,4293	no	coding-synonymous	ABCC12	NM_033226.2		24,436,6041	GG,GA,AA		0.0814,10.836,3.7225		163/1360	48174766	484,12518	2201	4300	6501	SO:0001819	synonymous_variant	94160	exon4			CAGTCCAATGCCA	AY040220	CCDS10730.1	16q12.1	2012-03-14			ENSG00000140798	ENSG00000140798		"""ATP binding cassette transporters / subfamily C"""	14640	protein-coding gene	gene with protein product		607041				11435397, 11483364	Standard	NM_033226		Approved	MRP9	uc002efc.1	Q96J65	OTTHUMG00000133143	ENST00000311303.3:c.489T>C	16.37:g.48174766A>G		94.0	0.0	0		103.0	47.0	0.456311	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Silent	SNP	ENST00000311303.3	37	CCDS10730.1																																																																																			A|0.955;G|0.045	0.045	strong		0.537	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226	
VWA5B1	127731	hgsc.bcm.edu	37	1	20640969	20640969	+	Silent	SNP	G	G	A	rs114916291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:20640969G>A	ENST00000375079.2	+	4	643	c.447G>A	c.(445-447)tcG>tcA	p.S149S	VWA5B1_ENST00000289825.4_5'UTR|VWA5B1_ENST00000289815.8_Silent_p.S149S|RP4-745E8.2_ENST00000444923.1_RNA|VWA5B1_ENST00000375083.4_Silent_p.S149S	NM_001039500.2	NP_001034589.2	Q5TIE3	VW5B1_HUMAN	von Willebrand factor A domain containing 5B1	149	VIT. {ECO:0000255|PROSITE- ProRule:PRU00801}.					extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(3)|kidney(1)|prostate(1)|skin(1)	7						GCACCTCCTCGGAGCTCCCAA	0.617													G|||	76	0.0151757	0.0499	0.0072	5008	,	,		17445	0.0		0.005	False		,,,				2504	0.0				p.S149S		Atlas-SNP	.											.	VWA5B1	44	.	0			c.G447A						PASS	.	G		66,1318		3,60,629	46.0	45.0	46.0		447	-11.2	0.5	1	dbSNP_132	46	37,3145		0,37,1554	no	coding-synonymous	VWA5B1	NM_001039500.2		3,97,2183	AA,AG,GG		1.1628,4.7688,2.2558		149/1216	20640969	103,4463	692	1591	2283	SO:0001819	synonymous_variant	127731	exon4			CTCCTCGGAGCTC	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.447G>A	1.37:g.20640969G>A		115.0	0.0	0		115.0	68.0	0.591304	NM_001039500	A4IF35|A4IF36|Q3ZCM4|Q6ZUB4|Q96M71	Silent	SNP	ENST00000375079.2	37																																																																																				G|0.988;A|0.012	0.012	strong		0.617	VWA5B1-001	NOVEL	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000007945.4	XM_001722222	
CCDC18	343099	hgsc.bcm.edu	37	1	93720153	93720153	+	Missense_Mutation	SNP	G	G	T	rs61729705	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:93720153G>T	ENST00000343253.7	+	24	3823	c.3321G>T	c.(3319-3321)agG>agT	p.R1107S	CCDC18_ENST00000338949.4_3'UTR|CCDC18_ENST00000401026.3_Missense_Mutation_p.R1108S|CCDC18_ENST00000557479.1_Missense_Mutation_p.R1226S|CCDC18_ENST00000334652.5_3'UTR			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	1107										breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		CACAACAAAGGATGAAAGAAA	0.323													G|||	487	0.0972444	0.3366	0.0288	5008	,	,		19033	0.0159		0.002	False		,,,				2504	0.0041				p.R1108S		Atlas-SNP	.											.	CCDC18	93	.	0			c.G3324T						PASS	.	G	SER/ARG	1093,2575		157,779,898	125.0	131.0	129.0		3324	0.4	1.0	1	dbSNP_129	129	13,8157		1,11,4073	yes	missense	CCDC18	NM_206886.3	110	158,790,4971	TT,TG,GG		0.1591,29.7983,9.3428	benign	1108/1300	93720153	1106,10732	1834	4085	5919	SO:0001583	missense	343099	exon24			ACAAAGGATGAAA			1p22.1	2008-02-05			ENSG00000122483	ENSG00000122483			30370	protein-coding gene	gene with protein product						12601173	Standard	XM_006710609		Approved	NY-SAR-41	uc021opx.1	Q5T9S5	OTTHUMG00000010598	ENST00000343253.7:c.3321G>T	1.37:g.93720153G>T	ENSP00000343377:p.Arg1107Ser	217.0	0.0	0		200.0	90.0	0.45	NM_206886	Q6ZU17	Missense_Mutation	SNP	ENST00000343253.7	37		175|175	0.08012820512820513|0.08012820512820513	150|150	0.3048780487804878|0.3048780487804878	12|12	0.03314917127071823|0.03314917127071823	11|11	0.019230769230769232|0.019230769230769232	2|2	0.002638522427440633|0.002638522427440633	G|G	5.074|5.074	0.199375|0.199375	0.09652|0.09652	0.297983|0.297983	0.001591|0.001591	ENSG00000122483|ENSG00000122483	ENST00000370276|ENST00000343253;ENST00000401026;ENST00000557479	.|.	.|.	.|.	5.02|5.02	0.449|0.449	0.16619|0.16619	.|.	.|0.782786	.|0.12361	.|N	.|0.475673	T|T	0.06462|0.06462	0.0166|0.0166	N|N	0.12182|0.12182	0.205|0.205	0.09310|0.09310	P|P	0.99999902352|0.99999902352	.|P;B	.|0.35575	.|0.51;0.006	.|B;B	.|0.36666	.|0.23;0.005	T|T	0.30149|0.30149	-0.9988|-0.9988	4|8	.|0.21540	.|T	.|0.41	.|.	5.0771|5.0771	0.14638|0.14638	0.5374:0.1787:0.2838:0.0|0.5374:0.1787:0.2838:0.0	rs61729705|rs61729705	.|26;1226	.|Q5T9S4;G3V388	.|.;.	V|S	1161|1107;1108;1226	.|.	.|ENSP00000343377:R1107S	G|R	+|+	2|3	0|2	CCDC18|CCDC18	93492741|93492741	1.000000|1.000000	0.71417|0.71417	0.977000|0.977000	0.42913|0.42913	0.453000|0.453000	0.32348|0.32348	0.703000|0.703000	0.25646|0.25646	0.243000|0.243000	0.21327|0.21327	-0.143000|-0.143000	0.13931|0.13931	GGA|AGG	A|0.000;G|0.947;T|0.053	0.053	strong		0.323	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886	
MAPK10	5602	hgsc.bcm.edu	37	4	86950354	86950354	+	Silent	SNP	A	A	G	rs148438622	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:86950354A>G	ENST00000359221.3	-	13	1774	c.1248T>C	c.(1246-1248)ccT>ccC	p.P416P	MAPK10_ENST00000395157.3_Silent_p.P271P|MAPK10_ENST00000395166.1_Silent_p.P378P|MAPK10_ENST00000395161.2_Silent_p.P416P|MAPK10_ENST00000395169.3_Silent_p.P378P|MAPK10_ENST00000395160.3_Silent_p.P271P|MAPK10_ENST00000361569.2_Silent_p.P416P|MAPK10_ENST00000449047.2_Silent_p.P271P			P53779	MK10_HUMAN	mitogen-activated protein kinase 10	416					activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|JUN phosphorylation (GO:0007258)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|JUN kinase activity (GO:0004705)|MAP kinase kinase activity (GO:0004708)			breast(1)|central_nervous_system(1)|stomach(1)	3		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.243)		OV - Ovarian serous cystadenocarcinoma(123;0.002)		GAGTACCTGAAGGAGAAGGCT	0.353																																					p.P416P		Atlas-SNP	.											MAPK10_ENST00000449047,colon,carcinoma,-2,2	MAPK10	106	2	0			c.T1248C						PASS	.	A	,,,	5,4401	11.4+/-27.6	0,5,2198	215.0	200.0	205.0		1248,1134,813,1248	6.0	1.0	4	dbSNP_134	205	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MAPK10	NM_002753.3,NM_138980.2,NM_138981.2,NM_138982.2	,,,	0,5,6498	GG,GA,AA		0.0,0.1135,0.0384	,,,	416/423,378/427,271/278,416/465	86950354	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	5602	exon13			ACCTGAAGGAGAA	U07620	CCDS3612.1, CCDS3613.1, CCDS34026.1, CCDS43247.1	4q22-q23	2011-06-09			ENSG00000109339	ENSG00000109339	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinases"""	6872	protein-coding gene	gene with protein product		602897		PRKM10		8654373, 12436199	Standard	NM_002753		Approved	JNK3, p493F12, p54bSAPK	uc003hpt.3	P53779	OTTHUMG00000130604	ENST00000359221.3:c.1248T>C	4.37:g.86950354A>G		103.0	0.0	0		100.0	45.0	0.45	NM_002753	A6NFS3|A6NG28|B3KQ94|Q15707|Q49AP1	Silent	SNP	ENST00000359221.3	37	CCDS34026.1	.	.	.	.	.	.	.	.	.	.	A	10.37	1.331983	0.24167	0.001135	0.0	ENSG00000109339	ENST00000515400	.	.	.	5.96	5.96	0.96718	.	.	.	.	.	T	0.63850	0.2546	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62955	-0.6744	4	.	.	.	-10.1507	11.1954	0.48709	0.9281:0.0:0.0718:0.0	.	.	.	.	L	329	.	.	F	-	1	0	MAPK10	87169378	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.314000	0.51943	2.278000	0.76064	0.533000	0.62120	TTC	A|1.000;G|0.000	0.000	strong		0.353	MAPK10-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000361363.2		
ACVR1B	91	hgsc.bcm.edu	37	12	52370181	52370181	+	Silent	SNP	G	G	A	rs115556161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52370181G>A	ENST00000257963.4	+	3	479	c.402G>A	c.(400-402)ccG>ccA	p.P134P	ACVR1B_ENST00000415850.2_Silent_p.P134P|ACVR1B_ENST00000541224.1_Silent_p.P134P|ACVR1B_ENST00000542485.1_Silent_p.P82P|ACVR1B_ENST00000426655.2_Silent_p.P134P	NM_004302.4|NM_020328.3	NP_004293.1|NP_064733.3	P36896	ACV1B_HUMAN	activin A receptor, type IB	134					activin receptor signaling pathway (GO:0032924)|central nervous system development (GO:0007417)|development of primary female sexual characteristics (GO:0046545)|extrinsic apoptotic signaling pathway (GO:0097191)|G1/S transition of mitotic cell cycle (GO:0000082)|hair follicle development (GO:0001942)|in utero embryonic development (GO:0001701)|negative regulation of cell growth (GO:0030308)|nodal signaling pathway (GO:0038092)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of activin receptor signaling pathway (GO:0032927)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of trophoblast cell migration (GO:1901165)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	activin receptor activity, type I (GO:0016361)|ATP binding (GO:0005524)|inhibin binding (GO:0034711)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|SMAD binding (GO:0046332)|transforming growth factor beta-activated receptor activity (GO:0005024)|transmembrane receptor protein serine/threonine kinase activity (GO:0004675)|ubiquitin protein ligase binding (GO:0031625)			breast(5)|endometrium(4)|kidney(5)|large_intestine(12)|lung(10)|ovary(1)|pancreas(6)|prostate(1)	44				BRCA - Breast invasive adenocarcinoma(357;0.104)	Adenosine triphosphate(DB00171)	TCGCCGGCCCGGTGTTCCTCC	0.542													G|||	30	0.00599042	0.0219	0.0014	5008	,	,		19147	0.0		0.0	False		,,,				2504	0.0				p.P134P		Atlas-SNP	.											.	ACVR1B	167	.	0			c.G402A						PASS	.	G	,,	52,4354	52.9+/-88.7	0,52,2151	162.0	157.0	159.0		402,246,402	-10.8	0.7	12	dbSNP_132	159	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	ACVR1B	NM_004302.4,NM_020327.3,NM_020328.3	,,	0,53,6450	AA,AG,GG		0.0116,1.1802,0.4075	,,	134/506,82/454,134/547	52370181	53,12953	2203	4300	6503	SO:0001819	synonymous_variant	91	exon3			CGGCCCGGTGTTC		CCDS8816.1, CCDS44893.1, CCDS44894.1, CCDS44893.2, CCDS44894.2	12q13	2006-11-09			ENSG00000135503	ENSG00000135503			172	protein-coding gene	gene with protein product		601300		ACVRLK4		8397373	Standard	NM_020327		Approved	ALK4, SKR2, ActRIB	uc010snn.2	P36896	OTTHUMG00000167920	ENST00000257963.4:c.402G>A	12.37:g.52370181G>A		154.0	0.0	0		167.0	85.0	0.508982	NM_020328	B7Z5L8|B7Z5W5|Q15479|Q15480|Q15481|Q15482	Silent	SNP	ENST00000257963.4	37	CCDS8816.1																																																																																			G|0.994;A|0.006	0.006	strong		0.542	ACVR1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397000.1	NM_020328	
RAB4A	5867	hgsc.bcm.edu	37	1	229431613	229431613	+	Silent	SNP	T	T	C	rs114366150	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229431613T>C	ENST00000366690.4	+	4	454	c.246T>C	c.(244-246)taT>taC	p.Y82Y	RAB4A_ENST00000473894.1_3'UTR	NM_004578.2	NP_004569.2	P20338	RAB4A_HUMAN	RAB4A, member RAS oncogene family	82					antigen processing and presentation (GO:0019882)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|regulation of endocytosis (GO:0030100)|small GTPase mediated signal transduction (GO:0007264)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|vesicle (GO:0031982)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|protein transporter activity (GO:0008565)			central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(6)|ovary(1)|skin(1)	11	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.178)				CGAGAAGTTATTACCGAGGCG	0.522													T|||	9	0.00179712	0.0053	0.0029	5008	,	,		18011	0.0		0.0	False		,,,				2504	0.0				p.Y82Y	Esophageal Squamous(11;250 603 9619 16563)	Atlas-SNP	.											.	RAB4A	29	.	0			c.T246C						PASS	.	T		34,4372	39.2+/-71.8	0,34,2169	76.0	78.0	77.0		246	-5.4	0.8	1	dbSNP_132	77	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RAB4A	NM_004578.2		0,35,6468	CC,CT,TT		0.0116,0.7717,0.2691		82/219	229431613	35,12971	2203	4300	6503	SO:0001819	synonymous_variant	5867	exon4			AAGTTATTACCGA	BC004309	CCDS31050.1, CCDS73046.1	1q42-q43	2014-04-03		2002-02-28	ENSG00000168118	ENSG00000168118		"""RAB, member RAS oncogene"""	9781	protein-coding gene	gene with protein product		179511		RAB4			Standard	NM_004578		Approved	HRES-1/RAB4	uc001hth.4	P20338	OTTHUMG00000037627	ENST00000366690.4:c.246T>C	1.37:g.229431613T>C		68.0	0.0	0		96.0	41.0	0.427083	NM_004578	Q5T7P7|Q9BQ44	Silent	SNP	ENST00000366690.4	37	CCDS31050.1																																																																																			T|0.998;C|0.002	0.002	strong		0.522	RAB4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091727.3	NM_004578	
CCDC102B	79839	hgsc.bcm.edu	37	18	66678192	66678192	+	Missense_Mutation	SNP	G	G	C	rs9963788	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:66678192G>C	ENST00000360242.5	+	7	1402	c.1285G>C	c.(1285-1287)Gcc>Ccc	p.A429P	CCDC102B_ENST00000584156.1_Missense_Mutation_p.A429P|CCDC102B_ENST00000319445.6_Missense_Mutation_p.A429P	NM_024781.2	NP_079057	Q68D86	C102B_HUMAN	coiled-coil domain containing 102B	429			A -> P (in dbSNP:rs9963788).							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)				CCTTCAACATGCCTACTATAA	0.323													G|||	354	0.0706869	0.2572	0.0202	5008	,	,		17747	0.0		0.0	False		,,,				2504	0.0				p.A429P		Atlas-SNP	.											.	CCDC102B	92	.	0			c.G1285C						PASS	.	G	PRO/ALA,PRO/ALA	913,3493	333.9+/-303.2	116,681,1406	68.0	66.0	67.0		1285,1285	4.5	0.1	18	dbSNP_119	67	9,8591	4.3+/-15.6	0,9,4291	yes	missense,missense	CCDC102B	NM_001093729.1,NM_024781.2	27,27	116,690,5697	CC,CG,GG		0.1047,20.7217,7.089	probably-damaging,probably-damaging	429/514,429/514	66678192	922,12084	2203	4300	6503	SO:0001583	missense	79839	exon9			CAACATGCCTACT	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.1285G>C	18.37:g.66678192G>C	ENSP00000353377:p.Ala429Pro	97.0	0.0	0		104.0	104.0	1	NM_001093729	Q7Z467|Q8NDK7|Q9H5C1	Missense_Mutation	SNP	ENST00000360242.5	37	CCDS11996.2	127	0.05815018315018315	122	0.24796747967479674	5	0.013812154696132596	0	0.0	0	0.0	G	12.64	1.997195	0.35226	0.207217	0.001047	ENSG00000150636	ENST00000319445;ENST00000360242	T;T	0.12879	2.64;2.64	5.4	4.53	0.55603	.	0.266261	0.26851	N	0.022162	T	0.00012	0.0000	L	0.46157	1.445	0.09310	P	1.0	D	0.89917	1.0	D	0.66979	0.948	T	0.21759	-1.0236	9	0.59425	D	0.04	-2.2619	9.8768	0.41209	0.0944:0.0:0.9056:0.0	rs9963788;rs52813873;rs59666069;rs9963788	429	Q68D86	C102B_HUMAN	P	429	ENSP00000316237:A429P;ENSP00000353377:A429P	ENSP00000316237:A429P	A	+	1	0	CCDC102B	64829172	0.997000	0.39634	0.131000	0.22000	0.981000	0.71138	3.552000	0.53705	1.276000	0.44395	0.650000	0.86243	GCC	G|0.928;C|0.072	0.072	strong		0.323	CCDC102B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256225.2	NM_024781	
ITGA2B	3674	hgsc.bcm.edu	37	17	42457087	42457087	+	Silent	SNP	C	C	T	rs79289329	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:42457087C>T	ENST00000262407.5	-	18	1879	c.1848G>A	c.(1846-1848)gtG>gtA	p.V616V	ITGA2B_ENST00000353281.4_Silent_p.V616V	NM_000419.3	NP_000410.2	P08514	ITA2B_HUMAN	integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41)	616					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of leukocyte migration (GO:0002687)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)	extracellular matrix binding (GO:0050840)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			biliary_tract(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(8)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.191)	Abciximab(DB00054)|Tirofiban(DB00775)	CTCCATGCAGCACGACAGCAG	0.607													C|||	26	0.00519169	0.0174	0.0043	5008	,	,		19396	0.0		0.0	False		,,,				2504	0.0				p.V616V		Atlas-SNP	.											.	ITGA2B	88	.	0			c.G1848A						PASS	.	C		70,4336	61.7+/-98.7	0,70,2133	109.0	106.0	107.0		1848	1.2	0.9	17	dbSNP_132	107	0,8600		0,0,4300	no	coding-synonymous	ITGA2B	NM_000419.3		0,70,6433	TT,TC,CC		0.0,1.5887,0.5382		616/1040	42457087	70,12936	2203	4300	6503	SO:0001819	synonymous_variant	3674	exon18			ATGCAGCACGACA		CCDS32665.1	17q21.32	2014-09-17	2006-02-22			ENSG00000005961		"""CD molecules"", ""Integrins"""	6138	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 93"""	607759	"""integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41B)"""	GP2B			Standard	NM_000419		Approved	CD41B, CD41, PPP1R93	uc002igt.1	P08514		ENST00000262407.5:c.1848G>A	17.37:g.42457087C>T		107.0	0.0	0		116.0	52.0	0.448276	NM_000419	B2RCY8|O95366|Q14443|Q17R67	Silent	SNP	ENST00000262407.5	37	CCDS32665.1																																																																																			C|0.994;T|0.006	0.006	strong		0.607	ITGA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439823.1		
AFF4	27125	hgsc.bcm.edu	37	5	132232148	132232148	+	Missense_Mutation	SNP	C	C	G	rs138811630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:132232148C>G	ENST00000265343.5	-	11	2553	c.2174G>C	c.(2173-2175)aGa>aCa	p.R725T	AFF4_ENST00000378595.3_Missense_Mutation_p.R725T	NM_014423.3	NP_055238.1	Q9UHB7	AFF4_HUMAN	AF4/FMR2 family, member 4	725					spermatid development (GO:0007286)|transcription from RNA polymerase II promoter (GO:0006366)	mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	sequence-specific DNA binding transcription factor activity (GO:0003700)		SEPT8/AFF4(2)	breast(2)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(7)|lung(11)|ovary(3)|pancreas(1)|prostate(3)|skin(2)	43		all_cancers(142;0.145)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TCCTGGTATTCTAGTCAAAAG	0.453													C|||	2	0.000399361	0.0015	0.0	5008	,	,		18395	0.0		0.0	False		,,,				2504	0.0				p.R725T	Ovarian(126;889 1733 2942 10745 11605)	Atlas-SNP	.											.	AFF4	120	.	0			c.G2174C						PASS	.	C	THR/ARG	8,4398	12.9+/-30.5	0,8,2195	125.0	125.0	125.0		2174	4.9	1.0	5	dbSNP_134	125	0,8600		0,0,4300	yes	missense	AFF4	NM_014423.3	71	0,8,6495	GG,GC,CC		0.0,0.1816,0.0615	probably-damaging	725/1164	132232148	8,12998	2203	4300	6503	SO:0001583	missense	27125	exon11			GGTATTCTAGTCA	AF197927	CCDS4164.1	5q31	2006-04-28			ENSG00000072364	ENSG00000072364			17869	protein-coding gene	gene with protein product	"""ALL1 fused gene from 5q31"""	604417				10588740	Standard	XM_005271963		Approved	AF5Q31, MCEF	uc003kyd.3	Q9UHB7	OTTHUMG00000059838	ENST00000265343.5:c.2174G>C	5.37:g.132232148C>G	ENSP00000265343:p.Arg725Thr	173.0	0.0	0		196.0	89.0	0.454082	NM_014423	B2RP19|B7WPD2|Q498B2|Q59FB3|Q6P592|Q8TDR1|Q9P0E4	Missense_Mutation	SNP	ENST00000265343.5	37	CCDS4164.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	21.2	4.115328	0.77323	0.001816	0.0	ENSG00000072364	ENST00000265343;ENST00000378595	T;T	0.78481	-1.18;-1.18	4.9	4.9	0.64082	.	0.000000	0.85682	D	0.000000	D	0.89385	0.6700	M	0.85777	2.775	0.58432	D	0.999998	D;D	0.67145	0.996;0.991	D;D	0.77557	0.99;0.987	D	0.91090	0.4906	10	0.72032	D	0.01	-16.5422	18.443	0.90673	0.0:1.0:0.0:0.0	.	725;725	Q9UHB7-2;Q9UHB7	.;AFF4_HUMAN	T	725	ENSP00000265343:R725T;ENSP00000367858:R725T	ENSP00000265343:R725T	R	-	2	0	AFF4	132260047	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.593000	0.82686	2.417000	0.82017	0.563000	0.77884	AGA	C|0.999;G|0.001	0.001	strong		0.453	AFF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133049.1	NM_014423	
CCDC116	164592	hgsc.bcm.edu	37	22	21991224	21991224	+	Silent	SNP	C	C	T	rs45533832	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:21991224C>T	ENST00000292779.3	+	5	1868	c.1707C>T	c.(1705-1707)acC>acT	p.T569T		NM_152612.2	NP_689825.2	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	0										endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(5)	22	Colorectal(54;0.105)					CTGCCTGCACCGGCATGGGTT	0.577													C|||	124	0.0247604	0.0893	0.0086	5008	,	,		20745	0.0		0.0	False		,,,				2504	0.0				p.T569T		Atlas-SNP	.											.	CCDC116	56	.	0			c.C1707T						PASS	.	C		279,4127	155.5+/-188.7	7,265,1931	77.0	78.0	78.0		1707	-7.8	0.0	22	dbSNP_127	78	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	CCDC116	NM_152612.2		7,269,6227	TT,TC,CC		0.0465,6.3323,2.1759		569/614	21991224	283,12723	2203	4300	6503	SO:0001819	synonymous_variant	164592	exon5			CTGCACCGGCATG	BC033499	CCDS13791.1	22q11.21	2006-06-27			ENSG00000161180	ENSG00000161180			26688	protein-coding gene	gene with protein product						12477932	Standard	NM_152612		Approved	FLJ36046	uc002zve.3	Q8IYX3	OTTHUMG00000150821	ENST00000292779.3:c.1707C>T	22.37:g.21991224C>T		87.0	0.0	0		90.0	44.0	0.488889	NM_152612	Q8N9Y9	Silent	SNP	ENST00000292779.3	37	CCDS13791.1																																																																																			C|0.974;T|0.026	0.026	strong		0.577	CCDC116-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320199.1	NM_152612	
MSH2	4436	hgsc.bcm.edu	37	2	47637246	47637246	+	Missense_Mutation	SNP	A	A	G	rs17217772|rs63751227|rs63750924	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:47637246A>G	ENST00000233146.2	+	3	603	c.380A>G	c.(379-381)aAt>aGt	p.N127S	MSH2_ENST00000406134.1_Missense_Mutation_p.N127S|MSH2_ENST00000543555.1_Missense_Mutation_p.N61S	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	127			N -> S (in HNPCC1; shows significantly decreased repair efficiency when associated with variant Pro-328; presumed to enhance cancer risk considerably when associated with Pro-328; this concomitant defect with another variant could explain its recurrent occurrence in CRC patients; dbSNP:rs17217772). {ECO:0000269|PubMed:12655564, ECO:0000269|Ref.9}.		ATP catabolic process (GO:0006200)|B cell differentiation (GO:0030183)|B cell mediated immunity (GO:0019724)|cell cycle arrest (GO:0007050)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|intra-S DNA damage checkpoint (GO:0031573)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|isotype switching (GO:0045190)|maintenance of DNA repeat elements (GO:0043570)|male gonad development (GO:0008584)|meiotic gene conversion (GO:0006311)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reciprocal meiotic recombination (GO:0045128)|oxidative phosphorylation (GO:0006119)|positive regulation of helicase activity (GO:0051096)|postreplication repair (GO:0006301)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSalpha complex (GO:0032301)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|guanine/thymine mispair binding (GO:0032137)|heteroduplex DNA loop binding (GO:0000404)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|Y-form DNA binding (GO:0000403)	p.0?(2)|p.?(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(5)|large_intestine(50)|lung(18)|ovary(5)|prostate(2)|skin(3)|small_intestine(1)|stomach(2)|urinary_tract(1)	112		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TCTCCTGGCAATctctctcag	0.333			"""D, Mis, N, F, S"""		"""colorectal, endometrial, ovarian"""	"""colorectal, endometrial, ovarian"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				A|||	124	0.0247604	0.087	0.0115	5008	,	,		17721	0.0		0.001	False		,,,				2504	0.0				p.N127S		Atlas-SNP	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p22-p21	4436	mutS homolog 2 (E. coli)		E	.	MSH2	198	.	3	Whole gene deletion(2)|Unknown(1)	haematopoietic_and_lymphoid_tissue(3)	c.A380G	GRCh37	CD982801|CM011415|CM081337	MSH2	D|M	rs17217772	PASS	.	A	SER/ASN	339,4067	176.2+/-205.4	17,305,1881	178.0	180.0	180.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	380	4.6	1.0	2	dbSNP_123	180	4,8596	3.7+/-12.6	0,4,4296	no	missense	MSH2	NM_000251.1	46	17,309,6177	GG,GA,AA		0.0465,7.6941,2.6372	possibly-damaging	127/935	47637246	343,12663	2203	4300	6503	SO:0001583	missense	4436	exon3	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	CTGGCAATCTCTC	U03911	CCDS1834.1, CCDS58709.1	2p21	2014-09-17	2013-09-12		ENSG00000095002	ENSG00000095002			7325	protein-coding gene	gene with protein product		609309	"""mutS (E. coli) homolog 2 (colon cancer, nonpolyposis type 1)"", ""mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)"""	COCA1		8484120, 9843200	Standard	NM_000251		Approved	HNPCC, HNPCC1	uc002rvy.2	P43246	OTTHUMG00000128861	ENST00000233146.2:c.380A>G	2.37:g.47637246A>G	ENSP00000233146:p.Asn127Ser	103.0	0.0	0		88.0	44.0	0.5	NM_000251	B4E2Z2|O75488	Missense_Mutation	SNP	ENST00000233146.2	37	CCDS1834.1	41|41	0.018772893772893772|0.018772893772893772	36|36	0.07317073170731707|0.07317073170731707	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	A|A	15.07|15.07	2.724903|2.724903	0.48833|0.48833	0.076941|0.076941	4.65E-4|4.65E-4	ENSG00000095002|ENSG00000095002	ENST00000413880|ENST00000233146;ENST00000454849;ENST00000543555;ENST00000406134;ENST00000419559;ENST00000432737;ENST00000453755;ENST00000448533;ENST00000394792	.|D;D;D;D	.|0.89485	.|-2.52;-2.52;-2.52;-2.52	5.73|5.73	4.59|4.59	0.56863|0.56863	.|DNA mismatch repair protein MutS-like, N-terminal (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.62551|0.62551	0.2437|0.2437	M|M	0.93150|0.93150	3.385|3.385	0.80722|0.80722	D|D	1|1	.|P;P	.|0.51057	.|0.941;0.912	.|P;P	.|0.60068	.|0.812;0.868	T|T	0.77913|0.77913	-0.2410|-0.2410	6|10	0.18276|0.87932	T|D	0.48|0	-16.5115|-16.5115	11.6216|11.6216	0.51121|0.51121	0.9307:0.0:0.0693:0.0|0.9307:0.0:0.0693:0.0	rs17217772;rs60111901|rs17217772;rs60111901	.|127;127	.|E9PHA6;P43246	.|.;MSH2_HUMAN	V|S	13|127;61;61;127;127;127;127;127;127	.|ENSP00000233146:N127S;ENSP00000411482:N61S;ENSP00000442697:N61S;ENSP00000384199:N127S	ENSP00000402969:I13V|ENSP00000233146:N127S	I|N	+|+	1|2	0|0	MSH2|MSH2	47490750|47490750	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.064000|0.064000	0.16182|0.16182	9.227000|9.227000	0.95236|0.95236	1.008000|1.008000	0.39264|0.39264	-0.322000|-0.322000	0.08575|0.08575	ATC|AAT	A|0.965;G|0.035	0.035	strong		0.333	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3		
LRRC71	149499	hgsc.bcm.edu	37	1	156902678	156902678	+	Missense_Mutation	SNP	G	G	A	rs11264585	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156902678G>A	ENST00000337428.7	+	15	1751	c.1597G>A	c.(1597-1599)Gcc>Acc	p.A533T	ARHGEF11_ENST00000487682.1_5'Flank|LRRC71_ENST00000490146.1_3'UTR	NM_144702.2	NP_653303.2	Q8N4P6	LRC71_HUMAN	leucine rich repeat containing 71	533			A -> T (in dbSNP:rs11264585).							endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|stomach(1)	12						TCCTGCGTACGCCATAATCCA	0.498													G|||	121	0.0241613	0.0862	0.0101	5008	,	,		18240	0.0		0.0	False		,,,				2504	0.0				p.A533T		Atlas-SNP	.											.	LRRC71	33	.	0			c.G1597A						PASS	.	G	THR/ALA	265,3689		9,247,1721	48.0	46.0	47.0		1597	-11.0	0.0	1	dbSNP_120	47	3,8317		0,3,4157	yes	missense	LRRC71	NM_144702.2	58	9,250,5878	AA,AG,GG		0.0361,6.7021,2.1835	benign	533/560	156902678	268,12006	1977	4160	6137	SO:0001583	missense	149499	exon15			GCGTACGCCATAA	BC033790	CCDS44249.1	1q23.1	2011-02-14	2011-02-14	2011-02-14	ENSG00000160838	ENSG00000160838			26556	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 92"""	C1orf92		14702039	Standard	NM_144702		Approved	FLJ32884	uc001fqm.2	Q8N4P6	OTTHUMG00000041298	ENST00000337428.7:c.1597G>A	1.37:g.156902678G>A	ENSP00000336661:p.Ala533Thr	98.0	0.0	0		115.0	57.0	0.495652	NM_144702	Q96M24	Missense_Mutation	SNP	ENST00000337428.7	37	CCDS44249.1	34	0.015567765567765568	28	0.056910569105691054	6	0.016574585635359115	0	0.0	0	0.0	G	1.828	-0.470466	0.04445	0.067021	3.61E-4	ENSG00000160838	ENST00000337428	T	0.18810	2.19	5.48	-11.0	0.00169	.	1.768440	0.02711	N	0.112830	T	0.01695	0.0054	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22417	-1.0217	10	0.12766	T	0.61	-0.0908	4.8021	0.13301	0.2877:0.1877:0.4323:0.0923	rs11264585;rs52828876;rs11264585	533	Q8N4P6	LRC71_HUMAN	T	533	ENSP00000336661:A533T	ENSP00000336661:A533T	A	+	1	0	LRRC71	155169302	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.651000	0.05372	-2.183000	0.00763	-1.149000	0.01842	GCC	G|0.981;A|0.019	0.019	strong		0.498	LRRC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098961.1	NM_144702	
MERTK	10461	hgsc.bcm.edu	37	2	112740561	112740561	+	Silent	SNP	A	A	G	rs115203717	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:112740561A>G	ENST00000295408.4	+	8	1544	c.1287A>G	c.(1285-1287)gcA>gcG	p.A429A	MERTK_ENST00000421804.2_Silent_p.A429A|MERTK_ENST00000409780.1_Silent_p.A253A			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	429	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|leukocyte migration (GO:0050900)|natural killer cell differentiation (GO:0001779)|negative regulation of lymphocyte activation (GO:0051250)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of phagocytosis (GO:0050766)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|secretion by cell (GO:0032940)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|rhabdomere (GO:0016028)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(10)	46						GGCAGAGTGCAGGGATTTCCG	0.448													A|||	28	0.00559105	0.0197	0.0029	5008	,	,		19646	0.0		0.0	False		,,,				2504	0.0				p.A429A		Atlas-SNP	.											.	MERTK	112	.	0			c.A1287G						PASS	.	A		48,4358	50.9+/-86.3	1,46,2156	111.0	106.0	108.0		1287	-9.6	0.0	2	dbSNP_132	108	0,8600		0,0,4300	no	coding-synonymous	MERTK	NM_006343.2		1,46,6456	GG,GA,AA		0.0,1.0894,0.3691		429/1000	112740561	48,12958	2203	4300	6503	SO:0001819	synonymous_variant	10461	exon8			GAGTGCAGGGATT	U08023	CCDS2094.1	2q14.1	2014-06-26	2014-06-26		ENSG00000153208	ENSG00000153208		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7027	protein-coding gene	gene with protein product		604705	"""c-mer proto-oncogene tyrosine kinase"""			8086340, 10343112	Standard	XM_005263565		Approved	mer, RP38	uc002thk.1	Q12866	OTTHUMG00000131278	ENST00000295408.4:c.1287A>G	2.37:g.112740561A>G		151.0	0.0	0		123.0	54.0	0.439024	NM_006343	Q9HBB4	Silent	SNP	ENST00000295408.4	37	CCDS2094.1																																																																																			A|0.995;G|0.005	0.005	strong		0.448	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2		
COL6A6	131873	hgsc.bcm.edu	37	3	130289687	130289687	+	Silent	SNP	C	C	T	rs59562634	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:130289687C>T	ENST00000358511.6	+	6	2458	c.2427C>T	c.(2425-2427)gaC>gaT	p.D809D	COL6A6_ENST00000453409.2_Silent_p.D809D	NM_001102608.1	NP_001096078.1	A6NMZ7	CO6A6_HUMAN	collagen, type VI, alpha 6	809	Nonhelical region.|VWFA 5. {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 matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				NS(2)|breast(5)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(30)|lung(57)|ovary(8)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	134						AAGTTTTAGACGTTGTGTTTG	0.388													T|||	352	0.0702875	0.2526	0.0245	5008	,	,		20800	0.0		0.001	False		,,,				2504	0.0				p.D809D		Atlas-SNP	.											.	COL6A6	497	.	0			c.C2427T						PASS	.	T		838,2942		86,666,1138	85.0	88.0	87.0		2427	-7.7	0.0	3	dbSNP_129	87	16,8238		0,16,4111	no	coding-synonymous	COL6A6	NM_001102608.1		86,682,5249	TT,TC,CC		0.1938,22.1693,7.0966		809/2264	130289687	854,11180	1890	4127	6017	SO:0001819	synonymous_variant	131873	exon6			TTTAGACGTTGTG	AL713792	CCDS46911.1	3q22.1	2013-01-16			ENSG00000206384	ENSG00000206384		"""Collagens"""	27023	protein-coding gene	gene with protein product							Standard	NM_001102608		Approved		uc010htl.3	A6NMZ7	OTTHUMG00000159653	ENST00000358511.6:c.2427C>T	3.37:g.130289687C>T		76.0	0.0	0		75.0	74.0	0.986667	NM_001102608	A7DZQ0|A7DZQ1|A7DZQ2|Q69YT0	Silent	SNP	ENST00000358511.6	37	CCDS46911.1																																																																																			C|0.945;T|0.055	0.055	strong		0.388	COL6A6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356705.5	NM_001102608	
ECSIT	51295	hgsc.bcm.edu	37	19	11618846	11618846	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11618846G>C	ENST00000270517.7	-	5	891	c.756C>G	c.(754-756)gaC>gaG	p.D252E	ECSIT_ENST00000591104.1_Missense_Mutation_p.D252E|ECSIT_ENST00000591352.1_5'UTR|ZNF653_ENST00000293771.5_5'Flank|ECSIT_ENST00000588998.1_Missense_Mutation_p.D38E|ZNF653_ENST00000593191.1_5'Flank|CTC-398G3.6_ENST00000585656.1_5'Flank|ECSIT_ENST00000252440.7_Missense_Mutation_p.D252E|ECSIT_ENST00000592312.1_Missense_Mutation_p.D136E|ECSIT_ENST00000417981.2_Missense_Mutation_p.D38E	NM_016581.4	NP_057665.2	Q9BQ95	ECSIT_HUMAN	ECSIT signalling integrator	252					BMP signaling pathway (GO:0030509)|innate immune response (GO:0045087)|mesoderm formation (GO:0001707)|oxidation-reduction process (GO:0055114)|regulation of oxidoreductase activity (GO:0051341)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	oxidoreductase activity, acting on NAD(P)H (GO:0016651)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	11						CACCTGTTGAGTCTTTGGGCA	0.552																																					p.D252E		Atlas-SNP	.											.	ECSIT	32	.	0			c.C756G						PASS	.						104.0	112.0	109.0					19																	11618846		2203	4300	6503	SO:0001583	missense	51295	exon5			TGTTGAGTCTTTG	BC005119	CCDS12262.1, CCDS45979.1, CCDS45980.1, CCDS59353.1	19p13.2	2013-05-24	2013-05-24			ENSG00000130159		"""Mitochondrial respiratory chain complex assembly factors"""	29548	protein-coding gene	gene with protein product	"""signaling intermediate in Toll pathway evolutionarily conserved ortholog (mouse)"""	608388	"""ECSIT homolog (Drosophila)"""			10465784, 22982022	Standard	NM_001142464		Approved	SITPEC	uc002msb.3	Q9BQ95		ENST00000270517.7:c.756C>G	19.37:g.11618846G>C	ENSP00000270517:p.Asp252Glu	129.0	0.0	0		143.0	76.0	0.531469	NM_001142464	E9PAN9|K7EMM0|Q96HQ7|Q9NYI1	Missense_Mutation	SNP	ENST00000270517.7	37	CCDS12262.1	.	.	.	.	.	.	.	.	.	.	G	10.47	1.360534	0.24598	.	.	ENSG00000130159	ENST00000270517;ENST00000417981;ENST00000252440	T;T;T	0.77098	-1.07;1.56;-1.07	3.81	0.321	0.15883	.	0.520943	0.20641	N	0.088408	T	0.68952	0.3057	M	0.65975	2.015	0.09310	N	1	B;B;B	0.15930	0.015;0.008;0.003	B;B;B	0.19946	0.027;0.009;0.015	T	0.54397	-0.8300	10	0.26408	T	0.33	-23.9198	5.4189	0.16390	0.117:0.4096:0.4734:0.0	.	38;252;252	E9PAN9;Q9BQ95-2;Q9BQ95	.;.;ECSIT_HUMAN	E	252;38;252	ENSP00000270517:D252E;ENSP00000412712:D38E;ENSP00000252440:D252E	ENSP00000252440:D252E	D	-	3	2	ECSIT	11479846	0.109000	0.22037	0.016000	0.15963	0.074000	0.17049	0.357000	0.20199	0.312000	0.23038	0.561000	0.74099	GAC	.	.	none		0.552	ECSIT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442603.2	NM_016581	
IL1R1	3554	hgsc.bcm.edu	37	2	102781466	102781466	+	Silent	SNP	A	A	G	rs144946641	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:102781466A>G	ENST00000410023.1	+	4	612	c.294A>G	c.(292-294)gtA>gtG	p.V98V	IL1R1_ENST00000409329.1_Silent_p.V98V|IL1R1_ENST00000233946.3_Silent_p.V98V|IL1R1_ENST00000424272.1_Silent_p.V98V|IL1R1_ENST00000409929.1_Silent_p.V98V|IL1R1_ENST00000409589.1_Silent_p.V98V|IL1R1_ENST00000409288.1_Silent_p.V98V			P14778	IL1R1_HUMAN	interleukin 1 receptor, type I	98	Ig-like C2-type 1.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|interleukin-1-mediated signaling pathway (GO:0070498)|regulation of inflammatory response (GO:0050727)|response to interleukin-1 (GO:0070555)	cell surface (GO:0009986)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type I, activating receptor activity (GO:0004909)|platelet-derived growth factor receptor binding (GO:0005161)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)	p.V98V(1)		breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|prostate(2)|skin(3)	19					Anakinra(DB00026)	ATTGCGTGGTAAGGTAAGAGA	0.358													A|||	16	0.00319489	0.0121	0.0	5008	,	,		18836	0.0		0.0	False		,,,				2504	0.0				p.V98V		Atlas-SNP	.											IL1R1,NS,carcinoma,0,1	IL1R1	52	1	1	Substitution - coding silent(1)	lung(1)	c.A294G						PASS	.	A		24,4382	30.8+/-60.4	0,24,2179	99.0	90.0	93.0		294	-5.0	0.3	2	dbSNP_134	93	0,8600		0,0,4300	no	coding-synonymous	IL1R1	NM_000877.2		0,24,6479	GG,GA,AA		0.0,0.5447,0.1845		98/570	102781466	24,12982	2203	4300	6503	SO:0001819	synonymous_variant	3554	exon3			CGTGGTAAGGTAA	M27492	CCDS2055.1, CCDS74547.1	2q12	2013-01-29			ENSG00000115594	ENSG00000115594		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5993	protein-coding gene	gene with protein product		147810		IL1R, IL1RA		1833184, 10191101	Standard	XM_005263929		Approved	D2S1473, CD121A	uc002tbr.3	P14778	OTTHUMG00000130783	ENST00000410023.1:c.294A>G	2.37:g.102781466A>G		81.0	0.0	0		93.0	44.0	0.473118	NM_000877	Q587I7	Silent	SNP	ENST00000410023.1	37	CCDS2055.1																																																																																			A|0.998;G|0.002	0.002	strong		0.358	IL1R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253299.1		
DNAH9	1770	hgsc.bcm.edu	37	17	11592928	11592928	+	Silent	SNP	C	C	T	rs35922062	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:11592928C>T	ENST00000262442.4	+	20	3857	c.3789C>T	c.(3787-3789)atC>atT	p.I1263I	DNAH9_ENST00000454412.2_Silent_p.I1263I	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	1263	Stem. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		CCAGGCACATCGAGATCCAGC	0.493													c|||	58	0.0115815	0.0424	0.0029	5008	,	,		19643	0.0		0.0	False		,,,				2504	0.0				p.I1263I		Atlas-SNP	.											.	DNAH9	695	.	0			c.C3789T						PASS	.	T		164,4242	111.6+/-149.8	6,152,2045	115.0	106.0	109.0		3789	-11.2	0.0	17	dbSNP_126	109	1,8599		0,1,4299	no	coding-synonymous	DNAH9	NM_001372.3		6,153,6344	TT,TC,CC		0.0116,3.7222,1.2686		1263/4487	11592928	165,12841	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon20			GCACATCGAGATC	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.3789C>T	17.37:g.11592928C>T		75.0	0.0	0		88.0	46.0	0.522727	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			C|0.988;T|0.012	0.012	strong		0.493	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
ZNF831	128611	hgsc.bcm.edu	37	20	57766397	57766397	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:57766397C>T	ENST00000371030.2	+	1	323	c.323C>T	c.(322-324)cCg>cTg	p.P108L		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	108	Pro-rich.						metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					GTGGGGAAGCCGGCGGCCCCT	0.701																																					p.P108L		Atlas-SNP	.											.	ZNF831	287	.	0			c.C323T						PASS	.						9.0	12.0	11.0					20																	57766397		2020	4160	6180	SO:0001583	missense	128611	exon1			GGAAGCCGGCGGC	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 174"""	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.323C>T	20.37:g.57766397C>T	ENSP00000360069:p.Pro108Leu	35.0	0.0	0		47.0	25.0	0.531915	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	37	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	C	12.91	2.079440	0.36662	.	.	ENSG00000124203	ENST00000371030	T	0.05649	3.41	5.2	3.14	0.36123	.	.	.	.	.	T	0.03739	0.0106	N	0.19112	0.55	0.09310	N	1	P	0.42908	0.793	B	0.31547	0.132	T	0.39722	-0.9600	9	0.66056	D	0.02	-0.6362	7.8433	0.29410	0.2296:0.6849:0.0:0.0855	.	108	Q5JPB2	ZN831_HUMAN	L	108	ENSP00000360069:P108L	ENSP00000360069:P108L	P	+	2	0	ZNF831	57199792	0.703000	0.27826	0.694000	0.30210	0.923000	0.55619	1.411000	0.34702	1.194000	0.43101	0.561000	0.74099	CCG	.	.	none		0.701	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457	
RGS3	5998	hgsc.bcm.edu	37	9	116356389	116356389	+	Intron	SNP	C	C	T	rs57845277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116356389C>T	ENST00000374140.2	+	23	3289				RGS3_ENST00000343817.5_Intron|RGS3_ENST00000374134.3_Intron|RGS3_ENST00000462143.1_Intron|RGS3_ENST00000394646.3_Intron|RGS3_ENST00000462403.1_Missense_Mutation_p.R64W|RGS3_ENST00000350696.5_Intron|RGS3_ENST00000342620.5_Intron	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3						inactivation of MAPK activity (GO:0000188)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						GTCCCAGCCCCGGCTTGTGCC	0.637													C|||	54	0.0107827	0.0393	0.0029	5008	,	,		15146	0.0		0.0	False		,,,				2504	0.0				p.R64W		Atlas-SNP	.											.	RGS3	251	.	0			c.C190T						PASS	.	C	,,,,TRP/ARG	146,4260		5,136,2062	66.0	74.0	71.0		,,,,190	-5.5	0.0	9	dbSNP_129	71	1,8599		0,1,4299	no	intron,intron,intron,intron,missense	RGS3	NM_021106.3,NM_130795.2,NM_134427.1,NM_144488.4,NM_144489.2	,,,,101	5,137,6361	TT,TC,CC		0.0116,3.3137,1.1302	,,,,	,,,,64/312	116356389	147,12859	2203	4300	6503	SO:0001627	intron_variant	5998	exon1			CAGCCCCGGCTTG	AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"""Regulators of G-protein signaling"""	9999	protein-coding gene	gene with protein product		602189	"""regulator of G-protein signalling 3"""			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.3081-321C>T	9.37:g.116356389C>T		273.0	0.0	0		259.0	94.0	0.362934	NM_144489	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	37	CCDS43869.1	17	0.007783882783882784	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	0	0.0	C	1.749	-0.489752	0.04352	0.033137	1.16E-4	ENSG00000138835	ENST00000462403	T	0.62232	0.04	4.25	-5.51	0.02568	.	.	.	.	.	T	0.12390	0.0301	N	0.08118	0	0.20074	N	0.999939	B	0.02656	0.0	B	0.01281	0.0	T	0.09707	-1.0662	9	0.87932	D	0	.	0.1774	0.00120	0.2449:0.2726:0.1703:0.3122	rs57845277	64	Q5VZ06	.	W	64	ENSP00000436168:R64W	ENSP00000436168:R64W	R	+	1	2	RGS3	115396210	0.000000	0.05858	0.010000	0.14722	0.220000	0.24768	-2.218000	0.01219	-1.939000	0.01044	-1.946000	0.00489	CGG	C|0.988;T|0.012	0.012	strong		0.637	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790	
CCDC132	55610	hgsc.bcm.edu	37	7	92926102	92926102	+	Missense_Mutation	SNP	A	A	G	rs374290264		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:92926102A>G	ENST00000305866.5	+	15	1344	c.1216A>G	c.(1216-1218)Ata>Gta	p.I406V	CCDC132_ENST00000317751.6_Missense_Mutation_p.I137V|CCDC132_ENST00000535481.1_Missense_Mutation_p.I126V|CCDC132_ENST00000541136.1_Missense_Mutation_p.I217V|CCDC132_ENST00000544910.1_Missense_Mutation_p.I376V	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	406						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)			TGATTTGTCTATATTCAAATA	0.294																																					p.I406V		Atlas-SNP	.											.	CCDC132	136	.	0			c.A1216G						PASS	.	A	VAL/ILE	2,3616		0,2,1807	89.0	86.0	87.0		1216	4.8	1.0	7		87	0,8124		0,0,4062	no	missense	CCDC132	NM_017667.2	29	0,2,5869	GG,GA,AA		0.0,0.0553,0.017	benign	406/965	92926102	2,11740	1809	4062	5871	SO:0001583	missense	55610	exon15			TTGTCTATATTCA	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.1216A>G	7.37:g.92926102A>G	ENSP00000307666:p.Ile406Val	67.0	0.0	0		75.0	32.0	0.426667	NM_017667	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Missense_Mutation	SNP	ENST00000305866.5	37	CCDS43617.1	.	.	.	.	.	.	.	.	.	.	A	9.350	1.065336	0.20067	5.53E-4	0.0	ENSG00000004766	ENST00000305866;ENST00000544910;ENST00000541136;ENST00000535481;ENST00000317751	T	0.41065	1.01	4.82	4.82	0.62117	.	0.178206	0.47455	D	0.000238	T	0.22205	0.0535	N	0.03608	-0.345	0.27582	N	0.949545	B;B;B	0.12630	0.001;0.006;0.0	B;B;B	0.10450	0.001;0.005;0.0	T	0.10800	-1.0614	10	0.30078	T	0.28	-3.5357	14.7032	0.69168	1.0:0.0:0.0:0.0	.	126;376;406	B4DS55;F5H5U7;Q96JG6	.;.;CC132_HUMAN	V	406;376;217;126;137	ENSP00000325582:I137V	ENSP00000307666:I406V	I	+	1	0	CCDC132	92764038	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	7.164000	0.77533	1.951000	0.56629	0.455000	0.32223	ATA	.	.	weak		0.294	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667	
CCDC130	81576	hgsc.bcm.edu	37	19	13873793	13873793	+	Missense_Mutation	SNP	C	C	A	rs138278370	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:13873793C>A	ENST00000586600.1	+	11	1605	c.1102C>A	c.(1102-1104)Cag>Aag	p.Q368K	MRI1_ENST00000040663.6_5'Flank|MRI1_ENST00000319545.8_5'Flank|CCDC130_ENST00000221554.8_Missense_Mutation_p.Q368K			P13994	CC130_HUMAN	coiled-coil domain containing 130	368					response to virus (GO:0009615)					endometrium(2)|kidney(1)|large_intestine(3)|ovary(1)|skin(2)|urinary_tract(1)	10			OV - Ovarian serous cystadenocarcinoma(19;6.02e-23)|Epithelial(5;2.58e-18)			AGGCTCCTCCCAGGAGGCAGC	0.667													C|||	22	0.00439297	0.0159	0.0014	5008	,	,		13510	0.0		0.0	False		,,,				2504	0.0				p.Q368K		Atlas-SNP	.											.	CCDC130	25	.	0			c.C1102A						PASS	.	C	LYS/GLN	82,4310		0,82,2114	14.0	17.0	16.0		1102	4.5	0.0	19	dbSNP_134	16	1,8579		0,1,4289	yes	missense	CCDC130	NM_030818.2	53	0,83,6403	AA,AC,CC		0.0117,1.867,0.6398	benign	368/397	13873793	83,12889	2196	4290	6486	SO:0001583	missense	81576	exon10			TCCTCCCAGGAGG	AF250306	CCDS12296.1	19p13.13	2008-02-05				ENSG00000104957			28118	protein-coding gene	gene with protein product						3203696	Standard	NM_030818		Approved	MGC10471	uc002mxc.1	P13994		ENST00000586600.1:c.1102C>A	19.37:g.13873793C>A	ENSP00000465776:p.Gln368Lys	52.0	0.0	0		40.0	13.0	0.325	NM_030818	Q9BQ72	Missense_Mutation	SNP	ENST00000586600.1	37	CCDS12296.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	11.27	1.590016	0.28357	0.01867	1.17E-4	ENSG00000104957	ENST00000221554	T	0.27557	1.66	4.49	4.49	0.54785	.	0.852666	0.09747	N	0.761109	T	0.13970	0.0338	L	0.57536	1.79	0.24401	N	0.994709	B;B	0.27625	0.183;0.183	B;B	0.25506	0.061;0.061	T	0.37407	-0.9707	10	0.06494	T	0.89	-10.5446	8.8286	0.35069	0.0:0.8959:0.0:0.1041	.	368;368	B3KUZ1;P13994	.;CC130_HUMAN	K	368	ENSP00000221554:Q368K	ENSP00000221554:Q368K	Q	+	1	0	CCDC130	13734793	0.003000	0.15002	0.033000	0.17914	0.220000	0.24768	0.327000	0.19663	2.230000	0.72887	0.491000	0.48974	CAG	C|0.994;A|0.006	0.006	strong		0.667	CCDC130-001	KNOWN	alternative_5_UTR|upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453216.2	NM_030818	
SLC24A1	9187	hgsc.bcm.edu	37	15	65918277	65918277	+	Missense_Mutation	SNP	C	C	T	rs35398714	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:65918277C>T	ENST00000261892.6	+	2	2146	c.1859C>T	c.(1858-1860)gCc>gTc	p.A620V	SLC24A1_ENST00000546330.1_Missense_Mutation_p.A620V|SLC24A1_ENST00000339868.6_Missense_Mutation_p.A620V|SLC24A1_ENST00000544319.2_Missense_Mutation_p.A620V|SLC24A1_ENST00000537259.1_Missense_Mutation_p.A620V|SLC24A1_ENST00000399033.4_Missense_Mutation_p.A620V	NM_001254740.1|NM_004727.2	NP_001241669.1|NP_004718.1	O60721	NCKX1_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 1	620					calcium ion transport (GO:0006816)|ion transport (GO:0006811)|phototransduction, visible light (GO:0007603)|response to light intensity (GO:0009642)|rhodopsin mediated signaling pathway (GO:0016056)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|outer membrane (GO:0019867)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			breast(2)|endometrium(7)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						AGGCCAGTGGCCAAGGTCATG	0.537													C|||	20	0.00399361	0.0151	0.0	5008	,	,		23355	0.0		0.0	False		,,,				2504	0.0				p.A620V		Atlas-SNP	.											.	SLC24A1	58	.	0			c.C1859T						PASS	.	C	VAL/ALA	40,4044		0,40,2002	101.0	98.0	99.0		1859	4.0	0.8	15	dbSNP_126	99	0,8416		0,0,4208	yes	missense	SLC24A1	NM_004727.2	64	0,40,6210	TT,TC,CC		0.0,0.9794,0.32	benign	620/1100	65918277	40,12460	2042	4208	6250	SO:0001583	missense	9187	exon2			CAGTGGCCAAGGT	AF062922	CCDS45284.1, CCDS73742.1, CCDS73743.1, CCDS73744.1	15q22.31	2014-01-28			ENSG00000074621	ENSG00000074621		"""Solute carriers"""	10975	protein-coding gene	gene with protein product		603617				9856482	Standard	NM_004727		Approved	NCKX1, NCKX, RODX, KIAA0702, HsT17412, CSNB1D	uc010ujf.2	O60721	OTTHUMG00000167960	ENST00000261892.6:c.1859C>T	15.37:g.65918277C>T	ENSP00000261892:p.Ala620Val	75.0	0.0	0		61.0	33.0	0.540984	NM_004727	O43485|O75184|Q17RM9	Missense_Mutation	SNP	ENST00000261892.6	37	CCDS45284.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	C	13.30	2.196553	0.38806	0.009794	0.0	ENSG00000074621	ENST00000537259;ENST00000261892;ENST00000339868;ENST00000544319;ENST00000399033;ENST00000546330	T;T;T;T;T;T	0.65916	0.08;-0.16;-0.15;0.12;-0.18;-0.15	6.06	3.97	0.46021	.	0.354666	0.29737	N	0.011329	T	0.33235	0.0856	L	0.35793	1.09	0.25586	N	0.986742	B;B;B;B;B	0.28026	0.084;0.051;0.051;0.198;0.125	B;B;B;B;B	0.33846	0.046;0.02;0.02;0.171;0.119	T	0.28396	-1.0045	10	0.30078	T	0.28	.	6.3771	0.21513	0.0:0.6781:0.1434:0.1785	rs35398714	620;620;620;620;620	O60721-2;Q17RM9;O60721;F5H127;B4E1W0	.;.;NCKX1_HUMAN;.;.	V	620	ENSP00000439693:A620V;ENSP00000261892:A620V;ENSP00000341837:A620V;ENSP00000445163:A620V;ENSP00000381991:A620V;ENSP00000439190:A620V	ENSP00000261892:A620V	A	+	2	0	SLC24A1	63705331	1.000000	0.71417	0.763000	0.31416	0.072000	0.16883	2.208000	0.42797	0.705000	0.31890	0.655000	0.94253	GCC	C|0.995;T|0.005	0.005	strong		0.537	SLC24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397304.1	NM_004727	
RDH8	50700	hgsc.bcm.edu	37	19	10132358	10132358	+	Missense_Mutation	SNP	G	G	A	rs142753796	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:10132358G>A	ENST00000171214.1	+	6	1118	c.869G>A	c.(868-870)cGc>cAc	p.R290H	RDH8_ENST00000591589.1_Missense_Mutation_p.R310H	NM_015725.2	NP_056540.2	Q9NYR8	RDH8_HUMAN	retinol dehydrogenase 8 (all-trans)	290					estrogen biosynthetic process (GO:0006703)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|steroid biosynthetic process (GO:0006694)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|NADP-retinol dehydrogenase activity (GO:0052650)|retinol dehydrogenase activity (GO:0004745)			endometrium(3)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|prostate(1)	21			Epithelial(33;4.24e-05)		Vitamin A(DB00162)	CGCTGTCCACGCCTCCTCAAC	0.607													G|||	3	0.000599042	0.0023	0.0	5008	,	,		17925	0.0		0.0	False		,,,				2504	0.0				p.R310H		Atlas-SNP	.											.	RDH8	51	.	0			c.G929A						PASS	.	G	HIS/ARG	7,4399	12.9+/-30.5	0,7,2196	113.0	108.0	110.0		869	0.6	1.0	19	dbSNP_134	110	0,8600		0,0,4300	yes	missense	RDH8	NM_015725.2	29	0,7,6496	AA,AG,GG		0.0,0.1589,0.0538	benign	290/312	10132358	7,12999	2203	4300	6503	SO:0001583	missense	50700	exon6			GTCCACGCCTCCT	AF229845	CCDS12223.1, CCDS12223.2	19p13.2	2011-09-14				ENSG00000080511	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	14423	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 28C, member 2"""	608575				10753906, 19027726	Standard	NM_015725		Approved	PRRDH, SDR28C2	uc002mmr.4	Q9NYR8		ENST00000171214.1:c.869G>A	19.37:g.10132358G>A	ENSP00000171214:p.Arg290His	108.0	0.0	0		95.0	54.0	0.568421	NM_015725	Q9H838	Missense_Mutation	SNP	ENST00000171214.1	37		1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	12.22	1.874004	0.33069	0.001589	0.0	ENSG00000080511	ENST00000171214	D	0.82803	-1.65	4.23	0.581	0.17407	.	0.728843	0.13435	N	0.388095	T	0.67059	0.2853	N	0.21142	0.635	0.22142	N	0.999337	B	0.11235	0.004	B	0.06405	0.002	T	0.53322	-0.8455	10	0.33940	T	0.23	.	5.0034	0.14275	0.2203:0.3107:0.469:0.0	.	290	Q9NYR8	RDH8_HUMAN	H	290	ENSP00000171214:R290H	ENSP00000171214:R290H	R	+	2	0	RDH8	9993358	0.044000	0.20184	0.991000	0.47740	0.717000	0.41224	1.418000	0.34782	0.730000	0.32425	0.297000	0.19635	CGC	G|0.999;A|0.001	0.001	strong		0.607	RDH8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			
BRSK1	84446	hgsc.bcm.edu	37	19	55823421	55823421	+	Silent	SNP	G	G	C	rs113284733	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55823421G>C	ENST00000309383.1	+	19	2599	c.2322G>C	c.(2320-2322)ggG>ggC	p.G774G	CTD-2105E13.14_ENST00000596786.1_RNA|BRSK1_ENST00000326848.7_Silent_p.G469G|BRSK1_ENST00000590333.1_Silent_p.G790G	NM_032430.1	NP_115806.1	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1	774					axonogenesis (GO:0007409)|cellular response to DNA damage stimulus (GO:0006974)|centrosome duplication (GO:0051298)|establishment of cell polarity (GO:0030010)|G2 DNA damage checkpoint (GO:0031572)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|protein phosphorylation (GO:0006468)|response to UV (GO:0009411)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(15)|ovary(2)|prostate(2)|skin(6)|stomach(1)	48		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0474)		CCACCAACGGGACCCCTCTGC	0.706													G|||	16	0.00319489	0.0113	0.0014	5008	,	,		6575	0.0		0.0	False		,,,				2504	0.0				p.G774G		Atlas-SNP	.											.	BRSK1	192	.	0			c.G2322C						PASS	.	G		13,3847		0,13,1917	6.0	7.0	7.0		2322	2.6	1.0	19	dbSNP_132	7	0,7676		0,0,3838	no	coding-synonymous	BRSK1	NM_032430.1		0,13,5755	CC,CG,GG		0.0,0.3368,0.1127		774/779	55823421	13,11523	1930	3838	5768	SO:0001819	synonymous_variant	84446	exon19			CAACGGGACCCCT	AB058714	CCDS12921.1	19q13.4	2008-02-05				ENSG00000160469			18994	protein-coding gene	gene with protein product		609235				14976552	Standard	NM_032430		Approved	KIAA1811	uc002qkg.3	Q8TDC3		ENST00000309383.1:c.2322G>C	19.37:g.55823421G>C		71.0	0.0	0		60.0	27.0	0.45	NM_032430	F1DG44|Q5J5B5|Q8NDD0|Q8NDR4|Q8TDC2|Q96AV4|Q96JL4	Silent	SNP	ENST00000309383.1	37	CCDS12921.1																																																																																			G|0.998;C|0.002	0.002	strong		0.706	BRSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452787.1	NM_032430	
ACTBL2	345651	hgsc.bcm.edu	37	5	56778213	56778213	+	Missense_Mutation	SNP	C	C	T	rs73757391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:56778213C>T	ENST00000423391.1	-	1	423	c.322G>A	c.(322-324)Gag>Aag	p.E108K	CTD-2023N9.1_ENST00000506106.1_RNA|AC025470.1_ENST00000584598.1_RNA	NM_001017992.3	NP_001017992.1	Q562R1	ACTBL_HUMAN	actin, beta-like 2	108						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(7)|ovary(3)|pancreas(1)|prostate(2)	28		Lung NSC(810;0.000135)|Prostate(74;0.055)|Breast(144;0.0707)|Ovarian(174;0.182)		OV - Ovarian serous cystadenocarcinoma(10;4.24e-37)		AGGGGTGCCTCGGTGAGGAGG	0.527													C|||	126	0.0251597	0.0946	0.0014	5008	,	,		23302	0.0		0.0	False		,,,				2504	0.0				p.E108K		Atlas-SNP	.											.	ACTBL2	65	.	0			c.G322A						PASS	.	C	LYS/GLU	340,4066	179.0+/-207.6	20,300,1883	105.0	89.0	95.0		322	4.0	0.9	5	dbSNP_130	95	2,8598	2.2+/-6.3	0,2,4298	yes	missense	ACTBL2	NM_001017992.2	56	20,302,6181	TT,TC,CC		0.0233,7.7167,2.6296	possibly-damaging	108/377	56778213	342,12664	2203	4300	6503	SO:0001583	missense	345651	exon1			GTGCCTCGGTGAG		CCDS34163.1	5q11.2	2014-08-08			ENSG00000169067	ENSG00000169067			17780	protein-coding gene	gene with protein product		614835					Standard	NM_001017992		Approved	DKFZp686D0972	uc003jrm.3	Q562R1	OTTHUMG00000162330	ENST00000423391.1:c.322G>A	5.37:g.56778213C>T	ENSP00000416706:p.Glu108Lys	169.0	0.0	0		187.0	99.0	0.529412	NM_001017992	B2RPJ1|Q562R2|Q562S9|Q562X8	Missense_Mutation	SNP	ENST00000423391.1	37	CCDS34163.1	45	0.020604395604395604	44	0.08943089430894309	1	0.0027624309392265192	0	0.0	0	0.0	C	13.74	2.327453	0.41197	0.077167	2.33E-4	ENSG00000169067	ENST00000423391	D	0.96940	-4.18	4.91	4.04	0.47022	Actin/actin-like conserved site (1);	0.000000	0.64402	D	0.000005	D	0.82774	0.5110	H	0.98295	4.195	0.48762	D	0.999703	D	0.89917	1.0	D	0.78314	0.991	T	0.76862	-0.2802	10	0.87932	D	0	.	11.3815	0.49761	0.0:0.9109:0.0:0.0891	.	108	Q562R1	ACTBL_HUMAN	K	108	ENSP00000416706:E108K	ENSP00000416706:E108K	E	-	1	0	ACTBL2	56813970	1.000000	0.71417	0.920000	0.36463	0.468000	0.32798	5.904000	0.69886	1.279000	0.44446	0.655000	0.94253	GAG	C|0.973;T|0.027	0.027	strong		0.527	ACTBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368579.1	NM_001017992	
CXorf36	79742	hgsc.bcm.edu	37	X	45059838	45059838	+	Splice_Site	SNP	C	C	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:45059838C>A	ENST00000398000.2	-	1	308		c.e1+1		RP11-342D14.1_ENST00000438181.1_RNA|CXorf36_ENST00000377934.4_Splice_Site|RP11-342D14.1_ENST00000450527.1_RNA	NM_176819.3	NP_789789.2	Q9H7Y0	DIA1R_HUMAN	chromosome X open reading frame 36							extracellular region (GO:0005576)				endometrium(1)|large_intestine(2)|lung(4)	7						GATATTCTGACCTTATTTCTT	0.368																																					.		Atlas-SNP	.											.	CXorf36	53	.	0			c.233+1G>T						PASS	.						45.0	43.0	43.0					X																	45059838		2203	4299	6502	SO:0001630	splice_region_variant	79742	exon2			TTCTGACCTTATT	AF289581	CCDS14266.1, CCDS48096.1	Xp11.3-p11.23	2012-08-03			ENSG00000147113	ENSG00000147113			25866	protein-coding gene	gene with protein product						11944989, 21283809	Standard	NM_176819		Approved	FLJ14103, DIA1R	uc004dgg.2	Q9H7Y0	OTTHUMG00000021403	ENST00000398000.2:c.233+1G>T	X.37:g.45059838C>A		155.0	0.0	0		127.0	67.0	0.527559	NM_176819	A8MUU5|B2RPN7|Q6UWJ5	Splice_Site	SNP	ENST00000398000.2	37	CCDS48096.1	.	.	.	.	.	.	.	.	.	.	C	17.24	3.340498	0.60963	.	.	ENSG00000147113	ENST00000398000;ENST00000377934	.	.	.	5.0	5.0	0.66597	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.7275	0.77774	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	CXorf36	44944782	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	5.738000	0.68613	2.074000	0.62210	0.415000	0.27848	.	.	.	none		0.368	CXorf36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056333.2	NM_024689	Intron
SPIRE2	84501	hgsc.bcm.edu	37	16	89927102	89927102	+	Missense_Mutation	SNP	G	G	A	rs28478911		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89927102G>A	ENST00000378247.3	+	10	1517	c.1474G>A	c.(1474-1476)Gcg>Acg	p.A492T	SPIRE2_ENST00000393062.2_Missense_Mutation_p.A492T	NM_032451.1	NP_115827.1	Q8WWL2	SPIR2_HUMAN	spire-type actin nucleation factor 2	492					actin cytoskeleton organization (GO:0030036)|cleavage furrow formation (GO:0036089)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|intracellular transport (GO:0046907)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasmic vesicle membrane (GO:0030659)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(10)|upper_aerodigestive_tract(2)|urinary_tract(1)	21		Lung NSC(15;5.15e-06)|all_lung(18;8.38e-06)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0286)		TACCTGTCCCGCGAGTGTCTC	0.642											OREG0024056	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	0.0008	0.0	5008	,	,		14998	0.0		0.0	False		,,,				2504	0.0				p.A492T		Atlas-SNP	.											SPIRE2,colon,carcinoma,-1,1	SPIRE2	63	1	0			c.G1474A						PASS	.	G	THR/ALA	3,4371		0,3,2184	29.0	28.0	28.0		1474	1.9	0.0	16	dbSNP_125	28	0,8572		0,0,4286	no	missense	SPIRE2	NM_032451.1	58	0,3,6470	AA,AG,GG		0.0,0.0686,0.0232	benign	492/715	89927102	3,12943	2187	4286	6473	SO:0001583	missense	84501	exon10			TGTCCCGCGAGTG	AL834408	CCDS32516.1	16q24	2013-08-27	2013-08-27			ENSG00000204991			30623	protein-coding gene	gene with protein product		609217	"""spire homolog 2 (Drosophila)"", ""spire family actin nucleation factor 2"""			11347906	Standard	NM_032451		Approved	spir-2, KIAA1832	uc002foz.1	Q8WWL2		ENST00000378247.3:c.1474G>A	16.37:g.89927102G>A	ENSP00000367494:p.Ala492Thr	67.0	0.0	0	1271	76.0	41.0	0.539474	NM_032451	A4QPB1|Q2TA98|Q6P433|Q8ND47|Q96JJ5	Missense_Mutation	SNP	ENST00000378247.3	37	CCDS32516.1	.	.	.	.	.	.	.	.	.	.	G	6.872	0.530358	0.13127	6.86E-4	0.0	ENSG00000204991	ENST00000378247;ENST00000393062	T;T	0.43688	0.95;0.94	5.08	1.87	0.25490	.	0.915637	0.09208	N	0.833668	T	0.25382	0.0617	N	0.22421	0.69	0.09310	N	0.999999	B;B;B;B	0.15719	0.001;0.014;0.008;0.001	B;B;B;B	0.10450	0.001;0.005;0.002;0.001	T	0.27571	-1.0070	10	0.15066	T	0.55	-9.4382	6.2595	0.20891	0.1685:0.1545:0.6769:0.0	rs28478911	359;492;444;492	Q8WWL2-4;Q8WWL2-2;Q8WWL2-3;Q8WWL2	.;.;.;SPIR2_HUMAN	T	492	ENSP00000367494:A492T;ENSP00000376782:A492T	ENSP00000367494:A492T	A	+	1	0	SPIRE2	88454603	0.002000	0.14202	0.001000	0.08648	0.000000	0.00434	1.200000	0.32247	0.668000	0.31126	-0.794000	0.03295	GCG	G|1.000;|0.000	.	weak		0.642	SPIRE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421843.1	XM_047462	
C2CD3	26005	hgsc.bcm.edu	37	11	73759251	73759251	+	Splice_Site	SNP	T	T	C	rs1632242|rs200356969	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:73759251T>C	ENST00000334126.7	-	28	5720	c.5494A>G	c.(5494-5496)Aga>Gga	p.R1832G	C2CD3_ENST00000313663.7_Splice_Site_p.R1832G			Q4AC94	C2CD3_HUMAN	C2 calcium-dependent domain containing 3	1832			R -> G (in dbSNP:rs1632242).		brain development (GO:0007420)|centriole elongation (GO:0061511)|embryonic digit morphogenesis (GO:0042733)|heart looping (GO:0001947)|in utero embryonic development (GO:0001701)|neural plate axis specification (GO:0021997)|neural tube development (GO:0021915)|nonmotile primary cilium assembly (GO:0035058)|protein localization to centrosome (GO:0071539)|protein processing (GO:0016485)|regulation of proteolysis (GO:0030162)|regulation of smoothened signaling pathway (GO:0008589)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)				NS(1)|breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(26)|ovary(4)|pancreas(2)|prostate(1)|skin(3)	64	Breast(11;4.16e-06)					TTCACTCACCTCCCAGGAGAG	0.438													T|||	243	0.0485224	0.1778	0.0115	5008	,	,		19079	0.0		0.0	False		,,,				2504	0.0				p.R1832G		Atlas-SNP	.											.	C2CD3	288	.	0			c.A5494G						PASS	.						56.0	52.0	53.0					11																	73759251		2200	4293	6493	SO:0001630	splice_region_variant	26005	exon28			CTCACCTCCCAGG	BC035599	CCDS31636.1, CCDS66167.1	11q13.4	2014-02-12	2007-10-17		ENSG00000168014	ENSG00000168014			24564	protein-coding gene	gene with protein product		615944					Standard	XM_005273897		Approved	DKFZP586P0123	uc001ouu.2	Q4AC94	OTTHUMG00000168110	ENST00000334126.7:c.5495+1A>G	11.37:g.73759251T>C		97.0	0.0	0		99.0	42.0	0.424242	NM_015531	C9JR55|E2QRD1|Q2NLE1|Q3C1U9|Q6ZU92|Q8IYM4|Q8NB87|Q8NDH7|Q9Y4M2	Missense_Mutation	SNP	ENST00000334126.7	37		76|76	0.0347985347985348|0.0347985347985348	71|71	0.1443089430894309|0.1443089430894309	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	0|0	0.0|0.0	T|T	11.88|11.88	1.770709|1.770709	0.31320|0.31320	.|.	.|.	ENSG00000168014|ENSG00000168014	ENST00000538361|ENST00000334126;ENST00000313663;ENST00000313681;ENST00000414160	.|T;T;T	.|0.15952	.|2.73;2.77;2.38	4.75|4.75	4.75|4.75	0.60458|0.60458	.|.	.|0.440230	.|0.27172	.|N	.|0.020590	T|T	0.00144|0.00144	0.0004|0.0004	M|M	0.72894|0.72894	2.215|2.215	0.34135|0.34135	P|P	0.334317|0.334317	.|P	.|0.35272	.|0.493	.|B	.|0.33620	.|0.167	T|T	0.09292|0.09292	-1.0681|-1.0681	4|9	.|0.44086	.|T	.|0.13	-5.0634|-5.0634	10.8098|10.8098	0.46540|0.46540	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs1632242;rs52837313;rs1632242|rs1632242;rs52837313;rs1632242	.|1832	.|Q4AC94-1	.|.	G|G	65|1832;1832;1813;640	.|ENSP00000334379:R1832G;ENSP00000323339:R1832G;ENSP00000388750:R640G	.|ENSP00000323339:R1832G	E|R	-|-	2|1	0|2	C2CD3|C2CD3	73436899|73436899	0.997000|0.997000	0.39634|0.39634	0.981000|0.981000	0.43875|0.43875	0.172000|0.172000	0.22775|0.22775	2.829000|2.829000	0.48128|0.48128	2.114000|2.114000	0.64651|0.64651	0.533000|0.533000	0.62120|0.62120	GAG|AGA	T|0.962;C|0.038	0.038	strong		0.438	C2CD3-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015531	Missense_Mutation
KIRREL3	84623	hgsc.bcm.edu	37	11	126294661	126294661	+	Silent	SNP	G	G	A	rs34844660	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:126294661G>A	ENST00000525144.2	-	17	2400	c.2151C>T	c.(2149-2151)agC>agT	p.S717S	KIRREL3_ENST00000529097.2_Silent_p.S705S|KIRREL3_ENST00000416561.2_Silent_p.S184S	NM_032531.3	NP_115920.1	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 (Drosophila)	717	Ser-rich.				hemopoiesis (GO:0030097)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(5)|large_intestine(11)|lung(8)|ovary(3)|prostate(1)	29	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		AGCTGCTGTCGCTGAGGGAGC	0.627													G|||	69	0.013778	0.0514	0.0014	5008	,	,		19048	0.0		0.0	False		,,,				2504	0.0				p.S717S		Atlas-SNP	.											.	KIRREL3	183	.	0			c.C2151T						PASS	.	G		148,4198		0,148,2025	74.0	82.0	79.0		2151	4.0	1.0	11	dbSNP_126	79	0,8562		0,0,4281	no	coding-synonymous	KIRREL3	NM_032531.3		0,148,6306	AA,AG,GG		0.0,3.4054,1.1466		717/779	126294661	148,12760	2173	4281	6454	SO:0001819	synonymous_variant	84623	exon17			GCTGTCGCTGAGG	AB058770	CCDS53723.1, CCDS55796.1, CCDS73413.1	11q24	2013-01-29			ENSG00000149571	ENSG00000149571		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	23204	protein-coding gene	gene with protein product		607761				12424224, 11347906	Standard	NM_032531		Approved	NEPH2, KIAA1867, KIRRE	uc001qea.3	Q8IZU9	OTTHUMG00000165831	ENST00000525144.2:c.2151C>T	11.37:g.126294661G>A		115.0	0.0	0		109.0	54.0	0.495413	NM_032531	Q3MIJ7|Q6UWJ9|Q6UWL5|Q96JG0	Silent	SNP	ENST00000525144.2	37	CCDS53723.1																																																																																			G|0.992;A|0.008	0.008	strong		0.627	KIRREL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386479.2	NM_032531	
DNAH17	8632	hgsc.bcm.edu	37	17	76570924	76570924	+	Silent	SNP	G	G	A	rs61745225	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:76570924G>A	ENST00000585328.1	-	2	340	c.216C>T	c.(214-216)ctC>ctT	p.L72L	DNAH17_ENST00000389840.5_Silent_p.L72L	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	72	Stem. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			CTTTGGACTTGAGGGACTGGG	0.557													G|||	358	0.0714856	0.2496	0.0375	5008	,	,		17437	0.0		0.002	False		,,,				2504	0.0				p.L72L		Atlas-SNP	.											.	DNAH17	347	.	0			c.C216T						PASS	.	G		781,3257		77,627,1315	118.0	126.0	123.0		216	4.1	1.0	17	dbSNP_129	123	15,8343		0,15,4164	no	coding-synonymous	DNAH17	NM_173628.3		77,642,5479	AA,AG,GG		0.1795,19.3413,6.4214		72/4463	76570924	796,11600	2019	4179	6198	SO:0001819	synonymous_variant	8632	exon2			GGACTTGAGGGAC	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"""Axonemal dyneins"""	2946	protein-coding gene	gene with protein product		610063	"""dynein, axonemal, heavy polypeptide 17"", ""dynein, axonemal, heavy chain like 1"", ""dynein, axonemal, heavy like 1"""	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.216C>T	17.37:g.76570924G>A		206.0	0.0	0		205.0	85.0	0.414634	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				G|0.948;A|0.052	0.052	strong		0.557	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
NFASC	23114	hgsc.bcm.edu	37	1	204939763	204939763	+	Silent	SNP	C	C	T	rs6690894	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:204939763C>T	ENST00000401399.1	+	10	1222	c.1023C>T	c.(1021-1023)gaC>gaT	p.D341D	NFASC_ENST00000404907.1_Silent_p.D352D|NFASC_ENST00000539706.1_Silent_p.D352D|NFASC_ENST00000339876.6_Silent_p.D341D|NFASC_ENST00000360049.4_Silent_p.D352D|NFASC_ENST00000338586.6_Silent_p.D341D|NFASC_ENST00000404076.1_Silent_p.D335D|NFASC_ENST00000367169.4_Silent_p.D341D|NFASC_ENST00000338515.6_Silent_p.D341D|NFASC_ENST00000403080.1_Silent_p.D341D|NFASC_ENST00000367172.4_Silent_p.D341D|NFASC_ENST00000367171.4_Silent_p.D341D|NFASC_ENST00000367170.4_Silent_p.D341D|NFASC_ENST00000513543.1_Silent_p.D352D			O94856	NFASC_HUMAN	neurofascin	341	Ig-like C2-type 4.				axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			ACTGGCTGGACGAACCCAAGA	0.552													C|||	104	0.0207668	0.0764	0.0029	5008	,	,		18345	0.0		0.0	False		,,,				2504	0.001				p.D352D		Atlas-SNP	.											.	NFASC	396	.	0			c.C1056T						PASS	.	C	,,,,,	288,4118	158.9+/-191.5	13,262,1928	87.0	76.0	80.0		1023,1023,1056,1056,1005,1056	-8.8	0.4	1	dbSNP_116	80	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NFASC	NM_001005388.2,NM_001005389.1,NM_001160331.1,NM_001160332.1,NM_001160333.1,NM_015090.3	,,,,,	13,263,6227	TT,TC,CC		0.0116,6.5365,2.2221	,,,,,	341/1241,341/620,352/1190,352/1175,335/614,352/1170	204939763	289,12717	2203	4300	6503	SO:0001819	synonymous_variant	23114	exon11			GCTGGACGAACCC	AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	29866	protein-coding gene	gene with protein product		609145	"""neurofascin homolog (chicken)"""			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.1023C>T	1.37:g.204939763C>T		101.0	0.0	0		131.0	60.0	0.458015	NM_015090	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Silent	SNP	ENST00000401399.1	37	CCDS53460.1	30	0.013736263736263736	29	0.05894308943089431	1	0.0027624309392265192	0	0.0	0	0.0	C	8.636	0.894786	0.17613	0.065365	1.16E-4	ENSG00000163531	ENST00000367173	.	.	.	5.64	-8.77	0.00827	.	.	.	.	.	T	0.12475	0.0303	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.68655	-0.5351	4	.	.	.	.	17.7033	0.88301	0.0:0.1936:0.0:0.8064	rs6690894;rs6690894	.	.	.	M	311	.	.	T	+	2	0	NFASC	203206386	0.189000	0.23263	0.369000	0.25952	0.985000	0.73830	-0.441000	0.06879	-2.495000	0.00514	-0.797000	0.03246	ACG	C|0.974;T|0.026	0.026	strong		0.552	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388	
ZNF212	7988	hgsc.bcm.edu	37	7	148947564	148947564	+	Silent	SNP	C	C	T	rs138413836	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:148947564C>T	ENST00000335870.2	+	2	467	c.339C>T	c.(337-339)aaC>aaT	p.N113N		NM_012256.3	NP_036388.2	Q9UDV6	ZN212_HUMAN	zinc finger protein 212	113					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|identical protein binding (GO:0042802)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(4)|ovary(1)|prostate(1)	9	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00171)			GGCTGGAGAACGTGGAGAACC	0.617													C|||	13	0.00259585	0.0091	0.0014	5008	,	,		15049	0.0		0.0	False		,,,				2504	0.0				p.N113N		Atlas-SNP	.											.	ZNF212	28	.	0			c.C339T						PASS	.	C		33,4373	37.6+/-69.7	0,33,2170	68.0	83.0	78.0		339	3.2	1.0	7	dbSNP_134	78	0,8600		0,0,4300	no	coding-synonymous	ZNF212	NM_012256.3		0,33,6470	TT,TC,CC		0.0,0.749,0.2537		113/496	148947564	33,12973	2203	4300	6503	SO:0001819	synonymous_variant	7988	exon2			GGAGAACGTGGAG	U38864	CCDS5896.1	7q36.1	2013-01-08			ENSG00000170260	ENSG00000170260		"""Zinc fingers, C2H2-type"", ""-"""	13004	protein-coding gene	gene with protein product		602386				9169157	Standard	NM_012256		Approved	C2H2-150	uc003wfp.3	Q9UDV6	OTTHUMG00000158968	ENST00000335870.2:c.339C>T	7.37:g.148947564C>T		87.0	0.0	0		104.0	59.0	0.567308	NM_012256	B2RCF4|Q13396|Q8N664	Silent	SNP	ENST00000335870.2	37	CCDS5896.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	9.867	1.197790	0.22037	0.00749	0.0	ENSG00000170260	ENST00000481584	.	.	.	5.95	3.17	0.36434	.	.	.	.	.	T	0.49115	0.1538	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44922	-0.9296	4	.	.	.	-30.1409	7.8161	0.29260	0.0:0.7392:0.0:0.2608	.	.	.	.	C	11	.	.	R	+	1	0	ZNF212	148578497	0.992000	0.36948	1.000000	0.80357	0.983000	0.72400	1.139000	0.31504	0.412000	0.25729	-0.222000	0.12452	CGT	C|0.999;T|0.001	0.001	strong		0.617	ZNF212-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352710.1	NM_012256	
RBM12	10137	hgsc.bcm.edu	37	20	34241530	34241530	+	Missense_Mutation	SNP	T	T	C	rs17092928	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34241530T>C	ENST00000374114.3	-	3	1978	c.1715A>G	c.(1714-1716)aAt>aGt	p.N572S	CPNE1_ENST00000397443.1_Intron|RP1-309K20.6_ENST00000541176.2_Intron|RBM12_ENST00000359646.1_Missense_Mutation_p.N572S|RBM12_ENST00000374104.3_Missense_Mutation_p.N572S|CPNE1_ENST00000397442.1_Intron|CPNE1_ENST00000317677.5_5'UTR|CPNE1_ENST00000397445.1_Intron|CPNE1_ENST00000352393.4_Intron|CPNE1_ENST00000317619.3_Intron|CPNE1_ENST00000397446.1_Intron	NM_001198838.1|NM_001198840.1|NM_006047.5	NP_001185767.1|NP_001185769.1|NP_006038.2	Q9NTZ6	RBM12_HUMAN	RNA binding motif protein 12	572			N -> S (in dbSNP:rs17092928).			nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(7)|kidney(1)|large_intestine(3)|lung(14)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	36	Lung NSC(9;0.00608)|all_lung(11;0.00918)		BRCA - Breast invasive adenocarcinoma(18;0.00953)			ATGTACAGCATTTTCATCCAC	0.408													T|||	124	0.0247604	0.09	0.0072	5008	,	,		22183	0.0		0.0	False		,,,				2504	0.0				p.N572S		Atlas-SNP	.											.	RBM12	93	.	0			c.A1715G						PASS	.	T	SER/ASN,SER/ASN,,,SER/ASN,SER/ASN,,,,	267,4139	150.7+/-184.7	3,261,1939	194.0	187.0	189.0		1715,1715,,,1715,1715,,,,	3.7	1.0	20	dbSNP_123	189	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense,intron,utr-5,missense,missense,intron,intron,intron,intron	CPNE1,RBM12	NM_001198838.1,NM_001198840.1,NM_001198863.1,NM_003915.5,NM_006047.5,NM_152838.3,NM_152925.2,NM_152926.2,NM_152927.2,NM_152928.2	46,46,,,46,46,,,,	3,265,6235	CC,CT,TT		0.0465,6.0599,2.0837	benign,benign,,,benign,benign,,,,	572/933,572/933,,,572/933,572/933,,,,	34241530	271,12735	2203	4300	6503	SO:0001583	missense	10137	exon2			ACAGCATTTTCAT	AJ289772	CCDS13261.1	20q11.21	2013-02-12			ENSG00000244462	ENSG00000244462		"""RNA binding motif (RRM) containing"""	9898	protein-coding gene	gene with protein product		607179				11435693	Standard	NM_006047		Approved	HRIHFB2091, KIAA0765, SWAN	uc021wcq.1	Q9NTZ6	OTTHUMG00000032350	ENST00000374114.3:c.1715A>G	20.37:g.34241530T>C	ENSP00000363228:p.Asn572Ser	149.0	0.0	0		148.0	78.0	0.527027	NM_001198840	B3KRU2|E1P5R6|O94865|Q8N3B1|Q9H196	Missense_Mutation	SNP	ENST00000374114.3	37	CCDS13261.1	48	0.02197802197802198	43	0.08739837398373984	5	0.013812154696132596	0	0.0	0	0.0	T	8.105	0.777613	0.16120	0.060599	4.65E-4	ENSG00000244462	ENST00000374114;ENST00000359646;ENST00000374104;ENST00000349942	T;T;T	0.15487	2.42;2.42;2.42	4.83	3.69	0.42338	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.200400	0.42682	N	0.000670	T	0.00496	0.0016	L	0.38175	1.15	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.17289	-1.0374	10	0.37606	T	0.19	-5.5476	10.7607	0.46264	0.0:0.0756:0.0:0.9244	rs17092928;rs52836153;rs17092928	572	Q9NTZ6	RBM12_HUMAN	S	572;572;572;371	ENSP00000363228:N572S;ENSP00000352668:N572S;ENSP00000363217:N572S	ENSP00000339879:N371S	N	-	2	0	RBM12	33704944	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.686000	0.61700	0.827000	0.34685	0.460000	0.39030	AAT	T|0.978;C|0.022	0.022	strong		0.408	RBM12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078894.1	NM_006047	
ZNF217	7764	hgsc.bcm.edu	37	20	52192308	52192308	+	Missense_Mutation	SNP	A	A	C	rs61758384	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:52192308A>C	ENST00000371471.2	-	4	3420	c.2995T>G	c.(2995-2997)Tgt>Ggt	p.C999G	RP4-724E16.2_ENST00000424252.1_RNA|ZNF217_ENST00000302342.3_Missense_Mutation_p.C999G			O75362	ZN217_HUMAN	zinc finger protein 217	999					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleoplasm (GO:0005654)	metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(13)|lung(17)|ovary(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	50	all_cancers(1;6.75e-17)|all_epithelial(1;1.76e-18)|Breast(2;3.83e-14)|Lung NSC(4;9.04e-07)|all_lung(4;2.5e-06)|Ovarian(1;0.0398)		BRCA - Breast invasive adenocarcinoma(1;9.88e-17)|Epithelial(1;1.56e-14)|all cancers(1;9.44e-13)|STAD - Stomach adenocarcinoma(23;0.0474)|Colorectal(105;0.198)			GCAGGCACACAAGTGTAAAGT	0.527													A|||	51	0.0101837	0.0356	0.0058	5008	,	,		21128	0.0		0.0	False		,,,				2504	0.0				p.C999G		Atlas-SNP	.											ZNF217,NS,carcinoma,+1,1	ZNF217	227	1	0			c.T2995G						PASS	.	A	GLY/CYS	187,4219	116.3+/-154.2	1,185,2017	61.0	58.0	59.0		2995	4.8	0.0	20	dbSNP_129	59	2,8598	2.2+/-6.3	0,2,4298	yes	missense	ZNF217	NM_006526.2	159	1,187,6315	CC,CA,AA		0.0233,4.2442,1.4532	possibly-damaging	999/1049	52192308	189,12817	2203	4300	6503	SO:0001583	missense	7764	exon3			GCACACAAGTGTA	AF041259	CCDS13443.1	20q13.2	2013-01-08			ENSG00000171940	ENSG00000171940		"""Zinc fingers, C2H2-type"""	13009	protein-coding gene	gene with protein product		602967				9671742	Standard	NM_006526		Approved	ZABC1	uc002xwq.4	O75362	OTTHUMG00000032764	ENST00000371471.2:c.2995T>G	20.37:g.52192308A>C	ENSP00000360526:p.Cys999Gly	32.0	0.0	0		40.0	17.0	0.425	NM_006526	E1P5Y6|Q14DB8	Missense_Mutation	SNP	ENST00000371471.2	37	CCDS13443.1	18	0.008241758241758242	16	0.032520325203252036	2	0.0055248618784530384	0	0.0	0	0.0	A	16.16	3.044296	0.55110	0.042442	2.33E-4	ENSG00000171940	ENST00000371471;ENST00000302342;ENST00000437222;ENST00000395971	T;T	0.11821	2.74;2.74	4.79	4.79	0.61399	.	0.463445	0.23003	N	0.053056	T	0.07773	0.0195	L	0.59436	1.845	0.19945	N	0.999949	D	0.71674	0.998	P	0.60682	0.878	T	0.01081	-1.1458	10	0.72032	D	0.01	-8.6365	12.5619	0.56286	1.0:0.0:0.0:0.0	rs61758384	999	O75362	ZN217_HUMAN	G	999;999;87;159	ENSP00000360526:C999G;ENSP00000304308:C999G	ENSP00000304308:C999G	C	-	1	0	ZNF217	51625715	0.948000	0.32251	0.008000	0.14137	0.003000	0.03518	5.216000	0.65246	1.791000	0.52520	0.528000	0.53228	TGT	A|0.985;C|0.015	0.015	strong		0.527	ZNF217-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079757.2	NM_006526	
ZNF667	63934	hgsc.bcm.edu	37	19	56952615	56952615	+	Silent	SNP	A	A	G	rs61740673	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56952615A>G	ENST00000504904.3	-	7	2468	c.1749T>C	c.(1747-1749)taT>taC	p.Y583Y	ZNF667_ENST00000292069.6_Silent_p.Y583Y|ZNF667_ENST00000591790.1_3'UTR|ZNF667_ENST00000342634.3_Silent_p.Y711Y			Q5HYK9	ZN667_HUMAN	zinc finger protein 667	583					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(18)|pancreas(1)|skin(1)|upper_aerodigestive_tract(3)	38		Colorectal(82;0.000256)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0615)		TACTACATTCATAGGGTTTCT	0.398													A|||	158	0.0315495	0.0961	0.0159	5008	,	,		20645	0.0		0.0159	False		,,,				2504	0.0041				p.Y583Y		Atlas-SNP	.											ZNF667,NS,NS,-2,1	ZNF667	95	1	0			c.T1749C						PASS	.	A		393,4013	197.7+/-221.8	16,361,1826	120.0	115.0	117.0		1749	-0.7	0.4	19	dbSNP_129	117	96,8504	53.1+/-113.8	0,96,4204	no	coding-synonymous	ZNF667	NM_022103.3		16,457,6030	GG,GA,AA		1.1163,8.9197,3.7598		583/611	56952615	489,12517	2203	4300	6503	SO:0001819	synonymous_variant	63934	exon5			ACATTCATAGGGT		CCDS12944.1	19q13.43	2013-01-08				ENSG00000198046		"""Zinc fingers, C2H2-type"", ""-"""	28854	protein-coding gene	gene with protein product		611024					Standard	NM_022103		Approved	FLJ14011	uc002qnd.3	Q5HYK9		ENST00000504904.3:c.1749T>C	19.37:g.56952615A>G		98.0	0.0	0		94.0	40.0	0.425532	NM_022103	B2RMS6|B9EK36|Q6B093|Q9H807	Silent	SNP	ENST00000504904.3	37	CCDS12944.1																																																																																			A|0.965;G|0.035	0.035	strong		0.398	ZNF667-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458394.1	NM_022103	
PITRM1	10531	hgsc.bcm.edu	37	10	3187831	3187831	+	Missense_Mutation	SNP	C	C	T	rs34837384	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:3187831C>T	ENST00000224949.4	-	21	2448	c.2414G>A	c.(2413-2415)cGg>cAg	p.R805Q	PITRM1_ENST00000451104.2_Missense_Mutation_p.R707Q|PITRM1_ENST00000464395.1_5'UTR|PITRM1-AS1_ENST00000441377.1_RNA|PITRM1_ENST00000380989.2_Missense_Mutation_p.R806Q|PITRM1-AS1_ENST00000598280.1_RNA|PITRM1_ENST00000380994.1_Missense_Mutation_p.R363Q|PITRM1-AS1_ENST00000601046.1_RNA			Q5JRX3	PREP_HUMAN	pitrilysin metallopeptidase 1	805			R -> Q (in dbSNP:rs34837384).		positive regulation of catalytic activity (GO:0043085)|proteolysis (GO:0006508)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enzyme activator activity (GO:0008047)|metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|urinary_tract(3)	33						CTTTTTACTCCGACCGATGCT	0.547													C|||	45	0.00898562	0.0325	0.0029	5008	,	,		17900	0.0		0.0	False		,,,				2504	0.0				p.R806Q		Atlas-SNP	.											.	PITRM1	109	.	0			c.G2417A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	145,3603		5,135,1734	51.0	52.0	52.0		2417,2120,2414	3.4	0.0	10	dbSNP_126	52	1,7975		0,1,3987	yes	missense,missense,missense	PITRM1	NM_001242307.1,NM_001242309.1,NM_014889.3	43,43,43	5,136,5721	TT,TC,CC		0.0125,3.8687,1.2453	benign,benign,benign	806/1039,707/940,805/1038	3187831	146,11578	1874	3988	5862	SO:0001583	missense	10531	exon21			TTACTCCGACCGA	AB029027	CCDS55699.1, CCDS55700.1, CCDS59208.1	10p15.2	2008-07-30	2005-08-17		ENSG00000107959	ENSG00000107959			17663	protein-coding gene	gene with protein product	"""PreP peptidasome"""		"""pitrilysin metalloproteinase 1"""			1036083, 10470851, 16849325	Standard	NM_014889		Approved	MP1, KIAA1104, hMP1, PreP	uc009xhv.2	Q5JRX3	OTTHUMG00000017557	ENST00000224949.4:c.2414G>A	10.37:g.3187831C>T	ENSP00000224949:p.Arg805Gln	100.0	0.0	0		81.0	41.0	0.506173	NM_001242307	B3KMJ6|B4E0J8|C9JSL2|E7ES23|O95204|Q2M2G6|Q4VBR1|Q5JRW7|Q7L5Z7|Q9BSI6|Q9BVJ5|Q9UPP8	Missense_Mutation	SNP	ENST00000224949.4	37	CCDS59208.1	15	0.006868131868131868	15	0.03048780487804878	0	0.0	0	0.0	0	0.0	c	13.97	2.394997	0.42512	0.038687	1.25E-4	ENSG00000107959	ENST00000224949;ENST00000380980;ENST00000380989;ENST00000380994;ENST00000451104;ENST00000424714	T;T;T;T;T	0.54866	1.57;1.57;1.57;1.57;0.55	5.29	3.43	0.39272	Peptidase M16, C-terminal (1);Metalloenzyme, LuxS/M16 peptidase-like, metal-binding (1);	0.301189	0.35495	N	0.003174	T	0.14570	0.0352	L	0.46947	1.48	0.09310	N	1	B;B;B;B;B	0.24043	0.017;0.045;0.056;0.056;0.096	B;B;B;B;B	0.26969	0.005;0.046;0.075;0.075;0.075	T	0.08126	-1.0737	10	0.17369	T	0.5	-8.921	12.181	0.54211	0.0:0.8592:0.0:0.1408	rs34837384	798;707;806;805;798	E9PDX6;E7ES23;C9JSL2;Q5JRX3;B4DH07	.;.;.;PREP_HUMAN;.	Q	805;798;806;363;707;24	ENSP00000224949:R805Q;ENSP00000370377:R806Q;ENSP00000370382:R363Q;ENSP00000401201:R707Q;ENSP00000402072:R24Q	ENSP00000224949:R805Q	R	-	2	0	PITRM1	3177831	0.021000	0.18746	0.004000	0.12327	0.004000	0.04260	1.792000	0.38754	0.725000	0.32318	0.462000	0.41574	CGG	C|0.992;T|0.008	0.008	strong		0.547	PITRM1-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000046469.2		
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249530	71249530	+	Silent	SNP	T	T	C	rs532438179|rs369043826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71249530T>C	ENST00000398534.3	+	1	460	c.429T>C	c.(427-429)tgT>tgC	p.C143C		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	143	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						AGCCCTGCTGTTCCCAGTCCA	0.612																																					p.C143C		Atlas-SNP	.											KRTAP5-8,NS,carcinoma,+1,1	KRTAP5-8	28	1	0			c.T429C						scavenged	.						146.0	159.0	155.0					11																	71249530		2200	4294	6494	SO:0001819	synonymous_variant	57830	exon1			CTGCTGTTCCCAG	AB126077	CCDS41683.1	11q13.4	2008-02-05			ENSG00000241233	ENSG00000241233		"""Keratin associated proteins"""	23603	protein-coding gene	gene with protein product						15144888	Standard	NM_021046		Approved	KRTAP5.8, UHSKerB, KRTAP5-2	uc001oqr.1	O75690	OTTHUMG00000057571	ENST00000398534.3:c.429T>C	11.37:g.71249530T>C		157.0	1.0	0.00636943		229.0	16.0	0.069869	NM_021046	Q6L8G7|Q6UTX6	Silent	SNP	ENST00000398534.3	37	CCDS41683.1																																																																																			.	.	none		0.612	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046	
FAM134B	54463	hgsc.bcm.edu	37	5	16475209	16475209	+	Missense_Mutation	SNP	G	G	C	rs34432513	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:16475209G>C	ENST00000306320.9	-	9	1221	c.1135C>G	c.(1135-1137)Cag>Gag	p.Q379E	FAM134B_ENST00000399793.2_Missense_Mutation_p.Q238E	NM_001034850.2	NP_001030022.1	Q9H6L5	F134B_HUMAN	family with sequence similarity 134, member B	379			Q -> E (in dbSNP:rs34432513).		sensory perception of pain (GO:0019233)	cis-Golgi network (GO:0005801)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(2)|skin(1)	16						CTGTCCAACTGTTCCTTCTTT	0.453													G|||	57	0.0113818	0.0393	0.0058	5008	,	,		20685	0.0		0.001	False		,,,				2504	0.0				p.Q379E		Atlas-SNP	.											.	FAM134B	72	.	0			c.C1135G						PASS	.	G	GLU/GLN,GLU/GLN	137,3809		4,129,1840	165.0	161.0	162.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1135,712	3.9	0.0	5	dbSNP_126	162	2,8320		0,2,4159	yes	missense,missense	FAM134B	NM_001034850.1,NM_019000.3	29,29	4,131,5999	CC,CG,GG		0.024,3.4719,1.133	benign,benign	379/498,238/357	16475209	139,12129	1973	4161	6134	SO:0001583	missense	54463	exon9			CCAACTGTTCCTT	BC053326	CCDS43304.1, CCDS43305.1	5p15.1	2014-09-17			ENSG00000154153	ENSG00000154153			25964	protein-coding gene	gene with protein product		613114				19838196, 24327336	Standard	NM_001034850		Approved	FLJ20152	uc003jfs.3	Q9H6L5	OTTHUMG00000161788	ENST00000306320.9:c.1135C>G	5.37:g.16475209G>C	ENSP00000304642:p.Gln379Glu	196.0	0.0	0		206.0	104.0	0.504854	NM_001034850	Q69YN8|Q9H6K6|Q9H764|Q9NXM8	Missense_Mutation	SNP	ENST00000306320.9	37	CCDS43304.1	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	G	0.004	-2.276501	0.00254	0.034719	2.4E-4	ENSG00000154153	ENST00000399793;ENST00000306320	T;T	0.43688	0.96;0.94	5.7	3.86	0.44501	.	0.782790	0.11830	N	0.525295	T	0.01976	0.0062	N	0.25647	0.755	0.09310	N	1	B;B	0.23442	0.085;0.034	B;B	0.19666	0.026;0.022	T	0.10823	-1.0613	10	0.02654	T	1	-0.8582	10.5977	0.45347	0.0:0.1293:0.6027:0.2681	rs34432513	379;238	Q9H6L5;Q9H6L5-2	F134B_HUMAN;.	E	238;379	ENSP00000382691:Q238E;ENSP00000304642:Q379E	ENSP00000304642:Q379E	Q	-	1	0	FAM134B	16528209	0.617000	0.27043	0.001000	0.08648	0.391000	0.30476	4.123000	0.57917	0.704000	0.31869	0.655000	0.94253	CAG	G|0.984;C|0.016	0.016	strong		0.453	FAM134B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000366090.1	NM_001034850	
CNTN4	152330	hgsc.bcm.edu	37	3	2787338	2787338	+	Silent	SNP	G	G	A	rs116041691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:2787338G>A	ENST00000397461.1	+	5	699	c.315G>A	c.(313-315)tcG>tcA	p.S105S	CNTN4_ENST00000427331.1_Silent_p.S105S|CNTN4_ENST00000418658.1_Silent_p.S105S	NM_001206955.1	NP_001193884.1	Q8IWV2	CNTN4_HUMAN	contactin 4	105	Ig-like C2-type 1.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|brain development (GO:0007420)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|neuron cell-cell adhesion (GO:0007158)|neuron projection development (GO:0031175)|regulation of synaptic plasticity (GO:0048167)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(19)|ovary(2)|pancreas(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		CGACAAACTCGTTTGGAACAA	0.408													G|||	28	0.00559105	0.0212	0.0	5008	,	,		17052	0.0		0.0	False		,,,				2504	0.0				p.S105S		Atlas-SNP	.											CNTN4_ENST00000418658,NS,carcinoma,0,1	CNTN4	335	1	0			c.G315A						PASS	.	G	,	64,3818		1,62,1878	146.0	137.0	140.0		315,315	-7.4	0.7	3	dbSNP_132	140	1,8275		0,1,4137	no	coding-synonymous,coding-synonymous	CNTN4	NM_001206955.1,NM_175607.2	,	1,63,6015	AA,AG,GG		0.0121,1.6486,0.5346	,	105/1027,105/1027	2787338	65,12093	1941	4138	6079	SO:0001819	synonymous_variant	152330	exon6			AAACTCGTTTGGA	AW665944	CCDS2558.1, CCDS43041.1	3p26.3	2013-02-11			ENSG00000144619	ENSG00000144619		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2174	protein-coding gene	gene with protein product		607280				8586965, 12202991	Standard	NM_175607		Approved	BIG-2	uc003bpc.3	Q8IWV2	OTTHUMG00000119031	ENST00000397461.1:c.315G>A	3.37:g.2787338G>A		105.0	0.0	0		78.0	48.0	0.615385	NM_175607	B2RAX3|Q8IX14|Q8TC35	Silent	SNP	ENST00000397461.1	37	CCDS43041.1																																																																																			G|0.996;A|0.004	0.004	strong		0.408	CNTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239236.2		
NUP133	55746	hgsc.bcm.edu	37	1	229636561	229636561	+	Missense_Mutation	SNP	C	C	T	rs75411588	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229636561C>T	ENST00000261396.3	-	4	546	c.455G>A	c.(454-456)aGt>aAt	p.S152N	NUP133_ENST00000537506.1_Missense_Mutation_p.S136N|NUP133_ENST00000366678.3_Missense_Mutation_p.S152N	NM_018230.2	NP_060700.2	Q8WUM0	NU133_HUMAN	nucleoporin 133kDa	152					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 export from nucleus (GO:0006406)|nuclear pore organization (GO:0006999)|paraxial mesoderm development (GO:0048339)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|breast(7)|endometrium(1)|kidney(6)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(3)|skin(3)|stomach(4)	56	Breast(184;0.104)|Ovarian(103;0.249)	Prostate(94;0.167)				TAAGTCGGCACTCCAGTGGAA	0.388													C|||	163	0.0325479	0.1135	0.0115	5008	,	,		19355	0.0		0.003	False		,,,				2504	0.002				p.S152N		Atlas-SNP	.											.	NUP133	111	.	0			c.G455A						PASS	.	C	ASN/SER	400,4006	198.4+/-222.2	12,376,1815	59.0	58.0	58.0		455	2.0	0.7	1	dbSNP_131	58	7,8593	6.4+/-24.3	0,7,4293	yes	missense	NUP133	NM_018230.2	46	12,383,6108	TT,TC,CC		0.0814,9.0785,3.1293	benign	152/1157	229636561	407,12599	2203	4300	6503	SO:0001583	missense	55746	exon4			TCGGCACTCCAGT		CCDS1579.1	1q42.13	2008-02-05	2002-08-29		ENSG00000069248	ENSG00000069248			18016	protein-coding gene	gene with protein product		607613	"""nucleoporin 133kD"""			11684705	Standard	NM_018230		Approved	FLJ10814	uc001htn.3	Q8WUM0	OTTHUMG00000039462	ENST00000261396.3:c.455G>A	1.37:g.229636561C>T	ENSP00000261396:p.Ser152Asn	55.0	0.0	0		77.0	38.0	0.493506	NM_018230	B2RAZ8|Q5T8N0|Q9H9W2|Q9NV71|Q9NVC4	Missense_Mutation	SNP	ENST00000261396.3	37	CCDS1579.1	46	0.021062271062271064	42	0.08536585365853659	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	C	9.530	1.110704	0.20714	0.090785	8.14E-4	ENSG00000069248	ENST00000366681;ENST00000261396;ENST00000366679;ENST00000537506;ENST00000366678	T;T;T;T	0.23754	1.89;1.89;1.89;1.89	5.93	1.98	0.26296	WD40/YVTN repeat-like-containing domain (1);Nucleoporin, Nup133/Nup155-like, N-terminal (1);	0.372720	0.33813	N	0.004533	T	0.00524	0.0017	L	0.32530	0.975	0.47214	D	0.999358	B	0.09022	0.002	B	0.08055	0.003	T	0.21042	-1.0257	10	0.16420	T	0.52	-7.1368	6.2296	0.20728	0.0:0.558:0.1243:0.3178	.	152	Q8WUM0	NU133_HUMAN	N	152;152;152;136;152	ENSP00000261396:S152N;ENSP00000355640:S152N;ENSP00000443496:S136N;ENSP00000355639:S152N	ENSP00000261396:S152N	S	-	2	0	NUP133	227703184	0.996000	0.38824	0.673000	0.29887	0.384000	0.30261	0.731000	0.26058	0.845000	0.35118	0.557000	0.71058	AGT	C|0.972;T|0.028	0.028	strong		0.388	NUP133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095224.1	NM_018230	
DCP1B	196513	hgsc.bcm.edu	37	12	2102455	2102455	+	Silent	SNP	A	A	C	rs150415068	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:2102455A>C	ENST00000280665.6	-	3	373	c.294T>G	c.(292-294)ccT>ccG	p.P98P	DCP1B_ENST00000541700.1_5'UTR|DCP1B_ENST00000397173.4_5'UTR	NM_152640.3	NP_689853.3	Q8IZD4	DCP1B_HUMAN	decapping mRNA 1B	98					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)	hydrolase activity (GO:0016787)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(10)|skin(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00193)			AGAGAAGGAAAGGGTCCTGGA	0.403													A|||	4	0.000798722	0.0	0.0014	5008	,	,		19112	0.0		0.003	False		,,,				2504	0.0				p.P98P		Atlas-SNP	.											DCP1B,rectum,carcinoma,0,6	DCP1B	63	6	0			c.T294G						PASS	.	A		2,4404	4.2+/-10.8	0,2,2201	148.0	156.0	153.0		294	0.6	1.0	12	dbSNP_134	153	19,8581	13.3+/-46.6	0,19,4281	no	coding-synonymous	DCP1B	NM_152640.3		0,21,6482	CC,CA,AA		0.2209,0.0454,0.1615		98/618	2102455	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	196513	exon3			AAGGAAAGGGTCC	AY146652	CCDS31727.1	12p13.33	2013-05-02	2013-05-02		ENSG00000151065	ENSG00000151065			24451	protein-coding gene	gene with protein product		609843	"""DCP1 decapping enzyme homolog B (S. cerevisiae)"""			12417715, 15067023	Standard	NM_152640		Approved	FLJ31638	uc001qjx.1	Q8IZD4	OTTHUMG00000168113	ENST00000280665.6:c.294T>G	12.37:g.2102455A>C		146.0	0.0	0		185.0	85.0	0.459459	NM_152640	B4DRD1|Q86XH9|Q96BP8|Q96MZ8	Silent	SNP	ENST00000280665.6	37	CCDS31727.1																																																																																			A|0.998;C|0.002	0.002	strong		0.403	DCP1B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398244.1	NM_152640	
APOH	350	hgsc.bcm.edu	37	17	64216797	64216797	+	Missense_Mutation	SNP	G	G	T	rs114459902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:64216797G>T	ENST00000205948.6	-	5	516	c.479C>A	c.(478-480)gCt>gAt	p.A160D		NM_000042.2	NP_000033.2	P02749	APOH_HUMAN	apolipoprotein H (beta-2-glycoprotein I)	160	Sushi 3. {ECO:0000255|PROSITE- ProRule:PRU00302}.				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)			ATTGTTTCCAGCTGATGGCTT	0.408													G|||	29	0.00579073	0.0212	0.0014	5008	,	,		19051	0.0		0.0	False		,,,				2504	0.0				p.A160D	Melanoma(155;624 1882 16869 48804 51309)	Atlas-SNP	.											.	APOH	45	.	0			c.C479A						PASS	.	G	ASP/ALA	83,4323	70.3+/-108.2	0,83,2120	127.0	123.0	124.0		479	0.9	0.0	17	dbSNP_133	124	0,8600		0,0,4300	yes	missense	APOH	NM_000042.2	126	0,83,6420	TT,TG,GG		0.0,1.8838,0.6382	benign	160/346	64216797	83,12923	2203	4300	6503	SO:0001583	missense	350	exon5			TTTCCAGCTGATG		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.479C>A	17.37:g.64216797G>T	ENSP00000205948:p.Ala160Asp	156.0	0.0	0		147.0	57.0	0.387755	NM_000042	B2R9M3|Q9UCN7	Missense_Mutation	SNP	ENST00000205948.6	37	CCDS11663.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	g	4.559	0.103783	0.08731	0.018838	0.0	ENSG00000091583	ENST00000205948	T	0.30448	1.53	5.2	0.92	0.19397	Complement control module (2);Sushi/SCR/CCP (3);	0.940200	0.09067	N	0.853424	T	0.11665	0.0284	L	0.53729	1.69	0.09310	N	0.999999	B	0.29378	0.243	B	0.22601	0.04	T	0.25398	-1.0133	10	0.15066	T	0.55	.	4.9343	0.13932	0.3059:0.0:0.5587:0.1354	.	160	P02749	APOH_HUMAN	D	160	ENSP00000205948:A160D	ENSP00000205948:A160D	A	-	2	0	APOH	61647259	0.000000	0.05858	0.013000	0.15412	0.335000	0.28730	-0.346000	0.07760	0.036000	0.15547	-0.271000	0.10264	GCT	G|0.993;T|0.007	0.007	strong		0.408	APOH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446926.1	NM_000042	
OR10T2	128360	hgsc.bcm.edu	37	1	158369210	158369210	+	Missense_Mutation	SNP	A	A	G	rs6660222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158369210A>G	ENST00000334438.1	-	1	46	c.47T>C	c.(46-48)gTg>gCg	p.V16A		NM_001004475.1	NP_001004475.1	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T, member 2	16			V -> A (in dbSNP:rs6660222).			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(4)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_hematologic(112;0.0378)					GGAGAAACCCACCAGGATGAA	0.448													A|||	103	0.0205671	0.0772	0.0	5008	,	,		18704	0.0		0.0	False		,,,				2504	0.001				p.V16A		Atlas-SNP	.											.	OR10T2	76	.	0			c.T47C						PASS	.	A	ALA/VAL	237,4169	128.2+/-165.1	5,227,1971	35.0	39.0	37.0		47	4.7	0.9	1	dbSNP_116	37	0,8600		0,0,4300	yes	missense	OR10T2	NM_001004475.1	64	5,227,6271	GG,GA,AA		0.0,5.379,1.8222	benign	16/315	158369210	237,12769	2203	4300	6503	SO:0001583	missense	128360	exon1			AAACCCACCAGGA	AB065643	CCDS30895.1	1q23.1	2012-08-09			ENSG00000186306	ENSG00000186306		"""GPCR / Class A : Olfactory receptors"""	14816	protein-coding gene	gene with protein product							Standard	NM_001004475		Approved		uc010pih.2	Q8NGX3	OTTHUMG00000017521	ENST00000334438.1:c.47T>C	1.37:g.158369210A>G	ENSP00000334115:p.Val16Ala	96.0	0.0	0		111.0	53.0	0.477477	NM_001004475	Q6IF98	Missense_Mutation	SNP	ENST00000334438.1	37	CCDS30895.1	38	0.0173992673992674	38	0.07723577235772358	0	0.0	0	0.0	0	0.0	A	10.40	1.341006	0.24339	0.05379	0.0	ENSG00000186306	ENST00000334438	T	0.01406	4.93	4.65	4.65	0.58169	.	0.000000	0.34411	U	0.003988	T	0.00637	0.0021	L	0.41710	1.295	0.20764	N	0.99986	B	0.34161	0.439	B	0.36666	0.23	T	0.48658	-0.9016	10	0.87932	D	0	.	4.0026	0.09587	0.7202:0.0:0.0962:0.1837	rs6660222;rs52824469;rs56643236;rs6660222	16	Q8NGX3	O10T2_HUMAN	A	16	ENSP00000334115:V16A	ENSP00000334115:V16A	V	-	2	0	OR10T2	156635834	0.176000	0.23096	0.922000	0.36590	0.528000	0.34623	1.079000	0.30766	1.939000	0.56221	0.482000	0.46254	GTG	A|0.976;G|0.024	0.024	strong		0.448	OR10T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046371.1	NM_001004475	
LRRFIP2	9209	hgsc.bcm.edu	37	3	37144480	37144480	+	Missense_Mutation	SNP	G	G	A	rs143314448	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:37144480G>A	ENST00000336686.4	-	15	888	c.808C>T	c.(808-810)Cgc>Tgc	p.R270C	LRRFIP2_ENST00000354379.4_Intron|LRRFIP2_ENST00000421307.1_Missense_Mutation_p.R270C|LRRFIP2_ENST00000440230.1_Intron|LRRFIP2_ENST00000421276.2_Intron|LRRFIP2_ENST00000396428.2_Intron			Q9Y608	LRRF2_HUMAN	leucine rich repeat (in FLII) interacting protein 2	270	DVL3-binding.|Ser-rich.				Wnt signaling pathway (GO:0016055)		LRR domain binding (GO:0030275)	p.0?(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						CGATTGGAGCGACTGAAATAA	0.403													G|||	5	0.000998403	0.0038	0.0	5008	,	,		15844	0.0		0.0	False		,,,				2504	0.0				p.R270C		Atlas-SNP	.											.	LRRFIP2	71	.	1	Whole gene deletion(1)	ovary(1)	c.C808T						PASS	.	G	,CYS/ARG,	12,4386		0,12,2187	79.0	61.0	67.0		,808,	6.2	1.0	3	dbSNP_134	67	0,8592		0,0,4296	yes	intron,missense,intron	LRRFIP2	NM_001134369.1,NM_006309.2,NM_017724.2	,180,	0,12,6483	AA,AG,GG		0.0,0.2729,0.0924	,probably-damaging,	,270/722,	37144480	12,12978	2199	4296	6495	SO:0001583	missense	9209	exon16			TGGAGCGACTGAA	AF115509	CCDS2664.1, CCDS2665.1, CCDS46791.1, CCDS63592.1	3p22.1	2008-07-18			ENSG00000093167	ENSG00000093167			6703	protein-coding gene	gene with protein product		614043				10366446	Standard	NM_017724		Approved	HUFI-2	uc003cgp.2	Q9Y608	OTTHUMG00000130796	ENST00000336686.4:c.808C>T	3.37:g.37144480G>A	ENSP00000338727:p.Arg270Cys	102.0	0.0	0		81.0	39.0	0.481481	NM_006309	A8K649|A8MXR0|B4DY63|Q68CV3|Q9NXH5	Missense_Mutation	SNP	ENST00000336686.4	37	CCDS2664.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	33	5.265897	0.95399	0.002729	0.0	ENSG00000093167	ENST00000421307;ENST00000336686	T;T	0.56275	0.47;0.47	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.63628	0.2527	N	0.22421	0.69	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.64859	-0.6308	10	0.66056	D	0.02	-8.9955	20.4549	0.99139	0.0:0.0:1.0:0.0	.	270	Q9Y608	LRRF2_HUMAN	C	270	ENSP00000392217:R270C;ENSP00000338727:R270C	ENSP00000338727:R270C	R	-	1	0	LRRFIP2	37119484	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	6.226000	0.72277	2.937000	0.99478	0.650000	0.86243	CGC	G|0.999;A|0.001	0.001	strong		0.403	LRRFIP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000253335.3	NM_006309	
NOD1	10392	hgsc.bcm.edu	37	7	30491081	30491081	+	Missense_Mutation	SNP	G	G	A	rs151170709	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:30491081G>A	ENST00000222823.4	-	6	2477	c.1952C>T	c.(1951-1953)aCg>aTg	p.T651M		NM_006092.2	NP_006083.1	Q9Y239	NOD1_HUMAN	nucleotide-binding oligomerization domain containing 1	651					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of MAPK activity (GO:0000187)|apoptotic process (GO:0006915)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-8 biosynthetic process (GO:0042228)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of tumor necrosis factor production (GO:0032760)|protein oligomerization (GO:0051259)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|identical protein binding (GO:0042802)|peptidoglycan binding (GO:0042834)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|skin(2)	39						CCAGATGAACGTGGGCATGGC	0.622													G|||	4	0.000798722	0.003	0.0	5008	,	,		18686	0.0		0.0	False		,,,				2504	0.0				p.T651M		Atlas-SNP	.											.	NOD1	79	.	0			c.C1952T						PASS	.	G	MET/THR	18,4388	26.2+/-53.5	0,18,2185	44.0	45.0	45.0		1952	5.6	1.0	7	dbSNP_134	45	0,8600		0,0,4300	yes	missense	NOD1	NM_006092.2	81	0,18,6485	AA,AG,GG		0.0,0.4085,0.1384	probably-damaging	651/954	30491081	18,12988	2203	4300	6503	SO:0001583	missense	10392	exon6			ATGAACGTGGGCA	AF126484	CCDS5427.1	7p15-p14	2006-12-08	2006-12-08	2006-12-08	ENSG00000106100	ENSG00000106100		"""Nucleotide-binding domain and leucine rich repeat containing"""	16390	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 1"", ""NLR family, CARD domain containing 1"""	605980	"""caspase recruitment domain family, member 4"""	CARD4		10224040, 10329646	Standard	NM_006092		Approved	NLRC1, CLR7.1	uc003tav.3	Q9Y239	OTTHUMG00000023923	ENST00000222823.4:c.1952C>T	7.37:g.30491081G>A	ENSP00000222823:p.Thr651Met	53.0	0.0	0		63.0	34.0	0.539683	NM_006092	B4DTU3|Q549U4|Q8IWF5	Missense_Mutation	SNP	ENST00000222823.4	37	CCDS5427.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	17.46	3.395795	0.62177	0.004085	0.0	ENSG00000106100	ENST00000222823	T	0.71103	-0.54	5.61	5.61	0.85477	.	0.192032	0.52532	D	0.000072	T	0.70046	0.3179	M	0.63428	1.95	0.80722	D	1	D	0.71674	0.998	P	0.54706	0.759	T	0.74636	-0.3599	10	0.49607	T	0.09	.	12.283	0.54776	0.0:0.0:0.7325:0.2675	.	651	Q9Y239	NOD1_HUMAN	M	651	ENSP00000222823:T651M	ENSP00000222823:T651M	T	-	2	0	NOD1	30457606	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.689000	0.68234	2.652000	0.90054	0.655000	0.94253	ACG	G|0.998;A|0.002	0.002	strong		0.622	NOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250443.2		
SLC44A2	57153	hgsc.bcm.edu	37	19	10713212	10713212	+	Silent	SNP	G	G	A	rs115559926	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:10713212G>A	ENST00000407327.4	+	1	27	c.6G>A	c.(4-6)gaG>gaA	p.E2E		NM_001145056.1	NP_001138528.1	Q8IWA5	CTL2_HUMAN	solute carrier family 44 (choline transporter), member 2	2					choline transport (GO:0015871)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	choline transmembrane transporter activity (GO:0015220)|signal transducer activity (GO:0004871)			NS(1)|breast(3)|endometrium(5)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	27			Epithelial(33;8.7e-06)|all cancers(31;2.77e-05)		Choline(DB00122)	CGGCCATGGAGGACGAGCGGA	0.771													G|||	86	0.0171725	0.0643	0.0014	5008	,	,		6430	0.0		0.0	False		,,,				2504	0.0				p.E2E		Atlas-SNP	.											.	SLC44A2	56	.	0			c.G6A						PASS	.						7.0	12.0	11.0					19																	10713212		643	1532	2175	SO:0001819	synonymous_variant	57153	exon1			CATGGAGGACGAG	AF070636	CCDS12245.1, CCDS54216.1	19p13.2	2014-08-12	2013-07-17		ENSG00000129353	ENSG00000129353		"""Solute carriers"""	17292	protein-coding gene	gene with protein product		606106				10677542, 15715662	Standard	NM_001145056		Approved	CTL2	uc002mpf.3	Q8IWA5	OTTHUMG00000180585	ENST00000407327.4:c.6G>A	19.37:g.10713212G>A		21.0	0.0	0		21.0	13.0	0.619048	NM_001145056	B2RBB1|B3KNH3|B4DFJ0|F2Q9D7|Q658V1|Q658Z2|Q6PJV7|Q8N2F0|Q9NY68	Silent	SNP	ENST00000407327.4	37	CCDS54216.1																																																																																			G|0.986;A|0.014	0.014	strong		0.771	SLC44A2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452044.1		
RARS2	57038	hgsc.bcm.edu	37	6	88279282	88279282	+	Silent	SNP	T	T	C	rs7748563	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:88279282T>C	ENST00000369536.5	-	2	108	c.63A>G	c.(61-63)ccA>ccG	p.P21P		NM_020320.3	NP_064716.2	Q5T160	SYRM_HUMAN	arginyl-tRNA synthetase 2, mitochondrial	21					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)	arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	22		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0456)		TCAAGTTTTCTGGTGGAAGAT	0.313													T|||	68	0.0135783	0.0477	0.0058	5008	,	,		18264	0.0		0.001	False		,,,				2504	0.0				p.P21P		Atlas-SNP	.											.	RARS2	61	.	0			c.A63G						PASS	.	T		160,4246	107.8+/-146.2	5,150,2048	110.0	113.0	112.0		63	2.8	1.0	6	dbSNP_116	112	0,8600		0,0,4300	no	coding-synonymous	RARS2	NM_020320.3		5,150,6348	CC,CT,TT		0.0,3.6314,1.2302		21/579	88279282	160,12846	2203	4300	6503	SO:0001819	synonymous_variant	57038	exon2			GTTTTCTGGTGGA	AK093934	CCDS5011.1	6q16.1	2011-07-01	2007-09-27	2007-02-23	ENSG00000146282	ENSG00000146282	6.1.1.19	"""Aminoacyl tRNA synthetases / Class I"""	21406	protein-coding gene	gene with protein product	"""arginine tRNA ligase 2, mitochondrial (putative)"""	611524	"""arginyl-tRNA synthetase-like"""	RARSL		17847012	Standard	NM_020320		Approved	MGC14993, MGC23778, PRO1992, dJ382I10.6, DALRD2	uc003pme.3	Q5T160	OTTHUMG00000015178	ENST00000369536.5:c.63A>G	6.37:g.88279282T>C		137.0	0.0	0		157.0	71.0	0.452229	NM_020320	B2RDT7|Q96FU5|Q9H8K8	Silent	SNP	ENST00000369536.5	37	CCDS5011.1	23	0.010531135531135532	20	0.04065040650406504	3	0.008287292817679558	0	0.0	0	0.0	T	14.17	2.456129	0.43634	0.036314	0.0	ENSG00000146282	ENST00000369523	.	.	.	5.2	2.75	0.32379	.	.	.	.	.	T	0.41026	0.1141	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33137	-0.9880	5	0.39692	T	0.17	.	5.3844	0.16211	0.0:0.0915:0.177:0.7315	rs7748563;rs7748563	.	.	.	G	9	.	ENSP00000358536:R9G	R	-	1	2	RARS2	88336001	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	0.869000	0.27996	0.374000	0.24650	0.528000	0.53228	AGA	T|0.987;C|0.013	0.013	strong		0.313	RARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041448.1	NM_020320	
ALG3	10195	hgsc.bcm.edu	37	3	183963000	183963000	+	Silent	SNP	A	A	G	rs2233464	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:183963000A>G	ENST00000397676.3	-	4	621	c.591T>C	c.(589-591)ggT>ggC	p.G197G	ALG3_ENST00000445626.2_Silent_p.G149G|ALG3_ENST00000463495.1_5'Flank|ALG3_ENST00000455059.1_Silent_p.G157G|ALG3_ENST00000418734.2_Silent_p.G141G|EIF2B5_ENST00000444495.1_Intron	NM_005787.5	NP_005778.1	Q92685	ALG3_HUMAN	ALG3, alpha-1,3- mannosyltransferase	197					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-1,3-mannosyltransferase activity (GO:0000033)|dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity (GO:0052925)			kidney(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	9	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			AAAAGCAGCAACCCCAGCCCC	0.542													G|||	247	0.0493211	0.1808	0.0115	5008	,	,		20053	0.0		0.0	False		,,,				2504	0.0				p.G197G		Atlas-SNP	.											.	ALG3	48	.	0			c.T591C						PASS	.	G	,	483,3459		24,435,1512	36.0	42.0	40.0		447,591	2.0	1.0	3	dbSNP_98	40	4,8306		0,4,4151	no	coding-synonymous,coding-synonymous	ALG3	NM_001006941.2,NM_005787.5	,	24,439,5663	GG,GA,AA		0.0481,12.2527,3.9749	,	149/391,197/439	183963000	487,11765	1971	4155	6126	SO:0001819	synonymous_variant	10195	exon4			GCAGCAACCCCAG	BC002839	CCDS46967.1, CCDS46968.1	3q27.3	2013-02-26	2013-02-26		ENSG00000214160	ENSG00000214160	2.4.1.258	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	23056	protein-coding gene	gene with protein product	"""carbohydrate deficient glycoprotein syndrome type IV"", ""dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase"", ""dol-P-Man dependent alpha-1,3- mannosyltransferase"""	608750	"""asparagine-linked glycosylation 3 homolog (yeast, alpha-1,3-mannosyltransferase)"", ""asparagine-linked glycosylation 3, alpha-1,3- mannosyltransferase homolog (S. cerevisiae)"""			1058125	Standard	NM_005787		Approved	NOT56L, Not56, CDGS4, D16Ertd36e	uc003fne.2	Q92685	OTTHUMG00000156823	ENST00000397676.3:c.591T>C	3.37:g.183963000A>G		128.0	0.0	0		136.0	67.0	0.492647	NM_005787	A8JZZ6|Q9BT71	Silent	SNP	ENST00000397676.3	37	CCDS46968.1																																																																																			A|0.962;G|0.038	0.038	strong		0.542	ALG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346033.1	NM_005787	
CD163	9332	hgsc.bcm.edu	37	12	7636027	7636027	+	Silent	SNP	A	A	G	rs78817356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:7636027A>G	ENST00000359156.4	-	12	3226	c.3024T>C	c.(3022-3024)tgT>tgC	p.C1008C	CD163_ENST00000396620.3_Silent_p.C1041C|CD163_ENST00000541972.1_Silent_p.C996C|CD163_ENST00000432237.2_Silent_p.C1008C|CD163_ENST00000539632.1_5'UTR	NM_004244.5	NP_004235.4	Q86VB7	C163A_HUMAN	CD163 molecule	1008	SRCR 9. {ECO:0000255|PROSITE- ProRule:PRU00196}.				acute-phase response (GO:0006953)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(33)|ovary(6)|pancreas(2)|prostate(1)|skin(5)|urinary_tract(4)	76					WF10(DB05389)	GTCTGGCAGGACAATCCCACA	0.507													A|||	144	0.028754	0.1014	0.013	5008	,	,		-128	0.0		0.001	False		,,,				2504	0.0				p.C1008C		Atlas-SNP	.											.	CD163	221	.	0			c.T3024C						PASS	.	A	,	305,4101	164.4+/-196.0	6,293,1904	131.0	112.0	118.0		3024,3024	0.5	1.0	12	dbSNP_131	118	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	CD163	NM_004244.5,NM_203416.3	,	6,294,6203	GG,GA,AA		0.0116,6.9224,2.3528	,	1008/1157,1008/1122	7636027	306,12700	2203	4300	6503	SO:0001819	synonymous_variant	9332	exon12			GGCAGGACAATCC	Z22968	CCDS8578.1, CCDS53742.1	12p13	2006-03-28	2006-03-28		ENSG00000177575	ENSG00000177575		"""CD molecules"""	1631	protein-coding gene	gene with protein product		605545	"""CD163 antigen"""			10403791, 8370408	Standard	NM_004244		Approved	M130, MM130	uc001qsz.3	Q86VB7	OTTHUMG00000168353	ENST00000359156.4:c.3024T>C	12.37:g.7636027A>G		131.0	0.0	0		123.0	58.0	0.471545	NM_203416	C9JIG2|Q07898|Q07899|Q07900|Q07901|Q2VLH7	Silent	SNP	ENST00000359156.4	37	CCDS8578.1	42	0.019230769230769232	35	0.07113821138211382	7	0.019337016574585635	0	0.0	0	0.0	A	10.17	1.275594	0.23307	0.069224	1.16E-4	ENSG00000177575	ENST00000537626	.	.	.	5.4	0.458	0.16670	.	.	.	.	.	T	0.08313	0.0207	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.04103	-1.0977	4	.	.	.	.	8.3663	0.32389	0.6729:0.0:0.3271:0.0	.	.	.	.	A	21	.	.	V	-	2	0	CD163	7527294	0.000000	0.05858	0.998000	0.56505	0.984000	0.73092	-0.124000	0.10595	0.121000	0.18284	-0.388000	0.06559	GTC	A|0.978;G|0.022	0.022	strong		0.507	CD163-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000399396.2	NM_004244, NM_203416	
ADAMTSL5	339366	hgsc.bcm.edu	37	19	1506799	1506799	+	Silent	SNP	C	C	T	rs79538691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1506799C>T	ENST00000413997.2	-	10	1010	c.1011G>A	c.(1009-1011)gtG>gtA	p.V337V	ADAMTSL5_ENST00000330475.4_Silent_p.V327V|ADAMTSL5_ENST00000590562.1_5'UTR|CTB-25B13.9_ENST00000590252.1_RNA|ADAMTSL5_ENST00000395467.2_Silent_p.V96V			Q6ZMM2	ATL5_HUMAN	ADAMTS-like 5	337						extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	10		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		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)		GCTGAGGCTCCACCCCCCGGG	0.711													C|||	101	0.0201677	0.0756	0.0014	5008	,	,		10308	0.0		0.0	False		,,,				2504	0.0				p.V327V		Atlas-SNP	.											.	ADAMTSL5	24	.	0			c.G981A						PASS	.	C		192,3668		2,188,1740	7.0	10.0	9.0		981	1.9	0.8	19	dbSNP_131	9	1,7767		0,1,3883	no	coding-synonymous	ADAMTSL5	NM_213604.2		2,189,5623	TT,TC,CC		0.0129,4.9741,1.6598		327/472	1506799	193,11435	1930	3884	5814	SO:0001819	synonymous_variant	339366	exon10			AGGCTCCACCCCC	BC040620	CCDS12071.1	19p13.3	2008-02-05	2006-02-07	2006-02-07		ENSG00000185761			27912	protein-coding gene	gene with protein product			"""thrombospondin, type I, domain containing 6"""	THSD6			Standard	NM_213604		Approved		uc002ltd.2	Q6ZMM2		ENST00000413997.2:c.1011G>A	19.37:g.1506799C>T		36.0	0.0	0		50.0	25.0	0.5	NM_213604	B4DXK7|Q8IW95	Silent	SNP	ENST00000413997.2	37																																																																																				C|0.982;T|0.018	0.018	strong		0.711	ADAMTSL5-202	KNOWN	basic	protein_coding	protein_coding		XM_294919	
C1QL2	165257	hgsc.bcm.edu	37	2	119915750	119915750	+	Silent	SNP	G	G	T	rs113019193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:119915750G>T	ENST00000272520.3	-	1	715	c.96C>A	c.(94-96)atC>atA	p.I32I		NM_182528.3	NP_872334.2	Q7Z5L3	C1QL2_HUMAN	complement component 1, q subcomponent-like 2	32					protein oligomerization (GO:0051259)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)				NS(1)|endometrium(1)|large_intestine(3)|pancreas(1)|prostate(1)	7						AAGGGTCGCAGATCATGCGGC	0.721										HNSCC(49;0.14)			G|||	87	0.0173722	0.0628	0.0043	5008	,	,		7998	0.0		0.001	False		,,,				2504	0.0				p.I32I		Atlas-SNP	.											.	C1QL2	25	.	0			c.C96A						PASS	.	G		134,3240		1,132,1554	6.0	7.0	7.0		96	3.3	1.0	2	dbSNP_132	7	8,7550		0,8,3771	no	coding-synonymous	C1QL2	NM_182528.3		1,140,5325	TT,TG,GG		0.1058,3.9715,1.2989		32/288	119915750	142,10790	1687	3779	5466	SO:0001819	synonymous_variant	165257	exon1			GTCGCAGATCATG	AF525315	CCDS42737.1	2q14.2	2009-05-20			ENSG00000144119	ENSG00000144119			24181	protein-coding gene	gene with protein product	"""C1q and tumor necrosis factor related protein 10"""	614330				18783346	Standard	NM_182528		Approved	CTRP10, C1QTNF10	uc002tlo.2	Q7Z5L3	OTTHUMG00000153271	ENST00000272520.3:c.96C>A	2.37:g.119915750G>T		7.0	0.0	0		7.0	4.0	0.571429	NM_182528		Silent	SNP	ENST00000272520.3	37	CCDS42737.1																																																																																			G|0.981;T|0.019	0.019	strong		0.721	C1QL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330527.2	NM_182528	
ISYNA1	51477	hgsc.bcm.edu	37	19	18547209	18547209	+	Silent	SNP	G	G	A	rs61743954	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18547209G>A	ENST00000338128.8	-	6	907	c.690C>T	c.(688-690)aaC>aaT	p.N230N	ISYNA1_ENST00000457269.4_Silent_p.N176N|ISYNA1_ENST00000317018.6_Silent_p.N28N|ISYNA1_ENST00000545187.1_Silent_p.N80N|ISYNA1_ENST00000578963.1_Silent_p.N102N	NM_001170938.1|NM_016368.4	NP_001164409.1|NP_057452.1	Q9NPH2	INO1_HUMAN	inositol-3-phosphate synthase 1	230					inositol biosynthetic process (GO:0006021)|inositol phosphate metabolic process (GO:0043647)|phospholipid biosynthetic process (GO:0008654)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	inositol-3-phosphate synthase activity (GO:0004512)			breast(1)|endometrium(1)|kidney(2)|lung(4)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(2)	12						AGCGCTCCGTGTTCGCCGTCC	0.632																																					p.N230N		Atlas-SNP	.											.	ISYNA1	31	.	0			c.C690T						PASS	.	G	,,	205,4201	129.8+/-166.5	5,195,2003	104.0	93.0	97.0		528,240,690	1.6	0.5	19	dbSNP_129	97	54,8546	34.8+/-89.0	0,54,4246	no	coding-synonymous,coding-synonymous,coding-synonymous	ISYNA1	NM_001170938.1,NM_001170939.1,NM_016368.4	,,	5,249,6249	AA,AG,GG		0.6279,4.6527,1.9914	,,	176/505,80/409,230/559	18547209	259,12747	2203	4300	6503	SO:0001819	synonymous_variant	51477	exon6			CTCCGTGTTCGCC		CCDS12379.1, CCDS54234.1, CCDS62603.1	19p13.11	2014-09-04			ENSG00000105655	ENSG00000105655	5.5.1.4		29821	protein-coding gene	gene with protein product	"""myo-inositol 1-phosphate synthase"""	611670				15024000, 12941308	Standard	NM_016368		Approved	Ino1, INOS, IPS	uc002njd.2	Q9NPH2	OTTHUMG00000179027	ENST00000338128.8:c.690C>T	19.37:g.18547209G>A		44.0	0.0	0		36.0	12.0	0.333333	NM_016368	B3KRT1|G5E9U0|Q6NXT5|Q7Z525|Q9BT65|Q9H2Y2|Q9NSU0|Q9NVW7	Silent	SNP	ENST00000338128.8	37	CCDS12379.1																																																																																			G|0.982;A|0.018	0.018	strong		0.632	ISYNA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444469.2	NM_016368	
MYH4	4622	hgsc.bcm.edu	37	17	10354747	10354747	+	Missense_Mutation	SNP	C	C	T	rs200121484		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:10354747C>T	ENST00000255381.2	-	28	3871	c.3761G>A	c.(3760-3762)cGc>cAc	p.R1254H	RP11-799N11.1_ENST00000581304.1_RNA|CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_017533.2	NP_060003.2	Q9Y623	MYH4_HUMAN	myosin, heavy chain 4, skeletal muscle	1254					actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|membrane organization (GO:0061024)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to activity (GO:0014823)	muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin filament (GO:0032982)|sarcomere (GO:0030017)	ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|microfilament motor activity (GO:0000146)	p.R1254H(1)		NS(4)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(72)|ovary(10)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	149						CTCTAGGGTGCGGCACATTTT	0.418													C|||	1	0.000199681	0.0008	0.0	5008	,	,		11762	0.0		0.0	False		,,,				2504	0.0				p.R1254H		Atlas-SNP	.											MYH4,caecum,carcinoma,0,1	MYH4	349	1	1	Substitution - Missense(1)	large_intestine(1)	c.G3761A						PASS	.	C	HIS/ARG	5,4401	9.9+/-24.2	0,5,2198	159.0	139.0	146.0		3761	3.6	1.0	17		146	0,8600		0,0,4300	yes	missense	MYH4	NM_017533.2	29	0,5,6498	TT,TC,CC		0.0,0.1135,0.0384	probably-damaging	1254/1940	10354747	5,13001	2203	4300	6503	SO:0001583	missense	4622	exon28			AGGGTGCGGCACA		CCDS11154.1	17p13.1	2013-09-19	2006-09-29		ENSG00000264424	ENSG00000264424		"""Myosins / Myosin superfamily : Class II"""	7574	protein-coding gene	gene with protein product		160742	"""myosin, heavy polypeptide 4, skeletal muscle"""			8518795	Standard	NM_017533		Approved	MYH2B, MyHC-2B, MyHC-IIb	uc002gmn.3	Q9Y623	OTTHUMG00000130365	ENST00000255381.2:c.3761G>A	17.37:g.10354747C>T	ENSP00000255381:p.Arg1254His	198.0	0.0	0		202.0	99.0	0.490099	NM_017533		Missense_Mutation	SNP	ENST00000255381.2	37	CCDS11154.1	.	.	.	.	.	.	.	.	.	.	C	17.94	3.511257	0.64522	0.001135	0.0	ENSG00000141048	ENST00000255381	T	0.78924	-1.22	5.62	3.64	0.41730	Myosin tail (1);	0.000000	0.37219	U	0.002181	T	0.76300	0.3968	M	0.65975	2.015	0.44359	D	0.997257	B	0.18863	0.031	B	0.26770	0.073	T	0.73688	-0.3904	10	0.59425	D	0.04	.	12.8771	0.57996	0.0:0.8666:0.0:0.1334	.	1254	Q9Y623	MYH4_HUMAN	H	1254	ENSP00000255381:R1254H	ENSP00000255381:R1254H	R	-	2	0	MYH4	10295472	0.952000	0.32445	0.963000	0.40424	0.878000	0.50629	2.224000	0.42945	0.845000	0.35118	0.655000	0.94253	CGC	.	.	weak		0.418	MYH4-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252731.1	NM_017533	
POU5F1B	5462	hgsc.bcm.edu	37	8	128428721	128428721	+	Silent	SNP	C	C	T	rs192151034	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:128428721C>T	ENST00000465342.2	+	2	1767	c.610C>T	c.(610-612)Ctg>Ttg	p.L204L	CASC8_ENST00000501396.1_RNA|CASC8_ENST00000502082.1_RNA|POU5F1B_ENST00000391675.1_Silent_p.L204L|CASC8_ENST00000523825.1_RNA			Q06416	P5F1B_HUMAN	POU class 5 homeobox 1B	204	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(1)|prostate(1)|urinary_tract(1)	3						GCGGCCCTTGCTGCAGAAGTG	0.502													c|||	78	0.0155751	0.053	0.0115	5008	,	,		19515	0.0		0.0	False		,,,				2504	0.0				p.L204L		Atlas-SNP	.											.	POU5F1B	32	.	0			c.C610T						PASS	.	C		73,1311		2,69,621	17.0	21.0	20.0		610	1.1	0.8	8		20	0,3180		0,0,1590	no	coding-synonymous	POU5F1B	NM_001159542.1		2,69,2211	TT,TC,CC		0.0,5.2746,1.5995		204/360	128428721	73,4491	692	1590	2282	SO:0001819	synonymous_variant	5462	exon1			CCCTTGCTGCAGA	AF268615	CCDS55274.1	8q24.21	2011-06-20	2009-04-15	2009-04-15	ENSG00000212993	ENSG00000212993		"""Homeoboxes / POU class"""	9223	protein-coding gene	gene with protein product		615739	"""POU domain class 5, transcription factor 1 pseudogene 1"", ""POU class 5 homeobox 1 pseudogene 1"""	OTF3P1, POU5F1P1		1408763	Standard	NM_001159542		Approved	OTF3C	uc003ysf.3	Q06416	OTTHUMG00000157807	ENST00000465342.2:c.610C>T	8.37:g.128428721C>T		124.0	0.0	0		159.0	86.0	0.540881	NM_001159542	D5K9S4|D5K9S9|D5K9T0|D5K9T1|D5K9T3|D5K9U3|D5K9U6|D5K9V4|D5K9V6|D5K9W0|D5K9W2|D5K9W7|D5K9X2|D5K9X3|D5K9X5|D5K9X8|D5K9X9|E9LRB1|E9LRB2|E9LRH5|E9LRH6|E9LRH7|E9LRK4|E9LRK5|E9LRK7|E9LRK8|E9LRM7|E9LRM9|E9LRN2|E9LRN4|E9LRN5|E9LRP8|E9LRQ0|E9LRQ2|E9LRQ3|E9LRQ4|E9LRQ5|E9LRS3|Q2VIK6|Q9BZV7|Q9BZV9	Silent	SNP	ENST00000465342.2	37	CCDS55274.1																																																																																			C|0.985;T|0.015	0.015	strong		0.502	POU5F1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349649.2	NM_001159542	
PRAM1	84106	hgsc.bcm.edu	37	19	8564288	8564288	+	Missense_Mutation	SNP	C	C	T	rs58466313	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8564288C>T	ENST00000423345.4	-	2	924	c.404G>A	c.(403-405)gGg>gAg	p.G135E	PRAM1_ENST00000255612.3_Missense_Mutation_p.G135E			Q96QH2	PRAM_HUMAN	PML-RARA regulated adaptor molecule 1	183	8 X 12 AA repeats of K-P-P-[PQ]-P-[EQ]- [VAF]-T-D-L-P-K.|Pro-rich.				integrin-mediated signaling pathway (GO:0007229)|regulation of neutrophil degranulation (GO:0043313)		lipid binding (GO:0008289)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(5)|prostate(1)|skin(1)	19						CGGAGTGGCCCCCAGCTGTGG	0.657													T|||	813	0.16234	0.5802	0.0519	5008	,	,		12320	0.0		0.004	False		,,,				2504	0.0061				p.G135E		Atlas-SNP	.											.	PRAM1	53	.	0			c.G404A						PASS	.	T	GLU/GLY	1453,2153		274,905,624	35.0	39.0	38.0		404	3.3	0.0	19	dbSNP_129	38	54,7706		2,50,3828	yes	missense	PRAM1	NM_032152.4	98	276,955,4452	TT,TC,CC		0.6959,40.294,13.2588	benign	135/671	8564288	1507,9859	1803	3880	5683	SO:0001583	missense	84106	exon2			GTGGCCCCCAGCT	BC028012	CCDS45954.1, CCDS45954.2	19p13.2	2009-01-21				ENSG00000133246			30091	protein-coding gene	gene with protein product		606466				11301322, 15572693	Standard	NM_032152		Approved	PML-RAR	uc002mkd.3	Q96QH2		ENST00000423345.4:c.404G>A	19.37:g.8564288C>T	ENSP00000408342:p.Gly135Glu	100.0	0.0	0		106.0	105.0	0.990566	NM_032152	Q8N6W7	Missense_Mutation	SNP	ENST00000423345.4	37	CCDS45954.2	286	0.13095238095238096	266	0.540650406504065	18	0.049723756906077346	0	0.0	2	0.002638522427440633	T	0.056	-1.237003	0.01493	0.40294	0.006959	ENSG00000133246	ENST00000255612;ENST00000423345	T;T	0.11385	2.78;2.78	4.32	3.31	0.37934	.	0.543293	0.15485	N	0.259864	T	0.00012	0.0000	N	0.00926	-1.1	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44159	-0.9346	9	0.02654	T	1	.	2.7649	0.05317	0.1891:0.2063:0.0:0.6046	rs58466313	135;183	Q96QH2-2;Q96QH2	.;PRAM_HUMAN	E	135	ENSP00000255612:G135E;ENSP00000408342:G135E	ENSP00000255612:G135E	G	-	2	0	PRAM1	8470288	0.008000	0.16893	0.008000	0.14137	0.015000	0.08874	1.805000	0.38883	0.811000	0.34303	-0.340000	0.08031	GGG	C|0.891;T|0.109	0.109	strong		0.657	PRAM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397040.3	NM_032152	
MUC17	140453	hgsc.bcm.edu	37	7	100680336	100680336	+	Missense_Mutation	SNP	C	C	T	rs74687161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100680336C>T	ENST00000306151.4	+	3	5703	c.5639C>T	c.(5638-5640)gCc>gTc	p.A1880V		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1880	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					ACAACAGTGGCCAGTTCTGAA	0.498													-|||	251	0.0501198	0.1823	0.0144	5008	,	,		24216	0.0		0.0	False		,,,				2504	0.0				p.A1880V		Atlas-SNP	.											.	MUC17	804	.	0			c.C5639T						PASS	.	C	VAL/ALA	665,3741		90,485,1628	240.0	251.0	247.0		5639	-0.3	0.0	7	dbSNP_131	247	6,8594		0,6,4294	no	missense	MUC17	NM_001040105.1	64	90,491,5922	TT,TC,CC		0.0698,15.0931,5.1592	benign	1880/4494	100680336	671,12335	2203	4300	6503	SO:0001583	missense	140453	exon3			CAGTGGCCAGTTC	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.5639C>T	7.37:g.100680336C>T	ENSP00000302716:p.Ala1880Val	130.0	0.0	0		120.0	59.0	0.491667	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	79	0.036172161172161175	77	0.1565040650406504	2	0.0055248618784530384	0	0.0	0	0.0	c	3.374	-0.127886	0.06753	0.150931	6.98E-4	ENSG00000169876	ENST00000306151	T	0.02656	4.21	0.824	-0.353	0.12594	.	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B	0.16802	0.019	B	0.08055	0.003	T	0.45977	-0.9224	8	0.18276	T	0.48	.	5.508	0.16864	0.0:0.7655:0.0:0.2345	.	1880	Q685J3	MUC17_HUMAN	V	1880	ENSP00000302716:A1880V	ENSP00000302716:A1880V	A	+	2	0	MUC17	100467056	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.179000	0.16840	-0.086000	0.12550	0.134000	0.15878	GCC	C|0.958;T|0.042	0.042	strong		0.498	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
SIDT1	54847	hgsc.bcm.edu	37	3	113323785	113323785	+	Missense_Mutation	SNP	G	G	T	rs61732220	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:113323785G>T	ENST00000264852.4	+	14	2092	c.1366G>T	c.(1366-1368)Gcg>Tcg	p.A456S	SIDT1_ENST00000463226.1_3'UTR|SIDT1_ENST00000393830.3_Missense_Mutation_p.A456S	NM_017699.2	NP_060169.2	Q9NXL6	SIDT1_HUMAN	SID1 transmembrane family, member 1	456					dsRNA transport (GO:0033227)	integral component of membrane (GO:0016021)	RNA transmembrane transporter activity (GO:0051033)			breast(1)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(11)|liver(2)|lung(15)|ovary(3)|pancreas(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50						TGTGTTTTACGCGCTGCCCGT	0.468													G|||	91	0.0181709	0.0666	0.0043	5008	,	,		15956	0.0		0.0	False		,,,				2504	0.0				p.A456S		Atlas-SNP	.											.	SIDT1	99	.	0			c.G1366T						PASS	.	G	SER/ALA	281,4125	155.2+/-188.4	10,261,1932	129.0	119.0	122.0		1366	5.9	1.0	3	dbSNP_129	122	2,8598	2.2+/-6.3	0,2,4298	yes	missense	SIDT1	NM_017699.2	99	10,263,6230	TT,TG,GG		0.0233,6.3777,2.1759	benign	456/828	113323785	283,12723	2203	4300	6503	SO:0001583	missense	54847	exon14			TTTTACGCGCTGC	AK000181	CCDS2974.1	3q13.31	2009-11-26			ENSG00000072858	ENSG00000072858			25967	protein-coding gene	gene with protein product		606816					Standard	NM_017699		Approved	FLJ20174, SID-1	uc003eak.3	Q9NXL6	OTTHUMG00000159299	ENST00000264852.4:c.1366G>T	3.37:g.113323785G>T	ENSP00000264852:p.Ala456Ser	75.0	0.0	0		78.0	41.0	0.525641	NM_017699	Q17RR4	Missense_Mutation	SNP	ENST00000264852.4	37	CCDS2974.1	34	0.015567765567765568	33	0.06707317073170732	1	0.0027624309392265192	0	0.0	0	0.0	G	15.33	2.801458	0.50315	0.063777	2.33E-4	ENSG00000072858	ENST00000264852;ENST00000393830	T;T	0.21361	2.01;2.01	5.88	5.88	0.94601	.	0.090977	0.47852	D	0.000207	T	0.02193	0.0068	L	0.51914	1.62	0.80722	D	1	B;B	0.29766	0.215;0.256	B;B	0.37047	0.154;0.24	T	0.01460	-1.1349	10	0.26408	T	0.33	-3.7185	20.2441	0.98394	0.0:0.0:1.0:0.0	rs61732220	456;456	Q9NXL6-2;Q9NXL6	.;SIDT1_HUMAN	S	456	ENSP00000264852:A456S;ENSP00000377416:A456S	ENSP00000264852:A456S	A	+	1	0	SIDT1	114806475	1.000000	0.71417	1.000000	0.80357	0.066000	0.16364	9.697000	0.98697	2.774000	0.95407	0.655000	0.94253	GCG	G|0.981;T|0.019	0.019	strong		0.468	SIDT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317564.1	NM_017699	
LMBR1L	55716	hgsc.bcm.edu	37	12	49498635	49498635	+	Silent	SNP	G	G	T	rs141166526	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:49498635G>T	ENST00000267102.8	-	4	567	c.225C>A	c.(223-225)gcC>gcA	p.A75A	LMBR1L_ENST00000395141.4_Silent_p.A70A|LMBR1L_ENST00000547382.1_Silent_p.A75A|LMBR1L_ENST00000553204.1_5'UTR	NM_018113.2	NP_060583.2	Q6UX01	LMBRL_HUMAN	limb development membrane protein 1-like	75	LCN1-binding.				endocytosis (GO:0006897)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						CAGCACCCAGGGCAATTGCCA	0.587													G|||	22	0.00439297	0.0166	0.0	5008	,	,		22882	0.0		0.0	False		,,,				2504	0.0				p.A75A		Atlas-SNP	.											LMBR1L_ENST00000267102,colon,carcinoma,-1,2	LMBR1L	61	2	0			c.C225A						PASS	.	G		50,4356	48.9+/-83.8	0,50,2153	108.0	78.0	88.0		225	5.2	1.0	12	dbSNP_134	88	0,8600		0,0,4300	no	coding-synonymous	LMBR1L	NM_018113.2		0,50,6453	TT,TG,GG		0.0,1.1348,0.3844		75/490	49498635	50,12956	2203	4300	6503	SO:0001819	synonymous_variant	55716	exon4			ACCCAGGGCAATT	AB033000	CCDS8780.2, CCDS73466.1	12q13.12	2013-08-05	2013-08-05		ENSG00000139636	ENSG00000139636			18268	protein-coding gene	gene with protein product		610007	"""limb region 1 homolog (mouse)-like"""			10574461, 11287427	Standard	XM_005269022		Approved	FLJ10494, KIAA1174	uc001rth.4	Q6UX01	OTTHUMG00000150511	ENST00000267102.8:c.225C>A	12.37:g.49498635G>T		76.0	0.0	0		67.0	33.0	0.492537	NM_018113	Q969J4|Q96BY8|Q96HN8|Q9NT09|Q9NVE1|Q9NVU9|Q9ULP6	Silent	SNP	ENST00000267102.8	37	CCDS8780.2																																																																																			G|0.996;T|0.004	0.004	strong		0.587	LMBR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318696.1	NM_018113	
OR4C16	219428	hgsc.bcm.edu	37	11	55340057	55340057	+	Missense_Mutation	SNP	G	G	A	rs144962866	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55340057G>A	ENST00000314634.3	+	1	454	c.454G>A	c.(454-456)Gtg>Atg	p.V152M		NM_001004701.2	NP_001004701.2	Q8NGL9	OR4CG_HUMAN	olfactory receptor, family 4, subfamily C, member 16 (gene/pseudogene)	152						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(3)|large_intestine(1)|lung(28)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41		all_epithelial(135;0.0748)				GGGATCCTGTGTGCATTCTTT	0.488													g|||	34	0.00678914	0.025	0.0014	5008	,	,		19716	0.0		0.0	False		,,,				2504	0.0				p.V152M		Atlas-SNP	.											.	OR4C16	104	.	0			c.G454A						PASS	.	G	MET/VAL	101,4301	79.9+/-118.3	2,97,2102	149.0	137.0	141.0		454	-2.6	0.3	11	dbSNP_134	141	0,8592		0,0,4296	yes	missense	OR4C16	NM_001004701.2	21	2,97,6398	AA,AG,GG		0.0,2.2944,0.7773	benign	152/311	55340057	101,12893	2201	4296	6497	SO:0001583	missense	219428	exon1			TCCTGTGTGCATT	AB065773	CCDS31502.1	11q11	2013-10-10	2013-10-10		ENSG00000181935	ENSG00000181935		"""GPCR / Class A : Olfactory receptors"""	15172	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily C, member 16"""				Standard	NM_001004701		Approved		uc010rih.2	Q8NGL9	OTTHUMG00000165198	ENST00000314634.3:c.454G>A	11.37:g.55340057G>A	ENSP00000324913:p.Val152Met	144.0	0.0	0		159.0	85.0	0.534591	NM_001004701	Q6IEV8	Missense_Mutation	SNP	ENST00000314634.3	37	CCDS31502.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	G	9.386	1.074257	0.20227	0.022944	0.0	ENSG00000181935	ENST00000314634	T	0.39997	1.05	4.83	-2.58	0.06228	GPCR, rhodopsin-like superfamily (1);	0.267871	0.27139	N	0.020760	T	0.16428	0.0395	L	0.39566	1.225	0.09310	N	1	B	0.18461	0.028	B	0.32211	0.142	T	0.25363	-1.0134	10	0.62326	D	0.03	.	5.5455	0.17061	0.4732:0.1409:0.3859:0.0	.	152	Q8NGL9	OR4CG_HUMAN	M	152	ENSP00000324913:V152M	ENSP00000324913:V152M	V	+	1	0	OR4C16	55096633	0.000000	0.05858	0.326000	0.25389	0.412000	0.31113	-3.095000	0.00607	-0.293000	0.08986	-0.272000	0.10252	GTG	G|0.994;A|0.006	0.006	strong		0.488	OR4C16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382627.1	NM_001004701	
RANBP1	5902	hgsc.bcm.edu	37	22	20112868	20112868	+	Silent	SNP	C	C	T	rs111311060	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:20112868C>T	ENST00000331821.3	+	4	450	c.348C>T	c.(346-348)agC>agT	p.S116S	SNORA77_ENST00000578179.1_RNA|RANBP1_ENST00000430524.1_Silent_p.S26S|RANBP1_ENST00000402752.1_Silent_p.S116S	NM_002882.2	NP_002873.1	P43487	RANG_HUMAN	RAN binding protein 1	116	RanBD1. {ECO:0000255|PROSITE- ProRule:PRU00164}.				intracellular transport (GO:0046907)|positive regulation of mitotic centrosome separation (GO:0046604)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)|spindle organization (GO:0007051)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	GDP-dissociation inhibitor activity (GO:0005092)|GTPase activator activity (GO:0005096)|Ran GTPase binding (GO:0008536)			breast(1)|large_intestine(1)|lung(1)|ovary(1)	4	Colorectal(54;0.0993)					ACGCAGGTAGCGACCGTGCCT	0.607													C|||	15	0.00299521	0.0113	0.0	5008	,	,		18036	0.0		0.0	False		,,,				2504	0.0				p.S116S		Atlas-SNP	.											.	RANBP1	19	.	0			c.C348T						PASS	.	C		33,4373	38.4+/-70.7	0,33,2170	62.0	57.0	59.0		348	-10.0	0.4	22	dbSNP_132	59	0,8600		0,0,4300	no	coding-synonymous	RANBP1	NM_002882.2		0,33,6470	TT,TC,CC		0.0,0.749,0.2537		116/202	20112868	33,12973	2203	4300	6503	SO:0001819	synonymous_variant	5902	exon4			AGGTAGCGACCGT	D38076	CCDS13775.1, CCDS63408.1, CCDS74823.1	22q11.21	2008-06-16			ENSG00000099901	ENSG00000099901			9847	protein-coding gene	gene with protein product		601180				7616957, 10330396	Standard	NM_001278639		Approved	HTF9A	uc002zro.1	P43487	OTTHUMG00000150490	ENST00000331821.3:c.348C>T	22.37:g.20112868C>T		166.0	0.0	0		180.0	91.0	0.505556	NM_002882	Q53EY3	Silent	SNP	ENST00000331821.3	37	CCDS13775.1																																																																																			C|0.997;T|0.003	0.003	strong		0.607	RANBP1-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343733.1	NM_002882	
PCNXL3	399909	hgsc.bcm.edu	37	11	65403666	65403666	+	Silent	SNP	C	C	T	rs61732727	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:65403666C>T	ENST00000355703.3	+	33	6020	c.5481C>T	c.(5479-5481)gcC>gcT	p.A1827A	SIPA1_ENST00000534313.1_5'Flank|MIR4690_ENST00000578459.1_RNA	NM_032223.2	NP_115599.2	Q9H6A9	PCX3_HUMAN	pecanex-like 3 (Drosophila)	1827	Gly-rich.					integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)	13						GCTGTGGCGCCGGCTGCAATA	0.632													C|||	160	0.0319489	0.1112	0.0173	5008	,	,		17328	0.0		0.001	False		,,,				2504	0.0				p.A1827A		Atlas-SNP	.											.	PCNXL3	140	.	0			c.C5481T						PASS	.	C		352,3732		7,338,1697	27.0	32.0	30.0		5481	-7.7	0.9	11	dbSNP_129	30	4,8360		0,4,4178	no	coding-synonymous	PCNXL3	NM_032223.2		7,342,5875	TT,TC,CC		0.0478,8.619,2.8599		1827/2035	65403666	356,12092	2042	4182	6224	SO:0001819	synonymous_variant	399909	exon33			TGGCGCCGGCTGC	BX640978	CCDS44650.1	11q12.1	2008-07-21			ENSG00000197136	ENSG00000197136			18760	protein-coding gene	gene with protein product						15146197	Standard	NM_032223		Approved	FLJ22427	uc001oey.2	Q9H6A9	OTTHUMG00000166539	ENST00000355703.3:c.5481C>T	11.37:g.65403666C>T		138.0	0.0	0		151.0	78.0	0.516556	NM_032223	Q6MZN8	Silent	SNP	ENST00000355703.3	37	CCDS44650.1																																																																																			C|0.974;T|0.026	0.026	strong		0.632	PCNXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390321.1	NM_032223	
PCED1B	91523	hgsc.bcm.edu	37	12	47629179	47629179	+	Silent	SNP	G	G	T	rs79990001	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:47629179G>T	ENST00000546455.1	+	4	1064	c.333G>T	c.(331-333)tcG>tcT	p.S111S	RP11-493L12.3_ENST00000547748.1_RNA|PCED1B_ENST00000432328.1_Silent_p.S111S			Q96HM7	PED1B_HUMAN	PC-esterase domain containing 1B	111							hydrolase activity (GO:0016787)										AGCTGCAGTCGGGCGAGCACG	0.572													G|||	122	0.024361	0.0877	0.0072	5008	,	,		17862	0.0		0.001	False		,,,				2504	0.0				p.S111S		Atlas-SNP	.											FAM113B,rectum,carcinoma,+1,1	.	.	1	0			c.G333T						PASS	.	G		310,4096	167.3+/-198.3	8,294,1901	104.0	116.0	112.0		333	-8.4	0.0	12	dbSNP_132	112	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FAM113B	NM_138371.1		8,295,6200	TT,TG,GG		0.0116,7.0359,2.3912		111/433	47629179	311,12695	2203	4300	6503	SO:0001819	synonymous_variant	91523	exon2			GCAGTCGGGCGAG	BC016154	CCDS8752.1	12q13.11	2012-06-11	2012-06-11	2012-06-11	ENSG00000179715	ENSG00000179715			28255	protein-coding gene	gene with protein product			"""family with sequence similarity 113, member B"""	FAM113B		20056006	Standard	NM_138371		Approved	MGC16044	uc001rpq.3	Q96HM7	OTTHUMG00000169617	ENST00000546455.1:c.333G>T	12.37:g.47629179G>T		36.0	0.0	0		45.0	25.0	0.555556	NM_138371	Q96B20	Silent	SNP	ENST00000546455.1	37	CCDS8752.1																																																																																			G|0.974;T|0.026	0.026	strong		0.572	PCED1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405079.1	NM_138371	
MRPL15	29088	hgsc.bcm.edu	37	8	55047893	55047893	+	Missense_Mutation	SNP	G	G	A	rs200980911	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:55047893G>A	ENST00000260102.4	+	1	124	c.50G>A	c.(49-51)cGg>cAg	p.R17Q		NM_014175.3	NP_054894.1	Q9P015	RM15_HUMAN	mitochondrial ribosomal protein L15	17					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)|skin(3)	10		Lung NSC(129;0.109)|all_epithelial(80;0.134)|all_lung(136;0.181)	OV - Ovarian serous cystadenocarcinoma(7;4.3e-07)|Epithelial(17;5.79e-05)|all cancers(17;0.000458)			GACCTACTCCGGGGCCTGCCG	0.677													g|||	8	0.00159744	0.0045	0.0029	5008	,	,		12630	0.0		0.0	False		,,,				2504	0.0				p.R17Q		Atlas-SNP	.											.	MRPL15	26	.	0			c.G50A						PASS	.	G	GLN/ARG	20,4078		0,20,2029	11.0	13.0	12.0		50	5.1	0.5	8		12	0,8010		0,0,4005	yes	missense	MRPL15	NM_014175.3	43	0,20,6034	AA,AG,GG		0.0,0.488,0.1652	benign	17/297	55047893	20,12088	2049	4005	6054	SO:0001583	missense	29088	exon1			TACTCCGGGGCCT	AB051619	CCDS6158.1	8q11.2-q13	2012-09-13			ENSG00000137547	ENSG00000137547		"""Mitochondrial ribosomal proteins / large subunits"""	14054	protein-coding gene	gene with protein product		611828				11543634	Standard	NM_014175		Approved	RPML7, MRP-L7, HSPC145, L15mt, MRP-L15	uc003xsa.2	Q9P015	OTTHUMG00000164315	ENST00000260102.4:c.50G>A	8.37:g.55047893G>A	ENSP00000260102:p.Arg17Gln	237.0	0.0	0		222.0	106.0	0.477477	NM_014175	Q96Q54|Q9H0Y1	Missense_Mutation	SNP	ENST00000260102.4	37	CCDS6158.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	G	19.81	3.897077	0.72639	0.00488	0.0	ENSG00000137547	ENST00000260102;ENST00000519831	.	.	.	5.07	5.07	0.68467	.	0.111607	0.64402	D	0.000010	T	0.68714	0.3031	L	0.52759	1.655	0.45648	D	0.998575	D	0.69078	0.997	D	0.70227	0.968	T	0.73827	-0.3860	9	0.54805	T	0.06	-19.3451	18.8755	0.92332	0.0:0.0:1.0:0.0	.	17	Q9P015	RM15_HUMAN	Q	17	.	ENSP00000260102:R17Q	R	+	2	0	MRPL15	55210446	0.990000	0.36364	0.459000	0.27081	0.769000	0.43574	5.342000	0.65970	2.533000	0.85409	0.650000	0.86243	CGG	G|0.997;A|0.003	0.003	strong		0.677	MRPL15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378254.1	NM_014175	
PWP2	5822	hgsc.bcm.edu	37	21	45538685	45538685	+	Missense_Mutation	SNP	C	C	T	rs150440839	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45538685C>T	ENST00000291576.7	+	9	1149	c.1022C>T	c.(1021-1023)tCg>tTg	p.S341L		NM_005049.2	NP_005040.2	Q15269	PWP2_HUMAN	PWP2 periodic tryptophan protein homolog (yeast)	341					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(6)|large_intestine(6)|lung(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	21				STAD - Stomach adenocarcinoma(101;0.172)|Colorectal(79;0.2)		ATCAATAGCTCGGGGGACTGG	0.607													C|||	13	0.00259585	0.0098	0.0	5008	,	,		16887	0.0		0.0	False		,,,				2504	0.0				p.S341L		Atlas-SNP	.											.	PWP2	64	.	0			c.C1022T						PASS	.	C	LEU/SER	38,4368	43.1+/-76.7	0,38,2165	127.0	99.0	108.0		1022	5.1	0.9	21	dbSNP_134	108	0,8600		0,0,4300	yes	missense	PWP2	NM_005049.2	145	0,38,6465	TT,TC,CC		0.0,0.8625,0.2922	benign	341/920	45538685	38,12968	2203	4300	6503	SO:0001583	missense	5822	exon9			ATAGCTCGGGGGA		CCDS33579.1	21q22.3	2013-01-10	2001-11-28	2006-11-24	ENSG00000241945	ENSG00000241945		"""WD repeat domain containing"""	9711	protein-coding gene	gene with protein product		601475	"""PWP2 (periodic tryptophan protein, yeast) homolog"""	PWP2H		8893822	Standard	NM_005049		Approved	EHOC-17, UTP1	uc002zeb.3	Q15269	OTTHUMG00000086893	ENST00000291576.7:c.1022C>T	21.37:g.45538685C>T	ENSP00000291576:p.Ser341Leu	176.0	0.0	0		188.0	95.0	0.505319	NM_005049	B2RAG8|Q96A77	Missense_Mutation	SNP	ENST00000291576.7	37	CCDS33579.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	19.96	3.924314	0.73213	0.008625	0.0	ENSG00000241945	ENST00000291576	T	0.44881	0.91	5.05	5.05	0.67936	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (2);WD40-repeat-containing domain (1);	0.462069	0.24755	N	0.035863	T	0.22205	0.0535	L	0.59436	1.845	0.41576	D	0.988714	P	0.39352	0.669	B	0.27887	0.084	T	0.32214	-0.9915	10	0.49607	T	0.09	-12.9707	16.9482	0.86236	0.0:1.0:0.0:0.0	.	341	Q15269	PWP2_HUMAN	L	341	ENSP00000291576:S341L	ENSP00000291576:S341L	S	+	2	0	PWP2	44363113	1.000000	0.71417	0.933000	0.37362	0.909000	0.53808	5.017000	0.64047	2.501000	0.84356	0.555000	0.69702	TCG	C|0.996;T|0.004	0.004	strong		0.607	PWP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195736.3	NM_005049	
ABCB5	340273	hgsc.bcm.edu	37	7	20725366	20725366	+	Silent	SNP	T	T	G	rs115722120	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:20725366T>G	ENST00000404938.2	+	16	2569	c.1917T>G	c.(1915-1917)acT>acG	p.T639T	ABCB5_ENST00000258738.6_Silent_p.T194T	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	639					antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						CATATTCTACTGAAAGAAAGA	0.368													T|||	18	0.00359425	0.0129	0.0	5008	,	,		16557	0.0		0.001	False		,,,				2504	0.0				p.T639T		Atlas-SNP	.											.	ABCB5	357	.	0			c.T1917G						PASS	.	T	,	61,4345	58.1+/-94.6	0,61,2142	94.0	85.0	88.0		1917,582	1.8	0.0	7	dbSNP_132	88	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ABCB5	NM_001163941.1,NM_178559.5	,	0,61,6442	GG,GT,TT		0.0,1.3845,0.469	,	639/1258,194/813	20725366	61,12945	2203	4300	6503	SO:0001819	synonymous_variant	340273	exon16			TTCTACTGAAAGA	U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"""ATP binding cassette transporters / subfamily B"""	46	protein-coding gene	gene with protein product	"""P-glycoprotein ABCB5"", ""ATP-binding cassette protein"""	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	ENST00000404938.2:c.1917T>G	7.37:g.20725366T>G		181.0	0.0	0		185.0	85.0	0.459459	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Silent	SNP	ENST00000404938.2	37	CCDS55090.1																																																																																			T|0.995;G|0.005	0.005	strong		0.368	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	
FREM1	158326	hgsc.bcm.edu	37	9	14863863	14863863	+	Silent	SNP	A	A	G	rs61740262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:14863863A>G	ENST00000380880.3	-	3	1056	c.273T>C	c.(271-273)taT>taC	p.Y91Y	FREM1_ENST00000380881.4_Silent_p.Y91Y|FREM1_ENST00000422223.2_Silent_p.Y91Y			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	91					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)		CATTGTGAACATACTTGACTT	0.393													A|||	159	0.0317492	0.112	0.013	5008	,	,		22501	0.0		0.001	False		,,,				2504	0.001				p.Y91Y		Atlas-SNP	.											.	FREM1	261	.	0			c.T273C						PASS	.	A		313,3603		19,275,1664	115.0	113.0	113.0		273	2.9	0.8	9	dbSNP_129	113	12,8276		0,12,4132	yes	coding-synonymous	FREM1	NM_144966.5		19,287,5796	GG,GA,AA		0.1448,7.9928,2.6631		91/2180	14863863	325,11879	1958	4144	6102	SO:0001819	synonymous_variant	158326	exon4			GTGAACATACTTG	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.273T>C	9.37:g.14863863A>G		107.0	0.0	0		121.0	65.0	0.53719	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Silent	SNP	ENST00000380880.3	37	CCDS47952.1																																																																																			A|0.975;G|0.025	0.025	strong		0.393	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
EIF3M	10480	hgsc.bcm.edu	37	11	32610617	32610617	+	Missense_Mutation	SNP	G	G	T	rs140562244	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:32610617G>T	ENST00000531120.1	+	4	437	c.374G>T	c.(373-375)tGc>tTc	p.C125F	EIF3M_ENST00000524896.1_Intron	NM_006360.4	NP_006351.2			eukaryotic translation initiation factor 3, subunit M											breast(3)|endometrium(4)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	16	Breast(20;0.109)					ACAGTGTATTGCAGCCTTATT	0.408																																					p.C125F		Atlas-SNP	.											.	EIF3M	37	.	0			c.G374T						PASS	.	G	PHE/CYS	14,4390	14.3+/-33.2	0,14,2188	115.0	102.0	106.0		374	5.8	1.0	11	dbSNP_134	106	0,8598		0,0,4299	yes	missense	EIF3M	NM_006360.3	205	0,14,6487	TT,TG,GG		0.0,0.3179,0.1077	benign	125/375	32610617	14,12988	2202	4299	6501	SO:0001583	missense	10480	exon4			TGTATTGCAGCCT	AK131064	CCDS7880.1	11p13	2012-12-13	2007-07-27	2007-07-27	ENSG00000149100	ENSG00000149100			24460	protein-coding gene	gene with protein product	"""transport and golgi organization 7 homolog (Drosophila)"""	609641	"""PCI domain containing 1 (herpesvirus entry mediator)"""	PCID1		15919898, 15919899	Standard	NM_006360		Approved	hfl-B5, FLJ29030, GA17, eIF3m, TANGO7	uc001mtu.4	Q7L2H7	OTTHUMG00000166258	ENST00000531120.1:c.374G>T	11.37:g.32610617G>T	ENSP00000436049:p.Cys125Phe	119.0	0.0	0		154.0	21.0	0.136364	NM_006360		Missense_Mutation	SNP	ENST00000531120.1	37	CCDS7880.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	14.72	2.618767	0.46736	0.003179	0.0	ENSG00000149100	ENST00000531120;ENST00000323213;ENST00000533439	T;T	0.36878	1.23;1.23	5.81	5.81	0.92471	.	0.000000	0.85682	D	0.000000	T	0.45498	0.1345	L	0.59436	1.845	0.80722	D	1	D	0.61080	0.989	P	0.62014	0.897	T	0.27536	-1.0071	10	0.12766	T	0.61	-25.8093	20.0797	0.97768	0.0:0.0:1.0:0.0	.	125	Q7L2H7	EIF3M_HUMAN	F	125;62;62	ENSP00000436049:C125F;ENSP00000319910:C62F	ENSP00000319910:C62F	C	+	2	0	EIF3M	32567193	1.000000	0.71417	1.000000	0.80357	0.365000	0.29674	9.476000	0.97823	2.752000	0.94435	0.467000	0.42956	TGC	G|0.998;T|0.002	0.002	strong		0.408	EIF3M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388762.2	NM_006360	
FES	2242	hgsc.bcm.edu	37	15	91436965	91436965	+	Silent	SNP	C	C	T	rs2227989	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:91436965C>T	ENST00000328850.3	+	17	2269	c.2127C>T	c.(2125-2127)gcC>gcT	p.A709A	FES_ENST00000450438.2_Silent_p.A581A|FES_ENST00000444422.2_Silent_p.A639A|FES_ENST00000394300.3_Silent_p.A651A|FES_ENST00000414248.2_Silent_p.A581A|FES_ENST00000394302.1_Silent_p.A568A	NM_002005.3	NP_001996.1	P07332	FES_HUMAN	FES proto-oncogene, tyrosine kinase	709	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell proliferation (GO:0008283)|multicellular organismal development (GO:0007275)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of myeloid cell differentiation (GO:0045639)|positive regulation of neuron projection development (GO:0010976)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell adhesion (GO:0030155)|regulation of cell differentiation (GO:0045595)|regulation of cell motility (GO:2000145)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of mast cell degranulation (GO:0043304)|regulation of vesicle-mediated transport (GO:0060627)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|microtubule cytoskeleton (GO:0015630)	ATP binding (GO:0005524)|immunoglobulin receptor binding (GO:0034987)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|phosphatidylinositol binding (GO:0035091)|protein tyrosine kinase activity (GO:0004713)			lung(2)|ovary(1)	3	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.229)			GAGAGGAAGCCGATGGGGTCT	0.597													T|||	396	0.0790735	0.2829	0.0274	5008	,	,		19349	0.0		0.003	False		,,,				2504	0.0				p.A709A		Atlas-SNP	.											.	FES	102	.	0			c.C2127T						PASS	.	T	,,,	1132,3264	713.0+/-408.2	156,820,1222	69.0	77.0	74.0		1953,1917,1743,2127	-10.7	0.1	15	dbSNP_98	74	15,8581	816.6+/-406.9	0,15,4283	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FES	NM_001143783.1,NM_001143784.1,NM_001143785.1,NM_002005.3	,,,	156,835,5505	TT,TC,CC		0.1745,25.7507,8.8285	,,,	651/765,639/753,581/695,709/823	91436965	1147,11845	2198	4298	6496	SO:0001819	synonymous_variant	2242	exon17			GGAAGCCGATGGG	X52192	CCDS10365.1, CCDS45349.1, CCDS45350.1, CCDS45351.1	15q26.1	2014-06-26	2014-06-26		ENSG00000182511	ENSG00000182511	2.7.10.1	"""SH2 domain containing"""	3657	protein-coding gene	gene with protein product	"""Oncogene FES, feline sarcoma virus"", ""c-fes/fps protein"""	190030	"""feline sarcoma (Snyder-Theilen) viral (v-fes)/Fujinami avian sarcoma (PRCII) viral (v-fps) oncogene homolog"", ""feline sarcoma oncogene"""			1870997	Standard	NM_002005		Approved	FPS	uc002bpv.3	P07332	OTTHUMG00000044456	ENST00000328850.3:c.2127C>T	15.37:g.91436965C>T		104.0	1.0	0.00961538		70.0	70.0	1	NM_002005	B2R6E6|B4DUD0|E9PC94|E9PC95|Q2VXS7|Q2VXS8|Q2VXT0|Q6GTU5	Silent	SNP	ENST00000328850.3	37	CCDS10365.1																																																																																			C|0.910;T|0.090	0.090	strong		0.597	FES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313497.1	NM_002005	
MUC4	4585	hgsc.bcm.edu	37	3	195509605	195509605	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195509605T>C	ENST00000463781.3	-	2	9305	c.8846A>G	c.(8845-8847)gAc>gGc	p.D2949G	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D2949G	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)		TGAGGAAGTGTCGGTGACAGG	0.587																																					p.D2949G		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,1	MUC4	1505	1	0			c.A8846G						scavenged	.						10.0	8.0	9.0					3																	195509605		648	1502	2150	SO:0001583	missense	4585	exon2			GAAGTGTCGGTGA	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.8846A>G	3.37:g.195509605T>C	ENSP00000417498:p.Asp2949Gly	292.0	2.0	0.00684932		204.0	29.0	0.142157	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	6.649	0.488291	0.12641	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32753	1.45;1.44	.	.	.	.	.	.	.	.	T	0.16938	0.0407	N	0.19112	0.55	0.09310	N	1	P	0.50617	0.937	B	0.42319	0.383	T	0.13683	-1.0500	7	.	.	.	.	5.3345	0.15949	0.0:1.0E-4:0.0:0.9999	.	2821	E7ESK3	.	G	2949	ENSP00000417498:D2949G;ENSP00000420243:D2949G	.	D	-	2	0	MUC4	196994384	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.288000	0.08377	0.000000	0.14550	0.000000	0.15137	GAC	T|0.625;C|0.375	0.375	strong		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
COL21A1	81578	hgsc.bcm.edu	37	6	55925698	55925698	+	Missense_Mutation	SNP	A	A	C	rs545860371		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:55925698A>C	ENST00000244728.5	-	26	2740	c.2343T>G	c.(2341-2343)gaT>gaG	p.D781E	COL21A1_ENST00000535941.1_Missense_Mutation_p.D781E|COL21A1_ENST00000467045.1_5'UTR|COL21A1_ENST00000370819.1_Missense_Mutation_p.D778E|COL21A1_ENST00000370808.2_Missense_Mutation_p.D181E	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	781	Collagen-like 5.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|prostate(2)	41	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			CGGGCTTCCCATCCAAACCTG	0.473													A|||	1	0.000199681	0.0	0.0	5008	,	,		15984	0.001		0.0	False		,,,				2504	0.0				p.D781E		Atlas-SNP	.											.	COL21A1	201	.	0			c.T2343G						PASS	.						44.0	43.0	43.0					6																	55925698		1837	4081	5918	SO:0001583	missense	81578	exon26			CTTCCCATCCAAA	AF330693	CCDS55025.1	6p12.3-p11.2	2013-01-16			ENSG00000124749	ENSG00000124749		"""Collagens"""	17025	protein-coding gene	gene with protein product		610002				11566190	Standard	XR_241922		Approved		uc003pcs.3	Q96P44	OTTHUMG00000014907	ENST00000244728.5:c.2343T>G	6.37:g.55925698A>C	ENSP00000244728:p.Asp781Glu	96.0	0.0	0		92.0	23.0	0.25	NM_030820	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Missense_Mutation	SNP	ENST00000244728.5	37	CCDS55025.1	.	.	.	.	.	.	.	.	.	.	A	11.01	1.513616	0.27123	.	.	ENSG00000124749	ENST00000244728;ENST00000370819;ENST00000535941;ENST00000370811;ENST00000370808	D;D;D;D	0.93133	-3.17;-3.17;-3.17;-3.16	4.9	3.74	0.42951	.	0.191909	0.35739	N	0.003010	T	0.80336	0.4604	N	0.25201	0.72	0.32304	N	0.56468	D;D;P;D	0.57571	0.975;0.98;0.789;0.98	P;P;B;P	0.52454	0.573;0.699;0.444;0.699	T	0.75255	-0.3382	10	0.07644	T	0.81	.	4.3365	0.11089	0.6951:0.0:0.1586:0.1463	.	181;781;781;138	Q96P44-2;B7ZLK3;Q96P44;B3KU30	.;.;COLA1_HUMAN;.	E	781;778;781;778;181	ENSP00000244728:D781E;ENSP00000359855:D778E;ENSP00000444384:D781E;ENSP00000359844:D181E	ENSP00000244728:D781E	D	-	3	2	COL21A1	56033657	1.000000	0.71417	0.996000	0.52242	0.986000	0.74619	1.167000	0.31847	0.830000	0.34757	0.533000	0.62120	GAT	.	.	none		0.473	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2		
ANGPTL1	9068	hgsc.bcm.edu	37	1	178834231	178834231	+	Silent	SNP	T	T	C	rs6689778	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:178834231T>C	ENST00000234816.2	-	3	1128	c.681A>G	c.(679-681)caA>caG	p.Q227Q	ANGPTL1_ENST00000367629.1_Silent_p.Q227Q|RALGPS2_ENST00000367635.3_Intron|RALGPS2_ENST00000367634.2_Intron	NM_004673.3	NP_004664.1	O95841	ANGL1_HUMAN	angiopoietin-like 1	227					transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			breast(2)|endometrium(1)|large_intestine(2)|lung(7)|pancreas(1)|skin(1)	14						GAGTATACTGTTGGCTGTTAG	0.498													A|||	283	0.0565096	0.2035	0.0202	5008	,	,		18124	0.0		0.0	False		,,,				2504	0.0				p.Q227Q		Atlas-SNP	.											.	ANGPTL1	41	.	0			c.A681G						PASS	.	A	,	822,3584		80,662,1461	118.0	108.0	111.0		681,	-8.9	0.1	1	dbSNP_116	111	4,8596		0,4,4296	no	coding-synonymous,intron	ANGPTL1,RALGPS2	NM_004673.3,NM_152663.3	,	80,666,5757	CC,CT,TT		0.0465,18.6564,6.3509	,	227/492,	178834231	826,12180	2203	4300	6503	SO:0001819	synonymous_variant	9068	exon3			ATACTGTTGGCTG	AF107253	CCDS1327.1	1q25.2	2013-02-06			ENSG00000116194	ENSG00000116194		"""Fibrinogen C domain containing"""	489	protein-coding gene	gene with protein product	"""angioarrestin"""	603874		ANGPT3		10025962, 9286704	Standard	NM_004673		Approved	ANG3, AngY, ARP1	uc001gma.3	O95841	OTTHUMG00000035075	ENST00000234816.2:c.681A>G	1.37:g.178834231T>C		110.0	0.0	0		128.0	48.0	0.375	NM_004673	Q5T5Z5	Silent	SNP	ENST00000234816.2	37	CCDS1327.1																																																																																			T|0.939;C|0.061	0.061	strong		0.498	ANGPTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084924.1	NM_004673	
ZNF679	168417	hgsc.bcm.edu	37	7	63727210	63727210	+	Missense_Mutation	SNP	G	G	A	rs142919190	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:63727210G>A	ENST00000421025.1	+	5	1468	c.1199G>A	c.(1198-1200)aGt>aAt	p.S400N	ZNF679_ENST00000255746.4_Missense_Mutation_p.S400N	NM_001159524.1|NM_153363.2	NP_001152996.1|NP_699194.2	Q8IYX0	ZN679_HUMAN	zinc finger protein 679	400					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(2)|kidney(3)|lung(11)|skin(1)|stomach(1)	18						AATCATAAGAGTATGCATACT	0.338													.|||	38	0.00758786	0.0287	0.0	5008	,	,		18314	0.0		0.0	False		,,,				2504	0.0				p.S400N		Atlas-SNP	.											ZNF679,NS,carcinoma,0,1	ZNF679	80	1	0			c.G1199A						PASS	.	G	ASN/SER	29,1355		0,29,663	26.0	25.0	25.0		1199	0.8	0.5	7	dbSNP_134	25	0,3182		0,0,1591	no	missense	ZNF679	NM_153363.2	46	0,29,2254	AA,AG,GG		0.0,2.0954,0.6351	benign	400/412	63727210	29,4537	692	1591	2283	SO:0001583	missense	168417	exon5			ATAAGAGTATGCA	BC033523	CCDS47592.1	7q11.21	2013-01-08			ENSG00000197123	ENSG00000197123		"""Zinc fingers, C2H2-type"", ""-"""	28650	protein-coding gene	gene with protein product	"""hypothetical protein MGC42415"""					12477932	Standard	NM_153363		Approved	MGC42415	uc003tsx.3	Q8IYX0	OTTHUMG00000156486	ENST00000421025.1:c.1199G>A	7.37:g.63727210G>A	ENSP00000416809:p.Ser400Asn	24.0	0.0	0		34.0	20.0	0.588235	NM_153363		Missense_Mutation	SNP	ENST00000421025.1	37	CCDS47592.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	11.97	1.796444	0.31777	0.020954	0.0	ENSG00000197123	ENST00000421025;ENST00000255746	T;T	0.01139	5.28;5.28	0.819	0.819	0.18785	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00496	0.0016	N	0.11818	0.18	0.21020	N	0.999808	B	0.25007	0.116	B	0.28011	0.085	T	0.49560	-0.8927	9	0.62326	D	0.03	.	6.9957	0.24780	0.0:0.0:1.0:0.0	.	400	Q8IYX0	ZN679_HUMAN	N	400	ENSP00000416809:S400N;ENSP00000255746:S400N	ENSP00000255746:S400N	S	+	2	0	ZNF679	63364645	0.000000	0.05858	0.476000	0.27291	0.477000	0.33069	-0.030000	0.12308	0.191000	0.20236	0.194000	0.17425	AGT	G|0.997;A|0.003	0.003	strong		0.338	ZNF679-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344317.2	NM_153363	
DENND2A	27147	hgsc.bcm.edu	37	7	140225578	140225578	+	Silent	SNP	G	G	A	rs61737086	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140225578G>A	ENST00000275884.6	-	15	2937	c.2520C>T	c.(2518-2520)gaC>gaT	p.D840D	DENND2A_ENST00000537639.1_Silent_p.D840D|DENND2A_ENST00000496613.1_Silent_p.D840D			Q9ULE3	DEN2A_HUMAN	DENN/MADD domain containing 2A	840	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|retrograde transport, endosome to Golgi (GO:0042147)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(22)|ovary(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	49	Melanoma(164;0.00956)					TGTTGACGAGGTCAACCACAA	0.537													G|||	248	0.0495208	0.171	0.0101	5008	,	,		18548	0.0		0.0	False		,,,				2504	0.0153				p.D840D		Atlas-SNP	.											.	DENND2A	132	.	0			c.C2520T						PASS	.	G		507,3455		30,447,1504	49.0	53.0	52.0		2520	2.6	1.0	7	dbSNP_129	52	4,8336		0,4,4166	no	coding-synonymous	DENND2A	NM_015689.3		30,451,5670	AA,AG,GG		0.048,12.7966,4.1538		840/1010	140225578	511,11791	1981	4170	6151	SO:0001819	synonymous_variant	27147	exon14			GACGAGGTCAACC	AB033103	CCDS43659.1	7q34	2012-10-03	2005-08-17	2005-08-17	ENSG00000146966	ENSG00000146966		"""DENN/MADD domain containing"""	22212	protein-coding gene	gene with protein product			"""KIAA1277"""	KIAA1277			Standard	NM_015689		Approved	FAM31D	uc010lnj.3	Q9ULE3	OTTHUMG00000157411	ENST00000275884.6:c.2520C>T	7.37:g.140225578G>A		92.0	0.0	0		111.0	60.0	0.540541	NM_015689	C9JUI3|Q1RMD5|Q86XY0	Silent	SNP	ENST00000275884.6	37	CCDS43659.1																																																																																			G|0.968;A|0.032	0.032	strong		0.537	DENND2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348742.1	NM_015689	
CDYL	9425	hgsc.bcm.edu	37	6	4892381	4892381	+	Silent	SNP	C	C	T	rs734783	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:4892381C>T	ENST00000328908.5	+	4	752	c.621C>T	c.(619-621)acC>acT	p.T207T	CDYL_ENST00000449732.2_Silent_p.T21T|CDYL_ENST00000397588.3_Silent_p.T153T|CDYL_ENST00000472453.1_Intron|CDYL_ENST00000343762.5_Silent_p.T21T			Q9Y232	CDYL1_HUMAN	chromodomain protein, Y-like	207	Interaction with EZH2.				regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|methylated histone binding (GO:0035064)|transcription corepressor activity (GO:0003714)			breast(2)|kidney(2)|large_intestine(9)|lung(13)|skin(1)|stomach(2)|urinary_tract(1)	30	Ovarian(93;0.11)	all_hematologic(90;0.0901)|Lung NSC(90;0.244)		OV - Ovarian serous cystadenocarcinoma(45;0.182)		AGAGCAGGACCGCAGTGGACG	0.587													C|||	250	0.0499201	0.18	0.0159	5008	,	,		19239	0.0		0.001	False		,,,				2504	0.0				p.T153T		Atlas-SNP	.											.	CDYL	74	.	0			c.C459T						PASS	.	C	,,	664,3742	284.3+/-277.5	59,546,1598	66.0	67.0	67.0		63,63,459	3.8	0.8	6	dbSNP_86	67	20,8580	14.6+/-50.1	0,20,4280	no	coding-synonymous,coding-synonymous,coding-synonymous	CDYL	NM_001143970.1,NM_001143971.1,NM_004824.3	,,	59,566,5878	TT,TC,CC		0.2326,15.0704,5.2591	,,	21/413,21/413,153/545	4892381	684,12322	2203	4300	6503	SO:0001819	synonymous_variant	9425	exon2			CAGGACCGCAGTG	AF081258	CCDS4491.2, CCDS47364.1	6p25.1	2010-05-04	2003-09-12		ENSG00000153046	ENSG00000153046			1811	protein-coding gene	gene with protein product	"""CDY-like, autosomal"", ""testis-specific chromodomain Y-like protein"""	603778	"""chromodomain protein, Y chromosome-like"""			10192397	Standard	NM_001143970		Approved	DKFZP586C1622, CDYL1	uc003mwj.3	Q9Y232	OTTHUMG00000014170	ENST00000328908.5:c.621C>T	6.37:g.4892381C>T		54.0	0.0	0		91.0	47.0	0.516484	NM_004824	A8K6D6|B4DLG4|Q0VDG7|Q32NC5|Q5VX99|Q6P7T5|Q9BWZ2|Q9Y424	Silent	SNP	ENST00000328908.5	37																																																																																				C|0.956;T|0.044	0.044	strong		0.587	CDYL-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000039736.1	NM_004824	
PCCA	5095	hgsc.bcm.edu	37	13	100992428	100992428	+	Missense_Mutation	SNP	A	A	T	rs112237881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:100992428A>T	ENST00000376285.1	+	18	1596	c.1558A>T	c.(1558-1560)Agt>Tgt	p.S520C	PCCA_ENST00000376286.4_Missense_Mutation_p.S494C|PCCA_ENST00000376279.3_Missense_Mutation_p.S520C	NM_000282.3	NP_000273.2	P05165	PCCA_HUMAN	propionyl CoA carboxylase, alpha polypeptide	520					biotin metabolic process (GO:0006768)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)	ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|propionyl-CoA carboxylase activity (GO:0004658)			breast(1)|endometrium(1)|kidney(1)|large_intestine(12)|lung(8)|prostate(1)|skin(2)	26	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Biotin(DB00121)	GCTAACCAAGAGTGAGAAGAA	0.348													A|||	14	0.00279553	0.0098	0.0014	5008	,	,		20036	0.0		0.0	False		,,,				2504	0.0				p.S520C		Atlas-SNP	.											.	PCCA	59	.	0			c.A1558T						PASS	.	A	CYS/SER,CYS/SER,CYS/SER	18,4388	25.3+/-52.1	0,18,2185	145.0	133.0	137.0		1558,1480,1558	4.1	0.0	13	dbSNP_132	137	0,8600		0,0,4300	yes	missense,missense,missense	PCCA	NM_000282.3,NM_001127692.2,NM_001178004.1	112,112,112	0,18,6485	TT,TA,AA		0.0,0.4085,0.1384	benign,benign,benign	520/729,494/703,520/682	100992428	18,12988	2203	4300	6503	SO:0001583	missense	5095	exon18			ACCAAGAGTGAGA	X14608	CCDS9496.2, CCDS45065.1, CCDS53878.1	13q32	2011-01-14	2010-04-30		ENSG00000175198	ENSG00000175198	6.4.1.3		8653	protein-coding gene	gene with protein product		232000	"""propionyl Coenzyme A carboxylase, alpha polypeptide"""			1427880	Standard	NM_000282		Approved		uc001voo.3	P05165	OTTHUMG00000017284	ENST00000376285.1:c.1558A>T	13.37:g.100992428A>T	ENSP00000365462:p.Ser520Cys	88.0	0.0	0		94.0	43.0	0.457447	NM_001178004	B4DKY8|B4DPF9|C9JPQ8|Q15979|Q8WXQ7	Missense_Mutation	SNP	ENST00000376285.1	37	CCDS9496.2	6|6	0.0027472527472527475|0.0027472527472527475	5|5	0.01016260162601626|0.01016260162601626	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	A|A	11.63|11.63	1.697151|1.697151	0.30142|0.30142	0.004085|0.004085	0.0|0.0	ENSG00000175198|ENSG00000175198	ENST00000443601|ENST00000376286;ENST00000376279;ENST00000376285;ENST00000424527;ENST00000376254;ENST00000536640	.|D;D;D;D	.|0.97186	.|-4.27;-4.25;-4.28;-1.72	5.3|5.3	4.08|4.08	0.47627|0.47627	.|.	.|1.227710	.|0.05174	.|N	.|0.499995	D|D	0.94165|0.94165	0.8128|0.8128	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.29886	.|0.26;0.221;0.26	.|B;B;B	.|0.41440	.|0.246;0.357;0.246	D|D	0.88437|0.88437	0.3039|0.3039	5|10	.|0.66056	.|D	.|0.02	.|.	11.3631|11.3631	0.49655|0.49655	0.693:0.307:0.0:0.0|0.693:0.307:0.0:0.0	.|.	.|520;494;520	.|C9JPQ8;P05165-2;P05165	.|.;.;PCCA_HUMAN	S|C	111|494;520;520;54;111;16	.|ENSP00000365463:S494C;ENSP00000365456:S520C;ENSP00000365462:S520C;ENSP00000396050:S54C	.|ENSP00000365430:S111C	R|S	+|+	3|1	2|0	PCCA|PCCA	99790429|99790429	0.447000|0.447000	0.25673|0.25673	0.022000|0.022000	0.16811|0.16811	0.327000|0.327000	0.28475|0.28475	1.075000|1.075000	0.30716|0.30716	0.923000|0.923000	0.37045|0.37045	0.528000|0.528000	0.53228|0.53228	AGA|AGT	A|0.997;T|0.003	0.003	strong		0.348	PCCA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045627.2		
FKBP14	55033	hgsc.bcm.edu	37	7	30054492	30054492	+	Silent	SNP	C	C	T	rs142474407	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:30054492C>T	ENST00000222803.5	-	4	670	c.495G>A	c.(493-495)aaG>aaA	p.K165K	AC007285.6_ENST00000419103.1_RNA|AC007285.6_ENST00000422239.1_RNA	NM_017946.3	NP_060416.1	Q9NWM8	FKB14_HUMAN	FK506 binding protein 14, 22 kDa	165	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|chaperone-mediated protein folding (GO:0061077)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|large_intestine(2)|lung(2)	5						CAAACTCCTTCTTTAAATATG	0.348													C|||	10	0.00199681	0.0076	0.0	5008	,	,		14950	0.0		0.0	False		,,,				2504	0.0				p.K165K		Atlas-SNP	.											.	FKBP14	18	.	0			c.G495A						PASS	.	C		39,4367	38.4+/-70.7	1,37,2165	85.0	80.0	82.0		495	5.0	1.0	7	dbSNP_134	82	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FKBP14	NM_017946.2		1,38,6464	TT,TC,CC		0.0116,0.8852,0.3076		165/212	30054492	40,12966	2203	4300	6503	SO:0001819	synonymous_variant	55033	exon4			CTCCTTCTTTAAA	AK000738	CCDS5423.1	7p15	2014-09-17	2002-08-29		ENSG00000106080	ENSG00000106080		"""EF-hand domain containing"""	18625	protein-coding gene	gene with protein product		614505	"""FK506 binding protein 14 (22 kDa)"""			12036304	Standard	NM_017946		Approved	FLJ20731, FKBP22	uc003tal.2	Q9NWM8	OTTHUMG00000023442	ENST00000222803.5:c.495G>A	7.37:g.30054492C>T		63.0	0.0	0		66.0	42.0	0.636364	NM_017946		Silent	SNP	ENST00000222803.5	37	CCDS5423.1																																																																																			C|0.997;T|0.003	0.003	strong		0.348	FKBP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214229.1	NM_017946	
ZNF765	91661	hgsc.bcm.edu	37	19	53911041	53911041	+	Missense_Mutation	SNP	A	A	G	rs116731689	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:53911041A>G	ENST00000396408.3	+	4	350	c.233A>G	c.(232-234)gAa>gGa	p.E78G	ZNF765_ENST00000594030.1_Intron	NM_001040185.1	NP_001035275.1	Q7L2R6	ZN765_HUMAN	zinc finger protein 765	78	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)			endometrium(1)|lung(3)	4				GBM - Glioblastoma multiforme(134;0.00379)		CAAAGACATGAAAGTCATCAC	0.378													.|||	152	0.0303514	0.1112	0.0029	5008	,	,		19693	0.0		0.003	False		,,,				2504	0.0				p.E78G		Atlas-SNP	.											.	ZNF765	61	.	0			c.A233G						PASS	.	A	GLY/GLU	374,4018	175.9+/-205.1	16,342,1838	73.0	74.0	74.0		233	1.2	0.0	19	dbSNP_132	74	6,8586	3.0+/-9.4	0,6,4290	yes	missense	ZNF765	NM_001040185.1	98	16,348,6128	GG,GA,AA		0.0698,8.5155,2.9267	benign	78/524	53911041	380,12604	2196	4296	6492	SO:0001583	missense	91661	exon4			GACATGAAAGTCA	BC017357	CCDS46171.1	19q13.41	2013-01-08				ENSG00000196417		"""Zinc fingers, C2H2-type"", ""-"""	25092	protein-coding gene	gene with protein product						12477932	Standard	XR_430215		Approved		uc002qbm.3	Q7L2R6		ENST00000396408.3:c.233A>G	19.37:g.53911041A>G	ENSP00000379689:p.Glu78Gly	209.0	0.0	0		264.0	129.0	0.488636	NM_001040185	A8MYG0|B4DF18|B7ZAI5|B9EIL1|Q9BV49	Missense_Mutation	SNP	ENST00000396408.3	37	CCDS46171.1	47	0.02152014652014652	44	0.08943089430894309	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	A	13.11	2.139154	0.37728	0.085155	6.98E-4	ENSG00000196417	ENST00000396408;ENST00000505866	T;T	0.08896	3.04;4.0	1.21	1.21	0.21127	Krueppel-associated box (1);	.	.	.	.	T	0.00241	0.0007	N	0.17082	0.46	0.09310	N	1	B	0.34241	0.444	B	0.38880	0.284	T	0.47471	-0.9115	8	.	.	.	.	4.4592	0.11657	1.0:0.0:0.0:0.0	.	78	Q7L2R6	ZN765_HUMAN	G	78;25	ENSP00000379689:E78G;ENSP00000421579:E25G	.	E	+	2	0	ZNF765	58602853	0.000000	0.05858	0.013000	0.15412	0.045000	0.14185	0.406000	0.21032	0.523000	0.28482	0.147000	0.16070	GAA	A|0.975;G|0.025	0.025	strong		0.378	ZNF765-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371603.1	NM_138372	
UNC45A	55898	hgsc.bcm.edu	37	15	91485730	91485730	+	Missense_Mutation	SNP	C	C	G	rs115978927	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:91485730C>G	ENST00000418476.2	+	7	791	c.751C>G	c.(751-753)Cag>Gag	p.Q251E	UNC45A_ENST00000553671.2_Intron|UNC45A_ENST00000394275.2_Missense_Mutation_p.Q236E	NM_018671.3	NP_061141.2	Q9H3U1	UN45A_HUMAN	unc-45 homolog A (C. elegans)	251					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			CGTGGAAAGCCAGGCTGTGTC	0.557													C|||	48	0.00958466	0.0325	0.0072	5008	,	,		19205	0.0		0.0	False		,,,				2504	0.0				p.Q251E		Atlas-SNP	.											.	UNC45A	57	.	0			c.C751G						PASS	.	C	GLU/GLN,GLU/GLN	99,4297	79.3+/-117.8	1,97,2100	118.0	109.0	112.0		706,751	4.6	1.0	15	dbSNP_132	112	1,8595	1.2+/-3.3	0,1,4297	yes	missense,missense	UNC45A	NM_001039675.1,NM_018671.3	29,29	1,98,6397	GG,GC,CC		0.0116,2.252,0.7697	benign,benign	236/930,251/945	91485730	100,12892	2198	4298	6496	SO:0001583	missense	55898	exon7			GAAAGCCAGGCTG		CCDS10367.1, CCDS42082.1	15q26.1	2008-02-05			ENSG00000140553	ENSG00000140553			30594	protein-coding gene	gene with protein product	"""smooth muscle cell associated protein-1"""	611219				12356907	Standard	XM_005254963		Approved	SMAP-1, GC-UNC45	uc002bqg.3	Q9H3U1	OTTHUMG00000141261	ENST00000418476.2:c.751C>G	15.37:g.91485730C>G	ENSP00000407487:p.Gln251Glu	100.0	0.0	0		85.0	38.0	0.447059	NM_018671	A8K6F7|Q7L3Y6|Q9H3U8|Q9NSE8|Q9NSE9	Missense_Mutation	SNP	ENST00000418476.2	37	CCDS10367.1	14	0.00641025641025641	12	0.024390243902439025	2	0.0055248618784530384	0	0.0	0	0.0	C	3.104	-0.184173	0.06340	0.02252	1.16E-4	ENSG00000140553	ENST00000394275;ENST00000418476	T;T	0.44482	0.92;0.92	5.5	4.56	0.56223	Armadillo-like helical (1);Armadillo-type fold (1);	0.329961	0.31051	N	0.008356	T	0.06872	0.0175	N	0.01109	-1.01	0.28195	N	0.927606	B;B;B;B	0.12630	0.004;0.006;0.0;0.0	B;B;B;B	0.08055	0.002;0.003;0.001;0.001	T	0.12708	-1.0537	10	0.02654	T	1	-19.8406	13.9263	0.63964	0.0:0.6338:0.3662:0.0	.	251;243;251;236	B4DZL0;B4DLE6;Q9H3U1;A8K6F7	.;.;UN45A_HUMAN;.	E	236;251	ENSP00000377816:Q236E;ENSP00000407487:Q251E	ENSP00000377816:Q236E	Q	+	1	0	UNC45A	89286734	0.984000	0.35163	1.000000	0.80357	0.929000	0.56500	3.726000	0.54977	1.405000	0.46838	0.558000	0.71614	CAG	C|0.991;G|0.009	0.009	strong		0.557	UNC45A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000280406.2	NM_018671	
SLC6A3	6531	hgsc.bcm.edu	37	5	1409226	1409226	+	Silent	SNP	G	G	C	rs8179035	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:1409226G>C	ENST00000270349.9	-	11	1540	c.1413C>G	c.(1411-1413)gtC>gtG	p.V471V	SLC6A3_ENST00000453492.2_Silent_p.V471V	NM_001044.4	NP_001035.1	Q01959	SC6A3_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 3	471			V -> I (in dbSNP:rs75916702). {ECO:0000269|PubMed:21179162}.		adenohypophysis development (GO:0021984)|aging (GO:0007568)|cation transmembrane transport (GO:0098655)|cell death (GO:0008219)|dopamine biosynthetic process (GO:0042416)|dopamine catabolic process (GO:0042420)|dopamine transport (GO:0015872)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|neurotransmitter biosynthetic process (GO:0042136)|positive regulation of multicellular organism growth (GO:0040018)|prepulse inhibition (GO:0060134)|regulation of dopamine metabolic process (GO:0042053)|response to cAMP (GO:0051591)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to iron ion (GO:0010039)|response to nicotine (GO:0035094)|sensory perception of smell (GO:0007608)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	axon (GO:0030424)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine transmembrane transporter activity (GO:0005329)|dopamine:sodium symporter activity (GO:0005330)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)			breast(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(19)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38			OV - Ovarian serous cystadenocarcinoma(19;0.00928)|all cancers(22;0.0262)		Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Benzatropine(DB00245)|Benzphetamine(DB00865)|Bupropion(DB01156)|Chloroprocaine(DB01161)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Cocaine(DB00907)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Diethylpropion(DB00937)|Diphenylpyraline(DB01146)|Dopamine(DB00988)|Duloxetine(DB00476)|Ephedra(DB01363)|Escitalopram(DB01175)|Fencamfamine(DB01463)|Imipramine(DB00458)|Ioflupane I 123(DB08824)|Lisdexamfetamine(DB01255)|Loxapine(DB00408)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Mirtazapine(DB00370)|Modafinil(DB00745)|Nefazodone(DB01149)|Pethidine(DB00454)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Procaine(DB00721)|Pseudoephedrine(DB00852)|Sertraline(DB01104)|Sibutramine(DB01105)|Trimipramine(DB00726)|Venlafaxine(DB00285)	GGAGCGTGAAGACGTAGATGC	0.572													G|||	21	0.00419329	0.0129	0.0029	5008	,	,		17164	0.0		0.002	False		,,,				2504	0.0				p.V471V		Atlas-SNP	.											SLC6A3,NS,carcinoma,-1,1	SLC6A3	102	1	0			c.C1413G						PASS	.	G		59,4343	55.5+/-91.7	0,59,2142	56.0	49.0	51.0		1413	0.7	1.0	5	dbSNP_125	51	1,8589		0,1,4294	no	coding-synonymous	SLC6A3	NM_001044.4		0,60,6436	CC,CG,GG		0.0116,1.3403,0.4618		471/621	1409226	60,12932	2201	4295	6496	SO:0001819	synonymous_variant	6531	exon11			CGTGAAGACGTAG		CCDS3863.1	5p15.3	2013-07-19	2013-07-19		ENSG00000142319	ENSG00000142319		"""Solute carriers"""	11049	protein-coding gene	gene with protein product	"""dopamine transporter"""	126455	"""solute carrier family 6 (neurotransmitter transporter, dopamine), member 3"", ""dopamine transporter 1"""	DAT1		1406597	Standard	NM_001044		Approved	DAT	uc003jck.3	Q01959	OTTHUMG00000131016	ENST00000270349.9:c.1413C>G	5.37:g.1409226G>C		44.0	0.0	0		63.0	32.0	0.507937	NM_001044	A2RUN4|Q14996	Silent	SNP	ENST00000270349.9	37	CCDS3863.1																																																																																			G|0.995;C|0.005	0.005	strong		0.572	SLC6A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253650.3	NM_001044	
POLRMT	5442	hgsc.bcm.edu	37	19	622304	622304	+	Missense_Mutation	SNP	G	G	A	rs41545023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:622304G>A	ENST00000588649.2	-	9	1780	c.1696C>T	c.(1696-1698)Ccc>Tcc	p.P566S	LLNLR-299G3.1_ENST00000607288.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	566					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)			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)		AGGGGCCAGGGCTGCTCCCGC	0.706													G|||	32	0.00638978	0.0212	0.0058	5008	,	,		13734	0.0		0.0	False		,,,				2504	0.0				p.P566S		Atlas-SNP	.											.	POLRMT	91	.	0			c.C1696T						PASS	.	G	SER/PRO	59,4143		0,59,2042	5.0	6.0	6.0		1696	3.0	1.0	19	dbSNP_127	6	0,8252		0,0,4126	no	missense	POLRMT	NM_005035.3	74	0,59,6168	AA,AG,GG		0.0,1.4041,0.4737	benign	566/1231	622304	59,12395	2101	4126	6227	SO:0001583	missense	5442	exon9			GCCAGGGCTGCTC		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.1696C>T	19.37:g.622304G>A	ENSP00000465759:p.Pro566Ser	34.0	0.0	0		42.0	23.0	0.547619	NM_005035	O60370	Missense_Mutation	SNP	ENST00000588649.2	37	CCDS12036.1	.	.	.	.	.	.	.	.	.	.	.	7.555	0.663560	0.14710	0.014041	0.0	ENSG00000099821	ENST00000215591	T	0.41065	1.01	4.15	3.02	0.34903	.	0.759629	0.13016	N	0.420516	T	0.26231	0.0640	M	0.64170	1.965	0.26553	N	0.973879	B	0.22683	0.073	B	0.20184	0.028	T	0.12553	-1.0543	10	0.30078	T	0.28	-50.68	2.8775	0.05636	0.1015:0.271:0.4629:0.1646	rs41545023	566	O00411	RPOM_HUMAN	S	566	ENSP00000215591:P566S	ENSP00000215591:P566S	P	-	1	0	POLRMT	573304	0.788000	0.28762	1.000000	0.80357	0.557000	0.35523	1.680000	0.37607	2.309000	0.77851	0.561000	0.74099	CCC	.	.	weak		0.706	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035	
FREM1	158326	hgsc.bcm.edu	37	9	14857744	14857744	+	Missense_Mutation	SNP	A	A	C	rs145369669	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:14857744A>C	ENST00000380880.3	-	5	1418	c.635T>G	c.(634-636)cTg>cGg	p.L212R	FREM1_ENST00000380881.4_Missense_Mutation_p.L212R|FREM1_ENST00000422223.2_Missense_Mutation_p.L212R			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	212					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)		TTTTGCTCTCAGTTCTAGAAT	0.428													A|||	18	0.00359425	0.0136	0.0	5008	,	,		19720	0.0		0.0	False		,,,				2504	0.0				p.L212R		Atlas-SNP	.											.	FREM1	261	.	0			c.T635G						PASS	.	A	ARG/LEU	53,3683		0,53,1815	71.0	70.0	70.0		635	4.9	1.0	9	dbSNP_134	70	0,8198		0,0,4099	yes	missense	FREM1	NM_144966.5	102	0,53,5914	CC,CA,AA		0.0,1.4186,0.4441	benign	212/2180	14857744	53,11881	1868	4099	5967	SO:0001583	missense	158326	exon6			GCTCTCAGTTCTA	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.635T>G	9.37:g.14857744A>C	ENSP00000370262:p.Leu212Arg	59.0	0.0	0		84.0	43.0	0.511905	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Missense_Mutation	SNP	ENST00000380880.3	37	CCDS47952.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	a	6.809	0.518344	0.13005	0.014186	0.0	ENSG00000164946	ENST00000380881;ENST00000422223;ENST00000380880	T;T;T	0.11385	2.78;2.78;2.78	6.03	4.86	0.63082	.	0.387478	0.27668	N	0.018341	T	0.04634	0.0126	N	0.22421	0.69	0.09310	N	0.999998	P	0.51791	0.948	B	0.39876	0.312	T	0.36237	-0.9756	10	0.25751	T	0.34	-4.1637	10.3897	0.44162	0.7497:0.0:0.0:0.2503	.	212	Q5H8C1	FREM1_HUMAN	R	212	ENSP00000370263:L212R;ENSP00000412940:L212R;ENSP00000370262:L212R	ENSP00000370257:L212R	L	-	2	0	FREM1	14847744	0.590000	0.26815	0.952000	0.39060	0.064000	0.16182	4.254000	0.58798	2.314000	0.78098	0.456000	0.33151	CTG	A|0.997;C|0.003	0.003	strong		0.428	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
FAM109B	150368	hgsc.bcm.edu	37	22	42473586	42473586	+	Missense_Mutation	SNP	C	C	T	rs61736039	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:42473586C>T	ENST00000321753.3	+	3	476	c.289C>T	c.(289-291)Cgc>Tgc	p.R97C	snoU13_ENST00000458891.1_RNA|SMDT1_ENST00000331479.3_5'Flank	NM_001002034.2	NP_001002034.2	Q6ICB4	SESQ2_HUMAN	family with sequence similarity 109, member B	97	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				endosome organization (GO:0007032)|receptor recycling (GO:0001881)|retrograde transport, endosome to Golgi (GO:0042147)	clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(2)|liver(2)|lung(1)|prostate(1)	8						CCCTGGAGTGCGCCCACACCT	0.662													C|||	111	0.0221645	0.0794	0.0058	5008	,	,		16709	0.0		0.002	False		,,,				2504	0.0				p.R97C		Atlas-SNP	.											.	FAM109B	22	.	0			c.C289T						PASS	.	C	CYS/ARG	356,4050	184.0+/-211.4	14,328,1861	69.0	73.0	72.0		289	4.0	0.8	22	dbSNP_129	72	2,8598	2.2+/-6.3	0,2,4298	yes	missense	FAM109B	NM_001002034.2	180	14,330,6159	TT,TC,CC		0.0233,8.0799,2.7526	probably-damaging	97/260	42473586	358,12648	2203	4300	6503	SO:0001583	missense	150368	exon3			GGAGTGCGCCCAC	BX648402	CCDS33655.1	22q13.2	2013-01-10			ENSG00000177096	ENSG00000177096		"""Pleckstrin homology (PH) domain containing"""	27161	protein-coding gene	gene with protein product		614240				12477932	Standard	NM_001002034		Approved	DKFZp686J07229	uc003bbz.3	Q6ICB4	OTTHUMG00000151285	ENST00000321753.3:c.289C>T	22.37:g.42473586C>T	ENSP00000312753:p.Arg97Cys	100.0	0.0	0		129.0	60.0	0.465116	NM_001002034	Q3SXQ3|Q8N6L9	Missense_Mutation	SNP	ENST00000321753.3	37	CCDS33655.1	33	0.01510989010989011	32	0.06504065040650407	1	0.0027624309392265192	0	0.0	0	0.0	C	14.36	2.512399	0.44660	0.080799	2.33E-4	ENSG00000177096	ENST00000321753;ENST00000419475	T;T	0.76839	-1.05;-1.05	5.01	3.95	0.45737	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.211920	0.38492	N	0.001667	T	0.33206	0.0855	M	0.83012	2.62	0.51012	D	0.999905	D	0.76494	0.999	P	0.61201	0.885	T	0.69738	-0.5064	10	0.66056	D	0.02	-12.5019	13.5179	0.61551	0.2769:0.7231:0.0:0.0	rs61736039	97	Q6ICB4	SESQ2_HUMAN	C	97	ENSP00000312753:R97C;ENSP00000396170:R97C	ENSP00000312753:R97C	R	+	1	0	FAM109B	40803532	1.000000	0.71417	0.758000	0.31321	0.031000	0.12232	3.245000	0.51407	2.299000	0.77371	0.655000	0.94253	CGC	C|0.975;T|0.025	0.025	strong		0.662	FAM109B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322084.1	NM_001002034	
WDFY4	57705	hgsc.bcm.edu	37	10	50165258	50165258	+	Missense_Mutation	SNP	G	G	A	rs61733228	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:50165258G>A	ENST00000325239.5	+	51	8089	c.8062G>A	c.(8062-8064)Gtc>Atc	p.V2688I	WDFY4_ENST00000413659.2_3'UTR|WDFY4_ENST00000465910.1_3'UTR	NM_020945.1	NP_065996.1	Q6ZS81	WDFY4_HUMAN	WDFY family member 4	2688	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.					integral component of membrane (GO:0016021)				NS(2)|breast(5)|central_nervous_system(4)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(3)|pancreas(2)|prostate(5)|skin(6)|stomach(1)	48						CATGAGTGACGTCAGGGAGCT	0.577													g|||	35	0.00698882	0.0257	0.0	5008	,	,		21298	0.001		0.0	False		,,,				2504	0.0				p.V2688I		Atlas-SNP	.											.	WDFY4	205	.	0			c.G8062A						PASS	.		ILE/VAL	34,1350		0,34,658	86.0	93.0	91.0		8062	5.6	1.0	10	dbSNP_129	91	0,3182		0,0,1591	yes	missense	WDFY4	NM_020945.1	29	0,34,2249	AA,AG,GG		0.0,2.4566,0.7446	probably-damaging	2688/3185	50165258	34,4532	692	1591	2283	SO:0001583	missense	57705	exon52			AGTGACGTCAGGG	AK074085	CCDS44385.1	10q11.23	2013-01-10			ENSG00000128815	ENSG00000128815		"""WD repeat domain containing"""	29323	protein-coding gene	gene with protein product		613316	"""chromosome 10 open reading frame 64"""	C10orf64		10997877	Standard	NM_020945		Approved	KIAA1607, Em:AC060234.3, FLJ45748	uc001jha.4	Q6ZS81	OTTHUMG00000018180	ENST00000325239.5:c.8062G>A	10.37:g.50165258G>A	ENSP00000320563:p.Val2688Ile	105.0	0.0	0		79.0	44.0	0.556962	NM_020945	B9ZVP2|Q86WZ4|Q8N4A3|Q8TEN7|Q96BE1|Q9H7H8|Q9HCG5	Missense_Mutation	SNP	ENST00000325239.5	37	CCDS44385.1	24|24	0.01098901098901099|0.01098901098901099	22|22	0.044715447154471545|0.044715447154471545	0|0	0.0|0.0	2|2	0.0034965034965034965|0.0034965034965034965	0|0	0.0|0.0	g|g	34|34	5.379064|5.379064	0.95945|0.95945	0.024566|0.024566	0.0|0.0	ENSG00000128815|ENSG00000128815	ENST00000312002|ENST00000426033;ENST00000325239;ENST00000544136	.|T	.|0.81330	.|-1.48	5.57|5.57	5.57|5.57	0.84162|0.84162	.|BEACH domain (4);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.73869|0.73869	0.3642|0.3642	M|M	0.81802|0.81802	2.56|2.56	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|0.994;1.0	.|D;D	.|0.81914	.|0.975;0.995	T|T	0.82857|0.82857	-0.0250|-0.0250	5|9	.|.	.|.	.|.	.|.	18.5788|18.5788	0.91164|0.91164	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs61733228|rs61733228	.|151;2688	.|B4DWY9;Q6ZS81	.|.;WDFY4_HUMAN	H|I	1778|2688;2688;151	.|ENSP00000320563:V2688I	.|.	R|V	+|+	2|1	0|0	WDFY4|WDFY4	49835264|49835264	1.000000|1.000000	0.71417|0.71417	0.983000|0.983000	0.44433|0.44433	0.993000|0.993000	0.82548|0.82548	7.927000|7.927000	0.87577|0.87577	2.628000|2.628000	0.89032|0.89032	0.645000|0.645000	0.84053|0.84053	CGT|GTC	G|0.988;A|0.012	0.012	strong		0.577	WDFY4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_033379	
FLT4	2324	hgsc.bcm.edu	37	5	180058720	180058720	+	Silent	SNP	G	G	A	rs150736691	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:180058720G>A	ENST00000261937.6	-	2	195	c.117C>T	c.(115-117)caC>caT	p.H39H	FLT4_ENST00000424276.2_5'UTR|FLT4_ENST00000502649.1_Silent_p.H39H|FLT4_ENST00000393347.3_Silent_p.H39H	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	39	Ig-like C2-type 1.				blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TGTCGATGACGTGTGACTCCT	0.637																																					p.H39H	Colon(97;1075 1466 27033 27547 35871)	Atlas-SNP	.											.	FLT4	356	.	0			c.C117T						PASS	.	G	,	20,4384	27.2+/-55.0	0,20,2182	114.0	95.0	101.0		117,117	1.4	0.0	5	dbSNP_134	101	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	FLT4	NM_002020.4,NM_182925.4	,	0,20,6482	AA,AG,GG		0.0,0.4541,0.1538	,	39/1299,39/1364	180058720	20,12984	2202	4300	6502	SO:0001819	synonymous_variant	2324	exon2			GATGACGTGTGAC	X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.117C>T	5.37:g.180058720G>A		45.0	0.0	0		51.0	30.0	0.588235	NM_182925	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Silent	SNP	ENST00000261937.6	37	CCDS4457.1																																																																																			G|0.999;A|0.001	0.001	strong		0.637	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253527.4		
SCAF1	58506	hgsc.bcm.edu	37	19	50156762	50156762	+	Missense_Mutation	SNP	A	A	T	rs201628577		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50156762A>T	ENST00000360565.3	+	7	3240	c.3116A>T	c.(3115-3117)gAg>gTg	p.E1039V		NM_021228.2	NP_067051.2	Q9H7N4	SFR19_HUMAN	SR-related CTD-associated factor 1	1039	Glu-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(2)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	20		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00113)|GBM - Glioblastoma multiforme(134;0.0204)		gaggaggaggagCAGCAGCCT	0.692																																					p.E1039V		Atlas-SNP	.											.	SCAF1	78	.	0			c.A3116T						PASS	.	A	VAL/GLU	4,4388		0,4,2192	9.0	12.0	11.0		3116	4.7	1.0	19		11	0,8566		0,0,4283	no	missense	SCAF1	NM_021228.2	121	0,4,6475	TT,TA,AA		0.0,0.0911,0.0309	possibly-damaging	1039/1313	50156762	4,12954	2196	4283	6479	SO:0001583	missense	58506	exon7			AGGAGGAGCAGCA	AK024444	CCDS33074.1	19q13.3-q13.4	2011-01-10			ENSG00000126461	ENSG00000126461			30403	protein-coding gene	gene with protein product						11461075	Standard	NM_021228		Approved	SR-A1, FLJ00034	uc002poq.3	Q9H7N4		ENST00000360565.3:c.3116A>T	19.37:g.50156762A>T	ENSP00000353769:p.Glu1039Val	33.0	0.0	0		27.0	12.0	0.444444	NM_021228	Q7Z5V7|Q8WVA1|Q9NR59	Missense_Mutation	SNP	ENST00000360565.3	37	CCDS33074.1	.	.	.	.	.	.	.	.	.	.	A	10.60	1.395512	0.25205	9.11E-4	0.0	ENSG00000126461	ENST00000360565	T	0.33865	1.39	5.74	4.67	0.58626	.	.	.	.	.	T	0.25344	0.0616	N	0.19112	0.55	0.24915	N	0.992013	P	0.41131	0.739	B	0.41332	0.354	T	0.05784	-1.0864	8	.	.	.	-21.1177	9.6199	0.39714	0.8441:0.0:0.0:0.1559	.	1039	Q9H7N4	SFR19_HUMAN	V	1039	ENSP00000353769:E1039V	.	E	+	2	0	SCAF1	54848574	1.000000	0.71417	1.000000	0.80357	0.216000	0.24613	1.552000	0.36244	2.189000	0.69895	0.533000	0.62120	GAG	.	.	weak		0.692	SCAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465764.1	NM_021228	
PTCD3	55037	hgsc.bcm.edu	37	2	86358214	86358214	+	Missense_Mutation	SNP	G	G	C	rs146203968		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:86358214G>C	ENST00000254630.7	+	16	1317	c.1251G>C	c.(1249-1251)caG>caC	p.Q417H		NM_017952.5	NP_060422.4	Q96EY7	PTCD3_HUMAN	pentatricopeptide repeat domain 3	417					mitochondrial translation (GO:0032543)|regulation of translation (GO:0006417)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|rRNA binding (GO:0019843)			NS(1)|breast(2)|endometrium(3)|kidney(4)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	22						AGTTTTTTCAGTCAGCCATGA	0.318													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16645	0.0		0.0	False		,,,				2504	0.0				p.Q417H		Atlas-SNP	.											.	PTCD3	51	.	0			c.G1251C						PASS	.	G	HIS/GLN	1,4405	2.1+/-5.4	0,1,2202	78.0	78.0	78.0		1251	1.9	1.0	2	dbSNP_134	78	0,8592		0,0,4296	no	missense	PTCD3	NM_017952.5	24	0,1,6498	CC,CG,GG		0.0,0.0227,0.0077	benign	417/690	86358214	1,12997	2203	4296	6499	SO:0001583	missense	55037	exon16			TTTTCAGTCAGCC		CCDS33235.1	2p11.2	2014-02-12	2012-02-24		ENSG00000132300	ENSG00000132300			24717	protein-coding gene	gene with protein product		614918				8889548	Standard	NM_017952		Approved	FLJ20758, DKFZp666K071	uc002sqw.2	Q96EY7	OTTHUMG00000153168	ENST00000254630.7:c.1251G>C	2.37:g.86358214G>C	ENSP00000254630:p.Gln417His	154.0	0.0	0		142.0	65.0	0.457746	NM_017952	A6NHD2|D6W5M1|Q597H0|Q658Y9|Q9BUZ8|Q9NWL0	Missense_Mutation	SNP	ENST00000254630.7	37	CCDS33235.1	.	.	.	.	.	.	.	.	.	.	G	9.979	1.227623	0.22542	2.27E-4	0.0	ENSG00000132300	ENST00000254630	T	0.31769	1.48	6.16	1.9	0.25705	.	0.469117	0.24400	N	0.038860	T	0.22704	0.0548	L	0.44542	1.39	0.58432	D	0.999994	B;B	0.09022	0.002;0.001	B;B	0.11329	0.006;0.003	T	0.06481	-1.0824	10	0.56958	D	0.05	-1.4753	5.8329	0.18590	0.2275:0.0:0.6349:0.1376	.	8;417	Q96EY7-2;Q96EY7	.;PTCD3_HUMAN	H	417	ENSP00000254630:Q417H	ENSP00000254630:Q417H	Q	+	3	2	PTCD3	86211725	0.976000	0.34144	0.999000	0.59377	0.903000	0.53119	0.568000	0.23623	0.488000	0.27723	-0.158000	0.13435	CAG	G|1.000;C|0.000	0.000	weak		0.318	PTCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329854.1	NM_017952	
BZRAP1	9256	hgsc.bcm.edu	37	17	56388356	56388356	+	Silent	SNP	C	C	T	rs61745692	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:56388356C>T	ENST00000343736.4	-	19	3463	c.3300G>A	c.(3298-3300)gcG>gcA	p.A1100A	BZRAP1_ENST00000268893.6_Silent_p.A1040A|BZRAP1_ENST00000355701.3_Silent_p.A1100A			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	1100	Pro-rich.					cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)			cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					AAGCAAGGGGCGCTCTGGCCT	0.692													C|||	151	0.0301518	0.1097	0.0086	5008	,	,		16644	0.0		0.0	False		,,,				2504	0.0				p.A1100A		Atlas-SNP	.											BZRAP1_ENST00000355701,caecum,carcinoma,0,2	BZRAP1	287	2	0			c.G3300A						PASS	.	C	,	391,4007		15,361,1823	17.0	22.0	20.0		3300,3120	-3.6	0.3	17	dbSNP_129	20	3,8591		0,3,4294	no	coding-synonymous,coding-synonymous	BZRAP1	NM_004758.2,NM_024418.1	,	15,364,6117	TT,TC,CC		0.0349,8.8904,3.0326	,	1100/1858,1040/1798	56388356	394,12598	2199	4297	6496	SO:0001819	synonymous_variant	9256	exon19			AAGGGGCGCTCTG	AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.3300G>A	17.37:g.56388356C>T		163.0	0.0	0		161.0	86.0	0.534162	NM_004758	O75111|Q8N5W3	Silent	SNP	ENST00000343736.4	37	CCDS11605.1																																																																																			C|0.968;T|0.032	0.032	strong		0.692	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758	
SRGAP3	9901	hgsc.bcm.edu	37	3	9034605	9034605	+	Missense_Mutation	SNP	C	C	G	rs150617309	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:9034605C>G	ENST00000383836.3	-	20	2970	c.2543G>C	c.(2542-2544)gGg>gCg	p.G848A	SRGAP3_ENST00000360413.3_Missense_Mutation_p.G824A	NM_014850.3	NP_055665.1	O43295	SRGP3_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	848					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)		SRGAP3/RAF1(6)	breast(1)|endometrium(2)|kidney(21)|large_intestine(7)|lung(13)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	54				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		CATCACCCCCCCAAAGCCGTA	0.557			T	RAF1	pilocytic astrocytoma																																p.G848A		Atlas-SNP	.		Dom	yes		3	3p25.3	9901	SLIT-ROBO Rho GTPase activating protein 3		M	.	SRGAP3	146	.	0			c.G2543C						PASS	.						83.0	79.0	81.0					3																	9034605		2203	4300	6503	SO:0001583	missense	9901	exon20			ACCCCCCCAAAGC	AB007871	CCDS2572.1, CCDS33689.1	3p25.3	2011-07-04	2004-11-12	2004-11-12	ENSG00000196220	ENSG00000196220		"""Rho GTPase activating proteins"""	19744	protein-coding gene	gene with protein product		606525	"""SLIT-ROBO Rho GTPase activating protein 2"""	SRGAP2		12195014	Standard	NM_014850		Approved	KIAA0411, MEGAP, WRP, ARHGAP14	uc003brf.2	O43295	OTTHUMG00000090589	ENST00000383836.3:c.2543G>C	3.37:g.9034605C>G	ENSP00000373347:p.Gly848Ala	70.0	0.0	0		69.0	36.0	0.521739	NM_014850	Q8IX13|Q8IZV8	Missense_Mutation	SNP	ENST00000383836.3	37	CCDS2572.1	.	.	.	.	.	.	.	.	.	.	C	5.202	0.222874	0.09863	.	.	ENSG00000196220	ENST00000383836;ENST00000360413	T;T	0.22134	1.97;2.37	5.17	5.17	0.71159	.	0.270733	0.35708	N	0.003023	T	0.12860	0.0312	N	0.22421	0.69	0.47621	D	0.999477	B;B	0.09022	0.002;0.001	B;B	0.10450	0.005;0.002	T	0.04551	-1.0943	10	0.02654	T	1	.	13.9514	0.64118	0.0:0.8479:0.1521:0.0	.	824;848	O43295-2;O43295	.;SRGP2_HUMAN	A	848;824	ENSP00000373347:G848A;ENSP00000353587:G824A	ENSP00000353587:G824A	G	-	2	0	SRGAP3	9009605	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.779000	0.55379	2.410000	0.81850	0.591000	0.81541	GGG	C|1.000;G|0.000	0.000	alt		0.557	SRGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207137.3		
ZNF781	163115	hgsc.bcm.edu	37	19	38160255	38160255	+	Silent	SNP	A	A	C	rs73932934	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38160255A>C	ENST00000590008.1	-	5	1647	c.795T>G	c.(793-795)ctT>ctG	p.L265L	ZNF781_ENST00000593040.1_5'Flank|ZNF781_ENST00000358582.4_Silent_p.L265L|ZFP30_ENST00000586732.1_Intron			Q8N8C0	ZN781_HUMAN	zinc finger protein 781	265					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)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24						CAATTGTTAAAAGCTCTACCA	0.383													A|||	189	0.0377396	0.1354	0.0144	5008	,	,		20442	0.0		0.0	False		,,,				2504	0.0				p.L265L		Atlas-SNP	.											.	ZNF781	66	.	0			c.T795G						PASS	.	A		401,4005	196.7+/-221.0	20,361,1822	87.0	91.0	90.0		795	1.4	0.0	19	dbSNP_130	90	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	ZNF781	NM_152605.3		20,364,6119	CC,CA,AA		0.0349,9.1012,3.1063		265/328	38160255	404,12602	2203	4300	6503	SO:0001819	synonymous_variant	163115	exon4			TGTTAAAAGCTCT	AK097019	CCDS12507.1	19q13.12	2013-01-08				ENSG00000196381		"""Zinc fingers, C2H2-type"""	26745	protein-coding gene	gene with protein product							Standard	NM_152605		Approved	FLJ37549	uc002ogy.2	Q8N8C0		ENST00000590008.1:c.795T>G	19.37:g.38160255A>C		93.0	0.0	0		77.0	37.0	0.480519	NM_152605	Q2VPJ8	Silent	SNP	ENST00000590008.1	37	CCDS12507.1																																																																																			A|0.967;C|0.033	0.033	strong		0.383	ZNF781-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000459495.2	NM_152605	
CNTNAP2	26047	hgsc.bcm.edu	37	7	146829390	146829390	+	Silent	SNP	C	C	T	rs78543192	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:146829390C>T	ENST00000361727.3	+	8	1653	c.1137C>T	c.(1135-1137)aaC>aaT	p.N379N		NM_014141.5	NP_054860.1	Q9UHC6	CNTP2_HUMAN	contactin associated protein-like 2	379					adult behavior (GO:0030534)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|cerebral cortex development (GO:0021987)|clustering of voltage-gated potassium channels (GO:0045163)|learning (GO:0007612)|limbic system development (GO:0021761)|neuron projection development (GO:0031175)|neuron recognition (GO:0008038)|protein localization to juxtaparanode region of axon (GO:0071205)|social behavior (GO:0035176)|striatum development (GO:0021756)|superior temporal gyrus development (GO:0071109)|thalamus development (GO:0021794)|transmission of nerve impulse (GO:0019226)|vocalization behavior (GO:0071625)	axolemma (GO:0030673)|axon (GO:0030424)|cell surface (GO:0009986)|dendrite (GO:0030425)|early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|juxtaparanode region of axon (GO:0044224)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|perikaryon (GO:0043204)|voltage-gated potassium channel complex (GO:0008076)	enzyme binding (GO:0019899)			NS(3)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(105)|ovary(9)|pancreas(2)|prostate(5)|skin(7)|stomach(3)|upper_aerodigestive_tract(6)|urinary_tract(3)	188	Melanoma(164;0.153)	all_cancers(3;3.51e-10)|all_epithelial(3;1.4e-05)|Myeloproliferative disorder(3;0.00452)|Lung NSC(3;0.0067)|all_lung(3;0.00794)	OV - Ovarian serous cystadenocarcinoma(82;0.0319)			TCTTTTTCAACGCTACAAGTT	0.458										HNSCC(39;0.1)			T|||	30	0.00599042	0.0219	0.0014	5008	,	,		20040	0.0		0.0	False		,,,				2504	0.0				p.N379N		Atlas-SNP	.											CNTNAP2,colon,carcinoma,0,2	CNTNAP2	392	2	0			c.C1137T						PASS	.	T		66,4340	820.5+/-416.4	0,66,2137	126.0	121.0	122.0		1137	3.3	1.0	7	dbSNP_132	122	0,8600		0,0,4300	no	coding-synonymous	CNTNAP2	NM_014141.5		0,66,6437	TT,TC,CC		0.0,1.498,0.5075		379/1332	146829390	66,12940	2203	4300	6503	SO:0001819	synonymous_variant	26047	exon8			TTTCAACGCTACA	AF193613	CCDS5889.1	7q35	2008-02-04			ENSG00000174469	ENSG00000174469			13830	protein-coding gene	gene with protein product		604569				10624965, 10048485	Standard	NM_014141		Approved	Caspr2, KIAA0868, NRXN4	uc003weu.2	Q9UHC6	OTTHUMG00000152743	ENST00000361727.3:c.1137C>T	7.37:g.146829390C>T		110.0	0.0	0		116.0	51.0	0.439655	NM_014141	D3DWG2|Q14DG2|Q52LV1|Q5H9Q7|Q9UQ12	Silent	SNP	ENST00000361727.3	37	CCDS5889.1																																																																																			C|0.995;T|0.005	0.005	strong		0.458	CNTNAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327668.1		
CLCA4	22802	hgsc.bcm.edu	37	1	87043733	87043733	+	Silent	SNP	C	C	T	rs2231601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:87043733C>T	ENST00000370563.3	+	12	2142	c.2100C>T	c.(2098-2100)taC>taT	p.Y700Y	RP4-651E10.4_ENST00000456587.1_RNA	NM_012128.3	NP_036260.2	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	700					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44		Lung NSC(277;0.238)		all cancers(265;0.0202)|Epithelial(280;0.0404)		GAGCCGCGTACATACCAGGCT	0.403													C|||	204	0.0407348	0.149	0.0101	5008	,	,		17663	0.0		0.0	False		,,,				2504	0.0				p.Y700Y		Atlas-SNP	.											.	CLCA4	131	.	0			c.C2100T						PASS	.	C		472,3276		21,430,1423	42.0	41.0	41.0		2100	-7.0	0.0	1	dbSNP_98	41	0,8218		0,0,4109	no	coding-synonymous	CLCA4	NM_012128.3		21,430,5532	TT,TC,CC		0.0,12.5934,3.9445		700/920	87043733	472,11494	1874	4109	5983	SO:0001819	synonymous_variant	22802	exon12			CGCGTACATACCA	AF127035	CCDS41355.1	1p31-p22	2012-02-26	2009-01-29		ENSG00000016602	ENSG00000016602			2018	protein-coding gene	gene with protein product			"""chloride channel, calcium activated, family member 4"", ""chloride channel regulator 4"""			10437792	Standard	NM_012128		Approved	CaCC2	uc009wcs.3	Q14CN2	OTTHUMG00000010260	ENST00000370563.3:c.2100C>T	1.37:g.87043733C>T		125.0	0.0	0		91.0	38.0	0.417582	NM_012128	A8MQC9|B7Z1Q5|Q6UX81|Q9UNF7	Silent	SNP	ENST00000370563.3	37	CCDS41355.1																																																																																			C|0.976;T|0.024	0.024	strong		0.403	CLCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028292.1	NM_012128	
SDF2	6388	hgsc.bcm.edu	37	17	26982341	26982341	+	Silent	SNP	A	A	G	rs35579310	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:26982341A>G	ENST00000247020.4	-	2	610	c.312T>C	c.(310-312)caT>caC	p.H104H	SDF2_ENST00000592250.1_5'UTR	NM_006923.3	NP_008854.2	Q99470	SDF2_HUMAN	stromal cell-derived factor 2	104	MIR 2. {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)					AGTGGTGACTATGGAGGTTTC	0.537													A|||	47	0.00938498	0.0325	0.0058	5008	,	,		21075	0.0		0.0	False		,,,				2504	0.0				p.H104H		Atlas-SNP	.											.	SDF2	17	.	0			c.T312C						PASS	.	A		123,4283	91.6+/-130.3	1,121,2081	156.0	134.0	141.0		312	-0.8	1.0	17	dbSNP_126	141	0,8600		0,0,4300	no	coding-synonymous	SDF2	NM_006923.2		1,121,6381	GG,GA,AA		0.0,2.7916,0.9457		104/212	26982341	123,12883	2203	4300	6503	SO:0001819	synonymous_variant	6388	exon2			GTGACTATGGAGG	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.312T>C	17.37:g.26982341A>G		119.0	0.0	0		137.0	58.0	0.423358	NM_006923	Q9BQ79	Silent	SNP	ENST00000247020.4	37	CCDS11238.1																																																																																			A|0.991;G|0.009	0.009	strong		0.537	SDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255965.2	NM_006923	
FGFR3	2261	hgsc.bcm.edu	37	4	1803251	1803251	+	Silent	SNP	T	T	C	rs2305181	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:1803251T>C	ENST00000260795.2	+	4	705	c.603T>C	c.(601-603)atT>atC	p.I201I	FGFR3_ENST00000481110.2_Silent_p.I201I|FGFR3_ENST00000440486.2_Silent_p.I201I|FGFR3_ENST00000352904.1_Silent_p.I201I|FGFR3_ENST00000412135.2_Silent_p.I201I|FGFR3_ENST00000340107.4_Silent_p.I201I			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	201	Ig-like C2-type 2.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)			NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	AGCACCGCATTGGAGGCATCA	0.721		1	"""Mis, T"""	"""IGH@, ETV6"""	"""bladder, MM, T-cell lymphoma"""		"""Hypochondroplasia, Thanatophoric dysplasia"""		Saethre-Chotzen syndrome;Muenke syndrome				N|||	527	0.105232	0.3359	0.0461	5008	,	,		10686	0.0298		0.0119	False		,,,				2504	0.0092				p.I201I		Atlas-SNP	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"""L, E"""	.	FGFR3	3320	.	0			c.T603C						PASS	.	C	,,	1007,3249		98,811,1219	7.0	7.0	7.0		603,603,603	-6.3	0.9	4	dbSNP_100	7	68,8282		1,66,4108	no	coding-synonymous,coding-synonymous,coding-synonymous	FGFR3	NM_000142.4,NM_001163213.1,NM_022965.3	,,	99,877,5327	CC,CT,TT		0.8144,23.6607,8.5277	,,	201/807,201/809,201/695	1803251	1075,11531	2128	4175	6303	SO:0001819	synonymous_variant	2261	exon5	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	CCGCATTGGAGGC	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3690	protein-coding gene	gene with protein product		134934	"""achondroplasia, thanatophoric dwarfism"""	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.603T>C	4.37:g.1803251T>C		29.0	0.0	0		36.0	15.0	0.416667	NM_001163213	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Silent	SNP	ENST00000260795.2	37	CCDS3353.1																																																																																			T|0.879;C|0.121	0.121	strong		0.721	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142	
HPGD	3248	hgsc.bcm.edu	37	4	175414444	175414444	+	Missense_Mutation	SNP	T	T	G	rs200207595		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:175414444T>G	ENST00000296522.6	-	6	966	c.520A>C	c.(520-522)Agt>Cgt	p.S174R	HPGD_ENST00000542498.1_Intron|HPGD_ENST00000510901.1_Missense_Mutation_p.S53R|HPGD_ENST00000296521.7_Intron|HPGD_ENST00000541923.1_Missense_Mutation_p.S53R|HPGD_ENST00000422112.2_Missense_Mutation_p.S106R	NM_000860.5|NM_001145816.2|NM_001256301.1|NM_001256307.1	NP_000851.2|NP_001139288.1|NP_001243230.1|NP_001243236.1	P15428	PGDH_HUMAN	hydroxyprostaglandin dehydrogenase 15-(NAD)	174					arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|ductus arteriosus closure (GO:0097070)|female pregnancy (GO:0007565)|lipoxin metabolic process (GO:2001300)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|ovulation (GO:0030728)|parturition (GO:0007567)|prostaglandin metabolic process (GO:0006693)|small molecule metabolic process (GO:0044281)|thrombin receptor signaling pathway (GO:0070493)|transforming growth factor beta receptor signaling pathway (GO:0007179)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	15-hydroxyprostaglandin dehydrogenase (NAD+) activity (GO:0016404)|catalytic activity (GO:0003824)|NAD binding (GO:0051287)|NAD+ binding (GO:0070403)|prostaglandin E receptor activity (GO:0004957)|protein homodimerization activity (GO:0042803)			kidney(1)|lung(3)|prostate(3)	7		Prostate(90;0.00763)|Melanoma(52;0.0179)|Renal(120;0.0376)|Breast(14;0.0991)|all_hematologic(60;0.124)|all_neural(102;0.196)		all cancers(43;2.6e-18)|Epithelial(43;4.19e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.23e-09)|GBM - Glioblastoma multiforme(59;0.00176)|STAD - Stomach adenocarcinoma(60;0.00299)|LUSC - Lung squamous cell carcinoma(193;0.0253)		CTCACACCACTGTTCATAAGA	0.363																																					p.S174R		Atlas-SNP	.											.	HPGD	19	.	0			c.A520C						PASS	.	T	ARG/SER,	4,4402	8.1+/-20.4	0,4,2199	96.0	91.0	93.0		520,	5.6	1.0	4		93	0,8598		0,0,4299	yes	missense,intron	HPGD	NM_000860.4,NM_001145816.1	110,	0,4,6498	GG,GT,TT		0.0,0.0908,0.0308	possibly-damaging,	174/267,	175414444	4,13000	2203	4299	6502	SO:0001583	missense	3248	exon6			CACCACTGTTCAT		CCDS3821.1, CCDS54821.1, CCDS58933.1, CCDS58934.1, CCDS58935.1	4q34-q35	2011-09-14			ENSG00000164120	ENSG00000164120	1.1.1.141	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	5154	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 36C, member 1"""	601688				19027726	Standard	NM_000860		Approved	SDR36C1	uc003itu.3	P15428	OTTHUMG00000160772	ENST00000296522.6:c.520A>C	4.37:g.175414444T>G	ENSP00000296522:p.Ser174Arg	135.0	0.0	0		121.0	53.0	0.438017	NM_000860	B4DTA4|B4DU74|B4DV57|D3DP43|E7EV11|O00749|Q06F08|Q12998	Missense_Mutation	SNP	ENST00000296522.6	37	CCDS3821.1	.	.	.	.	.	.	.	.	.	.	T	16.52	3.146678	0.57151	9.08E-4	0.0	ENSG00000164120	ENST00000296522;ENST00000510901;ENST00000422112;ENST00000541923;ENST00000506910;ENST00000514584	D;D;T;D;D;D	0.82433	-1.61;-1.61;-1.29;-1.61;-1.61;-1.61	5.58	5.58	0.84498	NAD(P)-binding domain (1);	0.099373	0.64402	D	0.000001	T	0.79816	0.4511	L	0.31371	0.925	0.80722	D	1	P;D;D	0.71674	0.925;0.98;0.998	B;P;P	0.60682	0.446;0.595;0.878	T	0.76613	-0.2895	10	0.02654	T	1	.	9.2337	0.37453	0.2704:0.0:0.0:0.7296	.	106;174;53	E7EV11;P15428;B4DU74	.;PGDH_HUMAN;.	R	174;53;106;53;53;53	ENSP00000296522:S174R;ENSP00000422418:S53R;ENSP00000398720:S106R;ENSP00000438017:S53R;ENSP00000423066:S53R;ENSP00000423110:S53R	ENSP00000296522:S174R	S	-	1	0	HPGD	175651019	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.963000	0.56773	2.119000	0.64992	0.533000	0.62120	AGT	.	.	weak		0.363	HPGD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362228.3		
RAI1	10743	hgsc.bcm.edu	37	17	17696526	17696526	+	Silent	SNP	G	G	A	rs61999281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:17696526G>A	ENST00000353383.1	+	3	733	c.264G>A	c.(262-264)caG>caA	p.Q88Q	RAI1_ENST00000261641.6_Silent_p.Q88Q	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	88					circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		TGCCCACACAGCAAGGCCTGC	0.687													G|||	105	0.0209665	0.0749	0.0086	5008	,	,		12762	0.0		0.0	False		,,,				2504	0.0				p.Q88Q		Atlas-SNP	.											.	RAI1	121	.	0			c.G264A						PASS	.	G		283,4099		11,261,1919	12.0	14.0	14.0		264	1.9	0.7	17	dbSNP_129	14	1,8583		0,1,4291	no	coding-synonymous	RAI1	NM_030665.3		11,262,6210	AA,AG,GG		0.0116,6.4582,2.1903		88/1907	17696526	284,12682	2191	4292	6483	SO:0001819	synonymous_variant	10743	exon3			CACACAGCAAGGC	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.264G>A	17.37:g.17696526G>A		69.0	0.0	0		89.0	40.0	0.449438	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Silent	SNP	ENST00000353383.1	37	CCDS11188.1																																																																																			G|0.980;A|0.020	0.020	strong		0.687	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
FKBPL	63943	hgsc.bcm.edu	37	6	32097089	32097089	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32097089C>T	ENST00000375156.3	-	2	739	c.469G>A	c.(469-471)Ggg>Agg	p.G157R	ATF6B_ENST00000468502.1_5'Flank|ATF6B_ENST00000375203.3_5'Flank|ATF6B_ENST00000375201.4_5'Flank	NM_022110.3	NP_071393.2	Q9UIM3	FKBPL_HUMAN	FK506 binding protein like	157					chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)|response to radiation (GO:0009314)	endoplasmic reticulum membrane (GO:0005789)	FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)										ATGAGCTCCCCCCAAGTTTCC	0.592																																					p.G157R		Atlas-SNP	.											.	FKBPL	25	.	0			c.G469A						PASS	.						188.0	201.0	196.0					6																	32097089		2203	4300	6503	SO:0001583	missense	63943	exon2			GCTCCCCCCAAGT	AF139374	CCDS4738.1	6p21.3	2013-12-13	2001-11-28		ENSG00000204315	ENSG00000204315		"""Tetratricopeptide (TTC) repeat domain containing"""	13949	protein-coding gene	gene with protein product	"""WAF-1/CIP1 stabilizing protein 39"""		"""FK506-binding protein like"""			9056895	Standard	NM_022110		Approved	DIR1, NG7, WISp39	uc003nzr.3	Q9UIM3	OTTHUMG00000031129	ENST00000375156.3:c.469G>A	6.37:g.32097089C>T	ENSP00000364298:p.Gly157Arg	103.0	0.0	0		94.0	51.0	0.542553	NM_022110	A8K5V3|B0UYX8|Q9H5G3	Missense_Mutation	SNP	ENST00000375156.3	37	CCDS4738.1	.	.	.	.	.	.	.	.	.	.	C	18.73	3.686625	0.68157	.	.	ENSG00000204315	ENST00000375156	T	0.80994	-1.44	5.23	3.46	0.39613	.	0.000000	0.42548	D	0.000691	T	0.47820	0.1466	N	0.24115	0.695	0.38007	D	0.934418	B	0.32829	0.386	B	0.29353	0.101	T	0.42172	-0.9467	10	0.23891	T	0.37	-13.8519	9.3205	0.37962	0.0:0.8274:0.0:0.1726	.	157	Q9UIM3	FKBPL_HUMAN	R	157	ENSP00000364298:G157R	ENSP00000364298:G157R	G	-	1	0	FKBPL	32205067	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.754000	0.47532	0.793000	0.33875	0.462000	0.41574	GGG	.	.	none		0.592	FKBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076221.2		
MUC4	4585	hgsc.bcm.edu	37	3	195511236	195511236	+	Missense_Mutation	SNP	G	G	T	rs534701413		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195511236G>T	ENST00000463781.3	-	2	7674	c.7215C>A	c.(7213-7215)gaC>gaA	p.D2405E	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D2405E	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)		CTGAGGAAGTGTCGGTGACAG	0.587																																					p.D2405E		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-2,3	MUC4	1505	3	0			c.C7215A						PASS	.						35.0	37.0	37.0					3																	195511236		689	1589	2278	SO:0001583	missense	4585	exon2			GGAAGTGTCGGTG	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.7215C>A	3.37:g.195511236G>T	ENSP00000417498:p.Asp2405Glu	637.0	0.0	0		235.0	19.0	0.0808511	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	G	8.514	0.867217	0.17250	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29655	1.58;1.56	.	.	.	.	.	.	.	.	T	0.31199	0.0789	N	0.19112	0.55	0.09310	N	1	P	0.37781	0.608	P	0.55508	0.777	T	0.36163	-0.9759	7	.	.	.	.	6.6894	0.23163	2.0E-4:0.0:0.9998:0.0	.	2405	E7ESK3	.	E	2405	ENSP00000417498:D2405E;ENSP00000420243:D2405E	.	D	-	3	2	MUC4	196995631	0.000000	0.05858	0.004000	0.12327	0.079000	0.17450	-3.039000	0.00633	0.482000	0.27582	0.000000	0.15137	GAC	.	.	none		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ZFP82	284406	hgsc.bcm.edu	37	19	36884651	36884651	+	Silent	SNP	C	C	A	rs114627398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36884651C>A	ENST00000392161.3	-	5	833	c.591G>T	c.(589-591)ccG>ccT	p.P197P	ZFP82_ENST00000392171.1_Silent_p.P197P	NM_133466.2	NP_597723.1	Q8N141	ZFP82_HUMAN	ZFP82 zinc finger protein	197					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(7)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						TACATTCATACGGTTTTTCAC	0.408													G|||	68	0.0135783	0.0499	0.0029	5008	,	,		22380	0.0		0.0	False		,,,				2504	0.0				p.P197P		Atlas-SNP	.											.	ZFP82	71	.	0			c.G591T						PASS	.	G		150,4256		4,142,2057	88.0	78.0	81.0		591	-4.1	1.0	19	dbSNP_132	81	2,8598		0,2,4298	no	coding-synonymous	ZFP82	NM_133466.2		4,144,6355	AA,AC,CC		0.0233,3.4044,1.1687		197/533	36884651	152,12854	2203	4300	6503	SO:0001819	synonymous_variant	284406	exon5			TTCATACGGTTTT	AL834267	CCDS12493.1	19q13.13	2013-01-08	2012-11-27	2008-07-01		ENSG00000181007		"""Zinc fingers, C2H2-type"", ""-"""	28682	protein-coding gene	gene with protein product			"""zinc finger protein 545"", ""zinc finger protein 82 homolog (mouse)"", ""zinc finger protein 82"""	ZNF545		11853319	Standard	NM_133466		Approved	MGC45380, KIAA1948	uc002ody.1	Q8N141		ENST00000392161.3:c.591G>T	19.37:g.36884651C>A		168.0	0.0	0		176.0	90.0	0.511364	NM_133466	Q8NC63|Q8TF53	Silent	SNP	ENST00000392161.3	37	CCDS12493.1																																																																																			C|0.989;A|0.011	0.011	strong		0.408	ZFP82-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109552.2	NM_133466	
TAB2	23118	hgsc.bcm.edu	37	6	149699333	149699333	+	Silent	SNP	A	A	G	rs13215304	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:149699333A>G	ENST00000367456.1	+	4	859	c.282A>G	c.(280-282)ggA>ggG	p.G94G	TAB2_ENST00000286332.5_Silent_p.G94G|TAB2_ENST00000536230.1_Silent_p.G62G|TAB2_ENST00000538427.1_Silent_p.G94G|TAB2_ENST00000392282.1_Silent_p.G94G			Q9NYJ8	TAB2_HUMAN	TGF-beta activated kinase 1/MAP3K7 binding protein 2	94					activation of MAPK activity (GO:0000187)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein kinase activity (GO:0045860)|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)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|endosome membrane (GO:0010008)|plasma membrane (GO:0005886)	K63-linked polyubiquitin binding (GO:0070530)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|urinary_tract(1)	22						GAAGAGAAGGAAGTAGGATGA	0.428													A|||	55	0.0109824	0.0	0.0288	5008	,	,		20789	0.001		0.0328	False		,,,				2504	0.001				p.G94G		Atlas-SNP	.											TAB2,NS,carcinoma,+2,1	TAB2	55	1	0			c.A282G						scavenged	.	A		32,4374	36.0+/-67.5	0,32,2171	132.0	115.0	120.0		282	3.3	1.0	6	dbSNP_121	120	268,8332	103.1+/-164.3	4,260,4036	no	coding-synonymous	TAB2	NM_015093.4		4,292,6207	GG,GA,AA		3.1163,0.7263,2.3066		94/694	149699333	300,12706	2203	4300	6503	SO:0001819	synonymous_variant	23118	exon5			AGAAGGAAGTAGG	AF241230	CCDS5214.1	6q25.1	2010-08-05	2010-02-05	2010-02-05	ENSG00000055208	ENSG00000055208			17075	protein-coding gene	gene with protein product		605101	"""mitogen-activated protein kinase kinase kinase 7 interacting protein 2"""	MAP3K7IP2		9872452, 10882101	Standard	XR_250046		Approved	KIAA0733	uc010kib.2	Q9NYJ8	OTTHUMG00000015783	ENST00000367456.1:c.282A>G	6.37:g.149699333A>G		132.0	1.0	0.00757576		141.0	70.0	0.496454	NM_015093	B2RCC4|E1P5A0|O94838|Q6I9W8|Q76N06|Q9UFP7	Silent	SNP	ENST00000367456.1	37	CCDS5214.1																																																																																			A|0.977;G|0.023	0.023	strong		0.428	TAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042633.3		
ECT2	1894	hgsc.bcm.edu	37	3	172480580	172480580	+	Missense_Mutation	SNP	A	A	G	rs138074177	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:172480580A>G	ENST00000392692.3	+	10	1165	c.989A>G	c.(988-990)tAt>tGt	p.Y330C	ECT2_ENST00000232458.5_Missense_Mutation_p.Y299C|ECT2_ENST00000427830.1_Missense_Mutation_p.Y299C|ECT2_ENST00000540509.1_Missense_Mutation_p.Y330C|ECT2_ENST00000417960.1_Missense_Mutation_p.Y298C|ECT2_ENST00000441497.2_Missense_Mutation_p.Y299C	NM_001258315.1	NP_001245244.1	Q9H8V3	ECT2_HUMAN	epithelial cell transforming 2	330	BRCT 2. {ECO:0000255|PROSITE- ProRule:PRU00033}.				activation of protein kinase activity (GO:0032147)|activation of Rac GTPase activity (GO:0032863)|activation of Rho GTPase activity (GO:0032862)|apoptotic signaling pathway (GO:0097190)|cell morphogenesis (GO:0000902)|cellular response to calcium ion (GO:0071277)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to ionizing radiation (GO:0071479)|cytokinesis (GO:0000910)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of cytokinesis (GO:0032467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of Rho GTPase activity (GO:0032321)|protein homooligomerization (GO:0051260)|protein transport (GO:0015031)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|centralspindlin complex (GO:0097149)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|tight junction (GO:0005923)	GTPase activator activity (GO:0005096)|protein homodimerization activity (GO:0042803)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(5)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	Ovarian(172;0.00197)|Breast(254;0.158)		Lung(28;1.33e-14)|LUSC - Lung squamous cell carcinoma(14;1.48e-14)			AAGAAACTTTATGTTGTCAAG	0.313													A|||	2	0.000399361	0.0008	0.0	5008	,	,		17827	0.0		0.001	False		,,,				2504	0.0				p.Y330C		Atlas-SNP	.											.	ECT2	79	.	0			c.A989G						PASS	.	A	CYS/TYR	3,4403	6.2+/-15.9	0,3,2200	89.0	90.0	90.0		896	4.7	1.0	3	dbSNP_134	90	2,8596	2.2+/-6.3	0,2,4297	yes	missense	ECT2	NM_018098.4	194	0,5,6497	GG,GA,AA		0.0233,0.0681,0.0384	probably-damaging	299/884	172480580	5,12999	2203	4299	6502	SO:0001583	missense	1894	exon10			AACTTTATGTTGT	AA206473	CCDS3220.1, CCDS58860.1	3q26.1-q26.2	2014-03-11	2014-03-11		ENSG00000114346	ENSG00000114346		"""Rho guanine nucleotide exchange factors"""	3155	protein-coding gene	gene with protein product		600586	"""epithelial cell transforming sequence 2 oncogene"""			8464478, 10579713	Standard	NM_018098		Approved	ARHGEF31	uc003fil.2	Q9H8V3	OTTHUMG00000156762	ENST00000392692.3:c.989A>G	3.37:g.172480580A>G	ENSP00000376457:p.Tyr330Cys	163.0	0.0	0		144.0	74.0	0.513889	NM_001258315	Q0MT80|Q2M269|Q6U836|Q9NSV8|Q9NVW9	Missense_Mutation	SNP	ENST00000392692.3	37	CCDS58860.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	A|A	16.30|16.30	3.083153|3.083153	0.55861|0.55861	6.81E-4|6.81E-4	2.33E-4|2.33E-4	ENSG00000114346|ENSG00000114346	ENST00000444250|ENST00000232458;ENST00000392692;ENST00000427830;ENST00000417960;ENST00000441497;ENST00000540509	.|T;T;T;T;T;T	.|0.79141	.|-1.24;-1.24;-1.24;-1.24;-1.24;-1.24	5.84|5.84	4.65|4.65	0.58169|0.58169	.|.	.|0.105654	.|0.64402	.|D	.|0.000003	D|D	0.85106|0.85106	0.5621|0.5621	M|M	0.73598|0.73598	2.24|2.24	0.53688|0.53688	D|D	0.999974|0.999974	.|P;D;P;P	.|0.58620	.|0.783;0.983;0.941;0.929	.|B;P;P;P	.|0.61003	.|0.325;0.882;0.753;0.525	D|D	0.85632|0.85632	0.1271|0.1271	5|10	.|0.62326	.|D	.|0.03	-13.9317|-13.9317	11.9979|11.9979	0.53214|0.53214	0.8666:0.0:0.0:0.1334|0.8666:0.0:0.0:0.1334	.|.	.|330;330;299;298	.|Q9H8V3;Q9H8V3-3;G5E9L8;Q9H8V3-2	.|ECT2_HUMAN;.;.;.	V|C	2|299;330;299;298;299;330	.|ENSP00000232458:Y299C;ENSP00000376457:Y330C;ENSP00000401910:Y299C;ENSP00000415876:Y298C;ENSP00000412259:Y299C;ENSP00000443160:Y330C	.|ENSP00000232458:Y299C	M|Y	+|+	1|2	0|0	ECT2|ECT2	173963274|173963274	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	4.323000|4.323000	0.59221|0.59221	0.990000|0.990000	0.38787|0.38787	0.482000|0.482000	0.46254|0.46254	ATG|TAT	A|0.999;G|0.001	0.001	strong		0.313	ECT2-003	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345994.2	NM_018098	
DOCK4	9732	hgsc.bcm.edu	37	7	111400275	111400275	+	Missense_Mutation	SNP	T	T	C	rs374962931		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:111400275T>C	ENST00000437633.1	-	39	4353	c.4097A>G	c.(4096-4098)aAc>aGc	p.N1366S	DOCK4_ENST00000428084.1_Missense_Mutation_p.N1375S|DOCK4_ENST00000494651.2_Missense_Mutation_p.N249S	NM_014705.3	NP_055520.3	Q8N1I0	DOCK4_HUMAN	dedicator of cytokinesis 4	1366	DHR-2.				cell chemotaxis (GO:0060326)|positive regulation of Rac GTPase activity (GO:0032855)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|stereocilium (GO:0032420)|stereocilium bundle (GO:0032421)	guanyl-nucleotide exchange factor activity (GO:0005085)|PDZ domain binding (GO:0030165)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|receptor tyrosine kinase binding (GO:0030971)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(13)|lung(31)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(4)	72		Acute lymphoblastic leukemia(1;0.0441)				ATCGGGCTGGTTGGCGTGCTG	0.552																																					p.N1366S		Atlas-SNP	.											.	DOCK4	365	.	0			c.A4097G						PASS	.	T	SER/ASN	2,4310		0,2,2154	184.0	186.0	185.0		4097	4.6	1.0	7		185	0,8506		0,0,4253	no	missense	DOCK4	NM_014705.3	46	0,2,6407	CC,CT,TT		0.0,0.0464,0.0156	benign	1366/1967	111400275	2,12816	2156	4253	6409	SO:0001583	missense	9732	exon39			GGCTGGTTGGCGT		CCDS47688.1	7q31.1	2007-08-07			ENSG00000128512	ENSG00000128512			19192	protein-coding gene	gene with protein product		607679				12432077, 12628187	Standard	XM_006716188		Approved	FLJ34238, KIAA0716	uc003vfx.3	Q8N1I0	OTTHUMG00000155077	ENST00000437633.1:c.4097A>G	7.37:g.111400275T>C	ENSP00000404179:p.Asn1366Ser	128.0	0.0	0		139.0	63.0	0.453237	NM_014705	O14584|O94824|Q8NB45	Missense_Mutation	SNP	ENST00000437633.1	37	CCDS47688.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	11.83|11.83	1.755933|1.755933	0.31137|0.31137	4.64E-4|4.64E-4	0.0|0.0	ENSG00000128512|ENSG00000128512	ENST00000352877;ENST00000428084;ENST00000494651;ENST00000437633;ENST00000342288|ENST00000423057;ENST00000445943	T;T;T|.	0.05996|.	4.12;3.36;4.12|.	4.62|4.62	4.62|4.62	0.57501|0.57501	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.53965|0.53965	0.1829|0.1829	L|L	0.29908|0.29908	0.895|0.895	0.49798|0.49798	D|D	0.999821|0.999821	B;B;B;B;B|.	0.28998|.	0.112;0.178;0.22;0.23;0.178|.	B;B;B;B;B|.	0.30716|.	0.023;0.051;0.119;0.119;0.084|.	T|T	0.50931|0.50931	-0.8769|-0.8769	10|5	0.02654|.	T|.	1|.	.|.	14.4645|14.4645	0.67475|0.67475	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	273;249;1411;1366;1375|.	B7Z2K9;F5GXW1;Q149N5;Q8N1I0;Q8N1I0-2|.	.;.;.;DOCK4_HUMAN;.|.	S|A	1354;1375;249;1366;1363|827;1399	ENSP00000410746:N1375S;ENSP00000440944:N249S;ENSP00000404179:N1366S|.	ENSP00000345432:N1363S|.	N|T	-|-	2|1	0|0	DOCK4|DOCK4	111187511|111187511	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	6.086000|6.086000	0.71352|0.71352	2.066000|2.066000	0.61787|0.61787	0.482000|0.482000	0.46254|0.46254	AAC|ACC	.	.	weak		0.552	DOCK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338369.4	NM_014705	
MYO18B	84700	hgsc.bcm.edu	37	22	26423124	26423124	+	Missense_Mutation	SNP	G	G	C	rs6004901	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:26423124G>C	ENST00000407587.2	+	43	7356	c.7187G>C	c.(7186-7188)gGc>gCc	p.G2396A	MYO18B_ENST00000536101.1_Missense_Mutation_p.G2395A|MYO18B_ENST00000335473.7_Missense_Mutation_p.G2395A			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2395						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						GACGATGCGGGCTGTCCAGAC	0.592													G|||	488	0.0974441	0.2663	0.0476	5008	,	,		15885	0.004		0.0348	False		,,,				2504	0.0654				p.G2395A		Atlas-SNP	.											.	MYO18B	322	.	0			c.G7184C						PASS	.	G	ALA/GLY	855,3101		95,665,1218	66.0	72.0	70.0		7184	-1.6	0.0	22	dbSNP_114	70	253,8029		6,241,3894	yes	missense	MYO18B	NM_032608.5	60	101,906,5112	CC,CG,GG		3.0548,21.6127,9.0538	benign	2395/2568	26423124	1108,11130	1978	4141	6119	SO:0001583	missense	84700	exon43			ATGCGGGCTGTCC	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.7187G>C	22.37:g.26423124G>C	ENSP00000386096:p.Gly2396Ala	86.0	0.0	0		88.0	39.0	0.443182	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		166|166	0.076007326007326|0.076007326007326	119|119	0.241869918699187|0.241869918699187	22|22	0.06077348066298342|0.06077348066298342	4|4	0.006993006993006993|0.006993006993006993	21|21	0.027704485488126648|0.027704485488126648	G|G	0.007|0.007	-1.985354|-1.985354	0.00443|0.00443	0.216127|0.216127	0.030548|0.030548	ENSG00000133454|ENSG00000133454	ENST00000543971|ENST00000536101;ENST00000335473;ENST00000407587	.|D;D;D	.|0.86956	.|-2.17;-2.17;-2.19	5.12|5.12	-1.6|-1.6	0.08426|0.08426	.|.	.|0.491877	.|0.18417	.|N	.|0.141867	T|T	0.00073|0.00073	0.0002|0.0002	L|L	0.45581|0.45581	1.43|1.43	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B;B;B	.|0.06786	.|0.001;0.001;0.001;0.001;0.001	.|B;B;B;B;B	.|0.08055	.|0.003;0.001;0.001;0.003;0.003	T|T	0.02877|0.02877	-1.1099|-1.1099	4|9	.|0.19147	.|T	.|0.46	.|.	1.509|1.509	0.02492|0.02492	0.1649:0.2383:0.3545:0.2424|0.1649:0.2383:0.3545:0.2424	rs6004901;rs52824215;rs6004901|rs6004901;rs52824215;rs6004901	.|1908;2397;2395;2396;2395	.|Q8IUG5-2;B0QYF5;Q8IUG5;F5GXR6;F5GYU7	.|.;.;MY18B_HUMAN;.;.	P|A	345|2395;2395;2396	.|ENSP00000441229:G2395A;ENSP00000334563:G2395A;ENSP00000386096:G2396A	.|ENSP00000334563:G2395A	A|G	+|+	1|2	0|0	MYO18B|MYO18B	24753124|24753124	0.003000|0.003000	0.15002|0.15002	0.011000|0.011000	0.14972|0.14972	0.130000|0.130000	0.20726|0.20726	0.135000|0.135000	0.15952|0.15952	0.154000|0.154000	0.19237|0.19237	-0.264000|-0.264000	0.10439|0.10439	GCT|GGC	G|0.912;C|0.088	0.088	strong		0.592	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
LAMTOR1	55004	hgsc.bcm.edu	37	11	71817250	71817250	+	5'Flank	SNP	G	G	A	rs181092713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71817250G>A	ENST00000278671.5	-	0	0				LRTOMT_ENST00000307198.7_Missense_Mutation_p.V118I|LRTOMT_ENST00000419228.1_Missense_Mutation_p.V78I|LRTOMT_ENST00000439209.1_Intron|LAMTOR1_ENST00000535107.1_5'Flank|LAMTOR1_ENST00000545249.1_5'Flank|snoU13_ENST00000459046.1_RNA|LRTOMT_ENST00000435085.1_Missense_Mutation_p.V118I|LAMTOR1_ENST00000538404.1_5'Flank	NM_017907.2	NP_060377.1	Q6IAA8	LTOR1_HUMAN	late endosomal/lysosomal adaptor, MAPK and MTOR activator 1						cell growth (GO:0016049)|cellular protein localization (GO:0034613)|cellular response to amino acid stimulus (GO:0071230)|cholesterol homeostasis (GO:0042632)|endosome localization (GO:0032439)|endosome organization (GO:0007032)|lysosome localization (GO:0032418)|lysosome organization (GO:0007040)|positive regulation of GTPase activity (GO:0043547)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of TOR signaling (GO:0032008)|regulation of cholesterol efflux (GO:0010874)|regulation of cholesterol esterification (GO:0010872)|regulation of cholesterol import (GO:0060620)|regulation of receptor recycling (GO:0001919)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|late endosome membrane (GO:0031902)|lysosome (GO:0005764)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|Ragulator complex (GO:0071986)				cervix(1)	1						CATGGGGCCTGTCAAAGGTCA	0.562													G|||	14	0.00279553	0.0106	0.0	5008	,	,		18621	0.0		0.0	False		,,,				2504	0.0				p.V118I		Atlas-SNP	.											.	LRTOMT	20	.	0			c.G352A						PASS	.	G	ILE/VAL	21,1363		0,21,671	35.0	38.0	37.0		352	1.4	1.0	11		37	0,3182		0,0,1591	no	missense	LRTOMT	NM_001145308.2	29	0,21,2262	AA,AG,GG		0.0,1.5173,0.4599	benign	118/292	71817250	21,4545	692	1591	2283	SO:0001631	upstream_gene_variant	220074	exon7			GGGCCTGTCAAAG	AK000632	CCDS8209.1	11q13.4	2011-05-18	2011-02-15	2011-02-15	ENSG00000149357	ENSG00000149357			26068	protein-coding gene	gene with protein product	"""p27kip1 releasing factor from RhoA"", ""protein associated with DRMs and endosomes"""	613510	"""chromosome 11 open reading frame 59"""	C11orf59		12358155	Standard	NM_017907		Approved	FLJ20625, p18, p27RF-Rho, Pdro, Ragulator1	uc001ort.3	Q6IAA8	OTTHUMG00000167869		11.37:g.71817250G>A	Exception_encountered	13.0	0.0	0		15.0	6.0	0.4	NM_001145309	Q8WZ09|Q9NWT0	Missense_Mutation	SNP	ENST00000278671.5	37	CCDS8209.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	13.30	2.195071	0.38806	0.015173	0.0	ENSG00000184154	ENST00000419228;ENST00000435085;ENST00000307198	T;T;T	0.21734	1.99;1.99;1.99	4.59	1.43	0.22495	.	.	.	.	.	T	0.05364	0.0142	N	0.21240	0.645	0.21445	N	0.99969	B;B	0.06786	0.0;0.001	B;B	0.08055	0.001;0.003	T	0.26573	-1.0099	9	0.38643	T	0.18	-3.0892	2.2276	0.03988	0.1802:0.2893:0.404:0.1265	.	118;78	Q8WZ04;Q8WZ04-2	TOMT_HUMAN;.	I	78;118;118	ENSP00000392233:V78I;ENSP00000409789:V118I;ENSP00000305742:V118I	ENSP00000305742:V78I	V	+	1	0	LRTOMT	71494898	0.617000	0.27043	0.999000	0.59377	0.980000	0.70556	1.049000	0.30392	0.642000	0.30620	0.462000	0.41574	GTC	G|0.998;A|0.002	0.002	strong		0.562	LAMTOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396733.1	NM_017907	
DNAH9	1770	hgsc.bcm.edu	37	17	11687721	11687721	+	Silent	SNP	G	G	A	rs16945337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:11687721G>A	ENST00000262442.4	+	41	7994	c.7926G>A	c.(7924-7926)gcG>gcA	p.A2642A	DNAH9_ENST00000454412.2_Silent_p.A2642A	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	2642	AAA 3. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		ACTTCCCGGCGTCCCTGCAGA	0.542													G|||	239	0.0477236	0.0877	0.0058	5008	,	,		17425	0.002		0.0348	False		,,,				2504	0.0838				p.A2642A		Atlas-SNP	.											DNAH9,NS,carcinoma,+1,1	DNAH9	695	1	0			c.G7926A						PASS	.	G		358,4048	185.0+/-212.2	14,330,1859	177.0	169.0	172.0		7926	-2.6	0.0	17	dbSNP_123	172	195,8405	86.1+/-148.5	0,195,4105	no	coding-synonymous	DNAH9	NM_001372.3		14,525,5964	AA,AG,GG		2.2674,8.1253,4.2519		2642/4487	11687721	553,12453	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon41			CCCGGCGTCCCTG	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.7926G>A	17.37:g.11687721G>A		200.0	0.0	0		192.0	91.0	0.473958	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			G|0.956;A|0.044	0.044	strong		0.542	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
MUC4	4585	hgsc.bcm.edu	37	3	195515113	195515113	+	Missense_Mutation	SNP	A	A	G	rs71321849	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195515113A>G	ENST00000463781.3	-	2	3797	c.3338T>C	c.(3337-3339)gTa>gCa	p.V1113A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.V1113A	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	544					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)		ACCTGTGGATACTGAGGAAGT	0.567													.|||	247	0.0493211	0.1679	0.0202	5008	,	,		17898	0.001		0.005	False		,,,				2504	0.0051				p.V1113A		Atlas-SNP	.											.	MUC4	1505	.	0			c.T3338C						PASS	.						12.0	7.0	9.0					3																	195515113		666	1536	2202	SO:0001583	missense	4585	exon2			GTGGATACTGAGG	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.3338T>C	3.37:g.195515113A>G	ENSP00000417498:p.Val1113Ala	169.0	0.0	0		335.0	34.0	0.101493	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	2.657	-0.280535	0.05642	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32272	1.46;1.46	0.814	-1.63	0.08345	.	.	.	.	.	T	0.16041	0.0386	N	0.19112	0.55	0.09310	N	1	B	0.15473	0.013	B	0.21546	0.035	T	0.32322	-0.9911	8	.	.	.	.	5.3188	0.15870	0.6312:0.0:0.3688:0.0	.	1113	E7ESK3	.	A	1113	ENSP00000417498:V1113A;ENSP00000420243:V1113A	.	V	-	2	0	MUC4	196999508	0.000000	0.05858	0.000000	0.03702	0.285000	0.27093	-0.337000	0.07852	-0.728000	0.04882	0.055000	0.15244	GTA	A|0.500;G|0.500	0.500	strong		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PDK2	5164	hgsc.bcm.edu	37	17	48174794	48174794	+	Silent	SNP	C	C	T	rs11546968	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48174794C>T	ENST00000503176.1	+	2	287	c.126C>T	c.(124-126)agC>agT	p.S42S	PDK2_ENST00000007708.3_5'UTR|PDK2_ENST00000511026.1_3'UTR	NM_002611.4	NP_002602.2	Q15119	PDK2_HUMAN	pyruvate dehydrogenase kinase, isozyme 2	42					cellular metabolic process (GO:0044237)|cellular response to nutrient (GO:0031670)|cellular response to reactive oxygen species (GO:0034614)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of cellular ketone metabolic process (GO:0010565)|regulation of gluconeogenesis (GO:0006111)|regulation of glucose metabolic process (GO:0010906)|regulation of pH (GO:0006885)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrial pyruvate dehydrogenase complex (GO:0005967)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)			central_nervous_system(4)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	20						CAGGATCCAGCAATGCCTGTG	0.552									Autosomal Dominant Polycystic Kidney Disease				C|||	15	0.00299521	0.0113	0.0	5008	,	,		20973	0.0		0.0	False		,,,				2504	0.0				p.S42S		Atlas-SNP	.											.	PDK2	41	.	0			c.C126T						PASS	.	C	,,,	53,4353	52.9+/-88.7	0,53,2150	80.0	64.0	69.0		,,126,126	3.2	1.0	17	dbSNP_120	69	5,8595	4.3+/-15.6	0,5,4295	no	utr-5,utr-5,coding-synonymous,coding-synonymous	PDK2	NM_001199898.1,NM_001199899.1,NM_001199900.1,NM_002611.4	,,,	0,58,6445	TT,TC,CC		0.0581,1.2029,0.4459	,,,	,,42/200,42/408	48174794	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	5164	exon2	Familial Cancer Database	ADPKD	ATCCAGCAATGCC	L42451	CCDS11559.1, CCDS56039.1	17q21.33	2012-07-18	2005-11-16		ENSG00000005882	ENSG00000005882			8810	protein-coding gene	gene with protein product		602525	"""pyruvate dehydrogenase kinase, isoenzyme 2"""			7499431	Standard	NM_001199898		Approved	PDHK2	uc002iqc.3	Q15119	OTTHUMG00000161948	ENST00000503176.1:c.126C>T	17.37:g.48174794C>T		47.0	0.0	0		56.0	33.0	0.589286	NM_002611	A8K3A7|B3KNW0|Q6P515|Q9BS05	Silent	SNP	ENST00000503176.1	37	CCDS11559.1																																																																																			C|0.997;T|0.003	0.003	strong		0.552	PDK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366492.2	NM_002611	
MED12	9968	hgsc.bcm.edu	37	X	70339715	70339715	+	Silent	SNP	A	A	G	rs201566660		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:70339715A>G	ENST00000374080.3	+	3	416	c.384A>G	c.(382-384)caA>caG	p.Q128Q	MED12_ENST00000333646.6_Silent_p.Q128Q|MED12_ENST00000374102.1_Silent_p.Q128Q			Q93074	MED12_HUMAN	mediator complex subunit 12	128					androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					CACTCACGCAACTAGCCAAAA	0.502			"""M, S"""		uterine leiomyoma		Opitz-Kaveggia Syndrome						.|||	9	0.00238411	0.0061	0.0014	3775	,	,		15678	0.0		0.0	False		,,,				2504	0.0				p.Q128Q		Atlas-SNP	.		Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	MED12	984	.	0			c.A384G						PASS	.	A		31,3377		0,27,4,1392,566	33.0	32.0	33.0		384	-3.8	1.0	X		33	0,6498		0,0,0,2353,1792	no	coding-synonymous	MED12	NM_005120.2		0,27,4,3745,2358	GG,GA,G,AA,A		0.0,0.9096,0.3129		128/2178	70339715	31,9875	1989	4145	6134	SO:0001819	synonymous_variant	9968	exon3			CACGCAACTAGCC	U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"""trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)"", ""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)"", ""FG syndrome 1"""	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.384A>G	X.37:g.70339715A>G		121.0	0.0	0		152.0	68.0	0.447368	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	Silent	SNP	ENST00000374080.3	37	CCDS43970.1	2	0.0012055455093429777	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	0	0.0	.	6.865	0.528992	0.13127	0.009096	0.0	ENSG00000184634	ENST00000429213	.	.	.	5.73	-3.76	0.04359	.	.	.	.	.	T	0.33585	0.0868	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.35226	-0.9797	4	.	.	.	-1.517	4.2759	0.10809	0.1879:0.4151:0.308:0.089	.	.	.	.	S	113	.	.	N	+	2	0	MED12	70256440	1.000000	0.71417	0.980000	0.43619	0.912000	0.54170	0.874000	0.28065	-0.477000	0.06832	-1.276000	0.01395	AAC	A|0.999;G|0.001	0.001	strong		0.502	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120	
PRKAR1B	5575	hgsc.bcm.edu	37	7	720274	720274	+	Silent	SNP	A	A	G	rs200458521	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:720274A>G	ENST00000406797.1	-	3	441	c.267T>C	c.(265-267)ccT>ccC	p.P89P	PRKAR1B_ENST00000544935.1_Silent_p.P89P|PRKAR1B_ENST00000537384.1_Silent_p.P89P|PRKAR1B_ENST00000403562.1_Silent_p.P89P|PRKAR1B_ENST00000360274.4_Silent_p.P89P	NM_001164761.1	NP_001158233.1	P31321	KAP1_HUMAN	protein kinase, cAMP-dependent, regulatory, type I, beta	89	Dimerization and phosphorylation.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein phosphorylation (GO:0006468)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)			endometrium(4)|large_intestine(1)|liver(1)|lung(10)|prostate(1)	17		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0181)|Epithelial(4;5.75e-19)|OV - Ovarian serous cystadenocarcinoma(56;2.01e-18)|all cancers(6;3.96e-16)|BRCA - Breast invasive adenocarcinoma(126;0.152)		CCTTCACCACAGGGTTCGGGG	0.632													a|||	9	0.00179712	0.0061	0.0014	5008	,	,		15949	0.0		0.0	False		,,,				2504	0.0				p.P89P		Atlas-SNP	.											.	PRKAR1B	32	.	0			c.T267C						PASS	.	A	,,,,,	22,4384	24.3+/-50.5	0,22,2181	51.0	51.0	51.0		267,267,267,267,267,267	-9.8	0.1	7		51	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRKAR1B	NM_001164758.1,NM_001164759.1,NM_001164760.1,NM_001164761.1,NM_001164762.1,NM_002735.2	,,,,,	0,22,6481	GG,GA,AA		0.0,0.4993,0.1692	,,,,,	89/382,89/382,89/382,89/382,89/382,89/382	720274	22,12984	2203	4300	6503	SO:0001819	synonymous_variant	5575	exon3			CACCACAGGGTTC	M65066	CCDS34579.1	7p22.3	2013-09-19			ENSG00000188191	ENSG00000188191	2.7.11.1		9390	protein-coding gene	gene with protein product		176911				1358799, 3479018	Standard	NM_002735		Approved		uc003siw.2	P31321	OTTHUMG00000151411	ENST00000406797.1:c.267T>C	7.37:g.720274A>G		52.0	0.0	0		35.0	14.0	0.4	NM_001164760	Q8N422	Silent	SNP	ENST00000406797.1	37	CCDS34579.1																																																																																			A|0.998;G|0.002	0.002	strong		0.632	PRKAR1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322525.1		
SERPINB12	89777	hgsc.bcm.edu	37	18	61234144	61234144	+	Missense_Mutation	SNP	G	G	A	rs56812375	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61234144G>A	ENST00000269491.1	+	7	1118	c.1118G>A	c.(1117-1119)cGa>cAa	p.R373Q	SERPINB12_ENST00000382768.1_Missense_Mutation_p.R393Q	NM_080474.1	NP_536722.1	Q96P63	SPB12_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 12	373					hematopoietic progenitor cell differentiation (GO:0002244)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of protein catabolic process (GO:0042177)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	enzyme binding (GO:0019899)|serine-type endopeptidase inhibitor activity (GO:0004867)			kidney(1)|large_intestine(5)|lung(19)|skin(1)	26						AGGTCACTACGATCTTGGGTG	0.453													G|||	172	0.034345	0.1256	0.0086	5008	,	,		21067	0.0		0.0	False		,,,				2504	0.0				p.R373Q		Atlas-SNP	.											SERPINB12,colon,carcinoma,0,1	SERPINB12	55	1	0			c.G1118A						PASS	.	G	GLN/ARG	455,3951	218.1+/-236.3	27,401,1775	78.0	77.0	77.0		1118	3.3	0.0	18	dbSNP_129	77	1,8599		0,1,4299	yes	missense	SERPINB12	NM_080474.1	43	27,402,6074	AA,AG,GG		0.0116,10.3268,3.5061	benign	373/406	61234144	456,12550	2203	4300	6503	SO:0001583	missense	89777	exon7			CACTACGATCTTG	AF411191	CCDS11984.1	18q21.33	2014-02-18	2005-08-18		ENSG00000166634	ENSG00000166634		"""Serine (or cysteine) peptidase inhibitors"""	14220	protein-coding gene	gene with protein product		615662	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 12"""			24172014	Standard	NM_080474		Approved	YUKOPIN	uc010xen.2	Q96P63	OTTHUMG00000132789	ENST00000269491.1:c.1118G>A	18.37:g.61234144G>A	ENSP00000269491:p.Arg373Gln	73.0	0.0	0		72.0	33.0	0.458333	NM_080474	Q3SYB4	Missense_Mutation	SNP	ENST00000269491.1	37	CCDS11984.1	46	0.021062271062271064	43	0.08739837398373984	3	0.008287292817679558	0	0.0	0	0.0	G	6.154	0.396700	0.11638	0.103268	1.16E-4	ENSG00000166634	ENST00000269491;ENST00000382768	D;D	0.84146	-1.81;-1.81	6.01	3.29	0.37713	Serpin domain (3);	2.339550	0.01636	N	0.023778	T	0.08179	0.0204	N	0.16656	0.425	0.09310	N	1	B;B	0.26363	0.147;0.004	B;B	0.29524	0.103;0.001	T	0.49303	-0.8954	10	0.12766	T	0.61	.	7.6332	0.28251	0.0:0.6835:0.1241:0.1924	rs56812375;rs61741590	393;373	Q3SYB4;Q96P63	.;SPB12_HUMAN	Q	373;393	ENSP00000269491:R373Q;ENSP00000372218:R393Q	ENSP00000269491:R373Q	R	+	2	0	SERPINB12	59385124	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.232000	0.09055	0.892000	0.36259	-0.133000	0.14855	CGA	G|0.972;A|0.028	0.028	strong		0.453	SERPINB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256197.1	NM_080474	
OR1J1	347168	hgsc.bcm.edu	37	9	125239449	125239449	+	Missense_Mutation	SNP	G	G	A	rs192344372	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:125239449G>A	ENST00000259357.2	-	1	786	c.757C>T	c.(757-759)Cgg>Tgg	p.R253W	RP11-542K23.9_ENST00000412262.2_RNA	NM_001004451.1	NP_001004451.1	Q8NGS3	OR1J1_HUMAN	olfactory receptor, family 1, subfamily J, member 1	253						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(4)|lung(6)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	16						ATAATTGTCCGATAATAGATA	0.453													C|||	3	0.000599042	0.0023	0.0	5008	,	,		23406	0.0		0.0	False		,,,				2504	0.0				p.R253W		Atlas-SNP	.											OR1J1,colon,carcinoma,0,1	OR1J1	46	1	0			c.C757T						PASS	.						135.0	129.0	131.0					9																	125239449		2203	4300	6503	SO:0001583	missense	347168	exon1			TTGTCCGATAATA	AL353767	CCDS35120.1	9q33.2	2013-09-20			ENSG00000136834	ENSG00000136834		"""GPCR / Class A : Olfactory receptors"""	8208	protein-coding gene	gene with protein product							Standard	NM_001004451		Approved	hg32	uc011lyu.2	Q8NGS3	OTTHUMG00000020603	ENST00000259357.2:c.757C>T	9.37:g.125239449G>A	ENSP00000259357:p.Arg253Trp	125.0	0.0	0		137.0	92.0	0.671533	NM_001004451	A3KFL8|Q6IF10|Q96R88	Missense_Mutation	SNP	ENST00000259357.2	37	CCDS35120.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	18.97	3.734988	0.69189	.	.	ENSG00000136834	ENST00000259357	T	0.37058	1.22	4.93	4.93	0.64822	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	D	0.000015	T	0.23965	0.0580	N	0.24115	0.695	0.35696	D	0.81525	P	0.36874	0.572	B	0.26614	0.071	T	0.35176	-0.9799	10	0.87932	D	0	.	14.8875	0.70582	0.0:0.8554:0.1446:0.0	.	253	Q8NGS3	OR1J1_HUMAN	W	253	ENSP00000259357:R253W	ENSP00000259357:R253W	R	-	1	2	OR1J1	124279270	0.076000	0.21285	1.000000	0.80357	0.049000	0.14656	1.108000	0.31123	1.482000	0.48325	-0.181000	0.13052	CGG	G|0.999;A|0.001	0.001	strong		0.453	OR1J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053931.1		
PGPEP1L	145814	hgsc.bcm.edu	37	15	99512877	99512877	+	Missense_Mutation	SNP	C	C	T	rs78254881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:99512877C>T	ENST00000378919.6	-	4	353	c.148G>A	c.(148-150)Gtc>Atc	p.V50I	RP11-654A16.3_ENST00000559468.1_RNA|PGPEP1L_ENST00000535714.1_5'UTR	NM_001102612.2	NP_001096082.2	A6NFU8	PGPIL_HUMAN	pyroglutamyl-peptidase I-like	50							cysteine-type peptidase activity (GO:0008234)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(2)|skin(1)|stomach(1)	14						ACATGCACGACGAGCTGTGTG	0.602													C|||	66	0.0131789	0.0469	0.0058	5008	,	,		16700	0.0		0.0	False		,,,				2504	0.0				p.V50I		Atlas-SNP	.											.	PGPEP1L	26	.	0			c.G148A						PASS	.	C	ILE/VAL,	145,4113		4,137,1988	77.0	82.0	80.0		148,	0.1	0.1	15	dbSNP_131	80	5,8489		0,5,4242	yes	missense,utr-5	PGPEP1L	NM_001102612.2,NM_001167902.1	29,	4,142,6230	TT,TC,CC		0.0589,3.4054,1.1763	benign,	50/197,	99512877	150,12602	2129	4247	6376	SO:0001583	missense	145814	exon4			GCACGACGAGCTG		CCDS53977.1, CCDS58400.1	15q26.3	2010-02-16			ENSG00000183571	ENSG00000183571			27080	protein-coding gene	gene with protein product							Standard	NM_001102612		Approved		uc002bum.3	A6NFU8		ENST00000378919.6:c.148G>A	15.37:g.99512877C>T	ENSP00000368199:p.Val50Ile	71.0	0.0	0		74.0	39.0	0.527027	NM_001102612	H0YF86	Missense_Mutation	SNP	ENST00000378919.6	37	CCDS53977.1	25	0.011446886446886446	20	0.04065040650406504	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	C	4.380	0.070062	0.08436	0.034054	5.89E-4	ENSG00000183571	ENST00000378919;ENST00000535714	T	0.54279	0.58	4.36	0.0993	0.14502	.	.	.	.	.	T	0.11024	0.0269	L	0.41573	1.285	0.09310	N	1	B	0.22346	0.068	B	0.18561	0.022	T	0.12502	-1.0545	9	0.40728	T	0.16	-23.075	3.4626	0.07539	0.1898:0.3126:0.0:0.4976	.	50	A6NFU8	PGPIL_HUMAN	I	50;43	ENSP00000368199:V50I	ENSP00000368199:V50I	V	-	1	0	PGPEP1L	97330400	0.000000	0.05858	0.065000	0.19835	0.005000	0.04900	0.029000	0.13666	0.141000	0.18875	-0.827000	0.03088	GTC	C|0.986;T|0.014	0.014	strong		0.602	PGPEP1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000415703.1	NM_001102612.2	
CSF3R	1441	hgsc.bcm.edu	37	1	36933493	36933493	+	Silent	SNP	G	G	A	rs3917998	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:36933493G>A	ENST00000373106.1	-	14	2341	c.1794C>T	c.(1792-1794)atC>atT	p.I598I	CSF3R_ENST00000373104.1_Silent_p.I598I|CSF3R_ENST00000440588.2_Silent_p.I598I|CSF3R_ENST00000338937.5_Silent_p.I598I|CSF3R_ENST00000418048.2_Silent_p.I598I|CSF3R_ENST00000373103.1_Silent_p.I598I|CSF3R_ENST00000487540.2_5'UTR|CSF3R_ENST00000361632.4_Silent_p.I598I|CSF3R_ENST00000331941.5_Silent_p.I598I	NM_000760.3	NP_000751.1	Q99062	CSF3R_HUMAN	colony stimulating factor 3 receptor (granulocyte)	598	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|defense response (GO:0006952)|neutrophil chemotaxis (GO:0030593)|odontogenesis of dentin-containing tooth (GO:0042475)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)|receptor activity (GO:0004872)			central_nervous_system(3)|endometrium(2)|kidney(3)|large_intestine(9)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)			Filgrastim(DB00099)|Pegfilgrastim(DB00019)	CCATGAGGTGGATGTGATACA	0.632													G|||	39	0.00778754	0.0287	0.0014	5008	,	,		18146	0.0		0.0	False		,,,				2504	0.0				p.I598I		Atlas-SNP	.											.	CSF3R	157	.	0			c.C1794T						PASS	.	G	,,	110,4296	85.3+/-124.0	1,108,2094	62.0	72.0	68.0		1794,1794,1794	0.9	0.8	1	dbSNP_108	68	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	CSF3R	NM_000760.3,NM_156039.3,NM_172313.2	,,	1,113,6389	AA,AG,GG		0.0581,2.4966,0.8842	,,	598/837,598/864,598/784	36933493	115,12891	2203	4300	6503	SO:0001819	synonymous_variant	1441	exon14			GAGGTGGATGTGA	M59820	CCDS412.1, CCDS413.1, CCDS414.1	1p35-p34.3	2014-09-17			ENSG00000119535	ENSG00000119535		"""CD molecules"", ""Fibronectin type III domain containing"""	2439	protein-coding gene	gene with protein product		138971		CD114		1371413	Standard	NM_000760		Approved	GCSFR	uc001cax.2	Q99062	OTTHUMG00000008010	ENST00000373106.1:c.1794C>T	1.37:g.36933493G>A		131.0	0.0	0		142.0	69.0	0.485915	NM_156039		Silent	SNP	ENST00000373106.1	37	CCDS413.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	G	1.164	-0.642824	0.03531	0.024966	5.81E-4	ENSG00000119535	ENST00000464465	.	.	.	5.33	0.847	0.18961	.	.	.	.	.	T	0.37625	0.1010	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.31166	-0.9953	4	.	.	.	-20.3197	6.8146	0.23822	0.0808:0.1894:0.6261:0.1037	rs3917998;rs3917998	.	.	.	F	150	.	.	S	-	2	0	CSF3R	36706080	0.985000	0.35326	0.819000	0.32651	0.078000	0.17371	0.083000	0.14871	0.245000	0.21373	-0.797000	0.03246	TCC	G|0.991;A|0.009	0.009	strong		0.632	CSF3R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021997.2	NM_156039	
ABCC2	1244	hgsc.bcm.edu	37	10	101604107	101604107	+	Missense_Mutation	SNP	C	C	T	rs17216317	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:101604107C>T	ENST00000370449.4	+	28	3985	c.3872C>T	c.(3871-3873)cCg>cTg	p.P1291L		NM_000392.3	NP_000383	Q92887	MRP2_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 2	1291			P -> L (altered transporter activity; dbSNP:rs17216317). {ECO:0000269|PubMed:22290738}.		cellular chloride ion homeostasis (GO:0030644)|drug transmembrane transport (GO:0006855)|prostaglandin transport (GO:0015732)|response to arsenic-containing substance (GO:0046685)|response to estrogen (GO:0043627)|response to heat (GO:0009408)|response to methotrexate (GO:0031427)|response to oxidative stress (GO:0006979)|thyroid hormone transport (GO:0070327)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intercellular canaliculus (GO:0046581)|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)			NS(1)|breast(5)|endometrium(9)|kidney(2)|large_intestine(20)|liver(1)|lung(20)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	67		Colorectal(252;0.234)		Epithelial(162;2.77e-10)|all cancers(201;2.47e-08)	Adenosine triphosphate(DB00171)|Aminohippurate(DB00345)|Arsenic trioxide(DB01169)|Atorvastatin(DB01076)|Canagliflozin(DB08907)|Carbamazepine(DB00564)|Carboplatin(DB00958)|Cisplatin(DB00515)|Clotrimazole(DB00257)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Eprosartan(DB00876)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Ezetimibe(DB00973)|Furosemide(DB00695)|Fusidic Acid(DB02703)|Gadoxetate(DB08884)|Glutathione(DB00143)|Glyburide(DB01016)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Ivermectin(DB00602)|Lamivudine(DB00709)|Leucovorin(DB00650)|Levetiracetam(DB01202)|Lomefloxacin(DB00978)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nifedipine(DB01115)|Norgestimate(DB00957)|Ofloxacin(DB01165)|Olmesartan(DB00275)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Pravastatin(DB00175)|Probenecid(DB01032)|Quinidine(DB00908)|Reserpine(DB00206)|Rifampicin(DB01045)|Ritonavir(DB00503)|Saquinavir(DB01232)|Simvastatin(DB00641)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Sulfasalazine(DB00795)|Sulfinpyrazone(DB01138)|Sunitinib(DB01268)|Tamoxifen(DB00675)|Telmisartan(DB00966)|Tenofovir(DB00300)|Tetrahydrofolic acid(DB00116)|Ursodeoxycholic acid(DB01586)|Vasopressin(DB00067)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)	AAGAGGCCTCCGCCAGATTGG	0.532													C|||	55	0.0109824	0.0363	0.0086	5008	,	,		20061	0.0		0.001	False		,,,				2504	0.0				p.P1291L		Atlas-SNP	.											.	ABCC2	160	.	0			c.C3872T						PASS	.		LEU/PRO	145,4261	101.2+/-139.8	3,139,2061	95.0	89.0	91.0		3872	5.8	1.0	10	dbSNP_126	91	3,8597	2.2+/-6.3	0,3,4297	yes	missense	ABCC2	NM_000392.3	98	3,142,6358	TT,TC,CC		0.0349,3.291,1.1379	probably-damaging	1291/1546	101604107	148,12858	2203	4300	6503	SO:0001583	missense	1244	exon28			GGCCTCCGCCAGA	U63970	CCDS7484.1	10q24	2012-03-14			ENSG00000023839	ENSG00000023839		"""ATP binding cassette transporters / subfamily C"""	53	protein-coding gene	gene with protein product		601107	"""canalicular multispecific organic anion transporter 1"""	CMOAT		8797578, 9284939	Standard	XM_006717630		Approved	DJS, MRP2, cMRP	uc001kqf.2	Q92887	OTTHUMG00000018895	ENST00000370449.4:c.3872C>T	10.37:g.101604107C>T	ENSP00000359478:p.Pro1291Leu	62.0	0.0	0		62.0	33.0	0.532258	NM_000392	B2RMT8|Q14022|Q5T2B1|Q92500|Q92798|Q99663|Q9UMS2	Missense_Mutation	SNP	ENST00000370449.4	37	CCDS7484.1	15	0.006868131868131868	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	0	0.0	C	18.14	3.557532	0.65425	0.03291	3.49E-4	ENSG00000023839	ENST00000370449	D	0.89681	-2.55	5.79	5.79	0.91817	.	0.099134	0.64402	D	0.000001	D	0.84556	0.5498	M	0.65320	2	0.80722	D	1	D	0.69078	0.997	D	0.64687	0.928	D	0.87880	0.2677	10	0.87932	D	0	-8.0E-4	15.6234	0.76829	0.1379:0.8621:0.0:0.0	rs17216317;rs52825311;rs61667815	1291	Q92887	MRP2_HUMAN	L	1291	ENSP00000359478:P1291L	ENSP00000359478:P1291L	P	+	2	0	ABCC2	101594097	1.000000	0.71417	0.968000	0.41197	0.881000	0.50899	5.706000	0.68362	2.733000	0.93635	0.655000	0.94253	CCG	C|0.988;T|0.012	0.012	strong		0.532	ABCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049825.1	NM_000392	
APRT	353	hgsc.bcm.edu	37	16	88874545	88874545	+	IGR	SNP	G	G	T	rs3218720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88874545G>T	ENST00000378364.3	-	0	947				CDT1_ENST00000301019.4_Silent_p.L500L	NM_000485.2	NP_000476.1	P07741	APT_HUMAN	adenine phosphoribosyltransferase						adenine salvage (GO:0006168)|AMP salvage (GO:0044209)|cellular response to insulin stimulus (GO:0032869)|grooming behavior (GO:0007625)|lactation (GO:0007595)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	adenine binding (GO:0002055)|adenine phosphoribosyltransferase activity (GO:0003999)|AMP binding (GO:0016208)			cervix(1)|endometrium(1)|liver(1)	3				BRCA - Breast invasive adenocarcinoma(80;0.0477)	Adenine(DB00173)|Adenosine monophosphate(DB00131)	AGCACCTGCTGCTCCTCTCCG	0.662													G|||	217	0.0433307	0.1581	0.0115	5008	,	,		18032	0.0		0.0	False		,,,				2504	0.0				p.L500L		Atlas-SNP	.											.	CDT1	30	.	0			c.G1500T						PASS	.	G		651,3741		50,551,1595	42.0	31.0	35.0		1500	2.8	0.1	16	dbSNP_106	35	6,8592		0,6,4293	no	coding-synonymous	CDT1	NM_030928.3		50,557,5888	TT,TG,GG		0.0698,14.8224,5.0577		500/547	88874545	657,12333	2196	4299	6495	SO:0001628	intergenic_variant	81620	exon10			CCTGCTGCTCCTC		CCDS32511.1, CCDS45546.1	16q24	2012-10-02				ENSG00000198931	2.4.2.7		626	protein-coding gene	gene with protein product		102600					Standard	NM_000485		Approved		uc002flv.3	P07741			16.37:g.88874545G>T		131.0	0.0	0		121.0	118.0	0.975207	NM_030928	G5E9J2|Q3KP55|Q68DF9	Silent	SNP	ENST00000378364.3	37	CCDS32511.1																																																																																			G|0.953;T|0.047	0.047	strong		0.662	APRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430000.2	NM_000485	
TMC3	342125	hgsc.bcm.edu	37	15	81641872	81641872	+	Missense_Mutation	SNP	G	G	T	rs61740148	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:81641872G>T	ENST00000359440.5	-	11	1255	c.1120C>A	c.(1120-1122)Cca>Aca	p.P374T	RP11-761I4.3_ENST00000560851.1_RNA|TMC3_ENST00000558726.1_Missense_Mutation_p.P375T|RP11-761I4.3_ENST00000559781.1_RNA	NM_001080532.1	NP_001074001.1			transmembrane channel-like 3											autonomic_ganglia(2)|breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	34						AAGGCTGATGGTGCTATCATG	0.577													G|||	58	0.0115815	0.0408	0.0058	5008	,	,		16696	0.0		0.0	False		,,,				2504	0.0				p.P374T		Atlas-SNP	.											.	TMC3	112	.	0			c.C1120A						PASS	.	G	THR/PRO	172,4164		3,166,1999	107.0	111.0	110.0		1120	5.0	0.6	15	dbSNP_129	110	1,8523		0,1,4261	yes	missense	TMC3	NM_001080532.1	38	3,167,6260	TT,TG,GG		0.0117,3.9668,1.3453	probably-damaging	374/1101	81641872	173,12687	2168	4262	6430	SO:0001583	missense	342125	exon11			CTGATGGTGCTAT	AY263163	CCDS45324.1	15q24.3	2006-11-24				ENSG00000188869			22995	protein-coding gene	gene with protein product						12906855, 12812529	Standard	NM_001080532		Approved		uc021ssk.1	Q7Z5M5		ENST00000359440.5:c.1120C>A	15.37:g.81641872G>T	ENSP00000352413:p.Pro374Thr	218.0	0.0	0		211.0	99.0	0.469194	NM_001080532		Missense_Mutation	SNP	ENST00000359440.5	37	CCDS45324.1	20	0.009157509157509158	18	0.036585365853658534	2	0.0055248618784530384	0	0.0	0	0.0	G	16.89	3.247828	0.59103	0.039668	1.17E-4	ENSG00000188869	ENST00000359440	D	0.91237	-2.81	5.02	5.02	0.67125	.	0.129405	0.53938	D	0.000052	D	0.87466	0.6184	M	0.85041	2.73	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.89179	0.3542	10	0.87932	D	0	-13.1745	18.3718	0.90409	0.0:0.0:1.0:0.0	.	374;374	Q7Z5M5-2;Q7Z5M5	.;TMC3_HUMAN	T	374	ENSP00000352413:P374T	ENSP00000352413:P374T	P	-	1	0	TMC3	79428927	1.000000	0.71417	0.619000	0.29118	0.082000	0.17680	9.398000	0.97281	2.322000	0.78497	0.655000	0.94253	CCA	G|0.990;T|0.010	0.010	strong		0.577	TMC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417795.3	NM_181841	
RELN	5649	hgsc.bcm.edu	37	7	103251218	103251218	+	Missense_Mutation	SNP	T	T	C	rs3025962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:103251218T>C	ENST00000428762.1	-	22	3091	c.2932A>G	c.(2932-2934)Aca>Gca	p.T978A	RELN_ENST00000424685.2_Missense_Mutation_p.T978A|RELN_ENST00000343529.5_Missense_Mutation_p.T978A	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	978			T -> A (in dbSNP:rs3025962).		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)		CTTGCTGATGTAAATTCCTGA	0.413													T|||	92	0.0183706	0.0651	0.0086	5008	,	,		18923	0.0		0.0	False		,,,				2504	0.0				p.T978A	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.A2932G						PASS	.	T	ALA/THR,ALA/THR	211,4195	131.0+/-167.6	4,203,1996	146.0	123.0	131.0		2932,2932	6.1	1.0	7	dbSNP_102	131	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense	RELN	NM_005045.3,NM_173054.2	58,58	4,206,6293	CC,CT,TT		0.0349,4.7889,1.6454	probably-damaging,probably-damaging	978/3461,978/3459	103251218	214,12792	2203	4300	6503	SO:0001583	missense	5649	exon22			CTGATGTAAATTC		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.2932A>G	7.37:g.103251218T>C	ENSP00000392423:p.Thr978Ala	73.0	0.0	0		75.0	34.0	0.453333	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	T	23.6	4.434312	0.83776	0.047889	3.49E-4	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.24908	1.83;2.09;1.83	6.08	6.08	0.98989	.	0.000000	0.85682	D	0.000000	T	0.06325	0.0163	M	0.61703	1.905	0.58432	D	0.999994	D;D	0.76494	0.999;0.982	D;D	0.83275	0.996;0.952	T	0.01235	-1.1410	10	0.62326	D	0.03	.	15.2149	0.73258	0.0:0.0:0.0:1.0	rs3025962;rs52799777;rs3025962	978;978	P78509-2;P78509	.;RELN_HUMAN	A	978	ENSP00000392423:T978A;ENSP00000345694:T978A;ENSP00000388446:T978A	ENSP00000345694:T978A	T	-	1	0	RELN	103038454	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	7.358000	0.79466	2.333000	0.79357	0.533000	0.62120	ACA	T|0.978;C|0.022	0.022	strong		0.413	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
PBOV1	59351	hgsc.bcm.edu	37	6	138539372	138539372	+	Missense_Mutation	SNP	C	C	T	rs73774688	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:138539372C>T	ENST00000527246.2	-	1	255	c.161G>A	c.(160-162)cGa>cAa	p.R54Q	KIAA1244_ENST00000251691.4_Intron	NM_021635.2	NP_067648.1	Q9GZY1	PBOV1_HUMAN	prostate and breast cancer overexpressed 1	54						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)	1	Breast(32;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.00055)|GBM - Glioblastoma multiforme(68;0.000674)		TTCTTTTTTTCGAAATACCTt	0.398													C|||	33	0.00658946	0.0234	0.0029	5008	,	,		20845	0.0		0.0	False		,,,				2504	0.0				p.R54Q		Atlas-SNP	.											PBOV1_ENST00000527246,NS,carcinoma,-1,2	PBOV1	12	2	0			c.G161A						PASS	.	C	GLN/ARG,	107,4299	69.2+/-107.0	0,107,2096	124.0	121.0	122.0		161,	0.7	0.0	6	dbSNP_130	122	0,8600		0,0,4300	yes	missense,intron	KIAA1244,PBOV1	NM_021635.2,NM_020340.4	43,	0,107,6396	TT,TC,CC		0.0,2.4285,0.8227	probably-damaging,	54/136,	138539372	107,12899	2203	4300	6503	SO:0001583	missense	59351	exon1			TTTTTTCGAAATA	AF189269	CCDS5190.1	6q23.3	2012-02-09			ENSG00000254440	ENSG00000254440			21079	protein-coding gene	gene with protein product		605669				12553037, 11156405	Standard	NM_021635		Approved	UC28, UROC28	uc003qhv.3	Q9GZY1	OTTHUMG00000167040	ENST00000527246.2:c.161G>A	6.37:g.138539372C>T	ENSP00000432353:p.Arg54Gln	178.0	0.0	0		160.0	75.0	0.46875	NM_021635		Missense_Mutation	SNP	ENST00000527246.2	37	CCDS5190.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	C	6.594	0.478015	0.12521	0.024285	0.0	ENSG00000254440	ENST00000527246	T	0.43294	0.95	2.62	0.733	0.18289	.	.	.	.	.	T	0.05868	0.0153	N	0.08118	0	0.09310	N	1	D	0.56035	0.974	B	0.32342	0.144	T	0.16394	-1.0404	9	0.87932	D	0	.	5.1595	0.15054	0.0:0.6937:0.0:0.3063	.	54	Q9GZY1	PBOV1_HUMAN	Q	54	ENSP00000432353:R54Q	ENSP00000432353:R54Q	R	-	2	0	PBOV1	138581065	0.004000	0.15560	0.005000	0.12908	0.122000	0.20287	0.148000	0.16224	0.034000	0.15491	-0.880000	0.02959	CGA	C|0.991;T|0.009	0.009	strong		0.398	PBOV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392617.1	NM_021635	
CAST	831	hgsc.bcm.edu	37	5	96082128	96082128	+	Splice_Site	SNP	C	C	T	rs78054235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:96082128C>T	ENST00000341926.3	+	15	1196	c.1034C>T	c.(1033-1035)aCg>aTg	p.T345M	CAST_ENST00000509903.1_Splice_Site_p.T310M|CAST_ENST00000325674.7_Splice_Site_p.T393M|CAST_ENST00000395812.2_Splice_Site_p.T387M|CAST_ENST00000309190.5_Splice_Site_p.T323M|CAST_ENST00000348386.3_3'UTR|CAST_ENST00000508608.1_Splice_Site_p.T391M|CAST_ENST00000515663.1_Splice_Site_p.T68M|CAST_ENST00000338252.3_Splice_Site_p.T332M|CAST_ENST00000508579.1_Splice_Site_p.T60M|CAST_ENST00000359176.4_Splice_Site_p.T409M|CAST_ENST00000510756.1_Splice_Site_p.T406M|CAST_ENST00000395813.1_Splice_Site_p.T428M|CAST_ENST00000504465.1_Splice_Site_p.T273M|CAST_ENST00000508830.1_Splice_Site_p.T428M|CAST_ENST00000511049.1_Splice_Site_p.T331M|CAST_ENST00000511782.1_Splice_Site_p.T331M			P20810	ICAL_HUMAN	calpastatin	345					negative regulation of endopeptidase activity (GO:0010951)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)	cysteine-type endopeptidase inhibitor activity (GO:0004869)|endopeptidase inhibitor activity (GO:0004866)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(5)|ovary(1)|skin(2)	22		all_cancers(142;5.27e-07)|all_epithelial(76;8.21e-10)|all_lung(232;0.000396)|Lung NSC(167;0.000539)|Ovarian(225;0.024)|Colorectal(57;0.0341)|Breast(839;0.244)		all cancers(79;6.85e-15)		AAACCAGCCACGGTAAATTTT	0.418													c|||	63	0.0125799	0.0454	0.0014	5008	,	,		20246	0.0		0.0	False		,,,				2504	0.002				p.T387M		Atlas-SNP	.											.	CAST	58	.	0			c.C1160T						PASS	.	T	MET/THR,MET/THR,MET/THR	135,4271	98.0+/-136.7	2,131,2070	121.0	125.0	124.0		1160,995,968	1.3	1.0	5	dbSNP_131	124	2,8598	2.2+/-6.3	0,2,4298	yes	missense-near-splice,missense-near-splice,missense-near-splice	CAST	NM_001042440.2,NM_001190442.1,NM_173060.3	81,81,81	2,133,6368	TT,TC,CC		0.0233,3.064,1.0534	benign,benign,benign	387/751,332/696,323/687	96082128	137,12869	2203	4300	6503	SO:0001630	splice_region_variant	831	exon15			CAGCCACGGTAAA	AF327443	CCDS4082.1, CCDS54882.1, CCDS54883.1, CCDS75279.1	5q15	2012-09-20			ENSG00000153113	ENSG00000153113			1515	protein-coding gene	gene with protein product		114090				8340353, 14685690, 15820218	Standard	NM_173060		Approved		uc003klx.3	P20810	OTTHUMG00000128413	ENST00000341926.3:c.1035+1C>T	5.37:g.96082128C>T		199.0	0.0	0		225.0	112.0	0.497778	NM_001042440	B7Z468|G5E946|G5E9D3|O95360|Q05DE8|Q7Z4K0|Q96D08|Q9H1Z5	Missense_Mutation	SNP	ENST00000341926.3	37		21|21	0.009615384615384616|0.009615384615384616	20|20	0.04065040650406504|0.04065040650406504	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	c|c	8.238|8.238	0.806130|0.806130	0.16467|0.16467	0.03064|0.03064	2.33E-4|2.33E-4	ENSG00000153113|ENSG00000153113	ENST00000437034|ENST00000338252;ENST00000508830;ENST00000511097;ENST00000395813;ENST00000359176;ENST00000325674;ENST00000395812;ENST00000510756;ENST00000508608;ENST00000341926;ENST00000511049;ENST00000309190;ENST00000510156;ENST00000504465;ENST00000509903;ENST00000511782;ENST00000508579;ENST00000503828;ENST00000515663	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.22743	.|2.24;2.24;1.94;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24;2.24	6.17|6.17	1.3|1.3	0.21679|0.21679	.|.	.|0.548082	.|0.21244	.|N	.|0.077779	T|T	0.05731|0.05731	0.0150|0.0150	L|L	0.36672|0.36672	1.1|1.1	0.24426|0.24426	N|N	0.994593|0.994593	.|P;P;B;D;B;D;B;B;B;B;B;P;B;P;B;B;B	.|0.59767	.|0.867;0.79;0.366;0.962;0.43;0.986;0.132;0.055;0.178;0.284;0.055;0.84;0.245;0.741;0.451;0.378;0.178	.|B;B;B;B;B;P;B;B;B;B;B;B;B;B;B;B;B	.|0.57057	.|0.345;0.199;0.108;0.417;0.21;0.812;0.131;0.021;0.057;0.1;0.061;0.234;0.058;0.287;0.066;0.058;0.197	T|T	0.03043|0.03043	-1.1079|-1.1079	5|10	.|0.46703	.|T	.|0.11	-0.1946|-0.1946	5.1484|5.1484	0.14996|0.14996	0.1336:0.5121:0.0:0.3543|0.1336:0.5121:0.0:0.3543	.|.	.|273;193;391;68;96;68;331;310;323;304;345;393;387;409;406;428;332	.|E9PDE4;B7Z8S8;B7Z468;E7EQA0;Q86YM9;E7EPY6;E7EVY3;E9PCH5;G5E946;P20810-4;P20810;P20810-5;G5E9D3;P20810-7;E7ESM9;P20810-6;P20810-2	.|.;.;.;.;.;.;.;.;.;.;ICAL_HUMAN;.;.;.;.;.;.	W|M	97|332;428;393;428;409;393;387;406;391;345;331;323;345;273;310;331;60;60;68	.|ENSP00000343421:T332M;ENSP00000425721:T428M;ENSP00000422951:T393M;ENSP00000379158:T428M;ENSP00000352098:T409M;ENSP00000320319:T393M;ENSP00000379157:T387M;ENSP00000422176:T406M;ENSP00000422677:T391M;ENSP00000339914:T345M;ENSP00000421130:T331M;ENSP00000312523:T323M;ENSP00000422325:T345M;ENSP00000425670:T273M;ENSP00000426946:T310M;ENSP00000423638:T331M;ENSP00000425787:T60M;ENSP00000422807:T60M;ENSP00000422929:T68M	.|ENSP00000312523:T323M	R|T	+|+	1|2	2|0	CAST|CAST	96107884|96107884	0.001000|0.001000	0.12720|0.12720	0.998000|0.998000	0.56505|0.56505	0.117000|0.117000	0.20001|0.20001	-0.754000|-0.754000	0.04787|0.04787	0.168000|0.168000	0.19655|0.19655	-0.733000|-0.733000	0.03571|0.03571	CGG|ACG	C|0.988;T|0.012	0.012	strong		0.418	CAST-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000250199.2	NM_173062	Missense_Mutation
C16orf82	162083	hgsc.bcm.edu	37	16	27078462	27078462	+	lincRNA	SNP	T	T	C	rs114324679	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27078462T>C	ENST00000505035.1	+	0	435				RP11-673P17.2_ENST00000565783.1_RNA			Q7Z2V1	TNT_HUMAN	chromosome 16 open reading frame 82																		CATGCAGGAGTGGCTCAGGAG	0.607													C|||	96	0.0191693	0.0711	0.0014	5008	,	,		17070	0.0		0.001	False		,,,				2504	0.0				p.V49A		Atlas-SNP	.											.	.	.	.	0			c.T146C						PASS	.	C	ALA/VAL	219,4001		6,207,1897	21.0	26.0	24.0		146	-3.7	0.0	16	dbSNP_132	24	6,8484		0,6,4239	yes	missense	C16orf82	NM_001145545.1	64	6,213,6136	CC,CT,TT		0.0707,5.1896,1.7703	benign	49/155	27078462	225,12485	2110	4245	6355			162083	exon1			CAGGAGTGGCTCA	BC031257		16p12.1	2013-01-24			ENSG00000234186	ENSG00000234186			30755	other	unknown						12477932	Standard	NM_001145545		Approved	TNT	uc010vcm.2	Q7Z2V1	OTTHUMG00000161986		16.37:g.27078462T>C		76.0	0.0	0		98.0	48.0	0.489796	NM_001145545	B9EGC2|Q8NEF0	Missense_Mutation	SNP	ENST00000505035.1	37																																																																																				T|0.984;C|0.016	0.016	strong		0.607	C16orf82-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000366634.1	NM_001145545	
FNDC7	163479	hgsc.bcm.edu	37	1	109273351	109273351	+	Missense_Mutation	SNP	C	C	A	rs76462144	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:109273351C>A	ENST00000370017.3	+	9	1957	c.1680C>A	c.(1678-1680)aaC>aaA	p.N560K	FNDC7_ENST00000271311.2_Missense_Mutation_p.N561K	NM_001144937.1	NP_001138409.1	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	560	Fibronectin type-III 7. {ECO:0000255|PROSITE-ProRule:PRU00316}.					extracellular region (GO:0005576)				breast(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(6)|ovary(1)|skin(4)|stomach(1)|urinary_tract(1)	20		all_lung(203;0.00439)|Lung NSC(277;0.00683)|all_epithelial(167;0.00728)		Colorectal(144;0.0314)|Lung(183;0.0924)|COAD - Colon adenocarcinoma(174;0.119)|Epithelial(280;0.173)|all cancers(265;0.244)		CAGTAATCAACGTGAGCTGGA	0.453													C|||	140	0.0279553	0.1006	0.0086	5008	,	,		19811	0.0		0.001	False		,,,				2504	0.0				p.N560K		Atlas-SNP	.											FNDC7_ENST00000370017,NS,carcinoma,0,2	FNDC7	113	2	0			c.C1680A						PASS	.	C	LYS/ASN	382,4024	193.3+/-218.5	18,346,1839	151.0	133.0	139.0		1680	-0.3	1.0	1	dbSNP_131	139	4,8596	3.7+/-12.6	0,4,4296	yes	missense	FNDC7	NM_001144937.1	94	18,350,6135	AA,AC,CC		0.0465,8.67,2.9679	probably-damaging	560/734	109273351	386,12620	2203	4300	6503	SO:0001583	missense	163479	exon9			AATCAACGTGAGC		CCDS44185.1	1p13.3	2013-02-11			ENSG00000143107	ENSG00000143107		"""Fibronectin type III domain containing"""	26668	protein-coding gene	gene with protein product						12477932	Standard	NM_001144937		Approved	FLJ35838	uc001dvx.3	Q5VTL7	OTTHUMG00000011120	ENST00000370017.3:c.1680C>A	1.37:g.109273351C>A	ENSP00000359034:p.Asn560Lys	176.0	0.0	0		153.0	77.0	0.503268	NM_001144937	A1L468|E9PAZ5|Q6PF16|Q8NA51	Missense_Mutation	SNP	ENST00000370017.3	37	CCDS44185.1	67|67	0.030677655677655676|0.030677655677655676	63|63	0.12804878048780488|0.12804878048780488	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	0|0	0.0|0.0	C|C	19.57|19.57	3.852633|3.852633	0.71719|0.71719	0.0867|0.0867	4.65E-4|4.65E-4	ENSG00000143107|ENSG00000143107	ENST00000370017;ENST00000271311|ENST00000445274	D;D|.	0.99220|.	-5.58;-5.58|.	6.05|6.05	-0.336|-0.336	0.12658|0.12658	Fibronectin, type III (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.58337|0.58337	0.2115|0.2115	M|M	0.72894|0.72894	2.215|2.215	0.48135|0.48135	D|D	0.999597|0.999597	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.999;0.998|.	T|T	0.62300|0.62300	-0.6883|-0.6883	10|5	0.05833|.	T|.	0.94|.	-25.7874|-25.7874	12.6633|12.6633	0.56826|0.56826	0.0:0.563:0.0:0.437|0.0:0.563:0.0:0.437	.|.	561;560|.	Q5VTL7;E9PAZ5|.	FNDC7_HUMAN;.|.	K|S	560;561|336	ENSP00000359034:N560K;ENSP00000271311:N561K|.	ENSP00000271311:N561K|.	N|R	+|+	3|1	2|0	FNDC7|FNDC7	109074874|109074874	0.002000|0.002000	0.14202|0.14202	0.998000|0.998000	0.56505|0.56505	0.989000|0.989000	0.77384|0.77384	-1.351000|-1.351000	0.02622|0.02622	0.023000|0.023000	0.15187|0.15187	0.655000|0.655000	0.94253|0.94253	AAC|CGT	A|0.027;C|0.973;T|0.000	0.027	strong		0.453	FNDC7-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030589.4	NM_173532	
NBPF3	84224	hgsc.bcm.edu	37	1	21795287	21795287	+	Silent	SNP	G	G	A	rs10157037	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:21795287G>A	ENST00000318249.5	+	3	590	c.240G>A	c.(238-240)tcG>tcA	p.S80S	NBPF3_ENST00000318220.6_Silent_p.S24S|NBPF3_ENST00000342104.5_Silent_p.S80S|NBPF3_ENST00000454000.2_Intron	NM_032264.3	NP_115640.1	Q9H094	NBPF3_HUMAN	neuroblastoma breakpoint family, member 3	80						cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	20		all_lung(284;2.16e-05)|Lung NSC(340;2.19e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00432)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0181)|OV - Ovarian serous cystadenocarcinoma(117;7.53e-27)|COAD - Colon adenocarcinoma(152;1.18e-05)|GBM - Glioblastoma multiforme(114;3.47e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000143)|STAD - Stomach adenocarcinoma(196;0.00306)|KIRC - Kidney renal clear cell carcinoma(1967;0.00645)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		ACAAGAAATCGCGCCCCCAGC	0.502											OREG0013205	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	.|||	267	0.0533147	0.1467	0.0951	5008	,	,		17981	0.001		0.002	False		,,,				2504	0.0041				p.K80K		Atlas-SNP	.											.	NBPF3	55	.	0			c.A240A						PASS	.	G		498,3908		32,434,1737	85.0	99.0	94.0		240	-2.3	0.0	1	dbSNP_119	94	57,8543		1,55,4244	no	coding-synonymous	NBPF3	NM_032264.2		33,489,5981	AA,AG,GG		0.6628,11.3028,4.2673		80/634	21795287	555,12451	2203	4300	6503	SO:0001819	synonymous_variant	84224	exon3			GAAATCGCGCCCC	BC024011	CCDS216.1, CCDS57976.1, CCDS57977.1	1p36.12	2013-01-17			ENSG00000142794	ENSG00000142794		"""neuroblastoma breakpoint family"""	25076	protein-coding gene	gene with protein product		612992				11230166, 16079250	Standard	NM_032264		Approved	AE2	uc001ber.4	Q9H094	OTTHUMG00000002944	ENST00000318249.5:c.240G>A	1.37:g.21795287G>A		195.0	0.0	0	751	191.0	95.0	0.497382	NM_001256416	A8K965|B4DSP2|I3L0I8|Q3BBW1|Q5VTG2|Q5VTG3|Q5VTG4|Q8IX78|Q8ND86|Q8TC96	Silent	SNP	ENST00000318249.5	37	CCDS216.1																																																																																			G|0.953;A|0.047	0.047	strong		0.502	NBPF3-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_032264	
FLG2	388698	hgsc.bcm.edu	37	1	152324397	152324397	+	Silent	SNP	G	G	A	rs79983774	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152324397G>A	ENST00000388718.5	-	3	5937	c.5865C>T	c.(5863-5865)caC>caT	p.H1955H	FLG-AS1_ENST00000445097.1_RNA|FLG-AS1_ENST00000392688.2_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	1955					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)			TGTACTCACTGTGGCCAGATC	0.532													g|||	341	0.0680911	0.2421	0.0231	5008	,	,		27530	0.0		0.005	False		,,,				2504	0.0				p.H1955H		Atlas-SNP	.											.	FLG2	431	.	0			c.C5865T						PASS	.	G		841,3565	331.8+/-302.1	70,701,1432	329.0	310.0	316.0		5865	-2.1	0.0	1	dbSNP_131	316	25,8575	17.9+/-57.8	0,25,4275	no	coding-synonymous	FLG2	NM_001014342.2		70,726,5707	AA,AG,GG		0.2907,19.0876,6.6585		1955/2392	152324397	866,12140	2203	4300	6503	SO:0001819	synonymous_variant	388698	exon3			CTCACTGTGGCCA	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.5865C>T	1.37:g.152324397G>A		383.0	0.0	0		426.0	211.0	0.495305	NM_001014342	Q9H4U1	Silent	SNP	ENST00000388718.5	37	CCDS30861.1																																																																																			G|0.940;A|0.060	0.060	strong		0.532	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
HMHA1	23526	hgsc.bcm.edu	37	19	1085690	1085690	+	Silent	SNP	G	G	A	rs149960692	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1085690G>A	ENST00000313093.2	+	23	3327	c.3096G>A	c.(3094-3096)tcG>tcA	p.S1032S	HMHA1_ENST00000536472.1_Silent_p.S900S|HMHA1_ENST00000590214.1_Silent_p.S1059S|HMHA1_ENST00000586866.1_Silent_p.S1036S|HMHA1_ENST00000543365.1_Silent_p.S915S|POLR2E_ENST00000585838.1_5'Flank|HMHA1_ENST00000539243.2_Silent_p.S1048S|HMHA1_ENST00000590577.1_Silent_p.S667S|HMHA1_ENST00000591169.1_3'UTR	NM_012292.3	NP_036424.2	Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	1032					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(7)|ovary(1)|prostate(2)	16		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|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)		ATTCGGACTCGGACCTAGAGG	0.617													g|||	36	0.0071885	0.0272	0.0	5008	,	,		17360	0.0		0.0	False		,,,				2504	0.0				p.S1048S		Atlas-SNP	.											.	HMHA1	78	.	0			c.G3144A						PASS	.	G		87,4271		1,85,2093	10.0	13.0	12.0		3096	-6.4	1.0	19	dbSNP_134	12	1,8533		0,1,4266	no	coding-synonymous	HMHA1	NM_012292.2		1,86,6359	AA,AG,GG		0.0117,1.9963,0.6826		1032/1137	1085690	88,12804	2179	4267	6446	SO:0001819	synonymous_variant	23526	exon23			GGACTCGGACCTA	D86976	CCDS32863.1, CCDS58637.1, CCDS74242.1, CCDS74243.1	19p13.3	2011-09-07				ENSG00000180448		"""Rho GTPase activating proteins"""	17102	protein-coding gene	gene with protein product		601155				9820596, 9039502	Standard	NM_012292		Approved	KIAA0223, HA-1, ARHGAP45	uc010xgd.2	Q92619		ENST00000313093.2:c.3096G>A	19.37:g.1085690G>A		129.0	0.0	0		119.0	63.0	0.529412	NM_001258328	B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	Silent	SNP	ENST00000313093.2	37	CCDS32863.1																																																																																			G|0.993;A|0.007	0.007	strong		0.617	HMHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458026.1		
CEACAM8	1088	hgsc.bcm.edu	37	19	43093718	43093718	+	Silent	SNP	C	C	T	rs10413332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43093718C>T	ENST00000244336.5	-	3	695	c.594G>A	c.(592-594)agG>agA	p.R198R	LIPE-AS1_ENST00000594624.2_RNA|CEACAM8_ENST00000599005.1_Intron|LIPE-AS1_ENST00000594688.1_RNA	NM_001816.3	NP_001807.2	P31997	CEAM8_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 8	198	Ig-like C2-type 1.				immune response (GO:0006955)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	16		Prostate(69;0.00899)				GAGTGAGGGTCCTGTTGCCAT	0.522													C|||	355	0.0708866	0.2542	0.0231	5008	,	,		18633	0.0		0.003	False		,,,				2504	0.0				p.R198R		Atlas-SNP	.											.	CEACAM8	44	.	0			c.G594A						PASS	.	C		874,3532	341.2+/-306.6	92,690,1421	271.0	241.0	251.0		594	1.3	0.6	19	dbSNP_119	251	18,8582	10.5+/-38.8	0,18,4282	no	coding-synonymous	CEACAM8	NM_001816.3		92,708,5703	TT,TC,CC		0.2093,19.8366,6.8584		198/350	43093718	892,12114	2203	4300	6503	SO:0001819	synonymous_variant	1088	exon3			GAGGGTCCTGTTG	D90064	CCDS12610.1	19q13.2	2013-01-29			ENSG00000124469	ENSG00000124469		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1820	protein-coding gene	gene with protein product		615747		CGM6		2208113, 2306228	Standard	NM_001816		Approved	CD66b	uc002oud.2	P31997	OTTHUMG00000151124	ENST00000244336.5:c.594G>A	19.37:g.43093718C>T		243.0	0.0	0		291.0	123.0	0.42268	NM_001816	O60399|Q16574	Silent	SNP	ENST00000244336.5	37	CCDS12610.1																																																																																			C|0.938;T|0.062	0.062	strong		0.522	CEACAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321430.1		
ITGAL	3683	hgsc.bcm.edu	37	16	30495496	30495496	+	Silent	SNP	C	C	T	rs7191097	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:30495496C>T	ENST00000356798.6	+	9	1098	c.918C>T	c.(916-918)ccC>ccT	p.P306P	RP11-297C4.3_ENST00000562525.1_RNA|RP11-297C4.2_ENST00000569459.1_RNA|ITGAL_ENST00000433423.2_Intron|ITGAL_ENST00000358164.5_Silent_p.P223P|RNU7-61P_ENST00000515897.1_RNA	NM_002209.2	NP_002200.2	P20701	ITAL_HUMAN	integrin, alpha L (antigen CD11A (p180), lymphocyte function-associated antigen 1; alpha polypeptide)	306	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|cellular component movement (GO:0006928)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|inflammatory response (GO:0006954)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of T cell proliferation (GO:0042102)|receptor clustering (GO:0043113)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integrin alphaL-beta2 complex (GO:0034687)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|ICAM-3 receptor activity (GO:0030369)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(10)|kidney(4)|large_intestine(12)|lung(32)|ovary(3)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	76					Antithymocyte globulin(DB00098)|Efalizumab(DB00095)|Lovastatin(DB00227)	CATCAAAACCCGCGAGCGAGT	0.468													C|||	423	0.0844649	0.3086	0.0159	5008	,	,		18600	0.0		0.004	False		,,,				2504	0.0				p.P306P	NSCLC(110;1462 1641 3311 33990 49495)	Atlas-SNP	.											.	ITGAL	149	.	0			c.C918T						PASS	.	C	,	1274,3120	434.7+/-344.0	192,890,1115	110.0	112.0	111.0		669,918	-3.8	0.0	16	dbSNP_116	111	27,8573	17.9+/-57.8	1,25,4274	no	coding-synonymous,coding-synonymous	ITGAL	NM_001114380.1,NM_002209.2	,	193,915,5389	TT,TC,CC		0.314,28.9941,10.0123	,	223/1087,306/1171	30495496	1301,11693	2197	4300	6497	SO:0001819	synonymous_variant	3683	exon9			AAAACCCGCGAGC		CCDS32433.1, CCDS45461.1	16p13.1-p11	2010-03-23				ENSG00000005844		"""CD molecules"", ""Integrins"""	6148	protein-coding gene	gene with protein product		153370		CD11A		3284962	Standard	NM_002209		Approved	LFA-1	uc002dyi.4	P20701		ENST00000356798.6:c.918C>T	16.37:g.30495496C>T		63.0	0.0	0		61.0	61.0	1	NM_002209	O43746|Q45H73|Q96HB1|Q9UBC8	Silent	SNP	ENST00000356798.6	37	CCDS32433.1																																																																																			C|0.900;T|0.100	0.100	strong		0.468	ITGAL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434508.2		
ZNF492	57615	hgsc.bcm.edu	37	19	22847917	22847917	+	Silent	SNP	T	T	C	rs201040917		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22847917T>C	ENST00000456783.2	+	4	1690	c.1446T>C	c.(1444-1446)tgT>tgC	p.C482C	CTC-457E21.9_ENST00000601860.1_RNA	NM_020855.2	NP_065906.1	Q9P255	ZN492_HUMAN	zinc finger protein 492	482					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(6)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		all_cancers(12;0.0266)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00203)|Hepatocellular(1079;0.244)				GTGAAGAATGTGGCAAAGCCT	0.373																																					p.C482C		Atlas-SNP	.											ZNF492_ENST00000456783,NS,carcinoma,+1,1	ZNF492	129	1	0			c.T1446C						scavenged	.	T		172,3876		2,168,1854	27.0	39.0	36.0		1446	1.1	0.5	19	dbSNP_134	36	4,8488		0,4,4242	no	coding-synonymous	ZNF492	NM_020855.2		2,172,6096	CC,CT,TT		0.0471,4.249,1.4035		482/532	22847917	176,12364	2024	4246	6270	SO:0001819	synonymous_variant	57615	exon4			AGAATGTGGCAAA	AB040906	CCDS46032.1	19p13.11	2013-01-08				ENSG00000229676		"""Zinc fingers, C2H2-type"""	23707	protein-coding gene	gene with protein product			"""zinc finger protein 115 (Y20)"""	ZNF115		10819331	Standard	NM_020855		Approved	KIAA1473	uc002nqw.3	Q9P255		ENST00000456783.2:c.1446T>C	19.37:g.22847917T>C		310.0	1.0	0.00322581		26.0	23.0	0.884615	NM_020855	Q08EI7|Q08EI8	Silent	SNP	ENST00000456783.2	37	CCDS46032.1																																																																																			T|0.500;C|0.500	0.500	weak		0.373	ZNF492-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464581.1	NM_020855	
WNT3A	89780	hgsc.bcm.edu	37	1	228238443	228238443	+	Missense_Mutation	SNP	G	G	A	rs61743220	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228238443G>A	ENST00000284523.1	+	3	478	c.400G>A	c.(400-402)Gcc>Acc	p.A134T	WNT3A_ENST00000366753.2_Missense_Mutation_p.A134T	NM_033131.3	NP_149122.1	P56704	WNT3A_HUMAN	wingless-type MMTV integration site family, member 3A	134					axis elongation involved in somitogenesis (GO:0090245)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment (GO:0061317)|cell proliferation in forebrain (GO:0021846)|cellular protein localization (GO:0034613)|cellular response to retinoic acid (GO:0071300)|COP9 signalosome assembly (GO:0010387)|dorsal/ventral neural tube patterning (GO:0021904)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|hemopoiesis (GO:0030097)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|inner ear morphogenesis (GO:0042472)|mammary gland development (GO:0030879)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron projection development (GO:0010977)|neuron differentiation (GO:0030182)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|paraxial mesodermal cell fate commitment (GO:0048343)|platelet aggregation (GO:0070527)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation (GO:2000081)|positive regulation of cardiac muscle cell differentiation (GO:2000727)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of collateral sprouting in absence of injury (GO:0048697)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of dermatome development (GO:0061184)|positive regulation of mesodermal cell fate specification (GO:0048337)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of receptor internalization (GO:0002092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-anal tail morphogenesis (GO:0036342)|regulation of microtubule cytoskeleton organization (GO:0070507)|skeletal muscle cell differentiation (GO:0035914)|spinal cord association neuron differentiation (GO:0021527)|Wnt signaling pathway involved in forebrain neuroblast division (GO:0021874)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|transcription coactivator activity (GO:0003713)			kidney(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	12		Prostate(94;0.0405)				AGGCACGGCCGCCATCTGTGG	0.627													G|||	31	0.0061901	0.0234	0.0	5008	,	,		17447	0.0		0.0	False		,,,				2504	0.0				p.A134T		Atlas-SNP	.											.	WNT3A	40	.	0			c.G400A						PASS	.	G	THR/ALA	115,4291	86.3+/-125.0	1,113,2089	80.0	72.0	75.0		400	-2.0	0.0	1	dbSNP_129	75	0,8600		0,0,4300	yes	missense	WNT3A	NM_033131.3	58	1,113,6389	AA,AG,GG		0.0,2.6101,0.8842	benign	134/353	228238443	115,12891	2203	4300	6503	SO:0001583	missense	89780	exon3			ACGGCCGCCATCT	AB060284	CCDS1564.1	1q42	2013-02-28			ENSG00000154342	ENSG00000154342		"""Wingless-type MMTV integration sites"", ""Endogenous ligands"""	15983	protein-coding gene	gene with protein product		606359				11414706	Standard	NM_033131		Approved		uc001hrq.2	P56704	OTTHUMG00000037593	ENST00000284523.1:c.400G>A	1.37:g.228238443G>A	ENSP00000284523:p.Ala134Thr	189.0	0.0	0		167.0	79.0	0.473054	NM_033131	Q3SY79|Q3SY80|Q969P2	Missense_Mutation	SNP	ENST00000284523.1	37	CCDS1564.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	G	0.524	-0.860772	0.02610	0.026101	0.0	ENSG00000154342	ENST00000284523;ENST00000366753	T;T	0.75367	-0.93;-0.93	4.78	-1.98	0.07480	.	0.443415	0.23894	N	0.043517	T	0.15782	0.0380	N	0.00771	-1.2	0.24533	N	0.994101	B;B	0.06786	0.0;0.001	B;B	0.09377	0.002;0.004	T	0.25984	-1.0116	10	0.10377	T	0.69	.	12.1436	0.54012	0.6823:0.0:0.3177:0.0	rs61743220	134;134	P56704;Q3SY79	WNT3A_HUMAN;.	T	134	ENSP00000284523:A134T;ENSP00000355715:A134T	ENSP00000284523:A134T	A	+	1	0	WNT3A	226305066	0.916000	0.31088	0.005000	0.12908	0.134000	0.20937	1.632000	0.37102	-0.810000	0.04375	-1.094000	0.02160	GCC	G|0.992;A|0.008	0.008	strong		0.627	WNT3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091648.1	NM_033131	
LCN15	389812	hgsc.bcm.edu	37	9	139657874	139657874	+	Missense_Mutation	SNP	G	G	C	rs11145871	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139657874G>C	ENST00000316144.5	-	4	377	c.353C>G	c.(352-354)tCc>tGc	p.S118C	LCN15_ENST00000482511.1_5'UTR	NM_203347.1	NP_976222.1	Q6UWW0	LCN15_HUMAN	lipocalin 15	118					lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	small molecule binding (GO:0036094)|transporter activity (GO:0005215)			endometrium(1)|lung(1)	2						GACGGCGAAGGAGCTGTAGTC	0.642													G|||	14	0.00279553	0.0098	0.0014	5008	,	,		8323	0.0		0.0	False		,,,				2504	0.0				p.S118C		Atlas-SNP	.											.	LCN15	11	.	0			c.C353G						PASS	.	G	CYS/SER	55,4351	54.2+/-90.2	1,53,2149	83.0	75.0	77.0		353	3.8	0.3	9	dbSNP_120	77	0,8600		0,0,4300	yes	missense	LCN15	NM_203347.1	112	1,53,6449	CC,CG,GG		0.0,1.2483,0.4229	probably-damaging	118/185	139657874	55,12951	2203	4300	6503	SO:0001583	missense	389812	exon4			GCGAAGGAGCTGT		CCDS7006.1	9q34.3	2011-10-24			ENSG00000177984	ENSG00000177984		"""Lipocalins"""	33777	protein-coding gene	gene with protein product							Standard	NM_203347		Approved	UNQ2541, PRO6093	uc004cjd.3	Q6UWW0	OTTHUMG00000020943	ENST00000316144.5:c.353C>G	9.37:g.139657874G>C	ENSP00000313833:p.Ser118Cys	37.0	0.0	0		37.0	21.0	0.567568	NM_203347		Missense_Mutation	SNP	ENST00000316144.5	37	CCDS7006.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	G	14.93	2.681579	0.47991	0.012483	0.0	ENSG00000177984	ENST00000316144	T	0.08720	3.06	3.76	3.76	0.43208	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	1.023620	0.07803	N	0.956885	T	0.17577	0.0422	M	0.71581	2.175	0.09310	N	1	D	0.69078	0.997	P	0.58077	0.832	T	0.08700	-1.0709	10	0.62326	D	0.03	.	11.2408	0.48968	0.0:0.0:1.0:0.0	rs11145871	118	Q6UWW0	LCN15_HUMAN	C	118	ENSP00000313833:S118C	ENSP00000313833:S118C	S	-	2	0	LCN15	138777695	0.919000	0.31177	0.273000	0.24645	0.776000	0.43924	2.771000	0.47670	2.104000	0.64026	0.561000	0.74099	TCC	G|0.994;C|0.006	0.006	strong		0.642	LCN15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055114.2	NM_203347	
SCN1A	6323	hgsc.bcm.edu	37	2	166900425	166900425	+	Silent	SNP	C	C	T	rs145035963		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:166900425C>T	ENST00000303395.4	-	11	1796	c.1797G>A	c.(1795-1797)gaG>gaA	p.E599E	AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000595268.1_RNA|SCN1A_ENST00000423058.2_Silent_p.E599E|SCN1A_ENST00000409050.1_Silent_p.E599E|AC010127.3_ENST00000599041.1_RNA|SCN1A_ENST00000375405.3_Silent_p.E599E			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	599					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TCTCGTTATCCTCAAAGGTGC	0.527													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20315	0.0		0.0	False		,,,				2504	0.0				p.E599E		Atlas-SNP	.											.	SCN1A	641	.	0			c.G1797A						PASS	.	C	,,,	4,4402	8.1+/-20.4	0,4,2199	168.0	148.0	155.0		1797,1797,1797,1797	3.3	1.0	2	dbSNP_134	155	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SCN1A	NM_001165963.1,NM_001165964.1,NM_001202435.1,NM_006920.4	,,,	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	,,,	599/2010,599/1982,599/2010,599/1999	166900425	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	6323	exon11			GTTATCCTCAAAG	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10585	protein-coding gene	gene with protein product		182389	"""febrile convulsions 3"""	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.1797G>A	2.37:g.166900425C>T		213.0	0.0	0		195.0	111.0	0.569231	NM_001165964	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Silent	SNP	ENST00000303395.4	37	CCDS54413.1																																																																																			C|1.000;T|0.000	0.000	strong		0.527	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920	
NEIL2	252969	hgsc.bcm.edu	37	8	11640853	11640853	+	Silent	SNP	C	C	T	rs112549959	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11640853C>T	ENST00000284503.6	+	4	1232	c.633C>T	c.(631-633)ggC>ggT	p.G211G	NEIL2_ENST00000528323.1_Silent_p.G95G|NEIL2_ENST00000455213.2_Silent_p.G211G|NEIL2_ENST00000436750.3_Silent_p.G211G|NEIL2_ENST00000403422.3_Silent_p.G150G	NM_145043.2	NP_659480.1	Q969S2	NEIL2_HUMAN	nei endonuclease VIII-like 2 (E. coli)	211					base-excision repair (GO:0006284)|nucleotide-excision repair (GO:0006289)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)	damaged DNA binding (GO:0003684)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|upper_aerodigestive_tract(1)	10	all_epithelial(15;0.103)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.166)		AAGCTCTAGGCCAGGCTCAGC	0.517								Base excision repair (BER), DNA glycosylases					C|||	22	0.00439297	0.0159	0.0014	5008	,	,		23388	0.0		0.0	False		,,,				2504	0.0				p.G211G		Atlas-SNP	.											.	NEIL2	14	.	0			c.C633T						PASS	.	C	,,,	45,4361	48.2+/-83.0	0,45,2158	119.0	104.0	109.0		633,450,285,633	-3.7	0.1	8	dbSNP_132	109	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NEIL2	NM_001135746.1,NM_001135747.1,NM_001135748.1,NM_145043.2	,,,	0,45,6458	TT,TC,CC		0.0,1.0213,0.346	,,,	211/333,150/272,95/217,211/333	11640853	45,12961	2203	4300	6503	SO:0001819	synonymous_variant	252969	exon4			TCTAGGCCAGGCT	AK056206	CCDS5984.1, CCDS47802.1, CCDS47803.1	8p23.1	2010-04-27	2010-04-27		ENSG00000154328	ENSG00000154328			18956	protein-coding gene	gene with protein product		608933	"""nei like 2 (E. coli)"""			12097317, 17686777	Standard	NM_145043		Approved	NEH2, FLJ31644, MGC2832, MGC4505	uc003wue.2	Q969S2	OTTHUMG00000090753	ENST00000284503.6:c.633C>T	8.37:g.11640853C>T		180.0	0.0	0		207.0	97.0	0.468599	NM_001135746	B4DFR7|Q7Z3Q7|Q8N842|Q8NG52	Silent	SNP	ENST00000284503.6	37	CCDS5984.1																																																																																			C|0.996;T|0.004	0.004	strong		0.517	NEIL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207583.3	NM_145043	
TSPYL5	85453	hgsc.bcm.edu	37	8	98289922	98289922	+	Missense_Mutation	SNP	C	C	T	rs200123082	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:98289922C>T	ENST00000322128.3	-	1	254	c.151G>A	c.(151-153)Gca>Aca	p.A51T		NM_033512.2	NP_277047.2	Q86VY4	TSYL5_HUMAN	TSPY-like 5	51					cellular response to gamma radiation (GO:0071480)|nucleosome assembly (GO:0006334)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein ubiquitination (GO:0031398)|regulation of growth (GO:0040008)	nucleus (GO:0005634)				cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(3)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	20	Breast(36;2.56e-06)					TGCACCTGTGCCGCCTGGGTG	0.746													C|||	37	0.00738818	0.0257	0.0043	5008	,	,		10609	0.0		0.0	False		,,,				2504	0.0				p.A51T		Atlas-SNP	.											.	TSPYL5	48	.	0			c.G151A						PASS	.	C	THR/ALA	59,4045		1,57,1994	5.0	7.0	6.0		151	1.2	0.0	8		6	2,8036		0,2,4017	yes	missense	TSPYL5	NM_033512.2	58	1,59,6011	TT,TC,CC		0.0249,1.4376,0.5024	possibly-damaging	51/418	98289922	61,12081	2052	4019	6071	SO:0001583	missense	85453	exon1			CCTGTGCCGCCTG	AB051537	CCDS34927.1	8q22.1	2011-05-24			ENSG00000180543	ENSG00000180543			29367	protein-coding gene	gene with protein product		614721				11214970	Standard	NM_033512		Approved	KIAA1750	uc003yhy.3	Q86VY4	OTTHUMG00000164857	ENST00000322128.3:c.151G>A	8.37:g.98289922C>T	ENSP00000322802:p.Ala51Thr	29.0	0.0	0		32.0	18.0	0.5625	NM_033512	B3KRF0|Q9C0B3	Missense_Mutation	SNP	ENST00000322128.3	37	CCDS34927.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	C	2.842	-0.240359	0.05944	0.014376	2.49E-4	ENSG00000180543	ENST00000322128	T	0.23754	1.89	4.03	1.24	0.21308	.	0.260319	0.20293	N	0.095194	T	0.04998	0.0134	N	0.20986	0.625	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	T	0.32719	-0.9896	10	0.02654	T	1	-1.04	3.5525	0.07851	0.1976:0.5914:0.0:0.211	.	51	Q86VY4	TSYL5_HUMAN	T	51	ENSP00000322802:A51T	ENSP00000322802:A51T	A	-	1	0	TSPYL5	98359098	0.996000	0.38824	0.014000	0.15608	0.014000	0.08584	2.417000	0.44653	0.261000	0.21753	-0.258000	0.10820	GCA	C|0.994;T|0.006	0.006	strong		0.746	TSPYL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380611.1	NM_033512	
APOC2	344	hgsc.bcm.edu	37	19	45452429	45452429	+	Missense_Mutation	SNP	A	A	C	rs5126	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45452429A>C	ENST00000590360.1	+	4	351	c.229A>C	c.(229-231)Aaa>Caa	p.K77Q	APOC2_ENST00000585786.1_3'UTR|APOC4-APOC2_ENST00000589057.1_Missense_Mutation_p.K154Q|APOC2_ENST00000592257.1_3'UTR|APOC2_ENST00000252490.4_Missense_Mutation_p.K77Q|APOC4_ENST00000419266.2_3'UTR|APOC2_ENST00000591597.1_Missense_Mutation_p.K63Q			P02655	APOC2_HUMAN	apolipoprotein C-II	77	Lipoprotein lipase cofactor.		K -> Q (in Africa; dbSNP:rs5126). {ECO:0000269|PubMed:10391210, ECO:0000269|PubMed:3944271}.		cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|chylomicron remnant clearance (GO:0034382)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle clearance (GO:0034384)|lipid catabolic process (GO:0016042)|lipoprotein metabolic process (GO:0042157)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of lipid metabolic process (GO:0045833)|negative regulation of receptor-mediated endocytosis (GO:0048261)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of phospholipid catabolic process (GO:0060697)|positive regulation of triglyceride catabolic process (GO:0010898)|positive regulation of very-low-density lipoprotein particle remodeling (GO:0010902)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)|triglyceride-rich lipoprotein particle remodeling (GO:0034370)|very-low-density lipoprotein particle remodeling (GO:0034372)	chylomicron (GO:0042627)|early endosome (GO:0005769)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate-density lipoprotein particle (GO:0034363)|low-density lipoprotein particle (GO:0034362)|spherical high-density lipoprotein particle (GO:0034366)|very-low-density lipoprotein particle (GO:0034361)	lipase inhibitor activity (GO:0055102)|lipid binding (GO:0008289)|lipoprotein lipase activator activity (GO:0060230)|phospholipase activator activity (GO:0016004)|phospholipase binding (GO:0043274)|protein homodimerization activity (GO:0042803)			kidney(1)|large_intestine(1)|liver(1)|lung(3)	6	Lung NSC(12;0.00858)|all_lung(12;0.0197)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.00327)|Epithelial(262;0.174)		CTTGTACAGCAAAAGCACAGC	0.567													A|||	39	0.00778754	0.0287	0.0014	5008	,	,		15843	0.0		0.0	False		,,,				2504	0.0				p.K77Q		Atlas-SNP	.											.	APOC2	9	.	0			c.A229C						PASS	.	A	GLN/LYS	85,4321	47.5+/-82.1	1,83,2119	79.0	66.0	71.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	229	2.0	0.4	19	dbSNP_52	71	0,8600		0,0,4300	yes	missense	APOC2	NM_000483.4	53	1,83,6419	CC,CA,AA		0.0,1.9292,0.6535	probably-damaging	77/102	45452429	85,12921	2203	4300	6503	SO:0001583	missense	344	exon4			TACAGCAAAAGCA	X00568	CCDS12650.1	19q13.2	2013-01-24			ENSG00000234906	ENSG00000234906		"""Apolipoproteins"""	609	protein-coding gene	gene with protein product		608083					Standard	NM_000483		Approved			P02655	OTTHUMG00000180847	ENST00000590360.1:c.229A>C	19.37:g.45452429A>C	ENSP00000466775:p.Lys77Gln	122.0	0.0	0		123.0	59.0	0.479675	NM_000483	C0JYY4|Q9BS39|Q9UDE3|Q9UNK3	Missense_Mutation	SNP	ENST00000590360.1	37	CCDS12650.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	A	15.05	2.717211	0.48622	0.019292	0.0	ENSG00000234906	ENST00000252490	D	0.86164	-2.08	4.25	1.97	0.26223	ApoC-II domain (1);	0.331465	0.21058	U	0.080867	T	0.66616	0.2807	M	0.77820	2.39	0.19300	N	0.999973	P	0.39216	0.664	B	0.36504	0.226	T	0.68573	-0.5373	10	0.48119	T	0.1	-0.0013	4.4429	0.11582	0.621:0.2662:0.1128:0.0	rs5126;rs52806093;rs5126	77	P02655	APOC2_HUMAN	Q	77	ENSP00000252490:K77Q	ENSP00000252490:K77Q	K	+	1	0	APOC2	50144269	0.077000	0.21312	0.448000	0.26945	0.770000	0.43624	0.076000	0.14712	0.113000	0.18004	0.323000	0.21402	AAA	A|0.991;C|0.009	0.009	strong		0.567	APOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453261.1	NM_000483	
SPATA2	9825	hgsc.bcm.edu	37	20	48522263	48522263	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:48522263C>T	ENST00000422556.1	-	3	1805	c.1456G>A	c.(1456-1458)Gct>Act	p.A486T	SPATA2_ENST00000289431.5_Missense_Mutation_p.A486T|SPATA2_ENST00000543716.1_Missense_Mutation_p.A349T	NM_001135773.1	NP_001129245.1	Q9UM82	SPAT2_HUMAN	spermatogenesis associated 2	486					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)	20	Hepatocellular(150;0.133)		BRCA - Breast invasive adenocarcinoma(9;4.03e-06)			TAATGGTAAGCGCTGAGGCAG	0.562																																					p.A486T		Atlas-SNP	.											.	SPATA2	36	.	0			c.G1456A						PASS	.						167.0	154.0	159.0					20																	48522263		2203	4300	6503	SO:0001583	missense	9825	exon3			GGTAAGCGCTGAG	AB018300	CCDS13422.1	20q13.13	2014-06-13			ENSG00000158480	ENSG00000158480			14681	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 145"""	607662					Standard	NM_001135773		Approved	KIAA0757, PD1, tamo, PPP1R145	uc002xuw.3	Q9UM82	OTTHUMG00000032704	ENST00000422556.1:c.1456G>A	20.37:g.48522263C>T	ENSP00000416799:p.Ala486Thr	342.0	0.0	0		371.0	188.0	0.506739	NM_006038	E1P626|O94857	Missense_Mutation	SNP	ENST00000422556.1	37	CCDS13422.1	.	.	.	.	.	.	.	.	.	.	C	15.06	2.721788	0.48728	.	.	ENSG00000158480	ENST00000289431;ENST00000422556;ENST00000543716	T;T;T	0.48201	0.83;0.83;0.82	5.08	0.988	0.19796	.	0.293281	0.28198	N	0.016236	T	0.40570	0.1122	L	0.59436	1.845	0.36765	D	0.883515	B	0.18968	0.032	B	0.14023	0.01	T	0.36601	-0.9741	10	0.42905	T	0.14	-10.862	10.0211	0.42044	0.0:0.7242:0.0:0.2758	.	486	Q9UM82	SPAT2_HUMAN	T	486;486;349	ENSP00000289431:A486T;ENSP00000416799:A486T;ENSP00000438855:A349T	ENSP00000289431:A486T	A	-	1	0	SPATA2	47955670	1.000000	0.71417	0.974000	0.42286	0.448000	0.32197	2.904000	0.48719	0.057000	0.16193	0.455000	0.32223	GCT	.	.	none		0.562	SPATA2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079658.1	NM_006038	
URB2	9816	hgsc.bcm.edu	37	1	229770827	229770827	+	Missense_Mutation	SNP	C	C	T	rs115641620	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229770827C>T	ENST00000258243.2	+	4	603	c.467C>T	c.(466-468)tCg>tTg	p.S156L		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	156						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						CTTTGCTGGTCGGCCTGCAGG	0.587													C|||	43	0.00858626	0.0318	0.0014	5008	,	,		21011	0.0		0.0	False		,,,				2504	0.0				p.S156L		Atlas-SNP	.											.	URB2	152	.	0			c.C467T						PASS	.	C	LEU/SER	113,4293	87.8+/-126.4	1,111,2091	62.0	53.0	56.0		467	-7.6	0.0	1	dbSNP_132	56	1,8599		0,1,4299	no	missense	URB2	NM_014777.2	145	1,112,6390	TT,TC,CC		0.0116,2.5647,0.8765	benign	156/1525	229770827	114,12892	2203	4300	6503	SO:0001583	missense	9816	exon4			GCTGGTCGGCCTG	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.467C>T	1.37:g.229770827C>T	ENSP00000258243:p.Ser156Leu	108.0	0.0	0		117.0	62.0	0.529915	NM_014777	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	37	CCDS31052.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	C	0.017	-1.506370	0.00992	0.025647	1.16E-4	ENSG00000135763	ENST00000258243	T	0.09911	2.93	5.68	-7.55	0.01327	.	0.884065	0.09779	N	0.756927	T	0.01558	0.0050	N	0.04994	-0.135	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40251	-0.9573	9	.	.	.	-0.0083	19.9267	0.97106	0.0:0.1135:0.0:0.8865	.	156	Q14146	URB2_HUMAN	L	156	ENSP00000258243:S156L	.	S	+	2	0	URB2	227837450	0.045000	0.20229	0.000000	0.03702	0.006000	0.05464	0.359000	0.20233	-1.352000	0.02194	-1.684000	0.00734	TCG	C|0.992;T|0.008	0.008	strong		0.587	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777	
GABPA	2551	hgsc.bcm.edu	37	21	27107251	27107251	+	5'UTR	SNP	C	C	G	rs71649640	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:27107251C>G	ENST00000354828.3	+	0	371				ATP5J_ENST00000400093.3_Intron|ATP5J_ENST00000400090.3_Intron|ATP5J_ENST00000400094.1_5'Flank|ATP5J_ENST00000457143.2_Splice_Site_p.G6R|ATP5J_ENST00000284971.3_5'UTR|GABPA_ENST00000400075.3_5'Flank|ATP5J_ENST00000400099.1_Intron|ATP5J_ENST00000400087.3_Intron	NM_001197297.1	NP_001184226.1	Q06546	GABPA_HUMAN	GA binding protein transcription factor, alpha subunit 60kDa						cell differentiation (GO:0030154)|in utero embryonic development (GO:0001701)|negative regulation of megakaryocyte differentiation (GO:0045653)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|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 transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	24						CACGCCTACCCGCCATCGCAA	0.662													C|||	60	0.0119808	0.0446	0.0014	5008	,	,		16320	0.0		0.0	False		,,,				2504	0.0				p.G6R		Atlas-SNP	.											.	ATP5J	13	.	0			c.G16C						PASS	.	C	,,ARG/GLY,,	126,3852		2,122,1865	15.0	22.0	20.0		,,16,,	3.9	1.0	21	dbSNP_130	20	1,8301		0,1,4150	yes	intron,intron,missense-near-splice,utr-5,intron	ATP5J	NM_001003696.1,NM_001003697.1,NM_001003701.1,NM_001003703.1,NM_001685.4	,,125,,	2,123,6015	GG,GC,CC		0.012,3.1674,1.0342	,,,,	,,6/117,,	27107251	127,12153	1989	4151	6140	SO:0001623	5_prime_UTR_variant	522	exon1			CCTACCCGCCATC		CCDS13575.1	21q21-q22.1	2008-07-31	2002-08-29		ENSG00000154727	ENSG00000154727			4071	protein-coding gene	gene with protein product	"""human nuclear respiratory factor-2 subunit alpha"", ""nuclear respiratory factor 2 alpha subunit"""	600609	"""GA-binding protein transcription factor, alpha subunit (60kD)"""			8441384	Standard	NM_002040		Approved	E4TF1A, NFT2, NRF2, E4TF1-60, NRF2A	uc002yly.4	Q06546	OTTHUMG00000078443	ENST00000354828.3:c.-157C>G	21.37:g.27107251C>G		100.0	0.0	0		99.0	52.0	0.525253	NM_001003701	Q12939	Missense_Mutation	SNP	ENST00000354828.3	37	CCDS13575.1	20	0.009157509157509158	20	0.04065040650406504	0	0.0	0	0.0	0	0.0	C	21.0	4.088791	0.76756	0.031674	1.2E-4	ENSG00000154723	ENST00000457143	.	.	.	4.83	3.92	0.45320	.	.	.	.	.	T	0.29817	0.0745	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.46062	-0.9218	5	0.37606	T	0.19	.	11.0432	0.47844	0.0:0.8121:0.1879:0.0	.	.	.	.	R	6	.	ENSP00000389649:G6R	G	-	1	0	ATP5J	26029122	0.918000	0.31147	0.990000	0.47175	0.998000	0.95712	1.903000	0.39858	1.359000	0.45940	0.655000	0.94253	GGA	C|0.990;G|0.010	0.010	strong		0.662	GABPA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171365.1	NM_002040	
ZNF804B	219578	hgsc.bcm.edu	37	7	88963401	88963401	+	Missense_Mutation	SNP	C	C	T	rs141118086	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:88963401C>T	ENST00000333190.4	+	4	1714	c.1105C>T	c.(1105-1107)Cca>Tca	p.P369S		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	369							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			TTCCTTCAGCCCACCAAACAT	0.393										HNSCC(36;0.09)			C|||	81	0.0161741	0.0575	0.0058	5008	,	,		18756	0.0		0.001	False		,,,				2504	0.0				p.P369S		Atlas-SNP	.											.	ZNF804B	322	.	0			c.C1105T						PASS	.	C	SER/PRO	239,4165	136.1+/-172.1	7,225,1970	43.0	48.0	46.0		1105	3.1	0.8	7	dbSNP_134	46	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ZNF804B	NM_181646.2	74	7,226,6269	TT,TC,CC		0.0116,5.4269,1.8456	probably-damaging	369/1350	88963401	240,12764	2202	4300	6502	SO:0001583	missense	219578	exon4			TTCAGCCCACCAA	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"""zinc finger 804B"""				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.1105C>T	7.37:g.88963401C>T	ENSP00000329638:p.Pro369Ser	87.0	0.0	0		83.0	34.0	0.409639	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	37	CCDS5613.1	26	0.011904761904761904	24	0.04878048780487805	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	11.61	1.688835	0.29962	0.054269	1.16E-4	ENSG00000182348	ENST00000333190	T	0.05199	3.48	4.86	3.07	0.35406	.	0.639011	0.14589	N	0.310354	T	0.01092	0.0036	M	0.67953	2.075	0.09310	N	1	B	0.34372	0.451	B	0.23150	0.044	T	0.17623	-1.0363	10	0.41790	T	0.15	-1.6547	11.2317	0.48916	0.0:0.8527:0.0:0.1473	.	369	A4D1E1	Z804B_HUMAN	S	369	ENSP00000329638:P369S	ENSP00000329638:P369S	P	+	1	0	ZNF804B	88801337	0.052000	0.20516	0.793000	0.32043	0.997000	0.91878	1.203000	0.32284	0.670000	0.31165	0.655000	0.94253	CCA	C|0.986;T|0.014	0.014	strong		0.393	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646	
XYLT1	64131	hgsc.bcm.edu	37	16	17353090	17353090	+	Missense_Mutation	SNP	G	G	C	rs113276942	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:17353090G>C	ENST00000261381.6	-	3	752	c.668C>G	c.(667-669)gCc>gGc	p.A223G		NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	223					cellular response to heat (GO:0034605)|chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GTTGGCTGCGGCTCTGTCCCC	0.592													G|||	265	0.0529153	0.1914	0.0173	5008	,	,		17039	0.0		0.0	False		,,,				2504	0.0				p.A223G		Atlas-SNP	.											XYLT1,NS,carcinoma,+1,1	XYLT1	147	1	0			c.C668G						PASS	.	G	GLY/ALA	697,3697	288.1+/-279.7	67,563,1567	106.0	117.0	113.0		668	4.5	0.0	16	dbSNP_132	113	19,8581	11.2+/-40.8	0,19,4281	yes	missense	XYLT1	NM_022166.3	60	67,582,5848	CC,CG,GG		0.2209,15.8625,5.5102	benign	223/960	17353090	716,12278	2197	4300	6497	SO:0001583	missense	64131	exon3			GCTGCGGCTCTGT	AJ277441	CCDS10569.1	16p12	2013-02-25			ENSG00000103489	ENSG00000103489	2.4.2.26	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	15516	protein-coding gene	gene with protein product	"""protein xylosyltransferase 1"""	608124				11099377	Standard	NM_022166		Approved	XT-I, PXYLT1	uc002dfa.3	Q86Y38	OTTHUMG00000129975	ENST00000261381.6:c.668C>G	16.37:g.17353090G>C	ENSP00000261381:p.Ala223Gly	143.0	0.0	0		197.0	110.0	0.558376	NM_022166	Q9H1B6	Missense_Mutation	SNP	ENST00000261381.6	37	CCDS10569.1	89	0.04075091575091575	81	0.16463414634146342	8	0.022099447513812154	0	0.0	0	0.0	G	9.870	1.198774	0.22121	0.158625	0.002209	ENSG00000103489	ENST00000261381	T	0.04809	3.55	5.43	4.47	0.54385	.	0.429861	0.27500	N	0.019098	T	0.00039	0.0001	L	0.44542	1.39	0.09310	N	1	B	0.32245	0.361	B	0.19148	0.024	T	0.49021	-0.8982	10	0.31617	T	0.26	-19.7884	11.4244	0.50001	0.1501:0.0:0.8499:0.0	.	223	Q86Y38	XYLT1_HUMAN	G	223	ENSP00000261381:A223G	ENSP00000261381:A223G	A	-	2	0	XYLT1	17260591	0.015000	0.18098	0.011000	0.14972	0.446000	0.32137	1.886000	0.39688	1.296000	0.44742	0.655000	0.94253	GCC	G|0.950;C|0.050	0.050	strong		0.592	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	NM_022166	
HPS5	11234	hgsc.bcm.edu	37	11	18330522	18330522	+	Silent	SNP	A	A	G	rs146455658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:18330522A>G	ENST00000349215.3	-	6	859	c.582T>C	c.(580-582)ctT>ctC	p.L194L	HPS5_ENST00000438420.2_Silent_p.L80L|HPS5_ENST00000531848.1_Silent_p.L80L|HPS5_ENST00000396253.3_Silent_p.L80L	NM_181507.1	NP_852608.1	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5	194					blood coagulation (GO:0007596)|organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						AGGATCGAGTAAGTGAAGATA	0.388									Hermansky-Pudlak syndrome				A|||	2	0.000399361	0.0008	0.0014	5008	,	,		16667	0.0		0.0	False		,,,				2504	0.0				p.L194L		Atlas-SNP	.											.	HPS5	70	.	0			c.T582C						PASS	.	A	,,	15,4383	22.3+/-47.3	0,15,2184	136.0	118.0	124.0		240,582,240	0.2	1.0	11	dbSNP_134	124	0,8586		0,0,4293	no	coding-synonymous,coding-synonymous,coding-synonymous	HPS5	NM_007216.3,NM_181507.1,NM_181508.1	,,	0,15,6477	GG,GA,AA		0.0,0.3411,0.1155	,,	80/1016,194/1130,80/1016	18330522	15,12969	2199	4293	6492	SO:0001819	synonymous_variant	11234	exon6	Familial Cancer Database	HPS, HPS1-8	TCGAGTAAGTGAA	AB023234	CCDS7836.1, CCDS7837.1	11p14	2014-06-18			ENSG00000110756	ENSG00000110756			17022	protein-coding gene	gene with protein product		607521				10231032, 10094488	Standard	NM_181507		Approved		uc001mod.1	Q9UPZ3	OTTHUMG00000166612	ENST00000349215.3:c.582T>C	11.37:g.18330522A>G		97.0	0.0	0		88.0	40.0	0.454545	NM_181507	A8K6J8|A8K8S1|D3DQX9|D3DQY0|O95942|Q8N4U0	Silent	SNP	ENST00000349215.3	37	CCDS7836.1																																																																																			A|0.999;G|0.001	0.001	strong		0.388	HPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390808.1	NM_181507	
PNO1	56902	hgsc.bcm.edu	37	2	68385240	68385240	+	Silent	SNP	C	C	G	rs61735657	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:68385240C>G	ENST00000263657.2	+	1	265	c.174C>G	c.(172-174)ccC>ccG	p.P58P	WDR92_ENST00000409164.1_5'Flank|WDR92_ENST00000492039.2_5'Flank|WDR92_ENST00000295121.6_5'Flank|RP11-474G23.1_ENST00000406334.3_Silent_p.T150T|WDR92_ENST00000406245.2_5'Flank	NM_020143.2	NP_064528.1	Q9NRX1	PNO1_HUMAN	partner of NOB1 homolog (S. cerevisiae)	58						nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(1)|lung(2)	4						CGAAGAGGCCCGTCTTCCCAC	0.672													C|||	109	0.0217652	0.0779	0.0	5008	,	,		15102	0.0		0.001	False		,,,				2504	0.0051				p.P58P	NSCLC(83;642 1410 13044 32832 40058)	Atlas-SNP	.											.	PNO1	17	.	0			c.C174G						PASS	.	C		289,4109		7,275,1917	13.0	19.0	17.0		174	-4.9	0.9	2	dbSNP_129	17	17,8575		0,17,4279	no	coding-synonymous	PNO1	NM_020143.2		7,292,6196	GG,GC,CC		0.1979,6.5712,2.3557		58/253	68385240	306,12684	2199	4296	6495	SO:0001819	synonymous_variant	56902	exon1			GAGGCCCGTCTTC	AF164799	CCDS1885.1	2p14	2010-07-06			ENSG00000115946	ENSG00000115946			32790	protein-coding gene	gene with protein product	"""RNA binding protein"""		"""KH-type RNA binding protein 1"", ""KH-type RNA-binding protein 1"""	KHRBP1		15497447	Standard	NM_020143		Approved	RRP20	uc002seh.3	Q9NRX1	OTTHUMG00000129563	ENST00000263657.2:c.174C>G	2.37:g.68385240C>G		56.0	0.0	0		78.0	39.0	0.5	NM_020143	A8K6Q0|Q53G13|Q8WVB8	Silent	SNP	ENST00000263657.2	37	CCDS1885.1																																																																																			C|0.979;G|0.021	0.021	strong		0.672	PNO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251756.1	NM_020143	
SMARCAL1	50485	hgsc.bcm.edu	37	2	217285104	217285104	+	Missense_Mutation	SNP	C	C	G	rs2066522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:217285104C>G	ENST00000357276.4	+	5	1275	c.945C>G	c.(943-945)agC>agG	p.S315R	SMARCAL1_ENST00000358207.5_Missense_Mutation_p.S315R	NM_014140.3	NP_054859.2	Q9NZC9	SMAL1_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a-like 1	315			S -> R (in dbSNP:rs2066522).		cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA metabolic process (GO:0006259)|DNA strand renaturation (GO:0000733)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|replication fork processing (GO:0031297)	nucleus (GO:0005634)|site of double-strand break (GO:0035861)	annealing helicase activity (GO:0036310)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)			NS(1)|breast(3)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(15)|ovary(3)|prostate(1)|skin(1)	42		Renal(323;0.0458)		Epithelial(149;9.48e-06)|all cancers(144;0.000621)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.0111)		CCTCCACCAGCAGTGAGGGAC	0.572									Schimke Immuno-Osseous Dysplasia				C|||	170	0.0339457	0.0809	0.0331	5008	,	,		17373	0.0		0.0338	False		,,,				2504	0.0061				p.S315R		Atlas-SNP	.											SMARCAL1,right_upper_lobe,carcinoma,+1,1	SMARCAL1	93	1	0			c.C945G						scavenged	.	C	ARG/SER,ARG/SER	353,4053	181.9+/-209.8	17,319,1867	90.0	73.0	79.0		945,945	-0.2	0.0	2	dbSNP_98	79	249,8351	99.3+/-160.8	2,245,4053	yes	missense,missense	SMARCAL1	NM_001127207.1,NM_014140.3	110,110	19,564,5920	GG,GC,CC		2.8953,8.0118,4.6286	possibly-damaging,possibly-damaging	315/955,315/955	217285104	602,12404	2203	4300	6503	SO:0001583	missense	50485	exon5	Familial Cancer Database	SIOD	CACCAGCAGTGAG	AF210833	CCDS2403.1	2q35	2014-09-17			ENSG00000138375	ENSG00000138375			11102	protein-coding gene	gene with protein product	"""HepA-related protein"", ""ATP-driven annealing helicase"""	606622				10713074, 10857751, 18974355	Standard	NM_014140		Approved	HHARP, HARP	uc002vgd.4	Q9NZC9	OTTHUMG00000133055	ENST00000357276.4:c.945C>G	2.37:g.217285104C>G	ENSP00000349823:p.Ser315Arg	164.0	1.0	0.00609756		160.0	76.0	0.475	NM_014140	A6NEH0|Q53R00|Q96AY1|Q9NXQ5|Q9UFH3|Q9UI93	Missense_Mutation	SNP	ENST00000357276.4	37	CCDS2403.1	65	0.02976190476190476	36	0.07317073170731707	9	0.024861878453038673	0	0.0	20	0.026385224274406333	C	19.69	3.875544	0.72180	0.080118	0.028953	ENSG00000138375	ENST00000357276;ENST00000358207;ENST00000427645;ENST00000392128;ENST00000412913	D;D;T;D;T	0.85955	-2.04;-2.04;1.51;-2.05;0.68	3.96	-0.186	0.13272	.	1.145540	0.06356	N	0.710693	T	0.14614	0.0353	L	0.36672	1.1	0.09310	N	1	P	0.43287	0.802	B	0.31614	0.133	T	0.38436	-0.9661	10	0.38643	T	0.18	.	7.9086	0.29776	0.0:0.6035:0.0:0.3965	rs2066522;rs2266768;rs52816735;rs2066522	315	Q9NZC9	SMAL1_HUMAN	R	315;315;214;179;35	ENSP00000349823:S315R;ENSP00000350940:S315R;ENSP00000392997:S214R;ENSP00000375974:S179R;ENSP00000390248:S35R	ENSP00000349823:S315R	S	+	3	2	SMARCAL1	216993349	0.000000	0.05858	0.001000	0.08648	0.897000	0.52465	0.450000	0.21762	0.000000	0.14550	0.561000	0.74099	AGC	C|0.957;G|0.043	0.043	strong		0.572	SMARCAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256671.2		
PLEKHG4B	153478	hgsc.bcm.edu	37	5	143359	143359	+	Missense_Mutation	SNP	G	G	A	rs114876243	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:143359G>A	ENST00000283426.6	+	2	657	c.607G>A	c.(607-609)Gtc>Atc	p.V203I	Y_RNA_ENST00000362670.1_RNA	NM_052909.3	NP_443141.3	Q96PX9	PKH4B_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 4B	203							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(1)|large_intestine(2)|lung(2)|prostate(3)|skin(3)	11			all cancers(22;0.0253)|Lung(60;0.113)	Kidney(1;0.119)		GTCCGGGGTCGTCACCCTCCC	0.637													G|||	85	0.0169728	0.0643	0.0	5008	,	,		19147	0.0		0.0	False		,,,				2504	0.0				p.V203I		Atlas-SNP	.											.	PLEKHG4B	167	.	0			c.G607A						PASS	.	G	ILE/VAL	217,4189		9,199,1995	34.0	39.0	37.0		607	-3.8	0.0	5	dbSNP_132	37	3,8589		0,3,4293	yes	missense	PLEKHG4B	NM_052909.3	29	9,202,6288	AA,AG,GG		0.0349,4.9251,1.6926	benign	203/1272	143359	220,12778	2203	4296	6499	SO:0001583	missense	153478	exon2			GGGGTCGTCACCC	BC008352	CCDS34124.1	5p15.33	2013-01-11			ENSG00000153404	ENSG00000153404		"""Pleckstrin homology (PH) domain containing"""	29399	protein-coding gene	gene with protein product						11572484	Standard	NM_052909		Approved	KIAA1909	uc003jak.2	Q96PX9	OTTHUMG00000161570	ENST00000283426.6:c.607G>A	5.37:g.143359G>A	ENSP00000283426:p.Val203Ile	61.0	0.0	0		49.0	24.0	0.489796	NM_052909		Missense_Mutation	SNP	ENST00000283426.6	37	CCDS34124.1	22	0.010073260073260074	22	0.044715447154471545	0	0.0	0	0.0	0	0.0	.	0.015	-1.543641	0.00934	0.049251	3.49E-4	ENSG00000153404	ENST00000283426;ENST00000502646	T;T	0.18174	2.23;2.23	2.87	-3.76	0.04359	.	.	.	.	.	T	0.00754	0.0025	N	0.04090	-0.28	0.09310	N	1	B	0.13145	0.007	B	0.04013	0.001	T	0.38308	-0.9667	9	0.05620	T	0.96	.	7.5065	0.27547	0.5943:0.0:0.4057:0.0	.	203	Q96PX9	PKH4B_HUMAN	I	203;117	ENSP00000283426:V203I;ENSP00000422493:V117I	ENSP00000283426:V203I	V	+	1	0	PLEKHG4B	196359	0.000000	0.05858	0.001000	0.08648	0.108000	0.19459	-0.481000	0.06552	-0.665000	0.05317	-0.752000	0.03492	GTC	G|0.985;A|0.015	0.015	strong		0.637	PLEKHG4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365359.1	NM_052909	
TNFRSF21	27242	hgsc.bcm.edu	37	6	47251772	47251772	+	Missense_Mutation	SNP	C	C	T	rs148459670	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:47251772C>T	ENST00000296861.2	-	3	1538	c.1145G>A	c.(1144-1146)cGg>cAg	p.R382Q		NM_014452.3	NP_055267.1	O75509	TNR21_HUMAN	tumor necrosis factor receptor superfamily, member 21	382					adaptive immune response (GO:0002250)|apoptotic process (GO:0006915)|B cell apoptotic process (GO:0001783)|cellular lipid metabolic process (GO:0044255)|cellular response to tumor necrosis factor (GO:0071356)|humoral immune response (GO:0006959)|myelination (GO:0042552)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of interleukin-10 secretion (GO:2001180)|negative regulation of interleukin-13 secretion (GO:2000666)|negative regulation of interleukin-5 secretion (GO:2000663)|negative regulation of myelination (GO:0031642)|negative regulation of T cell proliferation (GO:0042130)|neuron apoptotic process (GO:0051402)|oligodendrocyte apoptotic process (GO:0097252)|regulation of oligodendrocyte differentiation (GO:0048713)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|lung(7)|pancreas(1)|skin(2)	21			Lung(136;0.189)			GGGATCCTGCCGGGGCCCCTT	0.527													C|||	2	0.000399361	0.0015	0.0	5008	,	,		17459	0.0		0.0	False		,,,				2504	0.0				p.R382Q		Atlas-SNP	.											.	TNFRSF21	61	.	0			c.G1145A						PASS	.	C	GLN/ARG	3,4403	6.2+/-15.9	0,3,2200	91.0	99.0	96.0		1145	6.2	1.0	6	dbSNP_134	96	0,8600		0,0,4300	yes	missense	TNFRSF21	NM_014452.3	43	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	probably-damaging	382/656	47251772	3,13003	2203	4300	6503	SO:0001583	missense	27242	exon3			TCCTGCCGGGGCC	AF068868	CCDS4921.1	6p21.1	2011-08-11			ENSG00000146072	ENSG00000146072		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	13469	protein-coding gene	gene with protein product	"""death receptor 6"""	605732				9714541	Standard	NM_014452		Approved	DR6, CD358	uc003oyv.3	O75509	OTTHUMG00000014796	ENST00000296861.2:c.1145G>A	6.37:g.47251772C>T	ENSP00000296861:p.Arg382Gln	227.0	0.0	0		269.0	137.0	0.509294	NM_014452	B2RDI9|Q0D2P5|Q96D86	Missense_Mutation	SNP	ENST00000296861.2	37	CCDS4921.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.892611	0.91889	6.81E-4	0.0	ENSG00000146072	ENST00000296861;ENST00000419206	T	0.66099	-0.19	6.17	6.17	0.99709	.	0.162308	0.56097	D	0.000032	T	0.65450	0.2692	L	0.59436	1.845	0.47374	D	0.999408	D	0.71674	0.998	P	0.56788	0.806	T	0.68689	-0.5342	10	0.87932	D	0	.	13.9957	0.64397	0.0:0.9315:0.0:0.0685	.	382	O75509	TNR21_HUMAN	Q	382;71	ENSP00000296861:R382Q	ENSP00000296861:R382Q	R	-	2	0	TNFRSF21	47359731	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.682000	0.54656	2.941000	0.99782	0.655000	0.94253	CGG	C|1.000;T|0.000	0.000	strong		0.527	TNFRSF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040814.1	NM_014452	
DUOX1	53905	hgsc.bcm.edu	37	15	45444572	45444572	+	Silent	SNP	T	T	C	rs114272662	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:45444572T>C	ENST00000321429.4	+	26	3689	c.3282T>C	c.(3280-3282)tcT>tcC	p.S1094S	CTD-2651B20.1_ENST00000558039.1_lincRNA|DUOX1_ENST00000389037.3_Silent_p.S1094S|DUOX1_ENST00000561166.1_Silent_p.S740S	NM_017434.3	NP_059130.2	Q9NRD9	DUOX1_HUMAN	dual oxidase 1	1094	Ferric oxidoreductase.|Interaction with TXNDC11. {ECO:0000250}.				cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide biosynthetic process (GO:0050665)|hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|superoxide anion generation (GO:0042554)|thyroid hormone generation (GO:0006590)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|NADP binding (GO:0050661)|peroxidase activity (GO:0004601)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(5)|large_intestine(13)|lung(16)|ovary(6)|prostate(1)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)	57		all_cancers(109;5.7e-11)|all_epithelial(112;4.65e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;5.77e-18)|GBM - Glioblastoma multiforme(94;5.11e-07)|COAD - Colon adenocarcinoma(120;0.071)|Colorectal(133;0.0717)		CCAGCATCTCTTTCATGTTCT	0.602													T|||	137	0.0273562	0.0976	0.0086	5008	,	,		20873	0.0		0.002	False		,,,				2504	0.0				p.S1094S		Atlas-SNP	.											.	DUOX1	125	.	0			c.T3282C						PASS	.	T	,	415,3981	202.1+/-225.0	17,381,1800	212.0	155.0	174.0		3282,3282	2.2	1.0	15	dbSNP_132	174	7,8589	5.0+/-18.6	0,7,4291	no	coding-synonymous,coding-synonymous	DUOX1	NM_017434.3,NM_175940.1	,	17,388,6091	CC,CT,TT		0.0814,9.4404,3.2482	,	1094/1552,1094/1552	45444572	422,12570	2198	4298	6496	SO:0001819	synonymous_variant	53905	exon26			CATCTCTTTCATG	AF213465	CCDS32221.1	15q21	2013-01-10				ENSG00000137857		"""EF-hand domain containing"""	3062	protein-coding gene	gene with protein product	"""NADPH thyroid oxidase 1"", ""flavoprotein NADPH oxidase"", ""nicotinamide adenine dinucleotide phosphate oxidase"""	606758				10806195	Standard	XM_005254463		Approved	NOXEF1, THOX1, LNOX1	uc001zut.1	Q9NRD9		ENST00000321429.4:c.3282T>C	15.37:g.45444572T>C		194.0	1.0	0.00515464		219.0	116.0	0.52968	NM_017434	A6NH28|Q14C94|Q6ZMB3|Q6ZR09|Q9NZC1	Silent	SNP	ENST00000321429.4	37	CCDS32221.1																																																																																			T|0.968;C|0.032	0.032	strong		0.602	DUOX1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416251.1	NM_017434	
GSE1	23199	hgsc.bcm.edu	37	16	85690900	85690900	+	Missense_Mutation	SNP	G	G	A	rs35446008	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:85690900G>A	ENST00000253458.7	+	8	1506	c.1330G>A	c.(1330-1332)Ggc>Agc	p.G444S	GSE1_ENST00000393243.1_Missense_Mutation_p.G371S|RN7SL381P_ENST00000577658.1_RNA|GSE1_ENST00000405402.2_Missense_Mutation_p.G340S	NM_014615.2	NP_055430.1	Q14687	GSE1_HUMAN	Gse1 coiled-coil protein	444				G -> S (in Ref. 1; BAA11499). {ECO:0000305}.													GAAGGATGCCGGCCTGCAGGC	0.642													G|||	67	0.0133786	0.0484	0.0043	5008	,	,		16388	0.0		0.0	False		,,,				2504	0.0				p.G444S		Atlas-SNP	.											.	.	.	.	0			c.G1330A						PASS	.	G	SER/GLY,SER/GLY	180,4216	110.4+/-148.6	4,172,2022	51.0	51.0	51.0		1018,1330	4.0	0.9	16	dbSNP_126	51	1,8597	1.2+/-3.3	0,1,4298	yes	missense,missense	KIAA0182	NM_001134473.1,NM_014615.2	56,56	4,173,6320	AA,AG,GG		0.0116,4.0946,1.393	benign,benign	340/1114,444/1218	85690900	181,12813	2198	4299	6497	SO:0001583	missense	23199	exon8			GATGCCGGCCTGC	D80004	CCDS10952.1, CCDS45539.1, CCDS62007.1	16q24.1	2012-12-07	2012-12-07	2012-10-02	ENSG00000131149	ENSG00000131149			28979	protein-coding gene	gene with protein product	"""genetic suppressor element 1"""		"""KIAA0182"", ""Gse1 coiled-coil protein homolog (mouse)"""	KIAA0182		8724849, 8786132	Standard	NM_014615		Approved		uc002fix.4	Q14687	OTTHUMG00000137650	ENST00000253458.7:c.1330G>A	16.37:g.85690900G>A	ENSP00000253458:p.Gly444Ser	101.0	0.0	0		92.0	46.0	0.5	NM_014615	D3DUM4|Q8IY61|Q96GA4|Q9BW09	Missense_Mutation	SNP	ENST00000253458.7	37	CCDS10952.1	23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	G	8.046	0.765024	0.15914	0.040946	1.16E-4	ENSG00000131149	ENST00000405402;ENST00000253458;ENST00000393243	T;T;T	0.30981	1.51;1.51;1.51	5.07	4.04	0.47022	.	0.488693	0.24152	N	0.041074	T	0.02083	0.0065	N	0.01705	-0.755	0.22457	N	0.999083	B;B	0.32203	0.325;0.36	B;B	0.21151	0.033;0.027	T	0.14227	-1.0480	10	0.18276	T	0.48	-34.1225	12.2615	0.54652	0.0:0.0:0.702:0.298	rs35446008	371;444	Q14687-3;Q14687	.;GSE1_HUMAN	S	340;444;371	ENSP00000384839:G340S;ENSP00000253458:G444S;ENSP00000376934:G371S	ENSP00000253458:G444S	G	+	1	0	KIAA0182	84248401	0.732000	0.28121	0.941000	0.38009	0.471000	0.32888	1.422000	0.34826	2.367000	0.80283	0.561000	0.74099	GGC	G|0.985;A|0.015	0.015	strong		0.642	GSE1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325527.1	NM_014615	
ZNF141	7700	hgsc.bcm.edu	37	4	367290	367290	+	Missense_Mutation	SNP	A	A	G	rs61733102	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:367290A>G	ENST00000240499.7	+	4	1213	c.1064A>G	c.(1063-1065)aAt>aGt	p.N355S	ZNF141_ENST00000505939.1_Intron|ZNF141_ENST00000512994.1_Intron	NM_003441.2	NP_003432.1	Q15928	ZN141_HUMAN	zinc finger protein 141	355					anatomical structure morphogenesis (GO:0009653)|limb morphogenesis (GO:0035108)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|kidney(3)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(1)	18						TCAAAACTGAATGAACATAAG	0.408													a|||	13	0.00259585	0.0098	0.0	5008	,	,		20026	0.0		0.0	False		,,,				2504	0.0				p.N355S		Atlas-SNP	.											.	ZNF141	48	.	0			c.A1064G						PASS	.	A	SER/ASN	33,4373	36.8+/-68.6	0,33,2170	37.0	40.0	39.0		1064	-2.5	0.0	4	dbSNP_129	39	0,8596		0,0,4298	no	missense	ZNF141	NM_003441.2	46	0,33,6468	GG,GA,AA		0.0,0.749,0.2538	benign	355/475	367290	33,12969	2203	4298	6501	SO:0001583	missense	7700	exon4			AACTGAATGAACA	L15309	CCDS33931.1	4p16.3	2013-01-08	2006-06-13			ENSG00000131127		"""Zinc fingers, C2H2-type"", ""-"""	12926	protein-coding gene	gene with protein product		194648	"""zinc finger protein 141 (clone pHZ-44)"""	D4S90		8268908	Standard	NM_003441		Approved	pHZ-44	uc003gaa.2	Q15928		ENST00000240499.7:c.1064A>G	4.37:g.367290A>G	ENSP00000240499:p.Asn355Ser	35.0	0.0	0		61.0	31.0	0.508197	NM_003441	Q6DK07	Missense_Mutation	SNP	ENST00000240499.7	37	CCDS33931.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	10.25	1.299693	0.23650	0.00749	0.0	ENSG00000131127	ENST00000240499	T	0.03272	3.99	1.24	-2.48	0.06423	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01558	0.0050	N	0.25992	0.78	0.09310	N	1	B	0.12013	0.005	B	0.11329	0.006	T	0.46762	-0.9168	8	.	.	.	.	2.176	0.03862	0.556:0.0:0.1963:0.2477	rs61733102	355	Q15928	ZN141_HUMAN	S	355	ENSP00000240499:N355S	.	N	+	2	0	ZNF141	357290	0.000000	0.05858	0.001000	0.08648	0.756000	0.42949	-0.780000	0.04654	-1.529000	0.01754	-0.856000	0.03024	AAT	A|0.998;G|0.002	0.002	strong		0.408	ZNF141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357710.1	NM_003441	
CD200R1L	344807	hgsc.bcm.edu	37	3	112545875	112545875	+	Missense_Mutation	SNP	G	G	A	rs61740125	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:112545875G>A	ENST00000398214.1	-	4	869	c.644C>T	c.(643-645)aCt>aTt	p.T215I	CD200R1L_ENST00000448932.1_Missense_Mutation_p.T194I|CD200R1L_ENST00000488794.1_Missense_Mutation_p.T194I	NM_001008784.2	NP_001008784.2	Q6Q8B3	MO2R2_HUMAN	CD200 receptor 1-like	215	Ig-like C2-type.					integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|urinary_tract(2)	19						CTTGTTGCCAGTCAAATGGGA	0.453													G|||	201	0.0401358	0.0968	0.0115	5008	,	,		19144	0.002		0.001	False		,,,				2504	0.0634				p.T215I		Atlas-SNP	.											.	CD200R1L	47	.	0			c.C644T						PASS	.	G	ILE/THR,ILE/THR	351,4045	164.4+/-196.0	7,337,1854	66.0	70.0	68.0		644,581	3.5	0.3	3	dbSNP_129	68	6,8592	5.0+/-18.6	0,6,4293	yes	missense,missense	CD200R1L	NM_001008784.2,NM_001199215.1	89,89	7,343,6147	AA,AG,GG		0.0698,7.9845,2.7474	probably-damaging,probably-damaging	215/272,194/251	112545875	357,12637	2198	4299	6497	SO:0001583	missense	344807	exon4			TTGCCAGTCAAAT	AY284976	CCDS43131.1, CCDS56267.1	3q13.2	2014-05-15	2008-10-08		ENSG00000206531	ENSG00000206531		"""Immunoglobulin superfamily / C2-set domain containing"""	24665	protein-coding gene	gene with protein product	"""CD200 receptor 2"""						Standard	NM_001008784		Approved	CD200RLa, CD200R2	uc003dzi.1	Q6Q8B3	OTTHUMG00000159283	ENST00000398214.1:c.644C>T	3.37:g.112545875G>A	ENSP00000381272:p.Thr215Ile	130.0	0.0	0		141.0	141.0	1	NM_001008784	Q6WHB7	Missense_Mutation	SNP	ENST00000398214.1	37	CCDS43131.1	71	0.03250915750915751	65	0.13211382113821138	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	G	16.52	3.146835	0.57151	0.079845	6.98E-4	ENSG00000206531	ENST00000398214;ENST00000488794;ENST00000448932	T;T;T	0.76578	-1.03;-1.03;-1.03	4.35	3.45	0.39498	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.276049	0.31279	N	0.007923	T	0.07324	0.0185	M	0.87547	2.89	0.34063	P	0.342499	D	0.76494	0.999	D	0.72982	0.979	T	0.63220	-0.6686	9	0.72032	D	0.01	.	10.1628	0.42862	0.0:0.2033:0.7967:0.0	.	215	Q6Q8B3	MO2R2_HUMAN	I	215;194;194	ENSP00000381272:T215I;ENSP00000418413:T194I;ENSP00000415132:T194I	ENSP00000381272:T215I	T	-	2	0	CD200R1L	114028565	0.138000	0.22547	0.331000	0.25455	0.900000	0.52787	2.570000	0.45981	1.126000	0.42016	0.655000	0.94253	ACT	G|0.979;A|0.021	0.021	strong		0.453	CD200R1L-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354365.1	NM_001008784	
ITGA11	22801	hgsc.bcm.edu	37	15	68603345	68603345	+	Missense_Mutation	SNP	C	C	T	rs146663204	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:68603345C>T	ENST00000315757.7	-	26	3247	c.3161G>A	c.(3160-3162)cGt>cAt	p.R1054H	ITGA11_ENST00000423218.2_Missense_Mutation_p.R1055H	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	1054					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						CTGTGGAGCACGACGCAAGTC	0.607													C|||	22	0.00439297	0.0166	0.0	5008	,	,		17947	0.0		0.0	False		,,,				2504	0.0				p.R1054H		Atlas-SNP	.											.	ITGA11	110	.	0			c.G3161A						PASS	.	C	HIS/ARG	64,4062		1,62,2000	37.0	38.0	38.0		3161	-0.7	0.0	15	dbSNP_134	38	0,8378		0,0,4189	yes	missense	ITGA11	NM_001004439.1	29	1,62,6189	TT,TC,CC		0.0,1.5511,0.5118	benign	1054/1189	68603345	64,12440	2063	4189	6252	SO:0001583	missense	22801	exon26			GGAGCACGACGCA	AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"""Integrins"""	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.3161G>A	15.37:g.68603345C>T	ENSP00000327290:p.Arg1054His	76.0	0.0	0		88.0	33.0	0.375	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Missense_Mutation	SNP	ENST00000315757.7	37	CCDS45291.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	0.254	-1.004438	0.02112	0.015511	0.0	ENSG00000137809	ENST00000315757;ENST00000423218;ENST00000535491	T;T	0.51325	0.71;0.8	4.72	-0.744	0.11101	.	0.394401	0.31051	N	0.008356	T	0.11024	0.0269	N	0.05383	-0.06	0.09310	N	0.99999	B;B	0.11235	0.0;0.004	B;B	0.08055	0.002;0.003	T	0.13522	-1.0506	10	0.23891	T	0.37	.	8.4623	0.32936	0.0:0.5066:0.0:0.4934	.	1054;1054	A8K8T0;Q9UKX5	.;ITA11_HUMAN	H	1054;1055;689	ENSP00000327290:R1054H;ENSP00000403392:R1055H	ENSP00000327290:R1054H	R	-	2	0	ITGA11	66390399	0.024000	0.19004	0.024000	0.17045	0.267000	0.26476	0.065000	0.14466	0.021000	0.15133	0.655000	0.94253	CGT	C|0.997;T|0.003	0.003	strong		0.607	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211	
EPHA10	284656	hgsc.bcm.edu	37	1	38197214	38197214	+	Missense_Mutation	SNP	G	G	A	rs141193695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:38197214G>A	ENST00000373048.4	-	7	1531	c.1532C>T	c.(1531-1533)gCg>gTg	p.A511V	EPHA10_ENST00000330210.7_Missense_Mutation_p.A6V|EPHA10_ENST00000427468.2_Missense_Mutation_p.A511V|EPHA10_ENST00000540011.1_Missense_Mutation_p.A6V|EPHA10_ENST00000446149.2_5'UTR	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	511	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)			NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				GACTGTGGGCGCCCCTGTCTT	0.587													G|||	4	0.000798722	0.003	0.0	5008	,	,		15942	0.0		0.0	False		,,,				2504	0.0				p.A511V		Atlas-SNP	.											EPHA10,colon,carcinoma,+1,1	EPHA10	120	1	0			c.C1532T						PASS	.	G	VAL/ALA	16,3888		0,16,1936	106.0	106.0	106.0		1532	2.9	0.3	1	dbSNP_134	106	1,8293		0,1,4146	yes	missense	EPHA10	NM_001099439.1	64	0,17,6082	AA,AG,GG		0.0121,0.4098,0.1394	possibly-damaging	511/1009	38197214	17,12181	1952	4147	6099	SO:0001583	missense	284656	exon7			GTGGGCGCCCCTG	AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.1532C>T	1.37:g.38197214G>A	ENSP00000362139:p.Ala511Val	99.0	0.0	0		86.0	38.0	0.44186	NM_001099439	A4FU89|J3KPB5|Q6NW42	Missense_Mutation	SNP	ENST00000373048.4	37	CCDS41305.1	47	0.02152014652014652	14	0.028455284552845527	4	0.011049723756906077	9	0.015734265734265736	20	0.026385224274406333	G	11.32	1.603665	0.28534	0.004098	1.21E-4	ENSG00000183317	ENST00000330210;ENST00000427468;ENST00000540011;ENST00000373048	T;T;T;T	0.76448	-1.02;0.36;-1.02;0.36	4.77	2.89	0.33648	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.526148	0.16039	N	0.232481	T	0.42268	0.1195	L	0.47016	1.485	0.09310	N	1	B	0.19331	0.035	B	0.10450	0.005	T	0.41305	-0.9516	9	.	.	.	.	5.1724	0.15118	0.172:0.0:0.6615:0.1665	.	511	Q5JZY3	EPHAA_HUMAN	V	6;511;6;511	ENSP00000330379:A6V;ENSP00000397746:A511V;ENSP00000441822:A6V;ENSP00000362139:A511V	.	A	-	2	0	EPHA10	37969801	0.972000	0.33761	0.319000	0.25293	0.345000	0.29048	3.224000	0.51238	0.605000	0.29947	0.563000	0.77884	GCG	G|0.979;A|0.021	0.021	strong		0.587	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641	
COL18A1	80781	hgsc.bcm.edu	37	21	46900062	46900062	+	Missense_Mutation	SNP	G	G	A	rs61738822	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46900062G>A	ENST00000359759.4	+	10	2656	c.2635G>A	c.(2635-2637)Gac>Aac	p.D879N	COL18A1_ENST00000400337.2_Missense_Mutation_p.D464N|COL18A1_ENST00000355480.5_Missense_Mutation_p.D644N			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	879	Nonhelical region 3 (NC3).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		CTTCAGACACGACAAGCTGGT	0.642													G|||	17	0.00339457	0.0121	0.0014	5008	,	,		14900	0.0		0.0	False		,,,				2504	0.0				p.D644N		Atlas-SNP	.											.	COL18A1	129	.	0			c.G1930A						PASS	.	G	ASN/ASP,ASN/ASP	53,3705		0,53,1826	17.0	22.0	21.0		1930,1390	3.2	0.9	21	dbSNP_129	21	0,8226		0,0,4113	yes	missense,missense	COL18A1	NM_030582.3,NM_130445.2	23,23	0,53,5939	AA,AG,GG		0.0,1.4103,0.4423	possibly-damaging,possibly-damaging	644/1520,464/1340	46900062	53,11931	1879	4113	5992	SO:0001583	missense	80781	exon10			AGACACGACAAGC		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.2635G>A	21.37:g.46900062G>A	ENSP00000352798:p.Asp879Asn	44.0	0.0	0		76.0	41.0	0.539474	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	37		8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	17.19	3.325962	0.60743	0.014103	0.0	ENSG00000182871	ENST00000400337;ENST00000400347;ENST00000355480;ENST00000359759;ENST00000539645	D;D;D	0.90788	-2.72;-2.73;-2.64	3.19	3.19	0.36642	.	0.545209	0.16627	N	0.206240	D	0.88385	0.6422	L	0.56769	1.78	0.40960	D	0.984616	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.992;0.997;0.997	D	0.89130	0.3509	10	0.59425	D	0.04	.	10.0536	0.42230	0.0:0.0:1.0:0.0	rs61738822	879;644;464	P39060;P39060-1;P39060-2	COIA1_HUMAN;.;.	N	464;464;644;879;879	ENSP00000383191:D464N;ENSP00000347665:D644N;ENSP00000352798:D879N	ENSP00000347665:D644N	D	+	1	0	COL18A1	45724490	1.000000	0.71417	0.858000	0.33744	0.334000	0.28698	5.592000	0.67543	1.812000	0.52913	0.561000	0.74099	GAC	G|0.996;A|0.004	0.004	strong		0.642	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
PRAMEF2	65122	hgsc.bcm.edu	37	1	12918903	12918903	+	Silent	SNP	G	G	A	rs17038644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12918903G>A	ENST00000240189.2	+	2	126	c.39G>A	c.(37-39)gcG>gcA	p.A13A		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	13					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(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	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;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		TGGAGCTGGCGGGGCAGAGCC	0.562													.|||	197	0.0393371	0.0908	0.0144	5008	,	,		19026	0.0298		0.0189	False		,,,				2504	0.0184				p.A13A		Atlas-SNP	.											.	PRAMEF2	85	.	0			c.G39A						PASS	.	A		276,4126	143.8+/-178.8	19,238,1944	88.0	99.0	95.0		39	-1.7	0.0	1	dbSNP_123	95	7,8587		0,7,4290	no	coding-synonymous	PRAMEF2	NM_023014.1		19,245,6234	AA,AG,GG		0.0815,6.2699,2.1776		13/475	12918903	283,12713	2201	4297	6498	SO:0001819	synonymous_variant	65122	exon2			GCTGGCGGGGCAG		CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"""-"""	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.39G>A	1.37:g.12918903G>A		358.0	1.0	0.0027933		452.0	227.0	0.502212	NM_023014		Silent	SNP	ENST00000240189.2	37	CCDS149.1																																																																																			G|0.978;A|0.022	0.022	strong		0.562	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
KRTAP10-7	386675	hgsc.bcm.edu	37	21	46021546	46021546	+	Missense_Mutation	SNP	C	C	G	rs116074123	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46021546C>G	ENST00000380102.2	+	1	1050	c.1025C>G	c.(1024-1026)gCc>gGc	p.A342G	TSPEAR_ENST00000323084.4_Intron	NM_198689.2	NP_941962.1	P60409	KR107_HUMAN	keratin associated protein 10-7	342	30 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				breast(1)|large_intestine(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	8						TCCTGCCAGGCCAGCTGCTGC	0.711													-|||	183	0.0365415	0.1331	0.0101	5008	,	,		15282	0.0		0.0	False		,,,				2504	0.0				p.A337G		Atlas-SNP	.											.	KRTAP10-7	41	.	0			c.C1010G						PASS	.	C	,GLY/ALA	439,3945		20,399,1773	32.0	38.0	36.0		,1025	3.7	1.0	21	dbSNP_132	36	4,8554		0,4,4275	no	intron,missense	TSPEAR,KRTAP10-7	NM_144991.2,NM_198689.2	,60	20,403,6048	GG,GC,CC		0.0467,10.0137,3.423	,benign	,342/376	46021546	443,12499	2192	4279	6471	SO:0001583	missense	386675	exon2			GCCAGGCCAGCTG	AJ566385	CCDS74803.1	21q22.3	2014-04-10			ENSG00000205441	ENSG00000272804		"""Keratin associated proteins"""	22970	protein-coding gene	gene with protein product				KRTAP18-7			Standard	NM_198689		Approved	KAP10.7, KAP18.7	uc002zfn.4	P60409	OTTHUMG00000188307	ENST00000380102.2:c.1025C>G	21.37:g.46021546C>G	ENSP00000369445:p.Ala342Gly	59.0	0.0	0		114.0	83.0	0.72807	NM_198689	Q0VDJ8|Q70LJ2	Missense_Mutation	SNP	ENST00000380102.2	37		50	0.022893772893772892	45	0.09146341463414634	5	0.013812154696132596	0	0.0	0	0.0	c	11.47	1.647906	0.29336	0.100137	4.67E-4	ENSG00000205441	ENST00000380102	T	0.00675	5.88	3.73	3.73	0.42828	.	.	.	.	.	T	0.00039	0.0001	N	0.24115	0.695	0.19575	N	0.999963	B	0.17038	0.02	B	0.14023	0.01	T	0.52586	-0.8556	9	0.72032	D	0.01	.	7.4909	0.27460	0.0:0.8767:0.0:0.1233	.	337	P60409-2	.	G	342	ENSP00000369445:A342G	ENSP00000369445:A342G	A	+	2	0	KRTAP10-7	44845974	0.490000	0.26012	1.000000	0.80357	0.413000	0.31143	1.890000	0.39728	1.805000	0.52779	0.467000	0.42956	GCC	C|0.974;G|0.026	0.026	strong		0.711	KRTAP10-7-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000128038.1	NM_198689	
CD101	9398	hgsc.bcm.edu	37	1	117576631	117576631	+	Missense_Mutation	SNP	C	C	T	rs34248572	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:117576631C>T	ENST00000256652.4	+	9	3032	c.2974C>T	c.(2974-2976)Cgg>Tgg	p.R992W	CD101_ENST00000369470.1_Missense_Mutation_p.R992W|RP11-27K13.3_ENST00000445523.1_RNA|RP11-27K13.3_ENST00000421254.1_RNA|CD101_ENST00000467588.1_3'UTR	NM_001256106.1|NM_001256109.1|NM_001256111.1|NM_004258.4	NP_001243035.1|NP_001243038.1|NP_001243040.1|NP_004249.2	Q93033	IGSF2_HUMAN	CD101 molecule	992			R -> W (in dbSNP:rs34248572).		cell surface receptor signaling pathway (GO:0007166)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)			NS(1)|breast(1)|endometrium(6)|kidney(3)|large_intestine(14)|lung(18)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						TTCCAACACACGGAAAGAAAA	0.517													C|||	117	0.0233626	0.0817	0.0115	5008	,	,		19361	0.001		0.0	False		,,,				2504	0.0				p.R992W		Atlas-SNP	.											CD101,NS,carcinoma,-1,1	CD101	95	1	0			c.C2974T						PASS	.	C	TRP/ARG	286,4120	157.0+/-190.0	13,260,1930	123.0	112.0	116.0		2974	-0.3	0.0	1	dbSNP_126	116	5,8595	3.0+/-9.4	0,5,4295	yes	missense	CD101	NM_004258.3	101	13,265,6225	TT,TC,CC		0.0581,6.4911,2.2374	probably-damaging	992/1022	117576631	291,12715	2203	4300	6503	SO:0001583	missense	9398	exon9			AACACACGGAAAG	Z33642	CCDS891.1	1p13	2013-01-29	2009-10-27	2009-10-27	ENSG00000134256	ENSG00000134256		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5949	protein-coding gene	gene with protein product		604516	"""immunoglobulin superfamily, member 2"""	IGSF2		7722300	Standard	NM_004258		Approved	V7	uc010oxb.2	Q93033	OTTHUMG00000012029	ENST00000256652.4:c.2974C>T	1.37:g.117576631C>T	ENSP00000256652:p.Arg992Trp	138.0	0.0	0		112.0	53.0	0.473214	NM_001256109	Q15856	Missense_Mutation	SNP	ENST00000256652.4	37	CCDS891.1	48	0.02197802197802198	45	0.09146341463414634	3	0.008287292817679558	0	0.0	0	0.0	C	14.76	2.631571	0.46944	0.064911	5.81E-4	ENSG00000134256	ENST00000256652;ENST00000369470	T;T	0.03772	3.81;3.81	5.83	-0.273	0.12915	.	1.475580	0.04746	N	0.423700	T	0.01523	0.0049	N	0.14661	0.345	0.09310	N	1	D	0.63880	0.993	B	0.44315	0.446	T	0.49234	-0.8961	10	0.72032	D	0.01	-0.5271	9.27	0.37666	0.5351:0.3393:0.1256:0.0	rs34248572	992	Q93033	IGSF2_HUMAN	W	992	ENSP00000256652:R992W;ENSP00000358482:R992W	ENSP00000256652:R992W	R	+	1	2	CD101	117378154	0.000000	0.05858	0.000000	0.03702	0.250000	0.25880	-0.056000	0.11787	0.306000	0.22856	0.563000	0.77884	CGG	C|0.972;T|0.028	0.028	strong		0.517	CD101-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033274.1	NM_004258	
FASLG	356	hgsc.bcm.edu	37	1	172628488	172628488	+	Silent	SNP	G	G	A	rs61756244	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:172628488G>A	ENST00000367721.2	+	1	331	c.147G>A	c.(145-147)ccG>ccA	p.P49P	FASLG_ENST00000340030.3_Silent_p.P49P	NM_000639.1	NP_000630.1	P48023	TNFL6_HUMAN	Fas ligand (TNF superfamily, member 6)	49	Poly-Pro.|Pro-rich.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell-cell signaling (GO:0007267)|cellular chloride ion homeostasis (GO:0030644)|endosomal lumen acidification (GO:0048388)|extrinsic apoptotic signaling pathway (GO:0097191)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|immune response (GO:0006955)|inflammatory cell apoptotic process (GO:0006925)|necroptotic process (GO:0070266)|necroptotic signaling pathway (GO:0097527)|negative regulation of angiogenesis (GO:0016525)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|response to growth factor (GO:0070848)|response to lipopolysaccharide (GO:0032496)|retinal cell programmed cell death (GO:0046666)|signal transduction (GO:0007165)|T cell apoptotic process (GO:0070231)|transcription, DNA-templated (GO:0006351)	caveola (GO:0005901)|cytoplasmic membrane-bounded vesicle (GO:0016023)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	receptor binding (GO:0005102)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(12)|prostate(1)|skin(1)	19						caccaccaccgccaccgccac	0.662													G|||	242	0.0483227	0.1717	0.0216	5008	,	,		10744	0.0		0.0	False		,,,				2504	0.0				p.P49P	Ovarian(28;486 876 30334 44033)	Atlas-SNP	.											.	FASLG	44	.	0			c.G147A						PASS	.	G		714,3692	267.4+/-267.8	68,578,1557	56.0	57.0	57.0		147	-8.6	0.0	1	dbSNP_129	57	7,8593	3.7+/-12.6	0,7,4293	no	coding-synonymous	FASLG	NM_000639.1		68,585,5850	AA,AG,GG		0.0814,16.2052,5.5436		49/282	172628488	721,12285	2203	4300	6503	SO:0001819	synonymous_variant	356	exon1			ACCACCGCCACCG	U11821	CCDS1304.1	1q23	2014-09-17	2005-01-07	2005-01-07	ENSG00000117560	ENSG00000117560		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"", ""Endogenous ligands"""	11936	protein-coding gene	gene with protein product		134638	"""tumor necrosis factor (ligand) superfamily, member 6"""	APT1LG1, TNFSF6		7826947, 9022072	Standard	NM_000639		Approved	FasL, CD178	uc001gis.3	P48023	OTTHUMG00000034841	ENST00000367721.2:c.147G>A	1.37:g.172628488G>A		139.0	0.0	0		136.0	60.0	0.441176	NM_000639	Q9BZP9	Silent	SNP	ENST00000367721.2	37	CCDS1304.1																																																																																			G|0.944;A|0.056	0.056	strong		0.662	FASLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084276.1		
TPRN	286262	hgsc.bcm.edu	37	9	140086940	140086940	+	Silent	SNP	C	C	T	rs115446132	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140086940C>T	ENST00000409012.4	-	2	2015	c.1929G>A	c.(1927-1929)gtG>gtA	p.V643V	TPRN_ENST00000321773.2_Silent_p.V582V|TPRN_ENST00000541945.1_5'Flank	NM_001128228.2	NP_001121700.2	Q4KMQ1	TPRN_HUMAN	taperin	643					sensory perception of sound (GO:0007605)	stereocilium (GO:0032420)				breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(2)	8						TCTCGGGTCTCACGCTGCTCA	0.642													C|||	20	0.00399361	0.0129	0.0043	5008	,	,		17266	0.0		0.0	False		,,,				2504	0.0				p.V643V		Atlas-SNP	.											.	TPRN	28	.	0			c.G1929A						PASS	.	C		48,4356	46.7+/-81.2	0,48,2154	33.0	26.0	28.0		1929	3.0	0.0	9	dbSNP_132	28	0,8596		0,0,4298	no	coding-synonymous	TPRN	NM_001128228.2		0,48,6452	TT,TC,CC		0.0,1.0899,0.3692		643/712	140086940	48,12952	2202	4298	6500	SO:0001819	synonymous_variant	286262	exon2			GGGTCTCACGCTG	AK074735	CCDS56594.1	9q34.3	2011-01-06	2010-03-24	2010-03-24	ENSG00000176058	ENSG00000176058			26894	protein-coding gene	gene with protein product		613354	"""chromosome 9 open reading frame 75"", ""deafness, autosomal recessive 79"""	C9orf75, DFNB79		20170898, 20170899	Standard	NM_001128228		Approved	FLJ90254	uc004clu.3	Q4KMQ1	OTTHUMG00000020984	ENST00000409012.4:c.1929G>A	9.37:g.140086940C>T		93.0	0.0	0		71.0	41.0	0.577465	NM_001128228	B7ZKU5|Q5VSG5|Q5VSG6|Q6IPP2|Q8NCH2	Silent	SNP	ENST00000409012.4	37	CCDS56594.1																																																																																			C|0.996;T|0.004	0.004	strong		0.642	TPRN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055323.3	NM_173691	
HSH2D	84941	hgsc.bcm.edu	37	19	16263946	16263946	+	Silent	SNP	C	C	T	rs1870354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16263946C>T	ENST00000253680.6	+	6	840	c.309C>T	c.(307-309)gaC>gaT	p.D103D	HSH2D_ENST00000397372.4_Splice_Site|HSH2D_ENST00000593154.2_Silent_p.D103D|HSH2D_ENST00000588246.1_Silent_p.D103D			Q96JZ2	HSH2D_HUMAN	hematopoietic SH2 domain containing	103	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of mitochondrial depolarization (GO:0051902)|positive regulation of signal transduction (GO:0009967)|T cell activation (GO:0042110)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)				central_nervous_system(1)|kidney(1)|large_intestine(2)	4						CCTCGCTGGACGCCCTGGTCA	0.617													C|||	96	0.0191693	0.0696	0.0043	5008	,	,		17099	0.0		0.001	False		,,,				2504	0.0				p.D103D		Atlas-SNP	.											.	HSH2D	16	.	0			c.C309T						PASS	.	C		236,3872		5,226,1823	26.0	30.0	29.0		309	-3.9	0.2	19	dbSNP_92	29	3,8351		0,3,4174	no	coding-synonymous	HSH2D	NM_032855.2		5,229,5997	TT,TC,CC		0.0359,5.7449,1.9178		103/353	16263946	239,12223	2054	4177	6231	SO:0001819	synonymous_variant	84941	exon6			GCTGGACGCCCTG	AK027792	CCDS74304.1	19p13.12	2013-02-14				ENSG00000196684		"""SH2 domain containing"""	24920	protein-coding gene	gene with protein product		608349				11700021	Standard	NM_032855		Approved	ALX, HSH2, FLJ14886	uc002ndp.4	Q96JZ2		ENST00000253680.6:c.309C>T	19.37:g.16263946C>T		73.0	0.0	0		55.0	33.0	0.6	NM_032855	B5ME72|Q6ZNG7	Silent	SNP	ENST00000253680.6	37		30	0.013736263736263736	27	0.054878048780487805	3	0.008287292817679558	0	0.0	0	0.0	C	0.017	-1.489323	0.01018	0.057449	3.59E-4	ENSG00000196684	ENST00000397372	.	.	.	4.63	-3.9	0.04181	.	.	.	.	.	.	.	.	.	.	.	0.22253	N	0.999254	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.8363	0.13466	0.0:0.3118:0.3055:0.3827	rs1870354;rs1870354	.	.	.	.	-1	.	.	.	+	.	.	HSH2D	16124946	0.000000	0.05858	0.227000	0.23927	0.006000	0.05464	-2.127000	0.01315	-0.294000	0.08973	-0.949000	0.02662	.	C|0.986;T|0.014	0.014	strong		0.617	HSH2D-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_032855	
NOL8	55035	hgsc.bcm.edu	37	9	95078413	95078413	+	Missense_Mutation	SNP	T	T	C	rs41305617	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95078413T>C	ENST00000535387.1	-	6	493	c.494A>G	c.(493-495)aAa>aGa	p.K165R	NOL8_ENST00000542053.1_Missense_Mutation_p.K97R|NOL8_ENST00000545558.1_Missense_Mutation_p.K165R|NOL8_ENST00000358855.4_Missense_Mutation_p.K97R|NOL8_ENST00000442668.2_Missense_Mutation_p.K165R					nucleolar protein 8											endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						GGGATCATATTTGATGATGTT	0.363													T|||	47	0.00938498	0.0023	0.0144	5008	,	,		20765	0.0		0.0338	False		,,,				2504	0.0				p.K165R		Atlas-SNP	.											.	NOL8	118	.	0			c.A494G						PASS	.	T	ARG/LYS	16,3702		0,16,1843	96.0	85.0	89.0		494	5.1	1.0	9	dbSNP_127	89	231,7979		3,225,3877	yes	missense	NOL8	NM_017948.5	26	3,241,5720	CC,CT,TT		2.8136,0.4303,2.0708	probably-damaging	165/1168	95078413	247,11681	1859	4105	5964	SO:0001583	missense	55035	exon7			TCATATTTGATGA	AB109030	CCDS47993.1, CCDS59135.1	9q22.32	2013-02-12	2004-01-12	2004-01-14	ENSG00000198000	ENSG00000198000		"""RNA binding motif (RRM) containing"""	23387	protein-coding gene	gene with protein product		611534	"""chromosome 9 open reading frame 34"""	C9orf34		12477932	Standard	NM_017948		Approved	FLJ20736, Nop132	uc022bjx.1	Q76FK4	OTTHUMG00000020221	ENST00000535387.1:c.494A>G	9.37:g.95078413T>C	ENSP00000441300:p.Lys165Arg	223.0	0.0	0		242.0	91.0	0.376033	NM_017948		Missense_Mutation	SNP	ENST00000535387.1	37	CCDS47993.1	33	0.01510989010989011	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	24	0.0316622691292876	T	21.3	4.129430	0.77549	0.004303	0.028136	ENSG00000198000	ENST00000442668;ENST00000375594;ENST00000358855;ENST00000545558;ENST00000535387;ENST00000542053;ENST00000432670;ENST00000433029;ENST00000421075;ENST00000411621;ENST00000535807	T;T;T;T;T;T;T;T	0.54479	2.12;2.06;2.12;2.32;2.06;1.84;0.57;0.66	5.07	5.07	0.68467	.	0.000000	0.85682	D	0.000000	T	0.40815	0.1132	L	0.39147	1.195	0.47659	D	0.999482	D	0.89917	1.0	D	0.87578	0.998	T	0.60949	-0.7161	10	0.87932	D	0	-23.0153	15.1284	0.72500	0.0:0.0:0.0:1.0	rs41305617	165	Q76FK4	NOL8_HUMAN	R	165;167;97;165;165;97;165;165;165;97;97	ENSP00000401177:K165R;ENSP00000351723:K97R;ENSP00000441140:K165R;ENSP00000441300:K165R;ENSP00000440709:K97R;ENSP00000414112:K165R;ENSP00000412471:K165R;ENSP00000390143:K165R	ENSP00000351723:K97R	K	-	2	0	NOL8	94118234	1.000000	0.71417	1.000000	0.80357	0.536000	0.34869	7.001000	0.76297	2.021000	0.59480	0.528000	0.53228	AAA	T|0.986;C|0.014	0.014	strong		0.363	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948	
GPR98	84059	hgsc.bcm.edu	37	5	90136732	90136732	+	Missense_Mutation	SNP	C	C	G	rs61748627	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:90136732C>G	ENST00000405460.2	+	78	17045	c.16949C>G	c.(16948-16950)aCc>aGc	p.T5650S	GPR98_ENST00000425867.2_Missense_Mutation_p.T1311S	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	5650					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		GTGCTCCATACCATCAGCATG	0.408													C|||	28	0.00559105	0.0204	0.0014	5008	,	,		19148	0.0		0.0	False		,,,				2504	0.0				p.T5650S		Atlas-SNP	.											.	GPR98	605	.	0			c.C16949G						PASS	.	C	SER/THR	47,3955		1,45,1955	75.0	75.0	75.0		16949	-6.1	0.0	5	dbSNP_129	75	1,8377		0,1,4188	yes	missense	GPR98	NM_032119.3	58	1,46,6143	GG,GC,CC		0.0119,1.1744,0.3877	benign	5650/6307	90136732	48,12332	2001	4189	6190	SO:0001583	missense	84059	exon78			TCCATACCATCAG	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.16949C>G	5.37:g.90136732C>G	ENSP00000384582:p.Thr5650Ser	63.0	0.0	0		58.0	30.0	0.517241	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	25	0.011446886446886446	24	0.04878048780487805	1	0.0027624309392265192	0	0.0	0	0.0	C	1.382	-0.583061	0.03827	0.011744	1.19E-4	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000425867	T;T	0.28069	1.63;1.63	6.16	-6.11	0.02131	.	0.807701	0.12567	N	0.457630	T	0.01454	0.0047	N	0.04508	-0.205	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.33111	-0.9881	9	.	.	.	.	9.7985	0.40751	0.4619:0.4027:0.1354:0.0	rs61748627	1311;5650;1311	E7EML1;Q8WXG9;Q8WXG9-2	.;GPR98_HUMAN;.	S	5650;5650;1311	ENSP00000384582:T5650S;ENSP00000392618:T1311S	.	T	+	2	0	GPR98	90172488	0.001000	0.12720	0.001000	0.08648	0.233000	0.25261	-0.112000	0.10791	-0.739000	0.04809	-0.885000	0.02943	ACC	C|0.988;G|0.012	0.012	strong		0.408	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
OGFR	11054	hgsc.bcm.edu	37	20	61444900	61444900	+	Missense_Mutation	SNP	A	A	C	rs61735508	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:61444900A>C	ENST00000290291.6	+	7	1958	c.1933A>C	c.(1933-1935)Agc>Cgc	p.S645R	OGFR_ENST00000370461.1_Missense_Mutation_p.S593R	NM_007346.2	NP_031372.2	Q9NZT2	OGFR_HUMAN	opioid growth factor receptor	645	7 X 20 AA approximate tandem repeats of [ST]-P-S-E-T-P-G-P-[SR]-P-A-G-P-[AT]- [GR]-D-E-P-A-[EK].				opioid receptor signaling pathway (GO:0038003)|regulation of cell growth (GO:0001558)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	opioid receptor activity (GO:0004985)			endometrium(2)|kidney(1)|lung(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)	17	Breast(26;3.65e-08)					CCCAGGCCCCAGCCCGGCAGG	0.692													a|||	178	0.0355431	0.1233	0.0086	5008	,	,		13505	0.0		0.004	False		,,,				2504	0.0051				p.S645R		Atlas-SNP	.											.	OGFR	63	.	0			c.A1933C						PASS	.	A	ARG/SER	255,4123		7,241,1941	24.0	29.0	28.0		1933	-0.6	0.0	20	dbSNP_129	28	10,8570		0,10,4280	no	missense	OGFR	NM_007346.2	110	7,251,6221	CC,CA,AA		0.1166,5.8246,2.0451	possibly-damaging	645/678	61444900	265,12693	2189	4290	6479	SO:0001583	missense	11054	exon7			GGCCCCAGCCCGG	AF109134	CCDS13504.1	20q13.3	2008-05-02			ENSG00000060491	ENSG00000060491			15768	protein-coding gene	gene with protein product		606459				10677613	Standard	NM_007346		Approved	7-60	uc002ydj.3	Q9NZT2	OTTHUMG00000032937	ENST00000290291.6:c.1933A>C	20.37:g.61444900A>C	ENSP00000290291:p.Ser645Arg	64.0	0.0	0		64.0	37.0	0.578125	NM_007346	O96029|Q4VXW5|Q96CM2|Q9BQW1|Q9H4H0|Q9H7J5|Q9NZT3|Q9NZT4	Missense_Mutation	SNP	ENST00000290291.6	37	CCDS13504.1	60	0.027472527472527472	53	0.10772357723577236	4	0.011049723756906077	1	0.0017482517482517483	2	0.002638522427440633	A	6.697	0.497303	0.12762	0.058246	0.001166	ENSG00000060491	ENST00000290291;ENST00000357163;ENST00000370469;ENST00000370461	T;T	0.13089	2.62;2.62	0.584	-0.628	0.11537	.	.	.	.	.	T	0.00109	0.0003	N	0.03608	-0.345	0.09310	N	1	P;P;P	0.52842	0.956;0.956;0.956	P;P;P	0.45829	0.494;0.494;0.494	T	0.18493	-1.0335	9	0.22109	T	0.4	.	1.7819	0.03033	0.4838:0.0:0.2359:0.2802	rs61735508	645;628;645	B3KMQ6;Q05BV5;Q9NZT2	.;.;OGFR_HUMAN	R	645;625;480;593	ENSP00000290291:S645R;ENSP00000359491:S593R	ENSP00000290291:S645R	S	+	1	0	OGFR	60915345	0.004000	0.15560	0.002000	0.10522	0.050000	0.14768	-0.440000	0.06888	-0.224000	0.09928	0.076000	0.15429	AGC	A|0.975;C|0.025	0.025	strong		0.692	OGFR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080067.1		
TTN	7273	hgsc.bcm.edu	37	2	179577870	179577870	+	Silent	SNP	T	T	C	rs61232800	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179577870T>C	ENST00000591111.1	-	91	26264	c.26040A>G	c.(26038-26040)acA>acG	p.T8680T	TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Silent_p.T7753T|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Silent_p.T8997T			Q8WZ42	TITIN_HUMAN	titin	12837	Ig-like 69.				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)			TAGCTATACATGTGTAGTCAC	0.388													T|||	122	0.024361	0.0893	0.0058	5008	,	,		22217	0.0		0.0	False		,,,				2504	0.0				p.T8997T		Atlas-SNP	.											.	TTN	18412	.	0			c.A26991G						PASS	.	T	,,,	265,3699		10,245,1727	90.0	90.0	90.0		,23259,,	-11.7	0.5	2	dbSNP_129	90	13,8331		0,13,4159	no	intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	10,258,5886	CC,CT,TT		0.1558,6.6852,2.2587	,,,	,7753/33424,,	179577870	278,12030	1982	4172	6154	SO:0001819	synonymous_variant	7273	exon93			TATACATGTGTAG	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.26040A>G	2.37:g.179577870T>C		285.0	0.0	0		288.0	134.0	0.465278	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|0.981;C|0.019	0.019	strong		0.388	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
NOS1	4842	hgsc.bcm.edu	37	12	117691490	117691490	+	Silent	SNP	G	G	A	rs9658446	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:117691490G>A	ENST00000338101.4	-	17	2707	c.2703C>T	c.(2701-2703)ccC>ccT	p.P901P	NOS1_ENST00000344089.3_3'UTR|NOS1_ENST00000317775.6_Silent_p.P867P			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		CTCTGAGGTCGGGCCCATCGC	0.562													G|||	163	0.0325479	0.0983	0.0202	5008	,	,		18019	0.0		0.002	False		,,,				2504	0.0174				p.P901P	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											NOS1,NS,carcinoma,0,1	NOS1	240	1	0			c.C2703T						PASS	.	G	,,,	340,3958		15,310,1824	90.0	97.0	95.0		2601,1593,1593,2703	-7.8	0.8	12	dbSNP_119	95	26,8488		0,26,4231	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NOS1	NM_000620.4,NM_001204213.1,NM_001204214.1,NM_001204218.1	,,,	15,336,6055	AA,AG,GG		0.3054,7.9107,2.8567	,,,	867/1435,531/1099,531/1099,901/1469	117691490	366,12446	2149	4257	6406	SO:0001819	synonymous_variant	4842	exon18			GAGGTCGGGCCCA		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.2703C>T	12.37:g.117691490G>A		121.0	0.0	0		149.0	51.0	0.342282	NM_001204218		Silent	SNP	ENST00000338101.4	37	CCDS55890.1																																																																																			G|0.985;A|0.015	0.015	strong		0.562	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1		
TRAPPC9	83696	hgsc.bcm.edu	37	8	140999002	140999002	+	Silent	SNP	G	G	A	rs28710457	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:140999002G>A	ENST00000438773.2	-	19	2875	c.2742C>T	c.(2740-2742)acC>acT	p.T914T	TRAPPC9_ENST00000389328.4_Silent_p.T1012T|TRAPPC9_ENST00000389327.3_Silent_p.T905T	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	914					cell differentiation (GO:0030154)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						GCTCATGCTCGGTGGAGTTGA	0.567													G|||	54	0.0107827	0.0378	0.0014	5008	,	,		19691	0.003		0.0	False		,,,				2504	0.0				p.T1012T		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.C3036T						PASS	.	G	,	125,3835		1,123,1856	29.0	26.0	27.0		2742,3036	-9.6	0.5	8	dbSNP_125	27	1,7655		0,1,3827	no	coding-synonymous,coding-synonymous	TRAPPC9	NM_001160372.1,NM_031466.5	,	1,124,5683	AA,AG,GG		0.0131,3.1566,1.0847	,	914/1149,1012/1247	140999002	126,11490	1980	3828	5808	SO:0001819	synonymous_variant	83696	exon19			ATGCTCGGTGGAG	BC006206	CCDS34946.1, CCDS55278.1	8q24.3	2010-10-22			ENSG00000167632	ENSG00000167632		"""Trafficking protein particle complex"""	30832	protein-coding gene	gene with protein product	"""TRAPP 120 kDa subunit"", ""tularik gene 1"""	611966				11572484	Standard	NM_031466		Approved	IKBKBBP, NIBP, KIAA1882, T1, TRS120, MRT13	uc003yvh.2	Q96Q05	OTTHUMG00000164187	ENST00000438773.2:c.2742C>T	8.37:g.140999002G>A		49.0	0.0	0		62.0	30.0	0.483871	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Silent	SNP	ENST00000438773.2	37	CCDS55278.1	21	0.009615384615384616	17	0.034552845528455285	1	0.0027624309392265192	3	0.005244755244755245	0	0.0	G	6.618	0.482489	0.12581	0.031566	1.31E-4	ENSG00000167632	ENST00000520857	.	.	.	5.62	-9.63	0.00544	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	4.9498	0.14008	0.0885:0.1092:0.2516:0.5507	rs28710457	.	.	.	X	758	.	.	R	-	1	2	TRAPPC9	141068184	0.262000	0.24073	0.460000	0.27093	0.679000	0.39708	-0.500000	0.06405	-2.040000	0.00916	-2.131000	0.00343	CGA	G|0.986;A|0.014	0.014	strong		0.567	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466	
PCDHB16	57717	hgsc.bcm.edu	37	5	140562756	140562756	+	Missense_Mutation	SNP	C	C	G	rs28398442	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140562756C>G	ENST00000361016.2	+	1	1777	c.622C>G	c.(622-624)Cta>Gta	p.L208V		NM_020957.1	NP_066008.1	Q9NRJ7	PCDBG_HUMAN	protocadherin beta 16	208	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(10)|kidney(3)|large_intestine(14)|lung(29)|ovary(5)|pancreas(2)|prostate(3)|skin(1)|urinary_tract(1)	69			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGAGCCTCAACTAAGATTAAC	0.502													C|||	58	0.0115815	0.0431	0.0014	5008	,	,		17472	0.0		0.0	False		,,,				2504	0.0				p.L208V		Atlas-SNP	.											.	PCDHB16	159	.	0			c.C622G						PASS	.	C	VAL/LEU	154,4252	107.3+/-145.7	3,148,2052	65.0	66.0	65.0		622	-8.7	0.0	5	dbSNP_125	65	0,8600		0,0,4300	yes	missense	PCDHB16	NM_020957.1	32	3,148,6352	GG,GC,CC		0.0,3.4952,1.1841	benign	208/777	140562756	154,12852	2203	4300	6503	SO:0001583	missense	57717	exon1			CCTCAACTAAGAT	AF217757	CCDS4251.1	5q31	2014-04-11			ENSG00000196963			"""Cadherins / Protocadherins : Clustered"""	14546	other	protocadherin	"""cadherin ME1"", ""protocadherin-3x"", ""PCDHbeta 16"""	606345				11230163, 11322959	Standard	NM_020957		Approved	PCDHB8a, PCDH3X, KIAA1621, PCDH-BETA16, ME1	uc003liv.3	Q9NRJ7	OTTHUMG00000188325	ENST00000361016.2:c.622C>G	5.37:g.140562756C>G	ENSP00000354293:p.Leu208Val	65.0	0.0	0		73.0	39.0	0.534247	NM_020957	B3KPK5|Q8IYD5|Q96SE9|Q9HCF1	Missense_Mutation	SNP	ENST00000361016.2	37	CCDS4251.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	C	2.179	-0.387934	0.04932	0.034952	0.0	ENSG00000196963	ENST00000361016	T	0.49139	0.79	4.69	-8.68	0.00859	Cadherin (4);Cadherin-like (1);	0.962534	0.08410	N	0.950091	T	0.07098	0.0180	L	0.38531	1.155	0.09310	N	1	B	0.21452	0.056	B	0.27170	0.077	T	0.27606	-1.0069	10	0.41790	T	0.15	.	1.2389	0.01958	0.2632:0.3205:0.2274:0.189	rs28398442	208	Q9NRJ7	PCDBG_HUMAN	V	208	ENSP00000354293:L208V	ENSP00000354293:L208V	L	+	1	2	PCDHB16	140542940	0.000000	0.05858	0.001000	0.08648	0.191000	0.23601	-4.894000	0.00173	-1.135000	0.02895	-0.176000	0.13171	CTA	C|0.991;G|0.009	0.009	strong		0.502	PCDHB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251800.1	NM_020957	
ECM1	1893	hgsc.bcm.edu	37	1	150482639	150482639	+	Silent	SNP	C	C	T	rs74352693	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:150482639C>T	ENST00000369047.4	+	5	491	c.366C>T	c.(364-366)caC>caT	p.H122H	ECM1_ENST00000470432.1_3'UTR|ECM1_ENST00000346569.6_Silent_p.H122H|ECM1_ENST00000369049.4_Silent_p.H149H	NM_004425.3	NP_004416.2	Q16610	ECM1_HUMAN	extracellular matrix protein 1	122					angiogenesis (GO:0001525)|biomineral tissue development (GO:0031214)|inflammatory response (GO:0006954)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of peptidase activity (GO:0010466)|ossification (GO:0001503)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of T cell migration (GO:2000404)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type 2 immune response (GO:0002828)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	enzyme binding (GO:0019899)|laminin binding (GO:0043236)|protease binding (GO:0002020)|protein C-terminus binding (GO:0008022)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|urinary_tract(1)	22	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.29e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			CTCTCCAGCACCCCAATGAAC	0.587													C|||	81	0.0161741	0.0575	0.0072	5008	,	,		18178	0.0		0.0	False		,,,				2504	0.0				p.H149H	Melanoma(156;1696 2560 11093 19685)	Atlas-SNP	.											.	ECM1	96	.	0			c.C447T						PASS	.	C	,,	203,4203	126.1+/-163.2	7,189,2007	138.0	139.0	139.0		447,366,366	-1.3	0.0	1	dbSNP_132	139	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	ECM1	NM_001202858.1,NM_004425.3,NM_022664.2	,,	7,192,6304	TT,TC,CC		0.0349,4.6074,1.5839	,,	149/568,122/541,122/416	150482639	206,12800	2203	4300	6503	SO:0001819	synonymous_variant	1893	exon5			CCAGCACCCCAAT	U68186	CCDS953.1, CCDS954.1, CCDS55632.1	1q21	2008-02-05			ENSG00000143369	ENSG00000143369			3153	protein-coding gene	gene with protein product		602201				9367673, 9501329	Standard	NM_004425		Approved		uc001eus.3	Q16610	OTTHUMG00000012806	ENST00000369047.4:c.366C>T	1.37:g.150482639C>T		101.0	0.0	0		110.0	51.0	0.463636	NM_001202858	A8K8S0|B4DW49|B4DY60|O43266|Q5T5G4|Q5T5G5|Q5T5G6|Q8IZ60	Silent	SNP	ENST00000369047.4	37	CCDS953.1																																																																																			C|0.982;T|0.018	0.018	strong		0.587	ECM1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035832.2	NM_004425	
PODXL2	50512	hgsc.bcm.edu	37	3	127387388	127387388	+	Silent	SNP	C	C	T	rs34716022	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:127387388C>T	ENST00000342480.6	+	5	1350	c.1311C>T	c.(1309-1311)agC>agT	p.S437S		NM_015720.2	NP_056535.1	Q9NZ53	PDXL2_HUMAN	podocalyxin-like 2	437					leukocyte tethering or rolling (GO:0050901)	integral component of plasma membrane (GO:0005887)	glycosaminoglycan binding (GO:0005539)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	26						TCTCTCTGAGCAAGCCCAGCG	0.682													C|||	315	0.0628994	0.2239	0.0231	5008	,	,		17746	0.0		0.003	False		,,,				2504	0.0				p.S437S		Atlas-SNP	.											.	PODXL2	53	.	0			c.C1311T						PASS	.	C		750,3654		52,646,1504	22.0	19.0	20.0		1311	4.3	1.0	3	dbSNP_126	20	8,8586		0,8,4289	no	coding-synonymous	PODXL2	NM_015720.2		52,654,5793	TT,TC,CC		0.0931,17.03,5.8317		437/606	127387388	758,12240	2202	4297	6499	SO:0001819	synonymous_variant	50512	exon5			TCTGAGCAAGCCC	AF219137	CCDS3044.1	3q21.3	2005-02-18			ENSG00000114631	ENSG00000114631			17936	protein-coding gene	gene with protein product	"""endoglycan"""					10722749	Standard	NM_015720		Approved	PODLX2, endoglycan	uc003ejq.3	Q9NZ53	OTTHUMG00000159642	ENST00000342480.6:c.1311C>T	3.37:g.127387388C>T		230.0	0.0	0		253.0	133.0	0.525692	NM_015720	Q6UVY4|Q8WUV6	Silent	SNP	ENST00000342480.6	37	CCDS3044.1																																																																																			C|0.938;T|0.062	0.062	strong		0.682	PODXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356638.1	NM_015720	
HELQ	113510	hgsc.bcm.edu	37	4	84374692	84374692	+	Missense_Mutation	SNP	A	A	G	rs17006837	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:84374692A>G	ENST00000295488.3	-	2	866	c.704T>C	c.(703-705)cTg>cCg	p.L235P	HELQ_ENST00000440639.2_5'Flank|MRPS18C_ENST00000295491.4_5'Flank|MRPS18C_ENST00000507019.1_5'Flank|HELQ_ENST00000510985.1_Missense_Mutation_p.L235P|MRPS18C_ENST00000507349.1_5'Flank	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	235			L -> P (in dbSNP:rs17006837).		double-strand break repair via homologous recombination (GO:0000724)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						ATTATGGGGCAGTTCCTCATT	0.378								Other identified genes with known or suspected DNA repair function					a|||	675	0.134784	0.4894	0.0331	5008	,	,		20460	0.0		0.004	False		,,,				2504	0.001				p.L235P		Atlas-SNP	.											.	HELQ	95	.	0			c.T704C						PASS	.	G	PRO/LEU	1835,2571	527.1+/-372.1	367,1101,735	132.0	138.0	136.0		704	-1.4	0.0	4	dbSNP_123	136	27,8573	16.0+/-53.3	0,27,4273	yes	missense	HELQ	NM_133636.2	98	367,1128,5008	GG,GA,AA		0.314,41.6478,14.3165	benign	235/1102	84374692	1862,11144	2203	4300	6503	SO:0001583	missense	113510	exon2			TGGGGCAGTTCCT	AF436845	CCDS3603.1, CCDS75158.1	4q21.23	2009-02-26			ENSG00000163312	ENSG00000163312			18536	protein-coding gene	gene with protein product		606769				11751861	Standard	XM_005262711		Approved	Hel308	uc003hom.3	Q8TDG4	OTTHUMG00000130423	ENST00000295488.3:c.704T>C	4.37:g.84374692A>G	ENSP00000295488:p.Leu235Pro	124.0	0.0	0		123.0	64.0	0.520325	NM_133636	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Missense_Mutation	SNP	ENST00000295488.3	37	CCDS3603.1	202	0.0924908424908425	187	0.3800813008130081	12	0.03314917127071823	0	0.0	3	0.00395778364116095	a	9.849	1.193106	0.21954	0.416478	0.00314	ENSG00000163312	ENST00000295488;ENST00000510985	T;T	0.69926	0.03;-0.44	5.43	-1.43	0.08884	.	0.989793	0.08215	N	0.980008	T	0.00012	0.0000	L	0.59436	1.845	0.80722	P	0.0	P;B;D;B	0.57571	0.8;0.06;0.98;0.006	B;B;P;B	0.56700	0.278;0.018;0.804;0.003	T	0.20840	-1.0263	9	0.32370	T	0.25	-34.7802	6.3635	0.21441	0.6213:0.1187:0.2599:0.0	rs17006837;rs61470575;rs17006837	235;235;198;235	E3W980;E3W982;Q8TDG4-2;Q8TDG4	.;.;.;HELQ_HUMAN	P	235	ENSP00000295488:L235P;ENSP00000424539:L235P	ENSP00000295488:L235P	L	-	2	0	HELQ	84593716	0.000000	0.05858	0.006000	0.13384	0.002000	0.02628	0.386000	0.20702	-0.126000	0.11682	-1.060000	0.02296	CTG	A|0.864;G|0.136	0.136	strong		0.378	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636	
TM7SF2	7108	hgsc.bcm.edu	37	11	64882441	64882441	+	Silent	SNP	G	G	A	rs33981236	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:64882441G>A	ENST00000279263.7	+	7	942	c.780G>A	c.(778-780)gcG>gcA	p.A260A	AP003068.12_ENST00000527789.1_RNA|TM7SF2_ENST00000345348.5_Silent_p.A260A|TM7SF2_ENST00000540748.1_Silent_p.A144A|TM7SF2_ENST00000531029.1_3'UTR	NM_003273.2	NP_003264.2	O76062	ERG24_HUMAN	transmembrane 7 superfamily member 2	260					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	delta14-sterol reductase activity (GO:0050613)			lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						TCATGCTGGCGTTTGGGGACA	0.617													G|||	152	0.0303514	0.0681	0.0187	5008	,	,		20654	0.0317		0.003	False		,,,				2504	0.0143				p.A260A		Atlas-SNP	.											TM7SF2,NS,carcinoma,+1,1	TM7SF2	30	1	0			c.G780A						PASS	.	G		201,4019		2,197,1911	171.0	181.0	178.0		780	-2.3	1.0	11	dbSNP_126	178	14,8428		0,14,4207	no	coding-synonymous	TM7SF2	NM_003273.2		2,211,6118	AA,AG,GG		0.1658,4.763,1.698		260/419	64882441	215,12447	2110	4221	6331	SO:0001819	synonymous_variant	7108	exon7			GCTGGCGTTTGGG	BC012857	CCDS41669.1, CCDS60846.1	11q13.1	2013-05-23			ENSG00000149809	ENSG00000149809	1.3.1.70		11863	protein-coding gene	gene with protein product	"""delta(14)-sterol reductase"""	603414				9615229, 9286704	Standard	NM_003273		Approved	ANG1, DHCR14A, NET47	uc001oct.4	O76062	OTTHUMG00000165603	ENST00000279263.7:c.780G>A	11.37:g.64882441G>A		130.0	0.0	0		174.0	93.0	0.534483	NM_003273	A8K4H0|O95982|Q8IY06|Q96E64|Q96GZ1	Silent	SNP	ENST00000279263.7	37	CCDS41669.1	62	0.028388278388278388	33	0.06707317073170732	7	0.019337016574585635	19	0.033216783216783216	3	0.00395778364116095	G	6.877	0.531230	0.13127	0.04763	0.001658	ENSG00000149809	ENST00000528802	.	.	.	5.23	-2.3	0.06785	.	.	.	.	.	T	0.03520	0.0101	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.21655	-1.0239	4	.	.	.	-10.0796	0.2725	0.00233	0.2909:0.1876:0.2797:0.2419	rs33981236	.	.	.	H	88	.	.	R	+	2	0	TM7SF2	64639017	0.000000	0.05858	0.991000	0.47740	0.658000	0.38924	-1.832000	0.01696	-0.207000	0.10187	-1.332000	0.01269	CGT	G|0.981;A|0.019	0.019	strong		0.617	TM7SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385234.1	NM_003273	
DEFB135	613209	hgsc.bcm.edu	37	8	11842019	11842019	+	Missense_Mutation	SNP	G	G	A	rs73663074	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:11842019G>A	ENST00000382208.2	+	2	154	c.154G>A	c.(154-156)Gaa>Aaa	p.E52K		NM_001033017.2	NP_001028189.2	Q30KP9	DB135_HUMAN	defensin, beta 135	52					defense response to bacterium (GO:0042742)	extracellular region (GO:0005576)				endometrium(1)|large_intestine(2)|prostate(1)	4						TCTAAAAAACGAACAATATCG	0.388													G|||	220	0.0439297	0.1422	0.013	5008	,	,		20406	0.0		0.0	False		,,,				2504	0.0235				p.E52K		Atlas-SNP	.											.	DEFB135	7	.	0			c.G154A						PASS	.	G	LYS/GLU	467,3281		28,411,1435	112.0	110.0	111.0		154	3.3	0.1	8	dbSNP_130	111	10,8190		0,10,4090	yes	missense	DEFB135	NM_001033017.2	56	28,421,5525	AA,AG,GG		0.122,12.46,3.9923	possibly-damaging	52/78	11842019	477,11471	1874	4100	5974	SO:0001583	missense	613209	exon2			AAAAACGAACAAT	DQ012025	CCDS43710.1	8p23.1	2009-05-27			ENSG00000205883	ENSG00000205883		"""Defensins, beta"""	32400	protein-coding gene	gene with protein product						16033865	Standard	NM_001033017		Approved		uc003wuw.1	Q30KP9	OTTHUMG00000158719	ENST00000382208.2:c.154G>A	8.37:g.11842019G>A	ENSP00000371643:p.Glu52Lys	105.0	0.0	0		103.0	57.0	0.553398	NM_001033017	Q4QY37	Missense_Mutation	SNP	ENST00000382208.2	37	CCDS43710.1	89	0.04075091575091575	86	0.17479674796747968	3	0.008287292817679558	0	0.0	0	0.0	G	17.23	3.337441	0.60963	0.1246	0.00122	ENSG00000205883	ENST00000382208	T	0.73575	-0.76	3.34	3.34	0.38264	.	0.000000	0.33005	N	0.005386	T	0.01029	0.0034	.	.	.	0.80722	P	0.0	D	0.89917	1.0	D	0.87578	0.998	T	0.47328	-0.9126	8	0.87932	D	0	-25.449	10.4608	0.44578	0.0:0.0:1.0:0.0	.	52	Q30KP9	DB135_HUMAN	K	52	ENSP00000371643:E52K	ENSP00000371643:E52K	E	+	1	0	DEFB135	11879428	0.515000	0.26210	0.053000	0.19242	0.001000	0.01503	2.965000	0.49200	2.157000	0.67596	0.561000	0.74099	GAA	G|0.959;A|0.041	0.041	strong		0.388	DEFB135-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351888.1	NM_001033017	
TRPV6	55503	hgsc.bcm.edu	37	7	142573613	142573613	+	Silent	SNP	C	C	T	rs79832568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:142573613C>T	ENST00000359396.3	-	7	1052	c.807G>A	c.(805-807)acG>acA	p.T269T	RP11-114L10.2_ENST00000438839.1_RNA	NM_018646.3	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel, subfamily V, member 6	269					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|regulation of calcium ion-dependent exocytosis (GO:0017158)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)			breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	42	Melanoma(164;0.059)					GTGGTCCATACGTCCACTGGG	0.532													C|||	117	0.0233626	0.0779	0.0144	5008	,	,		10275	0.0		0.004	False		,,,				2504	0.0				p.T269T		Atlas-SNP	.											.	TRPV6	108	.	0			c.G807A						PASS	.	C		327,4079	172.7+/-202.6	19,289,1895	214.0	162.0	180.0		807	-9.9	0.0	7	dbSNP_131	180	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous	TRPV6	NM_018646.2		19,303,6181	TT,TC,CC		0.1628,7.4217,2.6219		269/726	142573613	341,12665	2203	4300	6503	SO:0001819	synonymous_variant	55503	exon7			TCCATACGTCCAC	AJ277909	CCDS5874.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000165125	ENSG00000165125		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	14006	protein-coding gene	gene with protein product		606680	"""epithelial calcium channel 2"""	ECAC2		11097838, 11549322, 16382100, 16717058	Standard	NM_018646		Approved	CaT1	uc003wbx.2	Q9H1D0	OTTHUMG00000157158	ENST00000359396.3:c.807G>A	7.37:g.142573613C>T		167.0	0.0	0		170.0	83.0	0.488235	NM_018646	A4D2I8|Q8TDL3|Q8WXR8|Q96LC5|Q9H1D1|Q9H296	Silent	SNP	ENST00000359396.3	37	CCDS5874.1																																																																																			C|0.976;T|0.024	0.024	strong		0.532	TRPV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347662.1	NM_014274	
PARP14	54625	hgsc.bcm.edu	37	3	122419993	122419993	+	Silent	SNP	C	C	T	rs16833421	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122419993C>T	ENST00000474629.2	+	6	2858	c.2592C>T	c.(2590-2592)gcC>gcT	p.A864A		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	864	Macro 1. {ECO:0000255|PROSITE- ProRule:PRU00490}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		CGGGCAATGCCACCATCTCCA	0.612													C|||	169	0.033746	0.1188	0.0173	5008	,	,		19518	0.0		0.0	False		,,,				2504	0.0				p.A864A		Atlas-SNP	.											.	PARP14	242	.	0			c.C2592T						PASS	.	C		326,3758		15,296,1731	33.0	35.0	34.0		2592	-0.9	0.0	3	dbSNP_123	34	3,8335		0,3,4166	yes	coding-synonymous	PARP14	NM_017554.2		15,299,5897	TT,TC,CC		0.036,7.9824,2.6485		864/1802	122419993	329,12093	2042	4169	6211	SO:0001819	synonymous_variant	54625	exon6			CAATGCCACCATC	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"""Poly (ADP-ribose) polymerases"""	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.2592C>T	3.37:g.122419993C>T		56.0	0.0	0		75.0	37.0	0.493333	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Silent	SNP	ENST00000474629.2	37	CCDS46894.1																																																																																			C|0.965;T|0.035	0.035	strong		0.612	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554	
MYLK	4638	hgsc.bcm.edu	37	3	123452859	123452859	+	Silent	SNP	C	C	T	rs115018449	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:123452859C>T	ENST00000475616.1	-	7	983	c.984G>A	c.(982-984)tcG>tcA	p.S328S	MYLK_ENST00000360304.3_Silent_p.S328S|MYLK_ENST00000346322.5_Silent_p.S328S|MYLK_ENST00000360772.3_Silent_p.S328S|MYLK_ENST00000359169.1_Silent_p.S328S			Q15746	MYLK_HUMAN	myosin light chain kinase	328					actin filament organization (GO:0007015)|aorta smooth muscle tissue morphogenesis (GO:0060414)|bleb assembly (GO:0032060)|cellular hypotonic response (GO:0071476)|muscle contraction (GO:0006936)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|smooth muscle contraction (GO:0006939)|tonic smooth muscle contraction (GO:0014820)	cell-cell junction (GO:0005911)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|metal ion binding (GO:0046872)|myosin light chain kinase activity (GO:0004687)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		CCGTTCTGGGCGAGTCCTTGC	0.647													C|||	12	0.00239617	0.0091	0.0	5008	,	,		14936	0.0		0.0	False		,,,				2504	0.0				p.S328S		Atlas-SNP	.											MYLK,caecum,carcinoma,0,1	MYLK	224	1	0			c.G984A						PASS	.	C	,,,	42,4364	43.1+/-76.7	0,42,2161	47.0	51.0	49.0		984,984,984,984	-10.9	0.0	3	dbSNP_132	49	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MYLK	NM_053025.3,NM_053026.3,NM_053027.3,NM_053028.3	,,,	0,42,6461	TT,TC,CC		0.0,0.9532,0.3229	,,,	328/1915,328/1846,328/1864,328/1795	123452859	42,12964	2203	4300	6503	SO:0001819	synonymous_variant	4638	exon10			TCTGGGCGAGTCC	X85337	CCDS3023.1, CCDS43141.1, CCDS46896.1, CCDS46897.1, CCDS58849.1	3q21	2013-02-11	2008-01-23		ENSG00000065534	ENSG00000065534	2.7.11.18	"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7590	protein-coding gene	gene with protein product	"""smooth muscle myosin light chain kinase"""	600922	"""myosin, light polypeptide kinase"""			8575746	Standard	NM_053026		Approved	MLCK, smMLCK, MYLK1, MLCK1	uc003ego.3	Q15746	OTTHUMG00000141304	ENST00000475616.1:c.984G>A	3.37:g.123452859C>T		114.0	0.0	0		149.0	65.0	0.436242	NM_053025	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Silent	SNP	ENST00000475616.1	37	CCDS46896.1																																																																																			C|0.998;T|0.002	0.002	strong		0.647	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025	
BPIFA2	140683	hgsc.bcm.edu	37	20	31761885	31761885	+	Splice_Site	SNP	G	G	T	rs61734343	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:31761885G>T	ENST00000253362.2	+	4	449	c.303G>T	c.(301-303)ggG>ggT	p.G101G	BPIFA2_ENST00000354932.5_Splice_Site_p.G101G			Q96DR5	BPIA2_HUMAN	BPI fold containing family A, member 2	101						extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)										TTTCACACAGGTTGAAAATCA	0.537													G|||	23	0.00459265	0.0174	0.0	5008	,	,		19612	0.0		0.0	False		,,,				2504	0.0				p.G101G		Atlas-SNP	.											.	.	.	.	0			c.G303T						PASS	.	G		72,4334	64.1+/-101.4	0,72,2131	164.0	110.0	128.0		303	0.6	0.6	20	dbSNP_129	128	3,8597	3.0+/-9.4	0,3,4297	yes	coding-synonymous-near-splice	BPIFA2	NM_080574.2		0,75,6428	TT,TG,GG		0.0349,1.6341,0.5767		101/250	31761885	75,12931	2203	4300	6503	SO:0001630	splice_region_variant	140683	exon4			ACACAGGTTGAAA	AF432917	CCDS13214.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000131050	ENSG00000131050		"""BPI fold containing"""	16203	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 70"""	C20orf70		11971875	Standard	NM_080574		Approved	bA49G10.1, SPLUNC2, PSP	uc002wyo.1	Q96DR5	OTTHUMG00000032244	ENST00000253362.2:c.303-1G>T	20.37:g.31761885G>T		121.0	0.0	0		138.0	58.0	0.42029	NM_080574	Q9BQQ0	Silent	SNP	ENST00000253362.2	37	CCDS13214.1																																																																																			A|0.003;G|0.992;T|0.005	0.005	strong		0.537	BPIFA2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257117.1	NM_080574	Silent
PFKP	5214	hgsc.bcm.edu	37	10	3177944	3177944	+	Silent	SNP	C	C	T	rs61731934	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:3177944C>T	ENST00000381125.4	+	21	2215	c.2139C>T	c.(2137-2139)acC>acT	p.T713T	PITRM1_ENST00000464395.1_5'Flank|PFKP_ENST00000381075.2_Silent_p.T705T|PFKP_ENST00000381072.1_Silent_p.T131T	NM_002627.4	NP_002618.1	Q01813	PFKAP_HUMAN	phosphofructokinase, platelet	713	C-terminal regulatory PFK domain 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|fructose 6-phosphate metabolic process (GO:0006002)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	6-phosphofructokinase activity (GO:0003872)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein complex binding (GO:0032403)			breast(2)|central_nervous_system(4)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	31				GBM - Glioblastoma multiforme(1;0.000975)|all cancers(11;0.00351)|Epithelial(11;0.142)		AATTTACCACCGATGATTCCA	0.413													C|||	53	0.0105831	0.0356	0.0043	5008	,	,		18020	0.0		0.001	False		,,,				2504	0.002				p.T713T		Atlas-SNP	.											PFKP_ENST00000381075,NS,carcinoma,+2,2	PFKP	182	2	0			c.C2139T						PASS	.	C	,	224,4182	130.6+/-167.2	9,206,1988	62.0	63.0	63.0		2115,2139	-7.3	0.0	10	dbSNP_129	63	5,8595	5.0+/-18.6	0,5,4295	yes	coding-synonymous,coding-synonymous	PFKP	NM_001242339.1,NM_002627.4	,	9,211,6283	TT,TC,CC		0.0581,5.084,1.7607	,	705/777,713/785	3177944	229,12777	2203	4300	6503	SO:0001819	synonymous_variant	5214	exon21			TACCACCGATGAT	AK092597	CCDS7059.1, CCDS55698.1	10p15.3-p15.2	2006-08-25			ENSG00000067057	ENSG00000067057	2.7.1.11		8878	protein-coding gene	gene with protein product	"""Phosphofructokinase, platelet type"""	171840					Standard	NM_002627		Approved	PFK-C, PFKF	uc001igp.3	Q01813	OTTHUMG00000017556	ENST00000381125.4:c.2139C>T	10.37:g.3177944C>T		51.0	0.0	0		76.0	40.0	0.526316	NM_002627	B3KS15|Q5VSR7|Q5VSR8	Silent	SNP	ENST00000381125.4	37	CCDS7059.1	19	0.0086996336996337	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	0	0.0	c	2.293	-0.362014	0.05103	0.05084	5.81E-4	ENSG00000067057	ENST00000433193	.	.	.	5.21	-7.26	0.01466	.	.	.	.	.	T	0.19846	0.0477	.	.	.	0.48288	D	0.999629	.	.	.	.	.	.	T	0.59413	-0.7459	4	.	.	.	.	13.2504	0.60048	0.0:0.5807:0.1633:0.256	rs61731934	.	.	.	L	66	.	.	P	+	2	0	PFKP	3167944	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-5.635000	0.00108	-1.087000	0.03081	-1.012000	0.02466	CCG	C|0.983;T|0.017	0.017	strong		0.413	PFKP-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046454.1	NM_002627	
ABCA8	10351	hgsc.bcm.edu	37	17	66928468	66928468	+	Missense_Mutation	SNP	G	G	C	rs62638729|rs386798698	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:66928468G>C	ENST00000269080.2	-	6	895	c.758C>G	c.(757-759)gCc>gGc	p.A253G	ABCA8_ENST00000586539.1_Missense_Mutation_p.A253G|ABCA8_ENST00000430352.2_Missense_Mutation_p.A253G	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	253					transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					TGTCATCAAGGCCTTCATCCT	0.388													C|||	380	0.0758786	0.2716	0.0231	5008	,	,		20420	0.0		0.005	False		,,,				2504	0.0				p.A253G		Atlas-SNP	.											.	ABCA8	213	.	0			c.C758G						PASS	.						89.0	81.0	84.0					17																	66928468		2203	4300	6503	SO:0001583	missense	10351	exon6			ATCAAGGCCTTCA	AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"""ATP binding cassette transporters / subfamily A"""	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.758C>G	17.37:g.66928468G>C	ENSP00000269080:p.Ala253Gly	80.0	0.0	0		99.0	46.0	0.464646	NM_007168	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	37	CCDS11680.1	132	0.06043956043956044	120	0.24390243902439024	10	0.027624309392265192	0	0.0	2	0.002638522427440633	C	5.598	0.295055	0.10622	.	.	ENSG00000141338	ENST00000269080;ENST00000430352;ENST00000541225;ENST00000428549	D;D	0.87571	-2.27;-2.27	4.85	-0.973	0.10297	.	0.589518	0.15272	N	0.271169	T	0.00039	0.0001	N	0.00483	-1.445	0.09310	N	1	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.01281	0.0;0.0;0.0;0.0;0.0	T	0.18398	-1.0338	10	0.52906	T	0.07	.	6.2111	0.20630	0.1354:0.2547:0.5285:0.0813	rs62638729	192;253;253;253;253	F5H6Z4;A1L3U3;B4DJ11;C9JQE6;O94911	.;.;.;.;ABCA8_HUMAN	G	253;253;192;253	ENSP00000269080:A253G;ENSP00000402814:A253G	ENSP00000269080:A253G	A	-	2	0	ABCA8	64440063	0.000000	0.05858	0.000000	0.03702	0.505000	0.33919	-0.762000	0.04745	-0.174000	0.10743	-0.224000	0.12420	GCC	G|0.945;C|0.055	0.055	strong		0.388	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168	
CIB1	10519	hgsc.bcm.edu	37	15	90771787	90771787	+	IGR	SNP	G	G	A	rs16944065	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90771787G>A	ENST00000328649.6	-	0	1247				SEMA4B_ENST00000332496.6_Missense_Mutation_p.S809N|SEMA4B_ENST00000379122.3_Intron|SEMA4B_ENST00000411539.2_Missense_Mutation_p.S809N	NM_006384.3	NP_006375.2	Q99828	CIB1_HUMAN	calcium and integrin binding 1 (calmyrin)						angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cell division (GO:0051301)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to growth factor stimulus (GO:0071363)|cellular response to nerve growth factor stimulus (GO:1990090)|cellular response to tumor necrosis factor (GO:0071356)|cytoplasmic microtubule organization (GO:0031122)|double-strand break repair (GO:0006302)|endomitotic cell cycle (GO:0007113)|extrinsic apoptotic signaling pathway (GO:0097191)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of megakaryocyte differentiation (GO:0045653)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of neuron projection development (GO:0010977)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|platelet formation (GO:0030220)|positive regulation of calcineurin-NFAT signaling cascade (GO:0070886)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of male germ cell proliferation (GO:2000256)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of cell division (GO:0051302)|regulation of cell proliferation (GO:0042127)|response to ischemia (GO:0002931)|spermatid development (GO:0007286)|thrombopoietin-mediated signaling pathway (GO:0038163)	cell periphery (GO:0071944)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|protein anchor (GO:0043495)|Ras GTPase binding (GO:0017016)			lung(1)|prostate(1)	2	Melanoma(11;0.00551)|Lung NSC(78;0.0141)|all_lung(78;0.0303)		BRCA - Breast invasive adenocarcinoma(143;0.00269)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.217)			AGGCCACTCAGCATCCAAGAC	0.652													G|||	47	0.00938498	0.0348	0.0014	5008	,	,		16568	0.0		0.0	False		,,,				2504	0.0				p.S809N		Atlas-SNP	.											.	SEMA4B	51	.	0			c.G2426A						PASS	.	G	ASN/SER,ASN/SER	156,3862		0,156,1853	29.0	34.0	32.0		2426,2426	4.8	1.0	15	dbSNP_123	32	3,8309		0,3,4153	yes	missense,missense	SEMA4B	NM_020210.3,NM_198925.2	46,46	0,159,6006	AA,AG,GG		0.0361,3.8825,1.2895	benign,benign	809/838,809/838	90771787	159,12171	2009	4156	6165	SO:0001628	intergenic_variant	10509	exon15			CACTCAGCATCCA	U82226	CCDS10360.1, CCDS73781.1	15q25.3-q26	2013-01-10			ENSG00000185043	ENSG00000185043		"""EF-hand domain containing"""	16920	protein-coding gene	gene with protein product		602293				9030514, 10826701	Standard	NM_006384		Approved	SIP2-28, CALMYRIN, CIB, KIP	uc031qtq.1	Q99828	OTTHUMG00000149808		15.37:g.90771787G>A		58.0	0.0	0		70.0	30.0	0.428571	NM_020210	B5BU40|H6WJF3|O00693|O00735|Q6IB49|Q96J54|Q99971	Missense_Mutation	SNP	ENST00000328649.6	37	CCDS10360.1	45	0.020604395604395604	23	0.046747967479674794	4	0.011049723756906077	6	0.01048951048951049	12	0.0158311345646438	G	12.52	1.963517	0.34659	0.038825	3.61E-4	ENSG00000185033	ENST00000332496;ENST00000411539	T;T	0.21543	2.0;2.0	4.75	4.75	0.60458	.	0.102022	0.64402	D	0.000003	T	0.01558	0.0050	N	0.11560	0.145	0.80722	D	1	B;B	0.26120	0.142;0.072	B;B	0.23018	0.043;0.031	T	0.20140	-1.0284	10	0.34782	T	0.22	.	10.5938	0.45325	0.0988:0.0:0.9012:0.0	rs16944065;rs16944065	809;804	Q2NL81;Q9NPR2	.;SEM4B_HUMAN	N	809	ENSP00000332204:S809N;ENSP00000394720:S809N	ENSP00000332204:S809N	S	+	2	0	SEMA4B	88572791	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	3.820000	0.55693	2.624000	0.88883	0.561000	0.74099	AGC	G|0.979;A|0.021	0.021	strong		0.652	CIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313419.1		
C19orf54	284325	hgsc.bcm.edu	37	19	41248532	41248532	+	Silent	SNP	G	G	A	rs36071297	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41248532G>A	ENST00000378313.2	-	6	981	c.862C>T	c.(862-864)Ctg>Ttg	p.L288L	C19orf54_ENST00000598485.2_Intron|C19orf54_ENST00000470681.1_3'UTR|C19orf54_ENST00000594163.1_5'Flank|C19orf54_ENST00000339153.3_Silent_p.L116L|C19orf54_ENST00000598729.1_Silent_p.L116L	NM_198476.3	NP_940878.3	Q5BKX5	CS054_HUMAN	chromosome 19 open reading frame 54	288										breast(1)|lung(1)|urinary_tract(2)	4			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			TGCTTGGACAGCAGGTAGACA	0.657													G|||	137	0.0273562	0.0998	0.0072	5008	,	,		19677	0.0		0.0	False		,,,				2504	0.0				p.L288L		Atlas-SNP	.											.	C19orf54	13	.	0			c.C862T						PASS	.	G		321,4085	170.1+/-200.6	11,299,1893	43.0	38.0	39.0		862	5.5	1.0	19	dbSNP_126	39	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	C19orf54	NM_198476.3		11,302,6190	AA,AG,GG		0.0349,7.2855,2.4912		288/352	41248532	324,12682	2203	4300	6503	SO:0001819	synonymous_variant	284325	exon6			TGGACAGCAGGTA	AK123126	CCDS12564.2	19q13.2	2012-10-26			ENSG00000188493	ENSG00000188493			24758	protein-coding gene	gene with protein product							Standard	NM_198476		Approved	FLJ41131	uc002oou.1	Q5BKX5	OTTHUMG00000150174	ENST00000378313.2:c.862C>T	19.37:g.41248532G>A		127.0	0.0	0		145.0	78.0	0.537931	NM_198476	A8MSZ5|B4DNU7	Silent	SNP	ENST00000378313.2	37	CCDS12564.2																																																																																			G|0.905;A|0.095	0.095	strong		0.657	C19orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316701.1	NM_198476	
HRNR	388697	hgsc.bcm.edu	37	1	152193049	152193049	+	Silent	SNP	C	C	T	rs114845154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152193049C>T	ENST00000368801.2	-	3	1131	c.1056G>A	c.(1054-1056)gaG>gaA	p.E352E	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	352					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CTGAGCCAGACTCATGTTGCC	0.557													C|||	95	0.0189696	0.0696	0.0043	5008	,	,		22156	0.0		0.0	False		,,,				2504	0.0				p.E352E		Atlas-SNP	.											HRNR,NS,carcinoma,-2,1	HRNR	403	1	0			c.G1056A						PASS	.	C		188,4218	120.8+/-158.4	2,184,2017	118.0	121.0	120.0		1056	-8.3	0.0	1	dbSNP_132	120	0,8600		0,0,4300	no	coding-synonymous	HRNR	NM_001009931.1		2,184,6317	TT,TC,CC		0.0,4.2669,1.4455		352/2851	152193049	188,12818	2203	4300	6503	SO:0001819	synonymous_variant	388697	exon3			GCCAGACTCATGT	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.1056G>A	1.37:g.152193049C>T		114.0	0.0	0		123.0	54.0	0.439024	NM_001009931	Q5DT20|Q5U1F4	Silent	SNP	ENST00000368801.2	37	CCDS30859.1																																																																																			C|0.985;T|0.015	0.015	strong		0.557	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
CEP89	84902	hgsc.bcm.edu	37	19	33406328	33406328	+	Missense_Mutation	SNP	G	G	A	rs113919201	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33406328G>A	ENST00000305768.5	-	14	1568	c.1480C>T	c.(1480-1482)Cgt>Tgt	p.R494C		NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	494					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						CATTTGGCACGTAAAATCTCC	0.423													G|||	36	0.0071885	0.025	0.0043	5008	,	,		15861	0.0		0.0	False		,,,				2504	0.0				p.R494C		Atlas-SNP	.											CEP89,NS,carcinoma,+1,1	CEP89	82	1	0			c.C1480T						PASS	.	G	CYS/ARG	99,4307	79.9+/-118.3	3,93,2107	123.0	109.0	114.0		1480	3.5	0.0	19	dbSNP_132	114	0,8600		0,0,4300	yes	missense	CEP89	NM_032816.3	180	3,93,6407	AA,AG,GG		0.0,2.2469,0.7612	benign	494/784	33406328	99,12907	2203	4300	6503	SO:0001583	missense	84902	exon14			TGGCACGTAAAAT	AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"""coiled-coil domain containing 123"""	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.1480C>T	19.37:g.33406328G>A	ENSP00000306105:p.Arg494Cys	218.0	1.0	0.00458716		244.0	128.0	0.52459	NM_032816	B9EGA6|Q8N5J8	Missense_Mutation	SNP	ENST00000305768.5	37	CCDS32987.1	15	0.006868131868131868	12	0.024390243902439025	3	0.008287292817679558	0	0.0	0	0.0	G	6.345	0.431801	0.12045	0.022469	0.0	ENSG00000121289	ENST00000305768	D	0.88201	-2.35	5.6	3.45	0.39498	.	1.178400	0.05586	N	0.573762	T	0.80385	0.4613	L	0.60455	1.87	0.24756	N	0.992952	B;B	0.14438	0.004;0.01	B;B	0.09377	0.004;0.002	T	0.71318	-0.4629	10	0.52906	T	0.07	1.9766	11.2548	0.49048	0.0701:0.1277:0.8023:0.0	.	247;494	Q96ST8-2;Q96ST8	.;CEP89_HUMAN	C	494	ENSP00000306105:R494C	ENSP00000306105:R494C	R	-	1	0	CEP89	38098168	0.414000	0.25408	0.000000	0.03702	0.009000	0.06853	1.725000	0.38074	0.708000	0.31955	0.591000	0.81541	CGT	G|0.991;A|0.009	0.009	strong		0.423	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816	
GPC3	2719	hgsc.bcm.edu	37	X	132730541	132730541	+	Silent	SNP	A	A	G	rs2314298	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:132730541A>G	ENST00000370818.3	-	7	1945	c.1500T>C	c.(1498-1500)gaT>gaC	p.D500D	GPC3_ENST00000394299.2_Silent_p.D523D|GPC3_ENST00000543339.1_Silent_p.D446D	NM_001164618.1|NM_004484.3	NP_001158090.1|NP_004475.1	P51654	GPC3_HUMAN	glypican 3	500					anatomical structure morphogenesis (GO:0009653)|anterior/posterior axis specification (GO:0009948)|body morphogenesis (GO:0010171)|bone mineralization (GO:0030282)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cell proliferation involved in metanephros development (GO:0072203)|chondroitin sulfate metabolic process (GO:0030204)|coronary vasculature development (GO:0060976)|embryonic hindlimb morphogenesis (GO:0035116)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lung development (GO:0030324)|mesenchymal cell proliferation involved in ureteric bud development (GO:0072138)|mesonephric duct morphogenesis (GO:0072180)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of growth (GO:0045926)|negative regulation of smoothened signaling pathway (GO:0045879)|osteoclast differentiation (GO:0030316)|phototransduction, visible light (GO:0007603)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of endocytosis (GO:0045807)|positive regulation of glucose import (GO:0046326)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	anchored component of plasma membrane (GO:0046658)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	peptidyl-dipeptidase inhibitor activity (GO:0060422)			breast(1)|endometrium(4)|kidney(3)|large_intestine(8)|lung(17)|prostate(1)|skin(2)	36	Acute lymphoblastic leukemia(192;0.000127)					CATCTTCATCATCACCGCAGT	0.448			"""T, D, Mis, N, F, S"""			Wilms tumour			Simpson-Golabi-Behmel syndrome				a|||	247	0.0654305	0.1823	0.0086	3775	,	,		13843	0.0		0.0	False		,,,				2504	0.0				p.D523D		Atlas-SNP	.	yes	Rec/X		Simpson-Golabi-Behmel syndrome	X	Xq26.1	2719	glypican 3		O	.	GPC3	88	.	0			c.T1569C						PASS	.	A	,,,	844,2991		83,548,130,1001,441	240.0	203.0	216.0		1569,1452,1338,1500	-8.8	0.0	X	dbSNP_100	216	9,6719		0,6,3,2422,1869	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GPC3	NM_001164617.1,NM_001164618.1,NM_001164619.1,NM_004484.3	,,,	83,554,133,3423,2310	GG,GA,G,AA,A		0.1338,22.0078,8.0754	,,,	523/604,484/565,446/527,500/581	132730541	853,9710	2203	4300	6503	SO:0001819	synonymous_variant	2719	exon8	Familial Cancer Database	SGBS	TTCATCATCACCG	L47125	CCDS14638.1, CCDS55496.1	Xq26	2014-09-17			ENSG00000147257	ENSG00000147257		"""Proteoglycans / Cell Surface : Glypicans"""	4451	protein-coding gene	gene with protein product	"""glypican proteoglycan 3"""	300037		SDYS		8589713, 9787072	Standard	NM_004484		Approved	OCI-5, SGBS, SGBS1, SGB, DGSX	uc010nrn.2	P51654	OTTHUMG00000022448	ENST00000370818.3:c.1500T>C	X.37:g.132730541A>G		421.0	0.0	0		461.0	297.0	0.644252	NM_001164617	C9JLE3|G3V1R0|Q2L880|Q2L882	Silent	SNP	ENST00000370818.3	37	CCDS14638.1	88	0.05304400241109102	57	0.1313364055299539	1	0.002777777777777778	0	0.0	0	0.0	a	2.240	-0.373954	0.05034	0.220078	0.001338	ENSG00000147257	ENST00000406757	.	.	.	4.73	-8.77	0.00827	.	.	.	.	.	T	0.00039	0.0001	.	.	.	0.21290	P	0.99973057	.	.	.	.	.	.	T	0.40997	-0.9533	3	.	.	.	.	17.6231	0.88087	0.3063:0.0:0.6937:0.0	rs2314298;rs60128560;rs2314298	.	.	.	T	230	.	.	M	-	2	0	GPC3	132558207	0.013000	0.17824	0.034000	0.17996	0.609000	0.37215	-1.591000	0.02100	-2.800000	0.00352	-3.172000	0.00057	ATG	A|0.905;G|0.095	0.095	strong		0.448	GPC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058356.1	NM_004484	
CIZ1	25792	hgsc.bcm.edu	37	9	130941451	130941451	+	Silent	SNP	C	C	T	rs45536439	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:130941451C>T	ENST00000393608.1	-	8	1237	c.1035G>A	c.(1033-1035)gcG>gcA	p.A345A	CIZ1_ENST00000476727.2_Intron|CIZ1_ENST00000538431.1_Silent_p.A345A|CIZ1_ENST00000325721.8_Silent_p.A316A|CIZ1_ENST00000357558.5_Silent_p.A345A|CIZ1_ENST00000372948.3_Silent_p.A345A|CIZ1_ENST00000372954.1_Silent_p.A321A|CIZ1_ENST00000372938.5_Silent_p.A345A|CIZ1_ENST00000541172.1_Silent_p.A244A|CIZ1_ENST00000277465.4_Silent_p.A345A	NM_012127.2	NP_036259.2	Q9ULV3	CIZ1_HUMAN	CDKN1A interacting zinc finger protein 1	345	Gln-rich.				maintenance of protein location in nucleus (GO:0051457)|positive regulation of DNA-dependent DNA replication initiation (GO:0032298)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|liver(1)|lung(9)|ovary(3)|prostate(2)|urinary_tract(2)	35						TCTGTGTTTGCGCCTGCTTCT	0.617													C|||	174	0.0347444	0.1225	0.0159	5008	,	,		20540	0.0		0.001	False		,,,				2504	0.0				p.A375A		Atlas-SNP	.											.	CIZ1	75	.	0			c.G1125A						PASS	.	C	,,,,	553,3853	248.7+/-256.4	38,477,1688	63.0	64.0	64.0		1035,1035,1020,963,1035	-5.6	0.9	9	dbSNP_127	64	13,8587	7.7+/-29.5	0,13,4287	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CIZ1	NM_001131015.1,NM_001131016.1,NM_001131017.1,NM_001131018.1,NM_012127.2	,,,,	38,490,5975	TT,TC,CC		0.1512,12.5511,4.3518	,,,,	345/843,345/899,340/838,321/819,345/899	130941451	566,12440	2203	4300	6503	SO:0001819	synonymous_variant	25792	exon8			TGTTTGCGCCTGC	AB030835	CCDS6894.1, CCDS48033.1, CCDS48034.1, CCDS75910.1	9q34.1	2012-10-05			ENSG00000148337	ENSG00000148337			16744	protein-coding gene	gene with protein product		611420				10529385	Standard	NM_001131015		Approved	LSFR1, ZNF356	uc011mas.2	Q9ULV3	OTTHUMG00000020735	ENST00000393608.1:c.1035G>A	9.37:g.130941451C>T		118.0	0.0	0		118.0	70.0	0.59322	NM_001257975	A8K9J8|B4E131|B7ZAS8|Q5SYW3|Q5SYW5|Q8WU72|Q9H868|Q9NYM8|Q9UHK4|Q9Y3F9|Q9Y3G0	Silent	SNP	ENST00000393608.1	37	CCDS6894.1																																																																																			C|0.961;T|0.039	0.039	strong		0.617	CIZ1-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054399.1	NM_012127	
CDC42BPB	9578	hgsc.bcm.edu	37	14	103406169	103406169	+	Silent	SNP	C	C	T	rs60475222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:103406169C>T	ENST00000361246.2	-	33	4995	c.4707G>A	c.(4705-4707)agG>agA	p.R1569R	RP11-365N19.2_ENST00000560931.1_RNA	NM_006035.3	NP_006026.3			CDC42 binding protein kinase beta (DMPK-like)											NS(1)|breast(4)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(11)|liver(1)|lung(14)|ovary(2)|prostate(2)|skin(3)|stomach(1)	49		Melanoma(154;0.155)		Colorectal(3;0.0129)|READ - Rectum adenocarcinoma(2;0.0419)|Epithelial(152;0.0474)|all cancers(159;0.199)		GCTCCTACCGCCTCTGCTGCA	0.597													C|||	35	0.00698882	0.0257	0.0014	5008	,	,		19254	0.0		0.0	False		,,,				2504	0.0				p.R1569R		Atlas-SNP	.											.	CDC42BPB	123	.	0			c.G4707A						PASS	.	C		110,4296	86.8+/-125.4	2,106,2095	147.0	158.0	155.0		4707	3.4	1.0	14	dbSNP_129	155	0,8600		0,0,4300	no	coding-synonymous	CDC42BPB	NM_006035.3		2,106,6395	TT,TC,CC		0.0,2.4966,0.8458		1569/1712	103406169	110,12896	2203	4300	6503	SO:0001819	synonymous_variant	9578	exon33			CTACCGCCTCTGC	AF128625	CCDS9978.1	14q32.32	2010-05-12	2001-11-28		ENSG00000198752	ENSG00000198752			1738	protein-coding gene	gene with protein product		614062	"""CDC42-binding protein kinase beta (DMPK-like)"""			10198171	Standard	NM_006035		Approved	MRCKB, KIAA1124	uc001ymi.1	Q9Y5S2		ENST00000361246.2:c.4707G>A	14.37:g.103406169C>T		163.0	0.0	0		216.0	96.0	0.444444	NM_006035		Silent	SNP	ENST00000361246.2	37	CCDS9978.1																																																																																			C|0.992;T|0.008	0.008	strong		0.597	CDC42BPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415711.1	NM_006035	
CTF1	1489	hgsc.bcm.edu	37	16	30910830	30910830	+	Silent	SNP	C	C	T	rs8059269	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:30910830C>T	ENST00000279804.2	+	2	157	c.120C>T	c.(118-120)taC>taT	p.Y40Y	CTF1_ENST00000395019.3_Silent_p.Y39Y	NM_001142544.1|NM_001330.3	NP_001136016.1|NP_001321.1	Q16619	CTF1_HUMAN	cardiotrophin 1	40					cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|leukemia inhibitory factor signaling pathway (GO:0048861)|muscle organ development (GO:0007517)|nervous system development (GO:0007399)|neuron development (GO:0048666)|positive regulation of cell proliferation (GO:0008284)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	leukemia inhibitory factor receptor binding (GO:0005146)			large_intestine(1)|urinary_tract(1)	2			Colorectal(24;0.198)			TCACCAAATACGCTGAGCAGC	0.592													C|||	143	0.0285543	0.1051	0.0058	5008	,	,		11807	0.0		0.0	False		,,,				2504	0.0				p.Y40Y		Atlas-SNP	.											.	CTF1	3	.	0			c.C120T						PASS	.	C	,	349,4045	180.5+/-208.7	14,321,1862	67.0	61.0	63.0		117,120	-0.7	1.0	16	dbSNP_116	63	4,8596	2.2+/-6.3	0,4,4296	no	coding-synonymous,coding-synonymous	CTF1	NM_001142544.1,NM_001330.3	,	14,325,6158	TT,TC,CC		0.0465,7.9426,2.7166	,	39/201,40/202	30910830	353,12641	2197	4300	6497	SO:0001819	synonymous_variant	1489	exon2			CAAATACGCTGAG	U43030	CCDS10694.1, CCDS45464.1	16p11.2	2014-09-17			ENSG00000150281	ENSG00000150281			2499	protein-coding gene	gene with protein product		600435				8833032	Standard	NM_001330		Approved	CT-1, CT1	uc002dzw.3	Q16619	OTTHUMG00000132413	ENST00000279804.2:c.120C>T	16.37:g.30910830C>T		194.0	0.0	0		188.0	83.0	0.441489	NM_001330	A8MVX4|Q5U5Y7	Silent	SNP	ENST00000279804.2	37	CCDS10694.1																																																																																			C|0.965;T|0.035	0.035	strong		0.592	CTF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255550.1	NM_001330	
CLCA4	22802	hgsc.bcm.edu	37	1	87045696	87045696	+	Missense_Mutation	SNP	G	G	C	rs2231604	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:87045696G>C	ENST00000370563.3	+	14	2470	c.2428G>C	c.(2428-2430)Gta>Cta	p.V810L	RP4-651E10.4_ENST00000456587.1_RNA	NM_012128.3	NP_036260.2	Q14CN2	CLCA4_HUMAN	chloride channel accessory 4	810			V -> L (in dbSNP:rs2231604). {ECO:0000269|PubMed:15489334}.		chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(7)|liver(2)|lung(21)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44		Lung NSC(277;0.238)		all cancers(265;0.0202)|Epithelial(280;0.0404)		TGCTCTTCAAGTAAATACTAC	0.333													G|||	275	0.0549121	0.1944	0.0115	5008	,	,		18080	0.005		0.0	False		,,,				2504	0.0051				p.V810L		Atlas-SNP	.											.	CLCA4	131	.	0			c.G2428C						PASS	.	G	LEU/VAL	642,3036		52,538,1249	57.0	51.0	53.0		2428	4.9	0.9	1	dbSNP_98	53	2,8174		0,2,4086	yes	missense	CLCA4	NM_012128.3	32	52,540,5335	CC,CG,GG		0.0245,17.4551,5.4328	probably-damaging	810/920	87045696	644,11210	1839	4088	5927	SO:0001583	missense	22802	exon14			CTTCAAGTAAATA	AF127035	CCDS41355.1	1p31-p22	2012-02-26	2009-01-29		ENSG00000016602	ENSG00000016602			2018	protein-coding gene	gene with protein product			"""chloride channel, calcium activated, family member 4"", ""chloride channel regulator 4"""			10437792	Standard	NM_012128		Approved	CaCC2	uc009wcs.3	Q14CN2	OTTHUMG00000010260	ENST00000370563.3:c.2428G>C	1.37:g.87045696G>C	ENSP00000359594:p.Val810Leu	110.0	0.0	0		149.0	59.0	0.395973	NM_012128	A8MQC9|B7Z1Q5|Q6UX81|Q9UNF7	Missense_Mutation	SNP	ENST00000370563.3	37	CCDS41355.1	109	0.04990842490842491	102	0.2073170731707317	5	0.013812154696132596	2	0.0034965034965034965	0	0.0	G	14.30	2.494809	0.44352	0.174551	2.45E-4	ENSG00000016602	ENST00000370563	T	0.03717	3.83	5.82	4.91	0.64330	.	0.000000	0.64402	D	0.000001	T	0.04048	0.0113	M	0.80847	2.515	0.09310	P	1.0	P;P	0.47350	0.894;0.894	P;P	0.45071	0.468;0.468	T	0.25398	-1.0133	9	0.44086	T	0.13	-20.4313	10.9104	0.47106	0.071:0.1305:0.7984:0.0	rs2231604;rs52796222;rs2231604	362;810	Q9NXP1;Q14CN2	.;CLCA4_HUMAN	L	810	ENSP00000359594:V810L	ENSP00000359594:V810L	V	+	1	0	CLCA4	86818284	0.999000	0.42202	0.888000	0.34837	0.308000	0.27856	2.265000	0.43311	1.477000	0.48234	-0.237000	0.12165	GTA	G|0.950;C|0.050	0.050	strong		0.333	CLCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028292.1	NM_012128	
PSG6	5675	hgsc.bcm.edu	37	19	43414875	43414875	+	Missense_Mutation	SNP	A	A	C	rs59587483	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43414875A>C	ENST00000292125.2	-	3	607	c.563T>G	c.(562-564)aTg>aGg	p.M188R	PSG6_ENST00000187910.2_Missense_Mutation_p.M188R|PSG6_ENST00000402603.4_Missense_Mutation_p.M188R	NM_002782.4	NP_002773.1	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6	188	Ig-like C2-type 1.		M -> R (in dbSNP:rs59587483).		female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(19)|ovary(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	44		Prostate(69;0.00899)				CCTGTGAGTCATAGGGAGGTT	0.488																																					p.M188R		Atlas-SNP	.											.	PSG6	89	.	0			c.T563G						PASS	.	G	ARG/MET,ARG/MET	490,3912		33,424,1744	229.0	231.0	230.0		563,563	-3.3	0.0	19	dbSNP_129	230	4,8596		0,4,4296	yes	missense,missense	PSG6	NM_001031850.2,NM_002782.3	91,91	33,428,6040	CC,CA,AA		0.0465,11.1313,3.7994	,	188/425,188/436	43414875	494,12508	2201	4300	6501	SO:0001583	missense	5675	exon3			TGAGTCATAGGGA		CCDS12613.1, CCDS33038.1	19q13.2	2013-01-29			ENSG00000170848	ENSG00000170848		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9523	protein-coding gene	gene with protein product		176395				1690992	Standard	NM_002782		Approved			Q00889	OTTHUMG00000151127	ENST00000292125.2:c.563T>G	19.37:g.43414875A>C	ENSP00000292125:p.Met188Arg	278.0	0.0	0		294.0	133.0	0.452381	NM_001031850	O75244|Q15224|Q15235|Q549K1	Missense_Mutation	SNP	ENST00000292125.2	37	CCDS12613.1	74	0.03388278388278388	67	0.13617886178861788	5	0.013812154696132596	2	0.0034965034965034965	0	0.0	N	0.033	-1.323644	0.01309	0.111313	4.65E-4	ENSG00000170848	ENST00000187910;ENST00000402603;ENST00000292125;ENST00000402456	T;T;T	0.00705	5.81;5.81;5.81	1.64	-3.28	0.05033	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00012	0.0000	L	0.29908	0.895	0.80722	P	0.0	B;B;B	0.30973	0.018;0.074;0.302	B;B;B	0.28709	0.048;0.056;0.093	T	0.42361	-0.9456	8	0.51188	T	0.08	.	2.1928	0.03904	0.4901:0.193:0.0:0.3168	rs59587483	188;188;188	Q00889;Q00889-2;B5MCE1	PSG6_HUMAN;.;.	R	188	ENSP00000187910:M188R;ENSP00000385736:M188R;ENSP00000292125:M188R	ENSP00000187910:M188R	M	-	2	0	PSG6	48106715	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.991000	0.00318	-0.913000	0.03832	-1.229000	0.01577	ATG	A|0.960;C|0.040	0.040	strong		0.488	PSG6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321436.1	NM_002782	
SH2D4A	63898	hgsc.bcm.edu	37	8	19221784	19221784	+	Missense_Mutation	SNP	A	A	G	rs35319139	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:19221784A>G	ENST00000265807.3	+	7	1319	c.908A>G	c.(907-909)aAa>aGa	p.K303R	SH2D4A_ENST00000518040.1_Missense_Mutation_p.K258R|SH2D4A_ENST00000519207.1_Missense_Mutation_p.K303R	NM_001174160.1|NM_022071.3	NP_001167631.1|NP_071354.2	Q9H788	SH24A_HUMAN	SH2 domain containing 4A	303					negative regulation of phosphatase activity (GO:0010923)	cytoplasm (GO:0005737)	phosphatase binding (GO:0019902)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|stomach(1)	16				Colorectal(111;0.0732)		TATCCTCAAAAACCTCTTAGG	0.473													A|||	113	0.0225639	0.0825	0.0043	5008	,	,		16415	0.0		0.001	False		,,,				2504	0.0				p.K303R		Atlas-SNP	.											.	SH2D4A	49	.	0			c.A908G						PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS	338,4068	177.6+/-206.5	7,324,1872	52.0	50.0	51.0		908,773,908	2.1	0.0	8	dbSNP_126	51	0,8600		0,0,4300	yes	missense,missense,missense	SH2D4A	NM_001174159.1,NM_001174160.1,NM_022071.3	26,26,26	7,324,6172	GG,GA,AA		0.0,7.6714,2.5988	benign,benign,benign	303/455,258/410,303/455	19221784	338,12668	2203	4300	6503	SO:0001583	missense	63898	exon7			CTCAAAAACCTCT	AY190323	CCDS6009.1, CCDS55206.1	8p21	2013-02-14			ENSG00000104611	ENSG00000104611		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""SH2 domain containing"""	26102	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 38"""	614968					Standard	NM_022071		Approved	FLJ20967, SH2A, PPP1R38	uc003wzc.3	Q9H788	OTTHUMG00000097005	ENST00000265807.3:c.908A>G	8.37:g.19221784A>G	ENSP00000265807:p.Lys303Arg	89.0	0.0	0		67.0	32.0	0.477612	NM_022071	B4DDR1|Q5XKC1|Q6NXE9|Q86YM2|Q96C88|Q9H7F7	Missense_Mutation	SNP	ENST00000265807.3	37	CCDS6009.1	36	0.016483516483516484	34	0.06910569105691057	2	0.0055248618784530384	0	0.0	0	0.0	A	6.884	0.532610	0.13127	0.076714	0.0	ENSG00000104611	ENST00000265807;ENST00000518040;ENST00000519207	T;T;T	0.12672	2.66;2.66;2.66	5.75	2.12	0.27331	.	0.818608	0.11013	N	0.609227	T	0.00300	0.0009	N	0.04203	-0.255	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.45440	-0.9261	10	0.11794	T	0.64	.	4.2604	0.10739	0.6516:0.1741:0.1743:0.0	rs35319139	258;303	B4DDR1;Q9H788	.;SH24A_HUMAN	R	303;258;303	ENSP00000265807:K303R;ENSP00000429482:K258R;ENSP00000428684:K303R	ENSP00000265807:K303R	K	+	2	0	SH2D4A	19266064	0.000000	0.05858	0.000000	0.03702	0.779000	0.44077	0.275000	0.18698	0.443000	0.26582	0.460000	0.39030	AAA	A|0.973;G|0.027	0.027	strong		0.473	SH2D4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214094.1	NM_022071	
SLC47A2	146802	hgsc.bcm.edu	37	17	19607432	19607432	+	Silent	SNP	C	C	T	rs34169093	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:19607432C>T	ENST00000325411.5	-	11	1127	c.1077G>A	c.(1075-1077)gcG>gcA	p.A359A	SLC47A2_ENST00000350657.5_Silent_p.A337A|SLC47A2_ENST00000463318.1_5'UTR	NM_152908.3	NP_690872.2	Q86VL8	S47A2_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 2	359					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antiporter activity (GO:0015297)|drug transmembrane transporter activity (GO:0015238)			endometrium(2)|kidney(3)|large_intestine(2)|lung(1)|ovary(1)	9	all_cancers(12;2.3e-05)|all_epithelial(12;0.0024)|Breast(13;0.245)				Aciclovir(DB00787)	GCACAGTATCCGCAGCCCCCA	0.617													C|||	311	0.0621006	0.1831	0.0187	5008	,	,		18054	0.0		0.0268	False		,,,				2504	0.0297				p.A359A		Atlas-SNP	.											.	SLC47A2	61	.	0			c.G1077A						PASS	.	C	,	663,3743	278.7+/-274.4	51,561,1591	50.0	49.0	50.0		969,1077	-0.3	0.0	17	dbSNP_126	50	237,8363	94.7+/-156.6	2,233,4065	no	coding-synonymous,coding-synonymous	SLC47A2	NM_001099646.1,NM_152908.3	,	53,794,5656	TT,TC,CC		2.7558,15.0477,6.9199	,	323/567,359/603	19607432	900,12106	2203	4300	6503	SO:0001819	synonymous_variant	146802	exon11			AGTATCCGCAGCC	AB250364	CCDS11211.1, CCDS58530.1	17p11.2	2013-07-17	2013-07-17		ENSG00000180638	ENSG00000180638		"""Solute carriers"""	26439	protein-coding gene	gene with protein product	"""multidrug and toxin extrusion 2"""	609833				16996621, 16807400	Standard	NM_152908		Approved	FLJ31196, MATE2, MATE2-K	uc002gwf.4	Q86VL8	OTTHUMG00000059464	ENST00000325411.5:c.1077G>A	17.37:g.19607432C>T		45.0	0.0	0		39.0	20.0	0.512821	NM_152908	A0JBX9|A0P8Z7|Q63HJ9|Q8IV44|Q96NA1	Silent	SNP	ENST00000325411.5	37	CCDS11211.1																																																																																			C|0.935;T|0.065	0.065	strong		0.617	SLC47A2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132242.2	NM_152908	
ENAM	10117	hgsc.bcm.edu	37	4	71508869	71508869	+	Missense_Mutation	SNP	T	T	C	rs2609428	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:71508869T>C	ENST00000396073.3	+	9	2007	c.1726T>C	c.(1726-1728)Ttt>Ctt	p.F576L	ENAM_ENST00000472903.1_Intron	NM_031889.2	NP_114095.2	Q9NRM1	ENAM_HUMAN	enamelin	576			F -> L (in dbSNP:rs2609428).		amelogenesis (GO:0097186)|biomineral tissue development (GO:0031214)	proteinaceous extracellular matrix (GO:0005578)				haematopoietic_and_lymphoid_tissue(1)|ovary(3)|upper_aerodigestive_tract(2)	6			Lung(101;0.235)			CTCTCCACCTTTTAAGGAAGA	0.443													T|||	197	0.0393371	0.1346	0.0144	5008	,	,		20189	0.0		0.0089	False		,,,				2504	0.0				p.F576L		Atlas-SNP	.											.	ENAM	140	.	0			c.T1726C						PASS	.	T	LEU/PHE	528,3878	231.7+/-245.5	27,474,1702	161.0	168.0	166.0		1726	3.5	0.9	4	dbSNP_100	166	29,8571	18.5+/-59.3	0,29,4271	yes	missense	ENAM	NM_031889.2	22	27,503,5973	CC,CT,TT		0.3372,11.9837,4.2826	benign	576/1143	71508869	557,12449	2203	4300	6503	SO:0001583	missense	10117	exon9			CCACCTTTTAAGG	AF125373	CCDS3544.2	4q13.3	2008-02-05			ENSG00000132464	ENSG00000132464			3344	protein-coding gene	gene with protein product		606585	"""amelogenesis imperfecta 2, hypocalcification (autosomal dominant)"""	AIH2		11978766	Standard	NM_031889		Approved		uc011caw.1	Q9NRM1	OTTHUMG00000129914	ENST00000396073.3:c.1726T>C	4.37:g.71508869T>C	ENSP00000379383:p.Phe576Leu	125.0	0.0	0		137.0	62.0	0.452555	NM_031889	Q17RI5|Q9H3D1	Missense_Mutation	SNP	ENST00000396073.3	37	CCDS3544.2	80	0.03663003663003663	72	0.14634146341463414	5	0.013812154696132596	0	0.0	3	0.00395778364116095	T	12.85	2.062285	0.36373	0.119837	0.003372	ENSG00000132464	ENST00000396073	T	0.40756	1.02	5.83	3.45	0.39498	.	0.216214	0.33438	N	0.004920	T	0.00109	0.0003	N	0.20574	0.59	0.41757	P	0.010307999999999984	B	0.23735	0.09	B	0.26969	0.075	T	0.14008	-1.0488	9	0.05620	T	0.96	-5.2885	6.2822	0.21013	0.0:0.1986:0.0:0.8014	rs2609428;rs2609428	576	Q9NRM1	ENAM_HUMAN	L	576	ENSP00000379383:F576L	ENSP00000379383:F576L	F	+	1	0	ENAM	71727733	0.757000	0.28394	0.948000	0.38648	0.909000	0.53808	0.881000	0.28173	1.034000	0.39945	0.533000	0.62120	TTT	T|0.952;C|0.048	0.048	strong		0.443	ENAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252166.3	NM_031889	
MAML3	55534	hgsc.bcm.edu	37	4	140811114	140811114	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:140811114C>T	ENST00000509479.2	-	2	2332	c.1476G>A	c.(1474-1476)caG>caA	p.Q492Q	MAML3_ENST00000398940.1_Silent_p.Q31Q|MAML3_ENST00000327122.5_Silent_p.Q336Q	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					gctgctgctgctgctgctgtt	0.542																																					p.Q492Q		Atlas-SNP	.											MAML3_ENST00000509479,colon,carcinoma,0,4	MAML3	192	4	0			c.G1476A						scavenged	.						15.0	19.0	18.0					4																	140811114		2185	4284	6469	SO:0001819	synonymous_variant	55534	exon2			CTGCTGCTGCTGC	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"""mastermind (drosophila)-like 3"""	608991	"""trinucleotide repeat containing 3"""	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.1476G>A	4.37:g.140811114C>T		87.0	1.0	0.0114943		98.0	6.0	0.0612245	NM_018717		Silent	SNP	ENST00000509479.2	37	CCDS54805.1																																																																																			.	.	none		0.542	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2		
HOMEZ	57594	hgsc.bcm.edu	37	14	23744826	23744826	+	Missense_Mutation	SNP	T	T	A	rs35076736|rs76331664|rs67447855	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:23744826T>A	ENST00000357460.5	-	2	1775	c.1611A>T	c.(1609-1611)gaA>gaT	p.E537D	HOMEZ_ENST00000431326.2_Missense_Mutation_p.E539D|HOMEZ_ENST00000561013.1_Missense_Mutation_p.E539D	NM_020834.2	NP_065885.2	Q8IX15	HOMEZ_HUMAN	homeobox and leucine zipper encoding	537	Poly-Asp.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(5)|lung(7)	12	all_cancers(95;5.54e-06)			GBM - Glioblastoma multiforme(265;0.00643)		catcatcatcttcctcctcct	0.483																																					p.E537D		Atlas-SNP	.											.	HOMEZ	80	.	0			c.A1611T						PASS	.						39.0	39.0	39.0					14																	23744826		2192	4262	6454	SO:0001583	missense	57594	exon2			ATCATCTTCCTCC	AB037864	CCDS45085.1	14q11.2	2011-06-20	2007-02-15	2007-02-15		ENSG00000215271		"""Homeoboxes / ZF class"""	20164	protein-coding gene	gene with protein product		608119	"""KIAA1443"""	KIAA1443		12925734	Standard	NM_020834		Approved		uc001wja.2	Q8IX15		ENST00000357460.5:c.1611A>T	14.37:g.23744826T>A	ENSP00000350049:p.Glu537Asp	159.0	0.0	0		135.0	15.0	0.111111	NM_020834	A1L445|B4DZ80|F8WCA3|Q6P049|Q86XB6|Q9P2A5	Missense_Mutation	SNP	ENST00000357460.5	37	CCDS45085.1	.	.	.	.	.	.	.	.	.	.	T	0.034	-1.315721	0.01331	.	.	ENSG00000215271	ENST00000357460;ENST00000431326	T;T	0.63744	-0.06;-0.06	.	.	.	Armadillo-like helical (1);	.	.	.	.	T	0.45478	0.1344	N	0.08118	0	0.09310	N	1	B;B	0.32829	0.386;0.267	B;B	0.42462	0.388;0.217	T	0.47812	-0.9088	7	0.87932	D	0	.	.	.	.	.	539;537	F8WCA3;Q8IX15	.;HOMEZ_HUMAN	D	537;539	ENSP00000350049:E537D;ENSP00000406579:E539D	ENSP00000350049:E537D	E	-	3	2	HOMEZ	22814666	0.017000	0.18338	0.112000	0.21494	0.037000	0.13140	-2.594000	0.00896	0.319000	0.23209	0.314000	0.21332	GAA	.	.	weak		0.483	HOMEZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000416939.2	NM_020834	
PROSER2	254427	hgsc.bcm.edu	37	10	11912381	11912381	+	Silent	SNP	G	G	A	rs191542752	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:11912381G>A	ENST00000277570.5	+	4	1438	c.1284G>A	c.(1282-1284)ctG>ctA	p.L428L	PROSER2-AS1_ENST00000453242.1_RNA|PROSER2_ENST00000379200.1_Silent_p.L232L|PROSER2-AS1_ENST00000445498.1_RNA	NM_153256.3	NP_694988.3	Q86WR7	PRSR2_HUMAN	proline and serine rich 2	428																	TGCGGAAGCTGGGGCTGCTCA	0.726													G|||	45	0.00898562	0.031	0.0058	5008	,	,		11702	0.0		0.0	False		,,,				2504	0.0				p.L428L		Atlas-SNP	.											.	.	.	.	0			c.G1284A						PASS	.	G		34,2126		0,34,1046	1.0	1.0	1.0		1284	-10.4	0.7	10		1	1,4447		0,1,2223	no	coding-synonymous	C10orf47	NM_153256.3		0,35,3269	AA,AG,GG		0.0225,1.5741,0.5297		428/436	11912381	35,6573	1080	2224	3304	SO:0001819	synonymous_variant	254427	exon4			GAAGCTGGGGCTG	BC017269	CCDS7085.1	10p14	2014-02-19	2014-02-19	2012-12-05	ENSG00000148426	ENSG00000148426			23728	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 47"", ""proline and serine-rich protein 2"""	C10orf47		12477932	Standard	NM_153256		Approved	MGC35403	uc001ikx.3	Q86WR7	OTTHUMG00000017673	ENST00000277570.5:c.1284G>A	10.37:g.11912381G>A		20.0	0.0	0		19.0	10.0	0.526316	NM_153256	D3DRR8|Q5W0J9|Q5W0K0|Q5W0K1|Q5W0K2|Q6PJC8|Q8N317	Silent	SNP	ENST00000277570.5	37	CCDS7085.1																																																																																			G|0.993;A|0.007	0.007	strong		0.726	PROSER2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090189.2	NM_153256	
AQP7	364	hgsc.bcm.edu	37	9	33385134	33385134	+	3'UTR	SNP	C	C	T	rs61073250	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:33385134C>T	ENST00000537089.1	-	0	1298				AQP7_ENST00000377425.4_3'UTR			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)			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)		TTGGGCAATACGGTTATCCCG	0.562													c|||	234	0.0467252	0.1732	0.0072	5008	,	,		18995	0.0		0.0	False		,,,				2504	0.0				p.V300I		Atlas-SNP	.											.	AQP7	58	.	0			c.G898A						PASS	.	C	ILE/VAL	519,3887	236.1+/-248.4	25,469,1709	142.0	140.0	141.0		898	0.9	0.0	9	dbSNP_129	141	8,8592	6.4+/-24.3	0,8,4292	no	missense	AQP7	NM_001170.1	29	25,477,6001	TT,TC,CC		0.093,11.7794,4.052	benign	300/343	33385134	527,12479	2203	4300	6503	SO:0001624	3_prime_UTR_variant	364	exon8			GCAATACGGTTAT	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.*482G>A	9.37:g.33385134C>T		113.0	0.0	0		150.0	87.0	0.58	NM_001170	Q08E94|Q5T5L9|Q8NHM3	Missense_Mutation	SNP	ENST00000537089.1	37		76	0.0347985347985348	73	0.1483739837398374	3	0.008287292817679558	0	0.0	0	0.0	c	10.83	1.461549	0.26248	0.117794	9.3E-4	ENSG00000165269	ENST00000379507;ENST00000297988	D;D	0.86164	-2.07;-2.08	3.75	0.85	0.18980	.	.	.	.	.	T	0.01124	0.0037	L	0.32530	0.975	0.09310	N	1	B	0.26602	0.154	B	0.17098	0.017	T	0.04128	-1.0975	9	0.39692	T	0.17	0.5079	3.07	0.06227	0.2121:0.5537:0.0:0.2342	rs61073250	300	O14520	AQP7_HUMAN	I	299;300	ENSP00000368821:V299I;ENSP00000297988:V300I	ENSP00000297988:V300I	V	-	1	0	AQP7	33375134	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.123000	0.10611	-0.001000	0.14495	-0.354000	0.07668	GTA	C|0.964;T|0.036	0.036	strong		0.562	AQP7-202	KNOWN	basic	protein_coding	protein_coding		NM_001170	
BCAR3	8412	hgsc.bcm.edu	37	1	94049576	94049576	+	Splice_Site	SNP	A	A	G	rs78645541	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:94049576A>G	ENST00000370244.1	-	8	1320	c.1032T>C	c.(1030-1032)atT>atC	p.I344I	BCAR3_ENST00000539242.1_Splice_Site_p.I20I|BCAR3_ENST00000370247.3_Splice_Site_p.I253I|BCAR3_ENST00000466632.1_5'UTR|BCAR3_ENST00000370243.1_Splice_Site_p.I344I|BCAR3_ENST00000260502.6_Splice_Site_p.I344I	NM_001261408.1	NP_001248337.1	O75815	BCAR3_HUMAN	breast cancer anti-estrogen resistance 3	344					lens morphogenesis in camera-type eye (GO:0002089)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)		guanyl-nucleotide exchange factor activity (GO:0005085)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)	25		all_lung(203;0.00145)|Lung NSC(277;0.00662)		all cancers(265;0.0126)|GBM - Glioblastoma multiforme(16;0.0467)|Epithelial(280;0.166)		GAAACATACCAATCGGCAGGT	0.522													A|||	34	0.00678914	0.025	0.0014	5008	,	,		18298	0.0		0.0	False		,,,				2504	0.0				p.I344I		Atlas-SNP	.											.	BCAR3	62	.	0			c.T1032C						PASS	.	A		122,4284	91.6+/-130.3	1,120,2082	95.0	93.0	93.0		1032	0.0	0.9	1	dbSNP_131	93	0,8600		0,0,4300	yes	coding-synonymous-near-splice	BCAR3	NM_003567.2		1,120,6382	GG,GA,AA		0.0,2.769,0.938		344/826	94049576	122,12884	2203	4300	6503	SO:0001630	splice_region_variant	8412	exon6			CATACCAATCGGC	U92715	CCDS745.1, CCDS58010.1	1p22.1	2013-02-14			ENSG00000137936	ENSG00000137936		"""SH2 domain containing"""	973	protein-coding gene	gene with protein product		604704				9582273	Standard	NM_001261408		Approved	NSP2, SH2D3B	uc001dpz.4	O75815	OTTHUMG00000010301	ENST00000370244.1:c.1033+1T>C	1.37:g.94049576A>G		144.0	0.0	0		146.0	81.0	0.554795	NM_001261409	D3DT43|Q5TEW3|Q6UW40|Q9BR50	Silent	SNP	ENST00000370244.1	37	CCDS745.1																																																																																			A|0.992;G|0.008	0.008	strong		0.522	BCAR3-003	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028420.1		Silent
FMO2	2327	hgsc.bcm.edu	37	1	171162583	171162583	+	Missense_Mutation	SNP	T	T	C	rs2020860	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:171162583T>C	ENST00000209929.7	+	3	400	c.242T>C	c.(241-243)tTc>tCc	p.F81S	FMO2_ENST00000529935.1_3'UTR|FMO2_ENST00000441535.1_Missense_Mutation_p.F81S			P31512	FMO4_HUMAN	flavin containing monooxygenase 2 (non-functional)	81					drug catabolic process (GO:0042737)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|prostate(1)|skin(2)|stomach(3)|urinary_tract(1)	22	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					TTTCCAAACTTCCTGCATAAT	0.353													T|||	516	0.103035	0.298	0.0476	5008	,	,		16096	0.002		0.0447	False		,,,				2504	0.0429				p.F81S		Atlas-SNP	.											FMO2,colon,carcinoma,+1,1	FMO2	66	1	0			c.T242C						PASS	.	T	SER/PHE	1075,3331	373.0+/-320.6	151,773,1279	75.0	76.0	75.0		242	5.4	1.0	1	dbSNP_98	75	409,8191	123.1+/-182.0	13,383,3904	yes	missense	FMO2	NM_001460.2	155	164,1156,5183	CC,CT,TT		4.7558,24.3985,11.4101	probably-damaging	81/472	171162583	1484,11522	2203	4300	6503	SO:0001583	missense	2327	exon3			CAAACTTCCTGCA	BC005894	CCDS1293.1	1q24.3	2011-08-04	2006-07-17		ENSG00000094963	ENSG00000094963			3770	protein-coding gene	gene with protein product		603955	"""flavin containing monooxygenase 2"""			1417778, 9804831	Standard	XR_426768		Approved		uc001ghk.1	Q99518	OTTHUMG00000035504	ENST00000209929.7:c.242T>C	1.37:g.171162583T>C	ENSP00000209929:p.Phe81Ser	66.0	0.0	0		55.0	24.0	0.436364	NM_001460	Q53XR0	Missense_Mutation	SNP	ENST00000209929.7	37	CCDS1293.1	205	0.09386446886446886	156	0.3170731707317073	18	0.049723756906077346	0	0.0	31	0.040897097625329816	T	22.7	4.324261	0.81580	0.243985	0.047558	ENSG00000094963	ENST00000209929;ENST00000441535	T;T	0.60920	0.15;0.15	5.44	5.44	0.79542	.	0.172296	0.53938	D	0.000041	T	0.81754	0.4889	H	0.97265	3.97	0.23834	P	0.99671674	D	0.76494	0.999	D	0.78314	0.991	D	0.88765	0.3260	9	0.87932	D	0	-14.2724	15.165	0.72818	0.0:0.0:0.0:1.0	rs2020860;rs2266704;rs56518508;rs57046818;rs2020860	81	Q99518	FMO2_HUMAN	S	81	ENSP00000209929:F81S;ENSP00000405905:F81S	ENSP00000209929:F81S	F	+	2	0	FMO2	169429207	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	2.960000	0.49161	2.062000	0.61559	0.533000	0.62120	TTC	T|0.895;C|0.105	0.105	strong		0.353	FMO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086216.2	NM_001460	
XPR1	9213	hgsc.bcm.edu	37	1	180804033	180804033	+	Silent	SNP	C	C	T	rs61742073	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:180804033C>T	ENST00000367590.4	+	10	1356	c.1158C>T	c.(1156-1158)ttC>ttT	p.F386F	XPR1_ENST00000367589.3_Silent_p.F386F	NM_004736.3	NP_004727.2	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor 1	386					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)			breast(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	35						CAGCCCCCTTCCATAAGGTAG	0.403													C|||	258	0.0515176	0.1808	0.0259	5008	,	,		19539	0.0		0.001	False		,,,				2504	0.0				p.F386F		Atlas-SNP	.											.	XPR1	76	.	0			c.C1158T						PASS	.	C	,	636,3770	267.1+/-267.6	45,546,1612	64.0	65.0	64.0		1158,1158	4.3	1.0	1	dbSNP_129	64	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous	XPR1	NM_001135669.1,NM_004736.3	,	45,550,5908	TT,TC,CC		0.0465,14.4349,4.9208	,	386/632,386/697	180804033	640,12366	2203	4300	6503	SO:0001819	synonymous_variant	9213	exon10			CCCCTTCCATAAG	AF099082	CCDS1340.1, CCDS44284.1	1q25.1	2013-07-18	2010-04-23		ENSG00000143324	ENSG00000143324			12827	protein-coding gene	gene with protein product		605237	"""xenotropic and polytropic retrovirus receptor"""			9990033	Standard	NM_004736		Approved	SYG1, X3	uc001goi.3	Q9UBH6	OTTHUMG00000035116	ENST00000367590.4:c.1158C>T	1.37:g.180804033C>T		71.0	0.0	0		67.0	30.0	0.447761	NM_004736	O95719|Q7L8K9|Q8IW20|Q9NT19|Q9UFB9	Silent	SNP	ENST00000367590.4	37	CCDS1340.1																																																																																			C|0.949;T|0.051	0.051	strong		0.403	XPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084996.2	NM_004736	
RBP1	5947	hgsc.bcm.edu	37	3	139257727	139257727	+	Missense_Mutation	SNP	T	T	C	rs34674353	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:139257727T>C	ENST00000483943.2	-	2	334	c.334A>G	c.(334-336)Atg>Gtg	p.M112V	RBP1_ENST00000492918.1_Missense_Mutation_p.M112V|RP11-319G6.1_ENST00000381790.3_RNA|RBP1_ENST00000232219.2_Missense_Mutation_p.M112V|RP11-319G6.1_ENST00000515247.1_RNA	NM_001130993.1	NP_001124465.1	P09455	RET1_HUMAN	retinol binding protein 1, cellular	50					phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|vitamin A metabolic process (GO:0006776)	cytosol (GO:0005829)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			endometrium(1)|large_intestine(2)|lung(1)|prostate(1)	5					Acitretin(DB00459)|Vitamin A(DB00162)	CGGATGATCATATGGTCACCG	0.532													T|||	48	0.00958466	0.034	0.0043	5008	,	,		19972	0.0		0.0	False		,,,				2504	0.0				p.M112V		Atlas-SNP	.											.	RBP1	39	.	0			c.A334G						PASS	.	T	VAL/MET,VAL/MET,VAL/MET	98,4308	79.3+/-117.8	0,98,2105	242.0	194.0	210.0		334,334,334	5.3	1.0	3	dbSNP_126	210	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense	RBP1	NM_002899.3,NM_001130993.1,NM_001130992.1	21,21,21	0,100,6403	CC,CT,TT		0.0233,2.2242,0.7689	benign,benign,benign	112/198,112/154,112/158	139257727	100,12906	2203	4300	6503	SO:0001583	missense	5947	exon2			TGATCATATGGTC		CCDS3110.2, CCDS46925.1, CCDS46926.1	3q21-q23	2013-03-01	2001-11-28		ENSG00000114115	ENSG00000114115		"""Fatty acid binding protein family"""	9919	protein-coding gene	gene with protein product		180260	"""retinol-binding protein 1, cellular"""			1654334, 9858824	Standard	NM_002899		Approved	CRABP-I, CRBP1, CRBP, RBPC, CRBPI	uc003eti.2	P09455	OTTHUMG00000155751	ENST00000483943.2:c.334A>G	3.37:g.139257727T>C	ENSP00000424813:p.Met112Val	260.0	0.0	0		274.0	141.0	0.514599	NM_002899	A8K2Q0|B7Z7A0|E7EWV0|F2Z2F2|Q6FGX8	Missense_Mutation	SNP	ENST00000483943.2	37	CCDS46925.1	13	0.005952380952380952	11	0.022357723577235773	2	0.0055248618784530384	0	0.0	0	0.0	T	14.91	2.676656	0.47886	0.022242	2.33E-4	ENSG00000114115	ENST00000232219;ENST00000483943;ENST00000492918	T;T;T	0.21031	2.03;2.03;2.03	5.28	5.28	0.74379	Calycin-like (1);Lipocalin/cytosolic fatty-acid binding protein domain (1);Calycin (1);	0.057277	0.64402	D	0.000002	T	0.12050	0.0293	L	0.33485	1.01	0.45979	D	0.998796	P;P;B	0.37548	0.599;0.543;0.04	P;B;B	0.45167	0.472;0.243;0.072	T	0.02484	-1.1152	10	0.28530	T	0.3	.	14.3982	0.67025	0.0:0.0:0.0:1.0	rs34674353	112;112;50	F2Z2F2;E7EWV0;P09455	.;.;RET1_HUMAN	V	112	ENSP00000232219:M112V;ENSP00000424813:M112V;ENSP00000429166:M112V	ENSP00000232219:M112V	M	-	1	0	RBP1	140740417	1.000000	0.71417	0.999000	0.59377	0.834000	0.47266	4.774000	0.62339	1.988000	0.58038	0.455000	0.32223	ATG	T|0.992;C|0.008	0.008	strong		0.532	RBP1-003	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000341497.2	NM_002899	
MTERF4	130916	hgsc.bcm.edu	37	2	242036769	242036769	+	Silent	SNP	G	G	A	rs10171090	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242036769G>A	ENST00000391980.2	-	3	652	c.594C>T	c.(592-594)gtC>gtT	p.V198V	MTERFD2_ENST00000464344.2_Intron|MTERFD2_ENST00000495694.1_Intron|MTERFD2_ENST00000406593.1_Silent_p.V10V|MTERFD2_ENST00000407095.3_Silent_p.V198V	NM_182501.3	NP_872307.2	Q7Z6M4	MTEF4_HUMAN		198					rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)	rRNA binding (GO:0019843)			endometrium(3)|large_intestine(6)|lung(5)|ovary(1)|skin(2)|urinary_tract(3)	20		all_cancers(19;4.67e-31)|all_epithelial(40;8.67e-13)|Breast(86;0.000141)|Renal(207;0.00528)|Ovarian(221;0.104)|Esophageal squamous(248;0.131)|all_lung(227;0.17)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;2.47e-32)|all cancers(36;1.79e-29)|OV - Ovarian serous cystadenocarcinoma(60;2.59e-14)|Kidney(56;3.21e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;2.81e-06)|Lung(119;0.000509)|LUSC - Lung squamous cell carcinoma(224;0.00442)|Colorectal(34;0.0129)|COAD - Colon adenocarcinoma(134;0.0886)		TGAGAAGCCTGACAGTGTCGT	0.473													G|||	111	0.0221645	0.0772	0.013	5008	,	,		21463	0.0		0.0	False		,,,				2504	0.0				p.V198V		Atlas-SNP	.											.	MTERFD2	33	.	0			c.C594T						PASS	.	G		262,4144	148.8+/-183.1	9,244,1950	101.0	87.0	92.0		594	-1.5	0.0	2	dbSNP_119	92	0,8600		0,0,4300	no	coding-synonymous	MTERFD2	NM_182501.3		9,244,6250	AA,AG,GG		0.0,5.9464,2.0145		198/382	242036769	262,12744	2203	4300	6503	SO:0001819	synonymous_variant	130916	exon3			AAGCCTGACAGTG																												ENST00000391980.2:c.594C>T	2.37:g.242036769G>A		129.0	0.0	0		118.0	52.0	0.440678	NM_182501	A8K6K0|Q9P0E0	Silent	SNP	ENST00000391980.2	37	CCDS2544.1																																																																																			G|0.978;A|0.022	0.022	strong		0.473	MTERFD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323798.4		
GBA	2629	hgsc.bcm.edu	37	1	155210498	155210498	+	Missense_Mutation	SNP	T	T	C	rs150466109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:155210498T>C	ENST00000327247.5	-	3	270	c.38A>G	c.(37-39)aAg>aGg	p.K13R	GBA_ENST00000368373.3_Missense_Mutation_p.K13R|GBA_ENST00000428024.3_Intron|GBA_ENST00000427500.3_Missense_Mutation_p.K13R|GBA_ENST00000493842.1_5'UTR|GBA_ENST00000536770.1_Missense_Mutation_p.K13R	NM_001005741.2|NM_001005742.2	NP_001005741.1|NP_001005742.1	P04062	GLCM_HUMAN	glucosidase, beta, acid	13					carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|cellular response to tumor necrosis factor (GO:0071356)|ceramide biosynthetic process (GO:0046513)|glucosylceramide catabolic process (GO:0006680)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of MAP kinase activity (GO:0043407)|positive regulation of protein dephosphorylation (GO:0035307)|regulation of water loss via skin (GO:0033561)|response to estrogen (GO:0043627)|response to glucocorticoid (GO:0051384)|response to pH (GO:0009268)|response to testosterone (GO:0033574)|response to thyroid hormone (GO:0097066)|skin morphogenesis (GO:0043589)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingosine biosynthetic process (GO:0046512)|termination of signal transduction (GO:0023021)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)	glucosylceramidase activity (GO:0004348)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(9)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	26	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)		Velaglucerase alfa(DB06720)	ACTCAAAGGCTTGGGACATTC	0.557									Gaucher disease type I				t|||	118	0.0235623	0.084	0.0072	5008	,	,		19504	0.002		0.0	False		,,,				2504	0.0				p.K13R		Atlas-SNP	.											.	GBA	46	.	0			c.A38G	GRCh37	CM065215	GBA	M	rs150466109	PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS,,ARG/LYS	312,4094	166.9+/-198.0	11,290,1902	154.0	142.0	146.0		38,38,38,,38	-0.4	0.0	1	dbSNP_134	146	3,8597	2.2+/-6.3	0,3,4297	no	missense,missense,missense,intron,missense	GBA	NM_000157.3,NM_001005741.2,NM_001005742.2,NM_001171811.1,NM_001171812.1	26,26,26,,26	11,293,6199	CC,CT,TT		0.0349,7.0813,2.422	benign,benign,benign,,benign	13/537,13/537,13/537,,13/488	155210498	315,12691	2203	4300	6503	SO:0001583	missense	2629	exon3	Familial Cancer Database	glucocerebrosidase insufficiency	AAAGGCTTGGGAC	M19285	CCDS1102.1, CCDS53373.1, CCDS53374.1	1q22	2010-01-19	2010-01-19		ENSG00000177628	ENSG00000177628	3.2.1.21		4177	protein-coding gene	gene with protein product		606463	"""glucosylceramidase"", ""glucosidase, beta; acid (includes glucosylceramidase)"""	GLUC		3359914	Standard	NM_001005742		Approved	GBA1	uc001fjl.3	P04062	OTTHUMG00000035841	ENST00000327247.5:c.38A>G	1.37:g.155210498T>C	ENSP00000314508:p.Lys13Arg	53.0	0.0	0		60.0	31.0	0.516667	NM_001005742	A8K796|B7Z5G2|B7Z6S1|J3KQG4|J3KQK9|Q16545|Q4VX22|Q6I9R6|Q9UMJ8	Missense_Mutation	SNP	ENST00000327247.5	37	CCDS1102.1	44	0.020146520146520148	43	0.08739837398373984	1	0.0027624309392265192	0	0.0	0	0.0	T	5.065	0.197635	0.09652	0.070813	3.49E-4	ENSG00000177628	ENST00000427500;ENST00000368373;ENST00000327247;ENST00000536770;ENST00000402928	D;D;D;D	0.99474	-5.59;-5.62;-5.62;-5.97	3.32	-0.397	0.12423	.	1.116300	0.07210	U	0.859048	D	0.90789	0.7108	N	0.03608	-0.345	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	D	0.91133	0.4939	10	0.24483	T	0.36	.	2.0673	0.03605	0.2405:0.2836:0.0:0.4759	.	13;13;13	B7Z5G2;F5H241;P04062	.;.;GLCM_HUMAN	R	13	ENSP00000402577:K13R;ENSP00000357357:K13R;ENSP00000314508:K13R;ENSP00000445560:K13R	ENSP00000314508:K13R	K	-	2	0	GBA	153477122	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.370000	0.07523	0.052000	0.16007	0.482000	0.46254	AAG	T|0.979;C|0.021	0.021	strong		0.557	GBA-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087204.1	NM_000157	
WDR87	83889	hgsc.bcm.edu	37	19	38380501	38380501	+	Silent	SNP	G	G	A	rs143655348	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38380501G>A	ENST00000303868.5	-	6	3917	c.3693C>T	c.(3691-3693)ggC>ggT	p.G1231G	WDR87_ENST00000447313.2_Silent_p.G1270G	NM_031951.3	NP_114157.3	Q6ZQQ6	WDR87_HUMAN	WD repeat domain 87	1231										NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|prostate(1)|skin(3)|stomach(1)	36						TTGACCTGCGGCCAGATATTC	0.468													G|||	23	0.00459265	0.0166	0.0014	5008	,	,		18970	0.0		0.0	False		,,,				2504	0.0				p.G1231G		Atlas-SNP	.											.	WDR87	191	.	0			c.C3693T						PASS	.	G		26,1358		1,24,667	130.0	101.0	110.0		3693	-3.6	0.0	19	dbSNP_134	110	0,3182		0,0,1591	no	coding-synonymous	WDR87	NM_031951.3		1,24,2258	AA,AG,GG		0.0,1.8786,0.5694		1231/2874	38380501	26,4540	692	1591	2283	SO:0001819	synonymous_variant	83889	exon6			CCTGCGGCCAGAT	AK128826	CCDS46063.1, CCDS74356.1	19q13.13	2013-01-09			ENSG00000171804	ENSG00000171804		"""WD repeat domain containing"""	29934	protein-coding gene	gene with protein product							Standard	XM_005259304		Approved	NYD-SP11	uc010efu.2	Q6ZQQ6	OTTHUMG00000048187	ENST00000303868.5:c.3693C>T	19.37:g.38380501G>A		207.0	1.0	0.00483092		195.0	95.0	0.487179	NM_031951	Q9BWV9	Silent	SNP	ENST00000303868.5	37	CCDS46063.1																																																																																			G|0.994;A|0.006	0.006	strong		0.468	WDR87-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314628.2	XM_940478	
TG	7038	hgsc.bcm.edu	37	8	133953676	133953676	+	Missense_Mutation	SNP	A	A	G	rs61744679	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133953676A>G	ENST00000220616.4	+	26	5162	c.5122A>G	c.(5122-5124)Att>Gtt	p.I1708V	TG_ENST00000542445.1_Intron|TG_ENST00000377869.1_Missense_Mutation_p.I1651V	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	1708					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		GTACAACCCCATTGTGTTCTC	0.502													A|||	140	0.0279553	0.1014	0.0086	5008	,	,		22921	0.0		0.0	False		,,,				2504	0.0				p.I1708V		Atlas-SNP	.											.	TG	416	.	0			c.A5122G						PASS	.	A	VAL/ILE	382,4024	193.0+/-218.2	19,344,1840	170.0	143.0	153.0		5122	-0.3	0.0	8	dbSNP_129	153	3,8597	3.0+/-9.4	0,3,4297	yes	missense	TG	NM_003235.4	29	19,347,6137	GG,GA,AA		0.0349,8.67,2.9602	benign	1708/2769	133953676	385,12621	2203	4300	6503	SO:0001583	missense	7038	exon26			AACCCCATTGTGT	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.5122A>G	8.37:g.133953676A>G	ENSP00000220616:p.Ile1708Val	241.0	0.0	0		286.0	144.0	0.503497	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	61	0.027930402930402932	57	0.11585365853658537	4	0.011049723756906077	0	0.0	0	0.0	A	0	-2.653927	0.00109	0.0867	3.49E-4	ENSG00000042832	ENST00000377869;ENST00000543313;ENST00000220616	T;T	0.60548	0.18;0.18	5.81	-0.269	0.12930	.	1.039030	0.07593	N	0.922337	T	0.00210	0.0006	N	0.00268	-1.735	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.12604	-1.0541	10	0.02654	T	1	.	4.2539	0.10708	0.2662:0.0:0.4355:0.2983	rs61744679	1708	P01266	THYG_HUMAN	V	1651;514;1708	ENSP00000367100:I1651V;ENSP00000220616:I1708V	ENSP00000220616:I1708V	I	+	1	0	TG	134022858	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	0.340000	0.19892	0.055000	0.16094	-1.652000	0.00757	ATT	A|0.964;G|0.036	0.036	strong		0.502	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
TMEM44	93109	hgsc.bcm.edu	37	3	194325103	194325103	+	Silent	SNP	G	G	A	rs745169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:194325103G>A	ENST00000392432.2	-	10	1435	c.1230C>T	c.(1228-1230)ccC>ccT	p.P410P	TMEM44_ENST00000473092.1_Silent_p.P363P|TMEM44_ENST00000347147.4_Silent_p.P363P|TMEM44_ENST00000381975.3_Missense_Mutation_p.P362L|TMEM44_ENST00000273580.7_Silent_p.P363P	NM_001166305.1	NP_001159777.1	Q2T9K0	TMM44_HUMAN	transmembrane protein 44	410						integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|urinary_tract(1)	8	all_cancers(143;1.41e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;4.34e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;9.06e-06)		GGTACGACGGGGGGTCCTGCA	0.657													G|||	314	0.0626997	0.2277	0.0101	5008	,	,		15940	0.002		0.001	False		,,,				2504	0.0031				p.P362L		Atlas-SNP	.											.	TMEM44	42	.	0			c.C1085T						PASS	.	G	,,LEU/PRO,	772,3568		78,616,1476	29.0	26.0	27.0		1089,1230,1085,1089	-5.4	0.4	3	dbSNP_86	27	9,8525		0,9,4258	yes	coding-synonymous,coding-synonymous,missense,coding-synonymous	TMEM44	NM_001011655.2,NM_001166305.1,NM_001166306.1,NM_138399.4	,,98,	78,625,5734	AA,AG,GG		0.1055,17.788,6.0665	,,,	363/429,410/476,362/397,363/439	194325103	781,12093	2170	4267	6437	SO:0001819	synonymous_variant	93109	exon9			CGACGGGGGGTCC	AL833026	CCDS3308.1, CCDS33921.1, CCDS3308.2, CCDS54698.1, CCDS54699.1	3q29	2005-08-16			ENSG00000145014	ENSG00000145014			25120	protein-coding gene	gene with protein product							Standard	NM_138399		Approved	DKFZp686O18124	uc010hzn.3	Q2T9K0	OTTHUMG00000156023	ENST00000392432.2:c.1230C>T	3.37:g.194325103G>A		104.0	0.0	0		131.0	65.0	0.496183	NM_001166306	A1L3V7|B7ZLZ5|B7ZLZ6|C9JJ62|E9PGA9|Q0P6F7|Q6ZT47|Q8IXR1|Q8N4G3	Missense_Mutation	SNP	ENST00000392432.2	37	CCDS54699.1	106	0.048534798534798536	102	0.2073170731707317	4	0.011049723756906077	0	0.0	0	0.0	G	11.04	1.523178	0.27211	0.17788	0.001055	ENSG00000145014	ENST00000381975;ENST00000429560	T	0.35789	1.29	5.23	-5.43	0.02632	.	0.095734	0.42964	D	0.000626	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999837588	B;B	0.09022	0.002;0.0	B;B	0.08055	0.003;0.002	T	0.09552	-1.0669	8	0.66056	D	0.02	-23.756	7.3059	0.26447	0.3646:0.466:0.1694:0.0	rs745169;rs745169	94;362	Q6PL43;Q2T9K0-4	.;.	L	362;94	ENSP00000371402:P362L	ENSP00000371402:P362L	P	-	2	0	TMEM44	195806392	0.819000	0.29175	0.431000	0.26735	0.097000	0.18754	-0.564000	0.05936	-1.360000	0.02172	0.447000	0.29281	CCC	G|0.930;A|0.070	0.070	strong		0.657	TMEM44-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000342750.1	NM_138399	
CCBL2	56267	hgsc.bcm.edu	37	1	89453966	89453966	+	Missense_Mutation	SNP	G	G	A	rs74100109	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:89453966G>A	ENST00000260508.4	-	2	405	c.68C>T	c.(67-69)tCt>tTt	p.S23F	CCBL2_ENST00000446900.2_5'UTR|RBMXL1_ENST00000413769.1_5'UTR|RBMXL1_ENST00000399794.2_5'UTR|CCBL2_ENST00000370485.2_Missense_Mutation_p.S23F|CCBL2_ENST00000370491.3_Intron|RBMXL1_ENST00000321792.5_Intron	NM_001008661.2	NP_001008661.1	Q6YP21	KAT3_HUMAN	cysteine conjugate-beta lyase 2	23					2-oxoglutarate metabolic process (GO:0006103)|biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)|cellular nitrogen compound metabolic process (GO:0034641)|kynurenine metabolic process (GO:0070189)|L-kynurenine metabolic process (GO:0097052)|small molecule metabolic process (GO:0044281)|tryptophan catabolic process (GO:0006569)	mitochondrion (GO:0005739)	cysteine-S-conjugate beta-lyase activity (GO:0047804)|kynurenine-glyoxylate transaminase activity (GO:0047315)|kynurenine-oxoglutarate transaminase activity (GO:0016212)|poly(A) RNA binding (GO:0044822)|pyridoxal phosphate binding (GO:0030170)			endometrium(3)|kidney(4)|large_intestine(2)|lung(4)|ovary(2)|skin(2)|soft_tissue(1)	18		Lung NSC(277;0.123)		all cancers(265;0.0117)|Epithelial(280;0.0341)		GATTTTGGAAGAAGAAATTGT	0.348													G|||	45	0.00898562	0.0318	0.0043	5008	,	,		17385	0.0		0.0	False		,,,				2504	0.0				p.S23F		Atlas-SNP	.											.	CCBL2	138	.	0			c.C68T						PASS	.	G	PHE/SER,,,	148,4258	96.2+/-134.9	4,140,2059	58.0	64.0	62.0		68,,,	4.6	1.0	1	dbSNP_130	62	0,8600		0,0,4300	yes	missense,intron,utr-5,intron	CCBL2,RBMXL1	NM_001008661.2,NM_001008662.2,NM_001162536.2,NM_019610.5	155,,,	4,140,6359	AA,AG,GG		0.0,3.3591,1.1379	benign,,,	23/455,,,	89453966	148,12858	2203	4300	6503	SO:0001583	missense	56267	exon2			TTGGAAGAAGAAA	AF091090	CCDS30766.1, CCDS30767.1	1p22.2	2009-06-23			ENSG00000137944	ENSG00000137944			33238	protein-coding gene	gene with protein product		610656				16376499	Standard	NM_001008662		Approved	RBM1, RP11-82K18.3, KAT3	uc001dmp.2	Q6YP21	OTTHUMG00000010617	ENST00000260508.4:c.68C>T	1.37:g.89453966G>A	ENSP00000260508:p.Ser23Phe	266.0	0.0	0		328.0	159.0	0.484756	NM_001008661	B3KQ13|O95335|Q5JS27|Q5T9T7|Q5T9T8|Q6AI27|Q6ICW1|Q9BVY5	Missense_Mutation	SNP	ENST00000260508.4	37	CCDS30766.1	13	0.005952380952380952	11	0.022357723577235773	2	0.0055248618784530384	0	0.0	0	0.0	G	9.181	1.023703	0.19433	0.033591	0.0	ENSG00000137944	ENST00000260508;ENST00000370485;ENST00000370486	T;T	0.72725	-0.68;-0.52	5.5	4.58	0.56647	.	0.894418	0.09587	N	0.782010	T	0.43233	0.1238	N	0.22421	0.69	0.80722	D	1	B	0.25169	0.119	B	0.24269	0.052	T	0.42447	-0.9451	10	0.52906	T	0.07	-4.0555	9.248	0.37539	0.0959:0.0:0.9041:0.0	.	23	Q6YP21	KAT3_HUMAN	F	23	ENSP00000260508:S23F;ENSP00000359517:S23F	ENSP00000260508:S23F	S	-	2	0	CCBL2	89226554	0.999000	0.42202	0.970000	0.41538	0.267000	0.26476	3.285000	0.51716	2.588000	0.87417	0.650000	0.86243	TCT	G|0.988;A|0.012	0.012	strong		0.348	CCBL2-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000029300.3	NM_001008661	
FUT1	2523	hgsc.bcm.edu	37	19	49253717	49253717	+	Silent	SNP	G	G	T	rs838138	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49253717G>T	ENST00000310160.3	-	4	1796	c.822C>A	c.(820-822)acC>acA	p.T274T	FUT1_ENST00000601931.1_5'Flank	NM_000148.3	NP_000139.1	P19526	FUT1_HUMAN	fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase, H blood group)	274					carbohydrate metabolic process (GO:0005975)|L-fucose catabolic process (GO:0042355)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	fucosyltransferase activity (GO:0008417)|galactoside 2-alpha-L-fucosyltransferase activity (GO:0008107)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(3)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	17		all_lung(116;1.7e-06)|all_epithelial(76;3.52e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000135)|all cancers(93;0.000354)|Epithelial(262;0.0191)|GBM - Glioblastoma multiforme(486;0.0222)		CGCCCTGGGAGGTGTCGATGT	0.577													G|||	267	0.0533147	0.1884	0.0259	5008	,	,		20123	0.0		0.0	False		,,,				2504	0.0				p.T274T		Atlas-SNP	.											.	FUT1	44	.	0			c.C822A						PASS	.	G		653,3753	279.0+/-274.6	52,549,1602	166.0	127.0	140.0		822	1.1	0.3	19	dbSNP_86	140	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	FUT1	NM_000148.3		52,551,5900	TT,TG,GG		0.0233,14.8207,5.0361		274/366	49253717	655,12351	2203	4300	6503	SO:0001819	synonymous_variant	2523	exon4			CTGGGAGGTGTCG		CCDS12733.1	19q13.33	2014-07-19	2006-01-19		ENSG00000174951	ENSG00000174951	2.4.1.69	"""Blood group antigens"", ""Fucosyltransferases"""	4012	protein-coding gene	gene with protein product		211100	"""fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase, Bombay phenotype included)"", ""fucosyltransferase 1 (galactoside 2-alpha-L-fucosyltransferase)"""	H, HSC			Standard	NM_000148		Approved		uc002pkk.3	P19526		ENST00000310160.3:c.822C>A	19.37:g.49253717G>T		77.0	0.0	0		55.0	55.0	1	NM_000148	O14505|O14506|O14507	Silent	SNP	ENST00000310160.3	37	CCDS12733.1																																																																																			G|0.955;T|0.045	0.045	strong		0.577	FUT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466194.1	NM_000148	
C1orf27	54953	hgsc.bcm.edu	37	1	186355168	186355168	+	Missense_Mutation	SNP	A	A	G	rs115570554	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:186355168A>G	ENST00000287859.6	+	4	408	c.283A>G	c.(283-285)Att>Gtt	p.I95V	C1orf27_ENST00000432021.3_Missense_Mutation_p.I95V|C1orf27_ENST00000367470.3_Missense_Mutation_p.I95V|C1orf27_ENST00000419367.3_Intron	NM_017847.5	NP_060317.3	Q5SWX8	ODR4_HUMAN	chromosome 1 open reading frame 27	95						integral component of membrane (GO:0016021)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)	9						AGTATTTATTATTACTACTTT	0.289													A|||	21	0.00419329	0.0151	0.0014	5008	,	,		15027	0.0		0.0	False		,,,				2504	0.0				p.I95V		Atlas-SNP	.											.	C1orf27	41	.	0			c.A283G						PASS	.	A	VAL/ILE,,VAL/ILE	36,3532		0,36,1748	54.0	51.0	52.0		283,,283	2.5	1.0	1	dbSNP_132	52	0,8118		0,0,4059	yes	missense,intron,missense	C1orf27	NM_001164245.1,NM_001164246.1,NM_017847.5	29,,29	0,36,5807	GG,GA,AA		0.0,1.009,0.3081	benign,,benign	95/432,,95/455	186355168	36,11650	1784	4059	5843	SO:0001583	missense	54953	exon4			TTTATTATTACTA	BC003397	CCDS53448.1, CCDS53449.1, CCDS53450.1	1q25	2012-06-25			ENSG00000157181	ENSG00000157181			24299	protein-coding gene	gene with protein product	"""transactivated by recombinant transforming growth factor beta"""	609335				12868032	Standard	NM_017847		Approved	FLJ20505, odr-4, TTG1	uc021pgj.1	Q5SWX8	OTTHUMG00000035579	ENST00000287859.6:c.283A>G	1.37:g.186355168A>G	ENSP00000287859:p.Ile95Val	41.0	0.0	0		56.0	24.0	0.428571	NM_001164245	B4DNY0|E9PFR7|Q19CC6|Q8WYB6|Q9BTS2|Q9H6A6|Q9NX06	Missense_Mutation	SNP	ENST00000287859.6	37	CCDS53448.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	A	1.145	-0.648372	0.03506	0.01009	0.0	ENSG00000157181	ENST00000367470;ENST00000432021;ENST00000287859	T;T;T	0.38401	1.14;1.14;1.14	4.97	2.47	0.30058	.	0.271361	0.41500	N	0.000862	T	0.12860	0.0312	L	0.29908	0.895	0.33076	D	0.535996	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.22382	-1.0218	10	0.05833	T	0.94	-21.9948	4.69	0.12776	0.6635:0.1637:0.1728:0.0	.	95;95	Q5SWX8-2;Q5SWX8	.;ODR4_HUMAN	V	95	ENSP00000356440:I95V;ENSP00000402029:I95V;ENSP00000287859:I95V	ENSP00000287859:I95V	I	+	1	0	C1orf27	184621791	0.727000	0.28069	0.998000	0.56505	0.985000	0.73830	0.258000	0.18387	0.851000	0.35264	-0.263000	0.10527	ATT	A|0.997;G|0.003	0.003	strong		0.289	C1orf27-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086352.2	NM_017847	
PDE9A	5152	hgsc.bcm.edu	37	21	44192574	44192574	+	Missense_Mutation	SNP	C	C	T	rs147305658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:44192574C>T	ENST00000291539.6	+	19	1772	c.1712C>T	c.(1711-1713)aCg>aTg	p.T571M	PDE9A_ENST00000335440.6_Missense_Mutation_p.T469M|PDE9A_ENST00000470987.1_3'UTR|PDE9A_ENST00000349112.3_Missense_Mutation_p.T443M|PDE9A_ENST00000398224.3_Missense_Mutation_p.T444M|PDE9A_ENST00000398236.3_Missense_Mutation_p.T485M|PDE9A_ENST00000398225.3_Missense_Mutation_p.T530M|PDE9A_ENST00000398227.3_Missense_Mutation_p.T411M|PDE9A_ENST00000328862.6_Missense_Mutation_p.T545M|PDE9A_ENST00000539837.1_Missense_Mutation_p.T443M|PDE9A_ENST00000398234.3_Missense_Mutation_p.T470M|PDE9A_ENST00000398232.3_Missense_Mutation_p.T504M|PDE9A_ENST00000335512.4_Missense_Mutation_p.T511M|PDE9A_ENST00000398229.3_Missense_Mutation_p.T437M|PDE9A_ENST00000380328.2_Missense_Mutation_p.T518M	NM_002606.2	NP_002597.1	O76083	PDE9A_HUMAN	phosphodiesterase 9A	571					blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|metabolic process (GO:0008152)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|perikaryon (GO:0043204)|plasma membrane (GO:0005886)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|metal ion binding (GO:0046872)			breast(1)|endometrium(4)|large_intestine(6)|lung(8)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Caffeine(DB00201)	GACAGCTTGACGTCTGGGGCC	0.527													C|||	3	0.000599042	0.0023	0.0	5008	,	,		18440	0.0		0.0	False		,,,				2504	0.0				p.T571M		Atlas-SNP	.											.	PDE9A	69	.	0			c.C1712T						PASS	.	C	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	23,4381	29.9+/-59.1	0,23,2179	68.0	55.0	59.0		1532,1331,1328,1553,1409,1091,1091,1454,1232,1061,1310,1406,1091,1061,1511,1589,1634,1091,1091,1712	1.4	0.0	21	dbSNP_134	59	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	PDE9A	NM_001001567.1,NM_001001568.1,NM_001001569.1,NM_001001570.1,NM_001001571.1,NM_001001572.1,NM_001001573.1,NM_001001574.1,NM_001001575.1,NM_001001576.1,NM_001001577.1,NM_001001578.1,NM_001001579.1,NM_001001580.1,NM_001001581.1,NM_001001582.1,NM_001001583.1,NM_001001584.2,NM_001001585.1,NM_002606.2	81,81,81,81,81,81,81,81,81,81,81,81,81,81,81,81,81,81,81,81	0,23,6479	TT,TC,CC		0.0,0.5223,0.1769	benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	511/534,444/467,443/466,518/541,470/493,364/387,364/387,485/508,411/434,354/377,437/460,469/492,364/387,354/377,504/527,530/553,545/568,364/387,364/387,571/594	44192574	23,12981	2202	4300	6502	SO:0001583	missense	5152	exon19			GCTTGACGTCTGG	AF048837	CCDS13690.1, CCDS33567.1, CCDS33568.1, CCDS33569.1, CCDS33570.1, CCDS33571.1, CCDS42941.1, CCDS42942.1, CCDS42943.1, CCDS42944.1, CCDS42945.1, CCDS42946.1, CCDS42947.1	21q22.3	2005-11-29			ENSG00000160191	ENSG00000160191	3.1.4.17	"""Phosphodiesterases"""	8795	protein-coding gene	gene with protein product		602973				9624146	Standard	NM_001001584		Approved		uc002zbm.3	O76083	OTTHUMG00000086825	ENST00000291539.6:c.1712C>T	21.37:g.44192574C>T	ENSP00000291539:p.Thr571Met	100.0	0.0	0		62.0	38.0	0.612903	NM_002606	B2RBI5|B4DFI5|D3DSJ8|D3DSJ9|O75490|O75491|O95225|Q53Y40|Q5QD39|Q86SF7|Q86SI6|Q86SJ3|Q86WN3|Q86WN4|Q86WN5|Q86WN6|Q86WN7|Q86WN8|Q86WN9|Q86WP0	Missense_Mutation	SNP	ENST00000291539.6	37	CCDS13690.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	8.057	0.767372	0.15983	0.005223	0.0	ENSG00000160191	ENST00000335512;ENST00000539837;ENST00000291539;ENST00000380328;ENST00000398232;ENST00000398234;ENST00000398236;ENST00000328862;ENST00000335440;ENST00000398225;ENST00000398229;ENST00000398227;ENST00000349112;ENST00000398224	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.69926	-0.4;-0.39;-0.42;-0.41;-0.44;-0.4;-0.4;-0.43;-0.41;-0.42;-0.4;-0.4;-0.39;-0.4	3.3	1.42	0.22433	.	2.420000	0.01711	N	0.027724	T	0.45756	0.1358	L	0.32530	0.975	0.09310	N	1	P;B;B;P;P;P;B;B;B;B;B;P;B;B;B	0.45044	0.588;0.069;0.145;0.759;0.849;0.759;0.145;0.069;0.145;0.145;0.301;0.849;0.301;0.145;0.308	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.36244	0.216;0.028;0.04;0.176;0.176;0.115;0.093;0.013;0.079;0.049;0.124;0.176;0.22;0.102;0.048	T	0.48055	-0.9068	10	0.48119	T	0.1	.	6.1538	0.20326	0.0:0.7003:0.1902:0.1095	.	504;485;470;545;530;463;511;354;411;437;443;469;518;444;571	O76083-13;O76083-8;O76083-6;O76083-15;O76083-14;O76083-16;O76083-2;O76083-10;O76083-9;O76083-11;O76083-4;O76083-12;O76083-5;O76083-3;O76083	.;.;.;.;.;.;.;.;.;.;.;.;.;.;PDE9A_HUMAN	M	511;443;571;518;504;470;485;545;469;530;437;411;443;444	ENSP00000335242:T511M;ENSP00000441899:T443M;ENSP00000291539:T571M;ENSP00000369685:T518M;ENSP00000381287:T504M;ENSP00000381289:T470M;ENSP00000381291:T485M;ENSP00000328699:T545M;ENSP00000335365:T469M;ENSP00000381281:T530M;ENSP00000381285:T437M;ENSP00000381283:T411M;ENSP00000344730:T443M;ENSP00000381280:T444M	ENSP00000291539:T571M	T	+	2	0	PDE9A	43065643	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.028000	0.13644	0.392000	0.25172	-0.234000	0.12200	ACG	C|0.999;T|0.001	0.001	strong		0.527	PDE9A-016	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000195466.1		
OR6C76	390326	hgsc.bcm.edu	37	12	55820358	55820358	+	Silent	SNP	G	G	A	rs12322458	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:55820358G>A	ENST00000328314.3	+	1	321	c.321G>A	c.(319-321)acG>acA	p.T107T		NM_001005183.1	NP_001005183.1	A6NM76	O6C76_HUMAN	olfactory receptor, family 6, subfamily C, member 76	107						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						TTGGCTCAACGGAGTTTTTCC	0.408													g|||	97	0.019369	0.0673	0.0115	5008	,	,		15616	0.0		0.0	False		,,,				2504	0.0				p.T107T		Atlas-SNP	.											.	OR6C76	98	.	0			c.G321A						PASS	.			262,4144	140.0+/-175.5	7,248,1948	116.0	128.0	124.0		321	-1.2	0.7	12	dbSNP_120	124	3,8593	3.0+/-9.4	0,3,4295	no	coding-synonymous	OR6C76	NM_001005183.1		7,251,6243	AA,AG,GG		0.0349,5.9464,2.0381		107/313	55820358	265,12737	2203	4298	6501	SO:0001819	synonymous_variant	390326	exon1			CTCAACGGAGTTT		CCDS31823.1	12q13.2	2013-09-23			ENSG00000185821	ENSG00000185821		"""GPCR / Class A : Olfactory receptors"""	31305	protein-coding gene	gene with protein product							Standard	NM_001005183		Approved		uc010spm.2	A6NM76	OTTHUMG00000169956	ENST00000328314.3:c.321G>A	12.37:g.55820358G>A		165.0	0.0	0		152.0	72.0	0.473684	NM_001005183		Silent	SNP	ENST00000328314.3	37	CCDS31823.1																																																																																			G|0.978;A|0.022	0.022	strong		0.408	OR6C76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406675.1	NM_001005183	
ANK1	286	hgsc.bcm.edu	37	8	41522407	41522407	+	Intron	SNP	G	G	C	rs112350393	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:41522407G>C	ENST00000347528.4	-	40	5478				ANK1_ENST00000396945.1_Intron|RP11-930P14.1_ENST00000520418.1_RNA|ANK1_ENST00000352337.4_Intron|ANK1_ENST00000265709.8_Intron|ANK1_ENST00000457297.1_Missense_Mutation_p.D45E|ANK1_ENST00000379758.2_Intron|ANK1_ENST00000522231.1_Missense_Mutation_p.D45E|ANK1_ENST00000314214.8_Missense_Mutation_p.D45E|RP11-930P14.1_ENST00000585088.1_RNA|ANK1_ENST00000289734.7_Intron|ANK1_ENST00000522543.1_Missense_Mutation_p.D45E|ANK1_ENST00000396942.1_Intron|RP11-930P14.1_ENST00000522388.1_RNA	NM_020475.2|NM_020476.2|NM_020477.2	NP_065208.2|NP_065209.2|NP_065210.2	P16157	ANK1_HUMAN	ankyrin 1, erythrocytic						axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|ER to Golgi vesicle-mediated transport (GO:0006888)|erythrocyte development (GO:0048821)|exocytosis (GO:0006887)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|monovalent inorganic cation transport (GO:0015672)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of organelle organization (GO:0010638)|protein targeting to plasma membrane (GO:0072661)|signal transduction (GO:0007165)	axolemma (GO:0030673)|basolateral plasma membrane (GO:0016323)|cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|M band (GO:0031430)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|cytoskeletal adaptor activity (GO:0008093)|enzyme binding (GO:0019899)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(4)|endometrium(9)|kidney(1)|large_intestine(26)|lung(62)|ovary(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	122	Ovarian(28;0.00541)|Colorectal(14;0.0398)|Lung SC(25;0.211)	all_lung(54;0.000626)|Lung NSC(58;0.00245)|Esophageal squamous(32;0.0559)|Hepatocellular(245;0.0663)|Renal(179;0.188)	OV - Ovarian serous cystadenocarcinoma(14;0.000984)|Lung(22;0.00108)|Colorectal(10;0.00245)|LUSC - Lung squamous cell carcinoma(45;0.00392)|COAD - Colon adenocarcinoma(11;0.0264)			CCAGCTCCTTGTCCAGCTCCT	0.612													G|||	147	0.029353	0.1104	0.0014	5008	,	,		18468	0.0		0.0	False		,,,				2504	0.0				p.D45E		Atlas-SNP	.											.	ANK1	497	.	0			c.C135G						PASS	.	G	,GLU/ASP,,,,,GLU/ASP,GLU/ASP	405,4001	200.8+/-224.0	31,343,1829	80.0	58.0	65.0		,135,,,,,135,135	4.6	1.0	8	dbSNP_132	65	4,8596	3.0+/-9.4	0,4,4296	yes	intron,missense,intron,intron,intron,intron,missense,missense	ANK1	NM_000037.3,NM_001142445.1,NM_001142446.1,NM_020475.2,NM_020476.2,NM_020477.2,NM_020478.4,NM_020480.4	,45,,,,,45,45	31,347,6125	CC,CG,GG		0.0465,9.192,3.1447	,,,,,,,	,45/157,,,,,45/156,45/110	41522407	409,12597	2203	4300	6503	SO:0001627	intron_variant	286	exon1			CTCCTTGTCCAGC	M28880	CCDS6119.1, CCDS6121.1, CCDS6122.1, CCDS47849.1, CCDS55227.1	8p11.21	2013-01-10			ENSG00000029534	ENSG00000029534		"""Ankyrin repeat domain containing"""	492	protein-coding gene	gene with protein product		612641		ANK		1689849	Standard	NM_001142445		Approved	SPH1	uc003xom.3	P16157	OTTHUMG00000150281	ENST00000347528.4:c.5395-1147C>G	8.37:g.41522407G>C		68.0	0.0	0		63.0	28.0	0.444444	NM_020478	A0PJN8|A6NJ23|E5RFL7|O43400|Q13768|Q53ER1|Q59FP2|Q8N604|Q99407	Missense_Mutation	SNP	ENST00000347528.4	37	CCDS6119.1	36	0.016483516483516484	36	0.07317073170731707	0	0.0	0	0.0	0	0.0	G	24.8	4.569350	0.86439	0.09192	4.65E-4	ENSG00000029534	ENST00000457297;ENST00000522231;ENST00000522543;ENST00000314214;ENST00000348036;ENST00000335651	D;D;D	0.87334	-1.81;-2.24;-2.19	5.51	4.63	0.57726	.	.	.	.	.	T	0.41534	0.1163	M	0.67953	2.075	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.83275	0.996;0.994;0.996;0.996	T	0.72087	-0.4396	9	0.72032	D	0.01	.	12.8445	0.57821	0.078:0.0:0.9219:0.0	.	45;45;45;45	Q6PK32;A0PJN8;Q53ER1;E5RFL7	.;.;.;.	E	45	ENSP00000428750:D45E;ENSP00000430368:D45E;ENSP00000319123:D45E	ENSP00000319123:D45E	D	-	3	2	ANK1	41641564	1.000000	0.71417	1.000000	0.80357	0.830000	0.47004	4.545000	0.60698	2.585000	0.87301	0.563000	0.77884	GAC	G|0.969;C|0.031	0.031	strong		0.612	ANK1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317297.1	NM_020475	
THAP11	57215	hgsc.bcm.edu	37	16	67876805	67876805	+	Silent	SNP	A	A	G	rs28434205	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67876805A>G	ENST00000303596.1	+	1	593	c.348A>G	c.(346-348)caA>caG	p.Q116Q	CENPT_ENST00000562787.1_Intron	NM_020457.2	NP_065190.2	Q96EK4	THA11_HUMAN	THAP domain containing 11	116	Gln-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.Q116Q(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|urinary_tract(1)	8		Acute lymphoblastic leukemia(13;0.000299)|all_hematologic(13;0.0184)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.00412)|Epithelial(162;0.018)|all cancers(182;0.118)		aacagcagcaacagcagcagc	0.682																																					p.Q116Q		Atlas-SNP	.											THAP11,bladder,carcinoma,0,3	THAP11	27	3	1	Substitution - coding silent(1)	lung(1)	c.A348G						PASS	.	G	,	14,3828		0,14,1907	21.0	26.0	24.0		348,	-3.2	0.7	16	dbSNP_125	24	20,7612		0,20,3796	no	coding-synonymous,intron	THAP11,CENPT	NM_020457.2,NM_025082.3	,	0,34,5703	GG,GA,AA		0.2621,0.3644,0.2963	,	116/315,	67876805	34,11440	1921	3816	5737	SO:0001819	synonymous_variant	57215	exon1			GCAGCAACAGCAG	AB015338	CCDS10847.1	16q22.1	2013-01-25			ENSG00000168286	ENSG00000168286		"""THAP (C2CH-type zinc finger) domain containing"""	23194	protein-coding gene	gene with protein product		609119				12575992, 8325628	Standard	NM_020457		Approved	HRIHFB2206, CTG-B45d, CTG-B43a	uc002euo.3	Q96EK4	OTTHUMG00000137546	ENST00000303596.1:c.348A>G	16.37:g.67876805A>G		19.0	0.0	0		19.0	7.0	0.368421	NM_020457	A4UCT5|A8K002|O94795	Silent	SNP	ENST00000303596.1	37	CCDS10847.1																																																																																			A|0.991;G|0.009	0.009	strong		0.682	THAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268879.1	NM_020457	
FMN2	56776	hgsc.bcm.edu	37	1	240371409	240371409	+	Silent	SNP	G	G	T	rs373533409	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:240371409G>T	ENST00000319653.9	+	5	3527	c.3297G>T	c.(3295-3297)ccG>ccT	p.P1099P		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1099	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TACCCCCTCCGCCCCCTCTAC	0.731																																					p.P1099P		Atlas-SNP	.											FMN2,NS,neuroblastoma,0,1	FMN2	451	1	0			c.G3297T						scavenged	.						6.0	8.0	8.0					1																	240371409		2016	4072	6088	SO:0001819	synonymous_variant	56776	exon5			CCCTCCGCCCCCT	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3297G>T	1.37:g.240371409G>T		142.0	0.0	0		149.0	7.0	0.0469799	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																			.	.	none		0.731	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
EIF1AD	84285	hgsc.bcm.edu	37	11	65767578	65767578	+	Missense_Mutation	SNP	G	G	A	rs35497370	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:65767578G>A	ENST00000312234.2	-	3	476	c.142C>T	c.(142-144)Cgc>Tgc	p.R48C	BANF1_ENST00000445560.2_5'Flank|EIF1AD_ENST00000533544.1_Missense_Mutation_p.R48C|EIF1AD_ENST00000529964.1_Missense_Mutation_p.R48C|EIF1AD_ENST00000525767.1_5'UTR|BANF1_ENST00000527348.1_5'Flank|EIF1AD_ENST00000527249.1_Missense_Mutation_p.R48C|BANF1_ENST00000533166.1_5'Flank|EIF1AD_ENST00000526451.1_Missense_Mutation_p.R48C|BANF1_ENST00000312175.2_5'Flank	NM_001242481.1|NM_001242482.1|NM_001242483.1|NM_032325.3	NP_001229410.1|NP_001229411.1|NP_001229412.1|NP_115701.2	Q8N9N8	EIF1A_HUMAN	eukaryotic translation initiation factor 1A domain containing	48	S1-like. {ECO:0000255|PROSITE- ProRule:PRU00181}.					intermediate filament cytoskeleton (GO:0045111)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	translation initiation factor activity (GO:0003743)			lung(5)	5						ACCAGGAAGCGCTGCCCTTGG	0.517													G|||	16	0.00319489	0.0113	0.0014	5008	,	,		21003	0.0		0.0	False		,,,				2504	0.0				p.R48C		Atlas-SNP	.											EIF1AD,colon,carcinoma,+1,1	EIF1AD	10	1	0			c.C142T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	29,4373	36.0+/-67.5	0,29,2172	128.0	115.0	119.0		142,142,142,142,142,142,142	5.3	1.0	11	dbSNP_126	119	0,8592		0,0,4296	yes	missense,missense,missense,missense,missense,missense,missense	EIF1AD	NM_001242481.1,NM_001242482.1,NM_001242483.1,NM_001242484.1,NM_001242485.1,NM_001242486.1,NM_032325.3	180,180,180,180,180,180,180	0,29,6468	AA,AG,GG		0.0,0.6588,0.2232	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	48/166,48/166,48/166,48/166,48/166,48/166,48/166	65767578	29,12965	2201	4296	6497	SO:0001583	missense	84285	exon3			GGAAGCGCTGCCC	AK094129	CCDS8124.1	11q13.1	2009-05-27				ENSG00000175376			28147	protein-coding gene	gene with protein product						12477932	Standard	NM_001242482		Approved	MGC11102, haponin	uc001ogn.2	Q8N9N8		ENST00000312234.2:c.142C>T	11.37:g.65767578G>A	ENSP00000309175:p.Arg48Cys	110.0	0.0	0		91.0	47.0	0.516484	NM_001242483	B2R4N5|Q9BSC1	Missense_Mutation	SNP	ENST00000312234.2	37	CCDS8124.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	26.8	4.770117	0.90108	0.006588	0.0	ENSG00000175376	ENST00000526451;ENST00000312234;ENST00000529964;ENST00000533544;ENST00000527249;ENST00000530462;ENST00000532707;ENST00000527051	T;T;T;T;T;T;T;T	0.46451	0.87;0.87;0.87;0.87;0.87;0.87;0.87;0.87	5.31	5.31	0.75309	Nucleic acid-binding, OB-fold-like (1);RNA-binding domain, S1, IF1 type (2);Nucleic acid-binding, OB-fold (1);	0.170574	0.50627	D	0.000112	T	0.51381	0.1671	M	0.62723	1.935	0.80722	D	1	D	0.60575	0.988	P	0.61477	0.889	T	0.58532	-0.7620	10	0.59425	D	0.04	.	16.4684	0.84092	0.0:0.0:1.0:0.0	rs35497370	48	Q8N9N8	EIF1A_HUMAN	C	48	ENSP00000436644:R48C;ENSP00000309175:R48C;ENSP00000435942:R48C;ENSP00000434056:R48C;ENSP00000435439:R48C;ENSP00000435891:R48C;ENSP00000433320:R48C;ENSP00000432135:R48C	ENSP00000309175:R48C	R	-	1	0	EIF1AD	65524154	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	2.963000	0.49184	2.488000	0.83962	0.561000	0.74099	CGC	G|0.997;A|0.003	0.003	strong		0.517	EIF1AD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391072.1	NM_032325	
OR4K15	81127	hgsc.bcm.edu	37	14	20443751	20443751	+	Missense_Mutation	SNP	T	T	G	rs139828094	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20443751T>G	ENST00000305051.5	+	1	149	c.74T>G	c.(73-75)aTg>aGg	p.M25R		NM_001005486.1	NP_001005486.1	Q8NH41	OR4KF_HUMAN	olfactory receptor, family 4, subfamily K, member 15	25						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(2)|large_intestine(6)|lung(23)|ovary(1)|prostate(2)|skin(1)|stomach(1)	39	all_cancers(95;0.00108)		Epithelial(56;9.96e-07)|all cancers(55;3.58e-06)	GBM - Glioblastoma multiforme(265;0.00327)		CCAAAATCGATGAATGAGACA	0.383													T|||	23	0.00459265	0.0174	0.0	5008	,	,		20008	0.0		0.0	False		,,,				2504	0.0				p.M25R		Atlas-SNP	.											.	OR4K15	82	.	0			c.T74G						PASS	.	T	ARG/MET	56,4350		0,56,2147	103.0	104.0	103.0		74	2.0	1.0	14	dbSNP_134	103	2,8596		0,2,4297	yes	missense	OR4K15	NM_001005486.1	91	0,58,6444	GG,GT,TT		0.0233,1.271,0.446	probably-damaging	25/349	20443751	58,12946	2203	4299	6502	SO:0001583	missense	81127	exon1			AATCGATGAATGA		CCDS32026.1	14q11.2	2013-09-23			ENSG00000169488	ENSG00000169488		"""GPCR / Class A : Olfactory receptors"""	15353	protein-coding gene	gene with protein product							Standard	NM_001005486		Approved	OR4K15Q	uc010tkx.2	Q8NH41	OTTHUMG00000170635	ENST00000305051.5:c.74T>G	14.37:g.20443751T>G	ENSP00000304077:p.Met25Arg	187.0	0.0	0		193.0	102.0	0.528497	NM_001005486	B9EIL3|Q6IEZ4	Missense_Mutation	SNP	ENST00000305051.5	37	CCDS32026.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	.	12.07	1.827026	0.32329	0.01271	2.33E-4	ENSG00000169488	ENST00000305051	T	0.01414	4.92	3.26	1.98	0.26296	.	0.000000	0.53938	D	0.000058	T	0.02970	0.0088	M	0.90595	3.13	0.22754	N	0.998776	D	0.63880	0.993	D	0.67382	0.951	T	0.12941	-1.0528	10	0.72032	D	0.01	.	2.5999	0.04864	0.2303:0.1328:0.0:0.6369	.	25	Q8NH41	OR4KF_HUMAN	R	25	ENSP00000304077:M25R	ENSP00000304077:M25R	M	+	2	0	OR4K15	19513591	0.762000	0.28451	0.970000	0.41538	0.716000	0.41182	1.136000	0.31467	1.335000	0.45486	0.383000	0.25322	ATG	T|0.994;G|0.006	0.006	strong		0.383	OR4K15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409883.1		
AKNAD1	254268	hgsc.bcm.edu	37	1	109395230	109395230	+	Silent	SNP	A	A	G	rs142279898	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:109395230A>G	ENST00000370001.3	-	2	325	c.57T>C	c.(55-57)taT>taC	p.Y19Y	AKNAD1_ENST00000369995.3_Silent_p.Y19Y|AKNAD1_ENST00000357393.4_Intron|AKNAD1_ENST00000369994.1_Silent_p.Y19Y	NM_152763.4	NP_689976.2	Q5T1N1	AKND1_HUMAN	AKNA domain containing 1	19						cytoplasm (GO:0005737)				breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(10)|ovary(3)|prostate(6)|skin(3)|stomach(2)	32						GGTCCCCATCATAAGGCAAAT	0.438													A|||	15	0.00299521	0.0113	0.0	5008	,	,		19172	0.0		0.0	False		,,,				2504	0.0				p.Y19Y		Atlas-SNP	.											.	AKNAD1	83	.	0			c.T57C						PASS	.	A		29,4377	33.5+/-64.1	0,29,2174	72.0	72.0	72.0		57	-0.7	1.0	1	dbSNP_134	72	0,8598		0,0,4299	no	coding-synonymous	AKNAD1	NM_152763.3		0,29,6473	GG,GA,AA		0.0,0.6582,0.223		19/837	109395230	29,12975	2203	4299	6502	SO:0001819	synonymous_variant	254268	exon2			CCCATCATAAGGC	AK095517	CCDS791.2	1p13.3	2009-10-29	2009-10-29	2009-10-29	ENSG00000162641	ENSG00000162641			28398	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 62"""	C1orf62			Standard	NM_152763		Approved	MGC26989	uc001dwa.4	Q5T1N1	OTTHUMG00000011231	ENST00000370001.3:c.57T>C	1.37:g.109395230A>G		83.0	0.0	0		99.0	49.0	0.494949	NM_152763	B9EK62|Q5T1N0|Q8N990|Q8NCN9	Silent	SNP	ENST00000370001.3	37	CCDS791.2																																																																																			A|0.998;G|0.002	0.002	strong		0.438	AKNAD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030923.2	NM_152763	
GLIS3	169792	hgsc.bcm.edu	37	9	4118262	4118262	+	Missense_Mutation	SNP	C	C	A	rs75462592	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:4118262C>A	ENST00000324333.10	-	3	944	c.751G>T	c.(751-753)Ggc>Tgc	p.G251C	GLIS3_ENST00000381971.3_Missense_Mutation_p.G406C	NM_152629.3	NP_689842.3	Q8NEA6	GLIS3_HUMAN	GLIS family zinc finger 3	251					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|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)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(12)|lung(4)|ovary(2)|prostate(1)|skin(1)	26		Acute lymphoblastic leukemia(2;0.00464)|Breast(48;0.148)		Lung(2;0.00163)|GBM - Glioblastoma multiforme(50;0.00301)|LUSC - Lung squamous cell carcinoma(2;0.0148)		TTGACCAGGCCTGGCTGCAGG	0.721													C|||	66	0.0131789	0.0469	0.0058	5008	,	,		10239	0.0		0.0	False		,,,				2504	0.0				p.G406C		Atlas-SNP	.											.	GLIS3	152	.	0			c.G1216T						PASS	.	C	CYS/GLY,CYS/GLY	67,3403		1,65,1669	5.0	6.0	5.0		1216,751	5.5	0.4	9	dbSNP_131	5	2,6878		0,2,3438	yes	missense,missense	GLIS3	NM_001042413.1,NM_152629.3	159,159	1,67,5107	AA,AC,CC		0.0291,1.9308,0.6667	possibly-damaging,possibly-damaging	406/931,251/776	4118262	69,10281	1735	3440	5175	SO:0001583	missense	169792	exon4			CCAGGCCTGGCTG	BC033899	CCDS6451.1, CCDS43784.1	9p24.2	2008-05-02	2004-07-16	2004-07-16	ENSG00000107249	ENSG00000107249		"""Zinc fingers, C2H2-type"""	28510	protein-coding gene	gene with protein product		610192	"""zinc finger protein 515"""	ZNF515		14500813	Standard	NM_152629		Approved	MGC33662	uc003zhx.1	Q8NEA6	OTTHUMG00000019463	ENST00000324333.10:c.751G>T	9.37:g.4118262C>A	ENSP00000325494:p.Gly251Cys	10.0	0.0	0		24.0	18.0	0.75	NM_001042413	B1AL19|Q1PHK5	Missense_Mutation	SNP	ENST00000324333.10	37	CCDS6451.1	15	0.006868131868131868	14	0.028455284552845527	1	0.0027624309392265192	0	0.0	0	0.0	C	12.40	1.925708	0.34002	0.019308	2.91E-4	ENSG00000107249	ENST00000324333;ENST00000381971	T;T	0.10960	2.84;2.82	5.49	5.49	0.81192	.	0.299519	0.22308	U	0.061772	T	0.04770	0.0129	N	0.22421	0.69	0.09310	N	0.999999	D;D	0.57257	0.979;0.964	P;B	0.50378	0.639;0.436	T	0.05115	-1.0905	10	0.38643	T	0.18	.	19.359	0.94428	0.0:1.0:0.0:0.0	.	406;251	Q8NEA6-2;Q8NEA6	.;GLIS3_HUMAN	C	251;406	ENSP00000325494:G251C;ENSP00000371398:G406C	ENSP00000325494:G251C	G	-	1	0	GLIS3	4108262	0.000000	0.05858	0.385000	0.26158	0.649000	0.38597	1.002000	0.29796	2.555000	0.86185	0.655000	0.94253	GGC	C|0.993;A|0.007	0.007	strong		0.721	GLIS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051559.1	NM_152629	
MAP2K2	5605	hgsc.bcm.edu	37	19	4110552	4110552	+	Silent	SNP	C	C	G	rs10424722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4110552C>G	ENST00000262948.5	-	3	658	c.405G>C	c.(403-405)ggG>ggC	p.G135G	MAP2K2_ENST00000599345.1_5'UTR|MAP2K2_ENST00000394867.4_Silent_p.G38G	NM_030662.3	NP_109587.1	P36507	MP2K2_HUMAN	mitogen-activated protein kinase kinase 2	135	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|MAPK cascade (GO:0000165)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine autophosphorylation (GO:0036289)|positive regulation of cell motility (GO:2000147)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|Ras protein signal transduction (GO:0007265)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of stress-activated MAPK cascade (GO:0032872)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|peroxisomal membrane (GO:0005778)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|scaffold protein binding (GO:0097110)						Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)	Bosutinib(DB06616)|Trametinib(DB08911)	TGTAGAAGGCCCCGTAGAAGC	0.602													C|||	239	0.0477236	0.1755	0.0101	5008	,	,		16819	0.0		0.0	False		,,,				2504	0.0				p.G135G		Atlas-SNP	.											.	MAP2K2	72	.	0			c.G405C						PASS	.	C		628,3778	272.8+/-271.0	51,526,1626	87.0	74.0	79.0		405	-3.6	1.0	19	dbSNP_119	79	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	MAP2K2	NM_030662.3		51,531,5921	GG,GC,CC		0.0581,14.2533,4.867		135/401	4110552	633,12373	2203	4300	6503	SO:0001819	synonymous_variant	5605	exon3			GAAGGCCCCGTAG	L11285	CCDS12120.1	19p13.3	2014-09-17			ENSG00000126934	ENSG00000126934	2.7.12.2	"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6842	protein-coding gene	gene with protein product		601263		PRKMK2		8388392	Standard	NM_030662		Approved	MEK2	uc002lzk.3	P36507	OTTHUMG00000134286	ENST00000262948.5:c.405G>C	19.37:g.4110552C>G		45.0	0.0	0		56.0	38.0	0.678571	NM_030662		Silent	SNP	ENST00000262948.5	37	CCDS12120.1																																																																																			C|0.956;G|0.044	0.044	strong		0.602	MAP2K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258957.2		
MAL2	114569	hgsc.bcm.edu	37	8	120233968	120233968	+	Missense_Mutation	SNP	G	G	A	rs2303398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:120233968G>A	ENST00000276681.6	+	3	376	c.274G>A	c.(274-276)Gct>Act	p.A92T	RP11-4K16.2_ENST00000522828.1_lincRNA|MAL2_ENST00000521748.1_3'UTR	NM_052886.2	NP_443118.1	Q969L2	MAL2_HUMAN	mal, T-cell differentiation protein 2 (gene/pseudogene)	92	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.		A -> T (in dbSNP:rs2303398).			cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)						all_cancers(13;1.91e-26)|Lung NSC(37;8.61e-08)|Ovarian(258;0.018)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.000967)			TGGCATGGTGGCTCAAATTGA	0.433													A|||	563	0.11242	0.3238	0.0331	5008	,	,		19676	0.0308		0.0	False		,,,				2504	0.0828				p.A92T		Atlas-SNP	.											.	.	.	.	0			c.G274A						PASS	.	A	THR/ALA	1171,2763		182,807,978	128.0	127.0	127.0		275	5.2	1.0	8	dbSNP_100	127	21,8295		0,21,4137	yes	missense	MAL2	NM_052886.2	58	182,828,5115	AA,AG,GG		0.2525,29.7661,9.7306	benign	92/177	120233968	1192,11058	1967	4158	6125	SO:0001583	missense	114569	exon3			ATGGTGGCTCAAA	AL117612	CCDS75780.1	8q23	2011-01-26	2011-01-26			ENSG00000147676			13634	protein-coding gene	gene with protein product	"""MAL proteolipid protein 2"""	609684				11549320	Standard	NM_052886		Approved		uc003yop.3	Q969L2		ENST00000276681.6:c.274G>A	8.37:g.120233968G>A	ENSP00000475434:p.Ala92Thr	138.0	0.0	0		135.0	88.0	0.651852	NM_052886	B2R520|Q6ZMD9	Missense_Mutation	SNP	ENST00000276681.6	37																																																																																				G|0.895;A|0.105	0.105	strong		0.433	MAL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052886	
INCENP	3619	hgsc.bcm.edu	37	11	61906216	61906216	+	Missense_Mutation	SNP	G	G	A	rs61751226	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61906216G>A	ENST00000394818.3	+	6	1349	c.1147G>A	c.(1147-1149)Gag>Aag	p.E383K	INCENP_ENST00000278849.4_Missense_Mutation_p.E383K	NM_001040694.1	NP_001035784.1	Q9NQS7	INCE_HUMAN	inner centromere protein antigens 135/155kDa	383					chromosome segregation (GO:0007059)|cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	central element (GO:0000801)|chromocenter (GO:0010369)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lateral element (GO:0000800)|microtubule (GO:0005874)|midbody (GO:0030496)|pericentric heterochromatin (GO:0005721)|protein complex (GO:0043234)|spindle (GO:0005819)				breast(1)|endometrium(1)|kidney(6)|large_intestine(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19						CGAGGAGGCTGAGCCTGTGGC	0.642													G|||	58	0.0115815	0.0159	0.0	5008	,	,		17187	0.0		0.0	False		,,,				2504	0.0378				p.E383K		Atlas-SNP	.											.	INCENP	122	.	0			c.G1147A						PASS	.	G	LYS/GLU,LYS/GLU	83,4321	72.0+/-110.0	2,79,2121	47.0	53.0	51.0		1147,1147	1.9	0.0	11	dbSNP_129	51	1,8597		0,1,4298	yes	missense,missense	INCENP	NM_020238.2,NM_001040694.1	56,56	2,80,6419	AA,AG,GG		0.0116,1.8847,0.6461	benign,benign	383/915,383/919	61906216	84,12918	2202	4299	6501	SO:0001583	missense	3619	exon6			GAGGCTGAGCCTG	AF282265	CCDS31582.1, CCDS44624.1	11q12.3	2013-01-17	2002-08-29		ENSG00000149503	ENSG00000149503			6058	protein-coding gene	gene with protein product		604411	"""inner centromere protein antigens (135kD, 155kD)"""			1860899, 11453556	Standard	NM_001040694		Approved	FLJ31633	uc001nsw.1	Q9NQS7	OTTHUMG00000167470	ENST00000394818.3:c.1147G>A	11.37:g.61906216G>A	ENSP00000378295:p.Glu383Lys	44.0	0.0	0		50.0	26.0	0.52	NM_001040694	A8MQD2|Q5Y192	Missense_Mutation	SNP	ENST00000394818.3	37	CCDS44624.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	G	9.415	1.081416	0.20309	0.018847	1.16E-4	ENSG00000149503	ENST00000394818;ENST00000278849	T;T	0.16743	2.37;2.32	4.98	1.93	0.25924	.	0.347185	0.24786	N	0.035604	T	0.05731	0.0150	M	0.68952	2.095	0.09310	N	1	P;B;B	0.43788	0.817;0.208;0.132	B;B;B	0.36666	0.23;0.038;0.017	T	0.12682	-1.0538	10	0.08381	T	0.77	.	4.7767	0.13182	0.1895:0.1777:0.6328:0.0	rs61751226	383;383;383	B3KPD3;Q9NQS7-2;Q9NQS7	.;.;INCE_HUMAN	K	383	ENSP00000378295:E383K;ENSP00000278849:E383K	ENSP00000278849:E383K	E	+	1	0	INCENP	61662792	0.351000	0.24887	0.039000	0.18376	0.000000	0.00434	2.664000	0.46783	0.816000	0.34421	-0.768000	0.03414	GAG	G|0.995;A|0.005	0.005	strong		0.642	INCENP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000394723.2	NM_020238	
C2orf16	84226	hgsc.bcm.edu	37	2	27804114	27804114	+	Missense_Mutation	SNP	C	C	T	rs13392197	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:27804114C>T	ENST00000408964.2	+	1	4726	c.4675C>T	c.(4675-4677)Cat>Tat	p.H1559Y	ZNF512_ENST00000413371.2_5'Flank|ZNF512_ENST00000379717.1_5'Flank|AC074091.1_ENST00000408604.1_RNA|ZNF512_ENST00000416005.2_5'Flank|ZNF512_ENST00000556601.1_5'Flank|RP11-158I13.2_ENST00000505973.1_RNA|ZNF512_ENST00000355467.4_5'Flank	NM_032266.3	NP_115642.3	Q68DN1	CB016_HUMAN	chromosome 2 open reading frame 16	1559	Arg-rich.		H -> Y (in dbSNP:rs13392197).			extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(33)|urinary_tract(1)	47	Acute lymphoblastic leukemia(172;0.155)					GAGAACCCGTCATAACCCCTC	0.537													C|||	59	0.0117812	0.0408	0.0043	5008	,	,		18030	0.0		0.002	False		,,,				2504	0.0				p.H1559Y		Atlas-SNP	.											.	C2orf16	357	.	0			c.C4675T						PASS	.	C	TYR/HIS	130,3650		3,124,1763	118.0	118.0	118.0		4675	-5.8	0.0	2	dbSNP_121	118	3,8217		0,3,4107	yes	missense	C2orf16	NM_032266.3	83	3,127,5870	TT,TC,CC		0.0365,3.4392,1.1083	benign	1559/1985	27804114	133,11867	1890	4110	6000	SO:0001583	missense	84226	exon1			ACCCGTCATAACC	AL136898	CCDS42666.1	2p23.3	2013-09-20			ENSG00000221843	ENSG00000221843			25275	protein-coding gene	gene with protein product	"""P-S-E-R-S-H-H-S repeats containing"""						Standard	NM_032266		Approved	DKFZp434G118	uc002rkz.4	Q68DN1	OTTHUMG00000159099	ENST00000408964.2:c.4675C>T	2.37:g.27804114C>T	ENSP00000386190:p.His1559Tyr	90.0	0.0	0		81.0	44.0	0.54321	NM_032266	B9EIQ4|Q53S01|Q8ND64|Q9H088	Missense_Mutation	SNP	ENST00000408964.2	37	CCDS42666.1	24	0.01098901098901099	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	5.555	0.287230	0.10513	0.034392	3.65E-4	ENSG00000221843	ENST00000408964	T	0.04809	3.55	4.05	-5.76	0.02376	.	.	.	.	.	T	0.00552	0.0018	N	0.25647	0.755	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.47699	-0.9097	9	0.08381	T	0.77	.	2.2504	0.04042	0.1341:0.3469:0.1054:0.4136	rs13392197;rs52835437;rs13392197	1559	Q68DN1	CB016_HUMAN	Y	1559	ENSP00000386190:H1559Y	ENSP00000386190:H1559Y	H	+	1	0	C2orf16	27657618	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.314000	0.01125	-1.329000	0.02258	-0.379000	0.06801	CAT	C|0.983;T|0.017	0.017	strong		0.537	C2orf16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353292.1	NM_032266	
C15orf54	400360	hgsc.bcm.edu	37	15	39544809	39544809	+	Missense_Mutation	SNP	G	G	C	rs115130297	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:39544809G>C	ENST00000318578.3	+	2	841	c.473G>C	c.(472-474)aGg>aCg	p.R158T	RP11-624L4.1_ENST00000560484.1_RNA|RP11-624L4.1_ENST00000558209.1_RNA|RP11-624L4.1_ENST00000561058.1_RNA|C15orf54_ENST00000561223.1_Missense_Mutation_p.R158T	NM_207445.2	NP_997328.1	Q8N8G6	CO054_HUMAN	chromosome 15 open reading frame 54	158										NS(1)|haematopoietic_and_lymphoid_tissue(2)|lung(2)	5		all_cancers(109;5.39e-14)|all_epithelial(112;3.14e-12)|Lung NSC(122;9.74e-10)|all_lung(180;2.23e-08)|Melanoma(134;0.091)|Colorectal(260;0.198)		GBM - Glioblastoma multiforme(113;1.19e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0706)		AGGGGAGAGAGGGGACATTTT	0.448													G|||	16	0.00319489	0.0121	0.0	5008	,	,		21387	0.0		0.0	False		,,,				2504	0.0				p.R158T		Atlas-SNP	.											.	C15orf54	18	.	0			c.G473C						PASS	.	G	THR/ARG	28,4372	34.3+/-65.2	0,28,2172	98.0	84.0	88.0		473	0.3	0.0	15	dbSNP_132	88	0,8594		0,0,4297	yes	missense	C15orf54	NM_207445.2	71	0,28,6469	CC,CG,GG		0.0,0.6364,0.2155	benign	158/184	39544809	28,12966	2200	4297	6497	SO:0001583	missense	400360	exon2			GAGAGAGGGGACA		CCDS10049.1	15q14	2014-09-10			ENSG00000175746	ENSG00000175746			33797	protein-coding gene	gene with protein product							Standard	NM_207445		Approved	FLJ39531	uc001zkg.2	Q8N8G6	OTTHUMG00000129843	ENST00000318578.3:c.473G>C	15.37:g.39544809G>C	ENSP00000323686:p.Arg158Thr	145.0	0.0	0		165.0	88.0	0.533333	NM_207445	B7ZVZ9	Missense_Mutation	SNP	ENST00000318578.3	37	CCDS10049.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	G	4.682	0.126814	0.08931	0.006364	0.0	ENSG00000175746	ENST00000318578	T	0.39406	1.08	3.57	0.297	0.15762	.	.	.	.	.	T	0.09247	0.0228	N	0.08118	0	0.09310	N	1	B	0.25312	0.123	B	0.16289	0.015	T	0.15235	-1.0444	9	0.87932	D	0	.	2.1381	0.03768	0.1165:0.1939:0.4906:0.199	.	158	Q8N8G6	CO054_HUMAN	T	158	ENSP00000323686:R158T	ENSP00000323686:R158T	R	+	2	0	C15orf54	37332101	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-0.520000	0.06252	-0.036000	0.13669	0.609000	0.83330	AGG	G|0.997;C|0.003	0.003	strong		0.448	C15orf54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252083.1	NM_207445	
PLSCR5	389158	hgsc.bcm.edu	37	3	146311832	146311832	+	Missense_Mutation	SNP	G	G	T	rs12107687	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:146311832G>T	ENST00000443512.1	-	4	1331	c.328C>A	c.(328-330)Cgt>Agt	p.R110S	PLSCR5_ENST00000492200.1_Missense_Mutation_p.R110S|PLSCR5_ENST00000482567.1_Missense_Mutation_p.R98S	NM_001085420.1	NP_001078889.1	A0PG75	PLS5_HUMAN	phospholipid scramblase family, member 5	110			R -> S (in dbSNP:rs12107687).							endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|urinary_tract(1)	12						CAGAAAGTACGATTGAAGCAG	0.433													G|||	76	0.0151757	0.0545	0.0058	5008	,	,		14788	0.0		0.0	False		,,,				2504	0.0				p.R110S		Atlas-SNP	.											.	PLSCR5	35	.	0			c.C328A						PASS	.	G	SER/ARG	192,3650		3,186,1732	141.0	139.0	139.0		328	5.7	1.0	3	dbSNP_120	139	2,8270		0,2,4134	yes	missense	PLSCR5	NM_001085420.1	110	3,188,5866	TT,TG,GG		0.0242,4.9974,1.6015	probably-damaging	110/272	146311832	194,11920	1921	4136	6057	SO:0001583	missense	389158	exon4			AAGTACGATTGAA	AY436642	CCDS46931.1	3q24	2004-06-28			ENSG00000231213	ENSG00000231213			19952	protein-coding gene	gene with protein product							Standard	NM_001085420		Approved		uc010hvc.3	A0PG75	OTTHUMG00000159437	ENST00000443512.1:c.328C>A	3.37:g.146311832G>T	ENSP00000390111:p.Arg110Ser	141.0	0.0	0		142.0	72.0	0.507042	NM_001085420	B2RXK5	Missense_Mutation	SNP	ENST00000443512.1	37	CCDS46931.1	20	0.009157509157509158	19	0.03861788617886179	1	0.0027624309392265192	0	0.0	0	0.0	G	19.70	3.876593	0.72180	0.049974	2.42E-4	ENSG00000231213	ENST00000492200;ENST00000482567;ENST00000443512	T;T;T	0.56103	0.48;0.48;0.48	5.69	5.69	0.88448	Tubby, C-terminal (1);	.	.	.	.	T	0.44456	0.1294	H	0.94222	3.51	0.39506	D	0.968276	D;D	0.89917	0.984;1.0	P;D	0.83275	0.871;0.996	T	0.76570	-0.2911	9	0.87932	D	0	-22.5708	14.6371	0.68696	0.0:0.0:0.8546:0.1454	rs12107687;rs52836343;rs12107687	98;110	B2RXK5;A0PG75	.;PLS5_HUMAN	S	110;98;110	ENSP00000417184:R110S;ENSP00000418626:R98S;ENSP00000390111:R110S	ENSP00000390111:R110S	R	-	1	0	PLSCR5	147794522	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.190000	0.58365	2.679000	0.91253	0.650000	0.86243	CGT	G|0.987;T|0.013	0.013	strong		0.433	PLSCR5-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355365.1	XM_371670	
IVL	3713	hgsc.bcm.edu	37	1	152883036	152883036	+	Missense_Mutation	SNP	C	C	T	rs4459054	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152883036C>T	ENST00000368764.3	+	2	827	c.763C>T	c.(763-765)Ctc>Ttc	p.L255F	IVL_ENST00000392667.2_Missense_Mutation_p.L109F			P07476	INVO_HUMAN	involucrin	255	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].				isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			gcagctggagctctctgagca	0.657													C|||	107	0.0213658	0.0779	0.0058	5008	,	,		19088	0.0		0.0	False		,,,				2504	0.0				p.L255F		Atlas-SNP	.											IVL,NS,carcinoma,-2,1	IVL	100	1	0			c.C763T						PASS	.		PHE/LEU	213,3727		5,203,1762	10.0	10.0	10.0		763	-0.7	0.0	1	dbSNP_111	10	3,7787		0,3,3892	no	missense	IVL	NM_005547.2	22	5,206,5654	TT,TC,CC		0.0385,5.4061,1.8414	benign	255/586	152883036	216,11514	1970	3895	5865	SO:0001583	missense	3713	exon2			CTGGAGCTCTCTG	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.763C>T	1.37:g.152883036C>T	ENSP00000357753:p.Leu255Phe	169.0	0.0	0		208.0	88.0	0.423077	NM_005547	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	37	CCDS1030.1	31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	C	0.147	-1.096036	0.01843	0.054061	3.85E-4	ENSG00000163207	ENST00000368764;ENST00000392667	T;T	0.11821	2.96;2.74	0.329	-0.658	0.11428	.	.	.	.	.	T	0.01835	0.0058	L	0.29908	0.895	0.09310	N	1	B	0.32245	0.361	B	0.28305	0.088	T	0.47328	-0.9126	9	0.11794	T	0.64	.	4.7855	0.13223	0.3488:0.6511:0.0:1.0E-4	rs4459054;rs7413034	255	P07476	INVO_HUMAN	F	255;109	ENSP00000357753:L255F;ENSP00000376435:L109F	ENSP00000357753:L255F	L	+	1	0	IVL	151149660	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.401000	0.07232	-0.793000	0.04475	0.123000	0.15791	CTC	C|0.986;T|0.014	0.014	strong		0.657	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547	
RBM20	282996	hgsc.bcm.edu	37	10	112540884	112540884	+	Missense_Mutation	SNP	C	C	A	rs7908490	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:112540884C>A	ENST00000369519.3	+	2	575	c.517C>A	c.(517-519)Ccc>Acc	p.P173T		NM_001134363.1	NP_001127835.1	Q5T481	RBM20_HUMAN	RNA binding motif protein 20	173			P -> T (in dbSNP:rs7908490).		heart development (GO:0007507)|mRNA processing (GO:0006397)|positive regulation of RNA splicing (GO:0033120)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(4)|kidney(3)|large_intestine(1)|ovary(1)|skin(2)	12						TGCCTTTTCACCCCCCAGCCA	0.597													C|||	135	0.0269569	0.0976	0.0086	5008	,	,		19513	0.0		0.0	False		,,,				2504	0.0				p.P173T		Atlas-SNP	.											.	RBM20	50	.	0			c.C517A						PASS	.	C	THR/PRO	98,1286		2,94,596	34.0	33.0	33.0		517	1.5	0.1	10	dbSNP_116	33	0,3182		0,0,1591	yes	missense	RBM20	NM_001134363.1	38	2,94,2187	AA,AC,CC		0.0,7.0809,2.1463	probably-damaging	173/1228	112540884	98,4468	692	1591	2283	SO:0001583	missense	282996	exon2			TTTTCACCCCCCA	BX648563	CCDS44477.1	10q25.3	2014-09-17			ENSG00000203867	ENSG00000203867		"""RNA binding motif (RRM) containing"""	27424	protein-coding gene	gene with protein product		613171					Standard	NM_001134363		Approved		uc001kzf.2	Q5T481	OTTHUMG00000019043	ENST00000369519.3:c.517C>A	10.37:g.112540884C>A	ENSP00000358532:p.Pro173Thr	129.0	0.0	0		129.0	54.0	0.418605	NM_001134363	A6NIP5|B5A868|Q5JVI1	Missense_Mutation	SNP	ENST00000369519.3	37	CCDS44477.1	43	0.019688644688644688	39	0.07926829268292683	4	0.011049723756906077	0	0.0	0	0.0	C	11.77	1.736804	0.30774	0.070809	0.0	ENSG00000203867	ENST00000369519;ENST00000539821	D	0.89617	-2.54	5.51	1.54	0.23209	.	.	.	.	.	T	0.13543	0.0328	N	0.14661	0.345	0.09310	N	1	B	0.30824	0.296	B	0.19946	0.027	T	0.43458	-0.9390	9	0.34782	T	0.22	.	0.4254	0.00463	0.2389:0.2976:0.228:0.2354	rs7908490;rs7908490	173	Q5T481	RBM20_HUMAN	T	173	ENSP00000358532:P173T	ENSP00000358532:P173T	P	+	1	0	RBM20	112530874	0.009000	0.17119	0.087000	0.20705	0.988000	0.76386	0.078000	0.14761	0.279000	0.22186	0.591000	0.81541	CCC	C|0.970;A|0.030	0.030	strong		0.597	RBM20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050339.2	NM_001134363	
ROS1	6098	hgsc.bcm.edu	37	6	117681560	117681560	+	Silent	SNP	G	G	T	rs140639104	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:117681560G>T	ENST00000368508.3	-	22	3588	c.3390C>A	c.(3388-3390)gcC>gcA	p.A1130A	GOPC_ENST00000467125.1_Intron|ROS1_ENST00000368507.3_Silent_p.A1125A	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	1130	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		TAGATGTAAAGGCCCTAACCT	0.368			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""								G|||	12	0.00239617	0.0083	0.0014	5008	,	,		17507	0.0		0.0	False		,,,				2504	0.0				p.A1130A		Atlas-SNP	.		Dom	yes		6	6q22	6098	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)		"""O, E"""	.	ROS1	728	.	0			c.C3390A						PASS	.	G		37,4369	41.6+/-74.8	0,37,2166	81.0	76.0	78.0		3390	1.1	1.0	6	dbSNP_134	78	0,8600		0,0,4300	no	coding-synonymous	ROS1	NM_002944.2		0,37,6466	TT,TG,GG		0.0,0.8398,0.2845		1130/2348	117681560	37,12969	2203	4300	6503	SO:0001819	synonymous_variant	6098	exon22			TGTAAAGGCCCTA	M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"""Fibronectin type III domain containing"""	10261	protein-coding gene	gene with protein product		165020	"""v-ros avian UR2 sarcoma virus oncogene homolog 1"", ""v-ros UR2 sarcoma virus oncogene homolog 1 (avian)"", ""c-ros oncogene 1 , receptor tyrosine kinase"""			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.3390C>A	6.37:g.117681560G>T		75.0	0.0	0		73.0	24.0	0.328767	NM_002944	Q15368|Q5TDB5	Silent	SNP	ENST00000368508.3	37	CCDS5116.1																																																																																			G|0.998;T|0.002	0.002	strong		0.368	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1		
LRIT2	340745	hgsc.bcm.edu	37	10	85981756	85981756	+	Missense_Mutation	SNP	G	G	T	rs74145770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:85981756G>T	ENST00000372113.4	-	3	1578	c.1573C>A	c.(1573-1575)Cca>Aca	p.P525T	LRIT2_ENST00000538192.1_Missense_Mutation_p.P535T	NM_001017924.2	NP_001017924.1	A6NDA9	LRIT2_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 2	525						integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(13)|ovary(3)|prostate(6)|urinary_tract(1)	32						CAGACAGCTGGATGTTCTCTA	0.592													G|||	227	0.0453275	0.1672	0.0086	5008	,	,		19768	0.0		0.0	False		,,,				2504	0.0				p.P525T		Atlas-SNP	.											.	LRIT2	81	.	0			c.C1573A						PASS	.	G	THR/PRO	600,3806	252.1+/-258.6	50,500,1653	117.0	105.0	109.0		1573	-5.7	0.0	10	dbSNP_130	109	18,8582	12.6+/-44.7	0,18,4282	yes	missense	LRIT2	NM_001017924.2	38	50,518,5935	TT,TG,GG		0.2093,13.6178,4.7517	benign	525/551	85981756	618,12388	2203	4300	6503	SO:0001583	missense	340745	exon3			CAGCTGGATGTTC		CCDS31234.1, CCDS60581.1	10q23.2	2013-01-11	2007-06-19	2007-06-19	ENSG00000204033	ENSG00000204033		"""Immunoglobulin superfamily / I-set domain containing"""	23443	protein-coding gene	gene with protein product			"""leucine rich repeat containing 22"""	LRRC22			Standard	NM_001017924		Approved	AC022389.4	uc001kcy.3	A6NDA9	OTTHUMG00000018633	ENST00000372113.4:c.1573C>A	10.37:g.85981756G>T	ENSP00000361185:p.Pro525Thr	159.0	0.0	0		208.0	119.0	0.572115	NM_001017924	B7ZME6	Missense_Mutation	SNP	ENST00000372113.4	37	CCDS31234.1	91	0.041666666666666664	87	0.17682926829268292	4	0.011049723756906077	0	0.0	0	0.0	G	0.610	-0.825514	0.02734	0.136178	0.002093	ENSG00000204033	ENST00000372113;ENST00000538192	T;T	0.16597	2.33;2.33	4.57	-5.65	0.02459	.	1.918670	0.02557	N	0.096284	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.12013	0.005;0.001	B;B	0.06405	0.002;0.001	T	0.31336	-0.9947	9	0.13108	T	0.6	.	3.6424	0.08172	0.1993:0.4518:0.2433:0.1056	.	535;525	B7ZME6;A6NDA9	.;LRIT2_HUMAN	T	525;535	ENSP00000361185:P525T;ENSP00000438264:P535T	ENSP00000361185:P525T	P	-	1	0	LRIT2	85971736	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.226000	0.09139	-1.353000	0.02191	0.655000	0.94253	CCA	G|0.957;T|0.043	0.043	strong		0.592	LRIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049110.4	XM_291697	
NLRC4	58484	hgsc.bcm.edu	37	2	32463353	32463353	+	Missense_Mutation	SNP	A	A	G	rs202095832		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:32463353A>G	ENST00000404025.2	-	7	2857	c.2369T>C	c.(2368-2370)cTg>cCg	p.L790P	NLRC4_ENST00000342905.6_Missense_Mutation_p.L125P|NLRC4_ENST00000402280.1_Missense_Mutation_p.L790P|NLRC4_ENST00000360906.5_Missense_Mutation_p.L790P			Q9NPP4	NLRC4_HUMAN	NLR family, CARD domain containing 4	790					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of innate immune response (GO:0002218)|defense response to bacterium (GO:0042742)|detection of bacterium (GO:0016045)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of apoptotic process (GO:0043065)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein homooligomerization (GO:0051260)|pyroptosis (GO:0070269)	cytosol (GO:0005829)|intracellular (GO:0005622)|IPAF inflammasome complex (GO:0072557)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(1)|ovary(3)|skin(2)|stomach(2)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					CATCTTCTTCAGGTTTTTCAG	0.368													A|||	1	0.000199681	0.0008	0.0	5008	,	,		19319	0.0		0.0	False		,,,				2504	0.0				p.L790P		Atlas-SNP	.											.	NLRC4	165	.	0			c.T2369C						PASS	.	A	PRO/LEU,PRO/LEU,PRO/LEU	3,4403	6.2+/-15.9	0,3,2200	101.0	101.0	101.0		2369,2369,2369	4.6	0.9	2		101	0,8600		0,0,4300	no	missense,missense,missense	NLRC4	NM_001199138.1,NM_001199139.1,NM_021209.4	98,98,98	0,3,6500	GG,GA,AA		0.0,0.0681,0.0231	probably-damaging,probably-damaging,probably-damaging	790/1025,790/1025,790/1025	32463353	3,13003	2203	4300	6503	SO:0001583	missense	58484	exon6			TTCTTCAGGTTTT	AF376061	CCDS33174.1	2p22-p21	2008-08-27	2006-12-08	2006-12-08	ENSG00000091106	ENSG00000091106		"""Nucleotide-binding domain and leucine rich repeat containing"""	16412	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 4"", ""NOD-like receptor C4"""	606831	"""caspase recruitment domain family, member 12"""	CARD12		11374873	Standard	NM_021209		Approved	CLAN1, ipaf, CLANA, CLANB, CLANC, CLAND, CLR2.1, CLAN	uc021vfq.1	Q9NPP4	OTTHUMG00000152107	ENST00000404025.2:c.2369T>C	2.37:g.32463353A>G	ENSP00000385090:p.Leu790Pro	91.0	0.0	0		113.0	61.0	0.539823	NM_001199138	A8K9F8|B2RBQ3|B3KTF0|D6W580|Q96J81|Q96J82|Q96J83	Missense_Mutation	SNP	ENST00000404025.2	37	CCDS33174.1	.	.	.	.	.	.	.	.	.	.	A	12.13	1.846213	0.32606	6.81E-4	0.0	ENSG00000091106	ENST00000360906;ENST00000402280;ENST00000342905;ENST00000404025	T;T;T;T	0.57752	0.38;0.38;0.38;0.38	4.63	4.63	0.57726	.	0.000000	0.31949	N	0.006818	T	0.64527	0.2606	M	0.63843	1.955	0.34053	D	0.656327	D;D	0.71674	0.998;0.994	D;P	0.65874	0.939;0.879	T	0.71251	-0.4648	9	0.34782	T	0.22	-3.8349	10.6228	0.45489	1.0:0.0:0.0:0.0	.	125;790	Q9NPP4-2;Q9NPP4	.;NLRC4_HUMAN	P	790;790;125;790	ENSP00000354159:L790P;ENSP00000385428:L790P;ENSP00000339666:L125P;ENSP00000385090:L790P	ENSP00000339666:L125P	L	-	2	0	NLRC4	32316857	0.984000	0.35163	0.947000	0.38551	0.111000	0.19643	1.992000	0.40737	2.088000	0.63022	0.533000	0.62120	CTG	.	.	weak		0.368	NLRC4-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325222.2	NM_021209	
EXPH5	23086	hgsc.bcm.edu	37	11	108383560	108383560	+	Missense_Mutation	SNP	T	T	A	rs10890850	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:108383560T>A	ENST00000265843.4	-	6	2784	c.2674A>T	c.(2674-2676)Aat>Tat	p.N892Y	EXPH5_ENST00000524840.1_5'Flank|EXPH5_ENST00000428840.1_Missense_Mutation_p.N816Y|EXPH5_ENST00000525344.1_Missense_Mutation_p.N885Y|EXPH5_ENST00000443411.1_Missense_Mutation_p.N704Y	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	892			N -> Y (in dbSNP:rs10890850).		intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		AGGGAAGAATTCTTTGATGGT	0.438													T|||	270	0.0539137	0.1316	0.0115	5008	,	,		19382	0.0119		0.002	False		,,,				2504	0.0757				p.N892Y		Atlas-SNP	.											.	EXPH5	193	.	0			c.A2674T						PASS	.	T	TYR/ASN	493,3909	229.8+/-244.2	29,435,1737	182.0	167.0	172.0		2674	-2.0	0.0	11	dbSNP_120	172	9,8587	7.1+/-27.0	0,9,4289	yes	missense	EXPH5	NM_015065.2	143	29,444,6026	AA,AT,TT		0.1047,11.1995,3.8621	benign	892/1990	108383560	502,12496	2201	4298	6499	SO:0001583	missense	23086	exon6			AAGAATTCTTTGA		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.2674A>T	11.37:g.108383560T>A	ENSP00000265843:p.Asn892Tyr	126.0	0.0	0		130.0	86.0	0.661538	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	37	CCDS8341.1	59	0.027014652014652016	46	0.09349593495934959	5	0.013812154696132596	7	0.012237762237762238	1	0.0013192612137203166	T	14.92	2.680490	0.47886	0.111995	0.001047	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000526312;ENST00000533052	T;T;T;T;T;T	0.04603	4.17;4.1;3.95;4.17;4.02;3.59	5.74	-1.97	0.07503	.	0.712890	0.13437	N	0.387972	T	0.00109	0.0003	L	0.44542	1.39	0.09310	N	1	P	0.49090	0.919	B	0.43445	0.42	T	0.40813	-0.9543	10	0.72032	D	0.01	-0.8859	6.5046	0.22188	0.0:0.4682:0.1578:0.3739	rs10890850;rs10890850	892	Q8NEV8	EXPH5_HUMAN	Y	892;816;704;885;816;704	ENSP00000265843:N892Y;ENSP00000391966:N816Y;ENSP00000411390:N704Y;ENSP00000432546:N885Y;ENSP00000432683:N816Y;ENSP00000446434:N704Y	ENSP00000265843:N892Y	N	-	1	0	EXPH5	107888770	0.000000	0.05858	0.002000	0.10522	0.230000	0.25150	-0.173000	0.09854	-0.270000	0.09285	0.460000	0.39030	AAT	T|0.967;A|0.033	0.033	strong		0.438	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
MUC4	4585	hgsc.bcm.edu	37	3	195511397	195511397	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195511397G>A	ENST00000463781.3	-	2	7513	c.7054C>T	c.(7054-7056)Cct>Tct	p.P2352S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P2352S	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)		ACATGAAGAGGGGTGGCGTGA	0.587																																					p.P2352S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,+1,3	MUC4	1505	3	0			c.C7054T						scavenged	.						16.0	14.0	14.0					3																	195511397		675	1561	2236	SO:0001583	missense	4585	exon2			GAAGAGGGGTGGC	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.7054C>T	3.37:g.195511397G>A	ENSP00000417498:p.Pro2352Ser	377.0	1.0	0.00265252		142.0	9.0	0.0633803	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	G	5.636	0.301959	0.10678	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29655	1.56;1.56	.	.	.	.	.	.	.	.	T	0.12050	0.0293	N	0.08118	0	0.09310	N	1	B	0.14438	0.01	B	0.06405	0.002	T	0.31475	-0.9942	7	.	.	.	.	4.3952	0.11360	0.3325:0.0:0.6675:0.0	rs6799339	2352	E7ESK3	.	S	2352	ENSP00000417498:P2352S;ENSP00000420243:P2352S	.	P	-	1	0	MUC4	196995792	0.025000	0.19082	0.006000	0.13384	0.066000	0.16364	0.045000	0.14013	-0.417000	0.07461	0.064000	0.15345	CCT	.	.	none		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ABCA6	23460	hgsc.bcm.edu	37	17	67109493	67109493	+	Silent	SNP	A	A	G	rs2058128	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:67109493A>G	ENST00000284425.2	-	15	2085	c.1911T>C	c.(1909-1911)ctT>ctC	p.L637L		NM_080284.2	NP_525023.2	Q8N139	ABCA6_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 6	637	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(6)|endometrium(5)|kidney(17)|large_intestine(18)|lung(20)|ovary(3)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	82	Breast(10;5.65e-12)					GTTCATCTAAAAGCAAAATCT	0.363													G|||	631	0.125998	0.4531	0.0447	5008	,	,		20176	0.0		0.001	False		,,,				2504	0.0				p.L637L		Atlas-SNP	.											.	ABCA6	210	.	0			c.T1911C						PASS	.	G		1650,2756	653.9+/-399.7	293,1064,846	57.0	56.0	57.0		1911	-4.0	0.7	17	dbSNP_94	57	11,8587	817.7+/-406.9	0,11,4288	no	coding-synonymous	ABCA6	NM_080284.2		293,1075,5134	GG,GA,AA		0.1279,37.4489,12.773		637/1618	67109493	1661,11343	2203	4299	6502	SO:0001819	synonymous_variant	23460	exon15			ATCTAAAAGCAAA	U66680	CCDS11683.1	17q21	2012-03-14			ENSG00000154262	ENSG00000154262		"""ATP binding cassette transporters / subfamily A"""	36	protein-coding gene	gene with protein product		612504				8894702	Standard	NM_080284		Approved	EST155051	uc002jhw.1	Q8N139		ENST00000284425.2:c.1911T>C	17.37:g.67109493A>G		53.0	0.0	0		64.0	30.0	0.46875	NM_080284	Q6NSH9|Q8N856|Q8WWZ6	Silent	SNP	ENST00000284425.2	37	CCDS11683.1																																																																																			A|0.876;G|0.124	0.124	strong		0.363	ABCA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450463.1	NM_080284	
ODF1	4956	hgsc.bcm.edu	37	8	103573086	103573086	+	Missense_Mutation	SNP	T	T	C	rs11995900	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:103573086T>C	ENST00000285402.3	+	2	883	c.727T>C	c.(727-729)Ttt>Ctt	p.F243L	ODF1_ENST00000518835.1_Missense_Mutation_p.F36L	NM_024410.3	NP_077721.2	Q14990	ODFP1_HUMAN	outer dense fiber of sperm tails 1	243			F -> L (in dbSNP:rs11995900).		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	nucleus (GO:0005634)|outer dense fiber (GO:0001520)				NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(14;2.76e-05)|all_epithelial(15;4.54e-08)|Lung NSC(17;4.08e-05)|all_lung(17;9.15e-05)		OV - Ovarian serous cystadenocarcinoma(57;0.000125)|STAD - Stomach adenocarcinoma(118;0.0826)			TGGAAGCCGATTTTCCTGTAG	0.537													T|||	386	0.0770767	0.2587	0.0303	5008	,	,		19863	0.0129		0.0099	False		,,,				2504	0.0				p.F243L		Atlas-SNP	.											.	ODF1	55	.	0			c.T727C						PASS	.	T	LEU/PHE	1038,3368	365.1+/-317.3	121,796,1286	93.0	100.0	97.0		727	4.0	1.0	8	dbSNP_120	97	37,8563	22.8+/-68.1	0,37,4263	yes	missense	ODF1	NM_024410.3	22	121,833,5549	CC,CT,TT		0.4302,23.5588,8.2654	benign	243/251	103573086	1075,11931	2203	4300	6503	SO:0001583	missense	4956	exon2			AGCCGATTTTCCT	M93131	CCDS6293.1	8q22	2011-09-05	2002-10-21		ENSG00000155087	ENSG00000155087		"""Heat shock proteins / HSPB"""	8113	protein-coding gene	gene with protein product	"""cancer/testis antigen 133"""	182878	"""outer dense fibre of sperm tails 1"""			8305202	Standard	NM_024410		Approved	ODFPG, ODF27, RT7, HSPB10, CT133	uc003ykt.2	Q14990	OTTHUMG00000164719	ENST00000285402.3:c.727T>C	8.37:g.103573086T>C	ENSP00000285402:p.Phe243Leu	93.0	0.0	0		79.0	31.0	0.392405	NM_024410	Q3SX72	Missense_Mutation	SNP	ENST00000285402.3	37	CCDS6293.1	170	0.07783882783882784	146	0.2967479674796748	11	0.03038674033149171	9	0.015734265734265736	4	0.005277044854881266	T	15.81	2.942523	0.53079	0.235588	0.004302	ENSG00000155087	ENST00000285402;ENST00000518835	T;T	0.29655	1.56;1.73	5.18	3.95	0.45737	.	0.114042	0.40302	N	0.001133	T	0.00012	0.0000	N	0.22421	0.69	0.32344	P	0.559367	B	0.11235	0.004	B	0.12156	0.007	T	0.24083	-1.0170	9	0.87932	D	0	-31.0421	8.7103	0.34380	0.1694:0.0:0.0:0.8306	rs11995900;rs52827661;rs59122996;rs11995900	243	Q14990	ODFP1_HUMAN	L	243;36	ENSP00000285402:F243L;ENSP00000430023:F36L	ENSP00000285402:F243L	F	+	1	0	ODF1	103642262	0.945000	0.32115	1.000000	0.80357	0.997000	0.91878	2.400000	0.44504	2.106000	0.64143	0.528000	0.53228	TTT	T|0.911;C|0.089	0.089	strong		0.537	ODF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379884.1		
PON2	5445	hgsc.bcm.edu	37	7	95039394	95039394	+	Missense_Mutation	SNP	C	C	G	rs17876152	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:95039394C>G	ENST00000222572.3	-	6	760	c.514G>C	c.(514-516)Gtt>Ctt	p.V172L	PON2_ENST00000536183.1_Missense_Mutation_p.V193L|PON2_ENST00000483292.1_5'UTR|PON2_ENST00000433091.2_Missense_Mutation_p.V160L			Q15165	PON2_HUMAN	paraoxonase 2	172			V -> L (in dbSNP:rs17876152). {ECO:0000269|Ref.5}.		aromatic compound catabolic process (GO:0019439)|response to oxidative stress (GO:0006979)	extracellular region (GO:0005576)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arylesterase activity (GO:0004064)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|prostate(1)	9	all_cancers(62;9.35e-11)|all_epithelial(64;3.37e-09)		STAD - Stomach adenocarcinoma(171;0.0151)			GCCGGTCCAACAGCTGTGATG	0.358													C|||	54	0.0107827	0.0378	0.0014	5008	,	,		15286	0.0		0.002	False		,,,				2504	0.001				p.V172L	GBM(42;803 823 13649 23368 31463)	Atlas-SNP	.											.	PON2	32	.	0			c.G514C						PASS	.	C	LEU/VAL,LEU/VAL	149,4257	104.3+/-142.8	2,145,2056	82.0	78.0	79.0		514,478	5.0	1.0	7	dbSNP_124	79	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	PON2	NM_000305.2,NM_001018161.1	32,32	2,147,6354	GG,GC,CC		0.0233,3.3818,1.161	benign,benign	172/355,160/343	95039394	151,12855	2203	4300	6503	SO:0001583	missense	5445	exon6			GTCCAACAGCTGT	M63012, AF001601	CCDS5640.1, CCDS47644.1	7q21.3	2014-03-14			ENSG00000105854	ENSG00000105854	3.1.1.2	"""Paraoxonases"""	9205	protein-coding gene	gene with protein product	"""paraoxonase nirs"", ""arylesterase 2"""	602447				8661009, 9714608	Standard	XM_005250453		Approved		uc003unv.3	Q15165	OTTHUMG00000153948	ENST00000222572.3:c.514G>C	7.37:g.95039394C>G	ENSP00000222572:p.Val172Leu	83.0	0.0	0		108.0	58.0	0.537037	NM_000305	A4D1H7|B2RCP9|B4DJD5|O15114|O15115|O75856|Q5FBX7|Q86YL0	Missense_Mutation	SNP	ENST00000222572.3	37	CCDS5640.1	18	0.008241758241758242	18	0.036585365853658534	0	0.0	0	0.0	0	0.0	C	9.490	1.100457	0.20552	0.033818	2.33E-4	ENSG00000105854	ENST00000536183;ENST00000355659;ENST00000433091;ENST00000222572	T;T;T	0.40756	2.27;1.02;2.27	4.97	4.97	0.65823	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.85682	D	0.000000	T	0.11067	0.0270	L	0.58302	1.8	0.51767	D	0.999939	B;B	0.12013	0.005;0.005	B;B	0.18263	0.021;0.021	T	0.03240	-1.1057	10	0.20519	T	0.43	-18.3381	10.5089	0.44849	0.0:0.7892:0.1357:0.0752	rs17876152;rs58276578	172;172	A4D1H7;Q15165	.;PON2_HUMAN	L	193;170;160;172	ENSP00000440282:V193L;ENSP00000404622:V160L;ENSP00000222572:V172L	ENSP00000222572:V172L	V	-	1	0	PON2	94877330	0.359000	0.24955	1.000000	0.80357	0.502000	0.33828	0.451000	0.21779	2.754000	0.94517	0.650000	0.86243	GTT	C|0.983;G|0.017	0.017	strong		0.358	PON2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333142.1	NM_000305	
TAF1	6872	hgsc.bcm.edu	37	X	70595132	70595132	+	Silent	SNP	T	T	C	rs5981106	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:70595132T>C	ENST00000373790.4	+	4	579	c.528T>C	c.(526-528)acT>acC	p.T176T	TAF1_ENST00000276072.3_Silent_p.T176T|TAF1_ENST00000449580.1_Silent_p.T176T|TAF1_ENST00000423759.1_Silent_p.T176T	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	176	Protein kinase 1.				cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				ATTCTATTACTGGTGGTAAGT	0.438													C|||	293	0.0776159	0.2012	0.0274	3775	,	,		12232	0.0		0.005	False		,,,				2504	0.0031				p.T176T		Atlas-SNP	.											.	TAF1	439	.	0			c.T528C						PASS	.	C	,	921,2914		89,609,134,934,437	96.0	82.0	87.0		528,528	-6.1	0.0	X	dbSNP_114	87	38,6690		0,28,10,2400,1862	no	coding-synonymous,coding-synonymous	TAF1	NM_004606.3,NM_138923.2	,	89,637,144,3334,2299	CC,CT,C,TT,T		0.5648,24.0156,9.0789	,	176/1894,176/1873	70595132	959,9604	2203	4300	6503	SO:0001819	synonymous_variant	6872	exon4			TATTACTGGTGGT		CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"""Chromatin-modifying enzymes / K-acetyltransferases"""	11535	protein-coding gene	gene with protein product		313650	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD"", ""dystonia 3 (with Parkinsonism)"""	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.528T>C	X.37:g.70595132T>C		141.0	0.0	0		158.0	67.0	0.424051	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Silent	SNP	ENST00000373790.4	37	CCDS35325.1																																																																																			T|0.891;C|0.109	0.109	strong		0.438	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606	
MFRP	83552	hgsc.bcm.edu	37	11	119216867	119216867	+	Missense_Mutation	SNP	G	G	C	rs139436396	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:119216867G>C	ENST00000530681.1	-	3	304	c.160C>G	c.(160-162)Cgg>Ggg	p.R54G	MFRP_ENST00000555262.1_Missense_Mutation_p.R54G|C1QTNF5_ENST00000445041.2_5'UTR|MFRP_ENST00000360167.4_Missense_Mutation_p.R54G|MFRP_ENST00000449574.2_Missense_Mutation_p.R54G|MFRP_ENST00000529147.1_5'UTR	NM_001278431.1	NP_001265360.1	Q9BY79	MFRP_HUMAN	membrane frizzled-related protein	54			R -> G (in dbSNP:rs139436396). {ECO:0000269|PubMed:16352475}.		embryo development (GO:0009790)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)|urinary_tract(1)	18		Medulloblastoma(222;0.0523)|Breast(348;0.174)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.84e-05)		CGAGGACGCCGACCTGCGGGT	0.642													G|||	55	0.0109824	0.0371	0.0086	5008	,	,		17805	0.0		0.0	False		,,,				2504	0.0				p.R54G		Atlas-SNP	.											.	MFRP	63	.	0			c.C160G						PASS	.	G	,GLY/ARG	111,4267		2,107,2080	19.0	18.0	18.0		,160	4.3	0.8	11	dbSNP_134	18	1,8565		0,1,4282	yes	utr-5,missense	MFRP,C1QTNF5	NM_015645.3,NM_031433.2	,125	2,108,6362	CC,CG,GG		0.0117,2.5354,0.8653	,benign	,54/580	119216867	112,12832	2189	4283	6472	SO:0001583	missense	83552	exon3			GACGCCGACCTGC	AB055505	CCDS8421.1	11q23.3	2014-01-28			ENSG00000235718	ENSG00000235718			18121	protein-coding gene	gene with protein product	"""membrane-type frizzled-related protein"", ""complement C1q tumor necrosis factor-related protein 5 precursor variant 1"""	606227				11263980	Standard	NM_031433		Approved	FLJ30570, rd6, NNO2, C1QTNF5	uc001pwj.2	Q9BY79		ENST00000530681.1:c.160C>G	11.37:g.119216867G>C	ENSP00000456533:p.Arg54Gly	48.0	0.0	0		46.0	23.0	0.5	NM_031433	B0YJ36|B0YJ37|B4DHN8|Q335M3|Q96DQ9	Missense_Mutation	SNP	ENST00000530681.1	37	CCDS8421.1	15	0.006868131868131868	15	0.03048780487804878	0	0.0	0	0.0	0	0.0	G	17.80	3.477400	0.63849	0.025354	1.17E-4	ENSG00000235718	ENST00000555262;ENST00000449574;ENST00000360167	T;T;T	0.67698	-0.28;-0.28;1.88	5.24	4.27	0.50696	.	0.647065	0.15397	N	0.264485	T	0.29126	0.0724	L	0.27053	0.805	0.24539	N	0.994075	P;B	0.39157	0.662;0.319	B;B	0.37833	0.259;0.097	T	0.26643	-1.0097	10	0.30078	T	0.28	-13.8891	13.6734	0.62438	0.0:0.1544:0.8456:0.0	.	54;54	B4DHN8;Q9BY79	.;MFRP_HUMAN	G	54	ENSP00000450509:R54G;ENSP00000391664:R54G;ENSP00000353291:R54G	ENSP00000353291:R54G	R	-	1	2	MFRP	118722077	0.010000	0.17322	0.842000	0.33263	0.537000	0.34900	0.833000	0.27504	2.601000	0.87937	0.655000	0.94253	CGG	G|0.990;C|0.010	0.010	strong		0.642	MFRP-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000415179.1	NM_031433	
RASA2	5922	hgsc.bcm.edu	37	3	141248572	141248572	+	Missense_Mutation	SNP	A	A	C	rs144759014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:141248572A>C	ENST00000452898.1	+	4	413	c.378A>C	c.(376-378)gaA>gaC	p.E126D	RASA2_ENST00000286364.3_Missense_Mutation_p.E126D	NM_006506.2	NP_006497.2	Q15283	RASA2_HUMAN	RAS p21 protein activator 2	126					intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)			NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	34						TCAAAAAAGAAGACTTGTGTA	0.318													A|||	3	0.000599042	0.0023	0.0	5008	,	,		15787	0.0		0.0	False		,,,				2504	0.0				p.E126D		Atlas-SNP	.											RASA2_ENST00000286364,temporal_lobe,glioma,+2,2	RASA2	169	2	0			c.A378C						PASS	.	A	ASP/GLU	7,4399	12.9+/-30.5	0,7,2196	72.0	74.0	74.0		378	4.7	1.0	3	dbSNP_134	74	0,8598		0,0,4299	yes	missense	RASA2	NM_006506.2	45	0,7,6495	CC,CA,AA		0.0,0.1589,0.0538	possibly-damaging	126/850	141248572	7,12997	2203	4299	6502	SO:0001583	missense	5922	exon4			AAAAGAAGACTTG	AF115573	CCDS3117.1	3q22-q23	2013-01-10			ENSG00000155903	ENSG00000155903		"""Pleckstrin homology (PH) domain containing"""	9872	protein-coding gene	gene with protein product		601589				8699317	Standard	NM_006506		Approved	GAP1M	uc003etz.1	Q15283	OTTHUMG00000160221	ENST00000452898.1:c.378A>C	3.37:g.141248572A>C	ENSP00000391677:p.Glu126Asp	35.0	0.0	0		42.0	17.0	0.404762	NM_006506	A8K7K1|G3V0F9|O00695|Q15284|Q92594|Q99577|Q9UEQ2	Missense_Mutation	SNP	ENST00000452898.1	37		.	.	.	.	.	.	.	.	.	.	A	16.18	3.051372	0.55218	0.001589	0.0	ENSG00000155903	ENST00000286364;ENST00000452898	T;T	0.70869	-0.52;-0.52	5.84	4.68	0.58851	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.055137	0.64402	D	0.000001	T	0.70064	0.3181	M	0.80183	2.485	0.46356	D	0.999007	B;B;B	0.23490	0.051;0.086;0.051	B;B;B	0.31686	0.063;0.134;0.063	T	0.63060	-0.6721	10	0.21014	T	0.42	.	8.3803	0.32468	0.8469:0.0:0.1531:0.0	.	126;126;126	A8K7K1;G3V0F9;Q15283	.;.;RASA2_HUMAN	D	126	ENSP00000286364:E126D;ENSP00000391677:E126D	ENSP00000286364:E126D	E	+	3	2	RASA2	142731262	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	1.541000	0.36126	1.030000	0.39839	0.533000	0.62120	GAA	A|1.000;C|0.000	0.000	strong		0.318	RASA2-201	KNOWN	basic	protein_coding	protein_coding		NM_006506	
MT-CO1	4512	hgsc.bcm.edu	37	M	6071	6071	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:6071T>C	ENST00000361624.2	+	1	168	c.168T>C	c.(166-168)gtT>gtC	p.V56V	MT-TL1_ENST00000386347.1_RNA|MT-ATP6_ENST00000361899.2_5'Flank|MT-TD_ENST00000387419.1_RNA|MT-TA_ENST00000387392.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-TS1_ENST00000387416.2_RNA|MT-TY_ENST00000387409.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ATP8_ENST00000361851.1_5'Flank|MT-TN_ENST00000387400.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-TI_ENST00000387365.1_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-CO2_ENST00000361739.1_5'Flank			P00395	COX1_HUMAN	mitochondrially encoded cytochrome c oxidase I	56					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex IV (GO:0005751)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(4)|endometrium(25)|kidney(19)|lung(3)|prostate(3)	54						ATCTACAACGTTATCGTCACA	0.498																																					p.V56V		Atlas-SNP	.											.	.	.	.	0			c.T168C						PASS	.																																			SO:0001819	synonymous_variant	5742	exon1			CAACGTTATCGTC			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198804	ENSG00000198804		"""Mitochondrial respiratory chain complex / Complex IV"""	7419	protein-coding gene	gene with protein product		516030	"""cytochrome c oxidase I"""	MTCO1		7219534	Standard			Approved	COX1, COI		P00395		ENST00000361624.2:c.168T>C	M.37:g.6071T>C		13.0	0.0	0		12.0	12.0	1	ENST00000361624	Q34770	Silent	SNP	ENST00000361624.2	37																																																																																				.	.	none		0.498	MT-CO1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024028	
KCNT1	57582	hgsc.bcm.edu	37	9	138651648	138651648	+	Silent	SNP	A	A	G	rs61739517	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:138651648A>G	ENST00000263604.3	+	11	921	c.921A>G	c.(919-921)ccA>ccG	p.P307P	KCNT1_ENST00000490355.2_Silent_p.P307P|KCNT1_ENST00000486577.2_Silent_p.P287P|KCNT1_ENST00000487664.1_Silent_p.P281P|KCNT1_ENST00000371757.2_Silent_p.P326P|KCNT1_ENST00000491806.2_Silent_p.P293P|KCNT1_ENST00000488444.2_Silent_p.P307P|KCNT1_ENST00000298480.5_Silent_p.P326P			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	307					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		AGATCTGGCCATCGCAGCTGC	0.642													A|||	142	0.0283546	0.1051	0.0043	5008	,	,		20814	0.0		0.0	False		,,,				2504	0.0				p.P326P		Atlas-SNP	.											.	KCNT1	139	.	0			c.A978G						PASS	.	A		385,4021	194.0+/-219.0	20,345,1838	137.0	98.0	111.0		978	-9.7	0.7	9	dbSNP_129	111	4,8596	1.2+/-3.3	0,4,4296	no	coding-synonymous	KCNT1	NM_020822.2		20,349,6134	GG,GA,AA		0.0465,8.7381,2.9909		326/1236	138651648	389,12617	2203	4300	6503	SO:0001819	synonymous_variant	57582	exon11			CTGGCCATCGCAG	AB037843	CCDS35175.1, CCDS35175.2, CCDS65188.1	9q34.3	2012-07-05			ENSG00000107147	ENSG00000107147		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18865	protein-coding gene	gene with protein product		608167				10718198, 16382103	Standard	NM_020822		Approved	KCa4.1, KIAA1422	uc011mdq.2	Q5JUK3	OTTHUMG00000020917	ENST00000263604.3:c.921A>G	9.37:g.138651648A>G		135.0	0.0	0		116.0	39.0	0.336207	NM_020822	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	Silent	SNP	ENST00000263604.3	37																																																																																				A|0.967;G|0.033	0.033	strong		0.642	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_020822	
ACACB	32	hgsc.bcm.edu	37	12	109637234	109637234	+	Silent	SNP	G	G	T	rs73398054	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:109637234G>T	ENST00000338432.7	+	18	2774	c.2655G>T	c.(2653-2655)acG>acT	p.T885T	ACACB_ENST00000377848.3_Silent_p.T885T|ACACB_ENST00000377854.5_Silent_p.T885T			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	885					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	GCAATAAGACGTGTGTGTTTG	0.552													G|||	34	0.00678914	0.0234	0.0043	5008	,	,		18076	0.0		0.0	False		,,,				2504	0.0				p.T885T		Atlas-SNP	.											.	ACACB	330	.	0			c.G2655T						PASS	.						146.0	131.0	136.0					12																	109637234		2203	4300	6503	SO:0001819	synonymous_variant	32	exon17			TAAGACGTGTGTG	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 2"""	601557	"""acetyl-Coenzyme A carboxylase beta"""			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.2655G>T	12.37:g.109637234G>T		109.0	0.0	0		96.0	46.0	0.479167	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Silent	SNP	ENST00000338432.7	37	CCDS31898.1																																																																																			A|0.006;G|0.992;T|0.002	0.002	strong		0.552	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
MOAP1	64112	hgsc.bcm.edu	37	14	93652734	93652734	+	5'Flank	SNP	C	C	T	rs61744704	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:93652734C>T	ENST00000556883.1	-	0	0				TMEM251_ENST00000283534.4_Silent_p.A38A|TMEM251_ENST00000415050.2_Silent_p.A76A|MOAP1_ENST00000298894.4_5'Flank|RP11-371E8.4_ENST00000557048.1_Intron|RP11-371E8.4_ENST00000557574.1_Silent_p.A38A			Q96BY2	MOAP1_HUMAN	modulator of apoptosis 1						apoptotic signaling pathway (GO:0097190)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of apoptotic process (GO:0043065)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:0001844)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)	13		all_cancers(154;0.00528)|Acute lymphoblastic leukemia(33;0.0497)|all_epithelial(191;0.125)|all_neural(303;0.13)		Epithelial(152;0.178)|all cancers(159;0.2)|COAD - Colon adenocarcinoma(157;0.204)		ACAGGCTGGCCTTGGAACACA	0.478													C|||	20	0.00399361	0.0151	0.0	5008	,	,		18903	0.0		0.0	False		,,,				2504	0.0				p.A76A		Atlas-SNP	.											.	.	.	.	0			c.C228T						PASS	.	C	,	42,3868		0,42,1913	165.0	163.0	164.0		228,114	-0.2	1.0	14	dbSNP_129	164	0,8292		0,0,4146	no	coding-synonymous,coding-synonymous	C14orf109	NM_001098621.1,NM_015676.1	,	0,42,6059	TT,TC,CC		0.0,1.0742,0.3442	,	76/170,38/132	93652734	42,12160	1955	4146	6101	SO:0001631	upstream_gene_variant	26175	exon2			GCTGGCCTTGGAA	BC015044	CCDS9908.1	14q32.12	2012-02-09			ENSG00000165943	ENSG00000165943		"""Paraneoplastic Ma antigens"""	16658	protein-coding gene	gene with protein product	"""paraneoplastic Ma antigen family member 4"""	609485				11060313	Standard	NM_022151		Approved	MAP-1, PNMA4	uc001ybj.3	Q96BY2	OTTHUMG00000169184		14.37:g.93652734C>T	Exception_encountered	246.0	0.0	0		263.0	133.0	0.505703	NM_001098621	B2RDF6|Q9H833|Q9HAS1	Silent	SNP	ENST00000556883.1	37	CCDS9908.1																																																																																			C|0.997;T|0.003	0.003	strong		0.478	MOAP1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412685.1		
ERP27	121506	hgsc.bcm.edu	37	12	15070169	15070169	+	Silent	SNP	T	T	A	rs35203261	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:15070169T>A	ENST00000266397.2	-	5	1092	c.519A>T	c.(517-519)ccA>ccT	p.P173P	ERP27_ENST00000544881.1_5'UTR|ERP27_ENST00000540097.1_Silent_p.P72P	NM_152321.2	NP_689534.1	Q96DN0	ERP27_HUMAN	endoplasmic reticulum protein 27	173						endoplasmic reticulum (GO:0005783)				breast(2)|cervix(2)|endometrium(2)|kidney(3)|large_intestine(4)|lung(3)|prostate(2)|skin(1)	19						CTTCATACTCTGGGGAGGCCT	0.458													T|||	123	0.0245607	0.09	0.0043	5008	,	,		20881	0.0		0.0	False		,,,				2504	0.001				p.P173P		Atlas-SNP	.											.	ERP27	37	.	0			c.A519T						PASS	.	T		319,4087	170.5+/-200.9	8,303,1892	216.0	184.0	195.0		519	0.8	1.0	12	dbSNP_126	195	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	ERP27	NM_152321.2		8,307,6188	AA,AT,TT		0.0465,7.2401,2.4835		173/274	15070169	323,12683	2203	4300	6503	SO:0001819	synonymous_variant	121506	exon5			ATACTCTGGGGAG	AK056677	CCDS8670.1, CCDS73450.1	12p12.3	2011-10-19	2009-02-23	2007-03-26	ENSG00000139055	ENSG00000139055		"""Protein disulfide isomerases"""	26495	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 8"""	610642	"""chromosome 12 open reading frame 46"", ""endoplasmic reticulum protein 27 kDa"""	C12orf46		12975309, 16940051	Standard	XM_005253303		Approved	FLJ32115, ERp27, PDIA8	uc001rco.3	Q96DN0	OTTHUMG00000168741	ENST00000266397.2:c.519A>T	12.37:g.15070169T>A		229.0	0.0	0		229.0	102.0	0.445415	NM_152321		Silent	SNP	ENST00000266397.2	37	CCDS8670.1																																																																																			T|0.980;A|0.020	0.020	strong		0.458	ERP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400868.1	NM_152321	
CEACAM8	1088	hgsc.bcm.edu	37	19	43093793	43093793	+	Silent	SNP	G	G	A	rs10418988	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43093793G>A	ENST00000244336.5	-	3	620	c.519C>T	c.(517-519)aaC>aaT	p.N173N	LIPE-AS1_ENST00000594624.2_RNA|CEACAM8_ENST00000599005.1_Intron|LIPE-AS1_ENST00000594688.1_RNA	NM_001816.3	NP_001807.2	P31997	CEAM8_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 8	173	Ig-like C2-type 1.				immune response (GO:0006955)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	16		Prostate(69;0.00899)				GGTAGGTTGTGTTCTGAGTCT	0.567													G|||	102	0.0203674	0.0719	0.0072	5008	,	,		17179	0.0		0.002	False		,,,				2504	0.0				p.N173N		Atlas-SNP	.											.	CEACAM8	44	.	0			c.C519T						PASS	.	G		240,4166	141.5+/-176.9	6,228,1969	220.0	192.0	201.0		519	1.4	0.5	19	dbSNP_119	201	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous	CEACAM8	NM_001816.3		6,239,6258	AA,AG,GG		0.1279,5.4471,1.9299		173/350	43093793	251,12755	2203	4300	6503	SO:0001819	synonymous_variant	1088	exon3			GGTTGTGTTCTGA	D90064	CCDS12610.1	19q13.2	2013-01-29			ENSG00000124469	ENSG00000124469		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1820	protein-coding gene	gene with protein product		615747		CGM6		2208113, 2306228	Standard	NM_001816		Approved	CD66b	uc002oud.2	P31997	OTTHUMG00000151124	ENST00000244336.5:c.519C>T	19.37:g.43093793G>A		206.0	0.0	0		231.0	104.0	0.450216	NM_001816	O60399|Q16574	Silent	SNP	ENST00000244336.5	37	CCDS12610.1																																																																																			G|0.977;A|0.023	0.023	strong		0.567	CEACAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321430.1		
EML2	24139	hgsc.bcm.edu	37	19	46142624	46142624	+	Missense_Mutation	SNP	A	A	C	rs201822741	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:46142624A>C	ENST00000245925.3	-	1	61	c.11T>G	c.(10-12)tTt>tGt	p.F4C	EML2_ENST00000587152.1_Intron|EML2_ENST00000536630.1_Intron|EML2_ENST00000589876.1_Missense_Mutation_p.F4C|MIR330_ENST00000362196.1_RNA|AC006132.1_ENST00000593161.1_5'Flank	NM_012155.2	NP_036287.1	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like 2	4					negative regulation of microtubule polymerization (GO:0031115)|regulation of microtubule nucleation (GO:0010968)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|urinary_tract(1)	31		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)		CCCAGCTCCAAAGCTACTCAT	0.726													A|||	48	0.00958466	0.0325	0.0072	5008	,	,		12182	0.0		0.0	False		,,,				2504	0.0				p.F4C		Atlas-SNP	.											.	EML2	64	.	0			c.T11G						PASS	.		,,CYS/PHE	90,4006		0,90,1958	15.0	17.0	16.0		,,11	4.6	1.0	19	dbSNP_134	16	1,8033		0,1,4016	yes	intron,intron,missense	EML2	NM_001193268.1,NM_001193269.1,NM_012155.2	,,205	0,91,5974	CC,CA,AA		0.0124,2.1973,0.7502	,,	,,4/650	46142624	91,12039	2048	4017	6065	SO:0001583	missense	24139	exon1			GCTCCAAAGCTAC	AF103939	CCDS12670.1, CCDS54280.1, CCDS59399.1	19q13.32	2013-01-10				ENSG00000125746		"""WD repeat domain containing"""	18035	protein-coding gene	gene with protein product	"""echinoderm MT-associated protein (EMAP)-like protein 70"", ""microtubule-associated protein like echinoderm EMAP"""					11694528, 10521658	Standard	NM_012155		Approved	EMAP2, ELP70, EMAP-2	uc010xxm.2	O95834		ENST00000245925.3:c.11T>G	19.37:g.46142624A>C	ENSP00000245925:p.Phe4Cys	45.0	0.0	0		56.0	29.0	0.517857	NM_012155	B7Z3I2|B7Z3Q9|K7ERL7|Q59EN8|Q8N5A2|Q9UG50	Missense_Mutation	SNP	ENST00000245925.3	37	CCDS12670.1	13	0.005952380952380952	8	0.016260162601626018	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	A	14.61	2.585437	0.46110	0.021973	1.24E-4	ENSG00000125746	ENST00000245925	T	0.26067	1.76	4.58	4.58	0.56647	.	1.865290	0.03249	U	0.181627	T	0.26666	0.0652	L	0.29908	0.895	0.80722	D	1	D;B	0.76494	0.999;0.118	D;B	0.74674	0.984;0.053	T	0.03034	-1.1080	10	0.59425	D	0.04	44.314	10.2951	0.43618	1.0:0.0:0.0:0.0	.	4;4	B7Z918;O95834	.;EMAL2_HUMAN	C	4	ENSP00000245925:F4C	ENSP00000245925:F4C	F	-	2	0	EML2	50834464	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.633000	0.54295	1.932000	0.55993	0.454000	0.30748	TTT	A|0.994;C|0.006	0.006	strong		0.726	EML2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459608.1	NM_012155	
DSE	29940	hgsc.bcm.edu	37	6	116720466	116720466	+	Missense_Mutation	SNP	G	G	T	rs76186865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:116720466G>T	ENST00000331677.3	+	3	497	c.53G>T	c.(52-54)tGc>tTc	p.C18F	DSE_ENST00000452085.3_Missense_Mutation_p.C18F|DSE_ENST00000540275.1_3'UTR|DSE_ENST00000359564.2_Missense_Mutation_p.C18F|DSE_ENST00000537543.1_Missense_Mutation_p.C37F			Q9UL01	DSE_HUMAN	dermatan sulfate epimerase	18					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	chondroitin-glucuronate 5-epimerase activity (GO:0047757)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35		all_cancers(87;0.00019)|all_epithelial(87;0.000416)|Ovarian(999;0.133)|Colorectal(196;0.234)		Epithelial(106;0.00915)|OV - Ovarian serous cystadenocarcinoma(136;0.0149)|GBM - Glioblastoma multiforme(226;0.0189)|all cancers(137;0.0262)		TATTTGCTTTGCTTTGTGTCA	0.498													G|||	175	0.0349441	0.1263	0.0058	5008	,	,		17864	0.0		0.004	False		,,,				2504	0.0				p.C18F		Atlas-SNP	.											.	DSE	98	.	0			c.G53T						PASS	.	G	PHE/CYS,PHE/CYS	409,3997	201.1+/-224.2	28,353,1822	78.0	72.0	74.0		53,53	4.8	0.1	6	dbSNP_131	74	23,8577	16.0+/-53.3	1,21,4278	yes	missense,missense	DSE	NM_001080976.1,NM_013352.2	205,205	29,374,6100	TT,TG,GG		0.2674,9.2828,3.3215	benign,benign	18/959,18/959	116720466	432,12574	2203	4300	6503	SO:0001583	missense	29940	exon2			TGCTTTGCTTTGT	AF098066	CCDS5107.1	6q22	2008-02-05	2007-01-29	2007-01-29	ENSG00000111817	ENSG00000111817	5.1.3.19		21144	protein-coding gene	gene with protein product		605942	"""squamous cell carcinoma antigen recognized by T cells 2"""	SART2		11920522, 16505484	Standard	NM_001080976		Approved	DSEPI	uc003pws.3	Q9UL01	OTTHUMG00000015434	ENST00000331677.3:c.53G>T	6.37:g.116720466G>T	ENSP00000332151:p.Cys18Phe	100.0	0.0	0		78.0	34.0	0.435897	NM_001080976	Q5R3K6	Missense_Mutation	SNP	ENST00000331677.3	37	CCDS5107.1	70	0.03205128205128205	67	0.13617886178861788	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	7.264	0.605736	0.14002	0.092828	0.002674	ENSG00000111817	ENST00000430252;ENST00000452085;ENST00000537543;ENST00000331677;ENST00000359564	T;T;T;T;T	0.22336	1.96;1.96;1.96;1.96;1.96	5.65	4.76	0.60689	.	0.151973	0.64402	D	0.000006	T	0.10766	0.0263	L	0.36672	1.1	0.44373	D	0.997279	B;B	0.18968	0.032;0.013	B;B	0.18561	0.022;0.009	T	0.02424	-1.1161	10	0.62326	D	0.03	-6.9295	15.1889	0.73028	0.0684:0.0:0.9316:0.0	.	37;18	B7Z765;Q9UL01	.;DSE_HUMAN	F	18;18;37;18;18	ENSP00000397597:C18F;ENSP00000404049:C18F;ENSP00000441152:C37F;ENSP00000332151:C18F;ENSP00000352567:C18F	ENSP00000332151:C18F	C	+	2	0	DSE	116827159	1.000000	0.71417	0.104000	0.21259	0.051000	0.14879	5.884000	0.69729	2.941000	0.99782	0.655000	0.94253	TGC	G|0.970;T|0.030	0.030	strong		0.498	DSE-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041940.2	NM_013352	
CDC27	996	hgsc.bcm.edu	37	17	45234301	45234301	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:45234301C>A	ENST00000066544.3	-	7	913	c.820G>T	c.(820-822)Gct>Tct	p.A274S	CDC27_ENST00000531206.1_Missense_Mutation_p.A274S|CDC27_ENST00000528748.1_5'Flank|CDC27_ENST00000446365.2_Missense_Mutation_p.A213S|CDC27_ENST00000527547.1_Missense_Mutation_p.A274S	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	274					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.A274S(3)		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						GGACTAAGAGCTGCTGGTCCT	0.363																																					p.A274S		Atlas-SNP	.											CDC27_ENST00000531206,NS,carcinoma,+1,10	CDC27	337	10	3	Substitution - Missense(3)	prostate(3)	c.G820T						scavenged	.						62.0	65.0	64.0					17																	45234301		2201	4292	6493	SO:0001583	missense	996	exon7			TAAGAGCTGCTGG	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.820G>T	17.37:g.45234301C>A	ENSP00000066544:p.Ala274Ser	76.0	1.0	0.0131579		46.0	2.0	0.0434783	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	C	13.06	2.125822	0.37533	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	T;T;T;T;T	0.68181	-0.31;-0.3;-0.05;-0.31;0.78	5.64	4.68	0.58851	.	0.058237	0.64402	D	0.000002	T	0.46171	0.1379	N	0.11560	0.145	0.50039	D	0.999845	B;B;B;B	0.23442	0.085;0.079;0.073;0.003	B;B;B;B	0.22880	0.013;0.028;0.042;0.004	T	0.36212	-0.9757	10	0.25106	T	0.35	-20.3108	12.4418	0.55629	0.0:0.9186:0.0:0.0814	.	213;274;274;274	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	S	274;274;213;274;274	ENSP00000066544:A274S;ENSP00000434614:A274S;ENSP00000392802:A213S;ENSP00000437339:A274S;ENSP00000432105:A274S	ENSP00000066544:A274S	A	-	1	0	CDC27	42589300	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.048000	0.41278	1.400000	0.46741	0.460000	0.39030	GCT	.	.	none		0.363	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
FAM179B	23116	hgsc.bcm.edu	37	14	45431636	45431636	+	Silent	SNP	C	C	T	rs141982460	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:45431636C>T	ENST00000361577.3	+	1	226	c.12C>T	c.(10-12)gcC>gcT	p.A4A	KLHL28_ENST00000355081.2_5'Flank|KLHL28_ENST00000396128.4_5'Flank|FAM179B_ENST00000361462.2_Silent_p.A4A|KLHL28_ENST00000553817.1_5'Flank|FAM179B_ENST00000382233.2_Silent_p.A4A	NM_015091.2	NP_055906.2	Q9Y4F4	F179B_HUMAN	family with sequence similarity 179, member B	4										endometrium(4)|kidney(5)|large_intestine(12)|lung(16)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	45						TGGCGGCTGCCCCCTCCGCGC	0.617													C|||	4	0.000798722	0.003	0.0	5008	,	,		16675	0.0		0.0	False		,,,				2504	0.0				p.A4A		Atlas-SNP	.											.	FAM179B	115	.	0			c.C12T						PASS	.	C		24,4370		0,24,2173	21.0	24.0	23.0		12	0.9	0.3	14	dbSNP_134	23	0,8568		0,0,4284	no	coding-synonymous	FAM179B	NM_015091.2		0,24,6457	TT,TC,CC		0.0,0.5462,0.1852		4/1721	45431636	24,12938	2197	4284	6481	SO:0001819	synonymous_variant	23116	exon1			GGCTGCCCCCTCC	AB007883	CCDS9681.1	14q21.3	2008-07-21	2008-07-21	2008-07-21	ENSG00000198718	ENSG00000198718			19959	protein-coding gene	gene with protein product			"""KIAA0423"""	KIAA0423			Standard	XM_005267451		Approved		uc001wvv.3	Q9Y4F4	OTTHUMG00000140264	ENST00000361577.3:c.12C>T	14.37:g.45431636C>T		51.0	0.0	0		60.0	29.0	0.483333	NM_015091	Q68D66|Q6PG27	Silent	SNP	ENST00000361577.3	37	CCDS9681.1																																																																																			C|0.998;T|0.002	0.002	strong		0.617	FAM179B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000276791.1	XM_113781	
PIK3C2G	5288	hgsc.bcm.edu	37	12	18473933	18473933	+	Missense_Mutation	SNP	T	T	G	rs201637656		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:18473933T>G	ENST00000266497.5	+	6	1213	c.1175T>G	c.(1174-1176)cTt>cGt	p.L392R	PIK3C2G_ENST00000538779.1_Missense_Mutation_p.L392R|PIK3C2G_ENST00000535651.1_Missense_Mutation_p.L392R|PIK3C2G_ENST00000433979.1_Missense_Mutation_p.L392R|RERGL_ENST00000541632.1_5'Flank			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	392					chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				CTGAATCAACTTCTAGAATTT	0.303																																					p.L392R		Atlas-SNP	.											PIK3C2G_ENST00000433979,NS,carcinoma,+1,2	PIK3C2G	315	2	0			c.T1175G						PASS	.	T	ARG/LEU	3,3597		0,3,1797	50.0	49.0	49.0		1175	4.6	1.0	12		49	0,8118		0,0,4059	yes	missense	PIK3C2G	NM_004570.4	102	0,3,5856	GG,GT,TT		0.0,0.0833,0.0256	probably-damaging	392/1446	18473933	3,11715	1800	4059	5859	SO:0001583	missense	5288	exon7			ATCAACTTCTAGA	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"""phosphoinositide-3-kinase, class 2, gamma polypeptide"""			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.1175T>G	12.37:g.18473933T>G	ENSP00000266497:p.Leu392Arg	287.0	0.0	0		256.0	121.0	0.472656	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	37	CCDS44839.1	.	.	.	.	.	.	.	.	.	.	T	16.78	3.216850	0.58452	8.33E-4	0.0	ENSG00000139144	ENST00000535651;ENST00000433979;ENST00000266497;ENST00000538779	T;T;T;T	0.65916	1.12;-0.18;-0.18;-0.08	4.57	4.57	0.56435	.	0.000000	0.52532	D	0.000071	T	0.72787	0.3504	M	0.63843	1.955	0.42403	D	0.992574	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.71184	0.957;0.972;0.938	T	0.72516	-0.4269	10	0.40728	T	0.16	-22.2094	10.628	0.45519	0.0:0.0:0.0:1.0	.	391;392;392	B7ZLY6;F5H369;O75747	.;.;P3C2G_HUMAN	R	392	ENSP00000443850:L392R;ENSP00000404845:L392R;ENSP00000266497:L392R;ENSP00000445381:L392R	ENSP00000266497:L392R	L	+	2	0	PIK3C2G	18365200	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.773000	0.55333	2.281000	0.76405	0.528000	0.53228	CTT	.	.	weak		0.303	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570	
KIAA1456	57604	hgsc.bcm.edu	37	8	12879016	12879016	+	Silent	SNP	T	T	A	rs75377133	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:12879016T>A	ENST00000524591.2	+	5	1317	c.828T>A	c.(826-828)gtT>gtA	p.V276V	KIAA1456_ENST00000447063.2_Intron	NM_001099677.1|NM_020844.2	NP_001093147.1|NP_065895.2	Q9P272	K1456_HUMAN	KIAA1456	276							methyltransferase activity (GO:0008168)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)	7						ACACAGAAGTTTGGGCCAGTA	0.418													T|||	107	0.0213658	0.0794	0.0014	5008	,	,		19745	0.0		0.001	False		,,,				2504	0.0				p.V276V		Atlas-SNP	.											.	KIAA1456	20	.	0			c.T828A						PASS	.	T	,	301,3443		12,277,1583	81.0	78.0	79.0		450,828	-9.9	0.0	8	dbSNP_132	79	3,8199		0,3,4098	no	coding-synonymous,coding-synonymous	KIAA1456	NM_001099677.1,NM_020844.2	,	12,280,5681	AA,AT,TT		0.0366,8.0395,2.5448	,	150/329,276/455	12879016	304,11642	1872	4101	5973	SO:0001819	synonymous_variant	57604	exon5			AGAAGTTTGGGCC	BC035082	CCDS47808.1	8p22	2013-10-04	2011-02-23	2011-02-23	ENSG00000250305	ENSG00000250305			26725	protein-coding gene	gene with protein product		615666	"""chromosome 8 open reading frame 79"""	C8orf79		23381944	Standard	NM_020844		Approved	FLJ36980	uc010lsq.3	Q8N9K7	OTTHUMG00000165477	ENST00000524591.2:c.828T>A	8.37:g.12879016T>A		91.0	0.0	0		112.0	47.0	0.419643	NM_020844	Q96AW6	Silent	SNP	ENST00000524591.2	37	CCDS47808.1																																																																																			T|0.989;A|0.011	0.011	strong		0.418	KIAA1456-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383262.2	NM_001099677	
SNAPC4	6621	hgsc.bcm.edu	37	9	139292751	139292751	+	Splice_Site	SNP	C	C	T	rs7031489	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139292751C>T	ENST00000298532.2	-	1	498	c.130G>A	c.(130-132)Gat>Aat	p.D44N		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa											biliary_tract(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	33		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		AGGGGCTTACCTGCTTCAGAA	0.557													C|||	36	0.0071885	0.0257	0.0029	5008	,	,		15053	0.0		0.0	False		,,,				2504	0.0				p.D44N		Atlas-SNP	.											.	SNAPC4	82	.	0			c.G130A						PASS	.	C	ASN/ASP	86,4320	73.1+/-111.1	0,86,2117	105.0	108.0	107.0		130	4.2	0.8	9	dbSNP_116	107	12,8588	9.1+/-34.3	0,12,4288	yes	missense-near-splice	SNAPC4	NM_003086.2	23	0,98,6405	TT,TC,CC		0.1395,1.9519,0.7535	benign	44/1470	139292751	98,12908	2203	4300	6503	SO:0001630	splice_region_variant	6621	exon1			GCTTACCTGCTTC	AF032387	CCDS6998.1	9q34.3	2008-07-21	2002-08-29		ENSG00000165684	ENSG00000165684			11137	protein-coding gene	gene with protein product		602777	"""small nuclear RNA activating complex, polypeptide 4, 190kD"""			9418884	Standard	XM_005266096		Approved	SNAP190, PTFalpha, FLJ13451	uc004chh.3	Q5SXM2	OTTHUMG00000020929	ENST00000298532.2:c.130+1G>A	9.37:g.139292751C>T		88.0	0.0	0		91.0	30.0	0.32967	NM_003086		Missense_Mutation	SNP	ENST00000298532.2	37	CCDS6998.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	c	12.43	1.935886	0.34189	0.019519	0.001395	ENSG00000165684	ENST00000298532	T	0.28895	1.59	4.18	4.18	0.49190	.	0.853272	0.10561	N	0.660279	T	0.15609	0.0376	L	0.46157	1.445	0.26436	N	0.975854	B	0.32245	0.361	B	0.29440	0.102	T	0.05835	-1.0861	9	.	.	.	-10.7631	14.4014	0.67050	0.0:1.0:0.0:0.0	rs7031489;rs7031489	44	Q5SXM2	SNPC4_HUMAN	N	44	ENSP00000298532:D44N	.	D	-	1	0	SNAPC4	138412572	0.988000	0.35896	0.779000	0.31741	0.410000	0.31052	3.351000	0.52232	2.327000	0.79052	0.651000	0.88453	GAT	C|0.991;T|0.009	0.009	strong		0.557	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	Missense_Mutation
GSDMA	284110	hgsc.bcm.edu	37	17	38122117	38122117	+	Silent	SNP	G	G	A	rs16965465	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:38122117G>A	ENST00000301659.4	+	2	295	c.177G>A	c.(175-177)acG>acA	p.T59T		NM_178171.4	NP_835465.2	Q96QA5	GSDMA_HUMAN	gasdermin A	59					apoptotic process (GO:0006915)	perinuclear region of cytoplasm (GO:0048471)				NS(1)|endometrium(2)|large_intestine(3)|lung(1)	7						CCGACTACACGCTGCTGGATG	0.637													A|||	351	0.0700879	0.2315	0.036	5008	,	,		17304	0.0		0.0149	False		,,,				2504	0.0051				p.T59T		Atlas-SNP	.											GSDMA,NS,carcinoma,+1,1	GSDMA	26	1	0			c.G177A						PASS	.	A		683,3313		60,563,1375	21.0	24.0	23.0		177	1.0	1.0	17	dbSNP_123	23	53,8223		1,51,4086	no	coding-synonymous	GSDMA	NM_178171.4		61,614,5461	AA,AG,GG		0.6404,17.0921,5.9974		59/446	38122117	736,11536	1998	4138	6136	SO:0001819	synonymous_variant	284110	exon2			CTACACGCTGCTG	AB093591	CCDS45669.1	17q21.2	2008-07-31	2008-07-31	2008-07-31		ENSG00000167914			13311	protein-coding gene	gene with protein product		611218	"""gasdermin"", ""gasdermin 1"""	GSDM, GSDM1		12883658, 15010812, 17350798	Standard	NM_178171		Approved	FLJ39120	uc002htl.1	Q96QA5		ENST00000301659.4:c.177G>A	17.37:g.38122117G>A		56.0	0.0	0		42.0	16.0	0.380952	NM_178171	Q32MC5|Q86VE7|Q8N1M6	Silent	SNP	ENST00000301659.4	37	CCDS45669.1																																																																																			G|0.930;A|0.070	0.070	strong		0.637	GSDMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446847.1	NM_178171	
SPTA1	6708	hgsc.bcm.edu	37	1	158587368	158587368	+	Missense_Mutation	SNP	T	T	C	rs111980420	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158587368T>C	ENST00000368147.4	-	47	6739	c.6559A>G	c.(6559-6561)Aaa>Gaa	p.K2187E		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	2187					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CCTGTTTCTTTGAGCAATGAT	0.343													T|||	50	0.00998403	0.0363	0.0029	5008	,	,		21215	0.0		0.0	False		,,,				2504	0.0				p.K2187E		Atlas-SNP	.											.	SPTA1	720	.	0			c.A6559G						PASS	.	T	GLU/LYS	109,3607		1,107,1750	110.0	101.0	104.0		6559	4.0	1.0	1	dbSNP_132	104	1,8199		0,1,4099	yes	missense	SPTA1	NM_003126.2	56	1,108,5849	CC,CT,TT		0.0122,2.9333,0.9231	benign	2187/2420	158587368	110,11806	1858	4100	5958	SO:0001583	missense	6708	exon47			TTTCTTTGAGCAA	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.6559A>G	1.37:g.158587368T>C	ENSP00000357129:p.Lys2187Glu	231.0	0.0	0		190.0	112.0	0.589474	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	T	5.051	0.195152	0.09599	0.029333	1.22E-4	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.53423	0.62;0.62	5.15	4.01	0.46588	.	0.000000	0.33792	N	0.004556	T	0.07728	0.0194	N	0.12182	0.205	0.34813	D	0.737938	B	0.10296	0.003	B	0.09377	0.004	T	0.27262	-1.0079	10	0.02654	T	1	.	5.5016	0.16831	0.0:0.0873:0.1765:0.7361	.	2187	P02549	SPTA1_HUMAN	E	2187;2184	ENSP00000357130:K2187E;ENSP00000357129:K2184E	ENSP00000357129:K2184E	K	-	1	0	SPTA1	156853992	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.835000	0.48175	1.068000	0.40764	0.533000	0.62120	AAA	T|0.994;C|0.006	0.006	strong		0.343	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
XPR1	9213	hgsc.bcm.edu	37	1	180849394	180849394	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:180849394A>G	ENST00000367590.4	+	14	2189	c.1991A>G	c.(1990-1992)aAc>aGc	p.N664S	XPR1_ENST00000367589.3_Missense_Mutation_p.N599S	NM_004736.3	NP_004727.2	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor 1	664					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)			breast(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	35						TGGAAGTACAACCAGAGCATA	0.512																																					p.N664S		Atlas-SNP	.											.	XPR1	76	.	0			c.A1991G						PASS	.						155.0	146.0	149.0					1																	180849394		2203	4300	6503	SO:0001583	missense	9213	exon14			AGTACAACCAGAG	AF099082	CCDS1340.1, CCDS44284.1	1q25.1	2013-07-18	2010-04-23		ENSG00000143324	ENSG00000143324			12827	protein-coding gene	gene with protein product		605237	"""xenotropic and polytropic retrovirus receptor"""			9990033	Standard	NM_004736		Approved	SYG1, X3	uc001goi.3	Q9UBH6	OTTHUMG00000035116	ENST00000367590.4:c.1991A>G	1.37:g.180849394A>G	ENSP00000356562:p.Asn664Ser	111.0	0.0	0		130.0	66.0	0.507692	NM_004736	O95719|Q7L8K9|Q8IW20|Q9NT19|Q9UFB9	Missense_Mutation	SNP	ENST00000367590.4	37	CCDS1340.1	.	.	.	.	.	.	.	.	.	.	A	8.539	0.872854	0.17322	.	.	ENSG00000143324	ENST00000367590;ENST00000367589	T	0.40476	1.03	5.56	1.18	0.20946	.	0.390605	0.32002	N	0.006729	T	0.10852	0.0265	N	0.00823	-1.155	0.20821	N	0.999847	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	T	0.35649	-0.9780	10	0.06891	T	0.86	-0.9318	7.5346	0.27702	0.4444:0.0:0.5556:0.0	.	599;664	Q9UBH6-2;Q9UBH6	.;XPR1_HUMAN	S	664;599	ENSP00000356562:N664S	ENSP00000356561:N599S	N	+	2	0	XPR1	179116017	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	1.285000	0.33261	0.243000	0.21327	-0.462000	0.05337	AAC	.	.	none		0.512	XPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084996.2	NM_004736	
GCLC	2729	hgsc.bcm.edu	37	6	53365102	53365102	+	Silent	SNP	C	C	T	rs17881359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:53365102C>T	ENST00000229416.6	-	14	2007	c.1524G>A	c.(1522-1524)acG>acA	p.T508T	RP1-27K12.4_ENST00000508884.1_RNA	NM_001197115.1|NM_001498.3	NP_001184044.1|NP_001489.1	P48506	GSH1_HUMAN	glutamate-cysteine ligase, catalytic subunit	508					apoptotic mitochondrial changes (GO:0008637)|cell redox homeostasis (GO:0045454)|cellular nitrogen compound metabolic process (GO:0034641)|cysteine metabolic process (GO:0006534)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|L-ascorbic acid metabolic process (GO:0019852)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|regulation of blood vessel size (GO:0050880)|regulation of mitochondrial depolarization (GO:0051900)|response to arsenic-containing substance (GO:0046685)|response to heat (GO:0009408)|response to hormone (GO:0009725)|response to nitrosative stress (GO:0051409)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|glutamate-cysteine ligase complex (GO:0017109)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|coenzyme binding (GO:0050662)|glutamate binding (GO:0016595)|glutamate-cysteine ligase activity (GO:0004357)|magnesium ion binding (GO:0000287)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22	Lung NSC(77;0.0137)				L-Cysteine(DB00151)|Vitamin E(DB00163)	CAGCGAGCTCCGTGCTGTTCT	0.567													C|||	28	0.00559105	0.0204	0.0014	5008	,	,		18765	0.0		0.0	False		,,,				2504	0.0				p.T508T		Atlas-SNP	.											.	GCLC	58	.	0			c.G1524A						PASS	.	C	,	76,4330	67.0+/-104.6	0,76,2127	148.0	129.0	136.0		1410,1524	-10.5	0.0	6	dbSNP_124	136	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	GCLC	NM_001197115.1,NM_001498.3	,	0,76,6427	TT,TC,CC		0.0,1.7249,0.5843	,	470/600,508/638	53365102	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	2729	exon14			GAGCTCCGTGCTG	M90656	CCDS4952.1, CCDS75471.1	6p12	2008-02-05				ENSG00000001084	6.3.2.2		4311	protein-coding gene	gene with protein product		606857		GLCLC, GLCL		1350904	Standard	NM_001498		Approved	GCS	uc003pbw.2	P48506		ENST00000229416.6:c.1524G>A	6.37:g.53365102C>T		179.0	0.0	0		176.0	82.0	0.465909	NM_001498	Q14399	Silent	SNP	ENST00000229416.6	37	CCDS4952.1																																																																																			C|0.994;T|0.006	0.006	strong		0.567	GCLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359710.2		
SPHKAP	80309	hgsc.bcm.edu	37	2	228882588	228882588	+	Silent	SNP	T	T	C	rs73994847	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:228882588T>C	ENST00000392056.3	-	7	3028	c.2982A>G	c.(2980-2982)aaA>aaG	p.K994K	SPHKAP_ENST00000344657.5_Silent_p.K994K	NM_001142644.1	NP_001136116.1	Q2M3C7	SPKAP_HUMAN	SPHK1 interactor, AKAP domain containing	994						extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|Z disc (GO:0030018)	protein kinase A binding (GO:0051018)			NS(5)|breast(5)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(25)|lung(86)|ovary(6)|pancreas(1)|prostate(6)|skin(17)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	185		Renal(207;0.025)|all_hematologic(139;0.15)|all_lung(227;0.204)|Acute lymphoblastic leukemia(138;0.205)|Esophageal squamous(248;0.23)		Epithelial(121;8.17e-11)|all cancers(144;7.92e-08)|Lung(261;0.0168)|LUSC - Lung squamous cell carcinoma(224;0.0232)		GAGGCTTGTGTTTCCTCACAG	0.537													T|||	177	0.0353435	0.1301	0.0072	5008	,	,		20344	0.0		0.0	False		,,,				2504	0.0				p.K994K		Atlas-SNP	.											.	SPHKAP	750	.	0			c.A2982G						PASS	.	T	,	552,3854	246.8+/-255.3	32,488,1683	83.0	74.0	77.0		2982,2982	-4.0	1.0	2	dbSNP_130	77	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	SPHKAP	NM_001142644.1,NM_030623.3	,	32,493,5978	CC,CT,TT		0.0581,12.5284,4.2826	,	994/1701,994/1672	228882588	557,12449	2203	4300	6503	SO:0001819	synonymous_variant	80309	exon7			CTTGTGTTTCCTC		CCDS33389.1, CCDS46537.1	2q36.3	2010-08-20			ENSG00000153820	ENSG00000153820		"""A-kinase anchor proteins"""	30619	protein-coding gene	gene with protein product	"""sphingosine kinase type 1-interacting protein"""	611646				12080051, 11214970	Standard	NM_030623		Approved	SKIP	uc002vpq.2	Q2M3C7	OTTHUMG00000153584	ENST00000392056.3:c.2982A>G	2.37:g.228882588T>C		85.0	0.0	0		101.0	53.0	0.524752	NM_030623	Q68DA3|Q68DR8|Q9C0I5	Silent	SNP	ENST00000392056.3	37	CCDS46537.1																																																																																			T|0.953;C|0.047	0.047	strong		0.537	SPHKAP-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000331750.1	NM_030623	
TENM4	26011	hgsc.bcm.edu	37	11	78387356	78387356	+	Silent	SNP	C	C	T	rs59660398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:78387356C>T	ENST00000278550.7	-	30	5799	c.5337G>A	c.(5335-5337)gcG>gcA	p.A1779A		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1779					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										CAGTCTGCAGCGCCACCTCCA	0.632													C|||	301	0.0601038	0.2224	0.0101	5008	,	,		15294	0.0		0.0	False		,,,				2504	0.0				p.A1779A		Atlas-SNP	.											.	.	.	.	0			c.G5337A						PASS	.	C		802,3514		60,682,1416	30.0	37.0	35.0		5337	-9.4	0.2	11	dbSNP_129	35	15,8485		0,15,4235	no	coding-synonymous	ODZ4	NM_001098816.2		60,697,5651	TT,TC,CC		0.1765,18.582,6.3748		1779/2770	78387356	817,11999	2158	4250	6408	SO:0001819	synonymous_variant	26011	exon30			CTGCAGCGCCACC	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"""odz, odd Oz/ten-m homolog 4 (Drosophila)"""	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.5337G>A	11.37:g.78387356C>T		67.0	0.0	0		88.0	39.0	0.443182	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Silent	SNP	ENST00000278550.7	37	CCDS44688.1																																																																																			C|0.963;T|0.037	0.037	strong		0.632	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
PTPN1	5770	hgsc.bcm.edu	37	20	49191191	49191191	+	Splice_Site	SNP	A	A	G	rs35414863	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:49191191A>G	ENST00000371621.3	+	5	666	c.492A>G	c.(490-492)acA>acG	p.T164T	RP4-530I15.9_ENST00000431019.1_RNA|PTPN1_ENST00000541713.1_Splice_Site_p.T91T	NM_001278618.1|NM_002827.2	NP_001265547.1|NP_002818.1	P18031	PTN1_HUMAN	protein tyrosine phosphatase, non-receptor type 1	164	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|endoplasmic reticulum unfolded protein response (GO:0030968)|insulin receptor signaling pathway (GO:0008286)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|peptidyl-tyrosine dephosphorylation (GO:0035335)|peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity (GO:1990264)|platelet activation (GO:0030168)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|regulation of endocytosis (GO:0030100)|regulation of hepatocyte growth factor receptor signaling pathway (GO:1902202)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of signal transduction (GO:0009966)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|sorting endosome (GO:0097443)	enzyme binding (GO:0019899)|ephrin receptor binding (GO:0046875)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|skin(2)	16		Lung NSC(126;0.163)			Tiludronate(DB01133)	aAAACCTTACAGTGAGTATAG	0.398													A|||	113	0.0225639	0.0772	0.0144	5008	,	,		21947	0.0		0.001	False		,,,				2504	0.0				p.T164T		Atlas-SNP	.											.	PTPN1	36	.	0			c.A492G						PASS	.	A		344,4062	179.7+/-208.2	11,322,1870	117.0	116.0	117.0		492	-10.3	0.0	20	dbSNP_126	117	19,8581	13.3+/-46.6	0,19,4281	yes	coding-synonymous-near-splice	PTPN1	NM_002827.2		11,341,6151	GG,GA,AA		0.2209,7.8075,2.791		164/436	49191191	363,12643	2203	4300	6503	SO:0001630	splice_region_variant	5770	exon5			CCTTACAGTGAGT		CCDS13430.1, CCDS63309.1	20q13.1-q13.2	2011-06-09			ENSG00000196396	ENSG00000196396		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9642	protein-coding gene	gene with protein product		176885		PTP1B		2164224	Standard	NM_002827		Approved		uc002xvl.3	P18031	OTTHUMG00000032729	ENST00000371621.3:c.492+1A>G	20.37:g.49191191A>G		89.0	0.0	0		99.0	51.0	0.515152	NM_002827	Q5TGD8|Q9BQV9|Q9NQQ4	Silent	SNP	ENST00000371621.3	37	CCDS13430.1																																																																																			A|0.976;G|0.024	0.024	strong		0.398	PTPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079694.2		Silent
NLGN4X	57502	hgsc.bcm.edu	37	X	5821468	5821468	+	Silent	SNP	C	C	G	rs61741754	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:5821468C>G	ENST00000381095.3	-	5	1878	c.1251G>C	c.(1249-1251)cgG>cgC	p.R417R	NLGN4X_ENST00000275857.6_Silent_p.R417R|NLGN4X_ENST00000381093.2_Silent_p.R437R|NLGN4X_ENST00000381092.1_Silent_p.R417R|NLGN4X_ENST00000538097.1_Silent_p.R417R	NM_001282145.1|NM_001282146.1|NM_181332.1	NP_001269074.1|NP_001269075.1|NP_851849.1	Q8N0W4	NLGNX_HUMAN	neuroligin 4, X-linked	417					adult behavior (GO:0030534)|brainstem development (GO:0003360)|cell-cell junction organization (GO:0045216)|cerebellum development (GO:0021549)|learning (GO:0007612)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|neuron cell-cell adhesion (GO:0007158)|neuron differentiation (GO:0030182)|organ growth (GO:0035265)|presynaptic membrane assembly (GO:0097105)|social behavior (GO:0035176)|synapse organization (GO:0050808)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|excitatory synapse (GO:0060076)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|chloride ion binding (GO:0031404)|neurexin family protein binding (GO:0042043)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)			breast(1)|cervix(2)|endometrium(4)|large_intestine(21)|lung(39)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)	81						TGATAGTCTCCCGCAAAGTGT	0.542													c|||	232	0.061457	0.1604	0.0259	3775	,	,		12595	0.0		0.002	False		,,,				2504	0.0				p.R417R		Atlas-SNP	.											.	NLGN4X	191	.	0			c.G1251C						PASS	.	G	,	580,2948		38,395,109,1058,437	6.0	7.0	7.0		1251,1251	-1.2	0.0	X	dbSNP_134	7	4,6426		0,4,0,2331,1760	no	coding-synonymous,coding-synonymous	NLGN4X	NM_020742.2,NM_181332.1	,	38,399,109,3389,2197	GG,GC,G,CC,C		0.0622,16.4399,5.8646	,	417/817,417/817	5821468	584,9374	2037	4095	6132	SO:0001819	synonymous_variant	57502	exon5			AGTCTCCCGCAAA	AB033086	CCDS14126.1	Xp22.33	2008-02-05	2004-05-21	2004-05-26	ENSG00000146938	ENSG00000146938			14287	protein-coding gene	gene with protein product		300427	"""neuroligin 4"""	NLGN4		10574462	Standard	XM_005274564		Approved	KIAA1260, NLGN, HLNX	uc004crr.3	Q8N0W4	OTTHUMG00000021093	ENST00000381095.3:c.1251G>C	X.37:g.5821468C>G		173.0	0.0	0		229.0	125.0	0.545852	NM_181332	Q6UX10|Q9ULG0	Silent	SNP	ENST00000381095.3	37	CCDS14126.1																																																																																			C|0.870;G|0.130	0.130	strong		0.542	NLGN4X-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000055673.1	NM_020742	
TRIM17	51127	hgsc.bcm.edu	37	1	228601506	228601506	+	Missense_Mutation	SNP	C	C	T	rs116188608	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228601506C>T	ENST00000366697.2	-	2	1473	c.517G>A	c.(517-519)Gag>Aag	p.E173K	TRIM17_ENST00000366698.2_Missense_Mutation_p.E173K|TRIM17_ENST00000295033.3_Missense_Mutation_p.E173K|TRIM17_ENST00000456946.2_Missense_Mutation_p.E173K			Q9Y577	TRI17_HUMAN	tripartite motif containing 17	173					protein autoubiquitination (GO:0051865)	intracellular (GO:0005622)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)	10		Prostate(94;0.0724)				ACCTGCCACTCGGCTAAGCTC	0.607													C|||	54	0.0107827	0.0378	0.0043	5008	,	,		16452	0.0		0.001	False		,,,				2504	0.0				p.E173K		Atlas-SNP	.											.	TRIM17	66	.	0			c.G517A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU	193,4213	121.3+/-158.8	1,191,2011	120.0	90.0	100.0		517,517,517	1.6	0.1	1	dbSNP_132	100	0,8600		0,0,4300	yes	missense,missense,missense	TRIM17	NM_001024940.2,NM_001134855.1,NM_016102.3	56,56,56	1,191,6311	TT,TC,CC		0.0,4.3804,1.4839	benign,benign,benign	173/478,173/344,173/478	228601506	193,12813	2203	4300	6503	SO:0001583	missense	51127	exon3			GCCACTCGGCTAA	AF156271	CCDS1571.1, CCDS44327.1	1q42	2013-01-09	2011-01-25	2001-11-30	ENSG00000162931	ENSG00000162931		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	13430	protein-coding gene	gene with protein product	"""ring finger protein 16"", ""RING finger protein terf"", ""testis RING finger protein"""	606123	"""tripartite motif-containing 17"""	RNF16		9792805, 10894938	Standard	NM_016102		Approved	terf, RBCC	uc001hsv.3	Q9Y577	OTTHUMG00000039974	ENST00000366697.2:c.517G>A	1.37:g.228601506C>T	ENSP00000355658:p.Glu173Lys	93.0	0.0	0		109.0	44.0	0.40367	NM_001024940	B4DVJ2|Q5VST8	Missense_Mutation	SNP	ENST00000366697.2	37	CCDS1571.1	15	0.006868131868131868	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	0	0.0	C	0.010	-1.780416	0.00634	0.043804	0.0	ENSG00000162931	ENST00000366697;ENST00000366698;ENST00000295033;ENST00000456946;ENST00000479800;ENST00000355586	T;T;T;T;T;T	0.18810	3.58;3.58;3.58;3.58;3.58;2.19	3.5	1.56	0.23342	.	0.000000	0.38663	N	0.001611	T	0.03520	0.0101	M	0.66939	2.045	0.09310	N	1	B;B	0.20550	0.046;0.004	B;B	0.17433	0.018;0.002	T	0.30149	-0.9988	10	0.08599	T	0.76	.	4.9406	0.13963	0.0:0.6631:0.2166:0.1203	.	173;173	Q9Y577-2;Q9Y577	.;TRI17_HUMAN	K	173;173;173;173;146;173	ENSP00000355658:E173K;ENSP00000355659:E173K;ENSP00000295033:E173K;ENSP00000403312:E173K;ENSP00000430468:E146K;ENSP00000347794:E173K	ENSP00000295033:E173K	E	-	1	0	TRIM17	226668129	0.008000	0.16893	0.143000	0.22291	0.036000	0.12997	0.247000	0.18179	0.452000	0.26830	-0.254000	0.11334	GAG	C|0.986;T|0.014	0.014	strong		0.607	TRIM17-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096439.2	NM_016102	
BRD7	29117	hgsc.bcm.edu	37	16	50368671	50368671	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:50368671C>G	ENST00000394688.3	-	7	997	c.838G>C	c.(838-840)Gga>Cga	p.G280R	BRD7_ENST00000394689.2_Missense_Mutation_p.G280R			Q9NPI1	BRD7_HUMAN	bromodomain containing 7	280					cell cycle (GO:0007049)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|urinary_tract(2)	22		all_cancers(37;0.0127)				TCGGCATCTCCAGAGTCCTCT	0.473																																					p.G280R		Atlas-SNP	.											.	BRD7	61	.	0			c.G838C						PASS	.						138.0	142.0	141.0					16																	50368671		2198	4300	6498	SO:0001583	missense	29117	exon7			CATCTCCAGAGTC	AF213969	CCDS10742.1, CCDS54007.1	16q12.1	2008-11-18	2002-01-14		ENSG00000166164	ENSG00000166164			14310	protein-coding gene	gene with protein product			"""bromodomain-containing 7"""			10526152, 18809673	Standard	NM_013263		Approved	CELTIX1, BP75	uc002ege.2	Q9NPI1	OTTHUMG00000133170	ENST00000394688.3:c.838G>C	16.37:g.50368671C>G	ENSP00000378180:p.Gly280Arg	136.0	0.0	0		194.0	58.0	0.298969	NM_013263	Q4VC09|Q8N2L9|Q96KA4|Q9BV48|Q9UH59	Missense_Mutation	SNP	ENST00000394688.3	37	CCDS10742.1	.	.	.	.	.	.	.	.	.	.	C	8.023	0.760146	0.15846	.	.	ENSG00000166164	ENST00000394688;ENST00000394689	T;T	0.30981	1.51;1.51	5.47	3.42	0.39159	.	0.486780	0.23583	N	0.046637	T	0.18173	0.0436	L	0.29908	0.895	0.09310	N	1	B;P	0.35923	0.393;0.528	B;B	0.37943	0.133;0.261	T	0.10636	-1.0621	10	0.14252	T	0.57	-13.1079	5.4568	0.16594	0.1802:0.6543:0.0:0.1655	.	280;280	Q9NPI1;Q9NPI1-2	BRD7_HUMAN;.	R	280	ENSP00000378180:G280R;ENSP00000378181:G280R	ENSP00000378180:G280R	G	-	1	0	BRD7	48926172	0.849000	0.29639	0.418000	0.26571	0.791000	0.44710	1.471000	0.35365	2.733000	0.93635	0.650000	0.86243	GGA	.	.	none		0.473	BRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256874.3	NM_013263	
LRP1	4035	hgsc.bcm.edu	37	12	57578696	57578696	+	Silent	SNP	C	C	T	rs140921686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:57578696C>T	ENST00000243077.3	+	39	6727	c.6261C>T	c.(6259-6261)cgC>cgT	p.R2087R		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	2087					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	GTGAGAACCGCGAGGTGGTTC	0.542													C|||	18	0.00359425	0.0023	0.0	5008	,	,		21048	0.0149		0.0	False		,,,				2504	0.0				p.R2087R		Atlas-SNP	.											.	LRP1	428	.	0			c.C6261T						PASS	.	C		6,4400	11.4+/-27.6	0,6,2197	189.0	162.0	171.0		6261	-10.3	0.7	12	dbSNP_134	171	0,8600		0,0,4300	no	coding-synonymous	LRP1	NM_002332.2		0,6,6497	TT,TC,CC		0.0,0.1362,0.0461		2087/4545	57578696	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	4035	exon39			GAACCGCGAGGTG	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.6261C>T	12.37:g.57578696C>T		110.0	0.0	0		144.0	79.0	0.548611	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			C|0.999;T|0.001	0.001	strong		0.542	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
PLA2R1	22925	hgsc.bcm.edu	37	2	160901403	160901403	+	Silent	SNP	C	C	T	rs35005192	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160901403C>T	ENST00000283243.7	-	2	581	c.375G>A	c.(373-375)ccG>ccA	p.P125P	PLA2R1_ENST00000392771.1_Silent_p.P125P	NM_001195641.1|NM_007366.4	NP_001182570.1|NP_031392.3	Q13018	PLA2R_HUMAN	phospholipase A2 receptor 1, 180kDa	125	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.				cytokine production (GO:0001816)|negative regulation of arachidonic acid secretion (GO:1900139)|negative regulation of phospholipase A2 activity (GO:1900138)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of arachidonic acid secretion (GO:0090238)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|replicative senescence (GO:0090399)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	carbohydrate binding (GO:0030246)|phospholipase binding (GO:0043274)|receptor activity (GO:0004872)		PLA2R1/RBMS1(2)	central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(17)|lung(20)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	60						AGTACTGCAGCGGGCCTGTGA	0.502													C|||	27	0.00539137	0.0204	0.0	5008	,	,		17735	0.0		0.0	False		,,,				2504	0.0				p.P125P		Atlas-SNP	.											.	PLA2R1	153	.	0			c.G375A						PASS	.	C	,,	59,4347	56.8+/-93.2	0,59,2144	82.0	82.0	82.0		375,375,375	-12.1	0.0	2	dbSNP_126	82	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	PLA2R1	NM_001007267.2,NM_001195641.1,NM_007366.4	,,	0,59,6444	TT,TC,CC		0.0,1.3391,0.4536	,,	125/1325,125/1462,125/1464	160901403	59,12947	2203	4300	6503	SO:0001819	synonymous_variant	22925	exon2			CTGCAGCGGGCCT	U17033	CCDS33309.1, CCDS42767.1	2q23-q24	2011-08-30	2002-08-29		ENSG00000153246	ENSG00000153246		"""C-type lectin domain containing"""	9042	protein-coding gene	gene with protein product		604939	"""phospholipase A2 receptor 1, 180kD"""			7721806, 7925459	Standard	NM_007366		Approved	PLA2G1R, PLA2IR, PLA2-R, CLEC13C	uc002ube.2	Q13018	OTTHUMG00000154087	ENST00000283243.7:c.375G>A	2.37:g.160901403C>T		132.0	0.0	0		137.0	58.0	0.423358	NM_001195641	B2RTU9|D3DPB1|Q13019|Q15095|Q53R45|Q53RR7	Silent	SNP	ENST00000283243.7	37	CCDS33309.1																																																																																			C|0.994;T|0.006	0.006	strong		0.502	PLA2R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333820.1		
MYO3B	140469	hgsc.bcm.edu	37	2	171256771	171256771	+	Missense_Mutation	SNP	C	C	T	rs148136770|rs552913139	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:171256771C>T	ENST00000408978.4	+	17	2008	c.1865C>T	c.(1864-1866)tCt>tTt	p.S622F	MYO3B_ENST00000602629.1_3'UTR|MYO3B_ENST00000334231.6_Missense_Mutation_p.S631F|MYO3B_ENST00000409044.3_Missense_Mutation_p.S622F	NM_138995.4	NP_620482.3	Q8WXR4	MYO3B_HUMAN	myosin IIIB	622	Myosin motor.				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)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium bundle tip (GO:0032426)	ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(25)|ovary(6)|pancreas(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	59						GCTATTTCCTCTCAACATCAG	0.408																																					p.S622F		Atlas-SNP	.											.	MYO3B	320	.	0			c.C1865T						PASS	.	C	PHE/SER,PHE/SER,PHE/SER	5,3711		0,5,1853	199.0	181.0	187.0		1865,1865,1865	6.0	1.0	2	dbSNP_134	187	0,8214		0,0,4107	yes	missense,missense,missense	MYO3B	NM_001083615.2,NM_001171642.1,NM_138995.3	155,155,155	0,5,5960	TT,TC,CC		0.0,0.1346,0.0419	possibly-damaging,possibly-damaging,possibly-damaging	622/1315,622/1276,622/1342	171256771	5,11925	1858	4107	5965	SO:0001583	missense	140469	exon17			TTTCCTCTCAACA		CCDS42773.1, CCDS46446.1	2q31.1-q31.2	2011-09-27			ENSG00000071909	ENSG00000071909		"""Myosins / Myosin superfamily : Class III"""	15576	protein-coding gene	gene with protein product		610040					Standard	NM_001083615		Approved		uc002ufy.3	Q8WXR4	OTTHUMG00000154002	ENST00000408978.4:c.1865C>T	2.37:g.171256771C>T	ENSP00000386213:p.Ser622Phe	166.0	0.0	0		129.0	56.0	0.434109	NM_001083615	B8ZZR2|Q53QE1|Q53T08|Q8IX64|Q8IX65|Q8IX66|Q8IX67|Q8IX68|Q96N94	Missense_Mutation	SNP	ENST00000408978.4	37	CCDS42773.1	3	0.0013736263736263737	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	0	0.0	C	32	5.164240	0.94727	0.001346	0.0	ENSG00000071909	ENST00000409044;ENST00000408978;ENST00000317915;ENST00000484338;ENST00000334231	T;T;T;T	0.79454	-1.27;-1.27;-1.25;-1.27	6.03	6.03	0.97812	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	D	0.89047	0.6604	M	0.86268	2.805	0.80722	D	1	D;P;P	0.58268	0.982;0.539;0.885	P;B;P	0.61132	0.884;0.281;0.688	D	0.89522	0.3779	10	0.87932	D	0	.	20.5568	0.99304	0.0:1.0:0.0:0.0	.	622;622;622	Q8WXR4-5;Q8WXR4-4;Q8WXR4	.;.;MYO3B_HUMAN	F	622;622;621;631;631	ENSP00000386497:S622F;ENSP00000386213:S622F;ENSP00000446237:S631F;ENSP00000335100:S631F	ENSP00000314213:S621F	S	+	2	0	MYO3B	170965017	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.818000	0.86416	2.861000	0.98227	0.655000	0.94253	TCT	C|0.999;T|0.001	0.001	strong		0.408	MYO3B-004	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333410.1		
SLC52A3	113278	hgsc.bcm.edu	37	20	744510	744510	+	Silent	SNP	G	G	A	rs3746806	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:744510G>A	ENST00000217254.7	-	3	946	c.705C>T	c.(703-705)ctC>ctT	p.L235L	SLC52A3_ENST00000473664.1_Intron|SLC52A3_ENST00000381944.3_Silent_p.L235L	NM_033409.3	NP_212134.3	Q9NQ40	S52A3_HUMAN	solute carrier family 52 (riboflavin transporter), member 3	235					cellular response to heat (GO:0034605)|riboflavin metabolic process (GO:0006771)|riboflavin transport (GO:0032218)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	riboflavin transporter activity (GO:0032217)										AGAACGCCACGAGGCAGCAGG	0.622																																					p.L235L		Atlas-SNP	.											C20orf54,colon,carcinoma,-2,1	.	.	1	0			c.C705T						PASS	.	G		140,4266	98.9+/-137.6	3,134,2066	80.0	72.0	75.0		705	0.5	0.0	20	dbSNP_107	75	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	C20orf54	NM_033409.3		3,137,6363	AA,AG,GG		0.0349,3.1775,1.0995		235/470	744510	143,12863	2203	4300	6503	SO:0001819	synonymous_variant	113278	exon3			CGCCACGAGGCAG	AL118502	CCDS13007.1	20p13	2013-07-17	2013-07-17	2012-02-29	ENSG00000101276	ENSG00000101276		"""Solute carriers"""	16187	protein-coding gene	gene with protein product	"""hypothetical protein LOC113278"""	613350	"""chromosome 20 open reading frame 54"""	C20orf54		11780052, 19122205	Standard	NM_033409		Approved	bA371L19.1, hRFT2, RFVT3	uc002wed.4	Q9NQ40	OTTHUMG00000031647	ENST00000217254.7:c.705C>T	20.37:g.744510G>A		71.0	0.0	0		87.0	37.0	0.425287	NM_033409	A8K6P1|Q5W1A0|Q5W1A1|Q8NCL7|Q96GD5	Silent	SNP	ENST00000217254.7	37	CCDS13007.1																																																																																			A|0.009;C|0.000;G|0.991	0.009	strong		0.622	SLC52A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077482.2	NM_033409	
AMOT	154796	hgsc.bcm.edu	37	X	112022687	112022687	+	Missense_Mutation	SNP	T	T	C	rs147791527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:112022687T>C	ENST00000524145.1	-	11	2769	c.2695A>G	c.(2695-2697)Act>Gct	p.T899A	MIR4329_ENST00000582643.1_RNA|AMOT_ENST00000371959.3_Missense_Mutation_p.T899A|AMOT_ENST00000371962.1_Missense_Mutation_p.T667A|AMOT_ENST00000304758.1_Missense_Mutation_p.T490A			Q4VCS5	AMOT_HUMAN	angiomotin	899					actin cytoskeleton organization (GO:0030036)|blood vessel endothelial cell migration (GO:0043534)|cell migration involved in gastrulation (GO:0042074)|cell-cell junction assembly (GO:0007043)|cellular protein localization (GO:0034613)|chemotaxis (GO:0006935)|establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|gastrulation with mouth forming second (GO:0001702)|hippo signaling (GO:0035329)|in utero embryonic development (GO:0001701)|negative regulation of angiogenesis (GO:0016525)|negative regulation of GTPase activity (GO:0034260)|negative regulation of vascular permeability (GO:0043116)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell size (GO:0045793)|positive regulation of embryonic development (GO:0040019)|positive regulation of stress fiber assembly (GO:0051496)|regulation of cell migration (GO:0030334)|regulation of small GTPase mediated signal transduction (GO:0051056)|vasculogenesis (GO:0001570)	actin filament (GO:0005884)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|ruffle (GO:0001726)|stress fiber (GO:0001725)|tight junction (GO:0005923)	angiostatin binding (GO:0043532)|receptor activity (GO:0004872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	43						gtggcagcagtggcagtgatg	0.607													T|||	32	0.00847682	0.0242	0.0	3775	,	,		10806	0.0		0.0	False		,,,				2504	0.0				p.T899A		Atlas-SNP	.											.	AMOT	204	.	0			c.A2695G						PASS	.	T	ALA/THR,ALA/THR	65,3719		0,54,11,1560,545	47.0	27.0	34.0		1468,2695	-1.9	0.0	X	dbSNP_134	34	0,6636		0,0,0,2405,1826	yes	missense,missense	AMOT	NM_133265.2,NM_001113490.1	58,58	0,54,11,3965,2371	CC,CT,C,TT,T		0.0,1.7178,0.6238	benign,benign	490/676,899/1085	112022687	65,10355	2170	4231	6401	SO:0001583	missense	154796	exon10			CAGCAGTGGCAGT	AB028994	CCDS14563.1, CCDS48154.1	Xq23	2006-02-08			ENSG00000126016	ENSG00000126016			17810	protein-coding gene	gene with protein product		300410				11257124, 16043488, 12406577	Standard	NM_001113490		Approved	KIAA1071	uc004epr.3	Q4VCS5	OTTHUMG00000022216	ENST00000524145.1:c.2695A>G	X.37:g.112022687T>C	ENSP00000429013:p.Thr899Ala	94.0	0.0	0		116.0	82.0	0.706897	NM_001113490	Q504X5|Q9HD27|Q9UPT1	Missense_Mutation	SNP	ENST00000524145.1	37	CCDS48154.1	14	0.008438818565400843	10	0.02066115702479339	0	0.0	0	0.0	0	0.0	T	7.595	0.671638	0.14776	0.017178	0.0	ENSG00000126016	ENST00000304758;ENST00000371959;ENST00000371962;ENST00000524145;ENST00000432214	T;T;T;T	0.39592	1.07;2.17;2.41;2.17	5.08	-1.92	0.07618	.	0.574197	0.15760	N	0.245998	T	0.10637	0.0260	L	0.36672	1.1	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16897	-1.0387	10	0.08599	T	0.76	0.0865	1.9616	0.03387	0.1442:0.3726:0.1459:0.3373	.	899	Q4VCS5	AMOT_HUMAN	A	490;899;667;899;139	ENSP00000305557:T490A;ENSP00000361027:T899A;ENSP00000361030:T667A;ENSP00000429013:T899A	ENSP00000305557:T490A	T	-	1	0	AMOT	111909343	0.990000	0.36364	0.019000	0.16419	0.904000	0.53231	1.464000	0.35288	-0.085000	0.12573	0.430000	0.28490	ACT	T|0.990;C|0.010	0.010	strong		0.607	AMOT-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378570.1	NM_133265	
CCDC37	348807	hgsc.bcm.edu	37	3	126142189	126142189	+	Silent	SNP	C	C	A	rs78360289	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:126142189C>A	ENST00000352312.1	+	12	1203	c.1104C>A	c.(1102-1104)ccC>ccA	p.P368P	CCDC37_ENST00000505024.1_Silent_p.P369P|CCDC37_ENST00000393425.1_Silent_p.P369P	NM_182628.2	NP_872434.2	Q494V2	CCD37_HUMAN	coiled-coil domain containing 37	368										NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|skin(3)	23				GBM - Glioblastoma multiforme(114;0.166)		CCATCCCCCCCACGCAGGAGG	0.662																																					p.P368P		Atlas-SNP	.											.	CCDC37	69	.	0			c.C1104A						PASS	.						41.0	36.0	38.0					3																	126142189		2203	4300	6503	SO:0001819	synonymous_variant	348807	exon12			CCCCCCCACGCAG	AK097402	CCDS3037.1	3q21.2	2014-07-31			ENSG00000163885	ENSG00000163885			26842	protein-coding gene	gene with protein product						23569216	Standard	NM_182628		Approved	FLJ40083, MIA1	uc003eiu.1	Q494V2	OTTHUMG00000162691	ENST00000352312.1:c.1104C>A	3.37:g.126142189C>A		128.0	0.0	0		148.0	79.0	0.533784	NM_182628	D3DNA8|Q494V1|Q494V4|Q8N838	Silent	SNP	ENST00000352312.1	37	CCDS3037.1																																																																																			C|0.992;T|0.008	.	alt		0.662	CCDC37-001	KNOWN	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000370099.4	NM_182628	
CALHM1	255022	hgsc.bcm.edu	37	10	105215071	105215071	+	Missense_Mutation	SNP	C	C	T	rs114015468	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:105215071C>T	ENST00000329905.5	-	2	1125	c.989G>A	c.(988-990)gGt>gAt	p.G330D	CALHM2_ENST00000369788.3_5'Flank|CALHM2_ENST00000260743.5_5'Flank|CALHM2_ENST00000393235.1_5'Flank|RP11-225H22.4_ENST00000411906.1_RNA	NM_001001412.3	NP_001001412.3	Q8IU99	CAHM1_HUMAN	calcium homeostasis modulator 1	330					ATP transport (GO:0015867)|cation transport (GO:0006812)|protein homooligomerization (GO:0051260)|regulation of ion transmembrane transport (GO:0034765)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)	calcium activated cation channel activity (GO:0005227)|calcium channel activity (GO:0005262)|identical protein binding (GO:0042802)|voltage-gated ion channel activity (GO:0005244)			large_intestine(2)|liver(1)|lung(5)|ovary(1)	9						CCGGGGCCCACCCCCAGCCCA	0.662													C|||	63	0.0125799	0.0477	0.0	5008	,	,		17190	0.0		0.0	False		,,,				2504	0.0				p.G330D		Atlas-SNP	.											.	CALHM1	33	.	0			c.G989A						PASS	.	C	ASP/GLY	151,4255	95.7+/-134.4	1,149,2053	30.0	27.0	28.0		989	1.8	0.0	10	dbSNP_132	28	1,8599	2.2+/-6.3	0,1,4299	yes	missense	CALHM1	NM_001001412.3	94	1,150,6352	TT,TC,CC		0.0116,3.4271,1.1687	benign	330/347	105215071	152,12854	2203	4300	6503	SO:0001583	missense	255022	exon2			GGCCCACCCCCAG	BC036208	CCDS7550.1	10q24.33	2008-07-02	2008-07-02	2008-07-02	ENSG00000185933	ENSG00000185933			23494	protein-coding gene	gene with protein product		612234	"""family with sequence similarity 26, member C"""	FAM26C		18585350	Standard	NM_001001412		Approved		uc001kxe.2	Q8IU99	OTTHUMG00000018991	ENST00000329905.5:c.989G>A	10.37:g.105215071C>T	ENSP00000329926:p.Gly330Asp	90.0	0.0	0		123.0	75.0	0.609756	NM_001001412	Q5W091	Missense_Mutation	SNP	ENST00000329905.5	37	CCDS7550.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	C	0.028	-1.354143	0.01256	0.034271	1.16E-4	ENSG00000185933	ENST00000329905	T	0.17054	2.3	4.8	1.83	0.25207	.	1.229190	0.05379	N	0.536826	T	0.01661	0.0053	N	0.08118	0	0.09310	N	1	B	0.22414	0.069	B	0.18561	0.022	T	0.36625	-0.9740	10	0.13108	T	0.6	-4.9354	5.3984	0.16283	0.0:0.5539:0.146:0.3001	.	330	Q8IU99	CAHM1_HUMAN	D	330	ENSP00000329926:G330D	ENSP00000329926:G330D	G	-	2	0	CALHM1	105205061	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	-0.057000	0.11768	0.169000	0.19679	-0.379000	0.06801	GGT	C|0.988;T|0.012	0.012	strong		0.662	CALHM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050165.1	NM_001001412	
MC1R	4157	hgsc.bcm.edu	37	16	89985984	89985984	+	Silent	SNP	G	G	A	rs3212364	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89985984G>A	ENST00000555147.1	+	1	1698	c.318G>A	c.(316-318)ctG>ctA	p.L106L	RP11-566K11.4_ENST00000554623.1_RNA|MC1R_ENST00000555427.1_Silent_p.L106L|TUBB3_ENST00000556922.1_Silent_p.L106L|RP11-566K11.7_ENST00000570217.1_RNA|TUBB3_ENST00000554444.1_5'Flank	NM_002386.3	NP_002377.4	Q01726	MSHR_HUMAN	melanocortin 1 receptor (alpha melanocyte stimulating hormone receptor)	106					G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|intracellular signal transduction (GO:0035556)|melanin biosynthetic process (GO:0042438)|multicellular organismal development (GO:0007275)|negative regulation of tumor necrosis factor production (GO:0032720)|pigmentation (GO:0043473)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sensory perception of pain (GO:0019233)|UV protection (GO:0009650)|UV-damage excision repair (GO:0070914)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled peptide receptor activity (GO:0008528)|melanocortin receptor activity (GO:0004977)|melanocyte-stimulating hormone receptor activity (GO:0004980)|ubiquitin protein ligase binding (GO:0031625)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	11		all_cancers(9;1.69e-11)|Lung NSC(15;8.94e-06)|all_lung(18;1.39e-05)|all_neural(9;0.00581)|all_hematologic(23;0.0194)		BRCA - Breast invasive adenocarcinoma(80;0.0273)		CCGGTGCACTGGTGGCCCGGG	0.647									Melanoma, Familial Clustering of				G|||	56	0.0111821	0.0401	0.0043	5008	,	,		18870	0.0		0.0	False		,,,				2504	0.0				p.L106L		Atlas-SNP	.											.	MC1R	20	.	0			c.G318A						PASS	.	G		179,4203		4,171,2016	42.0	51.0	48.0		318	4.8	0.2	16	dbSNP_106	48	2,8582		0,2,4290	no	coding-synonymous	MC1R	NM_002386.3		4,173,6306	AA,AG,GG		0.0233,4.0849,1.396		106/318	89985984	181,12785	2191	4292	6483	SO:0001819	synonymous_variant	4157	exon1	Familial Cancer Database		TGCACTGGTGGCC		CCDS56011.1	16q24.3	2012-10-05			ENSG00000258839	ENSG00000258839		"""GPCR / Class A : Melanocortin receptors"""	6929	protein-coding gene	gene with protein product		155555				8458079	Standard	NM_002386		Approved	MSH-R		Q01726		ENST00000555147.1:c.318G>A	16.37:g.89985984G>A		62.0	0.0	0		83.0	35.0	0.421687	NM_002386	Q66K38|Q6UR93|Q8WWX6|Q8WWX7|Q96I33|Q96RU4|Q9UBF7|Q9UN58|Q9UN59|Q9UN60|Q9UN61|Q9UN62	Silent	SNP	ENST00000555147.1	37	CCDS56011.1																																																																																			G|0.991;A|0.009	0.009	strong		0.647	MC1R-001	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412014.1	NM_002386	
C1orf158	93190	hgsc.bcm.edu	37	1	12819401	12819401	+	Silent	SNP	G	G	A	rs115263357	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12819401G>A	ENST00000288048.5	+	3	600	c.384G>A	c.(382-384)aaG>aaA	p.K128K	C1orf158_ENST00000376210.3_Silent_p.K90K	NM_152290.2	NP_689503.2	Q8N1D5	CA158_HUMAN	chromosome 1 open reading frame 158	128										central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(1)|ovary(1)|skin(2)|urinary_tract(3)	10	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.06e-06)|COAD - Colon adenocarcinoma(227;0.000273)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00575)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		TGCCAGAGAAGTCTGACTTTC	0.522													G|||	33	0.00658946	0.0227	0.0043	5008	,	,		20187	0.0		0.0	False		,,,				2504	0.0				p.K128K		Atlas-SNP	.											.	C1orf158	28	.	0			c.G384A						PASS	.	G		78,4328		0,78,2125	86.0	88.0	87.0		384	1.4	0.3	1	dbSNP_132	87	0,8600		0,0,4300	no	coding-synonymous	C1orf158	NM_152290.2		0,78,6425	AA,AG,GG		0.0,1.7703,0.5997		128/195	12819401	78,12928	2203	4300	6503	SO:0001819	synonymous_variant	93190	exon3			AGAGAAGTCTGAC	BX647383	CCDS147.1	1p36.21	2008-02-05			ENSG00000157330	ENSG00000157330			28567	protein-coding gene	gene with protein product						12477932	Standard	NM_152290		Approved	MGC35194	uc001auh.3	Q8N1D5	OTTHUMG00000001888	ENST00000288048.5:c.384G>A	1.37:g.12819401G>A		111.0	0.0	0		107.0	53.0	0.495327	NM_152290	Q5VUY4	Silent	SNP	ENST00000288048.5	37	CCDS147.1																																																																																			G|0.993;A|0.007	0.007	strong		0.522	C1orf158-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005325.1	NM_152290	
DCTN1	1639	hgsc.bcm.edu	37	2	74596321	74596321	+	Silent	SNP	T	T	C	rs13429423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74596321T>C	ENST00000361874.3	-	15	1922	c.1605A>G	c.(1603-1605)acA>acG	p.T535T	DCTN1_ENST00000409240.1_Silent_p.T498T|DCTN1_ENST00000407639.2_Silent_p.T401T|DCTN1_ENST00000409567.3_Silent_p.T515T|DCTN1_ENST00000409438.1_Silent_p.T401T|DCTN1_ENST00000495643.1_5'Flank|DCTN1_ENST00000409868.1_Silent_p.T518T|DCTN1_ENST00000394003.3_Silent_p.T528T	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	535					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|G2/M transition of mitotic cell cycle (GO:0000086)|melanosome transport (GO:0032402)|microtubule-based transport (GO:0010970)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nervous system development (GO:0007399)	cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|dynein complex (GO:0030286)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(1)|skin(3)	45						CCTGCTGGTTTGTCAGTTCCC	0.532													T|||	222	0.0443291	0.1611	0.013	5008	,	,		20259	0.0		0.0	False		,,,				2504	0.0				p.T535T		Atlas-SNP	.											.	DCTN1	110	.	0			c.A1605G						PASS	.	T	,,,,,	590,3816	259.5+/-263.1	37,516,1650	137.0	126.0	130.0		1545,1203,1494,1584,1605,1203	-3.8	1.0	2	dbSNP_121	130	6,8594	3.7+/-12.6	0,6,4294	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DCTN1	NM_001135040.2,NM_001135041.2,NM_001190836.1,NM_001190837.1,NM_004082.4,NM_023019.3	,,,,,	37,522,5944	CC,CT,TT		0.0698,13.3908,4.5825	,,,,,	515/1254,401/1140,498/1237,528/1272,535/1279,401/1145	74596321	596,12410	2203	4300	6503	SO:0001819	synonymous_variant	1639	exon15			CTGGTTTGTCAGT		CCDS1939.1, CCDS46341.1, CCDS46342.1, CCDS54368.1, CCDS54369.1	2p13	2014-09-17	2010-06-24		ENSG00000204843	ENSG00000204843			2711	protein-coding gene	gene with protein product	"""p150 glued homolog (Drosophila)"""	601143	"""dynactin 1 (p150, Glued (Drosophila) homolog)"""			1828535	Standard	NM_001190836		Approved		uc002skx.3	Q14203	OTTHUMG00000129963	ENST00000361874.3:c.1605A>G	2.37:g.74596321T>C		252.0	0.0	0		305.0	151.0	0.495082	NM_004082	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Silent	SNP	ENST00000361874.3	37	CCDS1939.1																																																																																			T|0.956;C|0.044	0.044	strong		0.532	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082	
ZNF566	84924	hgsc.bcm.edu	37	19	36940675	36940675	+	Missense_Mutation	SNP	T	T	C	rs35217571	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36940675T>C	ENST00000434377.2	-	5	542	c.461A>G	c.(460-462)cAc>cGc	p.H154R	ZNF566_ENST00000454319.1_Missense_Mutation_p.H155R|ZNF566_ENST00000424129.2_Missense_Mutation_p.H154R|ZNF566_ENST00000493391.1_Missense_Mutation_p.H50R|ZNF566_ENST00000392170.2_Missense_Mutation_p.H155R	NM_032838.4	NP_116227.1	Q969W8	ZN566_HUMAN	zinc finger protein 566	154					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)					GGATGGATGGTGACTCAAAGT	0.393													T|||	78	0.0155751	0.0575	0.0029	5008	,	,		19069	0.0		0.0	False		,,,				2504	0.0				p.H155R		Atlas-SNP	.											.	ZNF566	40	.	0			c.A464G						PASS	.	T	ARG/HIS,ARG/HIS,ARG/HIS,ARG/HIS	208,4198	129.0+/-165.8	6,196,2001	146.0	145.0	145.0		464,461,461,461	2.8	0.6	19	dbSNP_126	145	7,8593	5.7+/-21.5	0,7,4293	yes	missense,missense,missense,missense	ZNF566	NM_001145343.1,NM_001145344.1,NM_001145345.1,NM_032838.4	29,29,29,29	6,203,6294	CC,CT,TT		0.0814,4.7208,1.6531	benign,benign,benign,benign	155/420,154/419,154/419,154/419	36940675	215,12791	2203	4300	6503	SO:0001583	missense	84924	exon5			GGATGGTGACTCA	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.461A>G	19.37:g.36940675T>C	ENSP00000415520:p.His154Arg	183.0	0.0	0		159.0	89.0	0.559748	NM_001145343	B7ZL95|Q2M3J1	Missense_Mutation	SNP	ENST00000434377.2	37	CCDS12494.1	23	0.010531135531135532	23	0.046747967479674794	0	0.0	0	0.0	0	0.0	T	0.347	-0.946931	0.02304	0.047208	8.14E-4	ENSG00000186017	ENST00000454319;ENST00000434377;ENST00000392170;ENST00000424129;ENST00000452939;ENST00000427002	T;T;T;T;T;T	0.04862	3.66;3.65;3.66;3.65;3.54;6.16	3.77	2.76	0.32466	.	0.718904	0.12064	N	0.502915	T	0.00637	0.0021	L	0.28054	0.825	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.46582	-0.9181	10	0.20046	T	0.44	.	3.8345	0.08888	0.0:0.1142:0.2214:0.6644	rs35217571	155;154	B7ZL95;Q969W8	.;ZN566_HUMAN	R	155;154;155;154;154;155	ENSP00000394207:H155R;ENSP00000415520:H154R;ENSP00000376010:H155R;ENSP00000401259:H154R;ENSP00000411526:H154R;ENSP00000400651:H155R	ENSP00000376010:H155R	H	-	2	0	ZNF566	41632515	0.045000	0.20229	0.589000	0.28718	0.313000	0.28021	0.622000	0.24433	0.836000	0.34901	0.454000	0.30748	CAC	T|0.986;C|0.014	0.014	strong		0.393	ZNF566-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000341054.1	NM_032838	
PCNX	22990	hgsc.bcm.edu	37	14	71514668	71514668	+	Missense_Mutation	SNP	G	G	C	rs78161372	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:71514668G>C	ENST00000304743.2	+	22	4751	c.4305G>C	c.(4303-4305)ttG>ttC	p.L1435F	PCNX_ENST00000238570.5_Missense_Mutation_p.L1435F|PCNX_ENST00000439984.3_Missense_Mutation_p.L1324F	NM_014982.2	NP_055797.2	Q96RV3	PCX1_HUMAN	pecanex homolog (Drosophila)	1435						integral component of membrane (GO:0016021)				NS(2)|biliary_tract(1)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(14)|liver(2)|lung(40)|ovary(1)|prostate(7)|skin(2)|urinary_tract(1)	87			KIRC - Kidney renal clear cell carcinoma(12;0.206)	all cancers(60;0.00835)|BRCA - Breast invasive adenocarcinoma(234;0.00951)|OV - Ovarian serous cystadenocarcinoma(108;0.0417)		CCATGCTGTTGGATCTCTTCT	0.358													G|||	26	0.00519169	0.0174	0.0043	5008	,	,		15956	0.0		0.0	False		,,,				2504	0.0				p.L1435F		Atlas-SNP	.											.	PCNX	198	.	0			c.G4305C						PASS	.	G	PHE/LEU	62,4342	59.3+/-96.0	0,62,2140	129.0	120.0	123.0		4305	3.2	1.0	14	dbSNP_132	123	0,8598		0,0,4299	yes	missense	PCNX	NM_014982.2	22	0,62,6439	CC,CG,GG		0.0,1.4078,0.4768	possibly-damaging	1435/2342	71514668	62,12940	2202	4299	6501	SO:0001583	missense	22990	exon22			GCTGTTGGATCTC	AF233450, AB018348	CCDS9806.1	14q24.2	2014-07-03							19740	protein-coding gene	gene with protein product			"""pecanex-like 1 (Drosophila)"""	PCNXL1		9244429, 15777640	Standard	NM_014982		Approved	KIAA0995, KIAA0805, pecanex	uc001xmo.2	Q96RV3		ENST00000304743.2:c.4305G>C	14.37:g.71514668G>C	ENSP00000304192:p.Leu1435Phe	206.0	0.0	0		226.0	102.0	0.451327	NM_014982	B2RTR6|O94897|Q96AI7|Q9Y2J9	Missense_Mutation	SNP	ENST00000304743.2	37	CCDS9806.1	7|7	0.003205128205128205|0.003205128205128205	6|6	0.012195121951219513|0.012195121951219513	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	G|G	14.02|14.02	2.412251|2.412251	0.42817|0.42817	0.014078|0.014078	0.0|0.0	ENSG00000100731|ENSG00000100731	ENST00000304743;ENST00000238570;ENST00000439984|ENST00000554691	T;T;T|.	0.12147|.	3.14;3.11;2.71|.	5.41|5.41	3.19|3.19	0.36642|0.36642	.|.	0.212294|.	0.41001|.	D|.	0.000979|.	T|T	0.40619|0.40619	0.1124|0.1124	L|L	0.53249|0.53249	1.67|1.67	0.47819|0.47819	D|D	0.999528|0.999528	P;P;P|.	0.50272|.	0.879;0.609;0.933|.	P;B;B|.	0.47573|.	0.55;0.235;0.441|.	T|T	0.45041|0.45041	-0.9288|-0.9288	10|5	0.02654|.	T|.	1|.	.|.	2.1506|2.1506	0.03798|0.03798	0.3175:0.0:0.433:0.2494|0.3175:0.0:0.433:0.2494	.|.	1435;1324;1435|.	Q96RV3-3;B2RTR6;Q96RV3|.	.;.;PCX1_HUMAN|.	F|S	1435;1435;1324|494	ENSP00000304192:L1435F;ENSP00000238570:L1435F;ENSP00000396617:L1324F|.	ENSP00000238570:L1435F|.	L|W	+|+	3|2	2|0	PCNX|PCNX	70584421|70584421	0.927000|0.927000	0.31430|0.31430	0.978000|0.978000	0.43139|0.43139	0.996000|0.996000	0.88848|0.88848	0.071000|0.071000	0.14594|0.14594	1.412000|1.412000	0.46977|0.46977	0.655000|0.655000	0.94253|0.94253	TTG|TGG	G|0.995;C|0.005	0.005	strong		0.358	PCNX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412479.1	NM_014982	
OR2T3	343173	hgsc.bcm.edu	37	1	248636934	248636934	+	Missense_Mutation	SNP	G	G	T	rs148766825	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248636934G>T	ENST00000359594.2	+	1	308	c.283G>T	c.(283-285)Gat>Tat	p.D95Y		NM_001005495.1	NP_001005495.1	Q8NH03	OR2T3_HUMAN	olfactory receptor, family 2, subfamily T, member 3	95						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|endometrium(5)|lung(19)|ovary(1)|prostate(1)|skin(3)	31	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CACTGGAGATGATACCATTTC	0.552													.|||	287	0.0573083	0.2065	0.0173	5008	,	,		20624	0.0		0.001	False		,,,				2504	0.001				p.D95Y		Atlas-SNP	.											.	OR2T3	79	.	0			c.G283T						PASS	.	T	TYR/ASP	740,3640	744.5+/-411.6	104,532,1554	59.0	51.0	54.0		283	-3.5	0.0	1	dbSNP_134	54	11,8581	817.4+/-406.9	0,11,4285	no	missense	OR2T3	NM_001005495.1	160	104,543,5839	TT,TG,GG		0.128,16.895,5.7894	benign	95/319	248636934	751,12221	2190	4296	6486	SO:0001583	missense	343173	exon1			GGAGATGATACCA		CCDS31117.1	1q44	2012-08-09			ENSG00000196539	ENSG00000196539		"""GPCR / Class A : Olfactory receptors"""	14727	protein-coding gene	gene with protein product							Standard	NM_001005495		Approved		uc001iel.1	Q8NH03	OTTHUMG00000040452	ENST00000359594.2:c.283G>T	1.37:g.248636934G>T	ENSP00000352604:p.Asp95Tyr	635.0	2.0	0.00314961		441.0	278.0	0.630385	NM_001005495	B2RNJ1	Missense_Mutation	SNP	ENST00000359594.2	37	CCDS31117.1	101	0.04624542124542125	96	0.1951219512195122	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	t	5.919	0.353667	0.11182	0.16895	0.00128	ENSG00000196539	ENST00000359594	T	0.36340	1.26	2.65	-3.45	0.04781	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00012	0.0000	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22034	-1.0228	9	0.72032	D	0.01	.	1.1933	0.01869	0.4366:0.2119:0.224:0.1274	.	95	Q8NH03	OR2T3_HUMAN	Y	95	ENSP00000352604:D95Y	ENSP00000352604:D95Y	D	+	1	0	OR2T3	246703557	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	0.501000	0.22578	-2.758000	0.00371	-3.175000	0.00056	GAT	G|1.000;|0.000	.	weak		0.552	OR2T3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097348.1	NM_001005495	
GGT1	2678	hgsc.bcm.edu	37	22	25010746	25010746	+	Silent	SNP	T	T	C	rs4049881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:25010746T>C	ENST00000400382.1	+	6	923	c.168T>C	c.(166-168)gaT>gaC	p.D56D	GGT1_ENST00000248923.4_Silent_p.D56D|GGT1_ENST00000406383.2_Silent_p.D56D|GGT1_ENST00000400383.1_Silent_p.D56D|GGT1_ENST00000400380.1_Silent_p.D56D			P19440	GGT1_HUMAN	gamma-glutamyltransferase 1	56					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)	ATGGCAGGGATGCACTGCGGG	0.622													t|||	343	0.0684904	0.2209	0.0231	5008	,	,		14046	0.003		0.002	False		,,,				2504	0.0307				p.D56D		Atlas-SNP	.											.	GGT1	68	.	0			c.T168C						PASS	.	C	,,,	589,3461		50,489,1486	41.0	46.0	45.0		168,168,168,168	-7.5	0.0	22	dbSNP_108	45	5,8363		0,5,4179	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GGT1	NM_001032364.2,NM_001032365.2,NM_005265.2,NM_013430.2	,,,	50,494,5665	CC,CT,TT		0.0598,14.5432,4.7834	,,,	56/570,56/570,56/570,56/570	25010746	594,11824	2025	4184	6209	SO:0001819	synonymous_variant	2678	exon6			CAGGGATGCACTG	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.168T>C	22.37:g.25010746T>C		230.0	0.0	0		269.0	127.0	0.472119	NM_013430	Q08247|Q14404|Q8TBS1|Q9UMK1	Silent	SNP	ENST00000400382.1	37	CCDS42992.1																																																																																			T|0.970;C|0.030	0.030	strong		0.622	GGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250797.1	NM_013430	
AGRN	375790	hgsc.bcm.edu	37	1	978804	978804	+	Missense_Mutation	SNP	C	C	T	rs144164397	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:978804C>T	ENST00000379370.2	+	8	1620	c.1570C>T	c.(1570-1572)Cgg>Tgg	p.R524W		NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	524	Kazal-like 5. {ECO:0000255|PROSITE- ProRule:PRU00798}.				axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|clustering of voltage-gated sodium channels (GO:0045162)|extracellular matrix organization (GO:0030198)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuromuscular junction development (GO:0007528)|neurotransmitter receptor metabolic process (GO:0045213)|phototransduction, visible light (GO:0007603)|plasma membrane organization (GO:0007009)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of synaptic growth at neuromuscular junction (GO:0045887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor clustering (GO:0043113)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synapse organization (GO:0050808)	basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acetylcholine receptor regulator activity (GO:0030548)|calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|dystroglycan binding (GO:0002162)|heparan sulfate proteoglycan binding (GO:0043395)|laminin binding (GO:0043236)|sialic acid binding (GO:0033691)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	42	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)		TACCCTCGGGCGGGAGATCCA	0.687													C|||	6	0.00119808	0.003	0.0029	5008	,	,		13574	0.0		0.0	False		,,,				2504	0.0				p.R524W		Atlas-SNP	.											.	AGRN	110	.	0			c.C1570T						PASS	.	C	TRP/ARG	12,4360		0,12,2174	32.0	33.0	32.0		1570	3.8	0.6	1	dbSNP_134	32	0,8582		0,0,4291	yes	missense	AGRN	NM_198576.3	101	0,12,6465	TT,TC,CC		0.0,0.2745,0.0926	probably-damaging	524/2046	978804	12,12942	2186	4291	6477	SO:0001583	missense	375790	exon8			CTCGGGCGGGAGA	XM_372195	CCDS30551.1	1p36.33	2014-09-17		2007-02-16	ENSG00000188157	ENSG00000188157		"""Proteoglycans / Extracellular Matrix : Other"""	329	protein-coding gene	gene with protein product	"""agrin proteoglycan"""	103320				1851019, 12270958	Standard	NM_198576		Approved	AGRIN	uc001ack.2	O00468	OTTHUMG00000040778	ENST00000379370.2:c.1570C>T	1.37:g.978804C>T	ENSP00000368678:p.Arg524Trp	65.0	0.0	0		76.0	38.0	0.5	NM_198576	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Missense_Mutation	SNP	ENST00000379370.2	37	CCDS30551.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	15.96	2.987733	0.53934	0.002745	0.0	ENSG00000188157	ENST00000379370	T	0.04454	3.62	4.76	3.76	0.43208	Proteinase inhibitor I1, Kazal (1);Protease inhibitor, Kazal-type (1);	0.533856	0.15977	N	0.235503	T	0.20941	0.0504	M	0.82433	2.59	0.37536	D	0.918126	D	0.89917	1.0	D	0.77557	0.99	T	0.02275	-1.1184	10	0.87932	D	0	-11.7757	9.9656	0.41723	0.4775:0.5225:0.0:0.0	.	524	O00468	AGRIN_HUMAN	W	524	ENSP00000368678:R524W	ENSP00000368678:R524W	R	+	1	2	AGRN	968667	0.998000	0.40836	0.597000	0.28824	0.014000	0.08584	3.246000	0.51414	2.195000	0.70347	0.655000	0.94253	CGG	C|0.999;T|0.001	0.001	strong		0.687	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576	
SEC14L3	266629	hgsc.bcm.edu	37	22	30860831	30860831	+	Missense_Mutation	SNP	G	G	A	rs115090125	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30860831G>A	ENST00000215812.4	-	8	730	c.640C>T	c.(640-642)Cgc>Tgc	p.R214C	SEC14L3_ENST00000401751.1_Missense_Mutation_p.R155C|SEC14L3_ENST00000539629.1_Missense_Mutation_p.R155C|SEC14L3_ENST00000415957.2_Missense_Mutation_p.R155C|SEC14L3_ENST00000402286.1_Missense_Mutation_p.R137C|SEC14L3_ENST00000403066.1_Missense_Mutation_p.R155C|SEC14L3_ENST00000540910.1_Missense_Mutation_p.R137C	NM_174975.4	NP_777635.1	Q9UDX4	S14L3_HUMAN	SEC14-like 3 (S. cerevisiae)	214	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.		R -> H (in dbSNP:rs2269961).			extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			NS(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	19					Vitamin E(DB00163)	ATTTTCCTGCGAGTGTCCTCA	0.443													G|||	18	0.00359425	0.0129	0.0014	5008	,	,		23216	0.0		0.0	False		,,,				2504	0.0				p.R214C	Esophageal Squamous(108;290 1516 3584 23771 37333)	Atlas-SNP	.											.	SEC14L3	46	.	0			c.C640T						PASS	.	G	CYS/ARG	34,4372	40.0+/-72.8	0,34,2169	179.0	154.0	162.0		640	4.4	1.0	22	dbSNP_132	162	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SEC14L3	NM_174975.4	180	0,35,6468	AA,AG,GG		0.0116,0.7717,0.2691	probably-damaging	214/401	30860831	35,12971	2203	4300	6503	SO:0001583	missense	266629	exon8			TCCTGCGAGTGTC	AY158086	CCDS13877.1, CCDS58800.1, CCDS58801.1	22q12.2	2013-09-23			ENSG00000100012	ENSG00000100012			18655	protein-coding gene	gene with protein product		612824					Standard	NM_174975		Approved	TAP2	uc003ahy.3	Q9UDX4	OTTHUMG00000151259	ENST00000215812.4:c.640C>T	22.37:g.30860831G>A	ENSP00000215812:p.Arg214Cys	135.0	0.0	0		148.0	75.0	0.506757	NM_174975	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Missense_Mutation	SNP	ENST00000215812.4	37	CCDS13877.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	20.1	3.931583	0.73442	0.007717	1.16E-4	ENSG00000100012	ENST00000403066;ENST00000415957;ENST00000215812;ENST00000402286;ENST00000401751;ENST00000539629;ENST00000540910	T;T;T;T;T;T;T	0.79454	-1.27;-1.27;-1.27;-1.27;-1.27;-1.27;-1.27	5.5	4.43	0.53597	Cellular retinaldehyde-binding/triple function, C-terminal (5);	0.000000	0.85682	D	0.000000	D	0.86615	0.5975	M	0.91510	3.215	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.71414	0.973;0.973	D	0.90030	0.4134	10	0.87932	D	0	-11.635	14.7515	0.69530	0.0:0.0:0.8547:0.1453	.	137;214	E9PE57;Q9UDX4	.;S14L3_HUMAN	C	155;155;214;137;155;155;137	ENSP00000385941:R155C;ENSP00000401864:R155C;ENSP00000215812:R214C;ENSP00000385004:R137C;ENSP00000383896:R155C;ENSP00000444691:R155C;ENSP00000439752:R137C	ENSP00000215812:R214C	R	-	1	0	SEC14L3	29190831	1.000000	0.71417	0.996000	0.52242	0.707000	0.40811	4.312000	0.59154	2.593000	0.87608	0.655000	0.94253	CGC	G|0.997;A|0.003	0.003	strong		0.443	SEC14L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321950.4	NM_174975	
PYGM	5837	hgsc.bcm.edu	37	11	64520569	64520569	+	Silent	SNP	G	G	A	rs11231865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:64520569G>A	ENST00000164139.3	-	12	1892	c.1494C>T	c.(1492-1494)ccC>ccT	p.P498P	PYGM_ENST00000462303.1_5'Flank|PYGM_ENST00000377432.3_Silent_p.P410P	NM_005609.2	NP_005600.1	P11217	PYGM_HUMAN	phosphorylase, glycogen, muscle	498					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glycogen phosphorylase activity (GO:0008184)|nucleotide binding (GO:0000166)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CTGCCAGCCCGGGGTTACACA	0.572													G|||	177	0.0353435	0.1293	0.0058	5008	,	,		18308	0.0		0.002	False		,,,				2504	0.0				p.P498P		Atlas-SNP	.											.	PYGM	77	.	0			c.C1494T						PASS	.	G	,	539,3863	245.3+/-254.3	24,491,1686	202.0	231.0	221.0		1230,1494	-11.6	0.1	11	dbSNP_120	221	1,8593		0,1,4296	no	coding-synonymous,coding-synonymous	PYGM	NM_001164716.1,NM_005609.2	,	24,492,5982	AA,AG,GG		0.0116,12.2444,4.1551	,	410/755,498/843	64520569	540,12456	2201	4297	6498	SO:0001819	synonymous_variant	5837	exon12			CAGCCCGGGGTTA		CCDS8079.1, CCDS53659.1	11q12-q13.2	2013-03-01	2008-07-31		ENSG00000068976	ENSG00000068976	2.4.1.1	"""Glycogen phosphorylases"""	9726	protein-coding gene	gene with protein product	"""McArdle syndrome"", ""glycogen storage disease type V"", ""glycogen phosphorylase, muscle form"""	608455	"""phosphorylase, glycogen; muscle"""				Standard	NM_005609		Approved		uc001oax.4	P11217	OTTHUMG00000066835	ENST00000164139.3:c.1494C>T	11.37:g.64520569G>A		200.0	1.0	0.005		221.0	121.0	0.547511	NM_005609	A0AVK1|A6NDY6	Silent	SNP	ENST00000164139.3	37	CCDS8079.1																																																																																			G|0.963;A|0.037	0.037	strong		0.572	PYGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143254.2	NM_005609	
GRIN3A	116443	hgsc.bcm.edu	37	9	104432462	104432462	+	Silent	SNP	A	A	G	rs200841145	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:104432462A>G	ENST00000361820.3	-	3	2832	c.2232T>C	c.(2230-2232)ttT>ttC	p.F744F		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	744					calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	GGTTCATTAGAAACCTTCCAG	0.433													A|||	3	0.000599042	0.0015	0.0014	5008	,	,		19652	0.0		0.0	False		,,,				2504	0.0				p.F744F		Atlas-SNP	.											.	GRIN3A	186	.	0			c.T2232C						PASS	.	A		3,4403	6.2+/-15.9	0,3,2200	90.0	86.0	87.0		2232	5.4	1.0	9		87	0,8600		0,0,4300	no	coding-synonymous	GRIN3A	NM_133445.2		0,3,6500	GG,GA,AA		0.0,0.0681,0.0231		744/1116	104432462	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	116443	exon3			CATTAGAAACCTT		CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.2232T>C	9.37:g.104432462A>G		96.0	0.0	0		79.0	48.0	0.607595	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Silent	SNP	ENST00000361820.3	37	CCDS6758.1																																																																																			A|1.000;G|0.000	0.000	strong		0.433	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
CXorf65	158830	hgsc.bcm.edu	37	X	70325881	70325881	+	Silent	SNP	G	G	A	rs138762266	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:70325881G>A	ENST00000374251.5	-	3	267	c.219C>T	c.(217-219)taC>taT	p.Y73Y		NM_001025265.2	NP_001020436.1	A6NEN9	CX065_HUMAN	chromosome X open reading frame 65	73										breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(2)|lung(3)	10						TACAAACGTAGTAGGTGCTTC	0.443													G|||	10	0.00264901	0.0068	0.0014	3775	,	,		16348	0.0		0.0	False		,,,				2504	0.0				p.Y73Y		Atlas-SNP	.											.	CXorf65	23	.	0			c.C219T						PASS	.	G		41,3794		0,37,4,1595,567	169.0	128.0	142.0		219	3.1	0.9	X	dbSNP_134	142	0,6728		0,0,0,2428,1872	no	coding-synonymous	CXorf65	NM_001025265.2		0,37,4,4023,2439	AA,AG,A,GG,G		0.0,1.0691,0.3881		73/184	70325881	41,10522	2203	4300	6503	SO:0001819	synonymous_variant	158830	exon3			AACGTAGTAGGTG	BC144434	CCDS35324.1	Xq13.1	2009-03-06			ENSG00000204165	ENSG00000204165			33713	protein-coding gene	gene with protein product							Standard	NM_001025265		Approved		uc011mpo.2	A6NEN9	OTTHUMG00000021785	ENST00000374251.5:c.219C>T	X.37:g.70325881G>A		200.0	0.0	0		174.0	77.0	0.442529	NM_001025265		Silent	SNP	ENST00000374251.5	37	CCDS35324.1																																																																																			G|0.996;A|0.004	0.004	strong		0.443	CXorf65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057089.2	NM_001025265	
CYB5B	80777	hgsc.bcm.edu	37	16	69458746	69458746	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:69458746C>T	ENST00000512062.1	+	1	319	c.148C>T	c.(148-150)Cgc>Tgc	p.R50C	CYB5B_ENST00000561792.1_Missense_Mutation_p.R50C|CYB5B_ENST00000307892.8_Missense_Mutation_p.R54C|CYB5B_ENST00000515314.1_Missense_Mutation_p.R50C			O43169	CYB5B_HUMAN	cytochrome b5 type B (outer mitochondrial membrane)	50	Cytochrome b5 heme-binding. {ECO:0000255|PROSITE-ProRule:PRU00279}.				oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	heme binding (GO:0020037)|metal ion binding (GO:0046872)			endometrium(3)|kidney(3)|lung(2)	8		Ovarian(137;0.101)				CGATGTCACCCGCTTCCTCAA	0.592																																					p.R54C		Atlas-SNP	.											.	CYB5B	12	.	0			c.C160T						PASS	.						52.0	53.0	53.0					16																	69458746		2066	4196	6262	SO:0001583	missense	80777	exon1			GTCACCCGCTTCC		CCDS10880.2	16q22.1	2006-02-02			ENSG00000103018	ENSG00000103018			24374	protein-coding gene	gene with protein product		611964				11867265, 14733950	Standard	NM_030579		Approved	CYB5-M	uc002exg.1	O43169	OTTHUMG00000133020	ENST00000512062.1:c.148C>T	16.37:g.69458746C>T	ENSP00000423679:p.Arg50Cys	67.0	0.0	0		89.0	4.0	0.0449438	NM_030579	A8K6B1|Q96CC3|Q9BT35	Missense_Mutation	SNP	ENST00000512062.1	37		.	.	.	.	.	.	.	.	.	.	C	16.35	3.099759	0.56183	.	.	ENSG00000103018	ENST00000512062;ENST00000307892;ENST00000515314	T;T;T	0.77229	-1.08;-1.08;-1.08	5.88	2.86	0.33363	Cytochrome b5 (5);	0.620650	0.18955	N	0.126564	T	0.62344	0.2420	N	0.26092	0.79	0.58432	D	0.999999	B;B;B	0.30584	0.286;0.047;0.004	B;B;B	0.28638	0.092;0.012;0.005	T	0.57843	-0.7741	10	0.87932	D	0	-12.3637	6.394	0.21603	0.1369:0.6613:0.1316:0.0702	.	50;50;50	D6RFH4;O43169;Q5HYD9	.;CYB5B_HUMAN;.	C	50;54;50	ENSP00000423679:R50C;ENSP00000308430:R54C;ENSP00000421492:R50C	ENSP00000308430:R54C	R	+	1	0	CYB5B	68016247	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	1.771000	0.38542	0.382000	0.24878	0.655000	0.94253	CGC	.	.	none		0.592	CYB5B-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000256606.2	NM_030579	
SHROOM2	357	hgsc.bcm.edu	37	X	9863929	9863929	+	Missense_Mutation	SNP	G	G	A	rs146519576	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:9863929G>A	ENST00000380913.3	+	4	2071	c.1981G>A	c.(1981-1983)Ggc>Agc	p.G661S		NM_001649.2	NP_001640.1	Q13796	SHRM2_HUMAN	shroom family member 2	661					apical protein localization (GO:0045176)|brain development (GO:0007420)|camera-type eye development (GO:0043010)|camera-type eye morphogenesis (GO:0048593)|cell migration (GO:0016477)|cell-cell junction maintenance (GO:0045217)|cellular pigment accumulation (GO:0043482)|ear development (GO:0043583)|establishment of melanosome localization (GO:0032401)|eye pigment granule organization (GO:0008057)|lens morphogenesis in camera-type eye (GO:0002089)|melanosome organization (GO:0032438)|negative regulation of actin filament depolymerization (GO:0030835)|sodium ion transmembrane transport (GO:0035725)	apical plasma membrane (GO:0016324)|cell cortex (GO:0005938)|cell-cell adherens junction (GO:0005913)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|microtubule (GO:0005874)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|beta-catenin binding (GO:0008013)|ligand-gated sodium channel activity (GO:0015280)			breast(4)|central_nervous_system(2)|cervix(3)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(13)|ovary(3)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	57		Hepatocellular(5;0.000888)				GGATGGCACCGGCCGCTGGAG	0.652													G|||	6	0.0015894	0.0038	0.0014	3775	,	,		11713	0.0		0.0	False		,,,				2504	0.0				p.G661S		Atlas-SNP	.											.	SHROOM2	139	.	0			c.G1981A						PASS	.	G	SER/GLY	8,3745		0,6,2,1598,543	10.0	10.0	10.0		1981	1.2	0.0	X	dbSNP_134	10	4,6600		0,4,0,2400,1796	yes	missense	SHROOM2	NM_001649.2	56	0,10,2,3998,2339	AA,AG,A,GG,G		0.0606,0.2132,0.1159	benign	661/1617	9863929	12,10345	2149	4200	6349	SO:0001583	missense	357	exon4			GGCACCGGCCGCT	X83543	CCDS14135.1	Xp22.3	2008-02-05	2006-07-20	2006-07-20	ENSG00000146950	ENSG00000146950			630	protein-coding gene	gene with protein product		300103	"""apical protein, Xenopus laevis-like"", ""apical protein-like (Xenopus laevis)"""	APXL		7795590, 16615870	Standard	NM_001649		Approved		uc004csu.1	Q13796	OTTHUMG00000021121	ENST00000380913.3:c.1981G>A	X.37:g.9863929G>A	ENSP00000370299:p.Gly661Ser	106.0	0.0	0		138.0	63.0	0.456522	NM_001649	B9EIQ7	Missense_Mutation	SNP	ENST00000380913.3	37	CCDS14135.1	.	.	.	.	.	.	.	.	.	.	G	4.289	0.052893	0.08291	0.002132	6.06E-4	ENSG00000146950	ENST00000380913	T	0.39406	1.08	4.92	1.21	0.21127	Apx/shroom, ASD1 (1);	1.413420	0.04081	N	0.309622	T	0.28830	0.0715	L	0.44542	1.39	0.20196	N	0.999928	P	0.40398	0.716	B	0.25405	0.06	T	0.18335	-1.0340	10	0.11485	T	0.65	-1.4736	9.2772	0.37707	0.3048:0.0:0.6952:0.0	.	661	Q13796	SHRM2_HUMAN	S	661	ENSP00000370299:G661S	ENSP00000370299:G661S	G	+	1	0	SHROOM2	9823929	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.067000	0.14510	-0.181000	0.10619	-1.129000	0.01985	GGC	G|0.998;A|0.002	0.002	strong		0.652	SHROOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055721.1	NM_001649	
MGAM	8972	hgsc.bcm.edu	37	7	141754629	141754629	+	Missense_Mutation	SNP	G	G	C	rs145885349	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:141754629G>C	ENST00000549489.2	+	27	3330	c.3235G>C	c.(3235-3237)Gag>Cag	p.E1079Q	MGAM_ENST00000475668.2_Missense_Mutation_p.E1079Q	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	1079	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)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	CAGCACCCCTGAGGGTCAACT	0.448													g|||	21	0.00419329	0.0151	0.0014	5008	,	,		18921	0.0		0.0	False		,,,				2504	0.0				p.E1079Q		Atlas-SNP	.											MGAM_ENST00000549489,caecum,carcinoma,-2,3	MGAM	767	3	0			c.G3235C						PASS	.	G	GLN/GLU	46,3784		0,46,1869	135.0	129.0	131.0		3235	2.3	0.0	7	dbSNP_134	131	0,8230		0,0,4115	no	missense	MGAM	NM_004668.2	29	0,46,5984	CC,CG,GG		0.0,1.201,0.3814	possibly-damaging	1079/1858	141754629	46,12014	1915	4115	6030	SO:0001583	missense	8972	exon27			ACCCCTGAGGGTC	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.3235G>C	7.37:g.141754629G>C	ENSP00000447378:p.Glu1079Gln	169.0	0.0	0		191.0	94.0	0.492147	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	37	CCDS47727.1	6	0.0027472527472527475	4	0.008130081300813009	2	0.0055248618784530384	0	0.0	0	0.0	G	11.01	1.514051	0.27123	0.01201	0.0	ENSG00000257335	ENST00000549489;ENST00000475668;ENST00000548812	T	0.30714	1.52	4.24	2.31	0.28768	Glycoside hydrolase-type carbohydrate-binding (1);	0.422018	0.17369	N	0.176760	T	0.28001	0.0690	M	0.76838	2.35	0.09310	N	1	B	0.15719	0.014	B	0.11329	0.006	T	0.28235	-1.0050	10	0.54805	T	0.06	.	12.7162	0.57117	0.0:0.3182:0.6818:0.0	.	1079	O43451	MGA_HUMAN	Q	1079;1079;956	ENSP00000447378:E1079Q	ENSP00000316431:E956Q	E	+	1	0	MGAM	141401098	0.000000	0.05858	0.001000	0.08648	0.119000	0.20118	0.690000	0.25451	0.207000	0.20607	-0.515000	0.04445	GAG	G|0.997;C|0.003	0.003	strong		0.448	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
SARAF	51669	hgsc.bcm.edu	37	8	29927182	29927182	+	Missense_Mutation	SNP	G	G	A	rs34416759	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:29927182G>A	ENST00000256255.6	-	3	933	c.676C>T	c.(676-678)Cca>Tca	p.P226S	TMEM66_ENST00000536273.1_Missense_Mutation_p.P54S|TMEM66_ENST00000545648.1_Missense_Mutation_p.P54S	NM_016127.4	NP_057211.4	Q96BY9	SARAF_HUMAN		226					calcium ion transport (GO:0006816)|regulation of store-operated calcium entry (GO:2001256)	integral component of endoplasmic reticulum membrane (GO:0030176)				endometrium(2)|large_intestine(1)|lung(11)	14				KIRC - Kidney renal clear cell carcinoma(542;0.0993)|Kidney(114;0.119)		TTAAAGCCTGGGGGAGGAGGT	0.507													G|||	44	0.00878594	0.031	0.0043	5008	,	,		18064	0.0		0.0	False		,,,				2504	0.0				p.P226S		Atlas-SNP	.											.	TMEM66	23	.	0			c.C676T						PASS	.	G	SER/PRO	135,4271	95.3+/-134.0	4,127,2072	119.0	102.0	108.0		676	-0.4	0.0	8	dbSNP_126	108	0,8600		0,0,4300	yes	missense	TMEM66	NM_016127.4	74	4,127,6372	AA,AG,GG		0.0,3.064,1.038	benign	226/340	29927182	135,12871	2203	4300	6503	SO:0001583	missense	51669	exon3			AGCCTGGGGGAGG																												ENST00000256255.6:c.676C>T	8.37:g.29927182G>A	ENSP00000256255:p.Pro226Ser	126.0	0.0	0		159.0	64.0	0.402516	NM_016127	B3KQQ4|B7Z9J1|D3DSU7|H9MHJ8|H9MHJ9|Q53HE8|Q9UNZ3|Q9Y683	Missense_Mutation	SNP	ENST00000256255.6	37	CCDS6074.1	16|16	0.007326007326007326|0.007326007326007326	15|15	0.03048780487804878|0.03048780487804878	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	G|G	13.64|13.64	2.296786|2.296786	0.40594|0.40594	0.03064|0.03064	0.0|0.0	ENSG00000133872|ENSG00000133872	ENST00000518296|ENST00000256255;ENST00000545648;ENST00000541035;ENST00000536273;ENST00000523127;ENST00000522794	T|T;T;T;T;T	0.58940|0.57752	0.3|0.38;0.38;0.38;0.38;0.38	5.82|5.82	-0.4|-0.4	0.12411|0.12411	.|.	0.360290|0.360290	0.32244|0.32244	N|N	0.006371|0.006371	T|T	0.21427|0.21427	0.0516|0.0516	L|L	0.61036|0.61036	1.89|1.89	0.41958|0.41958	D|D	0.990696|0.990696	.|B;B	.|0.25390	.|0.125;0.125	.|B;B	.|0.27170	.|0.077;0.077	T|T	0.09751|0.09751	-1.0660|-1.0660	8|10	0.72032|0.48119	D|T	0.01|0.1	-4.2187|-4.2187	7.801|7.801	0.29174|0.29174	0.0663:0.457:0.3642:0.1125|0.0663:0.457:0.3642:0.1125	rs34416759|rs34416759	.|226;226	.|B3KQQ4;Q96BY9	.|.;TMM66_HUMAN	L|S	95|226;54;190;54;124;190	ENSP00000427769:P95L|ENSP00000256255:P226S;ENSP00000441351:P54S;ENSP00000441723:P54S;ENSP00000428323:P124S;ENSP00000429630:P190S	ENSP00000427769:P95L|ENSP00000256255:P226S	P|P	-|-	2|1	0|0	TMEM66|TMEM66	30046724|30046724	0.985000|0.985000	0.35326|0.35326	0.020000|0.020000	0.16555|0.16555	0.991000|0.991000	0.79684|0.79684	1.791000|1.791000	0.38744|0.38744	-0.381000|-0.381000	0.07882|0.07882	-0.182000|-0.182000	0.12963|0.12963	CCC|CCA	G|0.990;A|0.010	0.010	strong		0.507	TMEM66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257254.4		
ACTG2	72	hgsc.bcm.edu	37	2	74140616	74140616	+	Silent	SNP	C	C	T	rs34286914	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:74140616C>T	ENST00000409624.1	+	7	1099	c.456C>T	c.(454-456)atC>atT	p.I152I	ACTG2_ENST00000409731.3_Silent_p.I109I|ACTG2_ENST00000345517.3_Silent_p.I152I			P63267	ACTH_HUMAN	actin, gamma 2, smooth muscle, enteric	152					muscle contraction (GO:0006936)	blood microparticle (GO:0072562)|cell periphery (GO:0071944)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			large_intestine(3)|lung(14)|skin(1)	18						CCACAGGCATCGTCCTGGATT	0.507													C|||	124	0.0247604	0.0908	0.0043	5008	,	,		20140	0.0		0.001	False		,,,				2504	0.0				p.I152I		Atlas-SNP	.											.	ACTG2	37	.	0			c.C456T						PASS	.	C	,	388,4018	193.6+/-218.7	20,348,1835	106.0	98.0	101.0		327,456	-9.2	0.3	2	dbSNP_126	101	2,8598		0,2,4298	no	coding-synonymous,coding-synonymous	ACTG2	NM_001199893.1,NM_001615.3	,	20,350,6133	TT,TC,CC		0.0233,8.8062,2.9986	,	109/334,152/377	74140616	390,12616	2203	4300	6503	SO:0001819	synonymous_variant	72	exon6			AGGCATCGTCCTG		CCDS1930.1, CCDS56124.1	2p13.1	2008-05-20			ENSG00000163017	ENSG00000163017			145	protein-coding gene	gene with protein product		102545		ACTL3, ACTA3		1710027, 1673027	Standard	NM_001199893		Approved	ACTSG	uc002sjw.3	P63267	OTTHUMG00000129813	ENST00000409624.1:c.456C>T	2.37:g.74140616C>T		144.0	0.0	0		137.0	66.0	0.481752	NM_001615	B2R7E7|B4E315|D6W5H8|E9PG30|P12718|Q504R1|Q6FI22	Silent	SNP	ENST00000409624.1	37	CCDS1930.1																																																																																			C|0.976;T|0.024	0.024	strong		0.507	ACTG2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328086.1	NM_001615	
AGFG2	3268	hgsc.bcm.edu	37	7	100151719	100151719	+	Missense_Mutation	SNP	G	G	A	rs61742738	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100151719G>A	ENST00000300176.4	+	5	711	c.589G>A	c.(589-591)Gtc>Atc	p.V197I	AGFG2_ENST00000262935.4_Intron|AGFG2_ENST00000474713.1_3'UTR	NM_006076.4	NP_006067.3	O95081	AGFG2_HUMAN	ArfGAP with FG repeats 2	197					regulation of ARF GTPase activity (GO:0032312)	membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						CTCCAAGCCCGTCAGTCAGTC	0.597													G|||	203	0.0405351	0.143	0.0144	5008	,	,		19840	0.001		0.003	False		,,,				2504	0.0				p.V197I		Atlas-SNP	.											.	AGFG2	44	.	0			c.G589A						PASS	.	G	ILE/VAL	588,3818	259.2+/-262.9	40,508,1655	69.0	62.0	64.0		589	3.3	1.0	7	dbSNP_129	64	15,8585	10.5+/-38.8	0,15,4285	yes	missense	AGFG2	NM_006076.4	29	40,523,5940	AA,AG,GG		0.1744,13.3454,4.6363	benign	197/482	100151719	603,12403	2203	4300	6503	SO:0001583	missense	3268	exon5			AAGCCCGTCAGTC	AF015042	CCDS5697.1	7q22.1	2008-09-22	2008-09-22	2008-09-22	ENSG00000106351	ENSG00000106351		"""ADP-ribosylation factor GTPase activating proteins"""	5177	protein-coding gene	gene with protein product		604019	"""HIV-1 Rev binding protein-like"""	HRBL		9799793	Standard	XM_005250306		Approved	RABR	uc003uvf.3	O95081	OTTHUMG00000156029	ENST00000300176.4:c.589G>A	7.37:g.100151719G>A	ENSP00000300176:p.Val197Ile	83.0	0.0	0		86.0	43.0	0.5	NM_006076	O75429|Q96AB9|Q96GL4	Missense_Mutation	SNP	ENST00000300176.4	37	CCDS5697.1	76	0.0347985347985348	69	0.1402439024390244	5	0.013812154696132596	0	0.0	2	0.002638522427440633	G	6.520	0.464149	0.12402	0.133454	0.001744	ENSG00000106351	ENST00000300176	T	0.22945	1.93	5.1	3.31	0.37934	.	0.980801	0.08316	N	0.964634	T	0.00144	0.0004	N	0.25485	0.75	0.09310	P	0.9999999999537761	B	0.14438	0.01	B	0.06405	0.002	T	0.22695	-1.0209	9	0.23891	T	0.37	-29.7338	8.266	0.31815	0.1791:0.0:0.8209:0.0	rs61742738	197	O95081	AGFG2_HUMAN	I	197	ENSP00000300176:V197I	ENSP00000300176:V197I	V	+	1	0	AGFG2	99989655	0.823000	0.29233	0.979000	0.43373	0.187000	0.23431	1.897000	0.39799	0.877000	0.35895	-0.125000	0.14975	GTC	G|0.959;A|0.041	0.041	strong		0.597	AGFG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342769.1	NM_006076	
PTX4	390667	hgsc.bcm.edu	37	16	1536140	1536140	+	Missense_Mutation	SNP	C	C	T	rs386787711|rs79505704	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1536140C>T	ENST00000447419.2	-	3	1262	c.1237G>A	c.(1237-1239)Gga>Aga	p.G413R	PTX4_ENST00000293922.1_Missense_Mutation_p.G408R|PTX4_ENST00000440447.2_3'UTR			Q96A99	PTX4_HUMAN	pentraxin 4, long	413	Pentaxin.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						CTGTCGAATCCGCCCCCCACG	0.662													C|||	87	0.0173722	0.0643	0.0029	5008	,	,		16723	0.0		0.0	False		,,,				2504	0.0				p.G408R		Atlas-SNP	.											.	PTX4	46	.	0			c.G1222A						PASS	.						57.0	55.0	55.0					16																	1536140		2199	4300	6499	SO:0001583	missense	390667	exon3			CGAATCCGCCCCC		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"""chromosome 16 open reading frame 38"""	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.1237G>A	16.37:g.1536140C>T	ENSP00000445277:p.Gly413Arg	65.0	0.0	0		75.0	40.0	0.533333	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		43	0.019688644688644688	41	0.08333333333333333	2	0.0055248618784530384	0	0.0	0	0.0	C	13.11	2.138909	0.37728	.	.	ENSG00000251692	ENST00000447419;ENST00000293922	T;T	0.65364	-0.15;-0.15	5.45	3.39	0.38822	.	0.128923	0.51477	D	0.000092	T	0.09202	0.0227	M	0.63428	1.95	0.09310	N	0.999999	D	0.56287	0.975	P	0.55011	0.766	T	0.10382	-1.0632	10	0.18710	T	0.47	.	8.671	0.34149	0.0:0.7615:0.1535:0.085	.	408	Q96A99-2	.	R	413;408	ENSP00000445277:G413R;ENSP00000293922:G408R	ENSP00000293922:G408R	G	-	1	0	PTX4	1476141	0.000000	0.05858	0.048000	0.18961	0.000000	0.00434	0.922000	0.28734	1.318000	0.45170	-0.251000	0.11542	GGA	C|0.987;T|0.013	0.013	strong		0.662	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
IFNAR1	3454	hgsc.bcm.edu	37	21	34721782	34721782	+	Missense_Mutation	SNP	C	C	T	rs17875834	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:34721782C>T	ENST00000270139.3	+	8	1228	c.1076C>T	c.(1075-1077)aCg>aTg	p.T359M	IFNAR1_ENST00000416947.2_Missense_Mutation_p.T290M|IFNAR1_ENST00000442357.2_Missense_Mutation_p.T359M	NM_000629.2	NP_000620.2	P17181	INAR1_HUMAN	interferon (alpha, beta and omega) receptor 1	359	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.		T -> M (in dbSNP:rs17875834). {ECO:0000269|Ref.5}.		cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to virus (GO:0009615)|T cell activation (GO:0042110)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	type I interferon receptor activity (GO:0004905)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|skin(2)	14					"""""""Interferon Alfa-2a(DB00034)|""""Interferon Alfa-2b(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1a(DB00060)|Interferon beta-1b(DB00068)|Natural alpha interferon(DB05258)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)"""	TCTGGAAACACGCCTGTGATC	0.338													C|||	315	0.0628994	0.2307	0.0101	5008	,	,		17009	0.002		0.001	False		,,,				2504	0.0				p.T359M	Esophageal Squamous(73;817 1211 32990 35667 42746)	Atlas-SNP	.											IFNAR1,caecum,carcinoma,0,1	IFNAR1	44	1	0			c.C1076T						PASS	.	C	MET/THR	677,3729	286.0+/-278.5	47,583,1573	56.0	55.0	55.0		1076	-1.0	0.0	21	dbSNP_124	55	4,8594	3.0+/-9.4	0,4,4295	yes	missense	IFNAR1	NM_000629.2	81	47,587,5868	TT,TC,CC		0.0465,15.3654,5.2369	benign	359/558	34721782	681,12323	2203	4299	6502	SO:0001583	missense	3454	exon8			GAAACACGCCTGT		CCDS13624.1	21q22.1	2008-05-02			ENSG00000142166	ENSG00000142166		"""Interferons"""	5432	protein-coding gene	gene with protein product		107450		IFNAR		8181059	Standard	NM_000629		Approved	IFRC	uc002yrn.3	P17181	OTTHUMG00000065126	ENST00000270139.3:c.1076C>T	21.37:g.34721782C>T	ENSP00000270139:p.Thr359Met	117.0	0.0	0		106.0	49.0	0.462264	NM_000629	B2R6L9|B4DNT3|D3DSF0|Q53GW9|Q53H11|Q6PKD7|Q7M4L2|Q8WTZ2	Missense_Mutation	SNP	ENST00000270139.3	37	CCDS13624.1	130	0.05952380952380952	126	0.25609756097560976	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	C	8.320	0.823991	0.16678	0.153654	4.65E-4	ENSG00000142166	ENST00000416947;ENST00000270139;ENST00000442357	T;T;T	0.40756	1.02;1.02;1.55	4.43	-1.01	0.10169	Fibronectin, type III (2);Interferon alpha/beta receptor, beta chain (1);Immunoglobulin-like fold (1);	1.665550	0.02913	N	0.136918	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B	0.22146	0.065	B	0.11329	0.006	T	0.20538	-1.0272	9	0.45353	T	0.12	.	0.7942	0.01063	0.4848:0.1669:0.1883:0.16	rs17875834;rs17875834	359	P17181	INAR1_HUMAN	M	290;359;359	ENSP00000395606:T290M;ENSP00000270139:T359M;ENSP00000407406:T359M	ENSP00000270139:T359M	T	+	2	0	IFNAR1	33643652	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.564000	0.05936	-0.375000	0.07955	-0.272000	0.10252	ACG	C|0.930;T|0.070	0.070	strong		0.338	IFNAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139823.4		
SSPO	23145	hgsc.bcm.edu	37	7	149488909	149488909	+	RNA	SNP	C	C	T	rs893600	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149488909C>T	ENST00000378016.2	+	0	5250							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			TCACAGTGGACGGTGAATGGA	0.657													C|||	131	0.0261581	0.0946	0.0086	5008	,	,		18103	0.0		0.0	False		,,,				2504	0.0				p.D1750D		Atlas-SNP	.											.	.	.	.	0			c.C5250T						PASS	.	C		247,3859		6,235,1812	14.0	18.0	16.0		5254	-5.8	0.4	7	dbSNP_86	16	6,8318		0,6,4156	yes	coding-notMod3	SSPO	NM_198455.2		6,241,5968	TT,TC,CC		0.0721,6.0156,2.0354			149488909	253,12177	2053	4162	6215			23145	exon35			AGTGGACGGTGAA	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149488909C>T		188.0	0.0	0		159.0	77.0	0.484277	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	37																																																																																				C|0.979;T|0.021	0.021	strong		0.657	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
WWC3	55841	hgsc.bcm.edu	37	X	10085227	10085227	+	Silent	SNP	T	T	C	rs7058143	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:10085227T>C	ENST00000380861.4	+	11	1519	c.1128T>C	c.(1126-1128)cgT>cgC	p.R376R	WWC3_ENST00000454666.1_Silent_p.R376R	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	376	Ser-rich.				negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						CCTCCAGCCGTGGGTCTCTGG	0.672													C|||	774	0.205033	0.5401	0.0648	3775	,	,		12301	0.0		0.0149	False		,,,				2504	0.0				p.R376R		Atlas-SNP	.											.	WWC3	142	.	0			c.T1128C						PASS	.	C		2272,1558		575,780,342,277,224	36.0	44.0	41.0		1128	-3.3	0.3	X	dbSNP_116	41	142,6583		0,105,37,2323,1832	no	coding-synonymous	WWC3	NM_015691.3		575,885,379,2600,2056	CC,CT,C,TT,T		2.1115,40.6789,22.8707		376/1093	10085227	2414,8141	2198	4297	6495	SO:0001819	synonymous_variant	55841	exon11			CAGCCGTGGGTCT	AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"""WW, C2 and coiled-coil domain containing"""	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.1128T>C	X.37:g.10085227T>C		106.0	0.0	0		123.0	51.0	0.414634	NM_015691	A8KA96|Q659C1|Q9BTQ1	Silent	SNP	ENST00000380861.4	37	CCDS14136.1																																																																																			0|0.004;C|0.221	0.221	strong		0.672	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691	
CTNNBL1	56259	hgsc.bcm.edu	37	20	36396429	36396429	+	Missense_Mutation	SNP	C	C	G	rs186475150	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:36396429C>G	ENST00000361383.6	+	7	850	c.733C>G	c.(733-735)Ctg>Gtg	p.L245V	CTNNBL1_ENST00000405275.2_Missense_Mutation_p.L218V|CTNNBL1_ENST00000373473.1_Missense_Mutation_p.L58V|CTNNBL1_ENST00000473857.1_3'UTR	NM_030877.3	NP_110517.2	Q8WYA6	CTBL1_HUMAN	catenin, beta like 1	245					apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|positive regulation of apoptotic process (GO:0043065)|RNA splicing (GO:0008380)|somatic diversification of immunoglobulins (GO:0016445)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)|Prp19 complex (GO:0000974)|spliceosomal complex (GO:0005681)	enzyme binding (GO:0019899)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(6)|lung(6)|ovary(3)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				TCTACAGTGGCTGTTGAAGAG	0.517													C|||	15	0.00299521	0.0113	0.0	5008	,	,		18099	0.0		0.0	False		,,,				2504	0.0				p.L245V	Ovarian(184;582 2038 3273 4106 42608)	Atlas-SNP	.											.	CTNNBL1	78	.	0			c.C733G						PASS	.						108.0	108.0	108.0					20																	36396429		2203	4300	6503	SO:0001583	missense	56259	exon7			CAGTGGCTGTTGA	AL023804	CCDS13298.1	20q11.23-q12	2011-06-03	2002-05-27	2002-05-31	ENSG00000132792	ENSG00000132792			15879	protein-coding gene	gene with protein product	"""nuclear associated protein"""	611537	"""chromosome 20 open reading frame 33"""	C20orf33		12659813, 21385873	Standard	NM_030877		Approved	FLJ21108, P14L, P14, NAP, NYD-SP19	uc021wdj.1	Q8WYA6	OTTHUMG00000032428	ENST00000361383.6:c.733C>G	20.37:g.36396429C>G	ENSP00000355050:p.Leu245Val	180.0	0.0	0		199.0	107.0	0.537688	NM_030877	B4DE16|Q0VAL9|Q0VAM0|Q53HI8|Q5JWZ2|Q5JWZ3|Q5JWZ7|Q5JWZ8|Q8N454|Q8NCL2|Q8TBD6|Q96KD2|Q9H7A5|Q9NQF9|Q9NTX0|Q9Y3M7	Missense_Mutation	SNP	ENST00000361383.6	37	CCDS13298.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	C	18.66	3.670848	0.67814	.	.	ENSG00000132792	ENST00000361383;ENST00000405275;ENST00000373473	T;T;T	0.69806	-0.28;-0.28;-0.43	5.8	2.36	0.29203	Armadillo-like helical (1);Armadillo-type fold (1);	0.071705	0.64402	N	0.000019	T	0.58991	0.2161	M	0.76727	2.345	0.80722	D	1	D;D	0.57571	0.98;0.964	P;P	0.53401	0.725;0.629	T	0.70389	-0.4885	10	0.52906	T	0.07	-14.1169	11.9885	0.53161	0.0:0.7773:0.0:0.2227	.	245;58	Q8WYA6;Q8WYA6-2	CTBL1_HUMAN;.	V	245;218;58	ENSP00000355050:L245V;ENSP00000384355:L218V;ENSP00000362572:L58V	ENSP00000355050:L245V	L	+	1	2	CTNNBL1	35829843	1.000000	0.71417	0.988000	0.46212	0.998000	0.95712	0.916000	0.28651	0.797000	0.33971	0.655000	0.94253	CTG	C|0.995;G|0.005	0.005	strong		0.517	CTNNBL1-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079125.1	NM_030877	
GJB4	127534	hgsc.bcm.edu	37	1	35227306	35227306	+	Missense_Mutation	SNP	C	C	A	rs78499418	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:35227306C>A	ENST00000339480.1	+	2	821	c.451C>A	c.(451-453)Cgc>Agc	p.R151S	RP1-34M23.5_ENST00000542839.1_RNA	NM_153212.2	NP_694944.1	Q9NTQ9	CXB4_HUMAN	gap junction protein, beta 4, 30.3kDa	151					cell communication (GO:0007154)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|skin(1)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				TATCTTCCACCGCCTCTACAA	0.597													C|||	224	0.0447284	0.0991	0.0807	5008	,	,		20226	0.0317		0.0	False		,,,				2504	0.0051				p.R151S		Atlas-SNP	.											.	GJB4	51	.	0			c.C451A						PASS	.	C	SER/ARG	388,4018	195.7+/-220.2	16,356,1831	61.0	51.0	54.0		451	2.8	1.0	1	dbSNP_131	54	7,8593	5.0+/-18.6	0,7,4293	yes	missense	GJB4	NM_153212.2	110	16,363,6124	AA,AC,CC		0.0814,8.8062,3.0371	benign	151/267	35227306	395,12611	2203	4300	6503	SO:0001583	missense	127534	exon2			TTCCACCGCCTCT		CCDS383.1	1p35-p34	2008-05-14	2007-11-06		ENSG00000189433	ENSG00000189433		"""Ion channels / Gap junction proteins (connexins)"""	4286	protein-coding gene	gene with protein product	"""connexin 30.3"""	605425	"""gap junction protein, beta 4 (connexin 30.3)"", ""gap junction protein, beta 4"""				Standard	NM_153212		Approved	CX30.3	uc001bxv.1	Q9NTQ9	OTTHUMG00000004052	ENST00000339480.1:c.451C>A	1.37:g.35227306C>A	ENSP00000345868:p.Arg151Ser	73.0	0.0	0		75.0	41.0	0.546667	NM_153212	B3KQ82	Missense_Mutation	SNP	ENST00000339480.1	37	CCDS383.1	110	0.05036630036630037	58	0.11788617886178862	31	0.0856353591160221	21	0.03671328671328671	0	0.0	C	14.68	2.606763	0.46527	0.088062	8.14E-4	ENSG00000189433	ENST00000339480	D	0.95272	-3.66	5.73	2.76	0.32466	Gap junction protein, cysteine-rich domain (1);	0.176980	0.50627	D	0.000107	T	0.12050	0.0293	L	0.45352	1.415	0.53688	P	2.5000000000052758E-5	B	0.20780	0.048	B	0.20577	0.03	T	0.61865	-0.6975	9	0.32370	T	0.25	.	2.7568	0.05295	0.1289:0.5283:0.1251:0.2177	.	151	Q9NTQ9	CXB4_HUMAN	S	151	ENSP00000345868:R151S	ENSP00000345868:R151S	R	+	1	0	GJB4	34999893	0.000000	0.05858	0.951000	0.38953	0.977000	0.68977	-0.582000	0.05814	0.319000	0.23209	0.655000	0.94253	CGC	C|0.966;A|0.034	0.034	strong		0.597	GJB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011560.1	NM_153212	
ALKBH4	54784	hgsc.bcm.edu	37	7	102098035	102098035	+	Missense_Mutation	SNP	G	G	A	rs150409598	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:102098035G>A	ENST00000292566.3	-	3	754	c.715C>T	c.(715-717)Cgc>Tgc	p.R239C		NM_017621.3	NP_060091.1	Q9NXW9	ALKB4_HUMAN	alkB, alkylation repair homolog 4 (E. coli)	239					actomyosin structure organization (GO:0031032)|cleavage furrow ingression (GO:0036090)|protein demethylation (GO:0006482)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	contractile ring (GO:0070938)|cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)	actin binding (GO:0003779)|demethylase activity (GO:0032451)|metal ion binding (GO:0046872)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)			kidney(1)|lung(5)|skin(2)	8						AGCAGGGAGCGGGCGGGTAAG	0.701													G|||	22	0.00439297	0.0144	0.0029	5008	,	,		15602	0.0		0.0	False		,,,				2504	0.001				p.R239C		Atlas-SNP	.											.	ALKBH4	21	.	0			c.C715T						PASS	.	G	CYS/ARG	17,4385		0,17,2184	20.0	19.0	19.0		715	3.0	1.0	7	dbSNP_134	19	0,8590		0,0,4295	no	missense	ALKBH4	NM_017621.3	180	0,17,6479	AA,AG,GG		0.0,0.3862,0.1308	probably-damaging	239/303	102098035	17,12975	2201	4295	6496	SO:0001583	missense	54784	exon3			GGGAGCGGGCGGG	BC017096	CCDS5723.1	7q22.1	2006-02-09			ENSG00000160993	ENSG00000160993		"""Alkylation repair homologs"""	21900	protein-coding gene	gene with protein product		613302					Standard	NM_017621		Approved	FLJ20013	uc003uzl.3	Q9NXW9	OTTHUMG00000157720	ENST00000292566.3:c.715C>T	7.37:g.102098035G>A	ENSP00000292566:p.Arg239Cys	58.0	0.0	0		48.0	28.0	0.583333	NM_017621	Q53H92|Q9H6A4	Missense_Mutation	SNP	ENST00000292566.3	37	CCDS5723.1	16	0.007326007326007326	14	0.028455284552845527	2	0.0055248618784530384	0	0.0	0	0.0	G	15.57	2.873700	0.51695	0.003862	0.0	ENSG00000160993	ENST00000292566	T	0.15718	2.4	5.08	3.05	0.35203	Oxoglutarate/iron-dependent oxygenase (1);	0.100392	0.64402	N	0.000011	T	0.11153	0.0272	M	0.89658	3.05	0.80722	D	1	P	0.49447	0.924	P	0.45577	0.486	T	0.02805	-1.1108	10	0.59425	D	0.04	-5.0926	7.4982	0.27503	0.0954:0.0:0.6433:0.2613	.	239	Q9NXW9	ALKB4_HUMAN	C	239	ENSP00000292566:R239C	ENSP00000292566:R239C	R	-	1	0	ALKBH4	101885040	0.994000	0.37717	0.991000	0.47740	0.438000	0.31896	1.036000	0.30228	1.137000	0.42214	0.561000	0.74099	CGC	G|0.996;A|0.004	0.004	strong		0.701	ALKBH4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349503.1	NM_017621	
FBXO34	55030	hgsc.bcm.edu	37	14	55818162	55818162	+	Missense_Mutation	SNP	C	C	T	rs74050979	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:55818162C>T	ENST00000313833.4	+	2	1299	c.1054C>T	c.(1054-1056)Cct>Tct	p.P352S	FBXO34_ENST00000440021.1_Missense_Mutation_p.P352S	NM_017943.3	NP_060413.2	Q9NWN3	FBX34_HUMAN	F-box protein 34	352										breast(2)|kidney(2)|large_intestine(4)|lung(5)|ovary(3)|pancreas(1)|skin(2)|stomach(3)	22						GGATTGTGGCCCTTCAAGAGC	0.532													C|||	74	0.0147764	0.053	0.0058	5008	,	,		18923	0.0		0.0	False		,,,				2504	0.0				p.P352S		Atlas-SNP	.											.	FBXO34	61	.	0			c.C1054T						PASS	.	C	SER/PRO,SER/PRO	248,4158	143.8+/-178.8	7,234,1962	118.0	112.0	114.0		1054,1054	1.2	0.0	14	dbSNP_130	114	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	FBXO34	NM_017943.3,NM_152231.1	74,74	7,237,6259	TT,TC,CC		0.0349,5.6287,1.9299	benign,benign	352/712,352/712	55818162	251,12755	2203	4300	6503	SO:0001583	missense	55030	exon2			TGTGGCCCTTCAA	AK000732	CCDS32086.1	14q22.1	2004-08-24	2004-06-15			ENSG00000178974		"""F-boxes /  ""other"""""	20201	protein-coding gene	gene with protein product		609104	"""F-box only protein 34"""				Standard	NM_017943		Approved	FLJ20725, Fbx34	uc010aoo.3	Q9NWN3		ENST00000313833.4:c.1054C>T	14.37:g.55818162C>T	ENSP00000313159:p.Pro352Ser	195.0	0.0	0		207.0	90.0	0.434783	NM_017943	Q2VPB5|Q4VBP5|Q86TY4	Missense_Mutation	SNP	ENST00000313833.4	37	CCDS32086.1	30	0.013736263736263736	28	0.056910569105691054	2	0.0055248618784530384	0	0.0	0	0.0	C	2.024	-0.423983	0.04734	0.056287	3.49E-4	ENSG00000178974	ENST00000313833;ENST00000440021	T;T	0.17528	2.27;2.27	5.29	1.21	0.21127	.	0.444948	0.20885	N	0.083928	T	0.01695	0.0054	M	0.66939	2.045	0.09310	N	1	B	0.10296	0.003	B	0.15484	0.013	T	0.14090	-1.0485	10	0.36615	T	0.2	-19.68	8.4711	0.32986	0.0:0.6402:0.0:0.3598	.	352	Q9NWN3	FBX34_HUMAN	S	352	ENSP00000313159:P352S;ENSP00000394117:P352S	ENSP00000313159:P352S	P	+	1	0	FBXO34	54887915	0.000000	0.05858	0.001000	0.08648	0.034000	0.12701	0.391000	0.20784	0.388000	0.25054	0.650000	0.86243	CCT	C|0.979;T|0.021	0.021	strong		0.532	FBXO34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411322.1		
CYP4F12	66002	hgsc.bcm.edu	37	19	15794463	15794463	+	Missense_Mutation	SNP	G	G	C	rs57578760	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15794463G>C	ENST00000550308.1	+	7	1188	c.808G>C	c.(808-810)Gtc>Ctc	p.V270L	CYP4F12_ENST00000324632.10_Missense_Mutation_p.V270L	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	270					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	CACAGACGCTGTCATCCGGGA	0.537													.|||	73	0.0145767	0.0522	0.0043	5008	,	,		20833	0.0		0.001	False		,,,				2504	0.0				p.V270L		Atlas-SNP	.											.	CYP4F12	89	.	0			c.G808C						PASS	.	G	LEU/VAL	254,4142		0,254,1944	93.0	93.0	93.0		808	-1.0	0.1	19	dbSNP_129	93	2,8594		0,2,4296	no	missense	CYP4F12	NM_023944.3	32	0,256,6240	CC,CG,GG		0.0233,5.778,1.9704	possibly-damaging	270/525	15794463	256,12736	2198	4298	6496	SO:0001583	missense	66002	exon7			GACGCTGTCATCC	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.808G>C	19.37:g.15794463G>C	ENSP00000448998:p.Val270Leu	103.0	0.0	0		154.0	44.0	0.285714	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	25	0.011446886446886446	24	0.04878048780487805	1	0.0027624309392265192	0	0.0	0	0.0	.	11.57	1.677010	0.29783	0.05778	2.33E-4	ENSG00000186204	ENST00000550308;ENST00000324632	T;T	0.67698	-0.28;-0.28	2.47	-0.985	0.10256	.	0.093718	0.42172	U	0.000741	T	0.25680	0.0625	M	0.76002	2.32	0.31890	N	0.617322	P	0.51147	0.942	P	0.58577	0.841	T	0.62029	-0.6940	10	0.87932	D	0	.	6.6191	0.22792	0.3804:0.0:0.6196:0.0	rs57578760	270	Q9HCS2	CP4FC_HUMAN	L	270	ENSP00000448998:V270L;ENSP00000321821:V270L	ENSP00000321821:V270L	V	+	1	0	CYP4F12	15655463	0.981000	0.34729	0.078000	0.20375	0.184000	0.23303	1.826000	0.39092	-0.124000	0.11724	0.491000	0.48974	GTC	G|0.973;C|0.027	0.027	strong		0.537	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
AHNAK2	113146	hgsc.bcm.edu	37	14	105417731	105417731	+	Missense_Mutation	SNP	G	G	C	rs199870471	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105417731G>C	ENST00000333244.5	-	7	4176	c.4057C>G	c.(4057-4059)Ctg>Gtg	p.L1353V	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1353						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			GGTGCAGACAGGTCCACGGAG	0.597													.|||	284	0.0567093	0.0113	0.1311	5008	,	,		13717	0.0129		0.1153	False		,,,				2504	0.0501				p.L1353V		Atlas-SNP	.											.	AHNAK2	719	.	0			c.C4057G						PASS	.						125.0	106.0	114.0					14																	105417731		1812	2876	4688	SO:0001583	missense	113146	exon7			CAGACAGGTCCAC	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.4057C>G	14.37:g.105417731G>C	ENSP00000353114:p.Leu1353Val	364.0	0.0	0		261.0	108.0	0.413793	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	-	0.008	-1.901985	0.00517	.	.	ENSG00000185567	ENST00000333244	T	0.01933	4.55	4.27	0.17	0.15021	.	.	.	.	.	T	0.00784	0.0026	N	0.01529	-0.815	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.46721	-0.9171	9	0.02654	T	1	-1.5949	5.7398	0.18087	0.0:0.3359:0.4011:0.263	.	1353	Q8IVF2	AHNK2_HUMAN	V	1353	ENSP00000353114:L1353V	ENSP00000353114:L1353V	L	-	1	2	AHNAK2	104488776	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.272000	0.01165	-0.259000	0.09432	-1.901000	0.00528	CTG	.	.	weak		0.597	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
VPS9D1	9605	hgsc.bcm.edu	37	16	89778919	89778919	+	Silent	SNP	T	T	C	rs139626173	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89778919T>C	ENST00000389386.3	-	6	679	c.555A>G	c.(553-555)ctA>ctG	p.L185L	VPS9D1_ENST00000565452.1_5'Flank|VPS9D1-AS1_ENST00000562866.1_RNA|VPS9D1_ENST00000561976.1_Silent_p.L115L	NM_004913.2	NP_004904.2	Q9Y2B5	VP9D1_HUMAN	VPS9 domain containing 1	185					ATP synthesis coupled proton transport (GO:0015986)		GTPase activator activity (GO:0005096)|transporter activity (GO:0005215)										TCTGCCGCTGTAGAGAGAGGG	0.662													t|||	80	0.0159744	0.0575	0.0058	5008	,	,		12775	0.0		0.0	False		,,,				2504	0.0				p.L185L		Atlas-SNP	.											.	.	.	.	0			c.A555G						PASS	.			191,3575		3,185,1695	49.0	56.0	54.0		555	0.6	1.0	16	dbSNP_134	54	4,8210		0,4,4103	no	coding-synonymous	C16orf7	NM_004913.2		3,189,5798	CC,CT,TT		0.0487,5.0717,1.6277		185/632	89778919	195,11785	1883	4107	5990	SO:0001819	synonymous_variant	9605	exon6			CCGCTGTAGAGAG	AB018551	CCDS42220.1	16q24.3	2012-10-09	2012-10-09	2012-10-09	ENSG00000075399	ENSG00000075399			13526	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 7"""	C16orf7		10231027	Standard	NM_004913		Approved	ATP-BL	uc002fom.1	Q9Y2B5	OTTHUMG00000173219	ENST00000389386.3:c.555A>G	16.37:g.89778919T>C		42.0	0.0	0		38.0	27.0	0.710526	NM_004913		Silent	SNP	ENST00000389386.3	37	CCDS42220.1																																																																																			T|0.989;C|0.011	0.011	strong		0.662	VPS9D1-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422508.1	NM_004913	
ITPR2	3709	hgsc.bcm.edu	37	12	26816779	26816779	+	Splice_Site	SNP	C	C	T	rs77639758	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:26816779C>T	ENST00000381340.3	-	15	1968	c.1552G>A	c.(1552-1554)Gta>Ata	p.V518I		NM_002223.2	NP_002214.2	Q14571	ITPR2_HUMAN	inositol 1,4,5-trisphosphate receptor, type 2	518					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|cellular response to cAMP (GO:0071320)|cellular response to ethanol (GO:0071361)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|regulation of insulin secretion (GO:0050796)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transport (GO:0006810)	cell cortex (GO:0005938)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|phosphatidylinositol binding (GO:0035091)		ETV6/ITPR2(2)	biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(20)|liver(1)|lung(51)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	125	Colorectal(261;0.0847)				Caffeine(DB00201)	ATTCCAAATACCTATCAGGAA	0.338													C|||	19	0.00379393	0.0136	0.0014	5008	,	,		15680	0.0		0.0	False		,,,				2504	0.0				p.V518I		Atlas-SNP	.											.	ITPR2	270	.	0			c.G1552A						PASS	.	C	ILE/VAL	30,3602		0,30,1786	151.0	148.0	149.0		1552	4.5	1.0	12	dbSNP_131	149	0,8144		0,0,4072	yes	missense-near-splice	ITPR2	NM_002223.2	29	0,30,5858	TT,TC,CC		0.0,0.826,0.2548	benign	518/2702	26816779	30,11746	1816	4072	5888	SO:0001630	splice_region_variant	3709	exon15			CAAATACCTATCA	D26350	CCDS41764.1	12p11.23	2014-07-18	2011-04-28		ENSG00000123104	ENSG00000123104		"""Ion channels / Inositol triphosphate receptors"""	6181	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 48"""	600144	"""inositol 1,4,5-triphosphate receptor, type 2"""			8081734	Standard	XM_006719064		Approved	IP3R2, CFAP48	uc001rhg.3	Q14571	OTTHUMG00000169181	ENST00000381340.3:c.1552-1G>A	12.37:g.26816779C>T		68.0	0.0	0		74.0	38.0	0.513514	NM_002223	O94773	Missense_Mutation	SNP	ENST00000381340.3	37	CCDS41764.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	4.645	0.119815	0.08881	0.00826	0.0	ENSG00000123104	ENST00000381340	D	0.96885	-4.16	4.5	4.5	0.54988	Intracellular calcium-release channel (1);	0.053381	0.64402	D	0.000001	T	0.78317	0.4264	N	0.01242	-0.935	0.80722	D	1	B	0.02656	0.0	B	0.08055	0.003	T	0.77744	-0.2473	10	0.02654	T	1	.	5.5858	0.17274	0.0:0.7597:0.0:0.2403	.	518	Q14571	ITPR2_HUMAN	I	518	ENSP00000370744:V518I	ENSP00000370744:V518I	V	-	1	0	ITPR2	26708046	1.000000	0.71417	1.000000	0.80357	0.843000	0.47879	4.869000	0.63028	2.489000	0.83994	0.655000	0.94253	GTA	C|0.998;T|0.002	0.002	strong		0.338	ITPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402732.1	NM_002223	Missense_Mutation
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240577	39240577	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39240577A>G	ENST00000391417.4	+	1	119	c.119A>G	c.(118-120)tAc>tGc	p.Y40C		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	40	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						ACCACCTGCTACCGCCCCAGC	0.657																																					p.Y40C		Atlas-SNP	.											.	KRTAP4-7	49	.	0			c.A119G						PASS	.						13.0	22.0	19.0					17																	39240577		692	1590	2282	SO:0001583	missense	100132476	exon1			CCTGCTACCGCCC	AJ406939	CCDS45673.1	17q21.2	2013-06-25			ENSG00000240871	ENSG00000240871		"""Keratin associated proteins"""	18898	protein-coding gene	gene with protein product						11279113	Standard	NM_033061		Approved	KAP4.7	uc010wfn.2	Q9BYR0	OTTHUMG00000133582	ENST00000391417.4:c.119A>G	17.37:g.39240577A>G	ENSP00000375236:p.Tyr40Cys	106.0	0.0	0		135.0	16.0	0.118519	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	.	.	.	.	.	.	.	.	.	.	.	0.001	-2.883871	0.00061	.	.	ENSG00000240871;ENSG00000212722	ENST00000391417;ENST00000377734	T	0.00666	5.91	3.63	1.53	0.23141	.	0.603408	0.12340	N	0.477557	T	0.00412	0.0013	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.44390	-0.9331	9	0.02654	T	1	.	5.5941	0.17317	0.2179:0.1587:0.6234:0.0	.	40	Q9BYR0	KRA47_HUMAN	C	40	ENSP00000375236:Y40C	ENSP00000375236:Y40C	Y	+	2	0	KRTAP4-9;KRTAP4-7	36494103	0.873000	0.30073	0.022000	0.16811	0.001000	0.01503	1.032000	0.30178	-0.124000	0.11724	-2.594000	0.00164	TAC	.	.	none		0.657	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
HRCT1	646962	hgsc.bcm.edu	37	9	35906601	35906601	+	Missense_Mutation	SNP	C	C	A	rs565823201|rs112212538		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35906601C>A	ENST00000354323.2	+	1	413	c.317C>A	c.(316-318)cCc>cAc	p.P106H	LINC00961_ENST00000443779.1_lincRNA	NM_001039792.1	NP_001034881.1	Q6UXD1	HRCT1_HUMAN	histidine rich carboxyl terminus 1	106	His-rich.					integral component of membrane (GO:0016021)				NS(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(1)	4						caccaccacccccaccgccac	0.677																																					p.P106H		Atlas-SNP	.											.	HRCT1	14	.	0			c.C317A						PASS	.						6.0	6.0	6.0					9																	35906601		1795	3578	5373	SO:0001583	missense	646962	exon1			ACCACCCCCACCG		CCDS35012.1	9p13.3	2008-09-30			ENSG00000196196	ENSG00000196196			33872	protein-coding gene	gene with protein product						12975309	Standard	NM_001039792		Approved	LGLL338, PRO537, UNQ338	uc003zyr.1	Q6UXD1	OTTHUMG00000154146	ENST00000354323.2:c.317C>A	9.37:g.35906601C>A	ENSP00000346283:p.Pro106His	37.0	0.0	0		36.0	22.0	0.611111	NM_001039792	B7ZBJ1	Missense_Mutation	SNP	ENST00000354323.2	37	CCDS35012.1	337	0.1543040293040293	82	0.16666666666666666	47	0.1298342541436464	45	0.07867132867132867	163	0.21503957783641162	C	1.568	-0.535019	0.04082	.	.	ENSG00000196196	ENST00000354323	.	.	.	0.571	-1.14	0.09741	.	2.262810	0.02394	N	0.080002	T	0.00012	0.0000	N	0.04508	-0.205	0.80722	P	0.0	P	0.36944	0.574	B	0.32465	0.146	T	0.09751	-1.0660	7	0.87932	D	0	-19.8215	.	.	.	.	106	Q6UXD1	HRCT1_HUMAN	H	106	.	ENSP00000346283:P106H	P	+	2	0	HRCT1	35896601	0.000000	0.05858	0.011000	0.14972	0.341000	0.28922	-0.113000	0.10774	-1.188000	0.02705	-0.718000	0.03613	CCC	C|0.846;A|0.154	0.154	strong		0.677	HRCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334099.1	NM_001039792	
YY1AP1	55249	hgsc.bcm.edu	37	1	155629982	155629982	+	Missense_Mutation	SNP	C	C	T	rs145852062	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:155629982C>T	ENST00000295566.4	-	11	1880	c.1857G>A	c.(1855-1857)atG>atA	p.M619I	YY1AP1_ENST00000368340.5_Missense_Mutation_p.M691I|YY1AP1_ENST00000359205.5_Missense_Mutation_p.M562I|MSTO1_ENST00000538143.1_Intron|YY1AP1_ENST00000404643.1_Missense_Mutation_p.M553I|YY1AP1_ENST00000347088.5_Missense_Mutation_p.M573I|YY1AP1_ENST00000407221.1_Missense_Mutation_p.M542I|YY1AP1_ENST00000368330.2_Missense_Mutation_p.M573I|YY1AP1_ENST00000355499.4_Missense_Mutation_p.M573I|YY1AP1_ENST00000368339.5_Missense_Mutation_p.M711I|YY1AP1_ENST00000361831.5_Missense_Mutation_p.M562I|MSTO1_ENST00000452804.2_Intron|YY1AP1_ENST00000535662.1_Missense_Mutation_p.M419I|YY1AP1_ENST00000311573.5_Missense_Mutation_p.M542I	NM_001198906.1|NM_139118.2	NP_001185835.1|NP_620829.1	Q9H869	YYAP1_HUMAN	YY1 associated protein 1	619					regulation of cell cycle (GO:0051726)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(7)|ovary(2)|skin(2)|urinary_tract(2)	31	Hepatocellular(266;0.0997)|all_hematologic(923;0.145)					CAGGCTGGATCATGTTACAGC	0.537													C|||	100	0.0199681	0.0719	0.0072	5008	,	,		19458	0.0		0.0	False		,,,				2504	0.0				p.M711I		Atlas-SNP	.											.	YY1AP1	104	.	0			c.G2133A						PASS	.	C	,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET	286,4120	156.6+/-189.7	10,266,1927	87.0	80.0	83.0		,1521,1719,1857,1686,1659,2073,2133,1719,1719,1686,1686	2.5	1.0	1	dbSNP_134	83	2,8592	1.2+/-3.3	0,2,4295	no	utr-3,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	YY1AP1	NM_001198906.1,NM_139121.2,NM_139119.2,NM_139118.2,NM_018253.3,NM_001198905.1,NM_001198904.1,NM_001198903.1,NM_001198902.1,NM_001198901.1,NM_001198900.1,NM_001198899.1	,10,10,10,10,10,10,10,10,10,10,10	10,268,6222	TT,TC,CC		0.0233,6.4911,2.2154	,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign,benign	,507/685,573/751,619/797,562/740,553/731,691/869,711/889,573/751,573/751,562/740,562/740	155629982	288,12712	2203	4297	6500	SO:0001583	missense	55249	exon10			CTGGATCATGTTA	BC008766	CCDS1115.1, CCDS1116.1, CCDS55643.1, CCDS55644.1, CCDS55645.1	1q22	2009-05-07			ENSG00000163374	ENSG00000163374			30935	protein-coding gene	gene with protein product		607860				11710830	Standard	NM_139119		Approved	YY1AP, HCCA2, YAP		Q9H869	OTTHUMG00000035437	ENST00000295566.4:c.1857G>A	1.37:g.155629982C>T	ENSP00000295566:p.Met619Ile	291.0	1.0	0.00343643		320.0	162.0	0.50625	NM_001198903	B0QZ54|B4DMP2|B4E0I0|D3DV96|D3DV98|H7BY62|Q5VYZ1|Q5VYZ4|Q5VYZ7|Q7L4C3|Q7L5E2|Q8IXA6|Q8TEW5|Q8TF04|Q96HB6|Q9BQ64|Q9NV84	Missense_Mutation	SNP	ENST00000295566.4	37	CCDS1115.1	34	0.015567765567765568	31	0.06300813008130081	3	0.008287292817679558	0	0.0	0	0.0	c	13.31	2.198345	0.38806	0.064911	2.33E-4	ENSG00000163374	ENST00000359205;ENST00000355499;ENST00000311573;ENST00000347088;ENST00000361831;ENST00000368340;ENST00000295566;ENST00000368330;ENST00000407221;ENST00000404643;ENST00000368339;ENST00000535662	T;T;T;T;T;T;T;T;T;T;T;T	0.23552	1.96;1.96;1.97;1.96;1.96;1.92;1.95;1.96;1.97;1.98;1.9;1.97	2.53	2.53	0.30540	.	0.744128	0.12619	N	0.453204	T	0.13457	0.0326	L	0.47716	1.5	0.80722	D	1	B;B;B;B;B	0.21905	0.009;0.013;0.031;0.062;0.053	B;B;B;B;B	0.34652	0.015;0.02;0.187;0.068;0.013	T	0.08207	-1.0733	10	0.16896	T	0.51	.	13.0809	0.59114	0.0:1.0:0.0:0.0	.	711;553;619;573;691	B4DMP2;Q9H869-4;Q9H869;Q9H869-2;Q5VYZ1	.;.;YYAP1_HUMAN;.;.	I	562;573;542;573;562;691;619;573;542;553;711;419	ENSP00000352134:M562I;ENSP00000347686:M573I;ENSP00000311138:M542I;ENSP00000316079:M573I;ENSP00000355298:M562I;ENSP00000357324:M691I;ENSP00000295566:M619I;ENSP00000357314:M573I;ENSP00000385791:M542I;ENSP00000385390:M553I;ENSP00000357323:M711I;ENSP00000437926:M419I	ENSP00000295566:M619I	M	-	3	0	YY1AP1	153896606	1.000000	0.71417	0.995000	0.50966	0.972000	0.66771	2.589000	0.46145	1.419000	0.47118	0.306000	0.20318	ATG	C|0.981;T|0.019	0.019	strong		0.537	YY1AP1-043	PUTATIVE	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000086027.1	NM_139118	
LILRA6	79168	hgsc.bcm.edu	37	19	54744771	54744771	+	Silent	SNP	A	A	G	rs142457810	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54744771A>G	ENST00000396365.2	-	5	930	c.891T>C	c.(889-891)taT>taC	p.Y297Y	LILRA6_ENST00000440558.2_Silent_p.Y297Y|LILRA6_ENST00000391735.3_3'UTR|LILRA6_ENST00000419410.2_Silent_p.Y297Y|LILRA6_ENST00000245621.5_Silent_p.Y297Y|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000270464.5_Intron	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	297	Ig-like C2-type 1.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGTGTGCACCATAGCACCTGT	0.687																																					p.Y297Y		Atlas-SNP	.											.	LILRA6	75	.	0			c.T891C						PASS	.						57.0	71.0	67.0					19																	54744771		2203	4300	6503	SO:0001819	synonymous_variant	79168	exon5			TGCACCATAGCAC	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15495	protein-coding gene	gene with protein product			"""leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"""	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.891T>C	19.37:g.54744771A>G		380.0	1.0	0.00263158		471.0	124.0	0.26327	NM_024318		Silent	SNP	ENST00000396365.2	37	CCDS42610.1																																																																																			A|0.570;G|0.430	0.430	strong		0.687	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
MRS2	57380	hgsc.bcm.edu	37	6	24418749	24418749	+	Silent	SNP	G	G	A	rs141564147	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:24418749G>A	ENST00000378386.3	+	9	1143	c.1050G>A	c.(1048-1050)tcG>tcA	p.S350S	MRS2_ENST00000378353.1_Silent_p.S350S|MRS2_ENST00000543597.1_Silent_p.S59S|MRS2_ENST00000443868.2_Silent_p.S353S|MRS2_ENST00000483634.1_3'UTR|MRS2_ENST00000535061.1_Silent_p.S300S|MRS2_ENST00000274747.7_3'UTR	NM_020662.2	NP_065713.1	Q9HD23	MRS2_HUMAN	MRS2 magnesium transporter	350						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	magnesium ion transmembrane transporter activity (GO:0015095)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)|stomach(1)	12						TCTCTCTTTCGCTCTTTGGAC	0.443													G|||	18	0.00359425	0.0129	0.0014	5008	,	,		15837	0.0		0.0	False		,,,				2504	0.0				p.S350S		Atlas-SNP	.											.	MRS2	31	.	0			c.G1050A						PASS	.	G		50,4356	50.9+/-86.3	1,48,2154	171.0	167.0	168.0		1050	-10.8	0.0	6	dbSNP_134	168	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	MRS2	NM_020662.2		1,51,6451	AA,AG,GG		0.0349,1.1348,0.4075		350/444	24418749	53,12953	2203	4300	6503	SO:0001819	synonymous_variant	57380	exon9			TCTTTCGCTCTTT	AF288288	CCDS4552.1, CCDS69055.1, CCDS69056.1, CCDS75408.1	6p22.3-p22.1	2013-05-03	2013-05-03	2008-01-18	ENSG00000124532	ENSG00000124532			13785	protein-coding gene	gene with protein product			"""MRS2-like, magnesium homeostasis factor (S. cerevisiae)"", ""MRS2 magnesium homeostasis factor homolog (S. cerevisiae)"""	MRS2L			Standard	XM_005249242		Approved		uc003neb.3	Q9HD23	OTTHUMG00000014355	ENST00000378386.3:c.1050G>A	6.37:g.24418749G>A		278.0	0.0	0		261.0	118.0	0.452107	NM_020662	A8K4U3|B3KNN2|B4DQL2|Q5T3Y1|Q6NTG4|Q96KF8|Q9BVP1	Silent	SNP	ENST00000378386.3	37	CCDS4552.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	G	9.599	1.128145	0.20959	0.011348	3.49E-4	ENSG00000124532	ENST00000446191	.	.	.	5.41	-10.8	0.00216	.	.	.	.	.	T	0.13670	0.0331	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43393	-0.9394	4	.	.	.	-16.4762	0.5483	0.00658	0.2381:0.1624:0.2797:0.3198	.	.	.	.	H	169	.	.	R	+	2	0	MRS2	24526728	0.008000	0.16893	0.026000	0.17262	0.987000	0.75469	-1.057000	0.03486	-2.703000	0.00397	-0.163000	0.13421	CGC	G|0.996;A|0.004	0.004	strong		0.443	MRS2-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040002.1		
SRCAP	10847	hgsc.bcm.edu	37	16	30748715	30748715	+	Missense_Mutation	SNP	G	G	A	rs144295177		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:30748715G>A	ENST00000262518.4	+	34	7739	c.7354G>A	c.(7354-7356)Gct>Act	p.A2452T	SRCAP_ENST00000395059.2_Missense_Mutation_p.A2390T|SRCAP_ENST00000344771.4_Missense_Mutation_p.A2294T	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	2452	Pro-rich.				histone acetylation (GO:0016573)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|cervix(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(22)|liver(3)|lung(62)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(5)	136			Colorectal(24;0.198)			ttcagctccggctgcaattcc	0.587																																					p.A2452T		Atlas-SNP	.											.	SRCAP	298	.	0			c.G7354A						PASS	.	G	THR/ALA	3,4389	6.2+/-15.9	0,3,2193	124.0	89.0	101.0		7354	1.9	0.2	16	dbSNP_134	101	0,8596		0,0,4298	yes	missense	SRCAP	NM_006662.2	58	0,3,6491	AA,AG,GG		0.0,0.0683,0.0231	benign	2452/3231	30748715	3,12985	2196	4298	6494	SO:0001583	missense	10847	exon34			GCTCCGGCTGCAA	AB002307	CCDS10689.2	16p11.2	2009-08-06			ENSG00000080603	ENSG00000080603			16974	protein-coding gene	gene with protein product	"""Swi2/Snf2-related ATPase homolog (S. cerevisiae)"", ""domino homolog 1 (Drosophila)"""	611421				10347196, 9205841	Standard	NM_006662		Approved	KIAA0309, EAF1, SWR1, DOMO1	uc002dze.1	Q6ZRS2	OTTHUMG00000132393	ENST00000262518.4:c.7354G>A	16.37:g.30748715G>A	ENSP00000262518:p.Ala2452Thr	144.0	0.0	0		149.0	78.0	0.52349	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Missense_Mutation	SNP	ENST00000262518.4	37	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	G	8.548	0.874873	0.17395	6.83E-4	0.0	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	D;D;D	0.91521	-2.85;-2.85;-2.86	3.9	1.89	0.25635	.	.	.	.	.	T	0.77164	0.4090	N	0.08118	0	0.19575	N	0.999965	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.61441	-0.7062	9	0.17369	T	0.5	2.0848	6.8859	0.24199	0.1034:0.1777:0.7189:0.0	.	2390;2452	Q6ZRS2-2;Q6ZRS2	.;SRCAP_HUMAN	T	2452;2390;2294	ENSP00000262518:A2452T;ENSP00000378499:A2390T;ENSP00000343042:A2294T	ENSP00000262518:A2452T	A	+	1	0	SRCAP	30656216	0.830000	0.29337	0.206000	0.23566	0.629000	0.37895	1.913000	0.39956	0.317000	0.23160	0.306000	0.20318	GCT	G|1.000;A|0.000	0.000	weak		0.587	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662	
H6PD	9563	hgsc.bcm.edu	37	1	9322194	9322194	+	Silent	SNP	C	C	T	rs145706807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:9322194C>T	ENST00000377403.2	+	4	1124	c.822C>T	c.(820-822)ctC>ctT	p.L274L	H6PD_ENST00000602477.1_Silent_p.L285L	NM_001282587.1|NM_004285.3	NP_001269516.1|NP_004276.2	O95479	G6PE_HUMAN	hexose-6-phosphate dehydrogenase (glucose 1-dehydrogenase)	274	Glucose 1-dehydrogenase.				pentose-phosphate shunt (GO:0006098)|response to alcohol (GO:0097305)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)	6-phosphogluconolactonase activity (GO:0017057)|carbohydrate binding (GO:0030246)|glucose 1-dehydrogenase [NAD(P)] activity (GO:0047936)|glucose-6-phosphate dehydrogenase activity (GO:0004345)|NADP binding (GO:0050661)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|upper_aerodigestive_tract(1)	23	all_lung(157;0.23)	all_epithelial(116;1.28e-19)|all_lung(118;5.22e-06)|Lung NSC(185;1.98e-05)|Renal(390;0.000147)|Breast(348;0.00109)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;1.88e-07)|COAD - Colon adenocarcinoma(227;7.47e-05)|Kidney(185;0.000244)|KIRC - Kidney renal clear cell carcinoma(229;0.000905)|STAD - Stomach adenocarcinoma(132;0.00176)|BRCA - Breast invasive adenocarcinoma(304;0.00183)|READ - Rectum adenocarcinoma(331;0.0419)		TCCTCACCCTCGTGGCCATGG	0.637													C|||	2	0.000399361	0.0015	0.0	5008	,	,		19119	0.0		0.0	False		,,,				2504	0.0				p.L274L		Atlas-SNP	.											.	H6PD	71	.	0			c.C822T						PASS	.	C		7,4399	14.3+/-33.2	0,7,2196	68.0	63.0	65.0		822	-10.5	0.2	1	dbSNP_134	65	0,8600		0,0,4300	no	coding-synonymous	H6PD	NM_004285.3		0,7,6496	TT,TC,CC		0.0,0.1589,0.0538		274/792	9322194	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	9563	exon4			CACCCTCGTGGCC	AJ012590	CCDS101.1, CCDS72697.1	1p36	2008-02-05	2003-10-10		ENSG00000049239	ENSG00000049239	1.1.1.47		4795	protein-coding gene	gene with protein product		138090	"""glucose dehyrogenase"""	GDH		10349511	Standard	NM_001282587		Approved		uc001apt.3	O95479	OTTHUMG00000001768	ENST00000377403.2:c.822C>T	1.37:g.9322194C>T		195.0	0.0	0		213.0	126.0	0.591549	NM_004285	Q4TT33|Q66I35|Q68DT3	Silent	SNP	ENST00000377403.2	37	CCDS101.1																																																																																			C|0.999;T|0.001	0.001	strong		0.637	H6PD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004928.2	NM_004285	
RAB3D	9545	hgsc.bcm.edu	37	19	11436221	11436221	+	Silent	SNP	A	A	G	rs12981706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11436221A>G	ENST00000222120.3	-	5	773	c.513T>C	c.(511-513)aaT>aaC	p.N171N	TSPAN16_ENST00000316737.1_Intron|CTC-510F12.6_ENST00000586051.1_RNA|CTC-510F12.4_ENST00000586356.1_RNA|RAB3D_ENST00000589655.1_Silent_p.N171N	NM_004283.3	NP_004274.1	O95716	RAB3D_HUMAN	RAB3D, member RAS oncogene family	171					exocytosis (GO:0006887)|GTP catabolic process (GO:0006184)|peptidyl-cysteine methylation (GO:0018125)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)|zymogen granule (GO:0042588)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(3)|ovary(2)	14						CCTGCTTCACATTGATGTTCT	0.557													A|||	286	0.0571086	0.1762	0.0187	5008	,	,		14659	0.0		0.0318	False		,,,				2504	0.0082				p.N171N		Atlas-SNP	.											.	RAB3D	24	.	0			c.T513C						PASS	.	A	,	617,3789	268.6+/-268.5	43,531,1629	146.0	132.0	136.0		513,	-6.2	1.0	19	dbSNP_121	136	293,8307	108.0+/-168.7	3,287,4010	no	coding-synonymous,intron	RAB3D,TSPAN16	NM_004283.3,NM_012466.2	,	46,818,5639	GG,GA,AA		3.407,14.0036,6.9968	,	171/220,	11436221	910,12096	2203	4300	6503	SO:0001819	synonymous_variant	9545	exon5			CTTCACATTGATG	AF081353	CCDS12257.1	19p13.2	2012-10-02			ENSG00000105514	ENSG00000105514		"""RAB, member RAS oncogene"""	9779	protein-coding gene	gene with protein product	"""Rab3D upregulated with myeloid differentiation"", ""glioblastoma overexpressed"""	604350		GOV		10023084, 10072586	Standard	NM_004283		Approved	RAB16, D2-2, RAD3D	uc002mqx.3	O95716	OTTHUMG00000180835	ENST00000222120.3:c.513T>C	19.37:g.11436221A>G		46.0	0.0	0		48.0	16.0	0.333333	NM_004283		Silent	SNP	ENST00000222120.3	37	CCDS12257.1																																																																																			A|0.939;G|0.061;T|0.000	0.061	strong		0.557	RAB3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453211.1	NM_004283	
CXCR5	643	hgsc.bcm.edu	37	11	118764382	118764382	+	Silent	SNP	G	G	T	rs2230319	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:118764382G>T	ENST00000292174.4	+	2	305	c.129G>T	c.(127-129)ggG>ggT	p.G43G		NM_001716.4|NM_032966.2	NP_001707.1|NP_116743.1	P32302	CXCR5_HUMAN	chemokine (C-X-C motif) receptor 5	43					B cell activation (GO:0042113)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of cytokinesis (GO:0032467)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|G-protein coupled receptor activity (GO:0004930)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(5)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.62e-05)		CCACAGAGGGGCCCCTCATGG	0.597													G|||	275	0.0549121	0.202	0.0101	5008	,	,		17609	0.0		0.001	False		,,,				2504	0.0				p.G43G		Atlas-SNP	.											.	CXCR5	34	.	0			c.G129T						PASS	.	G	,	589,3811	259.8+/-263.3	34,521,1645	87.0	83.0	85.0		129,	-1.9	0.9	11	dbSNP_98	85	8,8582	5.7+/-21.5	0,8,4287	no	coding-synonymous,utr-5	CXCR5	NM_001716.4,NM_032966.2	,	34,529,5932	TT,TG,GG		0.0931,13.3864,4.5958	,	43/373,	118764382	597,12393	2200	4295	6495	SO:0001819	synonymous_variant	643	exon2			AGAGGGGCCCCTC	X68829	CCDS8402.1	11q23.3	2012-08-08	2008-01-22	2008-01-22	ENSG00000160683	ENSG00000160683		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : C-X-C motif"""	1060	protein-coding gene	gene with protein product		601613	"""Burkitt lymphoma receptor 1, GTP-binding protein"", ""Burkitt lymphoma receptor 1, GTP binding protein (chemokine (C-X-C motif) receptor 5)"""	BLR1		1425907	Standard	NM_001716		Approved	MDR15, CD185	uc001pue.4	P32302	OTTHUMG00000166345	ENST00000292174.4:c.129G>T	11.37:g.118764382G>T		97.0	0.0	0		114.0	67.0	0.587719	NM_001716	Q14811	Silent	SNP	ENST00000292174.4	37	CCDS8402.1																																																																																			G|0.952;T|0.048	0.048	strong		0.597	CXCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389309.1	NM_001716	
NOLC1	9221	hgsc.bcm.edu	37	10	103920255	103920255	+	Silent	SNP	T	T	A	rs145855726	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:103920255T>A	ENST00000605788.1	+	10	1381	c.1146T>A	c.(1144-1146)ggT>ggA	p.G382G	NOLC1_ENST00000603742.1_Silent_p.G101G|NOLC1_ENST00000405356.1_Silent_p.G392G|NOLC1_ENST00000488254.2_Silent_p.G383G	NM_001284389.1|NM_004741.3	NP_001271318.1|NP_004732.2	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1	382	11 X 12 AA approximate repeats of an acidic serine cluster.|Interacts with RPA194.				cell cycle (GO:0007049)|mitotic nuclear division (GO:0007067)|nucleolus organization (GO:0007000)|rRNA processing (GO:0006364)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	31		Colorectal(252;0.122)		Epithelial(162;5.19e-08)|all cancers(201;9.43e-07)		AGCCAGCTGGTACCACCAAGA	0.542													T|||	7	0.00139776	0.0053	0.0	5008	,	,		20457	0.0		0.0	False		,,,				2504	0.0				p.G382G		Atlas-SNP	.											.	NOLC1	61	.	0			c.T1146A						PASS	.	T		31,4375	36.0+/-67.5	0,31,2172	63.0	67.0	66.0		1146	-1.0	0.0	10	dbSNP_134	66	0,8600		0,0,4300	yes	coding-synonymous	NOLC1	NM_004741.3		0,31,6472	AA,AT,TT		0.0,0.7036,0.2384		382/700	103920255	31,12975	2203	4300	6503	SO:0001819	synonymous_variant	9221	exon10			AGCTGGTACCACC	Z34289	CCDS7530.1, CCDS65925.1, CCDS65926.1	10q24.32	2008-08-01			ENSG00000166197	ENSG00000166197			15608	protein-coding gene	gene with protein product		602394				7657714, 10567578	Standard	XM_005270273		Approved	P130, KIAA0035, NOPP140, NOPP130	uc001kuo.2	Q14978	OTTHUMG00000018944	ENST00000605788.1:c.1146T>A	10.37:g.103920255T>A		97.0	0.0	0		102.0	51.0	0.5	NM_004741	Q15030|Q5VV70|Q9BUV3	Silent	SNP	ENST00000605788.1	37	CCDS7530.1																																																																																			T|0.997;A|0.003	0.003	strong		0.542	NOLC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050012.2	NM_004741	
OR2H1	26716	hgsc.bcm.edu	37	6	29429732	29429732	+	Silent	SNP	T	T	C	rs61732184	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:29429732T>C	ENST00000377136.1	+	4	651	c.186T>C	c.(184-186)tcT>tcC	p.S62S	OR2H1_ENST00000396792.2_Silent_p.S62S|OR2H1_ENST00000442615.1_Silent_p.S62S|OR2H1_ENST00000377132.1_Silent_p.S62S|OR2H1_ENST00000377133.1_Silent_p.S62S|OR2H1_ENST00000473369.1_Intron			Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H, member 1	62						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(5)|lung(12)	17						TTTTCCTCTCTGACCTCTCCT	0.527													T|||	174	0.0347444	0.1044	0.013	5008	,	,		20433	0.0119		0.0119	False		,,,				2504	0.0031				p.S62S		Atlas-SNP	.											.	OR2H1	38	.	0			c.T186C						PASS	.	T		301,2721		17,267,1227	138.0	135.0	136.0		186	-0.0	1.0	6	dbSNP_129	136	33,5385		0,33,2676	no	coding-synonymous	OR2H1	NM_030883.3		17,300,3903	CC,CT,TT		0.6091,9.9603,3.9573		62/317	29429732	334,8106	1511	2709	4220	SO:0001819	synonymous_variant	26716	exon3			CCTCTCTGACCTC	AF044491	CCDS4660.1	6p22.1	2014-02-19	2002-02-28		ENSG00000204688	ENSG00000204688		"""GPCR / Class A : Olfactory receptors"""	8252	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily H, member 8"""	OR2H6, OR2H8			Standard	NM_030883		Approved	OR6-2	uc003nmi.3	Q9GZK4	OTTHUMG00000031050	ENST00000377136.1:c.186T>C	6.37:g.29429732T>C		256.0	0.0	0		303.0	139.0	0.458746	NM_030883	B0S7T4|O43629|O43661|O43662|Q5SUN6|Q9GZK9	Silent	SNP	ENST00000377136.1	37	CCDS4660.1																																																																																			T|0.964;C|0.036	0.036	strong		0.527	OR2H1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194014.3		
NDOR1	27158	hgsc.bcm.edu	37	9	140108468	140108468	+	Silent	SNP	C	C	T	rs114934623	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140108468C>T	ENST00000344894.5	+	5	543	c.460C>T	c.(460-462)Ctg>Ttg	p.L154L	NDOR1_ENST00000371521.4_Silent_p.L154L|NDOR1_ENST00000427047.2_Intron|NDOR1_ENST00000458322.2_Silent_p.L154L	NM_001144028.1|NM_014434.2	NP_001137500.1|NP_055249.1			NADPH dependent diflavin oxidoreductase 1											breast(1)|endometrium(5)|large_intestine(1)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	15	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		GGACAGGGTTCTGGGGCTGTA	0.711													C|||	26	0.00519169	0.0182	0.0029	5008	,	,		14886	0.0		0.0	False		,,,				2504	0.0				p.L154L		Atlas-SNP	.											.	NDOR1	71	.	0			c.C460T						PASS	.	C	,,,	43,4245		0,43,2101	18.0	22.0	21.0		460,,460,460	2.3	0.6	9	dbSNP_132	21	0,8378		0,0,4189	no	coding-synonymous,intron,coding-synonymous,coding-synonymous	NDOR1	NM_001144026.1,NM_001144027.1,NM_001144028.1,NM_014434.2	,,,	0,43,6290	TT,TC,CC		0.0,1.0028,0.3395	,,,	154/607,,154/591,154/598	140108468	43,12623	2144	4189	6333	SO:0001819	synonymous_variant	27158	exon5			AGGGTTCTGGGGC	BC015735	CCDS7036.1, CCDS48061.1, CCDS48062.1, CCDS48063.1	9q34.3	2008-02-05			ENSG00000188566	ENSG00000188566			29838	protein-coding gene	gene with protein product	"""NADPH dependent FMN and FAD containing oxidoreductase"""	606073				10625700, 12631275	Standard	XM_005266066		Approved	NR1, bA350O14.9	uc004clx.3	Q9UHB4	OTTHUMG00000020986	ENST00000344894.5:c.460C>T	9.37:g.140108468C>T		36.0	0.0	0		69.0	15.0	0.217391	NM_001144026		Silent	SNP	ENST00000344894.5	37	CCDS7036.1																																																																																			C|0.994;T|0.006	0.006	strong		0.711	NDOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254704.1	NM_014434	
HOXC10	3226	hgsc.bcm.edu	37	12	54379610	54379610	+	Silent	SNP	G	G	C	rs145093077		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:54379610G>C	ENST00000303460.4	+	1	641	c.567G>C	c.(565-567)tcG>tcC	p.S189S	HOXC-AS3_ENST00000513165.1_RNA|RP11-834C11.12_ENST00000513209.1_5'Flank|HOXC-AS3_ENST00000514702.1_RNA|HOXC-AS3_ENST00000509870.1_RNA|HOXC-AS3_ENST00000567780.1_RNA	NM_017409.3	NP_059105.2	Q9NYD6	HXC10_HUMAN	homeobox C10	189					anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|neuromuscular process (GO:0050905)|positive regulation of cell proliferation (GO:0008284)|proximal/distal pattern formation (GO:0009954)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system development (GO:0001501)|spinal cord motor neuron cell fate specification (GO:0021520)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			endometrium(2)|large_intestine(3)|lung(14)|pancreas(1)	20						ATCTGGAATCGCCTCAGCTGG	0.647																																					p.S189S		Atlas-SNP	.											.	HOXC10	42	.	0			c.G567C						PASS	.						32.0	36.0	35.0					12																	54379610		2203	4299	6502	SO:0001819	synonymous_variant	3226	exon1			GGAATCGCCTCAG		CCDS8868.1	12q13.13	2011-06-20	2005-12-22		ENSG00000180818	ENSG00000180818		"""Homeoboxes / ANTP class : HOXL subclass"""	5122	protein-coding gene	gene with protein product		605560	"""homeo box C10"""	HOX3I		1358459	Standard	NM_017409		Approved		uc001sen.3	Q9NYD6	OTTHUMG00000160031	ENST00000303460.4:c.567G>C	12.37:g.54379610G>C		72.0	0.0	0		106.0	49.0	0.462264	NM_017409	O15219|O15220|Q9BVD5	Silent	SNP	ENST00000303460.4	37	CCDS8868.1																																																																																			G|1.000;A|0.000	.	alt		0.647	HOXC10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358952.2		
SUN1	23353	hgsc.bcm.edu	37	7	878583	878583	+	Missense_Mutation	SNP	G	G	T	rs114826023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:878583G>T	ENST00000405266.1	+	2	250	c.226G>T	c.(226-228)Ggc>Tgc	p.G76C	SUN1_ENST00000401592.1_Missense_Mutation_p.G76C|SUN1_ENST00000389574.3_Missense_Mutation_p.G26C|SUN1_ENST00000456758.2_Missense_Mutation_p.G134C|SUN1_ENST00000425407.2_Missense_Mutation_p.G26C|SUN1_ENST00000457378.2_Missense_Mutation_p.G97C|SUN1_ENST00000403868.1_Missense_Mutation_p.G76C|SUN1_ENST00000469755.1_3'UTR|SUN1_ENST00000452783.2_Missense_Mutation_p.G76C			O94901	SUN1_HUMAN	Sad1 and UNC84 domain containing 1	76	LMNA-binding.				cytoskeletal anchoring at nuclear membrane (GO:0090286)|nuclear envelope organization (GO:0006998)|nuclear matrix anchoring at nuclear membrane (GO:0090292)	acrosomal membrane (GO:0002080)|integral component of nuclear inner membrane (GO:0005639)|nuclear envelope (GO:0005635)|SUN-KASH complex (GO:0034993)				NS(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						TGCCGACAGCGGCACCAGCAG	0.602													G|||	15	0.00299521	0.0113	0.0	5008	,	,		18035	0.0		0.0	False		,,,				2504	0.0				p.G97C		Atlas-SNP	.											.	SUN1	157	.	0			c.G289T						PASS	.	G	CYS/GLY,CYS/GLY,CYS/GLY,CYS/GLY,CYS/GLY	16,4036		0,16,2010	34.0	33.0	34.0		226,226,289,226,76	-2.4	0.0	7	dbSNP_132	34	0,8402		0,0,4201	yes	missense,missense,missense,missense,missense	SUN1	NM_001130965.2,NM_001171944.1,NM_001171945.1,NM_001171946.1,NM_025154.5	159,159,159,159,159	0,16,6211	TT,TG,GG		0.0,0.3949,0.1285	benign,benign,benign,benign,benign	76/786,76/683,97/279,76/258,26/703	878583	16,12438	2026	4201	6227	SO:0001583	missense	23353	exon4			GACAGCGGCACCA	AF202724	CCDS43533.1, CCDS47525.1, CCDS55078.1, CCDS55079.1, CCDS55080.1	7p22.3	2010-01-27	2010-01-27	2010-01-27	ENSG00000164828	ENSG00000164828			18587	protein-coding gene	gene with protein product	"""Sad1 unc-84 domain protein 1"""	607723	"""unc-84 homolog A (C. elegans)"""	UNC84A		11593002	Standard	NM_001130965		Approved	KIAA0810, FLJ12407	uc021zym.1	O94901	OTTHUMG00000151426	ENST00000405266.1:c.226G>T	7.37:g.878583G>T	ENSP00000384116:p.Gly76Cys	39.0	0.0	0		38.0	16.0	0.421053	NM_001171945	A5PL20|B3KMV7|B4DZF7|B7WNY4|B7WP53|E9PDU4|E9PF23|F8WD13|Q96CZ7|Q9HA14|Q9UH98	Missense_Mutation	SNP	ENST00000405266.1	37		10	0.004578754578754579	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	8.524	0.869408	0.17322	0.003949	0.0	ENSG00000164828	ENST00000456758;ENST00000389574;ENST00000457378;ENST00000452783;ENST00000435699;ENST00000440380;ENST00000439679;ENST00000424128;ENST00000457598;ENST00000421580;ENST00000405266;ENST00000401592;ENST00000403868;ENST00000297445;ENST00000425407;ENST00000450881	T;T;T;T;T;T;T;T;T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88;0.88	4.42	-2.43	0.06522	.	2.242240	0.01866	N	0.036910	T	0.06600	0.0169	N	0.00677	-1.265	0.09310	N	1	B;B;B;B;B	0.11235	0.0;0.001;0.001;0.004;0.0	B;B;B;B;B	0.12156	0.004;0.003;0.0;0.007;0.002	T	0.10474	-1.0628	10	0.46703	T	0.11	-1.7076	1.8943	0.03254	0.3095:0.0848:0.3628:0.2429	.	76;76;97;26;76	E9PDU4;E9PF23;F8WD13;O94901-5;O94901-3	.;.;.;.;.	C	134;26;97;76;76;76;76;76;76;76;76;76;76;76;26;51	ENSP00000388743:G134C;ENSP00000374225:G26C;ENSP00000395952:G97C;ENSP00000413439:G76C;ENSP00000388430:G76C;ENSP00000413188:G76C;ENSP00000404965:G76C;ENSP00000394381:G76C;ENSP00000384116:G76C;ENSP00000384015:G76C;ENSP00000383947:G76C;ENSP00000392309:G26C;ENSP00000392595:G51C	ENSP00000297445:G76C	G	+	1	0	SUN1	845109	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.218000	0.09240	-0.617000	0.05664	-0.266000	0.10368	GGC	G|0.997;T|0.003	0.003	strong		0.602	SUN1-001	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000322566.1	NM_025154	
ABCB5	340273	hgsc.bcm.edu	37	7	20766752	20766752	+	Missense_Mutation	SNP	G	G	T	rs35885925	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:20766752G>T	ENST00000404938.2	+	22	3367	c.2715G>T	c.(2713-2715)caG>caT	p.Q905H	ABCB5_ENST00000258738.6_Missense_Mutation_p.Q460H	NM_001163941.1	NP_001157413.1	Q2M3G0	ABCB5_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 5	905	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.		Q -> H (in dbSNP:rs35885925).		antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent (GO:0002485)|antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent (GO:0002489)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|cell differentiation (GO:0030154)|compound eye corneal lens development (GO:0048058)|positive regulation of antigen processing and presentation of peptide antigen via MHC class I (GO:0002591)|regulation of membrane potential (GO:0042391)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|efflux transmembrane transporter activity (GO:0015562)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(11)|liver(1)|lung(37)|ovary(1)|pancreas(1)|prostate(1)|skin(10)|upper_aerodigestive_tract(1)	77						AGATGCTTCAGACTCAACACA	0.358													G|||	104	0.0207668	0.0756	0.0058	5008	,	,		18547	0.0		0.0	False		,,,				2504	0.0				p.Q905H		Atlas-SNP	.											.	ABCB5	357	.	0			c.G2715T						PASS	.	G	HIS/GLN,HIS/GLN	270,4136	154.0+/-187.5	9,252,1942	99.0	105.0	103.0		2715,1380	1.6	0.7	7	dbSNP_126	103	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	ABCB5	NM_001163941.1,NM_178559.5	24,24	9,254,6240	TT,TG,GG		0.0233,6.128,2.0913	possibly-damaging,possibly-damaging	905/1258,460/813	20766752	272,12734	2203	4300	6503	SO:0001583	missense	340273	exon22			GCTTCAGACTCAA	U66692	CCDS5371.1, CCDS55090.1, CCDS55091.1, CCDS55092.1	7p14	2012-03-14			ENSG00000004846	ENSG00000004846		"""ATP binding cassette transporters / subfamily B"""	46	protein-coding gene	gene with protein product	"""P-glycoprotein ABCB5"", ""ATP-binding cassette protein"""	611785				8894702, 12960149	Standard	NM_001163942		Approved	EST422562, ABCB5beta, ABCB5alpha	uc010kuh.3	Q2M3G0	OTTHUMG00000094789	ENST00000404938.2:c.2715G>T	7.37:g.20766752G>T	ENSP00000384881:p.Gln905His	76.0	0.0	0		50.0	27.0	0.54	NM_001163941	A4D131|A7BKA4|B5MD19|B7WPL1|F8QQP8|F8QQP9|J3KQ04|Q2M3I5|Q5I5Q7|Q5I5Q8|Q6KG50|Q6XFQ5|Q8IXA1	Missense_Mutation	SNP	ENST00000404938.2	37	CCDS55090.1	36	0.016483516483516484	35	0.07113821138211382	1	0.0027624309392265192	0	0.0	0	0.0	G	5.753	0.323381	0.10900	0.06128	2.33E-4	ENSG00000004846	ENST00000404938;ENST00000258738	D;D	0.90197	-2.63;-2.63	4.43	1.61	0.23674	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.332317	0.24615	N	0.037015	T	0.39545	0.1082	L	0.55990	1.75	0.23260	N	0.998027	B;B;B	0.18310	0.027;0.01;0.003	B;B;B	0.21546	0.035;0.025;0.021	T	0.62900	-0.6756	10	0.46703	T	0.11	.	6.0759	0.19915	0.1851:0.1728:0.6421:0.0	rs35885925;rs57355100	905;83;460	A7BKA4;A0ASV4;Q2M3G0	.;.;ABCB5_HUMAN	H	905;460	ENSP00000384881:Q905H;ENSP00000258738:Q460H	ENSP00000258738:Q460H	Q	+	3	2	ABCB5	20733277	0.952000	0.32445	0.664000	0.29753	0.655000	0.38815	1.962000	0.40442	0.362000	0.24319	0.655000	0.94253	CAG	G|0.979;T|0.021	0.021	strong		0.358	ABCB5-004	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000326736.2	NM_178559	
FOXA2	3170	hgsc.bcm.edu	37	20	22563134	22563134	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:22563134A>G	ENST00000377115.4	-	3	909	c.728T>C	c.(727-729)tTc>tCc	p.F243S	FOXA2_ENST00000419308.2_Missense_Mutation_p.F249S	NM_153675.2	NP_710141.1	Q9Y261	FOXA2_HUMAN	forkhead box A2	243					adult locomotory behavior (GO:0008344)|cell development (GO:0048468)|cell differentiation in hindbrain (GO:0021533)|cell fate specification (GO:0001708)|chromatin modification (GO:0016568)|connective tissue development (GO:0061448)|dopaminergic neuron differentiation (GO:0071542)|dorsal/ventral neural tube patterning (GO:0021904)|ectoderm formation (GO:0001705)|endocrine pancreas development (GO:0031018)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|in utero embryonic development (GO:0001701)|lung epithelial cell differentiation (GO:0060487)|negative regulation of detection of glucose (GO:2000971)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of glucokinase activity (GO:0033132)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter by glucose (GO:0000433)|neuron fate specification (GO:0048665)|positive regulation of cell-cell adhesion mediated by cadherin (GO:2000049)|positive regulation of embryonic development (GO:0040019)|positive regulation of gastrulation (GO:2000543)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter by glucose (GO:0000432)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|primitive streak formation (GO:0090009)|regulation of blood coagulation (GO:0030193)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of steroid metabolic process (GO:0019218)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in detection of glucose (GO:2000976)|response to interleukin-6 (GO:0070741)|signal transduction involved in regulation of gene expression (GO:0023019)|somite rostral/caudal axis specification (GO:0032525)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(1)|lung(3)|ovary(2)|prostate(2)|urinary_tract(1)	22	Lung NSC(19;0.188)					GCCGTTCTCGAACATGTTGCC	0.662																																					p.F249S		Atlas-SNP	.											.	FOXA2	48	.	0			c.T746C						PASS	.						19.0	22.0	21.0					20																	22563134		2203	4300	6503	SO:0001583	missense	3170	exon2			TTCTCGAACATGT	AF147787	CCDS13147.1, CCDS46585.1	20p11	2008-04-10		2002-09-20	ENSG00000125798	ENSG00000125798		"""Forkhead boxes"""	5022	protein-coding gene	gene with protein product		600288	"""hepatocyte nuclear factor 3, beta"""	HNF3B		9119385, 11875061	Standard	NM_153675		Approved		uc002wsm.3	Q9Y261	OTTHUMG00000032041	ENST00000377115.4:c.728T>C	20.37:g.22563134A>G	ENSP00000366319:p.Phe243Ser	107.0	0.0	0		110.0	38.0	0.345455	NM_021784	Q8WUW4|Q96DF7	Missense_Mutation	SNP	ENST00000377115.4	37	CCDS13147.1	.	.	.	.	.	.	.	.	.	.	A	19.21	3.784481	0.70222	.	.	ENSG00000125798	ENST00000377115;ENST00000419308;ENST00000319993;ENST00000444877	D;D;D	0.96073	-3.9;-3.9;-3.9	4.98	3.87	0.44632	Winged helix-turn-helix transcription repressor DNA-binding (1);Transcription factor, fork head (3);	0.000000	0.64402	U	0.000006	D	0.97629	0.9223	M	0.88512	2.96	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.994;0.996	D	0.97315	0.9940	10	0.87932	D	0	.	10.4372	0.44443	0.9206:0.0:0.0794:0.0	.	243;249	Q9Y261;B0ZTD4	FOXA2_HUMAN;.	S	243;243;249;129	ENSP00000366319:F243S;ENSP00000400341:F243S;ENSP00000315955:F249S	ENSP00000315955:F249S	F	-	2	0	FOXA2	22511134	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.437000	0.80417	0.723000	0.32274	0.468000	0.43344	TTC	.	.	none		0.662	FOXA2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000078289.1		
FAM160A1	729830	hgsc.bcm.edu	37	4	152571711	152571711	+	Missense_Mutation	SNP	C	C	T	rs77993711	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:152571711C>T	ENST00000505231.1	+	9	2677	c.2518C>T	c.(2518-2520)Cat>Tat	p.H840Y	FAM160A1_ENST00000435205.1_Missense_Mutation_p.H840Y			Q05DH4	F16A1_HUMAN	family with sequence similarity 160, member A1	840										endometrium(2)|kidney(1)	3						TGCCAGTCGCCATCCCGTGAG	0.478													C|||	18	0.00359425	0.0136	0.0	5008	,	,		18392	0.0		0.0	False		,,,				2504	0.0				p.H840Y		Atlas-SNP	.											.	FAM160A1	60	.	0			c.C2518T						PASS	.	C	TYR/HIS	14,1370		0,14,678	40.0	46.0	44.0		2518	4.7	0.0	4	dbSNP_132	44	0,3182		0,0,1591	no	missense	FAM160A1	NM_001109977.1	83	0,14,2269	TT,TC,CC		0.0,1.0116,0.3066	benign	840/1041	152571711	14,4552	692	1591	2283	SO:0001583	missense	729830	exon11			AGTCGCCATCCCG		CCDS47146.1	4q31.3	2012-11-30			ENSG00000164142	ENSG00000164142			34237	protein-coding gene	gene with protein product							Standard	NM_001109977		Approved	FLJ43373	uc003imj.2	Q05DH4	OTTHUMG00000161675	ENST00000505231.1:c.2518C>T	4.37:g.152571711C>T	ENSP00000421580:p.His840Tyr	126.0	0.0	0		113.0	55.0	0.486726	NM_001109977	Q6ZUS2	Missense_Mutation	SNP	ENST00000505231.1	37	CCDS47146.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	0.040	-1.290594	0.01387	0.010116	0.0	ENSG00000164142	ENST00000435205;ENST00000505231	T;T	0.11930	2.73;2.73	4.68	4.68	0.58851	.	1.923240	0.02458	N	0.086292	T	0.08358	0.0208	L	0.44542	1.39	0.09310	N	1	B	0.24483	0.104	B	0.17433	0.018	T	0.13683	-1.0500	10	0.59425	D	0.04	.	9.8454	0.41024	0.0:0.779:0.1417:0.0794	.	840	Q05DH4	F16A1_HUMAN	Y	840	ENSP00000413196:H840Y;ENSP00000421580:H840Y	ENSP00000413196:H840Y	H	+	1	0	FAM160A1	152791161	0.006000	0.16342	0.004000	0.12327	0.035000	0.12851	2.082000	0.41605	2.320000	0.78422	0.655000	0.94253	CAT	C|0.995;T|0.005	0.005	strong		0.478	FAM160A1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365691.1	NM_001109977	
HUNK	30811	hgsc.bcm.edu	37	21	33371442	33371442	+	Missense_Mutation	SNP	T	T	C	rs150499320	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:33371442T>C	ENST00000270112.2	+	11	2450	c.2090T>C	c.(2089-2091)cTa>cCa	p.L697P		NM_014586.1	NP_055401.1	P57058	HUNK_HUMAN	hormonally up-regulated Neu-associated kinase	697					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|skin(2)|stomach(1)	30						CTGCAGCCCCTAGCCCCTGTG	0.582													T|||	5	0.000998403	0.0038	0.0	5008	,	,		17188	0.0		0.0	False		,,,				2504	0.0				p.L697P		Atlas-SNP	.											.	HUNK	74	.	0			c.T2090C						PASS	.	T	PRO/LEU	9,4397	14.3+/-33.2	0,9,2194	63.0	71.0	69.0		2090	-2.9	0.0	21	dbSNP_134	69	0,8600		0,0,4300	yes	missense	HUNK	NM_014586.1	98	0,9,6494	CC,CT,TT		0.0,0.2043,0.0692	benign	697/715	33371442	9,12997	2203	4300	6503	SO:0001583	missense	30811	exon11			AGCCCCTAGCCCC	AJ271722	CCDS13610.1	21q22.1	2008-06-05	2008-06-05		ENSG00000142149	ENSG00000142149			13326	protein-coding gene	gene with protein product		606532	"""hormonally upregulated Neu-associated kinase"""			10662544, 10830953	Standard	NM_014586		Approved		uc002yph.3	P57058	OTTHUMG00000085019	ENST00000270112.2:c.2090T>C	21.37:g.33371442T>C	ENSP00000270112:p.Leu697Pro	123.0	0.0	0		128.0	55.0	0.429688	NM_014586		Missense_Mutation	SNP	ENST00000270112.2	37	CCDS13610.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	T	3.433	-0.115606	0.06881	0.002043	0.0	ENSG00000142149	ENST00000270112	T	0.70164	-0.46	4.42	-2.92	0.05615	.	1.836150	0.03075	N	0.157723	T	0.39306	0.1073	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.40553	-0.9557	10	0.51188	T	0.08	-1.0E-4	10.8545	0.46792	0.0:0.2362:0.0:0.7638	.	697	P57058	HUNK_HUMAN	P	697	ENSP00000270112:L697P	ENSP00000270112:L697P	L	+	2	0	HUNK	32293313	0.002000	0.14202	0.011000	0.14972	0.070000	0.16714	-0.019000	0.12546	-0.588000	0.05882	-0.462000	0.05337	CTA	T|0.999;C|0.001	0.001	strong		0.582	HUNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192782.1	NM_014586	
OR2AE1	81392	hgsc.bcm.edu	37	7	99473801	99473801	+	Missense_Mutation	SNP	A	A	G	rs73403577	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99473801A>G	ENST00000316368.2	-	1	879	c.856T>C	c.(856-858)Tct>Cct	p.S286P		NM_001005276.1	NP_001005276.1	Q8NHA4	O2AE1_HUMAN	olfactory receptor, family 2, subfamily AE, member 1	286						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(2)	11	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					TAAATCAGAGAATTCAATGTG	0.453													G|||	372	0.0742812	0.2557	0.0288	5008	,	,		20421	0.001		0.002	False		,,,				2504	0.0112				p.S286P		Atlas-SNP	.											OR2AE1,rectum,carcinoma,+1,1	OR2AE1	32	1	0			c.T856C						PASS	.	G	PRO/SER	952,3454	734.8+/-410.6	103,746,1354	112.0	116.0	115.0		856	2.7	0.2	7	dbSNP_130	115	22,8578	818.3+/-406.9	0,22,4278	yes	missense	OR2AE1	NM_001005276.1	74	103,768,5632	GG,GA,AA		0.2558,21.6069,7.4889	benign	286/324	99473801	974,12032	2203	4300	6503	SO:0001583	missense	81392	exon1			TCAGAGAATTCAA	AC011904	CCDS34696.1	7q22.1	2014-02-19	2002-02-28		ENSG00000244623	ENSG00000244623		"""GPCR / Class A : Olfactory receptors"""	15087	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily AE, member 2"""	OR2AE2			Standard	NM_001005276		Approved		uc003usc.1	Q8NHA4	OTTHUMG00000156650	ENST00000316368.2:c.856T>C	7.37:g.99473801A>G	ENSP00000313936:p.Ser286Pro	169.0	0.0	0		150.0	74.0	0.493333	NM_001005276	B2RPD2	Missense_Mutation	SNP	ENST00000316368.2	37	CCDS34696.1	140	0.0641025641025641	127	0.258130081300813	12	0.03314917127071823	0	0.0	1	0.0013192612137203166	G	0.005	-2.228017	0.00280	0.216069	0.002558	ENSG00000244623	ENST00000316368	T	0.14516	2.5	3.56	2.68	0.31781	GPCR, rhodopsin-like superfamily (1);	0.201466	0.24843	N	0.035141	T	0.00012	0.0000	N	0.00081	-2.22	0.51012	P	9.099999999995223E-5	B	0.02656	0.0	B	0.01281	0.0	T	0.43475	-0.9389	9	0.02654	T	1	.	7.3678	0.26783	0.0999:0.1697:0.7304:0.0	.	286	Q8NHA4	O2AE1_HUMAN	P	286	ENSP00000313936:S286P	ENSP00000313936:S286P	S	-	1	0	OR2AE1	99311737	1.000000	0.71417	0.200000	0.23457	0.127000	0.20565	2.295000	0.43576	0.508000	0.28173	-3.352000	0.00042	TCT	A|0.933;G|0.067	0.067	strong		0.453	OR2AE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345053.1		
MUC17	140453	hgsc.bcm.edu	37	7	100682831	100682831	+	Missense_Mutation	SNP	C	C	G	rs34223735		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100682831C>G	ENST00000306151.4	+	3	8198	c.8134C>G	c.(8134-8136)Ctt>Gtt	p.L2712V		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	2712	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					GGCTAGCACCCTTTCAACAAC	0.493																																					p.L2712V		Atlas-SNP	.											.	MUC17	804	.	0			c.C8134G						PASS	.						257.0	264.0	262.0					7																	100682831		2203	4300	6503	SO:0001583	missense	140453	exon3			AGCACCCTTTCAA	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.8134C>G	7.37:g.100682831C>G	ENSP00000302716:p.Leu2712Val	120.0	0.0	0		146.0	9.0	0.0616438	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	0.020	-1.446165	0.01089	.	.	ENSG00000169876	ENST00000306151	T	0.04049	3.72	0.0465	0.0465	0.14256	.	.	.	.	.	T	0.02494	0.0076	N	0.17082	0.46	0.09310	N	1	B	0.17667	0.023	B	0.09377	0.004	T	0.48875	-0.8996	9	0.14656	T	0.56	.	3.6497	0.08198	2.0E-4:0.5059:0.4937:2.0E-4	rs34223735	2712	Q685J3	MUC17_HUMAN	V	2712	ENSP00000302716:L2712V	ENSP00000302716:L2712V	L	+	1	0	MUC17	100469551	0.018000	0.18449	0.005000	0.12908	0.081000	0.17604	-0.783000	0.04638	0.132000	0.18615	0.134000	0.15878	CTT	.	.	weak		0.493	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
FOXD4	2298	hgsc.bcm.edu	37	9	117637	117637	+	Silent	SNP	G	G	A	rs138098441	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117637G>A	ENST00000382500.2	-	1	780	c.483C>T	c.(481-483)tgC>tgT	p.C161C		NM_207305.4	NP_997188.2	Q12950	FOXD4_HUMAN	forkhead box D4	161					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)			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)		TCTTGACGAAGCAGTCGTTCA	0.637													.|||	119	0.023762	0.0847	0.0101	5008	,	,		14103	0.0		0.0	False		,,,				2504	0.0				p.C161C		Atlas-SNP	.											.	FOXD4	75	.	0			c.C483T						PASS	.	G		293,4087		3,287,1900	104.0	143.0	130.0		483	2.2	1.0	9	dbSNP_134	130	1,8567		0,1,4283	no	coding-synonymous	FOXD4	NM_207305.3		3,288,6183	AA,AG,GG		0.0117,6.6895,2.2706		161/440	117637	294,12654	2190	4284	6474	SO:0001819	synonymous_variant	2298	exon1			GACGAAGCAGTCG	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.483C>T	9.37:g.117637G>A		219.0	0.0	0		228.0	115.0	0.504386	NM_207305	B2RN05|B9EGL7|Q5VVK1|Q8WXT6	Silent	SNP	ENST00000382500.2	37	CCDS34975.1																																																																																			G|0.974;A|0.026	0.026	strong		0.637	FOXD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055433.1	NM_207305	
LMNTD1	160492	hgsc.bcm.edu	37	12	25671871	25671871	+	Silent	SNP	A	A	G	rs34028410	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:25671871A>G	ENST00000282881.6	-	7	1133	c.984T>C	c.(982-984)ccT>ccC	p.P328P	IFLTD1_ENST00000539744.1_Silent_p.P231P|IFLTD1_ENST00000458174.2_Silent_p.P349P|IFLTD1_ENST00000413632.2_Silent_p.P309P|IFLTD1_ENST00000445693.1_Silent_p.P265P	NM_152590.3	NP_689803.2	Q8N9Z9	LMTD1_HUMAN		328					cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22	all_lung(3;2.75e-22)|Lung NSC(3;1.77e-21)|all_hematologic(7;0.00656)|Colorectal(261;0.0847)					GGCTGCGATTAGGGAAAACGG	0.448													G|||	88	0.0175719	0.0628	0.0072	5008	,	,		20109	0.0		0.0	False		,,,				2504	0.0				p.P349P		Atlas-SNP	.											.	IFLTD1	121	.	0			c.T1047C						PASS	.	G	,,,	251,4155	803.2+/-415.7	5,241,1957	101.0	101.0	101.0		795,1047,927,984	-2.9	0.0	12	dbSNP_126	101	1,8599	819.2+/-406.8	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IFLTD1	NM_001145727.1,NM_001145728.1,NM_001145729.1,NM_152590.2	,,,	5,242,6256	GG,GA,AA		0.0116,5.6968,1.9376	,,,	265/326,349/410,309/370,328/389	25671871	252,12754	2203	4300	6503	SO:0001819	synonymous_variant	160492	exon8			GCGATTAGGGAAA																												ENST00000282881.6:c.984T>C	12.37:g.25671871A>G		117.0	0.0	0		151.0	79.0	0.523179	NM_001145728	B4DL27|B4DY70|Q8IY38	Silent	SNP	ENST00000282881.6	37	CCDS8704.1	20	0.009157509157509158	17	0.034552845528455285	3	0.008287292817679558	0	0.0	0	0.0	G	1.210	-0.629928	0.03610	0.056968	1.16E-4	ENSG00000152936	ENST00000543629	.	.	.	4.95	-2.93	0.05598	.	.	.	.	.	.	.	.	.	.	.	0.09310	N	0.999994	.	.	.	.	.	.	.	.	.	.	.	.	.	-13.2418	0.8046	0.01082	0.3824:0.1182:0.2583:0.241	rs34028410	.	.	.	Q	103	.	.	X	-	1	0	IFLTD1	25563138	0.330000	0.24705	0.000000	0.03702	0.293000	0.27360	0.047000	0.14056	-0.848000	0.04163	-0.930000	0.02707	TAA	A|0.980;G|0.020	0.020	strong		0.448	IFLTD1-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402279.1		
DNAH3	55567	hgsc.bcm.edu	37	16	20996868	20996868	+	Missense_Mutation	SNP	A	A	T	rs34179606	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:20996868A>T	ENST00000261383.3	-	48	7195	c.7196T>A	c.(7195-7197)aTc>aAc	p.I2399N	DNAH3_ENST00000415178.1_3'UTR	NM_017539.1	NP_060009.1	Q8TD57	DYH3_HUMAN	dynein, axonemal, heavy chain 3	2399	AAA 4. {ECO:0000250}.		I -> N (in dbSNP:rs34179606).		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)|microtubule motor activity (GO:0003777)			NS(3)|autonomic_ganglia(1)|breast(12)|central_nervous_system(3)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(42)|liver(2)|lung(57)|ovary(14)|pancreas(1)|prostate(7)|skin(11)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(6)	202				GBM - Glioblastoma multiforme(48;0.207)		GGCCTTGCTGATGTTGTTGAA	0.488													A|||	67	0.0133786	0.0507	0.0	5008	,	,		20170	0.0		0.0	False		,,,				2504	0.0				p.I2399N		Atlas-SNP	.											.	DNAH3	1142	.	0			c.T7196A						PASS	.	A	ASN/ILE	139,4263	98.9+/-137.6	2,135,2064	142.0	122.0	129.0		7196	4.8	1.0	16	dbSNP_126	129	3,8597	3.0+/-9.4	0,3,4297	yes	missense	DNAH3	NM_017539.1	149	2,138,6361	TT,TA,AA		0.0349,3.1577,1.0921	benign	2399/4117	20996868	142,12860	2201	4300	6501	SO:0001583	missense	55567	exon48			TTGCTGATGTTGT	U83574	CCDS10594.1	16p12.2	2008-08-01	2006-09-04		ENSG00000158486	ENSG00000158486		"""Axonemal dyneins"""	2949	protein-coding gene	gene with protein product		603334	"""dynein, axonemal, heavy polypeptide 3"""			9256245, 9373155	Standard	NM_017539		Approved	Dnahc3b, DLP3, Hsadhc3, DKFZp434N074	uc010vbe.2	Q8TD57	OTTHUMG00000090677	ENST00000261383.3:c.7196T>A	16.37:g.20996868A>T	ENSP00000261383:p.Ile2399Asn	79.0	0.0	0		66.0	35.0	0.530303	NM_017539	O00437|O15437|O43326|Q3C0H2|Q8WUP9|Q9UEM3|Q9UEM5|Q9UG35	Missense_Mutation	SNP	ENST00000261383.3	37	CCDS10594.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	A	12.96	2.093349	0.36952	0.031577	3.49E-4	ENSG00000158486	ENST00000261383	T	0.22945	1.93	4.79	4.79	0.61399	.	0.272346	0.29438	N	0.012143	T	0.06645	0.0170	L	0.48174	1.505	0.80722	D	1	P	0.39480	0.675	B	0.42343	0.384	T	0.00920	-1.1514	10	0.39692	T	0.17	.	10.7686	0.46308	0.9222:0.0:0.0778:0.0	rs34179606	2399	Q8TD57	DYH3_HUMAN	N	2399	ENSP00000261383:I2399N	ENSP00000261383:I2399N	I	-	2	0	DNAH3	20904369	0.994000	0.37717	0.975000	0.42487	0.937000	0.57800	2.961000	0.49168	1.930000	0.55929	0.533000	0.62120	ATC	A|0.989;T|0.011	0.011	strong		0.488	DNAH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207361.1	NM_017539	
TTC21B	79809	hgsc.bcm.edu	37	2	166781188	166781188	+	Splice_Site	SNP	G	G	A	rs16851307	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:166781188G>A	ENST00000243344.7	-	12	1524	c.1387C>T	c.(1387-1389)Cct>Tct	p.P463S		NM_024753.4	NP_079029.3	Q7Z4L5	TT21B_HUMAN	tetratricopeptide repeat domain 21B	463			P -> S (in dbSNP:rs16851307).		forebrain dorsal/ventral pattern formation (GO:0021798)|intraciliary retrograde transport (GO:0035721)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|protein localization to cilium (GO:0061512)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intraciliary transport particle A (GO:0030991)|nuclear chromatin (GO:0000790)				breast(2)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(9)|lung(28)|ovary(2)|pancreas(2)|skin(2)|urinary_tract(1)	58						GGACTTGCAGGCTAAACAAAA	0.353													G|||	55	0.0109824	0.0386	0.0058	5008	,	,		13522	0.0		0.0	False		,,,				2504	0.0				p.P463S		Atlas-SNP	.											.	TTC21B	130	.	0			c.C1387T						PASS	.	G	SER/PRO	192,4214	119.2+/-156.9	6,180,2017	46.0	46.0	46.0		1387	5.8	1.0	2	dbSNP_123	46	0,8600		0,0,4300	yes	missense-near-splice	TTC21B	NM_024753.3	74	6,180,6317	AA,AG,GG		0.0,4.3577,1.4762	benign	463/1317	166781188	192,12814	2203	4300	6503	SO:0001630	splice_region_variant	79809	exon12			TTGCAGGCTAAAC	AB082523	CCDS33315.1	2q24.3	2014-09-04			ENSG00000123607	ENSG00000123607		"""Tetratricopeptide (TTC) repeat domain containing"", ""Intraflagellar transport homologs"""	25660	protein-coding gene	gene with protein product		612014				12056414, 21258341	Standard	NM_024753		Approved	FLJ11457, JBTS11, NPHP12, IFT139, THM1	uc002udk.3	Q7Z4L5	OTTHUMG00000154083	ENST00000243344.7:c.1387-1C>T	2.37:g.166781188G>A		121.0	0.0	0		115.0	44.0	0.382609	NM_024753	A8MUZ3|Q3LIE4|Q53T84|Q6P4A1|Q6PIF5|Q8NCN3|Q96MA4|Q9HAK8	Missense_Mutation	SNP	ENST00000243344.7	37	CCDS33315.1	27	0.012362637362637362	25	0.0508130081300813	2	0.0055248618784530384	0	0.0	0	0.0	G	19.77	3.889969	0.72524	0.043577	0.0	ENSG00000123607	ENST00000243344	T	0.63417	-0.04	5.76	5.76	0.90799	.	0.049003	0.85682	D	0.000000	T	0.26195	0.0639	M	0.74389	2.26	0.80722	D	1	P	0.39748	0.686	B	0.38156	0.266	T	0.53927	-0.8369	10	0.36615	T	0.2	-18.9007	19.9766	0.97312	0.0:0.0:1.0:0.0	rs16851307;rs52837751;rs58123452;rs16851307	463	Q7Z4L5	TT21B_HUMAN	S	463	ENSP00000243344:P463S	ENSP00000243344:P463S	P	-	1	0	TTC21B	166489434	1.000000	0.71417	1.000000	0.80357	0.834000	0.47266	6.194000	0.72082	2.728000	0.93425	0.561000	0.74099	CCT	G|0.983;A|0.017	0.017	strong		0.353	TTC21B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333770.1	NM_024753	Missense_Mutation
LYSMD1	388695	hgsc.bcm.edu	37	1	151138250	151138250	+	5'UTR	SNP	G	G	T	rs113805704	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:151138250G>T	ENST00000368908.5	-	0	145				SCNM1_ENST00000368905.4_5'Flank|LYSMD1_ENST00000440902.2_Missense_Mutation_p.S3R	NM_212551.4	NP_997716.1	Q96S90	LYSM1_HUMAN	LysM, putative peptidoglycan-binding, domain containing 1											endometrium(2)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7	Lung SC(34;0.00471)|Ovarian(49;0.0147)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			TCAAAGGTCCGCTCCGCATAA	0.537													G|||	38	0.00758786	0.0287	0.0	5008	,	,		18656	0.0		0.0	False		,,,				2504	0.0				p.S3R		Atlas-SNP	.											.	LYSMD1	23	.	0			c.C9A						PASS	.	G	ARG/SER,,	33,1351		1,31,660	142.0	137.0	138.0		9,,	-8.1	0.0	1	dbSNP_132	138	1,3181		0,1,1590	yes	missense,intron,utr-5	LYSMD1,TNFAIP8L2-SCNM1	NM_001136543.1,NM_001204848.1,NM_212551.4	110,,	1,32,2250	TT,TG,GG		0.0314,2.3844,0.7446	,,	3/180,,	151138250	34,4532	692	1591	2283	SO:0001623	5_prime_UTR_variant	388695	exon1			AGGTCCGCTCCGC	BX647911	CCDS986.1, CCDS44218.1	1q21.2	2008-02-05			ENSG00000163155	ENSG00000163155			32070	protein-coding gene	gene with protein product						12477932	Standard	NM_212551		Approved	SB145, MGC35223, RP11-68I18.5	uc001ewy.3	Q96S90	OTTHUMG00000012260	ENST00000368908.5:c.-516C>A	1.37:g.151138250G>T		121.0	0.0	0		98.0	52.0	0.530612	NM_001136543	B4DQA1|Q69YX9	Missense_Mutation	SNP	ENST00000368908.5	37	CCDS986.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	G	16.76	3.211662	0.58452	0.023844	3.14E-4	ENSG00000163155	ENST00000440902	T	0.32988	1.43	4.06	-8.13	0.01073	.	.	.	.	.	T	0.05090	0.0136	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.27606	-1.0069	8	0.87932	D	0	.	0.7224	0.00943	0.307:0.2957:0.1987:0.1986	.	3	Q96S90-2	.	R	3	ENSP00000404059:S3R	ENSP00000404059:S3R	S	-	3	2	LYSMD1	149404874	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.795000	0.01752	-2.291000	0.00666	0.603000	0.83216	AGC	G|0.994;T|0.006	0.006	strong		0.537	LYSMD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034070.3	NM_212551	
OR6K2	81448	hgsc.bcm.edu	37	1	158669980	158669980	+	Missense_Mutation	SNP	G	G	A	rs111363268	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158669980G>A	ENST00000359610.2	-	1	506	c.463C>T	c.(463-465)Ccc>Tcc	p.P155S		NM_001005279.1	NP_001005279.1	Q8NGY2	OR6K2_HUMAN	olfactory receptor, family 6, subfamily K, member 2	155						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	46	all_hematologic(112;0.0378)					TCAGGAAGGGGTGTGATAAAG	0.488													G|||	119	0.023762	0.0847	0.0086	5008	,	,		23707	0.0		0.001	False		,,,				2504	0.0				p.P155S		Atlas-SNP	.											OR6K2,right_upper_lobe,carcinoma,+2,1	OR6K2	104	1	0			c.C463T						PASS	.	G	SER/PRO	340,4066	178.7+/-207.4	12,316,1875	123.0	107.0	113.0		463	3.9	0.1	1	dbSNP_132	113	2,8598	1.2+/-3.3	0,2,4298	yes	missense	OR6K2	NM_001005279.1	74	12,318,6173	AA,AG,GG		0.0233,7.7167,2.6296	possibly-damaging	155/325	158669980	342,12664	2203	4300	6503	SO:0001583	missense	81448	exon1			GAAGGGGTGTGAT	BK004196	CCDS30902.1	1q23.1	2012-08-09			ENSG00000196171	ENSG00000196171		"""GPCR / Class A : Olfactory receptors"""	15029	protein-coding gene	gene with protein product							Standard	NM_001005279		Approved		uc001fsu.1	Q8NGY2	OTTHUMG00000022768	ENST00000359610.2:c.463C>T	1.37:g.158669980G>A	ENSP00000352626:p.Pro155Ser	73.0	0.0	0		85.0	42.0	0.494118	NM_001005279	B9EH33|Q6IFR6	Missense_Mutation	SNP	ENST00000359610.2	37	CCDS30902.1	37	0.01694139194139194	36	0.07317073170731707	1	0.0027624309392265192	0	0.0	0	0.0	G	10.46	1.356369	0.24598	0.077167	2.33E-4	ENSG00000196171	ENST00000359610	T	0.29142	1.58	4.84	3.92	0.45320	GPCR, rhodopsin-like superfamily (1);	0.000000	0.37955	N	0.001874	T	0.06050	0.0157	N	0.00879	-1.12	0.09310	N	1	D	0.56035	0.974	P	0.60236	0.871	T	0.03807	-1.1002	10	0.18710	T	0.47	-12.7456	3.6905	0.08344	0.0886:0.1687:0.5679:0.1749	.	155	Q8NGY2	OR6K2_HUMAN	S	155	ENSP00000352626:P155S	ENSP00000352626:P155S	P	-	1	0	OR6K2	156936604	0.000000	0.05858	0.145000	0.22337	0.977000	0.68977	-0.103000	0.10940	1.232000	0.43678	0.650000	0.86243	CCC	G|0.977;A|0.023	0.023	strong		0.488	OR6K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059061.1	NM_001005279	
AKAP1	8165	hgsc.bcm.edu	37	17	55183726	55183726	+	Missense_Mutation	SNP	G	G	A	rs61731968	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:55183726G>A	ENST00000337714.3	+	2	1134	c.901G>A	c.(901-903)Gag>Aag	p.E301K	AKAP1_ENST00000539273.1_Missense_Mutation_p.E301K|AKAP1_ENST00000314126.3_Missense_Mutation_p.E301K|AKAP1_ENST00000572557.1_Missense_Mutation_p.E301K|AKAP1_ENST00000571629.1_Missense_Mutation_p.E301K	NM_003488.3	NP_003479.1	Q92667	AKAP1_HUMAN	A kinase (PRKA) anchor protein 1	301					blood coagulation (GO:0007596)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(2)|liver(1)|lung(7)|ovary(2)|pancreas(1)|skin(1)	14	Breast(9;5.46e-08)					TAGAGGTGTCGAGGGAGAACT	0.547													G|||	345	0.0688898	0.2496	0.0159	5008	,	,		18330	0.002		0.002	False		,,,				2504	0.0				p.E301K		Atlas-SNP	.											.	AKAP1	73	.	0			c.G901A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU	946,3460	357.1+/-313.8	103,740,1360	79.0	86.0	84.0		901,901,901	1.9	0.0	17	dbSNP_129	84	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense,missense	AKAP1	NM_001242902.1,NM_001242903.1,NM_003488.3	56,56,56	103,745,5655	AA,AG,GG		0.0581,21.4707,7.312	benign,benign,benign	301/904,301/904,301/904	55183726	951,12055	2203	4300	6503	SO:0001583	missense	8165	exon3			GGTGTCGAGGGAG	X97335	CCDS11594.1	17q22	2013-01-23			ENSG00000121057	ENSG00000121057		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Tudor domain containing"""	367	protein-coding gene	gene with protein product	"""protein kinase anchoring protein 1"", ""dual specificity A-kinase-anchoring protein 1"", ""protein phosphatase 1, regulatory subunit 43"", ""tudor domain containing 17"""	602449		PRKA1		8769136, 7499250	Standard	NM_003488		Approved	AKAP121, AKAP149, SAKAP84, S-AKAP84, AKAP84, D-AKAP1, PPP1R43, TDRD17	uc002iux.3	Q92667	OTTHUMG00000140369	ENST00000337714.3:c.901G>A	17.37:g.55183726G>A	ENSP00000337736:p.Glu301Lys	112.0	0.0	0		114.0	49.0	0.429825	NM_001242902	A8K8Q1|D3DTZ0|Q13320|Q9BW14	Missense_Mutation	SNP	ENST00000337714.3	37	CCDS11594.1	132	0.06043956043956044	127	0.258130081300813	3	0.008287292817679558	2	0.0034965034965034965	0	0.0	G	10.31	1.315692	0.23908	0.214707	5.81E-4	ENSG00000121057	ENST00000337714;ENST00000314126;ENST00000427138;ENST00000539273	T;T;T	0.17213	2.56;2.29;2.56	5.15	1.85	0.25348	.	1.753900	0.02141	N	0.057175	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.31599	0.33	B	0.18561	0.022	T	0.38329	-0.9666	9	0.21014	T	0.42	2.3366	2.2365	0.04010	0.3265:0.0:0.4319:0.2416	rs61731968	301	Q92667	AKAP1_HUMAN	K	301;301;343;301	ENSP00000337736:E301K;ENSP00000314075:E301K;ENSP00000443139:E301K	ENSP00000314075:E301K	E	+	1	0	AKAP1	52538725	0.000000	0.05858	0.000000	0.03702	0.086000	0.17979	-0.248000	0.08854	0.193000	0.20303	0.561000	0.74099	GAG	G|0.927;A|0.073	0.073	strong		0.547	AKAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277069.1		
MAN2B2	23324	hgsc.bcm.edu	37	4	6611560	6611560	+	Missense_Mutation	SNP	G	G	A	rs61733399	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:6611560G>A	ENST00000285599.3	+	13	2078	c.2042G>A	c.(2041-2043)cGc>cAc	p.R681H	MAN2B2_ENST00000504248.1_Missense_Mutation_p.R630H|MAN2B2_ENST00000504960.1_3'UTR	NM_015274.1	NP_056089.1	Q9Y2E5	MA2B2_HUMAN	mannosidase, alpha, class 2B, member 2	681					mannose metabolic process (GO:0006013)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	30						TATGCAATCCGCTCCCGGCTC	0.572													G|||	86	0.0171725	0.0613	0.0072	5008	,	,		18387	0.0		0.0	False		,,,				2504	0.0				p.R681H		Atlas-SNP	.											.	MAN2B2	80	.	0			c.G2042A						PASS	.		HIS/ARG	207,4199	128.6+/-165.4	4,199,2000	76.0	78.0	78.0		2042	0.2	0.0	4	dbSNP_129	78	3,8597	3.0+/-9.4	0,3,4297	yes	missense	MAN2B2	NM_015274.1	29	4,202,6297	AA,AG,GG		0.0349,4.6981,1.6146	benign	681/1010	6611560	210,12796	2203	4300	6503	SO:0001583	missense	23324	exon13			CAATCCGCTCCCG	BC033307	CCDS33951.1	4p16.2	2005-11-09			ENSG00000013288	ENSG00000013288			29623	protein-coding gene	gene with protein product	"""core-specific lysosomal alpha-1,6-Mannosidase"""					10231032, 16115860	Standard	XR_241647		Approved	KIAA0935	uc003gjf.1	Q9Y2E5	OTTHUMG00000160073	ENST00000285599.3:c.2042G>A	4.37:g.6611560G>A	ENSP00000285599:p.Arg681His	103.0	0.0	0		100.0	55.0	0.55	NM_015274	Q66MP2|Q86T67	Missense_Mutation	SNP	ENST00000285599.3	37	CCDS33951.1	30|30	0.013736263736263736|0.013736263736263736	25|25	0.0508130081300813|0.0508130081300813	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	0|0	0.0|0.0	g|g	0.366|0.366	-0.936607|-0.936607	0.02340|0.02340	0.046981|0.046981	3.49E-4|3.49E-4	ENSG00000013288|ENSG00000013288	ENST00000505907|ENST00000285599;ENST00000504248	.|T;T	.|0.78364	.|-1.17;-1.17	4.28|4.28	0.172|0.172	0.15031|0.15031	.|Glycosyl hydrolases 38, C-terminal (1);Glycoside hydrolase-type carbohydrate-binding (1);	.|0.616553	.|0.17323	.|N	.|0.178421	T|T	0.10465|0.10465	0.0256|0.0256	N|N	0.01705|0.01705	-0.755|-0.755	0.09310|0.09310	N|N	1|1	.|B;B;B	.|0.09022	.|0.002;0.001;0.002	.|B;B;B	.|0.08055	.|0.003;0.003;0.003	T|T	0.11348|0.11348	-1.0591|-1.0591	5|10	.|0.14656	.|T	.|0.56	-9.5755|-9.5755	4.7133|4.7133	0.12882|0.12882	0.4981:0.0:0.0855:0.4164|0.4981:0.0:0.0855:0.4164	rs61733399|rs61733399	.|630;681;681	.|E9PCD7;Q9Y2E5;Q9Y2E5-2	.|.;MA2B2_HUMAN;.	T|H	680|681;630	.|ENSP00000285599:R681H;ENSP00000423129:R630H	.|ENSP00000285599:R681H	A|R	+|+	1|2	0|0	MAN2B2|MAN2B2	6662461|6662461	0.000000|0.000000	0.05858|0.05858	0.015000|0.015000	0.15790|0.15790	0.083000|0.083000	0.17756|0.17756	0.078000|0.078000	0.14761|0.14761	-0.229000|-0.229000	0.09854|0.09854	-0.482000|-0.482000	0.04802|0.04802	GCT|CGC	G|0.981;A|0.019	0.019	strong		0.572	MAN2B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359106.2	NM_015274	
PTP4A1	7803	hgsc.bcm.edu	37	6	64289996	64289996	+	Silent	SNP	C	C	T	rs1681943	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:64289996C>T	ENST00000370651.3	+	6	1592	c.439C>T	c.(439-441)Ctg>Ttg	p.L147L	PTP4A1_ENST00000370650.2_Silent_p.L122L	NM_003463.3	NP_003454.1	Q93096	TP4A1_HUMAN	protein tyrosine phosphatase type IVA, member 1	147	Tyrosine-protein phosphatase.				cell cycle (GO:0007049)|multicellular organismal development (GO:0007275)|positive regulation of cell migration (GO:0030335)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)			large_intestine(3)|lung(4)|skin(1)	8	all_cancers(3;0.071)|all_epithelial(2;0.0146)|Lung NSC(77;0.175)		Epithelial(2;0.0365)|LUSC - Lung squamous cell carcinoma(74;0.0644)|all cancers(2;0.112)|Lung(124;0.13)			CAAGCAACTTCTGTATTTGGA	0.393													c|||	111	0.0221645	0.0825	0.0029	5008	,	,		16877	0.0		0.0	False		,,,				2504	0.0				p.L147L	Pancreas(91;1019 1502 28028 38110 51645)	Atlas-SNP	.											.	PTP4A1	13	.	0			c.C439T						PASS	.	C		303,4103	162.2+/-194.2	14,275,1914	101.0	101.0	101.0		439	-0.7	1.0	6	dbSNP_89	101	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	PTP4A1	NM_003463.3		14,278,6211	TT,TC,CC		0.0349,6.877,2.3528		147/174	64289996	306,12700	2203	4300	6503	SO:0001819	synonymous_variant	7803	exon6			CAACTTCTGTATT	U48296	CCDS4965.1	6q12	2011-06-09			ENSG00000112245	ENSG00000112245		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PRLs"""	9634	protein-coding gene	gene with protein product		601585				9642300	Standard	NM_003463		Approved	PTPCAAX1, PRL-1	uc003pel.3	Q93096	OTTHUMG00000014949	ENST00000370651.3:c.439C>T	6.37:g.64289996C>T		45.0	0.0	0		42.0	23.0	0.547619	NM_003463	B2R6C8|O00648|Q49A54	Silent	SNP	ENST00000370651.3	37	CCDS4965.1																																																																																			C|0.980;T|0.020	0.020	strong		0.393	PTP4A1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041083.2		
ARL4D	379	hgsc.bcm.edu	37	17	41477670	41477670	+	Silent	SNP	G	G	A	rs61749921	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:41477670G>A	ENST00000320033.4	+	2	777	c.570G>A	c.(568-570)agG>agA	p.R190R		NM_001661.3	NP_001652.2	P49703	ARL4D_HUMAN	ADP-ribosylation factor-like 4D	190					GTP catabolic process (GO:0006184)|protein secretion (GO:0009306)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|urinary_tract(1)	8		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.155)		TCCTCAAGAGGAAGAAGGCAG	0.622													G|||	83	0.0165735	0.0613	0.0029	5008	,	,		16722	0.0		0.0	False		,,,				2504	0.0				p.R190R		Atlas-SNP	.											.	ARL4D	16	.	0			c.G570A						PASS	.	G		190,4178		2,186,1996	19.0	19.0	19.0		570	-0.6	1.0	17	dbSNP_129	19	1,8523		0,1,4261	no	coding-synonymous	ARL4D	NM_001661.3		2,187,6257	AA,AG,GG		0.0117,4.3498,1.4815		190/202	41477670	191,12701	2184	4262	6446	SO:0001819	synonymous_variant	379	exon2			CAAGAGGAAGAAG	AB060692	CCDS11463.1	17q21.31	2014-05-09	2005-11-03	2005-11-03	ENSG00000175906	ENSG00000175906		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	656	protein-coding gene	gene with protein product		600732	"""ADP-ribosylation factor 4-like"""	ARF4L		7590735	Standard	NM_001661		Approved		uc002idt.3	P49703		ENST00000320033.4:c.570G>A	17.37:g.41477670G>A		67.0	0.0	0		49.0	28.0	0.571429	NM_001661	B2RC59|D3DX43	Silent	SNP	ENST00000320033.4	37	CCDS11463.1																																																																																			G|0.979;A|0.021	0.021	strong		0.622	ARL4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453481.2	NM_001661	
CEP192	55125	hgsc.bcm.edu	37	18	13068191	13068191	+	Silent	SNP	C	C	A	rs143595675	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:13068191C>A	ENST00000325971.8	+	21	4518	c.2925C>A	c.(2923-2925)ggC>ggA	p.G975G	CEP192_ENST00000430049.2_Silent_p.G1096G|CEP192_ENST00000506447.1_Silent_p.G1571G			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	975					centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						GGCTAGCAGGCCCTTCTGTGG	0.498													C|||	24	0.00479233	0.0174	0.0014	5008	,	,		16806	0.0		0.0	False		,,,				2504	0.0				p.G1571G		Atlas-SNP	.											.	CEP192	340	.	0			c.C4713A						PASS	.	C		51,4355	52.3+/-87.9	0,51,2152	72.0	74.0	73.0		4713	-5.3	0.0	18	dbSNP_134	73	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CEP192	NM_032142.3		0,52,6451	AA,AC,CC		0.0116,1.1575,0.3998		1571/2538	13068191	52,12954	2203	4300	6503	SO:0001819	synonymous_variant	55125	exon23			AGCAGGCCCTTCT	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.2925C>A	18.37:g.13068191C>A		76.0	0.0	0		110.0	55.0	0.5	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Silent	SNP	ENST00000325971.8	37																																																																																				C|0.996;A|0.004	0.004	strong		0.498	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
KRTAP10-4	386672	hgsc.bcm.edu	37	21	45994763	45994763	+	Silent	SNP	C	C	T	rs115169164	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45994763C>T	ENST00000400374.3	+	1	1158	c.1128C>T	c.(1126-1128)ccC>ccT	p.P376P	TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_5'Flank	NM_198687.1	NP_941960.1	P60372	KR104_HUMAN	keratin associated protein 10-4	376	36 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(4)|kidney(1)|large_intestine(1)|lung(9)|pancreas(1)|prostate(1)	18						GCTGCGTGCCCGTCCCTTCCT	0.711													.|||	103	0.0205671	0.0696	0.0144	5008	,	,		17408	0.0		0.0	False		,,,				2504	0.001				p.P376P		Atlas-SNP	.											.	KRTAP10-4	44	.	0			c.C1128T						PASS	.	C	,	273,4133	143.8+/-178.8	3,267,1933	59.0	72.0	68.0		,1128	2.3	0.1	21	dbSNP_132	68	1,8589		0,1,4294	no	intron,coding-synonymous	TSPEAR,KRTAP10-4	NM_144991.2,NM_198687.1	,	3,268,6227	TT,TC,CC		0.0116,6.1961,2.1083	,	,376/402	45994763	274,12722	2203	4295	6498	SO:0001819	synonymous_variant	386672	exon1			CGTGCCCGTCCCT	AB076351	CCDS42957.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000215454	ENSG00000215454		"""Keratin associated proteins"""	20521	protein-coding gene	gene with protein product			"""keratin associated protein 18-4"""	KRTAP18-4			Standard	NM_198687		Approved	KRTAP18.4, KAP10.4	uc002zfk.1	P60372	OTTHUMG00000057641	ENST00000400374.3:c.1128C>T	21.37:g.45994763C>T		127.0	0.0	0		104.0	52.0	0.5	NM_198687	Q08AS0	Silent	SNP	ENST00000400374.3	37	CCDS42957.1																																																																																			C|0.980;T|0.020	0.020	strong		0.711	KRTAP10-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128045.1	NM_198687	
MT-ND5	4540	hgsc.bcm.edu	37	M	13506	13506	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:13506C>T	ENST00000361567.2	+	1	1170	c.1170C>T	c.(1168-1170)taC>taT	p.Y390Y	MT-TT_ENST00000387460.2_RNA|MT-TE_ENST00000387459.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	390					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						ACAGGTTTCTACTCCAAAGAC	0.468																																					p.Y390Y		Atlas-SNP	.											.	.	.	.	0			c.C1170T						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			TTTCTACTCCAAA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.1170C>T	M.37:g.13506C>T		20.0	0.0	0		8.0	8.0	1	ENST00000361567	Q34773|Q8WCY3	Silent	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.468	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
STK38L	23012	hgsc.bcm.edu	37	12	27450671	27450671	+	Silent	SNP	G	G	T	rs56140810	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:27450671G>T	ENST00000389032.3	+	2	187	c.18G>T	c.(16-18)ggG>ggT	p.G6G	STK38L_ENST00000539577.1_Intron	NM_015000.3	NP_055815.1			serine/threonine kinase 38 like											breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)	12	Colorectal(261;0.0847)					TGACGGCAGGGACTACAACAA	0.373													G|||	124	0.0247604	0.0862	0.013	5008	,	,		18491	0.0		0.001	False		,,,				2504	0.0				p.G6G		Atlas-SNP	.											.	STK38L	44	.	0			c.G18T						PASS	.	G		384,4022	185.0+/-212.2	18,348,1837	90.0	90.0	90.0		18	5.2	1.0	12	dbSNP_129	90	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	STK38L	NM_015000.3		18,352,6133	TT,TG,GG		0.0465,8.7154,2.9832		6/465	27450671	388,12618	2203	4300	6503	SO:0001819	synonymous_variant	23012	exon2			GGCAGGGACTACA	AB023182	CCDS31761.1	12p11.23	2014-04-23			ENSG00000211455	ENSG00000211455			17848	protein-coding gene	gene with protein product	"""nuclear Dbf2-related 2"""	615836				16488889	Standard	NM_015000		Approved	KIAA0965, NDR2	uc001rhr.3	Q9Y2H1	OTTHUMG00000169284	ENST00000389032.3:c.18G>T	12.37:g.27450671G>T		56.0	0.0	0		68.0	32.0	0.470588	NM_015000		Silent	SNP	ENST00000389032.3	37	CCDS31761.1																																																																																			G|0.972;T|0.028	0.028	strong		0.373	STK38L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403297.1	NM_015000	
NOP14	8602	hgsc.bcm.edu	37	4	2955361	2955361	+	Missense_Mutation	SNP	T	T	G	rs111987238	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:2955361T>G	ENST00000314262.6	-	5	672	c.624A>C	c.(622-624)caA>caC	p.Q208H	NOP14_ENST00000416614.2_Missense_Mutation_p.Q208H|NOP14-AS1_ENST00000515194.1_RNA|NOP14_ENST00000502735.1_Missense_Mutation_p.Q208H|NOP14_ENST00000398071.4_Missense_Mutation_p.Q208H|NOP14-AS1_ENST00000503709.1_RNA	NM_003703.1	NP_003694.1	P78316	NOP14_HUMAN	NOP14 nucleolar protein	208					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|membrane (GO:0016020)|mitochondrion (GO:0005739)|Noc4p-Nop14p complex (GO:0030692)|nucleolus (GO:0005730)|nucleus (GO:0005634)|small-subunit processome (GO:0032040)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)			NS(1)|endometrium(2)|kidney(3)|large_intestine(9)|lung(12)|pancreas(1)|skin(1)|urinary_tract(1)	30						CTCGTTGAGCTTGTCTCTCCC	0.498													T|||	15	0.00299521	0.0106	0.0014	5008	,	,		19504	0.0		0.0	False		,,,				2504	0.0				p.Q208H		Atlas-SNP	.											.	NOP14	69	.	0			c.A624C						PASS	.	T	HIS/GLN	58,4348	56.8+/-93.2	0,58,2145	229.0	213.0	219.0		624	-1.6	0.2	4	dbSNP_132	219	0,8600		0,0,4300	yes	missense	NOP14	NM_003703.1	24	0,58,6445	GG,GT,TT		0.0,1.3164,0.4459	probably-damaging	208/858	2955361	58,12948	2203	4300	6503	SO:0001583	missense	8602	exon5			TTGAGCTTGTCTC	AB000467	CCDS33945.1	4p16.3	2012-12-10	2012-12-10	2008-10-13	ENSG00000087269	ENSG00000087269			16821	protein-coding gene	gene with protein product	"""NOP14 homolog (S. cerevisiae)"""	611526	"""chromosome 4 open reading frame 9"", ""nucleolar protein 14"", ""nucleolar protein 14 homolog (yeast)"", ""NOP14 nucleolar protein homolog (yeast)"""	C4orf9, NOL14		9734812, 11694595	Standard	XR_241655		Approved	RES4-25, UTP2	uc003ggj.1	P78316	OTTHUMG00000159911	ENST00000314262.6:c.624A>C	4.37:g.2955361T>G	ENSP00000315674:p.Gln208His	117.0	0.0	0		115.0	55.0	0.478261	NM_003703	D3DVR6|Q7LGI5|Q7Z6K0|Q8TBR6	Missense_Mutation	SNP	ENST00000314262.6	37	CCDS33945.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	T	12.38	1.921617	0.33908	0.013164	0.0	ENSG00000087269	ENST00000416614;ENST00000314262;ENST00000502735;ENST00000398071;ENST00000546137	T;T;T;T	0.50277	0.75;0.75;0.75;0.75	4.64	-1.62	0.08372	.	0.000000	0.85682	D	0.000000	T	0.54935	0.1889	M	0.91818	3.245	0.48762	D	0.999708	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.69953	-0.5005	10	0.87932	D	0	-37.2025	11.6825	0.51466	0.0:0.4263:0.0:0.5737	.	208;208	E9PFK5;P78316	.;NOP14_HUMAN	H	208;208;208;208;107	ENSP00000405068:Q208H;ENSP00000315674:Q208H;ENSP00000427415:Q208H;ENSP00000381146:Q208H	ENSP00000315674:Q208H	Q	-	3	2	NOP14	2925159	0.987000	0.35691	0.169000	0.22859	0.121000	0.20230	0.274000	0.18680	-0.361000	0.08125	-0.415000	0.06103	CAA	T|0.995;G|0.005	0.005	strong		0.498	NOP14-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000358135.2	NM_003703	
ABCB1	5243	hgsc.bcm.edu	37	7	87179256	87179256	+	Missense_Mutation	SNP	G	G	A	rs142600685		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:87179256G>A	ENST00000265724.3	-	14	1882	c.1465C>T	c.(1465-1467)Cgc>Tgc	p.R489C	ABCB1_ENST00000543898.1_Missense_Mutation_p.R425C	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	489	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	CGGCCATAGCGAATGTTTTCA	0.428													G|||	1	0.000199681	0.0008	0.0	5008	,	,		20930	0.0		0.0	False		,,,				2504	0.0				p.R489C		Atlas-SNP	.											ABCB1,NS,carcinoma,0,2	ABCB1	263	2	0			c.C1465T						PASS	.	G	CYS/ARG	6,4400	11.4+/-27.6	0,6,2197	236.0	218.0	224.0		1465	5.3	1.0	7	dbSNP_134	224	0,8600		0,0,4300	yes	missense	ABCB1	NM_000927.4	180	0,6,6497	AA,AG,GG		0.0,0.1362,0.0461	probably-damaging	489/1281	87179256	6,13000	2203	4300	6503	SO:0001583	missense	5243	exon14			CATAGCGAATGTT	M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563		"""CD molecules"", ""ATP binding cassette transporters / subfamily B"""	40	protein-coding gene	gene with protein product	"""multidrug resistance protein 1"""	171050	"""colchicin sensitivity"""	PGY1, MDR1, CLCS		3027054	Standard	NM_000927		Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.1465C>T	7.37:g.87179256G>A	ENSP00000265724:p.Arg489Cys	139.0	0.0	0		136.0	57.0	0.419118	NM_000927	A8K294|B5AK60|Q12755|Q14812	Missense_Mutation	SNP	ENST00000265724.3	37	CCDS5608.1	.	.	.	.	.	.	.	.	.	.	G	19.60	3.858540	0.71834	0.001362	0.0	ENSG00000085563	ENST00000543174;ENST00000265724;ENST00000543898	D;D	0.90955	-2.76;-2.76	6.16	5.29	0.74685	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.048148	0.85682	D	0.000000	D	0.93074	0.7795	M	0.64260	1.97	0.80722	D	1	B;P	0.49862	0.256;0.929	B;P	0.56216	0.116;0.794	D	0.93216	0.6604	10	0.54805	T	0.06	-11.5298	15.7393	0.77876	0.0651:0.0:0.9349:0.0	.	425;489	B5AK60;P08183	.;MDR1_HUMAN	C	270;489;425	ENSP00000265724:R489C;ENSP00000444095:R425C	ENSP00000265724:R489C	R	-	1	0	ABCB1	87017192	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	2.779000	0.47734	1.622000	0.50330	0.650000	0.86243	CGC	G|0.999;A|0.001	0.001	strong		0.428	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927	
TATDN2	9797	hgsc.bcm.edu	37	3	10311949	10311949	+	Silent	SNP	T	T	C	rs145595744	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:10311949T>C	ENST00000287652.4	+	4	2134	c.1083T>C	c.(1081-1083)tcT>tcC	p.S361S	RP11-438J1.1_ENST00000450534.1_3'UTR|TATDN2_ENST00000448281.2_Silent_p.S361S	NM_014760.3	NP_055575.3	Q93075	TATD2_HUMAN	TatD DNase domain containing 2	361					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|DNA catabolic process (GO:0006308)|endoplasmic reticulum unfolded protein response (GO:0030968)	intracellular organelle (GO:0043229)|nucleoplasm (GO:0005654)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(9)|pancreas(2)|prostate(1)|stomach(2)	28						CGGAGCCTTCTTCCTTCACCA	0.522													T|||	18	0.00359425	0.0136	0.0	5008	,	,		20081	0.0		0.0	False		,,,				2504	0.0				p.S361S		Atlas-SNP	.											.	TATDN2	59	.	0			c.T1083C						PASS	.	T		28,4378	34.3+/-65.2	1,26,2176	168.0	162.0	164.0		1083	-5.2	0.0	3	dbSNP_134	164	0,8600		0,0,4300	no	coding-synonymous	TATDN2	NM_014760.3		1,26,6476	CC,CT,TT		0.0,0.6355,0.2153		361/762	10311949	28,12978	2203	4300	6503	SO:0001819	synonymous_variant	9797	exon4			GCCTTCTTCCTTC	D86972	CCDS33698.1	3p25.3	2010-11-24			ENSG00000157014	ENSG00000157014			28988	protein-coding gene	gene with protein product						9039502	Standard	NM_014760		Approved	KIAA0218	uc003bvf.3	Q93075	OTTHUMG00000155361	ENST00000287652.4:c.1083T>C	3.37:g.10311949T>C		83.0	0.0	0		131.0	80.0	0.610687	NM_014760	Q3MIL9|Q5BKU0	Silent	SNP	ENST00000287652.4	37	CCDS33698.1																																																																																			T|0.997;C|0.003	0.003	strong		0.522	TATDN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339641.1	XM_376203	
FGFR2	2263	hgsc.bcm.edu	37	10	123310871	123310871	+	Missense_Mutation	SNP	A	A	G	rs755793	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:123310871A>G	ENST00000358487.5	-	5	829	c.557T>C	c.(556-558)aTg>aCg	p.M186T	FGFR2_ENST00000360144.3_Missense_Mutation_p.M97T|FGFR2_ENST00000359354.2_Missense_Mutation_p.M186T|FGFR2_ENST00000356226.4_Missense_Mutation_p.M71T|FGFR2_ENST00000357555.5_Missense_Mutation_p.M97T|FGFR2_ENST00000351936.6_Missense_Mutation_p.M186T|FGFR2_ENST00000369061.4_Missense_Mutation_p.M186T|FGFR2_ENST00000369059.1_Missense_Mutation_p.M71T|FGFR2_ENST00000369056.1_Missense_Mutation_p.M186T|FGFR2_ENST00000369060.4_Missense_Mutation_p.M186T|FGFR2_ENST00000346997.2_Missense_Mutation_p.M186T|FGFR2_ENST00000490349.1_5'UTR|FGFR2_ENST00000457416.2_Missense_Mutation_p.M186T	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2	186	Ig-like C2-type 2.		M -> T (in dbSNP:rs755793). {ECO:0000269|PubMed:11781872, ECO:0000269|PubMed:17344846, ECO:0000269|Ref.15}.		angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)			breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	CATGGTTGGCATTGGGTTCCC	0.517		5	Mis		"""gastric. NSCLC, endometrial"""		"""Crouzon, Pfeiffer, and Apert syndromes"""		Saethre-Chotzen syndrome;Apert syndrome				G|||	629	0.125599	0.3638	0.1066	5008	,	,		15709	0.0645		0.007	False		,,,				2504	0.002				p.M186T		Atlas-SNP	.		Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	.	FGFR2	758	.	0			c.T557C	GRCh37	CM071761	FGFR2	M	rs755793	PASS	.	G	THR/MET,THR/MET,THR/MET,THR/MET,THR/MET,THR/MET,THR/MET,THR/MET,THR/MET	1295,3111	698.3+/-406.3	194,907,1102	115.0	107.0	109.0		557,557,557,290,212,557,212,290,557	3.9	0.8	10	dbSNP_86	109	15,8585	818.8+/-406.8	0,15,4285	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense	FGFR2	NM_000141.4,NM_001144913.1,NM_001144914.1,NM_001144915.1,NM_001144916.1,NM_001144917.1,NM_001144918.1,NM_001144919.1,NM_022970.3	81,81,81,81,81,81,81,81,81	194,922,5387	GG,GA,AA		0.1744,29.3917,10.0723	benign,benign,benign,benign,benign,benign,benign,benign,benign	186/822,186/770,186/710,97/708,71/707,186/706,71/705,97/681,186/823	123310871	1310,11696	2203	4300	6503	SO:0001583	missense	2263	exon5	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	GTTGGCATTGGGT	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3689	protein-coding gene	gene with protein product	"""Crouzon syndrome"", ""Pfeiffer syndrome"""	176943	"""bacteria-expressed kinase"", ""keratinocyte growth factor receptor"", ""craniofacial dysostosis 1"", ""Jackson-Weiss syndrome"""	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.557T>C	10.37:g.123310871A>G	ENSP00000351276:p.Met186Thr	70.0	0.0	0		93.0	37.0	0.397849	NM_022970	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Missense_Mutation	SNP	ENST00000358487.5	37	CCDS31298.1	263	0.12042124542124542	176	0.35772357723577236	42	0.11602209944751381	40	0.06993006993006994	5	0.006596306068601583	G	0.006	-2.076963	0.00375	0.293917	0.001744	ENSG00000066468	ENST00000357555;ENST00000369062;ENST00000369061;ENST00000358487;ENST00000356226;ENST00000369060;ENST00000369059;ENST00000346997;ENST00000457416;ENST00000351936;ENST00000360144;ENST00000369056;ENST00000369058;ENST00000336553;ENST00000359354	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11	4.89	3.86	0.44501	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.389842	0.28279	N	0.015928	T	0.00012	0.0000	N	0.00855	-1.145	0.80722	P	0.0	B;B;B;B;B;B;B;B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B;B;B;B;B;B;B	0.09377	0.0;0.001;0.0;0.002;0.0;0.0;0.003;0.0;0.004;0.0;0.0;0.002	T	0.29941	-0.9995	9	0.02654	T	1	.	9.2544	0.37575	0.2804:0.0:0.7196:0.0	rs755793;rs52828989;rs60409063;rs755793	205;205;71;186;205;186;97;71;186;205;97;186	D3DRD9;D3DRD4;B5A963;B5A960;D3DRD5;P21802-18;P21802-21;P21802-20;P21802;D3DRE0;P21802-22;P21802-17	.;.;.;.;.;.;.;.;FGFR2_HUMAN;.;.;.	T	97;186;186;186;71;186;71;186;186;186;97;186;186;97;186	ENSP00000350166:M97T;ENSP00000358057:M186T;ENSP00000351276:M186T;ENSP00000348559:M71T;ENSP00000358056:M186T;ENSP00000358055:M71T;ENSP00000263451:M186T;ENSP00000410294:M186T;ENSP00000309878:M186T;ENSP00000353262:M97T;ENSP00000358052:M186T;ENSP00000358054:M186T;ENSP00000337665:M97T;ENSP00000352309:M186T	ENSP00000337665:M97T	M	-	2	0	FGFR2	123300861	0.028000	0.19301	0.838000	0.33150	0.277000	0.26821	1.098000	0.31000	1.065000	0.40693	-0.166000	0.13349	ATG	A|0.878;G|0.122	0.122	strong		0.517	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141	
ZNF658	26149	hgsc.bcm.edu	37	9	40784132	40784132	+	Silent	SNP	A	A	G	rs142151197	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:40784132A>G	ENST00000602553.1	-	4	507	c.213T>C	c.(211-213)gaT>gaC	p.D71D	ZNF658_ENST00000441795.1_Silent_p.D69D|ZNF658_ENST00000377626.3_Silent_p.D71D			Q5TYW1	ZN658_HUMAN	zinc finger protein 658	71	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			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)		TCAGGAATTCATCTTCTAAAG	0.433													A|||	68	0.0135783	0.0514	0.0	5008	,	,		13262	0.0		0.0	False		,,,				2504	0.0				p.D71D		Atlas-SNP	.											.	ZNF658	100	.	0			c.T213C						PASS	.	A		146,4260	97.1+/-135.8	1,144,2058	32.0	36.0	34.0		213	-3.4	0.0	9	dbSNP_134	34	2,8592	2.2+/-6.3	0,2,4295	no	coding-synonymous	ZNF658	NM_033160.5		1,146,6353	GG,GA,AA		0.0233,3.3137,1.1385		71/1060	40784132	148,12852	2203	4297	6500	SO:0001819	synonymous_variant	26149	exon4			GAATTCATCTTCT	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.213T>C	9.37:g.40784132A>G		233.0	0.0	0		264.0	93.0	0.352273	NM_033160	Q6PIP3|Q96M55|Q9H9S6|Q9UG02	Silent	SNP	ENST00000602553.1	37	CCDS35023.1																																																																																			.	.	weak		0.433	ZNF658-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467800.1	NM_033160	
OR6C76	390326	hgsc.bcm.edu	37	12	55820927	55820927	+	Missense_Mutation	SNP	C	C	T	rs73327795	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:55820927C>T	ENST00000328314.3	+	1	890	c.890C>T	c.(889-891)gCa>gTa	p.A297V		NM_001005183.1	NP_001005183.1	A6NM76	O6C76_HUMAN	olfactory receptor, family 6, subfamily C, member 76	297						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						GTGAAACAAGCATTTAAGGAT	0.353													c|||	104	0.0207668	0.0719	0.013	5008	,	,		14924	0.0		0.0	False		,,,				2504	0.0				p.A297V		Atlas-SNP	.											.	OR6C76	98	.	0			c.C890T						PASS	.		VAL/ALA	273,4133		6,261,1936	35.0	37.0	37.0		890	3.4	0.4	12	dbSNP_130	37	2,8590		0,2,4294	yes	missense	OR6C76	NM_001005183.1	64	6,263,6230	TT,TC,CC		0.0233,6.1961,2.1157	benign	297/313	55820927	275,12723	2203	4296	6499	SO:0001583	missense	390326	exon1			AACAAGCATTTAA		CCDS31823.1	12q13.2	2013-09-23			ENSG00000185821	ENSG00000185821		"""GPCR / Class A : Olfactory receptors"""	31305	protein-coding gene	gene with protein product							Standard	NM_001005183		Approved		uc010spm.2	A6NM76	OTTHUMG00000169956	ENST00000328314.3:c.890C>T	12.37:g.55820927C>T	ENSP00000328402:p.Ala297Val	70.0	0.0	0		54.0	31.0	0.574074	NM_001005183		Missense_Mutation	SNP	ENST00000328314.3	37	CCDS31823.1	41	0.018772893772893772	38	0.07723577235772358	3	0.008287292817679558	0	0.0	0	0.0	c	11.52	1.664546	0.29604	0.061961	2.33E-4	ENSG00000185821	ENST00000328314	T	0.44881	0.91	4.25	3.36	0.38483	.	0.000000	0.46442	U	0.000298	T	0.03095	0.0091	M	0.74647	2.275	0.09310	N	1	B	0.33940	0.433	B	0.35899	0.213	T	0.04811	-1.0925	10	0.59425	D	0.04	.	10.1138	0.42579	0.0:0.8992:0.0:0.1008	.	297	A6NM76	O6C76_HUMAN	V	297	ENSP00000328402:A297V	ENSP00000328402:A297V	A	+	2	0	OR6C76	54107194	0.109000	0.22037	0.419000	0.26584	0.684000	0.39900	2.983000	0.49345	1.154000	0.42482	-0.205000	0.12727	GCA	C|0.983;T|0.017	0.017	strong		0.353	OR6C76-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406675.1	NM_001005183	
MUC4	4585	hgsc.bcm.edu	37	3	195509559	195509559	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195509559G>A	ENST00000463781.3	-	2	9351	c.8892C>T	c.(8890-8892)acC>acT	p.T2964T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.T2964T	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.T2964T(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)		AGGAAGTGTCGGTGACAGGAA	0.582																																					p.T2964T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,2	MUC4	1505	2	1	Substitution - coding silent(1)	endometrium(1)	c.C8892T						PASS	.						9.0	8.0	8.0					3																	195509559		627	1488	2115	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.8892C>T	3.37:g.195509559G>A		261.0	0.0	0		187.0	24.0	0.128342	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			.	.	none		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
KIF20B	9585	hgsc.bcm.edu	37	10	91532574	91532574	+	Missense_Mutation	SNP	A	A	G	rs150021584	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:91532574A>G	ENST00000371728.3	+	32	5436	c.5371A>G	c.(5371-5373)Ata>Gta	p.I1791V	KIF20B_ENST00000416354.1_Missense_Mutation_p.I1821V|KIF20B_ENST00000478929.1_3'UTR|KIF20B_ENST00000260753.4_Missense_Mutation_p.I1751V	NM_001284259.1	NP_001271188.1	Q96Q89	KI20B_HUMAN	kinesin family member 20B	1791	Interaction with PIN1.				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						TCCTATTGATATATCAGGCCA	0.323													A|||	3	0.000599042	0.0023	0.0	5008	,	,		15182	0.0		0.0	False		,,,				2504	0.0				p.I1751V		Atlas-SNP	.											.	KIF20B	191	.	0			c.A5251G						PASS	.	A	VAL/ILE	17,4389	22.3+/-47.3	0,17,2186	137.0	137.0	137.0		5251	4.8	1.0	10	dbSNP_134	137	0,8600		0,0,4300	yes	missense	KIF20B	NM_016195.2	29	0,17,6486	GG,GA,AA		0.0,0.3858,0.1307	benign	1751/1781	91532574	17,12989	2203	4300	6503	SO:0001583	missense	9585	exon32			ATTGATATATCAG	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.5371A>G	10.37:g.91532574A>G	ENSP00000360793:p.Ile1791Val	407.0	1.0	0.002457		389.0	182.0	0.467866	NM_016195	A8MXM7|O43277|Q09471|Q2KQ73|Q32NE1|Q561V3|Q58EX8|Q5T9M8|Q5T9M9|Q5T9N0|Q5T9N1|Q7KZ68|Q7Z5E0|Q7Z5E1|Q7Z6M9|Q86X82|Q9H3R8|Q9H6Q9|Q9H755|Q9NTC1|Q9UFR5	Missense_Mutation	SNP	ENST00000371728.3	37		1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	19.08	3.757963	0.69648	0.003858	0.0	ENSG00000138182	ENST00000260753;ENST00000416354;ENST00000371728	T;T;T	0.54479	0.57;0.57;0.57	5.91	4.76	0.60689	.	0.125603	0.35235	N	0.003352	T	0.49983	0.1589	M	0.66939	2.045	0.80722	D	1	P;P	0.43287	0.702;0.802	B;B	0.40677	0.182;0.337	T	0.52961	-0.8505	10	0.66056	D	0.02	-7.6635	8.0076	0.30334	0.7238:0.1411:0.0:0.1351	.	1791;1751	Q96Q89;Q96Q89-3	KI20B_HUMAN;.	V	1751;1821;1791	ENSP00000260753:I1751V;ENSP00000411545:I1821V;ENSP00000360793:I1791V	ENSP00000260753:I1751V	I	+	1	0	KIF20B	91522554	1.000000	0.71417	0.991000	0.47740	0.989000	0.77384	2.459000	0.45023	1.027000	0.39758	0.533000	0.62120	ATA	A|0.999;G|0.001	0.001	strong		0.323	KIF20B-003	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000049330.1	NM_016195	
KLHDC4	54758	hgsc.bcm.edu	37	16	87743072	87743072	+	Missense_Mutation	SNP	C	C	T	rs61735154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:87743072C>T	ENST00000270583.5	-	10	1304	c.1246G>A	c.(1246-1248)Gaa>Aaa	p.E416K	KLHDC4_ENST00000347925.5_Missense_Mutation_p.E385K|KLHDC4_ENST00000566349.1_5'UTR|KLHDC4_ENST00000353170.5_Missense_Mutation_p.E359K	NM_017566.3	NP_060036.2	Q8TBB5	KLDC4_HUMAN	kelch domain containing 4	416										breast(2)|endometrium(3)|lung(10)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(2)	21				BRCA - Breast invasive adenocarcinoma(80;0.0283)		AGGCTGTCTTCGTCCTCAGAC	0.677													C|||	101	0.0201677	0.0726	0.0072	5008	,	,		12720	0.0		0.0	False		,,,				2504	0.0				p.E416K		Atlas-SNP	.											.	KLHDC4	45	.	0			c.G1246A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU	239,4155	133.7+/-170.0	4,231,1962	37.0	39.0	38.0		1075,1153,1246	5.3	0.2	16	dbSNP_129	38	0,8598		0,0,4299	no	missense,missense,missense	KLHDC4	NM_001184854.1,NM_001184856.1,NM_017566.3	56,56,56	4,231,6261	TT,TC,CC		0.0,5.4392,1.8396	benign,benign,benign	359/464,385/490,416/521	87743072	239,12753	2197	4299	6496	SO:0001583	missense	54758	exon10			TGTCTTCGTCCTC	AK001742	CCDS10963.1, CCDS54050.1, CCDS54051.1	16q24	2008-02-05			ENSG00000104731	ENSG00000104731			25272	protein-coding gene	gene with protein product							Standard	NM_001184854		Approved	DKFZp434G0522	uc002fki.3	Q8TBB5	OTTHUMG00000137657	ENST00000270583.5:c.1246G>A	16.37:g.87743072C>T	ENSP00000270583:p.Glu416Lys	34.0	0.0	0		62.0	32.0	0.516129	NM_017566	D3DUN3|D3DUN4|D3DUN5|Q96F29|Q9BVN3	Missense_Mutation	SNP	ENST00000270583.5	37	CCDS10963.1	41	0.018772893772893772	36	0.07317073170731707	5	0.013812154696132596	0	0.0	0	0.0	C	14.89	2.668986	0.47677	0.054392	0.0	ENSG00000104731	ENST00000270583;ENST00000347925;ENST00000353170	T;T;T	0.08807	3.83;3.05;3.59	5.27	5.27	0.74061	.	0.518149	0.21288	N	0.077021	T	0.00936	0.0031	M	0.69823	2.125	0.80722	D	1	B;D;D	0.57571	0.145;0.98;0.967	B;P;B	0.45449	0.04;0.481;0.229	T	0.27088	-1.0084	10	0.06757	T	0.87	-0.0563	17.8669	0.88797	0.0:1.0:0.0:0.0	.	359;385;416	Q8TBB5-2;Q8TBB5-3;Q8TBB5	.;.;KLDC4_HUMAN	K	416;385;359	ENSP00000270583:E416K;ENSP00000325717:E385K;ENSP00000262530:E359K	ENSP00000270583:E416K	E	-	1	0	KLHDC4	86300573	1.000000	0.71417	0.217000	0.23759	0.110000	0.19582	5.604000	0.67626	2.467000	0.83353	0.313000	0.20887	GAA	C|0.978;T|0.022	0.022	strong		0.677	KLHDC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269109.2	NM_017566	
USH1C	10083	hgsc.bcm.edu	37	11	17531057	17531057	+	Intron	SNP	C	C	A	rs139996942	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:17531057C>A	ENST00000318024.4	-	16	1393				USH1C_ENST00000527020.1_Intron|USH1C_ENST00000529563.1_Intron|USH1C_ENST00000005226.7_Missense_Mutation_p.R620L|USH1C_ENST00000527720.1_Intron	NM_005709.3	NP_005700.2	Q9Y6N9	USH1C_HUMAN	Usher syndrome 1C (autosomal recessive, severe)						auditory receptor cell differentiation (GO:0042491)|equilibrioception (GO:0050957)|G2/M transition of mitotic cell cycle (GO:0000086)|inner ear morphogenesis (GO:0042472)|parallel actin filament bundle assembly (GO:0030046)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	spectrin binding (GO:0030507)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(9)|lung(25)|ovary(1)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	48						GGGCAGTGGGCGGGTGGGAGT	0.637													C|||	55	0.0109824	0.0401	0.0029	5008	,	,		9520	0.0		0.0	False		,,,				2504	0.0				p.R620L		Atlas-SNP	.											USH1C,NS,carcinoma,-1,2	USH1C	157	2	0			c.G1859T	GRCh37	CM024263	ush1cpst	M	rs139996942	scavenged	.	C	,LEU/ARG	139,4261	97.6+/-136.3	3,133,2064	46.0	46.0	46.0		,1859	5.9	1.0	11	dbSNP_134	46	1,8585	1.2+/-3.3	0,1,4292	yes	intron,missense	USH1C	NM_005709.3,NM_153676.3	,102	3,134,6356	AA,AC,CC		0.0116,3.1591,1.0781	,benign	,620/900	17531057	140,12846	2200	4293	6493	SO:0001627	intron_variant	10083	exon18			AGTGGGCGGGTGG	AB006955	CCDS7825.1, CCDS31438.1, CCDS73265.1	11p14.3	2013-06-19	2004-05-19		ENSG00000006611	ENSG00000006611			12597	protein-coding gene	gene with protein product	"""harmonin"""	605242	"""deafness, autosomal recessive 18"""	DFNB18		10973247, 12107438	Standard	NM_005709		Approved	PDZ73, harmonin, NY-CO-37, NY-CO-38, PDZ-73, AIE-75, PDZD7C	uc001mne.3	Q9Y6N9	OTTHUMG00000166323	ENST00000318024.4:c.1285-7530G>T	11.37:g.17531057C>A		100.0	1.0	0.01		124.0	64.0	0.516129	NM_153676	A8K423|Q7RTU8|Q96B29|Q9UM04|Q9UM17|Q9UPC3	Missense_Mutation	SNP	ENST00000318024.4	37	CCDS31438.1	23	0.010531135531135532	21	0.042682926829268296	2	0.0055248618784530384	0	0.0	0	0.0	C	15.92	2.975208	0.53720	0.031591	1.16E-4	ENSG00000006611	ENST00000005226	T	0.37411	1.2	5.93	5.93	0.95920	.	0.378995	0.24557	N	0.037515	T	0.10165	0.0249	.	.	.	0.27896	N	0.93916	D	0.54207	0.965	B	0.44224	0.444	T	0.22277	-1.0221	9	0.66056	D	0.02	.	11.2233	0.48869	0.0:0.9172:0.0:0.0828	.	620	Q7RTU8	.	L	620	ENSP00000005226:R620L	ENSP00000005226:R620L	R	-	2	0	USH1C	17487633	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.046000	0.30354	2.814000	0.96858	0.591000	0.81541	CGC	C|0.988;A|0.012	0.012	strong		0.637	USH1C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000389146.1	NM_005709	
HRNR	388697	hgsc.bcm.edu	37	1	152191116	152191116	+	Missense_Mutation	SNP	C	C	T	rs138107632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152191116C>T	ENST00000368801.2	-	3	3064	c.2989G>A	c.(2989-2991)Ggc>Agc	p.G997S	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	997					establishment of skin barrier (GO:0061436)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinization (GO:0031424)	cornified envelope (GO:0001533)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(6)|central_nervous_system(2)|cervix(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|liver(1)|lung(84)|ovary(5)|prostate(6)|skin(12)|stomach(9)|upper_aerodigestive_tract(5)|urinary_tract(6)	192	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCATGTTGGCCGTGGCCCAAA	0.582													C|||	96	0.0191693	0.0696	0.0043	5008	,	,		24162	0.001		0.0	False		,,,				2504	0.0				p.G997S		Atlas-SNP	.											.	HRNR	403	.	0			c.G2989A						PASS	.	C	SER/GLY	190,4216	121.3+/-158.8	4,182,2017	136.0	140.0	139.0		2989	-1.5	0.0	1	dbSNP_134	139	0,8594		0,0,4297	no	missense	HRNR	NM_001009931.1	56	4,182,6314	TT,TC,CC		0.0,4.3123,1.4615	probably-damaging	997/2851	152191116	190,12810	2203	4297	6500	SO:0001583	missense	388697	exon3			GTTGGCCGTGGCC	AB104446	CCDS30859.1	1q21.3	2013-01-10			ENSG00000197915	ENSG00000197915		"""EF-hand domain containing"""	20846	protein-coding gene	gene with protein product	"""filaggrin family member 3"""						Standard	NM_001009931		Approved	S100a18, S100A16, FLG3	uc001ezt.2	Q86YZ3	OTTHUMG00000012243	ENST00000368801.2:c.2989G>A	1.37:g.152191116C>T	ENSP00000357791:p.Gly997Ser	221.0	1.0	0.00452489		266.0	124.0	0.466165	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	26	0.011904761904761904	22	0.044715447154471545	3	0.008287292817679558	1	0.0017482517482517483	0	0.0	C	9.275	1.046626	0.19748	0.043123	0.0	ENSG00000197915	ENST00000368801	T	0.01705	4.68	3.65	-1.49	0.08718	.	.	.	.	.	T	0.00271	0.0008	N	0.04297	-0.235	0.09310	N	1	D	0.57899	0.981	B	0.37943	0.261	T	0.37934	-0.9684	9	0.12430	T	0.62	.	7.1807	0.25770	0.0:0.4928:0.0:0.5072	.	997	Q86YZ3	HORN_HUMAN	S	997	ENSP00000357791:G997S	ENSP00000357791:G997S	G	-	1	0	HRNR	150457740	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.954000	0.03873	-0.422000	0.07405	0.556000	0.70494	GGC	C|0.985;T|0.015	0.015	strong		0.582	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
UACA	55075	hgsc.bcm.edu	37	15	70959576	70959576	+	Silent	SNP	C	C	T	rs61746327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:70959576C>T	ENST00000322954.6	-	16	3632	c.3447G>A	c.(3445-3447)gtG>gtA	p.V1149V	UACA_ENST00000379983.2_Silent_p.V1136V|UACA_ENST00000560441.1_Silent_p.V1134V|UACA_ENST00000539319.1_Silent_p.V1040V	NM_018003.2	NP_060473.2	Q9BZF9	UACA_HUMAN	uveal autoantigen with coiled-coil domains and ankyrin repeats	1149					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|negative regulation of inflammatory response (GO:0050728)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of protein import into nucleus (GO:0042307)|response to UV (GO:0009411)	apoptosome (GO:0043293)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(7)|kidney(4)|large_intestine(13)|lung(17)|ovary(2)|pancreas(1)|prostate(2)|skin(2)	50						GCAGTTTGGTCACTGTCTGCT	0.393													C|||	49	0.00978435	0.0356	0.0029	5008	,	,		20629	0.0		0.0	False		,,,				2504	0.0				p.V1149V		Atlas-SNP	.											.	UACA	235	.	0			c.G3447A						PASS	.	C	,	148,4250	100.7+/-139.4	1,146,2052	179.0	178.0	179.0		3408,3447	4.7	0.8	15	dbSNP_129	179	0,8594		0,0,4297	no	coding-synonymous,coding-synonymous	UACA	NM_001008224.1,NM_018003.2	,	1,146,6349	TT,TC,CC		0.0,3.3652,1.1392	,	1136/1404,1149/1417	70959576	148,12844	2199	4297	6496	SO:0001819	synonymous_variant	55075	exon16			TTTGGTCACTGTC	AF322916	CCDS10235.1, CCDS32280.1	15q22-q24	2013-01-10			ENSG00000137831	ENSG00000137831		"""Ankyrin repeat domain containing"""	15947	protein-coding gene	gene with protein product		612516				11162650, 10997877	Standard	NM_001008224		Approved	FLJ10128, KIAA1561	uc002asr.3	Q9BZF9	OTTHUMG00000133363	ENST00000322954.6:c.3447G>A	15.37:g.70959576C>T		149.0	0.0	0		161.0	68.0	0.42236	NM_018003	G3XAG2|Q14DD3|Q8N3B8|Q96NH6|Q9HCL1|Q9NWC6	Silent	SNP	ENST00000322954.6	37	CCDS10235.1																																																																																			C|0.989;T|0.011	0.011	strong		0.393	UACA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257199.2		
LRIT1	26103	hgsc.bcm.edu	37	10	85993923	85993923	+	Silent	SNP	C	C	T	rs149121025	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:85993923C>T	ENST00000372105.3	-	3	822	c.801G>A	c.(799-801)ttG>ttA	p.L267L		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	267	Ig-like C2-type.					integral component of endoplasmic reticulum membrane (GO:0030176)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|skin(1)	23						CTGTGCCACCCAAAAGGGACC	0.622													C|||	11	0.00219649	0.0083	0.0	5008	,	,		19368	0.0		0.0	False		,,,				2504	0.0				p.L267L		Atlas-SNP	.											LRIT1,NS,haematopoietic_neoplasm,0,1	LRIT1	73	1	0			c.G801A						PASS	.	C		27,4379	34.3+/-65.2	0,27,2176	73.0	72.0	72.0		801	5.9	1.0	10	dbSNP_134	72	0,8600		0,0,4300	no	coding-synonymous	LRIT1	NM_015613.2		0,27,6476	TT,TC,CC		0.0,0.6128,0.2076		267/624	85993923	27,12979	2203	4300	6503	SO:0001819	synonymous_variant	26103	exon3			GCCACCCAAAAGG	AB031547	CCDS7373.1	10q23	2013-02-11	2007-06-19	2007-06-19	ENSG00000148602	ENSG00000148602		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	23404	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 9"""		"""leucine rich repeat containing 21"""	LRRC21		10777785	Standard	NM_015613		Approved	PAL, DKFZP434K091, FIGLER9	uc001kcz.1	Q9P2V4	OTTHUMG00000018632	ENST00000372105.3:c.801G>A	10.37:g.85993923C>T		59.0	0.0	0		94.0	41.0	0.43617	NM_015613	Q0QD41|Q9Y4N7	Silent	SNP	ENST00000372105.3	37	CCDS7373.1																																																																																			C|0.998;T|0.002	0.002	strong		0.622	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613	
GDNF	2668	hgsc.bcm.edu	37	5	37835752	37835752	+	Intron	SNP	A	A	C	rs529935219	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37835752A>C	ENST00000326524.2	-	2	174				GDNF_ENST00000381826.4_Silent_p.S3S|GDNF_ENST00000344622.4_5'Flank|GDNF_ENST00000427982.1_Silent_p.S3S|GDNF_ENST00000515058.1_Intron	NM_000514.3	NP_000505.1	P39905	GDNF_HUMAN	glial cell derived neurotrophic factor						adult locomotory behavior (GO:0008344)|axon guidance (GO:0007411)|branching involved in ureteric bud morphogenesis (GO:0001658)|enteric nervous system development (GO:0048484)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|metanephros development (GO:0001656)|mRNA stabilization (GO:0048255)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neuron projection development (GO:0031175)|organ induction (GO:0001759)|peristalsis (GO:0030432)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of monooxygenase activity (GO:0032770)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of ureteric bud formation (GO:0072107)|postganglionic parasympathetic nervous system development (GO:0021784)|postsynaptic membrane organization (GO:0001941)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|regulation of morphogenesis of a branching structure (GO:0060688)|signal transduction (GO:0007165)|sympathetic nervous system development (GO:0048485)|ureteric bud formation (GO:0060676)	extracellular region (GO:0005576)	protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			NS(1)|endometrium(1)|large_intestine(2)|liver(1)|lung(8)|skin(2)	15	all_lung(31;0.00118)					TGTTAGGCAAAGACTGCATTT	0.418													A|||	11	0.00219649	0.0083	0.0	5008	,	,		19977	0.0		0.0	False		,,,				2504	0.0				p.S3S		Atlas-SNP	.											.	GDNF	56	.	0			c.T9G						PASS	.																																			SO:0001627	intron_variant	2668	exon1			AGGCAAAGACTGC		CCDS3922.1, CCDS3923.1, CCDS54845.1, CCDS54846.1, CCDS75237.1	5p13.1-p12	2014-01-30			ENSG00000168621	ENSG00000168621		"""Endogenous ligands"""	4232	protein-coding gene	gene with protein product	"""astrocyte-derived trophic factor"", ""glial cell line derived neurotrophic factor"", ""glial derived neurotrophic factor"""	600837				8493557	Standard	NM_199231		Approved	ATF1, ATF2, HFB1-GDNF	uc011cpg.2	P39905	OTTHUMG00000090809	ENST00000326524.2:c.26-828T>G	5.37:g.37835752A>C		141.0	0.0	0		128.0	50.0	0.390625	NM_001190468	B7WPK7|O95448|O95449|O95986|Q6FH33|Q96L44|Q9UD32|Q9UD33|Q9UMV2|Q9UP67|Q9UP97	Silent	SNP	ENST00000326524.2	37	CCDS3922.1																																																																																			.	.	none		0.418	GDNF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207606.1	NM_000514	
MAP2K1	5604	hgsc.bcm.edu	37	15	66779597	66779597	+	Silent	SNP	A	A	T	rs146869577	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:66779597A>T	ENST00000307102.5	+	8	1458	c.927A>T	c.(925-927)gcA>gcT	p.A309A	CTD-3185P2.1_ENST00000565387.1_RNA|MAP2K1_ENST00000566326.1_Silent_p.A133A|CTD-3185P2.2_ENST00000602360.1_RNA	NM_002755.3	NP_002746.1	Q02750	MP2K1_HUMAN	mitogen-activated protein kinase kinase 1	309	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cellular senescence (GO:0090398)|chemotaxis (GO:0006935)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|Golgi inheritance (GO:0048313)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|keratinocyte differentiation (GO:0030216)|labyrinthine layer development (GO:0060711)|MAPK cascade (GO:0000165)|melanosome transport (GO:0032402)|mitotic nuclear division (GO:0007067)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell proliferation (GO:0008285)|negative regulation of homotypic cell-cell adhesion (GO:0034111)|neurotrophin TRK receptor signaling pathway (GO:0048011)|placenta blood vessel development (GO:0060674)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of gene expression (GO:0010628)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|protein heterooligomerization (GO:0051291)|Ras protein signal transduction (GO:0007265)|regulation of early endosome to late endosome transport (GO:2000641)|regulation of Golgi inheritance (GO:0090170)|regulation of stress-activated MAPK cascade (GO:0032872)|regulation of vascular smooth muscle contraction (GO:0003056)|response to axon injury (GO:0048678)|response to glucocorticoid (GO:0051384)|response to oxidative stress (GO:0006979)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|vesicle transport along microtubule (GO:0047496)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite cytoplasm (GO:0032839)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|late endosome (GO:0005770)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perikaryon (GO:0043204)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activator activity (GO:0043539)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine phosphatase activity (GO:0004728)			endometrium(2)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(8)|urinary_tract(1)	20					Bosutinib(DB06616)|Trametinib(DB08911)	CTCCCATGGCAATTTTTGAGT	0.393													A|||	25	0.00499201	0.0182	0.0014	5008	,	,		20753	0.0		0.0	False		,,,				2504	0.0				p.A309A		Atlas-SNP	.											.	MAP2K1	115	.	0			c.A927T						PASS	.	A		61,4341	58.1+/-94.6	0,61,2140	141.0	130.0	134.0		927	-5.7	1.0	15	dbSNP_134	134	0,8598		0,0,4299	no	coding-synonymous	MAP2K1	NM_002755.3		0,61,6439	TT,TA,AA		0.0,1.3857,0.4692		309/394	66779597	61,12939	2201	4299	6500	SO:0001819	synonymous_variant	5604	exon8			CATGGCAATTTTT	L11284	CCDS10216.1	15q22.1-q22.33	2014-09-17			ENSG00000169032	ENSG00000169032	2.7.12.2	"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6840	protein-coding gene	gene with protein product		176872		PRKMK1		9465908, 8388392	Standard	NM_002755		Approved	MEK1, MAPKK1	uc010bhq.3	Q02750	OTTHUMG00000133196	ENST00000307102.5:c.927A>T	15.37:g.66779597A>T		133.0	0.0	0		115.0	51.0	0.443478	NM_002755		Silent	SNP	ENST00000307102.5	37	CCDS10216.1																																																																																			A|0.995;T|0.005	0.005	strong		0.393	MAP2K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256906.4		
TAC3	6866	hgsc.bcm.edu	37	12	57406234	57406234	+	Missense_Mutation	SNP	A	A	G	rs73334764	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:57406234A>G	ENST00000458521.2	-	6	454	c.295T>C	c.(295-297)Tct>Cct	p.S99P	TAC3_ENST00000415231.1_Missense_Mutation_p.S99P|TAC3_ENST00000441881.1_Missense_Mutation_p.S81P	NM_013251.3	NP_037383.1	Q9UHF0	TKNK_HUMAN	tachykinin 3	99					female pregnancy (GO:0007565)|neuropeptide signaling pathway (GO:0007218)|tachykinin receptor signaling pathway (GO:0007217)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			cervix(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|skin(1)	7						TCCGTAGGAGAGTCTAGGGTA	0.488													A|||	125	0.0249601	0.0893	0.0101	5008	,	,		16633	0.0		0.0	False		,,,				2504	0.0				p.S99P		Atlas-SNP	.											.	TAC3	11	.	0			c.T295C						PASS	.	A	PRO/SER,PRO/SER	347,4059	180.8+/-209.0	17,313,1873	73.0	66.0	68.0		241,295	-0.9	0.0	12	dbSNP_130	68	2,8598	1.2+/-3.3	0,2,4298	yes	missense,missense	TAC3	NM_001178054.1,NM_013251.3	74,74	17,315,6171	GG,GA,AA		0.0233,7.8756,2.6834	possibly-damaging,possibly-damaging	81/104,99/122	57406234	349,12657	2203	4300	6503	SO:0001583	missense	6866	exon6			TAGGAGAGTCTAG	AF186112	CCDS8928.1, CCDS53803.1	12q13-q21	2013-02-26	2008-07-31		ENSG00000166863	ENSG00000166863		"""Endogenous ligands"""	11521	protein-coding gene	gene with protein product	"""preprotachykinin-B"""	162330	"""neuromedin K"", ""neurokinin beta"""	NKNB		3479225, 10866201	Standard	NM_013251		Approved	ZNEUROK1, NKB	uc001smp.3	Q9UHF0	OTTHUMG00000156958	ENST00000458521.2:c.295T>C	12.37:g.57406234A>G	ENSP00000404056:p.Ser99Pro	77.0	0.0	0		83.0	42.0	0.506024	NM_013251	Q6IAG2|Q71BC6|Q71BC9	Missense_Mutation	SNP	ENST00000458521.2	37	CCDS8928.1	40	0.018315018315018316	36	0.07317073170731707	4	0.011049723756906077	0	0.0	0	0.0	A	10.20	1.285372	0.23478	0.078756	2.33E-4	ENSG00000166863	ENST00000458521;ENST00000441881;ENST00000415231	D;T;D	0.83250	-1.7;-1.07;-1.7	5.0	-0.857	0.10693	.	.	.	.	.	T	0.09512	0.0234	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.15263	-1.0443	9	0.40728	T	0.16	.	6.259	0.20889	0.1768:0.0:0.4637:0.3595	.	99;81	Q9UHF0;Q9UHF0-3	TKNK_HUMAN;.	P	99;81;99	ENSP00000404056:S99P;ENSP00000408208:S81P;ENSP00000402995:S99P	ENSP00000300108:S99P	S	-	1	0	TAC3	55692501	0.002000	0.14202	0.003000	0.11579	0.008000	0.06430	-0.120000	0.10660	0.002000	0.14630	-0.490000	0.04691	TCT	A|0.971;G|0.029	0.029	strong		0.488	TAC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346793.1	NM_001006667	
ARL14	80117	hgsc.bcm.edu	37	3	160395483	160395483	+	Missense_Mutation	SNP	C	C	A	rs35633732	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:160395483C>A	ENST00000320767.2	+	1	536	c.349C>A	c.(349-351)Cct>Act	p.P117T		NM_025047.2	NP_079323.1	Q8N4G2	ARL14_HUMAN	ADP-ribosylation factor-like 14	117			P -> T (in dbSNP:rs35633732).		small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)	GTP binding (GO:0005525)			lung(6)	6			Lung(72;7.02e-05)|LUSC - Lung squamous cell carcinoma(72;7.23e-05)			TAAAAATGTGCCTGTTGTTCT	0.443													C|||	224	0.0447284	0.1641	0.0086	5008	,	,		21657	0.0		0.001	False		,,,				2504	0.0				p.P117T		Atlas-SNP	.											.	ARL14	16	.	0			c.C349A						PASS	.	C	THR/PRO	635,3771	273.1+/-271.2	46,543,1614	75.0	69.0	71.0		349	5.9	0.8	3	dbSNP_126	71	7,8593	5.0+/-18.6	0,7,4293	yes	missense	ARL14	NM_025047.2	38	46,550,5907	AA,AC,CC		0.0814,14.4122,4.9362	probably-damaging	117/193	160395483	642,12364	2203	4300	6503	SO:0001583	missense	80117	exon1			AATGTGCCTGTTG	AK026248	CCDS3192.1	3q25.33	2014-05-09	2005-11-03	2005-11-03	ENSG00000179674	ENSG00000179674		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	22974	protein-coding gene	gene with protein product		614439	"""ADP-ribosylation factor 7"""	ARF7		15367757	Standard	NM_025047		Approved	FLJ22595	uc003fdq.3	Q8N4G2	OTTHUMG00000159031	ENST00000320767.2:c.349C>A	3.37:g.160395483C>A	ENSP00000323847:p.Pro117Thr	118.0	0.0	0		123.0	122.0	0.99187	NM_025047	Q9H655	Missense_Mutation	SNP	ENST00000320767.2	37	CCDS3192.1	122	0.055860805860805864	100	0.2032520325203252	5	0.013812154696132596	4	0.006993006993006993	13	0.017150395778364115	C	16.30	3.085550	0.55861	0.144122	8.14E-4	ENSG00000179674	ENST00000320767	T	0.74315	-0.83	5.95	5.95	0.96441	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	T	0.00496	0.0016	M	0.75150	2.29	0.09310	P	0.99999024684	D	0.89917	1.0	D	0.97110	1.0	T	0.02539	-1.1144	9	0.54805	T	0.06	-21.0946	19.3683	0.94473	0.0:1.0:0.0:0.0	rs35633732;rs35633732	117	Q8N4G2	ARL14_HUMAN	T	117	ENSP00000323847:P117T	ENSP00000323847:P117T	P	+	1	0	ARL14	161878177	0.994000	0.37717	0.842000	0.33263	0.656000	0.38851	3.803000	0.55560	2.822000	0.97130	0.563000	0.77884	CCT	C|0.942;A|0.058	0.058	strong		0.443	ARL14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352958.1	NM_025047	
SLC40A1	30061	hgsc.bcm.edu	37	2	190437572	190437572	+	Splice_Site	SNP	G	G	A	rs11568344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:190437572G>A	ENST00000261024.2	-	4	813	c.387C>T	c.(385-387)ctC>ctT	p.L129L	SLC40A1_ENST00000418714.1_5'Flank	NM_014585.5	NP_055400.1	Q9NP59	S40A1_HUMAN	solute carrier family 40 (iron-regulated transporter), member 1	129					anatomical structure morphogenesis (GO:0009653)|cellular iron ion homeostasis (GO:0006879)|endothelium development (GO:0003158)|iron ion transmembrane transport (GO:0034755)|lymphocyte homeostasis (GO:0002260)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of apoptotic process (GO:0043066)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|spleen trabecula formation (GO:0060345)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	iron ion transmembrane transporter activity (GO:0005381)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(117;0.000917)|Epithelial(96;0.014)|all cancers(119;0.0491)			GAGAACTTACGAGAACCCATC	0.383													G|||	164	0.0327476	0.118	0.0115	5008	,	,		19151	0.0		0.0	False		,,,				2504	0.0				p.L129L		Atlas-SNP	.											.	SLC40A1	51	.	0			c.C387T						PASS	.	G		492,3914	228.5+/-243.3	22,448,1733	77.0	73.0	74.0		387	0.8	1.0	2	dbSNP_121	74	4,8596	2.2+/-6.3	0,4,4296	yes	coding-synonymous-near-splice	SLC40A1	NM_014585.5		22,452,6029	AA,AG,GG		0.0465,11.1666,3.8136		129/572	190437572	496,12510	2203	4300	6503	SO:0001630	splice_region_variant	30061	exon4			ACTTACGAGAACC	AF215636	CCDS2299.1	2q32	2014-09-17	2003-06-04	2003-06-05	ENSG00000138449	ENSG00000138449		"""Solute carriers"""	10909	protein-coding gene	gene with protein product	"""ferroportin 1"""	604653	"""solute carrier family 11 (proton-coupled divalent metal ion transporters), member 3"""	SLC11A3		10828623	Standard	NM_014585		Approved	MTP1, IREG1, FPN1, HFE4	uc002uqp.4	Q9NP59	OTTHUMG00000132662	ENST00000261024.2:c.387+1C>T	2.37:g.190437572G>A		186.0	0.0	0		196.0	98.0	0.5	NM_014585	Q6FI62|Q7Z4F8|Q8IVB2|Q9NRL0	Silent	SNP	ENST00000261024.2	37	CCDS2299.1																																																																																			G|0.960;A|0.040	0.040	strong		0.383	SLC40A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255916.2		Silent
TLL2	7093	hgsc.bcm.edu	37	10	98240156	98240156	+	Missense_Mutation	SNP	T	T	A	rs61738802	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:98240156T>A	ENST00000357947.3	-	2	461	c.236A>T	c.(235-237)aAa>aTa	p.K79I	TLL2_ENST00000469598.1_5'UTR	NM_012465.3	NP_036597.1	Q9Y6L7	TLL2_HUMAN	tolloid-like 2	79					cell differentiation (GO:0030154)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(15)|lung(22)|ovary(1)|pancreas(1)|prostate(1)|skin(3)	58		Colorectal(252;0.0846)		Epithelial(162;1.51e-07)|all cancers(201;7.59e-06)		GTCTCTGGCTTTGTCAATGTG	0.502													T|||	19	0.00379393	0.0144	0.0	5008	,	,		22069	0.0		0.0	False		,,,				2504	0.0				p.K79I		Atlas-SNP	.											.	TLL2	122	.	0			c.A236T						PASS	.	T	ILE/LYS	66,4340	61.7+/-98.7	1,64,2138	285.0	234.0	251.0		236	3.4	0.4	10	dbSNP_129	251	1,8599		0,1,4299	yes	missense	TLL2	NM_012465.3	102	1,65,6437	AA,AT,TT		0.0116,1.498,0.5151	benign	79/1016	98240156	67,12939	2203	4300	6503	SO:0001583	missense	7093	exon2			CTGGCTTTGTCAA	AF059516	CCDS7449.1	10q23-q24	2008-07-29			ENSG00000095587	ENSG00000095587			11844	protein-coding gene	gene with protein product		606743				10516436	Standard	NM_012465		Approved		uc001kml.2	Q9Y6L7	OTTHUMG00000018833	ENST00000357947.3:c.236A>T	10.37:g.98240156T>A	ENSP00000350630:p.Lys79Ile	250.0	0.0	0		256.0	118.0	0.460938	NM_012465	A6NDK0|Q2M1H1|Q6PJN5|Q9UQ00	Missense_Mutation	SNP	ENST00000357947.3	37	CCDS7449.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	T	16.21	3.058034	0.55325	0.01498	1.16E-4	ENSG00000095587	ENST00000357947	T	0.16457	2.34	5.74	3.37	0.38596	.	0.384078	0.18126	U	0.150896	T	0.07863	0.0197	L	0.38175	1.15	0.24846	N	0.992434	B	0.34103	0.437	B	0.29716	0.106	T	0.22695	-1.0209	10	0.72032	D	0.01	.	4.0306	0.09708	0.0:0.1654:0.1858:0.6489	rs61738802	79	Q9Y6L7	TLL2_HUMAN	I	79	ENSP00000350630:K79I	ENSP00000350630:K79I	K	-	2	0	TLL2	98230146	0.920000	0.31207	0.364000	0.25888	0.337000	0.28794	1.236000	0.32683	0.959000	0.37980	0.459000	0.35465	AAA	T|0.986;A|0.014	0.014	strong		0.502	TLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049608.1		
NDUFS4	4724	hgsc.bcm.edu	37	5	52856572	52856572	+	Missense_Mutation	SNP	T	T	A	rs145347909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:52856572T>A	ENST00000296684.5	+	1	108	c.80T>A	c.(79-81)gTt>gAt	p.V27D		NM_002495.2	NP_002486.1	O43181	NDUS4_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 4, 18kDa (NADH-coenzyme Q reductase)	27					brain development (GO:0007420)|cAMP-mediated signaling (GO:0019933)|cellular metabolic process (GO:0044237)|cellular respiration (GO:0045333)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|mitochondrial respiratory chain complex I assembly (GO:0032981)|positive regulation of fibroblast proliferation (GO:0048146)|reactive oxygen species metabolic process (GO:0072593)|regulation of protein phosphorylation (GO:0001932)|respiratory electron transport chain (GO:0022904)|response to cAMP (GO:0051591)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(1)|ovary(1)|prostate(3)	10		Lung NSC(810;8.27e-05)|Breast(144;0.0848)				GCCCTTTCCGTTTCCAGGGTT	0.547													T|||	6	0.00119808	0.0038	0.0014	5008	,	,		15687	0.0		0.0	False		,,,				2504	0.0				p.V27D		Atlas-SNP	.											.	NDUFS4	17	.	0			c.T80A						PASS	.	T	ASP/VAL	9,4397	15.5+/-35.6	0,9,2194	108.0	97.0	101.0		80	-0.2	0.1	5	dbSNP_134	101	0,8600		0,0,4300	yes	missense	NDUFS4	NM_002495.2	152	0,9,6494	AA,AT,TT		0.0,0.2043,0.0692	possibly-damaging	27/176	52856572	9,12997	2203	4300	6503	SO:0001583	missense	4724	exon1			TTTCCGTTTCCAG	AF020351	CCDS3960.1	5q11.1	2011-07-04	2002-08-29		ENSG00000164258	ENSG00000164258		"""Mitochondrial respiratory chain complex / Complex I"""	7711	protein-coding gene	gene with protein product	"""complex I 18kDa subunit"""	602694	"""NADH dehydrogenase (ubiquinone) Fe-S protein 4 (18kD) (NADH-coenzyme Q reductase)"""			9463323, 9763677	Standard	NM_002495		Approved	AQDQ, CI-18	uc003jpe.2	O43181	OTTHUMG00000096987	ENST00000296684.5:c.80T>A	5.37:g.52856572T>A	ENSP00000296684:p.Val27Asp	63.0	0.0	0		80.0	39.0	0.4875	NM_002495	Q9BS69	Missense_Mutation	SNP	ENST00000296684.5	37	CCDS3960.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	T	12.86	2.065131	0.36470	0.002043	0.0	ENSG00000164258	ENST00000296684;ENST00000506765	T	0.69040	-0.37	4.72	-0.216	0.13153	.	1.026790	0.07670	N	0.935325	T	0.49236	0.1545	L	0.54323	1.7	0.19775	N	0.999952	B	0.29085	0.232	B	0.26517	0.07	T	0.38373	-0.9664	10	0.30854	T	0.27	-17.1517	7.242	0.26102	0.0:0.3826:0.0:0.6174	.	27	O43181	NDUS4_HUMAN	D	27;23	ENSP00000296684:V27D	ENSP00000296684:V27D	V	+	2	0	NDUFS4	52892329	0.912000	0.30974	0.063000	0.19743	0.310000	0.27922	0.131000	0.15870	-0.025000	0.13918	0.533000	0.62120	GTT	T|0.999;A|0.001	0.001	strong		0.547	NDUFS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214062.2	NM_002495	
SIDT2	51092	hgsc.bcm.edu	37	11	117062989	117062989	+	Missense_Mutation	SNP	C	C	T	rs12285035	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117062989C>T	ENST00000324225.4	+	20	2423	c.1892C>T	c.(1891-1893)aCg>aTg	p.T631M	SIDT2_ENST00000431081.2_Missense_Mutation_p.T628M|SIDT2_ENST00000532062.1_5'Flank	NM_001040455.1	NP_001035545.1	Q8NBJ9	SIDT2_HUMAN	SID1 transmembrane family, member 2	631			T -> M (in dbSNP:rs12285035).		cell morphogenesis (GO:0000902)|dsRNA transport (GO:0033227)|glucose homeostasis (GO:0042593)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to glucose (GO:0009749)|type B pancreatic cell development (GO:0003323)|type B pancreatic cell proliferation (GO:0044342)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	RNA transmembrane transporter activity (GO:0051033)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(11)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	36	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000219)|all cancers(92;0.00144)		AAAGGGAACACGGCGTTCTGG	0.617													C|||	83	0.0165735	0.0575	0.0086	5008	,	,		18145	0.0		0.001	False		,,,				2504	0.0				p.T631M		Atlas-SNP	.											.	SIDT2	82	.	0			c.C1892T						PASS	.	C	MET/THR	214,4188	129.8+/-166.5	6,202,1993	114.0	97.0	103.0		1892	3.4	0.9	11	dbSNP_120	103	2,8590	2.2+/-6.3	0,2,4294	yes	missense	SIDT2	NM_001040455.1	81	6,204,6287	TT,TC,CC		0.0233,4.8614,1.6623	benign	631/833	117062989	216,12778	2201	4296	6497	SO:0001583	missense	51092	exon20			GGAACACGGCGTT	AF151799	CCDS31682.1	11q23.3	2008-02-05			ENSG00000149577	ENSG00000149577			24272	protein-coding gene	gene with protein product						10810093, 12975309	Standard	NM_001040455		Approved	CGI-40	uc001pqh.1	Q8NBJ9	OTTHUMG00000167065	ENST00000324225.4:c.1892C>T	11.37:g.117062989C>T	ENSP00000314023:p.Thr631Met	98.0	0.0	0		93.0	93.0	1	NM_001040455	Q8NBY7|Q9Y357	Missense_Mutation	SNP	ENST00000324225.4	37	CCDS31682.1	34	0.015567765567765568	29	0.05894308943089431	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	C	9.873	1.199548	0.22121	0.048614	2.33E-4	ENSG00000149577	ENST00000324225;ENST00000278951;ENST00000431081	T;T;T	0.21932	1.98;1.98;1.98	5.47	3.36	0.38483	.	0.304899	0.37761	N	0.001945	T	0.00784	0.0026	N	0.02247	-0.625	0.35238	D	0.777525	B;B;B;B	0.16166	0.013;0.005;0.006;0.016	B;B;B;B	0.15484	0.007;0.003;0.008;0.013	T	0.22661	-1.0210	10	0.32370	T	0.25	-5.8591	8.774	0.34751	0.0:0.6961:0.0:0.3039	rs12285035;rs52809888;rs12285035	652;628;631;652	Q8NBJ9-2;F5H8L4;Q8NBJ9;C9JBG5	.;.;SIDT2_HUMAN;.	M	631;652;628	ENSP00000314023:T631M;ENSP00000278951:T652M;ENSP00000399635:T628M	ENSP00000278951:T652M	T	+	2	0	SIDT2	116568199	0.066000	0.20996	0.886000	0.34754	0.994000	0.84299	0.421000	0.21280	1.308000	0.44962	0.655000	0.94253	ACG	C|0.978;T|0.022	0.022	strong		0.617	SIDT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392836.1	NM_015996	
VWDE	221806	hgsc.bcm.edu	37	7	12409209	12409209	+	Missense_Mutation	SNP	G	G	A	rs77088407	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:12409209G>A	ENST00000275358.3	-	12	2911	c.2723C>T	c.(2722-2724)tCc>tTc	p.S908F		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	908						extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						AAAGCTTGGGGAACACGCACA	0.398													G|||	93	0.0185703	0.0688	0.0029	5008	,	,		19786	0.0		0.0	False		,,,				2504	0.0				p.S908F		Atlas-SNP	.											.	VWDE	123	.	0			c.C2723T						PASS	.	G	PHE/SER	59,1325		1,57,634	93.0	76.0	81.0		2723	-1.6	0.0	7	dbSNP_132	81	1,3181		0,1,1590	yes	missense	VWDE	NM_001135924.1	155	1,58,2224	AA,AG,GG		0.0314,4.263,1.3141	benign	908/1591	12409209	60,4506	692	1591	2283	SO:0001583	missense	221806	exon12			CTTGGGGAACACG		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.2723C>T	7.37:g.12409209G>A	ENSP00000275358:p.Ser908Phe	178.0	0.0	0		161.0	81.0	0.503106	NM_001135924	B7ZM77|Q96SQ3	Missense_Mutation	SNP	ENST00000275358.3	37	CCDS47544.1	31	0.014194139194139194	30	0.06097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	G	0	-2.705590	0.00096	0.04263	3.14E-4	ENSG00000146530	ENST00000275358;ENST00000536307	D	0.81579	-1.51	4.83	-1.63	0.08345	.	0.700766	0.14662	N	0.305885	T	0.10680	0.0261	N	0.04508	-0.205	0.21984	N	0.999433	B	0.02656	0.0	B	0.04013	0.001	T	0.14643	-1.0465	10	0.06236	T	0.91	.	9.7136	0.40260	0.6228:0.0:0.3772:0.0	.	908	Q8N2E2	VWDE_HUMAN	F	908;362	ENSP00000275358:S908F	ENSP00000275358:S908F	S	-	2	0	VWDE	12375734	1.000000	0.71417	0.015000	0.15790	0.012000	0.07955	1.322000	0.33689	-0.444000	0.07170	-1.099000	0.02127	TCC	G|0.985;A|0.015	0.015	strong		0.398	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
CLEC4A	50856	hgsc.bcm.edu	37	12	8290881	8290881	+	Nonstop_Mutation	SNP	T	T	C	rs74810750	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:8290881T>C	ENST00000229332.5	+	6	959	c.712T>C	c.(712-714)Tga>Cga	p.*238R	CLEC4A_ENST00000360500.3_Nonstop_Mutation_p.*199R|CLEC4A_ENST00000352620.3_Nonstop_Mutation_p.*205R|CLEC4A_ENST00000345999.3_Nonstop_Mutation_p.*166R	NM_016184.3|NM_194447.2|NM_194450.2	NP_057268.1|NP_919429.2|NP_919432.1	Q9UMR7	CLC4A_HUMAN	C-type lectin domain family 4, member A	0					cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(3)|large_intestine(2)|lung(4)|prostate(1)	11				Kidney(36;0.0915)		GATCCACTTATGAACTGAACA	0.393													t|||	32	0.00638978	0.0227	0.0029	5008	,	,		-128	0.0		0.0	False		,,,				2504	0.0				p.X238R		Atlas-SNP	.											.	CLEC4A	28	.	0			c.T712C						PASS	.	T	ARG/stop,ARG/stop,ARG/stop,ARG/stop	70,4336	64.1+/-101.4	1,68,2134	229.0	204.0	212.0		712,595,496,613	1.6	0.9	12	dbSNP_132	212	2,8598	2.2+/-6.3	0,2,4298	yes	stop-lost,stop-lost,stop-lost,stop-lost	CLEC4A	NM_016184.3,NM_194447.2,NM_194448.2,NM_194450.2	,,,	1,70,6432	CC,CT,TT		0.0233,1.5887,0.5536	,,,	238/238,199/199,166/166,205/205	8290881	72,12934	2203	4300	6503	SO:0001578	stop_lost	50856	exon6			CACTTATGAACTG	AJ133532	CCDS8590.1, CCDS8591.1, CCDS8592.1, CCDS41745.1	12p13	2005-02-09	2005-02-09	2005-02-09	ENSG00000111729	ENSG00000111729		"""C-type lectin domain containing"""	13257	protein-coding gene	gene with protein product		605306	"""C-type (calcium dependent, carbohydrate-recognition domain) lectin, superfamily member 6"""	CLECSF6		10438934	Standard	NM_016184		Approved	DCIR, DDB27	uc001qtz.1	Q9UMR7	OTTHUMG00000168571	ENST00000229332.5:c.712T>C	12.37:g.8290881T>C	ENSP00000229332:p.*238Argext*6	127.0	0.0	0		162.0	72.0	0.444444	NM_016184	Q17R69|Q8WXW9|Q9H2Z9|Q9NS33|Q9UI34	Missense_Mutation	SNP	ENST00000229332.5	37	CCDS8590.1	11	0.005036630036630037	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	0	0.0	T	7.275	0.607941	0.14002	0.015887	2.33E-4	ENSG00000111729	ENST00000229332;ENST00000345999;ENST00000352620;ENST00000360500	.	.	.	4.12	1.65	0.23941	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.3429	0.32254	0.0:0.0:0.3962:0.6038	.	.	.	.	R	238;166;205;199	.	.	X	+	1	0	CLEC4A	8182148	0.320000	0.24616	0.897000	0.35233	0.152000	0.21847	0.699000	0.25586	0.346000	0.23899	0.477000	0.44152	TGA	T|0.994;C|0.006	0.006	strong		0.393	CLEC4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400257.1	NM_194450	
CACNA1A	773	hgsc.bcm.edu	37	19	13323261	13323261	+	Silent	SNP	C	C	T	rs7249722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:13323261C>T	ENST00000360228.5	-	42	6125	c.6126G>A	c.(6124-6126)acG>acA	p.T2042T	CACNA1A_ENST00000573710.2_Silent_p.T2043T	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	2043					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	TCCATGTGCCCGTCTTCTGGA	0.647													C|||	48	0.00958466	0.0356	0.0014	5008	,	,		15991	0.0		0.0	False		,,,				2504	0.0				p.T2043T		Atlas-SNP	.											.	CACNA1A	715	.	0			c.G6129A						PASS	.	C	,,,,	100,3864		1,98,1883	30.0	34.0	33.0		6144,6129,6126,6135,6144	-8.6	0.8	19	dbSNP_116	33	1,8295		0,1,4147	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CACNA1A	NM_000068.3,NM_001127221.1,NM_001127222.1,NM_001174080.1,NM_023035.2	,,,,	1,99,6030	TT,TC,CC		0.0121,2.5227,0.8238	,,,,	2048/2267,2043/2262,2042/2507,2045/2264,2048/2513	13323261	101,12159	1982	4148	6130	SO:0001819	synonymous_variant	773	exon42			TGTGCCCGTCTTC	U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.6126G>A	19.37:g.13323261C>T		106.0	0.0	0		109.0	49.0	0.449541	NM_001127221	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Silent	SNP	ENST00000360228.5	37	CCDS45998.1																																																																																			C|0.996;T|0.004	0.004	strong		0.647	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2	NM_000068	
APOBEC3C	27350	hgsc.bcm.edu	37	22	39413957	39413957	+	Missense_Mutation	SNP	G	G	A	rs141108460		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:39413957G>A	ENST00000361441.4	+	3	641	c.361G>A	c.(361-363)Gcc>Acc	p.A121T	APOBEC3D_ENST00000381568.4_Intron	NM_014508.2	NP_055323.2	Q9NRW3	ABC3C_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3C	121					cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA demethylation (GO:0080111)|innate immune response (GO:0045087)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amidines (GO:0016814)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(3)|lung(1)|skin(1)	6	Melanoma(58;0.04)					CATCTTCACCGCCCGCCTCTA	0.587																																					p.A121T		Atlas-SNP	.											.	APOBEC3C	21	.	0			c.G361A						PASS	.	G	THR/ALA	1,4405		0,1,2202	113.0	118.0	117.0		361	-2.5	0.0	22	dbSNP_134	117	0,8600		0,0,4300	no	missense	APOBEC3C	NM_014508.2	58	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	121/191	39413957	1,13005	2203	4300	6503	SO:0001583	missense	27350	exon3			TTCACCGCCCGCC	AF165520	CCDS13983.1	22q13.1-q13.2	2014-01-28			ENSG00000244509	ENSG00000244509		"""Apolipoprotein B mRNA editing enzymes"""	17353	protein-coding gene	gene with protein product		607750				11863358	Standard	NM_014508		Approved	APOBEC1L, PBI, bK150C2.3, ARDC2, ARDC4, ARP5	uc003awr.3	Q9NRW3	OTTHUMG00000151087	ENST00000361441.4:c.361G>A	22.37:g.39413957G>A	ENSP00000355340:p.Ala121Thr	281.0	0.0	0		276.0	114.0	0.413043	NM_014508	B2R884|Q5JZ92|Q7Z2N7|Q96F12	Missense_Mutation	SNP	ENST00000361441.4	37	CCDS13983.1	.	.	.	.	.	.	.	.	.	.	.	15.12	2.740041	0.49045	2.27E-4	0.0	ENSG00000244509	ENST00000361441	T	0.67523	-0.27	2.01	-2.48	0.06423	APOBEC-like, N-terminal (1);Cytidine deaminase-like (1);	.	.	.	.	T	0.79936	0.4532	M	0.89095	3.005	0.38181	D	0.939611	D	0.89917	1.0	D	0.72982	0.979	T	0.79897	-0.1609	9	0.87932	D	0	.	8.5433	0.33406	0.0:0.0:0.4067:0.5932	.	121	Q9NRW3	ABC3C_HUMAN	T	121	ENSP00000355340:A121T	ENSP00000355340:A121T	A	+	1	0	APOBEC3C	37743903	0.644000	0.27277	0.035000	0.18076	0.027000	0.11550	0.674000	0.25218	-0.470000	0.06901	0.479000	0.44913	GCC	G|1.000;A|0.000	0.000	weak		0.587	APOBEC3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321241.2	NM_014508	
SIGLEC9	27180	hgsc.bcm.edu	37	19	51628395	51628395	+	Missense_Mutation	SNP	C	C	T	rs144549146		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51628395C>T	ENST00000250360.3	+	1	231	c.164C>T	c.(163-165)cCa>cTa	p.P55L	SIGLEC9_ENST00000440804.3_Missense_Mutation_p.P55L	NM_014441.2	NP_055256.1	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9	55	Ig-like V-type.				cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(3)|lung(25)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	45		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)		TACCCTGGCCCAGTAGTTCAT	0.602													.|||	1	0.000199681	0.0008	0.0	5008	,	,		16792	0.0		0.0	False		,,,				2504	0.0				p.P55L		Atlas-SNP	.											.	SIGLEC9	85	.	0			c.C164T						PASS	.	C	LEU/PRO,LEU/PRO	3,4403		0,3,2200	120.0	87.0	98.0		164,164	0.7	0.0	19	dbSNP_134	98	0,8600		0,0,4300	no	missense,missense	SIGLEC9	NM_001198558.1,NM_014441.2	98,98	0,3,6500	TT,TC,CC		0.0,0.0681,0.0231	possibly-damaging,possibly-damaging	55/480,55/464	51628395	3,13003	2203	4300	6503	SO:0001583	missense	27180	exon1			CTGGCCCAGTAGT	AF135027	CCDS12825.1, CCDS56100.1	19q13.3-q13.4	2013-01-29			ENSG00000129450	ENSG00000129450		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10878	protein-coding gene	gene with protein product		605640				10903842	Standard	NM_014441		Approved	CD329	uc002pvu.3	Q9Y336		ENST00000250360.3:c.164C>T	19.37:g.51628395C>T	ENSP00000250360:p.Pro55Leu	210.0	0.0	0		227.0	108.0	0.475771	NM_001198558	Q6GTU4|Q9BYI9	Missense_Mutation	SNP	ENST00000250360.3	37	CCDS12825.1	.	.	.	.	.	.	.	.	.	.	.	11.96	1.794120	0.31777	6.81E-4	0.0	ENSG00000129450	ENST00000440804;ENST00000250360	T;T	0.54071	0.59;0.59	2.88	0.675	0.17952	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	5.876730	0.00810	N	0.001498	T	0.62344	0.2420	M	0.80183	2.485	0.09310	N	1	P	0.41947	0.766	P	0.46208	0.507	T	0.41466	-0.9507	10	0.62326	D	0.03	.	4.9958	0.14237	0.0:0.6975:0.0:0.3025	.	55	Q9Y336	SIGL9_HUMAN	L	55	ENSP00000413861:P55L;ENSP00000250360:P55L	ENSP00000250360:P55L	P	+	2	0	SIGLEC9	56320207	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.035000	0.12205	0.010000	0.14839	0.397000	0.26171	CCA	C|1.000;T|0.000	0.000	strong		0.602	SIGLEC9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464224.1	NM_014441	
SEC24D	9871	hgsc.bcm.edu	37	4	119659518	119659518	+	Silent	SNP	G	G	A	rs1128403	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:119659518G>A	ENST00000280551.6	-	19	2632	c.2394C>T	c.(2392-2394)ctC>ctT	p.L798L	SEC24D_ENST00000419654.2_Silent_p.L354L|SEC24D_ENST00000505134.1_5'UTR|SEC24D_ENST00000379735.5_Silent_p.L799L|SEC24D_ENST00000511481.1_Silent_p.L429L|SEC24D_ENST00000429811.2_Silent_p.L354L			O94855	SC24D_HUMAN	SEC24 family member D	798					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|in utero embryonic development (GO:0001701)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(13)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37						AAGGCTGGTGGAGAACTGCTT	0.403													G|||	197	0.0393371	0.1309	0.0202	5008	,	,		19037	0.0		0.008	False		,,,				2504	0.002				p.L798L		Atlas-SNP	.											.	SEC24D	96	.	0			c.C2394T						PASS	.	G		499,3907	234.6+/-247.4	25,449,1729	100.0	89.0	93.0		2394	-10.1	0.1	4	dbSNP_86	93	28,8572	19.8+/-62.0	0,28,4272	no	coding-synonymous	SEC24D	NM_014822.2		25,477,6001	AA,AG,GG		0.3256,11.3255,4.052		798/1033	119659518	527,12479	2203	4300	6503	SO:0001819	synonymous_variant	9871	exon19			CTGGTGGAGAACT	AB018298	CCDS3710.1	4q26	2013-10-21	2013-10-21		ENSG00000150961	ENSG00000150961			10706	protein-coding gene	gene with protein product		607186	"""SEC24 (S. cerevisiae) related gene family, member D"", ""SEC24 family, member D (S. cerevisiae)"""			9872452, 10075675	Standard	NM_014822		Approved	KIAA0755	uc003ici.4	O94855	OTTHUMG00000132957	ENST00000280551.6:c.2394C>T	4.37:g.119659518G>A		170.0	0.0	0		178.0	75.0	0.421348	NM_014822	Q8IYI7	Silent	SNP	ENST00000280551.6	37	CCDS3710.1																																																																																			G|0.956;A|0.044	0.044	strong		0.403	SEC24D-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256514.4		
ERICH6	131831	hgsc.bcm.edu	37	3	150391789	150391789	+	Missense_Mutation	SNP	C	C	T	rs11919896	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:150391789C>T	ENST00000295910.6	-	11	1349	c.1297G>A	c.(1297-1299)Ggg>Agg	p.G433R	FAM194A_ENST00000491361.1_Missense_Mutation_p.G287R	NM_152394.3	NP_689607.2														NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						AACTTGCTCCCATGTTTGTAG	0.338													C|||	120	0.0239617	0.084	0.0101	5008	,	,		20313	0.0		0.002	False		,,,				2504	0.0				p.G433R		Atlas-SNP	.											.	FAM194A	91	.	0			c.G1297A						PASS	.	C	ARG/GLY	318,4088	171.2+/-201.5	8,302,1893	153.0	148.0	149.0		1297	4.9	0.5	3	dbSNP_120	149	2,8598	1.2+/-3.3	0,2,4298	yes	missense	FAM194A	NM_152394.3	125	8,304,6191	TT,TC,CC		0.0233,7.2174,2.4604	probably-damaging	433/664	150391789	320,12686	2203	4300	6503	SO:0001583	missense	131831	exon11			TGCTCCCATGTTT																												ENST00000295910.6:c.1297G>A	3.37:g.150391789C>T	ENSP00000295910:p.Gly433Arg	78.0	0.0	0		62.0	30.0	0.483871	NM_152394		Missense_Mutation	SNP	ENST00000295910.6	37	CCDS3151.2	48	0.02197802197802198	42	0.08536585365853659	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	C	19.68	3.873229	0.72180	0.072174	2.33E-4	ENSG00000163645	ENST00000295910;ENST00000491361;ENST00000313811	T;T	0.14893	2.47;2.47	4.94	4.94	0.65067	.	0.238409	0.29307	N	0.012528	T	0.01905	0.0060	M	0.68593	2.085	0.39844	D	0.973152	D	0.89917	1.0	D	0.97110	1.0	T	0.00144	-1.1994	10	0.54805	T	0.06	-12.8489	17.0788	0.86593	0.0:1.0:0.0:0.0	rs11919896;rs52830969;rs11919896	433	Q7L0X2	F194A_HUMAN	R	433;287;391	ENSP00000295910:G433R;ENSP00000419366:G287R	ENSP00000295910:G433R	G	-	1	0	FAM194A	151874479	0.965000	0.33210	0.523000	0.27875	0.854000	0.48673	3.537000	0.53590	2.540000	0.85666	0.655000	0.94253	GGG	C|0.970;T|0.030	0.030	strong		0.338	FAM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257666.1		
MCEE	84693	hgsc.bcm.edu	37	2	71351641	71351641	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:71351641T>C	ENST00000244217.5	-	2	90	c.73A>G	c.(73-75)Aca>Gca	p.T25A	AC007881.1_ENST00000578636.1_RNA	NM_032601.3	NP_115990.3	Q96PE7	MCEE_HUMAN	methylmalonyl CoA epimerase	25					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|L-methylmalonyl-CoA metabolic process (GO:0046491)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	metal ion binding (GO:0046872)|methylmalonyl-CoA epimerase activity (GO:0004493)			kidney(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	9						GCTCTTACTGTTGGAATGGGA	0.418																																					p.T25A		Atlas-SNP	.											.	MCEE	19	.	0			c.A73G						PASS	.						87.0	95.0	92.0					2																	71351641		2203	4300	6503	SO:0001583	missense	84693	exon2			TTACTGTTGGAAT	AF364547	CCDS1915.1	2p13.3	2011-05-12			ENSG00000124370	ENSG00000124370	5.1.99.1		16732	protein-coding gene	gene with protein product	"""glyoxalase domain containing 2"""	608419				16697227, 16752391, 16843692	Standard	NM_032601		Approved	GLOD2	uc002shs.2	Q96PE7	OTTHUMG00000129709	ENST00000244217.5:c.73A>G	2.37:g.71351641T>C	ENSP00000244217:p.Thr25Ala	55.0	0.0	0		51.0	25.0	0.490196	NM_032601	Q53TP1|Q8WW63	Missense_Mutation	SNP	ENST00000244217.5	37	CCDS1915.1	.	.	.	.	.	.	.	.	.	.	T	11.40	1.627801	0.28978	.	.	ENSG00000124370	ENST00000244217	T	0.62941	-0.01	5.33	-5.38	0.02673	.	0.745129	0.13573	N	0.377891	T	0.42494	0.1205	L	0.35723	1.085	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.26849	-1.0091	10	0.20519	T	0.43	-5.2959	9.1858	0.37170	0.1202:0.5708:0.0:0.3089	.	25	Q96PE7	MCEE_HUMAN	A	25	ENSP00000244217:T25A	ENSP00000244217:T25A	T	-	1	0	MCEE	71205149	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.466000	0.06672	-0.914000	0.03827	0.528000	0.53228	ACA	.	.	none		0.418	MCEE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251917.3	NM_032601	
DYX1C1	161582	hgsc.bcm.edu	37	15	55790053	55790053	+	Missense_Mutation	SNP	T	T	C	rs61733359	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:55790053T>C	ENST00000321149.3	-	3	495	c.128A>G	c.(127-129)aAc>aGc	p.N43S	DYX1C1_ENST00000348518.3_Missense_Mutation_p.N43S|DYX1C1_ENST00000457155.2_Missense_Mutation_p.N43S|DYX1C1-CCPG1_ENST00000565113.1_RNA|DYX1C1_ENST00000380679.1_Missense_Mutation_p.N43S|DYX1C1_ENST00000448430.2_Missense_Mutation_p.N43S	NM_130810.3	NP_570722.2	Q8WXU2	DYXC1_HUMAN	dyslexia susceptibility 1 candidate 1	43	CS. {ECO:0000255|PROSITE- ProRule:PRU00547}.|Mediates interaction with ESR1 and STUB1.				cilium movement (GO:0003341)|determination of left/right symmetry (GO:0007368)|inner dynein arm assembly (GO:0036159)|neuron migration (GO:0001764)|outer dynein arm assembly (GO:0036158)|regulation of intracellular estrogen receptor signaling pathway (GO:0033146)|regulation of proteasomal protein catabolic process (GO:0061136)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	estrogen receptor binding (GO:0030331)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18				all cancers(107;0.0118)|GBM - Glioblastoma multiforme(80;0.171)		TGGAGGAAAGTTGACCTATGC	0.363													T|||	15	0.00299521	0.0106	0.0014	5008	,	,		17266	0.0		0.0	False		,,,				2504	0.0				p.N43S		Atlas-SNP	.											.	DYX1C1	54	.	0			c.A128G						PASS	.	T	SER/ASN,SER/ASN,SER/ASN	59,4327	55.5+/-91.7	0,59,2134	81.0	81.0	81.0		128,128,128	3.6	1.0	15	dbSNP_129	81	1,8583		0,1,4291	yes	missense,missense,missense	DYX1C1	NM_001033559.2,NM_001033560.1,NM_130810.3	46,46,46	0,60,6425	CC,CT,TT		0.0116,1.3452,0.4626	benign,benign,benign	43/377,43/382,43/421	55790053	60,12910	2193	4292	6485	SO:0001583	missense	161582	exon3			GGAAAGTTGACCT		CCDS10154.1, CCDS32243.1, CCDS32244.1	15q21.3	2014-09-11			ENSG00000256061	ENSG00000256061		"""Tetratricopeptide (TTC) repeat domain containing"""	21493	protein-coding gene	gene with protein product		608706				12954984	Standard	NM_130810		Approved	EKN1, FLJ37882, CILD25	uc002adc.3	Q8WXU2	OTTHUMG00000132008	ENST00000321149.3:c.128A>G	15.37:g.55790053T>C	ENSP00000323275:p.Asn43Ser	50.0	0.0	0		37.0	19.0	0.513514	NM_001033560	Q6P5Y9|Q8N1S6	Missense_Mutation	SNP	ENST00000321149.3	37	CCDS10154.1	5	0.0022893772893772895	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	0	0.0	T	15.43	2.830177	0.50845	0.013452	1.16E-4	ENSG00000256061	ENST00000420792;ENST00000448430;ENST00000380679;ENST00000457155;ENST00000321149;ENST00000348518	T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59	4.72	3.56	0.40772	CS-like domain (1);CS domain (1);HSP20-like chaperone (1);	0.272597	0.33610	U	0.004729	T	0.10723	0.0262	N	0.17872	0.535	0.30138	N	0.804168	B;B;B	0.32526	0.057;0.119;0.374	B;B;B	0.34138	0.082;0.078;0.176	T	0.16958	-1.0385	10	0.02654	T	1	.	7.8669	0.29543	0.0:0.1574:0.0:0.8426	.	43;43;43	Q8WXU2-3;Q8WXU2;Q8WXU2-2	.;DYXC1_HUMAN;.	S	43	ENSP00000403412:N43S;ENSP00000370054:N43S;ENSP00000402640:N43S;ENSP00000323275:N43S;ENSP00000299561:N43S	ENSP00000323275:N43S	N	-	2	0	DYX1C1	53577345	1.000000	0.71417	0.980000	0.43619	0.984000	0.73092	1.407000	0.34657	1.984000	0.57885	0.459000	0.35465	AAC	T|0.995;C|0.005	0.005	strong		0.363	DYX1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254976.1	NM_130810	
TTC21A	199223	hgsc.bcm.edu	37	3	39166887	39166887	+	Missense_Mutation	SNP	C	C	T	rs74824603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:39166887C>T	ENST00000431162.2	+	11	1414	c.1280C>T	c.(1279-1281)gCg>gTg	p.A427V	TTC21A_ENST00000301819.6_Missense_Mutation_p.A427V|TTC21A_ENST00000440121.1_Missense_Mutation_p.A378V			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	427										NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(23)|ovary(1)|prostate(1)|skin(3)	50				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		GAGACCACAGCGCTCCTGAAG	0.552											OREG0015487	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	12	0.00239617	0.0083	0.0014	5008	,	,		22490	0.0		0.0	False		,,,				2504	0.0				p.A427V		Atlas-SNP	.											.	TTC21A	96	.	0			c.C1280T						PASS	.						74.0	74.0	74.0					3																	39166887		2029	4198	6227	SO:0001583	missense	199223	exon11			CCACAGCGCTCCT	AJ487015	CCDS43068.1, CCDS46800.1, CCDS43068.2	3p22.2	2014-09-04			ENSG00000168026	ENSG00000168026		"""Tetratricopeptide (TTC) repeat domain containing"""	30761	protein-coding gene	gene with protein product		611430					Standard	NM_145755		Approved	STI2	uc003cjc.2	Q8NDW8	OTTHUMG00000155973	ENST00000431162.2:c.1280C>T	3.37:g.39166887C>T	ENSP00000398211:p.Ala427Val	129.0	0.0	0	883	130.0	61.0	0.469231	NM_145755	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	37	CCDS46800.1	.	.	.	.	.	.	.	.	.	.	C	5.561	0.288299	0.10513	.	.	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.36157	1.27;1.27;1.27	5.73	0.827	0.18835	.	0.834776	0.10720	N	0.641804	T	0.21022	0.0506	L	0.34521	1.04	0.09310	N	1	B;B;B	0.21309	0.031;0.054;0.032	B;B;B	0.12156	0.007;0.004;0.005	T	0.24657	-1.0154	10	0.27785	T	0.31	-0.2644	1.2509	0.01982	0.2566:0.4043:0.1248:0.2143	.	378;427;427	Q8NDW8-6;Q8NDW8-7;Q8NDW8	.;.;TT21A_HUMAN	V	427;409;427;378	ENSP00000301819:A427V;ENSP00000398211:A427V;ENSP00000410882:A378V	ENSP00000301819:A427V	A	+	2	0	TTC21A	39141891	0.000000	0.05858	0.000000	0.03702	0.029000	0.11900	0.215000	0.17562	0.074000	0.16767	0.609000	0.83330	GCG	A|0.004;C|0.994;T|0.001	0.001	strong		0.552	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755	
PDE11A	50940	hgsc.bcm.edu	37	2	178592452	178592452	+	Silent	SNP	C	C	A	rs77341035	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:178592452C>A	ENST00000286063.6	-	12	2294	c.1977G>T	c.(1975-1977)cgG>cgT	p.R659R	PDE11A_ENST00000358450.4_Silent_p.R409R|PDE11A_ENST00000449286.2_Silent_p.R301R|PDE11A_ENST00000409504.1_Silent_p.R301R|PDE11A_ENST00000389683.3_Silent_p.R215R|PDE11A_ENST00000497003.1_5'UTR	NM_016953.3	NP_058649.3	Q9HCR9	PDE11_HUMAN	phosphodiesterase 11A	659	Catalytic. {ECO:0000250}.				blood coagulation (GO:0007596)|cAMP catabolic process (GO:0006198)|cGMP catabolic process (GO:0046069)|signal transduction (GO:0007165)	cytosol (GO:0005829)|perikaryon (GO:0043204)	3',5'-cyclic-GMP phosphodiesterase activity (GO:0047555)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(13)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(3)	58			OV - Ovarian serous cystadenocarcinoma(117;0.00121)|Epithelial(96;0.00455)|all cancers(119;0.02)		Caffeine(DB00201)|Tadalafil(DB00820)	ATAGAACCATCCGATAGTTTT	0.468									Primary Pigmented Nodular Adrenocortical Disease, Familial				C|||	54	0.0107827	0.0393	0.0029	5008	,	,		22848	0.0		0.0	False		,,,				2504	0.0				p.R659R		Atlas-SNP	.											.	PDE11A	283	.	0			c.G1977T						PASS	.	C	,,,	96,4310	77.8+/-116.1	0,96,2107	185.0	153.0	164.0		645,1227,903,1977	-7.6	0.9	2	dbSNP_131	164	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PDE11A	NM_001077196.1,NM_001077197.1,NM_001077358.1,NM_016953.3	,,,	0,97,6406	AA,AC,CC		0.0116,2.1788,0.7458	,,,	215/490,409/684,301/576,659/934	178592452	97,12909	2203	4300	6503	SO:0001819	synonymous_variant	50940	exon12	Familial Cancer Database	iPPNAD, PPNAD1, incl. familial micronodular adrenocortical hyperplasia, PPNAD2	AACCATCCGATAG	AJ251509	CCDS33334.1, CCDS42785.1, CCDS42786.1, CCDS46459.1	2q31.3	2010-06-22			ENSG00000128655	ENSG00000128655	3.1.4.17	"""Phosphodiesterases"""	8773	protein-coding gene	gene with protein product		604961				10725373	Standard	NM_001077196		Approved		uc002ulq.3	Q9HCR9	OTTHUMG00000154188	ENST00000286063.6:c.1977G>T	2.37:g.178592452C>A		105.0	0.0	0		112.0	54.0	0.482143	NM_016953	Q14CD1|Q53T16|Q96S76|Q9GZY7|Q9HB46|Q9NY45	Silent	SNP	ENST00000286063.6	37	CCDS33334.1	24	0.01098901098901099	22	0.044715447154471545	2	0.0055248618784530384	0	0.0	0	0.0	C	11.02	1.515710	0.27123	0.021788	1.16E-4	ENSG00000128655	ENST00000433879	.	.	.	5.67	-7.56	0.01322	.	.	.	.	.	T	0.10252	0.0251	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.39014	-0.9634	4	.	.	.	.	2.2102	0.03945	0.1021:0.2177:0.3161:0.3641	.	.	.	.	V	267	.	.	G	-	2	0	PDE11A	178300698	0.947000	0.32204	0.922000	0.36590	0.991000	0.79684	-0.087000	0.11215	-0.991000	0.03476	-0.290000	0.09829	GGA	C|0.989;A|0.011	0.011	strong		0.468	PDE11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334313.2		
SIPA1L2	57568	hgsc.bcm.edu	37	1	232575051	232575051	+	Silent	SNP	G	G	A	rs189356281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:232575051G>A	ENST00000366630.1	-	14	4192	c.3834C>T	c.(3832-3834)ctC>ctT	p.L1278L	SIPA1L2_ENST00000308942.4_Silent_p.L352L|SIPA1L2_ENST00000262861.4_Silent_p.L1278L			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	1278					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)				GCACAGGGCCGAGGATGGTGG	0.667													G|||	21	0.00419329	0.0144	0.0	5008	,	,		18627	0.0		0.002	False		,,,				2504	0.0				p.L1278L		Atlas-SNP	.											SIPA1L2,colon,carcinoma,-2,1	SIPA1L2	218	1	0			c.C3834T						scavenged	.	G		77,3971		0,77,1947	37.0	41.0	40.0		3834	-10.3	0.0	1		40	3,8363		0,3,4180	no	coding-synonymous	SIPA1L2	NM_020808.3		0,80,6127	AA,AG,GG		0.0359,1.9022,0.6444		1278/1723	232575051	80,12334	2024	4183	6207	SO:0001819	synonymous_variant	57568	exon13			AGGGCCGAGGATG	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.3834C>T	1.37:g.232575051G>A		106.0	1.0	0.00943396		123.0	61.0	0.495935	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Silent	SNP	ENST00000366630.1	37	CCDS41474.1																																																																																			G|0.996;A|0.004	0.004	strong		0.667	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839	
PCDHA9	9752	hgsc.bcm.edu	37	5	140229581	140229581	+	Missense_Mutation	SNP	G	G	C	rs59056023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140229581G>C	ENST00000532602.1	+	1	2534	c.1501G>C	c.(1501-1503)Gag>Cag	p.E501Q	PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA9_ENST00000378122.3_Missense_Mutation_p.E501Q|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	501	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.		E -> Q (in dbSNP:rs59056023).		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(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGGTTGGGCGAGCGCTCGCT	0.672													.|||	319	0.0636981	0.2307	0.0187	5008	,	,		14972	0.0		0.001	False		,,,				2504	0.0				p.E501Q	Melanoma(55;1800 1972 14909)	Atlas-SNP	.											.	PCDHA9	373	.	0			c.G1501C						PASS	.	G	GLN/GLU,,,,,,,,,,,GLN/GLU	877,3515	327.2+/-299.9	127,623,1446	59.0	65.0	63.0		1501,,,,,,,,,,,1501	3.6	1.0	5	dbSNP_129	63	7,8531	4.3+/-15.6	1,5,4263	no	missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHA9,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_014005.3,NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1	29,,,,,,,,,,,29	128,628,5709	CC,CG,GG		0.082,19.9681,6.8368	,,,,,,,,,,,	501/843,,,,,,,,,,,501/951	140229581	884,12046	2196	4269	6465	SO:0001583	missense	9752	exon1			TTGGGCGAGCGCT	AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"""Cadherins / Protocadherins : Clustered"""	8675	other	complex locus constituent	"""KIAA0345-like 5"""	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.1501G>C	5.37:g.140229581G>C	ENSP00000436042:p.Glu501Gln	300.0	1.0	0.00333333		346.0	173.0	0.5	NM_031857	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	37	CCDS54920.1	129	0.059065934065934064	109	0.22154471544715448	11	0.03038674033149171	1	0.0017482517482517483	8	0.010554089709762533	G	14.45	2.539010	0.45176	0.199681	8.2E-4	ENSG00000204961	ENST00000532602;ENST00000378122	T;T	0.53640	0.69;0.61	3.56	3.56	0.40772	Cadherin (4);Cadherin-like (1);	0.000000	0.31760	U	0.007116	T	0.00039	0.0001	N	0.25245	0.725	0.49687	P	1.8499999999999073E-4	P;P	0.48834	0.916;0.904	P;P	0.61722	0.893;0.631	T	0.06162	-1.0842	9	0.87932	D	0	.	8.4611	0.32927	0.0:0.1643:0.6673:0.1684	rs59056023	501;501	Q9Y5H5;Q9Y5H5-2	PCDA9_HUMAN;.	Q	501	ENSP00000436042:E501Q;ENSP00000367362:E501Q	ENSP00000367362:E501Q	E	+	1	0	PCDHA9	140209765	0.000000	0.05858	1.000000	0.80357	0.295000	0.27426	-0.372000	0.07504	1.973000	0.57446	0.306000	0.20318	GAG	G|0.939;C|0.061	0.061	strong		0.672	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857	
TSGA10	80705	hgsc.bcm.edu	37	2	99722135	99722135	+	Missense_Mutation	SNP	C	C	T	rs146207401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:99722135C>T	ENST00000393483.3	-	8	1080	c.236G>A	c.(235-237)cGa>cAa	p.R79Q	TSGA10_ENST00000478090.1_5'UTR|TSGA10_ENST00000539964.1_Missense_Mutation_p.R79Q|TSGA10_ENST00000410001.1_Missense_Mutation_p.R79Q|TSGA10_ENST00000355053.4_Missense_Mutation_p.R79Q|TSGA10_ENST00000542655.1_Missense_Mutation_p.R79Q	NM_025244.2	NP_079520.1	Q9BZW7	TSG10_HUMAN	testis specific, 10	79					cell projection assembly (GO:0030031)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|membrane (GO:0016020)|motile cilium (GO:0031514)|neuron projection (GO:0043005)|nucleus (GO:0005634)				NS(2)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	34						CATTTCTCGTCGAAGTCGGGT	0.368																																					p.R79Q		Atlas-SNP	.											.	TSGA10	81	.	0			c.G236A						PASS	.	C	GLN/ARG,GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	203.0	195.0	198.0		236,236	5.0	1.0	2	dbSNP_134	198	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	TSGA10	NM_025244.2,NM_182911.3	43,43	0,4,6499	TT,TC,CC		0.0233,0.0454,0.0308	probably-damaging,probably-damaging	79/699,79/699	99722135	4,13002	2203	4300	6503	SO:0001583	missense	80705	exon7			TCTCGTCGAAGTC	AF254756	CCDS2037.1	2q11.2	2009-08-06			ENSG00000135951	ENSG00000135951			14927	protein-coding gene	gene with protein product	"""cancer/testis antigen 79"""	607166				11179690	Standard	NM_025244		Approved	CEP4L, CT79	uc002szi.4	Q9BZW7	OTTHUMG00000130637	ENST00000393483.3:c.236G>A	2.37:g.99722135C>T	ENSP00000377123:p.Arg79Gln	73.0	0.0	0		66.0	30.0	0.454545	NM_182911	B7Z925|D3DVH7|Q8NEP0|Q9BWX0	Missense_Mutation	SNP	ENST00000393483.3	37	CCDS2037.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.031503	0.93575	4.54E-4	2.33E-4	ENSG00000135951	ENST00000393483;ENST00000410001;ENST00000355053;ENST00000539964;ENST00000409564;ENST00000393482;ENST00000542655	T;T;T;T;T;T;T	0.54675	0.56;0.56;0.56;0.56;0.56;0.56;0.56	4.99	4.99	0.66335	.	0.158903	0.29853	N	0.011034	T	0.64746	0.2626	L	0.59436	1.845	0.34409	D	0.696207	D;D	0.71674	0.998;0.998	P;P	0.59889	0.865;0.865	T	0.69423	-0.5149	10	0.28530	T	0.3	-6.6381	17.049	0.86513	0.0:1.0:0.0:0.0	.	79;79	B7Z925;Q9BZW7	.;TSG10_HUMAN	Q	79	ENSP00000377123:R79Q;ENSP00000386956:R79Q;ENSP00000347161:R79Q;ENSP00000444419:R79Q;ENSP00000386508:R79Q;ENSP00000377122:R79Q;ENSP00000445623:R79Q	ENSP00000347161:R79Q	R	-	2	0	TSGA10	99088567	0.999000	0.42202	1.000000	0.80357	0.997000	0.91878	4.326000	0.59241	2.601000	0.87937	0.650000	0.86243	CGA	C|0.999;T|0.001	0.001	strong		0.368	TSGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253125.1	NM_182911	
HEPHL1	341208	hgsc.bcm.edu	37	11	93844722	93844722	+	Silent	SNP	C	C	T	rs76467816	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:93844722C>T	ENST00000315765.9	+	19	3236	c.3228C>T	c.(3226-3228)tcC>tcT	p.S1076S		NM_001098672.1	NP_001092142.1	Q6MZM0	HPHL1_HUMAN	hephaestin-like 1	1076	Plastocyanin-like 6.				copper ion transport (GO:0006825)|oxidation-reduction process (GO:0055114)	integral component of membrane (GO:0016021)	copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(11)|lung(25)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	61		Acute lymphoblastic leukemia(157;2.34e-05)|all_hematologic(158;0.00824)				TTCCTTACTCCACCACATCTC	0.428													C|||	147	0.029353	0.1067	0.0086	5008	,	,		20649	0.0		0.0	False		,,,				2504	0.0				p.S1076S		Atlas-SNP	.											.	HEPHL1	144	.	0			c.C3228T						PASS	.	C		310,3668		15,280,1694	48.0	47.0	48.0		3228	-4.0	0.9	11	dbSNP_131	48	1,8347		0,1,4173	no	coding-synonymous	HEPHL1	NM_001098672.1		15,281,5867	TT,TC,CC		0.012,7.7929,2.5231		1076/1160	93844722	311,12015	1989	4174	6163	SO:0001819	synonymous_variant	341208	exon19			TTACTCCACCACA	BX641008	CCDS44710.1	11q21	2008-02-05			ENSG00000181333	ENSG00000181333			30477	protein-coding gene	gene with protein product							Standard	NM_001098672		Approved	DKFZp686F22190	uc001pep.2	Q6MZM0	OTTHUMG00000167751	ENST00000315765.9:c.3228C>T	11.37:g.93844722C>T		205.0	0.0	0		194.0	193.0	0.994845	NM_001098672	Q3C1W7	Silent	SNP	ENST00000315765.9	37	CCDS44710.1																																																																																			C|0.979;T|0.021	0.021	strong		0.428	HEPHL1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396103.2	XM_291947	
LEFTY1	10637	hgsc.bcm.edu	37	1	226074635	226074635	+	Missense_Mutation	SNP	C	C	T	rs61739581	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:226074635C>T	ENST00000272134.5	-	4	972	c.893G>A	c.(892-894)cGg>cAg	p.R298Q	RP4-559A3.7_ENST00000432920.2_3'UTR|LEFTY1_ENST00000492457.1_5'Flank	NM_020997.3	NP_066277.1	O75610	LFTY1_HUMAN	left-right determination factor 1	298					cell growth (GO:0016049)|determination of left/right symmetry (GO:0007368)|heart morphogenesis (GO:0003007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)				cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	10	Breast(184;0.197)					CGGGGGCTGCCGGCAGGTGCC	0.642													c|||	331	0.0660942	0.236	0.0245	5008	,	,		16397	0.0		0.002	False		,,,				2504	0.0				p.R298Q		Atlas-SNP	.											.	LEFTY1	30	.	0			c.G893A						PASS	.	C	GLN/ARG	866,3536		78,710,1413	16.0	20.0	19.0		893	-8.0	0.7	1	dbSNP_129	19	12,8578		0,12,4283	no	missense	LEFTY1	NM_020997.3	43	78,722,5696	TT,TC,CC		0.1397,19.6729,6.758	benign	298/367	226074635	878,12114	2201	4295	6496	SO:0001583	missense	10637	exon4			GGCTGCCGGCAGG	AF081507	CCDS1548.1	1q42.1	2008-02-05	2004-11-17	2004-11-17	ENSG00000243709	ENSG00000243709			6552	protein-coding gene	gene with protein product		603037	"""left-right determination, factor B"""	LEFTB		10053005, 10886363	Standard	NM_020997		Approved	LEFTYB	uc001hpo.3	O75610	OTTHUMG00000037443	ENST00000272134.5:c.893G>A	1.37:g.226074635C>T	ENSP00000272134:p.Arg298Gln	293.0	0.0	0		285.0	134.0	0.470175	NM_020997	B2R7U0|Q53H67|Q5TE94	Missense_Mutation	SNP	ENST00000272134.5	37	CCDS1548.1	124	0.056776556776556776	114	0.23170731707317074	10	0.027624309392265192	0	0.0	0	0.0	c	6.256	0.415350	0.11870	0.196729	0.001397	ENSG00000243709	ENST00000272134	D	0.83506	-1.73	4.0	-7.99	0.01131	Transforming growth factor-beta, C-terminal (3);	0.426594	0.27613	N	0.018587	T	0.00039	0.0001	N	0.11131	0.1	0.53688	P	2.6999999999999247E-5	B	0.02656	0.0	B	0.06405	0.002	T	0.23261	-1.0193	9	0.12430	T	0.62	.	3.7673	0.08627	0.2397:0.4502:0.0985:0.2116	.	298	O75610	LFTY1_HUMAN	Q	298	ENSP00000272134:R298Q	ENSP00000272134:R298Q	R	-	2	0	LEFTY1	224141258	0.810000	0.29049	0.721000	0.30653	0.735000	0.41995	-0.153000	0.10144	-2.307000	0.00653	-0.993000	0.02533	CGG	C|0.939;T|0.061	0.061	strong		0.642	LEFTY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091155.1	NM_020997	
RBPJL	11317	hgsc.bcm.edu	37	20	43945377	43945377	+	Missense_Mutation	SNP	C	C	A	rs35220957	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43945377C>A	ENST00000343694.3	+	12	1404	c.1332C>A	c.(1330-1332)agC>agA	p.S444R	RBPJL_ENST00000464504.1_3'UTR|RBPJL_ENST00000372741.3_Silent_p.R448R|RBPJL_ENST00000372743.1_Missense_Mutation_p.S443R	NM_001281448.1|NM_001281449.1|NM_014276.2	NP_001268377.1|NP_001268378.1|NP_055091.2	Q9UBG7	RBPJL_HUMAN	recombination signal binding protein for immunoglobulin kappa J region-like	444	IPT/TIG.				positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Myeloproliferative disorder(115;0.0122)				CCTTCTGCAGCGACTGGCGCT	0.701													C|||	73	0.0145767	0.0454	0.0072	5008	,	,		12791	0.0		0.004	False		,,,				2504	0.0041				p.S444R		Atlas-SNP	.											.	RBPJL	67	.	0			c.C1332A						PASS	.	C	ARG/SER	179,4221		1,177,2022	17.0	23.0	21.0		1332	-2.0	0.7	20	dbSNP_126	21	17,8571		0,17,4277	yes	missense	RBPJL	NM_014276.2	110	1,194,6299	AA,AC,CC		0.198,4.0682,1.5091	possibly-damaging	444/518	43945377	196,12792	2200	4294	6494	SO:0001583	missense	11317	exon12			CTGCAGCGACTGG	AB024964	CCDS13349.1, CCDS63283.1, CCDS63284.1	20q13.12	2013-10-18	2007-02-26	2007-02-26	ENSG00000124232	ENSG00000124232			13761	protein-coding gene	gene with protein product			"""recombining binding protein suppressor of hairless (Drosophila)-like"""	RBPSUHL		9929984	Standard	NM_014276		Approved	RBP-L, SUH, SUHL	uc002xns.3	Q9UBG7	OTTHUMG00000033055	ENST00000343694.3:c.1332C>A	20.37:g.43945377C>A	ENSP00000341243:p.Ser444Arg	45.0	0.0	0		39.0	25.0	0.641026	NM_014276	O95723|Q5QPU9|Q5QPV0|Q9ULV9	Missense_Mutation	SNP	ENST00000343694.3	37	CCDS13349.1	29	0.013278388278388278	22	0.044715447154471545	3	0.008287292817679558	0	0.0	4	0.005277044854881266	C	16.39	3.108689	0.56291	0.040682	0.00198	ENSG00000124232	ENST00000372743;ENST00000343694	T;T	0.17054	2.3;2.3	5.48	-2.02	0.07388	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.121014	0.56097	D	0.000034	T	0.02727	0.0082	L	0.42245	1.32	0.37489	D	0.916303	D	0.57257	0.979	P	0.48189	0.57	T	0.35101	-0.9802	10	0.19147	T	0.46	-19.8204	5.1298	0.14903	0.2229:0.4288:0.0:0.3483	rs35220957;rs59797878	444	Q9UBG7	RBPJL_HUMAN	R	443;444	ENSP00000361828:S443R;ENSP00000341243:S444R	ENSP00000341243:S444R	S	+	3	2	RBPJL	43378791	0.191000	0.23288	0.652000	0.29579	0.983000	0.72400	-0.568000	0.05909	-0.198000	0.10333	0.549000	0.68633	AGC	C|0.988;A|0.012	0.012	strong		0.701	RBPJL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080391.1	NM_014276	
ZNF213	7760	hgsc.bcm.edu	37	16	3190767	3190767	+	Missense_Mutation	SNP	G	G	A	rs143851164		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3190767G>A	ENST00000396878.3	+	6	1274	c.799G>A	c.(799-801)Gac>Aac	p.D267N	ZNF213_ENST00000574902.1_Missense_Mutation_p.D267N|ZNF213_ENST00000576416.1_Missense_Mutation_p.D267N|ZNF213_ENST00000416391.2_Missense_Mutation_p.D109N	NM_001134655.1|NM_004220.2	NP_001128127.1|NP_004211.1	O14771	ZN213_HUMAN	zinc finger protein 213	267	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	16						GACAGGCAGCGACGTGACTGT	0.692																																					p.D267N		Atlas-SNP	.											.	ZNF213	36	.	0			c.G799A						PASS	.	G	ASN/ASP,ASN/ASP	1,4387		0,1,2193	34.0	38.0	37.0		799,799	-0.4	0.0	16	dbSNP_134	37	0,8598		0,0,4299	no	missense,missense	ZNF213	NM_001134655.1,NM_004220.2	23,23	0,1,6492	AA,AG,GG		0.0,0.0228,0.0077	benign,benign	267/460,267/460	3190767	1,12985	2194	4299	6493	SO:0001583	missense	7760	exon6			GGCAGCGACGTGA	AF017433	CCDS10495.1	16p13.3	2014-05-13	2007-02-20	2007-02-20	ENSG00000085644	ENSG00000085644		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13005	protein-coding gene	gene with protein product		608387				9653642, 10023065	Standard	NM_004220		Approved	CR53, ZKSCAN21, ZSCAN53	uc010uws.2	O14771	OTTHUMG00000177519	ENST00000396878.3:c.799G>A	16.37:g.3190767G>A	ENSP00000380087:p.Asp267Asn	33.0	0.0	0		33.0	20.0	0.606061	NM_004220	A8K1B9|B4DMG6|Q96IS1	Missense_Mutation	SNP	ENST00000396878.3	37	CCDS10495.1	.	.	.	.	.	.	.	.	.	.	G	10.65	1.409959	0.25465	2.28E-4	0.0	ENSG00000085644	ENST00000396878;ENST00000416391	T;T	0.05319	3.46;3.46	4.23	-0.444	0.12245	Krueppel-associated box (1);	1.158390	0.06689	N	0.769413	T	0.03348	0.0097	N	0.08118	0	0.09310	N	1	B	0.13594	0.008	B	0.10450	0.005	T	0.44907	-0.9297	10	0.52906	T	0.07	.	3.1334	0.06431	0.099:0.3134:0.4223:0.1652	.	267	O14771	ZN213_HUMAN	N	267;109	ENSP00000380087:D267N;ENSP00000403892:D109N	ENSP00000380087:D267N	D	+	1	0	ZNF213	3130768	0.000000	0.05858	0.000000	0.03702	0.242000	0.25591	-0.566000	0.05922	-0.371000	0.08004	-1.048000	0.02349	GAC	G|1.000;A|0.000	0.000	weak		0.692	ZNF213-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437334.1	NM_004220	
BCL9L	283149	hgsc.bcm.edu	37	11	118773204	118773204	+	Silent	SNP	G	G	A	rs7119065	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:118773204G>A	ENST00000334801.3	-	6	2212	c.1248C>T	c.(1246-1248)gaC>gaT	p.D416D	BCL9L_ENST00000526143.1_5'UTR	NM_182557.2	NP_872363.1	Q86UU0	BCL9L_HUMAN	B-cell CLL/lymphoma 9-like	416	Necessary for interaction with CTNNB1. {ECO:0000250}.|Pro-rich.				canonical Wnt signaling pathway (GO:0060070)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell morphogenesis (GO:0022604)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	beta-catenin binding (GO:0008013)|transcription coactivator activity (GO:0003713)			NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(2)	56	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.66e-05)		GTCGCTCAATGTCTCGCAGCG	0.682													G|||	294	0.0587061	0.2156	0.0101	5008	,	,		12409	0.0		0.002	False		,,,				2504	0.0				p.D416D		Atlas-SNP	.											BCL9L_ENST00000392849,right_upper_lobe,carcinoma,-1,2	BCL9L	254	2	0			c.C1248T						PASS	.	G		615,3783		41,533,1625	27.0	30.0	29.0		1248	3.6	1.0	11	dbSNP_116	29	11,8575		0,11,4282	no	coding-synonymous	BCL9L	NM_182557.2		41,544,5907	AA,AG,GG		0.1281,13.9836,4.8213		416/1500	118773204	626,12358	2199	4293	6492	SO:0001819	synonymous_variant	283149	exon6			CTCAATGTCTCGC	AB094091	CCDS8403.1	11q23.3	2012-06-06				ENSG00000186174			23688	protein-coding gene	gene with protein product		609004				12964048	Standard	NM_182557		Approved	DLNB11	uc001pug.3	Q86UU0		ENST00000334801.3:c.1248C>T	11.37:g.118773204G>A		21.0	0.0	0		30.0	19.0	0.633333	NM_182557	A1A4C1|Q67FY1|Q6ZWJ0|Q6ZWK2	Silent	SNP	ENST00000334801.3	37	CCDS8403.1																																																																																			G|0.949;A|0.051	0.051	strong		0.682	BCL9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389653.1	NM_182557	
SSPO	23145	hgsc.bcm.edu	37	7	149481205	149481205	+	RNA	SNP	T	T	C	rs73727609	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149481205T>C	ENST00000378016.2	+	0	2687							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			AGTGCCACCATGAAGGAGTGC	0.652													T|||	76	0.0151757	0.056	0.0029	5008	,	,		17147	0.0		0.0	False		,,,				2504	0.0				p.M896T		Atlas-SNP	.											.	.	.	.	0			c.T2687C						PASS	.	T		157,3863		1,155,1854	14.0	18.0	17.0		2689	1.3	0.0	7	dbSNP_130	17	2,8280		0,2,4139	yes	coding-notMod3	SSPO	NM_198455.2		1,157,5993	CC,CT,TT		0.0241,3.9055,1.2925			149481205	159,12143	2010	4141	6151			23145	exon18			CCACCATGAAGGA	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149481205T>C		55.0	0.0	0		65.0	28.0	0.430769	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				T|0.986;C|0.014	0.014	strong		0.652	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
USP11	8237	hgsc.bcm.edu	37	X	47107038	47107038	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:47107038C>T	ENST00000218348.3	+	20	2694	c.2694C>T	c.(2692-2694)agC>agT	p.S898S	USP11_ENST00000377107.2_Silent_p.S855S	NM_004651.3	NP_004642.2	P51784	UBP11_HUMAN	ubiquitin specific peptidase 11	898	USP.				protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|ovary(3)|pancreas(1)|stomach(1)	40						ACAAGGACAGCGGCCAGTGGC	0.512																																					p.S898S		Atlas-SNP	.											.	USP11	93	.	0			c.C2694T						PASS	.						156.0	114.0	129.0					X																	47107038		2203	4300	6503	SO:0001819	synonymous_variant	8237	exon20			GGACAGCGGCCAG	U44839	CCDS14277.1	Xp11.23	2008-02-05	2005-08-08		ENSG00000102226	ENSG00000102226		"""Ubiquitin-specific peptidases"""	12609	protein-coding gene	gene with protein product		300050	"""ubiquitin specific protease 11"""			12838346	Standard	XM_005272674		Approved	UHX1	uc004dhp.3	P51784	OTTHUMG00000021437	ENST00000218348.3:c.2694C>T	X.37:g.47107038C>T		256.0	0.0	0		240.0	111.0	0.4625	NM_004651	B2RTX1|Q8IUG6|Q9BWE1	Silent	SNP	ENST00000218348.3	37	CCDS14277.1																																																																																			.	.	none		0.512	USP11-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_004651	
DSEL	92126	hgsc.bcm.edu	37	18	65180706	65180706	+	Silent	SNP	T	T	C	rs9959648	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:65180706T>C	ENST00000310045.7	-	2	2643	c.1170A>G	c.(1168-1170)caA>caG	p.Q390Q	CTD-2541J13.2_ENST00000581951.1_RNA|CTD-2541J13.2_ENST00000583493.1_RNA	NM_032160.2	NP_115536.1	Q8IZU8	DSEL_HUMAN	dermatan sulfate epimerase-like	380					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	isomerase activity (GO:0016853)|sulfotransferase activity (GO:0008146)			NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(25)|lung(23)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)				TACTCCACCTTTGGGCAGTTG	0.443													T|||	189	0.0377396	0.1362	0.013	5008	,	,		18891	0.0		0.0	False		,,,				2504	0.0				p.Q390Q		Atlas-SNP	.											.	DSEL	196	.	0			c.A1170G						PASS	.	T		566,3840	252.7+/-259.0	39,488,1676	117.0	104.0	108.0		1170	0.4	1.0	18	dbSNP_119	108	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	DSEL	NM_032160.2		39,491,5973	CC,CT,TT		0.0349,12.8461,4.3749		390/1223	65180706	569,12437	2203	4300	6503	SO:0001819	synonymous_variant	92126	exon2			CCACCTTTGGGCA	AF480435	CCDS11995.1	18q22.1	2007-01-29	2007-01-29	2007-01-29	ENSG00000171451	ENSG00000171451			18144	protein-coding gene	gene with protein product		611125	"""chromosome 18 open reading frame 4"""	C18orf4		16505484	Standard	NM_032160		Approved	NCAG1, FLJ11477	uc002lke.1	Q8IZU8	OTTHUMG00000132804	ENST00000310045.7:c.1170A>G	18.37:g.65180706T>C		67.0	0.0	0		68.0	68.0	1	NM_032160	Q17RH1|Q6P5Z3	Silent	SNP	ENST00000310045.7	37	CCDS11995.1																																																																																			T|0.949;C|0.051	0.051	strong		0.443	DSEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256221.1	NM_032160	
FASTKD1	79675	hgsc.bcm.edu	37	2	170413700	170413700	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170413700T>C	ENST00000453153.2	-	6	1425	c.1079A>G	c.(1078-1080)aAa>aGa	p.K360R	FASTKD1_ENST00000453929.2_Missense_Mutation_p.K360R	NM_024622.3	NP_078898.3	Q53R41	FAKD1_HUMAN	FAST kinase domains 1	360					cellular respiration (GO:0045333)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(5)|large_intestine(10)|lung(9)|ovary(4)|prostate(3)	37						AAGATACCTTTTAATCAGACA	0.378																																					p.K360R		Atlas-SNP	.											.	FASTKD1	86	.	0			c.A1079G						PASS	.						140.0	133.0	135.0					2																	170413700		2203	4300	6503	SO:0001583	missense	79675	exon6			TACCTTTTAATCA	AL832058	CCDS33318.1, CCDS63051.1	2q31.1	2008-02-05			ENSG00000138399	ENSG00000138399			26150	protein-coding gene	gene with protein product						11347906	Standard	NM_024622		Approved	FLJ21901	uc002uev.4	Q53R41	OTTHUMG00000154953	ENST00000453153.2:c.1079A>G	2.37:g.170413700T>C	ENSP00000400513:p.Lys360Arg	107.0	0.0	0		83.0	46.0	0.554217	NM_024622	Q8N583|Q8TEA9|Q96JM5|Q96N71|Q9H6T4	Missense_Mutation	SNP	ENST00000453153.2	37	CCDS33318.1	.	.	.	.	.	.	.	.	.	.	T	14.27	2.486556	0.44249	.	.	ENSG00000138399	ENST00000453153;ENST00000453929	T;T	0.18810	2.19;2.19	5.02	5.02	0.67125	.	0.200255	0.52532	D	0.000064	T	0.25901	0.0631	M	0.74881	2.28	0.33094	D	0.538328	P;B	0.48350	0.909;0.053	B;B	0.43623	0.425;0.039	T	0.42396	-0.9454	10	0.25751	T	0.34	.	10.0946	0.42466	0.0:0.0:0.1684:0.8316	.	360;360	Q53R41-2;Q53R41	.;FAKD1_HUMAN	R	360	ENSP00000400513:K360R;ENSP00000403229:K360R	ENSP00000400513:K360R	K	-	2	0	FASTKD1	170121946	1.000000	0.71417	1.000000	0.80357	0.848000	0.48234	3.291000	0.51764	2.006000	0.58801	0.533000	0.62120	AAA	.	.	none		0.378	FASTKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337788.2	NM_024622	
VWF	7450	hgsc.bcm.edu	37	12	6103072	6103072	+	Missense_Mutation	SNP	C	C	T	rs2229446	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:6103072C>T	ENST00000261405.5	-	37	6808	c.6554G>A	c.(6553-6555)cGg>cAg	p.R2185Q		NM_000552.3	NP_000543	P04275	VWF_HUMAN	von Willebrand factor	2185			R -> Q (in dbSNP:rs2229446).		blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|cell adhesion (GO:0007155)|cell-substrate adhesion (GO:0031589)|extracellular matrix organization (GO:0030198)|hemostasis (GO:0007599)|liver development (GO:0001889)|placenta development (GO:0001890)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein homooligomerization (GO:0051260)|response to wounding (GO:0009611)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule (GO:0031091)|platelet alpha granule lumen (GO:0031093)|proteinaceous extracellular matrix (GO:0005578)|Weibel-Palade body (GO:0033093)	chaperone binding (GO:0051087)|collagen binding (GO:0005518)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|immunoglobulin binding (GO:0019865)|integrin binding (GO:0005178)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|protein N-terminus binding (GO:0047485)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(41)|ovary(7)|pancreas(2)|prostate(6)|skin(15)|stomach(1)|upper_aerodigestive_tract(5)	129					Antihemophilic Factor(DB00025)	CCCGTTGGTCCGACAGAGGTG	0.552													C|||	342	0.0682907	0.2428	0.0245	5008	,	,		17441	0.0		0.002	False		,,,				2504	0.002				p.R2185Q		Atlas-SNP	.											VWF,rectum,carcinoma,-1,1	VWF	338	1	0			c.G6554A	GRCh37	CM070322	VWF	M	rs76342212	PASS	.	C	GLN/ARG	877,3529	337.0+/-304.7	89,699,1415	71.0	60.0	63.0		6554	5.3	1.0	12	dbSNP_131	63	13,8587	8.4+/-32.0	0,13,4287	yes	missense	VWF	NM_000552.3	43	89,712,5702	TT,TC,CC		0.1512,19.9047,6.843	probably-damaging	2185/2814	6103072	890,12116	2203	4300	6503	SO:0001583	missense	7450	exon37			TTGGTCCGACAGA		CCDS8539.1	12p13.3	2014-09-17			ENSG00000110799	ENSG00000110799		"""Endogenous ligands"""	12726	protein-coding gene	gene with protein product		613160		F8VWF		2251280	Standard	NM_000552		Approved		uc001qnn.1	P04275	OTTHUMG00000168265	ENST00000261405.5:c.6554G>A	12.37:g.6103072C>T	ENSP00000261405:p.Arg2185Gln	72.0	0.0	0		48.0	23.0	0.479167	NM_000552	Q8TCE8|Q99806	Missense_Mutation	SNP	ENST00000261405.5	37	CCDS8539.1	110	0.05036630036630037	102	0.2073170731707317	8	0.022099447513812154	0	0.0	0	0.0	C	22.3	4.275153	0.80580	0.199047	0.001512	ENSG00000110799	ENST00000261405	T	0.75367	-0.93	5.3	5.3	0.74995	Uncharacterised domain, cysteine-rich (2);	0.000000	0.40385	N	0.001115	T	0.00241	0.0007	L	0.43646	1.37	0.09310	P	1.0	D	0.89917	1.0	D	0.87578	0.998	T	0.01405	-1.1363	9	0.51188	T	0.08	.	17.9818	0.89144	0.0:1.0:0.0:0.0	rs2229446;rs11537643;rs52798162;rs11537643	2185	P04275	VWF_HUMAN	Q	2185	ENSP00000261405:R2185Q	ENSP00000261405:R2185Q	R	-	2	0	VWF	5973333	0.998000	0.40836	0.994000	0.49952	0.987000	0.75469	3.949000	0.56668	2.482000	0.83794	0.655000	0.94253	CGG	C|0.939;T|0.061	0.061	strong		0.552	VWF-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399020.1	NM_000552	
TNFAIP3	7128	hgsc.bcm.edu	37	6	138196066	138196066	+	Missense_Mutation	SNP	T	T	G	rs2230926	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:138196066T>G	ENST00000237289.4	+	3	446	c.380T>G	c.(379-381)tTc>tGc	p.F127C		NM_001270507.1|NM_001270508.1|NM_006290.3	NP_001257436.1|NP_001257437.1|NP_006281.1	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	127	OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.|TRAF-binding.		F -> C (in dbSNP:rs2230926). {ECO:0000269|Ref.3}.		apoptotic process (GO:0006915)|B-1 B cell homeostasis (GO:0001922)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of B cell activation (GO:0050869)|negative regulation of bone resorption (GO:0045779)|negative regulation of CD40 signaling pathway (GO:2000349)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of protein catabolic process (GO:0045732)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked deubiquitination (GO:0070536)|protein oligomerization (GO:0051259)|regulation of defense response to virus by host (GO:0050691)|regulation of germinal center formation (GO:0002634)|regulation of vascular wound healing (GO:0061043)|response to molecule of bacterial origin (GO:0002237)|tolerance induction to lipopolysaccharide (GO:0072573)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|protease binding (GO:0002020)|protein self-association (GO:0043621)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.0?(25)|p.L126fs*87(1)|p.W113_F140del(1)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(196)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	225	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		AAGGCGCTGTTCAGCACGCTC	0.498			"""D, N, F"""		"""marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"""								T|||	699	0.139577	0.4092	0.0778	5008	,	,		19066	0.0506		0.0239	False		,,,				2504	0.0297				p.F127C	GBM(130;153 1739 22295 28918 47987)	Atlas-SNP	.		Rec	yes		6	6q23	7128	"""tumor necrosis factor, alpha-induced protein 3"""		L	TNFAIP3,eye,lymphoid_neoplasm,0,1	TNFAIP3	340	1	27	Whole gene deletion(25)|Deletion - In frame(1)|Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(27)	c.T380G	GRCh37	CM083789	TNFAIP3	M	rs2230926	PASS	.	T	CYS/PHE	1570,2836	491.8+/-362.2	290,990,923	120.0	109.0	112.0	http://omim.org/entry/612378|http://www.ncbi.nlm.nih.gov/pubmed?term	380	-0.1	0.9	6	dbSNP_98	112	276,8324	103.6+/-164.7	10,256,4034	yes	missense	TNFAIP3	NM_006290.2	205	300,1246,4957	GG,GT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	3.2093,35.6332,14.1934	benign	127/791	138196066	1846,11160	2203	4300	6503	SO:0001583	missense	7128	exon3			CGCTGTTCAGCAC	M59465	CCDS5187.1	6q23-q25	2013-01-21			ENSG00000118503	ENSG00000118503		"""OTU domain containing"""	11896	protein-coding gene	gene with protein product		191163				2118515	Standard	NM_006290		Approved	A20, OTUD7C	uc031spw.1	P21580	OTTHUMG00000015664	ENST00000237289.4:c.380T>G	6.37:g.138196066T>G	ENSP00000237289:p.Phe127Cys	164.0	0.0	0		180.0	94.0	0.522222	NM_001270507	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Missense_Mutation	SNP	ENST00000237289.4	37	CCDS5187.1	270	0.12362637362637363	185	0.37601626016260165	27	0.07458563535911603	41	0.07167832167832168	17	0.022427440633245383	T	12.83	2.055887	0.36277	0.356332	0.032093	ENSG00000118503	ENST00000420009;ENST00000237289;ENST00000535574;ENST00000535332;ENST00000539356;ENST00000544646;ENST00000536070	T;T	0.30714	1.52;1.52	5.97	-0.0566	0.13805	Ovarian tumour, otubain (2);	0.318945	0.38897	N	0.001540	T	0.06554	0.0168	L	0.31926	0.97	0.29434	P	0.85964	B	0.13594	0.008	B	0.17722	0.019	T	0.23154	-1.0196	9	0.32370	T	0.25	-4.7828	3.4675	0.07555	0.2368:0.0676:0.1098:0.5858	rs2230926;rs5029942;rs52802446;rs61407535;rs2230926	127	P21580	TNAP3_HUMAN	C	127	ENSP00000401562:F127C;ENSP00000237289:F127C	ENSP00000237289:F127C	F	+	2	0	TNFAIP3	138237759	1.000000	0.71417	0.922000	0.36590	0.934000	0.57294	1.341000	0.33907	0.125000	0.18397	0.533000	0.62120	TTC	T|0.857;G|0.143	0.143	strong		0.498	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1		
PCDH12	51294	hgsc.bcm.edu	37	5	141336858	141336858	+	Missense_Mutation	SNP	C	C	T	rs140883612	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:141336858C>T	ENST00000231484.3	-	1	1769	c.559G>A	c.(559-561)Ggc>Agc	p.G187S	PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	187	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCATCAGGGCCCACAATGACA	0.507													C|||	42	0.00838658	0.0303	0.0029	5008	,	,		19922	0.0		0.0	False		,,,				2504	0.0				p.G187S		Atlas-SNP	.											.	PCDH12	133	.	0			c.G559A						PASS	.	C	SER/GLY	104,4302	81.4+/-119.9	0,104,2099	102.0	111.0	108.0		559	5.0	1.0	5	dbSNP_134	108	0,8600		0,0,4300	yes	missense	PCDH12	NM_016580.2	56	0,104,6399	TT,TC,CC		0.0,2.3604,0.7996	probably-damaging	187/1185	141336858	104,12902	2203	4300	6503	SO:0001583	missense	51294	exon1			CAGGGCCCACAAT	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"""Cadherins / Protocadherins : Non-clustered"""	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.559G>A	5.37:g.141336858C>T	ENSP00000231484:p.Gly187Ser	220.0	0.0	0		225.0	106.0	0.471111	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	37	CCDS4269.1	15	0.006868131868131868	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	0	0.0	C	10.27	1.304137	0.23736	0.023604	0.0	ENSG00000113555	ENST00000231484	T	0.19669	2.13	4.98	4.98	0.66077	Cadherin (4);Cadherin-like (1);	0.127172	0.52532	D	0.000076	T	0.10294	0.0252	L	0.39898	1.24	0.35472	D	0.797432	D	0.62365	0.991	P	0.60541	0.876	T	0.06058	-1.0848	10	0.13108	T	0.6	.	9.2129	0.37328	0.0:0.9043:0.0:0.0957	.	187	Q9NPG4	PCD12_HUMAN	S	187	ENSP00000231484:G187S	ENSP00000231484:G187S	G	-	1	0	PCDH12	141317042	0.001000	0.12720	1.000000	0.80357	0.554000	0.35429	0.429000	0.21412	2.605000	0.88082	0.655000	0.94253	GGC	C|0.991;T|0.009	0.009	strong		0.507	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580	
CBLC	23624	hgsc.bcm.edu	37	19	45285734	45285734	+	Silent	SNP	G	G	A	rs10416628	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45285734G>A	ENST00000270279.3	+	4	828	c.765G>A	c.(763-765)agG>agA	p.R255R	CBLC_ENST00000341505.4_Silent_p.R255R	NM_012116.3	NP_036248.3	Q9ULV8	CBLC_HUMAN	Cbl proto-oncogene C, E3 ubiquitin protein ligase	255	Cbl-PTB. {ECO:0000255|PROSITE- ProRule:PRU00839}.|SH2-like.				cell surface receptor signaling pathway (GO:0007166)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of epidermal growth factor-activated receptor activity (GO:0007175)|negative regulation of MAP kinase activity (GO:0043407)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|ligase activity (GO:0016874)|phosphotyrosine binding (GO:0001784)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|kidney(1)|lung(6)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	Lung NSC(12;0.00136)|all_lung(12;0.00371)	Ovarian(192;0.231)				AGGCCTGCAGGGACAAGCCAG	0.612			M		AML								G|||	144	0.028754	0.1021	0.013	5008	,	,		17150	0.0		0.0	False		,,,				2504	0.0				p.R255R		Atlas-SNP	.		Rec	yes		19	19q13.2	23624	Cas-Br-M (murine) ecotropic retroviral transforming sequence c		L	.	CBLC	41	.	0			c.G765A						PASS	.	G	,	407,3999		15,377,1811	62.0	57.0	59.0		765,765	-2.1	1.0	19	dbSNP_119	59	4,8596		0,4,4296	no	coding-synonymous,coding-synonymous	CBLC	NM_001130852.1,NM_012116.3	,	15,381,6107	AA,AG,GG		0.0465,9.2374,3.1601	,	255/429,255/475	45285734	411,12595	2203	4300	6503	SO:0001819	synonymous_variant	23624	exon4			CTGCAGGGACAAG	AB028645	CCDS12643.1, CCDS46109.1	19q13.2	2013-07-09	2013-07-09		ENSG00000142273	ENSG00000142273		"""RING-type (C3HC4) zinc fingers"""	15961	protein-coding gene	gene with protein product		608453	"""Cas-Br-M (murine) ectropic retroviral transforming sequence c"", ""Cas-Br-M (murine) ecotropic retroviral transforming sequence c"""			10362357, 10571044	Standard	NM_012116		Approved	CBL-3, CBL-SL, RNF57	uc002ozs.3	Q9ULV8	OTTHUMG00000150715	ENST00000270279.3:c.765G>A	19.37:g.45285734G>A		118.0	0.0	0		119.0	62.0	0.521008	NM_001130852	Q8N1E5|Q9Y5Z2|Q9Y5Z3	Silent	SNP	ENST00000270279.3	37	CCDS12643.1																																																																																			G|0.958;A|0.042	0.042	strong		0.612	CBLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319732.2	NM_012116	
BRD7	29117	hgsc.bcm.edu	37	16	50368626	50368626	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:50368626T>C	ENST00000394688.3	-	7	1042	c.883A>G	c.(883-885)Aaa>Gaa	p.K295E	BRD7_ENST00000394689.2_Missense_Mutation_p.K295E			Q9NPI1	BRD7_HUMAN	bromodomain containing 7	295					cell cycle (GO:0007049)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone acetylation (GO:0035066)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(4)|lung(7)|prostate(2)|urinary_tract(2)	22		all_cancers(37;0.0127)				TTTTACTTTTTATTTTCTTTG	0.488																																					p.K295E		Atlas-SNP	.											.	BRD7	61	.	0			c.A883G						PASS	.						95.0	110.0	105.0					16																	50368626		2192	4296	6488	SO:0001583	missense	29117	exon7			ACTTTTTATTTTC	AF213969	CCDS10742.1, CCDS54007.1	16q12.1	2008-11-18	2002-01-14		ENSG00000166164	ENSG00000166164			14310	protein-coding gene	gene with protein product			"""bromodomain-containing 7"""			10526152, 18809673	Standard	NM_013263		Approved	CELTIX1, BP75	uc002ege.2	Q9NPI1	OTTHUMG00000133170	ENST00000394688.3:c.883A>G	16.37:g.50368626T>C	ENSP00000378180:p.Lys295Glu	71.0	0.0	0		84.0	8.0	0.0952381	NM_013263	Q4VC09|Q8N2L9|Q96KA4|Q9BV48|Q9UH59	Missense_Mutation	SNP	ENST00000394688.3	37	CCDS10742.1	.	.	.	.	.	.	.	.	.	.	T	12.84	2.058696	0.36277	.	.	ENSG00000166164	ENST00000394688;ENST00000394689	T;T	0.52754	0.65;0.65	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.49321	0.1550	M	0.67953	2.075	0.47374	D	0.999409	B;B	0.27910	0.193;0.161	B;B	0.31442	0.13;0.079	T	0.45891	-0.9230	10	0.34782	T	0.22	.	14.6369	0.68696	0.0:0.0:0.0:1.0	.	295;295	Q9NPI1;Q9NPI1-2	BRD7_HUMAN;.	E	295	ENSP00000378180:K295E;ENSP00000378181:K295E	ENSP00000378180:K295E	K	-	1	0	BRD7	48926127	1.000000	0.71417	0.995000	0.50966	0.266000	0.26442	4.022000	0.57203	2.254000	0.74563	0.528000	0.53228	AAA	.	.	none		0.488	BRD7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000256874.3	NM_013263	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39253931	39253931	+	Missense_Mutation	SNP	G	G	A	rs150613353	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39253931G>A	ENST00000333822.4	-	1	462	c.406C>T	c.(406-408)Cgc>Tgc	p.R136C		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	136	25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						caagaggggcggcagcagctg	0.662													G|||	232	0.0463259	0.1664	0.0159	5008	,	,		14984	0.0		0.001	False		,,,				2504	0.0				p.R136C		Atlas-SNP	.											.	KRTAP4-8	57	.	0			c.C406T						PASS	.						6.0	8.0	8.0					17																	39253931		682	1556	2238	SO:0001583	missense	728224	exon1			AGGGGCGGCAGCA	AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"""Keratin associated proteins"""	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.406C>T	17.37:g.39253931G>A	ENSP00000328444:p.Arg136Cys	84.0	0.0	0		123.0	54.0	0.439024	NM_031960	A8MSH3	Missense_Mutation	SNP	ENST00000333822.4	37	CCDS45674.1	75	0.034340659340659344	69	0.1402439024390244	6	0.016574585635359115	0	0.0	0	0.0	.	12.52	1.962330	0.34659	.	.	ENSG00000204880	ENST00000333822	T	0.01484	4.84	3.73	3.73	0.42828	.	1.159130	0.06715	U	0.773946	T	0.00039	0.0001	M	0.75447	2.3	0.32957	P	0.47942799999999997	B	0.29936	0.262	B	0.19666	0.026	T	0.33701	-0.9858	9	0.66056	D	0.02	.	7.5536	0.27812	0.1225:0.0:0.8775:0.0	.	136	Q9BYQ9	KRA48_HUMAN	C	136	ENSP00000328444:R136C	ENSP00000328444:R136C	R	-	1	0	KRTAP4-8	36507457	0.000000	0.05858	0.820000	0.32676	0.259000	0.26198	-1.031000	0.03578	1.794000	0.52575	0.449000	0.29647	CGC	G|0.966;A|0.034	0.034	strong		0.662	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
ERN2	10595	hgsc.bcm.edu	37	16	23721865	23721865	+	Missense_Mutation	SNP	C	C	T	rs9932495	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:23721865C>T	ENST00000457008.2	-	3	243	c.205G>A	c.(205-207)Gtc>Atc	p.V69I	CTD-2385L22.1_ENST00000563611.1_RNA|ERN2_ENST00000256797.4_Missense_Mutation_p.V117I					endoplasmic reticulum to nucleus signaling 2											large_intestine(2)|lung(2)|ovary(2)	6				GBM - Glioblastoma multiforme(48;0.0156)		CCTTCGATGACGGGATCTGCA	0.507													C|||	104	0.0207668	0.0756	0.0014	5008	,	,		21483	0.0		0.001	False		,,,				2504	0.002				p.V117I		Atlas-SNP	.											.	ERN2	131	.	0			c.G349A						PASS	.	C	ILE/VAL	242,4152	141.1+/-176.5	7,228,1962	206.0	200.0	202.0		349	-3.1	0.4	16	dbSNP_119	202	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ERN2	NM_033266.3	29	7,229,6261	TT,TC,CC		0.0116,5.5075,1.8701	benign	117/975	23721865	243,12751	2197	4300	6497	SO:0001583	missense	10595	exon3			CGATGACGGGATC	AA527544	CCDS32407.1	16p12.2	2008-02-05	2007-08-14			ENSG00000134398			16942	protein-coding gene	gene with protein product		604034	"""ER to nucleus signalling 2"""			9755171, 11175748	Standard	NM_033266		Approved	IRE1b	uc002dma.4	Q76MJ5		ENST00000457008.2:c.205G>A	16.37:g.23721865C>T	ENSP00000413812:p.Val69Ile	156.0	0.0	0		99.0	51.0	0.515152	NM_033266		Missense_Mutation	SNP	ENST00000457008.2	37		31	0.014194139194139194	30	0.06097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	C	5.726	0.318420	0.10845	0.055075	1.16E-4	ENSG00000134398	ENST00000256797;ENST00000457008	T;T	0.21361	2.01;2.01	4.91	-3.07	0.05363	.	0.439897	0.27147	N	0.020713	T	0.00724	0.0024	N	0.05574	-0.02	0.25356	N	0.988828	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.28073	-1.0055	10	0.19147	T	0.46	.	6.6045	0.22718	0.0:0.4318:0.2707:0.2975	rs9932495;rs52791098;rs9932495	69;69	E7ETG2;A5YM65	.;.	I	117;69	ENSP00000256797:V117I;ENSP00000413812:V69I	ENSP00000256797:V117I	V	-	1	0	ERN2	23629366	0.991000	0.36638	0.383000	0.26132	0.543000	0.35085	0.246000	0.18160	-0.855000	0.04125	-0.379000	0.06801	GTC	C|0.981;T|0.019	0.019	strong		0.507	ERN2-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000434886.1		
GPATCH1	55094	hgsc.bcm.edu	37	19	33587298	33587298	+	Silent	SNP	C	C	T	rs114017497	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33587298C>T	ENST00000170564.2	+	7	1112	c.798C>T	c.(796-798)ggC>ggT	p.G266G		NM_018025.2	NP_060495.2	Q9BRR8	GPTC1_HUMAN	G patch domain containing 1	266					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)	nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(15)|prostate(4)|skin(4)	40	Esophageal squamous(110;0.137)					AGAGAGCTGGCGATCTTGGAG	0.413													C|||	37	0.00738818	0.0257	0.0043	5008	,	,		16637	0.0		0.0	False		,,,				2504	0.0				p.G266G	Pancreas(67;88 1713 4567 18227)	Atlas-SNP	.											.	GPATCH1	79	.	0			c.C798T						PASS	.	C		114,4292	87.3+/-125.9	4,106,2093	75.0	78.0	77.0		798	2.0	0.0	19	dbSNP_132	77	0,8600		0,0,4300	no	coding-synonymous	GPATCH1	NM_018025.2		4,106,6393	TT,TC,CC		0.0,2.5874,0.8765		266/932	33587298	114,12892	2203	4300	6503	SO:0001819	synonymous_variant	55094	exon7			AGCTGGCGATCTT	AF434677	CCDS12428.1	19q13.12	2013-01-28		2006-12-13		ENSG00000076650		"""G patch domain containing"""	24658	protein-coding gene	gene with protein product	"""evolutionarily conserved G patch domain containing"""			GPATC1		12477932	Standard	NM_018025		Approved	ECGP, FLJ10206, FLJ38686	uc002nug.1	Q9BRR8		ENST00000170564.2:c.798C>T	19.37:g.33587298C>T		167.0	0.0	0		152.0	73.0	0.480263	NM_018025	Q8IZV6|Q8N3B7|Q9NW94	Silent	SNP	ENST00000170564.2	37	CCDS12428.1																																																																																			C|0.991;T|0.009	0.009	strong		0.413	GPATCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450834.1	NM_018025	
RYR3	6263	hgsc.bcm.edu	37	15	34111969	34111969	+	Silent	SNP	C	C	T	rs58745096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:34111969C>T	ENST00000389232.4	+	77	10789	c.10719C>T	c.(10717-10719)gaC>gaT	p.D3573D	RYR3_ENST00000415757.3_Silent_p.D3568D	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	3573					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		AATTGGAAGACGACCCTTTGT	0.338													C|||	91	0.0181709	0.0666	0.0029	5008	,	,		14784	0.0		0.001	False		,,,				2504	0.0				p.D3573D		Atlas-SNP	.											RYR3,NS,carcinoma,0,1	RYR3	760	1	0			c.C10719T						PASS	.	C		163,3477		5,153,1662	318.0	297.0	303.0		10719	-6.1	0.9	15	dbSNP_129	303	2,8170		0,2,4084	no	coding-synonymous	RYR3	NM_001036.3		5,155,5746	TT,TC,CC		0.0245,4.478,1.3969		3573/4871	34111969	165,11647	1820	4086	5906	SO:0001819	synonymous_variant	6263	exon77			GGAAGACGACCCT		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.10719C>T	15.37:g.34111969C>T		168.0	0.0	0		174.0	87.0	0.5	NM_001036	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			C|0.984;T|0.016	0.016	strong		0.338	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
KRTAP19-6	337973	hgsc.bcm.edu	37	21	31914013	31914013	+	Missense_Mutation	SNP	G	G	A	rs115563631	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31914013G>A	ENST00000334046.5	-	1	170	c.140C>T	c.(139-141)tCa>tTa	p.S47L		NM_181612.2	NP_853643.1	Q3LI70	KR196_HUMAN	keratin associated protein 19-6	47						intermediate filament (GO:0005882)				breast(1)|large_intestine(2)|lung(5)|upper_aerodigestive_tract(1)	9						TTCACGGCATGATGGGCGGCA	0.507													g|||	55	0.0109824	0.0401	0.0029	5008	,	,		15048	0.0		0.0	False		,,,				2504	0.0				p.S47L		Atlas-SNP	.											.	KRTAP19-6	16	.	0			c.C140T						PASS	.	G	LEU/SER	161,4245	109.1+/-147.4	2,157,2044	110.0	120.0	117.0		140	2.1	0.0	21	dbSNP_132	117	3,8597	3.7+/-12.6	0,3,4297	yes	missense	KRTAP19-6	NM_181612.2	145	2,160,6341	AA,AG,GG		0.0349,3.6541,1.261	possibly-damaging	47/59	31914013	164,12842	2203	4300	6503	SO:0001583	missense	337973	exon1			CGGCATGATGGGC	AP001708	CCDS13598.1	21q22.1	2010-09-30			ENSG00000186925	ENSG00000186925		"""Keratin associated proteins"""	18941	protein-coding gene	gene with protein product						12359730	Standard	NM_181612		Approved	KAP19.6	uc002yok.1	Q3LI70	OTTHUMG00000057779	ENST00000334046.5:c.140C>T	21.37:g.31914013G>A	ENSP00000375107:p.Ser47Leu	94.0	0.0	0		94.0	42.0	0.446809	NM_181612	Q3LI71	Missense_Mutation	SNP	ENST00000334046.5	37	CCDS13598.1	17	0.007783882783882784	15	0.03048780487804878	2	0.0055248618784530384	0	0.0	0	0.0	g	7.582	0.668877	0.14776	0.036541	3.49E-4	ENSG00000186925	ENST00000334046;ENST00000437381	T	0.10005	2.92	3.96	2.1	0.27182	.	2.101130	0.03499	N	0.217738	T	0.02380	0.0073	.	.	.	0.09310	N	1	P	0.36616	0.561	B	0.36504	0.226	T	0.30179	-0.9987	9	0.87932	D	0	.	6.6627	0.23022	0.2276:0.0:0.7724:0.0	.	47	Q3LI70	KR196_HUMAN	L	47	ENSP00000375107:S47L	ENSP00000375107:S47L	S	-	2	0	KRTAP19-6	30835884	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-0.310000	0.08135	0.272000	0.22027	0.597000	0.82753	TCA	G|0.985;A|0.015	0.015	strong		0.507	KRTAP19-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128231.4		
DOCK7	85440	hgsc.bcm.edu	37	1	63119442	63119442	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:63119442C>T	ENST00000340370.5	-	4	360	c.343G>A	c.(343-345)Gac>Aac	p.D115N	DOCK7_ENST00000404627.2_Missense_Mutation_p.D115N|DOCK7_ENST00000251157.5_Missense_Mutation_p.D115N	NM_033407.2	NP_212132.2	Q96N67	DOCK7_HUMAN	dedicator of cytokinesis 7	115					activation of Rac GTPase activity (GO:0032863)|axonogenesis (GO:0007409)|establishment of neuroblast polarity (GO:0045200)|hematopoietic progenitor cell differentiation (GO:0002244)|interkinetic nuclear migration (GO:0022027)|microtubule cytoskeleton organization (GO:0000226)|neuron projection development (GO:0031175)|pigmentation (GO:0043473)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of neurogenesis (GO:0050767)|small GTPase mediated signal transduction (GO:0007264)	axon (GO:0030424)|basal part of cell (GO:0045178)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|neuron projection (GO:0043005)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rac GTPase binding (GO:0048365)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(19)|lung(42)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	92						CTTATACAGTCTCTAACATGT	0.303																																					p.D115N		Atlas-SNP	.											.	DOCK7	184	.	0			c.G343A						PASS	.						61.0	62.0	62.0					1																	63119442		2203	4297	6500	SO:0001583	missense	85440	exon4			TACAGTCTCTAAC		CCDS30734.1, CCDS60156.1, CCDS60157.1	1p32.1	2008-02-05			ENSG00000116641	ENSG00000116641			19190	protein-coding gene	gene with protein product		615730				12432077	Standard	NM_033407		Approved	KIAA1771, ZIR2	uc001daq.4	Q96N67	OTTHUMG00000013131	ENST00000340370.5:c.343G>A	1.37:g.63119442C>T	ENSP00000340742:p.Asp115Asn	129.0	0.0	0		149.0	45.0	0.302013	NM_001271999	Q00M63|Q2PPY7|Q45RE8|Q45RE9|Q5T1B9|Q5T1C0|Q6ZV32|Q8TB82|Q96NG6|Q96NI0|Q9C092	Missense_Mutation	SNP	ENST00000340370.5	37	CCDS30734.1	.	.	.	.	.	.	.	.	.	.	C	34	5.339631	0.95783	.	.	ENSG00000116641	ENST00000371140;ENST00000251157;ENST00000340370;ENST00000404627	T;T;T	0.49720	0.77;0.77;0.77	5.19	5.19	0.71726	.	0.000000	0.85682	D	0.000000	T	0.64193	0.2576	M	0.78049	2.395	0.80722	D	1	D;D;P;P;D	0.65815	0.992;0.995;0.923;0.923;0.993	D;D;P;P;D	0.66979	0.925;0.948;0.772;0.772;0.913	T	0.64330	-0.6433	10	0.48119	T	0.1	.	18.898	0.92432	0.0:1.0:0.0:0.0	.	115;115;115;115;115	Q96NI0;Q96N67-2;Q96N67-5;Q96N67-4;Q96N67-3	.;.;.;.;.	N	115	ENSP00000251157:D115N;ENSP00000340742:D115N;ENSP00000384446:D115N	ENSP00000251157:D115N	D	-	1	0	DOCK7	62892030	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.651000	0.83577	2.699000	0.92147	0.655000	0.94253	GAC	.	.	none		0.303	DOCK7-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036806.1	NM_033407	
TRRAP	8295	hgsc.bcm.edu	37	7	98558922	98558922	+	Silent	SNP	G	G	A	rs34983214	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:98558922G>A	ENST00000359863.4	+	45	6716	c.6507G>A	c.(6505-6507)acG>acA	p.T2169T	TRRAP_ENST00000355540.3_Silent_p.T2151T|TRRAP_ENST00000446306.3_Silent_p.T2150T	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	2169	Interaction with TP53.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			ATATCTGCACGGGCCTAGAAG	0.507													G|||	32	0.00638978	0.0219	0.0029	5008	,	,		14881	0.0		0.001	False		,,,				2504	0.0				p.T2169T		Atlas-SNP	.											.	TRRAP	863	.	0			c.G6507A						PASS	.	G		78,4328	68.1+/-105.8	0,78,2125	162.0	161.0	162.0		6453	-10.9	0.0	7	dbSNP_126	162	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TRRAP	NM_003496.3		0,80,6423	AA,AG,GG		0.0233,1.7703,0.6151		2151/3831	98558922	80,12926	2203	4300	6503	SO:0001819	synonymous_variant	8295	exon45			CTGCACGGGCCTA	AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.6507G>A	7.37:g.98558922G>A		81.0	0.0	0		94.0	46.0	0.489362	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Silent	SNP	ENST00000359863.4	37	CCDS59066.1	18	0.008241758241758242	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	7.407	0.633881	0.14322	0.017703	2.33E-4	ENSG00000196367	ENST00000456197	.	.	.	5.47	-10.9	0.00192	.	.	.	.	.	T	0.12860	0.0312	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37842	-0.9688	4	.	.	.	.	1.7278	0.02925	0.4473:0.1858:0.2241:0.1428	rs34983214	.	.	.	Q	1891	.	.	R	+	2	0	TRRAP	98396858	0.000000	0.05858	0.019000	0.16419	0.892000	0.51952	-2.537000	0.00939	-2.796000	0.00354	-0.136000	0.14681	CGG	G|0.993;A|0.007	0.007	strong		0.507	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496	
GFRA4	64096	hgsc.bcm.edu	37	20	3640568	3640568	+	Silent	SNP	C	C	T	rs74740423	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:3640568C>T	ENST00000319242.3	-	5	887	c.888G>A	c.(886-888)ccG>ccA	p.P296P	GFRA4_ENST00000290417.2_Silent_p.P266P			Q9GZZ7	GFRA4_HUMAN	GDNF family receptor alpha 4	296					negative regulation of ossification (GO:0030279)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	glial cell-derived neurotrophic factor receptor activity (GO:0016167)			large_intestine(1)|lung(2)	3						AGAGCAGGGCCGGGAGAGCCA	0.647													C|||	147	0.029353	0.1051	0.0115	5008	,	,		18655	0.0		0.0	False		,,,				2504	0.0				p.P296P		Atlas-SNP	.											.	GFRA4	10	.	0			c.G888A						PASS	.	C	,	405,3999		13,379,1810	29.0	30.0	29.0		798,888	2.8	0.3	20	dbSNP_131	29	3,8589		0,3,4293	no	coding-synonymous,coding-synonymous	GFRA4	NM_022139.3,NM_145762.2	,	13,382,6103	TT,TC,CC		0.0349,9.1962,3.1394	,	266/270,296/300	3640568	408,12588	2202	4296	6498	SO:0001819	synonymous_variant	64096	exon5			CAGGGCCGGGAGA	AF253318	CCDS13055.1, CCDS13056.1	20p13-p12	2008-07-16			ENSG00000125861	ENSG00000125861			13821	protein-coding gene	gene with protein product	"""persephin receptor"""					10958791, 15225646	Standard	XM_005260793		Approved		uc002win.3	Q9GZZ7	OTTHUMG00000031748	ENST00000319242.3:c.888G>A	20.37:g.3640568C>T		37.0	0.0	0		41.0	23.0	0.560976	NM_145762	Q5JT74|Q9H191|Q9H192	Silent	SNP	ENST00000319242.3	37	CCDS13056.1																																																																																			C|0.968;T|0.032	0.032	strong		0.647	GFRA4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077744.1	NM_145762	
ACOT1	641371	hgsc.bcm.edu	37	14	74009937	74009937	+	Missense_Mutation	SNP	A	A	G	rs377598014		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:74009937A>G	ENST00000311148.4	+	3	1152	c.844A>G	c.(844-846)Atc>Gtc	p.I282V	HEATR4_ENST00000553558.1_Intron|HEATR4_ENST00000560393.1_Intron|HEATR4_ENST00000334988.2_Intron|ACOT1_ENST00000557556.1_Missense_Mutation_p.I256V	NM_001037161.1	NP_001032238.1	Q86TX2	ACOT1_HUMAN	acyl-CoA thioesterase 1	282					acyl-CoA metabolic process (GO:0006637)|long-chain fatty acid metabolic process (GO:0001676)|very long-chain fatty acid metabolic process (GO:0000038)	cytosol (GO:0005829)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)			endometrium(1)|large_intestine(1)|lung(2)	4				OV - Ovarian serous cystadenocarcinoma(108;1.37e-45)|BRCA - Breast invasive adenocarcinoma(234;0.0033)		CAGAAATCGCATCAAGGTGAC	0.552																																					p.I282V		Atlas-SNP	.											.	ACOT1	12	.	0			c.A844G						PASS	.	A	VAL/ILE,,	1,4395		0,1,2197	84.0	65.0	72.0		844,,	-4.8	0.0	14		72	0,8584		0,0,4292	no	missense,intron,intron	HEATR4,ACOT1	NM_001037161.1,NM_001220484.1,NM_203309.2	29,,	0,1,6489	GG,GA,AA		0.0,0.0227,0.0077	,,	282/422,,	74009937	1,12979	2198	4292	6490	SO:0001583	missense	641371	exon3			AATCGCATCAAGG	DQ082754	CCDS32117.1	14q24.3	2013-09-20			ENSG00000184227	ENSG00000184227		"""Acyl CoA thioesterases"""	33128	protein-coding gene	gene with protein product		614313				16103133, 16940157	Standard	NM_001037161		Approved	ACH2, CTE-1, LACH2		Q86TX2	OTTHUMG00000171607	ENST00000311148.4:c.844A>G	14.37:g.74009937A>G	ENSP00000311224:p.Ile282Val	659.0	0.0	0		906.0	319.0	0.352097	NM_001037161	A1L173|Q3I5F9	Missense_Mutation	SNP	ENST00000311148.4	37	CCDS32117.1	.	.	.	.	.	.	.	.	.	.	-	7.679	0.688575	0.14973	2.27E-4	0.0	ENSG00000184227	ENST00000311148;ENST00000557556	T;T	0.28895	1.59;1.59	4.06	-4.76	0.03229	BAAT/Acyl-CoA thioester hydrolase C-terminal (1);	0.642575	0.16665	N	0.204604	T	0.14830	0.0358	N	0.25789	0.76	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35375	-0.9791	10	0.11794	T	0.64	-8.1147	9.7986	0.40751	0.127:0.2638:0.6092:0.0	.	282	Q86TX2	ACOT1_HUMAN	V	282;256	ENSP00000311224:I282V;ENSP00000451764:I256V	ENSP00000311224:I282V	I	+	1	0	ACOT1	73079690	0.000000	0.05858	0.014000	0.15608	0.043000	0.13939	-2.813000	0.00753	-0.728000	0.04882	0.324000	0.21423	ATC	.	.	weak		0.552	ACOT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414432.1	NM_001037161	
BTNL2	56244	hgsc.bcm.edu	37	6	32370859	32370859	+	Missense_Mutation	SNP	C	C	T	rs9461742	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32370859C>T	ENST00000374993.1	-	3	561	c.562G>A	c.(562-564)Gtg>Atg	p.V188M	BTNL2_ENST00000374995.3_Splice_Site_p.V148I|BTNL2_ENST00000454136.3_Missense_Mutation_p.V188M|BTNL2_ENST00000540315.1_Intron|BTNL2_ENST00000414363.1_Intron|BTNL2_ENST00000429232.2_Intron|BTNL2_ENST00000544175.1_Intron	NM_019602.1	NP_062548.1	Q9UIR0	BTNL2_HUMAN	butyrophilin-like 2 (MHC class II associated)	188	Ig-like V-type 2.		V -> M (in dbSNP:rs9461742).			integral component of membrane (GO:0016021)				central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|prostate(1)|urinary_tract(1)	19						TGCTCAGACACGGCCAGCAGC	0.587													C|||	29	0.00579073	0.0182	0.0058	5008	,	,		19224	0.0		0.0	False		,,,				2504	0.001				p.V188M		Atlas-SNP	.											.	BTNL2	50	.	0			c.G562A						PASS	.	C	MET/VAL	39,2983		0,39,1472	85.0	79.0	81.0		562	-8.9	0.0	6	dbSNP_119	81	4,5412		0,4,2704	no	missense	BTNL2	NM_019602.1	21	0,43,4176	TT,TC,CC		0.0739,1.2905,0.5096	probably-damaging	188/456	32370859	43,8395	1511	2708	4219	SO:0001583	missense	56244	exon3			CAGACACGGCCAG	AF186588		6p21.3	2014-01-14			ENSG00000204290	ENSG00000204290		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1142	protein-coding gene	gene with protein product		606000				10803852, 15735647	Standard	XM_006726138		Approved	HSBLMHC1, BTL-II, BTN7	uc003obg.1	Q9UIR0	OTTHUMG00000031102	ENST00000374993.1:c.562G>A	6.37:g.32370859C>T	ENSP00000364132:p.Val188Met	168.0	0.0	0		194.0	92.0	0.474227	NM_019602	A0PJV5|B0UYW9|B0V0N6|O98261|Q08E96|Q58R22|Q58R23|Q5JYF9|Q5MP42|Q5MP43|Q5RIF8|Q5SP08|Q5SP09|Q5SRW3|Q5SRW4|Q5SU36|Q95HK0	Missense_Mutation	SNP	ENST00000374993.1	37		14|14	0.00641025641025641|0.00641025641025641	12|12	0.024390243902439025|0.024390243902439025	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	C|C	8.531|8.531	0.871030|0.871030	0.17322|0.17322	0.012905|0.012905	7.39E-4|7.39E-4	ENSG00000204290|ENSG00000204290	ENST00000374995|ENST00000468270;ENST00000374993	T|T	0.02177|0.75704	4.41|-0.96	4.44|4.44	-8.89|-8.89	0.00785|0.00785	.|CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	2.023030|2.023030	0.02292|0.02292	N|N	0.070382|0.070382	T|T	0.43787|0.43787	0.1263|0.1263	L|L	0.50333|0.50333	1.59|1.59	0.09310|0.09310	N|N	1|1	.|P	.|0.50156	.|0.932	.|P	.|0.45232	.|0.474	T|T	0.61926|0.61926	-0.6962|-0.6962	8|10	0.27785|0.35671	T|T	0.31|0.21	.|.	3.5087|3.5087	0.07700|0.07700	0.2462:0.1048:0.4451:0.2038|0.2462:0.1048:0.4451:0.2038	rs9461742;rs9461742|rs9461742;rs9461742	.|188	.|Q9UIR0	.|BTNL2_HUMAN	I|M	148|188	ENSP00000364134:V148I|ENSP00000364132:V188M	ENSP00000364134:V148I|ENSP00000364132:V188M	V|V	-|-	1|1	0|0	BTNL2|BTNL2	32478837|32478837	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.015000|0.015000	0.08874|0.08874	-8.769000|-8.769000	0.00017|0.00017	-2.865000|-2.865000	0.00325|0.00325	-0.172000|-0.172000	0.13284|0.13284	GTT|GTG	C|0.992;T|0.008	0.008	strong		0.587	BTNL2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_019602	
C3	718	hgsc.bcm.edu	37	19	6711070	6711070	+	Missense_Mutation	SNP	C	C	G	rs11569422	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:6711070C>G	ENST00000245907.6	-	12	1499	c.1407G>C	c.(1405-1407)gaG>gaC	p.E469D		NM_000064.2	NP_000055.2	P01024	CO3_HUMAN	complement component 3	469			E -> D (in dbSNP:rs11569422).		complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|fatty acid metabolic process (GO:0006631)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of activation of membrane attack complex (GO:0001970)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic cell clearance (GO:2000427)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of glucose transport (GO:0010828)|positive regulation of lipid storage (GO:0010884)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of type IIa hypersensitivity (GO:0001798)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of complement activation (GO:0030449)|regulation of immune response (GO:0050776)|regulation of triglyceride biosynthetic process (GO:0010866)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	C5L2 anaphylatoxin chemotactic receptor binding (GO:0031715)|endopeptidase inhibitor activity (GO:0004866)|receptor binding (GO:0005102)			breast(5)|endometrium(7)|kidney(6)|large_intestine(18)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)	72				GBM - Glioblastoma multiforme(1328;1.36e-05)|Lung(535;0.00661)	Intravenous Immunoglobulin(DB00028)	CGTTGAGGGTCTCCCCGGGTC	0.602													C|||	81	0.0161741	0.059	0.0029	5008	,	,		16993	0.0		0.001	False		,,,				2504	0.0				p.E469D		Atlas-SNP	.											.	C3	192	.	0			c.G1407C						PASS	.	C	ASP/GLU	180,4226	116.7+/-154.6	1,178,2024	244.0	215.0	225.0		1407	-10.1	0.0	19	dbSNP_120	225	3,8597	3.0+/-9.4	0,3,4297	yes	missense	C3	NM_000064.2	45	1,181,6321	GG,GC,CC		0.0349,4.0853,1.407	benign	469/1664	6711070	183,12823	2203	4300	6503	SO:0001583	missense	718	exon12			GAGGGTCTCCCCG	J04763	CCDS32883.1	19p13.3-p13.2	2014-09-17			ENSG00000125730	ENSG00000125730	3.4.21.43	"""Complement system"", ""Endogenous ligands"""	1318	protein-coding gene	gene with protein product	"""C3a anaphylatoxin"", ""complement component C3a"", ""complement component C3b"", ""prepro-C3"""	120700					Standard	NM_000064		Approved	CPAMD1, ARMD9, C3a, C3b	uc002mfm.3	P01024	OTTHUMG00000150335	ENST00000245907.6:c.1407G>C	19.37:g.6711070C>G	ENSP00000245907:p.Glu469Asp	177.0	0.0	0		184.0	90.0	0.48913	NM_000064	A7E236	Missense_Mutation	SNP	ENST00000245907.6	37	CCDS32883.1	28	0.01282051282051282	27	0.054878048780487805	1	0.0027624309392265192	0	0.0	0	0.0	C	0.018	-1.468540	0.01053	0.040853	3.49E-4	ENSG00000125730	ENST00000245907	T	0.63417	-0.04	5.03	-10.1	0.00402	Alpha-2-macroglobulin, N-terminal 2 (1);	0.352724	0.35013	N	0.003502	T	0.03739	0.0106	N	0.04655	-0.195	0.09310	N	1	B	0.02656	0.0	B	0.13407	0.009	T	0.41448	-0.9508	10	0.02654	T	1	.	9.8878	0.41272	0.0906:0.1208:0.6374:0.1513	rs11569422	469	P01024	CO3_HUMAN	D	469	ENSP00000245907:E469D	ENSP00000245907:E469D	E	-	3	2	C3	6662070	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	-1.288000	0.02783	-0.902000	0.03886	-1.288000	0.01363	GAG	C|0.980;G|0.020	0.020	strong		0.602	C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317636.2	NM_000064	
MPZL2	10205	hgsc.bcm.edu	37	11	118133334	118133334	+	Silent	SNP	T	T	C	rs17122002	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:118133334T>C	ENST00000278937.2	-	3	383	c.255A>G	c.(253-255)caA>caG	p.Q85Q	MPZL2_ENST00000438295.2_Silent_p.Q85Q|MPZL2_ENST00000525647.1_5'Flank	NM_005797.3	NP_005788.1	O60487	MPZL2_HUMAN	myelin protein zero-like 2	85	Ig-like V-type.				anatomical structure morphogenesis (GO:0009653)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)|T cell differentiation in thymus (GO:0033077)	cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|skin(1)	11	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)		CACTCATGGGTTGGAAGGGAT	0.537													T|||	205	0.0409345	0.1467	0.013	5008	,	,		20403	0.0		0.002	False		,,,				2504	0.0				p.Q85Q		Atlas-SNP	.											.	MPZL2	20	.	0			c.A255G						PASS	.	T	,	655,3745	280.8+/-275.6	62,531,1607	62.0	57.0	59.0		255,255	-6.6	0.0	11	dbSNP_123	59	5,8587	4.3+/-15.6	0,5,4291	no	coding-synonymous,coding-synonymous	MPZL2	NM_005797.3,NM_144765.2	,	62,536,5898	CC,CT,TT		0.0582,14.8864,5.08	,	85/216,85/216	118133334	660,12332	2200	4296	6496	SO:0001819	synonymous_variant	10205	exon3			CATGGGTTGGAAG	AF275945	CCDS8393.1	11q24	2013-01-11	2007-08-01	2007-08-01		ENSG00000149573		"""Immunoglobulin superfamily / V-set domain containing"""	3496	protein-coding gene	gene with protein product		604873	"""epithelial V-like antigen 1"""	EVA1		9585423	Standard	NM_005797		Approved	EVA	uc001psn.3	O60487		ENST00000278937.2:c.255A>G	11.37:g.118133334T>C		167.0	0.0	0		120.0	70.0	0.583333	NM_005797	A8K2R1	Silent	SNP	ENST00000278937.2	37	CCDS8393.1																																																																																			T|0.954;C|0.046	0.046	strong		0.537	MPZL2-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392113.1	NM_005797	
WAS	7454	hgsc.bcm.edu	37	X	48546837	48546837	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:48546837G>A	ENST00000376701.4	+	9	1001	c.926G>A	c.(925-927)cGc>cAc	p.R309H		NM_000377.2	NP_000368.1	P42768	WASP_HUMAN	Wiskott-Aldrich syndrome	309					actin filament polymerization (GO:0030041)|actin filament-based movement (GO:0030048)|actin polymerization or depolymerization (GO:0008154)|blood coagulation (GO:0007596)|defense response (GO:0006952)|endosomal transport (GO:0016197)|epidermis development (GO:0008544)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|immune response (GO:0006955)|innate immune response (GO:0045087)|positive regulation of Arp2/3 complex-mediated actin nucleation (GO:2000601)|protein complex assembly (GO:0006461)|regulation of catalytic activity (GO:0050790)|T cell activation (GO:0042110)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|vesicle membrane (GO:0012506)	identical protein binding (GO:0042802)|phospholipase binding (GO:0043274)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)|small GTPase regulator activity (GO:0005083)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	28		all_lung(315;1.27e-10)				GAGATGAGGCGCCAGGGTGAG	0.562			"""Mis, N, F, S"""			lymphoma																															p.R309H		Atlas-SNP	.		X-linked recessive		Wiskott-Aldrich syndrome	X	Xp11.23-p11.22	7454	Wiskott-Aldrich syndrome		L	.	WAS	51	.	0			c.G926A						PASS	.						41.0	35.0	37.0					X																	48546837		2203	4300	6503	SO:0001583	missense	7454	exon9			TGAGGCGCCAGGG	AF115548	CCDS14303.1	Xp11.4-p11.21	2014-09-17	2012-07-12		ENSG00000015285	ENSG00000015285			12731	protein-coding gene	gene with protein product	"""eczema-thrombocytopenia"""	300392	"""thrombocytopenia 1 (X-linked)"", ""Wiskott-Aldrich syndrome (eczema-thrombocytopenia)"""	IMD2, THC		7795648	Standard	NM_000377		Approved	WASP	uc004dkm.4	P42768	OTTHUMG00000034483	ENST00000376701.4:c.926G>A	X.37:g.48546837G>A	ENSP00000365891:p.Arg309His	238.0	0.0	0		255.0	68.0	0.266667	NM_000377	Q9BU11|Q9UNJ9	Missense_Mutation	SNP	ENST00000376701.4	37	CCDS14303.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.110307	0.77210	.	.	ENSG00000015285	ENST00000376701	D	0.95918	-3.85	4.71	4.71	0.59529	Wiscott-Aldrich syndrome, C-terminal (1);	0.055809	0.64402	D	0.000002	D	0.96679	0.8916	L	0.57536	1.79	0.43947	D	0.99661	D	0.89917	1.0	D	0.69142	0.962	D	0.97151	0.9831	10	0.72032	D	0.01	-11.737	14.3592	0.66757	0.0:0.0:1.0:0.0	.	309	P42768	WASP_HUMAN	H	309	ENSP00000365891:R309H	ENSP00000365891:R309H	R	+	2	0	WAS	48431781	1.000000	0.71417	0.997000	0.53966	0.961000	0.63080	4.816000	0.62642	2.055000	0.61198	0.431000	0.28591	CGC	.	.	none		0.562	WAS-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083379.1	NM_000377	
CYP27A1	1593	hgsc.bcm.edu	37	2	219674482	219674482	+	Silent	SNP	G	G	A	rs692003	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:219674482G>A	ENST00000258415.4	+	2	865	c.438G>A	c.(436-438)ccG>ccA	p.P146P		NM_000784.3	NP_000775.1	Q02318	CP27A_HUMAN	cytochrome P450, family 27, subfamily A, polypeptide 1	146					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cholesterol metabolic process (GO:0008203)|small molecule metabolic process (GO:0044281)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)	cholestanetriol 26-monooxygenase activity (GO:0047749)|cholesterol 26-hydroxylase activity (GO:0031073)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid hydroxylase activity (GO:0008395)|vitamin D3 25-hydroxylase activity (GO:0030343)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|prostate(3)|urinary_tract(1)	26		Renal(207;0.0474)		Epithelial(149;9.48e-07)|all cancers(144;0.000171)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00981)	Chenodeoxycholic acid(DB06777)|Cholecalciferol(DB00169)|Ergocalciferol(DB00153)|Pegvisomant(DB00082)	CCTATGGGCCGTTCACCACGT	0.622													G|||	366	0.0730831	0.2632	0.0259	5008	,	,		16942	0.0		0.0	False		,,,				2504	0.0				p.P146P		Atlas-SNP	.											.	CYP27A1	52	.	0			c.G438A						PASS	.	G		877,3529	341.2+/-306.6	84,709,1410	90.0	78.0	82.0		438	2.9	0.9	2	dbSNP_83	82	8,8592	5.0+/-18.6	0,8,4292	no	coding-synonymous	CYP27A1	NM_000784.3		84,717,5702	AA,AG,GG		0.093,19.9047,6.8046		146/532	219674482	885,12121	2203	4300	6503	SO:0001819	synonymous_variant	1593	exon2			TGGGCCGTTCACC	BC017044	CCDS2423.1	2q35	2013-09-19	2003-01-14		ENSG00000135929	ENSG00000135929		"""Cytochrome P450s"""	2605	protein-coding gene	gene with protein product	"""cerebrotendinous xanthomatosis"""	606530	"""cytochrome P450, subfamily XXVIIA (steroid 27-hydroxylase, cerebrotendinous xanthomatosis), polypeptide 1"""	CYP27		2019602	Standard	NM_000784		Approved	CTX, CP27	uc002viz.4	Q02318	OTTHUMG00000048238	ENST00000258415.4:c.438G>A	2.37:g.219674482G>A		82.0	0.0	0		73.0	32.0	0.438356	NM_000784	A8K303|Q6LDB4|Q86YQ6	Silent	SNP	ENST00000258415.4	37	CCDS2423.1																																																																																			G|0.935;A|0.065	0.065	strong		0.622	CYP27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109734.4		
HSD3B1	3283	hgsc.bcm.edu	37	1	120057163	120057163	+	Silent	SNP	G	G	A	rs33913717	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:120057163G>A	ENST00000369413.3	+	4	1162	c.1017G>A	c.(1015-1017)gcG>gcA	p.A339A	HSD3B1_ENST00000235547.6_Silent_p.A341A|HSD3B1_ENST00000528909.1_Silent_p.A339A			P14060	3BHS1_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1	339					androgen biosynthetic process (GO:0006702)|estrogen biosynthetic process (GO:0006703)|glucocorticoid biosynthetic process (GO:0006704)|mineralocorticoid biosynthetic process (GO:0006705)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|smooth endoplasmic reticulum membrane (GO:0030868)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|steroid delta-isomerase activity (GO:0004769)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(18)|ovary(2)|prostate(1)|skin(1)	32	all_neural(166;0.219)	all_lung(203;3.16e-06)|Lung NSC(69;2.19e-05)|all_epithelial(167;0.000624)		Lung(183;0.0106)|LUSC - Lung squamous cell carcinoma(189;0.0554)	Trilostane(DB01108)	GAGATCTGGCGTATAAGCCAC	0.517													g|||	37	0.00738818	0.0272	0.0014	5008	,	,		21238	0.0		0.0	False		,,,				2504	0.0				p.A339A		Atlas-SNP	.											HSD3B1,caecum,carcinoma,+1,1	HSD3B1	53	1	0			c.G1017A						PASS	.	A		118,4288	89.2+/-127.9	7,104,2092	83.0	73.0	76.0		1017	-6.5	0.0	1	dbSNP_126	76	0,8600		0,0,4300	yes	coding-synonymous	HSD3B1	NM_000862.2		7,104,6392	AA,AG,GG		0.0,2.6782,0.9073		339/374	120057163	118,12888	2203	4300	6503	SO:0001819	synonymous_variant	3283	exon4			TCTGGCGTATAAG	S45679	CCDS903.1	1p12	2014-06-03			ENSG00000203857	ENSG00000203857	1.1.1.145, 5.3.3.1	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	5217	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 11E, member 1"""	109715		HSDB3, HSD3B		2779585, 19027726	Standard	NM_000862		Approved	SDR11E1	uc001ehv.1	P14060	OTTHUMG00000012525	ENST00000369413.3:c.1017G>A	1.37:g.120057163G>A		233.0	0.0	0		250.0	127.0	0.508	NM_000862	A8K691|Q14545|Q8IV65	Silent	SNP	ENST00000369413.3	37	CCDS903.1																																																																																			G|0.990;A|0.010	0.010	strong		0.517	HSD3B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000034993.3	NM_000862	
CD1E	913	hgsc.bcm.edu	37	1	158325819	158325819	+	Silent	SNP	G	G	A	rs61734678	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158325819G>A	ENST00000368167.3	+	4	1067	c.828G>A	c.(826-828)gcG>gcA	p.A276A	CD1E_ENST00000368160.3_Silent_p.A276A|CD1E_ENST00000368157.1_Intron|CD1E_ENST00000452291.2_Silent_p.A87A|CD1E_ENST00000368165.3_Silent_p.A186A|CD1E_ENST00000368164.3_Intron|CD1E_ENST00000368163.3_Intron|CD1E_ENST00000368156.1_Silent_p.A186A|CD1E_ENST00000368166.3_Silent_p.A87A|CD1E_ENST00000368155.3_Intron|CD1E_ENST00000368154.1_Intron|CD1E_ENST00000444681.2_Silent_p.A177A|CD1E_ENST00000434258.1_Silent_p.A274A|CD1E_ENST00000368161.3_Intron	NM_030893.3	NP_112155.2	P15812	CD1E_HUMAN	CD1e molecule	276	Ig-like.				antigen processing and presentation (GO:0019882)|immune response (GO:0006955)	endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	lipid binding (GO:0008289)			breast(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(27)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|urinary_tract(1)	49	all_hematologic(112;0.0378)					TGGATGTGGCGGCTGGGGAGG	0.607													G|||	70	0.0139776	0.0507	0.0043	5008	,	,		15775	0.0		0.0	False		,,,				2504	0.0				p.A276A		Atlas-SNP	.											CD1E,colon,carcinoma,+1,2	CD1E	129	2	0			c.G828A						PASS	.	G	,,,,,,,,,,,,	153,4253	104.3+/-142.8	6,141,2056	85.0	86.0	86.0		828,,,261,,558,,,261,,531,558,828	-8.6	0.0	1	dbSNP_129	86	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,intron,intron,coding-synonymous,intron,coding-synonymous,intron,intron,coding-synonymous,intron,coding-synonymous,coding-synonymous,coding-synonymous	CD1E	NM_001042583.2,NM_001042584.2,NM_001042585.2,NM_001042586.2,NM_001042587.2,NM_001185107.1,NM_001185108.1,NM_001185110.1,NM_001185112.1,NM_001185113.1,NM_001185114.1,NM_001185115.1,NM_030893.3	,,,,,,,,,,,,	6,142,6355	AA,AG,GG		0.0116,3.4725,1.1841	,,,,,,,,,,,,	276/377,,,87/188,,186/299,,,87/200,,177/290,186/287,276/389	158325819	154,12852	2203	4300	6503	SO:0001819	synonymous_variant	913	exon4			TGTGGCGGCTGGG	AJ289111	CCDS41417.1, CCDS41418.1, CCDS41419.1, CCDS41420.1, CCDS41421.1, CCDS41422.1, CCDS53387.1, CCDS53388.1, CCDS53389.1, CCDS53390.1, CCDS53384.1, CCDS53385.1, CCDS53386.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158488	ENSG00000158488		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1638	protein-coding gene	gene with protein product		188411	"""CD1E antigen, e polypeptide"", ""CD1e antigen"""			10948205	Standard	NM_001042585		Approved		uc001fse.3	P15812	OTTHUMG00000017515	ENST00000368167.3:c.828G>A	1.37:g.158325819G>A		219.0	0.0	0		249.0	114.0	0.457831	NM_030893	B4DZV3|E7EP01|Q5TDJ9|Q5TDK3|Q5TDK4|Q5TDK5|Q5TDK6|Q5TDK8|Q5TDL1|Q712E4|Q712E5|Q712E6|Q712E7|Q712E8|Q712E9|Q712F0|Q712F1|Q712F2|Q712F3|Q712F4|Q712F5|Q96TD0|Q96TD1|Q9UMM1|Q9Y5M3	Silent	SNP	ENST00000368167.3	37	CCDS41417.1																																																																																			G|0.988;A|0.012	0.012	strong		0.607	CD1E-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046353.3	NM_030893	
OBSCN	84033	hgsc.bcm.edu	37	1	228547691	228547691	+	Intron	SNP	C	C	T	rs367920745	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228547691C>T	ENST00000422127.1	+	80	18705				OBSCN_ENST00000366707.4_Intron|OBSCN_ENST00000570156.2_Intron|OBSCN_ENST00000366709.4_Silent_p.P3485P|OBSCN_ENST00000284548.11_Silent_p.P6366P	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF						apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GTGCGACCCCCGGAGGGGACC	0.647													C|||	36	0.0071885	0.0272	0.0	5008	,	,		17215	0.0		0.0	False		,,,				2504	0.0				p.P6366P		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C19098T						PASS	.	C	,	82,3694		1,80,1807	17.0	20.0	19.0		,19098	-8.8	0.0	1		19	0,8218		0,0,4109	no	intron,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	1,80,5916	TT,TC,CC		0.0,2.1716,0.6837	,	,6366/6621	228547691	82,11912	1888	4109	5997	SO:0001627	intron_variant	84033	exon81			GACCCCCGGAGGG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.18662-2586C>T	1.37:g.228547691C>T		128.0	0.0	0		164.0	83.0	0.506098	NM_052843	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			.	.	none		0.647	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
ABCA8	10351	hgsc.bcm.edu	37	17	66928460	66928460	+	Missense_Mutation	SNP	T	T	C	rs16973446	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:66928460T>C	ENST00000269080.2	-	6	903	c.766A>G	c.(766-768)Aca>Gca	p.T256A	ABCA8_ENST00000586539.1_Missense_Mutation_p.T256A|ABCA8_ENST00000430352.2_Missense_Mutation_p.T256A	NM_007168.2	NP_009099.1	O94911	ABCA8_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 8	256			T -> A (in dbSNP:rs16973446).		transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			breast(3)|central_nervous_system(2)|endometrium(9)|kidney(5)|large_intestine(19)|liver(1)|lung(30)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|urinary_tract(4)	83	Breast(10;4.56e-13)					CCCATCATTGTCATCAAGGCC	0.393													T|||	383	0.0764776	0.2738	0.0231	5008	,	,		20528	0.0		0.005	False		,,,				2504	0.0				p.T256A		Atlas-SNP	.											.	ABCA8	213	.	0			c.A766G						PASS	.	T	ALA/THR	1058,3348	384.9+/-325.5	129,800,1274	86.0	79.0	81.0		766	2.6	0.5	17	dbSNP_123	81	17,8583	12.6+/-44.7	0,17,4283	yes	missense	ABCA8	NM_007168.2	58	129,817,5557	CC,CT,TT		0.1977,24.0127,8.2654	benign	256/1582	66928460	1075,11931	2203	4300	6503	SO:0001583	missense	10351	exon6			TCATTGTCATCAA	AB020629	CCDS11680.1, CCDS74138.1, CCDS74139.1	17q24	2012-03-14			ENSG00000141338	ENSG00000141338		"""ATP binding cassette transporters / subfamily A"""	38	protein-coding gene	gene with protein product		612505					Standard	XM_005256938		Approved	KIAA0822	uc002jhp.3	O94911		ENST00000269080.2:c.766A>G	17.37:g.66928460T>C	ENSP00000269080:p.Thr256Ala	76.0	0.0	0		91.0	40.0	0.43956	NM_007168	A1L3U3|C9JQE6|Q86WW0	Missense_Mutation	SNP	ENST00000269080.2	37	CCDS11680.1	140	0.0641025641025641	128	0.2601626016260163	10	0.027624309392265192	0	0.0	2	0.002638522427440633	T	9.995	1.231776	0.22626	0.240127	0.001977	ENSG00000141338	ENST00000269080;ENST00000430352;ENST00000541225;ENST00000428549	D;D	0.82344	-1.6;-1.6	4.85	2.63	0.31362	.	1.596760	0.03628	N	0.237455	T	0.00039	0.0001	N	0.26130	0.795	0.47407	P	5.819999999999714E-4	B;B;B;B;B	0.22146	0.065;0.02;0.036;0.003;0.02	B;B;B;B;B	0.21360	0.03;0.02;0.021;0.012;0.034	T	0.04041	-1.0982	9	0.42905	T	0.14	.	6.2716	0.20956	0.0:0.1989:0.0:0.8011	rs16973446;rs16973446	195;256;256;256;256	F5H6Z4;A1L3U3;B4DJ11;C9JQE6;O94911	.;.;.;.;ABCA8_HUMAN	A	256;256;195;256	ENSP00000269080:T256A;ENSP00000402814:T256A	ENSP00000269080:T256A	T	-	1	0	ABCA8	64440055	0.856000	0.29760	0.510000	0.27712	0.553000	0.35397	1.060000	0.30530	0.444000	0.26612	-0.385000	0.06624	ACA	T|0.915;C|0.085	0.085	strong		0.393	ABCA8-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450172.1	NM_007168	
PLA2G4F	255189	hgsc.bcm.edu	37	15	42438380	42438380	+	Silent	SNP	G	G	A	rs80108792	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42438380G>A	ENST00000382396.4	-	14	1565	c.1479C>T	c.(1477-1479)taC>taT	p.Y493Y	PLA2G4F_ENST00000397272.3_Silent_p.Y495Y			Q68DD2	PA24F_HUMAN	phospholipase A2, group IVF	493	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)		TGTAAATGGGGTAAGGGTTCT	0.582													G|||	69	0.013778	0.0507	0.0014	5008	,	,		20601	0.0		0.001	False		,,,				2504	0.0				p.Y493Y		Atlas-SNP	.											.	PLA2G4F	75	.	0			c.C1479T						PASS	.	G		155,4251	105.6+/-144.1	4,147,2052	100.0	89.0	92.0		1479	-2.0	1.0	15	dbSNP_132	92	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	PLA2G4F	NM_213600.3		4,148,6350	AA,AG,GG		0.0116,3.5179,1.1996		493/850	42438380	156,12848	2203	4299	6502	SO:0001819	synonymous_variant	255189	exon14			AATGGGGTAAGGG		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.1479C>T	15.37:g.42438380G>A		109.0	0.0	0		90.0	47.0	0.522222	NM_213600	Q6ZMC8	Silent	SNP	ENST00000382396.4	37	CCDS32204.1																																																																																			G|0.988;A|0.012	0.012	strong		0.582	PLA2G4F-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000420463.1	NM_213600	
CLRN2	645104	hgsc.bcm.edu	37	4	17517141	17517141	+	Splice_Site	SNP	G	G	A	rs201838208	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:17517141G>A	ENST00000511148.2	+	1	354	c.252G>A	c.(250-252)acG>acA	p.T84T		NM_001079827.2	NP_001073296.1	A0PK11	CLRN2_HUMAN	clarin 2	84						integral component of membrane (GO:0016021)				breast(1)|kidney(1)|large_intestine(3)|lung(8)|pancreas(1)|upper_aerodigestive_tract(1)	15						CCCAATTCACGAGTGAGTATA	0.483													G|||	3	0.000599042	0.0023	0.0	5008	,	,		18289	0.0		0.0	False		,,,				2504	0.0				p.T84T		Atlas-SNP	.											.	CLRN2	40	.	0			c.G252A						PASS	.	G		5,3809		0,5,1902	46.0	45.0	45.0		252	-10.8	0.1	4		45	0,8216		0,0,4108	yes	coding-synonymous-near-splice	CLRN2	NM_001079827.2		0,5,6010	AA,AG,GG		0.0,0.1311,0.0416		84/233	17517141	5,12025	1907	4108	6015	SO:0001630	splice_region_variant	645104	exon1			ATTCACGAGTGAG		CCDS47032.1	4p15.32	2008-01-17			ENSG00000249581	ENSG00000249581			33939	protein-coding gene	gene with protein product						12080385	Standard	NM_001079827		Approved		uc003gpg.1	A0PK11	OTTHUMG00000160273	ENST00000511148.2:c.253+1G>A	4.37:g.17517141G>A		164.0	0.0	0		148.0	80.0	0.540541	NM_001079827		Silent	SNP	ENST00000511148.2	37	CCDS47032.1																																																																																			.	.	weak		0.483	CLRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359990.2	NM_001079827	Silent
MDC1	9656	hgsc.bcm.edu	37	6	30673013	30673013	+	Missense_Mutation	SNP	A	A	G	rs61733213	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:30673013A>G	ENST00000376406.3	-	10	4594	c.3947T>C	c.(3946-3948)aTg>aCg	p.M1316T	MDC1_ENST00000376405.2_Missense_Mutation_p.M1052T|MDC1-AS1_ENST00000442150.1_RNA	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	1316	Interaction with the PRKDC complex.|Pro-rich.			Missing (in Ref. 2; CAH18685). {ECO:0000305}.	DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						GACAGAGGACATATTTGTCCT	0.597								Other conserved DNA damage response genes					a|||	234	0.0467252	0.1278	0.0432	5008	,	,		19113	0.0208		0.0129	False		,,,				2504	0.001				p.M1316T		Atlas-SNP	.											.	MDC1	218	.	0			c.T3947C						PASS	.	C	THR/MET	480,3926	224.9+/-240.9	34,412,1757	141.0	152.0	148.0		3947	-1.8	0.0	6	dbSNP_129	148	95,8505	52.3+/-112.8	1,93,4206	no	missense	MDC1	NM_014641.2	81	35,505,5963	GG,GA,AA		1.1047,10.8942,4.421	benign	1316/2090	30673013	575,12431	2203	4300	6503	SO:0001583	missense	9656	exon10			GAGGACATATTTG	D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.3947T>C	6.37:g.30673013A>G	ENSP00000365588:p.Met1316Thr	322.0	1.0	0.00310559		363.0	186.0	0.512397	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Missense_Mutation	SNP	ENST00000376406.3	37	CCDS34384.1	100	0.045787545787545784	59	0.11991869918699187	16	0.04419889502762431	17	0.02972027972027972	8	0.010554089709762533	a	2.633	-0.285988	0.05605	0.108942	0.011047	ENSG00000137337	ENST00000376406;ENST00000376405	T;T	0.05139	3.49;3.49	3.32	-1.81	0.07882	.	0.445015	0.16677	N	0.204131	T	0.00637	0.0021	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.12837	0.008;0.004	T	0.42103	-0.9471	10	0.12103	T	0.63	.	3.1868	0.06603	0.299:0.311:0.0:0.3899	.	1052;1316	Q14676-2;Q14676	.;MDC1_HUMAN	T	1316;1052	ENSP00000365588:M1316T;ENSP00000365587:M1052T	ENSP00000365587:M1052T	M	-	2	0	MDC1	30780992	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.173000	0.03108	-0.789000	0.04498	-3.196000	0.00055	ATG	A|0.958;G|0.042	0.042	strong		0.597	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641	
PTPN23	25930	hgsc.bcm.edu	37	3	47454398	47454398	+	Missense_Mutation	SNP	C	C	T	rs140165828	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:47454398C>T	ENST00000265562.4	+	25	4711	c.4634C>T	c.(4633-4635)cCg>cTg	p.P1545L	PTPN23_ENST00000431726.1_Missense_Mutation_p.P1419L	NM_015466.2	NP_056281.1	Q9H3S7	PTN23_HUMAN	protein tyrosine phosphatase, non-receptor type 23	1545	Pro-rich.				cilium morphogenesis (GO:0060271)|negative regulation of epithelial cell migration (GO:0010633)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of adherens junction organization (GO:1903393)|positive regulation of early endosome to late endosome transport (GO:2000643)|positive regulation of homophilic cell adhesion (GO:1903387)|protein transport (GO:0015031)|ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|central_nervous_system(1)|large_intestine(5)|lung(7)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)	23				BRCA - Breast invasive adenocarcinoma(193;0.000271)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		TCTTCCTCCCCGCCCCCCCTT	0.701													C|||	9	0.00179712	0.0068	0.0	5008	,	,		11435	0.0		0.0	False		,,,				2504	0.0				p.P1545L		Atlas-SNP	.											PTPN23,NS,carcinoma,-1,1	PTPN23	85	1	0			c.C4634T						PASS	.	C	LEU/PRO	19,4375		0,19,2178	21.0	24.0	23.0		4634	3.9	0.8	3	dbSNP_134	23	0,8586		0,0,4293	yes	missense	PTPN23	NM_015466.2	98	0,19,6471	TT,TC,CC		0.0,0.4324,0.1464	probably-damaging	1545/1637	47454398	19,12961	2197	4293	6490	SO:0001583	missense	25930	exon25			CCTCCCCGCCCCC	AB025194	CCDS2754.1	3p21.3	2011-06-09			ENSG00000076201	ENSG00000076201		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	14406	protein-coding gene	gene with protein product		606584				11095967	Standard	NM_015466		Approved	DKFZP564F0923, KIAA1471, HD-PTP	uc003crf.1	Q9H3S7	OTTHUMG00000133520	ENST00000265562.4:c.4634C>T	3.37:g.47454398C>T	ENSP00000265562:p.Pro1545Leu	237.0	0.0	0		247.0	116.0	0.469636	NM_015466	A8K0D7|Q7KZF8|Q8N6Z5|Q9BSR5|Q9P257|Q9UG03|Q9UMZ4	Missense_Mutation	SNP	ENST00000265562.4	37	CCDS2754.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	13.75	2.328844	0.41197	0.004324	0.0	ENSG00000076201	ENST00000265562	T	0.02916	4.11	3.9	3.9	0.45041	.	0.171581	0.36932	N	0.002332	T	0.02929	0.0087	L	0.27053	0.805	0.50171	D	0.999851	D	0.64830	0.994	P	0.51453	0.67	T	0.50825	-0.8782	10	0.72032	D	0.01	-10.0851	11.2398	0.48962	0.0:0.8134:0.1866:0.0	.	1545	Q9H3S7	PTN23_HUMAN	L	1545	ENSP00000265562:P1545L	ENSP00000265562:P1545L	P	+	2	0	PTPN23	47429402	0.499000	0.26083	0.835000	0.33067	0.668000	0.39293	2.241000	0.43097	2.146000	0.66826	0.563000	0.77884	CCG	C|0.998;T|0.002	0.002	strong		0.701	PTPN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257492.2	NM_015466	
CHST12	55501	hgsc.bcm.edu	37	7	2472662	2472662	+	Missense_Mutation	SNP	G	G	C	rs11537796	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:2472662G>C	ENST00000258711.6	+	2	523	c.388G>C	c.(388-390)Ggc>Cgc	p.G130R		NM_001243794.1|NM_001243795.1|NM_018641.4	NP_001230723.1|NP_001230724.1|NP_061111.1	Q9NRB3	CHSTC_HUMAN	carbohydrate (chondroitin 4) sulfotransferase 12	130					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|chondroitin 4-sulfotransferase activity (GO:0047756)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(1)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	21		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0847)|OV - Ovarian serous cystadenocarcinoma(56;2.25e-13)		CGTGCTGCGGGGCTTCTGCGC	0.701													G|||	141	0.028155	0.0968	0.0159	5008	,	,		14367	0.0		0.002	False		,,,				2504	0.0				p.G130R		Atlas-SNP	.											.	CHST12	39	.	0			c.G388C						PASS	.	G	ARG/GLY	361,4045		25,311,1867	35.0	37.0	37.0		388	4.2	0.3	7	dbSNP_120	37	2,8598		0,2,4298	yes	missense	CHST12	NM_018641.4	125	25,313,6165	CC,CG,GG		0.0233,8.1934,2.791	benign	130/415	2472662	363,12643	2203	4300	6503	SO:0001583	missense	55501	exon2			CTGCGGGGCTTCT	AF239822	CCDS5333.1	7p22	2007-03-14			ENSG00000136213	ENSG00000136213	2.8.2.5	"""Sulfotransferases, membrane-bound"""	17423	protein-coding gene	gene with protein product		610129				10781601	Standard	NM_018641		Approved	C4S-2, C4ST2	uc021zyu.1	Q9NRB3	OTTHUMG00000023849	ENST00000258711.6:c.388G>C	7.37:g.2472662G>C	ENSP00000258711:p.Gly130Arg	17.0	0.0	0		21.0	10.0	0.47619	NM_018641	A4D1Z9|Q502W3|Q9NXY7	Missense_Mutation	SNP	ENST00000258711.6	37	CCDS5333.1	55	0.025183150183150184	48	0.0975609756097561	5	0.013812154696132596	0	0.0	2	0.002638522427440633	G	2.483	-0.319175	0.05386	0.081934	2.33E-4	ENSG00000136213	ENST00000258711;ENST00000432336	T;T	0.60548	0.18;1.03	5.09	4.18	0.49190	.	0.697828	0.14301	N	0.328271	T	0.01387	0.0045	N	0.22421	0.69	0.25416	N	0.988316	B	0.19583	0.037	B	0.18871	0.023	T	0.00978	-1.1493	10	0.17832	T	0.49	-6.2778	13.8779	0.63665	0.0:0.2917:0.7083:0.0	rs11537796	130	Q9NRB3	CHSTC_HUMAN	R	130	ENSP00000258711:G130R;ENSP00000411207:G130R	ENSP00000258711:G130R	G	+	1	0	CHST12	2439188	0.021000	0.18746	0.287000	0.24848	0.689000	0.40095	1.514000	0.35834	1.095000	0.41419	0.561000	0.74099	GGC	G|0.970;C|0.030	0.030	strong		0.701	CHST12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060170.3	NM_018641	
XCL1	6375	hgsc.bcm.edu	37	1	168549321	168549321	+	Missense_Mutation	SNP	G	G	C	rs56148248	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:168549321G>C	ENST00000367818.3	+	2	247	c.82G>C	c.(82-84)Gat>Cat	p.D28H		NM_002995.2	NP_002986.1	P47992	XCL1_HUMAN	chemokine (C motif) ligand 1	28					cell-cell signaling (GO:0007267)|cellular response to interleukin-4 (GO:0071353)|cellular response to transforming growth factor beta stimulus (GO:0071560)|immune response (GO:0006955)|mature natural killer cell chemotaxis (GO:0035782)|negative regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000562)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of T cell cytokine production (GO:0002725)|negative regulation of T-helper 1 cell activation (GO:2000518)|negative regulation of T-helper 1 type immune response (GO:0002826)|negative regulation of transcription, DNA-templated (GO:0045892)|neutrophil chemotaxis (GO:0030593)|positive regulation of B cell chemotaxis (GO:2000538)|positive regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000563)|positive regulation of CD8-positive, alpha-beta T cell proliferation (GO:2000566)|positive regulation of granzyme A production (GO:2000513)|positive regulation of granzyme B production (GO:0071663)|positive regulation of immunoglobulin production in mucosal tissue (GO:2000558)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of natural killer cell chemotaxis (GO:2000503)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of T cell cytokine production (GO:0002726)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T-helper 1 cell cytokine production (GO:2000556)|positive regulation of T-helper 2 cell cytokine production (GO:2000553)|positive regulation of thymocyte migration (GO:2000412)|positive regulation of transforming growth factor beta production (GO:0071636)|regulation of inflammatory response (GO:0050727)|release of sequestered calcium ion into cytosol (GO:0051209)|response to virus (GO:0009615)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)|chemokine receptor binding (GO:0042379)|protein homodimerization activity (GO:0042803)			kidney(2)|lung(7)|upper_aerodigestive_tract(1)	10	all_hematologic(923;0.208)					TGAAGTCTCAGATAAGAGGAC	0.433													G|||	160	0.0319489	0.115	0.0029	5008	,	,		19069	0.001		0.005	False		,,,				2504	0.0				p.D28H		Atlas-SNP	.											.	XCL1	16	.	0			c.G82C						PASS	.	G	HIS/ASP	274,4132		34,206,1963	129.0	132.0	131.0		82	0.2	0.0	1	dbSNP_129	131	4,8596		0,4,4296	no	missense	XCL1	NM_002995.2	81	34,210,6259	CC,CG,GG		0.0465,6.2188,2.1375	benign	28/115	168549321	278,12728	2203	4300	6503	SO:0001583	missense	6375	exon2			GTCTCAGATAAGA	D43768	CCDS1274.1	1q24.2	2014-01-30	2002-08-22	2002-08-23	ENSG00000143184	ENSG00000143184		"""Endogenous ligands"""	10645	protein-coding gene	gene with protein product		600250	"""small inducible cytokine subfamily C, member 1 (lymphotactin)"""	LTN, SCYC1		7602097, 7875320	Standard	NM_002995		Approved	LPTN, ATAC, SCM-1a, SCM-1, lymphotactin	uc001gfo.2	P47992	OTTHUMG00000034548	ENST00000367818.3:c.82G>C	1.37:g.168549321G>C	ENSP00000356792:p.Asp28His	281.0	0.0	0		161.0	68.0	0.42236	NM_002995	Q52MA8	Missense_Mutation	SNP	ENST00000367818.3	37	CCDS1274.1	44	0.020146520146520148	37	0.07520325203252033	2	0.0055248618784530384	1	0.0017482517482517483	4	0.005277044854881266	G	11.98	1.801914	0.31869	0.062188	4.65E-4	ENSG00000143184	ENST00000367818	T	0.03982	3.74	4.36	0.171	0.15026	Chemokine interleukin-8-like domain (2);	1.336140	0.04578	N	0.394548	T	0.02193	0.0068	L	0.29908	0.895	0.25228	N	0.98985	P	0.44309	0.832	P	0.49085	0.6	T	0.37009	-0.9724	9	0.62326	D	0.03	-0.0463	3.0265	0.06092	0.0977:0.3375:0.3913:0.1734	rs56148248	28	P47992	XCL1_HUMAN	H	28	ENSP00000356792:D28H	ENSP00000356792:D28H	D	+	1	0	XCL1	166815945	0.001000	0.12720	0.006000	0.13384	0.548000	0.35241	0.157000	0.16402	0.172000	0.19760	0.655000	0.94253	GAT	G|0.982;C|0.018	0.018	strong		0.433	XCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083612.1	NM_002995	
DLG2	1740	hgsc.bcm.edu	37	11	83182726	83182726	+	Silent	SNP	G	G	T	rs34857356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:83182726G>T	ENST00000532653.1	-	19	2322	c.2020C>A	c.(2020-2022)Cgg>Agg	p.R674R	DLG2_ENST00000330014.6_Silent_p.R613R|DLG2_ENST00000418306.2_Silent_p.R571R|DLG2_ENST00000524982.1_Silent_p.R688R|DLG2_ENST00000537455.1_Silent_p.R442R|DLG2_ENST00000376104.2_Silent_p.R797R|DLG2_ENST00000543673.1_Silent_p.R797R|DLG2_ENST00000398309.2_Silent_p.R692R|DLG2_ENST00000426717.2_Silent_p.R156R|DLG2_ENST00000404783.3_Silent_p.R170R|DLG2_ENST00000531015.1_Silent_p.R659R|DLG2_ENST00000376106.3_Silent_p.R156R|DLG2_ENST00000280241.8_Silent_p.R731R			Q14168	MPP2_HUMAN	discs, large homolog 2 (Drosophila)	389					nucleotide phosphorylation (GO:0046939)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	guanylate kinase activity (GO:0004385)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(11)|lung(35)|ovary(3)|pancreas(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	71		all_cancers(6;0.00791)|Acute lymphoblastic leukemia(157;4.44e-05)|all_hematologic(158;0.0036)				TCATTGATCCGATCCTTCATG	0.433													G|||	105	0.0209665	0.0688	0.013	5008	,	,		17636	0.0		0.005	False		,,,				2504	0.0				p.R797R		Atlas-SNP	.											DLG2_ENST00000418306,colon,carcinoma,+2,9	DLG2	448	9	0			c.C2389A						PASS	.	G	,,,,	221,3475		11,199,1638	67.0	65.0	65.0		2389,1711,466,2191,2074	4.2	1.0	11	dbSNP_126	65	11,8175		0,11,4082	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DLG2	NM_001142699.1,NM_001142700.1,NM_001142702.1,NM_001206769.1,NM_001364.3	,,,,	11,210,5720	TT,TG,GG		0.1344,5.9794,1.9525	,,,,	797/976,571/750,156/335,731/910,692/871	83182726	232,11650	1848	4093	5941	SO:0001819	synonymous_variant	1740	exon24			TGATCCGATCCTT	U32376	CCDS41696.1, CCDS44690.1, CCDS44691.1, CCDS44692.1, CCDS55782.1, CCDS73357.1	11q21	2012-04-17	2008-12-15		ENSG00000150672	ENSG00000150672		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	2901	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 58"""	603583	"""discs, large homolog 2, chapsyn-110 (Drosophila)"""			8755482, 9806853	Standard	NM_001142702		Approved	PSD-93, PSD93, chapsyn-110, PPP1R58	uc001pak.2	Q15700	OTTHUMG00000134309	ENST00000532653.1:c.2020C>A	11.37:g.83182726G>T		144.0	0.0	0		111.0	60.0	0.540541	NM_001142699	B4DGE9|B4DRJ0|B7Z3G8|E7EV80|E7EV91|E7EX01|Q53ES9|Q5CZB9|Q9BQJ2	Silent	SNP	ENST00000532653.1	37																																																																																				G|0.984;T|0.016	0.016	strong		0.433	DLG2-009	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000259253.2	NM_001364	
FAM174A	345757	hgsc.bcm.edu	37	5	99897880	99897880	+	Missense_Mutation	SNP	A	A	G	rs76060686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:99897880A>G	ENST00000312637.4	+	2	783	c.557A>G	c.(556-558)aAt>aGt	p.N186S	FAM174A_ENST00000505792.1_3'UTR	NM_198507.1	NP_940909.1	Q8TBP5	F174A_HUMAN	family with sequence similarity 174, member A	186						integral component of membrane (GO:0016021)				breast(2)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	9						TTTGATGCCAATCATCCTCGA	0.368													A|||	19	0.00379393	0.0144	0.0	5008	,	,		14171	0.0		0.0	False		,,,				2504	0.0				p.N186S		Atlas-SNP	.											.	FAM174A	13	.	0			c.A557G						PASS	.	A	SER/ASN	98,4308	78.3+/-116.7	1,96,2106	143.0	131.0	135.0		557	2.8	1.0	5	dbSNP_131	135	0,8600		0,0,4300	yes	missense	FAM174A	NM_198507.1	46	1,96,6406	GG,GA,AA		0.0,2.2242,0.7535	benign	186/191	99897880	98,12908	2203	4300	6503	SO:0001583	missense	345757	exon2			ATGCCAATCATCC	AY359108	CCDS4090.1	5q21.1	2008-06-19	2008-06-19	2008-06-19	ENSG00000174132	ENSG00000174132			24943	protein-coding gene	gene with protein product			"""transmembrane protein 157"""	TMEM157		12975309	Standard	NM_198507		Approved	UNQ1912	uc003knj.1	Q8TBP5	OTTHUMG00000128726	ENST00000312637.4:c.557A>G	5.37:g.99897880A>G	ENSP00000307954:p.Asn186Ser	206.0	0.0	0		242.0	117.0	0.483471	NM_198507	A8K0H4	Missense_Mutation	SNP	ENST00000312637.4	37	CCDS4090.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	A	12.69	2.014664	0.35511	0.022242	0.0	ENSG00000174132	ENST00000312637	T	0.50548	0.74	5.21	2.81	0.32909	.	0.211018	0.31145	N	0.008177	T	0.14700	0.0355	L	0.35644	1.08	0.35327	D	0.785245	B	0.31989	0.35	B	0.35655	0.207	T	0.20974	-1.0259	9	.	.	.	-11.1789	8.0143	0.30372	0.8295:0.0:0.1705:0.0	.	186	Q8TBP5	F174A_HUMAN	S	186	ENSP00000307954:N186S	.	N	+	2	0	FAM174A	99925779	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	1.898000	0.39809	0.319000	0.23209	0.383000	0.25322	AAT	A|0.992;G|0.008	0.008	strong		0.368	FAM174A-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000250631.2	NM_198507	
PREX1	57580	hgsc.bcm.edu	37	20	47274733	47274733	+	Missense_Mutation	SNP	T	T	C	rs62621889	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:47274733T>C	ENST00000371941.3	-	17	1937	c.1915A>G	c.(1915-1917)Atc>Gtc	p.I639V	PREX1_ENST00000396220.1_Missense_Mutation_p.I639V	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	639	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				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)			TTCTCCTCGATGTCAAAGCCA	0.672											OREG0026010	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	51	0.0101837	0.0378	0.0014	5008	,	,		19323	0.0		0.0	False		,,,				2504	0.0				p.I639V		Atlas-SNP	.											.	PREX1	441	.	0			c.A1915G						PASS	.	T	VAL/ILE	146,4260	102.5+/-141.1	1,144,2058	285.0	256.0	266.0		1915	3.9	1.0	20	dbSNP_129	266	1,8599	1.2+/-3.3	0,1,4299	yes	missense	PREX1	NM_020820.3	29	1,145,6357	CC,CT,TT		0.0116,3.3137,1.1302	benign	639/1660	47274733	147,12859	2203	4300	6503	SO:0001583	missense	57580	exon17			CCTCGATGTCAAA	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.1915A>G	20.37:g.47274733T>C	ENSP00000361009:p.Ile639Val	155.0	0.0	0	945	161.0	68.0	0.42236	NM_020820	E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	37	CCDS13410.1	15	0.006868131868131868	14	0.028455284552845527	1	0.0027624309392265192	0	0.0	0	0.0	T	12.08	1.832013	0.32421	0.033137	1.16E-4	ENSG00000124126	ENST00000371941;ENST00000396220	T;T	0.18016	2.24;2.24	4.98	3.86	0.44501	Winged helix-turn-helix transcription repressor DNA-binding (1);PDZ/DHR/GLGF (3);	0.406056	0.19926	U	0.102980	T	0.02494	0.0076	N	0.08118	0	0.34912	D	0.747534	B	0.02656	0.0	B	0.04013	0.001	T	0.12656	-1.0539	10	0.56958	D	0.05	.	6.8339	0.23925	0.0:0.0776:0.2974:0.625	rs62621889	639	Q8TCU6	PREX1_HUMAN	V	639	ENSP00000361009:I639V;ENSP00000379522:I639V	ENSP00000361009:I639V	I	-	1	0	PREX1	46708140	1.000000	0.71417	0.981000	0.43875	0.935000	0.57460	3.185000	0.50934	0.714000	0.32081	0.533000	0.62120	ATC	T|0.989;C|0.011	0.011	strong		0.672	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820	
HOXD8	3234	hgsc.bcm.edu	37	2	176995146	176995146	+	Missense_Mutation	SNP	G	G	A	rs192755857	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:176995146G>A	ENST00000313173.4	+	1	679	c.52G>A	c.(52-54)Gcg>Acg	p.A18T	HOXD-AS2_ENST00000440016.2_RNA|HOXD8_ENST00000548663.1_Missense_Mutation_p.A18T|HOXD8_ENST00000429017.1_Intron|HOXD8_ENST00000544999.1_Missense_Mutation_p.A18T|HOXD8_ENST00000450510.2_Missense_Mutation_p.A18T	NM_001199746.1|NM_019558.3	NP_001186675.1|NP_062458.1	P13378	HXD8_HUMAN	homeobox D8	18	Poly-Ala.				anterior/posterior axis specification, embryo (GO:0008595)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|lung(5)|skin(1)	9			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.195)	Colorectal(32;0.0224)|READ - Rectum adenocarcinoma(9;0.0556)		ggcggcggctgcggcggcggc	0.726													G|||	92	0.0183706	0.0681	0.0029	5008	,	,		5924	0.0		0.0	False		,,,				2504	0.0				p.A18T		Atlas-SNP	.											.	HOXD8	24	.	0			c.G52A						PASS	.						1.0	1.0	1.0					2																	176995146		405	891	1296	SO:0001583	missense	3234	exon1			GCGGCTGCGGCGG		CCDS2268.1, CCDS56148.1, CCDS56149.1	2q31.1	2011-06-20	2005-12-22		ENSG00000175879	ENSG00000175879		"""Homeoboxes / ANTP class : HOXL subclass"""	5139	protein-coding gene	gene with protein product		142985	"""homeo box D8"""	HOX4, HOX4E		1973146, 1358459	Standard	NM_001199747		Approved		uc002uko.3	P13378	OTTHUMG00000132513	ENST00000313173.4:c.52G>A	2.37:g.176995146G>A	ENSP00000315949:p.Ala18Thr	2.0	0.0	0		9.0	7.0	0.777778	NM_001199746	F8WBG7|Q5BL00|Q8IXZ1	Missense_Mutation	SNP	ENST00000313173.4	37	CCDS2268.1	76	0.0347985347985348	32	0.06504065040650407	8	0.022099447513812154	29	0.050699300699300696	7	0.009234828496042216	G	15.69	2.907048	0.52333	.	.	ENSG00000175879	ENST00000313173;ENST00000544999;ENST00000548663;ENST00000450510	D;D;D;D	0.93763	-3.28;-3.25;-3.0;-3.25	2.06	1.06	0.20224	.	.	.	.	.	T	0.30230	0.0758	N	0.08118	0	0.22968	N	0.998491	B;B	0.26081	0.124;0.141	B;B	0.17722	0.014;0.019	T	0.54036	-0.8353	9	0.14656	T	0.56	.	5.7146	0.17952	0.0:0.0:0.6812:0.3188	.	18;18	Q8IXZ1;P13378	.;HXD8_HUMAN	T	18	ENSP00000315949:A18T;ENSP00000437431:A18T;ENSP00000448196:A18T;ENSP00000409026:A18T	ENSP00000315949:A18T	A	+	1	0	HOXD8	176703392	0.986000	0.35501	0.504000	0.27639	0.610000	0.37248	0.000000	0.12993	-0.051000	0.13334	0.186000	0.17326	GCG	G|0.966;A|0.034	0.034	strong		0.726	HOXD8-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255694.1		
RGS9	8787	hgsc.bcm.edu	37	17	63221136	63221136	+	Missense_Mutation	SNP	C	C	T	rs116395890	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:63221136C>T	ENST00000262406.9	+	18	1491	c.1424C>T	c.(1423-1425)gCt>gTt	p.A475V	RGS9_ENST00000449996.3_Missense_Mutation_p.A472V|RGS9_ENST00000443584.3_Missense_Mutation_p.A472V	NM_003835.3	NP_003826.2	O75916	RGS9_HUMAN	regulator of G-protein signaling 9	475					dopamine receptor signaling pathway (GO:0007212)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|response to estrogen (GO:0043627)|rhodopsin mediated signaling pathway (GO:0016056)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|heterotrimeric G-protein complex (GO:0005834)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(8)|liver(2)|lung(12)|ovary(2)|prostate(3)|skin(3)	41						CAGCACATGGCTCCCAGCCCC	0.642													C|||	27	0.00539137	0.0197	0.0014	5008	,	,		17870	0.0		0.0	False		,,,				2504	0.0				p.A475V		Atlas-SNP	.											.	RGS9	82	.	0			c.C1424T						PASS	.	C	VAL/ALA,VAL/ALA	66,4064		0,66,1999	96.0	112.0	107.0		1415,1424	3.6	0.0	17	dbSNP_132	107	0,8416		0,0,4208	yes	missense,missense	RGS9	NM_001081955.2,NM_003835.3	64,64	0,66,6207	TT,TC,CC		0.0,1.5981,0.5261	possibly-damaging,possibly-damaging	472/672,475/675	63221136	66,12480	2065	4208	6273	SO:0001583	missense	8787	exon18			ACATGGCTCCCAG	AF071476	CCDS42373.1, CCDS45764.1	17q24	2008-07-18	2007-08-14			ENSG00000108370		"""Regulators of G-protein signaling"""	10004	protein-coding gene	gene with protein product	"""regulator of G protein signalling 9"", ""regulator of G protein signalling 9L"", ""regulator of G-protein signaling 9L"""	604067	"""regulator of G-protein signalling 9"""			9765512	Standard	NM_003835		Approved	PERRS, RGS9L, MGC26458, MGC111763	uc002jfe.3	O75916		ENST00000262406.9:c.1424C>T	17.37:g.63221136C>T	ENSP00000262406:p.Ala475Val	95.0	0.0	0		96.0	49.0	0.510417	NM_003835	A8K3C0|O75573|Q696R2|Q8TD64|Q8TD65|Q9HC32|Q9HC33	Missense_Mutation	SNP	ENST00000262406.9	37	CCDS42373.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	C	14.11	2.437293	0.43224	0.015981	0.0	ENSG00000108370	ENST00000262406;ENST00000449996	T;T	0.33216	1.42;1.42	4.56	3.58	0.41010	.	0.420099	0.26742	N	0.022729	T	0.09379	0.0231	N	0.19112	0.55	0.09310	N	1	B;B;B	0.31548	0.099;0.22;0.328	B;B;B	0.24394	0.025;0.024;0.053	T	0.17623	-1.0363	10	0.62326	D	0.03	.	12.4444	0.55643	0.0:0.915:0.0:0.085	.	475;475;472	A8K1G1;O75916;O75916-5	.;RGS9_HUMAN;.	V	475;472	ENSP00000262406:A475V;ENSP00000396329:A472V	ENSP00000262406:A475V	A	+	2	0	RGS9	60651598	0.176000	0.23096	0.018000	0.16275	0.782000	0.44232	2.127000	0.42035	2.450000	0.82876	0.561000	0.74099	GCT	C|0.994;T|0.006	0.006	strong		0.642	RGS9-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000445885.1	NM_003835	
LBH	81606	hgsc.bcm.edu	37	2	30457288	30457288	+	Missense_Mutation	SNP	C	C	T	rs144194149	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:30457288C>T	ENST00000395323.3	+	2	252	c.44C>T	c.(43-45)tCg>tTg	p.S15L	LBH_ENST00000406087.1_Missense_Mutation_p.S15L|LBH_ENST00000401506.1_Missense_Mutation_p.S21L|LBH_ENST00000467242.1_3'UTR|LBH_ENST00000404397.1_Missense_Mutation_p.S15L|LBH_ENST00000407930.2_5'UTR	NM_030915.3	NP_112177.2	Q53QV2	LBH_HUMAN	limb bud and heart development	15					multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(2)|large_intestine(1)|lung(2)	5	Acute lymphoblastic leukemia(172;0.155)					TATCTGAGATCGGCCAAGATG	0.537													C|||	12	0.00239617	0.0076	0.0029	5008	,	,		20573	0.0		0.0	False		,,,				2504	0.0				p.S15L		Atlas-SNP	.											.	LBH	14	.	0			c.C44T						PASS	.	C	LEU/SER	58,4348	56.8+/-93.2	1,56,2146	138.0	116.0	124.0		44	4.5	1.0	2	dbSNP_134	124	0,8600		0,0,4300	yes	missense	LBH	NM_030915.3	145	1,56,6446	TT,TC,CC		0.0,1.3164,0.4459	possibly-damaging	15/106	30457288	58,12948	2203	4300	6503	SO:0001583	missense	81606	exon2			TGAGATCGGCCAA	AF110224	CCDS33173.1	2p23.1	2012-12-07	2012-12-07		ENSG00000213626	ENSG00000213626			29532	protein-coding gene	gene with protein product		611763	"""limb bud and heart development homolog (mouse)"""			11230166, 11336496	Standard	NM_030915		Approved		uc002rne.2	Q53QV2	OTTHUMG00000152051	ENST00000395323.3:c.44C>T	2.37:g.30457288C>T	ENSP00000378733:p.Ser15Leu	171.0	0.0	0		186.0	98.0	0.526882	NM_030915	B2RBC2|Q9H0Q1	Missense_Mutation	SNP	ENST00000395323.3	37	CCDS33173.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	21.8	4.205678	0.79127	0.013164	0.0	ENSG00000213626	ENST00000395323;ENST00000406087;ENST00000404397;ENST00000401506	.	.	.	4.47	4.47	0.54385	.	0.250189	0.33895	N	0.004451	T	0.51126	0.1656	L	0.56769	1.78	0.80722	D	1	D	0.62365	0.991	P	0.47134	0.539	T	0.60915	-0.7168	9	0.46703	T	0.11	-7.442	14.6316	0.68660	0.0:1.0:0.0:0.0	.	15	Q53QV2	LBH_HUMAN	L	15;15;15;21	.	ENSP00000378733:S15L	S	+	2	0	LBH	30310792	0.992000	0.36948	0.990000	0.47175	0.952000	0.60782	3.080000	0.50112	2.028000	0.59812	0.455000	0.32223	TCG	C|0.996;T|0.004	0.004	strong		0.537	LBH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325091.1	NM_030915	
ATAD3A	55210	hgsc.bcm.edu	37	1	1458944	1458944	+	Silent	SNP	C	C	T	rs112145664	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1458944C>T	ENST00000378755.5	+	9	1198	c.1104C>T	c.(1102-1104)ctC>ctT	p.L368L	ATAD3A_ENST00000536055.1_Silent_p.L241L|ATAD3A_ENST00000378756.3_Silent_p.L320L	NM_018188.3	NP_060658.3	Q9NVI7	ATD3A_HUMAN	ATPase family, AAA domain containing 3A	368					cell growth (GO:0016049)|negative regulation of apoptotic process (GO:0043066)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(4)|kidney(6)|large_intestine(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.12e-36)|OV - Ovarian serous cystadenocarcinoma(86;2.18e-22)|Colorectal(212;0.000164)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00233)|BRCA - Breast invasive adenocarcinoma(365;0.00469)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0347)|Lung(427;0.147)		GTGTTGTGCTCAGTGTAAGTC	0.711													N|||	109	0.0217652	0.0756	0.0115	5008	,	,		12972	0.001		0.0	False		,,,				2504	0.0				p.L368L		Atlas-SNP	.											.	ATAD3A	35	.	0			c.C1104T						PASS	.	G	,,	346,4060	177.3+/-206.3	11,324,1868	57.0	56.0	56.0		960,723,1104	2.9	0.9	1	dbSNP_132	56	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	ATAD3A	NM_001170535.1,NM_001170536.1,NM_018188.3	,,	11,326,6166	TT,TC,CC		0.0233,7.8529,2.6757	,,	320/587,241/508,368/635	1458944	348,12658	2203	4300	6503	SO:0001819	synonymous_variant	55210	exon9			TGTGCTCAGTGTA	AK025865	CCDS31.1, CCDS53259.1, CCDS53260.1	1p36.33	2010-04-21		2007-02-08	ENSG00000197785	ENSG00000197785		"""ATPases / AAA-type"""	25567	protein-coding gene	gene with protein product		612316				12477932	Standard	NM_018188		Approved	FLJ10709	uc001afz.2	Q9NVI7	OTTHUMG00000000575	ENST00000378755.5:c.1104C>T	1.37:g.1458944C>T		139.0	0.0	0		186.0	106.0	0.569892	NM_018188	B3KPB3|D2K8Q1|G3V1I6|Q5SV23|Q8N275|Q96A50	Silent	SNP	ENST00000378755.5	37	CCDS31.1	43	0.019688644688644688	37	0.07520325203252033	6	0.016574585635359115	0	0.0	0	0.0	c	0.686	-0.796159	0.02862	0.078529	2.33E-4	ENSG00000197785	ENST00000339113	.	.	.	4.8	2.93	0.34026	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.355	0.66730	0.0:0.5744:0.4256:0.0	.	.	.	.	X	306	.	.	Q	+	1	0	ATAD3A	1448807	1.000000	0.71417	0.865000	0.33974	0.004000	0.04260	0.553000	0.23391	0.465000	0.27167	-1.655000	0.00754	CAG	C|0.974;T|0.026	0.026	strong		0.711	ATAD3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000001365.1	NM_018188	
SF3A3	10946	hgsc.bcm.edu	37	1	38433762	38433762	+	Silent	SNP	G	G	A	rs59294668	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:38433762G>A	ENST00000373019.4	-	15	2281	c.1326C>T	c.(1324-1326)aaC>aaT	p.N442N	SF3A3_ENST00000448721.2_Silent_p.N389N	NM_006802.2	NP_006793.1	Q12874	SF3A3_HUMAN	splicing factor 3a, subunit 3, 60kDa	442					gene expression (GO:0010467)|mRNA 3'-splice site recognition (GO:0000389)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(1)|lung(3)|prostate(2)	12	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				AGTGAGCAGTGTTTGGGATGC	0.448													G|||	79	0.0157748	0.0545	0.0101	5008	,	,		22415	0.0		0.0	False		,,,				2504	0.0				p.N442N		Atlas-SNP	.											.	SF3A3	37	.	0			c.C1326T						PASS	.	G		199,4207	123.3+/-160.7	7,185,2011	184.0	174.0	177.0		1326	-0.1	1.0	1	dbSNP_129	177	0,8600		0,0,4300	no	coding-synonymous	SF3A3	NM_006802.2		7,185,6311	AA,AG,GG		0.0,4.5166,1.5301		442/502	38433762	199,12807	2203	4300	6503	SO:0001819	synonymous_variant	10946	exon15			AGCAGTGTTTGGG	U08815	CCDS428.1	1p34.3	2012-06-07	2002-08-29		ENSG00000183431	ENSG00000183431			10767	protein-coding gene	gene with protein product		605596	"""splicing factor 3a, subunit 3, 60kD"""			7816610, 8022796	Standard	NM_006802		Approved	SF3a60, SAP61, PRP9, PRPF9	uc001cci.3	Q12874	OTTHUMG00000004438	ENST00000373019.4:c.1326C>T	1.37:g.38433762G>A		478.0	2.0	0.0041841		500.0	294.0	0.588	NM_006802	D3DPT5|Q15460|Q5VT87	Silent	SNP	ENST00000373019.4	37	CCDS428.1																																																																																			G|0.983;A|0.017	0.017	strong		0.448	SF3A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012976.1	NM_006802	
ATP1A2	477	hgsc.bcm.edu	37	1	160104950	160104950	+	Silent	SNP	C	C	T	rs61734529	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:160104950C>T	ENST00000361216.3	+	15	2069	c.1980C>T	c.(1978-1980)tgC>tgT	p.C660C	ATP1A2_ENST00000392233.3_Silent_p.C660C	NM_000702.3	NP_000693.1	P50993	AT1A2_HUMAN	ATPase, Na+/K+ transporting, alpha 2 polypeptide	660					adult locomotory behavior (GO:0008344)|ATP biosynthetic process (GO:0006754)|ATP hydrolysis coupled proton transport (GO:0015991)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|locomotion (GO:0040011)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of heart contraction (GO:0045822)|negative regulation of striated muscle contraction (GO:0045988)|neurotransmitter uptake (GO:0001504)|potassium ion import (GO:0010107)|potassium ion transport (GO:0006813)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of smooth muscle contraction (GO:0006940)|regulation of striated muscle contraction (GO:0006942)|regulation of the force of heart contraction (GO:0002026)|regulation of vasoconstriction (GO:0019229)|relaxation of cardiac muscle (GO:0055119)|response to nicotine (GO:0035094)|sodium ion export from cell (GO:0036376)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|visual learning (GO:0008542)	caveola (GO:0005901)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|endosome (GO:0005768)|plasma membrane (GO:0005886)|sodium:potassium-exchanging ATPase complex (GO:0005890)|synapse (GO:0045202)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|metal ion binding (GO:0046872)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)			NS(1)|autonomic_ganglia(1)|breast(4)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(30)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	69	all_cancers(52;1.11e-16)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)|LUSC - Lung squamous cell carcinoma(543;0.246)			CCAAGGCATGCGTGGTGCACG	0.612													C|||	104	0.0207668	0.0779	0.0014	5008	,	,		22206	0.0		0.0	False		,,,				2504	0.0				p.C660C		Atlas-SNP	.											.	ATP1A2	167	.	0			c.C1980T						PASS	.	C		301,4105	164.0+/-195.7	10,281,1912	99.0	72.0	81.0		1980	-6.2	0.4	1	dbSNP_129	81	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ATP1A2	NM_000702.3		10,283,6210	TT,TC,CC		0.0233,6.8316,2.3297		660/1021	160104950	303,12703	2203	4300	6503	SO:0001819	synonymous_variant	477	exon15			GGCATGCGTGGTG	AB018321	CCDS1196.1	1q23.2	2014-09-17	2010-04-20		ENSG00000018625	ENSG00000018625	3.6.3.9	"""ATPases / P-type"""	800	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-2"", ""sodium pump subunit alpha-2"", ""sodium-potassium ATPase catalytic subunit alpha-2"""	182340	"""migraine, hemiplegic 2"", ""ATPase, Na+/K+ transporting, alpha 2 (+) polypeptide"""	MHP2		9403481	Standard	NM_000702		Approved	FHM2	uc001fvc.3	P50993	OTTHUMG00000024080	ENST00000361216.3:c.1980C>T	1.37:g.160104950C>T		356.0	0.0	0		414.0	216.0	0.521739	NM_000702	D3DVE4|Q07059|Q5JW74|Q86UZ5|Q9UQ25	Silent	SNP	ENST00000361216.3	37	CCDS1196.1	34	0.015567765567765568	34	0.06910569105691057	0	0.0	0	0.0	0	0.0	C	9.163	1.019313	0.19355	0.068316	2.33E-4	ENSG00000018625	ENST00000447527	.	.	.	4.44	-6.19	0.02078	.	.	.	.	.	T	0.47173	0.1431	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60662	-0.7219	4	.	.	.	.	13.6226	0.62146	0.0:0.609:0.0:0.391	rs61734529	.	.	.	V	371	.	.	A	+	2	0	ATP1A2	158371574	0.002000	0.14202	0.400000	0.26346	0.942000	0.58702	-1.400000	0.02504	-1.346000	0.02211	0.511000	0.50034	GCG	C|0.978;T|0.022	0.022	strong		0.612	ATP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060642.2	NM_000702	
DCANP1	140947	hgsc.bcm.edu	37	5	134782396	134782396	+	Missense_Mutation	SNP	T	T	A	rs67187482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:134782396T>A	ENST00000503143.2	-	1	642	c.403A>T	c.(403-405)Agt>Tgt	p.S135C	TIFAB_ENST00000537858.1_3'UTR	NM_130848.2	NP_570900.1	Q8TF63	DCNP1_HUMAN		135						nucleus (GO:0005634)				endometrium(1)|lung(1)|prostate(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			AGTCTGAAACTACAAACCAGA	0.547													T|||	430	0.0858626	0.2867	0.0418	5008	,	,		19738	0.0		0.0179	False		,,,				2504	0.0041				p.S135C		Atlas-SNP	.											.	C5orf20	16	.	0			c.A403T						PASS	.	T	CYS/SER	1116,3290	402.4+/-332.3	149,818,1236	132.0	143.0	139.0		403	-1.8	0.0	5	dbSNP_130	139	119,8481	61.7+/-123.6	1,117,4182	yes	missense	C5orf20	NM_130848.2	112	150,935,5418	AA,AT,TT		1.3837,25.3291,9.4956	benign	135/245	134782396	1235,11771	2203	4300	6503	SO:0001583	missense	140947	exon1			TGAAACTACAAAC																												ENST00000503143.2:c.403A>T	5.37:g.134782396T>A	ENSP00000421871:p.Ser135Cys	104.0	0.0	0		100.0	42.0	0.42	NM_130848		Missense_Mutation	SNP	ENST00000503143.2	37	CCDS4186.1	163	0.07463369963369963	132	0.2682926829268293	14	0.03867403314917127	0	0.0	17	0.022427440633245383	T	4.521	0.096694	0.08681	0.253291	0.013837	ENSG00000251380	ENST00000503143	T	0.39056	1.1	2.85	-1.79	0.07932	.	.	.	.	.	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	0.32508	-0.9904	8	0.87932	D	0	.	4.0496	0.09790	0.3788:0.41:0.0:0.2112	.	135	Q8TF63	DCNP1_HUMAN	C	135	ENSP00000421871:S135C	ENSP00000421871:S135C	S	-	1	0	C5orf20	134810295	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.310000	0.19356	-0.278000	0.09180	-0.892000	0.02923	AGT	T|0.905;A|0.095	0.095	strong		0.547	C5orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372531.1		
EPPK1	83481	hgsc.bcm.edu	37	8	144946271	144946271	+	Missense_Mutation	SNP	C	C	T	rs58368323	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144946271C>T	ENST00000525985.1	-	2	1222	c.1151G>A	c.(1150-1152)gGg>gAg	p.G384E				P58107	EPIPL_HUMAN	epiplakin 1	384						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GTCCACTAGCCCCTTCTTCAT	0.672													C|||	224	0.0447284	0.1604	0.013	5008	,	,		15903	0.0		0.003	False		,,,				2504	0.0				p.G384E		Atlas-SNP	.											.	EPPK1	199	.	0			c.G1151A						PASS	.	C	GLU/GLY	400,3414		19,362,1526	6.0	7.0	7.0		1151	-1.4	0.7	8	dbSNP_129	7	6,8126		0,6,4060	yes	missense	EPPK1	NM_031308.1	98	19,368,5586	TT,TC,CC		0.0738,10.4877,3.3986	benign	384/2420	144946271	406,11540	1907	4066	5973	SO:0001583	missense	83481	exon1			ACTAGCCCCTTCT	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.1151G>A	8.37:g.144946271C>T	ENSP00000436337:p.Gly384Glu	95.0	0.0	0		72.0	34.0	0.472222	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		83	0.038003663003663	70	0.14227642276422764	4	0.011049723756906077	2	0.0034965034965034965	7	0.009234828496042216	C	9.565	1.119374	0.20877	0.104877	7.38E-4	ENSG00000227184	ENST00000525985	T	0.72835	-0.69	4.96	-1.43	0.08884	.	.	.	.	.	T	0.00524	0.0017	N	0.25789	0.76	0.09310	N	0.999997	B	0.12013	0.005	B	0.09377	0.004	T	0.00870	-1.1533	9	0.16896	T	0.51	.	10.042	0.42164	0.0:0.6982:0.0:0.3018	rs58368323	384	E9PPU0	.	E	384	ENSP00000436337:G384E	ENSP00000436337:G384E	G	-	2	0	EPPK1	145018259	0.000000	0.05858	0.663000	0.29738	0.564000	0.35744	-0.181000	0.09740	-0.542000	0.06249	-0.409000	0.06214	GGG	C|0.961;T|0.039	0.039	strong		0.672	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
ENDOU	8909	hgsc.bcm.edu	37	12	48110150	48110150	+	Silent	SNP	G	G	A	rs61734364	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:48110150G>A	ENST00000422538.3	-	6	806	c.684C>T	c.(682-684)gaC>gaT	p.D228D	ENDOU_ENST00000545824.2_Silent_p.D165D|ENDOU_ENST00000229003.3_Silent_p.D187D|ENDOU_ENST00000542202.1_De_novo_Start_OutOfFrame|RP1-197B17.3_ENST00000547799.1_lincRNA	NM_001172439.1	NP_001165910.1	P21128	ENDOU_HUMAN	endonuclease, polyU-specific	228					female pregnancy (GO:0007565)|immune response (GO:0006955)|proteolysis (GO:0006508)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	endoribonuclease activity (GO:0004521)|growth factor activity (GO:0008083)|manganese ion binding (GO:0030145)|polysaccharide binding (GO:0030247)|RNA binding (GO:0003723)|scavenger receptor activity (GO:0005044)|serine-type peptidase activity (GO:0008236)			autonomic_ganglia(1)|endometrium(2)|large_intestine(4)|lung(2)|ovary(3)|pancreas(1)|stomach(1)	14						TGAGGAAGGCGTCCTGCTCGG	0.592											OREG0021752	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	109	0.0217652	0.0756	0.0101	5008	,	,		17569	0.001		0.001	False		,,,				2504	0.0				p.D228D		Atlas-SNP	.											.	ENDOU	39	.	0			c.C684T						PASS	.	G	,,	344,4062	180.5+/-208.7	12,320,1871	136.0	124.0	128.0		684,495,561	-9.6	0.0	12	dbSNP_129	128	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	ENDOU	NM_001172439.1,NM_001172440.1,NM_006025.3	,,	12,323,6168	AA,AG,GG		0.0349,7.8075,2.668	,,	228/411,165/348,187/370	48110150	347,12659	2203	4300	6503	SO:0001819	synonymous_variant	8909	exon6			GAAGGCGTCCTGC	M32402	CCDS8754.1, CCDS53784.1, CCDS53785.1	12q13.1	2011-08-31			ENSG00000111405	ENSG00000111405		"""Serine peptidases / Serine peptidases"""	14369	protein-coding gene	gene with protein product		606720				2350438, 1710108, 15755742, 18936097	Standard	NM_006025		Approved	PP11, P11, PRSS26	uc001rpu.2	P21128	OTTHUMG00000169670	ENST00000422538.3:c.684C>T	12.37:g.48110150G>A		193.0	0.0	0	952	204.0	93.0	0.455882	NM_001172439	B2RBJ3|B3KQS7|B7Z6E1|Q2NKJ4	Silent	SNP	ENST00000422538.3	37	CCDS53785.1																																																																																			A|0.024;G|0.975;T|0.000	0.024	strong		0.592	ENDOU-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000405352.1	NM_006025.2	
ANGPT4	51378	hgsc.bcm.edu	37	20	861853	861853	+	Silent	SNP	G	G	A	rs6086328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:861853G>A	ENST00000381922.3	-	5	1014	c.912C>T	c.(910-912)gtC>gtT	p.V304V	ANGPT4_ENST00000546022.1_Silent_p.V304V	NM_015985.2	NP_057069.1	Q9Y264	ANGP4_HUMAN	angiopoietin 4	304	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular response to hypoxia (GO:0071456)|leukocyte migration (GO:0050900)|negative regulation of angiogenesis (GO:0016525)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)	27						GGATGGTGTAGACACCACTGG	0.572													G|||	335	0.066893	0.2405	0.0216	5008	,	,		18573	0.0		0.002	False		,,,				2504	0.0				p.V304V	Pancreas(181;481 2077 3259 31286 49856)	Atlas-SNP	.											.	ANGPT4	77	.	0			c.C912T						PASS	.	G		986,3420	370.0+/-319.4	106,774,1323	74.0	62.0	66.0		912	4.9	1.0	20	dbSNP_114	66	14,8586	9.1+/-34.3	0,14,4286	no	coding-synonymous	ANGPT4	NM_015985.2		106,788,5609	AA,AG,GG		0.1628,22.3786,7.6888		304/504	861853	1000,12006	2203	4300	6503	SO:0001819	synonymous_variant	51378	exon5			GGTGTAGACACCA	AF074332	CCDS13009.1	20p13	2013-02-06			ENSG00000101280	ENSG00000101280		"""Fibrinogen C domain containing"""	487	protein-coding gene	gene with protein product		603705				10051567, 10218486	Standard	NM_015985		Approved		uc002wei.3	Q9Y264	OTTHUMG00000031652	ENST00000381922.3:c.912C>T	20.37:g.861853G>A		121.0	0.0	0		111.0	48.0	0.432432	NM_015985	B4E3J9|Q5TFF4|Q9H4Z4	Silent	SNP	ENST00000381922.3	37	CCDS13009.1																																																																																			A|0.066;G|0.934	0.066	strong		0.572	ANGPT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077493.1	NM_015985	
MUC4	4585	hgsc.bcm.edu	37	3	195505828	195505828	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195505828G>T	ENST00000463781.3	-	2	13082	c.12623C>A	c.(12622-12624)cCt>cAt	p.P4208H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P4208H	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)		GACAGGAAGAGGGGTGGCGTG	0.592																																					p.P4208H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,3	MUC4	1505	3	0			c.C12623A						PASS	.						17.0	16.0	16.0					3																	195505828		688	1570	2258	SO:0001583	missense	4585	exon2			GGAAGAGGGGTGG	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.12623C>A	3.37:g.195505828G>T	ENSP00000417498:p.Pro4208His	246.0	0.0	0		292.0	24.0	0.0821918	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	4.993	0.184423	0.09495	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.36340	1.46;1.26	.	.	.	.	.	.	.	.	T	0.33235	0.0856	N	0.19112	0.55	0.23101	N	0.998295	D	0.56521	0.976	P	0.62298	0.9	T	0.14392	-1.0474	7	.	.	.	.	3.6132	0.08067	2.0E-4:0.4969:0.5026:2.0E-4	.	4080	E7ESK3	.	H	4208	ENSP00000417498:P4208H;ENSP00000420243:P4208H	.	P	-	2	0	MUC4	196990607	.	.	0.019000	0.16419	0.029000	0.11900	.	.	0.088000	0.17205	0.089000	0.15464	CCT	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
COTL1	23406	hgsc.bcm.edu	37	16	84651452	84651452	+	Silent	SNP	G	G	C	rs144159131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84651452G>C	ENST00000262428.4	-	1	231	c.69C>G	c.(67-69)gcC>gcG	p.A23A	COTL1_ENST00000564057.1_5'UTR	NM_021149.2	NP_066972.1	Q14019	COTL1_HUMAN	coactosin-like F-actin binding protein 1	23	ADF-H. {ECO:0000255|PROSITE- ProRule:PRU00599}.				defense response to fungus (GO:0050832)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	actin binding (GO:0003779)|enzyme binding (GO:0019899)			endometrium(1)|large_intestine(1)|liver(1)|lung(2)|skin(1)	6						ACCAGATGACGGCCGAGCCGT	0.706													g|||	3	0.000599042	0.0015	0.0	5008	,	,		7761	0.0		0.0	False		,,,				2504	0.001				p.A23A		Atlas-SNP	.											.	COTL1	17	.	0			c.C69G						PASS	.			4,4354		0,4,2175	19.0	15.0	16.0		69	-5.9	1.0	16	dbSNP_134	16	0,8534		0,0,4267	no	coding-synonymous	COTL1	NM_021149.2		0,4,6442	CC,CG,GG		0.0,0.0918,0.031		23/143	84651452	4,12888	2179	4267	6446	SO:0001819	synonymous_variant	23406	exon1			GATGACGGCCGAG	L54057	CCDS10947.1	16q24.1	2014-03-05	2014-03-05	2002-08-01	ENSG00000103187	ENSG00000103187			18304	protein-coding gene	gene with protein product		606748	"""coactosin-like 1 (Dictyostelium)"""			10051563, 9326934, 16924104	Standard	NM_021149		Approved	CLP	uc002fid.3	Q14019	OTTHUMG00000137634	ENST00000262428.4:c.69C>G	16.37:g.84651452G>C		22.0	0.0	0		35.0	16.0	0.457143	NM_021149	B2RDU3|D3DUL9|Q86XM5	Silent	SNP	ENST00000262428.4	37	CCDS10947.1																																																																																			G|0.999;C|0.001	0.001	strong		0.706	COTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269075.1	NM_021149	
BCL6B	255877	hgsc.bcm.edu	37	17	6930927	6930927	+	Missense_Mutation	SNP	G	G	A	rs201522060	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:6930927G>A	ENST00000293805.5	+	9	1521	c.1429G>A	c.(1429-1431)Ggg>Agg	p.G477R		NM_181844.3	NP_862827	Q8N143	BCL6B_HUMAN	B-cell CLL/lymphoma 6, member B	477					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			skin(1)	1						CCACATTCTCGGGGGGCCCTA	0.627													G|||	7	0.00139776	0.0045	0.0014	5008	,	,		17141	0.0		0.0	False		,,,				2504	0.0				p.G477R		Atlas-SNP	.											.	BCL6B	85	.	0			c.G1429A						PASS	.	G	ARG/GLY	15,3949		0,15,1967	49.0	54.0	53.0		1429	5.5	1.0	17		53	1,8327		0,1,4163	yes	missense	BCL6B	NM_181844.3	125	0,16,6130	AA,AG,GG		0.012,0.3784,0.1302	probably-damaging	477/480	6930927	16,12276	1982	4164	6146	SO:0001583	missense	255877	exon9			ATTCTCGGGGGGC	AI672318	CCDS42248.1	17p13.1	2014-06-10	2010-04-14		ENSG00000161940	ENSG00000161940		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	1002	protein-coding gene	gene with protein product		608992	"""zinc finger protein 62"", ""B-cell CLL/lymphoma 6, member B (zinc finger protein)"""	ZNF62		9632807	Standard	NM_181844		Approved	ZBTB28, BAZF	uc010clt.1	Q8N143	OTTHUMG00000177882	ENST00000293805.5:c.1429G>A	17.37:g.6930927G>A	ENSP00000293805:p.Gly477Arg	65.0	0.0	0		86.0	44.0	0.511628	NM_181844	Q6PCB4	Missense_Mutation	SNP	ENST00000293805.5	37	CCDS42248.1	.	.	.	.	.	.	.	.	.	.	G	14.52	2.560429	0.45590	0.003784	1.2E-4	ENSG00000161940	ENST00000293805	T	0.07114	3.22	5.47	5.47	0.80525	.	0.340325	0.32161	N	0.006486	T	0.08133	0.0203	L	0.29908	0.895	0.38463	D	0.94726	B	0.22541	0.071	B	0.14578	0.011	T	0.15636	-1.0430	10	0.51188	T	0.08	.	14.8178	0.70048	0.0:0.0:1.0:0.0	.	477	Q8N143	BCL6B_HUMAN	R	477	ENSP00000293805:G477R	ENSP00000293805:G477R	G	+	1	0	BCL6B	6871651	0.978000	0.34361	0.999000	0.59377	0.849000	0.48306	4.025000	0.57225	2.584000	0.87258	0.462000	0.41574	GGG	.	.	weak		0.627	BCL6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439455.2	NM_181844	
C9orf172	389813	hgsc.bcm.edu	37	9	139740900	139740900	+	Silent	SNP	C	C	T	rs147735504	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139740900C>T	ENST00000436881.1	+	1	2034	c.2034C>T	c.(2032-2034)aaC>aaT	p.N678N	PHPT1_ENST00000545326.1_5'Flank|PHPT1_ENST00000371661.1_5'Flank|PHPT1_ENST00000247665.10_5'Flank	NM_001080482.2	NP_001073951.2	C9J069	CI172_HUMAN	chromosome 9 open reading frame 172	678										endometrium(2)|large_intestine(1)|lung(6)	9						CCATGTTCAACGCCTGCCTCT	0.682													c|||	31	0.0061901	0.0227	0.0014	5008	,	,		10471	0.0		0.0	False		,,,				2504	0.0				p.N678N		Atlas-SNP	.											.	C9orf172	23	.	0			c.C2034T						PASS	.	C		90,4048		0,90,1979	23.0	28.0	27.0		2034	3.2	1.0	9	dbSNP_134	27	1,8323		0,1,4161	no	coding-synonymous	C9orf172	NM_001080482.2		0,91,6140	TT,TC,CC		0.012,2.175,0.7302		678/977	139740900	91,12371	2069	4162	6231	SO:0001819	synonymous_variant	389813	exon1			GTTCAACGCCTGC		CCDS48059.1	9q34.3	2012-04-03			ENSG00000232434	ENSG00000232434			37284	protein-coding gene	gene with protein product							Standard	NM_001080482		Approved		uc011meh.2	C9J069		ENST00000436881.1:c.2034C>T	9.37:g.139740900C>T		41.0	0.0	0		38.0	16.0	0.421053	NM_001080482		Silent	SNP	ENST00000436881.1	37	CCDS48059.1																																																																																			C|0.994;T|0.006	0.006	strong		0.682	C9orf172-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080482	
WDSUB1	151525	hgsc.bcm.edu	37	2	160104988	160104988	+	Missense_Mutation	SNP	T	T	C	rs74475652	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160104988T>C	ENST00000409990.3	-	10	1424	c.1168A>G	c.(1168-1170)Att>Gtt	p.I390V	WDSUB1_ENST00000392796.3_Missense_Mutation_p.I390V|WDSUB1_ENST00000358147.4_Missense_Mutation_p.I298V|WDSUB1_ENST00000359774.4_Missense_Mutation_p.I390V|WDSUB1_ENST00000409124.1_Intron	NM_001128213.1	NP_001121685	Q8N9V3	WSDU1_HUMAN	WD repeat, sterile alpha motif and U-box domain containing 1	390	SAM. {ECO:0000255|PROSITE- ProRule:PRU00184}.						ubiquitin-protein transferase activity (GO:0004842)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(3)|prostate(1)|stomach(3)	16						AGCTCTTCAATTTTCCTCAGC	0.388													T|||	219	0.04373	0.1604	0.0086	5008	,	,		19089	0.0		0.001	False		,,,				2504	0.0				p.I390V		Atlas-SNP	.											.	WDSUB1	39	.	0			c.A1168G						PASS	.	T	VAL/ILE,VAL/ILE,VAL/ILE	583,3823	258.3+/-262.4	45,493,1665	100.0	101.0	101.0		1168,1168,1168	3.5	1.0	2	dbSNP_131	101	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense	WDSUB1	NM_001128212.1,NM_001128213.1,NM_152528.2	29,29,29	45,495,5963	CC,CT,TT		0.0233,13.232,4.4979	benign,benign,benign	390/477,390/477,390/477	160104988	585,12421	2203	4300	6503	SO:0001583	missense	151525	exon10			CTTCAATTTTCCT	AK093494	CCDS2208.1	2q24.2	2013-01-28	2006-02-17	2005-03-25	ENSG00000196151	ENSG00000196151		"""WD repeat domain containing"", ""Sterile alpha motif (SAM) domain containing"", ""U-box domain containing"""	26697	protein-coding gene	gene with protein product			"""WD repeat and SAM domain containing 1"", ""WD repeat, SAM and U-box domain containing 1"""	WDSAM1		12477932	Standard	NM_152528		Approved	UBOX6, FLJ36175	uc002ual.4	Q8N9V3	OTTHUMG00000132028	ENST00000409990.3:c.1168A>G	2.37:g.160104988T>C	ENSP00000387078:p.Ile390Val	101.0	0.0	0		91.0	44.0	0.483516	NM_152528	Q53TI9|Q8N6N8	Missense_Mutation	SNP	ENST00000409990.3	37	CCDS2208.1	64	0.029304029304029304	62	0.12601626016260162	2	0.0055248618784530384	0	0.0	0	0.0	T	11.96	1.793785	0.31685	0.13232	2.33E-4	ENSG00000196151	ENST00000359774;ENST00000358147;ENST00000392796;ENST00000409990	T;T;T;T	0.51325	0.71;0.71;0.71;0.71	5.97	3.55	0.40652	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	0.114020	0.64402	N	0.000011	T	0.00552	0.0018	M	0.64997	1.995	0.09310	P	1.0	B;B	0.24258	0.009;0.1	B;B	0.28465	0.007;0.09	T	0.08785	-1.0705	9	0.38643	T	0.18	.	10.5342	0.44994	0.0:0.132:0.0:0.868	.	298;390	Q8N9V3-2;Q8N9V3	.;WSDU1_HUMAN	V	390;298;390;390	ENSP00000352820:I390V;ENSP00000350866:I298V;ENSP00000376545:I390V;ENSP00000387078:I390V	ENSP00000350866:I298V	I	-	1	0	WDSUB1	159813234	1.000000	0.71417	0.993000	0.49108	0.992000	0.81027	3.080000	0.50112	0.486000	0.27676	0.528000	0.53228	ATT	T|0.958;C|0.042	0.042	strong		0.388	WDSUB1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333339.1	NM_152528	
BMP3	651	hgsc.bcm.edu	37	4	81952658	81952658	+	Missense_Mutation	SNP	C	C	G	rs61729824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:81952658C>G	ENST00000282701.2	+	1	540	c.220C>G	c.(220-222)Cgg>Ggg	p.R74G		NM_001201.2	NP_001192.2	P12645	BMP3_HUMAN	bone morphogenetic protein 3	74					cartilage development (GO:0051216)|cell differentiation (GO:0030154)|cell-cell signaling (GO:0007267)|growth (GO:0040007)|ossification (GO:0001503)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system development (GO:0001501)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	BMP receptor binding (GO:0070700)|receptor binding (GO:0005102)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(4)|pancreas(1)|prostate(1)|stomach(1)|urinary_tract(1)	29						CCAGGCGGCCCGGACACCGGG	0.687													c|||	28	0.00559105	0.0197	0.0029	5008	,	,		13952	0.0		0.0	False		,,,				2504	0.0				p.R74G		Atlas-SNP	.											.	BMP3	59	.	0			c.C220G						PASS	.						18.0	21.0	20.0					4																	81952658		2199	4298	6497	SO:0001583	missense	651	exon1			GCGGCCCGGACAC	M22491	CCDS3588.1	4q21	2013-02-06	2008-05-22		ENSG00000152785	ENSG00000152785		"""Bone morphogenetic proteins"""	1070	protein-coding gene	gene with protein product	"""osteogenin"""	112263	"""bone morphogenetic protein 3 (osteogenic)"""				Standard	NM_001201		Approved		uc003hmg.4	P12645	OTTHUMG00000130292	ENST00000282701.2:c.220C>G	4.37:g.81952658C>G	ENSP00000282701:p.Arg74Gly	78.0	0.0	0		103.0	47.0	0.456311	NM_001201	Q4VAS5	Missense_Mutation	SNP	ENST00000282701.2	37	CCDS3588.1	.	.	.	.	.	.	.	.	.	.	c	7.074	0.568893	0.13560	.	.	ENSG00000152785	ENST00000282701	T	0.64803	-0.12	3.44	2.6	0.31112	Transforming growth factor-beta, N-terminal (1);	1.192490	0.06406	N	0.719754	T	0.41880	0.1178	N	0.08118	0	0.09310	N	1	B	0.25007	0.116	B	0.28849	0.095	T	0.35649	-0.9780	10	0.22109	T	0.4	.	7.0017	0.24813	0.0:0.875:0.0:0.125	.	74	P12645	BMP3_HUMAN	G	74	ENSP00000282701:R74G	ENSP00000282701:R74G	R	+	1	2	BMP3	82171682	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-0.383000	0.07398	1.034000	0.39945	-0.215000	0.12644	CGG	C|0.988;T|0.012	.	alt		0.687	BMP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252634.1		
SCAF11	9169	hgsc.bcm.edu	37	12	46321417	46321417	+	Silent	SNP	G	G	A	rs11574971	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:46321417G>A	ENST00000369367.3	-	11	2300	c.2067C>T	c.(2065-2067)acC>acT	p.T689T	SCAF11_ENST00000549162.1_Silent_p.T497T|SCAF11_ENST00000550629.1_5'Flank|SCAF11_ENST00000465950.1_Silent_p.T374T|SCAF11_ENST00000419565.2_Silent_p.T689T	NM_004719.2	NP_004710.2	Q99590	SCAFB_HUMAN	SR-related CTD-associated factor 11	689					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|spliceosomal complex assembly (GO:0000245)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(8)|large_intestine(17)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	69						TAGGATGTTCGGTCAGCGATT	0.318													G|||	549	0.109625	0.3775	0.0259	5008	,	,		13728	0.004		0.002	False		,,,				2504	0.0266				p.T689T		Atlas-SNP	.											.	SCAF11	145	.	0			c.C2067T						PASS	.	G		1384,3022	457.5+/-351.6	235,914,1054	160.0	162.0	161.0		2067	1.9	0.0	12	dbSNP_120	161	14,8586	9.8+/-36.6	0,14,4286	no	coding-synonymous	SCAF11	NM_004719.2		235,928,5340	AA,AG,GG		0.1628,31.4117,10.7489		689/1464	46321417	1398,11608	2203	4300	6503	SO:0001819	synonymous_variant	9169	exon11			ATGTTCGGTCAGC	Y11251	CCDS8748.2	12q13.11	2013-01-09	2011-01-10	2011-01-10	ENSG00000139218	ENSG00000139218		"""RING-type (C3HC4) zinc fingers"""	10784	protein-coding gene	gene with protein product		603668	"""splicing factor, arginine/serine-rich 2, interacting protein"", ""serine/arginine-rich splicing factor 2, interacting protein"""	SFRS2IP, SRSF2IP		9224939, 9447963	Standard	NM_004719		Approved	SIP1, SRRP129, CASP11	uc001rox.3	Q99590	OTTHUMG00000149930	ENST00000369367.3:c.2067C>T	12.37:g.46321417G>A		76.0	0.0	0		90.0	45.0	0.5	NM_004719	A6NEU9|A6NLW5|Q8IW59	Silent	SNP	ENST00000369367.3	37	CCDS8748.2																																																																																			G|0.894;A|0.106	0.106	strong		0.318	SCAF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313992.2	NM_004719	
PLXNB2	23654	hgsc.bcm.edu	37	22	50720430	50720430	+	Silent	SNP	G	G	C	rs56110807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:50720430G>C	ENST00000449103.1	-	20	3338	c.3198C>G	c.(3196-3198)gcC>gcG	p.A1066A	PLXNB2_ENST00000359337.4_Silent_p.A1066A|PLXNB2_ENST00000496720.1_5'Flank			O15031	PLXB2_HUMAN	plexin B2	1066	IPT/TIG 3.				brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)			breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		TGAGGTTGTAGGCCTCTGGCT	0.612													G|||	436	0.0870607	0.3169	0.0245	5008	,	,		17944	0.0		0.0	False		,,,				2504	0.0				p.A1066A		Atlas-SNP	.											.	PLXNB2	172	.	0			c.C3198G						PASS	.	G		954,3276		106,742,1267	54.0	61.0	59.0		3198	2.5	1.0	22	dbSNP_129	59	2,8428		0,2,4213	no	coding-synonymous	PLXNB2	NM_012401.3		106,744,5480	CC,CG,GG		0.0237,22.5532,7.5513		1066/1839	50720430	956,11704	2115	4215	6330	SO:0001819	synonymous_variant	23654	exon20			GTTGTAGGCCTCT		CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"""Plexins"""	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.3198C>G	22.37:g.50720430G>C		48.0	0.0	0		41.0	23.0	0.560976	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Silent	SNP	ENST00000449103.1	37	CCDS43035.1	154	0.07051282051282051	144	0.2926829268292683	10	0.027624309392265192	0	0.0	0	0.0	G	6.393	0.440700	0.12104	0.225532	2.37E-4	ENSG00000196576	ENST00000427829	.	.	.	4.63	2.46	0.29980	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.20538	-1.0272	3	.	.	.	.	10.4218	0.44354	0.1674:0.0:0.8326:0.0	rs56110807	.	.	.	R	84	.	.	P	-	2	0	PLXNB2	49062557	1.000000	0.71417	1.000000	0.80357	0.432000	0.31715	2.715000	0.47210	1.146000	0.42352	0.313000	0.20887	CCT	G|0.953;C|0.047	0.047	strong		0.612	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401	
TNFSF12	8742	hgsc.bcm.edu	37	17	7460514	7460514	+	Silent	SNP	G	G	A	rs143039184	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7460514G>A	ENST00000293825.6	+	7	860	c.597G>A	c.(595-597)gcG>gcA	p.A199A	TNFSF13_ENST00000380535.4_5'Flank|TNFSF13_ENST00000396542.1_5'Flank|TNFSF12-TNFSF13_ENST00000293826.4_Intron|TNFSF12_ENST00000462811.1_3'UTR|TNFSF13_ENST00000396545.4_5'Flank|TNFSF13_ENST00000483039.1_5'Flank|TNFSF13_ENST00000338784.4_5'Flank|TNFSF12_ENST00000557233.1_Intron|TNFSF13_ENST00000349228.4_5'Flank	NM_003809.2	NP_003800.1	O43508	TNF12_HUMAN	tumor necrosis factor (ligand) superfamily, member 12	199					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell differentiation (GO:0030154)|endothelial cell migration (GO:0043542)|immune response (GO:0006955)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)	cytokine activity (GO:0005125)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|large_intestine(5)|prostate(2)	11		Prostate(122;0.157)				CAGCCACTGCGGCGAGTTCCC	0.667													G|||	7	0.00139776	0.003	0.0043	5008	,	,		13746	0.0		0.0	False		,,,				2504	0.0				p.A199A		Atlas-SNP	.											.	TNFSF12	20	.	0			c.G597A						PASS	.	G	,	14,4392	21.2+/-45.6	0,14,2189	83.0	65.0	71.0		597,	-7.7	0.0	17	dbSNP_134	71	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,intron	TNFSF12,TNFSF12-TNFSF13	NM_003809.2,NM_172089.3	,	0,18,6485	AA,AG,GG		0.0465,0.3177,0.1384	,	199/250,	7460514	18,12988	2203	4300	6503	SO:0001819	synonymous_variant	8742	exon7			CACTGCGGCGAGT	AF030099	CCDS11109.1	17p13.1	2008-02-01			ENSG00000239697	ENSG00000239697		"""Tumor necrosis factor (ligand) superfamily"""	11927	protein-coding gene	gene with protein product		602695				9405449, 9560343	Standard	NM_003809		Approved	TWEAK, DR3LG, APO3L		O43508	OTTHUMG00000108148	ENST00000293825.6:c.597G>A	17.37:g.7460514G>A		87.0	0.0	0		84.0	45.0	0.535714	NM_003809	Q8IZK7|Q8WUZ7	Silent	SNP	ENST00000293825.6	37	CCDS11109.1																																																																																			G|0.999;A|0.001	0.001	strong		0.667	TNFSF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226951.2	NM_003809	
TG	7038	hgsc.bcm.edu	37	8	133899438	133899438	+	Silent	SNP	C	C	T	rs61742713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:133899438C>T	ENST00000220616.4	+	9	1861	c.1821C>T	c.(1819-1821)acC>acT	p.T607T	TG_ENST00000377869.1_Silent_p.T607T	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	607	Thyroglobulin type-1 5. {ECO:0000255|PROSITE-ProRule:PRU00500}.				hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		GCTCCCAGACCTGTGAGCAGA	0.473													C|||	108	0.0215655	0.0802	0.0029	5008	,	,		21407	0.0		0.0	False		,,,				2504	0.0				p.T607T		Atlas-SNP	.											.	TG	416	.	0			c.C1821T						PASS	.	C		290,4116	160.0+/-192.4	12,266,1925	148.0	132.0	137.0		1821	5.0	0.7	8	dbSNP_129	137	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TG	NM_003235.4		12,268,6223	TT,TC,CC		0.0233,6.5819,2.2451		607/2769	133899438	292,12714	2203	4300	6503	SO:0001819	synonymous_variant	7038	exon9			CCAGACCTGTGAG	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.1821C>T	8.37:g.133899438C>T		141.0	0.0	0		149.0	77.0	0.516779	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1																																																																																			C|0.974;T|0.026	0.026	strong		0.473	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
SEL1L3	23231	hgsc.bcm.edu	37	4	25806279	25806279	+	Missense_Mutation	SNP	T	T	C	rs16877591	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:25806279T>C	ENST00000399878.3	-	10	1782	c.1660A>G	c.(1660-1662)Att>Gtt	p.I554V	SEL1L3_ENST00000502949.1_Missense_Mutation_p.I401V|SEL1L3_ENST00000264868.5_Missense_Mutation_p.I519V	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	554			I -> V (in dbSNP:rs16877591).			integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						ATAGAGCTAATTTGGTGAAGA	0.423													T|||	315	0.0628994	0.2307	0.013	5008	,	,		19704	0.001		0.0	False		,,,				2504	0.0				p.I554V		Atlas-SNP	.											.	SEL1L3	62	.	0			c.A1660G						PASS	.	T	VAL/ILE	657,3117		65,527,1295	105.0	101.0	102.0		1660	4.8	1.0	4	dbSNP_123	102	5,8259		0,5,4127	yes	missense	SEL1L3	NM_015187.3	29	65,532,5422	CC,CT,TT		0.0605,17.4086,5.4993	benign	554/1133	25806279	662,11376	1887	4132	6019	SO:0001583	missense	23231	exon10			AGCTAATTTGGTG	BC009945	CCDS47037.1, CCDS75113.1	4p15.2	2009-09-24			ENSG00000091490	ENSG00000091490			29108	protein-coding gene	gene with protein product	"""KIAA0746 protein"""					9872452	Standard	XM_005248143		Approved	KIAA0746	uc003gru.4	Q68CR1	OTTHUMG00000160331	ENST00000399878.3:c.1660A>G	4.37:g.25806279T>C	ENSP00000382767:p.Ile554Val	237.0	0.0	0		237.0	120.0	0.506329	NM_015187	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Missense_Mutation	SNP	ENST00000399878.3	37	CCDS47037.1	103	0.04716117216117216	98	0.1991869918699187	5	0.013812154696132596	0	0.0	0	0.0	T	2.128	-0.399879	0.04865	0.174086	6.05E-4	ENSG00000091490	ENST00000399878;ENST00000264868;ENST00000502949	T;T;T	0.15139	2.64;2.67;2.45	6.02	4.84	0.62591	Tetratricopeptide-like helical (1);	0.609972	0.19314	N	0.117326	T	0.00012	0.0000	L	0.46157	1.445	0.35888	P	0.17056099999999996	B	0.09022	0.002	B	0.04013	0.001	T	0.35251	-0.9796	9	0.22706	T	0.39	-16.5487	1.9195	0.03304	0.1312:0.1514:0.1366:0.5808	rs16877591;rs56773321;rs16877591	554	Q68CR1	SE1L3_HUMAN	V	554;519;401	ENSP00000382767:I554V;ENSP00000264868:I519V;ENSP00000425438:I401V	ENSP00000264868:I519V	I	-	1	0	SEL1L3	25415377	0.939000	0.31865	1.000000	0.80357	0.338000	0.28826	0.314000	0.19432	1.093000	0.41377	0.533000	0.62120	ATT	T|0.933;C|0.067	0.067	strong		0.423	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187	
C5orf42	65250	hgsc.bcm.edu	37	5	37158363	37158363	+	Missense_Mutation	SNP	G	G	A	rs16903518	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37158363G>A	ENST00000508244.1	-	38	7868	c.7775C>T	c.(7774-7776)cCt>cTt	p.P2592L	C5orf42_ENST00000274258.7_Missense_Mutation_p.P1472L|C5orf42_ENST00000425232.2_Missense_Mutation_p.P2592L			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	2592			P -> L (in dbSNP:rs16903518).			integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			GGGTGACCAAGGTTTCTCTGA	0.368													G|||	122	0.024361	0.09	0.0043	5008	,	,		17612	0.0		0.0	False		,,,				2504	0.0				p.P2592L		Atlas-SNP	.											.	C5orf42	422	.	0			c.C7775T						PASS	.	G	LEU/PRO	340,4066	177.3+/-206.3	13,314,1876	129.0	125.0	127.0		7775	3.0	0.0	5	dbSNP_123	127	2,8598	2.2+/-6.3	0,2,4298	yes	missense	C5orf42	NM_023073.3	98	13,316,6174	AA,AG,GG		0.0233,7.7167,2.6296	benign	2592/3198	37158363	342,12664	2203	4300	6503	SO:0001583	missense	65250	exon39			GACCAAGGTTTCT		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.7775C>T	5.37:g.37158363G>A	ENSP00000421690:p.Pro2592Leu	157.0	0.0	0		183.0	92.0	0.502732	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Missense_Mutation	SNP	ENST00000508244.1	37	CCDS34146.2	45	0.020604395604395604	43	0.08739837398373984	2	0.0055248618784530384	0	0.0	0	0.0	G	7.667	0.686250	0.14973	0.077167	2.33E-4	ENSG00000197603	ENST00000508244;ENST00000425232;ENST00000274258;ENST00000514429;ENST00000388739	T;T;T;T	0.70631	-0.5;-0.5;1.32;1.35	4.88	3.02	0.34903	.	0.626374	0.14293	N	0.328786	T	0.05410	0.0143	L	0.46157	1.445	0.09310	N	0.999998	B;B	0.06786	0.001;0.001	B;B	0.12156	0.004;0.007	T	0.19257	-1.0311	10	0.62326	D	0.03	.	8.7051	0.34349	0.2574:0.0:0.7426:0.0	rs16903518;rs52830390;rs16903518	2592;1472	E9PH94;Q9H799	.;CE042_HUMAN	L	2592;2592;1472;1640;1472	ENSP00000421690:P2592L;ENSP00000389014:P2592L;ENSP00000274258:P1472L;ENSP00000424223:P1640L	ENSP00000274258:P1472L	P	-	2	0	C5orf42	37194120	0.609000	0.26975	0.007000	0.13788	0.048000	0.14542	1.796000	0.38794	0.704000	0.31869	0.563000	0.77884	CCT	G|0.970;A|0.030	0.030	strong		0.368	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073	
UCP3	7352	hgsc.bcm.edu	37	11	73717247	73717247	+	Missense_Mutation	SNP	C	C	T	rs2229707	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:73717247C>T	ENST00000314032.4	-	3	856	c.304G>A	c.(304-306)Gtc>Atc	p.V102I	UCP3_ENST00000426995.2_Missense_Mutation_p.V102I|UCP3_ENST00000348534.4_Missense_Mutation_p.V102I	NM_003356.3	NP_003347.1	P55916	UCP3_HUMAN	uncoupling protein 3 (mitochondrial, proton carrier)	102			V -> I (in obesity; dbSNP:rs2229707). {ECO:0000269|PubMed:9769326}.		aging (GO:0007568)|cellular metabolic process (GO:0044237)|cellular response to hormone stimulus (GO:0032870)|fatty acid metabolic process (GO:0006631)|lipid metabolic process (GO:0006629)|mitochondrial transport (GO:0006839)|proton transport (GO:0015992)|respiratory electron transport chain (GO:0022904)|respiratory gaseous exchange (GO:0007585)|response to activity (GO:0014823)|response to cold (GO:0009409)|response to glucocorticoid (GO:0051384)|response to hypoxia (GO:0001666)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|response to superoxide (GO:0000303)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	oxidative phosphorylation uncoupler activity (GO:0017077)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	12	Breast(11;2.08e-05)					ACCTGCTTGACGGAGTCATAG	0.627													C|||	216	0.043131	0.1513	0.013	5008	,	,		19077	0.0		0.005	False		,,,				2504	0.002				p.V102I		Atlas-SNP	.											.	UCP3	31	.	0			c.G304A	GRCh37	CM981987	UCP3	M	rs2229707	PASS	.	C	ILE/VAL,ILE/VAL	524,3876	236.8+/-248.8	36,452,1712	44.0	43.0	44.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	304,304	5.8	1.0	11	dbSNP_98	44	12,8574	9.1+/-34.3	0,12,4281	yes	missense,missense	UCP3	NM_003356.3,NM_022803.2	29,29	36,464,5993	TT,TC,CC		0.1398,11.9091,4.1275	benign,benign	102/313,102/276	73717247	536,12450	2200	4293	6493	SO:0001583	missense	7352	exon3			GCTTGACGGAGTC	AF001787	CCDS8229.1, CCDS44677.1	11q13.4	2013-05-22				ENSG00000175564		"""Solute carriers"""	12519	protein-coding gene	gene with protein product		602044				9480760, 9196039	Standard	NM_003356		Approved	SLC25A9	uc001our.3	P55916		ENST00000314032.4:c.304G>A	11.37:g.73717247C>T	ENSP00000323740:p.Val102Ile	67.0	0.0	0		76.0	32.0	0.421053	NM_003356	O60475|Q96HL3	Missense_Mutation	SNP	ENST00000314032.4	37	CCDS8229.1	81	0.03708791208791209	75	0.1524390243902439	3	0.008287292817679558	0	0.0	3	0.00395778364116095	C	15.72	2.915545	0.52546	0.119091	0.001398	ENSG00000175564	ENST00000314032;ENST00000348534;ENST00000426995	T;T;T	0.78816	-1.21;-1.21;-1.21	5.76	5.76	0.90799	Mitochondrial carrier domain (2);	0.054467	0.64402	D	0.000001	T	0.00967	0.0032	L	0.39020	1.185	0.22933	P	0.99854677	B	0.20459	0.045	B	0.23275	0.045	T	0.24764	-1.0151	9	0.59425	D	0.04	-25.6915	19.5566	0.95351	0.0:1.0:0.0:0.0	rs2229707;rs2734830;rs2229707	102	P55916	UCP3_HUMAN	I	102	ENSP00000323740:V102I;ENSP00000343615:V102I;ENSP00000392143:V102I	ENSP00000323740:V102I	V	-	1	0	UCP3	73394895	1.000000	0.71417	0.990000	0.47175	0.261000	0.26267	5.621000	0.67743	2.724000	0.93272	0.561000	0.74099	GTC	C|0.964;T|0.036	0.036	strong		0.627	UCP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398200.1	NM_003356	
BMP10	27302	hgsc.bcm.edu	37	2	69093288	69093288	+	Missense_Mutation	SNP	G	G	T	rs2231345	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:69093288G>T	ENST00000295379.1	-	2	908	c.750C>A	c.(748-750)aaC>aaA	p.N250K		NM_014482.1	NP_055297.1	O95393	BMP10_HUMAN	bone morphogenetic protein 10	250			N -> K (in dbSNP:rs2231345).		activin receptor signaling pathway (GO:0032924)|adult heart development (GO:0007512)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heart trabecula formation (GO:0060347)|negative regulation of cardiac muscle hypertrophy (GO:0010614)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of endothelial cell migration (GO:0010596)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation involved in heart morphogenesis (GO:2000138)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cardiac muscle contraction (GO:0055117)|sarcomere organization (GO:0045214)|ventricular cardiac muscle cell development (GO:0055015)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Z disc (GO:0030018)	hormone activity (GO:0005179)|receptor serine/threonine kinase binding (GO:0033612)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(15)|ovary(2)	27						TGAGCAAAGGGTTATGCTTAT	0.488													G|||	78	0.0155751	0.0537	0.0101	5008	,	,		22010	0.0		0.0	False		,,,				2504	0.0				p.N250K		Atlas-SNP	.											.	BMP10	70	.	0			c.C750A						PASS	.	G	LYS/ASN	212,4194	129.4+/-166.1	8,196,1999	106.0	94.0	98.0		750	-0.1	0.6	2	dbSNP_98	98	0,8600		0,0,4300	yes	missense	BMP10	NM_014482.1	94	8,196,6299	TT,TG,GG		0.0,4.8116,1.63	benign	250/425	69093288	212,12794	2203	4300	6503	SO:0001583	missense	27302	exon2			CAAAGGGTTATGC	AF101441	CCDS1890.1	2p13.2	2014-09-17			ENSG00000163217	ENSG00000163217		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	20869	protein-coding gene	gene with protein product		608748				10072785	Standard	NM_014482		Approved		uc002sez.1	O95393	OTTHUMG00000129573	ENST00000295379.1:c.750C>A	2.37:g.69093288G>T	ENSP00000295379:p.Asn250Lys	346.0	0.0	0		349.0	168.0	0.481375	NM_014482	Q53R17|Q6NTE0	Missense_Mutation	SNP	ENST00000295379.1	37	CCDS1890.1	34	0.015567765567765568	29	0.05894308943089431	5	0.013812154696132596	0	0.0	0	0.0	G	0.876	-0.730477	0.03135	0.048116	0.0	ENSG00000163217	ENST00000295379	T	0.63417	-0.04	5.44	-0.119	0.13543	Transforming growth factor-beta, N-terminal (1);	0.340366	0.33457	N	0.004893	T	0.02193	0.0068	N	0.01705	-0.755	0.26995	N	0.965051	B	0.09022	0.002	B	0.06405	0.002	T	0.07501	-1.0769	10	0.05620	T	0.96	.	0.5561	0.00671	0.2685:0.2748:0.2527:0.204	rs2231345;rs52835894;rs2231345	250	O95393	BMP10_HUMAN	K	250	ENSP00000295379:N250K	ENSP00000295379:N250K	N	-	3	2	BMP10	68946792	0.130000	0.22417	0.596000	0.28811	0.989000	0.77384	-0.205000	0.09411	-0.164000	0.10927	0.655000	0.94253	AAC	G|0.979;T|0.021	0.021	strong		0.488	BMP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251768.1	NM_014482	
PKD1	5310	hgsc.bcm.edu	37	16	2156153	2156153	+	Missense_Mutation	SNP	C	C	G	rs28369051	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2156153C>G	ENST00000262304.4	-	19	7850	c.7642G>C	c.(7642-7644)Gag>Cag	p.E2548Q	PKD1_ENST00000561991.1_5'UTR|PKD1_ENST00000423118.1_Missense_Mutation_p.E2548Q	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	2548	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.		E -> Q (in dbSNP:rs28369051). {ECO:0000269|PubMed:10577909}.		anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						AGGCCCACCTCGAAGTGTGGC	0.701													c|||	192	0.0383387	0.1392	0.0115	5008	,	,		16164	0.0		0.0	False		,,,				2504	0.0				p.E2548Q		Atlas-SNP	.											.	PKD1	184	.	0			c.G7642C						PASS	.		GLN/GLU,GLN/GLU	303,3739		5,293,1723	5.0	8.0	7.0		7642,7642	-4.0	0.0	16	dbSNP_125	7	2,8128		0,2,4063	no	missense,missense	PKD1	NM_000296.3,NM_001009944.2	29,29	5,295,5786	GG,GC,CC		0.0246,7.4963,2.5058	benign,benign	2548/4303,2548/4304	2156153	305,11867	2021	4065	6086	SO:0001583	missense	5310	exon19			CCACCTCGAAGTG	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9008	protein-coding gene	gene with protein product	"""polycystin 1"", ""transient receptor potential cation channel, subfamily P, member 1"""	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.7642G>C	16.37:g.2156153C>G	ENSP00000262304:p.Glu2548Gln	223.0	0.0	0		296.0	138.0	0.466216	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	79	0.036172161172161175	74	0.15040650406504066	5	0.013812154696132596	0	0.0	0	0.0	c	2.890	-0.229927	0.06022	0.074963	2.46E-4	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101;ENST00000382481	T;T	0.68624	-0.34;-0.34	5.14	-4.01	0.04045	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);Polycystin cation channel (1);	1.060040	0.07309	N	0.875540	T	0.00178	0.0005	N	0.02011	-0.69	0.80722	P	0.0	B;B	0.21688	0.059;0.053	B;B	0.20384	0.012;0.029	T	0.04090	-1.0978	9	0.13108	T	0.6	.	6.7917	0.23703	0.0891:0.3434:0.4431:0.1245	rs28369051	2548;2548	P98161-3;P98161	.;PKD1_HUMAN	Q	2548;2548;1899;827	ENSP00000262304:E2548Q;ENSP00000399501:E2548Q	ENSP00000262304:E2548Q	E	-	1	0	PKD1	2096154	0.000000	0.05858	0.001000	0.08648	0.967000	0.64934	-2.425000	0.01028	-0.502000	0.06596	0.544000	0.68410	GAG	C|0.972;G|0.028	0.028	strong		0.701	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
URB1	9875	hgsc.bcm.edu	37	21	33711077	33711077	+	Silent	SNP	C	C	T	rs58130645	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:33711077C>T	ENST00000382751.3	-	26	4564	c.4449G>A	c.(4447-4449)tcG>tcA	p.S1483S		NM_014825.2	NP_055640.2	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog (S. cerevisiae)	1483						nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(3)|skin(1)|stomach(1)	19						GCAGAAACAGCGAGTGCTGCA	0.592													C|||	91	0.0181709	0.0651	0.0058	5008	,	,		15666	0.0		0.001	False		,,,				2504	0.0				p.S1483S		Atlas-SNP	.											.	URB1	176	.	0			c.G4449A						PASS	.						56.0	57.0	56.0					21																	33711077		692	1591	2283	SO:0001819	synonymous_variant	9875	exon26			AAACAGCGAGTGC	AB011111	CCDS46645.1	21q22.11	2006-11-28	2006-11-28	2006-11-28	ENSG00000142207	ENSG00000142207			17344	protein-coding gene	gene with protein product	nucleolar preribosomal-associated protein 1	608865	"""chromosome 21 open reading frame 108"""	C21orf108		9628581	Standard	NM_014825		Approved	KIAA0539, NPA1	uc002ypn.2	O60287	OTTHUMG00000064919	ENST00000382751.3:c.4449G>A	21.37:g.33711077C>T		99.0	0.0	0		127.0	62.0	0.488189	NM_014825	D3DSE5|Q96NX1|Q9NYQ1	Silent	SNP	ENST00000382751.3	37	CCDS46645.1																																																																																			C|0.986;T|0.014	0.014	strong		0.592	URB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139400.2		
LAMA1	284217	hgsc.bcm.edu	37	18	7040197	7040197	+	Missense_Mutation	SNP	T	T	C	rs62619829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:7040197T>C	ENST00000389658.3	-	10	1393	c.1300A>G	c.(1300-1302)Aca>Gca	p.T434A		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	434	Laminin EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				TTTTCTCCTGTATAACCTTCC	0.507													T|||	77	0.0153754	0.0552	0.0058	5008	,	,		19191	0.0		0.0	False		,,,				2504	0.0				p.T434A		Atlas-SNP	.											.	LAMA1	458	.	0			c.A1300G						PASS	.	T	ALA/THR	190,4216	118.8+/-156.5	2,186,2015	150.0	136.0	141.0		1300	1.4	0.9	18	dbSNP_129	141	5,8595	4.3+/-15.6	0,5,4295	yes	missense	LAMA1	NM_005559.3	58	2,191,6310	CC,CT,TT		0.0581,4.3123,1.4993	benign	434/3076	7040197	195,12811	2203	4300	6503	SO:0001583	missense	284217	exon10			CTCCTGTATAACC	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.1300A>G	18.37:g.7040197T>C	ENSP00000374309:p.Thr434Ala	71.0	0.0	0		106.0	52.0	0.490566	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	18	0.008241758241758242	16	0.032520325203252036	2	0.0055248618784530384	0	0.0	0	0.0	T	2.627	-0.287315	0.05605	0.043123	5.81E-4	ENSG00000101680	ENST00000389658	T	0.60797	0.16	5.32	1.35	0.21983	EGF-like, laminin (4);	0.395100	0.27622	N	0.018551	T	0.08133	0.0203	N	0.12831	0.26	0.25331	N	0.989032	B	0.02656	0.0	B	0.08055	0.003	T	0.10042	-1.0647	10	0.06891	T	0.86	.	8.4468	0.32847	0.0:0.5006:0.0:0.4994	rs62619829	434	P25391	LAMA1_HUMAN	A	434	ENSP00000374309:T434A	ENSP00000374309:T434A	T	-	1	0	LAMA1	7030197	0.000000	0.05858	0.947000	0.38551	0.982000	0.71751	-0.882000	0.04174	0.407000	0.25591	-0.146000	0.13790	ACA	T|0.986;C|0.014	0.014	strong		0.507	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
IWS1	55677	hgsc.bcm.edu	37	2	128261099	128261099	+	Missense_Mutation	SNP	C	C	T	rs34785867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128261099C>T	ENST00000295321.4	-	4	1532	c.1273G>A	c.(1273-1275)Gta>Ata	p.V425I	AC010976.2_ENST00000599001.1_RNA|IWS1_ENST00000455721.2_Missense_Mutation_p.V432I|IWS1_ENST00000486662.1_5'Flank	NM_017969.2	NP_060439.2	Q96ST2	IWS1_HUMAN	IWS1 homolog (S. cerevisiae)	425	Glu-rich.		V -> I (in dbSNP:rs34785867).		mRNA processing (GO:0006397)|mRNA transport (GO:0051028)|regulation of histone H3-K36 trimethylation (GO:2001253)|regulation of histone H4 acetylation (GO:0090239)|regulation of mRNA export from nucleus (GO:0010793)|regulation of mRNA processing (GO:0050684)|regulation of transcription, DNA-templated (GO:0006355)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(2)|kidney(6)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0735)		TTGTCTGATACAGCATCACTG	0.383													C|||	98	0.0195687	0.0711	0.0058	5008	,	,		15170	0.0		0.0	False		,,,				2504	0.0				p.V425I		Atlas-SNP	.											.	IWS1	61	.	0			c.G1273A						PASS	.	C	ILE/VAL	309,4097	167.3+/-198.3	10,289,1904	128.0	111.0	117.0		1273	-6.2	0.0	2	dbSNP_126	117	2,8598	1.2+/-3.3	0,2,4298	yes	missense	IWS1	NM_017969.2	29	10,291,6202	TT,TC,CC		0.0233,7.0132,2.3912	benign	425/820	128261099	311,12695	2203	4300	6503	SO:0001583	missense	55677	exon4			CTGATACAGCATC	AK000868	CCDS2146.1	2q14.3	2006-03-17			ENSG00000163166	ENSG00000163166			25467	protein-coding gene	gene with protein product							Standard	NM_017969		Approved	DKFZp761G0123, FLJ10006, FLJ14655, FLJ32319	uc002ton.2	Q96ST2	OTTHUMG00000131527	ENST00000295321.4:c.1273G>A	2.37:g.128261099C>T	ENSP00000295321:p.Val425Ile	176.0	0.0	0		185.0	184.0	0.994595	NM_017969	Q2TB65|Q6P157|Q8N3E8|Q96MI7|Q9NV97|Q9NWH8	Missense_Mutation	SNP	ENST00000295321.4	37	CCDS2146.1	27	0.012362637362637362	25	0.0508130081300813	2	0.0055248618784530384	0	0.0	0	0.0	C	10.39	1.337907	0.24253	0.070132	2.33E-4	ENSG00000163166	ENST00000295321;ENST00000433551;ENST00000455721	T;T	0.31247	2.33;1.5	5.67	-6.15	0.02105	.	1.260290	0.05632	N	0.581936	T	0.01124	0.0037	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.24440	-1.0160	10	0.37606	T	0.19	0.5854	9.4352	0.38635	0.1086:0.6567:0.1211:0.1136	rs34785867	425	Q96ST2	IWS1_HUMAN	I	425;378;432	ENSP00000295321:V425I;ENSP00000399245:V432I	ENSP00000295321:V425I	V	-	1	0	IWS1	127977569	0.000000	0.05858	0.003000	0.11579	0.981000	0.71138	-0.215000	0.09279	-1.101000	0.03027	-0.793000	0.03317	GTA	C|0.977;T|0.023	0.023	strong		0.383	IWS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254384.2	NM_017969	
PCDHA1	56147	hgsc.bcm.edu	37	5	140167175	140167175	+	Missense_Mutation	SNP	T	T	C	rs61743801	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140167175T>C	ENST00000504120.2	+	1	1300	c.1300T>C	c.(1300-1302)Tcg>Ccg	p.S434P	PCDHA1_ENST00000394633.3_Missense_Mutation_p.S434P|PCDHA1_ENST00000378133.3_Missense_Mutation_p.S434P	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	434	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(34)|prostate(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(3)	70			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGCTCGCCTTCGCTGTGGGC	0.627													.|||	72	0.014377	0.0537	0.0014	5008	,	,		17483	0.0		0.0	False		,,,				2504	0.0				p.S434P		Atlas-SNP	.											.	PCDHA1	387	.	0			c.T1300C						PASS	.	T	PRO/SER,PRO/SER,PRO/SER	236,4170	135.3+/-171.4	10,216,1977	82.0	88.0	86.0		1300,1300,1300	-3.1	0.7	5	dbSNP_129	86	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense,missense	PCDHA1	NM_018900.2,NM_031410.1,NM_031411.1	74,74,74	10,217,6275	CC,CT,TT		0.0116,5.3563,1.8225	,,	434/951,434/808,434/687	140167175	237,12767	2203	4299	6502	SO:0001583	missense	56147	exon1			TCGCCTTCGCTGT	AF152479	CCDS54912.1, CCDS54913.1	5q31	2010-11-26				ENSG00000204970		"""Cadherins / Protocadherins : Clustered"""	8663	other	complex locus constituent	"""KIAA0345-like 13"""	606307				10380929	Standard	NM_018900		Approved			Q9Y5I3		ENST00000504120.2:c.1300T>C	5.37:g.140167175T>C	ENSP00000420840:p.Ser434Pro	159.0	0.0	0		166.0	81.0	0.487952	NM_031411	O75288|Q9NRT7	Missense_Mutation	SNP	ENST00000504120.2	37	CCDS54913.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	t	4.310	0.056796	0.08339	0.053563	1.16E-4	ENSG00000204970	ENST00000504120;ENST00000394633;ENST00000378133	T;T;T	0.44881	0.91;0.91;0.91	3.89	-3.14	0.05250	Cadherin (5);Cadherin-like (1);	0.679068	0.12024	N	0.506656	T	0.02047	0.0064	N	0.02539	-0.55	0.09310	N	1	B;B;B	0.17852	0.024;0.002;0.023	B;B;B	0.32022	0.139;0.002;0.03	T	0.30563	-0.9974	10	0.13853	T	0.58	.	2.4978	0.04626	0.1149:0.2142:0.4488:0.2221	rs61743801	434;434;434	Q9Y5I3;Q9Y5I3-2;Q9Y5I3-3	PCDA1_HUMAN;.;.	P	434	ENSP00000420840:S434P;ENSP00000378129:S434P;ENSP00000367373:S434P	ENSP00000367373:S434P	S	+	1	0	PCDHA1	140147359	0.000000	0.05858	0.741000	0.31004	0.719000	0.41307	-0.511000	0.06321	-0.192000	0.10432	0.369000	0.22263	TCG	T|0.983;C|0.017	0.017	strong		0.627	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900	
PTX4	390667	hgsc.bcm.edu	37	16	1536138	1536138	+	Silent	SNP	T	T	C	rs386787711|rs114122805	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1536138T>C	ENST00000447419.2	-	3	1264	c.1239A>G	c.(1237-1239)ggA>ggG	p.G413G	PTX4_ENST00000293922.1_Silent_p.G408G|PTX4_ENST00000440447.2_3'UTR			Q96A99	PTX4_HUMAN	pentraxin 4, long	413	Pentaxin.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						AGCTGTCGAATCCGCCCCCCA	0.662													T|||	87	0.0173722	0.0643	0.0029	5008	,	,		16736	0.0		0.0	False		,,,				2504	0.0				p.G408G		Atlas-SNP	.											.	PTX4	46	.	0			c.A1224G						PASS	.						59.0	56.0	57.0					16																	1536138		2199	4300	6499	SO:0001819	synonymous_variant	390667	exon3			GTCGAATCCGCCC		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"""chromosome 16 open reading frame 38"""	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.1239A>G	16.37:g.1536138T>C		66.0	0.0	0		77.0	41.0	0.532468	NM_001013658		Silent	SNP	ENST00000447419.2	37																																																																																				T|0.980;C|0.020	0.020	strong		0.662	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
KCNN1	3780	hgsc.bcm.edu	37	19	18084775	18084775	+	Silent	SNP	G	G	A	rs75754669	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18084775G>A	ENST00000222249.9	+	3	397	c.78G>A	c.(76-78)ccG>ccA	p.P26P	RNA5SP468_ENST00000516782.1_RNA	NM_002248.3	NP_002239.2	Q92952	KCNN1_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1	26					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			endometrium(1)|kidney(1)|lung(5)|urinary_tract(1)	8					Miconazole(DB01110)|Procaine(DB00721)	GAGACCCTCCGGACCCTGAGG	0.736													G|||	47	0.00938498	0.0348	0.0014	5008	,	,		10833	0.0		0.0	False		,,,				2504	0.0				p.P26P		Atlas-SNP	.											.	KCNN1	74	.	0			c.G78A						PASS	.	G		61,3441		0,61,1690	6.0	9.0	8.0		78	-0.2	0.2	19	dbSNP_131	8	2,7602		0,2,3800	no	coding-synonymous	KCNN1	NM_002248.3		0,63,5490	AA,AG,GG		0.0263,1.7419,0.5673		26/544	18084775	63,11043	1751	3802	5553	SO:0001819	synonymous_variant	3780	exon3			CCCTCCGGACCCT	U69883	CCDS67611.1	19p13.1	2012-07-05				ENSG00000105642		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6290	protein-coding gene	gene with protein product		602982				8781233, 10516439, 16382103	Standard	NM_002248		Approved	KCa2.1, hSK1	uc002nht.3	Q92952		ENST00000222249.9:c.78G>A	19.37:g.18084775G>A		1.0	0.0	0		5.0	4.0	0.8	NM_002248	Q5KR10|Q6DJU4	Silent	SNP	ENST00000222249.9	37																																																																																				G|0.990;A|0.010	0.010	strong		0.736	KCNN1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471896.2	NM_002248	
FCGR2B	2213	hgsc.bcm.edu	37	1	161645058	161645058	+	Missense_Mutation	SNP	T	T	G	rs148534844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:161645058T>G	ENST00000358671.5	+	6	853	c.772T>G	c.(772-774)Tac>Gac	p.Y258D	FCGR2B_ENST00000367960.5_Missense_Mutation_p.Y251D|FCGR2B_ENST00000367962.4_Missense_Mutation_p.Y258D|FCGR2B_ENST00000236937.9_Intron|FCGR2B_ENST00000403078.3_Intron|RP11-25K21.1_ENST00000453111.1_RNA|FCGR2B_ENST00000367961.4_Missense_Mutation_p.Y251D	NM_001002275.2|NM_004001.4	NP_001002275.1|NP_003992.3	P31994	FCG2B_HUMAN	Fc fragment of IgG, low affinity IIb, receptor (CD32)	258			Y -> D (in dbSNP:rs148534844). {ECO:0000269|PubMed:8466861}.		immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|viral process (GO:0016032)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)						all_cancers(52;4.89e-16)|all_hematologic(112;0.0207)		BRCA - Breast invasive adenocarcinoma(70;0.00376)		Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Antithymocyte globulin(DB00098)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Intravenous Immunoglobulin(DB00028)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	TCTCCCAGGATACCCTGAGTG	0.612			T	?	ALL																																p.Y258D		Atlas-SNP	.		Dom	yes		1	1q23	2213	"""Fc fragment of IgG, low affinity IIb, receptor for (CD32)"""		L	.	FCGR2B	33	.	0			c.T772G						PASS	.	T	,,ASP/TYR,ASP/TYR,ASP/TYR	54,4350		0,54,2148	31.0	29.0	29.0		,,769,751,772	-1.8	0.6	1	dbSNP_134	29	1,8599		0,1,4299	no	intron,intron,missense,missense,missense	FCGR2B	NM_001002273.2,NM_001002274.2,NM_001002275.2,NM_001190828.1,NM_004001.4	,,160,160,160	0,55,6447	GG,GT,TT		0.0116,1.2262,0.4229	,,benign,benign,benign	,,257/310,251/304,258/311	161645058	55,12949	2202	4300	6502	SO:0001583	missense	2213	exon6			CCAGGATACCCTG	BC031992	CCDS30924.1, CCDS30925.1, CCDS53414.1	1q23	2013-01-11	2005-02-02		ENSG00000072694	ENSG00000072694		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3618	protein-coding gene	gene with protein product		604590	"""Fc fragment of IgG, low affinity IIb, receptor for (CD32)"""	FCG2, FCGR2		2139735	Standard	NM_004001		Approved	CD32, CD32B	uc001gaz.2	P31994	OTTHUMG00000034470	ENST00000358671.5:c.772T>G	1.37:g.161645058T>G	ENSP00000351497:p.Tyr258Asp	324.0	0.0	0		331.0	141.0	0.425982	NM_004001	A6H8N3|O95649|Q53X85|Q5VXA9|Q8NIA1	Missense_Mutation	SNP	ENST00000358671.5	37	CCDS30924.1	23	0.010531135531135532	19	0.03861788617886179	4	0.011049723756906077	0	0.0	0	0.0	A	9.704	1.155245	0.21454	0.012262	1.16E-4	ENSG00000072694	ENST00000367962;ENST00000367960;ENST00000367961;ENST00000358671	T;T;T;T	0.27557	4.78;1.66;1.66;4.78	5.06	-1.78	0.07957	.	1.572250	0.03874	N	0.276032	T	0.04318	0.0119	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.11329	0.006;0.002	T	0.27806	-1.0063	10	0.31617	T	0.26	.	3.8406	0.08912	0.4674:0.0:0.1509:0.3817	.	251;258	P31994-3;P31994	.;FCG2B_HUMAN	D	258;251;251;258	ENSP00000356939:Y258D;ENSP00000356937:Y251D;ENSP00000356938:Y251D;ENSP00000351497:Y258D	ENSP00000351497:Y258D	Y	+	1	0	FCGR2B	159911682	0.585000	0.26774	0.642000	0.29436	0.834000	0.47266	0.095000	0.15127	-0.667000	0.05303	-0.384000	0.06662	TAC	T|0.992;G|0.008	0.008	strong		0.612	FCGR2B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000083337.4	NM_004001	
PLCXD3	345557	hgsc.bcm.edu	37	5	41382536	41382536	+	Silent	SNP	C	C	T	rs16871312	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:41382536C>T	ENST00000377801.3	-	2	278	c.204G>A	c.(202-204)gtG>gtA	p.V68V	PLCXD3_ENST00000328457.3_Silent_p.V68V			Q63HM9	PLCX3_HUMAN	phosphatidylinositol-specific phospholipase C, X domain containing 3	68	PI-PLC X-box. {ECO:0000255|PROSITE- ProRule:PRU00270}.				lipid catabolic process (GO:0016042)		phosphoric diester hydrolase activity (GO:0008081)|signal transducer activity (GO:0004871)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(4)|lung(21)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37						GCTTTTTGGCCACAGTTCCAA	0.448													C|||	356	0.0710863	0.2632	0.0115	5008	,	,		17078	0.0		0.0	False		,,,				2504	0.0				p.V68V		Atlas-SNP	.											.	PLCXD3	86	.	0			c.G204A						PASS	.	C		1023,3383	371.2+/-319.9	129,765,1309	59.0	65.0	63.0		204	-0.2	1.0	5	dbSNP_123	63	8,8592	4.3+/-15.6	0,8,4292	no	coding-synonymous	PLCXD3	NM_001005473.2		129,773,5601	TT,TC,CC		0.093,23.2183,7.9271		68/322	41382536	1031,11975	2203	4300	6503	SO:0001819	synonymous_variant	345557	exon2			TTTGGCCACAGTT		CCDS34150.1	5p13.1	2004-09-09			ENSG00000182836	ENSG00000182836			31822	protein-coding gene	gene with protein product							Standard	NM_001005473		Approved		uc003jmm.1	Q63HM9	OTTHUMG00000162076	ENST00000377801.3:c.204G>A	5.37:g.41382536C>T		32.0	0.0	0		36.0	36.0	1	NM_001005473	A6NL04	Silent	SNP	ENST00000377801.3	37	CCDS34150.1																																																																																			C|0.907;T|0.093	0.093	strong		0.448	PLCXD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367109.1	XM_293875	
FNDC1	84624	hgsc.bcm.edu	37	6	159647584	159647584	+	Silent	SNP	G	G	A	rs12110595	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:159647584G>A	ENST00000297267.9	+	9	1352	c.1152G>A	c.(1150-1152)gcG>gcA	p.A384A	FNDC1_ENST00000480856.1_3'UTR|FNDC1_ENST00000340366.6_Silent_p.A384A	NM_032532.2	NP_115921.2	Q4ZHG4	FNDC1_HUMAN	fibronectin type III domain containing 1	384	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cellular response to hypoxia (GO:0071456)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein transport (GO:0051223)	cell-cell junction (GO:0005911)|extracellular region (GO:0005576)|mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(29)|liver(2)|lung(23)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)	93		Breast(66;0.000781)|Ovarian(120;0.0308)|Prostate(117;0.195)		OV - Ovarian serous cystadenocarcinoma(65;2.6e-16)|BRCA - Breast invasive adenocarcinoma(81;1.06e-05)		CTTGGGATGCGCTACCAGAGA	0.473													G|||	264	0.0527157	0.1876	0.0216	5008	,	,		20701	0.001		0.0	False		,,,				2504	0.0				p.A384A		Atlas-SNP	.											.	FNDC1	250	.	0			c.G1152A						PASS	.	G		716,3112		66,584,1264	97.0	94.0	95.0		1152	-10.6	0.0	6	dbSNP_120	95	8,8254		0,8,4123	no	coding-synonymous	FNDC1	NM_032532.2		66,592,5387	AA,AG,GG		0.0968,18.7043,5.9884		384/1895	159647584	724,11366	1914	4131	6045	SO:0001819	synonymous_variant	84624	exon9			GGATGCGCTACCA	AB058769	CCDS47512.1	6q25	2013-02-11			ENSG00000164694	ENSG00000164694		"""Fibronectin type III domain containing"""	21184	protein-coding gene	gene with protein product		609991	"""fibronectin type III domain containing 2"""	FNDC2		11347906	Standard	NM_032532		Approved	bA243O10.1, KIAA1866, dJ322A24.1	uc010kjv.3	Q4ZHG4	OTTHUMG00000015927	ENST00000297267.9:c.1152G>A	6.37:g.159647584G>A		85.0	0.0	0		50.0	17.0	0.34	NM_032532	A6H8X2|B7ZBR4|B7ZBR5|B9EK49|Q5JPI0|Q5VU31|Q5VU32|Q5VXX4|Q70CQ6|Q96JG1	Silent	SNP	ENST00000297267.9	37	CCDS47512.1	111	0.050824175824175824	103	0.20934959349593496	8	0.022099447513812154	0	0.0	0	0.0	G	7.656	0.683920	0.14907	0.187043	9.68E-4	ENSG00000164694	ENST00000329629	T	0.03181	4.02	5.29	-10.6	0.00265	.	0.279587	0.34777	N	0.003696	T	0.00845	0.0028	.	.	.	0.09310	P	0.999999999722547	.	.	.	.	.	.	T	0.17899	-1.0354	6	0.40728	T	0.16	-5.1754	3.7308	0.08492	0.176:0.081:0.3814:0.3616	rs12110595;rs57583348;rs12110595	.	.	.	T	343	ENSP00000333297:A343T	ENSP00000333297:A343T	A	+	1	0	FNDC1	159567572	0.002000	0.14202	0.028000	0.17463	0.773000	0.43773	-1.392000	0.02523	-2.325000	0.00638	-1.283000	0.01379	GCT	G|0.929;A|0.071	0.071	strong		0.473	FNDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042897.3	NM_032532	
EME1	146956	hgsc.bcm.edu	37	17	48453219	48453219	+	Missense_Mutation	SNP	G	G	A	rs114836030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48453219G>A	ENST00000338165.4	+	2	732	c.650G>A	c.(649-651)aGa>aAa	p.R217K	MRPL27_ENST00000225969.4_5'Flank|MRPL27_ENST00000503633.1_5'Flank|MRPL27_ENST00000507088.1_5'Flank|EME1_ENST00000393271.2_Missense_Mutation_p.R217K|MRPL27_ENST00000442592.3_5'Flank|EME1_ENST00000511648.2_Missense_Mutation_p.R217K	NM_152463.2	NP_689676.2	Q96AY2	EME1_HUMAN	essential meiotic structure-specific endonuclease 1	217					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cytoplasm (GO:0005737)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	DNA binding (GO:0003677)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(4)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	19	Breast(11;5.62e-19)		BRCA - Breast invasive adenocarcinoma(22;2.43e-08)			CGGCAGCAGAGACAAGCAAGG	0.507								Direct reversal of damage;Homologous recombination					G|||	34	0.00678914	0.0227	0.0058	5008	,	,		22256	0.0		0.0	False		,,,				2504	0.0				p.R217K		Atlas-SNP	.											.	EME1	39	.	0			c.G650A						PASS	.	G	LYS/ARG,LYS/ARG	79,4327	68.7+/-106.4	1,77,2125	82.0	83.0	83.0		650,650	0.3	0.0	17	dbSNP_132	83	0,8600		0,0,4300	yes	missense,missense	EME1	NM_001166131.1,NM_152463.2	26,26	1,77,6425	AA,AG,GG		0.0,1.793,0.6074	benign,benign	217/584,217/571	48453219	79,12927	2203	4300	6503	SO:0001583	missense	146956	exon2			AGCAGAGACAAGC	BC016470	CCDS11565.1, CCDS54141.1	17q21.33	2013-07-03	2013-07-03			ENSG00000154920			24965	protein-coding gene	gene with protein product	"""SLX2 structure-specific endonuclease subunit homolog A (S. cerevisiae)"""	610885	"""essential meiotic endonuclease 1 homolog 1 (S. pombe)"""			12721304	Standard	NM_001166131		Approved	FLJ31364, MMS4L, SLX2A	uc010dbp.2	Q96AY2		ENST00000338165.4:c.650G>A	17.37:g.48453219G>A	ENSP00000339897:p.Arg217Lys	64.0	0.0	0		78.0	35.0	0.448718	NM_152463	Q96N62	Missense_Mutation	SNP	ENST00000338165.4	37	CCDS11565.1	10	0.004578754578754579	8	0.016260162601626018	2	0.0055248618784530384	0	0.0	0	0.0	G	0.100	-1.152905	0.01700	0.01793	0.0	ENSG00000154920	ENST00000338165;ENST00000393271;ENST00000511648	T;T;T	0.10860	2.83;2.87;2.87	5.11	0.34	0.15985	.	1.089720	0.07057	N	0.833034	T	0.03095	0.0091	L	0.34521	1.04	0.09310	N	1	B;B	0.20052	0.041;0.011	B;B	0.14578	0.011;0.003	T	0.42464	-0.9450	10	0.07644	T	0.81	0.1474	5.5521	0.17095	0.4065:0.1533:0.4403:0.0	.	217;217	Q96AY2-2;Q96AY2	.;EME1_HUMAN	K	217	ENSP00000339897:R217K;ENSP00000376952:R217K;ENSP00000421700:R217K	ENSP00000339897:R217K	R	+	2	0	EME1	45808218	0.000000	0.05858	0.000000	0.03702	0.142000	0.21351	0.423000	0.21313	0.189000	0.20188	-0.145000	0.13849	AGA	G|0.994;A|0.006	0.006	strong		0.507	EME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367118.3	NM_152463	
HERC2	8924	hgsc.bcm.edu	37	15	28424100	28424100	+	Silent	SNP	C	C	T	rs9806328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:28424100C>T	ENST00000261609.7	-	59	9204	c.9096G>A	c.(9094-9096)acG>acA	p.T3032T		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		GGATGGGCACCGTCCCGCTGG	0.612													C|||	716	0.142971	0.5166	0.0375	5008	,	,		11324	0.004		0.001	False		,,,				2504	0.002				p.T3032T		Atlas-SNP	.											.	HERC2	501	.	0			c.G9096A						PASS	.	C		1921,2485	549.9+/-377.9	410,1101,692	82.0	84.0	83.0		9096	-11.2	0.1	15	dbSNP_119	83	7,8593	4.3+/-15.6	0,7,4293	no	coding-synonymous	HERC2	NM_004667.4		410,1108,4985	TT,TC,CC		0.0814,43.5996,14.8239		3032/4835	28424100	1928,11078	2203	4300	6503	SO:0001819	synonymous_variant	8924	exon59			GGGCACCGTCCCG	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.9096G>A	15.37:g.28424100C>T		76.0	0.0	0		92.0	37.0	0.402174	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			C|0.864;T|0.136	0.136	strong		0.612	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
KRTAP4-4	84616	hgsc.bcm.edu	37	17	39316841	39316841	+	Missense_Mutation	SNP	A	A	T	rs444509|rs535200131	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39316841A>T	ENST00000390661.3	-	1	142	c.103T>A	c.(103-105)Tgc>Agc	p.C35S		NM_032524.1	NP_115913.1	Q9BYR3	KRA44_HUMAN	keratin associated protein 4-4	35	26 X 5 AA repeats of C-C-[GRQVCH]-[SPT]- [VSTQR].		C -> S (in dbSNP:rs444509).			keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(5)	7		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			GGGCGGCAGCAGGTGGTCCTG	0.647													A|||	522	0.104233	0.3782	0.0288	5008	,	,		19513	0.0		0.002	False		,,,				2504	0.0				p.C35S		Atlas-SNP	.											.	KRTAP4-4	21	.	0			c.T103A						PASS	.	A	SER/CYS	1206,3164		166,874,1145	38.0	53.0	48.0		103	4.5	1.0	17	dbSNP_80	48	3,8589		0,3,4293	no	missense	KRTAP4-4	NM_032524.1	112	166,877,5438	TT,TA,AA		0.0349,27.5973,9.3273	possibly-damaging	35/167	39316841	1209,11753	2185	4296	6481	SO:0001583	missense	84616	exon1			GGCAGCAGGTGGT	AJ406936	CCDS11383.1	17q21.2	2013-06-25			ENSG00000171396	ENSG00000171396		"""Keratin associated proteins"""	16928	protein-coding gene	gene with protein product			"""keratin associated protein 4-13"""	KRTAP4-13		11279113	Standard	NM_032524		Approved	KAP4.4, KAP4.13	uc002hwc.3	Q9BYR3	OTTHUMG00000133428	ENST00000390661.3:c.103T>A	17.37:g.39316841A>T	ENSP00000375076:p.Cys35Ser	171.0	0.0	0		147.0	147.0	1	NM_032524	Q9BYU7	Missense_Mutation	SNP	ENST00000390661.3	37	CCDS11383.1	187	0.08562271062271062	176	0.35772357723577236	11	0.03038674033149171	0	0.0	0	0.0	.	14.47	2.545823	0.45280	0.275973	3.49E-4	ENSG00000171396	ENST00000390661	T	0.04406	3.63	4.52	4.52	0.55395	.	0.000000	0.44688	U	0.000438	T	0.00012	0.0000	M	0.93150	3.385	0.34592	P	0.28444	P	0.38551	0.636	P	0.47827	0.558	T	0.34179	-0.9839	9	0.44086	T	0.13	.	11.8038	0.52143	1.0:0.0:0.0:0.0	rs444509;rs61402488	35	Q9BYR3	KRA44_HUMAN	S	35	ENSP00000375076:C35S	ENSP00000375076:C35S	C	-	1	0	KRTAP4-4	36570367	1.000000	0.71417	0.961000	0.40146	0.964000	0.63967	2.062000	0.41413	1.660000	0.50760	0.443000	0.29094	TGC	A|0.912;T|0.088	0.088	strong		0.647	KRTAP4-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257291.1		
FAM183A	440585	hgsc.bcm.edu	37	1	43621973	43621973	+	Missense_Mutation	SNP	C	C	T	rs59274667	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:43621973C>T	ENST00000335282.4	+	4	394	c.394C>T	c.(394-396)Cac>Tac	p.H132Y	FAM183A_ENST00000409337.1_3'UTR|FAM183A_ENST00000410048.1_Missense_Mutation_p.H104Y	NM_001101376.2	NP_001094846.2	A6NL82	F183A_HUMAN	family with sequence similarity 183, member A	132										kidney(1)|large_intestine(1)|lung(2)|ovary(3)	7						AGGAGATGATCACCACAAGTA	0.473													C|||	26	0.00519169	0.0197	0.0	5008	,	,		22333	0.0		0.0	False		,,,				2504	0.0				p.H132Y		Atlas-SNP	.											.	FAM183A	28	.	0			c.C394T						PASS	.	C	TYR/HIS	67,3987		1,65,1961	126.0	127.0	127.0		394	-0.6	0.0	1	dbSNP_129	127	0,8370		0,0,4185	yes	missense	FAM183A	NM_001101376.2	83	1,65,6146	TT,TC,CC		0.0,1.6527,0.5393	benign	132/135	43621973	67,12357	2027	4185	6212	SO:0001583	missense	440585	exon4			GATGATCACCACA	AI192630, AI375550, AL139138	CCDS44126.1	1p34.2	2008-08-11			ENSG00000186973	ENSG00000186973			34347	protein-coding gene	gene with protein product						11181995	Standard	NM_001101376		Approved	LOC440585, hCG23177	uc009vwo.3	A6NL82	OTTHUMG00000007286	ENST00000335282.4:c.394C>T	1.37:g.43621973C>T	ENSP00000334415:p.His132Tyr	99.0	0.0	0		120.0	60.0	0.5	NM_001101376	B7ZBL8	Missense_Mutation	SNP	ENST00000335282.4	37	CCDS44126.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	C	10.05	1.243842	0.22796	0.016527	0.0	ENSG00000186973	ENST00000409706;ENST00000410048;ENST00000409337;ENST00000410025;ENST00000335282	.	.	.	4.08	-0.601	0.11638	.	1.498380	0.03915	N	0.282630	T	0.10637	0.0260	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.18272	-1.0342	9	0.49607	T	0.09	.	3.0707	0.06230	0.2209:0.3721:0.0:0.4069	rs59274667;rs61738384	132	A6NL82	F183A_HUMAN	Y	132;104;42;80;132	.	ENSP00000334415:H132Y	H	+	1	0	FAM183A	43394560	0.000000	0.05858	0.000000	0.03702	0.129000	0.20672	-0.229000	0.09098	-0.092000	0.12417	-0.768000	0.03414	CAC	C|0.996;T|0.004	0.004	strong		0.473	FAM183A-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019024.3	NM_001101376	
CCDC129	223075	hgsc.bcm.edu	37	7	31691582	31691582	+	Missense_Mutation	SNP	G	G	A	rs80081783	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:31691582G>A	ENST00000407970.3	+	13	2779	c.2741G>A	c.(2740-2742)cGt>cAt	p.R914H	CCDC129_ENST00000409210.1_Missense_Mutation_p.R822H|CCDC129_ENST00000451887.2_Missense_Mutation_p.R940H|CCDC129_ENST00000319386.3_Missense_Mutation_p.R766H	NM_001257967.1|NM_194300.3	NP_001244896.1|NP_919276.2	Q6ZRS4	CC129_HUMAN	coiled-coil domain containing 129	914										cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(31)	44						CAAACGTTACGTGAGGCCCTG	0.478													G|||	30	0.00599042	0.0227	0.0	5008	,	,		17400	0.0		0.0	False		,,,				2504	0.0				p.R940H		Atlas-SNP	.											LOC223075,right_lower_lobe,carcinoma,-1,2	CCDC129	127	2	0			c.G2819A						PASS	.	G	HIS/ARG	56,4350	55.5+/-91.7	0,56,2147	69.0	60.0	63.0		2741	5.2	0.0	7	dbSNP_133	63	0,8600		0,0,4300	yes	missense	CCDC129	NM_194300.2	29	0,56,6447	AA,AG,GG		0.0,1.271,0.4306	probably-damaging	914/1045	31691582	56,12950	2203	4300	6503	SO:0001583	missense	223075	exon13			CGTTACGTGAGGC	AK128026	CCDS5435.2, CCDS59050.1, CCDS75577.1	7p14.3	2006-08-21			ENSG00000180347	ENSG00000180347			27363	protein-coding gene	gene with protein product						14702039	Standard	NM_001257967		Approved	FLJ38344	uc011kad.1	Q6ZRS4	OTTHUMG00000128611	ENST00000407970.3:c.2741G>A	7.37:g.31691582G>A	ENSP00000384416:p.Arg914His	168.0	0.0	0		153.0	77.0	0.503268	NM_001257968	A2RU17|B3KTI9|B4DHB0|B4E2R1|F5H3V5	Missense_Mutation	SNP	ENST00000407970.3	37	CCDS5435.2	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	26.1	4.700031	0.88924	0.01271	0.0	ENSG00000180347	ENST00000319386;ENST00000407970;ENST00000451887;ENST00000538406;ENST00000409210	T;T;T;T	0.56103	0.48;0.48;0.48;0.48	5.21	5.21	0.72293	.	0.000000	0.50627	D	0.000101	T	0.55862	0.1947	M	0.71581	2.175	0.09310	N	0.999998	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.79784	0.966;0.993;0.993;0.984	T	0.59910	-0.7365	10	0.87932	D	0	-17.7013	14.263	0.66097	0.0:0.0:1.0:0.0	.	940;924;914;766	F5H3V5;F5H2J8;Q6ZRS4;Q6ZRS4-2	.;.;CC129_HUMAN;.	H	766;914;940;924;822	ENSP00000313062:R766H;ENSP00000384416:R914H;ENSP00000395835:R940H;ENSP00000387214:R822H	ENSP00000313062:R766H	R	+	2	0	CCDC129	31658107	0.944000	0.32072	0.031000	0.17742	0.664000	0.39144	2.657000	0.46724	2.437000	0.82529	0.561000	0.74099	CGT	G|0.995;A|0.005	0.005	strong		0.478	CCDC129-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318975.1	NM_194300	
ERI2	112479	hgsc.bcm.edu	37	16	20809240	20809240	+	Missense_Mutation	SNP	G	G	T	rs61746707	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:20809240G>T	ENST00000357967.4	-	9	1924	c.1882C>A	c.(1882-1884)Caa>Aaa	p.Q628K	ERI2_ENST00000569729.1_3'UTR|ERI2_ENST00000563117.1_Missense_Mutation_p.Q535K|ERI2_ENST00000300005.3_Intron|ERI2_ENST00000389345.5_Missense_Mutation_p.Q363K|ERI2_ENST00000564349.1_Missense_Mutation_p.Q535K	NM_001142725.1	NP_001136197.1	A8K979	ERI2_HUMAN	ERI1 exoribonuclease family member 2	628							exonuclease activity (GO:0004527)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|prostate(2)	11						CTGTTTTCTTGGTATTTCCCG	0.413													G|||	74	0.0147764	0.0545	0.0014	5008	,	,		17542	0.0		0.001	False		,,,				2504	0.0				p.Q628K		Atlas-SNP	.											.	ERI2	50	.	0			c.C1882A						PASS	.	G	LYS/GLN,	53,1331		1,51,640	115.0	94.0	100.0		1882,	3.4	1.0	16	dbSNP_129	100	0,3182		0,0,1591	no	missense,intron	ERI2	NM_001142725.1,NM_080663.2	53,	1,51,2231	TT,TG,GG		0.0,3.8295,1.1608	benign,	628/692,	20809240	53,4513	692	1591	2283	SO:0001583	missense	112479	exon9			TTTCTTGGTATTT	BC010503	CCDS10590.1, CCDS45436.1	16p12.3	2014-02-18	2009-10-07	2008-12-16	ENSG00000196678	ENSG00000196678		"""Enhanced RNAi three prime mRNA exonucleases"""	30541	protein-coding gene	gene with protein product	"""enhanced RNAi three prime mRNA exonuclease homolog 2 (C.elegans)"", ""exoribonuclease 2"", ""zinc finger, GRF-type containing 5"""		"""exonuclease domain containing 1"""	EXOD1		10819331	Standard	NM_080663		Approved	KIAA1504, MGC16943, ZGRF5	uc010vbb.1	A8K979	OTTHUMG00000131557	ENST00000357967.4:c.1882C>A	16.37:g.20809240G>T	ENSP00000350651:p.Gln628Lys	189.0	0.0	0		248.0	114.0	0.459677	NM_001142725	Q6ZSJ2|Q96FR9|Q9P224|Q9Y6V3	Missense_Mutation	SNP	ENST00000357967.4	37	CCDS45436.1	28	0.01282051282051282	28	0.056910569105691054	0	0.0	0	0.0	0	0.0	G	9.624	1.134740	0.21123	0.038295	0.0	ENSG00000196678	ENST00000357967;ENST00000389345	T;T	0.18338	2.26;2.22	5.57	3.44	0.39384	Zinc finger, GRF-type (1);	0.400221	0.26349	N	0.024900	T	0.01029	0.0034	N	0.25245	0.725	0.23204	N	0.99813	B	0.17465	0.022	B	0.15052	0.012	T	0.21586	-1.0241	10	0.33940	T	0.23	-3.6176	8.303	0.32025	0.0:0.2738:0.4857:0.2405	.	628	A8K979	ERI2_HUMAN	K	628;363	ENSP00000350651:Q628K;ENSP00000373996:Q363K	ENSP00000350651:Q628K	Q	-	1	0	ERI2	20716741	0.998000	0.40836	1.000000	0.80357	0.562000	0.35680	2.069000	0.41481	1.450000	0.47717	0.591000	0.81541	CAA	G|0.987;T|0.013	0.013	strong		0.413	ERI2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_080663	
C7orf65	401335	hgsc.bcm.edu	37	7	47698737	47698737	+	Missense_Mutation	SNP	A	A	C	rs114109572	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:47698737A>C	ENST00000408988.2	+	3	402	c.367A>C	c.(367-369)Act>Cct	p.T123P		NM_001123065.1	NP_001116537.1	Q6ZTY9	CG065_HUMAN	chromosome 7 open reading frame 65	123										endometrium(1)|lung(2)	3						AAATGGTTTCACTGACCCCTG	0.537													A|||	8	0.00159744	0.0061	0.0	5008	,	,		19526	0.0		0.0	False		,,,				2504	0.0				p.T123P		Atlas-SNP	.											.	C7orf65	18	.	0			c.A367C						PASS	.	A	PRO/THR	16,3120		0,16,1552	126.0	114.0	118.0		367	0.6	0.0	7	dbSNP_132	118	0,7164		0,0,3582	yes	missense	C7orf65	NM_001123065.1	38	0,16,5134	CC,CA,AA		0.0,0.5102,0.1553	probably-damaging	123/152	47698737	16,10284	1568	3582	5150	SO:0001583	missense	401335	exon3			GGTTTCACTGACC		CCDS43580.1	7p12.3	2009-02-11			ENSG00000221845	ENSG00000221845			34432	protein-coding gene	gene with protein product							Standard	NM_001123065		Approved	FLJ44108	uc010kyp.1	Q6ZTY9	OTTHUMG00000155550	ENST00000408988.2:c.367A>C	7.37:g.47698737A>C	ENSP00000386198:p.Thr123Pro	100.0	0.0	0		83.0	35.0	0.421687	NM_001123065	A4D2F8	Missense_Mutation	SNP	ENST00000408988.2	37	CCDS43580.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	A	6.306	0.424633	0.11928	0.005102	0.0	ENSG00000221845	ENST00000408988	.	.	.	0.559	0.559	0.17272	.	.	.	.	.	T	0.26011	0.0634	N	0.08118	0	0.09310	N	1	D	0.69078	0.997	D	0.68483	0.958	T	0.16928	-1.0386	7	0.87932	D	0	.	.	.	.	.	123	Q6ZTY9	CG065_HUMAN	P	123	.	ENSP00000386198:T123P	T	+	1	0	C7orf65	47665262	0.000000	0.05858	0.008000	0.14137	0.008000	0.06430	0.017000	0.13399	0.469000	0.27268	0.459000	0.35465	ACT	A|0.999;C|0.001	0.001	strong		0.537	C7orf65-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340616.1	NM_001123065	
APOF	319	hgsc.bcm.edu	37	12	56755300	56755300	+	Silent	SNP	A	A	C	rs11575217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56755300A>C	ENST00000398189.3	-	2	767	c.690T>G	c.(688-690)gcT>gcG	p.A230A	STAT2_ENST00000418572.2_5'Flank|STAT2_ENST00000557235.1_5'Flank|STAT2_ENST00000314128.4_5'Flank|APOF_ENST00000541105.1_Silent_p.A212A	NM_001638.2	NP_001629.1	Q13790	APOF_HUMAN	apolipoprotein F	230					cholesterol efflux (GO:0033344)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|triglyceride metabolic process (GO:0006641)	extracellular region (GO:0005576)|high-density lipoprotein particle (GO:0034364)|low-density lipoprotein particle (GO:0034362)	cholesterol binding (GO:0015485)|lipid transporter activity (GO:0005319)|receptor binding (GO:0005102)			breast(1)|lung(3)|prostate(1)|stomach(1)	6						CTGACATCCCAGCCATGGTCA	0.517													A|||	212	0.0423323	0.1528	0.0144	5008	,	,		20580	0.0		0.0	False		,,,				2504	0.0				p.A230A		Atlas-SNP	.											.	APOF	13	.	0			c.T690G						PASS	.	A		449,3449		26,397,1526	68.0	70.0	69.0		690	-11.0	0.0	12	dbSNP_120	69	0,8286		0,0,4143	no	coding-synonymous	APOF	NM_001638.2		26,397,5669	CC,CA,AA		0.0,11.5187,3.6852		230/327	56755300	449,11735	1949	4143	6092	SO:0001819	synonymous_variant	319	exon2			CATCCCAGCCATG	L27050	CCDS44923.1	12q13	2013-01-24				ENSG00000175336		"""Apolipoproteins"""	615	protein-coding gene	gene with protein product		107760				8093033	Standard	NM_001638		Approved		uc001sle.1	Q13790		ENST00000398189.3:c.690T>G	12.37:g.56755300A>C		150.0	0.0	0		126.0	53.0	0.420635	NM_001638	Q8TC13	Silent	SNP	ENST00000398189.3	37	CCDS44923.1																																																																																			A|0.945;C|0.055	0.055	strong		0.517	APOF-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410076.1		
CSMD3	114788	hgsc.bcm.edu	37	8	114111156	114111156	+	Missense_Mutation	SNP	C	C	T	rs73701331	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:114111156C>T	ENST00000297405.5	-	5	990	c.746G>A	c.(745-747)aGt>aAt	p.S249N	CSMD3_ENST00000519485.1_5'UTR|CSMD3_ENST00000455883.2_Missense_Mutation_p.S249N|CSMD3_ENST00000343508.3_Missense_Mutation_p.S209N|CSMD3_ENST00000352409.3_Missense_Mutation_p.S249N	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	249	CUB 2. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TATGATGCCACTGGATCCTCT	0.388										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			C|||	47	0.00938498	0.034	0.0	5008	,	,		16287	0.002		0.0	False		,,,				2504	0.0				p.S249N		Atlas-SNP	.											.	CSMD3	2325	.	0			c.G746A						PASS	.	C	ASN/SER,ASN/SER,ASN/SER	106,4300	82.9+/-121.4	2,102,2099	124.0	107.0	112.0		746,746,626	5.3	1.0	8	dbSNP_130	112	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	46,46,46	2,103,6398	TT,TC,CC		0.0116,2.4058,0.8227	possibly-damaging,possibly-damaging,possibly-damaging	249/3539,249/3708,209/3668	114111156	107,12899	2203	4300	6503	SO:0001583	missense	114788	exon5			ATGCCACTGGATC	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.746G>A	8.37:g.114111156C>T	ENSP00000297405:p.Ser249Asn	109.0	0.0	0		125.0	63.0	0.504	NM_052900	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	15	0.006868131868131868	14	0.028455284552845527	0	0.0	1	0.0017482517482517483	0	0.0	C	17.36	3.370151	0.61624	0.024058	1.16E-4	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000455883;ENST00000352409	T;T;T;T	0.18502	2.21;2.21;2.21;2.21	5.32	5.32	0.75619	CUB (5);	0.058984	0.64402	D	0.000003	T	0.09686	0.0238	L	0.27944	0.81	0.30352	N	0.784714	P;P;D;P	0.65815	0.763;0.844;0.995;0.753	B;B;D;P	0.75020	0.288;0.445;0.985;0.671	T	0.05920	-1.0856	10	0.02654	T	1	.	19.3517	0.94389	0.0:1.0:0.0:0.0	.	249;249;249;209	Q7Z407-3;Q7Z407-4;Q7Z407;Q7Z407-2	.;.;CSMD3_HUMAN;.	N	209;249;249;249	ENSP00000345799:S209N;ENSP00000297405:S249N;ENSP00000412263:S249N;ENSP00000343124:S249N	ENSP00000297405:S249N	S	-	2	0	CSMD3	114180332	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	4.889000	0.63171	2.660000	0.90430	0.591000	0.81541	AGT	C|0.990;T|0.010	0.010	strong		0.388	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
PHC2	1912	hgsc.bcm.edu	37	1	33820520	33820520	+	Silent	SNP	G	G	A	rs79627057	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:33820520G>A	ENST00000257118.5	-	7	1364	c.1311C>T	c.(1309-1311)ccC>ccT	p.P437P	PHC2_ENST00000373422.3_Silent_p.P42P|RP11-415J8.5_ENST00000432703.1_RNA|PHC2_ENST00000419414.2_Silent_p.P437P|PHC2_ENST00000373416.1_5'UTR|PHC2_ENST00000431992.1_Silent_p.P408P	NM_198040.2	NP_932157.1	Q8IXK0	PHC2_HUMAN	polyhomeotic homolog 2 (Drosophila)	437					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)				GCACGCCCTCGGGATGTCCAT	0.607													G|||	94	0.01877	0.0651	0.0115	5008	,	,		18903	0.0		0.0	False		,,,				2504	0.0				p.P437P		Atlas-SNP	.											.	PHC2	78	.	0			c.C1311T						PASS	.	G		237,4169	140.4+/-175.9	12,213,1978	72.0	69.0	70.0		1311	-8.6	0.4	1	dbSNP_131	70	0,8600		0,0,4300	no	coding-synonymous	PHC2	NM_198040.2		12,213,6278	AA,AG,GG		0.0,5.379,1.8222		437/859	33820520	237,12769	2203	4300	6503	SO:0001819	synonymous_variant	1912	exon7			GCCCTCGGGATGT	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.1311C>T	1.37:g.33820520G>A		90.0	0.0	0		110.0	46.0	0.418182	NM_198040	A1L4Q1|A8KA40|D3DPR2|Q2TAL3|Q5T0C1|Q6NUJ6|Q6ZQR1|Q8N306|Q8TAG8|Q96BL4|Q9Y4Y7	Silent	SNP	ENST00000257118.5	37	CCDS378.1																																																																																			G|0.981;A|0.019	0.019	strong		0.607	PHC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000011895.1	NM_198040	
FCRL2	79368	hgsc.bcm.edu	37	1	157736673	157736673	+	Silent	SNP	C	C	T	rs34445670	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:157736673C>T	ENST00000361516.3	-	7	1299	c.1251G>A	c.(1249-1251)ctG>ctA	p.L417L	FCRL2_ENST00000469986.1_Silent_p.L164L|FCRL2_ENST00000368181.4_Silent_p.L133L|FCRL2_ENST00000392274.3_Silent_p.L417L	NM_030764.3	NP_110391.2	Q96LA5	FCRL2_HUMAN	Fc receptor-like 2	417					cell-cell signaling (GO:0007267)|positive regulation of signal transduction (GO:0009967)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|skin(2)	51	all_hematologic(112;0.0378)		LUSC - Lung squamous cell carcinoma(543;0.24)			AGGCATACAACAGCAAAGCAA	0.418													C|||	92	0.0183706	0.0643	0.0086	5008	,	,		19517	0.0		0.001	False		,,,				2504	0.0				p.L417L		Atlas-SNP	.											.	FCRL2	104	.	0			c.G1251A						PASS	.	C		271,4135	152.5+/-186.2	9,253,1941	135.0	126.0	129.0		1251	-0.2	0.0	1	dbSNP_126	129	0,8600		0,0,4300	no	coding-synonymous	FCRL2	NM_030764.3		9,253,6241	TT,TC,CC		0.0,6.1507,2.0837		417/509	157736673	271,12735	2203	4300	6503	SO:0001819	synonymous_variant	79368	exon7			ATACAACAGCAAA	AF319438	CCDS1168.1	1q23.1	2013-01-14	2002-01-14	2005-03-23	ENSG00000132704	ENSG00000132704		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14875	protein-coding gene	gene with protein product		606509	"""SH2 domain-containing phosphatase anchor protein 1"""	SPAP1		11162587	Standard	NM_030764		Approved	FCRH2, IRTA4, CD307b	uc001fre.2	Q96LA5	OTTHUMG00000019399	ENST00000361516.3:c.1251G>A	1.37:g.157736673C>T		325.0	0.0	0		336.0	150.0	0.446429	NM_030764	A0N0M5|A1L307|A6NMS0|Q6NTA1|Q9BZI4|Q9BZI5|Q9BZI6	Silent	SNP	ENST00000361516.3	37	CCDS1168.1																																																																																			C|0.983;T|0.017	0.017	strong		0.418	FCRL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051408.2	NM_030764	
METTL11B	149281	hgsc.bcm.edu	37	1	170136808	170136808	+	Silent	SNP	G	G	T	rs61745740	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:170136808G>T	ENST00000439373.2	+	4	869	c.762G>T	c.(760-762)ctG>ctT	p.L254L		NM_001136107.1	NP_001129579.1	Q5VVY1	NTM1B_HUMAN	methyltransferase like 11B	254						nucleus (GO:0005634)	methyltransferase activity (GO:0008168)			NS(1)|breast(2)|endometrium(3)|prostate(2)	8						AGAGTGGGCTGGTGGTGCTGG	0.577													G|||	14	0.00279553	0.0106	0.0	5008	,	,		18267	0.0		0.0	False		,,,				2504	0.0				p.L254L		Atlas-SNP	.											.	METTL11B	18	.	0			c.G762T						PASS	.	G		16,1368		0,16,676	53.0	54.0	54.0		762	5.2	1.0	1	dbSNP_129	54	0,3182		0,0,1591	no	coding-synonymous	METTL11B	NM_001136107.1		0,16,2267	TT,TG,GG		0.0,1.1561,0.3504		254/284	170136808	16,4550	692	1591	2283	SO:0001819	synonymous_variant	149281	exon4			TGGGCTGGTGGTG	AL445203, CAH72139	CCDS44275.1	1q24.2	2012-11-05	2008-06-11	2008-06-11	ENSG00000203740	ENSG00000203740			31932	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 184"""	C1orf184			Standard	NM_001136107		Approved	HOMT1B	uc009wvv.1	Q5VVY1	OTTHUMG00000035959	ENST00000439373.2:c.762G>T	1.37:g.170136808G>T		96.0	0.0	0		106.0	45.0	0.424528	NM_001136107	B2RXI0	Silent	SNP	ENST00000439373.2	37	CCDS44275.1																																																																																			G|0.999;T|0.001	0.001	strong		0.577	METTL11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087586.2	NM_001136107	
ARID2	196528	hgsc.bcm.edu	37	12	46245077	46245077	+	Silent	SNP	G	G	A	rs7296694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:46245077G>A	ENST00000334344.6	+	15	3343	c.3171G>A	c.(3169-3171)tcG>tcA	p.S1057S	ARID2_ENST00000457135.1_5'Flank|ARID2_ENST00000422737.1_Silent_p.S908S|ARID2_ENST00000479608.1_3'UTR|ARID2_ENST00000444670.1_Silent_p.S667S	NM_152641.2	NP_689854.2	Q68CP9	ARID2_HUMAN	AT rich interactive domain 2 (ARID, RFX-like)	1057	Gln-rich.				chromatin modification (GO:0016568)|nucleosome disassembly (GO:0006337)|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)|autonomic_ganglia(1)|breast(7)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(21)|liver(20)|lung(34)|ovary(7)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	116	Lung SC(27;0.192)|Renal(347;0.236)	Lung NSC(34;0.106)|all_lung(34;0.22)	OV - Ovarian serous cystadenocarcinoma(5;0.00691)	GBM - Glioblastoma multiforme(48;0.0153)		CTGGTGAGTCGAGTCTGATTA	0.493			"""N, S, F"""		hepatocellular carcinoma								G|||	501	0.10004	0.3442	0.0202	5008	,	,		22635	0.004		0.001	False		,,,				2504	0.0276				p.S1057S		Atlas-SNP	.		Rec	yes		12	12q12	196528	AT rich interactive domain 2		E	.	ARID2	311	.	0			c.G3171A						PASS	.	G		1229,3177	426.4+/-341.1	182,865,1156	148.0	131.0	137.0		3171	-11.8	0.0	12	dbSNP_116	137	9,8591	6.4+/-24.3	0,9,4291	yes	coding-synonymous	ARID2	NM_152641.2		182,874,5447	AA,AG,GG		0.1047,27.8938,9.5187		1057/1836	46245077	1238,11768	2203	4300	6503	SO:0001819	synonymous_variant	196528	exon15			TGAGTCGAGTCTG		CCDS31783.1	12q13.11	2013-02-07			ENSG00000189079	ENSG00000189079		"""-"""	18037	protein-coding gene	gene with protein product		609539					Standard	NM_152641		Approved	KIAA1557, DKFZp686G052, FLJ30619, BAF200	uc001ros.1	Q68CP9	OTTHUMG00000150487	ENST00000334344.6:c.3171G>A	12.37:g.46245077G>A		116.0	0.0	0		120.0	58.0	0.483333	NM_152641	Q15KG9|Q5EB51|Q645I3|Q6ZRY5|Q7Z3I5|Q86T28|Q96SJ6|Q9HCL5	Silent	SNP	ENST00000334344.6	37	CCDS31783.1																																																																																			G|0.905;A|0.095	0.095	strong		0.493	ARID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318380.2	XM_350875	
SPTA1	6708	hgsc.bcm.edu	37	1	158626382	158626382	+	Missense_Mutation	SNP	G	G	A	rs34706737	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158626382G>A	ENST00000368147.4	-	20	3050	c.2870C>T	c.(2869-2871)gCt>gTt	p.A957V		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	957			A -> V (in dbSNP:rs34706737).		actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					ATTCCGCAGAGCTTTCATACT	0.398													G|||	173	0.0345447	0.1248	0.0101	5008	,	,		16513	0.0		0.001	False		,,,				2504	0.0				p.A957V		Atlas-SNP	.											.	SPTA1	720	.	0			c.C2870T						PASS	.	G	VAL/ALA	340,3368		17,306,1531	170.0	174.0	173.0		2870	2.5	0.0	1	dbSNP_126	173	11,8171		0,11,4080	yes	missense	SPTA1	NM_003126.2	64	17,317,5611	AA,AG,GG		0.1344,9.1694,2.9521	possibly-damaging	957/2420	158626382	351,11539	1854	4091	5945	SO:0001583	missense	6708	exon20			CGCAGAGCTTTCA	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.2870C>T	1.37:g.158626382G>A	ENSP00000357129:p.Ala957Val	83.0	0.0	0		72.0	30.0	0.416667	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	73	0.033424908424908424	69	0.1402439024390244	4	0.011049723756906077	0	0.0	0	0.0	G	16.62	3.174122	0.57692	0.091694	0.001344	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.52295	0.67;0.67	5.5	2.53	0.30540	.	0.000000	0.32120	N	0.006555	T	0.42154	0.1190	M	0.66297	2.02	0.40998	D	0.9849	P	0.46952	0.887	P	0.53722	0.733	T	0.31943	-0.9925	10	0.39692	T	0.17	.	9.6117	0.39668	0.0:0.1322:0.4583:0.4095	rs34706737	957	P02549	SPTA1_HUMAN	V	957	ENSP00000357130:A957V;ENSP00000357129:A957V	ENSP00000357129:A957V	A	-	2	0	SPTA1	156893006	0.999000	0.42202	0.038000	0.18304	0.494000	0.33585	2.748000	0.47483	0.395000	0.25257	0.655000	0.94253	GCT	G|0.976;A|0.024	0.024	strong		0.398	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
PKP1	5317	hgsc.bcm.edu	37	1	201282334	201282334	+	Missense_Mutation	SNP	G	G	A	rs34626929	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:201282334G>A	ENST00000352845.3	+	3	347	c.347G>A	c.(346-348)cGc>cAc	p.R116H	PKP1_ENST00000367324.3_Missense_Mutation_p.R116H|PKP1_ENST00000263946.3_Missense_Mutation_p.R116H			Q13835	PKP1_HUMAN	plakophilin 1	116			R -> H (in dbSNP:rs34626929).		apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intermediate filament bundle assembly (GO:0045110)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|lamin binding (GO:0005521)|signal transducer activity (GO:0004871)|structural constituent of epidermis (GO:0030280)			NS(2)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(5)|prostate(1)	22						GACAACAGGCGCTTCAGCTCC	0.582													G|||	125	0.0249601	0.093	0.0014	5008	,	,		15377	0.0		0.001	False		,,,				2504	0.0				p.R116H		Atlas-SNP	.											.	PKP1	127	.	0			c.G347A						PASS	.	G	HIS/ARG,HIS/ARG	335,4069		12,311,1879	12.0	14.0	13.0		347,347	4.2	1.0	1	dbSNP_126	13	5,8591		0,5,4293	yes	missense,missense	PKP1	NM_000299.3,NM_001005337.2	29,29	12,316,6172	AA,AG,GG		0.0582,7.6067,2.6154	probably-damaging,probably-damaging	116/748,116/727	201282334	340,12660	2202	4298	6500	SO:0001583	missense	5317	exon3			ACAGGCGCTTCAG	X79293	CCDS30966.1, CCDS30967.1	1q32	2014-06-18	2014-06-18		ENSG00000081277	ENSG00000081277		"""Armadillo repeat containing"""	9023	protein-coding gene	gene with protein product	"""ectodermal dysplasia/skin fragility syndrome"""	601975	"""plakophilin 1 (ectodermal dysplasia/skin fragility syndrome)"""			9272178	Standard	NM_001005337		Approved	B6P	uc001gwd.3	Q13835	OTTHUMG00000035729	ENST00000352845.3:c.347G>A	1.37:g.201282334G>A	ENSP00000295597:p.Arg116His	223.0	0.0	0		226.0	126.0	0.557522	NM_001005337	O00645|Q14CA0|Q15152	Missense_Mutation	SNP	ENST00000352845.3	37	CCDS30966.1	39	0.017857142857142856	39	0.07926829268292683	0	0.0	0	0.0	0	0.0	G	19.95	3.921490	0.73213	0.076067	5.82E-4	ENSG00000081277	ENST00000367324;ENST00000263946;ENST00000352845	T;T;T	0.77750	-1.12;-1.05;-1.05	4.25	4.25	0.50352	.	0.085098	0.50627	D	0.000107	T	0.22085	0.0532	L	0.29908	0.895	0.50467	D	0.999874	D;D	0.89917	0.999;1.0	P;D	0.68621	0.904;0.959	T	0.62553	-0.6830	10	0.46703	T	0.11	-3.6844	15.3441	0.74320	0.0:0.0:1.0:0.0	rs34626929	116;116	Q13835-2;Q13835	.;PKP1_HUMAN	H	116	ENSP00000356293:R116H;ENSP00000263946:R116H;ENSP00000295597:R116H	ENSP00000263946:R116H	R	+	2	0	PKP1	199548957	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	6.051000	0.71072	2.373000	0.80994	0.491000	0.48974	CGC	G|0.974;A|0.026	0.026	strong		0.582	PKP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086897.1	NM_000299	
ZNF780A	284323	hgsc.bcm.edu	37	19	40581677	40581677	+	Silent	SNP	G	G	A	rs337795	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40581677G>A	ENST00000595687.2	-	6	881	c.672C>T	c.(670-672)aaC>aaT	p.N224N	ZNF780A_ENST00000340963.5_Silent_p.N224N|ZNF780A_ENST00000455521.1_Silent_p.N225N|AC005614.5_ENST00000595508.1_RNA|ZNF780A_ENST00000594395.1_Silent_p.N225N|ZNF780A_ENST00000414720.2_Intron|ZNF780A_ENST00000450241.2_Silent_p.N190N	NM_001010880.2	NP_001010880.2	O75290	Z780A_HUMAN	zinc finger protein 780A	224					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|upper_aerodigestive_tract(3)|urinary_tract(1)	31	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					TTCCACATTCGTTACATTCAA	0.398													G|||	385	0.076877	0.2761	0.0274	5008	,	,		22376	0.0		0.001	False		,,,				2504	0.0				p.N225N		Atlas-SNP	.											.	ZNF780A	156	.	0			c.C675T						PASS	.	G	,,,	1084,3322	393.5+/-328.9	143,798,1262	92.0	92.0	92.0		672,675,672,	-3.5	0.8	19	dbSNP_79	92	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous,coding-synonymous,coding-synonymous,intron	ZNF780A	NM_001010880.2,NM_001142577.1,NM_001142578.1,NM_001142579.1	,,,	143,809,5551	AA,AG,GG		0.1279,24.6028,8.4192	,,,	224/642,225/643,224/642,	40581677	1095,11911	2203	4300	6503	SO:0001819	synonymous_variant	284323	exon6			ACATTCGTTACAT	AK091274	CCDS33026.2, CCDS46078.1, CCDS46079.1	19q13.2	2014-02-12	2006-08-15		ENSG00000197782	ENSG00000197782		"""Zinc fingers, C2H2-type"", ""-"""	27603	protein-coding gene	gene with protein product							Standard	NM_001142577		Approved	ZNF780	uc010xvh.2	O75290	OTTHUMG00000155119	ENST00000595687.2:c.672C>T	19.37:g.40581677G>A		89.0	0.0	0		139.0	139.0	1	NM_001142577	E9PB48|Q6ZN87	Silent	SNP	ENST00000595687.2	37	CCDS33026.2																																																																																			G|0.928;A|0.072	0.072	strong		0.398	ZNF780A-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000470066.1	NM_001010880	
PARP14	54625	hgsc.bcm.edu	37	3	122437536	122437536	+	Missense_Mutation	SNP	C	C	T	rs61732767	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122437536C>T	ENST00000474629.2	+	14	4804	c.4538C>T	c.(4537-4539)gCg>gTg	p.A1513V	PARP14_ENST00000475640.1_3'UTR	NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	1513					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		GAAATTGAGGCGATGATCAAG	0.388													C|||	54	0.0107827	0.0363	0.0086	5008	,	,		21623	0.0		0.0	False		,,,				2504	0.0				p.A1513V		Atlas-SNP	.											.	PARP14	242	.	0			c.C4538T						PASS	.	C	VAL/ALA	89,3737		3,83,1827	209.0	205.0	206.0		4538	-3.8	0.0	3	dbSNP_129	206	1,8273		0,1,4136	yes	missense	PARP14	NM_017554.2	64	3,84,5963	TT,TC,CC		0.0121,2.3262,0.7438	benign	1513/1802	122437536	90,12010	1913	4137	6050	SO:0001583	missense	54625	exon14			TTGAGGCGATGAT	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"""Poly (ADP-ribose) polymerases"""	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.4538C>T	3.37:g.122437536C>T	ENSP00000418194:p.Ala1513Val	164.0	0.0	0		138.0	51.0	0.369565	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Missense_Mutation	SNP	ENST00000474629.2	37	CCDS46894.1	20	0.009157509157509158	16	0.032520325203252036	4	0.011049723756906077	0	0.0	0	0.0	C	12.90	2.075995	0.36662	0.023262	1.21E-4	ENSG00000173193	ENST00000474629;ENST00000398162;ENST00000310290;ENST00000398157	T	0.31510	1.49	5.05	-3.77	0.04346	.	1.394450	0.04317	N	0.350052	T	0.04815	0.0130	L	0.29908	0.895	0.09310	N	1	B;P	0.37330	0.166;0.59	B;B	0.26094	0.035;0.066	T	0.11324	-1.0592	10	0.30078	T	0.28	.	1.8967	0.03259	0.3644:0.238:0.2884:0.1093	rs61732767	1513;1513	Q460N5-4;Q460N5	.;PAR14_HUMAN	V	1513;1432;116;509	ENSP00000418194:A1513V	ENSP00000310633:A116V	A	+	2	0	PARP14	123920226	0.000000	0.05858	0.005000	0.12908	0.945000	0.59286	0.740000	0.26188	-0.515000	0.06479	-0.271000	0.10264	GCG	C|0.990;T|0.010	0.010	strong		0.388	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554	
RBPJL	11317	hgsc.bcm.edu	37	20	43938284	43938284	+	Missense_Mutation	SNP	G	G	A	rs35032855	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43938284G>A	ENST00000343694.3	+	3	281	c.209G>A	c.(208-210)cGg>cAg	p.R70Q	MATN4_ENST00000372751.4_5'Flank|RBPJL_ENST00000372741.3_Missense_Mutation_p.R70Q|RBPJL_ENST00000372743.1_Missense_Mutation_p.R70Q|MATN4_ENST00000537548.1_5'Flank|MATN4_ENST00000360607.6_5'Flank|MATN4_ENST00000353917.5_5'Flank|MATN4_ENST00000342716.4_5'Flank	NM_001281448.1|NM_001281449.1|NM_014276.2	NP_001268377.1|NP_001268378.1|NP_055091.2	Q9UBG7	RBPJL_HUMAN	recombination signal binding protein for immunoglobulin kappa J region-like	70					positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|kidney(1)|large_intestine(5)|lung(3)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		Myeloproliferative disorder(115;0.0122)				CAGACTGTGCGGATCCTGCAT	0.607													G|||	57	0.0113818	0.034	0.0058	5008	,	,		19804	0.0		0.004	False		,,,				2504	0.0041				p.R70Q		Atlas-SNP	.											.	RBPJL	67	.	0			c.G209A						PASS	.	G	GLN/ARG	165,4241	109.5+/-147.8	3,159,2041	114.0	93.0	100.0		209	5.5	1.0	20	dbSNP_126	100	17,8583	12.6+/-44.7	0,17,4283	yes	missense	RBPJL	NM_014276.2	43	3,176,6324	AA,AG,GG		0.1977,3.7449,1.3994	benign	70/518	43938284	182,12824	2203	4300	6503	SO:0001583	missense	11317	exon3			CTGTGCGGATCCT	AB024964	CCDS13349.1, CCDS63283.1, CCDS63284.1	20q13.12	2013-10-18	2007-02-26	2007-02-26	ENSG00000124232	ENSG00000124232			13761	protein-coding gene	gene with protein product			"""recombining binding protein suppressor of hairless (Drosophila)-like"""	RBPSUHL		9929984	Standard	NM_014276		Approved	RBP-L, SUH, SUHL	uc002xns.3	Q9UBG7	OTTHUMG00000033055	ENST00000343694.3:c.209G>A	20.37:g.43938284G>A	ENSP00000341243:p.Arg70Gln	119.0	0.0	0		93.0	39.0	0.419355	NM_014276	O95723|Q5QPU9|Q5QPV0|Q9ULV9	Missense_Mutation	SNP	ENST00000343694.3	37	CCDS13349.1	23	0.010531135531135532	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	20.6	4.012876	0.75161	0.037449	0.001977	ENSG00000124232	ENST00000372743;ENST00000372741;ENST00000343694	D;D;D	0.82711	-1.64;-1.64;-1.64	5.53	5.53	0.82687	LAG1, DNA binding (2);p53-like transcription factor, DNA-binding (1);	0.860937	0.10327	N	0.688044	T	0.41213	0.1149	N	0.22421	0.69	0.20307	N	0.999911	P;P	0.46621	0.881;0.708	B;B	0.35073	0.195;0.189	T	0.57573	-0.7788	10	0.66056	D	0.02	-7.9496	12.2068	0.54356	0.0:0.0:0.7307:0.2693	rs35032855	70;70	Q5QPV1;Q9UBG7	.;RBPJL_HUMAN	Q	70	ENSP00000361828:R70Q;ENSP00000361826:R70Q;ENSP00000341243:R70Q	ENSP00000341243:R70Q	R	+	2	0	RBPJL	43371698	0.992000	0.36948	0.998000	0.56505	0.917000	0.54804	1.776000	0.38594	2.622000	0.88805	0.456000	0.33151	CGG	G|0.988;A|0.012	0.012	strong		0.607	RBPJL-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080391.1	NM_014276	
EPPK1	83481	hgsc.bcm.edu	37	8	144942097	144942097	+	Silent	SNP	G	G	A	rs73375119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144942097G>A	ENST00000525985.1	-	2	5396	c.5325C>T	c.(5323-5325)caC>caT	p.H1775H				P58107	EPIPL_HUMAN	epiplakin 1	1775						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			ATTGCAACACGTGTCTCGTGG	0.522													G|||	67	0.0133786	0.0477	0.0043	5008	,	,		20496	0.0		0.001	False		,,,				2504	0.0				p.H1775H		Atlas-SNP	.											EPPK1,NS,NS,-1,1	EPPK1	199	1	0			c.C5325T						PASS	.	G		178,3790		4,170,1810	125.0	120.0	122.0		5325	-10.2	0.0	8	dbSNP_130	122	1,8341		0,1,4170	no	coding-synonymous	EPPK1	NM_031308.1		4,171,5980	AA,AG,GG		0.012,4.4859,1.4541		1775/2420	144942097	179,12131	1984	4171	6155	SO:0001819	synonymous_variant	83481	exon1			CAACACGTGTCTC	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.5325C>T	8.37:g.144942097G>A		247.0	1.0	0.00404858		260.0	132.0	0.507692	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																				G|0.984;A|0.016	0.016	strong		0.522	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
CASC5	57082	hgsc.bcm.edu	37	15	40916272	40916272	+	Silent	SNP	G	G	A	rs34758606	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:40916272G>A	ENST00000346991.5	+	11	4278	c.3888G>A	c.(3886-3888)gcG>gcA	p.A1296A	CASC5_ENST00000399668.2_Silent_p.A1270A			Q8NG31	CASC5_HUMAN	cancer susceptibility candidate 5	1296					acrosome assembly (GO:0001675)|attachment of spindle microtubules to kinetochore (GO:0008608)|CENP-A containing nucleosome assembly (GO:0034080)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of phosphatase activity (GO:0010923)|nucleosome assembly (GO:0006334)|protein localization to kinetochore (GO:0034501)|spindle assembly checkpoint (GO:0071173)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(1)|breast(7)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(13)|lung(16)|skin(3)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_cancers(109;2.03e-18)|all_epithelial(112;4.26e-15)|Lung NSC(122;1.12e-10)|all_lung(180;2.59e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;4.99e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0861)|COAD - Colon adenocarcinoma(120;0.211)		TGGAAAAAGCGCAAGTTGAAA	0.363													G|||	68	0.0135783	0.0484	0.0058	5008	,	,		20456	0.0		0.0	False		,,,				2504	0.0				p.A1296A		Atlas-SNP	.											.	CASC5	269	.	0			c.G3888A						PASS	.	G	,	134,3578		6,122,1728	87.0	81.0	83.0		3810,3888	-4.3	0.0	15	dbSNP_126	83	1,8199		0,1,4099	no	coding-synonymous,coding-synonymous	CASC5	NM_144508.3,NM_170589.3	,	6,123,5827	AA,AG,GG		0.0122,3.6099,1.1333	,	1270/2317,1296/2343	40916272	135,11777	1856	4100	5956	SO:0001819	synonymous_variant	57082	exon11			AAAAGCGCAAGTT	AF173994	CCDS42023.1, CCDS42024.1	15q14	2013-07-03			ENSG00000137812	ENSG00000137812		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	24054	protein-coding gene	gene with protein product	"""cancer/testis antigen 29"", ""kinetochore null 1 homolog (C. elegans)"", ""blinkin, bub-linking kinetochore protein"", ""protein phosphatase 1, regulatory subunit 55"""	609173				10980622, 10780384, 18045986	Standard	NM_170589		Approved	D40, AF15Q14, CT29, hKNL-1, KNL1, hSpc105, PPP1R55, Spc7	uc010bbt.1	Q8NG31	OTTHUMG00000166532	ENST00000346991.5:c.3888G>A	15.37:g.40916272G>A		75.0	0.0	0		98.0	55.0	0.561224	NM_170589	Q8NHE1|Q8WXA6|Q9HCK2|Q9NR92	Silent	SNP	ENST00000346991.5	37	CCDS42023.1																																																																																			G|0.991;A|0.009	0.009	strong		0.363	CASC5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390224.2	NM_144508	
CELA3A	10136	hgsc.bcm.edu	37	1	22328207	22328207	+	Missense_Mutation	SNP	G	G	A	rs11541414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:22328207G>A	ENST00000290122.3	+	1	59	c.40G>A	c.(40-42)Gtt>Att	p.V14I	CELA3A_ENST00000374663.1_Missense_Mutation_p.V14I|RN7SL768P_ENST00000584415.1_RNA	NM_005747.4	NP_005738.4	P09093	CEL3A_HUMAN	chymotrypsin-like elastase family, member 3A	14					cholesterol metabolic process (GO:0008203)|digestion (GO:0007586)|proteolysis (GO:0006508)		serine-type endopeptidase activity (GO:0004252)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						CCTTGTGGCCGTTGGTAAGAC	0.537													G|||	284	0.0567093	0.1755	0.0187	5008	,	,		18400	0.0258		0.0109	False		,,,				2504	0.002				p.V14I		Atlas-SNP	.											.	CELA3A	35	.	0			c.G40A						PASS	.	G	ILE/VAL	543,3853	244.7+/-253.9	48,447,1703	198.0	197.0	197.0		40	1.4	1.0	1	dbSNP_120	197	97,8503	54.8+/-115.7	2,93,4205	no	missense	CELA3A	NM_005747.4	29	50,540,5908	AA,AG,GG		1.1279,12.3521,4.9246		14/271	22328207	640,12356	2198	4300	6498	SO:0001583	missense	10136	exon1			GTGGCCGTTGGTA	D00306	CCDS220.1	1p36.12	2009-05-05	2009-05-05	2009-05-05	ENSG00000142789	ENSG00000142789			15944	protein-coding gene	gene with protein product	"""protease E"""		"""elastase 3A, pancreatic (protease E)"", ""elastase 3A, pancreatic"""	ELA3A		2826474, 2460440	Standard	NM_005747		Approved	ELA3		P09093	OTTHUMG00000002755	ENST00000290122.3:c.40G>A	1.37:g.22328207G>A	ENSP00000290122:p.Val14Ile	270.0	0.0	0		264.0	135.0	0.511364	NM_005747	B1AQ53|Q9BRW4	Missense_Mutation	SNP	ENST00000290122.3	37	CCDS220.1	121	0.0554029304029304	91	0.18495934959349594	5	0.013812154696132596	21	0.03671328671328671	4	0.005277044854881266	G	4.477	0.088340	0.08583	0.123521	0.011279	ENSG00000142789	ENST00000290122;ENST00000374663	D;D	0.92911	-2.37;-3.13	3.38	1.44	0.22558	.	.	.	.	.	T	0.00552	0.0018	N	0.13098	0.295	0.58432	P	6.999999999979245E-6	B	0.16802	0.019	B	0.04013	0.001	T	0.21211	-1.0252	8	0.22706	T	0.39	-4.0293	4.8356	0.13464	0.0:0.6486:0.224:0.1274	rs11541414;rs12129372	14	P09093	CEL3A_HUMAN	I	14	ENSP00000290122:V14I;ENSP00000363795:V14I	ENSP00000290122:V14I	V	+	1	0	CELA3A	22200794	0.882000	0.30256	0.999000	0.59377	0.226000	0.24999	-0.001000	0.12947	0.265000	0.21872	-1.210000	0.01631	GTT	G|0.950;A|0.050	0.050	strong		0.537	CELA3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007791.1	NM_005747	
NOTCH1	4851	hgsc.bcm.edu	37	9	139390958	139390958	+	Silent	SNP	T	T	C	rs11574911	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139390958T>C	ENST00000277541.6	-	34	7308	c.7233A>G	c.(7231-7233)ccA>ccG	p.P2411P		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	2411	Poly-Pro.				anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P2412P(1)|p.P2412del(1)		breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		GTGGTGGTGGTGGCGGCTGCA	0.642			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)			T|||	160	0.0319489	0.1112	0.0144	5008	,	,		14401	0.0		0.003	False		,,,				2504	0.0				p.P2411P		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	NOTCH1,NS,lymphoid_neoplasm,0,1	NOTCH1	1980	1	2	Substitution - coding silent(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(2)	c.A7233G						PASS	.	T		313,3979		8,297,1841	22.0	30.0	27.0		7233	-1.5	0.0	9	dbSNP_120	27	17,8511		0,17,4247	no	coding-synonymous	NOTCH1	NM_017617.3		8,314,6088	CC,CT,TT		0.1993,7.2926,2.5741		2411/2556	139390958	330,12490	2146	4264	6410	SO:0001819	synonymous_variant	4851	exon34			TGGTGGTGGCGGC	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.7233A>G	9.37:g.139390958T>C		26.0	0.0	0		31.0	11.0	0.354839	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			T|0.968;C|0.032	0.032	strong		0.642	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
DSC2	1824	hgsc.bcm.edu	37	18	28681903	28681903	+	Missense_Mutation	SNP	T	T	C	rs868333	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:28681903T>C	ENST00000280904.6	-	1	475	c.32A>G	c.(31-33)aAc>aGc	p.N11S	RP11-408H20.2_ENST00000581836.1_RNA|DSC2_ENST00000251081.6_Missense_Mutation_p.N11S	NM_024422.3	NP_077740.1	Q02487	DSC2_HUMAN	desmocollin 2	11			N -> S (in dbSNP:rs868333). {ECO:0000269|PubMed:20031617}.		bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell-cardiac muscle cell adhesion (GO:0086042)|cell adhesion (GO:0007155)|cellular response to starvation (GO:0009267)|homophilic cell adhesion (GO:0007156)|regulation of heart rate by cardiac conduction (GO:0086091)|ventricular cardiac muscle cell action potential (GO:0086005)	cell-cell adherens junction (GO:0005913)|cytoplasmic vesicle (GO:0031410)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(2)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|prostate(1)|skin(1)	21			OV - Ovarian serous cystadenocarcinoma(10;0.0241)			GAGGGCTCCGTTCCAGGAGCC	0.751													C|||	428	0.0854633	0.3116	0.0216	5008	,	,		8187	0.001		0.0	False		,,,				2504	0.0				p.N11S		Atlas-SNP	.											.	DSC2	168	.	0			c.A32G						PASS	.						1.0	2.0	2.0					18																	28681903		1051	2094	3145	SO:0001583	missense	1824	exon1			GCTCCGTTCCAGG	X56807	CCDS11892.1, CCDS11893.1	18q12.1	2014-09-17			ENSG00000134755	ENSG00000134755		"""Cadherins / Major cadherins"""	3036	protein-coding gene	gene with protein product		125645		DSC3		7774948	Standard	NM_024422		Approved	CDHF2	uc002kwl.4	Q02487	OTTHUMG00000131981	ENST00000280904.6:c.32A>G	18.37:g.28681903T>C	ENSP00000280904:p.Asn11Ser	25.0	0.0	0		10.0	5.0	0.5	NM_024422		Missense_Mutation	SNP	ENST00000280904.6	37	CCDS11892.1	169	0.07738095238095238	156	0.3170731707317073	7	0.019337016574585635	5	0.008741258741258742	1	0.0013192612137203166	C	7.222	0.597497	0.13875	.	.	ENSG00000134755	ENST00000251081;ENST00000280904;ENST00000399347	T;T	0.57107	0.45;0.42	4.55	3.59	0.41128	.	.	.	.	.	T	0.00012	0.0000	N	0.00289	-1.7	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.38001	-0.9681	8	0.02654	T	1	.	4.9282	0.13903	0.2229:0.6676:0.0:0.1095	rs868333	11;11	Q02487;Q02487-2	DSC2_HUMAN;.	S	11	ENSP00000251081:N11S;ENSP00000280904:N11S	ENSP00000251081:N11S	N	-	2	0	DSC2	26935901	0.000000	0.05858	0.506000	0.27664	0.417000	0.31264	0.324000	0.19610	1.139000	0.42245	-0.186000	0.12905	AAC	T|0.923;C|0.077	0.077	strong		0.751	DSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254943.1	NM_004949	
MUC4	4585	hgsc.bcm.edu	37	3	195509322	195509322	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195509322G>A	ENST00000463781.3	-	2	9588	c.9129C>T	c.(9127-9129)gtC>gtT	p.V3043V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.V3043V	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	984					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.V3043V(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)		AAGTGTCGGTGACAGGAAGCG	0.612																																					p.V3043V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - coding silent(1)	kidney(1)	c.C9129T						PASS	.																																			SO:0001819	synonymous_variant	4585	exon2			GTCGGTGACAGGA	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.9129C>T	3.37:g.195509322G>A		127.0	0.0	0		177.0	11.0	0.0621469	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			.	.	none		0.612	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TMPRSS4	56649	hgsc.bcm.edu	37	11	117978578	117978578	+	Missense_Mutation	SNP	G	G	A	rs1894176	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117978578G>A	ENST00000437212.3	+	6	744	c.530G>A	c.(529-531)cGg>cAg	p.R177Q	TMPRSS4_ENST00000523251.1_Missense_Mutation_p.R137Q|TMPRSS4_ENST00000522824.1_Missense_Mutation_p.R172Q|TMPRSS4_ENST00000534111.1_Missense_Mutation_p.R175Q|TMPRSS4_ENST00000522307.1_Missense_Mutation_p.R30Q			Q9NRS4	TMPS4_HUMAN	transmembrane protease, serine 4	177	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.		R -> Q (in dbSNP:rs1894176).		proteolysis (GO:0006508)	integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			breast(2)|central_nervous_system(2)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)	19	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0431)|all_hematologic(192;0.164)|Breast(348;0.183)|all_neural(223;0.238)		BRCA - Breast invasive adenocarcinoma(274;4.16e-05)|Epithelial(105;0.00204)		CTTCGCATGCGGAACTCAAGT	0.547													G|||	204	0.0407348	0.1415	0.0216	5008	,	,		19296	0.0		0.002	False		,,,				2504	0.0				p.R177Q		Atlas-SNP	.											TMPRSS4,NS,carcinoma,-1,1	TMPRSS4	46	1	0			c.G530A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	452,3948	216.1+/-234.9	26,400,1774	67.0	60.0	62.0		515,524,410,530	-7.9	0.0	11	dbSNP_92	62	13,8579	9.1+/-34.3	0,13,4283	yes	missense,missense,missense,missense	TMPRSS4	NM_001083947.1,NM_001173551.1,NM_001173552.1,NM_019894.3	43,43,43,43	26,413,6057	AA,AG,GG		0.1513,10.2727,3.5791	benign,benign,benign,benign	172/433,175/436,137/398,177/438	117978578	465,12527	2200	4296	6496	SO:0001583	missense	56649	exon6			GCATGCGGAACTC	AF179224	CCDS31684.1, CCDS44743.1, CCDS53716.1, CCDS53717.1	11q23.3	2010-04-13			ENSG00000137648	ENSG00000137648		"""Serine peptidases / Transmembrane"""	11878	protein-coding gene	gene with protein product	"""transmembrane serine protease 3"", ""membrane-type serine protease 2"", ""type II membrane serine protease"""	606565				10825129	Standard	NM_001083947		Approved	TMPRSS3, MT-SP2	uc021qrd.1	Q9NRS4	OTTHUMG00000164122	ENST00000437212.3:c.530G>A	11.37:g.117978578G>A	ENSP00000416037:p.Arg177Gln	57.0	0.0	0		51.0	35.0	0.686275	NM_019894	A8MU84|B0YJB0|B7Z8C5|E7ERX8|Q5XKQ6|Q6UX37|Q9NZA5	Missense_Mutation	SNP	ENST00000437212.3	37	CCDS31684.1	84	0.038461538461538464	78	0.15853658536585366	6	0.016574585635359115	0	0.0	0	0.0	G	2.686	-0.274296	0.05679	0.102727	0.001513	ENSG00000137648	ENST00000534111;ENST00000522307;ENST00000523251;ENST00000437212;ENST00000522824;ENST00000522151	T;D;T;T;T;T	0.88201	0.21;-2.35;0.21;0.21;0.21;0.21	5.31	-7.95	0.01148	Speract/scavenger receptor-related (2);	1.636540	0.03489	N	0.216335	T	0.00384	0.0012	N	0.00642	-1.3	0.80722	P	0.0	B;B;B;B;B	0.15719	0.014;0.014;0.008;0.005;0.005	B;B;B;B;B	0.04013	0.001;0.001;0.0;0.001;0.001	T	0.33752	-0.9856	9	0.13108	T	0.6	.	4.6674	0.12673	0.2857:0.1209:0.4751:0.1183	rs1894176;rs1894176	152;137;30;177;175	B7Z900;E7ERX8;E7ESG9;Q9NRS4;Q9NRS4-3	.;.;.;TMPS4_HUMAN;.	Q	175;30;137;177;172;124	ENSP00000435184:R175Q;ENSP00000428814:R30Q;ENSP00000429209:R137Q;ENSP00000416037:R177Q;ENSP00000430547:R172Q;ENSP00000428407:R124Q	ENSP00000416037:R177Q	R	+	2	0	TMPRSS4	117483788	0.000000	0.05858	0.033000	0.17914	0.003000	0.03518	-1.134000	0.03228	-1.008000	0.03404	-1.105000	0.02106	CGG	G|0.955;A|0.045	0.045	strong		0.547	TMPRSS4-004	KNOWN	non_canonical_polymorphism|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377328.2	NM_019894	
C1orf53	388722	hgsc.bcm.edu	37	1	197872001	197872001	+	Silent	SNP	G	G	A	rs73083807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:197872001G>A	ENST00000367393.3	+	1	225	c.222G>A	c.(220-222)gcG>gcA	p.A74A		NM_001024594.2	NP_001019765.1	Q5VUE5	CA053_HUMAN	chromosome 1 open reading frame 53	74										endometrium(1)|lung(1)	2						AGTTAACCGCGGCGGAGCGAC	0.756													G|||	123	0.0245607	0.0877	0.0101	5008	,	,		10681	0.0		0.0	False		,,,				2504	0.0				p.A74A		Atlas-SNP	.											.	C1orf53	18	.	0			c.G222A						PASS	.	G		263,3423		4,255,1584	7.0	8.0	8.0		222	0.1	0.0	1	dbSNP_130	8	3,8019		0,3,4008	no	coding-synonymous	C1orf53	NM_001024594.2		4,258,5592	AA,AG,GG		0.0374,7.1351,2.272		74/146	197872001	266,11442	1843	4011	5854	SO:0001819	synonymous_variant	388722	exon1			AACCGCGGCGGAG	BC038214	CCDS44290.1	1q31.3	2011-01-26			ENSG00000203724	ENSG00000203724			30003	protein-coding gene	gene with protein product						15897902	Standard	NM_001024594		Approved		uc001guh.3	Q5VUE5	OTTHUMG00000035659	ENST00000367393.3:c.222G>A	1.37:g.197872001G>A		20.0	0.0	0		15.0	7.0	0.466667	NM_001024594	A1L4N2|Q5VUE4	Silent	SNP	ENST00000367393.3	37	CCDS44290.1																																																																																			G|0.972;A|0.028	0.028	strong		0.756	C1orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086555.1	NM_001024594	
AHR	196	hgsc.bcm.edu	37	7	17379157	17379157	+	Missense_Mutation	SNP	G	G	A	rs4986826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:17379157G>A	ENST00000242057.4	+	10	2351	c.1708G>A	c.(1708-1710)Gtt>Att	p.V570I		NM_001621.4	NP_001612.1	P35869	AHR_HUMAN	aryl hydrocarbon receptor	570			V -> I (in dbSNP:rs4986826). {ECO:0000269|PubMed:10739168, ECO:0000269|PubMed:11689007}.		apoptotic process (GO:0006915)|blood vessel development (GO:0001568)|cell cycle (GO:0007049)|circadian regulation of gene expression (GO:0032922)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|regulation of B cell proliferation (GO:0030888)|regulation of gene expression (GO:0010468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to toxic substance (GO:0009636)|response to xenobiotic stimulus (GO:0009410)|transcription from RNA polymerase II promoter (GO:0006366)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosolic aryl hydrocarbon receptor complex (GO:0034752)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|enhancer binding (GO:0035326)|Hsp90 protein binding (GO:0051879)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(11)|ovary(1)|pancreas(1)|urinary_tract(3)	33	Lung NSC(10;0.0392)|all_lung(11;0.0754)				Atorvastatin(DB01076)|Flutamide(DB00499)|Ginseng(DB01404)|Leflunomide(DB01097)|Mexiletine(DB00379)|Nimodipine(DB00393)	TTCTGGTGAGGTTGACTTCAG	0.363													G|||	113	0.0225639	0.0756	0.0144	5008	,	,		21431	0.0		0.002	False		,,,				2504	0.001				p.V570I		Atlas-SNP	.											.	AHR	89	.	0			c.G1708A						PASS	.	G	ILE/VAL	285,4121	151.8+/-185.6	14,257,1932	67.0	71.0	69.0		1708	3.4	0.4	7	dbSNP_111	69	17,8583	11.9+/-42.8	0,17,4283	yes	missense	AHR	NM_001621.4	29	14,274,6215	AA,AG,GG		0.1977,6.4685,2.322	benign	570/849	17379157	302,12704	2203	4300	6503	SO:0001583	missense	196	exon10			GGTGAGGTTGACT	L19872	CCDS5366.1	7p15	2013-05-21			ENSG00000106546	ENSG00000106546		"""Basic helix-loop-helix proteins"""	348	protein-coding gene	gene with protein product		600253				8125016	Standard	NM_001621		Approved	bHLHe76	uc011jxz.1	P35869	OTTHUMG00000149967	ENST00000242057.4:c.1708G>A	7.37:g.17379157G>A	ENSP00000242057:p.Val570Ile	53.0	0.0	0		43.0	27.0	0.627907	NM_001621	A4D130|Q13728|Q13803|Q13804	Missense_Mutation	SNP	ENST00000242057.4	37	CCDS5366.1	49	0.022435897435897436	41	0.08333333333333333	8	0.022099447513812154	0	0.0	0	0.0	G	9.679	1.148672	0.21288	0.064685	0.001977	ENSG00000106546	ENST00000242057	T	0.24723	1.84	6.16	3.44	0.39384	.	0.396190	0.28322	N	0.015763	T	0.01489	0.0048	M	0.63428	1.95	0.18873	N	0.999986	B	0.31009	0.303	B	0.33799	0.17	T	0.02132	-1.1208	10	0.38643	T	0.18	.	12.061	0.53562	0.15:0.0:0.85:0.0	rs4986826;rs52830926;rs58070269;rs4986826	570	P35869	AHR_HUMAN	I	570	ENSP00000242057:V570I	ENSP00000242057:V570I	V	+	1	0	AHR	17345682	0.908000	0.30866	0.408000	0.26446	0.911000	0.54048	1.786000	0.38694	0.498000	0.27948	0.650000	0.86243	GTT	G|0.974;A|0.026	0.026	strong		0.363	AHR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314620.2	NM_001621	
OBSCN	84033	hgsc.bcm.edu	37	1	228404864	228404864	+	Missense_Mutation	SNP	G	G	A	rs141921462	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228404864G>A	ENST00000422127.1	+	8	2572	c.2528G>A	c.(2527-2529)cGc>cAc	p.R843H	OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000570156.2_Missense_Mutation_p.R843H|OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000284548.11_Missense_Mutation_p.R843H	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	843	Ig-like 8.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TCCGGTGAGCGCTTCTTGCAG	0.662													G|||	36	0.0071885	0.0272	0.0	5008	,	,		16092	0.0		0.0	False		,,,				2504	0.0				p.R843H		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G2528A						PASS	.	G	HIS/ARG,HIS/ARG	124,4184		1,122,2031	64.0	72.0	69.0		2528,2528	-2.1	0.0	1	dbSNP_134	69	1,8503		0,1,4251	yes	missense,missense	OBSCN	NM_001098623.1,NM_052843.2	29,29	1,123,6282	AA,AG,GG		0.0118,2.8784,0.9756	probably-damaging,probably-damaging	843/7969,843/6621	228404864	125,12687	2154	4252	6406	SO:0001583	missense	84033	exon8			GTGAGCGCTTCTT	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.2528G>A	1.37:g.228404864G>A	ENSP00000409493:p.Arg843His	94.0	0.0	0		91.0	57.0	0.626374	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	.	8.071	0.770330	0.15983	0.028784	1.18E-4	ENSG00000154358	ENST00000284548;ENST00000422127	T;T	0.52057	0.68;0.68	4.79	-2.11	0.07187	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.987508	0.08243	N	0.975792	T	0.20659	0.0497	L	0.58101	1.795	0.09310	N	0.999998	B;D	0.64830	0.008;0.994	B;P	0.48454	0.003;0.578	T	0.31110	-0.9955	10	0.14656	T	0.56	.	7.3341	0.26599	0.6513:0.0:0.2172:0.1315	.	843;843	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	H	843	ENSP00000284548:R843H;ENSP00000409493:R843H	ENSP00000284548:R843H	R	+	2	0	OBSCN	226471487	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.113000	0.03296	-0.663000	0.05331	-0.768000	0.03414	CGC	G|0.996;A|0.004	0.004	strong		0.662	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
ACSM2A	123876	hgsc.bcm.edu	37	16	20476974	20476974	+	Missense_Mutation	SNP	C	C	T	rs13332099	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:20476974C>T	ENST00000573854.1	+	3	427	c.313C>T	c.(313-315)Cgt>Tgt	p.R105C	ACSM2A_ENST00000575690.1_Missense_Mutation_p.R105C|ACSM2A_ENST00000396104.2_Missense_Mutation_p.R105C|ACSM2A_ENST00000417235.2_Missense_Mutation_p.R26C|ACSM2A_ENST00000424070.1_Missense_Mutation_p.R105C|ACSM2A_ENST00000219054.6_Missense_Mutation_p.R105C|ACSM2A_ENST00000536134.1_5'UTR|ACSM2A_ENST00000575558.1_3'UTR	NM_001010845.2	NP_001010845	Q08AH3	ACS2A_HUMAN	acyl-CoA synthetase medium-chain family member 2A	105					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)	p.R105G(1)		breast(2)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(34)|ovary(1)|skin(6)|stomach(1)	51						TGGCCTGCAGCGTGGGGATCG	0.577													C|||	31	0.0061901	0.0212	0.0029	5008	,	,		20999	0.0		0.0	False		,,,				2504	0.001				p.R105C		Atlas-SNP	.											ACSM2A,NS,carcinoma,-2,1	ACSM2A	120	1	1	Substitution - Missense(1)	lung(1)	c.C313T						PASS	.	C	CYS/ARG	79,4327	68.1+/-105.8	1,77,2125	121.0	101.0	108.0		313	2.8	1.0	16	dbSNP_121	108	0,8600		0,0,4300	no	missense	ACSM2A	NM_001010845.2	180	1,77,6425	TT,TC,CC		0.0,1.793,0.6074	benign	105/578	20476974	79,12927	2203	4300	6503	SO:0001583	missense	123876	exon4			CTGCAGCGTGGGG	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.313C>T	16.37:g.20476974C>T	ENSP00000459451:p.Arg105Cys	502.0	0.0	0		521.0	179.0	0.34357	NM_001010845	B3KTT9|O75202	Missense_Mutation	SNP	ENST00000573854.1	37	CCDS32401.1	14	0.00641025641025641	13	0.026422764227642278	1	0.0027624309392265192	0	0.0	0	0.0	C	11.81	1.750666	0.31046	0.01793	0.0	ENSG00000183747	ENST00000417235;ENST00000219054;ENST00000424070;ENST00000396104	T;T;T;T	0.52295	0.67;0.67;0.67;0.67	3.76	2.79	0.32731	AMP-dependent synthetase/ligase (1);	0.189594	0.27262	N	0.020171	T	0.19967	0.0480	M	0.84326	2.69	0.30993	N	0.721168	P;P	0.37636	0.485;0.603	B;B	0.28916	0.096;0.096	T	0.46569	-0.9182	10	0.56958	D	0.05	-6.0087	6.554	0.22450	0.1772:0.7202:0.0:0.1026	rs13332099	26;105	B7Z8R0;Q08AH3	.;ACS2A_HUMAN	C	26;105;105;105	ENSP00000392169:R26C;ENSP00000219054:R105C;ENSP00000394904:R105C;ENSP00000379411:R105C	ENSP00000219054:R105C	R	+	1	0	ACSM2A	20384475	0.515000	0.26210	0.989000	0.46669	0.734000	0.41952	1.158000	0.31737	0.694000	0.31654	0.298000	0.19748	CGT	C|0.993;T|0.007	0.007	strong		0.577	ACSM2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436764.1	NM_001010845	
DKK3	27122	hgsc.bcm.edu	37	11	12023868	12023868	+	Silent	SNP	A	A	G	rs79628149	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:12023868A>G	ENST00000396505.2	-	3	568	c.330T>C	c.(328-330)caT>caC	p.H110H	DKK3_ENST00000525493.1_Silent_p.H110H|DKK3_ENST00000450094.2_Silent_p.H110H|DKK3_ENST00000527132.1_Intron|DKK3_ENST00000326932.4_Silent_p.H110H	NM_015881.5	NP_056965.3	Q9UBP4	DKK3_HUMAN	dickkopf WNT signaling pathway inhibitor 3	110					adrenal gland development (GO:0030325)|anatomical structure morphogenesis (GO:0009653)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of transcription, DNA-templated (GO:0045892)|Wnt signaling pathway (GO:0016055)	extracellular space (GO:0005615)				breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|ovary(1)|pancreas(1)	8				Epithelial(150;0.000502)		CTCGGTGCACATGGATGGTAT	0.433													A|||	45	0.00898562	0.028	0.0101	5008	,	,		18698	0.0		0.001	False		,,,				2504	0.0				p.H110H		Atlas-SNP	.											.	DKK3	35	.	0			c.T330C						PASS	.	A	,,	109,4293	86.3+/-125.0	0,109,2092	308.0	260.0	276.0		330,330,330	-11.1	0.1	11	dbSNP_132	276	0,8588		0,0,4294	no	coding-synonymous,coding-synonymous,coding-synonymous	DKK3	NM_001018057.1,NM_013253.4,NM_015881.5	,,	0,109,6386	GG,GA,AA		0.0,2.4761,0.8391	,,	110/351,110/351,110/351	12023868	109,12881	2201	4294	6495	SO:0001819	synonymous_variant	27122	exon2			GTGCACATGGATG	AF177396	CCDS7808.1	11p15.3	2013-05-15	2013-05-15		ENSG00000050165	ENSG00000050165			2893	protein-coding gene	gene with protein product	"""regulated in glioma"""	605416	"""dickkopf (Xenopus laevis) homolog 3"", ""dickkopf 3 homolog (Xenopus laevis)"""			10570958	Standard	XM_006718177		Approved	REIC, RIG	uc001mjv.3	Q9UBP4	OTTHUMG00000165709	ENST00000396505.2:c.330T>C	11.37:g.12023868A>G		362.0	1.0	0.00276243		361.0	164.0	0.454294	NM_001018057	A8K1I2|D3DQW1|Q9ULB7	Silent	SNP	ENST00000396505.2	37	CCDS7808.1																																																																																			A|0.991;G|0.009	0.009	strong		0.433	DKK3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385863.1	NM_013253	
LYPD1	116372	hgsc.bcm.edu	37	2	133403647	133403647	+	Missense_Mutation	SNP	T	T	C	rs139508764	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:133403647T>C	ENST00000397463.2	-	3	669	c.397A>G	c.(397-399)Aaa>Gaa	p.K133E	LYPD1_ENST00000345008.6_Missense_Mutation_p.K81E|GPR39_ENST00000470071.1_3'UTR|GPR39_ENST00000329321.3_3'UTR	NM_144586.5	NP_653187.3	Q8N2G4	LYPD1_HUMAN	LY6/PLAUR domain containing 1	133				K -> R (in Ref. 2; BAC85518). {ECO:0000305}.		anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)				lung(2)	2						AGGGCTAATTTGAGGAACAGG	0.612													T|||	16	0.00319489	0.0113	0.0014	5008	,	,		16585	0.0		0.0	False		,,,				2504	0.0				p.K133E		Atlas-SNP	.											.	LYPD1	11	.	0			c.A397G						PASS	.	T	GLU/LYS,,GLU/LYS	34,3886		1,32,1927	66.0	73.0	71.0		241,,397	-1.4	0.0	2	dbSNP_134	71	0,8316		0,0,4158	yes	missense,utr-3,missense	GPR39,LYPD1	NM_001077427.2,NM_001508.2,NM_144586.5	56,,56	1,32,6085	CC,CT,TT		0.0,0.8673,0.2779	benign,,benign	81/90,,133/142	133403647	34,12202	1960	4158	6118	SO:0001583	missense	116372	exon3			CTAATTTGAGGAA	AK075487	CCDS42759.1, CCDS46416.1	2q21.2	2008-02-05		2005-08-30	ENSG00000150551	ENSG00000150551			28431	protein-coding gene	gene with protein product		610450		LYPDC1		12477932	Standard	NM_144586		Approved	MGC29643	uc002ttn.3	Q8N2G4	OTTHUMG00000153609	ENST00000397463.2:c.397A>G	2.37:g.133403647T>C	ENSP00000380605:p.Lys133Glu	180.0	0.0	0		158.0	85.0	0.537975	NM_144586	H7BXW6|Q6ZP52|Q6ZWI4|Q96AC2	Missense_Mutation	SNP	ENST00000397463.2	37	CCDS42759.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	T	8.848	0.943963	0.18281	0.008673	0.0	ENSG00000150551	ENST00000409034;ENST00000397463;ENST00000345008	D;D	0.82526	-1.62;-1.62	5.55	-1.42	0.08913	.	1.164150	0.06065	N	0.658974	T	0.58680	0.2139	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.50833	-0.8781	10	0.42905	T	0.14	-15.7811	8.1786	0.31296	0.0:0.1191:0.444:0.4369	.	133;149	Q8N2G4;Q8N2G4-3	LYPD1_HUMAN;.	E	156;133;81	ENSP00000380605:K133E;ENSP00000340563:K81E	ENSP00000340563:K81E	K	-	1	0	LYPD1	133120117	0.001000	0.12720	0.021000	0.16686	0.724000	0.41520	-0.106000	0.10890	-0.206000	0.10203	0.529000	0.55759	AAA	T|0.998;C|0.002	0.002	strong		0.612	LYPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331821.1	NM_144586	
VLDLR	7436	hgsc.bcm.edu	37	9	2643175	2643175	+	Missense_Mutation	SNP	G	G	C	rs34080096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:2643175G>C	ENST00000382100.3	+	5	820	c.464G>C	c.(463-465)aGt>aCt	p.S155T	VLDLR_ENST00000382099.2_Missense_Mutation_p.S155T|RP11-125B21.2_ENST00000599229.1_RNA	NM_003383.3	NP_003374.3	P98155	VLDLR_HUMAN	very low density lipoprotein receptor	155	LDL-receptor class A 4. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cholesterol metabolic process (GO:0008203)|glycoprotein transport (GO:0034436)|lipid transport (GO:0006869)|memory (GO:0007613)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|positive regulation of dendrite development (GO:1900006)|positive regulation of protein kinase activity (GO:0045860)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|signal transduction (GO:0007165)|ventral spinal cord development (GO:0021517)|very-low-density lipoprotein particle clearance (GO:0034447)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|glycoprotein binding (GO:0001948)|glycoprotein transporter activity (GO:0034437)|low-density lipoprotein receptor activity (GO:0005041)|reelin receptor activity (GO:0038025)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	24				GBM - Glioblastoma multiforme(50;0.0668)|Lung(218;0.123)		ATAACATGTAGTCCCGACGAG	0.473													G|||	15	0.00299521	0.0106	0.0014	5008	,	,		20805	0.0		0.0	False		,,,				2504	0.0				p.S155T		Atlas-SNP	.											.	VLDLR	68	.	0			c.G464C						PASS	.	G	THR/SER,THR/SER	36,4370	40.8+/-73.8	0,36,2167	116.0	122.0	120.0		464,464	4.6	0.0	9	dbSNP_126	120	0,8600		0,0,4300	yes	missense,missense	VLDLR	NM_001018056.1,NM_003383.3	58,58	0,36,6467	CC,CG,GG		0.0,0.8171,0.2768	benign,benign	155/846,155/874	2643175	36,12970	2203	4300	6503	SO:0001583	missense	7436	exon5			CATGTAGTCCCGA		CCDS6446.1, CCDS34979.1	9p24	2014-01-24			ENSG00000147852	ENSG00000147852		"""Low density lipoprotein receptors"""	12698	protein-coding gene	gene with protein product		192977				8294473	Standard	XM_006716864		Approved	CARMQ1, CHRMQ1, VLDLRCH	uc003zhk.1	P98155	OTTHUMG00000019447	ENST00000382100.3:c.464G>C	9.37:g.2643175G>C	ENSP00000371532:p.Ser155Thr	40.0	0.0	0		38.0	22.0	0.578947	NM_003383	B2RMZ7|D3DRH6|Q5VVF6	Missense_Mutation	SNP	ENST00000382100.3	37	CCDS6446.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	13.70	2.315185	0.40996	0.008171	0.0	ENSG00000147852	ENST00000382100;ENST00000382096;ENST00000382099	D;D;D	0.95588	-3.75;-3.75;-3.75	5.5	4.61	0.57282	.	0.091415	0.48286	D	0.000195	D	0.86789	0.6017	L	0.28776	0.89	0.80722	D	1	B;B;B	0.14805	0.003;0.004;0.011	B;B;B	0.29353	0.013;0.022;0.101	D	0.85668	0.1293	10	0.33940	T	0.23	.	14.3118	0.66422	0.0706:0.0:0.9294:0.0	rs34080096	155;155;155	P98155-2;Q5VVF5;P98155	.;.;VLDLR_HUMAN	T	155;114;155	ENSP00000371532:S155T;ENSP00000371528:S114T;ENSP00000371531:S155T	ENSP00000371528:S114T	S	+	2	0	VLDLR	2633175	1.000000	0.71417	0.028000	0.17463	0.199000	0.23934	5.517000	0.67061	1.558000	0.49541	0.655000	0.94253	AGT	G|0.996;C|0.004	0.004	strong		0.473	VLDLR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051519.2	NM_003383	
WDR36	134430	hgsc.bcm.edu	37	5	110432841	110432841	+	Silent	SNP	T	T	C	rs17132775	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:110432841T>C	ENST00000513710.2	+	3	427	c.423T>C	c.(421-423)taT>taC	p.Y141Y	WDR36_ENST00000506538.2_Silent_p.Y141Y|WDR36_ENST00000505303.1_Silent_p.Y85Y			Q8NI36	WDR36_HUMAN	WD repeat domain 36	141					regulation of axon extension (GO:0030516)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|rRNA processing (GO:0006364)|visual perception (GO:0007601)	nucleus (GO:0005634)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(9)|kidney(4)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(142;2.72e-05)|all_epithelial(76;4.4e-07)|Prostate(80;0.00955)|Lung NSC(167;0.0418)|Ovarian(225;0.0443)|Colorectal(57;0.0465)|all_lung(232;0.0508)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;1.39e-08)|Epithelial(69;1.82e-07)|all cancers(49;2.04e-05)|COAD - Colon adenocarcinoma(37;0.111)		TTGCTGCTTATGGAAATGTTT	0.388													T|||	212	0.0423323	0.1558	0.0072	5008	,	,		15681	0.0		0.001	False		,,,				2504	0.0				p.Y141Y		Atlas-SNP	.											.	WDR36	111	.	0			c.T423C						PASS	.	T		647,3757	277.5+/-273.7	44,559,1599	179.0	171.0	174.0		423	2.0	1.0	5	dbSNP_123	174	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	WDR36	NM_139281.2		44,567,5891	CC,CT,TT		0.093,14.6912,5.0369		141/952	110432841	655,12349	2202	4300	6502	SO:0001819	synonymous_variant	134430	exon3			TGCTTATGGAAAT	AF385437	CCDS4102.1	5q22.2	2013-01-09			ENSG00000134987	ENSG00000134987		"""WD repeat domain containing"""	30696	protein-coding gene	gene with protein product		609669	"""glaucoma 1, open angle, G"""	GLC1G		15590835, 15677485	Standard	NM_139281		Approved	TA-WDRP, UTP21	uc003kpd.3	Q8NI36	OTTHUMG00000128790	ENST00000513710.2:c.423T>C	5.37:g.110432841T>C		165.0	0.0	0		133.0	133.0	1	NM_139281	A2RUS4|Q68E02|Q8N1Q2	Silent	SNP	ENST00000513710.2	37	CCDS4102.1																																																																																			T|0.951;C|0.049	0.049	strong		0.388	WDR36-008	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000373504.3	NM_139281	
CAP2	10486	hgsc.bcm.edu	37	6	17426846	17426846	+	Silent	SNP	T	T	C	rs59744718	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:17426846T>C	ENST00000229922.2	+	3	679	c.147T>C	c.(145-147)ttT>ttC	p.F49F	CAP2_ENST00000465994.1_Silent_p.F49F|CAP2_ENST00000489374.1_Silent_p.F49F|CAP2_ENST00000378990.2_Silent_p.F49F|CAP2_ENST00000493172.1_Silent_p.F49F	NM_006366.2	NP_006357.1	P40123	CAP2_HUMAN	CAP, adenylate cyclase-associated protein, 2 (yeast)	49					activation of adenylate cyclase activity (GO:0007190)|axon guidance (GO:0007411)|cytoskeleton organization (GO:0007010)|establishment or maintenance of cell polarity (GO:0007163)|signal transduction (GO:0007165)	plasma membrane (GO:0005886)				breast(3)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(4)|urinary_tract(1)	27	Breast(50;0.0333)|Ovarian(93;0.0386)	all_hematologic(90;0.0466)	all cancers(50;0.194)|Epithelial(50;0.227)			TGGAAGCCTTTGACAAGCTGA	0.537													T|||	173	0.0345447	0.0915	0.0173	5008	,	,		18857	0.0308		0.003	False		,,,				2504	0.0061				p.F49F		Atlas-SNP	.											.	CAP2	61	.	0			c.T147C						PASS	.	T		352,4054	181.9+/-209.8	13,326,1864	113.0	102.0	105.0		147	1.8	1.0	6	dbSNP_129	105	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous	CAP2	NM_006366.2		13,340,6150	CC,CT,TT		0.1628,7.9891,2.8141		49/478	17426846	366,12640	2203	4300	6503	SO:0001819	synonymous_variant	10486	exon3			AGCCTTTGACAAG	BC008481	CCDS4539.1	6p22.3	2008-02-05			ENSG00000112186	ENSG00000112186			20039	protein-coding gene	gene with protein product						7962207, 8761950	Standard	NM_006366		Approved		uc003ncb.3	P40123	OTTHUMG00000014311	ENST00000229922.2:c.147T>C	6.37:g.17426846T>C		117.0	0.0	0		153.0	153.0	1	NM_006366	B2R5Y3|B7Z1C4|B7Z214|Q6IAY2	Silent	SNP	ENST00000229922.2	37	CCDS4539.1																																																																																			T|0.967;C|0.033	0.033	strong		0.537	CAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039952.2		
GUCA1A	2978	hgsc.bcm.edu	37	6	42141360	42141360	+	Silent	SNP	C	C	T	rs116114043	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42141360C>T	ENST00000394237.1	+	3	985	c.9C>T	c.(7-9)aaC>aaT	p.N3N	GUCA1A_ENST00000053469.4_Silent_p.N3N|GUCA1A_ENST00000372958.1_Silent_p.N3N|GUCA1A_ENST00000541991.1_Silent_p.N3N			P43080	GUC1A_HUMAN	guanylate cyclase activator 1A (retina)	3					phototransduction, visible light (GO:0007603)|positive regulation of cGMP biosynthetic process (GO:0030828)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)	7	Colorectal(47;0.196)		STAD - Stomach adenocarcinoma(11;5.54e-05)|Epithelial(12;0.000167)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			CAATGGGCAACGTGATGGAGG	0.607													C|||	20	0.00399361	0.0151	0.0	5008	,	,		20437	0.0		0.0	False		,,,				2504	0.0				p.N3N		Atlas-SNP	.											.	GUCA1A	18	.	0			c.C9T						PASS	.	C		59,4347	56.8+/-93.2	0,59,2144	117.0	97.0	104.0		9	2.2	1.0	6	dbSNP_132	104	0,8600		0,0,4300	no	coding-synonymous	GUCA1A	NM_000409.3		0,59,6444	TT,TC,CC		0.0,1.3391,0.4536		3/202	42141360	59,12947	2203	4300	6503	SO:0001819	synonymous_variant	2978	exon3			GGGCAACGTGATG		CCDS4864.1	6p21.1	2013-06-06			ENSG00000048545	ENSG00000048545		"""EF-hand domain containing"""	4678	protein-coding gene	gene with protein product	"""cone dystrophy 3"""	600364	"""chromosome 6 open reading frame 131"""	GUCA, GUCA1, C6orf131		9425234	Standard	NM_000409		Approved	GCAP, GCAP1, COD3, dJ139D8.6, CORD14	uc003orx.3	P43080	OTTHUMG00000014696	ENST00000394237.1:c.9C>T	6.37:g.42141360C>T		54.0	0.0	0		36.0	19.0	0.527778	NM_000409	B3KWT4|Q7Z6T1|Q9NU14	Silent	SNP	ENST00000394237.1	37	CCDS4864.1																																																																																			C|0.995;T|0.005	0.005	strong		0.607	GUCA1A-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316582.1		
SLC35B2	347734	hgsc.bcm.edu	37	6	44223292	44223292	+	Silent	SNP	C	C	T	rs35112470	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:44223292C>T	ENST00000393812.3	-	4	593	c.450G>A	c.(448-450)acG>acA	p.T150T	SLC35B2_ENST00000538577.1_Silent_p.T57T|SLC35B2_ENST00000393810.1_3'UTR|SLC35B2_ENST00000537814.1_Silent_p.T17T|SLC35B2_ENST00000495706.1_5'UTR|MIR4647_ENST00000583964.1_RNA	NM_178148.2	NP_835361.1	Q8TB61	S35B2_HUMAN	solute carrier family 35 (adenosine 3'-phospho 5'-phosphosulfate transporter), member B2	150					3'-phospho-5'-adenylyl sulfate transmembrane transport (GO:1902559)|3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|3'-phosphoadenosine 5'-phosphosulfate transport (GO:0046963)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|xenobiotic metabolic process (GO:0006805)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	3'-phosphoadenosine 5'-phosphosulfate transmembrane transporter activity (GO:0046964)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(2)|kidney(3)|large_intestine(2)|lung(4)|ovary(2)|urinary_tract(1)	15	all_cancers(18;2e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			ACTGCGAGTCCGTAAAGCGCT	0.587													C|||	114	0.0227636	0.0855	0.0014	5008	,	,		18748	0.0		0.0	False		,,,				2504	0.0				p.T150T		Atlas-SNP	.											.	SLC35B2	40	.	0			c.G450A						PASS	.	C		296,4110	162.2+/-194.2	7,282,1914	94.0	93.0	93.0		450	-11.6	0.5	6	dbSNP_126	93	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	SLC35B2	NM_178148.2		7,289,6207	TT,TC,CC		0.0814,6.7181,2.3297		150/433	44223292	303,12703	2203	4300	6503	SO:0001819	synonymous_variant	347734	exon4			CGAGTCCGTAAAG	AK075456	CCDS34462.1, CCDS69127.1, CCDS75462.1, CCDS75463.1	6p12.1-p11.21	2013-07-17	2013-07-17		ENSG00000157593	ENSG00000157593		"""Solute carriers"""	16872	protein-coding gene	gene with protein product		610788	"""solute carrier family 35, member B2"""				Standard	NM_001286517		Approved	UGTrel4	uc003oxd.3	Q8TB61	OTTHUMG00000014760	ENST00000393812.3:c.450G>A	6.37:g.44223292C>T		114.0	0.0	0		126.0	72.0	0.571429	NM_178148	B4DDU9|F5H7Y9|Q2VY06|Q53GA3|Q5T9W1|Q5T9W2|Q7Z2G3|Q8NBK6|Q96AR6	Silent	SNP	ENST00000393812.3	37	CCDS34462.1																																																																																			C|0.977;T|0.023	0.023	strong		0.587	SLC35B2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040724.2		
AKNA	80709	hgsc.bcm.edu	37	9	117104368	117104368	+	Silent	SNP	G	G	A	rs73548990	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117104368G>A	ENST00000307564.4	-	20	3956	c.3795C>T	c.(3793-3795)ccC>ccT	p.P1265P	AKNA_ENST00000374075.5_Silent_p.P1184P|AKNA_ENST00000374088.3_Silent_p.P1265P|AKNA_ENST00000492875.1_5'UTR|AKNA_ENST00000374079.4_Silent_p.P210P|AKNA_ENST00000223791.3_Silent_p.P725P	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	1265					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						GGGTATCAGCGGGAGGCGGTC	0.567													G|||	130	0.0259585	0.093	0.0072	5008	,	,		18549	0.0		0.002	False		,,,				2504	0.0				p.P1265P		Atlas-SNP	.											.	AKNA	119	.	0			c.C3795T						PASS	.	G		303,4103	164.0+/-195.7	7,289,1907	52.0	51.0	51.0		3795	1.6	0.0	9	dbSNP_130	51	1,8599		0,1,4299	no	coding-synonymous	AKNA	NM_030767.4		7,290,6206	AA,AG,GG		0.0116,6.877,2.3374		1265/1440	117104368	304,12702	2203	4300	6503	SO:0001819	synonymous_variant	80709	exon20			ATCAGCGGGAGGC	AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.3795C>T	9.37:g.117104368G>A		79.0	0.0	0		50.0	34.0	0.68	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Silent	SNP	ENST00000307564.4	37	CCDS6805.1	56	0.02564102564102564	51	0.10365853658536585	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	4.086	0.013849	0.07959	0.06877	1.16E-4	ENSG00000106948	ENST00000320310	.	.	.	4.95	1.61	0.23674	.	0.482521	0.19304	N	0.117578	T	0.01189	0.0039	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.03130	-1.1069	6	0.87932	D	0	-5.6524	5.4261	0.16427	0.1935:0.0:0.6201:0.1863	.	.	.	.	L	276	.	ENSP00000314538:P276L	P	-	2	0	AKNA	116144189	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-1.483000	0.02318	0.275000	0.22094	-0.244000	0.11960	CCG	G|0.978;A|0.022	0.022	strong		0.567	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767	
RPUSD1	113000	hgsc.bcm.edu	37	16	836111	836111	+	Missense_Mutation	SNP	G	G	T	rs112366818	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:836111G>T	ENST00000561734.1	-	5	1021	c.778C>A	c.(778-780)Cct>Act	p.P260T	RPUSD1_ENST00000565809.1_3'UTR|CHTF18_ENST00000455171.2_5'Flank|RPUSD1_ENST00000007264.2_Missense_Mutation_p.P260T|RPUSD1_ENST00000567114.1_Missense_Mutation_p.P131T|MSLNL_ENST00000442466.1_5'Flank|CHTF18_ENST00000317063.6_5'Flank|CHTF18_ENST00000262315.9_5'Flank			Q9UJJ7	RUSD1_HUMAN	RNA pseudouridylate synthase domain containing 1	260	Pro-rich.				pseudouridine synthesis (GO:0001522)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			endometrium(3)|lung(2)|skin(2)	7		Hepatocellular(780;0.00335)				TCGGGGTCAGGGTCGGGGGTG	0.721													G|||	227	0.0453275	0.1641	0.0115	5008	,	,		13109	0.0		0.002	False		,,,				2504	0.0				p.P260T		Atlas-SNP	.											.	RPUSD1	19	.	0			c.C778A						PASS	.	G	THR/PRO	471,3899		25,421,1739	18.0	24.0	22.0		778	4.2	1.0	16	dbSNP_132	22	3,8555		0,3,4276	yes	missense	RPUSD1	NM_058192.2	38	25,424,6015	TT,TG,GG		0.0351,10.778,3.6665	possibly-damaging	260/313	836111	474,12454	2185	4279	6464	SO:0001583	missense	113000	exon6			GGTCAGGGTCGGG	AE006465	CCDS10426.1	16p13.3	2013-02-11	2005-01-31	2005-01-31	ENSG00000007376	ENSG00000007376		"""RNA pseudouridylate synthase domain containing"""	14173	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 40"""	C16orf40			Standard	NM_058192		Approved	RLUCL, MGC19600	uc002ckb.3	Q9UJJ7	OTTHUMG00000047840	ENST00000561734.1:c.778C>A	16.37:g.836111G>T	ENSP00000455026:p.Pro260Thr	59.0	0.0	0		72.0	71.0	0.986111	NM_058192	D3DU66	Missense_Mutation	SNP	ENST00000561734.1	37	CCDS10426.1	79	0.036172161172161175	75	0.1524390243902439	4	0.011049723756906077	0	0.0	0	0.0	G	10.09	1.256160	0.22965	0.10778	3.51E-4	ENSG00000007376	ENST00000007264	T	0.16743	2.32	4.21	4.21	0.49690	.	0.832292	0.11055	N	0.604570	T	0.00109	0.0003	L	0.44542	1.39	0.20703	N	0.999863	P	0.52316	0.952	P	0.45998	0.5	T	0.08554	-1.0716	10	0.72032	D	0.01	-9.908	12.1354	0.53968	0.0:0.0:1.0:0.0	.	260	Q9UJJ7	RUSD1_HUMAN	T	260	ENSP00000007264:P260T	ENSP00000007264:P260T	P	-	1	0	RPUSD1	776112	0.991000	0.36638	0.987000	0.45799	0.161000	0.22273	2.137000	0.42130	1.920000	0.55613	0.456000	0.33151	CCT	G|0.962;T|0.038	0.038	strong		0.721	RPUSD1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420620.1	NM_058192	
MIER2	54531	hgsc.bcm.edu	37	19	307282	307282	+	Missense_Mutation	SNP	T	T	C	rs35042658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:307282T>C	ENST00000264819.4	-	13	1463	c.1453A>G	c.(1453-1455)Agc>Ggc	p.S485G	CTD-3113P16.5_ENST00000591533.1_RNA	NM_017550.1	NP_060020.1	Q8N344	MIER2_HUMAN	mesoderm induction early response 1, family member 2	485			S -> G (in dbSNP:rs35042658).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			endometrium(4)|kidney(1)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	22		all_cancers(10;1.05e-30)|all_epithelial(18;3.04e-19)|Acute lymphoblastic leukemia(61;4.36e-14)|all_hematologic(61;4.84e-09)|Lung NSC(49;2.49e-05)|all_lung(49;4.36e-05)|Breast(49;0.000304)		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)		TCCACATGGCTGGAGATGAGG	0.647													T|||	249	0.0497204	0.1808	0.013	5008	,	,		15517	0.0		0.001	False		,,,				2504	0.0				p.S485G		Atlas-SNP	.											.	MIER2	51	.	0			c.A1453G						PASS	.	T	GLY/SER	552,3848		29,494,1677	28.0	25.0	26.0		1453	3.0	0.2	19	dbSNP_126	26	9,8589		0,9,4290	yes	missense	MIER2	NM_017550.1	56	29,503,5967	CC,CT,TT		0.1047,12.5455,4.316	benign	485/546	307282	561,12437	2200	4299	6499	SO:0001583	missense	54531	exon13			CATGGCTGGAGAT	AB033019	CCDS32855.1	19p13.3	2008-02-05	2006-04-20	2006-04-20		ENSG00000105556			29210	protein-coding gene	gene with protein product			"""KIAA1193"""	KIAA1193		10574462	Standard	NM_017550		Approved		uc002lok.1	Q8N344		ENST00000264819.4:c.1453A>G	19.37:g.307282T>C	ENSP00000264819:p.Ser485Gly	133.0	0.0	0		161.0	85.0	0.52795	NM_017550	Q9ULM7	Missense_Mutation	SNP	ENST00000264819.4	37	CCDS32855.1	112	0.05128205128205128	108	0.21951219512195122	4	0.011049723756906077	0	0.0	0	0.0	T	5.043	0.193576	0.09599	0.125455	0.001047	ENSG00000105556	ENST00000264819	T	0.15834	2.39	4.02	3.0	0.34707	.	0.118436	0.38058	N	0.001834	T	0.00012	0.0000	N	0.25485	0.75	0.42449	P	0.007252000000000036	B	0.06786	0.001	B	0.04013	0.001	T	0.37934	-0.9684	9	0.33940	T	0.23	-8.985	5.2116	0.15320	0.0:0.2476:0.0:0.7524	rs35042658	485	Q8N344	MIER2_HUMAN	G	485	ENSP00000264819:S485G	ENSP00000264819:S485G	S	-	1	0	MIER2	258282	1.000000	0.71417	0.220000	0.23810	0.106000	0.19336	1.279000	0.33191	0.701000	0.31803	0.533000	0.62120	AGC	T|0.946;C|0.054	0.054	strong		0.647	MIER2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451784.1	XM_041843	
PKD1	5310	hgsc.bcm.edu	37	16	2166538	2166538	+	Missense_Mutation	SNP	G	G	A	rs149022148	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2166538G>A	ENST00000262304.4	-	8	1922	c.1714C>T	c.(1714-1716)Ccc>Tcc	p.P572S	RP11-304L19.2_ENST00000562027.1_RNA|PKD1_ENST00000423118.1_Missense_Mutation_p.P572S	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	572			P -> S (in dbSNP:rs149022148). {ECO:0000269|PubMed:11967008}.		anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						ACCTCCACGGGCTCGTGCGGG	0.682													g|||	204	0.0407348	0.1467	0.0144	5008	,	,		12972	0.0		0.0	False		,,,				2504	0.0				p.P572S		Atlas-SNP	.											PKD1,caecum,carcinoma,0,1	PKD1	184	1	0			c.C1714T						PASS	.	G	SER/PRO,SER/PRO	422,3878		16,390,1744	7.0	8.0	7.0		1714,1714	1.8	0.0	16	dbSNP_134	7	4,8436		0,4,4216	no	missense,missense	PKD1	NM_000296.3,NM_001009944.2	74,74	16,394,5960	AA,AG,GG		0.0474,9.814,3.3438	benign,benign	572/4303,572/4304	2166538	426,12314	2150	4220	6370	SO:0001583	missense	5310	exon8			CCACGGGCTCGTG	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9008	protein-coding gene	gene with protein product	"""polycystin 1"", ""transient receptor potential cation channel, subfamily P, member 1"""	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.1714C>T	16.37:g.2166538G>A	ENSP00000262304:p.Pro572Ser	104.0	0.0	0		85.0	45.0	0.529412	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	86	0.039377289377289376	81	0.16463414634146342	5	0.013812154696132596	0	0.0	0	0.0	G	8.927	0.962500	0.18583	0.09814	4.74E-4	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101	T;T	0.34472	1.36;1.36	4.27	1.83	0.25207	Polycystin cation channel (1);	0.410377	0.23245	N	0.050320	T	0.00109	0.0003	L	0.60455	1.87	0.80722	P	0.0	B;B	0.33171	0.4;0.179	B;B	0.30855	0.121;0.057	T	0.10941	-1.0608	9	0.11182	T	0.66	.	7.8856	0.29648	0.0:0.2683:0.5323:0.1994	.	572;572	P98161-3;P98161	.;PKD1_HUMAN	S	572;572;505	ENSP00000262304:P572S;ENSP00000399501:P572S	ENSP00000262304:P572S	P	-	1	0	PKD1	2106539	0.000000	0.05858	0.004000	0.12327	0.034000	0.12701	0.309000	0.19332	0.907000	0.36646	0.555000	0.69702	CCC	G|0.961;A|0.039	0.039	strong		0.682	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
AKAP9	10142	hgsc.bcm.edu	37	7	91622249	91622249	+	Missense_Mutation	SNP	C	C	A	rs138567837		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:91622249C>A	ENST00000359028.2	+	6	717	c.492C>A	c.(490-492)gaC>gaA	p.D164E	AKAP9_ENST00000358100.2_Missense_Mutation_p.D164E|AKAP9_ENST00000356239.3_Missense_Mutation_p.D152E|AKAP9_ENST00000394564.1_Missense_Mutation_p.D152E			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	164					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			GAGCACAAGACAGTCCGACTC	0.388			T	BRAF	papillary thyroid								C|||	1	0.000199681	0.0008	0.0	5008	,	,		16096	0.0		0.0	False		,,,				2504	0.0				p.D152E		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.C456A						PASS	.	C	GLU/ASP,GLU/ASP	4,4402	8.1+/-20.4	0,4,2199	107.0	105.0	106.0		456,456	1.5	1.0	7	dbSNP_134	106	0,8600		0,0,4300	yes	missense,missense	AKAP9	NM_005751.4,NM_147185.2	45,45	0,4,6499	AA,AC,CC		0.0,0.0908,0.0308	benign,benign	152/3908,152/3900	91622249	4,13002	2203	4300	6503	SO:0001583	missense	10142	exon5			ACAAGACAGTCCG	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.492C>A	7.37:g.91622249C>A	ENSP00000351922:p.Asp164Glu	87.0	0.0	0		74.0	33.0	0.445946	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	9.491	1.100713	0.20552	9.08E-4	0.0	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394565;ENST00000394564;ENST00000438114	T;T;T;T;T	0.28666	1.6;1.6;1.6;1.6;1.6	5.37	1.53	0.23141	.	0.681654	0.12148	N	0.495208	T	0.16981	0.0408	N	0.14661	0.345	0.09310	N	1	B;B;B;B	0.19817	0.013;0.01;0.039;0.005	B;B;B;B	0.15870	0.008;0.006;0.014;0.008	T	0.24584	-1.0156	10	0.30854	T	0.27	.	8.8667	0.35291	0.0:0.6341:0.0:0.3659	.	152;152;164;152	Q99996-2;Q99996-3;A4D1E4;Q6PJH3	.;.;.;.	E	152;164;164;164;164;152;103	ENSP00000348573:D152E;ENSP00000351922:D164E;ENSP00000350813:D164E;ENSP00000378065:D152E;ENSP00000391704:D103E	ENSP00000348573:D152E	D	+	3	2	AKAP9	91460185	0.943000	0.32029	0.981000	0.43875	0.717000	0.41224	0.068000	0.14531	0.061000	0.16311	-0.150000	0.13652	GAC	C|1.000;A|0.000	0.000	strong		0.388	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
MUC17	140453	hgsc.bcm.edu	37	7	100678032	100678032	+	Missense_Mutation	SNP	T	T	C	rs147173571		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:100678032T>C	ENST00000306151.4	+	3	3399	c.3335T>C	c.(3334-3336)cTg>cCg	p.L1112P		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1112	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					AGCACCAGGCTGGTGGTCAGT	0.512																																					p.L1112P		Atlas-SNP	.											.	MUC17	804	.	0			c.T3335C						PASS	.						494.0	394.0	428.0					7																	100678032		2203	4300	6503	SO:0001583	missense	140453	exon3			CCAGGCTGGTGGT	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.3335T>C	7.37:g.100678032T>C	ENSP00000302716:p.Leu1112Pro	163.0	0.0	0		352.0	33.0	0.09375	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	C	0.149	-1.093913	0.01858	.	.	ENSG00000169876	ENST00000306151	T	0.03212	4.01	0.693	-0.391	0.12446	.	.	.	.	.	T	0.01320	0.0043	N	0.01576	-0.805	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48055	-0.9068	8	0.25751	T	0.34	.	.	.	.	.	1112	Q685J3	MUC17_HUMAN	P	1112	ENSP00000302716:L1112P	ENSP00000302716:L1112P	L	+	2	0	MUC17	100464752	0.000000	0.05858	0.001000	0.08648	0.004000	0.04260	-6.070000	0.00082	-0.165000	0.10908	-1.364000	0.01208	CTG	.	.	weak		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
SULF2	55959	hgsc.bcm.edu	37	20	46292910	46292910	+	Missense_Mutation	SNP	C	C	T	rs10048853	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:46292910C>T	ENST00000359930.4	-	15	2872	c.2021G>A	c.(2020-2022)cGc>cAc	p.R674H	SULF2_ENST00000467815.1_Missense_Mutation_p.R674H|SULF2_ENST00000484875.1_Missense_Mutation_p.R674H|SULF2_ENST00000361612.4_Missense_Mutation_p.R674H	NM_018837.3	NP_061325.1	Q8IWU5	SULF2_HUMAN	sulfatase 2	674			R -> H (in dbSNP:rs10048853).		bone development (GO:0060348)|cartilage development (GO:0051216)|chondrocyte development (GO:0002063)|embryonic skeletal system development (GO:0048706)|esophagus smooth muscle contraction (GO:0014846)|glial cell-derived neurotrophic factor receptor signaling pathway (GO:0035860)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|heparan sulfate proteoglycan metabolic process (GO:0030201)|innervation (GO:0060384)|kidney development (GO:0001822)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation vascular endothelial growth factor production (GO:0010575)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	arylsulfatase activity (GO:0004065)|calcium ion binding (GO:0005509)|N-acetylglucosamine-6-sulfatase activity (GO:0008449)			breast(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(22)|ovary(4)|pancreas(1)|prostate(5)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	54						GTGCTTGAGGCGGCCTTTGTG	0.607											OREG0026005	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	90	0.0179712	0.0582	0.0159	5008	,	,		17857	0.0		0.002	False		,,,				2504	0.0				p.R674H		Atlas-SNP	.											.	SULF2	131	.	0			c.G2021A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG	189,4217	116.7+/-154.6	4,181,2018	55.0	47.0	50.0		2021,2021,2021	3.1	1.0	20	dbSNP_119	50	3,8597	2.2+/-6.3	0,3,4297	yes	missense,missense,missense	SULF2	NM_001161841.1,NM_018837.3,NM_198596.2	29,29,29	4,184,6315	TT,TC,CC		0.0349,4.2896,1.4762	benign,benign,benign	674/871,674/871,674/868	46292910	192,12814	2203	4300	6503	SO:0001583	missense	55959	exon15			TTGAGGCGGCCTT	AY101176	CCDS13408.1, CCDS13409.1, CCDS13409.2	20q13.12-q13.13	2008-05-14			ENSG00000196562	ENSG00000196562			20392	protein-coding gene	gene with protein product		610013				12368295	Standard	NM_018837		Approved	KIAA1247, HSULF-2, SULF-2	uc002xto.3	Q8IWU5	OTTHUMG00000032675	ENST00000359930.4:c.2021G>A	20.37:g.46292910C>T	ENSP00000353007:p.Arg674His	92.0	0.0	0	938	106.0	57.0	0.537736	NM_001161841	E1P5U6|Q5JYE1|Q6UX86|Q96SG2|Q9H1H0|Q9UJR3|Q9ULH3	Missense_Mutation	SNP	ENST00000359930.4	37	CCDS13408.1	25|25	0.011446886446886446|0.011446886446886446	16|16	0.032520325203252036|0.032520325203252036	7|7	0.019337016574585635|0.019337016574585635	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	C|C	13.33|13.33	2.203972|2.203972	0.38905|0.38905	0.042896|0.042896	3.49E-4|3.49E-4	ENSG00000196562|ENSG00000196562	ENST00000495544|ENST00000359930;ENST00000484875;ENST00000361612;ENST00000371978;ENST00000467815	.|T;T;T;T	.|0.22134	.|1.97;1.97;1.97;1.97	5.08|5.08	3.1|3.1	0.35709|0.35709	.|Alkaline-phosphatase-like, core domain (1);	.|0.302855	.|0.32769	.|N	.|0.005668	T|T	0.01523|0.01523	0.0049|0.0049	N|N	0.04959|0.04959	-0.14|-0.14	0.29204|0.29204	N|N	0.875005|0.875005	.|B;B	.|0.09022	.|0.002;0.001	.|B;B	.|0.06405	.|0.002;0.001	T|T	0.29518|0.29518	-1.0009|-1.0009	5|10	.|0.13108	.|T	.|0.6	-22.8637|-22.8637	4.1427|4.1427	0.10201|0.10201	0.0:0.5786:0.1901:0.2313|0.0:0.5786:0.1901:0.2313	rs10048853;rs10048853|rs10048853;rs10048853	.|674;674	.|Q8IWU5-2;Q8IWU5	.|.;SULF2_HUMAN	T|H	29|674;674;674;93;674	.|ENSP00000353007:R674H;ENSP00000418290:R674H;ENSP00000354662:R674H;ENSP00000418442:R674H	.|ENSP00000353007:R674H	A|R	-|-	1|2	0|0	SULF2|SULF2	45726317|45726317	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.796000|0.796000	0.44982|0.44982	1.968000|1.968000	0.40500|0.40500	0.689000|0.689000	0.31550|0.31550	-0.254000|-0.254000	0.11334|0.11334	GCC|CGC	C|0.983;T|0.017	0.017	strong		0.607	SULF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079606.1	NM_018837	
ECE2	9718	hgsc.bcm.edu	37	3	183967500	183967500	+	Silent	SNP	A	A	C	rs2233461	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:183967500A>C	ENST00000402825.3	+	1	18	c.18A>C	c.(16-18)gcA>gcC	p.A6A	ALG3_ENST00000397676.3_5'Flank|ALG3_ENST00000445626.2_5'Flank|ALG3_ENST00000455059.1_5'Flank|ALG3_ENST00000418734.2_5'Flank|ECE2_ENST00000324557.4_Silent_p.A6A|EIF2B5_ENST00000444495.1_Intron	NM_014693.3	NP_055508.3	O60344	ECE2_HUMAN	endothelin converting enzyme 2	6	Methyltransferase-like region.				brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|cell-cell signaling (GO:0007267)|heart development (GO:0007507)|peptide hormone processing (GO:0016486)	cytoplasmic vesicle membrane (GO:0030659)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|methyltransferase activity (GO:0008168)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(13)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(4)	49	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			CTCCAGGGGCAGGTAGGGCGC	0.672											OREG0015944	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	246	0.0491214	0.1793	0.013	5008	,	,		15078	0.0		0.0	False		,,,				2504	0.0				p.A6A		Atlas-SNP	.											.	ECE2	303	.	0			c.A18C						PASS	.	C	,	533,3863		28,477,1693	18.0	21.0	20.0		18,18	-10.9	0.0	3	dbSNP_98	20	4,8584		0,4,4290	no	coding-synonymous,coding-synonymous	ECE2	NM_014693.3,NM_032331.3	,	28,481,5983	CC,CA,AA		0.0466,12.1247,4.1359	,	6/884,6/256	183967500	537,12447	2198	4294	6492	SO:0001819	synonymous_variant	9718	exon1			AGGGGCAGGTAGG	AF428263	CCDS3255.1, CCDS33899.1, CCDS3256.2, CCDS43179.1, CCDS46969.1	3q27.1	2007-07-26			ENSG00000145194	ENSG00000145194			13275	protein-coding gene	gene with protein product		610145				11718899	Standard	NM_032331		Approved	KIAA0604, MGC2408	uc003fni.4	O60344	OTTHUMG00000150551	ENST00000402825.3:c.18A>C	3.37:g.183967500A>C		51.0	0.0	0	1988	58.0	34.0	0.586207	NM_014693	A5PLK8|Q6NTG7|Q6UW36|Q8NFD7|Q96NX3|Q96NX4|Q9BRZ8	Silent	SNP	ENST00000402825.3	37	CCDS3256.2																																																																																			A|0.943;C|0.057	0.057	strong		0.672	ECE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318874.3	NM_014693	
CLEC16A	23274	hgsc.bcm.edu	37	16	11133681	11133681	+	Silent	SNP	C	C	T	rs61740118	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:11133681C>T	ENST00000409790.1	+	14	1838	c.1608C>T	c.(1606-1608)aaC>aaT	p.N536N	CLEC16A_ENST00000465491.1_3'UTR|CLEC16A_ENST00000409552.3_Silent_p.N518N	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A									p.0?(1)		breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						CCACCTACAACCACCCGCTAG	0.552													C|||	64	0.0127796	0.0477	0.0014	5008	,	,		18259	0.0		0.0	False		,,,				2504	0.0				p.N536N		Atlas-SNP	.											.	CLEC16A	101	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.C1608T						PASS	.	C		139,3971		5,129,1921	57.0	61.0	59.0		1608	4.3	1.0	16	dbSNP_129	59	0,8386		0,0,4193	no	coding-synonymous	CLEC16A	NM_015226.2		5,129,6114	TT,TC,CC		0.0,3.382,1.1124		536/1054	11133681	139,12357	2055	4193	6248	SO:0001819	synonymous_variant	23274	exon13			CTACAACCACCCG	AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"""C-type lectin domain containing"""	29013	protein-coding gene	gene with protein product		611303	"""KIAA0350"""	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.1608C>T	16.37:g.11133681C>T		99.0	0.0	0		97.0	44.0	0.453608	NM_015226		Silent	SNP	ENST00000409790.1	37	CCDS45409.1																																																																																			C|0.989;T|0.011	0.011	strong		0.552	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226	
LRRC43	254050	hgsc.bcm.edu	37	12	122674807	122674807	+	Missense_Mutation	SNP	T	T	C	rs77473460	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:122674807T>C	ENST00000339777.4	+	5	821	c.793T>C	c.(793-795)Tac>Cac	p.Y265H	LRRC43_ENST00000425921.1_Missense_Mutation_p.Y80H	NM_152759.4	NP_689972.3	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43	265	LRRCT.									NS(1)|endometrium(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(2)	19	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000312)|Epithelial(86;0.000539)|BRCA - Breast invasive adenocarcinoma(302;0.225)		CTTGGTGCCCTACTACCGCGG	0.637													T|||	195	0.0389377	0.1415	0.0101	5008	,	,		20541	0.0		0.001	False		,,,				2504	0.0				p.Y265H		Atlas-SNP	.											.	LRRC43	105	.	0			c.T793C						PASS	.	T	HIS/TYR,HIS/TYR	502,3826		30,442,1692	84.0	95.0	92.0		793,238	-1.6	0.9	12	dbSNP_131	92	4,8530		0,4,4263	yes	missense,missense	LRRC43	NM_001098519.1,NM_152759.4	83,83	30,446,5955	CC,CT,TT		0.0469,11.5989,3.9341	possibly-damaging,possibly-damaging	265/657,80/472	122674807	506,12356	2164	4267	6431	SO:0001583	missense	254050	exon5			GTGCCCTACTACC	AK124107	CCDS45001.1	12q24.31	2014-09-11			ENSG00000158113	ENSG00000158113			28562	protein-coding gene	gene with protein product						12477932	Standard	NM_152759		Approved	MGC35140	uc009zxm.3	Q8N309	OTTHUMG00000168915	ENST00000339777.4:c.793T>C	12.37:g.122674807T>C	ENSP00000344233:p.Tyr265His	186.0	0.0	0		176.0	82.0	0.465909	NM_001098519	Q6ZVT9	Missense_Mutation	SNP	ENST00000339777.4	37	CCDS45001.1	78	0.03571428571428571	75	0.1524390243902439	3	0.008287292817679558	0	0.0	0	0.0	T	9.271	1.045795	0.19748	0.115989	4.69E-4	ENSG00000158113	ENST00000537729;ENST00000339777;ENST00000289014;ENST00000425921	T;T;T	0.23348	1.91;1.91;1.91	5.22	-1.59	0.08453	.	0.926504	0.09255	N	0.827363	T	0.00073	0.0002	N	0.13043	0.29	0.09310	N	1	B	0.18461	0.028	B	0.11329	0.006	T	0.37911	-0.9685	10	0.15499	T	0.54	-14.8888	1.3937	0.02256	0.1943:0.3528:0.2254:0.2275	.	265	Q8N309	LRC43_HUMAN	H	80;265;136;80	ENSP00000438751:Y80H;ENSP00000344233:Y265H;ENSP00000416628:Y80H	ENSP00000289014:Y136H	Y	+	1	0	LRRC43	121240760	0.000000	0.05858	0.934000	0.37439	0.988000	0.76386	0.172000	0.16704	0.039000	0.15632	0.459000	0.35465	TAC	T|0.977;C|0.023	0.023	strong		0.637	LRRC43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401589.1	NM_152759	
CSMD3	114788	hgsc.bcm.edu	37	8	113668453	113668453	+	Silent	SNP	A	A	G	rs11992014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:113668453A>G	ENST00000297405.5	-	18	3178	c.2934T>C	c.(2932-2934)agT>agC	p.S978S	CSMD3_ENST00000455883.2_Silent_p.S874S|CSMD3_ENST00000343508.3_Silent_p.S938S|CSMD3_ENST00000352409.3_Silent_p.S978S	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	978	CUB 5. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						ATATAAAATTACTGCTACTAA	0.348										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			A|||	156	0.0311502	0.1112	0.0115	5008	,	,		12832	0.0		0.001	False		,,,				2504	0.0				p.S978S		Atlas-SNP	.											CSMD3_ENST00000343508,NS,carcinoma,-2,2	CSMD3	2325	2	0			c.T2934C						PASS	.	A	,,	382,4024	189.5+/-215.6	17,348,1838	67.0	74.0	72.0		2622,2934,2814	2.5	1.0	8	dbSNP_120	72	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	,,	17,353,6133	GG,GA,AA		0.0581,8.67,2.9755	,,	874/3539,978/3708,938/3668	113668453	387,12619	2203	4300	6503	SO:0001819	synonymous_variant	114788	exon18			AAAATTACTGCTA	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.2934T>C	8.37:g.113668453A>G		95.0	0.0	0		132.0	132.0	1	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																			A|0.971;G|0.029	0.029	strong		0.348	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
VPS13A	23230	hgsc.bcm.edu	37	9	79936579	79936579	+	Missense_Mutation	SNP	G	G	A	rs73467962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:79936579G>A	ENST00000360280.3	+	44	6007	c.5747G>A	c.(5746-5748)aGt>aAt	p.S1916N	VPS13A_ENST00000376636.3_Missense_Mutation_p.S1877N|VPS13A_ENST00000376634.4_Missense_Mutation_p.S1916N|VPS13A_ENST00000357409.5_Missense_Mutation_p.S1916N	NM_033305.2	NP_150648.2	Q96RL7	VP13A_HUMAN	vacuolar protein sorting 13 homolog A (S. cerevisiae)	1916					cell death (GO:0008219)|Golgi to endosome transport (GO:0006895)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|protein localization (GO:0008104)|protein transport (GO:0015031)|social behavior (GO:0035176)	dense core granule (GO:0031045)|intracellular (GO:0005622)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(28)|liver(1)|lung(42)|ovary(3)|pancreas(3)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)|urinary_tract(1)	104						GAAAGTTTAAGTATGGATTAT	0.343													G|||	72	0.014377	0.0537	0.0014	5008	,	,		16144	0.0		0.0	False		,,,				2504	0.0				p.S1916N		Atlas-SNP	.											.	VPS13A	735	.	0			c.G5747A						PASS	.	G	ASN/SER,ASN/SER,ASN/SER,ASN/SER	183,4223	118.4+/-156.1	3,177,2023	84.0	82.0	82.0		5630,5747,5747,5747	1.9	1.0	9	dbSNP_130	82	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense,missense	VPS13A	NM_001018037.1,NM_001018038.2,NM_015186.3,NM_033305.2	46,46,46,46	3,178,6322	AA,AG,GG		0.0116,4.1534,1.4147	benign,benign,benign,benign	1877/3136,1916/3070,1916/3096,1916/3175	79936579	184,12822	2203	4300	6503	SO:0001583	missense	23230	exon44			GTTTAAGTATGGA	AB023203	CCDS6655.1, CCDS6656.1, CCDS47983.1, CCDS55321.1	9q21	2014-01-30	2006-04-04	2004-02-11	ENSG00000197969	ENSG00000197969			1908	protein-coding gene	gene with protein product	"""chorein"""	605978	"""chorea acanthocytosis"", ""vacuolar protein sorting 13A (yeast)"""	CHAC		9382101, 11381253	Standard	NM_001018038		Approved	KIAA0986	uc004akr.3	Q96RL7	OTTHUMG00000020055	ENST00000360280.3:c.5747G>A	9.37:g.79936579G>A	ENSP00000353422:p.Ser1916Asn	99.0	0.0	0		125.0	75.0	0.6	NM_001018038	Q5JSX9|Q5JSY0|Q5VYR5|Q702P4|Q709D0|Q86YF8|Q96S61|Q9H995|Q9Y2J1	Missense_Mutation	SNP	ENST00000360280.3	37	CCDS6655.1	19|19	0.0086996336996337|0.0086996336996337	19|19	0.03861788617886179|0.03861788617886179	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	6.184|6.184	0.402055|0.402055	0.11696|0.11696	0.041534|0.041534	1.16E-4|1.16E-4	ENSG00000197969|ENSG00000197969	ENST00000376634;ENST00000376636;ENST00000360280;ENST00000357409|ENST00000419472	T;T;T;T|.	0.47869|.	1.0;0.83;0.91;1.0|.	5.8|5.8	1.87|1.87	0.25490|0.25490	.|.	0.321368|.	0.38111|.	N|.	0.001815|.	T|T	0.08044|0.08044	0.0201|0.0201	N|N	0.11560|0.11560	0.145|0.145	0.80722|0.80722	D|D	1|1	B;B;B;B;B|.	0.16802|.	0.004;0.005;0.019;0.019;0.019|.	B;B;B;B;B|.	0.18871|.	0.006;0.012;0.01;0.023;0.023|.	T|T	0.01899|0.01899	-1.1251|-1.1251	10|5	0.37606|.	T|.	0.19|.	.|.	5.1895|5.1895	0.15203|0.15203	0.3604:0.1441:0.4955:0.0|0.3604:0.1441:0.4955:0.0	.|.	168;1877;1916;1916;1916|.	B1ALW4;Q96RL7-3;Q96RL7;Q96RL7-2;Q96RL7-4|.	.;.;VP13A_HUMAN;.;.|.	N|I	1916;1877;1916;1916|169	ENSP00000365821:S1916N;ENSP00000365823:S1877N;ENSP00000353422:S1916N;ENSP00000349985:S1916N|.	ENSP00000349985:S1916N|.	S|V	+|+	2|1	0|0	VPS13A|VPS13A	79126399|79126399	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.867000|0.867000	0.49689|0.49689	1.688000|1.688000	0.37690|0.37690	0.347000|0.347000	0.23924|0.23924	-0.373000|-0.373000	0.07131|0.07131	AGT|GTA	G|0.987;A|0.013	0.013	strong		0.343	VPS13A-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052753.2	NM_015186	
SPEF2	79925	hgsc.bcm.edu	37	5	35694454	35694454	+	Missense_Mutation	SNP	A	A	G	rs12332369	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:35694454A>G	ENST00000356031.3	+	13	2118	c.1964A>G	c.(1963-1965)gAa>gGa	p.E655G	SPEF2_ENST00000509059.1_Intron|SPEF2_ENST00000440995.2_Intron|CTD-2113L7.1_ENST00000510433.1_RNA	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	655			E -> G (in dbSNP:rs12332369).		axoneme assembly (GO:0035082)|brain morphogenesis (GO:0048854)|embryonic neurocranium morphogenesis (GO:0048702)|fertilization (GO:0009566)|immune system development (GO:0002520)|multicellular organismal aging (GO:0010259)|respiratory system development (GO:0060541)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|manchette (GO:0002177)|sperm midpiece (GO:0097225)				breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	37	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			ACAGAAGGTGAAACAATGCTT	0.368													A|||	114	0.0227636	0.0832	0.0058	5008	,	,		17502	0.0		0.0	False		,,,				2504	0.0				p.E655G		Atlas-SNP	.											.	SPEF2	324	.	0			c.A1964G						PASS	.	A	GLY/GLU	258,3442		10,238,1602	93.0	86.0	88.0		1964	3.7	0.9	5	dbSNP_120	88	1,8215		0,1,4107	yes	missense	SPEF2	NM_024867.3	98	10,239,5709	GG,GA,AA		0.0122,6.973,2.1735	benign	655/1823	35694454	259,11657	1850	4108	5958	SO:0001583	missense	79925	exon13			AAGGTGAAACAAT	AB051557	CCDS3910.1, CCDS43309.1	5p13.2	2010-05-04			ENSG00000152582	ENSG00000152582			26293	protein-coding gene	gene with protein product	"""cancer/testis antigen 122"""	610172				11214970, 16549801, 17610085	Standard	NM_024867		Approved	KPL2, FLJ23577, CT122	uc003jjo.3	Q9C093	OTTHUMG00000131111	ENST00000356031.3:c.1964A>G	5.37:g.35694454A>G	ENSP00000348314:p.Glu655Gly	166.0	0.0	0		180.0	89.0	0.494444	NM_024867	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Missense_Mutation	SNP	ENST00000356031.3	37	CCDS43309.1	39	0.017857142857142856	37	0.07520325203252033	2	0.0055248618784530384	0	0.0	0	0.0	A	11.23	1.576102	0.28092	0.06973	1.22E-4	ENSG00000152582	ENST00000356031	T	0.06449	3.3	3.74	3.74	0.42951	.	0.984296	0.08306	N	0.966202	T	0.00300	0.0009	N	0.22421	0.69	0.80722	D	1	B	0.16166	0.016	B	0.09377	0.004	T	0.46965	-0.9153	10	0.33940	T	0.23	.	9.1268	0.36821	1.0:0.0:0.0:0.0	rs12332369;rs52800439;rs12332369	655	Q9C093	SPEF2_HUMAN	G	655	ENSP00000348314:E655G	ENSP00000348314:E655G	E	+	2	0	SPEF2	35730211	0.746000	0.28272	0.862000	0.33874	0.140000	0.21249	2.047000	0.41269	1.941000	0.56285	0.260000	0.18958	GAA	A|0.973;G|0.027	0.027	strong		0.368	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722	
OR6P1	128366	hgsc.bcm.edu	37	1	158533219	158533219	+	Missense_Mutation	SNP	A	A	C	rs114956415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158533219A>C	ENST00000334632.1	-	1	175	c.176T>G	c.(175-177)aTg>aGg	p.M59R		NM_001160325.1	NP_001153797.1	Q8NGX9	OR6P1_HUMAN	olfactory receptor, family 6, subfamily P, member 1	59						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(4)|lung(1)	6						GAAAAAGTACATGGGACGATG	0.448													A|||	79	0.0157748	0.0582	0.0029	5008	,	,		20152	0.0		0.0	False		,,,				2504	0.0				p.M59R		Atlas-SNP	.											.	OR6P1	47	.	0			c.T176G						PASS	.	A	ARG/MET	78,1306		3,72,617	41.0	47.0	45.0		176	5.0	1.0	1	dbSNP_132	45	1,3181		0,1,1590	yes	missense	OR6P1	NM_001160325.1	91	3,73,2207	CC,CA,AA		0.0314,5.6358,1.7302	probably-damaging	59/318	158533219	79,4487	692	1591	2283	SO:0001583	missense	128366	exon1			AAGTACATGGGAC	BK004193	CCDS53391.1	1q23.1	2012-08-09			ENSG00000186440	ENSG00000186440		"""GPCR / Class A : Olfactory receptors"""	15036	protein-coding gene	gene with protein product							Standard	NM_001160325		Approved		uc010pim.2	Q8NGX9	OTTHUMG00000019633	ENST00000334632.1:c.176T>G	1.37:g.158533219A>C	ENSP00000334721:p.Met59Arg	96.0	0.0	0		86.0	41.0	0.476744	NM_001160325	Q6IFR9	Missense_Mutation	SNP	ENST00000334632.1	37	CCDS53391.1	26	0.011904761904761904	26	0.052845528455284556	0	0.0	0	0.0	0	0.0	A	14.53	2.561606	0.45590	0.056358	3.14E-4	ENSG00000186440	ENST00000334632	T	0.09911	2.93	5.0	5.0	0.66597	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000027	T	0.28101	0.0693	H	0.98426	4.23	0.52099	D	0.999948	P	0.51351	0.944	P	0.48114	0.567	T	0.54476	-0.8288	10	0.87932	D	0	.	13.8199	0.63313	1.0:0.0:0.0:0.0	.	59	Q8NGX9	OR6P1_HUMAN	R	59	ENSP00000334721:M59R	ENSP00000334721:M59R	M	-	2	0	OR6P1	156799843	1.000000	0.71417	1.000000	0.80357	0.061000	0.15899	8.965000	0.93393	2.100000	0.63781	0.482000	0.46254	ATG	A|0.987;C|0.013	0.013	strong		0.448	OR6P1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051848.1		
GALNT12	79695	hgsc.bcm.edu	37	9	101594219	101594219	+	Silent	SNP	A	A	G	rs16917929	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:101594219A>G	ENST00000375011.3	+	4	897	c.897A>G	c.(895-897)caA>caG	p.Q299Q		NM_024642.4	NP_078918.3	Q8IXK2	GLT12_HUMAN	polypeptide N-acetylgalactosaminyltransferase 12	299					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(1)|endometrium(2)|large_intestine(3)|lung(8)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	17		Acute lymphoblastic leukemia(62;0.0559)				TACGGATGCAATCCCCCGTCG	0.572													A|||	206	0.0411342	0.1513	0.0086	5008	,	,		14266	0.0		0.0	False		,,,				2504	0.0				p.Q299Q		Atlas-SNP	.											.	GALNT12	37	.	0			c.A897G						PASS	.	A		592,3814	257.7+/-262.0	43,506,1654	65.0	49.0	54.0		897	-4.0	0.6	9	dbSNP_123	54	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	GALNT12	NM_024642.4		43,509,5951	GG,GA,AA		0.0349,13.4362,4.5748		299/582	101594219	595,12411	2203	4300	6503	SO:0001819	synonymous_variant	79695	exon4			GATGCAATCCCCC	AB078146	CCDS6737.1	9q22.33	2014-03-13	2014-03-13		ENSG00000119514	ENSG00000119514	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	19877	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 12"""	610290	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 12 (GalNAc-T12)"""			12135769	Standard	NM_024642		Approved	GalNAc-T12	uc004ayz.3	Q8IXK2	OTTHUMG00000020348	ENST00000375011.3:c.897A>G	9.37:g.101594219A>G		98.0	0.0	0		89.0	56.0	0.629214	NM_024642	Q5TCF7|Q8NG54|Q96CT9|Q9H771	Silent	SNP	ENST00000375011.3	37	CCDS6737.1																																																																																			A|0.954;G|0.046	0.046	strong		0.572	GALNT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053382.1	NM_024642	
HIST3H3	8290	hgsc.bcm.edu	37	1	228612994	228612994	+	Silent	SNP	T	T	C	rs61741017	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228612994T>C	ENST00000366696.1	-	1	32	c.33A>G	c.(31-33)tcA>tcG	p.S11S		NM_003493.2	NP_003484.1	Q16695	H31T_HUMAN	histone cluster 3, H3	11					telomere maintenance (GO:0000723)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			large_intestine(1)|lung(2)|prostate(2)|skin(1)	6		Prostate(94;0.0724)				TGCCACCCGTTGACTTGCGCG	0.652													c|||	80	0.0159744	0.0567	0.0058	5008	,	,		14474	0.0		0.001	False		,,,				2504	0.0				p.S11S		Atlas-SNP	.											.	HIST3H3	20	.	0			c.A33G						PASS	.	C		249,4147	735.3+/-410.7	1,247,1950	42.0	50.0	47.0		33	-7.2	0.0	1	dbSNP_129	47	0,8592		0,0,4296	no	coding-synonymous	HIST3H3	NM_003493.2		1,247,6246	CC,CT,TT		0.0,5.6642,1.9172		11/137	228612994	249,12739	2198	4296	6494	SO:0001819	synonymous_variant	8290	exon1			ACCCGTTGACTTG	Z49861	CCDS1572.1	1q42.13	2012-09-19	2006-10-11	2003-02-21	ENSG00000168148	ENSG00000168148		"""Histones / Replication-dependent"""	4778	protein-coding gene	gene with protein product		602820	"""H3 histone family, member T"", ""histone 3, H3"""	H3FT		8834248, 12408966	Standard	NM_003493		Approved	H3t, H3/g, H3.4	uc001hsx.1	Q16695	OTTHUMG00000040044	ENST00000366696.1:c.33A>G	1.37:g.228612994T>C		160.0	0.0	0		143.0	64.0	0.447552	NM_003493	B2R5K3|Q6FGU4	Silent	SNP	ENST00000366696.1	37	CCDS1572.1																																																																																			T|0.984;C|0.016	0.016	strong		0.652	HIST3H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096595.2	NM_003493	
MT-CYB	4519	hgsc.bcm.edu	37	M	14911	14911	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:14911C>T	ENST00000361789.2	+	1	165	c.165C>T	c.(163-165)taC>taT	p.Y55Y	MT-TT_ENST00000387460.2_RNA|MT-TE_ENST00000387459.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-ND6_ENST00000361681.2_5'Flank|MT-TH_ENST00000387441.1_RNA			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	55					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						GCCATACACTACTCACCAGAC	0.532																																					p.Y55Y		Atlas-SNP	.											.	.	.	.	0			c.C165T						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			GCACTACTCACCA			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156		ENST00000361789.2:c.165C>T	M.37:g.14911C>T		45.0	0.0	0		40.0	40.0	1	ENST00000361789	Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	Silent	SNP	ENST00000361789.2	37																																																																																				.	.	none		0.532	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024038	
MST1L	11223	hgsc.bcm.edu	37	1	17084057	17084057	+	RNA	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17084057C>T	ENST00000455405.2	-	0	655							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										GTGCACATCTCGCTCTCCCGC	0.587																																					p.E622K		Atlas-SNP	.											.	.	.	.	0			c.G1864A						PASS	.																																					11223	exon14			ACATCTCGCTCTC	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.17084057C>T		1115.0	0.0	0		1363.0	118.0	0.0865737	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	15.05	2.717424	0.48622	.	.	ENSG00000186715	ENST00000334998;ENST00000442552	.	.	.	.	.	.	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.42420	D	0.000706	T	0.65943	0.2740	.	.	.	.	.	.	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.71196	-0.4664	6	0.56958	D	0.05	.	6.7402	0.23431	0.0:0.9998:0.0:2.0E-4	.	622;648	Q2TV78-2;Q2TV78	.;MSTP9_HUMAN	K	622;648	.	ENSP00000439273:E622K	E	-	1	0	MST1P9	16956644	1.000000	0.71417	0.477000	0.27303	0.000000	0.00434	4.380000	0.59581	0.502000	0.28037	0.000000	0.15137	GAG	.	.	none		0.587	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
GALNT2	2590	hgsc.bcm.edu	37	1	230391058	230391058	+	Silent	SNP	G	G	A	rs75919037	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:230391058G>A	ENST00000366672.4	+	11	1176	c.1104G>A	c.(1102-1104)acG>acA	p.T368T	GALNT2_ENST00000541865.1_Missense_Mutation_p.V244I|GALNT2_ENST00000543760.1_Silent_p.T330T	NM_004481.3	NP_004472.1	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2	368					cellular protein metabolic process (GO:0044267)|immunoglobulin biosynthetic process (GO:0002378)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(5)|skin(2)	32	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				ACCCCTACACGTTCCCGGGTG	0.587													G|||	10	0.00199681	0.0076	0.0	5008	,	,		19672	0.0		0.0	False		,,,				2504	0.0				p.T368T		Atlas-SNP	.											GALNT2,ear,carcinoma,+1,1	GALNT2	83	1	0			c.G1104A						PASS	.	G		42,4364	45.3+/-79.5	0,42,2161	173.0	129.0	144.0		1104	-8.4	0.7	1	dbSNP_132	144	0,8600		0,0,4300	no	coding-synonymous	GALNT2	NM_004481.3		0,42,6461	AA,AG,GG		0.0,0.9532,0.3229		368/572	230391058	42,12964	2203	4300	6503	SO:0001819	synonymous_variant	2590	exon11			CTACACGTTCCCG	BC041120	CCDS1582.1	1q41-q42	2014-03-13	2014-03-13		ENSG00000143641	ENSG00000143641	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4124	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 2"""	602274	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2)"""			9592121, 7592619	Standard	NM_004481		Approved	GalNAc-T2	uc010pwa.1	Q10471	OTTHUMG00000037771	ENST00000366672.4:c.1104G>A	1.37:g.230391058G>A		133.0	0.0	0		115.0	69.0	0.6	NM_004481	A8K1Y3|B7Z8V8|C5HU00|Q9NPY4	Silent	SNP	ENST00000366672.4	37	CCDS1582.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	2.687	-0.274072	0.05679	0.009532	0.0	ENSG00000143641	ENST00000541865	T	0.41065	1.01	4.97	-8.41	0.00961	.	.	.	.	.	T	0.19525	0.0469	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.35847	-0.9772	6	0.59425	D	0.04	.	1.101	0.01683	0.1909:0.2919:0.1871:0.3301	.	.	.	.	I	244	ENSP00000444346:V244I	ENSP00000444346:V244I	V	+	1	0	GALNT2	228457681	0.000000	0.05858	0.694000	0.30210	0.977000	0.68977	-2.466000	0.00994	-1.729000	0.01364	-0.244000	0.11960	GTT	G|0.996;A|0.004	0.004	strong		0.587	GALNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092158.1	NM_004481	
CAPN12	147968	hgsc.bcm.edu	37	19	39234723	39234723	+	Missense_Mutation	SNP	C	C	T	rs112433506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39234723C>T	ENST00000328867.4	-	1	391	c.83G>A	c.(82-84)cGg>cAg	p.R28Q	CAPN12_ENST00000601953.1_Intron	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	28					proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(60;2.87e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)			GCTCTGGCCCCGAAAAAGCTG	0.632													c|||	11	0.00219649	0.0083	0.0	5008	,	,		14500	0.0		0.0	False		,,,				2504	0.0				p.R28Q		Atlas-SNP	.											.	CAPN12	43	.	0			c.G83A						PASS	.	C	GLN/ARG	26,4380	29.9+/-59.1	0,26,2177	61.0	57.0	58.0		83	3.7	0.3	19	dbSNP_132	58	0,8600		0,0,4300	yes	missense	CAPN12	NM_144691.3	43	0,26,6477	TT,TC,CC		0.0,0.5901,0.1999	benign	28/720	39234723	26,12980	2203	4300	6503	SO:0001583	missense	147968	exon1			TGGCCCCGAAAAA	BC014027	CCDS12519.1	19q13.2	2014-08-12			ENSG00000182472	ENSG00000182472		"""EF-hand domain containing"""	13249	protein-coding gene	gene with protein product		608839					Standard	NM_144691		Approved		uc002ojd.1	Q6ZSI9	OTTHUMG00000182525	ENST00000328867.4:c.83G>A	19.37:g.39234723C>T	ENSP00000331636:p.Arg28Gln	65.0	0.0	0		63.0	30.0	0.47619	NM_144691		Missense_Mutation	SNP	ENST00000328867.4	37	CCDS12519.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	c	12.17	1.858222	0.32791	0.005901	0.0	ENSG00000182472	ENST00000328867	T	0.41065	1.01	4.74	3.7	0.42460	Peptidase C2, calpain, catalytic domain (1);	0.749962	0.11830	N	0.525296	T	0.18087	0.0434	L	0.39898	1.24	0.09310	N	1	P	0.37997	0.614	B	0.27887	0.084	T	0.07616	-1.0763	10	0.13853	T	0.58	.	5.2383	0.15458	0.2025:0.6908:0.0:0.1066	.	28	Q6ZSI9	CAN12_HUMAN	Q	28	ENSP00000331636:R28Q	ENSP00000331636:R28Q	R	-	2	0	CAPN12	43926563	0.001000	0.12720	0.349000	0.25694	0.717000	0.41224	-0.261000	0.08694	1.204000	0.43247	0.457000	0.33378	CGG	C|0.998;T|0.002	0.002	strong		0.632	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1		
TRANK1	9881	hgsc.bcm.edu	37	3	36887863	36887863	+	Silent	SNP	G	G	A	rs142584752	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:36887863G>A	ENST00000429976.2	-	16	5182	c.4935C>T	c.(4933-4935)acC>acT	p.T1645T	TRANK1_ENST00000301807.6_Silent_p.T1095T|TRANK1_ENST00000428977.2_Silent_p.T1095T|TRANK1_ENST00000463984.1_5'UTR	NM_014831.2	NP_055646.2	O15050	TRNK1_HUMAN	tetratricopeptide repeat and ankyrin repeat containing 1	1645							ATP binding (GO:0005524)|hydrolase activity (GO:0016787)			NS(2)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(20)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	73						GTGTGATGGCGGTGTACAGCT	0.448													G|||	14	0.00279553	0.0106	0.0	5008	,	,		18174	0.0		0.0	False		,,,				2504	0.0				p.T1645T		Atlas-SNP	.											.	TRANK1	398	.	0			c.C4935T						PASS	.	G		30,3826		1,28,1899	56.0	54.0	55.0		4935	-10.3	0.4	3	dbSNP_134	55	1,8267		0,1,4133	no	coding-synonymous	TRANK1	NM_014831.2		1,29,6032	AA,AG,GG		0.0121,0.778,0.2557		1645/2926	36887863	31,12093	1928	4134	6062	SO:0001819	synonymous_variant	9881	exon16			GATGGCGGTGTAC	AK096678	CCDS46789.1, CCDS46789.2	3p22.2	2013-01-11			ENSG00000168016	ENSG00000168016		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29011	protein-coding gene	gene with protein product	"""lupus brain antigen 1"", ""KIAA0342"""					9205841	Standard	NM_014831		Approved	LBA1, KIAA0342	uc003cgj.3	O15050	OTTHUMG00000155848	ENST00000429976.2:c.4935C>T	3.37:g.36887863G>A		175.0	0.0	0		224.0	92.0	0.410714	NM_014831	Q8N8K0	Silent	SNP	ENST00000429976.2	37	CCDS46789.2																																																																																			G|0.998;A|0.002	0.002	strong		0.448	TRANK1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014831	
MT-ND5	4540	hgsc.bcm.edu	37	M	12540	12540	+	Nonstop_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:12540A>G	ENST00000361567.2	+	1	204	c.204A>G	c.(202-204)tgA>tgG	p.*68W	MT-TR_ENST00000387439.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	68					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						AACTGACACTGAGCCACAACC	0.408																																					p.W68W		Atlas-SNP	.											.	.	.	.	0			c.A204G						PASS	.																																			SO:0001578	stop_lost	0	exon1			ACACTGAGCCACA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.204A>G	M.37:g.12540A>G	Exception_encountered	8.0	0.0	0		18.0	18.0	1	ENST00000361567	Q34773|Q8WCY3	Silent	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.408	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
PADI6	353238	hgsc.bcm.edu	37	1	17727847	17727847	+	RNA	SNP	T	T	C	rs183565903	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:17727847T>C	ENST00000434762.2	+	0	2049							Q6TGC4	PADI6_HUMAN	peptidyl arginine deiminase, type VI						cytoplasm organization (GO:0007028)|cytoskeleton organization (GO:0007010)|protein citrullination (GO:0018101)|regulation of translation by machinery localization (GO:0043143)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(2)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000337)|Lung NSC(340;0.000419)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00488)|BRCA - Breast invasive adenocarcinoma(304;7.59e-06)|COAD - Colon adenocarcinoma(227;1.18e-05)|Kidney(64;0.000186)|KIRC - Kidney renal clear cell carcinoma(64;0.00272)|STAD - Stomach adenocarcinoma(196;0.0134)|READ - Rectum adenocarcinoma(331;0.0655)|Lung(427;0.189)	L-Citrulline(DB00155)	ACTTTGACTGTTACCTGACAG	0.552													T|||	4	0.000798722	0.0015	0.0029	5008	,	,		19527	0.0		0.0	False		,,,				2504	0.0				p.C666C		Atlas-SNP	.											.	PADI6	51	.	0			c.T1998C						PASS	.	T		5,3961		0,5,1978	60.0	64.0	63.0		1999	-1.8	0.9	1		63	0,8346		0,0,4173	no	coding-synonymous	PADI6	NM_207421.3		0,5,6151	CC,CT,TT		0.0,0.1261,0.0406		666/695	17727847	5,12307	1983	4173	6156			353238	exon17			TGACTGTTACCTG	AY422079	CCDS72715.1	1p36.13	2014-07-10			ENSG00000256049	ENSG00000276747	3.5.3.15	"""Peptidyl arginine deiminases"""	20449	protein-coding gene	gene with protein product		610363				15087120	Standard	NM_207421		Approved		uc001bak.1	Q6TGC4	OTTHUMG00000002372		1.37:g.17727847T>C		128.0	0.0	0		121.0	52.0	0.429752	NM_207421	Q330K5|Q70SX3	Silent	SNP	ENST00000434762.2	37																																																																																				T|1.000;C|0.000	0.000	strong		0.552	PADI6-001	KNOWN	basic	processed_transcript	processed_transcript	OTTHUMT00000006804.4	NM_207421	
C1orf127	148345	hgsc.bcm.edu	37	1	11009703	11009703	+	Missense_Mutation	SNP	C	C	T	rs1281012	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11009703C>T	ENST00000377008.4	-	10	1213	c.767G>A	c.(766-768)cGg>cAg	p.R256Q	C1orf127_ENST00000377004.4_Missense_Mutation_p.R423Q			Q8N9H9	CA127_HUMAN	chromosome 1 open reading frame 127	256	Pro-rich.		R -> Q (in dbSNP:rs1281012).							NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(5)	32	Ovarian(185;0.249)	Lung NSC(185;0.000226)|all_lung(284;0.000302)|Renal(390;0.000469)|Colorectal(325;0.0062)|Breast(348;0.0139)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0731)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.71e-07)|COAD - Colon adenocarcinoma(227;7.79e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000305)|Kidney(185;0.000785)|KIRC - Kidney renal clear cell carcinoma(229;0.00262)|READ - Rectum adenocarcinoma(331;0.0509)		GTCGGAAGGCCGGTGCAGGAG	0.622													C|||	347	0.0692891	0.2042	0.0144	5008	,	,		17273	0.004		0.0427	False		,,,				2504	0.0204				p.R423Q		Atlas-SNP	.											.	C1orf127	134	.	0			c.G1268A						PASS	.	C	GLN/ARG	725,3675		66,593,1541	40.0	34.0	36.0		1268	-6.4	0.0	1	dbSNP_87	36	333,8267		4,325,3971	yes	missense	C1orf127	NM_001170754.1	43	70,918,5512	TT,TC,CC		3.8721,16.4773,8.1385	benign	423/824	11009703	1058,11942	2200	4300	6500	SO:0001583	missense	148345	exon11			GAAGGCCGGTGCA	AK094437	CCDS53267.1	1p36.22	2008-02-05			ENSG00000175262	ENSG00000175262			26730	protein-coding gene	gene with protein product						14702039	Standard	NM_001170754		Approved	FLJ37118	uc010oao.2	Q8N9H9	OTTHUMG00000002032	ENST00000377008.4:c.767G>A	1.37:g.11009703C>T	ENSP00000366207:p.Arg256Gln	118.0	0.0	0		121.0	60.0	0.495868	NM_001170754	A0AVG8|A6NKM7|Q5VXJ2	Missense_Mutation	SNP	ENST00000377008.4	37		167|167	0.07646520146520147|0.07646520146520147	123|123	0.25|0.25	4|4	0.011049723756906077|0.011049723756906077	1|1	0.0017482517482517483|0.0017482517482517483	39|39	0.051451187335092345|0.051451187335092345	C|C	1.843|1.843	-0.467033|-0.467033	0.04476|0.04476	0.164773|0.164773	0.038721|0.038721	ENSG00000175262|ENSG00000175262	ENST00000418570|ENST00000377004;ENST00000377008	.|T;T	.|0.29142	.|1.58;1.58	3.98|3.98	-6.39|-6.39	0.01951|0.01951	.|.	.|6.202500	.|0.00166	.|N	.|0.000011	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.02539|0.02539	-0.55|-0.55	0.80722|0.80722	P|P	0.0|0.0	.|B;B	.|0.09022	.|0.002;0.002	.|B;B	.|0.01281	.|0.0;0.0	T|T	0.18999|0.18999	-1.0319|-1.0319	4|9	.|0.23891	.|T	.|0.37	.|.	2.3424|2.3424	0.04263|0.04263	0.1182:0.3558:0.1181:0.4079|0.1182:0.3558:0.1181:0.4079	rs1281012;rs1281012|rs1281012;rs1281012	.|274;256	.|B7ZLG7;Q8N9H9	.|.;CA127_HUMAN	S|Q	258|423;256	.|ENSP00000366203:R423Q;ENSP00000366207:R256Q	.|ENSP00000366203:R423Q	G|R	-|-	1|2	0|0	C1orf127|C1orf127	10932290|10932290	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-1.451000|-1.451000	0.02387|0.02387	-1.615000|-1.615000	0.01573|0.01573	-1.314000|-1.314000	0.01303|0.01303	GGC|CGG	C|0.907;T|0.093	0.093	strong		0.622	C1orf127-202	KNOWN	basic	protein_coding	protein_coding		NM_173507	
SPAG17	200162	hgsc.bcm.edu	37	1	118598362	118598362	+	Missense_Mutation	SNP	A	A	G	rs138706127	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:118598362A>G	ENST00000336338.5	-	19	2781	c.2716T>C	c.(2716-2718)Tct>Cct	p.S906P		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	906						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		TTACTTTTAGATTCTTTAATG	0.303													A|||	23	0.00459265	0.0174	0.0	5008	,	,		16823	0.0		0.0	False		,,,				2504	0.0				p.S906P		Atlas-SNP	.											SPAG17,NS,haematopoietic_neoplasm,0,1	SPAG17	263	1	0			c.T2716C						scavenged	.	A	PRO/SER	93,4307	73.6+/-111.7	1,91,2108	67.0	68.0	68.0		2716	4.4	1.0	1	dbSNP_134	68	1,8595	1.2+/-3.3	0,1,4297	yes	missense	SPAG17	NM_206996.2	74	1,92,6405	GG,GA,AA		0.0116,2.1136,0.7233	possibly-damaging	906/2224	118598362	94,12902	2200	4298	6498	SO:0001583	missense	200162	exon19			TTTTAGATTCTTT		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.2716T>C	1.37:g.118598362A>G	ENSP00000337804:p.Ser906Pro	64.0	1.0	0.015625		60.0	38.0	0.633333	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	A	13.34	2.206952	0.39003	0.021136	1.16E-4	ENSG00000155761	ENST00000336338	T	0.30981	1.51	5.55	4.42	0.53409	.	0.557030	0.19693	N	0.108216	T	0.14787	0.0357	L	0.59436	1.845	0.27117	N	0.962222	B	0.18166	0.026	B	0.19391	0.025	T	0.18304	-1.0341	10	0.72032	D	0.01	.	9.3895	0.38363	0.9185:0.0:0.0815:0.0	.	906	Q6Q759	SPG17_HUMAN	P	906	ENSP00000337804:S906P	ENSP00000337804:S906P	S	-	1	0	SPAG17	118399885	1.000000	0.71417	0.999000	0.59377	0.166000	0.22503	2.832000	0.48152	1.112000	0.41740	0.477000	0.44152	TCT	A|0.993;G|0.007	0.007	strong		0.303	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
XCL1	6375	hgsc.bcm.edu	37	1	168549325	168549325	+	Missense_Mutation	SNP	A	A	G	rs61546281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:168549325A>G	ENST00000367818.3	+	2	251	c.86A>G	c.(85-87)aAg>aGg	p.K29R		NM_002995.2	NP_002986.1	P47992	XCL1_HUMAN	chemokine (C motif) ligand 1	29					cell-cell signaling (GO:0007267)|cellular response to interleukin-4 (GO:0071353)|cellular response to transforming growth factor beta stimulus (GO:0071560)|immune response (GO:0006955)|mature natural killer cell chemotaxis (GO:0035782)|negative regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000562)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of T cell cytokine production (GO:0002725)|negative regulation of T-helper 1 cell activation (GO:2000518)|negative regulation of T-helper 1 type immune response (GO:0002826)|negative regulation of transcription, DNA-templated (GO:0045892)|neutrophil chemotaxis (GO:0030593)|positive regulation of B cell chemotaxis (GO:2000538)|positive regulation of CD4-positive, alpha-beta T cell proliferation (GO:2000563)|positive regulation of CD8-positive, alpha-beta T cell proliferation (GO:2000566)|positive regulation of granzyme A production (GO:2000513)|positive regulation of granzyme B production (GO:0071663)|positive regulation of immunoglobulin production in mucosal tissue (GO:2000558)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of leukocyte chemotaxis (GO:0002690)|positive regulation of natural killer cell chemotaxis (GO:2000503)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of T cell chemotaxis (GO:0010820)|positive regulation of T cell cytokine production (GO:0002726)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|positive regulation of T-helper 1 cell cytokine production (GO:2000556)|positive regulation of T-helper 2 cell cytokine production (GO:2000553)|positive regulation of thymocyte migration (GO:2000412)|positive regulation of transforming growth factor beta production (GO:0071636)|regulation of inflammatory response (GO:0050727)|release of sequestered calcium ion into cytosol (GO:0051209)|response to virus (GO:0009615)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	chemokine activity (GO:0008009)|chemokine receptor binding (GO:0042379)|protein homodimerization activity (GO:0042803)			kidney(2)|lung(7)|upper_aerodigestive_tract(1)	10	all_hematologic(923;0.208)					GTCTCAGATAAGAGGACCTGT	0.443													A|||	162	0.0323482	0.1165	0.0029	5008	,	,		19121	0.001		0.005	False		,,,				2504	0.0				p.K29R		Atlas-SNP	.											.	XCL1	16	.	0			c.A86G						PASS	.	A	ARG/LYS	158,4248		35,88,2080	131.0	134.0	133.0		86	-0.5	0.0	1	dbSNP_129	133	2,8598		0,2,4298	no	missense	XCL1	NM_002995.2	26	35,90,6378	GG,GA,AA		0.0233,3.586,1.2302	benign	29/115	168549325	160,12846	2203	4300	6503	SO:0001583	missense	6375	exon2			CAGATAAGAGGAC	D43768	CCDS1274.1	1q24.2	2014-01-30	2002-08-22	2002-08-23	ENSG00000143184	ENSG00000143184		"""Endogenous ligands"""	10645	protein-coding gene	gene with protein product		600250	"""small inducible cytokine subfamily C, member 1 (lymphotactin)"""	LTN, SCYC1		7602097, 7875320	Standard	NM_002995		Approved	LPTN, ATAC, SCM-1a, SCM-1, lymphotactin	uc001gfo.2	P47992	OTTHUMG00000034548	ENST00000367818.3:c.86A>G	1.37:g.168549325A>G	ENSP00000356792:p.Lys29Arg	292.0	0.0	0		170.0	68.0	0.4	NM_002995	Q52MA8	Missense_Mutation	SNP	ENST00000367818.3	37	CCDS1274.1	41	0.018772893772893772	35	0.07113821138211382	1	0.0027624309392265192	1	0.0017482517482517483	4	0.005277044854881266	A	4.417	0.077069	0.08485	0.03586	2.33E-4	ENSG00000143184	ENST00000367818	T	0.04809	3.55	4.36	-0.539	0.11865	Chemokine interleukin-8-like domain (3);	0.562682	0.17985	N	0.155390	T	0.00936	0.0031	N	0.26162	0.8	0.25269	N	0.989532	B	0.10296	0.003	B	0.08055	0.003	T	0.48317	-0.9046	9	0.16896	T	0.51	-0.7914	7.4105	0.27016	0.483:0.0:0.517:0.0	rs61546281	29	P47992	XCL1_HUMAN	R	29	ENSP00000356792:K29R	ENSP00000356792:K29R	K	+	2	0	XCL1	166815949	0.000000	0.05858	0.002000	0.10522	0.518000	0.34316	-0.858000	0.04281	0.011000	0.14865	0.533000	0.62120	AAG	A|0.981;G|0.019	0.019	strong		0.443	XCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083612.1	NM_002995	
ALMS1	7840	hgsc.bcm.edu	37	2	73676189	73676189	+	Silent	SNP	C	C	T	rs77517267	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:73676189C>T	ENST00000264448.6	+	8	2643	c.2532C>T	c.(2530-2532)gaC>gaT	p.D844D	ALMS1_ENST00000409009.1_Silent_p.D802D|ALMS1_ENST00000377715.1_Silent_p.D844D	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	844	34 X 47 AA approximate tandem repeat.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						GACCAGCTGACGGAAAGACTG	0.507													C|||	183	0.0365415	0.1324	0.0115	5008	,	,		19422	0.0		0.0	False		,,,				2504	0.0				p.D844D		Atlas-SNP	.											ALMS1,NS,carcinoma,+2,1	ALMS1	384	1	0			c.C2532T						PASS	.	C		414,3376		30,354,1511	76.0	79.0	78.0		2532	-6.5	0.0	2	dbSNP_132	78	3,8219		0,3,4108	no	coding-synonymous	ALMS1	NM_015120.4		30,357,5619	TT,TC,CC		0.0365,10.9235,3.4715		844/4168	73676189	417,11595	1895	4111	6006	SO:0001819	synonymous_variant	7840	exon8			AGCTGACGGAAAG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.2532C>T	2.37:g.73676189C>T		141.0	0.0	0		157.0	79.0	0.503185	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	37	CCDS42697.1																																																																																			C|0.976;T|0.024	0.024	strong		0.507	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
ZNF814	730051	hgsc.bcm.edu	37	19	58386314	58386314	+	Silent	SNP	G	G	A	rs111313171	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58386314G>A	ENST00000435989.2	-	3	678	c.444C>T	c.(442-444)taC>taT	p.Y148Y	ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597832.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	148					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						CACTCCCTCTGTAGGGTTTCT	0.483													.|||	397	0.0792732	0.2821	0.0331	5008	,	,		22387	0.0		0.001	False		,,,				2504	0.0				p.Y148Y		Atlas-SNP	.											.	ZNF814	93	.	0			c.C444T						PASS	.	G		365,1019		52,261,379	59.0	50.0	53.0		444	-5.5	0.0	19	dbSNP_132	53	7,3173		0,7,1583	no	coding-synonymous	ZNF814	NM_001144989.1		52,268,1962	AA,AG,GG		0.2201,26.3728,8.1507		148/856	58386314	372,4192	692	1590	2282	SO:0001819	synonymous_variant	730051	exon3			CCCTCTGTAGGGT		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"""Zinc fingers, C2H2-type"", ""-"""	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.444C>T	19.37:g.58386314G>A		744.0	1.0	0.00134409		779.0	332.0	0.426187	NM_001144989	A6NF35	Silent	SNP	ENST00000435989.2	37	CCDS46212.1																																																																																			G|0.941;A|0.059	0.059	strong		0.483	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708	
SEC61A2	55176	hgsc.bcm.edu	37	10	12200092	12200092	+	Silent	SNP	A	A	G	rs61731911	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:12200092A>G	ENST00000298428.9	+	9	1052	c.963A>G	c.(961-963)ctA>ctG	p.L321L	SEC61A2_ENST00000304267.8_Silent_p.L321L|SEC61A2_ENST00000379033.3_Silent_p.L299L|SEC61A2_ENST00000379020.4_Intron|SEC61A2_ENST00000495368.1_3'UTR	NM_018144.3	NP_060614.2	Q9H9S3	S61A2_HUMAN	Sec61 alpha 2 subunit (S. cerevisiae)	321					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)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	ribosome binding (GO:0043022)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Renal(717;0.228)				TAAATTTACTAGGACAGTGGG	0.373													A|||	91	0.0181709	0.0651	0.0072	5008	,	,		16175	0.0		0.0	False		,,,				2504	0.0				p.L321L		Atlas-SNP	.											.	SEC61A2	48	.	0			c.A963G						PASS	.	A	,,	258,4148	145.7+/-180.5	6,246,1951	83.0	77.0	79.0		963,897,963	-1.3	1.0	10	dbSNP_129	79	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	SEC61A2	NM_001142627.1,NM_001142628.1,NM_018144.3	,,	6,246,6251	GG,GA,AA		0.0,5.8557,1.9837	,,	321/438,299/455,321/477	12200092	258,12748	2203	4300	6503	SO:0001819	synonymous_variant	55176	exon9			TTTACTAGGACAG	AF346603	CCDS7088.1, CCDS44358.1, CCDS44359.1	10p14	2004-01-06			ENSG00000065665	ENSG00000065665			17702	protein-coding gene	gene with protein product							Standard	NM_018144		Approved	FLJ10578	uc001ile.2	Q9H9S3	OTTHUMG00000017679	ENST00000298428.9:c.963A>G	10.37:g.12200092A>G		141.0	0.0	0		142.0	82.0	0.577465	NM_001142627	A8K8D0|B4DX72|F8W773	Silent	SNP	ENST00000298428.9	37	CCDS7088.1																																																																																			A|0.974;G|0.026	0.026	strong		0.373	SEC61A2-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046795.1	NM_018144	
ALMS1	7840	hgsc.bcm.edu	37	2	73786188	73786188	+	Missense_Mutation	SNP	A	A	G	rs34071195	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:73786188A>G	ENST00000264448.6	+	15	10411	c.10300A>G	c.(10300-10302)Aaa>Gaa	p.K3434E	ALMS1_ENST00000409009.1_Missense_Mutation_p.K3392E	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	3434			K -> E (in dbSNP:rs34071195).		endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CATTACACAGAAAGAGGAGAT	0.468													A|||	92	0.0183706	0.0658	0.0072	5008	,	,		16247	0.0		0.0	False		,,,				2504	0.0				p.K3434E		Atlas-SNP	.											.	ALMS1	384	.	0			c.A10300G						PASS	.	A	GLU/LYS	195,3577		8,179,1699	101.0	101.0	101.0		10300	3.8	1.0	2	dbSNP_126	101	2,8234		0,2,4116	yes	missense	ALMS1	NM_015120.4	56	8,181,5815	GG,GA,AA		0.0243,5.1697,1.6406	probably-damaging	3434/4168	73786188	197,11811	1886	4118	6004	SO:0001583	missense	7840	exon15			ACACAGAAAGAGG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.10300A>G	2.37:g.73786188A>G	ENSP00000264448:p.Lys3434Glu	131.0	0.0	0		143.0	70.0	0.48951	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	37	CCDS42697.1	29	0.013278388278388278	26	0.052845528455284556	3	0.008287292817679558	0	0.0	0	0.0	A	18.42	3.620149	0.66787	0.051697	2.43E-4	ENSG00000116127	ENST00000409009;ENST00000264448	T;T	0.07327	3.2;3.2	3.75	3.75	0.43078	.	0.162704	0.29239	N	0.012727	T	0.02848	0.0085	L	0.48642	1.525	0.80722	D	1	P;D;P	0.64830	0.886;0.994;0.932	P;D;P	0.72982	0.55;0.979;0.546	T	0.00158	-1.1976	10	0.72032	D	0.01	.	9.1435	0.36919	1.0:0.0:0.0:0.0	rs34071195	3434;3392;3434	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	E	3392;3434	ENSP00000386627:K3392E;ENSP00000264448:K3434E	ENSP00000264448:K3434E	K	+	1	0	ALMS1	73639696	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	2.265000	0.43311	1.946000	0.56461	0.377000	0.23210	AAA	A|0.991;G|0.009	0.009	strong		0.468	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
SORBS2	8470	hgsc.bcm.edu	37	4	186545346	186545346	+	Missense_Mutation	SNP	A	A	T	rs61736043	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:186545346A>T	ENST00000284776.7	-	13	1734	c.1225T>A	c.(1225-1227)Tta>Ata	p.L409I	SORBS2_ENST00000498125.1_Intron|SORBS2_ENST00000431808.1_Missense_Mutation_p.L409I|SORBS2_ENST00000319471.9_Intron|SORBS2_ENST00000437304.2_Intron|SORBS2_ENST00000393528.3_Intron|SORBS2_ENST00000449407.2_Intron|SORBS2_ENST00000448662.2_Intron|SORBS2_ENST00000418609.1_Missense_Mutation_p.L313I|SORBS2_ENST00000355634.5_Missense_Mutation_p.L509I	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	409					actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		TCCTCACATAACAGGGAGCCC	0.577													A|||	57	0.0113818	0.0416	0.0029	5008	,	,		18529	0.0		0.0	False		,,,				2504	0.0				p.L509I	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-SNP	.											.	SORBS2	300	.	0			c.T1525A						PASS	.	A	ILE/LEU,ILE/LEU,,,,,,	170,4236	112.5+/-150.6	2,166,2035	63.0	58.0	60.0		937,1225,,,,,,	-10.1	0.0	4	dbSNP_129	60	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,intron,intron,intron,intron,intron,intron	SORBS2	NM_001145674.1,NM_021069.4,NM_001145670.1,NM_001145671.1,NM_001145672.1,NM_001145673.1,NM_001145675.1,NM_003603.5	5,5,,,,,,	2,167,6334	TT,TA,AA		0.0116,3.8584,1.3148	probably-damaging,probably-damaging,,,,,,	313/1005,409/1101,,,,,,	186545346	171,12835	2203	4300	6503	SO:0001583	missense	8470	exon16			CACATAACAGGGA		CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"""Arg/Abl interacting protein"""					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.1225T>A	4.37:g.186545346A>T	ENSP00000284776:p.Leu409Ile	249.0	1.0	0.00401606		253.0	121.0	0.478261	NM_001270771	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Missense_Mutation	SNP	ENST00000284776.7	37	CCDS3845.1	23	0.010531135531135532	21	0.042682926829268296	2	0.0055248618784530384	0	0.0	0	0.0	A	11.06	1.528292	0.27299	0.038584	1.16E-4	ENSG00000154556	ENST00000284776;ENST00000431808;ENST00000418609;ENST00000355634	T;T;T;T	0.37411	1.31;1.31;1.2;1.29	5.72	-10.1	0.00402	.	0.248771	0.33180	N	0.005188	T	0.14399	0.0348	L	0.42245	1.32	0.09310	N	1	D;D;D	0.71674	0.998;0.998;0.995	D;D;P	0.75020	0.985;0.984;0.792	T	0.63470	-0.6630	10	0.45353	T	0.12	-2.604	18.4155	0.90568	0.2035:0.0853:0.7112:0.0	rs61736043	313;509;409	B7Z3X6;B3KPQ7;O94875	.;.;SRBS2_HUMAN	I	409;409;313;509	ENSP00000284776:L409I;ENSP00000411764:L409I;ENSP00000397482:L313I;ENSP00000347852:L509I	ENSP00000284776:L409I	L	-	1	2	SORBS2	186782340	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.844000	0.04345	-2.307000	0.00653	-0.479000	0.04858	TTA	A|0.977;T|0.023	0.023	strong		0.577	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603	
TLR5	7100	hgsc.bcm.edu	37	1	223285042	223285042	+	Silent	SNP	G	G	A	rs5744169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:223285042G>A	ENST00000540964.1	-	4	1793	c.1332C>T	c.(1330-1332)ctC>ctT	p.L444L	TLR5_ENST00000342210.6_Silent_p.L444L			O60602	TLR5_HUMAN	toll-like receptor 5	444			Missing (in 10% of the population; abolishes flagellin signaling; associated with resistance to SLEB1). {ECO:0000269|PubMed:14623910}.		cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of cytokine secretion (GO:0050707)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor signaling pathway (GO:0002224)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor binding (GO:0005149)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				GBM - Glioblastoma multiforme(131;0.0851)		GTACCCGTAGGAGAAAGTAGA	0.418													G|||	101	0.0201677	0.0734	0.0029	5008	,	,		19084	0.0		0.002	False		,,,				2504	0.0				p.L444L		Atlas-SNP	.											.	TLR5	86	.	0			c.C1332T						PASS	.	G		315,4091	163.3+/-195.1	11,293,1899	82.0	85.0	84.0		1332	-2.9	0.9	1	dbSNP_114	84	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	TLR5	NM_003268.5		11,296,6196	AA,AG,GG		0.0349,7.1493,2.445		444/859	223285042	318,12688	2203	4300	6503	SO:0001819	synonymous_variant	7100	exon6			CCGTAGGAGAAAG		CCDS31033.1	1q32.3-q42	2014-01-29			ENSG00000187554	ENSG00000187554			11851	protein-coding gene	gene with protein product	"""Toll/interleukin-1 receptor-like protein 3"""	603031	"""systemic lupus erythematosus susceptibility 1"""	SLEB1		9435236, 16027372	Standard	NM_003268		Approved	TIL3, FLJ10052, MGC126430, MGC126431	uc001hnw.2	O60602	OTTHUMG00000037937	ENST00000540964.1:c.1332C>T	1.37:g.223285042G>A		136.0	0.0	0		143.0	63.0	0.440559	NM_003268	B1AZ05|B3Y633|B9VJ63|D1CS80|D3DTB8|O15456|Q32MI2|Q32MI3	Silent	SNP	ENST00000540964.1	37	CCDS31033.1																																																																																			G|0.976;A|0.024	0.024	strong		0.418	TLR5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_003268	
PKD1L1	168507	hgsc.bcm.edu	37	7	47933494	47933494	+	Missense_Mutation	SNP	C	C	T	rs17131915	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:47933494C>T	ENST00000289672.2	-	15	2484	c.2434G>A	c.(2434-2436)Gac>Aac	p.D812N		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	812	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.		D -> N (in dbSNP:rs17131915).		detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						GCCCCAGGGTCGTCAGGGTCG	0.612													T|||	104	0.0207668	0.0741	0.0014	5008	,	,		17811	0.005		0.0	False		,,,				2504	0.0				p.D812N		Atlas-SNP	.											.	PKD1L1	328	.	0			c.G2434A						PASS	.	T	ASN/ASP	237,4169		5,227,1971	47.0	36.0	40.0		2434	-8.5	0.0	7	dbSNP_123	40	0,8600		0,0,4300	yes	missense	PKD1L1	NM_138295.3	23	5,227,6271	TT,TC,CC		0.0,5.379,1.8222	benign	812/2850	47933494	237,12769	2203	4300	6503	SO:0001583	missense	168507	exon15			CAGGGTCGTCAGG	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.2434G>A	7.37:g.47933494C>T	ENSP00000289672:p.Asp812Asn	46.0	0.0	0		37.0	16.0	0.432432	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	46	0.021062271062271064	41	0.08333333333333333	1	0.0027624309392265192	4	0.006993006993006993	0	0.0	N	8.513	0.867001	0.17250	0.05379	0.0	ENSG00000158683	ENST00000289672	T	0.69306	-0.39	5.12	-8.54	0.00912	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	1.892900	0.03306	N	0.189835	T	0.01254	0.0041	N	0.00707	-1.245	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.09143	-1.0688	10	0.26408	T	0.33	-0.013	0.2929	0.00261	0.2928:0.2218:0.2594:0.226	rs17131915;rs52800675;rs17131915	812	Q8TDX9	PK1L1_HUMAN	N	812	ENSP00000289672:D812N	ENSP00000289672:D812N	D	-	1	0	PKD1L1	47900019	0.000000	0.05858	0.002000	0.10522	0.571000	0.35966	-3.364000	0.00496	-1.993000	0.00974	-0.389000	0.06534	GAC	C|0.974;T|0.026	0.026	strong		0.612	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
KIAA0196	9897	hgsc.bcm.edu	37	8	126087351	126087351	+	Silent	SNP	T	T	G	rs79464415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:126087351T>G	ENST00000318410.7	-	8	1216	c.867A>C	c.(865-867)gtA>gtC	p.V289V	KIAA0196_ENST00000517845.1_Silent_p.V141V	NM_014846.3	NP_055661.3	Q12768	STRUM_HUMAN	KIAA0196	289					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)			AAATACTAATTACCTGAAAGA	0.363													T|||	36	0.0071885	0.0272	0.0	5008	,	,		18432	0.0		0.0	False		,,,				2504	0.0				p.V289V		Atlas-SNP	.											.	KIAA0196	90	.	0			c.A867C						PASS	.	T		72,4334	64.7+/-102.0	0,72,2131	106.0	106.0	106.0		867	-3.3	1.0	8	dbSNP_131	106	1,8599		0,1,4299	no	coding-synonymous	KIAA0196	NM_014846.3		0,73,6430	GG,GT,TT		0.0116,1.6341,0.5613		289/1160	126087351	73,12933	2203	4300	6503	SO:0001819	synonymous_variant	9897	exon8			ACTAATTACCTGA		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.867A>C	8.37:g.126087351T>G		116.0	0.0	0		71.0	39.0	0.549296	NM_014846	A8K4R7|Q3KQX5|Q8TBQ2	Silent	SNP	ENST00000318410.7	37	CCDS6355.1																																																																																			T|0.994;G|0.006	0.006	strong		0.363	KIAA0196-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381369.1	NM_014846	
KIF19	124602	hgsc.bcm.edu	37	17	72340965	72340965	+	Silent	SNP	G	G	A	rs34914485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:72340965G>A	ENST00000389916.4	+	7	786	c.648G>A	c.(646-648)acG>acA	p.T216T		NM_153209.3	NP_694941.2	Q2TAC6	KIF19_HUMAN	kinesin family member 19	216	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|axonemal microtubule depolymerization (GO:0060404)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end specific microtubule depolymerization (GO:0070462)	cilium (GO:0005929)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(3)|lung(16)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	41						CCAACCAGACGTCCTCCCGCT	0.662													G|||	182	0.0363419	0.1278	0.0144	5008	,	,		16134	0.0		0.0	False		,,,				2504	0.0031				p.T216T		Atlas-SNP	.											.	KIF19	102	.	0			c.G648A						PASS	.	G		498,3906	217.4+/-235.8	20,458,1724	38.0	40.0	39.0		648	-4.4	1.0	17	dbSNP_126	39	10,8588	6.4+/-24.3	0,10,4289	no	coding-synonymous	KIF19	NM_153209.3		20,468,6013	AA,AG,GG		0.1163,11.3079,3.9071		216/999	72340965	508,12494	2202	4299	6501	SO:0001819	synonymous_variant	124602	exon7			CCAGACGTCCTCC	AK094619	CCDS32718.2	17q25	2007-02-13			ENSG00000196169	ENSG00000196169		"""Kinesins"""	26735	protein-coding gene	gene with protein product						11416179	Standard	NM_153209		Approved	FLJ37300, KIF19A	uc031rei.1	Q2TAC6	OTTHUMG00000150694	ENST00000389916.4:c.648G>A	17.37:g.72340965G>A		127.0	0.0	0		156.0	80.0	0.512821	NM_153209	A6NLG2|B7ZKR1|Q52M87|Q8N1X8|Q8TAB6	Silent	SNP	ENST00000389916.4	37	CCDS32718.2																																																																																			G|0.965;A|0.035	0.035	strong		0.662	KIF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319644.2	NM_153209	
KDM1A	23028	hgsc.bcm.edu	37	1	23409674	23409674	+	Silent	SNP	G	G	A	rs137940710	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:23409674G>A	ENST00000356634.3	+	19	2525	c.2376G>A	c.(2374-2376)ccG>ccA	p.P792P	KDM1A_ENST00000542151.1_Silent_p.P816P|RP1-184J9.2_ENST00000427154.1_RNA|KDM1A_ENST00000400181.4_Silent_p.P816P	NM_015013.3	NP_055828.2	O60341	KDM1A_HUMAN	lysine (K)-specific demethylase 1A	792	Demethylase activity.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|histone H3-K4 demethylation (GO:0034720)|histone H3-K9 demethylation (GO:0033169)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of DNA binding (GO:0043392)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of protein binding (GO:0032091)|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)|pituitary gland development (GO:0021983)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein demethylation (GO:0006482)|regulation of primitive erythrocyte differentiation (GO:0010725)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|demethylase activity (GO:0032451)|enzyme binding (GO:0019899)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-K4 specific) (GO:0032453)|histone demethylase activity (H3-K9 specific) (GO:0032454)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|MRF binding (GO:0043426)|oxidoreductase activity (GO:0016491)|p53 binding (GO:0002039)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(2)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						TAAAATAGCCGATTCCACGAC	0.438													G|||	21	0.00419329	0.0144	0.0029	5008	,	,		19038	0.0		0.0	False		,,,				2504	0.0				p.P816P		Atlas-SNP	.											.	KDM1A	49	.	0			c.G2448A						PASS	.	G	,	24,4382	30.8+/-60.4	0,24,2179	75.0	71.0	72.0		2448,2376	-1.3	1.0	1	dbSNP_134	72	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	KDM1A	NM_001009999.2,NM_015013.3	,	0,24,6479	AA,AG,GG		0.0,0.5447,0.1845	,	816/877,792/853	23409674	24,12982	2203	4300	6503	SO:0001819	synonymous_variant	23028	exon21			ATAGCCGATTCCA	AL031428	CCDS30627.1, CCDS53278.1	1p36.12	2011-07-01	2009-09-29	2009-09-29	ENSG00000004487	ENSG00000004487		"""Chromatin-modifying enzymes / K-demethylases"""	29079	protein-coding gene	gene with protein product		609132	"""amine oxidase (flavin containing) domain 2"", ""lysine (K)-specific demethylase 1"""	AOF2, KDM1		9628581, 12493763	Standard	NM_015013		Approved	KIAA0601, BHC110, LSD1	uc001bgj.2	O60341	OTTHUMG00000003220	ENST00000356634.3:c.2376G>A	1.37:g.23409674G>A		318.0	1.0	0.00314465		279.0	140.0	0.501792	NM_001009999	A8MWP9|Q5TH94|Q5TH95|Q86VT7|Q8IXK4|Q8NDP6|Q8TAZ3|Q96AW4	Silent	SNP	ENST00000356634.3	37	CCDS30627.1																																																																																			G|0.999;A|0.001	0.001	strong		0.438	KDM1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008880.3	NM_015013	
RNF213	57674	hgsc.bcm.edu	37	17	78263634	78263634	+	Silent	SNP	A	A	G	rs141921176	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78263634A>G	ENST00000582970.1	+	6	1253	c.1110A>G	c.(1108-1110)gcA>gcG	p.A370A	RNF213_ENST00000319921.4_Silent_p.A370A|RNF213_ENST00000508628.2_Silent_p.A419A|RNF213_ENST00000456466.1_Silent_p.A370A	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	370					ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			AAGTGAAGGCAAGGTAGGGAT	0.567													A|||	17	0.00339457	0.0129	0.0	5008	,	,		17512	0.0		0.0	False		,,,				2504	0.0				p.A370A		Atlas-SNP	.											.	RNF213	766	.	0			c.A1110G						PASS	.	A	,	61,4345	54.9+/-90.9	0,61,2142	63.0	66.0	65.0		1257,1110	-6.5	0.0	17	dbSNP_134	65	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous,coding-synonymous	RNF213	NM_020914.4,NM_020954.2	,	0,63,6440	GG,GA,AA		0.0233,1.3845,0.4844	,	419/5257,370/1064	78263634	63,12943	2203	4300	6503	SO:0001819	synonymous_variant	57674	exon6			GAAGGCAAGGTAG	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.1110A>G	17.37:g.78263634A>G		102.0	0.0	0		81.0	40.0	0.493827	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Silent	SNP	ENST00000582970.1	37	CCDS58606.1																																																																																			A|0.995;G|0.005	0.005	strong		0.567	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
AR	367	hgsc.bcm.edu	37	X	66765164	66765164	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:66765164A>T	ENST00000374690.3	+	1	700	c.176A>T	c.(175-177)cAg>cTg	p.Q59L	AR_ENST00000504326.1_Missense_Mutation_p.Q59L|AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Missense_Mutation_p.Q59L	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	59	Gln-rich.|Modulating.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	CTGCTgcagcagcagcagcag	0.677									Androgen Insensitivity Syndrome																												p.Q59L		Atlas-SNP	.											.	AR	249	.	0			c.A176T						PASS	.						7.0	10.0	9.0					X																	66765164		2055	4063	6118	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	TGCAGCAGCAGCA	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"""Nuclear hormone receptors"""	644	protein-coding gene	gene with protein product	"""testicular feminization"", ""Kennedy disease"""	313700	"""dihydrotestosterone receptor"", ""spinal and bulbar muscular atrophy"""	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.176A>T	X.37:g.66765164A>T	ENSP00000363822:p.Gln59Leu	64.0	0.0	0		68.0	4.0	0.0588235	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	37	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	12.32	1.901651	0.33535	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.69175	-0.38;-0.38;-0.38	.	.	.	.	1.117170	0.06949	N	0.814177	T	0.47060	0.1425	N	0.19112	0.55	0.09310	N	0.999999	B;B	0.34313	0.448;0.448	B;B	0.36534	0.227;0.227	T	0.31724	-0.9933	8	0.13108	T	0.6	.	.	.	.	.	59;59	E7EVX6;D3YPQ2	.;.	L	59	ENSP00000363822:Q59L;ENSP00000421155:Q59L;ENSP00000379359:Q59L	ENSP00000363822:Q59L	Q	+	2	0	AR	66681889	0.995000	0.38212	0.864000	0.33941	0.503000	0.33858	0.245000	0.18142	0.000000	0.14550	0.000000	0.15137	CAG	.	.	none		0.677	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044	
PTPN2	5771	hgsc.bcm.edu	37	18	12817348	12817348	+	Missense_Mutation	SNP	G	G	T	rs78174797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:12817348G>T	ENST00000309660.5	-	6	605	c.512C>A	c.(511-513)aCa>aAa	p.T171K	PTPN2_ENST00000327283.3_Missense_Mutation_p.T171K|PTPN2_ENST00000591115.1_Missense_Mutation_p.T194K|PTPN2_ENST00000353319.4_Missense_Mutation_p.T171K|PTPN2_ENST00000591497.1_Missense_Mutation_p.T142K	NM_002828.3	NP_002819.2	P17706	PTN2_HUMAN	protein tyrosine phosphatase, non-receptor type 2	171	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				B cell differentiation (GO:0030183)|cytokine-mediated signaling pathway (GO:0019221)|erythrocyte differentiation (GO:0030218)|glucose homeostasis (GO:0042593)|insulin receptor signaling pathway (GO:0008286)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemotaxis (GO:0050922)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of inflammatory response (GO:0050728)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of interleukin-2-mediated signaling pathway (GO:1902206)|negative regulation of interleukin-4-mediated signaling pathway (GO:1902215)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|negative regulation of lipid storage (GO:0010888)|negative regulation of macrophage colony-stimulating factor signaling pathway (GO:1902227)|negative regulation of macrophage differentiation (GO:0045650)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of positive thymic T cell selection (GO:1902233)|negative regulation of prolactin signaling pathway (GO:1902212)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of tumor necrosis factor-mediated signaling pathway (GO:0010804)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)|negative regulation of tyrosine phosphorylation of Stat1 protein (GO:0042512)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|negative regulation of tyrosine phosphorylation of Stat6 protein (GO:0042527)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of gluconeogenesis (GO:0045722)|regulation of hepatocyte growth factor receptor signaling pathway (GO:1902202)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|T cell differentiation (GO:0030217)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|syntaxin binding (GO:0019905)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|prostate(1)|skin(3)	13		Lung NSC(161;8.94e-06)				GTGAGATATTGTTCTGGTTTC	0.338													G|||	67	0.0133786	0.0477	0.0043	5008	,	,		17923	0.0		0.001	False		,,,				2504	0.0				p.T194K		Atlas-SNP	.											.	PTPN2	37	.	0			c.C581A						PASS	.	G	LYS/THR,LYS/THR,LYS/THR,LYS/THR	222,4184	119.2+/-156.9	3,216,1984	52.0	54.0	53.0		581,512,512,512	3.1	1.0	18	dbSNP_131	53	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense,missense	PTPN2	NM_001207013.1,NM_002828.3,NM_080422.2,NM_080423.2	78,78,78,78	3,217,6283	TT,TG,GG		0.0116,5.0386,1.7146	benign,benign,benign,benign	194/411,171/416,171/388,171/354	12817348	223,12783	2203	4300	6503	SO:0001583	missense	5771	exon7			GATATTGTTCTGG	M25393	CCDS11863.1, CCDS11864.1, CCDS11865.1, CCDS59306.1	18p11.3-p11.2	2011-06-09			ENSG00000175354	ENSG00000175354		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9650	protein-coding gene	gene with protein product		176887		PTPT		2164224	Standard	NM_002828		Approved	TCELLPTP, TC-PTP, TCPTP	uc002krp.3	P17706	OTTHUMG00000131702	ENST00000309660.5:c.512C>A	18.37:g.12817348G>T	ENSP00000311857:p.Thr171Lys	254.0	0.0	0		252.0	109.0	0.43254	NM_001207013	A8K955|A8MXU3|K7ENG3|Q96AU5|Q96HR2	Missense_Mutation	SNP	ENST00000309660.5	37	CCDS11865.1	34	0.015567765567765568	32	0.06504065040650407	2	0.0055248618784530384	0	0.0	0	0.0	G	10.90	1.481893	0.26598	0.050386	1.16E-4	ENSG00000175354	ENST00000327283;ENST00000353319;ENST00000341361;ENST00000309660	D;D;D	0.83419	-1.72;-1.72;-1.72	5.25	3.09	0.35607	Protein-tyrosine phosphatase, receptor/non-receptor type (4);	0.369486	0.22569	N	0.058367	T	0.14787	0.0357	N	0.21240	0.645	0.31241	N	0.695115	B;B;B;B;B	0.24132	0.025;0.013;0.098;0.055;0.016	B;B;B;B;B	0.18263	0.009;0.008;0.021;0.009;0.014	T	0.50775	-0.8788	10	0.49607	T	0.09	.	4.6107	0.12401	0.1352:0.0:0.4911:0.3736	.	171;171;148;171;171	P17706;P17706-2;Q59F91;Q96AU5;A8K3N4	PTN2_HUMAN;.;.;.;.	K	171;171;148;171	ENSP00000320298:T171K;ENSP00000320546:T171K;ENSP00000311857:T171K	ENSP00000311857:T171K	T	-	2	0	PTPN2	12807348	1.000000	0.71417	0.987000	0.45799	0.981000	0.71138	2.804000	0.47931	1.186000	0.42985	0.591000	0.81541	ACA	G|0.981;T|0.019	0.019	strong		0.338	PTPN2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254613.3	NM_002828, NM_080422, NM_080423	
CYP3A43	64816	hgsc.bcm.edu	37	7	99463556	99463556	+	Missense_Mutation	SNP	A	A	T	rs540214188	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:99463556A>T	ENST00000354829.2	+	13	1547	c.1444A>T	c.(1444-1446)Att>Ttt	p.I482F	CYP3A43_ENST00000342499.4_3'UTR|CYP3A43_ENST00000415413.1_Missense_Mutation_p.I271F|CYP3A43_ENST00000312017.5_3'UTR|CYP3A43_ENST00000222382.5_Missense_Mutation_p.I483F|CYP3A43_ENST00000417625.1_Missense_Mutation_p.I372F|CYP3A43_ENST00000444905.1_3'UTR|CYP3A43_ENST00000477658.1_3'UTR	NM_022820.3|NM_057095.1	NP_073731.1|NP_476436.1	Q9HB55	CP343_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 43	482			Missing (in allele CYP3A43*2).		small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)|skin(1)	19	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)				Dexamethasone(DB01234)|Dolutegravir(DB08930)|Ethosuximide(DB00593)|Oxazepam(DB00842)|Phenelzine(DB00780)|Praziquantel(DB01058)|Rifampicin(DB01045)|Rifapentine(DB01201)|Testosterone(DB00624)|Troleandomycin(DB01361)|Zalcitabine(DB00943)	CAATCTACCAATTCTTCAACC	0.338													A|||	292	0.0583067	0.2035	0.0216	5008	,	,		18384	0.001		0.002	False		,,,				2504	0.0051				p.I483F		Atlas-SNP	.											.	CYP3A43	52	.	0			c.A1447T						PASS	.						87.0	97.0	93.0					7																	99463556		2184	4300	6484	SO:0001583	missense	64816	exon13			CTACCAATTCTTC	AF319634	CCDS5675.1, CCDS5676.1, CCDS5677.1, CCDS64723.1	7q21.1	2007-12-14	2003-01-14		ENSG00000021461	ENSG00000021461		"""Cytochrome P450s"""	17450	protein-coding gene	gene with protein product		606534	"""cytochrome P450, subfamily IIIA, polypeptide 43"""			11160876, 11266076	Standard	NM_022820		Approved		uc003ury.1	Q9HB55	OTTHUMG00000156498	ENST00000354829.2:c.1444A>T	7.37:g.99463556A>T	ENSP00000346887:p.Ile482Phe	113.0	0.0	0		75.0	12.0	0.16	NM_022820	Q495Y1|Q75MK2|Q75MK3|Q9HB52|Q9HB53|Q9HB54|Q9HB57	Missense_Mutation	SNP	ENST00000354829.2	37	CCDS5676.1	.	.	.	.	.	.	.	.	.	.	A	10.34	1.321913	0.23994	.	.	ENSG00000021461	ENST00000354829;ENST00000417625;ENST00000415413;ENST00000222382	T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31	3.17	-6.34	0.01982	.	0.885559	0.09500	N	0.793766	T	0.24928	0.0605	N	0.01019	-1.045	0.22127	N	0.999348	B;B;B	0.11235	0.002;0.001;0.004	B;B;B	0.15052	0.003;0.006;0.012	T	0.16541	-1.0399	10	0.23891	T	0.37	.	0.423	0.00459	0.3831:0.1534:0.2286:0.2349	.	372;483;482	Q495Y1;Q75MK2;Q9HB55	.;.;CP343_HUMAN	F	482;372;271;483	ENSP00000346887:I482F;ENSP00000416581:I372F;ENSP00000401521:I271F;ENSP00000222382:I483F	ENSP00000222382:I483F	I	+	1	0	CYP3A43	99301492	0.000000	0.05858	0.000000	0.03702	0.483000	0.33249	-8.694000	0.00017	-2.343000	0.00623	0.172000	0.16884	ATT	.	.	none		0.338	CYP3A43-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000344379.1		
EXOC4	60412	hgsc.bcm.edu	37	7	133749077	133749077	+	Silent	SNP	C	C	T	rs139944066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:133749077C>T	ENST00000253861.4	+	18	2750	c.2721C>T	c.(2719-2721)gaC>gaT	p.D907D	EXOC4_ENST00000545148.1_Silent_p.D517D|EXOC4_ENST00000539845.1_Silent_p.D806D|EXOC4_ENST00000541309.1_Silent_p.D195D	NM_021807.3	NP_068579.3	Q96A65	EXOC4_HUMAN	exocyst complex component 4	907					cellular protein metabolic process (GO:0044267)|membrane organization (GO:0061024)|protein transport (GO:0015031)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|exocyst (GO:0000145)|growth cone membrane (GO:0032584)|membrane (GO:0016020)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)	protein N-terminus binding (GO:0047485)			NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(16)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	50		Esophageal squamous(399;0.129)				ACACAGCTGACGAGCTCCTGA	0.577													C|||	11	0.00219649	0.0083	0.0	5008	,	,		21152	0.0		0.0	False		,,,				2504	0.0				p.D907D		Atlas-SNP	.											.	EXOC4	118	.	0			c.C2721T						PASS	.	C		21,4385	28.1+/-56.4	0,21,2182	90.0	76.0	81.0		2721	-8.4	0.4	7	dbSNP_134	81	0,8600		0,0,4300	no	coding-synonymous	EXOC4	NM_021807.3		0,21,6482	TT,TC,CC		0.0,0.4766,0.1615		907/975	133749077	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	60412	exon18			AGCTGACGAGCTC	AL831989	CCDS5829.1, CCDS43648.1	7q31	2013-01-22	2005-11-01	2005-11-01	ENSG00000131558	ENSG00000131558			30389	protein-coding gene	gene with protein product		608185	"""SEC8-like 1 (S. cerevisiae)"""	SEC8L1		11214970, 12687004	Standard	XM_005250523		Approved	KIAA1699, MGC27170, SEC8, Sec8p	uc003vrk.3	Q96A65	OTTHUMG00000155259	ENST00000253861.4:c.2721C>T	7.37:g.133749077C>T		94.0	0.0	0		118.0	52.0	0.440678	NM_021807	E9PED2|Q541U8|Q9C0G4|Q9H9K0|Q9P102	Silent	SNP	ENST00000253861.4	37	CCDS5829.1																																																																																			C|0.997;T|0.003	0.003	strong		0.577	EXOC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339182.1	NM_021807	
DHRS2	10202	hgsc.bcm.edu	37	14	24114483	24114483	+	3'UTR	SNP	T	T	C	rs7156794	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24114483T>C	ENST00000250383.6	+	0	1340				DHRS2_ENST00000344777.7_Missense_Mutation_p.V292A	NM_005794.3	NP_005785.1	Q13268	DHRS2_HUMAN	dehydrogenase/reductase (SDR family) member 2						C21-steroid hormone metabolic process (GO:0008207)|cellular response to oxidative stress (GO:0034599)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|response to toxic substance (GO:0009636)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	carbonyl reductase (NADPH) activity (GO:0004090)			endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00659)		GGCGGCTGCGTAGCTGTGGTC	0.602													c|||	572	0.114217	0.4153	0.0303	5008	,	,		17144	0.0		0.002	False		,,,				2504	0.0				p.V292A		Atlas-SNP	.											.	DHRS2	78	.	0			c.T875C						PASS	.		,ALA/VAL	1524,2882	480.3+/-358.8	279,966,958	61.0	62.0	61.0		,875	-2.1	0.0	14	dbSNP_116	61	19,8581	12.6+/-44.7	0,19,4281	yes	utr-3,missense	DHRS2	NM_005794.3,NM_182908.4	,64	279,985,5239	CC,CT,TT		0.2209,34.5892,11.8638	,benign	,292/301	24114483	1543,11463	2203	4300	6503	SO:0001624	3_prime_UTR_variant	10202	exon9			GCTGCGTAGCTGT		CCDS9604.1, CCDS41927.1	14q11.2	2011-09-14			ENSG00000100867	ENSG00000100867		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	18349	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 1"""	615194				7556196, 11944995, 16685466, 19027726	Standard	NM_182908		Approved	HEP27, SDR25C1	uc001wkt.4	Q13268	OTTHUMG00000028771	ENST00000250383.6:c.*21T>C	14.37:g.24114483T>C		64.0	0.0	0		74.0	41.0	0.554054	NM_182908	D3DS54|Q53GS4|Q7Z789|Q9H2R2	Missense_Mutation	SNP	ENST00000250383.6	37	CCDS9604.1	198	0.09065934065934066	183	0.3719512195121951	14	0.03867403314917127	0	0.0	1	0.0013192612137203166	t	0.018	-1.479180	0.01035	0.345892	0.002209	ENSG00000100867	ENST00000344777	D	0.82984	-1.67	2.22	-2.14	0.07123	.	2.958940	0.01651	N	0.024553	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.22068	-1.0227	8	0.87932	D	0	.	0.3421	0.00335	0.2015:0.3173:0.1984:0.2828	rs7156794;rs60193895	270	Q13268-2	.	A	292	ENSP00000344674:V292A	ENSP00000344674:V292A	V	+	2	0	DHRS2	23184323	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.227000	0.09126	-0.620000	0.05641	-0.251000	0.11542	GTA	T|0.941;C|0.059	0.059	strong		0.602	DHRS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000071842.2	NM_182908	
RBM42	79171	hgsc.bcm.edu	37	19	36124822	36124822	+	Silent	SNP	C	C	A	rs147020112	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36124822C>A	ENST00000262633.4	+	7	1023	c.918C>A	c.(916-918)cgC>cgA	p.R306R	RBM42_ENST00000592202.1_Silent_p.R252R|RBM42_ENST00000360475.4_Silent_p.R277R|RBM42_ENST00000589559.1_Silent_p.R277R|RBM42_ENST00000589871.1_Silent_p.R284R|RBM42_ENST00000588161.1_Silent_p.R276R|RBM42_ENST00000586618.1_Intron	NM_024321.3	NP_077297.2	Q9BTD8	RBM42_HUMAN	RNA binding motif protein 42	306	Necessary for interaction with HNRNPK. {ECO:0000250}.|Pro-rich.					cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|large_intestine(7)|lung(9)|prostate(1)	21	all_lung(56;1.58e-07)|Lung NSC(56;2.43e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			AGGTCGTCCGCGGCCTCCTGC	0.731													C|||	79	0.0157748	0.0598	0.0	5008	,	,		14671	0.0		0.0	False		,,,				2504	0.0				p.R306R		Atlas-SNP	.											.	RBM42	40	.	0			c.C918A						PASS	.	C		157,4183		3,151,2016	7.0	9.0	8.0		918	-10.2	0.1	19	dbSNP_134	8	2,8482		0,2,4240	no	coding-synonymous	RBM42	NM_024321.3		3,153,6256	AA,AC,CC		0.0236,3.6175,1.2399		306/481	36124822	159,12665	2170	4242	6412	SO:0001819	synonymous_variant	79171	exon7			CGTCCGCGGCCTC	BC004204	CCDS12468.1	19q13.12	2013-02-12				ENSG00000126254		"""RNA binding motif (RRM) containing"""	28117	protein-coding gene	gene with protein product		613232				12477932	Standard	NM_024321		Approved	MGC10433	uc002oan.3	Q9BTD8		ENST00000262633.4:c.918C>A	19.37:g.36124822C>A		26.0	0.0	0		40.0	18.0	0.45	NM_024321	O00320|Q8N5R7|Q9BU66	Silent	SNP	ENST00000262633.4	37	CCDS12468.1																																																																																			C|0.990;A|0.010	0.010	strong		0.731	RBM42-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459057.2	NM_024321	
SLC35A5	55032	hgsc.bcm.edu	37	3	112292765	112292765	+	Silent	SNP	C	C	T	rs61732187	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:112292765C>T	ENST00000492406.1	+	5	673	c.390C>T	c.(388-390)agC>agT	p.S130S	SLC35A5_ENST00000460713.1_3'UTR	NM_017945.2	NP_060415.1	Q9BS91	S35A5_HUMAN	solute carrier family 35, member A5	130					nucleotide-sugar transport (GO:0015780)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	nucleotide-sugar transmembrane transporter activity (GO:0005338)|sugar:proton symporter activity (GO:0005351)			endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(4)|ovary(1)|skin(1)	11						CAAATTTTAGCATTATAACAA	0.353													C|||	119	0.023762	0.0832	0.013	5008	,	,		18592	0.0		0.0	False		,,,				2504	0.0				p.S130S		Atlas-SNP	.											.	SLC35A5	40	.	0			c.C390T						PASS	.	C		278,4128	156.6+/-189.7	8,262,1933	191.0	205.0	200.0		390	5.9	1.0	3	dbSNP_129	200	0,8600		0,0,4300	no	coding-synonymous	SLC35A5	NM_017945.2		8,262,6233	TT,TC,CC		0.0,6.3096,2.1375		130/425	112292765	278,12728	2203	4300	6503	SO:0001819	synonymous_variant	55032	exon5			TTTTAGCATTATA	AK000737	CCDS2967.1	3q13.13	2013-05-22			ENSG00000138459	ENSG00000138459		"""Solute carriers"""	20792	protein-coding gene	gene with protein product							Standard	NM_017945		Approved	FLJ20730	uc003dze.4	Q9BS91	OTTHUMG00000159263	ENST00000492406.1:c.390C>T	3.37:g.112292765C>T		168.0	0.0	0		183.0	183.0	1	NM_017945	D3DN66|Q69YY6|Q6ZMD6|Q9NWM9	Silent	SNP	ENST00000492406.1	37	CCDS2967.1																																																																																			C|0.976;T|0.024	0.024	strong		0.353	SLC35A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354184.1	NM_017945	
EXD3	54932	hgsc.bcm.edu	37	9	140247103	140247103	+	Missense_Mutation	SNP	C	C	T	rs115998217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:140247103C>T	ENST00000340951.4	-	11	1201	c.1006G>A	c.(1006-1008)Gtg>Atg	p.V336M	EXD3_ENST00000342129.4_Missense_Mutation_p.V16M	NM_017820.3	NP_060290.3	Q9NX53	MUT7B_HUMAN	exonuclease 3'-5' domain containing 3	0										NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(2)	12						CGGAGTTCCACAGCCACCGCA	0.701													C|||	163	0.0325479	0.1142	0.0101	5008	,	,		8184	0.001		0.004	False		,,,				2504	0.0				p.V336M		Atlas-SNP	.											.	EXD3	86	.	0			c.G1006A						PASS	.	C	MET/VAL	259,3395		3,253,1571	5.0	7.0	6.0		1006	-0.7	0.0	9	dbSNP_132	6	35,7739		0,35,3852	yes	missense	EXD3	NM_017820.3	21	3,288,5423	TT,TC,CC		0.4502,7.0881,2.5726	benign	336/877	140247103	294,11134	1827	3887	5714	SO:0001583	missense	54932	exon11			GTTCCACAGCCAC		CCDS48066.1, CCDS75942.1	9q34.3	2009-03-04			ENSG00000187609	ENSG00000187609			26023	protein-coding gene	gene with protein product							Standard	XM_005266093		Approved	LOC54932, FLJ20433, mut-7	uc004cmp.2	Q8N9H8	OTTHUMG00000156149	ENST00000340951.4:c.1006G>A	9.37:g.140247103C>T	ENSP00000340474:p.Val336Met	47.0	0.0	0		78.0	29.0	0.371795	NM_017820	Q6P1M1|Q8IXT8	Missense_Mutation	SNP	ENST00000340951.4	37	CCDS48066.1	84	0.038461538461538464	78	0.15853658536585366	3	0.008287292817679558	0	0.0	3	0.00395778364116095	C	10.88	1.476873	0.26511	0.070881	0.004502	ENSG00000187609	ENST00000342129;ENST00000340951	T;T	0.64085	-0.08;0.68	3.69	-0.678	0.11353	.	0.954002	0.08598	N	0.921938	T	0.00210	0.0006	N	0.22421	0.69	0.80722	P	0.0	P;P	0.46327	0.876;0.831	B;B	0.41036	0.346;0.254	T	0.01848	-1.1261	9	0.54805	T	0.06	.	4.8317	0.13443	0.0:0.5455:0.1562:0.2983	.	16;336	Q8N9H8-3;Q8N9H8	.;MUT7_HUMAN	M	16;336	ENSP00000343705:V16M;ENSP00000340474:V336M	ENSP00000340474:V336M	V	-	1	0	EXD3	139366924	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.999000	0.03697	-0.415000	0.07484	-0.494000	0.04653	GTG	C|0.960;T|0.040	0.040	strong		0.701	EXD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343182.1	NM_017820	
FKBP11	51303	hgsc.bcm.edu	37	12	49315821	49315821	+	Silent	SNP	T	T	C	rs148302547	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:49315821T>C	ENST00000550765.1	-	6	950	c.552A>G	c.(550-552)aaA>aaG	p.K184K	FKBP11_ENST00000444214.2_Silent_p.K82K|RP11-302B13.5_ENST00000398092.4_Intron|CCDC65_ENST00000266984.5_Intron|AC073610.5_ENST00000537495.1_3'UTR	NM_016594.2	NP_057678.1	Q9NYL4	FKB11_HUMAN	FK506 binding protein 11, 19 kDa	184					chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			kidney(1)|large_intestine(3)|lung(1)	5						TTTTGGAGACTTTGGGTCTAT	0.403													T|||	8	0.00159744	0.0053	0.0014	5008	,	,		18104	0.0		0.0	False		,,,				2504	0.0				p.K184K		Atlas-SNP	.											FKBP11,colon,carcinoma,-1,1	FKBP11	12	1	0			c.A552G						PASS	.	T	,	15,4391	15.5+/-35.6	0,15,2188	90.0	91.0	91.0		246,552	4.7	1.0	12	dbSNP_134	91	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous	FKBP11	NM_001143781.1,NM_016594.2	,	0,16,6487	CC,CT,TT		0.0116,0.3404,0.123	,	82/100,184/202	49315821	16,12990	2203	4300	6503	SO:0001819	synonymous_variant	51303	exon6			GGAGACTTTGGGT	AF238079	CCDS8773.1, CCDS44870.1, CCDS44871.1	12q13.12	2008-08-04	2002-08-29			ENSG00000134285			18624	protein-coding gene	gene with protein product		610571	"""FK506 binding protein 11 (19 kDa)"""			12036304, 16596453	Standard	NM_016594		Approved	FKBP19	uc001rsp.3	Q9NYL4		ENST00000550765.1:c.552A>G	12.37:g.49315821T>C		75.0	0.0	0		60.0	29.0	0.483333	NM_016594	B4DWB7	Silent	SNP	ENST00000550765.1	37	CCDS8773.1																																																																																			T|0.999;C|0.001	0.001	strong		0.403	FKBP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408927.1	NM_016594	
TNFRSF10C	8794	hgsc.bcm.edu	37	8	22960654	22960654	+	Missense_Mutation	SNP	C	C	T	rs10107826|rs374790272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:22960654C>T	ENST00000356864.3	+	1	552	c.20C>T	c.(19-21)aCc>aTc	p.T7I	TNFRSF10C_ENST00000397703.2_Missense_Mutation_p.T47I|TNFRSF10C_ENST00000520607.1_Intron|TNFRSF10C_ENST00000540813.1_5'UTR	NM_003841.3	NP_003832	O14798	TR10C_HUMAN	tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain	7					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)			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)		ATCCCCAAGACCCTAAAGTTC	0.711													C|||	208	0.0415335	0.149	0.0101	5008	,	,		14783	0.0		0.004	False		,,,				2504	0.0				p.T7I		Atlas-SNP	.											.	TNFRSF10C	30	.	0			c.C20T						PASS	.	C	ILE/THR	443,3961	170.9+/-201.2	25,393,1784	79.0	59.0	66.0		20	0.6	0.0	8	dbSNP_119	66	12,8584	5.7+/-21.5	0,12,4286	yes	missense	TNFRSF10C	NM_003841.3	89	25,405,6070	TT,TC,CC		0.1396,10.059,3.5	probably-damaging	7/260	22960654	455,12545	2202	4298	6500	SO:0001583	missense	8794	exon1			CCAAGACCCTAAA	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.20C>T	8.37:g.22960654C>T	ENSP00000349324:p.Thr7Ile	75.0	0.0	0		82.0	40.0	0.487805	NM_003841	O14755|Q08AS6|Q6FH98|Q6UXM5	Missense_Mutation	SNP	ENST00000356864.3	37	CCDS6037.1	56	0.02564102564102564	50	0.1016260162601626	4	0.011049723756906077	0	0.0	2	0.002638522427440633	C	4.995	0.184796	0.09495	0.10059	0.001396	ENSG00000173535	ENST00000397703;ENST00000356864;ENST00000544885	T	0.62364	0.03	1.76	0.639	0.17747	.	2.630870	0.02547	U	0.095275	T	0.01627	0.0052	N	0.19112	0.55	0.52099	P	5.100000000002325E-5	B	0.21225	0.053	B	0.06405	0.002	T	0.08186	-1.0734	9	0.52906	T	0.07	.	4.4054	0.11407	0.0:0.717:0.0:0.283	rs10107826;rs10107826	7	O14798	TR10C_HUMAN	I	47;7;7	ENSP00000349324:T7I	ENSP00000349324:T7I	T	+	2	0	TNFRSF10C	23016599	0.000000	0.05858	0.001000	0.08648	0.053000	0.15095	-0.737000	0.04877	-0.010000	0.14271	0.205000	0.17691	ACC	C|0.958;T|0.042	0.042	strong		0.711	TNFRSF10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215134.3		
TMC3	342125	hgsc.bcm.edu	37	15	81625028	81625028	+	Missense_Mutation	SNP	C	C	T	rs8031046	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:81625028C>T	ENST00000359440.5	-	22	3170	c.3035G>A	c.(3034-3036)aGa>aAa	p.R1012K	RP11-761I4.3_ENST00000560851.1_RNA|TMC3_ENST00000558726.1_Missense_Mutation_p.R1013K|RP11-761I4.3_ENST00000560973.1_RNA|RP11-761I4.3_ENST00000559781.1_RNA	NM_001080532.1	NP_001074001.1			transmembrane channel-like 3											autonomic_ganglia(2)|breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	34						TCGTGGCTTTCTGGGCACATA	0.582													T|||	836	0.166933	0.4728	0.062	5008	,	,		16882	0.0952		0.0517	False		,,,				2504	0.0204				p.R1012K		Atlas-SNP	.											.	TMC3	112	.	0			c.G3035A						PASS	.	T	LYS/ARG	1592,2362		345,902,730	35.0	40.0	39.0		3035	-9.0	0.0	15	dbSNP_116	39	440,7886		12,416,3735	yes	missense	TMC3	NM_001080532.1	26	357,1318,4465	TT,TC,CC		5.2847,40.263,16.5472	benign	1012/1101	81625028	2032,10248	1977	4163	6140	SO:0001583	missense	342125	exon22			GGCTTTCTGGGCA	AY263163	CCDS45324.1	15q24.3	2006-11-24				ENSG00000188869			22995	protein-coding gene	gene with protein product						12906855, 12812529	Standard	NM_001080532		Approved		uc021ssk.1	Q7Z5M5		ENST00000359440.5:c.3035G>A	15.37:g.81625028C>T	ENSP00000352413:p.Arg1012Lys	158.0	0.0	0		168.0	93.0	0.553571	NM_001080532		Missense_Mutation	SNP	ENST00000359440.5	37	CCDS45324.1	363	0.1662087912087912	240	0.4878048780487805	25	0.06906077348066299	61	0.10664335664335664	37	0.048812664907651716	T	4.161	0.028403	0.08054	0.40263	0.052847	ENSG00000188869	ENST00000359440	T	0.62232	0.04	5.42	-9.03	0.00737	.	0.406919	0.19362	N	0.116103	T	0.00012	0.0000	N	0.01742	-0.745	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.31916	-0.9926	9	0.02654	T	1	-0.4035	21.2883	0.99950	0.0:0.656:0.0:0.344	rs8031046;rs52825478;rs59441739;rs8031046	1012	Q7Z5M5	TMC3_HUMAN	K	1012	ENSP00000352413:R1012K	ENSP00000352413:R1012K	R	-	2	0	TMC3	79412083	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-0.956000	0.03865	-2.591000	0.00456	-1.213000	0.01624	AGA	C|0.811;T|0.189	0.189	strong		0.582	TMC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417795.3	NM_181841	
TMPRSS11B	132724	hgsc.bcm.edu	37	4	69100200	69100200	+	Silent	SNP	A	A	G	rs4431295	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:69100200A>G	ENST00000332644.5	-	5	611	c.450T>C	c.(448-450)ccT>ccC	p.P150P		NM_182502.3	NP_872308.2	Q86T26	TM11B_HUMAN	transmembrane protease, serine 11B	150	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.					extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|skin(1)	27						TAATGGAAGCAGGAACTGCAT	0.328													G|||	141	0.028155	0.1006	0.0086	5008	,	,		17100	0.0		0.0	False		,,,				2504	0.002				p.P150P		Atlas-SNP	.											.	TMPRSS11B	66	.	0			c.T450C						PASS	.	G		351,4055	794.2+/-415.3	20,311,1872	108.0	104.0	106.0		450	-8.9	0.0	4	dbSNP_111	106	14,8586	818.7+/-406.8	0,14,4286	no	coding-synonymous	TMPRSS11B	NM_182502.3		20,325,6158	GG,GA,AA		0.1628,7.9664,2.8064		150/417	69100200	365,12641	2203	4300	6503	SO:0001819	synonymous_variant	132724	exon5			GGAAGCAGGAACT	BX537945	CCDS3521.1	4q13.2	2010-04-13			ENSG00000185873	ENSG00000185873		"""Serine peptidases / Transmembrane"""	25398	protein-coding gene	gene with protein product							Standard	NM_182502		Approved		uc003hdw.4	Q86T26	OTTHUMG00000129301	ENST00000332644.5:c.450T>C	4.37:g.69100200A>G		83.0	0.0	0		108.0	56.0	0.518519	NM_182502	A8K4D9	Silent	SNP	ENST00000332644.5	37	CCDS3521.1																																																																																			A|0.970;G|0.030	0.030	strong		0.328	TMPRSS11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251431.2	NM_182502	
DCANP1	140947	hgsc.bcm.edu	37	5	134782443	134782443	+	Missense_Mutation	SNP	T	T	C	rs113429044	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:134782443T>C	ENST00000503143.2	-	1	595	c.356A>G	c.(355-357)aAg>aGg	p.K119R	TIFAB_ENST00000537858.1_3'UTR	NM_130848.2	NP_570900.1	Q8TF63	DCNP1_HUMAN		119						nucleus (GO:0005634)				endometrium(1)|lung(1)|prostate(1)	3			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			CTGGCCTGTCTTCCTTCTGCT	0.547													T|||	452	0.0902556	0.3033	0.0418	5008	,	,		19866	0.0		0.0179	False		,,,				2504	0.0041				p.K119R		Atlas-SNP	.											.	C5orf20	16	.	0			c.A356G						PASS	.	T	ARG/LYS	1160,3246	410.9+/-335.5	154,852,1197	112.0	120.0	117.0		356	0.2	0.0	5	dbSNP_132	117	119,8481	61.7+/-123.6	1,117,4182	yes	missense	C5orf20	NM_130848.2	26	155,969,5379	CC,CT,TT		1.3837,26.3277,9.8339	benign	119/245	134782443	1279,11727	2203	4300	6503	SO:0001583	missense	140947	exon1			CCTGTCTTCCTTC																												ENST00000503143.2:c.356A>G	5.37:g.134782443T>C	ENSP00000421871:p.Lys119Arg	83.0	0.0	0		83.0	37.0	0.445783	NM_130848		Missense_Mutation	SNP	ENST00000503143.2	37	CCDS4186.1	170	0.07783882783882784	139	0.28252032520325204	14	0.03867403314917127	0	0.0	17	0.022427440633245383	T	5.813	0.334340	0.11013	0.263277	0.013837	ENSG00000251380	ENST00000503143	T	0.37915	1.17	2.78	0.236	0.15471	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.58432	P	5.000000000032756E-6	B	0.16603	0.018	B	0.08055	0.003	T	0.36089	-0.9762	8	0.87932	D	0	.	3.1238	0.06400	0.5045:0.2511:0.0:0.2444	.	119	Q8TF63	DCNP1_HUMAN	R	119	ENSP00000421871:K119R	ENSP00000421871:K119R	K	-	2	0	C5orf20	134810342	0.000000	0.05858	0.013000	0.15412	0.047000	0.14425	-0.373000	0.07494	0.043000	0.15746	-0.669000	0.03829	AAG	T|0.902;C|0.098	0.098	strong		0.547	C5orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372531.1		
WDR93	56964	hgsc.bcm.edu	37	15	90274756	90274756	+	Silent	SNP	C	C	T	rs35502270	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90274756C>T	ENST00000268130.7	+	12	1394	c.1293C>T	c.(1291-1293)tgC>tgT	p.C431C	WDR93_ENST00000560294.1_Silent_p.C431C|WDR93_ENST00000444934.2_Silent_p.C148C	NM_020212.1	NP_064597.1	Q6P2C0	WDR93_HUMAN	WD repeat domain 93	431					electron transport chain (GO:0022900)		oxidoreductase activity, acting on NAD(P)H (GO:0016651)			NS(1)|breast(3)|endometrium(2)|kidney(4)|large_intestine(5)|liver(2)|lung(8)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	33	Lung NSC(78;0.0237)|all_lung(78;0.0478)		KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|BRCA - Breast invasive adenocarcinoma(143;0.128)			TGCTGGCCTGCGAGGATGGTG	0.617													C|||	134	0.0267572	0.0998	0.0029	5008	,	,		18890	0.0		0.0	False		,,,				2504	0.0				p.C431C		Atlas-SNP	.											.	WDR93	63	.	0			c.C1293T						PASS	.	C		363,4037	184.7+/-212.0	14,335,1851	208.0	181.0	190.0		1293	-4.6	0.9	15	dbSNP_126	190	3,8595	3.0+/-9.4	0,3,4296	no	coding-synonymous	WDR93	NM_020212.1		14,338,6147	TT,TC,CC		0.0349,8.25,2.8158		431/687	90274756	366,12632	2200	4299	6499	SO:0001819	synonymous_variant	56964	exon12			GGCCTGCGAGGAT		CCDS32326.1, CCDS66862.1, CCDS73779.1	15q26.1	2012-11-02						"""WD repeat domain containing"""	26924	protein-coding gene	gene with protein product							Standard	NM_020212		Approved		uc002boj.3	Q6P2C0		ENST00000268130.7:c.1293C>T	15.37:g.90274756C>T		131.0	0.0	0		147.0	72.0	0.489796	NM_020212	Q8N7Y8|Q9NP89	Silent	SNP	ENST00000268130.7	37	CCDS32326.1																																																																																			C|0.973;T|0.027	0.027	strong		0.617	WDR93-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416369.1	NM_020212	
REEP6	92840	hgsc.bcm.edu	37	19	1495327	1495327	+	Silent	SNP	C	C	T	rs79574672	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1495327C>T	ENST00000233596.3	+	2	254	c.150C>T	c.(148-150)ttC>ttT	p.F50F		NM_138393.1	NP_612402.1	Q96HR9	REEP6_HUMAN	receptor accessory protein 6	50					regulation of intracellular transport (GO:0032386)	apical part of cell (GO:0045177)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				lung(1)|ovary(1)	2		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		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)		ATCTGCTGTTCGGCTACGGAG	0.657													C|||	120	0.0239617	0.09	0.0014	5008	,	,		18573	0.0		0.0	False		,,,				2504	0.0				p.F50F		Atlas-SNP	.											REEP6_ENST00000395484,NS,carcinoma,-2,1	REEP6	21	1	0			c.C150T						PASS	.	C		322,4080	171.2+/-201.5	7,308,1886	114.0	100.0	105.0		150	1.9	1.0	19	dbSNP_131	105	0,8598		0,0,4299	no	coding-synonymous	REEP6	NM_138393.1		7,308,6185	TT,TC,CC		0.0,7.3149,2.4769		50/185	1495327	322,12678	2201	4299	6500	SO:0001819	synonymous_variant	92840	exon2			GCTGTTCGGCTAC	BC008201	CCDS12070.1	19p13.3	2012-12-20	2006-02-08	2006-02-07	ENSG00000115255	ENSG00000115255		"""Receptor accessory proteins"""	30078	protein-coding gene	gene with protein product	"""polyposis locus protein 1-like 1"", ""deleted in polyposis 1-like 1"""	609346	"""chromosome 19 open reading frame 32"""	C19orf32		16271481, 15550249	Standard	NM_138393		Approved	DP1L1, FLJ25383	uc002ltc.3	Q96HR9	OTTHUMG00000180072	ENST00000233596.3:c.150C>T	19.37:g.1495327C>T		169.0	0.0	0		182.0	85.0	0.467033	NM_138393	B2RE01|D6W5Z0|Q96LM0	Silent	SNP	ENST00000233596.3	37	CCDS12070.1	51	0.023351648351648352	51	0.10365853658536585	0	0.0	0	0.0	0	0.0	C	12.63	1.996371	0.35226	0.073149	0.0	ENSG00000115255	ENST00000395484	.	.	.	4.61	1.93	0.25924	.	.	.	.	.	T	0.03783	0.0107	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.11299	-1.0593	5	0.87932	D	0	-9.0609	8.2387	0.31645	0.0:0.6717:0.0:0.3283	.	.	.	.	W	118	.	ENSP00000378865:R118W	R	+	1	2	REEP6	1446327	0.890000	0.30428	0.982000	0.44146	0.017000	0.09413	-0.058000	0.11750	0.846000	0.35142	-0.354000	0.07668	CGG	C|0.974;T|0.026	0.026	strong		0.657	REEP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449623.1	NM_138393	
CD83	9308	hgsc.bcm.edu	37	6	14135394	14135394	+	Missense_Mutation	SNP	G	G	A	rs2230193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:14135394G>A	ENST00000379153.3	+	5	716	c.545G>A	c.(544-546)cGa>cAa	p.R182Q		NM_001040280.1|NM_001251901.1|NM_004233.3	NP_001035370.1|NP_001238830.1|NP_004224.1	Q01151	CD83_HUMAN	CD83 molecule	182			R -> Q (in dbSNP:rs2230193).		defense response (GO:0006952)|humoral immune response (GO:0006959)|negative regulation of interleukin-4 production (GO:0032713)|positive regulation of CD4-positive, alpha-beta T cell differentiation (GO:0043372)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-2 production (GO:0032743)|response to organic cyclic compound (GO:0014070)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(1)	12	Breast(50;0.00245)|Ovarian(93;0.137)	all_hematologic(90;0.117)				GGCATGGAACGAGCTTTTCTC	0.403													.|||	74	0.0147764	0.0545	0.0014	5008	,	,		21026	0.0		0.0	False		,,,				2504	0.001				p.R182Q		Atlas-SNP	.											.	CD83	23	.	0			c.G545A						PASS	.	G	GLN/ARG,GLN/ARG	202,4204	126.1+/-163.2	4,194,2005	103.0	105.0	104.0		542,545	-4.0	0.0	6	dbSNP_98	104	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense	CD83	NM_001040280.1,NM_004233.3	43,43	4,200,6299	AA,AG,GG		0.0698,4.5847,1.5993	benign,benign	181/205,182/206	14135394	208,12798	2203	4300	6503	SO:0001583	missense	9308	exon5			TGGAACGAGCTTT	Z11697	CCDS4532.1, CCDS75403.1	6p23	2013-01-11	2006-03-31		ENSG00000112149	ENSG00000112149		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1703	protein-coding gene	gene with protein product		604534	"""CD83 antigen (activated B lymphocytes, immunoglobulin superfamily)"", ""CD83 molecule """			1378080, 8422464	Standard	NM_001251901		Approved	HB15, BL11	uc003nbi.3	Q01151	OTTHUMG00000014283	ENST00000379153.3:c.545G>A	6.37:g.14135394G>A	ENSP00000368450:p.Arg182Gln	104.0	0.0	0		106.0	48.0	0.45283	NM_004233	Q5THX9	Missense_Mutation	SNP	ENST00000379153.3	37	CCDS4532.1	23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	G	9.394	1.076332	0.20227	0.045847	6.98E-4	ENSG00000112149	ENST00000379153	T	0.48201	0.82	5.0	-3.99	0.04069	.	1.449440	0.04161	N	0.322989	T	0.09862	0.0242	N	0.17082	0.46	0.09310	N	1	B	0.21147	0.052	B	0.10450	0.005	T	0.10200	-1.0640	10	0.25106	T	0.35	-23.8615	5.7782	0.18292	0.4997:0.2613:0.239:0.0	rs2230193;rs16874698;rs52804483;rs16874698	182	Q01151	CD83_HUMAN	Q	182	ENSP00000368450:R182Q	ENSP00000368450:R182Q	R	+	2	0	CD83	14243373	0.210000	0.23517	0.017000	0.16124	0.481000	0.33189	0.050000	0.14120	-0.988000	0.03489	-0.150000	0.13652	CGA	G|0.982;A|0.018	0.018	strong		0.403	CD83-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039916.1		
SGK223	157285	hgsc.bcm.edu	37	8	8176051	8176051	+	Silent	SNP	G	G	A	rs114220337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:8176051G>A	ENST00000520004.1	-	6	4098	c.3834C>T	c.(3832-3834)taC>taT	p.Y1278Y	SGK223_ENST00000330777.4_Silent_p.Y1278Y			Q86YV5	SG223_HUMAN		1282	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.						ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										CCTCCTGCCGGTAGTCTCTCT	0.647													G|||	123	0.0245607	0.0885	0.0072	5008	,	,		10988	0.0		0.001	False		,,,				2504	0.0				p.Y1278Y	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											SgK223,caecum,carcinoma,0,2	.	.	2	0			c.C3834T						PASS	.	G		299,3693		13,273,1710	16.0	21.0	19.0		3834	2.7	1.0	8	dbSNP_132	19	0,8286		0,0,4143	no	coding-synonymous	SGK223	NM_001080826.1		13,273,5853	AA,AG,GG		0.0,7.49,2.4353		1278/1403	8176051	299,11979	1996	4143	6139	SO:0001819	synonymous_variant	0	exon5			CTGCCGGTAGTCT																												ENST00000520004.1:c.3834C>T	8.37:g.8176051G>A		44.0	0.0	0		44.0	27.0	0.613636	NM_001080826	Q8N3N5	Silent	SNP	ENST00000520004.1	37	CCDS43706.1																																																																																			G|0.980;A|0.020	0.020	strong		0.647	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
EPB41L4B	54566	hgsc.bcm.edu	37	9	112017883	112017883	+	Silent	SNP	A	A	G	rs73529389	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:112017883A>G	ENST00000374566.3	-	11	1594	c.1077T>C	c.(1075-1077)gtT>gtC	p.V359V	EPB41L4B_ENST00000374557.4_Silent_p.V359V	NM_019114.3	NP_061987.3	Q9H329	E41LB_HUMAN	erythrocyte membrane protein band 4.1 like 4B	359	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actomyosin structure organization (GO:0031032)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)	structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CGTGGTGCTCAACTGCACACT	0.532													G|||	30	0.00599042	0.0219	0.0014	5008	,	,		20496	0.0		0.0	False		,,,				2504	0.0				p.V359V		Atlas-SNP	.											.	EPB41L4B	111	.	0			c.T1077C						PASS	.	G	,	79,3947		0,79,1934	131.0	125.0	127.0		1077,1077	-11.6	0.0	9	dbSNP_130	127	0,8322		0,0,4161	no	coding-synonymous,coding-synonymous	EPB41L4B	NM_018424.2,NM_019114.3	,	0,79,6095	GG,GA,AA		0.0,1.9622,0.6398	,	359/519,359/901	112017883	79,12269	2013	4161	6174	SO:0001819	synonymous_variant	54566	exon11			GTGCTCAACTGCA	AB032179	CCDS43859.1, CCDS43860.1	9q22.1-q22.3	2008-02-05			ENSG00000095203	ENSG00000095203			19818	protein-coding gene	gene with protein product		610340				10783258	Standard	NM_018424		Approved	EHM2	uc004bdz.1	Q9H329	OTTHUMG00000020470	ENST00000374566.3:c.1077T>C	9.37:g.112017883A>G		107.0	0.0	0		116.0	34.0	0.293103	NM_019114	Q5T4G5|Q5T4G6|Q9H328|Q9P2V3	Silent	SNP	ENST00000374566.3	37	CCDS43859.1																																																																																			A|0.997;G|0.003	0.003	strong		0.532	EPB41L4B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053592.1	NM_018424	
COL1A2	1278	hgsc.bcm.edu	37	7	94057007	94057007	+	Silent	SNP	C	C	T	rs34691365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:94057007C>T	ENST00000297268.6	+	49	3807	c.3336C>T	c.(3334-3336)taC>taT	p.Y1112Y		NM_000089.3	NP_000080.2	P08123	CO1A2_HUMAN	collagen, type I, alpha 2	1112					blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|leukocyte migration (GO:0050900)|odontogenesis (GO:0042476)|platelet activation (GO:0030168)|protein heterotrimerization (GO:0070208)|regulation of blood pressure (GO:0008217)|Rho protein signal transduction (GO:0007266)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|transforming growth factor beta receptor signaling pathway (GO:0007179)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)|protein binding, bridging (GO:0030674)		COL1A2/PLAG1(3)	NS(2)|breast(2)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(21)|lung(51)|ovary(2)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	115	all_cancers(62;2.46e-09)|all_epithelial(64;2.7e-08)		STAD - Stomach adenocarcinoma(171;0.0031)		Collagenase(DB00048)	ACTTTGGTTACGATGGAGACT	0.547										HNSCC(75;0.22)			C|||	27	0.00539137	0.0197	0.0	5008	,	,		18009	0.0		0.001	False		,,,				2504	0.0				p.Y1112Y		Atlas-SNP	.											.	COL1A2	240	.	0			c.C3336T						PASS	.	C		58,4348	56.2+/-92.4	1,56,2146	96.0	97.0	97.0		3336	-4.7	0.1	7	dbSNP_126	97	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	COL1A2	NM_000089.3		1,57,6445	TT,TC,CC		0.0116,1.3164,0.4536		1112/1367	94057007	59,12947	2203	4300	6503	SO:0001819	synonymous_variant	1278	exon49			TGGTTACGATGGA	Z74616	CCDS34682.1	7q21.3	2014-09-17	2002-02-13		ENSG00000164692	ENSG00000164692		"""Collagens"""	2198	protein-coding gene	gene with protein product	"""alpha 2(I)-collagen"", ""alpha-2 collagen type I"", ""type I procollagen"", ""collagen I, alpha-2 polypeptide"", ""collagen of skin, tendon and bone, alpha-2 chain"""	120160	"""osteogenesis imperfecta type IV"""	OI4		3857213, 2897363	Standard	NM_000089		Approved		uc003ung.1	P08123	OTTHUMG00000148675	ENST00000297268.6:c.3336C>T	7.37:g.94057007C>T		106.0	0.0	0		132.0	67.0	0.507576	NM_000089	P02464|Q13897|Q13997|Q13998|Q14038|Q14057|Q15177|Q15947|Q16480|Q16511|Q7Z5S6|Q9UEB6|Q9UEF9|Q9UM83|Q9UMI1|Q9UML5|Q9UMM6|Q9UPH0	Silent	SNP	ENST00000297268.6	37	CCDS34682.1																																																																																			C|0.995;T|0.005	0.005	strong		0.547	COL1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309045.2	NM_000089	
AHNAK	79026	hgsc.bcm.edu	37	11	62295149	62295149	+	Missense_Mutation	SNP	T	T	G	rs61524789	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:62295149T>G	ENST00000378024.4	-	5	7014	c.6740A>C	c.(6739-6741)aAa>aCa	p.K2247T	AHNAK_ENST00000530124.1_Intron|AHNAK_ENST00000257247.7_Intron	NM_001620.1	NP_001611.1	Q09666	AHNK_HUMAN	AHNAK nucleoprotein	2247			K -> T (in dbSNP:rs61524789).		protein oligomerization (GO:0051259)|regulation of RNA splicing (GO:0043484)|regulation of voltage-gated calcium channel activity (GO:1901385)	actin cytoskeleton (GO:0015629)|cell-cell contact zone (GO:0044291)|costamere (GO:0043034)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|vesicle (GO:0031982)	poly(A) RNA binding (GO:0044822)|S100 protein binding (GO:0044548)|structural molecule activity conferring elasticity (GO:0097493)			NS(3)|autonomic_ganglia(1)|breast(10)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(33)|large_intestine(40)|liver(1)|lung(108)|ovary(13)|pancreas(4)|prostate(5)|skin(16)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	268		Melanoma(852;0.155)				CTTGGGCATTTTCATCTTAGG	0.522													T|||	148	0.0295527	0.1051	0.0101	5008	,	,		20293	0.0		0.002	False		,,,				2504	0.0				p.K2247T		Atlas-SNP	.											.	AHNAK	532	.	0			c.A6740C						PASS	.	T	THR/LYS,	378,4026	192.6+/-218.0	16,346,1840	305.0	305.0	305.0		6740,	3.4	1.0	11	dbSNP_129	305	3,8595	2.2+/-6.3	0,3,4296	no	missense,intron	AHNAK	NM_001620.1,NM_024060.2	78,	16,349,6136	GG,GT,TT		0.0349,8.5831,2.9303	probably-damaging,	2247/5891,	62295149	381,12621	2202	4299	6501	SO:0001583	missense	79026	exon5			GGCATTTTCATCT	M80899	CCDS31584.1, CCDS44625.1	11q12-q13	2008-02-05	2007-03-30		ENSG00000124942	ENSG00000124942			347	protein-coding gene	gene with protein product	"""desmoyokin"""	103390	"""AHNAK nucleoprotein (desmoyokin)"""			7987395, 12153988	Standard	NM_024060		Approved	MGC5395	uc001ntl.3	Q09666	OTTHUMG00000167558	ENST00000378024.4:c.6740A>C	11.37:g.62295149T>G	ENSP00000367263:p.Lys2247Thr	210.0	0.0	0		274.0	131.0	0.478102	NM_001620	A1A586	Missense_Mutation	SNP	ENST00000378024.4	37	CCDS31584.1	73	0.033424908424908424	68	0.13821138211382114	3	0.008287292817679558	0	0.0	2	0.002638522427440633	T	16.14	3.038892	0.55003	0.085831	3.49E-4	ENSG00000124942	ENST00000244934;ENST00000378024	T	0.12147	2.71	3.38	3.38	0.38709	.	0.000000	0.39083	U	0.001465	T	0.00440	0.0014	H	0.95470	3.675	0.44660	D	0.997647	D	0.69078	0.997	D	0.77557	0.99	T	0.01743	-1.1283	10	0.62326	D	0.03	.	12.0108	0.53286	0.0:0.0:0.0:1.0	rs61524789	2247	Q09666	AHNK_HUMAN	T	336;2247	ENSP00000367263:K2247T	ENSP00000244934:K336T	K	-	2	0	AHNAK	62051725	1.000000	0.71417	0.997000	0.53966	0.777000	0.43975	5.886000	0.69743	1.546000	0.49388	0.242000	0.17961	AAA	T|0.965;G|0.035	0.035	strong		0.522	AHNAK-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395572.1	NM_024060	
FKBPL	63943	hgsc.bcm.edu	37	6	32096528	32096528	+	Silent	SNP	G	G	A	rs61747172	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32096528G>A	ENST00000375156.3	-	2	1300	c.1030C>T	c.(1030-1032)Ctg>Ttg	p.L344L	ATF6B_ENST00000468502.1_5'Flank|ATF6B_ENST00000375203.3_5'Flank|ATF6B_ENST00000375201.4_5'Flank	NM_022110.3	NP_071393.2	Q9UIM3	FKBPL_HUMAN	FK506 binding protein like	344					chaperone-mediated protein folding (GO:0061077)|protein peptidyl-prolyl isomerization (GO:0000413)|response to radiation (GO:0009314)	endoplasmic reticulum membrane (GO:0005789)	FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)										ATCTTGCGCAGACCCTGAGCC	0.537													G|||	10	0.00199681	0.0068	0.0014	5008	,	,		19239	0.0		0.0	False		,,,				2504	0.0				p.L344L		Atlas-SNP	.											.	FKBPL	25	.	0			c.C1030T						PASS	.	G		14,4392	21.2+/-45.6	0,14,2189	191.0	203.0	199.0		1030	3.1	0.9	6	dbSNP_129	199	0,8600		0,0,4300	no	coding-synonymous	FKBPL	NM_022110.3		0,14,6489	AA,AG,GG		0.0,0.3177,0.1076		344/350	32096528	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	63943	exon2			TGCGCAGACCCTG	AF139374	CCDS4738.1	6p21.3	2013-12-13	2001-11-28		ENSG00000204315	ENSG00000204315		"""Tetratricopeptide (TTC) repeat domain containing"""	13949	protein-coding gene	gene with protein product	"""WAF-1/CIP1 stabilizing protein 39"""		"""FK506-binding protein like"""			9056895	Standard	NM_022110		Approved	DIR1, NG7, WISp39	uc003nzr.3	Q9UIM3	OTTHUMG00000031129	ENST00000375156.3:c.1030C>T	6.37:g.32096528G>A		144.0	0.0	0		160.0	83.0	0.51875	NM_022110	A8K5V3|B0UYX8|Q9H5G3	Silent	SNP	ENST00000375156.3	37	CCDS4738.1																																																																																			G|0.998;A|0.002	0.002	strong		0.537	FKBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076221.2		
ST3GAL1	6482	hgsc.bcm.edu	37	8	134478178	134478178	+	Silent	SNP	A	A	G	rs112787936	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:134478178A>G	ENST00000319914.5	-	5	1489	c.462T>C	c.(460-462)tcT>tcC	p.S154S	ST3GAL1_ENST00000399640.2_Silent_p.S154S|ST3GAL1_ENST00000521180.1_Silent_p.S154S|ST3GAL1_ENST00000522652.1_Silent_p.S154S			Q11201	SIA4A_HUMAN	ST3 beta-galactoside alpha-2,3-sialyltransferase 1	154					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|N-acetylneuraminate metabolic process (GO:0006054)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein phosphorylation (GO:0006468)|sialylation (GO:0097503)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	beta-galactoside (CMP) alpha-2,3-sialyltransferase activity (GO:0003836)			endometrium(3)|large_intestine(2)|lung(11)|prostate(1)	17	all_epithelial(106;1.53e-23)|Lung NSC(106;3.15e-07)|all_lung(105;1.26e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.00721)			GCCCATAAGAAGACTCCCTCA	0.622													A|||	75	0.014976	0.0552	0.0029	5008	,	,		18246	0.0		0.0	False		,,,				2504	0.0				p.S154S		Atlas-SNP	.											.	ST3GAL1	39	.	0			c.T462C						PASS	.	A	,	201,4205	123.7+/-161.0	5,191,2007	94.0	93.0	93.0		462,462	1.8	0.3	8	dbSNP_132	93	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	ST3GAL1	NM_003033.3,NM_173344.2	,	5,193,6305	GG,GA,AA		0.0233,4.562,1.5608	,	154/341,154/341	134478178	203,12803	2203	4300	6503	SO:0001819	synonymous_variant	6482	exon6			ATAAGAAGACTCC	L29555	CCDS6373.1	8q24.22	2013-03-01	2003-01-14	2005-02-07	ENSG00000008513	ENSG00000008513	2.4.99.4	"""Sialyltransferases"""	10862	protein-coding gene	gene with protein product	"""ST3Gal I"""	607187	"""sialyltransferase 4A (beta-galactosidase alpha-2,3-sialytransferase)"""	SIAT4A		10504389, 7655169	Standard	NM_003033		Approved	ST3O, SIATFL, ST3GalA.1	uc003yuk.2	Q11201	OTTHUMG00000164534	ENST00000319914.5:c.462T>C	8.37:g.134478178A>G		146.0	0.0	0		160.0	82.0	0.5125	NM_173344	O60677|Q9UN51	Silent	SNP	ENST00000319914.5	37	CCDS6373.1																																																																																			A|0.984;G|0.016	0.016	strong		0.622	ST3GAL1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379132.1	NM_003033	
NUP188	23511	hgsc.bcm.edu	37	9	131755891	131755891	+	Silent	SNP	C	C	T	rs17485583	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131755891C>T	ENST00000372577.2	+	27	2956	c.2935C>T	c.(2935-2937)Ctg>Ttg	p.L979L		NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	979					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						GTGCCCACCCCTGCTGCATCG	0.562													C|||	169	0.033746	0.1203	0.0115	5008	,	,		20683	0.0		0.002	False		,,,				2504	0.0				p.L979L		Atlas-SNP	.											.	NUP188	140	.	0			c.C2935T						PASS	.	C		452,3954	218.1+/-236.3	17,418,1768	169.0	137.0	148.0		2935	5.6	1.0	9	dbSNP_123	148	6,8594	3.7+/-12.6	0,6,4294	no	coding-synonymous	NUP188	NM_015354.1		17,424,6062	TT,TC,CC		0.0698,10.2587,3.5215		979/1750	131755891	458,12548	2203	4300	6503	SO:0001819	synonymous_variant	23511	exon27			CCACCCCTGCTGC	D79991	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319			17859	protein-coding gene	gene with protein product		615587	"""KIAA0169"""	KIAA0169		11029043	Standard	NM_015354		Approved		uc004bws.2	Q5SRE5	OTTHUMG00000020768	ENST00000372577.2:c.2935C>T	9.37:g.131755891C>T		234.0	0.0	0		218.0	140.0	0.642202	NM_015354	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Silent	SNP	ENST00000372577.2	37	CCDS35156.1																																																																																			C|0.962;T|0.038	0.038	strong		0.562	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2		
CDYL2	124359	hgsc.bcm.edu	37	16	80642076	80642076	+	Silent	SNP	C	C	T	rs117351184	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:80642076C>T	ENST00000570137.2	-	6	1430	c.1275G>A	c.(1273-1275)agG>agA	p.R425R	CDYL2_ENST00000563890.1_Silent_p.R426R|CDYL2_ENST00000562812.1_Silent_p.R426R|CDYL2_ENST00000566173.1_Silent_p.R426R	NM_152342.2	NP_689555.2	Q8N8U2	CDYL2_HUMAN	chromodomain protein, Y-like 2	425						nucleus (GO:0005634)	catalytic activity (GO:0003824)			breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	21						ACACCAGCCCCCTGCTGCAGG	0.617													C|||	27	0.00539137	0.0	0.0029	5008	,	,		6251	0.0		0.0239	False		,,,				2504	0.001				p.R425R		Atlas-SNP	.											.	CDYL2	66	.	0			c.G1275A						PASS	.	C		15,4385		0,15,2185	36.0	26.0	30.0		1275	-5.3	0.9	16	dbSNP_132	30	120,8478		0,120,4179	no	coding-synonymous	CDYL2	NM_152342.2		0,135,6364	TT,TC,CC		1.3957,0.3409,1.0386		425/507	80642076	135,12863	2200	4299	6499	SO:0001819	synonymous_variant	124359	exon6			CAGCCCCCTGCTG	AK096185	CCDS32493.1	16q23.2	2008-02-05	2003-09-12			ENSG00000166446			23030	protein-coding gene	gene with protein product			"""chromodomain Y-like protein 2"""			12837688	Standard	NM_152342		Approved	FLJ38866	uc002ffs.3	Q8N8U2		ENST00000570137.2:c.1275G>A	16.37:g.80642076C>T		117.0	0.0	0		130.0	59.0	0.453846	NM_152342	Q7Z5I8	Silent	SNP	ENST00000570137.2	37	CCDS32493.1																																																																																			C|0.990;T|0.010	0.010	strong		0.617	CDYL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434727.2	NM_152342	
KRT33B	3884	hgsc.bcm.edu	37	17	39521517	39521517	+	Silent	SNP	C	C	T	rs553149537	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39521517C>T	ENST00000251646.3	-	5	835	c.786G>A	c.(784-786)tcG>tcA	p.S262S		NM_002279.4	NP_002270.1	Q14525	KT33B_HUMAN	keratin 33B	262	Coil 2.|Rod.				aging (GO:0007568)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)	p.S262S(1)		NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(6)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)	21		Breast(137;0.000496)				GCAGCTGCTCCGAGCTGGATA	0.617													C|||	4	0.000798722	0.0008	0.0	5008	,	,		18679	0.0		0.0	False		,,,				2504	0.0031				p.S262S		Atlas-SNP	.											KRT33B,caecum,carcinoma,0,1	KRT33B	46	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G786A						scavenged	.						51.0	51.0	51.0					17																	39521517		2189	4298	6487	SO:0001819	synonymous_variant	3884	exon5			CTGCTCCGAGCTG	X82634	CCDS11389.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000131738	ENSG00000131738		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6451	protein-coding gene	gene with protein product	"""hard keratin type I 3II"""	602762	"""keratin, hair, acidic, 3B"""	KRTHA3B		7565656, 16831889	Standard	NM_002279		Approved	Ha-3II	uc002hwl.4	Q14525	OTTHUMG00000133429	ENST00000251646.3:c.786G>A	17.37:g.39521517C>T		191.0	0.0	0		254.0	23.0	0.0905512	NM_002279	O76010	Silent	SNP	ENST00000251646.3	37	CCDS11389.1																																																																																			.	.	none		0.617	KRT33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257292.1	NM_002279	
LRP2	4036	hgsc.bcm.edu	37	2	170034473	170034473	+	Silent	SNP	G	G	A	rs139363553	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170034473G>A	ENST00000263816.3	-	53	10518	c.10233C>T	c.(10231-10233)ttC>ttT	p.F3411F	LRP2_ENST00000461418.1_5'UTR	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	3411					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	TGGTAATAGCGAAAGGGTGAG	0.433													G|||	7	0.00139776	0.0053	0.0	5008	,	,		20637	0.0		0.0	False		,,,				2504	0.0				p.F3411F		Atlas-SNP	.											.	LRP2	751	.	0			c.C10233T						PASS	.	G		25,4381	31.7+/-61.6	0,25,2178	169.0	146.0	154.0		10233	2.0	1.0	2	dbSNP_134	154	0,8600		0,0,4300	no	coding-synonymous	LRP2	NM_004525.2		0,25,6478	AA,AG,GG		0.0,0.5674,0.1922		3411/4656	170034473	25,12981	2203	4300	6503	SO:0001819	synonymous_variant	4036	exon53			AATAGCGAAAGGG		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.10233C>T	2.37:g.170034473G>A		346.0	1.0	0.00289017		268.0	116.0	0.432836	NM_004525	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																			G|0.999;A|0.001	0.001	strong		0.433	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
ABCA4	24	hgsc.bcm.edu	37	1	94505604	94505604	+	Missense_Mutation	SNP	A	A	C	rs61750126	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:94505604A>C	ENST00000370225.3	-	24	3688	c.3602T>G	c.(3601-3603)cTg>cGg	p.L1201R		NM_000350.2	NP_000341.2	P78363	ABCA4_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 4	1201			L -> R (in STGD1; may predispose to develop retinal toxicity after treatment with chloroquine and hydroxychloroquine; dbSNP:rs61750126). {ECO:0000269|PubMed:11384574, ECO:0000269|PubMed:11527935}.		phospholipid transfer to membrane (GO:0006649)|photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|photoreceptor disc membrane (GO:0097381)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|phospholipid-translocating ATPase activity (GO:0004012)|transporter activity (GO:0005215)			NS(2)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(10)|large_intestine(25)|lung(57)|ovary(4)|pancreas(1)|prostate(4)|skin(10)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	147		all_lung(203;0.000757)|Lung NSC(277;0.00335)		all cancers(265;0.00432)|GBM - Glioblastoma multiforme(16;0.00715)|Epithelial(280;0.171)		CTTACCATCCAGGACTTGTTC	0.547											OREG0013610	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	146	0.0291534	0.1051	0.0101	5008	,	,		20682	0.0		0.0	False		,,,				2504	0.0				p.L1201R		Atlas-SNP	.											.	ABCA4	275	.	0			c.T3602G	GRCh37	CM990042	ABCA4	M	rs61750126	PASS	.	A	ARG/LEU	412,3994	189.5+/-215.6	25,362,1816	131.0	106.0	115.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3602	5.5	1.0	1	dbSNP_129	115	4,8596	2.2+/-6.3	0,4,4296	yes	missense	ABCA4	NM_000350.2	102	25,366,6112	CC,CA,AA		0.0465,9.3509,3.1985	probably-damaging	1201/2274	94505604	416,12590	2203	4300	6503	SO:0001583	missense	24	exon24			CCATCCAGGACTT	U88667	CCDS747.1	1p22	2013-01-23			ENSG00000198691	ENSG00000198691		"""ATP binding cassette transporters / subfamily A"""	34	protein-coding gene	gene with protein product	"""Stargardt disease"""	601691	"""ATP-binding cassette transporter, retinal-specific"""	STGD1, ABCR, RP19, STGD		9490294	Standard	NM_000350		Approved	FFM, ARMD2, CORD3	uc001dqh.3	P78363	OTTHUMG00000010622	ENST00000370225.3:c.3602T>G	1.37:g.94505604A>C	ENSP00000359245:p.Leu1201Arg	92.0	0.0	0	1306	89.0	39.0	0.438202	NM_000350	O15112|O60438|O60915|Q0QD48|Q4LE31	Missense_Mutation	SNP	ENST00000370225.3	37	CCDS747.1	46	0.021062271062271064	44	0.08943089430894309	2	0.0055248618784530384	0	0.0	0	0.0	A	12.19	1.864956	0.32977	0.093509	4.65E-4	ENSG00000198691	ENST00000370225	D	0.86562	-2.14	5.54	5.54	0.83059	.	0.077785	0.50627	D	0.000119	T	0.76983	0.4064	L	0.53249	1.67	0.80722	A	1	B	0.18863	0.031	B	0.24269	0.052	T	0.73228	-0.4049	9	0.27082	T	0.32	.	13.1677	0.59581	1.0:0.0:0.0:0.0	rs61750126	1201	P78363	ABCA4_HUMAN	R	1201	ENSP00000359245:L1201R	ENSP00000359245:L1201R	L	-	2	0	ABCA4	94278192	1.000000	0.71417	0.997000	0.53966	0.864000	0.49448	4.771000	0.62318	2.326000	0.78906	0.533000	0.62120	CTG	A|0.968;C|0.032	0.032	strong		0.547	ABCA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029320.1	NM_000350	
CACNA1G	8913	hgsc.bcm.edu	37	17	48653144	48653144	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48653144C>T	ENST00000359106.5	+	8	1381	c.1381C>T	c.(1381-1383)Cgg>Tgg	p.R461W	CACNA1G_ENST00000515411.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000514717.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000515765.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000514079.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000512389.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000513964.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000507609.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000503485.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000513689.2_Missense_Mutation_p.R461W|CACNA1G_ENST00000354983.4_Missense_Mutation_p.R461W|CACNA1G_ENST00000507336.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000505165.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000502264.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000510115.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000360761.4_Missense_Mutation_p.R461W|CACNA1G_ENST00000515165.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000507896.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000416767.4_Missense_Mutation_p.R461W|CACNA1G_ENST00000510366.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000358244.5_Missense_Mutation_p.R461W|CACNA1G_ENST00000352832.5_Missense_Mutation_p.R461W|CACNA1G_ENST00000514181.1_Missense_Mutation_p.R461W|CACNA1G_ENST00000429973.2_Missense_Mutation_p.R461W|CACNA1G_ENST00000442258.2_Missense_Mutation_p.R461W|CACNA1G_ENST00000507510.2_Missense_Mutation_p.R461W	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	461					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	AGCAGGTGTGCGGGTTGGGCT	0.672																																					p.R461W		Atlas-SNP	.											.	CACNA1G	659	.	0			c.C1381T						PASS	.																																			SO:0001583	missense	8913	exon8			GGTGTGCGGGTTG	AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.1381C>T	17.37:g.48653144C>T	ENSP00000352011:p.Arg461Trp	56.0	0.0	0		78.0	44.0	0.564103	NM_001256360	D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Missense_Mutation	SNP	ENST00000359106.5	37	CCDS45730.1	.	.	.	.	.	.	.	.	.	.	c	11.34	1.610132	0.28712	.	.	ENSG00000006283	ENST00000360761;ENST00000352832;ENST00000416767;ENST00000354983;ENST00000442258;ENST00000502264;ENST00000512389;ENST00000513964;ENST00000514717;ENST00000510366;ENST00000503485;ENST00000507510;ENST00000507336;ENST00000513689;ENST00000507609;ENST00000510115;ENST00000515165;ENST00000514181;ENST00000515765;ENST00000514079;ENST00000358244;ENST00000359106;ENST00000429973;ENST00000515411;ENST00000505165;ENST00000507896	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97352	-4.2;-4.21;-4.35;-4.14;-4.2;-4.19;-4.23;-4.28;-4.25;-4.27;-4.28;-4.16;-4.16;-4.22;-4.2;-4.14;-4.23;-4.18;-4.15;-4.23;-4.2;-4.16;-4.22;-4.15;-4.22;-4.22	5.15	5.15	0.70609	.	0.317948	0.29783	N	0.011202	D	0.97241	0.9098	L	0.42632	1.34	0.37962	D	0.932991	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;B;D	0.89917	1.0;0.999;1.0;1.0;1.0;1.0;1.0;0.999;1.0;0.998;1.0;1.0;0.999;0.999;1.0;0.997;1.0;0.999;1.0;1.0;1.0;0.999;1.0;0.999;0.013;1.0	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;B;D	0.83275	0.991;0.918;0.984;0.996;0.959;0.984;0.994;0.959;0.994;0.918;0.947;0.975;0.945;0.947;0.994;0.918;0.965;0.926;0.959;0.991;0.988;0.945;0.947;0.918;0.003;0.985	D	0.98292	1.0514	10	0.66056	D	0.02	.	11.91	0.52733	0.2981:0.7019:0.0:0.0	.	461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461;461	Q19QZ5;Q19QZ1;Q19QZ4;Q19R07;Q19QY8;Q19R10;Q19QZ6;Q19QZ3;Q19R06;Q19R00;Q19R04;O43497-10;Q19QZ9;Q19QZ7;Q19R08;Q19QZ8;Q19R03;O43497-4;Q19R02;Q19R12;Q19R17;Q19R11;Q2TAC4;O43497;Q19R13;O43497-11	.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;CAC1G_HUMAN;.;.	W	461	ENSP00000353990:R461W;ENSP00000339302:R461W;ENSP00000392390:R461W;ENSP00000347078:R461W;ENSP00000409759:R461W;ENSP00000425522:R461W;ENSP00000426261:R461W;ENSP00000425451:R461W;ENSP00000422407:R461W;ENSP00000426814:R461W;ENSP00000427238:R461W;ENSP00000423112:R461W;ENSP00000420918:R461W;ENSP00000426172:R461W;ENSP00000423045:R461W;ENSP00000427173:R461W;ENSP00000426098:R461W;ENSP00000425698:R461W;ENSP00000426232:R461W;ENSP00000423317:R461W;ENSP00000350979:R461W;ENSP00000352011:R461W;ENSP00000414388:R461W;ENSP00000423155:R461W;ENSP00000422268:R461W;ENSP00000421518:R461W	ENSP00000339302:R461W	R	+	1	2	CACNA1G	46008143	0.991000	0.36638	0.995000	0.50966	0.137000	0.21094	2.463000	0.45058	2.388000	0.81334	0.655000	0.94253	CGG	.	.	none		0.672	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1	NM_018896	
USP40	55230	hgsc.bcm.edu	37	2	234398065	234398065	+	Missense_Mutation	SNP	G	G	A	rs34026756	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:234398065G>A	ENST00000427112.2	-	26	3109	c.3074C>T	c.(3073-3075)aCg>aTg	p.T1025M	USP40_ENST00000496298.1_5'UTR|USP40_ENST00000450966.1_Missense_Mutation_p.T1037M|USP40_ENST00000251722.6_Missense_Mutation_p.T1025M			Q9NVE5	UBP40_HUMAN	ubiquitin specific peptidase 40	1025			T -> M (in dbSNP:rs34026756).		ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(1)|endometrium(6)|kidney(5)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	30		Breast(86;0.0013)|Renal(207;0.00339)|all_hematologic(139;0.0116)|all_lung(227;0.0179)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0539)		Epithelial(121;1.71e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000407)|Lung(119;0.00277)|LUSC - Lung squamous cell carcinoma(224;0.00646)		CCTCTCCACCGTCCAGGCTCT	0.572													G|||	90	0.0179712	0.0658	0.0043	5008	,	,		17455	0.0		0.0	False		,,,				2504	0.0				p.T1037M		Atlas-SNP	.											USP40_ENST00000450966,NS,carcinoma,+1,2	USP40	174	2	0			c.C3110T						PASS	.	G	MET/THR	242,3748		6,230,1759	34.0	38.0	36.0		3110	4.6	0.9	2	dbSNP_126	36	2,8304		0,2,4151	yes	missense	USP40	NM_018218.2	81	6,232,5910	AA,AG,GG		0.0241,6.0652,1.9844	probably-damaging	1037/1248	234398065	244,12052	1995	4153	6148	SO:0001583	missense	55230	exon26			TCCACCGTCCAGG	AK001647	CCDS46547.1	2q37.1	2005-08-08	2005-08-08		ENSG00000085982	ENSG00000085982		"""Ubiquitin-specific peptidases"""	20069	protein-coding gene	gene with protein product		610570	"""ubiquitin specific protease 40"""			12838346	Standard	NM_018218		Approved	FLJ10785	uc010zmr.2	Q9NVE5	OTTHUMG00000153199	ENST00000427112.2:c.3074C>T	2.37:g.234398065G>A	ENSP00000387898:p.Thr1025Met	218.0	1.0	0.00458716		200.0	102.0	0.51	NM_018218	Q6NX38|Q70EL0	Missense_Mutation	SNP	ENST00000427112.2	37	CCDS46547.1	35|35	0.016025641025641024|0.016025641025641024	34|34	0.06910569105691057|0.06910569105691057	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	G|G	19.02|19.02	3.746166|3.746166	0.69418|0.69418	0.060652|0.060652	2.41E-4|2.41E-4	ENSG00000085982|ENSG00000085982	ENST00000454354;ENST00000430158|ENST00000450966;ENST00000251722;ENST00000427112	.|T;T;T	.|0.05580	.|3.42;3.42;3.42	5.5|5.5	4.57|4.57	0.56435|0.56435	.|.	.|0.947819	.|0.08861	.|N	.|0.883028	T|T	0.01730|0.01730	0.0055|0.0055	M|M	0.66939|0.66939	2.045|2.045	0.32511|0.32511	N|N	0.537508|0.537508	.|D;D	.|0.89917	.|1.0;0.999	.|D;P	.|0.63957	.|0.92;0.878	T|T	0.00967|0.00967	-1.1497|-1.1497	5|10	.|0.59425	.|D	.|0.04	.|.	15.0977|15.0977	0.72247|0.72247	0.0:0.0:0.8577:0.1423|0.0:0.0:0.8577:0.1423	rs34026756|rs34026756	.|1037;685	.|Q9NVE5-3;B4DN96	.|.;.	W|M	15;201|1037;1025;1025	.|ENSP00000415434:T1037M;ENSP00000251722:T1025M;ENSP00000387898:T1025M	.|ENSP00000251722:T1025M	R|T	-|-	1|2	2|0	USP40|USP40	234062804|234062804	1.000000|1.000000	0.71417|0.71417	0.945000|0.945000	0.38365|0.38365	0.606000|0.606000	0.37113|0.37113	3.308000|3.308000	0.51896|0.51896	2.571000|2.571000	0.86741|0.86741	0.650000|0.650000	0.86243|0.86243	CGG|ACG	G|0.985;A|0.015	0.015	strong		0.572	USP40-017	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397235.1	XM_114294	
PIGB	9488	hgsc.bcm.edu	37	15	55647617	55647617	+	Missense_Mutation	SNP	A	A	C	rs2444042	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:55647617A>C	ENST00000164305.5	+	12	1943	c.1652A>C	c.(1651-1653)aAg>aCg	p.K551T	DYX1C1-CCPG1_ENST00000565113.1_RNA|CCPG1_ENST00000310958.6_3'UTR|PIGB_ENST00000539642.1_Missense_Mutation_p.K356T|CCPG1_ENST00000442196.3_3'UTR	NM_004855.4	NP_004846.4	Q92521	PIGB_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class B	551			K -> T (in dbSNP:rs2444042).		C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	mannosyltransferase activity (GO:0000030)			endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	11				all cancers(107;0.0255)		TTCAACATGAAGATGAAATTC	0.368													A|||	96	0.0191693	0.0719	0.0014	5008	,	,		17374	0.0		0.0	False		,,,				2504	0.0				p.K551T		Atlas-SNP	.											.	PIGB	36	.	0			c.A1652C						PASS	.	A	,,,THR/LYS,	239,3401		7,225,1588	89.0	89.0	89.0		,,,1652,	3.4	0.3	15	dbSNP_100	89	2,8126		0,2,4062	yes	utr-3,utr-3,utr-3,missense,utr-3	CCPG1,PIGB	NM_001204450.1,NM_001204451.1,NM_004748.4,NM_004855.4,NM_020739.3	,,,78,	7,227,5650	CC,CA,AA		0.0246,6.5659,2.0479	,,,benign,	,,,551/555,	55647617	241,11527	1820	4064	5884	SO:0001583	missense	9488	exon12			ACATGAAGATGAA	D42138	CCDS61641.1	15q21.3	2013-02-26	2006-06-28		ENSG00000069943	ENSG00000069943		"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"", ""Phosphatidylinositol glycan anchor biosynthesis"""	8959	protein-coding gene	gene with protein product	"""GPI mannosyltransferase 3"", ""dol-P-Man dependent GPI mannosyltransferase"""	604122	"""phosphatidylinositol glycan, class B"""			8861954	Standard	NM_004855		Approved		uc002act.3	Q92521	OTTHUMG00000172654	ENST00000164305.5:c.1652A>C	15.37:g.55647617A>C	ENSP00000164305:p.Lys551Thr	94.0	0.0	0		103.0	47.0	0.456311	NM_004855	Q53FF9|Q8WVN7	Missense_Mutation	SNP	ENST00000164305.5	37		32	0.014652014652014652	31	0.06300813008130081	1	0.0027624309392265192	0	0.0	0	0.0	A	7.554	0.663207	0.14710	0.065659	2.46E-4	ENSG00000069943	ENST00000164305;ENST00000539642	T;T	0.59638	0.51;0.25	5.67	3.39	0.38822	.	3.113960	0.00954	N	0.003003	T	0.03827	0.0108	N	0.03608	-0.345	0.80722	D	1	B	0.31318	0.319	B	0.30029	0.11	T	0.02668	-1.1126	10	0.66056	D	0.02	9.0326	8.6085	0.33789	0.8432:0.0:0.1568:0.0	rs2444042;rs52826750;rs2444042	551	Q92521	PIGB_HUMAN	T	551;356	ENSP00000164305:K551T;ENSP00000438963:K356T	ENSP00000164305:K551T	K	+	2	0	PIGB	53434909	0.999000	0.42202	0.263000	0.24496	0.257000	0.26127	1.168000	0.31859	0.452000	0.26830	0.482000	0.46254	AAG	A|0.977;C|0.023	0.023	strong		0.368	PIGB-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000419687.1	NM_004855	
ASB15	142685	hgsc.bcm.edu	37	7	123267200	123267200	+	Missense_Mutation	SNP	C	C	T	rs73718440	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:123267200C>T	ENST00000451558.1	+	11	1255	c.734C>T	c.(733-735)tCg>tTg	p.S245L	RP11-390E23.3_ENST00000429396.1_RNA|ASB15_ENST00000451215.1_Missense_Mutation_p.S245L|RP11-390E23.3_ENST00000440504.1_RNA|ASB15_ENST00000540573.1_Missense_Mutation_p.S245L|ASB15_ENST00000275699.3_Missense_Mutation_p.S245L|RP11-390E23.3_ENST00000451016.1_RNA|ASB15_ENST00000434204.1_Missense_Mutation_p.S245L|RP11-390E23.3_ENST00000422401.1_RNA|RP11-390E23.3_ENST00000418409.1_RNA			Q8WXK1	ASB15_HUMAN	ankyrin repeat and SOCS box containing 15	245					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|kidney(1)|large_intestine(1)|lung(6)|skin(3)	12						GATGGGGCGTCGGTGCTGTTT	0.488													C|||	39	0.00778754	0.0295	0.0	5008	,	,		17121	0.0		0.0	False		,,,				2504	0.0				p.S245L		Atlas-SNP	.											.	ASB15	94	.	0			c.C734T						PASS	.	C	LEU/SER	96,4310	78.8+/-117.2	0,96,2107	178.0	141.0	153.0		734	5.6	0.8	7	dbSNP_130	153	1,8599		0,1,4299	yes	missense	ASB15	NM_080928.3	145	0,97,6406	TT,TC,CC		0.0116,2.1788,0.7458	probably-damaging	245/589	123267200	97,12909	2203	4300	6503	SO:0001583	missense	142685	exon7			GGGCGTCGGTGCT	AF403033	CCDS34742.1	7q31.31	2013-01-10	2011-01-25		ENSG00000146809	ENSG00000146809		"""Ankyrin repeat domain containing"""	19767	protein-coding gene	gene with protein product			"""ankyrin repeat and SOCS box-containing 15"""			12076535	Standard	XM_005250149		Approved	FLJ43370	uc003vkw.1	Q8WXK1	OTTHUMG00000157114	ENST00000451558.1:c.734C>T	7.37:g.123267200C>T	ENSP00000397655:p.Ser245Leu	277.0	0.0	0		315.0	149.0	0.473016	NM_080928	Q3ZCP3|Q3ZCP5|Q68D37	Missense_Mutation	SNP	ENST00000451558.1	37	CCDS34742.1	15	0.006868131868131868	15	0.03048780487804878	0	0.0	0	0.0	0	0.0	C	19.14	3.770300	0.69992	0.021788	1.16E-4	ENSG00000146809	ENST00000451558;ENST00000434204;ENST00000451215;ENST00000540573;ENST00000542545;ENST00000275699	T;T;T;T;T	0.16897	2.31;2.31;2.31;2.31;2.31	5.57	5.57	0.84162	Ankyrin repeat-containing domain (4);	0.000000	0.56097	D	0.000022	T	0.16557	0.0398	L	0.48642	1.525	0.46317	D	0.99898	D	0.89917	1.0	D	0.81914	0.995	T	0.00964	-1.1498	10	0.87932	D	0	-24.7501	19.5537	0.95331	0.0:1.0:0.0:0.0	.	245	Q8WXK1	ASB15_HUMAN	L	245;245;245;245;34;245	ENSP00000397655:S245L;ENSP00000390963:S245L;ENSP00000416433:S245L;ENSP00000438643:S245L;ENSP00000275699:S245L	ENSP00000275699:S245L	S	+	2	0	ASB15	123054436	0.989000	0.36119	0.802000	0.32245	0.453000	0.32348	3.285000	0.51716	2.614000	0.88457	0.557000	0.71058	TCG	C|0.993;T|0.007	0.007	strong		0.488	ASB15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347493.1		
UBASH3B	84959	hgsc.bcm.edu	37	11	122678778	122678778	+	Missense_Mutation	SNP	A	A	G	rs35343548	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:122678778A>G	ENST00000284273.5	+	13	2081	c.1706A>G	c.(1705-1707)aAt>aGt	p.N569S		NM_032873.4	NP_116262.2	Q8TF42	UBS3B_HUMAN	ubiquitin associated and SH3 domain containing B	569	Protein tyrosine phosphatase. {ECO:0000250}.		N -> S (in dbSNP:rs35343548).		negative regulation of platelet aggregation (GO:0090331)|negative regulation of protein kinase activity (GO:0006469)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(11)|prostate(1)|skin(2)|stomach(2)	26		Breast(109;0.00254)|Medulloblastoma(222;0.00877)|Lung NSC(97;0.0183)|all_lung(97;0.0186)|all_neural(223;0.0381)|all_hematologic(192;0.104)		BRCA - Breast invasive adenocarcinoma(274;1.37e-05)|OV - Ovarian serous cystadenocarcinoma(99;0.0463)		CCCCCAGGAAATAACATCCTG	0.473													A|||	33	0.00658946	0.0242	0.0014	5008	,	,		18186	0.0		0.0	False		,,,				2504	0.0				p.N569S		Atlas-SNP	.											.	UBASH3B	73	.	0			c.A1706G						PASS	.	A	SER/ASN	74,4330	66.4+/-103.9	0,74,2128	336.0	327.0	330.0		1706	4.7	1.0	11	dbSNP_126	330	2,8596		0,2,4297	yes	missense	UBASH3B	NM_032873.4	46	0,76,6425	GG,GA,AA		0.0233,1.6803,0.5845	benign	569/650	122678778	76,12926	2202	4299	6501	SO:0001583	missense	84959	exon13			CAGGAAATAACAT	AB075839	CCDS31694.1	11q24.1	2010-04-28	2010-04-28		ENSG00000154127	ENSG00000154127			29884	protein-coding gene	gene with protein product	"""SH3 domain-containing 70 kDa protein, suppressor of T-cell receptor signaling 1, nm23-phosphorylated unknown substrate"""	609201				11853319, 12370296	Standard	NM_032873		Approved	KIAA1959, STS-1	uc001pyi.4	Q8TF42	OTTHUMG00000166025	ENST00000284273.5:c.1706A>G	11.37:g.122678778A>G	ENSP00000284273:p.Asn569Ser	176.0	0.0	0		130.0	49.0	0.376923	NM_032873	Q53GT5|Q53GT8|Q8NBV7|Q96IG9|Q96NZ2	Missense_Mutation	SNP	ENST00000284273.5	37	CCDS31694.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	A	15.55	2.865578	0.51588	0.016803	2.33E-4	ENSG00000154127	ENST00000284273	T	0.27890	1.64	5.85	4.74	0.60224	Histidine phosphatase superfamily, clade-1 (1);	0.130095	0.64402	N	0.000002	T	0.10423	0.0255	L	0.27053	0.805	0.46376	D	0.999012	B	0.06786	0.001	B	0.08055	0.003	T	0.03514	-1.1029	10	0.48119	T	0.1	-8.6767	7.823	0.29298	0.7888:0.1392:0.072:0.0	rs35343548	569	Q8TF42	UBS3B_HUMAN	S	569	ENSP00000284273:N569S	ENSP00000284273:N569S	N	+	2	0	UBASH3B	122183988	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.395000	0.52558	1.061000	0.40601	0.533000	0.62120	AAT	A|0.992;G|0.008	0.008	strong		0.473	UBASH3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387499.1	NM_032873	
DMKN	93099	hgsc.bcm.edu	37	19	36002394	36002394	+	Silent	SNP	G	G	A	rs56743379|rs146822312		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36002394G>A	ENST00000339686.3	-	5	1013	c.837C>T	c.(835-837)ggC>ggT	p.G279G	DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000447113.2_Silent_p.G279G|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000451297.2_Silent_p.G279G|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000440396.1_Silent_p.G279G|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000424570.2_Silent_p.G279G|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000418261.1_Silent_p.G279G	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	279	Gly-rich.			G -> GSSSG (in Ref. 4; AAQ88778). {ECO:0000305}.		extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.S274_S290del(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			cactgctgccgccactgctgc	0.637																																					p.G279G		Atlas-SNP	.											.	DMKN	116	.	1	Deletion - In frame(1)	ovary(1)	c.C837T						PASS	.						26.0	20.0	22.0					19																	36002394		2165	4212	6377	SO:0001819	synonymous_variant	93099	exon5			GCTGCCGCCACTG	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.837C>T	19.37:g.36002394G>A		92.0	0.0	0		89.0	30.0	0.337079	NM_001126058	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Silent	SNP	ENST00000339686.3	37	CCDS12463.1																																																																																			G|0.933;A|0.067	0.067	strong		0.637	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
NCAPD3	23310	hgsc.bcm.edu	37	11	134055275	134055275	+	Missense_Mutation	SNP	C	C	T	rs61744119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:134055275C>T	ENST00000534548.2	-	17	2256	c.2192G>A	c.(2191-2193)aGg>aAg	p.R731K	RP11-700F16.3_ENST00000531710.1_RNA	NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	731					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	germinal vesicle (GO:0042585)|membrane (GO:0016020)|nuclear condensin complex (GO:0000799)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)	methylated histone binding (GO:0035064)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		GTAGTCCAGCCTGGGTGAGGA	0.433													c|||	20	0.00399361	0.0136	0.0029	5008	,	,		16996	0.0		0.0	False		,,,				2504	0.0				p.R731K		Atlas-SNP	.											.	NCAPD3	141	.	0			c.G2192A						PASS	.	T	LYS/ARG	55,4347	52.3+/-87.9	0,55,2146	67.0	64.0	65.0		2192	-2.9	0.6	11	dbSNP_129	65	0,8594		0,0,4297	yes	missense	NCAPD3	NM_015261.2	26	0,55,6443	TT,TC,CC		0.0,1.2494,0.4232	benign	731/1499	134055275	55,12941	2201	4297	6498	SO:0001583	missense	23310	exon17			TCCAGCCTGGGTG	AK124878	CCDS31723.1	11q25	2008-02-04			ENSG00000151503	ENSG00000151503			28952	protein-coding gene	gene with protein product		609276				7584044, 8619474, 14532007	Standard	NM_015261		Approved	hCAP-D3, CAP-D3, hHCP-6, KIAA0056, FLJ42888, hcp-6	uc001qhd.1	P42695	OTTHUMG00000167172	ENST00000534548.2:c.2192G>A	11.37:g.134055275C>T	ENSP00000433681:p.Arg731Lys	114.0	0.0	0		134.0	74.0	0.552239	NM_015261	A6NFS2|Q4KMQ9	Missense_Mutation	SNP	ENST00000534548.2	37	CCDS31723.1	6	0.0027472527472527475	5	0.01016260162601626	1	0.0027624309392265192	0	0.0	0	0.0	c	0.387	-0.925700	0.02377	0.012494	0.0	ENSG00000151503	ENST00000534548	T	0.16743	2.32	5.95	-2.94	0.05581	Armadillo-like helical (1);Armadillo-type fold (1);	0.333488	0.38164	N	0.001795	T	0.01387	0.0045	N	0.00104	-2.125	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45026	-0.9289	10	0.02654	T	1	-5.8849	6.0997	0.20041	0.087:0.072:0.1785:0.6625	.	731	P42695	CNDD3_HUMAN	K	731	ENSP00000433681:R731K	ENSP00000431612:R731K	R	-	2	0	NCAPD3	133560485	0.426000	0.25506	0.571000	0.28486	0.014000	0.08584	0.322000	0.19576	-1.200000	0.02662	-1.563000	0.00883	AGG	C|0.995;T|0.005	0.005	strong		0.433	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261	
CYBB	1536	hgsc.bcm.edu	37	X	37663234	37663234	+	Silent	SNP	G	G	A	rs2228117	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:37663234G>A	ENST00000378588.4	+	9	1069	c.1002G>A	c.(1000-1002)aaG>aaA	p.K334K	CYBB_ENST00000492288.1_3'UTR|CYBB_ENST00000545017.1_Silent_p.K302K|CYBB_ENST00000536160.1_Silent_p.K67K|TM4SF2_ENST00000465127.1_Intron	NM_000397.3	NP_000388.2	P04839	CY24B_HUMAN	cytochrome b-245, beta polypeptide	334	FAD-binding FR-type. {ECO:0000255|PROSITE-ProRule:PRU00716}.				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)|hydrogen peroxide biosynthetic process (GO:0050665)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|oxidation-reduction process (GO:0055114)|phagosome maturation (GO:0090382)|respiratory burst (GO:0045730)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|neuronal cell body (GO:0043025)|phagocytic vesicle membrane (GO:0030670)|rough endoplasmic reticulum (GO:0005791)	flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|superoxide-generating NADPH oxidase activity (GO:0016175)|voltage-gated ion channel activity (GO:0005244)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(20)|prostate(2)|skin(2)	32					Dextromethorphan(DB00514)	AGGTGTCCAAGCTGGAGTGGC	0.483													G|||	110	0.0291391	0.0719	0.0216	3775	,	,		14198	0.0		0.0	False		,,,				2504	0.0				p.K334K		Atlas-SNP	.											.	CYBB	62	.	0			c.G1002A						PASS	.	G		707,3126		70,466,101,1095,470	110.0	99.0	103.0		1002	-2.1	0.2	X	dbSNP_98	103	2,6726		0,2,0,2426,1872	no	coding-synonymous	CYBB	NM_000397.3		70,468,101,3521,2342	AA,AG,A,GG,G		0.0297,18.4451,6.7134		334/571	37663234	709,9852	2202	4300	6502	SO:0001819	synonymous_variant	1536	exon9			GTCCAAGCTGGAG	X04011	CCDS14242.1	Xp21.1	2014-09-17	2008-07-29		ENSG00000165168	ENSG00000165168		"""Cytochrome b genes"""	2578	protein-coding gene	gene with protein product		300481	"""chronic granulomatous disease"""	CGD			Standard	NM_000397		Approved	GP91-PHOX, NOX2	uc004ddr.2	P04839	OTTHUMG00000033175	ENST00000378588.4:c.1002G>A	X.37:g.37663234G>A		324.0	1.0	0.00308642		367.0	190.0	0.517711	NM_000397	A8K138|Q2PP16	Silent	SNP	ENST00000378588.4	37	CCDS14242.1																																																																																			0|0.006;A|0.061	0.061	strong		0.483	CYBB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080881.1		
MICALL2	79778	hgsc.bcm.edu	37	7	1488317	1488317	+	Silent	SNP	G	G	A	rs78897087	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:1488317G>A	ENST00000297508.7	-	3	448	c.273C>T	c.(271-273)gaC>gaT	p.D91D	MICALL2_ENST00000405088.4_Intron	NM_182924.3	NP_891554.1	Q8IY33	MILK2_HUMAN	MICAL-like 2	91	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.|Forms an intramolecular interaction with the C-terminal coiled coil domain keeping the protein in a closed conformation. {ECO:0000250}.				actin cytoskeleton reorganization (GO:0031532)|actin filament polymerization (GO:0030041)|endocytic recycling (GO:0032456)|neuron projection development (GO:0031175)|substrate adhesion-dependent cell spreading (GO:0034446)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|stress fiber (GO:0001725)|tight junction (GO:0005923)	actin filament binding (GO:0051015)|filamin binding (GO:0031005)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|lung(8)|ovary(2)|skin(2)	19		Ovarian(82;0.0253)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;6.01e-15)		TGCTCAGCCGGTCAGGCACCT	0.657													G|||	158	0.0315495	0.1135	0.0115	5008	,	,		15745	0.0		0.0	False		,,,				2504	0.0				p.D91D		Atlas-SNP	.											.	MICALL2	63	.	0			c.C273T						PASS	.			390,4016	190.9+/-216.7	20,350,1833	97.0	89.0	92.0		273	3.2	1.0	7	dbSNP_132	92	4,8594	3.7+/-12.6	0,4,4295	no	coding-synonymous	MICALL2	NM_182924.3		20,354,6128	AA,AG,GG		0.0465,8.8516,3.0298		91/905	1488317	394,12610	2203	4299	6502	SO:0001819	synonymous_variant	79778	exon3			CAGCCGGTCAGGC	BC037988	CCDS5324.1	7p22.3	2006-11-24			ENSG00000164877	ENSG00000164877			29672	protein-coding gene	gene with protein product	"""junctional Rab13-binding protein"""					12110185, 16525024	Standard	NM_182924		Approved	MGC46023, FLJ23471, MICAL-L2, JRAB	uc003skj.4	Q8IY33	OTTHUMG00000119021	ENST00000297508.7:c.273C>T	7.37:g.1488317G>A		123.0	0.0	0		122.0	122.0	1	NM_182924	D3YTD2|Q7RTP4|Q7Z655|Q8TEQ4|Q9H5F9	Silent	SNP	ENST00000297508.7	37	CCDS5324.1																																																																																			G|0.968;A|0.032	0.032	strong		0.657	MICALL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239223.2	NM_182924	
SPAG4	6676	hgsc.bcm.edu	37	20	34205080	34205080	+	Silent	SNP	C	C	T	rs116016997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34205080C>T	ENST00000374273.3	+	2	439	c.327C>T	c.(325-327)gtC>gtT	p.V109V	SPAG4_ENST00000462896.1_3'UTR	NM_003116.1	NP_003107.1	Q9NPE6	SPAG4_HUMAN	sperm associated antigen 4	109					spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|motile cilium (GO:0031514)	structural molecule activity (GO:0005198)			NS(1)|cervix(5)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)	21	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.0127)			CTCCAGTAGTCTCTGAGGAGC	0.637													C|||	107	0.0213658	0.0779	0.0058	5008	,	,		11937	0.0		0.0	False		,,,				2504	0.0				p.V109V		Atlas-SNP	.											.	SPAG4	36	.	0			c.C327T						PASS	.	C		232,4174		2,228,1973	24.0	26.0	25.0		327	2.1	0.8	20	dbSNP_132	25	3,8595		0,3,4296	no	coding-synonymous	SPAG4	NM_003116.1		2,231,6269	TT,TC,CC		0.0349,5.2655,1.8071		109/438	34205080	235,12769	2203	4299	6502	SO:0001819	synonymous_variant	6676	exon2			AGTAGTCTCTGAG	AF043344	CCDS13259.1	20q11.2	2010-04-23			ENSG00000061656	ENSG00000061656			11214	protein-coding gene	gene with protein product	"""acrosomal protein ACR55"", ""Sad1 and UNC84 domain containing 4"", ""cancer/testis antigen 127"""	603038				9691178, 10373309	Standard	NM_003116		Approved	SUN4, CT127	uc002xdb.1	Q9NPE6	OTTHUMG00000032352	ENST00000374273.3:c.327C>T	20.37:g.34205080C>T		65.0	0.0	0		83.0	35.0	0.421687	NM_003116	O43648	Silent	SNP	ENST00000374273.3	37	CCDS13259.1																																																																																			C|0.982;T|0.018	0.018	strong		0.637	SPAG4-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078896.1	NM_003116	
CLCN6	1185	hgsc.bcm.edu	37	1	11876692	11876692	+	Silent	SNP	G	G	A	rs57044879	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11876692G>A	ENST00000346436.6	+	4	286	c.234G>A	c.(232-234)gcG>gcA	p.A78A	CLCN6_ENST00000376492.3_3'UTR|CLCN6_ENST00000376496.3_Silent_p.A78A|CLCN6_ENST00000376487.3_Silent_p.A56A|CLCN6_ENST00000376497.3_Silent_p.A78A|CLCN6_ENST00000312413.6_Silent_p.A78A	NM_001286.3	NP_001277	P51797	CLCN6_HUMAN	chloride channel, voltage-sensitive 6	78					cell volume homeostasis (GO:0006884)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|response to mechanical stimulus (GO:0009612)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	antiporter activity (GO:0015297)|ATP binding (GO:0005524)|voltage-gated chloride channel activity (GO:0005247)			cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(12)|prostate(2)|skin(4)	36	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;6.13e-06)|COAD - Colon adenocarcinoma(227;0.000274)|BRCA - Breast invasive adenocarcinoma(304;0.000311)|Kidney(185;0.000816)|KIRC - Kidney renal clear cell carcinoma(229;0.00268)|STAD - Stomach adenocarcinoma(313;0.00743)|READ - Rectum adenocarcinoma(331;0.0649)		GATATGAGGCGGTGAAGTGGA	0.532													G|||	135	0.0269569	0.0938	0.0058	5008	,	,		19754	0.004		0.001	False		,,,				2504	0.002				p.A78A		Atlas-SNP	.											.	CLCN6	77	.	0			c.G234A						PASS	.	G	,,,	483,3923	220.7+/-238.1	24,435,1744	134.0	103.0	114.0		234,234,234,234	1.6	1.0	1	dbSNP_129	114	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CLCN6	NM_001286.2,NM_021735.2,NM_021736.2,NM_021737.2	,,,	24,443,6036	AA,AG,GG		0.093,10.9623,3.7752	,,,	78/870,78/321,78/354,78/309	11876692	491,12515	2203	4300	6503	SO:0001819	synonymous_variant	1185	exon4			TGAGGCGGTGAAG	X83378	CCDS138.1, CCDS57972.1	1p36	2012-09-26	2012-02-23		ENSG00000011021	ENSG00000011021		"""Ion channels / Chloride channels : Voltage-sensitive"""	2024	protein-coding gene	gene with protein product		602726	"""chloride channel 6"""			8543009	Standard	NM_001286		Approved	CLC-6, KIAA0046, ClC-6	uc001ate.5	P51797	OTTHUMG00000002299	ENST00000346436.6:c.234G>A	1.37:g.11876692G>A		158.0	0.0	0		192.0	111.0	0.578125	NM_001286	A8K1T4|B4DGT7|F8W9R3|O60818|O60819|O60820|O60821|P78520|P78521|Q17R81|Q5SNW2|Q5SNW3|Q5SNX1|Q5SNX2|Q5SNX3|Q99427|Q99428|Q99429	Silent	SNP	ENST00000346436.6	37	CCDS138.1																																																																																			G|0.971;A|0.029	0.029	strong		0.532	CLCN6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006639.2	NM_001286	
FAT3	120114	hgsc.bcm.edu	37	11	92624276	92624276	+	Silent	SNP	G	G	A	rs371790138	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:92624276G>A	ENST00000298047.6	+	27	13784	c.13767G>A	c.(13765-13767)gtG>gtA	p.V4589V	FAT3_ENST00000525166.1_Silent_p.V4439V|FAT3_ENST00000533797.1_Silent_p.V892V|FAT3_ENST00000409404.2_Silent_p.V4557V			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	4589					homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				AGACTCAAGTGTAGACATCAC	0.507										TCGA Ovarian(4;0.039)			G|||	3	0.000599042	0.0023	0.0	5008	,	,		20727	0.0		0.0	False		,,,				2504	0.0				p.V4557V		Atlas-SNP	.											.	FAT3	1822	.	0			c.G13671A						PASS	.	G		9,4135		0,9,2063	43.0	45.0	44.0		13671	3.8	1.0	11		44	0,8398		0,0,4199	no	coding-synonymous	FAT3	NM_001008781.2		0,9,6262	AA,AG,GG		0.0,0.2172,0.0718		4557/4558	92624276	9,12533	2072	4199	6271	SO:0001819	synonymous_variant	120114	exon25			TCAAGTGTAGACA	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.13767G>A	11.37:g.92624276G>A		60.0	0.0	0		48.0	24.0	0.5	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				.	.	weak		0.507	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
ZNF366	167465	hgsc.bcm.edu	37	5	71740073	71740073	+	Missense_Mutation	SNP	A	A	T	rs116305374	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:71740073A>T	ENST00000318442.5	-	5	2235	c.1745T>A	c.(1744-1746)cTg>cAg	p.L582Q	RP11-389C8.2_ENST00000564956.1_RNA	NM_152625.1	NP_689838.1	Q8N895	ZN366_HUMAN	zinc finger protein 366	582	Interaction with CTBP1.|Interaction with NRIP1.				negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|estrogen receptor binding (GO:0030331)|metal ion binding (GO:0046872)|transcription corepressor activity (GO:0003714)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(9)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	35		Lung NSC(167;0.0247)|Ovarian(174;0.0908)|Prostate(461;0.155)		OV - Ovarian serous cystadenocarcinoma(47;2.51e-53)		CAGACTCCTCAGGACACCGGC	0.607													A|||	9	0.00179712	0.0068	0.0	5008	,	,		15362	0.0		0.0	False		,,,				2504	0.0				p.L582Q		Atlas-SNP	.											.	ZNF366	108	.	0			c.T1745A						PASS	.	A	GLN/LEU	17,4379		0,17,2181	36.0	44.0	41.0		1745	5.9	1.0	5	dbSNP_133	41	0,8588		0,0,4294	yes	missense	ZNF366	NM_152625.1	113	0,17,6475	TT,TA,AA		0.0,0.3867,0.1309	probably-damaging	582/745	71740073	17,12967	2198	4294	6492	SO:0001583	missense	167465	exon5			CTCCTCAGGACAC	AK097115	CCDS4015.1	5q13.1	2013-01-08			ENSG00000178175	ENSG00000178175		"""Zinc fingers, C2H2-type"""	18316	protein-coding gene	gene with protein product		610159					Standard	NM_152625		Approved	FLJ39796	uc003kce.1	Q8N895	OTTHUMG00000100965	ENST00000318442.5:c.1745T>A	5.37:g.71740073A>T	ENSP00000313158:p.Leu582Gln	108.0	0.0	0		102.0	42.0	0.411765	NM_152625	Q5HYI9|Q7RTV4	Missense_Mutation	SNP	ENST00000318442.5	37	CCDS4015.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	20.9	4.063034	0.76187	0.003867	0.0	ENSG00000178175	ENST00000318442	T	0.09723	2.95	5.87	5.87	0.94306	.	0.000000	0.52532	D	0.000062	T	0.17023	0.0409	L	0.36672	1.1	0.47737	D	0.999503	D	0.63880	0.993	D	0.62955	0.909	T	0.07616	-1.0763	10	0.07482	T	0.82	-37.1713	11.6024	0.51010	0.931:0.0:0.069:0.0	.	582	Q8N895	ZN366_HUMAN	Q	582	ENSP00000313158:L582Q	ENSP00000313158:L582Q	L	-	2	0	ZNF366	71775829	1.000000	0.71417	0.992000	0.48379	0.753000	0.42808	6.038000	0.70964	2.371000	0.80710	0.533000	0.62120	CTG	A|0.999;T|0.001	0.001	strong		0.607	ZNF366-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218574.3		
GFM2	84340	hgsc.bcm.edu	37	5	74037369	74037369	+	Silent	SNP	C	C	T	rs35565659	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:74037369C>T	ENST00000296805.3	-	11	1372	c.915G>A	c.(913-915)ttG>ttA	p.L305L	GFM2_ENST00000509430.1_Silent_p.L305L|GFM2_ENST00000427854.2_Silent_p.L305L|GFM2_ENST00000345239.2_Silent_p.L305L	NM_032380.3	NP_115756.2			G elongation factor, mitochondrial 2											breast(2)|endometrium(2)|large_intestine(4)|lung(5)|prostate(1)	14		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Breast(144;0.231)		OV - Ovarian serous cystadenocarcinoma(47;1.86e-56)		CAGCTGGTAACAAATCAAAAT	0.303													C|||	152	0.0303514	0.1097	0.0101	5008	,	,		15822	0.0		0.0	False		,,,				2504	0.0				p.L305L		Atlas-SNP	.											.	GFM2	38	.	0			c.G915A						PASS	.	C	,,	392,4000		12,368,1816	42.0	44.0	43.0		915,915,915	3.1	1.0	5	dbSNP_126	43	5,8569		0,5,4282	no	coding-synonymous,coding-synonymous,coding-synonymous	GFM2	NM_032380.3,NM_170681.1,NM_170691.1	,,	12,373,6098	TT,TC,CC		0.0583,8.9253,3.0619	,,	305/780,305/514,305/733	74037369	397,12569	2196	4287	6483	SO:0001819	synonymous_variant	84340	exon11			TGGTAACAAATCA	AF111808	CCDS4023.1, CCDS4024.1, CCDS47232.1	5q13	2008-02-05			ENSG00000164347	ENSG00000164347			29682	protein-coding gene	gene with protein product		606544				11735030	Standard	NM_001281302		Approved	EFG2, FLJ21661	uc003kdh.1	Q969S9	OTTHUMG00000102058	ENST00000296805.3:c.915G>A	5.37:g.74037369C>T		279.0	0.0	0		247.0	110.0	0.445344	NM_032380		Silent	SNP	ENST00000296805.3	37	CCDS4023.1																																																																																			C|0.976;T|0.024	0.024	strong		0.303	GFM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219860.2	NM_032380	
MCM8	84515	hgsc.bcm.edu	37	20	5935303	5935303	+	Missense_Mutation	SNP	A	A	C	rs6117014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:5935303A>C	ENST00000378896.3	+	4	680	c.303A>C	c.(301-303)aaA>aaC	p.K101N	MCM8_ENST00000378886.2_Missense_Mutation_p.K101N|MCM8_ENST00000265187.4_Missense_Mutation_p.K101N|MCM8_ENST00000378883.1_Missense_Mutation_p.K101N	NM_001281520.1|NM_032485.4|NM_182802.1	NP_001268449.1|NP_115874.3|NP_877954.1	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	101			K -> N (in dbSNP:rs6117014).		cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)|G1/S transition of mitotic cell cycle (GO:0000082)|male gamete generation (GO:0048232)|mitotic cell cycle (GO:0000278)	MCM8-MCM9 complex (GO:0097362)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	23						CATTTGAAAAATTTTTCACAA	0.373													A|||	351	0.0700879	0.1626	0.1009	5008	,	,		19997	0.001		0.0199	False		,,,				2504	0.046				p.K101N		Atlas-SNP	.											.	MCM8	125	.	0			c.A303C						PASS	.	A	ASN/LYS,ASN/LYS	652,3750	276.0+/-272.9	51,550,1600	101.0	97.0	98.0		303,303	-10.4	0.5	20	dbSNP_114	98	183,8417	83.1+/-145.7	2,179,4119	yes	missense,missense	MCM8	NM_032485.4,NM_182802.1	94,94	53,729,5719	CC,CA,AA		2.1279,14.8114,6.4221	benign,benign	101/841,101/825	5935303	835,12167	2201	4300	6501	SO:0001583	missense	84515	exon4			TGAAAAATTTTTC	AJ439063	CCDS13094.1, CCDS13095.1, CCDS63226.1, CCDS63227.1	20p12.3	2007-04-04	2007-04-04	2003-07-09	ENSG00000125885	ENSG00000125885			16147	protein-coding gene	gene with protein product	"""REC homolog (Drosophila)"""	608187	"""chromosome 20 open reading frame 154"""	C20orf154		12527764	Standard	NM_032485		Approved	MGC4816, MGC12866, MGC119522, MGC119523, dJ967N21.5, REC	uc002wmi.3	Q9UJA3	OTTHUMG00000031822	ENST00000378896.3:c.303A>C	20.37:g.5935303A>C	ENSP00000368174:p.Lys101Asn	94.0	0.0	0		103.0	50.0	0.485437	NM_032485	B2RBG7|D3DW08|E7EQU7|Q495R4|Q495R6|Q495R7|Q86US4|Q969I5	Missense_Mutation	SNP	ENST00000378896.3	37	CCDS13094.1	145	0.06639194139194139	92	0.18699186991869918	29	0.08011049723756906	2	0.0034965034965034965	22	0.029023746701846966	A	11.02	1.515159	0.27123	0.148114	0.021279	ENSG00000125885	ENST00000378896;ENST00000378883;ENST00000399350;ENST00000378886;ENST00000265187	T;T;T;T	0.04119	3.7;3.7;3.7;3.7	5.37	-10.4	0.00318	Nucleic acid-binding, OB-fold-like (1);	0.302307	0.39475	N	0.001357	T	0.00012	0.0000	L	0.29908	0.895	0.27511	P	0.9516967	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.001;0.002;0.001	T	0.38265	-0.9669	9	0.11485	T	0.65	-1.2423	2.7834	0.05367	0.2356:0.137:0.3949:0.2325	rs6117014;rs52802444;rs6117014	101;101;101;101	Q9UJA3-2;E7EQU7;Q9UJA3-3;Q9UJA3	.;.;.;MCM8_HUMAN	N	101	ENSP00000368174:K101N;ENSP00000368161:K101N;ENSP00000368164:K101N;ENSP00000265187:K101N	ENSP00000265187:K101N	K	+	3	2	MCM8	5883303	0.041000	0.20044	0.522000	0.27862	0.993000	0.82548	-1.262000	0.02852	-1.754000	0.01321	-0.250000	0.11733	AAA	A|0.936;C|0.064	0.064	strong		0.373	MCM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077900.1	NM_032485	
ECM1	1893	hgsc.bcm.edu	37	1	150484016	150484016	+	Silent	SNP	G	G	A	rs78194273	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:150484016G>A	ENST00000369047.4	+	7	917	c.792G>A	c.(790-792)gaG>gaA	p.E264E	ECM1_ENST00000470432.1_3'UTR|ECM1_ENST00000346569.6_Intron|ECM1_ENST00000369049.4_Silent_p.E291E	NM_004425.3	NP_004416.2	Q16610	ECM1_HUMAN	extracellular matrix protein 1	264	2 X approximate repeats.				angiogenesis (GO:0001525)|biomineral tissue development (GO:0031214)|inflammatory response (GO:0006954)|negative regulation of bone mineralization (GO:0030502)|negative regulation of cytokine-mediated signaling pathway (GO:0001960)|negative regulation of peptidase activity (GO:0010466)|ossification (GO:0001503)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|regulation of T cell migration (GO:2000404)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of type 2 immune response (GO:0002828)|signal transduction (GO:0007165)	extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	enzyme binding (GO:0019899)|laminin binding (GO:0043236)|protease binding (GO:0002020)|protein C-terminus binding (GO:0008022)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|urinary_tract(1)	22	all_cancers(9;3.13e-53)|all_epithelial(9;3.74e-43)|all_lung(15;2.43e-34)|Lung NSC(24;8.86e-31)|Breast(34;0.000326)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0757)|all cancers(9;1.29e-21)|BRCA - Breast invasive adenocarcinoma(12;0.000734)|LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.206)			GGCAGGGGGAGGCTCGGTTCT	0.632													G|||	82	0.0163738	0.0582	0.0072	5008	,	,		16846	0.0		0.0	False		,,,				2504	0.0				p.E291E	Melanoma(156;1696 2560 11093 19685)	Atlas-SNP	.											.	ECM1	96	.	0			c.G873A						PASS	.	G	,,	207,4199	127.4+/-164.3	7,193,2003	52.0	50.0	51.0		873,792,	4.5	1.0	1	dbSNP_132	51	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous,intron	ECM1	NM_001202858.1,NM_004425.3,NM_022664.2	,,	7,196,6300	AA,AG,GG		0.0349,4.6981,1.6146	,,	291/568,264/541,	150484016	210,12796	2203	4300	6503	SO:0001819	synonymous_variant	1893	exon7			GGGGGAGGCTCGG	U68186	CCDS953.1, CCDS954.1, CCDS55632.1	1q21	2008-02-05			ENSG00000143369	ENSG00000143369			3153	protein-coding gene	gene with protein product		602201				9367673, 9501329	Standard	NM_004425		Approved		uc001eus.3	Q16610	OTTHUMG00000012806	ENST00000369047.4:c.792G>A	1.37:g.150484016G>A		88.0	0.0	0		99.0	54.0	0.545455	NM_001202858	A8K8S0|B4DW49|B4DY60|O43266|Q5T5G4|Q5T5G5|Q5T5G6|Q8IZ60	Silent	SNP	ENST00000369047.4	37	CCDS953.1																																																																																			G|0.984;A|0.016	0.016	strong		0.632	ECM1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035832.2	NM_004425	
LRP2	4036	hgsc.bcm.edu	37	2	170038097	170038097	+	Missense_Mutation	SNP	C	C	T	rs137983840	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170038097C>T	ENST00000263816.3	-	52	10315	c.10030G>A	c.(10030-10032)Gca>Aca	p.A3344T	LRP2_ENST00000461418.1_5'UTR	NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	3344					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	CCAATGTATGCGCGGTGACCC	0.483													C|||	8	0.00159744	0.0053	0.0014	5008	,	,		18886	0.0		0.0	False		,,,				2504	0.0				p.A3344T		Atlas-SNP	.											LRP2,NS,carcinoma,0,1	LRP2	751	1	0			c.G10030A						PASS	.	C	THR/ALA	23,4383	29.9+/-59.1	0,23,2180	151.0	123.0	132.0		10030	4.8	0.8	2	dbSNP_134	132	1,8599	1.2+/-3.3	0,1,4299	yes	missense	LRP2	NM_004525.2	58	0,24,6479	TT,TC,CC		0.0116,0.522,0.1845	probably-damaging	3344/4656	170038097	24,12982	2203	4300	6503	SO:0001583	missense	4036	exon52			TGTATGCGCGGTG		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.10030G>A	2.37:g.170038097C>T	ENSP00000263816:p.Ala3344Thr	197.0	0.0	0		183.0	82.0	0.448087	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	2	9.157509157509158E-4	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	0	0.0	C	17.25	3.341348	0.60963	0.00522	1.16E-4	ENSG00000081479	ENST00000263816;ENST00000536293	D	0.97811	-4.55	5.66	4.76	0.60689	Six-bladed beta-propeller, TolB-like (1);Growth factor, receptor (1);	0.170562	0.52532	D	0.000080	D	0.98327	0.9445	M	0.92169	3.28	0.80722	D	1	D	0.76494	0.999	P	0.62184	0.899	D	0.96079	0.9052	10	0.59425	D	0.04	.	16.2936	0.82761	0.0:0.7787:0.2213:0.0	.	3344	P98164	LRP2_HUMAN	T	3344;39	ENSP00000263816:A3344T	ENSP00000263816:A3344T	A	-	1	0	LRP2	169746343	0.991000	0.36638	0.788000	0.31933	0.219000	0.24729	2.604000	0.46274	2.661000	0.90470	0.655000	0.94253	GCA	C|0.999;T|0.001	0.001	strong		0.483	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
TCEB3	6924	hgsc.bcm.edu	37	1	24077554	24077554	+	Silent	SNP	T	T	C	rs35397069	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:24077554T>C	ENST00000418390.2	+	4	808	c.537T>C	c.(535-537)gaT>gaC	p.D179D	TCEB3_ENST00000609199.1_Silent_p.D153D	NM_003198.2	NP_003189.2	Q14241	ELOA1_HUMAN	transcription elongation factor B (SIII), polypeptide 3 (110kDa, elongin A)	179					gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|pancreas(1)|prostate(2)|skin(1)	19		Colorectal(325;3.46e-05)|Lung NSC(340;0.000112)|all_lung(284;0.00016)|Renal(390;0.000219)|Breast(348;0.0044)|Ovarian(437;0.00539)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;2.42e-24)|Colorectal(126;5.5e-08)|COAD - Colon adenocarcinoma(152;3.09e-06)|GBM - Glioblastoma multiforme(114;4.74e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000973)|KIRC - Kidney renal clear cell carcinoma(1967;0.00334)|STAD - Stomach adenocarcinoma(196;0.0127)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.0853)|LUSC - Lung squamous cell carcinoma(448;0.187)		AGAGGAGAGATGAGAGAAAGA	0.498													C|||	487	0.0972444	0.351	0.0303	5008	,	,		19697	0.0		0.001	False		,,,				2504	0.001				p.D179D		Atlas-SNP	.											.	TCEB3	61	.	0			c.T537C						PASS	.	C		1242,3164	704.4+/-407.1	172,898,1133	105.0	97.0	100.0		537	-11.1	0.1	1	dbSNP_126	100	22,8578	818.3+/-406.9	0,22,4278	no	coding-synonymous	TCEB3	NM_003198.2		172,920,5411	CC,CT,TT		0.2558,28.1888,9.7186		179/799	24077554	1264,11742	2203	4300	6503	SO:0001819	synonymous_variant	6924	exon4			GAGAGATGAGAGA	L47345	CCDS239.2	1p36.1	2010-06-22	2002-08-29		ENSG00000011007	ENSG00000011007			11620	protein-coding gene	gene with protein product		600786	"""transcription elongation factor B (SIII), polypeptide 3 (110kD, elongin A)"""			8586449, 7660129	Standard	NM_003198		Approved	SIII, TCEB3A	uc001bho.3	Q14241	OTTHUMG00000002957	ENST00000418390.2:c.537T>C	1.37:g.24077554T>C		148.0	0.0	0		159.0	68.0	0.427673	NM_003198	B2R7Q8|Q8IXH1	Silent	SNP	ENST00000418390.2	37	CCDS239.2																																																																																			T|0.913;C|0.087	0.087	strong		0.498	TCEB3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000008230.2	NM_003198	
VCAN	1462	hgsc.bcm.edu	37	5	82836912	82836912	+	Missense_Mutation	SNP	G	G	A	rs61733389	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:82836912G>A	ENST00000265077.3	+	8	8655	c.8090G>A	c.(8089-8091)cGt>cAt	p.R2697H	VCAN_ENST00000513016.1_3'UTR|VCAN-AS1_ENST00000513899.1_RNA|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000512590.2_Intron|VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000343200.5_Missense_Mutation_p.R1710H	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	2697	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	CCAATTCCTCGTAAGTCTGCC	0.453													A|||	154	0.0307508	0.1097	0.0086	5008	,	,		22255	0.0		0.003	False		,,,				2504	0.0				p.R2697H		Atlas-SNP	.											.	VCAN	498	.	0			c.G8090A						PASS	.	A	,HIS/ARG,,HIS/ARG	375,4031	781.0+/-414.5	12,351,1840	87.0	82.0	84.0		,5129,,8090	3.4	0.0	5	dbSNP_129	84	4,8596	806.0+/-407.3	0,4,4296	yes	intron,missense,intron,missense	VCAN	NM_001126336.2,NM_001164097.1,NM_001164098.1,NM_004385.4	,29,,29	12,355,6136	AA,AG,GG		0.0465,8.5111,2.914	,benign,,benign	,1710/2410,,2697/3397	82836912	379,12627	2203	4300	6503	SO:0001583	missense	1462	exon8			TTCCTCGTAAGTC	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.8090G>A	5.37:g.82836912G>A	ENSP00000265077:p.Arg2697His	92.0	0.0	0		87.0	51.0	0.586207	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	59	0.027014652014652016	57	0.11585365853658537	2	0.0055248618784530384	0	0.0	0	0.0	A	3.518	-0.098356	0.07010	0.085111	4.65E-4	ENSG00000038427	ENST00000265077;ENST00000343200	T;T	0.30714	1.52;1.52	6.17	3.43	0.39272	.	0.411591	0.25929	N	0.027400	T	0.00210	0.0006	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.01281	0.0;0.0	T	0.19031	-1.0318	10	0.33940	T	0.23	.	9.0379	0.36300	0.1951:0.1117:0.6933:0.0	rs61733389	1710;2697	P13611-2;P13611	.;CSPG2_HUMAN	H	2697;1710	ENSP00000265077:R2697H;ENSP00000340062:R1710H	ENSP00000265077:R2697H	R	+	2	0	VCAN	82872668	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.225000	0.09151	0.183000	0.20059	-1.569000	0.00873	CGT	G|0.967;A|0.033	0.033	strong		0.453	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
C12orf43	64897	hgsc.bcm.edu	37	12	121442833	121442833	+	Missense_Mutation	SNP	C	C	T	rs34543757	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:121442833C>T	ENST00000288757.3	-	5	447	c.425G>A	c.(424-426)cGc>cAc	p.R142H	C12orf43_ENST00000537817.1_Missense_Mutation_p.R143H|C12orf43_ENST00000536407.2_Intron|C12orf43_ENST00000445832.3_Missense_Mutation_p.R112H|C12orf43_ENST00000539736.1_Missense_Mutation_p.R131H|C12orf43_ENST00000366211.2_Missense_Mutation_p.R100H	NM_022895.1	NP_075046.1	Q96C57	CL043_HUMAN	chromosome 12 open reading frame 43	142										cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(10)	14	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TCGCTTTCGGCGGGGTTGGGG	0.527													.|||	31	0.0061901	0.0227	0.0	5008	,	,		13357	0.0		0.0	False		,,,				2504	0.001				p.R142H		Atlas-SNP	.											.	C12orf43	30	.	0			c.G425A						PASS	.	C	HIS/ARG	121,4283		2,117,2083	64.0	67.0	66.0		425	-0.7	0.0	12	dbSNP_126	66	0,8594		0,0,4297	yes	missense	C12orf43	NM_022895.1	29	2,117,6380	TT,TC,CC		0.0,2.7475,0.9309	benign	142/263	121442833	121,12877	2202	4297	6499	SO:0001583	missense	64897	exon5			TTTCGGCGGGGTT	AK022510	CCDS66486.1, CCDS66487.1	12q24.31	2012-05-30			ENSG00000157895	ENSG00000157895			25719	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_001286195		Approved	FLJ12448	uc001tzh.1	Q96C57	OTTHUMG00000169150	ENST00000288757.3:c.425G>A	12.37:g.121442833C>T	ENSP00000288757:p.Arg142His	84.0	0.0	0		100.0	57.0	0.57	NM_022895	Q53HF0|Q9H9Z7	Missense_Mutation	SNP	ENST00000288757.3	37	CCDS9210.1	15|15	0.006868131868131868|0.006868131868131868	15|15	0.03048780487804878|0.03048780487804878	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	C|C	10.27|10.27	1.304130|1.304130	0.23736|0.23736	0.027475|0.027475	0.0|0.0	ENSG00000157895|ENSG00000157895	ENST00000546272|ENST00000445832;ENST00000288757;ENST00000537817;ENST00000366211;ENST00000539736;ENST00000538296;ENST00000535367	.|T;T;T;T;T	.|0.49432	.|0.81;0.78;0.81;0.84;0.83	5.65|5.65	-0.735|-0.735	0.11137|0.11137	.|.	.|1.534110	.|0.03428	.|N	.|0.207380	T|T	0.11067|0.11067	0.0270|0.0270	N|N	0.21142|0.21142	0.635|0.635	0.09310|0.09310	N|N	1|1	.|B;B;B;B;B	.|0.19817	.|0.017;0.039;0.003;0.017;0.001	.|B;B;B;B;B	.|0.15052	.|0.007;0.012;0.003;0.007;0.002	T|T	0.03514|0.03514	-1.1029|-1.1029	5|10	.|0.17832	.|T	.|0.49	0.9065|0.9065	2.1|2.1	0.03677|0.03677	0.1243:0.427:0.2412:0.2075|0.1243:0.427:0.2412:0.2075	.|.	.|131;100;143;131;142	.|G5EA44;F6TFQ5;F5H7W8;B4DWJ9;Q96C57	.|.;.;.;.;CL043_HUMAN	T|H	95|112;142;143;100;131;79;96	.|ENSP00000409788:R112H;ENSP00000288757:R142H;ENSP00000442224:R143H;ENSP00000437803:R131H;ENSP00000442041:R79H	.|ENSP00000288757:R142H	A|R	-|-	1|2	0|0	C12orf43|C12orf43	119927216|119927216	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	-0.008000|-0.008000	0.12788|0.12788	-0.335000|-0.335000	0.08451|0.08451	-0.158000|-0.158000	0.13435|0.13435	GCC|CGC	C|0.990;G|0.000;T|0.009	0.009	strong		0.527	C12orf43-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022895	
PRSS27	83886	hgsc.bcm.edu	37	16	2762637	2762637	+	Missense_Mutation	SNP	A	A	G	rs61734617	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2762637A>G	ENST00000302641.3	-	6	911	c.857T>C	c.(856-858)tTg>tCg	p.L286S	AC092117.1_ENST00000410123.1_RNA	NM_031948.3	NP_114154.1	Q9BQR3	PRS27_HUMAN	protease, serine 27	286						extracellular region (GO:0005576)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)	8						CTGGCCGCCCAACCTCGCTGG	0.662													g|||	240	0.0479233	0.174	0.0101	5008	,	,		14544	0.0		0.003	False		,,,				2504	0.0				p.L286S		Atlas-SNP	.											.	PRSS27	20	.	0			c.T857C						PASS	.	G	SER/LEU	609,3777		37,535,1621	42.0	37.0	38.0		857	-2.0	0.0	16	dbSNP_129	38	4,8592		0,4,4294	yes	missense	PRSS27	NM_031948.3	145	37,539,5915	GG,GA,AA		0.0465,13.8851,4.7219	benign	286/291	2762637	613,12369	2193	4298	6491	SO:0001583	missense	83886	exon6			CCGCCCAACCTCG	AB056161	CCDS10476.1	16p13.3	2010-05-07			ENSG00000172382	ENSG00000172382		"""Serine peptidases / Serine peptidases"""	15475	protein-coding gene	gene with protein product		608018					Standard	NM_031948		Approved	MPN, pancreasin, CAPH2, marapsin	uc002crf.3	Q9BQR3	OTTHUMG00000128929	ENST00000302641.3:c.857T>C	16.37:g.2762637A>G	ENSP00000306390:p.Leu286Ser	164.0	0.0	0		171.0	82.0	0.479532	NM_031948		Missense_Mutation	SNP	ENST00000302641.3	37	CCDS10476.1	93	0.042582417582417584	90	0.18292682926829268	3	0.008287292817679558	0	0.0	0	0.0	.	2.610	-0.290913	0.05568	0.138851	4.65E-4	ENSG00000172382	ENST00000302641;ENST00000543965	D	0.88586	-2.4	4.96	-2.0	0.07433	.	5.046650	0.00575	N	0.000311	T	0.00412	0.0013	N	0.19112	0.55	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.50676	-0.8800	9	0.06625	T	0.88	.	2.0974	0.03671	0.3642:0.1178:0.3973:0.1207	.	286;250	Q9BQR3;B3KP25	PRS27_HUMAN;.	S	286;250	ENSP00000306390:L286S	ENSP00000306390:L286S	L	-	2	0	PRSS27	2702638	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.040000	0.13905	-1.081000	0.03105	-1.147000	0.01851	TTG	A|0.948;G|0.052	0.052	strong		0.662	PRSS27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250908.1	NM_031948	
SLC4A2	6522	hgsc.bcm.edu	37	7	150768849	150768849	+	Silent	SNP	C	C	T	rs11542749	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:150768849C>T	ENST00000485713.1	+	15	3305	c.2265C>T	c.(2263-2265)tgC>tgT	p.C755C	SLC4A2_ENST00000413384.2_Silent_p.C755C|SLC4A2_ENST00000310317.5_Silent_p.C673C|SLC4A2_ENST00000461735.1_Silent_p.C741C|RP11-148K1.12_ENST00000485974.1_RNA|SLC4A2_ENST00000392826.2_Silent_p.C746C	NM_001199692.1	NP_001186621.1	P04920	B3A2_HUMAN	solute carrier family 4 (anion exchanger), member 2	755	Membrane (anion exchange).				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	anion transmembrane transporter activity (GO:0008509)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(2)|liver(2)|lung(14)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	33			OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TGGTCTTCTGCCTGCTGGGTG	0.617													C|||	332	0.0662939	0.2027	0.036	5008	,	,		15252	0.0		0.0298	False		,,,				2504	0.0092				p.C755C		Atlas-SNP	.											.	SLC4A2	98	.	0			c.C2265T						PASS	.	C	,,,	593,3813	259.8+/-263.3	40,513,1650	83.0	90.0	88.0		2265,2238,2223,2265	1.9	1.0	7	dbSNP_120	88	256,8344	100.1+/-161.6	4,248,4048	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC4A2	NM_001199692.1,NM_001199693.1,NM_001199694.1,NM_003040.3	,,,	44,761,5698	TT,TC,CC		2.9767,13.4589,6.5278	,,,	755/1242,746/1233,741/1228,755/1242	150768849	849,12157	2203	4300	6503	SO:0001819	synonymous_variant	6522	exon15			CTTCTGCCTGCTG		CCDS5917.1, CCDS56520.1, CCDS56521.1	7q36.1	2013-07-19	2013-07-19		ENSG00000164889	ENSG00000164889		"""Solute carriers"""	11028	protein-coding gene	gene with protein product	"""anion exchanger 2 type a"", ""anion exchanger 2 type b1"", ""anion exchanger 2 type b2"""	109280	"""erythrocyte membrane protein band 3-like 1"", ""solute carrier family 4, anion exchanger, member 2 (erythrocyte membrane protein band 3-like 1)"""	EPB3L1, AE2		8434259	Standard	NM_003040		Approved	HKB3, BND3L, NBND3	uc003wit.4	P04920	OTTHUMG00000158443	ENST00000485713.1:c.2265C>T	7.37:g.150768849C>T		104.0	0.0	0		160.0	81.0	0.50625	NM_003040	B2R6T0|B4DIT0|D3DX05|F8W682|Q45EY5|Q969L3	Silent	SNP	ENST00000485713.1	37	CCDS5917.1																																																																																			C|0.927;T|0.073	0.073	strong		0.617	SLC4A2-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000351039.1	NM_003040	
LIPE	3991	hgsc.bcm.edu	37	19	42931004	42931004	+	Missense_Mutation	SNP	A	A	G	rs16975750	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42931004A>G	ENST00000244289.4	-	1	574	c.298T>C	c.(298-300)Tac>Cac	p.Y100H	LIPE-AS1_ENST00000457234.2_RNA|LIPE-AS1_ENST00000593740.2_RNA|LIPE-AS1_ENST00000594624.2_RNA|LIPE-AS1_ENST00000597203.1_RNA|CTB-50E14.4_ENST00000596781.1_RNA|LIPE-AS1_ENST00000594688.1_RNA	NM_005357.2	NP_005348.2	Q05469	LIPS_HUMAN	lipase, hormone-sensitive	100			Y -> H (in dbSNP:rs16975750). {ECO:0000269|Ref.3}.		cholesterol metabolic process (GO:0008203)|diacylglycerol catabolic process (GO:0046340)|lipid catabolic process (GO:0016042)|long-chain fatty acid catabolic process (GO:0042758)|protein phosphorylation (GO:0006468)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)	cytosol (GO:0005829)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)	hormone-sensitive lipase activity (GO:0033878)|triglyceride lipase activity (GO:0004806)			breast(2)|endometrium(4)|kidney(7)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	32		Prostate(69;0.00682)				CTTTGGATGTAAGGTGATTGC	0.502													G|||	393	0.0784744	0.2799	0.0288	5008	,	,		19320	0.0		0.003	False		,,,				2504	0.0				p.Y100H		Atlas-SNP	.											.	LIPE	83	.	0			c.T298C						PASS	.	G	HIS/TYR	997,3409	730.3+/-410.1	128,741,1334	167.0	172.0	171.0		298	-1.8	0.0	19	dbSNP_123	171	18,8582	818.6+/-406.8	0,18,4282	yes	missense	LIPE	NM_005357.2	83	128,759,5616	GG,GA,AA		0.2093,22.6282,7.8041	benign	100/1077	42931004	1015,11991	2203	4300	6503	SO:0001583	missense	3991	exon1			GGATGTAAGGTGA	L11706	CCDS12607.1	19q13.1-q13.2	2014-03-14			ENSG00000079435	ENSG00000079435	3.1.1.3		6621	protein-coding gene	gene with protein product		151750				8506334	Standard	NM_005357		Approved	HSL	uc002otr.3	Q05469	OTTHUMG00000182814	ENST00000244289.4:c.298T>C	19.37:g.42931004A>G	ENSP00000244289:p.Tyr100His	434.0	1.0	0.00230415		434.0	193.0	0.4447	NM_005357	Q3LRT2|Q6NSL7	Missense_Mutation	SNP	ENST00000244289.4	37	CCDS12607.1	152	0.0695970695970696	136	0.2764227642276423	13	0.03591160220994475	0	0.0	3	0.00395778364116095	G	0.044	-1.272008	0.01421	0.226282	0.002093	ENSG00000079435	ENST00000244289	T	0.21361	2.01	4.4	-1.76	0.08006	.	0.581795	0.14398	N	0.322096	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.42327	-0.9458	9	0.12430	T	0.62	-3.0127	1.9171	0.03299	0.4826:0.1392:0.2367:0.1415	rs16975750;rs52836316;rs58365984;rs16975750	100	Q05469	LIPS_HUMAN	H	100	ENSP00000244289:Y100H	ENSP00000244289:Y100H	Y	-	1	0	LIPE	47622844	0.018000	0.18449	0.025000	0.17156	0.087000	0.18053	-0.426000	0.07008	-0.446000	0.07149	-0.213000	0.12676	TAC	A|0.915;G|0.085	0.085	strong		0.502	LIPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463861.1	NM_005357	
ZNF71	58491	hgsc.bcm.edu	37	19	57132879	57132879	+	Missense_Mutation	SNP	G	G	A	rs79950845	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:57132879G>A	ENST00000328070.6	+	3	458	c.224G>A	c.(223-225)tGt>tAt	p.C75Y		NM_021216.4	NP_067039.1	Q9NQZ8	ZNF71_HUMAN	zinc finger protein 71	75					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|large_intestine(5)|lung(13)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	26				GBM - Glioblastoma multiforme(193;0.062)|Lung(386;0.0681)|LUSC - Lung squamous cell carcinoma(496;0.18)		GTACCCGCATGTCATGAACTG	0.622													G|||	99	0.0197684	0.0741	0.0014	5008	,	,		17597	0.0		0.0	False		,,,				2504	0.0				p.C75Y		Atlas-SNP	.											.	ZNF71	69	.	0			c.G224A						PASS	.	G	TYR/CYS	263,4143	149.5+/-183.7	5,253,1945	57.0	54.0	55.0		224	2.9	0.0	19	dbSNP_131	55	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ZNF71	NM_021216.4	194	5,254,6244	AA,AG,GG		0.0116,5.9691,2.0298	possibly-damaging	75/490	57132879	264,12742	2203	4300	6503	SO:0001583	missense	58491	exon3			CCGCATGTCATGA	X60074	CCDS12947.1	19q13.4	2013-01-08	2006-05-12			ENSG00000197951		"""Zinc fingers, C2H2-type"""	13141	protein-coding gene	gene with protein product		194545	"""zinc finger protein 71 (Cos26)"""			1639391	Standard	NM_021216		Approved	Cos26, EZFIT	uc002qnm.4	Q9NQZ8		ENST00000328070.6:c.224G>A	19.37:g.57132879G>A	ENSP00000328245:p.Cys75Tyr	72.0	0.0	0		77.0	43.0	0.558442	NM_021216	Q15919|Q9UC09|Q9UQD3	Missense_Mutation	SNP	ENST00000328070.6	37	CCDS12947.1	39	0.017857142857142856	38	0.07723577235772358	1	0.0027624309392265192	0	0.0	0	0.0	G	13.10	2.134948	0.37728	0.059691	1.16E-4	ENSG00000197951	ENST00000328070	T	0.07114	3.22	2.91	2.91	0.33838	.	.	.	.	.	T	0.00815	0.0027	M	0.91249	3.19	0.09310	N	1	B	0.26318	0.146	B	0.22753	0.041	T	0.04203	-1.0969	9	0.62326	D	0.03	.	9.5203	0.39131	0.0:0.0:1.0:0.0	.	75	Q9NQZ8	ZNF71_HUMAN	Y	75	ENSP00000328245:C75Y	ENSP00000328245:C75Y	C	+	2	0	ZNF71	61824691	0.006000	0.16342	0.002000	0.10522	0.001000	0.01503	0.648000	0.24828	1.942000	0.56320	0.561000	0.74099	TGT	G|0.976;A|0.024	0.024	strong		0.622	ZNF71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459798.2	NM_021216	
MT-ND5	4540	hgsc.bcm.edu	37	M	13105	13105	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:13105A>G	ENST00000361567.2	+	1	769	c.769A>G	c.(769-771)Atc>Gtc	p.I257V	MT-TR_ENST00000387439.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-TE_ENST00000387459.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	257			I -> V (in dbSNP:rs2853501). {ECO:0000269|PubMed:11553319, ECO:0000269|PubMed:7530363}.		cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						TTGTAGCAGGAATCTTCTTAC	0.517																																					p.I257V		Atlas-SNP	.											.	.	.	.	0			c.A769G						PASS	.																																			SO:0001583	missense	0	exon1			GCAGGAATCTTCT			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.769A>G	M.37:g.13105A>G	ENSP00000354813:p.Ile257Val	6.0	0.0	0		7.0	7.0	1	ENST00000361567	Q34773|Q8WCY3	Missense_Mutation	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.517	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
LILRA6	79168	hgsc.bcm.edu	37	19	54745659	54745659	+	Missense_Mutation	SNP	G	G	C	rs200657736		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54745659G>C	ENST00000396365.2	-	4	490	c.451C>G	c.(451-453)Cac>Gac	p.H151D	LILRA6_ENST00000440558.2_Missense_Mutation_p.H151D|LILRA6_ENST00000391735.3_Missense_Mutation_p.H151D|LILRA6_ENST00000419410.2_Missense_Mutation_p.H151D|LILRA6_ENST00000245621.5_Missense_Mutation_p.H151D|LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000270464.5_Missense_Mutation_p.H151D	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	151					immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		ACAAAATGGTGATATCCCTTC	0.592																																					p.H151D		Atlas-SNP	.											LILRA6,NS,carcinoma,0,2	LILRA6	75	2	0			c.C451G						scavenged	.						23.0	37.0	32.0					19																	54745659		2100	4266	6366	SO:0001583	missense	79168	exon4			AATGGTGATATCC	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15495	protein-coding gene	gene with protein product			"""leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"""	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.451C>G	19.37:g.54745659G>C	ENSP00000379651:p.His151Asp	500.0	1.0	0.002		875.0	120.0	0.137143	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	g	0	-2.647560	0.00111	.	.	ENSG00000244482	ENST00000440558;ENST00000270464;ENST00000419410;ENST00000391735;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T;T;T	0.10960	2.82;2.82;2.82;4.04;2.82;2.82	2.64	-5.28	0.02755	Immunoglobulin-like fold (1);	2.010510	0.02119	N	0.055507	T	0.01870	0.0059	N	0.00237	-1.79	0.09310	N	1	B;B;B;B;B;B	0.09022	0.002;0.0;0.002;0.0;0.0;0.0	B;B;B;B;B;B	0.08055	0.003;0.0;0.003;0.001;0.002;0.001	T	0.25537	-1.0129	10	0.02654	T	1	.	3.0381	0.06129	0.2388:0.2899:0.373:0.0983	.	151;151;151;151;151;151	C9JFH3;Q6PI73-2;Q6PI73;F8WCY4;D3YTC4;F8W6G6	.;.;LIRA6_HUMAN;.;.;.	D	151	ENSP00000390120:H151D;ENSP00000270464:H151D;ENSP00000411227:H151D;ENSP00000375615:H151D;ENSP00000379651:H151D;ENSP00000245621:H151D	ENSP00000245621:H151D	H	-	1	0	LILRA6	59437471	.	.	0.000000	0.03702	0.020000	0.10135	.	.	-3.099000	0.00245	-1.962000	0.00476	CAC	G|0.999;C|0.001	0.001	weak		0.592	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
CPB1	1360	hgsc.bcm.edu	37	3	148545789	148545789	+	Splice_Site	SNP	C	C	T	rs80013498	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:148545789C>T	ENST00000491148.1	+	3	406	c.72C>T	c.(70-72)ggC>ggT	p.G24G	CPB1_ENST00000282957.4_Splice_Site_p.G24G			P15086	CBPB1_HUMAN	carboxypeptidase B1 (tissue)	24						extracellular region (GO:0005576)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	38			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)			CATTATTCAGCGAGAAGGTGT	0.408													C|||	50	0.00998403	0.0356	0.0029	5008	,	,		21398	0.001		0.0	False		,,,				2504	0.0				p.G24G		Atlas-SNP	.											.	CPB1	74	.	0			c.C72T						PASS	.	C		163,4243	110.4+/-148.6	2,159,2042	101.0	103.0	102.0		72	-7.2	0.1	3	dbSNP_131	102	0,8600		0,0,4300	yes	coding-synonymous-near-splice	CPB1	NM_001871.2		2,159,6342	TT,TC,CC		0.0,3.6995,1.2533		24/418	148545789	163,12843	2203	4300	6503	SO:0001630	splice_region_variant	1360	exon2			ATTCAGCGAGAAG	AJ224866	CCDS33874.1	3q24	2012-02-10			ENSG00000153002	ENSG00000153002	3.4.17.2		2299	protein-coding gene	gene with protein product	"""pancreatic carboxypeptidase B"", ""tissue carboxypeptidase B"", ""protaminase"""	114852					Standard	XM_005247124		Approved		uc003ewl.3	P15086	OTTHUMG00000159520	ENST00000491148.1:c.72-1C>T	3.37:g.148545789C>T		111.0	0.0	0		146.0	71.0	0.486301	NM_001871	O60834|Q53XJ0|Q96BQ8	Silent	SNP	ENST00000491148.1	37	CCDS33874.1																																																																																			C|0.986;T|0.014	0.014	strong		0.408	CPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355928.1	NM_001871	Silent
TEKT5	146279	hgsc.bcm.edu	37	16	10769873	10769873	+	Silent	SNP	G	G	A	rs115325161	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:10769873G>A	ENST00000283025.2	-	5	1100	c.1029C>T	c.(1027-1029)aaC>aaT	p.N343N		NM_144674.1	NP_653275.1	Q96M29	TEKT5_HUMAN	tektin 5	343						cilium (GO:0005929)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)				breast(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(9)|lung(9)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(4)	34						AGATGCGGGCGTTGAAGGCCA	0.602													A|||	25	0.00499201	0.0174	0.0029	5008	,	,		21091	0.0		0.0	False		,,,				2504	0.0				p.N343N		Atlas-SNP	.											.	TEKT5	66	.	0			c.C1029T						PASS	.	A		72,4322	818.8+/-416.3	1,70,2126	153.0	126.0	135.0		1029	-3.3	0.1	16	dbSNP_132	135	0,8600		0,0,4300	no	coding-synonymous	TEKT5	NM_144674.1		1,70,6426	AA,AG,GG		0.0,1.6386,0.5541		343/486	10769873	72,12922	2197	4300	6497	SO:0001819	synonymous_variant	146279	exon5			GCGGGCGTTGAAG		CCDS10542.1	16p13.13	2014-01-21			ENSG00000153060	ENSG00000153060			26554	protein-coding gene	gene with protein product							Standard	NM_144674		Approved	FLJ32871, CT149	uc002czz.1	Q96M29	OTTHUMG00000129750	ENST00000283025.2:c.1029C>T	16.37:g.10769873G>A		86.0	0.0	0		101.0	56.0	0.554455	NM_144674	A1L3Z3	Silent	SNP	ENST00000283025.2	37	CCDS10542.1																																																																																			G|0.995;A|0.005	0.005	strong		0.602	TEKT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251963.1	NM_144674	
ZKSCAN4	387032	hgsc.bcm.edu	37	6	28219695	28219695	+	Missense_Mutation	SNP	G	G	A	rs62638680	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:28219695G>A	ENST00000377294.2	-	1	307	c.64C>T	c.(64-66)Ctc>Ttc	p.L22F	ZKSCAN4_ENST00000423974.2_Intron	NM_019110.3	NP_061983.2	Q969J2	ZKSC4_HUMAN	zinc finger with KRAB and SCAN domains 4	22					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	18						ACGGTCAGGAGCCCCGTCTGG	0.637													G|||	179	0.0357428	0.1082	0.0187	5008	,	,		15084	0.006		0.0139	False		,,,				2504	0.0031				p.L22F		Atlas-SNP	.											.	ZKSCAN4	42	.	0			c.C64T						PASS	.	G	PHE/LEU	433,3917		24,385,1766	63.0	69.0	67.0		64	-0.6	0.1	6	dbSNP_129	67	51,8447		0,51,4198	yes	missense	ZKSCAN4	NM_019110.3	22	24,436,5964	AA,AG,GG		0.6001,9.954,3.7671	benign	22/546	28219695	484,12364	2175	4249	6424	SO:0001583	missense	387032	exon1			TCAGGAGCCCCGT	AK056698	CCDS4647.1	6p21	2013-01-09	2007-02-20	2007-02-20	ENSG00000187626	ENSG00000187626		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13854	protein-coding gene	gene with protein product		611643	"""zinc finger protein 307"", ""zinc finger protein 427"""	ZNF307, ZNF427		12477932	Standard	NM_019110		Approved	p373c6.1, P1P373C6, FLJ32136, ZSCAN36	uc003nks.1	Q969J2	OTTHUMG00000014511	ENST00000377294.2:c.64C>T	6.37:g.28219695G>A	ENSP00000366509:p.Leu22Phe	82.0	0.0	0		102.0	101.0	0.990196	NM_019110	B2RE32|Q5U7L4	Missense_Mutation	SNP	ENST00000377294.2	37	CCDS4647.1	77	0.035256410256410256	52	0.10569105691056911	9	0.024861878453038673	5	0.008741258741258742	11	0.014511873350923483	G	16.83	3.231677	0.58777	0.09954	0.006001	ENSG00000187626	ENST00000377294	T	0.08896	3.04	4.21	-0.602	0.11634	.	.	.	.	.	T	0.02047	0.0064	L	0.27053	0.805	0.09310	N	0.999995	P	0.46706	0.883	P	0.44732	0.459	T	0.39901	-0.9591	9	0.46703	T	0.11	.	3.0342	0.06116	0.0972:0.1668:0.458:0.278	.	22	Q969J2	ZKSC4_HUMAN	F	22	ENSP00000366509:L22F	ENSP00000366509:L22F	L	-	1	0	ZKSCAN4	28327674	0.000000	0.05858	0.050000	0.19076	0.678000	0.39670	-0.612000	0.05616	0.044000	0.15775	0.563000	0.77884	CTC	G|0.968;A|0.032	0.032	strong		0.637	ZKSCAN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040179.1	NM_019110	
PKD1L1	168507	hgsc.bcm.edu	37	7	47927650	47927650	+	Missense_Mutation	SNP	G	G	A	rs79105203	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:47927650G>A	ENST00000289672.2	-	17	2824	c.2774C>T	c.(2773-2775)cCg>cTg	p.P925L		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	925	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						AGACAGATTCGGTATTTCACT	0.398													G|||	230	0.0459265	0.1641	0.0115	5008	,	,		21650	0.0		0.004	False		,,,				2504	0.001				p.P925L		Atlas-SNP	.											PKD1L1,colon,carcinoma,0,1	PKD1L1	328	1	0			c.C2774T						scavenged	.	G	LEU/PRO	738,3668	302.1+/-287.2	68,602,1533	123.0	115.0	118.0		2774	-4.2	0.0	7	dbSNP_132	118	85,8515	48.1+/-107.5	1,83,4216	yes	missense	PKD1L1	NM_138295.3	98	69,685,5749	AA,AG,GG		0.9884,16.7499,6.3278	benign	925/2850	47927650	823,12183	2203	4300	6503	SO:0001583	missense	168507	exon17			AGATTCGGTATTT	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.2774C>T	7.37:g.47927650G>A	ENSP00000289672:p.Pro925Leu	125.0	1.0	0.008		98.0	54.0	0.55102	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	100	0.045787545787545784	92	0.18699186991869918	5	0.013812154696132596	0	0.0	3	0.00395778364116095	G	7.863	0.726477	0.15439	0.167499	0.009884	ENSG00000158683	ENST00000289672	T	0.69306	-0.39	5.65	-4.17	0.03857	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	1.960750	0.02041	N	0.049260	T	0.00109	0.0003	L	0.27053	0.805	0.80722	P	0.0	B	0.17268	0.021	B	0.10450	0.005	T	0.04635	-1.0937	9	0.37606	T	0.19	0.0986	5.9318	0.19142	0.1912:0.0:0.3612:0.4476	.	925	Q8TDX9	PK1L1_HUMAN	L	925	ENSP00000289672:P925L	ENSP00000289672:P925L	P	-	2	0	PKD1L1	47894175	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.980000	0.01492	-0.571000	0.06014	-0.978000	0.02582	CCG	G|0.945;A|0.055	0.055	strong		0.398	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
RRAGC	64121	hgsc.bcm.edu	37	1	39325136	39325136	+	Silent	SNP	C	C	T	rs112925356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:39325136C>T	ENST00000373001.3	-	1	359	c.183G>A	c.(181-183)aaG>aaA	p.K61K	RP5-864K19.4_ENST00000456813.1_RNA|RP5-864K19.4_ENST00000433671.2_RNA	NM_022157.2	NP_071440.1			Ras-related GTP binding C											endometrium(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(1)	10	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)				GAATCCTCGGCTTGGAGCTGT	0.726													C|||	139	0.0277556	0.0658	0.0086	5008	,	,		6031	0.001		0.001	False		,,,				2504	0.045				p.K61K		Atlas-SNP	.											.	RRAGC	28	.	0			c.G183A						PASS	.	C		156,3314		2,152,1581	7.0	8.0	7.0		183	5.0	1.0	1	dbSNP_132	7	12,6612		0,12,3300	no	coding-synonymous	RRAGC	NM_022157.2		2,164,4881	TT,TC,CC		0.1812,4.4957,1.6644		61/400	39325136	168,9926	1735	3312	5047	SO:0001819	synonymous_variant	64121	exon1			CCTCGGCTTGGAG	AF323609	CCDS430.1	1p34	2008-02-05			ENSG00000116954	ENSG00000116954			19902	protein-coding gene	gene with protein product		608267				11073942	Standard	NM_022157		Approved	GTR2, FLJ13311	uc001ccq.3	Q9HB90	OTTHUMG00000000490	ENST00000373001.3:c.183G>A	1.37:g.39325136C>T		53.0	0.0	0		56.0	29.0	0.517857	NM_001271851		Silent	SNP	ENST00000373001.3	37	CCDS430.1																																																																																			C|0.978;T|0.022	0.022	strong		0.726	RRAGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001222.2	NM_022157	
ARSG	22901	hgsc.bcm.edu	37	17	66416511	66416511	+	Silent	SNP	C	C	T	rs35268505	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:66416511C>T	ENST00000448504.2	+	12	2281	c.1485C>T	c.(1483-1485)aaC>aaT	p.N495N	WIPI1_ENST00000589459.1_5'Flank|ARSG_ENST00000452479.2_Silent_p.N331N|ARSG_ENST00000582154.1_3'UTR|RP11-120M18.2_ENST00000592030.1_RNA	NM_014960.4	NP_055775.2	Q96EG1	ARSG_HUMAN	arylsulfatase G	495					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sulfur compound metabolic process (GO:0006790)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular space (GO:0005615)|lysosome (GO:0005764)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			NS(2)|endometrium(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|stomach(1)|urinary_tract(1)	26			BRCA - Breast invasive adenocarcinoma(8;5.34e-07)|LUSC - Lung squamous cell carcinoma(166;0.24)			ACATTGCCAACGACAACATCT	0.552													C|||	79	0.0157748	0.0575	0.0043	5008	,	,		20902	0.0		0.0	False		,,,				2504	0.0				p.N495N		Atlas-SNP	.											.	ARSG	55	.	0			c.C1485T						PASS	.	C		231,4175	136.5+/-172.5	2,227,1974	189.0	180.0	183.0		1485	-11.8	0.0	17	dbSNP_126	183	0,8600		0,0,4300	no	coding-synonymous	ARSG	NM_014960.3		2,227,6274	TT,TC,CC		0.0,5.2429,1.7761		495/526	66416511	231,12775	2203	4300	6503	SO:0001819	synonymous_variant	22901	exon12			TGCCAACGACAAC	AB023218	CCDS11676.1	17q24.2	2013-07-15	2006-02-15		ENSG00000141337	ENSG00000141337		"""Arylsulfatase family"""	24102	protein-coding gene	gene with protein product		610008				12461688, 16174644	Standard	NM_014960		Approved	KIAA1001	uc002jhc.2	Q96EG1	OTTHUMG00000179810	ENST00000448504.2:c.1485C>T	17.37:g.66416511C>T		238.0	0.0	0		240.0	125.0	0.520833	NM_001267727	Q6UXF2|Q9Y2K4	Silent	SNP	ENST00000448504.2	37	CCDS11676.1																																																																																			C|0.981;T|0.019	0.019	strong		0.552	ARSG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448369.1	NM_014960	
ACTN4	81	hgsc.bcm.edu	37	19	39212226	39212226	+	Missense_Mutation	SNP	C	C	T	rs140271107		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39212226C>T	ENST00000252699.2	+	12	1416	c.1340C>T	c.(1339-1341)tCg>tTg	p.S447L	ACTN4_ENST00000424234.2_Intron|ACTN4_ENST00000390009.3_Missense_Mutation_p.S228L	NM_004924.4	NP_004915.2	O43707	ACTN4_HUMAN	actinin, alpha 4	447					actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cellular component movement (GO:0051272)|positive regulation of pinocytosis (GO:0048549)|positive regulation of sodium:proton antiporter activity (GO:0032417)|protein localization to tight junction (GO:1902396)|protein transport (GO:0015031)|regulation of apoptotic process (GO:0042981)|response to hypoxia (GO:0001666)|tight junction assembly (GO:0070830)	cell-cell junction (GO:0005911)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|platelet alpha granule lumen (GO:0031093)|protein complex (GO:0043234)|pseudopodium (GO:0031143)|ribonucleoprotein complex (GO:0030529)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|nucleoside binding (GO:0001882)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|urinary_tract(3)	30	all_cancers(60;1.57e-05)|Ovarian(47;0.103)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			GCCACACTATCGGACATCAAA	0.632													C|||	1	0.000199681	0.0	0.0	5008	,	,		20965	0.0		0.001	False		,,,				2504	0.0				p.S447L	Colon(168;199 1940 10254 46213 46384)	Atlas-SNP	.											.	ACTN4	69	.	0			c.C1340T						PASS	.						125.0	101.0	109.0					19																	39212226		2203	4300	6503	SO:0001583	missense	81	exon12			CACTATCGGACAT	D89980	CCDS12518.1	19q13	2013-01-10			ENSG00000130402	ENSG00000130402		"""EF-hand domain containing"""	166	protein-coding gene	gene with protein product		604638	"""focal segmental glomerulosclerosis 1"""	FSGS1		9461087, 10700177	Standard	NM_004924		Approved		uc002oja.2	O43707	OTTHUMG00000137382	ENST00000252699.2:c.1340C>T	19.37:g.39212226C>T	ENSP00000252699:p.Ser447Leu	68.0	0.0	0		90.0	43.0	0.477778	NM_004924	A4K467|D6PXK4|O76048	Missense_Mutation	SNP	ENST00000252699.2	37	CCDS12518.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.50	3.636731	0.67130	.	.	ENSG00000130402	ENST00000252699;ENST00000445727;ENST00000390009	T;T	0.51325	0.71;0.71	4.21	4.21	0.49690	.	0.194257	0.34959	N	0.003557	T	0.54271	0.1848	M	0.65498	2.005	0.80722	D	1	B;B	0.32382	0.091;0.368	B;B	0.40636	0.335;0.154	T	0.61133	-0.7124	10	0.59425	D	0.04	.	15.8417	0.78852	0.0:1.0:0.0:0.0	.	447;447	E7EV83;O43707	.;ACTN4_HUMAN	L	447;447;228	ENSP00000252699:S447L;ENSP00000439497:S228L	ENSP00000252699:S447L	S	+	2	0	ACTN4	43904066	1.000000	0.71417	0.962000	0.40283	0.599000	0.36880	7.651000	0.83577	2.340000	0.79590	0.462000	0.41574	TCG	C|1.000;T|0.000	0.000	strong		0.632	ACTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268091.1		
TMEM19	55266	hgsc.bcm.edu	37	12	72094627	72094627	+	Missense_Mutation	SNP	C	C	G	rs74104122	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:72094627C>G	ENST00000266673.5	+	6	1457	c.863C>G	c.(862-864)aCt>aGt	p.T288S		NM_018279.3	NP_060749.2	Q96HH6	TMM19_HUMAN	transmembrane protein 19	288						integral component of membrane (GO:0016021)				large_intestine(1)|lung(8)	9		Breast(359;0.0889)		GBM - Glioblastoma multiforme(134;0.044)		GATGAAAGCACTGGCATGGTG	0.358													C|||	126	0.0251597	0.09	0.0086	5008	,	,		17302	0.0		0.001	False		,,,				2504	0.0				p.T288S		Atlas-SNP	.											.	TMEM19	35	.	0			c.C863G						PASS	.	C	SER/THR	319,4087	170.9+/-201.2	13,293,1897	195.0	174.0	181.0		863	5.0	1.0	12	dbSNP_130	181	3,8597	3.0+/-9.4	0,3,4297	yes	missense	TMEM19	NM_018279.3	58	13,296,6194	GG,GC,CC		0.0349,7.2401,2.4758	possibly-damaging	288/337	72094627	322,12684	2203	4300	6503	SO:0001583	missense	55266	exon6			AAAGCACTGGCAT	BC008596	CCDS9002.1	12q15	2004-03-04				ENSG00000139291			25605	protein-coding gene	gene with protein product						12477932	Standard	NM_018279		Approved	FLJ10936	uc001sws.3	Q96HH6	OTTHUMG00000169558	ENST00000266673.5:c.863C>G	12.37:g.72094627C>G	ENSP00000266673:p.Thr288Ser	157.0	0.0	0		188.0	95.0	0.505319	NM_018279	B2RDL2|Q53FY3|Q9NV41	Missense_Mutation	SNP	ENST00000266673.5	37	CCDS9002.1	45|45	0.020604395604395604|0.020604395604395604	43|43	0.08739837398373984|0.08739837398373984	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	0|0	0.0|0.0	C|C	10.59|10.59	1.393752|1.393752	0.25205|0.25205	0.072401|0.072401	3.49E-4|3.49E-4	ENSG00000139291|ENSG00000139291	ENST00000550787|ENST00000266673;ENST00000546795	.|.	.|.	.|.	5.93|5.93	5.03|5.03	0.67393|0.67393	.|.	.|0.100553	.|0.64402	.|N	.|0.000002	T|T	0.02649|0.02649	0.0080|0.0080	L|L	0.42245|0.42245	1.32|1.32	0.80722|0.80722	D|D	1|1	.|P	.|0.51537	.|0.946	.|P	.|0.48952	.|0.596	T|T	0.04165|0.04165	-1.0972|-1.0972	5|9	.|0.08837	.|T	.|0.75	-22.104|-22.104	12.1152|12.1152	0.53861|0.53861	0.0:0.8121:0.1216:0.0663|0.0:0.8121:0.1216:0.0663	.|.	.|288	.|Q96HH6	.|TMM19_HUMAN	Q|S	103|288;132	.|.	.|ENSP00000266673:T288S	H|T	+|+	3|2	2|0	TMEM19|TMEM19	70380894|70380894	0.990000|0.990000	0.36364|0.36364	0.993000|0.993000	0.49108|0.49108	0.973000|0.973000	0.67179|0.67179	1.858000|1.858000	0.39408|0.39408	1.463000|1.463000	0.47967|0.47967	0.655000|0.655000	0.94253|0.94253	CAC|ACT	C|0.976;G|0.024	0.024	strong		0.358	TMEM19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404801.1	NM_018279	
TMC2	117532	hgsc.bcm.edu	37	20	2582839	2582839	+	Missense_Mutation	SNP	T	T	A	rs140733869	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:2582839T>A	ENST00000358864.1	+	11	1320	c.1305T>A	c.(1303-1305)ttT>ttA	p.F435L	TMC2_ENST00000496948.1_3'UTR	NM_080751.2	NP_542789.2	Q8TDI7	TMC2_HUMAN	transmembrane channel-like 2	435					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|vestibular reflex (GO:0060005)	integral component of membrane (GO:0016021)|stereocilium bundle tip (GO:0032426)	voltage-gated calcium channel activity (GO:0005245)			NS(1)|breast(3)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35						TGGCCAACTTTCTCATCATCT	0.388													T|||	15	0.00299521	0.0106	0.0014	5008	,	,		20141	0.0		0.0	False		,,,				2504	0.0				p.F435L		Atlas-SNP	.											.	TMC2	121	.	0			c.T1305A						PASS	.	T	LEU/PHE	26,4380	32.6+/-62.9	0,26,2177	199.0	174.0	182.0		1305	-4.7	1.0	20	dbSNP_134	182	0,8600		0,0,4300	yes	missense	TMC2	NM_080751.2	22	0,26,6477	AA,AT,TT		0.0,0.5901,0.1999	possibly-damaging	435/907	2582839	26,12980	2203	4300	6503	SO:0001583	missense	117532	exon11			CAACTTTCTCATC	AF417580	CCDS13029.2	20p13	2010-08-05	2003-02-23		ENSG00000149488	ENSG00000149488			16527	protein-coding gene	gene with protein product		606707	"""transmembrane, cochlear expressed, 2"""	C20orf145		11850618, 12906855	Standard	XM_005260660		Approved	dJ686C3.3	uc002wgf.1	Q8TDI7	OTTHUMG00000031698	ENST00000358864.1:c.1305T>A	20.37:g.2582839T>A	ENSP00000351732:p.Phe435Leu	226.0	0.0	0		245.0	137.0	0.559184	NM_080751	Q5JXT0|Q5JXT1|Q6UWW4|Q6ZS41|Q8N9F3|Q9BYN2|Q9BYN3|Q9BYN4|Q9BYN5	Missense_Mutation	SNP	ENST00000358864.1	37	CCDS13029.2	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	T	17.98	3.520320	0.64747	0.005901	0.0	ENSG00000149488	ENST00000358864	T	0.80994	-1.44	5.58	-4.7	0.03288	.	0.171732	0.56097	D	0.000039	T	0.64811	0.2632	L	0.60845	1.875	0.39342	D	0.965601	B;B;P;P	0.45986	0.382;0.209;0.866;0.87	B;B;P;P	0.50570	0.064;0.031;0.644;0.542	T	0.76044	-0.3103	10	0.09084	T	0.74	-13.3661	15.7824	0.78272	0.0:0.7271:0.0:0.2729	.	266;267;435;435	B4DFB3;B7ZAE6;Q8TDI7-3;Q8TDI7	.;.;.;TMC2_HUMAN	L	435	ENSP00000351732:F435L	ENSP00000351732:F435L	F	+	3	2	TMC2	2530839	0.062000	0.20869	0.972000	0.41901	0.959000	0.62525	-0.545000	0.06069	-0.718000	0.04949	-1.151000	0.01829	TTT	T|0.997;A|0.003	0.003	strong		0.388	TMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077601.2		
TRPV6	55503	hgsc.bcm.edu	37	7	142573332	142573332	+	Silent	SNP	C	C	T	rs4987664	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:142573332C>T	ENST00000359396.3	-	8	1256	c.1011G>A	c.(1009-1011)ctG>ctA	p.L337L	RP11-114L10.2_ENST00000438839.1_RNA	NM_018646.3	NP_061116	Q9H1D0	TRPV6_HUMAN	transient receptor potential cation channel, subfamily V, member 6	337					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|regulation of calcium ion-dependent exocytosis (GO:0017158)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calmodulin binding (GO:0005516)			breast(1)|endometrium(1)|kidney(2)|large_intestine(11)|lung(15)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)	42	Melanoma(164;0.059)					TGATGTACAGCAGATATATGG	0.597													C|||	105	0.0209665	0.0726	0.013	5008	,	,		18895	0.0		0.0	False		,,,				2504	0.0				p.L337L		Atlas-SNP	.											.	TRPV6	108	.	0			c.G1011A						PASS	.	C		312,4094	167.3+/-198.3	17,278,1908	150.0	147.0	148.0		1011	1.6	0.4	7	dbSNP_113	148	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TRPV6	NM_018646.2		17,280,6206	TT,TC,CC		0.0233,7.0813,2.4143		337/726	142573332	314,12692	2203	4300	6503	SO:0001819	synonymous_variant	55503	exon8			GTACAGCAGATAT	AJ277909	CCDS5874.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000165125	ENSG00000165125		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	14006	protein-coding gene	gene with protein product		606680	"""epithelial calcium channel 2"""	ECAC2		11097838, 11549322, 16382100, 16717058	Standard	NM_018646		Approved	CaT1	uc003wbx.2	Q9H1D0	OTTHUMG00000157158	ENST00000359396.3:c.1011G>A	7.37:g.142573332C>T		47.0	0.0	0		49.0	28.0	0.571429	NM_018646	A4D2I8|Q8TDL3|Q8WXR8|Q96LC5|Q9H1D1|Q9H296	Silent	SNP	ENST00000359396.3	37	CCDS5874.1																																																																																			C|0.971;T|0.029	0.029	strong		0.597	TRPV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347662.1	NM_014274	
PARVG	64098	hgsc.bcm.edu	37	22	44586519	44586519	+	Missense_Mutation	SNP	C	C	A	rs3842780	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:44586519C>A	ENST00000444313.3	+	7	961	c.477C>A	c.(475-477)aaC>aaA	p.N159K	PARVG_ENST00000415224.1_Missense_Mutation_p.N159K|PARVG_ENST00000422871.1_Missense_Mutation_p.N159K	NM_022141.5	NP_071424.1	Q9HBI0	PARVG_HUMAN	parvin, gamma	159					actin cytoskeleton reorganization (GO:0031532)|cell-matrix adhesion (GO:0007160)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)	actin binding (GO:0003779)			endometrium(2)|kidney(1)|large_intestine(4)|lung(10)	17		Ovarian(80;0.024)|all_neural(38;0.0299)				TCCCAACCAACGTCCAGGTGG	0.602													C|||	70	0.0139776	0.053	0.0	5008	,	,		19412	0.0		0.0	False		,,,				2504	0.0				p.N159K		Atlas-SNP	.											PARVG,NS,carcinoma,0,1	PARVG	41	1	0			c.C477A						PASS	.	C	LYS/ASN,LYS/ASN,LYS/ASN	218,4188	133.7+/-170.0	2,214,1987	89.0	71.0	77.0		477,477,477	-2.7	0.0	22	dbSNP_107	77	0,8600		0,0,4300	yes	missense,missense,missense	PARVG	NM_001137605.1,NM_001137606.1,NM_022141.5	94,94,94	2,214,6287	AA,AC,CC		0.0,4.9478,1.6761	probably-damaging,probably-damaging,probably-damaging	159/332,159/332,159/332	44586519	218,12788	2203	4300	6503	SO:0001583	missense	64098	exon7			AACCAACGTCCAG	AF237772	CCDS14057.1	22q13.31	2013-01-24			ENSG00000138964	ENSG00000138964		"""Parvins"""	14654	protein-coding gene	gene with protein product		608122				11171322	Standard	NM_022141		Approved		uc003bep.4	Q9HBI0	OTTHUMG00000150473	ENST00000444313.3:c.477C>A	22.37:g.44586519C>A	ENSP00000391583:p.Asn159Lys	71.0	0.0	0		83.0	32.0	0.385542	NM_001137606	B4DDW5|E7EVM6|Q9BQX5|Q9NSG1	Missense_Mutation	SNP	ENST00000444313.3	37	CCDS14057.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	C	11.29	1.594965	0.28445	0.049478	0.0	ENSG00000138964	ENST00000422871;ENST00000444313;ENST00000415224	T;T;T	0.58506	0.33;0.33;0.33	3.46	-2.74	0.05932	Calponin homology domain (1);	0.347388	0.28130	N	0.016483	T	0.17450	0.0419	M	0.77313	2.365	0.30861	N	0.733509	P	0.50819	0.939	P	0.46253	0.509	T	0.53795	-0.8388	10	0.56958	D	0.05	-1.8351	8.7897	0.34843	0.0:0.5205:0.0:0.4795	rs3842780	159	Q9HBI0	PARVG_HUMAN	K	159	ENSP00000391453:N159K;ENSP00000391583:N159K;ENSP00000416761:N159K	ENSP00000349378:N159K	N	+	3	2	PARVG	42917852	0.015000	0.18098	0.018000	0.16275	0.401000	0.30781	-0.744000	0.04839	-0.298000	0.08921	0.561000	0.74099	AAC	C|0.985;A|0.015	0.015	strong		0.602	PARVG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318238.4	NM_022141	
CKAP2L	150468	hgsc.bcm.edu	37	2	113509891	113509891	+	Missense_Mutation	SNP	T	T	C	rs36046436	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:113509891T>C	ENST00000302450.6	-	5	1633	c.1555A>G	c.(1555-1557)Agt>Ggt	p.S519G	CKAP2L_ENST00000541405.1_Missense_Mutation_p.S354G	NM_152515.3	NP_689728.3	Q8IYA6	CKP2L_HUMAN	cytoskeleton associated protein 2-like	519			S -> G (in dbSNP:rs36046436).			centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(15)|skin(1)|upper_aerodigestive_tract(1)	28						TTAATTTTACTGGACAGTTCG	0.348													T|||	66	0.0131789	0.0492	0.0014	5008	,	,		17493	0.0		0.0	False		,,,				2504	0.0				p.S519G		Atlas-SNP	.											.	CKAP2L	54	.	0			c.A1555G						PASS	.	T	GLY/SER	207,4199	127.8+/-164.7	5,197,2001	253.0	252.0	252.0		1555	0.2	0.0	2	dbSNP_126	252	0,8600		0,0,4300	yes	missense	CKAP2L	NM_152515.3	56	5,197,6301	CC,CT,TT		0.0,4.6981,1.5916	benign	519/746	113509891	207,12799	2203	4300	6503	SO:0001583	missense	150468	exon5			TTTTACTGGACAG	AL832036	CCDS2100.1	2q13	2008-02-05			ENSG00000169607	ENSG00000169607			26877	protein-coding gene	gene with protein product						12477932	Standard	NM_152515		Approved	FLJ40629	uc002tie.2	Q8IYA6	OTTHUMG00000131313	ENST00000302450.6:c.1555A>G	2.37:g.113509891T>C	ENSP00000305204:p.Ser519Gly	396.0	0.0	0		382.0	184.0	0.481675	NM_152515	A8K915|B4DZE3|B7ZAC6|F5H0M5|Q53QF8|Q53RS8|Q8N1J8	Missense_Mutation	SNP	ENST00000302450.6	37	CCDS2100.1	20	0.009157509157509158	20	0.04065040650406504	0	0.0	0	0.0	0	0.0	T	5.135	0.210489	0.09757	0.046981	0.0	ENSG00000169607	ENST00000541405;ENST00000302450	T;T	0.22945	1.93;1.93	5.61	0.251	0.15540	.	0.735060	0.14028	N	0.346338	T	0.01730	0.0055	N	0.22421	0.69	0.09310	N	1	B;B	0.24426	0.034;0.103	B;B	0.25140	0.04;0.058	T	0.23583	-1.0184	10	0.21014	T	0.42	0.2974	1.8328	0.03133	0.1345:0.1548:0.1396:0.5711	rs36046436	108;519	Q8IYA6-2;Q8IYA6	.;CKP2L_HUMAN	G	354;519	ENSP00000438763:S354G;ENSP00000305204:S519G	ENSP00000305204:S519G	S	-	1	0	CKAP2L	113226362	0.001000	0.12720	0.041000	0.18516	0.163000	0.22366	0.999000	0.29757	0.391000	0.25143	-0.481000	0.04817	AGT	T|0.983;C|0.017	0.017	strong		0.348	CKAP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254082.2	NM_152515	
TRAPPC10	7109	hgsc.bcm.edu	37	21	45518396	45518396	+	Silent	SNP	G	G	A	rs115989144	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45518396G>A	ENST00000291574.4	+	21	3502	c.3327G>A	c.(3325-3327)tcG>tcA	p.S1109S		NM_003274.4	NP_003265.3	P48553	TPC10_HUMAN	trafficking protein particle complex 10	1109					sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	sodium ion transmembrane transporter activity (GO:0015081)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(8)|ovary(1)|prostate(2)|skin(2)|urinary_tract(4)	41						AGCATTTTTCGACAAAGCTTA	0.527													G|||	12	0.00239617	0.0091	0.0	5008	,	,		20869	0.0		0.0	False		,,,				2504	0.0				p.S1109S		Atlas-SNP	.											TRAPPC10,colon,carcinoma,+1,1	TRAPPC10	109	1	0			c.G3327A						PASS	.	G		35,4371	40.8+/-73.8	0,35,2168	103.0	103.0	103.0		3327	-11.1	0.0	21	dbSNP_132	103	0,8600		0,0,4300	no	coding-synonymous	TRAPPC10	NM_003274.4		0,35,6468	AA,AG,GG		0.0,0.7944,0.2691		1109/1260	45518396	35,12971	2203	4300	6503	SO:0001819	synonymous_variant	7109	exon21			TTTTTCGACAAAG	U19252	CCDS13704.1	21q22.3	2008-05-07	2008-05-07	2008-05-07	ENSG00000160218	ENSG00000160218		"""Trafficking protein particle complex"""	11868	protein-coding gene	gene with protein product	"""trafficking protein particle complex subunit 130"", ""TRAPP 130 kDa subunit"""	602103	"""transmembrane protein 1"""	TMEM1		7633421	Standard	NM_003274		Approved	EHOC-1, TRS130	uc002zea.3	P48553	OTTHUMG00000086894	ENST00000291574.4:c.3327G>A	21.37:g.45518396G>A		62.0	0.0	0		68.0	39.0	0.573529	NM_003274	Q3MIR2|Q86SI7|Q9UMD4|Q9Y4L3	Silent	SNP	ENST00000291574.4	37	CCDS13704.1																																																																																			G|0.996;A|0.004	0.004	strong		0.527	TRAPPC10-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000195737.1	NM_003274	
GRHL3	57822	hgsc.bcm.edu	37	1	24664220	24664220	+	Missense_Mutation	SNP	G	G	A	rs145470039	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:24664220G>A	ENST00000350501.5	+	6	908	c.781G>A	c.(781-783)Gtc>Atc	p.V261I	GRHL3_ENST00000342072.4_Missense_Mutation_p.V168I|GRHL3_ENST00000356046.2_Missense_Mutation_p.V215I|GRHL3_ENST00000236255.4_Missense_Mutation_p.V266I|GRHL3_ENST00000361548.4_Missense_Mutation_p.V261I	NM_198174.2	NP_937817.3	Q8TE85	GRHL3_HUMAN	grainyhead-like 3 (Drosophila)	261					central nervous system development (GO:0007417)|cochlea morphogenesis (GO:0090103)|ectoderm development (GO:0007398)|epidermis development (GO:0008544)|establishment of planar polarity (GO:0001736)|eyelid development in camera-type eye (GO:0061029)|pattern specification process (GO:0007389)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.V266I(1)		breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(3)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Colorectal(325;3.46e-05)|Renal(390;0.0007)|Lung NSC(340;0.00171)|all_lung(284;0.00226)|Ovarian(437;0.00348)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.19)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;8.72e-25)|Colorectal(126;4.38e-08)|COAD - Colon adenocarcinoma(152;1.84e-06)|GBM - Glioblastoma multiforme(114;0.000132)|BRCA - Breast invasive adenocarcinoma(304;0.00105)|STAD - Stomach adenocarcinoma(196;0.00151)|KIRC - Kidney renal clear cell carcinoma(1967;0.00377)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.143)		GTTCTACCCCGTCACCCTGCG	0.587													G|||	9	0.00179712	0.0061	0.0014	5008	,	,		20270	0.0		0.0	False		,,,				2504	0.0				p.V266I		Atlas-SNP	.											GRHL3_ENST00000350501,NS,carcinoma,0,4	GRHL3	69	4	1	Substitution - Missense(1)	ovary(1)	c.G796A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	16,4390	23.3+/-48.9	0,16,2187	98.0	84.0	89.0		781,781,796,643	4.1	0.8	1	dbSNP_134	89	0,8600		0,0,4300	yes	missense,missense,missense,missense	GRHL3	NM_198174.2,NM_198173.2,NM_021180.3,NM_001195010.1	29,29,29,29	0,16,6487	AA,AG,GG		0.0,0.3631,0.123	benign,benign,benign,benign	261/627,261/603,266/608,215/557	24664220	16,12990	2203	4300	6503	SO:0001583	missense	57822	exon6			TACCCCGTCACCC	AY231161	CCDS251.1, CCDS252.1, CCDS44088.1, CCDS252.2, CCDS53284.1	1p36	2008-02-05	2005-07-11	2005-07-11	ENSG00000158055	ENSG00000158055			25839	protein-coding gene	gene with protein product		608317	"""transcription factor CP2-like 4"""	TFCP2L4		12549979	Standard	NM_021180		Approved	SOM	uc021oiw.1	Q8TE85	OTTHUMG00000003040	ENST00000350501.5:c.781G>A	1.37:g.24664220G>A	ENSP00000288955:p.Val261Ile	93.0	0.0	0		79.0	37.0	0.468354	NM_021180	A2A297|B2RCL1|G3XAF0|Q5TH78|Q86Y06|Q8N407	Missense_Mutation	SNP	ENST00000350501.5	37	CCDS252.2	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	G	4.028	0.002793	0.07866	0.003631	0.0	ENSG00000158055	ENST00000361548;ENST00000342072;ENST00000350501;ENST00000356046;ENST00000236255	T;T;T;T;T	0.15017	2.46;2.46;2.46;2.46;2.46	5.97	4.12	0.48240	.	0.237878	0.42964	N	0.000623	T	0.03390	0.0098	N	0.02103	-0.685	0.32683	N	0.515251	B;B;B	0.18310	0.013;0.003;0.027	B;B;B	0.14578	0.008;0.006;0.011	T	0.30937	-0.9961	10	0.02654	T	1	-28.162	9.5371	0.39229	0.2343:0.0:0.7657:0.0	.	215;266;261	A2A297;Q8TE85-2;G3XAF0	.;.;.	I	261;168;261;215;266	ENSP00000354943:V261I;ENSP00000340543:V168I;ENSP00000288955:V261I;ENSP00000348333:V215I;ENSP00000236255:V266I	ENSP00000236255:V266I	V	+	1	0	GRHL3	24536807	0.796000	0.28864	0.822000	0.32727	0.992000	0.81027	1.375000	0.34295	0.868000	0.35678	0.655000	0.94253	GTC	G|0.997;A|0.003	0.003	strong		0.587	GRHL3-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000009047.2	NM_021180	
C4A	720	hgsc.bcm.edu	37	6	31963780	31963780	+	Silent	SNP	A	A	G	rs371801898	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:31963780A>G	ENST00000428956.2	+	26	3363	c.3279A>G	c.(3277-3279)gtA>gtG	p.V1093V	C4A_ENST00000498271.1_Silent_p.V1093V	NM_007293.2	NP_009224.2	P0C0L4	CO4A_HUMAN	complement component 4A (Rodgers blood group)	1093					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)	AGGAGCAGGTAGGAGGCTCGC	0.567													A|||	7	0.00139776	0.0053	0.0	5008	,	,		18057	0.0		0.0	False		,,,				2504	0.0				p.V1093V		Atlas-SNP	.											.	C4A	15	.	0			c.A3279G						PASS	.	A		6,3114		0,6,1554	19.0	17.0	18.0		3279	0.3	0.6	6		18	0,6998		0,0,3499	no	coding-synonymous	C4A	NM_007293.2		0,6,5053	GG,GA,AA		0.0,0.1923,0.0593		1093/1745	31963780	6,10112	1560	3499	5059	SO:0001819	synonymous_variant	720	exon26			GCAGGTAGGAGGC	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.3279A>G	6.37:g.31963780A>G		927.0	2.0	0.0021575		867.0	299.0	0.344867	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																																																																																			.	.	weak		0.567	C4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076364.3	NM_007293	
IGSF10	285313	hgsc.bcm.edu	37	3	151155197	151155197	+	Silent	SNP	T	T	C	rs141741834	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:151155197T>C	ENST00000282466.3	-	6	7151	c.7152A>G	c.(7150-7152)caA>caG	p.Q2384Q	IGSF10_ENST00000495443.1_5'UTR	NM_001178145.1|NM_001178146.1|NM_178822.4	NP_001171616.1|NP_001171617.1|NP_849144.2	Q6WRI0	IGS10_HUMAN	immunoglobulin superfamily, member 10	2384	Ig-like C2-type 10.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)	extracellular region (GO:0005576)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(24)|liver(4)|lung(43)|ovary(8)|prostate(4)|skin(9)|stomach(1)|urinary_tract(3)	116			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0517)			ACTGATAACTTTGTGGTCCAT	0.403													T|||	44	0.00878594	0.0333	0.0	5008	,	,		21182	0.0		0.0	False		,,,				2504	0.0				p.Q2384Q		Atlas-SNP	.											.	IGSF10	279	.	0			c.A7152G						PASS	.	T	,,	84,4322	70.9+/-108.8	0,84,2119	124.0	124.0	124.0		1233,1089,7152	-11.2	0.0	3	dbSNP_134	124	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	IGSF10	NM_001178145.1,NM_001178146.1,NM_178822.4	,,	0,84,6419	CC,CT,TT		0.0,1.9065,0.6459	,,	411/651,363/603,2384/2624	151155197	84,12922	2203	4300	6503	SO:0001819	synonymous_variant	285313	exon6			ATAACTTTGTGGT	AY273815	CCDS3160.1	3q25.1	2013-01-11			ENSG00000152580	ENSG00000152580		"""Immunoglobulin superfamily / I-set domain containing"""	26384	protein-coding gene	gene with protein product						12477932	Standard	NM_178822		Approved	FLJ25972, CMF608	uc011bod.2	Q6WRI0	OTTHUMG00000159856	ENST00000282466.3:c.7152A>G	3.37:g.151155197T>C		130.0	0.0	0		129.0	71.0	0.550388	NM_178822	Q86YJ9|Q8N772|Q8NA84	Silent	SNP	ENST00000282466.3	37	CCDS3160.1																																																																																			T|0.993;C|0.007	0.007	strong		0.403	IGSF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357782.1	NM_178822	
CRAMP1L	57585	hgsc.bcm.edu	37	16	1706480	1706480	+	Silent	SNP	C	C	G	rs80154657	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1706480C>G	ENST00000397412.3	+	10	1821	c.1722C>G	c.(1720-1722)ccC>ccG	p.P574P	CRAMP1L_ENST00000262317.4_Intron|CRAMP1L_ENST00000436138.3_Silent_p.P571P|CRAMP1L_ENST00000293925.5_Silent_p.P574P|LA16c-431H6.6_ENST00000454337.1_Intron			Q96RY5	CRML_HUMAN	Crm, cramped-like (Drosophila)	574						nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|lung(6)|pancreas(1)	22						TCATTGTCCCCGAGCAGTGCC	0.677													C|||	98	0.0195687	0.0726	0.0029	5008	,	,		15682	0.0		0.0	False		,,,				2504	0.0				p.P574P		Atlas-SNP	.											.	CRAMP1L	60	.	0			c.C1722G						PASS	.	C		168,3706		3,162,1772	15.0	16.0	16.0		1722	-10.0	0.0	16	dbSNP_132	16	1,8121		0,1,4060	no	coding-synonymous	CRAMP1L	NM_020825.3		3,163,5832	GG,GC,CC		0.0123,4.3366,1.4088		574/1270	1706480	169,11827	1937	4061	5998	SO:0001819	synonymous_variant	57585	exon9			TGTCCCCGAGCAG	AB037847	CCDS10440.2	16p13.3	2008-07-30	2001-11-28		ENSG00000007545	ENSG00000007545			14122	protein-coding gene	gene with protein product			"""Crm (Cramped Drosophila)-like"""				Standard	NM_020825		Approved	KIAA1426	uc010uvh.2	Q96RY5	OTTHUMG00000074087	ENST00000397412.3:c.1722C>G	16.37:g.1706480C>G		30.0	0.0	0		24.0	9.0	0.375	NM_020825	A8MZL1|B1AJY1|Q8NDN1|Q9P2C1	Silent	SNP	ENST00000397412.3	37	CCDS10440.2																																																																																			C|0.979;G|0.021	0.021	strong		0.677	CRAMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157297.4		
MUC16	94025	hgsc.bcm.edu	37	19	9070186	9070186	+	Missense_Mutation	SNP	C	C	T	rs1559171	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9070186C>T	ENST00000397910.4	-	3	17463	c.17260G>A	c.(17260-17262)Gcc>Acc	p.A5754T		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5756	Thr-rich.				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						TCCCCCATGGCGAAGGTGATA	0.468													t|||	100	0.0199681	0.0734	0.0043	5008	,	,		22084	0.0		0.0	False		,,,				2504	0.0				p.A5754T		Atlas-SNP	.											.	MUC16	4315	.	0			c.G17260A						PASS	.	T	THR/ALA	251,3819		11,229,1795	161.0	152.0	155.0		17260	-3.5	0.0	19	dbSNP_88	155	5,8383		0,5,4189	yes	missense	MUC16	NM_024690.2	58	11,234,5984	TT,TC,CC		0.0596,6.1671,2.0549	benign	5754/14508	9070186	256,12202	2035	4194	6229	SO:0001583	missense	94025	exon3			CCATGGCGAAGGT	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.17260G>A	19.37:g.9070186C>T	ENSP00000381008:p.Ala5754Thr	273.0	0.0	0		282.0	132.0	0.468085	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	28	0.01282051282051282	25	0.0508130081300813	3	0.008287292817679558	0	0.0	0	0.0	t	4.044	0.005793	0.07866	0.061671	5.96E-4	ENSG00000181143	ENST00000397910	T	0.20069	2.1	1.73	-3.46	0.04767	.	.	.	.	.	T	0.00724	0.0024	N	0.03608	-0.345	.	.	.	B	0.02656	0.0	B	0.01281	0.0	T	0.26503	-1.0101	8	0.87932	D	0	.	1.5797	0.02632	0.2079:0.4205:0.1629:0.2087	rs1559171;rs1559171	5754	B5ME49	.	T	5754	ENSP00000381008:A5754T	ENSP00000381008:A5754T	A	-	1	0	MUC16	8931186	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.346000	0.07760	-2.492000	0.00516	-0.521000	0.04368	GCC	C|0.987;T|0.013	0.013	strong		0.468	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
MCTP2	55784	hgsc.bcm.edu	37	15	94858808	94858808	+	Silent	SNP	G	G	A	rs146431277	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:94858808G>A	ENST00000357742.4	+	3	579	c.579G>A	c.(577-579)gcG>gcA	p.A193A	MCTP2_ENST00000331706.4_5'UTR|MCTP2_ENST00000451018.3_Silent_p.A193A|MCTP2_ENST00000543482.1_Silent_p.A193A	NM_018349.3	NP_060819.3	Q6DN12	MCTP2_HUMAN	multiple C2 domains, transmembrane 2	193	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				calcium-mediated signaling (GO:0019722)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(4)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|liver(1)|lung(12)|ovary(1)|pancreas(1)|skin(9)|stomach(2)	49	Lung NSC(78;0.0821)|all_lung(78;0.148)		BRCA - Breast invasive adenocarcinoma(143;0.0323)|OV - Ovarian serous cystadenocarcinoma(32;0.0593)			GCCCTTTTGCGTACCTCCTCA	0.547													g|||	8	0.00159744	0.0053	0.0	5008	,	,		17286	0.0		0.0	False		,,,				2504	0.001				p.A193A		Atlas-SNP	.											MCTP2,NS,adenoma,0,1	MCTP2	122	1	0			c.G579A						PASS	.	A	,	28,4366	34.3+/-65.2	0,28,2169	150.0	121.0	131.0		579,579	-12.1	0.0	15	dbSNP_134	131	1,8595	1.2+/-3.3	0,1,4297	no	coding-synonymous,coding-synonymous	MCTP2	NM_001159643.1,NM_018349.3	,	0,29,6466	AA,AG,GG		0.0116,0.6372,0.2232	,	193/824,193/879	94858808	29,12961	2197	4298	6495	SO:0001819	synonymous_variant	55784	exon3			TTTTGCGTACCTC	AK002037	CCDS32338.1, CCDS53975.1, CCDS53976.1	15q26.2	2006-02-08				ENSG00000140563			25636	protein-coding gene	gene with protein product						15528213	Standard	NM_018349		Approved	FLJ11175, FLJ33303	uc002btj.3	Q6DN12		ENST00000357742.4:c.579G>A	15.37:g.94858808G>A		191.0	0.0	0		203.0	105.0	0.517241	NM_001159643	A2RRC2|C6G483|C6G484|Q49AB0|Q8TAX2|Q9NUS2|Q9NUW7	Silent	SNP	ENST00000357742.4	37	CCDS32338.1																																																																																			G|0.998;A|0.002	0.002	strong		0.547	MCTP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415060.3	NM_018349	
ADCK2	90956	hgsc.bcm.edu	37	7	140374482	140374482	+	Silent	SNP	G	G	C	rs142577491	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:140374482G>C	ENST00000072869.4	+	2	1183	c.1005G>C	c.(1003-1005)ctG>ctC	p.L335L	ADCK2_ENST00000476491.1_Silent_p.L335L	NM_052853.3	NP_443085.2	Q7Z695	ADCK2_HUMAN	aarF domain containing kinase 2	335	Protein kinase.					integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|kidney(2)|large_intestine(2)|lung(5)|prostate(1)|skin(4)	15	Melanoma(164;0.00956)					GCCGAGTCCTGGGAGTTTTGC	0.542													C|||	6	0.00119808	0.0038	0.0014	5008	,	,		18388	0.0		0.0	False		,,,				2504	0.0				p.L335L		Atlas-SNP	.											.	ADCK2	37	.	0			c.G1005C						PASS	.	C		15,4391	823.8+/-416.5	0,15,2188	113.0	95.0	101.0		1005	-11.2	0.0	7	dbSNP_134	101	0,8600		0,0,4300	no	coding-synonymous	ADCK2	NM_052853.3		0,15,6488	CC,CG,GG		0.0,0.3404,0.1153		335/627	140374482	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	90956	exon2			AGTCCTGGGAGTT	AF131745	CCDS5861.1	7q34	2003-07-21			ENSG00000133597	ENSG00000133597			19039	protein-coding gene	gene with protein product							Standard	NM_052853		Approved	MGC20727	uc003vvy.1	Q7Z695	OTTHUMG00000157409	ENST00000072869.4:c.1005G>C	7.37:g.140374482G>C		113.0	0.0	0		124.0	71.0	0.572581	NM_052853	Q96CN6|Q9Y6T5	Silent	SNP	ENST00000072869.4	37	CCDS5861.1	2	9.157509157509158E-4	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	0	0.0	C	8.385	0.838441	0.16891	0.003404	0.0	ENSG00000133597	ENST00000483369	.	.	.	5.61	-11.2	0.00127	.	.	.	.	.	T	0.57755	0.2075	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.71537	-0.4563	4	.	.	.	-48.0441	14.5211	0.67851	0.0:0.1623:0.6463:0.1913	.	.	.	.	R	173	.	.	G	+	1	0	ADCK2	140020951	0.066000	0.20996	0.001000	0.08648	0.874000	0.50279	-0.756000	0.04777	-2.611000	0.00445	-1.093000	0.02169	GGG	G|0.999;C|0.001	0.001	strong		0.542	ADCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348734.1	NM_052853	
C15orf43	145645	hgsc.bcm.edu	37	15	45250685	45250685	+	Missense_Mutation	SNP	T	T	G	rs147135555	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:45250685T>G	ENST00000340827.3	+	3	278	c.261T>G	c.(259-261)atT>atG	p.I87M		NM_152448.2	NP_689661.1	Q8NHR7	CO043_HUMAN	chromosome 15 open reading frame 43	87										NS(1)|breast(2)|large_intestine(1)|lung(2)|skin(2)	8		all_cancers(109;3.68e-08)|all_epithelial(112;1.05e-06)|Lung NSC(122;1.42e-05)|all_lung(180;0.000112)|Melanoma(134;0.0192)		all cancers(107;7.64e-17)|GBM - Glioblastoma multiforme(94;2.03e-06)		GTCATTTCATTCTTCCTCCTG	0.408													T|||	18	0.00359425	0.0136	0.0	5008	,	,		18466	0.0		0.0	False		,,,				2504	0.0				p.I87M		Atlas-SNP	.											.	C15orf43	19	.	0			c.T261G						PASS	.	T	MET/ILE	52,4344	52.3+/-87.9	1,50,2147	79.0	74.0	75.0		261	-2.2	1.0	15	dbSNP_134	75	0,8596		0,0,4298	yes	missense	C15orf43	NM_152448.1	10	1,50,6445	GG,GT,TT		0.0,1.1829,0.4002	benign	87/221	45250685	52,12940	2198	4298	6496	SO:0001583	missense	145645	exon3			TTTCATTCTTCCT	BC029537	CCDS10115.1	15q21.1	2006-02-03			ENSG00000167014	ENSG00000167014			28520	protein-coding gene	gene with protein product							Standard	NM_152448		Approved	MGC33951	uc001zuk.4	Q8NHR7	OTTHUMG00000131264	ENST00000340827.3:c.261T>G	15.37:g.45250685T>G	ENSP00000340644:p.Ile87Met	98.0	0.0	0		132.0	63.0	0.477273	NM_152448		Missense_Mutation	SNP	ENST00000340827.3	37	CCDS10115.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	t	12.26	1.883358	0.33255	0.011829	0.0	ENSG00000167014	ENST00000340827	T	0.55234	0.53	4.45	-2.18	0.07037	.	0.349419	0.23496	N	0.047553	T	0.21881	0.0527	N	0.19112	0.55	0.22185	N	0.999309	B	0.15141	0.012	B	0.13407	0.009	T	0.08513	-1.0718	10	0.52906	T	0.07	.	5.0719	0.14611	0.0:0.4003:0.1728:0.4268	.	87	Q8NHR7	CO043_HUMAN	M	87	ENSP00000340644:I87M	ENSP00000340644:I87M	I	+	3	3	C15orf43	43037977	0.971000	0.33674	0.971000	0.41717	0.977000	0.68977	0.016000	0.13377	-0.254000	0.09500	0.523000	0.50628	ATT	T|0.997;G|0.003	0.003	strong		0.408	C15orf43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254032.1	NM_152448	
DUPD1	338599	hgsc.bcm.edu	37	10	76797660	76797660	+	Silent	SNP	C	C	T	rs1868624	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:76797660C>T	ENST00000338487.5	-	3	596	c.597G>A	c.(595-597)caG>caA	p.Q199Q		NM_001003892.1	NP_001003892.1	Q68J44	DUPD1_HUMAN	dual specificity phosphatase and pro isomerase domain containing 1	199	Tyrosine-protein phosphatase.				protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)	protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			breast(1)|endometrium(2)|lung(5)|ovary(2)|urinary_tract(1)	11	all_cancers(46;0.0207)|all_epithelial(25;0.00126)|Prostate(51;0.0112)|Ovarian(15;0.0348)					GCTGCACCAGCTGCTTGTCCA	0.657													C|||	34	0.00678914	0.0227	0.0058	5008	,	,		21195	0.0		0.0	False		,,,				2504	0.0				p.Q199Q		Atlas-SNP	.											.	DUPD1	30	.	0			c.G597A						PASS	.	C		89,4317	74.1+/-112.3	0,89,2114	60.0	60.0	60.0		597	4.1	1.0	10	dbSNP_92	60	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	DUPD1	NM_001003892.1		0,91,6412	TT,TC,CC		0.0233,2.02,0.6997		199/221	76797660	91,12915	2203	4300	6503	SO:0001819	synonymous_variant	338599	exon3			CACCAGCTGCTTG		CCDS31223.1	10q22.3	2011-06-09			ENSG00000188716	ENSG00000188716		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	23481	protein-coding gene	gene with protein product							Standard	NM_001003892		Approved	DUSP27	uc001jwq.1	Q68J44	OTTHUMG00000018512	ENST00000338487.5:c.597G>A	10.37:g.76797660C>T		69.0	0.0	0		75.0	34.0	0.453333	NM_001003892	B2RP93	Silent	SNP	ENST00000338487.5	37	CCDS31223.1																																																																																			C|0.959;T|0.041	0.041	strong		0.657	DUPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048777.2	XM_291741	
AMPD3	272	hgsc.bcm.edu	37	11	10526179	10526179	+	Silent	SNP	C	C	T	rs375685508		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:10526179C>T	ENST00000396554.3	+	14	2468	c.2127C>T	c.(2125-2127)agC>agT	p.S709S	AMPD3_ENST00000444303.2_Silent_p.S541S|AMPD3_ENST00000530864.1_3'UTR	NM_000480.2	NP_000471.1	Q01432	AMPD3_HUMAN	adenosine monophosphate deaminase 3	700					ADP metabolic process (GO:0046031)|AMP catabolic process (GO:0006196)|ATP metabolic process (GO:0046034)|energy homeostasis (GO:0097009)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(12)|ovary(1)|prostate(3)|skin(1)	25				all cancers(16;1.14e-08)|Epithelial(150;2.83e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0291)		CCAGGAACAGCGTGCTGCAGA	0.587																																					p.S709S		Atlas-SNP	.											.	AMPD3	68	.	0			c.C2127T						PASS	.	C	,,,,	0,4402		0,0,2201	177.0	141.0	154.0		2127,2100,2121,2100,1623	-9.7	0.5	11		154	1,8587	1.2+/-3.3	0,1,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	AMPD3	NM_000480.2,NM_001025389.1,NM_001025390.1,NM_001172430.1,NM_001172431.1	,,,,	0,1,6494	TT,TC,CC		0.0116,0.0,0.0077	,,,,	709/777,700/768,707/775,700/768,541/609	10526179	1,12989	2201	4294	6495	SO:0001819	synonymous_variant	272	exon14			GAACAGCGTGCTG	M84722	CCDS7802.1, CCDS41617.1, CCDS44537.1, CCDS53601.1	11p15	2010-02-10	2010-02-10			ENSG00000133805	3.5.4.6		470	protein-coding gene	gene with protein product	"""erythrocyte-specific AMP deaminase"""	102772	"""adenosine monophosphate deaminase (isoform E)"""			1400401	Standard	NM_001172430		Approved		uc001min.1	Q01432		ENST00000396554.3:c.2127C>T	11.37:g.10526179C>T		98.0	0.0	0		120.0	43.0	0.358333	NM_000480	A0AUX0|B7Z2S2|B7Z763|B7Z877	Silent	SNP	ENST00000396554.3	37	CCDS7802.1																																																																																			.	.	weak		0.587	AMPD3-001	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385783.2	NM_000480	
POLQ	10721	hgsc.bcm.edu	37	3	121207083	121207083	+	Missense_Mutation	SNP	C	C	A	rs3218639	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:121207083C>A	ENST00000264233.5	-	16	4823	c.4695G>T	c.(4693-4695)caG>caT	p.Q1565H		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1565					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		CTTCAACCATCTGAACAGAAT	0.338								DNA polymerases (catalytic subunits)					C|||	23	0.00459265	0.0159	0.0029	5008	,	,		20878	0.0		0.0	False		,,,				2504	0.0				p.Q1565H	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.G4695T						PASS	.	C	HIS/GLN	75,4331	65.8+/-103.3	1,73,2129	73.0	72.0	73.0		4695	5.3	1.0	3	dbSNP_106	73	0,8600		0,0,4300	yes	missense	POLQ	NM_199420.3	24	1,73,6429	AA,AC,CC		0.0,1.7022,0.5767	probably-damaging	1565/2591	121207083	75,12931	2203	4300	6503	SO:0001583	missense	10721	exon16			AACCATCTGAACA	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.4695G>T	3.37:g.121207083C>A	ENSP00000264233:p.Gln1565His	78.0	0.0	0		57.0	24.0	0.421053	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	14.28	2.488609	0.44249	0.017022	0.0	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.57436	0.4	6.17	5.3	0.74995	.	0.354292	0.29205	N	0.012838	T	0.41880	0.1178	L	0.36672	1.1	0.26824	N	0.968735	D;P	0.71674	0.998;0.865	D;B	0.66084	0.941;0.391	T	0.46190	-0.9209	10	0.48119	T	0.1	.	8.7602	0.34669	0.0:0.6832:0.1822:0.1345	rs3218639;rs52804917;rs3218639	1565;737	O75417;O75417-2	DPOLQ_HUMAN;.	H	1188;1565;1701	ENSP00000264233:Q1565H	ENSP00000264233:Q1565H	Q	-	3	2	POLQ	122689773	1.000000	0.71417	1.000000	0.80357	0.578000	0.36192	1.322000	0.33689	1.632000	0.50472	-0.140000	0.14226	CAG	C|0.993;A|0.007	0.007	strong		0.338	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
PIEZO1	9780	hgsc.bcm.edu	37	16	88780603	88780603	+	IGR	SNP	C	C	G	rs73262673	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:88780603C>G	ENST00000301015.9	-	0	8072				CTU2_ENST00000378384.3_Silent_p.T268T|MIR4722_ENST00000578292.1_RNA|CTU2_ENST00000567949.1_Silent_p.T426T|CTU2_ENST00000453996.2_Silent_p.T355T|CTU2_ENST00000312060.5_Silent_p.T355T	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1						cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1)	10						GGCTGCAGACCCAGTTCCCCT	0.632													C|||	245	0.0489217	0.177	0.0159	5008	,	,		16241	0.0		0.0	False		,,,				2504	0.0				p.T355T		Atlas-SNP	.											.	CTU2	66	.	0			c.C1065G						PASS	.	C	,	604,3774	262.8+/-265.1	38,528,1623	84.0	76.0	79.0		1065,1065	0.1	1.0	16	dbSNP_130	79	5,8587	4.3+/-15.6	0,5,4291	no	coding-synonymous,coding-synonymous	CTU2	NM_001012759.1,NM_001012762.1	,	38,533,5914	GG,GC,CC		0.0582,13.7963,4.6955	,	355/516,355/486	88780603	609,12361	2189	4296	6485	SO:0001628	intergenic_variant	348180	exon10			GCAGACCCAGTTC	D87071	CCDS54058.1	16q24.3	2011-08-31	2011-08-31	2011-08-31	ENSG00000103335	ENSG00000103335			28993	protein-coding gene	gene with protein product		611184	"""family with sequence similarity 38, member A"""	FAM38A		20813920, 21056836, 21299953, 21696149	Standard	NM_001142864		Approved	KIAA0233	uc010vpb.2	Q92508	OTTHUMG00000156776		16.37:g.88780603C>G		145.0	0.0	0		93.0	41.0	0.44086	NM_001012759	A6NHT9|A7E2B7|Q0KKZ9	Silent	SNP	ENST00000301015.9	37	CCDS54058.1																																																																																			C|0.960;G|0.040	0.040	strong		0.632	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
FREM2	341640	hgsc.bcm.edu	37	13	39263646	39263646	+	Missense_Mutation	SNP	G	G	A	rs58363253	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:39263646G>A	ENST00000280481.7	+	1	2381	c.2165G>A	c.(2164-2166)aGg>aAg	p.R722K		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	722			R -> K (in dbSNP:rs58363253).		cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		ACACCACTGAGGAAGAAGTGG	0.552													G|||	315	0.0628994	0.208	0.0231	5008	,	,		19051	0.001		0.0089	False		,,,				2504	0.0143				p.R722K		Atlas-SNP	.											.	FREM2	385	.	0			c.G2165A						PASS	.	G	LYS/ARG	745,3661	305.5+/-289.0	68,609,1526	67.0	64.0	65.0		2165	5.1	1.0	13	dbSNP_129	65	88,8512	49.8+/-109.6	1,86,4213	yes	missense	FREM2	NM_207361.4	26	69,695,5739	AA,AG,GG		1.0233,16.9088,6.4047	benign	722/3170	39263646	833,12173	2203	4300	6503	SO:0001583	missense	341640	exon1			CACTGAGGAAGAA	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.2165G>A	13.37:g.39263646G>A	ENSP00000280481:p.Arg722Lys	97.0	0.0	0		127.0	58.0	0.456693	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	96	0.04395604395604396	82	0.16666666666666666	9	0.024861878453038673	0	0.0	5	0.006596306068601583	G	11.87	1.768801	0.31320	0.169088	0.010233	ENSG00000150893	ENST00000280481	T	0.28255	1.62	5.97	5.13	0.70059	.	0.088825	0.64402	N	0.000001	T	0.00073	0.0002	L	0.49513	1.565	0.18873	P	0.9999848891	B	0.02656	0.0	B	0.06405	0.002	T	0.12708	-1.0537	9	0.17832	T	0.49	.	14.9829	0.71324	0.0679:0.0:0.932:0.0	rs58363253;rs61734231	722	Q5SZK8	FREM2_HUMAN	K	722	ENSP00000280481:R722K	ENSP00000280481:R722K	R	+	2	0	FREM2	38161646	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.884000	0.48562	1.541000	0.49316	0.655000	0.94253	AGG	G|0.949;A|0.051	0.051	strong		0.552	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
ZNF205	7755	hgsc.bcm.edu	37	16	3169321	3169321	+	Silent	SNP	C	C	T	rs59049520	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3169321C>T	ENST00000382192.3	+	7	865	c.660C>T	c.(658-660)ccC>ccT	p.P220P	RP11-473M20.14_ENST00000575139.1_RNA|ZNF205_ENST00000219091.4_Silent_p.P220P|RP11-473M20.14_ENST00000576490.1_RNA	NM_001278158.1|NM_003456.2	NP_001265087.1|NP_003447.2	O95201	ZN205_HUMAN	zinc finger protein 205	220					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hydrogen peroxide biosynthetic process (GO:0010729)|positive regulation of mitochondrial outer membrane permeabilization involved in apoptotic signaling pathway (GO:1901030)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(5)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	20						ATGTGAAGCCCTTCAGAACCA	0.657													C|||	281	0.0561102	0.2065	0.0101	5008	,	,		15886	0.0		0.001	False		,,,				2504	0.0				p.P220P		Atlas-SNP	.											.	ZNF205	42	.	0			c.C660T						PASS	.	C	,	701,3651		60,581,1535	41.0	37.0	38.0		660,660	1.8	0.2	16	dbSNP_129	38	8,8474		0,8,4233	no	coding-synonymous,coding-synonymous	ZNF205	NM_001042428.1,NM_003456.2	,	60,589,5768	TT,TC,CC		0.0943,16.1075,5.5244	,	220/555,220/555	3169321	709,12125	2176	4241	6417	SO:0001819	synonymous_variant	7755	exon7			GAAGCCCTTCAGA	AF060865	CCDS10494.2	16p13.3	2013-01-08			ENSG00000122386	ENSG00000122386		"""Zinc fingers, C2H2-type"", ""-"""	12996	protein-coding gene	gene with protein product		603436		ZNF210		9787081	Standard	NM_003456		Approved	Zfp13	uc002cub.3	O95201	OTTHUMG00000148676	ENST00000382192.3:c.660C>T	16.37:g.3169321C>T		88.0	0.0	0		83.0	52.0	0.626506	NM_003456	A8MZK0|D3DUB4|Q9BU95	Silent	SNP	ENST00000382192.3	37	CCDS10494.2																																																																																			C|0.944;T|0.056	0.056	strong		0.657	ZNF205-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309057.1	NM_003456	
ATP9A	10079	hgsc.bcm.edu	37	20	50310559	50310559	+	Silent	SNP	G	G	A	rs2031344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:50310559G>A	ENST00000338821.5	-	7	894	c.630C>T	c.(628-630)ctC>ctT	p.L210L	ATP9A_ENST00000311637.5_Intron|ATP9A_ENST00000402822.1_Intron	NM_006045.1	NP_006036.1	O75110	ATP9A_HUMAN	ATPase, class II, type 9A	210					phospholipid translocation (GO:0045332)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(2)|cervix(2)|endometrium(6)|kidney(1)|large_intestine(10)|lung(18)|ovary(5)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	48						CGGCCGTGGGGAGCCTCTGCG	0.627													G|||	70	0.0139776	0.0499	0.0043	5008	,	,		14542	0.0		0.001	False		,,,				2504	0.0				p.L210L		Atlas-SNP	.											.	ATP9A	135	.	0			c.C630T						PASS	.	G		171,4235	96.7+/-135.4	3,165,2035	42.0	45.0	44.0		630	-3.0	1.0	20	dbSNP_94	44	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ATP9A	NM_006045.1		3,166,6334	AA,AG,GG		0.0116,3.8811,1.3225		210/1048	50310559	172,12834	2203	4300	6503	SO:0001819	synonymous_variant	10079	exon7			CGTGGGGAGCCTC	AB014511	CCDS33489.1	20q13.2	2010-04-20	2007-09-19		ENSG00000054793	ENSG00000054793		"""ATPases / P-type"""	13540	protein-coding gene	gene with protein product		609126	"""ATPase, Class II, type 9A"""			9734811, 11015572	Standard	NM_006045		Approved	KIAA0611, ATPIIA	uc002xwg.1	O75110	OTTHUMG00000032751	ENST00000338821.5:c.630C>T	20.37:g.50310559G>A		218.0	0.0	0		188.0	82.0	0.43617	NM_006045	E1P5Y3|E1P5Y4|Q5TFW5|Q5TFW6|Q5TFW9|Q6ZMF3|Q9NQK6|Q9NQK7	Silent	SNP	ENST00000338821.5	37	CCDS33489.1																																																																																			G|0.985;A|0.015	0.015	strong		0.627	ATP9A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106494.1	NM_006045	
CENPE	1062	hgsc.bcm.edu	37	4	104080217	104080217	+	Missense_Mutation	SNP	A	A	C	rs75568479	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:104080217A>C	ENST00000265148.3	-	22	2640	c.2551T>G	c.(2551-2553)Tct>Gct	p.S851A	CENPE_ENST00000380026.3_Missense_Mutation_p.S826A	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	851					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)			NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		GCTTCTTTAGAGAGATTAACT	0.373													A|||	53	0.0105831	0.0318	0.0101	5008	,	,		17002	0.0		0.001	False		,,,				2504	0.0031				p.S851A		Atlas-SNP	.											.	CENPE	253	.	0			c.T2551G						PASS	.	A	ALA/SER	160,4246	105.6+/-144.1	4,152,2047	77.0	74.0	75.0		2551	4.9	0.1	4	dbSNP_131	75	15,8585	9.8+/-36.6	0,15,4285	yes	missense	CENPE	NM_001813.2	99	4,167,6332	CC,CA,AA		0.1744,3.6314,1.3455	probably-damaging	851/2702	104080217	175,12831	2203	4300	6503	SO:0001583	missense	1062	exon22			CTTTAGAGAGATT	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"""Kinesins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1856	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 61"""	117143	"""centromere protein E (312kD)"""			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.2551T>G	4.37:g.104080217A>C	ENSP00000265148:p.Ser851Ala	174.0	0.0	0		204.0	107.0	0.52451	NM_001813	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	24	0.01098901098901099	20	0.04065040650406504	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	A	11.57	1.679425	0.29783	0.036314	0.001744	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026;ENST00000503705	T;T;T	0.81163	-1.46;-1.46;-1.46	4.94	4.94	0.65067	.	.	.	.	.	T	0.51024	0.1650	M	0.62723	1.935	0.18873	N	0.999984	P;P	0.48089	0.732;0.905	B;B	0.41988	0.372;0.369	T	0.61471	-0.7056	9	0.32370	T	0.25	.	14.9037	0.70699	1.0:0.0:0.0:0.0	.	826;851	Q02224-3;Q02224	.;CENPE_HUMAN	A	851;851;826;851	ENSP00000265148:S851A;ENSP00000369365:S826A;ENSP00000423981:S851A	ENSP00000265148:S851A	S	-	1	0	CENPE	104299666	0.997000	0.39634	0.084000	0.20598	0.866000	0.49608	2.194000	0.42668	1.971000	0.57363	0.477000	0.44152	TCT	A|0.985;C|0.015	0.015	strong		0.373	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SLC35G6	643664	hgsc.bcm.edu	37	17	7385661	7385661	+	Missense_Mutation	SNP	A	A	G	rs192630658	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7385661A>G	ENST00000412468.2	+	2	473	c.358A>G	c.(358-360)Agt>Ggt	p.S120G	ZBTB4_ENST00000311403.4_Intron|ZBTB4_ENST00000380599.4_5'Flank|POLR2A_ENST00000322644.6_5'Flank|POLR2A_ENST00000572844.1_5'Flank	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	120	EamA 1.					integral component of membrane (GO:0016021)											ATGTGCCTACAGTGCGGTTCA	0.617													A|||	183	0.0365415	0.1309	0.013	5008	,	,		18822	0.0		0.001	False		,,,				2504	0.0				p.S120G		Atlas-SNP	.											.	.	.	.	0			c.A358G						PASS	.	A	GLY/SER,	467,3939	220.4+/-237.8	34,399,1770	139.0	139.0	139.0		358,	4.2	1.0	17		139	4,8596	3.7+/-12.6	0,4,4296	no	missense,intron	ZBTB4,SLC35G6	NM_001102614.1,NM_020899.3	56,	34,403,6066	GG,GA,AA		0.0465,10.5992,3.6214	possibly-damaging,	120/339,	7385661	471,12535	2203	4300	6503	SO:0001583	missense	643664	exon2			GCCTACAGTGCGG		CCDS45603.1	17p13.1	2013-05-22	2011-08-03	2011-08-03		ENSG00000259224		"""Solute carriers"""	31351	protein-coding gene	gene with protein product			"""transmembrane protein 21B"", ""acyl-malonyl condensing enzyme 1-like 3"""	TMEM21B, AMAC1L3			Standard	NM_001102614		Approved		uc010cmj.1	P0C7Q6		ENST00000412468.2:c.358A>G	17.37:g.7385661A>G	ENSP00000396523:p.Ser120Gly	214.0	1.0	0.0046729		220.0	119.0	0.540909	NM_001102614		Missense_Mutation	SNP	ENST00000412468.2	37	CCDS45603.1	63	0.028846153846153848	57	0.11585365853658537	5	0.013812154696132596	1	0.0017482517482517483	0	0.0	A	14.87	2.665416	0.47677	0.105992	4.65E-4	ENSG00000181222	ENST00000412468	T	0.52057	0.68	4.19	4.19	0.49359	.	.	.	.	.	T	0.00524	0.0017	N	0.24115	0.695	0.43740	D	0.996233	B	0.27286	0.174	B	0.33846	0.171	T	0.01925	-1.1246	9	0.27082	T	0.32	-4.3505	12.5602	0.56277	1.0:0.0:0.0:0.0	.	120	P0C7Q6	S35G6_HUMAN	G	120	ENSP00000396523:S120G	ENSP00000396523:S120G	S	+	1	0	SLC35G6	7326385	1.000000	0.71417	1.000000	0.80357	0.928000	0.56348	4.149000	0.58091	1.671000	0.50874	0.460000	0.39030	AGT	A|0.977;G|0.023	0.023	strong		0.617	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614	
SF3B1	23451	hgsc.bcm.edu	37	2	198266834	198266834	+	Missense_Mutation	SNP	T	T	C	rs559063155		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:198266834T>C	ENST00000335508.6	-	15	2189	c.2098A>G	c.(2098-2100)Aaa>Gaa	p.K700E	SNORA4_ENST00000365564.1_RNA|SF3B1_ENST00000462613.1_5'UTR	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	700					anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)	p.K700E(179)|p.Q699_K700del(2)		NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			GTCCGAACTTTCTGCTGCTCA	0.408			Mis		myelodysplastic syndrome								T|||	1	0.000199681	0.0	0.0	5008	,	,		17946	0.0		0.0	False		,,,				2504	0.001				p.K700E		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"""splicing factor 3b, subunit 1, 155kDa"""		L	SF3B1,NS,haematopoietic_neoplasm,0,263	SF3B1	1038	263	181	Substitution - Missense(179)|Deletion - In frame(2)	haematopoietic_and_lymphoid_tissue(153)|NS(20)|breast(5)|pancreas(2)|central_nervous_system(1)	c.A2098G						PASS	.																																			SO:0001583	missense	23451	exon15			GAACTTTCTGCTG	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"""splicing factor 3b, subunit 1, 155kD"""			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.2098A>G	2.37:g.198266834T>C	ENSP00000335321:p.Lys700Glu	173.0	0.0	0		214.0	70.0	0.327103	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	37	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	T	33	5.243295	0.95272	.	.	ENSG00000115524	ENST00000335508	T	0.63580	-0.05	6.02	6.02	0.97574	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.85609	0.5736	H	0.95504	3.68	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.89820	0.3988	10	0.87932	D	0	.	16.542	0.84395	0.0:0.0:0.0:1.0	.	700	O75533	SF3B1_HUMAN	E	700	ENSP00000335321:K700E	ENSP00000335321:K700E	K	-	1	0	SF3B1	197975079	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.555000	0.82223	2.304000	0.77564	0.528000	0.53228	AAA	.	.	none		0.408	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2		
FTHL17	53940	hgsc.bcm.edu	37	X	31089873	31089873	+	Missense_Mutation	SNP	A	A	T	rs73617043	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:31089873A>T	ENST00000359202.3	-	1	297	c.198T>A	c.(196-198)caT>caA	p.H66Q		NM_031894.2	NP_114100.1	Q9BXU8	FHL17_HUMAN	ferritin, heavy polypeptide-like 17	66	Ferritin-like diiron. {ECO:0000255|PROSITE-ProRule:PRU00085}.				cellular iron ion homeostasis (GO:0006879)|iron ion transport (GO:0006826)		ferric iron binding (GO:0008199)			endometrium(2)|large_intestine(2)|liver(1)|lung(13)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	23						GCTTCTGGGCATGCTCCATTT	0.592													A|||	11	0.00291391	0.0083	0.0	3775	,	,		13041	0.0		0.0	False		,,,				2504	0.0				p.H66Q		Atlas-SNP	.											.	FTHL17	99	.	0			c.T198A						PASS	.	A	GLN/HIS	31,3802		0,27,4,1604,567	73.0	66.0	69.0		198	-3.3	0.0	X	dbSNP_130	69	0,6728		0,0,0,2428,1872	yes	missense	FTHL17	NM_031894.2	24	0,27,4,4032,2439	TT,TA,T,AA,A		0.0,0.8088,0.2935	benign	66/184	31089873	31,10530	2202	4300	6502	SO:0001583	missense	53940	exon1			CTGGGCATGCTCC	AF285592	CCDS14227.1	Xp21.2	2010-07-06			ENSG00000132446	ENSG00000132446			3987	protein-coding gene	gene with protein product	"""cancer/testis antigen 38"""	300308				11279525	Standard	NM_031894		Approved	CT38	uc004dcl.1	Q9BXU8	OTTHUMG00000021332	ENST00000359202.3:c.198T>A	X.37:g.31089873A>T	ENSP00000368207:p.His66Gln	180.0	0.0	0		186.0	87.0	0.467742	NM_031894	Q6NT24|Q6NTE2	Missense_Mutation	SNP	ENST00000359202.3	37	CCDS14227.1	8	0.004822182037371911	5	0.0102880658436214	0	0.0	0	0.0	0	0.0	A	10.22	1.290499	0.23478	0.008088	0.0	ENSG00000132446	ENST00000359202	T	0.72051	-0.62	3.44	-3.29	0.05017	Ferritin/ribonucleotide reductase-like (1);Ferritin-related (1);Ferritin/DPS protein domain (1);Ferritin-like (1);	0.401704	0.26156	N	0.026011	T	0.48804	0.1520	M	0.70595	2.14	0.21220	N	0.999756	B	0.32800	0.385	B	0.29353	0.101	T	0.48822	-0.9001	10	0.59425	D	0.04	.	1.8231	0.03115	0.4037:0.1354:0.331:0.1299	.	66	Q9BXU8	FHL17_HUMAN	Q	66	ENSP00000368207:H66Q	ENSP00000368207:H66Q	H	-	3	2	FTHL17	30999794	0.001000	0.12720	0.000000	0.03702	0.002000	0.02628	-1.291000	0.02775	-1.082000	0.03101	-1.413000	0.01118	CAT	A|0.996;T|0.004	0.004	strong		0.592	FTHL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056178.1	NM_031894	
ALDH1L1	10840	hgsc.bcm.edu	37	3	125854404	125854404	+	Silent	SNP	C	C	T	rs114109734	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:125854404C>T	ENST00000393434.2	-	12	1795	c.1446G>A	c.(1444-1446)gcG>gcA	p.A482A	ALDH1L1_ENST00000452905.2_Silent_p.A381A|ALDH1L1_ENST00000472186.1_Silent_p.A482A|ALDH1L1_ENST00000273450.3_Silent_p.A492A|ALDH1L1_ENST00000393431.2_Silent_p.A482A	NM_012190.3	NP_036322.2	O75891	AL1L1_HUMAN	aldehyde dehydrogenase 1 family, member L1	482	Aldehyde dehydrogenase.				10-formyltetrahydrofolate catabolic process (GO:0009258)|biosynthetic process (GO:0009058)|one-carbon metabolic process (GO:0006730)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	catalytic activity (GO:0003824)|formyltetrahydrofolate dehydrogenase activity (GO:0016155)|hydroxymethyl-, formyl- and related transferase activity (GO:0016742)|methyltransferase activity (GO:0008168)|oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(5)|large_intestine(10)|lung(22)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	52				GBM - Glioblastoma multiforme(114;0.0462)	Tetrahydrofolic acid(DB00116)	CCCGGTCCCGCGCACTGATCT	0.632													C|||	15	0.00299521	0.0106	0.0014	5008	,	,		15773	0.0		0.0	False		,,,				2504	0.0				p.A492A		Atlas-SNP	.											.	ALDH1L1	138	.	0			c.G1476A						PASS	.	C		49,4357	50.9+/-86.3	0,49,2154	136.0	102.0	114.0		1446	-7.5	0.0	3	dbSNP_133	114	0,8600		0,0,4300	no	coding-synonymous	ALDH1L1	NM_012190.2		0,49,6454	TT,TC,CC		0.0,1.1121,0.3767		482/903	125854404	49,12957	2203	4300	6503	SO:0001819	synonymous_variant	10840	exon12			GTCCCGCGCACTG	AF052732	CCDS3034.1, CCDS58850.1, CCDS58851.1	3q21.2	2010-07-19		2005-01-27	ENSG00000144908	ENSG00000144908	1.5.1.6	"""Aldehyde dehydrogenases"""	3978	protein-coding gene	gene with protein product	"""cytosolic 10-formyltetrahydrofolate dehydrogenase"""	600249	"""formyltetrahydrofolate dehydrogenase"""	FTHFD			Standard	NM_012190		Approved	10-fTHF	uc031sbp.1	O75891	OTTHUMG00000125551	ENST00000393434.2:c.1446G>A	3.37:g.125854404C>T		75.0	0.0	0		79.0	35.0	0.443038	NM_001270364	B4DG36|E9PBX3|Q68CS1	Silent	SNP	ENST00000393434.2	37	CCDS3034.1																																																																																			C|0.996;T|0.004	0.004	strong		0.632	ALDH1L1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354391.1	NM_012190	
PVR	5817	hgsc.bcm.edu	37	19	45161070	45161070	+	Missense_Mutation	SNP	G	G	A	rs35365841	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:45161070G>A	ENST00000425690.3	+	5	1182	c.883G>A	c.(883-885)Gcc>Acc	p.A295T	PVR_ENST00000403059.4_Missense_Mutation_p.A295T|PVR_ENST00000406449.4_Missense_Mutation_p.A295T|PVR_ENST00000344956.4_Missense_Mutation_p.A295T|CTB-171A8.1_ENST00000590796.1_RNA	NM_006505.3	NP_006496.3	P15151	PVR_HUMAN	poliovirus receptor	295	Ig-like C2-type 2.		A -> T (in dbSNP:rs35365841).		adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|receptor activity (GO:0004872)			large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	6	Lung NSC(12;0.00608)|all_lung(12;0.0148)	Medulloblastoma(540;0.0425)|Ovarian(192;0.0728)|Prostate(69;0.081)|all_neural(266;0.112)		Epithelial(262;0.000601)		GGCCCAGGGCGCCCAGCTCCT	0.587											OREG0025540	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	257	0.0513179	0.1755	0.0259	5008	,	,		18444	0.0		0.001	False		,,,				2504	0.0061				p.A295T		Atlas-SNP	.											.	PVR	23	.	0			c.G883A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA	656,3750	279.9+/-275.1	61,534,1608	61.0	53.0	55.0		883,883,883,883	-10.2	0.0	19	dbSNP_126	55	8,8592	5.7+/-21.5	0,8,4292	yes	missense,missense,missense,missense	PVR	NM_001135768.1,NM_001135769.1,NM_001135770.1,NM_006505.3	58,58,58,58	61,542,5900	AA,AG,GG		0.093,14.8888,5.1053	benign,benign,benign,benign	295/373,295/365,295/393,295/418	45161070	664,12342	2203	4300	6503	SO:0001583	missense	5817	exon5			CAGGGCGCCCAGC	BC015542	CCDS12640.1, CCDS46105.1, CCDS46106.1, CCDS46107.1	19q13.2	2013-01-29			ENSG00000073008	ENSG00000073008		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9705	protein-coding gene	gene with protein product	"""nectin-like 5"""	173850		PVS		2170108	Standard	XM_005259120		Approved	CD155, HVED, Necl-5, NECL5, Tage4	uc002ozm.3	P15151	OTTHUMG00000151527	ENST00000425690.3:c.883G>A	19.37:g.45161070G>A	ENSP00000402060:p.Ala295Thr	84.0	0.0	0	929	93.0	42.0	0.451613	NM_001135769	B4DTS9|P15152|Q15267|Q15268|Q96BJ1	Missense_Mutation	SNP	ENST00000425690.3	37	CCDS12640.1	116	0.05311355311355311	101	0.20528455284552846	14	0.03867403314917127	0	0.0	1	0.0013192612137203166	G	10.75	1.438622	0.25900	0.148888	9.3E-4	ENSG00000073008	ENST00000344956;ENST00000425690;ENST00000406449;ENST00000403059	T;T;T;T	0.16743	2.32;2.32;2.32;2.32	5.08	-10.2	0.00374	Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	2.148170	0.02353	N	0.076098	T	0.00012	0.0000	N	0.12746	0.255	0.80722	P	0.0	B;B;B;B	0.30361	0.038;0.154;0.097;0.277	B;B;B;B	0.28305	0.027;0.049;0.031;0.088	T	0.22765	-1.0207	9	0.14252	T	0.57	.	1.6961	0.02862	0.118:0.3407:0.2586:0.2827	rs35365841	295;295;295;295	P15151-2;P15151-3;P15151-4;P15151	.;.;.;PVR_HUMAN	T	295	ENSP00000340870:A295T;ENSP00000402060:A295T;ENSP00000383907:A295T;ENSP00000385344:A295T	ENSP00000340870:A295T	A	+	1	0	PVR	49852910	0.000000	0.05858	0.000000	0.03702	0.123000	0.20343	-2.189000	0.01248	-2.865000	0.00325	-0.165000	0.13383	GCC	G|0.951;A|0.049	0.049	strong		0.587	PVR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000323017.2	NM_006505	
ZNF804B	219578	hgsc.bcm.edu	37	7	88964162	88964162	+	Missense_Mutation	SNP	T	T	G	rs150870900	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:88964162T>G	ENST00000333190.4	+	4	2475	c.1866T>G	c.(1864-1866)gaT>gaG	p.D622E		NM_181646.2	NP_857597.1	A4D1E1	Z804B_HUMAN	zinc finger protein 804B	622							metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(20)|lung(78)|ovary(5)|pancreas(5)|prostate(2)|skin(11)|soft_tissue(1)|upper_aerodigestive_tract(9)	144	all_hematologic(106;0.125)|Lung NSC(181;0.15)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0513)			ATGATATAGATGAGGACCTAT	0.383										HNSCC(36;0.09)			T|||	31	0.0061901	0.0204	0.0058	5008	,	,		19603	0.0		0.0	False		,,,				2504	0.0				p.D622E		Atlas-SNP	.											.	ZNF804B	322	.	0			c.T1866G						PASS	.	T	GLU/ASP	63,4343	59.3+/-96.0	0,63,2140	74.0	78.0	77.0		1866	-1.2	0.0	7	dbSNP_134	77	0,8600		0,0,4300	yes	missense	ZNF804B	NM_181646.2	45	0,63,6440	GG,GT,TT		0.0,1.4299,0.4844	benign	622/1350	88964162	63,12943	2203	4300	6503	SO:0001583	missense	219578	exon4			TATAGATGAGGAC	AK056672	CCDS5613.1	7q21.13	2012-10-05	2006-12-18		ENSG00000182348	ENSG00000182348			21958	protein-coding gene	gene with protein product			"""zinc finger 804B"""				Standard	NM_181646		Approved	FLJ32110	uc011khi.2	A4D1E1	OTTHUMG00000131037	ENST00000333190.4:c.1866T>G	7.37:g.88964162T>G	ENSP00000329638:p.Asp622Glu	83.0	0.0	0		102.0	46.0	0.45098	NM_181646	B2RTV2|Q7Z714|Q96MN7	Missense_Mutation	SNP	ENST00000333190.4	37	CCDS5613.1	8	0.003663003663003663	7	0.014227642276422764	1	0.0027624309392265192	0	0.0	0	0.0	T	0.048	-1.259050	0.01445	0.014299	0.0	ENSG00000182348	ENST00000333190	T	0.04454	3.62	5.49	-1.24	0.09435	.	0.337088	0.29376	N	0.012335	T	0.01189	0.0039	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.04013	0.001	T	0.46205	-0.9208	10	0.02654	T	1	-6.4004	6.3638	0.21443	0.0:0.1906:0.325:0.4844	.	622	A4D1E1	Z804B_HUMAN	E	622	ENSP00000329638:D622E	ENSP00000329638:D622E	D	+	3	2	ZNF804B	88802098	0.211000	0.23529	0.002000	0.10522	0.037000	0.13140	-0.303000	0.08210	-0.334000	0.08463	0.533000	0.62120	GAT	T|0.996;G|0.004	0.004	strong		0.383	ZNF804B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253683.2	NM_181646	
DNAH10	196385	hgsc.bcm.edu	37	12	124360037	124360037	+	Splice_Site	SNP	C	C	T	rs61732737	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124360037C>T	ENST00000409039.3	+	46	7869	c.7844C>T	c.(7843-7845)tCg>tTg	p.S2615L		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2615	AAA 3. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		GGCCACACCTCGGTAACTTGA	0.448													C|||	125	0.0249601	0.034	0.0086	5008	,	,		18069	0.0526		0.007	False		,,,				2504	0.0143				p.S2615L		Atlas-SNP	.											.	DNAH10	888	.	0			c.C7844T						PASS	.	C	LEU/SER	112,3600		3,106,1747	100.0	93.0	95.0		7844	3.3	1.0	12	dbSNP_129	95	57,8131		0,57,4037	yes	missense-near-splice	DNAH10	NM_207437.3	145	3,163,5784	TT,TC,CC		0.6961,3.0172,1.4202	benign	2615/4472	124360037	169,11731	1856	4094	5950	SO:0001630	splice_region_variant	196385	exon46			ACACCTCGGTAAC	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.7845+1C>T	12.37:g.124360037C>T		88.0	0.0	0		103.0	49.0	0.475728	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	64	0.029304029304029304	20	0.04065040650406504	3	0.008287292817679558	37	0.06468531468531469	4	0.005277044854881266	C	12.26	1.884048	0.33255	0.030172	0.006961	ENSG00000197653	ENST00000409039	T	0.39787	1.06	5.41	3.3	0.37823	.	2.437090	0.02760	N	0.118428	T	0.05640	0.0148	L	0.41415	1.275	0.80722	D	1	B	0.22080	0.064	B	0.16289	0.015	T	0.03524	-1.1028	10	0.34782	T	0.22	.	10.3793	0.44101	0.1914:0.7324:0.0:0.0762	rs61732737	2615	Q8IVF4	DYH10_HUMAN	L	2615	ENSP00000386770:S2615L	ENSP00000386770:S2615L	S	+	2	0	DNAH10	122925990	0.862000	0.29867	0.998000	0.56505	0.927000	0.56198	0.469000	0.22067	1.425000	0.47237	0.558000	0.71614	TCG	C|0.976;T|0.024	0.024	strong		0.448	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		Missense_Mutation
SLC9A4	389015	hgsc.bcm.edu	37	2	103142761	103142761	+	Missense_Mutation	SNP	A	A	T	rs115217520	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:103142761A>T	ENST00000295269.4	+	11	2451	c.1994A>T	c.(1993-1995)aAt>aTt	p.N665I		NM_001011552.3	NP_001011552.2	Q6AI14	SL9A4_HUMAN	solute carrier family 9, subfamily A (NHE4, cation proton antiporter 4), member 4	665					epithelial cell development (GO:0002064)|gastric acid secretion (GO:0001696)|ion transport (GO:0006811)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium:proton antiporter activity (GO:0015385)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						CCCTACGGGAATCCTCAGTCT	0.498													A|||	11	0.00219649	0.0083	0.0	5008	,	,		15709	0.0		0.0	False		,,,				2504	0.0				p.N665I		Atlas-SNP	.											.	SLC9A4	115	.	0			c.A1994T						PASS	.	A	ILE/ASN	27,4379	33.5+/-64.1	0,27,2176	126.0	118.0	121.0		1994	3.4	0.0	2	dbSNP_133	121	2,8598	2.2+/-6.3	0,2,4298	yes	missense	SLC9A4	NM_001011552.3	149	0,29,6474	TT,TA,AA		0.0233,0.6128,0.223	benign	665/799	103142761	29,12977	2203	4300	6503	SO:0001583	missense	389015	exon11			ACGGGAATCCTCA		CCDS33264.1	2q12.1	2013-05-22	2012-03-22		ENSG00000180251	ENSG00000180251		"""Solute carriers"""	11077	protein-coding gene	gene with protein product		600531	"""solute carrier family 9 (sodium/hydrogen exchanger), isoform 4"", ""solute carrier family 9 (sodium/hydrogen exchanger), member 4"""			8199403	Standard	NM_001011552		Approved	NHE4	uc002tbz.4	Q6AI14	OTTHUMG00000153093	ENST00000295269.4:c.1994A>T	2.37:g.103142761A>T	ENSP00000295269:p.Asn665Ile	123.0	0.0	0		131.0	59.0	0.450382	NM_001011552	Q69YK0	Missense_Mutation	SNP	ENST00000295269.4	37	CCDS33264.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	12.38	1.919817	0.33908	0.006128	2.33E-4	ENSG00000180251	ENST00000295269	T	0.46451	0.87	5.8	3.38	0.38709	.	2.143600	0.02112	N	0.054895	T	0.33294	0.0858	L	0.44542	1.39	0.09310	N	1	B	0.22604	0.072	B	0.26517	0.07	T	0.26292	-1.0107	10	0.42905	T	0.14	.	8.6644	0.34112	0.8465:0.0:0.1535:0.0	.	665	Q6AI14	SL9A4_HUMAN	I	665	ENSP00000295269:N665I	ENSP00000295269:N665I	N	+	2	0	SLC9A4	102509193	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.084000	0.14891	0.438000	0.26450	0.533000	0.62120	AAT	A|0.997;T|0.003	0.003	strong		0.498	SLC9A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329498.1	NM_001011552.3	
KRT14	3861	hgsc.bcm.edu	37	17	39741280	39741280	+	Silent	SNP	A	A	G	rs35849957	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39741280A>G	ENST00000167586.6	-	2	641	c.555T>C	c.(553-555)aaT>aaC	p.N185N		NM_000526.4	NP_000517	P02533	K1C14_HUMAN	keratin 14	185	Coil 1B.|Rod.				aging (GO:0007568)|cell junction assembly (GO:0034329)|epidermis development (GO:0008544)|epithelial cell differentiation (GO:0030855)|hair cycle (GO:0042633)|hemidesmosome assembly (GO:0031581)|intermediate filament bundle assembly (GO:0045110)|response to ionizing radiation (GO:0010212)|response to zinc ion (GO:0010043)	cell periphery (GO:0071944)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	keratin filament binding (GO:1990254)|structural constituent of cytoskeleton (GO:0005200)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(3)|lung(7)|ovary(1)|prostate(5)|skin(1)|stomach(1)	25		Breast(137;0.000307)				GCAGAAGGACATTGGCATTGT	0.507													.|||	299	0.0597045	0.2118	0.0216	5008	,	,		20159	0.0		0.004	False		,,,				2504	0.0				p.N185N		Atlas-SNP	.											.	KRT14	65	.	0			c.T555C						PASS	.	G		794,3612	751.1+/-412.2	71,652,1480	101.0	82.0	89.0		555	-7.0	0.0	17	dbSNP_126	89	6,8594	818.5+/-406.9	0,6,4294	no	coding-synonymous	KRT14	NM_000526.4		71,658,5774	GG,GA,AA		0.0698,18.0209,6.151		185/473	39741280	800,12206	2203	4300	6503	SO:0001819	synonymous_variant	3861	exon2			AAGGACATTGGCA	BC002690	CCDS11400.1	17q21.2	2013-06-20	2008-09-19		ENSG00000186847	ENSG00000186847		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6416	protein-coding gene	gene with protein product	"""epidermolysis bullosa simplex, Dowling-Meara, Koebner"""	148066	"""keratin 14 (epidermolysis bullosa simplex, Dowling-Meara, Koebner)"""	EBS3, EBS4		1717157, 16831889	Standard	NM_000526		Approved		uc002hxf.2	P02533	OTTHUMG00000133426	ENST00000167586.6:c.555T>C	17.37:g.39741280A>G		87.0	0.0	0		102.0	55.0	0.539216	NM_000526	Q14715|Q53XY3|Q9BUE3|Q9UBN2|Q9UBN3|Q9UCY4	Silent	SNP	ENST00000167586.6	37	CCDS11400.1																																																																																			A|0.944;G|0.056	0.056	strong		0.507	KRT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257289.1	NM_000526	
NKX3-2	579	hgsc.bcm.edu	37	4	13545610	13545610	+	Silent	SNP	C	C	T	rs10032202	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:13545610C>T	ENST00000382438.5	-	1	1064	c.429G>A	c.(427-429)gcG>gcA	p.A143A	AC006445.8_ENST00000501050.1_lincRNA	NM_001189.3	NP_001180.1	P78367	NKX32_HUMAN	NK3 homeobox 2	143					determination of left/right symmetry (GO:0007368)|embryonic skeletal system development (GO:0048706)|intestinal epithelial cell development (GO:0060576)|middle ear morphogenesis (GO:0042474)|negative regulation of apoptotic process (GO:0043066)|negative regulation of chondrocyte differentiation (GO:0032331)|organ formation (GO:0048645)|pancreas development (GO:0031016)|skeletal system development (GO:0001501)|skeletal system morphogenesis (GO:0048705)|spleen development (GO:0048536)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			breast(1)|large_intestine(1)|lung(4)|prostate(1)	7						CGCTCCGGCCCGCGGCTTCCT	0.731													C|||	196	0.0391374	0.1437	0.0058	5008	,	,		11648	0.0		0.002	False		,,,				2504	0.0				p.A143A		Atlas-SNP	.											.	NKX3-2	15	.	0			c.G429A						PASS	.	C		260,3434		1,258,1588	3.0	4.0	4.0		429	3.1	1.0	4	dbSNP_119	4	10,7596		0,10,3793	no	coding-synonymous	NKX3-2	NM_001189.3		1,268,5381	TT,TC,CC		0.1315,7.0384,2.3894		143/334	13545610	270,11030	1847	3803	5650	SO:0001819	synonymous_variant	579	exon1			CCGGCCCGCGGCT	AF009801	CCDS3410.1	4p16.3	2012-03-09	2007-07-26	2007-07-26	ENSG00000109705	ENSG00000109705		"""Homeoboxes / ANTP class : NKL subclass"""	951	protein-coding gene	gene with protein product		602183	"""bagpipe homeobox homolog 1 (Drosophila)"""	BAPX1		9344671	Standard	NM_001189		Approved	NKX3B, NKX3.2	uc003gmx.2	P78367	OTTHUMG00000090657	ENST00000382438.5:c.429G>A	4.37:g.13545610C>T		24.0	0.0	0		26.0	13.0	0.5	NM_001189	Q2M2I7	Silent	SNP	ENST00000382438.5	37	CCDS3410.1																																																																																			C|0.964;T|0.036	0.036	strong		0.731	NKX3-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207317.3		
PER3	8863	hgsc.bcm.edu	37	1	7887234	7887234	+	Missense_Mutation	SNP	C	C	T	rs35687686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:7887234C>T	ENST00000361923.2	+	17	2396	c.2221C>T	c.(2221-2223)Cgg>Tgg	p.R741W	PER3_ENST00000377532.3_Missense_Mutation_p.R749W|RP3-467L1.4_ENST00000451646.1_RNA	NM_016831.1	NP_058515.1	P56645	PER3_HUMAN	period circadian clock 3	741	CSNK1E binding domain. {ECO:0000250}.				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)			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)		GAAGCACAAGCGGAAGAAGCT	0.597													C|||	30	0.00599042	0.0197	0.0058	5008	,	,		15161	0.0		0.0	False		,,,				2504	0.0				p.R741W		Atlas-SNP	.											PER3,colon,carcinoma,0,1	PER3	95	1	0			c.C2221T						PASS	.	C	TRP/ARG	70,4246		1,68,2089	19.0	24.0	22.0		2221	1.6	0.1	1	dbSNP_126	22	1,8501		0,1,4250	yes	missense	PER3	NM_016831.1	101	1,69,6339	TT,TC,CC		0.0118,1.6219,0.5539	probably-damaging	741/1202	7887234	71,12747	2158	4251	6409	SO:0001583	missense	8863	exon17			CACAAGCGGAAGA	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.2221C>T	1.37:g.7887234C>T	ENSP00000355031:p.Arg741Trp	80.0	0.0	0		74.0	34.0	0.459459	NM_016831	Q5H8X4|Q5H8X5|Q969K6|Q96S77|Q96S78|Q9C0J3|Q9NSP9|Q9UGU8	Missense_Mutation	SNP	ENST00000361923.2	37	CCDS89.1	12	0.005494505494505495	10	0.02032520325203252	2	0.0055248618784530384	0	0.0	0	0.0	C	10.54	1.377888	0.24944	0.016219	1.18E-4	ENSG00000049246	ENST00000377532;ENST00000361923	T;T	0.13778	2.56;2.6	4.52	1.64	0.23874	.	2.148170	0.02588	N	0.099653	T	0.06188	0.0160	L	0.42529	1.33	0.09310	N	1	B;P;P;B	0.40180	0.179;0.581;0.705;0.179	B;B;B;B	0.31686	0.019;0.063;0.134;0.019	T	0.32161	-0.9917	10	0.87932	D	0	.	7.6166	0.28160	0.0:0.7331:0.0:0.2669	rs35687686	741;749;749;741	A2I2N5;A6H8X0;P56645-2;P56645	.;.;.;PER3_HUMAN	W	749;741	ENSP00000366755:R749W;ENSP00000355031:R741W	ENSP00000355031:R741W	R	+	1	2	PER3	7809821	0.991000	0.36638	0.061000	0.19648	0.054000	0.15201	0.501000	0.22578	0.181000	0.19994	0.561000	0.74099	CGG	C|0.993;T|0.007	0.007	strong		0.597	PER3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000003607.1	NM_016831	
UBR4	23352	hgsc.bcm.edu	37	1	19518855	19518855	+	Silent	SNP	T	T	C	rs147313932	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19518855T>C	ENST00000375254.3	-	11	1248	c.1221A>G	c.(1219-1221)caA>caG	p.Q407Q	UBR4_ENST00000375217.2_Silent_p.Q407Q|UBR4_ENST00000375226.2_Silent_p.Q407Q|UBR4_ENST00000375267.2_Silent_p.Q407Q	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	407					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)		CACCCAGCAATTGGAAATTCT	0.428													T|||	15	0.00299521	0.0106	0.0	5008	,	,		19894	0.001		0.0	False		,,,				2504	0.0				p.Q407Q		Atlas-SNP	.											.	UBR4	415	.	0			c.A1221G						PASS	.	T		13,4393	21.2+/-45.6	0,13,2190	79.0	81.0	80.0		1221	-11.2	0.0	1	dbSNP_134	80	0,8600		0,0,4300	no	coding-synonymous	UBR4	NM_020765.2		0,13,6490	CC,CT,TT		0.0,0.2951,0.1		407/5184	19518855	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	23352	exon11			CAGCAATTGGAAA	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.1221A>G	1.37:g.19518855T>C		76.0	0.0	0		78.0	37.0	0.474359	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																																																																																			T|0.999;C|0.001	0.001	strong		0.428	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
DNAH9	1770	hgsc.bcm.edu	37	17	11583245	11583245	+	Silent	SNP	G	G	A	rs8070788	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:11583245G>A	ENST00000262442.4	+	18	3593	c.3525G>A	c.(3523-3525)ttG>ttA	p.L1175L	DNAH9_ENST00000454412.2_Silent_p.L1175L	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	1175	Stem. {ECO:0000250}.				cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		CTATTGAATTGCTGAAGACCT	0.398													G|||	56	0.0111821	0.0408	0.0029	5008	,	,		19789	0.0		0.0	False		,,,				2504	0.0				p.L1175L		Atlas-SNP	.											.	DNAH9	695	.	0			c.G3525A						PASS	.	G		163,4243	111.2+/-149.4	6,151,2046	115.0	110.0	112.0		3525	4.6	1.0	17	dbSNP_116	112	1,8599		0,1,4299	no	coding-synonymous	DNAH9	NM_001372.3		6,152,6345	AA,AG,GG		0.0116,3.6995,1.261		1175/4487	11583245	164,12842	2203	4300	6503	SO:0001819	synonymous_variant	1770	exon18			TGAATTGCTGAAG	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.3525G>A	17.37:g.11583245G>A		82.0	0.0	0		80.0	37.0	0.4625	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Silent	SNP	ENST00000262442.4	37	CCDS11160.1																																																																																			G|0.988;A|0.012	0.012	strong		0.398	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
C17orf105	284067	hgsc.bcm.edu	37	17	41857869	41857869	+	Silent	SNP	C	C	T	rs73987086	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:41857869C>T	ENST00000449302.3	+	1	67	c.39C>T	c.(37-39)atC>atT	p.I13I	RP5-905N1.2_ENST00000591540.1_RNA|DUSP3_ENST00000397937.2_5'Flank|DUSP3_ENST00000226004.3_5'Flank|DUSP3_ENST00000591618.1_5'Flank	NM_001136483.1	NP_001129955.1	B2RV13	CQ105_HUMAN	chromosome 17 open reading frame 105	13																	ACCCTGTTATCGTCTCTAATC	0.443													C|||	262	0.0523163	0.1868	0.0202	5008	,	,		19742	0.0		0.001	False		,,,				2504	0.0				p.I13I		Atlas-SNP	.											.	C17orf105	3	.	0			c.C39T						PASS	.						159.0	137.0	144.0					17																	41857869		692	1591	2283	SO:0001819	synonymous_variant	284067	exon1			TGTTATCGTCTCT		CCDS45695.1	17q21.31	2012-10-23			ENSG00000231256	ENSG00000231256			37241	protein-coding gene	gene with protein product							Standard	NM_001136483		Approved		uc002ieg.3	B2RV13	OTTHUMG00000180890	ENST00000449302.3:c.39C>T	17.37:g.41857869C>T		98.0	0.0	0		139.0	67.0	0.482014	NM_001136483		Silent	SNP	ENST00000449302.3	37	CCDS45695.1																																																																																			C|0.953;T|0.047	0.047	strong		0.443	C17orf105-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453508.1	NM_001136483	
CSPG5	10675	hgsc.bcm.edu	37	3	47619025	47619025	+	Missense_Mutation	SNP	G	G	C	rs35863063	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:47619025G>C	ENST00000383738.2	-	2	2589	c.491C>G	c.(490-492)gCt>gGt	p.A164G	CSPG5_ENST00000264723.4_Missense_Mutation_p.A164G|CSPG5_ENST00000465441.1_5'Flank|CSPG5_ENST00000456150.1_Missense_Mutation_p.A26G	NM_001206943.1|NM_001206945.1	NP_001193872.1|NP_001193874.1	O95196	CSPG5_HUMAN	chondroitin sulfate proteoglycan 5 (neuroglycan C)	164					axon regeneration (GO:0031103)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|intracellular transport (GO:0046907)|nervous system development (GO:0007399)|regulation of growth (GO:0040008)|regulation of synaptic transmission (GO:0050804)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|Golgi-associated vesicle membrane (GO:0030660)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)	growth factor activity (GO:0008083)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|prostate(2)	22				BRCA - Breast invasive adenocarcinoma(193;0.000266)|KIRC - Kidney renal clear cell carcinoma(197;0.00551)|Kidney(197;0.00621)		GAGTTCAGAAGCTGGGCTCAG	0.652													G|||	97	0.019369	0.0696	0.0072	5008	,	,		14217	0.0		0.0	False		,,,				2504	0.0				p.A164G		Atlas-SNP	.											.	CSPG5	46	.	0			c.C491G						PASS	.	G	GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA,GLY/ALA	266,4134		10,246,1944	27.0	34.0	32.0		77,491,491,77,491	-4.3	0.0	3	dbSNP_126	32	1,8597		0,1,4298	yes	missense,missense,missense,missense,missense	CSPG5	NM_001206942.1,NM_001206943.1,NM_001206944.1,NM_001206945.1,NM_006574.3	60,60,60,60,60	10,247,6242	CC,CG,GG		0.0116,6.0455,2.0542	benign,benign,benign,benign,benign	26/402,164/567,164/478,26/429,164/540	47619025	267,12731	2200	4299	6499	SO:0001583	missense	10675	exon2			TCAGAAGCTGGGC	AF059274	CCDS2757.1, CCDS56252.1, CCDS56253.1, CCDS74930.1	3p21.3	2008-07-18			ENSG00000114646	ENSG00000114646			2467	protein-coding gene	gene with protein product		606775				9950058	Standard	NM_006574		Approved	NGC	uc003crp.4	O95196	OTTHUMG00000133518	ENST00000383738.2:c.491C>G	3.37:g.47619025G>C	ENSP00000373244:p.Ala164Gly	60.0	0.0	0		57.0	26.0	0.45614	NM_006574	Q71M39|Q71M40	Missense_Mutation	SNP	ENST00000383738.2	37	CCDS56253.1	38	0.0173992673992674	34	0.06910569105691057	4	0.011049723756906077	0	0.0	0	0.0	G	0.369	-0.934853	0.02340	0.060455	1.16E-4	ENSG00000114646	ENST00000456150;ENST00000383738;ENST00000264723	T;T;T	0.41400	1.0;1.0;1.0	3.92	-4.28	0.03732	Chondroitin sulphate attachment (1);	0.534137	0.14716	N	0.302660	T	0.00815	0.0027	N	0.04508	-0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.001	T	0.17289	-1.0374	10	0.09590	T	0.72	-0.5678	0.8637	0.01198	0.2327:0.2926:0.2766:0.1981	rs35863063	164;164	O95196;O95196-2	CSPG5_HUMAN;.	G	26;164;164	ENSP00000392096:A26G;ENSP00000373244:A164G;ENSP00000264723:A164G	ENSP00000264723:A164G	A	-	2	0	CSPG5	47594029	0.002000	0.14202	0.001000	0.08648	0.453000	0.32348	-1.165000	0.03132	-0.599000	0.05798	0.579000	0.79373	GCT	G|0.981;C|0.019	0.019	strong		0.652	CSPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257489.1	NM_006574	
TSHZ1	10194	hgsc.bcm.edu	37	18	73000131	73000131	+	Silent	SNP	G	G	A	rs35073557	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:73000131G>A	ENST00000580243.1	+	2	3117	c.2769G>A	c.(2767-2769)ccG>ccA	p.P923P	TSHZ1_ENST00000322038.5_Silent_p.P878P			Q6ZSZ6	TSH1_HUMAN	teashirt zinc finger homeobox 1	923					anterior/posterior pattern specification (GO:0009952)|middle ear morphogenesis (GO:0042474)|regulation of transcription, DNA-templated (GO:0006355)|soft palate development (GO:0060023)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(11)|liver(1)|lung(14)|ovary(1)|skin(6)|upper_aerodigestive_tract(2)	42		Esophageal squamous(42;0.129)|Prostate(75;0.142)|Melanoma(33;0.211)		Colorectal(1;0.000501)|READ - Rectum adenocarcinoma(2;0.00226)|BRCA - Breast invasive adenocarcinoma(31;0.246)		ACTTGGGCCCGCAGGAGAGGG	0.592													G|||	69	0.013778	0.0477	0.0086	5008	,	,		19023	0.0		0.0	False		,,,				2504	0.0				p.P878P		Atlas-SNP	.											.	TSHZ1	104	.	0			c.G2634A						PASS	.	G		230,4176	136.5+/-172.5	6,218,1979	56.0	53.0	54.0		2634	-9.1	1.0	18	dbSNP_126	54	0,8600		0,0,4300	no	coding-synonymous	TSHZ1	NM_005786.4		6,218,6279	AA,AG,GG		0.0,5.2202,1.7684		878/1033	73000131	230,12776	2203	4300	6503	SO:0001819	synonymous_variant	10194	exon2			GGGCCCGCAGGAG	AF039698	CCDS12009.1	18q22.3	2013-11-20	2007-07-16	2006-03-14	ENSG00000179981	ENSG00000179981		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	10669	protein-coding gene	gene with protein product		614427	"""serologically defined colon cancer antigen 33"", ""teashirt zinc finger 1"", ""teashirt family zinc finger 1"""	SDCCAG33		17586487	Standard	NM_005786		Approved	NY-CO-33, TSH1	uc002lly.4	Q6ZSZ6	OTTHUMG00000132859	ENST00000580243.1:c.2769G>A	18.37:g.73000131G>A		69.0	0.0	0		68.0	37.0	0.544118	NM_005786	O60534|Q4LE29|Q53EU4	Silent	SNP	ENST00000580243.1	37																																																																																				G|0.981;A|0.019	0.019	strong		0.592	TSHZ1-005	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000444913.1	NM_005786	
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254184	39254184	+	Silent	SNP	T	T	C	rs7217470	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39254184T>C	ENST00000333822.4	-	1	209	c.153A>G	c.(151-153)agA>agG	p.R51R		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	51	25 X 5 AA repeats of C-C-[IKRQVHEC]- [SPRT]-[STCVQPR].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(1)|prostate(1)	11						AGCACTGGGGTCTGCAGCAGC	0.652													T|||	241	0.048123	0.1732	0.0159	5008	,	,		15501	0.0		0.001	False		,,,				2504	0.0				p.R51R		Atlas-SNP	.											KRTAP4-8,NS,carcinoma,0,1	KRTAP4-8	57	1	0			c.A153G						scavenged	.	T		192,1192		14,164,514	14.0	17.0	16.0		153	-5.2	0.0	17	dbSNP_116	16	2,3172		0,2,1585	no	coding-synonymous	KRTAP4-8	NM_031960.2		14,166,2099	CC,CT,TT		0.063,13.8728,4.2563		51/186	39254184	194,4364	692	1587	2279	SO:0001819	synonymous_variant	728224	exon1			CTGGGGTCTGCAG	AJ406940	CCDS45674.1	17q21.2	2013-06-25			ENSG00000204880	ENSG00000204880		"""Keratin associated proteins"""	17230	protein-coding gene	gene with protein product						11279113	Standard	NM_031960		Approved	KAP4.8	uc010wfo.2	Q9BYQ9	OTTHUMG00000133580	ENST00000333822.4:c.153A>G	17.37:g.39254184T>C		101.0	1.0	0.00990099		146.0	83.0	0.568493	NM_031960	A8MSH3	Silent	SNP	ENST00000333822.4	37	CCDS45674.1																																																																																			T|0.820;C|0.180	0.180	strong		0.652	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
ADAM18	8749	hgsc.bcm.edu	37	8	39537616	39537616	+	Silent	SNP	C	C	T	rs28454772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:39537616C>T	ENST00000265707.5	+	16	1737	c.1692C>T	c.(1690-1692)gaC>gaT	p.D564D	ADAM18_ENST00000379866.1_Silent_p.D540D|ADAM18_ENST00000541111.1_5'UTR	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	564	Cys-rich.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(31)|ovary(1)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)	71		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)			ATAAAAGTGACGCTCAATCTA	0.383													c|||	402	0.0802716	0.2723	0.0317	5008	,	,		19440	0.002		0.0099	False		,,,				2504	0.0082				p.D564D		Atlas-SNP	.											ADAM18,colon,carcinoma,0,1	ADAM18	169	1	0			c.C1692T						PASS	.	A		1031,3375	381.6+/-324.1	128,775,1300	113.0	101.0	105.0		1692	0.3	0.0	8	dbSNP_125	105	60,8540	35.9+/-90.5	0,60,4240	no	coding-synonymous	ADAM18	NM_014237.2		128,835,5540	TT,TC,CC		0.6977,23.3999,8.3884		564/740	39537616	1091,11915	2203	4300	6503	SO:0001819	synonymous_variant	8749	exon16			AAGTGACGCTCAA	AJ133004	CCDS6113.1, CCDS55225.1	8p11.22	2008-08-07	2005-08-18		ENSG00000168619	ENSG00000168619		"""ADAM metallopeptidase domain containing"""	196	protein-coding gene	gene with protein product			"""a disintegrin and metalloproteinase domain 18"""			12200459	Standard	NM_014237		Approved	tMDCIII, ADAM27	uc003xni.3	Q9Y3Q7	OTTHUMG00000164040	ENST00000265707.5:c.1692C>T	8.37:g.39537616C>T		126.0	0.0	0		127.0	67.0	0.527559	NM_014237	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Silent	SNP	ENST00000265707.5	37	CCDS6113.1																																																																																			C|0.914;T|0.086	0.086	strong		0.383	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237	
NDUFAF7	55471	hgsc.bcm.edu	37	2	37459308	37459308	+	Missense_Mutation	SNP	C	C	G	rs2714473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:37459308C>G	ENST00000002125.4	+	2	155	c.115C>G	c.(115-117)Ccg>Gcg	p.P39A	NDUFAF7_ENST00000336237.6_Missense_Mutation_p.P39A|CEBPZ_ENST00000234170.5_5'Flank|NDUFAF7_ENST00000483999.1_Intron	NM_144736.4	NP_653337.1	Q7L592	NDUF7_HUMAN	NADH dehydrogenase (ubiquinone) complex I, assembly factor 7	39			P -> A (in dbSNP:rs2714473).		methylation (GO:0032259)|mitochondrial respiratory chain complex I assembly (GO:0032981)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	enzyme binding (GO:0019899)|methyltransferase activity (GO:0008168)										TGCAGAAAACCCGGTGACGCC	0.463													C|||	361	0.0720847	0.2564	0.0303	5008	,	,		19737	0.0		0.001	False		,,,				2504	0.0				p.P39A		Atlas-SNP	.											.	.	.	.	0			c.C115G						PASS	.	C	ALA/PRO,ALA/PRO	982,3424	366.1+/-317.7	113,756,1334	110.0	105.0	107.0		115,115	2.7	0.0	2	dbSNP_100	107	14,8586	8.4+/-32.0	0,14,4286	yes	missense,missense	C2orf56	NM_001083946.1,NM_144736.4	27,27	113,770,5620	GG,GC,CC		0.1628,22.2878,7.658	benign,benign	39/344,39/442	37459308	996,12010	2203	4300	6503	SO:0001583	missense	55471	exon2			GAAAACCCGGTGA		CCDS1788.1, CCDS42673.1	2p22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000003509	ENSG00000003509		"""Mitochondrial respiratory chain complex assembly factors"""	28816	protein-coding gene	gene with protein product	"""mitochondrial dysfunction protein A homolog"""	615898	"""chromosome 2 open reading frame 56"""	C2orf56			Standard	NM_144736		Approved	PRO1853, MidA	uc002rqa.4	Q7L592	OTTHUMG00000128468	ENST00000002125.4:c.115C>G	2.37:g.37459308C>G	ENSP00000002125:p.Pro39Ala	123.0	0.0	0		133.0	64.0	0.481203	NM_001083946	Q7Z399|Q9P1G3	Missense_Mutation	SNP	ENST00000002125.4	37	CCDS1788.1	107	0.04899267399267399	98	0.1991869918699187	9	0.024861878453038673	0	0.0	0	0.0	C	7.698	0.692572	0.15039	0.222878	0.001628	ENSG00000003509	ENST00000002125;ENST00000336237	T;T	0.40225	1.05;1.04	5.51	2.68	0.31781	.	1.761130	0.02616	N	0.102632	T	0.00012	0.0000	N	0.05467	-0.045	0.80722	P	0.0	B;B;B;B	0.15930	0.001;0.009;0.015;0.0	B;B;B;B	0.12837	0.003;0.004;0.008;0.004	T	0.17745	-1.0359	9	0.08599	T	0.76	0.7393	3.0899	0.06290	0.2362:0.4978:0.1281:0.1379	rs2714473;rs52835713;rs2714473	39;39;39;39	E7EUC2;B4DQY3;Q7L592-2;Q7L592	.;.;.;MIDA_HUMAN	A	39	ENSP00000002125:P39A;ENSP00000337431:P39A	ENSP00000002125:P39A	P	+	1	0	C2orf56	37312812	0.000000	0.05858	0.006000	0.13384	0.962000	0.63368	0.599000	0.24089	0.268000	0.21939	-0.319000	0.08680	CCG	C|0.931;G|0.069	0.069	strong		0.463	NDUFAF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250267.1	NM_144736	
ERC2	26059	hgsc.bcm.edu	37	3	56026204	56026204	+	Silent	SNP	C	C	T	rs61732592	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:56026204C>T	ENST00000288221.6	-	11	2391	c.2136G>A	c.(2134-2136)gcG>gcA	p.A712A		NM_015576.1	NP_056391.1	O15083	ERC2_HUMAN	ELKS/RAB6-interacting/CAST family member 2	712						cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|growth cone (GO:0030426)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)				breast(2)|endometrium(5)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|urinary_tract(1)	31				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)		GGTAGTAAGACGCCTCTTTAT	0.458													C|||	44	0.00878594	0.0325	0.0014	5008	,	,		19132	0.0		0.0	False		,,,				2504	0.0				p.A712A		Atlas-SNP	.											ERC2_ENST00000288221,caecum,carcinoma,-1,2	ERC2	221	2	0			c.G2136A						PASS	.	C		77,3739		2,73,1833	195.0	189.0	191.0		2136	1.6	1.0	3	dbSNP_129	191	1,8253		0,1,4126	no	coding-synonymous	ERC2	NM_015576.1		2,74,5959	TT,TC,CC		0.0121,2.0178,0.6462		712/958	56026204	78,11992	1908	4127	6035	SO:0001819	synonymous_variant	26059	exon11			GTAAGACGCCTCT	AB002376	CCDS46851.1	3p14.3	2006-08-14			ENSG00000187672	ENSG00000187672			31922	protein-coding gene	gene with protein product							Standard	NM_015576		Approved	CAST, CAST1, KIAA0378, SPBC110, Spc110, ELKSL	uc003dhr.1	O15083	OTTHUMG00000158390	ENST00000288221.6:c.2136G>A	3.37:g.56026204C>T		217.0	0.0	0		231.0	118.0	0.510823	NM_015576	Q2T9F6|Q86TK4	Silent	SNP	ENST00000288221.6	37	CCDS46851.1	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	C	6.971	0.549089	0.13312	0.020178	1.21E-4	ENSG00000187672	ENST00000492584	.	.	.	5.47	1.64	0.23874	.	.	.	.	.	T	0.15652	0.0377	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.06144	-1.0843	4	.	.	.	-11.4437	5.8817	0.18858	0.0:0.2089:0.3824:0.4087	.	.	.	.	H	363	.	.	R	-	2	0	ERC2	56001244	0.126000	0.22350	1.000000	0.80357	0.978000	0.69477	-0.482000	0.06544	0.039000	0.15632	-0.469000	0.05056	CGT	C|0.988;T|0.012	0.012	strong		0.458	ERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350884.2	NM_015576	
FAM193A	8603	hgsc.bcm.edu	37	4	2661342	2661342	+	Missense_Mutation	SNP	A	A	G	rs17164077	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:2661342A>G	ENST00000324666.5	+	7	925	c.574A>G	c.(574-576)Atg>Gtg	p.M192V	FAM193A_ENST00000505311.1_Missense_Mutation_p.M192V|FAM193A_ENST00000382839.3_Missense_Mutation_p.M192V|FAM193A_ENST00000545951.1_Missense_Mutation_p.M192V|FAM193A_ENST00000502458.1_Missense_Mutation_p.M216V	NM_001256666.1	NP_001243595.1	P78312	F193A_HUMAN	family with sequence similarity 193, member A	192			M -> V (in dbSNP:rs17164077). {ECO:0000269|PubMed:9734812}.							NS(2)|breast(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(12)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	40						CATGAGGCACATGTTATCGTC	0.488													A|||	339	0.0676917	0.2443	0.0202	5008	,	,		20584	0.0		0.002	False		,,,				2504	0.0				p.M216V		Atlas-SNP	.											FAM193A,colon,carcinoma,0,1	FAM193A	103	1	0			c.A646G						PASS	.	A	VAL/MET	918,3488	354.9+/-312.8	96,726,1381	97.0	91.0	93.0		574	-2.5	0.0	4	dbSNP_123	93	7,8593	4.3+/-15.6	0,7,4293	yes	missense	FAM193A	NM_003704.3	21	96,733,5674	GG,GA,AA		0.0814,20.8352,7.1121	benign	192/1225	2661342	925,12081	2203	4300	6503	SO:0001583	missense	8603	exon8			AGGCACATGTTAT	AB000459	CCDS33943.1, CCDS58874.1, CCDS58875.1, CCDS58876.1	4p16.3	2009-09-04	2009-09-04	2009-09-04					16822	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 8"""	C4orf8		9734812	Standard	NR_046335		Approved	RES4-22	uc010ick.3	P78312		ENST00000324666.5:c.574A>G	4.37:g.2661342A>G	ENSP00000324587:p.Met192Val	98.0	0.0	0		89.0	42.0	0.47191	NM_001256667	B7ZM85|B9EGR0|E9PFA1|O43607|P78311|P78313|Q9UEG8	Missense_Mutation	SNP	ENST00000324666.5	37	CCDS58875.1	109	0.04990842490842491	101	0.20528455284552846	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	A	12.59	1.983129	0.34942	0.208352	8.14E-4	ENSG00000125386	ENST00000382839;ENST00000324666;ENST00000545951;ENST00000502458;ENST00000513350	T;T;T;T;T	0.35048	1.41;1.82;1.4;1.43;1.33	5.82	-2.52	0.06346	.	0.074856	0.85682	N	0.000000	T	0.00039	0.0001	L	0.56769	1.78	0.23314	P	0.99792346	B;B;B;B;B	0.09022	0.001;0.001;0.002;0.001;0.001	B;B;B;B;B	0.06405	0.002;0.002;0.002;0.002;0.002	T	0.12863	-1.0531	9	0.56958	D	0.05	-7.4139	11.1394	0.48394	0.5558:0.0:0.4442:0.0	rs17164077	192;216;192;216;192	B9EGR0;E9PFA1;P78312;B7ZM85;P78312-2	.;.;F193A_HUMAN;.;.	V	192;192;192;216;46	ENSP00000372290:M192V;ENSP00000324587:M192V;ENSP00000443617:M192V;ENSP00000427505:M216V;ENSP00000427260:M46V	ENSP00000324587:M192V	M	+	1	0	FAM193A	2631140	0.995000	0.38212	0.043000	0.18650	0.738000	0.42128	2.222000	0.42926	-0.672000	0.05266	0.459000	0.35465	ATG	A|0.937;G|0.063	0.063	strong		0.488	FAM193A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360903.1	NM_003704	
NOL11	25926	hgsc.bcm.edu	37	17	65735054	65735054	+	Silent	SNP	A	A	G	rs151002760	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:65735054A>G	ENST00000253247.4	+	15	1885	c.1770A>G	c.(1768-1770)gcA>gcG	p.A590A	SNORA38B_ENST00000363524.1_RNA|NOL11_ENST00000535137.1_Silent_p.A408A	NM_015462.3	NP_056277.2	Q9H8H0	NOL11_HUMAN	nucleolar protein 11	590					maturation of SSU-rRNA (GO:0030490)|positive regulation of transcription of nuclear large rRNA transcript from RNA polymerase I promoter (GO:1901838)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|t-UTP complex (GO:0034455)	poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	11	all_cancers(12;1.54e-10)		BRCA - Breast invasive adenocarcinoma(8;7.48e-08)|Colorectal(3;0.0518)|COAD - Colon adenocarcinoma(4;0.0977)|LUSC - Lung squamous cell carcinoma(166;0.24)			TAAGTAATGCAATTCTTCATT	0.333													A|||	6	0.00119808	0.0045	0.0	5008	,	,		19461	0.0		0.0	False		,,,				2504	0.0				p.A590A		Atlas-SNP	.											.	NOL11	48	.	0			c.A1770G						PASS	.	A		45,4361	48.2+/-83.0	0,45,2158	165.0	150.0	155.0		1770	3.9	1.0	17	dbSNP_134	155	0,8600		0,0,4300	no	coding-synonymous	NOL11	NM_015462.3		0,45,6458	GG,GA,AA		0.0,1.0213,0.346		590/720	65735054	45,12961	2203	4300	6503	SO:0001819	synonymous_variant	25926	exon15			TAATGCAATTCTT	AK023702	CCDS11671.1	17q24.2	2005-08-08							24557	protein-coding gene	gene with protein product		615366				12477932	Standard	NM_015462		Approved	DKFZP586L0724	uc002jgd.1	Q9H8H0		ENST00000253247.4:c.1770A>G	17.37:g.65735054A>G		103.0	0.0	0		117.0	53.0	0.452991	NM_015462	B7Z5V9|Q7L5S1|Q9UG18	Silent	SNP	ENST00000253247.4	37	CCDS11671.1																																																																																			A|0.997;G|0.003	0.003	strong		0.333	NOL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448074.1	NM_015462	
ERMARD	55780	hgsc.bcm.edu	37	6	170155460	170155460	+	Missense_Mutation	SNP	C	C	A	rs61735516	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:170155460C>A	ENST00000366773.3	+	3	290	c.257C>A	c.(256-258)aCc>aAc	p.T86N	ERMARD_ENST00000392095.4_5'UTR|ERMARD_ENST00000366772.2_Missense_Mutation_p.T86N|ERMARD_ENST00000418781.3_Missense_Mutation_p.T86N|ERMARD_ENST00000588451.1_5'UTR	NM_001278532.1|NM_018341.1	NP_001265461.1|NP_060811.1	Q5T6L9	EMARD_HUMAN	ER membrane-associated RNA degradation	86					multicellular organismal development (GO:0007275)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)											TTATCTCTGACCAAGGGGCAA	0.458													C|||	45	0.00898562	0.0318	0.0043	5008	,	,		16421	0.0		0.0	False		,,,				2504	0.0				p.T86N		Atlas-SNP	.											.	C6orf70	63	.	0			c.C257A						PASS	.	C	ASN/THR	167,4239	111.2+/-149.4	1,165,2037	152.0	142.0	146.0		257	2.9	0.1	6	dbSNP_129	146	2,8598	2.2+/-6.3	0,2,4298	yes	missense	C6orf70	NM_018341.1	65	1,167,6335	AA,AC,CC		0.0233,3.7903,1.2994	possibly-damaging	86/679	170155460	169,12837	2203	4300	6503	SO:0001583	missense	55780	exon3			CTCTGACCAAGGG	AK002014	CCDS34576.1, CCDS64572.1, CCDS64573.1, CCDS64574.1	6q27	2013-08-28	2013-08-28	2013-08-28	ENSG00000130023	ENSG00000130023			21056	protein-coding gene	gene with protein product		615532	"""chromosome 6 open reading frame 70"""	C6orf70		23768067	Standard	NM_018341		Approved	FLJ11152, dJ266L20.3	uc003qxg.1	Q5T6L9	OTTHUMG00000016067	ENST00000366773.3:c.257C>A	6.37:g.170155460C>A	ENSP00000355735:p.Thr86Asn	268.0	0.0	0		297.0	149.0	0.501683	NM_018341	B4DFH0|F8WAF1|Q3ZCS8|Q5T6L8|Q9NUT5|Q9NVU2	Missense_Mutation	SNP	ENST00000366773.3	37	CCDS34576.1	22	0.010073260073260074	20	0.04065040650406504	2	0.0055248618784530384	0	0.0	0	0.0	C	9.157	1.017709	0.19355	0.037903	2.33E-4	ENSG00000130023	ENST00000366773;ENST00000366772;ENST00000418781	T	0.48201	0.82	5.72	2.91	0.33838	.	0.384232	0.25050	N	0.033534	T	0.26846	0.0657	L	0.56769	1.78	0.35175	D	0.771965	B;B	0.20052	0.041;0.006	B;B	0.16722	0.016;0.007	T	0.07731	-1.0757	10	0.56958	D	0.05	.	11.748	0.51832	0.1294:0.6211:0.2494:0.0	rs61735516	86;86	Q5T6L9-2;Q5T6L9	.;CF070_HUMAN	N	86	ENSP00000355735:T86N	ENSP00000355734:T86N	T	+	2	0	C6orf70	169897385	0.815000	0.29118	0.085000	0.20634	0.078000	0.17371	0.775000	0.26689	0.308000	0.22923	-0.310000	0.09108	ACC	C|0.987;A|0.013	0.013	strong		0.458	ERMARD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043238.2	NM_018341	
MYO7B	4648	hgsc.bcm.edu	37	2	128367556	128367556	+	Missense_Mutation	SNP	G	G	A	rs199654311	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128367556G>A	ENST00000409816.2	+	23	3189	c.3157G>A	c.(3157-3159)Ggt>Agt	p.G1053S	MYO7B_ENST00000389524.4_Missense_Mutation_p.G1053S|MYO7B_ENST00000428314.1_Missense_Mutation_p.G1053S			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1053	MyTH4 1. {ECO:0000255|PROSITE- ProRule:PRU00359}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		CAGGGAGCACGGTGCCCAGGT	0.642													G|||	13	0.00259585	0.0098	0.0	5008	,	,		17986	0.0		0.0	False		,,,				2504	0.0				p.G1053S		Atlas-SNP	.											.	MYO7B	359	.	0			c.G3157A						PASS	.	G	SER/GLY	32,4284		0,32,2126	29.0	33.0	32.0		3157	-6.9	0.0	2		32	0,8518		0,0,4259	yes	missense	MYO7B	NM_001080527.1	56	0,32,6385	AA,AG,GG		0.0,0.7414,0.2493	benign	1053/2117	128367556	32,12802	2158	4259	6417	SO:0001583	missense	4648	exon24			GAGCACGGTGCCC		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"""Myosins / Myosin superfamily : Class VII"""	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.3157G>A	2.37:g.128367556G>A	ENSP00000386461:p.Gly1053Ser	100.0	0.0	0		108.0	58.0	0.537037	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	37	CCDS46405.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	8.095	0.775454	0.16051	0.007414	0.0	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000409816	D;D;D	0.86164	-2.08;-2.08;-2.08	5.17	-6.92	0.01644	MyTH4 domain (2);	1.887620	0.02507	N	0.091055	T	0.52885	0.1762	N	0.00841	-1.15	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.64101	-0.6486	10	0.07030	T	0.85	.	10.025	0.42066	0.4891:0.1097:0.4012:0.0	.	1053	Q6PIF6	MYO7B_HUMAN	S	1053	ENSP00000374175:G1053S;ENSP00000415090:G1053S;ENSP00000386461:G1053S	ENSP00000374175:G1053S	G	+	1	0	MYO7B	128084026	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.438000	0.06905	-1.703000	0.01409	-0.140000	0.14226	GGT	G|0.999;A|0.001	0.001	strong		0.642	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
FBXW8	26259	hgsc.bcm.edu	37	12	117387465	117387465	+	Missense_Mutation	SNP	A	A	G	rs36021180	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:117387465A>G	ENST00000309909.5	+	4	713	c.631A>G	c.(631-633)Aca>Gca	p.T211A	FBXW8_ENST00000455858.2_Missense_Mutation_p.T145A			Q8N3Y1	FBXW8_HUMAN	F-box and WD repeat domain containing 8	211			T -> A (in dbSNP:rs36021180).		cell proliferation (GO:0008283)|Golgi organization (GO:0007030)|labyrinthine layer blood vessel development (GO:0060716)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|spongiotrophoblast layer development (GO:0060712)	Cul7-RING ubiquitin ligase complex (GO:0031467)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|SCF ubiquitin ligase complex (GO:0019005)				endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	22	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0353)		TGTTCCTGACACAGTTTTGTG	0.517													G|||	64	0.0127796	0.0454	0.0029	5008	,	,		24536	0.0		0.002	False		,,,				2504	0.0				p.T211A		Atlas-SNP	.											.	FBXW8	53	.	0			c.A631G						PASS	.	G	ALA/THR,ALA/THR	214,4192	806.9+/-415.9	6,202,1995	331.0	238.0	270.0		433,631	4.1	0.3	12	dbSNP_126	270	33,8567	817.8+/-406.9	0,33,4267	yes	missense,missense	FBXW8	NM_012174.1,NM_153348.2	58,58	6,235,6262	GG,GA,AA		0.3837,4.857,1.8991	benign,benign	145/533,211/599	117387465	247,12759	2203	4300	6503	SO:0001583	missense	26259	exon4			CCTGACACAGTTT	AF176707	CCDS9182.1, CCDS44988.1	12q24.23	2013-01-09	2007-02-08	2003-06-13				"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	13597	protein-coding gene	gene with protein product		609073	"""F-box only protein 29"", ""F-box and WD-40 domain protein 8"""	FBXO29		10531035, 10531037	Standard	NM_012174		Approved	FBX29, FBW6, FBW8	uc001twg.1	Q8N3Y1	OTTHUMG00000169329	ENST00000309909.5:c.631A>G	12.37:g.117387465A>G	ENSP00000310686:p.Thr211Ala	163.0	0.0	0		153.0	85.0	0.555556	NM_153348	Q9UK95	Missense_Mutation	SNP	ENST00000309909.5	37	CCDS9182.1	26	0.011904761904761904	23	0.046747967479674794	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	0.527	-0.859427	0.02610	0.04857	0.003837	ENSG00000174989	ENST00000309909;ENST00000455858;ENST00000505227	T;T	0.04454	3.62;3.62	5.05	4.09	0.47781	WD40/YVTN repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.116916	0.53938	N	0.000041	T	0.00328	0.0010	N	0.02011	-0.69	0.09310	N	0.999996	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.48670	-0.9015	10	0.14656	T	0.56	-3.3319	4.7195	0.12912	0.3949:0.0:0.6051:0.0	rs36021180;rs61748073	211;145	Q8N3Y1;Q8N3Y1-2	FBXW8_HUMAN;.	A	211;145;145	ENSP00000310686:T211A;ENSP00000389144:T145A	ENSP00000310686:T211A	T	+	1	0	FBXW8	115871848	0.960000	0.32886	0.276000	0.24689	0.163000	0.22366	4.018000	0.57174	1.377000	0.46286	-0.227000	0.12334	ACA	A|0.983;G|0.017	0.017	strong		0.517	FBXW8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403561.1	NM_012174	
PACS2	23241	hgsc.bcm.edu	37	14	105821457	105821457	+	Silent	SNP	G	G	A	rs61738367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105821457G>A	ENST00000325438.8	+	4	870	c.366G>A	c.(364-366)aaG>aaA	p.K122K	PACS2_ENST00000430725.2_Silent_p.K55K|PACS2_ENST00000447393.1_Silent_p.K122K|PACS2_ENST00000458164.2_Silent_p.K122K|PACS2_ENST00000547217.1_Silent_p.K92K			Q86VP3	PACS2_HUMAN	phosphofurin acidic cluster sorting protein 2	122					apoptotic process (GO:0006915)|autophagic vacuole assembly (GO:0000045)|protein localization to pre-autophagosomal structure (GO:0034497)|protein targeting to plasma membrane (GO:0072661)|viral process (GO:0016032)	endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)				endometrium(2)|kidney(2)|lung(7)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	21		all_cancers(154;0.0351)|all_epithelial(191;0.153)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.0145)|Epithelial(46;0.036)	Epithelial(152;0.138)		AGCGCTACAAGAACAGAACCA	0.602													G|||	56	0.0111821	0.0416	0.0	5008	,	,		19971	0.0		0.001	False		,,,				2504	0.0				p.K122K		Atlas-SNP	.											.	PACS2	75	.	0			c.G366A						PASS	.	G	,	200,4206	123.3+/-160.7	7,186,2010	78.0	64.0	69.0		366,366	-3.3	0.9	14	dbSNP_129	69	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	PACS2	NM_001100913.2,NM_015197.3	,	7,187,6309	AA,AG,GG		0.0116,4.5393,1.5454	,	122/894,122/890	105821457	201,12805	2203	4300	6503	SO:0001819	synonymous_variant	23241	exon4			CTACAAGAACAGA	AB011174	CCDS32168.1, CCDS45178.1, CCDS45178.2, CCDS58339.1	14q32	2005-02-15	2005-02-15	2005-02-15		ENSG00000179364			23794	protein-coding gene	gene with protein product		610423	"""phosphofurin acidic cluster sorting protein 1-like"""	PACS1L		15692567	Standard	NM_001100913		Approved	KIAA0602	uc001yqu.3	Q86VP3	OTTHUMG00000170450	ENST00000325438.8:c.366G>A	14.37:g.105821457G>A		105.0	0.0	0		97.0	48.0	0.494845	NM_001100913	A2VDJ9|G8JLK3|O60342|Q6P191|Q96FL7	Silent	SNP	ENST00000325438.8	37	CCDS32168.1																																																																																			G|0.986;A|0.014	0.014	strong		0.602	PACS2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000409209.1	XM_377355	
MUC4	4585	hgsc.bcm.edu	37	3	195515199	195515199	+	Silent	SNP	A	A	C	rs201720234	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195515199A>C	ENST00000463781.3	-	2	3711	c.3252T>G	c.(3250-3252)ggT>ggG	p.G1084G	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.G1084G	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	516					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)		GGGTGGTGTCACCTGTGGATG	0.567													.|||	158	0.0315495	0.1082	0.013	5008	,	,		18430	0.001		0.004	False		,,,				2504	0.001				p.G1084G		Atlas-SNP	.											.	MUC4	1505	.	0			c.T3252G						PASS	.																																			SO:0001819	synonymous_variant	4585	exon2			GGTGTCACCTGTG	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.3252T>G	3.37:g.195515199A>C		197.0	0.0	0		384.0	45.0	0.117188	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																																																																																			A|0.994;C|0.006	0.006	strong		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TM9SF3	56889	hgsc.bcm.edu	37	10	98282083	98282083	+	Silent	SNP	C	C	T	rs35359279	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:98282083C>T	ENST00000371142.4	-	15	1923	c.1707G>A	c.(1705-1707)gcG>gcA	p.A569A		NM_020123.3	NP_064508.3	Q9HD45	TM9S3_HUMAN	transmembrane 9 superfamily member 3	569						integral component of membrane (GO:0016021)				breast(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(2)|prostate(1)	15		Colorectal(252;0.158)		Epithelial(162;1.84e-09)|all cancers(201;2.84e-08)		TGTAACCAATCGCTCCTGCAA	0.338													C|||	47	0.00938498	0.0356	0.0	5008	,	,		18641	0.0		0.0	False		,,,				2504	0.0				p.A569A		Atlas-SNP	.											.	TM9SF3	45	.	0			c.G1707A						PASS	.	C		106,4300	82.9+/-121.4	3,100,2100	98.0	101.0	100.0		1707	-2.1	1.0	10	dbSNP_126	100	3,8595		0,3,4296	no	coding-synonymous	TM9SF3	NM_020123.3		3,103,6396	TT,TC,CC		0.0349,2.4058,0.8382		569/590	98282083	109,12895	2203	4299	6502	SO:0001819	synonymous_variant	56889	exon15			ACCAATCGCTCCT	AF160213, AF269150	CCDS7450.1	10q24.2	2006-04-12			ENSG00000077147	ENSG00000077147			21529	protein-coding gene	gene with protein product						11530251, 11595169	Standard	NM_020123		Approved	SMBP	uc001kmm.4	Q9HD45	OTTHUMG00000018834	ENST00000371142.4:c.1707G>A	10.37:g.98282083C>T		80.0	0.0	0		95.0	35.0	0.368421	NM_020123	Q5TB57|Q6UWE7|Q9NWL8|Q9P0G9|Q9UHW8	Silent	SNP	ENST00000371142.4	37	CCDS7450.1																																																																																			C|0.990;T|0.010	0.010	strong		0.338	TM9SF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049610.2	NM_020123	
TBC1D9B	23061	hgsc.bcm.edu	37	5	179297262	179297262	+	Silent	SNP	T	T	C	rs407437	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:179297262T>C	ENST00000356834.3	-	16	2755	c.2718A>G	c.(2716-2718)acA>acG	p.T906T	TBC1D9B_ENST00000519746.1_Silent_p.T82T|TBC1D9B_ENST00000355235.3_Silent_p.T906T|TBC1D9B_ENST00000444477.2_Silent_p.T64T	NM_198868.2	NP_942568.2	Q66K14	TBC9B_HUMAN	TBC1 domain family, member 9B (with GRAM domain)	906	EF-hand. {ECO:0000255|PROSITE- ProRule:PRU00448}.					integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|Rab GTPase activator activity (GO:0005097)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	28	all_cancers(89;0.000197)|all_epithelial(37;6.84e-05)|Renal(175;0.000159)|Lung NSC(126;0.00136)|all_lung(126;0.00243)	all_cancers(40;0.0236)|Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CACTCATCCCTGTCACGAACT	0.602													C|||	622	0.124201	0.444	0.0432	5008	,	,		19694	0.0		0.005	False		,,,				2504	0.0				p.T906T		Atlas-SNP	.											.	TBC1D9B	157	.	0			c.A2718G						PASS	.	C	,	1539,2867	670.9+/-402.4	283,973,947	104.0	111.0	109.0		2718,2718	-10.3	0.5	5	dbSNP_80	109	15,8585	818.5+/-406.9	0,15,4285	no	coding-synonymous,coding-synonymous	TBC1D9B	NM_015043.3,NM_198868.2	,	283,988,5232	CC,CT,TT		0.1744,34.9296,11.9483	,	906/1234,906/1251	179297262	1554,11452	2203	4300	6503	SO:0001819	synonymous_variant	23061	exon16			CATCCCTGTCACG	AB014576	CCDS4450.1, CCDS43408.1	5q35.3	2013-01-10			ENSG00000197226	ENSG00000197226		"""EF-hand domain containing"""	29097	protein-coding gene	gene with protein product						9734811	Standard	NM_198868		Approved	KIAA0676	uc003mlh.3	Q66K14	OTTHUMG00000130911	ENST00000356834.3:c.2718A>G	5.37:g.179297262T>C		104.0	0.0	0		70.0	30.0	0.428571	NM_198868	D3DWQ5|D3DWQ6|O75163|Q53EY0|Q6MZI2|Q96H49	Silent	SNP	ENST00000356834.3	37	CCDS43408.1																																																																																			T|0.882;C|0.118	0.118	strong		0.602	TBC1D9B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253501.3	NM_015043	
PALD1	27143	hgsc.bcm.edu	37	10	72324139	72324139	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:72324139C>T	ENST00000263563.6	+	19	2550	c.2282C>T	c.(2281-2283)gCg>gTg	p.A761V		NM_014431.2	NP_055246.2	Q9ULE6	PALD_HUMAN	phosphatase domain containing, paladin 1	761						cytosol (GO:0005829)											GCGAAAGAGGCGCAAGAAATG	0.617																																					p.A761V		Atlas-SNP	.											KIAA1274,NS,carcinoma,-1,1	.	.	1	0			c.C2282T						PASS	.						77.0	75.0	76.0					10																	72324139		2203	4300	6503	SO:0001583	missense	27143	exon19			AAGAGGCGCAAGA	AB033100	CCDS31215.1	10q22.2	2012-07-17	2012-07-17	2012-07-17	ENSG00000107719	ENSG00000107719			23530	protein-coding gene	gene with protein product		614656	"""paladin"", ""KIAA1274"""	PALD, KIAA1274			Standard	NM_014431		Approved		uc001jrd.4	Q9ULE6	OTTHUMG00000018411	ENST00000263563.6:c.2282C>T	10.37:g.72324139C>T	ENSP00000263563:p.Ala761Val	127.0	0.0	0		135.0	60.0	0.444444	NM_014431	B2RMS1|B9EGC6|Q5JTK7|Q5JTK8	Missense_Mutation	SNP	ENST00000263563.6	37	CCDS31215.1	.	.	.	.	.	.	.	.	.	.	c	10.63	1.404595	0.25378	.	.	ENSG00000107719	ENST00000263563;ENST00000373214	T	0.29917	1.55	4.9	2.42	0.29668	.	0.426837	0.24803	N	0.035474	T	0.24547	0.0595	L	0.47716	1.5	0.26423	N	0.976068	B	0.18610	0.029	B	0.12156	0.007	T	0.16158	-1.0412	10	0.40728	T	0.16	-12.6907	8.4465	0.32845	0.3575:0.52:0.0:0.1225	.	761	Q9ULE6	PALD_HUMAN	V	761;737	ENSP00000263563:A761V	ENSP00000263563:A761V	A	+	2	0	KIAA1274	71994145	1.000000	0.71417	0.147000	0.22382	0.613000	0.37349	1.533000	0.36040	0.168000	0.19655	-0.410000	0.06199	GCG	.	.	none		0.617	PALD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048515.2	NM_014431	
ZNF135	7694	hgsc.bcm.edu	37	19	58579464	58579464	+	Missense_Mutation	SNP	A	A	G	rs73938600	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58579464A>G	ENST00000313434.5	+	5	1713	c.1612A>G	c.(1612-1614)Att>Gtt	p.I538V	ZNF135_ENST00000359978.6_Intron|ZNF135_ENST00000511556.1_Missense_Mutation_p.I550V|ZNF135_ENST00000401053.4_Missense_Mutation_p.I562V|RN7SL526P_ENST00000469492.2_RNA|ZNF135_ENST00000506786.1_Missense_Mutation_p.I496V|ZNF135_ENST00000439855.2_Missense_Mutation_p.I538V	NM_003436.3	NP_003427.3	P52742	ZN135_HUMAN	zinc finger protein 135	538					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(26)|ovary(1)|skin(1)|urinary_tract(1)	41		Colorectal(82;0.000256)|all_neural(62;0.0412)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0161)		TGCTCCCCTCATTCAGCATCA	0.542													A|||	23	0.00459265	0.0159	0.0014	5008	,	,		19819	0.0		0.001	False		,,,				2504	0.0				p.I562V		Atlas-SNP	.											.	ZNF135	159	.	0			c.A1684G						PASS	.	A	,,VAL/ILE,VAL/ILE	74,4332	66.4+/-103.9	2,70,2131	80.0	76.0	77.0		,,1648,1684	3.4	1.0	19	dbSNP_130	77	2,8592	2.2+/-6.3	0,2,4295	no	utr-3,intron,missense,missense	ZNF135	NM_001164529.1,NM_001164530.1,NM_003436.3,NM_007134.1	,,29,29	2,72,6426	GG,GA,AA		0.0233,1.6795,0.5846	,,benign,benign	,,550/671,562/683	58579464	76,12924	2203	4297	6500	SO:0001583	missense	7694	exon4			CCCCTCATTCAGC	U09413	CCDS12970.1, CCDS12970.2, CCDS54329.1, CCDS54330.1, CCDS74471.1, CCDS74472.1	19q13.4	2013-01-08	2006-05-12			ENSG00000176293		"""Zinc fingers, C2H2-type"", ""-"""	12919	protein-coding gene	gene with protein product		604077	"""zinc finger protein 61"", ""zinc finger protein 135 (clone pHZ-17)"""	ZNF61, ZNF78L1		7557990, 1505991	Standard	NM_003436		Approved	pHZ-17	uc002qrg.3	P52742		ENST00000313434.5:c.1612A>G	19.37:g.58579464A>G	ENSP00000321406:p.Ile538Val	66.0	0.0	0		67.0	31.0	0.462687	NM_007134	B4DHH9|E9PEV2|F5GYY9|I3L0B3|Q5U5L3|Q8N1I7	Missense_Mutation	SNP	ENST00000313434.5	37		8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	A	3.025	-0.200904	0.06219	0.016795	2.33E-4	ENSG00000176293	ENST00000401053;ENST00000439855;ENST00000313434;ENST00000511556;ENST00000506786	T;T;T;T;T	0.35605	4.1;4.1;4.1;4.1;1.3	3.37	3.37	0.38596	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13030	0.0316	N	0.11364	0.135	0.09310	N	1	P;P	0.43287	0.591;0.802	B;P	0.48873	0.437;0.593	T	0.04650	-1.0936	9	0.23891	T	0.37	.	6.8432	0.23975	0.8839:0.0:0.1161:0.0	.	550;538	E9PEV2;P52742	.;ZN135_HUMAN	V	562;538;538;550;496	ENSP00000441410:I562V;ENSP00000444828:I538V;ENSP00000321406:I538V;ENSP00000422074:I550V;ENSP00000427691:I496V	ENSP00000321406:I538V	I	+	1	0	ZNF135	63271276	0.000000	0.05858	1.000000	0.80357	0.831000	0.47069	-1.095000	0.03356	1.545000	0.49373	0.455000	0.32223	ATT	.	.	weak		0.542	ZNF135-003	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000361899.2	NM_003436	
SYTL4	94121	hgsc.bcm.edu	37	X	99955925	99955925	+	Silent	SNP	T	T	C	rs16983588	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:99955925T>C	ENST00000372989.1	-	7	838	c.507A>G	c.(505-507)agA>agG	p.R169R	SYTL4_ENST00000276141.6_Silent_p.R169R|SYTL4_ENST00000454200.2_Silent_p.R169R|SYTL4_ENST00000455616.1_Silent_p.R169R|SYTL4_ENST00000263033.5_Silent_p.R169R|SYTL4_ENST00000372981.1_Silent_p.R169R	NM_080737.2	NP_542775.2	Q96C24	SYTL4_HUMAN	synaptotagmin-like 4	169					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|multivesicular body sorting pathway (GO:0071985)|negative regulation of insulin secretion (GO:0046676)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|synaptic vesicle (GO:0008021)	neurexin family protein binding (GO:0042043)|phospholipid binding (GO:0005543)|transporter activity (GO:0005215)|zinc ion binding (GO:0008270)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(2)	27					"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	GAATGATCTTTCTTCCTGGCC	0.408													t|||	572	0.151523	0.4077	0.0432	3775	,	,		13506	0.0		0.002	False		,,,				2504	0.001				p.R169R		Atlas-SNP	.											.	SYTL4	72	.	0			c.A507G						PASS	.		,,	1688,2147		321,777,269,534,302	142.0	127.0	133.0		507,507,507	3.4	1.0	X	dbSNP_123	133	24,6704		0,19,5,2409,1867	no	coding-synonymous,coding-synonymous,coding-synonymous	SYTL4	NM_001129896.2,NM_001174068.1,NM_080737.2	,,	321,796,274,2943,2169	CC,CT,C,TT,T		0.3567,44.0156,16.2075	,,	169/672,169/672,169/672	99955925	1712,8851	2203	4300	6503	SO:0001819	synonymous_variant	94121	exon6			GATCTTTCTTCCT		CCDS14472.1	Xq21.33	2008-07-31	2008-07-31		ENSG00000102362	ENSG00000102362			15588	protein-coding gene	gene with protein product	"""granuphilin-a"", ""exophilin-2"""	300723					Standard	NM_080737		Approved		uc010nnc.3	Q96C24	OTTHUMG00000022004	ENST00000372989.1:c.507A>G	X.37:g.99955925T>C		318.0	0.0	0		269.0	269.0	1	NM_001129896	Q5H9J3|Q5JPG8|Q8N9P4|Q9H4R0|Q9H4R1	Silent	SNP	ENST00000372989.1	37	CCDS14472.1																																																																																			0|0.004;C|0.166	0.166	strong		0.408	SYTL4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057488.1	NM_080737	
XIRP1	165904	hgsc.bcm.edu	37	3	39225549	39225549	+	Silent	SNP	G	G	C	rs36091974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:39225549G>C	ENST00000340369.3	-	2	5616	c.5388C>G	c.(5386-5388)ccC>ccG	p.P1796P	XIRP1_ENST00000396251.1_3'UTR|XIRP1_ENST00000421646.1_Silent_p.P479P	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	1796	Interaction with FLNC.				cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		CTGGGTTCCTGGGTGGCTCTG	0.602													G|||	121	0.0241613	0.0862	0.0086	5008	,	,		20643	0.0		0.001	False		,,,				2504	0.0				p.P1796P		Atlas-SNP	.											.	XIRP1	173	.	0			c.C5388G						PASS	.	G	,	362,4044	186.4+/-213.3	17,328,1858	126.0	132.0	130.0		,5388	2.4	0.0	3	dbSNP_126	130	3,8597	3.0+/-9.4	0,3,4297	yes	utr-3,coding-synonymous	XIRP1	NM_001198621.1,NM_194293.2	,	17,331,6155	CC,CG,GG		0.0349,8.2161,2.8064	,	,1796/1844	39225549	365,12641	2203	4300	6503	SO:0001819	synonymous_variant	165904	exon2			GTTCCTGGGTGGC	AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"""cardiomyopathy associated 1"""	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.5388C>G	3.37:g.39225549G>C		187.0	0.0	0		214.0	107.0	0.5	NM_194293	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Silent	SNP	ENST00000340369.3	37	CCDS2683.1																																																																																			G|0.973;C|0.027	0.027	strong		0.602	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522	
RIF1	55183	hgsc.bcm.edu	37	2	152321618	152321618	+	Missense_Mutation	SNP	G	G	A	rs2444258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:152321618G>A	ENST00000243326.5	+	29	6067	c.5584G>A	c.(5584-5586)Gtt>Att	p.V1862I	RIF1_ENST00000430328.2_Missense_Mutation_p.V1862I|RIF1_ENST00000453091.2_Missense_Mutation_p.V1862I|RIF1_ENST00000428287.2_Missense_Mutation_p.V1862I|RIF1_ENST00000444746.2_Missense_Mutation_p.V1862I			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		TTTTAAAACTGTTGGCCCGTG	0.368													G|||	370	0.0738818	0.2617	0.0317	5008	,	,		17559	0.0		0.002	False		,,,				2504	0.0				p.V1862I		Atlas-SNP	.											.	RIF1	244	.	0			c.G5584A						PASS	.	G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	986,3420	359.6+/-314.9	101,784,1318	57.0	63.0	61.0		5584,5584,5584,5584	-4.0	0.0	2	dbSNP_100	61	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense,missense,missense	RIF1	NM_001177663.1,NM_001177664.1,NM_001177665.1,NM_018151.4	29,29,29,29	101,789,5613	AA,AG,GG		0.0581,22.3786,7.6196	benign,benign,benign,benign	1862/2447,1862/2447,1862/2447,1862/2473	152321618	991,12015	2203	4300	6503	SO:0001583	missense	55183	exon30			AAAACTGTTGGCC	AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"""RAP1 interacting factor homolog (yeast)"""			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.5584G>A	2.37:g.152321618G>A	ENSP00000243326:p.Val1862Ile	84.0	0.0	0		97.0	29.0	0.298969	NM_018151	A0AVS0|Q9NS16	Missense_Mutation	SNP	ENST00000243326.5	37	CCDS2194.1	146	0.06684981684981685	137	0.2784552845528455	9	0.024861878453038673	0	0.0	0	0.0	G	10.51	1.369197	0.24771	0.223786	5.81E-4	ENSG00000080345	ENST00000444746;ENST00000453091;ENST00000428287;ENST00000243326;ENST00000430328	T;T;T;T;T	0.09723	2.96;2.95;2.95;2.96;2.95	5.68	-3.96	0.04106	.	1.726510	0.02579	N	0.098634	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B;B	0.29988	0.172;0.264	B;B	0.24269	0.023;0.052	T	0.41342	-0.9514	9	0.31617	T	0.26	0.8111	4.8656	0.13607	0.4276:0.089:0.3932:0.0902	rs2444258;rs52808590;rs60545876;rs2444258	1862;1862	Q5UIP0;Q5UIP0-2	RIF1_HUMAN;.	I	1862	ENSP00000390181:V1862I;ENSP00000414615:V1862I;ENSP00000415691:V1862I;ENSP00000243326:V1862I;ENSP00000416123:V1862I	ENSP00000243326:V1862I	V	+	1	0	RIF1	152029864	0.000000	0.05858	0.000000	0.03702	0.068000	0.16541	0.006000	0.13152	-0.725000	0.04901	0.650000	0.86243	GTT	G|0.918;A|0.082	0.082	strong		0.368	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3		
DCHS2	54798	hgsc.bcm.edu	37	4	155156875	155156875	+	Missense_Mutation	SNP	T	T	G	rs61746101	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:155156875T>G	ENST00000357232.4	-	25	7563	c.7564A>C	c.(7564-7566)Aat>Cat	p.N2522H		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2522	Cadherin 22. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		AAAGACACATTCACAAAAACA	0.408													T|||	214	0.0427316	0.1558	0.0086	5008	,	,		18956	0.0		0.002	False		,,,				2504	0.0				p.N2522H		Atlas-SNP	.											.	DCHS2	594	.	0			c.A7564C						PASS	.	T	HIS/ASN	567,3839	253.0+/-259.1	26,515,1662	81.0	82.0	82.0		7564	5.7	1.0	4	dbSNP_129	82	9,8591	6.4+/-24.3	0,9,4291	yes	missense	DCHS2	NM_017639.3	68	26,524,5953	GG,GT,TT		0.1047,12.8688,4.4287	probably-damaging	2522/2917	155156875	576,12430	2203	4300	6503	SO:0001583	missense	54798	exon25			ACACATTCACAAA	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.7564A>C	4.37:g.155156875T>G	ENSP00000349768:p.Asn2522His	74.0	0.0	0		97.0	48.0	0.494845	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	72	0.03296703296703297	71	0.1443089430894309	1	0.0027624309392265192	0	0.0	0	0.0	T	18.70	3.680330	0.68042	0.128688	0.001047	ENSG00000197410	ENST00000357232	T	0.60672	0.17	5.71	5.71	0.89125	Cadherin (3);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.01320	0.0043	L	0.58669	1.825	0.80722	D	1	D	0.89917	1.0	D	0.73708	0.981	T	0.04495	-1.0947	10	0.56958	D	0.05	.	15.9843	0.80138	0.0:0.0:0.0:1.0	.	2522	Q6V1P9	PCD23_HUMAN	H	2522	ENSP00000349768:N2522H	ENSP00000349768:N2522H	N	-	1	0	DCHS2	155376325	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.229000	0.58625	2.176000	0.68965	0.383000	0.25322	AAT	T|0.959;G|0.041	0.041	strong		0.408	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
OR5L2	26338	hgsc.bcm.edu	37	11	55595401	55595401	+	Missense_Mutation	SNP	A	A	G	rs148148644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55595401A>G	ENST00000378397.1	+	1	707	c.707A>G	c.(706-708)aAa>aGa	p.K236R		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	236						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|large_intestine(1)|lung(42)|ovary(1)|prostate(3)|skin(1)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	59		all_epithelial(135;0.208)				AGCAGGCACAAAGCTTTCTCC	0.488										HNSCC(27;0.073)			N|||	7	0.00139776	0.0053	0.0	5008	,	,		17988	0.0		0.0	False		,,,				2504	0.0				p.K236R		Atlas-SNP	.											.	OR5L2	135	.	0			c.A707G						PASS	.	A	ARG/LYS	43,4357		0,43,2157	177.0	150.0	159.0		707	5.2	1.0	11	dbSNP_134	159	0,8592		0,0,4296	yes	missense	OR5L2	NM_001004739.1	26	0,43,6453	GG,GA,AA		0.0,0.9773,0.331	benign	236/312	55595401	43,12949	2200	4296	6496	SO:0001583	missense	26338	exon1			GGCACAAAGCTTT	AB065782	CCDS31511.1	11q11	2012-08-09			ENSG00000205030	ENSG00000205030		"""GPCR / Class A : Olfactory receptors"""	8351	protein-coding gene	gene with protein product						1370859	Standard	NM_001004739		Approved	HTPCRX16, HSHTPCRX16	uc001nhy.1	Q8NGL0	OTTHUMG00000166812	ENST00000378397.1:c.707A>G	11.37:g.55595401A>G	ENSP00000367650:p.Lys236Arg	166.0	0.0	0		159.0	73.0	0.459119	NM_001004739	Q6IF66|Q96RB2	Missense_Mutation	SNP	ENST00000378397.1	37	CCDS31511.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	.	13.65	2.300050	0.40694	0.009773	0.0	ENSG00000205030	ENST00000378397	T	0.00360	7.86	5.24	5.24	0.73138	GPCR, rhodopsin-like superfamily (1);	0.110656	0.40640	N	0.001045	T	0.00300	0.0009	M	0.62723	1.935	0.39567	D	0.969221	B	0.31581	0.329	B	0.37304	0.246	T	0.77520	-0.2557	10	0.66056	D	0.02	-6.4806	14.3209	0.66487	1.0:0.0:0.0:0.0	.	236	Q8NGL0	OR5L2_HUMAN	R	236	ENSP00000367650:K236R	ENSP00000367650:K236R	K	+	2	0	OR5L2	55351977	1.000000	0.71417	0.998000	0.56505	0.029000	0.11900	2.879000	0.48522	2.115000	0.64714	0.514000	0.50259	AAA	A|0.997;G|0.003	0.003	strong		0.488	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739	
IQSEC2	23096	hgsc.bcm.edu	37	X	53263764	53263764	+	Silent	SNP	C	C	T	rs184087864		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:53263764C>T	ENST00000375368.5	-	14	4274	c.4074G>A	c.(4072-4074)ctG>ctA	p.L1358L	IQSEC2_ENST00000396435.3_Silent_p.L1368L|IQSEC2_ENST00000375365.2_3'UTR			Q5JU85	IQEC2_HUMAN	IQ motif and Sec7 domain 2	1358	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						TGTACAGGGGCAGTGGGGATG	0.672													c|||	294	0.0778808	0.2133	0.0173	3775	,	,		4478	0.0		0.0	False		,,,				2504	0.0				p.L1368L		Atlas-SNP	.											.	IQSEC2	195	.	0			c.G4104A						PASS	.						10.0	11.0	10.0					X																	53263764		689	1580	2269	SO:0001819	synonymous_variant	23096	exon15			CAGGGGCAGTGGG	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.4074G>A	X.37:g.53263764C>T		225.0	0.0	0		222.0	97.0	0.436937	NM_001111125	B3KT97|C7SDG1|O60275|Q5JUX1	Silent	SNP	ENST00000375368.5	37																																																																																				C|0.937;T|0.063	0.063	strong		0.672	IQSEC2-201	KNOWN	basic	protein_coding	protein_coding		XM_291345	
TERF2	7014	hgsc.bcm.edu	37	16	69401085	69401085	+	Missense_Mutation	SNP	G	G	T	rs34014829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:69401085G>T	ENST00000254942.3	-	7	981	c.965C>A	c.(964-966)cCa>cAa	p.P322Q	TERF2_ENST00000569611.2_5'Flank|TERF2_ENST00000603068.1_Missense_Mutation_p.P280Q	NM_005652.3	NP_005643.2	Q15554	TERF2_HUMAN	telomeric repeat binding factor 2	322					age-dependent telomere shortening (GO:0001309)|cell cycle (GO:0007049)|cellular senescence (GO:0090398)|in utero embryonic development (GO:0001701)|negative regulation of telomere maintenance (GO:0032205)|negative regulation of telomere maintenance via semi-conservative replication (GO:0032214)|positive regulation of telomere maintenance (GO:0032206)|protection from non-homologous end joining at telomere (GO:0031848)|protein localization to chromosome, telomeric region (GO:0070198)|telomere capping (GO:0016233)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)|telomere maintenance via telomere shortening (GO:0010834)|telomeric loop formation (GO:0031627)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|male germ cell nucleus (GO:0001673)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|double-stranded telomeric DNA binding (GO:0003691)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|telomeric DNA binding (GO:0042162)			NS(2)|breast(1)|large_intestine(3)|lung(1)	7		Ovarian(137;0.101)				AATGGTGGTTGGAGGATTCCG	0.453													G|||	28	0.00559105	0.0204	0.0014	5008	,	,		18068	0.0		0.0	False		,,,				2504	0.0				p.P322Q	Ovarian(13;63 524 30420 31710 34037)	Atlas-SNP	.											.	TERF2	24	.	0			c.C965A						PASS	.	G	GLN/PRO	80,4316	68.1+/-105.8	1,78,2119	49.0	50.0	49.0		839	6.2	1.0	16	dbSNP_126	49	0,8600		0,0,4300	yes	missense	TERF2	NM_005652.3	76	1,78,6419	TT,TG,GG		0.0,1.8198,0.6156	probably-damaging	280/501	69401085	80,12916	2198	4300	6498	SO:0001583	missense	7014	exon7			GTGGTTGGAGGAT		CCDS10879.1, CCDS10879.2	16q22.1	2008-02-05			ENSG00000132604	ENSG00000132604			11729	protein-coding gene	gene with protein product		602027		TRBF2		9326950, 10226653	Standard	NM_005652		Approved	TRF2	uc002exd.4	Q15554	OTTHUMG00000137566	ENST00000254942.3:c.965C>A	16.37:g.69401085G>T	ENSP00000254942:p.Pro322Gln	69.0	0.0	0		74.0	36.0	0.486486	NM_005652		Missense_Mutation	SNP	ENST00000254942.3	37		15	0.006868131868131868	14	0.028455284552845527	1	0.0027624309392265192	0	0.0	0	0.0	G	19.48	3.834956	0.71373	0.018198	0.0	ENSG00000132604	ENST00000254942	.	.	.	6.17	6.17	0.99709	.	0.265458	0.37761	N	0.001941	T	0.53270	0.1786	L	0.53249	1.67	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.62101	-0.6925	9	0.31617	T	0.26	-7.4119	16.3795	0.83443	0.0:0.0:1.0:0.0	rs34014829	280	Q15554	TERF2_HUMAN	Q	280	.	ENSP00000254942:P280Q	P	-	2	0	TERF2	67958586	1.000000	0.71417	0.998000	0.56505	0.894000	0.52154	3.792000	0.55476	2.941000	0.99782	0.655000	0.94253	CCA	G|0.991;T|0.009	0.009	strong		0.453	TERF2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000268944.2		
MYOM3	127294	hgsc.bcm.edu	37	1	24383873	24383873	+	Missense_Mutation	SNP	T	T	C	rs59805085	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:24383873T>C	ENST00000374434.3	-	37	4457	c.4295A>G	c.(4294-4296)aAg>aGg	p.K1432R	RP11-293P20.2_ENST00000439239.2_RNA|MYOM3_ENST00000330966.7_Missense_Mutation_p.K1435R|MYOM3_ENST00000338909.5_Missense_Mutation_p.K325R	NM_152372.3	NP_689585.3	Q5VTT5	MYOM3_HUMAN	myomesin 3	1432						M band (GO:0031430)	protein homodimerization activity (GO:0042803)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|kidney(6)|large_intestine(3)|lung(40)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	68		Colorectal(325;3.55e-05)|Renal(390;0.000703)|Lung NSC(340;0.001)|all_lung(284;0.0014)|Ovarian(437;0.00351)|Breast(348;0.0126)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;5.31e-24)|Colorectal(126;7.52e-08)|COAD - Colon adenocarcinoma(152;4.01e-06)|GBM - Glioblastoma multiforme(114;4.36e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00108)|KIRC - Kidney renal clear cell carcinoma(1967;0.00404)|STAD - Stomach adenocarcinoma(196;0.00966)|READ - Rectum adenocarcinoma(331;0.0678)|Lung(427;0.153)		CTTCAGCTCCTTGGGCTCGTC	0.577													T|||	277	0.0553115	0.2005	0.0159	5008	,	,		21478	0.0		0.001	False		,,,				2504	0.0				p.K1432R		Atlas-SNP	.											.	MYOM3	131	.	0			c.A4295G						PASS	.	T	ARG/LYS	524,3714		36,452,1631	75.0	74.0	74.0		4295	2.9	1.0	1	dbSNP_129	74	9,8473		0,9,4232	yes	missense	MYOM3	NM_152372.3	26	36,461,5863	CC,CT,TT		0.1061,12.3643,4.1903	benign	1432/1438	24383873	533,12187	2119	4241	6360	SO:0001583	missense	127294	exon37			AGCTCCTTGGGCT	AK093280	CCDS41281.1	1p36	2013-02-11	2012-10-17		ENSG00000142661	ENSG00000142661		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	26679	protein-coding gene	gene with protein product			"""myomesin family, member 3"""			18177667	Standard	NM_152372		Approved	FLJ35961	uc001bin.4	Q5VTT5	OTTHUMG00000002969	ENST00000374434.3:c.4295A>G	1.37:g.24383873T>C	ENSP00000363557:p.Lys1432Arg	147.0	0.0	0		158.0	83.0	0.525316	NM_152372	A6NF75|Q5VTT6|Q6AWC0|Q6AWC1|Q6NXF9|Q6ZRG7|Q7Z3G9|Q8NA11|Q96C54	Missense_Mutation	SNP	ENST00000374434.3	37	CCDS41281.1	85	0.03891941391941392	77	0.1565040650406504	8	0.022099447513812154	0	0.0	0	0.0	T	1.496	-0.553376	0.03996	0.123643	0.001061	ENSG00000142661	ENST00000338909;ENST00000374434;ENST00000330966;ENST00000374442	T;T;T	0.56103	0.48;0.56;0.56	5.24	2.88	0.33553	.	0.543380	0.19217	N	0.119765	T	0.00109	0.0003	N	0.22421	0.69	0.41520	P	0.01160899999999998	B;B	0.20459	0.01;0.045	B;B	0.17722	0.004;0.019	T	0.09707	-1.0662	9	0.06494	T	0.89	.	3.3931	0.07297	0.1436:0.0766:0.1321:0.6476	rs59805085	1432;325	Q5VTT5;Q5VTT5-3	MYOM3_HUMAN;.	R	325;1432;1435;326	ENSP00000342689:K325R;ENSP00000363557:K1432R;ENSP00000332670:K1435R	ENSP00000332670:K1435R	K	-	2	0	MYOM3	24256460	0.000000	0.05858	0.997000	0.53966	0.370000	0.29829	0.160000	0.16462	0.795000	0.33922	0.533000	0.62120	AAG	T|0.975;C|0.025	0.025	strong		0.577	MYOM3-001	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008272.2	NM_152372	
MCM8	84515	hgsc.bcm.edu	37	20	5943985	5943985	+	Silent	SNP	G	G	A	rs35102646	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:5943985G>A	ENST00000378896.3	+	8	1232	c.855G>A	c.(853-855)acG>acA	p.T285T	Y_RNA_ENST00000384650.1_RNA|MCM8_ENST00000378886.2_Silent_p.T285T|MCM8_ENST00000265187.4_Silent_p.T285T|MCM8_ENST00000378883.1_Silent_p.T285T	NM_001281520.1|NM_032485.4|NM_182802.1	NP_001268449.1|NP_115874.3|NP_877954.1	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	285					cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)|G1/S transition of mitotic cell cycle (GO:0000082)|male gamete generation (GO:0048232)|mitotic cell cycle (GO:0000278)	MCM8-MCM9 complex (GO:0097362)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	23						TCACAGTTACGATGGACTGGC	0.408													A|||	49	0.00978435	0.0363	0.0014	5008	,	,		16509	0.0		0.0	False		,,,				2504	0.0				p.T285T		Atlas-SNP	.											.	MCM8	125	.	0			c.G855A						PASS	.	A	,	87,4319	818.4+/-416.3	0,87,2116	123.0	107.0	112.0		855,855	-8.8	0.0	20	dbSNP_126	112	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	MCM8	NM_032485.4,NM_182802.1	,	0,87,6416	AA,AG,GG		0.0,1.9746,0.6689	,	285/841,285/825	5943985	87,12919	2203	4300	6503	SO:0001819	synonymous_variant	84515	exon8			AGTTACGATGGAC	AJ439063	CCDS13094.1, CCDS13095.1, CCDS63226.1, CCDS63227.1	20p12.3	2007-04-04	2007-04-04	2003-07-09	ENSG00000125885	ENSG00000125885			16147	protein-coding gene	gene with protein product	"""REC homolog (Drosophila)"""	608187	"""chromosome 20 open reading frame 154"""	C20orf154		12527764	Standard	NM_032485		Approved	MGC4816, MGC12866, MGC119522, MGC119523, dJ967N21.5, REC	uc002wmi.3	Q9UJA3	OTTHUMG00000031822	ENST00000378896.3:c.855G>A	20.37:g.5943985G>A		58.0	0.0	0		54.0	23.0	0.425926	NM_032485	B2RBG7|D3DW08|E7EQU7|Q495R4|Q495R6|Q495R7|Q86US4|Q969I5	Silent	SNP	ENST00000378896.3	37	CCDS13094.1																																																																																			G|0.992;A|0.008	0.008	strong		0.408	MCM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077900.1	NM_032485	
C6orf201	404220	hgsc.bcm.edu	37	6	4122279	4122279	+	Splice_Site	SNP	A	A	G	rs17137678	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:4122279A>G	ENST00000380175.4	+	4	1146	c.381A>G	c.(379-381)acA>acG	p.T127T	ECI2_ENST00000465828.1_Intron|ECI2_ENST00000413766.2_Intron|ECI2_ENST00000380125.2_Intron|C6orf201_ENST00000430835.2_Splice_Site_p.T127T|C6orf201_ENST00000333388.5_Splice_Site_p.T130T|ECI2_ENST00000361538.2_Intron|ECI2_ENST00000380118.3_Intron	NM_001085401.2	NP_001078870.1	Q7Z4U5	CF201_HUMAN	chromosome 6 open reading frame 201	127										central_nervous_system(1)|endometrium(3)|lung(2)	6	Ovarian(93;0.0925)	all_hematologic(90;0.0895)				GGACACAAACAGGTACATGCA	0.418													A|||	125	0.0249601	0.09	0.0086	5008	,	,		15796	0.0		0.0	False		,,,				2504	0.0				p.T127T		Atlas-SNP	.											.	C6orf201	17	.	0			c.A381G						PASS	.	A	,,,	308,3458		23,262,1598	63.0	61.0	62.0		381,,,	3.2	0.2	6	dbSNP_123	62	4,8226		0,4,4111	yes	coding-synonymous-near-splice,intron,intron,intron	ECI2,C6orf201	NM_001085401.1,NM_001166010.1,NM_006117.2,NM_206836.2	,,,	23,266,5709	GG,GA,AA		0.0486,8.1784,2.6009	,,,	127/141,,,	4122279	312,11684	1883	4115	5998	SO:0001630	splice_region_variant	404220	exon4			ACAAACAGGTACA	BC047663	CCDS43419.1	6p25.2	2012-02-21			ENSG00000185689	ENSG00000185689			21620	protein-coding gene	gene with protein product							Standard	NM_001085401		Approved	dJ1013A10.5	uc003mwa.4	Q7Z4U5	OTTHUMG00000014160	ENST00000380175.4:c.382+1A>G	6.37:g.4122279A>G		209.0	0.0	0		210.0	114.0	0.542857	NM_001085401	A6NLI6|Q6NXN5	Silent	SNP	ENST00000380175.4	37	CCDS43419.1																																																																																			A|0.978;G|0.022	0.022	strong		0.418	C6orf201-001	KNOWN	NMD_exception|basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000314019.2	NM_001085401	Silent
IL1R2	7850	hgsc.bcm.edu	37	2	102626187	102626187	+	Silent	SNP	G	G	A	rs2230401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:102626187G>A	ENST00000332549.3	+	3	460	c.231G>A	c.(229-231)acG>acA	p.T77T	IL1R2_ENST00000441002.1_Silent_p.T77T|IL1R2_ENST00000393414.2_Silent_p.T77T	NM_004633.3	NP_004624.1	P27930	IL1R2_HUMAN	interleukin 1 receptor, type II	77	Ig-like C2-type 1.				cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-1 receptor activity (GO:0004908)|interleukin-1, Type II, blocking receptor activity (GO:0004910)			breast(3)|endometrium(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(1)|skin(1)	28						CTGCTAGGACGGTCCCAGGAG	0.597													G|||	215	0.0429313	0.1551	0.013	5008	,	,		18355	0.0		0.001	False		,,,				2504	0.0				p.T77T	Pancreas(106;189 1628 2302 5133 12295)	Atlas-SNP	.											.	IL1R2	58	.	0			c.G231A						PASS	.	G	,	507,3899	234.6+/-247.4	31,445,1727	157.0	164.0	161.0		231,231	-3.7	0.0	2	dbSNP_98	161	12,8588	9.1+/-34.3	0,12,4288	no	coding-synonymous,coding-synonymous	IL1R2	NM_004633.3,NM_173343.1	,	31,457,6015	AA,AG,GG		0.1395,11.507,3.9905	,	77/399,77/399	102626187	519,12487	2203	4300	6503	SO:0001819	synonymous_variant	7850	exon3			TAGGACGGTCCCA	X59770	CCDS2054.1, CCDS58719.1	2q12	2013-01-11			ENSG00000115590	ENSG00000115590		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5994	protein-coding gene	gene with protein product		147811		IL1RB		10191101, 1833184	Standard	NM_004633		Approved	CD121b	uc002tbm.3	P27930	OTTHUMG00000130695	ENST00000332549.3:c.231G>A	2.37:g.102626187G>A		81.0	0.0	0		81.0	34.0	0.419753	NM_001261419	D3DVJ5|Q6LCE6|Q9UE68	Silent	SNP	ENST00000332549.3	37	CCDS2054.1																																																																																			G|0.958;A|0.042	0.042	strong		0.597	IL1R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253191.1	NM_004633	
AZU1	566	hgsc.bcm.edu	37	19	831811	831811	+	Silent	SNP	C	C	T	rs588442	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:831811C>T	ENST00000233997.2	+	5	711	c.690C>T	c.(688-690)acC>acT	p.T230T		NM_001700.3	NP_001691.1	P20160	CAP7_HUMAN	azurocidin 1	230	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cellular extravasation (GO:0045123)|defense response to Gram-negative bacterium (GO:0050829)|glial cell migration (GO:0008347)|induction of positive chemotaxis (GO:0050930)|inflammatory response (GO:0006954)|macrophage chemotaxis (GO:0048246)|microglial cell activation (GO:0001774)|monocyte activation (GO:0042117)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell adhesion (GO:0045785)|positive regulation of fractalkine biosynthetic process (GO:0050754)|positive regulation of interleukin-1 beta biosynthetic process (GO:0050725)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of phagocytosis (GO:0050766)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of vascular permeability (GO:0043114)	azurophil granule (GO:0042582)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)|toxic substance binding (GO:0015643)			NS(1)|endometrium(1)|kidney(1)|lung(4)|pancreas(1)|upper_aerodigestive_tract(2)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|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)		ACTTCTTCACCCGAGTGGCGC	0.711													C|||	405	0.0808706	0.2935	0.0216	5008	,	,		12838	0.0		0.002	False		,,,				2504	0.0				p.T230T		Atlas-SNP	.											.	AZU1	31	.	0			c.C690T						PASS	.	C		1054,3346		120,814,1266	32.0	36.0	35.0		690	0.8	0.1	19	dbSNP_83	35	6,8588		0,6,4291	no	coding-synonymous	AZU1	NM_001700.3		120,820,5557	TT,TC,CC		0.0698,23.9545,8.1576		230/252	831811	1060,11934	2200	4297	6497	SO:0001819	synonymous_variant	566	exon5			CTTCACCCGAGTG	X58794	CCDS12044.1	19p13.3	2012-03-30	2008-08-01		ENSG00000172232	ENSG00000172232			913	protein-coding gene	gene with protein product	"""cationic antimicrobial protein 37"", ""heparin-binding protein"", ""neutrophil azurocidin"""	162815				1919011	Standard	NM_001700		Approved	AZU, CAP37, AZAMP, HBP, NAZC, HUMAZUR	uc002lpz.1	P20160		ENST00000233997.2:c.690C>T	19.37:g.831811C>T		105.0	0.0	0		121.0	54.0	0.446281	NM_001700	P80014|Q52LG4|Q9UCM1|Q9UCT5	Silent	SNP	ENST00000233997.2	37	CCDS12044.1																																																																																			C|0.897;T|0.103	0.103	strong		0.711	AZU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457472.2	NM_001700	
KIAA0020	9933	hgsc.bcm.edu	37	9	2811522	2811522	+	Missense_Mutation	SNP	T	T	A	rs60717199	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:2811522T>A	ENST00000397885.2	-	15	1680	c.1474A>T	c.(1474-1476)Agc>Tgc	p.S492C		NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020	492	PUM-HD. {ECO:0000255|PROSITE- ProRule:PRU00318}.					endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(50;0.0319)		TGCAGGTAGCTTAACAAAGCT	0.473													T|||	109	0.0217652	0.0764	0.0101	5008	,	,		19686	0.0		0.001	False		,,,				2504	0.0				p.S492C		Atlas-SNP	.											.	KIAA0020	56	.	0			c.A1474T						PASS	.	T	CYS/SER	263,4143	148.8+/-183.1	7,249,1947	148.0	137.0	140.0		1474	4.8	0.8	9	dbSNP_129	140	3,8597	3.0+/-9.4	0,3,4297	yes	missense	KIAA0020	NM_014878.4	112	7,252,6244	AA,AT,TT		0.0349,5.9691,2.0452	probably-damaging	492/649	2811522	266,12740	2203	4300	6503	SO:0001583	missense	9933	exon15			GGTAGCTTAACAA	AL832239	CCDS6448.2	9p24.2	2012-11-29			ENSG00000080608	ENSG00000080608			29676	protein-coding gene	gene with protein product	"""penguin homolog (Drosophila)"", ""minor histocompatibility antigen HA-8"""	609960				7584026, 7584028, 21266351	Standard	NM_014878		Approved	XTP5, PEN, PUF6, hPUF-A, HA-8	uc003zhp.1	Q15397	OTTHUMG00000019450	ENST00000397885.2:c.1474A>T	9.37:g.2811522T>A	ENSP00000380982:p.Ser492Cys	107.0	0.0	0		102.0	42.0	0.411765	NM_014878	A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Missense_Mutation	SNP	ENST00000397885.2	37	CCDS6448.2	35	0.016025641025641024	32	0.06504065040650407	3	0.008287292817679558	0	0.0	0	0.0	T	19.38	3.816861	0.70912	0.059691	3.49E-4	ENSG00000080608	ENST00000397885	T	0.46063	0.88	5.97	4.84	0.62591	CPL (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.452768	0.30676	N	0.009106	T	0.07773	0.0195	M	0.63843	1.955	0.29221	N	0.87392	P;P	0.43607	0.544;0.812	P;P	0.54856	0.656;0.762	T	0.18147	-1.0346	10	0.66056	D	0.02	-29.6696	9.6157	0.39690	0.0:0.1502:0.0:0.8498	rs60717199	352;492	B2RDG4;Q15397	.;K0020_HUMAN	C	492	ENSP00000380982:S492C	ENSP00000380982:S492C	S	-	1	0	KIAA0020	2801522	1.000000	0.71417	0.841000	0.33234	0.884000	0.51177	2.579000	0.46059	1.089000	0.41292	0.533000	0.62120	AGC	T|0.980;A|0.020	0.020	strong		0.473	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3	NM_014878	
HELQ	113510	hgsc.bcm.edu	37	4	84361071	84361071	+	Missense_Mutation	SNP	G	G	A	rs6817280	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:84361071G>A	ENST00000295488.3	-	8	1915	c.1753C>T	c.(1753-1755)Cct>Tct	p.P585S	HELQ_ENST00000510985.1_Missense_Mutation_p.P518S	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	585	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.		P -> S (in dbSNP:rs6817280).		double-strand break repair via homologous recombination (GO:0000724)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						TTCTTACTAGGACAAAAAACT	0.303								Other identified genes with known or suspected DNA repair function					G|||	422	0.0842652	0.3026	0.0303	5008	,	,		16565	0.0		0.001	False		,,,				2504	0.0				p.P585S		Atlas-SNP	.											.	HELQ	95	.	0			c.C1753T						PASS	.	G	SER/PRO	1127,3279	391.0+/-327.9	138,851,1214	64.0	67.0	66.0		1753	5.7	1.0	4	dbSNP_116	66	14,8584	9.1+/-34.3	0,14,4285	yes	missense	HELQ	NM_133636.2	74	138,865,5499	AA,AG,GG		0.1628,25.5788,8.7742	possibly-damaging	585/1102	84361071	1141,11863	2203	4299	6502	SO:0001583	missense	113510	exon8			TACTAGGACAAAA	AF436845	CCDS3603.1, CCDS75158.1	4q21.23	2009-02-26			ENSG00000163312	ENSG00000163312			18536	protein-coding gene	gene with protein product		606769				11751861	Standard	XM_005262711		Approved	Hel308	uc003hom.3	Q8TDG4	OTTHUMG00000130423	ENST00000295488.3:c.1753C>T	4.37:g.84361071G>A	ENSP00000295488:p.Pro585Ser	335.0	1.0	0.00298507		376.0	192.0	0.510638	NM_133636	Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Missense_Mutation	SNP	ENST00000295488.3	37	CCDS3603.1	134	0.06135531135531135	122	0.24796747967479674	11	0.03038674033149171	0	0.0	1	0.0013192612137203166	G	21.9	4.217196	0.79352	0.255788	0.001628	ENSG00000163312	ENST00000295488;ENST00000510985	T;D	0.91686	-0.57;-2.89	5.68	5.68	0.88126	Helicase, C-terminal (1);	0.051961	0.85682	D	0.000000	T	0.00144	0.0004	L	0.28694	0.88	0.09310	P	0.99999999573404	D;P	0.71674	0.998;0.855	D;P	0.64687	0.928;0.474	T	0.42361	-0.9456	9	0.11485	T	0.65	.	19.7785	0.96405	0.0:0.0:1.0:0.0	rs6817280;rs6817280	518;585	E3W980;Q8TDG4	.;HELQ_HUMAN	S	585;518	ENSP00000295488:P585S;ENSP00000424539:P518S	ENSP00000295488:P585S	P	-	1	0	HELQ	84580095	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.458000	0.66679	2.675000	0.91044	0.655000	0.94253	CCT	G|0.916;A|0.084	0.084	strong		0.303	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1	NM_133636	
DCAF8L2	347442	hgsc.bcm.edu	37	X	27766474	27766474	+	Missense_Mutation	SNP	G	G	A	rs375048390		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:27766474G>A	ENST00000451261.2	+	5	1861	c.1462G>A	c.(1462-1464)Ggt>Agt	p.G488S		NM_001136533.1	NP_001130005.1	P0C7V8	DC8L2_HUMAN	DDB1 and CUL4 associated factor 8-like 2	488										central_nervous_system(1)|endometrium(9)|kidney(3)|lung(7)|pancreas(1)|skin(3)	24						TGTAGTGAGCGGTAGTGATTG	0.438													G|||	1	0.000264901	0.0008	0.0	3775	,	,		15465	0.0		0.0	False		,,,				2504	0.0				p.G488S		Atlas-SNP	.											.	DCAF8L2	79	.	0			c.G1462A						PASS	.	G	SER/GLY	2,1207		0,1,1,516,174	86.0	63.0	70.0		1462	3.8	0.8	X		70	0,2391		0,0,0,800,791	no	missense	DCAF8L2	NM_001136533.1	56	0,1,1,1316,965	AA,AG,A,GG,G		0.0,0.1654,0.0556	probably-damaging	488/632	27766474	2,3598	692	1591	2283	SO:0001583	missense	347442	exon1			GTGAGCGGTAGTG		CCDS59162.1	Xp22.11	2013-01-09	2009-07-17	2009-07-17		ENSG00000189186		"""WD repeat domain containing"""	31811	protein-coding gene	gene with protein product			"""WD repeat domain 42C"""	WDR42C			Standard	NM_001136533		Approved		uc011mjy.2	P0C7V8		ENST00000451261.2:c.1462G>A	X.37:g.27766474G>A	ENSP00000462745:p.Gly488Ser	295.0	1.0	0.00338983		250.0	138.0	0.552	NM_001136533	B2RXH9|J3KT06	Missense_Mutation	SNP	ENST00000451261.2	37	CCDS59162.1																																																																																			.	.	weak		0.438	DCAF8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056143.4	XM_293354	
SMCO1	255798	hgsc.bcm.edu	37	3	196235191	196235191	+	Missense_Mutation	SNP	A	A	G	rs73891273	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:196235191A>G	ENST00000397537.2	-	3	368	c.212T>C	c.(211-213)aTg>aCg	p.M71T		NM_001077657.1	NP_001071125.1	Q147U7	SMCO1_HUMAN	single-pass membrane protein with coiled-coil domains 1	71						integral component of membrane (GO:0016021)											ATTCAATTCCATTGAAGTGAG	0.358													.|||	265	0.0529153	0.1876	0.0231	5008	,	,		16968	0.0		0.001	False		,,,				2504	0.0				p.M71T		Atlas-SNP	.											C3orf43,NS,carcinoma,+1,1	C3orf43	25	1	0			c.T212C						PASS	.	A	THR/MET	559,3137		45,469,1334	62.0	60.0	60.0		212	5.5	1.0	3	dbSNP_130	60	5,8181		0,5,4088	yes	missense	C3orf43	NM_001077657.1	81	45,474,5422	GG,GA,AA		0.0611,15.1245,4.7467	possibly-damaging	71/215	196235191	564,11318	1848	4093	5941	SO:0001583	missense	255798	exon3			AATTCCATTGAAG	AK123917	CCDS43192.1	3q29	2013-03-08	2013-03-08	2013-03-08	ENSG00000214097	ENSG00000214097			27407	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 43"""	C3orf43			Standard	NM_001077657		Approved	FLJ41923, DKFZp313B0440		Q147U7	OTTHUMG00000155581	ENST00000397537.2:c.212T>C	3.37:g.196235191A>G	ENSP00000380671:p.Met71Thr	37.0	0.0	0		54.0	22.0	0.407407	NM_001077657	B3KW20	Missense_Mutation	SNP	ENST00000397537.2	37	CCDS43192.1	97	0.044413919413919416	90	0.18292682926829268	7	0.019337016574585635	0	0.0	0	0.0	A	14.07	2.425685	0.43020	0.151245	6.11E-4	ENSG00000214097	ENST00000397537	T	0.36699	1.24	5.46	5.46	0.80206	.	.	.	.	.	T	0.00073	0.0002	L	0.34521	1.04	0.30114	P	0.806335	B;B	0.32160	0.358;0.358	B;B	0.32762	0.152;0.152	T	0.11179	-1.0598	8	0.59425	D	0.04	-16.9577	13.0552	0.58975	1.0:0.0:0.0:0.0	.	71;63	Q147U7;E9PGG7	CC043_HUMAN;.	T	71	ENSP00000380671:M71T	ENSP00000380671:M71T	M	-	2	0	C3orf43	197719588	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	4.753000	0.62183	2.062000	0.61559	0.533000	0.62120	ATG	A|0.971;G|0.029	0.029	strong		0.358	SMCO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340776.1	NM_001006109	
ZNF142	7701	hgsc.bcm.edu	37	2	219515109	219515109	+	Missense_Mutation	SNP	T	T	G	rs61733648	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:219515109T>G	ENST00000449707.1	-	5	842	c.421A>C	c.(421-423)Aaa>Caa	p.K141Q	ZNF142_ENST00000411696.2_Missense_Mutation_p.K141Q	NM_001105537.1	NP_001099007.1	P52746	ZN142_HUMAN	zinc finger protein 142	141					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(7)|endometrium(7)|large_intestine(5)|lung(12)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	38		Renal(207;0.0474)		Epithelial(149;5.21e-07)|all cancers(144;0.000106)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)		CCTTGGCCTTTATCCACAGCC	0.527													T|||	67	0.0133786	0.0492	0.0029	5008	,	,		19332	0.0		0.0	False		,,,				2504	0.0				p.K141Q	Colon(170;867 1942 8995 15834 18053)	Atlas-SNP	.											.	ZNF142	190	.	0			c.A421C						PASS	.	T	GLN/LYS	162,3762		0,162,1800	230.0	233.0	232.0		421	4.1	0.0	2	dbSNP_129	232	1,8297		0,1,4148	yes	missense	ZNF142	NM_001105537.1	53	0,163,5948	GG,GT,TT		0.0121,4.1284,1.3337	possibly-damaging	141/1688	219515109	163,12059	1962	4149	6111	SO:0001583	missense	7701	exon5			GGCCTTTATCCAC	U09849	CCDS42817.1	2q35	2013-01-08	2006-06-13		ENSG00000115568	ENSG00000115568		"""Zinc fingers, C2H2-type"""	12927	protein-coding gene	gene with protein product		604083	"""zinc finger protein 142 (clone pHZ-49)"""				Standard	NM_001105537		Approved	KIAA0236, pHZ-49	uc002vin.4	P52746	OTTHUMG00000154736	ENST00000449707.1:c.421A>C	2.37:g.219515109T>G	ENSP00000408643:p.Lys141Gln	175.0	0.0	0		191.0	96.0	0.502618	NM_001105537	Q92510	Missense_Mutation	SNP	ENST00000449707.1	37	CCDS42817.1	22	0.010073260073260074	22	0.044715447154471545	0	0.0	0	0.0	0	0.0	T	8.836	0.941010	0.18281	0.041284	1.21E-4	ENSG00000115568	ENST00000449707;ENST00000411696	T;T	0.12984	2.63;2.63	5.2	4.05	0.47172	.	0.711144	0.13741	N	0.365968	T	0.02193	0.0068	L	0.44542	1.39	0.09310	N	1	P	0.39282	0.666	B	0.35859	0.212	T	0.21999	-1.0229	10	0.21014	T	0.42	-0.251	7.4012	0.26965	0.0:0.0962:0.0:0.9038	.	141	P52746	ZN142_HUMAN	Q	141	ENSP00000408643:K141Q;ENSP00000398798:K141Q	ENSP00000398798:K141Q	K	-	1	0	ZNF142	219223353	0.172000	0.23043	0.048000	0.18961	0.098000	0.18820	1.797000	0.38804	1.011000	0.39340	0.533000	0.62120	AAA	T|0.990;G|0.010	0.010	strong		0.527	ZNF142-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336833.1	NM_005081	
PRICKLE4	29964	hgsc.bcm.edu	37	6	41753136	41753136	+	Missense_Mutation	SNP	G	G	A	rs35880970	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:41753136G>A	ENST00000394260.1	+	3	320	c.320G>A	c.(319-321)cGc>cAc	p.R107H	PRICKLE4_ENST00000463606.1_3'UTR|PRICKLE4_ENST00000359201.5_Missense_Mutation_p.R147H|TOMM6_ENST00000398881.3_5'Flank|PRICKLE4_ENST00000394263.1_Missense_Mutation_p.R147H|PRICKLE4_ENST00000458694.1_Missense_Mutation_p.R147H|PRICKLE4_ENST00000394259.1_Missense_Mutation_p.R107H|TOMM6_ENST00000398884.3_5'Flank			Q2TBC4	PRIC4_HUMAN	prickle homolog 4 (Drosophila)	107	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.					nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	13	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;8.38e-05)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			GGGGAACAGCGCTGCTGGCAC	0.602													G|||	81	0.0161741	0.0537	0.0072	5008	,	,		17211	0.0		0.001	False		,,,				2504	0.0041				p.R147H		Atlas-SNP	.											.	PRICKLE4	29	.	0			c.G440A						PASS	.	G	HIS/ARG	225,4181	134.1+/-170.4	6,213,1984	51.0	50.0	50.0		440	2.9	0.6	6	dbSNP_126	50	17,8583	11.2+/-40.8	0,17,4283	yes	missense	PRICKLE4	NM_013397.5	29	6,230,6267	AA,AG,GG		0.1977,5.1067,1.8607	benign	147/385	41753136	242,12764	2203	4300	6503	SO:0001583	missense	29964	exon6			AACAGCGCTGCTG	AF216754	CCDS34449.1	6p21.1	2010-08-05	2007-09-18	2007-09-18	ENSG00000124593	ENSG00000124593			16805	protein-coding gene	gene with protein product		611389	"""chromosome 6 open reading frame 49"""	C6orf49		15702247	Standard	NM_013397		Approved	OEBT, DKFZp761H221	uc011duf.1	Q2TBC4	OTTHUMG00000014685	ENST00000394260.1:c.320G>A	6.37:g.41753136G>A	ENSP00000377803:p.Arg107His	89.0	0.0	0		79.0	77.0	0.974684	NM_013397	A2A3M0|A6PVU1|B3KQ15|Q5T3D4|Q9NSV1	Missense_Mutation	SNP	ENST00000394260.1	37		32	0.014652014652014652	28	0.056910569105691054	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	G	1.735	-0.493181	0.04322	0.051067	0.001977	ENSG00000124593	ENST00000458694;ENST00000359201;ENST00000394263;ENST00000394259;ENST00000394260	D;D;D;D;D	0.87491	-2.26;-2.26;-2.26;-2.26;-2.26	4.71	2.91	0.33838	.	0.859014	0.09926	N	0.737859	T	0.63988	0.2558	L	0.35542	1.07	0.09310	N	1	B	0.25169	0.119	B	0.22601	0.04	T	0.55817	-0.8081	10	0.42905	T	0.14	-6.1033	4.9115	0.13823	0.084:0.1478:0.6159:0.1523	rs35880970	147	Q2TBC4-3	.	H	147;147;147;107;107	ENSP00000404911:R147H;ENSP00000352128:R147H;ENSP00000377806:R147H;ENSP00000377802:R107H;ENSP00000377803:R107H	ENSP00000335185:R147H	R	+	2	0	PRICKLE4	41861114	0.024000	0.19004	0.631000	0.29282	0.275000	0.26752	0.519000	0.22862	0.587000	0.29643	-0.258000	0.10820	CGC	G|0.982;A|0.018	0.018	strong		0.602	PRICKLE4-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000303948.1	NM_013397	
KIF26B	55083	hgsc.bcm.edu	37	1	245775265	245775265	+	Silent	SNP	C	C	T	rs61741293	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:245775265C>T	ENST00000407071.2	+	9	2525	c.2085C>T	c.(2083-2085)agC>agT	p.S695S	RP11-522M21.2_ENST00000418402.1_RNA|KIF26B_ENST00000366518.4_Silent_p.S314S	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	695	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			TGGAGAAGAGCGGGAAAGGGG	0.587													C|||	71	0.0141773	0.0514	0.0029	5008	,	,		17393	0.0		0.001	False		,,,				2504	0.0				p.S695S		Atlas-SNP	.											.	KIF26B	343	.	0			c.C2085T						PASS	.	C		149,3979		1,147,1916	55.0	62.0	60.0		2085	0.9	1.0	1	dbSNP_129	60	4,8378		0,4,4187	no	coding-synonymous	KIF26B	NM_018012.3		1,151,6103	TT,TC,CC		0.0477,3.6095,1.223		695/2109	245775265	153,12357	2064	4191	6255	SO:0001819	synonymous_variant	55083	exon9			GAAGAGCGGGAAA	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"""Kinesins"""	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.2085C>T	1.37:g.245775265C>T		94.0	0.0	0		111.0	43.0	0.387387	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Silent	SNP	ENST00000407071.2	37	CCDS44342.1																																																																																			C|0.989;T|0.011	0.011	strong		0.587	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354	
DPH1	1801	hgsc.bcm.edu	37	17	1943525	1943525	+	Missense_Mutation	SNP	A	A	G	rs200693145	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:1943525A>G	ENST00000263083.6	+	8	823	c.778A>G	c.(778-780)Agc>Ggc	p.S260G	RP11-667K14.4_ENST00000572404.1_RNA|DPH1_ENST00000570477.1_Missense_Mutation_p.S180G|OVCA2_ENST00000572195.1_5'Flank	NM_001383.3	NP_001374.3	Q9BZG8	DPH1_HUMAN	diphthamide biosynthesis 1	260					cell proliferation (GO:0008283)|peptidyl-diphthamide biosynthetic process from peptidyl-histidine (GO:0017183)|translation (GO:0006412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|large_intestine(2)|lung(6)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	17						TGACCCATATAGCAAAGTCCT	0.557													A|||	6	0.00119808	0.0045	0.0	5008	,	,		19386	0.0		0.0	False		,,,				2504	0.0				p.S260G		Atlas-SNP	.											.	DPH1	32	.	0			c.A778G						PASS	.	A	GLY/SER	13,4155		0,13,2071	86.0	87.0	87.0		778	4.0	1.0	17		87	0,8422		0,0,4211	yes	missense	DPH1	NM_001383.3	56	0,13,6282	GG,GA,AA		0.0,0.3119,0.1033	benign	260/444	1943525	13,12577	2084	4211	6295	SO:0001583	missense	1801	exon8			CCATATAGCAAAG	S81752	CCDS42228.1	17p13.3	2013-05-02	2013-05-02	2005-06-03	ENSG00000108963	ENSG00000108963			3003	protein-coding gene	gene with protein product	"""ovarian tumor suppressor candidate 1"""	603527	"""diptheria toxin resistance protein required for diphthamide biosynthesis-like 1 (S. cerevisiae)"", ""DPH-like 1 (S. cerevisiae)"", ""DPH1 homolog (S. cerevisiae)"""	DPH2L, DPH2L1		8603384, 15485916, 22869748	Standard	NM_001383		Approved	OVCA1	uc002fts.3	Q9BZG8	OTTHUMG00000177724	ENST00000263083.6:c.778A>G	17.37:g.1943525A>G	ENSP00000263083:p.Ser260Gly	55.0	0.0	0		51.0	34.0	0.666667	NM_001383	D3DTI3|Q16439|Q4VBA2|Q9BTW7|Q9UCY0	Missense_Mutation	SNP	ENST00000263083.6	37	CCDS42228.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	10.42	1.346368	0.24426	0.003119	0.0	ENSG00000108963	ENST00000263083	T	0.49720	0.77	5.15	4.03	0.46877	.	0.040549	0.85682	N	0.000000	T	0.48241	0.1489	M	0.74647	2.275	0.50467	D	0.999871	B;B;B	0.14805	0.011;0.011;0.003	B;B;B	0.23852	0.049;0.049;0.033	T	0.43410	-0.9393	10	0.46703	T	0.11	-13.6359	10.1501	0.42788	0.9183:0.0:0.0817:0.0	.	270;270;260	E7ENH3;B4DNK0;Q9BZG8	.;.;DPH1_HUMAN	G	260	ENSP00000263083:S260G	ENSP00000263083:S260G	S	+	1	0	DPH1	1890275	1.000000	0.71417	0.990000	0.47175	0.054000	0.15201	4.836000	0.62789	0.748000	0.32831	0.459000	0.35465	AGC	A|1.000;G|0.000	0.000	strong		0.557	DPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000438660.1	NM_001383	
DHX40	79665	hgsc.bcm.edu	37	17	57652789	57652789	+	Silent	SNP	C	C	T	rs77178464	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:57652789C>T	ENST00000251241.4	+	7	1077	c.930C>T	c.(928-930)ctC>ctT	p.L310L	DHX40_ENST00000451169.2_Silent_p.L211L|DHX40_ENST00000425628.3_Silent_p.L233L	NM_024612.4	NP_078888.4	Q8IX18	DHX40_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 40	310	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.						ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|nucleic acid binding (GO:0003676)			endometrium(7)|large_intestine(6)|lung(6)|prostate(1)	20	all_neural(34;0.0878)|Medulloblastoma(34;0.0922)					ATACCACCCTCGATGGCTTGT	0.303													C|||	263	0.052516	0.1914	0.013	5008	,	,		16582	0.001		0.0	False		,,,				2504	0.0				p.L310L		Atlas-SNP	.											.	DHX40	40	.	0			c.C930T						PASS	.	C	,	569,3837	254.3+/-259.9	34,501,1668	112.0	107.0	109.0		699,930	-4.6	1.0	17	dbSNP_131	109	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	DHX40	NM_001166301.1,NM_024612.4	,	34,501,5967	TT,TC,CC		0.0,12.9142,4.3756	,	233/703,310/780	57652789	569,12435	2203	4299	6502	SO:0001819	synonymous_variant	79665	exon7			CACCCTCGATGGC	AF260270	CCDS11617.1, CCDS54150.1	17q22	2014-01-28	2003-06-13	2003-06-20		ENSG00000108406		"""DEAH-boxes"""	18018	protein-coding gene	gene with protein product		607570	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 40 (RNA helicase)"""	DDX40			Standard	NM_024612		Approved	ARG147, PAD, FLJ22060	uc002ixn.2	Q8IX18		ENST00000251241.4:c.930C>T	17.37:g.57652789C>T		392.0	1.0	0.00255102		386.0	201.0	0.520725	NM_024612	B3KTJ5|C9JR60|Q5JPH4|Q8TC86|Q8WY53|Q9BXM1|Q9H6M9	Silent	SNP	ENST00000251241.4	37	CCDS11617.1																																																																																			C|0.957;T|0.043	0.043	strong		0.303	DHX40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446095.1	NM_024612	
EPPK1	83481	hgsc.bcm.edu	37	8	144942934	144942934	+	Silent	SNP	C	C	T	rs114155737	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:144942934C>T	ENST00000525985.1	-	2	4559	c.4488G>A	c.(4486-4488)gcG>gcA	p.A1496A				P58107	EPIPL_HUMAN	epiplakin 1	1496						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GCCGCAGGGCCGCAGCCCTCC	0.672													C|||	59	0.0117812	0.0416	0.0043	5008	,	,		17427	0.0		0.001	False		,,,				2504	0.0				p.A1496A		Atlas-SNP	.											.	EPPK1	199	.	0			c.G4488A						PASS	.	C		163,4153		2,159,1997	19.0	22.0	21.0		4488	-9.0	0.0	8	dbSNP_132	21	4,8516		0,4,4256	no	coding-synonymous	EPPK1	NM_031308.1		2,163,6253	TT,TC,CC		0.0469,3.7766,1.301		1496/2420	144942934	167,12669	2158	4260	6418	SO:0001819	synonymous_variant	83481	exon1			CAGGGCCGCAGCC	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.4488G>A	8.37:g.144942934C>T		33.0	0.0	0		25.0	16.0	0.64	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																				C|0.987;T|0.013	0.013	strong		0.672	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
BRDT	676	hgsc.bcm.edu	37	1	92467626	92467626	+	Missense_Mutation	SNP	A	A	G	rs78267346	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:92467626A>G	ENST00000362005.3	+	17	2726	c.2308A>G	c.(2308-2310)Aat>Gat	p.N770D	BRDT_ENST00000394530.3_Missense_Mutation_p.N724D|BRDT_ENST00000399546.2_Missense_Mutation_p.N770D|BRDT_ENST00000402388.1_Missense_Mutation_p.N770D|BRDT_ENST00000370389.2_Missense_Mutation_p.N697D	NM_001242805.1	NP_001229734	Q58F21	BRDT_HUMAN	bromodomain, testis-specific	770					cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|histone displacement (GO:0001207)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|mRNA processing (GO:0006397)|positive regulation of transcription during meiosis (GO:0051039)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(24)|ovary(1)|prostate(4)|skin(2)|stomach(2)|urinary_tract(2)	56		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)		ACAGCTCTCAAATGGCATAAC	0.333													A|||	56	0.0111821	0.0401	0.0029	5008	,	,		17569	0.0		0.001	False		,,,				2504	0.0				p.N774D		Atlas-SNP	.											.	BRDT	133	.	0			c.A2320G						PASS	.	A	ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN,ASP/ASN	113,4293	86.8+/-125.4	2,109,2092	113.0	101.0	105.0		2308,2320,2170,2170,2089,2308,2308	1.3	0.0	1	dbSNP_132	105	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense,missense	BRDT	NM_001242805.1,NM_001242806.1,NM_001242807.1,NM_001242808.1,NM_001242810.1,NM_001726.3,NM_207189.2	23,23,23,23,23,23,23	2,109,6392	GG,GA,AA		0.0,2.5647,0.8688	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	770/948,774/952,724/902,724/902,697/875,770/948,770/948	92467626	113,12893	2203	4300	6503	SO:0001583	missense	676	exon16			CTCTCAAATGGCA	AF019085	CCDS735.1, CCDS55615.1, CCDS55616.1, CCDS72820.1	1p22.1	2010-12-23			ENSG00000137948	ENSG00000137948			1105	protein-coding gene	gene with protein product	"""cancer/testis antigen 9"""	602144				9367677	Standard	NM_001726		Approved	BRD6, CT9	uc010osz.2	Q58F21	OTTHUMG00000010113	ENST00000362005.3:c.2308A>G	1.37:g.92467626A>G	ENSP00000354568:p.Asn770Asp	275.0	0.0	0		297.0	159.0	0.535354	NM_001242806	A6NF68|B7Z811|B7Z890|B7ZAX7|D3DT32|O14789|Q05DQ4|Q6P5T1|Q7Z4A6|Q8IWI6	Missense_Mutation	SNP	ENST00000362005.3	37	CCDS735.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	A	8.950	0.968040	0.18659	0.025647	0.0	ENSG00000137948	ENST00000362005;ENST00000370389;ENST00000399546;ENST00000394530;ENST00000402388	T;T;T;T;T	0.57107	0.42;0.42;0.42;0.42;0.42	3.71	1.32	0.21799	.	0.438833	0.21441	N	0.074491	T	0.18341	0.0440	L	0.56769	1.78	0.09310	N	1	B;B;B;B	0.33694	0.421;0.421;0.16;0.421	B;B;B;B	0.29862	0.108;0.108;0.045;0.055	T	0.14504	-1.0470	10	0.18710	T	0.47	-3.342	3.8025	0.08764	0.6439:0.235:0.1211:0.0	.	724;724;774;770	B7ZAX7;B7Z811;B7Z890;Q58F21	.;.;.;BRDT_HUMAN	D	770;697;770;724;770	ENSP00000354568:N770D;ENSP00000359416:N697D;ENSP00000387822:N770D;ENSP00000378038:N724D;ENSP00000384051:N770D	ENSP00000354568:N770D	N	+	1	0	BRDT	92240214	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	0.214000	0.17541	0.274000	0.22072	0.533000	0.62120	AAT	A|0.988;G|0.012	0.012	strong		0.333	BRDT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027980.2	NM_207189	
CLDN14	23562	hgsc.bcm.edu	37	21	37833361	37833361	+	Silent	SNP	G	G	A	rs61745291	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:37833361G>A	ENST00000399137.1	-	3	1499	c.633C>T	c.(631-633)taC>taT	p.Y211Y	AP000695.6_ENST00000429588.1_RNA|AP000695.4_ENST00000428667.1_RNA|CLDN14_ENST00000399135.1_Silent_p.Y211Y|CLDN14_ENST00000342108.2_Silent_p.Y211Y|CLDN14_ENST00000399136.1_Silent_p.Y211Y|AP000695.4_ENST00000454980.1_RNA|CLDN14_ENST00000399139.1_Silent_p.Y211Y	NM_144492.2	NP_652763.1	O95500	CLD14_HUMAN	claudin 14	211					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|protein complex assembly (GO:0006461)|tight junction assembly (GO:0070830)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			endometrium(1)|lung(5)|skin(1)	7						CTGGTGGCTGGTAGGCAGGTG	0.657													G|||	118	0.0235623	0.0862	0.0043	5008	,	,		17127	0.0		0.001	False		,,,				2504	0.0				p.Y211Y		Atlas-SNP	.											.	CLDN14	25	.	0			c.C633T						PASS	.	G	,,,,	278,4128	154.4+/-187.8	11,256,1936	96.0	86.0	90.0		633,633,633,633,633	4.8	0.8	21	dbSNP_129	90	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CLDN14	NM_001146077.1,NM_001146078.1,NM_001146079.1,NM_012130.2,NM_144492.2	,,,,	11,258,6234	AA,AG,GG		0.0233,6.3096,2.1529	,,,,	211/240,211/240,211/240,211/240,211/240	37833361	280,12726	2203	4300	6503	SO:0001819	synonymous_variant	23562	exon3			TGGCTGGTAGGCA	AJ132445	CCDS13645.1	21q22.3	2008-07-31			ENSG00000159261	ENSG00000159261		"""Claudins"""	2035	protein-coding gene	gene with protein product		605608		DFNB29		11163249	Standard	NM_144492		Approved		uc002yvk.2	O95500	OTTHUMG00000086638	ENST00000399137.1:c.633C>T	21.37:g.37833361G>A		332.0	0.0	0		419.0	228.0	0.544153	NM_144492		Silent	SNP	ENST00000399137.1	37	CCDS13645.1																																																																																			G|0.976;A|0.024	0.024	strong		0.657	CLDN14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194697.1	NM_144492	
CEP250	11190	hgsc.bcm.edu	37	20	34084415	34084415	+	Silent	SNP	G	G	C	rs224376	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34084415G>C	ENST00000397527.1	+	25	3897	c.3177G>C	c.(3175-3177)ctG>ctC	p.L1059L	CEP250_ENST00000342580.4_Silent_p.L1003L	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	1059	Gln/Glu-rich.				centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			GCCTGACTCTGTCACTGATGG	0.453													G|||	31	0.0061901	0.0234	0.0	5008	,	,		19409	0.0		0.0	False		,,,				2504	0.0				p.L1059L		Atlas-SNP	.											.	CEP250	141	.	0			c.G3177C						PASS	.	G		131,4275	95.7+/-134.4	2,127,2074	72.0	68.0	69.0		3177	3.8	1.0	20	dbSNP_79	69	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	CEP250	NM_007186.3		2,130,6371	CC,CG,GG		0.0349,2.9732,1.0303		1059/2443	34084415	134,12872	2203	4300	6503	SO:0001819	synonymous_variant	11190	exon25			GACTCTGTCACTG	AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"""centrosomal protein 2"""	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.3177G>C	20.37:g.34084415G>C		60.0	0.0	0		64.0	32.0	0.5	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Silent	SNP	ENST00000397527.1	37	CCDS13255.1																																																																																			G|0.991;C|0.009	0.009	strong		0.453	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186	
NSUN3	63899	hgsc.bcm.edu	37	3	93845062	93845062	+	Missense_Mutation	SNP	A	A	G	rs61730354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:93845062A>G	ENST00000314622.4	+	6	962	c.751A>G	c.(751-753)Att>Gtt	p.I251V		NM_022072.3	NP_071355.1	Q9H649	NSUN3_HUMAN	NOP2/Sun domain family, member 3	251							methyltransferase activity (GO:0008168)|RNA binding (GO:0003723)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|skin(1)	18						CAGGTCTGCAATTAAGGCCTT	0.388													A|||	89	0.0177716	0.0537	0.0115	5008	,	,		18150	0.0		0.007	False		,,,				2504	0.0031				p.I251V		Atlas-SNP	.											.	NSUN3	33	.	0			c.A751G						PASS	.	A	VAL/ILE	193,4213	120.4+/-158.0	6,181,2016	52.0	49.0	50.0		751	3.3	1.0	3	dbSNP_129	50	93,8507	51.9+/-112.3	0,93,4207	yes	missense	NSUN3	NM_022072.3	29	6,274,6223	GG,GA,AA		1.0814,4.3804,2.199	benign	251/341	93845062	286,12720	2203	4300	6503	SO:0001583	missense	63899	exon6			TCTGCAATTAAGG	BC020602	CCDS2927.1	3q11.2	2009-11-23	2009-11-23		ENSG00000178694	ENSG00000178694		"""NOP2/Sun domain containing"""	26208	protein-coding gene	gene with protein product			"""NOL1/NOP2/Sun domain family 3"", ""NOL1/NOP2/Sun domain family, member 3"""			12477932	Standard	NM_022072		Approved	FLJ22609	uc003drl.1	Q9H649	OTTHUMG00000159025	ENST00000314622.4:c.751A>G	3.37:g.93845062A>G	ENSP00000318986:p.Ile251Val	124.0	0.0	0		150.0	82.0	0.546667	NM_022072	Q6PG41|Q8IXG9|Q9H6M2	Missense_Mutation	SNP	ENST00000314622.4	37	CCDS2927.1	25	0.011446886446886446	18	0.036585365853658534	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	A	9.012	0.982684	0.18889	0.043804	0.010814	ENSG00000178694	ENST00000314622	T	0.25579	1.79	5.64	3.29	0.37713	Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p (1);	0.121362	0.64402	D	0.000015	T	0.03136	0.0092	N	0.17723	0.515	0.35580	D	0.806204	B	0.21821	0.061	B	0.23574	0.047	T	0.16453	-1.0402	10	0.25751	T	0.34	-12.7984	7.4732	0.27361	0.6633:0.0:0.3367:0.0	rs61730354	251	Q9H649	NSUN3_HUMAN	V	251	ENSP00000318986:I251V	ENSP00000318986:I251V	I	+	1	0	NSUN3	95327752	0.993000	0.37304	1.000000	0.80357	0.720000	0.41350	0.754000	0.26390	0.964000	0.38108	0.377000	0.23210	ATT	A|0.982;G|0.018	0.018	strong		0.388	NSUN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352934.1	NM_022072	
PRICKLE1	144165	hgsc.bcm.edu	37	12	42862431	42862431	+	Silent	SNP	G	G	A	rs74081707	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:42862431G>A	ENST00000455697.1	-	5	870	c.585C>T	c.(583-585)gaC>gaT	p.D195D	PRICKLE1_ENST00000548696.1_Silent_p.D195D|RP11-328C8.4_ENST00000547824.1_RNA|PRICKLE1_ENST00000345127.3_Silent_p.D195D|PRICKLE1_ENST00000552240.1_Silent_p.D195D|PRICKLE1_ENST00000445766.2_Silent_p.D195D	NM_001144882.1|NM_001144883.1	NP_001138354.1|NP_001138355.1	Q96MT3	PRIC1_HUMAN	prickle homolog 1 (Drosophila)	195	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cardiac muscle cell myoblast differentiation (GO:2000691)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination (GO:0031398)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|liver(1)|lung(13)|ovary(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	47	all_cancers(12;4.25e-05)|Breast(8;0.176)			GBM - Glioblastoma multiforme(48;0.2)		TTTTTACCTCGTCACATGCTG	0.403													G|||	153	0.0305511	0.1097	0.0115	5008	,	,		20234	0.0		0.0	False		,,,				2504	0.0				p.D195D		Atlas-SNP	.											.	PRICKLE1	105	.	0			c.C585T						PASS	.	G	,,,	477,3929	223.9+/-240.3	23,431,1749	82.0	82.0	82.0		585,585,585,585	-6.4	0.9	12	dbSNP_130	82	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRICKLE1	NM_001144881.1,NM_001144882.1,NM_001144883.1,NM_153026.2	,,,	23,434,6046	AA,AG,GG		0.0349,10.8261,3.6906	,,,	195/832,195/832,195/832,195/832	42862431	480,12526	2203	4300	6503	SO:0001819	synonymous_variant	144165	exon5			TACCTCGTCACAT	AK056499	CCDS8742.1	12p11-q12	2010-08-13	2006-09-12			ENSG00000139174			17019	protein-coding gene	gene with protein product		608500	"""prickle-like 1 (Drosophila)"""			12525887, 18976727	Standard	NM_153026		Approved	FLJ31937, EPM1B	uc010skv.2	Q96MT3		ENST00000455697.1:c.585C>T	12.37:g.42862431G>A		90.0	0.0	0		81.0	45.0	0.555556	NM_001144882	Q14C83|Q71QF8|Q96N00	Silent	SNP	ENST00000455697.1	37	CCDS8742.1																																																																																			G|0.967;A|0.033	0.033	strong		0.403	PRICKLE1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404069.1		
C5orf42	65250	hgsc.bcm.edu	37	5	37244669	37244669	+	Silent	SNP	C	C	T	rs73750958	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37244669C>T	ENST00000508244.1	-	4	471	c.378G>A	c.(376-378)ggG>ggA	p.G126G	C5orf42_ENST00000274258.7_5'UTR|RN7SL37P_ENST00000490461.2_RNA|C5orf42_ENST00000425232.2_Silent_p.G126G			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	126						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			CAATTCTTTTCCCATTTCCAG	0.348													C|||	153	0.0305511	0.1127	0.0043	5008	,	,		18071	0.0		0.001	False		,,,				2504	0.0				p.G126G		Atlas-SNP	.											.	C5orf42	422	.	0			c.G378A						PASS	.	C		145,1239		8,129,555	70.0	61.0	64.0		378	1.9	1.0	5	dbSNP_130	64	0,3182		0,0,1591	no	coding-synonymous	C5orf42	NM_023073.3		8,129,2146	TT,TC,CC		0.0,10.4769,3.1756		126/3198	37244669	145,4421	692	1591	2283	SO:0001819	synonymous_variant	65250	exon5			TCTTTTCCCATTT		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.378G>A	5.37:g.37244669C>T		157.0	0.0	0		136.0	49.0	0.360294	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Silent	SNP	ENST00000508244.1	37	CCDS34146.2																																																																																			C|0.980;T|0.020	0.020	strong		0.348	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073	
PPCS	79717	hgsc.bcm.edu	37	1	42925501	42925501	+	Silent	SNP	A	A	G	rs142078638	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:42925501A>G	ENST00000372561.3	+	3	847	c.840A>G	c.(838-840)ctA>ctG	p.L280L	PPCS_ENST00000372556.3_3'UTR|PPCS_ENST00000372562.1_Silent_p.L107L|PPCS_ENST00000455780.1_Silent_p.L107L|PPCS_ENST00000472013.1_3'UTR	NM_024664.2	NP_078940.2	Q9HAB8	PPCS_HUMAN	phosphopantothenoylcysteine synthetase	280					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)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	phosphopantothenate--cysteine ligase activity (GO:0004632)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|skin(3)	12	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0333)				AGTTATTGCTATCAGAGGAAG	0.388													A|||	6	0.00119808	0.0015	0.0	5008	,	,		17283	0.004		0.0	False		,,,				2504	0.0				p.L280L		Atlas-SNP	.											.	PPCS	30	.	0			c.A840G						PASS	.	A	,	7,3669		0,7,1831	102.0	98.0	99.0		321,840	-10.5	0.6	1	dbSNP_134	99	0,8184		0,0,4092	no	coding-synonymous,coding-synonymous	PPCS	NM_001077447.1,NM_024664.2	,	0,7,5923	GG,GA,AA		0.0,0.1904,0.059	,	107/139,280/312	42925501	7,11853	1838	4092	5930	SO:0001819	synonymous_variant	79717	exon3			ATTGCTATCAGAG	AK021900	CCDS41311.1, CCDS41312.1	1p34.2	2008-02-05			ENSG00000127125	ENSG00000127125	6.3.2.5		25686	protein-coding gene	gene with protein product		609853				11923312	Standard	NM_024664		Approved	FLJ11838	uc001chl.3	Q9HAB8	OTTHUMG00000007332	ENST00000372561.3:c.840A>G	1.37:g.42925501A>G		139.0	0.0	0		123.0	56.0	0.455285	NM_024664	Q3KQT2|Q5VVM0	Silent	SNP	ENST00000372561.3	37	CCDS41311.1																																																																																			A|0.998;G|0.002	0.002	strong		0.388	PPCS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019166.1	NM_024664	
NSUN5	55695	hgsc.bcm.edu	37	7	72719048	72719048	+	Missense_Mutation	SNP	G	G	A	rs34913552	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:72719048G>A	ENST00000252594.6	-	5	562	c.547C>T	c.(547-549)Ccc>Tcc	p.P183S	NSUN5_ENST00000310326.8_Missense_Mutation_p.P183S|NSUN5_ENST00000438747.2_Missense_Mutation_p.P183S|NSUN5_ENST00000428206.1_Missense_Mutation_p.P145S			Q96P11	NSUN5_HUMAN	NOP2/Sun domain family, member 5	183			P -> S (in dbSNP:rs34913552).		rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|large_intestine(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	8		Lung NSC(55;0.163)				GGCATCAAGGGGTCCAGGAGA	0.567													g|||	189	0.0377396	0.1377	0.0101	5008	,	,		19720	0.0		0.0	False		,,,				2504	0.0				p.P183S		Atlas-SNP	.											.	NSUN5	47	.	0			c.C547T						PASS	.	A	SER/PRO,SER/PRO,SER/PRO,SER/PRO	445,3961	174.4+/-204.0	16,413,1774	19.0	20.0	20.0		547,433,547,547	-2.3	0.1	7	dbSNP_126	20	1,8579		0,1,4289	no	missense,missense,missense,missense	NSUN5	NM_001168347.1,NM_001168348.1,NM_018044.3,NM_148956.2	74,74,74,74	16,414,6063	AA,AG,GG		0.0117,10.0999,3.4345	benign,benign,benign,benign	183/471,145/392,183/430,183/467	72719048	446,12540	2203	4290	6493	SO:0001583	missense	55695	exon5			TCAAGGGGTCCAG	AF420249	CCDS5546.1, CCDS5547.1, CCDS55118.1, CCDS55119.1	7q11.23	2010-04-08	2009-11-23	2005-01-14	ENSG00000130305	ENSG00000130305		"""NOP2/Sun domain containing"""	16385	protein-coding gene	gene with protein product	"""NOP2/Sun domain family, member 5A"""	615732	"""Williams Beuren syndrome chromosome region 20A"", ""NOL1/NOP2/Sun domain family, member 5"""	WBSCR20, WBSCR20A		11978965, 12073013	Standard	NM_148956		Approved	NOL1R, p120, (NOL1), FLJ10267, NSUN5A, Ynl022cL	uc011kev.2	Q96P11	OTTHUMG00000129869	ENST00000252594.6:c.547C>T	7.37:g.72719048G>A	ENSP00000252594:p.Pro183Ser	568.0	0.0	0		496.0	155.0	0.3125	NM_148956	B3KX04|B4DP79|G3V0G9|Q6ZUI8|Q96HT9|Q9NW70	Missense_Mutation	SNP	ENST00000252594.6	37	CCDS5547.1	70	0.03205128205128205	59	0.11991869918699187	4	0.011049723756906077	3	0.005244755244755245	4	0.005277044854881266	g	0.011	-1.725772	0.00694	0.100999	1.17E-4	ENSG00000130305	ENST00000428206;ENST00000252594;ENST00000438747;ENST00000310326	T;T;T;T	0.09911	2.93;2.93;2.93;2.93	4.31	-2.31	0.06765	.	0.500976	0.23395	N	0.048648	T	0.00144	0.0004	M	0.69463	2.115	0.09310	N	1	B;B;B;B	0.23185	0.002;0.066;0.081;0.017	B;B;B;B	0.20384	0.01;0.029;0.021;0.018	T	0.42189	-0.9466	10	0.13853	T	0.58	.	7.9291	0.29891	0.3346:0.1027:0.5626:0.0	rs34913552	183;145;183;183	B4DP79;G3V0G9;Q96P11;Q96P11-2	.;.;NSUN5_HUMAN;.	S	145;183;183;183	ENSP00000393081:P145S;ENSP00000252594:P183S;ENSP00000388464:P183S;ENSP00000309126:P183S	ENSP00000252594:P183S	P	-	1	0	NSUN5	72356984	0.893000	0.30496	0.076000	0.20297	0.032000	0.12392	0.935000	0.28924	-0.731000	0.04862	-1.478000	0.00992	CCC	G|0.971;A|0.029	0.029	strong		0.567	NSUN5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252113.1	NM_148956	
SLC37A1	54020	hgsc.bcm.edu	37	21	43954850	43954850	+	Missense_Mutation	SNP	G	G	A	rs115669950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:43954850G>A	ENST00000352133.2	+	4	1163	c.181G>A	c.(181-183)Gtc>Atc	p.V61I	SLC37A1_ENST00000398341.3_Missense_Mutation_p.V61I			P57057	GLPT_HUMAN	solute carrier family 37 (glucose-6-phosphate transporter), member 1	61					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	transporter activity (GO:0005215)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|liver(2)|lung(3)	15						TGAAGCTGACGTCAGGTTCAG	0.602													G|||	91	0.0181709	0.0673	0.0029	5008	,	,		19958	0.0		0.0	False		,,,				2504	0.0				p.V61I		Atlas-SNP	.											.	SLC37A1	48	.	0			c.G181A						PASS	.	G	ILE/VAL	215,4191	130.6+/-167.2	6,203,1994	98.0	90.0	93.0		181	1.4	0.0	21	dbSNP_132	93	0,8600		0,0,4300	yes	missense	SLC37A1	NM_018964.3	29	6,203,6294	AA,AG,GG		0.0,4.8797,1.6531	benign	61/534	43954850	215,12791	2203	4300	6503	SO:0001583	missense	54020	exon5			GCTGACGTCAGGT	AJ269529	CCDS13689.1	21q22.3	2013-07-17	2013-07-17		ENSG00000160190	ENSG00000160190		"""Solute carriers"""	11024	protein-coding gene	gene with protein product		608094	"""solute carrier family 37 (glycerol-3-phosphate transporter), member 1"""			11112347	Standard	NM_018964		Approved		uc002zbi.3	P57057	OTTHUMG00000086803	ENST00000352133.2:c.181G>A	21.37:g.43954850G>A	ENSP00000344648:p.Val61Ile	101.0	0.0	0		118.0	68.0	0.576271	NM_018964	D3DSJ7|Q9HAQ1	Missense_Mutation	SNP	ENST00000352133.2	37	CCDS13689.1	22	0.010073260073260074	20	0.04065040650406504	2	0.0055248618784530384	0	0.0	0	0.0	G	3.524	-0.097237	0.07010	0.048797	0.0	ENSG00000160190	ENST00000398341;ENST00000352133	T;T	0.22743	1.94;1.94	4.36	1.44	0.22558	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.175660	0.06063	N	0.658658	T	0.01353	0.0044	N	0.08118	0	0.09310	N	1	B	0.14012	0.009	B	0.10450	0.005	T	0.34428	-0.9829	10	0.22706	T	0.39	-15.6473	2.5906	0.04841	0.1086:0.2627:0.4637:0.165	.	61	P57057	GLPT_HUMAN	I	61	ENSP00000381383:V61I;ENSP00000344648:V61I	ENSP00000344648:V61I	V	+	1	0	SLC37A1	42827919	0.009000	0.17119	0.000000	0.03702	0.010000	0.07245	1.076000	0.30729	0.170000	0.19704	0.655000	0.94253	GTC	G|0.984;A|0.016	0.016	strong		0.602	SLC37A1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195377.1		
RBM19	9904	hgsc.bcm.edu	37	12	114374887	114374887	+	Missense_Mutation	SNP	T	T	A	rs2290787	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:114374887T>A	ENST00000545145.2	-	16	2071	c.1993A>T	c.(1993-1995)Aca>Tca	p.T665S	RBM19_ENST00000392561.3_Missense_Mutation_p.T665S|RP11-780K2.1_ENST00000550206.1_RNA|RBM19_ENST00000261741.5_Missense_Mutation_p.T665S	NM_001146699.1	NP_001140171.1	Q9Y4C8	RBM19_HUMAN	RNA binding motif protein 19	665			T -> A (in dbSNP:rs2290787). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9734811}.		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)	p.T665A(1)		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)					TGTGGGGCTGTGCTGGAGAAG	0.527													C|||	386	0.0770767	0.2731	0.0317	5008	,	,		17578	0.0		0.003	False		,,,				2504	0.0				p.T665S		Atlas-SNP	.											RBM19,NS,carcinoma,0,1	RBM19	117	1	1	Substitution - Missense(1)	stomach(1)	c.A1993T						PASS	.						130.0	129.0	129.0					12																	114374887		2203	4300	6503	SO:0001583	missense	9904	exon16			GGGCTGTGCTGGA	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.1993A>T	12.37:g.114374887T>A	ENSP00000442053:p.Thr665Ser	205.0	0.0	0		188.0	85.0	0.452128	NM_001146699	A8K5X9|Q9BPY6|Q9UFN5	Missense_Mutation	SNP	ENST00000545145.2	37	CCDS9172.1	127	0.05815018315018315	112	0.22764227642276422	13	0.03591160220994475	0	0.0	2	0.002638522427440633	C	8.267	0.812524	0.16537	.	.	ENSG00000122965	ENST00000545145;ENST00000392561;ENST00000261741	T;T;T	0.05025	3.51;3.51;3.51	4.5	-7.42	0.01388	Nucleotide-binding, alpha-beta plait (1);	0.638273	0.16199	N	0.225012	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	0.33701	-0.9858	9	0.08599	T	0.76	0.174	2.1166	0.03715	0.1533:0.1255:0.303:0.4182	rs2290787;rs17856103;rs17856172	665	Q9Y4C8	RBM19_HUMAN	S	665	ENSP00000442053:T665S;ENSP00000376344:T665S;ENSP00000261741:T665S	ENSP00000261741:T665S	T	-	1	0	RBM19	112859270	0.076000	0.21285	0.052000	0.19188	0.226000	0.24999	-0.181000	0.09740	-2.257000	0.00695	-1.557000	0.00889	ACA	A|0.076;C|0.019;T|0.905	0.076	strong		0.527	RBM19-003	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405251.1	NM_016196	
KIAA1731	85459	hgsc.bcm.edu	37	11	93412587	93412587	+	Missense_Mutation	SNP	C	C	T	rs111783199	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:93412587C>T	ENST00000325212.6	+	7	796	c.634C>T	c.(634-636)Cgt>Tgt	p.R212C	KIAA1731_ENST00000411936.1_Missense_Mutation_p.R212C|KIAA1731_ENST00000344196.4_5'UTR			Q9C0D2	K1731_HUMAN	KIAA1731	212						centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)	11		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				GCCAGATGCTCGTTTGGCTGC	0.383													C|||	58	0.0115815	0.0431	0.0014	5008	,	,		16817	0.0		0.0	False		,,,				2504	0.0				p.R212C		Atlas-SNP	.											.	KIAA1731	173	.	0			c.C634T						PASS	.	C	CYS/ARG	33,1351		0,33,659	106.0	105.0	105.0		634	5.3	1.0	11	dbSNP_132	105	0,3182		0,0,1591	yes	missense	KIAA1731	NM_033395.1	180	0,33,2250	TT,TC,CC		0.0,2.3844,0.7227	probably-damaging	212/2602	93412587	33,4533	692	1591	2283	SO:0001583	missense	85459	exon7			GATGCTCGTTTGG	AB051518	CCDS44708.1	11q21	2014-03-11			ENSG00000166004	ENSG00000166004			29366	protein-coding gene	gene with protein product						20844083	Standard	NM_033395		Approved		uc009ywb.1	Q9C0D2	OTTHUMG00000167449	ENST00000325212.6:c.634C>T	11.37:g.93412587C>T	ENSP00000316681:p.Arg212Cys	134.0	0.0	0		132.0	75.0	0.568182	NM_033395	C9J5H9|C9JQY8|Q8N7L4|Q8N919|Q8N9B0|Q96LT8	Missense_Mutation	SNP	ENST00000325212.6	37	CCDS44708.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	C	17.45	3.393403	0.62066	0.023844	0.0	ENSG00000166004	ENST00000325212;ENST00000411936	T;T	0.11821	2.74;2.74	5.29	5.29	0.74685	.	0.165985	0.28889	N	0.013812	T	0.07863	0.0197	N	0.22421	0.69	0.80722	D	1	D	0.63880	0.993	P	0.47705	0.555	T	0.01480	-1.1344	10	0.46703	T	0.11	-2.4017	19.2977	0.94129	0.0:1.0:0.0:0.0	.	212	Q9C0D2	K1731_HUMAN	C	212	ENSP00000316681:R212C;ENSP00000406505:R212C	ENSP00000316681:R212C	R	+	1	0	KIAA1731	93052235	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.205000	0.65186	2.627000	0.88993	0.563000	0.77884	CGT	C|0.995;T|0.005	0.005	strong		0.383	KIAA1731-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000394640.1	NM_033395	
TG	7038	hgsc.bcm.edu	37	8	134108459	134108459	+	Missense_Mutation	SNP	G	G	C	rs61730222	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:134108459G>C	ENST00000220616.4	+	43	7454	c.7414G>C	c.(7414-7416)Gtg>Ctg	p.V2472L	SLA_ENST00000338087.5_Intron|SLA_ENST00000524345.1_Intron|SLA_ENST00000395352.3_Intron|TG_ENST00000542445.1_Missense_Mutation_p.V842L|SLA_ENST00000518565.1_Intron|TG_ENST00000377869.1_Missense_Mutation_p.V2415L|TG_ENST00000519543.1_Missense_Mutation_p.V605L|SLA_ENST00000517648.1_Intron	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	2472					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)		p.V2472M(1)		NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		GCTCCTGGCCGTGAGTGGCCC	0.502													G|||	90	0.0179712	0.0658	0.0043	5008	,	,		21243	0.0		0.0	False		,,,				2504	0.0				p.V2472L		Atlas-SNP	.											TG,colon,carcinoma,0,2	TG	416	2	1	Substitution - Missense(1)	large_intestine(1)	c.G7414C						PASS	.	G	,,LEU/VAL	250,4156	146.9+/-181.5	5,240,1958	171.0	160.0	164.0		,,7414	3.4	1.0	8	dbSNP_129	164	2,8598	1.2+/-3.3	0,2,4298	no	intron,intron,missense	SLA,TG	NM_001045556.2,NM_001045557.2,NM_003235.4	,,32	5,242,6256	CC,CG,GG		0.0233,5.6741,1.9376	,,possibly-damaging	,,2472/2769	134108459	252,12754	2203	4300	6503	SO:0001583	missense	7038	exon43			CTGGCCGTGAGTG	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.7414G>C	8.37:g.134108459G>C	ENSP00000220616:p.Val2472Leu	159.0	0.0	0		181.0	85.0	0.469613	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Missense_Mutation	SNP	ENST00000220616.4	37	CCDS34944.1	42|42	0.019230769230769232|0.019230769230769232	39|39	0.07926829268292683|0.07926829268292683	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	G|G	19.35|19.35	3.810956|3.810956	0.70797|0.70797	0.056741|0.056741	2.33E-4|2.33E-4	ENSG00000042832|ENSG00000042832	ENST00000519178|ENST00000377869;ENST00000543313;ENST00000220616;ENST00000542445;ENST00000519543	.|T;T;T;T	.|0.66815	.|-0.23;-0.23;-0.23;-0.23	5.46|5.46	3.42|3.42	0.39159|0.39159	.|Carboxylesterase, type B (1);	.|0.800184	.|0.11276	.|N	.|0.580893	T|T	0.05318|0.05318	0.0141|0.0141	L|L	0.33137|0.33137	0.985|0.985	0.80722|0.80722	D|D	1|1	.|P;B;P	.|0.45283	.|0.855;0.142;0.526	.|B;B;B	.|0.41571	.|0.36;0.014;0.172	T|T	0.11867|0.11867	-1.0570|-1.0570	5|10	.|0.66056	.|D	.|0.02	.|.	5.3896|5.3896	0.16237|0.16237	0.2809:0.0:0.7191:0.0|0.2809:0.0:0.7191:0.0	rs61730222|rs61730222	.|605;842;2472	.|E7EVM0;F5GWW5;P01266	.|.;.;THYG_HUMAN	P|L	927|2415;1278;2472;842;605	.|ENSP00000367100:V2415L;ENSP00000220616:V2472L;ENSP00000441693:V842L;ENSP00000430430:V605L	.|ENSP00000220616:V2472L	R|V	+|+	2|1	0|0	TG|TG	134177641|134177641	0.999000|0.999000	0.42202|0.42202	0.989000|0.989000	0.46669|0.46669	0.954000|0.954000	0.61252|0.61252	4.049000|4.049000	0.57397|0.57397	1.300000|1.300000	0.44818|0.44818	0.655000|0.655000	0.94253|0.94253	CGT|GTG	G|0.978;C|0.022	0.022	strong		0.502	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
ALOX15B	247	hgsc.bcm.edu	37	17	7942785	7942785	+	Missense_Mutation	SNP	C	C	G	rs78230493	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7942785C>G	ENST00000380183.4	+	2	368	c.229C>G	c.(229-231)Ccc>Gcc	p.P77A	ALOX15B_ENST00000380173.2_Missense_Mutation_p.P77A|ALOX15B_ENST00000572022.1_Missense_Mutation_p.P77A|ALOX15B_ENST00000573359.1_Missense_Mutation_p.P77A	NM_001141.2	NP_001132.2	O15296	LX15B_HUMAN	arachidonate 15-lipoxygenase, type B	77	PLAT. {ECO:0000255|PROSITE- ProRule:PRU00152}.				apoptotic process (GO:0006915)|arachidonic acid metabolic process (GO:0019369)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipid metabolic process (GO:0006629)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostate gland development (GO:0030850)|regulation of epithelial cell differentiation (GO:0030856)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arachidonate 15-lipoxygenase activity (GO:0050473)|arachidonate 8(S)-lipoxygenase activity (GO:0036403)|calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|lipid binding (GO:0008289)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	24						CCCAGTGCTGCCCCTGCTGGG	0.692													C|||	175	0.0349441	0.1241	0.0144	5008	,	,		9830	0.0		0.001	False		,,,				2504	0.0				p.P77A		Atlas-SNP	.											.	ALOX15B	66	.	0			c.C229G						PASS	.	C	ALA/PRO,ALA/PRO,ALA/PRO	282,4080		13,256,1912	8.0	9.0	9.0		229,229,229	-0.4	0.0	17	dbSNP_131	9	3,8557		0,3,4277	no	missense,missense,missense	ALOX15B	NM_001039130.1,NM_001039131.1,NM_001141.2	27,27,27	13,259,6189	GG,GC,CC		0.035,6.4649,2.2055	possibly-damaging,possibly-damaging,possibly-damaging	77/648,77/603,77/677	7942785	285,12637	2181	4280	6461	SO:0001583	missense	247	exon2			GTGCTGCCCCTGC	U78294	CCDS11128.1, CCDS32558.1, CCDS32559.1	17p13.1	2013-03-20	2006-01-16		ENSG00000179593	ENSG00000179593	1.13.11.33	"""Arachidonate lipoxygenases"""	434	protein-coding gene	gene with protein product		603697	"""arachidonate 15-lipoxygenase, second type"""			9177185	Standard	NM_001039130		Approved	15-LOX-2	uc002gju.3	O15296	OTTHUMG00000108181	ENST00000380183.4:c.229C>G	17.37:g.7942785C>G	ENSP00000369530:p.Pro77Ala	29.0	0.0	0		22.0	15.0	0.681818	NM_001141	D3DTR2|Q8IYQ2|Q8TEV3|Q8TEV4|Q8TEV5|Q8TEV6|Q9UKM4	Missense_Mutation	SNP	ENST00000380183.4	37	CCDS11128.1	69	0.03159340659340659	64	0.13008130081300814	5	0.013812154696132596	0	0.0	0	0.0	C	10.09	1.253985	0.22965	0.064649	3.5E-4	ENSG00000179593	ENST00000380173;ENST00000339694;ENST00000380183	T;T	0.20738	2.05;2.05	4.15	-0.36	0.12568	Lipoxygenase, LH2 (4);Lipase/lipooxygenase, PLAT/LH2 (1);	2.042930	0.02987	N	0.146355	T	0.00144	0.0004	N	0.08118	0	0.09310	N	1	B;B;B;B	0.22800	0.075;0.061;0.061;0.075	B;B;B;B	0.29524	0.071;0.043;0.043;0.103	T	0.31806	-0.9930	10	0.40728	T	0.16	-4.4415	7.6122	0.28137	0.0:0.6248:0.0:0.3752	.	77;77;77;77	B4DNW8;O15296-2;O15296-4;O15296	.;.;.;LX15B_HUMAN	A	77	ENSP00000369520:P77A;ENSP00000369530:P77A	ENSP00000344337:P77A	P	+	1	0	ALOX15B	7883510	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-0.527000	0.06200	-0.237000	0.09739	0.591000	0.81541	CCC	C|0.966;G|0.034	0.034	strong		0.692	ALOX15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226985.2		
TMEM104	54868	hgsc.bcm.edu	37	17	72784931	72784931	+	Silent	SNP	C	C	T	rs62638676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:72784931C>T	ENST00000335464.5	+	4	333	c.171C>T	c.(169-171)ttC>ttT	p.F57F	TMEM104_ENST00000582330.1_Silent_p.F57F|TMEM104_ENST00000582773.1_Silent_p.F57F|TMEM104_ENST00000417024.2_Silent_p.F70F	NM_017728.3	NP_060198.3	Q8NE00	TM104_HUMAN	transmembrane protein 104	57						integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(1)	19	all_lung(278;0.23)					CCCTCAGCTTCGTGACCACCA	0.587													c|||	157	0.0313498	0.115	0.0072	5008	,	,		18997	0.0		0.0	False		,,,				2504	0.0				p.F57F		Atlas-SNP	.											.	TMEM104	49	.	0			c.C171T						PASS	.	T		423,3983	206.2+/-227.9	22,379,1802	69.0	59.0	62.0		171	-9.1	0.2	17	dbSNP_129	62	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	TMEM104	NM_017728.3		22,382,6099	TT,TC,CC		0.0349,9.6005,3.2754		57/497	72784931	426,12580	2203	4300	6503	SO:0001819	synonymous_variant	54868	exon4			CAGCTTCGTGACC	AK074029	CCDS32723.1	17q25.1	2005-12-19				ENSG00000109066			25984	protein-coding gene	gene with protein product							Standard	NM_017728		Approved	FLJ20255, FLJ00021	uc002jls.4	Q8NE00		ENST00000335464.5:c.171C>T	17.37:g.72784931C>T		35.0	0.0	0		41.0	15.0	0.365854	NM_017728	Q8TEU1|Q9NT56|Q9NXH1	Silent	SNP	ENST00000335464.5	37	CCDS32723.1																																																																																			C|0.968;T|0.032	0.032	strong		0.587	TMEM104-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444442.1	NM_017728	
LMTK2	22853	hgsc.bcm.edu	37	7	97822990	97822990	+	Silent	SNP	G	G	A	rs56064038	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:97822990G>A	ENST00000297293.5	+	11	3506	c.3213G>A	c.(3211-3213)ccG>ccA	p.P1071P		NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	1071					early endosome to late endosome transport (GO:0045022)|endocytic recycling (GO:0032456)|negative regulation of catalytic activity (GO:0043086)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|myosin VI binding (GO:0070853)|protein phosphatase inhibitor activity (GO:0004864)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3)	59	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					CTCCCAACCCGGTCATTGTCA	0.632													G|||	76	0.0151757	0.0567	0.0014	5008	,	,		17179	0.0		0.0	False		,,,				2504	0.0				p.P1071P		Atlas-SNP	.											.	LMTK2	228	.	0			c.G3213A						PASS	.	G		192,4214	118.8+/-156.5	3,186,2014	34.0	33.0	34.0		3213	-10.7	0.1	7	dbSNP_129	34	3,8597	2.2+/-6.3	0,3,4297	no	coding-synonymous	LMTK2	NM_014916.3		3,189,6311	AA,AG,GG		0.0349,4.3577,1.4993		1071/1504	97822990	195,12811	2203	4300	6503	SO:0001819	synonymous_variant	22853	exon11			CAACCCGGTCATT	AB029002	CCDS5654.1	7q22.1	2014-06-12			ENSG00000164715	ENSG00000164715			17880	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 100"""	610989				15005709	Standard	NM_014916		Approved	KIAA1079, KPI2, KPI-2, cprk, LMR2, BREK, AATYK2, PPP1R100	uc003upd.2	Q8IWU2	OTTHUMG00000154256	ENST00000297293.5:c.3213G>A	7.37:g.97822990G>A		49.0	0.0	0		54.0	25.0	0.462963	NM_014916	A4D272|Q75MG7|Q9UPS3	Silent	SNP	ENST00000297293.5	37	CCDS5654.1																																																																																			G|0.985;A|0.015	0.015	strong		0.632	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334560.1	NM_014916	
SARDH	1757	hgsc.bcm.edu	37	9	136595253	136595253	+	Silent	SNP	C	C	T	rs35457000	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:136595253C>T	ENST00000371872.4	-	5	1004	c.747G>A	c.(745-747)gtG>gtA	p.V249V	SARDH_ENST00000298628.5_Silent_p.V249V|SARDH_ENST00000439388.1_Silent_p.V249V|SARDH_ENST00000371867.1_Silent_p.V160V|SARDH_ENST00000422262.2_Silent_p.V81V	NM_007101.3	NP_009032.2	Q9UL12	SARDH_HUMAN	sarcosine dehydrogenase	249					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|sarcosine dehydrogenase activity (GO:0008480)			central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(13)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	44				OV - Ovarian serous cystadenocarcinoma(145;3.21e-07)|Epithelial(140;2.37e-06)|all cancers(34;2.75e-05)		CGACCCGCCGCACCCCAAAAT	0.577													C|||	82	0.0163738	0.0598	0.0043	5008	,	,		17220	0.0		0.0	False		,,,				2504	0.0				p.V249V		Atlas-SNP	.											.	SARDH	112	.	0			c.G747A						PASS	.	C	,	174,4232	114.6+/-152.6	5,164,2034	92.0	85.0	88.0		747,747	3.1	1.0	9	dbSNP_126	88	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	SARDH	NM_001134707.1,NM_007101.3	,	5,166,6332	TT,TC,CC		0.0233,3.9492,1.3532	,	249/919,249/919	136595253	176,12830	2203	4300	6503	SO:0001819	synonymous_variant	1757	exon5			CCGCCGCACCCCA		CCDS6978.1	9q33-q34	2008-02-05			ENSG00000123453	ENSG00000123453	1.5.99.2		10536	protein-coding gene	gene with protein product		604455		DMGDHL1		10444331	Standard	NM_007101		Approved	SDH	uc004cep.4	Q9UL12	OTTHUMG00000020879	ENST00000371872.4:c.747G>A	9.37:g.136595253C>T		128.0	0.0	0		113.0	40.0	0.353982	NM_007101	B2RMR5|B4DPI2|B7ZLT6|Q5SYV0|Q9Y280|Q9Y2Y3	Silent	SNP	ENST00000371872.4	37	CCDS6978.1																																																																																			C|0.985;T|0.015	0.015	strong		0.577	SARDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054931.1		
EMCN	51705	hgsc.bcm.edu	37	4	101386643	101386643	+	Missense_Mutation	SNP	C	C	T	rs78403369	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:101386643C>T	ENST00000296420.4	-	4	491	c.313G>A	c.(313-315)Gta>Ata	p.V105I	EMCN_ENST00000511970.1_Missense_Mutation_p.V105I|EMCN_ENST00000305864.3_Missense_Mutation_p.V105I|EMCN_ENST00000502327.1_5'UTR	NM_001159694.1|NM_016242.3	NP_001153166.1|NP_057326.2	Q9ULC0	MUCEN_HUMAN	endomucin	105	Thr-rich.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)	13				OV - Ovarian serous cystadenocarcinoma(123;2.49e-08)		GTTACTGTTACGTTTGAAATG	0.363													C|||	82	0.0163738	0.0582	0.0043	5008	,	,		18744	0.0		0.002	False		,,,				2504	0.0				p.V105I		Atlas-SNP	.											.	EMCN	37	.	0			c.G313A						PASS	.	C	ILE/VAL,ILE/VAL	256,4150	146.1+/-180.8	8,240,1955	193.0	169.0	177.0		313,313	-5.4	0.0	4	dbSNP_132	177	32,8568	21.0+/-64.5	0,32,4268	yes	missense,missense	EMCN	NM_001159694.1,NM_016242.3	29,29	8,272,6223	TT,TC,CC		0.3721,5.8103,2.2144	possibly-damaging,possibly-damaging	105/249,105/262	101386643	288,12718	2203	4300	6503	SO:0001583	missense	51705	exon4			CTGTTACGTTTGA	AF205940	CCDS3655.1, CCDS54782.1	4q22.1	2008-02-05			ENSG00000164035	ENSG00000164035		"""Mucins"""	16041	protein-coding gene	gene with protein product		608350				11418125, 11594763	Standard	NM_016242		Approved	MUC14	uc003hvr.3	Q9ULC0	OTTHUMG00000131051	ENST00000296420.4:c.313G>A	4.37:g.101386643C>T	ENSP00000296420:p.Val105Ile	127.0	0.0	0		132.0	65.0	0.492424	NM_001159694	A8K716|B4E347|Q8NEY5|Q8WWE7|Q9NRM8	Missense_Mutation	SNP	ENST00000296420.4	37	CCDS3655.1	37	0.01694139194139194	33	0.06707317073170732	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	5.591	0.293797	0.10567	0.058103	0.003721	ENSG00000164035	ENST00000296420;ENST00000305864;ENST00000506300;ENST00000511970;ENST00000502569	.	.	.	3.93	-5.39	0.02664	.	5.984870	0.00541	N	0.000223	T	0.01695	0.0054	N	0.08118	0	0.09310	N	1	B;B;B	0.25667	0.107;0.131;0.131	B;B;B	0.17098	0.01;0.017;0.017	T	0.06481	-1.0824	9	0.19590	T	0.45	0.1434	13.3485	0.60589	0.0:0.2287:0.0:0.7713	.	105;105;105	Q9ULC0-2;B4E347;Q9ULC0	.;.;MUCEN_HUMAN	I	105;105;32;105;105	.	ENSP00000296420:V105I	V	-	1	0	EMCN	101605666	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.676000	0.00840	-1.586000	0.01632	-0.150000	0.13652	GTA	C|0.980;T|0.020	0.020	strong		0.363	EMCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253699.2	NM_016242	
FBN1	2200	hgsc.bcm.edu	37	15	48734008	48734008	+	Missense_Mutation	SNP	C	C	A	rs113577372	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:48734008C>A	ENST00000316623.5	-	50	6528	c.6073G>T	c.(6073-6075)Gcc>Tcc	p.A2025S		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	2025	EGF-like 35; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|kidney development (GO:0001822)|sequestering of BMP in extracellular matrix (GO:0035582)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|skeletal system development (GO:0001501)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(5)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|liver(1)|lung(49)|ovary(4)|pancreas(1)|prostate(9)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	139		all_lung(180;0.00279)		all cancers(107;4.24e-07)|GBM - Glioblastoma multiforme(94;1.41e-05)		GTGCCCAGGGCACAAATTTCT	0.448													C|||	10	0.00199681	0.0076	0.0	5008	,	,		19650	0.0		0.0	False		,,,				2504	0.0				p.A2025S		Atlas-SNP	.											.	FBN1	310	.	0			c.G6073T						PASS	.	C	SER/ALA	21,4375	29.0+/-57.7	0,21,2177	137.0	135.0	136.0		6073	5.9	1.0	15	dbSNP_132	136	0,8592		0,0,4296	yes	missense	FBN1	NM_000138.4	99	0,21,6473	AA,AC,CC		0.0,0.4777,0.1617	possibly-damaging	2025/2872	48734008	21,12967	2198	4296	6494	SO:0001583	missense	2200	exon50			CCAGGGCACAAAT	X63556	CCDS32232.1	15q21.1	2014-09-17	2006-04-25			ENSG00000166147			3603	protein-coding gene	gene with protein product	"""Marfan syndrome"""	134797	"""fibrillin 1 (Marfan syndrome)"""	FBN, MFS1, WMS		10036187, 12525539	Standard	NM_000138		Approved	MASS, OCTD, SGS	uc001zwx.2	P35555		ENST00000316623.5:c.6073G>T	15.37:g.48734008C>A	ENSP00000325527:p.Ala2025Ser	59.0	0.0	0		68.0	34.0	0.5	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Missense_Mutation	SNP	ENST00000316623.5	37	CCDS32232.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	C	12.59	1.982249	0.34942	0.004777	0.0	ENSG00000166147	ENST00000316623;ENST00000389087;ENST00000544030	D	0.91996	-2.95	5.94	5.94	0.96194	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.098253	0.64402	D	0.000001	T	0.77552	0.4147	N	0.01800	-0.715	0.80722	D	1	B	0.25850	0.136	B	0.29942	0.109	T	0.76753	-0.2843	10	0.17832	T	0.49	.	19.9452	0.97179	0.0:1.0:0.0:0.0	.	2025	P35555	FBN1_HUMAN	S	2025;593;915	ENSP00000325527:A2025S	ENSP00000325527:A2025S	A	-	1	0	FBN1	46521300	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.864000	0.39469	2.807000	0.96579	0.650000	0.86243	GCC	C|0.998;A|0.002	0.002	strong		0.448	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1		
INADL	10207	hgsc.bcm.edu	37	1	62393420	62393420	+	Missense_Mutation	SNP	C	C	T	rs61743112	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:62393420C>T	ENST00000371158.2	+	27	3703	c.3589C>T	c.(3589-3591)Ccg>Tcg	p.P1197S	INADL_ENST00000316485.6_Missense_Mutation_p.P1197S	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	1197					cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						AACTGCTCCACCGCCAATGAA	0.398													C|||	199	0.0397364	0.1415	0.0173	5008	,	,		17651	0.0		0.0	False		,,,				2504	0.0				p.P1197S		Atlas-SNP	.											.	INADL	179	.	0			c.C3589T						PASS	.	C	SER/PRO	478,3928	224.9+/-240.9	21,436,1746	102.0	94.0	97.0		3589	4.4	0.6	1	dbSNP_129	97	2,8598	2.2+/-6.3	0,2,4298	yes	missense	INADL	NM_176877.2	74	21,438,6044	TT,TC,CC		0.0233,10.8488,3.6906	possibly-damaging	1197/1802	62393420	480,12526	2203	4300	6503	SO:0001583	missense	10207	exon27			GCTCCACCGCCAA	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.3589C>T	1.37:g.62393420C>T	ENSP00000360200:p.Pro1197Ser	84.0	0.0	0		90.0	45.0	0.5	NM_176877	O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Missense_Mutation	SNP	ENST00000371158.2	37	CCDS617.2	86	0.039377289377289376	81	0.16463414634146342	5	0.013812154696132596	0	0.0	0	0.0	C	11.14	1.550134	0.27652	0.108488	2.33E-4	ENSG00000132849	ENST00000371158;ENST00000316485;ENST00000371156;ENST00000395513	T;T	0.16073	2.44;2.37	4.45	4.45	0.53987	.	0.000000	0.64402	D	0.000002	T	0.00144	0.0004	M	0.74258	2.255	0.09310	P	1.0	D;P;D	0.89917	0.959;0.726;1.0	P;B;D	0.79108	0.897;0.205;0.992	T	0.09335	-1.0679	9	0.08381	T	0.77	.	12.8308	0.57744	0.0:1.0:0.0:0.0	rs61743112	1197;1197;1197	F8W8T2;Q8NI35;Q8NI35-4	.;INADL_HUMAN;.	S	1197	ENSP00000360200:P1197S;ENSP00000326199:P1197S	ENSP00000326199:P1197S	P	+	1	0	INADL	62166008	0.949000	0.32298	0.641000	0.29422	0.012000	0.07955	3.927000	0.56499	2.465000	0.83290	0.650000	0.86243	CCG	C|0.959;T|0.041	0.041	strong		0.398	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
ZNF594	84622	hgsc.bcm.edu	37	17	5085806	5085806	+	Silent	SNP	G	G	A	rs114624606	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:5085806G>A	ENST00000399604.4	-	1	1886	c.1746C>T	c.(1744-1746)gaC>gaT	p.D582D	ZNF594_ENST00000575779.1_Silent_p.D582D			Q96JF6	ZN594_HUMAN	zinc finger protein 594	582					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(3)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	33						GTCTGATGAGGTCTGAGCTGC	0.453																																					p.D582D		Atlas-SNP	.											.	ZNF594	89	.	0			c.C1746T						PASS	.	G		95,3919		4,87,1916	149.0	144.0	145.0		1746	-2.1	0.0	17	dbSNP_132	145	1,8411		0,1,4205	no	coding-synonymous	ZNF594	NM_032530.1		4,88,6121	AA,AG,GG		0.0119,2.3667,0.7726		582/808	5085806	96,12330	2007	4206	6213	SO:0001819	synonymous_variant	84622	exon2			GATGAGGTCTGAG	AB058774	CCDS42241.1	17p13	2013-01-08			ENSG00000180626	ENSG00000180626		"""Zinc fingers, C2H2-type"""	29392	protein-coding gene	gene with protein product						11347906	Standard	NM_032530		Approved	KIAA1871	uc010cla.1	Q96JF6	OTTHUMG00000132059	ENST00000399604.4:c.1746C>T	17.37:g.5085806G>A		124.0	0.0	0		112.0	47.0	0.419643	NM_032530	Q6RFS0	Silent	SNP	ENST00000399604.4	37	CCDS42241.1																																																																																			G|0.990;A|0.010	0.010	strong		0.453	ZNF594-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438996.1	XM_290737	
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84683428	84683428	+	Missense_Mutation	SNP	A	A	G	rs17158450	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:84683428A>G	ENST00000286744.5	+	24	4332	c.4108A>G	c.(4108-4110)Acc>Gcc	p.T1370A	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.T1370A	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	1370	Ig-like C2-type 3.		T -> A (in dbSNP:rs17158450).			proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			CTGCATAGCCACCAATGCTCT	0.443													A|||	240	0.0479233	0.1717	0.0187	5008	,	,		20971	0.0		0.0	False		,,,				2504	0.0				p.T1370A		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.A4108G						PASS	.	A	ALA/THR	680,3726	286.6+/-278.8	50,580,1573	134.0	125.0	128.0		4108	2.7	1.0	15	dbSNP_123	128	7,8591	6.4+/-24.3	0,7,4292	yes	missense	ADAMTSL3	NM_207517.2	58	50,587,5865	GG,GA,AA		0.0814,15.4335,5.283	benign	1370/1692	84683428	687,12317	2203	4299	6502	SO:0001583	missense	57188	exon24			ATAGCCACCAATG	AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.4108A>G	15.37:g.84683428A>G	ENSP00000286744:p.Thr1370Ala	122.0	0.0	0		159.0	63.0	0.396226	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	94	0.04304029304029304	86	0.17479674796747968	8	0.022099447513812154	0	0.0	0	0.0	A	2.759	-0.258227	0.05791	0.154335	8.14E-4	ENSG00000156218	ENST00000286744	T	0.68903	-0.36	5.03	2.73	0.32206	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.188900	0.26149	N	0.026056	T	0.00210	0.0006	L	0.46741	1.465	0.30564	P	0.7641979999999999	B;B	0.17465	0.002;0.022	B;B	0.19946	0.01;0.027	T	0.06991	-1.0796	9	0.10111	T	0.7	.	8.0282	0.30448	0.7665:0.0:0.2335:0.0	rs17158450;rs52789838;rs17158450	1370;1370	P82987-2;P82987	.;ATL3_HUMAN	A	1370	ENSP00000286744:T1370A	ENSP00000286744:T1370A	T	+	1	0	ADAMTSL3	82474432	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	1.012000	0.29924	0.760000	0.33108	0.454000	0.30748	ACC	A|0.943;G|0.057	0.057	strong		0.443	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
CWF19L1	55280	hgsc.bcm.edu	37	10	101993024	101993024	+	Missense_Mutation	SNP	C	C	T	rs7922946	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:101993024C>T	ENST00000354105.4	-	14	1663	c.1577G>A	c.(1576-1578)cGg>cAg	p.R526Q	CWF19L1_ENST00000370379.1_Missense_Mutation_p.R241Q|CWF19L1_ENST00000478047.1_5'UTR|RP11-316M21.6_ENST00000444359.1_RNA	NM_018294.4	NP_060764.3	Q69YN2	C19L1_HUMAN	CWF19-like 1, cell cycle control (S. pombe)	526			R -> Q (in dbSNP:rs7922946).				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)		AAAGTCTTTCCGGAAGCGGCG	0.448													C|||	34	0.00678914	0.0257	0.0	5008	,	,		16484	0.0		0.0	False		,,,				2504	0.0				p.R526Q		Atlas-SNP	.											.	CWF19L1	39	.	0			c.G1577A						PASS	.	C	GLN/ARG	107,4299	83.4+/-121.9	1,105,2097	85.0	90.0	88.0		1577	2.5	1.0	10	dbSNP_116	88	0,8600		0,0,4300	yes	missense	CWF19L1	NM_018294.4	43	1,105,6397	TT,TC,CC		0.0,2.4285,0.8227	probably-damaging	526/539	101993024	107,12899	2203	4300	6503	SO:0001583	missense	55280	exon14			TCTTTCCGGAAGC	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.1577G>A	10.37:g.101993024C>T	ENSP00000326411:p.Arg526Gln	105.0	0.0	0		77.0	33.0	0.428571	NM_018294	B4DHX1|D3DR66|Q5W0I3|Q96HC3|Q9H865|Q9NV13	Missense_Mutation	SNP	ENST00000354105.4	37	CCDS7489.1	6	0.0027472527472527475	6	0.012195121951219513	0	0.0	0	0.0	0	0.0	C	21.5	4.159440	0.78226	0.024285	0.0	ENSG00000095485	ENST00000354105;ENST00000370379	T;T	0.30714	1.52;1.52	5.38	2.55	0.30701	Histidine triad motif (1);Cwf19-like protein, C-terminal domain-2 (1);	0.099847	0.64402	N	0.000004	T	0.31104	0.0786	M	0.79475	2.455	0.43168	D	0.994968	P;D;D	0.76494	0.815;0.993;0.999	B;P;P	0.60173	0.394;0.596;0.87	T	0.19063	-1.0317	10	0.41790	T	0.15	-3.3822	9.1705	0.37078	0.0:0.7604:0.0:0.2396	rs7922946;rs7922946	230;389;526	Q69YN2-2;Q69YN2-3;Q69YN2	.;.;C19L1_HUMAN	Q	526;241	ENSP00000326411:R526Q;ENSP00000359405:R241Q	ENSP00000326411:R526Q	R	-	2	0	CWF19L1	101983014	1.000000	0.71417	0.999000	0.59377	0.652000	0.38707	4.389000	0.59639	0.262000	0.21774	-0.219000	0.12488	CGG	C|0.993;T|0.007	0.007	strong		0.448	CWF19L1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018294	
SRF	6722	hgsc.bcm.edu	37	6	43146105	43146105	+	Silent	SNP	G	G	T	rs140883192	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:43146105G>T	ENST00000265354.4	+	5	1594	c.1236G>T	c.(1234-1236)ccG>ccT	p.P412P	SRF_ENST00000457278.2_Silent_p.P208P	NM_003131.2	NP_003122.1	P11831	SRF_HUMAN	serum response factor (c-fos serum response element-binding transcription factor)	412					angiogenesis involved in wound healing (GO:0060055)|associative learning (GO:0008306)|cardiac myofibril assembly (GO:0055003)|cardiac vascular smooth muscle cell differentiation (GO:0060947)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-matrix adhesion (GO:0007160)|cellular response to glucose stimulus (GO:0071333)|cellular senescence (GO:0090398)|contractile actin filament bundle assembly (GO:0030038)|developmental growth (GO:0048589)|dorsal aorta morphogenesis (GO:0035912)|epithelial cell-cell adhesion (GO:0090136)|epithelial structure maintenance (GO:0010669)|erythrocyte development (GO:0048821)|eyelid development in camera-type eye (GO:0061029)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula formation (GO:0060347)|hematopoietic stem cell differentiation (GO:0060218)|hippocampus development (GO:0021766)|long term synaptic depression (GO:0060292)|long-term memory (GO:0007616)|megakaryocyte development (GO:0035855)|mesoderm formation (GO:0001707)|morphogenesis of an epithelial sheet (GO:0002011)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|neuron development (GO:0048666)|neuron migration (GO:0001764)|neuron projection development (GO:0031175)|patterning of blood vessels (GO:0001569)|platelet activation (GO:0030168)|platelet formation (GO:0030220)|positive regulation of cell differentiation (GO:0045597)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of transcription by glucose (GO:0046016)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription via serum response element binding (GO:0010735)|positive thymic T cell selection (GO:0045059)|primitive streak formation (GO:0090009)|regulation of cell adhesion (GO:0030155)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of water loss via skin (GO:0033561)|response to cytokine (GO:0034097)|response to hormone (GO:0009725)|response to hypoxia (GO:0001666)|response to toxic substance (GO:0009636)|sarcomere organization (GO:0045214)|skin morphogenesis (GO:0043589)|stress fiber assembly (GO:0043149)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)|tight junction assembly (GO:0070830)|transcription from RNA polymerase II promoter (GO:0006366)|trophectodermal cell differentiation (GO:0001829)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|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 distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II transcription factor binding transcription factor activity (GO:0001076)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|serum response element binding (GO:0010736)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	12			Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.011)|OV - Ovarian serous cystadenocarcinoma(102;0.0423)			ACCCTAGCCCGCATGCGGTGA	0.607													G|||	31	0.0061901	0.0219	0.0014	5008	,	,		20467	0.0		0.001	False		,,,				2504	0.0				p.P412P		Atlas-SNP	.											.	SRF	24	.	0			c.G1236T						PASS	.	G		57,4349	55.5+/-91.7	0,57,2146	102.0	75.0	84.0		1236	4.7	1.0	6	dbSNP_134	84	0,8600		0,0,4300	no	coding-synonymous	SRF	NM_003131.2		0,57,6446	TT,TG,GG		0.0,1.2937,0.4383		412/509	43146105	57,12949	2203	4300	6503	SO:0001819	synonymous_variant	6722	exon5			TAGCCCGCATGCG	J03161	CCDS4889.1	6p	2008-02-05			ENSG00000112658	ENSG00000112658			11291	protein-coding gene	gene with protein product		600589				3203386	Standard	NM_003131		Approved	MCM1	uc003oui.3	P11831	OTTHUMG00000014722	ENST00000265354.4:c.1236G>T	6.37:g.43146105G>T		57.0	0.0	0		63.0	28.0	0.444444	NM_003131	Q5T648	Silent	SNP	ENST00000265354.4	37	CCDS4889.1																																																																																			G|0.997;T|0.003	0.003	strong		0.607	SRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040581.1	NM_003131	
CARD14	79092	hgsc.bcm.edu	37	17	78176193	78176193	+	Silent	SNP	G	G	A	rs35692270	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78176193G>A	ENST00000573882.1	+	17	2729	c.2193G>A	c.(2191-2193)gcG>gcA	p.A731A	RP11-334C17.5_ENST00000576824.1_RNA|CARD14_ENST00000392434.2_3'UTR|RP11-334C17.5_ENST00000573935.1_RNA|RP11-334C17.5_ENST00000572730.1_RNA|RP11-334C17.5_ENST00000573346.1_RNA|RP11-334C17.5_ENST00000570309.1_RNA|CARD14_ENST00000570421.1_Silent_p.A731A|CARD14_ENST00000344227.2_Silent_p.A731A			Q9BXL6	CAR14_HUMAN	caspase recruitment domain family, member 14	731					activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein phosphorylation (GO:0001934)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)			NS(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(11)|ovary(5)|prostate(1)|skin(1)	23	all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.017)|BRCA - Breast invasive adenocarcinoma(99;0.0908)			ATACTGCCGCGCACGGCACCA	0.632													G|||	32	0.00638978	0.0227	0.0029	5008	,	,		17093	0.0		0.0	False		,,,				2504	0.0				p.A731A		Atlas-SNP	.											.	CARD14	98	.	0			c.G2193A						PASS	.	G		115,4291	88.2+/-126.9	2,111,2090	51.0	41.0	44.0		2193	-4.0	0.0	17	dbSNP_126	44	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	CARD14	NM_024110.3		2,114,6387	AA,AG,GG		0.0349,2.6101,0.9073		731/1005	78176193	118,12888	2203	4300	6503	SO:0001819	synonymous_variant	79092	exon15			TGCCGCGCACGGC	AF322642	CCDS11768.1, CCDS58605.1	17q25.3	2014-09-04			ENSG00000141527	ENSG00000141527			16446	protein-coding gene	gene with protein product		607211	"""psoriasis susceptibility 2"""	PSORS2		11278692, 11356195, 22521418	Standard	NM_052819		Approved	CARMA2, BIMP2	uc031res.1	Q9BXL6	OTTHUMG00000177549	ENST00000573882.1:c.2193G>A	17.37:g.78176193G>A		70.0	0.0	0		78.0	35.0	0.448718	NM_024110	B8QQJ3|Q9BVB5	Silent	SNP	ENST00000573882.1	37	CCDS11768.1																																																																																			G|0.992;A|0.008	0.008	strong		0.632	CARD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437507.1		
RTP5	285093	hgsc.bcm.edu	37	2	242815157	242815157	+	Missense_Mutation	SNP	C	C	T	rs77317868	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242815157C>T	ENST00000343216.3	+	2	1478	c.1450C>T	c.(1450-1452)Cgc>Tgc	p.R484C		NM_173821.2	NP_776182.2																					TGTCATAAAGCGCAAGGGCGG	0.627													C|||	168	0.0335463	0.121	0.0086	5008	,	,		15580	0.0		0.002	False		,,,				2504	0.0				p.R484C		Atlas-SNP	.											.	.	.	.	0			c.C1450T						PASS	.	C	CYS/ARG	469,3695		27,415,1640	69.0	80.0	76.0		1450	-3.6	0.0	2	dbSNP_131	76	4,8400		0,4,4198	yes	missense	C2orf85	NM_173821.2	180	27,419,5838	TT,TC,CC		0.0476,11.2632,3.7635	benign	484/573	242815157	473,12095	2082	4202	6284	SO:0001583	missense	285093	exon2			ATAAAGCGCAAGG																												ENST00000343216.3:c.1450C>T	2.37:g.242815157C>T	ENSP00000345374:p.Arg484Cys	76.0	0.0	0		73.0	36.0	0.493151	NM_173821		Missense_Mutation	SNP	ENST00000343216.3	37	CCDS42843.1	49	0.022435897435897436	44	0.08943089430894309	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	.	7.258	0.604519	0.14002	0.112632	4.76E-4	ENSG00000188011	ENST00000343216	T	0.22539	1.95	2.14	-3.6	0.04570	.	.	.	.	.	T	0.00144	0.0004	N	0.03608	-0.345	0.09310	N	1	B	0.21225	0.053	B	0.06405	0.002	T	0.32322	-0.9911	9	0.87932	D	0	-7.0233	0.6619	0.00844	0.4047:0.248:0.1829:0.1644	.	484	Q14D33	CB085_HUMAN	C	484	ENSP00000345374:R484C	ENSP00000345374:R484C	R	+	1	0	C2orf85	242463830	0.000000	0.05858	0.000000	0.03702	0.242000	0.25591	-1.257000	0.02866	-0.945000	0.03681	0.196000	0.17591	CGC	C|0.973;T|0.027	0.027	strong		0.627	CXXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322310.1		
ZNF20	7568	hgsc.bcm.edu	37	19	12244624	12244624	+	Missense_Mutation	SNP	G	G	A	rs61743205	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12244624G>A	ENST00000334213.5	-	4	601	c.377C>T	c.(376-378)gCt>gTt	p.A126V	ZNF20_ENST00000600335.1_Intron|ZNF20_ENST00000485451.1_5'UTR|ZNF625-ZNF20_ENST00000430024.1_3'UTR	NM_001203250.1|NM_021143.3	NP_001190179.1|NP_066966.2	P17024	ZNF20_HUMAN	zinc finger protein 20	126					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|lung(6)	8						TCCAGTGTCAGCTCTGATATG	0.408													G|||	103	0.0205671	0.0764	0.0029	5008	,	,		20665	0.0		0.0	False		,,,				2504	0.0				p.A126V		Atlas-SNP	.											.	ZNF20	86	.	0			c.C377T						PASS	.	G	VAL/ALA,VAL/ALA	196,4082		3,190,1946	248.0	252.0	251.0		368,377	-0.3	0.0	19	dbSNP_129	251	1,8541		0,1,4270	yes	missense,missense	ZNF20	NM_001203250.1,NM_021143.3	64,64	3,191,6216	AA,AG,GG		0.0117,4.5816,1.5367	possibly-damaging,possibly-damaging	123/530,126/533	12244624	197,12623	2139	4271	6410	SO:0001583	missense	7568	exon4			GTGTCAGCTCTGA	X52344	CCDS45986.1	19p13.2	2013-01-08	2006-05-10		ENSG00000132010	ENSG00000132010		"""Zinc fingers, C2H2-type"", ""-"""	12992	protein-coding gene	gene with protein product		194557	"""zinc finger protein 20 (KOX 13)"""				Standard	NM_021143		Approved	KOX13	uc002mtf.2	P17024	OTTHUMG00000156409	ENST00000334213.5:c.377C>T	19.37:g.12244624G>A	ENSP00000335437:p.Ala126Val	182.0	0.0	0		182.0	88.0	0.483516	NM_021143	Q8N457|Q9UG41	Missense_Mutation	SNP	ENST00000334213.5	37	CCDS45986.1	39	0.017857142857142856	38	0.07723577235772358	1	0.0027624309392265192	0	0.0	0	0.0	G	4.410	0.075745	0.08485	0.045816	1.17E-4	ENSG00000132010	ENST00000334213;ENST00000292241;ENST00000418866	T;T	0.13420	3.41;2.59	0.94	-0.349	0.12609	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (1);	.	.	.	.	T	0.00241	0.0007	N	0.04148	-0.265	0.09310	N	1	P	0.44627	0.839	B	0.33454	0.164	T	0.38607	-0.9653	9	0.21540	T	0.41	.	4.7244	0.12935	0.0:0.4015:0.5985:0.0	.	126	P17024	ZNF20_HUMAN	V	126;126;123	ENSP00000335437:A126V;ENSP00000390115:A123V	ENSP00000292241:A126V	A	-	2	0	ZNF20	12105624	0.000000	0.05858	0.029000	0.17559	0.267000	0.26476	-1.626000	0.02035	-0.066000	0.12998	0.313000	0.20887	GCT	G|0.981;A|0.019	0.019	strong		0.408	ZNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344101.1	NM_021143	
VWA3B	200403	hgsc.bcm.edu	37	2	98779418	98779418	+	Missense_Mutation	SNP	G	G	A	rs77092382	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:98779418G>A	ENST00000477737.1	+	8	1297	c.1093G>A	c.(1093-1095)Gac>Aac	p.D365N	VWA3B_ENST00000435344.1_Missense_Mutation_p.D365N|VWA3B_ENST00000451075.2_Missense_Mutation_p.D215N	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	365										NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						TCCCAAGCCCGACGTGGCCAC	0.567													G|||	132	0.0263578	0.0946	0.0101	5008	,	,		16753	0.0		0.0	False		,,,				2504	0.0				p.D365N		Atlas-SNP	.											.	VWA3B	138	.	0			c.G1093A						PASS	.	G	ASN/ASP	319,3775		17,285,1745	56.0	64.0	62.0		1093	-9.4	0.0	2	dbSNP_131	62	4,8420		0,4,4208	no	missense	VWA3B	NM_144992.4	23	17,289,5953	AA,AG,GG		0.0475,7.7919,2.5803	benign	365/1295	98779418	323,12195	2047	4212	6259	SO:0001583	missense	200403	exon8			AAGCCCGACGTGG	AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.1093G>A	2.37:g.98779418G>A	ENSP00000417955:p.Asp365Asn	133.0	0.0	0		139.0	60.0	0.431655	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Missense_Mutation	SNP	ENST00000477737.1	37	CCDS42718.1	35	0.016025641025641024	33	0.06707317073170732	2	0.0055248618784530384	0	0.0	0	0.0	G	10.25	1.297516	0.23650	0.077919	4.75E-4	ENSG00000168658	ENST00000435344;ENST00000477737;ENST00000451075	T;T;T	0.23147	1.92;3.36;2.47	4.68	-9.37	0.00626	.	2.270810	0.02023	N	0.047965	T	0.00496	0.0016	N	0.04959	-0.14	0.09310	N	1	B;B;B	0.12630	0.006;0.001;0.002	B;B;B	0.04013	0.001;0.001;0.001	T	0.11179	-1.0598	10	0.34782	T	0.22	.	4.1345	0.10164	0.5431:0.1901:0.1706:0.0961	.	215;365;365	B7Z7Q7;Q502W6;Q502W6-8	.;VWA3B_HUMAN;.	N	365;365;215	ENSP00000401959:D365N;ENSP00000417955:D365N;ENSP00000389463:D215N	ENSP00000411168:D365N	D	+	1	0	VWA3B	98145850	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.018000	0.01444	-2.385000	0.00590	-0.781000	0.03364	GAC	G|0.981;A|0.019	0.019	strong		0.567	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992	
CSNK1G1	53944	hgsc.bcm.edu	37	15	64592522	64592522	+	Silent	SNP	T	T	C	rs7163558	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:64592522T>C	ENST00000303052.7	-	2	600	c.177A>G	c.(175-177)agA>agG	p.R59R	CSNK1G1_ENST00000607537.1_Silent_p.R59R|CTD-2116N17.1_ENST00000558783.1_5'Flank|CSNK1G1_ENST00000303032.6_Silent_p.R59R|CTD-2116N17.1_ENST00000606793.1_5'UTR	NM_022048.3	NP_071331.2	Q9HCP0	KC1G1_HUMAN	casein kinase 1, gamma 1	59	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|urinary_tract(1)	13						GCTTACCTAATCTGAGCTCTC	0.448													T|||	153	0.0305511	0.115	0.0014	5008	,	,		19957	0.0		0.0	False		,,,				2504	0.0				p.R59R		Atlas-SNP	.											.	CSNK1G1	56	.	0			c.A177G						PASS	.	T		401,4005	199.1+/-222.7	18,365,1820	253.0	243.0	246.0		177	5.4	1.0	15	dbSNP_116	246	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	CSNK1G1	NM_022048.3		18,372,6113	CC,CT,TT		0.0814,9.1012,3.137		59/423	64592522	408,12598	2203	4300	6503	SO:0001819	synonymous_variant	53944	exon2			ACCTAATCTGAGC	AB042562	CCDS10192.2	15q22.1-q22.31	2013-01-17			ENSG00000169118	ENSG00000169118			2454	protein-coding gene	gene with protein product		606274				11124537	Standard	NM_022048		Approved	CK1gamma1	uc002anf.3	Q9HCP0	OTTHUMG00000133019	ENST00000303052.7:c.177A>G	15.37:g.64592522T>C		147.0	0.0	0		190.0	91.0	0.478947	NM_022048	Q5JPH1|Q96AE9|Q9HCP1	Silent	SNP	ENST00000303052.7	37	CCDS10192.2																																																																																			T|0.968;C|0.032	0.032	strong		0.448	CSNK1G1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256605.1	NM_022048	
SEC14L3	266629	hgsc.bcm.edu	37	22	30864545	30864545	+	Missense_Mutation	SNP	T	T	A	rs115380280	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30864545T>A	ENST00000215812.4	-	5	463	c.373A>T	c.(373-375)Atg>Ttg	p.M125L	SEC14L3_ENST00000401751.1_Missense_Mutation_p.M66L|SEC14L3_ENST00000539629.1_Missense_Mutation_p.M66L|SEC14L3_ENST00000415957.2_Missense_Mutation_p.M66L|SEC14L3_ENST00000402286.1_Missense_Mutation_p.M48L|SEC14L3_ENST00000403066.1_Missense_Mutation_p.M66L|SEC14L3_ENST00000540910.1_Missense_Mutation_p.M48L	NM_174975.4	NP_777635.1	Q9UDX4	S14L3_HUMAN	SEC14-like 3 (S. cerevisiae)	125	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.					extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			NS(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(3)|ovary(3)|pancreas(1)|skin(2)|urinary_tract(1)	19					Vitamin E(DB00163)	CAGTCCCTCATCTTGGTCTTG	0.602													T|||	18	0.00359425	0.0129	0.0014	5008	,	,		18253	0.0		0.0	False		,,,				2504	0.0				p.M125L	Esophageal Squamous(108;290 1516 3584 23771 37333)	Atlas-SNP	.											.	SEC14L3	46	.	0			c.A373T						PASS	.	T	LEU/MET	33,4373	39.2+/-71.8	0,33,2170	176.0	130.0	145.0		373	4.6	1.0	22	dbSNP_132	145	0,8600		0,0,4300	yes	missense	SEC14L3	NM_174975.4	15	0,33,6470	AA,AT,TT		0.0,0.749,0.2537	benign	125/401	30864545	33,12973	2203	4300	6503	SO:0001583	missense	266629	exon5			CCCTCATCTTGGT	AY158086	CCDS13877.1, CCDS58800.1, CCDS58801.1	22q12.2	2013-09-23			ENSG00000100012	ENSG00000100012			18655	protein-coding gene	gene with protein product		612824					Standard	NM_174975		Approved	TAP2	uc003ahy.3	Q9UDX4	OTTHUMG00000151259	ENST00000215812.4:c.373A>T	22.37:g.30864545T>A	ENSP00000215812:p.Met125Leu	112.0	0.0	0		113.0	57.0	0.504425	NM_174975	E7EN74|E9PE57|Q495V8|Q495W0|Q495W1	Missense_Mutation	SNP	ENST00000215812.4	37	CCDS13877.1	2|2	9.157509157509158E-4|9.157509157509158E-4	2|2	0.0040650406504065045|0.0040650406504065045	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	T|T	10.11|10.11	1.260683|1.260683	0.23051|0.23051	0.00749|0.00749	0.0|0.0	ENSG00000100012|ENSG00000100012	ENST00000403066;ENST00000415957;ENST00000215812;ENST00000402286;ENST00000401751;ENST00000539629;ENST00000540910|ENST00000435069	T;T;T;T;T;T;T|.	0.72835|.	-0.69;-0.69;-0.69;-0.69;-0.69;-0.69;-0.69|.	4.55|4.55	4.55|4.55	0.56014|0.56014	Cellular retinaldehyde-binding/triple function, C-terminal (5);|.	0.222920|.	0.48286|.	D|.	0.000195|.	T|T	0.25754|0.25754	0.0627|0.0627	N|N	0.05592|0.05592	-0.015|-0.015	0.80722|0.80722	D|D	1|1	B;B|.	0.02656|.	0.0;0.0|.	B;B|.	0.08055|.	0.003;0.003|.	T|T	0.11251|0.11251	-1.0595|-1.0595	10|5	0.15952|.	T|.	0.53|.	-18.6063|-18.6063	9.2656|9.2656	0.37639|0.37639	0.205:0.0:0.0:0.795|0.205:0.0:0.0:0.795	.|.	48;125|.	E9PE57;Q9UDX4|.	.;S14L3_HUMAN|.	L|S	66;66;125;48;66;66;48|90	ENSP00000385941:M66L;ENSP00000401864:M66L;ENSP00000215812:M125L;ENSP00000385004:M48L;ENSP00000383896:M66L;ENSP00000444691:M66L;ENSP00000439752:M48L|.	ENSP00000215812:M125L|.	M|R	-|-	1|3	0|2	SEC14L3|SEC14L3	29194545|29194545	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	3.513000|3.513000	0.53414|0.53414	1.810000|1.810000	0.52873|0.52873	0.519000|0.519000	0.50382|0.50382	ATG|AGA	T|0.998;A|0.002	0.002	strong		0.602	SEC14L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321950.4	NM_174975	
KRTAP29-1	100533177	hgsc.bcm.edu	37	17	39458200	39458200	+	Missense_Mutation	SNP	C	C	T	rs115643796	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39458200C>T	ENST00000391353.1	-	1	903	c.904G>A	c.(904-906)Ggc>Agc	p.G302S		NM_001257309.1	NP_001244238.1	A8MX34	KR291_HUMAN	keratin associated protein 29-1	302	7 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)											GATTTGCAGCCACTCTGGTTA	0.512													C|||	77	0.0153754	0.056	0.0043	5008	,	,		22736	0.0		0.0	False		,,,				2504	0.0				p.G302S		Atlas-SNP	.											.	KRTAP29-1	2	.	0			c.G904A						PASS	.																																			SO:0001583	missense	100533177	exon1			TGCAGCCACTCTG		CCDS62183.1	17q21.2	2013-06-20			ENSG00000212658	ENSG00000212658		"""Keratin associated proteins"""	34211	protein-coding gene	gene with protein product							Standard	NM_001257309		Approved	KAP29.2	uc031rai.1	A8MX34	OTTHUMG00000133662	ENST00000391353.1:c.904G>A	17.37:g.39458200C>T	ENSP00000375148:p.Gly302Ser	142.0	0.0	0		152.0	73.0	0.480263	NM_001257309		Missense_Mutation	SNP	ENST00000391353.1	37		28	0.01282051282051282	24	0.04878048780487805	4	0.011049723756906077	0	0.0	0	0.0	C	11.47	1.648830	0.29336	.	.	ENSG00000212658	ENST00000391353	.	.	.	4.25	3.28	0.37604	.	.	.	.	.	T	0.02888	0.0086	.	.	.	.	.	.	.	.	.	.	.	.	T	0.16928	-1.0386	4	0.05959	T	0.93	.	7.7986	0.29162	0.0:0.8855:0.0:0.1145	.	.	.	.	S	302	.	ENSP00000375148:G302S	G	-	1	0	KRTAP29-1	36711726	0.008000	0.16893	0.746000	0.31095	0.834000	0.47266	0.971000	0.29396	0.995000	0.38917	0.455000	0.32223	GGC	C|0.987;T|0.013	0.013	strong		0.512	KRTAP29-1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257828.2		
DZIP1L	199221	hgsc.bcm.edu	37	3	137787173	137787173	+	Missense_Mutation	SNP	G	G	A	rs11917468	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:137787173G>A	ENST00000327532.2	-	13	2014	c.1652C>T	c.(1651-1653)gCc>gTc	p.A551V	DZIP1L_ENST00000488595.1_5'UTR	NM_173543.2	NP_775814.2	Q8IYY4	DZI1L_HUMAN	DAZ interacting zinc finger protein 1-like	551			A -> V (in dbSNP:rs11917468).		cilium assembly (GO:0042384)	ciliary basal body (GO:0036064)	metal ion binding (GO:0046872)			breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(2)|prostate(1)|skin(1)	35						CTTTGGCTGGGCCTCTCTGGT	0.577											OREG0015830	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	262	0.0523163	0.1868	0.0202	5008	,	,		16312	0.0		0.001	False		,,,				2504	0.0				p.A551V		Atlas-SNP	.											.	DZIP1L	88	.	0			c.C1652T						PASS	.	G	VAL/ALA	707,3699	290.1+/-280.8	50,607,1546	71.0	78.0	75.0		1652	-2.2	0.0	3	dbSNP_120	75	12,8588	9.1+/-34.3	0,12,4288	yes	missense	DZIP1L	NM_173543.2	64	50,619,5834	AA,AG,GG		0.1395,16.0463,5.5282	benign	551/768	137787173	719,12287	2203	4300	6503	SO:0001583	missense	199221	exon13			GGCTGGGCCTCTC	AK057406	CCDS3096.1, CCDS54645.1	3q22.3	2013-05-22	2013-05-22		ENSG00000158163	ENSG00000158163			26551	protein-coding gene	gene with protein product			"""DAZ interacting protein 1-like"""			12477932	Standard	NM_173543		Approved	FLJ32844, DZIP2	uc003erq.3	Q8IYY4	OTTHUMG00000159819	ENST00000327532.2:c.1652C>T	3.37:g.137787173G>A	ENSP00000332148:p.Ala551Val	209.0	0.0	0	1636	166.0	77.0	0.463855	NM_173543	C9JUG5|Q96M38	Missense_Mutation	SNP	ENST00000327532.2	37	CCDS3096.1	72	0.03296703296703297	66	0.13414634146341464	6	0.016574585635359115	0	0.0	0	0.0	G	3.102	-0.184558	0.06340	0.160463	0.001395	ENSG00000158163	ENST00000327532	T	0.39056	1.1	4.91	-2.15	0.07102	.	1.124280	0.06592	N	0.752174	T	0.00073	0.0002	N	0.02011	-0.69	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.17379	-1.0371	10	0.20046	T	0.44	0.1447	9.7913	0.40708	0.6267:0.0:0.3733:0.0	rs11917468;rs52808108;rs11917468	551	Q8IYY4	DZI1L_HUMAN	V	551	ENSP00000332148:A551V	ENSP00000332148:A551V	A	-	2	0	DZIP1L	139269863	0.000000	0.05858	0.000000	0.03702	0.128000	0.20619	-0.062000	0.11674	-0.389000	0.07786	0.650000	0.86243	GCC	G|0.948;A|0.052	0.052	strong		0.577	DZIP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357548.1	NM_173543	
TSPAN18	90139	hgsc.bcm.edu	37	11	44931308	44931308	+	Missense_Mutation	SNP	C	C	T	rs34282417	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:44931308C>T	ENST00000520358.2	+	5	531	c.116C>T	c.(115-117)aCc>aTc	p.T39I	TSPAN18_ENST00000340160.3_Missense_Mutation_p.T39I			Q96SJ8	TSN18_HUMAN	tetraspanin 18	39						integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(6)|lung(3)	10						GTGGACCCCACCGGCTTCCGG	0.667													C|||	17	0.00339457	0.0121	0.0014	5008	,	,		14867	0.0		0.0	False		,,,				2504	0.0				p.T39I		Atlas-SNP	.											.	TSPAN18	38	.	0			c.C116T						PASS	.	C	ILE/THR	46,4360	47.5+/-82.1	0,46,2157	45.0	49.0	48.0		116	5.0	1.0	11	dbSNP_126	48	0,8598		0,0,4299	yes	missense	TSPAN18	NM_130783.4	89	0,46,6456	TT,TC,CC		0.0,1.044,0.3537	probably-damaging	39/249	44931308	46,12958	2203	4299	6502	SO:0001583	missense	90139	exon4			ACCCCACCGGCTT	AY358087	CCDS7910.1	11p11.2	2013-02-14				ENSG00000157570		"""Tetraspanins"""	20660	protein-coding gene	gene with protein product						11756464	Standard	NM_130783		Approved	TSPAN	uc001mye.4	Q96SJ8		ENST00000520358.2:c.116C>T	11.37:g.44931308C>T	ENSP00000429993:p.Thr39Ile	96.0	0.0	0		87.0	44.0	0.505747	NM_130783	Q6UY44|Q8NBI9	Missense_Mutation	SNP	ENST00000520358.2	37	CCDS7910.1	9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	C	18.20	3.570526	0.65765	0.01044	0.0	ENSG00000157570	ENST00000533786;ENST00000533202;ENST00000520358;ENST00000520999;ENST00000340160;ENST00000520837	T;T;T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2;-1.2;-1.2	5.0	5.0	0.66597	.	0.000000	0.85682	D	0.000000	T	0.67859	0.2938	M	0.67517	2.055	0.80722	D	1	B;P	0.40050	0.143;0.7	B;B	0.42882	0.228;0.401	T	0.76041	-0.3104	10	0.40728	T	0.16	.	18.2971	0.90150	0.0:1.0:0.0:0.0	rs34282417	39;39	Q8WUV1;Q96SJ8	.;TSN18_HUMAN	I	39;39;39;49;39;49	ENSP00000433592:T39I;ENSP00000434625:T39I;ENSP00000429993:T39I;ENSP00000427942:T49I;ENSP00000339820:T39I;ENSP00000430343:T49I	ENSP00000339820:T39I	T	+	2	0	TSPAN18	44887884	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.845000	0.62853	2.319000	0.78375	0.561000	0.74099	ACC	C|0.995;T|0.005	0.005	strong		0.667	TSPAN18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376197.3	NM_130783	
ATP13A4	84239	hgsc.bcm.edu	37	3	193120459	193120459	+	Silent	SNP	G	G	A	rs9863164	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:193120459G>A	ENST00000342695.4	-	30	3895	c.3573C>T	c.(3571-3573)agC>agT	p.S1191S	ATP13A4_ENST00000392443.3_Silent_p.S1172S|ATP13A4_ENST00000482964.1_5'UTR|ATP13A4_ENST00000400270.2_Silent_p.S207S	NM_032279.2	NP_115655.2	Q4VNC1	AT134_HUMAN	ATPase type 13A4	1191						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(9)|lung(27)|ovary(2)|prostate(3)|skin(11)|upper_aerodigestive_tract(2)	71	all_cancers(143;1.76e-08)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(49;2.72e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;0.000109)		GTTCTTCATTGCTCTCAAATA	0.438													G|||	110	0.0219649	0.0802	0.0058	5008	,	,		18998	0.0		0.0	False		,,,				2504	0.0				p.S1191S		Atlas-SNP	.											.	ATP13A4	154	.	0			c.C3573T						PASS	.	G		302,4104	165.1+/-196.6	13,276,1914	91.0	89.0	90.0		3573	4.1	1.0	3	dbSNP_119	90	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	ATP13A4	NM_032279.2		13,280,6210	AA,AG,GG		0.0465,6.8543,2.3528		1191/1197	193120459	306,12700	2203	4300	6503	SO:0001819	synonymous_variant	84239	exon30			TTCATTGCTCTCA	AK095277	CCDS3304.2	3q29	2010-04-20			ENSG00000127249	ENSG00000127249		"""ATPases / P-type"""	25422	protein-coding gene	gene with protein product		609556				14702039, 12975309	Standard	XM_005247829		Approved	DKFZp761I1011, FLJ37958	uc003ftd.3	Q4VNC1	OTTHUMG00000074067	ENST00000342695.4:c.3573C>T	3.37:g.193120459G>A		99.0	0.0	0		108.0	49.0	0.453704	NM_032279	B7WPC7|Q6UY23|Q8N1Q9|Q9H043	Silent	SNP	ENST00000342695.4	37	CCDS3304.2																																																																																			G|0.974;A|0.026	0.026	strong		0.438	ATP13A4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157244.4	NM_032279	
PTOV1	53635	hgsc.bcm.edu	37	19	50361874	50361874	+	Silent	SNP	A	A	G	rs35389621	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:50361874A>G	ENST00000601675.1	+	10	1109	c.1005A>G	c.(1003-1005)acA>acG	p.T335T	PTOV1_ENST00000600603.1_Silent_p.T303T|AC018766.5_ENST00000601893.1_RNA|PTOV1_ENST00000599732.1_Silent_p.T335T|PTOV1_ENST00000598325.1_3'UTR|AC018766.5_ENST00000599259.1_RNA|AC018766.5_ENST00000593654.1_RNA|AC018766.4_ENST00000596624.1_RNA|PTOV1_ENST00000601638.1_Silent_p.T303T|PTOV1_ENST00000391842.1_Silent_p.T335T|PTOV1_ENST00000221557.9_Silent_p.T303T			Q86YD1	PTOV1_HUMAN	prostate tumor overexpressed 1	335	Interaction with FLOT1.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(5)|kidney(3)|large_intestine(2)|lung(5)|ovary(1)	16		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.0132)		ACCTGGAGACACTGAAGAGCC	0.667													A|||	48	0.00958466	0.034	0.0043	5008	,	,		16455	0.0		0.0	False		,,,				2504	0.0				p.T335T		Atlas-SNP	.											.	PTOV1	41	.	0			c.A1005G						PASS	.	A		125,4277	87.3+/-125.9	2,121,2078	43.0	30.0	35.0		1005	-5.7	0.3	19	dbSNP_126	35	0,8598		0,0,4299	no	coding-synonymous	PTOV1	NM_017432.3		2,121,6377	GG,GA,AA		0.0,2.8396,0.9615		335/417	50361874	125,12875	2201	4299	6500	SO:0001819	synonymous_variant	53635	exon10			GGAGACACTGAAG	AF238381	CCDS12782.1	19q13.33	2014-08-28	2008-09-12		ENSG00000104960	ENSG00000104960			9632	protein-coding gene	gene with protein product		610195				12598323, 15713644	Standard	XM_005258998		Approved		uc002pqf.1	Q86YD1	OTTHUMG00000183162	ENST00000601675.1:c.1005A>G	19.37:g.50361874A>G		99.0	0.0	0		85.0	43.0	0.505882	NM_017432	Q6UXX7|Q96BU3|Q9HBN4|Q9NYL1	Silent	SNP	ENST00000601675.1	37	CCDS12782.1																																																																																			A|0.990;G|0.010	0.010	strong		0.667	PTOV1-007	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465347.1	NM_017432	
SSPO	23145	hgsc.bcm.edu	37	7	149485987	149485987	+	RNA	SNP	T	T	A	rs893597	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149485987T>A	ENST00000378016.2	+	0	4206							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			AGGACGACTGTGGCGATGGCT	0.582													T|||	131	0.0261581	0.0946	0.0086	5008	,	,		22616	0.0		0.0	False		,,,				2504	0.0				p.C1402X		Atlas-SNP	.											.	.	.	.	0			c.T4206A						PASS	.	T		277,4091		10,257,1917	83.0	87.0	86.0		4210	1.2	1.0	7	dbSNP_86	86	4,8564		0,4,4280	yes	coding-notMod3	SSPO	NM_198455.2		10,261,6197	AA,AT,TT		0.0467,6.3416,2.1722			149485987	281,12655	2184	4284	6468			23145	exon29			CGACTGTGGCGAT	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149485987T>A		146.0	0.0	0		190.0	90.0	0.473684	NM_198455	Q76B61	Nonsense_Mutation	SNP	ENST00000378016.2	37																																																																																				T|0.977;A|0.023	0.023	strong		0.582	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
IPPK	64768	hgsc.bcm.edu	37	9	95411816	95411816	+	Silent	SNP	G	G	A	rs16908484	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95411816G>A	ENST00000287996.3	-	5	609	c.333C>T	c.(331-333)taC>taT	p.Y111Y		NM_022755.5	NP_073592.1	Q9H8X2	IPPK_HUMAN	inositol 1,3,4,5,6-pentakisphosphate 2-kinase	111					inositol phosphate metabolic process (GO:0043647)|inositol phosphorylation (GO:0052746)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|intracellular (GO:0005622)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|inositol pentakisphosphate 2-kinase activity (GO:0035299)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(2)|urinary_tract(1)	15						GGCACATAGCGTAACCACTGA	0.512													G|||	59	0.0117812	0.0424	0.0043	5008	,	,		19264	0.0		0.0	False		,,,				2504	0.0				p.Y111Y		Atlas-SNP	.											.	IPPK	34	.	0			c.C333T						PASS	.	G		156,4250	106.0+/-144.5	1,154,2048	165.0	127.0	140.0		333	-1.9	1.0	9	dbSNP_123	140	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	IPPK	NM_022755.5		1,155,6347	AA,AG,GG		0.0116,3.5406,1.2071		111/492	95411816	157,12849	2203	4300	6503	SO:0001819	synonymous_variant	64768	exon5			CATAGCGTAACCA	AK023225	CCDS6699.1	9q22.31	2010-12-02	2005-10-20	2005-10-20	ENSG00000127080	ENSG00000127080			14645	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 12"""	C9orf12		12084730	Standard	NM_022755		Approved	INSP5K2, FLJ13163, IP5K, IPK1	uc004asl.1	Q9H8X2	OTTHUMG00000020231	ENST00000287996.3:c.333C>T	9.37:g.95411816G>A		113.0	0.0	0		116.0	69.0	0.594828	NM_022755	Q5T9F7|Q9H7V8	Silent	SNP	ENST00000287996.3	37	CCDS6699.1																																																																																			G|0.986;A|0.014	0.014	strong		0.512	IPPK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053101.1	NM_022755	
C16orf58	64755	hgsc.bcm.edu	37	16	31519174	31519174	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31519174G>C	ENST00000327237.2	-	2	365	c.326C>G	c.(325-327)tCc>tGc	p.S109C	C16orf58_ENST00000567994.1_Missense_Mutation_p.S64C|C16orf58_ENST00000430477.2_Intron|C16orf58_ENST00000570164.1_Missense_Mutation_p.S109C|RP11-452L6.7_ENST00000569782.1_RNA			Q96GQ5	RUS1_HUMAN	chromosome 16 open reading frame 58	109						integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)	14						GGTGGCTAGGGAGCCGGAGAG	0.587																																					p.G109G		Atlas-SNP	.											.	C16orf58	28	.	0			c.G326G						PASS	.						32.0	27.0	29.0					16																	31519174		2189	4291	6480	SO:0001583	missense	64755	exon2			GCTAGGGAGCCGG	AK023930	CCDS10715.1	16p11.2	2013-03-04			ENSG00000140688	ENSG00000140688			25848	protein-coding gene	gene with protein product							Standard	NM_022744		Approved	FLJ13868	uc002eci.3	Q96GQ5	OTTHUMG00000132466	ENST00000327237.2:c.326C>G	16.37:g.31519174G>C	ENSP00000317579:p.Ser109Cys	64.0	0.0	0		99.0	51.0	0.515152	NM_022744	Q53GL8|Q8NAJ4|Q9BVY3|Q9H887	Silent	SNP	ENST00000327237.2	37	CCDS10715.1	.	.	.	.	.	.	.	.	.	.	G	29.6	5.018996	0.93462	.	.	ENSG00000140688	ENST00000327237;ENST00000452223;ENST00000541442	T	0.43294	0.95	5.45	5.45	0.79879	.	0.158717	0.56097	D	0.000026	T	0.59905	0.2228	M	0.74881	2.28	0.80722	D	1	P	0.45531	0.86	P	0.55667	0.781	T	0.62817	-0.6774	10	0.66056	D	0.02	-3.0354	14.7866	0.69808	0.0:0.0:1.0:0.0	.	109	Q96GQ5	CP058_HUMAN	C	109;63;109	ENSP00000317579:S109C	ENSP00000317579:S109C	S	-	2	0	C16orf58	31426675	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.068000	0.76748	2.559000	0.86315	0.655000	0.94253	TCC	.	.	none		0.587	C16orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255629.2	NM_022744	
ZC3H12D	340152	hgsc.bcm.edu	37	6	149777914	149777914	+	Missense_Mutation	SNP	G	G	T	rs200917878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:149777914G>T	ENST00000409806.3	-	4	886	c.568C>A	c.(568-570)Cag>Aag	p.Q190K	ZC3H12D_ENST00000542614.1_Missense_Mutation_p.Q190K|ZC3H12D_ENST00000416573.2_Missense_Mutation_p.Q190K|ZC3H12D_ENST00000389942.5_Missense_Mutation_p.Q190K			A2A288	ZC12D_HUMAN	zinc finger CCCH-type containing 12D	190					negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|prostate(1)	6		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.23e-11)|GBM - Glioblastoma multiforme(68;0.0921)		ACGCCGTCCTGCTCGTAGGCC	0.627													G|||	13	0.00259585	0.0076	0.0029	5008	,	,		12923	0.001		0.0	False		,,,				2504	0.0				p.Q190K		Atlas-SNP	.											.	ZC3H12D	21	.	0			c.C568A						PASS	.	G	LYS/GLN	63,4247		1,61,2093	85.0	95.0	92.0		568	1.6	1.0	6		92	1,8539		0,1,4269	yes	missense	ZC3H12D	NM_207360.2	53	1,62,6362	TT,TG,GG		0.0117,1.4617,0.4981	benign	190/528	149777914	64,12786	2155	4270	6425	SO:0001583	missense	340152	exon4			CGTCCTGCTCGTA			6q25.1	2012-07-05	2005-06-30	2005-06-30	ENSG00000178199	ENSG00000178199		"""Zinc fingers, CCCH-type domain containing"""	21175	protein-coding gene	gene with protein product	"""MCP induced protein 4"""	611106	"""chromosome 6 open reading frame 95"""	C6orf95		18178554	Standard	NM_207360		Approved	dJ281H8.1, MCPIP4	uc010kid.3	A2A288	OTTHUMG00000015786	ENST00000409806.3:c.568C>A	6.37:g.149777914G>T	ENSP00000386616:p.Gln190Lys	61.0	0.0	0		53.0	23.0	0.433962	NM_207360	A1L178|B2RXF4|B7WNU7|B9ZZP9|B9ZZQ0|Q6ZRW2	Missense_Mutation	SNP	ENST00000409806.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	10.37|10.37	1.330416|1.330416	0.24167|0.24167	0.014617|0.014617	1.17E-4|1.17E-4	ENSG00000178199|ENSG00000178199	ENST00000458251|ENST00000389942;ENST00000416573;ENST00000409806;ENST00000542614	.|T;T;T;T	.|0.38560	.|1.13;1.13;1.13;1.13	4.84|4.84	1.63|1.63	0.23807|0.23807	.|Ribonuclease Zc3h12a-like (1);	.|0.660796	.|0.14612	.|N	.|0.308967	T|T	0.01387|0.01387	0.0045|0.0045	N|N	0.00035|0.00035	-2.545|-2.545	0.20403|0.20403	N|N	0.999907|0.999907	.|B;B	.|0.10296	.|0.003;0.0	.|B;B	.|0.08055	.|0.003;0.001	T|T	0.47328|0.47328	-0.9126|-0.9126	5|10	.|0.02654	.|T	.|1	-11.5336|-11.5336	5.6416|5.6416	0.17567|0.17567	0.183:0.0:0.4125:0.4045|0.183:0.0:0.4125:0.4045	.|.	.|190;190	.|A2A288;B7WNU7	.|ZC12D_HUMAN;.	E|K	31|190	.|ENSP00000374592:Q190K;ENSP00000408686:Q190K;ENSP00000386616:Q190K;ENSP00000440813:Q190K	.|ENSP00000374592:Q190K	A|Q	-|-	2|1	0|0	ZC3H12D|ZC3H12D	149819607|149819607	0.890000|0.890000	0.30428|0.30428	0.999000|0.999000	0.59377|0.59377	0.998000|0.998000	0.95712|0.95712	1.503000|1.503000	0.35715|0.35715	0.574000|0.574000	0.29417|0.29417	0.561000|0.561000	0.74099|0.74099	GCA|CAG	.	.	weak		0.627	ZC3H12D-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000286400.2	NM_207360	
EIF2S3	1968	hgsc.bcm.edu	37	X	24073785	24073785	+	Silent	SNP	A	A	G	rs56229020	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:24073785A>G	ENST00000253039.4	+	2	376	c.123A>G	c.(121-123)acA>acG	p.T41T		NM_001415.3	NP_001406.1	P41091	IF2G_HUMAN	eukaryotic translation initiation factor 2, subunit 3 gamma, 52kDa	41	tr-type G. {ECO:0000255|PROSITE- ProRule:PRU01059}.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|GTP catabolic process (GO:0006184)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			breast(1)|cervix(1)|endometrium(4)|large_intestine(1)|lung(4)|ovary(1)	12						GACAAGCCACAATTAACATAG	0.348													A|||	10	0.00264901	0.0061	0.0014	3775	,	,		16856	0.0		0.001	False		,,,				2504	0.0				p.T41T		Atlas-SNP	.											.	EIF2S3	31	.	0			c.A123G						PASS	.	A		20,3815		0,19,1,1613,570	86.0	71.0	76.0		123	0.8	1.0	X	dbSNP_129	76	3,6725		0,2,1,2426,1871	no	coding-synonymous	EIF2S3	NM_001415.3		0,21,2,4039,2441	GG,GA,G,AA,A		0.0446,0.5215,0.2177		41/473	24073785	23,10540	2203	4300	6503	SO:0001819	synonymous_variant	1968	exon2			AGCCACAATTAAC	L19161	CCDS14210.1	Xp22.2-p22.1	2008-07-31	2002-08-29		ENSG00000130741	ENSG00000130741			3267	protein-coding gene	gene with protein product	"""eukaryotic translation initiation factor 2G"""	300161	"""eukaryotic translation initiation factor 2, subunit 3 (gamma, 52kD)"""	EIF2G		8106381, 9736774	Standard	NM_001415		Approved	EIF2gamma, EIF2	uc004dbc.3	P41091	OTTHUMG00000021262	ENST00000253039.4:c.123A>G	X.37:g.24073785A>G		364.0	0.0	0		370.0	169.0	0.456757	NM_001415	B5BTZ4	Silent	SNP	ENST00000253039.4	37	CCDS14210.1	4	0.0024110910186859553	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	A	9.881	1.201486	0.22121	0.005215	4.46E-4	ENSG00000130741	ENST00000423068	.	.	.	4.68	0.75	0.18387	.	.	.	.	.	T	0.42877	0.1222	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29458	-1.0011	4	.	.	.	.	4.9157	0.13844	0.6333:0.0:0.2319:0.1348	rs56229020	.	.	.	D	41	.	.	N	+	1	0	EIF2S3	23983706	0.992000	0.36948	1.000000	0.80357	0.903000	0.53119	0.389000	0.20751	0.110000	0.17919	0.339000	0.21740	AAT	A|0.998;G|0.002	0.002	strong		0.348	EIF2S3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056079.1	NM_001415	
UCN3	114131	hgsc.bcm.edu	37	10	5416027	5416027	+	Missense_Mutation	SNP	C	C	G	rs201708420	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:5416027C>G	ENST00000380433.3	+	2	572	c.344C>G	c.(343-345)cCc>cGc	p.P115R		NM_053049.2	NP_444277.2	Q969E3	UCN3_HUMAN	urocortin 3	115					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|cellular response to hypoxia (GO:0071456)|cellular response to nutrient levels (GO:0031669)|digestion (GO:0007586)|positive regulation of insulin secretion (GO:0032024)|positive regulation of membrane potential (GO:0045838)|response to corticosterone (GO:0051412)|response to glucose (GO:0009749)|response to immobilization stress (GO:0035902)|response to starvation (GO:0042594)	axon terminus (GO:0043679)|extracellular space (GO:0005615)|varicosity (GO:0043196)				endometrium(1)|large_intestine(1)	2						GCCAAGAGTCCCCACCGCACC	0.642													.|||	4	0.000798722	0.003	0.0	5008	,	,		10358	0.0		0.0	False		,,,				2504	0.0				p.P115R		Atlas-SNP	.											.	UCN3	13	.	0			c.C344G						PASS	.	C	ARG/PRO	4,4402	8.1+/-20.4	0,4,2199	74.0	76.0	76.0		344	1.7	0.0	10		76	0,8600		0,0,4300	yes	missense	UCN3	NM_053049.2	103	0,4,6499	GG,GC,CC		0.0,0.0908,0.0308	possibly-damaging	115/162	5416027	4,13002	2203	4300	6503	SO:0001583	missense	114131	exon2			AGAGTCCCCACCG	AF361943	CCDS7065.1	10p15.1	2013-02-28	2012-10-17		ENSG00000178473	ENSG00000178473		"""Endogenous ligands"""	17781	protein-coding gene	gene with protein product	"""stresscopin"", ""prepro-urocortin 3"""	605901				11416224	Standard	NM_053049		Approved	UCNIII, SPC	uc001ihx.1	Q969E3	OTTHUMG00000017594	ENST00000380433.3:c.344C>G	10.37:g.5416027C>G	ENSP00000369798:p.Pro115Arg	45.0	0.0	0		57.0	25.0	0.438596	NM_053049	Q496H2|Q5SR91	Missense_Mutation	SNP	ENST00000380433.3	37	CCDS7065.1	.	.	.	.	.	.	.	.	.	.	C	6.795	0.515627	0.12944	9.08E-4	0.0	ENSG00000178473	ENST00000380433	T	0.30182	1.54	5.49	1.67	0.24075	.	0.332477	0.29884	N	0.010946	T	0.18045	0.0433	N	0.22421	0.69	0.23144	N	0.998221	B	0.23490	0.086	B	0.21360	0.034	T	0.16630	-1.0396	10	0.59425	D	0.04	-11.4379	7.1327	0.25510	0.6324:0.291:0.0767:0.0	.	115	Q969E3	UCN3_HUMAN	R	115	ENSP00000369798:P115R	ENSP00000369798:P115R	P	+	2	0	UCN3	5406027	1.000000	0.71417	0.003000	0.11579	0.007000	0.05969	3.203000	0.51075	0.390000	0.25115	-0.500000	0.04577	CCC	.	.	weak		0.642	UCN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046547.1	NM_053049	
RAD51B	5890	hgsc.bcm.edu	37	14	68292187	68292187	+	Silent	SNP	T	T	C	rs114131734	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:68292187T>C	ENST00000487270.1	+	3	139	c.91T>C	c.(91-93)Tta>Cta	p.L31L	RAD51B_ENST00000471583.1_Silent_p.L31L|RAD51B_ENST00000488612.1_Silent_p.L31L|RAD51B_ENST00000390683.3_Silent_p.L31L|RAD51B_ENST00000487861.1_Silent_p.L31L	NM_133509.3	NP_598193.2	O15315	RA51B_HUMAN	RAD51 paralog B	31	Interaction with RAD51C.				ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|reciprocal meiotic recombination (GO:0007131)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Rad51B-Rad51C-Rad51D-XRCC2 complex (GO:0033063)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)		HMGA2/RAD51B(11)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	11						TTAGGACTTTTTATGTCTTTC	0.383								Direct reversal of damage					T|||	45	0.00898562	0.0325	0.0029	5008	,	,		16807	0.0		0.0	False		,,,				2504	0.0				p.L31L		Atlas-SNP	.											.	RAD51B	80	.	0			c.T91C						PASS	.	T	,,	162,4244	111.6+/-149.8	3,156,2044	118.0	113.0	115.0		91,91,91	0.4	1.0	14	dbSNP_132	115	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	RAD51B	NM_002877.5,NM_133509.3,NM_133510.3	,,	3,158,6342	CC,CT,TT		0.0233,3.6768,1.261	,,	31/351,31/385,31/351	68292187	164,12842	2203	4300	6503	SO:0001819	synonymous_variant	5890	exon3			GACTTTTTATGTC	U84138	CCDS9789.1, CCDS9790.1	14q23-q24.2	2013-07-02	2013-07-02	2011-07-01	ENSG00000182185	ENSG00000182185			9822	protein-coding gene	gene with protein product		602948	"""RAD51 (S. cerevisiae)-like 1"", ""RAD51-like 1 (S. cerevisiae)"", ""RAD51 homolog B (S. cerevisiae)"""	RAD51L1		6261043, 9207106	Standard	NM_002877		Approved	REC2, hREC2, R51H2	uc001xkf.2	O15315	OTTHUMG00000157530	ENST00000487270.1:c.91T>C	14.37:g.68292187T>C		81.0	0.0	0		70.0	29.0	0.414286	NM_133509	O60914|O75210|Q3Y4F8|Q6FHX8|Q86SY3|Q86SY4|Q86TR0|Q86U92|Q86U93|Q86U94|Q8N6H4|Q9UPL5	Silent	SNP	ENST00000487270.1	37	CCDS9789.1																																																																																			T|0.991;C|0.009	0.009	strong		0.383	RAD51B-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000349063.1		
SRPX	8406	hgsc.bcm.edu	37	X	38033415	38033415	+	Missense_Mutation	SNP	T	T	C	rs35474361	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:38033415T>C	ENST00000378533.3	-	3	453	c.347A>G	c.(346-348)aAa>aGa	p.K116R	SRPX_ENST00000538295.1_Missense_Mutation_p.K116R|TM4SF2_ENST00000465127.1_Intron|SRPX_ENST00000432886.2_Missense_Mutation_p.K116R|SRPX_ENST00000544439.1_Missense_Mutation_p.K96R|SRPX_ENST00000343800.6_Missense_Mutation_p.K103R	NM_006307.4	NP_006298.1	P78539	SRPX_HUMAN	sushi-repeat containing protein, X-linked	116	Sushi 1. {ECO:0000255|PROSITE- ProRule:PRU00302}.				autophagy (GO:0006914)|cell adhesion (GO:0007155)|negative regulation of cell proliferation involved in contact inhibition (GO:0060244)|phagolysosome assembly (GO:0001845)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|response to endoplasmic reticulum stress (GO:0034976)	autophagic vacuole (GO:0005776)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)				autonomic_ganglia(1)|breast(2)|endometrium(5)|large_intestine(5)|lung(10)|prostate(2)	25						CTACTCACGTTTGCAGATGAC	0.493													T|||	274	0.0725828	0.1952	0.0231	3775	,	,		15221	0.0		0.0	False		,,,				2504	0.0				p.K116R		Atlas-SNP	.											.	SRPX	53	.	0			c.A347G						PASS	.	T	ARG/LYS,ARG/LYS,ARG/LYS,ARG/LYS	901,2932		90,578,143,963,428	127.0	98.0	108.0		287,347,347,347	5.7	1.0	X	dbSNP_126	108	6,6722		0,5,1,2423,1871	yes	missense,missense,missense,missense	SRPX	NM_001170750.1,NM_001170751.1,NM_001170752.1,NM_006307.4	26,26,26,26	90,583,144,3386,2299	CC,CT,C,TT,T		0.0892,23.5064,8.5882	benign,benign,benign,benign	96/445,116/406,116/380,116/465	38033415	907,9654	2202	4300	6502	SO:0001583	missense	8406	exon3			TCACGTTTGCAGA	U78093	CCDS14245.1, CCDS55400.1, CCDS55401.1, CCDS55402.1	Xp21.1	2011-01-25	2011-01-25		ENSG00000101955	ENSG00000101955			11309	protein-coding gene	gene with protein product		300187	"""sushi-repeat-containing protein, X chromosome"", ""sushi-repeat-containing protein, X-linked"""			8634708, 8634709	Standard	NM_006307		Approved	ETX1	uc004ddy.2	P78539	OTTHUMG00000021362	ENST00000378533.3:c.347A>G	X.37:g.38033415T>C	ENSP00000367794:p.Lys116Arg	120.0	0.0	0		112.0	56.0	0.5	NM_001170751	A8K065|B3KWP8|B4DDB8|B4DQH5|F5H4D7|G3V1L0|Q4VX66|Q99652|Q99913	Missense_Mutation	SNP	ENST00000378533.3	37	CCDS14245.1	83	0.050030138637733576	51	0.11486486486486487	7	0.019444444444444445	0	0.0	0	0.0	T	1.424	-0.572093	0.03882	0.235064	8.92E-4	ENSG00000101955	ENST00000544439;ENST00000432886;ENST00000538295;ENST00000378533;ENST00000343800	T;T;T;T;T	0.73897	1.88;-0.79;1.88;1.88;1.87	5.7	5.7	0.88788	Complement control module (1);Sushi/SCR/CCP (1);	0.137867	0.64402	D	0.000003	T	0.00039	0.0001	N	0.13043	0.29	0.24140	P	0.99573811	B;B;B;B	0.24618	0.007;0.107;0.058;0.071	B;B;B;B	0.27262	0.043;0.078;0.022;0.038	T	0.04281	-1.0963	9	0.07644	T	0.81	-13.8523	14.935	0.70948	0.0:0.0:0.0:1.0	rs35474361	116;116;96;116	F5H4D7;B4DQH5;G3V1L0;P78539	.;.;.;SRPX_HUMAN	R	96;116;116;116;103	ENSP00000440758:K96R;ENSP00000411165:K116R;ENSP00000445034:K116R;ENSP00000367794:K116R;ENSP00000339211:K103R	ENSP00000339211:K103R	K	-	2	0	SRPX	37918359	1.000000	0.71417	1.000000	0.80357	0.385000	0.30292	3.342000	0.52159	1.909000	0.55274	0.486000	0.48141	AAA	T|0.921;C|0.079	0.079	strong		0.493	SRPX-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056243.1	NM_006307	
ZC3H4	23211	hgsc.bcm.edu	37	19	47584869	47584869	+	Silent	SNP	C	C	T	rs73943616	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:47584869C>T	ENST00000253048.5	-	11	1378	c.1341G>A	c.(1339-1341)ccG>ccA	p.P447P	ZC3H4_ENST00000594019.1_Intron|RN7SL533P_ENST00000584468.1_RNA	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	447							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		ACAGCTTACACGGGAAATCAC	0.522													C|||	133	0.0265575	0.093	0.0115	5008	,	,		20932	0.0		0.002	False		,,,				2504	0.0				p.P447P		Atlas-SNP	.											.	ZC3H4	96	.	0			c.G1341A						PASS	.	C		287,3833		14,259,1787	120.0	121.0	121.0		1341	-11.4	0.2	19	dbSNP_130	121	30,8360		0,30,4165	no	coding-synonymous	ZC3H4	NM_015168.1		14,289,5952	TT,TC,CC		0.3576,6.966,2.534		447/1304	47584869	317,12193	2060	4195	6255	SO:0001819	synonymous_variant	23211	exon11			CTTACACGGGAAA	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"""Zinc fingers, CCCH-type domain containing"""	17808	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 7"""	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.1341G>A	19.37:g.47584869C>T		139.0	0.0	0		144.0	84.0	0.583333	NM_015168	Q9Y420	Silent	SNP	ENST00000253048.5	37	CCDS42582.1																																																																																			C|0.986;T|0.014	0.014	strong		0.522	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1		
ZNF695	57116	hgsc.bcm.edu	37	1	247150631	247150631	+	Missense_Mutation	SNP	T	T	C	rs77178548	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:247150631T>C	ENST00000339986.7	-	4	1333	c.1186A>G	c.(1186-1188)Att>Gtt	p.I396V	ZNF695_ENST00000498046.2_Intron|ZNF695_ENST00000487338.2_Intron	NM_020394.4	NP_065127	Q8IW36	ZN695_HUMAN	zinc finger protein 695	396					regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			endometrium(1)|large_intestine(1)|lung(9)|prostate(1)|urinary_tract(1)	13	all_cancers(71;4.01e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			TTATGCTGAATAAGGTATGAG	0.398													T|||	157	0.0313498	0.1165	0.0043	5008	,	,		21162	0.0		0.0	False		,,,				2504	0.0				p.I396V		Atlas-SNP	.											.	ZNF695	55	.	0			c.A1186G						PASS	.	T	,VAL/ILE	387,3903		17,353,1775	51.0	55.0	53.0		,1186	0.6	0.0	1	dbSNP_132	53	3,8535		0,3,4266	no	intron,missense	ZNF695	NM_001204221.1,NM_020394.4	,29	17,356,6041	CC,CT,TT		0.0351,9.021,3.0402	,benign	,396/516	247150631	390,12438	2145	4269	6414	SO:0001583	missense	57116	exon4			GCTGAATAAGGTA		CCDS44344.1, CCDS55694.1	1q44	2013-01-08			ENSG00000197472	ENSG00000197472		"""Zinc fingers, C2H2-type"", ""-"""	30954	protein-coding gene	gene with protein product						12477932	Standard	NM_020394		Approved	SBZF3	uc009xgu.3	Q8IW36	OTTHUMG00000040707	ENST00000339986.7:c.1186A>G	1.37:g.247150631T>C	ENSP00000341236:p.Ile396Val	46.0	0.0	0		54.0	24.0	0.444444	NM_020394	Q5T0N9|Q5T0P1|Q5T0P3|Q7Z2W8|Q7Z648	Missense_Mutation	SNP	ENST00000339986.7	37	CCDS44344.1	54	0.024725274725274724	52	0.10569105691056911	2	0.0055248618784530384	0	0.0	0	0.0	T	11.16	1.556933	0.27827	0.09021	3.51E-4	ENSG00000197472	ENST00000339986	T	0.07216	3.21	0.642	0.642	0.17765	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00073	0.0002	N	0.02111	-0.68	0.09310	N	1	B	0.17465	0.022	B	0.08055	0.003	T	0.44742	-0.9308	9	0.66056	D	0.02	.	5.509	0.16870	0.0:1.0E-4:0.0:0.9999	.	396	Q8IW36	ZN695_HUMAN	V	396	ENSP00000341236:I396V	ENSP00000341236:I396V	I	-	1	0	ZNF695	245217254	0.000000	0.05858	0.009000	0.14445	0.744000	0.42396	-0.039000	0.12124	0.534000	0.28695	0.172000	0.16884	ATT	T|0.968;C|0.032	0.032	strong		0.398	ZNF695-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097823.5	NM_020394	
ZNF883	169834	hgsc.bcm.edu	37	9	115760381	115760381	+	lincRNA	SNP	G	G	A	rs113877750	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:115760381G>A	ENST00000427548.1	-	0	1432							P0CG24	ZN883_HUMAN	zinc finger protein 883						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										CAAGATTACTGTTCCGGGTAA	0.373													G|||	51	0.0101837	0.0371	0.0029	5008	,	,		18831	0.0		0.0	False		,,,				2504	0.0				p.N53N		Atlas-SNP	.											.	.	.	.	0			c.C159T						PASS	.	G		108,4228		3,102,2063	59.0	65.0	63.0		159	-0.9	0.0	9	dbSNP_132	63	1,8557		0,1,4278	no	coding-synonymous	ZNF883	NM_001101338.1		3,103,6341	AA,AG,GG		0.0117,2.4908,0.8454		53/380	115760381	109,12785	2168	4279	6447			169834	exon5			ATTACTGTTCCGG	AK095843		9q32	2010-07-23			ENSG00000228623	ENSG00000228623		"""Zinc fingers, C2H2-type"""	27271	protein-coding gene	gene with protein product							Standard	NM_001101338		Approved		uc011lwy.2	P0CG24	OTTHUMG00000020514		9.37:g.115760381G>A		100.0	0.0	0		93.0	34.0	0.365591	NM_001101338		Silent	SNP	ENST00000427548.1	37																																																																																				G|0.991;A|0.009	0.009	strong		0.373	ZNF883-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000053704.1	NM_001101338	
ZDHHC2	51201	hgsc.bcm.edu	37	8	17067959	17067959	+	Missense_Mutation	SNP	C	C	G	rs190630185	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:17067959C>G	ENST00000262096.8	+	10	1615	c.920C>G	c.(919-921)aCt>aGt	p.T307S		NM_016353.4	NP_057437.1	Q9UIJ5	ZDHC2_HUMAN	zinc finger, DHHC-type containing 2	307					protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|recycling endosome membrane (GO:0055038)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(1)|pancreas(1)|stomach(1)	8				Colorectal(111;0.0697)|COAD - Colon adenocarcinoma(73;0.244)		CAAGCATCTACTCCTGCAGGG	0.328													C|||	8	0.00159744	0.0	0.0	5008	,	,		16046	0.0		0.008	False		,,,				2504	0.0				p.T307S		Atlas-SNP	.											.	ZDHHC2	25	.	0			c.C920G						PASS	.	C	SER/THR	1,3667		0,1,1833	69.0	64.0	65.0		920	5.5	1.0	8		65	28,8156		0,28,4064	yes	missense	ZDHHC2	NM_016353.4	58	0,29,5897	GG,GC,CC		0.3421,0.0273,0.2447	benign	307/368	17067959	29,11823	1834	4092	5926	SO:0001583	missense	51201	exon10			CATCTACTCCTGC	AB023584	CCDS47810.1	8p22	2008-05-15			ENSG00000104219	ENSG00000104219		"""Zinc fingers, DHHC-type"""	18469	protein-coding gene	gene with protein product						10918388	Standard	NM_016353		Approved	ZNF372	uc003wxe.3	Q9UIJ5	OTTHUMG00000163860	ENST00000262096.8:c.920C>G	8.37:g.17067959C>G	ENSP00000262096:p.Thr307Ser	58.0	0.0	0		76.0	37.0	0.486842	NM_016353	D3DSP5	Missense_Mutation	SNP	ENST00000262096.8	37	CCDS47810.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	C	8.049	0.765606	0.15914	2.73E-4	0.003421	ENSG00000104219	ENST00000262096	T	0.41758	0.99	5.53	5.53	0.82687	.	0.075692	0.51477	D	0.000086	T	0.23210	0.0561	N	0.22421	0.69	0.43160	D	0.994945	B	0.11235	0.004	B	0.08055	0.003	T	0.13710	-1.0499	10	0.08179	T	0.78	-3.0288	19.8416	0.96692	0.0:1.0:0.0:0.0	.	307	Q9UIJ5	ZDHC2_HUMAN	S	307	ENSP00000262096:T307S	ENSP00000262096:T307S	T	+	2	0	ZDHHC2	17112330	0.998000	0.40836	0.996000	0.52242	0.427000	0.31564	4.020000	0.57189	2.774000	0.95407	0.585000	0.79938	ACT	C|0.997;G|0.003	0.003	strong		0.328	ZDHHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376014.2	NM_016353	
CWC25	54883	hgsc.bcm.edu	37	17	36963226	36963226	+	Silent	SNP	G	G	T	rs3785452	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:36963226G>T	ENST00000225428.5	-	7	991	c.694C>A	c.(694-696)Cgg>Agg	p.R232R	CWC25_ENST00000536127.1_Silent_p.R169R	NM_017748.3	NP_060218.1	Q9NXE8	CWC25_HUMAN	CWC25 spliceosome-associated protein homolog (S. cerevisiae)	232										central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(1)|lung(4)|upper_aerodigestive_tract(1)	14						TCAGAGTTCCGGACCTACATC	0.512													T|||	805	0.160743	0.4849	0.049	5008	,	,		18783	0.0556		0.0109	False		,,,				2504	0.0644				p.R232R		Atlas-SNP	.											.	CWC25	24	.	0			c.C694A						PASS	.	T		1555,2235		324,907,664	83.0	78.0	80.0		694	3.0	0.4	17	dbSNP_107	80	121,8119		0,121,3999	no	coding-synonymous	CWC25	NM_017748.3		324,1028,4663	TT,TG,GG		1.4684,41.029,13.9318		232/426	36963226	1676,10354	1895	4120	6015	SO:0001819	synonymous_variant	54883	exon7			AGTTCCGGACCTA	AK000298	CCDS45663.1	17q12	2010-01-26	2010-01-26	2010-01-26		ENSG00000273559			25989	protein-coding gene	gene with protein product			"""coiled-coil domain containing 49"""	CCDC49		19941820	Standard	NM_017748		Approved	FLJ20291	uc002hqu.4	Q9NXE8		ENST00000225428.5:c.694C>A	17.37:g.36963226G>T		137.0	0.0	0		131.0	131.0	1	NM_017748	A0JLM3|Q68DK5	Silent	SNP	ENST00000225428.5	37	CCDS45663.1																																																																																			G|0.860;T|0.140	0.140	strong		0.512	CWC25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442186.6	NM_017748	
CCSER1	401145	hgsc.bcm.edu	37	4	91230407	91230407	+	Silent	SNP	T	T	C	rs34445159	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:91230407T>C	ENST00000509176.1	+	2	1260	c.972T>C	c.(970-972)taT>taC	p.Y324Y	CCSER1_ENST00000432775.2_Silent_p.Y324Y|CCSER1_ENST00000333691.8_Silent_p.Y324Y	NM_001145065.1	NP_001138537.1	Q9C0I3	CCSE1_HUMAN	coiled-coil serine-rich protein 1	324																	CTGGGAAATATAGGTTAGAGG	0.413													T|||	23	0.00459265	0.0166	0.0014	5008	,	,		20571	0.0		0.0	False		,,,				2504	0.0				p.Y324Y		Atlas-SNP	.											.	.	.	.	0			c.T972C						PASS	.	T	,	68,3690		1,66,1812	124.0	117.0	119.0		972,972	1.3	1.0	4	dbSNP_126	119	1,8211		0,1,4105	no	coding-synonymous,coding-synonymous	FAM190A	NM_001145065.1,NM_207491.2	,	1,67,5917	CC,CT,TT		0.0122,1.8095,0.5764	,	324/901,324/678	91230407	69,11901	1879	4106	5985	SO:0001819	synonymous_variant	401145	exon2			GAAATATAGGTTA		CCDS47099.1, CCDS47100.1	4q22.1	2012-12-03	2012-12-03	2012-12-03	ENSG00000184305	ENSG00000184305			29349	protein-coding gene	gene with protein product			"""family with sequence similarity 190, member A"""	FAM190A		11214970	Standard	NM_001145065		Approved	KIAA1680	uc003hsv.4	Q9C0I3	OTTHUMG00000160950	ENST00000509176.1:c.972T>C	4.37:g.91230407T>C		178.0	0.0	0		218.0	92.0	0.422018	NM_001145065	Q4W5M0|Q86V57	Silent	SNP	ENST00000509176.1	37	CCDS47099.1																																																																																			T|0.995;C|0.005	0.005	strong		0.413	CCSER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363109.3	NM_001145065	
ALDH16A1	126133	hgsc.bcm.edu	37	19	49967996	49967996	+	Silent	SNP	G	G	A	rs10421522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49967996G>A	ENST00000293350.4	+	12	1708	c.1545G>A	c.(1543-1545)ccG>ccA	p.P515P	ALDH16A1_ENST00000540132.1_Silent_p.P352P|ALDH16A1_ENST00000455361.2_Silent_p.P464P|CTD-3148I10.9_ENST00000599536.1_3'UTR|ALDH16A1_ENST00000433981.2_Silent_p.P350P	NM_153329.3	NP_699160.2	Q8IZ83	A16A1_HUMAN	aldehyde dehydrogenase 16 family, member A1	515						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor (GO:0016620)			cervix(2)|endometrium(3)|kidney(2)|large_intestine(3)|lung(5)|skin(2)|urinary_tract(3)	20		all_lung(116;5.39e-06)|Lung NSC(112;1.97e-05)|all_neural(266;0.0966)|Ovarian(192;0.15)		OV - Ovarian serous cystadenocarcinoma(262;0.00156)|GBM - Glioblastoma multiforme(486;0.0251)		CAACCCTGCCGGCTGGGCCTG	0.617													g|||	197	0.0393371	0.1399	0.0159	5008	,	,		14923	0.0		0.001	False		,,,				2504	0.0				p.P515P		Atlas-SNP	.											.	ALDH16A1	54	.	0			c.G1545A						PASS	.	A	,	461,3945	218.4+/-236.5	24,413,1766	105.0	113.0	111.0		1392,1545	-8.9	0.0	19	dbSNP_119	111	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	ALDH16A1	NM_001145396.1,NM_153329.3	,	24,418,6061	AA,AG,GG		0.0581,10.463,3.583	,	464/752,515/803	49967996	466,12540	2203	4300	6503	SO:0001819	synonymous_variant	126133	exon12			CCTGCCGGCTGGG	AY007096	CCDS12766.1, CCDS46141.1	19q13.33	2014-08-12			ENSG00000161618	ENSG00000161618		"""Aldehyde dehydrogenases"""	28114	protein-coding gene	gene with protein product		613358					Standard	NM_153329		Approved	MGC10204	uc002pnt.3	Q8IZ83	OTTHUMG00000183163	ENST00000293350.4:c.1545G>A	19.37:g.49967996G>A		67.0	0.0	0		79.0	40.0	0.506329	NM_153329	B4DLQ1|C9JBH6|Q86YF0|Q8IYL4|Q8TEI8	Silent	SNP	ENST00000293350.4	37	CCDS12766.1																																																																																			G|0.964;A|0.036	0.036	strong		0.617	ALDH16A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465358.1	NM_153329	
OR8K1	390157	hgsc.bcm.edu	37	11	56113703	56113703	+	Silent	SNP	C	C	T	rs145394503	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:56113703C>T	ENST00000279783.2	+	1	283	c.189C>T	c.(187-189)acC>acT	p.T63T		NM_001002907.1	NP_001002907.1	Q8NGG5	OR8K1_HUMAN	olfactory receptor, family 8, subfamily K, member 1	63						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(8)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33	Esophageal squamous(21;0.00448)					AGCTACACACCCCCATGTACT	0.433										HNSCC(65;0.19)			C|||	35	0.00698882	0.0242	0.0029	5008	,	,		19161	0.0		0.001	False		,,,				2504	0.0				p.T63T		Atlas-SNP	.											.	OR8K1	93	.	0			c.C189T						PASS	.	C		108,4294	83.9+/-122.4	2,104,2095	165.0	149.0	154.0		189	-10.0	0.0	11	dbSNP_134	154	3,8589	2.2+/-6.3	0,3,4293	no	coding-synonymous	OR8K1	NM_001002907.1		2,107,6388	TT,TC,CC		0.0349,2.4534,0.8542		63/320	56113703	111,12883	2201	4296	6497	SO:0001819	synonymous_variant	390157	exon1			ACACACCCCCATG	AB065835	CCDS31528.1	11q11	2012-08-09			ENSG00000150261	ENSG00000150261		"""GPCR / Class A : Olfactory receptors"""	14831	protein-coding gene	gene with protein product							Standard	NM_001002907		Approved		uc010rjg.2	Q8NGG5	OTTHUMG00000166858	ENST00000279783.2:c.189C>T	11.37:g.56113703C>T		216.0	1.0	0.00462963		189.0	94.0	0.497355	NM_001002907	B9EJB1|Q6IFC3|Q96RC1	Silent	SNP	ENST00000279783.2	37	CCDS31528.1																																																																																			C|0.993;T|0.007	0.007	strong		0.433	OR8K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391605.1	NM_001002907	
ENDOD1	23052	hgsc.bcm.edu	37	11	94862340	94862340	+	Missense_Mutation	SNP	A	A	T	rs188091415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:94862340A>T	ENST00000278505.4	+	2	1218	c.1100A>T	c.(1099-1101)cAg>cTg	p.Q367L		NM_015036.2	NP_055851.1	O94919	ENDD1_HUMAN	endonuclease domain containing 1	367						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)				GTTACCAAGCAGGTGATTAAT	0.438													A|||	5	0.000998403	0.0038	0.0	5008	,	,		21650	0.0		0.0	False		,,,				2504	0.0				p.Q367L		Atlas-SNP	.											.	ENDOD1	26	.	0			c.A1100T						PASS	.	A	LEU/GLN	12,3830		0,12,1909	114.0	102.0	106.0		1100	4.9	1.0	11		106	0,8256		0,0,4128	yes	missense	ENDOD1	NM_015036.2	113	0,12,6037	TT,TA,AA		0.0,0.3123,0.0992	possibly-damaging	367/501	94862340	12,12086	1921	4128	6049	SO:0001583	missense	23052	exon2			CCAAGCAGGTGAT	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.1100A>T	11.37:g.94862340A>T	ENSP00000278505:p.Gln367Leu	165.0	0.0	0		145.0	89.0	0.613793	NM_015036	A8K6K8|Q6GQY5|Q8TAQ8	Missense_Mutation	SNP	ENST00000278505.4	37	CCDS41699.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	13.12	2.141283	0.37825	0.003123	0.0	ENSG00000149218	ENST00000278505	T	0.33865	1.39	6.03	4.88	0.63580	.	0.171913	0.40469	N	0.001086	T	0.26991	0.0661	M	0.67953	2.075	0.32644	N	0.52035	B	0.18461	0.028	B	0.17433	0.018	T	0.44360	-0.9333	10	0.87932	D	0	-24.9899	6.2791	0.20997	0.7766:0.0:0.0796:0.1438	.	367	O94919	ENDD1_HUMAN	L	367	ENSP00000278505:Q367L	ENSP00000278505:Q367L	Q	+	2	0	ENDOD1	94501988	0.987000	0.35691	0.993000	0.49108	0.553000	0.35397	1.425000	0.34859	1.066000	0.40716	0.455000	0.32223	CAG	A|0.998;T|0.002	0.002	strong		0.438	ENDOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396545.1	NM_015036	
RPGR	6103	hgsc.bcm.edu	37	X	38145918	38145918	+	Intron	SNP	C	C	T	rs201730068		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:38145918C>T	ENST00000339363.3	-	14	2688				RPGR_ENST00000378505.2_Silent_p.E778E|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000309513.3_Intron|RPGR_ENST00000318842.7_Intron|RPGR_ENST00000342811.3_Intron|RPGR_ENST00000338898.3_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						ccgctctttcctcctttttcc	0.537																																					p.E778E		Atlas-SNP	.											.	RPGR	175	.	0			c.G2334A						PASS	.						315.0	191.0	233.0					X																	38145918		1858	3627	5485	SO:0001627	intron_variant	6103	exon15			TCTTTCCTCCTTT	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+428G>A	X.37:g.38145918C>T		459.0	0.0	0		294.0	15.0	0.0510204	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	Silent	SNP	ENST00000339363.3	37																																																																																				.	.	none		0.537	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
PGAM4	441531	hgsc.bcm.edu	37	X	77225099	77225099	+	Missense_Mutation	SNP	C	C	T	rs6622613	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:77225099C>T	ENST00000458128.1	-	1	36	c.37G>A	c.(37-39)Gag>Aag	p.E13K	ATP7A_ENST00000343533.5_Intron|ATP7A_ENST00000350425.4_Intron|ATP7A_ENST00000341514.6_Intron	NM_001029891.2	NP_001025062.1	Q8N0Y7	PGAM4_HUMAN	phosphoglycerate mutase family member 4	13					glycolytic process (GO:0006096)|positive regulation of sperm motility (GO:1902093)	extracellular vesicular exosome (GO:0070062)|sperm principal piece (GO:0097228)	bisphosphoglycerate 2-phosphatase activity (GO:0004083)|bisphosphoglycerate mutase activity (GO:0004082)|phosphoglycerate mutase activity (GO:0004619)			endometrium(2)|lung(4)	6						CATGTGCTCTCGCCGTGCCGG	0.587													C|||	52	0.0137748	0.0363	0.0058	3775	,	,		12671	0.0		0.0	False		,,,				2504	0.0				p.E13K		Atlas-SNP	.											.	PGAM4	28	.	0			c.G37A						PASS	.	C	,LYS/GLU	101,3734		1,82,17,1549,554	55.0	54.0	54.0		,37	0.1	0.6	X	dbSNP_116	54	9,6713		0,7,2,2420,1866	no	intron,missense	ATP7A,PGAM4	NM_000052.4,NM_001029891.2	,56	1,89,19,3969,2420	TT,TC,T,CC,C		0.1339,2.6336,1.042	,possibly-damaging	,13/255	77225099	110,10447	2203	4295	6498	SO:0001583	missense	441531	exon1			TGCTCTCGCCGTG	AF465731	CCDS35338.1	Xq21.1	2011-02-09	2006-02-09		ENSG00000226784	ENSG00000226784			21731	protein-coding gene	gene with protein product		300567	"""phosphoglycerate mutase family 4"""			11961099, 9370262	Standard	NM_001029891		Approved	dJ1000K24.1, PGAM3, PGAM-B, PGAM1	uc004ecy.1	Q8N0Y7	OTTHUMG00000057865	ENST00000458128.1:c.37G>A	X.37:g.77225099C>T	ENSP00000412189:p.Glu13Lys	470.0	1.0	0.00212766		488.0	248.0	0.508197	NM_001029891	Q5JPN2|Q8NI24|Q8NI25|Q8NI26	Missense_Mutation	SNP	ENST00000458128.1	37	CCDS35338.1	13	0.007836045810729355	4	0.008298755186721992	4	0.011111111111111112	0	0.0	0	0.0	C	17.78	3.473730	0.63737	0.026336	0.001339	ENSG00000226784	ENST00000458128	D	0.83163	-1.69	0.119	0.119	0.14685	Histidine phosphatase superfamily, clade-1 (2);	0.000000	0.85682	U	0.000000	T	0.53916	0.1826	L	0.55743	1.74	0.22675	P	0.99886112	B	0.31077	0.307	B	0.35655	0.207	T	0.64266	-0.6448	8	.	.	.	-7.1432	6.135	0.20227	0.0:0.9996:0.0:4.0E-4	rs6622613	13	Q8N0Y7	PGAM4_HUMAN	K	13	ENSP00000412189:E13K	.	E	-	1	0	PGAM4	77111755	1.000000	0.71417	0.623000	0.29173	0.641000	0.38312	3.649000	0.54417	0.260000	0.21731	0.264000	0.19307	GAG	C|0.990;T|0.010	0.010	strong		0.587	PGAM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128371.2	NM_001029891	
UBE3A	7337	hgsc.bcm.edu	37	15	25616844	25616844	+	Silent	SNP	T	T	A	rs28528079	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:25616844T>A	ENST00000397954.2	-	4	485	c.486A>T	c.(484-486)gcA>gcT	p.A162A	SNHG14_ENST00000554726.1_RNA|UBE3A_ENST00000566215.1_Silent_p.A139A|UBE3A_ENST00000428984.2_Silent_p.A139A|UBE3A_ENST00000438097.1_Silent_p.A139A|UBE3A_ENST00000232165.3_Silent_p.A159A			Q05086	UBE3A_HUMAN	ubiquitin protein ligase E3A	162					androgen receptor signaling pathway (GO:0030521)|brain development (GO:0007420)|ovarian follicle development (GO:0001541)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prostate gland growth (GO:0060736)|protein autoubiquitination (GO:0051865)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|proteolysis (GO:0006508)|sperm entry (GO:0035037)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|proteasome complex (GO:0000502)	ligase activity (GO:0016874)|transcription coactivator activity (GO:0003713)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(3)|kidney(1)|large_intestine(14)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	38		all_cancers(20;3.47e-21)|Breast(32;0.00123)		all cancers(64;2.78e-08)|Epithelial(43;8.85e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0155)|Lung(196;0.0616)		TCTGTACCAATGCCTCAGCAC	0.363													T|||	167	0.0333466	0.1172	0.0144	5008	,	,		19091	0.0		0.001	False		,,,				2504	0.001				p.A162A		Atlas-SNP	.											.	UBE3A	109	.	0			c.A486T						PASS	.	T	,,	406,4000	196.0+/-220.5	19,368,1816	104.0	106.0	105.0		486,417,477	-0.7	1.0	15	dbSNP_125	105	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	UBE3A	NM_000462.3,NM_130838.1,NM_130839.2	,,	19,369,6115	AA,AT,TT		0.0116,9.2147,3.1293	,,	162/876,139/853,159/873	25616844	407,12599	2203	4300	6503	SO:0001819	synonymous_variant	7337	exon7			TACCAATGCCTCA	AF002224	CCDS32177.1, CCDS45191.1, CCDS45192.1	15q11.2	2014-09-17	2008-07-31		ENSG00000114062	ENSG00000114062	6.3.2.19		12496	protein-coding gene	gene with protein product	"""Angelman syndrome"""	601623	"""human papilloma virus E6-associated protein"""	EPVE6AP, HPVE6A		8221889	Standard	NM_130838		Approved	AS, ANCR, E6-AP, FLJ26981	uc001zas.3	Q05086		ENST00000397954.2:c.486A>T	15.37:g.25616844T>A		295.0	0.0	0		341.0	169.0	0.495601	NM_000462	A8K8Z9|P78355|Q93066|Q9UEP4|Q9UEP5|Q9UEP6|Q9UEP7|Q9UEP8|Q9UEP9	Silent	SNP	ENST00000397954.2	37	CCDS45192.1																																																																																			T|0.958;A|0.042	0.042	strong		0.363	UBE3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000434203.1	NM_000462	
FAM178B	51252	hgsc.bcm.edu	37	2	97543701	97543701	+	Missense_Mutation	SNP	G	G	A	rs34013660	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:97543701G>A	ENST00000417561.3	-	20	2376	c.2377C>T	c.(2377-2379)Cgc>Tgc	p.R793C	FAM178B_ENST00000470789.1_5'UTR|FAM178B_ENST00000393526.2_Missense_Mutation_p.R85C|FAM178B_ENST00000327896.3_Missense_Mutation_p.R613C|FAM178B_ENST00000490605.2_Missense_Mutation_p.R645C			Q8IXR5	F178B_HUMAN	family with sequence similarity 178, member B	793			R -> C (in dbSNP:rs34013660).							large_intestine(1)|ovary(1)	2						AGCATGGTGCGGTGCATGGCC	0.672													G|||	86	0.0171725	0.0635	0.0014	5008	,	,		16465	0.0		0.001	False		,,,				2504	0.0				p.R645C		Atlas-SNP	.											FAM178B_ENST00000417561,colon,carcinoma,+1,2	FAM178B	35	2	0			c.C1933T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG	256,4150	147.3+/-181.8	8,240,1955	77.0	64.0	68.0		1933,310,253	2.3	1.0	2	dbSNP_126	68	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense	FAM178B	NM_001122646.2,NM_001172667.1,NM_016490.4	180,180,180	8,242,6253	AA,AG,GG		0.0233,5.8103,1.9837	probably-damaging,probably-damaging,probably-damaging	645/680,104/139,85/120	97543701	258,12748	2203	4300	6503	SO:0001583	missense	51252	exon16			TGGTGCGGTGCAT	AF151068, BC039488	CCDS33252.1, CCDS46366.1, CCDS46366.2	2q11.2	2008-08-08			ENSG00000168754	ENSG00000168754			28036	protein-coding gene	gene with protein product						11042152	Standard	NM_001122646		Approved	LOC51252	uc002sxl.4	Q8IXR5	OTTHUMG00000155257	ENST00000417561.3:c.2377C>T	2.37:g.97543701G>A	ENSP00000413245:p.Arg793Cys	120.0	0.0	0		84.0	44.0	0.52381	NM_001122646	A8MXN2|E9PD86|Q8IUY0|Q9P0P4	Missense_Mutation	SNP	ENST00000417561.3	37		30	0.013736263736263736	29	0.05894308943089431	0	0.0	0	0.0	1	0.0013192612137203166	G	16.16	3.045853	0.55110	0.058103	2.33E-4	ENSG00000168754	ENST00000417561;ENST00000327896;ENST00000393526;ENST00000490605	T;T;T;T	0.60797	0.18;0.2;0.16;0.18	5.2	2.31	0.28768	.	.	.	.	.	T	0.14830	0.0358	M	0.62723	1.935	0.41162	D	0.986107	D	0.71674	0.998	P	0.53861	0.736	T	0.33369	-0.9871	9	0.87932	D	0	-4.1547	4.8677	0.13616	0.1825:0.0:0.636:0.1815	rs34013660	793	Q8IXR5	F178B_HUMAN	C	793;613;85;645	ENSP00000413245:R793C;ENSP00000333553:R613C;ENSP00000377160:R85C;ENSP00000429896:R645C	ENSP00000333553:R613C	R	-	1	0	FAM178B	96907428	0.594000	0.26849	0.988000	0.46212	0.405000	0.30901	0.542000	0.23222	0.161000	0.19458	0.455000	0.32223	CGC	G|0.979;A|0.021	0.021	strong		0.672	FAM178B-202	KNOWN	basic	protein_coding	protein_coding		NM_016490	
C16orf58	64755	hgsc.bcm.edu	37	16	31505252	31505252	+	Silent	SNP	C	C	T	rs34231527	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31505252C>T	ENST00000327237.2	-	7	747	c.708G>A	c.(706-708)acG>acA	p.T236T	C16orf58_ENST00000567994.1_Silent_p.T191T|C16orf58_ENST00000430477.2_Silent_p.T94T|C16orf58_ENST00000570164.1_Silent_p.T236T			Q96GQ5	RUS1_HUMAN	chromosome 16 open reading frame 58	236						integral component of membrane (GO:0016021)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)	14						GGTTCACCAGCGTCTCCTGGA	0.622													C|||	36	0.0071885	0.025	0.0043	5008	,	,		16051	0.0		0.0	False		,,,				2504	0.0				p.S236S		Atlas-SNP	.											.	C16orf58	28	.	0			c.C708A						PASS	.	C		101,4291	76.8+/-115.0	1,99,2096	34.0	36.0	36.0		708	-6.7	0.8	16	dbSNP_126	36	1,8599	1.2+/-3.3	0,1,4299	yes	coding-synonymous	C16orf58	NM_022744.2		1,100,6395	TT,TC,CC		0.0116,2.2996,0.7851		236/469	31505252	102,12890	2196	4300	6496	SO:0001819	synonymous_variant	64755	exon7			CACCAGCGTCTCC	AK023930	CCDS10715.1	16p11.2	2013-03-04			ENSG00000140688	ENSG00000140688			25848	protein-coding gene	gene with protein product							Standard	NM_022744		Approved	FLJ13868	uc002eci.3	Q96GQ5	OTTHUMG00000132466	ENST00000327237.2:c.708G>A	16.37:g.31505252C>T		78.0	0.0	0		124.0	63.0	0.508065	NM_022744	Q53GL8|Q8NAJ4|Q9BVY3|Q9H887	Silent	SNP	ENST00000327237.2	37	CCDS10715.1																																																																																			C|0.991;T|0.009	0.009	strong		0.622	C16orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255629.2	NM_022744	
CMPK2	129607	hgsc.bcm.edu	37	2	7005236	7005236	+	Missense_Mutation	SNP	G	G	T	rs575313172		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:7005236G>T	ENST00000256722.5	-	1	591	c.592C>A	c.(592-594)Ccc>Acc	p.P198T	CMPK2_ENST00000404168.1_Missense_Mutation_p.P198T|CMPK2_ENST00000458098.1_Missense_Mutation_p.P198T|CMPK2_ENST00000478738.1_Intron	NM_207315.3	NP_997198.2	Q5EBM0	CMPK2_HUMAN	cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial	198					cellular response to lipopolysaccharide (GO:0071222)|dTDP biosynthetic process (GO:0006233)|dUDP biosynthetic process (GO:0006227)|nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)|thymidylate kinase activity (GO:0004798)|UMP kinase activity (GO:0033862)			large_intestine(1)|lung(13)|prostate(1)|upper_aerodigestive_tract(1)	16	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					TGCAGCGGGGGCTCCGGGACG	0.721													G|||	1	0.000199681	0.0008	0.0	5008	,	,		11581	0.0		0.0	False		,,,				2504	0.0				p.P198T		Atlas-SNP	.											.	CMPK2	30	.	0			c.C592A						PASS	.						3.0	5.0	4.0					2																	7005236		1735	3836	5571	SO:0001583	missense	129607	exon1			GCGGGGGCTCCGG		CCDS42648.1, CCDS58695.1, CCDS58696.1	2p25.2	2008-01-25			ENSG00000134326	ENSG00000134326	2.7.4.14		27015	protein-coding gene	gene with protein product	"""cytidylate kinase 2"""	611787				17999954	Standard	NM_207315		Approved	TYKi, UMP-CMPK2	uc002qyo.4	Q5EBM0	OTTHUMG00000151629	ENST00000256722.5:c.592C>A	2.37:g.7005236G>T	ENSP00000256722:p.Pro198Thr	6.0	0.0	0		12.0	6.0	0.5	NM_001256478	A2RUB0|A5D8T2|B7ZM18|Q6ZRU2|Q96AL8	Missense_Mutation	SNP	ENST00000256722.5	37	CCDS42648.1	.	.	.	.	.	.	.	.	.	.	G	18.09	3.547309	0.65311	.	.	ENSG00000134326	ENST00000458098;ENST00000256722;ENST00000404168	T	0.57436	0.4	4.43	3.55	0.40652	.	0.061334	0.64402	D	0.000003	T	0.55065	0.1897	L	0.29908	0.895	0.38526	D	0.948847	D;D	0.67145	0.996;0.994	P;P	0.62014	0.897;0.663	T	0.60311	-0.7288	10	0.66056	D	0.02	-21.992	10.2012	0.43084	0.0989:0.0:0.9011:0.0	.	198;198	Q5EBM0-3;Q5EBM0	.;CMPK2_HUMAN	T	198	ENSP00000256722:P198T	ENSP00000256722:P198T	P	-	1	0	CMPK2	6922687	1.000000	0.71417	0.566000	0.28421	0.894000	0.52154	2.696000	0.47052	1.069000	0.40788	0.563000	0.77884	CCC	.	.	none		0.721	CMPK2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323339.2	NM_207315	
LMNTD1	160492	hgsc.bcm.edu	37	12	25673001	25673001	+	Silent	SNP	C	C	G	rs76419032	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:25673001C>G	ENST00000282881.6	-	6	893	c.744G>C	c.(742-744)gcG>gcC	p.A248A	IFLTD1_ENST00000539744.1_Silent_p.A151A|IFLTD1_ENST00000458174.2_Silent_p.A269A|IFLTD1_ENST00000413632.2_Silent_p.A229A|IFLTD1_ENST00000445693.1_Silent_p.A185A	NM_152590.3	NP_689803.2	Q8N9Z9	LMTD1_HUMAN		248	LTD.				cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22	all_lung(3;2.75e-22)|Lung NSC(3;1.77e-21)|all_hematologic(7;0.00656)|Colorectal(261;0.0847)					GGGTGTACCACGCAATGGCCT	0.343													G|||	88	0.0175719	0.0628	0.0072	5008	,	,		13235	0.0		0.0	False		,,,				2504	0.0				p.A269A		Atlas-SNP	.											.	IFLTD1	121	.	0			c.G807C						PASS	.	G	,,,	248,4158	801.2+/-415.6	5,238,1960	79.0	67.0	71.0		555,807,687,744	0.9	1.0	12	dbSNP_132	71	1,8599	818.4+/-406.9	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IFLTD1	NM_001145727.1,NM_001145728.1,NM_001145729.1,NM_152590.2	,,,	5,239,6259	GG,GC,CC		0.0116,5.6287,1.9145	,,,	185/326,269/410,229/370,248/389	25673001	249,12757	2203	4300	6503	SO:0001819	synonymous_variant	160492	exon7			GTACCACGCAATG																												ENST00000282881.6:c.744G>C	12.37:g.25673001C>G		108.0	0.0	0		112.0	65.0	0.580357	NM_001145728	B4DL27|B4DY70|Q8IY38	Silent	SNP	ENST00000282881.6	37	CCDS8704.1	20	0.009157509157509158	17	0.034552845528455285	3	0.008287292817679558	0	0.0	0	0.0	G	1.295	-0.606444	0.03717	0.056287	1.16E-4	ENSG00000152936	ENST00000543629	.	.	.	5.05	0.883	0.19177	.	.	.	.	.	T	0.06371	0.0164	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.07654	-1.0761	4	.	.	.	-5.3188	0.7606	0.01006	0.2856:0.1643:0.3812:0.1689	.	.	.	.	L	23	.	.	V	-	1	0	IFLTD1	25564268	1.000000	0.71417	0.983000	0.44433	0.110000	0.19582	0.968000	0.29357	0.060000	0.16281	-1.126000	0.01995	GTG	C|0.981;G|0.019	0.019	strong		0.343	IFLTD1-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402279.1		
ARFGAP3	26286	hgsc.bcm.edu	37	22	43195134	43195134	+	Missense_Mutation	SNP	C	C	T	rs36003980	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:43195134C>T	ENST00000263245.5	-	15	1663	c.1444G>A	c.(1444-1446)Gcc>Acc	p.A482T	ARFGAP3_ENST00000429508.2_Missense_Mutation_p.A410T|ARFGAP3_ENST00000437119.2_Missense_Mutation_p.A438T	NM_001142293.1|NM_014570.4	NP_001135765.1|NP_055385.3	Q9NP61	ARFG3_HUMAN	ADP-ribosylation factor GTPase activating protein 3	482			A -> T (in dbSNP:rs36003980).		intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|protein secretion (GO:0009306)|regulation of ARF GTPase activity (GO:0032312)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF GTPase activator activity (GO:0008060)|protein transporter activity (GO:0008565)|zinc ion binding (GO:0008270)			breast(3)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)	11						ATGTCGGGGGCGTTGGGCAGC	0.562													C|||	80	0.0159744	0.0575	0.0043	5008	,	,		17224	0.0		0.001	False		,,,				2504	0.0				p.A482T	GBM(58;544 1030 21460 27159 48838)	Atlas-SNP	.											.	ARFGAP3	48	.	0			c.G1444A						PASS	.	C	THR/ALA,THR/ALA	192,4214	120.8+/-158.4	4,184,2015	144.0	126.0	132.0		1312,1444	3.6	0.4	22	dbSNP_126	132	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	ARFGAP3	NM_001142293.1,NM_014570.4	58,58	4,187,6312	TT,TC,CC		0.0349,4.3577,1.4993	benign,benign	438/473,482/517	43195134	195,12811	2203	4300	6503	SO:0001583	missense	26286	exon15			CGGGGGCGTTGGG	AK002083	CCDS14042.1, CCDS46722.1	22q13.2	2009-11-30	2002-08-20	2002-08-23	ENSG00000242247	ENSG00000242247		"""ADP-ribosylation factor GTPase activating proteins"""	661	protein-coding gene	gene with protein product		612439	"""ADP-ribosylation factor GTPase activating protein 1"""	ARFGAP1		10704287, 11172815	Standard	NM_014570		Approved		uc003bdd.2	Q9NP61	OTTHUMG00000150718	ENST00000263245.5:c.1444G>A	22.37:g.43195134C>T	ENSP00000263245:p.Ala482Thr	65.0	0.0	0		76.0	43.0	0.565789	NM_014570	E9PB03|Q9BSC6|Q9H9J0|Q9NT10|Q9NUP5|Q9Y4V3|Q9Y4V4	Missense_Mutation	SNP	ENST00000263245.5	37	CCDS14042.1	27	0.012362637362637362	27	0.054878048780487805	0	0.0	0	0.0	0	0.0	C	11.57	1.678342	0.29783	0.043577	3.49E-4	ENSG00000242247	ENST00000263245;ENST00000429508;ENST00000437119	T;T;T	0.07021	3.4;3.23;3.35	4.65	3.63	0.41609	.	0.000000	0.85682	D	0.000000	T	0.01092	0.0036	L	0.48260	1.515	0.53005	D	0.999964	B;B	0.33212	0.066;0.402	B;B	0.20184	0.028;0.027	T	0.31943	-0.9925	10	0.51188	T	0.08	0.0519	11.8638	0.52482	0.0:0.9119:0.0:0.0881	rs36003980	438;482	E9PB03;Q9NP61	.;ARFG3_HUMAN	T	482;410;438	ENSP00000263245:A482T;ENSP00000393959:A410T;ENSP00000388791:A438T	ENSP00000263245:A482T	A	-	1	0	ARFGAP3	41525078	1.000000	0.71417	0.437000	0.26809	0.135000	0.20990	4.958000	0.63660	0.951000	0.37770	-0.137000	0.14449	GCC	C|0.983;T|0.017	0.017	strong		0.562	ARFGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319747.2	NM_014570	
HIST1H2BE	8344	hgsc.bcm.edu	37	6	26184082	26184082	+	Missense_Mutation	SNP	C	C	G	rs61978632	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:26184082C>G	ENST00000356530.3	+	1	125	c.59C>G	c.(58-60)aCc>aGc	p.T20S		NM_003523.2	NP_003514.2	P62807	H2B1C_HUMAN	histone cluster 1, H2be	20					antibacterial humoral response (GO:0019731)|chromatin organization (GO:0006325)|defense response to Gram-positive bacterium (GO:0050830)|innate immune response in mucosa (GO:0002227)|nucleosome assembly (GO:0006334)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			endometrium(1)|large_intestine(2)|lung(1)	4						AAGGCCGTGACCAAGGCGCAG	0.557													C|||	202	0.0403355	0.1339	0.0216	5008	,	,		19019	0.0		0.002	False		,,,				2504	0.0082				p.T20S		Atlas-SNP	.											.	HIST1H2BE	10	.	0			c.C59G						PASS	.	C	SER/THR	444,3962		21,402,1780	121.0	113.0	116.0		59	5.1	1.0	6	dbSNP_129	116	31,8569		0,31,4269	no	missense	HIST1H2BE	NM_003523.2	58	21,433,6049	GG,GC,CC		0.3605,10.0772,3.6522	benign	20/127	26184082	475,12531	2203	4300	6503	SO:0001583	missense	8344	exon1			CCGTGACCAAGGC	Z80780	CCDS4588.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000197697	ENSG00000274290		"""Histones / Replication-dependent"""	4753	protein-coding gene	gene with protein product		602805	"""H2B histone family, member H"", ""histone 1, H2be"""	H2BFH		9119399, 12408966	Standard	NM_003523		Approved	H2B/h, H2B.h	uc003ngt.3	P62807	OTTHUMG00000014427	ENST00000356530.3:c.59C>G	6.37:g.26184082C>G	ENSP00000348924:p.Thr20Ser	225.0	0.0	0		213.0	105.0	0.492958	NM_003523	P02278|Q3B872|Q4VB69|Q93078|Q93080	Missense_Mutation	SNP	ENST00000356530.3	37	CCDS4588.1	72	0.03296703296703297	64	0.13008130081300814	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	.	17.23	3.336510	0.60963	0.100772	0.003605	ENSG00000197697	ENST00000356530	T	0.22539	1.95	5.08	5.08	0.68730	.	0.000000	0.35040	U	0.003493	T	0.34308	0.0893	.	.	.	0.25861	P	0.9838228	.	.	.	.	.	.	T	0.09100	-1.0690	6	0.59425	D	0.04	.	17.8237	0.88657	0.0:1.0:0.0:0.0	rs61978632	.	.	.	S	20	ENSP00000348924:T20S	ENSP00000348924:T20S	T	+	2	0	HIST1H2BE	26292061	1.000000	0.71417	1.000000	0.80357	0.377000	0.30045	5.752000	0.68728	2.526000	0.85167	0.603000	0.83216	ACC	C|0.965;G|0.035	0.035	strong		0.557	HIST1H2BE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040090.1	NM_003523	
TNR	7143	hgsc.bcm.edu	37	1	175306758	175306758	+	Missense_Mutation	SNP	G	G	A	rs61731114	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:175306758G>A	ENST00000367674.2	-	19	4148	c.3440C>T	c.(3439-3441)aCt>aTt	p.T1147I	RP3-518E13.2_ENST00000569593.1_RNA|TNR_ENST00000263525.2_Missense_Mutation_p.T1147I			Q92752	TENR_HUMAN	tenascin R	1147	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|locomotory exploration behavior (GO:0035641)|long-term synaptic potentiation (GO:0060291)|negative regulation of axon extension involved in regeneration (GO:0048692)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of synaptic transmission (GO:0050805)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transmission of nerve impulse (GO:0051971)|synapse organization (GO:0050808)|telencephalon cell migration (GO:0022029)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)				NS(3)|breast(7)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|lung(98)|ovary(4)|pancreas(5)|prostate(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	177	Renal(580;0.146)					CCCACTCAAAGTGTCTCCATT	0.502													G|||	49	0.00978435	0.0303	0.013	5008	,	,		21455	0.0		0.0	False		,,,				2504	0.0				p.T1147I		Atlas-SNP	.											.	TNR	399	.	0			c.C3440T						PASS	.	G	ILE/THR	137,4269	96.7+/-135.4	4,129,2070	58.0	54.0	55.0		3440	5.4	1.0	1	dbSNP_129	55	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TNR	NM_003285.2	89	4,130,6369	AA,AG,GG		0.0116,3.1094,1.061	benign	1147/1359	175306758	138,12868	2203	4300	6503	SO:0001583	missense	7143	exon19			CTCAAAGTGTCTC	X98085	CCDS1318.1	1q24	2013-02-11	2012-07-12		ENSG00000116147	ENSG00000116147		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11953	protein-coding gene	gene with protein product	"""restrictin"", ""janusin"""	601995				8626505, 8940128	Standard	NM_003285		Approved		uc009wwu.1	Q92752	OTTHUMG00000034876	ENST00000367674.2:c.3440C>T	1.37:g.175306758G>A	ENSP00000356646:p.Thr1147Ile	143.0	0.0	0		131.0	71.0	0.541985	NM_003285	C9J563|Q15568|Q5R3G0	Missense_Mutation	SNP	ENST00000367674.2	37	CCDS1318.1	24	0.01098901098901099	20	0.04065040650406504	4	0.011049723756906077	0	0.0	0	0.0	G	22.4	4.278785	0.80692	0.031094	1.16E-4	ENSG00000116147	ENST00000367674;ENST00000263525;ENST00000367673	T;T	0.77229	-1.08;-1.08	5.37	5.37	0.77165	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 1 (1);	0.055231	0.64402	D	0.000001	T	0.47340	0.1440	M	0.62088	1.915	0.58432	D	0.999995	P	0.49253	0.921	B	0.43301	0.415	T	0.69997	-0.4993	10	0.59425	D	0.04	.	13.659	0.62354	0.0:0.0:0.8453:0.1547	.	1147	Q92752	TENR_HUMAN	I	1147;1147;1057	ENSP00000356646:T1147I;ENSP00000263525:T1147I	ENSP00000263525:T1147I	T	-	2	0	TNR	173573381	1.000000	0.71417	0.995000	0.50966	0.992000	0.81027	5.037000	0.64170	2.500000	0.84329	0.655000	0.94253	ACT	G|0.989;A|0.011	0.011	strong		0.502	TNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084414.4	NM_003285	
DYNC1H1	1778	hgsc.bcm.edu	37	14	102469273	102469273	+	Silent	SNP	T	T	C	rs75094258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:102469273T>C	ENST00000360184.4	+	23	5018	c.4854T>C	c.(4852-4854)taT>taC	p.Y1618Y		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	1618	Stem. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						TGGGAGAATATCTGGAAAGAG	0.458													T|||	27	0.00539137	0.0197	0.0014	5008	,	,		19492	0.0		0.0	False		,,,				2504	0.0				p.Y1618Y		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.T4854C						PASS	.	T		53,4353	52.9+/-88.7	1,51,2151	70.0	69.0	70.0		4854	4.5	1.0	14	dbSNP_132	70	0,8600		0,0,4300	no	coding-synonymous	DYNC1H1	NM_001376.4		1,51,6451	CC,CT,TT		0.0,1.2029,0.4075		1618/4647	102469273	53,12953	2203	4300	6503	SO:0001819	synonymous_variant	1778	exon23			AGAATATCTGGAA	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.4854T>C	14.37:g.102469273T>C		92.0	0.0	0		79.0	32.0	0.405063	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	37	CCDS9966.1																																																																																			T|0.994;C|0.006	0.006	strong		0.458	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
ABTB2	25841	hgsc.bcm.edu	37	11	34226140	34226140	+	Silent	SNP	G	G	T	rs77165558	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:34226140G>T	ENST00000435224.2	-	2	1405	c.981C>A	c.(979-981)acC>acA	p.T327T	ABTB2_ENST00000530814.1_5'UTR|ABTB2_ENST00000298992.2_Silent_p.T141T	NM_145804.2	NP_665803.2	Q8N961	ABTB2_HUMAN	ankyrin repeat and BTB (POZ) domain containing 2	327					cellular response to toxic substance (GO:0097237)	nucleus (GO:0005634)				breast(2)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)				ACTGCTCCAGGGTTCGGAGCT	0.637													G|||	142	0.0283546	0.1036	0.0072	5008	,	,		17394	0.0		0.0	False		,,,				2504	0.0				p.T327T		Atlas-SNP	.											ABTB2,NS,carcinoma,-2,1	ABTB2	101	1	0			c.C981A						PASS	.	G		392,4012	193.0+/-218.2	21,350,1831	45.0	43.0	44.0		981	-5.2	1.0	11	dbSNP_132	44	4,8592	3.0+/-9.4	0,4,4294	no	coding-synonymous	ABTB2	NM_145804.2		21,354,6125	TT,TG,GG		0.0465,8.901,3.0462		327/1026	34226140	396,12604	2202	4298	6500	SO:0001819	synonymous_variant	25841	exon2			CTCCAGGGTTCGG	AK056863	CCDS7890.1, CCDS7890.2	11p13	2013-10-02			ENSG00000166016	ENSG00000166016		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	23842	protein-coding gene	gene with protein product							Standard	NM_145804		Approved	DKFZP586C1619, BTBD22, ABTB2A	uc001mvl.2	Q8N961	OTTHUMG00000044382	ENST00000435224.2:c.981C>A	11.37:g.34226140G>T		45.0	0.0	0		33.0	17.0	0.515152	NM_145804	A8K6S9|E9PRW7|Q52LD6|Q6MZW4|Q8NB44	Silent	SNP	ENST00000435224.2	37	CCDS7890.2																																																																																			G|0.972;T|0.028	0.028	strong		0.637	ABTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388703.3	NM_145804	
KIF17	57576	hgsc.bcm.edu	37	1	21030956	21030956	+	Missense_Mutation	SNP	G	G	T	rs56750936	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:21030956G>T	ENST00000247986.2	-	5	1417	c.1107C>A	c.(1105-1107)agC>agA	p.S369R	KIF17_ENST00000375044.1_Missense_Mutation_p.S269R|KIF17_ENST00000400463.3_Missense_Mutation_p.S369R			Q9P2E2	KIF17_HUMAN	kinesin family member 17	369			S -> R (in dbSNP:rs56750936).		ATP catabolic process (GO:0006200)|cell projection organization (GO:0030030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|neurogenesis (GO:0022008)|protein complex localization (GO:0031503)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|intraciliary transport particle B (GO:0030992)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|endometrium(3)|kidney(3)|large_intestine(9)|liver(1)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50		all_lung(284;2.99e-05)|Lung NSC(340;3.26e-05)|Colorectal(325;3.46e-05)|Renal(390;9.67e-05)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|COAD - Colon adenocarcinoma(152;1.43e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000168)|Kidney(64;0.000221)|GBM - Glioblastoma multiforme(114;0.000651)|KIRC - Kidney renal clear cell carcinoma(64;0.0031)|STAD - Stomach adenocarcinoma(196;0.00336)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.209)		GGCTGCTGGGGCTCATCTGCT	0.607													G|||	135	0.0269569	0.0961	0.0101	5008	,	,		14173	0.0		0.0	False		,,,				2504	0.001				p.S369R		Atlas-SNP	.											.	KIF17	130	.	0			c.C1107A						PASS	.	G	ARG/SER,ARG/SER	369,4037	188.5+/-214.9	14,341,1848	85.0	73.0	77.0		1107,1107	3.4	1.0	1	dbSNP_129	77	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense	KIF17	NM_001122819.1,NM_020816.2	110,110	14,347,6142	TT,TG,GG		0.0698,8.3749,2.8833	benign,benign	369/1029,369/1030	21030956	375,12631	2203	4300	6503	SO:0001583	missense	57576	exon5			GCTGGGGCTCATC	AB037826	CCDS213.1, CCDS44079.1, CCDS72722.1	1p36.13	2012-08-01			ENSG00000117245	ENSG00000117245		"""Kinesins"""	19167	protein-coding gene	gene with protein product	"""kinesin-like protein KIF17"", ""KIF3-related motor protein"", ""KIF17 variant protein"""	605037				10846156	Standard	XR_241202		Approved	KIAA1405, KIF3X, KIF17B, OSM-3, KLP-2	uc001bdr.4	Q9P2E2	OTTHUMG00000002863	ENST00000247986.2:c.1107C>A	1.37:g.21030956G>T	ENSP00000247986:p.Ser369Arg	107.0	0.0	0		126.0	121.0	0.960317	NM_001122819	A2A3Q7|A2A3Q8|O95077|Q53YS6|Q5VWA9|Q6GSA8|Q8N411	Missense_Mutation	SNP	ENST00000247986.2	37	CCDS213.1	61	0.027930402930402932	57	0.11585365853658537	4	0.011049723756906077	0	0.0	0	0.0	G	2.171	-0.389993	0.04932	0.083749	6.98E-4	ENSG00000117245	ENST00000375044;ENST00000400463;ENST00000247986	T;T;T	0.70986	-0.53;-0.44;-0.44	5.26	3.4	0.38934	.	0.959805	0.08472	U	0.940858	T	0.01287	0.0042	N	0.22421	0.69	0.09310	N	1	B;B	0.30406	0.278;0.007	B;B	0.33960	0.173;0.011	T	0.01762	-1.1279	10	0.19590	T	0.45	.	8.9324	0.35680	0.2408:0.0:0.7592:0.0	rs56750936;rs61731590	369;369	Q9P2E2-3;Q9P2E2	.;KIF17_HUMAN	R	269;369;369	ENSP00000364184:S269R;ENSP00000383311:S369R;ENSP00000247986:S369R	ENSP00000247986:S369R	S	-	3	2	KIF17	20903543	0.011000	0.17503	0.984000	0.44739	0.078000	0.17371	0.251000	0.18257	0.733000	0.32492	-0.448000	0.05591	AGC	G|0.968;T|0.032	0.032	strong		0.607	KIF17-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276995.1	NM_020816	
FRAS1	80144	hgsc.bcm.edu	37	4	79396610	79396610	+	Silent	SNP	G	G	A	rs79849142	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:79396610G>A	ENST00000264895.6	+	54	8141	c.7701G>A	c.(7699-7701)aaG>aaA	p.K2567K		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	2567	Calx-beta 1.				cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						TCAGTGAGAAGGCAGGGTCTG	0.502													G|||	149	0.0297524	0.1074	0.0101	5008	,	,		22558	0.0		0.0	False		,,,				2504	0.0				p.K2567K		Atlas-SNP	.											.	FRAS1	779	.	0			c.G7701A						PASS	.	G		324,3850		17,290,1780	117.0	129.0	125.0		7701	1.3	1.0	4	dbSNP_132	125	3,8441		0,3,4219	no	coding-synonymous	FRAS1	NM_025074.6		17,293,5999	AA,AG,GG		0.0355,7.7623,2.5915		2567/4013	79396610	327,12291	2087	4222	6309	SO:0001819	synonymous_variant	80144	exon54			TGAGAAGGCAGGG	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.7701G>A	4.37:g.79396610G>A		220.0	1.0	0.00454545		220.0	110.0	0.5	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	37	CCDS54771.1	44	0.020146520146520148	41	0.08333333333333333	3	0.008287292817679558	0	0.0	0	0.0	G	9.007	0.981435	0.18812	0.077623	3.55E-4	ENSG00000138759	ENST00000512123	.	.	.	5.44	1.34	0.21922	.	.	.	.	.	T	0.02970	0.0088	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.03761	-1.1006	4	.	.	.	.	1.7426	0.02955	0.3312:0.1357:0.4093:0.1237	.	.	.	.	S	796	.	.	G	+	1	0	FRAS1	79615634	0.990000	0.36364	0.999000	0.59377	0.994000	0.84299	0.287000	0.18920	0.212000	0.20703	0.591000	0.81541	GGC	G|0.984;A|0.016	0.016	strong		0.502	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
PCDHA8	56140	hgsc.bcm.edu	37	5	140222430	140222430	+	Missense_Mutation	SNP	T	T	G	rs6873763	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140222430T>G	ENST00000531613.1	+	1	1524	c.1524T>G	c.(1522-1524)atT>atG	p.I508M	PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000378123.3_Missense_Mutation_p.I508M|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000527624.1_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	508	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(31)|ovary(2)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(6)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGAGCTACATTTCGGTGCACA	0.687													.|||	350	0.0698882	0.2564	0.0144	5008	,	,		12674	0.0		0.001	False		,,,				2504	0.0				p.I508M		Atlas-SNP	.											.	PCDHA8	366	.	0			c.T1524G						PASS	.	T	,,,,,,,MET/ILE,,,MET/ILE	994,3394	710.8+/-407.9	169,656,1369	62.0	70.0	67.0		,,,,,,,1524,,,1524	2.8	1.0	5	dbSNP_116	67	4,8526	800.3+/-407.4	0,4,4261	no	intron,intron,intron,intron,intron,intron,intron,missense,intron,intron,missense	PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031856.1	,,,,,,,10,,,10	169,660,5630	GG,GT,TT		0.0469,22.6527,7.7257	,,,,,,,,,,	,,,,,,,508/951,,,508/815	140222430	998,11920	2194	4265	6459	SO:0001583	missense	56140	exon1			CTACATTTCGGTG	AF152486	CCDS54919.1	5q31	2010-11-26				ENSG00000204962		"""Cadherins / Protocadherins : Clustered"""	8674	other	complex locus constituent	"""KIAA0345-like 6"""	606314				10380929	Standard	NM_018911		Approved			Q9Y5H6		ENST00000531613.1:c.1524T>G	5.37:g.140222430T>G	ENSP00000434655:p.Ile508Met	303.0	0.0	0		287.0	156.0	0.543554	NM_031856	B9EGT7|O75281	Missense_Mutation	SNP	ENST00000531613.1	37	CCDS54919.1	108	0.04945054945054945	101	0.20528455284552846	7	0.019337016574585635	0	0.0	0	0.0	G	11.04	1.520541	0.27211	0.226527	4.69E-4	ENSG00000204962	ENST00000531613;ENST00000378123	T;T	0.61274	0.12;0.12	3.72	2.85	0.33270	Cadherin (4);Cadherin-like (1);	0.000000	0.33199	U	0.005173	T	0.00073	0.0002	M	0.77486	2.375	0.43122	P	0.005152999999999963	P;P	0.45240	0.473;0.854	P;P	0.60068	0.868;0.729	T	0.06303	-1.0834	9	0.87932	D	0	.	8.018	0.30393	0.0:0.2626:0.4599:0.2775	rs6873763	508;508	Q9Y5H6;Q9Y5H6-2	PCDA8_HUMAN;.	M	508	ENSP00000434655:I508M;ENSP00000367363:I508M	ENSP00000367363:I508M	I	+	3	3	PCDHA8	140202614	0.030000	0.19436	1.000000	0.80357	0.083000	0.17756	-0.581000	0.05820	0.682000	0.31407	-0.741000	0.03529	ATT	T|0.933;G|0.067	0.067	strong		0.687	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911	
DUOX2	50506	hgsc.bcm.edu	37	15	45392382	45392382	+	Missense_Mutation	SNP	T	T	C	rs79393107	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:45392382T>C	ENST00000603300.1	-	24	3252	c.3050A>G	c.(3049-3051)gAg>gGg	p.E1017G	DUOX2_ENST00000389039.6_Missense_Mutation_p.E1017G	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	1017	Interaction with TXNDC11. {ECO:0000250}.				adenohypophysis morphogenesis (GO:0048855)|bone mineralization (GO:0030282)|cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|inner ear development (GO:0048839)|multicellular organism growth (GO:0035264)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|response to virus (GO:0009615)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|peroxidase activity (GO:0004601)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		CTGCATCTTCTCTTGCAGCGC	0.602													T|||	183	0.0365415	0.1293	0.0173	5008	,	,		20832	0.0		0.0	False		,,,				2504	0.0				p.E1017G		Atlas-SNP	.											.	DUOX2	137	.	0			c.A3050G						PASS	.	T	GLY/GLU	524,3872	240.6+/-251.3	40,444,1714	78.0	68.0	72.0		3050	5.4	1.0	15	dbSNP_131	72	3,8593	3.0+/-9.4	0,3,4295	yes	missense	DUOX2	NM_014080.4	98	40,447,6009	CC,CT,TT		0.0349,11.9199,4.0563	probably-damaging	1017/1549	45392382	527,12465	2198	4298	6496	SO:0001583	missense	50506	exon24			ATCTTCTCTTGCA	AF181972	CCDS10117.1	15q15.3-q21	2013-01-10			ENSG00000140279	ENSG00000140279		"""EF-hand domain containing"""	13273	protein-coding gene	gene with protein product	"""dual oxidase-like domains 2"", ""nicotinamide adenine dinucleotide phosphate oxidase"", ""flavoprotein NADPH oxidase"", ""NADPH thyroid oxidase 2"", ""NADH/NADPH thyroid oxidase p138-tox"", ""NADPH oxidase/peroxidase DUOX2"""	606759				10601291, 10806195	Standard	NM_014080		Approved	P138-TOX, P138(TOX), THOX2, LNOX2	uc010bea.3	Q9NRD8	OTTHUMG00000131355	ENST00000603300.1:c.3050A>G	15.37:g.45392382T>C	ENSP00000475084:p.Glu1017Gly	95.0	0.0	0		79.0	31.0	0.392405	NM_014080	A8MQ13|D2XI64|Q9NR02|Q9UHF9	Missense_Mutation	SNP	ENST00000603300.1	37	CCDS10117.1	58	0.026556776556776556	51	0.10365853658536585	7	0.019337016574585635	0	0.0	0	0.0	T	25.5	4.644005	0.87859	0.119199	3.49E-4	ENSG00000140279	ENST00000389039	.	.	.	5.45	5.45	0.79879	.	0.105054	0.64402	D	0.000003	T	0.02727	0.0082	M	0.76328	2.33	0.58432	D	0.999998	D	0.52996	0.957	P	0.52823	0.71	T	0.06698	-1.0812	9	0.34782	T	0.22	-29.5989	14.7059	0.69189	0.0:0.0:0.0:1.0	.	1017	Q9NRD8	DUOX2_HUMAN	G	1017	.	ENSP00000373691:E1017G	E	-	2	0	DUOX2	43179674	1.000000	0.71417	1.000000	0.80357	0.779000	0.44077	3.726000	0.54977	2.080000	0.62538	0.460000	0.39030	GAG	T|0.960;C|0.040	0.040	strong		0.602	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080	
ESX1	80712	hgsc.bcm.edu	37	X	103495007	103495007	+	Missense_Mutation	SNP	G	G	C	rs78191648	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:103495007G>C	ENST00000372588.4	-	4	1206	c.1123C>G	c.(1123-1125)Ctg>Gtg	p.L375V		NM_153448.3	NP_703149.1	Q8N693	ESX1_HUMAN	ESX homeobox 1	375	15 X 9 AA tandem repeats of P-P-x-x-P-x- P-P-x.				labyrinthine layer blood vessel development (GO:0060716)|labyrinthine layer morphogenesis (GO:0060713)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	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)|sequence-specific DNA binding (GO:0043565)			endometrium(2)|large_intestine(10)|lung(12)|ovary(1)|skin(2)	27						CTGGGTGGCAGAGGCGCCATG	0.667													T|||	187	0.0495364	0.1346	0.0101	3775	,	,		7462	0.0		0.001	False		,,,				2504	0.001				p.L375V	Pancreas(200;1705 2227 25194 28471 45274)	Atlas-SNP	.											.	ESX1	57	.	0			c.C1123G						PASS	.	T	VAL/LEU	553,3282		42,388,81,1202,490	36.0	34.0	35.0		1123	-8.3	0.0	X	dbSNP_131	35	7,6721		0,7,0,2421,1872	yes	missense	ESX1	NM_153448.3	32	42,395,81,3623,2362	CC,CG,C,GG,G		0.104,14.4198,5.3015	benign	375/407	103495007	560,10003	2203	4300	6503	SO:0001583	missense	80712	exon4			GTGGCAGAGGCGC	AL049631	CCDS14516.1	Xq22.2	2011-06-20	2007-07-11	2006-02-08	ENSG00000123576	ENSG00000123576		"""Homeoboxes / PRD class"""	14865	protein-coding gene	gene with protein product		300154	"""extraembryonic, spermatogenesis, homeobox 1 homolog (mouse)"""	ESX1L		11374906, 17242862	Standard	NM_153448		Approved	ESXR1	uc004ely.3	Q8N693	OTTHUMG00000022125	ENST00000372588.4:c.1123C>G	X.37:g.103495007G>C	ENSP00000361669:p.Leu375Val	53.0	0.0	0		53.0	29.0	0.54717	NM_153448	B0QYU3|Q7Z6K7	Missense_Mutation	SNP	ENST00000372588.4	37	CCDS14516.1	75	0.045207956600361664	55	0.1206140350877193	1	0.002777777777777778	0	0.0	0	0.0	T	0.004	-2.247286	0.00271	0.144198	0.00104	ENSG00000123576	ENST00000372588	T	0.73152	-0.72	4.14	-8.28	0.01013	.	.	.	.	.	T	0.00356	0.0011	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.10706	-1.0618	8	0.42905	T	0.14	0.5915	7.4597	0.27287	0.1697:0.6473:0.0849:0.0981	.	375	Q8N693	ESX1_HUMAN	V	375	ENSP00000361669:L375V	ENSP00000361669:L375V	L	-	1	2	ESX1	103381663	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-4.954000	0.00166	-3.304000	0.00192	-2.542000	0.00179	CTG	G|0.948;C|0.052	0.052	strong		0.667	ESX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057763.2	NM_153448	
CYP1B1	1545	hgsc.bcm.edu	37	2	38301803	38301803	+	Silent	SNP	C	C	G	rs9341249	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:38301803C>G	ENST00000260630.3	-	2	1130	c.729G>C	c.(727-729)gtG>gtC	p.V243V	CYP1B1-AS1_ENST00000589303.1_RNA|CYP1B1_ENST00000494864.1_Intron|CYP1B1_ENST00000407341.1_Silent_p.V243V|CYP1B1-AS1_ENST00000431999.1_RNA	NM_000104.3	NP_000095	Q16678	CP1B1_HUMAN	cytochrome P450, family 1, subfamily B, polypeptide 1	243					angiogenesis (GO:0001525)|arachidonic acid metabolic process (GO:0019369)|blood vessel morphogenesis (GO:0048514)|cell adhesion (GO:0007155)|cellular aromatic compound metabolic process (GO:0006725)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to organic cyclic compound (GO:0071407)|collagen fibril organization (GO:0030199)|endothelial cell migration (GO:0043542)|endothelial cell-cell adhesion (GO:0071603)|epoxygenase P450 pathway (GO:0019373)|estrogen metabolic process (GO:0008210)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|membrane lipid catabolic process (GO:0046466)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nitric oxide biosynthetic process (GO:0006809)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression involved in extracellular matrix organization (GO:1901313)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of reactive oxygen species metabolic process (GO:2000377)|response to toxic substance (GO:0009636)|retinal blood vessel morphogenesis (GO:0061304)|retinal metabolic process (GO:0042574)|retinol metabolic process (GO:0042572)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|toxin metabolic process (GO:0009404)|trabecular meshwork development (GO:0002930)|visual perception (GO:0007601)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|mitochondrion (GO:0005739)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)|oxygen binding (GO:0019825)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)	13		all_hematologic(82;0.21)			Amodiaquine(DB00613)|Arsenic trioxide(DB01169)|Biotin(DB00121)|Caffeine(DB00201)|Clozapine(DB00363)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Dexamethasone(DB01234)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Erlotinib(DB00530)|Estradiol(DB00783)|Estrone(DB00655)|Flutamide(DB00499)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Melatonin(DB01065)|Mitoxantrone(DB01204)|Omeprazole(DB00338)|Oxaliplatin(DB00526)|Paclitaxel(DB01229)|Phenobarbital(DB01174)|Primaquine(DB01087)|Procarbazine(DB01168)|Progesterone(DB00396)|Propofol(DB00818)|Tamoxifen(DB00675)|Testosterone(DB00624)|Theophylline(DB00277)	GCCAGGGCATCACGTCCACCA	0.627													c|||	383	0.0764776	0.2678	0.0159	5008	,	,		16495	0.0129		0.003	False		,,,				2504	0.002				p.V243V		Atlas-SNP	.											.	CYP1B1	39	.	0			c.G729C						PASS	.	A		917,3489	333.9+/-303.2	93,731,1379	43.0	41.0	42.0		729	1.5	1.0	2	dbSNP_119	42	21,8579	12.6+/-44.7	0,21,4279	yes	coding-synonymous	CYP1B1	NM_000104.3		93,752,5658	GG,GC,CC		0.2442,20.8125,7.2121		243/544	38301803	938,12068	2203	4300	6503	SO:0001819	synonymous_variant	1545	exon2			GGGCATCACGTCC	U56438	CCDS1793.1	2p22.2	2008-02-05	2003-01-14		ENSG00000138061	ENSG00000138061		"""Cytochrome P450s"""	2597	protein-coding gene	gene with protein product		601771	"""cytochrome P450, subfamily I (dioxin-inducible), polypeptide 1 (glaucoma 3, primary infantile)"""	GLC3A		8175734, 15128046	Standard	NM_000104		Approved	CP1B	uc002rqo.2	Q16678	OTTHUMG00000100970	ENST00000260630.3:c.729G>C	2.37:g.38301803C>G		107.0	0.0	0		148.0	148.0	1	NM_000104	Q5TZW8|Q93089|Q9H316	Silent	SNP	ENST00000260630.3	37	CCDS1793.1																																																																																			C|0.934;G|0.066	0.066	strong		0.627	CYP1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218580.3	NM_000104	
PLIN4	729359	hgsc.bcm.edu	37	19	4511913	4511913	+	Missense_Mutation	SNP	C	C	T	rs199927982	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4511913C>T	ENST00000301286.3	-	3	2016	c.2017G>A	c.(2017-2019)Gac>Aac	p.D673N		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	673	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						TTGGCCGTGTCTACACCTGTC	0.567													C|||	52	0.0103834	0.0386	0.0014	5008	,	,		29014	0.0		0.0	False		,,,				2504	0.0				p.D673N		Atlas-SNP	.											.	PLIN4	191	.	0			c.G2017A						PASS	.	G	ASN/ASP	151,4073		4,143,1965	139.0	148.0	145.0		2017	3.0	0.3	19	dbSNP_132	145	0,8444		0,0,4222	yes	missense	PLIN4	NM_001080400.1	23	4,143,6187	TT,TC,CC		0.0,3.5748,1.192	probably-damaging	673/1358	4511913	151,12517	2112	4222	6334	SO:0001583	missense	729359	exon3			CCGTGTCTACACC	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"""Perilipins"""	29393	protein-coding gene	gene with protein product		613247	"""KIAA1881"""	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.2017G>A	19.37:g.4511913C>T	ENSP00000301286:p.Asp673Asn	323.0	0.0	0		359.0	137.0	0.381616	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	27	0.012362637362637362	27	0.054878048780487805	0	0.0	0	0.0	0	0.0	C	13.17	2.155782	0.38021	0.035748	0.0	ENSG00000167676	ENST00000301286	T	0.11063	2.81	5.14	3.0	0.34707	.	0.287773	0.24191	U	0.040720	T	0.02970	0.0088	M	0.85197	2.74	0.20926	N	0.999825	P	0.49961	0.93	P	0.47044	0.535	T	0.04811	-1.0925	10	0.46703	T	0.11	-25.9696	7.1023	0.25344	0.0:0.6943:0.1443:0.1613	.	673	Q96Q06	PLIN4_HUMAN	N	673	ENSP00000301286:D673N	ENSP00000301286:D673N	D	-	1	0	PLIN4	4462913	0.000000	0.05858	0.349000	0.25694	0.008000	0.06430	-0.258000	0.08733	0.567000	0.29293	-0.757000	0.03467	GAC	C|0.988;T|0.012	0.012	strong		0.567	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
CBX2	84733	hgsc.bcm.edu	37	17	77755894	77755894	+	Intron	SNP	C	C	G	rs9912676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:77755894C>G	ENST00000310942.4	+	4	392				CBX2_ENST00000269399.5_Missense_Mutation_p.F194L	NM_005189.2	NP_005180.1	Q14781	CBX2_HUMAN	chromobox homolog 2						cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|development of primary sexual characteristics (GO:0045137)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)	16			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			AAGCACTCTTCCCTCCCAGGG	0.592													C|||	131	0.0261581	0.0961	0.0058	5008	,	,		17679	0.0		0.0	False		,,,				2504	0.0				p.F194L		Atlas-SNP	.											.	CBX2	50	.	0			c.C582G						PASS	.	C	,LEU/PHE	365,4037		13,339,1849	36.0	41.0	39.0		,582	0.7	0.0	17	dbSNP_119	39	3,8587		0,3,4292	yes	intron,missense	CBX2	NM_005189.2,NM_032647.3	,22	13,342,6141	GG,GC,CC		0.0349,8.2917,2.8325	,	,194/212	77755894	368,12624	2201	4295	6496	SO:0001627	intron_variant	84733	exon4			ACTCTTCCCTCCC	BC004252, BG354579	CCDS11764.1, CCDS32757.1	17q25.3	2010-07-06	2010-06-24		ENSG00000173894	ENSG00000173894			1552	protein-coding gene	gene with protein product	"""Pc class homolog (Drosophila)"""	602770	"""chromobox homolog 2 (Drosophila Pc class)"", ""cell division cycle associated 6"""	CDCA6		7782071, 2477932	Standard	NM_005189		Approved	MGC10561	uc002jxc.3	Q14781		ENST00000310942.4:c.288+294C>G	17.37:g.77755894C>G		92.0	0.0	0		116.0	42.0	0.362069	NM_032647	Q0VDA5|Q9BTB1	Missense_Mutation	SNP	ENST00000310942.4	37	CCDS32757.1	44	0.020146520146520148	42	0.08536585365853659	2	0.0055248618784530384	0	0.0	0	0.0	C	0.251	-1.006634	0.02112	0.082917	3.49E-4	ENSG00000173894	ENST00000269399	.	.	.	2.87	0.722	0.18225	.	.	.	.	.	T	0.00815	0.0027	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.13388	-1.0511	6	.	.	.	.	5.5063	0.16856	0.2264:0.553:0.2205:0.0	rs9912676	194	Q14781-2	.	L	194	.	.	F	+	3	2	CBX2	75370489	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.028000	0.13644	0.057000	0.16193	0.455000	0.32223	TTC	C|0.976;G|0.024	0.024	strong		0.592	CBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437040.1	NM_032647	
SLC45A4	57210	hgsc.bcm.edu	37	8	142228386	142228386	+	Silent	SNP	C	C	T	rs61995881	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:142228386C>T	ENST00000024061.3	-	4	1507	c.1200G>A	c.(1198-1200)ccG>ccA	p.P400P	SLC45A4_ENST00000519067.1_Silent_p.P400P|SLC45A4_ENST00000433583.2_Silent_p.P393P|SLC45A4_ENST00000517878.1_Silent_p.P451P	NM_001080431.1	NP_001073900.1	Q5BKX6	S45A4_HUMAN	solute carrier family 45, member 4						transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(6)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	31	all_cancers(97;1.52e-15)|all_epithelial(106;2.92e-14)|Lung NSC(106;1.23e-05)|all_lung(105;1.75e-05)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0493)			TGCTGCGCGACGGCTTGATCA	0.677													C|||	69	0.013778	0.0461	0.0086	5008	,	,		15669	0.0		0.0	False		,,,				2504	0.002				p.P400P		Atlas-SNP	.											.	SLC45A4	71	.	0			c.G1200A						PASS	.	C		212,4194	124.9+/-162.1	7,198,1998	46.0	44.0	45.0		1200	-2.3	0.9	8	dbSNP_129	45	0,8598		0,0,4299	no	coding-synonymous	SLC45A4	NM_001080431.1		7,198,6297	TT,TC,CC		0.0,4.8116,1.6303		400/799	142228386	212,12792	2203	4299	6502	SO:0001819	synonymous_variant	57210	exon4			GCGCGACGGCTTG	AB032952	CCDS34948.1, CCDS69550.1, CCDS75795.1	8q24.3	2013-05-22						"""Solute carriers"""	29196	protein-coding gene	gene with protein product							Standard	NM_001080431		Approved	KIAA1126	uc003ywd.1	Q5BKX6		ENST00000024061.3:c.1200G>A	8.37:g.142228386C>T		32.0	0.0	0		46.0	28.0	0.608696	NM_001080431	Q6ZRI2|Q9ULU3	Silent	SNP	ENST00000024061.3	37	CCDS34948.1																																																																																			C|0.986;T|0.014	0.014	strong		0.677	SLC45A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378571.3	XM_050325	
POMT2	29954	hgsc.bcm.edu	37	14	77786864	77786864	+	Missense_Mutation	SNP	G	G	T	rs8177536	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:77786864G>T	ENST00000261534.4	-	1	363	c.161C>A	c.(160-162)gCg>gAg	p.A54E	GSTZ1_ENST00000556627.1_5'Flank|GSTZ1_ENST00000216465.5_5'Flank|GSTZ1_ENST00000557053.1_5'Flank|GSTZ1_ENST00000349555.3_5'Flank|GSTZ1_ENST00000554279.1_5'Flank|GSTZ1_ENST00000393734.1_5'Flank|GSTZ1_ENST00000557639.1_5'Flank|GSTZ1_ENST00000361389.4_5'Flank	NM_013382.5	NP_037514.2	Q9UKY4	POMT2_HUMAN	protein-O-mannosyltransferase 2	54			A -> E (in dbSNP:rs8177536).			endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	dolichyl-phosphate-mannose-protein mannosyltransferase activity (GO:0004169)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|large_intestine(1)|liver(1)|lung(5)|ovary(1)|prostate(1)|skin(1)	14			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0292)		CCAGCCGACCGCCTCGAAGCG	0.711													G|||	162	0.0323482	0.1188	0.0072	5008	,	,		11629	0.0		0.0	False		,,,				2504	0.0				p.A54E		Atlas-SNP	.											.	POMT2	47	.	0			c.C161A						PASS	.	G	GLU/ALA	359,3731		14,331,1700	11.0	10.0	10.0		161	-1.7	0.0	14	dbSNP_117	10	3,8235		0,3,4116	yes	missense	POMT2	NM_013382.5	107	14,334,5816	TT,TG,GG		0.0364,8.7775,2.9364	benign	54/751	77786864	362,11966	2045	4119	6164	SO:0001583	missense	29954	exon1			CCGACCGCCTCGA	AF105020	CCDS9857.1	14q24	2014-09-17			ENSG00000009830	ENSG00000009830	2.4.1.109	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	19743	protein-coding gene	gene with protein product		607439				11162531, 12460945	Standard	NM_013382		Approved	LGMD2N	uc001xti.2	Q9UKY4	OTTHUMG00000171556	ENST00000261534.4:c.161C>A	14.37:g.77786864G>T	ENSP00000261534:p.Ala54Glu	32.0	0.0	0		41.0	27.0	0.658537	NM_013382	Q9NSG6|Q9P1W0|Q9P1W2	Missense_Mutation	SNP	ENST00000261534.4	37	CCDS9857.1	72	0.03296703296703297	70	0.14227642276422764	2	0.0055248618784530384	0	0.0	0	0.0	G	9.945	1.218430	0.22373	0.087775	3.64E-4	ENSG00000009830	ENST00000261534	T	0.76709	-1.04	5.34	-1.66	0.08265	.	0.721535	0.12751	N	0.442179	T	0.00412	0.0013	N	0.08118	0	0.80722	P	0.0	B	0.06786	0.001	B	0.04013	0.001	T	0.07271	-1.0781	9	0.02654	T	1	-1.3895	2.5294	0.04699	0.1453:0.2152:0.4208:0.2187	rs8177536;rs8177536	54	Q9UKY4	POMT2_HUMAN	E	54	ENSP00000261534:A54E	ENSP00000261534:A54E	A	-	2	0	POMT2	76856617	0.000000	0.05858	0.041000	0.18516	0.017000	0.09413	-0.222000	0.09190	-0.024000	0.13941	-0.136000	0.14681	GCG	G|0.920;T|0.080	0.080	strong		0.711	POMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414155.1	NM_013382	
FGFR3	2261	hgsc.bcm.edu	37	4	1803704	1803704	+	Silent	SNP	T	T	C	rs2234909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:1803704T>C	ENST00000260795.2	+	6	984	c.882T>C	c.(880-882)aaT>aaC	p.N294N	FGFR3_ENST00000481110.2_Silent_p.N294N|FGFR3_ENST00000474521.1_3'UTR|FGFR3_ENST00000440486.2_Silent_p.N294N|FGFR3_ENST00000352904.1_Silent_p.N294N|FGFR3_ENST00000412135.2_Silent_p.N294N|FGFR3_ENST00000340107.4_Silent_p.N294N			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	294	Ig-like C2-type 3.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)	p.N294N(5)		NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	TGGAGGTGAATGGCAGCAAGG	0.672		1	"""Mis, T"""	"""IGH@, ETV6"""	"""bladder, MM, T-cell lymphoma"""		"""Hypochondroplasia, Thanatophoric dysplasia"""		Saethre-Chotzen syndrome;Muenke syndrome				N|||	1039	0.207468	0.3707	0.1441	5008	,	,		12849	0.0744		0.17	False		,,,				2504	0.2076				p.N294N		Atlas-SNP	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"""L, E"""	FGFR3_ENST00000340107,caecum,carcinoma,+2,11	FGFR3	3320	11	5	Substitution - coding silent(5)	upper_aerodigestive_tract(3)|skin(2)	c.T882C						PASS	.	C	,,	1504,2902	654.3+/-399.7	251,1002,950	47.0	42.0	44.0		882,882,882	-6.8	0.9	4	dbSNP_98	44	1278,7320	749.7+/-407.4	98,1082,3119	no	coding-synonymous,coding-synonymous,coding-synonymous	FGFR3	NM_000142.4,NM_001163213.1,NM_022965.3	,,	349,2084,4069	CC,CT,TT		14.8639,34.1353,21.3934	,,	294/807,294/809,294/695	1803704	2782,10222	2203	4299	6502	SO:0001819	synonymous_variant	2261	exon7	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	GGTGAATGGCAGC	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3690	protein-coding gene	gene with protein product		134934	"""achondroplasia, thanatophoric dwarfism"""	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.882T>C	4.37:g.1803704T>C		112.0	0.0	0		97.0	50.0	0.515464	NM_001163213	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Silent	SNP	ENST00000260795.2	37	CCDS3353.1																																																																																			T|0.799;C|0.201	0.201	strong		0.672	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142	
KRTAP13-3	337960	hgsc.bcm.edu	37	21	31797919	31797919	+	Silent	SNP	G	G	A	rs73356706	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31797919G>A	ENST00000390690.2	-	1	367	c.312C>T	c.(310-312)tcC>tcT	p.S104S		NM_181622.1	NP_853653.1	Q3SY46	KR133_HUMAN	keratin associated protein 13-3	104						intermediate filament (GO:0005882)				endometrium(1)|large_intestine(1)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	14						AGCAGCTATTGGATCCAAAAC	0.532													-|||	210	0.0419329	0.1505	0.0144	5008	,	,		18568	0.0		0.001	False		,,,				2504	0.0				p.S104S		Atlas-SNP	.											.	KRTAP13-3	47	.	0			c.C312T						PASS	.	G		432,3908		23,386,1761	51.0	57.0	55.0		312	3.4	0.3	21	dbSNP_130	55	9,8569		0,9,4280	no	coding-synonymous	KRTAP13-3	NM_181622.1		23,395,6041	AA,AG,GG		0.1049,9.9539,3.4138		104/173	31797919	441,12477	2170	4289	6459	SO:0001819	synonymous_variant	337960	exon1			GCTATTGGATCCA	AP001708	CCDS13591.1	21q22.1	2006-03-13			ENSG00000240432	ENSG00000240432		"""Keratin associated proteins"""	18925	protein-coding gene	gene with protein product						12359730	Standard	NM_181622		Approved	KAP13.3	uc002yob.1	Q3SY46	OTTHUMG00000057776	ENST00000390690.2:c.312C>T	21.37:g.31797919G>A		132.0	0.0	0		107.0	47.0	0.439252	NM_181622	Q3LI78	Silent	SNP	ENST00000390690.2	37	CCDS13591.1																																																																																			G|0.975;A|0.025	0.025	strong		0.532	KRTAP13-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128228.2		
CCDC134	79879	hgsc.bcm.edu	37	22	42209767	42209767	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:42209767C>T	ENST00000255784.5	+	6	609	c.505C>T	c.(505-507)Ctg>Ttg	p.L169L	CCDC134_ENST00000402061.3_Intron	NM_024821.2	NP_079097.1	Q9H6E4	CC134_HUMAN	coiled-coil domain containing 134	169						extracellular region (GO:0005576)|membrane (GO:0016020)				large_intestine(1)|lung(2)|ovary(2)|skin(1)	6						GGCCCAGGAGCTGGGGATCAG	0.532																																					p.L169L		Atlas-SNP	.											.	CCDC134	19	.	0			c.C505T						PASS	.						100.0	96.0	97.0					22																	42209767		2203	4300	6503	SO:0001819	synonymous_variant	79879	exon6			CAGGAGCTGGGGA	AL021453	CCDS33654.1	22q13.2	2010-12-24			ENSG00000100147	ENSG00000100147			26185	protein-coding gene	gene with protein product						18087676	Standard	NM_024821		Approved	FLJ22349	uc003bbh.1	Q9H6E4	OTTHUMG00000151262	ENST00000255784.5:c.505C>T	22.37:g.42209767C>T		99.0	0.0	0		96.0	45.0	0.46875	NM_024821		Silent	SNP	ENST00000255784.5	37	CCDS33654.1																																																																																			.	.	none		0.532	CCDC134-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000321964.1	NM_024821	
GFAP	2670	hgsc.bcm.edu	37	17	42985453	42985453	+	Silent	SNP	G	G	T	rs146298944	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:42985453G>T	ENST00000253408.5	-	8	1301	c.1236C>A	c.(1234-1236)acC>acA	p.T412T	GFAP_ENST00000588735.1_Silent_p.T38T	NM_002055.4	NP_002046.1	P14136	GFAP_HUMAN	glial fibrillary acidic protein	412	Tail.				astrocyte development (GO:0014002)|Bergmann glial cell differentiation (GO:0060020)|extracellular matrix organization (GO:0030198)|intermediate filament organization (GO:0045109)|long-term synaptic potentiation (GO:0060291)|negative regulation of neuron projection development (GO:0010977)|neuron projection regeneration (GO:0031102)|positive regulation of Schwann cell proliferation (GO:0010625)|regulation of neurotransmitter uptake (GO:0051580)|response to wounding (GO:0009611)	astrocyte projection (GO:0097449)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intermediate filament (GO:0005882)|membrane (GO:0016020)	structural constituent of cytoskeleton (GO:0005200)			endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(11)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23		Prostate(33;0.0959)				GCATCTCCACGGTCTTCACCA	0.592													G|||	5	0.000998403	0.0038	0.0	5008	,	,		19484	0.0		0.0	False		,,,				2504	0.0				p.T412T		Atlas-SNP	.											GFAP,colon,carcinoma,0,1	GFAP	88	1	0			c.C1236A						PASS	.	G		20,4386	27.2+/-55.0	0,20,2183	231.0	198.0	209.0		1236	-10.3	0.1	17	dbSNP_134	209	0,8600		0,0,4300	no	coding-synonymous	GFAP	NM_002055.4		0,20,6483	TT,TG,GG		0.0,0.4539,0.1538		412/433	42985453	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	2670	exon8			CTCCACGGTCTTC	S40719	CCDS11491.1, CCDS45708.1, CCDS59296.1	17q21	2013-01-16						"""Intermediate filaments type III"""	4235	protein-coding gene	gene with protein product	"""intermediate filament protein"""	137780				9693047	Standard	NM_002055		Approved	FLJ45472	uc002ihq.3	P14136		ENST00000253408.5:c.1236C>A	17.37:g.42985453G>T		155.0	0.0	0		149.0	70.0	0.469799	NM_002055	B2RD44|D3DX59|E9PAX3|Q53H98|Q5D055|Q6ZQS3|Q7Z5J6|Q7Z5J7|Q96KS4|Q96P18|Q9UFD0	Silent	SNP	ENST00000253408.5	37	CCDS11491.1																																																																																			G|0.999;T|0.001	0.001	strong		0.592	GFAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448701.1	NM_002055	
PCDHA3	56145	hgsc.bcm.edu	37	5	140180964	140180964	+	Missense_Mutation	SNP	C	C	A	rs7731327	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140180964C>A	ENST00000522353.2	+	1	182	c.182C>A	c.(181-183)cCg>cAg	p.P61Q	PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000532566.2_Missense_Mutation_p.P61Q|PCDHA2_ENST00000520672.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018906.2	NP_061729.1	Q9Y5H8	PCDA3_HUMAN	protocadherin alpha 3	61	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		P -> Q (in dbSNP:rs7731327).		cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(16)|kidney(3)|large_intestine(19)|lung(36)|ovary(7)|prostate(8)|skin(3)|stomach(1)	95			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGCTGGTGCCGCGCCTGTTC	0.612													.|||	285	0.0569089	0.208	0.013	5008	,	,		16771	0.0		0.001	False		,,,				2504	0.0				p.P61Q		Atlas-SNP	.											PCDHA3_ENST00000522353,NS,carcinoma,-1,2	PCDHA3	396	2	0			c.C182A						PASS	.	C	,,GLN/PRO,,GLN/PRO	789,3617		66,657,1480	51.0	63.0	59.0		,,182,,182	3.6	1.0	5	dbSNP_116	59	5,8583		0,5,4289	no	intron,intron,missense,intron,missense	PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_031411.1,NM_031497.1	,,76,,76	66,662,5769	AA,AC,CC		0.0582,17.9074,6.1105	,,,,	,,61/951,,61/825	140180964	794,12200	2203	4294	6497	SO:0001583	missense	56145	exon1			TGGTGCCGCGCCT	AF152481	CCDS54915.1	5q31	2010-11-26				ENSG00000255408		"""Cadherins / Protocadherins : Clustered"""	8669	other	complex locus constituent	"""KIAA0345-like 11"""	606309				10380929	Standard	NM_018906		Approved	PCDH-ALPHA3		Q9Y5H8		ENST00000522353.2:c.182C>A	5.37:g.140180964C>A	ENSP00000429808:p.Pro61Gln	75.0	0.0	0		84.0	32.0	0.380952	NM_031497	O75286	Missense_Mutation	SNP	ENST00000522353.2	37	CCDS54915.1	88	0.040293040293040296	82	0.16666666666666666	6	0.016574585635359115	0	0.0	0	0.0	c	13.35	2.210033	0.39003	0.179074	5.82E-4	ENSG00000255408	ENST00000522353;ENST00000532566	T;T	0.26067	1.76;1.76	4.48	3.59	0.41128	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	0.203527	0.23851	U	0.043957	T	0.00039	0.0001	M	0.66297	2.02	0.46798	P	8.000000000000229E-4	P;P	0.42871	0.792;0.48	B;B	0.37508	0.224;0.252	T	0.16158	-1.0412	9	0.62326	D	0.03	.	13.352	0.60607	0.0:0.9179:0.0:0.0821	rs7731327	61;61	Q9Y5H8-2;Q9Y5H8	.;PCDA3_HUMAN	Q	61	ENSP00000429808:P61Q;ENSP00000434086:P61Q	ENSP00000429808:P61Q	P	+	2	0	PCDHA3	140161148	0.000000	0.05858	1.000000	0.80357	0.984000	0.73092	-0.420000	0.07062	2.228000	0.72767	0.586000	0.80456	CCG	C|0.949;A|0.051	0.051	strong		0.612	PCDHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372848.2	NM_018906	
NOL7	51406	hgsc.bcm.edu	37	6	13615767	13615767	+	Silent	SNP	T	T	C	rs75029999	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:13615767T>C	ENST00000451315.2	+	1	209	c.177T>C	c.(175-177)ttT>ttC	p.F59F	AL441883.1_ENST00000600057.1_3'UTR|RP1-223E5.4_ENST00000566170.1_RNA	NM_016167.3	NP_057251.2	Q9UMY1	NOL7_HUMAN	nucleolar protein 7, 27kDa	59						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|large_intestine(3)|lung(1)	5	Breast(50;0.00669)|Ovarian(93;0.0634)	all_hematologic(90;0.135)	Epithelial(50;0.176)			ACGATGAGTTTGACGATGAGG	0.706											OREG0017200	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	40	0.00798722	0.028	0.0043	5008	,	,		15084	0.0		0.0	False		,,,				2504	0.0				p.F59F		Atlas-SNP	.											.	NOL7	18	.	0			c.T177C						PASS	.	T		71,4223		1,69,2077	8.0	10.0	9.0		177	-7.7	0.0	6	dbSNP_132	9	1,8465		0,1,4232	no	coding-synonymous	NOL7	NM_016167.3		1,70,6309	CC,CT,TT		0.0118,1.6535,0.5643		59/258	13615767	72,12688	2147	4233	6380	SO:0001819	synonymous_variant	51406	exon1			TGAGTTTGACGAT	AF172066	CCDS4528.1	6p23	2008-05-23	2004-02-10		ENSG00000225921	ENSG00000225921			21040	protein-coding gene	gene with protein product		611533	"""chromosome 6 open reading frame 90"", ""polyglutamine binding protein 3"""	C6orf90, PQBP3		16205646	Standard	NM_016167		Approved	NOP27, RARG-1, dJ223E5.2	uc003naz.3	Q9UMY1	OTTHUMG00000014277	ENST00000451315.2:c.177T>C	6.37:g.13615767T>C		48.0	0.0	0	688	67.0	32.0	0.477612	NM_016167	Q5T297|Q9Y3U7	Silent	SNP	ENST00000451315.2	37	CCDS4528.1																																																																																			T|0.994;C|0.006	0.006	strong		0.706	NOL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039904.1	NM_016167	
VWDE	221806	hgsc.bcm.edu	37	7	12414314	12414314	+	Splice_Site	SNP	C	C	G	rs138469050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:12414314C>G	ENST00000275358.3	-	9	1505		c.e9+1			NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains							extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						CAGAAAATTACCTGCCATCAA	0.279													C|||	57	0.0113818	0.0416	0.0029	5008	,	,		13055	0.0		0.0	False		,,,				2504	0.0				.		Atlas-SNP	.											.	VWDE	123	.	0			c.1316+1G>C						PASS	.	C		43,1341		1,41,650	124.0	111.0	115.0			4.0	1.0	7	dbSNP_134	115	1,3157		0,1,1578	no	splice-5	VWDE	NM_001135924.1		1,42,2228	GG,GC,CC		0.0317,3.1069,0.9687			12414314	44,4498	692	1579	2271	SO:0001630	splice_region_variant	221806	exon10			AAATTACCTGCCA		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.1316+1G>C	7.37:g.12414314C>G		178.0	0.0	0		171.0	81.0	0.473684	NM_001135924	B7ZM77|Q96SQ3	Splice_Site	SNP	ENST00000275358.3	37	CCDS47544.1	14	0.00641025641025641	12	0.024390243902439025	2	0.0055248618784530384	0	0.0	0	0.0	C	20.5	4.001307	0.74818	0.031069	3.17E-4	ENSG00000146530	ENST00000275358	.	.	.	4.01	4.01	0.46588	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.3189	0.82938	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	VWDE	12380839	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.194000	0.77789	2.073000	0.62155	0.591000	0.81541	.	C|0.994;G|0.006	0.006	strong		0.279	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	Intron
ADAMDEC1	27299	hgsc.bcm.edu	37	8	24256512	24256512	+	Silent	SNP	T	T	C	rs7005258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24256512T>C	ENST00000256412.4	+	9	1108	c.888T>C	c.(886-888)tcT>tcC	p.S296S	RP11-624C23.1_ENST00000519689.1_RNA|ADAMDEC1_ENST00000522298.1_Silent_p.S217S|RP11-624C23.1_ENST00000523578.1_RNA|ADAMDEC1_ENST00000538205.1_Silent_p.S217S	NM_014479.3	NP_055294.1	O15204	ADEC1_HUMAN	ADAM-like, decysin 1	296	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				immune response (GO:0006955)|negative regulation of cell adhesion (GO:0007162)	extracellular region (GO:0005576)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|large_intestine(4)|skin(2)|stomach(1)	9		Prostate(55;0.0181)		Colorectal(74;0.016)|COAD - Colon adenocarcinoma(73;0.0646)|BRCA - Breast invasive adenocarcinoma(99;0.168)		GGCACAGTTCTAACCTGGGGA	0.517													C|||	88	0.0175719	0.0635	0.0058	5008	,	,		18805	0.0		0.0	False		,,,				2504	0.0				p.S296S	Ovarian(147;687 1849 3699 25981 31337)	Atlas-SNP	.											.	ADAMDEC1	69	.	0			c.T888C						PASS	.	C	,,	261,4145	803.2+/-415.7	11,239,1953	102.0	90.0	94.0		651,651,888	-0.3	0.0	8	dbSNP_116	94	2,8598	819.2+/-406.8	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	ADAMDEC1	NM_001145271.1,NM_001145272.1,NM_014479.3	,,	11,241,6251	CC,CT,TT		0.0233,5.9237,2.0221	,,	217/392,217/392,296/471	24256512	263,12743	2203	4300	6503	SO:0001819	synonymous_variant	27299	exon9			CAGTTCTAACCTG	Y13323	CCDS6044.1, CCDS55212.1	8p12	2008-08-07			ENSG00000134028	ENSG00000134028			16299	protein-coding gene	gene with protein product		606393				9271581, 12037602	Standard	NM_001145271		Approved	M12.219	uc003xdz.2	O15204	OTTHUMG00000097858	ENST00000256412.4:c.888T>C	8.37:g.24256512T>C		114.0	0.0	0		133.0	56.0	0.421053	NM_014479	B7ZAK5	Silent	SNP	ENST00000256412.4	37	CCDS6044.1																																																																																			T|0.977;C|0.023	0.023	strong		0.517	ADAMDEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215149.2	NM_014479	
GAS2L3	283431	hgsc.bcm.edu	37	12	101018061	101018061	+	Missense_Mutation	SNP	C	C	T	rs61748063	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:101018061C>T	ENST00000539410.1	+	9	1864	c.1478C>T	c.(1477-1479)tCa>tTa	p.S493L	GAS2L3_ENST00000547754.1_Missense_Mutation_p.S493L|GAS2L3_ENST00000266754.5_Missense_Mutation_p.S493L|GAS2L3_ENST00000537247.1_Missense_Mutation_p.S389L			Q86XJ1	GA2L3_HUMAN	growth arrest-specific 2 like 3	493					actin cytoskeleton organization (GO:0030036)|cell cycle arrest (GO:0007050)|microtubule cytoskeleton organization (GO:0000226)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	actin binding (GO:0003779)|microtubule binding (GO:0008017)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(15)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35						GCTGCACATTCAAATTCATCC	0.363													C|||	17	0.00339457	0.0008	0.0086	5008	,	,		20148	0.0		0.008	False		,,,				2504	0.002				p.S493L		Atlas-SNP	.											.	GAS2L3	76	.	0			c.C1478T						PASS	.	C	LEU/SER	6,4398	11.4+/-27.6	0,6,2196	61.0	65.0	64.0		1478	-0.2	0.0	12	dbSNP_129	64	50,8550	32.8+/-85.7	0,50,4250	yes	missense	GAS2L3	NM_174942.1	145	0,56,6446	TT,TC,CC		0.5814,0.1362,0.4306	benign	493/695	101018061	56,12948	2202	4300	6502	SO:0001583	missense	283431	exon10			CACATTCAAATTC	AK095594	CCDS9079.1	12q23.1	2014-09-11			ENSG00000139354	ENSG00000139354			27475	protein-coding gene	gene with protein product							Standard	NM_174942		Approved		uc001thu.3	Q86XJ1	OTTHUMG00000170439	ENST00000539410.1:c.1478C>T	12.37:g.101018061C>T	ENSP00000439672:p.Ser493Leu	40.0	0.0	0		57.0	30.0	0.526316	NM_174942	B2RCN2	Missense_Mutation	SNP	ENST00000539410.1	37	CCDS9079.1	11	0.005036630036630037	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	5	0.006596306068601583	C	0.060	-1.227601	0.01518	0.001362	0.005814	ENSG00000139354	ENST00000266754;ENST00000547754;ENST00000537247;ENST00000539410	T;T;T;T	0.22743	1.96;1.96;1.94;1.96	4.93	-0.166	0.13351	.	1.089570	0.07116	N	0.843066	T	0.06142	0.0159	N	0.02315	-0.6	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.37478	-0.9704	10	0.23302	T	0.38	-1.9276	10.8995	0.47043	0.0:0.4908:0.0:0.5092	rs61748063	493	Q86XJ1	GA2L3_HUMAN	L	493;493;389;493	ENSP00000266754:S493L;ENSP00000448955:S493L;ENSP00000442406:S389L;ENSP00000439672:S493L	ENSP00000266754:S493L	S	+	2	0	GAS2L3	99542192	0.000000	0.05858	0.000000	0.03702	0.198000	0.23893	-0.585000	0.05794	-0.113000	0.11958	-0.793000	0.03317	TCA	C|0.995;T|0.005	0.005	strong		0.363	GAS2L3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409143.1	NM_174942	
OBSCN	84033	hgsc.bcm.edu	37	1	228461055	228461055	+	Intron	SNP	T	T	C	rs113996842	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228461055T>C	ENST00000422127.1	+	18	5181				RP5-1139B12.2_ENST00000602517.1_RNA|OBSCN_ENST00000366709.4_Intron|OBSCN_ENST00000359599.6_Silent_p.C495C|RP5-1139B12.3_ENST00000602947.1_RNA|OBSCN_ENST00000570156.2_Silent_p.C2023C|RP5-1139B12.3_ENST00000602529.1_RNA|OBSCN_ENST00000366707.4_Intron|OBSCN_ENST00000284548.11_Intron	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF						apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CGCTGAGCTGTGAGGTGGCCC	0.637													T|||	15	0.00299521	0.0106	0.0014	5008	,	,		17510	0.0		0.0	False		,,,				2504	0.0				p.C2023C		Atlas-SNP	.											.	OBSCN	2142	.	0			c.T6069C						PASS	.																																			SO:0001627	intron_variant	84033	exon21			GAGCTGTGAGGTG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.5138-416T>C	1.37:g.228461055T>C		283.0	0.0	0		290.0	140.0	0.482759	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			T|0.997;C|0.003	0.003	strong		0.637	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
PKDREJ	10343	hgsc.bcm.edu	37	22	46656562	46656562	+	Silent	SNP	A	A	G	rs7287371	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46656562A>G	ENST00000253255.5	-	1	2657	c.2658T>C	c.(2656-2658)taT>taC	p.Y886Y		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	886	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		TGAGTGTTGGATAAAAACAAT	0.388													A|||	265	0.0529153	0.1899	0.0144	5008	,	,		21079	0.0		0.0	False		,,,				2504	0.0041				p.Y886Y		Atlas-SNP	.											.	PKDREJ	195	.	0			c.T2658C						PASS	.	A		777,3629	311.9+/-292.3	72,633,1498	83.0	84.0	83.0		2658	-10.1	0.0	22	dbSNP_116	83	14,8586	9.8+/-36.6	0,14,4286	no	coding-synonymous	PKDREJ	NM_006071.1		72,647,5784	GG,GA,AA		0.1628,17.635,6.0818		886/2254	46656562	791,12215	2203	4300	6503	SO:0001819	synonymous_variant	10343	exon1			TGTTGGATAAAAA	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like"", ""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like"", ""polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"""			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.2658T>C	22.37:g.46656562A>G		142.0	0.0	0		139.0	74.0	0.532374	NM_006071	B1AJY3|O95850	Silent	SNP	ENST00000253255.5	37	CCDS14073.1																																																																																			A|0.942;G|0.058	0.058	strong		0.388	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
TAF1	6872	hgsc.bcm.edu	37	X	70586196	70586196	+	Missense_Mutation	SNP	C	C	T	rs139510844	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:70586196C>T	ENST00000373790.4	+	1	83	c.32C>T	c.(31-33)aCa>aTa	p.T11I	TAF1_ENST00000276072.3_Missense_Mutation_p.T11I|TAF1_ENST00000449580.1_Missense_Mutation_p.T11I|TAF1_ENST00000423759.1_Missense_Mutation_p.T11I	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	11	Protein kinase 1.				cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				CTGCTGCGGACAGCAGCTACC	0.562													c|||	27	0.00715232	0.0189	0.0029	3775	,	,		5194	0.0		0.0	False		,,,				2504	0.0				p.T11I		Atlas-SNP	.											.	TAF1	439	.	0			c.C32T						PASS	.	C	ILE/THR,ILE/THR	98,3737		0,86,12,1546,559	66.0	56.0	59.0		32,32	-5.4	0.0	X	dbSNP_134	59	0,6728		0,0,0,2428,1872	yes	missense,missense	TAF1	NM_004606.3,NM_138923.2	89,89	0,86,12,3974,2431	TT,TC,T,CC,C		0.0,2.5554,0.9278	possibly-damaging,possibly-damaging	11/1894,11/1873	70586196	98,10465	2203	4300	6503	SO:0001583	missense	6872	exon1			TGCGGACAGCAGC		CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"""Chromatin-modifying enzymes / K-acetyltransferases"""	11535	protein-coding gene	gene with protein product		313650	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD"", ""dystonia 3 (with Parkinsonism)"""	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.32C>T	X.37:g.70586196C>T	ENSP00000362895:p.Thr11Ile	303.0	1.0	0.00330033		351.0	183.0	0.521368	NM_004606	A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Missense_Mutation	SNP	ENST00000373790.4	37	CCDS35325.1	12	0.007233273056057866	6	0.012345679012345678	1	0.002777777777777778	1	0.0017482517482517483	0	0.0	.	10.35	1.325295	0.24080	0.025554	0.0	ENSG00000147133	ENST00000373790;ENST00000449580;ENST00000423759;ENST00000276072	T;T;T;T	0.08720	3.06;3.12;3.13;3.08	4.36	-5.37	0.02681	.	4.117550	0.00760	N	0.001123	T	0.01254	0.0041	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.09377	0.002;0.004	T	0.34304	-0.9834	10	0.39692	T	0.17	.	4.0791	0.09917	0.4281:0.2007:0.0:0.3712	.	11;11	P21675;P21675-2	TAF1_HUMAN;.	I	11	ENSP00000362895:T11I;ENSP00000389000:T11I;ENSP00000406549:T11I;ENSP00000276072:T11I	ENSP00000276072:T11I	T	+	2	0	TAF1	70502921	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.175000	0.03102	-1.604000	0.01595	0.399000	0.26434	ACA	C|0.989;T|0.011	0.011	strong		0.562	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606	
MASP2	10747	hgsc.bcm.edu	37	1	11087687	11087687	+	Missense_Mutation	SNP	C	C	T	rs12085877	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11087687C>T	ENST00000400897.3	-	11	1331	c.1316G>A	c.(1315-1317)cGc>cAc	p.R439H	RP4-635E18.8_ENST00000607145.1_RNA	NM_006610.3	NP_006601.2	O00187	MASP2_HUMAN	mannan-binding lectin serine peptidase 2	439			R -> H (in dbSNP:rs12085877).		complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|complement component C4b binding (GO:0001855)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			biliary_tract(1)|endometrium(2)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	Ovarian(185;0.249)	Lung NSC(185;1.04e-05)|all_lung(284;1.31e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.071)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.12e-07)|COAD - Colon adenocarcinoma(227;7.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)|STAD - Stomach adenocarcinoma(313;0.192)		TCCTGTTGTGCGGGCTGATAG	0.443													C|||	144	0.028754	0.1036	0.0101	5008	,	,		19654	0.0		0.0	False		,,,				2504	0.0				p.R439H	GBM(35;611 746 20780 22741 36496)	Atlas-SNP	.											MASP2,NS,carcinoma,-1,1	MASP2	71	1	0			c.G1316A						PASS	.	C	HIS/ARG	413,3987		16,381,1803	59.0	62.0	61.0		1316	-0.5	0.0	1	dbSNP_120	61	3,8595		0,3,4296	yes	missense	MASP2	NM_006610.3	29	16,384,6099	TT,TC,CC		0.0349,9.3864,3.2005	benign	439/687	11087687	416,12582	2200	4299	6499	SO:0001583	missense	10747	exon11			GTTGTGCGGGCTG	X98400	CCDS123.1, CCDS124.1	1p36.3-p36.2	2014-09-17	2005-08-17		ENSG00000009724	ENSG00000009724			6902	protein-coding gene	gene with protein product		605102	"""mannan-binding lectin serine protease 2"", ""mannan-binding lectin serine peptidase 1 pseudogene 1"", ""mannan-binding lectin serine protease 1 pseudogene 1"""	MASP1P1		9087411, 9777418	Standard	NM_006610		Approved		uc001aru.3	O00187	OTTHUMG00000002121	ENST00000400897.3:c.1316G>A	1.37:g.11087687C>T	ENSP00000383690:p.Arg439His	104.0	0.0	0		100.0	44.0	0.44	NM_006610	A8K458|A8MWJ2|O75754|Q5TEQ5|Q5TER0|Q96QG4|Q9BZH0|Q9H498|Q9H499|Q9UBP3|Q9UC48|Q9ULC7|Q9UMV3|Q9Y270	Missense_Mutation	SNP	ENST00000400897.3	37	CCDS123.1	54	0.024725274725274724	50	0.1016260162601626	4	0.011049723756906077	0	0.0	0	0.0	C	11.07	1.530812	0.27387	0.093864	3.49E-4	ENSG00000009724	ENST00000400897	D	0.92858	-3.12	5.45	-0.488	0.12056	Peptidase cysteine/serine, trypsin-like (1);Complement control module (1);	0.541857	0.18692	N	0.133825	T	0.12050	0.0293	L	0.28400	0.85	0.21802	N	0.99953	B	0.11235	0.004	B	0.06405	0.002	T	0.50363	-0.8837	10	0.35671	T	0.21	.	0.5192	0.00609	0.2067:0.2927:0.1873:0.3133	rs12085877;rs52829987;rs12085877	439	O00187	MASP2_HUMAN	H	439	ENSP00000383690:R439H	ENSP00000383690:R439H	R	-	2	0	MASP2	11010274	0.000000	0.05858	0.005000	0.12908	0.027000	0.11550	-0.560000	0.05964	0.002000	0.14630	0.563000	0.77884	CGC	C|0.971;T|0.029	0.029	strong		0.443	MASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006072.1	NM_006610	
TMEM82	388595	hgsc.bcm.edu	37	1	16069664	16069664	+	Missense_Mutation	SNP	T	T	C	rs61740067	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:16069664T>C	ENST00000375782.1	+	3	449	c.311T>C	c.(310-312)gTg>gCg	p.V104A	TMEM82_ENST00000465575.1_3'UTR|RP11-169K16.4_ENST00000418525.1_RNA	NM_001013641.1	NP_001013663.1	A0PJX8	TMM82_HUMAN	transmembrane protein 82	104	Leu-rich.					integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(2)|lung(5)|prostate(1)|skin(1)	13		Colorectal(325;0.00108)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0798)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.73e-07)|COAD - Colon adenocarcinoma(227;3.49e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000114)|KIRC - Kidney renal clear cell carcinoma(229;0.00244)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CTCCGGGCCGTGTCCACGCTG	0.701													T|||	115	0.0229633	0.0817	0.0101	5008	,	,		13676	0.0		0.0	False		,,,				2504	0.0				p.V104A		Atlas-SNP	.											.	TMEM82	30	.	0			c.T311C						PASS	.	T	ALA/VAL	248,4156	138.4+/-174.2	7,234,1961	39.0	37.0	38.0		311	4.4	0.8	1	dbSNP_129	38	0,8594		0,0,4297	yes	missense	TMEM82	NM_001013641.1	64	7,234,6258	CC,CT,TT		0.0,5.6312,1.908	benign	104/344	16069664	248,12750	2202	4297	6499	SO:0001583	missense	388595	exon3			GGGCCGTGTCCAC		CCDS30608.1	1p36.13	2008-02-05				ENSG00000162460			32350	protein-coding gene	gene with protein product							Standard	NM_001013641		Approved		uc001axc.4	A0PJX8		ENST00000375782.1:c.311T>C	1.37:g.16069664T>C	ENSP00000364938:p.Val104Ala	67.0	0.0	0		80.0	29.0	0.3625	NM_001013641	B2RP27|Q5VVD4	Missense_Mutation	SNP	ENST00000375782.1	37	CCDS30608.1	53	0.024267399267399268	48	0.0975609756097561	5	0.013812154696132596	0	0.0	0	0.0	T	18.43	3.622000	0.66787	0.056312	0.0	ENSG00000162460	ENST00000375782	T	0.57595	0.39	4.44	4.44	0.53790	.	0.248154	0.34002	N	0.004349	T	0.01976	0.0062	M	0.72894	2.215	0.32890	D	0.511731	P	0.49559	0.925	B	0.38264	0.269	T	0.49370	-0.8947	10	0.66056	D	0.02	-21.6084	13.99	0.64359	0.0:0.0:0.0:1.0	rs61740067	104	A0PJX8	TMM82_HUMAN	A	104	ENSP00000364938:V104A	ENSP00000364938:V104A	V	+	2	0	TMEM82	15942251	0.731000	0.28111	0.774000	0.31636	0.905000	0.53344	3.834000	0.55798	1.763000	0.52060	0.459000	0.35465	GTG	T|0.982;C|0.018	0.018	strong		0.701	TMEM82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008471.2	NM_001013641	
ZNF286B	729288	hgsc.bcm.edu	37	17	18566422	18566422	+	Missense_Mutation	SNP	C	C	T	rs146829975	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18566422C>T	ENST00000545289.1	-	5	647	c.397G>A	c.(397-399)Gaa>Aaa	p.E133K	ZNF286B_ENST00000285274.5_3'UTR	NM_001145045.1	NP_001138517.1	P0CG31	Z286B_HUMAN	zinc finger protein 286B	133					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						TTGCATGATTCTGCTTTGGAA	0.408													.|||	165	0.0329473	0.118	0.0115	5008	,	,		22416	0.0		0.001	False		,,,				2504	0.0				p.E133K		Atlas-SNP	.											.	ZNF286B	75	.	0			c.G397A						PASS	.	C	LYS/GLU	110,1274		4,102,586	90.0	80.0	83.0		397	1.6	1.0	17	dbSNP_134	83	1,3179		0,1,1589	no	missense	ZNF286B	NM_001145045.1	56	4,103,2175	TT,TC,CC		0.0314,7.948,2.4321	benign	133/523	18566422	111,4453	692	1590	2282	SO:0001583	missense	729288	exon5			ATGATTCTGCTTT		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.397G>A	17.37:g.18566422C>T	ENSP00000461413:p.Glu133Lys	416.0	0.0	0		381.0	149.0	0.391076	NM_001145045		Missense_Mutation	SNP	ENST00000545289.1	37	CCDS58523.1																																																																																			C|0.975;T|0.025	0.025	strong		0.408	ZNF286B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_001723047	
MYBL2	4605	hgsc.bcm.edu	37	20	42310449	42310449	+	Missense_Mutation	SNP	G	G	A	rs150704861	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:42310449G>A	ENST00000217026.4	+	3	267	c.140G>A	c.(139-141)aGg>aAg	p.R47K	MYBL2_ENST00000396863.4_Intron	NM_002466.2	NP_002457.1	P10244	MYBB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog-like 2	47	HTH myb-type 1. {ECO:0000255|PROSITE- ProRule:PRU00625}.				G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|spindle assembly involved in mitosis (GO:0090307)	Myb complex (GO:0031523)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	46		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			GCCCTGGTGAGGCAGTTTGGA	0.617													G|||	5	0.000998403	0.003	0.0014	5008	,	,		17008	0.0		0.0	False		,,,				2504	0.0				p.R47K		Atlas-SNP	.											.	MYBL2	82	.	0			c.G140A						PASS	.	G	LYS/ARG	11,4395	17.9+/-39.9	0,11,2192	80.0	67.0	71.0		140	3.7	1.0	20	dbSNP_134	71	0,8600		0,0,4300	yes	missense	MYBL2	NM_002466.2	26	0,11,6492	AA,AG,GG		0.0,0.2497,0.0846	benign	47/701	42310449	11,12995	2203	4300	6503	SO:0001583	missense	4605	exon3			TGGTGAGGCAGTT		CCDS13322.1, CCDS63276.1	20q13.1	2013-07-09	2013-07-09		ENSG00000101057	ENSG00000101057			7548	protein-coding gene	gene with protein product		601415				8812502	Standard	NM_002466		Approved	BMYB, B-MYB	uc002xlb.1	P10244	OTTHUMG00000033062	ENST00000217026.4:c.140G>A	20.37:g.42310449G>A	ENSP00000217026:p.Arg47Lys	135.0	0.0	0		122.0	49.0	0.401639	NM_002466	B2RBS5|B7Z8D9|F8W6N6|Q53F07	Missense_Mutation	SNP	ENST00000217026.4	37	CCDS13322.1	.	.	.	.	.	.	.	.	.	.	G	13.64	2.297518	0.40694	0.002497	0.0	ENSG00000101057	ENST00000217026	T	0.12774	2.65	5.61	3.68	0.42216	Transcription regulator HTH, Myb-type, DNA-binding (1);Myb, DNA-binding (1);SANT domain, DNA binding (1);Homeodomain-related (1);Homeodomain-like (1);	0.198434	0.53938	N	0.000054	T	0.05640	0.0148	N	0.03224	-0.385	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.31503	-0.9941	10	0.35671	T	0.21	-32.0158	7.5543	0.27814	0.3171:0.0:0.6829:0.0	.	47	P10244	MYBB_HUMAN	K	47	ENSP00000217026:R47K	ENSP00000217026:R47K	R	+	2	0	MYBL2	41743863	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.841000	0.48223	0.872000	0.35775	0.655000	0.94253	AGG	G|0.998;A|0.002	0.002	strong		0.617	MYBL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080408.1	NM_002466	
OR10AG1	282770	hgsc.bcm.edu	37	11	55735091	55735091	+	Silent	SNP	C	C	T	rs12292026	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55735091C>T	ENST00000312345.2	-	1	899	c.849G>A	c.(847-849)ctG>ctA	p.L283L		NM_001005491.1	NP_001005491.1	Q8NH19	O10AG_HUMAN	olfactory receptor, family 10, subfamily AG, member 1	283						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(24)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	40	Esophageal squamous(21;0.0137)					CTTTGTTCCTCAGGGTATATA	0.328													C|||	121	0.0241613	0.0862	0.0101	5008	,	,		18729	0.0		0.0	False		,,,				2504	0.0				p.L283L		Atlas-SNP	.											.	OR10AG1	100	.	0			c.G849A						PASS	.	C		306,4096	161.4+/-193.6	17,272,1912	55.0	61.0	59.0		849	3.2	1.0	11	dbSNP_120	59	6,8586	5.7+/-21.5	0,6,4290	no	coding-synonymous	OR10AG1	NM_001005491.1		17,278,6202	TT,TC,CC		0.0698,6.9514,2.4011		283/302	55735091	312,12682	2201	4296	6497	SO:0001819	synonymous_variant	282770	exon1			GTTCCTCAGGGTA	AB065594	CCDS31514.1	11q11	2012-08-09			ENSG00000174970	ENSG00000174970		"""GPCR / Class A : Olfactory receptors"""	19607	protein-coding gene	gene with protein product							Standard	NM_001005491		Approved		uc010rit.2	Q8NH19	OTTHUMG00000166824	ENST00000312345.2:c.849G>A	11.37:g.55735091C>T		115.0	0.0	0		106.0	55.0	0.518868	NM_001005491	B2RNH4|Q6IEU3	Silent	SNP	ENST00000312345.2	37	CCDS31514.1																																																																																			C|0.974;T|0.026	0.026	strong		0.328	OR10AG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391531.1	NM_001005491	
ST7L	54879	hgsc.bcm.edu	37	1	113068651	113068651	+	Missense_Mutation	SNP	C	C	T	rs12069022	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:113068651C>T	ENST00000358039.4	-	15	2016	c.1712G>A	c.(1711-1713)gGt>gAt	p.G571D	WNT2B_ENST00000369686.5_3'UTR|ST7L_ENST00000369669.1_Missense_Mutation_p.G388D|ST7L_ENST00000490067.1_Missense_Mutation_p.G554D|ST7L_ENST00000360743.4_Missense_Mutation_p.G540D|ST7L_ENST00000544629.1_Missense_Mutation_p.G506D	NM_017744.4|NM_138727.3	NP_060214.2|NP_620055.1	Q8TDW4	ST7L_HUMAN	suppression of tumorigenicity 7 like	571			G -> D (in dbSNP:rs12069022).		negative regulation of cell growth (GO:0030308)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(4)|large_intestine(3)|lung(1)|prostate(2)|stomach(1)|urinary_tract(3)	15	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		agaactcaaacctaggtcttc	0.478													C|||	174	0.0347444	0.1263	0.0101	5008	,	,		18280	0.0		0.0	False		,,,				2504	0.0				p.G571D		Atlas-SNP	.											.	ST7L	31	.	0			c.G1712A						PASS	.	C	ASP/GLY,ASP/GLY,ASP/GLY	441,3965	212.5+/-232.4	23,395,1785	114.0	113.0	113.0		1712,1661,1619	1.9	0.1	1	dbSNP_120	113	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense	ST7L	NM_017744.4,NM_138727.3,NM_138728.2	94,94,94	23,398,6082	TT,TC,CC		0.0349,10.0091,3.4138	probably-damaging,probably-damaging,probably-damaging	571/576,554/559,540/545	113068651	444,12562	2203	4300	6503	SO:0001583	missense	54879	exon15			CTCAAACCTAGGT	AB081317	CCDS848.1, CCDS849.1, CCDS850.1, CCDS852.1	1p13.1	2008-06-06			ENSG00000007341	ENSG00000007341			18441	protein-coding gene	gene with protein product						12012006	Standard	NM_138729		Approved	FLJ20284, STLR, ST7R, FAM4B	uc001ecd.3	Q8TDW4	OTTHUMG00000011753	ENST00000358039.4:c.1712G>A	1.37:g.113068651C>T	ENSP00000350734:p.Gly571Asp	61.0	0.0	0		73.0	38.0	0.520548	NM_017744	A8K4S7|Q49AH6|Q5TEI4|Q5U5K6|Q6N067|Q7Z2Z0|Q7Z3C2|Q8N7P8|Q8TDW1|Q8TDW2|Q8TDW3|Q9NXF3	Missense_Mutation	SNP	ENST00000358039.4	37	CCDS848.1	44	0.020146520146520148	42	0.08536585365853659	2	0.0055248618784530384	0	0.0	0	0.0	C	15.95	2.984826	0.53934	0.100091	3.49E-4	ENSG00000007341	ENST00000358039;ENST00000360743;ENST00000369673;ENST00000544629;ENST00000369669;ENST00000490067	T;T;T;T;T	0.19394	2.43;2.24;2.15;2.39;2.43	3.81	1.87	0.25490	.	1.917730	0.02054	N	0.050248	T	0.04003	0.0112	N	0.08118	0	0.20563	N	0.999889	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.04013	0.0;0.001;0.001;0.0;0.0	T	0.32052	-0.9921	10	0.87932	D	0	.	5.8421	0.18639	0.0:0.7468:0.0:0.2532	rs12069022;rs12069022	506;506;554;540;571	B7Z3J2;F5H2P3;Q8TDW4-3;Q8TDW4-2;Q8TDW4	.;.;.;.;ST7L_HUMAN	D	571;540;321;506;388;554	ENSP00000350734:G571D;ENSP00000353972:G540D;ENSP00000445499:G506D;ENSP00000358683:G388D;ENSP00000417140:G554D	ENSP00000350734:G571D	G	-	2	0	ST7L	112870174	0.000000	0.05858	0.071000	0.20095	0.353000	0.29299	0.130000	0.15850	0.558000	0.29135	-0.119000	0.15052	GGT	C|0.963;T|0.037	0.037	strong		0.478	ST7L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032504.3		
OSBPL6	114880	hgsc.bcm.edu	37	2	179226431	179226431	+	Silent	SNP	A	A	G	rs145291582	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179226431A>G	ENST00000190611.4	+	13	1552	c.1176A>G	c.(1174-1176)gcA>gcG	p.A392A	OSBPL6_ENST00000315022.2_Silent_p.A396A|OSBPL6_ENST00000357080.4_Silent_p.A361A|OSBPL6_ENST00000409631.1_Silent_p.A392A|OSBPL6_ENST00000392505.2_Silent_p.A417A|OSBPL6_ENST00000409045.3_Silent_p.A361A|OSBPL6_ENST00000359685.3_Silent_p.A392A	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	392					lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			TGAAGTCTGCATTTAATAGCA	0.438													a|||	19	0.00379393	0.0136	0.0014	5008	,	,		20040	0.0		0.0	False		,,,				2504	0.0				p.A417A		Atlas-SNP	.											OSBPL6,NS,carcinoma,+1,1	OSBPL6	178	1	0			c.A1251G						PASS	.	A	,,,,	58,4348	55.5+/-91.7	0,58,2145	104.0	98.0	100.0		1251,1083,1176,1176,1188	-11.1	0.2	2	dbSNP_134	100	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OSBPL6	NM_001201480.1,NM_001201481.1,NM_001201482.1,NM_032523.3,NM_145739.2	,,,,	0,58,6445	GG,GA,AA		0.0,1.3164,0.4459	,,,,	417/960,361/904,392/899,392/935,396/939	179226431	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	114880	exon14			GTCTGCATTTAAT	AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156		"""Oxysterol binding proteins"""	16388	protein-coding gene	gene with protein product	"""OSBP-related protein 6"""	606734				11483621	Standard	NM_001201480		Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000190611.4:c.1176A>G	2.37:g.179226431A>G		290.0	0.0	0		289.0	144.0	0.49827	NM_001201480	B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Silent	SNP	ENST00000190611.4	37	CCDS2277.1																																																																																			A|0.995;G|0.005	0.005	strong		0.438	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523	
CD33	945	hgsc.bcm.edu	37	19	51742839	51742839	+	Missense_Mutation	SNP	A	A	G	rs35632246	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51742839A>G	ENST00000262262.4	+	7	1012	c.991A>G	c.(991-993)Act>Gct	p.T331A	CD33_ENST00000421133.2_Missense_Mutation_p.T204A|CD33_ENST00000600557.1_3'UTR	NM_001772.3	NP_001763.3	P20138	CD33_HUMAN	CD33 molecule	331			T -> A (in dbSNP:rs35632246).		cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|negative regulation of cell proliferation (GO:0008285)|signal transduction (GO:0007165)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(15)|skin(1)|stomach(1)	24		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000224)|OV - Ovarian serous cystadenocarcinoma(262;0.00468)	Gemtuzumab ozogamicin(DB00056)	TGCCGCCCCTACTGTGGAGAT	0.517													a|||	62	0.0123802	0.0454	0.0029	5008	,	,		18838	0.0		0.0	False		,,,				2504	0.0				p.T331A		Atlas-SNP	.											.	CD33	55	.	0			c.A991G						PASS	.	A	ALA/THR,ALA/THR	194,4212	121.3+/-158.8	6,182,2015	115.0	99.0	105.0		610,991	-5.0	0.0	19	dbSNP_126	105	2,8598	1.2+/-3.3	0,2,4298	yes	missense,missense	CD33	NM_001082618.1,NM_001772.3	58,58	6,184,6313	GG,GA,AA		0.0233,4.4031,1.507	benign,benign	204/238,331/365	51742839	196,12810	2203	4300	6503	SO:0001583	missense	945	exon7			GCCCCTACTGTGG	M23197	CCDS33084.1, CCDS46157.1, CCDS54299.1	19q13.3	2013-01-29	2006-03-28		ENSG00000105383	ENSG00000105383		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1659	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 3"""	159590	"""CD33 antigen (gp67)"""			3139766, 9465907	Standard	NM_001772		Approved	SIGLEC3, SIGLEC-3, p67, FLJ00391	uc002pwa.2	P20138		ENST00000262262.4:c.991A>G	19.37:g.51742839A>G	ENSP00000262262:p.Thr331Ala	133.0	0.0	0		116.0	57.0	0.491379	NM_001772	B4E3P8|C9JEN7|F8WAL2|Q8TD24	Missense_Mutation	SNP	ENST00000262262.4	37	CCDS33084.1	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	A	3.525	-0.096917	0.07010	0.044031	2.33E-4	ENSG00000105383	ENST00000262262;ENST00000421133	T;T	0.04758	3.56;3.56	2.51	-5.02	0.02982	.	.	.	.	.	T	0.00552	0.0018	L	0.39147	1.195	0.09310	N	1	B;B	0.15141	0.012;0.012	B;B	0.11329	0.006;0.006	T	0.44528	-0.9322	9	0.22706	T	0.39	.	3.2402	0.06778	0.2436:0.0:0.2473:0.5091	rs35632246	204;331	C9JEN7;P20138	.;CD33_HUMAN	A	331;204	ENSP00000262262:T331A;ENSP00000410126:T204A	ENSP00000262262:T331A	T	+	1	0	CD33	56434651	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	-1.760000	0.01806	-1.514000	0.01786	0.260000	0.18958	ACT	A|0.986;G|0.014	0.014	strong		0.517	CD33-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464199.2	NM_001772	
EPS8	2059	hgsc.bcm.edu	37	12	15776095	15776095	+	Silent	SNP	C	C	T	rs1126786	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:15776095C>T	ENST00000281172.5	-	20	2788	c.2352G>A	c.(2350-2352)ttG>ttA	p.L784L	EPS8_ENST00000543523.1_Silent_p.L784L|EPS8_ENST00000543612.1_Silent_p.L784L|EPS8_ENST00000542903.1_Silent_p.L524L|EPS8_ENST00000540613.1_Silent_p.L524L	NM_004447.5	NP_004438.3	Q12929	EPS8_HUMAN	epidermal growth factor receptor pathway substrate 8	784	Effector region. {ECO:0000250}.|Helix bundle 4. {ECO:0000250}.				actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|actin filament bundle assembly (GO:0051017)|actin polymerization-dependent cell motility (GO:0070358)|adult locomotory behavior (GO:0008344)|barbed-end actin filament capping (GO:0051016)|behavioral response to ethanol (GO:0048149)|cell proliferation (GO:0008283)|dendritic cell migration (GO:0036336)|epidermal growth factor receptor signaling pathway (GO:0007173)|exit from mitosis (GO:0010458)|positive regulation of signal transduction (GO:0009967)|Rac protein signal transduction (GO:0016601)|regulation of actin filament length (GO:0030832)|regulation of cell shape (GO:0008360)|signal transduction (GO:0007165)	cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|postsynaptic density (GO:0014069)|ruffle membrane (GO:0032587)|stereocilium (GO:0032420)|vesicle (GO:0031982)	actin binding (GO:0003779)|Rac GTPase binding (GO:0048365)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	33		all_epithelial(100;1.87e-05)|Breast(259;0.000286)|Hepatocellular(102;0.244)		BRCA - Breast invasive adenocarcinoma(232;4.29e-05)|GBM - Glioblastoma multiforme(207;0.0264)		GTCATACCTCCAATGCAGCTT	0.418													T|||	882	0.176118	0.5507	0.0562	5008	,	,		17316	0.0536		0.0209	False		,,,				2504	0.0409				p.L784L		Atlas-SNP	.											.	EPS8	70	.	0			c.G2352A						PASS	.	T		2128,2278	599.1+/-389.2	529,1070,604	131.0	135.0	133.0		2352	-0.9	0.7	12	dbSNP_86	133	204,8396	810.5+/-407.1	2,200,4098	no	coding-synonymous	EPS8	NM_004447.5		531,1270,4702	TT,TC,CC		2.3721,48.2978,17.9302		784/823	15776095	2332,10674	2203	4300	6503	SO:0001819	synonymous_variant	2059	exon20			TACCTCCAATGCA	U12535	CCDS31753.1	12p12.3	2008-05-02				ENSG00000151491			3420	protein-coding gene	gene with protein product		600206				8084614	Standard	NM_004447		Approved		uc001rdb.3	Q12929		ENST00000281172.5:c.2352G>A	12.37:g.15776095C>T		148.0	0.0	0		158.0	76.0	0.481013	NM_004447	A6NMC3|A8K6W2|A8KA66|B4DX66|Q8N6J0	Silent	SNP	ENST00000281172.5	37	CCDS31753.1																																																																																			T|0.130;G|0.153;C|0.674;A|0.042	0.130	strong		0.418	EPS8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401093.1		
TRAF2	7186	hgsc.bcm.edu	37	9	139814931	139814931	+	Silent	SNP	G	G	T	rs17244166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139814931G>T	ENST00000247668.2	+	8	976	c.924G>T	c.(922-924)cgG>cgT	p.R308R	TRAF2_ENST00000536468.1_Silent_p.R308R|TRAF2_ENST00000359662.3_Silent_p.R360R	NM_021138.3	NP_066961.2	Q12933	TRAF2_HUMAN	TNF receptor-associated factor 2	308				Missing (in Ref. 2; BAB70792). {ECO:0000305}.	activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular protein complex assembly (GO:0043623)|cellular response to nitric oxide (GO:0071732)|innate immune response (GO:0045087)|negative regulation of glial cell apoptotic process (GO:0034351)|negative regulation of neuron death (GO:1901215)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|programmed necrotic cell death (GO:0097300)|protein autoubiquitination (GO:0051865)|protein catabolic process (GO:0030163)|protein complex assembly (GO:0006461)|protein heterooligomerization (GO:0051291)|protein homotrimerization (GO:0070207)|protein K63-linked ubiquitination (GO:0070534)|regulation of apoptotic process (GO:0042981)|regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001239)|regulation of immunoglobulin secretion (GO:0051023)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	CD40 receptor complex (GO:0035631)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|membrane raft (GO:0045121)|ubiquitin ligase complex (GO:0000151)	CD40 receptor binding (GO:0005174)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|ligase activity (GO:0016874)|protein phosphatase binding (GO:0019903)|signal transducer activity (GO:0004871)|sphingolipid binding (GO:0046625)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.229)	OV - Ovarian serous cystadenocarcinoma(145;4.48e-06)|Epithelial(140;9.55e-06)		GGCAGCACCGGCTGGACCAAG	0.597													G|||	30	0.00599042	0.0219	0.0014	5008	,	,		15208	0.0		0.0	False		,,,				2504	0.0				p.R308R		Atlas-SNP	.											.	TRAF2	46	.	0			c.G924T						PASS	.	G		114,4290	85.8+/-124.5	1,112,2089	30.0	33.0	32.0		924	-1.9	1.0	9	dbSNP_123	32	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TRAF2	NM_021138.3		1,113,6388	TT,TG,GG		0.0116,2.5886,0.8843		308/502	139814931	115,12889	2202	4300	6502	SO:0001819	synonymous_variant	7186	exon8			GCACCGGCTGGAC	U12597	CCDS7013.1	9q34	2013-01-09			ENSG00000127191	ENSG00000127191		"""RING-type (C3HC4) zinc fingers"""	12032	protein-coding gene	gene with protein product		601895				7639698	Standard	NM_021138		Approved	TRAP3	uc004cjv.3	Q12933	OTTHUMG00000020952	ENST00000247668.2:c.924G>T	9.37:g.139814931G>T		61.0	0.0	0		77.0	29.0	0.376623	NM_021138	A8K107|B4DPJ7|Q7Z337|Q96NT2	Silent	SNP	ENST00000247668.2	37	CCDS7013.1																																																																																			G|0.989;T|0.011	0.011	strong		0.597	TRAF2-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055166.1	NM_021138	
RP1L1	94137	hgsc.bcm.edu	37	8	10464474	10464474	+	Silent	SNP	G	G	T	rs113172380	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:10464474G>T	ENST00000382483.3	-	4	7357	c.7134C>A	c.(7132-7134)ctC>ctA	p.L2378L		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	2458					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		CGAGACTTCCGAGTGCCTGGT	0.532													G|||	15	0.00299521	0.0113	0.0	5008	,	,		17727	0.0		0.0	False		,,,				2504	0.0				p.L2378L		Atlas-SNP	.											RP1L1,NS,carcinoma,-2,1	RP1L1	453	1	0			c.C7134A						PASS	.	G		27,3811		0,27,1892	110.0	114.0	113.0		7134	-7.2	0.0	8	dbSNP_132	113	0,8234		0,0,4117	no	coding-synonymous	RP1L1	NM_178857.5		0,27,6009	TT,TG,GG		0.0,0.7035,0.2237		2378/2401	10464474	27,12045	1919	4117	6036	SO:0001819	synonymous_variant	94137	exon4			ACTTCCGAGTGCC	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.7134C>A	8.37:g.10464474G>T		56.0	0.0	0		68.0	46.0	0.676471	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	37	CCDS43708.1																																																																																			G|0.996;T|0.004	0.004	strong		0.532	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
OR13C5	138799	hgsc.bcm.edu	37	9	107361009	107361009	+	Missense_Mutation	SNP	C	C	G	rs73508187	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107361009C>G	ENST00000374779.2	-	1	779	c.686G>C	c.(685-687)aGc>aCc	p.S229T		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	229						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						CTCCGAAGAGCTAATTTTGAA	0.428													C|||	65	0.0129792	0.0454	0.0072	5008	,	,		22160	0.0		0.0	False		,,,				2504	0.0				p.S229T		Atlas-SNP	.											.	OR13C5	60	.	0			c.G686C						PASS	.	C	THR/SER	125,4281	92.5+/-131.2	0,125,2078	122.0	115.0	117.0		686	-1.2	0.0	9	dbSNP_130	117	1,8599	1.2+/-3.3	0,1,4299	yes	missense	OR13C5	NM_001004482.1	58	0,126,6377	GG,GC,CC		0.0116,2.837,0.9688	benign	229/319	107361009	126,12880	2203	4300	6503	SO:0001583	missense	138799	exon1			GAAGAGCTAATTT		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.686G>C	9.37:g.107361009C>G	ENSP00000363911:p.Ser229Thr	183.0	0.0	0		210.0	132.0	0.628571	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Missense_Mutation	SNP	ENST00000374779.2	37	CCDS35091.1	27	0.012362637362637362	25	0.0508130081300813	2	0.0055248618784530384	0	0.0	0	0.0	C	10.96	1.499301	0.26861	0.02837	1.16E-4	ENSG00000255800	ENST00000374779	T	0.38722	1.12	4.03	-1.21	0.09524	GPCR, rhodopsin-like superfamily (1);	1.008970	0.07986	U	0.986370	T	0.05777	0.0151	L	0.29908	0.895	0.09310	N	1	B	0.22800	0.075	B	0.32022	0.139	T	0.36915	-0.9728	10	0.59425	D	0.04	.	5.1916	0.15212	0.0:0.2959:0.4158:0.2883	.	229	Q8NGS8	O13C5_HUMAN	T	229	ENSP00000363911:S229T	ENSP00000363911:S229T	S	-	2	0	OR13C5	106400830	0.000000	0.05858	0.000000	0.03702	0.174000	0.22865	-5.456000	0.00121	-0.113000	0.11958	0.423000	0.28283	AGC	C|0.990;G|0.010	0.010	strong		0.428	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
LCN15	389812	hgsc.bcm.edu	37	9	139657900	139657900	+	Silent	SNP	C	C	G	rs11145872	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:139657900C>G	ENST00000316144.5	-	4	351	c.327G>C	c.(325-327)gtG>gtC	p.V109V	LCN15_ENST00000482511.1_5'UTR	NM_203347.1	NP_976222.1	Q6UWW0	LCN15_HUMAN	lipocalin 15	109					lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	small molecule binding (GO:0036094)|transporter activity (GO:0005215)			endometrium(1)|lung(1)	2						CCACGATGCGCACGTCCAGGT	0.642													C|||	14	0.00279553	0.0098	0.0014	5008	,	,		8406	0.0		0.0	False		,,,				2504	0.0				p.V109V		Atlas-SNP	.											.	LCN15	11	.	0			c.G327C						PASS	.	C		56,4350	54.9+/-90.9	1,54,2148	76.0	67.0	70.0		327	3.9	1.0	9	dbSNP_120	70	0,8600		0,0,4300	no	coding-synonymous	LCN15	NM_203347.1		1,54,6448	GG,GC,CC		0.0,1.271,0.4306		109/185	139657900	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	389812	exon4			GATGCGCACGTCC		CCDS7006.1	9q34.3	2011-10-24			ENSG00000177984	ENSG00000177984		"""Lipocalins"""	33777	protein-coding gene	gene with protein product							Standard	NM_203347		Approved	UNQ2541, PRO6093	uc004cjd.3	Q6UWW0	OTTHUMG00000020943	ENST00000316144.5:c.327G>C	9.37:g.139657900C>G		36.0	0.0	0		32.0	20.0	0.625	NM_203347		Silent	SNP	ENST00000316144.5	37	CCDS7006.1																																																																																			C|0.994;G|0.006	0.006	strong		0.642	LCN15-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055114.2	NM_203347	
AQP2	359	hgsc.bcm.edu	37	12	50344958	50344958	+	Silent	SNP	C	C	T	rs60629501	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:50344958C>T	ENST00000199280.3	+	1	430	c.345C>T	c.(343-345)gaC>gaT	p.D115D	RP11-469H8.6_ENST00000552379.1_RNA|RP11-469H8.6_ENST00000550530.1_RNA	NM_000486.5	NP_000477.1	P41181	AQP2_HUMAN	aquaporin 2 (collecting duct)	115					actin filament depolymerization (GO:0030042)|aging (GO:0007568)|apoptotic process (GO:0006915)|cell volume homeostasis (GO:0006884)|cellular response to copper ion (GO:0071280)|cellular response to mercury ion (GO:0071288)|cellular response to water deprivation (GO:0042631)|excretion (GO:0007588)|female pregnancy (GO:0007565)|glycerol transport (GO:0015793)|hyperosmotic response (GO:0006972)|metanephric collecting duct development (GO:0072205)|positive regulation of calcium ion transport (GO:0051928)|renal water transport (GO:0003097)|response to calcium ion (GO:0051592)|response to glucagon (GO:0033762)|response to lipopolysaccharide (GO:0032496)|response to lithium ion (GO:0010226)|response to salt stress (GO:0009651)|response to starvation (GO:0042594)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|clathrin-coated vesicle (GO:0030136)|early endosome (GO:0005769)|exocytic vesicle (GO:0070382)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|recycling endosome (GO:0055037)|rough endoplasmic reticulum (GO:0005791)|trans-Golgi network (GO:0005802)|transport vesicle membrane (GO:0030658)	glycerol transmembrane transporter activity (GO:0015168)|water channel activity (GO:0015250)|water transmembrane transporter activity (GO:0005372)			breast(1)|central_nervous_system(1)|cervix(1)|large_intestine(1)|lung(4)|ovary(2)	10						TCCGCGGGGACCTGGCTGTCA	0.627													C|||	61	0.0121805	0.0431	0.0058	5008	,	,		18198	0.0		0.0	False		,,,				2504	0.0				p.D115D		Atlas-SNP	.											.	AQP2	34	.	0			c.C345T						PASS	.	C		173,4225		2,169,2028	16.0	17.0	17.0		345	0.7	1.0	12	dbSNP_129	17	0,8590		0,0,4295	no	coding-synonymous	AQP2	NM_000486.5		2,169,6323	TT,TC,CC		0.0,3.9336,1.332		115/272	50344958	173,12815	2199	4295	6494	SO:0001819	synonymous_variant	359	exon1			CGGGGACCTGGCT		CCDS8792.1	12q12-q13	2014-09-17				ENSG00000167580		"""Ion channels / Aquaporins"""	634	protein-coding gene	gene with protein product		107777				7512890	Standard	NM_000486		Approved		uc001rvn.3	P41181		ENST00000199280.3:c.345C>T	12.37:g.50344958C>T		69.0	0.0	0		83.0	43.0	0.518072	NM_000486	Q9UD68	Silent	SNP	ENST00000199280.3	37	CCDS8792.1																																																																																			C|0.988;T|0.012	0.012	strong		0.627	AQP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405540.1	NM_000486	
RPL31	6160	hgsc.bcm.edu	37	2	101619211	101619211	+	Silent	SNP	C	C	T	rs141007382	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:101619211C>T	ENST00000264258.3	+	2	649	c.48C>T	c.(46-48)gcC>gcT	p.A16A	RPL31_ENST00000409038.1_Silent_p.A16A|RPL31_ENST00000409000.1_Silent_p.A16A|RPL31_ENST00000409733.1_Silent_p.A16A|RPL31_ENST00000409320.3_Silent_p.A16A|RPL31_ENST00000409650.1_Silent_p.A16A|RPL31_ENST00000409028.4_Silent_p.A16A|RPL31_ENST00000409711.1_Silent_p.A16A|AC016738.4_ENST00000452364.1_RNA	NM_000993.4	NP_000984.1	P62899	RL31_HUMAN	ribosomal protein L31	16					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			kidney(1)|large_intestine(2)|lung(1)|prostate(1)|urinary_tract(3)	8						GCCGTTCTGCCATCAACGAAG	0.532													C|||	5	0.000998403	0.0038	0.0	5008	,	,		19707	0.0		0.0	False		,,,				2504	0.0				p.A16A		Atlas-SNP	.											.	RPL31	12	.	0			c.C48T						PASS	.	C	,,	13,4393	19.1+/-41.9	0,13,2190	71.0	66.0	68.0		48,48,48	2.5	1.0	2	dbSNP_134	68	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	RPL31	NM_000993.4,NM_001098577.2,NM_001099693.1	,,	0,13,6490	TT,TC,CC		0.0,0.2951,0.1	,,	16/126,16/129,16/122	101619211	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	6160	exon2			TTCTGCCATCAAC	X15940	CCDS2049.1, CCDS46373.1, CCDS46374.1	2q11.2	2011-04-06			ENSG00000071082	ENSG00000071082		"""L ribosomal proteins"""	10334	protein-coding gene	gene with protein product						2780320, 11875025	Standard	NM_000993		Approved	L31	uc010fiu.1	P62899	OTTHUMG00000130687	ENST00000264258.3:c.48C>T	2.37:g.101619211C>T		183.0	0.0	0		219.0	114.0	0.520548	NM_001098577	B7Z4K2|D3DVJ4|P12947|Q53SQ5|Q6IRZ0|Q6LBJ6	Silent	SNP	ENST00000264258.3	37	CCDS2049.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	13.12	2.141667	0.37825	0.002951	0.0	ENSG00000071082	ENST00000441435	.	.	.	5.38	2.51	0.30379	.	.	.	.	.	T	0.56587	0.1995	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50939	-0.8768	4	.	.	.	.	8.4008	0.32586	0.1258:0.7401:0.0:0.1341	.	.	.	.	L	4	.	.	P	+	2	0	RPL31	100985643	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.039000	0.49791	0.839000	0.34971	-0.150000	0.13652	CCA	C|0.999;T|0.001	0.001	strong		0.532	RPL31-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253182.3	NM_001098577	
MOK	5891	hgsc.bcm.edu	37	14	102700028	102700028	+	Missense_Mutation	SNP	T	T	C	rs34965156	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:102700028T>C	ENST00000361847.2	-	8	920	c.689A>G	c.(688-690)aAa>aGa	p.K230R	MOK_ENST00000519058.1_5'UTR|MOK_ENST00000522867.1_5'UTR|MOK_ENST00000524370.1_5'UTR|MOK_ENST00000561150.1_5'UTR|MOK_ENST00000517966.1_5'UTR|MOK_ENST00000522534.1_5'UTR|MOK_ENST00000524214.1_Missense_Mutation_p.K200R|MOK_ENST00000523231.1_5'UTR|MOK_ENST00000193029.6_5'UTR|MOK_ENST00000520266.1_5'UTR|MOK_ENST00000522874.1_Missense_Mutation_p.K229R	NM_014226.1	NP_055041.1	Q9UQ07	MOK_HUMAN	MOK protein kinase	230	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		K -> R (in dbSNP:rs34965156). {ECO:0000269|PubMed:17344846}.		protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)										TACTTACTGTTTGAACTTGGT	0.532													T|||	258	0.0515176	0.1876	0.0115	5008	,	,		19334	0.0		0.002	False		,,,				2504	0.0				p.K230R		Atlas-SNP	.											.	.	.	.	0			c.A689G						PASS	.	T	ARG/LYS	689,3717		61,567,1575	189.0	147.0	161.0		689	5.2	1.0	14	dbSNP_126	161	17,8583		0,17,4283	yes	missense	MOK	NM_014226.1	26	61,584,5858	CC,CT,TT		0.1977,15.6378,5.4283	benign	230/420	102700028	706,12300	2203	4300	6503	SO:0001583	missense	5891	exon8			TACTGTTTGAACT	AB022694	CCDS9971.1, CCDS61552.1	14q32	2014-04-23	2011-09-06	2011-09-06	ENSG00000080823	ENSG00000080823			9833	protein-coding gene	gene with protein product		605762	"""renal tumor antigen"""	RAGE		8781117, 10421840	Standard	NM_014226		Approved	RAGE1, STK30	uc001ylm.4	Q9UQ07	OTTHUMG00000164896	ENST00000361847.2:c.689A>G	14.37:g.102700028T>C	ENSP00000355304:p.Lys230Arg	216.0	0.0	0		225.0	113.0	0.502222	NM_014226	B2R6Z4|B7Z7P6|E7ER76|E7ERR8|Q92790|Q93067	Missense_Mutation	SNP	ENST00000361847.2	37	CCDS9971.1	99	0.04532967032967033	92	0.18699186991869918	5	0.013812154696132596	0	0.0	2	0.002638522427440633	.	14.82	2.649258	0.47362	0.156378	0.001977	ENSG00000080823	ENST00000522874;ENST00000361847;ENST00000524214	T;T;T	0.64803	-0.12;-0.12;-0.12	5.2	5.2	0.72013	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.054522	0.64402	D	0.000001	T	0.00073	0.0002	N	0.11313	0.125	0.09310	P	1.0	B;B	0.21225	0.021;0.053	B;B	0.26517	0.044;0.07	T	0.04752	-1.0929	9	0.46703	T	0.11	-1.1389	15.0926	0.72207	0.0:0.0:0.0:1.0	rs34965156	200;230	E7ERR8;Q9UQ07	.;MOK_HUMAN	R	229;230;200	ENSP00000429469:K229R;ENSP00000355304:K230R;ENSP00000428942:K200R	ENSP00000355304:K230R	K	-	2	0	RAGE	101769781	1.000000	0.71417	0.985000	0.45067	0.870000	0.49936	4.211000	0.58507	1.978000	0.57642	0.482000	0.46254	AAA	T|0.940;C|0.060	0.060	strong		0.532	MOK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380848.3		
FHL2	2274	hgsc.bcm.edu	37	2	106002854	106002854	+	Silent	SNP	G	G	A	rs11537578	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:106002854G>A	ENST00000409807.1	-	2	454	c.120C>T	c.(118-120)tgC>tgT	p.C40C	FHL2_ENST00000408995.1_Silent_p.C40C|FHL2_ENST00000344213.4_Silent_p.C150C|FHL2_ENST00000358129.4_Silent_p.C40C|FHL2_ENST00000336660.5_Silent_p.C40C|FHL2_ENST00000393353.3_Silent_p.C40C|FHL2_ENST00000322142.8_Silent_p.C40C|FHL2_ENST00000393352.3_Silent_p.C40C|FHL2_ENST00000607522.1_Silent_p.C40C|FHL2_ENST00000409177.1_Silent_p.C156C			Q14192	FHL2_HUMAN	four and a half LIM domains 2	40	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				androgen receptor signaling pathway (GO:0030521)|atrial cardiac muscle cell development (GO:0055014)|cellular lipid metabolic process (GO:0044255)|heart trabecula formation (GO:0060347)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast differentiation (GO:0001649)|positive regulation of transcription, DNA-templated (GO:0045893)|response to hormone (GO:0009725)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|ventricular cardiac muscle cell development (GO:0055015)	actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|M band (GO:0031430)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Z disc (GO:0030018)	androgen receptor binding (GO:0050681)|identical protein binding (GO:0042802)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	9						CACACTCCTCGCAGGTGTTGG	0.607													G|||	58	0.0115815	0.0416	0.0043	5008	,	,		16948	0.0		0.0	False		,,,				2504	0.0				p.C40C		Atlas-SNP	.											.	FHL2	18	.	0			c.C120T						PASS	.	G	,,,	166,4240	111.2+/-149.4	4,158,2041	71.0	66.0	68.0		120,120,120,120	-5.8	0.6	2	dbSNP_120	68	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FHL2	NM_001039492.2,NM_001450.3,NM_201555.1,NM_201557.3	,,,	4,159,6340	AA,AG,GG		0.0116,3.7676,1.284	,,,	40/280,40/280,40/280,40/280	106002854	167,12839	2203	4300	6503	SO:0001819	synonymous_variant	2274	exon3			CTCCTCGCAGGTG		CCDS2070.1	2q12.2	2014-09-17			ENSG00000115641	ENSG00000115641			3703	protein-coding gene	gene with protein product		602633				8753811	Standard	NM_201557		Approved	SLIM3, DRAL	uc002tcy.3	Q14192	OTTHUMG00000153120	ENST00000409807.1:c.120C>T	2.37:g.106002854G>A		116.0	0.0	0		138.0	72.0	0.521739	NM_001039492	Q13229|Q13644|Q2I5I4|Q5TM15|Q9P294	Silent	SNP	ENST00000409807.1	37	CCDS2070.1																																																																																			G|0.989;A|0.011	0.011	strong		0.607	FHL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329654.1		
AK8	158067	hgsc.bcm.edu	37	9	135601126	135601126	+	Silent	SNP	G	G	A	rs28477720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:135601126G>A	ENST00000298545.3	-	13	1910	c.1389C>T	c.(1387-1389)ttC>ttT	p.F463F	AK8_ENST00000477396.1_5'UTR	NM_152572.2	NP_689785.1	Q96MA6	KAD8_HUMAN	adenylate kinase 8	463	Adenylate kinase 2.				nucleoside diphosphate phosphorylation (GO:0006165)|nucleoside triphosphate biosynthetic process (GO:0009142)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)	adenylate kinase activity (GO:0004017)|ATP binding (GO:0005524)|cytidylate kinase activity (GO:0004127)|nucleoside diphosphate kinase activity (GO:0004550)			NS(1)|kidney(2)|large_intestine(4)|lung(11)|pancreas(2)|prostate(1)|urinary_tract(2)	23						CGATGTATTCGAAGACTGTGT	0.532													G|||	151	0.0301518	0.1089	0.0086	5008	,	,		18753	0.0		0.001	False		,,,				2504	0.0				p.F463F		Atlas-SNP	.											.	AK8	45	.	0			c.C1389T						PASS	.	G		452,3954		24,404,1775	80.0	61.0	67.0		1389	-1.5	0.8	9	dbSNP_125	67	3,8597		0,3,4297	no	coding-synonymous	AK8	NM_152572.2		24,407,6072	AA,AG,GG		0.0349,10.2587,3.4984		463/480	135601126	455,12551	2203	4300	6503	SO:0001819	synonymous_variant	158067	exon13			GTATTCGAAGACT	AK093446	CCDS6954.1	9q34.13	2013-04-29	2010-12-07	2010-12-07	ENSG00000165695	ENSG00000165695	2.7.4.3	"""Adenylate kinases"""	26526	protein-coding gene	gene with protein product		615365	"""chromosome 9 open reading frame 98"""	C9orf98		21080915	Standard	NM_152572		Approved	FLJ32704	uc004cbu.1	Q96MA6	OTTHUMG00000021009	ENST00000298545.3:c.1389C>T	9.37:g.135601126G>A		127.0	0.0	0		117.0	89.0	0.760684	NM_152572	A8K821|Q8N9W9	Silent	SNP	ENST00000298545.3	37	CCDS6954.1																																																																																			G|0.966;A|0.034	0.034	strong		0.532	AK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055413.1	NM_152572	
ARNTL2	56938	hgsc.bcm.edu	37	12	27543141	27543141	+	Missense_Mutation	SNP	G	G	C	rs74988383	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:27543141G>C	ENST00000266503.5	+	9	906	c.888G>C	c.(886-888)gaG>gaC	p.E296D	ARNTL2_ENST00000542388.1_Missense_Mutation_p.E211D|ARNTL2_ENST00000544915.1_Missense_Mutation_p.E262D|ARNTL2_ENST00000311001.5_Missense_Mutation_p.E282D|RP11-165P7.1_ENST00000500498.2_RNA|ARNTL2_ENST00000546179.1_Missense_Mutation_p.E259D|ARNTL2_ENST00000261178.5_Missense_Mutation_p.E248D|ARNTL2_ENST00000395901.2_Missense_Mutation_p.E259D			Q8WYA1	BMAL2_HUMAN	aryl hydrocarbon receptor nuclear translocator-like 2	296					circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|positive regulation of circadian rhythm (GO:0042753)|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)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	E-box binding (GO:0070888)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(1)|skin(2)|urinary_tract(1)	21	Colorectal(261;0.0847)|Lung SC(9;0.184)					TCAAAGAAGAGCATGGATGCT	0.373													G|||	31	0.0061901	0.0227	0.0014	5008	,	,		17221	0.0		0.0	False		,,,				2504	0.0				p.E296D		Atlas-SNP	.											.	ARNTL2	54	.	0			c.G888C						PASS	.	G	ASP/GLU	136,4270	97.1+/-135.8	1,134,2068	94.0	92.0	92.0		888	-2.6	0.3	12	dbSNP_132	92	3,8597	3.0+/-9.4	0,3,4297	yes	missense	ARNTL2	NM_020183.3	45	1,137,6365	CC,CG,GG		0.0349,3.0867,1.0687	benign	296/637	27543141	139,12867	2203	4300	6503	SO:0001583	missense	56938	exon9			AGAAGAGCATGGA	AF246961	CCDS8712.1, CCDS58219.1, CCDS58220.1, CCDS58221.1, CCDS58222.1	12p12.2-p11.2	2013-05-21			ENSG00000029153	ENSG00000029153		"""Basic helix-loop-helix proteins"""	18984	protein-coding gene	gene with protein product		614517				10864977, 10964693	Standard	NM_020183		Approved	BMAL2, MOP9, CLIF, PASD9, bHLHe6	uc001rht.2	Q8WYA1	OTTHUMG00000169257	ENST00000266503.5:c.888G>C	12.37:g.27543141G>C	ENSP00000266503:p.Glu296Asp	100.0	0.0	0		83.0	43.0	0.518072	NM_020183	B7Z429|F5H402|Q8WYA2|Q8WYA3|Q8WYA4|Q96J63|Q9H2M4|Q9NS70|Q9NYQ4|Q9NYQ5	Missense_Mutation	SNP	ENST00000266503.5	37	CCDS8712.1	13|13	0.005952380952380952|0.005952380952380952	13|13	0.026422764227642278|0.026422764227642278	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	17.22|17.22	3.334286|3.334286	0.60853|0.60853	0.030867|0.030867	3.49E-4|3.49E-4	ENSG00000029153|ENSG00000029153	ENST00000544915;ENST00000395901;ENST00000546179;ENST00000311001;ENST00000261178;ENST00000266503;ENST00000542388|ENST00000457040	T;T;T;T;T;T;T|.	0.08720|.	3.16;3.17;3.06;3.16;3.18;3.16;3.19|.	3.71|3.71	-2.58|-2.58	0.06228|0.06228	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.37571|0.37571	0.1008|0.1008	M|M	0.70903|0.70903	2.155|2.155	0.38371|0.38371	D|D	0.944876|0.944876	P;D;P;P;B;B|.	0.53151|.	0.907;0.958;0.907;0.907;0.161;0.09|.	P;P;P;P;B;B|.	0.60345|.	0.686;0.873;0.801;0.686;0.137;0.103|.	T|T	0.58601|0.58601	-0.7608|-0.7608	10|5	0.56958|.	D|.	0.05|.	.|.	10.3192|10.3192	0.43756|0.43756	0.6174:0.0:0.3826:0.0|0.6174:0.0:0.3826:0.0	.|.	259;262;259;248;282;296|.	F5H402;Q8WYA1-5;Q8WYA1-3;Q8WYA1-4;Q8WYA1-2;Q8WYA1|.	.;.;.;.;.;BMAL2_HUMAN|.	D|T	262;259;259;282;248;296;211|248	ENSP00000442438:E262D;ENSP00000379238:E259D;ENSP00000438545:E259D;ENSP00000312247:E282D;ENSP00000261178:E248D;ENSP00000266503:E296D;ENSP00000445836:E211D|.	ENSP00000261178:E248D|.	E|S	+|+	3|2	2|0	ARNTL2|ARNTL2	27434408|27434408	0.865000|0.865000	0.29922|0.29922	0.275000|0.275000	0.24674|0.24674	0.946000|0.946000	0.59487|0.59487	-0.103000|-0.103000	0.10940|0.10940	-0.470000|-0.470000	0.06901|0.06901	0.655000|0.655000	0.94253|0.94253	GAG|AGC	G|0.991;C|0.009	0.009	strong		0.373	ARNTL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403162.1	NM_020183	
MIP	4284	hgsc.bcm.edu	37	12	56847384	56847384	+	Silent	SNP	G	G	A	rs36032520	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56847384G>A	ENST00000257979.4	-	2	544	c.516C>T	c.(514-516)caC>caT	p.H172H	MIP_ENST00000555551.1_5'UTR	NM_012064.3	NP_036196.1	P30301	MIP_HUMAN	major intrinsic protein of lens fiber	172					canalicular bile acid transport (GO:0015722)|lens development in camera-type eye (GO:0002088)|response to stimulus (GO:0050896)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)|water transport (GO:0006833)	gap junction (GO:0005921)|integral component of plasma membrane (GO:0005887)|intracellular canaliculus (GO:0046691)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|structural constituent of eye lens (GO:0005212)|transporter activity (GO:0005215)|water channel activity (GO:0015250)			kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(3)|urinary_tract(1)	16						CCCCAAAGAGGTGCCCCAGGG	0.562													G|||	9	0.00179712	0.0068	0.0	5008	,	,		20604	0.0		0.0	False		,,,				2504	0.0				p.H172H		Atlas-SNP	.											.	MIP	39	.	0			c.C516T						PASS	.	G		39,4367	43.8+/-77.6	0,39,2164	57.0	53.0	54.0		516	3.0	1.0	12	dbSNP_126	54	0,8600		0,0,4300	no	coding-synonymous	MIP	NM_012064.3		0,39,6464	AA,AG,GG		0.0,0.8852,0.2999		172/264	56847384	39,12967	2203	4300	6503	SO:0001819	synonymous_variant	4284	exon2			AAAGAGGTGCCCC		CCDS8919.1	12q13	2012-10-02				ENSG00000135517		"""Ion channels / Aquaporins"""	7103	protein-coding gene	gene with protein product	aquaporin 0	154050				1840563, 7536742	Standard	NM_012064		Approved	MP26, LIM1, AQP0	uc001slh.3	P30301		ENST00000257979.4:c.516C>T	12.37:g.56847384G>A		85.0	0.0	0		84.0	40.0	0.47619	NM_012064	Q17R41	Silent	SNP	ENST00000257979.4	37	CCDS8919.1																																																																																			G|0.998;A|0.002	0.002	strong		0.562	MIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409620.1	NM_012064	
CAPZA1	829	hgsc.bcm.edu	37	1	113202386	113202386	+	Silent	SNP	C	C	T	rs12074157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:113202386C>T	ENST00000263168.3	+	7	1242	c.570C>T	c.(568-570)ggC>ggT	p.G190G	CAPZA1_ENST00000476936.1_3'UTR	NM_006135.2	NP_006126.1	P52907	CAZA1_HUMAN	capping protein (actin filament) muscle Z-line, alpha 1	190					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|blood coagulation (GO:0007596)|cellular component movement (GO:0006928)|innate immune response (GO:0045087)|protein complex assembly (GO:0006461)	actin cytoskeleton (GO:0015629)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|F-actin capping protein complex (GO:0008290)|WASH complex (GO:0071203)	actin binding (GO:0003779)			breast(1)|kidney(2)|large_intestine(2)|lung(3)|prostate(1)	9	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		AGGTGGTTGGCGTGCTTAAGA	0.403													c|||	179	0.0357428	0.1301	0.0101	5008	,	,		16515	0.0		0.0	False		,,,				2504	0.0				p.G190G		Atlas-SNP	.											CAPZA1,colon,carcinoma,0,1	CAPZA1	16	1	0			c.C570T						PASS	.	C		459,3947	217.1+/-235.6	24,411,1768	94.0	89.0	91.0		570	4.4	1.0	1	dbSNP_120	91	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	CAPZA1	NM_006135.2		24,414,6065	TT,TC,CC		0.0349,10.4176,3.5522		190/287	113202386	462,12544	2203	4300	6503	SO:0001819	synonymous_variant	829	exon7			GGTTGGCGTGCTT	U56637	CCDS30805.1	1p13.2	2014-05-09			ENSG00000116489	ENSG00000116489			1488	protein-coding gene	gene with protein product		601580				7665558, 9119363	Standard	NM_006135		Approved		uc001ecj.1	P52907	OTTHUMG00000011769	ENST00000263168.3:c.570C>T	1.37:g.113202386C>T		77.0	0.0	0		86.0	35.0	0.406977	NM_006135	Q53FQ6|Q6FHD5	Silent	SNP	ENST00000263168.3	37	CCDS30805.1																																																																																			C|0.968;T|0.032	0.032	strong		0.403	CAPZA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032567.2	NM_006135	
WWOX	51741	hgsc.bcm.edu	37	16	78458807	78458807	+	Missense_Mutation	SNP	C	C	G	rs7201683	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:78458807C>G	ENST00000566780.1	+	7	1012	c.646C>G	c.(646-648)Cta>Gta	p.L216V	WWOX_ENST00000539474.2_Intron|WWOX_ENST00000402655.2_Intron|WWOX_ENST00000408984.3_Missense_Mutation_p.L216V|WWOX_ENST00000406884.2_Intron	NM_016373.2	NP_057457.1	Q9NZC7	WWOX_HUMAN	WW domain containing oxidoreductase	216	Interaction with MAPT. {ECO:0000250}.|Mediates targeting to the mitochondria. {ECO:0000250}.		L -> V (in dbSNP:rs7201683).		cellular response to transforming growth factor beta stimulus (GO:0071560)|extrinsic apoptotic signaling pathway (GO:0097191)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of Wnt signaling pathway (GO:0030178)|osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal system morphogenesis (GO:0048705)|steroid metabolic process (GO:0008202)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	coenzyme binding (GO:0050662)|cofactor binding (GO:0048037)|enzyme binding (GO:0019899)|oxidoreductase activity (GO:0016491)|protein dimerization activity (GO:0046983)			large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)	7		all_cancers(2;1.97e-181)|all_epithelial(2;3.85e-160)|all_lung(2;2.03e-39)|Lung NSC(2;7.16e-35)|Colorectal(2;6.96e-21)|all_hematologic(2;1.13e-16)|Melanoma(2;5.16e-06)|all_neural(2;8.84e-06)|Renal(2;5.26e-05)|Medulloblastoma(2;0.00498)|Breast(2;0.00631)|Lung SC(2;0.0261)|Prostate(104;0.167)		UCEC - Uterine corpus endometrioid carcinoma (2;0.012)|Epithelial(1;2.65e-39)|all cancers(1;3.26e-34)|STAD - Stomach adenocarcinoma(1;5.1e-20)|COAD - Colon adenocarcinoma(1;1.04e-11)|Colorectal(1;3.4e-11)|OV - Ovarian serous cystadenocarcinoma(1;1.01e-10)|BRCA - Breast invasive adenocarcinoma(1;0.00196)|Kidney(780;0.232)		AACTTTTGCTCTACCCTGGAG	0.468													C|||	197	0.0393371	0.1218	0.0202	5008	,	,		19087	0.0		0.0089	False		,,,				2504	0.0133				p.L216V		Atlas-SNP	.											.	WWOX	98	.	0			c.C646G						PASS	.	C	VAL/LEU	370,3528		15,340,1594	281.0	282.0	282.0		646	1.1	0.0	16	dbSNP_116	282	102,8180		1,100,4040	yes	missense	WWOX	NM_016373.2	32	16,440,5634	GG,GC,CC		1.2316,9.492,3.8752	possibly-damaging	216/415	78458807	472,11708	1949	4141	6090	SO:0001583	missense	51741	exon7			TTTGCTCTACCCT	AF187015	CCDS42196.1, CCDS42197.1	16q23.3-q24.1	2012-08-15	2002-01-14		ENSG00000186153	ENSG00000186153	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	12799	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 41C, member 1"""	605131	"""WW domain-containing oxidoreductase"""			10786676, 10861292, 19027726	Standard	XR_243411		Approved	FOR, WOX1, SDR41C1	uc002ffk.3	Q9NZC7	OTTHUMG00000176851	ENST00000566780.1:c.646C>G	16.37:g.78458807C>G	ENSP00000457230:p.Leu216Val	176.0	0.0	0		196.0	100.0	0.510204	NM_016373	A8K323|Q5MYT5|Q96KM3|Q96RF2|Q9BTT8|Q9NPC9|Q9NRF4|Q9NRF5|Q9NRF6|Q9NRK1|Q9NZC5	Missense_Mutation	SNP	ENST00000566780.1	37	CCDS42196.1	79	0.036172161172161175	64	0.13008130081300814	9	0.024861878453038673	0	0.0	6	0.0079155672823219	C	0.015	-1.539831	0.00934	0.09492	0.012316	ENSG00000186153	ENST00000408984;ENST00000299644	T	0.21191	2.02	5.66	1.14	0.20703	NAD(P)-binding domain (1);	0.170005	0.43416	D	0.000569	T	0.00109	0.0003	N	0.16016	0.355	0.80722	P	0.0	B	0.14805	0.011	B	0.22601	0.04	T	0.23691	-1.0181	9	0.40728	T	0.16	.	8.0658	0.30659	0.0:0.5003:0.1647:0.335	rs7201683;rs52793545;rs7201683	216	Q9NZC7	WWOX_HUMAN	V	216;59	ENSP00000386161:L216V	ENSP00000299644:L59V	L	+	1	2	WWOX	77016308	0.006000	0.16342	0.043000	0.18650	0.121000	0.20230	0.216000	0.17585	-0.215000	0.10063	-0.797000	0.03246	CTA	C|0.956;G|0.044	0.044	strong		0.468	WWOX-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434328.1		
CD109	135228	hgsc.bcm.edu	37	6	74524757	74524757	+	Silent	SNP	T	T	G	rs58562849	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:74524757T>G	ENST00000287097.5	+	30	3934	c.3822T>G	c.(3820-3822)tcT>tcG	p.S1274S	CD109_ENST00000422508.2_Silent_p.S1197S|CD109_ENST00000437994.2_Silent_p.S1257S			Q6YHK3	CD109_HUMAN	CD109 molecule	1274					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GACGAAGATCTATCCAAAATC	0.328													T|||	132	0.0263578	0.0953	0.0086	5008	,	,		14879	0.0		0.0	False		,,,				2504	0.0				p.S1274S		Atlas-SNP	.											.	CD109	170	.	0			c.T3822G						PASS	.	T	,,	323,4083	172.3+/-202.3	13,297,1893	99.0	101.0	100.0		3771,3591,3822	-5.2	0.0	6	dbSNP_129	100	5,8591	4.3+/-15.6	0,5,4293	no	coding-synonymous,coding-synonymous,coding-synonymous	CD109	NM_001159587.1,NM_001159588.1,NM_133493.3	,,	13,302,6186	GG,GT,TT		0.0582,7.3309,2.5227	,,	1257/1429,1197/1369,1274/1446	74524757	328,12674	2203	4298	6501	SO:0001819	synonymous_variant	135228	exon30			AAGATCTATCCAA	AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"""CD molecules"""	21685	protein-coding gene	gene with protein product		608859	"""CD109 antigen (Gov platelet alloantigens)"""			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.3822T>G	6.37:g.74524757T>G		73.0	0.0	0		56.0	33.0	0.589286	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Silent	SNP	ENST00000287097.5	37	CCDS4982.1																																																																																			T|0.971;G|0.029	0.029	strong		0.328	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493	
FHOD1	29109	hgsc.bcm.edu	37	16	67266065	67266065	+	Silent	SNP	T	T	C	rs34888644	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67266065T>C	ENST00000258201.4	-	14	2326	c.2079A>G	c.(2077-2079)acA>acG	p.T693T		NM_013241.2	NP_037373.2	Q9Y613	FHOD1_HUMAN	formin homology 2 domain containing 1	693	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.|Interaction with ROCK1.				positive regulation of stress fiber assembly (GO:0051496)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			breast(4)|endometrium(3)|kidney(3)|large_intestine(5)|lung(7)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	34		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)		GGTCCAGCACTGTGGTCATTG	0.582													T|||	375	0.0748802	0.2201	0.013	5008	,	,		18790	0.003		0.003	False		,,,				2504	0.0706				p.T693T		Atlas-SNP	.											.	FHOD1	86	.	0			c.A2079G						PASS	.	T		797,3599	319.1+/-295.9	76,645,1477	147.0	122.0	131.0		2079	-0.9	1.0	16	dbSNP_126	131	8,8592	3.7+/-12.6	0,8,4292	no	coding-synonymous	FHOD1	NM_013241.2		76,653,5769	CC,CT,TT		0.093,18.1301,6.1942		693/1165	67266065	805,12191	2198	4300	6498	SO:0001819	synonymous_variant	29109	exon14			CAGCACTGTGGTC	AF113615	CCDS10834.1	16q22	2008-02-22			ENSG00000135723	ENSG00000135723			17905	protein-coding gene	gene with protein product		606881				10352228, 16112087	Standard	NM_013241		Approved	FHOS	uc002esl.3	Q9Y613	OTTHUMG00000137521	ENST00000258201.4:c.2079A>G	16.37:g.67266065T>C		418.0	1.0	0.00239234		452.0	223.0	0.493363	NM_013241	Q59F76|Q6Y1F2|Q76MS8|Q8N521	Silent	SNP	ENST00000258201.4	37	CCDS10834.1																																																																																			T|0.919;C|0.081	0.081	strong		0.582	FHOD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268844.2		
RHBDD1	84236	hgsc.bcm.edu	37	2	227860232	227860232	+	Silent	SNP	C	C	T	rs61745917	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:227860232C>T	ENST00000341329.3	+	7	1184	c.942C>T	c.(940-942)agC>agT	p.S314S	RHBDD1_ENST00000392062.2_Silent_p.S314S|RHBDD1_ENST00000493526.1_3'UTR	NM_032276.3	NP_115652.2	Q8TEB9	RHBL4_HUMAN	rhomboid domain containing 1	314	VCP/p97-interacting motif (VIM). {ECO:0000250}.				apoptotic process (GO:0006915)|cellular response to unfolded protein (GO:0034620)|cellular response to UV (GO:0034644)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|membrane protein intracellular domain proteolysis (GO:0031293)|membrane protein proteolysis (GO:0033619)|negative regulation of apoptotic process (GO:0043066)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein processing (GO:0010954)|positive regulation of secretion (GO:0051047)|post-translational protein modification (GO:0043687)|spermatid differentiation (GO:0048515)	endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum quality control compartment (GO:0044322)|integral component of endoplasmic reticulum membrane (GO:0030176)|mitochondrion (GO:0005739)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)			breast(1)|large_intestine(5)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19		Renal(207;0.023)|all_lung(227;0.13)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;1.47e-11)|all cancers(144;1.52e-08)|Lung(261;0.0128)|LUSC - Lung squamous cell carcinoma(224;0.0175)		GATTCGATAGCCAGTGAGGTG	0.448													C|||	29	0.00579073	0.0212	0.0014	5008	,	,		18839	0.0		0.0	False		,,,				2504	0.0				p.S314S		Atlas-SNP	.											.	RHBDD1	34	.	0			c.C942T						PASS	.	C	,	58,4348	57.4+/-93.9	0,58,2145	67.0	61.0	63.0		942,942	2.4	0.8	2	dbSNP_129	63	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	RHBDD1	NM_001167608.1,NM_032276.3	,	0,58,6445	TT,TC,CC		0.0,1.3164,0.4459	,	314/316,314/316	227860232	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	84236	exon9			CGATAGCCAGTGA	AK074258	CCDS2464.1	2q36.3	2012-07-09			ENSG00000144468	ENSG00000144468			23081	protein-coding gene	gene with protein product						12838346	Standard	NM_032276		Approved	DKFZp547E052	uc002voi.3	Q8TEB9	OTTHUMG00000133178	ENST00000341329.3:c.942C>T	2.37:g.227860232C>T		179.0	0.0	0		188.0	95.0	0.505319	NM_001167608	Q495B9|Q53S43|Q5EBM8|Q6P5V8|Q8IV60|Q9H057	Silent	SNP	ENST00000341329.3	37	CCDS2464.1																																																																																			C|0.996;T|0.004	0.004	strong		0.448	RHBDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256885.2		
C1orf112	55732	hgsc.bcm.edu	37	1	169796197	169796197	+	Missense_Mutation	SNP	T	T	C	rs142988055	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:169796197T>C	ENST00000286031.6	+	11	1554	c.854T>C	c.(853-855)tTt>tCt	p.F285S	C1orf112_ENST00000413811.2_Missense_Mutation_p.F256S|C1orf112_ENST00000498289.1_3'UTR|C1orf112_ENST00000359326.4_Missense_Mutation_p.F285S	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	285										breast(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(8)|lung(9)|ovary(1)|skin(1)|stomach(1)	34	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)					CCCAGCAAGTTTCCTCCAAGC	0.388													T|||	89	0.0177716	0.0658	0.0029	5008	,	,		14059	0.0		0.0	False		,,,				2504	0.0				p.F285S		Atlas-SNP	.											.	C1orf112	74	.	0			c.T854C						PASS	.	T	SER/PHE	258,4148	144.2+/-179.2	8,242,1953	87.0	87.0	87.0		854	5.0	1.0	1	dbSNP_134	87	0,8600		0,0,4300	yes	missense	C1orf112	NM_018186.2	155	8,242,6253	CC,CT,TT		0.0,5.8557,1.9837	probably-damaging	285/854	169796197	258,12748	2203	4300	6503	SO:0001583	missense	55732	exon11			GCAAGTTTCCTCC	AL354614	CCDS1285.1	1q24.2	2012-06-26			ENSG00000000460	ENSG00000000460			25565	protein-coding gene	gene with protein product						12477932	Standard	NM_018186		Approved	FLJ10706	uc001ggq.3	Q9NSG2	OTTHUMG00000035821	ENST00000286031.6:c.854T>C	1.37:g.169796197T>C	ENSP00000286031:p.Phe285Ser	242.0	0.0	0		242.0	125.0	0.516529	NM_018186	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Missense_Mutation	SNP	ENST00000286031.6	37	CCDS1285.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	T	18.57	3.652833	0.67472	0.058557	0.0	ENSG00000000460	ENST00000413811;ENST00000359326;ENST00000286031	T;T;T	0.58210	0.35;0.35;0.35	5.04	5.04	0.67666	.	0.088478	0.85682	D	0.000000	T	0.64034	0.2562	M	0.78637	2.42	0.46011	D	0.998815	D;P;D	0.61080	0.979;0.91;0.989	P;P;D	0.66084	0.776;0.821;0.941	T	0.70317	-0.4905	10	0.72032	D	0.01	-12.7977	13.0228	0.58799	0.0:0.0:0.0:1.0	.	256;227;285	B4E0A9;B4DGF2;Q9NSG2	.;.;CA112_HUMAN	S	256;285;285	ENSP00000389257:F256S;ENSP00000352276:F285S;ENSP00000286031:F285S	ENSP00000286031:F285S	F	+	2	0	C1orf112	168062821	1.000000	0.71417	1.000000	0.80357	0.897000	0.52465	3.338000	0.52128	2.002000	0.58637	0.528000	0.53228	TTT	T|0.984;C|0.016	0.016	strong		0.388	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186	
BCAR1	9564	hgsc.bcm.edu	37	16	75269730	75269730	+	Missense_Mutation	SNP	G	G	A	rs61729593	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:75269730G>A	ENST00000162330.5	-	5	1193	c.1067C>T	c.(1066-1068)cCg>cTg	p.P356L	BCAR1_ENST00000535626.2_Missense_Mutation_p.P208L|BCAR1_ENST00000566982.1_5'UTR|BCAR1_ENST00000420641.3_Missense_Mutation_p.P374L|BCAR1_ENST00000538440.2_Missense_Mutation_p.P356L|BCAR1_ENST00000393422.2_Missense_Mutation_p.P374L|BCAR1_ENST00000393420.6_Missense_Mutation_p.P374L|BCAR1_ENST00000418647.3_Missense_Mutation_p.P402L|BCAR1_ENST00000546196.1_Missense_Mutation_p.P327L|BCAR1_ENST00000542031.2_Missense_Mutation_p.P354L	NM_001170717.1|NM_014567.3	NP_001164188.1|NP_055382.2	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	356	Substrate for kinases. {ECO:0000250}.				actin filament organization (GO:0007015)|antigen receptor-mediated signaling pathway (GO:0050851)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell division (GO:0051301)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epidermal growth factor receptor signaling pathway (GO:0007173)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell migration (GO:0010595)|regulation of apoptotic process (GO:0042981)|regulation of cell growth (GO:0001558)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(5)|endometrium(1)|kidney(6)|large_intestine(1)|liver(1)|lung(13)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)	35				BRCA - Breast invasive adenocarcinoma(221;0.169)		CTCGGCCGGCGGGGAGTCTGG	0.716													G|||	36	0.0071885	0.0257	0.0029	5008	,	,		14012	0.0		0.0	False		,,,				2504	0.0				p.P402L		Atlas-SNP	.											.	BCAR1	184	.	0			c.C1205T						PASS	.	G	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	38,4262		0,38,2112	7.0	8.0	8.0		1205,1121,1121,1121,1067,1061,623,437,1067	3.3	0.3	16	dbSNP_129	8	2,8398		0,2,4198	no	missense,missense,missense,missense,missense,missense,missense,missense,missense	BCAR1	NM_001170714.1,NM_001170715.1,NM_001170716.1,NM_001170717.1,NM_001170718.1,NM_001170719.1,NM_001170720.1,NM_001170721.1,NM_014567.3	98,98,98,98,98,98,98,98,98	0,40,6310	AA,AG,GG		0.0238,0.8837,0.315	benign,benign,benign,benign,benign,benign,benign,benign,benign	402/917,374/889,374/889,374/889,356/871,354/869,208/723,146/661,356/871	75269730	40,12660	2150	4200	6350	SO:0001583	missense	9564	exon6			GCCGGCGGGGAGT	AJ242987	CCDS10915.1, CCDS54037.1, CCDS54038.1, CCDS54039.1, CCDS54040.1, CCDS54041.1, CCDS54042.1, CCDS54043.1	16q22-q23	2011-04-13			ENSG00000050820	ENSG00000050820		"""Cas scaffolding proteins"""	971	protein-coding gene	gene with protein product	"""Crk-associated substrate"", ""Cas scaffolding protein family member 1"""	602941				8413311, 10639512	Standard	NM_001170714		Approved	P130Cas, Crkas, CAS, CASS1	uc010vnb.2	P56945	OTTHUMG00000137604	ENST00000162330.5:c.1067C>T	16.37:g.75269730G>A	ENSP00000162330:p.Pro356Leu	22.0	0.0	0		33.0	15.0	0.454545	NM_001170714	B3KWD7|B4DEV4|B4DGB5|B4DIW5|B7Z7X7|E9PCL5|E9PCV2|F5GXA2|F5GXV6|F5H7Z0|F8WA69|Q6QEF7	Missense_Mutation	SNP	ENST00000162330.5	37	CCDS10915.1	19	0.0086996336996337	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	G	8.927	0.962569	0.18583	0.008837	2.38E-4	ENSG00000050820	ENST00000162330;ENST00000393422;ENST00000420641;ENST00000538440;ENST00000418647;ENST00000535626;ENST00000393420;ENST00000542031;ENST00000546196	T;T;T;T;T;T;T;T;T	0.41065	1.12;1.66;1.47;1.23;1.4;1.01;1.3;1.13;2.9	4.29	3.29	0.37713	.	0.858926	0.10058	N	0.721285	T	0.14399	0.0348	L	0.47716	1.5	0.29586	N	0.848804	B;B;B;B;B;B;B;B;B	0.10296	0.001;0.003;0.002;0.001;0.002;0.0;0.0;0.001;0.0	B;B;B;B;B;B;B;B;B	0.09377	0.0;0.004;0.001;0.002;0.001;0.0;0.002;0.001;0.001	T	0.18555	-1.0333	10	0.21014	T	0.42	-13.6226	9.512	0.39082	0.113:0.0:0.887:0.0	.	374;208;402;354;374;374;356;356;146	B4DIW5;F5GXV6;E9PCL5;F5GXA2;F8WA69;E9PCV2;F5H7Z0;P56945;B3KWE2	.;.;.;.;.;.;.;BCAR1_HUMAN;.	L	356;374;374;356;402;208;374;354;327	ENSP00000162330:P356L;ENSP00000377074:P374L;ENSP00000392708:P374L;ENSP00000443841:P356L;ENSP00000391669:P402L;ENSP00000440370:P208L;ENSP00000377072:P374L;ENSP00000440415:P354L;ENSP00000442161:P327L	ENSP00000162330:P356L	P	-	2	0	BCAR1	73827231	0.006000	0.16342	0.262000	0.24481	0.052000	0.14988	1.241000	0.32743	0.871000	0.35750	0.558000	0.71614	CCG	G|0.991;A|0.009	0.009	strong		0.716	BCAR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269017.1	NM_014567	
OR10H4	126541	hgsc.bcm.edu	37	19	16060453	16060453	+	Silent	SNP	T	T	C	rs115548355	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16060453T>C	ENST00000322107.1	+	1	636	c.636T>C	c.(634-636)tgT>tgC	p.C212C		NM_001004465.1	NP_001004465.1	Q8NGA5	O10H4_HUMAN	olfactory receptor, family 10, subfamily H, member 4	212						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	17						TGATAGGCTGTTTATTCCTCA	0.488													.|||	43	0.00858626	0.0318	0.0014	5008	,	,		23791	0.0		0.0	False		,,,				2504	0.0				p.C212C		Atlas-SNP	.											.	OR10H4	48	.	0			c.T636C						PASS	.	T		200,4206	125.7+/-162.9	6,188,2009	295.0	266.0	276.0		636	-0.8	0.8	19	dbSNP_132	276	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	OR10H4	NM_001004465.1		6,189,6308	CC,CT,TT		0.0116,4.5393,1.5454		212/317	16060453	201,12805	2203	4300	6503	SO:0001819	synonymous_variant	126541	exon1			AGGCTGTTTATTC	AC011517	CCDS32941.1	19p13.12	2013-09-24			ENSG00000176231	ENSG00000176231		"""GPCR / Class A : Olfactory receptors"""	15388	protein-coding gene	gene with protein product							Standard	NM_001004465		Approved		uc010xov.2	Q8NGA5	OTTHUMG00000182268	ENST00000322107.1:c.636T>C	19.37:g.16060453T>C		389.0	1.0	0.00257069		390.0	196.0	0.502564	NM_001004465	Q6IFJ2|Q96R57	Silent	SNP	ENST00000322107.1	37	CCDS32941.1																																																																																			T|0.988;C|0.012	0.012	strong		0.488	OR10H4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460311.1		
ZNF254	9534	hgsc.bcm.edu	37	19	24310074	24310074	+	Silent	SNP	T	T	C	rs61737179	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:24310074T>C	ENST00000357002.4	+	4	1387	c.1272T>C	c.(1270-1272)caT>caC	p.H424H	ZNF254_ENST00000342944.6_Silent_p.H339H	NM_001278661.1|NM_001278662.1|NM_001278664.1|NM_001278677.1|NM_001278678.1|NM_203282.2	NP_001265590.1|NP_001265591.1|NP_001265593.1|NP_001265606.1|NP_001265607.1|NP_975011.3	O75437	ZN254_HUMAN	zinc finger protein 254	424					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)						all_cancers(12;0.086)|all_lung(12;0.00528)|Lung NSC(12;0.00731)|all_epithelial(12;0.0186)				TTACTACACATAAGATAATTC	0.338													T|||	119	0.023762	0.0862	0.0072	5008	,	,		21190	0.0		0.0	False		,,,				2504	0.0				p.H424H		Atlas-SNP	.											.	ZNF254	88	.	0			c.T1272C						PASS	.	T		243,4161	134.9+/-171.1	7,229,1966	37.0	40.0	39.0		1272	1.1	0.1	19	dbSNP_129	39	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ZNF254	NM_203282.2		7,230,6265	CC,CT,TT		0.0116,5.5177,1.8763		424/660	24310074	244,12760	2202	4300	6502	SO:0001819	synonymous_variant	9534	exon4			TACACATAAGATA	AF054180	CCDS32983.1, CCDS62622.1, CCDS62623.1, CCDS74323.1, CCDS74324.1	19p13	2013-01-08				ENSG00000213096		"""Zinc fingers, C2H2-type"", ""-"""	13047	protein-coding gene	gene with protein product		604768	"""zinc finger protein 539"""	ZNF91L, ZNF539		9653160	Standard	NM_001278661		Approved	HD-ZNF1, BMZF-5	uc002nru.3	O75437		ENST00000357002.4:c.1272T>C	19.37:g.24310074T>C		59.0	0.0	0		68.0	28.0	0.411765	NM_203282	A4QPC0|Q86XL7	Silent	SNP	ENST00000357002.4	37	CCDS32983.1																																																																																			T|0.979;C|0.021	0.021	strong		0.338	ZNF254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466453.1	NM_004876	
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324190	39324190	+	Missense_Mutation	SNP	A	A	G	rs377224840		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39324190A>G	ENST00000391356.2	-	1	234	c.235T>C	c.(235-237)Tgc>Cgc	p.C79R		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	79	29 X 5 AA repeats of C-C-[GIKRQVH]-[SPT]- [STA].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			ggcctgcagcaactggaaatg	0.612																																					p.C79R		Atlas-SNP	.											.	KRTAP4-3	40	.	0			c.T235C						PASS	.	A	ARG/CYS	147,2777		0,147,1315	3.0	5.0	4.0		235	4.6	1.0	17		4	1,6765		0,1,3382	no	missense	KRTAP4-3	NM_033187.1	180	0,148,4697	GG,GA,AA		0.0148,5.0274,1.5273	possibly-damaging	79/196	39324190	148,9542	1462	3383	4845	SO:0001583	missense	85290	exon1			TGCAGCAACTGGA	AJ406935	CCDS42331.1	17q21.2	2013-06-25			ENSG00000196156	ENSG00000196156		"""Keratin associated proteins"""	18908	protein-coding gene	gene with protein product							Standard	NM_033187		Approved	KAP4.3	uc010cxl.3	Q9BYR4	OTTHUMG00000133639	ENST00000391356.2:c.235T>C	17.37:g.39324190A>G	ENSP00000375151:p.Cys79Arg	392.0	1.0	0.00255102		166.0	73.0	0.439759	NM_033187		Missense_Mutation	SNP	ENST00000391356.2	37	CCDS42331.1	.	.	.	.	.	.	.	.	.	.	.	12.37	1.918720	0.33908	0.050274	1.48E-4	ENSG00000196156	ENST00000391356	T	0.03689	3.84	4.57	4.57	0.56435	.	0.000000	0.34362	U	0.004039	T	0.01523	0.0049	M	0.94142	3.5	0.48571	D	0.999674	P	0.38827	0.649	B	0.39185	0.293	T	0.00288	-1.1845	10	0.66056	D	0.02	.	7.092	0.25289	0.8963:0.0:0.1037:0.0	.	79	Q9BYR4	KRA43_HUMAN	R	79	ENSP00000375151:C79R	ENSP00000375151:C79R	C	-	1	0	KRTAP4-3	36577716	0.718000	0.27976	0.995000	0.50966	0.018000	0.09664	1.969000	0.40510	1.799000	0.52666	0.496000	0.49642	TGC	.	.	weak		0.612	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1		
VWDE	221806	hgsc.bcm.edu	37	7	12443312	12443312	+	Missense_Mutation	SNP	C	C	T	rs139879021	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:12443312C>T	ENST00000275358.3	-	1	219	c.31G>A	c.(31-33)Gcg>Acg	p.A11T		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	11						extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						AACATCAGCGCGATCACCAGC	0.721													C|||	33	0.00658946	0.0234	0.0029	5008	,	,		14305	0.0		0.0	False		,,,				2504	0.0				p.A11T		Atlas-SNP	.											.	VWDE	123	.	0			c.G31A						PASS	.	C	THR/ALA	33,1351		1,31,660	20.0	27.0	25.0		31	2.4	0.0	7	dbSNP_134	25	1,3181		0,1,1590	yes	missense	VWDE	NM_001135924.1	58	1,32,2250	TT,TC,CC		0.0314,2.3844,0.7446	benign	11/1591	12443312	34,4532	692	1591	2283	SO:0001583	missense	221806	exon1			TCAGCGCGATCAC		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.31G>A	7.37:g.12443312C>T	ENSP00000275358:p.Ala11Thr	14.0	0.0	0		28.0	14.0	0.5	NM_001135924	B7ZM77|Q96SQ3	Missense_Mutation	SNP	ENST00000275358.3	37	CCDS47544.1	9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	C	13.20	2.164755	0.38217	0.023844	3.14E-4	ENSG00000146530	ENST00000275358;ENST00000541006	D	0.82344	-1.6	3.28	2.38	0.29361	.	1.817110	0.02839	N	0.127729	T	0.58293	0.2112	L	0.36672	1.1	0.09310	N	1	P	0.43431	0.807	B	0.29663	0.105	T	0.61431	-0.7064	10	0.37606	T	0.19	.	7.8381	0.29382	0.2478:0.7522:0.0:0.0	.	11	Q8N2E2	VWDE_HUMAN	T	11	ENSP00000275358:A11T	ENSP00000275358:A11T	A	-	1	0	VWDE	12409837	0.001000	0.12720	0.005000	0.12908	0.107000	0.19398	0.623000	0.24447	0.953000	0.37825	0.491000	0.48974	GCG	C|0.996;T|0.004	0.004	strong		0.721	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
TNXB	7148	hgsc.bcm.edu	37	6	32046832	32046832	+	Silent	SNP	C	C	T	rs61998180	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:32046832C>T	ENST00000375244.3	-	11	4554	c.4353G>A	c.(4351-4353)ccG>ccA	p.P1451P	TNXB_ENST00000375247.2_Silent_p.P1451P|RNA5SP206_ENST00000516703.1_RNA			P22105	TENX_HUMAN	tenascin XB	1538					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)	p.P1538P(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CGGCGGACACCGGGCCCACGC	0.662													C|||	18	0.00359425	0.0129	0.0014	5008	,	,		15860	0.0		0.0	False		,,,				2504	0.0				p.P1451P		Atlas-SNP	.											TNXB_ENST00000375247,NS,carcinoma,0,1	TNXB	553	1	1	Substitution - coding silent(1)	breast(1)	c.G4353A						PASS	.	C		11,2573		0,11,1281	38.0	43.0	41.0		4353	-2.3	0.8	6	dbSNP_129	41	0,5136		0,0,2568	no	coding-synonymous	TNXB	NM_019105.6		0,11,3849	TT,TC,CC		0.0,0.4257,0.1425		1451/4243	32046832	11,7709	1292	2568	3860	SO:0001819	synonymous_variant	7148	exon11			GGACACCGGGCCC	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.4353G>A	6.37:g.32046832C>T		86.0	0.0	0		137.0	71.0	0.518248	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	37																																																																																				C|0.987;T|0.013	0.013	weak		0.662	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
INTS3	65123	hgsc.bcm.edu	37	1	153740285	153740285	+	Silent	SNP	G	G	A	rs61736048	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:153740285G>A	ENST00000318967.2	+	21	2794	c.2226G>A	c.(2224-2226)acG>acA	p.T742T	INTS3_ENST00000456435.1_Silent_p.T536T|INTS3_ENST00000435409.2_Silent_p.T742T|INTS3_ENST00000512605.1_Silent_p.T536T|INTS3_ENST00000476843.1_3'UTR	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	integrator complex subunit 3	743					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|mitotic cell cycle checkpoint (GO:0007093)|response to ionizing radiation (GO:0010212)|snRNA processing (GO:0016180)	integrator complex (GO:0032039)|nucleus (GO:0005634)|SOSS complex (GO:0070876)				breast(1)|cervix(4)|endometrium(10)|kidney(1)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			GCCACCTCACGCCCTCCATCT	0.592													G|||	61	0.0121805	0.0446	0.0029	5008	,	,		18290	0.0		0.0	False		,,,				2504	0.0				p.T742T		Atlas-SNP	.											.	INTS3	83	.	0			c.G2226A						PASS	.	G		170,4236	112.9+/-151.0	2,166,2035	91.0	75.0	81.0		2226	-11.7	0.1	1	dbSNP_129	81	0,8600		0,0,4300	no	coding-synonymous	INTS3	NM_023015.3		2,166,6335	AA,AG,GG		0.0,3.8584,1.3071		742/1043	153740285	170,12836	2203	4300	6503	SO:0001819	synonymous_variant	65123	exon21			CCTCACGCCCTCC	BX640950	CCDS1052.1	1q21.3	2012-03-16	2006-03-15	2006-03-15	ENSG00000143624	ENSG00000143624			26153	protein-coding gene	gene with protein product	"""sensor of single-strand DNA complex subunit A"""	611347	"""chromosome 1 open reading frame 60"""	C1orf60		16239144	Standard	NM_023015		Approved	FLJ21919, INT3, SOSS-A	uc001fct.3	Q68E01	OTTHUMG00000037089	ENST00000318967.2:c.2226G>A	1.37:g.153740285G>A		74.0	0.0	0		76.0	38.0	0.5	NM_023015	A8K1W0|B4DQC8|B4E3U9|D3DV57|Q4G0E5|Q5VUQ5|Q5VUQ6|Q5VUR0|Q5VUR1|Q68DJ1|Q69YR5|Q6AI57|Q6DKG7|Q6MZQ4|Q6MZZ9|Q8NC46|Q8TB23|Q9H6S9	Silent	SNP	ENST00000318967.2	37	CCDS1052.1																																																																																			G|0.983;A|0.017	0.017	strong		0.592	INTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090045.2	NM_023015	
PTRF	284119	hgsc.bcm.edu	37	17	40556951	40556951	+	Silent	SNP	C	C	T	rs112332573	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:40556951C>T	ENST00000357037.5	-	2	1346	c.927G>A	c.(925-927)gcG>gcA	p.A309A		NM_012232.5	NP_036364.2			polymerase I and transcript release factor											breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)|urinary_tract(1)	17		all_cancers(22;0.00146)|Breast(137;0.00116)|all_epithelial(22;0.0134)		BRCA - Breast invasive adenocarcinoma(366;0.193)		TCTTGGAGCGCGCGTACACCA	0.647													C|||	92	0.0183706	0.0696	0.0	5008	,	,		12868	0.0		0.0	False		,,,				2504	0.0				p.A309A		Atlas-SNP	.											.	PTRF	48	.	0			c.G927A						PASS	.	C		259,4147	148.4+/-182.8	10,239,1954	104.0	89.0	94.0		927	0.5	1.0	17	dbSNP_132	94	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	PTRF	NM_012232.5		10,244,6249	TT,TC,CC		0.0581,5.8783,2.0298		309/391	40556951	264,12742	2203	4300	6503	SO:0001819	synonymous_variant	284119	exon2			GGAGCGCGCGTAC	AF000421	CCDS11425.1	17q21.31	2011-04-20				ENSG00000177469			9688	protein-coding gene	gene with protein product		603198				9582279	Standard	NM_012232		Approved	cavin-1, CAVIN1	uc002hzo.3	Q6NZI2		ENST00000357037.5:c.927G>A	17.37:g.40556951C>T		135.0	0.0	0		172.0	92.0	0.534884	NM_012232		Silent	SNP	ENST00000357037.5	37	CCDS11425.1																																																																																			C|0.981;T|0.019	0.019	strong		0.647	PTRF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449938.1	NM_012232	
TTC16	158248	hgsc.bcm.edu	37	9	130485476	130485476	+	Missense_Mutation	SNP	A	A	C	rs115363266	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:130485476A>C	ENST00000373289.3	+	7	816	c.736A>C	c.(736-738)Aag>Cag	p.K246Q	PTRH1_ENST00000419060.1_Intron|PTRH1_ENST00000429848.1_Intron|TTC16_ENST00000393748.4_Missense_Mutation_p.K70Q|TTC16_ENST00000489226.1_3'UTR	NM_144965.1	NP_659402.1	Q8NEE8	TTC16_HUMAN	tetratricopeptide repeat domain 16	246										central_nervous_system(2)|endometrium(3)|lung(7)|ovary(3)|pancreas(2)|prostate(4)|skin(1)	22						GCTGCTCCAGAAGATGGTGGC	0.662													A|||	136	0.0271565	0.0983	0.0086	5008	,	,		19586	0.0		0.0	False		,,,				2504	0.0				p.K246Q		Atlas-SNP	.											.	TTC16	55	.	0			c.A736C						PASS	.	A	GLN/LYS	459,3947	211.5+/-231.7	30,399,1774	55.0	56.0	55.0		736	0.1	0.1	9	dbSNP_132	55	0,8600		0,0,4300	yes	missense	TTC16	NM_144965.1	53	30,399,6074	CC,CA,AA		0.0,10.4176,3.5291	benign	246/874	130485476	459,12547	2203	4300	6503	SO:0001583	missense	158248	exon7			CTCCAGAAGATGG	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.736A>C	9.37:g.130485476A>C	ENSP00000362386:p.Lys246Gln	118.0	0.0	0		100.0	62.0	0.62	NM_144965	B4DYG4|B5ME24|Q5JU66|Q96M72	Missense_Mutation	SNP	ENST00000373289.3	37	CCDS6875.1	69|69	0.03159340659340659|0.03159340659340659	66|66	0.13414634146341464|0.13414634146341464	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	A|A	7.212|7.212	0.595622|0.595622	0.13875|0.13875	0.104176|0.104176	0.0|0.0	ENSG00000167094|ENSG00000167094	ENST00000373288|ENST00000373289;ENST00000393748;ENST00000316259	.|T	.|0.54866	.|0.55	5.08|5.08	0.119|0.119	0.14685|0.14685	.|Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	.|1.102050	.|0.06828	.|N	.|0.793373	T|T	0.00637|0.00637	0.0021|0.0021	L|L	0.53249|0.53249	1.67|1.67	0.09310|0.09310	N|N	1|1	.|P;B;P	.|0.51351	.|0.944;0.022;0.944	.|B;B;B	.|0.44044	.|0.439;0.013;0.439	T|T	0.02491|0.02491	-1.1151|-1.1151	6|10	0.87932|0.46703	D|T	0|0.11	-1.776|-1.776	7.3747|7.3747	0.26821|0.26821	0.6016:0.0:0.3984:0.0|0.6016:0.0:0.3984:0.0	.|.	.|233;198;246	.|B4DZ42;B4DH05;Q8NEE8	.|.;.;TTC16_HUMAN	A|Q	71|246;70;191	.|ENSP00000362386:K246Q	ENSP00000362385:E71A|ENSP00000319048:K191Q	E|K	+|+	2|1	0|0	TTC16|TTC16	129525297|129525297	0.005000|0.005000	0.15991|0.15991	0.113000|0.113000	0.21522|0.21522	0.358000|0.358000	0.29455|0.29455	0.441000|0.441000	0.21611|0.21611	-0.113000|-0.113000	0.11958|0.11958	0.374000|0.374000	0.22700|0.22700	GAA|AAG	A|0.962;C|0.038	0.038	strong		0.662	TTC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054224.1	NM_144965	
TAS1R3	83756	hgsc.bcm.edu	37	1	1269488	1269488	+	Missense_Mutation	SNP	G	G	A	rs112507608	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1269488G>A	ENST00000339381.5	+	6	2235	c.2203G>A	c.(2203-2205)Gcc>Acc	p.A735T		NM_152228.1	NP_689414	Q7RTX0	TS1R3_HUMAN	taste receptor, type 1, member 3	735					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			kidney(2)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.88e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.146)		CCTAGCGCACGCCACCAATGC	0.677													g|||	299	0.0597045	0.2148	0.0202	5008	,	,		18080	0.0		0.001	False		,,,				2504	0.0				p.A735T		Atlas-SNP	.											.	TAS1R3	39	.	0			c.G2203A						PASS	.	G	THR/ALA	825,3533		76,673,1430	31.0	17.0	22.0		2203	-1.0	0.0	1	dbSNP_132	22	6,8566		0,6,4280	yes	missense	TAS1R3	NM_152228.1	58	76,679,5710	AA,AG,GG		0.07,18.9307,6.4269	benign	735/853	1269488	831,12099	2179	4286	6465	SO:0001583	missense	83756	exon6			GCGCACGCCACCA	AC026283	CCDS30556.1	1p36	2012-08-22			ENSG00000169962	ENSG00000169962		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	15661	protein-coding gene	gene with protein product		605865				11319557	Standard	XM_006710939		Approved	T1R3	uc010nyk.2	Q7RTX0	OTTHUMG00000003071	ENST00000339381.5:c.2203G>A	1.37:g.1269488G>A	ENSP00000344411:p.Ala735Thr	71.0	0.0	0		61.0	29.0	0.47541	NM_152228	Q5TA49|Q8NGW9	Missense_Mutation	SNP	ENST00000339381.5	37	CCDS30556.1	110	0.05036630036630037	102	0.2073170731707317	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	G	5.972	0.363238	0.11296	0.189307	7.0E-4	ENSG00000169962	ENST00000339381	D	0.88741	-2.42	4.35	-1.05	0.10036	GPCR, family 3, C-terminal (2);	0.499914	0.20112	N	0.098990	T	0.00210	0.0006	L	0.33485	1.01	0.80722	P	0.0	B	0.18166	0.026	B	0.14578	0.011	T	0.24119	-1.0169	9	0.62326	D	0.03	.	9.7028	0.40198	0.4805:0.0:0.5195:0.0	.	735	Q7RTX0	TS1R3_HUMAN	T	735	ENSP00000344411:A735T	ENSP00000344411:A735T	A	+	1	0	TAS1R3	1259351	0.001000	0.12720	0.001000	0.08648	0.011000	0.07611	0.420000	0.21263	-0.093000	0.12396	0.456000	0.33151	GCC	G|0.933;A|0.067	0.067	strong		0.677	TAS1R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008493.1		
PABPC1	26986	hgsc.bcm.edu	37	8	101721705	101721705	+	Missense_Mutation	SNP	G	G	T	rs201017624	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:101721705G>T	ENST00000318607.5	-	8	2355	c.1227C>A	c.(1225-1227)ttC>ttA	p.F409L	AP001205.1_ENST00000579868.1_RNA|PABPC1_ENST00000519596.1_5'UTR|PABPC1_ENST00000519004.1_Missense_Mutation_p.F364L|PABPC1_ENST00000522387.1_Missense_Mutation_p.F377L	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	409					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|mRNA stabilization (GO:0048255)|negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) binding (GO:0008143)|poly(A) RNA binding (GO:0044822)|poly(U) RNA binding (GO:0008266)|protein C-terminus binding (GO:0008022)|translation activator activity (GO:0008494)			breast(2)|endometrium(4)|kidney(15)|large_intestine(4)|lung(13)|prostate(1)|skin(1)	40	all_cancers(14;6.8e-05)|all_epithelial(15;3.16e-07)|Lung NSC(17;0.000453)|all_lung(17;0.00125)		Epithelial(11;6.37e-11)|all cancers(13;1.11e-08)|OV - Ovarian serous cystadenocarcinoma(57;3.91e-05)|STAD - Stomach adenocarcinoma(118;0.206)			TAGCTGCCATGAAGTAACCTG	0.488													g|||	1288	0.257188	0.2943	0.2089	5008	,	,		21380	0.2649		0.2107	False		,,,				2504	0.2812				p.F409L		Atlas-SNP	.											.	PABPC1	76	.	0			c.C1227A						PASS	.						101.0	92.0	95.0					8																	101721705		2203	4300	6503	SO:0001583	missense	26986	exon8			TGCCATGAAGTAA	Y00345	CCDS6289.1	8q22.2-q23	2013-02-12	2004-04-20		ENSG00000070756	ENSG00000070756		"""RNA binding motif (RRM) containing"""	8554	protein-coding gene	gene with protein product		604679	"""poly(A)-binding protein, cytoplasmic 2"""	PAB1, PABPC2		2885805	Standard	XM_005250861		Approved	PABP1, PABPL1	uc003yjs.1	P11940	OTTHUMG00000164779	ENST00000318607.5:c.1227C>A	8.37:g.101721705G>T	ENSP00000313007:p.Phe409Leu	200.0	0.0	0		264.0	48.0	0.181818	NM_002568	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	.|.|.	g|g|g	17.00|17.00|17.00	3.276204|3.276204|3.276204	0.59649|0.59649|0.59649	.|.|.	.|.|.	ENSG00000070756|ENSG00000070756|ENSG00000070756	ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387|ENST00000519596|ENST00000517403;ENST00000519100	T;T;T|.|.	0.29142|.|.	1.67;1.58;2.65|.|.	5.37|5.37|5.37	4.5|4.5|4.5	0.54988|0.54988|0.54988	.|.|.	0.000000|.|.	0.64402|.|.	D|.|.	0.000001|.|.	T|T|.	0.61160|0.61160|.	0.2325|0.2325|.	L|L|L	0.46819|0.46819|0.46819	1.47|1.47|1.47	0.58432|0.58432|0.58432	D|D|D	0.999997|0.999997|0.999997	B;B;B|.|.	0.23937|.|.	0.094;0.024;0.009|.|.	B;B;B|.|.	0.19946|.|.	0.027;0.01;0.013|.|.	T|T|.	0.58747|0.58747|.	-0.7582|-0.7582|.	10|5|.	0.49607|.|.	T|.|.	0.09|.|.	.|.|.	14.6297|14.6297|14.6297	0.68647|0.68647|0.68647	0.0702:0.0:0.9298:0.0|0.0702:0.0:0.9298:0.0|0.0702:0.0:0.9298:0.0	.|.|.	377;409;409|.|.	E7ERJ7;B3KT93;P11940|.|.	.;.;PABP1_HUMAN|.|.	L|N|X	409;409;364;377|242|62;278	ENSP00000313007:F409L;ENSP00000429594:F364L;ENSP00000429395:F377L|.|.	ENSP00000313007:F409L|.|.	F|H|S	-|-|-	3|1|2	2|0|0	PABPC1|PABPC1|PABPC1	101790881|101790881|101790881	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	1.000000|1.000000|1.000000	0.80357|0.80357|0.80357	0.996000|0.996000|0.996000	0.88848|0.88848|0.88848	7.998000|7.998000|7.998000	0.88491|0.88491|0.88491	1.419000|1.419000|1.419000	0.47118|0.47118|0.47118	-0.119000|-0.119000|-0.119000	0.15052|0.15052|0.15052	TTC|CAT|TCA	G|0.944;T|0.057	0.057	strong		0.488	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
RFX4	5992	hgsc.bcm.edu	37	12	107114548	107114548	+	Silent	SNP	G	G	A	rs73391388	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:107114548G>A	ENST00000392842.1	+	13	1659	c.1245G>A	c.(1243-1245)aaG>aaA	p.K415K	RP11-482D24.3_ENST00000552415.1_RNA|RFX4_ENST00000229387.5_Silent_p.K321K|RFX4_ENST00000357881.4_Silent_p.K424K|RP11-144F15.1_ENST00000551505.1_Intron	NM_213594.2	NP_998759.1	Q33E94	RFX4_HUMAN	regulatory factor X, 4 (influences HLA class II expression)	415	Necessary for dimerization.				cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|dorsal spinal cord development (GO:0021516)|midbrain development (GO:0030901)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of protein processing (GO:0070613)|telencephalon development (GO:0021537)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			NS(2)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(20)|pancreas(1)|upper_aerodigestive_tract(1)	35						TGGCTGCCAAGAGACAAGGGT	0.493													G|||	53	0.0105831	0.0378	0.0043	5008	,	,		20153	0.0		0.0	False		,,,				2504	0.0				p.K424K		Atlas-SNP	.											.	RFX4	218	.	0			c.G1272A						PASS	.	G	,,	175,4231	115.4+/-153.4	2,171,2030	89.0	81.0	84.0		1272,963,1245	5.6	1.0	12	dbSNP_130	84	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous,coding-synonymous,coding-synonymous	RFX4	NM_001206691.1,NM_032491.5,NM_213594.2	,,	2,178,6323	AA,AG,GG		0.0814,3.9719,1.3994	,,	424/745,321/642,415/736	107114548	182,12824	2203	4300	6503	SO:0001819	synonymous_variant	5992	exon13			TGCCAAGAGACAA	AB044245	CCDS9106.1, CCDS9108.1, CCDS55880.1	12q24	2008-08-05			ENSG00000111783	ENSG00000111783			9985	protein-coding gene	gene with protein product		603958				8600444, 11682486	Standard	NM_213594		Approved		uc001tlt.3	Q33E94	OTTHUMG00000169173	ENST00000392842.1:c.1245G>A	12.37:g.107114548G>A		165.0	0.0	0		156.0	66.0	0.423077	NM_001206691	A8K5Y0|B2RDW4|Q33DW6|Q33DW7|Q33E95|Q6YM53|Q8MHQ1|Q8NC78|Q8NDF9|Q8SNA1|Q96S80|Q9BXI0	Silent	SNP	ENST00000392842.1	37	CCDS9106.1																																																																																			G|0.988;A|0.012	0.012	strong		0.493	RFX4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402707.1	NM_032491	
SUPV3L1	6832	hgsc.bcm.edu	37	10	70940052	70940052	+	Missense_Mutation	SNP	C	C	T	rs33998366	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:70940052C>T	ENST00000359655.4	+	1	65	c.5C>T	c.(4-6)tCc>tTc	p.S2F	SUPV3L1_ENST00000483572.1_3'UTR	NM_003171.3	NP_003162.2	Q8IYB8	SUV3_HUMAN	suppressor of var1, 3-like 1 (S. cerevisiae)	2			S -> F (in dbSNP:rs33998366).		ATP catabolic process (GO:0006200)|chromatin maintenance (GO:0070827)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|mitochondrial mRNA catabolic process (GO:0000958)|mitochondrial mRNA surveillance (GO:0035946)|mitochondrial ncRNA surveillance (GO:0035945)|mitochondrial RNA 3'-end processing (GO:0000965)|mitochondrial RNA surveillance (GO:2000827)|mitochondrion morphogenesis (GO:0070584)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell growth (GO:0030307)|positive regulation of mitochondrial RNA catabolic process (GO:0000962)|RNA catabolic process (GO:0006401)	mitochondrial degradosome (GO:0045025)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	3'-5' RNA helicase activity (GO:0034458)|ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(5)|kidney(5)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GCCTCGATGTCCTTCTCCCGT	0.692													C|||	218	0.0435304	0.1573	0.013	5008	,	,		16089	0.0		0.001	False		,,,				2504	0.0				p.S2F		Atlas-SNP	.											.	SUPV3L1	61	.	0			c.C5T						PASS	.	C	PHE/SER	537,3867	208.5+/-229.5	33,471,1698	25.0	29.0	28.0		5	4.9	1.0	10	dbSNP_126	28	2,8596	2.2+/-6.3	0,2,4297	yes	missense	SUPV3L1	NM_003171.3	155	33,473,5995	TT,TC,CC		0.0233,12.1935,4.1455	probably-damaging	2/787	70940052	539,12463	2202	4299	6501	SO:0001583	missense	6832	exon1			CGATGTCCTTCTC	AF042169	CCDS7287.1	10q22.1	2008-08-01	2001-11-28		ENSG00000156502	ENSG00000156502			11471	protein-coding gene	gene with protein product		605122	"""suppressor of var1 (S.cerevisiae) 3-like 1"""			9925937, 16176273	Standard	XM_005270068		Approved	SUV3	uc001jpe.1	Q8IYB8	OTTHUMG00000018375	ENST00000359655.4:c.5C>T	10.37:g.70940052C>T	ENSP00000352678:p.Ser2Phe	52.0	0.0	0		52.0	24.0	0.461538	NM_003171	A8K301|O43630	Missense_Mutation	SNP	ENST00000359655.4	37	CCDS7287.1	89	0.04075091575091575	81	0.16463414634146342	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	C	22.0	4.227112	0.79576	0.121935	2.33E-4	ENSG00000156502	ENST00000359655;ENST00000422378	T;T	0.35973	1.43;1.28	5.78	4.88	0.63580	.	0.080168	0.50627	N	0.000116	T	0.00073	0.0002	N	0.22421	0.69	0.31663	N	0.645286	P	0.35077	0.483	B	0.33392	0.163	T	0.02789	-1.1110	10	0.87932	D	0	-0.6733	8.3656	0.32385	0.1559:0.7643:0.0:0.0797	rs33998366	2	Q8IYB8	SUV3_HUMAN	F	2	ENSP00000352678:S2F;ENSP00000409072:S2F	ENSP00000352678:S2F	S	+	2	0	SUPV3L1	70610058	0.672000	0.27530	1.000000	0.80357	0.919000	0.55068	1.022000	0.30052	2.729000	0.93468	0.655000	0.94253	TCC	C|0.961;T|0.039	0.039	strong		0.692	SUPV3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048396.2	NM_003171	
BAIAP3	8938	hgsc.bcm.edu	37	16	1391419	1391419	+	Silent	SNP	T	T	C	rs73485660	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1391419T>C	ENST00000324385.5	+	8	923	c.765T>C	c.(763-765)ccT>ccC	p.P255P	BAIAP3_ENST00000421665.2_Silent_p.P220P|BAIAP3_ENST00000426824.3_Silent_p.P220P|BAIAP3_ENST00000568887.1_Silent_p.P192P|BAIAP3_ENST00000397489.1_Silent_p.P237P|BAIAP3_ENST00000397488.2_Silent_p.P237P|BAIAP3_ENST00000562208.1_Silent_p.P197P	NM_003933.4	NP_003924.2	O94812	BAIP3_HUMAN	BAI1-associated protein 3	255	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				G-protein coupled receptor signaling pathway (GO:0007186)|neurotransmitter secretion (GO:0007269)		protein C-terminus binding (GO:0008022)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(25)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	42		Hepatocellular(780;0.0893)				GACCCCTGCCTGCCAAGTGCA	0.677													C|||	42	0.00838658	0.031	0.0014	5008	,	,		17741	0.0		0.0	False		,,,				2504	0.0				p.P255P		Atlas-SNP	.											.	BAIAP3	88	.	0			c.T765C						PASS	.	C	,,,,	113,4283		0,113,2085	61.0	56.0	58.0		660,660,591,576,765	-9.4	0.1	16	dbSNP_130	58	0,8594		0,0,4297	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BAIAP3	NM_001199096.1,NM_001199097.1,NM_001199098.1,NM_001199099.1,NM_003933.4	,,,,	0,113,6382	CC,CT,TT		0.0,2.5705,0.8699	,,,,	220/1117,220/1153,197/1130,192/1125,255/1188	1391419	113,12877	2198	4297	6495	SO:0001819	synonymous_variant	8938	exon8			CCTGCCTGCCAAG	AB017111	CCDS10434.1, CCDS55978.1, CCDS55979.1, CCDS58402.1, CCDS58403.1, CCDS66894.1	16p13.3	2008-07-04			ENSG00000007516	ENSG00000007516			948	protein-coding gene	gene with protein product		604009				9790924	Standard	NM_003933		Approved	BAP3, KIAA0734	uc002clk.2	O94812	OTTHUMG00000047833	ENST00000324385.5:c.765T>C	16.37:g.1391419T>C		124.0	0.0	0		126.0	65.0	0.515873	NM_003933	A2A2B2|B2RCD7|B4DGS5|B4DIK3|B4DRK9|B4DRP1|E7EUB9|H3BUH8|H3BVI3|H7C2Q1|O94839|Q2M226|Q658J2|Q76N05|Q96RZ3|Q9UJK1	Silent	SNP	ENST00000324385.5	37	CCDS10434.1																																																																																			T|0.989;C|0.011	0.011	strong		0.677	BAIAP3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109056.3		
MT-ND4	4538	hgsc.bcm.edu	37	M	10792	10792	+	Silent	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrM:10792A>G	ENST00000361381.2	+	1	33	c.33A>G	c.(31-33)ttA>ttG	p.L11L	MT-TR_ENST00000387439.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-TK_ENST00000387421.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	11					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						ACAATTATATTACTACCACTG	0.383																																					p.L11L		Atlas-SNP	.											.	.	.	.	0			c.A33G						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			TATATTACTACCA			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.33A>G	M.37:g.10792A>G		6.0	0.0	0		9.0	9.0	1	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Silent	SNP	ENST00000361381.2	37																																																																																				.	.	none		0.383	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
KCNK15	60598	hgsc.bcm.edu	37	20	43374694	43374694	+	Missense_Mutation	SNP	T	T	C	rs144556326	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:43374694T>C	ENST00000372861.3	+	1	274	c.143T>C	c.(142-144)cTc>cCc	p.L48P	RP11-445H22.4_ENST00000445420.1_RNA|RP11-445H22.4_ENST00000427303.1_RNA	NM_022358.3	NP_071753.2	Q9H427	KCNKF_HUMAN	potassium channel, subfamily K, member 15	48					regulation of ion transmembrane transport (GO:0034765)	integral component of membrane (GO:0016021)	potassium channel activity (GO:0005267)			NS(1)|endometrium(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(2)	10		Myeloproliferative disorder(115;0.0122)				CGGGGCGCTCTCCGGAGGAAG	0.706													T|||	106	0.0211661	0.0726	0.0144	5008	,	,		11543	0.0		0.0	False		,,,				2504	0.0				p.L48P		Atlas-SNP	.											.	KCNK15	19	.	0			c.T143C						PASS	.	T	PRO/LEU	166,4206		2,162,2022	10.0	15.0	13.0		143	2.9	0.9	20	dbSNP_134	13	6,8538		0,6,4266	yes	missense	KCNK15	NM_022358.3	98	2,168,6288	CC,CT,TT		0.0702,3.7969,1.3317	probably-damaging	48/331	43374694	172,12744	2186	4272	6458	SO:0001583	missense	60598	exon1			GCGCTCTCCGGAG	AF257081	CCDS13337.1	20q13.12	2012-03-07			ENSG00000124249	ENSG00000124249		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	13814	protein-coding gene	gene with protein product		607368		KCNK11, KCNK14		11409881, 11431495, 16382106	Standard	NM_022358		Approved	K2p15.1, dJ781B1.1, KT3.3, KIAA0237, TASK5, TASK-5	uc002xmr.3	Q9H427	OTTHUMG00000032544	ENST00000372861.3:c.143T>C	20.37:g.43374694T>C	ENSP00000361952:p.Leu48Pro	41.0	0.0	0		37.0	15.0	0.405405	NM_022358	Q52LL3|Q9HBC8	Missense_Mutation	SNP	ENST00000372861.3	37	CCDS13337.1	43	0.019688644688644688	36	0.07317073170731707	7	0.019337016574585635	0	0.0	0	0.0	T	14.77	2.635968	0.47049	0.037969	7.02E-4	ENSG00000124249	ENST00000372861	T	0.17854	2.25	4.04	2.91	0.33838	.	0.349704	0.29892	N	0.010923	T	0.03827	0.0108	M	0.87180	2.865	0.80722	D	1	D	0.63880	0.993	P	0.61070	0.883	T	0.00295	-1.1839	10	0.87932	D	0	.	8.6904	0.34262	0.1705:0.0:0.0:0.8295	.	48	Q9H427	KCNKF_HUMAN	P	48	ENSP00000361952:L48P	ENSP00000361952:L48P	L	+	2	0	KCNK15	42808108	0.968000	0.33430	0.914000	0.36105	0.012000	0.07955	4.497000	0.60367	0.577000	0.29470	0.455000	0.32223	CTC	T|0.981;C|0.019	0.019	strong		0.706	KCNK15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079378.2	NM_022358	
ZNF286B	729288	hgsc.bcm.edu	37	17	18565915	18565915	+	Missense_Mutation	SNP	G	G	A	rs73291461	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:18565915G>A	ENST00000545289.1	-	5	1154	c.904C>T	c.(904-906)Cgt>Tgt	p.R302C	ZNF286B_ENST00000285274.5_3'UTR	NM_001145045.1	NP_001138517.1	P0CG31	Z286B_HUMAN	zinc finger protein 286B	302					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						TTACATTCACGGCATTCAAAG	0.398													.|||	424	0.0846645	0.3071	0.0202	5008	,	,		21283	0.0		0.002	False		,,,				2504	0.002				p.R302C		Atlas-SNP	.											.	ZNF286B	75	.	0			c.C904T						PASS	.	T	CYS/ARG	317,1067		31,255,406	74.0	66.0	69.0		904	0.1	0.9	17	dbSNP_130	69	13,3169		0,13,1578	no	missense	ZNF286B	NM_001145045.1	180	31,268,1984	AA,AG,GG		0.4085,22.9046,7.2273	benign	302/523	18565915	330,4236	692	1591	2283	SO:0001583	missense	729288	exon5			ATTCACGGCATTC		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.904C>T	17.37:g.18565915G>A	ENSP00000461413:p.Arg302Cys	330.0	0.0	0		299.0	130.0	0.434783	NM_001145045		Missense_Mutation	SNP	ENST00000545289.1	37	CCDS58523.1																																																																																			G|0.943;A|0.057	0.057	strong		0.398	ZNF286B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_001723047	
UBXN6	80700	hgsc.bcm.edu	37	19	4446164	4446164	+	Missense_Mutation	SNP	G	G	A	rs34179017	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4446164G>A	ENST00000301281.6	-	10	1206	c.1082C>T	c.(1081-1083)gCg>gTg	p.A361V	CTB-50L17.7_ENST00000588798.1_RNA|UBXN6_ENST00000394765.3_Missense_Mutation_p.A308V|MIR4746_ENST00000579802.1_RNA	NM_025241.2	NP_079517.1	Q9BZV1	UBXN6_HUMAN	UBX domain protein 6	361	UBX. {ECO:0000255|PROSITE- ProRule:PRU00215}.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)				NS(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|skin(1)	12						CCCGTACACCGCCCCCAGCCG	0.711													G|||	32	0.00638978	0.0242	0.0	5008	,	,		14161	0.0		0.0	False		,,,				2504	0.0				p.A361V		Atlas-SNP	.											.	UBXN6	27	.	0			c.C1082T						PASS	.	G	VAL/ALA,VAL/ALA	76,4324		1,74,2125	15.0	19.0	18.0		923,1082	-1.2	0.0	19	dbSNP_126	18	0,8590		0,0,4295	yes	missense,missense	UBXN6	NM_001171091.1,NM_025241.2	64,64	1,74,6420	AA,AG,GG		0.0,1.7273,0.5851	benign,benign	308/389,361/442	4446164	76,12914	2200	4295	6495	SO:0001583	missense	80700	exon10			TACACCGCCCCCA	AF272893	CCDS12129.1, CCDS54201.1	19p13	2008-07-25	2008-07-25	2008-07-25		ENSG00000167671		"""UBX domain containing"""	14928	protein-coding gene	gene with protein product		611946	"""UBX domain-containing 1"", ""UBX domain containing 1"""	UBXD1		11342112	Standard	NM_025241		Approved	UBXDC2	uc002man.2	Q9BZV1		ENST00000301281.6:c.1082C>T	19.37:g.4446164G>A	ENSP00000301281:p.Ala361Val	97.0	0.0	0		102.0	50.0	0.490196	NM_025241	D6W626|Q96AH1|Q96IK9|Q9BZV0	Missense_Mutation	SNP	ENST00000301281.6	37	CCDS12129.1	12	0.005494505494505495	12	0.024390243902439025	0	0.0	0	0.0	0	0.0	G	5.191	0.220842	0.09863	0.017273	0.0	ENSG00000167671	ENST00000301281;ENST00000394765	T;T	0.44881	0.91;0.91	5.15	-1.23	0.09465	UBX (3);	0.540957	0.20913	N	0.083423	T	0.14399	0.0348	L	0.48260	1.515	0.09310	N	0.999999	B;B	0.23540	0.047;0.087	B;B	0.22880	0.013;0.042	T	0.10019	-1.0648	10	0.25106	T	0.35	-7.5495	4.4434	0.11586	0.2944:0.0:0.4642:0.2414	rs34179017;rs34179017	308;361	Q9BZV1-2;Q9BZV1	.;UBXN6_HUMAN	V	361;308	ENSP00000301281:A361V;ENSP00000378246:A308V	ENSP00000301281:A361V	A	-	2	0	UBXN6	4397164	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	0.189000	0.17037	-0.230000	0.09840	0.561000	0.74099	GCG	G|0.992;A|0.008	0.008	strong		0.711	UBXN6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458447.3	NM_025241	
OR51F1	256892	hgsc.bcm.edu	37	11	4791012	4791012	+	Missense_Mutation	SNP	C	C	T	rs146706676	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:4791012C>T	ENST00000380383.1	-	1	156	c.157G>A	c.(157-159)Gtg>Atg	p.V53M	MMP26_ENST00000477339.1_Intron|OR51F1_ENST00000343430.3_Missense_Mutation_p.V46M|MMP26_ENST00000380390.1_Intron			A6NGY5	O51F1_HUMAN	olfactory receptor, family 51, subfamily F, member 1	53						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	22		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.0778)		Epithelial(150;5.87e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0045)|LUSC - Lung squamous cell carcinoma(625;0.192)		AACAGGATCACGCTGTTCCCA	0.478													C|||	4	0.000798722	0.003	0.0	5008	,	,		20537	0.0		0.0	False		,,,				2504	0.0				p.V46M		Atlas-SNP	.											.	OR51F1	60	.	0			c.G136A						PASS	.	C	MET/VAL	15,4387	22.3+/-47.3	0,15,2186	66.0	63.0	64.0		136	1.0	1.0	11	dbSNP_134	64	0,8596		0,0,4298	yes	missense	OR51F1	NM_001004752.1	21	0,15,6484	TT,TC,CC		0.0,0.3408,0.1154	benign	46/313	4791012	15,12983	2201	4298	6499	SO:0001583	missense	256892	exon1			GGATCACGCTGTT	BK004771	CCDS31359.1	11p15.4	2012-08-09		2004-03-10	ENSG00000188069	ENSG00000188069		"""GPCR / Class A : Olfactory receptors"""	15196	protein-coding gene	gene with protein product				OR51F1P			Standard	NM_001004752		Approved		uc010qyl.2	A6NGY5	OTTHUMG00000066503	ENST00000380383.1:c.157G>A	11.37:g.4791012C>T	ENSP00000369744:p.Val53Met	80.0	0.0	0		75.0	34.0	0.453333	NM_001004752		Missense_Mutation	SNP	ENST00000380383.1	37		.	.	.	.	.	.	.	.	.	.	C	0.094	-1.162853	0.01673	0.003408	0.0	ENSG00000188069	ENST00000343430;ENST00000380383	T;T	0.00451	7.35;7.35	4.81	1.05	0.20165	GPCR, rhodopsin-like superfamily (1);	0.193258	0.36234	N	0.002716	T	0.00109	0.0003	N	0.00595	-1.35	0.22762	N	0.998768	B	0.02656	0.0	B	0.01281	0.0	T	0.26916	-1.0089	10	0.18710	T	0.47	.	3.1994	0.06645	0.1376:0.0783:0.1435:0.6405	.	53	A6NGY5	O51F1_HUMAN	M	46;53	ENSP00000345163:V46M;ENSP00000369744:V53M	ENSP00000345163:V46M	V	-	1	0	OR51F1	4747588	0.000000	0.05858	0.993000	0.49108	0.775000	0.43874	-1.227000	0.02950	0.008000	0.14787	-0.385000	0.06624	GTG	C|0.999;T|0.001	0.001	strong		0.478	OR51F1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001004752	
KIRREL2	84063	hgsc.bcm.edu	37	19	36349721	36349721	+	Silent	SNP	G	G	A	rs57079408	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36349721G>A	ENST00000360202.5	+	4	675	c.477G>A	c.(475-477)ctG>ctA	p.L159L	KIRREL2_ENST00000592409.1_Silent_p.L159L|KIRREL2_ENST00000262625.7_Silent_p.L159L|NPHS1_ENST00000591817.1_Intron|KIRREL2_ENST00000347900.6_Silent_p.L109L	NM_032123.5|NM_199180.2	NP_115499.4|NP_954649.2	Q6UWL6	KIRR2_HUMAN	kin of IRRE like 2 (Drosophila)	159	Ig-like C2-type 2.				cell adhesion (GO:0007155)|negative regulation of protein phosphorylation (GO:0001933)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|slit diaphragm (GO:0036057)				breast(2)|central_nervous_system(1)|endometrium(6)|large_intestine(6)|liver(2)|lung(22)|ovary(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	48	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CTGAATTGCTGTGGTTCCGAG	0.592													G|||	35	0.00698882	0.0242	0.0043	5008	,	,		18517	0.0		0.0	False		,,,				2504	0.0				p.L159L		Atlas-SNP	.											.	KIRREL2	170	.	0			c.G477A						PASS	.	G	,,	87,4319	72.0+/-110.0	0,87,2116	107.0	103.0	104.0		477,327,477	2.1	1.0	19	dbSNP_129	104	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	KIRREL2	NM_032123.5,NM_199179.2,NM_199180.2	,,	0,87,6416	AA,AG,GG		0.0,1.9746,0.6689	,,	159/634,109/584,159/709	36349721	87,12919	2203	4300	6503	SO:0001819	synonymous_variant	84063	exon4			ATTGCTGTGGTTC	AL136654	CCDS12479.1, CCDS12480.1, CCDS12481.1	19q13.13	2013-01-29				ENSG00000126259		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18816	protein-coding gene	gene with protein product		607762				12837264, 12504092	Standard	NM_199180		Approved	NLG1, NEPH3, FILTRIN, DKFZp564A1164, MGC15718	uc002ocb.4	Q6UWL6		ENST00000360202.5:c.477G>A	19.37:g.36349721G>A		246.0	1.0	0.00406504		215.0	104.0	0.483721	NM_199180	C9JHF1|C9JJ76|F1T0I2|Q6P1R1|Q7Z5P1|Q7Z5P2|Q96IQ8|Q9H0T1	Silent	SNP	ENST00000360202.5	37	CCDS12481.1																																																																																			G|0.994;A|0.006	0.006	strong		0.592	KIRREL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452561.1	NM_032123	
MBOAT2	129642	hgsc.bcm.edu	37	2	9013424	9013424	+	Missense_Mutation	SNP	C	C	T	rs34573615	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:9013424C>T	ENST00000305997.3	-	8	895	c.697G>A	c.(697-699)Gtt>Att	p.V233I	MBOAT2_ENST00000486484.1_5'UTR	NM_138799.2	NP_620154.2	Q6ZWT7	MBOA2_HUMAN	membrane bound O-acyltransferase domain containing 2	233					glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)		MBOAT2/PRKCE(2)	endometrium(2)|kidney(1)|large_intestine(9)|lung(2)|skin(1)	15	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)					TTCTGAACAACCGCAGTCTGA	0.398													C|||	71	0.0141773	0.0212	0.0086	5008	,	,		19264	0.003		0.004	False		,,,				2504	0.0307				p.V233I	Ovarian(194;1699 3813 22401)	Atlas-SNP	.											.	MBOAT2	36	.	0			c.G697A						PASS	.	C	ILE/VAL	69,4337	62.3+/-99.4	1,67,2135	83.0	81.0	82.0		697	5.2	0.1	2	dbSNP_126	82	13,8587	9.8+/-36.6	0,13,4287	yes	missense	MBOAT2	NM_138799.2	29	1,80,6422	TT,TC,CC		0.1512,1.566,0.6305	probably-damaging	233/521	9013424	82,12924	2203	4300	6503	SO:0001583	missense	129642	exon8			GAACAACCGCAGT	BC016005	CCDS1660.1	2p25	2008-02-05	2006-06-29	2006-06-29	ENSG00000143797	ENSG00000143797			25193	protein-coding gene	gene with protein product		611949	"""O-acyltransferase (membrane bound) domain containing 2"""	OACT2			Standard	NM_138799		Approved	FLJ14415, FLJ90298	uc002qzg.1	Q6ZWT7	OTTHUMG00000090363	ENST00000305997.3:c.697G>A	2.37:g.9013424C>T	ENSP00000302177:p.Val233Ile	97.0	0.0	0		95.0	61.0	0.642105	NM_138799	A9EDR2|Q8NCE7|Q96KY4	Missense_Mutation	SNP	ENST00000305997.3	37	CCDS1660.1	20	0.009157509157509158	14	0.028455284552845527	4	0.011049723756906077	0	0.0	2	0.002638522427440633	C	26.8	4.769230	0.90020	0.01566	0.001512	ENSG00000143797	ENST00000305997	T	0.72615	-0.67	5.22	5.22	0.72569	.	0.173169	0.50627	D	0.000119	T	0.71888	0.3393	M	0.88775	2.98	0.80722	D	1	D;D	0.61697	0.99;0.99	D;D	0.64506	0.92;0.926	D	0.83693	0.0178	10	0.72032	D	0.01	-23.1005	18.7799	0.91928	0.0:1.0:0.0:0.0	rs34573615	233;233	B7Z3I3;Q6ZWT7	.;MBOA2_HUMAN	I	233	ENSP00000302177:V233I	ENSP00000302177:V233I	V	-	1	0	MBOAT2	8930875	1.000000	0.71417	0.062000	0.19696	0.024000	0.10985	7.292000	0.78731	2.418000	0.82041	0.460000	0.39030	GTT	C|0.994;T|0.006	0.006	strong		0.398	MBOAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206735.1	NM_138799	
SMARCA2	6595	hgsc.bcm.edu	37	9	2029196	2029196	+	Silent	SNP	G	G	A	rs10964470	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:2029196G>A	ENST00000382203.1	+	2	383	c.174G>A	c.(172-174)ccG>ccA	p.P58P	SMARCA2_ENST00000349721.2_Silent_p.P58P|SMARCA2_ENST00000357248.2_Silent_p.P58P|SMARCA2_ENST00000382194.1_Silent_p.P58P			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	58					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)		ATCCTATGCCGACGATGGGGT	0.527													G|||	245	0.0489217	0.1778	0.0115	5008	,	,		19068	0.0		0.002	False		,,,				2504	0.0				p.P58P		Atlas-SNP	.											.	SMARCA2	313	.	0			c.G174A						PASS	.	G	,	635,3771	271.0+/-269.9	44,547,1612	42.0	36.0	38.0		174,174	-11.2	0.0	9	dbSNP_120	38	2,8598	1.2+/-3.3	0,2,4298	yes	coding-synonymous,coding-synonymous	SMARCA2	NM_003070.3,NM_139045.2	,	44,549,5910	AA,AG,GG		0.0233,14.4122,4.8977	,	58/1591,58/1573	2029196	637,12369	2203	4300	6503	SO:0001819	synonymous_variant	6595	exon2			TATGCCGACGATG	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.174G>A	9.37:g.2029196G>A		91.0	0.0	0		111.0	56.0	0.504505	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	Silent	SNP	ENST00000382203.1	37	CCDS34977.1																																																																																			G|0.950;A|0.050	0.050	strong		0.527	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070	
IRF4	3662	hgsc.bcm.edu	37	6	393330	393330	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:393330C>A	ENST00000380956.4	+	2	304	c.178C>A	c.(178-180)Cag>Aag	p.Q60K	IRF4_ENST00000495137.1_Intron	NM_001195286.1|NM_002460.3	NP_001182215.1|NP_002451.2	Q15306	IRF4_HUMAN	interferon regulatory factor 4	60					cytokine-mediated signaling pathway (GO:0019221)|defense response to protozoan (GO:0042832)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of DNA binding (GO:0043388)|positive regulation of interleukin-10 biosynthetic process (GO:0045082)|positive regulation of interleukin-13 biosynthetic process (GO:0045368)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 biosynthetic process (GO:0045404)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of T-helper cell differentiation (GO:0045622)|T cell activation (GO:0042110)|T-helper 17 cell lineage commitment (GO:0072540)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear nucleosome (GO:0000788)|nucleus (GO:0005634)	protein-lysine N-methyltransferase activity (GO:0016279)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.Q60K(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|ovary(2)	5		Breast(5;0.0155)|all_lung(73;0.0691)|all_hematologic(90;0.0895)		OV - Ovarian serous cystadenocarcinoma(45;0.03)|BRCA - Breast invasive adenocarcinoma(62;0.0702)		CGCGGGCAAGCAGGACTACAA	0.692			T	IGH@	MM																																p.Q60K		Atlas-SNP	.		Dom	yes		6	6p25-p23	3662	interferon regulatory factor 4		L	IRF4_ENST00000380956,NS,lymphoid_neoplasm,-2,2	IRF4	65	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C178A						PASS	.						29.0	26.0	27.0					6																	393330		2201	4300	6501	SO:0001583	missense	3662	exon2			GGCAAGCAGGACT	U52682	CCDS4469.1	6p25-p23	2008-08-29			ENSG00000137265	ENSG00000137265			6119	protein-coding gene	gene with protein product		601900		MUM1		8921401, 18417578	Standard	NM_002460		Approved	LSIRF	uc003msz.4	Q15306	OTTHUMG00000016294	ENST00000380956.4:c.178C>A	6.37:g.393330C>A	ENSP00000370343:p.Gln60Lys	69.0	0.0	0		75.0	31.0	0.413333	NM_001195286	Q5VUI7|Q99660	Missense_Mutation	SNP	ENST00000380956.4	37	CCDS4469.1	.	.	.	.	.	.	.	.	.	.	C	34	5.402639	0.96030	.	.	ENSG00000137265	ENST00000380956;ENST00000412334	D	0.97505	-4.41	4.58	4.58	0.56647	Interferon regulatory factor, conserved site (1);Winged helix-turn-helix transcription repressor DNA-binding (1);Interferon regulatory factor DNA-binding domain (4);	0.115641	0.64402	D	0.000010	D	0.97297	0.9116	L	0.53561	1.675	0.80722	D	1	P;P;D	0.69078	0.852;0.624;0.997	P;P;D	0.74348	0.813;0.61;0.983	D	0.96246	0.9179	10	0.30854	T	0.27	-22.6787	17.6301	0.88104	0.0:1.0:0.0:0.0	.	60;60;60	F2Z3D5;Q15306-2;Q15306	.;.;IRF4_HUMAN	K	60;90	ENSP00000370343:Q60K	ENSP00000370343:Q60K	Q	+	1	0	IRF4	338330	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	6.909000	0.75735	2.399000	0.81585	0.306000	0.20318	CAG	.	.	none		0.692	IRF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043638.1		
ACOT1	641371	hgsc.bcm.edu	37	14	74008304	74008304	+	Missense_Mutation	SNP	G	G	A	rs146335256	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:74008304G>A	ENST00000311148.4	+	2	873	c.565G>A	c.(565-567)Gct>Act	p.A189T	HEATR4_ENST00000553558.1_Intron|HEATR4_ENST00000560393.1_Intron|HEATR4_ENST00000334988.2_Intron|ACOT1_ENST00000557556.1_Missense_Mutation_p.A189T	NM_001037161.1	NP_001032238.1	Q86TX2	ACOT1_HUMAN	acyl-CoA thioesterase 1	189					acyl-CoA metabolic process (GO:0006637)|long-chain fatty acid metabolic process (GO:0001676)|very long-chain fatty acid metabolic process (GO:0000038)	cytosol (GO:0005829)	acyl-CoA hydrolase activity (GO:0047617)|carboxylic ester hydrolase activity (GO:0052689)|palmitoyl-CoA hydrolase activity (GO:0016290)			endometrium(1)|large_intestine(1)|lung(2)	4				OV - Ovarian serous cystadenocarcinoma(108;1.37e-45)|BRCA - Breast invasive adenocarcinoma(234;0.0033)		GATGGCTCTGGCTTACTATAA	0.527													-|||	78	0.0155751	0.0552	0.0072	5008	,	,		9026	0.0		0.0	False		,,,				2504	0.0				p.A189T		Atlas-SNP	.											.	ACOT1	12	.	0			c.G565A						PASS	.	G	THR/ALA,,	147,3835		36,75,1880	224.0	174.0	192.0		565,,	3.6	1.0	14	dbSNP_134	192	2,7196		1,0,3598	no	missense,intron,intron	HEATR4,ACOT1	NM_001037161.1,NM_001220484.1,NM_203309.2	58,,	37,75,5478	AA,AG,GG		0.0278,3.6916,1.3327	,,	189/422,,	74008304	149,11031	1991	3599	5590	SO:0001583	missense	641371	exon2			GCTCTGGCTTACT	DQ082754	CCDS32117.1	14q24.3	2013-09-20			ENSG00000184227	ENSG00000184227		"""Acyl CoA thioesterases"""	33128	protein-coding gene	gene with protein product		614313				16103133, 16940157	Standard	NM_001037161		Approved	ACH2, CTE-1, LACH2		Q86TX2	OTTHUMG00000171607	ENST00000311148.4:c.565G>A	14.37:g.74008304G>A	ENSP00000311224:p.Ala189Thr	241.0	0.0	0		258.0	257.0	0.996124	NM_001037161	A1L173|Q3I5F9	Missense_Mutation	SNP	ENST00000311148.4	37	CCDS32117.1	21	0.009615384615384616	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	0	0.0	-	15.12	2.737774	0.49045	0.036916	2.78E-4	ENSG00000184227	ENST00000311148;ENST00000557556	T;T	0.42513	0.97;0.97	3.61	3.61	0.41365	.	0.149549	0.64402	D	0.000013	T	0.42743	0.1216	H	0.94345	3.525	0.54753	D	0.999987	D;D	0.89917	1.0;1.0	D;D	0.79108	0.992;0.992	T	0.75634	-0.3250	10	0.87932	D	0	-10.4661	15.853	0.78947	0.0:0.0:1.0:0.0	.	189;189	E9KL42;Q86TX2	.;ACOT1_HUMAN	T	189	ENSP00000311224:A189T;ENSP00000451764:A189T	ENSP00000311224:A189T	A	+	1	0	ACOT1	73078057	1.000000	0.71417	1.000000	0.80357	0.046000	0.14306	5.637000	0.67854	2.022000	0.59522	0.423000	0.28283	GCT	G|0.989;A|0.011	0.011	strong		0.527	ACOT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414432.1	NM_001037161	
SIGLEC9	27180	hgsc.bcm.edu	37	19	51628622	51628622	+	Missense_Mutation	SNP	A	A	C	rs16988910	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51628622A>C	ENST00000250360.3	+	1	458	c.391A>C	c.(391-393)Aaa>Caa	p.K131Q	SIGLEC9_ENST00000440804.3_Missense_Mutation_p.K131Q	NM_014441.2	NP_055256.1	Q9Y336	SIGL9_HUMAN	sialic acid binding Ig-like lectin 9	131	Ig-like V-type.		K -> Q (in dbSNP:rs16988910).		cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(3)|lung(25)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	45		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.000826)|OV - Ovarian serous cystadenocarcinoma(262;0.00295)		ATGGAATTATAAACATCACCG	0.498													.|||	482	0.096246	0.3495	0.0288	5008	,	,		19570	0.0		0.0	False		,,,				2504	0.0				p.K131Q		Atlas-SNP	.											.	SIGLEC9	85	.	0			c.A391C						PASS	.	A	GLN/LYS,GLN/LYS	1306,3100		197,912,1094	54.0	54.0	54.0		391,391	-6.1	0.0	19	dbSNP_123	54	9,8591		0,9,4291	yes	missense,missense	SIGLEC9	NM_001198558.1,NM_014441.2	53,53	197,921,5385	CC,CA,AA		0.1047,29.6414,10.1107	benign,benign	131/480,131/464	51628622	1315,11691	2203	4300	6503	SO:0001583	missense	27180	exon1			AATTATAAACATC	AF135027	CCDS12825.1, CCDS56100.1	19q13.3-q13.4	2013-01-29			ENSG00000129450	ENSG00000129450		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10878	protein-coding gene	gene with protein product		605640				10903842	Standard	NM_014441		Approved	CD329	uc002pvu.3	Q9Y336		ENST00000250360.3:c.391A>C	19.37:g.51628622A>C	ENSP00000250360:p.Lys131Gln	60.0	0.0	0		54.0	28.0	0.518519	NM_001198558	Q6GTU4|Q9BYI9	Missense_Mutation	SNP	ENST00000250360.3	37	CCDS12825.1	177	0.08104395604395605	167	0.3394308943089431	10	0.027624309392265192	0	0.0	0	0.0	.	2.109	-0.404270	0.04832	0.296414	0.001047	ENSG00000129450	ENST00000440804;ENST00000250360	T;T	0.45668	0.89;0.89	3.03	-6.06	0.02165	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	3.634600	0.01116	N	0.005689	T	0.00012	0.0000	L	0.35542	1.07	0.80722	P	0.0	B	0.13145	0.007	B	0.11329	0.006	T	0.28138	-1.0053	9	0.19147	T	0.46	.	0.854	0.01178	0.2909:0.3232:0.227:0.1589	rs16988910;rs57111846;rs16988910	131	Q9Y336	SIGL9_HUMAN	Q	131	ENSP00000413861:K131Q;ENSP00000250360:K131Q	ENSP00000250360:K131Q	K	+	1	0	SIGLEC9	56320434	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.430000	0.02434	-1.179000	0.02737	-0.476000	0.04901	AAA	A|0.895;C|0.105	0.105	strong		0.498	SIGLEC9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464224.1	NM_014441	
RSBN1L	222194	hgsc.bcm.edu	37	7	77325919	77325919	+	Missense_Mutation	SNP	G	G	A	rs79095281	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:77325919G>A	ENST00000334955.8	+	1	160	c.133G>A	c.(133-135)Gtc>Atc	p.V45I	RSBN1L-AS1_ENST00000440088.1_lincRNA|RSBN1L_ENST00000445288.1_5'Flank	NM_198467.2	NP_940869.2	Q6PCB5	RSBNL_HUMAN	round spermatid basic protein 1-like	45						nucleus (GO:0005634)				central_nervous_system(1)|endometrium(12)|large_intestine(2)|lung(8)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						CGCCAAGAAGGTCCGGACTGA	0.677													G|||	139	0.0277556	0.1029	0.0043	5008	,	,		14173	0.0		0.0	False		,,,				2504	0.0				p.V45I		Atlas-SNP	.											.	RSBN1L	74	.	0			c.G133A						PASS	.	G	ILE/VAL	329,3439		19,291,1574	34.0	45.0	41.0		133	2.1	1.0	7	dbSNP_131	41	3,8221		0,3,4109	yes	missense	RSBN1L	NM_198467.2	29	19,294,5683	AA,AG,GG		0.0365,8.7314,2.7685	benign	45/847	77325919	332,11660	1884	4112	5996	SO:0001583	missense	222194	exon1			AAGAAGGTCCGGA	AK124517	CCDS43607.1	7q21.11	2004-08-11			ENSG00000187257	ENSG00000187257			24765	protein-coding gene	gene with protein product						12477932	Standard	NM_198467		Approved	FLJ42526, FLJ45813, MGC71764	uc010ldt.1	Q6PCB5	OTTHUMG00000155517	ENST00000334955.8:c.133G>A	7.37:g.77325919G>A	ENSP00000334040:p.Val45Ile	60.0	0.0	0		67.0	39.0	0.58209	NM_198467	C9K0P1|Q6ZS58|Q6ZVI9|Q86X48	Missense_Mutation	SNP	ENST00000334955.8	37	CCDS43607.1	47	0.02152014652014652	45	0.09146341463414634	2	0.0055248618784530384	0	0.0	0	0.0	G	12.96	2.095669	0.36952	0.087314	3.65E-4	ENSG00000187257	ENST00000334955	.	.	.	4.02	2.14	0.27477	.	0.551396	0.14695	N	0.303893	T	0.01124	0.0037	N	0.14661	0.345	0.80722	D	1	B	0.09022	0.002	B	0.08055	0.003	T	0.03184	-1.1063	9	0.19147	T	0.46	-2.8559	7.0249	0.24934	0.2286:0.0:0.7714:0.0	.	45	Q6PCB5	RSBNL_HUMAN	I	45	.	ENSP00000334040:V45I	V	+	1	0	RSBN1L	77163855	0.998000	0.40836	0.998000	0.56505	0.557000	0.35523	0.398000	0.20899	0.421000	0.25980	0.313000	0.20887	GTC	G|0.973;A|0.027	0.027	strong		0.677	RSBN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340455.3	NM_198467	
LRPPRC	10128	hgsc.bcm.edu	37	2	44172496	44172496	+	Silent	SNP	T	T	C	rs145963884	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:44172496T>C	ENST00000260665.7	-	22	2328	c.2271A>G	c.(2269-2271)gtA>gtG	p.V757V		NM_133259.3	NP_573566.2	P42704	LPPRC_HUMAN	leucine-rich pentatricopeptide repeat containing	757					mitochondrion transport along microtubule (GO:0047497)|mRNA transport (GO:0051028)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of mitochondrial translation (GO:0070129)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed nuclear chromosome (GO:0000794)|cytoskeleton (GO:0005856)|membrane (GO:0016020)|microtubule (GO:0005874)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(3)|endometrium(3)|kidney(5)|large_intestine(9)|lung(15)|ovary(2)|prostate(2)|skin(2)	41		all_hematologic(82;0.166)|Acute lymphoblastic leukemia(82;0.17)				GCTTTGCCAATACTCTTACAA	0.378													T|||	5	0.000998403	0.0038	0.0	5008	,	,		22524	0.0		0.0	False		,,,				2504	0.0				p.V757V		Atlas-SNP	.											.	LRPPRC	105	.	0			c.A2271G						PASS	.	T		7,4399	12.9+/-30.5	0,7,2196	137.0	122.0	127.0		2271	-0.7	1.0	2	dbSNP_134	127	0,8598		0,0,4299	no	coding-synonymous	LRPPRC	NM_133259.3		0,7,6495	CC,CT,TT		0.0,0.1589,0.0538		757/1395	44172496	7,12997	2203	4299	6502	SO:0001819	synonymous_variant	10128	exon22			TGCCAATACTCTT	M92439	CCDS33189.1	2p21	2012-02-24	2012-02-24		ENSG00000138095	ENSG00000138095			15714	protein-coding gene	gene with protein product		607544	"""Leigh syndrome, French-Canadian type (cytochrome oxidase deficiency)"""	LSFC		8012652, 8619474, 22045337	Standard	NM_133259		Approved	GP130, LRP130	uc002rtr.2	P42704	OTTHUMG00000152782	ENST00000260665.7:c.2271A>G	2.37:g.44172496T>C		96.0	0.0	0		130.0	54.0	0.415385	NM_133259	A0PJE3|A8K1V1|Q53PC0|Q53QN7|Q6ZUD8|Q7Z7A6|Q96D84	Silent	SNP	ENST00000260665.7	37	CCDS33189.1																																																																																			T|0.999;C|0.001	0.001	strong		0.378	LRPPRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327823.1	NM_133259	
FBXW9	84261	hgsc.bcm.edu	37	19	12805525	12805525	+	Silent	SNP	G	G	C	rs10416965	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12805525G>C	ENST00000380339.3	-	3	597	c.561C>G	c.(559-561)ctC>ctG	p.L187L	FBXW9_ENST00000544494.1_5'UTR|FBXW9_ENST00000393261.3_Silent_p.L187L|FBXW9_ENST00000587955.1_Silent_p.L177L			Q5XUX1	FBXW9_HUMAN	F-box and WD repeat domain containing 9	187					SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)					cervix(1)|lung(4)|ovary(1)|prostate(1)	7						CCGACAGACAGAGTGACCCAC	0.632													G|||	749	0.149561	0.5348	0.0461	5008	,	,		18468	0.0		0.0099	False		,,,				2504	0.0				p.L187L		Atlas-SNP	.											.	FBXW9	30	.	0			c.C561G						PASS	.	G		1693,2405		363,967,719	62.0	68.0	66.0		561	-2.5	0.1	19	dbSNP_119	66	131,8263		1,129,4067	no	coding-synonymous	FBXW9	NM_032301.2		364,1096,4786	CC,CG,GG		1.5606,41.3128,14.6013		187/459	12805525	1824,10668	2049	4197	6246	SO:0001819	synonymous_variant	84261	exon3			CAGACAGAGTGAC	BC004290	CCDS12278.2	19p13.2	2013-01-09	2007-02-08		ENSG00000132004	ENSG00000132004		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	28136	protein-coding gene	gene with protein product		609074	"""F-box and WD-40 domain protein 9"""			12477932	Standard	NM_032301		Approved	MGC10870, Fbw9	uc002mum.1	Q5XUX1	OTTHUMG00000150152	ENST00000380339.3:c.561C>G	19.37:g.12805525G>C		70.0	0.0	0		82.0	41.0	0.5	NM_032301	B3KVP7|Q9BT89	Silent	SNP	ENST00000380339.3	37																																																																																				G|0.921;C|0.079	0.079	strong		0.632	FBXW9-201	KNOWN	basic	protein_coding	protein_coding		NM_032301	
MYOM2	9172	hgsc.bcm.edu	37	8	2050564	2050564	+	Silent	SNP	G	G	A	rs34460811	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:2050564G>A	ENST00000262113.4	+	21	2868	c.2727G>A	c.(2725-2727)gcG>gcA	p.A909A	MYOM2_ENST00000523438.1_Silent_p.A334A	NM_003970.2	NP_003961.2	P54296	MYOM2_HUMAN	myomesin 2	909	Fibronectin type-III 5. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Ig-like C2-type 3.				muscle contraction (GO:0006936)	M band (GO:0031430)|mitochondrion (GO:0005739)|myosin filament (GO:0032982)	structural constituent of muscle (GO:0008307)			autonomic_ganglia(2)|breast(4)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(11)|kidney(2)|large_intestine(17)|lung(39)|ovary(5)|prostate(1)|skin(10)|upper_aerodigestive_tract(3)	104		Ovarian(12;0.0572)|Colorectal(14;0.0844)|Hepatocellular(245;0.217)		BRCA - Breast invasive adenocarcinoma(11;1.85e-05)|Colorectal(4;0.0101)|READ - Rectum adenocarcinoma(4;0.148)|COAD - Colon adenocarcinoma(4;0.179)		TGGTAGAGGCGAGACCAGGTA	0.498													G|||	45	0.00898562	0.0333	0.0014	5008	,	,		21003	0.0		0.0	False		,,,				2504	0.0				p.A909A		Atlas-SNP	.											.	MYOM2	251	.	0			c.G2727A						PASS	.	G		115,4291	86.8+/-125.4	2,111,2090	61.0	53.0	55.0		2727	-7.8	0.2	8	dbSNP_126	55	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MYOM2	NM_003970.2		2,112,6389	AA,AG,GG		0.0116,2.6101,0.8919		909/1466	2050564	116,12890	2203	4300	6503	SO:0001819	synonymous_variant	9172	exon21			AGAGGCGAGACCA		CCDS5957.1	8p23.3	2014-06-06	2012-10-17		ENSG00000036448	ENSG00000036448		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7614	protein-coding gene	gene with protein product		603509	"""myomesin (M-protein) 2 (165kD)"", ""myomesin (M-protein) 2, 165kDa"""				Standard	XM_006716237		Approved		uc003wpx.4	P54296	OTTHUMG00000129175	ENST00000262113.4:c.2727G>A	8.37:g.2050564G>A		53.0	0.0	0		53.0	21.0	0.396226	NM_003970	Q7Z3Y2	Silent	SNP	ENST00000262113.4	37	CCDS5957.1																																																																																			G|0.991;A|0.009	0.009	strong		0.498	MYOM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251249.1	NM_003970	
ADAM28	10863	hgsc.bcm.edu	37	8	24184088	24184088	+	Silent	SNP	G	G	T	rs113950884	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:24184088G>T	ENST00000265769.4	+	10	1022	c.912G>T	c.(910-912)acG>acT	p.T304T	RP11-624C23.1_ENST00000518988.1_RNA|ADAM28_ENST00000518516.1_3'UTR|ADAM28_ENST00000397649.3_Silent_p.T51T|RP11-624C23.1_ENST00000523700.1_RNA|RP11-624C23.1_ENST00000519689.1_RNA|ADAM28_ENST00000540823.1_Silent_p.T71T|ADAM28_ENST00000437154.2_Silent_p.T304T|RP11-624C23.1_ENST00000523578.1_RNA	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	304	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		TTGCTGGAACGACTGTGGGTC	0.348													G|||	3	0.000599042	0.0023	0.0	5008	,	,		17957	0.0		0.0	False		,,,				2504	0.0				p.T304T	NSCLC(193;488 2149 22258 34798 40734)	Atlas-SNP	.											.	ADAM28	100	.	0			c.G912T						PASS	.	G	,	20,4386	27.2+/-55.0	0,20,2183	316.0	276.0	289.0		912,912	-11.0	0.0	8	dbSNP_132	289	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	ADAM28	NM_014265.4,NM_021777.3	,	0,20,6483	TT,TG,GG		0.0,0.4539,0.1538	,	304/776,304/541	24184088	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	10863	exon10			TGGAACGACTGTG	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.912G>T	8.37:g.24184088G>T		217.0	0.0	0		216.0	106.0	0.490741	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Silent	SNP	ENST00000265769.4	37	CCDS34865.1																																																																																			G|0.998;T|0.002	0.002	strong		0.348	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778	
CACNA1H	8912	hgsc.bcm.edu	37	16	1255206	1255206	+	Silent	SNP	C	C	T	rs28365123	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1255206C>T	ENST00000348261.5	+	11	2792	c.2544C>T	c.(2542-2544)ggC>ggT	p.G848G	RP11-616M22.3_ENST00000564700.1_RNA|CACNA1H_ENST00000565831.1_Silent_p.G848G|CACNA1H_ENST00000358590.4_Silent_p.G848G	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	848			G -> S (in ECA6). {ECO:0000269|PubMed:12891677}.		aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	TGGCCTGCGGCCCTCTGGGCT	0.612													c|||	290	0.0579073	0.2057	0.0216	5008	,	,		14068	0.0		0.003	False		,,,				2504	0.0				p.G848G		Atlas-SNP	.											.	CACNA1H	317	.	0			c.C2544T						PASS	.		,	677,3501		66,545,1478	74.0	79.0	77.0		2544,2544	1.9	0.9	16	dbSNP_126	77	5,8423		0,5,4209	no	coding-synonymous,coding-synonymous	CACNA1H	NM_001005407.1,NM_021098.2	,	66,550,5687	TT,TC,CC		0.0593,16.2039,5.4101	,	848/2348,848/2354	1255206	682,11924	2089	4214	6303	SO:0001819	synonymous_variant	8912	exon11			CTGCGGCCCTCTG	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.2544C>T	16.37:g.1255206C>T		67.0	0.0	0		65.0	38.0	0.584615	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	37	CCDS45375.1																																																																																			C|0.953;T|0.047	0.047	strong		0.612	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
TREML1	340205	hgsc.bcm.edu	37	6	41117586	41117586	+	Missense_Mutation	SNP	T	T	G	rs34254490	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:41117586T>G	ENST00000426005.2	-	6	735	c.692A>C	c.(691-693)cAc>cCc	p.H231P	TREML1_ENST00000373127.4_3'UTR|TREML1_ENST00000437044.2_Missense_Mutation_p.H120P	NM_178174.2	NP_835468.1	Q86YW5	TRML1_HUMAN	triggering receptor expressed on myeloid cells-like 1	231	Pro-rich.		H -> P (in dbSNP:rs34254490).		calcium-mediated signaling (GO:0019722)|innate immune response (GO:0045087)|platelet activation (GO:0030168)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|platelet alpha granule (GO:0031091)				breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)	13	Ovarian(28;0.0418)|Colorectal(47;0.196)					AAGCCTAATGTGTGGTACATC	0.507													T|||	138	0.0275559	0.1029	0.0029	5008	,	,		19751	0.0		0.0	False		,,,				2504	0.0				p.H231P		Atlas-SNP	.											.	TREML1	20	.	0			c.A692C						PASS	.	T	PRO/HIS	347,4059	175.9+/-205.1	18,311,1874	174.0	154.0	161.0		692	4.5	0.0	6	dbSNP_126	161	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TREML1	NM_178174.2	77	18,312,6173	GG,GT,TT		0.0116,7.8756,2.6757	benign	231/312	41117586	348,12658	2203	4300	6503	SO:0001583	missense	340205	exon6			CTAATGTGTGGTA	AF534822	CCDS4851.1, CCDS64420.1, CCDS64421.1	6p21.1	2013-01-11			ENSG00000161911	ENSG00000161911		"""Immunoglobulin superfamily / V-set domain containing"""	20434	protein-coding gene	gene with protein product	"""TREM-like transcript 1"""	609714				12393607, 12645956	Standard	NM_178174		Approved	TLT1, dJ238O23.3	uc011duc.3	Q86YW5	OTTHUMG00000016231	ENST00000426005.2:c.692A>C	6.37:g.41117586T>G	ENSP00000402855:p.His231Pro	138.0	0.0	0		148.0	77.0	0.52027	NM_178174	Q496B3|Q8IWY1|Q8IWY2	Missense_Mutation	SNP	ENST00000426005.2	37	CCDS4851.1	49	0.022435897435897436	49	0.09959349593495935	0	0.0	0	0.0	0	0.0	T	12.67	2.007412	0.35415	0.078756	1.16E-4	ENSG00000161911	ENST00000373127;ENST00000437044	T	0.46819	0.86	5.71	4.52	0.55395	.	0.532842	0.17347	N	0.177556	T	0.16385	0.0394	N	0.19112	0.55	0.09310	N	1	B;B	0.22683	0.073;0.072	B;B	0.25405	0.06;0.027	T	0.18053	-1.0349	10	0.66056	D	0.02	.	9.718	0.40286	0.0:0.0:0.1745:0.8255	rs34254490;rs60023904	120;231	Q86YW5-3;Q86YW5	.;TRML1_HUMAN	P	231;120	ENSP00000400405:H120P	ENSP00000362219:H231P	H	-	2	0	TREML1	41225564	0.001000	0.12720	0.001000	0.08648	0.184000	0.23303	0.517000	0.22832	0.954000	0.37851	0.533000	0.62120	CAC	T|0.975;G|0.025	0.025	strong		0.507	TREML1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043538.2	NM_178174	
EPHA7	2045	hgsc.bcm.edu	37	6	93982100	93982100	+	Silent	SNP	C	C	T	rs34302170	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:93982100C>T	ENST00000369303.4	-	6	1549	c.1365G>A	c.(1363-1365)ctG>ctA	p.L455L		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	455	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		CACTCCGCTGCAGTACTCTCT	0.438													C|||	206	0.0411342	0.152	0.0029	5008	,	,		18429	0.0		0.003	False		,,,				2504	0.0				p.L455L		Atlas-SNP	.											.	EPHA7	251	.	0			c.G1365A						PASS	.	C		517,3889	237.7+/-249.4	30,457,1716	204.0	194.0	197.0		1365	5.7	1.0	6	dbSNP_126	197	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	EPHA7	NM_004440.3		30,464,6009	TT,TC,CC		0.0814,11.734,4.0289		455/999	93982100	524,12482	2203	4300	6503	SO:0001819	synonymous_variant	2045	exon6			CCGCTGCAGTACT	L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3390	protein-coding gene	gene with protein product		602190	"""EphA7"""			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.1365G>A	6.37:g.93982100C>T		224.0	0.0	0		174.0	92.0	0.528736	NM_004440	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Silent	SNP	ENST00000369303.4	37	CCDS5031.1																																																																																			C|0.963;T|0.037	0.037	strong		0.438	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1		
CCT8L2	150160	hgsc.bcm.edu	37	22	17071899	17071899	+	Silent	SNP	G	G	A	rs547801677	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:17071899G>A	ENST00000359963.3	-	1	1801	c.1542C>T	c.(1540-1542)ctC>ctT	p.L514L		NM_014406.4	NP_055221.1	Q96SF2	TCPQM_HUMAN	chaperonin containing TCP1, subunit 8 (theta)-like 2	514					anion transport (GO:0006820)|cellular protein metabolic process (GO:0044267)|potassium ion transmembrane transport (GO:0071805)|transport (GO:0006810)	cytoplasm (GO:0005737)	anion channel activity (GO:0005253)|ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)			breast(3)|endometrium(7)|kidney(1)|large_intestine(8)|liver(2)|lung(37)|ovary(3)|prostate(3)|skin(2)|stomach(1)	67	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				CTACAGTCACGAGCTGTAGCA	0.498													g|||	3	0.000599042	0.0	0.0	5008	,	,		18283	0.003		0.0	False		,,,				2504	0.0				p.L514L		Atlas-SNP	.											CCT8L2,NS,carcinoma,-2,2	CCT8L2	150	2	0			c.C1542T						PASS	.						103.0	96.0	98.0					22																	17071899		2203	4298	6501	SO:0001819	synonymous_variant	150160	exon1			AGTCACGAGCTGT	AP003553	CCDS13738.1	22q11.1	2011-09-01			ENSG00000198445	ENSG00000198445			15553	protein-coding gene	gene with protein product							Standard	NM_014406		Approved	CESK1	uc002zlp.1	Q96SF2	OTTHUMG00000141302	ENST00000359963.3:c.1542C>T	22.37:g.17071899G>A		148.0	0.0	0		173.0	94.0	0.543353	NM_014406	A4QPH3|Q9UJS3	Silent	SNP	ENST00000359963.3	37	CCDS13738.1																																																																																			.	.	none		0.498	CCT8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280580.1		
ZNF354C	30832	hgsc.bcm.edu	37	5	178505831	178505831	+	Missense_Mutation	SNP	A	A	G	rs57271258	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:178505831A>G	ENST00000315475.6	+	5	704	c.398A>G	c.(397-399)gAg>gGg	p.E133G		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	133					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.E133G(1)		endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|urinary_tract(3)	30	all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309)	all_cancers(40;0.19)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.247)		TTTGAGAGCGAGATAGAAGAA	0.378													G|||	122	0.024361	0.0862	0.0115	5008	,	,		20349	0.0		0.0	False		,,,				2504	0.0				p.E133G		Atlas-SNP	.											ZNF354C,caecum,carcinoma,0,1	ZNF354C	77	1	1	Substitution - Missense(1)	large_intestine(1)	c.A398G						PASS	.	G	GLY/GLU	312,4094	788.4+/-414.9	9,294,1900	90.0	95.0	93.0		398	1.0	0.0	5	dbSNP_129	93	0,8600		0,0,4300	yes	missense	ZNF354C	NM_014594.1	98	9,294,6200	GG,GA,AA		0.0,7.0813,2.3989	benign	133/555	178505831	312,12694	2203	4300	6503	SO:0001583	missense	30832	exon5			AGAGCGAGATAGA		CCDS4443.1	5q35	2013-01-08			ENSG00000177932	ENSG00000177932		"""Zinc fingers, C2H2-type"", ""-"""	16736	protein-coding gene	gene with protein product						10786630	Standard	NM_014594		Approved	KID3	uc003mju.3	Q86Y25	OTTHUMG00000130888	ENST00000315475.6:c.398A>G	5.37:g.178505831A>G	ENSP00000324064:p.Glu133Gly	187.0	0.0	0		179.0	99.0	0.553073	NM_014594	Q6P4P9|Q8NFX1	Missense_Mutation	SNP	ENST00000315475.6	37	CCDS4443.1	30	0.013736263736263736	27	0.054878048780487805	3	0.008287292817679558	0	0.0	0	0.0	G	7.305	0.613748	0.14066	0.070813	0.0	ENSG00000177932	ENST00000315475	T	0.05786	3.39	3.87	1.04	0.20106	.	.	.	.	.	T	0.00241	0.0007	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48747	-0.9008	9	0.16896	T	0.51	1.603	3.2954	0.06964	0.3129:0.0:0.505:0.182	rs57271258	133	Q86Y25	Z354C_HUMAN	G	133	ENSP00000324064:E133G	ENSP00000324064:E133G	E	+	2	0	ZNF354C	178438437	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.082000	0.03400	-0.148000	0.11234	-0.930000	0.02707	GAG	A|0.974;G|0.026	0.026	strong		0.378	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2		
ZNF444	55311	hgsc.bcm.edu	37	19	56671359	56671359	+	Missense_Mutation	SNP	C	C	G	rs145075834	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56671359C>G	ENST00000337080.3	+	5	1140	c.773C>G	c.(772-774)aCc>aGc	p.T258S	ZNF444_ENST00000592949.1_Missense_Mutation_p.T257S	NM_001253792.1|NM_018337.3	NP_001240721.1|NP_060807.2	Q8N0Y2	ZN444_HUMAN	zinc finger protein 444	258					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(1)|endometrium(1)|lung(5)	7		Colorectal(82;3.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0531)		TGTGGCAAGACCTTCTACTGG	0.746													C|||	62	0.0123802	0.0461	0.0014	5008	,	,		9131	0.0		0.0	False		,,,				2504	0.0				p.T258S		Atlas-SNP	.											.	ZNF444	15	.	0			c.C773G						PASS	.	C	SER/THR	95,3577		0,95,1741	3.0	2.0	3.0		773	3.4	1.0	19	dbSNP_134	3	0,7290		0,0,3645	yes	missense	ZNF444	NM_018337.2	58	0,95,5386	GG,GC,CC		0.0,2.5871,0.8666	probably-damaging	258/328	56671359	95,10867	1836	3645	5481	SO:0001583	missense	55311	exon5			GCAAGACCTTCTA	AB052954	CCDS12939.1, CCDS59426.1	19q13.43	2013-01-09			ENSG00000167685	ENSG00000167685		"""-"", ""Zinc fingers, C2H2-type"""	16052	protein-coding gene	gene with protein product		607874				11978792, 19760602	Standard	NM_001253792		Approved	ZSCAN17, FLJ11137, EZF2	uc002qmm.3	Q8N0Y2		ENST00000337080.3:c.773C>G	19.37:g.56671359C>G	ENSP00000338860:p.Thr258Ser	21.0	0.0	0		6.0	6.0	1	NM_018337	Q8TEQ9|Q8WU35|Q9NUU1	Missense_Mutation	SNP	ENST00000337080.3	37	CCDS12939.1	29	0.013278388278388278	28	0.056910569105691054	1	0.0027624309392265192	0	0.0	0	0.0	C	13.37	2.215791	0.39102	0.025871	0.0	ENSG00000167685	ENST00000337080	T	0.27402	1.67	3.43	3.43	0.39272	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.203463	0.24681	N	0.036467	T	0.01454	0.0047	N	0.01473	-0.845	0.24823	N	0.992574	B;P	0.48089	0.106;0.905	B;P	0.47118	0.047;0.538	T	0.07986	-1.0744	10	0.21540	T	0.41	.	12.7548	0.57328	0.0:1.0:0.0:0.0	.	257;258	Q8N0Y2-2;Q8N0Y2	.;ZN444_HUMAN	S	258	ENSP00000338860:T258S	ENSP00000338860:T258S	T	+	2	0	ZNF444	61363171	0.072000	0.21174	1.000000	0.80357	0.965000	0.64279	0.403000	0.20982	1.938000	0.56188	0.455000	0.32223	ACC	C|0.987;G|0.013	0.013	strong		0.746	ZNF444-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457503.1	NM_018337	
KNOP1	400506	hgsc.bcm.edu	37	16	19726124	19726124	+	Silent	SNP	G	G	A	rs58543897	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:19726124G>A	ENST00000219837.7	-	2	312	c.234C>T	c.(232-234)tgC>tgT	p.C78C	IQCK_ENST00000320394.6_5'Flank|KNOP1_ENST00000568230.1_5'Flank|AC002550.5_ENST00000565916.1_RNA	NM_001012991.2	NP_001013009.2	Q1ED39	KNOP1_HUMAN	lysine-rich nucleolar protein 1	78	Lys-rich.					nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)										CATGCTCCTCGCAAAGGGTGC	0.542													G|||	271	0.0541134	0.1906	0.0245	5008	,	,		18472	0.0		0.002	False		,,,				2504	0.0				p.C78C		Atlas-SNP	.											.	C16orf88	41	.	0			c.C234T						PASS	.	G		700,3352		55,590,1381	65.0	64.0	64.0		234	-9.2	0.0	16	dbSNP_129	64	22,8366		0,22,4172	no	coding-synonymous	C16orf88	NM_001012991.2		55,612,5553	AA,AG,GG		0.2623,17.2754,5.8039		78/459	19726124	722,11718	2026	4194	6220	SO:0001819	synonymous_variant	400506	exon2			CTCCTCGCAAAGG	BC047010	CCDS42127.1	16p12.3	2013-03-12	2013-03-12	2013-03-12	ENSG00000103550	ENSG00000103550			34404	protein-coding gene	gene with protein product	"""family with sequence similarity 191, member A"", ""testis-specific gene 118"""		"""chromosome 16 open reading frame 88"""	C16orf88			Standard	NM_001012991		Approved	101F10.1, FAM191A, TSG118	uc002dgq.3	Q1ED39		ENST00000219837.7:c.234C>T	16.37:g.19726124G>A		91.0	0.0	0		107.0	54.0	0.504673	NM_001012991	O43328|Q5FWF3	Silent	SNP	ENST00000219837.7	37	CCDS42127.1																																																																																			G|0.972;A|0.028	0.028	strong		0.542	KNOP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435993.2	NM_001012991	
TDP1	55775	hgsc.bcm.edu	37	14	90429858	90429858	+	Missense_Mutation	SNP	G	G	A	rs28365054	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:90429858G>A	ENST00000335725.4	+	3	650	c.400G>A	c.(400-402)Gcc>Acc	p.A134T	TDP1_ENST00000357382.3_5'UTR|TDP1_ENST00000555880.1_Missense_Mutation_p.A134T|TDP1_ENST00000393454.2_Missense_Mutation_p.A134T|TDP1_ENST00000393452.3_Missense_Mutation_p.A134T|TDP1_ENST00000555565.1_Intron	NM_018319.3	NP_060789.2	Q9NUW8	TYDP1_HUMAN	tyrosyl-DNA phosphodiesterase 1	134			A -> T (in dbSNP:rs28365054). {ECO:0000269|Ref.3}.		cell death (GO:0008219)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	3'-tyrosyl-DNA phosphodiesterase activity (GO:0017005)|double-stranded DNA binding (GO:0003690)|exonuclease activity (GO:0004527)|single-stranded DNA binding (GO:0003697)			NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|urinary_tract(1)	25		all_cancers(154;0.185)		COAD - Colon adenocarcinoma(157;0.23)		TGGCGCTCCCGCCTGCCACAG	0.527								Repair of DNA-protein crosslinks					G|||	530	0.105831	0.3336	0.0447	5008	,	,		20317	0.0089		0.0199	False		,,,				2504	0.0297				p.A134T		Atlas-SNP	.											.	TDP1	47	.	0			c.G400A						PASS	.	G	THR/ALA,THR/ALA	1239,3167	411.7+/-335.8	181,877,1145	48.0	45.0	46.0		400,400	-2.6	0.0	14	dbSNP_126	46	179,8421	80.1+/-142.7	3,173,4124	yes	missense,missense	TDP1	NM_001008744.1,NM_018319.3	58,58	184,1050,5269	AA,AG,GG		2.0814,28.1207,10.9027	benign,benign	134/609,134/609	90429858	1418,11588	2203	4300	6503	SO:0001583	missense	55775	exon3			GCTCCCGCCTGCC	AF182002	CCDS9888.1	14q32.11	2008-08-11				ENSG00000042088			18884	protein-coding gene	gene with protein product		607198				11839309, 12244316	Standard	XM_005267847		Approved	FLJ11090, SCAN1	uc001xxz.3	Q9NUW8		ENST00000335725.4:c.400G>A	14.37:g.90429858G>A	ENSP00000337353:p.Ala134Thr	80.0	0.0	0		99.0	54.0	0.545455	NM_018319	Q2HXX4|Q86TV8|Q96BK7|Q9NZM7|Q9NZM8	Missense_Mutation	SNP	ENST00000335725.4	37	CCDS9888.1	195	0.08928571428571429	155	0.3150406504065041	19	0.052486187845303865	8	0.013986013986013986	13	0.017150395778364115	G	6.023	0.372548	0.11409	0.281207	0.020814	ENSG00000042088	ENST00000393452;ENST00000554180;ENST00000393454;ENST00000553617;ENST00000335725;ENST00000556867;ENST00000553527;ENST00000553989;ENST00000556498;ENST00000555880	T;T;T;T;T;T;T;T;T;T	0.30981	1.51;2.25;1.75;2.22;1.75;1.87;1.87;1.87;1.91;1.52	5.36	-2.62	0.06152	.	1.082140	0.06853	N	0.797624	T	0.00012	0.0000	N	0.13043	0.29	0.58432	P	1.0000000000287557E-6	B;B;B;B	0.09022	0.001;0.001;0.001;0.002	B;B;B;B	0.06405	0.001;0.001;0.002;0.0	T	0.44390	-0.9331	9	0.13108	T	0.6	-10.0622	5.7326	0.18049	0.4341:0.0:0.4386:0.1273	rs28365054;rs35332925;rs28365054	134;134;134;134	G3V2F4;E7EPD8;G3V4W8;Q9NUW8	.;.;.;TYDP1_HUMAN	T	134;134;134;35;134;134;134;134;134;134	ENSP00000377098:A134T;ENSP00000450872:A134T;ENSP00000377099:A134T;ENSP00000450708:A35T;ENSP00000337353:A134T;ENSP00000452279:A134T;ENSP00000451358:A134T;ENSP00000452333:A134T;ENSP00000452183:A134T;ENSP00000450628:A134T	ENSP00000337353:A134T	A	+	1	0	TDP1	89499611	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.012000	0.13287	-0.617000	0.05664	-1.300000	0.01332	GCC	G|0.892;A|0.108	0.108	strong		0.527	TDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411239.1	NM_018319	
HOXD9	3235	hgsc.bcm.edu	37	2	176988765	176988765	+	Silent	SNP	C	C	T	rs35649704	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:176988765C>T	ENST00000249499.6	+	2	1330	c.921C>T	c.(919-921)aaC>aaT	p.N307N	HOXD-AS2_ENST00000440016.2_RNA	NM_014213.3	NP_055028.3	P28356	HXD9_HUMAN	homeobox D9	307					adult locomotory behavior (GO:0008344)|anterior/posterior pattern specification (GO:0009952)|embryonic forelimb morphogenesis (GO:0035115)|embryonic skeletal system morphogenesis (GO:0048704)|hindlimb morphogenesis (GO:0035137)|mammary gland development (GO:0030879)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(3)|lung(5)|prostate(1)	10			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.195)	Colorectal(32;0.0226)|READ - Rectum adenocarcinoma(9;0.0556)		TCCTCTTCAACATGTACCTCA	0.537													C|||	83	0.0165735	0.0613	0.0029	5008	,	,		17944	0.0		0.0	False		,,,				2504	0.0				p.N307N	GBM(47;924 952 7959 9248 12176)	Atlas-SNP	.											.	HOXD9	49	.	0			c.C921T						PASS	.	C		186,4220	118.8+/-156.5	4,178,2021	94.0	105.0	101.0		921	3.9	1.0	2	dbSNP_126	101	0,8600		0,0,4300	no	coding-synonymous	HOXD9	NM_014213.3		4,178,6321	TT,TC,CC		0.0,4.2215,1.4301		307/353	176988765	186,12820	2203	4300	6503	SO:0001819	synonymous_variant	3235	exon2			CTTCAACATGTAC		CCDS2267.2	2q31.1	2011-06-20	2005-12-22		ENSG00000128709	ENSG00000128709		"""Homeoboxes / ANTP class : HOXL subclass"""	5140	protein-coding gene	gene with protein product		142982	"""homeo box D9"""	HOX4C, HOX4		1973146, 1358459	Standard	NM_014213		Approved		uc010zex.2	P28356	OTTHUMG00000132516	ENST00000249499.6:c.921C>T	2.37:g.176988765C>T		162.0	0.0	0		170.0	86.0	0.505882	NM_014213	Q86ST1	Silent	SNP	ENST00000249499.6	37	CCDS2267.2																																																																																			C|0.987;T|0.013	0.013	strong		0.537	HOXD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255698.4		
C1orf168	199920	hgsc.bcm.edu	37	1	57186000	57186000	+	Silent	SNP	G	G	A	rs76493848	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:57186000G>A	ENST00000343433.6	-	18	2057	c.1977C>T	c.(1975-1977)taC>taT	p.Y659Y		NM_001004303.4	NP_001004303.3	Q5VWT5	CA168_HUMAN	chromosome 1 open reading frame 168	659										NS(1)|breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(13)|ovary(3)|skin(6)|stomach(1)|urinary_tract(2)	46						TCTCTTTGTCGTACTGAAATG	0.303													G|||	66	0.0131789	0.0469	0.0058	5008	,	,		15674	0.0		0.0	False		,,,				2504	0.0				p.Y659Y		Atlas-SNP	.											.	C1orf168	102	.	0			c.C1977T						PASS	.	G		207,4199	122.5+/-159.9	2,203,1998	52.0	52.0	52.0		1977	-0.1	0.6	1	dbSNP_132	52	3,8587	1.2+/-3.3	0,3,4292	no	coding-synonymous	C1orf168	NM_001004303.4		2,206,6290	AA,AG,GG		0.0349,4.6981,1.6159		659/729	57186000	210,12786	2203	4295	6498	SO:0001819	synonymous_variant	199920	exon18			TTTGTCGTACTGA	BX648439	CCDS30729.1	1p32.2	2011-02-22			ENSG00000187889	ENSG00000187889			27295	protein-coding gene	gene with protein product						14702039	Standard	NM_001004303		Approved	RP4-758N20.2, FLJ43208	uc001cym.4	Q5VWT5	OTTHUMG00000008281	ENST00000343433.6:c.1977C>T	1.37:g.57186000G>A		103.0	0.0	0		86.0	41.0	0.476744	NM_001004303	Q63HM3|Q6ZUY6	Silent	SNP	ENST00000343433.6	37	CCDS30729.1																																																																																			G|0.987;A|0.013	0.013	strong		0.303	C1orf168-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022751.2	NM_001004303	
CR1L	1379	hgsc.bcm.edu	37	1	207890818	207890818	+	Missense_Mutation	SNP	G	G	A	rs113806677	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:207890818G>A	ENST00000508064.2	+	11	1484	c.1424G>A	c.(1423-1425)tGt>tAt	p.C475Y		NM_175710.1	NP_783641.1	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	475	Sushi 8. {ECO:0000255|PROSITE- ProRule:PRU00302}.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|receptor complex (GO:0043235)				endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						GAAATCTTTTGTCCAAATCCT	0.388													g|||	139	0.0277556	0.1014	0.0072	5008	,	,		18100	0.0		0.0	False		,,,				2504	0.0				p.C475Y		Atlas-SNP	.											CR1L_ENST00000508064,NS,carcinoma,-1,1	CR1L	97	1	0			c.G1424A						PASS	.	G	TYR/CYS	344,3278		18,308,1485	80.0	74.0	76.0		1424	3.0	0.1	1	dbSNP_132	76	1,8137		0,1,4068	yes	missense	CR1L	NM_175710.1	194	18,309,5553	AA,AG,GG		0.0123,9.4975,2.9337	probably-damaging	475/570	207890818	345,11415	1811	4069	5880	SO:0001583	missense	1379	exon11			TCTTTTGTCCAAA	AY114160	CCDS44310.1	1q32.1	2008-02-05			ENSG00000197721	ENSG00000197721		"""Complement system"""	2335	protein-coding gene	gene with protein product		605886				2295627	Standard	NM_175710		Approved		uc001hga.4	Q2VPA4	OTTHUMG00000036354	ENST00000508064.2:c.1424G>A	1.37:g.207890818G>A	ENSP00000421736:p.Cys475Tyr	262.0	0.0	0		210.0	112.0	0.533333	NM_175710	Q32MC9|Q8NEU7	Missense_Mutation	SNP	ENST00000508064.2	37	CCDS44310.1	52	0.023809523809523808	50	0.1016260162601626	2	0.0055248618784530384	0	0.0	0	0.0	.	14.21	2.467416	0.43839	0.094975	1.23E-4	ENSG00000197721	ENST00000508064	D	0.99784	-6.74	3.01	3.01	0.34805	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	D	0.95401	0.8507	H	0.99719	4.725	0.25098	N	0.99081	D	0.89917	1.0	D	0.97110	1.0	T	0.80630	-0.1297	9	0.87932	D	0	.	10.1225	0.42630	0.0:0.0:1.0:0.0	.	475	Q2VPA4	CR1L_HUMAN	Y	475	ENSP00000421736:C475Y	ENSP00000421736:C475Y	C	+	2	0	CR1L	205957441	0.981000	0.34729	0.142000	0.22268	0.288000	0.27193	4.125000	0.57931	1.639000	0.50556	0.305000	0.20034	TGT	G|0.976;A|0.024	0.024	strong		0.388	CR1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390247.1	XM_114735	
SRP68	6730	hgsc.bcm.edu	37	17	74060168	74060168	+	Silent	SNP	T	T	C	rs58471646	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:74060168T>C	ENST00000307877.2	-	4	611	c.450A>G	c.(448-450)cgA>cgG	p.R150R	SRP68_ENST00000355113.5_Silent_p.R49R|SRP68_ENST00000539137.1_Silent_p.R112R	NM_014230.3	NP_055045.2	Q9UHB9	SRP68_HUMAN	signal recognition particle 68kDa	150					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)|ribosome (GO:0005840)|signal recognition particle, endoplasmic reticulum targeting (GO:0005786)	7S RNA binding (GO:0008312)|endoplasmic reticulum signal peptide binding (GO:0030942)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			NS(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(5)|lung(4)|ovary(2)|prostate(3)	23						GAAACCGTTTTCGGGGTTCAG	0.502													T|||	393	0.0784744	0.2806	0.0317	5008	,	,		19465	0.0		0.0	False		,,,				2504	0.0				p.R150R		Atlas-SNP	.											SRP68,rectum,carcinoma,-1,1	SRP68	61	1	0			c.A450G						scavenged	.	T		1023,3383	380.2+/-323.6	119,785,1299	189.0	162.0	171.0		450	0.2	1.0	17	dbSNP_129	171	19,8581	11.2+/-40.8	0,19,4281	no	coding-synonymous	SRP68	NM_014230.2		119,804,5580	CC,CT,TT		0.2209,23.2183,8.0117		150/628	74060168	1042,11964	2203	4300	6503	SO:0001819	synonymous_variant	6730	exon4			CCGTTTTCGGGGT	AF195951	CCDS11738.1, CCDS58600.1, CCDS58601.1	17q25.1	2010-04-30	2002-08-29		ENSG00000167881	ENSG00000167881			11302	protein-coding gene	gene with protein product		604858	"""signal recognition particle 68kD"""			10618370	Standard	NM_014230		Approved		uc002jqk.2	Q9UHB9		ENST00000307877.2:c.450A>G	17.37:g.74060168T>C		222.0	1.0	0.0045045		273.0	115.0	0.421245	NM_014230	B3KUU5|B3KWY7|G3V1U4|Q8NCJ4|Q8WUK2	Silent	SNP	ENST00000307877.2	37	CCDS11738.1																																																																																			T|0.925;C|0.075	0.075	strong		0.502	SRP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449487.1	NM_014230	
HMHA1	23526	hgsc.bcm.edu	37	19	1079968	1079968	+	Silent	SNP	G	G	A	rs34047143	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1079968G>A	ENST00000313093.2	+	13	1785	c.1554G>A	c.(1552-1554)gcG>gcA	p.A518A	HMHA1_ENST00000536472.1_Silent_p.A358A|HMHA1_ENST00000590214.1_Silent_p.A545A|HMHA1_ENST00000586866.1_Silent_p.A522A|HMHA1_ENST00000543365.1_Silent_p.A401A|HMHA1_ENST00000539243.2_Silent_p.A534A|HMHA1_ENST00000590577.1_Silent_p.A153A	NM_012292.3	NP_036424.2	Q92619	HMHA1_HUMAN	histocompatibility (minor) HA-1	518					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|lung(7)|ovary(1)|prostate(2)	16		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|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)		TGCAGACGGCGCCGCTGCCCG	0.672													G|||	176	0.0351438	0.1309	0.0043	5008	,	,		15158	0.0		0.0	False		,,,				2504	0.0				p.A534A		Atlas-SNP	.											.	HMHA1	78	.	0			c.G1602A						PASS	.	G		481,3925	223.3+/-239.8	28,425,1750	74.0	80.0	78.0		1554	-6.9	1.0	19	dbSNP_126	78	0,8600		0,0,4300	no	coding-synonymous	HMHA1	NM_012292.2		28,425,6050	AA,AG,GG		0.0,10.9169,3.6983		518/1137	1079968	481,12525	2203	4300	6503	SO:0001819	synonymous_variant	23526	exon13			GACGGCGCCGCTG	D86976	CCDS32863.1, CCDS58637.1, CCDS74242.1, CCDS74243.1	19p13.3	2011-09-07				ENSG00000180448		"""Rho GTPase activating proteins"""	17102	protein-coding gene	gene with protein product		601155				9820596, 9039502	Standard	NM_012292		Approved	KIAA0223, HA-1, ARHGAP45	uc010xgd.2	Q92619		ENST00000313093.2:c.1554G>A	19.37:g.1079968G>A		78.0	0.0	0		84.0	42.0	0.5	NM_001258328	B4DTS4|F6QP70|Q6P189|Q7LE26|Q86WS1|Q8HX84|Q9GJN9|Q9GJP0|Q9GJP1|Q9MY24	Silent	SNP	ENST00000313093.2	37	CCDS32863.1																																																																																			G|0.962;A|0.038	0.038	strong		0.672	HMHA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458026.1		
GNMT	27232	hgsc.bcm.edu	37	6	42930877	42930877	+	Silent	SNP	G	G	A	rs147291064	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:42930877G>A	ENST00000372808.3	+	4	529	c.519G>A	c.(517-519)ctG>ctA	p.L173L		NM_018960.4	NP_061833.1	Q14749	GNMT_HUMAN	glycine N-methyltransferase	173					cellular protein modification process (GO:0006464)|glycogen metabolic process (GO:0005977)|methionine metabolic process (GO:0006555)|one-carbon metabolic process (GO:0006730)|protein homotetramerization (GO:0051289)|regulation of gluconeogenesis (GO:0006111)|S-adenosylmethionine metabolic process (GO:0046500)	cytoplasm (GO:0005737)	folic acid binding (GO:0005542)|glycine binding (GO:0016594)|glycine N-methyltransferase activity (GO:0017174)			kidney(2)|large_intestine(1)|lung(1)	4	Colorectal(47;0.196)		all cancers(41;0.00196)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0461)		Glycine(DB00145)|S-Adenosylmethionine(DB00118)	GGGGCCTACTGGTCATTGATC	0.602													G|||	47	0.00938498	0.034	0.0029	5008	,	,		11061	0.0		0.0	False		,,,				2504	0.0				p.L173L		Atlas-SNP	.											.	GNMT	13	.	0			c.G519A						PASS	.	G		88,4318	74.7+/-112.8	0,88,2115	42.0	40.0	41.0		519	3.9	1.0	6	dbSNP_134	41	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	GNMT	NM_018960.4		0,91,6412	AA,AG,GG		0.0349,1.9973,0.6997		173/296	42930877	91,12915	2203	4300	6503	SO:0001819	synonymous_variant	27232	exon4			CCTACTGGTCATT	AF101475	CCDS4876.1	6p12	2008-02-05			ENSG00000124713	ENSG00000124713			4415	protein-coding gene	gene with protein product		606628				10843803, 9495250	Standard	NM_018960		Approved		uc003otd.3	Q14749	OTTHUMG00000014712	ENST00000372808.3:c.519G>A	6.37:g.42930877G>A		65.0	0.0	0		82.0	39.0	0.47561	NM_018960	Q5T8W2|Q9NNZ1|Q9NS24	Silent	SNP	ENST00000372808.3	37	CCDS4876.1																																																																																			G|0.993;A|0.007	0.007	strong		0.602	GNMT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040568.1	NM_018960	
LPP	4026	hgsc.bcm.edu	37	3	188327555	188327555	+	Missense_Mutation	SNP	T	T	C	rs7645635	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:188327555T>C	ENST00000312675.4	+	6	1282	c.1036T>C	c.(1036-1038)Tat>Cat	p.Y346H	LPP_ENST00000448637.1_Missense_Mutation_p.Y346H|LPP_ENST00000543006.1_Missense_Mutation_p.Y346H|LPP_ENST00000471917.1_3'UTR	NM_001167672.1|NM_005578.3	NP_001161144.1|NP_005569.1	Q93052	LPP_HUMAN	LIM domain containing preferred translocation partner in lipoma	346	Pro-rich.		Y -> H (in dbSNP:rs7645635).		cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)		HMGA2/LPP(161)	NS(1)|breast(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		TCCTGGGATGTATCCAGTCAC	0.522			T	"""HMGA2, MLL, C12orf9"""	"""lipoma, leukemia"""								T|||	1002	0.20008	0.7126	0.0764	5008	,	,		18753	0.0		0.005	False		,,,				2504	0.002				p.Y346H		Atlas-SNP	.		Dom	yes		3	3q28	4026	LIM domain containing preferred translocation partner in lipoma		"""L, M"""	.	LPP	72	.	0			c.T1036C						PASS	.	T	HIS/TYR,,HIS/TYR	2581,1825		769,1043,391	42.0	42.0	42.0		1036,,1036	6.2	0.9	3	dbSNP_116	42	34,8564		0,34,4265	yes	missense,intron,missense	LPP	NM_001167671.1,NM_001167672.1,NM_005578.3	83,,83	769,1077,4656	CC,CT,TT		0.3954,41.4208,20.1092	probably-damaging,,probably-damaging	346/613,,346/613	188327555	2615,10389	2203	4299	6502	SO:0001583	missense	4026	exon6			GGGATGTATCCAG	AL833171	CCDS3291.1	3q27-q28	2004-03-02	2002-01-14		ENSG00000145012	ENSG00000145012			6679	protein-coding gene	gene with protein product		600700	"""LIM domain-containing preferred translocation partner in lipoma"""			8812423	Standard	XM_005247453		Approved		uc003frs.2	Q93052	OTTHUMG00000156387	ENST00000312675.4:c.1036T>C	3.37:g.188327555T>C	ENSP00000318089:p.Tyr346His	116.0	0.0	0		111.0	52.0	0.468468	NM_005578	A1L4L6|D3DNV6|Q8NFX5	Missense_Mutation	SNP	ENST00000312675.4	37	CCDS3291.1	360	0.16483516483516483	328	0.6666666666666666	28	0.07734806629834254	0	0.0	4	0.005277044854881266	T	16.16	3.043406	0.55003	0.585792	0.003954	ENSG00000145012	ENST00000448637;ENST00000312675;ENST00000543006;ENST00000415906	T;T;T;T	0.54866	1.79;0.55;0.55;1.41	6.17	6.17	0.99709	.	0.188754	0.37348	N	0.002140	T	0.00012	0.0000	M	0.66939	2.045	0.22050	P	0.999392708	D;D	0.89917	1.0;0.999	D;D	0.91635	0.999;0.965	T	0.47611	-0.9104	9	0.15499	T	0.54	.	16.0034	0.80327	0.0:0.0:0.0:1.0	rs7645635;rs52823079;rs57290235;rs7645635	346;346	C9JUT4;Q93052	.;LPP_HUMAN	H	346;346;346;183	ENSP00000393602:Y346H;ENSP00000318089:Y346H;ENSP00000438891:Y346H;ENSP00000393008:Y183H	ENSP00000318089:Y346H	Y	+	1	0	LPP	189810249	1.000000	0.71417	0.850000	0.33497	0.194000	0.23727	5.358000	0.66064	2.371000	0.80710	0.533000	0.62120	TAT	T|0.786;C|0.214	0.214	strong		0.522	LPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344030.1	NM_005578	
MYO7B	4648	hgsc.bcm.edu	37	2	128378009	128378009	+	Missense_Mutation	SNP	G	G	A	rs199900811	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128378009G>A	ENST00000409816.2	+	25	3447	c.3415G>A	c.(3415-3417)Ggc>Agc	p.G1139S	MYO7B_ENST00000389524.4_Missense_Mutation_p.G1139S|MYO7B_ENST00000409090.1_5'UTR|MYO7B_ENST00000428314.1_Missense_Mutation_p.G1139S			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1139	MyTH4 1. {ECO:0000255|PROSITE- ProRule:PRU00359}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		CCTCTGCCTCGGCTGCTTCCC	0.607													G|||	13	0.00259585	0.0098	0.0	5008	,	,		14187	0.0		0.0	False		,,,				2504	0.0				p.G1139S		Atlas-SNP	.											.	MYO7B	359	.	0			c.G3415A						PASS	.	G	SER/GLY	30,3642		0,30,1806	33.0	36.0	35.0		3415	4.2	1.0	2		35	0,8174		0,0,4087	yes	missense	MYO7B	NM_001080527.1	56	0,30,5893	AA,AG,GG		0.0,0.817,0.2533	probably-damaging	1139/2117	128378009	30,11816	1836	4087	5923	SO:0001583	missense	4648	exon26			TGCCTCGGCTGCT		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"""Myosins / Myosin superfamily : Class VII"""	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.3415G>A	2.37:g.128378009G>A	ENSP00000386461:p.Gly1139Ser	205.0	0.0	0		236.0	120.0	0.508475	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	37	CCDS46405.1	6	0.0027472527472527475	2	0.0040650406504065045	0	0.0	3	0.005244755244755245	1	0.0013192612137203166	.	26.3	4.726017	0.89298	0.00817	0.0	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000409816	D;D;D	0.91407	-2.84;-2.84;-2.84	4.16	4.16	0.48862	MyTH4 domain (3);	0.000000	0.85682	D	0.000000	D	0.91074	0.7191	L	0.48986	1.54	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	D	0.89742	0.3934	10	0.25106	T	0.35	.	17.0488	0.86513	0.0:0.0:1.0:0.0	.	1139	Q6PIF6	MYO7B_HUMAN	S	1139	ENSP00000374175:G1139S;ENSP00000415090:G1139S;ENSP00000386461:G1139S	ENSP00000374175:G1139S	G	+	1	0	MYO7B	128094479	1.000000	0.71417	1.000000	0.80357	0.911000	0.54048	8.993000	0.93524	2.318000	0.78349	0.456000	0.33151	GGC	G|0.997;A|0.003	0.003	strong		0.607	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
SPTA1	6708	hgsc.bcm.edu	37	1	158623092	158623092	+	Missense_Mutation	SNP	T	T	A	rs145054175	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158623092T>A	ENST00000368147.4	-	22	3340	c.3160A>T	c.(3160-3162)Acc>Tcc	p.T1054S		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1054					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TGGCGCTGGGTGATGTTTCCT	0.517													T|||	25	0.00499201	0.0182	0.0014	5008	,	,		15465	0.0		0.0	False		,,,				2504	0.0				p.T1054S		Atlas-SNP	.											SPTA1,NS,carcinoma,+1,1	SPTA1	720	1	0			c.A3160T						scavenged	.	T	SER/THR	56,3900		0,56,1922	118.0	122.0	120.0		3160	-1.3	0.2	1	dbSNP_134	120	0,8344		0,0,4172	yes	missense	SPTA1	NM_003126.2	58	0,56,6094	AA,AT,TT		0.0,1.4156,0.4553	benign	1054/2420	158623092	56,12244	1978	4172	6150	SO:0001583	missense	6708	exon22			GCTGGGTGATGTT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.3160A>T	1.37:g.158623092T>A	ENSP00000357129:p.Thr1054Ser	137.0	2.0	0.0145985		124.0	62.0	0.5	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	T	12.06	1.823290	0.32237	0.014156	0.0	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.65916	-0.18;-0.18	5.15	-1.33	0.09172	Src homology-3 domain (1);	2.011270	0.03053	N	0.154860	T	0.13457	0.0326	N	0.03608	-0.345	0.09310	N	1	B	0.10296	0.003	B	0.09377	0.004	T	0.07790	-1.0754	10	0.10636	T	0.68	.	8.2403	0.31656	0.0:0.5787:0.1365:0.2848	.	1054	P02549	SPTA1_HUMAN	S	1054	ENSP00000357130:T1054S;ENSP00000357129:T1054S	ENSP00000357129:T1054S	T	-	1	0	SPTA1	156889716	0.008000	0.16893	0.150000	0.22450	0.671000	0.39405	0.091000	0.15046	-0.379000	0.07906	-1.139000	0.01908	ACC	T|0.996;A|0.004	0.004	strong		0.517	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
SIGLEC12	89858	hgsc.bcm.edu	37	19	51994926	51994926	+	Missense_Mutation	SNP	T	T	C	rs7245807	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:51994926T>C	ENST00000291707.3	-	8	1812	c.1757A>G	c.(1756-1758)tAt>tGt	p.Y586C	SIGLEC12_ENST00000598614.1_Missense_Mutation_p.Y468C	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	586			Y -> C (in dbSNP:rs7245807).		cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|biliary_tract(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(1)|lung(23)|ovary(4)|prostate(2)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)	61		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		GGAGTACTCATAGCCGATGGC	0.572													t|||	234	0.0467252	0.1437	0.0144	5008	,	,		14528	0.0327		0.001	False		,,,				2504	0.0				p.Y586C		Atlas-SNP	.											.	SIGLEC12	243	.	0			c.A1757G						PASS	.	T	CYS/TYR,CYS/TYR	523,3883		36,451,1716	122.0	106.0	111.0		1403,1757	-4.5	0.0	19	dbSNP_116	111	5,8595		0,5,4295	yes	missense,missense	SIGLEC12	NM_033329.1,NM_053003.2	194,194	36,456,6011	CC,CT,TT		0.0581,11.8702,4.0597	benign,benign	468/478,586/596	51994926	528,12478	2203	4300	6503	SO:0001583	missense	89858	exon8			TACTCATAGCCGA	AF282256	CCDS12833.1, CCDS59416.1	19q13.41	2013-01-29	2011-06-29	2004-10-20	ENSG00000254521	ENSG00000254521		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15482	protein-coding gene	gene with protein product		606094	"""SIGLEC-like 1"", ""sialic acid binding Ig-like lectin 12"""	SIGLECL1		11409877, 11328818, 21555517	Standard	NM_053003		Approved	SLG, S2V, Siglec-XII, Siglec-12, Siglec-L1	uc002pwx.1	Q96PQ1	OTTHUMG00000165524	ENST00000291707.3:c.1757A>G	19.37:g.51994926T>C	ENSP00000291707:p.Tyr586Cys	113.0	0.0	0		124.0	71.0	0.572581	NM_053003	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	37	CCDS12833.1	91	0.041666666666666664	66	0.13414634146341464	6	0.016574585635359115	19	0.033216783216783216	0	0.0	.	0.031	-1.337170	0.01287	0.118702	5.81E-4	ENSG00000254521	ENST00000291707	T	0.04654	3.58	2.23	-4.47	0.03525	.	.	.	.	.	T	0.00039	0.0001	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.39502	-0.9611	9	0.44086	T	0.13	.	0.9451	0.01364	0.1876:0.1548:0.2634:0.3942	rs7245807;rs59181054;rs7245807	586;468	Q96PQ1;Q96PQ1-2	SIG12_HUMAN;.	C	586	ENSP00000291707:Y586C	ENSP00000291707:Y586C	Y	-	2	0	SIGLEC12	56686738	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.806000	0.00361	-5.302000	0.00017	-1.158000	0.01797	TAT	T|0.956;C|0.044	0.044	strong		0.572	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003	
PTGFR	5737	hgsc.bcm.edu	37	1	78959081	78959081	+	Missense_Mutation	SNP	T	T	C	rs115994459	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:78959081T>C	ENST00000370757.3	+	2	890	c.653T>C	c.(652-654)tTg>tCg	p.L218S	PTGFR_ENST00000370756.3_Missense_Mutation_p.L218S|PTGFR_ENST00000370758.1_Missense_Mutation_p.L218S	NM_000959.3	NP_000950.1	P43088	PF2R_HUMAN	prostaglandin F receptor (FP)	218					calcium-mediated signaling using intracellular calcium source (GO:0035584)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of apoptotic process (GO:0043066)|parturition (GO:0007567)|response to lipopolysaccharide (GO:0032496)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	prostaglandin F receptor activity (GO:0004958)			breast(6)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	33				Colorectal(170;0.248)	Bimatoprost(DB00905)|Dinoprost Tromethamine(DB01160)|Latanoprost(DB00654)|Tafluprost(DB08819)|Travoprost(DB00287)	GTTTCATTGTTGTGCAATGCA	0.378													T|||	22	0.00439297	0.0129	0.0058	5008	,	,		20200	0.0		0.001	False		,,,				2504	0.0				p.L218S		Atlas-SNP	.											.	PTGFR	121	.	0			c.T653C						PASS	.	T	SER/LEU,SER/LEU	58,4348	58.1+/-94.6	1,56,2146	62.0	65.0	64.0		653,653	4.7	0.6	1	dbSNP_132	64	0,8600		0,0,4300	yes	missense,missense	PTGFR	NM_000959.3,NM_001039585.1	145,145	1,56,6446	CC,CT,TT		0.0,1.3164,0.4459	benign,benign	218/360,218/298	78959081	58,12948	2203	4300	6503	SO:0001583	missense	5737	exon2			CATTGTTGTGCAA	AF004021	CCDS686.1, CCDS30759.1	1p31.1	2012-08-08			ENSG00000122420	ENSG00000122420		"""GPCR / Class A : Prostanoid receptors"""	9600	protein-coding gene	gene with protein product		600563				8300593, 7759114	Standard	XM_006710781		Approved	FP	uc001din.3	P43088	OTTHUMG00000009644	ENST00000370757.3:c.653T>C	1.37:g.78959081T>C	ENSP00000359793:p.Leu218Ser	126.0	0.0	0		142.0	61.0	0.429577	NM_000959	A8K9Y0|Q2KHP3|Q6RYQ6|Q9P1X4	Missense_Mutation	SNP	ENST00000370757.3	37	CCDS686.1	9	0.004120879120879121	6	0.012195121951219513	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	T	12.84	2.059053	0.36373	0.013164	0.0	ENSG00000122420	ENST00000370758;ENST00000370757;ENST00000370756	T;T;T	0.38887	1.11;1.11;1.11	5.85	4.73	0.59995	GPCR, rhodopsin-like superfamily (1);	0.414998	0.24801	N	0.035481	T	0.12817	0.0311	N	0.16903	0.455	0.34244	D	0.677948	B;B	0.16166	0.001;0.016	B;B	0.17433	0.008;0.018	T	0.05784	-1.0864	10	0.33940	T	0.23	-2.4004	11.3546	0.49609	0.0:0.0715:0.0:0.9285	.	218;218	P43088;P43088-2	PF2R_HUMAN;.	S	218	ENSP00000359794:L218S;ENSP00000359793:L218S;ENSP00000359792:L218S	ENSP00000359792:L218S	L	+	2	0	PTGFR	78731669	1.000000	0.71417	0.551000	0.28230	0.878000	0.50629	3.960000	0.56752	1.168000	0.42723	0.533000	0.62120	TTG	T|0.995;C|0.005	0.005	strong		0.378	PTGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026582.1	NM_000959	
CEMP1	752014	hgsc.bcm.edu	37	16	2580912	2580912	+	Missense_Mutation	SNP	T	T	C	rs13331643	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2580912T>C	ENST00000567119.1	-	1	497	c.163A>G	c.(163-165)Aag>Gag	p.K55E	AMDHD2_ENST00000565570.1_3'UTR|AMDHD2_ENST00000413459.3_3'UTR|CEMP1_ENST00000565480.1_Intron|MIR3178_ENST00000581887.1_RNA|CEMP1_ENST00000382350.1_Missense_Mutation_p.K55E|AMDHD2_ENST00000302956.4_3'UTR	NM_001048212.3	NP_001041677.1	Q6PRD7	CEMP1_HUMAN	cementum protein 1	55			K -> E (in dbSNP:rs13331643).			cytoplasm (GO:0005737)				lung(1)|skin(1)	2						GCGCACCCCTTAGGAAGTGGC	0.657													C|||	358	0.0714856	0.2564	0.0231	5008	,	,		20272	0.0		0.002	False		,,,				2504	0.001				p.K55E		Atlas-SNP	.											.	CEMP1	17	.	0			c.A163G						PASS	.	C	,GLU/LYS	839,3203		88,663,1270	36.0	42.0	40.0		,163	-0.1	0.0	16	dbSNP_121	40	12,8334		0,12,4161	yes	utr-3,missense	AMDHD2,CEMP1	NM_001145815.1,NM_001048212.3	,56	88,675,5431	CC,CT,TT		0.1438,20.7571,6.8696	,benign	,55/248	2580912	851,11537	2021	4173	6194	SO:0001583	missense	752014	exon1			ACCCCTTAGGAAG	AY584596	CCDS42108.1	16p13.3	2006-09-22							32553	protein-coding gene	gene with protein product	"""cementum protein-23"""	611113				16263347	Standard	NM_001048212		Approved	CP-23	uc002cqr.3	Q6PRD7		ENST00000567119.1:c.163A>G	16.37:g.2580912T>C	ENSP00000457380:p.Lys55Glu	79.0	0.0	0		85.0	85.0	1	NM_001048212	B2RUY1	Missense_Mutation	SNP	ENST00000567119.1	37	CCDS42108.1	124	0.056776556776556776	118	0.23983739837398374	6	0.016574585635359115	0	0.0	0	0.0	C	4.436	0.080653	0.08533	0.207571	0.001438	ENSG00000205923	ENST00000382350	T	0.54675	0.56	0.977	-0.126	0.13515	.	.	.	.	.	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	0.18681	-1.0329	8	0.87932	D	0	.	1.8024	0.03073	0.3218:0.4366:0.0:0.2416	rs13331643;rs13331643	55	Q6PRD7	CEMP1_HUMAN	E	55	ENSP00000371787:K55E	ENSP00000371787:K55E	K	-	1	0	CEMP1	2520913	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.745000	0.04834	-0.526000	0.06383	-1.124000	0.02001	AAG	T|0.955;C|0.045	0.045	strong		0.657	CEMP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435686.1	NM_001048212	
CGN	57530	hgsc.bcm.edu	37	1	151496718	151496718	+	Missense_Mutation	SNP	C	C	T	rs16833336	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:151496718C>T	ENST00000271636.7	+	7	1418	c.1285C>T	c.(1285-1287)Cgc>Tgc	p.R429C		NM_020770.2	NP_065821.1	Q9P2M7	CING_HUMAN	cingulin	423	Glu-rich.				transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|myosin complex (GO:0016459)|tight junction (GO:0005923)	actin binding (GO:0003779)|motor activity (GO:0003774)			NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	Ovarian(49;0.0273)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		LUSC - Lung squamous cell carcinoma(543;0.181)			GAACATGAAGCGCCTCTTGGA	0.433													C|||	189	0.0377396	0.1377	0.0058	5008	,	,		20806	0.0		0.003	False		,,,				2504	0.0				p.R429C		Atlas-SNP	.											CGN,colon,carcinoma,-1,2	CGN	106	2	0			c.C1285T						PASS	.	C	CYS/ARG	482,3924	225.6+/-241.4	29,424,1750	72.0	67.0	69.0		1285	4.0	1.0	1	dbSNP_123	69	6,8594	4.3+/-15.6	0,6,4294	yes	missense	CGN	NM_020770.2	180	29,430,6044	TT,TC,CC		0.0698,10.9396,3.7521	benign	429/1204	151496718	488,12518	2203	4300	6503	SO:0001583	missense	57530	exon7			ATGAAGCGCCTCT	AB037740	CCDS999.1	1q21	2008-02-05			ENSG00000143375	ENSG00000143375			17429	protein-coding gene	gene with protein product		609473				11042084, 12529927	Standard	NM_020770		Approved	KIAA1319	uc009wmw.3	Q9P2M7	OTTHUMG00000012497	ENST00000271636.7:c.1285C>T	1.37:g.151496718C>T	ENSP00000271636:p.Arg429Cys	67.0	0.0	0		85.0	34.0	0.4	NM_020770	A6H8L3|A7MD22|Q5T386|Q9NR25	Missense_Mutation	SNP	ENST00000271636.7	37	CCDS999.1	79	0.036172161172161175	77	0.1565040650406504	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	15.65	2.896561	0.52121	0.109396	6.98E-4	ENSG00000143375	ENST00000271636	T	0.63417	-0.04	4.95	4.02	0.46733	.	0.429980	0.25004	N	0.033881	T	0.19248	0.0462	N	0.08118	0	0.26850	N	0.96819	P	0.46327	0.876	B	0.34452	0.183	T	0.04781	-1.0927	10	0.72032	D	0.01	0.3796	10.5107	0.44860	0.1942:0.8058:0.0:0.0	rs16833336;rs16833336	423	Q9P2M7	CING_HUMAN	C	429	ENSP00000271636:R429C	ENSP00000271636:R429C	R	+	1	0	CGN	149763342	0.706000	0.27856	0.997000	0.53966	0.893000	0.52053	0.899000	0.28417	1.041000	0.40125	0.491000	0.48974	CGC	C|0.961;T|0.039	0.039	strong		0.433	CGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034900.3	NM_020770	
CD109	135228	hgsc.bcm.edu	37	6	74521948	74521948	+	Silent	SNP	G	G	T	rs61063525	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:74521948G>T	ENST00000287097.5	+	29	3835	c.3723G>T	c.(3721-3723)acG>acT	p.T1241T	CD109_ENST00000422508.2_Silent_p.T1164T|CD109_ENST00000437994.2_Silent_p.T1224T			Q6YHK3	CD109_HUMAN	CD109 molecule	1241			T -> M (in dbSNP:rs2917862). {ECO:0000269|PubMed:11861284, ECO:0000269|PubMed:17974005}.		negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TACAGCCAACGGCAGTTAATA	0.328													T|||	132	0.0263578	0.0953	0.0086	5008	,	,		20405	0.0		0.0	False		,,,				2504	0.0				p.T1241T		Atlas-SNP	.											.	CD109	170	.	0			c.G3723T						PASS	.	T	,,	324,4082	796.3+/-415.4	13,298,1892	146.0	139.0	142.0		3672,3492,3723	0.0	0.0	6	dbSNP_129	142	5,8595	818.7+/-406.8	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	CD109	NM_001159587.1,NM_001159588.1,NM_133493.3	,,	13,303,6187	TT,TG,GG		0.0581,7.3536,2.5296	,,	1224/1429,1164/1369,1241/1446	74521948	329,12677	2203	4300	6503	SO:0001819	synonymous_variant	135228	exon29			GCCAACGGCAGTT	AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"""CD molecules"""	21685	protein-coding gene	gene with protein product		608859	"""CD109 antigen (Gov platelet alloantigens)"""			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.3723G>T	6.37:g.74521948G>T		187.0	0.0	0		193.0	84.0	0.435233	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Silent	SNP	ENST00000287097.5	37	CCDS4982.1																																																																																			G|0.971;T|0.029	0.029	strong		0.328	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493	
OGT	8473	hgsc.bcm.edu	37	X	70777435	70777435	+	Silent	SNP	G	G	A	rs34739713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:70777435G>A	ENST00000373719.3	+	12	1732	c.1515G>A	c.(1513-1515)gtG>gtA	p.V505V	OGT_ENST00000373701.3_Silent_p.V495V	NM_181672.2|NM_181673.2	NP_858058.1|NP_858059.1	O15294	OGT1_HUMAN	O-linked N-acetylglucosamine (GlcNAc) transferase	505					apoptotic process (GO:0006915)|cellular response to retinoic acid (GO:0071300)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of protein ubiquitination (GO:0031397)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of catalytic activity (GO:0043085)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of histone H3-K27 methylation (GO:0061087)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glycolytic process (GO:0006110)|regulation of insulin receptor signaling pathway (GO:0046626)|regulation of Rac protein signal transduction (GO:0035020)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone acetyltransferase complex (GO:0000123)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)|MLL5-L complex (GO:0070688)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	acetylglucosaminyltransferase activity (GO:0008375)|enzyme activator activity (GO:0008047)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein N-acetylglucosaminyltransferase activity (GO:0016262)|protein O-GlcNAc transferase activity (GO:0097363)			breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|liver(3)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Renal(35;0.156)					TGCCTTCTGTGCATCCTCATC	0.433													G|||	160	0.0423841	0.1127	0.0144	3775	,	,		14352	0.0		0.001	False		,,,				2504	0.0				p.V505V		Atlas-SNP	.											.	OGT	207	.	0			c.G1515A						PASS	.	G	,	533,3302		27,404,75,1201,496	158.0	104.0	122.0		1515,1485	1.5	1.0	X	dbSNP_126	122	2,6726		0,2,0,2426,1872	no	coding-synonymous,coding-synonymous	OGT	NM_181672.2,NM_181673.2	,	27,406,75,3627,2368	AA,AG,A,GG,G		0.0297,13.8983,5.0648	,	505/1047,495/1037	70777435	535,10028	2203	4300	6503	SO:0001819	synonymous_variant	8473	exon12			TTCTGTGCATCCT	U77413	CCDS14414.1, CCDS35502.1	Xq13	2013-07-24	2012-05-04		ENSG00000147162	ENSG00000147162	2.4.1.255	"""Tetratricopeptide (TTC) repeat domain containing"""	8127	protein-coding gene	gene with protein product	"""UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase"""	300255	"""O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)"""			9083068	Standard	NM_181672		Approved	O-GLCNAC, HRNT1, MGC22921, FLJ23071	uc004eaa.2	O15294	OTTHUMG00000033316	ENST00000373719.3:c.1515G>A	X.37:g.70777435G>A		156.0	0.0	0		185.0	90.0	0.486486	NM_181672	Q7Z3K0|Q8WWM8|Q96CC1|Q9UG57	Silent	SNP	ENST00000373719.3	37	CCDS14414.1																																																																																			G|0.947;A|0.053	0.053	strong		0.433	OGT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000081829.3	NM_003605, NM_181672	
FLG	2312	hgsc.bcm.edu	37	1	152276603	152276603	+	Missense_Mutation	SNP	C	C	T	rs111939167		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152276603C>T	ENST00000368799.1	-	3	10794	c.10759G>A	c.(10759-10761)Ggt>Agt	p.G3587S	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3587	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGCCCGTGACCGGCTCTGTCT	0.562									Ichthyosis																												p.G3587S		Atlas-SNP	.											FLG,NS,carcinoma,0,1	FLG	900	1	0			c.G10759A						PASS	.						176.0	237.0	216.0					1																	152276603		2200	4294	6494	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CGTGACCGGCTCT	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.10759G>A	1.37:g.152276603C>T	ENSP00000357789:p.Gly3587Ser	609.0	0.0	0		581.0	297.0	0.511188	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	3.513	-0.099425	0.07010	.	.	ENSG00000143631	ENST00000368799	T	0.00902	5.56	3.24	-6.48	0.01896	.	.	.	.	.	T	0.00144	0.0004	N	0.25890	0.77	0.09310	N	1	P	0.47106	0.89	B	0.41646	0.362	T	0.48790	-0.9004	9	0.05436	T	0.98	.	1.8762	0.03219	0.2398:0.387:0.2291:0.1442	.	3587	P20930	FILA_HUMAN	S	3587	ENSP00000357789:G3587S	ENSP00000357789:G3587S	G	-	1	0	FLG	150543227	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.237000	0.00545	-3.276000	0.00198	-0.507000	0.04495	GGT	T|1.000;|0.000	1.000	weak		0.562	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
BRD4	23476	hgsc.bcm.edu	37	19	15355540	15355540	+	Missense_Mutation	SNP	G	G	A	rs149185763	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15355540G>A	ENST00000263377.2	-	12	2413	c.2192C>T	c.(2191-2193)cCc>cTc	p.P731L		NM_058243.2	NP_490597.1	O60885	BRD4_HUMAN	bromodomain containing 4	731					cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|chromosome segregation (GO:0007059)|histone H3-K14 acetylation (GO:0044154)|histone H4-K12 acetylation (GO:0043983)|inner cell mass cell proliferation (GO:0001833)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA binding (GO:0043388)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of phosphorylation of RNA polymerase II C-terminal domain (GO:1901407)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|positive transcription elongation factor complex b (GO:0008024)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|urinary_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(3;3.02e-24)|Epithelial(3;4.71e-20)|all cancers(3;2.26e-18)			CTCCCTCCCGGGGTGCCCCTT	0.582			T	C15orf55	lethal midline carcinoma of young people								G|||	13	0.00259585	0.0098	0.0	5008	,	,		13894	0.0		0.0	False		,,,				2504	0.0				p.P731L		Atlas-SNP	.		Dom	yes		19	19p13.1	23476	bromodomain containing 4		E	.	BRD4	172	.	0			c.C2192T						PASS	.	G	LEU/PRO	16,4390	23.3+/-48.9	0,16,2187	144.0	141.0	142.0		2192	3.4	0.8	19	dbSNP_134	142	0,8600		0,0,4300	yes	missense	BRD4	NM_058243.2	98	0,16,6487	AA,AG,GG		0.0,0.3631,0.123	probably-damaging	731/1363	15355540	16,12990	2203	4300	6503	SO:0001583	missense	23476	exon12			CTCCCGGGGTGCC	Y12059	CCDS12328.1, CCDS46004.1	19p13.12	2013-09-20	2002-01-14		ENSG00000141867	ENSG00000141867			13575	protein-coding gene	gene with protein product	"""chromosome-associated protein"""	608749	"""bromodomain-containing 4"""			10938129	Standard	NM_058243		Approved	HUNKI, MCAP, CAP, HUNK1	uc002nar.3	O60885	OTTHUMG00000183252	ENST00000263377.2:c.2192C>T	19.37:g.15355540G>A	ENSP00000263377:p.Pro731Leu	107.0	0.0	0		142.0	71.0	0.5	NM_058243	O60433|Q4G0X8|Q86YS8|Q96PD3	Missense_Mutation	SNP	ENST00000263377.2	37	CCDS12328.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	14.84	2.654846	0.47467	0.003631	0.0	ENSG00000141867	ENST00000263377	T	0.07216	3.21	4.48	3.43	0.39272	.	1.004540	0.08020	N	0.991771	T	0.08980	0.0222	L	0.36672	1.1	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.07751	-1.0756	10	0.42905	T	0.14	-1.3945	10.1453	0.42760	0.1003:0.0:0.8997:0.0	.	731	O60885	BRD4_HUMAN	L	731	ENSP00000263377:P731L	ENSP00000263377:P731L	P	-	2	0	BRD4	15216540	1.000000	0.71417	0.803000	0.32268	0.934000	0.57294	6.710000	0.74670	0.868000	0.35678	0.561000	0.74099	CCC	A|0.001;G|0.999	0.001	strong		0.582	BRD4-001	KNOWN	overlapping_uORF|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465800.3	NM_058243	
CSMD2	114784	hgsc.bcm.edu	37	1	34174737	34174737	+	Silent	SNP	A	A	G	rs10914765	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:34174737A>G	ENST00000373380.1	-	1	367	c.147T>C	c.(145-147)atT>atC	p.I49I	CSMD2_ENST00000373381.4_Silent_p.I1176I|CSMD2_ENST00000373388.2_5'UTR			Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	1136	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				CTTTCAGCTGAATTCCCTTCC	0.453													A|||	205	0.0409345	0.087	0.0101	5008	,	,		20724	0.0		0.001	False		,,,				2504	0.0838				p.I1136I		Atlas-SNP	.											.	CSMD2	946	.	0			c.T3408C						PASS	.	A		313,4093	170.1+/-200.6	10,293,1900	132.0	124.0	127.0		3408	4.4	1.0	1	dbSNP_120	127	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	CSMD2	NM_052896.3		10,297,6196	GG,GA,AA		0.0465,7.1039,2.4373		1136/3488	34174737	317,12689	2203	4300	6503	SO:0001819	synonymous_variant	114784	exon22			CAGCTGAATTCCC	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373380.1:c.147T>C	1.37:g.34174737A>G		94.0	0.0	0		105.0	52.0	0.495238	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Silent	SNP	ENST00000373380.1	37																																																																																				A|0.972;G|0.028	0.028	strong		0.453	CSMD2-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000030635.4	NM_052896	
CYP2C8	1558	hgsc.bcm.edu	37	10	96818106	96818106	+	Missense_Mutation	SNP	T	T	A	rs11572103	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:96818106T>A	ENST00000371270.3	-	5	899	c.805A>T	c.(805-807)Atc>Ttc	p.I269F	CYP2C8_ENST00000535898.1_Missense_Mutation_p.I167F|CYP2C8_ENST00000539050.1_Missense_Mutation_p.I183F	NM_000770.3|NM_001198853.1|NM_001198855.1	NP_000761.3|NP_001185782.1|NP_001185784.1	P10632	CP2C8_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 8	269			I -> F (in allele CYP2C8*2; only found in African-Americans; dbSNP:rs11572103). {ECO:0000269|PubMed:11668219, ECO:0000269|PubMed:12429347, ECO:0000269|PubMed:15469410, ECO:0000269|Ref.5}.		arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|omega-hydroxylase P450 pathway (GO:0097267)|organic acid metabolic process (GO:0006082)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)			breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(6)|skin(3)	21		Colorectal(252;0.0397)		all cancers(201;6.21e-05)	Abiraterone(DB05812)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Almotriptan(DB00918)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Antipyrine(DB01435)|Apixaban(DB06605)|Atorvastatin(DB01076)|Azelastine(DB00972)|Benzyl alcohol(DB06770)|Bezafibrate(DB01393)|Bortezomib(DB00188)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Candesartan(DB00796)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cisapride(DB00604)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dapsone(DB00250)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Domperidone(DB01184)|Eltrombopag(DB06210)|Enzalutamide(DB08899)|Erlotinib(DB00530)|Estradiol(DB00783)|Eszopiclone(DB00402)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Felodipine(DB01023)|Fenofibrate(DB01039)|Fluorouracil(DB00544)|Fluvastatin(DB01095)|Fosphenytoin(DB01320)|Gemfibrozil(DB01241)|Halofantrine(DB01218)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Ifosfamide(DB01181)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Liotrix(DB01583)|Loperamide(DB00836)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Meloxicam(DB00814)|Methadone(DB00333)|Metronidazole(DB00916)|Mirtazapine(DB00370)|Mometasone(DB00764)|Montelukast(DB00471)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Naloxone(DB01183)|Naproxen(DB00788)|Nicardipine(DB00622)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Omeprazole(DB00338)|Oxybutynin(DB01062)|Paclitaxel(DB01229)|Paramethadione(DB00617)|Paroxetine(DB00715)|Pazopanib(DB06589)|Pentamidine(DB00738)|Perphenazine(DB00850)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Ponatinib(DB08901)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quinidine(DB00908)|Quinine(DB00468)|Raloxifene(DB00481)|Regorafenib(DB08896)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Salmeterol(DB00938)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Simvastatin(DB00641)|Sitagliptin(DB01261)|Sorafenib(DB00398)|Spironolactone(DB00421)|Sulfadiazine(DB00359)|Sulfamethoxazole(DB01015)|Sulfaphenazole(DB06729)|Sulfinpyrazone(DB01138)|Tamoxifen(DB00675)|Tazarotene(DB00799)|Temazepam(DB00231)|Terbinafine(DB00857)|Testosterone(DB00624)|Theophylline(DB00277)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Torasemide(DB00214)|Trametinib(DB08911)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Verapamil(DB00661)|Vismodegib(DB08828)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zidovudine(DB00495)|Zopiclone(DB01198)	TCCATTTTGATCAGGAAGCAA	0.358													T|||	274	0.0547125	0.1891	0.0115	5008	,	,		17668	0.0		0.004	False		,,,				2504	0.0123				p.I269F		Atlas-SNP	.											.	CYP2C8	73	.	0			c.A805T	GRCh37	CM016067	CYP2C8	M	rs11572103	PASS	.	T	PHE/ILE,PHE/ILE,PHE/ILE,PHE/ILE	690,3716	289.5+/-280.5	68,554,1581	156.0	139.0	145.0		805,595,499,595	4.2	0.8	10	dbSNP_120	145	30,8570	21.0+/-64.5	0,30,4270	yes	missense,missense,missense,missense	CYP2C8	NM_000770.3,NM_001198853.1,NM_001198854.1,NM_001198855.1	21,21,21,21	68,584,5851	AA,AT,TT		0.3488,15.6605,5.5359	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	269/491,199/421,167/389,199/421	96818106	720,12286	2203	4300	6503	SO:0001583	missense	1558	exon5			TTTTGATCAGGAA	M17397	CCDS7438.1, CCDS55721.1, CCDS73166.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138115	ENSG00000138115		"""Cytochrome P450s"""	2622	protein-coding gene	gene with protein product		601129	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 8"""			7841444	Standard	NM_001198853		Approved	CPC8	uc001kkb.3	P10632	OTTHUMG00000018804	ENST00000371270.3:c.805A>T	10.37:g.96818106T>A	ENSP00000360317:p.Ile269Phe	138.0	0.0	0		136.0	73.0	0.536765	NM_000770	A8K9N8|B0AZN2|B7Z1F6|Q5VX93|Q8WWB1|Q9UCZ9	Missense_Mutation	SNP	ENST00000371270.3	37	CCDS7438.1	85	0.03891941391941392	82	0.16666666666666666	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	T	13.62	2.290753	0.40494	0.156605	0.003488	ENSG00000138115	ENST00000371270;ENST00000535868;ENST00000535898;ENST00000539050	T;T;T	0.68624	-0.34;-0.34;-0.34	4.17	4.17	0.49024	.	0.225081	0.35235	U	0.003341	T	0.00524	0.0017	M	0.66378	2.025	0.23903	P	0.99651506	P;D;D;D	0.59767	0.898;0.961;0.986;0.961	P;P;P;P	0.57101	0.622;0.675;0.795;0.813	T	0.32134	-0.9918	9	0.72032	D	0.01	.	11.4277	0.50020	0.0:0.0:0.0:1.0	rs11572103;rs52833642;rs58027822;rs11572103	183;167;237;269	F5H7Q9;B7Z1F6;B7Z8S1;P10632	.;.;.;CP2C8_HUMAN	F	269;236;167;183	ENSP00000360317:I269F;ENSP00000445062:I167F;ENSP00000442343:I183F	ENSP00000360317:I269F	I	-	1	0	CYP2C8	96808096	0.980000	0.34600	0.793000	0.32043	0.156000	0.22039	1.316000	0.33620	1.642000	0.50584	0.254000	0.18369	ATC	T|0.950;A|0.050	0.050	strong		0.358	CYP2C8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049499.2	NM_000770	
RREB1	6239	hgsc.bcm.edu	37	6	7231736	7231736	+	Missense_Mutation	SNP	G	G	T	rs116295722	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:7231736G>T	ENST00000349384.6	+	10	3718	c.3404G>T	c.(3403-3405)aGc>aTc	p.S1135I	RREB1_ENST00000379933.3_Missense_Mutation_p.S1135I|RREB1_ENST00000379938.2_Missense_Mutation_p.S1135I|RREB1_ENST00000334984.6_Missense_Mutation_p.S1135I	NM_001003698.3	NP_001003698.1	Q92766	RREB1_HUMAN	ras responsive element binding protein 1	1135					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|Ras protein signal transduction (GO:0007265)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear body (GO:0016604)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(18)|ovary(5)|pancreas(2)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58	Ovarian(93;0.0398)	all_hematologic(90;0.0384)|Prostate(151;0.191)				CCAGCCAGCAGCCCAGAGGCT	0.687													G|||	12	0.00239617	0.0091	0.0	5008	,	,		13021	0.0		0.0	False		,,,				2504	0.0				p.S1135I		Atlas-SNP	.											.	RREB1	242	.	0			c.G3404T						PASS	.	G	ILE/SER,ILE/SER,ILE/SER,ILE/SER	17,4291		0,17,2137	8.0	12.0	11.0		3404,3404,3404,3404	5.7	1.0	6	dbSNP_132	11	1,8493		0,1,4246	yes	missense,missense,missense,missense	RREB1	NM_001003698.3,NM_001003699.3,NM_001003700.1,NM_001168344.1	142,142,142,142	0,18,6383	TT,TG,GG		0.0118,0.3946,0.1406	probably-damaging,probably-damaging,probably-damaging,probably-damaging	1135/1688,1135/1743,1135/1477,1135/1688	7231736	18,12784	2154	4247	6401	SO:0001583	missense	6239	exon10			CCAGCAGCCCAGA	U26914	CCDS34335.1, CCDS34336.1, CCDS54963.1	6p25	2013-01-08			ENSG00000124782	ENSG00000124782		"""Zinc fingers, C2H2-type"""	10449	protein-coding gene	gene with protein product	"""hindsight homolog (drosophila)"""	602209				9367691, 18394891	Standard	NM_001003698		Approved	HNT	uc003mxb.3	Q92766	OTTHUMG00000014201	ENST00000349384.6:c.3404G>T	6.37:g.7231736G>T	ENSP00000305560:p.Ser1135Ile	104.0	0.0	0		110.0	58.0	0.527273	NM_001003700	A2RRF5|E2GM80|E2GM81|O75567|O75568|Q5VYB2|Q6BEP5|Q6BEP6|Q6BEP8|Q86SU2|Q9Y474	Missense_Mutation	SNP	ENST00000349384.6	37	CCDS34336.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	G	17.76	3.469337	0.63625	0.003946	1.18E-4	ENSG00000124782	ENST00000379933;ENST00000379938;ENST00000349384;ENST00000334984	T;T;T;T	0.13307	2.6;2.7;2.6;2.6	5.73	5.73	0.89815	.	0.089674	0.47455	D	0.000240	T	0.21186	0.0510	M	0.62723	1.935	0.38993	D	0.959191	D;D;D	0.67145	0.993;0.993;0.996	P;P;D	0.65010	0.9;0.855;0.931	T	0.00778	-1.1570	10	0.72032	D	0.01	-50.0022	10.0245	0.42063	0.1544:0.0:0.8456:0.0	.	1135;1135;1135	Q92766-3;Q92766;Q92766-2	.;RREB1_HUMAN;.	I	1135	ENSP00000369265:S1135I;ENSP00000369270:S1135I;ENSP00000305560:S1135I;ENSP00000335574:S1135I	ENSP00000335574:S1135I	S	+	2	0	RREB1	7176735	0.693000	0.27728	0.999000	0.59377	0.626000	0.37791	1.532000	0.36029	2.695000	0.91970	0.655000	0.94253	AGC	G|0.997;T|0.003	0.003	strong		0.687	RREB1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000352985.1		
SCARB2	950	hgsc.bcm.edu	37	4	77102148	77102148	+	Missense_Mutation	SNP	G	G	C	rs143558324	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:77102148G>C	ENST00000264896.2	-	3	731	c.382C>G	c.(382-384)Cct>Gct	p.P128A	SCARB2_ENST00000452464.2_Intron	NM_005506.3	NP_005497.1	Q14108	SCRB2_HUMAN	scavenger receptor class B, member 2	128					cell adhesion (GO:0007155)|protein targeting to lysosome (GO:0006622)	extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	enzyme binding (GO:0019899)|receptor activity (GO:0004872)			breast(1)|endometrium(4)|kidney(4)|large_intestine(7)|lung(3)|prostate(2)|skin(1)	22			Lung(101;0.196)			TCAATTTTAGGGTCTCCAACA	0.323													G|||	6	0.00119808	0.0045	0.0	5008	,	,		15540	0.0		0.0	False		,,,				2504	0.0				p.P128A		Atlas-SNP	.											.	SCARB2	47	.	0			c.C382G						PASS	.	G	,ALA/PRO	19,4383	26.2+/-53.5	0,19,2182	103.0	104.0	104.0		,382	3.2	0.9	4	dbSNP_134	104	0,8598		0,0,4299	yes	intron,missense	SCARB2	NM_001204255.1,NM_005506.3	,27	0,19,6481	CC,CG,GG		0.0,0.4316,0.1462	,benign	,128/479	77102148	19,12981	2201	4299	6500	SO:0001583	missense	950	exon3			TTTTAGGGTCTCC	D12676	CCDS3577.1, CCDS56335.1	4q21.1	2014-07-11	2002-09-06	2002-09-06	ENSG00000138760	ENSG00000138760			1665	protein-coding gene	gene with protein product		602257	"""CD36 antigen (collagen type I receptor, thrombospondin receptor)-like 2 (lysosomal integral membrane protein II)"""	CD36L2		1374238	Standard	NM_005506		Approved	HLGP85, LIMPII, SR-BII, LIMP-2	uc003hju.2	Q14108	OTTHUMG00000130099	ENST00000264896.2:c.382C>G	4.37:g.77102148G>C	ENSP00000264896:p.Pro128Ala	61.0	0.0	0		61.0	33.0	0.540984	NM_005506	B4DKD8|E7EM68|Q53Y63	Missense_Mutation	SNP	ENST00000264896.2	37	CCDS3577.1	.	.	.	.	.	.	.	.	.	.	G	12.17	1.857612	0.32791	0.004316	0.0	ENSG00000138760	ENST00000264896	T	0.72282	-0.64	5.87	3.17	0.36434	.	0.189182	0.64402	N	0.000018	T	0.75034	0.3795	M	0.71206	2.165	0.80722	D	1	B	0.29481	0.245	B	0.43575	0.424	T	0.66697	-0.5858	10	0.09590	T	0.72	.	16.5946	0.84792	0.0:0.3673:0.6327:0.0	.	128	Q14108	SCRB2_HUMAN	A	128	ENSP00000264896:P128A	ENSP00000264896:P128A	P	-	1	0	SCARB2	77321172	1.000000	0.71417	0.946000	0.38457	0.282000	0.26991	3.001000	0.49488	0.452000	0.26830	-0.176000	0.13171	CCT	G|0.999;C|0.001	0.001	strong		0.323	SCARB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252403.1	NM_005506	
TCHHL1	126637	hgsc.bcm.edu	37	1	152060495	152060495	+	Missense_Mutation	SNP	C	C	T	rs76137589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152060495C>T	ENST00000368806.1	-	2	189	c.125G>A	c.(124-126)gGg>gAg	p.G42E		NM_001008536.1	NP_001008536.1	Q5QJ38	TCHL1_HUMAN	trichohyalin-like 1	42							calcium ion binding (GO:0005509)			breast(4)|endometrium(1)|kidney(2)|large_intestine(9)|lung(33)|ovary(2)|prostate(1)|skin(7)|stomach(1)	60	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.246)			AAAAAAGTCCCCAAACTCGCC	0.458													c|||	59	0.0117812	0.0431	0.0029	5008	,	,		19439	0.0		0.0	False		,,,				2504	0.0				p.G42E		Atlas-SNP	.											.	TCHHL1	132	.	0			c.G125A						PASS	.	C	GLU/GLY	196,4210		8,180,2015	183.0	181.0	182.0		125	-0.3	0.9	1	dbSNP_131	182	0,8600		0,0,4300	yes	missense	TCHHL1	NM_001008536.1	98	8,180,6315	TT,TC,CC		0.0,4.4485,1.507	possibly-damaging	42/905	152060495	196,12810	2203	4300	6503	SO:0001583	missense	126637	exon2			AAGTCCCCAAACT		CCDS30857.1	1q21.3	2011-10-11	2004-10-05	2006-01-27	ENSG00000182898	ENSG00000182898		"""S100 calcium binding proteins"""	31796	protein-coding gene	gene with protein product			"""S100 calcium binding protein A17"""	S100A17, THHL1			Standard	NM_001008536		Approved		uc001ezo.1	Q5QJ38	OTTHUMG00000013058	ENST00000368806.1:c.125G>A	1.37:g.152060495C>T	ENSP00000357796:p.Gly42Glu	127.0	0.0	0		120.0	51.0	0.425	NM_001008536	B2RPK8|Q5VTJ9	Missense_Mutation	SNP	ENST00000368806.1	37	CCDS30857.1	21	0.009615384615384616	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	0	0.0	.	11.72	1.721614	0.30503	0.044485	0.0	ENSG00000182898	ENST00000368806	T	0.10573	2.86	6.0	-0.34	0.12643	S100/CaBP-9k-type, calcium binding, subdomain (1);EF-hand-like domain (1);	0.624434	0.13321	N	0.396729	T	0.05593	0.0147	L	0.58969	1.84	0.29774	N	0.834538	D	0.56746	0.977	P	0.51324	0.666	T	0.28004	-1.0057	10	0.20519	T	0.43	-1.2812	5.8572	0.18727	0.0:0.5081:0.1244:0.3675	.	42	Q5QJ38	TCHL1_HUMAN	E	42	ENSP00000357796:G42E	ENSP00000357796:G42E	G	-	2	0	TCHHL1	150327119	0.666000	0.27475	0.918000	0.36340	0.264000	0.26372	-0.095000	0.11077	-0.059000	0.13154	-0.136000	0.14681	GGG	C|0.985;T|0.015	0.015	strong		0.458	TCHHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036638.2	XM_060104	
GPATCH4	54865	hgsc.bcm.edu	37	1	156565389	156565389	+	Silent	SNP	C	C	T	rs145851878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156565389C>T	ENST00000438976.2	-	8	774	c.744G>A	c.(742-744)aaG>aaA	p.K248K	GPATCH4_ENST00000368232.4_Silent_p.K243K|GPATCH4_ENST00000497287.1_5'Flank			Q5T3I0	GPTC4_HUMAN	G patch domain containing 4	243							poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(2)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(2)|skin(3)|stomach(1)	17	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GTCGCCTTTTCTTCTTCTTGC	0.468													C|||	68	0.0135783	0.0499	0.0029	5008	,	,		22178	0.0		0.0	False		,,,				2504	0.0				p.K248K		Atlas-SNP	.											.	GPATCH4	34	.	0			c.G744A						PASS	.	C	,	172,4234	115.4+/-153.4	4,164,2035	332.0	314.0	320.0		744,729	1.0	0.4	1	dbSNP_134	320	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	GPATCH4	NM_015590.3,NM_182679.2	,	4,164,6335	TT,TC,CC		0.0,3.9038,1.3225	,	248/376,243/371	156565389	172,12834	2203	4300	6503	SO:0001819	synonymous_variant	54865	exon8			CCTTTTCTTCTTC	BC056904	CCDS1146.1, CCDS44245.1	1q22	2013-01-28		2006-12-13	ENSG00000160818	ENSG00000160818		"""G patch domain containing"""	25982	protein-coding gene	gene with protein product				GPATC4		12477932	Standard	NM_015590		Approved	FLJ20249, DKFZP434F1735	uc001fpl.3	Q5T3I0	OTTHUMG00000033203	ENST00000438976.2:c.744G>A	1.37:g.156565389C>T		237.0	0.0	0		284.0	130.0	0.457746	NM_015590	Q5T3I1|Q6ZUE7|Q8IWG8|Q9NXH4	Silent	SNP	ENST00000438976.2	37	CCDS44245.1																																																																																			C|0.988;T|0.012	0.012	strong		0.468	GPATCH4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386947.1	NM_017725	
TRIB1	10221	hgsc.bcm.edu	37	8	126448674	126448674	+	Missense_Mutation	SNP	G	G	T	rs16900603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:126448674G>T	ENST00000519576.1	+	2	650	c.387G>T	c.(385-387)gaG>gaT	p.E129D	TRIB1_ENST00000311922.3_Missense_Mutation_p.E360D|TRIB1_ENST00000520847.1_Missense_Mutation_p.E194D					tribbles pseudokinase 1											NS(1)|large_intestine(2)|lung(2)|prostate(2)|urinary_tract(1)	8	all_hematologic(1;4.97e-05)|Ovarian(258;0.00167)|all_neural(195;0.00294)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.000918)			TTGTTCCAGAGTACCAGGAGG	0.473													G|||	147	0.029353	0.1051	0.0101	5008	,	,		20227	0.0		0.001	False		,,,				2504	0.0				p.E360D		Atlas-SNP	.											.	TRIB1	73	.	0			c.G1080T						PASS	.	G	ASP/GLU	353,4053	181.5+/-209.5	15,323,1865	83.0	85.0	84.0		1080	2.7	1.0	8	dbSNP_123	84	4,8596	3.7+/-12.6	0,4,4296	yes	missense	TRIB1	NM_025195.2	45	15,327,6161	TT,TG,GG		0.0465,8.0118,2.7449	benign	360/373	126448674	357,12649	2203	4300	6503	SO:0001583	missense	10221	exon3			TCCAGAGTACCAG	AF205437	CCDS6357.1, CCDS64971.1	8q24.13	2013-10-03	2013-10-03			ENSG00000173334			16891	protein-coding gene	gene with protein product		609461	"""tribbles homolog 1 (Drosophila)"""			9342215, 16715410	Standard	NM_001282985		Approved	C8FW, GIG2, TRB1	uc003yrx.3	Q96RU8		ENST00000519576.1:c.387G>T	8.37:g.126448674G>T	ENSP00000428879:p.Glu129Asp	114.0	0.0	0		134.0	75.0	0.559702	NM_025195		Missense_Mutation	SNP	ENST00000519576.1	37		39	0.017857142857142856	35	0.07113821138211382	4	0.011049723756906077	0	0.0	0	0.0	G	0.601	-0.829096	0.02734	0.080118	4.65E-4	ENSG00000173334	ENST00000311922;ENST00000520847;ENST00000519576	T;T;T	0.47177	0.88;0.85;1.12	5.88	2.65	0.31530	.	0.241181	0.21003	N	0.081838	T	0.00936	0.0031	N	0.08118	0	0.23903	N	0.996519	B	0.11235	0.004	B	0.10450	0.005	T	0.17410	-1.0370	10	0.02654	T	1	-15.0092	5.2841	0.15692	0.0985:0.2463:0.5295:0.1257	rs16900603;rs52815805;rs16900603	360	Q96RU8	TRIB1_HUMAN	D	360;194;129	ENSP00000312150:E360D;ENSP00000429063:E194D;ENSP00000428879:E129D	ENSP00000312150:E360D	E	+	3	2	TRIB1	126517856	0.026000	0.19158	0.998000	0.56505	0.850000	0.48378	-0.005000	0.12855	0.811000	0.34303	-0.305000	0.09177	GAG	G|0.974;T|0.026	0.026	strong		0.473	TRIB1-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000381433.1	NM_025195	
NAPG	8774	hgsc.bcm.edu	37	18	10539774	10539774	+	Missense_Mutation	SNP	C	C	T	rs2228300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:10539774C>T	ENST00000322897.6	+	6	343	c.274C>T	c.(274-276)Cca>Tca	p.P92S	NAPG_ENST00000542979.1_Missense_Mutation_p.P10S	NM_003826.2	NP_003817.1	Q99747	SNAG_HUMAN	N-ethylmaleimide-sensitive factor attachment protein, gamma	92			P -> S (in dbSNP:rs16974765).		intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|protein complex assembly (GO:0006461)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|mitochondrion (GO:0005739)				large_intestine(2)|lung(2)	4						GCAGAAACTACCAGAGGCCGT	0.438													C|||	217	0.0433307	0.1573	0.013	5008	,	,		17838	0.0		0.0	False		,,,				2504	0.0				p.P92S		Atlas-SNP	.											.	NAPG	18	.	0			c.C274T						PASS	.	C	SER/PRO	498,3326		28,442,1442	64.0	64.0	64.0		274	4.1	0.1	18	dbSNP_123	64	1,8233		0,1,4116	yes	missense	NAPG	NM_003826.2	74	28,443,5558	TT,TC,CC		0.0121,13.023,4.1383	possibly-damaging	92/313	10539774	499,11559	1912	4117	6029	SO:0001583	missense	8774	exon6			AAACTACCAGAGG	U78107	CCDS45827.1	18p11.21	2013-02-28			ENSG00000134265	ENSG00000134265			7642	protein-coding gene	gene with protein product	"""gamma SNAP"""	603216				9269766	Standard	NM_003826		Approved		uc002kon.3	Q99747	OTTHUMG00000179119	ENST00000322897.6:c.274C>T	18.37:g.10539774C>T	ENSP00000324628:p.Pro92Ser	132.0	0.0	0		115.0	48.0	0.417391	NM_003826	B4DFC9|Q9BUV1	Missense_Mutation	SNP	ENST00000322897.6	37	CCDS45827.1	74	0.03388278388278388	69	0.1402439024390244	5	0.013812154696132596	0	0.0	0	0.0	C	10.89	1.479069	0.26511	0.13023	1.21E-4	ENSG00000134265	ENST00000322897;ENST00000542979	T;T	0.75050	-0.9;-0.9	5.82	4.06	0.47325	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.00580	0.0019	L	0.34521	1.04	0.09310	P	0.99999957713	P	0.37101	0.582	B	0.25987	0.065	T	0.28650	-1.0037	9	0.06625	T	0.88	-10.0671	11.8346	0.52316	0.0:0.8645:0.0:0.1355	rs2228300	92	Q99747	SNAG_HUMAN	S	92;10	ENSP00000324628:P92S;ENSP00000442849:P10S	ENSP00000324628:P92S	P	+	1	0	NAPG	10529774	1.000000	0.71417	0.125000	0.21846	0.551000	0.35334	5.446000	0.66600	0.820000	0.34516	0.561000	0.74099	CCA	C|0.965;T|0.035	0.035	strong		0.438	NAPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444873.1	NM_003826	
GPRASP2	114928	hgsc.bcm.edu	37	X	101970662	101970662	+	Missense_Mutation	SNP	A	A	G	rs113336462	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:101970662A>G	ENST00000535209.1	+	4	1696	c.865A>G	c.(865-867)Agc>Ggc	p.S289G	GPRASP2_ENST00000332262.5_Missense_Mutation_p.S289G|GPRASP2_ENST00000543253.1_Missense_Mutation_p.S289G			Q96D09	GASP2_HUMAN	G protein-coupled receptor associated sorting protein 2	289						cytoplasm (GO:0005737)	beta-amyloid binding (GO:0001540)			breast(3)|endometrium(5)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	30						GGATGAGGCCAGCAACCCATT	0.507													.|||	50	0.013245	0.0371	0.0014	3775	,	,		14521	0.0		0.0	False		,,,				2504	0.0				p.S289G		Atlas-SNP	.											.	GPRASP2	89	.	0			c.A865G						PASS	.	G	GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER,GLY/SER	148,3687		2,116,28,1514,543	112.0	111.0	112.0		865,865,865,865,865,865	1.3	0.0	X	dbSNP_132	112	0,6728		0,0,0,2428,1872	yes	missense,missense,missense,missense,missense,missense	GPRASP2,ARMCX5-GPRASP2	NM_001004051.3,NM_001184874.2,NM_001184875.2,NM_001184876.2,NM_001199818.1,NM_138437.5	56,56,56,56,56,56	2,116,28,3942,2415	GG,GA,G,AA,A		0.0,3.8592,1.4011	benign,benign,benign,benign,benign,benign	289/839,289/839,289/839,289/839,289/839,289/839	101970662	148,10415	2203	4300	6503	SO:0001583	missense	114928	exon4			GAGGCCAGCAACC	AK094646	CCDS14501.1	Xq22.1	2014-03-21			ENSG00000158301	ENSG00000158301		"""Armadillo repeat containing"""	25169	protein-coding gene	gene with protein product						15086532, 16221301	Standard	NM_138437		Approved	GASP2, FLJ37327		Q96D09	OTTHUMG00000022059	ENST00000535209.1:c.865A>G	X.37:g.101970662A>G	ENSP00000437394:p.Ser289Gly	130.0	0.0	0		157.0	64.0	0.407643	NM_138437	D3DXA0|Q8NAB4	Missense_Mutation	SNP	ENST00000535209.1	37	CCDS14501.1	15	0.009041591320072333	11	0.022727272727272728	0	0.0	0	0.0	0	0.0	G	0.001	-3.165628	0.00028	0.038592	0.0	ENSG00000158301	ENST00000543253;ENST00000535209;ENST00000332262	T;T;T	0.06218	3.33;3.33;3.33	4.2	1.33	0.21861	.	0.304465	0.24078	N	0.041755	T	0.00524	0.0017	N	0.02539	-0.55	0.18873	N	0.999988	B	0.02656	0.0	B	0.01281	0.0	T	0.46373	-0.9196	10	0.22706	T	0.39	-0.1711	4.5595	0.12152	0.2852:0.0:0.5594:0.1554	.	289	Q96D09	GASP2_HUMAN	G	289	ENSP00000437872:S289G;ENSP00000437394:S289G;ENSP00000339057:S289G	ENSP00000339057:S289G	S	+	1	0	GPRASP2	101857318	0.826000	0.29277	0.037000	0.18230	0.001000	0.01503	0.260000	0.18424	-0.074000	0.12820	-0.834000	0.03071	AGC	A|0.986;G|0.014	0.014	strong		0.507	GPRASP2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057626.2	NM_138437	
ADCY7	113	hgsc.bcm.edu	37	16	50344627	50344627	+	Silent	SNP	C	C	T	rs140505854	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:50344627C>T	ENST00000394697.2	+	19	2530	c.2190C>T	c.(2188-2190)ttC>ttT	p.F730F	ADCY7_ENST00000254235.3_Silent_p.F730F			P51828	ADCY7_HUMAN	adenylate cyclase 7	730					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to ethanol (GO:0071361)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|maternal process involved in female pregnancy (GO:0060135)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cAMP biosynthetic process (GO:0030819)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(5)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	35		all_cancers(37;0.0127)		GBM - Glioblastoma multiforme(240;0.195)		TCCTGGGCTTCATCGCCTGCT	0.617													C|||	2	0.000399361	0.0015	0.0	5008	,	,		18686	0.0		0.0	False		,,,				2504	0.0				p.F730F		Atlas-SNP	.											.	ADCY7	90	.	0			c.C2190T						PASS	.	C		4,4392	8.1+/-20.4	0,4,2194	107.0	78.0	88.0		2190	1.1	0.2	16	dbSNP_134	88	0,8600		0,0,4300	no	coding-synonymous	ADCY7	NM_001114.3		0,4,6494	TT,TC,CC		0.0,0.091,0.0308		730/1081	50344627	4,12992	2198	4300	6498	SO:0001819	synonymous_variant	113	exon18			GGGCTTCATCGCC	D25538	CCDS10741.1, CCDS73882.1	16q12.1	2013-02-04			ENSG00000121281	ENSG00000121281	4.6.1.1	"""Adenylate cyclases"""	238	protein-coding gene	gene with protein product		600385				7860067	Standard	NM_001286057		Approved	KIAA0037, AC7	uc002egd.1	P51828	OTTHUMG00000133172	ENST00000394697.2:c.2190C>T	16.37:g.50344627C>T		127.0	0.0	0		142.0	71.0	0.5	NM_001114	A0AVA6	Silent	SNP	ENST00000394697.2	37	CCDS10741.1																																																																																			C|1.000;T|0.000	0.000	weak		0.617	ADCY7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256877.3		
KRTAP4-5	85289	hgsc.bcm.edu	37	17	39305775	39305775	+	Missense_Mutation	SNP	T	T	C	rs535144703|rs141265645|rs58117746	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39305775T>C	ENST00000343246.4	-	1	279	c.245A>G	c.(244-246)cAg>cGg	p.Q82R		NM_033188.3	NP_149445.3	Q9BYR2	KRA45_HUMAN	keratin associated protein 4-5	82	26 X 5 AA repeats of C-C-[GRQVCHIEK]- [SPTR]-[VSTQYC].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(4)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			gcaggtggtctggcagcagca	0.657																																					p.Q82R		Atlas-SNP	.											KRTAP4-5,NS,carcinoma,+1,1	KRTAP4-5	34	1	0			c.A245G						PASS	.						14.0	21.0	18.0					17																	39305775		2102	4214	6316	SO:0001583	missense	85289	exon1			GTGGTCTGGCAGC	AJ406937	CCDS32650.1	17q21.2	2013-06-25			ENSG00000198271	ENSG00000198271		"""Keratin associated proteins"""	18899	protein-coding gene	gene with protein product						11279113	Standard	NM_033188		Approved	KAP4.5	uc002hwb.3	Q9BYR2	OTTHUMG00000133638	ENST00000343246.4:c.245A>G	17.37:g.39305775T>C	ENSP00000340546:p.Gln82Arg	137.0	0.0	0		87.0	53.0	0.609195	NM_033188		Missense_Mutation	SNP	ENST00000343246.4	37	CCDS32650.1	.	.	.	.	.	.	.	.	.	.	.	1.564	-0.535892	0.04082	.	.	ENSG00000198271	ENST00000343246	T	0.00581	6.42	2.44	-3.27	0.05048	.	.	.	.	.	T	0.00271	0.0008	N	0.04260	-0.245	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35001	-0.9806	9	0.11794	T	0.64	.	3.3098	0.07013	0.2034:0.3821:0.0:0.4145	.	87	Q9BYR2	KRA45_HUMAN	R	82	ENSP00000340546:Q82R	ENSP00000340546:Q82R	Q	-	2	0	KRTAP4-5	36559301	0.000000	0.05858	0.009000	0.14445	0.001000	0.01503	-1.539000	0.02202	-0.998000	0.03446	-1.710000	0.00715	CAG	.	.	weak		0.657	KRTAP4-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257783.1		
OR8H3	390152	hgsc.bcm.edu	37	11	55890066	55890066	+	Missense_Mutation	SNP	G	G	A	rs140843028	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:55890066G>A	ENST00000313472.3	+	1	218	c.218G>A	c.(217-219)aGt>aAt	p.S73N		NM_001005201.1	NP_001005201.1	Q8N146	OR8H3_HUMAN	olfactory receptor, family 8, subfamily H, member 3	73						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(30)|ovary(2)|prostate(1)|skin(3)|stomach(1)	42	Esophageal squamous(21;0.00693)					ATTGACCTCAGTTACTCAACT	0.448													G|||	73	0.0145767	0.0499	0.0101	5008	,	,		20989	0.0		0.0	False		,,,				2504	0.0				p.S73N		Atlas-SNP	.											.	OR8H3	92	.	0			c.G218A						PASS	.	G	ASN/SER	175,4227	115.0+/-153.0	4,167,2030	255.0	252.0	253.0		218	-0.2	0.9	11	dbSNP_134	253	4,8582	4.3+/-15.6	0,4,4289	no	missense	OR8H3	NM_001005201.1	46	4,171,6319	AA,AG,GG		0.0466,3.9755,1.3782	possibly-damaging	73/313	55890066	179,12809	2201	4293	6494	SO:0001583	missense	390152	exon1			ACCTCAGTTACTC	AB065840	CCDS31519.1	11q11	2012-08-09			ENSG00000181761	ENSG00000181761		"""GPCR / Class A : Olfactory receptors"""	15309	protein-coding gene	gene with protein product							Standard	NM_001005201		Approved		uc001nii.1	Q8N146	OTTHUMG00000166833	ENST00000313472.3:c.218G>A	11.37:g.55890066G>A	ENSP00000323928:p.Ser73Asn	368.0	0.0	0		390.0	160.0	0.410256	NM_001005201	Q6IFB7	Missense_Mutation	SNP	ENST00000313472.3	37	CCDS31519.1	26	0.011904761904761904	22	0.044715447154471545	4	0.011049723756906077	0	0.0	0	0.0	G	11.76	1.735059	0.30774	0.039755	4.66E-4	ENSG00000181761	ENST00000313472	T	0.01359	4.98	3.44	-0.164	0.13359	GPCR, rhodopsin-like superfamily (1);	0.421176	0.23038	N	0.052645	T	0.00875	0.0029	M	0.86864	2.845	0.09310	N	1	D	0.56287	0.975	P	0.52267	0.694	T	0.26849	-1.0091	10	0.87932	D	0	.	3.7935	0.08730	0.0939:0.291:0.4667:0.1484	.	73	Q8N146	OR8H3_HUMAN	N	73	ENSP00000323928:S73N	ENSP00000323928:S73N	S	+	2	0	OR8H3	55646642	0.006000	0.16342	0.902000	0.35471	0.267000	0.26476	1.600000	0.36762	0.075000	0.16796	0.173000	0.16961	AGT	G|0.986;A|0.014	0.014	weak		0.448	OR8H3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391541.1	NM_001005201	
JAK1	3716	hgsc.bcm.edu	37	1	65300305	65300305	+	Silent	SNP	T	T	C	rs369143723		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:65300305T>C	ENST00000342505.4	-	25	3653	c.3405A>G	c.(3403-3405)caA>caG	p.Q1135Q		NM_002227.2	NP_002218.2	P23458	JAK1_HUMAN	Janus kinase 1	1135	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-2-mediated signaling pathway (GO:0038110)|intracellular signal transduction (GO:0035556)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to antibiotic (GO:0046677)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(48)|kidney(3)|large_intestine(8)|liver(2)|lung(19)|ovary(1)|prostate(12)|skin(1)|soft_tissue(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	120				BRCA - Breast invasive adenocarcinoma(111;0.0485)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	GATTGGATGGTTGGAATTCCC	0.313			Mis		ALL																																p.Q1135Q		Atlas-SNP	.		Dom	yes		1	1p32.3-p31.3	3716	Janus kinase 1		L	.	JAK1	209	.	0			c.A3405G						PASS	.	T		1,3603		0,1,1801	104.0	98.0	100.0		3405	-4.4	0.6	1		100	0,8148		0,0,4074	no	coding-synonymous	JAK1	NM_002227.2		0,1,5875	CC,CT,TT		0.0,0.0277,0.0085		1135/1155	65300305	1,11751	1802	4074	5876	SO:0001819	synonymous_variant	3716	exon25			GGATGGTTGGAAT	M64174	CCDS41346.1	1p32.3-p31.3	2009-07-10	2009-04-23		ENSG00000162434	ENSG00000162434	2.7.10.1		6190	protein-coding gene	gene with protein product		147795		JAK1B		1848670, 7698020	Standard	NM_002227		Approved	JAK1A, JTK3	uc001dbu.1	P23458	OTTHUMG00000009310	ENST00000342505.4:c.3405A>G	1.37:g.65300305T>C		142.0	0.0	0		166.0	78.0	0.46988	NM_002227	Q59GQ2|Q9UD26	Silent	SNP	ENST00000342505.4	37	CCDS41346.1																																																																																			.	.	none		0.313	JAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025791.1	NM_002227	
ARHGAP23	57636	hgsc.bcm.edu	37	17	36623157	36623157	+	Silent	SNP	G	G	A	rs12326006	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:36623157G>A	ENST00000431231.2	+	7	1301	c.1233G>A	c.(1231-1233)ctG>ctA	p.L411L	ARHGAP23_ENST00000443378.1_Silent_p.L317L|ARHGAP23_ENST00000437668.3_Silent_p.L411L	NM_001199417.1	NP_001186346.1	Q9P227	RHG23_HUMAN	Rho GTPase activating protein 23	411					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(8)|kidney(6)|lung(1)|skin(1)|stomach(2)	20						TGCAGGGCCTGGATGACCTCG	0.706													G|||	273	0.0545128	0.1974	0.0173	5008	,	,		13202	0.0		0.0	False		,,,				2504	0.0				p.L411L		Atlas-SNP	.											.	ARHGAP23	48	.	0			c.G1233A						PASS	.						3.0	4.0	4.0					17																	36623157		622	1470	2092	SO:0001819	synonymous_variant	57636	exon7			GGGCCTGGATGAC	AB040934	CCDS56027.1	17q12	2014-05-06			ENSG00000225485	ENSG00000275832		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	29293	protein-coding gene	gene with protein product		610590				10819331, 15254754	Standard	NM_001199417		Approved	KIAA1501	uc021twd.1	Q9P227	OTTHUMG00000188547	ENST00000431231.2:c.1233G>A	17.37:g.36623157G>A		70.0	0.0	0		74.0	74.0	1	NM_001199417		Silent	SNP	ENST00000431231.2	37	CCDS56027.1																																																																																			G|0.964;A|0.036	0.036	strong		0.706	ARHGAP23-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441789.1	XM_290799	
PRR25	388199	hgsc.bcm.edu	37	16	855732	855732	+	Missense_Mutation	SNP	C	C	T	rs115484509	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:855732C>T	ENST00000301698.1	+	1	290	c.290C>T	c.(289-291)gCg>gTg	p.A97V		NM_001013638.1	NP_001013660.1	Q96S07	PRR25_HUMAN	proline rich 25	97										large_intestine(1)|lung(1)|skin(1)	3						TCAGGAACAGCGCAGCCGCTC	0.652													C|||	129	0.0257588	0.0938	0.0072	5008	,	,		17511	0.0		0.0	False		,,,				2504	0.0				p.A97V		Atlas-SNP	.											PRR25,NS,carcinoma,+1,1	PRR25	27	1	0			c.C290T						PASS	.	C	VAL/ALA	307,3571		16,275,1648	21.0	28.0	26.0		290	-0.5	0.0	16	dbSNP_132	26	1,8279		0,1,4139	yes	missense	PRR25	NM_001013638.1	64	16,276,5787	TT,TC,CC		0.0121,7.9165,2.5333	possibly-damaging	97/403	855732	308,11850	1939	4140	6079	SO:0001583	missense	388199	exon1			GAACAGCGCAGCC	BC156145	CCDS45372.1	16p13.3	2009-09-11			ENSG00000167945	ENSG00000167945			37230	protein-coding gene	gene with protein product						11157797	Standard	NM_001013638		Approved	gs64	uc010uut.2	Q96S07		ENST00000301698.1:c.290C>T	16.37:g.855732C>T	ENSP00000301698:p.Ala97Val	53.0	0.0	0		68.0	68.0	1	NM_001013638		Missense_Mutation	SNP	ENST00000301698.1	37	CCDS45372.1	44	0.020146520146520148	41	0.08333333333333333	3	0.008287292817679558	0	0.0	0	0.0	C	8.111	0.778895	0.16120	0.079165	1.21E-4	ENSG00000167945	ENST00000301698	T	0.38401	1.14	0.701	-0.467	0.12150	.	.	.	.	.	T	0.00815	0.0027	N	0.19112	0.55	0.09310	N	1	P	0.39964	0.697	B	0.29440	0.102	T	0.07121	-1.0789	8	0.87932	D	0	.	.	.	.	.	97	Q96S07	PRR25_HUMAN	V	97	ENSP00000301698:A97V	ENSP00000301698:A97V	A	+	2	0	PRR25	795733	0.000000	0.05858	0.013000	0.15412	0.030000	0.12068	-0.594000	0.05733	-0.199000	0.10317	0.313000	0.20887	GCG	C|0.977;T|0.023	0.023	strong		0.652	PRR25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440563.1	NM_001013638	
CTSG	1511	hgsc.bcm.edu	37	14	25045386	25045386	+	Missense_Mutation	SNP	C	C	G	rs61737123	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:25045386C>G	ENST00000216336.2	-	1	80	c.44G>C	c.(43-45)gGg>gCg	p.G15A		NM_001911.2	NP_001902.1	P08311	CATG_HUMAN	cathepsin G	15					angiotensin maturation (GO:0002003)|cellular protein metabolic process (GO:0044267)|defense response to fungus (GO:0050832)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|immune response (GO:0006955)|negative regulation of growth of symbiont in host (GO:0044130)|neutrophil mediated killing of gram-positive bacterium (GO:0070946)|positive regulation of immune response (GO:0050778)|proteolysis (GO:0006508)|response to lipopolysaccharide (GO:0032496)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)	heparin binding (GO:0008201)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			autonomic_ganglia(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(265;0.0269)		TGCCTCAGCCCCAGTGGGTAG	0.527													C|||	68	0.0135783	0.0492	0.0043	5008	,	,		18510	0.0		0.0	False		,,,				2504	0.0				p.G15A		Atlas-SNP	.											.	CTSG	63	.	0			c.G44C						PASS	.	C	ALA/GLY	228,4178	128.6+/-165.4	7,214,1982	63.0	54.0	57.0		44	1.1	0.0	14	dbSNP_129	57	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CTSG	NM_001911.2	60	7,216,6280	GG,GC,CC		0.0233,5.1748,1.7684	probably-damaging	15/256	25045386	230,12776	2203	4300	6503	SO:0001583	missense	1511	exon1			TCAGCCCCAGTGG	M16117	CCDS9631.1	14q12	2013-02-25			ENSG00000100448	ENSG00000100448		"""Cathepsins"", ""Endogenous ligands"""	2532	protein-coding gene	gene with protein product		116830				2569462	Standard	NM_001911		Approved	CG	uc001wpq.3	P08311	OTTHUMG00000140182	ENST00000216336.2:c.44G>C	14.37:g.25045386C>G	ENSP00000216336:p.Gly15Ala	77.0	0.0	0		83.0	37.0	0.445783	NM_001911	Q6IBJ6|Q9UCA5|Q9UCU6	Missense_Mutation	SNP	ENST00000216336.2	37	CCDS9631.1	22	0.010073260073260074	20	0.04065040650406504	2	0.0055248618784530384	0	0.0	0	0.0	c	11.21	1.572963	0.28092	0.051748	2.33E-4	ENSG00000100448	ENST00000216336	D	0.92752	-3.1	5.29	1.14	0.20703	Peptidase cysteine/serine, trypsin-like (1);	0.801389	0.10545	N	0.662150	T	0.49406	0.1555	L	0.28400	0.85	0.09310	N	1	B	0.25312	0.123	B	0.21360	0.034	T	0.57774	-0.7753	10	0.06236	T	0.91	.	6.4789	0.22051	0.0:0.6773:0.1397:0.1829	rs61737123	15	P08311	CATG_HUMAN	A	15	ENSP00000216336:G15A	ENSP00000216336:G15A	G	-	2	0	CTSG	24115226	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	0.884000	0.28214	0.309000	0.22966	0.655000	0.94253	GGG	C|0.969;G|0.031	0.031	strong		0.527	CTSG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276536.2	NM_001911	
FREM2	341640	hgsc.bcm.edu	37	13	39264083	39264083	+	Missense_Mutation	SNP	C	C	G	rs7329939	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:39264083C>G	ENST00000280481.7	+	1	2818	c.2602C>G	c.(2602-2604)Ctc>Gtc	p.L868V		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	868			L -> V (in dbSNP:rs7329939).		cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		CTCTTTCACTCTCACTCAGGC	0.507													C|||	315	0.0628994	0.208	0.0231	5008	,	,		21471	0.001		0.0089	False		,,,				2504	0.0143				p.L868V		Atlas-SNP	.											.	FREM2	385	.	0			c.C2602G						PASS	.	C	VAL/LEU	745,3661	306.3+/-289.4	68,609,1526	101.0	88.0	92.0		2602	5.8	1.0	13	dbSNP_116	92	88,8512	49.8+/-109.6	1,86,4213	yes	missense	FREM2	NM_207361.4	32	69,695,5739	GG,GC,CC		1.0233,16.9088,6.4047	benign	868/3170	39264083	833,12173	2203	4300	6503	SO:0001583	missense	341640	exon1			TTCACTCTCACTC	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.2602C>G	13.37:g.39264083C>G	ENSP00000280481:p.Leu868Val	112.0	0.0	0		114.0	64.0	0.561404	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	96	0.04395604395604396	82	0.16666666666666666	9	0.024861878453038673	0	0.0	5	0.006596306068601583	C	10.04	1.240711	0.22711	0.169088	0.010233	ENSG00000150893	ENST00000280481	T	0.43294	0.95	5.8	5.8	0.92144	.	0.062991	0.64402	D	0.000004	T	0.00109	0.0003	N	0.25647	0.755	0.19575	P	0.9999648898	B	0.30824	0.296	B	0.27262	0.078	T	0.03068	-1.1076	9	0.33940	T	0.23	.	20.0609	0.97674	0.0:1.0:0.0:0.0	rs7329939;rs52807873;rs7329939	868	Q5SZK8	FREM2_HUMAN	V	868	ENSP00000280481:L868V	ENSP00000280481:L868V	L	+	1	0	FREM2	38162083	0.038000	0.19896	1.000000	0.80357	0.329000	0.28539	0.383000	0.20651	2.755000	0.94549	0.655000	0.94253	CTC	C|0.947;G|0.053	0.053	strong		0.507	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
OR8B2	26595	hgsc.bcm.edu	37	11	124253042	124253042	+	Silent	SNP	G	G	A	rs142893914	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124253042G>A	ENST00000375013.2	-	1	216	c.198C>T	c.(196-198)ctC>ctT	p.L66L		NM_001005468.1	NP_001005468.1	Q96RD0	OR8B2_HUMAN	olfactory receptor, family 8, subfamily B, member 2	66						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(13)|ovary(1)	23		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;0.0277)		CAATGAAGGAGAGATTGAAGA	0.398													g|||	90	0.0179712	0.0605	0.0115	5008	,	,		22840	0.0		0.002	False		,,,				2504	0.0				p.L66L		Atlas-SNP	.											.	OR8B2	42	.	0			c.C198T						PASS	.	G		271,4131	153.7+/-187.2	8,255,1938	154.0	143.0	147.0		198	-8.4	0.0	11	dbSNP_134	147	5,8587	4.3+/-15.6	0,5,4291	no	coding-synonymous	OR8B2	NM_001005468.1		8,260,6229	AA,AG,GG		0.0582,6.1563,2.1241		66/314	124253042	276,12718	2201	4296	6497	SO:0001819	synonymous_variant	26595	exon1			GAAGGAGAGATTG	AB065826	CCDS31708.1	11q24.1	2012-08-09			ENSG00000204293	ENSG00000204293		"""GPCR / Class A : Olfactory receptors"""	8471	protein-coding gene	gene with protein product							Standard	XM_005271500		Approved		uc010sai.2	Q96RD0	OTTHUMG00000165982	ENST00000375013.2:c.198C>T	11.37:g.124253042G>A		242.0	0.0	0		175.0	87.0	0.497143	NM_001005468	Q8NGH2	Silent	SNP	ENST00000375013.2	37	CCDS31708.1																																																																																			.	.	weak		0.398	OR8B2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387290.1	NM_001005468	
RHBDF1	64285	hgsc.bcm.edu	37	16	113027	113027	+	Missense_Mutation	SNP	G	G	A	rs78541046	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:113027G>A	ENST00000262316.6	-	5	758	c.616C>T	c.(616-618)Cgc>Tgc	p.R206C	RHBDF1_ENST00000454039.2_Missense_Mutation_p.R206C	NM_022450.3	NP_071895.3	Q96CC6	RHDF1_HUMAN	rhomboid 5 homolog 1 (Drosophila)	206					cell migration (GO:0016477)|cell proliferation (GO:0008283)|negative regulation of protein secretion (GO:0050709)|protein transport (GO:0015031)|proteolysis (GO:0006508)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of protein secretion (GO:0050708)	endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	18		all_cancers(16;2.56e-05)|all_epithelial(16;0.000116)|Hepatocellular(780;0.0068)|Lung NSC(18;0.0795)|all_lung(18;0.159)				TCTCGCTTGCGCCGCCGCGGG	0.701													G|||	19	0.00379393	0.0144	0.0	5008	,	,		13623	0.0		0.0	False		,,,				2504	0.0				p.R206C		Atlas-SNP	.											.	RHBDF1	54	.	0			c.C616T						PASS	.	G	CYS/ARG	46,4332		1,44,2144	27.0	32.0	30.0		616	5.1	1.0	16	dbSNP_131	30	0,8578		0,0,4289	yes	missense	RHBDF1	NM_022450.3	180	1,44,6433	AA,AG,GG		0.0,1.0507,0.355	probably-damaging	206/856	113027	46,12910	2189	4289	6478	SO:0001583	missense	64285	exon5			GCTTGCGCCGCCG	BC014425	CCDS32344.1	16p13.3	2008-02-05	2006-02-22		ENSG00000007384	ENSG00000007384			20561	protein-coding gene	gene with protein product		614403	"""chromosome 16 open reading frame 8"", ""rhomboid family 1 (Drosophila)"""	C16orf8		8318735, 15965977	Standard	NM_022450		Approved	EGFR-RS, FLJ2235, Dist1	uc002cfl.4	Q96CC6	OTTHUMG00000060719	ENST00000262316.6:c.616C>T	16.37:g.113027G>A	ENSP00000262316:p.Arg206Cys	96.0	0.0	0		140.0	80.0	0.571429	NM_022450	Q04842|Q1W6H2|Q4TT59|Q96S34|Q9H6E1	Missense_Mutation	SNP	ENST00000262316.6	37	CCDS32344.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	.	24.2	4.509855	0.85282	0.010507	0.0	ENSG00000007384	ENST00000262316;ENST00000454039	T;T	0.80304	-1.36;-1.36	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	D	0.86406	0.5925	M	0.74258	2.255	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.994;0.998;0.999	D	0.88684	0.3204	10	0.62326	D	0.03	-33.0545	17.4836	0.87682	0.0:0.0:1.0:0.0	.	206;229;206	F5GWL4;B4E3Q0;Q96CC6	.;.;RHDF1_HUMAN	C	206	ENSP00000262316:R206C;ENSP00000392133:R206C	ENSP00000262316:R206C	R	-	1	0	RHBDF1	53027	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.266000	0.65525	2.354000	0.79902	0.462000	0.41574	CGC	G|0.996;A|0.004	0.004	strong		0.701	RHBDF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134178.2	NM_022450	
OR51V1	283111	hgsc.bcm.edu	37	11	5221132	5221132	+	Missense_Mutation	SNP	G	G	A	rs61736992	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5221132G>A	ENST00000321255.1	-	1	798	c.799C>T	c.(799-801)Ctc>Ttc	p.L267F		NM_001004760.2	NP_001004760.2	Q9H2C8	O51V1_HUMAN	olfactory receptor, family 51, subfamily V, member 1	267					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)			endometrium(1)|kidney(2)|large_intestine(13)|lung(19)|skin(2)|upper_aerodigestive_tract(2)	39		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;2.83e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACCATTGTGAGGCTAATGATA	0.483													G|||	126	0.0251597	0.0378	0.0086	5008	,	,		19744	0.0		0.0189	False		,,,				2504	0.0521				p.L267F		Atlas-SNP	.											.	OR51V1	77	.	0			c.C799T						PASS	.	G	PHE/LEU	182,4220	116.3+/-154.2	1,180,2020	134.0	117.0	123.0		799	1.4	0.0	11	dbSNP_129	123	209,8387	89.4+/-151.6	4,201,4093	yes	missense	OR51V1	NM_001004760.2	22	5,381,6113	AA,AG,GG		2.4314,4.1345,3.0082	probably-damaging	267/322	5221132	391,12607	2201	4298	6499	SO:0001583	missense	283111	exon1			TTGTGAGGCTAAT	BK004432	CCDS31375.1	11p15.4	2012-08-09			ENSG00000176742	ENSG00000176742		"""GPCR / Class A : Olfactory receptors"""	19597	protein-coding gene	gene with protein product				OR51A12			Standard	NM_001004760		Approved		uc010qyz.2	Q9H2C8	OTTHUMG00000066671	ENST00000321255.1:c.799C>T	11.37:g.5221132G>A	ENSP00000321729:p.Leu267Phe	117.0	0.0	0		104.0	58.0	0.557692	NM_001004760		Missense_Mutation	SNP	ENST00000321255.1	37	CCDS31375.1	32	0.014652014652014652	15	0.03048780487804878	6	0.016574585635359115	0	0.0	11	0.014511873350923483	G	10.05	1.243241	0.22796	0.041345	0.024314	ENSG00000176742	ENST00000321255	T	0.72835	-0.69	5.27	1.37	0.22104	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40144	N	0.001163	T	0.56992	0.2023	M	0.85373	2.75	0.09310	N	1	D	0.89917	1.0	D	0.97110	1.0	T	0.63972	-0.6516	10	0.87932	D	0	.	8.363	0.32369	0.3867:0.0:0.6133:0.0	.	267	Q9H2C8	O51V1_HUMAN	F	267	ENSP00000321729:L267F	ENSP00000321729:L267F	L	-	1	0	OR51V1	5177708	0.000000	0.05858	0.001000	0.08648	0.008000	0.06430	-0.502000	0.06390	0.103000	0.17682	0.655000	0.94253	CTC	G|0.975;A|0.025	0.025	strong		0.483	OR51V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142965.1	NM_001004760	
UBE2L3	7332	hgsc.bcm.edu	37	22	21965298	21965298	+	Silent	SNP	C	C	G	rs61133050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:21965298C>G	ENST00000342192.4	+	3	474	c.276C>G	c.(274-276)gcC>gcG	p.A92A	UBE2L3_ENST00000545681.1_Silent_p.A60A|UBE2L3_ENST00000458578.2_Silent_p.A150A	NM_003347.3	NP_003338.1	P68036	UB2L3_HUMAN	ubiquitin-conjugating enzyme E2L 3	92					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to steroid hormone stimulus (GO:0071383)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein K11-linked ubiquitination (GO:0070979)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activator activity (GO:0097027)|ubiquitin-protein transferase activity (GO:0004842)		UBE2L3/KRAS(2)	large_intestine(4)	4	Colorectal(54;0.105)					TAATTAGTGCCGAAAACTGGA	0.512													T|||	162	0.0323482	0.1172	0.0101	5008	,	,		17052	0.0		0.0	False		,,,				2504	0.0				p.A150A		Atlas-SNP	.											.	UBE2L3	11	.	0			c.C450G						PASS	.	T		393,4013		18,357,1828	38.0	38.0	38.0		276	4.6	1.0	22	dbSNP_129	38	4,8596		0,4,4296	no	coding-synonymous	UBE2L3	NM_003347.2		18,361,6124	GG,GC,CC		0.0465,8.9197,3.0524		92/155	21965298	397,12609	2203	4300	6503	SO:0001819	synonymous_variant	7332	exon3			TAGTGCCGAAAAC	AJ000519	CCDS13790.1, CCDS58795.1, CCDS58796.1	22q11.2	2007-02-05			ENSG00000185651	ENSG00000185651		"""Ubiquitin-conjugating enzymes E2"""	12488	protein-coding gene	gene with protein product		603721				8672131, 9693040	Standard	NM_001256356		Approved	UBCH7	uc031rxe.1	P68036	OTTHUMG00000150823	ENST00000342192.4:c.276C>G	22.37:g.21965298C>G		446.0	0.0	0		459.0	203.0	0.442266	NM_001256355	B2R4A7|B4DDG1|B4DSZ4|E7EWS7|P51966|P70653|Q9HAV1	Silent	SNP	ENST00000342192.4	37	CCDS13790.1																																																																																			C|0.964;G|0.036	0.036	strong		0.512	UBE2L3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320219.1	NM_198157	
CYP11B1	1584	hgsc.bcm.edu	37	8	143958291	143958291	+	Silent	SNP	C	C	T	rs61751154		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:143958291C>T	ENST00000292427.4	-	4	638	c.606G>A	c.(604-606)ttG>ttA	p.L202L	CYP11B1_ENST00000377675.3_Silent_p.L273L|CYP11B1_ENST00000517471.1_Silent_p.L202L	NM_000497.3	NP_000488.3	P15538	C11B1_HUMAN	cytochrome P450, family 11, subfamily B, polypeptide 1	202					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)|glucocorticoid biosynthetic process (GO:0006704)|glucose homeostasis (GO:0042593)|immune response (GO:0006955)|mineralocorticoid biosynthetic process (GO:0006705)|regulation of blood pressure (GO:0008217)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|sterol metabolic process (GO:0016125)|xenobiotic metabolic process (GO:0006805)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|steroid 11-beta-monooxygenase activity (GO:0004507)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(10)|lung(36)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	67	all_cancers(97;4.74e-11)|all_epithelial(106;2.06e-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)				Cimetidine(DB00501)|Clotrimazole(DB00257)|Etomidate(DB00292)|Fluconazole(DB00196)|Hydrocortisone(DB00741)|Ketoconazole(DB01026)|Metoclopramide(DB01233)|Metyrapone(DB01011)|Miconazole(DB01110)|Mitotane(DB00648)|Phenytoin(DB00252)|Spironolactone(DB00421)	CAAAAAGAGCCAAGTTGCTGG	0.642									Familial Hyperaldosteronism type I				.|||	1	0.000199681	0.0008	0.0	5008	,	,		19690	0.0		0.0	False		,,,				2504	0.0				p.L202L		Atlas-SNP	.											CYP11B1,right_lower_lobe,carcinoma,0,1	CYP11B1	128	1	0			c.G606A						scavenged	.						37.0	38.0	38.0					8																	143958291		2203	4300	6503	SO:0001819	synonymous_variant	1584	exon4	Familial Cancer Database	Dexamethasone Sensitive Aldosteronism, FH-I	AAGAGCCAAGTTG	D16153	CCDS6392.1, CCDS34953.1	8q21-q22	2013-06-19	2003-01-14		ENSG00000160882	ENSG00000160882	1.14.15.4	"""Cytochrome P450s"""	2591	protein-coding gene	gene with protein product	"""steroid 11-beta-monooxygenase"""	610613	"""cytochrome P450, subfamily XIB (steroid 11-beta-hydroxylase), polypeptide 1"""	CYP11B		1303253	Standard	XM_005250807		Approved	P450C11, FHI, CPN1	uc003yxi.3	P15538	OTTHUMG00000164637	ENST00000292427.4:c.606G>A	8.37:g.143958291C>T		140.0	1.0	0.00714286		184.0	24.0	0.130435	NM_000497	Q14095|Q4VAQ8|Q4VAQ9|Q9UML2	Silent	SNP	ENST00000292427.4	37	CCDS6392.1																																																																																			C|0.025;T|0.975	0.975	strong		0.642	CYP11B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379475.2		
RNF151	146310	hgsc.bcm.edu	37	16	2018580	2018580	+	Missense_Mutation	SNP	G	G	A	rs62038784	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2018580G>A	ENST00000569714.1	+	4	400	c.392G>A	c.(391-393)cGg>cAg	p.R131Q	RNF151_ENST00000321392.3_Missense_Mutation_p.R130Q|RNF151_ENST00000569210.2_3'UTR	NM_174903.4	NP_777563.2	Q2KHN1	RN151_HUMAN	ring finger protein 151	131					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			kidney(1)|lung(1)	2						GCAGAGCACCGGCAGCATTGC	0.706													G|||	204	0.0407348	0.118	0.0159	5008	,	,		15035	0.0069		0.0179	False		,,,				2504	0.0123				p.R131Q		Atlas-SNP	.											.	RNF151	12	.	0			c.G392A						PASS	.	G	GLN/ARG	323,3615		11,301,1657	10.0	10.0	10.0		392	-6.3	0.0	16	dbSNP_129	10	101,8157		1,99,4029	no	missense	RNF151	NM_174903.4	43	12,400,5686	AA,AG,GG		1.2231,8.2021,3.4765	benign	131/246	2018580	424,11772	1969	4129	6098	SO:0001583	missense	146310	exon4			AGCACCGGCAGCA	BC029501	CCDS58405.1	16p13.3	2013-01-09			ENSG00000179580	ENSG00000179580		"""RING-type (C3HC4) zinc fingers"""	23235	protein-coding gene	gene with protein product						12477932	Standard	NM_174903		Approved		uc002cnt.1	Q2KHN1	OTTHUMG00000176852	ENST00000569714.1:c.392G>A	16.37:g.2018580G>A	ENSP00000456566:p.Arg131Gln	73.0	0.0	0		77.0	44.0	0.571429	NM_174903	Q8NHS5	Missense_Mutation	SNP	ENST00000569714.1	37	CCDS58405.1	67	0.030677655677655676	49	0.09959349593495935	6	0.016574585635359115	4	0.006993006993006993	8	0.010554089709762533	g	1.782	-0.481785	0.04383	0.082021	0.012231	ENSG00000179580	ENST00000321392	T	0.29142	1.58	5.25	-6.3	0.02007	Zinc finger, TRAF-type (1);TRAF-like (1);Zinc finger, SIAH-type (1);	0.679770	0.13596	N	0.376216	T	0.00384	0.0012	L	0.33485	1.01	0.09310	N	1	B	0.22683	0.073	B	0.16289	0.015	T	0.22138	-1.0225	10	0.12430	T	0.62	-5.4708	7.1367	0.25533	0.5424:0.0:0.3431:0.1145	rs62038784	131	Q2KHN1	RN151_HUMAN	Q	130	ENSP00000325794:R130Q	ENSP00000325794:R130Q	R	+	2	0	RNF151	1958581	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.062000	0.11674	-1.696000	0.01421	-1.119000	0.02030	CGG	G|0.970;A|0.030	0.030	strong		0.706	RNF151-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434030.1	NM_174903	
DNAI2	64446	hgsc.bcm.edu	37	17	72306239	72306239	+	Silent	SNP	C	C	G	rs144035254	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:72306239C>G	ENST00000311014.6	+	11	1498	c.1431C>G	c.(1429-1431)acC>acG	p.T477T	RP11-647F2.2_ENST00000585167.1_RNA|DNAI2_ENST00000582036.1_Silent_p.T465T|AC103809.1_ENST00000516976.1_RNA|DNAI2_ENST00000446837.2_Silent_p.T477T|DNAI2_ENST00000307504.5_Silent_p.T334T|DNAI2_ENST00000579490.1_Silent_p.T534T			Q9GZS0	DNAI2_HUMAN	dynein, axonemal, intermediate chain 2	477					cilium assembly (GO:0042384)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(6)|liver(2)|lung(19)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	39						GGACAACCACCCTGCTGGAGG	0.627									Kartagener syndrome				C|||	27	0.00539137	0.0204	0.0	5008	,	,		12200	0.0		0.0	False		,,,				2504	0.0				p.T477T		Atlas-SNP	.											.	DNAI2	102	.	0			c.C1431G						PASS	.	C	,	65,4341	61.1+/-98.1	1,63,2139	53.0	49.0	50.0		1395,1431	-4.8	0.9	17	dbSNP_134	50	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	DNAI2	NM_001172810.1,NM_023036.4	,	1,64,6438	GG,GC,CC		0.0116,1.4753,0.5075	,	465/594,477/606	72306239	66,12940	2203	4300	6503	SO:0001819	synonymous_variant	64446	exon11	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AACCACCCTGCTG	AF250288	CCDS11697.1, CCDS58589.1	17q25	2013-02-19	2006-09-04			ENSG00000171595		"""Axonemal dyneins"", ""WD repeat domain containing"""	18744	protein-coding gene	gene with protein product	"""dynein intermediate chain 2"""	605483	"""dynein, axonemal, intermediate polypeptide 2"""			11153919, 21953912	Standard	NM_023036		Approved	CILD9, DIC2	uc002jkf.3	Q9GZS0		ENST00000311014.6:c.1431C>G	17.37:g.72306239C>G		69.0	0.0	0		72.0	30.0	0.416667	NM_023036	C9J0S6|Q8IUW4|Q9H179|Q9NT53	Silent	SNP	ENST00000311014.6	37	CCDS11697.1																																																																																			C|0.996;G|0.004	0.004	strong		0.627	DNAI2-001	KNOWN	NMD_exception|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000442537.1	NM_023036	
CACNA1H	8912	hgsc.bcm.edu	37	16	1245062	1245062	+	Silent	SNP	C	C	T	rs59794024	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1245062C>T	ENST00000348261.5	+	3	638	c.390C>T	c.(388-390)tcC>tcT	p.S130S	CACNA1H_ENST00000565831.1_Silent_p.S130S|CACNA1H_ENST00000358590.4_Silent_p.S130S	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	130					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	AGTGCGGCTCCGAGCGCTGCA	0.647											OREG0023543	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	c|||	215	0.0429313	0.1551	0.0144	5008	,	,		8995	0.0		0.0	False		,,,				2504	0.0				p.S130S		Atlas-SNP	.											.	CACNA1H	317	.	0			c.C390T						PASS	.		,	470,3718		28,414,1652	79.0	86.0	84.0		390,390	-9.0	0.7	16	dbSNP_129	84	3,8407		0,3,4202	no	coding-synonymous,coding-synonymous	CACNA1H	NM_001005407.1,NM_021098.2	,	28,417,5854	TT,TC,CC		0.0357,11.2225,3.7546	,	130/2348,130/2354	1245062	473,12125	2094	4205	6299	SO:0001819	synonymous_variant	8912	exon3			CGGCTCCGAGCGC	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.390C>T	16.37:g.1245062C>T		80.0	0.0	0	594	77.0	34.0	0.441558	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Silent	SNP	ENST00000348261.5	37	CCDS45375.1																																																																																			C|0.967;T|0.033	0.033	strong		0.647	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
GPR176	11245	hgsc.bcm.edu	37	15	40094431	40094431	+	Silent	SNP	C	C	T	rs76578471	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:40094431C>T	ENST00000561100.1	-	3	1315	c.450G>A	c.(448-450)ctG>ctA	p.L150L	GPR176_ENST00000299092.3_Silent_p.L149L|GPR176_ENST00000543580.1_Silent_p.L105L|RP11-37C7.1_ENST00000558616.1_RNA|GPR176_ENST00000560729.1_5'UTR	NM_007223.1	NP_009154.1	Q14439	GP176_HUMAN	G protein-coupled receptor 176	150					G-protein coupled receptor signaling pathway (GO:0007186)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(3)|liver(1)|lung(9)|ovary(2)|pancreas(1)|skin(2)	23		all_cancers(109;4.05e-15)|all_epithelial(112;2.96e-13)|Lung NSC(122;8.53e-11)|all_lung(180;2.71e-09)|Melanoma(134;0.091)|Colorectal(260;0.198)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;4.4e-06)|BRCA - Breast invasive adenocarcinoma(123;0.123)		TTTTCCTCTCCAGTGGATAGA	0.438											OREG0023053	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	67	0.0133786	0.0477	0.0058	5008	,	,		21801	0.0		0.0	False		,,,				2504	0.0				p.L150L		Atlas-SNP	.											.	GPR176	41	.	0			c.G450A						PASS	.	C		112,4294	86.3+/-125.0	0,112,2091	70.0	61.0	64.0		450	4.8	1.0	15	dbSNP_132	64	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GPR176	NM_007223.1		0,113,6390	TT,TC,CC		0.0116,2.542,0.8688		150/516	40094431	113,12893	2203	4300	6503	SO:0001819	synonymous_variant	11245	exon3			CCTCTCCAGTGGA	BC067106	CCDS10051.1, CCDS61588.1, CCDS61589.1	15q14-q15.1	2012-08-21			ENSG00000166073	ENSG00000166073		"""GPCR / Class A : Orphans"""	32370	protein-coding gene	gene with protein product		612183				7893747	Standard	NM_007223		Approved	Gm1012	uc010uck.2	Q14439	OTTHUMG00000129873	ENST00000561100.1:c.450G>A	15.37:g.40094431C>T		39.0	0.0	0	890	47.0	21.0	0.446809	NM_007223	Q6NXF6	Silent	SNP	ENST00000561100.1	37	CCDS10051.1																																																																																			C|0.989;T|0.011	0.011	strong		0.438	GPR176-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252117.2	NM_007223	
DHRS1	115817	hgsc.bcm.edu	37	14	24768220	24768220	+	Silent	SNP	G	G	T	rs150092528		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:24768220G>T	ENST00000288111.7	-	2	369	c.93C>A	c.(91-93)ggC>ggA	p.G31G	NOP9_ENST00000267425.3_5'Flank|NOP9_ENST00000396802.3_5'Flank|DHRS1_ENST00000396813.1_Silent_p.G31G	NM_001136050.2	NP_001129522.1	Q96LJ7	DHRS1_HUMAN	dehydrogenase/reductase (SDR family) member 1	31						endoplasmic reticulum (GO:0005783)|mitochondrial inner membrane (GO:0005743)	oxidoreductase activity (GO:0016491)			cervix(1)|endometrium(1)|large_intestine(2)|lung(2)	6				GBM - Glioblastoma multiforme(265;2.81e-08)|OV - Ovarian serous cystadenocarcinoma(311;0.0442)		AAACTGTGGCGCCTGCTTTGC	0.582																																					p.G31G		Atlas-SNP	.											.	DHRS1	21	.	0			c.C93A						PASS	.	G	,	1,4405	2.1+/-5.4	0,1,2202	67.0	60.0	63.0		93,93	-8.8	0.9	14	dbSNP_134	63	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	DHRS1	NM_001136050.2,NM_138452.2	,	0,1,6502	TT,TG,GG		0.0,0.0227,0.0077	,	31/314,31/314	24768220	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	115817	exon2			TGTGGCGCCTGCT	AK058159	CCDS9623.1	14q11.2	2011-09-14			ENSG00000157379	ENSG00000157379	1.1.-.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	16445	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 19C, member 1"""	610410				12153138, 19027726	Standard	NM_138452		Approved	FLJ25430, MGC20204, SDR19C1	uc001wok.3	Q96LJ7	OTTHUMG00000029333	ENST00000288111.7:c.93C>A	14.37:g.24768220G>T		59.0	0.0	0		69.0	25.0	0.362319	NM_138452	D3DS71|Q8NDG3|Q96B59|Q96CQ5	Silent	SNP	ENST00000288111.7	37	CCDS9623.1																																																																																			G|1.000;T|0.000	0.000	weak		0.582	DHRS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073168.4	NM_138452	
FER	2241	hgsc.bcm.edu	37	5	108281862	108281862	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:108281862C>T	ENST00000281092.4	+	11	1652	c.1268C>T	c.(1267-1269)tCt>tTt	p.S423F	FER_ENST00000536402.1_Silent_p.L319L|FER_ENST00000438717.2_Missense_Mutation_p.S248F	NM_005246.2	NP_005237.2	P16591	FER_HUMAN	fer (fps/fes related) tyrosine kinase	423					actin cytoskeleton reorganization (GO:0031532)|cell proliferation (GO:0008283)|cell-cell adhesion mediated by cadherin (GO:0044331)|cellular response to insulin stimulus (GO:0032869)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to reactive oxygen species (GO:0034614)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|diapedesis (GO:0050904)|extracellular matrix-cell signaling (GO:0035426)|Fc-epsilon receptor signaling pathway (GO:0038095)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|interleukin-6-mediated signaling pathway (GO:0070102)|intracellular signal transduction (GO:0035556)|Kit signaling pathway (GO:0038109)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of mast cell activation involved in immune response (GO:0033007)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|regulation of fibroblast migration (GO:0010762)|regulation of lamellipodium assembly (GO:0010591)|regulation of protein phosphorylation (GO:0001932)|response to lipopolysaccharide (GO:0032496)|response to platelet-derived growth factor (GO:0036119)|substrate adhesion-dependent cell spreading (GO:0034446)|tyrosine phosphorylation of Stat3 protein (GO:0042503)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nucleus (GO:0005634)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			NS(2)|biliary_tract(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(12)|ovary(1)|skin(2)|stomach(1)|urinary_tract(2)	32		all_cancers(142;2.86e-06)|all_epithelial(76;9.81e-08)|Prostate(80;0.00972)|Lung NSC(167;0.039)|Ovarian(225;0.0448)|all_lung(232;0.0496)|Colorectal(57;0.0986)|Breast(839;0.152)		OV - Ovarian serous cystadenocarcinoma(64;6.77e-10)|Epithelial(69;4.13e-08)|COAD - Colon adenocarcinoma(37;0.0174)		AAATTTGAATCTATTCGTCAT	0.373																																					p.S423F	Colon(146;1051 1799 9836 27344 47401)	Atlas-SNP	.											.	FER	100	.	0			c.C1268T						PASS	.						129.0	134.0	132.0					5																	108281862		2202	4300	6502	SO:0001583	missense	2241	exon11			TTGAATCTATTCG	J03358	CCDS4098.1	5q21	2013-02-14	2008-02-07		ENSG00000151422	ENSG00000151422	2.7.10.1	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""SH2 domain containing"""	3655	protein-coding gene	gene with protein product	"""phosphoprotein NCP94"", ""protein phosphatase 1, regulatory subunit 74"""	176942					Standard	NM_005246		Approved	TYK3, PPP1R74	uc003kop.1	P16591	OTTHUMG00000128751	ENST00000281092.4:c.1268C>T	5.37:g.108281862C>T	ENSP00000281092:p.Ser423Phe	77.0	0.0	0		70.0	4.0	0.0571429	NM_005246	B2RCR4|B4DSQ2|H2FLB8	Missense_Mutation	SNP	ENST00000281092.4	37	CCDS4098.1	.	.	.	.	.	.	.	.	.	.	C	19.61	3.859764	0.71834	.	.	ENSG00000151422	ENST00000281092;ENST00000438717	T;T	0.75367	-0.92;-0.93	5.45	5.45	0.79879	.	0.045955	0.85682	D	0.000000	T	0.68842	0.3045	N	0.22421	0.69	0.49213	D	0.999767	P	0.37955	0.612	B	0.41088	0.347	T	0.72261	-0.4345	10	0.66056	D	0.02	-12.8969	19.6346	0.95724	0.0:1.0:0.0:0.0	.	423	P16591	FER_HUMAN	F	423;248	ENSP00000281092:S423F;ENSP00000394297:S248F	ENSP00000281092:S423F	S	+	2	0	FER	108309761	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.910000	0.75741	2.720000	0.93068	0.491000	0.48974	TCT	.	.	none		0.373	FER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250664.1	NM_005246	
CEBPZ	10153	hgsc.bcm.edu	37	2	37454998	37454998	+	Silent	SNP	A	A	G	rs1803251	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:37454998A>G	ENST00000234170.5	-	2	1483	c.1338T>C	c.(1336-1338)aaT>aaC	p.N446N		NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	446					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|endometrium(2)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28		all_hematologic(82;0.21)				GAGCCATTTGATTTAAAAAGC	0.343													A|||	451	0.0900559	0.32	0.0389	5008	,	,		21260	0.0		0.001	False		,,,				2504	0.0				p.N446N		Atlas-SNP	.											.	CEBPZ	68	.	0			c.T1338C						PASS	.	A		1241,3163	393.3+/-328.8	184,873,1145	69.0	70.0	70.0		1338	3.0	1.0	2	dbSNP_89	70	15,8585	8.4+/-32.0	0,15,4285	no	coding-synonymous	CEBPZ	NM_005760.2		184,888,5430	GG,GA,AA		0.1744,28.1789,9.6586		446/1055	37454998	1256,11748	2202	4300	6502	SO:0001819	synonymous_variant	10153	exon2			CATTTGATTTAAA	M37197	CCDS1787.1	2p22.3	2008-09-03	2008-09-03		ENSG00000115816	ENSG00000115816			24218	protein-coding gene	gene with protein product		612828				2247079, 12534345	Standard	NM_005760		Approved	CBF2, CTF2	uc002rpz.3	Q03701	OTTHUMG00000100960	ENST00000234170.5:c.1338T>C	2.37:g.37454998A>G		61.0	0.0	0		68.0	36.0	0.529412	NM_005760	Q8NE75	Silent	SNP	ENST00000234170.5	37	CCDS1787.1																																																																																			A|0.912;G|0.088	0.088	strong		0.343	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218569.2	NM_005760	
NELFA	7469	hgsc.bcm.edu	37	4	1985668	1985668	+	Silent	SNP	G	G	A	rs2234574	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:1985668G>A	ENST00000411638.2	-	9	1224	c.1209C>T	c.(1207-1209)gtC>gtT	p.V403V	NELFA_ENST00000542778.1_Silent_p.V268V|MIR943_ENST00000401286.1_RNA|NELFA_ENST00000382882.3_Silent_p.V414V	NM_005663.4	NP_005654.3	Q9H3P2	NELFA_HUMAN	negative elongation factor complex member A	403					gene expression (GO:0010467)|multicellular organismal development (GO:0007275)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|positive regulation of viral transcription (GO:0050434)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	cytoplasm (GO:0005737)|NELF complex (GO:0032021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)										TGGTAGGGGCGACAGCCGGAG	0.682													G|||	137	0.0273562	0.0825	0.013	5008	,	,		13899	0.0129		0.002	False		,,,				2504	0.0041				p.V414V		Atlas-SNP	.											.	.	.	.	0			c.C1242T						PASS	.	G		286,4120	156.6+/-189.7	5,276,1922	42.0	45.0	44.0		1242	-2.0	0.0	4	dbSNP_98	44	13,8585	9.1+/-34.3	0,13,4286	no	coding-synonymous	WHSC2	NM_005663.4		5,289,6208	AA,AG,GG		0.1512,6.4911,2.2993		414/540	1985668	299,12705	2203	4299	6502	SO:0001819	synonymous_variant	7469	exon9			AGGGGCGACAGCC	AF101434	CCDS3358.2	4p16.3	2013-01-31	2013-01-31	2013-01-31	ENSG00000185049	ENSG00000185049			12768	protein-coding gene	gene with protein product		606026	"""Wolf-Hirschhorn syndrome candidate 2"""	WHSC2		10409432	Standard	NM_005663		Approved	NELF-A	uc003gem.3	Q9H3P2	OTTHUMG00000089967	ENST00000411638.2:c.1209C>T	4.37:g.1985668G>A		70.0	0.0	0		126.0	66.0	0.52381	NM_005663	A2A2T1|O95392	Silent	SNP	ENST00000411638.2	37																																																																																				G|0.977;A|0.023	0.023	strong		0.682	NELFA-015	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000473007.1	NM_005663	
CLDN23	137075	hgsc.bcm.edu	37	8	8559917	8559917	+	Silent	SNP	G	G	A	rs61754917	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:8559917G>A	ENST00000519106.1	+	1	470	c.9G>A	c.(7-9)acG>acA	p.T3T		NM_194284.2	NP_919260.2	Q96B33	CLD23_HUMAN	claudin 23	3					calcium-independent cell-cell adhesion (GO:0016338)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|tight junction assembly (GO:0070830)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	identical protein binding (GO:0042802)|structural molecule activity (GO:0005198)			endometrium(2)	2		Hepatocellular(245;0.217)		COAD - Colon adenocarcinoma(149;0.071)|READ - Rectum adenocarcinoma(644;0.238)		GGATGCGGACGCCGGTGGTGA	0.736													G|||	31	0.0061901	0.0219	0.0029	5008	,	,		12030	0.0		0.0	False		,,,				2504	0.0				p.T3T		Atlas-SNP	.											.	CLDN23	5	.	0			c.G9A						PASS	.	G		90,3868		0,90,1889	9.0	13.0	11.0		9	2.2	1.0	8	dbSNP_129	11	0,8248		0,0,4124	no	coding-synonymous	CLDN23	NM_194284.2		0,90,6013	AA,AG,GG		0.0,2.2739,0.7373		3/293	8559917	90,12116	1979	4124	6103	SO:0001819	synonymous_variant	137075	exon1			GCGGACGCCGGTG	AK123547	CCDS55195.1	8p23.1	2006-04-12				ENSG00000253958		"""Claudins"""	17591	protein-coding gene	gene with protein product		609203				12736707	Standard	NM_194284		Approved	CLDNL	uc003wsi.3	Q96B33		ENST00000519106.1:c.9G>A	8.37:g.8559917G>A		6.0	0.0	0		7.0	6.0	0.857143	NM_194284	Q08AJ3	Silent	SNP	ENST00000519106.1	37	CCDS55195.1																																																																																			G|0.995;A|0.005	0.005	strong		0.736	CLDN23-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374721.1	NM_194284	
ELP2	55250	hgsc.bcm.edu	37	18	33744465	33744465	+	Missense_Mutation	SNP	A	A	G	rs73428967	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:33744465A>G	ENST00000358232.6	+	18	1852	c.1789A>G	c.(1789-1791)Att>Gtt	p.I597V	ELP2_ENST00000442325.2_Missense_Mutation_p.I662V|ELP2_ENST00000423854.2_Missense_Mutation_p.I527V|ELP2_ENST00000350494.6_Missense_Mutation_p.I592V|ELP2_ENST00000542050.1_3'UTR|ELP2_ENST00000542824.1_Missense_Mutation_p.I527V|ELP2_ENST00000351393.6_Missense_Mutation_p.I571V	NM_018255.2	NP_060725.1	Q6IA86	ELP2_HUMAN	elongator acetyltransferase complex subunit 2	597					chromatin organization (GO:0006325)|regulation of JAK-STAT cascade (GO:0046425)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription elongation from RNA polymerase II promoter (GO:0006368)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|Elongator holoenzyme complex (GO:0033588)|nucleolus (GO:0005730)|transcription elongation factor complex (GO:0008023)				NS(1)|breast(4)|kidney(2)|large_intestine(8)|lung(10)|ovary(1)|skin(2)|urinary_tract(2)	30						TGCAGCTATCATTCTTTGGAA	0.368													A|||	15	0.00299521	0.0113	0.0	5008	,	,		19841	0.0		0.0	False		,,,				2504	0.0				p.I662V		Atlas-SNP	.											.	ELP2	70	.	0			c.A1984G						PASS	.	A	VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE,VAL/ILE	52,4354	52.3+/-87.9	1,50,2152	118.0	113.0	115.0		1984,1774,1711,1579,1579,1789	5.8	1.0	18	dbSNP_130	115	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense	ELP2	NM_001242875.1,NM_001242876.1,NM_001242877.1,NM_001242878.1,NM_001242879.1,NM_018255.2	29,29,29,29,29,29	1,50,6452	GG,GA,AA		0.0,1.1802,0.3998	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	662/892,592/822,571/801,527/757,527/757,597/827	33744465	52,12954	2203	4300	6503	SO:0001583	missense	55250	exon19			GCTATCATTCTTT	AK001741	CCDS11918.1, CCDS56065.1, CCDS56066.1, CCDS56067.1, CCDS56068.1, CCDS56069.1	18q12.1	2013-01-10	2012-08-08	2007-04-20	ENSG00000134759	ENSG00000134759		"""Elongator acetyltransferase complex subunits"", ""WD repeat domain containing"""	18248	protein-coding gene	gene with protein product			"""signal transducer and activator of transcription 3 interacting protein 1"", ""elongation protein 2 homolog (S. cerevisiae)"""	STATIP1		11714725, 10954736	Standard	NM_001242875		Approved	FLJ10879, StIP	uc002kzk.2	Q6IA86	OTTHUMG00000132589	ENST00000358232.6:c.1789A>G	18.37:g.33744465A>G	ENSP00000350967:p.Ile597Val	143.0	0.0	0		176.0	80.0	0.454545	NM_001242875	A8KAI6|B4DTG0|B4DXP0|E7EP23|E9PCX0|Q53GZ0|Q687Y8|Q8N5C2|Q96GV4|Q96PI7|Q9H9N0|Q9NV81	Missense_Mutation	SNP	ENST00000358232.6	37	CCDS11918.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	18.12	3.554080	0.65425	0.011802	0.0	ENSG00000134759	ENST00000358232;ENST00000351393;ENST00000442325;ENST00000423854;ENST00000350494;ENST00000542824	T;T;T;T;T;T	0.65364	-0.15;2.26;1.09;2.26;0.0;-0.15	5.79	5.79	0.91817	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.103034	0.64402	D	0.000005	T	0.62756	0.2454	M	0.67625	2.065	0.54753	D	0.999986	P;P;P;P;P;P	0.49090	0.879;0.879;0.881;0.919;0.619;0.868	P;P;P;P;P;P	0.52031	0.688;0.688;0.527;0.672;0.511;0.472	T	0.66308	-0.5956	10	0.33940	T	0.23	-26.4385	14.0849	0.64949	1.0:0.0:0.0:0.0	.	592;662;527;527;571;597	B4DTG0;E7EP23;E9PCX0;Q6IA86-2;Q6IA86-3;Q6IA86	.;.;.;.;.;ELP2_HUMAN	V	597;571;662;527;592;527	ENSP00000350967:I597V;ENSP00000257191:I571V;ENSP00000414851:I662V;ENSP00000391202:I527V;ENSP00000316051:I592V;ENSP00000443800:I527V	ENSP00000316051:I592V	I	+	1	0	ELP2	31998463	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.037000	0.49775	2.208000	0.71279	0.533000	0.62120	ATT	A|0.997;G|0.003	0.003	strong		0.368	ELP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255800.2	NM_018255	
SHC2	25759	hgsc.bcm.edu	37	19	422229	422229	+	Missense_Mutation	SNP	C	C	T	rs61750917	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:422229C>T	ENST00000264554.6	-	11	1536	c.1537G>A	c.(1537-1539)Gtc>Atc	p.V513I		NM_012435.2	NP_036567.2	P98077	SHC2_HUMAN	SHC (Src homology 2 domain containing) transforming protein 2	513	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				activation of MAPK activity (GO:0000187)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)	cytosol (GO:0005829)				endometrium(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	21		all_cancers(10;1.13e-36)|all_epithelial(18;1.46e-23)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.1e-06)|all_lung(49;1.55e-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)		GGGTTGGTGACGCTGTCTCGC	0.672													C|||	93	0.0185703	0.0651	0.0086	5008	,	,		14638	0.0		0.001	False		,,,				2504	0.0				p.V513I		Atlas-SNP	.											SHC2,colon,carcinoma,0,1	SHC2	47	1	0			c.G1537A						PASS	.	C	ILE/VAL	310,4082		12,286,1898	23.0	29.0	27.0		1537	-1.1	1.0	19	dbSNP_129	27	2,8592		0,2,4295	yes	missense	SHC2	NM_012435.2	29	12,288,6193	TT,TC,CC		0.0233,7.0583,2.4026	benign	513/583	422229	312,12674	2196	4297	6493	SO:0001583	missense	25759	exon11			TGGTGACGCTGTC	AB001451	CCDS45891.1	19p13.3	2013-02-14				ENSG00000129946		"""SH2 domain containing"""	29869	protein-coding gene	gene with protein product	"""neuronal Shc adaptor homolog"""	605217				7527937, 9507002	Standard	NM_012435		Approved	SLI, SCK, SHCB	uc002loq.4	P98077		ENST00000264554.6:c.1537G>A	19.37:g.422229C>T	ENSP00000264554:p.Val513Ile	128.0	0.0	0		136.0	62.0	0.455882	NM_012435	O60230|Q9NPL5|Q9UCX4	Missense_Mutation	SNP	ENST00000264554.6	37	CCDS45891.1	37	0.01694139194139194	34	0.06910569105691057	3	0.008287292817679558	0	0.0	0	0.0	C	8.377	0.836675	0.16891	0.070583	2.33E-4	ENSG00000129946	ENST00000264554	D	0.88431	-2.38	4.76	-1.12	0.09808	SH2 motif (5);	0.368945	0.29624	N	0.011635	T	0.16642	0.0400	N	0.02985	-0.445	0.24255	N	0.995303	B	0.12630	0.006	B	0.14023	0.01	T	0.49351	-0.8949	10	0.37606	T	0.19	-39.6557	8.286	0.31928	0.0:0.4041:0.0:0.5959	.	513	P98077	SHC2_HUMAN	I	513	ENSP00000264554:V513I	ENSP00000264554:V513I	V	-	1	0	SHC2	373229	0.748000	0.28294	0.991000	0.47740	0.309000	0.27889	-0.010000	0.12743	0.029000	0.15352	-0.812000	0.03155	GTC	C|0.981;T|0.019	0.019	strong		0.672	SHC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451840.3		
DCAF4L2	138009	hgsc.bcm.edu	37	8	88885256	88885256	+	Missense_Mutation	SNP	G	G	A	rs146716352	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:88885256G>A	ENST00000319675.3	-	1	1040	c.944C>T	c.(943-945)tCc>tTc	p.S315F		NM_152418.3	NP_689631.1	Q8NA75	DC4L2_HUMAN	DDB1 and CUL4 associated factor 4-like 2	315										breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|liver(2)|lung(40)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	83						TAGGTAGGCGGAGTTATTCAC	0.542													G|||	11	0.00219649	0.0083	0.0	5008	,	,		19579	0.0		0.0	False		,,,				2504	0.0				p.S315F		Atlas-SNP	.											.	DCAF4L2	187	.	0			c.C944T						PASS	.	G	PHE/SER	45,4361	46.7+/-81.2	0,45,2158	108.0	102.0	104.0		944	0.1	0.0	8	dbSNP_134	104	0,8600		0,0,4300	yes	missense	DCAF4L2	NM_152418.3	155	0,45,6458	AA,AG,GG		0.0,1.0213,0.346	benign	315/396	88885256	45,12961	2203	4300	6503	SO:0001583	missense	138009	exon1			TAGGCGGAGTTAT	AL833507	CCDS6245.1	8q21.3	2013-01-09	2009-07-17	2009-07-17		ENSG00000176566		"""WD repeat domain containing"""	26657	protein-coding gene	gene with protein product			"""WD repeat domain 21C"""	WDR21C		14702039	Standard	NM_152418		Approved		uc003ydz.3	Q8NA75		ENST00000319675.3:c.944C>T	8.37:g.88885256G>A	ENSP00000316496:p.Ser315Phe	199.0	0.0	0		185.0	87.0	0.47027	NM_152418		Missense_Mutation	SNP	ENST00000319675.3	37	CCDS6245.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	14.00	2.405976	0.42715	0.010213	0.0	ENSG00000176566	ENST00000319675	T	0.22945	1.93	1.39	0.0752	0.14398	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.113194	0.64402	D	0.000008	T	0.07773	0.0195	N	0.14661	0.345	0.22096	N	0.999368	B	0.25521	0.128	B	0.25614	0.062	T	0.24548	-1.0157	10	0.22706	T	0.39	.	5.3547	0.16055	0.0:0.0:0.3197:0.6803	.	315	Q8NA75	DC4L2_HUMAN	F	315	ENSP00000316496:S315F	ENSP00000316496:S315F	S	-	2	0	DCAF4L2	88954372	1.000000	0.71417	0.009000	0.14445	0.009000	0.06853	2.530000	0.45641	-0.175000	0.10725	-0.518000	0.04402	TCC	G|0.997;A|0.003	0.003	strong		0.542	DCAF4L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375302.1	NM_152418	
KIAA1671	85379	hgsc.bcm.edu	37	22	25570285	25570285	+	Silent	SNP	C	C	T	rs56351192	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:25570285C>T	ENST00000406486.4	+	9	5115	c.4728C>T	c.(4726-4728)tcC>tcT	p.S1576S	KIAA1671_ENST00000358431.3_Silent_p.S1576S|KIAA1671_ENST00000401395.1_Silent_p.S83S			Q9BY89	K1671_HUMAN	KIAA1671	1576										autonomic_ganglia(1)|breast(1)|endometrium(2)|lung(2)|prostate(1)|stomach(2)	9						CTTCTCTGTCCTCCCAAACGG	0.602													C|||	111	0.0221645	0.0779	0.0086	5008	,	,		17838	0.0		0.002	False		,,,				2504	0.0				p.S1576S		Atlas-SNP	.											.	KIAA1671	28	.	0			c.C4728T						PASS	.						27.0	31.0	30.0					22																	25570285		692	1591	2283	SO:0001819	synonymous_variant	85379	exon6			TCTGTCCTCCCAA		CCDS46676.1	22q11.23	2009-07-09			ENSG00000197077	ENSG00000197077			29345	protein-coding gene	gene with protein product						15289310	Standard	NM_001145206		Approved		uc003abn.3	Q9BY89	OTTHUMG00000150841	ENST00000406486.4:c.4728C>T	22.37:g.25570285C>T		184.0	0.0	0		156.0	155.0	0.99359	NM_001145206	B0QYF2|B7ZW08|Q5THZ5	Silent	SNP	ENST00000406486.4	37	CCDS46676.1																																																																																			C|0.981;T|0.019	0.019	strong		0.602	KIAA1671-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320306.6	NM_001145206	
DDX24	57062	hgsc.bcm.edu	37	14	94526812	94526812	+	Silent	SNP	C	C	T	rs11845400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:94526812C>T	ENST00000330836.5	-	5	1676	c.1545G>A	c.(1543-1545)caG>caA	p.Q515Q	DDX24_ENST00000555054.1_Silent_p.Q472Q|DDX24_ENST00000544005.1_Silent_p.Q265Q	NM_020414.3	NP_065147.1	Q9GZR7	DDX24_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 24	515	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				RNA metabolic process (GO:0016070)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			cervix(3)|endometrium(4)|kidney(4)|large_intestine(5)|lung(3)|ovary(2)|skin(1)|urinary_tract(1)	23		all_cancers(154;0.12)		Epithelial(152;0.114)|all cancers(159;0.19)|COAD - Colon adenocarcinoma(157;0.207)		GAGCAGGAGCCTGATGCACCA	0.473													C|||	202	0.0403355	0.1483	0.0043	5008	,	,		21521	0.0		0.002	False		,,,				2504	0.001				p.Q515Q		Atlas-SNP	.											.	DDX24	82	.	0			c.G1545A						PASS	.	C		558,3848	249.6+/-257.0	33,492,1678	192.0	177.0	182.0		1545	-1.5	1.0	14	dbSNP_120	182	39,8561	26.3+/-74.7	0,39,4261	no	coding-synonymous	DDX24	NM_020414.3		33,531,5939	TT,TC,CC		0.4535,12.6645,4.5902		515/860	94526812	597,12409	2203	4300	6503	SO:0001819	synonymous_variant	57062	exon5			AGGAGCCTGATGC	AF214731	CCDS9918.1	14q32	2013-07-16	2013-07-16			ENSG00000089737		"""DEAD-boxes"""	13266	protein-coding gene	gene with protein product		606181	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 24"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 24"""			10936056, 18289627	Standard	NM_020414		Approved		uc001ycj.3	Q9GZR7		ENST00000330836.5:c.1545G>A	14.37:g.94526812C>T		197.0	0.0	0		228.0	118.0	0.517544	NM_020414	E7EMJ4|Q4V9L5	Silent	SNP	ENST00000330836.5	37	CCDS9918.1																																																																																			C|0.952;T|0.048	0.048	strong		0.473	DDX24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412861.1	NM_020414	
NCOA3	8202	hgsc.bcm.edu	37	20	46264805	46264805	+	Missense_Mutation	SNP	C	C	T	rs2230781	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:46264805C>T	ENST00000371998.3	+	12	1866	c.1675C>T	c.(1675-1677)Cca>Tca	p.P559S	NCOA3_ENST00000372004.3_Missense_Mutation_p.P559S|NCOA3_ENST00000371997.3_Missense_Mutation_p.P569S|NCOA3_ENST00000341724.6_Missense_Mutation_p.P569S			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	559	Ser-rich.		P -> S (in dbSNP:rs2230781). {ECO:0000269|Ref.5}.		androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						TATTACCCAACCAAGTAAAGT	0.443													C|||	96	0.0191693	0.0651	0.0101	5008	,	,		17392	0.0		0.003	False		,,,				2504	0.0				p.P569S		Atlas-SNP	.											.	NCOA3	156	.	0			c.C1705T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO,SER/PRO	246,4160	143.1+/-178.2	7,232,1964	90.0	89.0	89.0		1675,1705,1675,1675	3.7	0.8	20	dbSNP_98	89	4,8596	3.0+/-9.4	0,4,4296	yes	missense,missense,missense,missense	NCOA3	NM_001174087.1,NM_001174088.1,NM_006534.3,NM_181659.2	74,74,74,74	7,236,6260	TT,TC,CC		0.0465,5.5833,1.9222	benign,benign,benign,benign	559/1424,569/1416,559/1421,559/1425	46264805	250,12756	2203	4300	6503	SO:0001583	missense	8202	exon12			ACCCAACCAAGTA	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7670	protein-coding gene	gene with protein product	"""receptor-associated coactivator 3"", ""thyroid hormone receptor activator molecule 1"""	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.1675C>T	20.37:g.46264805C>T	ENSP00000361066:p.Pro559Ser	134.0	0.0	0		155.0	87.0	0.56129	NM_001174088	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Missense_Mutation	SNP	ENST00000371998.3	37	CCDS13407.1	38	0.0173992673992674	33	0.06707317073170732	3	0.008287292817679558	0	0.0	2	0.002638522427440633	C	8.392	0.839981	0.16891	0.055833	4.65E-4	ENSG00000124151	ENST00000340189;ENST00000341724;ENST00000372004;ENST00000371998;ENST00000371997	T;T;T;T	0.16743	2.32;2.32;2.32;2.32	5.72	3.7	0.42460	.	0.351919	0.27627	N	0.018540	T	0.01061	0.0035	L	0.44542	1.39	0.26797	N	0.969286	B;B;B;B;B;B	0.25312	0.088;0.123;0.088;0.088;0.029;0.038	B;B;B;B;B;B	0.30572	0.103;0.117;0.103;0.103;0.098;0.071	T	0.24870	-1.0148	10	0.05833	T	0.94	-3.6234	16.0462	0.80722	0.0:0.7459:0.2541:0.0	rs2230781;rs52817019;rs2230781	559;569;563;559;559;559	A8K0W8;Q9Y6Q9-3;Q59EE8;Q0IIN7;Q9Y6Q9-5;Q9Y6Q9	.;.;.;.;.;NCOA3_HUMAN	S	559;569;559;559;569	ENSP00000342123:P569S;ENSP00000361073:P559S;ENSP00000361066:P559S;ENSP00000361065:P569S	ENSP00000345671:P559S	P	+	1	0	NCOA3	45698212	0.993000	0.37304	0.828000	0.32881	0.927000	0.56198	1.799000	0.38824	0.693000	0.31634	0.655000	0.94253	CCA	C|0.981;T|0.019	0.019	strong		0.443	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	
ANKRD24	170961	hgsc.bcm.edu	37	19	4216829	4216829	+	Missense_Mutation	SNP	G	G	A	rs61738959	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4216829G>A	ENST00000600132.1	+	18	1948	c.1672G>A	c.(1672-1674)Gga>Aga	p.G558R	ANKRD24_ENST00000318934.4_Missense_Mutation_p.G558R|ANKRD24_ENST00000262970.5_Missense_Mutation_p.G648R	NM_133475.1	NP_597732.1	Q8TF21	ANR24_HUMAN	ankyrin repeat domain 24	558										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)|skin(1)	21				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0233)|STAD - Stomach adenocarcinoma(1328;0.181)		CAAAGTTAACGGAGCCGAGAC	0.592													G|||	102	0.0203674	0.0749	0.0043	5008	,	,		18749	0.0		0.0	False		,,,				2504	0.0				p.G558R		Atlas-SNP	.											.	ANKRD24	180	.	0			c.G1672A						PASS	.	G	ARG/GLY	191,3851		8,175,1838	19.0	21.0	21.0		1672	3.5	0.0	19	dbSNP_129	21	4,8382		0,4,4189	yes	missense	ANKRD24	NM_133475.1	125	8,179,6027	AA,AG,GG		0.0477,4.7254,1.569	probably-damaging	558/1147	4216829	195,12233	2021	4193	6214	SO:0001583	missense	170961	exon18			GTTAACGGAGCCG	AB075861	CCDS45925.1	19p13.3	2013-01-10				ENSG00000089847		"""Ankyrin repeat domain containing"""	29424	protein-coding gene	gene with protein product						11853319	Standard	NM_133475		Approved	KIAA1981	uc010dtt.1	Q8TF21		ENST00000600132.1:c.1672G>A	19.37:g.4216829G>A	ENSP00000471252:p.Gly558Arg	35.0	0.0	0		29.0	14.0	0.482759	NM_133475	O75268|O95781	Missense_Mutation	SNP	ENST00000600132.1	37	CCDS45925.1	36	0.016483516483516484	35	0.07113821138211382	1	0.0027624309392265192	0	0.0	0	0.0	g	17.79	3.476233	0.63737	0.047254	4.77E-4	ENSG00000089847	ENST00000318934;ENST00000262970	T;T	0.39406	1.08;1.12	3.54	3.54	0.40534	.	0.251067	0.20840	N	0.084734	T	0.04998	0.0134	L	0.29908	0.895	0.26508	N	0.974647	D;D	0.67145	0.993;0.996	P;P	0.62089	0.794;0.898	T	0.01834	-1.1264	10	0.15952	T	0.53	-12.2673	12.9066	0.58156	0.0:0.0:1.0:0.0	rs61738959	558;648	Q8TF21;Q8TF21-2	ANR24_HUMAN;.	R	558;648	ENSP00000321731:G558R;ENSP00000262970:G648R	ENSP00000262970:G648R	G	+	1	0	ANKRD24	4167829	0.332000	0.24722	0.008000	0.14137	0.088000	0.18126	0.933000	0.28897	2.288000	0.76882	0.313000	0.20887	GGA	G|0.982;A|0.018	0.018	strong		0.592	ANKRD24-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458188.1	XM_114000	
LGALS16	148003	hgsc.bcm.edu	37	19	40148584	40148584	+	Missense_Mutation	SNP	T	T	C	rs10403702	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:40148584T>C	ENST00000392051.3	+	2	145	c.77T>C	c.(76-78)cTg>cCg	p.L26P		NM_001190441.1	NP_001177370.1			lectin, galactoside-binding, soluble, 16																		AAAGGGACACTGATCGACTCT	0.478													.|||	304	0.0607029	0.2209	0.0159	5008	,	,		23871	0.0		0.001	False		,,,				2504	0.0				p.L26P		Atlas-SNP	.											.	LGALS16	6	.	0			c.T77C						PASS	.																																			SO:0001583	missense	148003	exon2			GGACACTGATCGA		CCDS54267.1	19q13.2	2011-08-04			ENSG00000249861	ENSG00000249861		"""Lectins, galactoside-binding"""	40039	protein-coding gene	gene with protein product						19497882	Standard	NM_001190441		Approved		uc021uun.1	A8MUM7		ENST00000392051.3:c.77T>C	19.37:g.40148584T>C	ENSP00000375904:p.Leu26Pro	107.0	0.0	0		123.0	71.0	0.577236	NM_001190441		Missense_Mutation	SNP	ENST00000392051.3	37	CCDS54267.1	132	0.06043956043956044	124	0.25203252032520324	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	.	0.003	-2.453243	0.00175	.	.	ENSG00000249861	ENST00000392051	T	0.04194	3.68	1.21	0.065	0.14355	.	.	.	.	.	T	0.00012	0.0000	N	0.00510	-1.415	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45673	-0.9245	8	0.42905	T	0.14	.	3.8659	0.09016	0.0:0.4602:0.0:0.5398	rs10403702;rs10403702	26	A8MUM7	LEG16_HUMAN	P	26	ENSP00000375904:L26P	ENSP00000375904:L26P	L	+	2	0	LGALS16	44840424	0.000000	0.05858	0.007000	0.13788	0.200000	0.23975	-0.442000	0.06871	-0.172000	0.10779	-1.033000	0.02402	CTG	T|0.912;C|0.088	0.088	strong		0.478	LGALS16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465022.1		
CASS4	57091	hgsc.bcm.edu	37	20	55027509	55027509	+	Missense_Mutation	SNP	C	C	T	rs34899200	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:55027509C>T	ENST00000360314.3	+	6	1502	c.1277C>T	c.(1276-1278)tCg>tTg	p.S426L	CASS4_ENST00000371336.3_Missense_Mutation_p.S426L|CASS4_ENST00000434344.1_Intron	NM_001164116.1	NP_001157588.1	Q9NQ75	CASS4_HUMAN	Cas scaffolding protein family member 4	426	Ser-rich.				cell adhesion (GO:0007155)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|membrane (GO:0016020)	phosphorelay sensor kinase activity (GO:0000155)			breast(1)|endometrium(5)|kidney(1)|large_intestine(7)|lung(26)|ovary(4)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	54						AGCTCTTCCTCGGAGGAGTCA	0.572													C|||	94	0.01877	0.0681	0.0043	5008	,	,		20870	0.0		0.001	False		,,,				2504	0.0				p.S426L		Atlas-SNP	.											CASS4,rectum,adenoma,-1,1	CASS4	121	1	0			c.C1277T						PASS	.	C	LEU/SER,,LEU/SER,LEU/SER	242,4164	137.7+/-173.5	9,224,1970	44.0	40.0	41.0		1115,,1277,1277	2.7	0.0	20	dbSNP_126	41	5,8593	4.3+/-15.6	0,5,4294	yes	missense,intron,missense,missense	CASS4	NM_001164114.1,NM_001164115.1,NM_001164116.1,NM_020356.3	145,,145,145	9,229,6264	TT,TC,CC		0.0582,5.4925,1.8994	possibly-damaging,,possibly-damaging,possibly-damaging	372/733,,426/787,426/787	55027509	247,12757	2203	4299	6502	SO:0001583	missense	57091	exon5			CTTCCTCGGAGGA	AJ276678	CCDS33492.1, CCDS54475.1	20q13.31	2011-04-13	2008-04-14	2008-04-15	ENSG00000087589	ENSG00000087589		"""Cas scaffolding proteins"""	15878	protein-coding gene	gene with protein product	"""HEF-like protein"", ""HEF1-Efs-p130Cas-like"""		"""chromosome 20 open reading frame 32"""	C20orf32			Standard	NM_020356		Approved	HEFL, HEPL	uc002xxr.2	Q9NQ75	OTTHUMG00000032788	ENST00000360314.3:c.1277C>T	20.37:g.55027509C>T	ENSP00000353462:p.Ser426Leu	82.0	0.0	0		87.0	45.0	0.517241	NM_020356	E1P5Z8|Q5QPD6|Q96K09|Q9BYL5	Missense_Mutation	SNP	ENST00000360314.3	37	CCDS33492.1	31	0.014194139194139194	30	0.06097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	C	15.20	2.762107	0.49468	0.054925	5.82E-4	ENSG00000087589	ENST00000360314;ENST00000371336	T;T	0.16597	2.33;2.33	5.6	2.65	0.31530	.	0.315398	0.35708	N	0.003026	T	0.01940	0.0061	M	0.76002	2.32	0.09310	N	1	B;B;B	0.31640	0.225;0.333;0.225	B;B;B	0.25506	0.028;0.061;0.028	T	0.04537	-1.0944	10	0.42905	T	0.14	-1.5677	11.146	0.48430	0.0:0.8005:0.0:0.1995	rs34899200	372;426;426	B4DII4;Q9NQ75-2;Q9NQ75	.;.;CASS4_HUMAN	L	426	ENSP00000353462:S426L;ENSP00000360387:S426L	ENSP00000353462:S426L	S	+	2	0	CASS4	54460916	0.617000	0.27043	0.002000	0.10522	0.864000	0.49448	2.043000	0.41231	0.416000	0.25844	-0.157000	0.13467	TCG	C|0.984;T|0.016	0.016	strong		0.572	CASS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079789.2	NM_020356	
ARNTL2	56938	hgsc.bcm.edu	37	12	27543028	27543028	+	Splice_Site	SNP	G	G	A	rs113615248	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:27543028G>A	ENST00000266503.5	+	9	793		c.e9-1		ARNTL2_ENST00000542388.1_Splice_Site|ARNTL2_ENST00000544915.1_Splice_Site|ARNTL2_ENST00000311001.5_Splice_Site|RP11-165P7.1_ENST00000500498.2_RNA|ARNTL2_ENST00000546179.1_Splice_Site|ARNTL2_ENST00000261178.5_Splice_Site|ARNTL2_ENST00000395901.2_Splice_Site			Q8WYA1	BMAL2_HUMAN	aryl hydrocarbon receptor nuclear translocator-like 2						circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|positive regulation of circadian rhythm (GO:0042753)|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)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	E-box binding (GO:0070888)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			breast(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(1)|skin(2)|urinary_tract(1)	21	Colorectal(261;0.0847)|Lung SC(9;0.184)					CTGCACGAAAGCTGGTTTGCA	0.383													G|||	31	0.0061901	0.0227	0.0014	5008	,	,		17019	0.0		0.0	False		,,,				2504	0.0				.		Atlas-SNP	.											.	ARNTL2	54	.	0			c.665-1G>A						PASS	.	G		135,4271	96.7+/-135.4	1,133,2069	153.0	151.0	152.0			2.2	0.2	12	dbSNP_132	152	3,8597	3.0+/-9.4	0,3,4297	yes	splice-3	ARNTL2	NM_020183.3		1,136,6366	AA,AG,GG		0.0349,3.064,1.061			27543028	138,12868	2203	4300	6503	SO:0001630	splice_region_variant	56938	exon7			ACGAAAGCTGGTT	AF246961	CCDS8712.1, CCDS58219.1, CCDS58220.1, CCDS58221.1, CCDS58222.1	12p12.2-p11.2	2013-05-21			ENSG00000029153	ENSG00000029153		"""Basic helix-loop-helix proteins"""	18984	protein-coding gene	gene with protein product		614517				10864977, 10964693	Standard	NM_020183		Approved	BMAL2, MOP9, CLIF, PASD9, bHLHe6	uc001rht.2	Q8WYA1	OTTHUMG00000169257	ENST00000266503.5:c.776-1G>A	12.37:g.27543028G>A		172.0	0.0	0		151.0	78.0	0.516556	NM_001248005	B7Z429|F5H402|Q8WYA2|Q8WYA3|Q8WYA4|Q96J63|Q9H2M4|Q9NS70|Q9NYQ4|Q9NYQ5	Splice_Site	SNP	ENST00000266503.5	37	CCDS8712.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	G	17.45	3.393650	0.62066	0.03064	3.49E-4	ENSG00000029153	ENST00000544915;ENST00000395901;ENST00000546179;ENST00000311001;ENST00000261178;ENST00000266503;ENST00000457040;ENST00000542388	.	.	.	3.14	2.25	0.28309	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.6704	0.34147	0.1092:0.0:0.8908:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ARNTL2	27434295	1.000000	0.71417	0.181000	0.23098	0.664000	0.39144	7.551000	0.82182	0.675000	0.31264	0.655000	0.94253	.	G|0.991;A|0.009	0.009	strong		0.383	ARNTL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403162.1	NM_020183	Intron
PELI2	57161	hgsc.bcm.edu	37	14	56763743	56763743	+	Silent	SNP	G	G	T	rs112097284	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:56763743G>T	ENST00000267460.4	+	6	1408	c.1122G>T	c.(1120-1122)tcG>tcT	p.S374S		NM_021255.2	NP_067078.1	Q9HAT8	PELI2_HUMAN	pellino E3 ubiquitin protein ligase family member 2	374					innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein phosphorylation (GO:0001934)|protein ubiquitination (GO:0016567)|Toll signaling pathway (GO:0008063)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)	cytosol (GO:0005829)	ligase activity (GO:0016874)			kidney(6)|large_intestine(3)|lung(11)|ovary(1)|skin(1)	22						ACGTGTGCTCGGAGAAGTCTG	0.547													G|||	114	0.0227636	0.084	0.0043	5008	,	,		20479	0.0		0.0	False		,,,				2504	0.0				p.S374S		Atlas-SNP	.											.	PELI2	55	.	0			c.G1122T						PASS	.	G		307,4099	164.7+/-196.3	15,277,1911	170.0	147.0	155.0		1122	-4.0	1.0	14	dbSNP_132	155	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	PELI2	NM_021255.2		15,279,6209	TT,TG,GG		0.0233,6.9678,2.3758		374/421	56763743	309,12697	2203	4300	6503	SO:0001819	synonymous_variant	57161	exon6			GTGCTCGGAGAAG	AF302502	CCDS9726.1	14q21	2012-02-23	2012-02-23		ENSG00000139946	ENSG00000139946		"""Pellino homologs"""	8828	protein-coding gene	gene with protein product		614798	"""pellino (Drosophila) homolog 2"", ""pellino homolog 2 (Drosophila)"""			11306823, 12860405	Standard	XM_006720211		Approved		uc001xch.3	Q9HAT8	OTTHUMG00000152336	ENST00000267460.4:c.1122G>T	14.37:g.56763743G>T		76.0	0.0	0		71.0	34.0	0.478873	NM_021255	B2RDY5	Silent	SNP	ENST00000267460.4	37	CCDS9726.1																																																																																			G|0.979;T|0.021	0.021	strong		0.547	PELI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276925.1		
OR10T2	128360	hgsc.bcm.edu	37	1	158369025	158369025	+	Missense_Mutation	SNP	T	T	C	rs6662597	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158369025T>C	ENST00000334438.1	-	1	231	c.232A>G	c.(232-234)Atc>Gtc	p.I78V		NM_001004475.1	NP_001004475.1	Q8NGX3	O10T2_HUMAN	olfactory receptor, family 10, subfamily T, member 2	78			I -> V (in dbSNP:rs6662597).			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(4)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	34	all_hematologic(112;0.0378)					TGAGGGATGATGACAAAAGTG	0.502													T|||	63	0.0125799	0.0477	0.0	5008	,	,		20910	0.0		0.0	False		,,,				2504	0.0				p.I78V		Atlas-SNP	.											.	OR10T2	76	.	0			c.A232G						PASS	.	T	VAL/ILE	143,4263	99.4+/-138.0	3,137,2063	96.0	95.0	96.0		232	4.7	1.0	1	dbSNP_116	96	0,8600		0,0,4300	yes	missense	OR10T2	NM_001004475.1	29	3,137,6363	CC,CT,TT		0.0,3.2456,1.0995	possibly-damaging	78/315	158369025	143,12863	2203	4300	6503	SO:0001583	missense	128360	exon1			GGATGATGACAAA	AB065643	CCDS30895.1	1q23.1	2012-08-09			ENSG00000186306	ENSG00000186306		"""GPCR / Class A : Olfactory receptors"""	14816	protein-coding gene	gene with protein product							Standard	NM_001004475		Approved		uc010pih.2	Q8NGX3	OTTHUMG00000017521	ENST00000334438.1:c.232A>G	1.37:g.158369025T>C	ENSP00000334115:p.Ile78Val	96.0	0.0	0		91.0	53.0	0.582418	NM_001004475	Q6IF98	Missense_Mutation	SNP	ENST00000334438.1	37	CCDS30895.1	21	0.009615384615384616	21	0.042682926829268296	0	0.0	0	0.0	0	0.0	T	16.66	3.184032	0.57800	0.032456	0.0	ENSG00000186306	ENST00000334438	T	0.00611	6.23	4.73	4.73	0.59995	GPCR, rhodopsin-like superfamily (1);	0.000000	0.39759	U	0.001269	T	0.00271	0.0008	L	0.41573	1.285	0.09310	N	0.999995	P	0.36282	0.546	B	0.31442	0.13	T	0.50668	-0.8801	10	0.37606	T	0.19	.	13.3352	0.60515	0.0:0.0:0.0:1.0	rs6662597;rs52820437;rs56418545;rs6662597	78	Q8NGX3	O10T2_HUMAN	V	78	ENSP00000334115:I78V	ENSP00000334115:I78V	I	-	1	0	OR10T2	156635649	0.969000	0.33509	1.000000	0.80357	0.999000	0.98932	2.867000	0.48428	1.973000	0.57446	0.528000	0.53228	ATC	T|0.985;C|0.015	0.015	strong		0.502	OR10T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046371.1	NM_001004475	
LMNTD1	160492	hgsc.bcm.edu	37	12	25672945	25672945	+	Missense_Mutation	SNP	T	T	C	rs34326830	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:25672945T>C	ENST00000282881.6	-	6	949	c.800A>G	c.(799-801)gAa>gGa	p.E267G	IFLTD1_ENST00000539744.1_Missense_Mutation_p.E170G|IFLTD1_ENST00000458174.2_Missense_Mutation_p.E288G|IFLTD1_ENST00000413632.2_Missense_Mutation_p.E248G|IFLTD1_ENST00000445693.1_Missense_Mutation_p.E204G	NM_152590.3	NP_689803.2	Q8N9Z9	LMTD1_HUMAN		267			E -> G (in dbSNP:rs34326830).		cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22	all_lung(3;2.75e-22)|Lung NSC(3;1.77e-21)|all_hematologic(7;0.00656)|Colorectal(261;0.0847)					TCTGTTAAATTCAACGTCAGC	0.388													T|||	88	0.0175719	0.0628	0.0072	5008	,	,		13538	0.0		0.0	False		,,,				2504	0.0				p.E288G		Atlas-SNP	.											.	IFLTD1	121	.	0			c.A863G						PASS	.	T	GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU	251,4155	144.6+/-179.5	5,241,1957	138.0	121.0	126.0		611,863,743,800	5.1	1.0	12	dbSNP_126	126	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense,missense	IFLTD1	NM_001145727.1,NM_001145728.1,NM_001145729.1,NM_152590.2	98,98,98,98	5,242,6256	CC,CT,TT		0.0116,5.6968,1.9376	probably-damaging,probably-damaging,probably-damaging,probably-damaging	204/326,288/410,248/370,267/389	25672945	252,12754	2203	4300	6503	SO:0001583	missense	160492	exon7			TTAAATTCAACGT																												ENST00000282881.6:c.800A>G	12.37:g.25672945T>C	ENSP00000282881:p.Glu267Gly	169.0	0.0	0		155.0	81.0	0.522581	NM_001145728	B4DL27|B4DY70|Q8IY38	Missense_Mutation	SNP	ENST00000282881.6	37	CCDS8704.1	20|20	0.009157509157509158|0.009157509157509158	17|17	0.034552845528455285|0.034552845528455285	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	T|T	19.78|19.78	3.891505|3.891505	0.72524|0.72524	0.056968|0.056968	1.16E-4|1.16E-4	ENSG00000152936|ENSG00000152936	ENST00000282881;ENST00000539744;ENST00000458174;ENST00000445693;ENST00000413632;ENST00000545543|ENST00000543629	T;T;T;T;T;T|.	0.18502|.	2.35;2.43;2.33;2.38;2.28;2.21|.	5.05|5.05	5.05|5.05	0.67936|0.67936	.|.	.|.	.|.	.|.	.|.	T|.	0.05410|.	0.0143|.	L|L	0.32530|0.32530	0.975|0.975	0.29530|0.29530	N|N	0.852852|0.852852	P;P;D;D|.	0.76494|.	0.734;0.946;0.972;0.999|.	B;P;P;D|.	0.64144|.	0.421;0.637;0.723;0.922|.	T|.	0.04635|.	-1.0937|.	9|.	0.87932|.	D|.	0|.	4.219|4.219	11.112|11.112	0.48239|0.48239	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs34326830|rs34326830	204;288;248;267|.	Q8N9Z9-3;Q8N9Z9-5;Q8N9Z9-4;Q8N9Z9|.	.;.;.;ILFT1_HUMAN|.	G|W	267;170;288;204;248;97|41	ENSP00000282881:E267G;ENSP00000443132:E170G;ENSP00000407353:E288G;ENSP00000407043:E204G;ENSP00000393150:E248G;ENSP00000443596:E97G|.	ENSP00000282881:E267G|.	E|X	-|-	2|3	0|0	IFLTD1|IFLTD1	25564212|25564212	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.842000|0.842000	0.47809|0.47809	3.758000|3.758000	0.55220|0.55220	2.134000|2.134000	0.65973|0.65973	0.477000|0.477000	0.44152|0.44152	GAA|TGA	T|0.980;C|0.020	0.020	strong		0.388	IFLTD1-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402279.1		
CYP4F12	66002	hgsc.bcm.edu	37	19	15793238	15793238	+	Silent	SNP	C	C	T	rs144258147	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15793238C>T	ENST00000550308.1	+	6	945	c.565C>T	c.(565-567)Ctg>Ttg	p.L189L	CYP4F12_ENST00000324632.10_Silent_p.L189L	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	189					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)	p.L189V(1)		NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	CAGCAGTTGTCTGGACATGTT	0.557													.|||	31	0.0061901	0.0227	0.0	5008	,	,		20398	0.0		0.001	False		,,,				2504	0.0				p.L189L		Atlas-SNP	.											.	CYP4F12	89	.	1	Substitution - Missense(1)	urinary_tract(1)	c.C565T						PASS	.						81.0	78.0	79.0					19																	15793238		2203	4300	6503	SO:0001819	synonymous_variant	66002	exon6			AGTTGTCTGGACA	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.565C>T	19.37:g.15793238C>T		270.0	0.0	0		342.0	74.0	0.216374	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Silent	SNP	ENST00000550308.1	37	CCDS42517.1																																																																																			C|0.990;T|0.010	0.010	strong		0.557	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
ZNF211	10520	hgsc.bcm.edu	37	19	58152182	58152182	+	Missense_Mutation	SNP	G	G	A	rs34897843	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58152182G>A	ENST00000347302.3	+	3	507	c.328G>A	c.(328-330)Gac>Aac	p.D110N	ZNF211_ENST00000544273.1_Missense_Mutation_p.D122N|ZNF211_ENST00000420680.1_Missense_Mutation_p.D114N|ZNF211_ENST00000391703.3_Missense_Mutation_p.D49N|ZNF211_ENST00000254182.7_Missense_Mutation_p.D101N|ZNF211_ENST00000541801.1_Missense_Mutation_p.D101N|ZNF211_ENST00000299871.5_Missense_Mutation_p.D175N|ZNF211_ENST00000240731.4_Missense_Mutation_p.D123N	NM_198855.2	NP_942152.1	Q13398	ZN211_HUMAN	zinc finger protein 211	110			D -> N (in dbSNP:rs34897843).		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)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		CCAGAATGCCGACTCCTGTGA	0.453													g|||	32	0.00638978	0.0204	0.0043	5008	,	,		21518	0.0		0.001	False		,,,				2504	0.001				p.D175N		Atlas-SNP	.											.	ZNF211	78	.	0			c.G523A						PASS	.	A	ASN/ASP,ASN/ASP	123,4283	91.1+/-129.8	1,121,2081	98.0	98.0	98.0		367,328	-0.9	0.0	19	dbSNP_126	98	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	ZNF211	NM_006385.3,NM_198855.2	23,23	1,122,6380	AA,AG,GG		0.0116,2.7916,0.9534	benign,benign	123/578,110/565	58152182	124,12882	2203	4300	6503	SO:0001583	missense	10520	exon5			AATGCCGACTCCT	U38904	CCDS12956.1, CCDS12957.1, CCDS58686.1, CCDS58687.1, CCDS58688.1, CCDS74468.1	19q13.4	2013-01-08			ENSG00000121417	ENSG00000121417		"""Zinc fingers, C2H2-type"", ""-"""	13003	protein-coding gene	gene with protein product		601856				7633419, 9096115	Standard	NM_006385		Approved	ZNF-25, CH2H2-25	uc031rng.1	Q13398	OTTHUMG00000168012	ENST00000347302.3:c.328G>A	19.37:g.58152182G>A	ENSP00000339562:p.Asp110Asn	251.0	0.0	0		242.0	115.0	0.475207	NM_001265597	B4DH10|B4DLC9|B4E3C9|B9ZVS7|B9ZVW1|F8WDV2|Q05BQ7|Q2TAL7|Q59EG4|Q59G36|Q5EBL6	Missense_Mutation	SNP	ENST00000347302.3	37	CCDS12957.1	13|13	0.005952380952380952|0.005952380952380952	11|11	0.022357723577235773|0.022357723577235773	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	G|G	10.25|10.25	1.298596|1.298596	0.23650|0.23650	0.027916|0.027916	1.16E-4|1.16E-4	ENSG00000121417|ENSG00000121417	ENST00000420680;ENST00000347302;ENST00000254182;ENST00000391703;ENST00000541801;ENST00000299871;ENST00000544273;ENST00000240731|ENST00000407202	T;T;T;T;T;T;T;T|.	0.06768|.	3.31;3.33;3.26;3.27;3.26;3.37;3.33;3.33|.	3.7|3.7	-0.942|-0.942	0.10398|0.10398	.|.	.|.	.|.	.|.	.|.	T|T	0.02304|0.02304	0.0071|0.0071	N|N	0.01493|0.01493	-0.835|-0.835	0.09310|0.09310	N|N	1|1	B;B;B;P;B;B|.	0.39060|.	0.091;0.038;0.001;0.657;0.011;0.011|.	B;B;B;B;B;B|.	0.31812|.	0.013;0.008;0.0;0.136;0.004;0.006|.	T|T	0.30297|0.30297	-0.9983|-0.9983	9|5	0.20519|.	T|.	0.43|.	.|.	0.6887|0.6887	0.00887|0.00887	0.1784:0.3318:0.1832:0.3066|0.1784:0.3318:0.1832:0.3066	rs34897843|rs34897843	114;122;175;101;110;123|.	Q13398-4;Q13398-3;F8WDV2;Q13398-2;Q13398;B9ZVW1|.	.;.;.;.;ZN211_HUMAN;.|.	N|Q	114;110;101;49;101;175;122;123|113	ENSP00000399193:D114N;ENSP00000339562:D110N;ENSP00000254182:D101N;ENSP00000375584:D49N;ENSP00000442601:D101N;ENSP00000299871:D175N;ENSP00000441386:D122N;ENSP00000240731:D123N|.	ENSP00000240731:D123N|.	D|R	+|+	1|2	0|0	ZNF211|ZNF211	62843994|62843994	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.248000|0.248000	0.25809|0.25809	-0.035000|-0.035000	0.12205|0.12205	-0.041000|-0.041000	0.13558|0.13558	-1.230000|-1.230000	0.01575|0.01575	GAC|CGA	G|0.991;A|0.009	0.009	strong		0.453	ZNF211-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000397502.1		
CDH19	28513	hgsc.bcm.edu	37	18	64235877	64235877	+	Missense_Mutation	SNP	G	G	A	rs114375304	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:64235877G>A	ENST00000540086.1	-	3	512	c.266C>T	c.(265-267)aCt>aTt	p.T89I	CDH19_ENST00000262150.2_Missense_Mutation_p.T89I	NM_001271028.1	NP_001257957.1	Q96JQ0	PCD16_HUMAN	cadherin 19, type 2	190	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(22)|ovary(1)|prostate(3)|skin(7)	61		Esophageal squamous(42;0.0132)				AATGATAAAAGTACTTCCAGC	0.398													G|||	71	0.0141773	0.0499	0.0072	5008	,	,		16014	0.0		0.0	False		,,,				2504	0.0				p.T89I		Atlas-SNP	.											CDH19,NS,carcinoma,-1,1	CDH19	141	1	0			c.C266T						PASS	.	G	ILE/THR	266,4140	150.3+/-184.3	15,236,1952	94.0	93.0	94.0		266	1.9	0.1	18	dbSNP_132	94	2,8594	2.2+/-6.3	0,2,4296	yes	missense	CDH19	NM_021153.2	89	15,238,6248	AA,AG,GG		0.0233,6.0372,2.0612	benign	89/773	64235877	268,12734	2203	4298	6501	SO:0001583	missense	28513	exon3			ATAAAAGTACTTC	AJ007607	CCDS11994.1, CCDS59325.1	18q22.1	2010-01-26			ENSG00000071991	ENSG00000071991		"""Cadherins / Major cadherins"""	1758	protein-coding gene	gene with protein product		603016				10995570	Standard	NM_021153		Approved	CDH7	uc002lkc.2	Q9H159	OTTHUMG00000132802	ENST00000540086.1:c.266C>T	18.37:g.64235877G>A	ENSP00000439593:p.Thr89Ile	107.0	0.0	0		107.0	49.0	0.457944	NM_021153	O15098	Missense_Mutation	SNP	ENST00000540086.1	37	CCDS59325.1	29	0.013278388278388278	26	0.052845528455284556	3	0.008287292817679558	0	0.0	0	0.0	G	9.972	1.225826	0.22542	0.060372	2.33E-4	ENSG00000071991	ENST00000262150;ENST00000540086;ENST00000454642	T;T	0.51817	0.69;0.69	5.48	1.91	0.25777	Cadherin (5);Cadherin-like (1);	0.572976	0.18606	N	0.136310	T	0.01661	0.0053	N	0.02665	-0.54	0.22127	N	0.999345	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.19943	-1.0290	10	0.02654	T	1	.	7.9396	0.29950	0.7547:0.0:0.2453:0.0	.	89;89	F5H1K0;Q9H159	.;CAD19_HUMAN	I	89;89;34	ENSP00000262150:T89I;ENSP00000439593:T89I	ENSP00000262150:T89I	T	-	2	0	CDH19	62386857	0.762000	0.28451	0.145000	0.22337	0.830000	0.47004	3.161000	0.50747	0.396000	0.25283	-0.469000	0.05056	ACT	G|0.980;A|0.020	0.020	strong		0.398	CDH19-005	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000442285.1	NM_021153	
ADD1	118	hgsc.bcm.edu	37	4	2896419	2896419	+	Silent	SNP	G	G	A	rs112813723	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:2896419G>A	ENST00000398129.1	+	5	722	c.702G>A	c.(700-702)gtG>gtA	p.V234V	ADD1_ENST00000264758.7_Silent_p.V234V|ADD1_ENST00000513328.2_Silent_p.V234V|ADD1_ENST00000503455.2_Silent_p.V234V|ADD1_ENST00000355842.3_Silent_p.V234V|ADD1_ENST00000446856.1_Silent_p.V234V|ADD1_ENST00000398125.1_Silent_p.V234V|ADD1_ENST00000398123.2_Silent_p.V234V			P35611	ADDA_HUMAN	adducin 1 (alpha)	234					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)		GCCCGGACGTGAAGTGCGTCG	0.542													G|||	49	0.00978435	0.0356	0.0014	5008	,	,		14014	0.0		0.001	False		,,,				2504	0.0				p.V234V	Esophageal Squamous(71;505 1201 20414 34538 37449)	Atlas-SNP	.											.	ADD1	56	.	0			c.G702A						PASS	.	G	,,,	140,4266	98.9+/-137.6	3,134,2066	63.0	54.0	57.0		702,702,702,702	-4.3	0.1	4	dbSNP_132	57	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ADD1	NM_001119.4,NM_014189.3,NM_014190.3,NM_176801.2	,,,	3,136,6364	AA,AG,GG		0.0233,3.1775,1.0918	,,,	234/738,234/769,234/632,234/663	2896419	142,12864	2203	4300	6503	SO:0001819	synonymous_variant	118	exon6			GGACGTGAAGTGC	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.702G>A	4.37:g.2896419G>A		240.0	0.0	0		294.0	148.0	0.503401	NM_014190	A2A3N8|A2A3P0|B4DI79|D3DVR3|D3DVR4|D3DVR5|Q13734|Q14729|Q16156|Q86XM2|Q9UJB6	Silent	SNP	ENST00000398129.1	37	CCDS43205.1																																																																																			G|0.988;A|0.012	0.012	strong		0.542	ADD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242840.1	NM_014189	
DNAH17	8632	hgsc.bcm.edu	37	17	76447617	76447617	+	Silent	SNP	A	A	G	rs34002770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:76447617A>G	ENST00000585328.1	-	66	10777	c.10653T>C	c.(10651-10653)gaT>gaC	p.D3551D	DNAH17_ENST00000389840.5_Silent_p.D3542D|DNAH17_ENST00000586052.1_5'UTR	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	3542	AAA 5. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			CCTCGAGTCCATCCCTGGTGA	0.562													A|||	146	0.0291534	0.1044	0.0086	5008	,	,		21631	0.0		0.002	False		,,,				2504	0.0				p.D3556D		Atlas-SNP	.											.	DNAH17	347	.	0			c.T10668C						PASS	.	A		376,4030	191.9+/-217.4	17,342,1844	301.0	246.0	265.0		10668	-3.6	0.8	17	dbSNP_126	265	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	DNAH17	NM_173628.3		17,346,6140	GG,GA,AA		0.0465,8.5338,2.9217		3556/4463	76447617	380,12626	2203	4300	6503	SO:0001819	synonymous_variant	8632	exon66			GAGTCCATCCCTG	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"""Axonemal dyneins"""	2946	protein-coding gene	gene with protein product		610063	"""dynein, axonemal, heavy polypeptide 17"", ""dynein, axonemal, heavy chain like 1"", ""dynein, axonemal, heavy like 1"""	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.10653T>C	17.37:g.76447617A>G		237.0	0.0	0		267.0	125.0	0.468165	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				A|0.969;G|0.031	0.031	strong		0.562	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
MUC4	4585	hgsc.bcm.edu	37	3	195515726	195515726	+	Missense_Mutation	SNP	G	G	C	rs55697302	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195515726G>C	ENST00000463781.3	-	2	3184	c.2725C>G	c.(2725-2727)Cag>Gag	p.Q909E	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.Q909E	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	914	Ser-rich.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CTCTGAGTCTGGGCCATCCGG	0.602													.|||	462	0.0922524	0.3018	0.0202	5008	,	,		19609	0.002		0.007	False		,,,				2504	0.0409				p.Q909E		Atlas-SNP	.											.	MUC4	1505	.	0			c.C2725G						PASS	.		,,GLU/GLN	1021,3177		130,761,1208	113.0	115.0	114.0		,,2725	1.9	0.0	3	dbSNP_129	114	46,8360		0,46,4157	yes	intron,intron,missense	MUC4	NM_004532.5,NM_138297.4,NM_018406.6	,,29	130,807,5365	CC,CG,GG		0.5472,24.3211,8.4656	,,benign	,,909/5413	195515726	1067,11537	2099	4203	6302	SO:0001583	missense	4585	exon2			GAGTCTGGGCCAT	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.2725C>G	3.37:g.195515726G>C	ENSP00000417498:p.Gln909Glu	226.0	0.0	0		275.0	136.0	0.494545	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	154	0.07051282051282051	139	0.28252032520325204	10	0.027624309392265192	1	0.0017482517482517483	4	0.005277044854881266	g	3.831	-0.035685	0.07497	0.243211	0.005472	ENSG00000145113	ENST00000463781;ENST00000475231;ENST00000392409	T;T	0.42513	0.97;0.99	2.78	1.9	0.25705	.	1.330860	0.05376	N	0.536212	T	0.00012	0.0000	N	0.19112	0.55	0.80722	P	0.0	B;B	0.29508	0.141;0.246	B;B	0.20955	0.031;0.032	T	0.17992	-1.0351	9	0.06891	T	0.86	-1.2845	4.3272	0.11046	0.1349:0.2358:0.6293:0.0	rs55697302	909;914	E7ESK3;Q99102	.;MUC4_HUMAN	E	909;909;883	ENSP00000417498:Q909E;ENSP00000420243:Q909E	ENSP00000376209:Q883E	Q	-	1	0	MUC4	197000121	0.001000	0.12720	0.002000	0.10522	0.010000	0.07245	0.850000	0.27737	0.742000	0.32697	0.579000	0.79373	CAG	G|0.942;C|0.058	0.058	strong		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ZNF230	7773	hgsc.bcm.edu	37	19	44514859	44514859	+	Missense_Mutation	SNP	C	C	T	rs147553354	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:44514859C>T	ENST00000429154.2	+	5	896	c.668C>T	c.(667-669)cCa>cTa	p.P223L		NM_006300.3	NP_006291.2	Q9UIE0	ZN230_HUMAN	zinc finger protein 230	223					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(10)|skin(1)|stomach(3)|urinary_tract(2)	22		Prostate(69;0.0352)				GGAGAGAAACCATTCAAATGT	0.428													C|||	11	0.00219649	0.0083	0.0	5008	,	,		22817	0.0		0.0	False		,,,				2504	0.0				p.P223L	GBM(175;914 2069 22996 47111 52600)	Atlas-SNP	.											.	ZNF230	44	.	0			c.C668T						PASS	.	C	LEU/PRO	37,4369	40.0+/-72.8	0,37,2166	101.0	103.0	103.0		668	2.7	0.1	19	dbSNP_134	103	0,8600		0,0,4300	yes	missense	ZNF230	NM_006300.3	98	0,37,6466	TT,TC,CC		0.0,0.8398,0.2845	benign	223/475	44514859	37,12969	2203	4300	6503	SO:0001583	missense	7773	exon5			AGAAACCATTCAA	U95044	CCDS33044.1	19q13.31	2013-01-08				ENSG00000159882		"""Zinc fingers, C2H2-type"", ""-"""	13024	protein-coding gene	gene with protein product							Standard	NM_006300		Approved	FDZF2	uc002oyb.1	Q9UIE0		ENST00000429154.2:c.668C>T	19.37:g.44514859C>T	ENSP00000409318:p.Pro223Leu	110.0	0.0	0		120.0	50.0	0.416667	NM_006300	O15322|Q504X7|Q86W84|Q9P1U6	Missense_Mutation	SNP	ENST00000429154.2	37	CCDS33044.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	13.17	2.158672	0.38119	0.008398	0.0	ENSG00000159882	ENST00000429154	T	0.27557	1.66	2.67	2.67	0.31697	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.29256	0.0728	M	0.80422	2.495	0.80722	D	1	B	0.25105	0.118	B	0.26310	0.068	T	0.44697	-0.9311	9	0.66056	D	0.02	.	12.4612	0.55733	0.0:1.0:0.0:0.0	.	223	Q9UIE0	ZN230_HUMAN	L	223	ENSP00000409318:P223L	ENSP00000409318:P223L	P	+	2	0	ZNF230	49206699	0.016000	0.18221	0.064000	0.19789	0.067000	0.16453	1.315000	0.33608	1.468000	0.48064	0.407000	0.27541	CCA	C|0.998;T|0.002	0.002	strong		0.428	ZNF230-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460456.1		
OR4D9	390199	hgsc.bcm.edu	37	11	59282960	59282960	+	Missense_Mutation	SNP	C	C	G	rs113146895	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:59282960C>G	ENST00000329328.3	+	1	575	c.575C>G	c.(574-576)aCc>aGc	p.T192S		NM_001004711.1	NP_001004711.1	Q8NGE8	OR4D9_HUMAN	olfactory receptor, family 4, subfamily D, member 9	192						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(2)|large_intestine(3)|lung(14)|prostate(5)|upper_aerodigestive_tract(1)	26						TGCACTGACACCTTCACTCTG	0.453													C|||	108	0.0215655	0.0802	0.0029	5008	,	,		21548	0.0		0.0	False		,,,				2504	0.0				p.T192S		Atlas-SNP	.											.	OR4D9	47	.	0			c.C575G						PASS	.	C	SER/THR	263,4139	149.5+/-183.7	9,245,1947	189.0	162.0	171.0		575	3.5	0.1	11	dbSNP_132	171	1,8589		0,1,4294	yes	missense	OR4D9	NM_001004711.1	58	9,246,6241	GG,GC,CC		0.0116,5.9746,2.032	possibly-damaging	192/315	59282960	264,12728	2201	4295	6496	SO:0001583	missense	390199	exon1			CTGACACCTTCAC	AB065861	CCDS31564.1	11q12.1	2012-08-09	2003-12-15		ENSG00000172742	ENSG00000172742		"""GPCR / Class A : Olfactory receptors"""	15178	protein-coding gene	gene with protein product			"""olfactory receptor, family 4, subfamily D, member 9 pseudogene"""				Standard	NM_001004711		Approved		uc010rkv.2	Q8NGE8	OTTHUMG00000167343	ENST00000329328.3:c.575C>G	11.37:g.59282960C>G	ENSP00000328563:p.Thr192Ser	176.0	0.0	0		169.0	82.0	0.485207	NM_001004711	Q6IFF3	Missense_Mutation	SNP	ENST00000329328.3	37	CCDS31564.1	53	0.024267399267399268	52	0.10569105691056911	1	0.0027624309392265192	0	0.0	0	0.0	C	11.61	1.689273	0.29962	0.059746	1.16E-4	ENSG00000172742	ENST00000329328	T	0.00207	8.55	4.44	3.52	0.40303	GPCR, rhodopsin-like superfamily (1);	0.000000	0.42964	U	0.000628	T	0.00012	0.0000	M	0.78916	2.43	0.09310	N	1	D	0.53151	0.958	P	0.59825	0.864	T	0.37174	-0.9717	10	0.72032	D	0.01	-12.673	11.2423	0.48977	0.0:0.9081:0.0:0.0919	.	192	Q8NGE8	OR4D9_HUMAN	S	192	ENSP00000328563:T192S	ENSP00000328563:T192S	T	+	2	0	OR4D9	59039536	0.004000	0.15560	0.109000	0.21407	0.328000	0.28507	0.698000	0.25571	0.977000	0.38444	0.557000	0.71058	ACC	C|0.979;G|0.021	0.021	strong		0.453	OR4D9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394237.1	NM_001004711	
PRAMEF2	65122	hgsc.bcm.edu	37	1	12919145	12919145	+	Missense_Mutation	SNP	G	G	A	rs149655365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:12919145G>A	ENST00000240189.2	+	2	368	c.281G>A	c.(280-282)cGc>cAc	p.R94H		NM_023014.1	NP_075390.1	O60811	PRAM2_HUMAN	PRAME family member 2	94					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(2)|endometrium(1)|kidney(2)|large_intestine(2)|lung(22)|prostate(6)|skin(3)|upper_aerodigestive_tract(4)	42	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;2.4e-06)|Kidney(185;4.89e-05)|COAD - Colon adenocarcinoma(227;0.000152)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CAGAAGGATCGCCCCAGGTGA	0.552													.|||	204	0.0407348	0.1498	0.0086	5008	,	,		23772	0.0		0.0	False		,,,				2504	0.0				p.R94H		Atlas-SNP	.											.	PRAMEF2	85	.	0			c.G281A						PASS	.	G	HIS/ARG	545,3857	236.1+/-248.4	53,439,1709	141.0	155.0	150.0		281	-0.6	0.0	1	dbSNP_134	150	3,8583	2.2+/-6.3	0,3,4290	no	missense	PRAMEF2	NM_023014.1	29	53,442,5999	AA,AG,GG		0.0349,12.3807,4.2193	benign	94/475	12919145	548,12440	2201	4293	6494	SO:0001583	missense	65122	exon2			AGGATCGCCCCAG		CCDS149.1	1p36.21	2013-01-17			ENSG00000120952	ENSG00000120952		"""-"""	28841	protein-coding gene	gene with protein product							Standard	NM_023014		Approved	FLJ43580	uc001aum.1	O60811	OTTHUMG00000001986	ENST00000240189.2:c.281G>A	1.37:g.12919145G>A	ENSP00000240189:p.Arg94His	156.0	0.0	0		195.0	100.0	0.512821	NM_023014		Missense_Mutation	SNP	ENST00000240189.2	37	CCDS149.1	77	0.035256410256410256	72	0.14634146341463414	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	4.603	0.111991	0.08831	0.123807	3.49E-4	ENSG00000120952	ENST00000240189	T	0.04758	3.56	0.842	-0.64	0.11493	.	1.317630	0.05044	N	0.476841	T	0.00039	0.0001	L	0.42632	1.34	0.09310	N	1	B	0.21309	0.054	B	0.17979	0.02	T	0.46884	-0.9159	10	0.13853	T	0.58	.	3.5838	0.07963	0.0:0.0:0.5309:0.4691	.	94	O60811	PRAM2_HUMAN	H	94	ENSP00000240189:R94H	ENSP00000240189:R94H	R	+	2	0	PRAMEF2	12841732	0.000000	0.05858	0.040000	0.18447	0.062000	0.15995	-5.853000	0.00094	-0.190000	0.10465	0.194000	0.17425	CGC	G|0.957;A|0.043	0.043	strong		0.552	PRAMEF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005517.1	NM_023014	
SEPT9	10801	hgsc.bcm.edu	37	17	75471762	75471762	+	Intron	SNP	G	G	A	rs312821	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:75471762G>A	ENST00000427177.1	+	4	847				SEPT9_ENST00000591198.1_Intron|SEPT9_ENST00000427674.2_Intron|SEPT9_ENST00000590917.1_Intron|SEPT9_ENST00000592420.1_Intron|SEPT9_ENST00000590294.1_Intron|SEPT9_ENST00000591088.1_Intron|SEPT9_ENST00000592481.1_Intron|SEPT9_ENST00000585930.1_Intron|RP11-75C10.9_ENST00000591110.1_RNA|SEPT9_ENST00000541152.2_Intron|SEPT9_ENST00000423034.2_Intron|SEPT9_ENST00000449803.2_Intron|SEPT9_ENST00000592951.1_Intron|SEPT9_ENST00000329047.8_Intron|SEPT9_ENST00000588690.1_Intron|SEPT9_ENST00000431235.2_Intron|SEPT9_ENST00000427180.1_Silent_p.T54T	NM_001113491.1	NP_001106963.1	Q9UHD8	SEPT9_HUMAN	septin 9						cell cycle (GO:0007049)|cell division (GO:0051301)|GTP catabolic process (GO:0006184)|protein heterooligomerization (GO:0051291)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|perinuclear region of cytoplasm (GO:0048471)|stress fiber (GO:0001725)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			autonomic_ganglia(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(2)	16			BRCA - Breast invasive adenocarcinoma(99;0.153)			CTGGGCCCACGCTGGGCCGGG	0.642													G|||	387	0.0772764	0.2799	0.0231	5008	,	,		18847	0.0		0.001	False		,,,				2504	0.0				p.T54T		Atlas-SNP	.											.	SEPT9	105	.	0			c.G162A						PASS	.	G	,,,,,,	718,2418		83,552,933	35.0	38.0	37.0		,,,,162,,	-1.7	0.0	17	dbSNP_79	37	18,7146		0,18,3564	no	intron,intron,intron,intron,coding-synonymous,intron,intron	SEPT9	NM_001113491.1,NM_001113492.1,NM_001113493.1,NM_001113494.1,NM_001113495.1,NM_001113496.1,NM_006640.4	,,,,,,	83,570,4497	AA,AG,GG		0.2513,22.8954,7.1456	,,,,,,	,,,,54/475,,	75471762	736,9564	1568	3582	5150	SO:0001627	intron_variant	10801	exon1			GCCCACGCTGGGC	AB023208	CCDS45790.1, CCDS45791.1, CCDS45792.1, CCDS45793.1, CCDS45794.1, CCDS45795.1, CCDS74166.1	17q25.3	2014-09-17	2005-01-11	2005-01-12	ENSG00000184640	ENSG00000184640		"""Septins"""	7323	protein-coding gene	gene with protein product	"""Ov/Br septin"""	604061	"""MLL septin-like fusion"""	MSF		10339604, 10485469	Standard	NM_006640		Approved	MSF1, KIAA0991, PNUTL4, AF17q25, SeptD1	uc002jts.4	Q9UHD8		ENST00000427177.1:c.722-6464G>A	17.37:g.75471762G>A		66.0	0.0	0		83.0	44.0	0.53012	NM_001113495	A8K2V3|B3KPM0|B4DTL9|B4E0N2|B4E274|B7Z654|Q96QF3|Q96QF4|Q96QF5|Q9HA04|Q9UG40|Q9Y5W4	Silent	SNP	ENST00000427177.1	37	CCDS45790.1																																																																																			G|0.937;A|0.063	0.063	strong		0.642	SEPT9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000436304.2	NM_006640	
FAT3	120114	hgsc.bcm.edu	37	11	92616006	92616006	+	Silent	SNP	C	C	T	rs58474174	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:92616006C>T	ENST00000298047.6	+	23	12401	c.12384C>T	c.(12382-12384)taC>taT	p.Y4128Y	FAT3_ENST00000525166.1_Silent_p.Y3978Y|FAT3_ENST00000533797.1_Silent_p.Y463Y|FAT3_ENST00000409404.2_Silent_p.Y4128Y			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	4128	EGF-like 4; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				CGCCGGGCTACGTGGGCCAGT	0.632										TCGA Ovarian(4;0.039)			C|||	182	0.0363419	0.1309	0.0115	5008	,	,		15044	0.0		0.001	False		,,,				2504	0.0				p.Y4128Y		Atlas-SNP	.											.	FAT3	1822	.	0			c.C12384T						PASS	.	C		392,3806		19,354,1726	62.0	79.0	73.0		12384	1.9	1.0	11	dbSNP_129	73	2,8424		0,2,4211	no	coding-synonymous	FAT3	NM_001008781.2		19,356,5937	TT,TC,CC		0.0237,9.3378,3.121		4128/4558	92616006	394,12230	2099	4213	6312	SO:0001819	synonymous_variant	120114	exon23			GGGCTACGTGGGC	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.12384C>T	11.37:g.92616006C>T		140.0	0.0	0		115.0	47.0	0.408696	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				C|0.976;T|0.024	0.024	strong		0.632	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
CDH23	64072	hgsc.bcm.edu	37	10	73551088	73551088	+	Silent	SNP	G	G	A	rs55964031	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73551088G>A	ENST00000224721.6	+	46	6269	c.6264G>A	c.(6262-6264)ccG>ccA	p.P2088P		NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2083	Cadherin 20. {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)	p.P2088P(1)		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						AGAACTGCCCGCCTGGTAAGC	0.627													G|||	135	0.0269569	0.0976	0.0072	5008	,	,		16895	0.0		0.001	False		,,,				2504	0.0				p.P2083P		Atlas-SNP	.											CDH23,NS,carcinoma,0,1	CDH23	365	1	1	Substitution - coding silent(1)	prostate(1)	c.G6249A						scavenged	.	G		276,3814		11,254,1780	42.0	43.0	43.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	6249	-8.6	1.0	10	dbSNP_129	43	4,8364		0,4,4180	no	coding-synonymous	CDH23	NM_022124.5		11,258,5960	AA,AG,GG		0.0478,6.7482,2.2476		2083/3355	73551088	280,12178	2045	4184	6229	SO:0001819	synonymous_variant	64072	exon45			CTGCCCGCCTGGT	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.6264G>A	10.37:g.73551088G>A		80.0	1.0	0.0125		90.0	44.0	0.488889	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																				G|0.974;A|0.026	0.026	strong		0.627	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
LPA	4018	hgsc.bcm.edu	37	6	160977167	160977167	+	Silent	SNP	G	G	T	rs375904594		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:160977167G>T	ENST00000316300.5	-	30	4907	c.4863C>A	c.(4861-4863)ggC>ggA	p.G1621G	LPA_ENST00000447678.1_Silent_p.G1621G			P08519	APOA_HUMAN	lipoprotein, Lp(a)	4129	Kringle 15. {ECO:0000255|PROSITE- ProRule:PRU00121}.				blood circulation (GO:0008015)|lipid metabolic process (GO:0006629)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|negative regulation of endopeptidase activity (GO:0010951)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|plasma lipoprotein particle (GO:0034358)	apolipoprotein binding (GO:0034185)|endopeptidase inhibitor activity (GO:0004866)|fibronectin binding (GO:0001968)|heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|lung(54)|ovary(4)|pancreas(1)|prostate(2)|skin(10)|stomach(1)|urinary_tract(1)	107		Breast(66;0.000496)|Ovarian(120;0.0303)|Prostate(117;0.0965)		OV - Ovarian serous cystadenocarcinoma(65;2.5e-17)|BRCA - Breast invasive adenocarcinoma(81;6.48e-06)	Aminocaproic Acid(DB00513)	GATAACTCTGGCCATTACCAT	0.483																																					p.G1621G		Atlas-SNP	.											LPA,right_upper_lobe,carcinoma,-1,1	LPA	237	1	0			c.C4863A						scavenged	.	T		0,4376		0,0,2188	154.0	156.0	155.0		4863	-5.5	0.0	6		155	1,8599		0,1,4299	no	coding-synonymous	LPA	NM_005577.2		0,1,6487	TT,TG,GG		0.0116,0.0,0.0077		1621/2041	160977167	1,12975	2188	4300	6488	SO:0001819	synonymous_variant	4018	exon31			ACTCTGGCCATTA	X06290	CCDS43523.1	6q25-q26	2012-10-02			ENSG00000198670	ENSG00000198670			6667	protein-coding gene	gene with protein product		152200		LP		3670400	Standard	NM_005577		Approved		uc003qtl.3	P08519	OTTHUMG00000015956	ENST00000316300.5:c.4863C>A	6.37:g.160977167G>T		342.0	2.0	0.00584795		361.0	33.0	0.0914127	NM_005577	Q5VTD7|Q9UD88	Silent	SNP	ENST00000316300.5	37	CCDS43523.1																																																																																			.	.	weak		0.483	LPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042957.1	NM_005577	
APTX	54840	hgsc.bcm.edu	37	9	32984803	32984803	+	Missense_Mutation	SNP	C	C	T	rs150886026	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:32984803C>T	ENST00000379819.1	-	6	637	c.638G>A	c.(637-639)cGt>cAt	p.R213H	APTX_ENST00000463596.1_Missense_Mutation_p.R199H|APTX_ENST00000468275.1_Missense_Mutation_p.R199H|APTX_ENST00000309615.3_Missense_Mutation_p.R213H|APTX_ENST00000476858.1_Missense_Mutation_p.R159H|APTX_ENST00000379813.3_Missense_Mutation_p.R199H|APTX_ENST00000397172.3_Missense_Mutation_p.R141H|APTX_ENST00000379825.2_Missense_Mutation_p.R213H|APTX_ENST00000379817.2_Missense_Mutation_p.R199H|APTX_ENST00000436040.2_Intron			Q7Z2E3	APTX_HUMAN	aprataxin	213	HIT. {ECO:0000255|PROSITE- ProRule:PRU00464}.		R -> H (in AOA; dbSNP:rs150886026). {ECO:0000269|PubMed:11586300}.		cell death (GO:0008219)|cellular response to DNA damage stimulus (GO:0006974)|dephosphorylation (GO:0016311)|DNA catabolic process, exonucleolytic (GO:0000738)|DNA ligation (GO:0006266)|double-strand break repair (GO:0006302)|polynucleotide 3' dephosphorylation (GO:0098506)|regulation of protein stability (GO:0031647)|response to hydrogen peroxide (GO:0042542)|single strand break repair (GO:0000012)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA 5'-adenosine monophosphate hydrolase activity (GO:0033699)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)|phosphoglycolate phosphatase activity (GO:0008967)|phosphoprotein binding (GO:0051219)|polynucleotide 3'-phosphatase activity (GO:0046403)|protein N-terminus binding (GO:0047485)			endometrium(1)|lung(1)|ovary(2)|prostate(2)	6			LUSC - Lung squamous cell carcinoma(29;0.0302)	GBM - Glioblastoma multiforme(74;0.105)		CCAATGGTAACGGGCCTTTGG	0.473								Editing and processing nucleases					C|||	31	0.0061901	0.0197	0.0058	5008	,	,		21579	0.0		0.0	False		,,,				2504	0.001				p.R213H		Atlas-SNP	.											.	APTX	44	.	0			c.G638A	GRCh37	CM012895	APTX	M	rs150886026	PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	80,4326	69.2+/-107.0	0,80,2123	162.0	146.0	152.0		638,596,476,596,422,434,638,596	4.0	0.8	9	dbSNP_134	152	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense,missense,missense	APTX	NM_001195248.1,NM_001195249.1,NM_001195250.1,NM_001195251.1,NM_001195252.1,NM_001195254.1,NM_175069.2,NM_175073.2	29,29,29,29,29,29,29,29	0,80,6423	TT,TC,CC		0.0,1.8157,0.6151	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	213/357,199/343,159/303,199/293,141/285,145/289,213/307,199/343	32984803	80,12926	2203	4300	6503	SO:0001583	missense	54840	exon6			TGGTAACGGGCCT	AK000164	CCDS47956.1, CCDS56568.1, CCDS75827.1	9p13.3	2014-01-28	2003-04-03		ENSG00000137074	ENSG00000137074			15984	protein-coding gene	gene with protein product		606350	"""ataxia 1, early onset with hypoalbuminemia"""	AXA1		11586299, 11586300	Standard	NM_175069		Approved	FLJ20157, AOA, AOA1, EAOH, EOAHA	uc003zry.3	Q7Z2E3	OTTHUMG00000019759	ENST00000379819.1:c.638G>A	9.37:g.32984803C>T	ENSP00000369147:p.Arg213His	108.0	0.0	0		112.0	63.0	0.5625	NM_001195248	A8MTN4|D3DRK9|D3DRL0|Q0P662|Q5T781|Q5T782|Q5T784|Q6JV81|Q6JV82|Q6JV85|Q7Z2F3|Q7Z336|Q7Z5R5|Q7Z6V7|Q7Z6V8|Q9NXM5	Missense_Mutation	SNP	ENST00000379819.1	37		9	0.004120879120879121	8	0.016260162601626018	1	0.0027624309392265192	0	0.0	0	0.0	C	13.81	2.348650	0.41599	0.018157	0.0	ENSG00000137074	ENST00000379825;ENST00000309615;ENST00000397172;ENST00000379817;ENST00000379819;ENST00000468275;ENST00000463596;ENST00000476858;ENST00000344355;ENST00000379813;ENST00000379812;ENST00000473221;ENST00000477119	D;D;D;D;D;D;D;D;D;D;D;D	0.95656	-3.77;-3.77;-2.86;-2.86;-2.86;-2.86;-2.86;-2.86;-2.86;-3.77;-3.77;-3.77	5.81	3.96	0.45880	Histidine triad motif (1);Histidine triad-like motif (1);	0.047355	0.85682	D	0.000000	D	0.92257	0.7544	M	0.64170	1.965	0.80722	D	1	D;P;P;P;P	0.64830	0.994;0.864;0.632;0.769;0.632	P;B;B;B;B	0.55785	0.784;0.304;0.288;0.352;0.288	D	0.91337	0.5094	10	0.52906	T	0.07	-11.4381	11.0972	0.48152	0.0:0.8459:0.0:0.1541	.	159;141;213;145;213	C9JZ40;Q7Z2E3-3;Q5T782;Q7Z2E3-5;Q7Z2E3	.;.;.;.;APTX_HUMAN	H	213;213;141;199;213;199;199;159;194;199;141;159;145	ENSP00000369153:R213H;ENSP00000311547:R213H;ENSP00000380357:R141H;ENSP00000369145:R199H;ENSP00000369147:R213H;ENSP00000420263:R199H;ENSP00000419846:R199H;ENSP00000419042:R159H;ENSP00000369141:R199H;ENSP00000369140:R141H;ENSP00000419020:R159H;ENSP00000417649:R145H	ENSP00000311547:R213H	R	-	2	0	APTX	32974803	1.000000	0.71417	0.798000	0.32154	0.012000	0.07955	6.082000	0.71318	1.451000	0.47736	0.655000	0.94253	CGT	C|0.994;T|0.006	0.006	strong		0.473	APTX-003	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000052028.2	NM_017692	
SMTN	6525	hgsc.bcm.edu	37	22	31478942	31478942	+	Intron	SNP	G	G	A	rs73408133	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:31478942G>A	ENST00000347557.2	+	2	138				SMTN_ENST00000333137.7_Intron|SMTN_ENST00000358743.1_Intron|SMTN_ENST00000475548.1_Intron|RP3-412A9.16_ENST00000609017.1_RNA	NM_001207017.1|NM_006932.4	NP_001193946.1|NP_008863.3	P53814	SMTN_HUMAN	smoothelin						muscle organ development (GO:0007517)|smooth muscle contraction (GO:0006939)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	actin binding (GO:0003779)|structural constituent of muscle (GO:0008307)			breast(2)|endometrium(2)|large_intestine(5)|lung(9)|ovary(3)|pancreas(1)|prostate(3)	25						gcagactggcggccaagctgg	0.612											OREG0026470	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	217	0.0433307	0.1596	0.0086	5008	,	,		16659	0.0		0.0	False		,,,				2504	0.0				p.A12A		Atlas-SNP	.											.	SMTN	219	.	0			c.G36A						PASS	.																																			SO:0001627	intron_variant	6525	exon1			ACTGGCGGCCAAG	AY061972	CCDS13886.1, CCDS13887.1, CCDS13888.1, CCDS74845.1, CCDS74846.1	22q12	2006-01-27			ENSG00000183963	ENSG00000183963			11126	protein-coding gene	gene with protein product		602127				9244445, 8707825	Standard	NM_006932		Approved		uc011ale.2	P53814	OTTHUMG00000151203	ENST00000347557.2:c.-80-223G>A	22.37:g.31478942G>A		76.0	0.0	0	825	100.0	38.0	0.38	NM_001207017	O00569|O95769|O95937|Q8N4H8|Q8WWW1|Q8WWW2|Q9P1S8|Q9UIT1|Q9UIT2	Silent	SNP	ENST00000347557.2	37	CCDS13886.1																																																																																			G|0.963;A|0.037	0.037	strong		0.612	SMTN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321766.1	NM_134270	
PKD1L2	114780	hgsc.bcm.edu	37	16	81242184	81242184	+	RNA	SNP	T	T	C	rs9927930	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:81242184T>C	ENST00000525539.1	-	0	671				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						CCACCTGGCATGACTGTAGCT	0.562													T|||	184	0.0367412	0.1339	0.0101	5008	,	,		20552	0.0		0.0	False		,,,				2504	0.0				p.S224S		Atlas-SNP	.											.	PKD1L2	361	.	0			c.A672G						PASS	.	T	,	433,3807		22,389,1709	75.0	73.0	74.0		672,672	-8.6	0.6	16	dbSNP_119	74	3,8453		0,3,4225	no	coding-synonymous,coding-synonymous	PKD1L2	NM_001076780.1,NM_052892.3	,	22,392,5934	CC,CT,TT		0.0355,10.2123,3.4342	,	224/992,224/2460	81242184	436,12260	2120	4228	6348			114780	exon4			CTGGCATGACTGT	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81242184T>C		37.0	0.0	0		47.0	21.0	0.446809	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Silent	SNP	ENST00000525539.1	37																																																																																				T|0.951;C|0.049	0.049	strong		0.562	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
OR52E2	119678	hgsc.bcm.edu	37	11	5080523	5080523	+	Missense_Mutation	SNP	A	A	G	rs144077173	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:5080523A>G	ENST00000321522.2	-	1	334	c.335T>C	c.(334-336)aTg>aCg	p.M112T		NM_001005164.2	NP_001005164.2	Q8NGJ4	O52E2_HUMAN	olfactory receptor, family 52, subfamily E, member 2	112						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|lung(13)|ovary(2)|skin(3)	20		Medulloblastoma(188;0.0061)|all_neural(188;0.0479)|Breast(177;0.086)		Epithelial(150;1.03e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)|LUSC - Lung squamous cell carcinoma(625;0.191)		TGCTGACTCCATAAGTGTGAA	0.468													a|||	3	0.000599042	0.0	0.0	5008	,	,		22727	0.003		0.0	False		,,,				2504	0.0				p.M112T		Atlas-SNP	.											.	OR52E2	63	.	0			c.T335C						PASS	.	G	THR/MET	3,4399	8.1+/-20.4	0,3,2198	75.0	71.0	72.0		335	1.4	0.7	11	dbSNP_134	72	0,8596		0,0,4298	yes	missense	OR52E2	NM_001005164.2	81	0,3,6496	GG,GA,AA		0.0,0.0682,0.0231	benign	112/326	5080523	3,12995	2201	4298	6499	SO:0001583	missense	119678	exon1			GACTCCATAAGTG	AB065800	CCDS31371.1	11p15.4	2012-08-09			ENSG00000176787	ENSG00000176787		"""GPCR / Class A : Olfactory receptors"""	14769	protein-coding gene	gene with protein product							Standard	NM_001005164		Approved		uc010qyw.2	Q8NGJ4	OTTHUMG00000066608	ENST00000321522.2:c.335T>C	11.37:g.5080523A>G	ENSP00000322088:p.Met112Thr	87.0	0.0	0		91.0	47.0	0.516484	NM_001005164		Missense_Mutation	SNP	ENST00000321522.2	37	CCDS31371.1	4	0.0018315018315018315	0	0.0	0	0.0	4	0.006993006993006993	0	0.0	a	2.241	-0.373782	0.05034	6.82E-4	0.0	ENSG00000176787	ENST00000321522	T	0.01613	4.73	3.77	1.43	0.22495	GPCR, rhodopsin-like superfamily (1);	0.185074	0.38111	N	0.001815	T	0.01222	0.0040	L	0.35249	1.045	0.09310	N	1	B	0.23316	0.083	B	0.25291	0.059	T	0.44697	-0.9311	10	0.54805	T	0.06	.	7.9034	0.29748	0.8183:0.0:0.1817:0.0	.	112	Q8NGJ4	O52E2_HUMAN	T	112	ENSP00000322088:M112T	ENSP00000322088:M112T	M	-	2	0	OR52E2	5037099	0.000000	0.05858	0.673000	0.29887	0.113000	0.19764	0.661000	0.25023	0.311000	0.23014	-0.259000	0.10710	ATG	A|0.999;G|0.001	0.001	strong		0.468	OR52E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142815.1	NM_001005164	
AIP	9049	hgsc.bcm.edu	37	11	67258362	67258362	+	Silent	SNP	C	C	A	rs35665586|rs267606585	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:67258362C>A	ENST00000279146.3	+	6	1009	c.891C>A	c.(889-891)gcC>gcA	p.A297A	PITPNM1_ENST00000526450.1_5'Flank	NM_003977.2	NP_003968.2	O00170	AIP_HUMAN	aryl hydrocarbon receptor interacting protein	297					negative regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051344)|protein maturation by protein folding (GO:0022417)|protein targeting to mitochondrion (GO:0006626)|regulation of protein kinase A signaling (GO:0010738)|signal transduction (GO:0007165)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GAF domain binding (GO:0036004)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|unfolded protein binding (GO:0051082)			central_nervous_system(1)|large_intestine(1)|lung(3)|skin(2)	7						TGGACCCAGCCCTGGCGCCTG	0.652									Familial Isolated Pituitary Adenoma				C|||	31	0.0061901	0.0219	0.0029	5008	,	,		16963	0.0		0.0	False		,,,				2504	0.0				p.A297A		Atlas-SNP	.											.	AIP	26	.	0			c.C891A						PASS	.	C		70,4322	61.1+/-98.1	1,68,2127	25.0	27.0	26.0		891	4.0	1.0	11	dbSNP_126	26	1,8585		0,1,4292	no	coding-synonymous	AIP	NM_003977.2		1,69,6419	AA,AC,CC		0.0116,1.5938,0.5471		297/331	67258362	71,12907	2196	4293	6489	SO:0001819	synonymous_variant	9049	exon6	Familial Cancer Database	FIPA, incl. Familial Isolated Somatotropinomas, FIS, IFS, Familial Acromegaly	CCCAGCCCTGGCG	U31913	CCDS8168.1	11q13.3	2014-09-17	2001-11-29		ENSG00000110711	ENSG00000110711			358	protein-coding gene	gene with protein product		605555	"""aryl hydrocarbon receptor-interacting protein"""			8972861, 9111057	Standard	NM_003977		Approved	XAP2, ARA9, FKBP16	uc001olv.3	O00170	OTTHUMG00000167674	ENST00000279146.3:c.891C>A	11.37:g.67258362C>A		149.0	0.0	0		148.0	70.0	0.472973	NM_003977	A0SZW3|A0SZW4|A0SZW5|A0SZW6|Q2M3Q2|Q99606	Silent	SNP	ENST00000279146.3	37	CCDS8168.1																																																																																			C|0.995;A|0.005	0.005	strong		0.652	AIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395516.1		
ANKRD45	339416	hgsc.bcm.edu	37	1	173596257	173596257	+	Missense_Mutation	SNP	A	A	T	rs12059066	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:173596257A>T	ENST00000333279.2	-	4	598	c.538T>A	c.(538-540)Tta>Ata	p.L180I		NM_198493.2	NP_940895.1	Q5TZF3	ANR45_HUMAN	ankyrin repeat domain 45	196										NS(2)|endometrium(2)|large_intestine(4)|lung(3)|skin(1)	12						GTAACAGCTAAAGAGACTTTT	0.373													A|||	965	0.192692	0.6989	0.0504	5008	,	,		20198	0.0		0.005	False		,,,				2504	0.001				p.L180I		Atlas-SNP	.											.	ANKRD45	36	.	0			c.T538A						PASS	.	A	ILE/LEU	2539,1867	632.6+/-395.9	756,1027,420	145.0	150.0	148.0		538	-3.8	0.0	1	dbSNP_120	148	32,8568	19.8+/-62.0	0,32,4268	yes	missense	ANKRD45	NM_198493.2	5	756,1059,4688	TT,TA,AA		0.3721,42.374,19.7678	benign	180/267	173596257	2571,10435	2203	4300	6503	SO:0001583	missense	339416	exon4			CAGCTAAAGAGAC		CCDS1309.1	1q25.1	2013-01-10			ENSG00000183831	ENSG00000183831		"""Ankyrin repeat domain containing"""	24786	protein-coding gene	gene with protein product	"""cancer/testis antigen 117"""						Standard	NM_198493		Approved	FLJ45235, CT117	uc001gja.1	Q5TZF3	OTTHUMG00000040546	ENST00000333279.2:c.538T>A	1.37:g.173596257A>T	ENSP00000331268:p.Leu180Ile	67.0	0.0	0		54.0	53.0	0.981481	NM_198493	A1A4G2|Q6ZST1	Missense_Mutation	SNP	ENST00000333279.2	37	CCDS1309.1	377	0.17261904761904762	353	0.717479674796748	20	0.055248618784530384	0	0.0	4	0.005277044854881266	A	11.25	1.583800	0.28268	0.57626	0.003721	ENSG00000183831	ENST00000333279	T	0.13778	2.56	5.35	-3.79	0.04320	.	1.555310	0.03916	N	0.282716	T	0.01870	0.0059	N	0.22421	0.69	0.80722	P	0.0	B	0.27068	0.167	B	0.19148	0.024	T	0.35895	-0.9770	9	0.36615	T	0.2	-17.7491	1.2921	0.02062	0.1379:0.3633:0.2467:0.2521	rs12059066;rs52822128;rs12059066	196	Q5TZF3	ANR45_HUMAN	I	180	ENSP00000331268:L180I	ENSP00000331268:L180I	L	-	1	2	ANKRD45	171862880	0.000000	0.05858	0.000000	0.03702	0.656000	0.38851	-0.559000	0.05971	-1.213000	0.02617	0.455000	0.32223	TTA	A|0.814;T|0.186	0.186	strong		0.373	ANKRD45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097580.2	NM_198493	
SIGLEC1	6614	hgsc.bcm.edu	37	20	3672746	3672746	+	Silent	SNP	G	G	A	rs34921899	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:3672746G>A	ENST00000344754.4	-	16	4133	c.4134C>T	c.(4132-4134)gcC>gcT	p.A1378A	SIGLEC1_ENST00000202578.4_Silent_p.A1378A	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	1378	Ig-like C2-type 14.				cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						CATGAGATAGGGCCAGCTCAG	0.637													G|||	103	0.0205671	0.0772	0.0014	5008	,	,		19801	0.0		0.0	False		,,,				2504	0.0				p.A1378A		Atlas-SNP	.											.	SIGLEC1	210	.	0			c.C4134T						PASS	.	G		234,4170	138.0+/-173.8	7,220,1975	45.0	37.0	40.0		4134	1.1	0.3	20	dbSNP_126	40	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	SIGLEC1	NM_023068.3		7,224,6271	AA,AG,GG		0.0465,5.3134,1.8302		1378/1710	3672746	238,12766	2202	4300	6502	SO:0001819	synonymous_variant	6614	exon16			AGATAGGGCCAGC	AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	11127	protein-coding gene	gene with protein product		600751	"""sialoadhesin"""	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.4134C>T	20.37:g.3672746G>A		39.0	0.0	0		41.0	22.0	0.536585	NM_023068	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Silent	SNP	ENST00000344754.4	37	CCDS13060.1	32	0.014652014652014652	31	0.06300813008130081	0	0.0	0	0.0	1	0.0013192612137203166	G	6.234	0.411258	0.11812	0.053134	4.65E-4	ENSG00000088827	ENST00000419548	.	.	.	5.5	1.12	0.20585	.	.	.	.	.	T	0.07098	0.0180	.	.	.	0.58432	D	0.999999	.	.	.	.	.	.	T	0.03193	-1.1062	4	.	.	.	.	3.0219	0.06078	0.1405:0.1464:0.5625:0.1506	rs34921899	.	.	.	S	192	.	.	P	-	1	0	SIGLEC1	3620746	0.613000	0.27009	0.313000	0.25210	0.552000	0.35366	0.539000	0.23175	-0.009000	0.14296	0.655000	0.94253	CCT	G|0.979;A|0.021	0.021	strong		0.637	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077761.2	NM_023068	
KDM1A	23028	hgsc.bcm.edu	37	1	23395037	23395037	+	Silent	SNP	T	T	C	rs145865107	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:23395037T>C	ENST00000356634.3	+	9	1262	c.1113T>C	c.(1111-1113)ccT>ccC	p.P371P	KDM1A_ENST00000542151.1_Silent_p.P395P|RP1-184J9.2_ENST00000427154.1_RNA|KDM1A_ENST00000400181.4_Silent_p.P395P	NM_015013.3	NP_055828.2	O60341	KDM1A_HUMAN	lysine (K)-specific demethylase 1A	371	Demethylase activity.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|histone H3-K4 demethylation (GO:0034720)|histone H3-K9 demethylation (GO:0033169)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of DNA binding (GO:0043392)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of protein binding (GO:0032091)|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)|pituitary gland development (GO:0021983)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein demethylation (GO:0006482)|regulation of primitive erythrocyte differentiation (GO:0010725)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|demethylase activity (GO:0032451)|enzyme binding (GO:0019899)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-K4 specific) (GO:0032453)|histone demethylase activity (H3-K9 specific) (GO:0032454)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|MRF binding (GO:0043426)|oxidoreductase activity (GO:0016491)|p53 binding (GO:0002039)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(2)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						TTCAGGTTCCTAAAGAGAAAG	0.348													T|||	22	0.00439297	0.0151	0.0029	5008	,	,		18338	0.0		0.0	False		,,,				2504	0.0				p.P395P		Atlas-SNP	.											.	KDM1A	49	.	0			c.T1185C						PASS	.	T	,	41,4365	43.8+/-77.6	0,41,2162	72.0	68.0	69.0		1185,1113	0.5	1.0	1	dbSNP_134	69	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	KDM1A	NM_001009999.2,NM_015013.3	,	0,42,6461	CC,CT,TT		0.0116,0.9305,0.3229	,	395/877,371/853	23395037	42,12964	2203	4300	6503	SO:0001819	synonymous_variant	23028	exon11			GGTTCCTAAAGAG	AL031428	CCDS30627.1, CCDS53278.1	1p36.12	2011-07-01	2009-09-29	2009-09-29	ENSG00000004487	ENSG00000004487		"""Chromatin-modifying enzymes / K-demethylases"""	29079	protein-coding gene	gene with protein product		609132	"""amine oxidase (flavin containing) domain 2"", ""lysine (K)-specific demethylase 1"""	AOF2, KDM1		9628581, 12493763	Standard	NM_015013		Approved	KIAA0601, BHC110, LSD1	uc001bgj.2	O60341	OTTHUMG00000003220	ENST00000356634.3:c.1113T>C	1.37:g.23395037T>C		98.0	0.0	0		130.0	71.0	0.546154	NM_001009999	A8MWP9|Q5TH94|Q5TH95|Q86VT7|Q8IXK4|Q8NDP6|Q8TAZ3|Q96AW4	Silent	SNP	ENST00000356634.3	37	CCDS30627.1																																																																																			T|0.998;C|0.002	0.002	strong		0.348	KDM1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008880.3	NM_015013	
CCDC157	550631	hgsc.bcm.edu	37	22	30765502	30765502	+	Silent	SNP	G	G	C	rs5749080	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:30765502G>C	ENST00000405659.1	+	4	1039	c.330G>C	c.(328-330)gcG>gcC	p.A110A	CCDC157_ENST00000338306.3_Silent_p.A110A			Q569K6	CC157_HUMAN	coiled-coil domain containing 157	110										central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(5)|skin(3)|upper_aerodigestive_tract(1)	15						CACAGGCTGCGGGGCCCTGCA	0.652													G|||	51	0.0101837	0.0378	0.0014	5008	,	,		17743	0.0		0.0	False		,,,				2504	0.0				p.A110A		Atlas-SNP	.											.	CCDC157	86	.	0			c.G330C						PASS	.						41.0	40.0	41.0					22																	30765502		2203	4300	6503	SO:0001819	synonymous_variant	550631	exon4			GGCTGCGGGGCCC	BC018040	CCDS33632.2	22q12.2	2009-03-05			ENSG00000187860	ENSG00000187860			33854	protein-coding gene	gene with protein product							Standard	NM_001017437		Approved		uc011aku.2	Q569K6	OTTHUMG00000151007	ENST00000405659.1:c.330G>C	22.37:g.30765502G>C		96.0	0.0	0		107.0	69.0	0.64486	NM_001017437	Q0VD76|Q9BYA4	Silent	SNP	ENST00000405659.1	37	CCDS33632.2																																																																																			A|0.198;C|0.000;G|0.802	0.000	strong		0.652	CCDC157-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320936.1	NM_001017437	
ZDHHC20	253832	hgsc.bcm.edu	37	13	21987823	21987823	+	Missense_Mutation	SNP	G	G	A	rs151151710	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:21987823G>A	ENST00000400590.3	-	4	536	c.338C>T	c.(337-339)gCt>gTt	p.A113V	ZDHHC20_ENST00000422251.1_Missense_Mutation_p.A113V|ZDHHC20_ENST00000320220.9_Missense_Mutation_p.A113V|ZDHHC20_ENST00000415724.1_Missense_Mutation_p.A113V|ZDHHC20_ENST00000542645.1_Missense_Mutation_p.A50V|ZDHHC20_ENST00000382466.3_Missense_Mutation_p.A113V|ZDHHC20_ENST00000494731.1_5'UTR			Q5W0Z9	ZDH20_HUMAN	zinc finger, DHHC-type containing 20	113					protein palmitoylation (GO:0018345)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	9		all_cancers(29;8.1e-16)|all_epithelial(30;3.63e-14)|all_lung(29;2.04e-13)|Lung SC(185;0.0367)		all cancers(112;0.000268)|Epithelial(112;0.000735)|OV - Ovarian serous cystadenocarcinoma(117;0.00517)|Lung(94;0.171)		GATAGGTAAAGCTCTTGCTGC	0.313													G|||	22	0.00439297	0.0159	0.0014	5008	,	,		14776	0.0		0.0	False		,,,				2504	0.0				p.A113V		Atlas-SNP	.											ZDHHC20_ENST00000382466,NS,carcinoma,0,2	ZDHHC20	36	2	0			c.C338T						PASS	.	G	VAL/ALA	66,3544		0,66,1739	117.0	101.0	106.0		338	3.1	1.0	13	dbSNP_134	106	0,8150		0,0,4075	yes	missense	ZDHHC20	NM_153251.3	64	0,66,5814	AA,AG,GG		0.0,1.8283,0.5612	benign	113/355	21987823	66,11694	1805	4075	5880	SO:0001583	missense	253832	exon4			GGTAAAGCTCTTG	AK090979	CCDS45017.1, CCDS73551.1	13q12.11	2008-10-21			ENSG00000180776	ENSG00000180776		"""Zinc fingers, DHHC-type"""	20749	protein-coding gene	gene with protein product							Standard	NM_153251		Approved	FLJ25952	uc001uoa.2	Q5W0Z9	OTTHUMG00000017410	ENST00000400590.3:c.338C>T	13.37:g.21987823G>A	ENSP00000383433:p.Ala113Val	58.0	0.0	0		51.0	25.0	0.490196	NM_153251	A8MTV9|C9JG20|I6L9D4|Q2TB82|Q6NVU8	Missense_Mutation	SNP	ENST00000400590.3	37		13	0.005952380952380952	12	0.024390243902439025	1	0.0027624309392265192	0	0.0	0	0.0	G	10.49	1.365289	0.24684	0.018283	0.0	ENSG00000180776	ENST00000400590;ENST00000320220;ENST00000382466;ENST00000542645;ENST00000415724;ENST00000422251	T;T;T;T;T	0.26373	1.74;1.74;1.74;1.74;1.74	5.59	3.12	0.35913	.	0.330632	0.39834	N	0.001258	T	0.06325	0.0163	N	0.10916	0.065	0.20764	N	0.999855	B;B	0.02656	0.0;0.0	B;B	0.16722	0.016;0.001	T	0.20174	-1.0283	10	0.44086	T	0.13	-10.0193	8.0652	0.30657	0.125:0.0:0.3373:0.5376	.	50;113	B4DRN8;Q5W0Z9-3	.;.	V	113;113;113;50;113;113	ENSP00000383433:A113V;ENSP00000313583:A113V;ENSP00000371905:A113V;ENSP00000443236:A50V;ENSP00000401232:A113V	ENSP00000313583:A113V	A	-	2	0	ZDHHC20	20885823	0.999000	0.42202	0.989000	0.46669	0.681000	0.39784	1.392000	0.34486	0.017000	0.15025	-1.579000	0.00862	GCT	G|0.994;A|0.006	0.006	strong		0.313	ZDHHC20-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000045994.1	NM_153251	
TEP1	7011	hgsc.bcm.edu	37	14	20873695	20873695	+	Missense_Mutation	SNP	A	A	G	rs148090256	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:20873695A>G	ENST00000262715.5	-	4	825	c.785T>C	c.(784-786)aTg>aCg	p.M262T	TEP1_ENST00000556935.1_Missense_Mutation_p.M262T	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	262	TROVE. {ECO:0000255|PROSITE- ProRule:PRU00343}.				RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		TGTATTGTTCATGTTTACTTC	0.463													A|||	33	0.00658946	0.0234	0.0029	5008	,	,		21319	0.0		0.0	False		,,,				2504	0.0				p.M262T		Atlas-SNP	.											TEP1,caecum,carcinoma,0,1	TEP1	224	1	0			c.T785C						PASS	.	A	THR/MET	82,4324	70.3+/-108.2	0,82,2121	116.0	111.0	113.0		785	-2.0	0.0	14	dbSNP_134	113	0,8600		0,0,4300	yes	missense	TEP1	NM_007110.4	81	0,82,6421	GG,GA,AA		0.0,1.8611,0.6305	benign	262/2628	20873695	82,12924	2203	4300	6503	SO:0001583	missense	7011	exon4			TTGTTCATGTTTA		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"""WD repeat domain containing"""	11726	protein-coding gene	gene with protein product	"""TROVE domain family, member 1"""	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.785T>C	14.37:g.20873695A>G	ENSP00000262715:p.Met262Thr	64.0	0.0	0		57.0	29.0	0.508772	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	7	0.003205128205128205	6	0.012195121951219513	1	0.0027624309392265192	0	0.0	0	0.0	A	5.089	0.202155	0.09652	0.018611	0.0	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935	T;T	0.14144	2.53;2.53	4.07	-1.99	0.07457	TROVE (2);	2.107970	0.01669	N	0.025498	T	0.05044	0.0135	L	0.29908	0.895	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.001;0.002	T	0.32534	-0.9903	10	0.49607	T	0.09	15.064	5.3797	0.16183	0.594:0.1384:0.2676:0.0	.	262;262	G3V5X7;Q99973	.;TEP1_HUMAN	T	262	ENSP00000262715:M262T;ENSP00000452574:M262T	ENSP00000262715:M262T	M	-	2	0	TEP1	19943535	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.762000	0.04745	-0.429000	0.07329	0.533000	0.62120	ATG	A|0.994;G|0.006	0.006	strong		0.463	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
WDR87	83889	hgsc.bcm.edu	37	19	38377417	38377417	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:38377417C>T	ENST00000303868.5	-	6	7001	c.6777G>A	c.(6775-6777)gaG>gaA	p.E2259E	WDR87_ENST00000447313.2_Silent_p.E2298E	NM_031951.3	NP_114157.3	Q6ZQQ6	WDR87_HUMAN	WD repeat domain 87	2259	Glu-rich.									NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|prostate(1)|skin(3)|stomach(1)	36						ttacctcctcctcctcccttt	0.483																																					p.E2259E		Atlas-SNP	.											.	WDR87	191	.	0			c.G6777A						PASS	.						58.0	46.0	50.0					19																	38377417		692	1591	2283	SO:0001819	synonymous_variant	83889	exon6			CTCCTCCTCCTCC	AK128826	CCDS46063.1, CCDS74356.1	19q13.13	2013-01-09			ENSG00000171804	ENSG00000171804		"""WD repeat domain containing"""	29934	protein-coding gene	gene with protein product							Standard	XM_005259304		Approved	NYD-SP11	uc010efu.2	Q6ZQQ6	OTTHUMG00000048187	ENST00000303868.5:c.6777G>A	19.37:g.38377417C>T		82.0	0.0	0		74.0	11.0	0.148649	NM_031951	Q9BWV9	Silent	SNP	ENST00000303868.5	37	CCDS46063.1																																																																																			.	.	none		0.483	WDR87-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314628.2	XM_940478	
SHROOM3	57619	hgsc.bcm.edu	37	4	77660550	77660550	+	Silent	SNP	T	T	C	rs61745983	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:77660550T>C	ENST00000296043.6	+	5	2177	c.1224T>C	c.(1222-1224)gaT>gaC	p.D408D		NM_020859.3	NP_065910.3	Q8TF72	SHRM3_HUMAN	shroom family member 3	408					actin cytoskeleton organization (GO:0030036)|apical protein localization (GO:0045176)|cell morphogenesis (GO:0000902)|cellular pigment accumulation (GO:0043482)|columnar/cuboidal epithelial cell development (GO:0002066)|neural tube closure (GO:0001843)|pattern specification process (GO:0007389)|regulation of cell shape (GO:0008360)	adherens junction (GO:0005912)|apical junction complex (GO:0043296)|apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|microtubule (GO:0005874)				NS(3)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(29)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	60			Lung(101;0.0903)			CTAGCCTTGATCAGAAACGGC	0.577													T|||	94	0.01877	0.0681	0.0058	5008	,	,		19865	0.0		0.0	False		,,,				2504	0.0				p.D408D		Atlas-SNP	.											.	SHROOM3	134	.	0			c.T1224C						PASS	.	T		262,4144	146.1+/-180.8	7,248,1948	45.0	45.0	45.0		1224	-1.7	1.0	4	dbSNP_129	45	1,8599	2.2+/-6.3	0,1,4299	no	coding-synonymous	SHROOM3	NM_020859.3		7,249,6247	CC,CT,TT		0.0116,5.9464,2.0221		408/1997	77660550	263,12743	2203	4300	6503	SO:0001819	synonymous_variant	57619	exon5			CCTTGATCAGAAA	AB055660	CCDS3579.2	4q21.1	2009-11-25			ENSG00000138771	ENSG00000138771			30422	protein-coding gene	gene with protein product		604570				10589677, 16615870	Standard	NM_020859		Approved	ShrmL, SHRM, KIAA1481, APXL3	uc011cbx.2	Q8TF72	OTTHUMG00000157075	ENST00000296043.6:c.1224T>C	4.37:g.77660550T>C		136.0	0.0	0		132.0	58.0	0.439394	NM_020859	Q5QTQ3|Q6ZRW3|Q96IR9|Q9P247	Silent	SNP	ENST00000296043.6	37	CCDS3579.2																																																																																			T|0.978;C|0.022	0.022	strong		0.577	SHROOM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252408.2	NM_020859	
TRAPPC12	51112	hgsc.bcm.edu	37	2	3425731	3425731	+	Missense_Mutation	SNP	G	G	A	rs35775829	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:3425731G>A	ENST00000324266.5	+	4	1439	c.1244G>A	c.(1243-1245)gGg>gAg	p.G415E	TRAPPC12_ENST00000382110.2_Missense_Mutation_p.G415E	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	415					vesicle-mediated transport (GO:0016192)												GGCAAGAGCGGGCTGCTCACC	0.587													G|||	30	0.00599042	0.0227	0.0	5008	,	,		18288	0.0		0.0	False		,,,				2504	0.0				p.G415E		Atlas-SNP	.											.	.	.	.	0			c.G1244A						PASS	.	G	GLU/GLY	107,4299	82.4+/-120.9	0,107,2096	32.0	31.0	31.0		1244	4.7	1.0	2	dbSNP_126	31	2,8598	2.2+/-6.3	0,2,4298	yes	missense	TTC15	NM_016030.5	98	0,109,6394	AA,AG,GG		0.0233,2.4285,0.8381	probably-damaging	415/736	3425731	109,12897	2203	4300	6503	SO:0001583	missense	51112	exon4			AGAGCGGGCTGCT	BC017475	CCDS1652.1	2p25.3	2013-01-10	2011-12-12	2011-12-12	ENSG00000171853	ENSG00000171853		"""Trafficking protein particle complex"", ""Tetratricopeptide (TTC) repeat domain containing"""	24284	protein-coding gene	gene with protein product		614139	"""tetratricopeptide repeat domain 15"""	TTC15		10810093, 21525244, 20562859	Standard	NM_016030		Approved	CGI-87, TTC-15	uc002qxm.1	Q8WVT3	OTTHUMG00000090328	ENST00000324266.5:c.1244G>A	2.37:g.3425731G>A	ENSP00000324318:p.Gly415Glu	133.0	0.0	0		176.0	87.0	0.494318	NM_016030	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Missense_Mutation	SNP	ENST00000324266.5	37	CCDS1652.1	10|10	0.004578754578754579|0.004578754578754579	10|10	0.02032520325203252|0.02032520325203252	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	28.0|28.0	4.879029|4.879029	0.91740|0.91740	0.024285|0.024285	2.33E-4|2.33E-4	ENSG00000171853|ENSG00000171853	ENST00000382110;ENST00000304601;ENST00000324266|ENST00000441983	T;T|.	0.53206|.	0.63;0.63|.	4.72|4.72	4.72|4.72	0.59763|0.59763	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.61924|0.61924	0.2386|0.2386	M|M	0.82323|0.82323	2.585|2.585	0.80722|0.80722	D|D	1|1	D;P|.	0.53312|.	0.959;0.93|.	P;P|.	0.52881|.	0.712;0.712|.	T|T	0.68462|0.68462	-0.5402|-0.5402	10|7	0.44086|0.18710	T|T	0.13|0.47	.|.	16.8604|16.8604	0.86016|0.86016	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs35775829|rs35775829	398;415|.	E7ENL7;Q8WVT3|.	.;TPC12_HUMAN|.	E|S	415;398;415|95	ENSP00000371544:G415E;ENSP00000324318:G415E|.	ENSP00000303612:G398E|ENSP00000409960:G95S	G|G	+|+	2|1	0|0	TTC15|TTC15	3404738|3404738	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.983000|0.983000	0.72400|0.72400	7.184000|7.184000	0.77705|0.77705	2.439000|2.439000	0.82584|0.82584	0.563000|0.563000	0.77884|0.77884	GGG|GGC	G|0.992;A|0.008	0.008	strong		0.587	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030	
DNAH10	196385	hgsc.bcm.edu	37	12	124288213	124288213	+	Missense_Mutation	SNP	G	G	A	rs77726895	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124288213G>A	ENST00000409039.3	+	16	2291	c.2266G>A	c.(2266-2268)Ggt>Agt	p.G756S		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	756	Stem. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		CAAAGGTATCGGTGACTATAT	0.428													G|||	78	0.0155751	0.053	0.0115	5008	,	,		19141	0.0		0.0	False		,,,				2504	0.0				p.G756S		Atlas-SNP	.											.	DNAH10	888	.	0			c.G2266A						PASS	.	G	SER/GLY	261,4143	140.4+/-175.9	8,245,1949	37.0	33.0	35.0		2266	2.9	0.1	12	dbSNP_131	35	14,8584	8.4+/-32.0	0,14,4285	yes	missense	DNAH10	NM_207437.3	56	8,259,6234	AA,AG,GG		0.1628,5.9264,2.1151	benign	756/4472	124288213	275,12727	2202	4299	6501	SO:0001583	missense	196385	exon16			GGTATCGGTGACT	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.2266G>A	12.37:g.124288213G>A	ENSP00000386770:p.Gly756Ser	61.0	0.0	0		37.0	23.0	0.621622	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	20	0.009157509157509158	18	0.036585365853658534	2	0.0055248618784530384	0	0.0	0	0.0	G	0.013	-1.611697	0.00835	0.059264	0.001628	ENSG00000197653	ENST00000409039	T	0.53640	0.61	4.78	2.86	0.33363	Dynein heavy chain, domain-1 (1);	0.636305	0.13044	N	0.418306	T	0.01765	0.0056	N	0.01505	-0.83	0.09310	N	1	B;B;B	0.10296	0.003;0.0;0.0	B;B;B	0.09377	0.004;0.003;0.004	T	0.15925	-1.0420	10	0.08381	T	0.77	.	8.2499	0.31710	0.0747:0.0:0.6468:0.2785	.	756;631;756	Q8IVF4-2;C4IXU6;Q8IVF4	.;.;DYH10_HUMAN	S	756	ENSP00000386770:G756S	ENSP00000386770:G756S	G	+	1	0	DNAH10	122854166	0.000000	0.05858	0.130000	0.21974	0.029000	0.11900	0.209000	0.17435	0.475000	0.27415	0.650000	0.86243	GGT	G|0.980;A|0.020	0.020	strong		0.428	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
LZTS1	11178	hgsc.bcm.edu	37	8	20107325	20107325	+	Missense_Mutation	SNP	G	G	C	rs114929298	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:20107325G>C	ENST00000381569.1	-	4	2056	c.1699C>G	c.(1699-1701)Ctg>Gtg	p.L567V	LZTS1_ENST00000522290.1_Missense_Mutation_p.L508V|LZTS1_ENST00000265801.6_Missense_Mutation_p.L567V			Q9Y250	LZTS1_HUMAN	leucine zipper, putative tumor suppressor 1	567					cell cycle (GO:0007049)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of macroautophagy (GO:0016242)|positive regulation of type I interferon production (GO:0032481)|regulation of dendrite morphogenesis (GO:0048814)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	apical plasma membrane (GO:0016324)|cell body (GO:0044297)|cell junction (GO:0030054)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|nucleoplasm (GO:0005654)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(16)|ovary(2)|skin(1)|urinary_tract(1)	29				Colorectal(74;0.0511)|COAD - Colon adenocarcinoma(73;0.207)		CCACGTGCCAGCTGCTGCAGG	0.617													g|||	19	0.00379393	0.0144	0.0	5008	,	,		18009	0.0		0.0	False		,,,				2504	0.0				p.L567V		Atlas-SNP	.											.	LZTS1	72	.	0			c.C1699G						PASS	.		VAL/LEU	46,4360	48.2+/-83.0	1,44,2158	86.0	87.0	87.0		1699	4.4	1.0	8	dbSNP_132	87	0,8600		0,0,4300	yes	missense	LZTS1	NM_021020.2	32	1,44,6458	CC,CG,GG		0.0,1.044,0.3537	probably-damaging	567/597	20107325	46,12960	2203	4300	6503	SO:0001583	missense	11178	exon3			GTGCCAGCTGCTG	AF123659	CCDS6015.1	8p22	2012-10-05			ENSG00000061337	ENSG00000061337			13861	protein-coding gene	gene with protein product		606551	"""F37/Esophageal cancer-related gene-coding leucine-zipper motif"""			10097140, 17349584	Standard	NM_021020		Approved	FEZ1	uc003wzr.3	Q9Y250	OTTHUMG00000097027	ENST00000381569.1:c.1699C>G	8.37:g.20107325G>C	ENSP00000370981:p.Leu567Val	135.0	0.0	0		121.0	71.0	0.586777	NM_021020	D3DSQ6|Q9Y5V7|Q9Y5V8|Q9Y5V9|Q9Y5W0|Q9Y5W1|Q9Y5W2	Missense_Mutation	SNP	ENST00000381569.1	37	CCDS6015.1	12	0.005494505494505495	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	g	13.50	2.257140	0.39896	0.01044	0.0	ENSG00000061337	ENST00000381569;ENST00000265801;ENST00000522290;ENST00000360248	T;T;T	0.31769	1.59;1.59;1.48	5.28	4.4	0.53042	.	0.075319	0.53938	D	0.000043	T	0.17408	0.0418	N	0.08118	0	0.58432	D	0.99999	P;D	0.76494	0.884;0.999	B;D	0.66847	0.41;0.947	T	0.08351	-1.0726	10	0.36615	T	0.2	-20.5699	12.9504	0.58397	0.0808:0.0:0.9192:0.0	.	508;567	Q9Y250-4;Q9Y250	.;LZTS1_HUMAN	V	567;567;508;544	ENSP00000370981:L567V;ENSP00000265801:L567V;ENSP00000429263:L508V	ENSP00000265801:L567V	L	-	1	2	LZTS1	20151605	1.000000	0.71417	1.000000	0.80357	0.779000	0.44077	3.266000	0.51569	2.454000	0.82982	0.543000	0.68304	CTG	G|0.995;C|0.005	0.005	strong		0.617	LZTS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214122.1	NM_021020	
RFPL3	10738	hgsc.bcm.edu	37	22	32756807	32756807	+	Silent	SNP	G	G	C	rs78565810	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:32756807G>C	ENST00000249007.4	+	2	1147	c.942G>C	c.(940-942)ggG>ggC	p.G314G	RFPL3S_ENST00000461833.1_5'UTR|RFPL3S_ENST00000400234.1_Silent_p.S77S|RFPL3_ENST00000397468.1_Silent_p.G285G|RFPL3S_ENST00000382084.4_Silent_p.S48S|RFPL3_ENST00000382088.3_Silent_p.G285G	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	314							zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						TCCGTCCTGGGGAGGCCAAAT	0.443													g|||	99	0.0197684	0.0734	0.0029	5008	,	,		15426	0.0		0.0	False		,,,				2504	0.0				p.G314G		Atlas-SNP	.											.	RFPL3	91	.	0			c.G942C						PASS	.	G	,	237,4113		2,233,1940	44.0	48.0	47.0		942,855	-0.6	0.0	22	dbSNP_131	47	0,8528		0,0,4264	no	coding-synonymous,coding-synonymous	RFPL3	NM_001098535.1,NM_006604.2	,	2,233,6204	CC,CG,GG		0.0,5.4483,1.8403	,	314/318,285/289	32756807	237,12641	2175	4264	6439	SO:0001819	synonymous_variant	10738	exon2			TCCTGGGGAGGCC	AJ010232	CCDS13904.1, CCDS43011.1	22q12	2006-04-25			ENSG00000128276	ENSG00000128276			9980	protein-coding gene	gene with protein product		605970				10508838	Standard	NM_006604		Approved		uc010gwn.3	O75679	OTTHUMG00000030290	ENST00000249007.4:c.942G>C	22.37:g.32756807G>C		198.0	0.0	0		216.0	86.0	0.398148	NM_001098535	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Silent	SNP	ENST00000249007.4	37	CCDS43011.1																																																																																			G|0.978;C|0.022	0.022	strong		0.443	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3	NM_006604	
RGS8	85397	hgsc.bcm.edu	37	1	182640848	182640848	+	5'UTR	SNP	G	G	A	rs115960776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:182640848G>A	ENST00000483095.2	-	0	98				RGS8_ENST00000491420.2_5'UTR|RGS8_ENST00000367556.1_5'UTR|RGS8_ENST00000367557.4_5'UTR|RGS8_ENST00000258302.4_Silent_p.S8S			P57771	RGS8_HUMAN	regulator of G-protein signaling 8						positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			haematopoietic_and_lymphoid_tissue(1)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	5						GGTCAGAGAGGCTTCGGGTTA	0.502													G|||	104	0.0207668	0.0749	0.0072	5008	,	,		20143	0.0		0.0	False		,,,				2504	0.0				p.S8S	Ovarian(189;1262 3804 41973)	Atlas-SNP	.											.	RGS8	51	.	0			c.C24T						PASS	.	G	,	243,4163	142.3+/-177.5	10,223,1970	173.0	176.0	175.0		,24	4.4	1.0	1	dbSNP_132	175	5,8595	3.7+/-12.6	0,5,4295	no	utr-5,coding-synonymous	RGS8	NM_001102450.1,NM_033345.2	,	10,228,6265	AA,AG,GG		0.0581,5.5152,1.9068	,	,8/199	182640848	248,12758	2203	4300	6503	SO:0001623	5_prime_UTR_variant	85397	exon2			AGAGAGGCTTCGG	AF297015	CCDS1349.1, CCDS41443.1	1q25	2008-07-18	2007-08-14		ENSG00000135824	ENSG00000135824		"""Regulators of G-protein signaling"""	16810	protein-coding gene	gene with protein product		607189	"""regulator of G-protein signalling 8"""			11318611	Standard	NM_001102450		Approved	MGC119067, MGC119068, MGC119069	uc001gpm.1	P57771	OTTHUMG00000035219	ENST00000483095.2:c.-160C>T	1.37:g.182640848G>A		286.0	0.0	0		215.0	80.0	0.372093	NM_033345	B4DGL9|Q3SYD2	Silent	SNP	ENST00000483095.2	37	CCDS41443.1																																																																																			G|0.981;A|0.019	0.019	strong		0.502	RGS8-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358979.1	NM_033345	
HERC6	55008	hgsc.bcm.edu	37	4	89338691	89338691	+	Missense_Mutation	SNP	A	A	G	rs190243300	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:89338691A>G	ENST00000264346.7	+	13	1732	c.1673A>G	c.(1672-1674)aAt>aGt	p.N558S	HERC6_ENST00000380265.5_Missense_Mutation_p.N558S	NM_017912.3	NP_060382.3	Q8IVU3	HERC6_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 6	558					hematopoietic progenitor cell differentiation (GO:0002244)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)	11		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000222)		GATCACTGTAATGTTAAAGCT	0.373													A|||	17	0.00339457	0.0083	0.0043	5008	,	,		17266	0.0		0.003	False		,,,				2504	0.0				p.N558S		Atlas-SNP	.											.	HERC6	104	.	0			c.A1673G						PASS	.	A	SER/ASN,SER/ASN	17,3737		0,17,1860	65.0	61.0	62.0		1673,1673	0.7	0.0	4		62	5,8207		0,5,4101	yes	missense,missense	HERC6	NM_001165136.1,NM_017912.3	46,46	0,22,5961	GG,GA,AA		0.0609,0.4529,0.1839	benign,benign	558/987,558/1023	89338691	22,11944	1877	4106	5983	SO:0001583	missense	55008	exon13			ACTGTAATGTTAA	AF336798	CCDS47098.1, CCDS54777.1	4q22	2012-02-23	2012-02-23		ENSG00000138642	ENSG00000138642			26072	protein-coding gene	gene with protein product		609249	"""hect domain and RLD 6"""				Standard	NM_001165136		Approved	FLJ20637	uc011cdi.2	Q8IVU3	OTTHUMG00000160983	ENST00000264346.7:c.1673A>G	4.37:g.89338691A>G	ENSP00000264346:p.Asn558Ser	53.0	0.0	0		59.0	24.0	0.40678	NM_017912	B4DIY5|Q5GC90|Q5GRH3|Q5HYM6|Q5JPB6|Q6PIF4|Q8NAN3|Q9NWS4	Missense_Mutation	SNP	ENST00000264346.7	37	CCDS47098.1	5	0.0022893772893772895	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	A	6.688	0.495465	0.12762	0.004529	6.09E-4	ENSG00000138642	ENST00000380265;ENST00000264346	T;T	0.38240	1.15;1.17	4.79	0.721	0.18219	.	0.377680	0.25885	N	0.027670	T	0.12220	0.0297	N	0.19112	0.55	0.09310	N	0.999999	B;B	0.20052	0.041;0.024	B;B	0.14578	0.011;0.005	T	0.18999	-1.0319	10	0.14252	T	0.57	.	6.1186	0.20139	0.6064:0.3068:0.0867:0.0	.	558;558	Q8IVU3-2;Q8IVU3	.;HERC6_HUMAN	S	558	ENSP00000369617:N558S;ENSP00000264346:N558S	ENSP00000264346:N558S	N	+	2	0	HERC6	89557714	0.001000	0.12720	0.002000	0.10522	0.001000	0.01503	0.982000	0.29539	0.414000	0.25790	-0.438000	0.05819	AAT	A|0.998;G|0.002	0.002	strong		0.373	HERC6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363259.2		
SERPINB3	6317	hgsc.bcm.edu	37	18	61323228	61323228	+	Missense_Mutation	SNP	C	C	G	rs61748838	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:61323228C>G	ENST00000283752.5	-	8	979	c.836G>C	c.(835-837)cGt>cCt	p.R279P	SERPINB11_ENST00000489748.1_RNA|SERPINB3_ENST00000332821.8_Missense_Mutation_p.R227P	NM_006919.2	NP_008850.1	P29508	SPB3_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 3	279					negative regulation of catalytic activity (GO:0043086)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of peptidase activity (GO:0010466)|negative regulation of proteolysis (GO:0045861)|regulation of proteolysis (GO:0030162)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle (GO:0031982)	serine-type endopeptidase inhibitor activity (GO:0004867)|virus receptor activity (GO:0001618)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|skin(5)|upper_aerodigestive_tract(2)	36						TAAATCGACACGTGTCTCTCT	0.413													c|||	286	0.0571086	0.205	0.0144	5008	,	,		20730	0.0		0.004	False		,,,				2504	0.001				p.R279P		Atlas-SNP	.											SERPINB3,caecum,carcinoma,0,1	SERPINB3	90	1	0			c.G836C						PASS	.	G	PRO/ARG	699,3707	292.4+/-282.0	53,593,1557	149.0	127.0	135.0		836	-0.9	0.0	18	dbSNP_129	135	15,8585	9.8+/-36.6	0,15,4285	no	missense	SERPINB3	NM_006919.2	103	53,608,5842	GG,GC,CC		0.1744,15.8647,5.4898	benign	279/391	61323228	714,12292	2203	4300	6503	SO:0001583	missense	6317	exon8			TCGACACGTGTCT	U19568	CCDS11987.1	18q21.3	2014-02-18	2005-08-18		ENSG00000057149	ENSG00000057149		"""Serine (or cysteine) peptidase inhibitors"""	10569	protein-coding gene	gene with protein product		600517	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 3"""	SCC, SCCA1		7724531, 24172014	Standard	NM_006919		Approved	T4-A, HsT1196	uc002lji.3	P29508	OTTHUMG00000060403	ENST00000283752.5:c.836G>C	18.37:g.61323228C>G	ENSP00000283752:p.Arg279Pro	232.0	0.0	0		230.0	121.0	0.526087	NM_006919	A6NDM2|B2RBT5|B3W5Y6|Q53H28|Q53YB5|Q86VF3|Q86W04|Q8IWL4|Q8IXI3|Q96J21|Q9BYF8	Missense_Mutation	SNP	ENST00000283752.5	37	CCDS11987.1	100	0.045787545787545784	92	0.18699186991869918	6	0.016574585635359115	0	0.0	2	0.002638522427440633	c	9.127	1.010414	0.19277	0.158647	0.001744	ENSG00000057149	ENST00000283752;ENST00000332821	D;D	0.84944	-1.92;-1.92	3.07	-0.89	0.10577	Serpin domain (3);	4.332970	0.00769	N	0.001198	T	0.00300	0.0009	N	0.16368	0.405	0.80722	P	0.0	B;B	0.20164	0.042;0.0	B;B	0.33454	0.164;0.007	T	0.36529	-0.9744	9	0.66056	D	0.02	.	0.3718	0.00381	0.2731:0.1823:0.1396:0.405	rs61748838	227;279	P29508-2;P29508	.;SPB3_HUMAN	P	279;227	ENSP00000283752:R279P;ENSP00000329498:R227P	ENSP00000283752:R279P	R	-	2	0	SERPINB3	59474208	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.785000	0.04628	-0.480000	0.06803	-2.438000	0.00212	CGT	C|0.940;G|0.060	0.060	strong		0.413	SERPINB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133791.1	NM_006919	
UGGT1	56886	hgsc.bcm.edu	37	2	128870784	128870784	+	Silent	SNP	A	A	G	rs149605444	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:128870784A>G	ENST00000259253.6	+	6	695	c.648A>G	c.(646-648)tcA>tcG	p.S216S	UGGT1_ENST00000375990.3_Silent_p.S192S	NM_020120.3	NP_064505.1	Q9NYU2	UGGG1_HUMAN	UDP-glucose glycoprotein glucosyltransferase 1	216					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)	UDP-glucose:glycoprotein glucosyltransferase activity (GO:0003980)|unfolded protein binding (GO:0051082)			NS(1)|breast(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(14)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	63						AGCTTATATCAAAAAGCAATG	0.353													A|||	25	0.00499201	0.0189	0.0	5008	,	,		15033	0.0		0.0	False		,,,				2504	0.0				p.S216S		Atlas-SNP	.											.	UGGT1	126	.	0			c.A648G						PASS	.	A		64,4342	58.1+/-94.6	1,62,2140	71.0	74.0	73.0		648	-1.1	0.1	2	dbSNP_134	73	0,8598		0,0,4299	no	coding-synonymous	UGGT1	NM_020120.3		1,62,6439	GG,GA,AA		0.0,1.4526,0.4922		216/1556	128870784	64,12940	2203	4299	6502	SO:0001819	synonymous_variant	56886	exon6			TATATCAAAAAGC	AF227905	CCDS2154.1	2q14.3	2009-07-23	2009-07-23	2009-07-23	ENSG00000136731	ENSG00000136731			15663	protein-coding gene	gene with protein product		605897	"""UDP-glucose ceramide glucosyltransferase-like 1"""	UGCGL1		10694380	Standard	NM_020120		Approved	HUGT1	uc002tps.3	Q9NYU2	OTTHUMG00000131570	ENST00000259253.6:c.648A>G	2.37:g.128870784A>G		243.0	0.0	0		290.0	132.0	0.455172	NM_020120	Q53QP2|Q53SL3|Q8IW30|Q9H8I4	Silent	SNP	ENST00000259253.6	37	CCDS2154.1																																																																																			A|0.995;G|0.005	0.005	strong		0.353	UGGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254435.2	NM_020120	
AGL	178	hgsc.bcm.edu	37	1	100353654	100353654	+	Silent	SNP	A	A	C	rs34230588	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:100353654A>C	ENST00000294724.4	+	21	3280	c.2802A>C	c.(2800-2802)gcA>gcC	p.A934A	AGL_ENST00000370165.3_Silent_p.A934A|AGL_ENST00000361302.3_Silent_p.A918A|AGL_ENST00000370161.2_Silent_p.A918A|AGL_ENST00000370163.3_Silent_p.A934A|AGL_ENST00000361522.4_Silent_p.A917A|AGL_ENST00000361915.3_Silent_p.A934A	NM_000028.2	NP_000019.2	P35573	GDE_HUMAN	amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase	934					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|inclusion body (GO:0016234)|isoamylase complex (GO:0043033)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)	4-alpha-glucanotransferase activity (GO:0004134)|amylo-alpha-1,6-glucosidase activity (GO:0004135)|glycogen debranching enzyme activity (GO:0004133)|polysaccharide binding (GO:0030247)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(9)|lung(35)|ovary(1)|prostate(4)|skin(3)|urinary_tract(1)	69		all_epithelial(167;2.2e-06)|all_lung(203;0.000295)|Lung NSC(277;0.00131)		Epithelial(280;0.15)|COAD - Colon adenocarcinoma(174;0.151)|Lung(183;0.209)|all cancers(265;0.237)		TTAAATATGCAGGTCTTCAAG	0.418													A|||	27	0.00539137	0.0204	0.0	5008	,	,		17736	0.0		0.0	False		,,,				2504	0.0				p.A934A		Atlas-SNP	.											.	AGL	137	.	0			c.A2802C						PASS	.	A	,,,,,	97,4309	78.8+/-117.2	1,95,2107	121.0	115.0	117.0		2802,2802,2802,2802,2751,2754	1.8	1.0	1	dbSNP_126	117	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	AGL	NM_000028.2,NM_000642.2,NM_000643.2,NM_000644.2,NM_000645.2,NM_000646.2	,,,,,	1,95,6407	CC,CA,AA		0.0,2.2015,0.7458	,,,,,	934/1533,934/1533,934/1533,934/1533,917/1516,918/1517	100353654	97,12909	2203	4300	6503	SO:0001819	synonymous_variant	178	exon21			ATATGCAGGTCTT	BC078663	CCDS759.1, CCDS760.1, CCDS761.1	1p21	2010-04-27	2010-04-27		ENSG00000162688	ENSG00000162688	2.4.1.25, 3.2.1.33		321	protein-coding gene	gene with protein product	"""glycogen debranching enzyme"", ""glycogen storage disease type III"""	610860	"""amylo-1, 6-glucosidase, 4-alpha-glucanotransferase"""			1505983	Standard	NM_000028		Approved		uc001dsi.1	P35573	OTTHUMG00000010803	ENST00000294724.4:c.2802A>C	1.37:g.100353654A>C		61.0	0.0	0		50.0	21.0	0.42	NM_000644	A6NCX7|A6NEK2|D3DT51|P78354|P78544|Q59H92|Q6AZ90|Q9UF08	Silent	SNP	ENST00000294724.4	37	CCDS759.1																																																																																			A|0.994;C|0.006	0.006	strong		0.418	AGL-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029778.1	NM_000028	
LAIR2	3904	hgsc.bcm.edu	37	19	55019379	55019379	+	Missense_Mutation	SNP	T	T	A	rs34429135	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55019379T>A	ENST00000301202.2	+	3	466	c.344T>A	c.(343-345)tTc>tAc	p.F115Y	LAIR2_ENST00000351841.2_Missense_Mutation_p.F115Y	NM_002288.4	NP_002279.2	Q6ISS4	LAIR2_HUMAN	leukocyte-associated immunoglobulin-like receptor 2	115	Ig-like C2-type.		F -> Y (in dbSNP:rs34429135).			extracellular region (GO:0005576)				central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(1)	18	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.0967)		CACAGTGACTTCCTGGAGCTG	0.577													T|||	284	0.0567093	0.2005	0.0245	5008	,	,		17434	0.0		0.002	False		,,,				2504	0.0				p.F115Y		Atlas-SNP	.											.	LAIR2	30	.	0			c.T344A						PASS	.	T	TYR/PHE,TYR/PHE	773,3633	307.7+/-290.2	60,653,1490	89.0	92.0	91.0		344,344	-7.6	0.0	19	dbSNP_126	91	14,8586	8.4+/-32.0	0,14,4286	yes	missense,missense	LAIR2	NM_002288.4,NM_021270.3	22,22	60,667,5776	AA,AT,TT		0.1628,17.5443,6.0511	benign,benign	115/153,115/136	55019379	787,12219	2203	4300	6503	SO:0001583	missense	3904	exon3			GTGACTTCCTGGA	AF013250	CCDS12897.1, CCDS12898.1	19q13.4	2013-01-29	2006-03-23		ENSG00000167618	ENSG00000167618		"""Leukocyte-associated Ig like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6478	protein-coding gene	gene with protein product		602993	"""leukocyte-associated Ig-like receptor 2"""			9285412	Standard	XM_005277264		Approved	CD306	uc002qgc.3	Q6ISS4	OTTHUMG00000065697	ENST00000301202.2:c.344T>A	19.37:g.55019379T>A	ENSP00000301202:p.Phe115Tyr	107.0	0.0	0		127.0	55.0	0.433071	NM_002288	Q6PEZ4	Missense_Mutation	SNP	ENST00000301202.2	37	CCDS12897.1	99	0.04532967032967033	87	0.17682926829268292	10	0.027624309392265192	0	0.0	2	0.002638522427440633	T	0.013	-1.619502	0.00828	0.175443	0.001628	ENSG00000167618	ENST00000301202;ENST00000351841	T;T	0.11277	2.79;2.79	3.77	-7.55	0.01327	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	8.928910	0.00166	N	0.000000	T	0.00012	0.0000	N	0.02315	-0.6	0.80722	P	0.0	B;B	0.06786	0.0;0.001	B;B	0.09377	0.001;0.004	T	0.35822	-0.9773	8	.	.	.	.	0.0766	0.00027	0.2872:0.2456:0.1969:0.2703	rs34429135	115;115	Q6ISS4-2;Q6ISS4	.;LAIR2_HUMAN	Y	115	ENSP00000301202:F115Y;ENSP00000301203:F115Y	.	F	+	2	0	LAIR2	59711191	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.540000	0.00218	-3.651000	0.00126	-0.907000	0.02831	TTC	T|0.943;A|0.057	0.057	strong		0.577	LAIR2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000140801.1		
PRKAR2B	5577	hgsc.bcm.edu	37	7	106791447	106791447	+	Silent	SNP	G	G	A	rs3729878	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:106791447G>A	ENST00000265717.4	+	7	1081	c.822G>A	c.(820-822)ctG>ctA	p.L274L		NM_002736.2	NP_002727.2	P31323	KAP3_HUMAN	protein kinase, cAMP-dependent, regulatory, type II, beta	274					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fatty acid metabolic process (GO:0006631)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|learning (GO:0007612)|mitotic cell cycle (GO:0000278)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase inhibitor activity (GO:0004862)|cAMP-dependent protein kinase regulator activity (GO:0008603)|protein kinase A catalytic subunit binding (GO:0034236)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	14						TTGAGTCACTGCCATTCCTTA	0.303													G|||	196	0.0391374	0.1422	0.0115	5008	,	,		14361	0.0		0.0	False		,,,				2504	0.0				p.L274L		Atlas-SNP	.											.	PRKAR2B	34	.	0			c.G822A						PASS	.	G		532,3874	238.4+/-249.8	30,472,1701	72.0	74.0	73.0		822	4.6	1.0	7	dbSNP_107	73	9,8587	7.1+/-27.0	0,9,4289	no	coding-synonymous	PRKAR2B	NM_002736.2		30,481,5990	AA,AG,GG		0.1047,12.0744,4.1609		274/419	106791447	541,12461	2203	4298	6501	SO:0001819	synonymous_variant	5577	exon7			GTCACTGCCATTC		CCDS5740.1	7q22.3	2010-04-22			ENSG00000005249	ENSG00000005249	2.7.11.1		9392	protein-coding gene	gene with protein product		176912		PRKAR2		1358799	Standard	NM_002736		Approved		uc003vdx.3	P31323	OTTHUMG00000137418	ENST00000265717.4:c.822G>A	7.37:g.106791447G>A		201.0	0.0	0		209.0	95.0	0.454545	NM_002736	A4D0R9	Silent	SNP	ENST00000265717.4	37	CCDS5740.1																																																																																			G|0.953;A|0.047	0.047	strong		0.303	PRKAR2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268386.1		
FAM135A	57579	hgsc.bcm.edu	37	6	71234960	71234960	+	Missense_Mutation	SNP	A	A	G	rs9455142	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:71234960A>G	ENST00000418814.2	+	15	2787	c.2173A>G	c.(2173-2175)Att>Gtt	p.I725V	FAM135A_ENST00000457062.2_Missense_Mutation_p.I512V|FAM135A_ENST00000505868.1_Missense_Mutation_p.I725V|FAM135A_ENST00000370479.3_Missense_Mutation_p.I512V|FAM135A_ENST00000505769.1_Intron|FAM135A_ENST00000361499.3_Missense_Mutation_p.I529V	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	725			I -> V (in dbSNP:rs9455142).							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						GTGTCTTTCTATTGGAGAATC	0.313													A|||	102	0.0203674	0.0726	0.0058	5008	,	,		20204	0.0		0.002	False		,,,				2504	0.0				p.I725V		Atlas-SNP	.											.	FAM135A	181	.	0			c.A2173G						PASS	.	A	VAL/ILE,VAL/ILE,VAL/ILE	299,4105	154.8+/-188.1	6,287,1909	47.0	52.0	51.0		1585,2173,1534	-12.1	0.0	6	dbSNP_119	51	4,8590	3.0+/-9.4	0,4,4293	yes	missense,missense,missense	FAM135A	NM_001105531.2,NM_001162529.1,NM_020819.4	29,29,29	6,291,6202	GG,GA,AA		0.0465,6.7893,2.3311	benign,benign,benign	529/1320,725/1516,512/1303	71234960	303,12695	2202	4297	6499	SO:0001583	missense	57579	exon13			CTTTCTATTGGAG	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.2173A>G	6.37:g.71234960A>G	ENSP00000410768:p.Ile725Val	65.0	0.0	0		60.0	22.0	0.366667	NM_001162529	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Missense_Mutation	SNP	ENST00000418814.2	37	CCDS55028.1	46	0.021062271062271064	43	0.08739837398373984	3	0.008287292817679558	0	0.0	0	0.0	A	0.009	-1.845019	0.00568	0.067893	4.65E-4	ENSG00000082269	ENST00000418814;ENST00000370479;ENST00000457062;ENST00000361499;ENST00000505868	T;T;T;T;T	0.38722	1.12;1.12;1.12;1.12;1.12	6.07	-12.1	0.00011	.	1.270720	0.04845	N	0.441304	T	0.06416	0.0165	N	0.03948	-0.315	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.001;0.001	T	0.38542	-0.9656	10	0.23891	T	0.37	.	18.3851	0.90464	0.7861:0.0739:0.1401:0.0	rs9455142;rs52822960;rs9455142	725;725;529;512	Q9P2D6-4;Q9P2D6;Q9P2D6-2;Q9P2D6-3	.;F135A_HUMAN;.;.	V	725;512;512;529;725	ENSP00000410768:I725V;ENSP00000359510:I512V;ENSP00000409201:I512V;ENSP00000354913:I529V;ENSP00000423307:I725V	ENSP00000354913:I529V	I	+	1	0	FAM135A	71291681	0.000000	0.05858	0.000000	0.03702	0.896000	0.52359	-0.852000	0.04308	-2.772000	0.00364	-0.959000	0.02639	ATT	A|0.974;G|0.026	0.026	strong		0.313	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819	
PANX1	24145	hgsc.bcm.edu	37	11	93913392	93913392	+	Missense_Mutation	SNP	G	G	T	rs74549886	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:93913392G>T	ENST00000227638.3	+	4	1555	c.1170G>T	c.(1168-1170)gaG>gaT	p.E390D	PANX1_ENST00000436171.2_Missense_Mutation_p.E390D	NM_015368.3	NP_056183.2	Q96RD7	PANX1_HUMAN	pannexin 1	390					calcium ion transport (GO:0006816)|cation transport (GO:0006812)|innate immune response (GO:0045087)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 alpha secretion (GO:0050717)|positive regulation of interleukin-1 beta secretion (GO:0050718)|protein hexamerization (GO:0034214)|response to ATP (GO:0033198)|response to ischemia (GO:0002931)|synaptic transmission (GO:0007268)	bleb (GO:0032059)|endoplasmic reticulum (GO:0005783)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calcium channel activity (GO:0005262)|gap junction hemi-channel activity (GO:0055077)|leak channel activity (GO:0022840)|receptor binding (GO:0005102)			endometrium(2)|large_intestine(2)|lung(13)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)			Probenecid(DB01032)	AGATGAGAGAGGAGCAGGGGA	0.532													G|||	180	0.0359425	0.1286	0.0115	5008	,	,		17647	0.0		0.002	False		,,,				2504	0.0				p.E390D		Atlas-SNP	.											.	PANX1	38	.	0			c.G1170T						PASS	.	G	ASP/GLU	484,3918	225.9+/-241.6	21,442,1738	68.0	64.0	66.0		1170	1.0	0.0	11	dbSNP_131	66	6,8590	4.3+/-15.6	0,6,4292	yes	missense	PANX1	NM_015368.3	45	21,448,6030	TT,TG,GG		0.0698,10.995,3.7698	benign	390/427	93913392	490,12508	2201	4298	6499	SO:0001583	missense	24145	exon4			GAGAGAGGAGCAG	AF093239	CCDS8296.1	11q14-q21	2011-12-02			ENSG00000110218	ENSG00000110218		"""Ion channels / Pannexins"""	8599	protein-coding gene	gene with protein product	"""innexin"""	608420				14597722	Standard	NM_015368		Approved	MRS1, UNQ2529, PX1	uc001per.3	Q96RD7	OTTHUMG00000167757	ENST00000227638.3:c.1170G>T	11.37:g.93913392G>T	ENSP00000227638:p.Glu390Asp	136.0	0.0	0		129.0	56.0	0.434109	NM_015368	O75968|Q543A0|Q6UW26|Q96AM9|Q96L77|Q96RS5	Missense_Mutation	SNP	ENST00000227638.3	37	CCDS8296.1	62	0.028388278388278388	57	0.11585365853658537	5	0.013812154696132596	0	0.0	0	0.0	G	12.51	1.958933	0.34565	0.10995	6.98E-4	ENSG00000110218	ENST00000227638;ENST00000436171	T;T	0.19250	2.17;2.16	5.22	0.965	0.19661	.	1.495480	0.03723	N	0.252178	T	0.00300	0.0009	M	0.67953	2.075	0.09310	N	1	B;B	0.32573	0.376;0.29	B;B	0.29785	0.049;0.107	T	0.16600	-1.0397	10	0.39692	T	0.17	-15.6543	4.6163	0.12428	0.3593:0.2803:0.3603:0.0	.	390;390	Q96RD7;Q96RD7-2	PANX1_HUMAN;.	D	390	ENSP00000227638:E390D;ENSP00000411461:E390D	ENSP00000227638:E390D	E	+	3	2	PANX1	93553040	0.059000	0.20769	0.005000	0.12908	0.026000	0.11368	0.183000	0.16919	0.606000	0.29965	0.655000	0.94253	GAG	G|0.968;T|0.032	0.032	strong		0.532	PANX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396121.1	NM_015368	
ILDR1	286676	hgsc.bcm.edu	37	3	121712271	121712271	+	Missense_Mutation	SNP	C	C	T	rs34883204	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:121712271C>T	ENST00000344209.5	-	7	1451	c.1325G>A	c.(1324-1326)cGc>cAc	p.R442H	ILDR1_ENST00000273691.3_Missense_Mutation_p.R398H|ILDR1_ENST00000460554.1_5'UTR|ILDR1_ENST00000393631.1_Missense_Mutation_p.R353H|ILDR1_ENST00000462014.1_Missense_Mutation_p.R410H	NM_001199799.1	NP_001186728.1	Q86SU0	ILDR1_HUMAN	immunoglobulin-like domain containing receptor 1	442	Arg-rich.				positive regulation of peptide hormone secretion (GO:0090277)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	high-density lipoprotein particle receptor activity (GO:0070506)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(10)|lung(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(114;0.156)		CTCCTGACAGCGGCTCCTGAA	0.672													C|||	202	0.0403355	0.1452	0.0144	5008	,	,		16784	0.0		0.0	False		,,,				2504	0.0				p.R442H		Atlas-SNP	.											ILDR1_ENST00000344209,colon,carcinoma,-1,2	ILDR1	120	2	0			c.G1325A						scavenged	.	C	HIS/ARG,HIS/ARG,HIS/ARG	528,3878		24,480,1699	22.0	24.0	23.0		1325,1058,1193	-0.6	0.2	3	dbSNP_126	23	8,8592		0,8,4292	yes	missense,missense,missense	ILDR1	NM_001199799.1,NM_001199800.1,NM_175924.3	29,29,29	24,488,5991	TT,TC,CC		0.093,11.9837,4.1212	probably-damaging,probably-damaging,probably-damaging	442/547,353/458,398/503	121712271	536,12470	2203	4300	6503	SO:0001583	missense	286676	exon7			TGACAGCGGCTCC	BC044240	CCDS3008.1, CCDS56270.1, CCDS56271.1	3q21.1	2013-10-11			ENSG00000145103	ENSG00000145103			28741	protein-coding gene	gene with protein product		609739	"""deafness, autosomal recessive 42"""	DFNB42		15641023, 21255762	Standard	NM_175924		Approved	MGC50831	uc003ees.3	Q86SU0	OTTHUMG00000159481	ENST00000344209.5:c.1325G>A	3.37:g.121712271C>T	ENSP00000345667:p.Arg442His	85.0	1.0	0.0117647		102.0	56.0	0.54902	NM_001199799	Q6ZP61|Q7Z578	Missense_Mutation	SNP	ENST00000344209.5	37	CCDS56271.1	78	0.03571428571428571	74	0.15040650406504066	4	0.011049723756906077	0	0.0	0	0.0	C	7.187	0.590696	0.13812	0.119837	9.3E-4	ENSG00000145103	ENST00000273691;ENST00000344209;ENST00000393631;ENST00000462014	T;T;D;T	0.82984	-1.18;-0.64;-1.67;-0.71	4.69	-0.554	0.11811	.	0.768774	0.12399	N	0.472300	T	0.01287	0.0042	M	0.61703	1.905	0.38075	P	0.06350900000000004	B;B;B;B	0.10296	0.003;0.001;0.003;0.003	B;B;B;B	0.06405	0.001;0.0;0.001;0.002	T	0.38156	-0.9674	9	0.45353	T	0.12	-5.2038	8.9045	0.35515	0.0:0.3969:0.0:0.6031	rs34883204	353;442;398;410	Q86SU0-5;Q86SU0;Q86SU0-2;Q86SU0-6	.;ILDR1_HUMAN;.;.	H	398;442;353;410	ENSP00000273691:R398H;ENSP00000345667:R442H;ENSP00000377251:R353H;ENSP00000419414:R410H	ENSP00000273691:R398H	R	-	2	0	ILDR1	123194961	0.000000	0.05858	0.161000	0.22692	0.133000	0.20885	-0.271000	0.08572	-0.338000	0.08413	-0.345000	0.07892	CGC	C|0.960;T|0.040	0.040	strong		0.672	ILDR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355666.1	NM_175924	
SPTA1	6708	hgsc.bcm.edu	37	1	158623103	158623103	+	Missense_Mutation	SNP	G	G	A	rs116297260	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158623103G>A	ENST00000368147.4	-	22	3329	c.3149C>T	c.(3148-3150)cCa>cTa	p.P1050L		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1050					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					GATGTTTCCTGGCTCTTCTCG	0.532													G|||	40	0.00798722	0.0295	0.0014	5008	,	,		15095	0.0		0.0	False		,,,				2504	0.0				p.P1050L		Atlas-SNP	.											.	SPTA1	720	.	0			c.C3149T						PASS	.	G	LEU/PRO	81,3859		0,81,1889	116.0	119.0	118.0		3149	3.3	0.9	1	dbSNP_132	118	0,8370		0,0,4185	yes	missense	SPTA1	NM_003126.2	98	0,81,6074	AA,AG,GG		0.0,2.0558,0.658	benign	1050/2420	158623103	81,12229	1970	4185	6155	SO:0001583	missense	6708	exon22			TTTCCTGGCTCTT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.3149C>T	1.37:g.158623103G>A	ENSP00000357129:p.Pro1050Leu	134.0	0.0	0		130.0	65.0	0.5	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	G	11.31	1.600501	0.28534	0.020558	0.0	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.31510	1.49;1.49	5.15	3.28	0.37604	Src homology-3 domain (1);	0.273133	0.19703	N	0.107990	T	0.06962	0.0177	N	0.22421	0.69	0.47123	D	0.999327	B	0.11235	0.004	B	0.10450	0.005	T	0.12863	-1.0531	10	0.28530	T	0.3	.	4.5022	0.11869	0.1722:0.0:0.5672:0.2606	.	1050	P02549	SPTA1_HUMAN	L	1050	ENSP00000357130:P1050L;ENSP00000357129:P1050L	ENSP00000357129:P1050L	P	-	2	0	SPTA1	156889727	1.000000	0.71417	0.878000	0.34440	0.726000	0.41606	4.176000	0.58269	0.762000	0.33152	0.655000	0.94253	CCA	G|0.995;A|0.005	0.005	strong		0.532	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
SEMA6A	57556	hgsc.bcm.edu	37	5	115827506	115827506	+	Silent	SNP	G	G	A	rs34096390	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:115827506G>A	ENST00000343348.6	-	7	1252	c.465C>T	c.(463-465)ttC>ttT	p.F155F	CTB-118N6.3_ENST00000510682.1_RNA|CTB-118N6.3_ENST00000508640.1_RNA|SEMA6A_ENST00000503962.1_5'UTR|SEMA6A_ENST00000257414.8_Silent_p.F155F|SEMA6A_ENST00000510263.1_Silent_p.F155F|CTB-118N6.3_ENST00000514214.1_RNA	NM_020796.3	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	155	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|centrosome localization (GO:0051642)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|positive regulation of neuron migration (GO:2001224)|semaphorin-plexin signaling pathway (GO:0071526)	axon (GO:0030424)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)		ATTCATCCCCGAATGGTTCCA	0.418													G|||	155	0.0309505	0.1112	0.0086	5008	,	,		21381	0.0		0.002	False		,,,				2504	0.0				p.F155F		Atlas-SNP	.											SEMA6A,NS,carcinoma,-2,1	SEMA6A	93	1	0			c.C465T						scavenged	.	G		326,3528		20,286,1621	120.0	118.0	118.0		465	-12.2	0.0	5	dbSNP_126	118	3,8247		0,3,4122	no	coding-synonymous	SEMA6A	NM_020796.3		20,289,5743	AA,AG,GG		0.0364,8.4587,2.7181		155/1031	115827506	329,11775	1927	4125	6052	SO:0001819	synonymous_variant	57556	exon7			ATCCCCGAATGGT	AB037789	CCDS47256.1, CCDS75288.1	5q23.1	2014-07-29			ENSG00000092421			"""Semaphorins"""	10738	protein-coding gene	gene with protein product	"""sema VIa"""	605885		SEMAQ		9204478, 10993894	Standard	XM_006714663		Approved	KIAA1368, SEMA6A1, SEMA, HT018	uc010jck.3	Q9H2E6	OTTHUMG00000162987	ENST00000343348.6:c.465C>T	5.37:g.115827506G>A		153.0	1.0	0.00653595		228.0	91.0	0.399123	NM_020796	Q9P2H9	Silent	SNP	ENST00000343348.6	37	CCDS47256.1																																																																																			G|0.979;A|0.021	0.021	strong		0.418	SEMA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371270.1	NM_020796	
LY75	4065	hgsc.bcm.edu	37	2	160735775	160735775	+	Missense_Mutation	SNP	C	C	T	rs77761086	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160735775C>T	ENST00000263636.4	-	9	1537	c.1510G>A	c.(1510-1512)Gat>Aat	p.D504N	LY75_ENST00000554112.1_Missense_Mutation_p.D504N|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.D504N|LY75_ENST00000553424.1_Missense_Mutation_p.D504N|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.D504N	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	504	C-type lectin 3. {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)			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)		CCTACCTCATCTGGAGGACAC	0.353													C|||	26	0.00519169	0.0197	0.0	5008	,	,		19467	0.0		0.0	False		,,,				2504	0.0				p.D504N		Atlas-SNP	.											.	LY75	151	.	0			c.G1510A						PASS	.	C	ASN/ASP,ASN/ASP,ASN/ASP	59,4345	58.1+/-94.6	0,59,2143	199.0	183.0	189.0		1510,1510,1510	2.4	0.4	2	dbSNP_131	189	0,8598		0,0,4299	yes	missense,missense,missense	LY75,LY75-CD302	NM_001198759.1,NM_001198760.1,NM_002349.3	23,23,23	0,59,6442	TT,TC,CC		0.0,1.3397,0.4538	benign,benign,benign	504/1874,504/1818,504/1723	160735775	59,12943	2202	4299	6501	SO:0001583	missense	4065	exon9			CCTCATCTGGAGG	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.1510G>A	2.37:g.160735775C>T	ENSP00000263636:p.Asp504Asn	117.0	0.0	0		92.0	35.0	0.380435	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	C	4.816	0.151794	0.09185	0.013397	0.0	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.55413	0.52;3.0;2.98;0.52;3.0	5.4	2.44	0.29823	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (1);	1.063440	0.07525	N	0.911197	T	0.41096	0.1144	M	0.82056	2.57	0.09310	N	1	B;B;B;B	0.16603	0.001;0.018;0.018;0.007	B;B;B;B	0.22386	0.005;0.039;0.017;0.009	T	0.44221	-0.9342	10	0.34782	T	0.22	-1.7808	11.0531	0.47903	0.0:0.6813:0.0:0.3187	.	122;504;504;504	Q59H44;O60449-3;O60449;O60449-2	.;.;LY75_HUMAN;.	N	504	ENSP00000451511:D504N;ENSP00000451446:D504N;ENSP00000263636:D504N;ENSP00000423463:D504N;ENSP00000421035:D504N	ENSP00000423463:D504N	D	-	1	0	LY75;LY75-CD302	160444021	0.095000	0.21747	0.411000	0.26484	0.053000	0.15095	0.244000	0.18124	0.025000	0.15241	-1.595000	0.00837	GAT	C|0.994;T|0.006	0.006	strong		0.353	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
KRT7	3855	hgsc.bcm.edu	37	12	52636843	52636843	+	Silent	SNP	G	G	A	rs10564	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:52636843G>A	ENST00000331817.5	+	6	1089	c.906G>A	c.(904-906)cgG>cgA	p.R302R	RP3-416H24.1_ENST00000546686.1_RNA	NM_005556.3	NP_005547.3	P08729	K2C7_HUMAN	keratin 7	302	Coil 2.|Rod.				viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(2)|stomach(1)|urinary_tract(1)	14				BRCA - Breast invasive adenocarcinoma(357;0.105)	Primaquine(DB01087)	ACGACCTCCGGAATACCCGGA	0.567													G|||	172	0.034345	0.1256	0.0086	5008	,	,		18629	0.0		0.0	False		,,,				2504	0.0				p.R302R		Atlas-SNP	.											KRT7,colon,carcinoma,+1,1	KRT7	48	1	0			c.G906A						PASS	.	G		434,3972	210.8+/-231.2	19,396,1788	74.0	69.0	70.0		906	-0.4	0.5	12	dbSNP_52	70	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	KRT7	NM_005556.3		19,398,6086	AA,AG,GG		0.0233,9.8502,3.3523		302/470	52636843	436,12570	2203	4300	6503	SO:0001819	synonymous_variant	3855	exon6			CCTCCGGAATACC		CCDS8822.1	12q13.13	2013-01-16			ENSG00000135480	ENSG00000135480		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6445	protein-coding gene	gene with protein product	"""keratin, type II cytoskeletal 7"", ""cytokeratin 7"", ""sarcolectin"", ""keratin, 55K type II cytoskeletal"""	148059				1713141, 16831889	Standard	XR_245927		Approved	K7, CK7, K2C7, SCL	uc001saa.1	P08729	OTTHUMG00000169580	ENST00000331817.5:c.906G>A	12.37:g.52636843G>A		95.0	0.0	0		85.0	44.0	0.517647	NM_005556	Q92676|Q9BUD8|Q9Y3R7	Silent	SNP	ENST00000331817.5	37	CCDS8822.1																																																																																			G|0.964;A|0.036	0.036	strong		0.567	KRT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404897.1	NM_005556	
DIS3L2	129563	hgsc.bcm.edu	37	2	232995462	232995462	+	Silent	SNP	A	A	G	rs75061164	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:232995462A>G	ENST00000409401.3	+	7	910	c.735A>G	c.(733-735)caA>caG	p.Q245Q	DIS3L2_ENST00000409307.1_Intron|DIS3L2_ENST00000470087.1_3'UTR|DIS3L2_ENST00000273009.6_Intron|DIS3L2_ENST00000360410.4_Intron|DIS3L2_ENST00000325385.7_Intron	NM_001257282.1	NP_001244211.1			DIS3 like 3'-5' exoribonuclease 2											breast(2)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(18)|ovary(1)|prostate(2)|urinary_tract(1)	40		all_hematologic(139;0.00809)|Renal(207;0.0113)|Acute lymphoblastic leukemia(138;0.0195)|all_lung(227;0.0465)|Lung NSC(271;0.136)		Epithelial(121;1.6e-13)|BRCA - Breast invasive adenocarcinoma(100;0.00104)|LUSC - Lung squamous cell carcinoma(224;0.0109)|Lung(119;0.0149)		CACGTGTCCAAATGGCTTTCA	0.408													A|||	66	0.0131789	0.0492	0.0014	5008	,	,		17265	0.0		0.0	False		,,,				2504	0.0				p.Q245Q		Atlas-SNP	.											.	DIS3L2	77	.	0			c.A735G						PASS	.	A		183,3565		5,173,1696	56.0	53.0	54.0			0.9	0.0	2	dbSNP_132	54	1,8213		0,1,4106	no	intron	DIS3L2	NM_152383.4		5,174,5802	GG,GA,AA		0.0122,4.8826,1.5382			232995462	184,11778	1874	4107	5981	SO:0001819	synonymous_variant	129563	exon7			TGTCCAAATGGCT	BC026166	CCDS42834.1, CCDS58752.1, CCDS58753.1	2q37.1	2014-09-17	2014-03-05		ENSG00000144535	ENSG00000144535			28648	protein-coding gene	gene with protein product		614184	"""family with sequence similarity 6, member A"", ""DIS3 mitotic control homolog (S. cerevisiae)-like 2"""	FAM6A		22306653, 23503588	Standard	NM_152383		Approved	FLJ36974, MGC42174	uc010fxz.3	Q8IYB7	OTTHUMG00000153385	ENST00000409401.3:c.735A>G	2.37:g.232995462A>G		121.0	0.0	0		135.0	72.0	0.533333	NM_001257282		Silent	SNP	ENST00000409401.3	37	CCDS58753.1																																																																																			A|0.984;G|0.016	0.016	strong		0.408	DIS3L2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000330976.1	NM_152383	
DROSHA	29102	hgsc.bcm.edu	37	5	31526531	31526531	+	Missense_Mutation	SNP	G	G	A	rs77034974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:31526531G>A	ENST00000511367.2	-	4	753	c.509C>T	c.(508-510)cCg>cTg	p.P170L	DROSHA_ENST00000513349.1_Missense_Mutation_p.P170L|DROSHA_ENST00000442743.1_Missense_Mutation_p.P170L|DROSHA_ENST00000504361.1_5'Flank|DROSHA_ENST00000344624.3_Missense_Mutation_p.P170L	NM_013235.4	NP_037367.3	Q9NRR4	RNC_HUMAN	drosha, ribonuclease type III	170	Pro-rich.			YQYPPGYSH -> RERERTSLE (in Ref. 4; CAB45133). {ECO:0000305}.	defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|gene expression (GO:0010467)|miRNA metabolic process (GO:0010586)|pre-miRNA processing (GO:0031054)|primary miRNA processing (GO:0031053)|ribosome biogenesis (GO:0042254)|RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA catabolic process (GO:0016075)	nucleoplasm (GO:0005654)	lipopolysaccharide binding (GO:0001530)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|ribonuclease III activity (GO:0004525)			breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(19)|lung(33)|ovary(2)|skin(1)	66						AGAATAGCCCGGAGGGTACTG	0.532													G|||	179	0.0357428	0.1293	0.0115	5008	,	,		13508	0.0		0.0	False		,,,				2504	0.0				p.P170L		Atlas-SNP	.											.	DROSHA	130	.	0			c.C509T						PASS	.	G	LEU/PRO,LEU/PRO	443,3287		29,385,1451	47.0	47.0	47.0		509,509	5.1	0.2	5	dbSNP_131	47	2,8200		0,2,4099	yes	missense,missense	DROSHA	NM_001100412.1,NM_013235.4	98,98	29,387,5550	AA,AG,GG		0.0244,11.8767,3.7295	possibly-damaging,possibly-damaging	170/1338,170/1375	31526531	445,11487	1865	4101	5966	SO:0001583	missense	29102	exon4			TAGCCCGGAGGGT	AF116910	CCDS47194.1, CCDS47195.1	5q11.2	2010-11-17	2010-10-28	2010-10-28	ENSG00000113360	ENSG00000113360	3.1.26.3		17904	protein-coding gene	gene with protein product	"""drosha, ribonuclease type III"", ""drosha, double-stranded RNA-specific endoribonuclease"""	608828	"""ribonuclease type III, nuclear"""	RNASEN		10713462, 10948199	Standard	NM_013235		Approved	RNASE3L, Etohi2, HSA242976, RN3	uc003jhg.2	Q9NRR4	OTTHUMG00000161976	ENST00000511367.2:c.509C>T	5.37:g.31526531G>A	ENSP00000425979:p.Pro170Leu	200.0	0.0	0		228.0	103.0	0.451754	NM_013235	E7EMP9|Q7Z5V2|Q86YH0|Q9NW73|Q9Y2V9|Q9Y4Y0	Missense_Mutation	SNP	ENST00000511367.2	37	CCDS47195.1	55	0.025183150183150184	51	0.10365853658536585	4	0.011049723756906077	0	0.0	0	0.0	G	10.57	1.386208	0.25031	0.118767	2.44E-4	ENSG00000113360	ENST00000511367;ENST00000344624;ENST00000442743;ENST00000513349;ENST00000265075;ENST00000382188;ENST00000507438	T;T;T;T;T	0.41400	1.56;1.56;1.0;1.0;1.02	5.12	5.12	0.69794	.	0.173463	0.48767	D	0.000168	T	0.00384	0.0012	N	0.14661	0.345	0.22989	N	0.998465	B;B;B	0.28760	0.221;0.033;0.081	B;B;B	0.16722	0.016;0.007;0.007	T	0.00466	-1.1722	10	0.26408	T	0.33	-10.9681	18.5802	0.91168	0.0:0.0:1.0:0.0	.	170;170;170	Q9NRR4-2;E7EMP9;Q9NRR4	.;.;RNC_HUMAN	L	170;170;170;170;163;163;170	ENSP00000425979:P170L;ENSP00000339845:P170L;ENSP00000409335:P170L;ENSP00000424161:P170L;ENSP00000430921:P170L	ENSP00000265075:P163L	P	-	2	0	DROSHA	31562288	0.989000	0.36119	0.199000	0.23439	0.255000	0.26057	4.682000	0.61671	2.366000	0.80165	0.655000	0.94253	CCG	G|0.974;A|0.026	0.026	strong		0.532	DROSHA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366561.3	NM_013235	
PPL	5493	hgsc.bcm.edu	37	16	4952511	4952511	+	Missense_Mutation	SNP	C	C	T	rs115478590	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4952511C>T	ENST00000345988.2	-	4	423	c.334G>A	c.(334-336)Gag>Aag	p.E112K	PPL_ENST00000590782.2_Missense_Mutation_p.E112K	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	112					keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						GTCACACGCTCCTTCAGCTGG	0.637													C|||	16	0.00319489	0.0113	0.0014	5008	,	,		18020	0.0		0.0	False		,,,				2504	0.0				p.E112K		Atlas-SNP	.											.	PPL	168	.	0			c.G334A						PASS	.	C	LYS/GLU	47,4347	48.9+/-83.8	0,47,2150	129.0	94.0	106.0		334	5.0	1.0	16	dbSNP_132	106	0,8600		0,0,4300	yes	missense	PPL	NM_002705.4	56	0,47,6450	TT,TC,CC		0.0,1.0696,0.3617	probably-damaging	112/1757	4952511	47,12947	2197	4300	6497	SO:0001583	missense	5493	exon4			CACGCTCCTTCAG	AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.334G>A	16.37:g.4952511C>T	ENSP00000340510:p.Glu112Lys	128.0	0.0	0		160.0	90.0	0.5625	NM_002705	O60314|O60454|Q14C98	Missense_Mutation	SNP	ENST00000345988.2	37	CCDS10526.1	10	0.004578754578754579	8	0.016260162601626018	2	0.0055248618784530384	0	0.0	0	0.0	C	25.4	4.631767	0.87660	0.010696	0.0	ENSG00000118898	ENST00000345988	T	0.36520	1.25	4.98	4.98	0.66077	.	0.126906	0.52532	D	0.000078	T	0.43523	0.1251	M	0.69823	2.125	0.45528	D	0.998484	D	0.69078	0.997	D	0.75020	0.985	T	0.58629	-0.7603	10	0.72032	D	0.01	.	16.4235	0.83790	0.0:1.0:0.0:0.0	.	112	O60437	PEPL_HUMAN	K	112	ENSP00000340510:E112K	ENSP00000340510:E112K	E	-	1	0	PPL	4892512	1.000000	0.71417	1.000000	0.80357	0.645000	0.38454	5.290000	0.65661	2.311000	0.77944	0.650000	0.86243	GAG	C|0.996;T|0.004	0.004	strong		0.637	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
PCDH7	5099	hgsc.bcm.edu	37	4	31144189	31144189	+	Silent	SNP	C	C	T	rs148629328	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:31144189C>T	ENST00000543491.1	+	3	3486	c.3486C>T	c.(3484-3486)cgC>cgT	p.R1162R				O60245	PCDH7_HUMAN	protocadherin 7	0					homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						TGCCGGTCCGCACTTCTCCGG	0.552													C|||	19	0.00379393	0.0144	0.0	5008	,	,		15274	0.0		0.0	False		,,,				2504	0.0				p.R1162R		Atlas-SNP	.											.	PCDH7	215	.	0			c.C3486T						PASS	.	C	,	56,3986		0,56,1965	91.0	91.0	91.0		3486,3462	2.1	1.0	4	dbSNP_134	91	2,8402		0,2,4200	no	coding-synonymous,coding-synonymous	PCDH7	NM_001173523.1,NM_032457.3	,	0,58,6165	TT,TC,CC		0.0238,1.3855,0.466	,	1162/1256,1154/1248	31144189	58,12388	2021	4202	6223	SO:0001819	synonymous_variant	5099	exon3			GGTCCGCACTTCT	AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"""Cadherins / Protocadherins : Non-clustered"""	8659	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 120"""	602988	"""BH-protocadherin (brain-heart)"""			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000543491.1:c.3486C>T	4.37:g.31144189C>T		102.0	0.0	0		114.0	54.0	0.473684	NM_001173523	O60246|O60247|Q4W5C4	Silent	SNP	ENST00000543491.1	37	CCDS54753.1	7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	5.456	0.269217	0.10349	0.013855	2.38E-4	ENSG00000169851	ENST00000511884	.	.	.	5.86	2.14	0.27477	.	.	.	.	.	T	0.51109	0.1655	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48364	-0.9042	4	.	.	.	.	10.4605	0.44577	0.0:0.731:0.0:0.269	.	.	.	.	Y	844	.	.	H	+	1	0	PCDH7	30753287	0.983000	0.35010	0.999000	0.59377	0.829000	0.46940	0.584000	0.23864	0.146000	0.19002	0.650000	0.86243	CAC	C|0.997;T|0.003	0.003	strong		0.552	PCDH7-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_032457, NM_002589	
ROCK2	9475	hgsc.bcm.edu	37	2	11484212	11484212	+	Silent	SNP	C	C	A	rs368832806	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:11484212C>A	ENST00000315872.6	-	1	499	c.51G>T	c.(49-51)gcG>gcT	p.A17A	ROCK2_ENST00000462366.1_Intron	NM_004850.3	NP_004841.2	O75116	ROCK2_HUMAN	Rho-associated, coiled-coil containing protein kinase 2	17					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|neural tube closure (GO:0001843)|positive regulation of centrosome duplication (GO:0010825)|protein phosphorylation (GO:0006468)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of circadian rhythm (GO:0042752)|regulation of establishment of cell polarity (GO:2000114)|regulation of focal adhesion assembly (GO:0051893)|regulation of keratinocyte differentiation (GO:0045616)|regulation of stress fiber assembly (GO:0051492)|rhythmic process (GO:0048511)|smooth muscle contraction (GO:0006939)	centrosome (GO:0005813)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole centrosome (GO:0031616)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(6)|lung(10)|prostate(1)|skin(4)|stomach(3)|urinary_tract(2)	43	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.137)|OV - Ovarian serous cystadenocarcinoma(76;0.162)		CGTCCCCCGGCGCGGTCTCGG	0.741													C|||	9	0.00179712	0.0061	0.0	5008	,	,		9307	0.001		0.0	False		,,,				2504	0.0				p.A17A		Atlas-SNP	.											ROCK2_ENST00000315872,NS,carcinoma,-2,2	ROCK2	224	2	0			c.G51T						PASS	.	C		7,3463		0,7,1728	10.0	12.0	11.0		51	-1.3	0.0	2		11	0,7918		0,0,3959	no	coding-synonymous	ROCK2	NM_004850.3		0,7,5687	AA,AC,CC		0.0,0.2017,0.0615		17/1389	11484212	7,11381	1735	3959	5694	SO:0001819	synonymous_variant	9475	exon1			CCCCGGCGCGGTC	D87931	CCDS42654.1	2p24	2013-01-10			ENSG00000134318	ENSG00000134318	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	10252	protein-coding gene	gene with protein product		604002				9933571	Standard	NM_004850		Approved		uc002rbd.1	O75116	OTTHUMG00000149916	ENST00000315872.6:c.51G>T	2.37:g.11484212C>A		28.0	0.0	0		53.0	35.0	0.660377	NM_004850	Q53QZ0|Q53SJ7|Q9UQN5	Silent	SNP	ENST00000315872.6	37	CCDS42654.1																																																																																			.	.	weak		0.741	ROCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313886.3		
FAT3	120114	hgsc.bcm.edu	37	11	92538351	92538351	+	Silent	SNP	C	C	T	rs56843577	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:92538351C>T	ENST00000298047.6	+	10	8946	c.8929C>T	c.(8929-8931)Ctg>Ttg	p.L2977L	FAT3_ENST00000525166.1_Silent_p.L2827L|FAT3_ENST00000409404.2_Silent_p.L2977L			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2977	Cadherin 27. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TGCTCTGGGCCTGGTGCAAAG	0.428										TCGA Ovarian(4;0.039)			C|||	81	0.0161741	0.059	0.0043	5008	,	,		19268	0.0		0.0	False		,,,				2504	0.0				p.L2977L		Atlas-SNP	.											.	FAT3	1822	.	0			c.C8929T						PASS	.	C		197,3563		4,189,1687	80.0	81.0	81.0		8929	5.1	1.0	11	dbSNP_129	81	0,8218		0,0,4109	no	coding-synonymous	FAT3	NM_001008781.2		4,189,5796	TT,TC,CC		0.0,5.2394,1.6447		2977/4558	92538351	197,11781	1880	4109	5989	SO:0001819	synonymous_variant	120114	exon10			CTGGGCCTGGTGC	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.8929C>T	11.37:g.92538351C>T		172.0	0.0	0		178.0	81.0	0.455056	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				C|0.988;T|0.012	0.012	strong		0.428	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
NEURL4	84461	hgsc.bcm.edu	37	17	7226082	7226082	+	Silent	SNP	G	G	A	rs116452797	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7226082G>A	ENST00000399464.2	-	16	2712	c.2697C>T	c.(2695-2697)acC>acT	p.T899T	NEURL4_ENST00000315614.7_Silent_p.T897T|NEURL4_ENST00000570460.1_Silent_p.T875T	NM_032442.2	NP_115818.2	Q96JN8	NEUL4_HUMAN	neuralized E3 ubiquitin protein ligase 4	899						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						AGGACTTCTCGGTGGCAGTGT	0.622													G|||	2	0.000399361	0.0015	0.0	5008	,	,		21184	0.0		0.0	False		,,,				2504	0.0				p.T899T		Atlas-SNP	.											.	NEURL4	192	.	0			c.C2697T						PASS	.	G	,	6,4132		0,6,2063	159.0	171.0	167.0		2691,2697	-4.8	1.0	17	dbSNP_132	167	0,8428		0,0,4214	no	coding-synonymous,coding-synonymous	NEURL4	NM_001005408.1,NM_032442.2	,	0,6,6277	AA,AG,GG		0.0,0.145,0.0477	,	897/1561,899/1563	7226082	6,12560	2069	4214	6283	SO:0001819	synonymous_variant	84461	exon16			CTTCTCGGTGGCA		CCDS42251.1, CCDS42252.1	17p13	2013-10-24	2013-10-24		ENSG00000215041	ENSG00000215041			34410	protein-coding gene	gene with protein product		615865	"""neuralized homolog 4 (Drosophila)"""			22261722, 22441691	Standard	NM_001005408		Approved	KIAA1787	uc002gga.1	Q96JN8	OTTHUMG00000132319	ENST00000399464.2:c.2697C>T	17.37:g.7226082G>A		72.0	0.0	0		100.0	52.0	0.52	NM_032442	Q6GPI8|Q96IU9|Q9H0B0	Silent	SNP	ENST00000399464.2	37	CCDS42251.1																																																																																			G|0.999;A|0.001	0.001	strong		0.622	NEURL4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255434.2	NM_032442	
CCDC40	55036	hgsc.bcm.edu	37	17	78032677	78032677	+	Silent	SNP	C	C	T	rs61734950	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:78032677C>T	ENST00000397545.4	+	9	1365	c.1338C>T	c.(1336-1338)ctC>ctT	p.L446L	CCDC40_ENST00000374876.4_Intron|CCDC40_ENST00000374877.3_Silent_p.L446L|CCDC40_ENST00000269318.5_Silent_p.L446L	NM_017950.3	NP_060420.2	Q4G0X9	CCD40_HUMAN	coiled-coil domain containing 40	446					axonemal dynein complex assembly (GO:0070286)|determination of digestive tract left/right asymmetry (GO:0071907)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|epithelial cilium movement (GO:0003351)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|heart looping (GO:0001947)|lung development (GO:0030324)|regulation of cilium beat frequency (GO:0003356)	cilium (GO:0005929)|cytoplasm (GO:0005737)				NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(7)|lung(12)|ovary(4)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	38	all_neural(118;0.167)		OV - Ovarian serous cystadenocarcinoma(97;0.0292)|BRCA - Breast invasive adenocarcinoma(99;0.149)			TGGACCAGCTCACCACTCGAG	0.562													C|||	292	0.0583067	0.1694	0.0159	5008	,	,		18404	0.0		0.001	False		,,,				2504	0.0573				p.L446L		Atlas-SNP	.											.	CCDC40	198	.	0			c.C1338T						PASS	.	C		578,3600		37,504,1548	87.0	91.0	90.0		1338	-3.2	0.8	17	dbSNP_129	90	3,8431		0,3,4214	no	coding-synonymous	CCDC40	NM_017950.3		37,507,5762	TT,TC,CC		0.0356,13.8344,4.6067		446/1143	78032677	581,12031	2089	4217	6306	SO:0001819	synonymous_variant	55036	exon9			CCAGCTCACCACT	AB046860	CCDS42395.1, CCDS58604.1	17q25.3	2013-11-15			ENSG00000141519	ENSG00000141519			26090	protein-coding gene	gene with protein product		613799				21131974	Standard	NM_017950		Approved	FLJ20753, KIAA1640, FLJ32021, CILD15, FAP172	uc010dht.3	Q4G0X9	OTTHUMG00000132707	ENST00000397545.4:c.1338C>T	17.37:g.78032677C>T		122.0	0.0	0		103.0	60.0	0.582524	NM_017950	A8MTD2|C9JTI9|C9JTJ0|C9JXW1|Q6PE47|Q9HCD2|Q9NWL5	Silent	SNP	ENST00000397545.4	37	CCDS42395.1																																																																																			C|0.972;T|0.028	0.028	strong		0.562	CCDC40-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256005.2	XM_371082	
RDX	5962	hgsc.bcm.edu	37	11	110118459	110118459	+	Silent	SNP	T	T	C	rs139953187	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:110118459T>C	ENST00000343115.4	-	10	1378	c.1059A>G	c.(1057-1059)caA>caG	p.Q353Q	RDX_ENST00000528900.1_Silent_p.Q6Q|RDX_ENST00000528498.1_Silent_p.Q353Q|RDX_ENST00000405097.1_Silent_p.Q353Q|RDX_ENST00000530301.1_Intron|RDX_ENST00000544551.1_Silent_p.Q217Q	NM_001260494.1|NM_002906.3	NP_001247423.1|NP_002897.1	P35241	RADI_HUMAN	radixin	353	Glu-rich.				actin filament capping (GO:0051693)|apical protein localization (GO:0045176)|establishment of endothelial barrier (GO:0061028)|microvillus assembly (GO:0030033)|positive regulation of gene expression (GO:0010628)	apical part of cell (GO:0045177)|cell tip (GO:0051286)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|stereocilium (GO:0032420)|T-tubule (GO:0030315)	poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(2)|large_intestine(3)|lung(8)|skin(1)|urinary_tract(1)	18		all_cancers(61;7.18e-13)|all_epithelial(67;2.61e-07)|Melanoma(852;1.46e-05)|all_hematologic(158;3.66e-05)|Acute lymphoblastic leukemia(157;3.95e-05)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Breast(348;0.0544)		Epithelial(105;1.13e-06)|BRCA - Breast invasive adenocarcinoma(274;9.75e-06)|all cancers(92;5.9e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0248)		GCTCTTCAATTTGTTTTAGAC	0.308													T|||	53	0.0105831	0.0333	0.0115	5008	,	,		17959	0.0		0.001	False		,,,				2504	0.0				p.Q353Q	Esophageal Squamous(55;25 1062 11040 28755 44273)	Atlas-SNP	.											.	RDX	59	.	0			c.A1059G						PASS	.	T		107,4289	79.3+/-117.8	1,105,2092	134.0	122.0	126.0		1059	2.8	1.0	11	dbSNP_134	126	1,8587	1.2+/-3.3	0,1,4293	no	coding-synonymous	RDX	NM_002906.3		1,106,6385	CC,CT,TT		0.0116,2.434,0.8318		353/584	110118459	108,12876	2198	4294	6492	SO:0001819	synonymous_variant	5962	exon10			TTCAATTTGTTTT	BC020751	CCDS8343.1, CCDS58171.1, CCDS58172.1, CCDS58173.1, CCDS58174.1	11q23	2008-03-17				ENSG00000137710			9944	protein-coding gene	gene with protein product		179410	"""deafness, autosomal recessive 24"""	DFNB24		8486357, 17226784	Standard	NM_001260492		Approved		uc031qdy.1	P35241		ENST00000343115.4:c.1059A>G	11.37:g.110118459T>C		193.0	0.0	0		163.0	99.0	0.607362	NM_001260493	A7YIJ8|A7YIK0|A7YIK3|B7Z9U6|F5H1A7|Q86Y61	Silent	SNP	ENST00000343115.4	37	CCDS8343.1																																																																																			T|0.989;C|0.011	0.011	strong		0.308	RDX-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390535.2	NM_002906	
CP	1356	hgsc.bcm.edu	37	3	148901300	148901300	+	Missense_Mutation	SNP	C	C	T	rs115552500	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:148901300C>T	ENST00000264613.6	-	13	2640	c.2378G>A	c.(2377-2379)cGt>cAt	p.R793H	CP_ENST00000462336.1_5'Flank	NM_000096.3	NP_000087	P00450	CERU_HUMAN	ceruloplasmin (ferroxidase)	793	F5/8 type A 3.|Plastocyanin-like 5.		R -> H. {ECO:0000269|PubMed:15557511}.		cellular iron ion homeostasis (GO:0006879)|copper ion transport (GO:0006825)|transmembrane transport (GO:0055085)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)	chaperone binding (GO:0051087)|copper ion binding (GO:0005507)|ferroxidase activity (GO:0004322)			breast(6)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	44		Prostate(884;0.00217)|Hepatocellular(537;0.00826)|Myeloproliferative disorder(1037;0.0122)|all_neural(597;0.0189)|Melanoma(1037;0.152)	LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)		Drotrecogin alfa(DB00055)	CACTGGAACACGGAATGTGCT	0.373													C|||	61	0.0121805	0.0234	0.013	5008	,	,		13349	0.001		0.0169	False		,,,				2504	0.0031				p.R793H		Atlas-SNP	.											.	CP	112	.	0			c.G2378A	GRCh37	CM045287	CP	M	rs115552500	PASS	.	C	HIS/ARG	89,4317	74.1+/-112.3	1,87,2115	133.0	118.0	123.0		2378	-1.8	0.0	3	dbSNP_132	123	79,8521	46.3+/-105.2	0,79,4221	yes	missense	CP	NM_000096.3	29	1,166,6336	TT,TC,CC		0.9186,2.02,1.2917	possibly-damaging	793/1066	148901300	168,12838	2203	4300	6503	SO:0001583	missense	1356	exon13			GGAACACGGAATG	M13536	CCDS3141.1	3q23-q25	2010-07-01			ENSG00000047457	ENSG00000047457	1.16.3.1		2295	protein-coding gene	gene with protein product		117700					Standard	NM_000096		Approved		uc003ewy.4	P00450	OTTHUMG00000159563	ENST00000264613.6:c.2378G>A	3.37:g.148901300C>T	ENSP00000264613:p.Arg793His	83.0	0.0	0		67.0	35.0	0.522388	NM_000096	Q14063|Q2PP18|Q9UKS4	Missense_Mutation	SNP	ENST00000264613.6	37	CCDS3141.1	25	0.011446886446886446	4	0.008130081300813009	8	0.022099447513812154	1	0.0017482517482517483	12	0.0158311345646438	C	14.94	2.684284	0.47991	0.0202	0.009186	ENSG00000047457	ENST00000264613;ENST00000494544	D;D	0.98937	-5.25;-5.25	5.39	-1.8	0.07907	Cupredoxin (2);	1.207680	0.05806	N	0.613068	D	0.93877	0.8041	L	0.49350	1.555	0.09310	N	1	P;P;P	0.47350	0.528;0.802;0.894	B;B;B	0.42653	0.279;0.394;0.394	D	0.90687	0.4610	10	0.42905	T	0.14	0.5473	6.2989	0.21101	0.0:0.338:0.3602:0.3019	.	793;793;793	A8K5A4;P00450;Q1L857	.;CERU_HUMAN;.	H	793;576	ENSP00000264613:R793H;ENSP00000420545:R576H	ENSP00000264613:R793H	R	-	2	0	CP	150383990	0.000000	0.05858	0.000000	0.03702	0.304000	0.27724	-0.336000	0.07863	-0.782000	0.04541	0.555000	0.69702	CGT	C|0.987;T|0.013	0.013	strong		0.373	CP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317498.1	NM_000096	
MRPL46	26589	hgsc.bcm.edu	37	15	89002888	89002888	+	Missense_Mutation	SNP	G	G	T	rs146290179		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:89002888G>T	ENST00000312475.4	-	4	837	c.796C>A	c.(796-798)Cca>Aca	p.P266T	MRPL46_ENST00000559538.1_5'UTR	NM_022163.3	NP_071446.2	Q9H2W6	RM46_HUMAN	mitochondrial ribosomal protein L46	266						mitochondrion (GO:0005739)|ribosome (GO:0005840)	hydrolase activity (GO:0016787)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)	5	Lung NSC(78;0.203)		BRCA - Breast invasive adenocarcinoma(143;0.188)			AGGTATTTTGGTTTCAAATAG	0.502																																					p.P266T		Atlas-SNP	.											.	MRPL46	13	.	0			c.C796A						PASS	.	G	THR/PRO	2,4400	4.2+/-10.8	0,2,2199	119.0	101.0	107.0		796	6.0	0.5	15	dbSNP_134	107	0,8598		0,0,4299	no	missense	MRPL46	NM_022163.3	38	0,2,6498	TT,TG,GG		0.0,0.0454,0.0154	possibly-damaging	266/280	89002888	2,12998	2201	4299	6500	SO:0001583	missense	26589	exon4			ATTTTGGTTTCAA	AF210056	CCDS10341.1	15q25.3	2012-10-08	2001-12-10	2001-12-14	ENSG00000259494	ENSG00000259494		"""Mitochondrial ribosomal proteins / large subunits"""	1192	protein-coding gene	gene with protein product		611851	"""chromosome 15 open reading frame 4"""	C15orf4		11761714, 11551941	Standard	NM_022163		Approved	LIECG2, P2ECSL	uc002bmj.2	Q9H2W6	OTTHUMG00000148683	ENST00000312475.4:c.796C>A	15.37:g.89002888G>T	ENSP00000312311:p.Pro266Thr	114.0	0.0	0		122.0	53.0	0.434426	NM_022163	B2RD75|Q9HBU8	Missense_Mutation	SNP	ENST00000312475.4	37	CCDS10341.1	.	.	.	.	.	.	.	.	.	.	G	17.01	3.278489	0.59758	4.54E-4	0.0	ENSG00000173867	ENST00000312475	T	0.48201	0.82	5.98	5.98	0.97165	.	0.102208	0.64402	D	0.000002	T	0.47967	0.1474	M	0.62154	1.92	0.58432	D	0.999993	P	0.51653	0.947	B	0.43916	0.436	T	0.44697	-0.9311	10	0.36615	T	0.2	.	12.628	0.56640	0.0824:0.0:0.9176:0.0	.	266	Q9H2W6	RM46_HUMAN	T	266	ENSP00000312311:P266T	ENSP00000312311:P266T	P	-	1	0	MRPL46	86803892	1.000000	0.71417	0.508000	0.27688	0.542000	0.35054	4.395000	0.59678	2.835000	0.97688	0.650000	0.86243	CCA	G|1.000;T|0.000	0.000	weak		0.502	MRPL46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309073.1	NM_022163	
MASP2	10747	hgsc.bcm.edu	37	1	11106648	11106648	+	Missense_Mutation	SNP	G	G	A	rs56392418	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:11106648G>A	ENST00000400897.3	-	3	392	c.377C>T	c.(376-378)cCg>cTg	p.P126L	MASP2_ENST00000400898.3_Missense_Mutation_p.P126L	NM_006610.3	NP_006601.2	O00187	MASP2_HUMAN	mannan-binding lectin serine peptidase 2	126	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.		P -> L (in MASPD; dbSNP:rs56392418). {ECO:0000269|PubMed:16029433, ECO:0000269|PubMed:17252003}.		complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|complement component C4b binding (GO:0001855)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)			biliary_tract(1)|endometrium(2)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	23	Ovarian(185;0.249)	Lung NSC(185;1.04e-05)|all_lung(284;1.31e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.071)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.12e-07)|COAD - Colon adenocarcinoma(227;7.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)|STAD - Stomach adenocarcinoma(313;0.192)		CCCCGTGAACGGCTTCTCGTT	0.607													G|||	181	0.0361422	0.1316	0.0101	5008	,	,		19642	0.0		0.0	False		,,,				2504	0.0				p.P126L	GBM(35;611 746 20780 22741 36496)	Atlas-SNP	.											.	MASP2	71	.	0			c.C377T	GRCh37	CM073192	MASP2	M	rs56392418	PASS	.	G	LEU/PRO,LEU/PRO	505,3901	231.7+/-245.5	22,461,1720	52.0	45.0	47.0		377,377	2.8	1.0	1	dbSNP_129	47	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	MASP2	NM_006610.3,NM_139208.2	98,98	22,463,6018	AA,AG,GG		0.0233,11.4616,3.8982	possibly-damaging,possibly-damaging	126/687,126/186	11106648	507,12499	2203	4300	6503	SO:0001583	missense	10747	exon3			GTGAACGGCTTCT	X98400	CCDS123.1, CCDS124.1	1p36.3-p36.2	2014-09-17	2005-08-17		ENSG00000009724	ENSG00000009724			6902	protein-coding gene	gene with protein product		605102	"""mannan-binding lectin serine protease 2"", ""mannan-binding lectin serine peptidase 1 pseudogene 1"", ""mannan-binding lectin serine protease 1 pseudogene 1"""	MASP1P1		9087411, 9777418	Standard	NM_006610		Approved		uc001aru.3	O00187	OTTHUMG00000002121	ENST00000400897.3:c.377C>T	1.37:g.11106648G>A	ENSP00000383690:p.Pro126Leu	109.0	0.0	0		130.0	50.0	0.384615	NM_139208	A8K458|A8MWJ2|O75754|Q5TEQ5|Q5TER0|Q96QG4|Q9BZH0|Q9H498|Q9H499|Q9UBP3|Q9UC48|Q9ULC7|Q9UMV3|Q9Y270	Missense_Mutation	SNP	ENST00000400897.3	37	CCDS123.1	70	0.03205128205128205	66	0.13414634146341464	4	0.011049723756906077	0	0.0	0	0.0	G	17.33	3.361797	0.61403	0.114616	2.33E-4	ENSG00000009724	ENST00000400897;ENST00000400898	T;T	0.26660	1.72;1.72	4.87	2.75	0.32379	CUB (5);	0.752220	0.12578	N	0.456686	T	0.00178	0.0005	L	0.33485	1.01	0.49051	D	0.999741	B;P	0.36183	0.179;0.542	B;B	0.33196	0.016;0.159	T	0.18461	-1.0336	10	0.66056	D	0.02	.	7.2086	0.25921	0.0979:0.0:0.6342:0.2678	rs56392418;rs61747086	126;126	O00187-2;O00187	.;MASP2_HUMAN	L	126	ENSP00000383690:P126L;ENSP00000383691:P126L	ENSP00000383690:P126L	P	-	2	0	MASP2	11029235	0.099000	0.21834	0.984000	0.44739	0.939000	0.58152	0.769000	0.26604	1.046000	0.40249	-0.251000	0.11542	CCG	G|0.964;A|0.036	0.036	strong		0.607	MASP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006072.1	NM_006610	
TCF7L1	83439	hgsc.bcm.edu	37	2	85510654	85510654	+	Missense_Mutation	SNP	T	T	A	rs115942112	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:85510654T>A	ENST00000282111.3	+	4	753	c.478T>A	c.(478-480)Tcc>Acc	p.S160T		NM_031283.2	NP_112573.1	Q9HCS4	TF7L1_HUMAN	transcription factor 7-like 1 (T-cell specific, HMG-box)	160	Pro-rich.				anterior/posterior axis specification, embryo (GO:0008595)|axial mesoderm morphogenesis (GO:0048319)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|chromatin organization (GO:0006325)|generation of neurons (GO:0048699)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of stem cell maintenance (GO:2000036)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(3)|skin(4)|upper_aerodigestive_tract(1)	18						CGATGTCCCCTCCAGCGCCAC	0.507													T|||	60	0.0119808	0.0393	0.0	5008	,	,		20302	0.005		0.0	False		,,,				2504	0.0031				p.S160T		Atlas-SNP	.											.	TCF7L1	44	.	0			c.T478A						PASS	.	T	THR/SER	134,4272	97.1+/-135.8	1,132,2070	257.0	224.0	235.0		478	3.1	1.0	2	dbSNP_132	235	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TCF7L1	NM_031283.2	58	1,133,6369	AA,AT,TT		0.0116,3.0413,1.038	benign	160/589	85510654	135,12871	2203	4300	6503	SO:0001583	missense	83439	exon4			GTCCCCTCCAGCG	X62870	CCDS1971.1	2p11.2	2008-02-05			ENSG00000152284	ENSG00000152284			11640	protein-coding gene	gene with protein product		604652		TCF3		1741298, 11085512	Standard	NM_031283		Approved		uc002soy.3	Q9HCS4	OTTHUMG00000130026	ENST00000282111.3:c.478T>A	2.37:g.85510654T>A	ENSP00000282111:p.Ser160Thr	106.0	0.0	0		131.0	57.0	0.435115	NM_031283	Q53R97|Q6PD70|Q9NP00	Missense_Mutation	SNP	ENST00000282111.3	37	CCDS1971.1	21	0.009615384615384616	21	0.042682926829268296	0	0.0	0	0.0	0	0.0	T	12.34	1.910078	0.33721	0.030413	1.16E-4	ENSG00000152284	ENST00000282111;ENST00000442813	D	0.98550	-4.99	5.44	3.08	0.35506	CTNNB1 binding, N-teminal (1);	0.586502	0.18208	N	0.148291	D	0.83608	0.5291	N	0.22421	0.69	0.26675	N	0.971648	B	0.33000	0.393	B	0.34536	0.185	D	0.84356	0.0535	10	0.56958	D	0.05	.	5.5742	0.17215	0.0:0.09:0.1841:0.7258	.	160	Q9HCS4	TF7L1_HUMAN	T	160;10	ENSP00000282111:S160T	ENSP00000282111:S160T	S	+	1	0	TCF7L1	85364165	0.989000	0.36119	0.998000	0.56505	0.988000	0.76386	0.065000	0.14466	0.382000	0.24878	0.533000	0.62120	TCC	T|0.989;A|0.011	0.011	strong		0.507	TCF7L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252301.2	NM_031283	
RNF207	388591	hgsc.bcm.edu	37	1	6267523	6267523	+	Silent	SNP	C	C	T	rs58587405	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:6267523C>T	ENST00000377939.4	+	3	403	c.276C>T	c.(274-276)ggC>ggT	p.G92G	RP1-120G22.11_ENST00000455744.1_RNA|RNF207_ENST00000377948.2_5'UTR	NM_207396.2	NP_997279.2	Q6ZRF8	RN207_HUMAN	ring finger protein 207	92						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(7)|ovary(2)	16	Ovarian(185;0.0634)	all_cancers(23;1.22e-38)|all_epithelial(116;4.25e-22)|all_lung(118;7.95e-08)|Lung NSC(185;1.6e-06)|all_neural(13;3.18e-06)|all_hematologic(16;8.99e-06)|Acute lymphoblastic leukemia(12;0.000365)|Breast(487;0.000496)|Renal(390;0.0007)|Colorectal(325;0.00104)|Glioma(11;0.00203)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)|Medulloblastoma(700;0.211)		Epithelial(90;4.84e-38)|GBM - Glioblastoma multiforme(13;5.77e-32)|OV - Ovarian serous cystadenocarcinoma(86;2.88e-19)|Colorectal(212;6.9e-08)|COAD - Colon adenocarcinoma(227;8.13e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|BRCA - Breast invasive adenocarcinoma(365;0.00108)|STAD - Stomach adenocarcinoma(132;0.00311)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.182)		CAGGGGATGGCGTGGAGGCGG	0.692													C|||	152	0.0303514	0.1059	0.0144	5008	,	,		10633	0.0		0.002	False		,,,				2504	0.0				p.G92G		Atlas-SNP	.											.	RNF207	45	.	0			c.C276T						PASS	.	C		427,3971		22,383,1794	23.0	26.0	25.0		276	3.6	0.4	1	dbSNP_129	25	5,8589		0,5,4292	no	coding-synonymous	RNF207	NM_207396.2		22,388,6086	TT,TC,CC		0.0582,9.709,3.3251		92/635	6267523	432,12560	2199	4297	6496	SO:0001819	synonymous_variant	388591	exon3			GGATGGCGTGGAG	AK128246	CCDS59.2	1p36.31	2008-11-19			ENSG00000158286	ENSG00000158286		"""RING-type (C3HC4) zinc fingers"""	32947	protein-coding gene	gene with protein product	"""OTTHUMG00000001089"""		"""chromosome 1 open reading frame 188"""	C1orf188			Standard	NM_207396		Approved	FLJ46380, FLJ32096	uc001amg.3	Q6ZRF8	OTTHUMG00000001089	ENST00000377939.4:c.276C>T	1.37:g.6267523C>T		214.0	0.0	0		294.0	152.0	0.517007	NM_207396	A2VCM8|B4DFR6|Q5TGS6|Q6ZS63|Q96MP2	Silent	SNP	ENST00000377939.4	37	CCDS59.2																																																																																			C|0.966;T|0.034	0.034	strong		0.692	RNF207-001	NOVEL	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003669.2	NM_207396	
CCDC92	80212	hgsc.bcm.edu	37	12	124421764	124421764	+	Silent	SNP	C	C	T	rs34241686	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:124421764C>T	ENST00000238156.3	-	5	1191	c.837G>A	c.(835-837)ccG>ccA	p.P279P	RP11-380L11.3_ENST00000602292.1_RNA|CCDC92_ENST00000545135.1_Silent_p.P262P|CCDC92_ENST00000545891.1_Silent_p.P262P|DNAH10OS_ENST00000514254.2_5'Flank|CCDC92_ENST00000544798.1_Intron	NM_025140.1	NP_079416.1	Q53HC0	CCD92_HUMAN	coiled-coil domain containing 92	279						centriole (GO:0005814)				large_intestine(5)|lung(2)	7	all_neural(191;0.101)|Medulloblastoma(191;0.163)			Epithelial(86;0.0002)|OV - Ovarian serous cystadenocarcinoma(86;0.000222)|all cancers(50;0.00129)|BRCA - Breast invasive adenocarcinoma(302;0.242)		TTTCGCGGGCCGGGCTGTGCT	0.701													C|||	27	0.00539137	0.0197	0.0	5008	,	,		12393	0.0		0.001	False		,,,				2504	0.0				p.P279P		Atlas-SNP	.											.	CCDC92	18	.	0			c.G837A						PASS	.	C		54,4342		0,54,2144	18.0	21.0	20.0		837	-9.9	0.1	12	dbSNP_126	20	4,8578		0,4,4287	no	coding-synonymous	CCDC92	NM_025140.1		0,58,6431	TT,TC,CC		0.0466,1.2284,0.4469		279/332	124421764	58,12920	2198	4291	6489	SO:0001819	synonymous_variant	80212	exon5			GCGGGCCGGGCTG	AK026124	CCDS9256.1	12q24.31	2011-09-02			ENSG00000119242	ENSG00000119242			29563	protein-coding gene	gene with protein product	"""limkain beta 2"""					12477932	Standard	NM_025140		Approved	FLJ22471	uc001ufw.1	Q53HC0	OTTHUMG00000168725	ENST00000238156.3:c.837G>A	12.37:g.124421764C>T		13.0	0.0	0		22.0	10.0	0.454545	NM_025140	B3KNQ0|Q9H697	Silent	SNP	ENST00000238156.3	37	CCDS9256.1																																																																																			C|0.996;T|0.004	0.004	strong		0.701	CCDC92-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400780.2	NM_025140	
IGLL1	3543	hgsc.bcm.edu	37	22	23917176	23917176	+	Silent	SNP	G	G	A	rs115303391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:23917176G>A	ENST00000330377.2	-	2	417	c.300C>T	c.(298-300)agC>agT	p.S100S	AP000345.2_ENST00000454863.1_RNA|IGLL1_ENST00000249053.3_Intron|AP000345.2_ENST00000458318.1_RNA	NM_020070.3	NP_064455.1	P15814	IGLL1_HUMAN	immunoglobulin lambda-like polypeptide 1	100	J region (By similarity to lambda light- chain).				immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				kidney(1)|large_intestine(1)|lung(5)|skin(4)|stomach(1)	12						GCTGGGTCCCGCTGCCAAACA	0.577													g|||	176	0.0351438	0.1263	0.0115	5008	,	,		17917	0.0		0.001	False		,,,				2504	0.0				p.S100S		Atlas-SNP	.											.	IGLL1	27	.	0			c.C300T						PASS	.	G	,	537,3869		35,467,1701	70.0	59.0	63.0		300,	-3.2	0.0	22	dbSNP_132	63	11,8589		0,11,4289	no	coding-synonymous,intron	IGLL1	NM_020070.2,NM_152855.1	,	35,478,5990	AA,AG,GG		0.1279,12.1879,4.2134	,	100/214,	23917176	548,12458	2203	4300	6503	SO:0001819	synonymous_variant	3543	exon2			GGTCCCGCTGCCA	X52204	CCDS13809.1, CCDS13810.1	22q11.23	2014-09-17			ENSG00000128322	ENSG00000128322		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	5870	protein-coding gene	gene with protein product		146770		IGLL		3139558, 2511029	Standard	NM_020070		Approved	IGVPB, IGL5, 14.1, CD179B	uc002zxd.3	P15814	OTTHUMG00000150673	ENST00000330377.2:c.300C>T	22.37:g.23917176G>A		110.0	0.0	0		154.0	72.0	0.467532	NM_020070	Q0P681	Silent	SNP	ENST00000330377.2	37	CCDS13809.1																																																																																			G|0.965;A|0.035	0.035	strong		0.577	IGLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319569.1	NM_020070	
MICALL1	85377	hgsc.bcm.edu	37	22	38302469	38302469	+	Missense_Mutation	SNP	C	C	T	rs146549351	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:38302469C>T	ENST00000215957.6	+	1	166	c.40C>T	c.(40-42)Cgc>Tgc	p.R14C		NM_033386.3	NP_203744.1	Q8N3F8	MILK1_HUMAN	MICAL-like 1	14	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				endocytosis (GO:0006897)|membrane tubulation (GO:0097320)|neuron projection development (GO:0031175)|protein localization to endosome (GO:0036010)|protein targeting to membrane (GO:0006612)|receptor-mediated endocytosis (GO:0006898)|retrograde transport, endosome to plasma membrane (GO:1990126)|slow endocytic recycling (GO:0032458)	extrinsic component of membrane (GO:0019898)|late endosome (GO:0005770)|recycling endosome membrane (GO:0055038)	identical protein binding (GO:0042802)|phosphatidic acid binding (GO:0070300)|Rab GTPase binding (GO:0017137)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	24	Melanoma(58;0.045)					CTGGTGCCGCCGCCAGTGCGA	0.786													c|||	50	0.00998403	0.0371	0.0014	5008	,	,		3679	0.0		0.0	False		,,,				2504	0.0				p.R14C		Atlas-SNP	.											.	MICALL1	53	.	0			c.C40T						PASS	.		CYS/ARG	44,3156		1,42,1557	4.0	4.0	4.0		40	1.0	1.0	22	dbSNP_134	4	0,6182		0,0,3091	no	missense	MICALL1	NM_033386.3	180	1,42,4648	TT,TC,CC		0.0,1.375,0.469	probably-damaging	14/864	38302469	44,9338	1600	3091	4691	SO:0001583	missense	85377	exon1			TGCCGCCGCCAGT	BK000466	CCDS13961.1	22q13.1	2006-11-24			ENSG00000100139	ENSG00000100139			29804	protein-coding gene	gene with protein product	"""molecule interacting with Rab13"""					11258795, 12110185	Standard	NM_033386		Approved	MIRAB13, KIAA1668, MICAL-L1	uc003aui.3	Q8N3F8	OTTHUMG00000150670	ENST00000215957.6:c.40C>T	22.37:g.38302469C>T	ENSP00000215957:p.Arg14Cys	5.0	0.0	0		4.0	4.0	1	NM_033386	Q5TI16|Q7RTP5|Q8N3N8|Q9BVL9|Q9BY92|Q9UH43|Q9UH44|Q9UH45	Missense_Mutation	SNP	ENST00000215957.6	37	CCDS13961.1	128	0.05860805860805861	70	0.14227642276422764	22	0.06077348066298342	12	0.02097902097902098	24	0.0316622691292876	c	14.95	2.687334	0.48097	0.01375	0.0	ENSG00000100139	ENST00000215957	D	0.95342	-3.68	2.15	1.04	0.20106	Calponin homology domain (5);	.	.	.	.	T	0.15046	0.0363	M	0.92317	3.295	0.80722	D	1	B	0.14438	0.01	B	0.14023	0.01	T	0.69442	-0.5144	9	0.87932	D	0	.	8.698	0.34307	0.0:0.8737:0.0:0.1263	.	14	Q8N3F8	MILK1_HUMAN	C	14	ENSP00000215957:R14C	ENSP00000215957:R14C	R	+	1	0	MICALL1	36632415	1.000000	0.71417	0.985000	0.45067	0.590000	0.36582	4.587000	0.60991	0.179000	0.19938	0.165000	0.16767	CGC	C|0.942;T|0.058	0.058	strong		0.786	MICALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319545.4	NM_033386	
MED14	9282	hgsc.bcm.edu	37	X	40551993	40551993	+	Silent	SNP	G	G	A	rs10127014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:40551993G>A	ENST00000324817.1	-	14	1930	c.1812C>T	c.(1810-1812)acC>acT	p.T604T		NM_004229.3	NP_004220.2	O60244	MED14_HUMAN	mediator complex subunit 14	604	Interaction with SREBF1.				androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			NS(2)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(7)|lung(8)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						TCTGTTTCCCGGTTTTTGTAC	0.433													G|||	105	0.0278146	0.0719	0.0029	3775	,	,		13717	0.0		0.0	False		,,,				2504	0.0082				p.T604T		Atlas-SNP	.											.	MED14	108	.	0			c.C1812T						PASS	.	G		275,3560		4,230,37,1398,534	137.0	113.0	121.0		1812	-9.3	0.0	X	dbSNP_119	121	0,6728		0,0,0,2428,1872	no	coding-synonymous	MED14	NM_004229.3		4,230,37,3826,2406	AA,AG,A,GG,G		0.0,7.1708,2.6034		604/1455	40551993	275,10288	2203	4300	6503	SO:0001819	synonymous_variant	9282	exon14			TTTCCCGGTTTTT	AB006651	CCDS14254.1	Xp11.4	2008-05-14	2007-07-30	2007-07-30	ENSG00000180182	ENSG00000180182			2370	protein-coding gene	gene with protein product		300182	"""cofactor required for Sp1 transcriptional activation, subunit 2, 150kDa"""	CXorf4, CRSP2		9989412, 9598311	Standard	NM_004229		Approved	EXLM1, CRSP150, TRAP170, RGR1, CSRP	uc004dex.4	O60244	OTTHUMG00000024107	ENST00000324817.1:c.1812C>T	X.37:g.40551993G>A		178.0	0.0	0		236.0	128.0	0.542373	NM_004229	Q4KMR7|Q9UNB3	Silent	SNP	ENST00000324817.1	37	CCDS14254.1																																																																																			G|0.966;A|0.034	0.034	strong		0.433	MED14-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060692.1	NM_004229	
HAPLN2	60484	hgsc.bcm.edu	37	1	156593928	156593928	+	Missense_Mutation	SNP	G	G	T	rs149573918	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156593928G>T	ENST00000255039.1	+	4	822	c.415G>T	c.(415-417)Gtg>Ttg	p.V139L	HAPLN2_ENST00000494218.1_3'UTR	NM_021817.2	NP_068589.1	Q9GZV7	HPLN2_HUMAN	hyaluronan and proteoglycan link protein 2	139	Ig-like V-type.				cell adhesion (GO:0007155)|establishment of blood-nerve barrier (GO:0008065)|extracellular matrix assembly (GO:0085029)	proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			NS(1)|endometrium(2)|large_intestine(1)|lung(1)|skin(1)|urinary_tract(1)	7	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GGACGAGAGCGTGGCGCTGAC	0.692													G|||	68	0.0135783	0.0499	0.0029	5008	,	,		14129	0.0		0.0	False		,,,				2504	0.0				p.V139L		Atlas-SNP	.											.	HAPLN2	20	.	0			c.G415T						PASS	.	G	LEU/VAL	162,4192		4,154,2019	42.0	36.0	38.0		415	1.9	1.0	1	dbSNP_134	38	2,8482		0,2,4240	yes	missense	HAPLN2	NM_021817.2	32	4,156,6259	TT,TG,GG		0.0236,3.7207,1.2775	benign	139/341	156593928	164,12674	2177	4242	6419	SO:0001583	missense	60484	exon4			GAGAGCGTGGCGC	AB049054	CCDS1148.1	1q23.1	2013-01-11			ENSG00000132702	ENSG00000132702		"""Immunoglobulin superfamily / V-set domain containing"""	17410	protein-coding gene	gene with protein product	"""brain link protein 1"""					11027579, 11873941	Standard	NM_021817		Approved	BRAL1	uc001fpn.1	Q9GZV7	OTTHUMG00000033205	ENST00000255039.1:c.415G>T	1.37:g.156593928G>T	ENSP00000255039:p.Val139Leu	170.0	0.0	0		213.0	99.0	0.464789	NM_021817	Q5T3J0	Missense_Mutation	SNP	ENST00000255039.1	37	CCDS1148.1	16	0.007326007326007326	15	0.03048780487804878	1	0.0027624309392265192	0	0.0	0	0.0	G	13.59	2.283640	0.40394	0.037207	2.36E-4	ENSG00000132702	ENST00000255039;ENST00000544775;ENST00000456112	T;T	0.26957	1.7;1.7	4.04	1.89	0.25635	Immunoglobulin subtype (1);Immunoglobulin-like (1);	0.225805	0.35838	N	0.002959	T	0.05090	0.0136	N	0.17379	0.485	0.32704	N	0.512539	B	0.10296	0.003	B	0.18871	0.023	T	0.29731	-1.0002	10	0.27082	T	0.32	-15.0291	7.6488	0.28336	0.0:0.1512:0.5635:0.2853	.	139	Q9GZV7	HPLN2_HUMAN	L	139;112;139	ENSP00000255039:V139L;ENSP00000388835:V139L	ENSP00000255039:V139L	V	+	1	0	HAPLN2	154860552	0.867000	0.29959	1.000000	0.80357	0.971000	0.66376	0.920000	0.28705	0.995000	0.38917	0.655000	0.94253	GTG	G|0.986;T|0.014	0.014	strong		0.692	HAPLN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081039.1	NM_021817	
GUCA1C	9626	hgsc.bcm.edu	37	3	108627024	108627024	+	Missense_Mutation	SNP	T	T	C	rs16854916	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:108627024T>C	ENST00000261047.3	-	4	607	c.475A>G	c.(475-477)Atg>Gtg	p.M159V	GUCA1C_ENST00000393963.3_Missense_Mutation_p.H172R	NM_005459.3	NP_005450.3	O95843	GUC1C_HUMAN	guanylate cyclase activator 1C	159	EF-hand 4. {ECO:0000255|PROSITE- ProRule:PRU00448}.		M -> V (in dbSNP:rs16854916).		phototransduction, visible light (GO:0007603)|positive regulation of guanylate cyclase activity (GO:0031284)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|signal transduction (GO:0007165)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)			endometrium(2)|large_intestine(1)|liver(1)|lung(8)|pancreas(1)|skin(1)	14						TCTTTTGCCATGCCATTGATA	0.398													T|||	76	0.0151757	0.056	0.0029	5008	,	,		17705	0.0		0.0	False		,,,				2504	0.0				p.M159V	NSCLC(157;1360 1999 30631 40189 44208)	Atlas-SNP	.											.	GUCA1C	39	.	0			c.A475G						PASS	.	T	VAL/MET	184,4222	119.6+/-157.3	3,178,2022	84.0	82.0	83.0		475	-0.5	0.0	3	dbSNP_123	83	1,8599	1.2+/-3.3	0,1,4299	yes	missense	GUCA1C	NM_005459.3	21	3,179,6321	CC,CT,TT		0.0116,4.1761,1.4224	benign	159/210	108627024	185,12821	2203	4300	6503	SO:0001583	missense	9626	exon4			TTGCCATGCCATT	AF110002	CCDS2954.1	3q13.1	2013-01-10			ENSG00000138472	ENSG00000138472		"""EF-hand domain containing"""	4680	protein-coding gene	gene with protein product	"""guanylyl cyclase-activating protein 3"""	605128				10037746, 11860507	Standard	NM_005459		Approved	GCAP3	uc003dxj.2	O95843	OTTHUMG00000159204	ENST00000261047.3:c.475A>G	3.37:g.108627024T>C	ENSP00000261047:p.Met159Val	101.0	0.0	0		115.0	52.0	0.452174	NM_005459	O95844|Q9UNM0	Missense_Mutation	SNP	ENST00000261047.3	37	CCDS2954.1	29|29	0.013278388278388278|0.013278388278388278	28|28	0.056910569105691054|0.056910569105691054	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	T|T	0.866|0.866	-0.733700|-0.733700	0.03111|0.03111	0.041761|0.041761	1.16E-4|1.16E-4	ENSG00000138472|ENSG00000138472	ENST00000393963|ENST00000261047	T|T	0.66638|0.71817	-0.22|-0.6	5.67|5.67	-0.534|-0.534	0.11883|0.11883	.|EF-hand-like domain (1);	.|1.183010	.|0.05826	.|N	.|0.616757	T|T	0.06508|0.06508	0.0167|0.0167	N|N	0.05280|0.05280	-0.08|-0.08	0.09310|0.09310	N|N	1|1	B|B	0.13145|0.02656	0.007|0.0	B|B	0.10450|0.01281	0.005|0.0	T|T	0.08597|0.08597	-1.0714|-1.0714	9|10	0.41790|0.07175	T|T	0.15|0.84	.|.	3.7193|3.7193	0.08450|0.08450	0.1218:0.0744:0.2242:0.5796|0.1218:0.0744:0.2242:0.5796	rs16854916;rs52837740;rs56517263;rs16854916|rs16854916;rs52837740;rs56517263;rs16854916	172|159	C9JNI2|O95843	.|GUC1C_HUMAN	R|V	172|159	ENSP00000377535:H172R|ENSP00000261047:M159V	ENSP00000377535:H172R|ENSP00000261047:M159V	H|M	-|-	2|1	0|0	GUCA1C|GUCA1C	110109714|110109714	0.002000|0.002000	0.14202|0.14202	0.000000|0.000000	0.03702|0.03702	0.322000|0.322000	0.28314|0.28314	0.442000|0.442000	0.21628|0.21628	0.073000|0.073000	0.16731|0.16731	-0.461000|-0.461000	0.05368|0.05368	CAT|ATG	T|0.982;C|0.018	0.018	strong		0.398	GUCA1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353819.1	NM_005459	
C16orf82	162083	hgsc.bcm.edu	37	16	27078547	27078547	+	lincRNA	SNP	G	G	C	rs386790113|rs201942674|rs114049498	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:27078547G>C	ENST00000505035.1	+	0	520				RP11-673P17.2_ENST00000565783.1_RNA			Q7Z2V1	TNT_HUMAN	chromosome 16 open reading frame 82																		TGCAGCACCCGAGGCCAGAGG	0.652													C|||	228	0.0455272	0.1346	0.0086	5008	,	,		16840	0.0		0.004	False		,,,				2504	0.0409				p.P77P		Atlas-SNP	.											.	.	.	.	0			c.G231C						PASS	.	C		249,4131		11,227,1952	22.0	30.0	27.0		231	3.1	0.0	16	dbSNP_132	27	73,8505		0,73,4216	no	coding-synonymous	C16orf82	NM_001145545.1		11,300,6168	CC,CG,GG		0.851,5.6849,2.485		77/155	27078547	322,12636	2190	4289	6479			162083	exon1			GCACCCGAGGCCA	BC031257		16p12.1	2013-01-24			ENSG00000234186	ENSG00000234186			30755	other	unknown						12477932	Standard	NM_001145545		Approved	TNT	uc010vcm.2	Q7Z2V1	OTTHUMG00000161986		16.37:g.27078547G>C		61.0	0.0	0		66.0	28.0	0.424242	NM_001145545	B9EGC2|Q8NEF0	Silent	SNP	ENST00000505035.1	37																																																																																				G|0.968;C|0.032	0.032	strong		0.652	C16orf82-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000366634.1	NM_001145545	
PRRC2C	23215	hgsc.bcm.edu	37	1	171553209	171553209	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:171553209C>T	ENST00000338920.4	+	29	7755	c.7518C>T	c.(7516-7518)tcC>tcT	p.S2506S	PRRC2C_ENST00000392078.3_Silent_p.S2508S|PRRC2C_ENST00000367742.3_Silent_p.S2508S|PRRC2C_ENST00000426496.2_Silent_p.S2441S	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	2506	Gln-rich.				hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										AGGCACAATCCGGTCTTGCCT	0.463																																					p.S2506S		Atlas-SNP	.											.	.	.	.	0			c.C7518T						PASS	.						181.0	172.0	175.0					1																	171553209		2203	4300	6503	SO:0001819	synonymous_variant	23215	exon29			ACAATCCGGTCTT	AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"""BAT2 domain containing 1"", ""HLA-B associated transcript 2-like 2"""	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.7518C>T	1.37:g.171553209C>T		254.0	0.0	0		272.0	133.0	0.488971	NM_015172	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Silent	SNP	ENST00000338920.4	37	CCDS1296.2	.	.	.	.	.	.	.	.	.	.	C	5.989	0.366324	0.11352	.	.	ENSG00000117523	ENST00000495585	.	.	.	5.98	-12.0	0.00017	.	.	.	.	.	T	0.19805	0.0476	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.54702	-0.8254	4	.	.	.	.	4.6701	0.12685	0.2829:0.418:0.1692:0.1299	.	.	.	.	L	989	.	.	P	+	2	0	PRRC2C	169819833	0.000000	0.05858	0.002000	0.10522	0.916000	0.54674	-2.380000	0.01066	-4.069000	0.00076	-2.084000	0.00378	CCG	.	.	none		0.463	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4	NM_015172	
CDC42BPA	8476	hgsc.bcm.edu	37	1	227348245	227348245	+	Splice_Site	SNP	G	G	A	rs34614709	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:227348245G>A	ENST00000366769.3	-	6	1983	c.692C>T	c.(691-693)aCg>aTg	p.T231M	CDC42BPA_ENST00000535525.1_Splice_Site_p.T231M|CDC42BPA_ENST00000334218.5_Splice_Site_p.T231M|CDC42BPA_ENST00000366764.2_Splice_Site_p.T231M|CDC42BPA_ENST00000366767.3_Splice_Site_p.T231M|CDC42BPA_ENST00000366765.3_Splice_Site_p.T231M|CDC42BPA_ENST00000366766.2_Splice_Site_p.T231M	NM_003607.3	NP_003598.2			CDC42 binding protein kinase alpha (DMPK-like)											NS(1)|breast(4)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(12)|lung(32)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|urinary_tract(2)	77		all_cancers(173;0.156)|Prostate(94;0.0792)				TTTATTTACCGTTCCATCTTC	0.318													G|||	29	0.00579073	0.0219	0.0	5008	,	,		16832	0.0		0.0	False		,,,				2504	0.0				p.T231M		Atlas-SNP	.											.	CDC42BPA	528	.	0			c.C692T						PASS	.	G	MET/THR,MET/THR	77,4329	68.7+/-106.4	1,75,2127	130.0	139.0	136.0		692,692	5.2	1.0	1	dbSNP_126	136	1,8599	1.2+/-3.3	0,1,4299	yes	missense-near-splice,missense-near-splice	CDC42BPA	NM_003607.3,NM_014826.4	81,81	1,76,6426	AA,AG,GG		0.0116,1.7476,0.5997	probably-damaging,probably-damaging	231/1720,231/1639	227348245	78,12928	2203	4300	6503	SO:0001630	splice_region_variant	8476	exon6			TTTACCGTTCCAT	U59305	CCDS1558.1, CCDS1559.1	1q42.11	2011-11-23	2001-11-28		ENSG00000143776	ENSG00000143776			1737	protein-coding gene	gene with protein product	"""myotonic dystrophy kinase-related Cdc42-binding kinase"""	603412	"""CDC42-binding protein kinase alpha (DMPK-like)"""				Standard	NM_003607		Approved	MRCKA, PK428, FLJ23347, KIAA0451, MRCK	uc001hqr.3	Q5VT25	OTTHUMG00000037618	ENST00000366769.3:c.693+1C>T	1.37:g.227348245G>A		311.0	0.0	0		305.0	136.0	0.445902	NM_003607		Missense_Mutation	SNP	ENST00000366769.3	37	CCDS1558.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	25.7	4.667652	0.88348	0.017476	1.16E-4	ENSG00000143776	ENST00000366769;ENST00000366767;ENST00000334218;ENST00000366766;ENST00000366764;ENST00000535525;ENST00000366765	T;T;T;T;T;T;T	0.66099	-0.19;-0.19;-0.19;-0.19;-0.19;-0.19;-0.19	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	T	0.60741	0.2292	L	0.55743	1.74	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;0.998;0.999	T	0.65084	-0.6254	10	0.22109	T	0.4	.	17.4674	0.87637	0.0:0.0:1.0:0.0	rs34614709	231;231;231;231	F5H5N0;Q5VT25-4;Q5VT25-3;Q5VT25-5	.;.;.;.	M	231	ENSP00000355731:T231M;ENSP00000355729:T231M;ENSP00000335341:T231M;ENSP00000355728:T231M;ENSP00000355726:T231M;ENSP00000443275:T231M;ENSP00000355727:T231M	ENSP00000335341:T231M	T	-	2	0	CDC42BPA	225414868	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.035000	0.93752	2.394000	0.81467	0.585000	0.79938	ACG	G|0.995;A|0.005	0.005	strong		0.318	CDC42BPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091696.1	NM_014826	Missense_Mutation
EFCAB12	90288	hgsc.bcm.edu	37	3	129137245	129137245	+	Missense_Mutation	SNP	T	T	G	rs116798859	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:129137245T>G	ENST00000505956.1	-	3	695	c.533A>C	c.(532-534)cAg>cCg	p.Q178P	EFCAB12_ENST00000326085.3_Missense_Mutation_p.Q178P	NM_207307.1	NP_997190.1	Q6NXP0	EFC12_HUMAN	EF-hand calcium binding domain 12	178							calcium ion binding (GO:0005509)										CAGCTGGAGCTGGGGCACCAT	0.607													T|||	163	0.0325479	0.1157	0.013	5008	,	,		14537	0.0		0.001	False		,,,				2504	0.0				p.Q178P		Atlas-SNP	.											.	.	.	.	0			c.A533C						PASS	.	T	PRO/GLN	316,3492		6,304,1594	31.0	30.0	30.0		533	-2.7	1.0	3	dbSNP_132	30	5,8221		0,5,4108	yes	missense	C3orf25	NM_207307.1	76	6,309,5702	GG,GT,TT		0.0608,8.2983,2.6674	probably-damaging	178/573	129137245	321,11713	1904	4113	6017	SO:0001583	missense	90288	exon3			TGGAGCTGGGGCA	AK096099	CCDS54638.1	3q21.3	2013-01-10	2012-07-20	2012-07-20	ENSG00000172771	ENSG00000172771		"""EF-hand domain containing"""	28061	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 25"""	C3orf25			Standard	NM_207307		Approved		uc003emg.3	Q6NXP0	OTTHUMG00000159464	ENST00000505956.1:c.533A>C	3.37:g.129137245T>G	ENSP00000420854:p.Gln178Pro	72.0	0.0	0		68.0	41.0	0.602941	NM_207307	Q69YX4	Missense_Mutation	SNP	ENST00000505956.1	37	CCDS54638.1	47	0.02152014652014652	41	0.08333333333333333	6	0.016574585635359115	0	0.0	0	0.0	T	13.32	2.201720	0.38905	0.082983	6.08E-4	ENSG00000172771	ENST00000505956;ENST00000326085;ENST00000503957	T;T;T	0.33438	2.47;2.47;1.41	4.82	-2.68	0.06041	.	0.623436	0.14251	N	0.331422	T	0.01353	0.0044	L	0.34521	1.04	0.23802	N	0.99681	D	0.58620	0.983	P	0.56700	0.804	T	0.02983	-1.1086	10	0.40728	T	0.16	-17.8429	1.6546	0.02779	0.4769:0.0911:0.1374:0.2946	.	178	Q6NXP0	CC025_HUMAN	P	178;178;28	ENSP00000420854:Q178P;ENSP00000324241:Q178P;ENSP00000421462:Q28P	ENSP00000324241:Q178P	Q	-	2	0	C3orf25	130619935	0.954000	0.32549	0.988000	0.46212	0.232000	0.25224	-0.068000	0.11561	-0.177000	0.10690	0.459000	0.35465	CAG	T|0.975;G|0.025	0.025	strong		0.607	EFCAB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355530.1	NM_207307	
ZCCHC18	644353	hgsc.bcm.edu	37	X	103359334	103359334	+	Missense_Mutation	SNP	C	C	T	rs61745269	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:103359334C>T	ENST00000537356.3	+	2	1946	c.532C>T	c.(532-534)Ctt>Ttt	p.L178F	SLC25A53_ENST00000357421.4_Intron|ZCCHC18_ENST00000422784.1_Intron			P0CG32	ZCC18_HUMAN	zinc finger, CCHC domain containing 18	178							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)										CTTGCAACAGCTTCTTTTAGG	0.498													C|||	164	0.0434437	0.118	0.0101	3775	,	,		14288	0.0		0.001	False		,,,				2504	0.0				p.L178F		Atlas-SNP	.											.	.	.	.	0			c.C532T						PASS	.	C	,PHE/LEU	164,1045		12,119,21,386,154	40.0	32.0	35.0		,532	2.7	0.3	X	dbSNP_129	35	1,2390		0,1,0,799,791	yes	intron,missense	MCART6,ZCCHC18	NM_001012755.3,NM_001143978.1	,22	12,120,21,1185,945	TT,TC,T,CC,C		0.0418,13.5649,4.5833	,benign	,178/404	103359334	165,3435	692	1591	2283	SO:0001583	missense	644353	exon3			CAACAGCTTCTTT	AF086548	CCDS65304.1	Xq22.2	2013-01-31	2009-02-03		ENSG00000166707	ENSG00000166707		"""Zinc fingers, CCHC domain containing"", ""Paraneoplastic Ma antigens"""	32459	protein-coding gene	gene with protein product	"""paraneoplastic Ma antigen family member 7B"""		"""zinc finger, CCHC domain containing 12 pseudogene 1"""				Standard	NM_001143978		Approved	SIZN2, PNMA7B	uc011msh.2	P0CG32	OTTHUMG00000022123	ENST00000537356.3:c.532C>T	X.37:g.103359334C>T	ENSP00000473824:p.Leu178Phe	314.0	0.0	0		259.0	148.0	0.571429	NM_001143978		Missense_Mutation	SNP	ENST00000537356.3	37																																																																																				C|0.962;T|0.038	0.038	strong		0.498	ZCCHC18-006	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471686.1	NM_001143978	
PPFIBP1	8496	hgsc.bcm.edu	37	12	27842052	27842052	+	Silent	SNP	G	G	A	rs61730962	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:27842052G>A	ENST00000318304.8	+	26	2902	c.2619G>A	c.(2617-2619)ctG>ctA	p.L873L	PPFIBP1_ENST00000542629.1_Silent_p.L842L|PPFIBP1_ENST00000537927.1_Silent_p.L720L|PPFIBP1_ENST00000228425.6_Silent_p.L867L	NM_001198916.1|NM_177444.2	NP_001185845.1|NP_803193	Q86W92	LIPB1_HUMAN	PTPRF interacting protein, binding protein 1 (liprin beta 1)	873	SAM 3. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)			PPFIBP1/ALK(3)	central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(13)|prostate(2)|skin(1)	32	Lung SC(9;0.0873)					TCAACCTTCTGATTGGGGCTG	0.473													G|||	274	0.0547125	0.2005	0.0115	5008	,	,		18229	0.0		0.001	False		,,,				2504	0.0				p.L873L		Atlas-SNP	.											.	PPFIBP1	153	.	0			c.G2619A						PASS	.	G	,,,	720,3686	299.0+/-285.6	56,608,1539	130.0	117.0	121.0		2160,2526,2601,2619	4.4	1.0	12	dbSNP_129	121	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PPFIBP1	NM_001198915.1,NM_001198916.1,NM_003622.3,NM_177444.2	,,,	56,612,5835	AA,AG,GG		0.0465,16.3414,5.5667	,,,	720/859,842/981,867/1006,873/1012	27842052	724,12282	2203	4300	6503	SO:0001819	synonymous_variant	8496	exon26			CCTTCTGATTGGG	AF034802	CCDS8713.1, CCDS55812.1, CCDS55813.1, CCDS55814.1	12p12.1	2013-01-10						"""Sterile alpha motif (SAM) domain containing"""	9249	protein-coding gene	gene with protein product		603141				9624153, 11836260	Standard	NM_003622		Approved	L2, hSGT2, hSgt2p, SGT2	uc001ric.2	Q86W92		ENST00000318304.8:c.2619G>A	12.37:g.27842052G>A		137.0	0.0	0		167.0	84.0	0.502994	NM_177444	O75336|Q86X70|Q9NY03|Q9ULJ0	Silent	SNP	ENST00000318304.8	37	CCDS55812.1																																																																																			G|0.949;A|0.051	0.051	strong		0.473	PPFIBP1-007	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000402877.1	NM_003622	
ARMC1	55156	hgsc.bcm.edu	37	8	66517549	66517549	+	Silent	SNP	T	T	C	rs16932266	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:66517549T>C	ENST00000276569.3	-	6	850	c.606A>G	c.(604-606)tcA>tcG	p.S202S	ARMC1_ENST00000458464.2_Silent_p.S100S	NM_018120.4	NP_060590.1	Q9NVT9	ARMC1_HUMAN	armadillo repeat containing 1	202					metal ion transport (GO:0030001)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)			cervix(1)|endometrium(3)|large_intestine(1)|lung(8)|skin(1)	14			Epithelial(68;0.103)|OV - Ovarian serous cystadenocarcinoma(28;0.235)			TAACCTTGGTTGATGCTATTG	0.323													T|||	109	0.0217652	0.0257	0.0288	5008	,	,		18451	0.0248		0.0159	False		,,,				2504	0.0143				p.S202S		Atlas-SNP	.											.	ARMC1	22	.	0			c.A606G						PASS	.	T		105,4301	81.4+/-119.9	2,101,2100	114.0	110.0	111.0		606	-0.1	1.0	8	dbSNP_123	111	126,8474	65.3+/-127.6	1,124,4175	no	coding-synonymous	ARMC1	NM_018120.4		3,225,6275	CC,CT,TT		1.4651,2.3831,1.7761		202/283	66517549	231,12775	2203	4300	6503	SO:0001819	synonymous_variant	55156	exon6			CTTGGTTGATGCT	BC011607	CCDS6181.1, CCDS69490.1	8q12.3	2013-02-14			ENSG00000104442	ENSG00000104442		"""Armadillo repeat containing"""	17684	protein-coding gene	gene with protein product							Standard	XM_005251264		Approved	FLJ10511, Arcp	uc003xvl.3	Q9NVT9	OTTHUMG00000164374	ENST00000276569.3:c.606A>G	8.37:g.66517549T>C		190.0	0.0	0		193.0	103.0	0.533679	NM_018120	B4E2W7|Q9H018|Q9H820	Silent	SNP	ENST00000276569.3	37	CCDS6181.1																																																																																			T|0.984;C|0.016	0.016	strong		0.323	ARMC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378480.1	NM_018120	
UBR3	130507	hgsc.bcm.edu	37	2	170684548	170684548	+	Silent	SNP	G	G	A	rs79036304	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:170684548G>A	ENST00000272793.5	+	1	581	c.531G>A	c.(529-531)gtG>gtA	p.V177V	UBR3_ENST00000418381.1_Silent_p.V177V			Q6ZT12	UBR3_HUMAN	ubiquitin protein ligase E3 component n-recognin 3 (putative)	177					embryo development (GO:0009790)|in utero embryonic development (GO:0001701)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)|suckling behavior (GO:0001967)|ubiquitin-dependent protein catabolic process (GO:0006511)	integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(3)|stomach(1)	33						ACAGCAACGTGATGCGGGAGA	0.726													g|||	320	0.0638978	0.174	0.0461	5008	,	,		9387	0.0109		0.0258	False		,,,				2504	0.0215				p.V177V		Atlas-SNP	.											.	UBR3	182	.	0			c.G531A						PASS	.						6.0	6.0	6.0					2																	170684548		685	1551	2236	SO:0001819	synonymous_variant	130507	exon1			CAACGTGATGCGG	AL834144	CCDS2238.2	2q31.1	2008-06-23	2008-06-23	2007-11-29	ENSG00000144357	ENSG00000144357		"""Ubiquitin protein ligase E3 component n-recognins"""	30467	protein-coding gene	gene with protein product		613831	"""zinc finger protein 650"""	ZNF650		17462990	Standard	NM_172070		Approved	KIAA2024, DKFZp434P117, FLJ37422	uc010zdi.2	Q6ZT12	OTTHUMG00000132229	ENST00000272793.5:c.531G>A	2.37:g.170684548G>A		26.0	0.0	0		16.0	9.0	0.5625	NM_172070	B4DZR7|Q2KHN5|Q6ZR55|Q6ZSC2|Q8IVE7|Q8ND96	Silent	SNP	ENST00000272793.5	37																																																																																				G|0.940;A|0.060	0.060	strong		0.726	UBR3-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000255290.2	NM_172070	
HSPA8	3312	hgsc.bcm.edu	37	11	122931337	122931337	+	Silent	SNP	T	T	C	rs147610984	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:122931337T>C	ENST00000532636.1	-	3	494	c.375A>G	c.(373-375)acA>acG	p.T125T	HSPA8_ENST00000533540.1_Intron|HSPA8_ENST00000534319.1_5'Flank|HSPA8_ENST00000526110.1_Silent_p.T125T|SNORD14D_ENST00000384390.1_RNA|HSPA8_ENST00000526862.1_5'Flank|HSPA8_ENST00000227378.3_Silent_p.T125T|HSPA8_ENST00000534624.1_Silent_p.T125T|HSPA8_ENST00000453788.2_Silent_p.T125T|SNORD14E_ENST00000364009.1_RNA|SNORD14C_ENST00000365382.1_RNA			P11142	HSP7C_HUMAN	heat shock 70kDa protein 8	125					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone mediated protein folding requiring cofactor (GO:0051085)|clathrin coat disassembly (GO:0072318)|gene expression (GO:0010467)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|negative regulation of fibril organization (GO:1902904)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotransmitter secretion (GO:0007269)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein refolding (GO:0042026)|regulation of cell cycle (GO:0051726)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	blood microparticle (GO:0072562)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Prp19 complex (GO:0000974)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)			breast(1)|central_nervous_system(7)|endometrium(1)|kidney(9)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	36		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		CCTTCATCTTTGTCAGAACCA	0.488													T|||	41	0.0081869	0.0303	0.0014	5008	,	,		19288	0.0		0.0	False		,,,				2504	0.0				p.T125T	Colon(21;486 594 5900 6733 14272)	Atlas-SNP	.											.	HSPA8	168	.	0			c.A375G						PASS	.	T	,	123,4281	91.6+/-130.3	1,121,2080	94.0	97.0	96.0		375,375	-2.6	1.0	11	dbSNP_134	96	0,8598		0,0,4299	no	coding-synonymous,coding-synonymous	HSPA8	NM_006597.4,NM_153201.2	,	1,121,6379	CC,CT,TT		0.0,2.7929,0.946	,	125/647,125/494	122931337	123,12879	2202	4299	6501	SO:0001819	synonymous_variant	3312	exon3			CATCTTTGTCAGA	Y00371	CCDS8440.1, CCDS44754.1	11q24.1	2011-09-02	2002-08-29		ENSG00000109971	ENSG00000109971		"""Heat shock proteins / HSP70"""	5241	protein-coding gene	gene with protein product		600816	"""heat shock 70kD protein 8"""	HSPA10		8530083, 3037489	Standard	NM_006597		Approved	HSC71, HSC70, HSP73	uc001pyo.3	P11142	OTTHUMG00000166030	ENST00000532636.1:c.375A>G	11.37:g.122931337T>C		118.0	0.0	0		132.0	56.0	0.424242	NM_006597	Q9H3R6	Silent	SNP	ENST00000532636.1	37	CCDS8440.1																																																																																			T|0.989;C|0.011	0.011	strong		0.488	HSPA8-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387515.1		
ZNF433	163059	hgsc.bcm.edu	37	19	12127370	12127370	+	Silent	SNP	G	G	A	rs79787738	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12127370G>A	ENST00000344980.6	-	4	482	c.312C>T	c.(310-312)tgC>tgT	p.C104C	ZNF433_ENST00000419886.2_Silent_p.C69C|CTD-2006C1.2_ENST00000476474.1_RNA|CTD-2006C1.2_ENST00000406892.2_RNA|CTD-2006C1.2_ENST00000495324.1_RNA	NM_001080411.1	NP_001073880.1	Q8N7K0	ZN433_HUMAN	zinc finger protein 433	104					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(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(1)|prostate(1)|skin(1)	14						CACTGCTTTCGCATGATTTTA	0.408													G|||	15	0.00299521	0.0106	0.0014	5008	,	,		19210	0.0		0.0	False		,,,				2504	0.0				p.C104C		Atlas-SNP	.											.	ZNF433	49	.	0			c.C312T						PASS	.	G		67,4277		0,67,2105	93.0	93.0	93.0		312	-2.4	0.0	19	dbSNP_132	93	2,8572		0,2,4285	no	coding-synonymous	ZNF433	NM_001080411.1		0,69,6390	AA,AG,GG		0.0233,1.5424,0.5341		104/674	12127370	69,12849	2172	4287	6459	SO:0001819	synonymous_variant	163059	exon4			GCTTTCGCATGAT	AK098300	CCDS45983.1	19p13.13	2013-01-08			ENSG00000197647	ENSG00000197647		"""Zinc fingers, C2H2-type"", ""-"""	20811	protein-coding gene	gene with protein product							Standard	NM_001080411		Approved	FLJ40981	uc002msy.1	Q8N7K0	OTTHUMG00000156427	ENST00000344980.6:c.312C>T	19.37:g.12127370G>A		167.0	0.0	0		161.0	72.0	0.447205	NM_001080411	Q86VX3	Silent	SNP	ENST00000344980.6	37	CCDS45983.1																																																																																			G|0.994;A|0.006	0.006	strong		0.408	ZNF433-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403716.1	NM_152602	
ZNF585B	92285	hgsc.bcm.edu	37	19	37697988	37697988	+	Missense_Mutation	SNP	T	T	C	rs145040657		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:37697988T>C	ENST00000532828.2	-	2	277	c.26A>G	c.(25-27)cAg>cGg	p.Q9R	ZNF585B_ENST00000527838.1_Missense_Mutation_p.Q9R|ZNF585B_ENST00000534363.1_5'Flank|CTC-454I21.3_ENST00000585860.2_Missense_Mutation_p.Q9R	NM_152279.3	NP_689492.3	Q52M93	Z585B_HUMAN	zinc finger protein 585B	9					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(3)|endometrium(1)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)	29			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			TGAGGATTTCTGGGGTGAGGT	0.532													T|||	1	0.000199681	0.0008	0.0	5008	,	,		19866	0.0		0.0	False		,,,				2504	0.0				p.Q9R	Melanoma(93;882 1454 18863 28917 48427)	Atlas-SNP	.											.	ZNF585B	91	.	0			c.A26G						PASS	.	T	ARG/GLN	5,4401	9.9+/-24.2	0,5,2198	120.0	104.0	109.0		26	0.6	0.0	19	dbSNP_134	109	0,8600		0,0,4300	yes	missense	ZNF585B	NM_152279.3	43	0,5,6498	CC,CT,TT		0.0,0.1135,0.0384	benign	9/770	37697988	5,13001	2203	4300	6503	SO:0001583	missense	92285	exon2			GATTTCTGGGGTG	AK027834	CCDS12500.1	19q13.13	2013-01-08				ENSG00000245680		"""Zinc fingers, C2H2-type"", ""-"""	30948	protein-coding gene	gene with protein product						12477932	Standard	NM_152279		Approved	FLJ14928, SZFP41	uc002ofq.3	Q52M93		ENST00000532828.2:c.26A>G	19.37:g.37697988T>C	ENSP00000433773:p.Gln9Arg	76.0	0.0	0		77.0	39.0	0.506494	NM_152279	Q8IZD3|Q96JW6	Missense_Mutation	SNP	ENST00000532828.2	37	CCDS12500.1	.	.	.	.	.	.	.	.	.	.	T	8.991	0.977714	0.18812	0.001135	0.0	ENSG00000245680	ENST00000532828;ENST00000527838	T;T	0.06933	3.24;6.86	1.79	0.647	0.17796	.	.	.	.	.	T	0.06690	0.0171	L	0.52573	1.65	0.09310	N	1	B	0.31655	0.334	B	0.15870	0.014	T	0.32534	-0.9903	9	0.87932	D	0	.	3.6073	0.08048	0.374:0.0:0.0:0.626	.	9	Q52M93	Z585B_HUMAN	R	9	ENSP00000433773:Q9R;ENSP00000435268:Q9R	ENSP00000432760:Q9R	Q	-	2	0	ZNF585B	42389828	0.048000	0.20356	0.004000	0.12327	0.700000	0.40528	0.118000	0.15605	0.117000	0.18138	0.260000	0.18958	CAG	T|1.000;C|0.000	0.000	strong		0.532	ZNF585B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388272.2	NM_152279	
EOMES	8320	hgsc.bcm.edu	37	3	27758756	27758756	+	Silent	SNP	G	G	A	rs6783101	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:27758756G>A	ENST00000295743.4	-	6	2069	c.1866C>T	c.(1864-1866)ccC>ccT	p.P622P	EOMES_ENST00000449599.1_Silent_p.P641P|EOMES_ENST00000537516.1_Silent_p.P346P|EOMES_ENST00000461503.1_5'Flank			O95936	EOMES_HUMAN	eomesodermin	622	Required for transcription activation. {ECO:0000250}.				brain development (GO:0007420)|cardioblast differentiation (GO:0010002)|CD8-positive, alpha-beta T cell differentiation involved in immune response (GO:0002302)|cell differentiation involved in embryonic placenta development (GO:0060706)|cerebral cortex neuron differentiation (GO:0021895)|cerebral cortex regionalization (GO:0021796)|endoderm formation (GO:0001706)|endodermal cell fate specification (GO:0001714)|interferon-gamma production (GO:0032609)|mesoderm formation (GO:0001707)|mesodermal to mesenchymal transition involved in gastrulation (GO:0060809)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|olfactory bulb development (GO:0021772)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|skeletal muscle cell differentiation (GO:0035914)|stem cell maintenance (GO:0019827)|trophectodermal cell differentiation (GO:0001829)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(1)	21						TGATGGAAGGGGGTGTCTCTA	0.463													G|||	182	0.0363419	0.1316	0.0115	5008	,	,		18478	0.0		0.0	False		,,,				2504	0.0				p.P622P		Atlas-SNP	.											.	EOMES	65	.	0			c.C1866T						PASS	.	G		548,3858	247.5+/-255.7	26,496,1681	118.0	122.0	121.0		1866	-1.7	1.0	3	dbSNP_116	121	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous	EOMES	NM_005442.2		26,503,5974	AA,AG,GG		0.0814,12.4376,4.2673		622/687	27758756	555,12451	2203	4300	6503	SO:0001819	synonymous_variant	8320	exon6			GGAAGGGGGTGTC	BC025363	CCDS2646.1, CCDS63585.1	3p24.1	2011-06-13	2010-06-24		ENSG00000163508	ENSG00000163508		"""T-boxes"""	3372	protein-coding gene	gene with protein product	"""T-box brain2"""	604615	"""eomesodermin (Xenopus laevis) homolog"""			9888994, 9434949	Standard	NM_005442		Approved	TBR2	uc003cdy.4	O95936	OTTHUMG00000130570	ENST00000295743.4:c.1866C>T	3.37:g.27758756G>A		197.0	0.0	0		212.0	99.0	0.466981	NM_005442	B7Z4I2|B7ZA51|G3XAI5|Q8TAZ2|Q9UPM7	Silent	SNP	ENST00000295743.4	37	CCDS2646.1																																																																																			G|0.963;A|0.037	0.037	strong		0.463	EOMES-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252995.1	NM_005442	
COG7	91949	hgsc.bcm.edu	37	16	23403744	23403744	+	Silent	SNP	A	A	G	rs8057712	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:23403744A>G	ENST00000307149.5	-	16	2288	c.2103T>C	c.(2101-2103)ccT>ccC	p.P701P	COG7_ENST00000569635.1_Intron	NM_153603.3	NP_705831.1	P83436	COG7_HUMAN	component of oligomeric golgi complex 7	701					intracellular protein transport (GO:0006886)|protein glycosylation (GO:0006486)|protein localization to Golgi apparatus (GO:0034067)|protein localization to organelle (GO:0033365)|protein stabilization (GO:0050821)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	Golgi apparatus (GO:0005794)|Golgi transport complex (GO:0017119)|membrane (GO:0016020)				breast(1)|central_nervous_system(1)|endometrium(7)|large_intestine(9)|liver(1)|lung(7)|urinary_tract(1)	27				GBM - Glioblastoma multiforme(48;0.0401)		GGCTCAGCTCAGGGATCTGTA	0.597													G|||	540	0.107827	0.2625	0.1268	5008	,	,		18783	0.0169		0.0258	False		,,,				2504	0.0634				p.P701P		Atlas-SNP	.											COG7,NS,malignant_melanoma,-2,1	COG7	62	1	0			c.T2103C						PASS	.	G		947,3447	733.6+/-410.5	98,751,1348	107.0	92.0	97.0		2103	-11.0	0.3	16	dbSNP_116	97	254,8346	807.9+/-407.2	4,246,4050	no	coding-synonymous	COG7	NM_153603.3		102,997,5398	GG,GA,AA		2.9535,21.5521,9.2427		701/771	23403744	1201,11793	2197	4300	6497	SO:0001819	synonymous_variant	91949	exon16			CAGCTCAGGGATC	AF070568	CCDS10610.1	16p12.2	2008-02-05			ENSG00000168434	ENSG00000168434		"""Components of oligomeric golgi complex"""	18622	protein-coding gene	gene with protein product		606978				11980916	Standard	NM_153603		Approved		uc002dlo.3	P83436	OTTHUMG00000094807	ENST00000307149.5:c.2103T>C	16.37:g.23403744A>G		127.0	0.0	0		132.0	59.0	0.44697	NM_153603	Q6UWU7	Silent	SNP	ENST00000307149.5	37	CCDS10610.1																																																																																			A|0.910;G|0.090	0.090	strong		0.597	COG7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211625.1		
PPIAL4G	644591	hgsc.bcm.edu	37	1	143767730	143767730	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:143767730C>T	ENST00000419275.1	-	1	151	c.119G>A	c.(118-120)aGc>aAc	p.S40N		NM_001123068.1	NP_001116540.1	A2BFH1	PAL4G_HUMAN	peptidylprolyl isomerase A (cyclophilin A)-like 4G	40	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				protein folding (GO:0006457)	cytoplasm (GO:0005737)	peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|endometrium(2)|kidney(1)|lung(8)|ovary(1)|skin(1)	14						CTCTCCAGTGCTCAGAGCACG	0.473																																					p.S40N		Atlas-SNP	.											.	PPIAL4G	22	.	0			c.G119A						PASS	.						84.0	81.0	82.0					1																	143767730		1568	3562	5130	SO:0001583	missense	644591	exon1			CCAGTGCTCAGAG		CCDS41375.1, CCDS41375.2	1q21.1	2010-06-03			ENSG00000236334	ENSG00000236334			33996	protein-coding gene	gene with protein product							Standard	NM_001123068		Approved		uc001ejt.3	A2BFH1	OTTHUMG00000013629	ENST00000419275.1:c.119G>A	1.37:g.143767730C>T	ENSP00000393845:p.Ser40Asn	1116.0	0.0	0		1225.0	155.0	0.126531	NM_001123068	A1L431	Missense_Mutation	SNP	ENST00000419275.1	37	CCDS41375.1	.	.	.	.	.	.	.	.	.	.	.	14.94	2.685463	0.47991	.	.	ENSG00000236334	ENST00000419275	T	0.44482	0.92	0.523	-0.795	0.10915	Peptidyl-prolyl cis-trans isomerase, cyclophilin-type (3);Cyclophilin-like (1);	0.235838	0.42682	U	0.000663	T	0.16342	0.0393	L	0.49571	1.57	0.23010	N	0.99844	B	0.22480	0.07	B	0.35114	0.196	T	0.35475	-0.9787	10	0.35671	T	0.21	.	4.7838	0.13215	0.0:0.7163:0.0:0.2837	.	40	A2BFH1	PAL4G_HUMAN	N	40	ENSP00000393845:S40N	ENSP00000393845:S40N	S	-	2	0	PPIAL4G	142559253	1.000000	0.71417	0.814000	0.32528	0.857000	0.48899	2.074000	0.41529	-0.252000	0.09528	0.403000	0.27427	AGC	.	.	none		0.473	PPIAL4G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037969.1	NM_001123068	
GRM8	2918	hgsc.bcm.edu	37	7	126173902	126173902	+	Missense_Mutation	SNP	G	G	C	rs61753365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:126173902G>C	ENST00000339582.2	-	9	2342	c.1534C>G	c.(1534-1536)Ccg>Gcg	p.P512A	GRM8_ENST00000480995.1_Intron|GRM8_ENST00000358373.3_Missense_Mutation_p.P512A|GRM8_ENST00000444921.2_Missense_Mutation_p.P512A			O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8	512					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|negative regulation of cAMP biosynthetic process (GO:0030818)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(16)|lung(62)|ovary(5)|pancreas(1)|prostate(1)|skin(14)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(4)	125		Prostate(267;0.186)				ACAGACGCCGGGTGAGTATGT	0.488										HNSCC(24;0.065)			G|||	89	0.0177716	0.0635	0.0072	5008	,	,		17794	0.0		0.0	False		,,,				2504	0.0				p.P512A		Atlas-SNP	.											GRM8,NS,carcinoma,+2,1	GRM8	377	1	0			c.C1534G						scavenged	.	G	ALA/PRO,ALA/PRO	274,4132	149.2+/-183.4	11,252,1940	53.0	57.0	56.0		1534,1534	5.8	1.0	7	dbSNP_129	56	3,8597		0,3,4297	yes	missense,missense	GRM8	NM_000845.2,NM_001127323.1	27,27	11,255,6237	CC,CG,GG		0.0349,6.2188,2.1298	probably-damaging,probably-damaging	512/909,512/909	126173902	277,12729	2203	4300	6503	SO:0001583	missense	2918	exon8			ACGCCGGGTGAGT		CCDS5794.1, CCDS47696.1	7q31.3-q32.1	2012-08-29			ENSG00000179603	ENSG00000179603		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4600	protein-coding gene	gene with protein product		601116				8824806	Standard	NM_000845		Approved	GLUR8, GPRC1H, mGlu8, MGLUR8	uc003vlr.2	O00222	OTTHUMG00000022888	ENST00000339582.2:c.1534C>G	7.37:g.126173902G>C	ENSP00000344173:p.Pro512Ala	99.0	1.0	0.010101		111.0	54.0	0.486486	NM_000845	A4D0Y3|B0FZ74|B0M0L0|O15493|O95945|O95946|Q3MIV9|Q52M02|Q6J165	Missense_Mutation	SNP	ENST00000339582.2	37	CCDS5794.1	32	0.014652014652014652	29	0.05894308943089431	3	0.008287292817679558	0	0.0	0	0.0	G	20.9	4.059053	0.76074	0.062188	3.49E-4	ENSG00000179603	ENST00000339582;ENST00000444921;ENST00000358373	D;D;D	0.92699	-3.09;-3.09;-3.09	5.8	5.8	0.92144	GPCR, family 3, nine cysteines domain (1);	0.000000	0.85682	D	0.000000	D	0.85805	0.5782	H	0.94582	3.555	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	D	0.86401	0.1742	10	0.87932	D	0	.	19.0428	0.93008	0.0:0.0:1.0:0.0	rs61753365	512;512	O00222-2;O00222	.;GRM8_HUMAN	A	512	ENSP00000344173:P512A;ENSP00000409790:P512A;ENSP00000351142:P512A	ENSP00000344173:P512A	P	-	1	0	GRM8	125961138	1.000000	0.71417	0.971000	0.41717	0.816000	0.46133	9.859000	0.99545	2.758000	0.94735	0.643000	0.83706	CCG	G|0.968;C|0.032	0.032	strong		0.488	GRM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059209.4		
TMEM64	169200	hgsc.bcm.edu	37	8	91638019	91638019	+	Silent	SNP	T	T	C	rs61741096	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:91638019T>C	ENST00000458549.2	-	3	1200	c.1023A>G	c.(1021-1023)gtA>gtG	p.V341V	TMEM64_ENST00000519519.1_Silent_p.V80V|TMEM64_ENST00000418210.2_Silent_p.V289V	NM_001008495.3	NP_001008495.2	Q6YI46	TMM64_HUMAN	transmembrane protein 64	341					cytosolic calcium ion homeostasis (GO:0051480)|positive regulation of bone resorption (GO:0045780)|positive regulation of osteoclast differentiation (GO:0045672)|regulation of ATPase activity (GO:0043462)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)	2			BRCA - Breast invasive adenocarcinoma(11;0.0598)			TTTCACAAGCTACAATAGCTG	0.353													T|||	24	0.00479233	0.0174	0.0	5008	,	,		17444	0.0		0.001	False		,,,				2504	0.0				p.V341V		Atlas-SNP	.											.	TMEM64	31	.	0			c.A1023G						PASS	.	T	,	57,4349	52.9+/-88.7	0,57,2146	95.0	87.0	89.0		1023,867	0.2	1.0	8	dbSNP_129	89	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous	TMEM64	NM_001008495.3,NM_001146273.1	,	0,58,6445	CC,CT,TT		0.0116,1.2937,0.4459	,	341/381,289/329	91638019	58,12948	2203	4300	6503	SO:0001819	synonymous_variant	169200	exon3			ACAAGCTACAATA	AL834364	CCDS34920.2, CCDS55260.1	8q21.3	2005-08-09			ENSG00000180694	ENSG00000180694			25441	protein-coding gene	gene with protein product							Standard	NM_001008495		Approved	DKFZp762C1112	uc003yen.2	Q6YI46	OTTHUMG00000157185	ENST00000458549.2:c.1023A>G	8.37:g.91638019T>C		156.0	0.0	0		151.0	68.0	0.450331	NM_001008495	B4DUC0|F5GXM4|Q2HIZ7|Q8N3G6	Silent	SNP	ENST00000458549.2	37	CCDS34920.2																																																																																			T|0.996;C|0.004	0.004	strong		0.353	TMEM64-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347825.1	NM_001008495	
SLX4	84464	hgsc.bcm.edu	37	16	3640893	3640893	+	Missense_Mutation	SNP	C	C	A	rs79448721	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:3640893C>A	ENST00000294008.3	-	12	3386	c.2746G>T	c.(2746-2748)Gcc>Tcc	p.A916S		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	916	Interaction with PLK1 and TERF2-TERF2IP.				DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						GTGGTGGCGGCCTCATCTCTT	0.657								Direct reversal of damage					C|||	53	0.0105831	0.0393	0.0014	5008	,	,		15331	0.0		0.0	False		,,,				2504	0.0				p.A916S		Atlas-SNP	.											.	SLX4	173	.	0			c.G2746T						PASS	.	C	SER/ALA	146,4248	101.2+/-139.8	3,140,2054	88.0	89.0	88.0		2746	-4.9	0.0	16	dbSNP_131	88	1,8599	1.2+/-3.3	0,1,4299	yes	missense	SLX4	NM_032444.2	99	3,141,6353	AA,AC,CC		0.0116,3.3227,1.1313	benign	916/1835	3640893	147,12847	2197	4300	6497	SO:0001583	missense	84464	exon12			TGGCGGCCTCATC	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.2746G>T	16.37:g.3640893C>A	ENSP00000294008:p.Ala916Ser	308.0	0.0	0		343.0	168.0	0.489796	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	18	0.008241758241758242	17	0.034552845528455285	1	0.0027624309392265192	0	0.0	0	0.0	C	6.127	0.391716	0.11581	0.033227	1.16E-4	ENSG00000188827	ENST00000294008	T	0.01139	5.28	5.04	-4.9	0.03094	.	1.567630	0.03656	N	0.241881	T	0.00412	0.0013	L	0.43152	1.355	0.09310	N	1	B	0.14438	0.01	B	0.11329	0.006	T	0.48525	-0.9028	10	0.09843	T	0.71	.	3.8877	0.09105	0.3555:0.2957:0.0:0.3488	.	916	Q8IY92	SLX4_HUMAN	S	916	ENSP00000294008:A916S	ENSP00000294008:A916S	A	-	1	0	SLX4	3580894	0.004000	0.15560	0.000000	0.03702	0.009000	0.06853	-0.251000	0.08818	-1.230000	0.02561	0.561000	0.74099	GCC	C|0.990;A|0.010	0.010	strong		0.657	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
CDH23	64072	hgsc.bcm.edu	37	10	73377069	73377069	+	Silent	SNP	C	C	T	rs7903475	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73377069C>T	ENST00000224721.6	+	10	1073	c.1068C>T	c.(1066-1068)tcC>tcT	p.S356S	CDH23_ENST00000398842.3_Silent_p.S351S|CDH23_ENST00000461841.3_Silent_p.S396S|CDH23_ENST00000398809.4_Silent_p.S351S|CDH23_ENST00000299366.7_Silent_p.S396S	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	351	Cadherin 4. {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						TCAACAGCTCCGAGTACAGCG	0.547													C|||	368	0.0734824	0.2625	0.0259	5008	,	,		21110	0.0		0.003	False		,,,				2504	0.0				p.S351S		Atlas-SNP	.											.	CDH23	365	.	0			c.C1053T						PASS	.	C	,,,,	967,3407	328.0+/-300.3	116,735,1336	83.0	86.0	85.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1053,1053,1053,1053,1053	-10.9	0.2	10	dbSNP_116	85	12,8568	7.7+/-29.5	0,12,4278	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CDH23	NM_001171930.1,NM_001171931.1,NM_001171932.1,NM_022124.5,NM_052836.3	,,,,	116,747,5614	TT,TC,CC		0.1399,22.1079,7.5575	,,,,	351/1382,351/1062,351/407,351/3355,351/531	73377069	979,11975	2187	4290	6477	SO:0001819	synonymous_variant	64072	exon11			CAGCTCCGAGTAC	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.1068C>T	10.37:g.73377069C>T		112.0	0.0	0		108.0	52.0	0.481481	NM_052836	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																				C|0.932;T|0.068	0.068	strong		0.547	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
STARD8	9754	hgsc.bcm.edu	37	X	67938392	67938392	+	Missense_Mutation	SNP	C	C	T	rs58255923	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:67938392C>T	ENST00000252336.6	+	5	1768	c.1396C>T	c.(1396-1398)Ccc>Tcc	p.P466S	STARD8_ENST00000374597.3_Missense_Mutation_p.P466S|STARD8_ENST00000374599.3_Missense_Mutation_p.P546S	NM_014725.4	NP_055540.2	Q92502	STAR8_HUMAN	StAR-related lipid transfer (START) domain containing 8	466				P -> S (in Ref. 1; BAA11506). {ECO:0000305}.	regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)	GTPase activator activity (GO:0005096)|lipid binding (GO:0008289)			NS(2)|breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(2)	50						GGCTGCGGGGCCCCTGGCTGG	0.587													C|||	148	0.0392053	0.0991	0.0173	3775	,	,		10820	0.0		0.005	False		,,,				2504	0.0				p.P546S		Atlas-SNP	.											.	STARD8	282	.	0			c.C1636T						PASS	.	C	SER/PRO,SER/PRO,SER/PRO	468,3367		23,336,86,1273,485	46.0	39.0	41.0		1636,1396,1396	1.8	0.0	X	dbSNP_129	41	22,6706		0,15,7,2413,1865	yes	missense,missense,missense	STARD8	NM_001142503.2,NM_001142504.2,NM_014725.4	74,74,74	23,351,93,3686,2350	TT,TC,T,CC,C		0.327,12.2034,4.6388	benign,benign,benign	546/1104,466/1024,466/1024	67938392	490,10073	2203	4300	6503	SO:0001583	missense	9754	exon6			GCGGGGCCCCTGG	D80011	CCDS14390.1, CCDS48134.1	Xq13.1	2011-09-13	2007-08-16		ENSG00000130052	ENSG00000130052		"""Rho GTPase activating proteins"", ""StAR-related lipid transfer (START) domain containing"""	19161	protein-coding gene	gene with protein product		300689	"""START domain containing 8"""			8724849	Standard	NM_001142504		Approved	KIAA0189, ARHGAP38	uc004dxb.3	Q92502	OTTHUMG00000021748	ENST00000252336.6:c.1396C>T	X.37:g.67938392C>T	ENSP00000252336:p.Pro466Ser	156.0	0.0	0		147.0	75.0	0.510204	NM_001142503	A8K6T2|D3DVT9|Q5JST0|Q68DG7	Missense_Mutation	SNP	ENST00000252336.6	37	CCDS14390.1	48	0.028933092224231464	28	0.059322033898305086	5	0.014124293785310734	0	0.0	1	0.0013192612137203166	C	1.597	-0.527487	0.04141	0.122034	0.00327	ENSG00000130052	ENST00000252336;ENST00000374599;ENST00000374597	T;T;T	0.06218	3.33;3.33;3.33	4.26	1.76	0.24704	.	0.487629	0.17593	N	0.168718	T	0.00039	0.0001	N	0.00347	-1.61	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.39722	-0.9600	9	0.06494	T	0.89	.	3.9538	0.09380	0.0:0.1325:0.2824:0.5851	rs58255923;rs61736965	546;466	Q92502-2;Q92502	.;STAR8_HUMAN	S	466;546;466	ENSP00000252336:P466S;ENSP00000363727:P546S;ENSP00000363725:P466S	ENSP00000252336:P466S	P	+	1	0	STARD8	67855117	0.000000	0.05858	0.002000	0.10522	0.932000	0.56968	0.017000	0.13399	0.106000	0.17784	-0.340000	0.08031	CCC	C|0.955;T|0.045	0.045	strong		0.587	STARD8-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057026.2	NM_014725	
SSPO	23145	hgsc.bcm.edu	37	7	149526071	149526071	+	RNA	SNP	G	G	A	rs142321773	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149526071G>A	ENST00000378016.2	+	0	15128							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CCCTCTTGCCGCAGGGAGGCT	0.667													G|||	21	0.00419329	0.0159	0.0	5008	,	,		14491	0.0		0.0	False		,,,				2504	0.0				p.R5042H		Atlas-SNP	.											.	.	.	.	0			c.G15125A						PASS	.	G	HIS/ARG	46,4080		1,44,2018	42.0	53.0	49.0		15144	-1.8	0.0	7	dbSNP_134	49	1,8405		0,1,4202	no	missense	SSPO	NM_198455.2	29	1,45,6220	AA,AG,GG		0.0119,1.1149,0.375	benign	5042/5148	149526071	47,12485	2063	4203	6266			23145	exon107			CTTGCCGCAGGGA	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149526071G>A		129.0	0.0	0		114.0	56.0	0.491228	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				G|0.997;A|0.003	0.003	strong		0.667	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
SYTL2	54843	hgsc.bcm.edu	37	11	85435742	85435742	+	Intron	SNP	C	C	T	rs146372321	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:85435742C>T	ENST00000528231.1	-	7	1737				SYTL2_ENST00000316356.4_Intron|SYTL2_ENST00000525423.1_Silent_p.K586K|SYTL2_ENST00000527523.1_Intron|SYTL2_ENST00000354566.3_Silent_p.K586K|SYTL2_ENST00000389960.4_Intron|SYTL2_ENST00000524452.1_Intron|SYTL2_ENST00000359152.5_Silent_p.K1110K	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2						exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		GAGCCTCGGCCTTTTCTACTG	0.443													C|||	30	0.00599042	0.0219	0.0014	5008	,	,		18228	0.0		0.0	False		,,,				2504	0.0				p.K586K		Atlas-SNP	.											.	SYTL2	231	.	0			c.G1758A						PASS	.	C	,,,,	79,4327	62.3+/-99.4	0,79,2124	67.0	65.0	66.0		,,,1758,1758	1.0	0.1	11	dbSNP_134	66	0,8598		0,0,4299	no	intron,intron,intron,coding-synonymous,coding-synonymous	SYTL2	NM_001162951.1,NM_001162953.1,NM_032943.3,NM_206927.2,NM_206928.2	,,,,	0,79,6423	TT,TC,CC		0.0,1.793,0.6075	,,,,	,,,586/1273,586/1257	85435742	79,12925	2203	4299	6502	SO:0001627	intron_variant	54843	exon1			CTCGGCCTTTTCT	AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"""chromosome 11 synaptotagmin"", ""breast cancer-associated antigen SGA-72M"", ""protein phosphatase 1, regulatory subunit 151"""	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.1459+3196G>A	11.37:g.85435742C>T		117.0	0.0	0		117.0	47.0	0.401709	NM_206927	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Silent	SNP	ENST00000528231.1	37	CCDS53688.1																																																																																			C|0.995;T|0.005	0.005	strong		0.443	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927	
KIAA1683	80726	hgsc.bcm.edu	37	19	18368748	18368748	+	Missense_Mutation	SNP	C	C	T	rs61740685		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:18368748C>T	ENST00000600328.3	-	4	2978	c.2785G>A	c.(2785-2787)Gca>Aca	p.A929T	KIAA1683_ENST00000600359.3_Missense_Mutation_p.A883T|PDE4C_ENST00000596647.1_5'Flank|KIAA1683_ENST00000392413.4_Missense_Mutation_p.A1116T|PDE4C_ENST00000355502.3_5'Flank			Q9H0B3	K1683_HUMAN	KIAA1683	929	IQ 2. {ECO:0000255|PROSITE- ProRule:PRU00116}.					mitochondrion (GO:0005739)|nucleus (GO:0005634)				breast(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	37						GTGATCACTGCGAGGATGCGG	0.677													C|||	1	0.000199681	0.0	0.0	5008	,	,		16152	0.0		0.001	False		,,,				2504	0.0				p.A1116T		Atlas-SNP	.											.	KIAA1683	190	.	0			c.G3346A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA	1,4401	2.1+/-5.4	0,1,2200	58.0	57.0	57.0		3346,2647,2785	3.5	0.0	19	dbSNP_129	57	6,8590	5.0+/-18.6	0,6,4292	yes	missense,missense,missense	KIAA1683	NM_001145304.1,NM_001145305.1,NM_025249.3	58,58,58	0,7,6492	TT,TC,CC		0.0698,0.0227,0.0539	probably-damaging,probably-damaging,probably-damaging	1116/1368,883/1135,929/1181	18368748	7,12991	2201	4298	6499	SO:0001583	missense	80726	exon4			TCACTGCGAGGAT	AB051470	CCDS32958.1, CCDS46017.1, CCDS46018.1	19p13.1	2008-02-05				ENSG00000130518			29350	protein-coding gene	gene with protein product						11214970, 11230166	Standard	NM_025249		Approved		uc010ebn.2	Q9H0B3		ENST00000600328.3:c.2785G>A	19.37:g.18368748C>T	ENSP00000470780:p.Ala929Thr	99.0	0.0	0		84.0	40.0	0.47619	NM_001145304	B4DYH2|E9PDE0|E9PH54|Q2KHR5|Q8N4G8|Q96M14|Q9C0I0	Missense_Mutation	SNP	ENST00000600328.3	37	CCDS32958.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	18.27	3.587572	0.66105	2.27E-4	6.98E-4	ENSG00000130518	ENST00000392413;ENST00000359737;ENST00000427634;ENST00000392412;ENST00000411671	T;T;T	0.46819	0.86;0.86;0.86	3.5	3.5	0.40072	.	0.000000	0.32671	N	0.005798	T	0.67373	0.2886	M	0.83603	2.65	0.09310	N	1	D;D	0.89917	1.0;0.999	D;D	0.83275	0.992;0.996	T	0.57877	-0.7735	10	0.51188	T	0.08	-16.8658	10.7032	0.45939	0.0:1.0:0.0:0.0	.	1116;929	E9PDE0;Q9H0B3	.;K1683_HUMAN	T	1116;929;883;193;543	ENSP00000376213:A1116T;ENSP00000352774:A929T;ENSP00000404501:A883T	ENSP00000352774:A929T	A	-	1	0	KIAA1683	18229748	0.809000	0.29036	0.021000	0.16686	0.006000	0.05464	3.249000	0.51437	1.971000	0.57363	0.313000	0.20887	GCA	C|0.999;T|0.001	0.001	strong		0.677	KIAA1683-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466312.3		
FAM47C	442444	hgsc.bcm.edu	37	X	37028762	37028762	+	Missense_Mutation	SNP	C	C	G	rs61730910	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:37028762C>G	ENST00000358047.3	+	1	2331	c.2279C>G	c.(2278-2280)tCt>tGt	p.S760C		NM_001013736.2	NP_001013758.1	Q5HY64	FA47C_HUMAN	family with sequence similarity 47, member C	760										breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	120						ACTCGCGTATCTCATCTCCGC	0.632													c|||	23	0.00609272	0.0166	0.0014	3775	,	,		11549	0.0		0.0	False		,,,				2504	0.0				p.S760C		Atlas-SNP	.											.	FAM47C	267	.	0			c.C2279G						PASS	.	C	CYS/SER	66,3767		3,52,8,1576,563	46.0	44.0	45.0		2279	0.9	0.0	X	dbSNP_129	45	0,6728		0,0,0,2428,1872	yes	missense	FAM47C	NM_001013736.2	112	3,52,8,4004,2435	GG,GC,G,CC,C		0.0,1.7219,0.6249	probably-damaging	760/1036	37028762	66,10495	2202	4300	6502	SO:0001583	missense	442444	exon1			GCGTATCTCATCT	AK125992	CCDS35227.1	Xp21.1	2006-07-04			ENSG00000198173	ENSG00000198173			25301	protein-coding gene	gene with protein product							Standard	NM_001013736		Approved		uc004ddl.2	Q5HY64	OTTHUMG00000024025	ENST00000358047.3:c.2279C>G	X.37:g.37028762C>G	ENSP00000367913:p.Ser760Cys	123.0	0.0	0		150.0	80.0	0.533333	NM_001013736	Q6ZU46	Missense_Mutation	SNP	ENST00000358047.3	37	CCDS35227.1	8	0.004822182037371911	6	0.012244897959183673	1	0.0027624309392265192	0	0.0	0	0.0	-	5.654	0.305291	0.10678	0.017219	0.0	ENSG00000198173	ENST00000358047	T	0.20332	2.08	0.895	0.895	0.19247	.	.	.	.	.	T	0.21631	0.0521	M	0.81341	2.54	0.09310	N	1	D	0.58268	0.982	P	0.58873	0.847	T	0.08932	-1.0698	9	0.62326	D	0.03	.	3.8459	0.08934	0.0:0.67:0.0:0.33	rs61730910	760	Q5HY64	FA47C_HUMAN	C	760	ENSP00000367913:S760C	ENSP00000367913:S760C	S	+	2	0	FAM47C	36938683	0.005000	0.15991	0.002000	0.10522	0.002000	0.02628	0.436000	0.21526	0.163000	0.19507	0.165000	0.16767	TCT	C|0.993;G|0.007	0.007	strong		0.632	FAM47C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060508.1	NM_001013736	
PPT1	5538	hgsc.bcm.edu	37	1	40535945	40535945	+	IGR	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:40535945A>G	ENST00000433473.3	-	0	2740				CAP1_ENST00000372805.3_Missense_Mutation_p.I370V|CAP1_ENST00000479759.1_3'UTR|CAP1_ENST00000340450.3_Missense_Mutation_p.I369V|CAP1_ENST00000372797.3_Missense_Mutation_p.I370V|CAP1_ENST00000372802.1_Missense_Mutation_p.I369V|CAP1_ENST00000372792.2_Missense_Mutation_p.I370V|CAP1_ENST00000372798.1_Missense_Mutation_p.I369V	NM_000310.3	NP_000301.1	P50897	PPT1_HUMAN	palmitoyl-protein thioesterase 1						adult locomotory behavior (GO:0008344)|associative learning (GO:0008306)|brain development (GO:0007420)|cell death (GO:0008219)|cellular protein catabolic process (GO:0044257)|cofactor metabolic process (GO:0051186)|cofactor transport (GO:0051181)|grooming behavior (GO:0007625)|lipid catabolic process (GO:0016042)|lysosomal lumen acidification (GO:0007042)|membrane raft organization (GO:0031579)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of neuron apoptotic process (GO:0043524)|nervous system development (GO:0007399)|neuron development (GO:0048666)|neurotransmitter secretion (GO:0007269)|pinocytosis (GO:0006907)|positive regulation of pinocytosis (GO:0048549)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein catabolic process (GO:0030163)|protein depalmitoylation (GO:0002084)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|regulation of phospholipase A2 activity (GO:0032429)|regulation of synapse structure and activity (GO:0050803)|sphingolipid catabolic process (GO:0030149)|visual perception (GO:0007601)	axon (GO:0030424)|cytosol (GO:0005829)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)	palmitoyl-(protein) hydrolase activity (GO:0008474)|palmitoyl-CoA hydrolase activity (GO:0016290)			endometrium(5)|large_intestine(1)|lung(3)|ovary(1)|stomach(1)	11	Lung NSC(20;3.43e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1e-18)|Epithelial(16;3.6e-17)|all cancers(16;1.1e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			AATTAACTCCATTACAGTAGG	0.458																																					p.I370V		Atlas-SNP	.											.	CAP1	38	.	0			c.A1108G						PASS	.						81.0	77.0	78.0					1																	40535945		2020	4170	6190	SO:0001628	intergenic_variant	10487	exon10			AACTCCATTACAG	U44772	CCDS447.1, CCDS44119.1	1p32	2014-09-17	2008-07-31		ENSG00000131238	ENSG00000131238	3.1.2.22		9325	protein-coding gene	gene with protein product	"""ceroid-lipofuscinosis, neuronal 1, infantile"""	600722		PPT		7637805, 8325646	Standard	NM_000310		Approved	CLN1, INCL	uc001cfb.2	P50897	OTTHUMG00000004495		1.37:g.40535945A>G		128.0	0.0	0		154.0	82.0	0.532468	NM_006367	B4DY24|Q6FGQ4	Missense_Mutation	SNP	ENST00000433473.3	37	CCDS447.1	.	.	.	.	.	.	.	.	.	.	A	16.24	3.066402	0.55539	.	.	ENSG00000131236	ENST00000372797;ENST00000372802;ENST00000372792;ENST00000538246;ENST00000372798;ENST00000340450;ENST00000372805	T;T;T;T;T;T	0.08896	3.05;3.04;3.05;3.04;3.04;3.05	5.34	5.34	0.76211	CARP motif (1);Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal (1);Adenylate cyclase-associated CAP, C-terminal (2);C-CAP/cofactor C-like domain (1);	0.000000	0.85682	D	0.000000	T	0.11707	0.0285	L	0.48986	1.54	0.80722	D	1	B;B	0.33807	0.061;0.426	B;B	0.36534	0.149;0.227	T	0.03829	-1.1000	10	0.46703	T	0.11	-17.1934	14.503	0.67734	1.0:0.0:0.0:0.0	.	317;370	E7ENY9;Q01518	.;CAP1_HUMAN	V	370;369;370;347;369;369;370	ENSP00000361883:I370V;ENSP00000361888:I369V;ENSP00000361878:I370V;ENSP00000361884:I369V;ENSP00000344832:I369V;ENSP00000361891:I370V	ENSP00000344832:I369V	I	+	1	0	CAP1	40308532	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.437000	0.80417	1.996000	0.58369	0.528000	0.53228	ATT	.	.	none		0.458	PPT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000013126.2	NM_000310	
KRTAP5-8	57830	hgsc.bcm.edu	37	11	71249532	71249532	+	Missense_Mutation	SNP	C	C	G	rs532438179|rs11234084|rs369043826	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:71249532C>G	ENST00000398534.3	+	1	462	c.431C>G	c.(430-432)tCc>tGc	p.S144C		NM_021046.2	NP_066384.2	O75690	KRA58_HUMAN	keratin associated protein 5-8	144	9 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			cervix(1)|endometrium(1)|lung(2)|skin(1)|stomach(1)	6						CCCTGCTGTTCCCAGTCCAGC	0.612																																					p.S144C		Atlas-SNP	.											.	KRTAP5-8	28	.	0			c.C431G						PASS	.						148.0	160.0	156.0					11																	71249532		2200	4294	6494	SO:0001583	missense	57830	exon1			GCTGTTCCCAGTC	AB126077	CCDS41683.1	11q13.4	2008-02-05			ENSG00000241233	ENSG00000241233		"""Keratin associated proteins"""	23603	protein-coding gene	gene with protein product						15144888	Standard	NM_021046		Approved	KRTAP5.8, UHSKerB, KRTAP5-2	uc001oqr.1	O75690	OTTHUMG00000057571	ENST00000398534.3:c.431C>G	11.37:g.71249532C>G	ENSP00000420723:p.Ser144Cys	158.0	0.0	0		222.0	9.0	0.0405405	NM_021046	Q6L8G7|Q6UTX6	Missense_Mutation	SNP	ENST00000398534.3	37	CCDS41683.1	.	.	.	.	.	.	.	.	.	.	-	3.125	-0.179750	0.06380	.	.	ENSG00000241233	ENST00000398534	T	0.01197	5.19	1.57	-2.99	0.05497	.	.	.	.	.	T	0.00552	0.0018	N	0.02213	-0.635	0.21861	N	0.999505	B	0.02656	0.0	B	0.01281	0.0	T	0.44314	-0.9336	9	0.02654	T	1	.	12.0511	0.53507	0.0:0.7645:0.2355:0.0	rs11234084	144	O75690	KRA58_HUMAN	C	144	ENSP00000420723:S144C	ENSP00000420723:S144C	S	+	2	0	KRTAP5-8	70927180	0.000000	0.05858	0.375000	0.26029	0.014000	0.08584	-0.627000	0.05521	-0.723000	0.04915	-0.951000	0.02657	TCC	.	.	weak		0.612	KRTAP5-8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127954.1	NM_021046	
SLA2	84174	hgsc.bcm.edu	37	20	35242745	35242745	+	Missense_Mutation	SNP	C	C	T	rs34834764	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:35242745C>T	ENST00000262866.4	-	7	1050	c.628G>A	c.(628-630)Gtg>Atg	p.V210M	SLA2_ENST00000360672.2_Missense_Mutation_p.C193Y	NM_032214.3|NM_175077.2	NP_115590.1|NP_778252.1	Q9H6Q3	SLAP2_HUMAN	Src-like-adaptor 2	210	SLA C-terminal.		V -> M (in dbSNP:rs34834764).		antigen receptor-mediated signaling pathway (GO:0050851)|B cell mediated immunity (GO:0019724)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of B cell activation (GO:0050869)|negative regulation of calcium-mediated signaling (GO:0050849)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of signal transduction (GO:0009967)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)	cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome membrane (GO:0010008)|late endosome (GO:0005770)|plasma membrane (GO:0005886)	protein N-terminus binding (GO:0047485)|SH3/SH2 adaptor activity (GO:0005070)			endometrium(1)|lung(2)|skin(2)	5	Breast(12;0.114)	Myeloproliferative disorder(115;0.00878)				GTCCTCTGCACAGTCACAGGT	0.572													C|||	149	0.0297524	0.1067	0.0115	5008	,	,		21213	0.0		0.0	False		,,,				2504	0.0				p.V210M	Ovarian(59;720 1165 26994 46188 51693)	Atlas-SNP	.											.	SLA2	12	.	0			c.G628A						PASS	.	C	MET/VAL,TYR/CYS	374,4032	191.2+/-216.9	17,340,1846	152.0	144.0	147.0		628,578	5.4	1.0	20	dbSNP_126	147	1,8599		0,1,4299	yes	missense,missense	SLA2	NM_032214.2,NM_175077.1	21,194	17,341,6145	TT,TC,CC		0.0116,8.4884,2.8833	probably-damaging,probably-damaging	210/262,193/211	35242745	375,12631	2203	4300	6503	SO:0001583	missense	84174	exon7			TCTGCACAGTCAC	AF326353	CCDS13282.1, CCDS13283.1	20q11.23	2013-02-14			ENSG00000101082	ENSG00000101082		"""SH2 domain containing"""	17329	protein-coding gene	gene with protein product		606577		C20orf156		11696592	Standard	NM_032214		Approved	FLJ21992, SLAP-2	uc002xfv.3	Q9H6Q3	OTTHUMG00000032393	ENST00000262866.4:c.628G>A	20.37:g.35242745C>T	ENSP00000262866:p.Val210Met	176.0	0.0	0		205.0	105.0	0.512195	NM_032214	A8K648|E1P5U1|E1P5U2|Q5TH27|Q5TH28|Q8WY18|Q96QI4|Q9H135	Missense_Mutation	SNP	ENST00000262866.4	37	CCDS13282.1	45|45	0.020604395604395604|0.020604395604395604	42|42	0.08536585365853659|0.08536585365853659	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	C|C	15.68|15.68	2.904261|2.904261	0.52333|0.52333	0.084884|0.084884	1.16E-4|1.16E-4	ENSG00000101082|ENSG00000101082	ENST00000360672|ENST00000262866	T|T	0.74632|0.79033	-0.86|-1.23	5.43|5.43	5.43|5.43	0.79202|0.79202	.|.	.|0.131339	.|0.49916	.|D	.|0.000132	T|T	0.09862|0.09862	0.0242|0.0242	.|.	.|.	.|.	0.26547|0.26547	N|N	0.973972|0.973972	B|B	0.14012|0.29988	0.009|0.264	B|B	0.04013|0.33846	0.001|0.171	T|T	0.36187|0.36187	-0.9758|-0.9758	8|9	0.45353|0.39692	T|T	0.12|0.17	-19.6165|-19.6165	16.7763|16.7763	0.85551|0.85551	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs34834764|rs34834764	193|210	Q9H6Q3-2|Q9H6Q3	.|SLAP2_HUMAN	Y|M	193|210	ENSP00000353890:C193Y|ENSP00000262866:V210M	ENSP00000353890:C193Y|ENSP00000262866:V210M	C|V	-|-	2|1	0|0	SLA2|SLA2	34676159|34676159	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.904000|0.904000	0.53231|0.53231	2.488000|2.488000	0.45276|0.45276	2.824000|2.824000	0.97209|0.97209	0.655000|0.655000	0.94253|0.94253	TGT|GTG	C|0.968;T|0.032	0.032	strong		0.572	SLA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079037.2	NM_175077	
ACP5	54	hgsc.bcm.edu	37	19	11685948	11685948	+	Silent	SNP	A	A	G	rs77911902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11685948A>G	ENST00000592828.1	-	7	1257	c.855T>C	c.(853-855)acT>acC	p.T285T	ACP5_ENST00000412435.2_Silent_p.T285T|ACP5_ENST00000433365.2_Silent_p.T285T|ACP5_ENST00000218758.5_Silent_p.T285T|ZNF627_ENST00000588651.1_Intron|ACP5_ENST00000590420.1_Missense_Mutation_p.L43P	NM_001111034.1	NP_001104504.1	P13686	PPA5_HUMAN	acid phosphatase 5, tartrate resistant	285					bone morphogenesis (GO:0060349)|bone resorption (GO:0045453)|defense response to Gram-positive bacterium (GO:0050830)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of nitric oxide biosynthetic process (GO:0045019)|negative regulation of superoxide anion generation (GO:0032929)|negative regulation of tumor necrosis factor production (GO:0032720)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|riboflavin metabolic process (GO:0006771)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)	acid phosphatase activity (GO:0003993)|ferric iron binding (GO:0008199)|ferrous iron binding (GO:0008198)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(4)|pancreas(1)	9						GTGAGTCTTCAGTCCCATAGT	0.572													A|||	148	0.0295527	0.1051	0.013	5008	,	,		21260	0.0		0.0	False		,,,				2504	0.0				p.T285T		Atlas-SNP	.											.	ACP5	30	.	0			c.T855C						PASS	.		,,,	478,3928	225.9+/-241.6	21,436,1746	100.0	86.0	91.0		855,855,855,855	-1.6	0.0	19	dbSNP_131	91	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ACP5	NM_001111034.1,NM_001111035.1,NM_001111036.1,NM_001611.3	,,,	21,443,6039	GG,GA,AA		0.0814,10.8488,3.729	,,,	285/326,285/326,285/326,285/326	11685948	485,12521	2203	4300	6503	SO:0001819	synonymous_variant	54	exon6			GTCTTCAGTCCCA	X14618	CCDS12265.1	19p13.2	2012-10-02			ENSG00000102575	ENSG00000102575	3.1.3.2		124	protein-coding gene	gene with protein product	"""tartrate-resistant acid phosphatase"""	171640				8449511, 2338077	Standard	NM_001611		Approved	TRAP	uc002msj.4	P13686	OTTHUMG00000182036	ENST00000592828.1:c.855T>C	19.37:g.11685948A>G		163.0	0.0	0		158.0	80.0	0.506329	NM_001111034	A8K3V2|Q2TAB1|Q6IAS6|Q9UCJ5|Q9UCJ6|Q9UCJ7	Silent	SNP	ENST00000592828.1	37	CCDS12265.1																																																																																			A|0.967;G|0.033	0.033	strong		0.572	ACP5-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458881.1		
TSPEAR	54084	hgsc.bcm.edu	37	21	45929192	45929192	+	Silent	SNP	G	G	A	rs115847549	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45929192G>A	ENST00000323084.4	-	10	1709	c.1644C>T	c.(1642-1644)taC>taT	p.Y548Y	TSPEAR_ENST00000397916.1_Silent_p.Y480Y|TSPEAR-AS1_ENST00000451035.1_RNA|TSPEAR-AS1_ENST00000430181.1_RNA	NM_001272037.1|NM_144991.2	NP_001258966.1|NP_659428.2	Q8WU66	TSEAR_HUMAN	thrombospondin-type laminin G domain and EAR repeats	548					sensory perception of sound (GO:0007605)	cell surface (GO:0009986)|ciliary membrane (GO:0060170)|extracellular region (GO:0005576)|stereocilium (GO:0032420)				breast(1)|central_nervous_system(6)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	37						TCTCCACATCGTAGCTGTGAC	0.537													G|||	41	0.0081869	0.0287	0.0043	5008	,	,		13812	0.0		0.0	False		,,,				2504	0.0				p.Y548Y		Atlas-SNP	.											.	TSPEAR	110	.	0			c.C1644T						PASS	.	G		138,4268	100.7+/-139.4	6,126,2071	202.0	127.0	152.0		1644	-1.0	0.9	21	dbSNP_132	152	19,8581	13.3+/-46.6	0,19,4281	no	coding-synonymous	TSPEAR	NM_144991.2		6,145,6352	AA,AG,GG		0.2209,3.1321,1.2071		548/670	45929192	157,12849	2203	4300	6503	SO:0001819	synonymous_variant	54084	exon10			CACATCGTAGCTG	AJ487962	CCDS13712.1, CCDS74801.1	21q22.3	2012-10-30	2011-01-25	2011-01-25	ENSG00000175894	ENSG00000175894			1268	protein-coding gene	gene with protein product		612920	"""chromosome 21 open reading frame 29"", ""deafness, autosomal recessive 98"""	C21orf29, DFNB98		12095917, 22678063	Standard	NM_144991		Approved	MGC11251, TSP-EAR	uc002zfe.1	Q8WU66	OTTHUMG00000041215	ENST00000323084.4:c.1644C>T	21.37:g.45929192G>A		133.0	0.0	0		184.0	97.0	0.527174	NM_144991		Silent	SNP	ENST00000323084.4	37	CCDS13712.1																																																																																			G|0.988;A|0.012	0.012	strong		0.537	TSPEAR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098761.1	NM_144991	
WNT9A	7483	hgsc.bcm.edu	37	1	228109696	228109696	+	Silent	SNP	G	G	A	rs112703157	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228109696G>A	ENST00000272164.5	-	4	631	c.621C>T	c.(619-621)atC>atT	p.I207I		NM_003395.2	NP_003386.1	O14904	WNT9A_HUMAN	wingless-type MMTV integration site family, member 9A	207					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)				CCCCAGCCTTGATCACCTGGC	0.677													G|||	122	0.024361	0.0862	0.0115	5008	,	,		17033	0.0		0.0	False		,,,				2504	0.0				p.I207I		Atlas-SNP	.											.	WNT9A	39	.	0			c.C621T						PASS	.	G		318,4080		6,306,1887	34.0	35.0	34.0		621	3.4	1.0	1	dbSNP_132	34	2,8592		0,2,4295	no	coding-synonymous	WNT9A	NM_003395.2		6,308,6182	AA,AG,GG		0.0233,7.2306,2.4631		207/366	228109696	320,12672	2199	4297	6496	SO:0001819	synonymous_variant	7483	exon4			AGCCTTGATCACC	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.621C>T	1.37:g.228109696G>A		69.0	0.0	0		84.0	30.0	0.357143	NM_003395	A6NLW2|Q2M2J3|Q5VWU0|Q96S50	Silent	SNP	ENST00000272164.5	37	CCDS31045.1																																																																																			G|0.977;A|0.023	0.023	strong		0.677	WNT9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091646.1	NM_003395	
MAST4	375449	hgsc.bcm.edu	37	5	66461583	66461583	+	Silent	SNP	C	C	T	rs56201012	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:66461583C>T	ENST00000403625.2	+	29	6871	c.6576C>T	c.(6574-6576)caC>caT	p.H2192H	MAST4_ENST00000405643.1_Silent_p.H2013H|MAST4_ENST00000404260.3_Silent_p.H2195H|MAST4_ENST00000261569.7_Silent_p.H1998H|MAST4_ENST00000403666.1_Silent_p.H2003H	NM_001164664.1	NP_001158136.1	O15021	MAST4_HUMAN	microtubule associated serine/threonine kinase family member 4	2195	Pro-rich.					cytoplasm (GO:0005737)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|kidney(2)|lung(6)|ovary(2)	13		Lung NSC(167;8.56e-06)|Prostate(74;0.00637)|Ovarian(174;0.0563)|Breast(144;0.0586)|Colorectal(97;0.245)		Lung(70;0.011)		GCAGCAGCCACAAGCCCCGGC	0.667													C|||	92	0.0183706	0.0673	0.0043	5008	,	,		14359	0.0		0.0	False		,,,				2504	0.0				p.H2192H		Atlas-SNP	.											.	MAST4	218	.	0			c.C6576T						PASS	.	C	,	176,3520		6,164,1678	6.0	10.0	9.0		6576,6009	1.2	0.0	5	dbSNP_129	9	0,8114		0,0,4057	no	coding-synonymous,coding-synonymous	MAST4	NM_001164664.1,NM_015183.2	,	6,164,5735	TT,TC,CC		0.0,4.7619,1.4903	,	2192/2624,2003/2435	66461583	176,11634	1848	4057	5905	SO:0001819	synonymous_variant	375449	exon29			CAGCCACAAGCCC	AY830839	CCDS47224.1, CCDS47225.1, CCDS54861.1, CCDS75254.1	5q12.3	2007-06-20			ENSG00000069020	ENSG00000069020			19037	protein-coding gene	gene with protein product						9205841	Standard	NM_198828		Approved	KIAA0303	uc021xzk.1	O15021	OTTHUMG00000152471	ENST00000403625.2:c.6576C>T	5.37:g.66461583C>T		75.0	0.0	0		89.0	40.0	0.449438	NM_001164664	A6NL49|B5ME48|Q05EE6|Q6ZN07|Q8N4X4|Q96LY3	Silent	SNP	ENST00000403625.2	37	CCDS54861.1	21	0.009615384615384616	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	0	0.0	C	0.038	-1.299299	0.01364	0.047619	0.0	ENSG00000069020	ENST00000443808	.	.	.	5.0	1.16	0.20824	.	.	.	.	.	.	.	.	.	.	.	0.22389	N	0.999143	.	.	.	.	.	.	.	.	.	.	.	.	.	-3.25	3.4785	0.07594	0.1768:0.386:0.0:0.4373	rs56201012;rs61910710	.	.	.	X	1249	.	.	Q	+	1	0	MAST4	66497339	0.016000	0.18221	0.007000	0.13788	0.092000	0.18411	-0.102000	0.10956	0.022000	0.15160	-0.140000	0.14226	CAA	C|0.990;T|0.010	0.010	strong		0.667	MAST4-001	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326324.2		
PCDHA1	56147	hgsc.bcm.edu	37	5	140167520	140167520	+	Missense_Mutation	SNP	G	G	A	rs150585640	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140167520G>A	ENST00000504120.2	+	1	1645	c.1645G>A	c.(1645-1647)Gtg>Atg	p.V549M	PCDHA1_ENST00000394633.3_Intron|PCDHA1_ENST00000378133.3_Missense_Mutation_p.V549M	NM_018900.2	NP_061723.1	Q9Y5I3	PCDA1_HUMAN	protocadherin alpha 1	549	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(34)|prostate(3)|skin(4)|upper_aerodigestive_tract(5)|urinary_tract(3)	70			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGGCAGCAACGTGACGCTGCA	0.672													.|||	71	0.0141773	0.053	0.0014	5008	,	,		16239	0.0		0.0	False		,,,				2504	0.0				p.V549M		Atlas-SNP	.											.	PCDHA1	387	.	0			c.G1645A						PASS	.	G	MET/VAL,MET/VAL,	233,4173	136.1+/-172.1	9,215,1979	78.0	81.0	80.0		1645,1645,	2.7	1.0	5	dbSNP_134	80	1,8589	1.2+/-3.3	0,1,4294	no	missense,missense,intron	PCDHA1	NM_018900.2,NM_031410.1,NM_031411.1	21,21,	9,216,6273	AA,AG,GG		0.0116,5.2882,1.8006	,,	549/951,549/808,	140167520	234,12762	2203	4295	6498	SO:0001583	missense	56147	exon1			AGCAACGTGACGC	AF152479	CCDS54912.1, CCDS54913.1	5q31	2010-11-26				ENSG00000204970		"""Cadherins / Protocadherins : Clustered"""	8663	other	complex locus constituent	"""KIAA0345-like 13"""	606307				10380929	Standard	NM_018900		Approved			Q9Y5I3		ENST00000504120.2:c.1645G>A	5.37:g.140167520G>A	ENSP00000420840:p.Val549Met	81.0	0.0	0		120.0	60.0	0.5	NM_031410	O75288|Q9NRT7	Missense_Mutation	SNP	ENST00000504120.2	37	CCDS54913.1	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	g	16.14	3.037929	0.54896	0.052882	1.16E-4	ENSG00000204970	ENST00000504120;ENST00000378133	T;T	0.53640	0.61;0.61	3.59	2.71	0.32032	Cadherin (5);Cadherin-like (1);	0.209202	0.23219	N	0.050600	T	0.16896	0.0406	M	0.83384	2.64	0.23997	N	0.996224	D;D	0.65815	0.995;0.988	P;P	0.50192	0.634;0.501	T	0.25847	-1.0120	10	0.66056	D	0.02	.	7.0109	0.24861	0.0968:0.1747:0.7285:0.0	.	549;549	Q9Y5I3;Q9Y5I3-3	PCDA1_HUMAN;.	M	549	ENSP00000420840:V549M;ENSP00000367373:V549M	ENSP00000367373:V549M	V	+	1	0	PCDHA1	140147704	0.967000	0.33354	0.987000	0.45799	0.935000	0.57460	2.495000	0.45337	0.621000	0.30232	0.555000	0.69702	GTG	G|0.961;A|0.039	0.039	strong		0.672	PCDHA1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000389127.1	NM_018900	
SUPT20HL2	170067	hgsc.bcm.edu	37	X	24329793	24329793	+	IGR	SNP	C	C	T	rs139232512		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:24329793C>T								AC096509.1 (24999 upstream) : AC004552.1 (37132 downstream)																							AGCTGGACGGCGCCTGCTAGC	0.637													C|||	170	0.0450331	0.1218	0.013	3775	,	,		10526	0.0		0.0	False		,,,				2504	0.0				p.R547H		Atlas-SNP	.											.	.	.	.	0			c.G1640A						PASS	.	C	HIS/ARG	385,2240		27,253,78,778,431	11.0	11.0	11.0		1640	-1.0	0.0	X	dbSNP_134	11	4,5486		0,4,0,1912,1658	yes	missense	FAM48B2	NM_001136233.1	29	27,257,78,2690,2089	TT,TC,T,CC,C		0.0729,14.6667,4.7936	possibly-damaging	547/818	24329793	389,7726	1567	3574	5141	SO:0001628	intergenic_variant	170067	exon1			GGACGGCGCCTGC																													X.37:g.24329793C>T		194.0	0.0	0		223.0	129.0	0.578475	NM_001136233		Missense_Mutation	SNP		37																																																																																				C|0.963;T|0.037	0.037	strong	0	0.637								
BCAN	63827	hgsc.bcm.edu	37	1	156621251	156621251	+	Missense_Mutation	SNP	C	C	T	rs12065791	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:156621251C>T	ENST00000329117.5	+	7	1403	c.1067C>T	c.(1066-1068)tCg>tTg	p.S356L	BCAN_ENST00000361588.5_Missense_Mutation_p.S356L|RP11-284F21.7_ENST00000448869.1_RNA	NM_021948.4	NP_068767.3	Q96GW7	PGCB_HUMAN	brevican	356			S -> L (in dbSNP:rs12065791).		carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hippocampus development (GO:0021766)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)|hyaluronic acid binding (GO:0005540)			cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	55	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					GCCACAGACTCGGCCCAGCCT	0.557													C|||	237	0.0473243	0.1687	0.0173	5008	,	,		18259	0.0		0.002	False		,,,				2504	0.0				p.S356L		Atlas-SNP	.											.	BCAN	174	.	0			c.C1067T						PASS	.	C	LEU/SER,LEU/SER	656,3750	268.0+/-268.2	43,570,1590	47.0	44.0	45.0		1067,1067	5.2	1.0	1	dbSNP_120	45	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	BCAN	NM_021948.4,NM_198427.1	145,145	43,574,5886	TT,TC,CC		0.0465,14.8888,5.0746	benign,benign	356/912,356/672	156621251	660,12346	2203	4300	6503	SO:0001583	missense	63827	exon7			CAGACTCGGCCCA	BC027971	CCDS1149.1, CCDS1150.1	1q31	2013-05-07			ENSG00000132692	ENSG00000132692		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	23059	protein-coding gene	gene with protein product	"""chondroitin sulfate proteoglycan 7"", ""brevican proteoglycan"""	600347				11054543, 11873941	Standard	NM_021948		Approved	BEHAB, MGC13038, CSPG7	uc001fpp.3	Q96GW7	OTTHUMG00000033322	ENST00000329117.5:c.1067C>T	1.37:g.156621251C>T	ENSP00000331210:p.Ser356Leu	35.0	0.0	0		50.0	26.0	0.52	NM_198427	D3DVC2|Q5SZ10|Q5T3I5|Q8TBB9|Q9HBK1|Q9HBK4	Missense_Mutation	SNP	ENST00000329117.5	37	CCDS1149.1	88	0.040293040293040296	79	0.16056910569105692	7	0.019337016574585635	0	0.0	2	0.002638522427440633	C	9.099	1.003544	0.19121	0.148888	4.65E-4	ENSG00000132692	ENST00000329117;ENST00000361588	T;T	0.11495	2.77;2.77	5.17	5.17	0.71159	C-type lectin fold (1);C-type lectin-like (1);	0.474289	0.19636	N	0.109545	T	0.02533	0.0077	L	0.27053	0.805	0.32632	N	0.521804	P;B	0.42518	0.782;0.145	B;B	0.29077	0.098;0.041	T	0.45190	-0.9278	10	0.33141	T	0.24	-10.544	11.8228	0.52250	0.0:0.8238:0.1762:0.0	rs12065791;rs12065791	356;356	Q96GW7;Q96GW7-2	PGCB_HUMAN;.	L	356	ENSP00000331210:S356L;ENSP00000354925:S356L	ENSP00000331210:S356L	S	+	2	0	BCAN	154887875	0.998000	0.40836	0.995000	0.50966	0.125000	0.20455	3.340000	0.52143	2.692000	0.91855	0.655000	0.94253	TCG	C|0.949;T|0.051	0.051	strong		0.557	BCAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081844.2	NM_021948	
RGS3	5998	hgsc.bcm.edu	37	9	116224452	116224452	+	Missense_Mutation	SNP	G	G	A	rs16933949	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116224452G>A	ENST00000374140.2	+	4	595	c.386G>A	c.(385-387)aGg>aAg	p.R129K	RGS3_ENST00000317613.6_5'Flank|RGS3_ENST00000350696.5_Missense_Mutation_p.R129K	NM_001282923.1|NM_144488.4	NP_001269852.1|NP_652759.3	P49796	RGS3_HUMAN	regulator of G-protein signaling 3	129			R -> K (in dbSNP:rs16933949).		inactivation of MAPK activity (GO:0000188)|positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			cervix(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(22)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	48						GCCAGGAAGAGGATCACGCAT	0.537													G|||	288	0.057508	0.2088	0.0159	5008	,	,		16916	0.0		0.001	False		,,,				2504	0.0				p.R129K		Atlas-SNP	.											.	RGS3	251	.	0			c.G386A						PASS	.	G	LYS/ARG	726,3434		72,582,1426	77.0	81.0	79.0		386	-1.2	0.0	9	dbSNP_123	79	4,8432		0,4,4214	yes	missense	RGS3	NM_144488.4	26	72,586,5640	AA,AG,GG		0.0474,17.4519,5.7955	possibly-damaging	129/1199	116224452	730,11866	2080	4218	6298	SO:0001583	missense	5998	exon4			GGAAGAGGATCAC	AF006610	CCDS6797.1, CCDS6798.1, CCDS35113.1, CCDS35114.1, CCDS43869.1, CCDS65111.1	9q32	2008-02-05	2007-08-14		ENSG00000138835	ENSG00000138835		"""Regulators of G-protein signaling"""	9999	protein-coding gene	gene with protein product		602189	"""regulator of G-protein signalling 3"""			8602223, 11034339	Standard	NM_001276260		Approved	C2PA, FLJ20370, PDZ-RGS3	uc004bhq.4	P49796	OTTHUMG00000021048	ENST00000374140.2:c.386G>A	9.37:g.116224452G>A	ENSP00000363255:p.Arg129Lys	95.0	0.0	0		105.0	72.0	0.685714	NM_144488	A6NHA0|A8K0V1|B3KUB2|Q5VXB8|Q5VXC1|Q5VZ05|Q5VZ06|Q6ZRM5|Q8IUQ1|Q8NC47|Q8NFN4|Q8NFN5|Q8NFN6|Q8TD59|Q8TD68|Q8WV02|Q8WXA0	Missense_Mutation	SNP	ENST00000374140.2	37	CCDS43869.1	100	0.045787545787545784	93	0.18902439024390244	7	0.019337016574585635	0	0.0	0	0.0	G	6.337	0.430283	0.12045	0.174519	4.74E-4	ENSG00000138835	ENST00000374140;ENST00000350696	T;T	0.41065	1.01;1.01	4.39	-1.25	0.09405	.	.	.	.	.	T	0.00039	0.0001	N	0.12182	0.205	0.80722	P	0.0	B	0.06786	0.001	B	0.01281	0.0	T	0.15321	-1.0441	8	0.87932	D	0	.	7.8729	0.29576	0.5369:0.0:0.4631:0.0	rs16933949;rs59024905;rs16933949	129	P49796	RGS3_HUMAN	K	129	ENSP00000363255:R129K;ENSP00000259406:R129K	ENSP00000259406:R129K	R	+	2	0	RGS3	115264273	0.022000	0.18835	0.003000	0.11579	0.862000	0.49288	0.044000	0.13992	-0.349000	0.08274	0.591000	0.81541	AGG	G|0.957;A|0.043	0.043	strong		0.537	RGS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055561.3	NM_017790	
OR2T34	127068	hgsc.bcm.edu	37	1	248737419	248737419	+	Missense_Mutation	SNP	T	T	C	rs145854970		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248737419T>C	ENST00000328782.2	-	1	661	c.640A>G	c.(640-642)Acc>Gcc	p.T214A		NM_001001821.1	NP_001001821.1	Q8NGX1	O2T34_HUMAN	olfactory receptor, family 2, subfamily T, member 34	214						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|large_intestine(6)|lung(28)|ovary(2)|skin(2)|stomach(3)	43	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ATGATGGGGGTGAGAAGCATG	0.557																																					p.T214A		Atlas-SNP	.											OR2T34,NS,carcinoma,+1,2	OR2T34	72	2	0			c.A640G						scavenged	.						196.0	210.0	206.0					1																	248737419		2114	4300	6414	SO:0001583	missense	127068	exon1			TGGGGGTGAGAAG	BK004477	CCDS31120.1	1q44	2012-08-09			ENSG00000183310	ENSG00000183310		"""GPCR / Class A : Olfactory receptors"""	31256	protein-coding gene	gene with protein product							Standard	NM_001001821		Approved		uc001iep.1	Q8NGX1	OTTHUMG00000040387	ENST00000328782.2:c.640A>G	1.37:g.248737419T>C	ENSP00000330904:p.Thr214Ala	307.0	0.0	0		206.0	17.0	0.0825243	NM_001001821	B2RNJ8|Q6IEY5|Q96R31	Missense_Mutation	SNP	ENST00000328782.2	37	CCDS31120.1	.	.	.	.	.	.	.	.	.	.	.	8.088	0.773777	0.16051	.	.	ENSG00000183310	ENST00000328782	T	0.36520	1.25	2.37	-2.05	0.07321	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.15609	0.0376	N	0.11818	0.18	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22208	-1.0223	9	0.59425	D	0.04	.	0.341	0.00334	0.2537:0.2468:0.1387:0.3608	.	214	Q8NGX1	O2T34_HUMAN	A	214	ENSP00000330904:T214A	ENSP00000330904:T214A	T	-	1	0	OR2T34	246804042	0.000000	0.05858	0.035000	0.18076	0.091000	0.18340	-0.914000	0.04038	-0.298000	0.08921	-1.680000	0.00737	ACC	.	.	weak		0.557	OR2T34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097138.1	NM_001001821	
COL27A1	85301	hgsc.bcm.edu	37	9	116958283	116958283	+	Silent	SNP	G	G	A	rs10982098	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116958283G>A	ENST00000356083.3	+	7	2506	c.2115G>A	c.(2113-2115)ccG>ccA	p.P705P		NM_032888.2	NP_116277.2	Q8IZC6	CORA1_HUMAN	collagen, type XXVII, alpha 1	705	Collagen-like 2.|Pro-rich.|Triple-helical region.				extracellular matrix organization (GO:0030198)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|fibrillar collagen trimer (GO:0005583)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(30)|ovary(4)|prostate(6)|skin(3)|soft_tissue(1)|stomach(1)|urinary_tract(3)	80						CAGGACCTCCGGGACGAAAGG	0.592													G|||	39	0.00778754	0.0295	0.0	5008	,	,		19536	0.0		0.0	False		,,,				2504	0.0				p.P705P		Atlas-SNP	.											.	COL27A1	200	.	0			c.G2115A						PASS	.	G		101,4305	79.3+/-117.8	2,97,2104	160.0	134.0	143.0		2115	1.2	0.4	9	dbSNP_120	143	0,8600		0,0,4300	no	coding-synonymous	COL27A1	NM_032888.2		2,97,6404	AA,AG,GG		0.0,2.2923,0.7766		705/1861	116958283	101,12905	2203	4300	6503	SO:0001819	synonymous_variant	85301	exon7			ACCTCCGGGACGA	AB058773	CCDS6802.1	9q33.1	2013-01-16			ENSG00000196739	ENSG00000196739		"""Collagens"""	22986	protein-coding gene	gene with protein product		608461				12766169	Standard	NM_032888		Approved	KIAA1870, MGC11337, FLJ11895	uc011lxl.2	Q8IZC6	OTTHUMG00000020537	ENST00000356083.3:c.2115G>A	9.37:g.116958283G>A		78.0	0.0	0		77.0	27.0	0.350649	NM_032888	Q66K43|Q96JF7	Silent	SNP	ENST00000356083.3	37	CCDS6802.1																																																																																			G|0.993;A|0.007	0.007	strong		0.592	COL27A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053763.1	NM_032888	
LRRC14	9684	hgsc.bcm.edu	37	8	145740622	145740622	+	5'Flank	SNP	C	C	T	rs34948955	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145740622C>T	ENST00000292524.1	+	0	0				RECQL4_ENST00000532237.1_5'UTR|LRRC14_ENST00000529022.1_5'Flank|CTD-2517M22.17_ENST00000580385.1_RNA|RECQL4_ENST00000428558.2_Silent_p.T465T	NM_001272036.1|NM_014665.2	NP_001258965.1|NP_055480.1	Q15048	LRC14_HUMAN	leucine rich repeat containing 14											endometrium(1)|lung(3)|prostate(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			CCTCAGCCGGCGTCTCTGCAG	0.622													C|||	8	0.00159744	0.0	0.0014	5008	,	,		20490	0.0		0.007	False		,,,				2504	0.0				p.T465T		Atlas-SNP	.											RECQL4,brain,glioma,0,2	RECQL4	75	2	0			c.G1395A						scavenged	.	C		5,4245		0,5,2120	25.0	32.0	29.0		1395	-10.8	0.0	8	dbSNP_126	29	70,8422		0,70,4176	no	coding-synonymous	RECQL4	NM_004260.3		0,75,6296	TT,TC,CC		0.8243,0.1176,0.5886		465/1209	145740622	75,12667	2125	4246	6371	SO:0001631	upstream_gene_variant	9401	exon8			AGCCGGCGTCTCT	BC011377	CCDS6432.1	8q24.3	2012-08-20			ENSG00000160959	ENSG00000160959			20419	protein-coding gene	gene with protein product						7584026	Standard	NM_001272036		Approved	KIAA0014, LRRC14A	uc003zdk.3	Q15048	OTTHUMG00000165179		8.37:g.145740622C>T	Exception_encountered	111.0	1.0	0.00900901		115.0	49.0	0.426087	NM_004260	A8K0A8|D3DWM8	Silent	SNP	ENST00000292524.1	37	CCDS6432.1																																																																																			C|0.997;T|0.003	0.003	strong		0.622	LRRC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382494.1	NM_014665	
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011415	46011415	+	Silent	SNP	G	G	A	rs145570198		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46011415G>A	ENST00000400368.1	-	1	971	c.951C>T	c.(949-951)tgC>tgT	p.C317C	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	317	29 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(6)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23						GGACGGGCACGCAGCAGGTGG	0.687																																					p.C317C		Atlas-SNP	.											.	KRTAP10-6	57	.	0			c.C951T						PASS	.						70.0	84.0	79.0					21																	46011415		2202	4300	6502	SO:0001819	synonymous_variant	386674	exon1			GGGCACGCAGCAG	AB076353	CCDS42959.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000188155	ENSG00000188155		"""Keratin associated proteins"""	20523	protein-coding gene	gene with protein product			"""keratin associated protein 18-6"""	KRTAP18-6			Standard	NM_198688		Approved	KRTAP18.6, KAP18.6, KAP10.6	uc002zfm.3	P60371	OTTHUMG00000057634	ENST00000400368.1:c.951C>T	21.37:g.46011415G>A		358.0	0.0	0		261.0	58.0	0.222222	NM_198688		Silent	SNP	ENST00000400368.1	37	CCDS42959.1																																																																																			G|0.976;A|0.024	0.024	strong		0.687	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688	
LILRB2	10288	hgsc.bcm.edu	37	19	54782173	54782173	+	Missense_Mutation	SNP	A	A	C	rs4993130		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:54782173A>C	ENST00000391749.4	-	7	1470	c.1199T>G	c.(1198-1200)cTc>cGc	p.L400R	LILRB2_ENST00000471216.1_5'Flank|LILRB2_ENST00000391746.1_Missense_Mutation_p.L400R|LILRB2_ENST00000314446.5_Missense_Mutation_p.L400R|LILRB2_ENST00000434421.1_Missense_Mutation_p.L284R|LILRB2_ENST00000391748.1_Missense_Mutation_p.L400R	NM_001278406.1	NP_001265335.1	Q8N423	LIRB2_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 2	400	Ig-like C2-type 4.				cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|heterotypic cell-cell adhesion (GO:0034113)|immune response (GO:0006955)|immune response-inhibiting cell surface receptor signaling pathway (GO:0002767)|negative regulation of antigen processing and presentation (GO:0002578)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of T cell tolerance induction (GO:0002666)|regulation of dendritic cell differentiation (GO:2001198)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|inhibitory MHC class I receptor activity (GO:0032396)|MHC class I protein binding (GO:0042288)|MHC class Ib protein binding (GO:0023029)|protein phosphatase 1 binding (GO:0008157)|receptor activity (GO:0004872)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(30)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	44	Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GTCGGAGTTGAGTGAGCCGTA	0.582																																					p.L400R		Atlas-SNP	.											.	LILRB2	94	.	0			c.T1199G						PASS	.	C	ARG/LEU,ARG/LEU	1,4405	825.9+/-416.6	0,1,2202	113.0	105.0	107.0		1199,1199	-3.8	0.0	19	dbSNP_113	107	1,8599		0,1,4299	no	missense,missense	LILRB2	NM_005874.3,NM_001080978.2	102,102	0,2,6501	CC,CA,AA		0.0116,0.0227,0.0154	benign,benign	400/599,400/598	54782173	2,13004	2203	4300	6503	SO:0001583	missense	10288	exon7			GAGTTGAGTGAGC	AF000574	CCDS12886.1, CCDS42612.1, CCDS62791.1, CCDS62792.1	19q13.4	2013-01-11			ENSG00000131042	ENSG00000131042		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6606	protein-coding gene	gene with protein product		604815				9151699, 9079806	Standard	XM_006722966		Approved	LIR-2, ILT4, MIR-10, LIR2, CD85d, MIR10	uc002qfb.3	Q8N423	OTTHUMG00000064896	ENST00000391749.4:c.1199T>G	19.37:g.54782173A>C	ENSP00000375629:p.Leu400Arg	199.0	0.0	0		172.0	77.0	0.447674	NM_005874	A8MU67|C9JF29|O75017|Q8NHJ7|Q8NHJ8	Missense_Mutation	SNP	ENST00000391749.4	37	CCDS12886.1	.	.	.	.	.	.	.	.	.	.	C	0.006	-2.109135	0.00353	2.27E-4	1.16E-4	ENSG00000131042	ENST00000391748;ENST00000314446;ENST00000391749;ENST00000391746;ENST00000434421	T;T;T;T;T	0.00745	5.75;5.75;5.75;5.75;5.75	1.88	-3.77	0.04346	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	6.345920	0.00496	N	0.000144	T	0.00580	0.0019	N	0.05592	-0.015	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.17979	0.013;0.013;0.02	T	0.47471	-0.9115	10	0.19590	T	0.45	.	5.0707	0.14606	0.1536:0.252:0.0:0.5944	.	400;417;400	A8MU67;E7EVY1;Q8N423	.;.;LIRB2_HUMAN	R	400;400;400;400;284	ENSP00000375628:L400R;ENSP00000319960:L400R;ENSP00000375629:L400R;ENSP00000375626:L400R;ENSP00000410117:L284R	ENSP00000319960:L400R	L	-	2	0	LILRB2	59473985	0.000000	0.05858	0.000000	0.03702	0.061000	0.15899	-4.942000	0.00167	-5.508000	0.00013	-3.110000	0.00062	CTC	A|1.000;C|0.000	0.000	weak		0.582	LILRB2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000139510.1		
MUC4	4585	hgsc.bcm.edu	37	3	195507684	195507684	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195507684G>A	ENST00000463781.3	-	2	11226	c.10767C>T	c.(10765-10767)gaC>gaT	p.D3589D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.D3589D	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)		CTGAGGAAGCGTCGGTGACAA	0.592																																					p.D3589D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-2,1	MUC4	1505	1	0			c.C10767T						scavenged	.						4.0	4.0	4.0					3																	195507684		541	1355	1896	SO:0001819	synonymous_variant	4585	exon2			GGAAGCGTCGGTG	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.10767C>T	3.37:g.195507684G>A		203.0	0.0	0		51.0	24.0	0.470588	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CEACAM4	1089	hgsc.bcm.edu	37	19	42125709	42125709	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:42125709G>A	ENST00000221954.2	-	7	839	c.729C>T	c.(727-729)gtC>gtT	p.V243V		NM_001817.2	NP_001808.2	O75871	CEAM4_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 4	243						integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				NS(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|skin(3)|urinary_tract(1)	16						GAACCTAAGAGACCACATCTG	0.532																																					p.V243V		Atlas-SNP	.											CEACAM4,NS,neuroblastoma,0,1	CEACAM4	42	1	0			c.C729T						PASS	.						113.0	108.0	110.0					19																	42125709		2203	4300	6503	SO:0001819	synonymous_variant	1089	exon7			CTAAGAGACCACA	D90276	CCDS33033.1	19q13.2	2013-01-11			ENSG00000105352	ENSG00000105352		"""Immunoglobulin superfamily / V-set domain containing"""	1816	protein-coding gene	gene with protein product				CGM7		2050678	Standard	XM_005258434		Approved		uc002orh.1	O75871	OTTHUMG00000151065	ENST00000221954.2:c.729C>T	19.37:g.42125709G>A		100.0	0.0	0		114.0	54.0	0.473684	NM_001817	Q03715|Q7LDZ7	Silent	SNP	ENST00000221954.2	37	CCDS33033.1																																																																																			.	.	none		0.532	CEACAM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321148.1	NM_001817	
GAS2	2620	hgsc.bcm.edu	37	11	22770669	22770669	+	Silent	SNP	T	T	C	rs7122835	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:22770669T>C	ENST00000454584.2	+	6	782	c.477T>C	c.(475-477)taT>taC	p.Y159Y	GAS2_ENST00000278187.3_Silent_p.Y159Y|GAS2_ENST00000433790.1_Silent_p.Y159Y	NM_001143830.1	NP_001137302.1	O43903	GAS2_HUMAN	growth arrest-specific 2	159					apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|regulation of cell shape (GO:0008360)	actin filament (GO:0005884)|cytosol (GO:0005829)|membrane (GO:0016020)				breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|skin(4)|stomach(1)	24						TTTAAAGGTATGGTGTGGAGC	0.378													t|||	80	0.0159744	0.059	0.0029	5008	,	,		18402	0.0		0.0	False		,,,				2504	0.0				p.Y159Y		Atlas-SNP	.											.	GAS2	46	.	0			c.T477C						PASS	.	C	,,	212,4194	128.6+/-165.4	5,202,1996	73.0	76.0	75.0		477,477,477	4.7	1.0	11	dbSNP_116	75	3,8595	3.0+/-9.4	0,3,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	GAS2	NM_001143830.1,NM_005256.3,NM_177553.2	,,	5,205,6292	CC,CT,TT		0.0349,4.8116,1.6533	,,	159/314,159/314,159/314	22770669	215,12789	2203	4299	6502	SO:0001819	synonymous_variant	2620	exon6			AAGGTATGGTGTG	BC040470	CCDS7858.1	11p14.3	2005-10-11			ENSG00000148935	ENSG00000148935			4167	protein-coding gene	gene with protein product		602835				9521882	Standard	NM_005256		Approved		uc001mqo.3	O43903	OTTHUMG00000166071	ENST00000454584.2:c.477T>C	11.37:g.22770669T>C		116.0	0.0	0		121.0	56.0	0.46281	NM_177553	B2R9C8|D3DQZ0|Q6ICV8|Q7Z3X8	Silent	SNP	ENST00000454584.2	37	CCDS7858.1																																																																																			T|0.988;C|0.012	0.012	strong		0.378	GAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387717.1	NM_177553	
SLC24A1	9187	hgsc.bcm.edu	37	15	65917349	65917349	+	Missense_Mutation	SNP	G	G	C	rs34363823	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:65917349G>C	ENST00000261892.6	+	2	1218	c.931G>C	c.(931-933)Gtc>Ctc	p.V311L	SLC24A1_ENST00000546330.1_Missense_Mutation_p.V311L|SLC24A1_ENST00000339868.6_Missense_Mutation_p.V311L|SLC24A1_ENST00000544319.2_Missense_Mutation_p.V311L|SLC24A1_ENST00000537259.1_Missense_Mutation_p.V311L|SLC24A1_ENST00000399033.4_Missense_Mutation_p.V311L	NM_001254740.1|NM_004727.2	NP_001241669.1|NP_004718.1	O60721	NCKX1_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 1	311			V -> L (in dbSNP:rs34363823).		calcium ion transport (GO:0006816)|ion transport (GO:0006811)|phototransduction, visible light (GO:0007603)|response to light intensity (GO:0009642)|rhodopsin mediated signaling pathway (GO:0016056)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|outer membrane (GO:0019867)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			breast(2)|endometrium(7)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						CCAGGGAACAGTCCTGTTGCA	0.557													G|||	84	0.0167732	0.0348	0.0	5008	,	,		19814	0.002		0.005	False		,,,				2504	0.0317				p.V311L		Atlas-SNP	.											.	SLC24A1	58	.	0			c.G931C	GRCh37	CM025395	SLC24A1	M	rs34363823	PASS	.	G	LEU/VAL	116,3812		1,114,1849	71.0	76.0	74.0		931	0.3	0.0	15	dbSNP_126	74	52,8226		0,52,4087	yes	missense	SLC24A1	NM_004727.2	32	1,166,5936	CC,CG,GG		0.6282,2.9532,1.3764	benign	311/1100	65917349	168,12038	1964	4139	6103	SO:0001583	missense	9187	exon2			GGAACAGTCCTGT	AF062922	CCDS45284.1, CCDS73742.1, CCDS73743.1, CCDS73744.1	15q22.31	2014-01-28			ENSG00000074621	ENSG00000074621		"""Solute carriers"""	10975	protein-coding gene	gene with protein product		603617				9856482	Standard	NM_004727		Approved	NCKX1, NCKX, RODX, KIAA0702, HsT17412, CSNB1D	uc010ujf.2	O60721	OTTHUMG00000167960	ENST00000261892.6:c.931G>C	15.37:g.65917349G>C	ENSP00000261892:p.Val311Leu	39.0	0.0	0		39.0	17.0	0.435897	NM_004727	O43485|O75184|Q17RM9	Missense_Mutation	SNP	ENST00000261892.6	37	CCDS45284.1	26	0.011904761904761904	22	0.044715447154471545	0	0.0	0	0.0	4	0.005277044854881266	G	12.69	2.014890	0.35511	0.029532	0.006282	ENSG00000074621	ENST00000537259;ENST00000261892;ENST00000339868;ENST00000544319;ENST00000399033;ENST00000546330	T;T;T;T;T;T	0.66460	0.04;-0.19;-0.18;-0.19;-0.21;-0.18	5.47	0.277	0.15668	.	2.029760	0.02311	N	0.072094	T	0.35828	0.0945	L	0.47190	1.495	0.09310	N	1	B;B;B;P;P	0.46859	0.052;0.031;0.031;0.885;0.817	B;B;B;P;B	0.50659	0.007;0.01;0.005;0.647;0.444	T	0.40627	-0.9553	10	0.48119	T	0.1	.	4.6642	0.12657	0.2534:0.3026:0.444:0.0	rs34363823	311;311;311;311;311	O60721-2;Q17RM9;O60721;F5H127;B4E1W0	.;.;NCKX1_HUMAN;.;.	L	311	ENSP00000439693:V311L;ENSP00000261892:V311L;ENSP00000341837:V311L;ENSP00000445163:V311L;ENSP00000381991:V311L;ENSP00000439190:V311L	ENSP00000261892:V311L	V	+	1	0	SLC24A1	63704402	0.115000	0.22152	0.000000	0.03702	0.015000	0.08874	1.862000	0.39448	-0.082000	0.12640	-0.882000	0.02950	GTC	G|0.990;C|0.010	0.010	strong		0.557	SLC24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397304.1	NM_004727	
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324237	39324237	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39324237C>G	ENST00000391356.2	-	1	187	c.188G>C	c.(187-189)aGc>aCc	p.S63T		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	63	29 X 5 AA repeats of C-C-[GIKRQVH]-[SPT]- [STA].				aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)				breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(2)|upper_aerodigestive_tract(1)	12		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			cctgcagcagctgggtttgca	0.627																																					p.S63T		Atlas-SNP	.											KRTAP4-3,NS,carcinoma,-1,1	KRTAP4-3	40	1	0			c.G188C						scavenged	.						3.0	5.0	4.0					17																	39324237		1480	3536	5016	SO:0001583	missense	85290	exon1			CAGCAGCTGGGTT	AJ406935	CCDS42331.1	17q21.2	2013-06-25			ENSG00000196156	ENSG00000196156		"""Keratin associated proteins"""	18908	protein-coding gene	gene with protein product							Standard	NM_033187		Approved	KAP4.3	uc010cxl.3	Q9BYR4	OTTHUMG00000133639	ENST00000391356.2:c.188G>C	17.37:g.39324237C>G	ENSP00000375151:p.Ser63Thr	420.0	0.0	0		110.0	18.0	0.163636	NM_033187		Missense_Mutation	SNP	ENST00000391356.2	37	CCDS42331.1	.	.	.	.	.	.	.	.	.	.	.	0.578	-0.838330	0.02692	.	.	ENSG00000196156	ENST00000391356	T	0.01335	5.0	4.13	-2.75	0.05914	.	.	.	.	.	T	0.01061	0.0035	N	0.20881	0.62	0.09310	N	1	B	0.09022	0.002	B	0.11329	0.006	T	0.47573	-0.9107	9	0.14252	T	0.57	.	8.0489	0.30566	0.3482:0.2735:0.3783:0.0	.	63	Q9BYR4	KRA43_HUMAN	T	63	ENSP00000375151:S63T	ENSP00000375151:S63T	S	-	2	0	KRTAP4-3	36577763	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.870000	0.00346	-0.385000	0.07833	-2.956000	0.00083	AGC	.	.	none		0.627	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1		
GALK2	2585	hgsc.bcm.edu	37	15	49574223	49574223	+	Missense_Mutation	SNP	A	A	G	rs35507772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:49574223A>G	ENST00000560031.1	+	6	851	c.544A>G	c.(544-546)Att>Gtt	p.I182V	GALK2_ENST00000561014.1_3'UTR|GALK2_ENST00000559454.1_Missense_Mutation_p.I158V|GALK2_ENST00000327171.3_Missense_Mutation_p.I171V|GALK2_ENST00000544523.1_Missense_Mutation_p.I158V|GALK2_ENST00000396509.2_Missense_Mutation_p.I158V|GALK2_ENST00000543495.1_Missense_Mutation_p.I53V			Q01415	GALK2_HUMAN	galactokinase 2	182			I -> V (in dbSNP:rs35507772).		carbohydrate metabolic process (GO:0005975)|galactose metabolic process (GO:0006012)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|galactokinase activity (GO:0004335)|N-acetylgalactosamine kinase activity (GO:0033858)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		all_lung(180;0.000325)		all cancers(107;3.71e-08)|GBM - Glioblastoma multiforme(94;7e-05)		TGAGCGTTACATTGGCACTGA	0.418													A|||	31	0.0061901	0.0227	0.0014	5008	,	,		20552	0.0		0.0	False		,,,				2504	0.0				p.I182V		Atlas-SNP	.											.	GALK2	78	.	0			c.A544G						PASS	.	A	VAL/ILE,VAL/ILE	85,4307	72.0+/-110.0	0,85,2111	132.0	124.0	126.0		511,544	5.8	1.0	15	dbSNP_126	126	0,8590		0,0,4295	yes	missense,missense	GALK2	NM_001001556.1,NM_002044.2	29,29	0,85,6406	GG,GA,AA		0.0,1.9353,0.6548	benign,benign	171/448,182/459	49574223	85,12897	2196	4295	6491	SO:0001583	missense	2585	exon6			CGTTACATTGGCA		CCDS32236.1, CCDS42034.1, CCDS73724.1	15q21.1-q21.2	2013-09-20			ENSG00000156958	ENSG00000156958	2.7.1.6		4119	protein-coding gene	gene with protein product		137028					Standard	XM_005254279		Approved	GK2	uc001zxj.1	Q01415	OTTHUMG00000172325	ENST00000560031.1:c.544A>G	15.37:g.49574223A>G	ENSP00000453129:p.Ile182Val	133.0	0.0	0		134.0	75.0	0.559702	NM_002044	Q7Z4Q4	Missense_Mutation	SNP	ENST00000560031.1	37	CCDS42034.1	18	0.008241758241758242	17	0.034552845528455285	1	0.0027624309392265192	0	0.0	0	0.0	A	17.89	3.500334	0.64298	0.019353	0.0	ENSG00000156958	ENST00000327171;ENST00000396509;ENST00000543495;ENST00000544523	D;D;D	0.86562	-2.14;-2.14;-2.14	5.79	5.79	0.91817	Ribosomal protein S5 domain 2-type fold (1);GHMP kinase (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);	0.043082	0.85682	D	0.000000	T	0.62245	0.2412	N	0.11870	0.19	0.80722	D	1	B;B	0.32382	0.368;0.174	B;B	0.42062	0.374;0.213	T	0.72047	-0.4408	10	0.15499	T	0.54	-14.2408	16.1193	0.81336	1.0:0.0:0.0:0.0	rs35507772	182;171	Q01415;Q7Z4Q4	GALK2_HUMAN;.	V	171;182;53;158	ENSP00000316632:I171V;ENSP00000443220:I53V;ENSP00000440312:I158V	ENSP00000316632:I171V	I	+	1	0	GALK2	47361515	1.000000	0.71417	0.999000	0.59377	0.968000	0.65278	5.983000	0.70540	2.201000	0.70794	0.533000	0.62120	ATT	A|0.992;G|0.008	0.008	strong		0.418	GALK2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417854.1		
NADK	65220	hgsc.bcm.edu	37	1	1688719	1688719	+	Silent	SNP	C	C	A	rs78921781	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1688719C>A	ENST00000341426.5	-	4	515	c.294G>T	c.(292-294)ctG>ctT	p.L98L	NADK_ENST00000492768.1_5'UTR|NADK_ENST00000342348.5_Silent_p.L66L|NADK_ENST00000344463.4_Silent_p.L202L|NADK_ENST00000378625.1_Silent_p.L202L|NADK_ENST00000341991.3_Silent_p.L98L	NM_023018.4	NP_075394.3	O95544	NADK_HUMAN	NAD kinase	98					ATP metabolic process (GO:0046034)|NAD metabolic process (GO:0019674)|NADP biosynthetic process (GO:0006741)|phosphorylation (GO:0016310)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			NS(1)|autonomic_ganglia(1)|endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|stomach(1)|urinary_tract(1)	17	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;5.61e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;8.75e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.33e-23)|GBM - Glioblastoma multiforme(42;1.35e-07)|Colorectal(212;0.000203)|COAD - Colon adenocarcinoma(227;0.000225)|Kidney(185;0.00265)|STAD - Stomach adenocarcinoma(132;0.00655)|BRCA - Breast invasive adenocarcinoma(365;0.00855)|KIRC - Kidney renal clear cell carcinoma(229;0.0382)|Lung(427;0.207)		TGTTCCACGTCAGCCGCTGGC	0.552													C|||	27	0.00539137	0.0159	0.0014	5008	,	,		10189	0.001		0.004	False		,,,				2504	0.0				p.L202L		Atlas-SNP	.											.	NADK	79	.	0			c.G606T						PASS	.	C	,,,	69,4337	62.3+/-99.4	1,67,2135	97.0	98.0	98.0		294,606,198,294	5.7	1.0	1	dbSNP_133	98	7,8593	6.4+/-24.3	1,5,4294	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NADK	NM_001198993.1,NM_001198994.1,NM_001198995.1,NM_023018.4	,,,	2,72,6429	AA,AC,CC		0.0814,1.566,0.5843	,,,	98/447,202/592,66/415,98/447	1688719	76,12930	2203	4300	6503	SO:0001819	synonymous_variant	65220	exon6			CCACGTCAGCCGC	BC001709	CCDS30565.1, CCDS55561.1, CCDS55562.1	1p36.33	2013-04-29			ENSG00000008130	ENSG00000008130	2.7.1.23		29831	protein-coding gene	gene with protein product		611616				11594753	Standard	NM_023018		Approved	FLJ13052	uc001aie.3	O95544	OTTHUMG00000000942	ENST00000341426.5:c.294G>T	1.37:g.1688719C>A		71.0	0.0	0		73.0	39.0	0.534247	NM_001198994	A6NNN3|A8K296|B7Z434|F5GXR5|Q5QPS4|Q9H2P2|Q9H931	Silent	SNP	ENST00000341426.5	37	CCDS30565.1																																																																																			C|0.995;A|0.005	0.005	strong		0.552	NADK-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000002769.1	NM_023018	
OR4A5	81318	hgsc.bcm.edu	37	11	51411817	51411817	+	Silent	SNP	G	G	A	rs144502772	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:51411817G>A	ENST00000319760.6	-	1	631	c.579C>T	c.(577-579)ggC>ggT	p.G193G		NM_001005272.3	NP_001005272.3	Q8NH83	OR4A5_HUMAN	olfactory receptor, family 4, subfamily A, member 5	193						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)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(28)|ovary(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	49		all_lung(304;0.236)				CAACAGTGAGGCCTATAAAGT	0.428													.|||	30	0.00599042	0.0219	0.0014	5008	,	,		20435	0.0		0.0	False		,,,				2504	0.0				p.G193G		Atlas-SNP	.											.	OR4A5	116	.	0			c.C579T						PASS	.	G		102,4300		2,98,2101	62.0	55.0	57.0		579	-2.1	0.1	11	dbSNP_134	57	0,8590		0,0,4295	no	coding-synonymous	OR4A5	NM_001005272.3		2,98,6396	AA,AG,GG		0.0,2.3171,0.7851		193/316	51411817	102,12890	2201	4295	6496	SO:0001819	synonymous_variant	81318	exon1			AGTGAGGCCTATA	AB065506	CCDS73289.1	11p11.12	2012-08-09			ENSG00000221840	ENSG00000221840		"""GPCR / Class A : Olfactory receptors"""	15162	protein-coding gene	gene with protein product							Standard	NM_001005272		Approved		uc001nhi.2	Q8NH83	OTTHUMG00000166764	ENST00000319760.6:c.579C>T	11.37:g.51411817G>A		88.0	0.0	0		105.0	58.0	0.552381	NM_001005272	Q6IF84	Silent	SNP	ENST00000319760.6	37	CCDS31497.1																																																																																			G|0.993;A|0.007	0.007	strong		0.428	OR4A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391399.1	NM_001005272	
AHNAK2	113146	hgsc.bcm.edu	37	14	105417777	105417777	+	Silent	SNP	C	C	T	rs1960092	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105417777C>T	ENST00000333244.5	-	7	4130	c.4011G>A	c.(4009-4011)tcG>tcA	p.S1337S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1337						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			ACACCCCGAACGACGGCATCT	0.612													.|||	385	0.076877	0.2693	0.0173	5008	,	,		14219	0.0079		0.007	False		,,,				2504	0.002				p.S1337S		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G4011A						PASS	.	G		843,2819		207,429,1195	147.0	129.0	135.0		4011	-2.5	0.0	14	dbSNP_92	135	21,6593		3,15,3289	no	coding-synonymous	AHNAK2	NM_138420.2		210,444,4484	TT,TC,CC		0.3175,23.0202,8.4079		1337/5796	105417777	864,9412	1831	3307	5138	SO:0001819	synonymous_variant	113146	exon7			CCCGAACGACGGC	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.4011G>A	14.37:g.105417777C>T		374.0	0.0	0		255.0	254.0	0.996078	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			C|0.959;T|0.041	0.041	strong		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
OTUD7B	56957	hgsc.bcm.edu	37	1	149916584	149916584	+	Silent	SNP	C	C	G	rs200362140	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:149916584C>G	ENST00000369135.4	-	12	1998	c.1704G>C	c.(1702-1704)ggG>ggC	p.G568G		NM_020205.2	NP_064590.2	Q6GQQ9	OTU7B_HUMAN	OTU deubiquitinase 7B	568					mucosal immune response (GO:0002385)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|DNA binding (GO:0003677)|Lys48-specific deubiquitinase activity (GO:1990380)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)			CAGGCCCATCCCCAGCTGCCT	0.572													C|||	10	0.00199681	0.0076	0.0	5008	,	,		16047	0.0		0.0	False		,,,				2504	0.0				p.G568G		Atlas-SNP	.											.	OTUD7B	76	.	0			c.G1704C						PASS	.	C		16,4136		0,16,2060	73.0	82.0	79.0		1704	0.7	1.0	1		79	0,8438		0,0,4219	no	coding-synonymous	OTUD7B	NM_020205.2		0,16,6279	GG,GC,CC		0.0,0.3854,0.1271		568/844	149916584	16,12574	2076	4219	6295	SO:0001819	synonymous_variant	56957	exon12			CCCATCCCCAGCT	AJ293573	CCDS72903.1	1q21.2	2014-02-24	2014-02-24	2006-07-07	ENSG00000163113	ENSG00000264522		"""OTU domain containing"""	16683	protein-coding gene	gene with protein product		611748	"""zinc finger, A20 domain containing 1"", ""OTU domain containing 7B"""	ZA20D1		11463333, 23827681	Standard	NM_020205		Approved	CEZANNE	uc001etn.3	Q6GQQ9	OTTHUMG00000012291	ENST00000369135.4:c.1704G>C	1.37:g.149916584C>G		63.0	0.0	0		70.0	39.0	0.557143	NM_020205	B7Z643|D3DUZ8|Q5SZ60|Q8WWA7|Q9NQ53|Q9UFF4	Silent	SNP	ENST00000369135.4	37	CCDS41389.1																																																																																			C|0.999;G|0.001	0.001	strong		0.572	OTUD7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034146.3	NM_020205	
OR10K1	391109	hgsc.bcm.edu	37	1	158435572	158435572	+	Missense_Mutation	SNP	C	C	T	rs78779179|rs386635902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158435572C>T	ENST00000289451.2	+	1	301	c.221C>T	c.(220-222)aCc>aTc	p.T74I		NM_001004473.1	NP_001004473.1	Q8NGX5	O10K1_HUMAN	olfactory receptor, family 10, subfamily K, member 1	74						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)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	27	all_hematologic(112;0.0378)					ATTTGCTATACCTTTGTCATT	0.453													C|||	189	0.0377396	0.1354	0.013	5008	,	,		24656	0.0		0.001	False		,,,				2504	0.0				p.T74I		Atlas-SNP	.											.	OR10K1	80	.	0			c.C221T						PASS	.	C	ILE/THR	501,3905	216.4+/-235.1	27,447,1729	209.0	190.0	197.0		221	4.5	1.0	1	dbSNP_131	197	8,8592	6.4+/-24.3	0,8,4292	yes	missense	OR10K1	NM_001004473.1	89	27,455,6021	TT,TC,CC		0.093,11.3709,3.9136	probably-damaging	74/314	158435572	509,12497	2203	4300	6503	SO:0001583	missense	391109	exon1			GCTATACCTTTGT	AP002532	CCDS30897.1	1q23.1	2012-08-09			ENSG00000173285	ENSG00000173285		"""GPCR / Class A : Olfactory receptors"""	14693	protein-coding gene	gene with protein product							Standard	NM_001004473		Approved		uc010pij.2	Q8NGX5	OTTHUMG00000017517	ENST00000289451.2:c.221C>T	1.37:g.158435572C>T	ENSP00000289451:p.Thr74Ile	490.0	0.0	0		474.0	204.0	0.43038	NM_001004473	Q6IFS2	Missense_Mutation	SNP	ENST00000289451.2	37	CCDS30897.1	55	0.025183150183150184	49	0.09959349593495935	6	0.016574585635359115	0	0.0	0	0.0	c	13.70	2.316088	0.40996	0.113709	9.3E-4	ENSG00000173285	ENST00000289451	T	0.00444	7.4	4.5	4.5	0.54988	GPCR, rhodopsin-like superfamily (1);	0.000000	0.44285	D	0.000467	T	0.00384	0.0012	L	0.49778	1.585	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.53173	-0.8476	10	0.62326	D	0.03	.	10.4216	0.44354	0.0:0.9045:0.0:0.0955	.	74	Q8NGX5	O10K1_HUMAN	I	74	ENSP00000289451:T74I	ENSP00000289451:T74I	T	+	2	0	OR10K1	156702196	0.000000	0.05858	0.999000	0.59377	0.887000	0.51463	0.237000	0.17985	2.311000	0.77944	0.557000	0.71058	ACC	C|0.966;T|0.034	0.034	strong		0.453	OR10K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046367.1		
SSPO	23145	hgsc.bcm.edu	37	7	149506195	149506195	+	RNA	SNP	C	C	T	rs73727627	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149506195C>T	ENST00000378016.2	+	0	9187							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CTACAGGAACCGCACCCGAGG	0.682													C|||	125	0.0249601	0.0772	0.0115	5008	,	,		13530	0.001		0.002	False		,,,				2504	0.0123				p.R3063C		Atlas-SNP	.											.	.	.	.	0			c.C9187T						PASS	.	C		235,3871		4,227,1822	16.0	24.0	22.0		9195	5.2	1.0	7	dbSNP_130	22	32,8324		0,32,4146	no	coding-notMod3	SSPO	NM_198455.2		4,259,5968	TT,TC,CC		0.383,5.7233,2.1425			149506195	267,12195	2053	4178	6231			23145	exon63			AGGAACCGCACCC	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149506195C>T		259.0	1.0	0.003861		292.0	154.0	0.527397	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.978;T|0.022	0.022	strong		0.682	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
EXPH5	23086	hgsc.bcm.edu	37	11	108380609	108380609	+	Silent	SNP	C	C	T	rs115867994	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:108380609C>T	ENST00000265843.4	-	6	5735	c.5625G>A	c.(5623-5625)agG>agA	p.R1875R	EXPH5_ENST00000428840.1_Silent_p.R1799R|EXPH5_ENST00000525344.1_Silent_p.R1868R|EXPH5_ENST00000443411.1_Silent_p.R1687R	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1875					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		ATATTGCAGACCTGGGACCTG	0.418													C|||	66	0.0131789	0.0492	0.0014	5008	,	,		19501	0.0		0.0	False		,,,				2504	0.0				p.R1875R		Atlas-SNP	.											.	EXPH5	193	.	0			c.G5625A						PASS	.	C		174,4228	114.6+/-152.6	0,174,2027	62.0	63.0	63.0		5625	2.2	0.2	11	dbSNP_132	63	0,8596		0,0,4298	no	coding-synonymous	EXPH5	NM_015065.2		0,174,6325	TT,TC,CC		0.0,3.9527,1.3387		1875/1990	108380609	174,12824	2201	4298	6499	SO:0001819	synonymous_variant	23086	exon6			TGCAGACCTGGGA		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.5625G>A	11.37:g.108380609C>T		150.0	0.0	0		157.0	74.0	0.471338	NM_015065	Q2KHM1|Q9Y4D6	Silent	SNP	ENST00000265843.4	37	CCDS8341.1																																																																																			C|0.986;T|0.014	0.014	strong		0.418	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
DLG5	9231	hgsc.bcm.edu	37	10	79616520	79616520	+	Silent	SNP	G	G	C	rs12243930	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:79616520G>C	ENST00000372391.2	-	3	509	c.504C>G	c.(502-504)gcC>gcG	p.A168A	DLG5_ENST00000372388.2_Silent_p.A168A	NM_004747.3	NP_004738.3	Q8TDM6	DLG5_HUMAN	discs, large homolog 5 (Drosophila)	168					apical protein localization (GO:0045176)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|intracellular signal transduction (GO:0035556)|metanephric collecting duct development (GO:0072205)|midbrain development (GO:0030901)|negative regulation of cell proliferation (GO:0008285)|polarized epithelial cell differentiation (GO:0030859)|protein complex assembly (GO:0006461)|protein localization to adherens junction (GO:0071896)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|zonula adherens assembly (GO:0045186)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cytoskeletal protein binding (GO:0008092)|receptor signaling complex scaffold activity (GO:0030159)			breast(9)|central_nervous_system(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(8)|lung(17)|ovary(5)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	60	all_cancers(46;0.0316)|all_epithelial(25;0.00147)|Breast(12;0.0015)|Prostate(51;0.0146)		Epithelial(14;0.00105)|OV - Ovarian serous cystadenocarcinoma(4;0.00151)|all cancers(16;0.00446)			GCGTAGCAAAGGCCAGGCGCT	0.592													G|||	720	0.14377	0.5197	0.0432	5008	,	,		18218	0.0		0.003	False		,,,				2504	0.0				p.A168A		Atlas-SNP	.											.	DLG5	154	.	0			c.C504G						PASS	.	G		1939,2467	545.8+/-376.9	450,1039,714	46.0	48.0	47.0		504	4.5	1.0	10	dbSNP_120	47	24,8576	14.6+/-50.1	0,24,4276	no	coding-synonymous	DLG5	NM_004747.3		450,1063,4990	CC,CG,GG		0.2791,44.0082,15.093		168/1920	79616520	1963,11043	2203	4300	6503	SO:0001819	synonymous_variant	9231	exon3			AGCAAAGGCCAGG	U61843	CCDS7353.2	10q23	2008-07-09	2001-11-28		ENSG00000151208	ENSG00000151208			2904	protein-coding gene	gene with protein product		604090	"""discs, large (Drosophila) homolog 5"""			9738934	Standard	XM_005270276		Approved	P-dlg, KIAA0583	uc001jzk.3	Q8TDM6	OTTHUMG00000018548	ENST00000372391.2:c.504C>G	10.37:g.79616520G>C		206.0	0.0	0		198.0	95.0	0.479798	NM_004747	A6H8Y3|Q149N1|Q5T1H7|Q5T1H8|Q6DKG3|Q86WC0|Q8TDM7|Q9UE73|Q9Y4E3	Silent	SNP	ENST00000372391.2	37	CCDS7353.2																																																																																			G|0.857;C|0.143	0.143	strong		0.592	DLG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048900.2		
CEP250	11190	hgsc.bcm.edu	37	20	34091624	34091624	+	Silent	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34091624G>A	ENST00000397527.1	+	30	6147	c.5427G>A	c.(5425-5427)caG>caA	p.Q1809Q	CEP250_ENST00000342580.4_Silent_p.Q1753Q	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	1809	Gln/Glu-rich.				centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			ATGAGGCCCAGAGAGCCCTAG	0.597																																					p.Q1809Q		Atlas-SNP	.											.	CEP250	141	.	0			c.G5427A						PASS	.						55.0	59.0	58.0					20																	34091624		2203	4300	6503	SO:0001819	synonymous_variant	11190	exon30			GGCCCAGAGAGCC	AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"""centrosomal protein 2"""	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.5427G>A	20.37:g.34091624G>A		57.0	0.0	0		85.0	41.0	0.482353	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Silent	SNP	ENST00000397527.1	37	CCDS13255.1																																																																																			.	.	none		0.597	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186	
B3GNT2	10678	hgsc.bcm.edu	37	2	62449664	62449664	+	Silent	SNP	G	G	A	rs72893877	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:62449664G>A	ENST00000301998.4	+	2	561	c.309G>A	c.(307-309)acG>acA	p.T103T	B3GNT2_ENST00000405767.1_Silent_p.T103T	NM_006577.5	NP_006568.2	Q9NY97	B3GN2_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 2	103					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	galactosyltransferase activity (GO:0008378)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(6)|ovary(1)|pancreas(1)	18	Lung NSC(7;0.031)|all_lung(7;0.0634)		LUSC - Lung squamous cell carcinoma(7;3.55e-06)|Epithelial(17;0.0963)			TGAGGGTCACGTCGGTGGTTA	0.502													G|||	22	0.00439297	0.0151	0.0029	5008	,	,		18758	0.0		0.0	False		,,,				2504	0.0				p.T103T		Atlas-SNP	.											.	B3GNT2	34	.	0			c.G309A						PASS	.	G		63,4343	56.2+/-92.4	0,63,2140	216.0	242.0	233.0		309	-11.5	0.0	2	dbSNP_130	233	0,8600		0,0,4300	no	coding-synonymous	B3GNT2	NM_006577.5		0,63,6440	AA,AG,GG		0.0,1.4299,0.4844		103/398	62449664	63,12943	2203	4300	6503	SO:0001819	synonymous_variant	10678	exon2			GGTCACGTCGGTG	AB049584	CCDS1870.1	2p15	2013-02-19	2006-04-12	2006-04-12	ENSG00000170340	ENSG00000170340		"""Beta 3-glycosyltransferases"""	15629	protein-coding gene	gene with protein product		605581	"""UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 1"""	B3GNT1		9892646, 11042166	Standard	NM_006577		Approved	B3GNT-2, BETA3GNT, B3GN-T2, B3GN-T1	uc002sbs.3	Q9NY97	OTTHUMG00000129444	ENST00000301998.4:c.309G>A	2.37:g.62449664G>A		106.0	0.0	0		132.0	76.0	0.575758	NM_006577	Q54AC1|Q9NQQ9|Q9NQR0|Q9NUT9	Silent	SNP	ENST00000301998.4	37	CCDS1870.1																																																																																			G|0.996;A|0.004	0.004	strong		0.502	B3GNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251606.2	NM_006577	
ENAM	10117	hgsc.bcm.edu	37	4	71510368	71510368	+	Silent	SNP	C	C	T	rs61737041	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:71510368C>T	ENST00000396073.3	+	9	3506	c.3225C>T	c.(3223-3225)agC>agT	p.S1075S	ENAM_ENST00000472903.1_Intron	NM_031889.2	NP_114095.2	Q9NRM1	ENAM_HUMAN	enamelin	1075					amelogenesis (GO:0097186)|biomineral tissue development (GO:0031214)	proteinaceous extracellular matrix (GO:0005578)				haematopoietic_and_lymphoid_tissue(1)|ovary(3)|upper_aerodigestive_tract(2)	6			Lung(101;0.235)			CTCCATCTAGCGATGGAAGGC	0.433													C|||	40	0.00798722	0.0295	0.0014	5008	,	,		24126	0.0		0.0	False		,,,				2504	0.0				p.S1075S		Atlas-SNP	.											.	ENAM	140	.	0			c.C3225T						PASS	.	C		106,4300	82.4+/-120.9	2,102,2099	96.0	93.0	94.0		3225	4.2	1.0	4	dbSNP_129	94	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ENAM	NM_031889.2		2,103,6398	TT,TC,CC		0.0116,2.4058,0.8227		1075/1143	71510368	107,12899	2203	4300	6503	SO:0001819	synonymous_variant	10117	exon9			ATCTAGCGATGGA	AF125373	CCDS3544.2	4q13.3	2008-02-05			ENSG00000132464	ENSG00000132464			3344	protein-coding gene	gene with protein product		606585	"""amelogenesis imperfecta 2, hypocalcification (autosomal dominant)"""	AIH2		11978766	Standard	NM_031889		Approved		uc011caw.1	Q9NRM1	OTTHUMG00000129914	ENST00000396073.3:c.3225C>T	4.37:g.71510368C>T		254.0	0.0	0		266.0	127.0	0.477444	NM_031889	Q17RI5|Q9H3D1	Silent	SNP	ENST00000396073.3	37	CCDS3544.2																																																																																			C|0.993;T|0.007	0.007	strong		0.433	ENAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252166.3	NM_031889	
DMKN	93099	hgsc.bcm.edu	37	19	36002488	36002488	+	Missense_Mutation	SNP	C	C	A	rs57760262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36002488C>A	ENST00000339686.3	-	5	919	c.743G>T	c.(742-744)aGc>aTc	p.S248I	DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000447113.2_Missense_Mutation_p.S248I|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000451297.2_Missense_Mutation_p.S248I|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000440396.1_Missense_Mutation_p.S248I|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000424570.2_Missense_Mutation_p.S248I|DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000458071.1_5'Flank|DMKN_ENST00000418261.1_Missense_Mutation_p.S248I	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	248	Gly-rich.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(7)|ovary(1)|prostate(1)|skin(2)	27	all_lung(56;1.89e-08)|Lung NSC(56;2.9e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			CTGTGAGCCGCTGCCTCCCTG	0.637													C|||	173	0.0345447	0.1241	0.0101	5008	,	,		18431	0.0		0.002	False		,,,				2504	0.0				p.S248I		Atlas-SNP	.											DMKN,NS,carcinoma,+1,1	DMKN	116	1	0			c.G743T						PASS	.	C	ILE/SER,ILE/SER,ILE/SER,ILE/SER,ILE/SER,,	365,4041	183.6+/-211.2	14,337,1852	34.0	31.0	32.0		743,743,743,743,743,,	2.7	0.7	19	dbSNP_129	32	4,8596	3.0+/-9.4	0,4,4296	yes	missense,missense,missense,missense,missense,intron,intron	DMKN	NM_001126057.2,NM_001126058.2,NM_001190348.1,NM_001190349.1,NM_033317.4,NM_001126056.2,NM_001190347.1	142,142,142,142,142,,	14,341,6148	AA,AC,CC		0.0465,8.2842,2.8372	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,,	248/399,248/387,248/437,248/370,248/477,,	36002488	369,12637	2203	4300	6503	SO:0001583	missense	93099	exon5			GAGCCGCTGCCTC	BC035311	CCDS12463.1, CCDS42549.1, CCDS46051.1, CCDS46052.1, CCDS46053.1, CCDS46054.1, CCDS46054.2, CCDS54250.1, CCDS54251.1, CCDS54252.1	19q13.12	2008-10-27			ENSG00000161249	ENSG00000161249			25063	protein-coding gene	gene with protein product						16374476	Standard	NM_001035516		Approved	ZD52F10	uc002nzm.4	Q6E0U4	OTTHUMG00000048101	ENST00000339686.3:c.743G>T	19.37:g.36002488C>A	ENSP00000342012:p.Ser248Ile	82.0	0.0	0		76.0	40.0	0.526316	NM_001126058	A3EZ79|A3EZ80|A3EZ81|A3EZ82|A3EZ83|C9J4P6|C9J5N8|C9JAL3|Q32W58|Q32W62|Q32W63|Q32W64|Q32W65|Q32W66|Q32W67|Q6E0U5|Q6UXC7|Q96EW8|Q9BSY6	Missense_Mutation	SNP	ENST00000339686.3	37	CCDS12463.1	62	0.028388278388278388	56	0.11382113821138211	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	C	13.09	2.132916	0.37630	0.082842	4.65E-4	ENSG00000161249	ENST00000339686;ENST00000392207;ENST00000447113;ENST00000440396;ENST00000418261;ENST00000424570;ENST00000451297	T;T;T;T;T;T	0.49720	0.77;0.77;0.77;0.77;0.77;0.77	3.78	2.73	0.32206	.	0.880319	0.09618	N	0.777875	T	0.02012	0.0063	L	0.52573	1.65	0.24630	N	0.993629	D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.997	D;D;D;D;P	0.69479	0.964;0.964;0.964;0.964;0.899	T	0.01078	-1.1459	10	0.72032	D	0.01	-3.8258	7.2516	0.26152	0.0:0.8755:0.0:0.1245	rs57760262	248;248;248;248;248	E7EUS0;Q6E0U4-7;Q6E0U4-3;Q6E0U4-5;Q6E0U4	.;.;.;.;DMKN_HUMAN	I	248	ENSP00000342012:S248I;ENSP00000394908:S248I;ENSP00000415277:S248I;ENSP00000414743:S248I;ENSP00000388404:S248I;ENSP00000409513:S248I	ENSP00000342012:S248I	S	-	2	0	DMKN	40694328	0.006000	0.16342	0.659000	0.29680	0.091000	0.18340	0.717000	0.25851	0.948000	0.37687	0.561000	0.74099	AGC	C|0.967;A|0.033	0.033	strong		0.637	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
TMEM232	642987	hgsc.bcm.edu	37	5	109961032	109961032	+	Missense_Mutation	SNP	C	C	T	rs61730863	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:109961032C>T	ENST00000455884.2	-	7	754	c.704G>A	c.(703-705)cGt>cAt	p.R235H	TMEM232_ENST00000515518.2_5'UTR|TMEM232_ENST00000429839.2_Missense_Mutation_p.R235H			C9JQI7	TM232_HUMAN	transmembrane protein 232	235						integral component of membrane (GO:0016021)				breast(1)|kidney(2)	3						GGATTCAGAACGGAGTTCTCT	0.378													C|||	149	0.0297524	0.1104	0.0029	5008	,	,		17282	0.0		0.001	False		,,,				2504	0.0				p.R235H		Atlas-SNP	.											.	TMEM232	57	.	0			c.G704A						PASS	.	C	HIS/ARG	111,1273		6,99,587	227.0	195.0	204.0		704	-9.4	0.0	5	dbSNP_129	204	0,3182		0,0,1591	yes	missense	TMEM232	NM_001039763.3	29	6,99,2178	TT,TC,CC		0.0,8.0202,2.431	benign	235/658	109961032	111,4455	692	1591	2283	SO:0001583	missense	642987	exon7			TCAGAACGGAGTT	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.704G>A	5.37:g.109961032C>T	ENSP00000401477:p.Arg235His	153.0	0.0	0		168.0	89.0	0.529762	NM_001039763	B4DKF4	Missense_Mutation	SNP	ENST00000455884.2	37	CCDS47253.2	50	0.022893772893772892	49	0.09959349593495935	1	0.0027624309392265192	0	0.0	0	0.0	C	9.585	1.124637	0.20959	0.080202	0.0	ENSG00000186952	ENST00000429839;ENST00000455884;ENST00000511883	.	.	.	4.72	-9.44	0.00603	.	1.502430	0.03762	N	0.258267	T	0.00356	0.0011	N	0.05383	-0.06	0.09310	N	1	B;B;B	0.12630	0.006;0.002;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.06338	-1.0832	8	.	.	.	4.4953	4.058	0.09826	0.1922:0.274:0.4192:0.1145	.	235;235;117	C9JQI7;C9JQI7-2;E9PFK0	TM232_HUMAN;.;.	H	235	.	.	R	-	2	0	TMEM232	109988931	0.000000	0.05858	0.000000	0.03702	0.099000	0.18886	-2.983000	0.00661	-2.769000	0.00366	-0.340000	0.08031	CGT	C|0.975;T|0.025	0.025	strong		0.378	TMEM232-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372488.2	NM_001039763	
KRTAP4-4	84616	hgsc.bcm.edu	37	17	39316870	39316870	+	Missense_Mutation	SNP	T	T	C	rs385055	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39316870T>C	ENST00000390661.3	-	1	113	c.74A>G	c.(73-75)tAc>tGc	p.Y25C		NM_032524.1	NP_115913.1	Q9BYR3	KRA44_HUMAN	keratin associated protein 4-4	25	26 X 5 AA repeats of C-C-[GRQVCH]-[SPT]- [VSTQR].		Y -> C (in dbSNP:rs385055).			keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(5)	7		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000449)			GGTCTGGCAGTAGCTGGGACG	0.637													C|||	641	0.127995	0.466	0.0331	5008	,	,		19142	0.0		0.002	False		,,,				2504	0.0				p.Y25C		Atlas-SNP	.											KRTAP4-4,NS,carcinoma,-1,1	KRTAP4-4	21	1	0			c.A74G						PASS	.	C	CYS/TYR	1640,2760		330,980,890	50.0	68.0	62.0		74	4.6	0.9	17	dbSNP_80	62	10,8590		0,10,4290	no	missense	KRTAP4-4	NM_032524.1	194	330,990,5180	CC,CT,TT		0.1163,37.2727,12.6923	benign	25/167	39316870	1650,11350	2200	4300	6500	SO:0001583	missense	84616	exon1			TGGCAGTAGCTGG	AJ406936	CCDS11383.1	17q21.2	2013-06-25			ENSG00000171396	ENSG00000171396		"""Keratin associated proteins"""	16928	protein-coding gene	gene with protein product			"""keratin associated protein 4-13"""	KRTAP4-13		11279113	Standard	NM_032524		Approved	KAP4.4, KAP4.13	uc002hwc.3	Q9BYR3	OTTHUMG00000133428	ENST00000390661.3:c.74A>G	17.37:g.39316870T>C	ENSP00000375076:p.Tyr25Cys	188.0	1.0	0.00531915		134.0	134.0	1	NM_032524	Q9BYU7	Missense_Mutation	SNP	ENST00000390661.3	37	CCDS11383.1	231	0.10576923076923077	218	0.44308943089430897	13	0.03591160220994475	0	0.0	0	0.0	.	0.052	-1.247813	0.01469	0.372727	0.001163	ENSG00000171396	ENST00000390661	T	0.00571	6.5	4.62	4.62	0.57501	.	0.157197	0.29868	N	0.010999	T	0.00012	0.0000	N	0.00005	-3.295	0.42889	P	0.005808000000000035	B	0.02656	0.0	B	0.01281	0.0	T	0.19647	-1.0299	9	0.02654	T	1	.	10.7732	0.46336	0.0:0.9051:0.0:0.0949	rs385055;rs59740078	25	Q9BYR3	KRA44_HUMAN	C	25	ENSP00000375076:Y25C	ENSP00000375076:Y25C	Y	-	2	0	KRTAP4-4	36570396	0.010000	0.17322	0.851000	0.33527	0.345000	0.29048	0.694000	0.25512	0.943000	0.37553	-0.227000	0.12334	TAC	T|0.890;C|0.110	0.110	strong		0.637	KRTAP4-4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257291.1		
SLC26A10	65012	hgsc.bcm.edu	37	12	58019388	58019388	+	Missense_Mutation	SNP	C	C	T	rs114079678	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:58019388C>T	ENST00000320442.4	+	14	1863	c.1552C>T	c.(1552-1554)Cgg>Tgg	p.R518W	SLC26A10_ENST00000379218.2_3'UTR|SLC26A10_ENST00000490243.1_Intron	NM_133489.2	NP_597996.2	Q8NG04	S2610_HUMAN	solute carrier family 26, member 10	518	STAS. {ECO:0000255|PROSITE- ProRule:PRU00198}.					integral component of membrane (GO:0016021)	antiporter activity (GO:0015297)|sulfate transmembrane transporter activity (GO:0015116)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(7)	19	Melanoma(17;0.122)					GACACTGACCCGGGTAGGACT	0.587													C|||	6	0.00119808	0.0045	0.0	5008	,	,		19242	0.0		0.0	False		,,,				2504	0.0				p.R518W		Atlas-SNP	.											.	SLC26A10	89	.	0			c.C1552T						PASS	.	C	TRP/ARG	21,4385		0,21,2182	63.0	58.0	60.0		1552	1.2	0.8	12	dbSNP_133	60	1,8599		0,1,4299	yes	missense	SLC26A10	NM_133489.2	101	0,22,6481	TT,TC,CC		0.0116,0.4766,0.1692	probably-damaging	518/564	58019388	22,12984	2203	4300	6503	SO:0001583	missense	65012	exon14			CTGACCCGGGTAG		CCDS8949.2	12q13	2013-07-18			ENSG00000135502	ENSG00000135502		"""Solute carriers"""	14470	protein-coding gene	gene with protein product							Standard	NM_133489		Approved		uc001spe.3	Q8NG04	OTTHUMG00000128505	ENST00000320442.4:c.1552C>T	12.37:g.58019388C>T	ENSP00000320217:p.Arg518Trp	81.0	0.0	0		82.0	35.0	0.426829	NM_133489	A6NMJ2|B6ZDQ3|Q6ZWI7	Missense_Mutation	SNP	ENST00000320442.4	37	CCDS8949.2	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	.	9.455	1.091629	0.20471	0.004766	1.16E-4	ENSG00000135502	ENST00000320442	D	0.89343	-2.5	4.62	1.25	0.21368	Sulphate transporter/antisigma-factor antagonist STAS (4);	.	.	.	.	T	0.81531	0.4842	L	0.56199	1.76	0.41713	D	0.989468	B	0.27316	0.175	B	0.14023	0.01	T	0.76225	-0.3037	9	0.87932	D	0	.	1.6978	0.02866	0.2061:0.4624:0.1995:0.132	.	518	Q8NG04	S2610_HUMAN	W	518	ENSP00000320217:R518W	ENSP00000320217:R518W	R	+	1	2	SLC26A10	56305655	0.903000	0.30736	0.796000	0.32109	0.255000	0.26057	0.125000	0.15749	0.554000	0.29061	0.557000	0.71058	CGG	C|0.999;T|0.001	0.001	strong		0.587	SLC26A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250311.2		
ITPKC	80271	hgsc.bcm.edu	37	19	41223387	41223387	+	Missense_Mutation	SNP	A	A	T	rs145275994	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:41223387A>T	ENST00000263370.2	+	1	380	c.347A>T	c.(346-348)gAc>gTc	p.D116V	ADCK4_ENST00000243583.6_5'Flank|ADCK4_ENST00000324464.3_5'Flank|ADCK4_ENST00000450541.1_5'Flank	NM_025194.2	NP_079470.1	Q96DU7	IP3KC_HUMAN	inositol-trisphosphate 3-kinase C	116					inositol phosphate metabolic process (GO:0043647)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	14			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)			ACGGAGCCAGACAGGTCCAGC	0.602													A|||	17	0.00339457	0.0121	0.0014	5008	,	,		13975	0.0		0.0	False		,,,				2504	0.0				p.D116V		Atlas-SNP	.											.	ITPKC	36	.	0			c.A347T						PASS	.	A	VAL/ASP	41,4363	43.1+/-76.7	0,41,2161	52.0	59.0	57.0		347	1.9	0.0	19	dbSNP_134	57	0,8600		0,0,4300	yes	missense	ITPKC	NM_025194.2	152	0,41,6461	TT,TA,AA		0.0,0.931,0.3153	benign	116/684	41223387	41,12963	2202	4300	6502	SO:0001583	missense	80271	exon1			AGCCAGACAGGTC	Y11999	CCDS12563.1	19q13.1	2011-04-28	2011-04-28		ENSG00000086544	ENSG00000086544	2.7.1.127		14897	protein-coding gene	gene with protein product		606476	"""inositol 1,4,5-trisphosphate 3-kinase C"""			11085927	Standard	NM_025194		Approved	IP3KC, IP3-3KC	uc002oot.3	Q96DU7		ENST00000263370.2:c.347A>T	19.37:g.41223387A>T	ENSP00000263370:p.Asp116Val	53.0	0.0	0		95.0	44.0	0.463158	NM_025194	Q9UE25|Q9Y475	Missense_Mutation	SNP	ENST00000263370.2	37	CCDS12563.1	2	9.157509157509158E-4	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	0	0.0	A	2.482	-0.319454	0.05386	0.00931	0.0	ENSG00000086544	ENST00000263370	.	.	.	4.07	1.93	0.25924	.	0.659632	0.13336	N	0.395559	T	0.17789	0.0427	N	0.19112	0.55	0.19775	N	0.999958	B	0.17667	0.023	B	0.15870	0.014	T	0.17107	-1.0380	9	0.27785	T	0.31	-3.0482	6.4104	0.21688	0.7762:0.0:0.2238:0.0	.	116	Q96DU7	IP3KC_HUMAN	V	116	.	ENSP00000263370:D116V	D	+	2	0	ITPKC	45915227	0.122000	0.22280	0.001000	0.08648	0.323000	0.28346	0.708000	0.25719	0.248000	0.21435	0.397000	0.26171	GAC	A|0.997;T|0.003	0.003	strong		0.602	ITPKC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463104.1	NM_025194	
EMC1	23065	hgsc.bcm.edu	37	1	19549250	19549250	+	Missense_Mutation	SNP	C	C	T	rs371524055	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19549250C>T	ENST00000477853.1	-	20	2497	c.2455G>A	c.(2455-2457)Gcc>Acc	p.A819T	EMC1_ENST00000375208.3_Missense_Mutation_p.A797T|RP1-43E13.2_ENST00000437898.1_RNA|EMC1_ENST00000375199.3_Missense_Mutation_p.A818T|EMC1_ENST00000480380.1_5'Flank	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	819						ER membrane protein complex (GO:0072546)|integral component of membrane (GO:0016021)											AAGGCGGTGGCGTTGTATTGC	0.602													C|||	4	0.000798722	0.003	0.0	5008	,	,		18529	0.0		0.0	False		,,,				2504	0.0				p.A819T		Atlas-SNP	.											.	.	.	.	0			c.G2455A						PASS	.	C	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	121.0	107.0	111.0		2455	6.0	1.0	1		111	0,8600		0,0,4300	no	missense	KIAA0090	NM_015047.1	58	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	819/994	19549250	1,13005	2203	4300	6503	SO:0001583	missense	23065	exon20			CGGTGGCGTTGTA		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.2455G>A	1.37:g.19549250C>T	ENSP00000420608:p.Ala819Thr	191.0	0.0	0		199.0	105.0	0.527638	NM_015047	A8K6F3|Q14700|Q5TG62|Q63HL0|Q63HL3|Q8NBH8	Missense_Mutation	SNP	ENST00000477853.1	37	CCDS190.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.93|14.93	2.680976|2.680976	0.47886|0.47886	2.27E-4|2.27E-4	0.0|0.0	ENSG00000127463|ENSG00000127463	ENST00000477853;ENST00000375199;ENST00000375208;ENST00000486405|ENST00000375197	T;T;T|.	0.24723|.	1.84;1.84;1.84|.	5.98|5.98	5.98|5.98	0.97165|0.97165	Domain of unknown function DUF1620 (1);|.	0.085825|.	0.85682|.	D|.	0.000000|.	T|T	0.51856|0.51856	0.1699|0.1699	N|N	0.26092|0.26092	0.79|0.79	0.80722|0.80722	D|D	1|1	B;B;P;P|.	0.39520|.	0.334;0.101;0.625;0.676|.	B;B;B;B|.	0.32289|.	0.063;0.063;0.088;0.143|.	T|T	0.45160|0.45160	-0.9280|-0.9280	10|5	0.21014|.	T|.	0.42|.	-26.1445|-26.1445	12.3448|12.3448	0.55114|0.55114	0.0:0.9228:0.0:0.0772|0.0:0.9228:0.0:0.0772	.|.	797;818;818;819|.	Q8N766-4;Q8N766-2;Q8N766-3;Q8N766|.	.;.;.;K0090_HUMAN|.	T|H	819;818;797;64|552	ENSP00000420608:A819T;ENSP00000364345:A818T;ENSP00000364354:A797T|.	ENSP00000364345:A818T|.	A|R	-|-	1|2	0|0	KIAA0090|KIAA0090	19421837|19421837	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.732000|0.732000	0.41865|0.41865	5.405000|5.405000	0.66351|0.66351	2.838000|2.838000	0.97847|0.97847	0.655000|0.655000	0.94253|0.94253	GCC|CGC	.	.	none		0.602	EMC1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000007076.2	NM_015047	
OR52L1	338751	hgsc.bcm.edu	37	11	6007992	6007992	+	Silent	SNP	A	A	G	rs115266467	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:6007992A>G	ENST00000332249.4	-	1	223	c.169T>C	c.(169-171)Tta>Cta	p.L57L		NM_001005173.2	NP_001005173.2	Q8NGH7	O52L1_HUMAN	olfactory receptor, family 52, subfamily L, member 1	57						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)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(11)|pancreas(1)|skin(3)|soft_tissue(1)	30		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.98e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTGCCCACTAAAGCAAGGAGG	0.512													.|||	116	0.0231629	0.0809	0.013	5008	,	,		22867	0.0		0.0	False		,,,				2504	0.0				p.L57L	Melanoma(121;653 1666 10547 22796 51255)	Atlas-SNP	.											.	OR52L1	100	.	0			c.T169C						PASS	.	G		204,3818		9,186,1816	75.0	75.0	75.0		169	0.5	0.9	11	dbSNP_132	75	6,8360		0,6,4177	no	coding-synonymous	OR52L1	NM_001005173.2		9,192,5993	GG,GA,AA		0.0717,5.0721,1.6952		57/330	6007992	210,12178	2011	4183	6194	SO:0001819	synonymous_variant	338751	exon1			CCACTAAAGCAAG	AB065819	CCDS44529.1	11p15.4	2012-08-09			ENSG00000183313	ENSG00000183313		"""GPCR / Class A : Olfactory receptors"""	14785	protein-coding gene	gene with protein product							Standard	NM_001005173		Approved		uc001mcd.2	Q8NGH7	OTTHUMG00000165374	ENST00000332249.4:c.169T>C	11.37:g.6007992A>G		135.0	0.0	0		163.0	74.0	0.453988	NM_001005173	B2RPA6|Q6IFK9	Silent	SNP	ENST00000332249.4	37	CCDS44529.1																																																																																			A|0.989;G|0.011	0.011	strong		0.512	OR52L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383754.1	NM_001005173	
SLC25A42	284439	hgsc.bcm.edu	37	19	19217081	19217081	+	Silent	SNP	C	C	A	rs61740506	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:19217081C>A	ENST00000318596.7	+	6	535	c.384C>A	c.(382-384)gcC>gcA	p.A128A	SLC25A42_ENST00000600275.1_3'UTR	NM_178526.4	NP_848621.2	Q86VD7	S2542_HUMAN	solute carrier family 25, member 42	128					ADP transport (GO:0015866)|AMP transport (GO:0080121)|ATP transport (GO:0015867)|coenzyme A transmembrane transport (GO:0035349)|metabolic process (GO:0008152)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	adenosine-diphosphatase activity (GO:0043262)|ADP transmembrane transporter activity (GO:0015217)|AMP transmembrane transporter activity (GO:0080122)|ATP transmembrane transporter activity (GO:0005347)|coenzyme A transmembrane transporter activity (GO:0015228)			cervix(1)|large_intestine(2)|lung(3)	6			OV - Ovarian serous cystadenocarcinoma(5;5.4e-06)|Epithelial(12;0.000497)			TGTTCAGAGCCCTGCCCCCTT	0.682													C|||	113	0.0225639	0.0749	0.0072	5008	,	,		14862	0.0		0.005	False		,,,				2504	0.0041				p.A128A		Atlas-SNP	.											.	SLC25A42	18	.	0			c.C384A						PASS	.	C		360,4046	184.0+/-211.4	12,336,1855	80.0	85.0	83.0		384	0.3	1.0	19	dbSNP_129	83	34,8566	23.4+/-69.3	0,34,4266	no	coding-synonymous	SLC25A42	NM_178526.3		12,370,6121	AA,AC,CC		0.3953,8.1707,3.0294		128/319	19217081	394,12612	2203	4300	6503	SO:0001819	synonymous_variant	284439	exon6			CAGAGCCCTGCCC		CCDS32966.1	19p13.11	2013-05-22			ENSG00000181035	ENSG00000181035		"""Solute carriers"""	28380	protein-coding gene	gene with protein product		610823				16949250, 19429682	Standard	NM_178526		Approved	MGC26694	uc002nlf.3	Q86VD7		ENST00000318596.7:c.384C>A	19.37:g.19217081C>A		113.0	0.0	0		91.0	43.0	0.472527	NM_178526	D2T2J5|O14553|O43378	Silent	SNP	ENST00000318596.7	37	CCDS32966.1																																																																																			C|0.976;A|0.024	0.024	strong		0.682	SLC25A42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465931.1	NM_178526	
CD109	135228	hgsc.bcm.edu	37	6	74524724	74524724	+	Silent	SNP	G	G	A	rs59555720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:74524724G>A	ENST00000287097.5	+	30	3901	c.3789G>A	c.(3787-3789)gtG>gtA	p.V1263V	CD109_ENST00000422508.2_Silent_p.V1186V|CD109_ENST00000437994.2_Silent_p.V1246V			Q6YHK3	CD109_HUMAN	CD109 molecule	1263					negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of wound healing (GO:0061045)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)|transforming growth factor beta binding (GO:0050431)			NS(2)|biliary_tract(1)|breast(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(2)|lung(26)|ovary(2)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TATATAATGTGAAGGCTTCTG	0.308													G|||	132	0.0263578	0.0953	0.0086	5008	,	,		15195	0.0		0.0	False		,,,				2504	0.0				p.V1263V		Atlas-SNP	.											.	CD109	170	.	0			c.G3789A						PASS	.	G	,,	321,4085	168.7+/-199.5	13,295,1895	80.0	87.0	84.0		3738,3558,3789	5.4	1.0	6	dbSNP_129	84	5,8593	4.3+/-15.6	0,5,4294	no	coding-synonymous,coding-synonymous,coding-synonymous	CD109	NM_001159587.1,NM_001159588.1,NM_133493.3	,,	13,300,6189	AA,AG,GG		0.0582,7.2855,2.5069	,,	1246/1429,1186/1369,1263/1446	74524724	326,12678	2203	4299	6502	SO:0001819	synonymous_variant	135228	exon30			TAATGTGAAGGCT	AF410459	CCDS4982.1, CCDS55038.1, CCDS55039.1	6q14.1	2008-02-05	2006-03-28		ENSG00000156535	ENSG00000156535		"""CD molecules"""	21685	protein-coding gene	gene with protein product		608859	"""CD109 antigen (Gov platelet alloantigens)"""			11861284, 11861285	Standard	XM_005248659		Approved	FLJ38569, DKFZp762L1111, CPAMD7	uc003php.3	Q6YHK3	OTTHUMG00000015040	ENST00000287097.5:c.3789G>A	6.37:g.74524724G>A		67.0	0.0	0		66.0	36.0	0.545455	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Silent	SNP	ENST00000287097.5	37	CCDS4982.1																																																																																			G|0.971;A|0.029	0.029	strong		0.308	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493	
LMNB2	84823	hgsc.bcm.edu	37	19	2432450	2432450	+	Silent	SNP	C	C	G	rs11882908	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2432450C>G	ENST00000582871.1	-	9	1580	c.1494G>C	c.(1492-1494)acG>acC	p.T498T	LMNB2_ENST00000475819.1_5'Flank|LMNB2_ENST00000325327.3_Silent_p.T518T	NM_032737.3	NP_116126.3	Q03252	LMNB2_HUMAN	lamin B2	498	LTD.|Tail.					lamin filament (GO:0005638)|nuclear inner membrane (GO:0005637)	structural molecule activity (GO:0005198)			NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18		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)		TGTACTTGGGCGTGAACTTGT	0.632													C|||	143	0.0285543	0.1059	0.0043	5008	,	,		14898	0.0		0.0	False		,,,				2504	0.0				p.T518T		Atlas-SNP	.											LMNB2,NS,carcinoma,0,2	LMNB2	40	2	0			c.G1554C						scavenged	.	C		491,3915	228.5+/-243.3	26,439,1738	300.0	225.0	250.0		1494	-8.2	0.9	19	dbSNP_120	250	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	LMNB2	NM_032737.2		26,442,6035	GG,GC,CC		0.0349,11.1439,3.7982		498/601	2432450	494,12512	2203	4300	6503	SO:0001819	synonymous_variant	84823	exon9			CTTGGGCGTGAAC	M94362	CCDS12090.1, CCDS12090.2	19p13.3	2013-01-16			ENSG00000176619	ENSG00000176619		"""Intermediate filaments type V, lamins"""	6638	protein-coding gene	gene with protein product		150341		LMN2		1630457	Standard	NM_032737		Approved		uc002lvy.4	Q03252	OTTHUMG00000150626	ENST00000582871.1:c.1494G>C	19.37:g.2432450C>G		104.0	1.0	0.00961538		79.0	34.0	0.43038	NM_032737	O75292|Q14734|Q96DF6	Silent	SNP	ENST00000582871.1	37																																																																																				C|0.960;G|0.040	0.040	strong		0.632	LMNB2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_032737	
CCDC158	339965	hgsc.bcm.edu	37	4	77288833	77288833	+	Missense_Mutation	SNP	C	C	T	rs17001824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:77288833C>T	ENST00000388914.3	-	11	1596	c.1444G>A	c.(1444-1446)Gaa>Aaa	p.E482K		NM_001042784.1	NP_001036249.1	Q5M9N0	CD158_HUMAN	coiled-coil domain containing 158	482										breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(1)	56						GTCAACTCTTCTACTACTTTG	0.453													C|||	103	0.0205671	0.0734	0.0086	5008	,	,		19288	0.0		0.0	False		,,,				2504	0.0				p.E482K		Atlas-SNP	.											.	CCDC158	114	.	0			c.G1444A						PASS	.	C	LYS/GLU	235,3573		12,211,1681	72.0	70.0	70.0		1444	5.7	1.0	4	dbSNP_123	70	8,8232		1,6,4113	yes	missense	CCDC158	NM_001042784.1	56	13,217,5794	TT,TC,CC		0.0971,6.1712,2.0169	possibly-damaging	482/1114	77288833	243,11805	1904	4120	6024	SO:0001583	missense	339965	exon11			ACTCTTCTACTAC	BC035224	CCDS43242.1	4q21.1	2009-04-06			ENSG00000163749	ENSG00000163749			26374	protein-coding gene	gene with protein product						12477932	Standard	NM_001042784		Approved	FLJ25770	uc003hkb.4	Q5M9N0	OTTHUMG00000160916	ENST00000388914.3:c.1444G>A	4.37:g.77288833C>T	ENSP00000373566:p.Glu482Lys	98.0	0.0	0		127.0	58.0	0.456693	NM_001042784	Q8IYQ1|Q8N7D4|Q8N7E3	Missense_Mutation	SNP	ENST00000388914.3	37	CCDS43242.1	32	0.014652014652014652	29	0.05894308943089431	3	0.008287292817679558	0	0.0	0	0.0	C	26.5	4.747697	0.89663	0.061712	9.71E-4	ENSG00000163749	ENST00000388914	T	0.78364	-1.17	5.71	5.71	0.89125	.	0.000000	0.64402	D	0.000019	T	0.36826	0.0981	N	0.19112	0.55	0.80722	D	1	D	0.71674	0.998	D	0.78314	0.991	T	0.66077	-0.6013	9	.	.	.	.	17.6416	0.88138	0.0:1.0:0.0:0.0	rs17001824;rs17001824	482	Q5M9N0	CD158_HUMAN	K	482	ENSP00000373566:E482K	.	E	-	1	0	CCDC158	77507857	0.999000	0.42202	0.963000	0.40424	0.995000	0.86356	5.178000	0.65037	2.711000	0.92665	0.563000	0.77884	GAA	C|0.981;T|0.019	0.019	strong		0.453	CCDC158-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362694.2	NM_001042784	
KIAA0020	9933	hgsc.bcm.edu	37	9	2837218	2837218	+	Missense_Mutation	SNP	T	T	C	rs112185565	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:2837218T>C	ENST00000397885.2	-	3	472	c.266A>G	c.(265-267)aAc>aGc	p.N89S		NM_014878.4	NP_055693.4	Q15397	K0020_HUMAN	KIAA0020	89						endoplasmic reticulum (GO:0005783)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(50;0.0319)		TCTCTTCTTGTTGAATTTATT	0.433													T|||	2	0.000399361	0.0015	0.0	5008	,	,		18588	0.0		0.0	False		,,,				2504	0.0				p.N89S		Atlas-SNP	.											.	KIAA0020	56	.	0			c.A266G						PASS	.	T	SER/ASN	6,3742		0,6,1868	226.0	222.0	223.0		266	-3.1	0.8	9	dbSNP_132	223	0,8196		0,0,4098	yes	missense	KIAA0020	NM_014878.4	46	0,6,5966	CC,CT,TT		0.0,0.1601,0.0502	benign	89/649	2837218	6,11938	1874	4098	5972	SO:0001583	missense	9933	exon3			TTCTTGTTGAATT	AL832239	CCDS6448.2	9p24.2	2012-11-29			ENSG00000080608	ENSG00000080608			29676	protein-coding gene	gene with protein product	"""penguin homolog (Drosophila)"", ""minor histocompatibility antigen HA-8"""	609960				7584026, 7584028, 21266351	Standard	NM_014878		Approved	XTP5, PEN, PUF6, hPUF-A, HA-8	uc003zhp.1	Q15397	OTTHUMG00000019450	ENST00000397885.2:c.266A>G	9.37:g.2837218T>C	ENSP00000380982:p.Asn89Ser	196.0	0.0	0		246.0	110.0	0.447154	NM_014878	A8K804|Q547G7|Q5SZY9|Q6IB47|Q96B27|Q96L78|Q96L79|Q96L80	Missense_Mutation	SNP	ENST00000397885.2	37	CCDS6448.2	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	2.871	-0.234057	0.05983	0.001601	0.0	ENSG00000080608	ENST00000397885	T	0.11277	2.79	3.73	-3.09	0.05331	.	1.455670	0.03867	N	0.274933	T	0.06554	0.0168	N	0.22421	0.69	0.09310	N	0.999993	B	0.02656	0.0	B	0.01281	0.0	T	0.38394	-0.9663	10	0.09084	T	0.74	-4.4541	7.1421	0.25562	0.0:0.4276:0.1305:0.4419	.	89	Q15397	K0020_HUMAN	S	89	ENSP00000380982:N89S	ENSP00000380982:N89S	N	-	2	0	KIAA0020	2827218	0.005000	0.15991	0.824000	0.32777	0.991000	0.79684	-0.410000	0.07151	-0.634000	0.05538	-0.263000	0.10527	AAC	T|0.999;C|0.001	0.001	strong		0.433	KIAA0020-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051529.3	NM_014878	
ACTA1	58	hgsc.bcm.edu	37	1	229567384	229567384	+	Silent	SNP	G	G	T	rs74897770	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:229567384G>T	ENST00000366684.3	-	7	1098	c.996C>A	c.(994-996)atC>atA	p.I332I	ACTA1_ENST00000366683.2_Silent_p.I244I	NM_001100.3	NP_001091.1	P68133	ACTS_HUMAN	actin, alpha 1, skeletal muscle	332					cell growth (GO:0016049)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|response to extracellular stimulus (GO:0009991)|response to lithium ion (GO:0010226)|response to mechanical stimulus (GO:0009612)|response to steroid hormone (GO:0048545)|skeletal muscle fiber adaptation (GO:0043503)|skeletal muscle fiber development (GO:0048741)|skeletal muscle thin filament assembly (GO:0030240)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|striated muscle thin filament (GO:0005865)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|myosin binding (GO:0017022)|structural constituent of cytoskeleton (GO:0005200)			endometrium(4)|large_intestine(4)|lung(18)|prostate(1)|urinary_tract(1)	28	Breast(184;0.0858)|Ovarian(103;0.103)	Prostate(94;0.167)				CCGGCGGGGCGATGATCTGCA	0.652													G|||	99	0.0197684	0.0734	0.0014	5008	,	,		13992	0.0		0.001	False		,,,				2504	0.0				p.I332I		Atlas-SNP	.											.	ACTA1	65	.	0			c.C996A						PASS	.	G		253,4153	146.5+/-181.1	10,233,1960	85.0	86.0	86.0		996	0.8	1.0	1	dbSNP_131	86	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ACTA1	NM_001100.3		10,235,6258	TT,TG,GG		0.0233,5.7422,1.9606		332/378	229567384	255,12751	2203	4300	6503	SO:0001819	synonymous_variant	58	exon7			CGGGGCGATGATC	J00068	CCDS1578.1	1q42.13	2014-09-17			ENSG00000143632	ENSG00000143632			129	protein-coding gene	gene with protein product	"""nemaline myopathy type 3"""	102610		ACTA		10072583, 6865942	Standard	NM_001100		Approved	NEM3	uc001htm.3	P68133	OTTHUMG00000038006	ENST00000366684.3:c.996C>A	1.37:g.229567384G>T		119.0	0.0	0		99.0	43.0	0.434343	NM_001100	P02568|P99020|Q5T8M9	Silent	SNP	ENST00000366684.3	37	CCDS1578.1																																																																																			G|0.982;T|0.018	0.018	strong		0.652	ACTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092781.1	NM_001100	
ETAA1	54465	hgsc.bcm.edu	37	2	67631541	67631541	+	Missense_Mutation	SNP	T	T	C	rs145096592	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:67631541T>C	ENST00000272342.5	+	5	1857	c.1727T>C	c.(1726-1728)tTc>tCc	p.F576S	ETAA1_ENST00000462772.1_Intron	NM_019002.3	NP_061875.2	Q9NY74	ETAA1_HUMAN	Ewing tumor-associated antigen 1	576						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(9)|ovary(3)|prostate(1)|stomach(3)|urinary_tract(1)	33						GTAGGTTCTTTCTTTGATGAT	0.363													T|||	4	0.000798722	0.003	0.0	5008	,	,		20046	0.0		0.0	False		,,,				2504	0.0				p.F576S		Atlas-SNP	.											.	ETAA1	88	.	0			c.T1727C						PASS	.	T	SER/PHE	14,4392	20.2+/-43.8	0,14,2189	80.0	84.0	83.0		1727	2.9	1.0	2	dbSNP_134	83	1,8597	1.2+/-3.3	0,1,4298	yes	missense	ETAA1	NM_019002.3	155	0,15,6487	CC,CT,TT		0.0116,0.3177,0.1153	benign	576/927	67631541	15,12989	2203	4299	6502	SO:0001583	missense	54465	exon5			GTTCTTTCTTTGA	AJ242682	CCDS1882.1	2p14	2014-02-12	2007-10-04		ENSG00000143971	ENSG00000143971			24648	protein-coding gene	gene with protein product		613196	"""Ewing's tumor-associated antigen 1"""			16003559	Standard	XM_005264374		Approved	ETAA16	uc002sdz.1	Q9NY74	OTTHUMG00000129545	ENST00000272342.5:c.1727T>C	2.37:g.67631541T>C	ENSP00000272342:p.Phe576Ser	106.0	0.0	0		108.0	56.0	0.518519	NM_019002	Q05BT7|Q53SC4	Missense_Mutation	SNP	ENST00000272342.5	37	CCDS1882.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	T	9.471	1.095577	0.20471	0.003177	1.16E-4	ENSG00000143971	ENST00000272342	T	0.19669	2.13	5.3	2.91	0.33838	.	0.634419	0.15834	N	0.242376	T	0.09686	0.0238	L	0.39898	1.24	0.26563	N	0.973703	P	0.42518	0.782	B	0.37650	0.255	T	0.07809	-1.0753	10	0.10902	T	0.67	-36.4777	8.156	0.31169	0.0:0.1631:0.0:0.8369	.	576	Q9NY74	ETAA1_HUMAN	S	576	ENSP00000272342:F576S	ENSP00000272342:F576S	F	+	2	0	ETAA1	67485045	0.146000	0.22672	0.998000	0.56505	0.629000	0.37895	1.768000	0.38511	1.046000	0.40249	0.533000	0.62120	TTC	T|0.999;C|0.001	0.001	strong		0.363	ETAA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251735.1	NM_019002	
GANC	2595	hgsc.bcm.edu	37	15	42644235	42644235	+	Silent	SNP	A	A	G	rs145163630	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42644235A>G	ENST00000318010.8	+	24	2883	c.2643A>G	c.(2641-2643)aaA>aaG	p.K881K	CAPN3_ENST00000356316.3_5'UTR|RP11-164J13.1_ENST00000495723.1_RNA	NM_198141.2	NP_937784.2	Q8TET4	GANC_HUMAN	glucosidase, alpha; neutral C	881					carbohydrate metabolic process (GO:0005975)		alpha-1,4-glucosidase activity (GO:0004558)|carbohydrate binding (GO:0030246)|maltose alpha-glucosidase activity (GO:0032450)			breast(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23		all_cancers(109;3.08e-16)|all_epithelial(112;7.48e-15)|Lung NSC(122;3.08e-09)|all_lung(180;1.48e-08)|Melanoma(134;0.0574)|Colorectal(260;0.153)		GBM - Glioblastoma multiforme(94;1.06e-06)	Miglitol(DB00491)	TAGATGGTAAAGATCAGCCTG	0.408													A|||	2	0.000399361	0.0015	0.0	5008	,	,		19780	0.0		0.0	False		,,,				2504	0.0				p.K881K		Atlas-SNP	.											.	GANC	57	.	0			c.A2643G						PASS	.	A		12,4394	16.8+/-37.8	0,12,2191	134.0	117.0	123.0		2643	1.8	0.2	15	dbSNP_134	123	0,8598		0,0,4299	no	coding-synonymous	GANC	NM_198141.2		0,12,6490	GG,GA,AA		0.0,0.2724,0.0923		881/915	42644235	12,12992	2203	4299	6502	SO:0001819	synonymous_variant	2595	exon24			TGGTAAAGATCAG	AF545045	CCDS10084.1	15q15.2	2012-10-02			ENSG00000214013	ENSG00000214013	3.2.1.20		4139	protein-coding gene	gene with protein product		104180				6995030, 12370436	Standard	NM_198141		Approved		uc001zpi.3	Q8TET4	OTTHUMG00000130487	ENST00000318010.8:c.2643A>G	15.37:g.42644235A>G		141.0	0.0	0		192.0	85.0	0.442708	NM_198141	Q52LQ4|Q8IWZ0|Q8IZM4|Q8IZM5	Silent	SNP	ENST00000318010.8	37	CCDS10084.1																																																																																			A|0.999;G|0.001	0.001	strong		0.408	GANC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252887.2	NM_198141	
KLHL20	27252	hgsc.bcm.edu	37	1	173725101	173725101	+	Silent	SNP	G	G	A	rs16846395	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:173725101G>A	ENST00000209884.4	+	6	1027	c.891G>A	c.(889-891)ccG>ccA	p.P297P	KLHL20_ENST00000546011.1_Silent_p.P108P	NM_014458.3	NP_055273.2	Q9Y2M5	KLH20_HUMAN	kelch-like family member 20	297					cytoskeleton organization (GO:0007010)|Golgi to endosome transport (GO:0006895)|negative regulation of apoptotic process (GO:0043066)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K33-linked ubiquitination (GO:1990390)|protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|response to interferon-alpha (GO:0035455)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|PML body (GO:0016605)|trans-Golgi network (GO:0005802)	interferon-gamma binding (GO:0019964)|ubiquitin-protein transferase activity (GO:0004842)			breast(3)|endometrium(6)|kidney(1)|large_intestine(8)|lung(14)|ovary(1)|upper_aerodigestive_tract(1)	34						TCCTATTGCCGCAAGAACGAC	0.403													G|||	472	0.0942492	0.3404	0.0274	5008	,	,		18997	0.0		0.003	False		,,,				2504	0.0				p.P297P	GBM(159;862 2695 6559 23041)	Atlas-SNP	.											.	KLHL20	54	.	0			c.G891A						PASS	.	G		1110,3296	397.2+/-330.3	139,832,1232	108.0	99.0	102.0		891	1.2	1.0	1	dbSNP_123	102	23,8577	15.3+/-51.7	0,23,4277	no	coding-synonymous	KLHL20	NM_014458.3		139,855,5509	AA,AG,GG		0.2674,25.1929,8.7114		297/610	173725101	1133,11873	2203	4300	6503	SO:0001819	synonymous_variant	27252	exon6			ATTGCCGCAAGAA	AB026190	CCDS1310.1	1q25.1	2013-01-30	2013-01-30		ENSG00000076321	ENSG00000076321		"""Kelch-like"", ""BTB/POZ domain containing"""	25056	protein-coding gene	gene with protein product			"""kelch-like 20 (Drosophila)"""			14668487, 20389280	Standard	NM_014458		Approved	KLEIP, KHLHX	uc001gjc.3	Q9Y2M5	OTTHUMG00000040548	ENST00000209884.4:c.891G>A	1.37:g.173725101G>A		125.0	0.0	0		119.0	60.0	0.504202	NM_014458	B3KMA0|B4DUR0|Q5TZF2|Q5ZF45|Q9H457	Silent	SNP	ENST00000209884.4	37	CCDS1310.1																																																																																			G|0.899;A|0.101	0.101	strong		0.403	KLHL20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097582.1	NM_014458	
KDM2B	84678	hgsc.bcm.edu	37	12	121877739	121877739	+	Silent	SNP	G	G	A	rs35674891	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:121877739G>A	ENST00000377071.4	-	22	3822	c.3750C>T	c.(3748-3750)caC>caT	p.H1250H	KDM2B_ENST00000536437.1_Intron|KDM2B_ENST00000542973.1_Silent_p.H618H|KDM2B_ENST00000377069.4_Silent_p.H1181H	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	1250					embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						GGTCGGTGACGTGGTTACAGT	0.602													G|||	75	0.014976	0.0567	0.0	5008	,	,		17032	0.0		0.0	False		,,,				2504	0.0				p.H1250H		Atlas-SNP	.											.	KDM2B	218	.	0			c.C3750T						PASS	.	G	,	235,4127		6,223,1952	123.0	146.0	138.0		3543,3750	-0.6	0.6	12	dbSNP_126	138	2,8542		0,2,4270	no	coding-synonymous,coding-synonymous	KDM2B	NM_001005366.1,NM_032590.4	,	6,225,6222	AA,AG,GG		0.0234,5.3874,1.8364	,	1181/1266,1250/1337	121877739	237,12669	2181	4272	6453	SO:0001819	synonymous_variant	84678	exon22			GGTGACGTGGTTA	AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"""F-boxes / Leucine-rich repeats"", ""Chromatin-modifying enzymes / K-demethylases"""	13610	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1B"""	609078	"""F-box and leucine-rich repeat protein 10"""	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.3750C>T	12.37:g.121877739G>A		105.0	0.0	0		122.0	54.0	0.442623	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Silent	SNP	ENST00000377071.4	37	CCDS41850.1																																																																																			G|0.990;A|0.010	0.010	strong		0.602	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590	
XPR1	9213	hgsc.bcm.edu	37	1	180772708	180772708	+	Silent	SNP	T	T	C	rs12078050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:180772708T>C	ENST00000367590.4	+	4	606	c.408T>C	c.(406-408)agT>agC	p.S136S	XPR1_ENST00000367589.3_Silent_p.S136S	NM_004736.3	NP_004727.2	Q9UBH6	XPR1_HUMAN	xenotropic and polytropic retrovirus receptor 1	136	SPX. {ECO:0000255|PROSITE- ProRule:PRU00714}.				G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)			breast(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	35						TGGCCTTCAGTGAGTTCTACC	0.408													C|||	258	0.0515176	0.1808	0.0259	5008	,	,		19232	0.0		0.001	False		,,,				2504	0.0				p.S136S		Atlas-SNP	.											.	XPR1	76	.	0			c.T408C						PASS	.	C	,	636,3770	767.9+/-413.5	45,546,1612	119.0	123.0	121.0		408,408	0.9	1.0	1	dbSNP_120	121	4,8596	819.1+/-406.8	0,4,4296	no	coding-synonymous,coding-synonymous	XPR1	NM_001135669.1,NM_004736.3	,	45,550,5908	CC,CT,TT		0.0465,14.4349,4.9208	,	136/632,136/697	180772708	640,12366	2203	4300	6503	SO:0001819	synonymous_variant	9213	exon4			CTTCAGTGAGTTC	AF099082	CCDS1340.1, CCDS44284.1	1q25.1	2013-07-18	2010-04-23		ENSG00000143324	ENSG00000143324			12827	protein-coding gene	gene with protein product		605237	"""xenotropic and polytropic retrovirus receptor"""			9990033	Standard	NM_004736		Approved	SYG1, X3	uc001goi.3	Q9UBH6	OTTHUMG00000035116	ENST00000367590.4:c.408T>C	1.37:g.180772708T>C		70.0	0.0	0		68.0	36.0	0.529412	NM_004736	O95719|Q7L8K9|Q8IW20|Q9NT19|Q9UFB9	Silent	SNP	ENST00000367590.4	37	CCDS1340.1																																																																																			T|0.942;C|0.058	0.058	strong		0.408	XPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084996.2	NM_004736	
HMCN1	83872	hgsc.bcm.edu	37	1	186026366	186026366	+	Splice_Site	SNP	C	C	T	rs140744695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:186026366C>T	ENST00000271588.4	+	46	7374	c.7145C>T	c.(7144-7146)gCt>gTt	p.A2382V	HMCN1_ENST00000367492.2_Splice_Site_p.A2382V	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2382					response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TGTCTTACAGCTCCTCCAAGC	0.363													C|||	2	0.000399361	0.0015	0.0	5008	,	,		17150	0.0		0.0	False		,,,				2504	0.0				p.A2382V		Atlas-SNP	.											.	HMCN1	797	.	0			c.C7145T						PASS	.	C	VAL/ALA	5,4401	9.9+/-24.2	0,5,2198	77.0	77.0	77.0		7145	-2.6	0.7	1	dbSNP_134	77	0,8598		0,0,4299	yes	missense-near-splice	HMCN1	NM_031935.2	64	0,5,6497	TT,TC,CC		0.0,0.1135,0.0384	benign	2382/5636	186026366	5,12999	2203	4299	6502	SO:0001630	splice_region_variant	83872	exon46			TTACAGCTCCTCC	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.7145-1C>T	1.37:g.186026366C>T		74.0	0.0	0		91.0	41.0	0.450549	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Missense_Mutation	SNP	ENST00000271588.4	37	CCDS30956.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	1.308	-0.602865	0.03744	0.001135	0.0	ENSG00000143341	ENST00000271588;ENST00000367492	T;T	0.72167	-0.63;-0.63	5.8	-2.64	0.06114	Immunoglobulin-like fold (1);	0.288142	0.38058	N	0.001832	T	0.32285	0.0824	N	0.00746	-1.225	0.34659	D	0.722457	B	0.09022	0.002	B	0.06405	0.002	T	0.31024	-0.9958	9	.	.	.	.	12.1208	0.53889	0.0:0.2184:0.0:0.7816	.	2382	Q96RW7	HMCN1_HUMAN	V	2382	ENSP00000271588:A2382V;ENSP00000356462:A2382V	.	A	+	2	0	HMCN1	184292989	0.973000	0.33851	0.699000	0.30290	0.417000	0.31264	1.939000	0.40213	-0.338000	0.08413	-0.142000	0.14014	GCT	C|0.999;T|0.001	0.001	strong		0.363	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	Missense_Mutation
PDE4DIP	9659	hgsc.bcm.edu	37	1	144873983	144873983	+	Silent	SNP	T	T	C	rs148165371	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:144873983T>C	ENST00000369354.3	-	31	5163	c.4974A>G	c.(4972-4974)ccA>ccG	p.P1658P	PDE4DIP_ENST00000313382.9_Silent_p.P1614P|PDE4DIP_ENST00000369359.4_Silent_p.P1794P|PDE4DIP_ENST00000530740.1_Intron|PDE4DIP_ENST00000369356.4_Silent_p.P1658P|PDE4DIP_ENST00000524974.1_5'UTR|RP4-791M13.5_ENST00000531288.1_RNA			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	1658					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TGGTTGATGATGGTTTAGAAG	0.473			T	PDGFRB	MPD								.|||	3	0.000599042	0.0023	0.0	5008	,	,		42684	0.0		0.0	False		,,,				2504	0.0				p.P1658P		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A4974G						PASS	.	T	,,	11,4395	17.9+/-39.9	0,11,2192	417.0	423.0	421.0		4842,4974,4974	5.3	1.0	1	dbSNP_134	421	0,8594		0,0,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	PDE4DIP	NM_001198832.1,NM_001198834.2,NM_014644.4	,,	0,11,6489	CC,CT,TT		0.0,0.2497,0.0846	,,	1614/2241,1658/2363,1658/2347	144873983	11,12989	2203	4297	6500	SO:0001819	synonymous_variant	9659	exon31			TGATGATGGTTTA	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.4974A>G	1.37:g.144873983T>C		355.0	0.0	0		418.0	111.0	0.26555	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Silent	SNP	ENST00000369354.3	37	CCDS30824.1																																																																																			T|0.999;C|0.001	0.001	strong		0.473	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
LAMB3	3914	hgsc.bcm.edu	37	1	209797061	209797061	+	Missense_Mutation	SNP	C	C	T	rs114174766	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:209797061C>T	ENST00000356082.4	-	16	2281	c.2147G>A	c.(2146-2148)cGg>cAg	p.R716Q	MIR4260_ENST00000583107.1_RNA|LAMB3_ENST00000367030.3_Missense_Mutation_p.R716Q|LAMB3_ENST00000391911.1_Missense_Mutation_p.R716Q	NM_000228.2	NP_000219.2	Q13751	LAMB3_HUMAN	laminin, beta 3	716	Domain II.				brown fat cell differentiation (GO:0050873)|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)	extracellular region (GO:0005576)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45				OV - Ovarian serous cystadenocarcinoma(81;0.0519)		GCTCAGCATCCGGAAGGCTCC	0.652													c|||	9	0.00179712	0.0061	0.0014	5008	,	,		19113	0.0		0.0	False		,,,				2504	0.0				p.R716Q		Atlas-SNP	.											.	LAMB3	136	.	0			c.G2147A						PASS	.	T	GLN/ARG,GLN/ARG,GLN/ARG	23,4383	29.0+/-57.7	0,23,2180	31.0	31.0	31.0		2147,2147,2147	1.2	0.7	1	dbSNP_132	31	0,8600		0,0,4300	yes	missense,missense,missense	LAMB3	NM_000228.2,NM_001017402.1,NM_001127641.1	43,43,43	0,23,6480	TT,TC,CC		0.0,0.522,0.1768	benign,benign,benign	716/1173,716/1173,716/1173	209797061	23,12983	2203	4300	6503	SO:0001583	missense	3914	exon16			AGCATCCGGAAGG	D37766	CCDS1487.1	1q32	2013-03-01	2002-08-29		ENSG00000196878	ENSG00000196878		"""Laminins"""	6490	protein-coding gene	gene with protein product		150310	"""laminin, beta 3 (nicein (125kD), kalinin (140kD), BM600 (125kD))"""	LAMNB1		8088808, 7774918	Standard	NM_001127641		Approved	nicein-125kDa, kalinin-140kDa, BM600-125kDa	uc001hhh.3	Q13751	OTTHUMG00000036360	ENST00000356082.4:c.2147G>A	1.37:g.209797061C>T	ENSP00000348384:p.Arg716Gln	101.0	0.0	0		75.0	37.0	0.493333	NM_000228	D3DT88|O14947|Q14733|Q9UJK4|Q9UJL1	Missense_Mutation	SNP	ENST00000356082.4	37	CCDS1487.1	4	0.0018315018315018315	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	c	6.857	0.527355	0.13066	0.00522	0.0	ENSG00000196878	ENST00000391911;ENST00000356082;ENST00000367030	T;T;T	0.35789	1.29;1.29;1.29	5.15	1.19	0.21007	.	0.666644	0.15639	N	0.251967	T	0.15435	0.0372	L	0.35723	1.085	0.18873	N	0.999981	B	0.16802	0.019	B	0.06405	0.002	T	0.23904	-1.0175	10	0.14252	T	0.57	.	4.7578	0.13093	0.1382:0.5549:0.0:0.3069	.	716	Q13751	LAMB3_HUMAN	Q	716	ENSP00000375778:R716Q;ENSP00000348384:R716Q;ENSP00000355997:R716Q	ENSP00000348384:R716Q	R	-	2	0	LAMB3	207863684	0.020000	0.18652	0.733000	0.30861	0.335000	0.28730	-0.012000	0.12699	0.043000	0.15746	-0.365000	0.07479	CGG	C|0.998;T|0.002	0.002	strong		0.652	LAMB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088525.2	NM_000228	
SNX18	112574	hgsc.bcm.edu	37	5	53814736	53814736	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:53814736G>C	ENST00000326277.3	+	1	1144	c.954G>C	c.(952-954)tgG>tgC	p.W318C	SNX18_ENST00000343017.6_Missense_Mutation_p.W318C|SNX18_ENST00000381410.4_Missense_Mutation_p.W318C	NM_052870.2	NP_443102.2	Q96RF0	SNX18_HUMAN	sorting nexin 18	318	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				cleavage furrow formation (GO:0036089)|endocytosis (GO:0006897)|endosomal transport (GO:0016197)|intracellular protein transport (GO:0006886)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|positive regulation of GTPase activity (GO:0043547)	cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)			endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)	18		Lung NSC(810;3.46e-05)|Breast(144;0.102)				ACTTCGACTGGCTGTACGCGC	0.622																																					p.W318C		Atlas-SNP	.											.	SNX18	102	.	0			c.G954C						PASS	.						48.0	45.0	46.0					5																	53814736		2203	4300	6503	SO:0001583	missense	112574	exon1			CGACTGGCTGTAC	AF395536	CCDS3962.1, CCDS43317.1, CCDS54851.1	5q11.2	2010-05-12	2008-03-11	2008-03-11	ENSG00000178996	ENSG00000178996		"""Sorting nexins"""	19245	protein-coding gene	gene with protein product			"""sorting nexin associated golgi protein 1"""	SNAG1		16782399, 17761170	Standard	NM_052870		Approved	SH3PX2, SH3PXD3B	uc003jpi.4	Q96RF0	OTTHUMG00000096994	ENST00000326277.3:c.954G>C	5.37:g.53814736G>C	ENSP00000317332:p.Trp318Cys	143.0	0.0	0		138.0	15.0	0.108696	NM_052870	B4E2B3|H7BXX3|Q05BB3|Q0VG02	Missense_Mutation	SNP	ENST00000326277.3	37	CCDS3962.1	.	.	.	.	.	.	.	.	.	.	G	15.12	2.740451	0.49045	.	.	ENSG00000178996	ENST00000343017;ENST00000381410;ENST00000326277	T;T;T	0.41400	1.0;1.0;1.0	4.8	3.94	0.45596	Phox homologous domain (5);	0.000000	0.85682	D	0.000000	T	0.69993	0.3173	M	0.91612	3.225	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.77598	-0.2528	10	0.87932	D	0	-9.487	13.0976	0.59202	0.0771:0.0:0.9229:0.0	.	318;318	Q96RF0;Q96RF0-2	SNX18_HUMAN;.	C	318	ENSP00000342276:W318C;ENSP00000370817:W318C;ENSP00000317332:W318C	ENSP00000317332:W318C	W	+	3	0	SNX18	53850493	1.000000	0.71417	1.000000	0.80357	0.591000	0.36615	9.638000	0.98445	1.250000	0.43966	-0.259000	0.10710	TGG	.	.	none		0.622	SNX18-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000214072.2		
DPPA4	55211	hgsc.bcm.edu	37	3	109049507	109049507	+	Silent	SNP	A	A	G	rs16834356	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:109049507A>G	ENST00000335658.6	-	5	597	c.543T>C	c.(541-543)aaT>aaC	p.N181N	DPPA4_ENST00000478791.1_5'UTR	NM_018189.3	NP_060659.3	Q7L190	DPPA4_HUMAN	developmental pluripotency associated 4	181					lung-associated mesenchyme development (GO:0060484)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(17)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25						GAGCAGTGGAATTTTCCAGGG	0.547													A|||	41	0.0081869	0.028	0.0043	5008	,	,		15162	0.0		0.001	False		,,,				2504	0.0				p.N181N		Atlas-SNP	.											.	DPPA4	56	.	0			c.T543C						PASS	.	A		122,4284	93.0+/-131.7	3,116,2084	71.0	77.0	75.0		543	-8.2	0.0	3	dbSNP_123	75	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DPPA4	NM_018189.3		3,117,6383	GG,GA,AA		0.0116,2.769,0.9457		181/305	109049507	123,12883	2203	4300	6503	SO:0001819	synonymous_variant	55211	exon5			AGTGGAATTTTCC	AK001575	CCDS33814.1	3q13.13	2014-01-28			ENSG00000121570	ENSG00000121570			19200	protein-coding gene	gene with protein product		614125					Standard	NM_018189		Approved	FLJ10713	uc003dxq.4	Q7L190	OTTHUMG00000159222	ENST00000335658.6:c.543T>C	3.37:g.109049507A>G		207.0	1.0	0.00483092		204.0	204.0	1	NM_018189	A8K4M7|Q9H9N5|Q9NVI6	Silent	SNP	ENST00000335658.6	37	CCDS33814.1																																																																																			A|0.991;G|0.009	0.009	strong		0.547	DPPA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353897.1	NM_018189	
NMT2	9397	hgsc.bcm.edu	37	10	15170387	15170387	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:15170387T>C	ENST00000378165.4	-	8	1041	c.961A>G	c.(961-963)Act>Gct	p.T321A	RPP38_ENST00000451677.1_Intron|NMT2_ENST00000378150.1_Missense_Mutation_p.T308A|NMT2_ENST00000540259.1_Missense_Mutation_p.T133A|NMT2_ENST00000535341.1_Missense_Mutation_p.T308A	NM_004808.2	NP_004799.1	O60551	NMT2_HUMAN	N-myristoyltransferase 2	321					intracellular transport of virus (GO:0075733)|N-terminal protein myristoylation (GO:0006499)|phototransduction, visible light (GO:0007603)|protein lipoylation (GO:0009249)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	catalytic activity (GO:0003824)|glycylpeptide N-tetradecanoyltransferase activity (GO:0004379)			breast(3)|endometrium(1)|kidney(4)|large_intestine(3)|lung(6)|ovary(1)|upper_aerodigestive_tract(3)	21						CTCTGTAAAGTCATATTTCTA	0.328																																					p.T321A	Melanoma(117;1345 1645 4130 12688 30625)	Atlas-SNP	.											.	NMT2	44	.	0			c.A961G						PASS	.						85.0	88.0	87.0					10																	15170387		2202	4300	6502	SO:0001583	missense	9397	exon8			GTAAAGTCATATT	AF043325	CCDS7109.1	10p13	2006-07-11			ENSG00000152465	ENSG00000152465			7858	protein-coding gene	gene with protein product		603801				9506952	Standard	NM_004808		Approved		uc001inz.1	O60551	OTTHUMG00000017723	ENST00000378165.4:c.961A>G	10.37:g.15170387T>C	ENSP00000367407:p.Thr321Ala	97.0	0.0	0		149.0	6.0	0.0402685	NM_004808	B0YJ49|Q53Y38|Q5VUC8|Q9BRB4	Missense_Mutation	SNP	ENST00000378165.4	37	CCDS7109.1	.	.	.	.	.	.	.	.	.	.	T	24.9	4.582566	0.86748	.	.	ENSG00000152465	ENST00000378165;ENST00000378150;ENST00000378143;ENST00000540259;ENST00000535341	T	0.50813	0.73	5.58	5.58	0.84498	Acyl-CoA N-acyltransferase (2);Myristoyl-CoA:protein N-myristoyltransferase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.77928	0.4204	H	0.95437	3.67	0.80722	D	1	D;D;D	0.65815	0.992;0.995;0.992	D;D;D	0.75020	0.985;0.985;0.985	D	0.85108	0.0961	10	0.87932	D	0	-19.6603	15.7488	0.77967	0.0:0.0:0.0:1.0	.	321;308;321	B2RCF3;Q5VUC6;O60551	.;.;NMT2_HUMAN	A	321;308;352;133;308	ENSP00000367407:T321A	ENSP00000367385:T352A	T	-	1	0	NMT2	15210393	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.040000	0.89188	2.115000	0.64714	0.533000	0.62120	ACT	.	.	none		0.328	NMT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046958.2	NM_004808	
VWA2	340706	hgsc.bcm.edu	37	10	116049199	116049199	+	Silent	SNP	C	C	T	rs148020287	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:116049199C>T	ENST00000392982.3	+	12	2323	c.2073C>T	c.(2071-2073)taC>taT	p.Y691Y	VWA2_ENST00000603594.1_Silent_p.Y691Y			Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	691	VWFA 3. {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)			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)		TGGCAGCTTACGCCGACCTGC	0.642													C|||	29	0.00579073	0.0212	0.0014	5008	,	,		18395	0.0		0.0	False		,,,				2504	0.0				p.Y691Y		Atlas-SNP	.											VWA2,caecum,carcinoma,0,1	VWA2	64	1	0			c.C2073T						PASS	.	C		62,4344	58.7+/-95.3	0,62,2141	126.0	100.0	109.0		2073	-0.5	0.1	10	dbSNP_134	109	0,8600		0,0,4300	no	coding-synonymous	VWA2	NM_198496.1		0,62,6441	TT,TC,CC		0.0,1.4072,0.4767		691/726	116049199	62,12944	2203	4300	6503	SO:0001819	synonymous_variant	340706	exon12			AGCTTACGCCGAC	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.2073C>T	10.37:g.116049199C>T		139.0	0.0	0		162.0	93.0	0.574074	NM_001272046	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Silent	SNP	ENST00000392982.3	37																																																																																				C|0.994;T|0.006	0.006	strong		0.642	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496	
ECI2	10455	hgsc.bcm.edu	37	6	4119492	4119492	+	Silent	SNP	T	T	C	rs10708	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:4119492T>C	ENST00000380118.3	-	8	849	c.813A>G	c.(811-813)ccA>ccG	p.P271P	ECI2_ENST00000465828.1_Silent_p.P241P|ECI2_ENST00000413766.2_Silent_p.P104P|ECI2_ENST00000380125.2_Silent_p.P241P|C6orf201_ENST00000430835.2_Intron|C6orf201_ENST00000333388.5_Intron|C6orf201_ENST00000380175.4_Intron|ECI2_ENST00000361538.2_Silent_p.P241P			O75521	ECI2_HUMAN	enoyl-CoA delta isomerase 2	271	ECH-like.				fatty acid catabolic process (GO:0009062)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	dodecenoyl-CoA delta-isomerase activity (GO:0004165)|fatty-acyl-CoA binding (GO:0000062)|receptor binding (GO:0005102)			endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	11						GGTGACTAAATGGTGTATGAA	0.378													T|||	214	0.0427316	0.1536	0.0159	5008	,	,		18618	0.0		0.0	False		,,,				2504	0.0				p.P271P		Atlas-SNP	.											.	ECI2	59	.	0			c.A813G						PASS	.	T	,,,	590,3816	258.9+/-262.7	51,488,1664	77.0	79.0	78.0		,723,723,813	-5.8	0.7	6	dbSNP_130	78	6,8594	5.0+/-18.6	0,6,4294	no	intron,coding-synonymous,coding-synonymous,coding-synonymous	ECI2,C6orf201	NM_001085401.1,NM_001166010.1,NM_006117.2,NM_206836.2	,,,	51,494,5958	CC,CT,TT		0.0698,13.3908,4.5825	,,,	,241/365,241/365,271/395	4119492	596,12410	2203	4300	6503	SO:0001819	synonymous_variant	10455	exon8			ACTAAATGGTGTA	AF069301	CCDS4490.1, CCDS43420.1, CCDS43420.2	6p24.3	2011-03-15	2011-03-15	2011-03-15	ENSG00000198721	ENSG00000198721			14601	protein-coding gene	gene with protein product	"""acyl-Coenzyme A binding domain containing 2"", "" Hepatocellular carcinoma-associated antigen 88"""	608024	"""peroxisomal D3,D2-enoyl-CoA isomerase"""	PECI		10419495	Standard	NM_206836		Approved	ACBD2, DRS1, HCA88	uc003mwf.3	O75521	OTTHUMG00000014158	ENST00000380118.3:c.813A>G	6.37:g.4119492T>C		80.0	0.0	0		56.0	27.0	0.482143	NM_206836	Q5JYK5|Q5JYK7|Q7L124|Q8N0X0|Q9BUE9|Q9H0T9|Q9NQH1|Q9NYH7|Q9UN55	Silent	SNP	ENST00000380118.3	37	CCDS43420.2																																																																																			T|0.962;C|0.038	0.038	strong		0.378	ECI2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039716.4	NM_006117	
POLE	5426	hgsc.bcm.edu	37	12	133201327	133201327	+	Missense_Mutation	SNP	T	T	A	rs73481453	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:133201327T>A	ENST00000320574.5	-	49	6860	c.6817A>T	c.(6817-6819)Acc>Tcc	p.T2273S	POLE_ENST00000535270.1_Missense_Mutation_p.T2246S	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	2273					base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)			NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	CACTCCAGGGTCTCCAGGAGG	0.612								DNA polymerases (catalytic subunits)					T|||	25	0.00499201	0.0189	0.0	5008	,	,		18347	0.0		0.0	False		,,,				2504	0.0				p.T2273S		Atlas-SNP	.											.	POLE	416	.	0			c.A6817T						PASS	.	T	SER/THR	62,4344	58.7+/-95.3	2,58,2143	81.0	82.0	82.0		6817	2.4	1.0	12	dbSNP_130	82	1,8599	1.2+/-3.3	0,1,4299	yes	missense	POLE	NM_006231.2	58	2,59,6442	AA,AT,TT		0.0116,1.4072,0.4844	benign	2273/2287	133201327	63,12943	2203	4300	6503	SO:0001583	missense	5426	exon49			CCAGGGTCTCCAG		CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"""DNA polymerases"""	9177	protein-coding gene	gene with protein product	"""DNA polymerase epsilon catalytic subunit A"""	174762	"""polymerase (DNA directed), epsilon"""			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.6817A>T	12.37:g.133201327T>A	ENSP00000322570:p.Thr2273Ser	169.0	0.0	0		154.0	72.0	0.467532	NM_006231	Q13533|Q86VH9	Missense_Mutation	SNP	ENST00000320574.5	37	CCDS9278.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	T	16.01	3.000426	0.54147	0.014072	1.16E-4	ENSG00000177084	ENST00000434528;ENST00000320574;ENST00000455752;ENST00000320557;ENST00000535270	T;T;T	0.02944	4.11;4.1;4.11	4.89	2.43	0.29744	.	0.285116	0.38436	N	0.001689	T	0.02193	0.0068	M	0.77103	2.36	0.41149	D	0.98601	B;B	0.12630	0.001;0.006	B;B	0.18263	0.005;0.021	T	0.20405	-1.0276	10	0.59425	D	0.04	.	7.0622	0.25131	0.1316:0.0728:0.0:0.7956	.	2273;483	Q07864;B3KS74	DPOE1_HUMAN;.	S	483;2273;2284;243;2246	ENSP00000322570:T2273S;ENSP00000406383:T2284S;ENSP00000445753:T2246S	ENSP00000322473:T243S	T	-	1	0	POLE	131711400	1.000000	0.71417	0.954000	0.39281	0.840000	0.47671	4.700000	0.61803	0.325000	0.23359	0.459000	0.35465	ACC	T|0.995;A|0.005	0.005	strong		0.612	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231	
FOCAD	54914	hgsc.bcm.edu	37	9	20978439	20978439	+	Missense_Mutation	SNP	A	A	C	rs149031092		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:20978439A>C	ENST00000380249.1	+	39	4727	c.4363A>C	c.(4363-4365)Atc>Ctc	p.I1455L	FOCAD_ENST00000338382.6_Missense_Mutation_p.I1455L|FOCAD_ENST00000605086.1_Missense_Mutation_p.I891L	NM_017794.3	NP_060264.3	Q5VW36	FOCAD_HUMAN	focadhesin	1455						focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)											ACCACCACTGATCCACAGTCT	0.458													A|||	1	0.000199681	0.0008	0.0	5008	,	,		19302	0.0		0.0	False		,,,				2504	0.0				p.I1455L		Atlas-SNP	.											.	.	.	.	0			c.A4363C						PASS	.	A	LEU/ILE	3,4403	6.2+/-15.9	0,3,2200	77.0	71.0	73.0		4363	-1.0	0.1	9	dbSNP_134	73	0,8600		0,0,4300	no	missense	KIAA1797	NM_017794.3	5	0,3,6500	CC,CA,AA		0.0,0.0681,0.0231	benign	1455/1802	20978439	3,13003	2203	4300	6503	SO:0001583	missense	54914	exon39			CCACTGATCCACA	AB058700	CCDS34993.1	9p21	2012-03-23	2012-03-23	2012-03-23	ENSG00000188352	ENSG00000188352			23377	protein-coding gene	gene with protein product		614606	"""KIAA1797"""	KIAA1797		22427331	Standard	XM_006716794		Approved	FLJ20375	uc003zog.1	Q5VW36	OTTHUMG00000066930	ENST00000380249.1:c.4363A>C	9.37:g.20978439A>C	ENSP00000369599:p.Ile1455Leu	138.0	0.0	0		152.0	80.0	0.526316	NM_017794	D3DRJ9|Q6ZME1|Q8IZG0|Q96JM8|Q96MS9|Q9BVF3|Q9NX87	Missense_Mutation	SNP	ENST00000380249.1	37	CCDS34993.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	12.27	1.888125	0.33348	6.81E-4	0.0	ENSG00000188352	ENST00000380249;ENST00000338382	T;T	0.21543	2.0;2.0	6.06	-0.993	0.10228	.	0.598323	0.18257	N	0.146776	T	0.15435	0.0372	L	0.51422	1.61	0.09310	N	1	B	0.09022	0.002	B	0.09377	0.004	T	0.16897	-1.0387	10	0.39692	T	0.17	-0.8041	5.9075	0.19008	0.399:0.252:0.349:0.0	.	1455	Q5VW36	K1797_HUMAN	L	1455	ENSP00000369599:I1455L;ENSP00000344307:I1455L	ENSP00000344307:I1455L	I	+	1	0	KIAA1797	20968439	0.409000	0.25368	0.067000	0.19924	0.828000	0.46876	0.494000	0.22467	-0.159000	0.11021	0.533000	0.62120	ATC	A|1.000;C|0.000	0.000	strong		0.458	FOCAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143442.1	NM_017794	
AKNA	80709	hgsc.bcm.edu	37	9	117103900	117103900	+	Missense_Mutation	SNP	T	T	C	rs2787344	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:117103900T>C	ENST00000307564.4	-	21	4141	c.3980A>G	c.(3979-3981)tAt>tGt	p.Y1327C	AKNA_ENST00000374075.5_Missense_Mutation_p.Y1246C|AKNA_ENST00000374088.3_Missense_Mutation_p.Y1327C|AKNA_ENST00000492875.1_5'UTR|AKNA_ENST00000374079.4_Missense_Mutation_p.Y272C|AKNA_ENST00000223791.3_Missense_Mutation_p.Y787C	NM_030767.4	NP_110394.3	Q7Z591	AKNA_HUMAN	AT-hook transcription factor	1327			Y -> C (in dbSNP:rs2787344).		positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	membrane (GO:0016020)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(7)|liver(2)|lung(22)|ovary(4)|stomach(2)	51						TGTTGCCAGATACCACAGTCC	0.622													T|||	395	0.0788738	0.2897	0.0173	5008	,	,		15911	0.0		0.0	False		,,,				2504	0.0				p.Y1327C		Atlas-SNP	.											.	AKNA	119	.	0			c.A3980G						PASS	.	T	CYS/TYR	981,3425	369.1+/-318.9	102,777,1324	56.0	62.0	60.0		3980	5.5	1.0	9	dbSNP_100	60	6,8594	4.3+/-15.6	0,6,4294	yes	missense	AKNA	NM_030767.4	194	102,783,5618	CC,CT,TT		0.0698,22.2651,7.5888	probably-damaging	1327/1440	117103900	987,12019	2203	4300	6503	SO:0001583	missense	80709	exon21			GCCAGATACCACA	AK024431	CCDS6805.1	9q32	2008-02-05			ENSG00000106948	ENSG00000106948			24108	protein-coding gene	gene with protein product		605729				11268217, 11853319	Standard	NM_030767		Approved	KIAA1968	uc004bis.3	Q7Z591	OTTHUMG00000020538	ENST00000307564.4:c.3980A>G	9.37:g.117103900T>C	ENSP00000303769:p.Tyr1327Cys	103.0	0.0	0		126.0	40.0	0.31746	NM_030767	Q05BK5|Q5T535|Q5T536|Q5T537|Q64FX6|Q64FX7|Q64FX8|Q64FY2|Q6ZMK0|Q6ZNL2|Q6ZTX0|Q8TET1|Q8TF33|Q96RR9|Q9H7P7	Missense_Mutation	SNP	ENST00000307564.4	37	CCDS6805.1	141|141	0.06456043956043957|0.06456043956043957	135|135	0.27439024390243905|0.27439024390243905	6|6	0.016574585635359115|0.016574585635359115	0|0	0.0|0.0	0|0	0.0|0.0	T|T	16.55|16.55	3.154873|3.154873	0.57259|0.57259	0.222651|0.222651	6.98E-4|6.98E-4	ENSG00000106948|ENSG00000106948	ENST00000320310|ENST00000307564;ENST00000374079;ENST00000374088;ENST00000223791;ENST00000374075	.|T;T;T;T;T	.|0.39592	.|1.99;1.07;1.99;1.73;1.97	5.5|5.5	5.5|5.5	0.81552|0.81552	.|.	.|0.000000	.|0.53938	.|D	.|0.000059	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.36672|0.36672	1.1|1.1	0.27590|0.27590	P|P	0.9492969|0.9492969	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.998;0.999	T|T	0.10567|0.10567	-1.0624|-1.0624	5|9	0.51188|0.72032	T|D	0.08|0.01	-18.4356|-18.4356	12.2902|12.2902	0.54815|0.54815	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs2787344;rs2787344|rs2787344;rs2787344	.|1327;1246	.|Q7Z591;Q7Z591-2	.|AKNA_HUMAN;.	V|C	338|1327;272;1327;787;1246	.|ENSP00000303769:Y1327C;ENSP00000363192:Y272C;ENSP00000363201:Y1327C;ENSP00000223791:Y787C;ENSP00000363188:Y1246C	ENSP00000314538:I338V|ENSP00000223791:Y787C	I|Y	-|-	1|2	0|0	AKNA|AKNA	116143721|116143721	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.450000|0.450000	0.32258|0.32258	4.341000|4.341000	0.59335|0.59335	2.209000|2.209000	0.71365|0.71365	0.533000|0.533000	0.62120|0.62120	ATC|TAT	T|0.919;C|0.081	0.081	strong		0.622	AKNA-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053767.2	NM_030767	
SCN9A	6335	hgsc.bcm.edu	37	2	167142979	167142979	+	Missense_Mutation	SNP	C	C	T	rs58022607	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:167142979C>T	ENST00000409435.1	-	10	1468	c.1469G>A	c.(1468-1470)aGt>aAt	p.S490N	AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Missense_Mutation_p.S491N|SCN9A_ENST00000409672.1_Missense_Mutation_p.S490N|SCN9A_ENST00000375387.4_Missense_Mutation_p.S491N			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	490			S -> N (in dbSNP:rs58022607). {ECO:0000269|PubMed:19763161}.		behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTCCTCTCCACTGGAGAGCTT	0.423													C|||	230	0.0459265	0.1551	0.0187	5008	,	,		19535	0.0		0.004	False		,,,				2504	0.0082				p.S490N		Atlas-SNP	.											.	SCN9A	296	.	0			c.G1469A						PASS	.	C	ASN/SER	464,3260		28,408,1426	111.0	104.0	106.0		1469	4.0	1.0	2	dbSNP_129	106	44,8140		3,38,4051	yes	missense	SCN9A	NM_002977.3	46	31,446,5477	TT,TC,CC		0.5376,12.4597,4.266	benign	490/1978	167142979	508,11400	1862	4092	5954	SO:0001583	missense	6335	exon11			TCTCCACTGGAGA	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10597	protein-coding gene	gene with protein product		603415	"""sodium channel, voltage-gated, type IX, alpha polypeptide"""			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.1469G>A	2.37:g.167142979C>T	ENSP00000386330:p.Ser490Asn	168.0	0.0	0		181.0	181.0	1	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Missense_Mutation	SNP	ENST00000409435.1	37	CCDS46441.1	95	0.043498168498168496	85	0.17276422764227642	8	0.022099447513812154	0	0.0	2	0.002638522427440633	C	11.89	1.773085	0.31411	0.124597	0.005376	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435;ENST00000454569;ENST00000452182	D;D;D;D;D;D	0.90900	-2.75;-2.75;-2.75;-2.75;-2.75;-2.75	5.82	4.01	0.46588	Domain of unknown function DUF3451 (1);	0.994312	0.08172	N	0.986830	T	0.01592	0.0051	M	0.66939	2.045	0.40162	P	0.022926000000000002	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.08055	0.003;0.003;0.003	T	0.53599	-0.8416	9	0.31617	T	0.26	.	6.4457	0.21875	0.2587:0.6092:0.0:0.1321	rs58022607	490;490;491	E7EUN6;Q15858;E9PF08	.;SCN9A_HUMAN;.	N	490;491;491;490;355;355	ENSP00000386306:S490N;ENSP00000364536:S491N;ENSP00000304748:S491N;ENSP00000386330:S490N;ENSP00000413212:S355N;ENSP00000393141:S355N	ENSP00000304748:S491N	S	-	2	0	SCN9A	166851225	0.956000	0.32656	1.000000	0.80357	0.897000	0.52465	0.338000	0.19858	1.468000	0.48064	0.484000	0.47621	AGT	C|0.964;T|0.036	0.036	strong		0.423	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	
TTN	7273	hgsc.bcm.edu	37	2	179613962	179613962	+	Intron	SNP	C	C	T	rs72648903	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179613962C>T	ENST00000591111.1	-	45	10585				TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Intron|TTN_ENST00000360870.5_Missense_Mutation_p.V4389I|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Intron			Q8WZ42	TITIN_HUMAN	titin						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)			TTAATAGTGACATCACTGAAA	0.343													C|||	95	0.0189696	0.0703	0.0029	5008	,	,		19175	0.0		0.0	False		,,,				2504	0.0				p.V4389I		Atlas-SNP	.											TTN_ENST00000360870,rectum,carcinoma,+1,1	TTN	18412	1	0			c.G13165A						PASS	.	C	,,ILE/VAL,,	221,4179	123.7+/-161.0	6,209,1985	57.0	62.0	60.0		,,13165,,	3.4	0.0	2	dbSNP_130	60	6,8586	3.7+/-12.6	0,6,4290	yes	intron,intron,missense,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,29,,	6,215,6275	TT,TC,CC		0.0698,5.0227,1.7472	,,,,	,,4389/5605,,	179613962	227,12765	2200	4296	6496	SO:0001627	intron_variant	7273	exon46			TAGTGACATCACT	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.10360+3888G>A	2.37:g.179613962C>T		74.0	0.0	0		83.0	28.0	0.337349	NM_133379	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		35	0.016025641025641024	34	0.06910569105691057	1	0.0027624309392265192	0	0.0	0	0.0	C	10.23	1.293061	0.23564	0.050227	6.98E-4	ENSG00000155657	ENST00000360870	T	0.60672	0.17	5.23	3.42	0.39159	.	.	.	.	.	T	0.04452	0.0122	N	0.24115	0.695	0.09310	N	0.999999	B	0.06786	0.001	B	0.06405	0.002	T	0.02126	-1.1209	9	0.16420	T	0.52	.	13.5505	0.61730	0.0:0.8613:0.0:0.1387	.	4389	Q8WZ42-6	.	I	4389	ENSP00000354117:V4389I	ENSP00000354117:V4389I	V	-	1	0	TTN	179322207	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	1.120000	0.31271	0.434000	0.26340	-2.010000	0.00438	GTC	C|0.980;T|0.020	0.020	strong		0.343	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
AHNAK2	113146	hgsc.bcm.edu	37	14	105417286	105417286	+	Missense_Mutation	SNP	G	G	A	rs149840830	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105417286G>A	ENST00000333244.5	-	7	4621	c.4502C>T	c.(4501-4503)cCg>cTg	p.P1501L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1501						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CCCGAACGACGGCATCTTGAA	0.607													.|||	272	0.0543131	0.2027	0.0058	5008	,	,		14935	0.0		0.0	False		,,,				2504	0.0				p.P1501L		Atlas-SNP	.											AHNAK2_ENST00000333244,colon,carcinoma,0,1	AHNAK2	719	1	0			c.C4502T						PASS	.	G	LEU/PRO	600,3288		124,352,1468	194.0	134.0	153.0		4502	4.2	0.9	14	dbSNP_134	153	13,8061		4,5,4028	no	missense	AHNAK2	NM_138420.2	98	128,357,5496	AA,AG,GG		0.161,15.4321,5.1246	probably-damaging	1501/5796	105417286	613,11349	1944	4037	5981	SO:0001583	missense	113146	exon7			AACGACGGCATCT	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.4502C>T	14.37:g.105417286G>A	ENSP00000353114:p.Pro1501Leu	370.0	0.0	0		355.0	337.0	0.949296	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	92	0.04212454212454213	90	0.18292682926829268	2	0.0055248618784530384	0	0.0	0	0.0	g	14.95	2.687349	0.48097	0.154321	0.00161	ENSG00000185567	ENST00000333244	T	0.03065	4.06	4.16	4.16	0.48862	.	.	.	.	.	T	0.00073	0.0002	H	0.95043	3.615	0.27144	P	0.9615793	D	0.89917	1.0	D	0.91635	0.999	T	0.05305	-1.0893	8	0.87932	D	0	-29.3229	16.1243	0.81382	0.0:0.0:1.0:0.0	.	1501	Q8IVF2	AHNK2_HUMAN	L	1501	ENSP00000353114:P1501L	ENSP00000353114:P1501L	P	-	2	0	AHNAK2	104488331	0.035000	0.19736	0.884000	0.34674	0.008000	0.06430	0.923000	0.28757	1.867000	0.54127	0.485000	0.47835	CCG	G|0.966;A|0.034	0.034	strong		0.607	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
NRIP1	8204	hgsc.bcm.edu	37	21	16337538	16337538	+	Silent	SNP	G	G	A	rs28587162	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:16337538G>A	ENST00000400202.1	-	3	3688	c.2976C>T	c.(2974-2976)agC>agT	p.S992S	AF127577.10_ENST00000446301.1_RNA|NRIP1_ENST00000318948.4_Silent_p.S992S|NRIP1_ENST00000400199.1_Silent_p.S992S			P48552	NRIP1_HUMAN	nuclear receptor interacting protein 1	992	Interaction with ZNF366.				androgen receptor signaling pathway (GO:0030521)|lipid storage (GO:0019915)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|ovarian follicle rupture (GO:0001543)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|glucocorticoid receptor binding (GO:0035259)|nuclear hormone receptor binding (GO:0035257)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			cervix(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(6)|lung(13)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	39				Epithelial(23;1.19e-05)|all cancers(11;4.64e-05)|COAD - Colon adenocarcinoma(22;0.000232)|Colorectal(24;0.0006)|OV - Ovarian serous cystadenocarcinoma(11;0.00418)|Lung(58;0.199)|LUSC - Lung squamous cell carcinoma(23;0.24)		CCATGCAACTGCTGGGCTGAG	0.428													G|||	112	0.0223642	0.0787	0.0115	5008	,	,		21468	0.0		0.0	False		,,,				2504	0.0				p.S992S		Atlas-SNP	.											.	NRIP1	103	.	0			c.C2976T						PASS	.	G		334,4072	175.9+/-205.1	15,304,1884	70.0	62.0	65.0		2976	4.0	0.0	21	dbSNP_125	65	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	NRIP1	NM_003489.3		15,305,6182	AA,AG,GG		0.0116,7.5806,2.5761		992/1159	16337538	335,12669	2203	4299	6502	SO:0001819	synonymous_variant	8204	exon4			GCAACTGCTGGGC	X84373	CCDS13568.1	21q11.2	2008-07-31			ENSG00000180530	ENSG00000180530			8001	protein-coding gene	gene with protein product	"""receptor interacting protein 140"", ""nuclear factor RIP140"""	602490				7641693, 9521594	Standard	NM_003489		Approved	RIP140	uc002yjx.2	P48552	OTTHUMG00000074323	ENST00000400202.1:c.2976C>T	21.37:g.16337538G>A		127.0	0.0	0		143.0	69.0	0.482517	NM_003489	Q8IWE8	Silent	SNP	ENST00000400202.1	37	CCDS13568.1																																																																																			G|0.979;A|0.021	0.021	strong		0.428	NRIP1-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157926.1	NM_003489	
ZNF208	7757	hgsc.bcm.edu	37	19	22155434	22155434	+	Missense_Mutation	SNP	T	T	C	rs139351235	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22155434T>C	ENST00000397126.4	-	4	2550	c.2402A>G	c.(2401-2403)gAt>gGt	p.D801G	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	801					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				GGGTTTCTCATCAGTATGAAT	0.363													N|||	152	0.0303514	0.1089	0.0115	5008	,	,		20788	0.0		0.0	False		,,,				2504	0.0				p.D801G		Atlas-SNP	.											.	ZNF208	817	.	0			c.A2402G						PASS	.	C	GLY/ASP	404,3794		23,358,1718	57.0	66.0	63.0		2402	2.6	0.1	19	dbSNP_134	63	3,8493		0,3,4245	no	missense	ZNF208	NM_007153.3	94	23,361,5963	CC,CT,TT		0.0353,9.6236,3.2062	benign	801/1281	22155434	407,12287	2099	4248	6347	SO:0001583	missense	7757	exon4			TTCTCATCAGTAT	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"""Zinc fingers, C2H2-type"", ""-"""	12999	protein-coding gene	gene with protein product	"""zinc finger protein 95"""	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.2402A>G	19.37:g.22155434T>C	ENSP00000380315:p.Asp801Gly	21.0	0.0	0		26.0	16.0	0.615385	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	61	0.027930402930402932	58	0.11788617886178862	3	0.008287292817679558	0	0.0	0	0.0	t	0.001	-2.962685	0.00049	0.096236	3.53E-4	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.11277	2.79	2.57	2.57	0.30868	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00073	0.0002	.	.	.	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.43327	-0.9398	7	0.02654	T	1	.	5.0553	0.14529	0.0:0.6551:0.213:0.1319	.	701	O43345	ZN208_HUMAN	G	801;701	ENSP00000380315:D801G	ENSP00000380315:D801G	D	-	2	0	ZNF208	21947274	0.000000	0.05858	0.123000	0.21794	0.158000	0.22134	-0.473000	0.06615	0.123000	0.18342	-1.171000	0.01739	GAT	T|0.972;C|0.028	0.028	strong		0.363	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153	
DSCAML1	57453	hgsc.bcm.edu	37	11	117329597	117329597	+	Silent	SNP	G	G	C	rs115831160	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117329597G>C	ENST00000321322.6	-	19	3622	c.3621C>G	c.(3619-3621)acC>acG	p.T1207T	DSCAML1_ENST00000527706.1_Silent_p.T937T	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	1147	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axonogenesis (GO:0007409)|brain development (GO:0007420)|cell fate determination (GO:0001709)|central nervous system development (GO:0007417)|dendrite self-avoidance (GO:0070593)|dorsal/ventral pattern formation (GO:0009953)|embryonic skeletal system morphogenesis (GO:0048704)|homophilic cell adhesion (GO:0007156)|negative regulation of cell adhesion (GO:0007162)	cell surface (GO:0009986)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)			breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(24)|lung(49)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	110	all_hematologic(175;0.0487)	Breast(348;0.0424)|Medulloblastoma(222;0.0523)|all_hematologic(192;0.232)		BRCA - Breast invasive adenocarcinoma(274;9.12e-06)|Epithelial(105;0.00172)		GCTCCCGCGTGGTGGTGATGT	0.652													G|||	5	0.000998403	0.0038	0.0	5008	,	,		20355	0.0		0.0	False		,,,				2504	0.0				p.T1207T		Atlas-SNP	.											.	DSCAML1	286	.	0			c.C3621G						PASS	.	G		14,4388	22.3+/-47.3	0,14,2187	104.0	95.0	98.0		3621	-7.8	0.7	11	dbSNP_132	98	2,8590	2.2+/-6.3	0,2,4294	no	coding-synonymous	DSCAML1	NM_020693.2		0,16,6481	CC,CG,GG		0.0233,0.318,0.1231		1207/2114	117329597	16,12978	2201	4296	6497	SO:0001819	synonymous_variant	57453	exon19			CCGCGTGGTGGTG		CCDS8384.1	11q22.2-q22.3	2013-02-11			ENSG00000177103	ENSG00000177103		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	14656	protein-coding gene	gene with protein product		611782				11453658	Standard	NM_020693		Approved	KIAA1132	uc001prh.1	Q8TD84	OTTHUMG00000167071	ENST00000321322.6:c.3621C>G	11.37:g.117329597G>C		100.0	0.0	0		118.0	48.0	0.40678	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Silent	SNP	ENST00000321322.6	37	CCDS8384.1																																																																																			G|0.999;C|0.001	0.001	strong		0.652	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693	
MYZAP	100820829	hgsc.bcm.edu	37	15	57925873	57925873	+	Missense_Mutation	SNP	G	G	C	rs148672365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:57925873G>C	ENST00000267853.5	+	8	961	c.867G>C	c.(865-867)gaG>gaC	p.E289D	GCOM1_ENST00000380561.2_Missense_Mutation_p.E258D|POLR2M_ENST00000380563.2_5'UTR|GCOM1_ENST00000587652.1_Missense_Mutation_p.E289D|GCOM1_ENST00000396180.1_Missense_Mutation_p.E258D|GCOM1_ENST00000572390.1_Missense_Mutation_p.E289D|GCOM1_ENST00000380568.3_Missense_Mutation_p.E289D|GCOM1_ENST00000380560.2_Missense_Mutation_p.E220D|GCOM1_ENST00000380569.2_Missense_Mutation_p.E289D|GCOM1_ENST00000574161.1_Missense_Mutation_p.E289D|MYZAP_ENST00000380565.4_Missense_Mutation_p.E289D			P0CAP1	MYZAP_HUMAN	myocardial zonula adherens protein	289					intracellular signal transduction (GO:0035556)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|I band (GO:0031674)											AAGCAGCAGAGATCAGCCTAG	0.478													G|||	20	0.00399361	0.0144	0.0014	5008	,	,		18055	0.0		0.0	False		,,,				2504	0.0				p.E289D		Atlas-SNP	.											.	GCOM1	66	.	0			c.G867C						PASS	.	G	ASP/GLU,ASP/GLU,ASP/GLU,ASP/GLU	70,4314	64.7+/-102.0	0,70,2122	128.0	127.0	128.0		867,867,867,867	3.5	1.0	15	dbSNP_134	128	0,8584		0,0,4292	yes	missense,missense,missense,missense	GCOM1	NM_001018090.3,NM_001018091.3,NM_001018100.3,NM_152451.6	45,45,45,45	0,70,6414	CC,CG,GG		0.0,1.5967,0.5398	probably-damaging,probably-damaging,probably-damaging,probably-damaging	289/551,289/446,289/467,289/439	57925873	70,12898	2192	4292	6484	SO:0001583	missense	145781	exon8			AGCAGAGATCAGC	FJ970029		15q21.3	2012-10-05			ENSG00000263155	ENSG00000263155			43444	protein-coding gene	gene with protein product	"""myocardium-enriched zonula adherens protein"""	614071				20093627, 21992629, 22160502	Standard	NM_001018100		Approved	MYOZAP, Gup, Gup1, GCOM1		P0CAP1	OTTHUMG00000132453	ENST00000267853.5:c.867G>C	15.37:g.57925873G>C	ENSP00000267853:p.Glu289Asp	170.0	0.0	0		162.0	79.0	0.487654	NM_001018090	D2E9U7|Q6EER8|Q6EES2|Q6EEV3|Q6EF00|Q6EF01|Q6EF02|Q6EF46|Q6EFN8|Q6EM48|Q6K046|Q6K050|Q6K051|Q6ZQZ3|Q8NC58|Q8NCF3|Q96DI5|Q96JB7|Q96NF5	Missense_Mutation	SNP	ENST00000267853.5	37	CCDS10162.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	G	18.62	3.663734	0.67700	0.015967	0.0	ENSG00000137878	ENST00000380569;ENST00000380561;ENST00000396180;ENST00000380560;ENST00000267853;ENST00000380565;ENST00000380568;ENST00000461709	T;T;T;T;T;T;T;T	0.33438	1.41;1.41;1.41;1.41;1.41;1.41;1.41;1.41	5.68	3.46	0.39613	.	0.000000	0.85682	D	0.000000	T	0.37019	0.0988	M	0.75615	2.305	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;0.999;1.0	D;D;D;D	0.87578	0.995;0.993;0.995;0.998	T	0.51911	-0.8645	10	0.62326	D	0.03	-34.0747	12.4064	0.55443	0.1663:0.0:0.8337:0.0	.	289;289;289;289	P0CAP1-2;P0CAP1-11;P0CAP1-4;P0CAP1	.;.;.;GCOM1_HUMAN	D	289;258;258;220;289;289;289;4	ENSP00000369943:E289D;ENSP00000369935:E258D;ENSP00000379483:E258D;ENSP00000369933:E220D;ENSP00000267853:E289D;ENSP00000369939:E289D;ENSP00000369942:E289D;ENSP00000431396:E4D	ENSP00000267853:E289D	E	+	3	2	GCOM1	55713165	1.000000	0.71417	0.998000	0.56505	0.916000	0.54674	1.551000	0.36233	1.394000	0.46624	0.563000	0.77884	GAG	G|0.994;C|0.006	0.006	strong		0.478	MYZAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255716.2	NM_001018100	
TANC1	85461	hgsc.bcm.edu	37	2	160019901	160019901	+	Missense_Mutation	SNP	C	C	T	rs55929944	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:160019901C>T	ENST00000263635.6	+	8	1027	c.790C>T	c.(790-792)Cgc>Tgc	p.R264C	TANC1_ENST00000454300.1_Missense_Mutation_p.R158C	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	264					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						GCTTCATGACCGCAGGGCAGA	0.522													C|||	163	0.0325479	0.1172	0.0086	5008	,	,		19708	0.0		0.002	False		,,,				2504	0.0				p.R264C		Atlas-SNP	.											.	TANC1	157	.	0			c.C790T						PASS	.	C	CYS/ARG,CYS/ARG	436,3492		33,370,1561	74.0	79.0	77.0		787,790	6.0	1.0	2	dbSNP_129	77	2,8292		0,2,4145	yes	missense,missense	TANC1	NM_001145909.1,NM_033394.2	180,180	33,372,5706	TT,TC,CC		0.0241,11.0998,3.5837	probably-damaging,probably-damaging	263/1391,264/1862	160019901	438,11784	1964	4147	6111	SO:0001583	missense	85461	exon8			CATGACCGCAGGG	AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29364	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.790C>T	2.37:g.160019901C>T	ENSP00000263635:p.Arg264Cys	280.0	0.0	0		278.0	165.0	0.593525	NM_033394	C9JD88|Q49AI8	Missense_Mutation	SNP	ENST00000263635.6	37	CCDS42766.1	62	0.028388278388278388	57	0.11585365853658537	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	C	15.63	2.890072	0.52014	0.110998	2.41E-4	ENSG00000115183	ENST00000454300;ENST00000263635	T;T	0.70869	-0.51;-0.52	6.04	6.04	0.98038	.	0.113037	0.64402	D	0.000007	T	0.02455	0.0075	L	0.54323	1.7	0.80722	D	1	B;B	0.24721	0.066;0.11	B;B	0.17722	0.01;0.019	T	0.25710	-1.0124	10	0.66056	D	0.02	.	20.5948	0.99439	0.0:1.0:0.0:0.0	rs55929944	263;264	B9EK39;Q9C0D5	.;TANC1_HUMAN	C	158;264	ENSP00000396339:R158C;ENSP00000263635:R264C	ENSP00000263635:R264C	R	+	1	0	TANC1	159728147	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.696000	0.54757	2.873000	0.98535	0.563000	0.77884	CGC	C|0.971;T|0.029	0.029	strong		0.522	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1		
MTSS1	9788	hgsc.bcm.edu	37	8	125575047	125575047	+	Silent	SNP	G	G	T	rs16899702	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:125575047G>T	ENST00000518547.1	-	10	1484	c.1011C>A	c.(1009-1011)ccC>ccA	p.P337P	MTSS1_ENST00000354184.4_Silent_p.P137P|MTSS1_ENST00000524090.1_Silent_p.P227P|MTSS1_ENST00000378017.3_Silent_p.P337P|MTSS1_ENST00000325064.5_Silent_p.P341P|MTSS1_ENST00000395508.2_Silent_p.P71P|MTSS1_ENST00000523587.1_5'UTR|NDUFB9_ENST00000522532.1_Intron|MTSS1_ENST00000431961.2_Silent_p.P137P	NM_001282971.1|NM_014751.4	NP_001269900.1|NP_055566.3	O43312	MTSS1_HUMAN	metastasis suppressor 1	337	Ser-rich.				actin cytoskeleton organization (GO:0030036)|actin filament polymerization (GO:0030041)|adherens junction maintenance (GO:0034334)|bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|cellular component movement (GO:0006928)|cellular response to fluid shear stress (GO:0071498)|epithelial cell proliferation involved in renal tubule morphogenesis (GO:2001013)|filopodium assembly (GO:0046847)|glomerulus morphogenesis (GO:0072102)|in utero embryonic development (GO:0001701)|magnesium ion homeostasis (GO:0010960)|microspike assembly (GO:0030035)|negative regulation of epithelial cell proliferation (GO:0050680)|nephron tubule epithelial cell differentiation (GO:0072160)|positive regulation of actin filament bundle assembly (GO:0032233)|renal tubule morphogenesis (GO:0061333)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)|identical protein binding (GO:0042802)|receptor binding (GO:0005102)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	37	Ovarian(258;0.00438)|all_neural(195;0.00459)|Hepatocellular(40;0.108)		STAD - Stomach adenocarcinoma(47;0.00288)			CTGGCGGCATGGGGGATGGTG	0.607													G|||	305	0.0609026	0.2201	0.0144	5008	,	,		18723	0.001		0.003	False		,,,				2504	0.0				p.P337P	Esophageal Squamous(160;622 1893 3862 8546 12509)	Atlas-SNP	.											.	MTSS1	79	.	0			c.C1011A						PASS	.	G		702,3704	291.8+/-281.7	69,564,1570	58.0	55.0	56.0		1011	-1.0	1.0	8	dbSNP_123	56	19,8581	14.0+/-48.4	0,19,4281	no	coding-synonymous	MTSS1	NM_014751.4		69,583,5851	TT,TG,GG		0.2209,15.9328,5.5436		337/756	125575047	721,12285	2203	4300	6503	SO:0001819	synonymous_variant	9788	exon10			CGGCATGGGGGAT	AF086645	CCDS6353.1, CCDS64968.1, CCDS64969.1	8p22	2008-02-05			ENSG00000170873	ENSG00000170873			20443	protein-coding gene	gene with protein product		608486				12482861, 12082544	Standard	XM_005251111		Approved	KIAA0429, MIMA, MIMB, MIM	uc003yrk.2	O43312	OTTHUMG00000048189	ENST00000518547.1:c.1011C>A	8.37:g.125575047G>T		88.0	0.0	0		93.0	50.0	0.537634	NM_014751	J3KNK6|Q8TCA2|Q96RX2	Silent	SNP	ENST00000518547.1	37	CCDS6353.1	116	0.05311355311355311	107	0.21747967479674796	8	0.022099447513812154	1	0.0017482517482517483	0	0.0	G	1.045	-0.677528	0.03378	0.159328	0.002209	ENSG00000170873	ENST00000519168;ENST00000523179	.	.	.	5.6	-0.986	0.10252	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.26780	-1.0093	3	.	.	.	-14.8982	2.3089	0.04181	0.1747:0.1927:0.435:0.1977	rs16899702;rs16899702	.	.	.	N	85;185	.	.	H	-	1	0	MTSS1	125644228	0.683000	0.27633	0.995000	0.50966	0.047000	0.14425	-0.264000	0.08658	-0.095000	0.12351	-0.156000	0.13503	CAT	G|0.936;T|0.064	0.064	strong		0.607	MTSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109625.3	NM_014751	
MED26	9441	hgsc.bcm.edu	37	19	16687870	16687870	+	Silent	SNP	G	G	A	rs61734286	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:16687870G>A	ENST00000263390.3	-	3	1033	c.771C>T	c.(769-771)gaC>gaT	p.D257D	CTD-3222D19.2_ENST00000409035.1_Silent_p.D265D|CTC-429P9.4_ENST00000593962.1_5'Flank	NM_004831.3	NP_004822.2	O95402	MED26_HUMAN	mediator complex subunit 26	257	Pro-rich.				gene expression (GO:0010467)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|RNA polymerase II transcription cofactor activity (GO:0001104)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)|skin(1)	8						CCGGAGTCTCGTCCACCCTGT	0.677													G|||	165	0.0329473	0.121	0.0072	5008	,	,		14022	0.0		0.0	False		,,,				2504	0.0				p.D257D		Atlas-SNP	.											.	MED26	25	.	0			c.C771T						PASS	.	G		407,3999	185.0+/-212.2	21,365,1817	30.0	32.0	31.0		771	-9.5	0.1	19	dbSNP_129	31	2,8598		0,2,4298	no	coding-synonymous	MED26	NM_004831.3		21,367,6115	AA,AG,GG		0.0233,9.2374,3.1447		257/601	16687870	409,12597	2203	4300	6503	SO:0001819	synonymous_variant	9441	exon3			AGTCTCGTCCACC	AF104253	CCDS12347.1	19p13.11	2008-02-05	2007-07-30	2007-07-30		ENSG00000105085			2376	protein-coding gene	gene with protein product		605043	"""cofactor required for Sp1 transcriptional activation, subunit 7, 70kDa"""	CRSP7		9989412	Standard	NM_004831		Approved	CRSP70	uc002nen.1	O95402		ENST00000263390.3:c.771C>T	19.37:g.16687870G>A		106.0	0.0	0		89.0	41.0	0.460674	NM_004831	A1A4S3|Q0VGB6	Silent	SNP	ENST00000263390.3	37	CCDS12347.1																																																																																			G|0.967;A|0.033	0.033	strong		0.677	MED26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461178.1	NM_004831	
PCDHA12	56137	hgsc.bcm.edu	37	5	140256275	140256275	+	Silent	SNP	G	G	A	rs73793508	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140256275G>A	ENST00000398631.2	+	1	1218	c.1218G>A	c.(1216-1218)tcG>tcA	p.S406S	PCDHA11_ENST00000398640.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA3_ENST00000522353.2_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	406	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATTACTACTCGTTGGTGCTGG	0.607													.|||	65	0.0129792	0.0484	0.0014	5008	,	,		20801	0.0		0.0	False		,,,				2504	0.0				p.S406S	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											PCDHA12,NS,carcinoma,+1,1	PCDHA12	196	1	0			c.G1218A						PASS	.	G	,,,,,,,,,,,,,,,	143,4263	102.1+/-140.7	3,137,2063	190.0	183.0	185.0		,,,1218,,,,,,,,,,,,1218	-9.9	0.0	5	dbSNP_130	185	0,8596		0,0,4298	no	intron,intron,intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031864.1	,,,,,,,,,,,,,,,	3,137,6361	AA,AG,GG		0.0,3.2456,1.0998	,,,,,,,,,,,,,,,	,,,406/942,,,,,,,,,,,,406/793	140256275	143,12859	2203	4298	6501	SO:0001819	synonymous_variant	56137	exon1			CTACTCGTTGGTG	AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"""Cadherins / Protocadherins : Clustered"""	8666	other	complex locus constituent	"""KIAA0345-like 2"""	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.1218G>A	5.37:g.140256275G>A		307.0	1.0	0.00325733		312.0	151.0	0.483974	NM_018903	O75278|Q2M1N8	Silent	SNP	ENST00000398631.2	37	CCDS47285.1																																																																																			G|0.990;A|0.010	0.010	strong		0.607	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903	
GNG12	55970	hgsc.bcm.edu	37	1	68171215	68171215	+	Silent	SNP	A	A	G	rs17130202	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:68171215A>G	ENST00000370982.3	-	4	337	c.138T>C	c.(136-138)caT>caC	p.H46H		NM_018841.5	NP_061329.3	Q9UBI6	GBG12_HUMAN	guanine nucleotide binding protein (G protein), gamma 12	46					cellular response to glucagon stimulus (GO:0071377)|cerebral cortex development (GO:0021987)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|response to lipopolysaccharide (GO:0032496)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|plasma membrane (GO:0005886)	PDZ domain binding (GO:0030165)|phosphate ion binding (GO:0042301)|signal transducer activity (GO:0004871)			lung(3)	3						CACTCCTGGCATGTTCCTCAC	0.393													A|||	54	0.0107827	0.0386	0.0043	5008	,	,		20621	0.0		0.0	False		,,,				2504	0.0				p.H46H		Atlas-SNP	.											.	GNG12	11	.	0			c.T138C						PASS	.	A		138,4268	99.4+/-138.0	2,134,2067	128.0	119.0	122.0		138	-4.2	1.0	1	dbSNP_123	122	0,8600		0,0,4300	no	coding-synonymous	GNG12	NM_018841.5		2,134,6367	GG,GA,AA		0.0,3.1321,1.061		46/73	68171215	138,12868	2203	4300	6503	SO:0001819	synonymous_variant	55970	exon4			CCTGGCATGTTCC	AF119663	CCDS30749.1	1p31.2	2008-02-05			ENSG00000172380	ENSG00000172380			19663	protein-coding gene	gene with protein product		615405				10819326	Standard	NM_018841		Approved		uc001dea.2	Q9UBI6	OTTHUMG00000009545	ENST00000370982.3:c.138T>C	1.37:g.68171215A>G		102.0	0.0	0		103.0	42.0	0.407767	NM_018841	Q69YP5|Q9BRV5	Silent	SNP	ENST00000370982.3	37	CCDS30749.1																																																																																			A|0.991;G|0.009	0.009	strong		0.393	GNG12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026355.2		
OR10G8	219869	hgsc.bcm.edu	37	11	123900968	123900968	+	Missense_Mutation	SNP	A	A	G	rs146815262	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:123900968A>G	ENST00000431524.1	+	1	672	c.639A>G	c.(637-639)atA>atG	p.I213M		NM_001004464.1	NP_001004464.1	Q8NGN5	O10G8_HUMAN	olfactory receptor, family 10, subfamily G, member 8	213						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(7)|large_intestine(2)|lung(21)|ovary(1)|prostate(5)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	44		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0521)		TTGTCCTGATAGTGCTGTCCT	0.552													A|||	5	0.000998403	0.0038	0.0	5008	,	,		21238	0.0		0.0	False		,,,				2504	0.0				p.I213M		Atlas-SNP	.											.	OR10G8	132	.	0			c.A639G						PASS	.	A	MET/ILE	11,4391	17.9+/-39.9	0,11,2190	187.0	162.0	171.0		639	0.0	0.8	11	dbSNP_134	171	0,8598		0,0,4299	yes	missense	OR10G8	NM_001004464.1	10	0,11,6489	GG,GA,AA		0.0,0.2499,0.0846	probably-damaging	213/312	123900968	11,12989	2201	4299	6500	SO:0001583	missense	219869	exon1			CCTGATAGTGCTG	AB065755	CCDS31704.1	11q24.1	2012-08-09			ENSG00000234560	ENSG00000234560		"""GPCR / Class A : Olfactory receptors"""	14845	protein-coding gene	gene with protein product							Standard	NM_001004464		Approved		uc001pzp.1	Q8NGN5	OTTHUMG00000165968	ENST00000431524.1:c.639A>G	11.37:g.123900968A>G	ENSP00000389072:p.Ile213Met	437.0	0.0	0		406.0	224.0	0.551724	NM_001004464	B2RNJ3|Q6IEV2	Missense_Mutation	SNP	ENST00000431524.1	37	CCDS31704.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	A	8.778	0.927449	0.18056	0.002499	0.0	ENSG00000234560	ENST00000431524	T	0.00333	8.07	2.91	0.0166	0.14109	GPCR, rhodopsin-like superfamily (1);	0.000000	0.52532	D	0.000074	T	0.00754	0.0025	M	0.89601	3.045	0.22571	N	0.998971	D	0.89917	1.0	D	0.97110	1.0	T	0.36089	-0.9762	10	0.72032	D	0.01	.	7.3929	0.26919	0.3109:0.0:0.0:0.6891	.	213	Q8NGN5	O10G8_HUMAN	M	213	ENSP00000389072:I213M	ENSP00000389072:I213M	I	+	3	3	OR10G8	123406178	0.000000	0.05858	0.808000	0.32385	0.060000	0.15804	-2.286000	0.01152	0.282000	0.22254	0.455000	0.32223	ATA	A|0.999;G|0.001	0.001	strong		0.552	OR10G8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387270.1	NM_001004464	
CELSR1	9620	hgsc.bcm.edu	37	22	46761135	46761135	+	Silent	SNP	G	G	T	rs9627424	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46761135G>T	ENST00000262738.3	-	32	8546	c.8547C>A	c.(8545-8547)acC>acA	p.T2849T		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2849					anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		CACCTTTGGGGGTGCTGTGGA	0.652													G|||	441	0.0880591	0.3177	0.0259	5008	,	,		17157	0.001		0.001	False		,,,				2504	0.001				p.T2849T		Atlas-SNP	.											.	CELSR1	242	.	0			c.C8547A						PASS	.	G		1269,3107	414.6+/-336.9	175,919,1094	28.0	27.0	27.0		8547	4.9	1.0	22	dbSNP_119	27	26,8564	16.6+/-54.9	0,26,4269	no	coding-synonymous	CELSR1	NM_014246.1		175,945,5363	TT,TG,GG		0.3027,28.9991,9.9877		2849/3015	46761135	1295,11671	2188	4295	6483	SO:0001819	synonymous_variant	9620	exon32			TTTGGGGGTGCTG	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	1850	protein-coding gene	gene with protein product	"""flamingo homolog 2 (Drosophila)"""	604523	"""cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"""			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.8547C>A	22.37:g.46761135G>T		75.0	0.0	0		55.0	28.0	0.509091	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	37	CCDS14076.1																																																																																			G|0.911;T|0.089	0.089	strong		0.652	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
ITGA11	22801	hgsc.bcm.edu	37	15	68650913	68650913	+	Silent	SNP	G	G	A	rs61729771	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:68650913G>A	ENST00000315757.7	-	6	569	c.483C>T	c.(481-483)acC>acT	p.T161T	ITGA11_ENST00000423218.2_Silent_p.T161T|ITGA11_ENST00000562826.1_5'UTR	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	161					cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						TGTCCATGTAGGTCTGGCACC	0.483													G|||	259	0.0517173	0.1853	0.0202	5008	,	,		22319	0.0		0.0	False		,,,				2504	0.0				p.T161T		Atlas-SNP	.											.	ITGA11	110	.	0			c.C483T						PASS	.	G		686,3688	269.5+/-269.1	42,602,1543	73.0	75.0	74.0		483	2.1	1.0	15	dbSNP_129	74	4,8592	3.7+/-12.6	0,4,4294	no	coding-synonymous	ITGA11	NM_001004439.1		42,606,5837	AA,AG,GG		0.0465,15.6836,5.32		161/1189	68650913	690,12280	2187	4298	6485	SO:0001819	synonymous_variant	22801	exon6			CATGTAGGTCTGG	AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"""Integrins"""	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.483C>T	15.37:g.68650913G>A		74.0	0.0	0		75.0	74.0	0.986667	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Silent	SNP	ENST00000315757.7	37	CCDS45291.1																																																																																			G|0.956;A|0.044	0.044	strong		0.483	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211	
GBP7	388646	hgsc.bcm.edu	37	1	89615023	89615023	+	Missense_Mutation	SNP	C	C	G	rs74098339	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:89615023C>G	ENST00000294671.2	-	7	1242	c.1104G>C	c.(1102-1104)atG>atC	p.M368I		NM_207398.2	NP_997281.2	Q8N8V2	GBP7_HUMAN	guanylate binding protein 7	368						membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Lung NSC(277;0.0908)		all cancers(265;0.00835)|Epithelial(280;0.0322)		AGGAGTACTCCATGAAGACTG	0.453													C|||	43	0.00858626	0.0303	0.0043	5008	,	,		17526	0.0		0.0	False		,,,				2504	0.0				p.M368I		Atlas-SNP	.											.	GBP7	57	.	0			c.G1104C						PASS	.	C	ILE/MET	143,4263	99.8+/-138.5	3,137,2063	97.0	93.0	95.0		1104	3.5	1.0	1	dbSNP_130	95	0,8600		0,0,4300	no	missense	GBP7	NM_207398.2	10	3,137,6363	GG,GC,CC		0.0,3.2456,1.0995	possibly-damaging	368/639	89615023	143,12863	2203	4300	6503	SO:0001583	missense	388646	exon7			GTACTCCATGAAG	AK096141	CCDS720.1	1p22.2	2008-02-05			ENSG00000213512	ENSG00000213512			29606	protein-coding gene	gene with protein product		612468					Standard	NM_207398		Approved	FLJ38822, GBP4L	uc001dna.2	Q8N8V2	OTTHUMG00000010659	ENST00000294671.2:c.1104G>C	1.37:g.89615023C>G	ENSP00000294671:p.Met368Ile	202.0	1.0	0.00495049		235.0	120.0	0.510638	NM_207398		Missense_Mutation	SNP	ENST00000294671.2	37	CCDS720.1	15	0.006868131868131868	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	0	0.0	C	8.920	0.960823	0.18583	0.032456	0.0	ENSG00000213512	ENST00000294671	T	0.02369	4.32	3.54	3.54	0.40534	Guanylate-binding protein, C-terminal (3);	0.154247	0.56097	D	0.000024	T	0.02649	0.0080	M	0.70903	2.155	0.34498	D	0.705737	B	0.32324	0.364	B	0.37943	0.261	T	0.22765	-1.0207	10	0.45353	T	0.12	.	12.621	0.56603	0.0:1.0:0.0:0.0	.	368	Q8N8V2	GBP7_HUMAN	I	368	ENSP00000294671:M368I	ENSP00000294671:M368I	M	-	3	0	GBP7	89387611	0.368000	0.25031	1.000000	0.80357	0.063000	0.16089	0.647000	0.24812	1.819000	0.53055	0.523000	0.50628	ATG	C|0.988;G|0.012	0.012	strong		0.453	GBP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029401.1	NM_207398	
NPTN	27020	hgsc.bcm.edu	37	15	73862606	73862606	+	Silent	SNP	C	C	T	rs35100473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:73862606C>T	ENST00000345330.4	-	6	1196	c.999G>A	c.(997-999)gtG>gtA	p.V333V	NPTN_ENST00000564551.1_5'Flank|NPTN_ENST00000351217.6_Silent_p.V217V|NPTN_ENST00000563691.1_Silent_p.V333V|NPTN_ENST00000545878.1_Silent_p.V333V|NPTN_ENST00000542234.1_Silent_p.V128V|NPTN_ENST00000287226.8_Missense_Mutation_p.C317Y|NPTN_ENST00000562924.1_Silent_p.V217V	NM_001161363.1|NM_012428.3	NP_001154835.1|NP_036560.1	Q9Y639	NPTN_HUMAN	neuroplastin	333					homophilic cell adhesion (GO:0007156)|long-term synaptic potentiation (GO:0060291)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein phosphorylation (GO:0001934)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|presynaptic membrane (GO:0042734)	cell adhesion molecule binding (GO:0050839)|type 1 fibroblast growth factor receptor binding (GO:0005105)			breast(2)|cervix(1)|endometrium(2)|large_intestine(2)|lung(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	13						GGTGGCTCCGCACCCTGAGGA	0.522													C|||	57	0.0113818	0.0393	0.0043	5008	,	,		16485	0.0		0.002	False		,,,				2504	0.0				p.V333V	Pancreas(101;1519 1568 9459 19537 41286)|Esophageal Squamous(143;1278 1787 35254 36835 44843)	Atlas-SNP	.											.	NPTN	35	.	0			c.G999A						PASS	.	C	,,,	139,4257	100.3+/-138.9	3,133,2062	80.0	75.0	76.0		999,651,999,651	0.3	1.0	15	dbSNP_126	76	0,8594		0,0,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NPTN	NM_001161363.1,NM_001161364.1,NM_012428.3,NM_017455.3	,,,	3,133,6359	TT,TC,CC		0.0,3.162,1.0701	,,,	333/395,217/279,333/399,217/283	73862606	139,12851	2198	4297	6495	SO:0001819	synonymous_variant	27020	exon6			GCTCCGCACCCTG	AF035287	CCDS10249.1, CCDS10250.1, CCDS58379.1, CCDS58380.1	15q24.1	2013-01-29	2006-02-22	2006-02-22	ENSG00000156642	ENSG00000156642		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17867	protein-coding gene	gene with protein product		612820	"""stromal cell derived factor receptor 1"""	SDFR1		8619474, 9110174	Standard	NM_012428		Approved	SDR1, GP55, GP65, np65, np55	uc002avs.3	Q9Y639	OTTHUMG00000137586	ENST00000345330.4:c.999G>A	15.37:g.73862606C>T		160.0	0.0	0		187.0	103.0	0.550802	NM_001161363	B2RAL7|B7Z4D3|B7ZLL2|Q17R52|Q59EJ9|Q6NVX7|Q9Y640	Silent	SNP	ENST00000345330.4	37	CCDS10249.1	21	0.009615384615384616	19	0.03861788617886179	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	16.12	3.034197	0.54896	0.03162	0.0	ENSG00000156642	ENST00000287226	T	0.67171	-0.25	5.6	0.321	0.15883	.	.	.	.	.	T	0.33411	0.0862	.	.	.	0.52501	D	0.999955	.	.	.	.	.	.	T	0.54516	-0.8282	6	0.87932	D	0	.	3.2099	0.06678	0.1208:0.4314:0.1233:0.3246	rs35100473	.	.	.	Y	317	ENSP00000287226:C317Y	ENSP00000287226:C317Y	C	-	2	0	NPTN	71649659	0.657000	0.27393	1.000000	0.80357	0.994000	0.84299	-0.201000	0.09464	0.055000	0.16094	-0.345000	0.07892	TGC	C|0.988;G|0.000;T|0.012	0.012	strong		0.522	NPTN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268980.1	NM_012428	
GDPGP1	390637	hgsc.bcm.edu	37	15	90784862	90784862	+	Missense_Mutation	SNP	G	G	A	rs75296384	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:90784862G>A	ENST00000558017.1	+	4	1142	c.722G>A	c.(721-723)gGa>gAa	p.G241E	GDPGP1_ENST00000329600.6_Missense_Mutation_p.G241E	NM_001013657.2	NP_001013679.2	Q6ZNW5	GDPP1_HUMAN	GDP-D-glucose phosphorylase 1	241					glucose metabolic process (GO:0006006)	cytoplasm (GO:0005737)	GDP-D-glucose phosphorylase activity (GO:0080048)|guanyl-nucleotide exchange factor activity (GO:0005085)|hydrolase activity (GO:0016787)|nucleotide binding (GO:0000166)|nucleotidyltransferase activity (GO:0016779)										CTGGACCCTGGAGGCCATTTG	0.617													G|||	174	0.0347444	0.1248	0.013	5008	,	,		17261	0.0		0.0	False		,,,				2504	0.0				p.G241E		Atlas-SNP	.											.	.	.	.	0			c.G722A						PASS	.	G	GLU/GLY	608,3790	264.4+/-266.0	41,526,1632	47.0	43.0	45.0		722	-2.9	0.0	15	dbSNP_131	45	9,8587	7.1+/-27.0	0,9,4289	yes	missense	C15orf58	NM_001013657.2	98	41,535,5921	AA,AG,GG		0.1047,13.8245,4.7483	benign	241/386	90784862	617,12377	2199	4298	6497	SO:0001583	missense	390637	exon4			ACCCTGGAGGCCA		CCDS32327.1	15q26.1	2012-05-04	2012-05-04	2012-05-04	ENSG00000183208	ENSG00000183208	2.7.7.78		34360	protein-coding gene	gene with protein product			"""chromosome 15 open reading frame 58"""	C15orf58		21507950	Standard	NM_001013657		Approved		uc002bpc.3	Q6ZNW5		ENST00000558017.1:c.722G>A	15.37:g.90784862G>A	ENSP00000452793:p.Gly241Glu	48.0	0.0	0		50.0	18.0	0.36	NM_001013657		Missense_Mutation	SNP	ENST00000558017.1	37	CCDS32327.1	64	0.029304029304029304	57	0.11585365853658537	7	0.019337016574585635	0	0.0	0	0.0	G	0.008	-1.878262	0.00537	0.138245	0.001047	ENSG00000183208	ENST00000329600	T	0.25579	1.79	5.95	-2.86	0.05717	.	1.014510	0.07864	N	0.966806	T	0.00109	0.0003	L	0.35341	1.055	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.34229	-0.9837	10	0.10902	T	0.67	0.0023	2.465	0.04550	0.4479:0.2093:0.2364:0.1065	.	241	Q6ZNW5	VTC2_HUMAN	E	241	ENSP00000368405:G241E	ENSP00000368405:G241E	G	+	2	0	C15orf58	88585866	0.000000	0.05858	0.000000	0.03702	0.142000	0.21351	0.507000	0.22675	-0.510000	0.06523	-0.150000	0.13652	GGA	G|0.962;A|0.038	0.038	strong		0.617	GDPGP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416973.1	NM_001013657	
CCDC160	347475	hgsc.bcm.edu	37	X	133378851	133378851	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:133378851C>T	ENST00000517294.1	+	3	404	c.21C>T	c.(19-21)caC>caT	p.H7H	CCDC160_ENST00000370809.4_Silent_p.H7H			A6NGH7	CC160_HUMAN	coiled-coil domain containing 160	7										endometrium(1)|kidney(2)|large_intestine(10)|lung(2)|prostate(1)|skin(1)	17						GAAGAAAACACTGGAAGGAGA	0.373																																					p.H7H		Atlas-SNP	.											.	CCDC160	38	.	0			c.C21T						PASS	.						20.0	18.0	19.0					X																	133378851		1825	4074	5899	SO:0001819	synonymous_variant	347475	exon2			AAAACACTGGAAG	BC017958	CCDS48171.1	Xq26.2	2010-02-17			ENSG00000203952	ENSG00000203952			37286	protein-coding gene	gene with protein product							Standard	NM_001101357		Approved		uc011mvj.2	A6NGH7	OTTHUMG00000164183	ENST00000517294.1:c.21C>T	X.37:g.133378851C>T		149.0	0.0	0		146.0	91.0	0.623288	NM_001101357		Silent	SNP	ENST00000517294.1	37	CCDS48171.1																																																																																			.	.	none		0.373	CCDC160-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377679.1	NM_001101357	
ZNF442	79973	hgsc.bcm.edu	37	19	12462873	12462873	+	Nonsense_Mutation	SNP	C	C	A	rs73507958	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:12462873C>A	ENST00000242804.4	-	5	799	c.217G>T	c.(217-219)Gaa>Taa	p.E73*	ZNF442_ENST00000438182.1_Nonsense_Mutation_p.E4*	NM_030824.2	NP_110451.1	Q9H7R0	ZN442_HUMAN	zinc finger protein 442	73	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(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	31						TTTGTGTCTTCCCATTTCATT	0.353													C|||	39	0.00778754	0.0287	0.0014	5008	,	,		16758	0.0		0.0	False		,,,				2504	0.0				p.E73X		Atlas-SNP	.											.	ZNF442	102	.	0			c.G217T						PASS	.	C	stop/GLU	83,4323	71.4+/-109.4	1,81,2121	123.0	111.0	115.0		217	-1.0	0.1	19	dbSNP_130	115	1,8599	1.2+/-3.3	0,1,4299	yes	stop-gained	ZNF442	NM_030824.2		1,82,6420	AA,AC,CC		0.0116,1.8838,0.6459		73/628	12462873	84,12922	2203	4300	6503	SO:0001587	stop_gained	79973	exon5			TGTCTTCCCATTT	AK024418	CCDS12271.1	19p13.13	2013-01-08			ENSG00000198342	ENSG00000198342		"""Zinc fingers, C2H2-type"", ""-"""	20877	protein-coding gene	gene with protein product							Standard	NM_030824		Approved	FLJ14356	uc002mtr.1	Q9H7R0	OTTHUMG00000156411	ENST00000242804.4:c.217G>T	19.37:g.12462873C>A	ENSP00000242804:p.Glu73*	133.0	0.0	0		118.0	61.0	0.516949	NM_030824	B4DJ48	Nonsense_Mutation	SNP	ENST00000242804.4	37	CCDS12271.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	C	13.54	2.268178	0.40095	0.018838	1.16E-4	ENSG00000198342	ENST00000242804;ENST00000438182;ENST00000424168	.	.	.	1.51	-0.994	0.10225	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.21540	T	0.41	.	3.7481	0.08556	0.0:0.4674:0.0:0.5326	.	.	.	.	X	73;4;4	.	ENSP00000242804:E73X	E	-	1	0	ZNF442	12323873	0.001000	0.12720	0.062000	0.19696	0.439000	0.31926	-0.419000	0.07071	-0.071000	0.12886	0.313000	0.20887	GAA	C|0.993;A|0.007	0.007	strong		0.353	ZNF442-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344109.1	NM_030824	
TUBB8	347688	hgsc.bcm.edu	37	10	94562	94562	+	Silent	SNP	G	G	A	rs145350711	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:94562G>A	ENST00000309812.4	-	3	332	c.270C>T	c.(268-270)ttC>ttT	p.F90F	TUBB8_ENST00000332708.5_Missense_Mutation_p.S54L|TUBB8_ENST00000413237.3_5'UTR|TUBB8_ENST00000447903.2_Silent_p.F18F	NM_177987.2	NP_817124.1	Q3ZCM7	TBB8_HUMAN	tubulin, beta 8 class VIII	90					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|cervix(1)|endometrium(4)|large_intestine(5)|lung(12)|ovary(2)|prostate(3)|skin(3)|stomach(1)	32		all_cancers(4;0.00131)|all_lung(4;0.000777)|Lung NSC(4;0.0043)|all_epithelial(10;0.0154)|Colorectal(49;0.235)		Epithelial(11;0.00341)|all cancers(11;0.00922)|OV - Ovarian serous cystadenocarcinoma(14;0.0508)|Lung(33;0.132)		CACCGAAGATGAAGTTGTCTG	0.637													g|||	2	0.000399361	0.0015	0.0	5008	,	,		15565	0.0		0.0	False		,,,				2504	0.0				p.F90F	Pancreas(192;2041 3010 9013 18103)	Atlas-SNP	.											.	TUBB8	62	.	0			c.C270T						PASS	.	G		16,4386	21.2+/-45.6	0,16,2185	42.0	52.0	49.0		270	0.1	0.0	10	dbSNP_134	49	0,8596		0,0,4298	no	coding-synonymous	TUBB8	NM_177987.2		0,16,6483	AA,AG,GG		0.0,0.3635,0.1231		90/445	94562	16,12982	2201	4298	6499	SO:0001819	synonymous_variant	347688	exon3			GAAGATGAAGTTG	AF355127	CCDS7051.1	10p15.3	2014-05-06			ENSG00000173876			"""Tubulins"""	20773	protein-coding gene	gene with protein product	"""class VIII beta-tubulin"""						Standard	NM_177987		Approved	bA631M21.2	uc001ifi.2	Q3ZCM7	OTTHUMG00000174803	ENST00000309812.4:c.270C>T	10.37:g.94562G>A		107.0	0.0	0		111.0	62.0	0.558559	NM_177987	Q5SQX9|Q8WZ78	Silent	SNP	ENST00000309812.4	37	CCDS7051.1	.	.	.	.	.	.	.	.	.	.	G	6.257	0.415577	0.11870	0.003635	0.0	ENSG00000173876	ENST00000332708	.	.	.	0.109	0.109	0.14578	.	.	.	.	.	T	0.55497	0.1924	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.55598	-0.8116	5	0.87932	D	0	.	2.6667	0.05054	0.4741:0.0:0.5259:0.0	.	.	.	.	L	54	.	ENSP00000371071:S54L	S	-	2	0	RP11-631M21.2	84562	0.988000	0.35896	0.031000	0.17742	0.032000	0.12392	0.081000	0.14823	0.181000	0.19994	0.184000	0.17185	TCA	G|0.999;A|0.001	0.001	strong		0.637	TUBB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467795.1	NM_177987	
HSPBAP1	79663	hgsc.bcm.edu	37	3	122496628	122496628	+	Missense_Mutation	SNP	A	A	C	rs16833517	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:122496628A>C	ENST00000306103.2	-	2	333	c.190T>G	c.(190-192)Tcg>Gcg	p.S64A	HSPBAP1_ENST00000465044.1_5'UTR|HSPBAP1_ENST00000383659.1_Missense_Mutation_p.S64A	NM_024610.5	NP_078886.2	Q96EW2	HBAP1_HUMAN	HSPB (heat shock 27kDa) associated protein 1	64			S -> A (in dbSNP:rs16833517).			cytoplasm (GO:0005737)				breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|urinary_tract(1)	16				GBM - Glioblastoma multiforme(114;0.0531)		AGGACCTGCGAAAGGTATTTA	0.413													A|||	256	0.0511182	0.1831	0.0202	5008	,	,		20190	0.0		0.0	False		,,,				2504	0.0				p.S64A		Atlas-SNP	.											HSPBAP1,NS,carcinoma,+1,1	HSPBAP1	32	1	0			c.T190G						PASS	.	A	ALA/SER	634,3772	274.0+/-271.7	39,556,1608	188.0	169.0	175.0		190	2.8	0.9	3	dbSNP_123	175	3,8597	3.0+/-9.4	0,3,4297	yes	missense	HSPBAP1	NM_024610.5	99	39,559,5905	CC,CA,AA		0.0349,14.3895,4.8977	benign	64/489	122496628	637,12369	2203	4300	6503	SO:0001583	missense	79663	exon2			CCTGCGAAAGGTA	AF400663	CCDS3017.1	3q21.1	2008-07-18	2002-08-29		ENSG00000169087	ENSG00000169087			16389	protein-coding gene	gene with protein product		608263	"""HSPB (heat shock 27kD) associated protein 1"""			11978969	Standard	NM_024610		Approved	FLJ22623, PASS1	uc003efu.2	Q96EW2	OTTHUMG00000159550	ENST00000306103.2:c.190T>G	3.37:g.122496628A>C	ENSP00000302562:p.Ser64Ala	275.0	0.0	0		346.0	191.0	0.552023	NM_024610	Q6P476|Q8N8J4|Q8NHH6|Q8WWF0	Missense_Mutation	SNP	ENST00000306103.2	37	CCDS3017.1	75	0.034340659340659344	67	0.13617886178861788	8	0.022099447513812154	0	0.0	0	0.0	A	9.139	1.013317	0.19277	0.143895	3.49E-4	ENSG00000169087	ENST00000383659;ENST00000306103	T;T	0.69040	-0.37;3.02	5.32	2.8	0.32819	.	0.105878	0.64402	N	0.000002	T	0.00496	0.0016	L	0.43757	1.38	0.37348	D	0.910665	B;B	0.28324	0.124;0.207	B;B	0.29353	0.057;0.101	T	0.02093	-1.1215	10	0.11485	T	0.65	.	6.8743	0.24139	0.6936:0.1567:0.0:0.1497	rs16833517;rs57105676;rs16833517	64;64	Q96EW2-2;Q96EW2	.;HBAP1_HUMAN	A	64	ENSP00000373155:S64A;ENSP00000302562:S64A	ENSP00000302562:S64A	S	-	1	0	HSPBAP1	123979318	1.000000	0.71417	0.943000	0.38184	0.390000	0.30446	2.466000	0.45084	0.405000	0.25532	0.528000	0.53228	TCG	A|0.951;C|0.049	0.049	strong		0.413	HSPBAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356161.1	NM_024610	
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46011544	46011544	+	Silent	SNP	G	G	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:46011544G>C	ENST00000400368.1	-	1	842	c.822C>G	c.(820-822)gtC>gtG	p.V274V	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	274	29 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(6)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23						CCCCAGAGCAGACGGGCACAC	0.647																																					p.V274V		Atlas-SNP	.											.	KRTAP10-6	57	.	0			c.C822G						PASS	.						112.0	115.0	114.0					21																	46011544		2203	4300	6503	SO:0001819	synonymous_variant	386674	exon1			AGAGCAGACGGGC	AB076353	CCDS42959.1	21q22.3	2006-03-13	2004-07-12	2004-07-14	ENSG00000188155	ENSG00000188155		"""Keratin associated proteins"""	20523	protein-coding gene	gene with protein product			"""keratin associated protein 18-6"""	KRTAP18-6			Standard	NM_198688		Approved	KRTAP18.6, KAP18.6, KAP10.6	uc002zfm.3	P60371	OTTHUMG00000057634	ENST00000400368.1:c.822C>G	21.37:g.46011544G>C		257.0	0.0	0		327.0	33.0	0.100917	NM_198688		Silent	SNP	ENST00000400368.1	37	CCDS42959.1																																																																																			.	.	none		0.647	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688	
GOLPH3	64083	hgsc.bcm.edu	37	5	32126441	32126441	+	Silent	SNP	G	G	A	rs34212503	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:32126441G>A	ENST00000265070.6	-	4	1089	c.774C>T	c.(772-774)gaC>gaT	p.D258D	GOLPH3_ENST00000512668.1_5'Flank	NM_022130.3	NP_071413.1	Q9H4A6	GOLP3_HUMAN	golgi phosphoprotein 3 (coat-protein)	258					cell adhesion molecule production (GO:0060352)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|gene expression (GO:0010467)|glycoprotein biosynthetic process (GO:0009101)|Golgi organization (GO:0007030)|Golgi to plasma membrane protein transport (GO:0043001)|Golgi vesicle budding (GO:0048194)|lamellipodium assembly (GO:0030032)|leukocyte tethering or rolling (GO:0050901)|positive regulation of protein secretion (GO:0050714)|positive regulation of TOR signaling (GO:0032008)|protein retention in Golgi apparatus (GO:0045053)|protein secretion (GO:0009306)|regulation of mitochondrion organization (GO:0010821)	cytosol (GO:0005829)|endosome (GO:0005768)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	enzyme binding (GO:0019899)|phosphatidylinositol-4-phosphate binding (GO:0070273)			kidney(2)|large_intestine(3)|lung(4)|ovary(1)|prostate(1)	11						CATACTGCTCGTCCAGAAGAG	0.557													G|||	219	0.04373	0.1604	0.0072	5008	,	,		19268	0.0		0.002	False		,,,				2504	0.0				p.D258D		Atlas-SNP	.											.	GOLPH3	25	.	0			c.C774T						PASS	.	G		495,3911	231.7+/-245.5	32,431,1740	103.0	86.0	92.0		774	-7.3	0.7	5	dbSNP_126	92	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	GOLPH3	NM_022130.3		32,439,6032	AA,AG,GG		0.093,11.2347,3.8674		258/299	32126441	503,12503	2203	4300	6503	SO:0001819	synonymous_variant	64083	exon4			CTGCTCGTCCAGA	AK075156	CCDS3896.1	5p13.2	2008-07-18			ENSG00000113384	ENSG00000113384			15452	protein-coding gene	gene with protein product	"""golgi peripheral membrane protein 1, 34 kDa"", ""golgi protein"", ""coat-protein"", ""golgi-associated protein"""	612207				11042173, 16263763	Standard	NM_022130		Approved	GPP34, GOPP1, MIDAS	uc003jhp.1	Q9H4A6	OTTHUMG00000090679	ENST00000265070.6:c.774C>T	5.37:g.32126441G>A		136.0	0.0	0		141.0	65.0	0.460993	NM_022130	Q9UIW5	Silent	SNP	ENST00000265070.6	37	CCDS3896.1																																																																																			G|0.966;A|0.034	0.034	strong		0.557	GOLPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207363.2	NM_022130	
PRPF4	9128	hgsc.bcm.edu	37	9	116041316	116041316	+	Silent	SNP	T	T	C	rs146246780	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116041316T>C	ENST00000374198.4	+	3	402	c.300T>C	c.(298-300)aaT>aaC	p.N100N	PRPF4_ENST00000374199.4_Silent_p.N99N	NM_001244926.1|NM_004697.4	NP_001231855.1|NP_004688.2	O43172	PRP4_HUMAN	pre-mRNA processing factor 4	100				HISERQAEVLAEFERRKRARQINVST -> ISASDRQKYWL SLREGSEPGRSMFPP (in Ref. 3; AAC02261). {ECO:0000305}.	gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	Cajal body (GO:0015030)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U4/U6 snRNP (GO:0071001)				NS(1)|breast(2)|endometrium(3)|large_intestine(6)|lung(6)|ovary(2)|pancreas(1)|prostate(2)	23						GGCAGATCAATGTTTCCACAG	0.473													T|||	7	0.00139776	0.0045	0.0014	5008	,	,		15580	0.0		0.0	False		,,,				2504	0.0				p.N100N		Atlas-SNP	.											.	PRPF4	56	.	0			c.T300C						PASS	.	T		14,4392	21.2+/-45.6	0,14,2189	95.0	91.0	92.0		300	0.2	1.0	9	dbSNP_134	92	0,8600		0,0,4300	no	coding-synonymous	PRPF4	NM_004697.3		0,14,6489	CC,CT,TT		0.0,0.3177,0.1076		100/523	116041316	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	9128	exon3			GATCAATGTTTCC	AF001687	CCDS6791.1, CCDS59142.1	9q31-q33	2013-10-03	2013-10-03		ENSG00000136875	ENSG00000136875		"""WD repeat domain containing"""	17349	protein-coding gene	gene with protein product	"""PRP4/STK/WD splicing factor"", ""U4/U6 small nuclear ribonucleoprotein Prp4"""	607795	"""PRP4 pre-mRNA processing factor 4 homolog (yeast)"""			9257651, 9404889	Standard	NM_004697		Approved	Prp4p, HPRP4, HPRP4P, PRP4, SNRNP60	uc004bgx.3	O43172	OTTHUMG00000020517	ENST00000374198.4:c.300T>C	9.37:g.116041316T>C		76.0	0.0	0		97.0	57.0	0.587629	NM_004697	O43445|O43864|Q5T1M8|Q96DG2|Q96IK4	Silent	SNP	ENST00000374198.4	37	CCDS6791.1																																																																																			T|0.999;C|0.001	0.001	strong		0.473	PRPF4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053708.2	NM_004697	
CNTN5	53942	hgsc.bcm.edu	37	11	100226900	100226900	+	Silent	SNP	G	G	A	rs34539243	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:100226900G>A	ENST00000524871.1	+	25	3542	c.3252G>A	c.(3250-3252)tcG>tcA	p.S1084S	CNTN5_ENST00000279463.3_Silent_p.S1084S|CNTN5_ENST00000524560.1_3'UTR|CNTN5_ENST00000528682.1_Silent_p.S1084S|CNTN5_ENST00000418526.2_Silent_p.S1010S	NM_014361.3	NP_055176.1	O94779	CNTN5_HUMAN	contactin 5	1084					cell adhesion (GO:0007155)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)				NS(2)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(12)|lung(38)|ovary(2)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	81		all_hematologic(158;1.22e-05)|Acute lymphoblastic leukemia(157;3.81e-05)|Melanoma(852;0.219)		BRCA - Breast invasive adenocarcinoma(274;0.00146)|KIRC - Kidney renal clear cell carcinoma(183;0.156)|Kidney(183;0.196)		CCACATCTTCGTCATCAGTCA	0.418													G|||	88	0.0175719	0.0651	0.0	5008	,	,		20062	0.0		0.002	False		,,,				2504	0.0				p.S1084S		Atlas-SNP	.											.	CNTN5	324	.	0			c.G3252A						PASS	.	G	,	209,3773		7,195,1789	143.0	139.0	140.0		3252,3030	-4.7	0.0	11	dbSNP_126	140	5,8327		0,5,4161	no	coding-synonymous,coding-synonymous	CNTN5	NM_014361.3,NM_175566.2	,	7,200,5950	AA,AG,GG		0.06,5.2486,1.7379	,	1084/1101,1010/1027	100226900	214,12100	1991	4166	6157	SO:0001819	synonymous_variant	53942	exon24			ATCTTCGTCATCA	AB013802	CCDS53696.1, CCDS53697.1, CCDS58168.1	11q22.1	2013-02-11			ENSG00000149972	ENSG00000149972		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2175	protein-coding gene	gene with protein product		607219					Standard	NM_014361		Approved	NB-2, hNB-2	uc021qpb.1	O94779	OTTHUMG00000167579	ENST00000524871.1:c.3252G>A	11.37:g.100226900G>A		115.0	0.0	0		94.0	56.0	0.595745	NM_001243270	A1L4P0|B7ZM07|E9PKE8|O94780|Q49AF3	Silent	SNP	ENST00000524871.1	37	CCDS53696.1																																																																																			G|0.988;A|0.012	0.012	strong		0.418	CNTN5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000395148.2	NM_014361	
LEFTY1	10637	hgsc.bcm.edu	37	1	226074436	226074436	+	Silent	SNP	G	G	C	rs35684337	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:226074436G>C	ENST00000272134.5	-	4	1171	c.1092C>G	c.(1090-1092)ctC>ctG	p.L364L	RP4-559A3.7_ENST00000432920.2_3'UTR|LEFTY1_ENST00000492457.1_5'Flank	NM_020997.3	NP_066277.1	O75610	LFTY1_HUMAN	left-right determination factor 1	364					cell growth (GO:0016049)|determination of left/right symmetry (GO:0007368)|heart morphogenesis (GO:0003007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)				cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	10	Breast(184;0.197)					CCTATGGCTGGAGCCTCCTTG	0.602													G|||	195	0.0389377	0.1354	0.0216	5008	,	,		18096	0.0		0.0	False		,,,				2504	0.001				p.L364L		Atlas-SNP	.											.	LEFTY1	30	.	0			c.C1092G						PASS	.	G		556,3840		26,504,1668	60.0	62.0	61.0		1092	1.1	0.8	1	dbSNP_126	61	0,8598		0,0,4299	no	coding-synonymous	LEFTY1	NM_020997.3		26,504,5967	CC,CG,GG		0.0,12.6479,4.2789		364/367	226074436	556,12438	2198	4299	6497	SO:0001819	synonymous_variant	10637	exon4			TGGCTGGAGCCTC	AF081507	CCDS1548.1	1q42.1	2008-02-05	2004-11-17	2004-11-17	ENSG00000243709	ENSG00000243709			6552	protein-coding gene	gene with protein product		603037	"""left-right determination, factor B"""	LEFTB		10053005, 10886363	Standard	NM_020997		Approved	LEFTYB	uc001hpo.3	O75610	OTTHUMG00000037443	ENST00000272134.5:c.1092C>G	1.37:g.226074436G>C		182.0	0.0	0		198.0	109.0	0.550505	NM_020997	B2R7U0|Q53H67|Q5TE94	Silent	SNP	ENST00000272134.5	37	CCDS1548.1																																																																																			G|0.963;C|0.037	0.037	strong		0.602	LEFTY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091155.1	NM_020997	
SCN10A	6336	hgsc.bcm.edu	37	3	38770198	38770198	+	Missense_Mutation	SNP	T	T	G	rs146028829		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:38770198T>G	ENST00000449082.2	-	15	2474	c.2475A>C	c.(2473-2475)gaA>gaC	p.E825D		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	825					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)	p.E825D(1)		NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	GGGGCCAGTCTTCATGGGGCG	0.517													T|||	1	0.000199681	0.0	0.0	5008	,	,		18556	0.0		0.001	False		,,,				2504	0.0				p.E825D		Atlas-SNP	.											SCN10A,NS,carcinoma,0,2	SCN10A	359	2	1	Substitution - Missense(1)	kidney(1)	c.A2475C						PASS	.	T	ASP/GLU	2,4404	4.2+/-10.8	0,2,2201	121.0	117.0	118.0		2475	-9.4	0.0	3	dbSNP_134	118	19,8581	14.6+/-50.1	0,19,4281	yes	missense	SCN10A	NM_006514.2	45	0,21,6482	GG,GT,TT		0.2209,0.0454,0.1615	benign	825/1957	38770198	21,12985	2203	4300	6503	SO:0001583	missense	6336	exon15			CCAGTCTTCATGG	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10582	protein-coding gene	gene with protein product		604427	"""sodium channel, voltage-gated, type X, alpha polypeptide"""			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.2475A>C	3.37:g.38770198T>G	ENSP00000390600:p.Glu825Asp	324.0	0.0	0		347.0	160.0	0.461095	NM_006514	A6NDQ1	Missense_Mutation	SNP	ENST00000449082.2	37	CCDS33736.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	3.068	-0.191656	0.06299	4.54E-4	0.002209	ENSG00000185313	ENST00000449082	D	0.98531	-4.98	4.73	-9.45	0.00600	Ion transport (1);	1.276660	0.04859	N	0.443792	D	0.93058	0.7790	N	0.16478	0.41	0.09310	N	1	B	0.06786	0.001	B	0.08055	0.003	D	0.86553	0.1836	10	0.45353	T	0.12	.	6.9757	0.24674	0.0871:0.3789:0.4161:0.1179	.	825	Q9Y5Y9	SCNAA_HUMAN	D	825	ENSP00000390600:E825D	ENSP00000390600:E825D	E	-	3	2	SCN10A	38745202	0.000000	0.05858	0.000000	0.03702	0.069000	0.16628	-1.935000	0.01550	-2.903000	0.00311	0.533000	0.62120	GAA	T|0.999;G|0.001	0.001	strong		0.517	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
MTFR2	113115	hgsc.bcm.edu	37	6	136560948	136560948	+	Silent	SNP	G	G	A	rs10484485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:136560948G>A	ENST00000420702.1	-	6	914	c.525C>T	c.(523-525)ggC>ggT	p.G175G	MTFR2_ENST00000451457.2_Silent_p.G175G	NM_001099286.1	NP_001092756.1	Q6P444	MTFR2_HUMAN	mitochondrial fission regulator 2	175					aerobic respiration (GO:0009060)|mitochondrial fission (GO:0000266)|mitochondrion organization (GO:0007005)	mitochondrion (GO:0005739)											CGTCACTCAAGCCAAAGGAAC	0.428													G|||	293	0.0585064	0.208	0.0231	5008	,	,		19229	0.0		0.002	False		,,,				2504	0.0				p.G175G		Atlas-SNP	.											.	.	.	.	0			c.C525T						PASS	.	G	,	786,3620	311.6+/-292.2	74,638,1491	38.0	33.0	35.0		525,525	1.3	0.0	6	dbSNP_119	35	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	FAM54A	NM_001099286.1,NM_138419.3	,	74,643,5786	AA,AG,GG		0.0581,17.8393,6.0818	,	175/386,175/386	136560948	791,12215	2203	4300	6503	SO:0001819	synonymous_variant	113115	exon6			ACTCAAGCCAAAG	BC011716	CCDS5176.1	6q23.2	2012-11-30	2012-11-29	2012-11-29	ENSG00000146410	ENSG00000146410			21115	protein-coding gene	gene with protein product			"""DUF729 domain containing 1"", ""family with sequence similarity 54, member A"""	DUFD1, FAM54A			Standard	NM_138419		Approved		uc003qgt.1	Q6P444	OTTHUMG00000015643	ENST00000420702.1:c.525C>T	6.37:g.136560948G>A		56.0	0.0	0		75.0	37.0	0.493333	NM_138419	A8K8D8|E1P585|Q5JWR7|Q6ZUE8|Q7L3U6|Q9BZ39	Silent	SNP	ENST00000420702.1	37	CCDS5176.1																																																																																			G|0.939;A|0.061	0.061	strong		0.428	MTFR2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042378.2	NM_138419	
CSMD3	114788	hgsc.bcm.edu	37	8	113662508	113662508	+	Silent	SNP	A	A	G	rs7839690	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:113662508A>G	ENST00000297405.5	-	19	3319	c.3075T>C	c.(3073-3075)gaT>gaC	p.D1025D	CSMD3_ENST00000455883.2_Silent_p.D921D|CSMD3_ENST00000343508.3_Silent_p.D985D|CSMD3_ENST00000352409.3_Silent_p.D1025D	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	1025	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						CAATGGAGAAATCATGACCAT	0.433										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)			A|||	132	0.0263578	0.0968	0.0058	5008	,	,		14812	0.0		0.0	False		,,,				2504	0.0				p.D1025D		Atlas-SNP	.											CSMD3_ENST00000343508,colon,carcinoma,-2,2	CSMD3	2325	2	0			c.T3075C						PASS	.	A	,,	311,4095	166.2+/-197.5	10,291,1902	147.0	147.0	147.0		2763,3075,2955	2.3	1.0	8	dbSNP_116	147	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	CSMD3	NM_052900.2,NM_198123.1,NM_198124.1	,,	10,296,6197	GG,GA,AA		0.0581,7.0586,2.4296	,,	921/3539,1025/3708,985/3668	113662508	316,12690	2203	4300	6503	SO:0001819	synonymous_variant	114788	exon19			GGAGAAATCATGA	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.3075T>C	8.37:g.113662508A>G		225.0	0.0	0		219.0	90.0	0.410959	NM_198123	Q96PZ3	Silent	SNP	ENST00000297405.5	37	CCDS6315.1																																																																																			A|0.972;G|0.028	0.028	strong		0.433	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
SLC35E4	339665	hgsc.bcm.edu	37	22	31032881	31032881	+	Silent	SNP	G	G	A	rs8136373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:31032881G>A	ENST00000343605.4	+	1	1243	c.444G>A	c.(442-444)ctG>ctA	p.L148L	SLC35E4_ENST00000300385.8_Silent_p.L148L|SLC35E4_ENST00000406566.1_Silent_p.L148L	NM_001001479.2	NP_001001479.1	Q6ICL7	S35E4_HUMAN	solute carrier family 35, member E4	148	EamA.|Leu-rich.					integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|skin(1)	10						TGTTCACCCTGGCCCTGTCGG	0.677													G|||	440	0.0878594	0.2988	0.0303	5008	,	,		14087	0.0		0.0149	False		,,,				2504	0.0092				p.L148L		Atlas-SNP	.											.	SLC35E4	22	.	0			c.G444A						PASS	.	G		1219,3185	391.9+/-328.3	165,889,1148	65.0	36.0	46.0		444	5.2	1.0	22	dbSNP_116	46	171,8429	72.9+/-135.5	1,169,4130	no	coding-synonymous	SLC35E4	NM_001001479.2		166,1058,5278	AA,AG,GG		1.9884,27.6794,10.689		148/351	31032881	1390,11614	2202	4300	6502	SO:0001819	synonymous_variant	339665	exon1			CACCCTGGCCCTG		CCDS13882.1	22q12.2	2013-05-22			ENSG00000100036	ENSG00000100036		"""Solute carriers"""	17058	protein-coding gene	gene with protein product							Standard	NM_001001479		Approved		uc003ais.1	Q6ICL7	OTTHUMG00000151110	ENST00000343605.4:c.444G>A	22.37:g.31032881G>A		46.0	0.0	0		39.0	38.0	0.974359	NM_001001479	Q567P0	Silent	SNP	ENST00000343605.4	37	CCDS13882.1																																																																																			G|0.900;A|0.100	0.100	strong		0.677	SLC35E4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321382.1	XM_290973	
ZNF678	339500	hgsc.bcm.edu	37	1	227842516	227842516	+	Missense_Mutation	SNP	G	G	C	rs61744724	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:227842516G>C	ENST00000343776.5	+	4	910	c.565G>C	c.(565-567)Gtt>Ctt	p.V189L	ZNF678_ENST00000608949.1_Intron|ZNF678_ENST00000397097.3_Missense_Mutation_p.V244L	NM_178549.3	NP_848644.2	Q5SXM1	ZN678_HUMAN	zinc finger protein 678	189					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(7)|pancreas(1)|prostate(1)	24		Prostate(94;0.0885)				ATGTGACAAAGTTTTTAATTG	0.373													G|||	82	0.0163738	0.059	0.0043	5008	,	,		18566	0.0		0.001	False		,,,				2504	0.0				p.V244L		Atlas-SNP	.											.	ZNF678	137	.	0			c.G730C						PASS	.	G	LEU/VAL	213,4193	124.5+/-161.8	3,207,1993	88.0	103.0	98.0		730	1.2	0.1	1	dbSNP_129	98	1,8597	1.2+/-3.3	0,1,4298	no	missense	ZNF678	NM_178549.3	32	3,208,6291	CC,CG,GG		0.0116,4.8343,1.6456	benign	244/581	227842516	214,12790	2203	4299	6502	SO:0001583	missense	339500	exon4			GACAAAGTTTTTA	BC042500		1q42.13	2013-01-08			ENSG00000181450	ENSG00000181450		"""Zinc fingers, C2H2-type"", ""-"""	28652	protein-coding gene	gene with protein product	"""hypothetical protein MGC42493"""					12477932	Standard	NM_178549		Approved	MGC42493	uc021pjy.1	Q5SXM1	OTTHUMG00000037700	ENST00000343776.5:c.565G>C	1.37:g.227842516G>C	ENSP00000344828:p.Val189Leu	56.0	0.0	0		60.0	30.0	0.5	NM_178549	Q8IVQ9	Missense_Mutation	SNP	ENST00000343776.5	37		27	0.012362637362637362	22	0.044715447154471545	1	0.0027624309392265192	4	0.006993006993006993	0	0.0	G	10.75	1.437218	0.25900	0.048343	1.16E-4	ENSG00000181450	ENST00000343776;ENST00000397097	T;T	0.35605	1.3;1.3	1.21	1.21	0.21127	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04724	0.0128	L	0.41415	1.275	0.19945	N	0.999946	P	0.36171	0.541	B	0.36608	0.229	T	0.09100	-1.0690	9	0.72032	D	0.01	.	5.6119	0.17410	0.0:0.3493:0.6507:0.0	rs61744724	189	Q5SXM1	ZN678_HUMAN	L	189;244	ENSP00000344828:V189L;ENSP00000440403:V244L	ENSP00000344828:V189L	V	+	1	0	ZNF678	225909139	0.001000	0.12720	0.092000	0.20876	0.083000	0.17756	-0.016000	0.12613	0.502000	0.28037	0.505000	0.49811	GTT	G|0.987;C|0.013	0.013	strong		0.373	ZNF678-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000091976.2	NM_178549	
CAPN9	10753	hgsc.bcm.edu	37	1	230916057	230916057	+	Missense_Mutation	SNP	T	T	G	rs79844715	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:230916057T>G	ENST00000271971.2	+	10	1360	c.1247T>G	c.(1246-1248)cTg>cGg	p.L416R	RP11-99J16__A.2_ENST00000412344.1_RNA|RP11-99J16__A.2_ENST00000428480.1_RNA|RP11-99J16__A.2_ENST00000452640.1_RNA|CAPN9_ENST00000366666.2_Missense_Mutation_p.L353R|CAPN9_ENST00000354537.1_Missense_Mutation_p.L390R	NM_006615.2	NP_006606.1	O14815	CAN9_HUMAN	calpain 9	416	Domain III.				digestion (GO:0007586)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	25	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.167)				GCCAATGTGCTGACAATCGGC	0.483													T|||	7	0.00139776	0.0045	0.0014	5008	,	,		17721	0.0		0.0	False		,,,				2504	0.0				p.L416R		Atlas-SNP	.											.	CAPN9	116	.	0			c.T1247G						PASS	.	T	ARG/LEU,ARG/LEU	23,4383	29.9+/-59.1	0,23,2180	124.0	112.0	116.0		1247,1169	5.5	1.0	1	dbSNP_131	116	0,8600		0,0,4300	yes	missense,missense	CAPN9	NM_006615.2,NM_016452.1	102,102	0,23,6480	GG,GT,TT		0.0,0.522,0.1768	probably-damaging,probably-damaging	416/691,390/665	230916057	23,12983	2203	4300	6503	SO:0001583	missense	10753	exon10			ATGTGCTGACAAT	AF022799	CCDS1586.1, CCDS31053.1	1q42.11-q42.3	2013-01-10	2004-11-11		ENSG00000135773	ENSG00000135773		"""EF-hand domain containing"""	1486	protein-coding gene	gene with protein product	"""novel calpain large subunit-4"""	606401	"""calpain 9 (nCL-4)"""			9524069, 10835488	Standard	XM_005273010		Approved	nCL-4, GC36	uc001htz.1	O14815	OTTHUMG00000037779	ENST00000271971.2:c.1247T>G	1.37:g.230916057T>G	ENSP00000271971:p.Leu416Arg	136.0	0.0	0		148.0	71.0	0.47973	NM_006615	B1APS1|B1AQI0|Q9NS74	Missense_Mutation	SNP	ENST00000271971.2	37	CCDS1586.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	T	10.03	1.239188	0.22711	0.00522	0.0	ENSG00000135773	ENST00000271971;ENST00000354537;ENST00000366666	D;D;D	0.88586	-2.4;-2.4;-2.4	5.54	5.54	0.83059	Peptidase C2, calpain, large subunit, domain III (2);Peptidase C2, calpain, domain III (1);	0.197529	0.44483	D	0.000444	D	0.92691	0.7677	M	0.88241	2.94	0.58432	D	0.999996	D;D;D	0.67145	0.996;0.991;0.993	D;P;P	0.64410	0.925;0.793;0.869	D	0.92319	0.5864	10	0.31617	T	0.26	.	15.3798	0.74645	0.0:0.0:0.0:1.0	.	353;390;416	E7ESS6;O14815-2;O14815	.;.;CAN9_HUMAN	R	416;390;353	ENSP00000271971:L416R;ENSP00000346538:L390R;ENSP00000355626:L353R	ENSP00000271971:L416R	L	+	2	0	CAPN9	228982680	1.000000	0.71417	0.998000	0.56505	0.017000	0.09413	3.833000	0.55790	2.112000	0.64535	0.524000	0.50904	CTG	T|0.998;G|0.002	0.002	strong		0.483	CAPN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092179.1	NM_006615	
SNAP91	9892	hgsc.bcm.edu	37	6	84303273	84303273	+	Silent	SNP	G	G	A	rs181491904	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:84303273G>A	ENST00000439399.2	-	18	1936	c.1620C>T	c.(1618-1620)acC>acT	p.T540T	SNAP91_ENST00000521743.1_Silent_p.T540T|SNAP91_ENST00000428679.2_Silent_p.T540T|SNAP91_ENST00000520302.1_Silent_p.T538T|SNAP91_ENST00000437520.1_Intron|SNAP91_ENST00000520213.1_Intron|SNAP91_ENST00000195649.6_Silent_p.T540T|SNAP91_ENST00000369694.2_Silent_p.T540T|SNAP91_ENST00000521485.1_Silent_p.T540T	NM_014841.2	NP_055656.1	O60641	AP180_HUMAN	synaptosomal-associated protein, 91kDa	540	Ala-rich.|Thr-rich.				clathrin coat assembly (GO:0048268)|protein transport (GO:0015031)	clathrin coat (GO:0030118)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|protein kinase binding (GO:0019901)			breast(2)|endometrium(2)|kidney(1)|large_intestine(4)|lung(22)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	37		all_cancers(76;0.000243)|Acute lymphoblastic leukemia(125;2.91e-07)|all_hematologic(105;0.000337)|all_epithelial(107;0.0575)		BRCA - Breast invasive adenocarcinoma(397;0.0967)		tggcagcggcggtggcagcag	0.577													G|||	20	0.00399361	0.0151	0.0	5008	,	,		15737	0.0		0.0	False		,,,				2504	0.0				p.T540T		Atlas-SNP	.											.	SNAP91	199	.	0			c.C1620T						PASS	.	G	,,,	20,4206		0,20,2093	15.0	21.0	19.0		1620,1614,,1620	2.3	0.1	6		19	1,8333		0,1,4166	no	coding-synonymous,coding-synonymous,intron,coding-synonymous	SNAP91	NM_001242792.1,NM_001242793.1,NM_001242794.1,NM_014841.2	,,,	0,21,6259	AA,AG,GG		0.012,0.4733,0.1672	,,,	540/908,538/878,,540/908	84303273	21,12539	2113	4167	6280	SO:0001819	synonymous_variant	9892	exon17			AGCGGCGGTGGCA	AB014556	CCDS47455.1, CCDS56437.1, CCDS56438.1	6q15	2012-12-07	2012-12-07		ENSG00000065609	ENSG00000065609			14986	protein-coding gene	gene with protein product		607923	"""synaptosomal-associated protein, 91 kDa (mouse) homolog"", ""synaptosomal-associated protein, 91kDa homolog (mouse)"""			9734811, 12493563, 10436022	Standard	NM_014841		Approved	KIAA0656, AP180, CALM	uc003pka.3	O60641	OTTHUMG00000015114	ENST00000439399.2:c.1620C>T	6.37:g.84303273G>A		96.0	0.0	0		105.0	57.0	0.542857	NM_001242792	A8K0L7|E5RI02|Q5JX13|Q68DL9|Q6P9D3|Q9NTY7	Silent	SNP	ENST00000439399.2	37	CCDS47455.1																																																																																			G|0.995;A|0.005	0.005	strong		0.577	SNAP91-007	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000375296.1		
AFAP1L2	84632	hgsc.bcm.edu	37	10	116056779	116056779	+	Silent	SNP	C	C	T	rs62641713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:116056779C>T	ENST00000304129.4	-	18	2417	c.2388G>A	c.(2386-2388)tcG>tcA	p.S796S	AFAP1L2_ENST00000491814.1_5'UTR|AFAP1L2_ENST00000369271.3_Silent_p.S792S|AFAP1L2_ENST00000545353.1_Silent_p.S849S			Q8N4X5	AF1L2_HUMAN	actin filament associated protein 1-like 2	796					inflammatory response (GO:0006954)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of interleukin-6 production (GO:0032675)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)	protein tyrosine kinase activator activity (GO:0030296)|SH2 domain binding (GO:0042169)|SH3 domain binding (GO:0017124)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|prostate(2)	21		Colorectal(252;0.175)|Breast(234;0.231)		Epithelial(162;0.0219)|all cancers(201;0.0561)		TGACCACGACCGAGAGAGGCC	0.567													C|||	206	0.0411342	0.1467	0.0115	5008	,	,		19382	0.001		0.003	False		,,,				2504	0.0				p.S796S		Atlas-SNP	.											.	AFAP1L2	90	.	0			c.G2388A						PASS	.	C	,	664,3742	280.8+/-275.6	62,540,1601	180.0	157.0	164.0		2388,2376	-10.9	0.1	10	dbSNP_129	164	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous,coding-synonymous	AFAP1L2	NM_001001936.1,NM_032550.2	,	62,547,5894	TT,TC,CC		0.0814,15.0704,5.1592	,	796/819,792/815	116056779	671,12335	2203	4300	6503	SO:0001819	synonymous_variant	84632	exon18			CACGACCGAGAGA	BC024314	CCDS31286.1, CCDS31287.1	10q26.11	2013-01-10	2007-02-07	2007-02-07	ENSG00000169129	ENSG00000169129		"""Pleckstrin homology (PH) domain containing"""	25901	protein-coding gene	gene with protein product		612420	"""KIAA1914"""	KIAA1914		11572484, 17412687	Standard	XM_005270239		Approved	FLJ14564, Em:AC005383.4, XB130	uc001lbn.3	Q8N4X5	OTTHUMG00000019086	ENST00000304129.4:c.2388G>A	10.37:g.116056779C>T		297.0	1.0	0.003367		337.0	337.0	1	NM_001001936	A8K6P7|B3KVQ8|Q2UZW3|Q8TB54|Q96PX4|Q96SY5	Silent	SNP	ENST00000304129.4	37	CCDS31286.1																																																																																			C|0.953;T|0.047	0.047	strong		0.567	AFAP1L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050462.1	NM_032550	
KANK2	25959	hgsc.bcm.edu	37	19	11289073	11289073	+	Missense_Mutation	SNP	C	C	T	rs115473443	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11289073C>T	ENST00000586659.1	-	6	1782	c.1468G>A	c.(1468-1470)Gca>Aca	p.A490T	KANK2_ENST00000355150.5_Missense_Mutation_p.A490T|KANK2_ENST00000589894.1_Missense_Mutation_p.A490T|KANK2_ENST00000432929.2_Missense_Mutation_p.A498T|KANK2_ENST00000589359.1_Missense_Mutation_p.A498T			Q63ZY3	KANK2_HUMAN	KN motif and ankyrin repeat domains 2	490					apoptotic process (GO:0006915)|negative regulation of cell proliferation (GO:0008285)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of programmed cell death (GO:0043069)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				endometrium(2)|large_intestine(1)|lung(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						GTGGGGTCTGCAACCTCCTCT	0.667													c|||	79	0.0157748	0.0575	0.0043	5008	,	,		10474	0.0		0.0	False		,,,				2504	0.0				p.A498T		Atlas-SNP	.											.	KANK2	47	.	0			c.G1492A						PASS	.		THR/ALA,THR/ALA	194,4212	115.9+/-153.8	4,186,2013	24.0	27.0	26.0		1468,1492	-3.0	0.0	19	dbSNP_132	26	4,8596	3.0+/-9.4	0,4,4296	yes	missense,missense	KANK2	NM_001136191.2,NM_015493.6	58,58	4,190,6309	TT,TC,CC		0.0465,4.4031,1.5224	benign,benign	490/852,498/860	11289073	198,12808	2203	4300	6503	SO:0001583	missense	25959	exon4			GGTCTGCAACCTC	AK000011	CCDS12255.1, CCDS54219.1	19p13.2	2013-01-10	2008-01-29	2008-01-29		ENSG00000197256		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	29300	protein-coding gene	gene with protein product		614610	"""matrix-remodelling associated 3"", ""ankyrin repeat domain 25"""	MXRA3, ANKRD25		10819331, 17996375, 19554261	Standard	NM_015493		Approved	KIAA1518	uc002mqm.3	Q63ZY3		ENST00000586659.1:c.1468G>A	19.37:g.11289073C>T	ENSP00000465650:p.Ala490Thr	81.0	0.0	0		102.0	45.0	0.441176	NM_015493	B0I1P4|Q3KQZ3|Q6GUF5|Q9H8S4|Q9NUP0|Q9P210	Missense_Mutation	SNP	ENST00000586659.1	37	CCDS12255.1	30	0.013736263736263736	26	0.052845528455284556	4	0.011049723756906077	0	0.0	0	0.0	C	6.571	0.473652	0.12521	0.044031	4.65E-4	ENSG00000197256	ENST00000432929;ENST00000355150	T;T	0.39406	1.08;1.1	5.45	-3.0	0.05480	.	0.449602	0.22279	N	0.062158	T	0.03348	0.0097	L	0.27053	0.805	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.08186	-1.0734	10	0.23891	T	0.37	-18.7177	6.2347	0.20756	0.1484:0.1981:0.0:0.6536	.	490;498	Q63ZY3;Q63ZY3-2	KANK2_HUMAN;.	T	498;490	ENSP00000395650:A498T;ENSP00000347276:A490T	ENSP00000347276:A490T	A	-	1	0	KANK2	11150073	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.342000	0.02645	-0.503000	0.06586	-0.144000	0.13903	GCA	C|0.985;T|0.015	0.015	strong		0.667	KANK2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453066.2	NM_015493	
ALK	238	hgsc.bcm.edu	37	2	29416750	29416750	+	Silent	SNP	A	A	G	rs55772745	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:29416750A>G	ENST00000389048.3	-	29	5109	c.4203T>C	c.(4201-4203)taT>taC	p.Y1401Y	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1401					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)		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)	CAAGTGGACCATATTCTATCG	0.488			"""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				A|||	114	0.0227636	0.0847	0.0029	5008	,	,		17238	0.0		0.0	False		,,,				2504	0.0				p.Y1401Y		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	.	ALK	533	.	0			c.T4203C						PASS	.			255,4149		7,241,1954	43.0	47.0	45.0		4203	-10.6	0.0	2	dbSNP_129	45	1,8599		0,1,4299	no	coding-synonymous	ALK	NM_004304.4		7,242,6253	GG,GA,AA		0.0116,5.7902,1.9686		1401/1621	29416750	256,12748	2202	4300	6502	SO:0001819	synonymous_variant	238	exon29	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	TGGACCATATTCT	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.4203T>C	2.37:g.29416750A>G		146.0	0.0	0		133.0	78.0	0.586466	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			A|0.979;G|0.021	0.021	strong		0.488	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
PKD1	5310	hgsc.bcm.edu	37	16	2162810	2162810	+	Missense_Mutation	SNP	G	G	A	rs147910505	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2162810G>A	ENST00000262304.4	-	13	3348	c.3140C>T	c.(3139-3141)tCg>tTg	p.S1047L	PKD1_ENST00000423118.1_Missense_Mutation_p.S1047L|RP11-304L19.4_ENST00000568795.1_RNA	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	1047	PKD 5. {ECO:0000255|PROSITE- ProRule:PRU00151}.				anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						CTCCACGGCCGAGTCCACCAG	0.682													g|||	5	0.000998403	0.003	0.0014	5008	,	,		9360	0.0		0.0	False		,,,				2504	0.0				p.S1047L		Atlas-SNP	.											.	PKD1	184	.	0			c.C3140T	GRCh37	CM074435	PKD1	M	rs147910505	PASS	.	G	LEU/SER,LEU/SER	16,4376	22.3+/-47.3	0,16,2180	50.0	53.0	52.0		3140,3140	5.0	1.0	16	dbSNP_134	52	0,8586		0,0,4293	no	missense,missense	PKD1	NM_000296.3,NM_001009944.2	145,145	0,16,6473	AA,AG,GG		0.0,0.3643,0.1233	possibly-damaging,possibly-damaging	1047/4303,1047/4304	2162810	16,12962	2196	4293	6489	SO:0001583	missense	5310	exon13			ACGGCCGAGTCCA	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9008	protein-coding gene	gene with protein product	"""polycystin 1"", ""transient receptor potential cation channel, subfamily P, member 1"""	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.3140C>T	16.37:g.2162810G>A	ENSP00000262304:p.Ser1047Leu	27.0	0.0	0		26.0	11.0	0.423077	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	.	.	.	.	.	.	.	.	.	.	g	15.48	2.845291	0.51164	0.003643	0.0	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101	T;T	0.62105	0.05;0.05	4.99	4.99	0.66335	PKD/Chitinase domain (1);Polycystin cation channel (1);PKD domain (2);	0.207794	0.41500	D	0.000864	T	0.74261	0.3693	M	0.68952	2.095	0.40941	D	0.984461	D;D	0.89917	1.0;0.997	D;D	0.91635	0.999;0.915	T	0.70506	-0.4853	10	0.02654	T	1	.	18.2979	0.90153	0.0:0.0:1.0:0.0	.	1047;1047	P98161-3;P98161	.;PKD1_HUMAN	L	1047;1047;762	ENSP00000262304:S1047L;ENSP00000399501:S1047L	ENSP00000262304:S1047L	S	-	2	0	PKD1	2102811	1.000000	0.71417	0.969000	0.41365	0.444000	0.32077	5.507000	0.66999	2.321000	0.78463	0.645000	0.84053	TCG	G|0.999;A|0.001	0.001	strong		0.682	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
CRELD1	78987	hgsc.bcm.edu	37	3	9984855	9984855	+	Splice_Site	SNP	C	C	T	rs79223485	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:9984855C>T	ENST00000383811.3	+	8	1511	c.912C>T	c.(910-912)ctC>ctT	p.L304L	CRELD1_ENST00000326434.5_Splice_Site_p.L304L|CRELD1_ENST00000397170.3_Splice_Site_p.L304L|CRELD1_ENST00000452070.1_Splice_Site_p.L304L|CRELD1_ENST00000489674.1_3'UTR	NM_015513.4	NP_056328	Q96HD1	CREL1_HUMAN	cysteine-rich with EGF-like domains 1	304					cardiac septum development (GO:0003279)|endocardial cushion development (GO:0003197)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|stomach(1)|urinary_tract(1)	14						CCAAGTGTCTCGGTGAGTCTC	0.612													C|||	106	0.0211661	0.0772	0.0058	5008	,	,		19596	0.0		0.0	False		,,,				2504	0.0				p.L304L		Atlas-SNP	.											.	CRELD1	48	.	0			c.C912T						PASS	.	C	,,	289,4117	156.6+/-189.7	12,265,1926	45.0	47.0	46.0		912,912,912	-1.4	1.0	3	dbSNP_132	46	3,8597	3.0+/-9.4	0,3,4297	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	CRELD1	NM_001031717.3,NM_001077415.2,NM_015513.4	,,	12,268,6223	TT,TC,CC		0.0349,6.5592,2.2451	,,	304/423,304/421,304/421	9984855	292,12714	2203	4300	6503	SO:0001630	splice_region_variant	78987	exon9			GTGTCTCGGTGAG	AF452623	CCDS2593.1, CCDS33693.1	3p25.3	2005-12-08	2004-02-13		ENSG00000163703	ENSG00000163703			14630	protein-coding gene	gene with protein product		607170	"""atrioventricular septal defect 2"""	AVSD2		10922384, 12137942	Standard	NM_015513		Approved		uc003buf.3	Q96HD1	OTTHUMG00000128653	ENST00000383811.3:c.913+1C>T	3.37:g.9984855C>T		107.0	0.0	0		102.0	43.0	0.421569	NM_001077415	A8MX90|B2RAA9|Q6I9X5|Q8NFT4|Q9Y409	Silent	SNP	ENST00000383811.3	37	CCDS2593.1																																																																																			C|0.975;T|0.025	0.025	strong		0.612	CRELD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250533.1	NM_015513	Silent
ANKRD36B	57730	hgsc.bcm.edu	37	2	98197010	98197010	+	RNA	SNP	G	G	A	rs2922614	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:98197010G>A	ENST00000443455.1	-	0	650							Q8N2N9	AN36B_HUMAN	ankyrin repeat domain 36B																		CTCACAGCAAGTAACAGTGGC	0.303													.|||	57	0.0113818	0.0401	0.0043	5008	,	,		20283	0.001		0.0	False		,,,				2504	0.0				p.L158F		Atlas-SNP	.											.	.	.	.	0			c.C472T						PASS	.	G	PHE/LEU	51,1333		1,49,642	161.0	125.0	136.0		472	-0.4	0.0	2	dbSNP_101	136	0,3182		0,0,1591	no	missense	ANKRD36B	NM_025190.3	22	1,49,2233	AA,AG,GG		0.0,3.685,1.117	benign	158/1354	98197010	51,4515	692	1591	2283			57730	exon4			CAGCAAGTAACAG	AK024934	CCDS74543.1	2q11.2	2013-01-11	2008-03-25	2008-03-25	ENSG00000196912	ENSG00000196912		"""Ankyrin repeat domain containing"""	29333	protein-coding gene	gene with protein product	"""melanoma-associated antigen"", ""CLL-associated antigen KW-1"""		"""KIAA1641"""	KIAA1641		10997877	Standard	NM_025190		Approved	FLJ21281	uc010yvc.1	Q8N2N9	OTTHUMG00000130547		2.37:g.98197010G>A		533.0	0.0	0		517.0	223.0	0.431335	NM_025190	Q08AK5|Q6IPR0|Q6PI49|Q8IZM7|Q8TDH6|Q96N30|Q9H759	Missense_Mutation	SNP	ENST00000443455.1	37																																																																																				G|0.984;A|0.016	0.016	strong		0.303	ANKRD36B-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000328967.2	NM_025190	
EPM2AIP1	9852	hgsc.bcm.edu	37	3	37033348	37033348	+	Silent	SNP	A	A	G	rs200289425	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:37033348A>G	ENST00000322716.5	-	1	1447	c.1221T>C	c.(1219-1221)gcT>gcC	p.A407A	MLH1_ENST00000458205.2_5'Flank|MLH1_ENST00000539477.1_5'Flank|MLH1_ENST00000435176.1_5'Flank|MLH1_ENST00000455445.2_5'Flank|MLH1_ENST00000231790.2_5'Flank|MLH1_ENST00000536378.1_5'Flank	NM_014805.3	NP_055620.1	Q7L775	EPMIP_HUMAN	EPM2A (laforin) interacting protein 1	407					positive regulation of glycogen (starch) synthase activity (GO:2000467)|positive regulation of glycogen biosynthetic process (GO:0045725)|response to insulin (GO:0032868)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(1)|large_intestine(7)|liver(1)|lung(12)|ovary(2)	27						GGTCAAAGGCAGCAGCAGCAA	0.383													A|||	4	0.000798722	0.003	0.0	5008	,	,		19336	0.0		0.0	False		,,,				2504	0.0				p.A407A		Atlas-SNP	.											.	EPM2AIP1	47	.	0			c.T1221C						PASS	.	A		4,3784		0,4,1890	93.0	95.0	95.0		1221	-2.3	1.0	3		95	0,8210		0,0,4105	no	coding-synonymous	EPM2AIP1	NM_014805.3		0,4,5995	GG,GA,AA		0.0,0.1056,0.0333		407/608	37033348	4,11994	1894	4105	5999	SO:0001819	synonymous_variant	9852	exon1			AAAGGCAGCAGCA	AB018309	CCDS46790.1	3p22.1	2003-03-26							19735	protein-coding gene	gene with protein product		607911					Standard	NM_014805		Approved	KIAA0766, FLJ11207	uc003cgk.3	Q7L775		ENST00000322716.5:c.1221T>C	3.37:g.37033348A>G		144.0	0.0	0		135.0	65.0	0.481481	NM_014805	O94866|Q9H3L3	Silent	SNP	ENST00000322716.5	37	CCDS46790.1																																																																																			A|0.999;G|0.001	0.001	strong		0.383	EPM2AIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470593.1	NM_014805	
NET1	10276	hgsc.bcm.edu	37	10	5498102	5498102	+	Missense_Mutation	SNP	C	C	T	rs34658946	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:5498102C>T	ENST00000355029.4	+	11	1392	c.1250C>T	c.(1249-1251)aCa>aTa	p.T417I	NET1_ENST00000380359.3_Missense_Mutation_p.T363I|NET1_ENST00000484741.1_3'UTR|NET1_ENST00000542715.1_Missense_Mutation_p.T236I	NM_001047160.2	NP_001040625.1	Q7Z628	ARHG8_HUMAN	neuroepithelial cell transforming 1	417	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.		T -> I (in dbSNP:rs34658946).		apoptotic signaling pathway (GO:0097190)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to ionizing radiation (GO:0071479)|myoblast migration (GO:0051451)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(4)|kidney(2)|large_intestine(9)|lung(5)|prostate(2)|skin(1)	23						CGGCCCGTCACACGGAACGAA	0.473													C|||	76	0.0151757	0.056	0.0029	5008	,	,		18225	0.0		0.0	False		,,,				2504	0.0				p.T417I		Atlas-SNP	.											.	NET1	82	.	0			c.C1250T						PASS	.	C	ILE/THR,ILE/THR	177,4229	115.4+/-153.4	4,169,2030	88.0	90.0	89.0		1250,1088	4.7	1.0	10	dbSNP_126	89	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	NET1	NM_001047160.1,NM_005863.3	89,89	4,170,6329	TT,TC,CC		0.0116,4.0172,1.3686	benign,benign	417/597,363/543	5498102	178,12828	2203	4300	6503	SO:0001583	missense	10276	exon11			CCGTCACACGGAA	AJ010046	CCDS7067.1, CCDS41483.1	10p15	2013-01-10	2008-09-12		ENSG00000173848	ENSG00000173848		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	14592	protein-coding gene	gene with protein product		606450				8649828	Standard	NR_073040		Approved	ARHGEF8, NET1A	uc001iia.4	Q7Z628	OTTHUMG00000017596	ENST00000355029.4:c.1250C>T	10.37:g.5498102C>T	ENSP00000347134:p.Thr417Ile	65.0	0.0	0		55.0	20.0	0.363636	NM_001047160	Q12773|Q96D82|Q99903|Q9UEN6	Missense_Mutation	SNP	ENST00000355029.4	37	CCDS41483.1	27	0.012362637362637362	25	0.0508130081300813	2	0.0055248618784530384	0	0.0	0	0.0	C	15.93	2.978394	0.53720	0.040172	1.16E-4	ENSG00000173848	ENST00000355029;ENST00000542715;ENST00000380359	T;T;T	0.31510	1.49;1.49;1.49	5.78	4.69	0.59074	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.43110	D	0.000603	T	0.06050	0.0157	L	0.49350	1.555	0.58432	D	0.999994	B;B	0.23490	0.048;0.086	B;B	0.34138	0.153;0.176	T	0.02491	-1.1151	10	0.48119	T	0.1	-20.9971	10.7957	0.46459	0.0:0.8395:0.0:0.1605	rs34658946	363;417	Q5SQI7;Q7Z628	.;ARHG8_HUMAN	I	417;236;363	ENSP00000347134:T417I;ENSP00000446452:T236I;ENSP00000369717:T363I	ENSP00000347134:T417I	T	+	2	0	NET1	5488102	0.967000	0.33354	0.997000	0.53966	0.951000	0.60555	2.640000	0.46579	2.735000	0.93741	0.557000	0.71058	ACA	C|0.984;T|0.016	0.016	strong		0.473	NET1-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046553.3	NM_005863	
SYNPO2	171024	hgsc.bcm.edu	37	4	119952589	119952589	+	Missense_Mutation	SNP	G	G	A	rs115012720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:119952589G>A	ENST00000429713.2	+	4	2841	c.2659G>A	c.(2659-2661)Gtg>Atg	p.V887M	SYNPO2_ENST00000307142.4_Missense_Mutation_p.V887M|SYNPO2_ENST00000434046.2_Missense_Mutation_p.V887M|SYNPO2_ENST00000448416.2_Intron	NM_001128933.1	NP_001122405.1	Q9UMS6	SYNP2_HUMAN	synaptopodin 2	887						actin cytoskeleton (GO:0015629)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|Z disc (GO:0030018)	14-3-3 protein binding (GO:0071889)|muscle alpha-actinin binding (GO:0051371)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(20)|lung(18)|ovary(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						GGAGAAGTATGTGGTCGATTC	0.562													G|||	28	0.00559105	0.0212	0.0	5008	,	,		20471	0.0		0.0	False		,,,				2504	0.0				p.V887M		Atlas-SNP	.											.	SYNPO2	353	.	0			c.G2659A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL	100,4306	80.4+/-118.8	1,98,2104	126.0	118.0	121.0		2659,2659,2659	5.8	1.0	4	dbSNP_132	121	3,8597	1.2+/-3.3	0,3,4297	yes	missense,missense,missense	SYNPO2	NM_001128933.1,NM_001128934.1,NM_133477.2	21,21,21	1,101,6401	AA,AG,GG		0.0349,2.2696,0.7919	probably-damaging,probably-damaging,probably-damaging	887/1094,887/1110,887/1262	119952589	103,12903	2203	4300	6503	SO:0001583	missense	171024	exon4			AAGTATGTGGTCG	AJ010482	CCDS34054.1, CCDS47128.1, CCDS47129.1, CCDS75185.1, CCDS75186.1	4q26	2008-08-29			ENSG00000172403	ENSG00000172403			17732	protein-coding gene	gene with protein product						11673475, 17828378	Standard	NM_133477		Approved	MYOPODIN	uc010inb.3	Q9UMS6	OTTHUMG00000161165	ENST00000429713.2:c.2659G>A	4.37:g.119952589G>A	ENSP00000395143:p.Val887Met	53.0	0.0	0		83.0	42.0	0.506024	NM_001128934	B2RWP6|B2Y8J9|Q9UK89|S5XAM4	Missense_Mutation	SNP	ENST00000429713.2	37	CCDS47129.1	8|8	0.003663003663003663|0.003663003663003663	8|8	0.016260162601626018|0.016260162601626018	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	18.38|18.38	3.611213|3.611213	0.66558|0.66558	0.022696|0.022696	3.49E-4|3.49E-4	ENSG00000172403|ENSG00000172403	ENST00000504178|ENST00000307142;ENST00000429713;ENST00000434046	.|T;T;T	.|0.25085	.|1.82;1.87;1.88	5.76|5.76	5.76|5.76	0.90799|0.90799	.|.	.|0.000000	.|0.56097	.|D	.|0.000026	T|T	0.39200|0.39200	0.1069|0.1069	M|M	0.79258|0.79258	2.445|2.445	0.80722|0.80722	D|D	1|1	.|D;D;D;D	.|0.89917	.|1.0;1.0;1.0;0.999	.|D;D;D;D	.|0.87578	.|0.998;0.994;0.986;0.99	T|T	0.43972|0.43972	-0.9358|-0.9358	5|9	.|.	.|.	.|.	-20.0199|-20.0199	19.9596|19.9596	0.97236|0.97236	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|887;887;887;887	.|B9EG60;Q9UMS6-2;E9PEM2;Q9UMS6	.|.;.;.;SYNP2_HUMAN	Y|M	838|887	.|ENSP00000306015:V887M;ENSP00000395143:V887M;ENSP00000390965:V887M	.|.	C|V	+|+	2|1	0|0	SYNPO2|SYNPO2	120172037|120172037	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.948000|0.948000	0.59901|0.59901	5.790000|5.790000	0.69038|0.69038	2.726000|2.726000	0.93360|0.93360	0.655000|0.655000	0.94253|0.94253	TGT|GTG	G|0.993;A|0.007	0.007	strong		0.562	SYNPO2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364020.1		
LUZP1	7798	hgsc.bcm.edu	37	1	23419914	23419914	+	Missense_Mutation	SNP	G	G	A	rs142425004	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:23419914G>A	ENST00000302291.4	-	4	1642	c.841C>T	c.(841-843)Cgc>Tgc	p.R281C	LUZP1_ENST00000314174.5_Missense_Mutation_p.R281C|LUZP1_ENST00000418342.1_Missense_Mutation_p.R281C|LUZP1_ENST00000374623.3_Missense_Mutation_p.R281C			Q86V48	LUZP1_HUMAN	leucine zipper protein 1	281					artery development (GO:0060840)|neural fold bending (GO:0021503)|ventricular septum development (GO:0003281)	membrane (GO:0016020)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(12)|upper_aerodigestive_tract(2)	31		Colorectal(325;3.46e-05)|Lung NSC(340;4.15e-05)|all_lung(284;6.64e-05)|Renal(390;0.000219)|Ovarian(437;0.00373)|Breast(348;0.00815)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;4.88e-27)|Colorectal(126;8.36e-08)|COAD - Colon adenocarcinoma(152;4.31e-06)|GBM - Glioblastoma multiforme(114;8.64e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00176)|STAD - Stomach adenocarcinoma(196;0.0146)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0967)|LUSC - Lung squamous cell carcinoma(448;0.199)		TCCTGATTGCGGTTCTTTTCA	0.388													G|||	20	0.00399361	0.0106	0.0014	5008	,	,		20491	0.005		0.0	False		,,,				2504	0.0				p.R281C		Atlas-SNP	.											LUZP1,NS,carcinoma,+1,1	LUZP1	83	1	0			c.C841T						PASS	.	G	CYS/ARG,CYS/ARG	28,4378	35.2+/-66.4	0,28,2175	217.0	203.0	208.0		841,841	4.1	1.0	1	dbSNP_134	208	0,8600		0,0,4300	yes	missense,missense	LUZP1	NM_001142546.1,NM_033631.3	180,180	0,28,6475	AA,AG,GG		0.0,0.6355,0.2153	probably-damaging,probably-damaging	281/1077,281/1077	23419914	28,12978	2203	4300	6503	SO:0001583	missense	7798	exon4			GATTGCGGTTCTT	BC051733	CCDS30628.1	1p36	2008-02-05			ENSG00000169641	ENSG00000169641			14985	protein-coding gene	gene with protein product		601422				8812416	Standard	NM_033631		Approved	LUZP	uc010odv.1	Q86V48	OTTHUMG00000003227	ENST00000302291.4:c.841C>T	1.37:g.23419914G>A	ENSP00000303758:p.Arg281Cys	341.0	0.0	0		313.0	147.0	0.469649	NM_033631	Q5TH93|Q8N4X3|Q8TEH1	Missense_Mutation	SNP	ENST00000302291.4	37	CCDS30628.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	G	16.53	3.149333	0.57151	0.006355	0.0	ENSG00000169641	ENST00000418342;ENST00000374623;ENST00000302291;ENST00000314174	T;T;T;T	0.15372	2.64;2.64;2.64;2.43	6.08	4.13	0.48395	.	0.000000	0.39909	N	0.001226	T	0.08980	0.0222	L	0.42245	1.32	0.42205	D	0.991782	P;P	0.41929	0.765;0.765	B;B	0.28139	0.086;0.086	T	0.08046	-1.0741	10	0.44086	T	0.13	.	13.9909	0.64367	0.0:0.0:0.5289:0.4711	.	281;281	Q86V48-2;Q86V48	.;LUZP1_HUMAN	C	281	ENSP00000393460:R281C;ENSP00000363752:R281C;ENSP00000303758:R281C;ENSP00000313705:R281C	ENSP00000303758:R281C	R	-	1	0	LUZP1	23292501	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	1.802000	0.38853	1.554000	0.49487	0.655000	0.94253	CGC	G|0.999;A|0.001	0.001	strong		0.388	LUZP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008900.3	NM_033631	
C16orf89	146556	hgsc.bcm.edu	37	16	5115811	5115811	+	Silent	SNP	G	G	A	rs35751409	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:5115811G>A	ENST00000315997.5	-	1	300	c.99C>T	c.(97-99)gcC>gcT	p.A33A	C16orf89_ENST00000422873.1_Silent_p.A71A|C16orf89_ENST00000350219.4_Silent_p.A71A|C16orf89_ENST00000474471.3_Silent_p.A33A|ALG1_ENST00000588623.1_Intron|C16orf89_ENST00000472572.3_Silent_p.A33A	NM_152459.4	NP_689672.4	Q6UX73	CP089_HUMAN	chromosome 16 open reading frame 89	33						cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	12						CTGCAATGGTGGCTTTACTTT	0.602													G|||	35	0.00698882	0.0265	0.0	5008	,	,		19948	0.0		0.0	False		,,,				2504	0.0				p.A33A		Atlas-SNP	.											.	C16orf89	64	.	0			c.C99T						PASS	.	G	,	111,4137		1,109,2014	61.0	66.0	64.0		99,99	-0.5	0.5	16	dbSNP_126	64	0,8502		0,0,4251	no	coding-synonymous,coding-synonymous	C16orf89	NM_001098514.2,NM_152459.4	,	1,109,6265	AA,AG,GG		0.0,2.613,0.8706	,	33/362,33/403	5115811	111,12639	2124	4251	6375	SO:0001819	synonymous_variant	146556	exon1			AATGGTGGCTTTA		CCDS42116.1, CCDS45404.1, CCDS42116.2, CCDS45404.2	16p13.3	2011-12-12			ENSG00000153446	ENSG00000153446			28687	protein-coding gene	gene with protein product						12975309, 20578903	Standard	NM_001098514		Approved	MGC45438	uc010bud.3	Q6UX73	OTTHUMG00000159314	ENST00000315997.5:c.99C>T	16.37:g.5115811G>A		127.0	0.0	0		143.0	61.0	0.426573	NM_001098514	B4DUM5|Q8N2I3|Q8N4T1	Silent	SNP	ENST00000315997.5	37	CCDS42116.2																																																																																			G|0.990;A|0.010	0.010	strong		0.602	C16orf89-001	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354524.1	NM_152459	
CDK2AP1	8099	hgsc.bcm.edu	37	12	123749834	123749834	+	Silent	SNP	G	G	A	rs76783415	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:123749834G>A	ENST00000261692.2	-	3	710	c.189C>T	c.(187-189)taC>taT	p.Y63Y	CDK2AP1_ENST00000535979.1_Silent_p.Y35Y|CDK2AP1_ENST00000544658.1_Silent_p.Y35Y|CDK2AP1_ENST00000538446.1_Silent_p.Y35Y|CDK2AP1_ENST00000542174.1_Silent_p.Y35Y|RP11-282O18.7_ENST00000602352.1_RNA	NM_001270433.1|NM_001270434.1|NM_004642.3	NP_001257362.1|NP_001257363.1|NP_004633.1	O14519	CDKA1_HUMAN	cyclin-dependent kinase 2 associated protein 1	63					cell cycle (GO:0007049)|DNA-dependent DNA replication (GO:0006261)|positive regulation of protein phosphorylation (GO:0001934)	nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	DNA polymerase binding (GO:0070182)			lung(2)|stomach(1)	3	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000554)|Epithelial(86;0.00178)		GCAGCTCCGCGTATTTGCTTT	0.582													G|||	152	0.0303514	0.1112	0.0072	5008	,	,		18220	0.0		0.0	False		,,,				2504	0.0				p.Y63Y		Atlas-SNP	.											.	CDK2AP1	8	.	0			c.C189T						PASS	.	G		443,3963	214.1+/-233.5	22,399,1782	137.0	129.0	132.0		189	-7.6	0.1	12	dbSNP_132	132	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	CDK2AP1	NM_004642.2		22,405,6076	AA,AG,GG		0.0698,10.0545,3.4523		63/116	123749834	449,12557	2203	4300	6503	SO:0001819	synonymous_variant	8099	exon3			CTCCGCGTATTTG	AB006077	CCDS9245.1, CCDS58289.1	12q24	2008-11-04	2008-11-04		ENSG00000111328	ENSG00000111328			14002	protein-coding gene	gene with protein product		602198	"""CDK2-associated protein 1"""			9331572, 9506968	Standard	NM_004642		Approved	DORC1, doc-1, DOC1, ST19, p12DOC-1	uc001ueq.4	O14519	OTTHUMG00000168854	ENST00000261692.2:c.189C>T	12.37:g.123749834G>A		147.0	0.0	0		148.0	77.0	0.52027	NM_004642	F5GYA4	Silent	SNP	ENST00000261692.2	37	CCDS9245.1																																																																																			G|0.970;A|0.030	0.030	strong		0.582	CDK2AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401387.1	NM_004642	
BSPRY	54836	hgsc.bcm.edu	37	9	116131916	116131916	+	Missense_Mutation	SNP	G	G	A	rs377189582		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:116131916G>A	ENST00000374183.4	+	6	742	c.703G>A	c.(703-705)Gat>Aat	p.D235N	BSPRY_ENST00000462085.1_3'UTR	NM_017688.2	NP_060158.2	Q5W0U4	BSPRY_HUMAN	B-box and SPRY domain containing	235	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				calcium ion transport (GO:0006816)	cell leading edge (GO:0031252)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|lung(4)|urinary_tract(1)	8						CATACGGATCGATGAGAGGAC	0.562																																					p.D235N		Atlas-SNP	.											.	BSPRY	21	.	0			c.G703A						PASS	.						85.0	85.0	85.0					9																	116131916		2012	4204	6216	SO:0001583	missense	54836	exon6			CGGATCGATGAGA	AJ276691	CCDS43868.1	9q33.1	2008-02-05			ENSG00000119411	ENSG00000119411			18232	protein-coding gene	gene with protein product						10978534, 11099500	Standard	NM_017688		Approved	FLJ20150	uc004bhg.4	Q5W0U4	OTTHUMG00000021006	ENST00000374183.4:c.703G>A	9.37:g.116131916G>A	ENSP00000363298:p.Asp235Asn	59.0	0.0	0		67.0	50.0	0.746269	NM_017688	B3KS19|Q96DJ2|Q9H4E4|Q9NXN0	Missense_Mutation	SNP	ENST00000374183.4	37	CCDS43868.1	.	.	.	.	.	.	.	.	.	.	G	19.66	3.868407	0.72065	.	.	ENSG00000119411	ENST00000374183	T	0.61274	0.12	5.6	4.7	0.59300	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	0.047007	0.85682	D	0.000000	T	0.67951	0.2948	M	0.92317	3.295	0.58432	D	0.999992	P	0.44195	0.828	B	0.41174	0.349	T	0.76429	-0.2962	10	0.59425	D	0.04	-17.9828	13.9619	0.64185	0.0733:0.0:0.9267:0.0	.	235	Q5W0U4	BSPRY_HUMAN	N	235	ENSP00000363298:D235N	ENSP00000363298:D235N	D	+	1	0	BSPRY	115171737	1.000000	0.71417	0.645000	0.29479	0.973000	0.67179	4.224000	0.58593	1.355000	0.45865	0.561000	0.74099	GAT	.	.	alt		0.562	BSPRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055399.1	NM_017688	
UMODL1	89766	hgsc.bcm.edu	37	21	43524188	43524188	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:43524188C>T	ENST00000408910.2	+	9	1510	c.1510C>T	c.(1510-1512)Cgc>Tgc	p.R504C	C21orf128_ENST00000329015.2_Intron|UMODL1_ENST00000400427.1_Missense_Mutation_p.R432C|UMODL1_ENST00000400424.2_Missense_Mutation_p.R432C|UMODL1_ENST00000408989.2_Missense_Mutation_p.R504C	NM_001004416.2	NP_001004416	Q5DID0	UROL1_HUMAN	uromodulin-like 1	504	SEA 1. {ECO:0000255|PROSITE- ProRule:PRU00188}.				adipose tissue development (GO:0060612)|cellular response to gonadotropin-releasing hormone (GO:0097211)|multicellular organismal reproductive process (GO:0048609)|regulation of apoptotic process (GO:0042981)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|peptidase inhibitor activity (GO:0030414)			breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(5)|lung(22)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	47						GCAGGGGACACGCGTGCAAGG	0.587																																					p.R504C	Pancreas(122;680 807 13940 14411 22888 25505 31742 36028 36332 38435)	Atlas-SNP	.											.	UMODL1	186	.	0			c.C1510T						PASS	.						48.0	50.0	49.0					21																	43524188		2203	4300	6503	SO:0001583	missense	89766	exon9			GGGACACGCGTGC		CCDS42935.1, CCDS42936.1, CCDS56214.1, CCDS56215.1	21q22.3	2008-07-04			ENSG00000177398	ENSG00000177398			12560	protein-coding gene	gene with protein product	"""olfactorin"""	613859				16026467	Standard	NM_173568		Approved		uc002zag.1	Q5DID0	OTTHUMG00000086788	ENST00000408910.2:c.1510C>T	21.37:g.43524188C>T	ENSP00000386147:p.Arg504Cys	49.0	0.0	0		47.0	7.0	0.148936	NM_173568	C9JCE6|Q5DIC9|Q6LA40|Q6LA41|Q8N216	Missense_Mutation	SNP	ENST00000408910.2	37	CCDS42936.1	.	.	.	.	.	.	.	.	.	.	C	8.034	0.762462	0.15914	.	.	ENSG00000177398	ENST00000400427;ENST00000400424;ENST00000408989;ENST00000408910	D;T;D;T	0.82167	-1.58;-0.65;-1.58;-0.67	3.67	0.744	0.18353	.	4.413020	0.00541	N	0.000220	D	0.85331	0.5672	L	0.47716	1.5	0.09310	N	0.999994	D;D;P	0.67145	0.98;0.996;0.939	P;P;P	0.59703	0.711;0.862;0.513	T	0.67321	-0.5700	10	0.37606	T	0.19	0.2373	4.6354	0.12521	0.0:0.4456:0.3484:0.206	.	432;504;504	Q5DID0-3;Q5DID0-2;Q5DID0	.;.;UROL1_HUMAN	C	432;432;504;504	ENSP00000383279:R432C;ENSP00000383276:R432C;ENSP00000386126:R504C;ENSP00000386147:R504C	ENSP00000383276:R432C	R	+	1	0	UMODL1	42397257	0.000000	0.05858	0.000000	0.03702	0.036000	0.12997	-0.543000	0.06084	0.140000	0.18849	0.655000	0.94253	CGC	.	.	none		0.587	UMODL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195292.2		
SYNE3	161176	hgsc.bcm.edu	37	14	95921722	95921722	+	Missense_Mutation	SNP	G	G	A	rs74079986	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:95921722G>A	ENST00000334258.5	-	5	1143	c.1129C>T	c.(1129-1131)Cgc>Tgc	p.R377C	SYNE3_ENST00000557275.1_Missense_Mutation_p.R377C|SYNE3_ENST00000553340.1_Missense_Mutation_p.R377C|SYNE3_ENST00000554873.1_Missense_Mutation_p.R134C	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	377					cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)			breast(1)|endometrium(2)|lung(25)	28						ACCGAGTAGCGTCTCCAGTGT	0.647													G|||	60	0.0119808	0.0439	0.0029	5008	,	,		17289	0.0		0.0	False		,,,				2504	0.0				p.R377C		Atlas-SNP	.											.	SYNE3	130	.	0			c.C1129T						PASS	.	G	CYS/ARG	174,4232	108.6+/-147.0	5,164,2034	29.0	32.0	31.0		1129	3.0	0.5	14	dbSNP_130	31	1,8597	1.2+/-3.3	0,1,4298	yes	missense	C14orf49	NM_152592.3	180	5,165,6332	AA,AG,GG		0.0116,3.9492,1.3457	possibly-damaging	377/976	95921722	175,12829	2203	4299	6502	SO:0001583	missense	161176	exon5			AGTAGCGTCTCCA	AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"""chromosome 14 open reading frame 49"""	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.1129C>T	14.37:g.95921722G>A	ENSP00000334308:p.Arg377Cys	79.0	0.0	0		75.0	45.0	0.6	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	37	CCDS9935.1	24	0.01098901098901099	22	0.044715447154471545	2	0.0055248618784530384	0	0.0	0	0.0	G	13.55	2.271639	0.40194	0.039492	1.16E-4	ENSG00000176438	ENST00000334258;ENST00000554873;ENST00000557275;ENST00000553340	T;T;T;T	0.37058	3.5;1.22;3.49;2.9	4.99	2.96	0.34315	.	1.317840	0.05603	N	0.576684	T	0.09730	0.0239	N	0.22421	0.69	0.25690	N	0.985697	D;D;D	0.64830	0.994;0.994;0.989	P;P;B	0.50617	0.646;0.646;0.443	T	0.12502	-1.0545	10	0.66056	D	0.02	-0.0728	5.3201	0.15876	0.1091:0.0:0.5537:0.3371	.	377;377;377	Q6ZMZ3-2;Q6ZMZ3-3;Q6ZMZ3	.;.;SYNE3_HUMAN	C	377;134;377;377	ENSP00000334308:R377C;ENSP00000452154:R134C;ENSP00000450562:R377C;ENSP00000450774:R377C	ENSP00000334308:R377C	R	-	1	0	C14orf49	94991475	0.999000	0.42202	0.468000	0.27192	0.258000	0.26162	3.690000	0.54713	1.110000	0.41699	0.455000	0.32223	CGC	G|0.988;A|0.012	0.012	strong		0.647	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592	
DSC1	1823	hgsc.bcm.edu	37	18	28712639	28712639	+	Silent	SNP	T	T	C	rs16961338	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:28712639T>C	ENST00000257198.5	-	14	2391	c.2130A>G	c.(2128-2130)acA>acG	p.T710T	RP11-408H20.2_ENST00000581836.1_RNA|RP11-408H20.3_ENST00000582307.1_RNA|DSC1_ENST00000257197.3_Silent_p.T710T	NM_024421.2	NP_077739.1	Q08554	DSC1_HUMAN	desmocollin 1	710					homophilic cell adhesion (GO:0007156)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	53			OV - Ovarian serous cystadenocarcinoma(10;0.00778)			CACAGAAACATGTAAACAGAA	0.318													T|||	149	0.0297524	0.1097	0.0058	5008	,	,		17598	0.0		0.0	False		,,,				2504	0.0				p.T710T		Atlas-SNP	.											.	DSC1	240	.	0			c.A2130G						PASS	.	T	,	391,4013	195.7+/-220.2	15,361,1826	76.0	72.0	73.0		2130,2130	-3.4	1.0	18	dbSNP_123	73	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous,coding-synonymous	DSC1	NM_004948.3,NM_024421.2	,	15,363,6124	CC,CT,TT		0.0233,8.8783,3.0221	,	710/841,710/895	28712639	393,12611	2202	4300	6502	SO:0001819	synonymous_variant	1823	exon14			GAAACATGTAAAC	AF293358	CCDS11894.1, CCDS11895.1	18q12.1	2010-01-26			ENSG00000134765	ENSG00000134765		"""Cadherins / Major cadherins"""	3035	protein-coding gene	gene with protein product		125643				8486729	Standard	NM_024421		Approved	CDHF1	uc002kwn.3	Q08554	OTTHUMG00000131982	ENST00000257198.5:c.2130A>G	18.37:g.28712639T>C		144.0	0.0	0		104.0	50.0	0.480769	NM_004948	Q9HB01	Silent	SNP	ENST00000257198.5	37	CCDS11894.1																																																																																			T|0.959;C|0.041	0.041	strong		0.318	DSC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254946.1	NM_004948, NM_024421	
CEP89	84902	hgsc.bcm.edu	37	19	33457328	33457328	+	Silent	SNP	C	C	T	rs150504912	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:33457328C>T	ENST00000305768.5	-	2	172	c.84G>A	c.(82-84)ccG>ccA	p.P28P	CEP89_ENST00000591863.1_5'Flank|CEP89_ENST00000590597.2_Silent_p.P28P	NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	28					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						CAGCTGCCTTCGGAGCAACGC	0.557													c|||	2	0.000399361	0.0008	0.0	5008	,	,		20181	0.001		0.0	False		,,,				2504	0.0				p.P28P		Atlas-SNP	.											CEP89,caecum,carcinoma,0,1	CEP89	82	1	0			c.G84A						scavenged	.	C		3,4403	6.2+/-15.9	0,3,2200	98.0	78.0	85.0		84	-7.9	1.0	19	dbSNP_134	85	0,8600		0,0,4300	no	coding-synonymous	CEP89	NM_032816.3		0,3,6500	TT,TC,CC		0.0,0.0681,0.0231		28/784	33457328	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	84902	exon2			TGCCTTCGGAGCA	AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"""coiled-coil domain containing 123"""	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.84G>A	19.37:g.33457328C>T		75.0	1.0	0.0133333		94.0	50.0	0.531915	NM_032816	B9EGA6|Q8N5J8	Silent	SNP	ENST00000305768.5	37	CCDS32987.1																																																																																			C|1.000;T|0.000	0.000	weak		0.557	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816	
KCNQ2	3785	hgsc.bcm.edu	37	20	62078184	62078184	+	Silent	SNP	G	G	C	rs145415996	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:62078184G>C	ENST00000359125.2	-	2	477	c.303C>G	c.(301-303)ctC>ctG	p.L101L	KCNQ2_ENST00000344425.5_Silent_p.L101L|KCNQ2_ENST00000354587.3_Silent_p.L101L|KCNQ2_ENST00000344462.4_Silent_p.L101L|KCNQ2_ENST00000370224.1_Silent_p.L101L|KCNQ2_ENST00000359689.1_Silent_p.L101L|KCNQ2_ENST00000360480.3_Silent_p.L101L|KCNQ2_ENST00000357249.2_Silent_p.L101L|RP11-358D14.2_ENST00000436263.1_RNA	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2	101					axon guidance (GO:0007411)|nervous system development (GO:0007399)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|liver(1)|lung(30)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	AGAAAACCAGGAGGAACCTGG	0.632													G|||	7	0.00139776	0.0053	0.0	5008	,	,		11541	0.0		0.0	False		,,,				2504	0.0				p.L101L		Atlas-SNP	.											.	KCNQ2	201	.	0			c.C303G						PASS	.	G	,,,,	22,4384	29.0+/-57.7	0,22,2181	80.0	75.0	77.0		303,303,303,303,303	0.6	1.0	20	dbSNP_134	77	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KCNQ2	NM_004518.4,NM_172106.1,NM_172107.2,NM_172108.3,NM_172109.1	,,,,	0,24,6479	CC,CG,GG		0.0233,0.4993,0.1845	,,,,	101/845,101/855,101/873,101/842,101/394	62078184	24,12982	2203	4300	6503	SO:0001819	synonymous_variant	3785	exon2			AACCAGGAGGAAC	AF033348	CCDS13518.1, CCDS13519.1, CCDS13520.1, CCDS13521.1, CCDS46629.1	20q13.33	2012-07-05			ENSG00000075043	ENSG00000075043		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6296	protein-coding gene	gene with protein product		602235		EBN, EBN1		9425895, 16382104	Standard	NM_172107		Approved	Kv7.2, ENB1, BFNC, KCNA11, HNSPC	uc002yex.3	O43526	OTTHUMG00000033049	ENST00000359125.2:c.303C>G	20.37:g.62078184G>C		114.0	0.0	0		91.0	39.0	0.428571	NM_172106	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Silent	SNP	ENST00000359125.2	37	CCDS13520.1																																																																																			G|0.998;C|0.002	0.002	strong		0.632	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109	
CHIA	27159	hgsc.bcm.edu	37	1	111854859	111854859	+	Missense_Mutation	SNP	C	C	T	rs61752461	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:111854859C>T	ENST00000369740.1	+	4	206	c.103C>T	c.(103-105)Cgg>Tgg	p.R35W	CHIA_ENST00000430615.1_Intron|CHIA_ENST00000483391.1_Intron|CHIA_ENST00000451398.2_Intron|CHIA_ENST00000343320.6_Missense_Mutation_p.R35W|CHIA_ENST00000353665.6_Intron	NM_001258001.1|NM_201653.3	NP_001244930.1|NP_970615.2	Q9BZP6	CHIA_HUMAN	chitinase, acidic	35					apoptotic process (GO:0006915)|cell wall chitin metabolic process (GO:0006037)|chitin catabolic process (GO:0006032)|chitin metabolic process (GO:0006030)|digestion (GO:0007586)|immune response (GO:0006955)|polysaccharide catabolic process (GO:0000272)|positive regulation of chemokine secretion (GO:0090197)|production of molecular mediator involved in inflammatory response (GO:0002532)|response to fungus (GO:0009620)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|chitin binding (GO:0008061)|chitinase activity (GO:0004568)|kinase binding (GO:0019900)|lysozyme activity (GO:0003796)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		all_cancers(81;3.23e-05)|all_epithelial(167;1.2e-05)|all_lung(203;0.000154)|Lung NSC(277;0.000304)		Colorectal(144;0.0115)|Lung(183;0.0292)|COAD - Colon adenocarcinoma(174;0.0314)|all cancers(265;0.0477)|Epithelial(280;0.0918)|LUSC - Lung squamous cell carcinoma(189;0.154)		GGCCCAGTACCGGCCAGGCCT	0.582													C|||	58	0.0115815	0.0393	0.0086	5008	,	,		18399	0.0		0.0	False		,,,				2504	0.0				p.R35W		Atlas-SNP	.											CHIA_ENST00000369740,NS,carcinoma,-2,1	CHIA	115	1	0			c.C103T						PASS	.	C	,TRP/ARG	170,4018		2,166,1926	70.0	74.0	73.0		,103	-0.2	0.2	1	dbSNP_129	73	0,8432		0,0,4216	yes	intron,missense	CHIA	NM_021797.2,NM_201653.2	,101	2,166,6142	TT,TC,CC		0.0,4.0592,1.3471	,probably-damaging	,35/477	111854859	170,12450	2094	4216	6310	SO:0001583	missense	27159	exon4			CAGTACCGGCCAG	AF290004	CCDS832.1, CCDS41368.1, CCDS58017.1	1p13.2	2008-05-14			ENSG00000134216	ENSG00000134216			17432	protein-coding gene	gene with protein product		606080				11085997	Standard	NM_021797		Approved	AMCase, TSA1902, CHIT2	uc001eas.4	Q9BZP6	OTTHUMG00000011165	ENST00000369740.1:c.103C>T	1.37:g.111854859C>T	ENSP00000358755:p.Arg35Trp	188.0	0.0	0		197.0	92.0	0.467005	NM_201653	Q32W79|Q32W80|Q3B866|Q5U5Z5|Q5VUV4|Q86UD8|Q9ULY3|Q9ULY4	Missense_Mutation	SNP	ENST00000369740.1	37	CCDS41368.1	26	0.011904761904761904	23	0.046747967479674794	3	0.008287292817679558	0	0.0	0	0.0	C	17.72	3.459828	0.63401	0.040592	0.0	ENSG00000134216	ENST00000369740;ENST00000343320	T;T	0.06933	3.24;3.24	5.08	-0.166	0.13351	Chitinase II (1);Glycoside hydrolase, family 18, catalytic domain (1);Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.000000	0.47852	U	0.000201	T	0.17874	0.0429	H	0.95294	3.65	0.80722	D	1	P	0.47484	0.896	P	0.51453	0.67	T	0.41998	-0.9477	10	0.66056	D	0.02	-8.6166	13.0776	0.59095	0.7282:0.2718:0.0:0.0	rs61752461	35	Q9BZP6	CHIA_HUMAN	W	35	ENSP00000358755:R35W;ENSP00000341828:R35W	ENSP00000341828:R35W	R	+	1	2	CHIA	111656382	0.000000	0.05858	0.241000	0.24154	0.789000	0.44602	-0.273000	0.08548	0.179000	0.19938	0.655000	0.94253	CGG	C|0.988;T|0.012	0.012	strong		0.582	CHIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030710.1		
CCDC151	115948	hgsc.bcm.edu	37	19	11537006	11537006	+	Silent	SNP	G	G	A	rs61739937	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:11537006G>A	ENST00000356392.4	-	7	1008	c.921C>T	c.(919-921)cgC>cgT	p.R307R	CCDC151_ENST00000586836.1_Silent_p.R116R|CCDC151_ENST00000591179.1_Silent_p.R247R|CCDC151_ENST00000545100.1_Silent_p.R253R	NM_145045.4	NP_659482.3	A5D8V7	CC151_HUMAN	coiled-coil domain containing 151	307										endometrium(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	12						TCTCCTCGGCGCGCTTCTTGC	0.627													G|||	129	0.0257588	0.09	0.0072	5008	,	,		14915	0.004		0.001	False		,,,				2504	0.0				p.R307R		Atlas-SNP	.											.	CCDC151	44	.	0			c.C921T						PASS	.	G		295,3731		14,267,1732	41.0	43.0	42.0		921	-8.9	0.1	19	dbSNP_129	42	2,8354		0,2,4176	no	coding-synonymous	CCDC151	NM_145045.4		14,269,5908	AA,AG,GG		0.0239,7.3274,2.3986		307/596	11537006	297,12085	2013	4178	6191	SO:0001819	synonymous_variant	115948	exon7			CTCGGCGCGCTTC		CCDS42501.1	19p13.2	2014-02-20				ENSG00000198003			28303	protein-coding gene	gene with protein product		615956				24067530	Standard	NM_145045		Approved	MGC20983	uc002mrs.3	A5D8V7		ENST00000356392.4:c.921C>T	19.37:g.11537006G>A		52.0	0.0	0		43.0	19.0	0.44186	NM_145045	B4DXT0|Q96CG5	Silent	SNP	ENST00000356392.4	37	CCDS42501.1																																																																																			G|0.986;A|0.014	0.014	strong		0.627	CCDC151-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458800.1	NM_145045	
NLRP4	147945	hgsc.bcm.edu	37	19	56369668	56369668	+	Silent	SNP	C	C	T	rs112565033	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:56369668C>T	ENST00000301295.6	+	3	1331	c.909C>T	c.(907-909)aaC>aaT	p.N303N	NLRP4_ENST00000587891.1_Silent_p.N228N|NLRP4_ENST00000346986.5_Silent_p.N303N	NM_134444.4	NP_604393.2	Q96MN2	NALP4_HUMAN	NLR family, pyrin domain containing 4	303	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(3)|ovary(6)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(8)	42		Colorectal(82;0.0002)|Ovarian(87;0.221)		GBM - Glioblastoma multiforme(193;0.0606)		GGGGATTCAACGAGAGTGATA	0.507													C|||	26	0.00519169	0.0189	0.0014	5008	,	,		18203	0.0		0.0	False		,,,				2504	0.0				p.N303N		Atlas-SNP	.											.	NLRP4	331	.	0			c.C909T						PASS	.	C		56,4350	56.2+/-92.4	0,56,2147	73.0	78.0	76.0		909	-8.2	0.0	19	dbSNP_132	76	0,8600		0,0,4300	yes	coding-synonymous	NLRP4	NM_134444.4		0,56,6447	TT,TC,CC		0.0,1.271,0.4306		303/995	56369668	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	147945	exon3			ATTCAACGAGAGT	AF479747	CCDS12936.1	19q13.43	2009-03-27	2006-12-08	2006-12-08				"""Nucleotide-binding domain and leucine rich repeat containing"""	22943	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 4"", ""cancer/testis antigen 58"""	609645	"""NACHT, leucine rich repeat and PYD containing 4"""	NALP4		12563287, 12019269	Standard	NM_134444		Approved	PYPAF4, FLJ32126, PAN2, RNH2, CLR19.5, CT58	uc002qmd.4	Q96MN2		ENST00000301295.6:c.909C>T	19.37:g.56369668C>T		174.0	0.0	0		143.0	78.0	0.545455	NM_134444	Q86W87|Q96AY6	Silent	SNP	ENST00000301295.6	37	CCDS12936.1																																																																																			C|0.994;T|0.006	0.006	strong		0.507	NLRP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457367.2	NM_134444	
EDIL3	10085	hgsc.bcm.edu	37	5	83433087	83433087	+	Silent	SNP	G	G	A	rs58219060	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:83433087G>A	ENST00000296591.5	-	5	859	c.441C>T	c.(439-441)ggC>ggT	p.G147G	EDIL3_ENST00000380138.3_Silent_p.G137G	NM_005711.3	NP_005702.3	O43854	EDIL3_HUMAN	EGF-like repeats and discoidin I-like domains 3	147	EGF-like 3. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|positive regulation of cell-substrate adhesion (GO:0010811)	extracellular vesicular exosome (GO:0070062)|vesicle (GO:0031982)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|prostate(5)|skin(3)	31		Lung NSC(167;0.000121)|all_lung(232;0.000154)|Ovarian(174;0.0425)		OV - Ovarian serous cystadenocarcinoma(54;4.3e-40)|Epithelial(54;4.79e-32)|all cancers(79;1.54e-26)		CCATAAATTCGCCTGGGCACT	0.393													G|||	159	0.0317492	0.118	0.0029	5008	,	,		16170	0.0		0.001	False		,,,				2504	0.0				p.G147G		Atlas-SNP	.											.	EDIL3	94	.	0			c.C441T						PASS	.	G		465,3941	220.7+/-238.1	23,419,1761	175.0	153.0	160.0		441	-4.0	1.0	5	dbSNP_129	160	4,8596	3.7+/-12.6	0,4,4296	yes	coding-synonymous	EDIL3	NM_005711.3		23,423,6057	AA,AG,GG		0.0465,10.5538,3.606		147/481	83433087	469,12537	2203	4300	6503	SO:0001819	synonymous_variant	10085	exon5			AAATTCGCCTGGG	U70312	CCDS4062.1, CCDS64195.1	5q14	2008-02-05			ENSG00000164176	ENSG00000164176			3173	protein-coding gene	gene with protein product		606018				9420328	Standard	NM_005711		Approved	DEL1	uc003kio.1	O43854	OTTHUMG00000119047	ENST00000296591.5:c.441C>T	5.37:g.83433087G>A		59.0	0.0	0		67.0	35.0	0.522388	NM_005711	B2R763|O43855|Q5D094|Q8N610	Silent	SNP	ENST00000296591.5	37	CCDS4062.1																																																																																			G|0.965;A|0.035	0.035	strong		0.393	EDIL3-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239258.1	NM_005711	
XPA	7507	hgsc.bcm.edu	37	9	100449436	100449436	+	Missense_Mutation	SNP	A	A	G	rs143374902	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:100449436A>G	ENST00000375128.4	-	4	561	c.497T>C	c.(496-498)gTg>gCg	p.V166A		NM_000380.3	NP_000371.1	P23025	XPA_HUMAN	xeroderma pigmentosum, complementation group A	166					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)|nucleotide-excision repair, DNA damage removal (GO:0000718)|response to oxidative stress (GO:0006979)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercellular bridge (GO:0045171)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(4)|large_intestine(1)|lung(4)|prostate(1)	11		Acute lymphoblastic leukemia(62;0.158)				ATTCTTCTTCACAATAAATTT	0.313			"""Mis, N, F, S"""			"""skin basal cell, skin squamous cell, melanoma"""		Nucleotide excision repair (NER)	Xeroderma Pigmentosum				A|||	10	0.00199681	0.0076	0.0	5008	,	,		15259	0.0		0.0	False		,,,				2504	0.0				p.V166A		Atlas-SNP	.	yes	Rec		Xeroderma pigmentosum (A)	9	9q22.3	7507	"""xeroderma pigmentosum, complementation group A"""		E	.	XPA	21	.	0			c.T497C						PASS	.	A	ALA/VAL	48,4358	48.9+/-83.8	0,48,2155	119.0	126.0	123.0		497	5.4	1.0	9	dbSNP_134	123	0,8596		0,0,4298	yes	missense	XPA	NM_000380.3	64	0,48,6453	GG,GA,AA		0.0,1.0894,0.3692	benign	166/274	100449436	48,12954	2203	4298	6501	SO:0001583	missense	7507	exon4	Familial Cancer Database	incl. XPA, XPB, XPC, XPD, XPE, XPF, XPG, XP Variant, XPV	TTCTTCACAATAA	D14533	CCDS6729.1	9q22.3	2014-09-17			ENSG00000136936	ENSG00000136936			12814	protein-coding gene	gene with protein product		611153					Standard	NM_000380		Approved	XPAC, XP1	uc004axr.4	P23025	OTTHUMG00000020330	ENST00000375128.4:c.497T>C	9.37:g.100449436A>G	ENSP00000364270:p.Val166Ala	76.0	0.0	0		71.0	55.0	0.774648	NM_000380	Q5T1U9|Q6LCW7|Q6LD02	Missense_Mutation	SNP	ENST00000375128.4	37	CCDS6729.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	A	15.65	2.896170	0.52121	0.010894	0.0	ENSG00000136936	ENST00000375128	T	0.59224	0.28	5.42	5.42	0.78866	DNA binding domain, putative (1);XPA C- terminal (1);	0.212392	0.44483	D	0.000454	T	0.48624	0.1510	L	0.48362	1.52	0.45852	D	0.998718	B	0.24426	0.103	B	0.36766	0.232	T	0.53063	-0.8491	10	0.40728	T	0.16	.	13.2937	0.60284	1.0:0.0:0.0:0.0	.	166	P23025	XPA_HUMAN	A	166	ENSP00000364270:V166A	ENSP00000364270:V166A	V	-	2	0	XPA	99489257	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.905000	0.92613	2.196000	0.70406	0.533000	0.62120	GTG	A|0.996;G|0.004	0.004	strong		0.313	XPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053332.1	NM_000380	
LMNTD1	160492	hgsc.bcm.edu	37	12	25672877	25672877	+	Missense_Mutation	SNP	C	C	T	rs34074522	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:25672877C>T	ENST00000282881.6	-	6	1017	c.868G>A	c.(868-870)Gct>Act	p.A290T	IFLTD1_ENST00000539744.1_Missense_Mutation_p.A193T|IFLTD1_ENST00000458174.2_Missense_Mutation_p.A311T|IFLTD1_ENST00000413632.2_Missense_Mutation_p.A271T|IFLTD1_ENST00000445693.1_Missense_Mutation_p.A227T	NM_152590.3	NP_689803.2	Q8N9Z9	LMTD1_HUMAN		290			A -> T (in dbSNP:rs34074522).		cell proliferation (GO:0008283)	cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|nuclear envelope (GO:0005635)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22	all_lung(3;2.75e-22)|Lung NSC(3;1.77e-21)|all_hematologic(7;0.00656)|Colorectal(261;0.0847)					GTTATTGTAGCTGTAGATGCT	0.383													T|||	88	0.0175719	0.0628	0.0072	5008	,	,		13260	0.0		0.0	False		,,,				2504	0.0				p.A311T		Atlas-SNP	.											IFLTD1_ENST00000458174,NS,carcinoma,+1,2	IFLTD1	121	2	0			c.G931A						PASS	.	T	THR/ALA,THR/ALA,THR/ALA,THR/ALA	251,4155	802.9+/-415.7	5,241,1957	210.0	187.0	195.0		679,931,811,868	-0.6	0.0	12	dbSNP_126	195	1,8599	818.9+/-406.8	0,1,4299	yes	missense,missense,missense,missense	IFLTD1	NM_001145727.1,NM_001145728.1,NM_001145729.1,NM_152590.2	58,58,58,58	5,242,6256	TT,TC,CC		0.0116,5.6968,1.9376	benign,benign,benign,benign	227/326,311/410,271/370,290/389	25672877	252,12754	2203	4300	6503	SO:0001583	missense	160492	exon7			TTGTAGCTGTAGA																												ENST00000282881.6:c.868G>A	12.37:g.25672877C>T	ENSP00000282881:p.Ala290Thr	159.0	0.0	0		119.0	50.0	0.420168	NM_001145728	B4DL27|B4DY70|Q8IY38	Missense_Mutation	SNP	ENST00000282881.6	37	CCDS8704.1	20|20	0.009157509157509158|0.009157509157509158	17|17	0.034552845528455285|0.034552845528455285	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	0|0	0.0|0.0	T|T	0.198|0.198	-1.047307|-1.047307	0.01981|0.01981	0.056968|0.056968	1.16E-4|1.16E-4	ENSG00000152936|ENSG00000152936	ENST00000282881;ENST00000539744;ENST00000458174;ENST00000445693;ENST00000413632;ENST00000539523;ENST00000545543|ENST00000543629	T;T;T;T;T;T;T|.	0.22336|.	2.67;2.68;2.67;2.66;2.53;1.96;2.54|.	4.68|4.68	-0.618|-0.618	0.11576|0.11576	.|.	.|.	.|.	.|.	.|.	T|T	0.00875|0.00875	0.0029|0.0029	N|N	0.01874|0.01874	-0.695|-0.695	0.09310|0.09310	N|N	1|1	B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0|.	B;B;B;B|.	0.04013|.	0.001;0.0;0.0;0.0|.	T|T	0.30179|0.30179	-0.9987|-0.9987	9|5	0.08599|.	T|.	0.76|.	-1.4413|-1.4413	4.4653|4.4653	0.11685|0.11685	0.1606:0.3771:0.0:0.4623|0.1606:0.3771:0.0:0.4623	rs34074522|rs34074522	227;311;271;290|.	Q8N9Z9-3;Q8N9Z9-5;Q8N9Z9-4;Q8N9Z9|.	.;.;.;ILFT1_HUMAN|.	T|N	290;193;311;227;271;7;120|64	ENSP00000282881:A290T;ENSP00000443132:A193T;ENSP00000407353:A311T;ENSP00000407043:A227T;ENSP00000393150:A271T;ENSP00000438160:A7T;ENSP00000443596:A120T|.	ENSP00000282881:A290T|.	A|S	-|-	1|2	0|0	IFLTD1|IFLTD1	25564144|25564144	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.002000|0.002000	0.02628|0.02628	-0.752000|-0.752000	0.04797|0.04797	-0.241000|-0.241000	0.09681|0.09681	-1.163000|-1.163000	0.01768|0.01768	GCT|AGC	C|0.980;T|0.020	0.020	strong		0.383	IFLTD1-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000402279.1		
SLC5A2	6524	hgsc.bcm.edu	37	16	31501642	31501642	+	Missense_Mutation	SNP	C	C	T	rs61746400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31501642C>T	ENST00000330498.3	+	14	1824	c.1805C>T	c.(1804-1806)cCg>cTg	p.P602L	C16orf58_ENST00000567994.1_3'UTR|SLC5A2_ENST00000564197.1_Intron|C16orf58_ENST00000327237.2_3'UTR|AC026471.6_ENST00000565137.1_RNA|C16orf58_ENST00000570164.1_3'UTR	NM_003041.3	NP_003032.1	P31639	SC5A2_HUMAN	solute carrier family 5 (sodium/glucose cotransporter), member 2	602					carbohydrate metabolic process (GO:0005975)|glucose transport (GO:0015758)|transmembrane transport (GO:0055085)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	low-affinity glucose:sodium symporter activity (GO:0005362)			endometrium(2)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	25					Canagliflozin(DB08907)|Dapagliflozin(DB06292)	CCCCAGGCCCCGGCACCAAGC	0.632													c|||	44	0.00878594	0.0325	0.0014	5008	,	,		16541	0.0		0.0	False		,,,				2504	0.0				p.P602L		Atlas-SNP	.											.	SLC5A2	58	.	0			c.C1805T						PASS	.	T	LEU/PRO,	75,4319		2,71,2124	16.0	18.0	18.0		1805,	-0.1	0.0	16	dbSNP_129	18	0,8600		0,0,4300	yes	missense,utr-3	SLC5A2,C16orf58	NM_003041.3,NM_022744.2	98,	2,71,6424	TT,TC,CC		0.0,1.7069,0.5772	benign,	602/673,	31501642	75,12919	2197	4300	6497	SO:0001583	missense	6524	exon14			AGGCCCCGGCACC		CCDS10714.1	16p11.2	2013-05-22			ENSG00000140675	ENSG00000140675		"""Solute carriers"""	11037	protein-coding gene	gene with protein product		182381		SGLT2		8244402	Standard	NM_003041		Approved		uc002ecf.4	P31639	OTTHUMG00000176620	ENST00000330498.3:c.1805C>T	16.37:g.31501642C>T	ENSP00000327943:p.Pro602Leu	84.0	0.0	0		75.0	31.0	0.413333	NM_003041	A2RRD2	Missense_Mutation	SNP	ENST00000330498.3	37	CCDS10714.1	17	0.007783882783882784	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	0	0.0	c	3.253	-0.152863	0.06585	0.017069	0.0	ENSG00000140675	ENST00000330498	D	0.91740	-2.9	5.22	-0.0727	0.13738	.	1.172050	0.06093	N	0.663966	T	0.68118	0.2966	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.65903	-0.6055	10	0.49607	T	0.09	.	8.1774	0.31289	0.0:0.5827:0.0:0.4173	rs61746400	602	P31639	SC5A2_HUMAN	L	602	ENSP00000327943:P602L	ENSP00000327943:P602L	P	+	2	0	SLC5A2	31409143	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.493000	0.22451	-0.230000	0.09840	-0.993000	0.02533	CCG	C|0.992;T|0.008	0.008	strong		0.632	SLC5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255627.2		
OR13C5	138799	hgsc.bcm.edu	37	9	107361038	107361038	+	Silent	SNP	C	C	T	rs75872480	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:107361038C>T	ENST00000374779.2	-	1	750	c.657G>A	c.(655-657)acG>acA	p.T219T		NM_001004482.1	NP_001004482.1	Q8NGS8	O13C5_HUMAN	olfactory receptor, family 13, subfamily C, member 5	219						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						AAATGATTAACGTGTAAGAGA	0.428													C|||	14	0.00279553	0.0106	0.0	5008	,	,		22708	0.0		0.0	False		,,,				2504	0.0				p.T219T		Atlas-SNP	.											OR13C5,NS,haematopoietic_neoplasm,-1,1	OR13C5	60	1	0			c.G657A						PASS	.	C		24,4382	30.8+/-60.4	0,24,2179	131.0	124.0	127.0		657	-8.1	0.0	9	dbSNP_131	127	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	OR13C5	NM_001004482.1		0,25,6478	TT,TC,CC		0.0116,0.5447,0.1922		219/319	107361038	25,12981	2203	4300	6503	SO:0001819	synonymous_variant	138799	exon1			GATTAACGTGTAA		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.657G>A	9.37:g.107361038C>T		173.0	0.0	0		212.0	134.0	0.632075	NM_001004482	B2RNE5|B9EGW5|Q6IF53	Silent	SNP	ENST00000374779.2	37	CCDS35091.1																																																																																			C|0.998;T|0.002	0.002	strong		0.428	OR13C5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053479.2	NM_001004482	
EPHB2	2048	hgsc.bcm.edu	37	1	23222008	23222008	+	Silent	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:23222008C>T	ENST00000400191.3	+	8	1653	c.1635C>T	c.(1633-1635)atC>atT	p.I545I	EPHB2_ENST00000374630.3_Silent_p.I545I|EPHB2_ENST00000465676.1_3'UTR|EPHB2_ENST00000374627.1_Silent_p.I540I|EPHB2_ENST00000374632.3_Silent_p.I545I	NM_004442.6|NM_017449.3	NP_004433.2|NP_059145.2	P29323	EPHB2_HUMAN	EPH receptor B2	545					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|camera-type eye morphogenesis (GO:0048593)|central nervous system projection neuron axonogenesis (GO:0021952)|commissural neuron axon guidance (GO:0071679)|corpus callosum development (GO:0022038)|dendritic spine development (GO:0060996)|dendritic spine morphogenesis (GO:0060997)|ephrin receptor signaling pathway (GO:0048013)|inner ear morphogenesis (GO:0042472)|learning (GO:0007612)|negative regulation of axonogenesis (GO:0050771)|nervous system development (GO:0007399)|optic nerve morphogenesis (GO:0021631)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse assembly (GO:0051965)|regulation of body fluid levels (GO:0050878)|retinal ganglion cell axon guidance (GO:0031290)|urogenital system development (GO:0001655)	axon (GO:0030424)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|protein tyrosine kinase activity (GO:0004713)|transmembrane-ephrin receptor activity (GO:0005005)			NS(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(17)|ovary(4)|pancreas(2)|prostate(3)|skin(8)|stomach(1)|urinary_tract(1)	56		Colorectal(325;3.46e-05)|Lung NSC(340;3.7e-05)|all_lung(284;5.45e-05)|Renal(390;0.000228)|Breast(348;0.0027)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0258)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0348)|OV - Ovarian serous cystadenocarcinoma(117;3.67e-26)|Colorectal(126;3.23e-08)|COAD - Colon adenocarcinoma(152;9.32e-07)|GBM - Glioblastoma multiforme(114;2.93e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000606)|KIRC - Kidney renal clear cell carcinoma(1967;0.00371)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.126)|Lung(427;0.153)		CACTCATCATCGGCTCCTCGG	0.592																																					p.I545I		Atlas-SNP	.											.	EPHB2	257	.	0			c.C1635T						PASS	.						139.0	120.0	126.0					1																	23222008		2203	4300	6503	SO:0001819	synonymous_variant	2048	exon8			CATCATCGGCTCC	AF025304	CCDS229.2, CCDS230.1	1p36.1-p35	2014-09-17	2004-10-28		ENSG00000133216	ENSG00000133216	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3393	protein-coding gene	gene with protein product		600997	"""EphB2"""	DRT, ERK, EPHT3		1648701	Standard	NM_017449		Approved	Hek5, Tyro5	uc001bge.3	P29323	OTTHUMG00000002881	ENST00000400191.3:c.1635C>T	1.37:g.23222008C>T		103.0	0.0	0		115.0	59.0	0.513043	NM_004442	O43477|Q5T0U6|Q5T0U7|Q5T0U8	Silent	SNP	ENST00000400191.3	37																																																																																				.	.	none		0.592	EPHB2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000008060.2	NM_017449	
UAP1	6675	hgsc.bcm.edu	37	1	162560209	162560209	+	Silent	SNP	G	G	A	rs61743694	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:162560209G>A	ENST00000367925.1	+	7	1298	c.1266G>A	c.(1264-1266)agG>agA	p.R422R	UAP1_ENST00000367926.4_Silent_p.R422R|UAP1_ENST00000367924.1_Silent_p.R422R|UAP1_ENST00000271469.3_Silent_p.R422R|RP11-359K18.4_ENST00000609669.1_RNA			Q16222	UAP1_HUMAN	UDP-N-acetylglucosamine pyrophosphorylase 1	422					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)|UDP-N-acetylglucosamine biosynthetic process (GO:0006048)	cytosol (GO:0005829)	carbohydrate binding (GO:0030246)|UDP-N-acetylglucosamine diphosphorylase activity (GO:0003977)			breast(2)|cervix(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(2)|skin(2)|stomach(1)	22	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			CTACTGCAAGGCATGCTTTGA	0.458													G|||	119	0.023762	0.0877	0.0043	5008	,	,		19084	0.0		0.0	False		,,,				2504	0.0				p.R422R		Atlas-SNP	.											.	UAP1	47	.	0			c.G1266A						PASS	.	G		377,4029	191.2+/-216.9	15,347,1841	174.0	159.0	164.0		1266	1.0	0.6	1	dbSNP_129	164	8,8592	5.0+/-18.6	0,8,4292	no	coding-synonymous	UAP1	NM_003115.4		15,355,6133	AA,AG,GG		0.093,8.5565,2.9602		422/506	162560209	385,12621	2203	4300	6503	SO:0001819	synonymous_variant	6675	exon8			TGCAAGGCATGCT	AB011004	CCDS1240.1	1q23.2	2014-07-31	2014-07-31		ENSG00000117143	ENSG00000117143	2.7.7.23		12457	protein-coding gene	gene with protein product		602862		SPAG2		9603950, 8025165	Standard	NM_003115		Approved	AGX1, AgX	uc001gce.4	Q16222	OTTHUMG00000034419	ENST00000367925.1:c.1266G>A	1.37:g.162560209G>A		167.0	0.0	0		162.0	88.0	0.54321	NM_003115	B2R6R8|Q5VTA9|Q5VTB0|Q5VTB1|Q96GM2	Silent	SNP	ENST00000367925.1	37																																																																																				G|0.969;A|0.031	0.031	strong		0.458	UAP1-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000083203.1	NM_003115	
CHAF1B	8208	hgsc.bcm.edu	37	21	37787615	37787615	+	Missense_Mutation	SNP	A	A	C	rs74900401	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:37787615A>C	ENST00000314103.5	+	13	1667	c.1516A>C	c.(1516-1518)Aag>Cag	p.K506Q		NM_005441.2	NP_005432.1	Q13112	CAF1B_HUMAN	chromatin assembly factor 1, subunit B (p60)	506			K -> Q (in dbSNP:rs2230638).		cell cycle (GO:0007049)|chromatin assembly (GO:0031497)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|protein complex assembly (GO:0006461)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|histone binding (GO:0042393)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(1)|lung(6)|ovary(2)|skin(2)	20						AACACCCTTAAAGACGGACAC	0.358													A|||	94	0.01877	0.0666	0.0086	5008	,	,		18323	0.0		0.0	False		,,,				2504	0.0				p.K506Q		Atlas-SNP	.											.	CHAF1B	47	.	0			c.A1516C						PASS	.	A	GLN/LYS	231,4175	137.7+/-173.5	11,209,1983	94.0	93.0	94.0		1516	5.3	1.0	21	dbSNP_131	94	3,8597	2.2+/-6.3	0,3,4297	no	missense	CHAF1B	NM_005441.2	53	11,212,6280	CC,CA,AA		0.0349,5.2429,1.7992	benign	506/560	37787615	234,12772	2203	4300	6503	SO:0001583	missense	8208	exon13			CCCTTAAAGACGG	U20980	CCDS13644.1	21q22.2	2013-01-10			ENSG00000159259	ENSG00000159259		"""WD repeat domain containing"""	1911	protein-coding gene	gene with protein product	"""M-phase phosphoprotein 7"", ""Chromatin assembly factor I, p60 subunit"", ""human chromatin assembly factor-I p60 subunit"""	601245				7600578, 8792829	Standard	NM_005441		Approved	CAF1P60, CAF-1, CAF1, CAF1A, MPP7, MPHOSPH7	uc002yvj.3	Q13112	OTTHUMG00000086606	ENST00000314103.5:c.1516A>C	21.37:g.37787615A>C	ENSP00000315700:p.Lys506Gln	38.0	0.0	0		50.0	20.0	0.4	NM_005441	Q99548	Missense_Mutation	SNP	ENST00000314103.5	37	CCDS13644.1	31	0.014194139194139194	27	0.054878048780487805	4	0.011049723756906077	0	0.0	0	0.0	A	15.24	2.773669	0.49786	0.052429	3.49E-4	ENSG00000159259	ENST00000314103	T	0.56444	0.46	5.27	5.27	0.74061	.	0.467856	0.25244	N	0.032064	T	0.09949	0.0244	L	0.34521	1.04	0.41488	D	0.988205	P	0.46706	0.883	B	0.41571	0.36	T	0.02868	-1.1100	10	0.28530	T	0.3	-21.6711	13.7766	0.63057	1.0:0.0:0.0:0.0	rs2230638;rs16994063;rs52813568;rs16994063	506	Q13112	CAF1B_HUMAN	Q	506	ENSP00000315700:K506Q	ENSP00000315700:K506Q	K	+	1	0	CHAF1B	36709485	1.000000	0.71417	0.995000	0.50966	0.553000	0.35397	5.445000	0.66594	1.991000	0.58162	0.533000	0.62120	AAG	A|0.984;C|0.016;T|0.000	0.016	strong		0.358	CHAF1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194616.2	NM_005441	
TMEM254	80195	hgsc.bcm.edu	37	10	81838864	81838864	+	Intron	SNP	A	A	G	rs61748824	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:81838864A>G	ENST00000372281.3	+	1	117				TMEM254-AS1_ENST00000448729.2_RNA|TMEM254-AS1_ENST00000432070.2_RNA|TMEM254_ENST00000372277.3_Intron|TMEM254_ENST00000372275.1_Intron|TMEM254_ENST00000372274.1_Intron|TMEM254-AS1_ENST00000412298.1_RNA	NM_001270372.1|NM_025125.3	NP_001257301.1|NP_079401.2	Q8TBM7	TM254_HUMAN	transmembrane protein 254							integral component of membrane (GO:0016021)											GAGGCCAGCAATGCGGCTACC	0.627													.|||	97	0.019369	0.0514	0.0144	5008	,	,		14740	0.001		0.004	False		,,,				2504	0.0143				p.N28S		Atlas-SNP	.											.	TMEM254	1	.	0			c.A83G						PASS	.																																			SO:0001627	intron_variant	80195	exon1			CCAGCAATGCGGC	BC022252	CCDS7363.1, CCDS58086.1, CCDS58087.1, CCDS73157.1	10q23.1	2012-11-06	2012-11-06	2012-11-06	ENSG00000133678	ENSG00000133678			25804	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 57"""	C10orf57		14702039	Standard	NM_025125		Approved	FLJ13263, bA369J21.6	uc010qlw.3	Q8TBM7	OTTHUMG00000018602	ENST00000372281.3:c.87+322A>G	10.37:g.81838864A>G		193.0	0.0	0		232.0	120.0	0.517241	NM_001270368	D3DWC8|Q53HP4|Q5JTC0|Q5JTC1|Q6IA45|Q9H8S6	Missense_Mutation	SNP	ENST00000372281.3	37	CCDS7363.1	24	0.01098901098901099	16	0.032520325203252036	7	0.019337016574585635	0	0.0	1	0.0013192612137203166	A	1.201	-0.632572	0.03584	.	.	ENSG00000133678	ENST00000372273	.	.	.	4.56	-2.15	0.07102	.	.	.	.	.	T	0.08313	0.0207	.	.	.	0.09310	N	0.999996	.	.	.	.	.	.	T	0.24584	-1.0156	4	.	.	.	-2.0324	4.9974	0.14247	0.458:0.1525:0.3894:0.0	rs61748824	.	.	.	V	25	.	.	M	+	1	0	C10orf57	81828844	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.359000	0.20233	-0.336000	0.08438	-0.959000	0.02639	ATG	A|0.988;G|0.012	0.012	strong		0.627	TMEM254-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049030.1	NM_025125	
FBN3	84467	hgsc.bcm.edu	37	19	8171068	8171068	+	Silent	SNP	G	G	A	rs7258713	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8171068G>A	ENST00000600128.1	-	38	5151	c.4737C>T	c.(4735-4737)tgC>tgT	p.C1579C	FBN3_ENST00000601739.1_Silent_p.C1579C|FBN3_ENST00000270509.2_Silent_p.C1579C			Q75N90	FBN3_HUMAN	fibrillin 3	1579	EGF-like 24; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						ACGTGTTGACGCAGTCACCCC	0.572													G|||	366	0.0730831	0.2428	0.0202	5008	,	,		20054	0.0		0.003	False		,,,				2504	0.0286				p.C1579C		Atlas-SNP	.											.	FBN3	300	.	0			c.C4737T						PASS	.	G		836,3570	331.5+/-302.0	86,664,1453	120.0	85.0	97.0		4737	0.9	0.8	19	dbSNP_116	97	25,8575	17.9+/-57.8	0,25,4275	no	coding-synonymous	FBN3	NM_032447.3		86,689,5728	AA,AG,GG		0.2907,18.9741,6.62		1579/2810	8171068	861,12145	2203	4300	6503	SO:0001819	synonymous_variant	84467	exon37			GTTGACGCAGTCA		CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.4737C>T	19.37:g.8171068G>A		69.0	0.0	0		82.0	42.0	0.512195	NM_032447	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																			G|0.925;A|0.075	0.075	strong		0.572	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2	NM_032447	
BUB1B	701	hgsc.bcm.edu	37	15	40512906	40512906	+	Silent	SNP	A	A	G	rs35611758	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:40512906A>G	ENST00000287598.6	+	23	3294	c.3099A>G	c.(3097-3099)aaA>aaG	p.K1033K	PAK6_ENST00000453867.1_Intron|BUB1B_ENST00000412359.3_Silent_p.K1047K|PAK6_ENST00000441369.1_Intron|RP11-133K1.2_ENST00000558658.1_Intron	NM_001211.5	NP_001202	O60566	BUB1B_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase B	1033	Protein kinase.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|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)|protein localization to chromosome, centromeric region (GO:0071459)|protein localization to kinetochore (GO:0034501)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|condensed chromosome kinetochore (GO:0000777)|condensed chromosome outer kinetochore (GO:0000940)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|perinuclear region of cytoplasm (GO:0048471)|spindle midzone (GO:0051233)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|endometrium(1)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(1)|stomach(2)|urinary_tract(2)	36		all_cancers(109;1.12e-18)|all_epithelial(112;1.61e-15)|Lung NSC(122;5.63e-11)|all_lung(180;1.4e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.83e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0556)		ACCTGAACAAAGCCTTATGGA	0.468			"""Mis, N, F, S"""			rhabdomyosarcoma			Mosaic Variegated Aneuploidy Syndrome				A|||	480	0.0958466	0.3502	0.0245	5008	,	,		19233	0.0		0.0	False		,,,				2504	0.0				p.K1033K		Atlas-SNP	.	yes	Rec		Mosaic variegated aneuploidy	15	15q15	701	BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast)		M	.	BUB1B	71	.	0			c.A3099G						PASS	.	A	,,	1160,3246	411.9+/-335.9	151,858,1194	139.0	133.0	135.0		,,3099	5.3	1.0	15	dbSNP_126	135	18,8582	13.3+/-46.6	0,18,4282	no	intron,intron,coding-synonymous	BUB1B,PAK6	NM_001128628.1,NM_001128629.1,NM_001211.5	,,	151,876,5476	GG,GA,AA		0.2093,26.3277,9.0574	,,	,,1033/1051	40512906	1178,11828	2203	4300	6503	SO:0001819	synonymous_variant	701	exon23	Familial Cancer Database	MVA, MVA syndrome, VMA syndrome, variegated mosaic aneuploidy syndrome, premature centromere division	GAACAAAGCCTTA	AF107297	CCDS10053.1	15q15	2014-09-17	2013-01-17		ENSG00000156970	ENSG00000156970			1149	protein-coding gene	gene with protein product		602860	"""budding uninhibited by benzimidazoles 1 (yeast homolog), beta"", ""budding uninhibited by benzimidazoles 1 homolog beta (yeast)"""			9889005	Standard	NM_001211		Approved	BUBR1, MAD3L, Bub1A, SSK1	uc001zkx.4	O60566	OTTHUMG00000129877	ENST00000287598.6:c.3099A>G	15.37:g.40512906A>G		151.0	0.0	0		137.0	73.0	0.532847	NM_001211	B2R6U0|B4DL09|B4DLG3|O60501|O60627|O60758|O75389|Q59HH6|Q8WV50|Q96KM4	Silent	SNP	ENST00000287598.6	37	CCDS10053.1																																																																																			A|0.915;G|0.085	0.085	strong		0.468	BUB1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252122.4		
C5orf45	51149	hgsc.bcm.edu	37	5	179285781	179285781	+	Missense_Mutation	SNP	G	G	A	rs199537217	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:179285781G>A	ENST00000292586.6	-	1	106	c.16C>T	c.(16-18)Cgt>Tgt	p.R6C	C5orf45_ENST00000521333.1_Missense_Mutation_p.R6C|C5orf45_ENST00000520698.1_Missense_Mutation_p.R6C|C5orf45_ENST00000403396.2_Missense_Mutation_p.A21V|C5orf45_ENST00000518219.1_Missense_Mutation_p.R6C|CTC-241N9.1_ENST00000499601.2_5'Flank|C5orf45_ENST00000518235.1_Missense_Mutation_p.R6C|C5orf45_ENST00000376931.2_Missense_Mutation_p.R6C|C5orf45_ENST00000523084.1_5'UTR	NM_016175.3	NP_057259.2	Q6NTE8	CE045_HUMAN	chromosome 5 open reading frame 45	6										breast(2)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)	12						ACCCGAGAACGCTGAAGCGAC	0.721													G|||	4	0.000798722	0.003	0.0	5008	,	,		14523	0.0		0.0	False		,,,				2504	0.0				p.R6C		Atlas-SNP	.											.	C5orf45	23	.	0			c.C16T						PASS	.	G	CYS/ARG,CYS/ARG	7,3989		0,7,1991	12.0	14.0	13.0		16,16	3.4	0.0	5		13	0,7610		0,0,3805	yes	missense,missense	C5orf45	NM_001017987.2,NM_016175.3	180,180	0,7,5796	AA,AG,GG		0.0,0.1752,0.0603	probably-damaging,probably-damaging	6/289,6/344	179285781	7,11599	1998	3805	5803	SO:0001583	missense	51149	exon1			GAGAACGCTGAAG		CCDS34318.1, CCDS34319.1	5q35.3	2008-07-10			ENSG00000161010	ENSG00000161010			30817	protein-coding gene	gene with protein product	"""truncated calcium binding protein"""						Standard	NM_016175		Approved	MGC65027, MGC78537, DKFZp686L2452, LOC51149	uc003mla.3	Q6NTE8	OTTHUMG00000163490	ENST00000292586.6:c.16C>T	5.37:g.179285781G>A	ENSP00000292586:p.Arg6Cys	59.0	0.0	0		50.0	27.0	0.54	NM_016175	B5MD09|E9PAK6|Q7Z3D8|Q9BUC1|Q9UN54	Missense_Mutation	SNP	ENST00000292586.6	37	CCDS34319.1	3|3	0.0013736263736263737|0.0013736263736263737	3|3	0.006097560975609756|0.006097560975609756	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	13.22|13.22	2.172040|2.172040	0.38315|0.38315	0.001752|0.001752	0.0|0.0	ENSG00000161010|ENSG00000161010	ENST00000403396|ENST00000518235;ENST00000520698;ENST00000376931;ENST00000518219;ENST00000292586;ENST00000521333	T|T;D;D;D;T;D	0.28454|0.82619	1.61|3.13;-1.63;-1.63;-1.63;3.13;-1.63	3.43|3.43	3.43|3.43	0.39272|0.39272	.|.	.|1.497770	.|0.04096	.|N	.|0.312148	T|T	0.70945|0.70945	0.3282|0.3282	N|N	0.22421|0.22421	0.69|0.69	0.09310|0.09310	N|N	1|1	.|D;D;D;D	.|0.60160	.|0.968;0.968;0.987;0.986	.|B;B;B;B	.|0.43809	.|0.432;0.335;0.432;0.432	T|T	0.67841|0.67841	-0.5566|-0.5566	7|10	0.87932|0.87932	D|D	0|0	-1.0479|-1.0479	10.2343|10.2343	0.43273|0.43273	0.1009:0.0:0.8991:0.0|0.1009:0.0:0.8991:0.0	.|.	.|6;6;6;6	.|E7EMV9;B7Z1T6;E9PAK6;Q6NTE8	.|.;.;.;CE045_HUMAN	V|C	21|6	ENSP00000384599:A21V|ENSP00000430298:R6C;ENSP00000427849:R6C;ENSP00000366130:R6C;ENSP00000428460:R6C;ENSP00000292586:R6C;ENSP00000429651:R6C	ENSP00000384599:A21V|ENSP00000292586:R6C	A|R	-|-	2|1	0|0	C5orf45|C5orf45	179218387|179218387	0.016000|0.016000	0.18221|0.18221	0.007000|0.007000	0.13788|0.13788	0.001000|0.001000	0.01503|0.01503	1.350000|1.350000	0.34010|0.34010	2.211000|2.211000	0.71520|0.71520	0.561000|0.561000	0.74099|0.74099	GCG|CGT	G|0.999;A|0.001	0.001	strong		0.721	C5orf45-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373760.2	NM_016175	
ATP6V1G3	127124	hgsc.bcm.edu	37	1	198498234	198498234	+	Missense_Mutation	SNP	C	C	G	rs16843254	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:198498234C>G	ENST00000367382.1	-	2	244	c.160G>C	c.(160-162)Gag>Cag	p.E54Q	ATP6V1G3_ENST00000367381.1_Missense_Mutation_p.E60Q|ATP6V1G3_ENST00000309309.7_3'UTR|ATP6V1G3_ENST00000489986.1_Missense_Mutation_p.E60Q|ATP6V1G3_ENST00000281087.2_Missense_Mutation_p.E54Q			Q96LB4	VATG3_HUMAN	ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G3	54			E -> Q (in dbSNP:rs16843254).		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)	cytosol (GO:0005829)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase complex (GO:0016471)	ATPase binding (GO:0051117)|hydrogen-exporting ATPase activity, phosphorylative mechanism (GO:0008553)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|prostate(1)	7						AGTCGAAACTCTTTATCTCTC	0.323													C|||	155	0.0309505	0.1142	0.0058	5008	,	,		9490	0.0		0.0	False		,,,				2504	0.0				p.E54Q		Atlas-SNP	.											.	ATP6V1G3	26	.	0			c.G160C						PASS	.	C	GLN/GLU,	460,3944	219.4+/-237.2	26,408,1768	148.0	140.0	143.0		160,	3.3	0.0	1	dbSNP_123	143	5,8593	3.7+/-12.6	0,5,4294	yes	missense,utr-3	ATP6V1G3	NM_133262.2,NM_133326.1	29,	26,413,6062	GG,GC,CC		0.0582,10.445,3.5764	possibly-damaging,	54/119,	198498234	465,12537	2202	4299	6501	SO:0001583	missense	127124	exon3			GAAACTCTTTATC	AY039760	CCDS1395.1, CCDS1396.1	1q32.2	2010-04-21	2006-01-13		ENSG00000151418	ENSG00000151418		"""ATPases / V-type"""	18265	protein-coding gene	gene with protein product			"""ATPase, H+ transporting, lysosomal 13kD, V1 subunit G isoform 3"", ""ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G isoform 3"""			9442887	Standard	NM_133262		Approved	ATP6G3, Vma10	uc001gup.3	Q96LB4	OTTHUMG00000035661	ENST00000367382.1:c.160G>C	1.37:g.198498234C>G	ENSP00000356352:p.Glu54Gln	66.0	0.0	0		100.0	58.0	0.58	NM_133262	Q495K2|Q495K4|Q5T9L6	Missense_Mutation	SNP	ENST00000367382.1	37	CCDS1395.1	62	0.028388278388278388	61	0.12398373983739837	1	0.0027624309392265192	0	0.0	0	0.0	C	8.216	0.801462	0.16397	0.10445	5.82E-4	ENSG00000151418	ENST00000367382;ENST00000367381;ENST00000281087;ENST00000489986	T;T;T;T	0.50548	0.74;0.79;0.74;0.79	5.19	3.31	0.37934	.	0.194878	0.53938	N	0.000054	T	0.01254	0.0041	L	0.53729	1.69	0.31164	N	0.704056	D;D	0.67145	0.996;0.989	P;P	0.60473	0.801;0.875	T	0.15780	-1.0425	10	0.15499	T	0.54	-20.9559	15.1522	0.72709	0.0:0.732:0.268:0.0	rs16843254;rs16843254	60;54	Q96LB4-4;Q96LB4	.;VATG3_HUMAN	Q	54;60;54;60	ENSP00000356352:E54Q;ENSP00000356351:E60Q;ENSP00000281087:E54Q;ENSP00000417171:E60Q	ENSP00000281087:E54Q	E	-	1	0	ATP6V1G3	196764857	1.000000	0.71417	0.044000	0.18714	0.074000	0.17049	3.337000	0.52120	0.682000	0.31407	-0.127000	0.14921	GAG	C|0.959;G|0.041	0.041	strong		0.323	ATP6V1G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086559.1	NM_133326	
RTP5	285093	hgsc.bcm.edu	37	2	242814778	242814778	+	Silent	SNP	C	C	T	rs7597435	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:242814778C>T	ENST00000343216.3	+	2	1099	c.1071C>T	c.(1069-1071)acC>acT	p.T357T		NM_173821.2	NP_776182.2																					CGGAGCCCACCGATGGCCCTG	0.612													C|||	204	0.0407348	0.1475	0.0101	5008	,	,		19528	0.0		0.002	False		,,,				2504	0.0				p.T357T		Atlas-SNP	.											.	.	.	.	0			c.C1071T						PASS	.	C		534,3442		35,464,1489	29.0	34.0	32.0		1071	-4.3	0.0	2	dbSNP_116	32	3,8279		0,3,4138	no	coding-synonymous	C2orf85	NM_173821.2		35,467,5627	TT,TC,CC		0.0362,13.4306,4.3808		357/573	242814778	537,11721	1988	4141	6129	SO:0001819	synonymous_variant	285093	exon2			GCCCACCGATGGC																												ENST00000343216.3:c.1071C>T	2.37:g.242814778C>T		182.0	0.0	0		198.0	88.0	0.444444	NM_173821		Silent	SNP	ENST00000343216.3	37	CCDS42843.1																																																																																			C|0.963;T|0.037	0.037	strong		0.612	CXXC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322310.1		
REG4	83998	hgsc.bcm.edu	37	1	120341193	120341193	+	Missense_Mutation	SNP	C	C	T	rs75358916	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:120341193C>T	ENST00000354219.1	-	6	775	c.336G>A	c.(334-336)atG>atA	p.M112I	REG4_ENST00000530654.1_Intron|REG4_ENST00000256585.5_Missense_Mutation_p.M112I	NM_001159352.1	NP_001152824.1	Q9BYZ8	REG4_HUMAN	regenerating islet-derived family, member 4	112	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)	heparin binding (GO:0008201)|mannan binding (GO:2001065)			central_nervous_system(1)|large_intestine(1)|lung(8)|ovary(2)|prostate(1)|skin(2)	15	all_cancers(5;4.81e-10)|all_epithelial(5;7.98e-11)|Melanoma(3;1.93e-05)|Breast(55;0.218)|all_neural(166;0.219)	all_lung(203;8.1e-07)|Lung NSC(69;5.89e-06)|all_epithelial(167;0.000959)		Lung(183;0.011)|LUSC - Lung squamous cell carcinoma(189;0.0588)		TGTACAGATACATGGCCCCAT	0.532													C|||	42	0.00838658	0.031	0.0014	5008	,	,		17162	0.0		0.0	False		,,,				2504	0.0				p.M112I		Atlas-SNP	.											.	REG4	36	.	0			c.G336A						PASS	.	C	ILE/MET,ILE/MET	128,4278	93.4+/-132.2	2,124,2077	201.0	185.0	190.0		336,336	-7.1	0.0	1	dbSNP_131	190	0,8600		0,0,4300	yes	missense,missense	REG4	NM_001159352.1,NM_032044.3	10,10	2,124,6377	TT,TC,CC		0.0,2.9051,0.9842	benign,benign	112/159,112/159	120341193	128,12878	2203	4300	6503	SO:0001583	missense	83998	exon5			CAGATACATGGCC	AY007243	CCDS906.1, CCDS53354.1	1p13.1-p12	2008-02-05			ENSG00000134193	ENSG00000134193			22977	protein-coding gene	gene with protein product	"""regenerating gene type IV"", "" gastrointestinal secretory protein"""	609846				11311942, 12455032	Standard	NM_032044		Approved	REG-IV, RELP, GISP	uc001eif.3	Q9BYZ8	OTTHUMG00000012175	ENST00000354219.1:c.336G>A	1.37:g.120341193C>T	ENSP00000346158:p.Met112Ile	203.0	1.0	0.00492611		225.0	120.0	0.533333	NM_032044	Q8NER6|Q8NER7	Missense_Mutation	SNP	ENST00000354219.1	37	CCDS906.1	16	0.007326007326007326	15	0.03048780487804878	1	0.0027624309392265192	0	0.0	0	0.0	C	9.514	1.106451	0.20632	0.029051	0.0	ENSG00000134193	ENST00000354219;ENST00000256585	T;T	0.07216	3.21;3.21	5.02	-7.05	0.01573	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	1.458410	0.04405	N	0.364865	T	0.01156	0.0038	N	0.11756	0.17	0.09310	N	1	B	0.02656	0.0	B	0.11329	0.006	T	0.43523	-0.9386	10	0.32370	T	0.25	0.8924	7.2514	0.26152	0.0:0.1828:0.4589:0.3583	.	112	Q9BYZ8	REG4_HUMAN	I	112	ENSP00000346158:M112I;ENSP00000256585:M112I	ENSP00000256585:M112I	M	-	3	0	REG4	120142716	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.742000	0.01835	-1.675000	0.01459	-0.893000	0.02921	ATG	C|0.991;T|0.009	0.009	strong		0.532	REG4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033675.1	NM_032044	
C19orf45	374877	hgsc.bcm.edu	37	19	7573225	7573225	+	Missense_Mutation	SNP	C	C	T	rs141790796		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:7573225C>T	ENST00000361664.2	+	9	1568	c.1427C>T	c.(1426-1428)cCc>cTc	p.P476L	CTD-2207O23.12_ENST00000599312.1_Intron	NM_198534.2	NP_940936.2	Q8NA69	CS045_HUMAN	chromosome 19 open reading frame 45	476										endometrium(1)|kidney(1)|liver(1)|lung(2)|ovary(2)|stomach(1)	8						GGCTTCGTGCCCCTGGGCACG	0.582																																					p.P476L		Atlas-SNP	.											.	C19orf45	36	.	0			c.C1427T						PASS	.						42.0	41.0	41.0					19																	7573225		2203	4300	6503	SO:0001583	missense	374877	exon9			TCGTGCCCCTGGG	BC029824	CCDS12179.2	19p13.2	2008-02-05			ENSG00000198723	ENSG00000198723			24745	protein-coding gene	gene with protein product						12477932	Standard	NM_198534		Approved	FLJ35784	uc002mgm.2	Q8NA69	OTTHUMG00000157183	ENST00000361664.2:c.1427C>T	19.37:g.7573225C>T	ENSP00000355241:p.Pro476Leu	124.0	0.0	0		139.0	10.0	0.0719424	NM_198534	Q8N115	Missense_Mutation	SNP	ENST00000361664.2	37	CCDS12179.2	.	.	.	.	.	.	.	.	.	.	C	14.42	2.530201	0.45073	.	.	ENSG00000198723	ENST00000361664	T	0.49139	0.79	4.15	3.09	0.35607	.	0.235290	0.36444	N	0.002596	T	0.43211	0.1237	M	0.63843	1.955	0.46798	D	0.999203	P	0.41597	0.756	B	0.39805	0.31	T	0.45702	-0.9243	10	0.87932	D	0	-24.0027	8.3255	0.32153	0.0:0.8889:0.0:0.1111	.	476	Q8NA69	CS045_HUMAN	L	476	ENSP00000355241:P476L	ENSP00000355241:P476L	P	+	2	0	C19orf45	7479225	0.647000	0.27304	0.555000	0.28281	0.064000	0.16182	1.178000	0.31981	1.090000	0.41315	0.462000	0.41574	CCC	C|1.000;A|0.000	.	alt		0.582	C19orf45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347808.1	NM_198534	
C5orf42	65250	hgsc.bcm.edu	37	5	37182940	37182940	+	Silent	SNP	T	T	A	rs73750949	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:37182940T>A	ENST00000508244.1	-	25	5436	c.5343A>T	c.(5341-5343)acA>acT	p.T1781T	C5orf42_ENST00000274258.7_Silent_p.T662T|C5orf42_ENST00000425232.2_Silent_p.T1781T			Q9H799	CE042_HUMAN	chromosome 5 open reading frame 42	1781						integral component of membrane (GO:0016021)				breast(5)|endometrium(3)|kidney(8)|large_intestine(24)|lung(28)|ovary(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	79	all_lung(31;0.000616)		COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.177)|Colorectal(62;0.202)			GAATGGCAGCTGTAGAGGTCT	0.363													T|||	144	0.028754	0.1067	0.0043	5008	,	,		18465	0.0		0.0	False		,,,				2504	0.0				p.T1781T		Atlas-SNP	.											.	C5orf42	422	.	0			c.A5343T						PASS	.	T		416,3990	203.1+/-225.7	20,376,1807	83.0	77.0	79.0		5343	1.2	1.0	5	dbSNP_130	79	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	C5orf42	NM_023073.3		20,377,6106	AA,AT,TT		0.0116,9.4417,3.2062		1781/3198	37182940	417,12589	2203	4300	6503	SO:0001819	synonymous_variant	65250	exon26			GGCAGCTGTAGAG		CCDS34146.1, CCDS34146.2	5p13.2	2014-01-28			ENSG00000197603	ENSG00000197603			25801	protein-coding gene	gene with protein product		614571				22264561	Standard	NM_023073		Approved	FLJ13231, JBTS17	uc011cpa.1	Q9H799	OTTHUMG00000160492	ENST00000508244.1:c.5343A>T	5.37:g.37182940T>A		79.0	0.0	0		78.0	41.0	0.525641	NM_023073	A8MUB7|B7ZLV7|Q4G174|Q6DK46|Q8N8L4|Q9H5T1|Q9H8T9	Silent	SNP	ENST00000508244.1	37	CCDS34146.2																																																																																			T|0.973;A|0.027	0.027	strong		0.363	C5orf42-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360806.1	NM_023073	
TXK	7294	hgsc.bcm.edu	37	4	48096101	48096101	+	Silent	SNP	A	A	G	rs73151620	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:48096101A>G	ENST00000264316.4	-	8	787	c.702T>C	c.(700-702)aaT>aaC	p.N234N	TXK_ENST00000510457.1_5'UTR	NM_003328.2	NP_003319.2	P42681	TXK_HUMAN	TXK tyrosine kinase	234	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				activation of phospholipase C activity (GO:0007202)|adaptive immune response (GO:0002250)|cytokine production (GO:0001816)|interferon-gamma production (GO:0032609)|interleukin-4 production (GO:0032633)|NK T cell differentiation (GO:0001865)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interferon-gamma-mediated signaling pathway (GO:0060335)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|T cell receptor signaling pathway (GO:0050852)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|RNA polymerase II regulatory region DNA binding (GO:0001012)			breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|prostate(2)	25						TACCGGCTGCATTGTGCTGGT	0.473													A|||	174	0.0347444	0.1263	0.0101	5008	,	,		17952	0.0		0.0	False		,,,				2504	0.0				p.N234N		Atlas-SNP	.											.	TXK	58	.	0			c.T702C						PASS	.	A		544,3862	245.6+/-254.5	32,480,1691	131.0	130.0	130.0		702	-9.1	0.2	4	dbSNP_130	130	3,8597	1.2+/-3.3	0,3,4297	no	coding-synonymous	TXK	NM_003328.2		32,483,5988	GG,GA,AA		0.0349,12.3468,4.2058		234/528	48096101	547,12459	2203	4300	6503	SO:0001819	synonymous_variant	7294	exon8			GGCTGCATTGTGC	L27071	CCDS3480.1	4p12	2013-02-14	2003-04-01		ENSG00000074966	ENSG00000074966	2.7.10.1	"""SH2 domain containing"""	12434	protein-coding gene	gene with protein product		600058	"""PTK4 protein tyrosine kinase 4"""	PTK4		7951233, 7528718	Standard	NM_003328		Approved	TKL, PSCTK5, BTKL, RLK	uc003gxx.4	P42681	OTTHUMG00000102065	ENST00000264316.4:c.702T>C	4.37:g.48096101A>G		87.0	0.0	0		92.0	92.0	1	NM_003328	Q14220	Silent	SNP	ENST00000264316.4	37	CCDS3480.1																																																																																			A|0.959;G|0.041	0.041	strong		0.473	TXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219869.7	NM_003328	
CPNE7	27132	hgsc.bcm.edu	37	16	89655120	89655120	+	Missense_Mutation	SNP	G	G	A	rs28568523	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:89655120G>A	ENST00000268720.5	+	12	1320	c.1190G>A	c.(1189-1191)cGg>cAg	p.R397Q	CPNE7_ENST00000319518.8_Missense_Mutation_p.R322Q	NM_014427.4	NP_055242.1	Q9UBL6	CPNE7_HUMAN	copine VII	397	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.		R -> Q (in dbSNP:rs28568523).		lipid metabolic process (GO:0006629)|transport (GO:0006810)	extracellular vesicular exosome (GO:0070062)	transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(8)|ovary(2)	17		all_hematologic(23;0.0748)		all cancers(4;3.63e-08)|OV - Ovarian serous cystadenocarcinoma(4;1.7e-06)|BRCA - Breast invasive adenocarcinoma(80;0.0147)		GGAGACCCGCGGAACAGCTGC	0.647													G|||	28	0.00559105	0.0144	0.0	5008	,	,		15442	0.002		0.007	False		,,,				2504	0.0				p.R397Q		Atlas-SNP	.											.	CPNE7	56	.	0			c.G1190A						PASS	.	G	GLN/ARG,GLN/ARG	43,4353	46.7+/-81.2	0,43,2155	129.0	98.0	108.0		1190,965	3.8	0.8	16	dbSNP_125	108	51,8549	33.3+/-86.6	0,51,4249	yes	missense,missense	CPNE7	NM_014427.4,NM_153636.2	43,43	0,94,6404	AA,AG,GG		0.593,0.9782,0.7233	probably-damaging,probably-damaging	397/634,322/559	89655120	94,12902	2198	4300	6498	SO:0001583	missense	27132	exon12			ACCCGCGGAACAG	AJ133798	CCDS10980.1, CCDS10981.1	16q24.3	2008-07-03			ENSG00000178773	ENSG00000178773			2320	protein-coding gene	gene with protein product		605689					Standard	NM_014427		Approved		uc002fnq.3	Q9UBL6	OTTHUMG00000138051	ENST00000268720.5:c.1190G>A	16.37:g.89655120G>A	ENSP00000268720:p.Arg397Gln	66.0	0.0	0		58.0	41.0	0.706897	NM_014427		Missense_Mutation	SNP	ENST00000268720.5	37	CCDS10980.1	10	0.004578754578754579	3	0.006097560975609756	0	0.0	1	0.0017482517482517483	6	0.0079155672823219	G	18.57	3.653381	0.67472	0.009782	0.00593	ENSG00000178773	ENST00000319518;ENST00000268720;ENST00000529800	T;T;T	0.18174	2.45;2.41;2.23	3.75	3.75	0.43078	von Willebrand factor, type A (2);	0.000000	0.85682	D	0.000000	T	0.18130	0.0435	M	0.64676	1.99	0.49798	D	0.999823	P;P	0.52316	0.907;0.952	P;B	0.46299	0.511;0.259	T	0.06481	-1.0824	10	0.49607	T	0.09	-8.211	15.5036	0.75719	0.0:0.0:1.0:0.0	rs28568523;rs28568523	322;397	Q9UBL6-2;Q9UBL6	.;CPNE7_HUMAN	Q	322;397;42	ENSP00000317374:R322Q;ENSP00000268720:R397Q;ENSP00000435876:R42Q	ENSP00000268720:R397Q	R	+	2	0	CPNE7	88182621	0.993000	0.37304	0.844000	0.33320	0.161000	0.22273	7.195000	0.77798	1.776000	0.52262	0.313000	0.20887	CGG	G|0.992;A|0.008	0.008	strong		0.647	CPNE7-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269929.2		
KIAA1755	85449	hgsc.bcm.edu	37	20	36856579	36856579	+	Silent	SNP	G	G	A	rs74723843	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:36856579G>A	ENST00000279024.4	-	6	2206	c.1935C>T	c.(1933-1935)ccC>ccT	p.P645P		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	645										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				TGACCAGACCGGGCTGTGGGG	0.602													g|||	114	0.0227636	0.0794	0.0101	5008	,	,		17204	0.0		0.0	False		,,,				2504	0.002				p.P645P		Atlas-SNP	.											.	KIAA1755	145	.	0			c.C1935T						PASS	.	G		301,4103	160.0+/-192.4	14,273,1915	36.0	37.0	37.0		1935	-9.6	0.0	20	dbSNP_131	37	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KIAA1755	NM_001029864.1		14,274,6214	AA,AG,GG		0.0116,6.8347,2.3224		645/1201	36856579	302,12702	2202	4300	6502	SO:0001819	synonymous_variant	85449	exon6			CAGACCGGGCTGT	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.1935C>T	20.37:g.36856579G>A		37.0	0.0	0		27.0	12.0	0.444444	NM_001029864	Q9C0A8	Silent	SNP	ENST00000279024.4	37	CCDS33467.1																																																																																			G|0.974;A|0.026	0.026	strong		0.602	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
PCDHB2	56133	hgsc.bcm.edu	37	5	140475958	140475958	+	Silent	SNP	G	G	T	rs371176940	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:140475958G>T	ENST00000194155.4	+	1	1732	c.1584G>T	c.(1582-1584)gcG>gcT	p.A528A		NM_018936.2	NP_061759.1	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2	528	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(22)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCCTGCAGGCGTTCGAGTTCC	0.706													g|||	5	0.000998403	0.0	0.0	5008	,	,		15707	0.0		0.0	False		,,,				2504	0.0051				p.A528A		Atlas-SNP	.											.	PCDHB2	163	.	0			c.G1584T						PASS	.						68.0	75.0	73.0					5																	140475958		2203	4299	6502	SO:0001819	synonymous_variant	56133	exon1			GCAGGCGTTCGAG	AF152495	CCDS4244.1	5q31	2010-01-26			ENSG00000112852	ENSG00000112852		"""Cadherins / Protocadherins : Clustered"""	8687	other	protocadherin		606328				10380929	Standard	NM_018936		Approved	PCDH-BETA2	uc003lil.3	Q9Y5E7	OTTHUMG00000129606	ENST00000194155.4:c.1584G>T	5.37:g.140475958G>T		209.0	0.0	0		205.0	10.0	0.0487805	NM_018936	Q4KMU1	Silent	SNP	ENST00000194155.4	37	CCDS4244.1																																																																																			.	.	alt		0.706	PCDHB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251801.2	NM_018936	
CC2D2B	387707	hgsc.bcm.edu	37	10	97779510	97779510	+	Missense_Mutation	SNP	T	T	C	rs9943393	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:97779510T>C	ENST00000344386.3	+	8	873	c.709T>C	c.(709-711)Tat>Cat	p.Y237H	ENTPD1-AS1_ENST00000416301.1_RNA|RP11-690P14.4_ENST00000475252.2_Intron|ENTPD1-AS1_ENST00000458228.1_RNA|CC2D2B_ENST00000371198.2_Intron|ENTPD1-AS1_ENST00000452728.1_RNA|ENTPD1-AS1_ENST00000454638.1_RNA|ENTPD1-AS1_ENST00000449197.1_RNA|ENTPD1-AS1_ENST00000451364.1_RNA|CC2D2B_ENST00000410012.2_Missense_Mutation_p.Y237H	NM_001001732.3	NP_001001732.2	Q6DHV5	C2D2B_HUMAN	coiled-coil and C2 domain containing 2B	237			Y -> H (in dbSNP:rs9943393).							large_intestine(1)|lung(7)|ovary(1)|urinary_tract(1)	10		Colorectal(252;0.158)		Epithelial(162;7.08e-08)|all cancers(201;2.71e-06)		ATTTTTTGACTATTCAAAGGA	0.338													T|||	67	0.0133786	0.0477	0.0043	5008	,	,		17685	0.0		0.001	False		,,,				2504	0.0				p.Y237H		Atlas-SNP	.											.	CC2D2B	46	.	0			c.T709C						PASS	.	T	HIS/TYR,HIS/TYR	124,3472		7,110,1681	105.0	107.0	106.0		709,709	3.7	1.0	10	dbSNP_119	106	3,8137		0,3,4067	yes	missense,missense	CC2D2B	NM_001001732.3,NM_001159747.1	83,83	7,113,5748	CC,CT,TT		0.0369,3.4483,1.0821	possibly-damaging,possibly-damaging	237/323,237/402	97779510	127,11609	1798	4070	5868	SO:0001583	missense	387707	exon8			TTTGACTATTCAA	BC075861	CCDS41555.1, CCDS53560.1	10q23.33	2008-11-06	2007-10-19	2007-10-19	ENSG00000188649	ENSG00000188649			31666	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 130"""	C10orf130			Standard	NM_001001732		Approved	bA248J23.4	uc010qop.2	Q6DHV5	OTTHUMG00000018820	ENST00000344386.3:c.709T>C	10.37:g.97779510T>C	ENSP00000343747:p.Tyr237His	271.0	0.0	0		288.0	127.0	0.440972	NM_001001732	A2A3E9|B4DYD4|E9PCC3|Q5VUS0	Missense_Mutation	SNP	ENST00000344386.3	37	CCDS41555.1	24	0.01098901098901099	23	0.046747967479674794	1	0.0027624309392265192	0	0.0	0	0.0	T	14.01	2.407470	0.42715	0.034483	3.69E-4	ENSG00000188649	ENST00000451649;ENST00000410012;ENST00000344386	T;T	0.70399	-0.48;-0.48	4.93	3.73	0.42828	.	.	.	.	.	T	0.22166	0.0534	L	0.44542	1.39	0.26525	N	0.974358	P;B	0.44195	0.828;0.392	B;B	0.42593	0.392;0.141	T	0.31194	-0.9952	9	0.39692	T	0.17	.	7.3082	0.26459	0.2619:0.0:0.0:0.7381	rs9943393;rs9943393	237;237	E9PCC3;Q6DHV5	.;C2D2B_HUMAN	H	237	ENSP00000386988:Y237H;ENSP00000343747:Y237H	ENSP00000343747:Y237H	Y	+	1	0	CC2D2B	97769500	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	2.130000	0.42064	2.072000	0.62099	0.454000	0.30748	TAT	T|0.988;C|0.012	0.012	strong		0.338	CC2D2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049573.3	NM_001001732	
GLIS1	148979	hgsc.bcm.edu	37	1	54060107	54060107	+	Missense_Mutation	SNP	A	A	G	rs34961060	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:54060107A>G	ENST00000312233.2	-	3	1035	c.469T>C	c.(469-471)Ttt>Ctt	p.F157L		NM_147193.2	NP_671726.2			GLIS family zinc finger 1											endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|skin(3)|urinary_tract(4)	24						TGAGGCCCAAAGAGCTCTGAA	0.657													A|||	183	0.0365415	0.1362	0.0029	5008	,	,		14987	0.0		0.001	False		,,,				2504	0.0				p.F157L		Atlas-SNP	.											.	GLIS1	52	.	0			c.T469C						PASS	.	A	LEU/PHE	429,3963		23,383,1790	15.0	18.0	17.0		469	2.4	0.8	1	dbSNP_126	17	4,8562		0,4,4279	yes	missense	GLIS1	NM_147193.2	22	23,387,6069	GG,GA,AA		0.0467,9.7678,3.3416	possibly-damaging	157/621	54060107	433,12525	2196	4283	6479	SO:0001583	missense	148979	exon3			GCCCAAAGAGCTC	AK093474	CCDS582.1	1p32.3	2008-02-05			ENSG00000174332	ENSG00000174332		"""Zinc fingers, C2H2-type"""	29525	protein-coding gene	gene with protein product		610378				12042312, 14500813	Standard	NM_147193		Approved	FLJ36155	uc001cvr.1	Q8NBF1	OTTHUMG00000008079	ENST00000312233.2:c.469T>C	1.37:g.54060107A>G	ENSP00000309653:p.Phe157Leu	68.0	0.0	0		63.0	31.0	0.492063	NM_147193		Missense_Mutation	SNP	ENST00000312233.2	37	CCDS582.1	79	0.036172161172161175	77	0.1565040650406504	2	0.0055248618784530384	0	0.0	0	0.0	A	16.69	3.192807	0.58017	0.097678	4.67E-4	ENSG00000174332	ENST00000312233	T	0.10573	2.86	5.07	2.43	0.29744	.	0.105911	0.41605	N	0.000847	T	0.00039	0.0001	L	0.29908	0.895	0.80722	P	0.0	B	0.06786	0.001	B	0.08055	0.003	T	0.39313	-0.9620	9	0.02654	T	1	.	7.8454	0.29422	0.7801:0.0:0.2199:0.0	rs34961060	157	Q8NBF1	GLIS1_HUMAN	L	157	ENSP00000309653:F157L	ENSP00000309653:F157L	F	-	1	0	GLIS1	53832695	1.000000	0.71417	0.814000	0.32528	0.822000	0.46500	2.049000	0.41288	0.888000	0.36160	0.379000	0.24179	TTT	A|0.968;G|0.032	0.032	strong		0.657	GLIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022109.1	NM_147193	
DNAJC17	55192	hgsc.bcm.edu	37	15	41068409	41068409	+	Missense_Mutation	SNP	C	C	T	rs73398528	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:41068409C>T	ENST00000220496.4	-	6	493	c.463G>A	c.(463-465)Gac>Aac	p.D155N		NM_018163.2	NP_060633.1	Q9NVM6	DJC17_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 17	155					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)		nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			endometrium(1)|kidney(1)|large_intestine(2)|pancreas(1)|skin(1)	6		all_cancers(109;4.16e-14)|all_epithelial(112;9.68e-12)|Lung NSC(122;3.19e-09)|all_lung(180;6.45e-08)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.91e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		AACCTCTGGTCACGCTCCTGG	0.622													C|||	294	0.0587061	0.2141	0.0144	5008	,	,		16797	0.001		0.0	False		,,,				2504	0.0				p.D155N		Atlas-SNP	.											.	DNAJC17	18	.	0			c.G463A						PASS	.	C	ASN/ASP	781,3625	315.2+/-294.0	55,671,1477	104.0	84.0	91.0		463	4.4	0.3	15	dbSNP_130	91	3,8597	2.2+/-6.3	0,3,4297	yes	missense	DNAJC17	NM_018163.2	23	55,674,5774	TT,TC,CC		0.0349,17.7258,6.028	benign	155/305	41068409	784,12222	2203	4300	6503	SO:0001583	missense	55192	exon6			TCTGGTCACGCTC	AK001496	CCDS10065.1	15q15.1	2014-02-12			ENSG00000104129	ENSG00000104129		"""Heat shock proteins / DNAJ (HSP40)"", ""RNA binding motif (RRM) containing"""	25556	protein-coding gene	gene with protein product						12477932	Standard	NM_018163		Approved	FLJ10634	uc001zms.2	Q9NVM6	OTTHUMG00000130065	ENST00000220496.4:c.463G>A	15.37:g.41068409C>T	ENSP00000220496:p.Asp155Asn	88.0	0.0	0		103.0	46.0	0.446602	NM_018163		Missense_Mutation	SNP	ENST00000220496.4	37	CCDS10065.1	103	0.04716117216117216	95	0.19308943089430894	7	0.019337016574585635	1	0.0017482517482517483	0	0.0	C	6.900	0.535565	0.13188	0.177258	3.49E-4	ENSG00000104129	ENST00000220496	T	0.18338	2.22	4.41	4.41	0.53225	.	0.289804	0.36444	N	0.002600	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.38394	-0.9663	9	0.21540	T	0.41	.	13.7416	0.62852	0.0:0.8449:0.1551:0.0	.	155	Q9NVM6	DJC17_HUMAN	N	155	ENSP00000220496:D155N	ENSP00000220496:D155N	D	-	1	0	DNAJC17	38855701	0.959000	0.32827	0.332000	0.25469	0.105000	0.19272	3.571000	0.53841	2.300000	0.77407	0.561000	0.74099	GAC	C|0.947;T|0.053	0.053	strong		0.622	DNAJC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252356.2	NM_018163	
SMYD2	56950	hgsc.bcm.edu	37	1	214507580	214507580	+	Missense_Mutation	SNP	A	A	G	rs34259050	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:214507580A>G	ENST00000366957.5	+	11	1172	c.1150A>G	c.(1150-1152)Atg>Gtg	p.M384V	SMYD2_ENST00000491455.1_3'UTR|SMYD2_ENST00000415093.2_3'UTR	NM_020197.2	NP_064582.2	Q9NRG4	SMYD2_HUMAN	SET and MYND domain containing 2	384					negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	histone methyltransferase activity (H3-K36 specific) (GO:0046975)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|RNA polymerase II core binding (GO:0000993)			breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(81;0.0122)|all cancers(67;0.0209)|GBM - Glioblastoma multiforme(131;0.106)|Epithelial(68;0.144)		CGTGGCCTCCATGTGGTTGAA	0.542													A|||	54	0.0107827	0.0098	0.0115	5008	,	,		20709	0.001		0.0209	False		,,,				2504	0.0112				p.M384V		Atlas-SNP	.											.	SMYD2	40	.	0			c.A1150G						PASS	.	A	VAL/MET	31,4375	36.0+/-67.5	0,31,2172	241.0	230.0	234.0		1150	5.1	1.0	1	dbSNP_126	234	199,8401	87.1+/-149.5	2,195,4103	yes	missense	SMYD2	NM_020197.2	21	2,226,6275	GG,GA,AA		2.314,0.7036,1.7684	benign	384/434	214507580	230,12776	2203	4300	6503	SO:0001583	missense	56950	exon11			GCCTCCATGTGGT	AF226053	CCDS31022.1	1q32.3	2011-07-01			ENSG00000143499	ENSG00000143499		"""Zinc fingers, MYND-type"", ""Chromatin-modifying enzymes / K-methyltransferases"""	20982	protein-coding gene	gene with protein product		610663					Standard	NM_020197		Approved	HSKM-B, ZMYND14, KMT3C	uc021pix.1	Q9NRG4	OTTHUMG00000037066	ENST00000366957.5:c.1150A>G	1.37:g.214507580A>G	ENSP00000355924:p.Met384Val	133.0	0.0	0		179.0	86.0	0.480447	NM_020197	B2R9P9|I6L9H7|Q4V765|Q5VSH9|Q96AI4	Missense_Mutation	SNP	ENST00000366957.5	37	CCDS31022.1	22	0.010073260073260074	4	0.008130081300813009	5	0.013812154696132596	1	0.0017482517482517483	12	0.0158311345646438	A	14.03	2.413182	0.42817	0.007036	0.02314	ENSG00000143499	ENST00000366957	T	0.61392	0.11	6.17	5.05	0.67936	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	T	0.30572	0.0769	L	0.48362	1.52	0.80722	D	1	B	0.26512	0.151	B	0.17979	0.02	T	0.21143	-1.0254	10	0.14656	T	0.56	-5.5028	12.297	0.54854	0.9345:0.0:0.0655:0.0	rs34259050	384	Q9NRG4	SMYD2_HUMAN	V	384	ENSP00000355924:M384V	ENSP00000355924:M384V	M	+	1	0	SMYD2	212574203	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	2.874000	0.48483	1.158000	0.42547	0.533000	0.62120	ATG	A|0.983;G|0.017	0.017	strong		0.542	SMYD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089998.1	NM_020197	
COL1A1	1277	hgsc.bcm.edu	37	17	48263786	48263786	+	Silent	SNP	G	G	A	rs34940368	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:48263786G>A	ENST00000225964.5	-	49	4015	c.3897C>T	c.(3895-3897)tgC>tgT	p.C1299C		NM_000088.3	NP_000079	P02452	CO1A1_HUMAN	collagen, type I, alpha 1	1299	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				blood coagulation (GO:0007596)|blood vessel development (GO:0001568)|bone trabecula formation (GO:0060346)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|cellular response to amino acid stimulus (GO:0071230)|cellular response to mechanical stimulus (GO:0071260)|cellular response to retinoic acid (GO:0071300)|cellular response to transforming growth factor beta stimulus (GO:0071560)|collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|embryonic skeletal system development (GO:0048706)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|intramembranous ossification (GO:0001957)|leukocyte migration (GO:0050900)|negative regulation of cell-substrate adhesion (GO:0010812)|osteoblast differentiation (GO:0001649)|platelet activation (GO:0030168)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterotrimerization (GO:0070208)|protein localization to nucleus (GO:0034504)|protein transport (GO:0015031)|response to cAMP (GO:0051591)|response to corticosteroid (GO:0031960)|response to estradiol (GO:0032355)|response to hydrogen peroxide (GO:0042542)|response to nutrient (GO:0007584)|response to peptide hormone (GO:0043434)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|skin morphogenesis (GO:0043589)|tooth mineralization (GO:0034505)|visual perception (GO:0007601)	collagen type I trimer (GO:0005584)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)		COL1A1/PDGFB(429)	NS(1)|breast(3)|central_nervous_system(8)|endometrium(3)|kidney(4)|large_intestine(17)|liver(3)|lung(18)|ovary(1)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	71					Collagenase(DB00048)	TGGGGTACACGCAGGTCTCAC	0.562			T	"""PDGFB, USP6"""	"""dermatofibrosarcoma protuberans, aneurysmal bone cyst """		Osteogenesis imperfecta						G|||	32	0.00638978	0.0227	0.0029	5008	,	,		22768	0.0		0.0	False		,,,				2504	0.0				p.C1299C		Atlas-SNP	.		Dom	yes		17	17q21.31-q22	1277	"""collagen, type I, alpha 1"""	yes	M	COL1A1,rectum,carcinoma,0,1	COL1A1	158	1	0			c.C3897T	GRCh37	CM012085	COL1A1	M	rs34940368	scavenged	.	G		75,4331	66.4+/-103.9	0,75,2128	160.0	143.0	149.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	3897	-0.3	1.0	17	dbSNP_126	149	0,8600		0,0,4300	no	coding-synonymous	COL1A1	NM_000088.3		0,75,6428	AA,AG,GG		0.0,1.7022,0.5767		1299/1465	48263786	75,12931	2203	4300	6503	SO:0001819	synonymous_variant	1277	exon49			GTACACGCAGGTC	Z74615	CCDS11561.1	17q21.33	2014-09-17			ENSG00000108821	ENSG00000108821		"""Collagens"""	2197	protein-coding gene	gene with protein product		120150				3178743, 2857713	Standard	NM_000088		Approved	OI4	uc002iqm.3	P02452	OTTHUMG00000148674	ENST00000225964.5:c.3897C>T	17.37:g.48263786G>A		134.0	1.0	0.00746269		141.0	63.0	0.446809	NM_000088	O76045|P78441|Q13896|Q13902|Q13903|Q14037|Q14992|Q15176|Q15201|Q16050|Q59F64|Q7KZ30|Q7KZ34|Q8IVI5|Q8N473|Q9UML6|Q9UMM7	Silent	SNP	ENST00000225964.5	37	CCDS11561.1																																																																																			G|0.994;A|0.006	0.006	strong		0.562	COL1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309036.2		
EPC2	26122	hgsc.bcm.edu	37	2	149528738	149528738	+	Missense_Mutation	SNP	A	A	G	rs34444151	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:149528738A>G	ENST00000258484.6	+	10	1536	c.1502A>G	c.(1501-1503)aAt>aGt	p.N501S		NM_015630.3	NP_056445.3	Q52LR7	EPC2_HUMAN	enhancer of polycomb homolog 2 (Drosophila)	501					chromatin modification (GO:0016568)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Piccolo NuA4 histone acetyltransferase complex (GO:0032777)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.0516)		TCTCGGACCAATGCTTCCAGT	0.378													A|||	43	0.00858626	0.0265	0.0029	5008	,	,		19522	0.0		0.0	False		,,,				2504	0.0061				p.N501S		Atlas-SNP	.											.	EPC2	57	.	0			c.A1502G						PASS	.	A	SER/ASN	71,3607		1,69,1769	55.0	54.0	54.0		1502	5.4	1.0	2	dbSNP_126	54	4,8166		0,4,4081	yes	missense	EPC2	NM_015630.3	46	1,73,5850	GG,GA,AA		0.049,1.9304,0.633	benign	501/808	149528738	75,11773	1839	4085	5924	SO:0001583	missense	26122	exon10			GGACCAATGCTTC	AF286904	CCDS46422.1	2q23	2008-02-05			ENSG00000135999	ENSG00000135999			24543	protein-coding gene	gene with protein product		611000					Standard	NM_015630		Approved	DKFZP566F2124	uc010zbt.2	Q52LR7	OTTHUMG00000153739	ENST00000258484.6:c.1502A>G	2.37:g.149528738A>G	ENSP00000258484:p.Asn501Ser	216.0	0.0	0		181.0	96.0	0.530387	NM_015630	B3KWT7|D3DP89|Q7L9J1|Q96RR7|Q9NUT8|Q9NVR1|Q9UFM9	Missense_Mutation	SNP	ENST00000258484.6	37	CCDS46422.1	18	0.008241758241758242	17	0.034552845528455285	1	0.0027624309392265192	0	0.0	0	0.0	A	14.04	2.415328	0.42817	0.019304	4.9E-4	ENSG00000135999	ENST00000258484	T	0.16324	2.35	5.36	5.36	0.76844	.	0.097920	0.64402	D	0.000002	T	0.05777	0.0151	L	0.40543	1.245	0.80722	D	1	B	0.25521	0.128	B	0.23018	0.043	T	0.01863	-1.1258	10	0.54805	T	0.06	-4.6206	15.6403	0.76993	1.0:0.0:0.0:0.0	rs34444151	501	Q52LR7	EPC2_HUMAN	S	501	ENSP00000258484:N501S	ENSP00000258484:N501S	N	+	2	0	EPC2	149245208	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.325000	0.59234	2.140000	0.66376	0.460000	0.39030	AAT	A|0.992;G|0.008	0.008	strong		0.378	EPC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332278.1	NM_015630	
TRIM72	493829	hgsc.bcm.edu	37	16	31235548	31235548	+	Silent	SNP	G	G	C	rs58585879	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31235548G>C	ENST00000322122.3	+	7	1190	c.906G>C	c.(904-906)ctG>ctC	p.L302L	RP11-388M20.9_ENST00000576745.1_lincRNA	NM_001008274.3	NP_001008275.2			tripartite motif containing 72, E3 ubiquitin protein ligase											breast(1)|endometrium(2)|large_intestine(2)|lung(9)|skin(1)	15						ACCCGAGCCTGGTGGTGTCTT	0.677													G|||	154	0.0307508	0.1067	0.0086	5008	,	,		12224	0.0		0.002	False		,,,				2504	0.0051				p.L302L		Atlas-SNP	.											.	TRIM72	32	.	0			c.G906C						PASS	.	G		414,3970		20,374,1798	22.0	23.0	23.0		906	2.3	1.0	16	dbSNP_129	23	6,8568		0,6,4281	no	coding-synonymous	TRIM72	NM_001008274.3		20,380,6079	CC,CG,GG		0.07,9.4434,3.2412		302/478	31235548	420,12538	2192	4287	6479	SO:0001819	synonymous_variant	493829	exon7			GAGCCTGGTGGTG	AK090695	CCDS32437.1	16p11.2	2014-02-10	2014-02-10					"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	32671	protein-coding gene	gene with protein product	"""mitsugumin 53"""	613288	"""tripartite motif-containing 72"", ""tripartite motif containing 72"""			20399744, 23354051	Standard	NM_001008274		Approved	MG53	uc002ebn.2	Q6ZMU5		ENST00000322122.3:c.906G>C	16.37:g.31235548G>C		25.0	0.0	0		33.0	10.0	0.30303	NM_001008274		Silent	SNP	ENST00000322122.3	37	CCDS32437.1																																																																																			G|0.966;C|0.034	0.034	strong		0.677	TRIM72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433567.1	NM_001008274	
KCNQ1	3784	hgsc.bcm.edu	37	11	2683252	2683252	+	Silent	SNP	C	C	T	rs17215465	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:2683252C>T	ENST00000155840.5	+	11	1563	c.1455C>T	c.(1453-1455)ttC>ttT	p.F485F	KCNQ1_ENST00000335475.5_Silent_p.F358F|KCNQ1OT1_ENST00000597346.1_RNA	NM_000218.2	NP_000209.2	P51787	KCNQ1_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 1	485					atrial cardiac muscle cell action potential (GO:0086014)|cardiac muscle contraction (GO:0060048)|cardiovascular system development (GO:0072358)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|gene silencing (GO:0016458)|male gonad development (GO:0008584)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of insulin secretion (GO:0046676)|positive regulation of gastric acid secretion (GO:0060454)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of heart contraction (GO:0008016)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of membrane repolarization (GO:0060306)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	basolateral plasma membrane (GO:0016323)|early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated potassium channel complex (GO:0008076)|zymogen granule membrane (GO:0042589)	calmodulin binding (GO:0005516)|delayed rectifier potassium channel activity (GO:0005251)|ion channel binding (GO:0044325)|outward rectifier potassium channel activity (GO:0015271)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|protein phosphatase 1 binding (GO:0008157)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)|voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization (GO:0086008)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)	21		all_epithelial(84;3.26e-05)|Breast(177;0.001)|Medulloblastoma(188;0.00111)|Ovarian(85;0.00158)|all_neural(188;0.00725)|all_lung(207;0.11)|Lung NSC(207;0.159)		BRCA - Breast invasive adenocarcinoma(625;0.00251)|Lung(200;0.131)	Bepridil(DB01244)|Indapamide(DB00808)	CCAACAGCTTCGCCGAGGACC	0.577													C|||	78	0.0155751	0.0514	0.0029	5008	,	,		17275	0.0		0.001	False		,,,				2504	0.0072				p.F485F		Atlas-SNP	.											.	KCNQ1	60	.	0			c.C1455T						PASS	.	C	,	211,4193	128.6+/-165.4	4,203,1995	170.0	158.0	162.0		1455,1074	-5.4	0.0	11	dbSNP_125	162	7,8591	5.0+/-18.6	0,7,4292	no	coding-synonymous,coding-synonymous	KCNQ1	NM_000218.2,NM_181798.1	,	4,210,6287	TT,TC,CC		0.0814,4.7911,1.6767	,	485/677,358/550	2683252	218,12784	2202	4299	6501	SO:0001819	synonymous_variant	3784	exon11			CAGCTTCGCCGAG	AF000571	CCDS7736.1	11p15.5	2014-09-17			ENSG00000053918	ENSG00000053918		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6294	protein-coding gene	gene with protein product	"""Jervell and Lange-Nielsen syndrome 1"""	607542		LQT, KCNA9		8528244, 16382104	Standard	NM_181798		Approved	Kv7.1, KCNA8, KVLQT1, JLNS1, LQT1	uc001lwn.3	P51787	OTTHUMG00000009900	ENST00000155840.5:c.1455C>T	11.37:g.2683252C>T		133.0	0.0	0		150.0	83.0	0.553333	NM_000218	O00347|O60607|O94787|Q14D14|Q7Z6G9|Q92960|Q9UMN8|Q9UMN9	Silent	SNP	ENST00000155840.5	37	CCDS7736.1																																																																																			C|0.983;T|0.017	0.017	strong		0.577	KCNQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027382.2	NM_000218	
ZNF708	7562	hgsc.bcm.edu	37	19	21476912	21476912	+	Missense_Mutation	SNP	C	C	T	rs112819776	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:21476912C>T	ENST00000356929.3	-	4	1053	c.856G>A	c.(856-858)Ggc>Agc	p.G286S		NM_021269.2	NP_067092.2	P17019	ZN708_HUMAN	zinc finger protein 708	222					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.G286C(1)		breast(1)|central_nervous_system(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(9)|ovary(2)|skin(2)|stomach(1)	32						AAAGCTTTGCCACATTCTTCA	0.383													C|||	27	0.00539137	0.0197	0.0014	5008	,	,		20573	0.0		0.0	False		,,,				2504	0.0				p.G286S		Atlas-SNP	.											ZNF708,NS,carcinoma,0,1	ZNF708	66	1	1	Substitution - Missense(1)	lung(1)	c.G856A						PASS	.	C	SER/GLY	64,4332		0,64,2134	51.0	55.0	54.0		856	1.0	0.6	19	dbSNP_132	54	1,8595		0,1,4297	no	missense	ZNF708	NM_021269.2	56	0,65,6431	TT,TC,CC		0.0116,1.4559,0.5003	possibly-damaging	286/564	21476912	65,12927	2198	4298	6496	SO:0001583	missense	7562	exon4			CTTTGCCACATTC	X52339	CCDS32980.1	19p12	2014-02-14	2006-08-22	2005-08-16	ENSG00000182141	ENSG00000182141		"""Zinc fingers, C2H2-type"", ""-"""	12945	protein-coding gene	gene with protein product			"""zinc finger protein 15-like 1 (KOX 8)"", ""zinc finger protein 708"", ""zinc finger protein 708 (KOX8)"""	ZNF15, ZNF15L1		2014798	Standard	NM_021269		Approved	KOX8	uc002npq.1	P17019	OTTHUMG00000182841	ENST00000356929.3:c.856G>A	19.37:g.21476912C>T	ENSP00000349401:p.Gly286Ser	31.0	0.0	0		23.0	9.0	0.391304	NM_021269	Q6ZMR0	Missense_Mutation	SNP	ENST00000356929.3	37	CCDS32980.1	13	0.005952380952380952	13	0.026422764227642278	0	0.0	0	0.0	0	0.0	.	13.82	2.351563	0.41700	0.014559	1.16E-4	ENSG00000182141	ENST00000356929	T	0.01455	4.87	1.05	1.05	0.20165	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01558	0.0050	L	0.43701	1.375	0.35437	D	0.794531	D	0.76494	0.999	D	0.81914	0.995	T	0.45614	-0.9249	9	0.62326	D	0.03	.	8.9689	0.35894	0.0:1.0:0.0:0.0	.	286	P17019	ZN708_HUMAN	S	286	ENSP00000349401:G286S	ENSP00000349401:G286S	G	-	1	0	ZNF708	21268752	0.049000	0.20398	0.552000	0.28243	0.491000	0.33493	0.979000	0.29500	0.482000	0.27582	0.485000	0.47835	GGC	C|0.994;T|0.006	0.006	strong		0.383	ZNF708-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463953.1	NM_021269	
DNAH14	127602	hgsc.bcm.edu	37	1	225393828	225393828	+	Missense_Mutation	SNP	A	A	G	rs143058170	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:225393828A>G	ENST00000445597.2	+	27	4852	c.4852A>G	c.(4852-4854)Aat>Gat	p.N1618D	DNAH14_ENST00000439375.2_Missense_Mutation_p.N2023D|DNAH14_ENST00000430092.1_Missense_Mutation_p.N2023D			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	1618					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						TGAAGTGGACAATCTCTCTCA	0.363													a|||	28	0.00559105	0.0204	0.0014	5008	,	,		16357	0.0		0.0	False		,,,				2504	0.0				p.N2023D		Atlas-SNP	.											.	DNAH14	300	.	0			c.A6067G						PASS	.	A	ASP/ASN	41,1343		0,41,651	74.0	68.0	70.0		6067	4.4	0.3	1	dbSNP_134	70	0,3182		0,0,1591	no	missense	DNAH14	NM_001373.1	23	0,41,2242	GG,GA,AA		0.0,2.9624,0.8979	benign	2023/4516	225393828	41,4525	692	1591	2283	SO:0001583	missense	127602	exon39			GTGGACAATCTCT	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.4852A>G	1.37:g.225393828A>G	ENSP00000409472:p.Asn1618Asp	62.0	0.0	0		48.0	19.0	0.395833	NM_001373	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		15	0.006868131868131868	15	0.03048780487804878	0	0.0	0	0.0	0	0.0	A	6.311	0.425409	0.11987	0.029624	0.0	ENSG00000185842	ENST00000445597;ENST00000430092;ENST00000439375	D;D;D	0.82893	-1.66;-1.66;-1.66	5.59	4.44	0.53790	.	.	.	.	.	T	0.35393	0.0930	N	0.03917	-0.325	0.80722	D	1	B	0.11235	0.004	B	0.16289	0.015	T	0.50021	-0.8876	9	0.02654	T	1	.	11.2778	0.49176	0.8633:0.0:0.0:0.1367	.	2023	Q0VDD8-4	.	D	1618;2023;2023	ENSP00000409472:N1618D;ENSP00000414402:N2023D;ENSP00000392061:N2023D	ENSP00000414402:N2023D	N	+	1	0	DNAH14	223460451	0.983000	0.35010	0.324000	0.25361	0.992000	0.81027	2.175000	0.42491	0.907000	0.36646	0.481000	0.45027	AAT	A|0.993;G|0.007	0.007	strong		0.363	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
ATP11AUN	400165	hgsc.bcm.edu	37	13	113333809	113333809	+	Missense_Mutation	SNP	G	G	A	rs114091399	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:113333809G>A	ENST00000356049.1	+	2	874	c.116G>A	c.(115-117)gGt>gAt	p.G39D		NM_207440.1	NP_997323.1	Q6ZP68	ATPUN_HUMAN		39										breast(1)|lung(2)|ovary(1)|prostate(1)	5	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)		all cancers(43;0.201)			GACCCGGCAGGTCTGGAGGGA	0.602													G|||	71	0.0141773	0.0507	0.0058	5008	,	,		14668	0.0		0.0	False		,,,				2504	0.0				p.G39D		Atlas-SNP	.											.	C13orf35	13	.	0			c.G116A						PASS	.	G	ASP/GLY	194,4212	122.5+/-159.9	3,188,2012	38.0	40.0	40.0		116	-0.7	0.0	13	dbSNP_132	40	9,8591	7.1+/-27.0	0,9,4291	yes	missense	C13orf35	NM_207440.1	94	3,197,6303	AA,AG,GG		0.1047,4.4031,1.5608	benign	39/122	113333809	203,12803	2203	4300	6503	SO:0001583	missense	400165	exon2			CGGCAGGTCTGGA																												ENST00000356049.1:c.116G>A	13.37:g.113333809G>A	ENSP00000348337:p.Gly39Asp	94.0	0.0	0		108.0	51.0	0.472222	NM_207440		Missense_Mutation	SNP	ENST00000356049.1	37	CCDS9526.1	25	0.011446886446886446	22	0.044715447154471545	3	0.008287292817679558	0	0.0	0	0.0	G	2.915	-0.224514	0.06061	0.044031	0.001047	ENSG00000197595	ENST00000356049	.	.	.	1.24	-0.688	0.11317	.	.	.	.	.	T	0.03390	0.0098	N	0.08118	0	0.09310	N	1	D	0.54601	0.967	P	0.46629	0.522	T	0.07597	-1.0764	8	0.87932	D	0	.	1.9567	0.03378	0.2212:0.0:0.4635:0.3153	.	39	Q6ZP68	CM035_HUMAN	D	39	.	ENSP00000348337:G39D	G	+	2	0	C13orf35	112381810	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-1.464000	0.02359	-0.287000	0.09064	-0.372000	0.07161	GGT	G|0.985;A|0.015	0.015	strong		0.602	C13orf35-001	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000126522.2		
CAPN12	147968	hgsc.bcm.edu	37	19	39227889	39227889	+	Silent	SNP	C	C	T	rs202082771	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39227889C>T	ENST00000328867.4	-	10	1577	c.1269G>A	c.(1267-1269)aaG>aaA	p.K423K	CAPN12_ENST00000601953.1_Silent_p.K274K|CTD-2540F13.2_ENST00000602255.1_RNA	NM_144691.3	NP_653292.2	Q6ZSI9	CAN12_HUMAN	calpain 12	423	Domain III.				proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(60;2.87e-05)|Ovarian(47;0.0454)		Lung(45;0.00416)|LUSC - Lung squamous cell carcinoma(53;0.00741)			GGACCGTGCACTTGGGCGTGC	0.692													C|||	11	0.00219649	0.0083	0.0	5008	,	,		5252	0.0		0.0	False		,,,				2504	0.0				p.K423K		Atlas-SNP	.											.	CAPN12	43	.	0			c.G1269A						PASS	.	C		14,4130		0,14,2058	15.0	13.0	14.0		1269	0.4	1.0	19		14	0,8264		0,0,4132	yes	coding-synonymous	CAPN12	NM_144691.3		0,14,6190	TT,TC,CC		0.0,0.3378,0.1128		423/720	39227889	14,12394	2072	4132	6204	SO:0001819	synonymous_variant	147968	exon10			CGTGCACTTGGGC	BC014027	CCDS12519.1	19q13.2	2014-08-12			ENSG00000182472	ENSG00000182472		"""EF-hand domain containing"""	13249	protein-coding gene	gene with protein product		608839					Standard	NM_144691		Approved		uc002ojd.1	Q6ZSI9	OTTHUMG00000182525	ENST00000328867.4:c.1269G>A	19.37:g.39227889C>T		28.0	0.0	0		35.0	20.0	0.571429	NM_144691		Silent	SNP	ENST00000328867.4	37	CCDS12519.1																																																																																			.	.	weak		0.692	CAPN12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462151.1		
BHLHB9	80823	hgsc.bcm.edu	37	X	102005371	102005371	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102005371A>T	ENST00000372735.1	+	4	2033	c.1448A>T	c.(1447-1449)aAt>aTt	p.N483I	BHLHB9_ENST00000447531.1_Missense_Mutation_p.N483I|BHLHB9_ENST00000361229.4_Missense_Mutation_p.N483I|BHLHB9_ENST00000457056.1_Missense_Mutation_p.N483I|BHLHB9_ENST00000448867.1_Missense_Mutation_p.N483I			Q6PI77	BHLH9_HUMAN	basic helix-loop-helix domain containing, class B, 9	483					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						GACATGATCAATATGAAGGCA	0.363																																					p.N483I		Atlas-SNP	.											.	BHLHB9	60	.	0			c.A1448T						PASS	.						120.0	119.0	119.0					X																	102005371		2203	4300	6503	SO:0001583	missense	80823	exon2			TGATCAATATGAA	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.1448A>T	X.37:g.102005371A>T	ENSP00000361820:p.Asn483Ile	438.0	0.0	0		429.0	59.0	0.137529	NM_001142530	Q9C0G2	Missense_Mutation	SNP	ENST00000372735.1	37	CCDS14502.1	.	.	.	.	.	.	.	.	.	.	A	13.45	2.240331	0.39598	.	.	ENSG00000198908	ENST00000457056;ENST00000361229;ENST00000447531;ENST00000448867;ENST00000372735	T;T;T;T;T	0.32272	1.46;1.46;1.46;1.46;1.46	4.24	1.84	0.25277	Armadillo-like helical (1);Armadillo-type fold (1);	0.647734	0.13738	N	0.366174	T	0.23210	0.0561	N	0.08118	0	0.09310	N	1	D	0.53462	0.96	P	0.57101	0.813	T	0.08411	-1.0723	9	.	.	.	-29.9634	5.1019	0.14764	0.7516:0.0:0.2484:0.0	.	483	Q6PI77	BHLH9_HUMAN	I	483	ENSP00000403226:N483I;ENSP00000354675:N483I;ENSP00000405893:N483I;ENSP00000391722:N483I;ENSP00000361820:N483I	.	N	+	2	0	BHLHB9	101892027	0.006000	0.16342	0.005000	0.12908	0.995000	0.86356	0.712000	0.25779	0.262000	0.21774	0.339000	0.21740	AAT	.	.	none		0.363	BHLHB9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057630.1	NM_030639	
OR8G5	219865	hgsc.bcm.edu	37	11	124135143	124135143	+	Missense_Mutation	SNP	G	G	A	rs200012972	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:124135143G>A	ENST00000524943.2	+	1	421	c.421G>A	c.(421-423)Gtt>Att	p.V141I	OR8G1_ENST00000341493.2_RNA	NM_001005198.1	NP_001005198.1	Q8NG78	OR8G5_HUMAN	olfactory receptor, family 8, subfamily G, member 5	141						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)						Breast(109;0.0157)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0523)		CTTCTTCCTCGTTTTTGCTAT	0.463													g|||	27	0.00539137	0.0197	0.0014	5008	,	,		23436	0.0		0.0	False		,,,				2504	0.0				p.V141I	Ovarian(169;523 1969 8640 31295 51256)	Atlas-SNP	.											.	.	.	.	0			c.G421A						PASS	.	G	ILE/VAL	38,4260		0,38,2111	165.0	155.0	158.0		421	-7.2	0.0	11		158	0,8562		0,0,4281	no	missense	OR8G5	NM_001005198.1	29	0,38,6392	AA,AG,GG		0.0,0.8841,0.2955		141/347	124135143	38,12822	2149	4281	6430	SO:0001583	missense	219865	exon1			TTCCTCGTTTTTG	BK004516	CCDS66256.1	11q24.1	2014-04-17		2004-03-10	ENSG00000255298	ENSG00000255298		"""GPCR / Class A : Olfactory receptors"""	19622	protein-coding gene	gene with protein product				OR8G5P, OR8G6			Standard	NM_001005198		Approved			Q8NG78	OTTHUMG00000186059	ENST00000524943.2:c.421G>A	11.37:g.124135143G>A	ENSP00000477014:p.Val141Ile	332.0	0.0	0		258.0	127.0	0.492248	NM_001005198	B2RND3|Q6IEU6	Missense_Mutation	SNP	ENST00000524943.2	37																																																																																				.	.	weak		0.463	OR8G5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000387283.2	NM_001005198	
NDUFV2	4729	hgsc.bcm.edu	37	18	9117899	9117899	+	Missense_Mutation	SNP	G	G	A	rs75362221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:9117899G>A	ENST00000318388.6	+	2	232	c.118G>A	c.(118-120)Gtg>Atg	p.V40M	RP11-143J12.3_ENST00000579467.1_RNA|NDUFV2_ENST00000400033.1_Missense_Mutation_p.V43M|RP11-21J18.1_ENST00000579126.1_RNA	NM_021074.4	NP_066552.2	P19404	NDUV2_HUMAN	NADH dehydrogenase (ubiquinone) flavoprotein 2, 24kDa	40					cardiac muscle tissue development (GO:0048738)|cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|nervous system development (GO:0007399)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|lung(4)|ovary(1)|stomach(1)	7						AGCTTTATTTGTGGTAAGTAA	0.289													G|||	20	0.00399361	0.0151	0.0	5008	,	,		17599	0.0		0.0	False		,,,				2504	0.0				p.V40M		Atlas-SNP	.											.	NDUFV2	17	.	0			c.G118A						PASS	.	G	MET/VAL	48,4358	45.3+/-79.5	0,48,2155	54.0	59.0	57.0		118	5.5	1.0	18	dbSNP_131	57	0,8588		0,0,4294	yes	missense	NDUFV2	NM_021074.4	21	0,48,6449	AA,AG,GG		0.0,1.0894,0.3694	benign	40/250	9117899	48,12946	2203	4294	6497	SO:0001583	missense	4729	exon2			TTATTTGTGGTAA	X84421	CCDS11842.1	18p11.22	2011-07-04	2002-08-29		ENSG00000178127	ENSG00000178127	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7717	protein-coding gene	gene with protein product	"""complex I 24kDa subunit"", ""NADH dehydrogenase [ubiquinone] flavoprotein 2, mitochondrial"""	600532	"""NADH dehydrogenase (ubiquinone) flavoprotein 2 (24kD)"""			9763677, 7607668	Standard	NM_021074		Approved	CI-24k	uc002knu.3	P19404	OTTHUMG00000131593	ENST00000318388.6:c.118G>A	18.37:g.9117899G>A	ENSP00000327268:p.Val40Met	126.0	0.0	0		123.0	52.0	0.422764	NM_021074	Q9BV41	Missense_Mutation	SNP	ENST00000318388.6	37	CCDS11842.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	G	17.70	3.453208	0.63290	0.010894	0.0	ENSG00000178127	ENST00000318388;ENST00000400033	T;T	0.52057	0.69;0.68	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.41858	0.1177	M	0.89478	3.035	0.80722	D	1	B	0.30406	0.278	B	0.32677	0.15	T	0.59595	-0.7425	10	0.72032	D	0.01	-16.8798	14.9056	0.70715	0.0709:0.0:0.9291:0.0	.	40	P19404	NDUV2_HUMAN	M	40;43	ENSP00000327268:V40M;ENSP00000382908:V43M	ENSP00000327268:V40M	V	+	1	0	NDUFV2	9107899	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	5.872000	0.69636	2.738000	0.93877	0.585000	0.79938	GTG	G|0.996;A|0.004	0.004	strong		0.289	NDUFV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254475.2	NM_021074	
NFATC3	4775	hgsc.bcm.edu	37	16	68225197	68225197	+	Silent	SNP	C	C	T	rs140991156	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:68225197C>T	ENST00000346183.3	+	9	2649	c.2625C>T	c.(2623-2625)acC>acT	p.T875T	SNORA48_ENST00000391143.1_RNA|NFATC3_ENST00000329524.4_Silent_p.T875T|NFATC3_ENST00000349223.5_Silent_p.T875T|NFATC3_ENST00000535127.2_3'UTR|NFATC3_ENST00000575270.1_Silent_p.T875T	NM_173165.2	NP_775188.1	Q12968	NFAC3_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 3	875					cellular respiration (GO:0045333)|cellular response to calcium ion (GO:0071277)|cellular response to lithium ion (GO:0071285)|Fc-epsilon receptor signaling pathway (GO:0038095)|heart development (GO:0007507)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|muscle cell development (GO:0055001)|patterning of blood vessels (GO:0001569)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|liver(1)|lung(19)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)	44		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0119)|Epithelial(162;0.0452)|all cancers(182;0.24)		CTGTGCATACCCTGCCTCATC	0.443																																					p.T875T		Atlas-SNP	.											.	NFATC3	190	.	0			c.C2625T						PASS	.	C	,,	4,4392	8.1+/-20.4	0,4,2194	199.0	181.0	187.0		2625,2625,2625	-1.8	0.4	16	dbSNP_134	187	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	NFATC3	NM_004555.3,NM_173163.2,NM_173165.2	,,	0,4,6494	TT,TC,CC		0.0,0.091,0.0308	,,	875/1069,875/1066,875/1076	68225197	4,12992	2198	4300	6498	SO:0001819	synonymous_variant	4775	exon9			GCATACCCTGCCT	L41067	CCDS10860.1, CCDS10861.1, CCDS10862.1	16q22	2009-11-24			ENSG00000072736	ENSG00000072736		"""Nuclear factor of activated T-cells"""	7777	protein-coding gene	gene with protein product		602698				7749981	Standard	NM_004555		Approved	NFAT4, NFATX	uc002evo.2	Q12968	OTTHUMG00000137555	ENST00000346183.3:c.2625C>T	16.37:g.68225197C>T		243.0	1.0	0.00411523		251.0	125.0	0.498008	NM_173163	O75211|Q14516|Q99840|Q99841|Q99842	Silent	SNP	ENST00000346183.3	37	CCDS10860.1																																																																																			C|1.000;T|0.000	0.000	strong		0.443	NFATC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268890.2	NM_004555	
CEACAM8	1088	hgsc.bcm.edu	37	19	43087428	43087428	+	Missense_Mutation	SNP	A	A	C	rs8103051	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43087428A>C	ENST00000244336.5	-	5	1121	c.1020T>G	c.(1018-1020)atT>atG	p.I340M	LIPE-AS1_ENST00000594624.2_RNA|CEACAM8_ENST00000599005.1_Missense_Mutation_p.I42M|LIPE-AS1_ENST00000594688.1_RNA	NM_001816.3	NP_001807.2	P31997	CEAM8_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 8	340			I -> M (in dbSNP:rs8103051).		immune response (GO:0006955)	anchored component of membrane (GO:0031225)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	16		Prostate(69;0.00899)				CCAGTACTCCAATCATGATGC	0.458													A|||	359	0.0716853	0.2572	0.0231	5008	,	,		21532	0.0		0.003	False		,,,				2504	0.0				p.I340M		Atlas-SNP	.											.	CEACAM8	44	.	0			c.T1020G						PASS	.	A	MET/ILE	878,3528	342.0+/-307.0	92,694,1417	99.0	89.0	93.0		1020	0.6	0.1	19	dbSNP_116	93	18,8582	10.5+/-38.8	0,18,4282	no	missense	CEACAM8	NM_001816.3	10	92,712,5699	CC,CA,AA		0.2093,19.9274,6.8891	probably-damaging	340/350	43087428	896,12110	2203	4300	6503	SO:0001583	missense	1088	exon5			TACTCCAATCATG	D90064	CCDS12610.1	19q13.2	2013-01-29			ENSG00000124469	ENSG00000124469		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1820	protein-coding gene	gene with protein product		615747		CGM6		2208113, 2306228	Standard	NM_001816		Approved	CD66b	uc002oud.2	P31997	OTTHUMG00000151124	ENST00000244336.5:c.1020T>G	19.37:g.43087428A>C	ENSP00000244336:p.Ile340Met	323.0	0.0	0		318.0	157.0	0.493711	NM_001816	O60399|Q16574	Missense_Mutation	SNP	ENST00000244336.5	37	CCDS12610.1	124	0.056776556776556776	110	0.22357723577235772	11	0.03038674033149171	0	0.0	3	0.00395778364116095	a	11.22	1.574497	0.28092	0.199274	0.002093	ENSG00000124469	ENST00000244336	T	0.21734	1.99	1.7	0.575	0.17374	.	.	.	.	.	T	0.00039	0.0001	M	0.78049	2.395	0.80722	P	0.0	D	0.76494	0.999	D	0.63488	0.915	T	0.05750	-1.0866	8	0.87932	D	0	.	3.7257	0.08474	0.6637:0.0:0.0:0.3363	rs8103051;rs8103051	340	P31997	CEAM8_HUMAN	M	340	ENSP00000244336:I340M	ENSP00000244336:I340M	I	-	3	3	CEACAM8	47779268	0.002000	0.14202	0.069000	0.20011	0.113000	0.19764	-0.125000	0.10579	0.101000	0.17610	0.254000	0.18369	ATT	A|0.937;C|0.063	0.063	strong		0.458	CEACAM8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321430.1		
BTN3A2	11118	hgsc.bcm.edu	37	6	26374571	26374571	+	Silent	SNP	G	G	A	rs115820857	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:26374571G>A	ENST00000356386.2	+	9	1169	c.981G>A	c.(979-981)tcG>tcA	p.S327S	BTN3A2_ENST00000377708.2_Silent_p.S327S|BTN3A2_ENST00000527422.1_Silent_p.S327S|BTN3A2_ENST00000396934.3_Silent_p.S304S|BTN3A2_ENST00000396948.1_Silent_p.S327S|BTN3A2_ENST00000508906.2_Silent_p.S285S	NM_001197246.2|NM_001197247.1|NM_007047.3	NP_001184175.1|NP_001184176.1|NP_008978.2	P78410	BT3A2_HUMAN	butyrophilin, subfamily 3, member A2	327				S -> L (in Ref. 2; AAC02655). {ECO:0000305}.	interferon-gamma secretion (GO:0072643)|T cell mediated immunity (GO:0002456)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(5)	10						AGGAGTCTTCGTCCGATACCA	0.473													G|||	75	0.014976	0.0552	0.0029	5008	,	,		16013	0.0		0.0	False		,,,				2504	0.0				p.S327S		Atlas-SNP	.											.	BTN3A2	44	.	0			c.G981A						PASS	.	G	,,,,	168,4238	110.8+/-149.0	1,166,2036	196.0	161.0	173.0		981,981,912,855,981	-1.2	0.0	6	dbSNP_132	173	12,8588	8.4+/-32.0	0,12,4288	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BTN3A2	NM_001197246.1,NM_001197247.1,NM_001197248.1,NM_001197249.1,NM_007047.3	,,,,	1,178,6324	AA,AG,GG		0.1395,3.813,1.384	,,,,	327/335,327/335,304/312,285/293,327/335	26374571	180,12826	2203	4300	6503	SO:0001819	synonymous_variant	11118	exon7			GTCTTCGTCCGAT	U90546	CCDS4605.1, CCDS56399.1, CCDS56400.1	6p22.1	2014-01-14			ENSG00000186470	ENSG00000186470		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1139	protein-coding gene	gene with protein product		613594				9149941	Standard	NM_007047		Approved	BTN3.2	uc010jqi.2	P78410	OTTHUMG00000014450	ENST00000356386.2:c.981G>A	6.37:g.26374571G>A		215.0	0.0	0		216.0	96.0	0.444444	NM_001197246	B4DRT7|B4E103|F5H791|F8W6E0|O00477|O15338|O75658|Q76PA0|Q9BU81|Q9NR44	Silent	SNP	ENST00000356386.2	37	CCDS4605.1																																																																																			G|0.988;A|0.012	0.012	strong		0.473	BTN3A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040113.2		
PRUNE	58497	hgsc.bcm.edu	37	1	150997155	150997155	+	Missense_Mutation	SNP	G	G	A	rs56805474	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:150997155G>A	ENST00000271620.3	+	4	560	c.404G>A	c.(403-405)tGc>tAc	p.C135Y	PRUNE_ENST00000368936.1_5'UTR|PRUNE_ENST00000368935.1_Intron|PRUNE_ENST00000467771.1_3'UTR|RNU6-884P_ENST00000363889.1_RNA|PRUNE_ENST00000368937.1_Intron|PRUNE_ENST00000271619.8_Intron|PRUNE_ENST00000368934.1_5'Flank	NM_021222.1	NP_067045.1	Q86TP1	PRUNE_HUMAN	prune exopolyphosphatase	135						cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	inorganic diphosphatase activity (GO:0004427)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	14	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			CCGAAACACTGCCCTCCCTGC	0.577											OREG0013792	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	g|||	156	0.0311502	0.1142	0.0043	5008	,	,		17672	0.0		0.002	False		,,,				2504	0.0				p.C135Y		Atlas-SNP	.											.	PRUNE	40	.	0			c.G404A						PASS	.	G	TYR/CYS	427,3979	208.8+/-229.8	19,389,1795	103.0	89.0	94.0		404	3.8	1.0	1	dbSNP_129	94	2,8598	2.2+/-6.3	0,2,4298	yes	missense	PRUNE	NM_021222.1	194	19,391,6093	AA,AG,GG		0.0233,9.6913,3.2985	possibly-damaging	135/454	150997155	429,12577	2203	4300	6503	SO:0001583	missense	58497	exon4			AACACTGCCCTCC	U67085	CCDS977.1	1q21.2	2013-04-29	2013-04-29		ENSG00000143363	ENSG00000143363	3.6.1.11		13420	protein-coding gene	gene with protein product			"""prune homolog (Drosophila)"""			10602478, 11687967, 18700747	Standard	NM_021222		Approved	DRES-17, HTCD37	uc001ewh.1	Q86TP1	OTTHUMG00000035062	ENST00000271620.3:c.404G>A	1.37:g.150997155G>A	ENSP00000271620:p.Cys135Tyr	106.0	0.0	0	1737	100.0	33.0	0.33	NM_021222	B2RCH8|B4DFL7|Q5SZF9|Q659E5|Q6P4E0|Q8N654|Q96JU5|Q9C071|Q9C072|Q9UIV0	Missense_Mutation	SNP	ENST00000271620.3	37	CCDS977.1	58	0.026556776556776556	57	0.11585365853658537	1	0.0027624309392265192	0	0.0	0	0.0	g	8.084	0.773045	0.16051	0.096913	2.33E-4	ENSG00000143363	ENST00000271620;ENST00000302413	T	0.30182	1.54	5.76	3.84	0.44239	Phosphoesterase, RecJ-like (1);	0.361754	0.29362	N	0.012374	T	0.09247	0.0228	N	0.22421	0.69	0.80722	D	1	D	0.53151	0.958	P	0.48334	0.574	T	0.06250	-1.0837	10	0.02654	T	1	.	9.1856	0.37168	0.0892:0.1831:0.7278:0.0	rs56805474	135	Q86TP1	PRUNE_HUMAN	Y	135;68	ENSP00000271620:C135Y	ENSP00000271620:C135Y	C	+	2	0	PRUNE	149263779	0.975000	0.34042	0.998000	0.56505	0.961000	0.63080	2.512000	0.45485	1.436000	0.47453	0.645000	0.84053	TGC	G|0.965;A|0.035	0.035	strong		0.577	PRUNE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084885.1	NM_021222	
TMEM8B	51754	hgsc.bcm.edu	37	9	35845998	35845998	+	Silent	SNP	G	G	C	rs34807292	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:35845998G>C	ENST00000377991.4	+	8	1321	c.306G>C	c.(304-306)acG>acC	p.T102T	TMEM8B_ENST00000377996.1_Silent_p.T102T|TMEM8B_ENST00000473947.1_3'UTR|TMEM8B_ENST00000377988.2_Silent_p.T102T|TMEM8B_ENST00000439587.2_Silent_p.T102T	NM_001042589.2	NP_001036054.1	A6NDV4	TMM8B_HUMAN	transmembrane protein 8B	102					cell-matrix adhesion (GO:0007160)|regulation of growth (GO:0040008)|regulation of mitotic cell cycle (GO:0007346)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|large_intestine(2)|lung(1)|ovary(1)	7						AAAACGTGACGGTGTTTGGAT	0.617													G|||	127	0.0253594	0.0908	0.0072	5008	,	,		16083	0.0		0.002	False		,,,				2504	0.0				p.T102T		Atlas-SNP	.											.	TMEM8B	53	.	0			c.G306C						PASS	.	G	,,	386,4020	191.9+/-217.4	17,352,1834	114.0	95.0	102.0		306,306,306	-2.7	1.0	9	dbSNP_126	102	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous	TMEM8B	NM_001042589.1,NM_001042590.1,NM_016446.3	,,	17,353,6133	CC,CG,GG		0.0116,8.7608,2.9755	,,	102/473,102/473,102/339	35845998	387,12619	2203	4300	6503	SO:0001819	synonymous_variant	51754	exon7			CGTGACGGTGTTT	BC043384	CCDS6595.1, CCDS43800.1	9p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000137103	ENSG00000137103			21427	protein-coding gene	gene with protein product	"""nasopharyngeal carcinoma expressed 6"""		"""chromosome 9 open reading frame 127"""	C9orf127		12918109, 8619474	Standard	NM_016446		Approved	NAG-5, NGX6	uc003zym.4	A6NDV4	OTTHUMG00000019885	ENST00000377991.4:c.306G>C	9.37:g.35845998G>C		65.0	0.0	0		50.0	24.0	0.48	NM_001042590	B3KQF3|O75539|Q49AB1|Q4KMX5|Q5TCW5|Q9HBY2|Q9P0U7	Silent	SNP	ENST00000377991.4	37	CCDS43800.1																																																																																			G|0.969;C|0.031	0.031	strong		0.617	TMEM8B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052388.2	NM_016446	
ZNF843	283933	hgsc.bcm.edu	37	16	31448168	31448168	+	Start_Codon_SNP	SNP	C	C	T	rs150789330	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31448168C>T	ENST00000315678.5	-	2	727	c.3G>A	c.(1-3)atG>atA	p.M1I	ZNF843_ENST00000564218.1_Start_Codon_SNP_p.M1I	NM_001136509.1	NP_001129981.1	Q8N446	ZN843_HUMAN	zinc finger protein 843	1							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			breast(2)|large_intestine(1)|prostate(1)	4						GGAGGCTTCTCATGAGCAGGG	0.627													C|||	12	0.00239617	0.0091	0.0	5008	,	,		18756	0.0		0.0	False		,,,				2504	0.0				p.M1I		Atlas-SNP	.											.	ZNF843	14	.	0			c.G3A						PASS	.	C	ILE/MET	18,1366		1,16,675	37.0	36.0	36.0		3	0.7	0.0	16	dbSNP_134	36	1,3181		0,1,1590	yes	missense	ZNF843	NM_001136509.1	10	1,17,2265	TT,TC,CC		0.0314,1.3006,0.4161	benign	1/349	31448168	19,4547	692	1591	2283	SO:0001582	initiator_codon_variant	283933	exon2			GCTTCTCATGAGC	BC036762	CCDS45471.1	16p11.2	2013-01-11			ENSG00000176723	ENSG00000176723		"""Zinc fingers, C2H2-type"""	28710	protein-coding gene	gene with protein product						12477932	Standard	NM_001136509		Approved	MGC46336	uc010vfm.1	Q8N446		ENST00000315678.5:c.3G>A	16.37:g.31448168C>T	ENSP00000322899:p.Met1Ile	55.0	0.0	0		64.0	37.0	0.578125	NM_001136509	A8K4U8	Missense_Mutation	SNP	ENST00000315678.5	37	CCDS45471.1	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	C	7.728	0.698715	0.15106	0.013006	3.14E-4	ENSG00000176723	ENST00000315678	T	0.01099	5.34	1.72	0.701	0.18104	.	.	.	.	.	T	0.00815	0.0027	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.55854	-0.8075	8	0.87932	D	0	.	5.7668	0.18231	0.0:0.8075:0.0:0.1925	.	1	Q8N446	ZN843_HUMAN	I	1	ENSP00000322899:M1I	ENSP00000322899:M1I	M	-	3	0	ZNF843	31355669	0.903000	0.30736	0.004000	0.12327	0.005000	0.04900	2.394000	0.44450	0.055000	0.16094	0.411000	0.27672	ATG	C|0.999;T|0.001	0.001	strong		0.627	ZNF843-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432843.1	NM_001136509	Missense_Mutation
RAB40AL	282808	hgsc.bcm.edu	37	X	102192372	102192372	+	Silent	SNP	G	G	A	rs61745023	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:102192372G>A	ENST00000218249.5	+	1	173	c.126G>A	c.(124-126)ccG>ccA	p.P42P	LL0XNC01-237H1.3_ENST00000413528.1_RNA	NM_001031834.1	NP_001027004.1	P0C0E4	RB40L_HUMAN	RAB40A, member RAS oncogene family-like	42					protein transport (GO:0015031)|protein ubiquitination (GO:0016567)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)			endometrium(4)|large_intestine(2)|lung(3)|ovary(3)	12						CCGAGTCCCCGTACAGTCACC	0.622													.|||	67	0.0177483	0.0477	0.0058	3775	,	,		11299	0.0		0.0	False		,,,				2504	0.0				p.P42P		Atlas-SNP	.											.	RAB40AL	33	.	0			c.G126A						PASS	.	G		213,3622		4,171,34,1457,537	115.0	109.0	111.0		126	-1.7	0.0	X	dbSNP_129	111	0,6728		0,0,0,2428,1872	no	coding-synonymous	RAB40AL	NM_001031834.1		4,171,34,3885,2409	AA,AG,A,GG,G		0.0,5.5541,2.0165		42/279	102192372	213,10350	2203	4300	6503	SO:0001819	synonymous_variant	282808	exon1			GTCCCCGTACAGT	BC101169	CCDS35353.1	Xq22.2	2008-02-05			ENSG00000102128	ENSG00000102128			25410	protein-coding gene	gene with protein product	"""Ras like GTPase"""	300405					Standard	NM_001031834		Approved	RAR2, RLGP	uc004ejs.3	P0C0E4	OTTHUMG00000022084	ENST00000218249.5:c.126G>A	X.37:g.102192372G>A		507.0	0.0	0		455.0	145.0	0.318681	NM_001031834	Q495H3	Silent	SNP	ENST00000218249.5	37	CCDS35353.1																																																																																			G|0.981;A|0.019	0.019	strong		0.622	RAB40AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057679.1	NM_001031834	
MUC2	4583	hgsc.bcm.edu	37	11	1093228	1093228	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:1093228A>G	ENST00000441003.2	+	30	5074	c.5047A>G	c.(5047-5049)Acg>Gcg	p.T1683A	MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.T1650A	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)	caccaccactacGGTGacccc	0.632																																					p.T1683A		Atlas-SNP	.											.	MUC2	614	.	0			c.A5047G						PASS	.						85.0	148.0	126.0					11																	1093228		1822	3322	5144	SO:0001583	missense	4583	exon30			ACCACTACGGTGA	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.5047A>G	11.37:g.1093228A>G	ENSP00000415183:p.Thr1683Ala	60.0	0.0	0		66.0	13.0	0.19697	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	A	3.524	-0.097228	0.07010	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.12465	2.97;2.68	1.75	0.234	0.15390	.	0.000000	0.34750	U	0.003714	T	0.04497	0.0123	.	.	.	0.09310	N	1	B	0.28933	0.228	B	0.21546	0.035	T	0.37126	-0.9719	9	0.11485	T	0.65	.	3.3046	0.06996	0.6291:0.0:0.0:0.3709	.	1683	E7EUV1	.	A	1683;1650	ENSP00000415183:T1683A;ENSP00000351956:T1650A	ENSP00000351956:T1650A	T	+	1	0	MUC2	1083228	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	-0.225000	0.09151	0.813000	0.34350	0.155000	0.16302	ACG	.	.	none		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
JSRP1	126306	hgsc.bcm.edu	37	19	2253641	2253641	+	Silent	SNP	G	G	T	rs200918439	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2253641G>T	ENST00000300961.6	-	5	478	c.414C>A	c.(412-414)ggC>ggA	p.G138G	JSRP1_ENST00000586471.2_Silent_p.G138G|MIR4321_ENST00000592276.1_RNA	NM_144616.3	NP_653217.1	Q96MG2	JSPR1_HUMAN	junctional sarcoplasmic reticulum protein 1	138	Pro-rich.				protein localization to membrane (GO:0072657)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|skeletal muscle contraction (GO:0003009)	membrane (GO:0016020)|sarcoplasmic reticulum (GO:0016529)				haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(1)|pancreas(1)|urinary_tract(1)	6				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GGAAAGCCGAGCCCAGCAGCG	0.716													G|||	54	0.0107827	0.0363	0.0072	5008	,	,		13645	0.0		0.001	False		,,,				2504	0.0				p.G138G		Atlas-SNP	.											.	JSRP1	18	.	0			c.C414A						PASS	.	G		103,3903		0,103,1900	6.0	10.0	9.0		414	1.9	1.0	19		9	8,7862		0,8,3927	no	coding-synonymous	JSRP1	NM_144616.3		0,111,5827	TT,TG,GG		0.1017,2.5711,0.9347		138/332	2253641	111,11765	2003	3935	5938	SO:0001819	synonymous_variant	126306	exon5			AGCCGAGCCCAGC	AK056978	CCDS12086.1	19p13.3	2010-03-23			ENSG00000167476	ENSG00000167476			24963	protein-coding gene	gene with protein product	"""homolog of mouse skeletal muscle sarcoplasmic reticulum protein JP-45"""	608743				12871958	Standard	NM_144616		Approved	JP-45, FLJ32416	uc002lvj.2	Q96MG2		ENST00000300961.6:c.414C>A	19.37:g.2253641G>T		31.0	0.0	0		24.0	15.0	0.625	NM_144616		Silent	SNP	ENST00000300961.6	37	CCDS12086.1																																																																																			G|0.996;T|0.004	0.004	strong		0.716	JSRP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451266.2	NM_144616	
SPANXN1	494118	hgsc.bcm.edu	37	X	144337286	144337286	+	Silent	SNP	G	G	A	rs75090998	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:144337286G>A	ENST00000370493.3	+	2	930	c.171G>A	c.(169-171)agG>agA	p.R57R		NM_001009614.2	NP_001009614.1	Q5VSR9	SPXN1_HUMAN	SPANX family, member N1	57										endometrium(2)|kidney(2)|lung(8)|prostate(1)|urinary_tract(1)	14	Acute lymphoblastic leukemia(192;6.56e-05)					TTTGCTACAGGAAAGCTAAGA	0.443													G|||	280	0.0741722	0.208	0.0072	3775	,	,		15977	0.0		0.0	False		,,,				2504	0.0				p.R57R		Atlas-SNP	.											.	SPANXN1	23	.	0			c.G171A						PASS	.	G		826,3009		83,540,120,1009,451	186.0	161.0	170.0		171	1.5	0.0	X	dbSNP_131	170	9,6716		1,5,2,2422,1867	no	coding-synonymous	SPANXN1	NM_001009614.2		84,545,122,3431,2318	AA,AG,A,GG,G		0.1338,21.5385,7.9072		57/73	144337286	835,9725	2203	4297	6500	SO:0001819	synonymous_variant	494118	exon2			CTACAGGAAAGCT		CCDS35421.1	Xq27.3	2009-03-25				ENSG00000203923			33174	protein-coding gene	gene with protein product	"""cancer/testis antigen family 11, member 6"""	300664				14973187, 17012309	Standard	NM_001009614		Approved	SPANX-N1, CT11.6	uc004fcb.2	Q5VSR9		ENST00000370493.3:c.171G>A	X.37:g.144337286G>A		374.0	0.0	0		365.0	363.0	0.994521	NM_001009614		Silent	SNP	ENST00000370493.3	37	CCDS35421.1																																																																																			G|0.919;A|0.081	0.081	strong		0.443	SPANXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058631.2	NM_001009614	
SPTA1	6708	hgsc.bcm.edu	37	1	158631106	158631106	+	Missense_Mutation	SNP	G	G	C	rs35121052	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:158631106G>C	ENST00000368147.4	-	18	2738	c.2558C>G	c.(2557-2559)aCa>aGa	p.T853R		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	853			T -> R (in dbSNP:rs35121052).		actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					TCCCCTTTCTGTTATCTCTTG	0.438													G|||	531	0.10603	0.382	0.0331	5008	,	,		17472	0.0		0.003	False		,,,				2504	0.0				p.T853R		Atlas-SNP	.											.	SPTA1	720	.	0			c.C2558G						PASS	.	G	ARG/THR	1121,2763		177,767,998	266.0	264.0	265.0		2558	3.9	1.0	1	dbSNP_126	265	21,8275		0,21,4127	yes	missense	SPTA1	NM_003126.2	71	177,788,5125	CC,CG,GG		0.2531,28.862,9.376	benign	853/2420	158631106	1142,11038	1942	4148	6090	SO:0001583	missense	6708	exon18			CTTTCTGTTATCT	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.2558C>G	1.37:g.158631106G>C	ENSP00000357129:p.Thr853Arg	311.0	0.0	0		338.0	165.0	0.488166	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	37	CCDS41423.1	192	0.08791208791208792	181	0.3678861788617886	11	0.03038674033149171	0	0.0	0	0.0	G	16.67	3.187725	0.57909	0.28862	0.002531	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.52057	0.68;0.68	4.81	3.9	0.45041	.	.	.	.	.	T	0.39145	0.1067	M	0.64997	1.995	0.23076	P	0.99833702	P	0.44659	0.84	P	0.51550	0.673	T	0.29243	-1.0018	8	0.18710	T	0.47	.	11.9273	0.52827	0.0851:0.0:0.9149:0.0	rs35121052;rs61126478	853	P02549	SPTA1_HUMAN	R	853	ENSP00000357130:T853R;ENSP00000357129:T853R	ENSP00000357129:T853R	T	-	2	0	SPTA1	156897730	1.000000	0.71417	1.000000	0.80357	0.643000	0.38383	5.076000	0.64413	1.249000	0.43950	0.650000	0.86243	ACA	G|0.933;C|0.067	0.067	strong		0.438	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
MLXIP	22877	hgsc.bcm.edu	37	12	122618417	122618417	+	Missense_Mutation	SNP	G	G	T	rs34702867	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:122618417G>T	ENST00000319080.7	+	9	1747	c.1615G>T	c.(1615-1617)Gtg>Ttg	p.V539L	MLXIP_ENST00000377037.2_Missense_Mutation_p.V129L|MLXIP_ENST00000538698.1_Missense_Mutation_p.V146L					MLX interacting protein											NS(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(7)|ovary(3)	20	all_neural(191;0.0837)|Medulloblastoma(191;0.163)	Lung NSC(355;0.0659)		OV - Ovarian serous cystadenocarcinoma(86;0.000599)|Epithelial(86;0.00102)|BRCA - Breast invasive adenocarcinoma(302;0.233)		GTTAACTTTTGTGCACCCCAA	0.607													G|||	194	0.038738	0.1422	0.0086	5008	,	,		14499	0.0		0.0	False		,,,				2504	0.0				p.V539L	Esophageal Squamous(105;787 1493 16200 18566 52466)	Atlas-SNP	.											.	MLXIP	46	.	0			c.G1615T						PASS	.	G	LEU/VAL	448,3490		28,392,1549	22.0	26.0	25.0		1205	4.2	1.0	12	dbSNP_126	25	6,8264		0,6,4129	yes	missense	MLXIP	NM_014938.3	32	28,398,5678	TT,TG,GG		0.0726,11.3763,3.7189	benign	539/920	122618417	454,11754	1969	4135	6104	SO:0001583	missense	22877	exon9			ACTTTTGTGCACC	AB020674	CCDS73540.1	12q21.31	2013-05-21				ENSG00000175727		"""Basic helix-loop-helix proteins"""	17055	protein-coding gene	gene with protein product		608090				10048485, 11073985	Standard	XM_006719290		Approved	MONDOA, KIAA0867, MIR, bHLHe36	uc001ubq.3	Q9HAP2		ENST00000319080.7:c.1615G>T	12.37:g.122618417G>T	ENSP00000312834:p.Val539Leu	55.0	0.0	0		38.0	14.0	0.368421	NM_014938		Missense_Mutation	SNP	ENST00000319080.7	37		73	0.033424908424908424	70	0.14227642276422764	3	0.008287292817679558	0	0.0	0	0.0	G	14.85	2.657247	0.47467	0.113763	7.26E-4	ENSG00000175727	ENST00000319080;ENST00000538698;ENST00000539039;ENST00000377037	D;D;D	0.84516	-1.86;-1.86;-1.86	5.09	4.19	0.49359	.	0.332806	0.28784	N	0.014156	T	0.02012	0.0063	.	.	.	0.24861	N	0.992344	B;B	0.31318	0.319;0.1	B;B	0.34301	0.179;0.03	T	0.00812	-1.1556	9	0.28530	T	0.3	-11.9952	12.6399	0.56705	0.0813:0.0:0.9187:0.0	rs34702867	539;539	Q9HAP2-3;Q9HAP2	.;MLXIP_HUMAN	L	539;146;146;129	ENSP00000312834:V539L;ENSP00000440769:V146L;ENSP00000366236:V129L	ENSP00000312834:V539L	V	+	1	0	MLXIP	121184370	1.000000	0.71417	0.977000	0.42913	0.967000	0.64934	4.310000	0.59141	1.097000	0.41459	0.655000	0.94253	GTG	G|0.973;T|0.027	0.027	strong		0.607	MLXIP-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000401718.2	NM_014938	
GPC1	2817	hgsc.bcm.edu	37	2	241404914	241404914	+	Silent	SNP	C	C	T	rs2228329	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:241404914C>T	ENST00000264039.2	+	8	1541	c.1293C>T	c.(1291-1293)gaC>gaT	p.D431D		NM_002081.2	NP_002072.2	P35052	GPC1_HUMAN	glypican 1	431					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|myelin assembly (GO:0032288)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|phototransduction, visible light (GO:0007603)|positive regulation of skeletal muscle cell differentiation (GO:2001016)|retinoid metabolic process (GO:0001523)|Schwann cell differentiation (GO:0014037)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	copper ion binding (GO:0005507)|fibroblast growth factor binding (GO:0017134)|laminin binding (GO:0043236)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	9		all_epithelial(40;2.79e-15)|Breast(86;2.41e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0335)|Lung NSC(271;0.106)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;4.51e-33)|all cancers(36;1.74e-30)|OV - Ovarian serous cystadenocarcinoma(60;4.73e-15)|Kidney(56;2.99e-09)|KIRC - Kidney renal clear cell carcinoma(57;3.23e-08)|BRCA - Breast invasive adenocarcinoma(100;9.1e-06)|Colorectal(34;0.000487)|Lung(119;0.0013)|LUSC - Lung squamous cell carcinoma(224;0.0154)|COAD - Colon adenocarcinoma(134;0.0194)|READ - Rectum adenocarcinoma(96;0.0949)		TCATGGGTGACGGCCTGGCCA	0.612													C|||	59	0.0117812	0.0416	0.0058	5008	,	,		19053	0.0		0.0	False		,,,				2504	0.0				p.D431D		Atlas-SNP	.											.	GPC1	32	.	0			c.C1293T						PASS	.	C		128,4278	93.0+/-131.7	2,124,2077	92.0	77.0	82.0		1293	-2.5	1.0	2	dbSNP_98	82	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GPC1	NM_002081.2		2,125,6376	TT,TC,CC		0.0116,2.9051,0.9918		431/559	241404914	129,12877	2203	4300	6503	SO:0001819	synonymous_variant	2817	exon8			GGGTGACGGCCTG	AK095397	CCDS2534.1	2q35-q37	2008-02-05			ENSG00000063660	ENSG00000063660		"""Proteoglycans / Cell Surface : Glypicans"""	4449	protein-coding gene	gene with protein product	"""glypican proteoglycan 1"""	600395				7774946	Standard	NM_002081		Approved	glypican	uc002vyw.4	P35052	OTTHUMG00000133349	ENST00000264039.2:c.1293C>T	2.37:g.241404914C>T		117.0	0.0	0		115.0	54.0	0.469565	NM_002081	B3KTD1|Q53QM4	Silent	SNP	ENST00000264039.2	37	CCDS2534.1	17	0.007783882783882784	15	0.03048780487804878	2	0.0055248618784530384	0	0.0	0	0.0	C	2.512	-0.312638	0.05422	0.029051	1.16E-4	ENSG00000063660	ENST00000420138;ENST00000455111	.	.	.	3.56	-2.52	0.06346	.	.	.	.	.	T	0.29389	0.0732	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.40459	-0.9562	4	.	.	.	-27.9108	9.046	0.36347	0.0:0.2401:0.0:0.7599	rs2228329;rs2228329	.	.	.	W	471;183	.	.	R	+	1	2	GPC1	241053587	0.000000	0.05858	0.965000	0.40720	0.315000	0.28087	-3.267000	0.00533	-0.465000	0.06953	-0.269000	0.10298	CGG	C|0.991;T|0.009	0.009	strong		0.612	GPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257179.3	NM_002081	
CPT1A	1374	hgsc.bcm.edu	37	11	68529027	68529027	+	Silent	SNP	A	A	G	rs2228503	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:68529027A>G	ENST00000265641.5	-	16	2158	c.2004T>C	c.(2002-2004)gcT>gcC	p.A668A	CPT1A_ENST00000376618.2_Silent_p.A668A|CPT1A_ENST00000539743.1_Silent_p.A668A|CPT1A_ENST00000540367.1_Silent_p.A668A|CPT1A_ENST00000537756.2_5'Flank	NM_001876.3	NP_001867.2	P50416	CPT1A_HUMAN	carnitine palmitoyltransferase 1A (liver)	668					carnitine metabolic process (GO:0009437)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|eating behavior (GO:0042755)|epithelial cell differentiation (GO:0030855)|fatty acid beta-oxidation (GO:0006635)|glucose metabolic process (GO:0006006)|long-chain fatty acid metabolic process (GO:0001676)|positive regulation of fatty acid beta-oxidation (GO:0032000)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	integral component of mitochondrial outer membrane (GO:0031307)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	carnitine O-palmitoyltransferase activity (GO:0004095)	p.A668A(1)		NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42	Esophageal squamous(3;3.28e-14)		LUAD - Lung adenocarcinoma(13;0.0676)|STAD - Stomach adenocarcinoma(18;0.142)		Glyburide(DB01016)|L-Carnitine(DB00583)|Perhexiline(DB01074)	GGGACTCCACAGCGAGATATT	0.473													G|||	63	0.0125799	0.0461	0.0014	5008	,	,		19324	0.0		0.001	False		,,,				2504	0.0				p.A668A		Atlas-SNP	.											CPT1A,colon,carcinoma,0,1	CPT1A	89	1	1	Substitution - coding silent(1)	large_intestine(1)	c.T2004C						PASS	.	G	,	117,4283	815.3+/-416.2	2,113,2085	176.0	173.0	174.0		2004,2004	-11.3	0.0	11	dbSNP_132	174	0,8588		0,0,4294	no	coding-synonymous,coding-synonymous	CPT1A	NM_001031847.2,NM_001876.3	,	2,113,6379	GG,GA,AA		0.0,2.6591,0.9008	,	668/757,668/774	68529027	117,12871	2200	4294	6494	SO:0001819	synonymous_variant	1374	exon16			CTCCACAGCGAGA	L39211	CCDS8185.1, CCDS31624.1	11q13.2	2007-07-26				ENSG00000110090	2.3.1.21		2328	protein-coding gene	gene with protein product		600528		CPT1		7892212, 9070950	Standard	NM_001876		Approved	CPT1-L, L-CPT1	uc001oog.4	P50416		ENST00000265641.5:c.2004T>C	11.37:g.68529027A>G		119.0	0.0	0		111.0	51.0	0.459459	NM_001876	Q8TCU0|Q9BWK0	Silent	SNP	ENST00000265641.5	37	CCDS8185.1																																																																																			A|0.991;G|0.009	0.009	strong		0.473	CPT1A-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397457.2	NM_001876	
SYT2	127833	hgsc.bcm.edu	37	1	202569555	202569555	+	Silent	SNP	C	C	T	rs907699	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:202569555C>T	ENST00000367267.1	-	7	1041	c.849G>A	c.(847-849)acG>acA	p.T283T	SYT2_ENST00000367268.4_Silent_p.T283T	NM_001136504.1	NP_001129976.1	Q8N9I0	SYT2_HUMAN	synaptotagmin II	283	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.|Phospholipid binding. {ECO:0000250}.				neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			NS(1)|breast(4)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|skin(2)|urinary_tract(1)	29			BRCA - Breast invasive adenocarcinoma(75;0.169)		Botulinum Toxin Type B(DB00042)	GCTTCCCGGCCGTGGGCACAT	0.607											OREG0014101	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	419	0.0836661	0.3011	0.0245	5008	,	,		20029	0.0		0.003	False		,,,				2504	0.001				p.T283T		Atlas-SNP	.											.	SYT2	51	.	0			c.G849A						PASS	.	C	,	1168,3238	411.7+/-335.8	150,868,1185	86.0	83.0	84.0		849,849	-4.4	0.7	1	dbSNP_86	84	45,8555	30.1+/-81.4	0,45,4255	no	coding-synonymous,coding-synonymous	SYT2	NM_001136504.1,NM_177402.4	,	150,913,5440	TT,TC,CC		0.5233,26.5093,9.3265	,	283/420,283/420	202569555	1213,11793	2203	4300	6503	SO:0001819	synonymous_variant	127833	exon7			CCCGGCCGTGGGC	AK090672	CCDS1427.1	1q32.1	2013-01-21			ENSG00000143858	ENSG00000143858		"""Synaptotagmins"""	11510	protein-coding gene	gene with protein product		600104				7749232	Standard	NM_177402		Approved		uc010pqb.2	Q8N9I0	OTTHUMG00000041388	ENST00000367267.1:c.849G>A	1.37:g.202569555C>T		87.0	0.0	0	2130	106.0	55.0	0.518868	NM_177402	Q496K5|Q8NBE5	Silent	SNP	ENST00000367267.1	37	CCDS1427.1																																																																																			C|0.917;T|0.083	0.083	strong		0.607	SYT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099157.1	NM_177402	
CXorf36	79742	hgsc.bcm.edu	37	X	45011018	45011018	+	Missense_Mutation	SNP	C	C	A	rs143817529		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:45011018C>A	ENST00000398000.2	-	5	1255	c.1181G>T	c.(1180-1182)cGc>cTc	p.R394L	CXorf36_ENST00000477281.1_5'UTR	NM_176819.3	NP_789789.2	Q9H7Y0	DIA1R_HUMAN	chromosome X open reading frame 36	394						extracellular region (GO:0005576)				endometrium(1)|large_intestine(2)|lung(4)	7						TGGGTCTGGGCGGATGCTGTC	0.572													C||||C|||	161|161	0.042649|0.042649	0.1188|0.1188	0.0043|0.0043	3775|3775	,|,	,|,		12325|12325	0.0|0.0		0.001|0.001	False|False		,,,|,,,				2504|2504	0.0|0.0				p.R394L		Atlas-SNP	.											.	CXorf36	53	.	0			c.G1181T						PASS	.	C	LEU/ARG	336,2291		19,221,77,819,432	63.0	57.0	59.0		1181	0.3	0.0	X	dbSNP_134	59	0,5498		0,0,0,1916,1666	yes	missense	CXorf36	NM_176819.3	102	19,221,77,2735,2098	AA,AC,A,CC,C		0.0,12.7903,4.1354	benign	394/434	45011018	336,7789	1568	3582	5150	SO:0001583	missense	79742	exon5			TCTGGGCGGATGC	AF289581	CCDS14266.1, CCDS48096.1	Xp11.3-p11.23	2012-08-03			ENSG00000147113	ENSG00000147113			25866	protein-coding gene	gene with protein product						11944989, 21283809	Standard	NM_176819		Approved	FLJ14103, DIA1R	uc004dgg.2	Q9H7Y0	OTTHUMG00000021403	ENST00000398000.2:c.1181G>T	X.37:g.45011018C>A	ENSP00000381086:p.Arg394Leu	121.0	0.0	0		109.0	108.0	0.990826	NM_176819	A8MUU5|B2RPN7|Q6UWJ5	Missense_Mutation	SNP	ENST00000398000.2	37	CCDS48096.1	50	0.030138637733574444	36	0.07692307692307693	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	1.583	-0.531173	0.04112	0.127903	0.0	ENSG00000147113	ENST00000398000	T	0.28895	1.59	5.17	0.326	0.15908	.	1.193830	0.06015	N	0.650241	T	0.00178	0.0005	N	0.16307	0.4	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.24476	-1.0159	9	0.27082	T	0.32	.	3.0329	0.06112	0.3241:0.4237:0.0931:0.1592	.	394	Q9H7Y0	CX036_HUMAN	L	394	ENSP00000381086:R394L	ENSP00000381086:R394L	R	-	2	0	CXorf36	44895962	0.000000	0.05858	0.001000	0.08648	0.055000	0.15305	-0.848000	0.04326	-0.006000	0.14370	-0.215000	0.12644	CGC	C|0.970;A|0.030	0.030	strong		0.572	CXorf36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056333.2	NM_024689	
WBSCR27	155368	hgsc.bcm.edu	37	7	73254871	73254871	+	Silent	SNP	A	A	G	rs61741292	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:73254871A>G	ENST00000297873.4	-	4	310	c.261T>C	c.(259-261)gcT>gcC	p.A87A		NM_152559.2	NP_689772.2	Q8N6F8	WBS27_HUMAN	Williams Beuren syndrome chromosome region 27	87										NS(1)|central_nervous_system(1)|lung(2)|prostate(1)	5		Lung NSC(55;0.159)				GGAAGCCTGGAGCCCGCAGCT	0.672													A|||	173	0.0345447	0.1263	0.0072	5008	,	,		14138	0.0		0.001	False		,,,				2504	0.0				p.A87A		Atlas-SNP	.											.	WBSCR27	21	.	0			c.T261C						PASS	.	A		341,3999		14,313,1843	14.0	17.0	16.0		261	-0.2	1.0	7	dbSNP_129	16	2,8534		0,2,4266	no	coding-synonymous	WBSCR27	NM_152559.2		14,315,6109	GG,GA,AA		0.0234,7.8571,2.6639		87/246	73254871	343,12533	2170	4268	6438	SO:0001819	synonymous_variant	155368	exon4			GCCTGGAGCCCGC	AF534110	CCDS5561.1	7q11.23	2004-07-05			ENSG00000165171	ENSG00000165171			19068	protein-coding gene	gene with protein product		612546					Standard	NM_152559		Approved		uc003tzj.2	Q8N6F8	OTTHUMG00000130033	ENST00000297873.4:c.261T>C	7.37:g.73254871A>G		111.0	0.0	0		95.0	95.0	1	NM_152559		Silent	SNP	ENST00000297873.4	37	CCDS5561.1																																																																																			A|0.974;G|0.026	0.026	strong		0.672	WBSCR27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252312.1	NM_152559	
SPAG17	200162	hgsc.bcm.edu	37	1	118634297	118634297	+	Missense_Mutation	SNP	A	A	C	rs150596428	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:118634297A>C	ENST00000336338.5	-	10	1356	c.1291T>G	c.(1291-1293)Tat>Gat	p.Y431D		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	431						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		TTCAGCAAATAATTGTAATAT	0.383													C|||	6	0.00119808	0.0045	0.0	5008	,	,		18256	0.0		0.0	False		,,,				2504	0.0				p.Y431D		Atlas-SNP	.											.	SPAG17	263	.	0			c.T1291G						PASS	.	C	ASP/TYR	28,4376	822.7+/-416.5	1,26,2175	89.0	85.0	86.0		1291	5.6	1.0	1	dbSNP_134	86	0,8600		0,0,4300	yes	missense	SPAG17	NM_206996.2	160	1,26,6475	CC,CA,AA		0.0,0.6358,0.2153	benign	431/2224	118634297	28,12976	2202	4300	6502	SO:0001583	missense	200162	exon10			GCAAATAATTGTA		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.1291T>G	1.37:g.118634297A>C	ENSP00000337804:p.Tyr431Asp	145.0	0.0	0		145.0	59.0	0.406897	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	.	.	.	.	.	.	.	.	.	.	C	7.275	0.607874	0.14002	0.006358	0.0	ENSG00000155761	ENST00000336338	T	0.67171	-0.25	5.59	5.59	0.84812	.	0.259606	0.43747	N	0.000525	T	0.07863	0.0197	N	0.00043	-2.47	0.26007	N	0.982046	B	0.02656	0.0	B	0.01281	0.0	T	0.33317	-0.9873	10	0.02654	T	1	.	16.0877	0.81070	0.1351:0.8649:0.0:0.0	.	431	Q6Q759	SPG17_HUMAN	D	431	ENSP00000337804:Y431D	ENSP00000337804:Y431D	Y	-	1	0	SPAG17	118435820	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	2.779000	0.47734	1.387000	0.46486	-0.127000	0.14921	TAT	A|0.997;C|0.003	0.003	strong		0.383	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
MAD1L1	8379	hgsc.bcm.edu	37	7	2275177	2275177	+	5'Flank	SNP	G	G	A	rs11547272	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:2275177G>A	ENST00000406869.1	-	0	0				FTSJ2_ENST00000242257.8_Silent_p.F107F|MAD1L1_ENST00000265854.7_5'Flank|FTSJ2_ENST00000440306.2_Missense_Mutation_p.S142L|FTSJ2_ENST00000486040.1_5'UTR|MAD1L1_ENST00000402746.1_5'Flank|MAD1L1_ENST00000399654.2_5'Flank|FTSJ2_ENST00000407040.1_Silent_p.F13F			Q9Y6D9	MD1L1_HUMAN	MAD1 mitotic arrest deficient-like 1 (yeast)						mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|regulation of metaphase plate congression (GO:0090235)	actin cytoskeleton (GO:0015629)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|spindle (GO:0005819)				central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(5)	36		Ovarian(82;0.0272)		UCEC - Uterine corpus endometrioid carcinoma (27;0.134)|OV - Ovarian serous cystadenocarcinoma(56;3.63e-14)		CCCCAAGCACGAAGCCAACAG	0.448													G|||	73	0.0145767	0.0537	0.0029	5008	,	,		22055	0.0		0.0	False		,,,				2504	0.0				p.F107F		Atlas-SNP	.											.	FTSJ2	22	.	0			c.C321T						PASS	.	G		246,4160	136.9+/-172.8	7,232,1964	49.0	47.0	48.0		321	-5.2	0.8	7	dbSNP_120	48	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	FTSJ2	NM_013393.1		7,235,6261	AA,AG,GG		0.0349,5.5833,1.9145		107/247	2275177	249,12757	2203	4300	6503	SO:0001631	upstream_gene_variant	29960	exon3			AAGCACGAAGCCA	U33822	CCDS43539.1	7p22	2013-01-17	2001-11-28		ENSG00000002822	ENSG00000002822			6762	protein-coding gene	gene with protein product		602686	"""MAD1 (mitotic arrest deficient, yeast, homolog)-like 1"""			10049595, 9546394	Standard	XM_005249876		Approved	HsMAD1, TXBP181, MAD1, PIG9, TP53I9	uc003slg.1	Q9Y6D9	OTTHUMG00000151493		7.37:g.2275177G>A	Exception_encountered	35.0	0.0	0		42.0	29.0	0.690476	NM_013393	B3KR41|Q13312|Q75MI0|Q86UM4|Q9UNH0	Silent	SNP	ENST00000406869.1	37	CCDS43539.1	30	0.013736263736263736	28	0.056910569105691054	2	0.0055248618784530384	0	0.0	0	0.0	G	15.89	2.967220	0.53507	0.055833	3.49E-4	ENSG00000122687	ENST00000440306	T	0.30714	1.52	5.47	-5.18	0.02840	.	.	.	.	.	T	0.05181	0.0138	.	.	.	0.22710	N	0.99883	.	.	.	.	.	.	T	0.39961	-0.9588	6	0.87932	D	0	.	14.6466	0.68764	0.5757:0.0:0.4243:0.0	rs11547272	.	.	.	L	142	ENSP00000392343:S142L	ENSP00000392343:S142L	S	-	2	0	FTSJ2	2241703	0.001000	0.12720	0.835000	0.33067	0.981000	0.71138	-1.403000	0.02497	-1.417000	0.02017	-0.137000	0.14449	TCG	G|0.982;C|0.000;A|0.018	0.018	strong		0.448	MAD1L1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322871.1	NM_003550	
SPHK2	56848	hgsc.bcm.edu	37	19	49133020	49133020	+	Missense_Mutation	SNP	G	G	A	rs11881285	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49133020G>A	ENST00000245222.4	+	7	2321	c.1955G>A	c.(1954-1956)cGg>cAg	p.R652Q	SPHK2_ENST00000443164.1_Intron|SPHK2_ENST00000600537.1_Missense_Mutation_p.R593Q|SPHK2_ENST00000598088.1_Missense_Mutation_p.R652Q|SPHK2_ENST00000599029.1_Intron|SPHK2_ENST00000340932.3_Missense_Mutation_p.R614Q|SPHK2_ENST00000599748.1_Missense_Mutation_p.R616Q	NM_001204158.2|NM_001243876.1|NM_020126.4	NP_001191087.1|NP_001230805.1|NP_064511.2	Q9NRA0	SPHK2_HUMAN	sphingosine kinase 2	652			R -> Q (in dbSNP:rs11881285).		blood vessel development (GO:0001568)|brain development (GO:0007420)|cell proliferation (GO:0008283)|lipid phosphorylation (GO:0046834)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|small molecule metabolic process (GO:0044281)|sphinganine-1-phosphate biosynthetic process (GO:0006669)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)|sphingosine metabolic process (GO:0006670)	cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	ATP binding (GO:0005524)|D-erythro-sphingosine kinase activity (GO:0017050)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|Ras GTPase binding (GO:0017016)|sphinganine kinase activity (GO:0008481)			NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(4)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	19		all_lung(116;0.000125)|Lung NSC(112;0.000202)|all_epithelial(76;0.000283)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		TGCCCGGGGCGGGAGCCCTGA	0.657													G|||	274	0.0547125	0.1959	0.0216	5008	,	,		14281	0.0		0.0	False		,,,				2504	0.0				p.R652Q		Atlas-SNP	.											.	SPHK2	62	.	0			c.G1955A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	687,3701		44,599,1551	13.0	14.0	13.0		1955,1847,1955,1778	0.8	0.0	19	dbSNP_120	13	3,8561		0,3,4279	yes	missense,missense,missense,missense	SPHK2	NM_020126.4,NM_001204160.2,NM_001204159.2,NM_001204158.2	43,43,43,43	44,602,5830	AA,AG,GG		0.035,15.6563,5.3274	benign,benign,benign,benign	652/655,616/619,652/655,593/596	49133020	690,12262	2194	4282	6476	SO:0001583	missense	56848	exon7			CGGGGCGGGAGCC	AF245447	CCDS12727.1, CCDS59404.1, CCDS59405.1, CCDS74414.1	19q13.33	2013-09-20			ENSG00000063176	ENSG00000063176			18859	protein-coding gene	gene with protein product		607092				10751414, 17895250	Standard	NM_020126		Approved		uc002pjs.3	Q9NRA0	OTTHUMG00000183318	ENST00000245222.4:c.1955G>A	19.37:g.49133020G>A	ENSP00000245222:p.Arg652Gln	150.0	1.0	0.00666667		165.0	165.0	1	NM_020126	A0T4C8|B4DU87|Q9BRN1|Q9H0Q2|Q9NWU7	Missense_Mutation	SNP	ENST00000245222.4	37	CCDS12727.1	94	0.04304029304029304	84	0.17073170731707318	10	0.027624309392265192	0	0.0	0	0.0	G	13.95	2.389587	0.42410	0.156563	3.5E-4	ENSG00000063176	ENST00000245222;ENST00000406269;ENST00000340932	T;T	0.26067	2.04;1.76	4.57	0.757	0.18427	.	1.133370	0.06720	N	0.774700	T	0.00039	0.0001	N	0.00926	-1.1	0.09310	N	1	B;B	0.10296	0.001;0.003	B;B	0.01281	0.0;0.0	T	0.29882	-0.9997	10	0.87932	D	0	.	4.2933	0.10888	0.1758:0.4248:0.3994:0.0	rs11881285;rs11881285	593;652	B4DU87;Q9NRA0	.;SPHK2_HUMAN	Q	652;625;614	ENSP00000245222:R652Q;ENSP00000341091:R614Q	ENSP00000245222:R652Q	R	+	2	0	SPHK2	53824832	0.005000	0.15991	0.003000	0.11579	0.039000	0.13416	0.222000	0.17699	0.076000	0.16826	0.555000	0.69702	CGG	G|0.942;A|0.058	0.058	strong		0.657	SPHK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466153.1		
DGKA	1606	hgsc.bcm.edu	37	12	56346891	56346891	+	Silent	SNP	C	C	T	rs199663532		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56346891C>T	ENST00000331886.5	+	22	2464	c.2010C>T	c.(2008-2010)acC>acT	p.T670T	DGKA_ENST00000551156.1_Silent_p.T670T|DGKA_ENST00000394147.1_Silent_p.T670T|DGKA_ENST00000549079.2_3'UTR	NM_001345.4	NP_001336.2	P23743	DGKA_HUMAN	diacylglycerol kinase, alpha 80kDa	670					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)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|diacylglycerol kinase activity (GO:0004143)|NAD+ kinase activity (GO:0003951)|phospholipid binding (GO:0005543)			breast(1)|endometrium(3)|large_intestine(1)|lung(11)|ovary(4)|pancreas(1)|skin(3)|urinary_tract(1)	25					Vitamin E(DB00163)	AAATCTATACCAAGCTCAAGA	0.532																																					p.T670T		Atlas-SNP	.											.	DGKA	70	.	0			c.C2010T						PASS	.						112.0	109.0	110.0					12																	56346891		2203	4300	6503	SO:0001819	synonymous_variant	1606	exon22			CTATACCAAGCTC	AF064767	CCDS8896.1	12q13.3	2013-01-10	2002-08-29			ENSG00000065357	2.7.1.107	"""EF-hand domain containing"""	2849	protein-coding gene	gene with protein product		125855	"""diacylglycerol kinase, alpha (80kD)"""	DAGK, DAGK1		8180475, 7959783	Standard	NM_001345		Approved	DGK-alpha	uc001sim.3	P23743		ENST00000331886.5:c.2010C>T	12.37:g.56346891C>T		123.0	0.0	0		108.0	48.0	0.444444	NM_201554	O75481|O75482|O75483|O95217|Q3ZE25|Q8IZ56|Q8N5Q2	Silent	SNP	ENST00000331886.5	37	CCDS8896.1																																																																																			.	.	none		0.532	DGKA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407291.1		
BRSK1	84446	hgsc.bcm.edu	37	19	55815072	55815072	+	Silent	SNP	C	C	T	rs17851414	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55815072C>T	ENST00000309383.1	+	12	1441	c.1164C>T	c.(1162-1164)agC>agT	p.S388S	BRSK1_ENST00000326848.7_Silent_p.S83S|BRSK1_ENST00000590333.1_Silent_p.S404S	NM_032430.1	NP_115806.1	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1	388					axonogenesis (GO:0007409)|cellular response to DNA damage stimulus (GO:0006974)|centrosome duplication (GO:0051298)|establishment of cell polarity (GO:0030010)|G2 DNA damage checkpoint (GO:0031572)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|protein phosphorylation (GO:0006468)|response to UV (GO:0009411)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(15)|ovary(2)|prostate(2)|skin(6)|stomach(1)	48		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0474)		CCATGCTGAGCCGTCACGGGA	0.617													C|||	156	0.0311502	0.115	0.0058	5008	,	,		15985	0.0		0.0	False		,,,				2504	0.0				p.S388S		Atlas-SNP	.											.	BRSK1	192	.	0			c.C1164T						PASS	.	C		400,4006		19,362,1822	63.0	72.0	69.0		1164	4.0	1.0	19	dbSNP_123	69	3,8597		0,3,4297	no	coding-synonymous	BRSK1	NM_032430.1		19,365,6119	TT,TC,CC		0.0349,9.0785,3.0986		388/779	55815072	403,12603	2203	4300	6503	SO:0001819	synonymous_variant	84446	exon12			GCTGAGCCGTCAC	AB058714	CCDS12921.1	19q13.4	2008-02-05				ENSG00000160469			18994	protein-coding gene	gene with protein product		609235				14976552	Standard	NM_032430		Approved	KIAA1811	uc002qkg.3	Q8TDC3		ENST00000309383.1:c.1164C>T	19.37:g.55815072C>T		158.0	0.0	0		122.0	60.0	0.491803	NM_032430	F1DG44|Q5J5B5|Q8NDD0|Q8NDR4|Q8TDC2|Q96AV4|Q96JL4	Silent	SNP	ENST00000309383.1	37	CCDS12921.1																																																																																			C|0.969;T|0.031	0.031	strong		0.617	BRSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452787.1	NM_032430	
PKD1L2	114780	hgsc.bcm.edu	37	16	81208348	81208348	+	RNA	SNP	G	G	T	rs745211	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:81208348G>T	ENST00000527937.1	-	0	636				PKD1L2_ENST00000533478.1_RNA|PKD1L2_ENST00000337114.4_RNA|PKD1L2_ENST00000525539.1_RNA|PKD1L2_ENST00000531391.1_RNA			Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						TCTATGCTCAGTGACTGTCCT	0.622													G|||	336	0.0670927	0.2443	0.0187	5008	,	,		18559	0.0		0.0	False		,,,				2504	0.0				p.L919M		Atlas-SNP	.											.	PKD1L2	361	.	0			c.C2755A						PASS	.	G	MET/LEU,MET/LEU	897,3165		103,691,1237	55.0	54.0	54.0		2755,2755	4.3	0.0	16	dbSNP_86	54	8,8374		0,8,4183	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	15,15	103,699,5420	TT,TG,GG		0.0954,22.0827,7.2726	probably-damaging,probably-damaging	919/992,919/2460	81208348	905,11539	2031	4191	6222			114780	exon16			TGCTCAGTGACTG	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81208348G>T		115.0	0.0	0		118.0	67.0	0.567797	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000527937.1	37		139|139	0.06364468864468864|0.06364468864468864	134|134	0.27235772357723576|0.27235772357723576	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	0|0	0.0|0.0	G|G	15.20|15.20	2.762411|2.762411	0.49468|0.49468	0.220827|0.220827	9.54E-4|9.54E-4	ENSG00000166473|ENSG00000166473	ENST00000531391;ENST00000337114;ENST00000527937|ENST00000526632	T;T;T|.	0.34667|.	2.35;4.96;1.35|.	4.33|4.33	4.33|4.33	0.51752|0.51752	Egg jelly receptor, REJ-like (1);|.	1.304660|.	0.05138|.	N|.	0.493678|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	D;D;B|.	0.89917|.	0.999;1.0;0.329|.	D;D;B|.	0.74348|.	0.967;0.983;0.077|.	T|T	0.03086|0.03086	-1.1074|-1.1074	8|3	0.87932|.	D|.	0|.	-5.2934|-5.2934	14.1184|14.1184	0.65169|0.65169	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs745211;rs52837063;rs745211|rs745211;rs52837063;rs745211	175;919;919|.	Q7Z442-6;Q7Z442-3;Q7Z442|.	.;.;PK1L2_HUMAN|.	M|N	234;919;175|446	ENSP00000436309:L234M;ENSP00000337397:L919M;ENSP00000432818:L175M|.	ENSP00000337397:L919M|.	L|T	-|-	1|2	2|0	PKD1L2|PKD1L2	79765849|79765849	0.108000|0.108000	0.22018|0.22018	0.003000|0.003000	0.11579|0.11579	0.003000|0.003000	0.03518|0.03518	3.794000|3.794000	0.55492|0.55492	2.116000|2.116000	0.64780|0.64780	0.555000|0.555000	0.69702|0.69702	CTG|ACT	G|0.924;T|0.076	0.076	strong		0.622	PKD1L2-007	KNOWN	basic|exp_conf	protein_coding	polymorphic_pseudogene	OTTHUMT00000387978.1		
PSMF1	9491	hgsc.bcm.edu	37	20	1106143	1106143	+	Silent	SNP	G	G	A	rs35517343	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:1106143G>A	ENST00000335877.6	+	2	308	c.132G>A	c.(130-132)ccG>ccA	p.P44P	PSMF1_ENST00000333082.3_Silent_p.P44P|PSMF1_ENST00000381898.4_5'UTR|PSMF1_ENST00000438768.2_Silent_p.P44P|PSMF1_ENST00000246015.4_Silent_p.P44P	NM_006814.3	NP_006805.2	Q92530	PSMF1_HUMAN	proteasome (prosome, macropain) inhibitor subunit 1 (PI31)	44	Important for homodimerization and interaction with FBXO7.				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)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of proteasomal protein catabolic process (GO:1901799)|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 polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|proteasome core complex (GO:0005839)	endopeptidase inhibitor activity (GO:0004866)|proteasome binding (GO:0070628)			endometrium(1)|kidney(1)|large_intestine(3)|lung(8)	13						CTTCCCAGCCGGGTCCCAATG	0.458													G|||	15	0.00299521	0.0113	0.0	5008	,	,		21820	0.0		0.0	False		,,,				2504	0.0				p.P44P		Atlas-SNP	.											.	PSMF1	27	.	0			c.G132A						PASS	.	G	,	61,4345	58.7+/-95.3	0,61,2142	77.0	70.0	72.0		132,132	-3.1	0.1	20	dbSNP_126	72	1,8599		0,1,4299	no	coding-synonymous,coding-synonymous	PSMF1	NM_006814.3,NM_178578.2	,	0,62,6441	AA,AG,GG		0.0116,1.3845,0.4767	,	44/272,44/272	1106143	62,12944	2203	4300	6503	SO:0001819	synonymous_variant	9491	exon2			CCAGCCGGGTCCC	D88378	CCDS13010.1	20p13	2008-07-02			ENSG00000125818	ENSG00000125818		"""Proteasome (prosome, macropain) subunits"""	9571	protein-coding gene	gene with protein product	"""proteasome inhibitor hP131 subunit"""					10363639	Standard	NM_006814		Approved	PI31	uc002wen.4	Q92530	OTTHUMG00000031656	ENST00000335877.6:c.132G>A	20.37:g.1106143G>A		90.0	0.0	0		106.0	52.0	0.490566	NM_006814	A0AVQ9|D3DVW3|Q9H4I1	Silent	SNP	ENST00000335877.6	37	CCDS13010.1																																																																																			G|0.995;A|0.005	0.005	strong		0.458	PSMF1-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077504.2	NM_178578	
TRAF1	7185	hgsc.bcm.edu	37	9	123671613	123671613	+	Silent	SNP	C	C	T	rs112060909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:123671613C>T	ENST00000373887.3	-	7	3372	c.927G>A	c.(925-927)ctG>ctA	p.L309L	TRAF1_ENST00000546084.1_Silent_p.L187L|TRAF1_ENST00000540010.1_Silent_p.L309L	NM_005658.4	NP_005649.1	Q13077	TRAF1_HUMAN	TNF receptor-associated factor 1	309	MATH. {ECO:0000255|PROSITE- ProRule:PRU00129}.				apoptotic process (GO:0006915)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein complex assembly (GO:0006461)|regulation of extrinsic apoptotic signaling pathway (GO:2001236)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(9)|ovary(4)|pancreas(1)|skin(2)	22						CATTCAGGTACAGCCGCAGGC	0.547													C|||	68	0.0135783	0.0492	0.0043	5008	,	,		20674	0.0		0.0	False		,,,				2504	0.0				p.L309L		Atlas-SNP	.											.	TRAF1	42	.	0			c.G927A						PASS	.	C	,,	179,4227	117.1+/-155.0	3,173,2027	173.0	163.0	167.0		927,561,927	-0.2	1.0	9	dbSNP_132	167	6,8594	5.7+/-21.5	0,6,4294	no	coding-synonymous,coding-synonymous,coding-synonymous	TRAF1	NM_001190945.1,NM_001190947.1,NM_005658.4	,,	3,179,6321	TT,TC,CC		0.0698,4.0626,1.4224	,,	309/417,187/295,309/417	123671613	185,12821	2203	4300	6503	SO:0001819	synonymous_variant	7185	exon7			CAGGTACAGCCGC	AK090468	CCDS6825.1, CCDS55335.1	9q33-q34	2008-02-05			ENSG00000056558	ENSG00000056558			12031	protein-coding gene	gene with protein product		601711				8069916	Standard	NM_001190945		Approved	EBI6	uc010mvl.2	Q13077	OTTHUMG00000020578	ENST00000373887.3:c.927G>A	9.37:g.123671613C>T		109.0	0.0	0		127.0	48.0	0.377953	NM_005658	B4DJ77|Q658U1|Q8NF13	Silent	SNP	ENST00000373887.3	37	CCDS6825.1																																																																																			C|0.983;T|0.017	0.017	strong		0.547	TRAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053843.1	NM_005658	
TTN	7273	hgsc.bcm.edu	37	2	179610619	179610619	+	Intron	SNP	C	C	G	rs16866489	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179610619C>G	ENST00000591111.1	-	46	10585				TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Intron|TTN_ENST00000360870.5_Missense_Mutation_p.S5503T|TTN-AS1_ENST00000578746.1_RNA|TTN-AS1_ENST00000582847.1_RNA|TTN_ENST00000359218.5_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Intron			Q8WZ42	TITIN_HUMAN	titin						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)			TTCAAAAAAACTGTCTGTGTA	0.378													C|||	29	0.00579073	0.0204	0.0029	5008	,	,		21580	0.0		0.0	False		,,,				2504	0.0				p.S5503T		Atlas-SNP	.											.	TTN	18412	.	0			c.G16508C						PASS	.	C	,,THR/SER,,	80,4326	70.9+/-108.8	0,80,2123	114.0	111.0	112.0		,,16508,,	5.1	1.0	2	dbSNP_123	112	2,8596	1.2+/-3.3	0,2,4297	yes	intron,intron,missense,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,58,,	0,82,6420	GG,GC,CC		0.0233,1.8157,0.6306	,,,,	,,5503/5605,,	179610619	82,12922	2203	4299	6502	SO:0001627	intron_variant	7273	exon46			AAAAAACTGTCTG	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.10361-3971G>C	2.37:g.179610619C>G		91.0	0.0	0		118.0	66.0	0.559322	NM_133379	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		13	0.005952380952380952	12	0.024390243902439025	1	0.0027624309392265192	0	0.0	0	0.0	C	12.68	2.011534	0.35511	0.018157	2.33E-4	ENSG00000155657	ENST00000360870;ENST00000306136	T	0.58210	0.35	5.94	5.06	0.68205	.	.	.	.	.	T	0.22704	0.0548	L	0.27053	0.805	0.80722	D	1	P	0.35272	0.493	B	0.33620	0.167	T	0.06770	-1.0808	9	0.30078	T	0.28	.	12.1518	0.54053	0.0:0.9185:0.0:0.0815	rs16866489;rs16866489	5503	Q8WZ42-6	.	T	5503;784	ENSP00000354117:S5503T	ENSP00000304714:S784T	S	-	2	0	TTN	179318864	1.000000	0.71417	1.000000	0.80357	0.591000	0.36615	2.864000	0.48404	2.816000	0.96949	0.563000	0.77884	AGT	C|0.992;G|0.008	0.008	strong		0.378	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
RYR3	6263	hgsc.bcm.edu	37	15	34030767	34030767	+	Silent	SNP	G	G	T	rs115185294	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:34030767G>T	ENST00000389232.4	+	50	7702	c.7632G>T	c.(7630-7632)ggG>ggT	p.G2544G	RYR3_ENST00000415757.3_Silent_p.G2544G	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	2544	4 X approximate repeats.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TTTTCTGGGGGATTTTTGACT	0.473											OREG0023032	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	36	0.0071885	0.025	0.0043	5008	,	,		18919	0.0		0.0	False		,,,				2504	0.0				p.G2544G		Atlas-SNP	.											.	RYR3	760	.	0			c.G7632T						PASS	.	G		61,3703		1,59,1822	96.0	104.0	102.0		7632	0.4	1.0	15	dbSNP_132	102	1,8205		0,1,4102	no	coding-synonymous	RYR3	NM_001036.3		1,60,5924	TT,TG,GG		0.0122,1.6206,0.518		2544/4871	34030767	62,11908	1882	4103	5985	SO:0001819	synonymous_variant	6263	exon50			CTGGGGGATTTTT		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.7632G>T	15.37:g.34030767G>T		65.0	0.0	0	844	59.0	25.0	0.423729	NM_001243996	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			G|0.994;T|0.006	0.006	strong		0.473	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
RFFL	117584	hgsc.bcm.edu	37	17	33348541	33348541	+	Missense_Mutation	SNP	C	C	T	rs34747500	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:33348541C>T	ENST00000315249.7	-	3	662	c.440G>A	c.(439-441)cGt>cAt	p.R147H	RFFL_ENST00000584655.1_Missense_Mutation_p.R147H|RFFL_ENST00000415395.2_Missense_Mutation_p.R147H|RFFL_ENST00000378516.2_Missense_Mutation_p.R147H|RFFL_ENST00000394597.2_Missense_Mutation_p.R147H|RFFL_ENST00000413582.2_Missense_Mutation_p.R147H|RFFL_ENST00000268850.7_Missense_Mutation_p.R147H|RFFL_ENST00000447669.2_Missense_Mutation_p.R147H|RAD51L3-RFFL_ENST00000593039.1_Intron					ring finger and FYVE-like domain containing E3 ubiquitin protein ligase											kidney(1)|large_intestine(2)|lung(3)	6		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0227)		GGTGGAGGCACGAGTCCTGTC	0.582													C|||	68	0.0135783	0.0356	0.0029	5008	,	,		19710	0.0188		0.0	False		,,,				2504	0.0				p.R147H		Atlas-SNP	.											.	RFFL	27	.	0			c.G440A						PASS	.	C	HIS/ARG	124,4282	91.6+/-130.3	3,118,2082	81.0	65.0	70.0		440	-4.3	0.4	17	dbSNP_126	70	1,8599	1.2+/-3.3	0,1,4299	yes	missense	RFFL	NM_001017368.1	29	3,119,6381	TT,TC,CC		0.0116,2.8143,0.9611	benign	147/364	33348541	125,12881	2203	4300	6503	SO:0001583	missense	117584	exon3			GAGGCACGAGTCC	AF434816	CCDS11286.1	17q12	2012-02-23	2012-02-23		ENSG00000092871	ENSG00000092871		"""RING-type (C3HC4) zinc fingers"""	24821	protein-coding gene	gene with protein product		609735	"""ring finger and FYVE-like domain containing"""			15229288	Standard	NR_037713		Approved	rififylin, fring, RNF189, RNF34L	uc002hin.1	Q8WZ73	OTTHUMG00000132933	ENST00000315249.7:c.440G>A	17.37:g.33348541C>T	ENSP00000326170:p.Arg147His	132.0	0.0	0		138.0	65.0	0.471014	NM_001017368		Missense_Mutation	SNP	ENST00000315249.7	37	CCDS11286.1	31	0.014194139194139194	16	0.032520325203252036	1	0.0027624309392265192	14	0.024475524475524476	0	0.0	C	7.587	0.669935	0.14776	0.028143	1.16E-4	ENSG00000092871	ENST00000315249;ENST00000394597;ENST00000378516;ENST00000268850;ENST00000413582;ENST00000415395	T;T;T;T;T;T	0.46451	0.87;0.87;0.89;0.91;0.89;0.87	5.65	-4.35	0.03656	.	1.494590	0.03679	N	0.245226	T	0.14184	0.0343	L	0.46157	1.445	0.19300	N	0.999975	B;B;B;B	0.10296	0.003;0.003;0.002;0.003	B;B;B;B	0.10450	0.005;0.003;0.001;0.001	T	0.33497	-0.9866	10	0.45353	T	0.12	-0.0021	7.6995	0.28615	0.1025:0.4344:0.0:0.4631	rs34747500	147;147;147;147	C9JN73;Q8WZ73-3;Q8WZ73;Q8WZ73-2	.;.;RFFL_HUMAN;.	H	147	ENSP00000326170:R147H;ENSP00000378096:R147H;ENSP00000367777:R147H;ENSP00000268850:R147H;ENSP00000408513:R147H;ENSP00000412322:R147H	ENSP00000268850:R147H	R	-	2	0	RFFL	30372654	0.000000	0.05858	0.450000	0.26969	0.123000	0.20343	-1.166000	0.03129	-0.526000	0.06383	-0.940000	0.02684	CGT	C|0.986;T|0.014	0.014	strong		0.582	RFFL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256460.2	NM_057178	
RALBP1	10928	hgsc.bcm.edu	37	18	9517221	9517221	+	Missense_Mutation	SNP	G	G	A	rs28552921	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:9517221G>A	ENST00000019317.4	+	3	846	c.623G>A	c.(622-624)cGg>cAg	p.R208Q	RNU2-27P_ENST00000516185.1_RNA|RALBP1_ENST00000383432.3_Missense_Mutation_p.R208Q|RP11-61L19.3_ENST00000609094.1_RNA			Q15311	RBP1_HUMAN	ralA binding protein 1	208	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				ATP catabolic process (GO:0006200)|chemotaxis (GO:0006935)|positive regulation of Cdc42 GTPase activity (GO:0043089)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|transport (GO:0006810)	cytosol (GO:0005829)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ATPase activity, coupled to movement of substances (GO:0043492)|GTPase activator activity (GO:0005096)|Rac GTPase activator activity (GO:0030675)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|lung(3)|upper_aerodigestive_tract(1)	14					Carbamazepine(DB00564)|Doxorubicin(DB00997)|Sorafenib(DB00398)|Vincristine(DB00541)	GATGGCATTCGGCTGCCAGCC	0.458													G|||	21	0.00419329	0.0159	0.0	5008	,	,		18073	0.0		0.0	False		,,,				2504	0.0				p.R208Q		Atlas-SNP	.											.	RALBP1	48	.	0			c.G623A						PASS	.	G	GLN/ARG	41,4365	45.3+/-79.5	0,41,2162	71.0	66.0	67.0		623	4.2	0.9	18	dbSNP_125	67	0,8600		0,0,4300	yes	missense	RALBP1	NM_006788.3	43	0,41,6462	AA,AG,GG		0.0,0.9305,0.3152	benign	208/656	9517221	41,12965	2203	4300	6503	SO:0001583	missense	10928	exon3			GCATTCGGCTGCC	L42542	CCDS11845.1	18p11.22	2006-04-22			ENSG00000017797	ENSG00000017797			9841	protein-coding gene	gene with protein product		605801				7673236	Standard	NM_006788		Approved	RLIP76, RIP1, RIP	uc002koc.3	Q15311	OTTHUMG00000131596	ENST00000019317.4:c.623G>A	18.37:g.9517221G>A	ENSP00000019317:p.Arg208Gln	366.0	1.0	0.00273224		380.0	179.0	0.471053	NM_006788	D3DUI0	Missense_Mutation	SNP	ENST00000019317.4	37	CCDS11845.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	G	11.16	1.558039	0.27827	0.009305	0.0	ENSG00000017797	ENST00000019317;ENST00000383432;ENST00000458039	T;T	0.22134	1.97;1.97	5.1	4.22	0.49857	Rho GTPase-activating protein domain (3);Rho GTPase activation protein (1);	0.120124	0.56097	D	0.000026	T	0.04724	0.0128	N	0.04768	-0.165	0.43489	D	0.995729	B	0.15473	0.013	B	0.04013	0.001	T	0.14476	-1.0471	10	0.14252	T	0.57	-0.6029	13.6511	0.62312	0.0752:0.0:0.9248:0.0	rs28552921	208	Q15311	RBP1_HUMAN	Q	208	ENSP00000019317:R208Q;ENSP00000372924:R208Q	ENSP00000019317:R208Q	R	+	2	0	RALBP1	9507221	0.992000	0.36948	0.879000	0.34478	0.997000	0.91878	3.800000	0.55537	1.264000	0.44198	0.655000	0.94253	CGG	G|0.996;A|0.004	0.004	strong		0.458	RALBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254479.1	NM_006788	
OR10G2	26534	hgsc.bcm.edu	37	14	22102315	22102315	+	Silent	SNP	A	A	G	rs61753931	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:22102315A>G	ENST00000542433.1	-	1	781	c.684T>C	c.(682-684)caT>caC	p.H228H		NM_001005466.1	NP_001005466.1	Q8NGC3	O10G2_HUMAN	olfactory receptor, family 10, subfamily G, member 2	228						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|prostate(1)|skin(2)|stomach(2)	22	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0142)		TCAGGATGGCATGGACTATGT	0.532													.|||	70	0.0139776	0.053	0.0	5008	,	,		17587	0.0		0.0	False		,,,				2504	0.0				p.H228H		Atlas-SNP	.											.	OR10G2	35	.	0			c.T684C						PASS	.	A		210,4082		33,144,1969	52.0	52.0	52.0		684	-1.2	0.9	14	dbSNP_129	52	4,8380		1,2,4189	no	coding-synonymous	OR10G2	NM_001005466.1		34,146,6158	GG,GA,AA		0.0477,4.8928,1.6882		228/311	22102315	214,12462	2146	4192	6338	SO:0001819	synonymous_variant	26534	exon1			GATGGCATGGACT		CCDS32047.1	14q11.2	2013-09-24			ENSG00000255582	ENSG00000255582		"""GPCR / Class A : Olfactory receptors"""	8170	protein-coding gene	gene with protein product						8188290	Standard	NM_001005466		Approved		uc010tmc.2	Q8NGC3	OTTHUMG00000168890	ENST00000542433.1:c.684T>C	14.37:g.22102315A>G		375.0	0.0	0		356.0	173.0	0.485955	NM_001005466	B2RPD0	Silent	SNP	ENST00000542433.1	37	CCDS32047.1																																																																																			A|0.983;G|0.017	0.017	strong		0.532	OR10G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401525.1		
ZC3H13	23091	hgsc.bcm.edu	37	13	46584500	46584500	+	Silent	SNP	G	G	A	rs79878411	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:46584500G>A	ENST00000242848.4	-	7	1077	c.729C>T	c.(727-729)ccC>ccT	p.P243P	ZC3H13_ENST00000282007.3_Silent_p.P243P|ZC3H13_ENST00000470308.1_5'UTR			Q5T200	ZC3HD_HUMAN	zinc finger CCCH-type containing 13	243							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(27)|lung(25)|ovary(2)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	79		Lung NSC(96;7.26e-05)|Breast(56;0.000118)|Prostate(109;0.00217)|Hepatocellular(98;0.0207)|Lung SC(185;0.0262)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;4.18e-05)		GGTCCAACAGGGGAGAAGATA	0.403													G|||	41	0.0081869	0.031	0.0	5008	,	,		15604	0.0		0.0	False		,,,				2504	0.0				p.P243P	Esophageal Squamous(187;747 2077 11056 31291 44172)	Atlas-SNP	.											.	ZC3H13	197	.	0			c.C729T						PASS	.	G		117,4289	87.8+/-126.4	1,115,2087	107.0	99.0	102.0		729	-1.8	0.5	13	dbSNP_132	102	0,8600		0,0,4300	no	coding-synonymous	ZC3H13	NM_015070.3		1,115,6387	AA,AG,GG		0.0,2.6555,0.8996		243/1565	46584500	117,12889	2203	4300	6503	SO:0001819	synonymous_variant	23091	exon7			CAACAGGGGAGAA	AB020660	CCDS9400.1	13q14.11	2012-07-05	2006-05-15	2006-05-15	ENSG00000123200	ENSG00000123200		"""Zinc fingers, CCCH-type domain containing"""	20368	protein-coding gene	gene with protein product			"""KIAA0853"""	KIAA0853		10048485	Standard	XM_005266301		Approved	DKFZp434D1812	uc001vas.1	Q5T200	OTTHUMG00000016863	ENST00000242848.4:c.729C>T	13.37:g.46584500G>A		115.0	0.0	0		162.0	70.0	0.432099	NM_015070	A2A323|O94936|Q5T1Z9|Q7Z7J3|Q8NDT6|Q9H0L6	Silent	SNP	ENST00000242848.4	37																																																																																				G|0.990;A|0.010	0.010	strong		0.403	ZC3H13-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000044789.1	NM_015070	
TRPM2	7226	hgsc.bcm.edu	37	21	45856963	45856963	+	Silent	SNP	T	T	C	rs11910471	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:45856963T>C	ENST00000397928.1	+	29	4525	c.4080T>C	c.(4078-4080)gaT>gaC	p.D1360D	snoZ6_ENST00000583496.1_RNA|TRPM2_ENST00000300482.5_Silent_p.D1360D|snoZ6_ENST00000581669.1_RNA|TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000397932.2_Silent_p.D1410D|TRPM2_ENST00000300481.9_Silent_p.D1306D	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	1360	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)			breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						GGAACGAGGATGGAGCCATCT	0.687													C|||	432	0.086262	0.3109	0.0288	5008	,	,		14340	0.0		0.001	False		,,,				2504	0.0				p.D1360D		Atlas-SNP	.											.	TRPM2	196	.	0			c.T4080C						PASS	.	C		892,2978		106,680,1149	92.0	66.0	75.0		4080	-6.6	0.2	21	dbSNP_120	75	8,7486		0,8,3739	no	coding-synonymous	TRPM2	NM_003307.3		106,688,4888	CC,CT,TT		0.1068,23.0491,7.9197		1360/1504	45856963	900,10464	1935	3747	5682	SO:0001819	synonymous_variant	7226	exon29			CGAGGATGGAGCC	AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Nudix motif containing"""	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.4080T>C	21.37:g.45856963T>C		45.0	0.0	0		54.0	31.0	0.574074	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Silent	SNP	ENST00000397928.1	37	CCDS13710.1																																																																																			T|0.901;C|0.099	0.099	strong		0.687	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307	
EXOC3L1	283849	hgsc.bcm.edu	37	16	67221494	67221494	+	Missense_Mutation	SNP	C	C	T	rs79820293	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:67221494C>T	ENST00000314586.6	-	5	914	c.674G>A	c.(673-675)cGt>cAt	p.R225H	EXOC3L1_ENST00000562887.1_Intron	NM_178516.3	NP_848611.2	Q86VI1	EX3L1_HUMAN	exocyst complex component 3-like 1	225	Mediates interaction with EXOC2, EXOC4 and EXOC5. {ECO:0000250}.				exocytosis (GO:0006887)|peptide hormone secretion (GO:0030072)	exocyst (GO:0000145)|secretory granule (GO:0030141)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	21						CTCCGCCACACGCACAGCAGC	0.687													C|||	107	0.0213658	0.0772	0.0043	5008	,	,		16224	0.0		0.002	False		,,,				2504	0.0				p.R225H		Atlas-SNP	.											.	EXOC3L1	52	.	0			c.G674A						PASS	.	C	HIS/ARG	242,4152		8,226,1963	28.0	33.0	32.0		674	5.8	1.0	16	dbSNP_131	32	1,8597		0,1,4298	yes	missense	EXOC3L1	NM_178516.3	29	8,227,6261	TT,TC,CC		0.0116,5.5075,1.8704	probably-damaging	225/747	67221494	243,12749	2197	4299	6496	SO:0001583	missense	283849	exon5			GCCACACGCACAG	AK092858	CCDS10832.1	16q22.1	2011-01-31	2011-01-31	2011-01-31	ENSG00000179044	ENSG00000179044			27540	protein-coding gene	gene with protein product		614117	"""exocyst complex component 3-like"""	EXOC3L		12477932	Standard	NM_178516		Approved	FLJ35539, FLJ35587	uc002erx.1	Q86VI1	OTTHUMG00000137508	ENST00000314586.6:c.674G>A	16.37:g.67221494C>T	ENSP00000325674:p.Arg225His	63.0	0.0	0		75.0	30.0	0.4	NM_178516	A8K7I9|Q8NAD2|Q8TEN2	Missense_Mutation	SNP	ENST00000314586.6	37	CCDS10832.1	49	0.022435897435897436	47	0.09552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	C	26.0	4.691637	0.88735	0.055075	1.16E-4	ENSG00000179044	ENST00000314586;ENST00000545725;ENST00000314553	T;T	0.34472	3.05;1.36	5.84	5.84	0.93424	.	0.000000	0.85682	D	0.000000	T	0.03695	0.0105	M	0.74881	2.28	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.996;0.998;0.999	T	0.04454	-1.0950	10	0.59425	D	0.04	-11.3738	18.7162	0.91677	0.0:1.0:0.0:0.0	.	164;164;225	F5H4W1;B7Z6U0;Q86VI1	.;.;EX3L1_HUMAN	H	225;164;169	ENSP00000325674:R225H;ENSP00000439910:R164H	ENSP00000325008:R169H	R	-	2	0	EXOC3L1	65778995	0.997000	0.39634	1.000000	0.80357	0.982000	0.71751	4.142000	0.58044	2.763000	0.94921	0.650000	0.86243	CGT	C|0.978;T|0.022	0.022	strong		0.687	EXOC3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268827.2	NM_178516	
ING1	3621	hgsc.bcm.edu	37	13	111368023	111368023	+	Missense_Mutation	SNP	C	C	G	rs56682720	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:111368023C>G	ENST00000375774.3	+	1	695	c.233C>G	c.(232-234)tCc>tGc	p.S78C	ING1_ENST00000333219.7_Intron|CARS2_ENST00000535398.1_5'Flank|ING1_ENST00000375775.3_Intron|ING1_ENST00000464141.1_Intron|ING1_ENST00000338450.7_Intron	NM_005537.4	NP_005528.3	Q9UK53	ING1_HUMAN	inhibitor of growth family, member 1	78					cell cycle (GO:0007049)|chromatin modification (GO:0016568)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|regulation of cell death (GO:0010941)	nucleus (GO:0005634)	methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(6)|lung(1)|ovary(1)	12	all_lung(23;3.61e-05)|Lung NSC(43;0.00144)|Lung SC(71;0.0753)|all_neural(89;0.077)|Medulloblastoma(90;0.148)		BRCA - Breast invasive adenocarcinoma(86;0.188)			CCGTGCTCTTCCGCCCTGCGG	0.672													C|||	189	0.0377396	0.1362	0.0101	5008	,	,		13851	0.0		0.002	False		,,,				2504	0.0				p.S78C		Atlas-SNP	.											.	ING1	106	.	0			c.C233G						PASS	.	C	CYS/SER,,,	544,3856		29,486,1685	69.0	63.0	65.0		233,,,	-8.2	0.0	13	dbSNP_129	65	6,8592		0,6,4293	yes	missense,intron,intron,intron	ING1	NM_005537.3,NM_198217.1,NM_198218.1,NM_198219.1	112,,,	29,492,5978	GG,GC,CC		0.0698,12.3636,4.2314	benign,,,	78/423,,,	111368023	550,12448	2200	4299	6499	SO:0001583	missense	3621	exon1			GCTCTTCCGCCCT		CCDS9515.1, CCDS9516.1, CCDS9517.1, CCDS9518.1	13q34	2013-01-28			ENSG00000153487	ENSG00000153487		"""Zinc fingers, PHD-type"""	6062	protein-coding gene	gene with protein product	"""inhibitor of growth 1"", ""tumor suppressor ING1"", ""growth inhibitor ING1"", ""growth inhibitory protein ING1"""	601566				8944021, 9186514	Standard	NM_198219		Approved	p33ING1, p33ING1b, p24ING1c, p33, p47, p47ING1a	uc001vri.3	Q9UK53	OTTHUMG00000017346	ENST00000375774.3:c.233C>G	13.37:g.111368023C>G	ENSP00000364929:p.Ser78Cys	70.0	0.0	0		86.0	42.0	0.488372	NM_005537	O00532|O43658|Q53ZR3|Q5T9G8|Q5T9G9|Q5T9H0|Q5T9H1|Q9H007|Q9HD98|Q9HD99|Q9NS83|Q9P0U6|Q9UBC6|Q9UIJ1|Q9UIJ2|Q9UIJ3|Q9UIJ4|Q9UK52	Missense_Mutation	SNP	ENST00000375774.3	37	CCDS9517.1	51	0.023351648351648352	49	0.09959349593495935	2	0.0055248618784530384	0	0.0	0	0.0	C	14.45	2.539810	0.45176	0.123636	6.98E-4	ENSG00000153487	ENST00000375774	T	0.35421	1.31	4.11	-8.22	0.01037	.	.	.	.	.	T	0.00178	0.0005	N	0.08118	0	0.80722	P	0.0	P	0.43352	0.804	B	0.36959	0.237	T	0.15607	-1.0431	8	0.87932	D	0	0.3496	0.192	0.00135	0.2844:0.1541:0.2434:0.318	rs56682720	78	Q9UK53	ING1_HUMAN	C	78	ENSP00000364929:S78C	ENSP00000364929:S78C	S	+	2	0	ING1	110166024	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.050000	0.00628	-2.327000	0.00636	-1.083000	0.02208	TCC	C|0.961;G|0.039	0.039	strong		0.672	ING1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045770.2	NM_005537	
SPAG4	6676	hgsc.bcm.edu	37	20	34204168	34204168	+	Silent	SNP	G	G	A	rs115161777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:34204168G>A	ENST00000374273.3	+	1	355	c.243G>A	c.(241-243)gcG>gcA	p.A81A		NM_003116.1	NP_003107.1	Q9NPE6	SPAG4_HUMAN	sperm associated antigen 4	81					spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|motile cilium (GO:0031514)	structural molecule activity (GO:0005198)			NS(1)|cervix(5)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)	21	Lung NSC(9;0.0053)|all_lung(11;0.00785)		BRCA - Breast invasive adenocarcinoma(18;0.0127)			AGAAGCCAGCGCCTCGGAGCC	0.731													G|||	107	0.0213658	0.0779	0.0058	5008	,	,		8847	0.0		0.0	False		,,,				2504	0.0				p.A81A		Atlas-SNP	.											.	SPAG4	36	.	0			c.G243A						PASS	.	G		185,3729		2,181,1774	5.0	8.0	7.0		243	4.6	1.0	20	dbSNP_132	7	4,7996		0,4,3996	no	coding-synonymous	SPAG4	NM_003116.1		2,185,5770	AA,AG,GG		0.05,4.7266,1.5864		81/438	34204168	189,11725	1957	4000	5957	SO:0001819	synonymous_variant	6676	exon1			GCCAGCGCCTCGG	AF043344	CCDS13259.1	20q11.2	2010-04-23			ENSG00000061656	ENSG00000061656			11214	protein-coding gene	gene with protein product	"""acrosomal protein ACR55"", ""Sad1 and UNC84 domain containing 4"", ""cancer/testis antigen 127"""	603038				9691178, 10373309	Standard	NM_003116		Approved	SUN4, CT127	uc002xdb.1	Q9NPE6	OTTHUMG00000032352	ENST00000374273.3:c.243G>A	20.37:g.34204168G>A		32.0	0.0	0		40.0	15.0	0.375	NM_003116	O43648	Silent	SNP	ENST00000374273.3	37	CCDS13259.1																																																																																			G|0.980;A|0.020	0.020	strong		0.731	SPAG4-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078896.1	NM_003116	
DCTD	1635	hgsc.bcm.edu	37	4	183814234	183814234	+	Silent	SNP	G	G	A	rs369366826		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:183814234G>A	ENST00000438320.2	-	5	698	c.408C>T	c.(406-408)gaC>gaT	p.D136D	DCTD_ENST00000357067.3_Silent_p.D147D|DCTD_ENST00000510370.1_Silent_p.D136D	NM_001921.2	NP_001912.2	P32321	DCTD_HUMAN	dCMP deaminase	136					nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide biosynthetic process (GO:0009165)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	dCMP deaminase activity (GO:0004132)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|urinary_tract(1)	18		all_lung(41;5.16e-14)|Lung NSC(41;1.33e-13)|Colorectal(36;0.00666)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.202)		all cancers(43;1.65e-24)|Epithelial(43;3.44e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.39e-10)|Colorectal(24;4.69e-07)|COAD - Colon adenocarcinoma(29;7.07e-05)|STAD - Stomach adenocarcinoma(60;0.000118)|GBM - Glioblastoma multiforme(59;0.000472)|LUSC - Lung squamous cell carcinoma(40;0.00984)|READ - Rectum adenocarcinoma(43;0.0419)	Cytarabine(DB00987)	CAGTTGCCTCGTCACTATCAT	0.507													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17184	0.0		0.0	False		,,,				2504	0.0				p.D147D		Atlas-SNP	.											.	DCTD	30	.	0			c.C441T						PASS	.	G	,	1,4405	2.1+/-5.4	0,1,2202	72.0	67.0	69.0		441,408	-10.8	0.0	4		69	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	DCTD	NM_001012732.1,NM_001921.2	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	147/190,136/179	183814234	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	1635	exon5			TGCCTCGTCACTA	L12136	CCDS3831.1, CCDS34108.1	4q35.1	2008-08-01			ENSG00000129187	ENSG00000129187	3.5.4.12		2710	protein-coding gene	gene with protein product		607638					Standard	XM_005262778		Approved		uc003ivg.3	P32321	OTTHUMG00000160685	ENST00000438320.2:c.408C>T	4.37:g.183814234G>A		215.0	0.0	0		233.0	110.0	0.472103	NM_001012732	B2R836|D3DP49|D3DP50|Q5M7Z8|Q9BVD8	Silent	SNP	ENST00000438320.2	37	CCDS3831.1																																																																																			.	.	weak		0.507	DCTD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361743.2		
RIN1	9610	hgsc.bcm.edu	37	11	66099888	66099888	+	Silent	SNP	C	C	T	rs61547186	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:66099888C>T	ENST00000311320.4	-	10	2337	c.2211G>A	c.(2209-2211)ggG>ggA	p.G737G	RIN1_ENST00000524804.1_5'Flank|RIN1_ENST00000424433.2_Intron|RIN1_ENST00000530056.1_Silent_p.G571G|RP11-867G23.12_ENST00000526655.1_RNA	NM_004292.2	NP_004283.2	Q13671	RIN1_HUMAN	Ras and Rab interactor 1	737					associative learning (GO:0008306)|endocytosis (GO:0006897)|memory (GO:0007613)|negative regulation of synaptic plasticity (GO:0031914)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|lung(8)|ovary(1)	14						CCCCAGCATCCCCATCTCCCT	0.647													C|||	153	0.0305511	0.1104	0.0101	5008	,	,		17960	0.0		0.0	False		,,,				2504	0.0				p.G737G		Atlas-SNP	.											.	RIN1	64	.	0			c.G2211A						PASS	.	C		437,3963	211.5+/-231.7	17,403,1780	156.0	151.0	153.0		2211	-2.9	0.0	11	dbSNP_129	153	2,8588	1.2+/-3.3	0,2,4293	no	coding-synonymous	RIN1	NM_004292.2		17,405,6073	TT,TC,CC		0.0233,9.9318,3.3795		737/784	66099888	439,12551	2200	4295	6495	SO:0001819	synonymous_variant	9610	exon10			AGCATCCCCATCT	L36463	CCDS31614.1	11q13.2	2005-09-18				ENSG00000174791			18749	protein-coding gene	gene with protein product		605965				9144171, 1849280	Standard	NM_004292		Approved		uc001ohn.1	Q13671		ENST00000311320.4:c.2211G>A	11.37:g.66099888C>T		181.0	0.0	0		182.0	182.0	1	NM_004292	O15010|Q00427|Q96CC8	Silent	SNP	ENST00000311320.4	37	CCDS31614.1																																																																																			C|0.969;T|0.031	0.031	strong		0.647	RIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392980.2	NM_004292	
NCR2	9436	hgsc.bcm.edu	37	6	41318578	41318578	+	Silent	SNP	T	T	C	rs115509322	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:41318578T>C	ENST00000373089.5	+	5	895	c.807T>C	c.(805-807)gaT>gaC	p.D269D	NCR2_ENST00000373086.3_3'UTR|NCR2_ENST00000373083.4_3'UTR	NM_004828.3	NP_004819.2	O95944	NCTR2_HUMAN	natural cytotoxicity triggering receptor 2	269	Poly-Asp.				cellular defense response (GO:0006968)|innate immune response (GO:0045087)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(1)	14	Ovarian(28;0.0327)|Colorectal(47;0.196)					agataagcgatgatgatgatg	0.398													T|||	43	0.00858626	0.0272	0.0058	5008	,	,		22654	0.0		0.003	False		,,,				2504	0.0				p.D269D		Atlas-SNP	.											.	NCR2	44	.	0			c.T807C						PASS	.	T	,,	118,4288	89.7+/-128.4	1,116,2086	95.0	89.0	91.0		,,807	-2.5	0.0	6	dbSNP_132	91	17,8583	12.6+/-44.7	0,17,4283	no	utr-3,utr-3,coding-synonymous	NCR2	NM_001199509.1,NM_001199510.1,NM_004828.3	,,	1,133,6369	CC,CT,TT		0.1977,2.6782,1.038	,,	,,269/277	41318578	135,12871	2203	4300	6503	SO:0001819	synonymous_variant	9436	exon5			AAGCGATGATGAT	AJ225109	CCDS4855.1, CCDS56428.1, CCDS56429.1	6p21.1	2013-01-11	2002-11-13	2002-11-15	ENSG00000096264	ENSG00000096264		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	6732	protein-coding gene	gene with protein product		604531	"""lymphocyte antigen 95 (activating NK-receptor; NK-p44)"""	LY95		10049942	Standard	NM_004828		Approved	NK-p44, CD336	uc003oqh.2	O95944	OTTHUMG00000014678	ENST00000373089.5:c.807T>C	6.37:g.41318578T>C		45.0	0.0	0		42.0	19.0	0.452381	NM_004828	Q9H562|Q9H563|Q9H564|Q9UMT1|Q9UMT2	Silent	SNP	ENST00000373089.5	37	CCDS4855.1																																																																																			T|0.990;C|0.010	0.010	strong		0.398	NCR2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040511.3		
PSG6	5675	hgsc.bcm.edu	37	19	43411150	43411150	+	Silent	SNP	G	G	A	rs78024453	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:43411150G>A	ENST00000292125.2	-	5	1208	c.1164C>T	c.(1162-1164)agC>agT	p.S388S	PSG6_ENST00000187910.2_Silent_p.S388S|PSG6_ENST00000402603.4_Silent_p.S295S	NM_002782.4	NP_002773.1	Q00889	PSG6_HUMAN	pregnancy specific beta-1-glycoprotein 6	388	Ig-like C2-type 3.				female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(19)|ovary(1)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)	44		Prostate(69;0.00899)				CATAGAGCCCGCTATGATTTG	0.458													.|||	116	0.0231629	0.0825	0.0101	5008	,	,		19776	0.0		0.0	False		,,,				2504	0.0				p.S388S		Atlas-SNP	.											.	PSG6	89	.	0			c.C1164T						PASS	.	T	,	343,4059		23,297,1881	192.0	203.0	199.0		1164,1164	-3.1	0.0	19	dbSNP_131	199	2,8596		0,2,4297	no	coding-synonymous,coding-synonymous	PSG6	NM_001031850.2,NM_002782.3	,	23,299,6178	AA,AG,GG		0.0233,7.7919,2.6538	,	388/425,388/436	43411150	345,12655	2201	4299	6500	SO:0001819	synonymous_variant	5675	exon5			GAGCCCGCTATGA		CCDS12613.1, CCDS33038.1	19q13.2	2013-01-29			ENSG00000170848	ENSG00000170848		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9523	protein-coding gene	gene with protein product		176395				1690992	Standard	NM_002782		Approved			Q00889	OTTHUMG00000151127	ENST00000292125.2:c.1164C>T	19.37:g.43411150G>A		199.0	0.0	0		171.0	70.0	0.409357	NM_001031850	O75244|Q15224|Q15235|Q549K1	Silent	SNP	ENST00000292125.2	37	CCDS12613.1																																																																																			G|0.976;A|0.024	0.024	strong		0.458	PSG6-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000321436.1	NM_002782	
OTOP2	92736	hgsc.bcm.edu	37	17	72926879	72926879	+	Silent	SNP	T	T	C	rs16967162	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:72926879T>C	ENST00000580223.1	+	5	1179	c.1149T>C	c.(1147-1149)tcT>tcC	p.S383S	OTOP2_ENST00000331427.4_Silent_p.S383S			Q7RTS6	OTOP2_HUMAN	otopetrin 2	383						integral component of membrane (GO:0016021)				breast(4)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|ovary(3)|prostate(4)|skin(1)|urinary_tract(2)	39	all_lung(278;0.172)|Lung NSC(278;0.207)					ACGCCATCTCTTACTACTCCA	0.637													C|||	334	0.0666933	0.2428	0.0187	5008	,	,		18213	0.0		0.0	False		,,,				2504	0.0				p.S383S		Atlas-SNP	.											.	OTOP2	81	.	0			c.T1149C						PASS	.	C		1004,3402	729.1+/-410.0	132,740,1331	72.0	63.0	66.0		1149	4.3	1.0	17	dbSNP_123	66	16,8584	818.5+/-406.9	0,16,4284	no	coding-synonymous	OTOP2	NM_178160.2		132,756,5615	CC,CT,TT		0.186,22.7871,7.8425		383/563	72926879	1020,11986	2203	4300	6503	SO:0001819	synonymous_variant	92736	exon6			CATCTCTTACTAC	BK000567	CCDS11708.1	17q25.3	2006-09-20				ENSG00000183034			19657	protein-coding gene	gene with protein product		607827				12651873	Standard	NM_178160		Approved		uc010wrp.2	Q7RTS6		ENST00000580223.1:c.1149T>C	17.37:g.72926879T>C		147.0	0.0	0		175.0	84.0	0.48	NM_178160		Silent	SNP	ENST00000580223.1	37	CCDS11708.1																																																																																			T|0.925;C|0.075	0.075	strong		0.637	OTOP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445306.1	NM_178160	
VWDE	221806	hgsc.bcm.edu	37	7	12409197	12409197	+	Missense_Mutation	SNP	C	C	G	rs78231473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:12409197C>G	ENST00000275358.3	-	12	2923	c.2735G>C	c.(2734-2736)aGt>aCt	p.S912T		NM_001135924.1	NP_001129396.1	Q8N2E2	VWDE_HUMAN	von Willebrand factor D and EGF domains	912						extracellular region (GO:0005576)				breast(4)|endometrium(2)|kidney(1)|skin(1)	8						GTCATAGGAACTAAAGCTTGG	0.383													C|||	93	0.0185703	0.0688	0.0029	5008	,	,		20375	0.0		0.0	False		,,,				2504	0.0				p.S912T		Atlas-SNP	.											VWDE_ENST00000275358,NS,carcinoma,+1,2	VWDE	123	2	0			c.G2735C						PASS	.	C	THR/SER	59,1325		1,57,634	84.0	68.0	73.0		2735	3.0	0.4	7	dbSNP_132	73	1,3181		0,1,1590	yes	missense	VWDE	NM_001135924.1	58	1,58,2224	GG,GC,CC		0.0314,4.263,1.3141	possibly-damaging	912/1591	12409197	60,4506	692	1591	2283	SO:0001583	missense	221806	exon12			TAGGAACTAAAGC		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.2735G>C	7.37:g.12409197C>G	ENSP00000275358:p.Ser912Thr	166.0	0.0	0		138.0	66.0	0.478261	NM_001135924	B7ZM77|Q96SQ3	Missense_Mutation	SNP	ENST00000275358.3	37	CCDS47544.1	29	0.013278388278388278	28	0.056910569105691054	1	0.0027624309392265192	0	0.0	0	0.0	C	0.328	-0.957594	0.02267	0.04263	3.14E-4	ENSG00000146530	ENST00000275358;ENST00000536307	D	0.82081	-1.57	4.83	3.03	0.35002	.	0.711350	0.14327	N	0.326598	T	0.27697	0.0681	L	0.42245	1.32	0.19575	N	0.999962	B	0.02656	0.0	B	0.06405	0.002	T	0.26573	-1.0099	10	0.12430	T	0.62	.	9.9581	0.41680	0.0:0.7396:0.12:0.1404	.	912	Q8N2E2	VWDE_HUMAN	T	912;366	ENSP00000275358:S912T	ENSP00000275358:S912T	S	-	2	0	VWDE	12375722	0.723000	0.28027	0.393000	0.26258	0.040000	0.13550	2.936000	0.48971	0.262000	0.21774	-0.795000	0.03280	AGT	C|0.986;G|0.014	0.014	strong		0.383	VWDE-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325870.3	XM_371878	
SREK1IP1	285672	hgsc.bcm.edu	37	5	64020241	64020241	+	Silent	SNP	T	T	C	rs16879016	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:64020241T>C	ENST00000513458.4	-	5	605	c.438A>G	c.(436-438)acA>acG	p.T146T		NM_173829.3	NP_776190.1	Q8N9Q2	SR1IP_HUMAN	SREK1-interacting protein 1	146					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)		nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(3)|ovary(1)	6						AACTATTAGGTGTAGAAGAAT	0.294													C|||	724	0.144569	0.4924	0.0519	5008	,	,		18873	0.0238		0.0109	False		,,,				2504	0.002				p.T146T		Atlas-SNP	.											.	SREK1IP1	28	.	0			c.A438G						PASS	.	C		1770,2634	619.0+/-393.3	360,1050,792	34.0	34.0	34.0		438	-9.1	0.0	5	dbSNP_123	34	59,8533	801.1+/-407.4	0,59,4237	no	coding-synonymous	SREK1IP1	NM_173829.3		360,1109,5029	CC,CT,TT		0.6867,40.1907,14.0736		146/156	64020241	1829,11167	2202	4296	6498	SO:0001819	synonymous_variant	285672	exon5			ATTAGGTGTAGAA	AK094073	CCDS34171.1	5q12.3	2010-09-20	2010-09-20	2010-09-20	ENSG00000153006	ENSG00000153006			26716	protein-coding gene	gene with protein product	"""p18 splicing regulatory protein"""		"""SFRS12-interacting protein 1"""	SFRS12IP1		15456940	Standard	NM_173829		Approved	FLJ36754, P18SRP	uc003jtk.3	Q8N9Q2	OTTHUMG00000162291	ENST00000513458.4:c.438A>G	5.37:g.64020241T>C		179.0	0.0	0		180.0	90.0	0.5	NM_173829	Q32NC8	Silent	SNP	ENST00000513458.4	37	CCDS34171.1																																																																																			T|0.886;C|0.114	0.114	strong		0.294	SREK1IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368457.4	NM_173829	
LARP6	55323	hgsc.bcm.edu	37	15	71128691	71128691	+	Silent	SNP	G	G	A	rs78188777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:71128691G>A	ENST00000299213.8	-	2	424	c.354C>T	c.(352-354)caC>caT	p.H118H		NM_018357.2	NP_060827.2	Q9BRS8	LARP6_HUMAN	La ribonucleoprotein domain family, member 6	118	HTH La-type RNA-binding. {ECO:0000255|PROSITE-ProRule:PRU00332}.				regulation of translation (GO:0006417)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(1)|large_intestine(5)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	19						TCCTCCTCACGTGTTTTAGCA	0.453													G|||	79	0.0157748	0.0567	0.0058	5008	,	,		20033	0.0		0.0	False		,,,				2504	0.0				p.H118H		Atlas-SNP	.											.	LARP6	43	.	0			c.C354T						PASS	.	G		219,4179	132.1+/-168.6	5,209,1985	124.0	123.0	123.0		354	-3.1	1.0	15	dbSNP_132	123	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous	LARP6	NM_018357.2		5,210,6281	AA,AG,GG		0.0116,4.9795,1.6933		118/492	71128691	220,12772	2199	4297	6496	SO:0001819	synonymous_variant	55323	exon2			CCTCACGTGTTTT	BC009446	CCDS10236.1, CCDS32281.1	15q23	2012-11-19			ENSG00000166173	ENSG00000166173		"""La ribonucleoprotein domain containing"""	24012	protein-coding gene	gene with protein product		611300				12477932	Standard	NM_018357		Approved	acheron, FLJ11196	uc002ass.3	Q9BRS8	OTTHUMG00000172179	ENST00000299213.8:c.354C>T	15.37:g.71128691G>A		250.0	0.0	0		206.0	93.0	0.451456	NM_018357	Q5XKE4|Q8N3N2|Q9NUR0	Silent	SNP	ENST00000299213.8	37	CCDS32281.1																																																																																			G|0.984;A|0.016	0.016	strong		0.453	LARP6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417197.2	NM_018357	
MOGAT2	80168	hgsc.bcm.edu	37	11	75431049	75431049	+	Missense_Mutation	SNP	C	C	T	rs35828061	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:75431049C>T	ENST00000198801.5	+	2	174	c.104C>T	c.(103-105)aCt>aTt	p.T35I	MOGAT2_ENST00000526712.1_5'UTR	NM_025098.2	NP_079374.2	Q3SYC2	MOGT2_HUMAN	monoacylglycerol O-acyltransferase 2	35					diacylglycerol biosynthetic process (GO:0006651)|glycerol metabolic process (GO:0006071)|intestinal absorption (GO:0050892)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	2-acylglycerol O-acyltransferase activity (GO:0003846)|acetyltransferase activity (GO:0016407)			NS(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	20	Ovarian(111;0.103)					GAGATCTGCACTGTGGGCTTC	0.592													C|||	122	0.024361	0.0908	0.0	5008	,	,		19209	0.0		0.002	False		,,,				2504	0.0				p.T35I		Atlas-SNP	.											MOGAT2,NS,carcinoma,+1,1	MOGAT2	49	1	0			c.C104T						PASS	.	C	ILE/THR	311,4089	169.8+/-200.3	8,295,1897	165.0	143.0	150.0		104	-7.3	0.0	11	dbSNP_126	150	6,8580	4.3+/-15.6	0,6,4287	yes	missense	MOGAT2	NM_025098.2	89	8,301,6184	TT,TC,CC		0.0699,7.0682,2.4411	benign	35/335	75431049	317,12669	2200	4293	6493	SO:0001583	missense	80168	exon2			TCTGCACTGTGGG	AY157608	CCDS8240.1	11q13.5	2008-02-05			ENSG00000166391	ENSG00000166391			23248	protein-coding gene	gene with protein product		610270				14970677	Standard	NM_025098		Approved	MGAT2, DGAT2L5, FLJ22644	uc010rru.2	Q3SYC2	OTTHUMG00000165341	ENST00000198801.5:c.104C>T	11.37:g.75431049C>T	ENSP00000198801:p.Thr35Ile	58.0	0.0	0		69.0	31.0	0.449275	NM_025098	A8K7I3|Q3SYC1|Q6ZQZ2|Q86UH6|Q9H630	Missense_Mutation	SNP	ENST00000198801.5	37	CCDS8240.1	37	0.01694139194139194	37	0.07520325203252033	0	0.0	0	0.0	0	0.0	C	2.919	-0.223665	0.06061	0.070682	6.99E-4	ENSG00000166391	ENST00000198801	T	0.09163	3.01	4.99	-7.32	0.01436	.	1.133530	0.06466	N	0.730377	T	0.00241	0.0007	N	0.04959	-0.14	0.20307	N	0.999911	B;B	0.06786	0.0;0.001	B;B	0.09377	0.0;0.004	T	0.42716	-0.9435	10	0.05833	T	0.94	2.7006	8.1687	0.31241	0.201:0.487:0.0:0.3121	rs35828061;rs61085918	35;35	Q3SYC2;Q3SYC2-3	MOGT2_HUMAN;.	I	35	ENSP00000198801:T35I	ENSP00000198801:T35I	T	+	2	0	MOGAT2	75108697	0.000000	0.05858	0.000000	0.03702	0.551000	0.35334	-2.562000	0.00920	-1.376000	0.02126	-1.300000	0.01332	ACT	C|0.974;T|0.026	0.026	strong		0.592	MOGAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383520.1	NM_025098	
ACOT7	11332	hgsc.bcm.edu	37	1	6324747	6324747	+	Silent	SNP	G	G	A	rs61739537	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:6324747G>A	ENST00000377855.2	-	9	1199	c.1053C>T	c.(1051-1053)acC>acT	p.T351T	ACOT7_ENST00000608083.1_Silent_p.T309T|ACOT7_ENST00000377845.3_Silent_p.T321T|ACOT7_ENST00000545482.1_Silent_p.T236T|ACOT7_ENST00000361521.4_Silent_p.T341T|ACOT7_ENST00000377842.3_Silent_p.T300T	NM_181864.2	NP_863654.1	O00154	BACH_HUMAN	acyl-CoA thioesterase 7	351					coenzyme A biosynthetic process (GO:0015937)|fatty acid catabolic process (GO:0009062)|long-chain fatty-acyl-CoA catabolic process (GO:0036116)|medium-chain fatty acid biosynthetic process (GO:0051792)|medium-chain fatty-acyl-CoA catabolic process (GO:0036114)|palmitic acid biosynthetic process (GO:1900535)	cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)	carboxylic ester hydrolase activity (GO:0052689)|fatty-acyl-CoA binding (GO:0000062)|long-chain fatty acyl-CoA binding (GO:0036042)|palmitoyl-CoA hydrolase activity (GO:0016290)|protein homodimerization activity (GO:0042803)	p.T341T(1)		kidney(1)|large_intestine(3)|lung(10)|pancreas(1)|prostate(1)	16	Ovarian(185;0.0634)|all_lung(157;0.175)	all_cancers(23;1.42e-38)|all_epithelial(116;3.96e-23)|all_lung(118;3.69e-08)|Lung NSC(185;8.52e-07)|all_hematologic(16;6.92e-06)|Colorectal(325;4.53e-05)|Acute lymphoblastic leukemia(12;5e-05)|all_neural(13;0.000164)|Breast(487;0.000688)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0393)|Medulloblastoma(700;0.211)		Epithelial(90;9.16e-37)|GBM - Glioblastoma multiforme(13;5.89e-29)|OV - Ovarian serous cystadenocarcinoma(86;7.63e-19)|Colorectal(212;1.27e-07)|COAD - Colon adenocarcinoma(227;2.06e-05)|Kidney(185;7.74e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00129)|BRCA - Breast invasive adenocarcinoma(365;0.00132)|STAD - Stomach adenocarcinoma(132;0.00195)|READ - Rectum adenocarcinoma(331;0.0481)		TCTCGTCCTCGGTCTCGGGCT	0.647													G|||	99	0.0197684	0.062	0.0086	5008	,	,		19936	0.0		0.0089	False		,,,				2504	0.002				p.T351T	GBM(74;673 1226 4974 11850 13190)	Atlas-SNP	.											ACOT7,NS,carcinoma,0,1	ACOT7	71	1	1	Substitution - coding silent(1)	pancreas(1)	c.C1053T						PASS	.	G	,,,	244,4160	138.4+/-174.2	9,226,1967	143.0	102.0	116.0		1023,1053,963,900	-7.1	0.9	1	dbSNP_129	116	69,8531	40.3+/-97.0	1,67,4232	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ACOT7	NM_007274.3,NM_181864.2,NM_181865.2,NM_181866.2	,,,	10,293,6199	AA,AG,GG		0.8023,5.5404,2.407	,,,	341/371,351/381,321/351,300/330	6324747	313,12691	2202	4300	6502	SO:0001819	synonymous_variant	11332	exon9			GTCCTCGGTCTCG	AB074417	CCDS65.1, CCDS66.1, CCDS67.1, CCDS30573.1	1p36	2008-08-14			ENSG00000097021	ENSG00000097021		"""Acyl CoA thioesterases"""	24157	protein-coding gene	gene with protein product	"""brain acyl CoA hydrolase"""	602587				10578051, 16103133, 16940157	Standard	XM_005263427		Approved	BACH, ACH1, ACT, CTE-II, LACH1, MGC1126, hBACH	uc001amt.3	O00154	OTTHUMG00000001295	ENST00000377855.2:c.1053C>T	1.37:g.6324747G>A		47.0	0.0	0		78.0	34.0	0.435897	NM_181864	A8K0K7|A8K232|A8K6B8|A8K837|B3KQ12|O43703|Q53Y78|Q5JYL2|Q5JYL3|Q5JYL4|Q5JYL5|Q5JYL6|Q5TGR4|Q9UJM9|Q9Y539|Q9Y540	Silent	SNP	ENST00000377855.2	37	CCDS65.1																																																																																			G|0.972;A|0.028	0.028	strong		0.647	ACOT7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000003773.1	NM_007274	
CNTN2	6900	hgsc.bcm.edu	37	1	205033518	205033518	+	Missense_Mutation	SNP	C	C	G	rs79431021	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:205033518C>G	ENST00000331830.4	+	11	1593	c.1309C>G	c.(1309-1311)Ctt>Gtt	p.L437V	AL583832.1_ENST00000515887.1_RNA	NM_005076.3	NP_005067.1	Q02246	CNTN2_HUMAN	contactin 2 (axonal)	437	Ig-like C2-type 5.				adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|cell adhesion (GO:0007155)|cellular protein localization (GO:0034613)|central nervous system myelination (GO:0022010)|cerebral cortex GABAergic interneuron migration (GO:0021853)|clustering of voltage-gated potassium channels (GO:0045163)|establishment of protein localization to juxtaparanode region of axon (GO:0071206)|learning (GO:0007612)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of adenosine receptor signaling pathway (GO:0060168)|positive regulation of protein processing (GO:0010954)|presynaptic membrane organization (GO:0097090)|receptor internalization (GO:0031623)|regulation of astrocyte differentiation (GO:0048710)|regulation of axon diameter (GO:0031133)|regulation of neuronal synaptic plasticity (GO:0048168)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|juxtaparanode region of axon (GO:0044224)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|synapse (GO:0045202)|voltage-gated potassium channel complex (GO:0008076)	carbohydrate binding (GO:0030246)|identical protein binding (GO:0042802)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(11)|lung(23)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	54	all_cancers(21;0.144)|Breast(84;0.0437)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			GGGAGAGATCCTTATCCCCTG	0.627													G|||	176	0.0351438	0.1112	0.0202	5008	,	,		13924	0.0		0.0129	False		,,,				2504	0.002				p.L437V	Melanoma(183;2548 2817 37099 41192)	Atlas-SNP	.											.	CNTN2	116	.	0			c.C1309G						PASS	.	G	VAL/LEU	380,4026	787.3+/-414.9	19,342,1842	91.0	107.0	101.0		1309	-7.0	0.0	1	dbSNP_132	101	148,8452	809.3+/-407.2	1,146,4153	yes	missense	CNTN2	NM_005076.3	32	20,488,5995	GG,GC,CC		1.7209,8.6246,4.0597	benign	437/1041	205033518	528,12478	2203	4300	6503	SO:0001583	missense	6900	exon11			GAGATCCTTATCC	X67734	CCDS1449.1	1q32.1	2013-02-11			ENSG00000184144	ENSG00000184144		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2172	protein-coding gene	gene with protein product		190197		TAX, AXT		8307567, 8586965	Standard	NM_005076		Approved	TAG-1, TAX1	uc001hbr.3	Q02246	OTTHUMG00000037105	ENST00000331830.4:c.1309C>G	1.37:g.205033518C>G	ENSP00000330633:p.Leu437Val	175.0	0.0	0		161.0	82.0	0.509317	NM_005076	P78432|Q5T054	Missense_Mutation	SNP	ENST00000331830.4	37	CCDS1449.1	76	0.0347985347985348	59	0.11991869918699187	7	0.019337016574585635	0	0.0	10	0.013192612137203167	G	0.460	-0.889703	0.02511	0.086246	0.017209	ENSG00000184144	ENST00000331830	T	0.66460	-0.21	5.33	-6.97	0.01616	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.302220	0.05908	N	0.631129	T	0.00496	0.0016	N	0.02985	-0.445	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.05241	-1.0897	10	0.15952	T	0.53	.	8.1491	0.31130	0.7102:0.0949:0.1004:0.0945	.	437;328	Q02246;Q68DA2	CNTN2_HUMAN;.	V	437	ENSP00000330633:L437V	ENSP00000330633:L437V	L	+	1	0	CNTN2	203300141	0.000000	0.05858	0.000000	0.03702	0.366000	0.29705	0.009000	0.13219	-1.704000	0.01407	-0.978000	0.02582	CTT	C|0.962;G|0.038	0.038	strong		0.627	CNTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090080.3	NM_005076	
AP5B1	91056	hgsc.bcm.edu	37	11	65547775	65547775	+	Silent	SNP	C	C	T	rs114368095	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:65547775C>T	ENST00000532090.2	-	2	399	c.189G>A	c.(187-189)caG>caA	p.Q63Q		NM_138368.4	NP_612377.4	Q2VPB7	AP5B1_HUMAN	adaptor-related protein complex 5, beta 1 subunit	63					endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-type membrane coat adaptor complex (GO:0030119)|lysosomal membrane (GO:0005765)				lung(1)	1						CGGGCCACAGCTGCGCAGGGT	0.667													C|||	130	0.0259585	0.0893	0.0173	5008	,	,		13769	0.0		0.0	False		,,,				2504	0.0				p.Q63Q		Atlas-SNP	.											.	AP5B1	40	.	0			c.G189A						PASS	.	C		220,3598		0,220,1689	5.0	7.0	6.0		18	3.2	1.0	11	dbSNP_132	6	4,8094		0,4,4045	no	coding-synonymous	DKFZp761E198	NM_138368.3		0,224,5734	TT,TC,CC		0.0494,5.7622,1.8798		6/822	65547775	224,11692	1909	4049	5958	SO:0001819	synonymous_variant	91056	exon2			CCACAGCTGCGCA	JQ313135	CCDS58146.1	11q13.1	2012-02-29			ENSG00000254470	ENSG00000254470			25104	protein-coding gene	gene with protein product		614367				22022230	Standard	NM_138368		Approved	PP1030, AP-5, DKFZp761E198	uc031qbm.1	Q2VPB7	OTTHUMG00000166593	ENST00000532090.2:c.189G>A	11.37:g.65547775C>T		41.0	0.0	0		51.0	19.0	0.372549	NM_138368	A1L0S6|H6WUK2|Q0D2Q2|Q8N3J7|Q8WYH6	Silent	SNP	ENST00000532090.2	37	CCDS58146.1																																																																																			C|0.975;T|0.025	0.025	strong		0.667	AP5B1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390636.2	NM_138368	
KRTAP13-2	337959	hgsc.bcm.edu	37	21	31744287	31744287	+	Missense_Mutation	SNP	C	C	T	rs113360916	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr21:31744287C>T	ENST00000399889.2	-	1	270	c.245G>A	c.(244-246)cGc>cAc	p.R82H		NM_181621.3	NP_853652.1	Q52LG2	KR132_HUMAN	keratin associated protein 13-2	82	5 X 10 AA approximate repeats.					intermediate filament (GO:0005882)				endometrium(1)|kidney(1)|lung(14)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	21						GGTTCTGGGGCGGTAGCAGGA	0.607													C|||	41	0.0081869	0.0295	0.0029	5008	,	,		19842	0.0		0.0	False		,,,				2504	0.0				p.R82H		Atlas-SNP	.											.	KRTAP13-2	29	.	0			c.G245A						PASS	.	C	HIS/ARG	124,4282	92.0+/-130.7	0,124,2079	59.0	59.0	59.0		245	1.4	0.1	21	dbSNP_132	59	2,8598	2.2+/-6.3	0,2,4298	yes	missense	KRTAP13-2	NM_181621.3	29	0,126,6377	TT,TC,CC		0.0233,2.8143,0.9688	benign	82/176	31744287	126,12880	2203	4300	6503	SO:0001583	missense	337959	exon1			CTGGGGCGGTAGC	AP001708	CCDS13589.1	21q22.1	2011-02-10			ENSG00000182816	ENSG00000182816		"""Keratin associated proteins"""	18923	protein-coding gene	gene with protein product						12359730	Standard	NM_181621		Approved	KAP13-2	uc002ynz.4	Q52LG2	OTTHUMG00000057793	ENST00000399889.2:c.245G>A	21.37:g.31744287C>T	ENSP00000382777:p.Arg82His	178.0	0.0	0		182.0	86.0	0.472527	NM_181621		Missense_Mutation	SNP	ENST00000399889.2	37	CCDS13589.1	15	0.006868131868131868	13	0.026422764227642278	2	0.0055248618784530384	0	0.0	0	0.0	C	7.773	0.707941	0.15239	0.028143	2.33E-4	ENSG00000182816	ENST00000399889	T	0.03496	3.91	4.26	1.36	0.22044	.	0.161204	0.28871	N	0.013862	T	0.00906	0.0030	L	0.39326	1.205	0.09310	N	1	B	0.24258	0.1	B	0.22601	0.04	T	0.46978	-0.9152	10	0.18710	T	0.47	.	4.1563	0.10263	0.1829:0.6128:0.0:0.2043	.	82	Q52LG2	KR132_HUMAN	H	82	ENSP00000382777:R82H	ENSP00000382777:R82H	R	-	2	0	KRTAP13-2	30666158	0.000000	0.05858	0.054000	0.19295	0.994000	0.84299	-1.818000	0.01717	0.138000	0.18790	0.655000	0.94253	CGC	C|0.990;T|0.010	0.010	strong		0.607	KRTAP13-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128245.1		
FBXO42	54455	hgsc.bcm.edu	37	1	16577948	16577948	+	Silent	SNP	G	G	A	rs61731119	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:16577948G>A	ENST00000375592.3	-	10	1587	c.1371C>T	c.(1369-1371)gaC>gaT	p.D457D		NM_018994.1	NP_061867.1	Q6P3S6	FBX42_HUMAN	F-box protein 42	457										autonomic_ganglia(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	26		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)		GTACAGGACTGTCCAAAGAAG	0.552													G|||	149	0.0297524	0.1074	0.0101	5008	,	,		17306	0.0		0.0	False		,,,				2504	0.0				p.D457D		Atlas-SNP	.											.	FBXO42	53	.	0			c.C1371T						PASS	.	G		386,4020	179.7+/-208.2	17,352,1834	29.0	33.0	32.0		1371	5.5	1.0	1	dbSNP_129	32	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	FBXO42	NM_018994.1		17,356,6130	AA,AG,GG		0.0465,8.7608,2.9986		457/718	16577948	390,12616	2203	4300	6503	SO:0001819	synonymous_variant	54455	exon10			AGGACTGTCCAAA	BC063864	CCDS30613.1	1p36.23-p36.11	2008-02-05			ENSG00000037637	ENSG00000037637		"""F-boxes /  ""other"""""	29249	protein-coding gene	gene with protein product		609109				10718198	Standard	XM_006710698		Approved	KIAA1332, Fbx42	uc001ayg.3	Q6P3S6	OTTHUMG00000002218	ENST00000375592.3:c.1371C>T	1.37:g.16577948G>A		181.0	0.0	0		159.0	87.0	0.54717	NM_018994	B3KP30|Q5TEU8|Q86XI0|Q8N3N4|Q8N5F8|Q9BRM0|Q9P2L4	Silent	SNP	ENST00000375592.3	37	CCDS30613.1																																																																																			G|0.973;A|0.027	0.027	strong		0.552	FBXO42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006285.1		
MUC4	4585	hgsc.bcm.edu	37	3	195512603	195512603	+	Missense_Mutation	SNP	T	T	C	rs79969373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195512603T>C	ENST00000463781.3	-	2	6307	c.5848A>G	c.(5848-5850)Acc>Gcc	p.T1950A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T1950A	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)		AGAGGGGTGGTGTGACCTGAG	0.597																																					p.T1950A		Atlas-SNP	.											.	MUC4	1505	.	0			c.A5848G						PASS	.						49.0	44.0	45.0					3																	195512603		691	1589	2280	SO:0001583	missense	4585	exon2			GGGTGGTGTGACC	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.5848A>G	3.37:g.195512603T>C	ENSP00000417498:p.Thr1950Ala	384.0	0.0	0		240.0	60.0	0.25	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	.	.	.	.	.	.	.	.	.	.	-	3.349	-0.132926	0.06711	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.26810	1.82;1.71	.	.	.	.	.	.	.	.	T	0.09818	0.0241	N	0.08118	0	0.09310	N	1	B	0.15141	0.012	B	0.04013	0.001	T	0.34502	-0.9826	7	.	.	.	.	2.8304	0.05498	3.0E-4:2.0E-4:0.4983:0.5012	.	1950	E7ESK3	.	A	1950	ENSP00000417498:T1950A;ENSP00000420243:T1950A	.	T	-	1	0	MUC4	196996998	0.028000	0.19301	0.042000	0.18584	0.032000	0.12392	-0.278000	0.08490	0.056000	0.16144	0.055000	0.15244	ACC	T|0.989;C|0.011	0.011	strong		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SARS2	54938	hgsc.bcm.edu	37	19	39416935	39416935	+	Silent	SNP	C	C	T	rs144229840	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39416935C>T	ENST00000221431.6	-	2	432	c.273G>A	c.(271-273)tcG>tcA	p.S91S	SARS2_ENST00000600042.1_Silent_p.S91S|SARS2_ENST00000448145.2_Silent_p.S91S|SARS2_ENST00000430193.3_Silent_p.S91S|SARS2_ENST00000594171.1_5'UTR|CTC-360G5.8_ENST00000599996.1_Missense_Mutation_p.D161N	NM_017827.3	NP_060297.1	Q9NP81	SYSM_HUMAN	seryl-tRNA synthetase 2, mitochondrial	91					gene expression (GO:0010467)|selenocysteinyl-tRNA(Sec) biosynthetic process (GO:0097056)|seryl-tRNA aminoacylation (GO:0006434)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|serine-tRNA ligase activity (GO:0004828)	p.S91S(1)		breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	15	all_cancers(60;2.74e-06)|all_epithelial(25;4.36e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			CCTGCCATGTCGAGATCTGGG	0.612													C|||	38	0.00758786	0.0265	0.0029	5008	,	,		19704	0.0		0.001	False		,,,				2504	0.0				p.S91S		Atlas-SNP	.											SARS2,rectum,carcinoma,0,1	SARS2	33	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G273A						PASS	.	C	,	75,4331	65.3+/-102.7	1,73,2129	50.0	42.0	45.0		273,273	-8.9	0.0	19	dbSNP_134	45	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	SARS2	NM_001145901.1,NM_017827.3	,	1,76,6426	TT,TC,CC		0.0349,1.7022,0.5997	,	91/521,91/519	39416935	78,12928	2203	4300	6503	SO:0001819	synonymous_variant	54938	exon2			CCATGTCGAGATC	AB029948	CCDS33017.1, CCDS54265.1	19q13.2	2014-05-06	2007-02-23			ENSG00000104835	6.1.1.11	"""Aminoacyl tRNA synthetases / Class II"""	17697	protein-coding gene	gene with protein product	"""serine tRNA ligase 2, mitochondrial"""	612804	"""serine-tRNA ligase, mitochondrial"", ""seryl-tRNA synthetase 2"""	SARSM		10764807	Standard	NM_001145901		Approved	FLJ20450, mtSerRS, SerRSmt, SARS, SERS, SYS	uc010xup.1	Q9NP81	OTTHUMG00000182691	ENST00000221431.6:c.273G>A	19.37:g.39416935C>T		39.0	0.0	0		26.0	12.0	0.461538	NM_001145901	A6NHW7|B4DE10|Q9BVP3	Silent	SNP	ENST00000221431.6	37	CCDS33017.1																																																																																			C|0.995;T|0.005	0.005	strong		0.612	SARS2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463139.1	NM_017827	
SPTAN1	6709	hgsc.bcm.edu	37	9	131395568	131395568	+	Silent	SNP	C	C	T	rs2228952	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131395568C>T	ENST00000372731.4	+	56	7484	c.7374C>T	c.(7372-7374)acC>acT	p.T2458T	SPTAN1_ENST00000358161.5_Silent_p.T2463T|WDR34_ENST00000483181.1_5'Flank|SPTAN1_ENST00000372739.3_Silent_p.T2463T	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	2458					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						AGCTCCCCACCGCGTTCGACT	0.632													C|||	116	0.0231629	0.0817	0.0101	5008	,	,		17940	0.0		0.001	False		,,,				2504	0.0				p.T2463T	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.C7389T						PASS	.	C	,,	348,4058	182.9+/-210.6	11,326,1866	83.0	72.0	76.0		7389,7314,7374	-10.7	0.0	9	dbSNP_98	76	5,8595	3.0+/-9.4	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	SPTAN1	NM_001130438.2,NM_001195532.1,NM_003127.3	,,	11,331,6161	TT,TC,CC		0.0581,7.8983,2.7141	,,	2463/2478,2438/2453,2458/2473	131395568	353,12653	2203	4300	6503	SO:0001819	synonymous_variant	6709	exon57			CCCCACCGCGTTC	M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"""EF-hand domain containing"""	11273	protein-coding gene	gene with protein product	"""alpha-fodrin"""	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.7374C>T	9.37:g.131395568C>T		80.0	0.0	0		77.0	52.0	0.675325	NM_001130438	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Silent	SNP	ENST00000372731.4	37	CCDS6905.1																																																																																			C|0.967;T|0.033	0.033	strong		0.632	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127	
C19orf57	79173	hgsc.bcm.edu	37	19	14006300	14006300	+	Missense_Mutation	SNP	C	C	A	rs58722011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14006300C>A	ENST00000586783.1	-	2	90	c.91G>T	c.(91-93)Gac>Tac	p.D31Y	C19orf57_ENST00000346736.2_Missense_Mutation_p.D31Y|C19orf57_ENST00000454313.1_Missense_Mutation_p.D31Y|C19orf57_ENST00000591586.1_Missense_Mutation_p.D31Y			Q0VDD7	CS057_HUMAN	chromosome 19 open reading frame 57	31					multicellular organismal development (GO:0007275)					breast(2)|kidney(1)|lung(3)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(19;2e-21)			CTCTGGGGGTCCCCATAGAAG	0.547													C|||	160	0.0319489	0.118	0.0058	5008	,	,		17727	0.0		0.0	False		,,,				2504	0.0				p.D31Y		Atlas-SNP	.											.	C19orf57	34	.	0			c.G91T						PASS	.	C	TYR/ASP	352,4054	182.9+/-210.6	15,322,1866	171.0	183.0	179.0		91	-1.8	0.0	19	dbSNP_129	179	1,8599	1.2+/-3.3	0,1,4299	yes	missense	C19orf57	NM_024323.3	160	15,323,6165	AA,AC,CC		0.0116,7.9891,2.7141	probably-damaging	31/638	14006300	353,12653	2203	4300	6503	SO:0001583	missense	79173	exon3			GGGGGTCCCCATA	BC012945	CCDS12299.1	19p13.12	2012-10-26			ENSG00000132016	ENSG00000132016			28153	protein-coding gene	gene with protein product						8228263	Standard	NM_024323		Approved	MGC11271	uc002mxl.1	Q0VDD7	OTTHUMG00000181851	ENST00000586783.1:c.91G>T	19.37:g.14006300C>A	ENSP00000465822:p.Asp31Tyr	146.0	0.0	0		174.0	79.0	0.454023	NM_024323	Q13411|Q8N825|Q96D63|Q9BU49	Missense_Mutation	SNP	ENST00000586783.1	37		60	0.027472527472527472	59	0.11991869918699187	1	0.0027624309392265192	0	0.0	0	0.0	C	12.10	1.837639	0.32513	0.079891	1.16E-4	ENSG00000132016	ENST00000454313;ENST00000346736	T;T	0.38401	1.14;1.14	4.12	-1.78	0.07957	.	1.528260	0.04542	N	0.388298	T	0.00300	0.0009	N	0.19112	0.55	0.09310	N	1	P	0.42620	0.785	B	0.37346	0.247	T	0.06661	-1.0814	10	0.56958	D	0.05	0.0377	4.2284	0.10590	0.0:0.4118:0.1831:0.4051	rs58722011	31	Q0VDD7-2	.	Y	31	ENSP00000404382:D31Y;ENSP00000254336:D31Y	ENSP00000254336:D31Y	D	-	1	0	C19orf57	13867300	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.800000	0.04555	-0.166000	0.10890	-0.743000	0.03520	GAC	C|0.974;A|0.026	0.026	strong		0.547	C19orf57-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000457947.1	NM_024323	
HTATSF1	27336	hgsc.bcm.edu	37	X	135593167	135593167	+	Silent	SNP	G	G	A	rs1058376	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:135593167G>A	ENST00000218364.4	+	9	1437	c.1263G>A	c.(1261-1263)gcG>gcA	p.A421A	HTATSF1_ENST00000535601.1_Silent_p.A421A	NM_014500.4	NP_055315.2	O43719	HTSF1_HUMAN	HIV-1 Tat specific factor 1	421	Mediates interaction with the P-TEFb complex.				regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(2)|endometrium(1)|kidney(2)|large_intestine(5)|lung(14)|ovary(3)|prostate(1)	30	Acute lymphoblastic leukemia(192;0.000127)					CTGGAATGGCGTTTGAAGAAC	0.448													g|||	513	0.135894	0.329	0.0447	3775	,	,		14100	0.0337		0.0089	False		,,,				2504	0.0041				p.A421A		Atlas-SNP	.											.	HTATSF1	66	.	0			c.G1263A						PASS	.	A	,	1427,2408		222,748,235,662,336	115.0	126.0	123.0		1263,1263	-3.1	0.0	X	dbSNP_86	123	73,6655		0,49,24,2379,1848	no	coding-synonymous,coding-synonymous	HTATSF1	NM_001163280.1,NM_014500.4	,	222,797,259,3041,2184	AA,AG,A,GG,G		1.085,37.2099,14.2005	,	421/756,421/756	135593167	1500,9063	2203	4300	6503	SO:0001819	synonymous_variant	27336	exon10			AATGGCGTTTGAA	U76992	CCDS14657.1	Xq26.3	2013-02-12	2006-01-09		ENSG00000102241	ENSG00000102241		"""RNA binding motif (RRM) containing"""	5276	protein-coding gene	gene with protein product		300346	"""HIV TAT specific factor 1"""			8849451	Standard	NM_014500		Approved	TAT-SF1	uc004ezx.3	O43719	OTTHUMG00000022510	ENST00000218364.4:c.1263G>A	X.37:g.135593167G>A		260.0	0.0	0		252.0	251.0	0.996032	NM_001163280	D3DWG9|Q59G06|Q99730	Silent	SNP	ENST00000218364.4	37	CCDS14657.1																																																																																			0|0.004;A|0.148	0.148	strong		0.448	HTATSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058497.1	NM_014500	
DCC	1630	hgsc.bcm.edu	37	18	50976898	50976898	+	Silent	SNP	G	G	A	rs35891220	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:50976898G>A	ENST00000442544.2	+	23	3874	c.3258G>A	c.(3256-3258)ccG>ccA	p.P1086P	DCC_ENST00000581580.1_Silent_p.P721P	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	1086					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)			NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		TGCACCCCCCGCATGGCAGTG	0.507													g|||	203	0.0405351	0.1172	0.0231	5008	,	,		17120	0.006		0.0119	False		,,,				2504	0.0143				p.P1086P		Atlas-SNP	.											DCC,colon,carcinoma,0,1	DCC	360	1	0			c.G3258A						scavenged	.	A		458,3948	219.1+/-236.9	22,414,1767	104.0	89.0	94.0		3258	-9.3	0.3	18	dbSNP_126	94	30,8570	19.8+/-62.0	0,30,4270	no	coding-synonymous	DCC	NM_005215.3		22,444,6037	AA,AG,GG		0.3488,10.3949,3.7521		1086/1448	50976898	488,12518	2203	4300	6503	SO:0001819	synonymous_variant	1630	exon23			CCCCCCGCATGGC	X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2701	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 1"""	120470	"""deleted in colorectal carcinoma"""			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.3258G>A	18.37:g.50976898G>A		117.0	1.0	0.00854701		127.0	64.0	0.503937	NM_005215		Silent	SNP	ENST00000442544.2	37	CCDS11952.1																																																																																			G|0.966;A|0.034	0.034	strong		0.507	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3	NM_005215	
LILRA1	11024	hgsc.bcm.edu	37	19	55107869	55107869	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:55107869T>G	ENST00000251372.3	+	7	1356	c.1174T>G	c.(1174-1176)Tcg>Gcg	p.S392A	LILRA1_ENST00000453777.1_Intron|LILRA1_ENST00000473156.1_3'UTR|LILRB1_ENST00000448689.1_Intron|LILRB1_ENST00000418536.2_Intron|LILRB1_ENST00000396321.2_Intron	NM_006863.2	NP_006854.1	O75019	LIRA1_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 1	392	Ig-like C2-type 4.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|transmembrane signaling receptor activity (GO:0004888)	p.S392T(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	47				GBM - Glioblastoma multiforme(193;0.0348)		CTCAGCCCACTCGGGGACCTA	0.587																																					p.S392A		Atlas-SNP	.											LILRA1,NS,carcinoma,0,2	LILRA1	105	2	1	Substitution - Missense(1)	lung(1)	c.T1174G						scavenged	.						144.0	135.0	138.0					19																	55107869		2203	4300	6503	SO:0001583	missense	11024	exon7			GCCCACTCGGGGA	AF025530	CCDS12901.1, CCDS62802.1	19q13.4	2013-01-11			ENSG00000104974	ENSG00000104974		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6602	protein-coding gene	gene with protein product		604810				9548455	Standard	NM_006863		Approved	LIR-6, CD85i, LIR6	uc002qgh.2	O75019	OTTHUMG00000065701	ENST00000251372.3:c.1174T>G	19.37:g.55107869T>G	ENSP00000251372:p.Ser392Ala	200.0	0.0	0		254.0	14.0	0.0551181	NM_006863	O75018|Q3MJA6	Missense_Mutation	SNP	ENST00000251372.3	37	CCDS12901.1	.	.	.	.	.	.	.	.	.	.	G	0.006	-2.088474	0.00367	.	.	ENSG00000104974	ENST00000251372	T	0.03553	3.89	1.8	-3.59	0.04583	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	0.846833	0.09755	N	0.760012	T	0.00608	0.0020	N	0.00123	-2.06	0.09310	N	1	B	0.02656	0.0	B	0.06405	0.002	T	0.33292	-0.9874	10	0.02654	T	1	.	0.6627	0.00845	0.4001:0.1718:0.2547:0.1734	.	392	O75019	LIRA1_HUMAN	A	392	ENSP00000251372:S392A	ENSP00000251372:S392A	S	+	1	0	LILRA1	59799681	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.554000	0.02172	-1.875000	0.01132	-0.982000	0.02568	TCG	.	.	none		0.587	LILRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000140807.2	NM_006863	
CDAN1	146059	hgsc.bcm.edu	37	15	43028207	43028207	+	Silent	SNP	G	G	C	rs143391538	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:43028207G>C	ENST00000356231.3	-	3	662	c.639C>G	c.(637-639)acC>acG	p.T213T		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	213					chromatin assembly (GO:0031497)|chromatin organization (GO:0006325)|negative regulation of DNA replication (GO:0008156)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	24		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		AGGTGAAGCAGGTCTTGGGCT	0.592													G|||	10	0.00199681	0.0076	0.0	5008	,	,		16376	0.0		0.0	False		,,,				2504	0.0				p.T213T		Atlas-SNP	.											.	CDAN1	70	.	0			c.C639G						PASS	.	G		15,4391	22.3+/-47.3	0,15,2188	107.0	124.0	118.0		639	-0.6	1.0	15	dbSNP_134	118	0,8598		0,0,4299	no	coding-synonymous	CDAN1	NM_138477.2		0,15,6487	CC,CG,GG		0.0,0.3404,0.1153		213/1228	43028207	15,12989	2203	4299	6502	SO:0001819	synonymous_variant	146059	exon3			GAAGCAGGTCTTG	AF525398	CCDS32209.1	15q15.2	2012-04-25	2012-04-25			ENSG00000140326			1713	protein-coding gene	gene with protein product		607465	"""congenital dyserythropoietic anemia, type I"""			8634422, 12434312	Standard	XM_005254177		Approved	CDA-I, CDAI	uc001zql.3	Q8IWY9		ENST00000356231.3:c.639C>G	15.37:g.43028207G>C		184.0	0.0	0		166.0	83.0	0.5	NM_138477	Q6NYD0|Q7Z7L5|Q969N3	Silent	SNP	ENST00000356231.3	37	CCDS32209.1																																																																																			G|0.998;C|0.002	0.002	strong		0.592	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300	
ATP6V0A4	50617	hgsc.bcm.edu	37	7	138417682	138417682	+	Silent	SNP	G	G	A	rs143883618	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:138417682G>A	ENST00000310018.2	-	17	2130	c.1848C>T	c.(1846-1848)ttC>ttT	p.F616F	ATP6V0A4_ENST00000393054.1_Silent_p.F616F|ATP6V0A4_ENST00000353492.4_Silent_p.F616F	NM_020632.2|NM_130840.2	NP_065683.2|NP_570855.2	Q9HBG4	VPP4_HUMAN	ATPase, H+ transporting, lysosomal V0 subunit a4	616					ATP hydrolysis coupled proton transport (GO:0015991)|cellular iron ion homeostasis (GO:0006879)|excretion (GO:0007588)|insulin receptor signaling pathway (GO:0008286)|interaction with host (GO:0051701)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|proton transport (GO:0015992)|regulation of pH (GO:0006885)|sensory perception of sound (GO:0007605)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|vacuolar proton-transporting V-type ATPase, V0 domain (GO:0000220)	ATPase binding (GO:0051117)|hydrogen ion transmembrane transporter activity (GO:0015078)			NS(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(15)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36						ACATGTTGATGAAGTGGATGA	0.398													G|||	24	0.00479233	0.0182	0.0	5008	,	,		17290	0.0		0.0	False		,,,				2504	0.0				p.F616F		Atlas-SNP	.											.	ATP6V0A4	93	.	0			c.C1848T						PASS	.	G	,,	74,4332	65.3+/-102.7	0,74,2129	116.0	110.0	112.0		1848,1848,1848	2.8	1.0	7	dbSNP_134	112	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	ATP6V0A4	NM_020632.2,NM_130840.2,NM_130841.2	,,	0,74,6429	AA,AG,GG		0.0,1.6795,0.569	,,	616/841,616/841,616/841	138417682	74,12932	2203	4300	6503	SO:0001819	synonymous_variant	50617	exon16			GTTGATGAAGTGG	AF245517	CCDS5849.1	7q34	2011-06-09	2006-01-20	2002-05-10	ENSG00000105929	ENSG00000105929		"""ATPases / V-type"""	866	protein-coding gene	gene with protein product		605239	"""ATPase, H+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1B"", ""ATPase, H+ transporting, lysosomal V0 subunit a isoform 4"", ""ATPase, H+ transporting, lysosomal V0 subunit A4"""	ATP6N1B, ATP6N2, RTA1C		10577919, 10973252	Standard	XM_005250393		Approved	RDRTA2, VPP2, RTADR, a4, Vph1, Stv1	uc003vuf.3	Q9HBG4	OTTHUMG00000157122	ENST00000310018.2:c.1848C>T	7.37:g.138417682G>A		144.0	0.0	0		124.0	63.0	0.508065	NM_130841	A4D1R4|A8KA80|Q32M47	Silent	SNP	ENST00000310018.2	37	CCDS5849.1																																																																																			G|0.995;A|0.005	0.005	strong		0.398	ATP6V0A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347514.1	NM_020632	
KCNV2	169522	hgsc.bcm.edu	37	9	2729705	2729705	+	Missense_Mutation	SNP	T	T	C	rs112673841	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:2729705T>C	ENST00000382082.3	+	2	1854	c.1616T>C	c.(1615-1617)cTc>cCc	p.L539P		NM_133497.3	NP_598004.1	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	539					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	35				GBM - Glioblastoma multiforme(50;0.0257)		AACCCACAGCTCACCCCAAGA	0.433													C|||	68	0.0135783	0.0492	0.0043	5008	,	,		19814	0.0		0.0	False		,,,				2504	0.0				p.L539P		Atlas-SNP	.											.	KCNV2	72	.	0			c.T1616C						PASS	.	C	PRO/LEU	195,4211	808.3+/-415.9	2,191,2010	92.0	87.0	89.0		1616	3.5	0.0	9	dbSNP_132	89	4,8596	819.1+/-406.8	0,4,4296	yes	missense	KCNV2	NM_133497.3	98	2,195,6306	CC,CT,TT		0.0465,4.4258,1.5301	benign	539/546	2729705	199,12807	2203	4300	6503	SO:0001583	missense	169522	exon2			CACAGCTCACCCC	AF348983	CCDS6447.1	9p24.2	2011-07-05			ENSG00000168263	ENSG00000168263		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	19698	protein-coding gene	gene with protein product		607604				12060745, 16382104	Standard	NM_133497		Approved	Kv8.2	uc003zho.2	Q8TDN2	OTTHUMG00000019449	ENST00000382082.3:c.1616T>C	9.37:g.2729705T>C	ENSP00000371514:p.Leu539Pro	93.0	0.0	0		103.0	52.0	0.504854	NM_133497	Q5T6X0	Missense_Mutation	SNP	ENST00000382082.3	37	CCDS6447.1	175	0.08012820512820513	58	0.11788617886178862	16	0.04419889502762431	36	0.06293706293706294	65	0.08575197889182058	C	0.271	-0.992832	0.02162	0.044258	4.65E-4	ENSG00000168263	ENST00000382082	D	0.96716	-4.1	5.47	3.52	0.40303	.	5.982730	0.00424	N	0.000068	T	0.08980	0.0222	N	0.00538	-1.39	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.70938	-0.4736	10	0.23302	T	0.38	.	5.3373	0.15965	0.2188:0.5872:0.1183:0.0758	.	539	Q8TDN2	KCNV2_HUMAN	P	539	ENSP00000371514:L539P	ENSP00000371514:L539P	L	+	2	0	KCNV2	2719705	0.000000	0.05858	0.010000	0.14722	0.081000	0.17604	0.370000	0.20433	1.461000	0.47929	-0.119000	0.15052	CTC	T|0.962;C|0.038	0.038	strong		0.433	KCNV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051528.1	NM_133497	
ZNF699	374879	hgsc.bcm.edu	37	19	9407468	9407468	+	Silent	SNP	G	G	A	rs189167193	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:9407468G>A	ENST00000591998.1	-	6	840	c.612C>T	c.(610-612)ttC>ttT	p.F204F	ZNF699_ENST00000308650.3_Silent_p.F204F|CTC-325H20.4_ENST00000591336.1_RNA			Q32M78	ZN699_HUMAN	zinc finger protein 699	204					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						AATGATCCACGAAGGCCTTTC	0.428													G|||	15	0.00299521	0.0113	0.0	5008	,	,		19156	0.0		0.0	False		,,,				2504	0.0				p.F204F		Atlas-SNP	.											.	ZNF699	67	.	0			c.C612T						PASS	.	G		36,3990		0,36,1977	154.0	140.0	145.0		612	-0.2	0.0	19		145	1,8385		0,1,4192	no	coding-synonymous	ZNF699	NM_198535.1		0,37,6169	AA,AG,GG		0.0119,0.8942,0.2981		204/643	9407468	37,12375	2013	4193	6206	SO:0001819	synonymous_variant	374879	exon5			ATCCACGAAGGCC	BC109268	CCDS42495.1	19p13.2	2013-01-08				ENSG00000196110		"""Zinc fingers, C2H2-type"", ""-"""	24750	protein-coding gene	gene with protein product	hangover homolog (Drosophila)	609571				16940975	Standard	NM_198535		Approved	FLJ38144, hang	uc002mlc.1	Q32M78		ENST00000591998.1:c.612C>T	19.37:g.9407468G>A		178.0	0.0	0		153.0	89.0	0.581699	NM_198535	Q8N9A1	Silent	SNP	ENST00000591998.1	37	CCDS42495.1																																																																																			G|0.998;A|0.002	0.002	strong		0.428	ZNF699-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449010.1	NM_198535	
PEX14	5195	hgsc.bcm.edu	37	1	10684422	10684422	+	Silent	SNP	C	C	A	rs35046754	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:10684422C>A	ENST00000356607.4	+	7	593	c.513C>A	c.(511-513)gcC>gcA	p.A171A	PEX14_ENST00000538836.1_Silent_p.A107A	NM_004565.2	NP_004556.1	O75381	PEX14_HUMAN	peroxisomal biogenesis factor 14	171					microtubule anchoring (GO:0034453)|negative regulation of protein binding (GO:0032091)|negative regulation of protein homotetramerization (GO:1901094)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|peroxisome organization (GO:0007031)|peroxisome transport along microtubule (GO:0036250)|protein complex assembly (GO:0006461)|protein homooligomerization (GO:0051260)|protein import into peroxisome matrix (GO:0016558)|protein import into peroxisome matrix, substrate release (GO:0044721)|protein import into peroxisome matrix, translocation (GO:0016561)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	beta-tubulin binding (GO:0048487)|microtubule binding (GO:0008017)|protein N-terminus binding (GO:0047485)|receptor binding (GO:0005102)|transcription corepressor activity (GO:0003714)			breast(3)|endometrium(1)|large_intestine(3)|lung(5)|prostate(1)	13	Ovarian(185;0.203)	all_lung(284;6.02e-06)|Lung NSC(185;9.62e-06)|Renal(390;0.000147)|Breast(348;0.000932)|Colorectal(325;0.00215)|Hepatocellular(190;0.00913)|Ovarian(437;0.023)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0292)|Colorectal(212;9.13e-08)|COAD - Colon adenocarcinoma(227;2.07e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000482)|Kidney(185;0.00174)|KIRC - Kidney renal clear cell carcinoma(229;0.00457)|STAD - Stomach adenocarcinoma(132;0.0249)|READ - Rectum adenocarcinoma(331;0.0419)		CGACCCTCGCCTCCGTCCAGG	0.622													C|||	63	0.0125799	0.0469	0.0014	5008	,	,		15967	0.0		0.0	False		,,,				2504	0.0				p.A171A		Atlas-SNP	.											.	PEX14	40	.	0			c.C513A						PASS	.	C		209,4197	127.4+/-164.3	9,191,2003	75.0	76.0	76.0		513	2.9	1.0	1	dbSNP_126	76	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	PEX14	NM_004565.2		9,193,6301	AA,AC,CC		0.0233,4.7435,1.6223		171/378	10684422	211,12795	2203	4300	6503	SO:0001819	synonymous_variant	5195	exon7			CCTCGCCTCCGTC	AF045186	CCDS30582.1	1p36.22	2008-05-14			ENSG00000142655	ENSG00000142655			8856	protein-coding gene	gene with protein product		601791				9653144	Standard	NM_004565		Approved		uc001arn.3	O75381	OTTHUMG00000001908	ENST00000356607.4:c.513C>A	1.37:g.10684422C>A		311.0	0.0	0		314.0	171.0	0.544586	NM_004565	B2R7N1|B3KML6|B7Z1N2|Q8WX51	Silent	SNP	ENST00000356607.4	37	CCDS30582.1																																																																																			C|0.986;A|0.014	0.014	strong		0.622	PEX14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005414.1		
TJP2	9414	hgsc.bcm.edu	37	9	71844124	71844124	+	Missense_Mutation	SNP	G	G	A	rs41277901	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:71844124G>A	ENST00000377245.4	+	10	1686	c.1478G>A	c.(1477-1479)aGa>aAa	p.R493K	TJP2_ENST00000265384.7_Missense_Mutation_p.R493K|TJP2_ENST00000453658.2_Missense_Mutation_p.R470K|TJP2_ENST00000535702.1_Missense_Mutation_p.R497K|TJP2_ENST00000348208.4_Missense_Mutation_p.R493K|TJP2_ENST00000539225.1_Missense_Mutation_p.R524K	NM_004817.3	NP_004808.2	Q9UDY2	ZO2_HUMAN	tight junction protein 2	493					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|hippo signaling (GO:0035329)|nucleotide phosphorylation (GO:0046939)|response to organic substance (GO:0010033)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	guanylate kinase activity (GO:0004385)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(5)|lung(9)|prostate(3)|skin(3)|soft_tissue(1)|upper_aerodigestive_tract(1)	35						GCAGCCCCGAGAACTTTTCTT	0.393													G|||	60	0.0119808	0.0356	0.0115	5008	,	,		19298	0.0		0.005	False		,,,				2504	0.0				p.R524K		Atlas-SNP	.											.	TJP2	120	.	0			c.G1571A						PASS	.	G	LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG,LYS/ARG	153,4253	106.5+/-144.9	0,153,2050	215.0	200.0	205.0		1409,1490,1571,1478,1478,1478	4.0	0.3	9	dbSNP_127	205	14,8586	11.2+/-40.8	0,14,4286	yes	missense,missense,missense,missense,missense,missense	TJP2	NM_001170414.1,NM_001170415.1,NM_001170416.1,NM_001170630.1,NM_004817.3,NM_201629.3	26,26,26,26,26,26	0,167,6336	AA,AG,GG		0.1628,3.4725,1.284	benign,benign,benign,benign,benign,benign	470/1021,497/1158,524/1222,493/994,493/1191,493/1044	71844124	167,12839	2203	4300	6503	SO:0001583	missense	9414	exon10			CCCCGAGAACTTT	L27476	CCDS6627.1, CCDS6628.1, CCDS55314.1, CCDS55315.1, CCDS55316.1, CCDS55317.1	9q13-q21	2012-07-12	2012-07-12		ENSG00000119139	ENSG00000119139			11828	protein-coding gene	gene with protein product	"""Friedreich ataxia region gene X104 (tight junction protein ZO-2)"", ""zona occludens 2"""	607709	"""deafness, autosomal dominant 51"""	DFNA51		7951235, 20602916	Standard	NM_001170630		Approved	ZO-2, X104, ZO2	uc011lrv.2	Q9UDY2	OTTHUMG00000019978	ENST00000377245.4:c.1478G>A	9.37:g.71844124G>A	ENSP00000366453:p.Arg493Lys	228.0	0.0	0		254.0	70.0	0.275591	NM_001170416	A2A3H9|B7Z2R8|B7Z7T6|F5H301|F5H886|Q15883|Q5VXL0|Q5VXL1|Q8N756|Q8NI14|Q99839|Q9UDY0|Q9UDY1	Missense_Mutation	SNP	ENST00000377245.4	37	CCDS6627.1	19	0.0086996336996337	13	0.026422764227642278	3	0.008287292817679558	0	0.0	3	0.00395778364116095	G	13.41	2.227582	0.39399	0.034725	0.001628	ENSG00000119139	ENST00000453658;ENST00000377245;ENST00000348208;ENST00000265384;ENST00000535702;ENST00000539225	T;T;T;T;T;T	0.08807	3.06;3.06;3.05;3.05;3.08;3.11	5.85	4.02	0.46733	PDZ/DHR/GLGF (1);	0.162144	0.56097	D	0.000036	T	0.01870	0.0059	L	0.29908	0.895	0.33647	D	0.608025	B;B;B;B;B	0.29136	0.234;0.007;0.004;0.007;0.021	B;B;B;B;B	0.28465	0.09;0.01;0.003;0.004;0.018	T	0.29731	-1.0002	10	0.24483	T	0.36	.	9.1425	0.36912	0.2159:0.0:0.7841:0.0	rs41277901;rs61731595	524;497;493;493;493	F5H301;F5H886;Q9UDY2-2;Q9UDY2;Q9UDY2-5	.;.;.;ZO2_HUMAN;.	K	470;493;493;493;497;524	ENSP00000392178:R470K;ENSP00000366453:R493K;ENSP00000345893:R493K;ENSP00000265384:R493K;ENSP00000442090:R497K;ENSP00000438262:R524K	ENSP00000265384:R493K	R	+	2	0	TJP2	71033944	1.000000	0.71417	0.285000	0.24819	0.979000	0.70002	4.172000	0.58243	1.481000	0.48307	0.557000	0.71058	AGA	G|0.988;A|0.012	0.012	strong		0.393	TJP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000052572.2	NM_201629	
COG2	22796	hgsc.bcm.edu	37	1	230810756	230810756	+	Missense_Mutation	SNP	T	T	A	rs6681346	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:230810756T>A	ENST00000366669.4	+	9	1027	c.912T>A	c.(910-912)aaT>aaA	p.N304K	COG2_ENST00000535166.1_Missense_Mutation_p.N188K|COG2_ENST00000534989.1_Missense_Mutation_p.N245K|COG2_ENST00000366668.3_Missense_Mutation_p.N304K	NM_001145036.1|NM_007357.2	NP_001138508.1|NP_031383.1	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2	304			N -> K (in dbSNP:rs6681346).		Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	cytosol (GO:0005829)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|Golgi transport complex (GO:0017119)	protein transporter activity (GO:0008565)			NS(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|urinary_tract(3)	27	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				AAAAAGGCAATACTGTTCCTG	0.368													T|||	475	0.0948482	0.2156	0.0231	5008	,	,		16747	0.0625		0.0159	False		,,,				2504	0.0971				p.N304K		Atlas-SNP	.											.	COG2	61	.	0			c.T912A						PASS	.	T	LYS/ASN,LYS/ASN	793,3613	316.9+/-294.8	78,637,1488	127.0	136.0	133.0		912,912	-2.2	0.3	1	dbSNP_116	133	90,8510	51.1+/-111.2	1,88,4211	yes	missense,missense	COG2	NM_001145036.1,NM_007357.2	94,94	79,725,5699	AA,AT,TT		1.0465,17.9982,6.7892	benign,benign	304/738,304/739	230810756	883,12123	2203	4300	6503	SO:0001583	missense	22796	exon9			AGGCAATACTGTT	Z34975	CCDS1584.1, CCDS44329.1	1q42.2	2008-02-05	2002-05-28	2002-05-31	ENSG00000135775	ENSG00000135775		"""Components of oligomeric golgi complex"""	6546	protein-coding gene	gene with protein product		606974	"""low density lipoprotein receptor defect C complementing"""	LDLC		7962052	Standard	NM_007357		Approved		uc001htw.3	Q14746	OTTHUMG00000037753	ENST00000366669.4:c.912T>A	1.37:g.230810756T>A	ENSP00000355629:p.Asn304Lys	104.0	0.0	0		101.0	49.0	0.485149	NM_007357	Q86U99	Missense_Mutation	SNP	ENST00000366669.4	37	CCDS1584.1	154	0.07051282051282051	104	0.21138211382113822	8	0.022099447513812154	34	0.05944055944055944	8	0.010554089709762533	T	11.50	1.658121	0.29425	0.179982	0.010465	ENSG00000135775	ENST00000366669;ENST00000535166;ENST00000366668;ENST00000534989	T;T;T;T	0.27256	1.68;1.68;1.68;1.68	5.92	-2.23	0.06930	.	0.182059	0.56097	D	0.000023	T	0.00012	0.0000	L	0.47716	1.5	0.21355	P	0.999712339	B;B	0.26195	0.144;0.045	B;B	0.18263	0.021;0.021	T	0.40021	-0.9585	9	0.07990	T	0.79	-16.6064	11.4718	0.50272	0.0:0.3913:0.0:0.6087	rs6681346;rs17848117;rs52807515;rs6681346	304;304	Q86U99;Q14746	.;COG2_HUMAN	K	304;188;304;245	ENSP00000355629:N304K;ENSP00000445724:N188K;ENSP00000355628:N304K;ENSP00000440349:N245K	ENSP00000355628:N304K	N	+	3	2	COG2	228877379	0.753000	0.28349	0.277000	0.24703	0.994000	0.84299	0.099000	0.15210	-0.398000	0.07679	0.533000	0.62120	AAT	T|0.922;A|0.078	0.078	strong		0.368	COG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092087.1	NM_007357	
IFIH1	64135	hgsc.bcm.edu	37	2	163128883	163128883	+	Silent	SNP	G	G	A	rs13418718	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:163128883G>A	ENST00000263642.2	-	13	2864	c.2469C>T	c.(2467-2469)gcC>gcT	p.A823A		NM_022168.3	NP_071451.2	Q9BYX4	IFIH1_HUMAN	interferon induced with helicase C domain 1	823	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|protein sumoylation (GO:0016925)|regulation of apoptotic process (GO:0042981)|regulation of type III interferon production (GO:0034344)|response to virus (GO:0009615)|viral process (GO:0016032)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|ribonucleoprotein complex binding (GO:0043021)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(3)|urinary_tract(1)	39						CATCAGCTCTGGCTCGACCAC	0.428													G|||	473	0.0944489	0.3374	0.0389	5008	,	,		19695	0.0		0.0	False		,,,				2504	0.0				p.A823A		Atlas-SNP	.											.	IFIH1	102	.	0			c.C2469T						PASS	.	G		1416,2990	462.1+/-353.1	226,964,1013	80.0	70.0	74.0		2469	1.3	1.0	2	dbSNP_121	74	7,8593	3.7+/-12.6	0,7,4293	no	coding-synonymous	IFIH1	NM_022168.2		226,971,5306	AA,AG,GG		0.0814,32.138,10.9411		823/1026	163128883	1423,11583	2203	4300	6503	SO:0001819	synonymous_variant	64135	exon13			AGCTCTGGCTCGA	AF095844	CCDS2217.1	2q24.2	2010-02-09			ENSG00000115267	ENSG00000115267			18873	protein-coding gene	gene with protein product	"""helicard"""	606951					Standard	NM_022168		Approved	MDA-5, Hlcd, MDA5, IDDM19	uc002uce.4	Q9BYX4	OTTHUMG00000132055	ENST00000263642.2:c.2469C>T	2.37:g.163128883G>A		248.0	0.0	0		188.0	106.0	0.56383	NM_022168	Q2NKL6|Q6DC96|Q86X56|Q96MX8|Q9H3G6	Silent	SNP	ENST00000263642.2	37	CCDS2217.1																																																																																			G|0.888;A|0.112	0.112	strong		0.428	IFIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255078.2	NM_022168	
ITIH3	3699	hgsc.bcm.edu	37	3	52840325	52840325	+	Silent	SNP	C	C	T	rs34397833	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:52840325C>T	ENST00000449956.2	+	18	1965	c.1959C>T	c.(1957-1959)caC>caT	p.H653H	ITIH3_ENST00000416872.2_Intron	NM_002217.3	NP_002208.3	Q06033	ITIH3_HUMAN	inter-alpha-trypsin inhibitor heavy chain 3	653					hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(6)|liver(1)|lung(6)|ovary(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(193;7e-05)|Kidney(197;0.000656)|KIRC - Kidney renal clear cell carcinoma(197;0.000794)|OV - Ovarian serous cystadenocarcinoma(275;0.0496)		GGGATCCCCACTTCATCATCC	0.582													C|||	219	0.04373	0.1581	0.013	5008	,	,		15639	0.0		0.0	False		,,,				2504	0.001				p.H653H		Atlas-SNP	.											.	ITIH3	132	.	0			c.C1959T						PASS	.	C		412,3666		24,364,1651	53.0	55.0	55.0		1959	4.6	1.0	3	dbSNP_126	55	1,8389		0,1,4194	no	coding-synonymous	ITIH3	NM_002217.3		24,365,5845	TT,TC,CC		0.0119,10.103,3.3125		653/891	52840325	413,12055	2039	4195	6234	SO:0001819	synonymous_variant	3699	exon18			TCCCCACTTCATC		CCDS46845.1	3p21.1	2011-10-26	2011-10-26		ENSG00000162267	ENSG00000162267			6168	protein-coding gene	gene with protein product	"""pre-alpha (globulin) inhibitor, H3 polypeptide"", ""inter-alpha-trypsin inhibitor heavy chain H3"""	146650	"""inter-alpha (globulin) inhibitor, H3 polypeptide"", ""inter-alpha (globulin) inhibitor H3"""			2465147, 10100603	Standard	NM_002217		Approved	H3P	uc003dfv.2	Q06033	OTTHUMG00000158956	ENST00000449956.2:c.1959C>T	3.37:g.52840325C>T		125.0	0.0	0		123.0	64.0	0.520325	NM_002217	Q3B7H5|Q53F06|Q6LAM2|Q99085	Silent	SNP	ENST00000449956.2	37	CCDS46845.1	75	0.034340659340659344	71	0.1443089430894309	4	0.011049723756906077	0	0.0	0	0.0	C	3.086	-0.187992	0.06299	0.10103	1.19E-4	ENSG00000162267	ENST00000398670;ENST00000536431	.	.	.	5.48	4.61	0.57282	.	.	.	.	.	T	0.00580	0.0019	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.00478	-1.1715	5	0.15952	T	0.53	-32.6536	13.5864	0.61933	0.0:0.9234:0.0:0.0766	rs34397833;rs61654726	.	.	.	F	654;642	.	ENSP00000381662:L654F	L	+	1	0	ITIH3	52815365	1.000000	0.71417	1.000000	0.80357	0.441000	0.31987	1.124000	0.31320	1.457000	0.47850	0.561000	0.74099	CTT	C|0.971;T|0.029	0.029	strong		0.582	ITIH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352668.2	NM_002217	
VPS33A	65082	hgsc.bcm.edu	37	12	122720423	122720423	+	Silent	SNP	G	G	A	rs34461198	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:122720423G>A	ENST00000267199.4	-	11	1462	c.1350C>T	c.(1348-1350)gcC>gcT	p.A450A	RP11-512M8.5_ENST00000535844.1_Silent_p.A411A	NM_022916.4	NP_075067.2	Q96AX1	VP33A_HUMAN	vacuolar protein sorting 33 homolog A (S. cerevisiae)	450					lysosome localization (GO:0032418)|melanosome localization (GO:0032400)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of developmental pigmentation (GO:0048070)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosomal membrane (GO:0005765)|perinuclear region of cytoplasm (GO:0048471)				NS(2)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(4)|lung(13)|ovary(1)|skin(2)	28	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000336)|Epithelial(86;0.000606)|BRCA - Breast invasive adenocarcinoma(302;0.23)		TCAGCAGGCCGGCCTTCTCCA	0.478													G|||	232	0.0463259	0.1702	0.0086	5008	,	,		18772	0.0		0.001	False		,,,				2504	0.0				p.A450A		Atlas-SNP	.											.	VPS33A	61	.	0			c.C1350T						PASS	.	G		696,3710	291.8+/-281.7	53,590,1560	208.0	192.0	197.0		1350	-11.7	0.0	12	dbSNP_126	197	17,8583	11.9+/-42.8	0,17,4283	no	coding-synonymous	VPS33A	NM_022916.4		53,607,5843	AA,AG,GG		0.1977,15.7966,5.4821		450/597	122720423	713,12293	2203	4300	6503	SO:0001819	synonymous_variant	65082	exon11			CAGGCCGGCCTTC	AK026048	CCDS9231.1	12q24.31	2008-06-23	2006-04-04		ENSG00000139719	ENSG00000139719			18179	protein-coding gene	gene with protein product		610034	"""vacuolar protein sorting 33A (yeast)"""			11250079	Standard	NM_022916		Approved		uc001ucd.3	Q96AX1	OTTHUMG00000168920	ENST00000267199.4:c.1350C>T	12.37:g.122720423G>A		240.0	0.0	0		253.0	125.0	0.494071	NM_022916	Q547V4|Q9H5Q0	Silent	SNP	ENST00000267199.4	37	CCDS9231.1																																																																																			G|0.944;A|0.056	0.056	strong		0.478	VPS33A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401607.2		
OVGP1	5016	hgsc.bcm.edu	37	1	111957721	111957721	+	Missense_Mutation	SNP	C	C	T	rs115512535	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:111957721C>T	ENST00000369732.3	-	11	1457	c.1402G>A	c.(1402-1404)Gga>Aga	p.G468R		NM_002557.3	NP_002548.3	Q12889	OVGP1_HUMAN	oviductal glycoprotein 1, 120kDa	468					binding of sperm to zona pellucida (GO:0007339)|carbohydrate metabolic process (GO:0005975)|chitin catabolic process (GO:0006032)|female pregnancy (GO:0007565)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|single fertilization (GO:0007338)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|egg coat (GO:0035805)|perivitelline space (GO:0098595)	chitinase activity (GO:0004568)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(13)|ovary(4)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	39		all_cancers(81;8.18e-06)|all_epithelial(167;5.64e-06)|all_lung(203;0.000152)|Lung NSC(277;0.000302)		Lung(183;0.0253)|Colorectal(144;0.033)|all cancers(265;0.0552)|Epithelial(280;0.0802)|COAD - Colon adenocarcinoma(174;0.123)|LUSC - Lung squamous cell carcinoma(189;0.14)		GTCTTCTCTCCTAGAGCTACA	0.498													C|||	11	0.00219649	0.0083	0.0	5008	,	,		20915	0.0		0.0	False		,,,				2504	0.0				p.G468R		Atlas-SNP	.											.	OVGP1	177	.	0			c.G1402A						PASS	.	C	ARG/GLY	57,4349	55.5+/-91.7	0,57,2146	121.0	104.0	110.0		1402	-0.9	0.0	1	dbSNP_132	110	1,8599	1.2+/-3.3	0,1,4299	yes	missense	OVGP1	NM_002557.3	125	0,58,6445	TT,TC,CC		0.0116,1.2937,0.4459	possibly-damaging	468/679	111957721	58,12948	2203	4300	6503	SO:0001583	missense	5016	exon11			TCTCTCCTAGAGC	U09550	CCDS834.1	1p13.2	2008-07-31	2008-07-31		ENSG00000085465	ENSG00000085465		"""Mucins"""	8524	protein-coding gene	gene with protein product	"""oviductin"""	603578	"""mucin 9"""	MUC9		7819450, 9341614	Standard	NM_002557		Approved	CHIT5	uc001eba.3	Q12889	OTTHUMG00000011746	ENST00000369732.3:c.1402G>A	1.37:g.111957721C>T	ENSP00000358747:p.Gly468Arg	298.0	0.0	0		300.0	134.0	0.446667	NM_002557	A0AV19|B9EGE1|Q15841	Missense_Mutation	SNP	ENST00000369732.3	37	CCDS834.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	C	17.36	3.368778	0.61624	0.012937	1.16E-4	ENSG00000085465	ENST00000369732;ENST00000369728;ENST00000434331	T	0.04317	3.65	4.86	-0.95	0.10372	.	0.931884	0.09108	N	0.847418	T	0.01489	0.0048	L	0.39898	1.24	0.09310	N	1	P;P	0.48764	0.675;0.915	B;B	0.41946	0.131;0.371	T	0.45977	-0.9224	10	0.40728	T	0.16	-0.097	5.5535	0.17103	0.0:0.5337:0.1411:0.3252	.	468;532	Q12889;Q59HH5	OVGP1_HUMAN;.	R	468;532;276	ENSP00000358747:G468R	ENSP00000358743:G532R	G	-	1	0	OVGP1	111759244	0.000000	0.05858	0.000000	0.03702	0.895000	0.52256	0.199000	0.17237	-0.209000	0.10156	0.585000	0.79938	GGA	C|0.997;T|0.003	0.003	strong		0.498	OVGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032461.1	NM_002557	
LRRIQ1	84125	hgsc.bcm.edu	37	12	85492658	85492658	+	Missense_Mutation	SNP	A	A	C	rs139758674	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:85492658A>C	ENST00000393217.2	+	13	3156	c.3095A>C	c.(3094-3096)gAg>gCg	p.E1032A		NM_001079910.1	NP_001073379.1	Q96JM4	LRIQ1_HUMAN	leucine-rich repeats and IQ motif containing 1	1032										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|liver(1)|lung(28)|ovary(5)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	83				GBM - Glioblastoma multiforme(134;0.212)		CCATCCTTGGAGAATCTTGTT	0.299													A|||	43	0.00858626	0.031	0.0029	5008	,	,		11103	0.0		0.0	False		,,,				2504	0.0				p.E1032A		Atlas-SNP	.											LRRIQ1_ENST00000393217,NS,carcinoma,-1,2	LRRIQ1	512	2	0			c.A3095C						scavenged	.	A	ALA/GLU	79,4325	69.8+/-107.6	1,77,2124	75.0	78.0	77.0		3095	0.4	0.0	12	dbSNP_134	77	2,8586	2.2+/-6.3	0,2,4292	yes	missense	LRRIQ1	NM_001079910.1	107	1,79,6416	CC,CA,AA		0.0233,1.7938,0.6235	benign	1032/1723	85492658	81,12911	2202	4294	6496	SO:0001583	missense	84125	exon13			CCTTGGAGAATCT	AK022365	CCDS41816.1	12q21	2008-02-05			ENSG00000133640	ENSG00000133640			25708	protein-coding gene	gene with protein product						11347906	Standard	NM_001079910		Approved	FLJ12303, KIAA1801	uc001tac.3	Q96JM4	OTTHUMG00000166185	ENST00000393217.2:c.3095A>C	12.37:g.85492658A>C	ENSP00000376910:p.Glu1032Ala	92.0	1.0	0.0108696		94.0	47.0	0.5	NM_001079910	Q567P4|Q9BS17|Q9HA36	Missense_Mutation	SNP	ENST00000393217.2	37	CCDS41816.1	10	0.004578754578754579	9	0.018292682926829267	1	0.0027624309392265192	0	0.0	0	0.0	A	6.385	0.439095	0.12104	0.017938	2.33E-4	ENSG00000133640	ENST00000256007;ENST00000378580;ENST00000393217	T	0.23348	1.91	5.18	0.447	0.16608	.	1.889910	0.03114	N	0.162924	T	0.08537	0.0212	N	0.20574	0.59	0.09310	N	1	B;B	0.25667	0.063;0.131	B;B	0.22386	0.039;0.039	T	0.21211	-1.0252	10	0.56958	D	0.05	.	4.26	0.10737	0.6323:0.0:0.2269:0.1408	.	1032;1007	Q96JM4;C9JI57	LRIQ1_HUMAN;.	A	1032;1007;1032	ENSP00000376910:E1032A	ENSP00000256007:E1032A	E	+	2	0	LRRIQ1	84016789	0.569000	0.26643	0.003000	0.11579	0.778000	0.44026	1.102000	0.31050	-0.162000	0.10964	0.477000	0.44152	GAG	A|0.995;C|0.005	0.005	strong		0.299	LRRIQ1-004	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388249.2	NM_032165	
RERE	473	hgsc.bcm.edu	37	1	8415621	8415621	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:8415621G>A	ENST00000337907.3	-	23	5159	c.4525C>T	c.(4525-4527)Ccc>Tcc	p.P1509S	RERE_ENST00000476556.1_Missense_Mutation_p.P955S|RERE_ENST00000400908.2_Missense_Mutation_p.P1509S|RERE_ENST00000400907.2_Missense_Mutation_p.P527S|RERE_ENST00000377464.1_Missense_Mutation_p.P1241S	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	1509	Pro-rich.				chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		GACATGGGGGGTGGGATGGCC	0.652																																					p.P1509S		Atlas-SNP	.											.	RERE	129	.	0			c.C4525T						PASS	.						15.0	17.0	16.0					1																	8415621		2198	4291	6489	SO:0001583	missense	473	exon23			TGGGGGGTGGGAT	AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"""GATA zinc finger domain containing"""	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.4525C>T	1.37:g.8415621G>A	ENSP00000338629:p.Pro1509Ser	43.0	0.0	0		58.0	36.0	0.62069	NM_012102	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Missense_Mutation	SNP	ENST00000337907.3	37	CCDS95.1	.	.	.	.	.	.	.	.	.	.	G	27.9	4.870072	0.91587	.	.	ENSG00000142599	ENST00000337907;ENST00000377464;ENST00000400907;ENST00000476556;ENST00000400908;ENST00000505225	T;T;T	0.47177	0.85;0.85;0.85	5.98	5.98	0.97165	.	.	.	.	.	T	0.64450	0.2599	L	0.60455	1.87	0.80722	D	1	D	0.54772	0.968	P	0.60117	0.869	T	0.61855	-0.6977	9	0.52906	T	0.07	-25.8584	19.4247	0.94737	0.0:0.0:1.0:0.0	.	1509	Q9P2R6	RERE_HUMAN	S	1509;1241;527;955;1509;165	ENSP00000338629:P1509S;ENSP00000366684:P1241S;ENSP00000383700:P1509S	ENSP00000338629:P1509S	P	-	1	0	RERE	8338208	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.807000	0.99171	2.843000	0.97960	0.585000	0.79938	CCC	.	.	none		0.652	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1		
TIMELESS	8914	hgsc.bcm.edu	37	12	56822690	56822690	+	Silent	SNP	C	C	T	rs11832580	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:56822690C>T	ENST00000553532.1	-	11	1431	c.1281G>A	c.(1279-1281)aaG>aaA	p.K427K	TIMELESS_ENST00000229201.4_Silent_p.K426K|TIMELESS_ENST00000554616.1_Intron					timeless circadian clock											NS(1)|breast(2)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(8)|lung(14)|ovary(7)|pancreas(2)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	49						AGGCAGCTTCCTTGCGGTCAG	0.532													C|||	256	0.0511182	0.1831	0.0187	5008	,	,		19438	0.0		0.001	False		,,,				2504	0.0				p.K427K		Atlas-SNP	.											.	TIMELESS	107	.	0			c.G1281A						PASS	.	C		702,3704	294.7+/-283.3	45,612,1546	109.0	95.0	100.0		1281	4.4	1.0	12	dbSNP_120	100	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	TIMELESS	NM_003920.3		45,616,5842	TT,TC,CC		0.0465,15.9328,5.4283		427/1209	56822690	706,12300	2203	4300	6503	SO:0001819	synonymous_variant	8914	exon11			AGCTTCCTTGCGG	AF098162	CCDS8918.1	12q13.3	2012-12-14	2012-12-14		ENSG00000111602	ENSG00000111602			11813	protein-coding gene	gene with protein product	"""Tof1 homolog (S. cerevisiae)"", ""timeless circadian clock 1"""	603887	"""timeless (Drosophila) homolog"", ""timeless homolog (Drosophila)"""			9856465	Standard	NM_003920		Approved	hTIM, TIM, TIM1	uc001slf.2	Q9UNS1	OTTHUMG00000170600	ENST00000553532.1:c.1281G>A	12.37:g.56822690C>T		127.0	0.0	0		119.0	54.0	0.453782	NM_003920		Silent	SNP	ENST00000553532.1	37	CCDS8918.1																																																																																			C|0.949;T|0.051	0.051	strong		0.532	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920	
ITIH1	3697	hgsc.bcm.edu	37	3	52823864	52823864	+	Missense_Mutation	SNP	A	A	T	rs61730358	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:52823864A>T	ENST00000273283.2	+	19	2339	c.2315A>T	c.(2314-2316)cAg>cTg	p.Q772L	ITIH1_ENST00000405128.3_Missense_Mutation_p.Q138L|ITIH1_ENST00000537050.1_Missense_Mutation_p.Q484L|ITIH1_ENST00000540715.1_Missense_Mutation_p.Q630L|ITIH1_ENST00000542827.1_3'UTR	NM_002215.3	NP_002206.2	P19827	ITIH1_HUMAN	inter-alpha-trypsin inhibitor heavy chain 1	772	Hyaluronan-binding.				hyaluronan metabolic process (GO:0030212)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(16)|lung(18)|ovary(4)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	52				BRCA - Breast invasive adenocarcinoma(193;7.04e-05)|Kidney(197;0.000659)|KIRC - Kidney renal clear cell carcinoma(197;0.000795)|OV - Ovarian serous cystadenocarcinoma(275;0.0498)		GTGCTGCGGCAGGACGGGTAA	0.627													A|||	96	0.0191693	0.0681	0.0086	5008	,	,		20037	0.0		0.0	False		,,,				2504	0.0				p.Q772L		Atlas-SNP	.											.	ITIH1	108	.	0			c.A2315T						PASS	.	A	LEU/GLN,LEU/GLN,LEU/GLN,LEU/GLN	272,4134	152.9+/-186.6	11,250,1942	55.0	54.0	54.0		1889,1451,1451,2315	5.4	1.0	3	dbSNP_129	54	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense,missense	ITIH1	NM_001166434.1,NM_001166435.1,NM_001166436.1,NM_002215.2	113,113,113,113	11,252,6240	TT,TA,AA		0.0233,6.1734,2.1067	benign,benign,benign,benign	630/770,484/624,484/624,772/912	52823864	274,12732	2203	4300	6503	SO:0001583	missense	3697	exon19			TGCGGCAGGACGG		CCDS2864.1, CCDS54595.1	3p21.1	2011-10-26	2011-10-26		ENSG00000055957	ENSG00000055957			6166	protein-coding gene	gene with protein product		147270	"""inter-alpha (globulin) inhibitor, H1 polypeptide"""			1385302, 10100603	Standard	NM_002215		Approved	H1P, IATIH, ITIH	uc003dfs.3	P19827	OTTHUMG00000150312	ENST00000273283.2:c.2315A>T	3.37:g.52823864A>T	ENSP00000273283:p.Gln772Leu	56.0	0.0	0		62.0	29.0	0.467742	NM_002215	A8K9N5|B2RAH9|B7Z558|B7Z8C0|F5H165|F5H7Y8|P78455|Q01746|Q562G1	Missense_Mutation	SNP	ENST00000273283.2	37	CCDS2864.1	36	0.016483516483516484	35	0.07113821138211382	1	0.0027624309392265192	0	0.0	0	0.0	A	15.98	2.991954	0.54041	0.061734	2.33E-4	ENSG00000055957	ENST00000273283;ENST00000540715;ENST00000537050;ENST00000428133;ENST00000405128	T;T;T;T;T	0.11712	2.75;2.75;2.75;2.75;2.75	5.42	5.42	0.78866	Inter-alpha-trypsin inhibitor heavy chain, C-terminal (1);	0.203207	0.43919	D	0.000515	T	0.01254	0.0041	L	0.49350	1.555	0.33937	D	0.642752	B;P;B;P	0.42337	0.006;0.776;0.425;0.661	B;B;B;P	0.48982	0.015;0.41;0.182;0.597	T	0.06534	-1.0821	10	0.40728	T	0.16	-18.8137	12.9885	0.58606	1.0:0.0:0.0:0.0	rs61730358	630;138;373;772	F5H165;B5MCP1;Q9P1C5;P19827	.;.;.;ITIH1_HUMAN	L	772;630;484;325;138	ENSP00000273283:Q772L;ENSP00000443973:Q630L;ENSP00000443847:Q484L;ENSP00000395836:Q325L;ENSP00000384589:Q138L	ENSP00000273283:Q772L	Q	+	2	0	ITIH1	52798904	1.000000	0.71417	0.993000	0.49108	0.101000	0.19017	5.862000	0.69560	2.043000	0.60533	0.460000	0.39030	CAG	A|0.981;T|0.019	0.019	strong		0.627	ITIH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317522.1	NM_002215	
SLC39A11	201266	hgsc.bcm.edu	37	17	70645366	70645366	+	Missense_Mutation	SNP	C	C	G	rs115567758	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:70645366C>G	ENST00000542342.2	-	8	822	c.734G>C	c.(733-735)gGc>gCc	p.G245A	SLC39A11_ENST00000255559.3_Missense_Mutation_p.G238A|SLC39A11_ENST00000579988.1_5'UTR	NM_001159770.1	NP_001153242.1	Q8N1S5	S39AB_HUMAN	solute carrier family 39, member 11	245					zinc ion transport (GO:0006829)	integral component of membrane (GO:0016021)	metal ion transmembrane transporter activity (GO:0046873)			endometrium(1)|large_intestine(4)|liver(2)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	16						GACAGCCAGGCCCTCGGGGAA	0.557													C|||	3	0.000599042	0.0023	0.0	5008	,	,		21013	0.0		0.0	False		,,,				2504	0.0				p.G245A	NSCLC(95;736 1527 12296 39625 41839)	Atlas-SNP	.											.	SLC39A11	32	.	0			c.G734C						PASS	.	C	ALA/GLY,ALA/GLY	25,4381	29.9+/-59.1	0,25,2178	47.0	51.0	50.0		734,713	5.1	1.0	17	dbSNP_132	50	0,8600		0,0,4300	yes	missense,missense	SLC39A11	NM_001159770.1,NM_139177.3	60,60	0,25,6478	GG,GC,CC		0.0,0.5674,0.1922	probably-damaging,probably-damaging	245/343,238/336	70645366	25,12981	2203	4300	6503	SO:0001583	missense	201266	exon8			GCCAGGCCCTCGG	AF331643	CCDS11690.1, CCDS54160.1	17q24.3-q25.1	2014-08-12	2013-07-17	2003-10-24	ENSG00000133195	ENSG00000133195		"""Solute carriers"""	14463	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 26"""	C17orf26		11707075	Standard	NM_139177		Approved		uc002jjb.3	Q8N1S5	OTTHUMG00000178306	ENST00000542342.2:c.734G>C	17.37:g.70645366C>G	ENSP00000445829:p.Gly245Ala	95.0	0.0	0		109.0	47.0	0.431193	NM_001159770	B2R8H7|Q8WZ81	Missense_Mutation	SNP	ENST00000542342.2	37	CCDS54160.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	15.55	2.865881	0.51588	0.005674	0.0	ENSG00000133195	ENST00000542342;ENST00000255559	T;T	0.48836	0.8;0.8	5.05	5.05	0.67936	.	0.000000	0.85682	D	0.000000	T	0.74642	0.3743	H	0.97051	3.93	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.85832	0.1392	10	0.87932	D	0	.	18.3766	0.90437	0.0:1.0:0.0:0.0	.	245;238	Q8N1S5;Q8N1S5-2	S39AB_HUMAN;.	A	245;238	ENSP00000445829:G245A;ENSP00000255559:G238A	ENSP00000255559:G238A	G	-	2	0	SLC39A11	68156961	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.013000	0.76373	2.504000	0.84457	0.655000	0.94253	GGC	C|0.999;G|0.001	0.001	strong		0.557	SLC39A11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441442.1		
LSG1	55341	hgsc.bcm.edu	37	3	194371925	194371925	+	Silent	SNP	A	A	G	rs35636619	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:194371925A>G	ENST00000265245.5	-	9	1508	c.1194T>C	c.(1192-1194)ggT>ggC	p.G398G	AC046143.2_ENST00000582474.1_RNA	NM_018385.2	NP_060855.2	Q9H089	LSG1_HUMAN	large 60S subunit nuclear export GTPase 1	398	CP-type G. {ECO:0000255|PROSITE- ProRule:PRU01058}.				GTP catabolic process (GO:0006184)|nuclear export (GO:0051168)|protein transport (GO:0015031)|ribosome biogenesis (GO:0042254)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(2)|endometrium(3)|large_intestine(2)|lung(9)	16	all_cancers(143;1.68e-08)|Ovarian(172;0.0634)		OV - Ovarian serous cystadenocarcinoma(49;4.34e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;7.55e-06)		TTGAACTCTTACCAACATTAG	0.418													A|||	13	0.00259585	0.0083	0.0014	5008	,	,		21914	0.0		0.001	False		,,,				2504	0.0				p.G398G		Atlas-SNP	.											.	LSG1	38	.	0			c.T1194C						PASS	.	A		13,4393	20.2+/-43.8	0,13,2190	162.0	146.0	151.0		1194	0.8	1.0	3	dbSNP_126	151	0,8600		0,0,4300	no	coding-synonymous	LSG1	NM_018385.2		0,13,6490	GG,GA,AA		0.0,0.2951,0.1		398/659	194371925	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	55341	exon9			ACTCTTACCAACA		CCDS33922.1	3q29	2013-08-21	2013-08-21		ENSG00000041802	ENSG00000041802			25652	protein-coding gene	gene with protein product		610780	"""large subunit GTPase 1 homolog (S. cerevisiae)"""			11230166	Standard	NM_018385		Approved	FLJ11301	uc003fui.3	Q9H089	OTTHUMG00000156021	ENST00000265245.5:c.1194T>C	3.37:g.194371925A>G		182.0	0.0	0		184.0	83.0	0.451087	NM_018385	A0JLT4|A0PJK3|A6NI18|Q7L9H8|Q9NUK8	Silent	SNP	ENST00000265245.5	37	CCDS33922.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	A	10.82	1.457387	0.26161	0.002951	0.0	ENSG00000041802	ENST00000437613	.	.	.	6.06	0.824	0.18818	.	.	.	.	.	T	0.40322	0.1112	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.28073	-1.0055	4	.	.	.	.	0.5788	0.00708	0.4085:0.17:0.2244:0.1971	rs35636619	.	.	.	A	132	.	.	V	-	2	0	LSG1	195853214	0.841000	0.29509	1.000000	0.80357	0.996000	0.88848	-0.065000	0.11617	0.549000	0.28973	0.533000	0.62120	GTA	A|0.999;G|0.001	0.001	strong		0.418	LSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342740.1	NM_018385	
ARNT2	9915	hgsc.bcm.edu	37	15	80843578	80843578	+	Missense_Mutation	SNP	G	G	A	rs150765047	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:80843578G>A	ENST00000303329.4	+	9	1081	c.916G>A	c.(916-918)Ggc>Agc	p.G306S	ARNT2_ENST00000527771.1_Missense_Mutation_p.G295S|ARNT2_ENST00000533983.1_Missense_Mutation_p.G295S	NM_014862.3	NP_055677.3	Q9HBZ2	ARNT2_HUMAN	aryl-hydrocarbon receptor nuclear translocator 2	306					central nervous system development (GO:0007417)|in utero embryonic development (GO:0001701)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell proliferation (GO:0008284)|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)|response to estradiol (GO:0032355)|response to hypoxia (GO:0001666)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	aryl hydrocarbon receptor binding (GO:0017162)|DNA binding (GO:0003677)|protein heterodimerization activity (GO:0046982)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			NS(1)|central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|ovary(1)|pancreas(2)|prostate(2)|skin(1)	35			BRCA - Breast invasive adenocarcinoma(143;0.134)			TGTGGGACAAGGCAGTAAATA	0.413													G|||	10	0.00199681	0.0076	0.0	5008	,	,		22886	0.0		0.0	False		,,,				2504	0.0				p.G306S		Atlas-SNP	.											.	ARNT2	88	.	0			c.G916A						PASS	.	G	SER/GLY	23,4383	29.9+/-59.1	0,23,2180	128.0	117.0	121.0		916	4.0	1.0	15	dbSNP_134	121	0,8600		0,0,4300	yes	missense	ARNT2	NM_014862.3	56	0,23,6480	AA,AG,GG		0.0,0.522,0.1768	benign	306/718	80843578	23,12983	2203	4300	6503	SO:0001583	missense	9915	exon9			GGACAAGGCAGTA	AB002305	CCDS32307.1	15q25.1	2013-05-21			ENSG00000172379	ENSG00000172379		"""Basic helix-loop-helix proteins"""	16876	protein-coding gene	gene with protein product		606036				11247670	Standard	NM_014862		Approved	KIAA0307, bHLHe1	uc002bfr.3	Q9HBZ2	OTTHUMG00000165478	ENST00000303329.4:c.916G>A	15.37:g.80843578G>A	ENSP00000307479:p.Gly306Ser	26.0	0.0	0		38.0	23.0	0.605263	NM_014862	B4DIS7|O15024|Q8IYC2	Missense_Mutation	SNP	ENST00000303329.4	37	CCDS32307.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	15.74	2.923805	0.52653	0.00522	0.0	ENSG00000172379	ENST00000360062;ENST00000303329;ENST00000540859	T	0.06142	3.34	4.9	3.98	0.46160	.	0.412872	0.25801	N	0.028211	T	0.03095	0.0091	N	0.16656	0.425	0.54753	D	0.999984	B	0.15719	0.014	B	0.17722	0.019	T	0.43163	-0.9408	10	0.18276	T	0.48	.	13.4258	0.61024	0.0763:0.0:0.9237:0.0	.	306	Q9HBZ2	ARNT2_HUMAN	S	295;306;306	ENSP00000307479:G306S	ENSP00000307479:G306S	G	+	1	0	ARNT2	78630633	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	4.471000	0.60182	1.060000	0.40578	0.655000	0.94253	GGC	G|0.999;A|0.001	0.001	strong		0.413	ARNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384389.2		
VNN1	8876	hgsc.bcm.edu	37	6	133015257	133015257	+	Missense_Mutation	SNP	C	C	G	rs45610032	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:133015257C>G	ENST00000367928.4	-	3	419	c.406G>C	c.(406-408)Gtg>Ctg	p.V136L		NM_004666.2	NP_004657.2	O95497	VNN1_HUMAN	vanin 1	136	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.		V -> L (in dbSNP:rs45610032). {ECO:0000269|Ref.4}.		acute inflammatory response (GO:0002526)|cellular component movement (GO:0006928)|chronic inflammatory response (GO:0002544)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|pantothenate metabolic process (GO:0015939)|positive regulation of T cell differentiation in thymus (GO:0033089)|response to oxidative stress (GO:0006979)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	GPI anchor binding (GO:0034235)|pantetheine hydrolase activity (GO:0017159)			NS(2)|endometrium(3)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)	31	Breast(56;0.135)			OV - Ovarian serous cystadenocarcinoma(155;0.0027)|GBM - Glioblastoma multiforme(226;0.0189)		ATATTTGCCACAACATAGATA	0.438													C|||	38	0.00758786	0.0265	0.0043	5008	,	,		16984	0.0		0.0	False		,,,				2504	0.0				p.V136L		Atlas-SNP	.											.	VNN1	69	.	0			c.G406C						PASS	.	C	LEU/VAL	119,4287	90.2+/-128.9	3,113,2087	155.0	139.0	144.0		406	6.1	1.0	6	dbSNP_127	144	5,8595	3.7+/-12.6	0,5,4295	no	missense	VNN1	NM_004666.2	32	3,118,6382	GG,GC,CC		0.0581,2.7009,0.9534	benign	136/514	133015257	124,12882	2203	4300	6503	SO:0001583	missense	8876	exon3			TTGCCACAACATA	AJ132099	CCDS5159.1	6q23-q24	2013-02-13			ENSG00000112299	ENSG00000112299	3.5.1.92	"""Vanins"""	12705	protein-coding gene	gene with protein product		603570				9790769	Standard	NM_004666		Approved	Tiff66	uc003qdo.3	O95497	OTTHUMG00000015587	ENST00000367928.4:c.406G>C	6.37:g.133015257C>G	ENSP00000356905:p.Val136Leu	224.0	0.0	0		233.0	115.0	0.493562	NM_004666	A8K310|Q4JFW6|Q4VAS7|Q4VAS8|Q4VAS9|Q9UF16|Q9UJF4	Missense_Mutation	SNP	ENST00000367928.4	37	CCDS5159.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	C	25.6	4.658625	0.88154	0.027009	5.81E-4	ENSG00000112299	ENST00000367928	D	0.89485	-2.52	6.07	6.07	0.98685	Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase (4);	0.000000	0.64402	D	0.000004	D	0.90140	0.6919	M	0.76002	2.32	0.58432	D	0.999998	P	0.37141	0.584	B	0.44044	0.439	D	0.89290	0.3618	10	0.52906	T	0.07	-8.8184	20.6439	0.99570	0.0:1.0:0.0:0.0	rs45610032	136	O95497	VNN1_HUMAN	L	136	ENSP00000356905:V136L	ENSP00000356905:V136L	V	-	1	0	VNN1	133056950	1.000000	0.71417	0.969000	0.41365	0.874000	0.50279	6.622000	0.74233	2.890000	0.99128	0.650000	0.86243	GTG	C|0.992;G|0.008	0.008	strong		0.438	VNN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042263.1		
MRPL32	64983	hgsc.bcm.edu	37	7	42971998	42971998	+	Missense_Mutation	SNP	A	A	G	rs111980169	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:42971998A>G	ENST00000223324.2	+	1	200	c.13A>G	c.(13-15)Atg>Gtg	p.M5V	PSMA2_ENST00000442788.1_5'Flank|PSMA2_ENST00000223321.4_5'Flank|PSMA2_ENST00000538645.1_5'Flank|PSMA2_ENST00000445517.1_5'Flank	NM_031903.2	NP_114109.1	Q9BYC8	RM32_HUMAN	mitochondrial ribosomal protein L32	5					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrial ribosome (GO:0005761)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(1)|kidney(1)|large_intestine(2)|lung(6)	10						GGCGCTGGCCATGCTGGTCTT	0.637													A|||	23	0.00459265	0.0174	0.0	5008	,	,		15207	0.0		0.0	False		,,,				2504	0.0				p.M5V		Atlas-SNP	.											.	MRPL32	25	.	0			c.A13G						PASS	.	A	VAL/MET	44,4362	46.7+/-81.2	0,44,2159	57.0	60.0	59.0		13	-11.6	0.0	7	dbSNP_132	59	0,8600		0,0,4300	yes	missense	MRPL32	NM_031903.2	21	0,44,6459	GG,GA,AA		0.0,0.9986,0.3383	benign	5/189	42971998	44,12962	2203	4300	6503	SO:0001583	missense	64983	exon1			CTGGCCATGCTGG	AB051343	CCDS5468.1	7p14	2012-09-13			ENSG00000106591	ENSG00000106591		"""Mitochondrial ribosomal proteins / large subunits"""	14035	protein-coding gene	gene with protein product		611839				11543634	Standard	NM_031903		Approved	HSPC283, L32mt, MRP-L32, bMRP-59b	uc003tia.3	Q9BYC8	OTTHUMG00000155180	ENST00000223324.2:c.13A>G	7.37:g.42971998A>G	ENSP00000223324:p.Met5Val	99.0	0.0	0		96.0	51.0	0.53125	NM_031903	Q96Q68|Q9P098	Missense_Mutation	SNP	ENST00000223324.2	37	CCDS5468.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	A	11.56	1.675863	0.29783	0.009986	0.0	ENSG00000106591	ENST00000223324	.	.	.	5.97	-11.6	0.00059	.	1.135090	0.06109	N	0.666822	T	0.09730	0.0239	L	0.42245	1.32	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.28427	-1.0044	9	0.02654	T	1	-2.6256	2.0049	0.03475	0.1081:0.2514:0.2373:0.4032	.	5	Q9BYC8	RM32_HUMAN	V	5	.	ENSP00000223324:M5V	M	+	1	0	MRPL32	42938523	0.000000	0.05858	0.005000	0.12908	0.224000	0.24922	-1.230000	0.02942	-1.610000	0.01583	0.477000	0.44152	ATG	A|0.995;G|0.005	0.005	strong		0.637	MRPL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338669.1	NM_031903	
TELO2	9894	hgsc.bcm.edu	37	16	1552107	1552107	+	Missense_Mutation	SNP	C	C	T	rs58099766	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:1552107C>T	ENST00000262319.6	+	12	1811	c.1532C>T	c.(1531-1533)gCt>gTt	p.A511V	TELO2_ENST00000564507.1_3'UTR	NM_016111.3	NP_057195.2	Q9Y4R8	TELO2_HUMAN	telomere maintenance 2	511			A -> V (in dbSNP:rs58099766).		regulation of TOR signaling (GO:0032006)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)	protein complex binding (GO:0032403)			NS(1)|endometrium(1)|kidney(5)|lung(9)|ovary(1)|skin(1)|urinary_tract(1)	19		Hepatocellular(780;0.219)				AGCAGCAAGGCTCCTGCCTAC	0.632													C|||	115	0.0229633	0.0847	0.0043	5008	,	,		15233	0.0		0.0	False		,,,				2504	0.0				p.A511V		Atlas-SNP	.											.	TELO2	44	.	0			c.C1532T						PASS	.	C	VAL/ALA	328,4070	172.7+/-202.6	14,300,1885	67.0	64.0	65.0		1532	0.3	0.1	16	dbSNP_129	65	1,8599		0,1,4299	yes	missense	TELO2	NM_016111.3	64	14,301,6184	TT,TC,CC		0.0116,7.4579,2.5312	benign	511/838	1552107	329,12669	2199	4300	6499	SO:0001583	missense	9894	exon12			GCAAGGCTCCTGC	AL080126	CCDS32363.1	16p13.3	2013-08-06	2013-08-06		ENSG00000100726	ENSG00000100726			29099	protein-coding gene	gene with protein product		611140	"""TEL2, telomere maintenance 2, homolog (S. cerevisiae)"""			9734811, 11230166, 12670948	Standard	NM_016111		Approved	KIAA0683, hCLK2, TEL2	uc002cly.3	Q9Y4R8	OTTHUMG00000044471	ENST00000262319.6:c.1532C>T	16.37:g.1552107C>T	ENSP00000262319:p.Ala511Val	63.0	0.0	0		68.0	36.0	0.529412	NM_016111	D3DU73|O75168|Q7LDV4|Q9BR21	Missense_Mutation	SNP	ENST00000262319.6	37	CCDS32363.1	48	0.02197802197802198	46	0.09349593495934959	2	0.0055248618784530384	0	0.0	0	0.0	C	10.54	1.379287	0.24944	0.074579	1.16E-4	ENSG00000100726	ENST00000437914;ENST00000262319	T	0.16743	2.32	5.67	0.301	0.15781	Telomere length regulation protein, conserved domain (1);	0.329093	0.36200	N	0.002734	T	0.00608	0.0020	M	0.76838	2.35	0.30705	N	0.749924	B	0.22800	0.075	B	0.24848	0.056	T	0.07309	-1.0779	10	0.29301	T	0.29	-4.6319	5.3866	0.16222	0.135:0.5696:0.0:0.2954	rs58099766	511	Q9Y4R8	TELO2_HUMAN	V	125;511	ENSP00000262319:A511V	ENSP00000262319:A511V	A	+	2	0	TELO2	1492108	0.983000	0.35010	0.139000	0.22197	0.033000	0.12548	2.614000	0.46359	0.055000	0.16094	0.655000	0.94253	GCT	C|0.972;T|0.028	0.028	strong		0.632	TELO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103602.2	NM_016111	
MYO1F	4542	hgsc.bcm.edu	37	19	8620636	8620636	+	Silent	SNP	C	C	T	rs73501540	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:8620636C>T	ENST00000338257.8	-	2	315	c.48G>A	c.(46-48)caG>caA	p.Q16Q		NM_012335.3	NP_036467.2	O00160	MYO1F_HUMAN	myosin IF	16					defense response to Gram-positive bacterium (GO:0050830)|negative regulation of cell adhesion (GO:0007162)|neutrophil degranulation (GO:0043312)|positive regulation of cell migration (GO:0030335)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of innate immune response (GO:0045088)	cortical actin cytoskeleton (GO:0030864)|filamentous actin (GO:0031941)|unconventional myosin complex (GO:0016461)	actin binding (GO:0003779)|ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(7)|lung(13)|ovary(3)|prostate(3)|skin(3)|urinary_tract(1)	42						CCACGCCGCTCTGCTTCACGT	0.637													C|||	320	0.0638978	0.2322	0.0187	5008	,	,		13239	0.0		0.0	False		,,,				2504	0.0				p.Q16Q		Atlas-SNP	.											.	MYO1F	128	.	0			c.G48A						PASS	.	C		799,3379		64,671,1354	83.0	90.0	87.0		48	1.9	1.0	19	dbSNP_130	87	10,8402		0,10,4196	no	coding-synonymous	MYO1F	NM_012335.3		64,681,5550	TT,TC,CC		0.1189,19.124,6.4257		16/1099	8620636	809,11781	2089	4206	6295	SO:0001819	synonymous_variant	4542	exon2			GCCGCTCTGCTTC	X98411	CCDS42494.1	19p13.3-p13.2	2011-09-27			ENSG00000142347	ENSG00000142347		"""Myosins / Myosin superfamily : Class I"""	7600	protein-coding gene	gene with protein product		601480				9119401, 8884266	Standard	NM_012335		Approved		uc002mkg.3	O00160	OTTHUMG00000156005	ENST00000338257.8:c.48G>A	19.37:g.8620636C>T		106.0	0.0	0		122.0	122.0	1	NM_012335	Q8WWN7	Silent	SNP	ENST00000338257.8	37	CCDS42494.1																																																																																			C|0.966;T|0.034	0.034	strong		0.637	MYO1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342716.2		
LRFN1	57622	hgsc.bcm.edu	37	19	39805188	39805188	+	Silent	SNP	C	C	T	rs115860908	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39805188C>T	ENST00000248668.4	-	1	788	c.789G>A	c.(787-789)ctG>ctA	p.L263L	CTC-246B18.8_ENST00000601911.1_RNA	NM_020862.1	NP_065913.1	Q9P244	LRFN1_HUMAN	leucine rich repeat and fibronectin type III domain containing 1	263	LRRCT.					cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				central_nervous_system(2)|cervix(1)|kidney(1)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	18	all_cancers(60;1.85e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;1.96e-27)|all cancers(26;2.05e-24)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)			TCAGCCGCCGCAGCCAGAGCA	0.682													C|||	131	0.0261581	0.0908	0.0144	5008	,	,		14203	0.0		0.001	False		,,,				2504	0.0				p.L263L		Atlas-SNP	.											.	LRFN1	59	.	0			c.G789A						PASS	.	C		280,4082		10,260,1911	14.0	19.0	17.0		789	0.8	1.0	19	dbSNP_132	17	7,8559		0,7,4276	no	coding-synonymous	LRFN1	NM_020862.1		10,267,6187	TT,TC,CC		0.0817,6.4191,2.22		263/772	39805188	287,12641	2181	4283	6464	SO:0001819	synonymous_variant	57622	exon1			CCGCCGCAGCCAG	BC014678	CCDS46071.1	19q13.2	2013-02-11				ENSG00000128011		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	29290	protein-coding gene	gene with protein product		612807				10819331, 16828986	Standard	NM_020862		Approved	KIAA1484, SALM2	uc002okw.2	Q9P244		ENST00000248668.4:c.789G>A	19.37:g.39805188C>T		44.0	0.0	0		51.0	34.0	0.666667	NM_020862	Q8TBS9	Silent	SNP	ENST00000248668.4	37	CCDS46071.1																																																																																			C|0.971;T|0.029	0.029	strong		0.682	LRFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463835.1	NM_020862	
TAS1R2	80834	hgsc.bcm.edu	37	1	19166894	19166894	+	Silent	SNP	G	G	A	rs11805253	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19166894G>A	ENST00000375371.3	-	6	1740	c.1719C>T	c.(1717-1719)gcC>gcT	p.A573A		NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	573					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cytokinesis (GO:0032467)|sensory perception of sweet taste (GO:0050916)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(10)|lung(14)|ovary(1)|pancreas(3)|prostate(1)|skin(3)|stomach(1)	45		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00466)|BRCA - Breast invasive adenocarcinoma(304;3.56e-05)|Kidney(64;0.000177)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)	Aspartame(DB00168)	AGCCCAGGGCGGCCAGCAGGG	0.612													G|||	262	0.0523163	0.1747	0.0303	5008	,	,		18191	0.001		0.003	False		,,,				2504	0.0061				p.A573A		Atlas-SNP	.											.	TAS1R2	134	.	0			c.C1719T						PASS	.	G		529,3877	237.7+/-249.4	32,465,1706	49.0	51.0	50.0		1719	-7.5	0.0	1	dbSNP_120	50	61,8539	36.9+/-92.0	1,59,4240	no	coding-synonymous	TAS1R2	NM_152232.2		33,524,5946	AA,AG,GG		0.7093,12.0064,4.5364		573/840	19166894	590,12416	2203	4300	6503	SO:0001819	synonymous_variant	80834	exon6			CAGGGCGGCCAGC		CCDS187.1	1p36.13	2012-08-22	2003-03-07		ENSG00000179002	ENSG00000179002		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	14905	protein-coding gene	gene with protein product		606226	"""G protein-coupled receptor 71"""	GPR71			Standard	NM_152232		Approved	T1R2, TR2	uc001bba.1	Q8TE23	OTTHUMG00000002442	ENST00000375371.3:c.1719C>T	1.37:g.19166894G>A		140.0	0.0	0		125.0	63.0	0.504	NM_152232	Q5TZ19	Silent	SNP	ENST00000375371.3	37	CCDS187.1																																																																																			G|0.959;A|0.041	0.041	strong		0.612	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1		
ZNF587	84914	hgsc.bcm.edu	37	19	58370744	58370744	+	Missense_Mutation	SNP	G	G	A	rs201869821	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:58370744G>A	ENST00000339656.5	+	3	1146	c.964G>A	c.(964-966)Ggg>Agg	p.G322R	ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000597652.1_5'Flank|ZNF814_ENST00000597832.1_Intron|ZNF587_ENST00000423137.1_Missense_Mutation_p.G321R|ZNF587_ENST00000419854.1_Missense_Mutation_p.G279R	NM_001204817.1|NM_032828.3	NP_001191746.1|NP_116217.1	Q96SQ5	ZN587_HUMAN	zinc finger protein 587	322					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	15		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0264)		CACTGGAGAAGGGCCTTATGA	0.473													.|||	671	0.133986	0.4274	0.0504	5008	,	,		18971	0.0526		0.0149	False		,,,				2504	0.0031				p.G322R	Pancreas(59;641 1233 1885 20055 50741)	Atlas-SNP	.											.	ZNF587	53	.	0			c.G964A						PASS	.	G	ARG/GLY,ARG/GLY	780,3588		221,338,1625	105.0	146.0	133.0		961,964	0.6	0.2	19	dbSNP_132	133	4,8596		0,4,4296	no	missense,missense	ZNF587	NM_001204817.1,NM_032828.3	125,125	221,342,5921	AA,AG,GG		0.0465,17.8571,6.0457	benign,benign	321/575,322/576	58370744	784,12184	2184	4300	6484	SO:0001583	missense	84914	exon3			GGAGAAGGGCCTT	AF294842	CCDS12964.1, CCDS56110.1	19q13.43	2013-01-08				ENSG00000198466		"""Zinc fingers, C2H2-type"", ""-"""	30955	protein-coding gene	gene with protein product						10520746	Standard	NM_032828		Approved	ZF6, FLJ14710, UBF-fl, FLJ20813	uc002qql.3	Q96SQ5	OTTHUMG00000154901	ENST00000339656.5:c.964G>A	19.37:g.58370744G>A	ENSP00000345479:p.Gly322Arg	232.0	0.0	0		201.0	63.0	0.313433	NM_032828	A0AV72|G3V0H5|Q6ZMK8	Missense_Mutation	SNP	ENST00000339656.5	37	CCDS12964.1	.	.	.	.	.	.	.	.	.	.	.	0.013	-1.627794	0.00813	0.178571	4.65E-4	ENSG00000198466	ENST00000376209;ENST00000423137;ENST00000339656;ENST00000540851;ENST00000419854	T;T;T	0.15603	2.41;2.41;2.41	1.76	0.637	0.17735	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00012	0.0000	N	0.00069	-2.28	0.27094	N	0.962789	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.42103	-0.9471	8	0.10902	T	0.67	.	5.5186	0.16919	0.8297:0.0:0.1703:0.0	.	321;322	G3V0H5;Q96SQ5	.;ZN587_HUMAN	R	279;321;322;322;279	ENSP00000393865:G321R;ENSP00000345479:G322R;ENSP00000406999:G279R	ENSP00000345479:G322R	G	+	1	0	ZNF587	63062556	0.000000	0.05858	0.162000	0.22713	0.192000	0.23643	1.091000	0.30915	-0.047000	0.13423	0.195000	0.17529	GGG	G|0.999;A|0.001	0.001	weak		0.473	ZNF587-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337594.2	NM_032828	
BEST1	7439	hgsc.bcm.edu	37	11	61730414	61730414	+	Intron	SNP	C	C	A	rs115379107	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:61730414C>A	ENST00000378043.4	+	10	2382				FTH1_ENST00000529631.1_Intron|BEST1_ENST00000301774.9_Silent_p.T224T|FTH1_ENST00000529191.1_Intron|BEST1_ENST00000449131.2_Silent_p.T536T|BEST1_ENST00000378042.3_Intron|BEST1_ENST00000534553.1_3'UTR	NM_004183.3	NP_004174.1	O76090	BEST1_HUMAN	bestrophin 1						chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|detection of light stimulus involved in visual perception (GO:0050908)|ion transmembrane transport (GO:0034220)|regulation of calcium ion transport (GO:0051924)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|visual perception (GO:0007601)	basolateral plasma membrane (GO:0016323)|chloride channel complex (GO:0034707)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	chloride channel activity (GO:0005254)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(9)|prostate(1)|skin(2)|urinary_tract(2)	25						TGTGCCCCACCCCAGCTTCCC	0.557													C|||	141	0.028155	0.1014	0.0101	5008	,	,		20189	0.0		0.0	False		,,,				2504	0.0				p.T536T		Atlas-SNP	.											.	BEST1	85	.	0			c.C1608A						PASS	.	C	,	329,4041		12,305,1868	69.0	76.0	74.0		1608,	-0.5	0.0	11	dbSNP_132	74	0,8586		0,0,4293	no	coding-synonymous,intron	BEST1	NM_001139443.1,NM_004183.3	,	12,305,6161	AA,AC,CC		0.0,7.5286,2.5394	,	536/605,	61730414	329,12627	2185	4293	6478	SO:0001627	intron_variant	7439	exon9			CCCCACCCCAGCT	AF057170	CCDS31580.1, CCDS44623.1	11q12	2013-02-14	2006-10-18	2006-10-18	ENSG00000167995	ENSG00000167995		"""Ion channels / Chloride channels : Calcium activated : Bestrophins"""	12703	protein-coding gene	gene with protein product	"""Best disease"""	607854	"""vitelliform macular dystrophy 2"""	VMD2		1302019, 17003041	Standard	NM_004183		Approved	BMD, BEST, RP50	uc001nsr.2	O76090	OTTHUMG00000167469	ENST00000378043.4:c.1739+49C>A	11.37:g.61730414C>A		201.0	0.0	0		163.0	84.0	0.515337	NM_001139443	A8K0W6|B7Z3J8|B7Z736|O75904|Q53YQ9|Q8IUR9|Q8IZ80	Silent	SNP	ENST00000378043.4	37	CCDS31580.1																																																																																			C|0.974;A|0.026	0.026	strong		0.557	BEST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394715.1	NM_004183	
ADCY2	108	hgsc.bcm.edu	37	5	7706989	7706989	+	Silent	SNP	C	C	T	rs75986905	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:7706989C>T	ENST00000338316.4	+	8	1331	c.1242C>T	c.(1240-1242)aaC>aaT	p.N414N	RP11-711G10.1_ENST00000514105.2_RNA|ADCY2_ENST00000537121.1_Silent_p.N234N	NM_020546.2	NP_065433.2	Q08462	ADCY2_HUMAN	adenylate cyclase 2 (brain)	414					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			NS(3)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|lung(56)|ovary(8)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	119						CCTTGGCCAACCACATGGAAG	0.502													C|||	68	0.0135783	0.0484	0.0058	5008	,	,		20791	0.0		0.0	False		,,,				2504	0.0				p.N414N		Atlas-SNP	.											.	ADCY2	337	.	0			c.C1242T						PASS	.	C		199,4207	124.5+/-161.8	4,191,2008	176.0	155.0	162.0		1242	-3.5	1.0	5	dbSNP_132	162	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ADCY2	NM_020546.2		4,193,6306	TT,TC,CC		0.0233,4.5166,1.5454		414/1092	7706989	201,12805	2203	4300	6503	SO:0001819	synonymous_variant	108	exon8			GGCCAACCACATG	AB028983	CCDS3872.2	5p15.3	2013-02-04			ENSG00000078295	ENSG00000078295	4.6.1.1	"""Adenylate cyclases"""	233	protein-coding gene	gene with protein product		103071				1427768	Standard	NM_020546		Approved	HBAC2, KIAA1060, AC2	uc003jdz.1	Q08462	OTTHUMG00000090476	ENST00000338316.4:c.1242C>T	5.37:g.7706989C>T		183.0	0.0	0		248.0	123.0	0.495968	NM_020546	B7Z2C1|Q2NKL8|Q9UDB2|Q9UPU2	Silent	SNP	ENST00000338316.4	37	CCDS3872.2																																																																																			C|0.985;T|0.015	0.015	strong		0.502	ADCY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206930.2	NM_020546	
TRMT11	60487	hgsc.bcm.edu	37	6	126319453	126319453	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:126319453C>T	ENST00000334379.5	+	5	500	c.379C>T	c.(379-381)Cga>Tga	p.R127*	TRMT11_ENST00000368332.3_Nonsense_Mutation_p.R127*|TRMT11_ENST00000450358.1_Nonsense_Mutation_p.R127*	NM_001031712.2	NP_001026882.2	Q7Z4G4	TRM11_HUMAN	tRNA methyltransferase 11 homolog (S. cerevisiae)	127					tRNA processing (GO:0008033)		methyltransferase activity (GO:0008168)|tRNA binding (GO:0000049)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				GBM - Glioblastoma multiforme(226;0.0356)		GAAAATCAAGCGAATAGATGT	0.303																																					p.R127X		Atlas-SNP	.											TRMT11,NS,carcinoma,-1,2	TRMT11	43	2	0			c.C379T						PASS	.						38.0	37.0	37.0					6																	126319453		2166	4290	6456	SO:0001587	stop_gained	60487	exon5			ATCAAGCGAATAG	AF182423	CCDS35496.1	6q11.1-q22.33	2009-06-15	2006-11-28	2006-11-28	ENSG00000066651	ENSG00000066651			21080	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 75"""	C6orf75			Standard	XM_006715546		Approved	MDS024, dJ187J11.2, TRM11, TRMT11-1	uc003qam.3	Q7Z4G4	OTTHUMG00000015515	ENST00000334379.5:c.379C>T	6.37:g.126319453C>T	ENSP00000333934:p.Arg127*	35.0	0.0	0		48.0	12.0	0.25	NM_001031712	E1P570|Q5JY11|Q6PGQ5|Q9HC13	Nonsense_Mutation	SNP	ENST00000334379.5	37	CCDS35496.1	.	.	.	.	.	.	.	.	.	.	C	36	5.666307	0.96745	.	.	ENSG00000066651	ENST00000334379;ENST00000450358;ENST00000368332;ENST00000444121;ENST00000446681	.	.	.	5.95	4.04	0.47022	.	0.174050	0.50627	D	0.000111	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07990	T	0.79	-10.3198	12.802	0.57591	0.508:0.492:0.0:0.0	.	.	.	.	X	127;127;127;64;64	.	ENSP00000333934:R127X	R	+	1	2	TRMT11	126361146	1.000000	0.71417	0.963000	0.40424	0.939000	0.58152	5.384000	0.66225	1.483000	0.48342	0.655000	0.94253	CGA	.	.	none		0.303	TRMT11-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_021820	
ZNF208	7757	hgsc.bcm.edu	37	19	22156470	22156470	+	Missense_Mutation	SNP	C	C	G	rs7255075	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:22156470C>G	ENST00000397126.4	-	4	1514	c.1366G>C	c.(1366-1368)Gaa>Caa	p.E456Q	ZNF208_ENST00000599916.1_Intron|ZNF208_ENST00000601773.1_Intron	NM_007153.3	NP_009084.2	O43345	ZN208_HUMAN	zinc finger protein 208	456			E -> Q (in dbSNP:rs7255075).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(18)|liver(1)|lung(71)|ovary(6)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	113		all_lung(12;0.0961)|Lung NSC(12;0.103)				CCACATTCTTCACATTTGTAG	0.378													c|||	152	0.0303514	0.1089	0.0101	5008	,	,		21690	0.0		0.001	False		,,,				2504	0.0				p.E456Q		Atlas-SNP	.											ZNF208_ENST00000428290,NS,carcinoma,+2,3	ZNF208	817	3	0			c.G1366C						PASS	.	C	GLN/GLU	499,3789		22,455,1667	73.0	79.0	77.0		1366	0.6	0.0	19	dbSNP_116	77	3,8513		0,3,4255	no	missense	ZNF208	NM_007153.3	29	22,458,5922	GG,GC,CC		0.0352,11.6371,3.9206	possibly-damaging	456/1281	22156470	502,12302	2144	4258	6402	SO:0001583	missense	7757	exon4			ATTCTTCACATTT	BC038199	CCDS54240.1	19p12	2013-01-08				ENSG00000160321		"""Zinc fingers, C2H2-type"", ""-"""	12999	protein-coding gene	gene with protein product	"""zinc finger protein 95"""	603977				9724325	Standard	NM_007153		Approved	PMIDP, ZNF95	uc021urr.1	O43345		ENST00000397126.4:c.1366G>C	19.37:g.22156470C>G	ENSP00000380315:p.Glu456Gln	64.0	0.0	0		80.0	36.0	0.45	NM_007153		Missense_Mutation	SNP	ENST00000397126.4	37	CCDS54240.1	63	0.028846153846153848	59	0.11991869918699187	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	C	12.09	1.832255	0.32421	0.116371	3.52E-4	ENSG00000160321	ENST00000397126;ENST00000428290	T	0.18960	2.18	2.83	0.577	0.17385	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00328	0.0010	.	.	.	0.80722	P	0.0	P	0.44816	0.844	P	0.55667	0.781	T	0.13953	-1.0490	7	0.18710	T	0.47	.	3.6064	0.08043	0.0:0.2616:0.1947:0.5437	rs7255075;rs52824395;rs58613552;rs7255075	456	O43345	ZN208_HUMAN	Q	456	ENSP00000380315:E456Q	ENSP00000380315:E456Q	E	-	1	0	ZNF208	21948310	0.000000	0.05858	0.000000	0.03702	0.358000	0.29455	-4.155000	0.00284	-0.314000	0.08716	0.306000	0.20318	GAA	C|0.961;G|0.039	0.039	strong		0.378	ZNF208-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464302.1	NM_007153	
LHB	3972	hgsc.bcm.edu	37	19	49519518	49519518	+	Missense_Mutation	SNP	G	G	T	rs116437960	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:49519518G>T	ENST00000221421.2	-	3	232	c.233C>A	c.(232-234)aCc>aAc	p.T78N	CTB-60B18.10_ENST00000600007.1_lincRNA	NM_000894.2	NP_000885.1	P01229	LSHB_HUMAN	luteinizing hormone beta polypeptide	78					cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|male gonad development (GO:0008584)|peptide hormone processing (GO:0016486)|progesterone biosynthetic process (GO:0006701)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	receptor binding (GO:0005102)			cervix(1)|endometrium(1)|large_intestine(1)|lung(4)|prostate(1)	8		all_epithelial(76;9.62e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		all cancers(93;0.000371)|OV - Ovarian serous cystadenocarcinoma(262;0.000503)|GBM - Glioblastoma multiforme(486;0.00518)|Epithelial(262;0.0427)		ATCACGGTAGGTGCACACCAC	0.677													G|||	71	0.0141773	0.0507	0.0058	5008	,	,		17306	0.0		0.0	False		,,,				2504	0.0				p.T78N		Atlas-SNP	.											.	LHB	20	.	0			c.C233A						PASS	.	G	ASN/THR	181,4223	113.3+/-151.4	8,165,2029	89.0	80.0	83.0		233	1.4	1.0	19	dbSNP_132	83	3,8595	3.0+/-9.4	0,3,4296	no	missense	LHB	NM_000894.2	65	8,168,6325	TT,TG,GG		0.0349,4.1099,1.4152	benign	78/142	49519518	184,12818	2202	4299	6501	SO:0001583	missense	3972	exon3			CGGTAGGTGCACA		CCDS12748.1	19q13.3	2013-02-26				ENSG00000104826		"""Endogenous ligands"""	6584	protein-coding gene	gene with protein product	"""lutropin, beta chain"", ""interstitial cell stimulating hormone, beta chain"", ""luteinizing hormone beta subunit"""	152780				1191677	Standard	NM_000894		Approved	LSH-B, CGB4, hLHB	uc002plt.3	P01229		ENST00000221421.2:c.233C>A	19.37:g.49519518G>T	ENSP00000221421:p.Thr78Asn	112.0	0.0	0		119.0	48.0	0.403361	NM_000894	Q9UDI0	Missense_Mutation	SNP	ENST00000221421.2	37	CCDS12748.1	23	0.010531135531135532	20	0.04065040650406504	3	0.008287292817679558	0	0.0	0	0.0	G	3.147	-0.175109	0.06421	0.041099	3.49E-4	ENSG00000104826	ENST00000221421;ENST00000391870	D	0.91792	-2.91	4.71	1.35	0.21983	Cystine knot (1);	0.000000	0.85682	D	0.000000	T	0.61185	0.2327	N	0.21448	0.665	0.45390	D	0.998374	B	0.10296	0.003	B	0.12156	0.007	T	0.66011	-0.6029	10	0.32370	T	0.25	-7.5582	11.6053	0.51029	0.0:0.0:0.6162:0.3838	.	78	P01229	LSHB_HUMAN	N	78;94	ENSP00000221421:T78N	ENSP00000221421:T78N	T	-	2	0	LHB	54211330	1.000000	0.71417	0.999000	0.59377	0.009000	0.06853	2.435000	0.44811	0.173000	0.19788	-3.593000	0.00028	ACC	G|0.988;T|0.012	0.012	strong		0.677	LHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466246.1	NM_000894	
OR10Q1	219960	hgsc.bcm.edu	37	11	57996289	57996289	+	Missense_Mutation	SNP	G	G	A	rs112800197	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:57996289G>A	ENST00000316770.2	-	1	101	c.59C>T	c.(58-60)gCg>gTg	p.A20V		NM_001004471.2	NP_001004471.1	Q8NGQ4	O10Q1_HUMAN	olfactory receptor, family 10, subfamily Q, member 1	20						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)	35		Breast(21;0.0589)				TGTGGTGAACGCACGGAACAC	0.507													g|||	51	0.0101837	0.0378	0.0014	5008	,	,		17105	0.0		0.0	False		,,,				2504	0.0				p.A20V		Atlas-SNP	.											.	OR10Q1	79	.	0			c.C59T						PASS	.	G	VAL/ALA	114,4248		1,112,2068	126.0	133.0	130.0		59	-1.3	0.0	11	dbSNP_132	130	0,8558		0,0,4279	yes	missense	OR10Q1	NM_001004471.2	64	1,112,6347	AA,AG,GG		0.0,2.6135,0.8824	benign	20/320	57996289	114,12806	2181	4279	6460	SO:0001583	missense	219960	exon1			GTGAACGCACGGA	AB065735	CCDS31547.1	11q12.1	2012-08-09			ENSG00000180475	ENSG00000180475		"""GPCR / Class A : Olfactory receptors"""	15134	protein-coding gene	gene with protein product							Standard	NM_001004471		Approved		uc010rkd.2	Q8NGQ4	OTTHUMG00000167542	ENST00000316770.2:c.59C>T	11.37:g.57996289G>A	ENSP00000314324:p.Ala20Val	209.0	0.0	0		212.0	103.0	0.485849	NM_001004471	Q6IFG4	Missense_Mutation	SNP	ENST00000316770.2	37	CCDS31547.1	20	0.009157509157509158	19	0.03861788617886179	1	0.0027624309392265192	0	0.0	0	0.0	G	2.409	-0.335766	0.05278	0.026135	0.0	ENSG00000180475	ENST00000316770	T	0.00330	8.08	4.98	-1.34	0.09143	.	0.376700	0.19161	N	0.121185	T	0.00039	0.0001	N	0.10760	0.04	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33574	-0.9863	10	0.51188	T	0.08	.	7.7104	0.28673	0.3775:0.1422:0.4802:0.0	.	20	Q8NGQ4	O10Q1_HUMAN	V	20	ENSP00000314324:A20V	ENSP00000314324:A20V	A	-	2	0	OR10Q1	57752865	0.000000	0.05858	0.000000	0.03702	0.206000	0.24218	-0.355000	0.07671	-0.439000	0.07222	-0.295000	0.09555	GCG	G|0.991;A|0.009	0.009	strong		0.507	OR10Q1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394706.1	NM_001004471	
KRTAP9-1	728318	hgsc.bcm.edu	37	17	39346197	39346197	+	Missense_Mutation	SNP	G	G	A	rs139370444	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39346197G>A	ENST00000398470.1	+	1	59	c.59G>A	c.(58-60)aGg>aAg	p.R20K	KRTAP9-1_ENST00000377723.3_Intron|KRTAP9-1_ENST00000318329.5_5'Flank	NM_001190460.1	NP_001177389.1	A8MXZ3	KRA91_HUMAN	keratin associated protein 9-1	20	30 X 5 AA repeats of C-C-[CGSVRQH]- [SQTNP]-[PTSI].					keratin filament (GO:0045095)				breast(1)|lung(3)	4						ACCTGCTGCAGGACAACCTGC	0.622													.|||	51	0.0101837	0.0371	0.0014	5008	,	,		18874	0.0		0.001	False		,,,				2504	0.0				p.R20K		Atlas-SNP	.											.	KRTAP9-1	34	.	0			c.G59A						PASS	.																																			SO:0001583	missense	728318	exon1			GCTGCAGGACAAC	AC006070	CCDS56029.1	17q21.2	2010-06-03			ENSG00000240542	ENSG00000240542		"""Keratin associated proteins"""	18912	protein-coding gene	gene with protein product			"""keratin associated protein 9-like 3"""	KRTAP9L3			Standard	NM_001190460		Approved	KAP9.1	uc021txf.1	A8MXZ3	OTTHUMG00000133636	ENST00000398470.1:c.59G>A	17.37:g.39346197G>A	ENSP00000381488:p.Arg20Lys	90.0	0.0	0		72.0	35.0	0.486111	NM_001190460		Missense_Mutation	SNP	ENST00000398470.1	37	CCDS56029.1	22	0.010073260073260074	21	0.042682926829268296	1	0.0027624309392265192	0	0.0	0	0.0	G	2.812	-0.246655	0.05867	.	.	ENSG00000240542	ENST00000398470	T	0.00616	6.2	3.53	0.028	0.14157	.	.	.	.	.	T	0.00241	0.0007	L	0.56769	1.78	0.09310	N	1	.	.	.	.	.	.	T	0.40776	-0.9545	7	0.06099	T	0.92	.	6.7368	0.23413	0.4053:0.0:0.5947:0.0	.	.	.	.	K	20	ENSP00000381488:R20K	ENSP00000381488:R20K	R	+	2	0	KRTAP9-1	36599723	0.000000	0.05858	0.001000	0.08648	0.089000	0.18198	0.179000	0.16840	0.163000	0.19507	0.467000	0.42956	AGG	G|0.992;A|0.008	0.008	strong		0.622	KRTAP9-1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257781.1		
PRKACA	5566	hgsc.bcm.edu	37	19	14204527	14204527	+	Silent	SNP	G	G	C	rs3729858	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:14204527G>C	ENST00000308677.4	-	9	1039	c.843C>G	c.(841-843)cgC>cgG	p.R281R	PRKACA_ENST00000590853.1_Intron|PRKACA_ENST00000589994.1_Silent_p.R273R|PRKACA_ENST00000350356.3_5'UTR|SAMD1_ENST00000541938.1_5'Flank	NM_002730.3	NP_002721.1	P17612	KAPCA_HUMAN	protein kinase, cAMP-dependent, catalytic, alpha	281	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|carbohydrate metabolic process (GO:0005975)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to glucagon stimulus (GO:0071377)|cellular response to glucose stimulus (GO:0071333)|cellular response to parathyroid hormone stimulus (GO:0071374)|cytosolic calcium ion homeostasis (GO:0051480)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mesoderm formation (GO:0001707)|mitotic cell cycle (GO:0000278)|negative regulation of smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:1901621)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of protein export from nucleus (GO:0046827)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of insulin secretion (GO:0050796)|regulation of osteoblast differentiation (GO:0045667)|regulation of proteasomal protein catabolic process (GO:0061136)|regulation of protein binding (GO:0043393)|regulation of protein processing (GO:0070613)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of synaptic transmission (GO:0050804)|regulation of tight junction assembly (GO:2000810)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sperm capacitation (GO:0048240)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	AMP-activated protein kinase complex (GO:0031588)|calcium channel complex (GO:0034704)|cAMP-dependent protein kinase complex (GO:0005952)|centrosome (GO:0005813)|ciliary base (GO:0097546)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|motile cilium (GO:0031514)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sperm midpiece (GO:0097225)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)|protein kinase A regulatory subunit binding (GO:0034237)|protein kinase binding (GO:0019901)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	16						GGTTCCCAAAGCGCTTGGTGA	0.547													G|||	29	0.00579073	0.0219	0.0	5008	,	,		20834	0.0		0.0	False		,,,				2504	0.0				p.R281R		Atlas-SNP	.											.	PRKACA	65	.	0			c.C843G						PASS	.	G	,	80,4326	69.2+/-107.0	1,78,2124	142.0	126.0	131.0		843,819	5.2	1.0	19	dbSNP_107	131	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PRKACA	NM_002730.3,NM_207518.1	,	1,78,6424	CC,CG,GG		0.0,1.8157,0.6151	,	281/352,273/344	14204527	80,12926	2203	4300	6503	SO:0001819	synonymous_variant	5566	exon9			CCCAAAGCGCTTG		CCDS12304.1, CCDS12305.1	19p13.1	2012-10-02				ENSG00000072062	2.7.11.1		9380	protein-coding gene	gene with protein product		601639				8884279	Standard	NM_002730		Approved	PKACa	uc002myc.3	P17612		ENST00000308677.4:c.843C>G	19.37:g.14204527G>C		179.0	0.0	0		165.0	85.0	0.515152	NM_002730	Q32P54|Q9H2Y0|Q9NRB4|Q9NRH9	Silent	SNP	ENST00000308677.4	37	CCDS12304.1																																																																																			G|0.995;C|0.005	0.005	strong		0.547	PRKACA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459004.1	NM_002730	
IFITM3	10410	hgsc.bcm.edu	37	11	320723	320723	+	Missense_Mutation	SNP	C	C	T	rs199582787	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:320723C>T	ENST00000399808.4	-	1	327	c.91G>A	c.(91-93)Gtg>Atg	p.V31M	RP11-326C3.11_ENST00000602429.1_RNA|RP11-326C3.14_ENST00000602809.1_lincRNA|RP11-326C3.10_ENST00000534271.1_RNA|RP11-326C3.11_ENST00000508004.2_RNA|RP11-326C3.11_ENST00000602756.1_RNA|IFITM3_ENST00000602735.1_Missense_Mutation_p.V10M|IFITM3_ENST00000526811.1_Missense_Mutation_p.V10M	NM_021034.2	NP_066362.2	Q01628	IFM3_HUMAN	interferon induced transmembrane protein 3	31					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|immune response (GO:0006955)|negative regulation of viral entry into host cell (GO:0046597)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral transcription (GO:0032897)|response to interferon-alpha (GO:0035455)|response to interferon-beta (GO:0035456)|response to interferon-gamma (GO:0034341)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|plasma membrane (GO:0005886)				central_nervous_system(7)|endometrium(7)|kidney(2)|large_intestine(1)|lung(1)	18		all_cancers(49;2e-09)|all_epithelial(84;3.36e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;8.85e-28)|Epithelial(43;5.52e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0327)|LUSC - Lung squamous cell carcinoma(625;0.122)		GCCCCCAGCACAGCCACCTCG	0.612																																					p.V31M		Atlas-SNP	.											IFITM3,brain,glioma,0,1	IFITM3	132	1	0			c.G91A						scavenged	.						87.0	98.0	95.0					11																	320723		1967	4140	6107	SO:0001583	missense	10410	exon1			CCAGCACAGCCAC	X57352	CCDS41585.1	11p15.5	2011-05-24	2011-05-24		ENSG00000142089	ENSG00000142089			5414	protein-coding gene	gene with protein product		605579	"""interferon induced transmembrane protein 3 (1-8U)"""			1906403, 16326387	Standard	NM_021034		Approved	1-8U	uc001lpa.2	Q01628		ENST00000399808.4:c.91G>A	11.37:g.320723C>T	ENSP00000382707:p.Val31Met	98.0	0.0	0		97.0	4.0	0.0412371	NM_021034	Q53Y76|Q96HK8|Q96J15	Missense_Mutation	SNP	ENST00000399808.4	37	CCDS41585.1	.	.	.	.	.	.	.	.	.	.	C	11.06	1.526447	0.27299	.	.	ENSG00000142089	ENST00000399808;ENST00000270031;ENST00000526811	T;T	0.79454	-1.03;-1.27	4.61	-4.91	0.03085	.	11.488500	0.02440	N	0.084490	T	0.64516	0.2605	L	0.39147	1.195	0.09310	N	1	B	0.16802	0.019	B	0.15484	0.013	T	0.46400	-0.9194	10	0.13108	T	0.6	0.9022	6.4601	0.21952	0.1231:0.361:0.0:0.5159	.	31	Q01628	IFM3_HUMAN	M	31;15;10	ENSP00000382707:V31M;ENSP00000432108:V10M	ENSP00000372047:V15M	V	-	1	0	IFITM3	310723	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-1.638000	0.02013	-0.562000	0.06086	-1.790000	0.00627	GTG	.	.	weak		0.612	IFITM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384765.1	NM_021034	
GTDC1	79712	hgsc.bcm.edu	37	2	144966208	144966208	+	Silent	SNP	T	T	C	rs16823579	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:144966208T>C	ENST00000392869.2	-	3	293	c.141A>G	c.(139-141)ttA>ttG	p.L47L	GTDC1_ENST00000467352.1_5'Flank|GTDC1_ENST00000409298.1_Silent_p.L47L|GTDC1_ENST00000392867.3_Silent_p.L47L|GTDC1_ENST00000344850.4_Silent_p.L47L|GTDC1_ENST00000409214.1_Silent_p.L47L|GTDC1_ENST00000241391.5_Silent_p.L47L|GTDC1_ENST00000542155.1_Silent_p.L47L|GTDC1_ENST00000463875.2_Intron	NM_001284234.1	NP_001271163.1	Q4AE62	GTDC1_HUMAN	glycosyltransferase-like domain containing 1	47					biosynthetic process (GO:0009058)		transferase activity, transferring glycosyl groups (GO:0016757)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|liver(1)|lung(17)|ovary(1)	25				BRCA - Breast invasive adenocarcinoma(221;0.0914)		GAGAGAAATATAAAGCAGATG	0.413													T|||	190	0.0379393	0.1384	0.0101	5008	,	,		16667	0.0		0.0	False		,,,				2504	0.0				p.L47L		Atlas-SNP	.											.	GTDC1	61	.	0			c.A141G						PASS	.	T	,,	568,3838	252.1+/-258.6	34,500,1669	81.0	82.0	82.0		141,141,141	-12.2	0.0	2	dbSNP_123	82	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	GTDC1	NM_001006636.3,NM_001164629.2,NM_024659.4	,,	34,502,5967	CC,CT,TT		0.0233,12.8915,4.3826	,,	47/459,47/459,47/374	144966208	570,12436	2203	4300	6503	SO:0001819	synonymous_variant	79712	exon4			GAAATATAAAGCA	AY281366	CCDS2185.1, CCDS33300.1, CCDS63029.1, CCDS74582.1, CCDS74583.1	2q22.3	2013-02-22			ENSG00000121964	ENSG00000121964		"""Glycosyltransferase group 1 domain containing"""	20887	protein-coding gene	gene with protein product	"""mannosyltransferase-like"""	610165				15068588, 21821951	Standard	NM_024659		Approved	FLJ11753, Hmat-Xa	uc010fnn.3	Q4AE62	OTTHUMG00000131835	ENST00000392869.2:c.141A>G	2.37:g.144966208T>C		94.0	0.0	0		64.0	41.0	0.640625	NM_001006636	A8K5P2|D3DP81|Q53SM7|Q53TC5|Q6P7E7|Q6PJB6|Q6WKW6|Q9HAE5	Silent	SNP	ENST00000392869.2	37	CCDS33300.1																																																																																			T|0.957;C|0.043	0.043	strong		0.413	GTDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254779.2	NM_024659	
ELK1	2002	hgsc.bcm.edu	37	X	47498400	47498400	+	Missense_Mutation	SNP	C	C	T	rs1059579	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:47498400C>T	ENST00000247161.3	-	3	647	c.548G>A	c.(547-549)aGt>aAt	p.S183N	ELK1_ENST00000592066.1_Missense_Mutation_p.S129N|ELK1_ENST00000376983.3_Missense_Mutation_p.S183N|ELK1_ENST00000343894.4_Intron	NM_005229.4	NP_005220.2	P19419	ELK1_HUMAN	ELK1, member of ETS oncogene family	183			S -> N (in dbSNP:rs1059579). {ECO:0000269|PubMed:2539641}.		cell differentiation (GO:0030154)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|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)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(2)|skin(2)	10						AGGAGCTGCACTGGGGAGCAC	0.672													T|||	537	0.142252	0.3366	0.0317	3775	,	,		12344	0.0625		0.005	False		,,,				2504	0.002				p.S183N		Atlas-SNP	.											.	ELK1	54	.	0			c.G548A						PASS	.	T	ASN/SER,ASN/SER	1349,2481		198,751,202,682,366	17.0	13.0	14.0		548,548	-0.9	0.3	X	dbSNP_86	14	28,6691		1,19,7,2407,1858	no	missense,missense	ELK1	NM_001114123.1,NM_005229.3	46,46	199,770,209,3089,2224	TT,TC,T,CC,C		0.4167,35.2219,13.0534	benign,benign	183/429,183/429	47498400	1377,9172	2199	4292	6491	SO:0001583	missense	2002	exon4			GCTGCACTGGGGA	M25269	CCDS14283.1, CCDS59165.1	Xp11.23	2010-07-20			ENSG00000126767	ENSG00000126767			3321	protein-coding gene	gene with protein product		311040				2539641	Standard	NM_001114123		Approved		uc010nhv.4	P19419	OTTHUMG00000021452	ENST00000247161.3:c.548G>A	X.37:g.47498400C>T	ENSP00000247161:p.Ser183Asn	186.0	0.0	0		180.0	59.0	0.327778	NM_001114123	B2R7H4|O75606|O95058|Q969X8|Q9UJM4	Missense_Mutation	SNP	ENST00000247161.3	37	CCDS14283.1	230	0.13863773357444242	123	0.33064516129032256	10	0.027932960893854747	26	0.046762589928057555	1	0.0013192612137203166	T	7.193	0.592017	0.13812	0.352219	0.004167	ENSG00000126767	ENST00000247161;ENST00000376983	T;T	0.21734	1.99;1.99	4.02	-0.858	0.10689	.	1.043230	0.07432	N	0.895821	T	0.00012	0.0000	N	0.02539	-0.55	0.09310	P	0.9999999769773	B	0.02656	0.0	B	0.01281	0.0	T	0.49679	-0.8914	9	0.16420	T	0.52	.	10.7665	0.46297	0.0:0.6834:0.0:0.3166	rs1059579	183	P19419	ELK1_HUMAN	N	183	ENSP00000247161:S183N;ENSP00000366182:S183N	ENSP00000247161:S183N	S	-	2	0	ELK1	47383344	0.256000	0.24012	0.318000	0.25279	0.616000	0.37450	-0.277000	0.08502	-0.454000	0.07066	-0.407000	0.06327	AGT	C|0.847;T|0.153	0.153	strong		0.672	ELK1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056436.1	NM_005229	
SEMA6B	10501	hgsc.bcm.edu	37	19	4558422	4558422	+	Silent	SNP	C	C	A	rs115168835	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4558422C>A	ENST00000586582.1	-	2	358	c.48G>T	c.(46-48)ctG>ctT	p.L16L	SEMA6B_ENST00000586965.1_Silent_p.L16L|SEMA6B_ENST00000301293.3_Silent_p.L16L	NM_032108.3	NP_115484.2	Q9H3T3	SEM6B_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	16					cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(2)|large_intestine(4)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		GTAGCAGCAGCAGAAGCAGCA	0.736											OREG0025169	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	94	0.01877	0.0696	0.0029	5008	,	,		9644	0.0		0.0	False		,,,				2504	0.0				p.L16L		Atlas-SNP	.											.	SEMA6B	51	.	0			c.G48T						PASS	.	C		155,3605		0,155,1725	3.0	5.0	4.0		48	2.6	1.0	19	dbSNP_132	4	1,7703		0,1,3851	no	coding-synonymous	SEMA6B	NM_032108.3		0,156,5576	AA,AC,CC		0.013,4.1223,1.3608		16/889	4558422	156,11308	1880	3852	5732	SO:0001819	synonymous_variant	10501	exon2			CAGCAGCAGAAGC	AB022433	CCDS12131.1	19p13.3	2008-07-22				ENSG00000167680		"""Semaphorins"""	10739	protein-coding gene	gene with protein product	"""Sema VIb"", ""semaphorin Z"", ""semaphorin VIB"""	608873		SEMAN		9361278	Standard	NM_032108		Approved	semaZ, SEMA-VIB, SEM-SEMA-Y	uc010dud.2	Q9H3T3		ENST00000586582.1:c.48G>T	19.37:g.4558422C>A		17.0	0.0	0	619	31.0	17.0	0.548387	NM_032108	A5PKU4|F6IB19|Q9NRK9	Silent	SNP	ENST00000586582.1	37	CCDS12131.1																																																																																			C|0.985;A|0.015	0.015	strong		0.736	SEMA6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458656.2	NM_032108	
FLG	2312	hgsc.bcm.edu	37	1	152281136	152281136	+	Missense_Mutation	SNP	C	C	T	rs78125326	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152281136C>T	ENST00000368799.1	-	3	6261	c.6226G>A	c.(6226-6228)Gca>Aca	p.A2076T	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2076	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGGCCACGTGCGGACTCTTTG	0.567									Ichthyosis				-|||	353	0.0704872	0.2496	0.0245	5008	,	,		29453	0.003		0.003	False		,,,				2504	0.0				p.A2076T		Atlas-SNP	.											.	FLG	900	.	0			c.G6226A						PASS	.	C	THR/ALA	898,3508		0,898,1305	315.0	259.0	278.0		6226	-4.7	0.0	1	dbSNP_131	278	11,8589		0,11,4289	no	missense	FLG	NM_002016.1	58	0,909,5594	TT,TC,CC		0.1279,20.3813,6.9891	benign	2076/4062	152281136	909,12097	2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CACGTGCGGACTC	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6226G>A	1.37:g.152281136C>T	ENSP00000357789:p.Ala2076Thr	482.0	0.0	0		915.0	460.0	0.502732	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	125	0.05723443223443223	114	0.23170731707317074	9	0.024861878453038673	1	0.0017482517482517483	1	0.0013192612137203166	c	4.927	0.172270	0.09391	0.203813	0.001279	ENSG00000143631	ENST00000368799	T	0.01705	4.68	2.33	-4.66	0.03329	.	.	.	.	.	T	0.00241	0.0007	N	0.11064	0.09	0.09310	N	1	B	0.14438	0.01	B	0.12156	0.007	T	0.44360	-0.9333	9	0.13108	T	0.6	.	1.7607	0.02992	0.1438:0.1924:0.1433:0.5205	.	2076	P20930	FILA_HUMAN	T	2076	ENSP00000357789:A2076T	ENSP00000357789:A2076T	A	-	1	0	FLG	150547760	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.201000	0.01236	-2.043000	0.00913	-0.330000	0.08379	GCA	C|0.942;T|0.058	0.058	strong		0.567	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
CTNNA2	1496	hgsc.bcm.edu	37	2	80620370	80620370	+	Missense_Mutation	SNP	T	T	C	rs61754542	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:80620370T>C	ENST00000402739.4	+	7	1096	c.1091T>C	c.(1090-1092)aTt>aCt	p.I364T	CTNNA2_ENST00000540488.1_Missense_Mutation_p.I364T|CTNNA2_ENST00000466387.1_Missense_Mutation_p.I364T|CTNNA2_ENST00000343114.3_Missense_Mutation_p.I43T|CTNNA2_ENST00000541047.1_Missense_Mutation_p.I364T|CTNNA2_ENST00000361291.4_Missense_Mutation_p.I398T|CTNNA2_ENST00000496558.1_Missense_Mutation_p.I364T	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	364					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						CCTCTCAACATTGCGATTGAT	0.294													T|||	69	0.013778	0.0499	0.0014	5008	,	,		16684	0.0		0.001	False		,,,				2504	0.001				p.I364T		Atlas-SNP	.											.	CTNNA2	462	.	0			c.T1091C						PASS	.	T	THR/ILE,THR/ILE	161,3487		4,153,1667	99.0	93.0	95.0		1091,1091	5.9	1.0	2	dbSNP_129	95	4,8156		0,4,4076	yes	missense,missense	CTNNA2	NM_001164883.1,NM_004389.3	89,89	4,157,5743	CC,CT,TT		0.049,4.4134,1.3974	benign,benign	364/861,364/906	80620370	165,11643	1824	4080	5904	SO:0001583	missense	1496	exon8			TCAACATTGCGAT		CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"""cadherin-associated protein, related"", ""cancer/testis antigen 114"""	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.1091T>C	2.37:g.80620370T>C	ENSP00000384638:p.Ile364Thr	237.0	0.0	0		227.0	93.0	0.409692	NM_001164883	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Missense_Mutation	SNP	ENST00000402739.4	37		24	0.01098901098901099	23	0.046747967479674794	0	0.0	0	0.0	1	0.0013192612137203166	T	8.517	0.867937	0.17250	0.044134	4.9E-4	ENSG00000066032	ENST00000466387;ENST00000496558;ENST00000361291;ENST00000402739;ENST00000541047;ENST00000540488;ENST00000343114;ENST00000409550	T;T;T;T;T;T;T;T	0.35789	1.29;1.29;1.29;1.29;1.29;1.29;2.59;1.3	5.88	5.88	0.94601	.	0.135082	0.52532	D	0.000073	T	0.02342	0.0072	N	0.02142	-0.665	0.37091	D	0.89945	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.001	T	0.16808	-1.0390	9	.	.	.	.	15.9407	0.79750	0.0:0.0:0.0:1.0	rs61754542	364;364;364	P26232;P26232-3;P26232-2	CTNA2_HUMAN;.;.	T	364;364;398;364;364;364;43;29	ENSP00000418191:I364T;ENSP00000419295:I364T;ENSP00000355398:I398T;ENSP00000384638:I364T;ENSP00000444675:I364T;ENSP00000441705:I364T;ENSP00000341500:I43T;ENSP00000386587:I29T	.	I	+	2	0	CTNNA2	80473881	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	2.197000	0.42696	2.243000	0.73865	0.533000	0.62120	ATT	T|0.992;C|0.008	0.008	strong		0.294	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389	
ANKRD45	339416	hgsc.bcm.edu	37	1	173596273	173596273	+	Silent	SNP	A	A	G	rs12059068	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:173596273A>G	ENST00000333279.2	-	4	582	c.522T>C	c.(520-522)taT>taC	p.Y174Y		NM_198493.2	NP_940895.1	Q5TZF3	ANR45_HUMAN	ankyrin repeat domain 45	190										NS(2)|endometrium(2)|large_intestine(4)|lung(3)|skin(1)	12						CTTTTGCAATATATTTTTTCA	0.388													A|||	965	0.192692	0.6989	0.0504	5008	,	,		19880	0.0		0.005	False		,,,				2504	0.001				p.Y174Y		Atlas-SNP	.											.	ANKRD45	36	.	0			c.T522C						PASS	.	A		2539,1867	632.6+/-395.9	756,1027,420	124.0	128.0	127.0		522	-0.2	0.9	1	dbSNP_120	127	32,8568	19.2+/-60.6	0,32,4268	no	coding-synonymous	ANKRD45	NM_198493.2		756,1059,4688	GG,GA,AA		0.3721,42.374,19.7678		174/267	173596273	2571,10435	2203	4300	6503	SO:0001819	synonymous_variant	339416	exon4			TGCAATATATTTT		CCDS1309.1	1q25.1	2013-01-10			ENSG00000183831	ENSG00000183831		"""Ankyrin repeat domain containing"""	24786	protein-coding gene	gene with protein product	"""cancer/testis antigen 117"""						Standard	NM_198493		Approved	FLJ45235, CT117	uc001gja.1	Q5TZF3	OTTHUMG00000040546	ENST00000333279.2:c.522T>C	1.37:g.173596273A>G		58.0	0.0	0		56.0	56.0	1	NM_198493	A1A4G2|Q6ZST1	Silent	SNP	ENST00000333279.2	37	CCDS1309.1																																																																																			A|0.781;G|0.219	0.219	strong		0.388	ANKRD45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097580.2	NM_198493	
TCF4	6925	hgsc.bcm.edu	37	18	52901894	52901894	+	Silent	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:52901894A>G	ENST00000356073.4	-	16	1982	c.1371T>C	c.(1369-1371)gaT>gaC	p.D457D	TCF4_ENST00000561992.1_Silent_p.D327D|TCF4_ENST00000566279.1_Silent_p.D397D|TCF4_ENST00000566286.1_Silent_p.D454D|TCF4_ENST00000568740.1_Silent_p.D432D|TCF4_ENST00000567880.1_Silent_p.D397D|TCF4_ENST00000570287.2_Silent_p.D297D|TCF4_ENST00000561831.3_Silent_p.D297D|TCF4_ENST00000398339.1_Silent_p.D559D|TCF4_ENST00000537578.1_Silent_p.D433D|TCF4_ENST00000543082.1_Silent_p.D415D|TCF4_ENST00000544241.2_Silent_p.D386D|TCF4_ENST00000540999.1_Silent_p.D433D|TCF4_ENST00000564999.1_Silent_p.D457D|TCF4_ENST00000537856.3_Silent_p.D327D|TCF4_ENST00000564403.2_Silent_p.D463D|TCF4_ENST00000565018.2_Silent_p.D457D|TCF4_ENST00000568673.1_Silent_p.D433D|TCF4_ENST00000570177.2_Silent_p.D327D|TCF4_ENST00000457482.3_Silent_p.D297D|TCF4_ENST00000354452.3_Silent_p.D457D|TCF4_ENST00000564228.1_Silent_p.D386D	NM_003199.2	NP_003190.1	P15884	ITF2_HUMAN	transcription factor 4	457					DNA-templated transcription, initiation (GO:0006352)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein-DNA complex assembly (GO:0065004)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|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)|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity (GO:0001011)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TFIIB-class binding transcription factor activity (GO:0001087)|TFIIB-class transcription factor binding (GO:0001093)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	41				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)		GGGCCACGCCATCTTCACGAT	0.597											OREG0024990	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D559D		Atlas-SNP	.											.	TCF4	178	.	0			c.T1677C						PASS	.						92.0	95.0	94.0					18																	52901894		2203	4300	6503	SO:0001819	synonymous_variant	6925	exon17			CACGCCATCTTCA	M74719	CCDS11960.1, CCDS42438.1, CCDS58623.1, CCDS58624.1, CCDS58625.1, CCDS58626.1, CCDS58627.1, CCDS58628.1, CCDS58629.1, CCDS58630.1, CCDS58631.1, CCDS59321.1	18q21.1	2013-05-21			ENSG00000196628	ENSG00000196628		"""Basic helix-loop-helix proteins"""	11634	protein-coding gene	gene with protein product		602272				9302263, 2308860	Standard	NM_001083962		Approved	SEF2-1B, ITF2, bHLHb19, E2-2	uc002lga.3	P15884	OTTHUMG00000132713	ENST00000356073.4:c.1371T>C	18.37:g.52901894A>G		70.0	0.0	0	988	85.0	46.0	0.541176	NM_001243226	B3KT62|B3KUC0|B4DT37|B4DUG3|B7Z5M6|B7Z6Y1|G0LNT9|G0LNU0|G0LNU1|G0LNU2|G0LNU4|G0LNU5|G0LNU8|G0LNU9|G0LNV0|G0LNV1|G0LNV2|H3BPQ1|Q08AP2|Q08AP3|Q15439|Q15440|Q15441	Silent	SNP	ENST00000356073.4	37	CCDS11960.1																																																																																			.	.	none		0.597	TCF4-002	KNOWN	upstream_uORF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256014.1	NM_003199	
RAD17	5884	hgsc.bcm.edu	37	5	68710032	68710032	+	Silent	SNP	G	G	A	rs145547419	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:68710032G>A	ENST00000509734.1	+	18	2637	c.1959G>A	c.(1957-1959)ctG>ctA	p.L653L	RAD17_ENST00000354312.3_Silent_p.L642L|RAD17_ENST00000358030.2_Silent_p.L477L|RAD17_ENST00000504177.1_3'UTR|RAD17_ENST00000521422.1_Silent_p.L477L|RAD17_ENST00000361732.2_Silent_p.L642L|RAD17_ENST00000345306.6_Silent_p.L642L|MARVELD2_ENST00000325631.5_5'Flank|RAD17_ENST00000282891.6_Silent_p.L556L|RAD17_ENST00000305138.4_Silent_p.L642L|RAD17_ENST00000380774.3_Silent_p.L653L|RAD17_ENST00000354868.5_Silent_p.L642L			O75943	RAD17_HUMAN	RAD17 homolog (S. pombe)	653	Interaction with MCM7.				cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of DNA replication (GO:0008156)|regulation of phosphorylation (GO:0042325)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)						Lung NSC(167;5.19e-05)|Prostate(74;0.0143)|Ovarian(174;0.0448)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;9.36e-57)|Epithelial(20;1.21e-52)|all cancers(19;3.34e-48)|Lung(70;0.0183)		CCAGTGAACTGCCTGCTAGCC	0.507								Other conserved DNA damage response genes																													p.L653L		Atlas-SNP	.											.	RAD17	49	.	0			c.G1959A						PASS	.	G	,,,,,,,	20,4386	28.1+/-56.4	0,20,2183	94.0	96.0	96.0		1926,1926,1959,1431,1668,1926,1926,1926	2.3	1.0	5	dbSNP_134	96	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RAD17	NM_002873.1,NM_133338.1,NM_133339.1,NM_133340.1,NM_133341.1,NM_133342.1,NM_133343.1,NM_133344.1	,,,,,,,	0,20,6483	AA,AG,GG		0.0,0.4539,0.1538	,,,,,,,	642/671,642/671,653/682,477/506,556/585,642/671,642/671,642/671	68710032	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	5884	exon16			TGAACTGCCTGCT	AF085736	CCDS4003.1, CCDS4004.1, CCDS4005.1, CCDS47226.1	5q13	2010-09-24	2001-11-28		ENSG00000152942	ENSG00000152942			9807	protein-coding gene	gene with protein product		603139	"""RAD1 (S. pombe) homolog"""			9869296, 9660800	Standard	NM_133343		Approved	Rad24, RAD17Sp, CCYC	uc003jwo.3	O75943	OTTHUMG00000099357	ENST00000509734.1:c.1959G>A	5.37:g.68710032G>A		113.0	0.0	0		118.0	53.0	0.449153	NM_133339	A8K8X2|D3DWA5|O75714|Q7Z3S4|Q9UNK7|Q9UNR7|Q9UNR8|Q9UPF5	Silent	SNP	ENST00000509734.1	37	CCDS4003.1																																																																																			G|0.998;A|0.002	0.002	strong		0.507	RAD17-008	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369171.1	NM_133344	
PPFIBP2	8495	hgsc.bcm.edu	37	11	7673049	7673049	+	Missense_Mutation	SNP	C	C	G	rs77975665	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:7673049C>G	ENST00000299492.4	+	23	2798	c.2410C>G	c.(2410-2412)Cca>Gca	p.P804A	PPFIBP2_ENST00000530582.1_3'UTR|PPFIBP2_ENST00000533792.1_Missense_Mutation_p.P646A|PPFIBP2_ENST00000530181.1_Missense_Mutation_p.P661A|PPFIBP2_ENST00000528883.1_Missense_Mutation_p.P692A	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	804					cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)	DNA binding (GO:0003677)|integrase activity (GO:0008907)			breast(8)|cervix(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		AGCTTACACACCACTGACCAC	0.612													C|||	445	0.0888578	0.2542	0.0418	5008	,	,		19239	0.0149		0.004	False		,,,				2504	0.0624				p.P804A		Atlas-SNP	.											.	PPFIBP2	87	.	0			c.C2410G						PASS	.	C	ALA/PRO	1038,3364	381.8+/-324.2	119,800,1282	117.0	116.0	117.0		2410	4.8	1.0	11	dbSNP_132	117	38,8554	26.3+/-74.7	0,38,4258	yes	missense	PPFIBP2	NM_003621.2	27	119,838,5540	GG,GC,CC		0.4423,23.5802,8.2807	probably-damaging	804/877	7673049	1076,11918	2201	4296	6497	SO:0001583	missense	8495	exon23			TACACACCACTGA	AF034803	CCDS31419.1, CCDS58116.1, CCDS58117.1	11p15.4	2013-01-10			ENSG00000166387	ENSG00000166387		"""Sterile alpha motif (SAM) domain containing"""	9250	protein-coding gene	gene with protein product		603142				9624153	Standard	NM_003621		Approved	Cclp1	uc001mfj.5	Q8ND30	OTTHUMG00000165617	ENST00000299492.4:c.2410C>G	11.37:g.7673049C>G	ENSP00000299492:p.Pro804Ala	53.0	0.0	0		46.0	13.0	0.282609	NM_003621	B7Z433|E9PK77|O75337|Q8WW26	Missense_Mutation	SNP	ENST00000299492.4	37	CCDS31419.1	146|146	0.06684981684981685|0.06684981684981685	118|118	0.23983739837398374|0.23983739837398374	12|12	0.03314917127071823|0.03314917127071823	13|13	0.022727272727272728|0.022727272727272728	3|3	0.00395778364116095|0.00395778364116095	C|C	9.478|9.478	1.097421|1.097421	0.20552|0.20552	0.235802|0.235802	0.004423|0.004423	ENSG00000166387|ENSG00000166387	ENST00000299492;ENST00000537211;ENST00000533792;ENST00000541115;ENST00000528883;ENST00000530181|ENST00000534552	T;T;T;T|.	0.36157|.	1.7;1.28;1.68;1.27|.	5.77|5.77	4.84|4.84	0.62591|0.62591	.|.	0.078622|.	0.53938|.	N|.	0.000047|.	T|T	0.00073|0.00073	0.0002|0.0002	M|M	0.76574|0.76574	2.34|2.34	0.09310|0.09310	P|P	0.99999648842|0.99999648842	B;B;P;B;B;B|.	0.36768|.	0.231;0.009;0.569;0.009;0.009;0.231|.	B;B;B;B;B;B|.	0.37480|.	0.128;0.016;0.251;0.01;0.016;0.08|.	T|T	0.00191|0.00191	-1.1936|-1.1936	9|5	0.15499|0.41790	T|T	0.54|0.15	-9.5207|-9.5207	15.0756|15.0756	0.72074|0.72074	0.0:0.846:0.154:0.0|0.0:0.846:0.154:0.0	.|.	692;692;727;646;661;804|.	E9PK77;B7Z433;F5GWB0;E9PP16;E9PMU1;Q8ND30|.	.;.;.;.;.;LIPB2_HUMAN|.	A|S	804;145;646;727;692;661|35	ENSP00000299492:P804A;ENSP00000436498:P646A;ENSP00000435469:P692A;ENSP00000437321:P661A|.	ENSP00000299492:P804A|ENSP00000436489:T35S	P|T	+|+	1|2	0|0	PPFIBP2|PPFIBP2	7629625|7629625	0.998000|0.998000	0.40836|0.40836	0.987000|0.987000	0.45799|0.45799	0.905000|0.905000	0.53344|0.53344	4.020000|4.020000	0.57189|0.57189	1.525000|1.525000	0.49052|0.49052	0.655000|0.655000	0.94253|0.94253	CCA|ACC	C|0.922;G|0.078	0.078	strong		0.612	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621	
CDH23	64072	hgsc.bcm.edu	37	10	73553177	73553177	+	Silent	SNP	C	C	T	rs41281332	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:73553177C>T	ENST00000224721.6	+	47	6512	c.6507C>T	c.(6505-6507)atC>atT	p.I2169I	CDH23_ENST00000398788.3_5'Flank	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2164	Cadherin 20. {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						CCATTCTGATCGATGACATCA	0.597													C|||	131	0.0261581	0.0946	0.0072	5008	,	,		18788	0.0		0.001	False		,,,				2504	0.0				p.I2164I		Atlas-SNP	.											.	CDH23	365	.	0			c.C6492T						PASS	.	C		294,3964		11,272,1846	75.0	82.0	80.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	6492	-2.9	1.0	10	dbSNP_127	80	4,8500		0,4,4248	no	coding-synonymous	CDH23	NM_022124.5		11,276,6094	TT,TC,CC		0.047,6.9047,2.3351		2164/3355	73553177	298,12464	2129	4252	6381	SO:0001819	synonymous_variant	64072	exon46			TCTGATCGATGAC	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.6507C>T	10.37:g.73553177C>T		105.0	0.0	0		120.0	63.0	0.525	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	37																																																																																				C|0.976;T|0.024	0.024	strong		0.597	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	
TRDN	10345	hgsc.bcm.edu	37	6	123759243	123759243	+	Missense_Mutation	SNP	C	C	T	rs35766971	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:123759243C>T	ENST00000398178.3	-	12	1037	c.1016G>A	c.(1015-1017)aGt>aAt	p.S339N	TRDN_ENST00000334268.4_Missense_Mutation_p.S339N|RP11-532N4.2_ENST00000427828.1_RNA|RP11-532N4.2_ENST00000587106.2_RNA|RP11-532N4.2_ENST00000418467.2_RNA|RP11-532N4.2_ENST00000434768.1_RNA|RP11-532N4.2_ENST00000587049.1_RNA|RP11-532N4.2_ENST00000589182.1_RNA	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin	339			S -> N (in dbSNP:rs35766971).		cellular calcium ion homeostasis (GO:0006874)|cytoplasmic microtubule organization (GO:0031122)|endoplasmic reticulum membrane organization (GO:0090158)|heart contraction (GO:0060047)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|myotube differentiation (GO:0014902)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|positive regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901846)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to organic cyclic compound (GO:0014070)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	41				GBM - Glioblastoma multiforme(226;0.184)		TTCCTTCTCACTTTTCTTTTT	0.353													C|||	66	0.0131789	0.0477	0.0043	5008	,	,		19093	0.0		0.0	False		,,,				2504	0.0				p.S340N		Atlas-SNP	.											TRDN,posterior_fossa,glioma,0,1	TRDN	88	1	0			c.G1019A						PASS	.	C	ASN/SER	123,3559		1,121,1719	124.0	119.0	121.0		1016	3.7	0.6	6	dbSNP_126	121	1,8137		0,1,4068	yes	missense	TRDN	NM_006073.2	46	1,122,5787	TT,TC,CC		0.0123,3.3406,1.0491	benign	339/730	123759243	124,11696	1841	4069	5910	SO:0001583	missense	10345	exon12			TTCTCACTTTTCT	U18985	CCDS59035.1, CCDS75511.1	6q22.31	2008-05-15			ENSG00000186439	ENSG00000186439			12261	protein-coding gene	gene with protein product		603283				7588753	Standard	NM_001251987		Approved		uc003pzj.2	Q13061	OTTHUMG00000015497	ENST00000398178.3:c.1016G>A	6.37:g.123759243C>T	ENSP00000381240:p.Ser339Asn	64.0	0.0	0		58.0	29.0	0.5	NM_001251987	A5D6W5|F5H2W7|Q6NSB8	Missense_Mutation	SNP	ENST00000398178.3	37	CCDS55053.1	19	0.0086996336996337	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	C	12.94	2.089922	0.36855	0.033406	1.23E-4	ENSG00000186439	ENST00000398178;ENST00000398161;ENST00000334268	T;T	0.62788	-0.0;-0.0	5.49	3.72	0.42706	.	0.724189	0.13174	N	0.408030	T	0.25457	0.0619	L	0.27053	0.805	0.43499	D	0.995746	B;B;B	0.23650	0.089;0.089;0.089	B;B;B	0.22152	0.025;0.025;0.038	T	0.09122	-1.0689	10	0.19590	T	0.45	6.1703	6.726	0.23357	0.125:0.3677:0.5073:0.0	rs35766971	339;340;339	Q5SWK9;Q8IVK2;Q13061	.;.;TRDN_HUMAN	N	339	ENSP00000381240:S339N;ENSP00000333984:S339N	ENSP00000333984:S339N	S	-	2	0	TRDN	123800942	0.970000	0.33590	0.602000	0.28890	0.991000	0.79684	1.640000	0.37186	0.812000	0.34326	0.650000	0.86243	AGT	C|0.991;T|0.009	0.009	strong		0.353	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
NCAPD3	23310	hgsc.bcm.edu	37	11	134038949	134038949	+	Splice_Site	SNP	G	G	T	rs7927108	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:134038949G>T	ENST00000534548.2	-	25	3166	c.3102C>A	c.(3100-3102)agC>agA	p.S1034R		NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	1034			S -> R (in dbSNP:rs7927108).		mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	germinal vesicle (GO:0042585)|membrane (GO:0016020)|nuclear condensin complex (GO:0000799)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)	methylated histone binding (GO:0035064)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		ACTCCCCGAAGCTGCAAAGGT	0.433													G|||	165	0.0329473	0.1195	0.0101	5008	,	,		20928	0.0		0.0	False		,,,				2504	0.0				p.S1034R		Atlas-SNP	.											.	NCAPD3	141	.	0			c.C3102A						PASS	.	G	ARG/SER	400,4002	198.1+/-222.0	11,378,1812	54.0	53.0	53.0		3102	-4.5	0.4	11	dbSNP_116	53	2,8592	2.2+/-6.3	0,2,4295	yes	missense-near-splice	NCAPD3	NM_015261.2	110	11,380,6107	TT,TG,GG		0.0233,9.0868,3.0933	benign	1034/1499	134038949	402,12594	2201	4297	6498	SO:0001630	splice_region_variant	23310	exon25			CCCGAAGCTGCAA	AK124878	CCDS31723.1	11q25	2008-02-04			ENSG00000151503	ENSG00000151503			28952	protein-coding gene	gene with protein product		609276				7584044, 8619474, 14532007	Standard	NM_015261		Approved	hCAP-D3, CAP-D3, hHCP-6, KIAA0056, FLJ42888, hcp-6	uc001qhd.1	P42695	OTTHUMG00000167172	ENST00000534548.2:c.3102-1C>A	11.37:g.134038949G>T		45.0	0.0	0		40.0	16.0	0.4	NM_015261	A6NFS2|Q4KMQ9	Missense_Mutation	SNP	ENST00000534548.2	37	CCDS31723.1	55	0.025183150183150184	53	0.10772357723577236	2	0.0055248618784530384	0	0.0	0	0.0	G	8.070	0.770068	0.15983	0.090868	2.33E-4	ENSG00000151503	ENST00000534548;ENST00000530396	T;T	0.46063	0.88;0.88	5.57	-4.49	0.03504	Armadillo-like helical (1);Armadillo-type fold (1);	0.288722	0.49305	N	0.000151	T	0.00384	0.0012	L	0.29908	0.895	0.80722	D	1	B	0.23937	0.094	B	0.28638	0.092	T	0.15292	-1.0442	10	0.13853	T	0.58	.	3.0773	0.06251	0.313:0.3092:0.2902:0.0876	rs7927108;rs52805171;rs7927108	1034	P42695	CNDD3_HUMAN	R	1034;70	ENSP00000433681:S1034R;ENSP00000435173:S70R	ENSP00000435173:S70R	S	-	3	2	NCAPD3	133544159	0.168000	0.22989	0.419000	0.26584	0.457000	0.32468	-0.280000	0.08468	-0.683000	0.05190	-0.258000	0.10820	AGC	G|0.966;T|0.034	0.034	strong		0.433	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261	Missense_Mutation
MUC4	4585	hgsc.bcm.edu	37	3	195515026	195515026	+	Missense_Mutation	SNP	G	G	C	rs200763050		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195515026G>C	ENST00000463781.3	-	2	3884	c.3425C>G	c.(3424-3426)aCt>aGt	p.T1142S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T1142S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	616					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.T1142S(3)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TACTGAGGAAGTGTCGGTGAC	0.567																																					p.T1142S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,4	MUC4	1505	4	3	Substitution - Missense(3)	skin(2)|kidney(1)	c.C3425G						PASS	.						11.0	7.0	8.0					3																	195515026		675	1482	2157	SO:0001583	missense	4585	exon2			GAGGAAGTGTCGG	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.3425C>G	3.37:g.195515026G>C	ENSP00000417498:p.Thr1142Ser	134.0	0.0	0		436.0	20.0	0.0458716	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	.	.	.	.	.	.	.	.	.	.	-	3.313	-0.140308	0.06669	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34667	1.35;1.35	0.545	-0.879	0.10613	.	.	.	.	.	T	0.31420	0.0796	N	0.14661	0.345	0.09310	N	1	D	0.60160	0.987	D	0.63488	0.915	T	0.16394	-1.0404	8	.	.	.	.	3.9497	0.09363	0.5686:0.0:0.4314:0.0	.	1142	E7ESK3	.	S	1142	ENSP00000417498:T1142S;ENSP00000420243:T1142S	.	T	-	2	0	MUC4	196999421	0.002000	0.14202	0.000000	0.03702	0.066000	0.16364	0.481000	0.22260	-0.332000	0.08489	0.064000	0.15345	ACT	G|0.998;C|0.002	0.002	weak		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
BRICD5	283870	hgsc.bcm.edu	37	16	2259673	2259673	+	Missense_Mutation	SNP	T	T	C	rs144886139	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:2259673T>C	ENST00000562360.1	-	5	472	c.473A>G	c.(472-474)cAc>cGc	p.H158R	BRICD5_ENST00000328540.3_Missense_Mutation_p.H158R|RP11-304L19.8_ENST00000561544.1_lincRNA			Q6PL45	BRID5_HUMAN	BRICHOS domain containing 5	158	BRICHOS. {ECO:0000255|PROSITE- ProRule:PRU00255}.					integral component of membrane (GO:0016021)											CTGGGTGTGGTGGGTGTCCTG	0.687													T|||	42	0.00838658	0.031	0.0014	5008	,	,		14172	0.0		0.0	False		,,,				2504	0.0				p.H158R		Atlas-SNP	.											C16orf79,NS,carcinoma,+1,1	.	.	1	0			c.A473G						PASS	.	T	ARG/HIS	108,4288	77.3+/-115.6	1,106,2091	55.0	68.0	64.0		473	-1.1	0.0	16	dbSNP_134	64	2,8598	1.2+/-3.3	0,2,4298	yes	missense	C16orf79	NM_182563.3	29	1,108,6389	CC,CT,TT		0.0233,2.4568,0.8464	benign	158/229	2259673	110,12886	2198	4300	6498	SO:0001583	missense	283870	exon5			GTGTGGTGGGTGT	BC039154	CCDS10463.1	16p13.3	2012-10-10	2012-10-10	2012-10-10	ENSG00000182685	ENSG00000182685		"""BRICHOS domain containing"""	28309	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 79"""	C16orf79		12477932	Standard	NM_182563		Approved	MGC21830	uc002cpi.2	Q6PL45	OTTHUMG00000128831	ENST00000562360.1:c.473A>G	16.37:g.2259673T>C	ENSP00000455052:p.His158Arg	91.0	0.0	0		85.0	42.0	0.494118	NM_182563	C9J7K2|Q8IXU9	Missense_Mutation	SNP	ENST00000562360.1	37	CCDS10463.1	18	0.008241758241758242	17	0.034552845528455285	1	0.0027624309392265192	0	0.0	0	0.0	T	6.160	0.397772	0.11696	0.024568	2.33E-4	ENSG00000182685	ENST00000328540	T	0.77877	-1.13	5.82	-1.09	0.09904	BRICHOS (2);	0.980375	0.08392	N	0.952853	T	0.27765	0.0683	.	.	.	0.09310	N	0.999999	B;B	0.06786	0.001;0.001	B;B	0.06405	0.002;0.001	T	0.19614	-1.0300	9	0.07813	T	0.8	-22.7577	5.497	0.16807	0.0:0.3998:0.2833:0.3169	.	158;158	Q6PL45;Q6PL45-2	CP079_HUMAN;.	R	158	ENSP00000332389:H158R	ENSP00000332389:H158R	H	-	2	0	C16orf79	2199674	0.000000	0.05858	0.002000	0.10522	0.081000	0.17604	0.005000	0.13129	-0.143000	0.11334	0.459000	0.35465	CAC	T|0.993;C|0.007	0.007	strong		0.687	BRICD5-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435091.1	NM_182563	
GNL3L	54552	hgsc.bcm.edu	37	X	54578725	54578725	+	Splice_Site	SNP	C	C	T	rs147602603	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chrX:54578725C>T	ENST00000336470.4	+	13	1321	c.1182C>T	c.(1180-1182)agC>agT	p.S394S	GNL3L_ENST00000360845.2_Splice_Site_p.S394S	NM_019067.5	NP_061940.1	Q9NVN8	GNL3L_HUMAN	guanine nucleotide binding protein-like 3 (nucleolar)-like	394					GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	30						CCCAATGCAGCGGGAAGATCA	0.507													C|||	7	0.0018543	0.0053	0.0	3775	,	,		13898	0.0		0.0	False		,,,				2504	0.0				p.S394S		Atlas-SNP	.											.	GNL3L	73	.	0			c.C1182T						PASS	.	C	,	19,3816		0,17,2,1615,569	169.0	132.0	144.0		1182,1182	-7.2	0.4	X	dbSNP_134	144	0,6728		0,0,0,2428,1872	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	GNL3L	NM_001184819.1,NM_019067.5	,	0,17,2,4043,2441	TT,TC,T,CC,C		0.0,0.4954,0.1799	,	394/583,394/583	54578725	19,10544	2203	4300	6503	SO:0001630	splice_region_variant	54552	exon13			ATGCAGCGGGAAG	AK001475	CCDS14360.1	Xp11.22	2010-03-17			ENSG00000130119	ENSG00000130119			25553	protein-coding gene	gene with protein product		300873				12477932	Standard	NM_019067		Approved	FLJ10613	uc004dth.2	Q9NVN8	OTTHUMG00000021629	ENST00000336470.4:c.1182-1C>T	X.37:g.54578725C>T		207.0	0.0	0		204.0	93.0	0.455882	NM_001184819		Silent	SNP	ENST00000336470.4	37	CCDS14360.1																																																																																			C|0.998;T|0.002	0.002	strong		0.507	GNL3L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056805.1	NM_019067	Silent
TNRC18	84629	hgsc.bcm.edu	37	7	5353252	5353252	+	Missense_Mutation	SNP	G	G	C	rs58819185	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:5353252G>C	ENST00000430969.1	-	27	7618	c.7270C>G	c.(7270-7272)Cca>Gca	p.P2424A	TNRC18_ENST00000399537.4_Missense_Mutation_p.P2424A	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2424	Pro-rich.						chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		AGGGGTGCTGGGGCCAGGGAG	0.726													G|||	321	0.0640974	0.2322	0.0144	5008	,	,		11967	0.0		0.004	False		,,,				2504	0.0				p.P2424A		Atlas-SNP	.											.	TNRC18	311	.	0			c.C7270G						PASS	.	G	ALA/PRO	536,2586		36,464,1061	11.0	12.0	11.0		7270	0.1	0.1	7	dbSNP_129	11	1,7155		0,1,3577	no	missense	TNRC18	NM_001080495.2	27	36,465,4638	CC,CG,GG		0.014,17.1685,5.2248	benign	2424/2969	5353252	537,9741	1561	3578	5139	SO:0001583	missense	84629	exon27			GTGCTGGGGCCAG	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.7270C>G	7.37:g.5353252G>C	ENSP00000395538:p.Pro2424Ala	119.0	0.0	0		155.0	66.0	0.425806	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	37	CCDS47534.1	109|109	0.04990842490842491|0.04990842490842491	101|101	0.20528455284552846|0.20528455284552846	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	4|4	0.005277044854881266|0.005277044854881266	g|g	0|0	-2.731061|-2.731061	0.00089|0.00089	0.171685|0.171685	1.4E-4|1.4E-4	ENSG00000182095|ENSG00000182095	ENST00000399537;ENST00000430969|ENST00000328270	T;T|.	0.12147|.	2.71;2.71|.	3.33|3.33	0.0546|0.0546	0.14311|0.14311	.|.	.|.	.|.	.|.	.|.	T|T	0.00039|0.00039	0.0001|0.0001	N|N	0.14661|0.14661	0.345|0.345	0.80722|0.80722	P|P	0.0|0.0	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.28004|0.28004	-1.0057|-1.0057	8|4	0.08381|.	T|.	0.77|.	.|.	8.9408|8.9408	0.35729|0.35729	0.0:0.4024:0.4584:0.1392|0.0:0.4024:0.4584:0.1392	rs58819185|rs58819185	2424|.	O15417|.	TNC18_HUMAN|.	A|R	2424|237	ENSP00000382452:P2424A;ENSP00000395538:P2424A|.	ENSP00000382452:P2424A|.	P|P	-|-	1|2	0|0	TNRC18|TNRC18	5319778|5319778	0.807000|0.807000	0.29009|0.29009	0.131000|0.131000	0.22000|0.22000	0.055000|0.055000	0.15305|0.15305	2.373000|2.373000	0.44266|0.44266	-0.063000|-0.063000	0.13065|0.13065	-3.803000|-3.803000	0.00020|0.00020	CCA|CCC	G|0.943;C|0.057	0.057	strong		0.726	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
PAPPA	5069	hgsc.bcm.edu	37	9	118950208	118950208	+	Silent	SNP	G	G	T	rs80284365	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:118950208G>T	ENST00000328252.3	+	2	1560	c.1191G>T	c.(1189-1191)gtG>gtT	p.V397V	PAPPA_ENST00000534838.1_5'Flank	NM_002581.3	NP_002572.2	Q13219	PAPP1_HUMAN	pregnancy-associated plasma protein A, pappalysin 1	397	Metalloprotease.				cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|female pregnancy (GO:0007565)|response to follicle-stimulating hormone (GO:0032354)|response to glucocorticoid (GO:0051384)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	endopeptidase activity (GO:0004175)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(9)|kidney(2)|large_intestine(23)|lung(33)|ovary(4)|pancreas(2)|prostate(5)|skin(7)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	98						AGCTGGACGTGCTGGAGGTGA	0.582													G|||	222	0.0443291	0.1581	0.0115	5008	,	,		19158	0.0		0.003	False		,,,				2504	0.002				p.V397V		Atlas-SNP	.											.	PAPPA	243	.	0			c.G1191T						PASS	.	G		626,3780	270.7+/-269.8	45,536,1622	71.0	61.0	64.0		1191	1.0	1.0	9	dbSNP_132	64	32,8568	20.4+/-63.3	1,30,4269	no	coding-synonymous	PAPPA	NM_002581.3		46,566,5891	TT,TG,GG		0.3721,14.2079,5.0592		397/1628	118950208	658,12348	2203	4300	6503	SO:0001819	synonymous_variant	5069	exon2			GGACGTGCTGGAG		CCDS6813.1	9q33.1	2014-03-05			ENSG00000182752	ENSG00000182752			8602	protein-coding gene	gene with protein product	"""insulin-like growth factor-dependent IGF binding protein-4 protease"", ""aspecific BCL2 ARE-binding protein 2"", ""differentially placenta 1 expressed protein"""	176385				7679961	Standard	NM_002581		Approved	PAPP-A, PAPPA1, IGFBP-4ase, PAPA, ASBABP2, DIPLA1	uc004bjn.3	Q13219	OTTHUMG00000021045	ENST00000328252.3:c.1191G>T	9.37:g.118950208G>T		77.0	0.0	0		78.0	52.0	0.666667	NM_002581	B1AMF9|Q08371|Q68G52|Q9UDK7	Silent	SNP	ENST00000328252.3	37	CCDS6813.1																																																																																			G|0.955;T|0.045	0.045	strong		0.582	PAPPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055546.1	NM_002581	
CEP192	55125	hgsc.bcm.edu	37	18	13056065	13056065	+	Missense_Mutation	SNP	C	C	G	rs61739695	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr18:13056065C>G	ENST00000325971.8	+	17	3281	c.1688C>G	c.(1687-1689)cCt>cGt	p.P563R	CEP192_ENST00000430049.2_Missense_Mutation_p.P684R|CEP192_ENST00000506447.1_Missense_Mutation_p.P1159R			Q8TEP8	CE192_HUMAN	centrosomal protein 192kDa	563					centrosome duplication (GO:0051298)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of phosphatase activity (GO:0010923)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	phosphatase binding (GO:0019902)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(36)|ovary(4)|pancreas(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						ACATCAAACCCTGAGGAATTG	0.512													C|||	61	0.0121805	0.0446	0.0029	5008	,	,		19222	0.0		0.0	False		,,,				2504	0.0				p.P1159R		Atlas-SNP	.											.	CEP192	340	.	0			c.C3476G						PASS	.	C	ARG/PRO	163,4243	108.2+/-146.6	2,159,2042	47.0	48.0	47.0		3476	0.8	0.0	18	dbSNP_129	47	1,8599	1.2+/-3.3	0,1,4299	yes	missense	CEP192	NM_032142.3	103	2,160,6341	GG,GC,CC		0.0116,3.6995,1.261	benign	1159/2538	13056065	164,12842	2203	4300	6503	SO:0001583	missense	55125	exon19			CAAACCCTGAGGA	AK074074	CCDS32792.1, CCDS32792.2	18p11.21	2014-02-20				ENSG00000101639		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	25515	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 62"""					11230166, 14654843	Standard	NM_032142		Approved	KIAA1569, FLJ10352, PPP1R62	uc010xac.2	Q8TEP8		ENST00000325971.8:c.1688C>G	18.37:g.13056065C>G	ENSP00000317156:p.Pro563Arg	91.0	0.0	0		68.0	35.0	0.514706	NM_032142	A0A060A9S4|E9PF99|Q8WYT8|Q9H0F4|Q9NW27	Missense_Mutation	SNP	ENST00000325971.8	37		23	0.010531135531135532	23	0.046747967479674794	0	0.0	0	0.0	0	0.0	C	5.196	0.221789	0.09863	0.036995	1.16E-4	ENSG00000101639	ENST00000506447;ENST00000325971;ENST00000399863;ENST00000430049	T;T;T	0.05382	3.46;3.45;3.46	4.19	0.836	0.18891	.	1.225170	0.05804	N	0.612700	T	0.00580	0.0019	N	0.16478	0.41	0.09310	N	1	B;B;B	0.11235	0.002;0.003;0.004	B;B;B	0.08055	0.002;0.003;0.003	T	0.46775	-0.9167	10	0.19147	T	0.46	0.3765	0.6935	0.00895	0.3617:0.2925:0.1361:0.2097	rs61739695	684;1159;563	C9JT09;E9PF99;Q8TEP8	.;.;CE192_HUMAN	R	1159;563;563;684	ENSP00000427550:P1159R;ENSP00000317156:P563R;ENSP00000389190:P684R	ENSP00000317156:P563R	P	+	2	0	CEP192	13046065	0.000000	0.05858	0.000000	0.03702	0.080000	0.17528	0.012000	0.13287	0.270000	0.21984	0.563000	0.77884	CCT	C|0.986;G|0.014	0.014	strong		0.512	CEP192-201	KNOWN	basic	protein_coding	protein_coding		NM_032142	
GPD1	2819	hgsc.bcm.edu	37	12	50498475	50498475	+	Missense_Mutation	SNP	A	A	G	rs2232202	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:50498475A>G	ENST00000301149.3	+	2	392	c.160A>G	c.(160-162)Atc>Gtc	p.I54V	GPD1_ENST00000547190.1_3'UTR|GPD1_ENST00000548814.1_Missense_Mutation_p.I54V	NM_001257199.1|NM_005276.3	NP_001244128.1|NP_005267.2	P21695	GPDA_HUMAN	glycerol-3-phosphate dehydrogenase 1 (soluble)	54			I -> V (in dbSNP:rs2232202). {ECO:0000269|PubMed:22226083}.		cellular lipid metabolic process (GO:0044255)|cellular response to cAMP (GO:0071320)|cellular response to tumor necrosis factor (GO:0071356)|gluconeogenesis (GO:0006094)|glycerol-3-phosphate catabolic process (GO:0046168)|glycerophosphate shuttle (GO:0006127)|glycerophospholipid biosynthetic process (GO:0046474)|NADH oxidation (GO:0006116)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of glycolytic process (GO:0045821)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycerol-3-phosphate dehydrogenase complex (GO:0009331)|mitochondrion (GO:0005739)	glycerol-3-phosphate dehydrogenase [NAD+] activity (GO:0004367)|glycerol-3-phosphate dehydrogenase activity (GO:0004368)|NAD binding (GO:0051287)			breast(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8						GACTGAGATCATCAACACGCA	0.542													A|||	56	0.0111821	0.0424	0.0	5008	,	,		20418	0.0		0.0	False		,,,				2504	0.0				p.I54V	NSCLC(141;1402 1905 9497 13391 44868)	Atlas-SNP	.											.	GPD1	23	.	0			c.A160G						PASS	.	A	VAL/ILE	177,4229	115.4+/-153.4	7,163,2033	126.0	112.0	117.0		160	5.7	1.0	12	dbSNP_98	117	1,8599		0,1,4299	yes	missense	GPD1	NM_005276.2	29	7,164,6332	GG,GA,AA		0.0116,4.0172,1.3686	probably-damaging	54/350	50498475	178,12828	2203	4300	6503	SO:0001583	missense	2819	exon2			GAGATCATCAACA		CCDS8799.1, CCDS58229.1	12q13.12	2013-09-20			ENSG00000167588	ENSG00000167588	1.1.1.8		4455	protein-coding gene	gene with protein product		138420					Standard	NM_005276		Approved		uc001rvz.4	P21695	OTTHUMG00000169813	ENST00000301149.3:c.160A>G	12.37:g.50498475A>G	ENSP00000301149:p.Ile54Val	130.0	0.0	0		98.0	41.0	0.418367	NM_005276	F8W1L5|Q8N1B0	Missense_Mutation	SNP	ENST00000301149.3	37	CCDS8799.1	22	0.010073260073260074	22	0.044715447154471545	0	0.0	0	0.0	0	0.0	A	26.3	4.724233	0.89298	0.040172	1.16E-4	ENSG00000167588	ENST00000301149;ENST00000547190;ENST00000548814	T;T	0.63913	-0.07;0.53	5.7	5.7	0.88788	Glycerol-3-phosphate dehydrogenase, NAD-dependent, N-terminal (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	T	0.57592	0.2064	M	0.89287	3.02	0.80722	D	1	D;D;D	0.76494	0.986;0.999;0.998	P;D;D	0.85130	0.908;0.99;0.997	T	0.78267	-0.2270	10	0.87932	D	0	-16.3048	16.2858	0.82720	1.0:0.0:0.0:0.0	rs2232202;rs52818556;rs2232202	54;54;54	B4DJ37;F8W1L5;P21695	.;.;GPDA_HUMAN	V	54	ENSP00000301149:I54V;ENSP00000446768:I54V	ENSP00000301149:I54V	I	+	1	0	GPD1	48784742	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.458000	0.80787	2.313000	0.78055	0.454000	0.30748	ATC	A|0.984;G|0.016	0.016	strong		0.542	GPD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406018.1		
HYDIN	54768	hgsc.bcm.edu	37	16	70954682	70954682	+	Missense_Mutation	SNP	G	G	A	rs143849088	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:70954682G>A	ENST00000393567.2	-	46	7747	c.7597C>T	c.(7597-7599)Cgg>Tgg	p.R2533W		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	2533					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				aggcgctcccgctccgccttc	0.697													G|||	17	0.00339457	0.0129	0.0	5008	,	,		19002	0.0		0.0	False		,,,				2504	0.0				p.R2533W		Atlas-SNP	.											.	HYDIN	788	.	0			c.C7597T						PASS	.	G	TRP/ARG	28,3858		0,28,1915	20.0	21.0	21.0		7594	-0.8	1.0	16	dbSNP_134	21	0,8242		0,0,4121	yes	missense	HYDIN	NM_032821.2	101	0,28,6036	AA,AG,GG		0.0,0.7205,0.2309	probably-damaging	2532/5121	70954682	28,12100	1943	4121	6064	SO:0001583	missense	54768	exon46			GCTCCCGCTCCGC	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.7597C>T	16.37:g.70954682G>A	ENSP00000377197:p.Arg2533Trp	82.0	0.0	0		88.0	43.0	0.488636	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	G	18.32	3.597425	0.66332	0.007205	0.0	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.01178	5.22	5.89	-0.796	0.10912	.	0.000000	0.33834	U	0.004514	T	0.01061	0.0035	N	0.14661	0.345	0.25478	N	0.987764	D	0.89917	1.0	D	0.72338	0.977	T	0.38134	-0.9675	10	0.72032	D	0.01	.	13.9873	0.64343	0.1005:0.0:0.6814:0.2181	.	2532	F8WD23	.	W	2533;2532	ENSP00000377197:R2533W	ENSP00000313052:R2532W	R	-	1	2	HYDIN	69512183	0.996000	0.38824	0.984000	0.44739	0.832000	0.47134	0.126000	0.15769	-0.426000	0.07360	-1.296000	0.01341	CGG	G|0.996;A|0.004	0.004	strong		0.697	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
ZNF479	90827	hgsc.bcm.edu	37	7	57187997	57187997	+	Missense_Mutation	SNP	A	A	T	rs146543279	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:57187997A>T	ENST00000331162.4	-	5	1395	c.1125T>A	c.(1123-1125)caT>caA	p.H375Q		NM_033273.1	NP_150376.1	Q96JC4	ZN479_HUMAN	zinc finger protein 479	375					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(53)|ovary(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	84			GBM - Glioblastoma multiforme(1;9.18e-12)			TCTCTCCAGTATGAATTCTCC	0.438													.|||	12	0.00239617	0.0091	0.0	5008	,	,		21893	0.0		0.0	False		,,,				2504	0.0				p.H375Q		Atlas-SNP	.											.	ZNF479	193	.	0			c.T1125A						PASS	.	A	GLN/HIS	39,4097		0,39,2029	42.0	43.0	43.0		1125	0.9	0.0	7	dbSNP_134	43	0,8454		0,0,4227	no	missense	ZNF479	NM_033273.1	24	0,39,6256	TT,TA,AA		0.0,0.9429,0.3098	probably-damaging	375/525	57187997	39,12551	2068	4227	6295	SO:0001583	missense	90827	exon5			TCCAGTATGAATT	AF277624	CCDS43590.1	7p11.2	2013-01-08			ENSG00000185177	ENSG00000185177		"""Zinc fingers, C2H2-type"", ""-"""	23258	protein-coding gene	gene with protein product						11410164	Standard	NM_033273		Approved	KR19	uc010kzo.3	Q96JC4	OTTHUMG00000156682	ENST00000331162.4:c.1125T>A	7.37:g.57187997A>T	ENSP00000333776:p.His375Gln	242.0	0.0	0		281.0	143.0	0.508897	NM_033273		Missense_Mutation	SNP	ENST00000331162.4	37	CCDS43590.1	4	0.0018315018315018315	4	0.008130081300813009	0	0.0	0	0.0	0	0.0	a	11.55	1.671267	0.29693	0.009429	0.0	ENSG00000185177	ENST00000331162	T	0.66995	-0.24	0.946	0.946	0.19549	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.71685	0.3369	M	0.86268	2.805	0.24579	N	0.993888	D	0.55385	0.971	D	0.65773	0.938	T	0.62501	-0.6841	9	0.87932	D	0	.	2.9462	0.05847	0.6852:0.0:0.3148:0.0	.	375	Q96JC4	ZN479_HUMAN	Q	375	ENSP00000333776:H375Q	ENSP00000333776:H375Q	H	-	3	2	ZNF479	57191939	0.998000	0.40836	0.011000	0.14972	0.010000	0.07245	0.567000	0.23608	0.339000	0.23719	0.329000	0.21502	CAT	A|0.998;T|0.002	0.002	strong		0.438	ZNF479-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345302.1	XM_291202	
PLA2G4B	100137049	hgsc.bcm.edu	37	15	42137201	42137201	+	Missense_Mutation	SNP	G	G	A	rs34807597	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42137201G>A	ENST00000452633.1	+	14	1524	c.1172G>A	c.(1171-1173)cGc>cAc	p.R391H	PLA2G4B_ENST00000542534.2_Missense_Mutation_p.R622H|PLA2G4B_ENST00000458483.1_Missense_Mutation_p.R391H|JMJD7-PLA2G4B_ENST00000382448.4_Missense_Mutation_p.R622H|JMJD7-PLA2G4B_ENST00000342159.4_Missense_Mutation_p.R622H			P0C869	PA24B_HUMAN	phospholipase A2, group IVB (cytosolic)	391	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.		R -> H (in dbSNP:rs34807597).		activation of signaling protein activity involved in unfolded protein response (GO:0006987)|arachidonic acid metabolic process (GO:0019369)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|parturition (GO:0007567)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)						all_cancers(109;1.84e-13)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		all cancers(2;1.08e-30)|Epithelial(2;1.43e-22)|OV - Ovarian serous cystadenocarcinoma(18;1.13e-17)|GBM - Glioblastoma multiforme(94;9.77e-07)|Colorectal(2;0.0129)|COAD - Colon adenocarcinoma(120;0.0371)		GAGCGTGCCCGCTTGGGCTAC	0.672													G|||	77	0.0153754	0.0552	0.0043	5008	,	,		15685	0.0		0.001	False		,,,				2504	0.0				p.R622H		Atlas-SNP	.											.	JMJD7-PLA2G4B	90	.	0			c.G1865A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG	189,4209		7,175,2017	16.0	17.0	17.0		1172,1865,1865	-1.9	0.4	15	dbSNP_126	17	3,8581		0,3,4289	yes	missense,missense,missense	JMJD7-PLA2G4B,PLA2G4B	NM_001114633.1,NM_001198588.1,NM_005090.3	29,29,29	7,178,6306	AA,AG,GG		0.0349,4.2974,1.479	benign,benign,benign	391/782,622/894,622/1013	42137201	192,12790	2199	4292	6491	SO:0001583	missense	8681	exon18			GTGCCCGCTTGGG	AF065215	CCDS45241.1	15q11.2-q21.3	2010-08-17			ENSG00000243708	ENSG00000243708	3.1.1.4		9036	protein-coding gene	gene with protein product		606088				9705332	Standard	NM_001114633		Approved	cPLA2-beta, HsT16992		P0C869	OTTHUMG00000156809	ENST00000452633.1:c.1172G>A	15.37:g.42137201G>A	ENSP00000396045:p.Arg391His	65.0	0.0	0		79.0	36.0	0.455696	NM_005090	B4DRT9|O95712|Q19KD5|Q19KD6|Q59GF9|Q8TB10|Q9UKV7	Missense_Mutation	SNP	ENST00000452633.1	37	CCDS45241.1	25	0.011446886446886446	22	0.044715447154471545	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	.	10.30	1.310981	0.23821	0.042974	3.49E-4	ENSG00000168970;ENSG00000168970;ENSG00000168970;ENSG00000243708	ENST00000382448;ENST00000342159;ENST00000458483;ENST00000452633	T;T;T;T	0.04603	3.59;3.59;3.59;3.59	5.51	-1.88	0.07713	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.492693	0.18810	N	0.130531	T	0.01156	0.0038	M	0.65498	2.005	0.09310	N	1	B;B;B;B	0.13594	0.008;0.0;0.003;0.003	B;B;B;B	0.12156	0.007;0.0;0.002;0.001	T	0.30001	-0.9993	10	0.62326	D	0.03	-2.658	5.6051	0.17374	0.6081:0.0:0.2403:0.1516	rs34807597	391;622;92;622	P0C869;P0C869-7;P0C869-4;P0C869-6	PA24B_HUMAN;.;.;.	H	622;622;391;391	ENSP00000371886:R622H;ENSP00000342785:R622H;ENSP00000416610:R391H;ENSP00000396045:R391H	ENSP00000342785:R622H	R	+	2	0	JMJD7-PLA2G4B;PLA2G4B	39924493	0.002000	0.14202	0.381000	0.26106	0.055000	0.15305	0.861000	0.27885	-0.138000	0.11434	0.561000	0.74099	CGC	G|0.984;A|0.016	0.016	strong		0.672	PLA2G4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345969.1	NM_001114633	
SLC38A8	146167	hgsc.bcm.edu	37	16	84050218	84050218	+	Silent	SNP	G	G	A	rs13334006	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:84050218G>A	ENST00000299709.3	-	8	1067	c.1068C>T	c.(1066-1068)acC>acT	p.T356T		NM_001080442.1	NP_001073911.1	A6NNN8	S38A8_HUMAN	solute carrier family 38, member 8	356					amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						CGAGCGTCACGGTGACCCACA	0.627													G|||	295	0.0589058	0.2156	0.0144	5008	,	,		20259	0.0		0.0	False		,,,				2504	0.0				p.T356T		Atlas-SNP	.											.	SLC38A8	60	.	0			c.C1068T						PASS	.	G		822,3578	326.1+/-299.4	78,666,1456	74.0	67.0	69.0		1068	-7.5	0.0	16	dbSNP_121	69	12,8588	7.7+/-29.5	0,12,4288	no	coding-synonymous	SLC38A8	NM_001080442.1		78,678,5744	AA,AG,GG		0.1395,18.6818,6.4154		356/436	84050218	834,12166	2200	4300	6500	SO:0001819	synonymous_variant	146167	exon8			CGTCACGGTGACC		CCDS32495.1	16q23.3	2013-05-22				ENSG00000166558		"""Solute carriers"""	32434	protein-coding gene	gene with protein product		615585					Standard	XM_006721135		Approved		uc002fhg.1	A6NNN8		ENST00000299709.3:c.1068C>T	16.37:g.84050218G>A		46.0	0.0	0		36.0	21.0	0.583333	NM_001080442		Silent	SNP	ENST00000299709.3	37	CCDS32495.1																																																																																			G|0.939;A|0.061	0.061	strong		0.627	SLC38A8-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432623.1	NM_001080442	
KBTBD6	89890	hgsc.bcm.edu	37	13	41706450	41706450	+	Silent	SNP	G	G	C	rs147388453	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:41706450G>C	ENST00000379485.1	-	1	432	c.198C>G	c.(196-198)acC>acG	p.T66T	KBTBD6_ENST00000499385.2_Intron	NM_152903.4	NP_690867.3	Q86V97	KBTB6_HUMAN	kelch repeat and BTB (POZ) domain containing 6	66	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.									NS(1)|breast(1)|endometrium(8)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|skin(4)|urinary_tract(4)	43		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;4.08e-09)|Epithelial(112;4.74e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000131)|GBM - Glioblastoma multiforme(144;0.000876)|BRCA - Breast invasive adenocarcinoma(63;0.0673)		CCACCTCGATGGTCACATCAC	0.607													G|||	43	0.00858626	0.031	0.0014	5008	,	,		18622	0.0		0.001	False		,,,				2504	0.0				p.T66T		Atlas-SNP	.											.	KBTBD6	83	.	0			c.C198G						PASS	.	G		152,4254	104.7+/-143.2	0,152,2051	89.0	89.0	89.0		198	3.7	1.0	13	dbSNP_134	89	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KBTBD6	NM_152903.4		0,153,6350	CC,CG,GG		0.0116,3.4498,1.1764		66/675	41706450	153,12853	2203	4300	6503	SO:0001819	synonymous_variant	89890	exon1			CTCGATGGTCACA	AK056633	CCDS9376.1	13q13.3	2013-01-08			ENSG00000165572	ENSG00000165572		"""BTB/POZ domain containing"""	25340	protein-coding gene	gene with protein product						12477932	Standard	NM_152903		Approved	DKFZp547E1912	uc001uxu.1	Q86V97	OTTHUMG00000016786	ENST00000379485.1:c.198C>G	13.37:g.41706450G>C		101.0	0.0	0		71.0	40.0	0.56338	NM_152903	Q5T6Y8|Q8N8L0|Q8NDM5|Q96MP6	Silent	SNP	ENST00000379485.1	37	CCDS9376.1																																																																																			G|0.988;C|0.012	0.012	strong		0.607	KBTBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044657.1	NM_152903	
CPNE3	8895	hgsc.bcm.edu	37	8	87558846	87558846	+	Missense_Mutation	SNP	G	G	C	rs41333046	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:87558846G>C	ENST00000521271.1	+	10	918	c.756G>C	c.(754-756)gaG>gaC	p.E252D	CPNE3_ENST00000198765.4_Missense_Mutation_p.E252D	NM_003909.3	NP_003900.1	O75131	CPNE3_HUMAN	copine III	252			E -> D (in dbSNP:rs41333046).		lipid metabolic process (GO:0006629)|protein phosphorylation (GO:0006468)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	calcium-dependent phospholipid binding (GO:0005544)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)|transporter activity (GO:0005215)			NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	23						GCATAAATGAGAAAAAAAGGC	0.308													G|||	571	0.114018	0.41	0.0303	5008	,	,		17040	0.004		0.003	False		,,,				2504	0.001				p.E252D		Atlas-SNP	.											CPNE3,NS,carcinoma,0,1	CPNE3	65	1	0			c.G756C						PASS	.	G	ASP/GLU	1372,3034	453.4+/-350.3	207,958,1038	90.0	103.0	98.0		756	1.6	1.0	8	dbSNP_127	98	14,8586	8.4+/-32.0	0,14,4286	yes	missense	CPNE3	NM_003909.3	45	207,972,5324	CC,CG,GG		0.1628,31.1394,10.6566	benign	252/538	87558846	1386,11620	2203	4300	6503	SO:0001583	missense	8895	exon10			AAATGAGAAAAAA	AB014536	CCDS6243.1	8q21	2008-07-03				ENSG00000085719			2316	protein-coding gene	gene with protein product		604207				9430674	Standard	NM_003909		Approved		uc003ydv.2	O75131		ENST00000521271.1:c.756G>C	8.37:g.87558846G>C	ENSP00000430934:p.Glu252Asp	265.0	0.0	0		270.0	141.0	0.522222	NM_003909	A8KA47|Q8IYA1	Missense_Mutation	SNP	ENST00000521271.1	37	CCDS6243.1	199|199	0.09111721611721611|0.09111721611721611	186|186	0.3780487804878049|0.3780487804878049	11|11	0.03038674033149171|0.03038674033149171	1|1	0.0017482517482517483|0.0017482517482517483	1|1	0.0013192612137203166|0.0013192612137203166	G|G	14.05|14.05	2.420410|2.420410	0.42918|0.42918	0.311394|0.311394	0.001628|0.001628	ENSG00000085719|ENSG00000085719	ENST00000198765;ENST00000521271|ENST00000517391	T;T|.	0.39787|.	1.06;1.06|.	5.52|5.52	1.62|1.62	0.23740|0.23740	C2 calcium/lipid-binding domain, CaLB (1);|.	0.106801|.	0.64402|.	D|.	0.000001|.	T|T	0.00012|0.00012	0.0000|0.0000	L|L	0.45352|0.45352	1.415|1.415	0.27719|0.27719	P|P	0.9451934|0.9451934	B|.	0.32051|.	0.354|.	B|.	0.26614|.	0.071|.	T|T	0.40739|0.40739	-0.9547|-0.9547	9|4	0.59425|.	D|.	0.04|.	-12.9148|-12.9148	9.7986|9.7986	0.40751|0.40751	0.5228:0.0:0.4772:0.0|0.5228:0.0:0.4772:0.0	rs41333046|rs41333046	252|.	O75131|.	CPNE3_HUMAN|.	D|T	252|141	ENSP00000198765:E252D;ENSP00000430934:E252D|.	ENSP00000198765:E252D|.	E|R	+|+	3|2	2|0	CPNE3|CPNE3	87627962|87627962	0.931000|0.931000	0.31567|0.31567	0.998000|0.998000	0.56505|0.56505	0.984000|0.984000	0.73092|0.73092	0.121000|0.121000	0.15667|0.15667	0.078000|0.078000	0.16900|0.16900	-0.355000|-0.355000	0.07637|0.07637	GAG|AGA	G|0.888;C|0.112	0.112	strong		0.308	CPNE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374994.1		
TFRC	7037	hgsc.bcm.edu	37	3	195787102	195787102	+	Silent	SNP	C	C	T	rs111276121	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195787102C>T	ENST00000360110.4	-	14	1654	c.1485G>A	c.(1483-1485)aaG>aaA	p.K495K	TFRC_ENST00000420415.1_Silent_p.K414K|TFRC_ENST00000465288.1_5'UTR|TFRC_ENST00000535031.1_Silent_p.K213K|TFRC_ENST00000540528.1_3'UTR|TFRC_ENST00000392396.3_Silent_p.K495K	NM_001128148.1	NP_001121620.1	P02786	TFR1_HUMAN	transferrin receptor	495					cellular iron ion homeostasis (GO:0006879)|iron ion import (GO:0097286)|osteoclast differentiation (GO:0030316)|positive regulation of bone resorption (GO:0045780)|transferrin transport (GO:0033572)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|coated pit (GO:0005905)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|vesicle (GO:0031982)	double-stranded RNA binding (GO:0003725)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|transferrin receptor activity (GO:0004998)			NS(1)|breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(10)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27	all_cancers(143;1.94e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;1.36e-24)|all cancers(36;3.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.17e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00233)	Gallium nitrate(DB05260)	TGGCAGAAACCTTGAAGTTGC	0.338			T	BCL6	NHL								C|||	9	0.00179712	0.0068	0.0	5008	,	,		19006	0.0		0.0	False		,,,				2504	0.0				p.K495K		Atlas-SNP	.		Dom	yes		3	3q29	7037	"""transferrin receptor (p90, CD71)"""		L	.	TFRC	54	.	0			c.G1485A						PASS	.	C	,	27,4379	33.5+/-64.1	0,27,2176	158.0	144.0	148.0		1485,1485	-0.4	1.0	3	dbSNP_132	148	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	TFRC	NM_001128148.1,NM_003234.2	,	0,27,6476	TT,TC,CC		0.0,0.6128,0.2076	,	495/761,495/761	195787102	27,12979	2203	4300	6503	SO:0001819	synonymous_variant	7037	exon14			AGAAACCTTGAAG	X01060	CCDS3312.1	3q29	2013-09-19	2013-09-19		ENSG00000072274	ENSG00000072274		"""CD molecules"""	11763	protein-coding gene	gene with protein product		190010	"""transferrin receptor (p90, CD71)"""				Standard	NM_003234		Approved	CD71, TFR1, p90	uc003fwa.4	P02786	OTTHUMG00000155714	ENST00000360110.4:c.1485G>A	3.37:g.195787102C>T		177.0	0.0	0		164.0	86.0	0.52439	NM_001128148	D3DXB0|Q1HE24|Q59G55|Q9UCN0|Q9UCU5|Q9UDF9|Q9UK21	Silent	SNP	ENST00000360110.4	37	CCDS3312.1																																																																																			C|0.997;T|0.003	0.003	strong		0.338	TFRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341346.1		
ATP10A	57194	hgsc.bcm.edu	37	15	25962057	25962057	+	Silent	SNP	C	C	T	rs115618637	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:25962057C>T	ENST00000356865.6	-	9	1707	c.1596G>A	c.(1594-1596)acG>acA	p.T532T		NM_024490.3	NP_077816.1	O60312	AT10A_HUMAN	ATPase, class V, type 10A	532			T -> M (in dbSNP:rs2066703).		ion transmembrane transport (GO:0034220)|phospholipid translocation (GO:0045332)|regulation of cell shape (GO:0008360)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|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)			NS(1)|breast(2)|endometrium(8)|kidney(2)|large_intestine(33)|liver(1)|lung(41)|ovary(3)|pancreas(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	103		all_cancers(20;5.16e-25)|all_lung(180;1.51e-14)|Acute lymphoblastic leukemia(1;2.53e-05)|all_hematologic(1;0.000267)|Breast(32;0.00125)		all cancers(64;9.48e-07)|Epithelial(43;1.69e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0252)|Lung(196;0.244)		TTGGGTCGGGCGTGATATCCT	0.577													C|||	11	0.00219649	0.0083	0.0	5008	,	,		15659	0.0		0.0	False		,,,				2504	0.0				p.T532T		Atlas-SNP	.											.	ATP10A	270	.	0			c.G1596A						PASS	.	C		36,4370	40.0+/-72.8	0,36,2167	85.0	63.0	71.0		1596	-10.8	0.2	15	dbSNP_132	71	0,8600		0,0,4300	no	coding-synonymous	ATP10A	NM_024490.3		0,36,6467	TT,TC,CC		0.0,0.8171,0.2768		532/1500	25962057	36,12970	2203	4300	6503	SO:0001819	synonymous_variant	57194	exon9			GTCGGGCGTGATA	AB011138	CCDS32178.1	15q12	2010-04-20	2007-09-19		ENSG00000206190	ENSG00000206190		"""ATPases / P-type"""	13542	protein-coding gene	gene with protein product		605855	"""ATPase, Class V, type 10C"", ""ATPase, Class V, type 10A"""	ATP10C		11015572, 9628581	Standard	NM_024490		Approved	ATPVA, ATPVC, KIAA0566	uc010ayu.3	O60312		ENST00000356865.6:c.1596G>A	15.37:g.25962057C>T		82.0	0.0	0		113.0	47.0	0.415929	NM_024490	Q4G0S9|Q969I4	Silent	SNP	ENST00000356865.6	37	CCDS32178.1																																																																																			C|0.998;T|0.002	0.002	strong		0.577	ATP10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414830.1	NM_024490	
USP18	11274	hgsc.bcm.edu	37	22	18644597	18644597	+	Missense_Mutation	SNP	G	G	A	rs143481018		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:18644597G>A	ENST00000215794.7	+	4	725	c.295G>A	c.(295-297)Gtc>Atc	p.V99I		NM_017414.3	NP_059110.2	Q9UMW8	UBP18_HUMAN	ubiquitin specific peptidase 18	99	USP.				cytokine-mediated signaling pathway (GO:0019221)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytosol (GO:0005829)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|stomach(1)	10						GAGGAGAAGCGTCCCTTTCCA	0.577																																					p.V99I		Atlas-SNP	.											.	USP18	22	.	0			c.G295A						PASS	.						23.0	20.0	21.0					22																	18644597		2202	4295	6497	SO:0001583	missense	11274	exon4			AGAAGCGTCCCTT	AJ243526	CCDS13752.1	22q11.2	2008-04-11	2005-08-08		ENSG00000184979	ENSG00000184979		"""Ubiquitin-specific peptidases"""	12616	protein-coding gene	gene with protein product		607057	"""ubiquitin specific protease 18"""			12838346	Standard	NM_017414		Approved		uc002zny.3	Q9UMW8	OTTHUMG00000150104	ENST00000215794.7:c.295G>A	22.37:g.18644597G>A	ENSP00000215794:p.Val99Ile	324.0	0.0	0		439.0	127.0	0.289294	NM_017414	Q53Y90|Q6IAD9|Q9NY71	Missense_Mutation	SNP	ENST00000215794.7	37	CCDS13752.1	.	.	.	.	.	.	.	.	.	.	.	16.12	3.034318	0.54896	.	.	ENSG00000184979	ENST00000215794	T	0.32023	1.47	5.57	2.19	0.27852	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.490245	0.22485	N	0.059456	T	0.24967	0.0606	N	0.26042	0.785	0.24638	N	0.993584	D	0.69078	0.997	P	0.57548	0.823	T	0.12863	-1.0531	10	0.08837	T	0.75	.	3.4873	0.07625	0.0914:0.1718:0.559:0.1778	.	99	Q9UMW8	UBP18_HUMAN	I	99	ENSP00000215794:V99I	ENSP00000215794:V99I	V	+	1	0	USP18	17024597	0.992000	0.36948	0.971000	0.41717	0.704000	0.40688	1.496000	0.35638	0.640000	0.30582	0.650000	0.86243	GTC	.	.	weak		0.577	USP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316368.1		
ZNF668	79759	hgsc.bcm.edu	37	16	31075439	31075439	+	Silent	SNP	G	G	A	rs34107331	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:31075439G>A	ENST00000538906.1	-	2	1126	c.342C>T	c.(340-342)tgC>tgT	p.C114C	ZNF668_ENST00000539836.3_Silent_p.C137C|ZNF668_ENST00000564456.1_5'Flank|ZNF668_ENST00000535577.1_Silent_p.C114C|ZNF668_ENST00000426488.2_Silent_p.C137C|ZNF668_ENST00000300849.4_Silent_p.C114C|AC135050.5_ENST00000568708.1_RNA|ZNF668_ENST00000394983.2_Silent_p.C114C	NM_001172668.1	NP_001166139	Q96K58	ZN668_HUMAN	zinc finger protein 668	114					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(6)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	27						CGCACTCGGGGCACGGAAAGG	0.706													G|||	38	0.00758786	0.0257	0.0058	5008	,	,		14213	0.0		0.0	False		,,,				2504	0.0				p.C137C	Colon(181;1111 1980 5060 10512 25785)	Atlas-SNP	.											.	ZNF668	121	.	0			c.C411T						PASS	.	G	,,,	130,4260		2,126,2067	22.0	23.0	23.0		342,411,342,342	0.9	1.0	16	dbSNP_126	23	1,8595		0,1,4297	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ZNF668	NM_001172668.1,NM_001172669.1,NM_001172670.1,NM_024706.4	,,,	2,127,6364	AA,AG,GG		0.0116,2.9613,1.0088	,,,	114/620,137/643,114/620,114/620	31075439	131,12855	2195	4298	6493	SO:0001819	synonymous_variant	79759	exon3			CTCGGGGCACGGA		CCDS10701.1, CCDS54003.1	16p11.2	2013-01-08			ENSG00000167394	ENSG00000167394		"""Zinc fingers, C2H2-type"""	25821	protein-coding gene	gene with protein product						12477932	Standard	NM_024706		Approved	FLJ13479	uc021tgt.1	Q96K58	OTTHUMG00000047357	ENST00000538906.1:c.342C>T	16.37:g.31075439G>A		7.0	0.0	0		14.0	7.0	0.5	NM_001172669	C9JHH8|F5H7E7|Q59EV1|Q8N669|Q9H8L4	Silent	SNP	ENST00000538906.1	37	CCDS10701.1																																																																																			G|0.990;A|0.010	0.010	strong		0.706	ZNF668-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108516.2	NM_024706	
WDR62	284403	hgsc.bcm.edu	37	19	36594404	36594404	+	Missense_Mutation	SNP	G	G	A	rs61743589	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:36594404G>A	ENST00000270301.7	+	30	3659	c.3659G>A	c.(3658-3660)cGt>cAt	p.R1220H	WDR62_ENST00000401500.2_Missense_Mutation_p.R1225H			O43379	WDR62_HUMAN	WD repeat domain 62	1220					cerebral cortex development (GO:0021987)|neurogenesis (GO:0022008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle pole (GO:0000922)				cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(15)|prostate(4)|stomach(2)|urinary_tract(3)	43	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			GCCAGCTCCCGTGCCAGGATA	0.652													G|||	112	0.0223642	0.0794	0.0101	5008	,	,		19415	0.0		0.0	False		,,,				2504	0.0				p.R1225H		Atlas-SNP	.											.	WDR62	102	.	0			c.G3674A						PASS	.	G	HIS/ARG,HIS/ARG	315,4091	168.7+/-199.5	11,293,1899	88.0	82.0	84.0		3674,3659	-9.4	0.0	19	dbSNP_129	84	5,8595	3.0+/-9.4	0,5,4295	yes	missense,missense	WDR62	NM_001083961.1,NM_173636.4	29,29	11,298,6194	AA,AG,GG		0.0581,7.1493,2.4604	benign,benign	1225/1524,1220/1519	36594404	320,12686	2203	4300	6503	SO:0001583	missense	284403	exon30			GCTCCCGTGCCAG	BX647726	CCDS33001.1, CCDS46059.1	19q13.12	2013-01-09	2005-05-09	2005-05-09	ENSG00000075702	ENSG00000075702		"""WD repeat domain containing"""	24502	protein-coding gene	gene with protein product		613583	"""chromosome 19 open reading frame 14"", ""microcephaly, primary autosomal recessive 2"""	C19orf14, MCPH2		19910486, 20729831, 20890278, 21496009	Standard	NM_001083961		Approved	DKFZP434J046, FLJ33298	uc002odd.2	O43379	OTTHUMG00000048139	ENST00000270301.7:c.3659G>A	19.37:g.36594404G>A	ENSP00000270301:p.Arg1220His	133.0	0.0	0		119.0	56.0	0.470588	NM_001083961	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Missense_Mutation	SNP	ENST00000270301.7	37	CCDS33001.1	33	0.01510989010989011	31	0.06300813008130081	2	0.0055248618784530384	0	0.0	0	0.0	G	1.107	-0.659223	0.03454	0.071493	5.81E-4	ENSG00000075702	ENST00000401500;ENST00000270301	T;T	0.48201	0.91;0.82	4.93	-9.42	0.00610	.	1.133150	0.06589	N	0.751672	T	0.01558	0.0050	N	0.12182	0.205	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.002	T	0.13845	-1.0494	10	0.13853	T	0.58	1.1471	9.9297	0.41514	0.2448:0.0:0.6539:0.1013	rs61743589	1225;1220	O43379-4;O43379	.;WDR62_HUMAN	H	1225;1220	ENSP00000384792:R1225H;ENSP00000270301:R1220H	ENSP00000270301:R1220H	R	+	2	0	WDR62	41286244	0.000000	0.05858	0.026000	0.17262	0.275000	0.26752	-0.741000	0.04855	-2.003000	0.00962	-1.360000	0.01215	CGT	G|0.981;A|0.019	0.019	strong		0.652	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671	
SDF2	6388	hgsc.bcm.edu	37	17	26988852	26988852	+	Missense_Mutation	SNP	C	C	T	rs35404078	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:26988852C>T	ENST00000247020.4	-	1	341	c.43G>A	c.(43-45)Gct>Act	p.A15T	SUPT6H_ENST00000347486.4_5'Flank|SUPT6H_ENST00000314616.6_5'Flank|SDF2_ENST00000592250.1_Intron	NM_006923.3	NP_008854.2	Q99470	SDF2_HUMAN	stromal cell-derived factor 2	15			A -> T (in dbSNP:rs35404078).		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)					GCTCCCACAGCGCTCCACAAA	0.592													C|||	47	0.00938498	0.0325	0.0058	5008	,	,		17083	0.0		0.0	False		,,,				2504	0.0				p.A15T		Atlas-SNP	.											.	SDF2	17	.	0			c.G43A						PASS	.	C	THR/ALA	125,4281	92.5+/-131.2	1,123,2079	152.0	133.0	139.0		43	4.5	1.0	17	dbSNP_126	139	0,8600		0,0,4300	yes	missense	SDF2	NM_006923.2	58	1,123,6379	TT,TC,CC		0.0,2.837,0.9611	benign	15/212	26988852	125,12881	2203	4300	6503	SO:0001583	missense	6388	exon1			CCACAGCGCTCCA	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.43G>A	17.37:g.26988852C>T	ENSP00000247020:p.Ala15Thr	92.0	0.0	0		97.0	45.0	0.463918	NM_006923	Q9BQ79	Missense_Mutation	SNP	ENST00000247020.4	37	CCDS11238.1	12	0.005494505494505495	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	0	0.0	C	13.72	2.321744	0.41096	0.02837	0.0	ENSG00000132581	ENST00000247020	D	0.84516	-1.86	5.54	4.54	0.55810	.	0.694941	0.13447	N	0.387194	T	0.60064	0.2240	L	0.47716	1.5	0.24340	N	0.994965	B;B	0.26147	0.143;0.143	B;B	0.15484	0.013;0.013	T	0.57522	-0.7797	10	0.13853	T	0.58	-4.1998	15.2037	0.73159	0.0:0.8229:0.177:0.0	rs35404078	15;15	Q6IBU4;Q99470	.;SDF2_HUMAN	T	15	ENSP00000247020:A15T	ENSP00000247020:A15T	A	-	1	0	SDF2	24012979	0.517000	0.26226	0.998000	0.56505	0.367000	0.29736	1.004000	0.29822	2.598000	0.87819	0.561000	0.74099	GCT	C|0.990;T|0.010	0.010	strong		0.592	SDF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255965.2	NM_006923	
CA6	765	hgsc.bcm.edu	37	1	9009452	9009452	+	Silent	SNP	C	C	T	rs61746465	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:9009452C>T	ENST00000377443.2	+	2	214	c.210C>T	c.(208-210)ggC>ggT	p.G70G	CA6_ENST00000480186.3_Silent_p.G70G|CA6_ENST00000476083.1_Intron|CA6_ENST00000377442.2_Intron|CA6_ENST00000377436.3_Silent_p.G70G	NM_001215.3	NP_001206.2	P23280	CAH6_HUMAN	carbonic anhydrase VI	70			G -> A (in dbSNP:rs2274329).		bicarbonate transport (GO:0015701)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|prostate(1)|skin(5)	16	Ovarian(185;0.112)|all_lung(157;0.143)	all_epithelial(116;1.02e-19)|all_lung(118;3.6e-06)|Lung NSC(185;7.94e-06)|Renal(390;0.000147)|Breast(348;0.00123)|Colorectal(325;0.00205)|Hepatocellular(190;0.00825)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.9e-07)|COAD - Colon adenocarcinoma(227;8.28e-05)|Kidney(185;0.000268)|KIRC - Kidney renal clear cell carcinoma(229;0.000971)|STAD - Stomach adenocarcinoma(132;0.00184)|BRCA - Breast invasive adenocarcinoma(304;0.00192)|READ - Rectum adenocarcinoma(331;0.0649)	Mafenide(DB06795)|Zonisamide(DB00909)	ATATGACAGGCTATGAGACCC	0.607													C|||	61	0.0121805	0.0439	0.0029	5008	,	,		20134	0.0		0.001	False		,,,				2504	0.0				p.G70G		Atlas-SNP	.											.	CA6	47	.	0			c.C210T						PASS	.	C		149,4257	102.1+/-140.7	5,139,2059	59.0	48.0	52.0		210	4.4	0.9	1	dbSNP_129	52	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	CA6	NM_001215.2		5,141,6357	TT,TC,CC		0.0233,3.3818,1.161		70/309	9009452	151,12855	2203	4300	6503	SO:0001819	synonymous_variant	765	exon2			GACAGGCTATGAG	M57892	CCDS30578.1, CCDS57970.1, CCDS57971.1	1p36.2	2008-02-05			ENSG00000131686	ENSG00000131686	4.2.1.1	"""Carbonic anhydrases"""	1380	protein-coding gene	gene with protein product		114780				9691177	Standard	NM_001215		Approved		uc031plc.1	P23280	OTTHUMG00000001763	ENST00000377443.2:c.210C>T	1.37:g.9009452C>T		102.0	0.0	0		111.0	64.0	0.576577	NM_001270500	E7EMQ1|Q5FBW3|Q5FC00|Q96QX8|Q9UF03	Silent	SNP	ENST00000377443.2	37	CCDS30578.1																																																																																			C|0.988;T|0.012	0.012	strong		0.607	CA6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000004911.1		
DENND2D	79961	hgsc.bcm.edu	37	1	111738589	111738589	+	Silent	SNP	A	A	T	rs34558744	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:111738589A>T	ENST00000357640.4	-	6	823	c.594T>A	c.(592-594)gcT>gcA	p.A198A	DENND2D_ENST00000473682.1_5'UTR|DENND2D_ENST00000369752.5_Silent_p.A195A	NM_024901.3	NP_079177.2	Q9H6A0	DEN2D_HUMAN	DENN/MADD domain containing 2D	198	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of Rab GTPase activity (GO:0032851)	cytoplasm (GO:0005737)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(1)|kidney(7)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	25		all_cancers(81;0.00198)|all_epithelial(167;0.000686)|all_lung(203;0.00318)|Lung NSC(277;0.00499)		Lung(183;0.0162)|Colorectal(144;0.069)|all cancers(265;0.0757)|LUSC - Lung squamous cell carcinoma(189;0.0845)|Epithelial(280;0.114)|COAD - Colon adenocarcinoma(174;0.14)		TCTTCCCAGGAGCAGGGAAGG	0.557													A|||	56	0.0111821	0.0401	0.0043	5008	,	,		18465	0.0		0.0	False		,,,				2504	0.0				p.A198A		Atlas-SNP	.											.	DENND2D	50	.	0			c.T594A						PASS	.	A		190,4216	121.7+/-159.2	6,178,2019	106.0	100.0	102.0		594	-0.2	1.0	1	dbSNP_126	102	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DENND2D	NM_024901.3		6,179,6318	TT,TA,AA		0.0116,4.3123,1.4686		198/472	111738589	191,12815	2203	4300	6503	SO:0001819	synonymous_variant	79961	exon6			CCCAGGAGCAGGG		CCDS831.1, CCDS60219.1	1p13.3	2014-02-12	2005-08-17		ENSG00000162777	ENSG00000162777		"""DENN/MADD domain containing"""	26192	protein-coding gene	gene with protein product		615111				12477932	Standard	NM_024901		Approved	FLJ22457, RP5-1180E21.2	uc001eal.2	Q9H6A0	OTTHUMG00000012356	ENST00000357640.4:c.594T>A	1.37:g.111738589A>T		49.0	0.0	0		70.0	33.0	0.471429	NM_024901	Q5T5V6|Q9BSU0	Silent	SNP	ENST00000357640.4	37	CCDS831.1																																																																																			A|0.988;T|0.012	0.012	strong		0.557	DENND2D-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000034456.1	NM_024901	
FAM135A	57579	hgsc.bcm.edu	37	6	71245978	71245978	+	Silent	SNP	G	G	A	rs9446260	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:71245978G>A	ENST00000418814.2	+	19	4595	c.3981G>A	c.(3979-3981)tcG>tcA	p.S1327S	FAM135A_ENST00000457062.2_Silent_p.S1114S|FAM135A_ENST00000505868.1_Silent_p.S1327S|FAM135A_ENST00000370479.3_Silent_p.S1114S|FAM135A_ENST00000505769.1_Silent_p.S907S|FAM135A_ENST00000361499.3_Silent_p.S1131S	NM_001105531.2|NM_001162529.1	NP_001099001.1|NP_001156001.1	Q9P2D6	F135A_HUMAN	family with sequence similarity 135, member A	1327										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						TTGGACATTCGTTGGGCAATT	0.333													G|||	128	0.0255591	0.0923	0.0058	5008	,	,		16102	0.0		0.002	False		,,,				2504	0.0				p.S1327S		Atlas-SNP	.											.	FAM135A	181	.	0			c.G3981A						PASS	.	G	,,	389,4015	196.4+/-220.7	12,365,1825	112.0	115.0	114.0		3393,3981,3342	-11.0	0.2	6	dbSNP_119	114	4,8594	3.7+/-12.6	0,4,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	FAM135A	NM_001105531.2,NM_001162529.1,NM_020819.4	,,	12,369,6120	AA,AG,GG		0.0465,8.8329,3.0226	,,	1131/1320,1327/1516,1114/1303	71245978	393,12609	2202	4299	6501	SO:0001819	synonymous_variant	57579	exon17			ACATTCGTTGGGC	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.3981G>A	6.37:g.71245978G>A		80.0	0.0	0		82.0	39.0	0.47561	NM_001162529	A2RRQ5|Q3C0H3|Q5JXK0|Q5JXK1|Q68DW0|Q6P081|Q9H0F2|Q9NU48|Q9NUQ5|Q9NXL5	Silent	SNP	ENST00000418814.2	37	CCDS55028.1																																																																																			G|0.972;A|0.028	0.028	strong		0.333	FAM135A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000041137.2	NM_020819	
SLC6A5	9152	hgsc.bcm.edu	37	11	20652291	20652291	+	Silent	SNP	C	C	T	rs143680068		TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:20652291C>T	ENST00000525748.1	+	10	1827	c.1554C>T	c.(1552-1554)ttC>ttT	p.F518F	SLC6A5_ENST00000528440.1_3'UTR	NM_004211.3	NP_004202.2	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 5	518					glycine import (GO:0036233)|synaptic transmission (GO:0007268)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(34)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	63					Glycine(DB00145)	TTGCCGGCTTCGTCATCTTCT	0.493													C|||	1	0.000199681	0.0008	0.0	5008	,	,		23670	0.0		0.0	False		,,,				2504	0.0				p.F518F		Atlas-SNP	.											.	SLC6A5	151	.	0			c.C1554T						PASS	.	C		9,4397	15.5+/-35.6	0,9,2194	204.0	173.0	183.0		1554	-9.9	0.5	11	dbSNP_134	183	0,8600		0,0,4300	no	coding-synonymous	SLC6A5	NM_004211.3		0,9,6494	TT,TC,CC		0.0,0.2043,0.0692		518/798	20652291	9,12997	2203	4300	6503	SO:0001819	synonymous_variant	9152	exon10			CGGCTTCGTCATC	AF085412	CCDS7854.1	11p15.1	2013-07-19	2013-07-19		ENSG00000165970	ENSG00000165970		"""Solute carriers"""	11051	protein-coding gene	gene with protein product	"""glycine transporter 2"""	604159	"""solute carrier family 6 (neurotransmitter transporter, glycine), member 5"""	NET1		9845349	Standard	NM_004211		Approved	GLYT2	uc001mqd.3	Q9Y345	OTTHUMG00000166024	ENST00000525748.1:c.1554C>T	11.37:g.20652291C>T		316.0	1.0	0.00316456		298.0	138.0	0.463087	NM_004211	O95288|Q4VAM7|Q9BX77	Silent	SNP	ENST00000525748.1	37	CCDS7854.1																																																																																			C|1.000;T|0.000	0.000	strong		0.493	SLC6A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387497.2	NM_004211	
KIAA1279	26128	hgsc.bcm.edu	37	10	70775329	70775329	+	Silent	SNP	G	G	A	rs16926021	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:70775329G>A	ENST00000361983.4	+	7	1125	c.1023G>A	c.(1021-1023)caG>caA	p.Q341Q		NM_015634.3	NP_056449.1	Q96EK5	KBP_HUMAN	KIAA1279	341					cell differentiation (GO:0030154)|mitochondrial transport (GO:0006839)|nervous system development (GO:0007399)	cytoskeleton (GO:0005856)|mitochondrion (GO:0005739)	kinesin binding (GO:0019894)			breast(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|skin(1)	14						TTGATAAACAGTCTGAACTTA	0.373													G|||	306	0.0611022	0.2148	0.0303	5008	,	,		18364	0.0		0.001	False		,,,				2504	0.0				p.Q341Q		Atlas-SNP	.											.	KIAA1279	35	.	0			c.G1023A						PASS	.	G		817,3589	310.2+/-291.5	78,661,1464	78.0	82.0	80.0		1023	-2.0	0.9	10	dbSNP_123	80	11,8589	5.7+/-21.5	0,11,4289	no	coding-synonymous	KIAA1279	NM_015634.3		78,672,5753	AA,AG,GG		0.1279,18.5429,6.3663		341/622	70775329	828,12178	2203	4300	6503	SO:0001819	synonymous_variant	26128	exon7			TAAACAGTCTGAA	BC012180	CCDS7284.1	10q22.1	2008-02-05			ENSG00000198954	ENSG00000198954			23419	protein-coding gene	gene with protein product		609367					Standard	NM_015634		Approved	DKFZP586B0923, TTC20	uc001joy.3	Q96EK5	OTTHUMG00000018363	ENST00000361983.4:c.1023G>A	10.37:g.70775329G>A		53.0	0.0	0		52.0	24.0	0.461538	NM_015634	A8K5M8|Q9BR89|Q9ULE1|Q9Y428	Silent	SNP	ENST00000361983.4	37	CCDS7284.1																																																																																			G|0.946;A|0.054	0.054	strong		0.373	KIAA1279-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048370.1	NM_015634	
PLA2G4B	100137049	hgsc.bcm.edu	37	15	42139875	42139875	+	Silent	SNP	A	A	G	rs34424865	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:42139875A>G	ENST00000452633.1	+	21	2515	c.2163A>G	c.(2161-2163)gcA>gcG	p.A721A	PLA2G4B_ENST00000542534.2_Silent_p.A952A|PLA2G4B_ENST00000458483.1_Silent_p.A721A|JMJD7-PLA2G4B_ENST00000382448.4_Silent_p.A952A|JMJD7-PLA2G4B_ENST00000342159.4_Missense_Mutation_p.Q890R			P0C869	PA24B_HUMAN	phospholipase A2, group IVB (cytosolic)	721	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|arachidonic acid metabolic process (GO:0019369)|calcium-mediated signaling (GO:0019722)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|glycerophospholipid biosynthetic process (GO:0046474)|glycerophospholipid catabolic process (GO:0046475)|inflammatory response (GO:0006954)|parturition (GO:0007567)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)						all_cancers(109;1.84e-13)|all_epithelial(112;5.15e-12)|Lung NSC(122;3.74e-08)|all_lung(180;1.81e-07)|Melanoma(134;0.0262)		all cancers(2;1.08e-30)|Epithelial(2;1.43e-22)|OV - Ovarian serous cystadenocarcinoma(18;1.13e-17)|GBM - Glioblastoma multiforme(94;9.77e-07)|Colorectal(2;0.0129)|COAD - Colon adenocarcinoma(120;0.0371)		AGGAGGCGGCAGCTGGGGAGG	0.617													a|||	78	0.0155751	0.0567	0.0029	5008	,	,		17421	0.0		0.001	False		,,,				2504	0.0				p.Q890R		Atlas-SNP	.											.	JMJD7-PLA2G4B	90	.	0			c.A2669G						PASS	.	A	,ARG/GLN,	196,4210		8,180,2015	74.0	66.0	69.0		2163,2669,2856	-9.6	0.0	15	dbSNP_126	69	3,8597		0,3,4297	yes	coding-synonymous,missense,coding-synonymous	JMJD7-PLA2G4B,PLA2G4B	NM_001114633.1,NM_001198588.1,NM_005090.3	,43,	8,183,6312	GG,GA,AA		0.0349,4.4485,1.5301	,,	721/782,890/894,952/1013	42139875	199,12807	2203	4300	6503	SO:0001819	synonymous_variant	8681	exon24			GGCGGCAGCTGGG	AF065215	CCDS45241.1	15q11.2-q21.3	2010-08-17			ENSG00000243708	ENSG00000243708	3.1.1.4		9036	protein-coding gene	gene with protein product		606088				9705332	Standard	NM_001114633		Approved	cPLA2-beta, HsT16992		P0C869	OTTHUMG00000156809	ENST00000452633.1:c.2163A>G	15.37:g.42139875A>G		92.0	0.0	0		91.0	49.0	0.538462	NM_001198588	B4DRT9|O95712|Q19KD5|Q19KD6|Q59GF9|Q8TB10|Q9UKV7	Missense_Mutation	SNP	ENST00000452633.1	37	CCDS45241.1	26	0.011904761904761904	24	0.04878048780487805	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	.	5.025	0.190237	0.09547	0.044485	3.49E-4	ENSG00000168970	ENST00000342159	T	0.01484	4.84	4.77	-9.55	0.00569	.	.	.	.	.	T	0.00241	0.0007	.	.	.	0.09310	N	0.999995	B	0.02656	0.0	B	0.01281	0.0	T	0.47249	-0.9132	8	0.87932	D	0	-0.1604	2.4723	0.04567	0.2543:0.1668:0.4127:0.1662	rs34424865	890	P0C869-7	.	R	890	ENSP00000342785:Q890R	ENSP00000342785:Q890R	Q	+	2	0	JMJD7-PLA2G4B	39927167	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-4.099000	0.00295	-2.603000	0.00450	-2.852000	0.00102	CAG	A|0.984;G|0.016	0.016	strong		0.617	PLA2G4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000345969.1	NM_001114633	
FAT1	2195	hgsc.bcm.edu	37	4	187542356	187542356	+	Missense_Mutation	SNP	C	C	T	rs56790426	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:187542356C>T	ENST00000441802.2	-	10	5593	c.5384G>A	c.(5383-5385)cGa>cAa	p.R1795Q		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1795	Cadherin 16. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						ATCAGCTGCTCGAATCACCAG	0.423										HNSCC(5;0.00058)			C|||	44	0.00878594	0.0325	0.0014	5008	,	,		22564	0.0		0.0	False		,,,				2504	0.0				p.R1795Q	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.G5384A						PASS	.	C	GLN/ARG	81,3883		1,79,1902	89.0	85.0	87.0		5384	4.7	1.0	4	dbSNP_129	87	1,8327		0,1,4163	yes	missense	FAT1	NM_005245.3	43	1,80,6065	TT,TC,CC		0.012,2.0434,0.6671	benign	1795/4589	187542356	82,12210	1982	4164	6146	SO:0001583	missense	2195	exon10			GCTGCTCGAATCA	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.5384G>A	4.37:g.187542356C>T	ENSP00000406229:p.Arg1795Gln	139.0	0.0	0		150.0	71.0	0.473333	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	C	8.328	0.825754	0.16749	0.020434	1.2E-4	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.01725	4.67	5.5	4.66	0.58398	Cadherin (4);Cadherin-like (1);	0.122272	0.56097	D	0.000036	T	0.00815	0.0027	N	0.25825	0.765	0.53005	D	0.999965	B	0.25007	0.116	B	0.23018	0.043	T	0.62586	-0.6823	10	0.21014	T	0.42	.	11.7859	0.52043	0.0:0.8082:0.1241:0.0676	rs56790426	1795	Q14517	FAT1_HUMAN	Q	1795;1797	ENSP00000406229:R1795Q	ENSP00000260147:R1797Q	R	-	2	0	FAT1	187779350	1.000000	0.71417	1.000000	0.80357	0.050000	0.14768	2.438000	0.44837	1.556000	0.49512	-0.150000	0.13652	CGA	C|0.993;T|0.007	0.007	strong		0.423	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
OR14I1	401994	hgsc.bcm.edu	37	1	248844695	248844695	+	Missense_Mutation	SNP	A	A	T	rs114135727	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:248844695A>T	ENST00000342623.3	-	1	934	c.911T>A	c.(910-912)gTg>gAg	p.V304E		NM_001004734.1	NP_001004734.1	A6ND48	O14I1_HUMAN	olfactory receptor, family 14, subfamily I, member 1	304						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(4)|large_intestine(2)|lung(24)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	35						ATATATCTTCACAAAGAGTCT	0.353													A|||	95	0.0189696	0.0703	0.0029	5008	,	,		17508	0.0		0.0	False		,,,				2504	0.0				p.V304E		Atlas-SNP	.											.	OR14I1	64	.	0			c.T911A						PASS	.	A	GLU/VAL	283,4123		10,263,1930	51.0	54.0	53.0		911	-2.2	0.0	1	dbSNP_132	53	0,8600		0,0,4300	yes	missense	OR14I1	NM_001004734.1	121	10,263,6230	TT,TA,AA		0.0,6.4231,2.1759	benign	304/312	248844695	283,12723	2203	4300	6503	SO:0001583	missense	401994	exon1			ATCTTCACAAAGA		CCDS31125.1	1q44	2012-08-09	2008-04-02	2008-04-02	ENSG00000189181	ENSG00000189181		"""GPCR / Class A : Olfactory receptors"""	19575	protein-coding gene	gene with protein product			"""olfactory receptor, family 5, subfamily BU, member 1"""	OR5BU1P, OR5BU1			Standard	NM_001004734		Approved		uc001ieu.1	A6ND48	OTTHUMG00000040378	ENST00000342623.3:c.911T>A	1.37:g.248844695A>T	ENSP00000339726:p.Val304Glu	43.0	0.0	0		51.0	24.0	0.470588	NM_001004734		Missense_Mutation	SNP	ENST00000342623.3	37	CCDS31125.1	39	0.017857142857142856	39	0.07926829268292683	0	0.0	0	0.0	0	0.0	.	0.008	-1.879400	0.00537	0.064231	0.0	ENSG00000189181	ENST00000342623	T	0.37235	1.21	2.84	-2.22	0.06952	.	2.383690	0.01770	N	0.031135	T	0.00637	0.0021	N	0.04373	-0.215	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.11084	-1.0602	10	0.06236	T	0.91	.	0.9342	0.01341	0.3966:0.2734:0.1869:0.1431	.	304	A6ND48	O14I1_HUMAN	E	304	ENSP00000339726:V304E	ENSP00000339726:V304E	V	-	2	0	OR14I1	246911318	0.000000	0.05858	0.001000	0.08648	0.006000	0.05464	-1.457000	0.02374	-0.041000	0.13558	-0.505000	0.04504	GTG	A|0.982;T|0.018	0.018	strong		0.353	OR14I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097128.1	NM_001004734	
BLOC1S2	282991	hgsc.bcm.edu	37	10	102046402	102046402	+	Silent	SNP	G	G	C	rs12250221	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr10:102046402G>C	ENST00000370372.2	-	1	67	c.15C>G	c.(13-15)gcC>gcG	p.A5A	BLOC1S2_ENST00000361832.2_5'UTR|BLOC1S2_ENST00000441611.1_5'Flank	NM_173809.4	NP_776170.2	Q6QNY1	BL1S2_HUMAN	biogenesis of lysosomal organelles complex-1, subunit 2	5					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|melanosome organization (GO:0032438)|microtubule nucleation (GO:0007020)|mitochondrial outer membrane permeabilization (GO:0097345)|neuron projection development (GO:0031175)|platelet dense granule organization (GO:0060155)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)	BLOC-1 complex (GO:0031083)|centrosome (GO:0005813)|gamma-tubulin complex (GO:0000930)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|recycling endosome (GO:0055037)	gamma-tubulin binding (GO:0043015)|protein C-terminus binding (GO:0008022)			large_intestine(1)|lung(2)|ovary(1)	4		Colorectal(252;0.117)		Epithelial(162;2.44e-10)|all cancers(201;1.97e-08)		GTACGCCCTCGGCTGCCGCCG	0.751													-|||	293	0.0585064	0.2148	0.0115	5008	,	,		12869	0.0		0.001	False		,,,				2504	0.0				p.A5A		Atlas-SNP	.											.	BLOC1S2	10	.	0			c.C15G						PASS	.			564,3608		30,504,1552	8.0	12.0	11.0		15	-6.3	0.1	10	dbSNP_120	11	10,8242		0,10,4116	no	coding-synonymous	BLOC1S2	NM_173809.2		30,514,5668	CC,CG,GG		0.1212,13.5187,4.6201		5/143	102046402	574,11850	2086	4126	6212	SO:0001819	synonymous_variant	282991	exon1			GCCCTCGGCTGCC	AK054697	CCDS7490.1, CCDS73179.1	10q24.31	2012-08-01	2008-08-11		ENSG00000196072	ENSG00000196072		"""Biogenesis of lysosomal organelles complex-1 subunits"""	20984	protein-coding gene	gene with protein product	"""centrosome protein oncogene"", ""Biogenesis of Lysosome-related Organelles complex-1 Subunit 2"", ""BLOC-1 subunit 2"""	609768				11483580, 15102850	Standard	NM_173809		Approved	MGC10120, FLJ30135, BLOS2	uc001kqw.2	Q6QNY1	OTTHUMG00000018908	ENST00000370372.2:c.15C>G	10.37:g.102046402G>C		75.0	0.0	0		53.0	22.0	0.415094	NM_173809	B4DQV2|Q5W040|Q8WUI8	Silent	SNP	ENST00000370372.2	37	CCDS7490.1																																																																																			G|0.949;C|0.051	0.051	strong		0.751	BLOC1S2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049861.2	NM_173809	
HSD17B4	3295	hgsc.bcm.edu	37	5	118877677	118877677	+	Silent	SNP	C	C	T	rs12714	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:118877677C>T	ENST00000256216.6	+	24	2332	c.2199C>T	c.(2197-2199)taC>taT	p.Y733Y	HSD17B4_ENST00000509514.1_Silent_p.Y471Y|HSD17B4_ENST00000414835.2_Silent_p.Y593Y|HSD17B4_ENST00000504811.1_Silent_p.Y758Y|HSD17B4_ENST00000510025.1_Silent_p.Y709Y|HSD17B4_ENST00000515320.1_Silent_p.Y715Y|HSD17B4_ENST00000513628.1_Silent_p.Y596Y|HSD17B4_ENST00000522415.1_3'UTR	NM_000414.3	NP_000405.1	P51659	DHB4_HUMAN	hydroxysteroid (17-beta) dehydrogenase 4	733	SCP2.				alpha-linolenic acid metabolic process (GO:0036109)|androgen metabolic process (GO:0008209)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|estrogen metabolic process (GO:0008210)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|medium-chain fatty-acyl-CoA metabolic process (GO:0036112)|metabolic process (GO:0008152)|osteoblast differentiation (GO:0001649)|oxidation-reduction process (GO:0055114)|Sertoli cell development (GO:0060009)|small molecule metabolic process (GO:0044281)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid metabolic process (GO:0000038)|very long-chain fatty-acyl-CoA metabolic process (GO:0036111)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	17-beta-hydroxysteroid dehydrogenase (NAD+) activity (GO:0044594)|3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity (GO:0033989)|isomerase activity (GO:0016853)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|pancreas(1)|prostate(2)|urinary_tract(2)	25		all_cancers(142;0.0206)|Prostate(80;0.0322)		OV - Ovarian serous cystadenocarcinoma(64;0.000247)|Epithelial(69;0.000849)|all cancers(49;0.0122)		TTAAAGACTACGCCAAGCTCT	0.408													T|||	249	0.0497204	0.146	0.0072	5008	,	,		15192	0.001		0.001	False		,,,				2504	0.0501				p.Y758Y	Colon(35;490 801 34689 41394 43344)	Atlas-SNP	.											.	HSD17B4	63	.	0			c.C2274T						PASS	.	T	,,	492,3912	780.4+/-414.4	32,428,1742	58.0	58.0	58.0		2199,2274,2145	-10.0	0.2	5	dbSNP_52	58	16,8584	818.4+/-406.9	0,16,4284	no	coding-synonymous,coding-synonymous,coding-synonymous	HSD17B4	NM_000414.3,NM_001199291.1,NM_001199292.1	,,	32,444,6026	TT,TC,CC		0.186,11.1717,3.9065	,,	733/737,758/762,715/719	118877677	508,12496	2202	4300	6502	SO:0001819	synonymous_variant	3295	exon25			AGACTACGCCAAG		CCDS4126.1, CCDS56378.1, CCDS56379.1	5q2	2011-09-20			ENSG00000133835	ENSG00000133835	4.2.1.107, 1.1.1.35	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 3"""	5213	protein-coding gene	gene with protein product	"""17beta-estradiol dehydrogenase type IV"", ""peroxisomal multifunctional protein 2"", ""17-beta-HSD IV"", ""17-beta-hydroxysteroid dehydrogenase 4"", ""D-bifunctional protein, peroxisomal"", ""D-3-hydroxyacyl-CoA dehydratase"", ""3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholest-24-enoyl-CoA hydratase"", ""beta-keto-reductase"", ""beta-hydroxyacyl dehydrogenase"", ""short chain dehydrogenase/reductase family 8C, member 1"""	601860				8938456, 19027726	Standard	NM_000414		Approved	MFE-2, DBP, SDR8C1	uc003ksj.3	P51659	OTTHUMG00000128899	ENST00000256216.6:c.2199C>T	5.37:g.118877677C>T		193.0	0.0	0		154.0	79.0	0.512987	NM_001199291	B4DNV1|B4DVS5|E9PB82|F5HE57	Silent	SNP	ENST00000256216.6	37	CCDS4126.1																																																																																			C|0.960;T|0.040	0.040	strong		0.408	HSD17B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250863.3	NM_000414	
PRR27	401137	hgsc.bcm.edu	37	4	71024268	71024268	+	Missense_Mutation	SNP	A	A	G	rs116632053	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:71024268A>G	ENST00000344526.5	+	3	488	c.299A>G	c.(298-300)aAt>aGt	p.N100S	C4orf40_ENST00000502441.2_Intron|C4orf40_ENST00000502294.1_Missense_Mutation_p.N100S	NM_214711.3	NP_999876.2	Q6MZM9	PRR27_HUMAN		100	Ala/Pro-rich.					extracellular vesicular exosome (GO:0070062)				breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						ACTCAGTTGAATGTTCCTCCT	0.512													A|||	48	0.00958466	0.0348	0.0029	5008	,	,		20664	0.0		0.0	False		,,,				2504	0.0				p.N100S		Atlas-SNP	.											.	C4orf40	19	.	0			c.A299G						PASS	.	A	SER/ASN	178,4228	115.4+/-153.4	1,176,2026	264.0	254.0	257.0		299	-7.7	0.0	4	dbSNP_132	257	1,8599	1.2+/-3.3	0,1,4299	yes	missense	C4orf40	NM_214711.3	46	1,177,6325	GG,GA,AA		0.0116,4.0399,1.3763	benign	100/220	71024268	179,12827	2203	4300	6503	SO:0001583	missense	401137	exon3			AGTTGAATGTTCC																												ENST00000344526.5:c.299A>G	4.37:g.71024268A>G	ENSP00000343172:p.Asn100Ser	209.0	0.0	0		213.0	100.0	0.469484	NM_214711	A8MXP0|Q6MZR6	Missense_Mutation	SNP	ENST00000344526.5	37	CCDS3535.1	11	0.005036630036630037	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	0	0.0	A	10.53	1.375740	0.24857	0.040399	1.16E-4	ENSG00000187533	ENST00000502294;ENST00000344526	T;T	0.34859	1.34;1.34	3.84	-7.67	0.01272	.	.	.	.	.	T	0.02767	0.0083	N	0.14661	0.345	0.09310	N	1	B	0.14438	0.01	B	0.13407	0.009	T	0.17992	-1.0351	9	0.13853	T	0.58	0.3329	1.6043	0.02681	0.3253:0.1509:0.0919:0.4319	.	100	Q6MZM9	CD040_HUMAN	S	100	ENSP00000426249:N100S;ENSP00000343172:N100S	ENSP00000343172:N100S	N	+	2	0	C4orf40	71058857	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-2.709000	0.00819	-2.592000	0.00456	-0.842000	0.03052	AAT	A|0.986;G|0.014	0.014	strong		0.512	C4orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251558.1		
SLC8A3	6547	hgsc.bcm.edu	37	14	70512964	70512964	+	Silent	SNP	G	G	A	rs144234198	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:70512964G>A	ENST00000381269.2	-	8	3237	c.2484C>T	c.(2482-2484)aaC>aaT	p.N828N	SLC8A3_ENST00000528359.1_Silent_p.N826N|SLC8A3_ENST00000533541.1_3'UTR|SLC8A3_ENST00000394330.2_Silent_p.N185N|SLC8A3_ENST00000216568.7_Silent_p.N199N|SLC8A3_ENST00000356921.2_Silent_p.N822N|SLC8A3_ENST00000534137.1_Silent_p.N825N|SLC8A3_ENST00000357887.3_Silent_p.N826N	NM_058240.2|NM_183002.1	NP_489479.1|NP_892114.1	P57103	NAC3_HUMAN	solute carrier family 8 (sodium/calcium exchanger), member 3	828					blood coagulation (GO:0007596)|calcium ion export from cell (GO:1990034)|calcium ion import into cell (GO:1990035)|calcium ion transport into cytosol (GO:0060402)|cell communication (GO:0007154)|cellular response to cAMP (GO:0071320)|hematopoietic progenitor cell differentiation (GO:0002244)|ion transport (GO:0006811)|telencephalon development (GO:0021537)|transmembrane transport (GO:0055085)	dendritic spine (GO:0043197)|integral component of membrane (GO:0016021)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)	calcium:sodium antiporter activity (GO:0005432)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(12)|lung(18)|ovary(2)|pancreas(2)|prostate(3)|skin(6)	54				BRCA - Breast invasive adenocarcinoma(234;0.0079)|all cancers(60;0.0102)|OV - Ovarian serous cystadenocarcinoma(108;0.0555)		CATTGACGGCGTTGCTGCCCG	0.602											OREG0022773	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.N828N		Atlas-SNP	.											SLC8A3_ENST00000357887,colon,carcinoma,0,2	SLC8A3	234	2	0			c.C2484T						PASS	.	G	,,,,,	1,4405	2.1+/-5.4	0,1,2202	49.0	43.0	45.0		597,2478,2475,2466,555,2484	-3.9	0.9	14	dbSNP_134	45	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SLC8A3	NM_001130417.1,NM_033262.3,NM_058240.2,NM_182932.1,NM_182936.1,NM_183002.1	,,,,,	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	,,,,,	199/299,826/926,825/925,822/922,185/285,828/928	70512964	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	6547	exon8			GACGGCGTTGCTG	AJ304852	CCDS9799.1, CCDS9800.1, CCDS35498.1, CCDS41967.1, CCDS45131.1, CCDS53904.1	14q24.1	2013-05-22	2008-09-02		ENSG00000100678	ENSG00000100678		"""Solute carriers"""	11070	protein-coding gene	gene with protein product		607991				8798769	Standard	XM_005268017		Approved	NCX3	uc001xly.3	P57103	OTTHUMG00000152342	ENST00000381269.2:c.2484C>T	14.37:g.70512964G>A		94.0	0.0	0	1122	148.0	71.0	0.47973	NM_183002	Q5K3P6|Q5K3P7|Q8IUE9|Q8IUF0|Q8NFI7|Q96QG1|Q96QG2	Silent	SNP	ENST00000381269.2	37	CCDS35498.1																																																																																			G|1.000;A|0.000	0.000	strong		0.602	SLC8A3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390736.1		
TTN	7273	hgsc.bcm.edu	37	2	179552895	179552895	+	Missense_Mutation	SNP	C	C	T	rs72650028	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:179552895C>T	ENST00000591111.1	-	125	31527	c.31303G>A	c.(31303-31305)Gtt>Att	p.V10435I	TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.V9508I|TTN-AS1_ENST00000589487.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000589830.1_RNA|TTN-AS1_ENST00000431752.1_RNA|TTN_ENST00000460472.2_Intron|TTN_ENST00000589042.1_Missense_Mutation_p.V10752I			Q8WZ42	TITIN_HUMAN	titin	0	Glu-rich.|Pro-rich.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TCTCTATAAACTGAAATGGAC	0.393													C|||	66	0.0131789	0.0477	0.0043	5008	,	,		19860	0.0		0.0	False		,,,				2504	0.0				p.V10752I		Atlas-SNP	.											.	TTN	18412	.	0			c.G32254A						PASS	.	C	ILE/VAL,,,	126,3626		1,124,1751	168.0	169.0	168.0		28522,,,	4.9	1.0	2	dbSNP_130	168	2,8194		0,2,4096	yes	missense,intron,intron,intron	TTN	NM_133378.4,NM_003319.4,NM_133432.3,NM_133437.3	29,,,	1,126,5847	TT,TC,CC		0.0244,3.3582,1.0713	possibly-damaging,,,	9508/33424,,,	179552895	128,11820	1876	4098	5974	SO:0001583	missense	7273	exon127			TATAAACTGAAAT	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.31303G>A	2.37:g.179552895C>T	ENSP00000465570:p.Val10435Ile	157.0	0.0	0		147.0	78.0	0.530612	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		22	0.010073260073260074	20	0.04065040650406504	2	0.0055248618784530384	0	0.0	0	0.0	C	14.87	2.665728	0.47677	0.033582	2.44E-4	ENSG00000155657	ENST00000342992	T	0.71222	-0.55	4.94	4.94	0.65067	Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.47985	0.1475	L	0.49778	1.585	0.80722	D	1	P	0.44690	0.841	P	0.55824	0.785	T	0.69355	-0.5167	9	0.87932	D	0	.	14.0185	0.64539	0.0:1.0:0.0:0.0	.	10435	Q8WZ42	TITIN_HUMAN	I	9508	ENSP00000343764:V9508I	ENSP00000343764:V9508I	V	-	1	0	TTN	179261140	0.996000	0.38824	1.000000	0.80357	0.951000	0.60555	2.506000	0.45433	2.460000	0.83146	0.467000	0.42956	GTT	C|0.991;T|0.009	0.009	strong		0.393	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
SHCBP1L	81626	hgsc.bcm.edu	37	1	182922003	182922003	+	Missense_Mutation	SNP	G	G	T	rs13373887	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:182922003G>T	ENST00000367547.3	-	1	502	c.266C>A	c.(265-267)gCg>gAg	p.A89E	SHCBP1L_ENST00000423786.1_5'Flank|SHCBP1L_ENST00000488956.1_5'UTR	NM_030933.2	NP_112195.2	Q9BZQ2	SHP1L_HUMAN	SHC SH2-domain binding protein 1-like	161										breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|pancreas(1)|prostate(1)|skin(2)	15						GGGCTCCTccgccgccgccgc	0.741													T|||	190	0.0379393	0.1293	0.0159	5008	,	,		11211	0.0		0.005	False		,,,				2504	0.0031				p.A89E		Atlas-SNP	.											.	SHCBP1L	64	.	0			c.C266A						PASS	.	T	GLU/ALA	443,3869		18,407,1731	6.0	7.0	7.0		266	0.0	0.0	1	dbSNP_121	7	23,8443		0,23,4210	yes	missense	SHCBP1L	NM_030933.2	107	18,430,5941	TT,TG,GG		0.2717,10.2737,3.6469	benign	89/654	182922003	466,12312	2156	4233	6389	SO:0001583	missense	81626	exon1			TCCTCCGCCGCCG	AF288397	CCDS30955.1	1q25	2011-01-24	2011-01-24	2011-01-24	ENSG00000157060	ENSG00000157060			16788	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 14"""	C1orf14		11318611	Standard	NM_030933		Approved		uc001gpu.3	Q9BZQ2	OTTHUMG00000035419	ENST00000367547.3:c.266C>A	1.37:g.182922003G>T	ENSP00000356518:p.Ala89Glu	33.0	0.0	0		37.0	28.0	0.756757	NM_030933	Q4G195|Q9BZQ3|Q9H2B6	Missense_Mutation	SNP	ENST00000367547.3	37	CCDS30955.1	66	0.03021978021978022	60	0.12195121951219512	5	0.013812154696132596	0	0.0	1	0.0013192612137203166	T	0.005	-2.169349	0.00315	0.102737	0.002717	ENSG00000157060	ENST00000367547;ENST00000287709	T	0.39229	1.09	3.96	0.04	0.14207	.	1.066270	0.07492	N	0.905864	T	0.00178	0.0005	N	0.01874	-0.695	0.21499	N	0.999663	B	0.02656	0.0	B	0.04013	0.001	T	0.09930	-1.0652	10	0.02654	T	1	.	4.0773	0.09911	0.0:0.2058:0.3591:0.4351	rs13373887	89	Q9BZQ2-3	.	E	89;158	ENSP00000356518:A89E	ENSP00000287709:A158E	A	-	2	0	SHCBP1L	181188626	.	.	0.003000	0.11579	0.009000	0.06853	.	.	-0.560000	0.06102	-0.865000	0.03005	GCG	G|0.965;T|0.035	0.035	strong		0.741	SHCBP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085956.1	NM_030933	
GMFG	9535	hgsc.bcm.edu	37	19	39826131	39826131	+	Missense_Mutation	SNP	G	G	T	rs1801733	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:39826131G>T	ENST00000597595.1	-	2	252	c.44C>A	c.(43-45)aCa>aAa	p.T15K	GMFG_ENST00000595636.1_Missense_Mutation_p.T15K|GMFG_ENST00000600322.1_5'UTR|GMFG_ENST00000253054.8_5'UTR|GMFG_ENST00000594700.1_Missense_Mutation_p.T15K|GMFG_ENST00000598034.1_Missense_Mutation_p.T15K|GMFG_ENST00000601387.1_Intron|GMFG_ENST00000602185.1_Intron	NM_004877.2	NP_004868.1	O60234	GMFG_HUMAN	glia maturation factor, gamma	15	ADF-H. {ECO:0000255|PROSITE- ProRule:PRU00599}.				negative regulation of protein kinase activity (GO:0006469)|positive regulation of catalytic activity (GO:0043085)|protein phosphorylation (GO:0006468)	intracellular (GO:0005622)	enzyme activator activity (GO:0008047)|protein kinase inhibitor activity (GO:0004860)			breast(1)|large_intestine(2)|liver(2)|lung(3)|skin(1)|stomach(1)	10	all_cancers(60;2.5e-07)|all_lung(34;4.03e-08)|Lung NSC(34;4.66e-08)|all_epithelial(25;6.4e-07)|Ovarian(47;0.0512)		Epithelial(26;1.15e-27)|all cancers(26;1.3e-24)|Lung(45;0.000278)|LUSC - Lung squamous cell carcinoma(53;0.000335)			CAGCTTTTCTGTTAGCTCTGG	0.572													G|||	79	0.0157748	0.056	0.0072	5008	,	,		17456	0.0		0.0	False		,,,				2504	0.0				p.T15K		Atlas-SNP	.											.	GMFG	16	.	0			c.C44A						PASS	.	G	LYS/THR	212,4194	127.0+/-164.0	8,196,1999	149.0	116.0	127.0		44	2.1	1.0	19	dbSNP_89	127	13,8587	9.8+/-36.6	0,13,4287	yes	missense	GMFG	NM_004877.2	78	8,209,6286	TT,TG,GG		0.1512,4.8116,1.73	benign	15/143	39826131	225,12781	2203	4300	6503	SO:0001583	missense	9535	exon2			TTTTCTGTTAGCT	AB001993	CCDS12532.1, CCDS74364.1	19q13.2	2014-08-12			ENSG00000130755	ENSG00000130755			4374	protein-coding gene	gene with protein product		604104				9545571, 9653160, 17127212	Standard	XM_005259440		Approved		uc002okz.4	O60234	OTTHUMG00000182811	ENST00000597595.1:c.44C>A	19.37:g.39826131G>T	ENSP00000472249:p.Thr15Lys	165.0	0.0	0		179.0	74.0	0.413408	NM_004877	Q6IB37	Missense_Mutation	SNP	ENST00000597595.1	37	CCDS12532.1	41	0.018772893772893772	37	0.07520325203252033	4	0.011049723756906077	0	0.0	0	0.0	G	0.825	-0.747109	0.03065	0.048116	0.001512	ENSG00000130755	ENST00000253054	.	.	.	4.18	2.07	0.26955	Actin-binding, cofilin/tropomyosin type (3);	0.077251	0.46442	N	0.000283	T	0.00241	0.0007	N	0.00265	-1.74	0.28216	N	0.926737	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.29640	-1.0005	9	0.02654	T	1	-19.027	1.2964	0.02070	0.1769:0.1034:0.1922:0.5276	rs1801733;rs52801314	15;15	O60234;Q6IB37	GMFG_HUMAN;.	K	15	.	ENSP00000253054:T15K	T	-	2	0	GMFG	44517971	0.864000	0.29904	0.990000	0.47175	0.765000	0.43378	0.310000	0.19356	0.188000	0.20168	-1.238000	0.01547	ACA	G|0.980;T|0.020	0.020	strong		0.572	GMFG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463839.1		
KDM1A	23028	hgsc.bcm.edu	37	1	23409803	23409803	+	Silent	SNP	G	G	A	rs150794224	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:23409803G>A	ENST00000356634.3	+	19	2654	c.2505G>A	c.(2503-2505)acG>acA	p.T835T	KDM1A_ENST00000542151.1_Silent_p.T859T|RP1-184J9.2_ENST00000427154.1_RNA|KDM1A_ENST00000400181.4_Silent_p.T859T	NM_015013.3	NP_055828.2	O60341	KDM1A_HUMAN	lysine (K)-specific demethylase 1A	835	Demethylase activity.				blood coagulation (GO:0007596)|cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|histone H3-K4 demethylation (GO:0034720)|histone H3-K9 demethylation (GO:0033169)|in utero embryonic development (GO:0001701)|muscle cell development (GO:0055001)|negative regulation of DNA binding (GO:0043392)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of histone H3-K4 methylation (GO:0051572)|negative regulation of histone H3-K9 methylation (GO:0051573)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of protein binding (GO:0032091)|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)|pituitary gland development (GO:0021983)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of hormone biosynthetic process (GO:0046886)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of stem cell proliferation (GO:2000648)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein demethylation (GO:0006482)|regulation of primitive erythrocyte differentiation (GO:0010725)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|demethylase activity (GO:0032451)|enzyme binding (GO:0019899)|flavin adenine dinucleotide binding (GO:0050660)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-K4 specific) (GO:0032453)|histone demethylase activity (H3-K9 specific) (GO:0032454)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|MRF binding (GO:0043426)|oxidoreductase activity (GO:0016491)|p53 binding (GO:0002039)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(2)|endometrium(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	23						CCATGTATACGCTGCCTCGCC	0.562													G|||	23	0.00459265	0.0159	0.0029	5008	,	,		18489	0.0		0.0	False		,,,				2504	0.0				p.T859T		Atlas-SNP	.											.	KDM1A	49	.	0			c.G2577A						PASS	.	G	,	43,4363	46.7+/-81.2	0,43,2160	84.0	70.0	75.0		2577,2505	-6.8	0.0	1	dbSNP_134	75	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	KDM1A	NM_001009999.2,NM_015013.3	,	0,44,6459	AA,AG,GG		0.0116,0.9759,0.3383	,	859/877,835/853	23409803	44,12962	2203	4300	6503	SO:0001819	synonymous_variant	23028	exon21			GTATACGCTGCCT	AL031428	CCDS30627.1, CCDS53278.1	1p36.12	2011-07-01	2009-09-29	2009-09-29	ENSG00000004487	ENSG00000004487		"""Chromatin-modifying enzymes / K-demethylases"""	29079	protein-coding gene	gene with protein product		609132	"""amine oxidase (flavin containing) domain 2"", ""lysine (K)-specific demethylase 1"""	AOF2, KDM1		9628581, 12493763	Standard	NM_015013		Approved	KIAA0601, BHC110, LSD1	uc001bgj.2	O60341	OTTHUMG00000003220	ENST00000356634.3:c.2505G>A	1.37:g.23409803G>A		89.0	0.0	0		69.0	43.0	0.623188	NM_001009999	A8MWP9|Q5TH94|Q5TH95|Q86VT7|Q8IXK4|Q8NDP6|Q8TAZ3|Q96AW4	Silent	SNP	ENST00000356634.3	37	CCDS30627.1																																																																																			G|0.997;A|0.003	0.003	strong		0.562	KDM1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000008880.3	NM_015013	
FAM129C	199786	hgsc.bcm.edu	37	19	17643125	17643125	+	Silent	SNP	C	C	T	rs73504248	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:17643125C>T	ENST00000335393.4	+	4	471	c.333C>T	c.(331-333)caC>caT	p.H111H	FAM129C_ENST00000300971.2_Silent_p.H111H|FAM129C_ENST00000352727.3_Silent_p.H111H|FAM129C_ENST00000599164.1_Silent_p.H80H|FAM129C_ENST00000449408.2_5'UTR|FAM129C_ENST00000601861.1_Silent_p.H80H|FAM129C_ENST00000332386.5_Silent_p.H111H|FAM129C_ENST00000597887.1_3'UTR|FAM129C_ENST00000600871.1_Silent_p.H57H|FAM129C_ENST00000595684.1_Silent_p.H111H|FAM129C_ENST00000599124.1_Silent_p.H80H	NM_173544.4	NP_775815	Q86XR2	NIBL2_HUMAN	family with sequence similarity 129, member C	111										autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(8)|liver(2)|lung(14)|ovary(1)|skin(3)|stomach(1)	33						TTCGGGGCCACCCACCCCGGT	0.647													C|||	105	0.0209665	0.0764	0.0058	5008	,	,		16326	0.0		0.0	False		,,,				2504	0.0				p.H111H		Atlas-SNP	.											.	FAM129C	110	.	0			c.C333T						PASS	.	C	,	316,4090	168.3+/-199.2	13,290,1900	67.0	66.0	66.0		333,333	-2.6	0.0	19	dbSNP_130	66	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	FAM129C	NM_001098524.1,NM_173544.4	,	13,292,6198	TT,TC,CC		0.0233,7.172,2.445	,	111/652,111/698	17643125	318,12688	2203	4300	6503	SO:0001819	synonymous_variant	199786	exon4			GGGCCACCCACCC	AY254198	CCDS12362.1, CCDS42521.1	19p13.11	2008-02-05				ENSG00000167483			24130	protein-coding gene	gene with protein product	B cell novel protein 1	609967				12886250	Standard	NM_173544		Approved	FLJ39802, BCNP1	uc021uqj.1	Q86XR2		ENST00000335393.4:c.333C>T	19.37:g.17643125C>T		168.0	0.0	0		219.0	219.0	1	NM_001098524	B4DNU3|B4DVN7|Q7Z6H6|Q86XR3|Q86XR4|Q8TEQ3	Silent	SNP	ENST00000335393.4	37	CCDS12362.1																																																																																			C|0.976;T|0.024	0.024	strong		0.647	FAM129C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464206.1	NM_173544	
CCDC65	85478	hgsc.bcm.edu	37	12	49308261	49308261	+	Silent	SNP	C	C	T	rs143088014	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:49308261C>T	ENST00000320516.4	+	3	563	c.375C>T	c.(373-375)gaC>gaT	p.D125D	RP11-302B13.5_ENST00000398092.4_Intron|CCDC65_ENST00000266984.5_Silent_p.D125D	NM_033124.4	NP_149115.2	Q8IXS2	CCD65_HUMAN	coiled-coil domain containing 65	125										breast(1)|large_intestine(4)|lung(7)|ovary(1)|skin(2)	15						ACAATGTTGACCAGCTCTTGG	0.537													C|||	8	0.00159744	0.0053	0.0014	5008	,	,		17358	0.0		0.0	False		,,,				2504	0.0				p.D125D		Atlas-SNP	.											.	CCDC65	41	.	0			c.C375T						PASS	.	C		15,4391	22.3+/-47.3	0,15,2188	85.0	74.0	78.0		375	1.2	1.0	12	dbSNP_134	78	1,8599		0,1,4299	no	coding-synonymous	CCDC65	NM_033124.4		0,16,6487	TT,TC,CC		0.0116,0.3404,0.123		125/485	49308261	16,12990	2203	4300	6503	SO:0001819	synonymous_variant	85478	exon3			TGTTGACCAGCTC		CCDS8772.1	12q13.12	2014-07-18			ENSG00000139537	ENSG00000139537			29937	protein-coding gene	gene with protein product		611088				17089017, 21700706	Standard	NM_033124		Approved	NYD-SP28, FLJ35732, FAP250, CILD27	uc001rso.3	Q8IXS2		ENST00000320516.4:c.375C>T	12.37:g.49308261C>T		62.0	0.0	0		67.0	25.0	0.373134	NM_033124	A6NJG5|B2RBE2|Q8N7G4|Q8NA91|Q96JA0	Silent	SNP	ENST00000320516.4	37	CCDS8772.1																																																																																			C|0.999;T|0.001	0.001	strong		0.537	CCDC65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408922.1	NM_033124	
FBXL5	26234	hgsc.bcm.edu	37	4	15627092	15627092	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:15627092A>G	ENST00000341285.3	-	9	1757	c.1633T>C	c.(1633-1635)Tat>Cat	p.Y545H	FBXL5_ENST00000412094.2_Missense_Mutation_p.Y528H|FBXL5_ENST00000382358.4_Missense_Mutation_p.Y419H	NM_001193534.1|NM_001193535.1|NM_012161.3	NP_001180463.1|NP_001180464.1|NP_036293.1	Q9UKA1	FBXL5_HUMAN	F-box and leucine-rich repeat protein 5	545					iron ion homeostasis (GO:0055072)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	perinuclear region of cytoplasm (GO:0048471)|SCF ubiquitin ligase complex (GO:0019005)|ubiquitin ligase complex (GO:0000151)	iron ion binding (GO:0005506)|ubiquitin-protein transferase activity (GO:0004842)			endometrium(2)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	13						TGACCACAATACGCAAAGGCT	0.423																																					p.Y545H		Atlas-SNP	.											.	FBXL5	52	.	0			c.T1633C						PASS	.						71.0	58.0	62.0					4																	15627092		2203	4300	6503	SO:0001583	missense	26234	exon9			CACAATACGCAAA	AF174591	CCDS3415.1, CCDS54745.1	4p15.33	2011-06-09			ENSG00000118564	ENSG00000118564		"""F-boxes / Leucine-rich repeats"""	13602	protein-coding gene	gene with protein product		605655				10531035	Standard	NM_012161		Approved	FBL4, FBL5, FLR1	uc003goc.2	Q9UKA1	OTTHUMG00000097097	ENST00000341285.3:c.1633T>C	4.37:g.15627092A>G	ENSP00000344866:p.Tyr545His	131.0	0.0	0		134.0	6.0	0.0447761	NM_012161	A8MSK4|B4DIB5|Q4W5A8|Q8NHP3|Q9NXN2|Q9P0I0|Q9P0X5|Q9UJT7|Q9UKC8	Missense_Mutation	SNP	ENST00000341285.3	37	CCDS3415.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.7|21.7	4.187808|4.187808	0.78789|0.78789	.|.	.|.	ENSG00000118564|ENSG00000118564	ENST00000513163|ENST00000341285;ENST00000412094;ENST00000382358	.|T;T;T	.|0.38401	.|1.17;1.19;1.14	5.72|5.72	5.72|5.72	0.89469|0.89469	.|.	.|0.108992	.|0.64402	.|D	.|0.000005	T|T	0.48095|0.48095	0.1481|0.1481	L|L	0.29908|0.29908	0.895|0.895	0.50467|0.50467	D|D	0.999876|0.999876	.|D;D	.|0.89917	.|1.0;0.999	.|D;D	.|0.85130	.|0.997;0.994	T|T	0.36601|0.36601	-0.9741|-0.9741	5|10	.|0.30078	.|T	.|0.28	-20.3568|-20.3568	16.0006|16.0006	0.80290|0.80290	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|528;545	.|Q9UKA1-2;Q9UKA1	.|.;FBXL5_HUMAN	A|H	465|545;528;419	.|ENSP00000344866:Y545H;ENSP00000408679:Y528H;ENSP00000371795:Y419H	.|ENSP00000344866:Y545H	V|Y	-|-	2|1	0|0	FBXL5|FBXL5	15236190|15236190	0.997000|0.997000	0.39634|0.39634	0.864000|0.864000	0.33941|0.33941	0.943000|0.943000	0.58893|0.58893	3.468000|3.468000	0.53086|0.53086	2.180000|2.180000	0.69256|0.69256	0.460000|0.460000	0.39030|0.39030	GTA|TAT	.	.	none		0.423	FBXL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214235.2		
FBXO22	26263	hgsc.bcm.edu	37	15	76205550	76205550	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:76205550C>T	ENST00000308275.3	+	3	391	c.286C>T	c.(286-288)Cgc>Tgc	p.R96C	FBXO22_ENST00000453211.2_Missense_Mutation_p.R96C|FBXO22_ENST00000540507.1_5'UTR	NM_147188.2	NP_671717.1	Q8NEZ5	FBX22_HUMAN	F-box protein 22	96					cellular protein modification process (GO:0006464)|cellular response to starvation (GO:0009267)|nucleocytoplasmic transport (GO:0006913)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein polyubiquitination (GO:0000209)|regulation of skeletal muscle fiber development (GO:0048742)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	21						GCAGAATGTTCGCATCTTACC	0.383																																					p.R96C		Atlas-SNP	.											FBXO22_ENST00000453211,NS,carcinoma,0,3	FBXO22	60	3	0			c.C286T						PASS	.						65.0	69.0	68.0					15																	76205550		2197	4294	6491	SO:0001583	missense	26263	exon3			AATGTTCGCATCT	AF174602	CCDS10287.1, CCDS45310.1	15q23	2008-10-03	2004-06-15		ENSG00000167196	ENSG00000167196		"""F-boxes /  ""other"""""	13593	protein-coding gene	gene with protein product	"""FIST domain containing 1"""	609096	"""F-box only protein 22"""			10531035, 10531037, 17855421	Standard	NM_147188		Approved	FBX22, FISTC1	uc002bbk.3	Q8NEZ5	OTTHUMG00000142841	ENST00000308275.3:c.286C>T	15.37:g.76205550C>T	ENSP00000307833:p.Arg96Cys	16.0	0.0	0		20.0	11.0	0.55	NM_012170	Q0D2P8|Q6PIL5|Q8IXW3|Q9H824|Q9UKC0	Missense_Mutation	SNP	ENST00000308275.3	37	CCDS10287.1	.	.	.	.	.	.	.	.	.	.	C	15.09	2.729883	0.48833	.	.	ENSG00000167196	ENST00000308275;ENST00000453211	.	.	.	5.95	5.95	0.96441	.	0.409490	0.29676	N	0.011486	T	0.39937	0.1097	N	0.08118	0	0.80722	D	1	P;D	0.57571	0.916;0.98	B;P	0.46049	0.23;0.502	T	0.37663	-0.9696	9	0.39692	T	0.17	-3.1292	17.1124	0.86679	0.0:1.0:0.0:0.0	.	96;96	Q8NEZ5;Q8NEZ5-3	FBX22_HUMAN;.	C	96	.	ENSP00000307833:R96C	R	+	1	0	FBXO22	73992605	0.995000	0.38212	0.523000	0.27875	0.842000	0.47809	2.942000	0.49018	2.824000	0.97209	0.655000	0.94253	CGC	.	.	none		0.383	FBXO22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286477.2	NM_147188	
MUC4	4585	hgsc.bcm.edu	37	3	195512734	195512734	+	Missense_Mutation	SNP	T	T	G	rs529505943	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195512734T>G	ENST00000463781.3	-	2	6176	c.5717A>C	c.(5716-5718)cAt>cCt	p.H1906P	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H1906P	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				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.H1906R(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)		GTCGGTGACATGAAGAGGGGT	0.567													.|||	5	0.000998403	0.0015	0.0	5008	,	,		42586	0.0		0.001	False		,,,				2504	0.002				p.H1906P		Atlas-SNP	.											MUC4_ENST00000463781,NS,malignant_melanoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	NS(2)	c.A5717C						scavenged	.						43.0	38.0	40.0					3																	195512734		690	1591	2281	SO:0001583	missense	4585	exon2			GTGACATGAAGAG	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.5717A>C	3.37:g.195512734T>G	ENSP00000417498:p.His1906Pro	399.0	2.0	0.00501253		327.0	27.0	0.0825688	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	.	.	.	.	.	.	.	.	.	.	-	5.462	0.270280	0.10349	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30714	1.53;1.52	0.844	-1.69	0.08186	.	.	.	.	.	T	0.09069	0.0224	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21042	-1.0257	8	.	.	.	.	2.2178	0.03964	0.0:0.333:0.3361:0.331	.	1906	E7ESK3	.	P	1906	ENSP00000417498:H1906P;ENSP00000420243:H1906P	.	H	-	2	0	MUC4	196997129	0.002000	0.14202	0.005000	0.12908	0.007000	0.05969	-0.537000	0.06128	-1.928000	0.01059	-1.950000	0.00486	CAT	.	.	none		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
PAPSS1	9061	hgsc.bcm.edu	37	4	108552787	108552787	+	Splice_Site	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:108552787T>C	ENST00000265174.4	-	11	2008	c.1736A>G	c.(1735-1737)cAc>cGc	p.H579R		NM_005443.4	NP_005434.4	O43252	PAPS1_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 1	579					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	adenylylsulfate kinase activity (GO:0004020)|ATP binding (GO:0005524)|nucleotidyltransferase activity (GO:0016779)|sulfate adenylyltransferase (ATP) activity (GO:0004781)			NS(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(5)|ovary(1)	16		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.49e-05)		TAAGACTTACTGTTCAGAGTC	0.403																																					p.H579R		Atlas-SNP	.											.	PAPSS1	57	.	0			c.A1736G						PASS	.						113.0	111.0	112.0					4																	108552787		2203	4300	6503	SO:0001630	splice_region_variant	9061	exon11			ACTTACTGTTCAG	Y10387	CCDS3676.1	4q24	2012-07-13			ENSG00000138801	ENSG00000138801	2.7.7.4, 2.7.1.25		8603	protein-coding gene	gene with protein product		603262				9576487, 9771708	Standard	NM_005443		Approved	ATPSK1, PAPSS	uc003hyk.3	O43252	OTTHUMG00000131210	ENST00000265174.4:c.1736+1A>G	4.37:g.108552787T>C		100.0	0.0	0		112.0	45.0	0.401786	NM_005443	O43841|O75332|Q96FB1|Q96TF4|Q9P1P9|Q9UE98	Missense_Mutation	SNP	ENST00000265174.4	37	CCDS3676.1	.	.	.	.	.	.	.	.	.	.	T	4.243	0.044005	0.08196	.	.	ENSG00000138801	ENST00000265174	T	0.26957	1.7	5.62	5.62	0.85841	Sulphate adenylyltransferase (2);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.188956	0.56097	D	0.000029	T	0.06096	0.0158	N	0.00125	-2.05	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.37267	-0.9713	9	.	.	.	-22.1456	15.8538	0.78960	0.0:0.0:0.0:1.0	.	579	O43252	PAPS1_HUMAN	R	579	ENSP00000265174:H579R	.	H	-	2	0	PAPSS1	108772236	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	1.979000	0.40608	2.141000	0.66446	0.528000	0.53228	CAC	.	.	none		0.403	PAPSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253946.2		Missense_Mutation
AHNAK2	113146	hgsc.bcm.edu	37	14	105416775	105416775	+	Silent	SNP	C	C	A	rs60880494	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105416775C>A	ENST00000333244.5	-	7	5132	c.5013G>T	c.(5011-5013)tcG>tcT	p.S1671S	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1671						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			TGCCTGGGGCCGACACCCCAA	0.602													.|||	107	0.0213658	0.0613	0.0058	5008	,	,		17088	0.005		0.001	False		,,,				2504	0.0164				p.S1671S		Atlas-SNP	.											.	AHNAK2	719	.	0			c.G5013T						PASS	.	T		136,3744		13,110,1817	190.0	222.0	212.0		5013	-5.7	0.0	14	dbSNP_129	212	15,8193		2,11,4091	no	coding-synonymous	AHNAK2	NM_138420.2		15,121,5908	AA,AC,CC		0.1827,3.5052,1.2492		1671/5796	105416775	151,11937	1940	4104	6044	SO:0001819	synonymous_variant	113146	exon7			TGGGGCCGACACC	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.5013G>T	14.37:g.105416775C>A		316.0	0.0	0		213.0	82.0	0.384977	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Silent	SNP	ENST00000333244.5	37	CCDS45177.1																																																																																			A|0.015;C|0.985	0.015	strong		0.602	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
LINC00283	100874057	hgsc.bcm.edu	37	13	103398453	103398453	+	RNA	SNP	C	C	A	rs141118373	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:103398453C>A	ENST00000430111.1	+	0	3894									long intergenic non-protein coding RNA 283																		TCTAAAGGACCCATTTGGAGA	0.408													C|||	57	0.0113818	0.0408	0.0043	5008	,	,		20326	0.0		0.0	False		,,,				2504	0.0				p.G1532C		Atlas-SNP	.											.	.	.	.	0			c.G4594T						PASS	.	C	CYS/GLY	29,1355		0,29,663	111.0	96.0	101.0		4594	-0.2	0.0	13	dbSNP_134	101	0,3180		0,0,1590	yes	missense	CCDC168	NM_001146197.1	159	0,29,2253	AA,AC,CC		0.0,2.0954,0.6354		1532/7082	103398453	29,4535	692	1590	2282			643677	exon4			AAGGACCCATTTG			13q33.1	2012-10-12	2011-08-10	2011-08-10	ENSG00000231633	ENSG00000231633		"""Long non-coding RNAs"""	38809	non-coding RNA	RNA, long non-coding			"""non-protein coding RNA 283"""	NCRNA00283			Standard			Approved				OTTHUMG00000017311		13.37:g.103398453C>A		199.0	0.0	0		206.0	108.0	0.524272	NM_001146197		Missense_Mutation	SNP	ENST00000430111.1	37																																																																																				C|0.991;A|0.009	0.009	strong		0.408	LINC00283-001	KNOWN	not_organism_supported|basic	antisense	antisense	OTTHUMT00000045714.1		
PEX19	5824	hgsc.bcm.edu	37	1	160253413	160253413	+	Silent	SNP	G	G	A	rs141911166	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:160253413G>A	ENST00000368072.5	-	2	108	c.87C>T	c.(85-87)ttC>ttT	p.F29F	PEX19_ENST00000440949.3_5'UTR|PEX19_ENST00000532508.1_5'UTR|DCAF8_ENST00000556710.1_Intron|DCAF8_ENST00000608310.1_Intron	NM_001193644.1|NM_002857.3	NP_001180573.1|NP_002848.1	P40855	PEX19_HUMAN	peroxisomal biogenesis factor 19	29	Docking to the peroxisome membrane and binding to PEX3.|Necessary for PEX19 function on peroxisome biogenesis.				chaperone-mediated protein folding (GO:0061077)|chaperone-mediated protein transport (GO:0072321)|establishment of protein localization to peroxisome (GO:0072663)|negative regulation of lipid binding (GO:1900131)|peroxisome fission (GO:0016559)|peroxisome membrane biogenesis (GO:0016557)|peroxisome organization (GO:0007031)|protein import into peroxisome membrane (GO:0045046)|protein stabilization (GO:0050821)|protein targeting to peroxisome (GO:0006625)|transmembrane transport (GO:0055085)	brush border membrane (GO:0031526)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|protein complex (GO:0043234)	ATPase binding (GO:0051117)|peroxisome membrane class-1 targeting sequence binding (GO:0036105)|protein N-terminus binding (GO:0047485)			cervix(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(2)	11	all_cancers(52;1.27e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			TGGCTTTATCGAAATCATCAA	0.532													G|||	2	0.000399361	0.0015	0.0	5008	,	,		18595	0.0		0.0	False		,,,				2504	0.0				p.F29F		Atlas-SNP	.											PEX19,NS,carcinoma,0,3	PEX19	34	3	0			c.C87T						PASS	.	G	,	5,4401	9.9+/-24.2	0,5,2198	81.0	75.0	77.0		87,87	1.1	1.0	1	dbSNP_134	77	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	PEX19	NM_001193644.1,NM_002857.3	,	0,5,6498	AA,AG,GG		0.0,0.1135,0.0384	,	29/280,29/300	160253413	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	5824	exon2			TTTATCGAAATCA	Y09048	CCDS1201.1	1q22	2008-07-18	2004-03-17	2004-03-19	ENSG00000162735	ENSG00000162735			9713	protein-coding gene	gene with protein product	"""housekeeping gene, 33kD"""	600279	"""peroxisomal farnesylated protein"""	PXF		9339377, 10051604	Standard	NM_002857		Approved	HK33, D1S2223E, PMP1, PMPI, PXMP1		P40855	OTTHUMG00000033112	ENST00000368072.5:c.87C>T	1.37:g.160253413G>A		81.0	0.0	0		103.0	53.0	0.514563	NM_002857	D3DVE7|Q5QNY4|Q8NI97	Silent	SNP	ENST00000368072.5	37	CCDS1201.1																																																																																			G|1.000;A|0.000	0.000	strong		0.532	PEX19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080642.2	NM_002857	
KRT16	3868	hgsc.bcm.edu	37	17	39767947	39767947	+	Silent	SNP	C	C	T	rs144914208	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:39767947C>T	ENST00000301653.4	-	2	622	c.558G>A	c.(556-558)gcG>gcA	p.A186A		NM_005557.3	NP_005548.2	P08779	K1C16_HUMAN	keratin 16	186	Coil 1B.|Rod.				aging (GO:0007568)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|epidermis development (GO:0008544)|hair cycle (GO:0042633)|intermediate filament cytoskeleton organization (GO:0045104)|negative regulation of cell migration (GO:0030336)	cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		Breast(137;0.000307)				AAATGGGCTGCGCATTCTCAA	0.577													c|||	105	0.0209665	0.0749	0.0072	5008	,	,		20382	0.0		0.001	False		,,,				2504	0.0				p.A186A		Atlas-SNP	.											KRT16,colon,carcinoma,-1,1	KRT16	45	1	0			c.G558A						PASS	.	T		282,4124	146.5+/-181.1	7,268,1928	29.0	27.0	28.0		558	-7.1	0.3	17	dbSNP_134	28	1,8593	1.2+/-3.3	0,1,4296	no	coding-synonymous	KRT16	NM_005557.3		7,269,6224	TT,TC,CC		0.0116,6.4004,2.1769		186/474	39767947	283,12717	2203	4297	6500	SO:0001819	synonymous_variant	3868	exon2			GGGCTGCGCATTC	S79867	CCDS11401.1	17q21.2	2013-01-16	2008-08-01		ENSG00000186832	ENSG00000186832		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6423	protein-coding gene	gene with protein product	"""focal non-epidermolytic palmoplantar keratoderma"""	148067				2451124, 16831889	Standard	NM_005557		Approved	NEPPK	uc002hxg.4	P08779	OTTHUMG00000133495	ENST00000301653.4:c.558G>A	17.37:g.39767947C>T		390.0	0.0	0		379.0	169.0	0.44591	NM_005557	A8K488|P30654|Q16402|Q9UBG8	Silent	SNP	ENST00000301653.4	37	CCDS11401.1																																																																																			C|0.978;T|0.022	0.022	strong		0.577	KRT16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257408.1	NM_005557	
PUS7L	83448	hgsc.bcm.edu	37	12	44130205	44130205	+	Silent	SNP	G	G	A	rs12309260	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:44130205G>A	ENST00000416848.2	-	7	2192	c.1704C>T	c.(1702-1704)gaC>gaT	p.D568D	PUS7L_ENST00000431332.3_Silent_p.D255D|PUS7L_ENST00000551923.1_Silent_p.D568D|PUS7L_ENST00000344862.5_Silent_p.D568D	NM_001098615.1|NM_001271826.1	NP_001092085.1|NP_001258755.1	Q9H0K6	PUS7L_HUMAN	pseudouridylate synthase 7 homolog (S. cerevisiae)-like	568	TRUD. {ECO:0000255|PROSITE- ProRule:PRU00342}.				pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(15)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	all_cancers(12;0.00027)	Lung NSC(34;0.114)|all_lung(34;0.24)		GBM - Glioblastoma multiforme(48;0.0402)		GGAAATTCTCGTCATCAATGT	0.373													G|||	61	0.0121805	0.0431	0.0043	5008	,	,		18654	0.0		0.001	False		,,,				2504	0.0				p.D568D		Atlas-SNP	.											.	PUS7L	73	.	0			c.C1704T						PASS	.	G	,,	178,4228	115.4+/-153.4	2,174,2027	158.0	146.0	150.0		1704,1704,1704	-5.5	0.0	12	dbSNP_120	150	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	PUS7L	NM_001098614.1,NM_001098615.1,NM_031292.3	,,	2,176,6325	AA,AG,GG		0.0233,4.0399,1.384	,,	568/702,568/702,568/702	44130205	180,12826	2203	4300	6503	SO:0001819	synonymous_variant	83448	exon7			ATTCTCGTCATCA	BX647494	CCDS8743.1, CCDS61104.1	12q12	2006-02-07				ENSG00000129317			25276	protein-coding gene	gene with protein product						11230166	Standard	NM_001098615		Approved	DKFZP434G1415	uc001rnr.5	Q9H0K6	OTTHUMG00000169423	ENST00000416848.2:c.1704C>T	12.37:g.44130205G>A		72.0	0.0	0		96.0	52.0	0.541667	NM_001098614	B3KUJ1|Q05CU0|Q6AHZ3|Q6NUP2	Silent	SNP	ENST00000416848.2	37	CCDS8743.1																																																																																			G|0.988;A|0.012	0.012	strong		0.373	PUS7L-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403931.1	NM_031292	
ATAD3C	219293	hgsc.bcm.edu	37	1	1403894	1403894	+	Missense_Mutation	SNP	A	A	G	rs145079480	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:1403894A>G	ENST00000378785.2	+	12	2215	c.1220A>G	c.(1219-1221)gAg>gGg	p.E407G		NM_001039211.2	NP_001034300.2	Q5T2N8	ATD3C_HUMAN	ATPase family, AAA domain containing 3C	407							ATP binding (GO:0005524)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|lung(4)	7	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		Epithelial(90;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		CCCGAGGACGAGCAACCCTCA	0.642													N|||	127	0.0253594	0.0923	0.0072	5008	,	,		14787	0.0		0.0	False		,,,				2504	0.0				p.E407G		Atlas-SNP	.											.	ATAD3C	23	.	0			c.A1220G						PASS	.	A	GLY/GLU	425,3979		20,385,1797	22.0	25.0	24.0		1220	-0.4	0.0	1	dbSNP_134	24	0,8590		0,0,4295	no	missense	ATAD3C	NM_001039211.2	98	20,385,6092	GG,GA,AA		0.0,9.6503,3.2707	benign	407/412	1403894	425,12569	2202	4295	6497	SO:0001583	missense	219293	exon12			AGGACGAGCAACC	AK091918	CCDS44039.1	1p36.33	2010-04-21		2007-02-08	ENSG00000215915	ENSG00000215915		"""ATPases / AAA-type"""	32151	protein-coding gene	gene with protein product							Standard	NM_001039211		Approved	FLJ34599	uc001aft.2	Q5T2N8	OTTHUMG00000000531	ENST00000378785.2:c.1220A>G	1.37:g.1403894A>G	ENSP00000368062:p.Glu407Gly	290.0	0.0	0		276.0	108.0	0.391304	NM_001039211	Q8N1Z5	Missense_Mutation	SNP	ENST00000378785.2	37	CCDS44039.1	60	0.027472527472527472	56	0.11382113821138211	4	0.011049723756906077	0	0.0	0	0.0	.	5.440	0.266325	0.10294	0.096503	0.0	ENSG00000215915	ENST00000378785	D	0.94184	-3.37	1.1	-0.358	0.12575	.	.	.	.	.	T	0.13329	0.0323	L	0.36672	1.1	0.80722	P	0.0	B	0.22480	0.07	B	0.19148	0.024	T	0.57980	-0.7717	8	0.34782	T	0.22	.	4.8484	0.13524	0.6826:0.3174:0.0:0.0	.	407	Q5T2N8	ATD3C_HUMAN	G	407	ENSP00000368062:E407G	ENSP00000368062:E407G	E	+	2	0	ATAD3C	1393757	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	0.745000	0.26259	-0.095000	0.12351	0.163000	0.16589	GAG	A|0.972;G|0.028	0.028	strong		0.642	ATAD3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001279.3	NM_001039211	
RGPD8	727851	hgsc.bcm.edu	37	2	113147751	113147751	+	Missense_Mutation	SNP	A	A	C	rs561418400	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:113147751A>C	ENST00000302558.3	-	20	2962	c.2771T>G	c.(2770-2772)tTt>tGt	p.F924C	RGPD8_ENST00000409750.1_Missense_Mutation_p.F784C	NM_001164463.1	NP_001157935.1	O14715	RGPD8_HUMAN	RANBP2-like and GRIP domain containing 8	924					protein targeting to Golgi (GO:0000042)	nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)			endometrium(4)|kidney(1)|lung(1)|prostate(3)|urinary_tract(1)	10						CGAAATGCCAAATTTAAATCC	0.398													.|||	287	0.0573083	0.2126	0.0086	5008	,	,		19416	0.0		0.0	False		,,,				2504	0.0				p.F924C		Atlas-SNP	.											.	RGPD8	81	.	0			c.T2771G						PASS	.						6.0	9.0	8.0					2																	113147751		655	1498	2153	SO:0001583	missense	727851	exon20			ATGCCAAATTTAA	AF012086	CCDS46394.1	2q13	2013-01-10	2005-12-20	2005-12-20	ENSG00000169629	ENSG00000169629		"""Tetratricopeptide (TTC) repeat domain containing"""	9849	protein-coding gene	gene with protein product		602752	"""RAN binding protein 2-like 1"""	RANBP2L1		9480752	Standard	NM_001164463		Approved	RanBP2alpha	uc002ths.2	O14715	OTTHUMG00000153289	ENST00000302558.3:c.2771T>G	2.37:g.113147751A>C	ENSP00000306637:p.Phe924Cys	627.0	0.0	0		720.0	230.0	0.319444	NM_001164463	Q5CZA8	Missense_Mutation	SNP	ENST00000302558.3	37	CCDS46394.1	.	.	.	.	.	.	.	.	.	.	-	11.55	1.670972	0.29693	.	.	ENSG00000169629	ENST00000302558;ENST00000409750	T;T	0.52983	0.65;0.64	2.33	2.33	0.28932	.	.	.	.	.	T	0.61223	0.2330	M	0.73598	2.24	0.80722	D	1	D	0.76494	0.999	D	0.66979	0.948	T	0.59359	-0.7469	9	0.37606	T	0.19	-28.0606	8.2389	0.31645	1.0:0.0:0.0:0.0	.	924	O14715	RGPD8_HUMAN	C	924;784	ENSP00000306637:F924C;ENSP00000386511:F784C	ENSP00000306637:F924C	F	-	2	0	RGPD8	112864222	1.000000	0.71417	0.998000	0.56505	0.288000	0.27193	8.054000	0.89451	1.076000	0.40961	0.147000	0.16070	TTT	.	.	none		0.398	RGPD8-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375951.1	XM_001722279	
LRRN4	164312	hgsc.bcm.edu	37	20	6021703	6021703	+	Missense_Mutation	SNP	C	C	T	rs116777692	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:6021703C>T	ENST00000378858.4	-	5	2412	c.2188G>A	c.(2188-2190)Gat>Aat	p.D730N		NM_152611.4	NP_689824.2	Q8WUT4	LRRN4_HUMAN	leucine rich repeat neuronal 4	730					long-term memory (GO:0007616)|visual learning (GO:0008542)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(2)	27						GGGTAATCATCAAAGGCCGGG	0.612													C|||	25	0.00499201	0.0189	0.0	5008	,	,		17219	0.0		0.0	False		,,,				2504	0.0				p.D730N		Atlas-SNP	.											.	LRRN4	54	.	0			c.G2188A						PASS	.	C	ASN/ASP	144,4262	91.6+/-130.3	3,138,2062	37.0	36.0	36.0		2188	2.0	0.0	20	dbSNP_132	36	1,8599		0,1,4299	yes	missense	LRRN4	NM_152611.3	23	3,139,6361	TT,TC,CC		0.0116,3.2683,1.1149	benign	730/741	6021703	145,12861	2203	4300	6503	SO:0001583	missense	164312	exon5			AATCATCAAAGGC	AL118505	CCDS13097.1	20p12.3	2013-02-11	2008-05-20	2008-05-20	ENSG00000125872	ENSG00000125872		"""Fibronectin type III domain containing"""	16208	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 75"""	C20orf75		15870286	Standard	NM_152611		Approved	dJ1056H1.1, NLRR4	uc002wmo.3	Q8WUT4	OTTHUMG00000031825	ENST00000378858.4:c.2188G>A	20.37:g.6021703C>T	ENSP00000368135:p.Asp730Asn	177.0	0.0	0		198.0	78.0	0.393939	NM_152611	A8K258|Q5JWV6|Q9H419	Missense_Mutation	SNP	ENST00000378858.4	37	CCDS13097.1	8	0.003663003663003663	8	0.016260162601626018	0	0.0	0	0.0	0	0.0	C	13.49	2.252207	0.39797	0.032683	1.16E-4	ENSG00000125872	ENST00000378858	T	0.61392	0.11	3.97	2.01	0.26516	.	0.648332	0.14770	N	0.299431	T	0.16514	0.0397	N	0.19112	0.55	0.09310	N	1	P	0.44877	0.845	B	0.43478	0.421	T	0.07366	-1.0776	10	0.09590	T	0.72	.	8.1533	0.31154	0.0:0.7545:0.1586:0.0869	.	730	Q8WUT4	LRRN4_HUMAN	N	730	ENSP00000368135:D730N	ENSP00000368135:D730N	D	-	1	0	LRRN4	5969703	0.075000	0.21258	0.001000	0.08648	0.305000	0.27757	1.403000	0.34612	0.618000	0.30179	0.655000	0.94253	GAT	C|0.990;T|0.010	0.010	strong		0.612	LRRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077907.2	NM_152611	
MYO19	80179	hgsc.bcm.edu	37	17	34859831	34859831	+	Silent	SNP	G	G	A	rs73276768	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:34859831G>A	ENST00000431794.3	-	20	2457	c.1935C>T	c.(1933-1935)ctC>ctT	p.L645L	MYO19_ENST00000268852.9_Silent_p.L445L	NM_001163735.1	NP_001157207.1	Q96H55	MYO19_HUMAN	myosin XIX	645	Myosin motor.					cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|urinary_tract(1)	20		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		TGGTCTCCACGAGGCCACAGG	0.632													G|||	22	0.00439297	0.0166	0.0	5008	,	,		18572	0.0		0.0	False		,,,				2504	0.0				p.L645L		Atlas-SNP	.											.	MYO19	130	.	0			c.C1935T						PASS	.	G	,	68,4038		3,62,1988	17.0	21.0	19.0		1935,1335	-11.3	0.9	17	dbSNP_130	19	1,8385		0,1,4192	no	coding-synonymous,coding-synonymous	MYO19	NM_001163735.1,NM_025109.5	,	3,63,6180	AA,AG,GG		0.0119,1.6561,0.5524	,	645/971,445/771	34859831	69,12423	2053	4193	6246	SO:0001819	synonymous_variant	80179	exon21			CTCCACGAGGCCA	BC008900	CCDS45654.1, CCDS54112.1, CCDS59283.1	17q12	2014-08-12	2007-09-26	2007-09-26	ENSG00000278259	ENSG00000278259		"""Myosins / Myosin superfamily : Class XIX"""	26234	protein-coding gene	gene with protein product			"""myosin head domain containing 1"""	MYOHD1		17877792, 19932026	Standard	NM_001033580		Approved	FLJ22865	uc010wcy.2	Q96H55	OTTHUMG00000188437	ENST00000431794.3:c.1935C>T	17.37:g.34859831G>A		37.0	0.0	0		45.0	19.0	0.422222	NM_001163735	Q59GS4|Q9H5X2	Silent	SNP	ENST00000431794.3	37	CCDS54112.1																																																																																			G|0.996;A|0.004	0.004	strong		0.632	MYO19-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451074.1	NM_025109	
TMEM140	55281	hgsc.bcm.edu	37	7	134849690	134849690	+	Missense_Mutation	SNP	T	T	C	rs76023601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:134849690T>C	ENST00000275767.3	+	2	720	c.497T>C	c.(496-498)aTa>aCa	p.I166T	C7orf49_ENST00000459937.1_Intron	NM_018295.3	NP_060765.4	Q9NV12	TM140_HUMAN	transmembrane protein 140	166						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(2)	5						CTCTTGCTTATAGCCATGGCT	0.567													T|||	9	0.00179712	0.0061	0.0	5008	,	,		20525	0.001		0.0	False		,,,				2504	0.0				p.I166T		Atlas-SNP	.											.	TMEM140	18	.	0			c.T497C						PASS	.	T	THR/ILE	27,4379	30.8+/-60.4	0,27,2176	48.0	48.0	48.0		497	0.2	0.0	7	dbSNP_131	48	0,8600		0,0,4300	yes	missense	TMEM140	NM_018295.3	89	0,27,6476	CC,CT,TT		0.0,0.6128,0.2076	benign	166/186	134849690	27,12979	2203	4300	6503	SO:0001583	missense	55281	exon2			TGCTTATAGCCAT	AK001862	CCDS5837.1	7q33	2006-03-17			ENSG00000146859	ENSG00000146859			21870	protein-coding gene	gene with protein product							Standard	NM_018295		Approved	FLJ11000	uc003vsi.3	Q9NV12	OTTHUMG00000155413	ENST00000275767.3:c.497T>C	7.37:g.134849690T>C	ENSP00000275767:p.Ile166Thr	146.0	0.0	0		214.0	98.0	0.457944	NM_018295	A4D1P9|Q8WUC3	Missense_Mutation	SNP	ENST00000275767.3	37	CCDS5837.1	4	0.0018315018315018315	3	0.006097560975609756	0	0.0	1	0.0017482517482517483	0	0.0	T	11.24	1.579014	0.28180	0.006128	0.0	ENSG00000146859	ENST00000275767;ENST00000456488	T	0.20069	2.1	5.28	0.166	0.14999	.	1.753430	0.02512	N	0.091627	T	0.08358	0.0208	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.28618	-1.0038	10	0.62326	D	0.03	-1.1492	5.0072	0.14293	0.0:0.1578:0.2972:0.545	.	166	Q9NV12	TM140_HUMAN	T	166;129	ENSP00000275767:I166T	ENSP00000275767:I166T	I	+	2	0	TMEM140	134500230	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.605000	0.24179	-0.098000	0.12285	-0.258000	0.10820	ATA	T|0.998;C|0.002	0.002	strong		0.567	TMEM140-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340017.2	NM_018295	
C16orf71	146562	hgsc.bcm.edu	37	16	4790304	4790304	+	Missense_Mutation	SNP	C	C	T	rs527269249|rs17137230	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:4790304C>T	ENST00000299320.5	+	4	905	c.427C>T	c.(427-429)Ccc>Tcc	p.P143S	C16orf71_ENST00000590191.1_Missense_Mutation_p.P157S|RP11-127I20.7_ENST00000588099.1_RNA	NM_139170.2	NP_631909.2	Q8IYS4	CP071_HUMAN	chromosome 16 open reading frame 71	143			P -> S (in dbSNP:rs17137230).							breast(1)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(1)	11						GGCCGAGGAGCCCCCCAGGTG	0.597													A|||	66	0.0131789	0.0469	0.0058	5008	,	,		15525	0.0		0.0	False		,,,				2504	0.0				p.P143S		Atlas-SNP	.											.	C16orf71	46	.	0			c.C427T						PASS	.	A	SER/PRO	250,4144		11,228,1958	67.0	74.0	72.0		427	3.0	0.2	16	dbSNP_123	72	3,8597		0,3,4297	yes	missense	C16orf71	NM_139170.2	74	11,231,6255	TT,TC,CC		0.0349,5.6896,1.9471	benign	143/521	4790304	253,12741	2197	4300	6497	SO:0001583	missense	146562	exon4			GAGGAGCCCCCCA	AF447587	CCDS10521.1	16p13.3	2008-02-05			ENSG00000166246	ENSG00000166246			25081	protein-coding gene	gene with protein product						12477932	Standard	XM_005255144		Approved	FLJ43261, DKFZp686H2240	uc002cxn.3	Q8IYS4	OTTHUMG00000129480	ENST00000299320.5:c.427C>T	16.37:g.4790304C>T	ENSP00000299320:p.Pro143Ser	156.0	0.0	0		192.0	103.0	0.536458	NM_139170	Q8NCV0	Missense_Mutation	SNP	ENST00000299320.5	37	CCDS10521.1	26	0.011904761904761904	25	0.0508130081300813	1	0.0027624309392265192	0	0.0	0	0.0	A	14.78	2.636363	0.47049	0.056896	3.49E-4	ENSG00000166246	ENST00000299320	T	0.08807	3.05	4.05	2.95	0.34219	.	0.488693	0.16973	N	0.192010	T	0.00412	0.0013	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.46470	-0.9189	10	0.23891	T	0.37	-3.9933	3.8797	0.09072	0.6631:0.2192:0.1178:0.0	rs17137230;rs52805275;rs17137230	143	Q8IYS4	CP071_HUMAN	S	143	ENSP00000299320:P143S	ENSP00000299320:P143S	P	+	1	0	C16orf71	4730305	0.001000	0.12720	0.189000	0.23252	0.035000	0.12851	0.195000	0.17155	0.253000	0.21552	-0.559000	0.04183	CCC	C|0.980;T|0.020	0.020	strong		0.597	C16orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251644.1	NM_139170	
PELP1	27043	hgsc.bcm.edu	37	17	4576623	4576623	+	Silent	SNP	G	G	A	rs191748391	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:4576623G>A	ENST00000574876.1	-	15	1784	c.1767C>T	c.(1765-1767)gcC>gcT	p.A589A	PELP1_ENST00000436683.2_Silent_p.A442A|AC091153.4_ENST00000441700.2_RNA|PELP1_ENST00000269230.7_Intron|PELP1_ENST00000301396.4_Silent_p.A733A|PELP1_ENST00000572293.1_Silent_p.A639A			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	589					cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						GAGGAGACGGGGCCAGCAGCA	0.647													G|||	4	0.000798722	0.003	0.0	5008	,	,		16322	0.0		0.0	False		,,,				2504	0.0				p.A589A		Atlas-SNP	.											.	PELP1	102	.	0			c.C1767T						PASS	.	G		8,4302		0,8,2147	18.0	30.0	26.0		1767	-11.1	0.0	17		26	0,8548		0,0,4274	no	coding-synonymous	PELP1	NM_014389.2		0,8,6421	AA,AG,GG		0.0,0.1856,0.0622		589/1131	4576623	8,12850	2155	4274	6429	SO:0001819	synonymous_variant	27043	exon15			AGACGGGGCCAGC		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"""proline, glutamic acid and leucine rich protein 1"""			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8		ENST00000574876.1:c.1767C>T	17.37:g.4576623G>A		161.0	0.0	0		194.0	97.0	0.5	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Silent	SNP	ENST00000574876.1	37	CCDS58503.1																																																																																			G|0.999;A|0.001	0.001	strong		0.647	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389	
MET	4233	hgsc.bcm.edu	37	7	116340269	116340269	+	Silent	SNP	C	C	T	rs28444388	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:116340269C>T	ENST00000318493.6	+	2	1318	c.1131C>T	c.(1129-1131)atC>atT	p.I377I	MET_ENST00000436117.2_Silent_p.I377I|MET_ENST00000397752.3_Silent_p.I377I			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			TCAACAAGATCGTCAACAAAA	0.433			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				C|||	311	0.0621006	0.2262	0.013	5008	,	,		19263	0.0		0.002	False		,,,				2504	0.001				p.I377I		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET	412	.	0			c.C1131T						PASS	.	C	,	744,3114		78,588,1263	105.0	97.0	100.0		1131,1131	-7.2	0.7	7	dbSNP_125	100	9,8271		0,9,4131	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	78,597,5394	TT,TC,CC		0.1087,19.2846,6.2037	,	377/1391,377/1409	116340269	753,11385	1929	4140	6069	SO:0001819	synonymous_variant	4233	exon2	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	CAAGATCGTCAAC	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"""hepatocyte growth factor receptor"""	164860	"""met proto-oncogene"""			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.1131C>T	7.37:g.116340269C>T		36.0	0.0	0		42.0	17.0	0.404762	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			C|0.967;T|0.033	0.033	strong		0.433	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
UBR4	23352	hgsc.bcm.edu	37	1	19467322	19467322	+	Silent	SNP	G	G	A	rs139618268	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19467322G>A	ENST00000375254.3	-	58	8580	c.8553C>T	c.(8551-8553)tcC>tcT	p.S2851S	UBR4_ENST00000375217.2_Intron|UBR4_ENST00000375226.2_Intron|UBR4_ENST00000375267.2_Silent_p.S2851S	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	2851					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)		CGTCCAGAGAGGAAGAGCTGG	0.622													G|||	3	0.000599042	0.0023	0.0	5008	,	,		19916	0.0		0.0	False		,,,				2504	0.0				p.S2851S		Atlas-SNP	.											.	UBR4	415	.	0			c.C8553T						PASS	.	G		17,4389	22.3+/-47.3	0,17,2186	66.0	60.0	62.0		8553	4.8	1.0	1	dbSNP_134	62	0,8600		0,0,4300	no	coding-synonymous	UBR4	NM_020765.2		0,17,6486	AA,AG,GG		0.0,0.3858,0.1307		2851/5184	19467322	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	23352	exon58			CAGAGAGGAAGAG	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.8553C>T	1.37:g.19467322G>A		57.0	0.0	0		67.0	34.0	0.507463	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Silent	SNP	ENST00000375254.3	37	CCDS189.1																																																																																			G|0.999;A|0.001	0.001	strong		0.622	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
SLC4A7	9497	hgsc.bcm.edu	37	3	27436247	27436247	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:27436247T>C	ENST00000295736.5	-	20	2922	c.2852A>G	c.(2851-2853)tAt>tGt	p.Y951C	SLC4A7_ENST00000446700.1_Missense_Mutation_p.Y943C|SLC4A7_ENST00000454389.1_Missense_Mutation_p.Y960C|SLC4A7_ENST00000388777.4_Missense_Mutation_p.Y501C|SLC4A7_ENST00000435667.2_Missense_Mutation_p.Y836C|SLC4A7_ENST00000428386.1_Missense_Mutation_p.Y827C|SLC4A7_ENST00000445684.1_Missense_Mutation_p.Y947C|SLC4A7_ENST00000425128.2_3'UTR|SLC4A7_ENST00000440156.1_Missense_Mutation_p.Y947C|SLC4A7_ENST00000437179.1_Missense_Mutation_p.Y832C|SLC4A7_ENST00000455077.1_Missense_Mutation_p.Y832C	NM_003615.4	NP_003606.3	Q9Y6M7	S4A7_HUMAN	solute carrier family 4, sodium bicarbonate cotransporter, member 7	951					auditory receptor cell development (GO:0060117)|bicarbonate transport (GO:0015701)|cochlear nucleus development (GO:0021747)|ion transport (GO:0006811)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal cell programmed cell death (GO:0046666)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			NS(2)|breast(3)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(9)|ovary(4)|skin(1)	38					Sodium bicarbonate(DB01390)	ATCAAGGTGATAGCCAGCTCC	0.393																																					p.Y951C		Atlas-SNP	.											.	SLC4A7	119	.	0			c.A2852G						PASS	.						101.0	93.0	96.0					3																	27436247		2203	4300	6503	SO:0001583	missense	9497	exon20			AGGTGATAGCCAG	AB012130	CCDS33721.1, CCDS58819.1, CCDS58820.1	3p24.1	2013-05-22			ENSG00000033867	ENSG00000033867		"""Solute carriers"""	11033	protein-coding gene	gene with protein product		603353		SLC4A6		10198178, 9610397	Standard	NM_003615		Approved	NBC3, SBC2	uc003cdv.4	Q9Y6M7	OTTHUMG00000155679	ENST00000295736.5:c.2852A>G	3.37:g.27436247T>C	ENSP00000295736:p.Tyr951Cys	80.0	0.0	0		85.0	47.0	0.552941	NM_003615	A6NIA8|B2CI53|B5M449|B5M451|B5M452|B5M453|B6DY52|B6DY53|C9JST9|D3K174|D3K175|O60350|Q6AHZ9|Q9HC88|Q9UIB9	Missense_Mutation	SNP	ENST00000295736.5	37	CCDS33721.1	.	.	.	.	.	.	.	.	.	.	T	24.4	4.526853	0.85706	.	.	ENSG00000033867	ENST00000419036;ENST00000295736;ENST00000428386;ENST00000454389;ENST00000440156;ENST00000437179;ENST00000446700;ENST00000455077;ENST00000445684;ENST00000435667;ENST00000388777;ENST00000428179	D;D;D;D;D;D;D;D;D;D;D;D	0.82167	-1.58;-1.58;-1.58;-1.58;-1.58;-1.58;-1.58;-1.58;-1.58;-1.58;-1.58;-1.58	5.84	5.84	0.93424	Bicarbonate transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.94095	0.8107	H	0.96365	3.81	0.80722	D	1	D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D	0.95792	0.8825	10	0.87932	D	0	.	16.2194	0.82247	0.0:0.0:0.0:1.0	.	947;832;943;947;960;501;827;951;832	E9PFN4;B5M452;E9PGC1;B5M453;E9PDL9;F8W7E6;Q9Y6M7-2;Q9Y6M7;B2CI53	.;.;.;.;.;.;.;S4A7_HUMAN;.	C	502;951;827;960;947;832;943;832;947;836;501;847	ENSP00000411031:Y502C;ENSP00000295736:Y951C;ENSP00000416368:Y827C;ENSP00000390394:Y960C;ENSP00000414797:Y947C;ENSP00000394252:Y832C;ENSP00000406605:Y943C;ENSP00000407382:Y832C;ENSP00000406804:Y947C;ENSP00000395336:Y836C;ENSP00000373429:Y501C;ENSP00000388703:Y847C	ENSP00000295736:Y951C	Y	-	2	0	SLC4A7	27411251	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.040000	0.89188	2.234000	0.73211	0.528000	0.53228	TAT	.	.	none		0.393	SLC4A7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000341230.2	NM_003615	
CELSR1	9620	hgsc.bcm.edu	37	22	46760102	46760102	+	Silent	SNP	C	C	T	rs6008778	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:46760102C>T	ENST00000262738.3	-	34	8825	c.8826G>A	c.(8824-8826)acG>acA	p.T2942T		NM_014246.1	NP_055061.1	Q9NYQ6	CELR1_HUMAN	cadherin, EGF LAG seven-pass G-type receptor 1	2942					anterior/posterior pattern specification (GO:0009952)|apical protein localization (GO:0045176)|central nervous system development (GO:0007417)|establishment of body hair planar orientation (GO:0048105)|establishment of planar polarity (GO:0001736)|establishment of planar polarity of embryonic epithelium (GO:0042249)|G-protein coupled receptor signaling pathway (GO:0007186)|hair follicle development (GO:0001942)|homophilic cell adhesion (GO:0007156)|inner ear morphogenesis (GO:0042472)|lateral sprouting involved in lung morphogenesis (GO:0060490)|locomotory behavior (GO:0007626)|neural tube closure (GO:0001843)|neuron migration (GO:0001764)|neuropeptide signaling pathway (GO:0007218)|orthogonal dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060488)|planar cell polarity pathway involved in neural tube closure (GO:0090179)|planar dichotomous subdivision of terminal units involved in lung branching morphogenesis (GO:0060489)|protein localization involved in establishment of planar polarity (GO:0090251)|regulation of actin cytoskeleton organization (GO:0032956)|Rho protein signal transduction (GO:0007266)|wound healing (GO:0042060)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)|protein dimerization activity (GO:0046983)|transmembrane signaling receptor activity (GO:0004888)			breast(8)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(13)|lung(27)|ovary(2)|pancreas(2)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(3)	95		Ovarian(80;0.00142)|Breast(42;0.00296)|all_neural(38;0.0416)|Colorectal(5;0.0766)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00643)|BRCA - Breast invasive adenocarcinoma(115;0.171)		GCGTCTGCTCCGTCAGCGTCA	0.662													C|||	272	0.0543131	0.1974	0.013	5008	,	,		15944	0.0		0.001	False		,,,				2504	0.001				p.T2942T		Atlas-SNP	.											.	CELSR1	242	.	0			c.G8826A						PASS	.	C		761,3639		66,629,1505	38.0	47.0	44.0		8826	-1.3	0.3	22	dbSNP_114	44	18,8570		0,18,4276	no	coding-synonymous	CELSR1	NM_014246.1		66,647,5781	TT,TC,CC		0.2096,17.2955,5.9978		2942/3015	46760102	779,12209	2200	4294	6494	SO:0001819	synonymous_variant	9620	exon34			CTGCTCCGTCAGC	AF231024	CCDS14076.1	22q13.31	2014-08-08	2013-02-18		ENSG00000075275	ENSG00000075275		"""Cadherins / Major cadherins"", ""-"", ""GPCR / Class B : Orphans"""	1850	protein-coding gene	gene with protein product	"""flamingo homolog 2 (Drosophila)"""	604523	"""cadherin, EGF LAG seven-pass G-type receptor 1, flamingo (Drosophila) homolog"""			9339365	Standard	XM_006724383		Approved	ME2, HFMI2, FMI2, CDHF9	uc003bhw.1	Q9NYQ6	OTTHUMG00000150423	ENST00000262738.3:c.8826G>A	22.37:g.46760102C>T		41.0	0.0	0		65.0	34.0	0.523077	NM_014246	O95722|Q5TH47|Q9BWQ5|Q9Y506|Q9Y526	Silent	SNP	ENST00000262738.3	37	CCDS14076.1																																																																																			C|0.948;T|0.052	0.052	strong		0.662	CELSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318037.1	NM_014246	
APC	324	hgsc.bcm.edu	37	5	112176556	112176556	+	Silent	SNP	G	G	A	rs34506289	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:112176556G>A	ENST00000457016.1	+	16	5645	c.5265G>A	c.(5263-5265)gcG>gcA	p.A1755A	CTC-554D6.1_ENST00000520401.1_Intron|APC_ENST00000257430.4_Silent_p.A1755A|APC_ENST00000508376.2_Silent_p.A1755A			P25054	APC_HUMAN	adenomatous polyposis coli	1755	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AAGCATCTGCGTCTTCTTCTG	0.398		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)			G|||	21	0.00419329	0.0068	0.0029	5008	,	,		19623	0.001		0.006	False		,,,				2504	0.0031				p.A1755A	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	.	APC	4158	.	2	Unknown(1)|Deletion - Frameshift(1)	soft_tissue(1)|skin(1)	c.G5265A						PASS	.	G	,,	43,4361	44.6+/-78.6	0,43,2159	56.0	55.0	56.0		5265,5265,5211	1.6	0.0	5	dbSNP_126	56	79,8517	43.6+/-101.6	1,77,4220	no	coding-synonymous,coding-synonymous,coding-synonymous	APC	NM_000038.5,NM_001127510.2,NM_001127511.2	,,	1,120,6379	AA,AG,GG		0.919,0.9764,0.9385	,,	1755/2844,1755/2844,1737/2826	112176556	122,12878	2202	4298	6500	SO:0001819	synonymous_variant	324	exon17	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	ATCTGCGTCTTCT	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.5265G>A	5.37:g.112176556G>A		114.0	0.0	0		109.0	41.0	0.376147	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																			G|0.992;A|0.008	0.008	strong		0.398	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
CREB3L3	84699	hgsc.bcm.edu	37	19	4171825	4171825	+	Silent	SNP	G	G	A	rs115268777	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:4171825G>A	ENST00000078445.2	+	10	1392	c.1245G>A	c.(1243-1245)acG>acA	p.T415T	CREB3L3_ENST00000602147.1_3'UTR|CREB3L3_ENST00000602257.1_Silent_p.T413T|CREB3L3_ENST00000252587.3_3'UTR|CREB3L3_ENST00000595923.1_Silent_p.T414T	NM_001271995.1|NM_001271996.1|NM_032607.1	NP_001258924.1|NP_001258925.1|NP_115996.1	Q68CJ9	CR3L3_HUMAN	cAMP responsive element binding protein 3-like 3	415					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	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)			breast(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|urinary_tract(3)	24				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0232)|STAD - Stomach adenocarcinoma(1328;0.18)		CCAATTCGACGGAGGAGCTGG	0.672													G|||	52	0.0103834	0.0393	0.0	5008	,	,		16107	0.0		0.0	False		,,,				2504	0.0				p.T415T		Atlas-SNP	.											.	CREB3L3	53	.	0			c.G1245A						PASS	.	G		158,4248	104.3+/-142.8	3,152,2048	37.0	41.0	40.0		1245	-4.7	0.0	19	dbSNP_132	40	1,8589	1.2+/-3.3	0,1,4294	no	coding-synonymous	CREB3L3	NM_032607.1		3,153,6342	AA,AG,GG		0.0116,3.586,1.2235		415/462	4171825	159,12837	2203	4295	6498	SO:0001819	synonymous_variant	84699	exon10			TTCGACGGAGGAG		CCDS12121.1, CCDS62498.1, CCDS62499.1, CCDS62500.1	19p13.3	2013-01-10				ENSG00000060566		"""basic leucine zipper proteins"""	18855	protein-coding gene	gene with protein product		611998				11353085	Standard	NM_032607		Approved	CREB-H	uc002lzl.4	Q68CJ9		ENST00000078445.2:c.1245G>A	19.37:g.4171825G>A		123.0	0.0	0		125.0	68.0	0.544	NM_032607	B2R7S6|B7ZL69|M0QYW7|Q6ZMC5|Q96TB9	Silent	SNP	ENST00000078445.2	37	CCDS12121.1																																																																																			G|0.988;A|0.012	0.012	strong		0.672	CREB3L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457922.1	NM_032607	
GAB4	128954	hgsc.bcm.edu	37	22	17472785	17472785	+	Silent	SNP	G	G	A	rs116325774	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:17472785G>A	ENST00000400588.1	-	2	563	c.456C>T	c.(454-456)ggC>ggT	p.G152G	GAB4_ENST00000523144.1_5'UTR	NM_001037814.1	NP_001032903.1	Q2WGN9	GAB4_HUMAN	GRB2-associated binding protein family, member 4	152	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.									breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(24)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	44		all_epithelial(15;0.112)|Lung NSC(13;0.248)				CCTGCCTGAAGCCACAGATCT	0.547													G|||	30	0.00599042	0.0227	0.0	5008	,	,		21341	0.0		0.0	False		,,,				2504	0.0				p.G152G		Atlas-SNP	.											GAB4,NS,carcinoma,-1,1	GAB4	95	1	0			c.C456T						scavenged	.	G		60,4346	55.5+/-91.7	1,58,2144	241.0	243.0	242.0		456	1.8	1.0	22	dbSNP_132	242	0,8600		0,0,4300	no	coding-synonymous	GAB4	NM_001037814.1		1,58,6444	AA,AG,GG		0.0,1.3618,0.4613		152/575	17472785	60,12946	2203	4300	6503	SO:0001819	synonymous_variant	128954	exon2			CCTGAAGCCACAG	AK057252	CCDS42976.1	22q11.2	2013-01-10			ENSG00000215568	ENSG00000215568		"""Pleckstrin homology (PH) domain containing"""	18325	protein-coding gene	gene with protein product							Standard	NM_001037814		Approved		uc002zlw.3	Q2WGN9	OTTHUMG00000149992	ENST00000400588.1:c.456C>T	22.37:g.17472785G>A		272.0	2.0	0.00735294		284.0	136.0	0.478873	NM_001037814		Silent	SNP	ENST00000400588.1	37	CCDS42976.1																																																																																			G|0.994;A|0.006	0.006	strong		0.547	GAB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315426.1	XM_372882	
IVL	3713	hgsc.bcm.edu	37	1	152882811	152882811	+	Missense_Mutation	SNP	G	G	A	rs75111974	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:152882811G>A	ENST00000368764.3	+	2	602	c.538G>A	c.(538-540)Gag>Aag	p.E180K	IVL_ENST00000392667.2_Missense_Mutation_p.E34K			P07476	INVO_HUMAN	involucrin	180	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].				isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			ggagcagcaggaggggcagct	0.647													G|||	107	0.0213658	0.0779	0.0058	5008	,	,		15888	0.0		0.0	False		,,,				2504	0.0				p.E180K		Atlas-SNP	.											.	IVL	100	.	0			c.G538A						PASS	.	G	LYS/GLU	255,4147		3,249,1949	13.0	15.0	14.0		538	0.1	0.0	1	dbSNP_131	14	2,8584		0,2,4291	no	missense	IVL	NM_005547.2	56	3,251,6240	AA,AG,GG		0.0233,5.7928,1.9787	possibly-damaging	180/586	152882811	257,12731	2201	4293	6494	SO:0001583	missense	3713	exon2			CAGCAGGAGGGGC	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.538G>A	1.37:g.152882811G>A	ENSP00000357753:p.Glu180Lys	126.0	0.0	0		205.0	112.0	0.546341	NM_005547	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	37	CCDS1030.1	31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	G	9.931	1.214712	0.22289	0.057928	2.33E-4	ENSG00000163207	ENST00000368764;ENST00000392667	T;T	0.11495	3.0;2.77	3.55	0.138	0.14793	.	.	.	.	.	T	0.03520	0.0101	L	0.38531	1.155	0.09310	N	1	P	0.38280	0.625	B	0.39738	0.308	T	0.39761	-0.9598	9	0.25106	T	0.35	.	12.3464	0.55124	0.0:0.5062:0.4938:0.0	rs62641593	180	P07476	INVO_HUMAN	K	180;34	ENSP00000357753:E180K;ENSP00000376435:E34K	ENSP00000357753:E180K	E	+	1	0	IVL	151149435	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	0.353000	0.20130	0.285000	0.22329	-0.662000	0.03851	GAG	G|0.980;A|0.020	0.020	strong		0.647	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547	
NOS1	4842	hgsc.bcm.edu	37	12	117685255	117685255	+	Silent	SNP	G	G	A	rs41410247	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr12:117685255G>A	ENST00000338101.4	-	18	2827	c.2823C>T	c.(2821-2823)ctC>ctT	p.L941L	NOS1_ENST00000344089.3_3'UTR|NOS1_ENST00000317775.6_Silent_p.L907L			Q8WY41	NANO1_HUMAN	nitric oxide synthase 1 (neuronal)	0					cell migration (GO:0016477)|epithelial cell migration (GO:0010631)|negative regulation of translation (GO:0017148)	cytoplasm (GO:0005737)|perinuclear region of cytoplasm (GO:0048471)	RNA binding (GO:0003723)|translation repressor activity (GO:0030371)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(21)|lung(43)|ovary(3)|pancreas(1)|prostate(6)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	117	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.0561)		GTTCTTCCAGGAGGGTGTCCA	0.552													G|||	37	0.00738818	0.0272	0.0014	5008	,	,		16371	0.0		0.0	False		,,,				2504	0.0				p.L941L	Esophageal Squamous(162;1748 2599 51982 52956)	Atlas-SNP	.											.	NOS1	240	.	0			c.C2823T						PASS	.	G	,,,	95,3833		0,95,1869	91.0	91.0	91.0		2721,1713,1713,2823	2.7	1.0	12	dbSNP_127	91	5,8315		0,5,4155	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NOS1	NM_000620.4,NM_001204213.1,NM_001204214.1,NM_001204218.1	,,,	0,100,6024	AA,AG,GG		0.0601,2.4185,0.8165	,,,	907/1435,571/1099,571/1099,941/1469	117685255	100,12148	1964	4160	6124	SO:0001819	synonymous_variant	4842	exon19			TTCCAGGAGGGTG		CCDS41842.1, CCDS55890.1	12q24.22	2013-09-19			ENSG00000089250	ENSG00000089250	1.14.13.39		7872	protein-coding gene	gene with protein product		163731		NOS		1385308, 7682706	Standard	NM_001204213		Approved	nNOS	uc001twn.2	P29475	OTTHUMG00000137376	ENST00000338101.4:c.2823C>T	12.37:g.117685255G>A		159.0	0.0	0		157.0	72.0	0.458599	NM_001204218		Silent	SNP	ENST00000338101.4	37	CCDS55890.1																																																																																			G|0.995;A|0.005	0.005	strong		0.552	NOS1-002	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000268053.1		
MUC4	4585	hgsc.bcm.edu	37	3	195511608	195511608	+	Silent	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:195511608T>C	ENST00000463781.3	-	2	7302	c.6843A>G	c.(6841-6843)gtA>gtG	p.V2281V	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000346145.4_Intron|MUC4_ENST00000475231.1_Silent_p.V2281V	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)		CACCTGTGGATACTGAGGAAA	0.582																																					p.V2281V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,1	MUC4	1505	1	0			c.A6843G						scavenged	.																																			SO:0001819	synonymous_variant	4585	exon2			TGTGGATACTGAG	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.6843A>G	3.37:g.195511608T>C		505.0	1.0	0.0019802		167.0	18.0	0.107784	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			.	.	none		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ZDHHC7	55625	hgsc.bcm.edu	37	16	85011548	85011548	+	Missense_Mutation	SNP	C	C	T	rs13334011	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:85011548C>T	ENST00000313732.4	-	6	953	c.601G>A	c.(601-603)Gtc>Atc	p.V201I	ZDHHC7_ENST00000569488.1_5'UTR|ZDHHC7_ENST00000564466.1_Missense_Mutation_p.V238I	NM_017740.2	NP_060210.2	Q9NXF8	ZDHC7_HUMAN	zinc finger, DHHC-type containing 7	201			V -> I (in dbSNP:rs13334011).		peptidyl-L-cysteine S-palmitoylation (GO:0018230)|protein palmitoylation (GO:0018345)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			large_intestine(6)|lung(4)	10						TGCCCTCGGACACAGGAGATG	0.443													C|||	134	0.0267572	0.0968	0.0086	5008	,	,		19553	0.0		0.0	False		,,,				2504	0.0				p.V238I		Atlas-SNP	.											.	ZDHHC7	55	.	0			c.G712A						PASS	.	C	ILE/VAL,ILE/VAL	332,4066	175.1+/-204.6	13,306,1880	138.0	130.0	133.0		712,601	5.2	1.0	16	dbSNP_121	133	7,8593	5.0+/-18.6	0,7,4293	yes	missense,missense	ZDHHC7	NM_001145548.1,NM_017740.2	29,29	13,313,6173	TT,TC,CC		0.0814,7.5489,2.6081	benign,benign	238/346,201/309	85011548	339,12659	2199	4300	6499	SO:0001583	missense	55625	exon7			CTCGGACACAGGA	AK000286	CCDS10950.1, CCDS45538.1	16q23.1	2010-02-09			ENSG00000153786	ENSG00000153786		"""Zinc fingers, DHHC-type"""	18459	protein-coding gene	gene with protein product	"""Sertoli cell gene with zinc finger domain-&#946;"""	614604					Standard	NM_017740		Approved	FLJ10792, ZNF370, FLJ20279, SERZ-B, SERZ1	uc002fiq.2	Q9NXF8	OTTHUMG00000137645	ENST00000313732.4:c.601G>A	16.37:g.85011548C>T	ENSP00000315604:p.Val201Ile	181.0	0.0	0		187.0	91.0	0.486631	NM_001145548	D3DUM1|Q8WV42|Q9NVD8	Missense_Mutation	SNP	ENST00000313732.4	37	CCDS10950.1	52	0.023809523809523808	50	0.1016260162601626	2	0.0055248618784530384	0	0.0	0	0.0	C	11.97	1.796547	0.31777	0.075489	8.14E-4	ENSG00000153786	ENST00000313732;ENST00000344861	T;T	0.39229	1.09;1.09	5.21	5.21	0.72293	.	0.056982	0.64402	D	0.000001	T	0.00845	0.0028	N	0.17631	0.505	0.58432	D	0.999999	B;B	0.12630	0.006;0.004	B;B	0.17979	0.02;0.02	T	0.01652	-1.1303	10	0.26408	T	0.33	-23.2644	17.7601	0.88462	0.0:1.0:0.0:0.0	rs13334011;rs56605352;rs13334011	238;201	Q9NXF8-2;Q9NXF8	.;ZDHC7_HUMAN	I	201;238	ENSP00000315604:V201I;ENSP00000341681:V238I	ENSP00000315604:V201I	V	-	1	0	ZDHHC7	83569049	1.000000	0.71417	0.995000	0.50966	0.805000	0.45488	3.515000	0.53429	2.428000	0.82296	0.561000	0.74099	GTC	C|0.962;T|0.038	0.038	strong		0.443	ZDHHC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269087.1	NM_017740	
CYP4F12	66002	hgsc.bcm.edu	37	19	15791081	15791081	+	Missense_Mutation	SNP	T	T	C	rs146740964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:15791081T>C	ENST00000550308.1	+	4	751	c.371T>C	c.(370-372)tTc>tCc	p.F124S	CYP4F12_ENST00000324632.10_Missense_Mutation_p.F124S	NM_023944.3	NP_076433	Q9HCS2	CP4FC_HUMAN	cytochrome P450, family 4, subfamily F, polypeptide 12	124					arachidonic acid metabolic process (GO:0019369)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|leukotriene B4 catabolic process (GO:0036101)|long-chain fatty acid metabolic process (GO:0001676)|negative regulation of blood coagulation (GO:0030195)|oxidation-reduction process (GO:0055114)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|very long-chain fatty acid metabolic process (GO:0000038)|vitamin E metabolic process (GO:0042360)|vitamin K biosynthetic process (GO:0042371)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			NS(1)|central_nervous_system(3)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	41	Acute lymphoblastic leukemia(2;0.0367)				Fingolimod(DB08868)	GATAATCTCTTCATCAGGTTC	0.572													.|||	103	0.0205671	0.0734	0.0072	5008	,	,		20653	0.0		0.001	False		,,,				2504	0.0				p.F124S		Atlas-SNP	.											.	CYP4F12	89	.	0			c.T371C						PASS	.	C	SER/PHE	125,4253		1,123,2065	133.0	138.0	136.0		371	-1.0	0.0	19	dbSNP_134	136	2,8586		0,2,4292	yes	missense	CYP4F12	NM_023944.3	155	1,125,6357	CC,CT,TT		0.0233,2.8552,0.9795	benign	124/525	15791081	127,12839	2189	4294	6483	SO:0001583	missense	66002	exon4			ATCTCTTCATCAG	AB035130	CCDS42517.1	19p13.1	2008-02-05	2003-01-14		ENSG00000186204	ENSG00000186204		"""Cytochrome P450s"""	18857	protein-coding gene	gene with protein product		611485	"""cytochrome P450, subfamily IVF, polypeptide 12"""			11162607	Standard	NM_023944		Approved		uc002nbl.3	Q9HCS2	OTTHUMG00000164477	ENST00000550308.1:c.371T>C	19.37:g.15791081T>C	ENSP00000448998:p.Phe124Ser	264.0	0.0	0		374.0	93.0	0.248663	NM_023944	E7ET51|O60389|Q5JPJ7|Q9HCS1	Missense_Mutation	SNP	ENST00000550308.1	37	CCDS42517.1	37	0.01694139194139194	34	0.06910569105691057	3	0.008287292817679558	0	0.0	0	0.0	.	3.728	-0.056179	0.07362	0.028552	2.33E-4	ENSG00000186204	ENST00000550308;ENST00000324632	T;T	0.70516	-0.49;-0.49	2.92	-1.0	0.10196	.	0.280349	0.26467	N	0.024209	T	0.08133	0.0203	N	0.17872	0.535	0.09310	N	1	B;P;B	0.34522	0.432;0.455;0.004	B;P;B	0.44811	0.344;0.461;0.091	T	0.20140	-1.0284	10	0.30078	T	0.28	.	4.0942	0.09983	0.1789:0.1265:0.0:0.6945	.	124;124;124	B4E2R2;B4E270;Q9HCS2	.;.;CP4FC_HUMAN	S	124	ENSP00000448998:F124S;ENSP00000321821:F124S	ENSP00000321821:F124S	F	+	2	0	CYP4F12	15652081	0.049000	0.20398	0.004000	0.12327	0.000000	0.00434	0.065000	0.14466	-0.503000	0.06586	-3.688000	0.00024	TTC	T|0.989;C|0.011	0.011	strong		0.572	CYP4F12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378938.9		
EHHADH	1962	hgsc.bcm.edu	37	3	184910042	184910042	+	Missense_Mutation	SNP	A	A	G	rs11927618	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr3:184910042A>G	ENST00000231887.3	-	7	2219	c.2144T>C	c.(2143-2145)tTg>tCg	p.L715S	EHHADH_ENST00000456310.1_Missense_Mutation_p.L619S|EHHADH-AS1_ENST00000417720.1_RNA	NM_001166415.1|NM_001966.3	NP_001159887.1|NP_001957.2	Q08426	ECHP_HUMAN	enoyl-CoA, hydratase/3-hydroxyacyl CoA dehydrogenase	715			L -> S (in dbSNP:rs11927618).		fatty acid beta-oxidation (GO:0006635)|internal protein amino acid acetylation (GO:0006475)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|peroxisome (GO:0005777)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|coenzyme binding (GO:0050662)|dodecenoyl-CoA delta-isomerase activity (GO:0004165)|enoyl-CoA hydratase activity (GO:0004300)|enzyme binding (GO:0019899)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|prostate(2)|skin(3)	24	all_cancers(143;4.04e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;1.98e-32)|OV - Ovarian serous cystadenocarcinoma(80;5.55e-21)			GGAGCCTGCCAAGCTTTGCCA	0.438													A|||	136	0.0271565	0.0976	0.0086	5008	,	,		19259	0.0		0.001	False		,,,				2504	0.0				p.L715S		Atlas-SNP	.											.	EHHADH	73	.	0			c.T2144C						PASS	.	A	SER/LEU,SER/LEU	328,4078	169.1+/-199.8	18,292,1893	71.0	77.0	75.0		1856,2144	5.9	1.0	3	dbSNP_120	75	2,8598		0,2,4298	yes	missense,missense	EHHADH	NM_001166415.1,NM_001966.3	145,145	18,294,6191	GG,GA,AA		0.0233,7.4444,2.5373	possibly-damaging,possibly-damaging	619/628,715/724	184910042	330,12676	2203	4300	6503	SO:0001583	missense	1962	exon7			CCTGCCAAGCTTT	L07077	CCDS33901.1, CCDS54694.1	3q26.3-q28	2012-07-13	2010-04-30		ENSG00000113790	ENSG00000113790	4.2.1.17, 1.1.1.35, 5.3.3.8		3247	protein-coding gene	gene with protein product		607037	"""enoyl-Coenzyme A, hydratase/3-hydroxyacyl Coenzyme A dehydrogenase"""	ECHD		8188243	Standard	NM_001966		Approved		uc003fpf.3	Q08426	OTTHUMG00000156698	ENST00000231887.3:c.2144T>C	3.37:g.184910042A>G	ENSP00000231887:p.Leu715Ser	126.0	0.0	0		128.0	67.0	0.523438	NM_001966	A8K6Y3|B4DWG3|D3DNU0|Q58EZ5	Missense_Mutation	SNP	ENST00000231887.3	37	CCDS33901.1	42	0.019230769230769232	38	0.07723577235772358	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	A	14.60	2.584965	0.46110	0.074444	2.33E-4	ENSG00000113790	ENST00000231887;ENST00000456310	T;T	0.75050	-0.49;-0.9	5.91	5.91	0.95273	.	0.563402	0.17628	N	0.167493	T	0.06690	0.0171	N	0.14661	0.345	0.80722	D	1	P	0.48834	0.916	B	0.41988	0.372	T	0.16571	-1.0398	10	0.33940	T	0.23	-11.2071	11.1978	0.48724	0.8307:0.0:0.0:0.1693	rs11927618;rs11927618	715	Q08426	ECHP_HUMAN	S	715;619	ENSP00000231887:L715S;ENSP00000387746:L619S	ENSP00000231887:L715S	L	-	2	0	EHHADH	186392736	0.991000	0.36638	0.998000	0.56505	0.771000	0.43674	2.683000	0.46943	2.254000	0.74563	0.533000	0.62120	TTG	A|0.975;G|0.025	0.025	strong		0.438	EHHADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345326.1		
PRSS38	339501	hgsc.bcm.edu	37	1	228003843	228003843	+	Silent	SNP	C	C	T	rs113353225	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:228003843C>T	ENST00000366757.3	+	2	225	c.201C>T	c.(199-201)ccC>ccT	p.P67P		NM_183062.2	NP_898885.1	A1L453	PRS38_HUMAN	protease, serine, 38	67	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						TCCCTGCGCCCGAGAGGAAGT	0.672													C|||	73	0.0145767	0.0537	0.0029	5008	,	,		14096	0.0		0.0	False		,,,				2504	0.0				p.P67P		Atlas-SNP	.											.	PRSS38	55	.	0			c.C201T						PASS	.	C		279,4127	151.8+/-185.6	4,271,1928	67.0	75.0	73.0		201	-8.3	0.0	1	dbSNP_132	73	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	PRSS38	NM_183062.2		4,272,6226	TT,TC,CC		0.0116,6.3323,2.1532		67/327	228003843	280,12724	2203	4299	6502	SO:0001819	synonymous_variant	339501	exon2			TGCGCCCGAGAGG		CCDS1563.1	1q42.13	2010-05-07			ENSG00000185888	ENSG00000185888		"""Serine peptidases / Serine peptidases"""	29625	protein-coding gene	gene with protein product	"""marapsin 2"""					12838346	Standard	NM_183062		Approved	MPN2	uc001hrh.3	A1L453	OTTHUMG00000037701	ENST00000366757.3:c.201C>T	1.37:g.228003843C>T		195.0	1.0	0.00512821		246.0	139.0	0.565041	NM_183062	Q7RTY6	Silent	SNP	ENST00000366757.3	37	CCDS1563.1																																																																																			C|0.982;T|0.018	0.018	strong		0.672	PRSS38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091981.1	NM_183062	
AHCTF1	25909	hgsc.bcm.edu	37	1	247013203	247013203	+	Silent	SNP	G	G	A	rs41308156	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:247013203G>A	ENST00000391829.2	-	33	6228	c.6105C>T	c.(6103-6105)aaC>aaT	p.N2035N	AHCTF1_ENST00000470300.1_5'UTR|AHCTF1_ENST00000366508.1_Silent_p.N2070N|AHCTF1_ENST00000326225.3_Silent_p.N2044N			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	2035	Disordered. {ECO:0000250}.|Necessary for nuclear localization. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			AAAGTTCCTCGTTTGGCACTA	0.383													G|||	221	0.0441294	0.1641	0.0058	5008	,	,		19777	0.0		0.0	False		,,,				2504	0.0				p.N2044N	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.C6132T						PASS	.	G		555,3851	241.8+/-252.1	29,497,1677	59.0	60.0	60.0		6132	0.8	0.9	1	dbSNP_127	60	5,8589	4.3+/-15.6	0,5,4292	no	coding-synonymous	AHCTF1	NM_015446.4		29,502,5969	AA,AG,GG		0.0582,12.5965,4.3077		2044/2276	247013203	560,12440	2203	4297	6500	SO:0001819	synonymous_variant	25909	exon33			TTCCTCGTTTGGC		CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"""ELYS transcription factor like protein TMBS62"""	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.6105C>T	1.37:g.247013203G>A		201.0	0.0	0		231.0	101.0	0.437229	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Silent	SNP	ENST00000391829.2	37																																																																																				.	.	weak		0.383	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446	
ECT2L	345930	hgsc.bcm.edu	37	6	139170412	139170412	+	Missense_Mutation	SNP	A	A	G	rs75962473	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:139170412A>G	ENST00000423192.1	+	8	1071	c.910A>G	c.(910-912)Atg>Gtg	p.M304V	ECT2L_ENST00000541398.1_Missense_Mutation_p.M235V|ECT2L_ENST00000367682.2_Missense_Mutation_p.M304V			Q008S8	ECT2L_HUMAN	epithelial cell transforming 2 like	304							Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(7)|lung(12)|skin(1)|upper_aerodigestive_tract(1)	30						CCAGATGGTGATGGAGAGTGT	0.398			"""N, Splice, Mis"""		ETP ALL								G|||	67	0.0133786	0.0477	0.0058	5008	,	,		15878	0.0		0.0	False		,,,				2504	0.0				p.M304V		Atlas-SNP	.		Rec	yes		6	6q24.1	345930	epithelial cell transforming sequence 2 oncogene-like		L	.	ECT2L	75	.	0			c.A910G						PASS	.	G	VAL/MET,VAL/MET	132,3612		4,124,1744	213.0	193.0	199.0		910,910	3.8	0.7	6	dbSNP_131	199	4,8222		0,4,4109	yes	missense,missense	ECT2L	NM_001077706.2,NM_001195037.2	21,21	4,128,5853	GG,GA,AA		0.0486,3.5256,1.1362	benign,benign	304/905,304/905	139170412	136,11834	1872	4113	5985	SO:0001583	missense	345930	exon8			ATGGTGATGGAGA		CCDS43508.1	6q24.1	2014-03-11	2014-03-11		ENSG00000203734	ENSG00000203734		"""Rho guanine nucleotide exchange factors"", ""F-boxes /  ""other"""""	21118	protein-coding gene	gene with protein product	"""lung specific F-box and DH domain containing protein"", ""F-box protein 49"""		"""chromosome 6 open reading frame 91"", ""epithelial cell transforming sequence 2 oncogene-like"""	C6orf91			Standard	NM_001077706		Approved	ARHGEF32, FBXO49, LFDH	uc021zfx.1	Q008S8	OTTHUMG00000015679	ENST00000423192.1:c.910A>G	6.37:g.139170412A>G	ENSP00000387388:p.Met304Val	120.0	0.0	0		132.0	69.0	0.522727	NM_001195037	B2RUV6|Q5JWK2|Q5JWK3|Q5JWK4	Missense_Mutation	SNP	ENST00000423192.1	37	CCDS43508.1	23	0.010531135531135532	20	0.04065040650406504	3	0.008287292817679558	0	0.0	0	0.0	G	0.004	-2.271576	0.00257	0.035256	4.86E-4	ENSG00000203734	ENST00000423192;ENST00000367682;ENST00000541398	T;T;T	0.72942	0.41;0.41;-0.7	5.6	3.8	0.43715	.	1.849090	0.04925	N	0.455693	T	0.14056	0.0340	N	0.01109	-1.01	0.19300	N	0.999979	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34950	-0.9808	10	0.02654	T	1	-0.0057	7.1142	0.25407	0.1538:0.1408:0.7055:0.0	.	235;304	F5H7S9;Q008S8	.;ECT2L_HUMAN	V	304;304;235	ENSP00000387388:M304V;ENSP00000356655:M304V;ENSP00000442307:M235V	ENSP00000356655:M304V	M	+	1	0	ECT2L	139212105	1.000000	0.71417	0.718000	0.30602	0.010000	0.07245	0.951000	0.29135	0.406000	0.25560	-0.186000	0.12905	ATG	A|0.992;G|0.008	0.008	strong		0.398	ECT2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042441.3	NM_001077706	
NOL8	55035	hgsc.bcm.edu	37	9	95081569	95081569	+	Silent	SNP	T	T	C	rs16908298	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:95081569T>C	ENST00000535387.1	-	4	350	c.351A>G	c.(349-351)ttA>ttG	p.L117L	NOL8_ENST00000542053.1_Silent_p.L49L|NOL8_ENST00000545558.1_Silent_p.L117L|NOL8_ENST00000358855.4_Silent_p.L49L|NOL8_ENST00000442668.2_Silent_p.L117L|NOL8_ENST00000543985.1_5'Flank					nucleolar protein 8											endometrium(3)|kidney(2)|large_intestine(5)|lung(5)|ovary(1)	16						CTGTCTTTTCTAACAAGTTGG	0.428													T|||	166	0.033147	0.1172	0.0159	5008	,	,		20037	0.0		0.0	False		,,,				2504	0.0				p.L117L		Atlas-SNP	.											.	NOL8	118	.	0			c.A351G						PASS	.	T		382,3474		15,352,1561	183.0	167.0	172.0		351	-3.3	0.0	9	dbSNP_123	172	9,8229		0,9,4110	no	coding-synonymous	NOL8	NM_017948.5		15,361,5671	CC,CT,TT		0.1092,9.9066,3.233		117/1168	95081569	391,11703	1928	4119	6047	SO:0001819	synonymous_variant	55035	exon5			CTTTTCTAACAAG	AB109030	CCDS47993.1, CCDS59135.1	9q22.32	2013-02-12	2004-01-12	2004-01-14	ENSG00000198000	ENSG00000198000		"""RNA binding motif (RRM) containing"""	23387	protein-coding gene	gene with protein product		611534	"""chromosome 9 open reading frame 34"""	C9orf34		12477932	Standard	NM_017948		Approved	FLJ20736, Nop132	uc022bjx.1	Q76FK4	OTTHUMG00000020221	ENST00000535387.1:c.351A>G	9.37:g.95081569T>C		284.0	0.0	0		241.0	156.0	0.647303	NM_017948		Silent	SNP	ENST00000535387.1	37	CCDS47993.1																																																																																			T|0.969;C|0.031	0.031	strong		0.428	NOL8-010	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000053082.2	NM_017948	
AHNAK2	113146	hgsc.bcm.edu	37	14	105414316	105414316	+	Missense_Mutation	SNP	G	G	A	rs145541349	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr14:105414316G>A	ENST00000333244.5	-	7	7591	c.7472C>T	c.(7471-7473)cCg>cTg	p.P2491L	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	2491						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CCCGAATGACGGCATCTTGAA	0.612													.|||	100	0.0199681	0.0741	0.0029	5008	,	,		18046	0.0		0.0	False		,,,				2504	0.0				p.P2491L		Atlas-SNP	.											AHNAK2_ENST00000333244,colon,carcinoma,+1,2	AHNAK2	719	2	0			c.C7472T						scavenged	.	G	LEU/PRO	217,3819		11,195,1812	175.0	202.0	193.0		7472	3.7	0.8	14	dbSNP_134	193	0,8354		0,0,4177	no	missense	AHNAK2	NM_138420.2	98	11,195,5989	AA,AG,GG		0.0,5.3766,1.7514	probably-damaging	2491/5796	105414316	217,12173	2018	4177	6195	SO:0001583	missense	113146	exon7			AATGACGGCATCT	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.7472C>T	14.37:g.105414316G>A	ENSP00000353114:p.Pro2491Leu	303.0	2.0	0.00660066		259.0	128.0	0.494208	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	31	0.014194139194139194	31	0.06300813008130081	0	0.0	0	0.0	0	0.0	g	16.25	3.069305	0.55539	0.053766	0.0	ENSG00000185567	ENST00000333244	T	0.03212	4.01	3.74	3.74	0.42951	.	.	.	.	.	T	0.03011	0.0089	H	0.95328	3.655	0.48632	D	0.999681	D	0.89917	1.0	D	0.97110	1.0	T	0.13469	-1.0508	9	0.42905	T	0.14	.	15.5871	0.76491	0.0:0.0:1.0:0.0	.	2491	Q8IVF2	AHNK2_HUMAN	L	2491	ENSP00000353114:P2491L	ENSP00000353114:P2491L	P	-	2	0	AHNAK2	104485361	0.998000	0.40836	0.839000	0.33178	0.181000	0.23173	3.089000	0.50183	1.642000	0.50584	0.485000	0.47835	CCG	G|0.988;A|0.012	0.012	strong		0.612	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
NEURL4	84461	hgsc.bcm.edu	37	17	7221454	7221454	+	Silent	SNP	G	G	A	rs73239601	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:7221454G>A	ENST00000399464.2	-	25	4005	c.3990C>T	c.(3988-3990)gcC>gcT	p.A1330A	RP11-542C16.2_ENST00000575474.1_Missense_Mutation_p.P144L|NEURL4_ENST00000574120.1_5'UTR|GPS2_ENST00000389167.5_5'Flank|GPS2_ENST00000380728.2_5'Flank|NEURL4_ENST00000315614.7_Silent_p.A1328A|NEURL4_ENST00000570460.1_Silent_p.A1306A|GPS2_ENST00000391950.3_5'Flank	NM_032442.2	NP_115818.2	Q96JN8	NEUL4_HUMAN	neuralized E3 ubiquitin protein ligase 4	1330						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GAGGACTAGCGGCAGGTGGTG	0.592													G|||	5	0.000998403	0.0038	0.0	5008	,	,		18299	0.0		0.0	False		,,,				2504	0.0				p.A1330A		Atlas-SNP	.											.	NEURL4	192	.	0			c.C3990T						PASS	.	G	,	22,4102		0,22,2040	82.0	93.0	89.0		3984,3990	1.4	0.1	17	dbSNP_130	89	1,8389		0,1,4194	no	coding-synonymous,coding-synonymous	NEURL4	NM_001005408.1,NM_032442.2	,	0,23,6234	AA,AG,GG		0.0119,0.5335,0.1838	,	1328/1561,1330/1563	7221454	23,12491	2062	4195	6257	SO:0001819	synonymous_variant	84461	exon25			ACTAGCGGCAGGT		CCDS42251.1, CCDS42252.1	17p13	2013-10-24	2013-10-24		ENSG00000215041	ENSG00000215041			34410	protein-coding gene	gene with protein product		615865	"""neuralized homolog 4 (Drosophila)"""			22261722, 22441691	Standard	NM_001005408		Approved	KIAA1787	uc002gga.1	Q96JN8	OTTHUMG00000132319	ENST00000399464.2:c.3990C>T	17.37:g.7221454G>A		97.0	0.0	0		87.0	43.0	0.494253	NM_032442	Q6GPI8|Q96IU9|Q9H0B0	Silent	SNP	ENST00000399464.2	37	CCDS42251.1																																																																																			G|0.999;A|0.001	0.001	strong		0.592	NEURL4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255434.2	NM_032442	
FSTL4	23105	hgsc.bcm.edu	37	5	132535225	132535225	+	Silent	SNP	G	G	A	rs61740558	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr5:132535225G>A	ENST00000265342.7	-	16	2340	c.2091C>T	c.(2089-2091)gaC>gaT	p.D697D	CTB-49A3.2_ENST00000509051.1_RNA	NM_015082.1	NP_055897.1	Q6MZW2	FSTL4_HUMAN	follistatin-like 4	697						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)	p.D697D(1)		autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(8)|skin(2)|upper_aerodigestive_tract(1)	23		all_cancers(142;0.244)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TGAAGCGCCCGTCGGGGGATG	0.607													G|||	110	0.0219649	0.0772	0.0115	5008	,	,		18282	0.0		0.0	False		,,,				2504	0.0				p.D697D		Atlas-SNP	.											FSTL4,colon,carcinoma,0,2	FSTL4	74	2	1	Substitution - coding silent(1)	large_intestine(1)	c.C2091T						PASS	.	G		270,4136	151.8+/-185.6	9,252,1942	49.0	52.0	51.0		2091	-4.1	0.6	5	dbSNP_129	51	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	FSTL4	NM_015082.1		9,258,6236	AA,AG,GG		0.0698,6.128,2.1221		697/843	132535225	276,12730	2203	4300	6503	SO:0001819	synonymous_variant	23105	exon16			GCGCCCGTCGGGG	AB028984	CCDS34238.1	5q31.1	2013-01-29			ENSG00000053108	ENSG00000053108		"""EF-hand domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	21389	protein-coding gene	gene with protein product						10470851, 15527507	Standard	NM_015082		Approved	KIAA1061	uc003kyn.1	Q6MZW2	OTTHUMG00000162729	ENST00000265342.7:c.2091C>T	5.37:g.132535225G>A		113.0	0.0	0		118.0	68.0	0.576271	NM_015082	Q8TBU0|Q9UPU1	Silent	SNP	ENST00000265342.7	37	CCDS34238.1																																																																																			G|0.980;A|0.020	0.020	strong		0.607	FSTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370212.1	XM_048786	
CHST5	23563	hgsc.bcm.edu	37	16	75564172	75564172	+	Silent	SNP	C	C	G	rs74355367	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:75564172C>G	ENST00000336257.3	-	3	1505	c.111G>C	c.(109-111)ctG>ctC	p.L37L	CHST5_ENST00000541075.1_Silent_p.L43L|RP11-77K12.7_ENST00000460606.1_3'UTR	NM_024533.4	NP_078809.2	Q9GZS9	CHST5_HUMAN	carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 5	37					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|N-acetylglucosamine metabolic process (GO:0006044)|protein sulfation (GO:0006477)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of Golgi membrane (GO:0031228)	N-acetylglucosamine 6-O-sulfotransferase activity (GO:0001517)|sulfotransferase activity (GO:0008146)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(2)	24						TGGTCTGTGCCAGGAGGAGCA	0.672													C|||	193	0.0385383	0.1422	0.0072	5008	,	,		17477	0.0		0.0	False		,,,				2504	0.0				p.L37L		Atlas-SNP	.											.	CHST5	47	.	0			c.G111C						PASS	.	C		537,3859	225.9+/-241.6	27,483,1688	32.0	28.0	29.0		111	1.1	1.0	16	dbSNP_131	29	16,8582	9.1+/-34.3	0,16,4283	no	coding-synonymous	CHST5	NM_024533.4		27,499,5971	GG,GC,CC		0.1861,12.2157,4.2558		37/412	75564172	553,12441	2198	4299	6497	SO:0001819	synonymous_variant	23563	exon3			CTGTGCCAGGAGG	AF176839	CCDS10919.1	16q23.1	2008-02-05			ENSG00000135702	ENSG00000135702		"""Sulfotransferases, membrane-bound"""	1973	protein-coding gene	gene with protein product		604817				10491328, 11017086	Standard	NM_024533		Approved	I-GLCNAC-6-ST, FLJ22167	uc002fei.3	Q9GZS9	OTTHUMG00000137610	ENST00000336257.3:c.111G>C	16.37:g.75564172C>G		95.0	0.0	0		114.0	52.0	0.45614	NM_024533	B2RV23|Q7LCN3|Q9UBY3	Silent	SNP	ENST00000336257.3	37	CCDS10919.1																																																																																			C|0.955;G|0.045	0.045	strong		0.672	CHST5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269025.2	NM_012126	
ZNF554	115196	hgsc.bcm.edu	37	19	2823100	2823100	+	Missense_Mutation	SNP	G	G	A	rs181024964	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:2823100G>A	ENST00000317243.5	+	2	314	c.116G>A	c.(115-117)cGc>cAc	p.R39H	ZNF554_ENST00000591265.1_Missense_Mutation_p.R39H	NM_001102651.1	NP_001096121.1	Q86TJ5	ZN554_HUMAN	zinc finger protein 554	39					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|liver(3)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	23		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)		TACCTGCCCCGCTGGTCCCAG	0.567													G|||	7	0.00139776	0.0045	0.0	5008	,	,		18086	0.001		0.0	False		,,,				2504	0.0				p.R39H		Atlas-SNP	.											.	ZNF554	47	.	0			c.G116A						PASS	.	G	HIS/ARG	7,3795		0,7,1894	51.0	55.0	54.0		116	0.6	0.0	19		54	0,8248		0,0,4124	yes	missense	ZNF554	NM_001102651.1	29	0,7,6018	AA,AG,GG		0.0,0.1841,0.0581	possibly-damaging	39/539	2823100	7,12043	1901	4124	6025	SO:0001583	missense	115196	exon2			TGCCCCGCTGGTC	AK027860	CCDS42462.1	19p13.3	2013-09-20			ENSG00000172006	ENSG00000172006		"""Zinc fingers, C2H2-type"", ""-"""	26629	protein-coding gene	gene with protein product						12477932	Standard	NM_001102651		Approved	FLJ34817	uc002lwm.2	Q86TJ5	OTTHUMG00000180493	ENST00000317243.5:c.116G>A	19.37:g.2823100G>A	ENSP00000321132:p.Arg39His	60.0	0.0	0		71.0	34.0	0.478873	NM_001102651	Q8NAT3|Q9BWN3	Missense_Mutation	SNP	ENST00000317243.5	37	CCDS42462.1	5	0.0022893772893772895	3	0.006097560975609756	0	0.0	2	0.0034965034965034965	0	0.0	G	6.811	0.518786	0.13005	0.001841	0.0	ENSG00000172006	ENST00000317243	T	0.07021	3.23	1.71	0.624	0.17659	Krueppel-associated box (1);	.	.	.	.	T	0.02267	0.0070	N	0.08118	0	0.09310	N	1	P	0.35050	0.482	B	0.24974	0.057	T	0.40813	-0.9543	9	0.56958	D	0.05	.	5.8806	0.18854	0.0:0.6302:0.3698:0.0	.	39	Q86TJ5	ZN554_HUMAN	H	39	ENSP00000321132:R39H	ENSP00000321132:R39H	R	+	2	0	ZNF554	2774100	0.000000	0.05858	0.041000	0.18516	0.029000	0.11900	-0.244000	0.08903	0.276000	0.22118	-0.502000	0.04539	CGC	G|0.998;A|0.002	0.002	strong		0.567	ZNF554-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451598.3	NM_152303	
PALLD	23022	hgsc.bcm.edu	37	4	169611765	169611765	+	Silent	SNP	C	C	T	rs17054482	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:169611765C>T	ENST00000505667.1	+	7	1520	c.1347C>T	c.(1345-1347)aaC>aaT	p.N449N	PALLD_ENST00000261509.6_Silent_p.N449N|PALLD_ENST00000335742.7_Silent_p.N67N|PALLD_ENST00000512127.1_Silent_p.N67N|PALLD_ENST00000333488.4_Silent_p.N326N			Q8WX93	PALLD_HUMAN	palladin, cytoskeletal associated protein	449	Ig-like C2-type 2.				cytoskeleton organization (GO:0007010)	actin filament (GO:0005884)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	muscle alpha-actinin binding (GO:0051371)			breast(4)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|liver(2)|lung(18)|ovary(3)|prostate(3)|skin(4)	48		Prostate(90;0.00996)|Renal(120;0.0203)|Melanoma(52;0.144)		GBM - Glioblastoma multiforme(119;0.204)		AACTGCAAAACACAGCCGTGG	0.498									Pancreatic Cancer, Familial Clustering of				c|||	210	0.0419329	0.1498	0.0159	5008	,	,		17440	0.0		0.001	False		,,,				2504	0.0				p.N449N	Esophageal Squamous(109;1482 1532 18347 40239 51172)	Atlas-SNP	.											.	PALLD	179	.	0			c.C1347T						PASS	.	T	,,	570,3836	251.8+/-258.4	41,488,1674	80.0	94.0	90.0		1347,201,1347	3.2	0.9	4	dbSNP_123	90	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous,coding-synonymous,coding-synonymous	PALLD	NM_001166108.1,NM_001166109.1,NM_016081.3	,,	41,496,5966	TT,TC,CC		0.093,12.9369,4.4441	,,	449/1124,67/778,449/1107	169611765	578,12428	2203	4300	6503	SO:0001819	synonymous_variant	23022	exon7	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1	GCAAAACACAGCC	AB023209	CCDS34098.1, CCDS54818.1, CCDS54819.1, CCDS54820.1	4q32.3	2013-01-11			ENSG00000129116	ENSG00000129116		"""Immunoglobulin superfamily / I-set domain containing"""	17068	protein-coding gene	gene with protein product		608092				10231032, 10931874	Standard	NM_001166108		Approved	KIAA0992, SIH002, CGI-151	uc011cjx.2	Q8WX93	OTTHUMG00000161097	ENST00000505667.1:c.1347C>T	4.37:g.169611765C>T		156.0	0.0	0		128.0	62.0	0.484375	NM_001166108	B3KTG2|B5MD56|B7ZMM5|Q7L3E0|Q7Z3W0|Q86WE8|Q8N1M2|Q9UGA0|Q9UQF5|Q9Y2J6|Q9Y3E9	Silent	SNP	ENST00000505667.1	37	CCDS54818.1																																																																																			C|0.962;T|0.038	0.038	strong		0.498	PALLD-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000363762.1	NM_016081	
ABCA7	10347	hgsc.bcm.edu	37	19	1058635	1058635	+	Missense_Mutation	SNP	C	C	T	rs73505232	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:1058635C>T	ENST00000263094.6	+	38	5399	c.5168C>T	c.(5167-5169)tCa>tTa	p.S1723L	ABCA7_ENST00000433129.1_Missense_Mutation_p.S1723L|ABCA7_ENST00000435683.2_Missense_Mutation_p.S1585L	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1723					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|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)		CAGTTCCAGTCACCCCTGCGC	0.552													C|||	196	0.0391374	0.143	0.0101	5008	,	,		17265	0.0		0.0	False		,,,				2504	0.0				p.S1723L		Atlas-SNP	.											.	ABCA7	174	.	0			c.C5168T						PASS	.	C	LEU/SER	578,3828	256.1+/-261.0	45,488,1670	60.0	62.0	61.0		5168	4.2	1.0	19	dbSNP_130	61	0,8600		0,0,4300	yes	missense	ABCA7	NM_019112.3	145	45,488,5970	TT,TC,CC		0.0,13.1185,4.4441	probably-damaging	1723/2147	1058635	578,12428	2203	4300	6503	SO:0001583	missense	10347	exon38			TCCAGTCACCCCT	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.5168C>T	19.37:g.1058635C>T	ENSP00000263094:p.Ser1723Leu	92.0	0.0	0		96.0	49.0	0.510417	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	37	CCDS12055.1	79	0.036172161172161175	74	0.15040650406504066	5	0.013812154696132596	0	0.0	0	0.0	C	20.3	3.973946	0.74246	0.131185	0.0	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.87650	-2.28;-2.28	4.23	4.23	0.50019	.	.	.	.	.	T	0.09730	0.0239	M	0.88450	2.955	0.28999	N	0.887598	P;D	0.61697	0.899;0.99	P;D	0.67103	0.735;0.949	T	0.35599	-0.9782	9	0.87932	D	0	.	15.318	0.74095	0.0:1.0:0.0:0.0	.	848;1723	D6W5Y0;Q8IZY2	.;ABCA7_HUMAN	L	1723	ENSP00000263094:S1723L;ENSP00000414062:S1723L	ENSP00000263094:S1723L	S	+	2	0	ABCA7	1009635	0.985000	0.35326	0.982000	0.44146	0.997000	0.91878	2.532000	0.45659	2.180000	0.69256	0.561000	0.74099	TCA	C|0.952;T|0.048	0.048	strong		0.552	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
ANKFN1	162282	hgsc.bcm.edu	37	17	54450073	54450073	+	Missense_Mutation	SNP	G	G	A	rs115263675	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:54450073G>A	ENST00000318698.2	+	6	712	c.677G>A	c.(676-678)aGt>aAt	p.S226N	ANKFN1_ENST00000566473.2_Missense_Mutation_p.S226N	NM_153228.2	NP_694960.2	Q8N957	ANKF1_HUMAN	ankyrin-repeat and fibronectin type III domain containing 1	226										NS(1)|breast(1)|cervix(2)|endometrium(4)|kidney(4)|large_intestine(11)|lung(27)|ovary(1)|prostate(1)|skin(1)	53						GAGAGGGTGAGTGAACTGTCT	0.502													G|||	77	0.0153754	0.056	0.0043	5008	,	,		17983	0.0		0.0	False		,,,				2504	0.0				p.S226N		Atlas-SNP	.											.	ANKFN1	115	.	0			c.G677A						PASS	.	G	ASN/SER	210,4196	128.2+/-165.1	3,204,1996	157.0	148.0	151.0		677	2.1	1.0	17	dbSNP_132	151	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ANKFN1	NM_153228.2	46	3,205,6295	AA,AG,GG		0.0116,4.7662,1.6223	benign	226/764	54450073	211,12795	2203	4300	6503	SO:0001583	missense	162282	exon6			GGGTGAGTGAACT	AK095654	CCDS32686.1	17q23.2	2014-02-12	2005-11-15		ENSG00000153930	ENSG00000153930		"""Ankyrin repeat domain containing"", ""Fibronectin type III domain containing"""	26766	protein-coding gene	gene with protein product							Standard	NM_153228		Approved	FLJ38335	uc002iun.1	Q8N957	OTTHUMG00000155010	ENST00000318698.2:c.677G>A	17.37:g.54450073G>A	ENSP00000321627:p.Ser226Asn	63.0	0.0	0		76.0	35.0	0.460526	NM_153228		Missense_Mutation	SNP	ENST00000318698.2	37	CCDS32686.1	29	0.013278388278388278	28	0.056910569105691054	1	0.0027624309392265192	0	0.0	0	0.0	G	6.241	0.412619	0.11812	0.047662	1.16E-4	ENSG00000153930	ENST00000318698	T	0.22539	1.95	5.64	2.14	0.27477	.	0.409722	0.29799	N	0.011164	T	0.00784	0.0026	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.33420	-0.9869	10	0.16896	T	0.51	-6.438	4.4468	0.11602	0.1486:0.2008:0.5381:0.1125	.	226	Q8N957	ANKF1_HUMAN	N	226	ENSP00000321627:S226N	ENSP00000321627:S226N	S	+	2	0	ANKFN1	51805072	0.802000	0.28943	0.995000	0.50966	0.985000	0.73830	0.633000	0.24598	1.317000	0.45149	0.462000	0.41574	AGT	G|0.982;A|0.018	0.018	strong		0.502	ANKFN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338043.1	NM_153228	
MGAM	8972	hgsc.bcm.edu	37	7	141719078	141719078	+	Missense_Mutation	SNP	A	A	G	rs114936410	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:141719078A>G	ENST00000549489.2	+	4	502	c.407A>G	c.(406-408)cAt>cGt	p.H136R	MGAM_ENST00000475668.2_Missense_Mutation_p.H136R	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	136					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)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TCCAAGAATCATAGCTACCAT	0.502													A|||	33	0.00658946	0.0234	0.0029	5008	,	,		18070	0.0		0.0	False		,,,				2504	0.0				p.H136R		Atlas-SNP	.											.	MGAM	767	.	0			c.A407G						PASS	.	A	ARG/HIS	70,4000		2,66,1967	86.0	90.0	89.0		407	3.7	1.0	7	dbSNP_132	89	0,8392		0,0,4196	yes	missense	MGAM	NM_004668.2	29	2,66,6163	GG,GA,AA		0.0,1.7199,0.5617	possibly-damaging	136/1858	141719078	70,12392	2035	4196	6231	SO:0001583	missense	8972	exon4			AGAATCATAGCTA	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.407A>G	7.37:g.141719078A>G	ENSP00000447378:p.His136Arg	46.0	0.0	0		38.0	15.0	0.394737	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	37	CCDS47727.1	21	0.009615384615384616	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	0	0.0	A	11.07	1.531130	0.27387	0.017199	0.0	ENSG00000257335	ENST00000465654;ENST00000549489;ENST00000497673;ENST00000475668;ENST00000548812	T;D;T	0.85339	-0.82;-1.97;0.55	4.85	3.7	0.42460	Glycoside hydrolase-type carbohydrate-binding (1);P-type trefoil (2);	0.276318	0.26251	N	0.025446	T	0.50752	0.1634	M	0.63843	1.955	0.32573	N	0.529585	P	0.44195	0.828	B	0.34385	0.181	T	0.74287	-0.3714	10	0.51188	T	0.08	.	8.8349	0.35107	0.9101:0.0:0.0899:0.0	.	136	O43451	MGA_HUMAN	R	136;136;136;136;13	ENSP00000419372:H136R;ENSP00000447378:H136R;ENSP00000417103:H136R	ENSP00000316431:H13R	H	+	2	0	MGAM	141365547	1.000000	0.71417	1.000000	0.80357	0.285000	0.27093	6.413000	0.73308	0.992000	0.38840	-0.476000	0.04901	CAT	A|0.990;G|0.010	0.010	strong		0.502	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
LGSN	51557	hgsc.bcm.edu	37	6	64004905	64004905	+	Missense_Mutation	SNP	T	T	A	rs2459568	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:64004905T>A	ENST00000370657.4	-	2	109	c.76A>T	c.(76-78)Aac>Tac	p.N26Y	LGSN_ENST00000370658.5_Missense_Mutation_p.N26Y			Q5TDP6	LGSN_HUMAN	lengsin, lens protein with glutamine synthetase domain	26			N -> Y (in dbSNP:rs2459568).		glutamine biosynthetic process (GO:0006542)	plasma membrane (GO:0005886)	glutamate-ammonia ligase activity (GO:0004356)			NS(1)|endometrium(2)|large_intestine(5)|lung(16)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	34						CTTAATGTGTTCATGCTGTTG	0.343													T|||	68	0.0135783	0.0499	0.0029	5008	,	,		18219	0.0		0.0	False		,,,				2504	0.0				p.N26Y		Atlas-SNP	.											.	LGSN	82	.	0			c.A76T						PASS	.	T	TYR/ASN,TYR/ASN	174,4232	114.2+/-152.2	4,166,2033	267.0	240.0	249.0		76,76	1.8	0.0	6	dbSNP_100	249	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	LGSN	NM_001143940.1,NM_016571.2	143,143	4,169,6330	AA,AT,TT		0.0349,3.9492,1.3609	benign,benign	26/209,26/510	64004905	177,12829	2203	4300	6503	SO:0001583	missense	51557	exon2			ATGTGTTCATGCT	AF242388	CCDS4964.1, CCDS55027.1	6q12	2013-09-19	2008-09-19	2008-09-19	ENSG00000146166	ENSG00000146166			21016	protein-coding gene	gene with protein product		611470	"""glutamate-ammonia ligase (glutamine synthetase) domain containing 1"""	GLULD1		12107412	Standard	NM_016571		Approved	LGS	uc003peh.3	Q5TDP6	OTTHUMG00000014946	ENST00000370657.4:c.76A>T	6.37:g.64004905T>A	ENSP00000359691:p.Asn26Tyr	302.0	0.0	0		362.0	163.0	0.450276	NM_016571	A1L421|Q0PVN9|Q0PVP0|Q9NYJ0	Missense_Mutation	SNP	ENST00000370657.4	37	CCDS4964.1	16	0.007326007326007326	14	0.028455284552845527	2	0.0055248618784530384	0	0.0	0	0.0	T	2.447	-0.327180	0.05350	0.039492	3.49E-4	ENSG00000146166	ENST00000370658;ENST00000370657	T;T	0.26660	1.72;1.83	4.71	1.8	0.24995	.	0.346161	0.36409	N	0.002618	T	0.02848	0.0085	N	0.02011	-0.69	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.10450	0.005;0.001;0.0	T	0.41142	-0.9525	10	0.46703	T	0.11	-6.0146	7.4053	0.26987	0.498:0.0:0.0:0.502	rs2459568;rs52826076;rs2459568	26;26;26	Q5TDP6-3;Q5TDP6-2;Q5TDP6	.;.;LGSN_HUMAN	Y	26	ENSP00000359692:N26Y;ENSP00000359691:N26Y	ENSP00000359691:N26Y	N	-	1	0	LGSN	64062864	0.001000	0.12720	0.003000	0.11579	0.007000	0.05969	0.975000	0.29449	0.746000	0.32786	-0.403000	0.06358	AAC	T|0.988;A|0.012	0.012	strong		0.343	LGSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041076.2	NM_016571	
CCDC28A	25901	hgsc.bcm.edu	37	6	139094936	139094936	+	Missense_Mutation	SNP	C	C	A	rs34538642	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:139094936C>A	ENST00000332797.6	+	1	280	c.125C>A	c.(124-126)tCc>tAc	p.S42Y		NM_015439.2	NP_056254.1	Q8IWP9	CC28A_HUMAN	coiled-coil domain containing 28A	42			S -> Y (in dbSNP:rs34538642).							autonomic_ganglia(1)|large_intestine(3)|lung(8)|ovary(1)	13				OV - Ovarian serous cystadenocarcinoma(155;0.000201)|GBM - Glioblastoma multiforme(68;0.000306)		AGGAGCGGGTCCCGGGATGTG	0.632													C|||	298	0.0595048	0.2148	0.0187	5008	,	,		16083	0.0		0.001	False		,,,				2504	0.0				p.S42Y		Atlas-SNP	.											.	CCDC28A	34	.	0			c.C125A						PASS	.	C	TYR/SER	746,3660	301.3+/-286.8	70,606,1527	83.0	103.0	96.0		125	-9.6	0.0	6	dbSNP_126	96	10,8590	7.7+/-29.5	0,10,4290	yes	missense	CCDC28A	NM_015439.2	144	70,616,5817	AA,AC,CC		0.1163,16.9315,5.8127	benign	42/275	139094936	756,12250	2203	4300	6503	SO:0001583	missense	25901	exon1			GCGGGTCCCGGGA	AY167571	CCDS5192.1	6q23.1-q24.1	2008-02-05	2005-09-12	2005-09-12	ENSG00000024862	ENSG00000024862			21098	protein-coding gene	gene with protein product		615353	"""chromosome 6 open reading frame 80"""	C6orf80			Standard	NM_015439		Approved	CCRL1AP, DKFZp586D0623	uc003qie.3	Q8IWP9	OTTHUMG00000015683	ENST00000332797.6:c.125C>A	6.37:g.139094936C>A	ENSP00000332716:p.Ser42Tyr	203.0	0.0	0		270.0	126.0	0.466667	NM_015439	E1P591|Q32NC7|Q66K67|Q96E23|Q9Y430	Missense_Mutation	SNP	ENST00000332797.6	37	CCDS5192.1	98	0.04487179487179487	95	0.19308943089430894	3	0.008287292817679558	0	0.0	0	0.0	C	4.671	0.124775	0.08931	0.169315	0.001163	ENSG00000024862	ENST00000332797	T	0.26067	1.76	4.79	-9.58	0.00559	.	5.212620	0.00597	N	0.000373	T	0.01730	0.0055	N	0.08118	0	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.22382	-1.0218	9	0.07175	T	0.84	6.5122	2.2197	0.03969	0.342:0.154:0.3568:0.1471	rs34538642	42	Q8IWP9	CC28A_HUMAN	Y	42	ENSP00000332716:S42Y	ENSP00000332716:S42Y	S	+	2	0	CCDC28A	139136629	0.000000	0.05858	0.000000	0.03702	0.068000	0.16541	-0.827000	0.04424	-2.758000	0.00371	-0.268000	0.10319	TCC	C|0.946;A|0.054	0.054	strong		0.632	CCDC28A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042444.1	NM_015439	
APOB	338	hgsc.bcm.edu	37	2	21258523	21258523	+	Missense_Mutation	SNP	C	C	T	rs61741625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:21258523C>T	ENST00000233242.1	-	7	878	c.751G>A	c.(751-753)Gct>Act	p.A251T	APOB_ENST00000399256.4_Missense_Mutation_p.A251T	NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	251	Heparin-binding.|Vitellogenin. {ECO:0000255|PROSITE- ProRule:PRU00557}.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TTCCTCTTAGCGTCCAGTGTG	0.502													C|||	13	0.00259585	0.0098	0.0	5008	,	,		21477	0.0		0.0	False		,,,				2504	0.0				p.A251T		Atlas-SNP	.											.	APOB	761	.	0			c.G751A						PASS	.	C	THR/ALA	34,4372	38.4+/-70.7	0,34,2169	130.0	105.0	114.0		751	-8.5	0.0	2	dbSNP_129	114	0,8600		0,0,4300	yes	missense	APOB	NM_000384.2	58	0,34,6469	TT,TC,CC		0.0,0.7717,0.2614	benign	251/4564	21258523	34,12972	2203	4300	6503	SO:0001583	missense	338	exon7			TCTTAGCGTCCAG	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.751G>A	2.37:g.21258523C>T	ENSP00000233242:p.Ala251Thr	120.0	0.0	0		106.0	58.0	0.54717	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	C	13.65	2.299459	0.40694	0.007717	0.0	ENSG00000084674	ENST00000233242;ENST00000535079;ENST00000399256	T;T	0.04809	3.55;3.55	5.73	-8.49	0.00931	Lipid transport protein, beta-sheet shell (1);Lipid transport protein, N-terminal (3);Vitellinogen, beta-sheet N-terminal (1);	1.266020	0.05424	N	0.544746	T	0.01029	0.0034	N	0.22421	0.69	0.09310	N	1	P	0.39520	0.676	B	0.32289	0.143	T	0.38628	-0.9652	10	0.21014	T	0.42	.	4.2167	0.10539	0.3063:0.3153:0.3062:0.0722	.	251	P04114	APOB_HUMAN	T	251	ENSP00000233242:A251T;ENSP00000382200:A251T	ENSP00000233242:A251T	A	-	1	0	APOB	21112028	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-1.261000	0.02855	-1.679000	0.01452	-1.193000	0.01689	GCT	C|0.997;T|0.003	0.003	strong		0.502	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
MATK	4145	hgsc.bcm.edu	37	19	3789321	3789321	+	5'Flank	SNP	G	G	A	rs74830030	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr19:3789321G>A	ENST00000310132.6	-	0	0				MATK_ENST00000395045.2_Nonsense_Mutation_p.R9*|MATK_ENST00000395040.2_5'Flank|MATK_ENST00000590821.1_5'UTR	NM_139355.2	NP_647612.1	P42679	MATK_HUMAN	megakaryocyte-associated tyrosine kinase						cell proliferation (GO:0008283)|mesoderm development (GO:0007498)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)	cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(13)|ovary(1)|skin(2)|stomach(2)|urinary_tract(1)	26		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00461)|STAD - Stomach adenocarcinoma(1328;0.18)		ccttctcttcgttcagcaggg	0.493													G|||	104	0.0207668	0.0726	0.0115	5008	,	,		19422	0.0		0.0	False		,,,				2504	0.0				p.R9X		Atlas-SNP	.											.	MATK	108	.	0			c.C25T						PASS	.	G	stop/ARG	253,4153	146.5+/-181.1	8,237,1958	46.0	44.0	45.0		25	-2.8	0.0	19	dbSNP_131	45	1,8599		0,1,4299	yes	stop-gained	MATK	NM_002378.3		8,238,6257	AA,AG,GG		0.0116,5.7422,1.9529		9/509	3789321	254,12752	2203	4300	6503	SO:0001631	upstream_gene_variant	4145	exon2			CTCTTCGTTCAGC	L18974	CCDS12113.1, CCDS12114.1, CCDS42468.1	19p13.3	2013-02-14						"""SH2 domain containing"""	6906	protein-coding gene	gene with protein product	"""Csk-homologous kinase"", ""tyrosine-protein kinase CTK"", ""protein kinase HYL"", ""hematopoietic consensus tyrosine-lacking kinase"", ""tyrosylprotein kinase"", ""hydroxyaryl-protein kinase"", ""Csk-type protein tyrosine kinase"", ""HYL tyrosine kinase"", ""tyrosine kinase MATK"", ""leukocyte carboxyl-terminal src kinase related"""	600038				8288563, 7530249	Standard	NM_139355		Approved	HYLTK, CTK, HYL, Lsk, CHK, HHYLTK, DKFZp434N1212, MGC1708, MGC2101	uc002lyt.3	P42679			19.37:g.3789321G>A	Exception_encountered	113.0	0.0	0		122.0	68.0	0.557377	NM_002378	B3KNZ9|Q9NST8	Nonsense_Mutation	SNP	ENST00000310132.6	37	CCDS12114.1	28	0.01282051282051282	25	0.0508130081300813	3	0.008287292817679558	0	0.0	0	0.0	G	19.36	3.813366	0.70912	0.057422	1.16E-4	ENSG00000007264	ENST00000395045	.	.	.	1.4	-2.8	0.05823	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.11794	T	0.64	2.4484	4.5873	0.12289	0.0:0.4596:0.3083:0.2321	.	.	.	.	X	9	.	ENSP00000378485:R9X	R	-	1	2	MATK	3740321	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.190000	0.09615	-0.756000	0.04703	0.455000	0.32223	CGA	G|0.980;A|0.020	0.020	strong		0.493	MATK-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453639.1	NM_139355	
PKN3	29941	hgsc.bcm.edu	37	9	131467782	131467782	+	Silent	SNP	C	C	T	rs55665019	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:131467782C>T	ENST00000291906.4	+	2	618	c.225C>T	c.(223-225)caC>caT	p.H75H		NM_013355.3	NP_037487.2	Q6P5Z2	PKN3_HUMAN	protein kinase N3	75					epithelial cell migration (GO:0010631)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(9)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	24						GGGAGCTGCACGCCCGAATCC	0.706													C|||	530	0.105831	0.3767	0.0317	5008	,	,		15403	0.0069		0.003	False		,,,				2504	0.0				p.H75H		Atlas-SNP	.											.	PKN3	62	.	0			c.C225T						PASS	.	C		1131,3035		106,919,1058	4.0	4.0	4.0		225	-10.4	0.1	9	dbSNP_129	4	36,8126		0,36,4045	no	coding-synonymous	PKN3	NM_013355.3		106,955,5103	TT,TC,CC		0.4411,27.1483,9.4663		75/890	131467782	1167,11161	2083	4081	6164	SO:0001819	synonymous_variant	29941	exon2			GCTGCACGCCCGA	AB019692	CCDS6908.1	9q34.13	2008-02-05			ENSG00000160447	ENSG00000160447			17999	protein-coding gene	gene with protein product		610714				10441506	Standard	NM_013355		Approved	PKNbeta	uc004bvw.3	Q6P5Z2	OTTHUMG00000020757	ENST00000291906.4:c.225C>T	9.37:g.131467782C>T		10.0	0.0	0		15.0	11.0	0.733333	NM_013355	Q9UM03	Silent	SNP	ENST00000291906.4	37	CCDS6908.1																																																																																			C|0.909;T|0.091	0.091	strong		0.706	PKN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054487.1	NM_013355	
CIRH1A	84916	hgsc.bcm.edu	37	16	69191012	69191012	+	Missense_Mutation	SNP	G	G	A	rs8056684	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:69191012G>A	ENST00000314423.7	+	12	1490	c.1313G>A	c.(1312-1314)cGc>cAc	p.R438H	CIRH1A_ENST00000563094.1_Missense_Mutation_p.R438H|CIRH1A_ENST00000352319.4_Intron			Q969X6	CIR1A_HUMAN	cirrhosis, autosomal recessive 1A (cirhin)	438			R -> H (in dbSNP:rs8056684).		maturation of SSU-rRNA (GO:0030490)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|t-UTP complex (GO:0034455)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(4)|prostate(1)|urinary_tract(1)	16				OV - Ovarian serous cystadenocarcinoma(108;0.125)		GCATTCCTTCGCTCTGCCCTT	0.443													G|||	28	0.00559105	0.0204	0.0014	5008	,	,		19933	0.0		0.0	False		,,,				2504	0.0				p.R438H	Melanoma(69;1156 1278 4951 8715 52012)	Atlas-SNP	.											.	CIRH1A	48	.	0			c.G1313A						PASS	.	G	HIS/ARG	91,4305	75.2+/-113.4	1,89,2108	97.0	89.0	92.0		1313	0.4	1.0	16	dbSNP_116	92	0,8600		0,0,4300	yes	missense	CIRH1A	NM_032830.2	29	1,89,6408	AA,AG,GG		0.0,2.0701,0.7002	benign	438/687	69191012	91,12905	2198	4300	6498	SO:0001583	missense	84916	exon12			TCCTTCGCTCTGC	AB075868	CCDS10872.1	16q22	2014-04-07			ENSG00000141076	ENSG00000141076		"""WD repeat domain containing"""	1983	protein-coding gene	gene with protein product	"""UTP4, small subunit (SSU) processome component, homolog (yeast)"""	607456				10820129, 20385600	Standard	NM_032830		Approved	NAIC, FLJ14728, KIAA1988, TEX292, CIRHIN, UTP4	uc002ews.4	Q969X6	OTTHUMG00000137570	ENST00000314423.7:c.1313G>A	16.37:g.69191012G>A	ENSP00000327179:p.Arg438His	111.0	0.0	0		155.0	69.0	0.445161	NM_032830	Q8NCD9|Q8TF14|Q96SP0|Q96SR9|Q96SZ9|Q96T13|Q9BWK6	Missense_Mutation	SNP	ENST00000314423.7	37	CCDS10872.1	17	0.007783882783882784	16	0.032520325203252036	1	0.0027624309392265192	0	0.0	0	0.0	G	11.42	1.632635	0.29068	0.020701	0.0	ENSG00000141076	ENST00000314423	T	0.29917	1.55	5.63	0.418	0.16429	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);	0.577687	0.20003	N	0.101285	T	0.04092	0.0114	N	0.04959	-0.14	0.22389	N	0.999142	B;B	0.10296	0.0;0.003	B;B	0.01281	0.0;0.0	T	0.18903	-1.0322	10	0.38643	T	0.18	.	7.8446	0.29419	0.5019:0.0:0.4981:0.0	rs8056684;rs52807145;rs8056684	438;438	Q969X6;Q969X6-3	CIR1A_HUMAN;.	H	438	ENSP00000327179:R438H	ENSP00000327179:R438H	R	+	2	0	CIRH1A	67748513	0.806000	0.28996	0.991000	0.47740	0.870000	0.49936	0.011000	0.13264	0.341000	0.23771	0.455000	0.32223	CGC	G|0.990;A|0.010	0.010	strong		0.443	CIRH1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268950.2	NM_032830	
S100A3	6274	hgsc.bcm.edu	37	1	153520898	153520898	+	Missense_Mutation	SNP	G	G	A	rs61731550	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:153520898G>A	ENST00000368713.3	-	2	260	c.64C>T	c.(64-66)Cgc>Tgc	p.R22C	S100A4_ENST00000368716.4_5'Flank|S100A4_ENST00000354332.4_5'Flank|S100A4_ENST00000368714.1_Intron|S100A3_ENST00000368712.1_Missense_Mutation_p.R22C	NM_002960.1	NP_002951.1	P33764	S10A3_HUMAN	S100 calcium binding protein A3	22	EF-hand 1.					cytoplasm (GO:0005737)|nucleolus (GO:0005730)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(1)|liver(1)|lung(1)	3	all_lung(78;5.98e-32)|Lung NSC(65;2.27e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			TCCCCACAGCGCCCTGCGTAT	0.622													G|||	51	0.0101837	0.0363	0.0043	5008	,	,		17589	0.0		0.0	False		,,,				2504	0.0				p.R22C		Atlas-SNP	.											.	S100A3	7	.	0			c.C64T						PASS	.	G	CYS/ARG	128,4278	94.4+/-133.1	2,124,2077	153.0	147.0	149.0		64	3.4	0.0	1	dbSNP_129	149	0,8600		0,0,4300	yes	missense	S100A3	NM_002960.1	180	2,124,6377	AA,AG,GG		0.0,2.9051,0.9842	probably-damaging	22/102	153520898	128,12878	2203	4300	6503	SO:0001583	missense	6274	exon2			CACAGCGCCCTGC	BC012893	CCDS1043.1	1q21	2008-02-05	2001-11-28		ENSG00000188015	ENSG00000188015		"""S100 calcium binding proteins"""	10493	protein-coding gene	gene with protein product		176992	"""S100 calcium-binding protein A3"""	S100E		8341667	Standard	NM_002960		Approved		uc001fca.1	P33764	OTTHUMG00000013550	ENST00000368713.3:c.64C>T	1.37:g.153520898G>A	ENSP00000357702:p.Arg22Cys	58.0	0.0	0		51.0	28.0	0.54902	NM_002960	D3DV51|Q6FGE4	Missense_Mutation	SNP	ENST00000368713.3	37	CCDS1043.1	17	0.007783882783882784	14	0.028455284552845527	3	0.008287292817679558	0	0.0	0	0.0	G	12.38	1.921365	0.33908	0.029051	0.0	ENSG00000188015	ENST00000368713;ENST00000368712	T;T	0.12039	2.72;2.72	5.42	3.43	0.39272	S100/CaBP-9k-type, calcium binding, subdomain (1);EF-hand-like domain (1);	0.495237	0.19790	N	0.106001	T	0.09512	0.0234	M	0.67569	2.06	0.18873	N	0.999985	D	0.64830	0.994	P	0.48770	0.589	T	0.09751	-1.0660	10	0.87932	D	0	.	6.1806	0.20470	0.094:0.0:0.7225:0.1835	.	22	P33764	S10A3_HUMAN	C	22	ENSP00000357702:R22C;ENSP00000357701:R22C	ENSP00000357701:R22C	R	-	1	0	S100A3	151787522	0.002000	0.14202	0.002000	0.10522	0.003000	0.03518	1.236000	0.32683	1.295000	0.44724	0.643000	0.83706	CGC	G|0.991;A|0.009	0.009	strong		0.622	S100A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037726.1	NM_002960	
MYH7B	57644	hgsc.bcm.edu	37	20	33568455	33568455	+	Silent	SNP	T	T	C	rs61746163	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr20:33568455T>C	ENST00000262873.7	+	6	635	c.543T>C	c.(541-543)gcT>gcC	p.A181A	MYH7B_ENST00000481922.1_3'UTR	NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	139	Myosin motor.					membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			CCGTAGTGGCTGCTTACAAGG	0.557													C|||	16	0.00319489	0.0121	0.0	5008	,	,		17350	0.0		0.0	False		,,,				2504	0.0				p.A181A		Atlas-SNP	.											.	MYH7B	145	.	0			c.T543C						PASS	.	C		58,4302	745.2+/-411.6	0,58,2122	100.0	111.0	107.0		543	-8.9	0.1	20	dbSNP_129	107	1,8587	799.2+/-407.4	0,1,4293	no	coding-synonymous	MYH7B	NM_020884.3		0,59,6415	CC,CT,TT		0.0116,1.3303,0.4557		181/1984	33568455	59,12889	2180	4294	6474	SO:0001819	synonymous_variant	57644	exon8			AGTGGCTGCTTAC	AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"""Myosins / Myosin superfamily : Class II"""	15906	protein-coding gene	gene with protein product		609928	"""myosin, heavy polypeptide 7B, cardiac muscle, beta"""			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.543T>C	20.37:g.33568455T>C		201.0	0.0	0		171.0	89.0	0.520468	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Silent	SNP	ENST00000262873.7	37	CCDS42869.1																																																																																			T|0.994;C|0.006	0.006	strong		0.557	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884	
PTP4A1	7803	hgsc.bcm.edu	37	6	64289968	64289968	+	Silent	SNP	G	G	T	rs1618240	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr6:64289968G>T	ENST00000370651.3	+	6	1564	c.411G>T	c.(409-411)cgG>cgT	p.R137R	PTP4A1_ENST00000370650.2_Silent_p.R112R	NM_003463.3	NP_003454.1	Q93096	TP4A1_HUMAN	protein tyrosine phosphatase type IVA, member 1	137	Tyrosine-protein phosphatase.				cell cycle (GO:0007049)|multicellular organismal development (GO:0007275)|positive regulation of cell migration (GO:0030335)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	protein tyrosine phosphatase activity (GO:0004725)			large_intestine(3)|lung(4)|skin(1)	8	all_cancers(3;0.071)|all_epithelial(2;0.0146)|Lung NSC(77;0.175)		Epithelial(2;0.0365)|LUSC - Lung squamous cell carcinoma(74;0.0644)|all cancers(2;0.112)|Lung(124;0.13)			CCAGAAAGCGGCGTGGAGCTT	0.403													G|||	100	0.0199681	0.0741	0.0029	5008	,	,		16055	0.0		0.0	False		,,,				2504	0.0				p.R137R	Pancreas(91;1019 1502 28028 38110 51645)	Atlas-SNP	.											.	PTP4A1	13	.	0			c.G411T						PASS	.	G		253,4153	143.5+/-178.5	12,229,1962	85.0	87.0	87.0		411	4.0	1.0	6	dbSNP_89	87	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	PTP4A1	NM_003463.3		12,232,6259	TT,TG,GG		0.0349,5.7422,1.9683		137/174	64289968	256,12750	2203	4300	6503	SO:0001819	synonymous_variant	7803	exon6			AAAGCGGCGTGGA	U48296	CCDS4965.1	6q12	2011-06-09			ENSG00000112245	ENSG00000112245		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PRLs"""	9634	protein-coding gene	gene with protein product		601585				9642300	Standard	NM_003463		Approved	PTPCAAX1, PRL-1	uc003pel.3	Q93096	OTTHUMG00000014949	ENST00000370651.3:c.411G>T	6.37:g.64289968G>T		32.0	0.0	0		29.0	16.0	0.551724	NM_003463	B2R6C8|O00648|Q49A54	Silent	SNP	ENST00000370651.3	37	CCDS4965.1																																																																																			G|0.980;T|0.020	0.020	strong		0.403	PTP4A1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041083.2		
SSPO	23145	hgsc.bcm.edu	37	7	149493519	149493519	+	RNA	SNP	C	C	T	rs57595625	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:149493519C>T	ENST00000378016.2	+	0	6595							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CCGCATGGTGCAGGCGAGGTT	0.617													C|||	145	0.0289537	0.1059	0.0072	5008	,	,		18965	0.0		0.0	False		,,,				2504	0.0				p.Q2199X		Atlas-SNP	.											.	.	.	.	0			c.C6595T						PASS	.	C		345,3947		8,329,1809	100.0	114.0	110.0		6599	3.6	1.0	7	dbSNP_129	110	3,8491		0,3,4244	yes	coding-notMod3	SSPO	NM_198455.2		8,332,6053	TT,TC,CC		0.0353,8.0382,2.7217			149493519	348,12438	2146	4247	6393			23145	exon44			ATGGTGCAGGCGA	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149493519C>T		135.0	0.0	0		139.0	73.0	0.52518	NM_198455	Q76B61	Nonsense_Mutation	SNP	ENST00000378016.2	37																																																																																				C|0.972;T|0.028	0.028	strong		0.617	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
C9orf3	84909	hgsc.bcm.edu	37	9	97563076	97563076	+	Missense_Mutation	SNP	C	C	T	rs34557833	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr9:97563076C>T	ENST00000375315.2	+	4	1156	c.1156C>T	c.(1156-1158)Cgc>Tgc	p.R386C	C9orf3_ENST00000297979.5_Missense_Mutation_p.R386C|C9orf3_ENST00000277198.2_Missense_Mutation_p.R386C|C9orf3_ENST00000395357.2_Missense_Mutation_p.R6C	NM_001193329.1	NP_001180258.1	Q8N6M6	AMPO_HUMAN	chromosome 9 open reading frame 3	386			R -> C (in dbSNP:rs34557833).		leukotriene biosynthetic process (GO:0019370)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23				OV - Ovarian serous cystadenocarcinoma(323;0.000275)		ATACCCCTGCCGCTTCCAGAA	0.507													C|||	30	0.00599042	0.0227	0.0	5008	,	,		20701	0.0		0.0	False		,,,				2504	0.0				p.R386C		Atlas-SNP	.											.	C9orf3	100	.	0			c.C1156T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG	58,4348	56.2+/-92.4	0,58,2145	102.0	94.0	97.0		1156,1156,1156	4.4	1.0	9	dbSNP_126	97	0,8600		0,0,4300	yes	missense,missense,missense	C9orf3	NM_001193329.1,NM_001193331.2,NM_032823.5	180,180,180	0,58,6445	TT,TC,CC		0.0,1.3164,0.4459	possibly-damaging,possibly-damaging,possibly-damaging	386/820,386/567,386/721	97563076	58,12948	2203	4300	6503	SO:0001583	missense	84909	exon5			CCCTGCCGCTTCC	AF043896	CCDS6713.1, CCDS55327.1, CCDS55328.1	9q22	2013-06-27			ENSG00000148120	ENSG00000148120			1361	protein-coding gene	gene with protein product	aminopeptidase O					15687497	Standard	NM_001193329		Approved	C90RF3, FLJ14675, APO, AOPEP, AP-O	uc004ava.3	Q8N6M6	OTTHUMG00000020276	ENST00000375315.2:c.1156C>T	9.37:g.97563076C>T	ENSP00000364464:p.Arg386Cys	130.0	0.0	0		141.0	88.0	0.624114	NM_001193331	Q5T9B1|Q5T9B3|Q5T9B4|Q8WUL6|Q96M23|Q96SS1	Missense_Mutation	SNP	ENST00000375315.2	37	CCDS55328.1	11	0.005036630036630037	11	0.022357723577235773	0	0.0	0	0.0	0	0.0	C	23.3	4.397577	0.83120	0.013164	0.0	ENSG00000148120	ENST00000277198;ENST00000297979;ENST00000375315;ENST00000424143;ENST00000428313;ENST00000395357	T;T;T;T;T;T	0.15952	4.18;2.39;2.74;2.43;2.38;4.18	5.28	4.38	0.52667	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.24084	0.0583	M	0.63843	1.955	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.999;0.998;0.995;0.998	T	0.13710	-1.0499	10	0.72032	D	0.01	-13.0857	15.6642	0.77213	0.1375:0.8625:0.0:0.0	rs34557833	386;386;386;386	Q8N6M6;Q8N6M6-4;Q8N6M6-2;Q8N6M6-3	AMPO_HUMAN;.;.;.	C	386;386;386;209;168;6	ENSP00000277198:R386C;ENSP00000297979:R386C;ENSP00000364464:R386C;ENSP00000402171:R209C;ENSP00000401854:R168C;ENSP00000378763:R6C	ENSP00000277198:R386C	R	+	1	0	C9orf3	96602897	1.000000	0.71417	1.000000	0.80357	0.951000	0.60555	4.291000	0.59025	1.432000	0.47375	0.650000	0.86243	CGC	C|0.995;T|0.005	0.005	strong		0.507	C9orf3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032823	
OGFOD3	79701	hgsc.bcm.edu	37	17	80373453	80373453	+	Missense_Mutation	SNP	G	G	A	rs61742456	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr17:80373453G>A	ENST00000313056.5	-	2	276	c.125C>T	c.(124-126)cCg>cTg	p.P42L	OGFOD3_ENST00000329197.5_Missense_Mutation_p.P42L|HEXDC_ENST00000337014.6_5'Flank|Y_RNA_ENST00000364369.1_RNA	NM_024648.2|NM_175902.4	NP_078924.1|NP_787098.3	Q6PK18	OGFD3_HUMAN	2-oxoglutarate and iron-dependent oxygenase domain containing 3	42						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)										CCTTAGCCACGGCCTCTGCCA	0.672													G|||	13	0.00259585	0.0038	0.0072	5008	,	,		15837	0.0		0.002	False		,,,				2504	0.001				p.P42L		Atlas-SNP	.											.	.	.	.	0			c.C125T						PASS	.	G	LEU/PRO,LEU/PRO	11,4395	15.5+/-35.6	0,11,2192	28.0	32.0	30.0		125,125	-6.8	0.0	17	dbSNP_129	30	32,8568	20.4+/-63.3	0,32,4268	yes	missense,missense	C17orf101	NM_024648.2,NM_175902.4	98,98	0,43,6460	AA,AG,GG		0.3721,0.2497,0.3306	benign,benign	42/320,42/332	80373453	43,12963	2203	4300	6503	SO:0001583	missense	79701	exon2			AGCCACGGCCTCT	BC023602	CCDS11811.1, CCDS11812.1	17q25.3	2012-10-23	2012-10-23	2012-10-23	ENSG00000181396	ENSG00000181396			26174	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 101"""	C17orf101		12477932	Standard	NM_175902		Approved	FLJ22222	uc002keu.2	Q6PK18		ENST00000313056.5:c.125C>T	17.37:g.80373453G>A	ENSP00000320116:p.Pro42Leu	35.0	0.0	0		54.0	32.0	0.592593	NM_175902	C9JDC8|Q8IZ37|Q9H6J2	Missense_Mutation	SNP	ENST00000313056.5	37	CCDS11811.1	5	0.0022893772893772895	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	10.25	1.299021	0.23650	0.002497	0.003721	ENSG00000181396	ENST00000313056;ENST00000329197	T;T	0.28895	2.05;1.59	5.0	-6.77	0.01727	.	0.937389	0.08845	N	0.885310	T	0.10078	0.0247	N	0.08118	0	0.09310	N	1	B;B	0.09022	0.0;0.002	B;B	0.04013	0.0;0.001	T	0.21280	-1.0250	10	0.27082	T	0.32	-1.2083	0.9917	0.01458	0.2458:0.3165:0.1245:0.3132	.	42;42	Q6PK18;Q6PK18-2	CQ101_HUMAN;.	L	42	ENSP00000320116:P42L;ENSP00000330075:P42L	ENSP00000320116:P42L	P	-	2	0	C17orf101	77966742	0.044000	0.20184	0.000000	0.03702	0.021000	0.10359	0.283000	0.18846	-1.664000	0.01479	-0.857000	0.03018	CCG	G|0.997;A|0.003	0.003	strong		0.672	OGFOD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442895.1	NM_175902	
PTPRJ	5795	hgsc.bcm.edu	37	11	48149352	48149352	+	Missense_Mutation	SNP	G	G	A	rs2229703	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:48149352G>A	ENST00000418331.2	+	7	1466	c.1114G>A	c.(1114-1116)Gtc>Atc	p.V372I	PTPRJ_ENST00000440289.2_Missense_Mutation_p.V372I	NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	372	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.		V -> I (in dbSNP:rs2229703).		contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)	p.V372L(1)		breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						GGTTTTTGACGTCACCGCTGT	0.498													G|||	156	0.0311502	0.1112	0.0115	5008	,	,		23784	0.0		0.0	False		,,,				2504	0.001				p.V372I		Atlas-SNP	.											PTPRJ_ENST00000418331,rectum,carcinoma,-1,5	PTPRJ	225	5	1	Substitution - Missense(1)	kidney(1)	c.G1114A						PASS	.	G	ILE/VAL,ILE/VAL	397,4005	197.7+/-221.8	9,379,1813	108.0	95.0	99.0		1114,1114	-11.5	0.0	11	dbSNP_98	99	4,8592	1.2+/-3.3	0,4,4294	yes	missense,missense	PTPRJ	NM_001098503.1,NM_002843.3	29,29	9,383,6107	AA,AG,GG		0.0465,9.0186,3.0851	benign,benign	372/540,372/1338	48149352	401,12597	2201	4298	6499	SO:0001583	missense	5795	exon7			TTTGACGTCACCG	U10886	CCDS7945.1, CCDS44596.1	11p11.2	2013-02-11			ENSG00000149177	ENSG00000149177		"""CD molecules"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9673	protein-coding gene	gene with protein product		600925				7937872, 7994032	Standard	NM_001098503		Approved	DEP1, HPTPeta, CD148	uc001ngp.4	Q12913	OTTHUMG00000166573	ENST00000418331.2:c.1114G>A	11.37:g.48149352G>A	ENSP00000400010:p.Val372Ile	73.0	0.0	0		96.0	38.0	0.395833	NM_001098503	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Missense_Mutation	SNP	ENST00000418331.2	37	CCDS7945.1	53	0.024267399267399268	48	0.0975609756097561	5	0.013812154696132596	0	0.0	0	0.0	G	4.166	0.029336	0.08054	0.090186	4.65E-4	ENSG00000149177	ENST00000278456;ENST00000418331;ENST00000440289	T;T	0.59906	0.23;0.23	5.75	-11.5	0.00074	Fibronectin, type III (4);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00637	0.0021	N	0.04297	-0.235	0.09310	N	1	B;P	0.36027	0.035;0.533	B;B	0.34652	0.024;0.187	T	0.28713	-1.0035	9	0.23302	T	0.38	.	9.7949	0.40728	0.1072:0.3001:0.5182:0.0745	rs2229703;rs16905649;rs56484607;rs16905649	372;372	Q12913;Q6P4H4	PTPRJ_HUMAN;.	I	372	ENSP00000400010:V372I;ENSP00000409733:V372I	ENSP00000278456:V372I	V	+	1	0	PTPRJ	48105928	0.000000	0.05858	0.000000	0.03702	0.188000	0.23474	-1.405000	0.02492	-3.757000	0.00111	-0.136000	0.14681	GTC	G|0.964;A|0.036	0.036	strong		0.498	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1		
CENPE	1062	hgsc.bcm.edu	37	4	104070041	104070041	+	Missense_Mutation	SNP	G	G	A	rs79431579	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr4:104070041G>A	ENST00000265148.3	-	28	3892	c.3803C>T	c.(3802-3804)aCt>aTt	p.T1268I	CENPE_ENST00000380026.3_Missense_Mutation_p.T1243I	NM_001813.2	NP_001804.2	Q02224	CENPE_HUMAN	centromere protein E, 312kDa	1268					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|kinetochore assembly (GO:0051382)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic chromosome movement towards spindle pole (GO:0007079)|mitotic metaphase plate congression (GO:0007080)|multicellular organismal development (GO:0007275)|positive regulation of protein kinase activity (GO:0045860)|regulation of mitotic metaphase/anaphase transition (GO:0030071)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|condensed chromosome, centromeric region (GO:0000779)|condensed nuclear chromosome kinetochore (GO:0000778)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|mitotic spindle midzone (GO:1990023)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinetochore binding (GO:0043515)|microtubule motor activity (GO:0003777)			NS(3)|breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(20)|lung(34)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(5)|urinary_tract(3)	101				OV - Ovarian serous cystadenocarcinoma(123;2.95e-08)		TAAGTCCTGAGTATTTATTAT	0.338													G|||	53	0.0105831	0.0318	0.0101	5008	,	,		19012	0.0		0.001	False		,,,				2504	0.0031				p.T1268I		Atlas-SNP	.											.	CENPE	253	.	0			c.C3803T						PASS	.	G	ILE/THR	160,4246	106.9+/-145.3	4,152,2047	138.0	143.0	141.0		3803	-6.5	0.0	4	dbSNP_131	141	15,8585	10.5+/-38.8	0,15,4285	yes	missense	CENPE	NM_001813.2	89	4,167,6332	AA,AG,GG		0.1744,3.6314,1.3455	benign	1268/2702	104070041	175,12831	2203	4300	6503	SO:0001583	missense	1062	exon28			TCCTGAGTATTTA	Z15005	CCDS34042.1, CCDS68768.1	4q24-q25	2013-11-05	2002-08-29			ENSG00000138778		"""Kinesins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1856	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 61"""	117143	"""centromere protein E (312kD)"""			7851898	Standard	NM_001286734		Approved	KIF10, PPP1R61	uc003hxb.1	Q02224		ENST00000265148.3:c.3803C>T	4.37:g.104070041G>A	ENSP00000265148:p.Thr1268Ile	203.0	0.0	0		185.0	92.0	0.497297	NM_001813	A6NKY9|A8K2U7|Q4LE75	Missense_Mutation	SNP	ENST00000265148.3	37	CCDS34042.1	24	0.01098901098901099	20	0.04065040650406504	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	G	11.01	1.512446	0.27123	0.036314	0.001744	ENSG00000138778	ENST00000265148;ENST00000394771;ENST00000380026	T;T	0.71341	-0.56;-0.56	4.06	-6.52	0.01872	.	.	.	.	.	T	0.11239	0.0274	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.14364	-1.0475	9	0.16896	T	0.51	.	6.5259	0.22301	0.2333:0.0:0.5348:0.232	.	1243;1268	Q02224-3;Q02224	.;CENPE_HUMAN	I	1268;1268;1243	ENSP00000265148:T1268I;ENSP00000369365:T1243I	ENSP00000265148:T1268I	T	-	2	0	CENPE	104289490	0.000000	0.05858	0.000000	0.03702	0.537000	0.34900	-1.463000	0.02361	-1.120000	0.02953	-1.155000	0.01812	ACT	G|0.985;A|0.015	0.015	strong		0.338	CENPE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
ACCSL	390110	hgsc.bcm.edu	37	11	44069589	44069589	+	Start_Codon_SNP	SNP	G	G	A	rs3094398	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:44069589G>A	ENST00000378832.1	+	1	59	c.3G>A	c.(1-3)atG>atA	p.M1I		NM_001031854.2	NP_001027025.2	Q4AC99	1A1L2_HUMAN	1-aminocyclopropane-1-carboxylate synthase homolog (Arabidopsis)(non-functional)-like	1					biosynthetic process (GO:0009058)		catalytic activity (GO:0003824)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|endometrium(6)|large_intestine(5)|lung(14)|ovary(5)|pancreas(1)|skin(2)	34						CCCGGAGTATGAGTCATCGGT	0.562													G|||	72	0.014377	0.053	0.0029	5008	,	,		20512	0.0		0.0	False		,,,				2504	0.0				p.M1I		Atlas-SNP	.											.	ACCSL	57	.	0			c.G3A						PASS	.	G	ILE/MET	158,3748		1,156,1796	58.0	60.0	59.0		3	0.3	0.0	11	dbSNP_103	59	0,8304		0,0,4152	yes	missense	ACCSL	NM_001031854.2	10	1,156,5948	AA,AG,GG		0.0,4.0451,1.294	benign	1/569	44069589	158,12052	1953	4152	6105	SO:0001582	initiator_codon_variant	390110	exon1			GAGTATGAGTCAT		CCDS41636.1	11p11.2	2008-11-26			ENSG00000205126	ENSG00000205126			34391	protein-coding gene	gene with protein product							Standard	NM_001031854		Approved		uc001mxw.1	Q4AC99	OTTHUMG00000166426	ENST00000378832.1:c.3G>A	11.37:g.44069589G>A	ENSP00000368109:p.Met1Ile	51.0	0.0	0		70.0	30.0	0.428571	NM_001031854		Missense_Mutation	SNP	ENST00000378832.1	37	CCDS41636.1	34	0.015567765567765568	33	0.06707317073170732	1	0.0027624309392265192	0	0.0	0	0.0	G	8.750	0.921130	0.17982	0.040451	0.0	ENSG00000205126	ENST00000378832	T	0.69040	-0.37	3.28	0.309	0.15820	.	0.437153	0.18726	N	0.132862	T	0.06554	0.0168	.	.	.	0.49299	D	0.999777	B	0.22003	0.063	B	0.14023	0.01	T	0.05666	-1.0871	9	0.46703	T	0.11	-1.1221	4.9599	0.14061	0.4511:0.0:0.5489:0.0	rs3094398;rs52832585;rs56504395;rs3094398	1	Q4AC99	1A1L2_HUMAN	I	1	ENSP00000368109:M1I	ENSP00000368109:M1I	M	+	3	0	ACCSL	44026165	0.115000	0.22152	0.024000	0.17045	0.018000	0.09664	0.130000	0.15850	0.065000	0.16485	0.563000	0.77884	ATG	G|0.977;A|0.023	0.023	strong		0.562	ACCSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389717.1	NM_001031854	Missense_Mutation
CCDC116	164592	hgsc.bcm.edu	37	22	21989230	21989230	+	Missense_Mutation	SNP	C	C	T	rs41279987	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr22:21989230C>T	ENST00000292779.3	+	4	1039	c.878C>T	c.(877-879)cCg>cTg	p.P293L	CCDC116_ENST00000607942.1_Missense_Mutation_p.P293L	NM_152612.2	NP_689825.2	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	293			P -> L (in dbSNP:rs41279987).							endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(5)	22	Colorectal(54;0.105)					GGCTACTGTCCGCTCCGTGAG	0.597													C|||	124	0.0247604	0.0893	0.0086	5008	,	,		19728	0.0		0.0	False		,,,				2504	0.0				p.P293L		Atlas-SNP	.											CCDC116,NS,carcinoma,-1,1	CCDC116	56	1	0			c.C878T						PASS	.	C	LEU/PRO	278,4128	155.5+/-188.7	7,264,1932	78.0	80.0	79.0		878	2.1	0.0	22	dbSNP_127	79	3,8597	3.0+/-9.4	0,3,4297	yes	missense	CCDC116	NM_152612.2	98	7,267,6229	TT,TC,CC		0.0349,6.3096,2.1605	benign	293/614	21989230	281,12725	2203	4300	6503	SO:0001583	missense	164592	exon4			ACTGTCCGCTCCG	BC033499	CCDS13791.1	22q11.21	2006-06-27			ENSG00000161180	ENSG00000161180			26688	protein-coding gene	gene with protein product						12477932	Standard	NM_152612		Approved	FLJ36046	uc002zve.3	Q8IYX3	OTTHUMG00000150821	ENST00000292779.3:c.878C>T	22.37:g.21989230C>T	ENSP00000292779:p.Pro293Leu	56.0	0.0	0		62.0	27.0	0.435484	NM_152612	Q8N9Y9	Missense_Mutation	SNP	ENST00000292779.3	37	CCDS13791.1	49	0.022435897435897436	45	0.09146341463414634	4	0.011049723756906077	0	0.0	0	0.0	C	11.67	1.706989	0.30232	0.063096	3.49E-4	ENSG00000161180	ENST00000292779	T	0.12465	2.68	4.39	2.13	0.27403	.	0.960630	0.08582	N	0.924354	T	0.00328	0.0010	L	0.34521	1.04	0.09310	N	1	P;P	0.38863	0.65;0.65	B;B	0.29524	0.103;0.064	T	0.33624	-0.9861	10	0.72032	D	0.01	-14.4612	4.7066	0.12853	0.2143:0.6741:0.0:0.1116	rs41279987	293;293	B7Z7H5;Q8IYX3-2	.;.	L	293	ENSP00000292779:P293L	ENSP00000292779:P293L	P	+	2	0	CCDC116	20319230	0.000000	0.05858	0.003000	0.11579	0.260000	0.26232	0.439000	0.21575	1.216000	0.43427	0.561000	0.74099	CCG	C|0.974;T|0.026	0.026	strong		0.597	CCDC116-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320199.1	NM_152612	
CALCRL	10203	hgsc.bcm.edu	37	2	188250275	188250275	+	Missense_Mutation	SNP	A	A	T	rs13391909	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr2:188250275A>T	ENST00000409998.1	-	5	829	c.48T>A	c.(46-48)ttT>ttA	p.F16L	CALCRL_ENST00000392370.3_Missense_Mutation_p.F16L|CALCRL_ENST00000410068.1_Missense_Mutation_p.F16L|AC007319.1_ENST00000453517.1_RNA|AC007319.1_ENST00000412276.1_RNA			Q16602	CALRL_HUMAN	calcitonin receptor-like	16			F -> L (in dbSNP:rs13391909).		adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|angiogenesis (GO:0001525)|calcium ion transport (GO:0006816)|cAMP biosynthetic process (GO:0006171)|cellular response to sucrose stimulus (GO:0071329)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|heart development (GO:0007507)|negative regulation of inflammatory response (GO:0050728)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|regulation of muscle contraction (GO:0006937)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	adrenomedullin receptor activity (GO:0001605)|calcitonin gene-related polypeptide receptor activity (GO:0001635)|calcitonin receptor activity (GO:0004948)|G-protein coupled receptor activity (GO:0004930)|protein transporter activity (GO:0008565)			endometrium(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(96;0.227)			TGCTTACCATAAAAAAAGGCA	0.274													A|||	207	0.0413339	0.1483	0.0159	5008	,	,		15603	0.0		0.0	False		,,,				2504	0.0				p.F16L		Atlas-SNP	.											.	CALCRL	73	.	0			c.T48A						PASS	.	A	LEU/PHE	527,3865		26,475,1695	30.0	33.0	32.0		48	-3.4	0.0	2	dbSNP_121	32	8,8520		0,8,4256	yes	missense	CALCRL	NM_005795.4	22	26,483,5951	TT,TA,AA		0.0938,11.9991,4.1409	benign	16/462	188250275	535,12385	2196	4264	6460	SO:0001583	missense	10203	exon3			TACCATAAAAAAA	U17473	CCDS2293.1	2q21.1-q21.3	2012-08-10			ENSG00000064989	ENSG00000064989		"""GPCR / Class B : Calcitonin receptors"""	16709	protein-coding gene	gene with protein product		114190				7818539, 8626685	Standard	NM_005795		Approved	CGRPR, CRLR	uc010frt.4	Q16602	OTTHUMG00000132636	ENST00000409998.1:c.48T>A	2.37:g.188250275A>T	ENSP00000386972:p.Phe16Leu	112.0	0.0	0		104.0	53.0	0.509615	NM_001271751	A8K6G5|A8KAD3|Q53S02|Q53TS5	Missense_Mutation	SNP	ENST00000409998.1	37	CCDS2293.1	96	0.04395604395604396	92	0.18699186991869918	4	0.011049723756906077	0	0.0	0	0.0	A	0.734	-0.779016	0.02929	0.119991	9.38E-4	ENSG00000064989	ENST00000392370;ENST00000409998;ENST00000410068;ENST00000447403;ENST00000410102	T;T;T;T;T	0.59906	1.04;1.04;1.04;1.57;0.23	5.81	-3.39	0.04868	.	1.007640	0.07990	N	0.986908	T	0.00039	0.0001	N	0.03608	-0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.07501	-1.0769	9	0.09843	T	0.71	.	4.5787	0.12248	0.3334:0.0:0.1511:0.5155	rs13391909;rs52830213;rs13391909	16	Q16602	CALRL_HUMAN	L	16	ENSP00000376177:F16L;ENSP00000386972:F16L;ENSP00000387190:F16L;ENSP00000415626:F16L;ENSP00000386599:F16L	ENSP00000376177:F16L	F	-	3	2	CALCRL	187958520	0.102000	0.21896	0.017000	0.16124	0.202000	0.24057	0.018000	0.13422	-0.859000	0.04105	-0.468000	0.05107	TTT	A|0.954;T|0.046	0.046	strong		0.274	CALCRL-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334648.1	NM_005795	
UBR4	23352	hgsc.bcm.edu	37	1	19482788	19482788	+	Missense_Mutation	SNP	T	T	C	rs145733997	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr1:19482788T>C	ENST00000375254.3	-	42	6076	c.6049A>G	c.(6049-6051)Att>Gtt	p.I2017V	UBR4_ENST00000375217.2_Missense_Mutation_p.I2017V|UBR4_ENST00000375226.2_Missense_Mutation_p.I2017V|UBR4_ENST00000375267.2_Missense_Mutation_p.I2017V	NM_020765.2	NP_065816.2	Q5T4S7	UBR4_HUMAN	ubiquitin protein ligase E3 component n-recognin 4	2017					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)		GCGGTGACAATTGCTAACTCG	0.433													T|||	15	0.00299521	0.0106	0.0	5008	,	,		21210	0.0		0.0	False		,,,				2504	0.001				p.I2017V		Atlas-SNP	.											.	UBR4	415	.	0			c.A6049G						PASS	.	T	VAL/ILE	11,4395	19.1+/-41.9	0,11,2192	132.0	119.0	123.0		6049	5.4	1.0	1	dbSNP_134	123	0,8600		0,0,4300	yes	missense	UBR4	NM_020765.2	29	0,11,6492	CC,CT,TT		0.0,0.2497,0.0846	benign	2017/5184	19482788	11,12995	2203	4300	6503	SO:0001583	missense	23352	exon42			TGACAATTGCTAA	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.6049A>G	1.37:g.19482788T>C	ENSP00000364403:p.Ile2017Val	204.0	0.0	0		192.0	95.0	0.494792	NM_020765	A8MPT2|A8MQ33|A8MQB1|O60646|O75050|Q4QRK5|Q5T4S8|Q5T4S9|Q5TBN8|Q5TBP2|Q6DKH8|Q6P4A4|Q7L8P7|Q8IXJ4|Q8TDN5|Q8WV67|Q9HA46|Q9P2N9|Q9UG82	Missense_Mutation	SNP	ENST00000375254.3	37	CCDS189.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	T	11.40	1.626757	0.28978	0.002497	0.0	ENSG00000127481	ENST00000375254;ENST00000375267;ENST00000375217;ENST00000375226;ENST00000417040;ENST00000419533	T;T;T;T;T	0.14391	2.51;2.51;2.51;2.51;3.45	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.08980	0.0222	N	0.01482	-0.84	0.80722	D	1	P	0.35745	0.518	P	0.47827	0.558	T	0.47636	-0.9102	10	0.09590	T	0.72	.	15.6048	0.76658	0.0:0.0:0.0:1.0	.	2017	Q5T4S7	UBR4_HUMAN	V	2017;2017;2017;2017;727;1233	ENSP00000364403:I2017V;ENSP00000364416:I2017V;ENSP00000364365:I2017V;ENSP00000364374:I2017V;ENSP00000404897:I727V	ENSP00000364365:I2017V	I	-	1	0	UBR4	19355375	1.000000	0.71417	0.999000	0.59377	0.988000	0.76386	5.563000	0.67352	2.270000	0.75569	0.482000	0.46254	ATT	T|0.999;C|0.001	0.001	strong		0.433	UBR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007085.1	NM_020765	
ABCC11	85320	hgsc.bcm.edu	37	16	48250031	48250031	+	Silent	SNP	T	T	C	rs11860868	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr16:48250031T>C	ENST00000394747.1	-	6	1294	c.945A>G	c.(943-945)ccA>ccG	p.P315P	ABCC11_ENST00000394748.1_Silent_p.P315P|ABCC11_ENST00000356608.2_Silent_p.P315P|ABCC11_ENST00000353782.5_Silent_p.P315P|ABCC11_ENST00000537808.1_Silent_p.P315P	NM_033151.3	NP_149163.2	Q96J66	ABCCB_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 11	315	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				organic anion transport (GO:0015711)|purine nucleotide transport (GO:0015865)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|organic anion transmembrane transporter activity (GO:0008514)|purine nucleotide transmembrane transporter activity (GO:0015216)			breast(3)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(3)|prostate(2)|skin(5)|urinary_tract(2)	83		all_cancers(37;0.127)|all_lung(18;0.132)|Breast(268;0.166)			Conjugated Estrogens(DB00286)|Folic Acid(DB00158)|Indomethacin(DB00328)|Methotrexate(DB00563)|Probenecid(DB01032)	TTACCGCCAGTGGGAAAACCA	0.473													C|||	295	0.0589058	0.2156	0.013	5008	,	,		21846	0.0		0.001	False		,,,				2504	0.0				p.P315P		Atlas-SNP	.											.	ABCC11	177	.	0			c.A945G						PASS	.	C	,,	768,3634	752.7+/-412.3	65,638,1498	128.0	132.0	130.0		945,945,945	-6.8	0.0	16	dbSNP_120	130	4,8596	819.1+/-406.8	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	ABCC11	NM_032583.3,NM_033151.3,NM_145186.2	,,	65,642,5794	CC,CT,TT		0.0465,17.4466,5.9375	,,	315/1383,315/1383,315/1345	48250031	772,12230	2201	4300	6501	SO:0001819	synonymous_variant	85320	exon6			CGCCAGTGGGAAA	AF367202	CCDS10732.1, CCDS10733.1	16q12	2012-03-14			ENSG00000121270	ENSG00000121270		"""ATP binding cassette transporters / subfamily C"""	14639	protein-coding gene	gene with protein product		607040				11483364, 11435397	Standard	NM_033151		Approved	MRP8	uc002efg.1	Q96J66	OTTHUMG00000133146	ENST00000394747.1:c.945A>G	16.37:g.48250031T>C		31.0	0.0	0		55.0	27.0	0.490909	NM_033151	Q8TDJ0|Q96JA6|Q9BX80	Silent	SNP	ENST00000394747.1	37	CCDS10732.1																																																																																			T|0.927;C|0.073	0.073	strong		0.473	ABCC11-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429984.1	NM_032583	
GRID2IP	392862	hgsc.bcm.edu	37	7	6554126	6554126	+	Missense_Mutation	SNP	C	C	A	rs115745154	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr7:6554126C>A	ENST00000457091.2	-	8	1302	c.1303G>T	c.(1303-1305)Gtg>Ttg	p.V435L	GRID2IP_ENST00000435185.1_Missense_Mutation_p.V252L|GRID2IP_ENST00000452113.1_Missense_Mutation_p.V245L	NM_001145118.1	NP_001138590.1	A4D2P6	GRD2I_HUMAN	glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein	435					long term synaptic depression (GO:0060292)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				endometrium(4)	4						GTGTCCAGCACAGGGTAGACG	0.562													C|||	76	0.0151757	0.0537	0.0029	5008	,	,		21578	0.0		0.003	False		,,,				2504	0.0				p.V435L		Atlas-SNP	.											.	GRID2IP	82	.	0			c.G1303T						PASS	.	C	LEU/VAL	54,1330		0,54,638	105.0	112.0	110.0		1303	4.6	1.0	7	dbSNP_132	110	4,3178		0,4,1587	yes	missense	GRID2IP	NM_001145118.1	32	0,58,2225	AA,AC,CC		0.1257,3.9017,1.2703	benign	435/1212	6554126	58,4508	692	1591	2283	SO:0001583	missense	392862	exon8			CCAGCACAGGGTA		CCDS47537.1	7p22	2007-10-05	2006-03-01		ENSG00000215045	ENSG00000215045			18464	protein-coding gene	gene with protein product		610639	"""glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein 1"""			14612983	Standard	NM_001145118		Approved		uc011jwx.2	A4D2P6	OTTHUMG00000155531	ENST00000457091.2:c.1303G>T	7.37:g.6554126C>A	ENSP00000397351:p.Val435Leu	31.0	0.0	0		51.0	27.0	0.529412	NM_001145118		Missense_Mutation	SNP	ENST00000457091.2	37	CCDS47537.1	32	0.014652014652014652	28	0.056910569105691054	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	28.6	4.930134	0.92389	0.039017	0.001257	ENSG00000215045	ENST00000452113;ENST00000435185;ENST00000457091	T;T;T	0.55588	0.51;0.51;0.53	4.61	4.61	0.57282	.	0.000000	0.64402	U	0.000001	T	0.22244	0.0536	M	0.63843	1.955	0.80722	D	1	D	0.64830	0.994	D	0.72625	0.978	T	0.56974	-0.7890	10	0.87932	D	0	.	15.3026	0.73966	0.0:1.0:0.0:0.0	.	435	A4D2P6	GRD2I_HUMAN	L	245;252;435	ENSP00000397887:V245L;ENSP00000408364:V252L;ENSP00000397351:V435L	ENSP00000408364:V252L	V	-	1	0	GRID2IP	6520651	1.000000	0.71417	0.988000	0.46212	0.970000	0.65996	5.714000	0.68422	2.263000	0.75096	0.563000	0.77884	GTG	C|0.986;A|0.014	0.014	strong		0.562	GRID2IP-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340534.1	XM_294249	
N4BP2L2	10443	hgsc.bcm.edu	37	13	33110539	33110539	+	Missense_Mutation	SNP	C	C	A	rs144941975	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr13:33110539C>A	ENST00000267068.3	-	2	790	c.626G>T	c.(625-627)gGt>gTt	p.G209V	N4BP2L2_ENST00000399396.3_Intron|N4BP2L2_ENST00000357505.6_Intron|N4BP2L2_ENST00000504114.1_Intron|N4BP2L2_ENST00000446957.2_Missense_Mutation_p.G209V	NM_014887.2	NP_055702.1	Q92802	N42L2_HUMAN	NEDD4 binding protein 2-like 2	209					negative regulation of hematopoietic stem cell differentiation (GO:1902037)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of hematopoietic stem cell proliferation (GO:1902035)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptional repressor complex (GO:0017053)	enzyme binding (GO:0019899)|RNA polymerase II transcription corepressor activity (GO:0001106)			kidney(4)|large_intestine(3)|liver(1)|lung(6)|skin(1)|urinary_tract(1)	16		Lung SC(185;0.0262)		all cancers(112;9.5e-07)|Epithelial(112;5.07e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.00196)|BRCA - Breast invasive adenocarcinoma(63;0.00438)|GBM - Glioblastoma multiforme(144;0.243)		ATTATTATGACCCTCATAAAA	0.338													C|||	8	0.00159744	0.0053	0.0014	5008	,	,		19947	0.0		0.0	False		,,,				2504	0.0				p.G209V		Atlas-SNP	.											.	N4BP2L2	90	.	0			c.G626T						PASS	.	C	VAL/GLY,	34,4372	37.6+/-69.7	0,34,2169	68.0	69.0	68.0		626,	-3.3	0.0	13	dbSNP_134	68	0,8600		0,0,4300	yes	missense,intron	N4BP2L2	NM_014887.2,NM_033111.3	109,	0,34,6469	AA,AC,CC		0.0,0.7717,0.2614	,	209/584,	33110539	34,12972	2203	4300	6503	SO:0001583	missense	10443	exon2			TTATGACCCTCAT	U50532	CCDS9346.1, CCDS45024.1, CCDS61307.1	13q13.1	2010-12-02			ENSG00000244754	ENSG00000244754			26916	protein-coding gene	gene with protein product	"""phosphonoformate immuno-associated protein 5"""	615788				8812419	Standard	NM_014887		Approved	CG005, PFAAP5	uc010abe.1	Q92802	OTTHUMG00000016700	ENST00000267068.3:c.626G>T	13.37:g.33110539C>A	ENSP00000267068:p.Gly209Val	121.0	0.0	0		100.0	40.0	0.4	NM_014887	A3KME8	Missense_Mutation	SNP	ENST00000267068.3	37	CCDS9346.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	5.665	0.307323	0.10733	0.007717	0.0	ENSG00000244754	ENST00000446957;ENST00000505213;ENST00000267068	T;T;T	0.42513	0.97;0.97;0.97	5.58	-3.31	0.04988	.	.	.	.	.	T	0.21347	0.0514	L	0.47716	1.5	0.09310	N	1	P;P	0.45902	0.868;0.454	B;B	0.34038	0.174;0.08	T	0.13150	-1.0520	9	0.62326	D	0.03	-15.1664	10.2296	0.43247	0.0:0.2989:0.0999:0.6013	.	209;209	D6R968;Q92802	.;N42L2_HUMAN	V	209	ENSP00000394239:G209V;ENSP00000423362:G209V;ENSP00000267068:G209V	ENSP00000267068:G209V	G	-	2	0	N4BP2L2	32008539	0.000000	0.05858	0.000000	0.03702	0.109000	0.19521	-0.411000	0.07142	-0.881000	0.03992	0.563000	0.77884	GGT	C|0.998;A|0.002	0.002	strong		0.338	N4BP2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044421.1	NM_014887	
LRRC14	9684	hgsc.bcm.edu	37	8	145745268	145745268	+	Silent	SNP	G	G	A	rs116791876	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr8:145745268G>A	ENST00000292524.1	+	2	305	c.159G>A	c.(157-159)acG>acA	p.T53T	RECQL4_ENST00000532237.1_5'Flank|LRRC14_ENST00000529022.1_Silent_p.T53T|RECQL4_ENST00000428558.2_5'Flank	NM_001272036.1|NM_014665.2	NP_001258965.1|NP_055480.1	Q15048	LRC14_HUMAN	leucine rich repeat containing 14	53										endometrium(1)|lung(3)|prostate(1)	5	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			TGGTACACACGTGGCCCTTCC	0.627													G|||	31	0.0061901	0.0212	0.0043	5008	,	,		21870	0.0		0.0	False		,,,				2504	0.0				p.T53T		Atlas-SNP	.											.	LRRC14	25	.	0			c.G159A						PASS	.	G		61,4345	58.1+/-94.6	0,61,2142	98.0	95.0	96.0		159	-8.8	0.0	8	dbSNP_132	96	1,8599	1.2+/-3.3	0,1,4299	yes	coding-synonymous	LRRC14	NM_014665.2		0,62,6441	AA,AG,GG		0.0116,1.3845,0.4767		53/494	145745268	62,12944	2203	4300	6503	SO:0001819	synonymous_variant	9684	exon3			ACACACGTGGCCC	BC011377	CCDS6432.1	8q24.3	2012-08-20			ENSG00000160959	ENSG00000160959			20419	protein-coding gene	gene with protein product						7584026	Standard	NM_001272036		Approved	KIAA0014, LRRC14A	uc003zdk.3	Q15048	OTTHUMG00000165179	ENST00000292524.1:c.159G>A	8.37:g.145745268G>A		147.0	0.0	0		144.0	85.0	0.590278	NM_001272036	A8K0A8|D3DWM8	Silent	SNP	ENST00000292524.1	37	CCDS6432.1																																																																																			G|0.994;A|0.006	0.006	strong		0.627	LRRC14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382494.1	NM_014665	
KIF23	9493	hgsc.bcm.edu	37	15	69714347	69714347	+	Silent	SNP	T	T	C	rs34969957	byFrequency	TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr15:69714347T>C	ENST00000260363.4	+	5	450	c.333T>C	c.(331-333)taT>taC	p.Y111Y	KIF23_ENST00000558585.1_5'Flank|KIF23_ENST00000559279.1_Silent_p.Y111Y|KIF23_ENST00000537891.1_5'Flank|KIF23_ENST00000395392.2_Silent_p.Y111Y|KIF23_ENST00000352331.4_Silent_p.Y111Y	NM_138555.2	NP_612565.1	Q02241	KIF23_HUMAN	kinesin family member 23	111	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|cytokinesis (GO:0000910)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle elongation (GO:0000022)|positive regulation of cytokinesis (GO:0032467)|spindle midzone assembly involved in mitosis (GO:0051256)	centralspindlin complex (GO:0097149)|centrosome (GO:0005813)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|intercellular bridge (GO:0045171)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			central_nervous_system(1)|endometrium(4)|large_intestine(7)|lung(6)|prostate(2)|skin(1)	21						TTTTTACATATGGTGTGACGG	0.408													T|||	60	0.0119808	0.0401	0.0043	5008	,	,		17202	0.0		0.003	False		,,,				2504	0.001				p.Y111Y		Atlas-SNP	.											.	KIF23	57	.	0			c.T333C						PASS	.	T	,	162,4236	110.8+/-149.0	4,154,2041	110.0	88.0	96.0		333,333	-0.3	1.0	15	dbSNP_126	96	6,8590	5.0+/-18.6	0,6,4292	no	coding-synonymous,coding-synonymous	KIF23	NM_004856.5,NM_138555.2	,	4,160,6333	CC,CT,TT		0.0698,3.6835,1.2929	,	111/857,111/961	69714347	168,12826	2199	4298	6497	SO:0001819	synonymous_variant	9493	exon5			TACATATGGTGTG	X67155	CCDS32278.1, CCDS32279.1	15q23	2008-03-03	2003-01-13	2003-01-17		ENSG00000137807		"""Kinesins"""	6392	protein-coding gene	gene with protein product		605064	"""kinesin-like 5 (mitotic kinesin-like protein 1)"""	KNSL5		1406973	Standard	NM_138555		Approved	MKLP1, MKLP-1	uc002asb.3	Q02241		ENST00000260363.4:c.333T>C	15.37:g.69714347T>C		175.0	0.0	0		180.0	90.0	0.5	NM_138555	Q8WVP0	Silent	SNP	ENST00000260363.4	37	CCDS32278.1																																																																																			T|0.985;C|0.015	0.015	strong		0.408	KIF23-201	KNOWN	basic|CCDS	protein_coding	protein_coding			
BACE1	23621	hgsc.bcm.edu	37	11	117186285	117186285	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6324-01A-11D-2210-10	TCGA-G8-6324-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	707a995c-8926-4885-9a96-14690480f680	b7d0d7b7-70a7-40a0-818b-06ef40f7f580	g.chr11:117186285T>C	ENST00000313005.6	-	1	687	c.227A>G	c.(226-228)tAc>tGc	p.Y76C	BACE1_ENST00000428381.2_Missense_Mutation_p.Y76C|BACE1_ENST00000514464.1_5'UTR|BACE1_ENST00000528053.1_Missense_Mutation_p.Y76C|BACE1_ENST00000445823.2_Missense_Mutation_p.Y76C|BACE1_ENST00000513780.1_Missense_Mutation_p.Y76C|AP000892.4_ENST00000504906.1_RNA	NM_012104.4|NM_138971.3|NM_138972.3|NM_138973.3	NP_036236|NP_620427.1|NP_620428.1|NP_620429.1	P56817	BACE1_HUMAN	beta-site APP-cleaving enzyme 1	76					beta-amyloid metabolic process (GO:0050435)|membrane protein ectodomain proteolysis (GO:0006509)|proteolysis (GO:0006508)	axon (GO:0030424)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	aspartic-type endopeptidase activity (GO:0004190)|beta-amyloid binding (GO:0001540)|beta-aspartyl-peptidase activity (GO:0008798)|enzyme binding (GO:0019899)			breast(2)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000563)|all cancers(92;0.0032)		CATCTCCACGTAGTAGCCCTG	0.677																																					p.Y76C		Atlas-SNP	.											.	BACE1	33	.	0			c.A227G						PASS	.						45.0	44.0	44.0					11																	117186285		2201	4296	6497	SO:0001583	missense	23621	exon1			TCCACGTAGTAGC	AF190725	CCDS8383.1, CCDS44739.1, CCDS44740.1, CCDS44741.1, CCDS55787.1, CCDS55786.1	11q23-q24	2011-07-27	2004-04-02	2004-04-02	ENSG00000186318	ENSG00000186318			933	protein-coding gene	gene with protein product		604252	"""beta-site APP-cleaving enzyme"""	BACE		10531052	Standard	NM_012104		Approved		uc001pqz.3	P56817	OTTHUMG00000160636	ENST00000313005.6:c.227A>G	11.37:g.117186285T>C	ENSP00000318585:p.Tyr76Cys	151.0	0.0	0		87.0	4.0	0.045977	NM_138972	A0M8W7|B0YIU9|E9PE65|H7BXJ9|Q9BYB9|Q9BYC0|Q9BYC1|Q9UJT5|Q9ULS1	Missense_Mutation	SNP	ENST00000313005.6	37	CCDS8383.1	.	.	.	.	.	.	.	.	.	.	T	23.5	4.420349	0.83559	.	.	ENSG00000186318	ENST00000313005;ENST00000528053;ENST00000428381;ENST00000513780;ENST00000445823	T;T;T;T;T	0.48201	0.82;0.82;0.82;0.82;0.82	4.99	4.99	0.66335	Peptidase aspartic (1);Peptidase aspartic, catalytic (1);	0.061196	0.64402	D	0.000002	T	0.72179	0.3428	M	0.89414	3.03	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;1.0	D;D;D;D;D	0.91635	0.999;0.998;0.982;0.964;0.999	T	0.78186	-0.2302	10	0.87932	D	0	.	12.6208	0.56601	0.0:0.0:0.0:1.0	.	76;76;76;76;76	Q76KP0;P56817;P56817-3;P56817-4;P56817-2	.;BACE1_HUMAN;.;.;.	C	76	ENSP00000318585:Y76C;ENSP00000431848:Y76C;ENSP00000402228:Y76C;ENSP00000424536:Y76C;ENSP00000403685:Y76C	ENSP00000318585:Y76C	Y	-	2	0	BACE1	116691495	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.012000	0.76366	1.866000	0.54105	0.533000	0.62120	TAC	.	.	none		0.677	BACE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361505.1		
